-- MySQL dump 10.14 Distrib 5.5.34-MariaDB, for Linux (x86_64) -- -- Host: localhost Database: oralgensearch -- ------------------------------------------------------ -- Server version 5.5.34-MariaDB /*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */; /*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */; /*!40101 SET @OLD_COLLATION_CONNECTION=@@COLLATION_CONNECTION */; /*!40101 SET NAMES utf8 */; /*!40103 SET @OLD_TIME_ZONE=@@TIME_ZONE */; /*!40103 SET TIME_ZONE='+00:00' */; /*!40014 SET @OLD_UNIQUE_CHECKS=@@UNIQUE_CHECKS, UNIQUE_CHECKS=0 */; /*!40014 SET @OLD_FOREIGN_KEY_CHECKS=@@FOREIGN_KEY_CHECKS, FOREIGN_KEY_CHECKS=0 */; /*!40101 SET @OLD_SQL_MODE=@@SQL_MODE, SQL_MODE='NO_AUTO_VALUE_ON_ZERO' */; /*!40111 SET @OLD_SQL_NOTES=@@SQL_NOTES, SQL_NOTES=0 */; -- -- Table structure for table `spieces` -- DROP TABLE IF EXISTS `spieces`; /*!40101 SET @saved_cs_client = @@character_set_client */; /*!40101 SET character_set_client = utf8 */; CREATE TABLE `spieces` ( `class` varchar(16) NOT NULL, `name` varchar(128) NOT NULL, `strain` varchar(32) NOT NULL, `s_code` varchar(16) NOT NULL, `overview` varchar(32768) NOT NULL ) ENGINE=InnoDB DEFAULT CHARSET=latin1; /*!40101 SET character_set_client = @saved_cs_client */; -- -- Dumping data for table `spieces` -- LOCK TABLES `spieces` WRITE; /*!40000 ALTER TABLE `spieces` DISABLE KEYS */; INSERT INTO `spieces` VALUES ('oral','Actinobacillus actinomycetemcomitans','HK1651','aact','Actinobacillus actinomycetemcomitans is a gram negative facultative anaerobe for which a complete genomic sequence is herein generously made available in advance of publication by David Dyer, Bruce Roe and colleagues at the University of Oklahoma. Their work on this genome was funded by NIDCR at the NIH. Strain HK1651 was employed for the sequencing project. For questions regarding the sequencing and the strain, contact David Dyer. A.actinomycetemcomitans is a typical cause of periodontitis but it may also be associated with systemic infections and it has been of current interest in relation to arterial plaques.
More than 3000 orfs are encoded in the 2.1 Mb circular chromosome. Approximately 35 orfs predicted by the LANL Oralgen project but not by Oklahoma University are included. Thus the core information in this database is a table of 3000 + annotated records. Each gene record is identified by a gene ID, AA00001 - AA03016; be forewarned that record designations have some discontinuities and some IDs utilize the number suffix 1. Basic summaries of specific information are available below in the Predefined Database Searches that contain links to the particular gene record. Specialized analysis sections of the database are available below in the Specialized Analysis section.
Browsing and searching are also facilitated by the \'Functional Classes\', \'EC Table\', and \'Biochemical Pathways\' summaries. For precise inquiries on the other hand, start with the search capabilities and their associated tables. We invite anyone with questions or suggestions to contact us ( oralgen@lanl.gov).
Seventy-seven references covering the years 2002-2004 and drawn from the molecular subset of Medline are included; please let us know of any pertinent reference that may have been omitted.
A plasmid sequence, pVT745, has been reported in association with A. actinomycetemcomitans and is included in this database. This plasmid sequence of approximately 5.5 kb encodes 13 orfs , some of which are orthologous to chromosomal genes. For further information about the plasmid, see Galli,D.M et al. J. Bacteriol. 183 (5), 1585-1594 (2001), PMID: 11160089; Chen J et al., J Bacteriol. 2002 Nov;184(21):5926-34 PMID: 12374826; Novak KF et al, Microbiology. 2001 Nov;147(Pt 11):3027-35, PMID: 11700353'),('oral','Actinomyces naeslundii','MG1','anae','Actinomyces species are Gram-positive, anaerobic bacteria that normally colonizes oral cavity in animals including humans. Actinomyces form the major component of oral plague and can cause opportunistic infections such as actinomycosis when invading tissues. Several other infections in which Actinomyces can play a role are: gingivitis, mild periodontitis and root surface tooth decay. However, it is not known to be the major player in causing severe periodontal disease. The complete genome of Actinomyces naeslundii MG1 was kindly provided prior to publication by Dr. Garry Myers. The sequencing was performed at J. Craig Venter Institute (JCVI) under the auspices of the NIDCR/NIH.
Actinomyces naeslundii MG1 genome consists of 3.04 Mbp and with G+C content of 68.5%. 87.6% of genome are known to be coding sequences. There are about 2800 protein coding genes. Currently, manual curation of coding regions and functional assignments have been performed. Machine-predicted coding regions were manually checked for errors in gene predictions and corrected where possible. Automated transporter analysis was done to identify potential transporters and manually checked to improve accuracy.
Insertion sequence analysis and cellular location predictions were also carried out. Please scroll down the left navigation menu to visit the analysis pages for Insertion Sequences and Cellular Location predictions. Metabolic pathway prediction is also done and results can be seen by following the link provide below. Please note that some analyses are not yet available and we removed links to these pages. Nine references drawn from the molecular subset of Medline were included from years 2004-2006. Please let us know of any pertinent reference that may have been omitted.'),('oral','Fusobacterium nucleatum','ATCC 25586','fnuc','Fusobacterium nucleatum comprises thirteen subspecies of which the strain ATCC 25586 is represented herein. The vincentii subspecies sequence as well as a plasmid sequence, pFN1, from strain 12230 (Wadsworth Anaerobe Lab) are available for comparative purposes. F. nucleatum, a gram-negative anaerobe, is a major concern for dental research, although its pathogenicity is effected indirectly insofar as it promotes aggregation and establishment of other dental pathogens.
The 2.17 Mb genome of Fusobacterium nucleatum ATCC 25586, was sequenced in 2002 by a team at Integrated Genomics, Chicago. The key publication describing this newly sequenced genome is Kapatral V., et al., 2002, \"Genome Sequence and Analysis of the Oral Bacterium Fusobacterium nucleatum Strain ATCC 25586\"; J.Bact. 184:2005-2018 (PMID: 11889109). A second genomic sequence for the the vincentii subspecies is available in GenBank as contigs and the publication associated with that sequence has been helpful in preparing the annotation herein (Kapatral et al., 2003, Genome Res 13:1180-1189; see the proteome comparison section). Approximately 54 additional and recent references pertaining to F. nucleatum have been extracted from a 2000-2003 molecular subset of PubMed. If we have overlooked any pertinent reference, please inform us (F. nucleatum references).
Three Fusobacteruium nucleatum plasmid sequences, pFN1, pPA52 and pKH9 are included in this section. To access the gene records for these, use the Gene Image Map or Basic Search below with query, \"Gene ID\" \"Contains\" \"plasmid name\". Publications concerning these plasmids are McKay et al., 1995 (PMID: 7753905), Haake et al., 2000 (PMID: 20115567) and Bachrach et al., 2004 (PMID: 15574887).
The core information in this database is the table of annotated records, 2067 predicted open reading frames taken directly from GenBank; Kapatral et al. 2002 report 2067 ORFs in their original manuscript of which 1394 have identifiable functions. Each gene record is identified by a gene id, FN0001-FN2019. Basic summaries of specific information are available below in the Predefined Database Searches and contain links to the complete gene record.
For a general perspective of the genome, we recommend you go to the Gene Image Map and browse blocks of coordinates. Caution: The entire 2.17 Mb genome can be viewed at one time, however this large file can cause some machines to freeze. Browsing and searching are also facilitated by the Functional Classes, EC Table, and Biochemical Pathways summaries. For precise inquiries on the other hand, start with the search capabilities and their associated tables. Fuller analyses of the proteome are underway, for example a table of proteins found in F. nucleatum vincentii and not in other Fusobacterium species, and bi-directional best hits between F. nucleatum ATCC 25586 and F. nucleatum vincentii proteins is presented in the proteome comparison section of the database. Finally, we would encourage anyone with questions or suggestions to contact us at oralgenlanl.gov.'),('oral','Fusobacterium nucleatum polymorphum','polymorphum','fnucp','Fusobacterium nucleatum is a Gram-negative anaerobic bacteria that is part of the oral bacterial community and dominant member of dental plaque biofilms. F. nucleatum is also known to contribute to tooth decay and gingivitis. Fusobacterium nucleatum subsp. polymorphum ATCC 10953 is a phenotypically well-characterized strain available and taxonomic studies have shown that it forms a separate phylogenetic brach from previously sequenced strains of F. nucleatum1. The complete genome sequence of Fusobacterium nucleatum subsp. polymorphum ATCC 10953 was done by The Human Genome Sequencing Center, Baylor College of Medicine. The paper describing the complete genome is by Karpathy et al, 2007, \"Genome Sequence of Fusobacterium nucleatum Subspecies Polymorphum — a Genetically Tractable Fusobacterium\". PLoS ONE. 2(7):e659.
The genome of F. nucleatum subsp. polymorphum ATCC 10953 contains a chromosome of approximately 2.4 Mbp and a plasmid (pFN3) of 11.9 Kbp. G+C content of the chromosome is about 27% and there are 2361 proteins are encoded in the genome. Each gene record is identified by a gene id, for example: FNP_0001 to FNP_2433. Annotated genome of F. nucleatum polymorphum was kindly provided by Dr. Sarah Highlander and Dr. George Weinstock from Baylor College of Medicine and we have manually checked and curated the annotation. The Genome Annotation ToolKit (ATK) was use to obtain evidence for determining final gene definitions.
Transporter analysis was automatically done using the TransAAP program to aid in identifying all potential transporters and manually compared with final annotation definitions to check accuracy of predictions. Several references pertaining to Fusobacterium nucleatum subsp. polymorphum that might be of interest to researchers in oral biology are summarized here. Please let us know if we have missed any relevent references.'),('oral','Porphyromonas gingivalis','W83 ','pgin','Porphyromonas gingivalis is a gram-negative oral anerobe found in periodontal lesions and associated with adult periodontal disease. Strain W83 was sequenced by The Institute for Genomic Research (TIGR) and a pre-published version became available June 2001. On this site General properties of P. gingivalis are available as well as an overview map of the genome and information summary through the Gene Image Map. A dynamic visualization tool with both linear and circular representations is available named BugBrowser.
The core information in this database is the table of annotated records, one for each of the more than 2000 predicted open reading frames. Each gene record is identified by a gene id, PG0001-PG1949. Simple summaries of specific information are available below in the Predefined Database Searches and contain links to the complete gene record. Comparisons between the open reading frames predicted by TIGR and by the LANL database team are summarized in three tables below.
The power of a relational database is demonstrated in the ability to search its information. We provide five search tools, each with different characteristics. The Basic Search allows a simple query of many fields for a text term. The Intermediate Search
Advanced Searchallows the user to search specific tables, to search a range of molecular weights or isoelectric points and to search the protein or nucleotide sequences for simple patterns. The Protein Motif Search allows searching protein sequences for sophisticated amino acid patterns.'),('oral','Porphyromonas gingivalis','ATCC 33277','pgin2','Porphyromonas gingivalis is a gram-negative anaerobic bacterium, which is often found in deep periodontal pockets of humans, is asaccharolytic and highly proteolytic. Porphyromonas gingivalis produces a broad array of potential virulence factors involved in tissue colonization and destruction as well as host defense perturbation. Porphyromonas gingivalis strains have been classified into virulent and less-virulent strains by mouse subcutaneous soft tissue abscess model analysis. P. gingivalis ATCC 33277 classified as a less-virulent strain is the type strain of P. gingivalis and has been widely used for characterization of pathophysiological features of the microorganism. The complete genome sequence of P. gingivalis ATCC 33277 was done by Hattori Laboratory at University of Tokyo. The paper describing the complete genome is by Naito M, et al. 2008 “Determination of the Genome Sequence of Porphyromonas gingivalis Strain ATCC 33277 and Genomic Comparison with Strain W83 Revealed Extensive Genome Rearrangements in P. gingivalis (DNA Research, 2008).
The genome of P. gingivalis ATCC 33277 contains a chromosome of approximately 2.35 Mbp. G+C content of the chromosome is about 48 % GC and there are 2090 protein-coding sequences (CDSs), 4 RNA operons, and 53 tRNA genes in the ATCC 33277 genome. By genomic comparison with the virulent strain W83, 461 ATCC 33277-specific and 415 W83-specific CDSs were identified. Annotated genome of P. gingivalis ATCC 33277 was initially provided by Hattori Laboratory and we are manually checking and curating the annotation. The Genome Annotation ToolKit (ATK) was use to obtain evidence for determining final gene definitions. Several references pertaining to P. gingivalis ATCC 33277 that might be of interest to researchers in oral biology are summarized here. Please let us know if we have missed any relevant references.'),('oral','Prevotella intermedia','17','pintnew','Prevotella intermedia (formerly Bacteroides intermedius) is a gram-negative anaerobic pathogen involved in periodontal infections including vertical bone loss. It is reported to co-aggregate with P.gingivalis. It also happens to share some transposases with P.gingivalis. A large-scale similarity study of this genome in relation to P. gingivalis, B. fragilis, B. thetaiotaomicron and C. hutchinsoniii is under way and will be appended to this Web site in the very near future.
The P. intermedia genome sequence was kindly provided prior to publication by John Heidelberg at TIGR and by Margaret Duncan at the Forsyth Institute. Kai Leung at the US Army Dental Research provided the source DNA for the strain. We have annotated and created records for approximately 2178 chromosomal orfs plus two orfs from a characterized plasmid (pYHBi) and 642 orfs from what appears to be a megaplasmid (megaplasmids have been reported for P. intermedia however this one has not been studied to our knowledge). Hence the core information of the relational database consists of records with IDs PI0001 to PI2178, pYHBi01 and pYHBi02, and pPI0001 to pPI0642.
Browsing and searching are facilitated by the \'Functional Classes\', \'EC Table\', and \'Biochemical Pathways\' summaries. For precise inquiries on the other hand, start with the search capabilities and their associated tables. We invite anyone with questions or suggestions to contact us (oralgen@lanl.gov).
Sixty-five references covering years 2002-2004 have been drawn from the molecular subset of MedLine and included herein. If any pertinent reference over this time period has been inadvertantly omitted, please let us know.'),('oral','Streptococcus gordonii','CH1','sgor','Streptococcus gordonii is a commensal bacteria that usually colonizes the human tooth surfaces and is an important member of community that forms dental plaque. This bacteria is known to be involved in development of dental caries and also considered as a potential causative agent of bacterial endocarditis. Streptococcus gordonii strain Challis is a laboratory strain used extensively due to its well-characterized transformation system. The primary publication describing the genome of Streptococcus gordonii is by Vickerman et al, 2007, \"Genome-wide transcriptional changes in Streptococcus gordonii in response to competence signaling peptide\". J Bacteriol. 189(21):7799-807.
The genome of Streptococcus gordonii was sequenced by The Institute for Genomic Research (TIGR) and work was funded by NIDCR. Genome size of Streptococcus gordonii is approximately 2.2 Mbp, has a G+C content of 42% and encodes 2051 proteins. Each gene record is identified by a gene id, for example: SGO_0001 to SGO_2051. Annotated genome of Streptococcus gordonii was kindly provided to us by Dr. Steven Gill from University at Buffalo (Previously from TIGR) and we have manually checked and curated the annotation. The Genome Annotation ToolKit (ATK) was used for determining final gene definitions.
Transporter analysis was automatically done using the TransAAP program to aid in identifying all potential transporters and manually compared with final annotation definitions to check accuracy of predictions. Several references pertaining to Streptococcus gordonii Challis that might be of interest to researchers in oral biology are summarized here. Please let us know if we have missed any relevent references.'),('oral','Streptococcus mitis','NCTC 12261','smit','Streptococcus mitis is a Gram-positive commensal bacteria commonly found in the human mouth, throat and nasopharynx. Although not known to be pathogenic Streptococcus mitis is phylogenetically related to pathogenic streptococci and thus we included it in our group of organisms for comparative genomic analysis. Strain NCTC 12261 of Streptococcus mitis is the type strain of this species has a genome of approximately 1.84 Mb and a GC content of 40%. Sequencing of Streptococcus mitis NCTC 12261 is not yet completed and analysis we present here is based on draft genome sequence available. For questions regarding the sequencing and the strain, please contact Dr. Hervé Tettelin.
Streptococcus mitis NCTC 12261 was sequenced by The Institute for Genomic Research (TIGR) and funded by NIDCR. The core information for the database is a table of 2149 predicted open reading frams (ORFs). Each gene record is identified by a gene id, for example: SMT0001 to SMT2149. Record designations have some discontinuities and some IDs have number suffix of 1, 2, 3 etc. We did not annotate this genome but use it as one of the organisms for comparative genomic analysis of oral streptococci.
Basic summaries of specific information are available below in the Predefined Database Searches which contain links to the complete gene record. For a general perspective of the genome, we recommend you go to the Gene Image Map and browse blocks of coordinates. Caution: The entire 1.84 Mb genome can be viewed at one time, however this large file can cause some machines to freeze. Browsing and searching are also facilitated by the [Functional Classes], [EC Table], and [Biochemical Pathways] summaries. For precise inquiries on the other hand, start with the search capabilities and their associated tables. We encourage anyone with questions or suggestions to contact us at oralgen@lanl.gov'),('oral','Streptococcus mutans','UA159','smut','The 2.03 Mb genome of Streptococcus mutans UA159, a serotype C strain, was sequenced in 2002 by teams at the University of Oklahoma Health Sciences Center, Department of Microbiology and Immunology, and the University of Oklahoma, Department of Chemistry and Biochemistry, working under the aegis of the National Institute of Dental and Craniofacial Research (NIDCR) within the National Institutes of Health. The key publication describing this newly sequenced genome is \"Genome sequence of Streptococcus mutans UA159, a cariogenic dental pathogen\" by Ajdic D, McShan WM, McLaughlin RE, Savic G, Chang J, Carson MB, Primeaux C, Tian R, Kenton S, Jia H, Lin S, Qian Y, Li S, Zh H, Najar F, Lai H, White J, Roe BA and Ferretti JJ, PNAS 99:14434-14439 (PMID: 12397186). Approximately 250 additional and recent references pertaining to S. mutans have been extracted from a 2000-2006 molecular subset of PubMed. If we have overlooked any pertinent reference, please inform us (S. mutans references). Dr. Dragana Ajdic has been especially helpful in the foundational curation of this database.
Two S. mutans related plasmids, pUA140 and pLM7, have been included in this section. To access the gene records for these, use the Gene Image Map. A publication concerning these plasmids is Zou et al., 2001 (PMID: 11591133).
The core information in this database is the table of annotated records, one for each of the 1966 (1963 in the Ajdic paper) predicted open reading frames. Each gene record is identified by a gene id, SMu0001-SMu1964. Basic summaries of specific information are available below in the Predefined Database Searches and contain links to the complete gene record. A table cross-referencing the gene ids used in this database and the gene ids found in the GenBank record can be used to resolve differences in naming conventions (ID cross-reference).
For a general perspective of the genome, we recommend you go to the Gene Image Map and browse blocks of coordinates. Caution: The entire 2.03 Mb genome can be viewed at one time, however this large file can cause some machines to freeze. Browsing and searching are also facilitated by the Functional Classes, EC Table, and Biochemical Pathways summaries. For precise inquiries on the other hand, start with the search capabilities and their associated tables. Fuller analyses of the proteome are underway, for example a table of proteins found in S. mutans and not in S. pneumoniae, S. pyogenes and S. agalactiae is presented in the Streptococcus proteome comparison section of the database. Finally, we would encourage anyone with questions or suggestions to contact us at std_db@lanl.gov.
A special section concerning bacteriocin operons and genes has been added (Bacteriocins) and records for such -- not characteristic of the UA159 genome (although see below) -- have been added. These new records have IDs MI0001 - MI0015, MII0001 - MII0007, MIII0001 - MIII0008 and Smb0001 - Smb0007. Some bacteriocin-like genes have been located on two potential genetic islands in S. mutans UA159 (Genomic Island Table).
Note: Genome sequence of S. mutansUA159 was recently updated in Genbank and gene coordinates of S. mutans UA159 in our database is updated (Nov 21, 2007) to reflect this change. A few gene records were removed or merged in this update. See below.
SMu0925: Deleted
SMu1408: Merged with SMu1407 (Annotated as sensor histidine kinase)
SMu1449: Merged with SMu1450 (Annotated as carbonic anhydrase (carbonate dehydratase))'),('oral','Streptococcus sanguinis','SK36','ssan','Strain SK36 of Streptococcus sanguinis (formerly Streptococcus sanguis) is found to have a genome of approximately 2.39 Mb encoding approximately 2300 proteins. The key publication reporting this work is Xu, Alves, Kitten et al., Journal of Bacteriology 189: 3166-3175, 2007. Dr. Todd Kitten of Virginia Commenwealth University has been helpful in the foundational curation of this database. Approximately 25 recent references pertaining to S. sanguinis have been extracted from a 2002-2007 molecular subset of PubMed (S. sanguinis references). If we have overlooked any pertinent refernce, please inform us.
S. sanguinis is reported to inhibit the growth of periodontopathic bacteria such as S. mutans. One study proposes that a bacteriocin (sanguicin) of approximately 65 Kd is responsible for this effect (Deng et al., 2004). The coding sequence for this proposed bacteriocin has not been identified, however a BLAST comparison of mutacin and SMB proteins against S. sanguinis reveals similarities with ABC-related elements, a subtilisin-like protein and a Dfp-like protein. We have yet toidentify some genomic islands that could encode bacteriocin-related proteins.
Xu et al. make note of a 70 kb region that may have arisen through horizontal gene transmission (HGT) (SSA_0463 to SSA_0541). This stretch is not obviously similar to other strep sequences (see below) but is similar to Listeria and Lactobaccili sequences and clearly encodes genes related to cobalamin and degradation of ethanolamine and propanediol. The authors also identify nearly 200 other SSA genes as potential HGT elements (see Comments herein).
Sanguinis infection is regarded to be a major cause of endocarditis. Paik et al. (2005) identified a handful of virulence factors that are, for the most part, housekeeping genes: fimA, sloC, purB, etc. The records for these are annotated herein.
The core information for the database is a table of 2274 predicted open reading frames. Each gene record is identified by a gene id, SSA_0001-SSA_2394. Two definitions may be provided for each gene: an Oralgen determined Definition derives from extensive BLAST analyses against S. mutans, S. agalactiae and S. thermophilus. Tri-directional and bi-directional best hit relationships (bets) coupled with co-annotation to attain consistency across these genome databases, yields what we designate a Species (plural) Definition. A detailed description of this methodology is forthcoming. The second definition is that provided by GenBank. In the absence of a reciprocal best hit relationship among the above-named streps, the Oralgen-derived Definition field will be empty (this informs the user that a pre-defined bet relationship to mutans, agalactiae or thermophilus genomes was not found). These records may have manual annotation that casts light upon their specious nature.
Basic summaries of specific information are available below in the Predefined Database Searches which contain links to the complete gene record.
For a general perspective of the genome, we recommend you go to the Gene Image Map and browse blocks of coordinates. Caution: The entire 2.39 Mb genome can be viewed at one time, however this large file can cause some machines to freeze. Browsing and searching are also facilitated by the [Functional Classes], [EC Table], and [Biochemical Pathways] summaries. For precise inquiries on the other hand, start with the search capabilities and their associated tables. We encourage anyone with questions or suggestions to contact us at oralgen_db@lanl.gov'),('oral','Tannerella forsythensis','ATCC 43037','tfor','Tannerella forsythensis is an anaerobic Gram-negative member of the Cytophaga-Bacteroides family implicated in periodontal diseases. T. forsythensis, P. gingivalis and T. denticola form a \"red complex\" of species associated with aggressive periodontal infections (Socransky et al., 1998; Holt and Ebersole, 2000). This organism was described as Bacteroides forsythus 1986 (Tanner et al. 1986) and reclassified to Tannerella forsythensis based upon its phylogenetic position by Sakamoto et al. 2002. Distinguishing biochemical characteristics are reviewed in Sakamoto et al. A proposal has been made to have the epithet name revised to \"forsythia\" (Maiden et al., 2003).
Strain ATCC 43037 was provided by Floyd Dewhirst and Mark F. J. Maiden at The Forsyth Institute. The resulting sequence was provided prior to publication by Steve Gill and colleagues at the TIGR Institute (\"Genome analysis of Bacteroides forsythus\" NIH/ National Institute of Dental and Craniofacial Research (U01-DE13914) awarded to TIGR; Steven R. Gill, PI.) We thank Dr. Anne Tanner of The Forsyth Institute for providing helpful background information and references. Twenty-one References covering years 1994-2005 have been drawn from the molecular subset of MedLine and included herein. Please contact us to include inadvertently omitted references.
The core information in this database is the table of annotated records, one for each of the 3034 predicted open reading frames. Annotation of the completed genome made use of penta-directional comparisons with the dentoti database and with BLAST similarities to the NR database. Each gene record is identified by a gene id, TF0001-TF3165. Basic summaries of specific information are available below in the Predefined Database Searches and contain links to the complete gene record. At this time, GenBank entries are not available for this genome.
For a general perspective of the genome, we recommend you go to the Gene Image Map and browse blocks of coordinates. Caution: The entire TF genome can be viewed at one time, however this large file can cause some machines to freeze. Browsing and searching are also facilitated by the Functional Classes, EC Table, and Biochemical Pathways summaries. For precise inquiries on the other hand, start with the search capabilities and their associated tables. Fuller analyses of the proteome are underway, for example a table of proteins found in the Bacteroides-related proteome comparison section of the database.
'),('oral','Treponema denticola','ATCC 35405','tden_new','Treponema denticola is an obligatory anaerobe for which a complete genomic sequence is herein generously made available in advance of publication by George Weinstock, Steven Norris and colleagues at the Baylor College of Medicine and the University of Texas--Houston. This sequence is in GenBank under gi number 42516522 and a paper has been submitted (Seshadri, R et al., Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes. PNAS 2004, PMID: 15064399). Work on this genome was funded by NIDCR at the NIH (5R01DE012488-03). Strain 35405 was employed for the sequencing project. For questions regarding the sequencing and the strain, contact George Weinstock.Nearly 2800 orfs are encoded in the 2.8 Mb circular chromosome. Approximately 45 orfs predicted by the LANL Oralgen project but not by Seshadri, et al. and GenBank are included. The core information in this database is a table of annotated records: each gene record is identified by a gene ID, TDE0001 - TDE2786; be forewarned that record designations have some discontinuities and some IDs utilize the number suffix 1. Basic summaries of specific information are available below in the Predefined Database Searches that contain links to the particular gene record. Specialized analysis sections of the database are available below in the Specialized Analysis section.
Browsing and searching are also facilitated by the \'Functional Classes\', \'EC Table\', and \'Biochemical Pathways\' summaries. For precise inquiries on the other hand, start with the search capabilities and their associated tables. We invite anyone with questions or suggestions to contact us (oralgen@lanl.gov).
Twenty-nine references covering years 2002-2004 have been drawn from the molecular subset of MedLine and included herein. If any pertinent reference over this time period has been inadvertantly omitted, please let us know.
A plasmid sequence, pTS1, has been reported in association with T.denticola and is included in this database. This plasmid sequence, of approximately 3.6 kb, encodes 4 or more orfs some of which are thought to be involved in replication and mobilization. For further information about the plasmid, see Chauhan and Kuramitsu, Plasmid (2004) 51: 61-65 PMID: 14711531.
'),('oral','Oral Plasmid Collection','','oralpp','The Oralgen Team has assembled here the complete sequences of 9 plasmids found in five well-studied oral bacterial pathogens. The nine plasmids vary in size from a 3.6 Kb cryptic plasmid in Treponema denticola to the 580 Kb megaplasmid discovered in Prevotella intermedia. These plasmids\' hosts occupy the same environment and it is anticipated that the plasmids may share other characteristics. This collection will facilitate comparison among themselves as well as comparison with the larger oral metagenome as it becomes available. PLASMIDS
|
Streptococcus agalactiae 2603V/R has a genome of approximately 2.16 Mb encoding about 2200 proteins and a GC content of 35.6%. The key publication reporting this work is by Tettelin et al. \"Complete genome sequence and comparative genomic analysis of an emerging human pathogen, serotype V Streptococcus agalactiae\". Proc Natl Acad Sci USA 2002, 99(19):12391-12396. Streptococcus agalactiae 2603V/R was sequenced by The Institute for Genomic Research (TIGR) and funded by NIAID. The core information for the database is a table of 2177 predicted open reading frams (ORFs). Each gene record is identified by a gene id, for example: SAG0001 to SAG2175. Record designations have some discontinuities and some IDs have number suffix of 1, 2, 3 etc. We did not annotate this genome but use it as one of the organisms for comparative genomic analysis of oral streptococci.
Basic summaries of specific information are available below in the Predefined Database Searches which contain links to the complete gene record. For a general perspective of the genome, we recommend you go to the Gene Image Map and browse blocks of coordinates. Caution: The entire 2.16 Mb genome can be viewed at one time, however this large file can cause some machines to freeze. Browsing and searching are also facilitated by the [Functional Classes], [EC Table], and [Biochemical Pathways] summaries. For precise inquiries on the other hand, start with the search capabilities and their associated tables. Please note that some analyses are not yet available and we removed links to these pages. We encourage anyone with questions or suggestions to contact us at oralgen@lanl.gov
'),('neighbor','Streptococcus pneumoniae','TIGR4','spne','Streptococcus pneumoniae belongs to Gram-positive cocci that colonize normal human nasopharyngeal flora. Many antigenic types are present and their classification are based on the capsular antigens. Common diseases associated with Streptococcus pneumoniae are, sinusitis, acute bacterial otitis media, and conjunctivitis. Pneumonia, meningitis, and bacteremia are also known causes of Streptococcus pneumoniae.Strain TIGR4 of Streptococcus pneumoniae is a highly virulent serotype 4 strain isolated from a 30 year old male patient in Norway. It is found to have a genome of approximately 2.16 Mb encoding approximately 2100 proteins and a GC content of 39.7%. The key publication reporting this work is Tettelin et al. \"Complete genome sequence of a virulent isolate of Streptococcus pneumoniae\". Science 2001, 293(5529):498-506. Streptococcus pneumoniae TIGR4 was sequenced by The Institute for Genomic Research (TIGR) and funded by NIAID and MGRI. The core information for the database is a table of 2125 predicted open reading frames. Each gene record is identified by a gene id, SP_0001-SP_2240. Record designations have some discontinuities and some IDs have number suffix of 1, 2, 3 etc. We did not annotate this genome but use it as one of the organisms for comparative genomic analysis of oral streptococci.
Basic summaries of specific information are available below in the Predefined Database Searches which contain links to the complete gene record. For a general perspective of the genome, we recommend you go to the Gene Image Map and browse blocks of coordinates. Caution: The entire 2.16 Mb genome can be viewed at one time, however this large file can cause some machines to freeze. Browsing and searching are also facilitated by the [Functional Classes], [EC Table], and [Biochemical Pathways] summaries. For precise inquiries on the other hand, start with the search capabilities and their associated tables. We encourage anyone with questions or suggestions to contact us at oralgen@lanl.gov'),('neighbor','Streptococcus thermophilus','CNRZ1066','sther','Streptococcus thermophilus is a Gram-positive lactic acid producing bacteria that are used in production of yogurt and cheese. Although mainly used in food industry, Streptococcus thermophilus is phylogenetically related to pathogenic streptococci and has potential for virulence and we included it in our group of organisms for comparative genomic analysis. Strain CNRZ1066 of Streptococcus thermophilus was isolated from yogurt in France. It has a genome of approximately 1.80 Mb encoding about 1900 proteins and a GC content of 39.1%.
The key publication reporting this work is Bolotin et al. \"Complete sequence and comparative genome analysis of the dairy bacterium Streptococcus thermophilus\". Nature biotechnology 2004, 22(12):1554-1558. Streptococcus thermophilus CNRZ1066 was sequenced by Institut National de la Recherche Agronomique, France and funded by Walloon Region and FNRS. The core information for the database is a table of 1916 predicted open reading frams (ORFs). Each gene record is identified by a gene id, for example: STr0001 to STr2025. Record designations have some discontinuities and some IDs have number suffix of 1, 2, 3 etc. We did not annotate this genome but use it as one of the organisms for comparative genomic analysis of oral streptococci.
Basic summaries of specific information are available below in the Predefined Database Searches which contain links to the complete gene record. For a general perspective of the genome, we recommend you go to the Gene Image Map and browse blocks of coordinates. Caution: The entire 1.80 Mb genome can be viewed at one time, however this large file can cause some machines to freeze. Browsing and searching are also facilitated by the [Functional Classes], [EC Table], and [Biochemical Pathways] summaries. For precise inquiries on the other hand, start with the search capabilities and their associated tables. We encourage anyone with questions or suggestions to contact us at oralgen@lanl.gov'),('neighbor','Streptococcus pyogenes','M1 GAS','spyo','Streptococcus pyogenes M1 GAS has a genome of approximately 1.85 Mb encoding about 1697 proteins and a GC content of 39%. The key publication reporting this work is by Ferretti et al. \"Complete genome sequence of an M1 strain of Streptococcus pyogenes.\". Proc Natl Acad Sci USA 2001 Apr 10;98(8):4658-63. We did not annotate this genome but use it as one of the organisms for comparative genomic analysis of oral Streptococci. Basic summaries of specific information are available below in the Predefined Database Searches which contain links to the complete gene record. For a general perspective of the genome, we recommend you go to the Gene Image Map and browse blocks of coordinates. Caution: The entire 2.16 Mb genome can be viewed at one time, however this large file can cause some machines to freeze. Browsing and searching are also facilitated by the [Functional Classes], [EC Table], and [Biochemical Pathways] summaries. For precise inquiries on the other hand, start with the search capabilities and their associated tables. Please note that some analyses are not yet available and we removed links to these pages. We encourage anyone with questions or suggestions to contact us at oralgen@lanl.gov '),('neighbor','Streptococcus in Toto','','streptoto',''),('uncurated','Actinomyces odontolyticus','ATCC 17982 ','aodo',''),('uncurated','Fusobacterium nucleatum vincentii','ATCC 49256','fnucv',''),('uncurated','Parvimonas micra','ATCC 33270','pmic',''),('virus','Human Herpesvirus 1 HSV-1','HSV-1','hhv1','Human herpesvirus 1, strain 17, commonly called herpes simplex virus 1, was sequenced by the McGeoch laboratory and published in a series of papers from 1985-1988. These are included in a comprehensive set of references from Medline (1980-6/2000), HSV-1 References. Human herpesvirus 1 is a member of the Herpesviridae family. General properties are available here, Herpesviridae Properties. Interesting genome information and properties specific to HSV-1 are available here, HSV-1 Properties.
An overview map of the genome and information summary is available through the Gene Image Map. The newest version of this map clearly depicts coterminal and overlapping genes, genes coding on opposite strands and repeats, all of which are common in the tightly packed genomes of herpesviruses. A double-stranded interactive visualization tool, called BugBrowser , is now available.
The core information in this database is the table of annotated records, one for each of 90 genes. Each gene record is identified by a gene id, HHVONE001-HHVONE077 (some with extensions to total 90). Seventy-eight of the genes are unique and six (gamma34.5, Orf-P, Orf-O, alpha0, alpha4, and the LAT) appear twice in the genome, once in each copy of the inverted repeats. Simple summaries of specific information are available below in the Predefined Database Searches and contain links to the complete gene record.
The power of a relational database is demonstrated in the ability to search it\'s information. We provide five search tools, each with different characteristics. The Basic Search allows a simple query of many fields for a text term. The Intermediate Search
Advanced Searchallows the user to search specific tables, to search a range of molecular weights or isoelectric points and to search the protein or nucleotide sequences for simple patterns. The Protein Motif Search allows searching protein sequences for sophisticated amino acid patterns. Repeat Search queries the repeat table for previously located nucleotide repeats.'),('virus','Human Herpesvirus 2 HSV-2','HSV-2','hhv2','Strain HG52 of Human Herpesvirus 2, commonly called herpes simplex virus 2, was sequenced by the McGeoch laboratory and published in 1998. The key publication describing this 155 kbp circular genome is \"The Genome Sequence of Herpes Simplex Virus type 2\" by Dolan, Jamieson, Cunningham, Barnett, and McGeoch, J Virol, March 1998, p. 2010-2021, Vol. 72, No. 3 and is included in a comprehensive set of HSV-2 References from Medline (1980-7/2001). Human Herpesvirus 2 is a member of the Herpesviridae family. General Herpesviridae properties are available (Herpesviridae Properties), as well as genome and proteome information specific to HSV-2 (HSV-2 Properties).
An overview map of the genome and information summary is available through the Gene Image Map. The newest version of this map clearly depicts coterminal and overlapping genes, genes coding on opposite strands and repeats, all of which are common in the tightly packed genomes of herpesviruses.
The core information in this database is the table of annotated records, one for each of 83 genes. Each gene record is identified by a gene id, HHVTW001-HHVTW077 (some with extensions to total 83). Seventy-five of the genes are unique and four (gamma34.5, Orf-P, alpha0 and alpha4) appear twice in the genome, once in each copy of the inverted repeats. Three of the genes (gamma 34.5, alpha0 and UL15) have one or two introns. Simple summaries of specific information are available below in the Predefined Database Searches and contain links to the complete gene record.
The power of a relational database is demonstrated in the ability to search its information. We provide five search tools, each with different characteristics. The Basic Search allows a simple query of many fields for a text term. The Intermediate Search
Advanced Searchallows the user to search specific tables, to search a range of molecular weights or isoelectric points and to search the protein or nucleotide sequences for simple patterns. The Protein Motif Search allows searching protein sequences for sophisticated amino acid patterns. Repeat Search queries the repeat table for previously located nucleotide repeats.'),('virus','Human Herpesvirus 5 HCMV','HCMV','hhv5','The laboratory strain AD169 of Human cytomegalovirus, HCMV, (also called human herpesvirus 5, HHV-5) was first sequenced in 1989. The key publication is Chee et al. Curr Top Microbiol Immunol. 1990;154:125-69, PMID: 2161319. In 1996 a 13 kbp and 15 kbp sequence was discovered in the low-passage Toledo strain that was missing from the Towne and AD169 strains respectively, see Cha et al. J Virol. 1996 Jan;70(1):78-83. PMID:8523595. The annotation presented here is based on a more recent sequence and annotation of AD169 by A.J. Davison et al. described in J Gen Virol. 2003 Jan;84(Pt 1):17-28. PMID: 12533697. We include the unique Towne and Toledo sequences as two separate inserts with coordinates matching their GenBank annotation. Summaries of more than thirty genes written by scientists in the HCMV research community are included in the comment section of the gene record, and a comprehensive list of HCMV References from Medline is provided. General properties of herpesviruses are reviewed here, Herpesviridae Properties Also take note of a new resource named HGXbase which contains 1300 human genes identified by expression studies as modulated by herpesvirus infection (HSV-1, HCMV and KSHV).
A graphic overview of the genome is available through the Gene Image Map. The core information in this database is the table of annotated records, one for each gene. Each gene record is identified by a gene id, HCMV000.5-HCMV203 for the AD169 genes and HCMVi01-HCMVi25 for unique genes in the Toledo and Towne inserts. Many spliced genes have been identified including, UL22A, UL36, UL37, UL119, UL123, UL128 and US3. Simple summaries of specific information are available below in the Predefined Database Searches including more than 20 identified Cellular Homologs.
The power of a relational database is demonstrated in the ability to search its information. We provide five search tools, each with different characteristics. The Basic Search allows a simple query of many fields for a text term. The Intermediate Search
Advanced Searchallows the user to search specific tables, to search a range of molecular weights or isoelectric points and to search the protein or nucleotide sequences for simple patterns. The Protein Motif Search allows searching protein sequences for sophisticated amino acid patterns. Repeat Search queries the repeat table for previously located nucleotide repeats. Tandem Repeats Finder locates 18 exact and inexact tandem repeats (minimum alignment score 50). Seven exact direct repeats, some with inverted components, (minimum length 20) are located with Reputer.'),('virus','Human Herpesvirus 8 KSHV','KSHV','hhv8','Human herpesvirus 8 from the BC-1 cell line was sequenced by the Moore/Chang Laboratory, Columbia University in 1996, except for a 3kb region at the far right end of the genome that was refractory to cloning. The key publication describing this genome is \"Nucleotide sequence of the Kaposi sarcoma-associated herpesvirus (HHV8)\" by Russo et al. Proc Natl Acad Sci U S A 1996 Dec 10;93(25):14862-7 and is included in a comprehensive set of KSHV References from Medline (12/1994-1/2002). A second genomic sequence of an isolate from a KS lesion was generated by the Neipel laboratory and published a year later (J Virol 1997 Jun;71(6):4187-92). Generally, less than 1% sequence variation is present between the two strains although hotspots of high sequence variability are present.
Kaposi\'s sarcoma, a vascular tumor seen very rarely except in immuno-suppressed people, was shown in 1994 to be closely associated with a sexually transmitted and newly identified member of the Herpesviridae family of viruses, namely Human herpesvirus 8. General properties of herpesviruses are reviewed here, Herpesviridae Properties.
An overview map of the genome and information summary is available through the Gene Image Map. The newest version of this map clearly depicts coterminal and overlapping genes, genes coding on opposite strands and repeats, all of which are common in the tightly packed genomes of herpesviruses. Expression Patterns illustrate the cellular localization of several important KSHV proteins.
The core information in this database is the table of annotated records, one for each of 87 genes. Each gene record is identified by a gene id, KSHV001-083 (some with extensions to total 87). Five spliced genes have been located, ORF50 (2 exons), K8 (3 exons), K10.5 (2 exons), K15 (8 exons) while K8.1 with 2 exons is known to be alternatively spliced. Simple summaries of specific information are available below in the Predefined Database Searches including 23 identified Cellular Homologs.
The power of a relational database is demonstrated in the ability to search its information. We provide five search tools, each with different characteristics. The Basic Search allows a simple query of many fields for a text term. The Intermediate Search
Advanced Searchallows the user to search specific tables, to search a range of molecular weights or isoelectric points and to search the protein or nucleotide sequences for simple patterns. The Protein Motif Search allows searching protein sequences for sophisticated amino acid patterns. Repeat Search queries the repeat table for previously located nucleotide repeats.'),('virus','Pseudorabies Virus PRV','PRV','prv1','The DNA sequence of Pseudorabies Virus (PRV), also called Suid Herpesvirus 1, presented here is based on the Kaplan strain with segments incorporated from five other strains and several new sequences. This sequence comes from a strategy by the Mettenleiter lab in Germany and the Enquist lab at Princeton University to solve the difficulty of precision sequencing a genome with 74% G+C content. The key publication describing this integrated genome is \"The Complete Annotated Sequence of the Pseudorabies Virus Genome\" by Klupp, Hengartner, Mettenleiter and Enquist, Journal of Virology (in press 2003).
Pseudorabies virus, a non-human pathogen, is included in this collection because of it\'s importance as an alphaherpesvirus model, both in cell biology and pathogenesis. In addition, the PRV genome provides a close, almost one to one, correspondence of genes to HSV-1, a sexually transmitted infection, and VZV, a common childhood infection causing chicken pox. The low sequence similarity of genes, but similar function, provides useful comparisons of gene action. The close relationship between transcript arrangement of PRV, HSV-1, and VZV increases the importance of this comparison. A comprehensive list of PRV References from Medline (1993-2003) is provided. General properties of herpesviruses are reviewed here, Herpesviridae Properties
A graphic overview of the genome is available through the Gene Image Map. The core information in this database is the table of annotated records, one for each gene. Each gene record is identified by a gene id, PRV001 - PRV077. Simple summaries of specific information are available below in the Predefined Database Searches including a complete UTR Table. A program called Tandem Repeats Finder located 77 exact and inexact tandem repeats (mi nimum alignment score 50). Fifty-eight exact direct repeats and 15 more with inverted components, (minimum length 20 bp) were located with Reputer.
The power of a relational database is demonstrated in the ability to search its information. We provide five search tools, each with different characteristics.The Basic Search allows a simple query of many fields for a text term. The Intermediate Search allows the user to search specific tables, to search a range of molecular weights or isoelectric points and to search the protein or nucleotide sequences for simple patterns. The Protein Motif Search allows searching protein sequences for sophisticated amino acid patterns.'),('uncurated','Aggregatibacter actinomycetemcomitans','D11S-1 ','AAD11S1','Aggregatibacter actinomycetemcomitans.
Aggregatibacter actinomycetemcomitans, previously Actinobacillus actinomycetemcomitans typically resides in the oral cavity of humans and animals and can cause a number of diseases. The bacterium, along with 3 other organisms, is the main culprit in periodontis, which results in devastation to the bone supporting the teeth. Adherence to oral surfaces is controlled through the tad (tight adherence) locus, which may express proteins that are involved in type IV secretion. The bacterium actively suppresses immune responses through a number of secreted proteins, two of which are toxins; leukotoxin and cytolethal distending toxin. This organism causes bone destruction by interfering with the osteoblast/osteoclast (bone-forming cell/bone resorption cell) control mechanisms that normally ensure constant bone remodeling through a number of expressed proteins. Aggregatibacter actinomycetemcomitans can also invade nonphagocytic cells and spread intercellularly, causing apoptotic destruction of host epithelial layers.\n\nThis major clonal lineages of the Gram-negative periodontal pathogen Aggregatibacter actinomycetemcomitans include serotype a, b, and c strains. A complete genome sequence of serotype c strain D11S-1, recovered from the subgingival plaque of a patient diagnosed with generalized aggressive periodontitis, is herein generously made available by Casey Chen and his colleagues at Herman Ostrow School of Dentistry of the University of Southern California. Their work on this genome was funded by NIDCR grant R01 DE12212 at the NIH. The genome paper for Strain D11S-1 has been published on Journal of Bacteriology, December 2009, p. 7378-7379, Vol. 191, No. 23 (PMID: 19820097) and its draft sequences has been deposited to the Genbank (Project ID: 41333). For questions regarding the sequencing and the strain, contact Casey Chen. \n\nAnother comparative genome paper covering the years until 2011 and drawn from the molecular subset of Medline are included (BMC Genomics. 2010 Sep 8;11:489. PMID:20825670), please let us know of any pertinent reference that may have been omitted. We invite anyone with questions or suggestions to contact us ( oralgen@lanl.gov).'),('uncurated','Aggregatibacter actinomycetemcomitans','D7S-1 ','AAD7S1','Aggregatibacter actinomycetemcomitans.
Aggregatibacter actinomycetemcomitans, previously Actinobacillus actinomycetemcomitans typically resides in the oral cavity of humans and animals and can cause a number of diseases. The bacterium, along with 3 other organisms, is the main culprit in periodontis, which results in devastation to the bone supporting the teeth. Adherence to oral surfaces is controlled through the tad (tight adherence) locus, which may express proteins that are involved in type IV secretion. The bacterium actively suppresses immune responses through a number of secreted proteins, two of which are toxins; leukotoxin and cytolethal distending toxin. This organism causes bone destruction by interfering with the osteoblast/osteoclast (bone-forming cell/bone resorption cell) control mechanisms that normally ensure constant bone remodeling through a number of expressed proteins. Aggregatibacter actinomycetemcomitans can also invade nonphagocytic cells and spread intercellularly, causing apoptotic destruction of host epithelial layers.\n\nThis major clonal lineages of the Gram-negative periodontal pathogen Aggregatibacter actinomycetemcomitans include serotype a, b, and c strains. A draft genome sequence of a naturally competent serotype a strain, D7S-1, isolated from a patient with aggressive periodontitis, is herein generously made available by Casey Chen and his colleagues at Herman Ostrow School of Dentistry of the University of Southern California. Their work on this genome was funded by NIDCR grant R01 DE12212 at the NIH. The genome paper for Strain D7S-1 has been published on Journal of Bacteriology, May 2010, p. 2643-2644, Vol. 192, No. 10 (PMID: 20348265) and its draft sequences has been deposited to the Genbank (Project ID: 46989). For questions regarding the sequencing and the strain, contact Casey Chen. \n\nAnother comparative genome paper covering the years until 2011 and drawn from the molecular subset of Medline are included (BMC Genomics. 2010 Sep 8;11:489. PMID:20825670), please let us know of any pertinent reference that may have been omitted. We invite anyone with questions or suggestions to contact us ( oralgen@lanl.gov).');
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