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Pacodom: Pathogen Protein Conserved Domains

Pacodom stores and allows searching for conserved domains of proteins from pathogen genomes analyzed in PHIDIAS. Boolean mode is supported for the following searchs, and the default mode is AND. A query quoted in parentheses, for example, "intracellular signaling", is considered as one phrase instead of individual words.

Search for pathogen proteins and containing conserved domains:
Genome:	All Bacillus anthracis (5 genomes) Bacillus anthracis plasmid pX02 Bacillus anthracis str. 'Ames Ancestor' plasmid pXO2 Bacillus anthracis str. A2012 plasmid pXO2 Bacillus anthracis str. Ames Bacillus anthracis str. Sterne Brucella (8 genomes) Brucella abortus bv. 1 str. 9-941 chromosome II Brucella abortus S19 chromosome 2 Brucella canis ATCC 23365 chromosome II Brucella melitensis 16M chromosome II Brucella melitensis biovar Abortus 2308 chromosome II Brucella ovis ATCC 25840 chromosome II Brucella suis 1330 chromosome II Brucella suis ATCC 23445 chromosome II Burkholderia mallei (4 genomes) Burkholderia mallei ATCC 23344 chromosome 2 Burkholderia mallei NCTC 10229 chromosome II Burkholderia mallei NCTC 10247 chromosome II Burkholderia mallei SAVP1 chromosome II Burkholderia pseudomallei (4 genomes) Burkholderia pseudomallei 1106a chromosome II Burkholderia pseudomallei 1710b chromosome II Burkholderia pseudomallei 668 chromosome II Burkholderia pseudomallei K96243 chromosome 2 Campylobacter jejuni (6 genomes) Campylobacter jejuni plasmid pCJ419 Campylobacter jejuni RM1221 Campylobacter jejuni subsp. doylei 269.97 Campylobacter jejuni subsp. jejuni 81-176 plasmid pVir Campylobacter jejuni subsp. jejuni 81116 Campylobacter jejuni subsp. jejuni NCTC 11168 Clostridium botulinum (8 genomes) Clostridium botulinum A str. ATCC 19397 Clostridium botulinum A str. ATCC 3502 plasmid pBOT3502 Clostridium botulinum A str. Hall Clostridium botulinum A3 str. Loch Maree plasmid pCLK Clostridium botulinum B str. Eklund 17B plasmid pCLL Clostridium botulinum B1 str. Okra plasmid pCLD Clostridium botulinum E3 str. Alaska E43 Clostridium botulinum F str. Langeland plasmid pCLI Clostridium perfringens (5 genomes) Clostridium perfringens plasmid pCW3 Clostridium perfringens ATCC 13124 Clostridium perfringens CPE str. F4969 plasmid pCPF4969 Clostridium perfringens SM101 plasmid 2 Clostridium perfringens str. 13 plasmid pCP13 Clostridium tetani (1 genomes) Clostridium tetani E88 plasmid pE88 Coxiella burnetii (5 genomes) Coxiella burnetii plasmid QpH1 Coxiella burnetii 'MSU Goat Q177' plasmid QpRS Coxiella burnetii Dugway 5J108-111 plasmid pQpDG Coxiella burnetii RSA 331 plasmid QpH1 Coxiella burnetii RSA 493 plasmid pQpH1 Crimean-Congo hemorrhagic fever virus (1 genomes) Crimean-Congo hemorrhagic fever virus segment S Cryptosporidium parvum (1 genomes) Cryptosporidium parvum Iowa II chromosome 8 Eastern equine encephalitis virus (1 genomes) Eastern equine encephalitis virus Escherichia coli (17 genomes) Escherichia coli plasmid R721 Escherichia coli 1520 plasmid pIP1206 Escherichia coli 536 Escherichia coli 53638 plasmid p53638_75 Escherichia coli APEC O1 plasmid pAPEC-O1-R Escherichia coli ATCC 8739 Escherichia coli CFT073 Escherichia coli E24377A plasmid pETEC_80 Escherichia coli HS Escherichia coli O157:H7 EDL933 plasmid pO157 Escherichia coli O157:H7 str. EC4115 plasmid pO157 Escherichia coli O157:H7 str. Sakai plasmid pOSAK1 Escherichia coli SE11 plasmid pSE11-6 Escherichia coli SMS-3-5 plasmid pSMS35_8 Escherichia coli str. K12 substr. DH10B Escherichia coli str. K12 substr. MG1655 Escherichia coli UTI89 plasmid pUTI89 Foot-and-mouth disease virus (7 genomes) Foot-and-mouth disease virus - type A Foot-and-mouth disease virus - type Asia 1 Foot-and-mouth disease virus - type C Foot-and-mouth disease virus - type O Foot-and-mouth disease virus - type SAT 1 Foot-and-mouth disease virus - type SAT 2 Foot-and-mouth disease virus - type SAT 3 Francisella tularensis (10 genomes) Francisella tularensis plasmid pOM1 Francisella tularensis subsp. holarctica Francisella tularensis subsp. holarctica FTNF002-00 Francisella tularensis subsp. holarctica OSU18 Francisella tularensis subsp. mediasiatica FSC147 Francisella tularensis subsp. novicida plasmid pFNL10 Francisella tularensis subsp. novicida U112 Francisella tularensis subsp. tularensis FSC198 Francisella tularensis subsp. tularensis SCHU S4 Francisella tularensis subsp. tularensis WY96-3418 Guanarito virus (1 genomes) Guanarito virus segment segment S Haemophilus influenzae (6 genomes) Haemophilus influenzae plasmid ICEhin1056 Haemophilus influenzae 86-028NP Haemophilus influenzae biotype aegyptius plasmid pF3031 Haemophilus influenzae PittEE Haemophilus influenzae PittGG Haemophilus influenzae Rd KW20 Hantavirus (9 genomes) Andes virus segment Segment S Dobrava-Belgrade virus segment segment S Hantaan virus segment segment S Hantavirus Z10 segment segment S Puumala virus segment segment S Seoul virus segment segment S Sin Nombre virus segment segment S Thottapalayam virus segment S Tula virus segment segment S Helicobacter (9 genomes) Helicobacter acinonychis str. Sheeba plasmid pHac1 Helicobacter hepaticus ATCC 51449 Helicobacter pylori plasmid pHPO100 Helicobacter pylori 26695 Helicobacter pylori G27 plasmid pHPG27 Helicobacter pylori HPAG1 plasmid pHPAG1 Helicobacter pylori J99 Helicobacter pylori P12 plasmid HPP12 Helicobacter pylori Shi470 Hepatitis A virus (1 genomes) Hepatitis A virus Hepatitis B virus (1 genomes) Hepatitis B virus Human immunodeficiency virus (2 genomes) Human immunodeficiency virus 1 Human immunodeficiency virus 2 Japanese encephalitis virus (1 genomes) Japanese encephalitis virus Junin virus (1 genomes) Junin virus segment segment S Lake Victoria marburgvirus (1 genomes) Lake Victoria marburgvirus Lassa virus (2 genomes) Lassa virus segment segment S Mopeia Lassa reassortant 29 segment S Legionella pneumophila (4 genomes) Legionella pneumophila str. Corby Legionella pneumophila str. Lens plasmid pLPL Legionella pneumophila str. Paris plasmid pLPP Legionella pneumophila subsp. pneumophila str. Philadelphia 1 Listeria monocytogenes (2 genomes) Listeria monocytogenes EGD-e Listeria monocytogenes str. 4b F2365 Louping ill virus (1 genomes) Louping ill virus Machupo virus (1 genomes) Machupo virus segment segment S Measles virus (1 genomes) Measles virus Mumps virus (1 genomes) Mumps virus Mycobacterium tuberculosis (4 genomes) Mycobacterium tuberculosis CDC1551 Mycobacterium tuberculosis F11 Mycobacterium tuberculosis H37Ra Mycobacterium tuberculosis H37Rv Neisseria meningitidis (5 genomes) Neisseria meningitidis plasmid pJS-B Neisseria meningitidis 053442 Neisseria meningitidis FAM18 Neisseria meningitidis MC58 Neisseria meningitidis Z2491 Newcastle disease virus (1 genomes) Newcastle disease virus Plasmodium falciparum (2 genomes) Plasmodium falciparum organelle mitochondrion Plasmodium falciparum 3D7 chromosome 9 Poliovirus (1 genomes) Poliovirus Powassan virus (1 genomes) Powassan virus Rabies virus (1 genomes) Rabies virus Reston ebolavirus (1 genomes) Reston ebolavirus Rickettsia prowazekii (1 genomes) Rickettsia prowazekii str. Madrid E Rickettsia rickettsii (2 genomes) Rickettsia rickettsii str. 'Sheila Smith' Rickettsia rickettsii str. Iowa Rift Valley fever virus (1 genomes) Rift Valley fever virus segment segment S Rotavirus (3 genomes) Adult diarrheal rotavirus strain J19 Rotavirus A segment 9 Rotavirus C segment 9 Rubella virus (1 genomes) Rubella virus Salmonella (31 genomes) Salmonella choleraesuis plasmid pSFD10 Salmonella enterica plasmid pOU1113 Salmonella enterica subsp. arizonae serovar 62:z4,z23:-- Salmonella enterica subsp. enterica serovar Agona str. SL483 plasmid unnamed Salmonella enterica subsp. enterica serovar Berta plasmid pBERT Salmonella enterica subsp. enterica serovar Brandenburg plasmid pUO-SbR5 Salmonella enterica subsp. enterica serovar Choleraesuis plasmid pOU7519 Salmonella enterica subsp. enterica serovar Choleraesuis str. SC plasmid pSCV50 Salmonella enterica subsp. enterica serovar Dublin plasmid pOU1115 Salmonella enterica subsp. enterica serovar Dublin str. CT_02021 plasmid pCT02021853_74 Salmonella enterica subsp. enterica serovar Enteritidis plasmid pSE34 Salmonella enterica subsp. enterica serovar Enteritidis str. P12 Salmonella enterica subsp. enterica serovar Gallinarum str. 287/ Salmonella enterica subsp. enterica serovar Heidelberg str. SL47 plasmid pSL476_91 Salmonella enterica subsp. enterica serovar Kentucky str. CVM291 plasmid pCVM29188_46 Salmonella enterica subsp. enterica serovar Newport plasmid pA172 Salmonella enterica subsp. enterica serovar Newport str. SL254 plasmid pSN254 Salmonella enterica subsp. enterica serovar Paratyphi A plasmid pGY1 Salmonella enterica subsp. enterica serovar Paratyphi A str. AKU Salmonella enterica subsp. enterica serovar Paratyphi A str. ATC Salmonella enterica subsp. enterica serovar Paratyphi B str. SPB Salmonella enterica subsp. enterica serovar Schwarzengrund str. plasmid pCVM19633_4 Salmonella enterica subsp. enterica serovar Typhi str. 404ty plasmid pBSSB1 Salmonella enterica subsp. enterica serovar Typhi str. CT18 plasmid pHCM2 Salmonella enterica subsp. enterica serovar Typhi str. Ty2 Salmonella enterica subsp. enterica serovar Typhimurium plasmid pTPqnrS-1a Salmonella enterica subsp. enterica serovar Virchow str. SL491 plasmid pSL491_5 Salmonella enteritidis plasmid pP Salmonella typhi plasmid R27 Salmonella typhimurium plasmid R64 Salmonella typhimurium LT2 plasmid pSLT Shigella (10 genomes) Shigella boydii CDC 3083-94 plasmid pBS512_7 Shigella boydii Sb227 plasmid pSB4_227 Shigella dysenteriae Sd197 plasmid pSD1_197 Shigella flexneri plasmid pWR501 Shigella flexneri 2a plasmid p2457TS2 Shigella flexneri 2a str. 2457T Shigella flexneri 2a str. 301 plasmid pCP301 Shigella flexneri 5 str. 8401 Shigella sonnei plasmid pKKTET7 Shigella sonnei Ss046 plasmid pSS_046 Streptococcus pneumoniae (7 genomes) Streptococcus pneumoniae plasmid pSpnP1 Streptococcus pneumoniae CGSP14 Streptococcus pneumoniae D39 plasmid pDP1 Streptococcus pneumoniae G54 Streptococcus pneumoniae Hungary19A-6 Streptococcus pneumoniae R6 Streptococcus pneumoniae TIGR4 Vaccinia virus (1 genomes) Vaccinia virus Varicella-zoster virus (1 genomes) Human herpesvirus 3 Variola virus (1 genomes) Variola virus Venezuelan equine encephalitis virus (1 genomes) Venezuelan equine encephalitis virus Vibrio (19 genomes) Vibrio cholerae plasmid pVCG4.1 Vibrio cholerae O1 biovar eltor str. N16961 chromosome II Vibrio cholerae O395 chromosome 2 Vibrio fischeri ES114 plasmid pES100 Vibrio fischeri MJ11 plasmid pMJ100 Vibrio harveyi ATCC BAA-1116 plasmid pVIBHAR Vibrio nigripulchritudo plasmid pSFn1 Vibrio parahaemolyticus plasmid pSA19 Vibrio parahaemolyticus RIMD 2210633 chromosome II Vibrio shilonii plasmid pAK1 Vibrio sp. 09022 plasmid p09022A Vibrio sp. 0908 plasmid p0908 Vibrio sp. 23023 plasmid p23023 Vibrio sp. 41 plasmid pPS41 Vibrio sp. TC68 plasmid pTC68 Vibrio tapetis plasmid pVT1 Vibrio vulnificus plasmid pR99 Vibrio vulnificus CMCP6 chromosome II Vibrio vulnificus YJ016 plasmid pYJ016 Western equine encephalitis virus (1 genomes) Western equine encephalomyelitis virus Yellow fever virus (1 genomes) Yellow fever virus Yersinia pestis (10 genomes) Yersinia pestis plasmid pYC Yersinia pestis Angola plasmid pMT-pPCP Yersinia pestis Antiqua plasmid pPCP Yersinia pestis biovar Microtus str. 91001 plasmid pPCP1 Yersinia pestis biovar Orientalis str. IP275 plasmid pIP1202 Yersinia pestis CA88-4125 plasmid pMT1 Yersinia pestis CO92 plasmid pPCP1 Yersinia pestis KIM plasmid pPCP1 Yersinia pestis Nepal516 plasmid pPCP Yersinia pestis Pestoides F plasmid MT
Protein GI:
Protein Accession:
Locus Tag:
Gene Sybmol:
Gene ID :
Description:

Search for conserved domains and related proteins:
Conserved domain database name:	All CDD COG KOG LOAD pfam PSSM
Conserved domain ID:
Conserved domain name:
Description:

NOTE: To search for conserved domains based on sequence similarity, please go to RPS BLAST.

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Statisitcs: The Pacodom module stores 7938 position-specific scoring matrices (PSSM) found from 153166 (75.9% of 201749) protein sequences. These 7938 PSSMs are assembled to form a customized RPS BLAST library for our RPS BLAST program.

Provenance: The data in Pacodom are originally extracted from NCBI CDD database and then processed using the workflow described below.

Pacodom workflow: