YRC Public Data Repository - Protein Structure Prediction

Protein:	RND_ECOLI
Organism:	Escherichia coli
Length:	375 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 RND_ECOLI.

Description	E-value	Query Range	Subject Range
gi\|26108465, gi\|... - gi\|26248062\|ref\|NP_754102.1\| ribonuclease D [Escherichia coli CFT073], gi\|26108465\|gb\|AAN80667.1\|AE0... gi\|91211019, gi\|... - gi\|91211019\|ref\|YP_541005.1\| ribonuclease D [Escherichia coli UTI89], gi\|91072593\|gb\|ABE07474.1\| rib... gi\|218689740, gi... - gi\|218689740\|ref\|YP_002397952.1\| ribonuclease D [Escherichia coli ED1a], gi\|218427304\|emb\|CAR08103.1... gi\|215265087, gi... - gi\|215487015\|ref\|YP_002329446.1\| ribonuclease D [Escherichia coli O127:H6 str. E2348/69], gi\|2152650... gi\|218365435, gi... - gi\|218558666\|ref\|YP_002391579.1\| ribonuclease D [Escherichia coli S88], gi\|218365435\|emb\|CAR03162.1\|...	272.0	[0..1]	[375..1]
gi\|15802217, gi\|... - gi\|15802217\|ref\|NP_288240.1\| ribonuclease D [Escherichia coli O157:H7 EDL933], gi\|12515844\|gb\|AAG567... gi\|25289176 - pir\|\|E85791 RNase D, processes tRNA precursor [imported] - Escherichia coli (strain O157:H7, substra...	271.0	[0..1]	[375..1]
gi\|254592826, gi... - gi\|254793426\|ref\|YP_003078263.1\| ribonuclease D [Escherichia coli O157:H7 str. TW14359], gi\|25459282... gi\|189355025, gi... - gi\|189402540\|ref\|ZP_02783120.2\| ribonuclease D [Escherichia coli O157:H7 str. EC4401], gi\|189355025\|... gi\|189010430, gi... - gi\|189010430\|ref\|ZP_02807242.2\| ribonuclease D [Escherichia coli O157:H7 str. EC4076], gi\|189000217\|... gi\|188024852, gi... - gi\|188024852\|ref\|ZP_02774388.2\| ribonuclease D [Escherichia coli O157:H7 str. EC4113], gi\|188016291\|... gi\|187776027, gi... - gi\|187776027\|ref\|ZP_02799888.2\| ribonuclease D [Escherichia coli O157:H7 str. EC4196], gi\|187769404\|... gi\|189376734, gi... - gi\|189406051\|ref\|ZP_02826040.2\| ribonuclease D [Escherichia coli O157:H7 str. EC508], gi\|189376734\|g... gi\|189405084, gi... - gi\|189405084\|ref\|ZP_02813223.2\| ribonuclease D [Escherichia coli O157:H7 str. EC869], gi\|189371954\|g... gi\|189404421, gi... - gi\|189404421\|ref\|ZP_02789258.2\| ribonuclease D [Escherichia coli O157:H7 str. EC4501], gi\|189365729\|... gi\|189360343, gi... - gi\|189403490\|ref\|ZP_02795783.2\| ribonuclease D [Escherichia coli O157:H7 str. EC4486], gi\|189360343\|... gi\|209768040, gi... - pir\|\|A99943 RNase D, processes tRNA precursor [imported] - Escherichia coli (strain O157:H7, substra... gi\|15831767, gi\|... - gi\|15831767\|ref\|NP_310540.1\| RNase D [Escherichia coli O157:H7], gi\|13361980\|dbj\|BAB35936.1\| RNase D... gi\|218352098, gi... - gi\|218695366\|ref\|YP_002403033.1\| ribonuclease D [Escherichia coli 55989], gi\|218352098\|emb\|CAU97835.... gi\|15831767, gi\|... - gi\|15831767\|ref\|NP_310540.1\| ribonuclease D [Escherichia coli O157:H7 str. Sakai], gi\|13361980\|dbj\|B... gi\|218361144, gi... - gi\|218554376\|ref\|YP_002387289.1\| ribonuclease D [Escherichia coli IAI1], gi\|218361144\|emb\|CAQ98727.1... gi\|217328853, gi... - gi\|217328853\|ref\|ZP_03444934.1\| ribonuclease D [Escherichia coli O157:H7 str. TW14588], gi\|217318200... gi\|209919169, gi... - gi\|209919169\|ref\|YP_002293253.1\| ribonuclease D [Escherichia coli SE11], gi\|209912428\|dbj\|BAG77502.1... gi\|157156075, gi... - gi\|157156075\|ref\|YP_001463104.1\| ribonuclease D [Escherichia coli E24377A], gi\|157078105\|gb\|ABV17813... gi\|218705302, gi... - gi\|218705302\|ref\|YP_002412821.1\| ribonuclease D [Escherichia coli UMN026], gi\|218432399\|emb\|CAR13290... gi\|194411930, gi... - gi\|194430003\|ref\|ZP_03062510.1\| ribonuclease D [Escherichia coli B171], gi\|194411930\|gb\|EDX28245.1\| ... gi\|192955385, gi... - gi\|193071290\|ref\|ZP_03052209.1\| ribonuclease D [Escherichia coli E110019], gi\|192955385\|gb\|EDV85869.... gi\|193066361, gi... - gi\|193066361\|ref\|ZP_03047410.1\| ribonuclease D [Escherichia coli E22], gi\|192926009\|gb\|EDV80654.1\| r... gi\|191168835, gi... - gi\|191168835\|ref\|ZP_03030609.1\| ribonuclease D [Escherichia coli B7A], gi\|190901115\|gb\|EDV60890.1\| r... gi\|209157942, gi... - gi\|209396542\|ref\|YP_002270881.1\| ribonuclease D [Escherichia coli O157:H7 str. EC4115], gi\|209157942... gi\|208818758, gi... - gi\|208818758\|ref\|ZP_03259078.1\| ribonuclease D [Escherichia coli O157:H7 str. EC4042], gi\|208738881\|... gi\|208816683, gi... - gi\|208816683\|ref\|ZP_03257803.1\| ribonuclease D [Escherichia coli O157:H7 str. EC4045], gi\|208731026\|... gi\|208810493, gi... - gi\|208810493\|ref\|ZP_03252369.1\| ribonuclease D [Escherichia coli O157:H7 str. EC4206], gi\|208725009\|...	271.0	[0..1]	[375..1]
gi\|81245204, gi\|... - gi\|82543793\|ref\|YP_407740.1\| ribonuclease D [Shigella boydii Sb227], gi\|81245204\|gb\|ABB65912.1\| RNas...	271.0	[0..1]	[375..1]
gi\|82776970, gi\|... - gi\|82776970\|ref\|YP_403319.1\| ribonuclease D [Shigella dysenteriae Sd197], gi\|81241118\|gb\|ABB61828.1\|...	270.0	[0..1]	[373..1]
gi\|110805403, gi... - gi\|110805403\|ref\|YP_688923.1\| ribonuclease D [Shigella flexneri 5 str. 8401], gi\|110614951\|gb\|ABF036... gi\|24051740, gi\|... - ref\|NP_707318.1\| RNase D, processes tRNA precursor [Shigella flexneri 2a str. 301], gb\|AAN43025.1\| ...	270.0	[0..1]	[375..1]
gi\|74311884, gi\|... - gi\|74311884\|ref\|YP_310303.1\| ribonuclease D [Shigella sonnei Ss046], gi\|73855361\|gb\|AAZ88068.1\| RNas...	267.0	[0..1]	[375..1]
gi\|110343513, gi... - gi\|110641921\|ref\|YP_669651.1\| ribonuclease D [Escherichia coli 536], gi\|110343513\|gb\|ABG69750.1\| rib... gi\|75241327 - gi\|75241327\|ref\|ZP_00725178.1\| COG0349: Ribonuclease D [Escherichia coli F11]	265.0	[0..5]	[375..1]
gi\|227837342, gi... - gi\|227885769\|ref\|ZP_04003574.1\| ribonuclease D [Escherichia coli 83972], gi\|227837342\|gb\|EEJ47808.1\|... gi\|237705754, gi... - gi\|237705754\|ref\|ZP_04536235.1\| ribonuclease D [Escherichia sp. 3_2_53FAA], gi\|226900511\|gb\|EEH86770... gi\|115513088, gi... - gi\|117623964\|ref\|YP_852877.1\| ribonuclease D [Escherichia coli APEC O1], gi\|115513088\|gb\|ABJ01163.1\|...	265.0	[0..5]	[375..1]
gi\|75513699 - gi\|75513699\|ref\|ZP_00736075.1\| COG0349: Ribonuclease D [Escherichia coli 53638] gi\|75195870 - gi\|75195870\|ref\|ZP_00705940.1\| COG0349: Ribonuclease D [Escherichia coli HS] gi\|83584989 - gi\|83584989\|ref\|ZP_00923644.1\| COG0349: Ribonuclease D [Escherichia coli 101-1] gi\|253324287, gi... - gi\|253773243\|ref\|YP_003036074.1\| ribonuclease D [Escherichia coli BL21(DE3)], gi\|253324287\|gb\|ACT288...	265.0	[0..5]	[375..1]

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Predicted Domain #1

Region A:
Residues: [1-375]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MNYQMITTDD ALASLCEAVR AFPAIALDTE FVRTRTYYPQ LGLIQLFDGE HLALIDPLGI  60
   61 TDWSPLKAIL RDPSITKFLH AGSEDLEVFL NVFGELPQPL IDTQILAAFC GRPMSWGFAS 120
  121 MVEEYSGVTL DKSESRTDWL ARPLTERQCE YAAADVWYLL PITAKLMVET EASGWLPAAL 180
  181 DECRLMQMRR QEVVAPEDAW RDITNAWQLR TRQLACLQLL ADWRLRKARE RDLAVNFVVR 240
  241 EEHLWSVARY MPGSLGELDS LGLSGSEIRF HGKTLLALVE KAQTLPEDAL PQPMLNLMDM 300
  301 PGYRKAFKAI KSLITDVSET HKISAELLAS RRQINQLLNW HWKLKPQNNL PELISGWRGE 360
  361 LMAEALHNLL QEYPQ

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	72.69897
Match:	1yt3A
Description:	Crystal Structure of Escherichia coli RNase D, an exoribonuclease involved in structured RNA processing
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
nuclease activity	1.81796593394339	bayes_pls_golite062009
catalytic activity	1.62277843225829	bayes_pls_golite062009
ribonuclease activity	1.27595421503132	bayes_pls_golite062009
endoribonuclease activity, producing 5'-phosphomonoesters	1.16743612214699	bayes_pls_golite062009
endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters	0.98004554864099	bayes_pls_golite062009
hydrolase activity, acting on ester bonds	0.882777779661113	bayes_pls_golite062009
hydrolase activity	0.65819530527327	bayes_pls_golite062009
endoribonuclease activity	0.424230530060369	bayes_pls_golite062009
exonuclease activity	0.39213900591465	bayes_pls_golite062009
exoribonuclease activity	0.18010377435387	bayes_pls_golite062009
DNA-directed RNA polymerase activity	0.16778637702032	bayes_pls_golite062009
RNA polymerase activity	0.16778637702032	bayes_pls_golite062009
endonuclease activity	0.150927275899469	bayes_pls_golite062009
exoribonuclease activity, producing 5'-phosphomonoesters	0.10987870963351	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: