YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|213999840
Organism:	Salmonella enterica subsp. enterica serovar Typhi str. E98-3139
Length:	294 amino acids
Reference:	Drew K, et al. (2011) The proteome folding project: Proteome-scale prediction of structure and function. Genome Res. 2011 Sep 16

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Top Sequence Alignment Hits

Listed below are up to the top 10 sequence alignment matches, by species, for the PSI-BLAST search against the protein sequence for gi|213999840.

Description	E-value	Query Range	Subject Range
gi\|205338512, gi... - gi\|205338512\|gb\|EDZ25276.1\| cytidine deaminase [Salmonella enterica subsp. enterica serovar Heidelbe... gi\|205335640, gi... - gi\|205335640\|gb\|EDZ22404.1\| cytidine deaminase [Salmonella enterica subsp. enterica serovar Kentucky... gi\|167991110, gi... - gi\|205330501\|gb\|EDZ17265.1\| cytidine deaminase [Salmonella enterica subsp. enterica serovar 4,[5],12... CDD_SALHS - Cytidine deaminase OS=Salmonella heidelberg (strain SL476) GN=cdd PE=3 SV=1 gi\|205345128, gi... - gi\|205345128\|gb\|EDZ31892.1\| cytidine deaminase [Salmonella enterica subsp. enterica serovar Weltevre... gi\|168466137, gi... - gi\|195631358\|gb\|EDX49918.1\| cytidine deaminase [Salmonella enterica subsp. enterica serovar Newport ... gi\|168259476, gi... - gi\|205350906\|gb\|EDZ37537.1\| cytidine deaminase [Salmonella enterica subsp. enterica serovar Hadar st... CDD_SALTY - Cytidine deaminase OS=Salmonella typhimurium GN=cdd PE=3 SV=1 lcl\|NC_016856.1_... - [gene=cdd] [protein=cytidine deaminase] [protein_id=YP_005238229.1] [location=2330719..2331603] gi\|238912625 - gi\|238912625\|ref\|ZP_04656462.1\| cytidine deaminase [Salmonella enterica subsp. enterica serovar Tenn... CDD_SALTY - Cytidine deaminase OS=Salmonella typhimurium GN=cdd PE=3 SV=1 CDD_SALPB - Cytidine deaminase OS=Salmonella paratyphi B (strain ATCC BAA-1250 / SPB7) GN=cdd PE=3 SV=1 CDD_SALG2 - Cytidine deaminase OS=Salmonella gallinarum (strain 287/91 / NCTC 13346) GN=cdd PE=3 SV=1 gi\|200388921, gi... - gi\|200388921\|ref\|ZP_03215533.1\| cytidine deaminase [Salmonella enterica subsp. enterica serovar Virc... CDD_SALTY - Cytidine deaminase OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) GN=cdd PE=3 SV=1 gi\|197261992, gi... - gi\|197261992\|ref\|ZP_03162066.1\| cytidine deaminase [Salmonella enterica subsp. enterica serovar Sain... gi\|194472954, gi... - gi\|194472954\|ref\|ZP_03078938.1\| cytidine deaminase [Salmonella enterica subsp. enterica serovar Kent... CDD_SALPB - Cytidine deaminase OS=Salmonella paratyphi B (strain ATCC BAA-1250 / SPB7) GN=cdd PE=3 SV=1 CDD_SALPC - Cytidine deaminase OS=Salmonella paratyphi C (strain RKS4594) GN=cdd PE=3 SV=1 CDD_SALEP - Cytidine deaminase OS=Salmonella enteritidis PT4 (strain P125109) GN=cdd PE=3 SV=1	4.0E-96	[1..294]	[1..294]
CDD_SALCH - Cytidine deaminase OS=Salmonella choleraesuis (strain SC-B67) GN=cdd PE=3 SV=1 CDD_SALCH - Cytidine deaminase OS=Salmonella choleraesuis GN=cdd PE=3 SV=1 CDD_SALCH - Cytidine deaminase OS=Salmonella choleraesuis GN=cdd PE=3 SV=1	2.0E-95	[1..294]	[1..294]
CDD_SALPA - Cytidine deaminase OS=Salmonella paratyphi A GN=cdd PE=3 SV=1 CDD_SALPA - Cytidine deaminase OS=Salmonella paratyphi A (strain ATCC 9150 / SARB42) GN=cdd PE=3 SV=1 CDD_SALPK - Cytidine deaminase OS=Salmonella paratyphi A (strain AKU_12601) GN=cdd PE=3 SV=1	2.0E-95	[1..294]	[1..294]
gi\|37198892, gi\|... - gi\|37680146\|ref\|NP_934755.1\| cytidine deaminase [Vibrio vulnificus YJ016], gi\|37198892\|dbj\|BAC94726....	2.0E-92	[1..290]	[8..297]
gi\|75242960, gi\|... - gi\|75242960\|ref\|ZP_00726666.1\| COG0295: Cytidine deaminase [Escherichia coli F11], gi\|191170069\|ref\|... sp\|B7UFF9\|CDD_ECO27 - Cytidine deaminase OS=Escherichia coli O127:H6 (strain E2348/69 / EPEC) GN=cdd PE=3 SV=1 CDD_ECOK1 - Cytidine deaminase OS=Escherichia coli O1:K1 / APEC GN=cdd PE=3 SV=1 CDD_ECOL6 - Cytidine deaminase OS=Escherichia coli O6 GN=cdd PE=3 SV=1 CDD_ECOL6 - Cytidine deaminase OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) GN=cdd PE=3 SV=1 CDD_ECO27 - Cytidine deaminase OS=Escherichia coli O127:H6 (strain E2348/69 / EPEC) GN=cdd PE=3 SV=1 CDD_ECO45 - Cytidine deaminase OS=Escherichia coli O45:K1 (strain S88 / ExPEC) GN=cdd PE=3 SV=1 CDD_ECOL5 - Cytidine deaminase OS=Escherichia coli O6:K15:H31 (strain 536 / UPEC) GN=cdd PE=3 SV=1 CDD_ECO81 - Cytidine deaminase OS=Escherichia coli O81 (strain ED1a) GN=cdd PE=3 SV=1 CDD_ECOLU - Cytidine deaminase OS=Escherichia coli O17:K52:H18 (strain UMN026 / ExPEC) GN=cdd PE=3 SV=1 gi\|226900974, gi... - gi\|237704608\|ref\|ZP_04535089.1\| cytidine deaminase [Escherichia sp. 3_2_53FAA], gi\|226900974\|gb\|EEH8... CDD_ECOUT - Cytidine deaminase OS=Escherichia coli (strain UTI89 / UPEC) GN=cdd PE=3 SV=1 gi\|227887198, gi... - gi\|227887198\|ref\|ZP_04005003.1\| cytidine deaminase [Escherichia coli 83972], gi\|227835548\|gb\|EEJ4601...	3.0E-92	[1..293]	[1..293]
gi\|27365698, gi\|... - gi\|27365698\|ref\|NP_761226.1\| cytidine deaminase [Vibrio vulnificus CMCP6], gi\|27361847\|gb\|AAO10753.1...	7.0E-92	[1..290]	[8..297]
CDD_VIBVU - Cytidine deaminase OS=Vibrio vulnificus (strain CMCP6) GN=cdd PE=3 SV=2 CDD_VIBVU - Cytidine deaminase OS=Vibrio vulnificus GN=cdd PE=3 SV=2	9.0E-92	[1..290]	[1..290]
EG10137 - cytidine /deoxycytidine deaminase / Cytidine deaminase; 2-deoxycytidine deaminase; mutants are 5-fluo... CDD_ECOBW - Cytidine deaminase OS=Escherichia coli (strain K12 / MC4100 / BW2952) GN=cdd PE=3 SV=1 gi\|242377785, gi... - gi\|251785512\|ref\|YP_002999816.1\| hypothetical protein B21_02031 [Escherichia coli BL21], gi\|24237778... gi\|253772930, gi... - gi\|254288919\|ref\|YP_003054667.1\| cytidine deaminase [Escherichia coli BL21(DE3)], gi\|253978226\|gb\|AC... CDD_ECOLI - Cytidine deaminase (EC 3.5.4.5) (Cytidine aminohydrolase) (CDA) - Escherichia coli gi\|253974058, gi... - gi\|254162157\|ref\|YP_003045265.1\| cytidine deaminase [Escherichia coli B str. REL606], gi\|253974058\|g... CDD_SHIF8 - Cytidine deaminase OS=Shigella flexneri serotype 5b (strain 8401) GN=cdd PE=3 SV=1 CDD_SHIFL - Cytidine deaminase OS=Shigella flexneri GN=cdd PE=3 SV=1 gi\|24113533, gi\|... - gi\|24113533\|ref\|NP_708043.1\| cytidine deaminase [Shigella flexneri 2a str. 301], gi\|24052577\|gb\|AAN4... CDD_SHIBS - Cytidine deaminase OS=Shigella boydii serotype 4 (strain Sb227) GN=cdd PE=3 SV=1 gi\|30041840, gi\|... - gi\|30063587\|ref\|NP_837758.1\| cytidine deaminase [Shigella flexneri 2a str. 2457T], gi\|30041840\|gb\|AA... EG10137 - cytidine /deoxycytidine deaminase / Cytidine deaminase; 2-deoxycytidine deaminase; mutants are 5-fluo... CDD_SHISS - Cytidine deaminase OS=Shigella sonnei (strain Ss046) GN=cdd PE=3 SV=1 gi\|75514518, gi\|... - gi\|75514518\|ref\|ZP_00736796.1\| COG0295: Cytidine deaminase [Escherichia coli 53638], gi\|188493466\|re... CDD_ECOSM - Cytidine deaminase OS=Escherichia coli (strain SMS-3-5 / SECEC) GN=cdd PE=3 SV=1 CDD_ECODH - Cytidine deaminase OS=Escherichia coli (strain K12 / DH10B) GN=cdd PE=3 SV=1 gi\|85675257, gi\|... - gi\|89108960\|ref\|AP_002740.1\| cytidine/deoxycytidine deaminase [Escherichia coli str. K-12 substr. W3... CDD_ECO8A - Cytidine deaminase OS=Escherichia coli O8 (strain IAI1) GN=cdd PE=3 SV=1 CDD_ECOSE - Cytidine deaminase OS=Escherichia coli (strain SE11) GN=cdd PE=3 SV=1 CDD_ECO55 - Cytidine deaminase OS=Escherichia coli (strain 55989 / EAEC) GN=cdd PE=3 SV=1 CDD_ECOHS - Cytidine deaminase OS=Escherichia coli O9:H4 (strain HS) GN=cdd PE=3 SV=1 gi\|75234031, gi\|... - gi\|75234031\|ref\|ZP_00718448.1\| COG0295: Cytidine deaminase [Escherichia coli E110019], gi\|193071075\|... gi\|83588124, gi\|... - gi\|83588124\|ref\|ZP_00926749.1\| COG0295: Cytidine deaminase [Escherichia coli 101-1], gi\|194435985\|re... CDD_SHIB3 - Cytidine deaminase OS=Shigella boydii serotype 18 (strain CDC 3083-94 / BS512) GN=cdd PE=3 SV=1	1.0E-91	[1..293]	[1..293]
gi\|75231518, gi\|... - gi\|75231518\|ref\|ZP_00717887.1\| COG0295: Cytidine deaminase [Escherichia coli B7A], gi\|191165451\|ref\|... CDD_ECO24 - Cytidine deaminase OS=Escherichia coli O139:H28 (strain E24377A / ETEC) GN=cdd PE=3 SV=1	2.0E-91	[1..293]	[1..293]

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Predicted Domain #1

Region A:
Residues: [1-294]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MHPRFQTAFA QLADNLQSAL APILADHHFP AMLTAEQVST LKNTAGLDED ALAFALLPLA  60
   61 AACARTDLSH FNVGAIARGV SGNWYFGANM EFLGATMQQT VHAEQSAISH AWLRGEKGLA 120
  121 AVTVNYTPCG HCRQFMNELN SGLDLRIHLP GRAPHTLRDY LPDAFGPKDL EIKTLLMDEQ 180
  181 DHGFTLTGNT LTQAAITAAN KSHMPYSHSP SGVALECKDG RIFTGSYAEN AAFNPTLPPL 240
  241 QGALNLLSLN GYDYADIQRA ILAEKGDAAL IQWDATAATL KALGCHNIDR VLLG

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	93.221849
Match:	1af2A
Description:	Two-domain cytidine deaminase
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
cytidine deaminase activity	4.42667374679603	bayes_pls_golite062009
deaminase activity	2.76997916054448	bayes_pls_golite062009
hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines	2.27736397496642	bayes_pls_golite062009
catalytic activity	1.70756445127105	bayes_pls_golite062009
hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	1.51294035758003	bayes_pls_golite062009
IMP cyclohydrolase activity	1.11605611485835	bayes_pls_golite062009
phosphoribosylaminoimidazolecarboxamide formyltransferase activity	0.827438033765078	bayes_pls_golite062009
hydrolase activity	0.339145951258927	bayes_pls_golite062009
cyclohydrolase activity	0.308525511259279	bayes_pls_golite062009
binding	0.255962198799579	bayes_pls_golite062009
hydroxymethyl-, formyl- and related transferase activity	0.1546696349714	bayes_pls_golite062009

TMHMM	2.0c	PSIPRED	v2.61
SignalP	3.0	COILS	1999
DISOPRED	v0.1	NCBI nr	06/2007
PSI-BLAST	2.2.18	FFAS	ffas03
PDB	06/2007	Pfam	22
HMMER	2.3.2

View Structure Prediction Details

Top Sequence Alignment Hits

Predicted functions: