YRC Public Data Repository - Protein Structure Prediction

Protein:	MNME_SHIB3
Organism:	Shigella boydii CDC 3083-94
Length:	454 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 MNME_SHIB3.

Description	E-value	Query Range	Subject Range
gi\|25319364 - gi\|25319364\|pir\|\|C86055 hypothetical protein thdF [imported] - Escherichia coli (strain O157:H7, su... gi\|12518545, gi\|... - gi\|15804300\|ref\|NP_290339.1\| tRNA modification GTPase TrmE [Escherichia coli O157:H7 EDL933], gi\|125...	430.0	[0..1]	[454..1]
gi\|254795709, gi... - gi\|254795709\|ref\|YP_003080546.1\| 5-methylaminomethyl-2-thiouridine-synthesizing GTPase [Escherichia ... gi\|25319352, gi\|... - pir\|\|A98209 hypothetical protein ECs4641 [imported] - Escherichia coli (strain O157:H7, substrain R... MNME_ECO57 - tRNA modification GTPase MnmE OS=Escherichia coli O157:H7 GN=mnmE PE=3 SV=1 gi\|208814185, gi... - gi\|208814185\|ref\|ZP_03255514.1\| tRNA modification GTPase TrmE [Escherichia coli O157:H7 str. EC4045]... gi\|208740195, gi... - gi\|208820072\|ref\|ZP_03260392.1\| tRNA modification GTPase TrmE [Escherichia coli O157:H7 str. EC4042]... MNME_ECO5E - tRNA modification GTPase MnmE OS=Escherichia coli O157:H7 (strain EC4115 / EHEC) GN=mnmE PE=3 SV=1 gi\|217324903, gi... - gi\|217324903\|ref\|ZP_03440987.1\| tRNA modification GTPase TrmE [Escherichia coli O157:H7 str. TW14588... gi\|189373460, gi... - gi\|189373460\|gb\|EDU91876.1\| tRNA modification GTPase TrmE [Escherichia coli O157:H7 str. EC869], gi\|... gi\|168798745, gi... - gi\|189378836\|gb\|EDU97252.1\| tRNA modification GTPase TrmE [Escherichia coli O157:H7 str. EC508], gi\|... gi\|195936329 - gi\|195936329\|ref\|ZP_03081711.1\| tRNA modification GTPase TrmE [Escherichia coli O157:H7 str. EC4024] gi\|208808040, gi... - gi\|208808040\|ref\|ZP_03250377.1\| tRNA modification GTPase TrmE [Escherichia coli O157:H7 str. EC4206]... gi\|189369584, gi... - gi\|189369584\|gb\|EDU88000.1\| tRNA modification GTPase TrmE [Escherichia coli O157:H7 str. EC4501], gi... gi\|189364418, gi... - gi\|189364418\|gb\|EDU82837.1\| tRNA modification GTPase TrmE [Escherichia coli O157:H7 str. EC4486], gi... gi\|168772255, gi... - gi\|187771576\|gb\|EDU35420.1\| tRNA modification GTPase TrmE [Escherichia coli O157:H7 str. EC4196], gi... gi\|168779932, gi... - gi\|189002302\|gb\|EDU71288.1\| tRNA modification GTPase TrmE [Escherichia coli O157:H7 str. EC4076], gi... gi\|15833895, gi\|... - gi\|15833895\|ref\|NP_312668.1\| tRNA modification GTPase TrmE [Escherichia coli O157:H7 str. Sakai], gi... gi\|168748574, gi... - gi\|188016998\|gb\|EDU55120.1\| tRNA modification GTPase TrmE [Escherichia coli O157:H7 str. EC4113], gi... gi\|189359120, gi... - gi\|189359120\|gb\|EDU77539.1\| tRNA modification GTPase TrmE [Escherichia coli O157:H7 str. EC4401], gi...	430.0	[0..1]	[454..1]
MNME_SHIFL - tRNA modification GTPase MnmE OS=Shigella flexneri GN=mnmE PE=3 SV=1 MNME_SHIF8 - tRNA modification GTPase MnmE OS=Shigella flexneri serotype 5b (strain 8401) GN=mnmE PE=3 SV=1 gi\|24054236, gi\|... - gi\|24114984\|ref\|NP_709494.1\| tRNA modification GTPase TrmE [Shigella flexneri 2a str. 301], gi\|24054... gi\|30065014, gi\|... - gi\|30065014\|ref\|NP_839185.1\| tRNA modification GTPase TrmE [Shigella flexneri 2a str. 2457T], gi\|300...	430.0	[0..1]	[454..1]
gi\|194413821, gi... - gi\|75210683\|ref\|ZP_00710824.1\| COG0486: Predicted GTPase [Escherichia coli B171], gi\|194428063\|ref\|Z... gi\|192930510, gi... - gi\|75258245\|ref\|ZP_00729693.1\| COG0486: Predicted GTPase [Escherichia coli E22], gi\|193063795\|ref\|ZP...	429.0	[0..1]	[454..1]
MNME_SHIDS - tRNA modification GTPase MnmE OS=Shigella dysenteriae serotype 1 (strain Sd197) GN=mnmE PE=3 SV=1	428.0	[0..1]	[454..1]
MNME_ECO45 - tRNA modification GTPase MnmE OS=Escherichia coli O45:K1 (strain S88 / ExPEC) GN=mnmE PE=3 SV=1 MNME_ECOL6, TRME... - tRNA modification GTPase trmE - Escherichia coli O6, tRNA modification GTPase MnmE OS=Escherichia co... gi\|227839207, gi... - gi\|227883929\|ref\|ZP_04001734.1\| tRNA modification GTPase TrmE [Escherichia coli 83972], gi\|227839207... gi\|226902772, gi... - gi\|237703508\|ref\|ZP_04533989.1\| tRNA modification GTPase mnmE [Escherichia sp. 3_2_53FAA], gi\|226902... gi\|191170442, gi... - gi\|75242505\|ref\|ZP_00726249.1\| COG0486: Predicted GTPase [Escherichia coli F11], gi\|191170442\|ref\|ZP... MNME_ECOK1 - tRNA modification GTPase MnmE OS=Escherichia coli O1:K1 / APEC GN=mnmE PE=3 SV=1 MNME_ECOUT - tRNA modification GTPase MnmE OS=Escherichia coli (strain UTI89 / UPEC) GN=mnmE PE=3 SV=1 MNME_ECOL6 - tRNA modification GTPase MnmE OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) GN=mnmE... MNME_ECOL5 - tRNA modification GTPase MnmE OS=Escherichia coli O6:K15:H31 (strain 536 / UPEC) GN=mnmE PE=3 SV=1	428.0	[0..1]	[454..1]
MNME_ECOSM - tRNA modification GTPase MnmE OS=Escherichia coli (strain SMS-3-5 / SECEC) GN=mnmE PE=3 SV=1 MNME_ECO81 - tRNA modification GTPase MnmE OS=Escherichia coli O81 (strain ED1a) GN=mnmE PE=3 SV=1 MNME_ESCF3 - tRNA modification GTPase MnmE OS=Escherichia fergusonii (strain ATCC 35469 / DSM 13698 / CDC 0568-73... gi\|194431305, gi... - gi\|83571504\|ref\|ZP_00922944.1\| COG0486: Predicted GTPase [Shigella dysenteriae 1012], gi\|194431305\|r... gi\|170124535, gi... - gi\|170767097\|ref\|ZP_02901550.1\| tRNA modification GTPase TrmE [Escherichia albertii TW07627], gi\|170...	428.0	[0..1]	[454..1]
gi\|253775659, gi... - gi\|254290408\|ref\|YP_003056156.1\| tRNA modification GTPase [Escherichia coli BL21(DE3)], gi\|253979715... gi\|242379246, gi... - gi\|251786973\|ref\|YP_003001277.1\| hypothetical protein B21_03534 [Escherichia coli BL21], gi\|24237924... MNME_ECOHS - tRNA modification GTPase MnmE OS=Escherichia coli O9:H4 (strain HS) GN=mnmE PE=3 SV=1 gi\|254163658, gi... - gi\|254163658\|ref\|YP_003046766.1\| tRNA modification GTPase [Escherichia coli B str. REL606], gi\|25397... gi\|83588429, gi\|... - gi\|83588429\|ref\|ZP_00927053.1\| COG0486: Predicted GTPase [Escherichia coli 101-1], gi\|194435686\|ref\|... MNME_ECO55 - tRNA modification GTPase MnmE OS=Escherichia coli (strain 55989 / EAEC) GN=mnmE PE=3 SV=1	428.0	[0..1]	[454..1]
gi\|290554 - gi\|290554\|gb\|AAA62057.1\| 50 kD protein	428.0	[0..1]	[454..1]
MNME_SHISS - tRNA modification GTPase MnmE OS=Shigella sonnei (strain Ss046) GN=mnmE PE=3 SV=1	427.0	[0..1]	[454..1]

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Predicted Domain #1

Region A:
Residues: [1-454]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSDNDTIVAQ ATPPGRGGVG ILRISGFKAR EVAETVLGKL PKPRYADYLP FKDADGSVLD  60
   61 QGIALWFPGP NSFTGEDVLE LQGHGGPVIL DLLLKRILTI PGLRIARPGE FSERAFLNDK 120
  121 LDLAQAEAIA DLIDASSEQA ARSALNSLQG AFSARVNHLV EALTHLRIYV EAAIDFPDEE 180
  181 IDFLSDGKIE AQLNDVIADL DAVRAEARQG SLLREGMKVV IAGRPNAGKS SLLNALAGRE 240
  241 AAIVTDIAGT TRDVLREHIH IDGMPLHIID TAGLREASDE VERIGIERAW QEIEQADRVL 300
  301 FMVDGTTTDA VDPAEIWPEF IARLPAKLPI TVVRNKADIT GETLGMSEVN GHALIRLSAR 360
  361 TGEGVDVLRN HLKQSMGFDT NMEGGFLARR RHLQALEQAA EHLQQGKAQL LGAWAGELLA 420
  421 EELRLAQQNL SEITGEFTSD DLLGRIFSSF CIGK

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	87.522879
Match:	1xzpA
Description:	Structure of the GTP-binding protein TrmE from Thermotoga maritima
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
methyltransferase activity	3.28983380541263	bayes_pls_golite062009
transferase activity, transferring one-carbon groups	3.20782575104451	bayes_pls_golite062009
catalytic activity	1.65079399897053	bayes_pls_golite062009
transferase activity	1.3676947912529	bayes_pls_golite062009
coenzyme binding	1.08379167900905	bayes_pls_golite062009
cofactor binding	0.96468813458034	bayes_pls_golite062009
ATP binding	0.60527666756293	bayes_pls_golite062009
aminomethyltransferase activity	0.573831999310668	bayes_pls_golite062009
adenyl ribonucleotide binding	0.573214556107072	bayes_pls_golite062009
nucleic acid binding	0.544057265221809	bayes_pls_golite062009
ligase activity	0.417681194526243	bayes_pls_golite062009
binding	0.394312443474767	bayes_pls_golite062009
RNA helicase activity	0.18362676509797	bayes_pls_golite062009
DNA binding	0.156173690421144	bayes_pls_golite062009
RNA-dependent ATPase activity	0.0388696977166548	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: