YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|75177969, gi\|...
Organism:	Shigella boydii CDC 3083-94
Length:	376 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|75177969, gi|....

Description	E-value	Query Range	Subject Range
gi\|110615753, gi... - gi\|110806205\|ref\|YP_689725.1\| ribonucleotide-diphosphate reductase subunit beta [Shigella flexneri 5... gi\|24052672, gi\|... - ref\|NP_708125.1\| ribonucleoside diphosphage reductase 1, beta subunit, B2 [Shigella flexneri 2a str....	431.0	[0..1]	[376..78]
gi\|226901077, gi... - gi\|237704711\|ref\|ZP_04535192.1\| ribonucleotide-diphosphate reductase subunit beta [Escherichia sp. 3... gi\|117624429, gi... - gi\|117624429\|ref\|YP_853342.1\| ribonucleotide-diphosphate reductase subunit beta [Escherichia coli AP...	422.0	[0..1]	[376..45]
gi\|75512711 - gi\|75512711\|ref\|ZP_00735213.1\| COG0208: Ribonucleotide reductase, beta subunit [Escherichia coli 536... gi\|75196277 - gi\|75196277\|ref\|ZP_00706347.1\| COG0208: Ribonucleotide reductase, beta subunit [Escherichia coli HS] gi\|217327202, gi... - gi\|217327202\|ref\|ZP_03443285.1\| ribonucleoside-diphosphate reductase, beta subunit [Escherichia coli... gi\|189403970, gi... - gi\|189403970\|ref\|ZP_02786340.2\| ribonucleoside-diphosphate reductase, beta subunit [Escherichia coli...	420.0	[0..1]	[376..18]
gi\|194424837, gi... - gi\|83588221\|ref\|ZP_00926846.1\| COG0208: Ribonucleotide reductase, beta subunit [Escherichia coli 101... gi\|75238026 - gi\|75238026\|ref\|ZP_00722031.1\| COG0208: Ribonucleotide reductase, beta subunit [Escherichia coli E11... gi\|75211646, gi\|... - gi\|75211646\|ref\|ZP_00711725.1\| COG0208: Ribonucleotide reductase, beta subunit [Escherichia coli B17...	420.0	[0..1]	[376..18]
gi\|30041924, gi\|... - gi\|30063669\|ref\|NP_837840.1\| ribonucleotide-diphosphate reductase beta subunit [Shigella flexneri 2a... gi\|193068232, gi... - gi\|193068232\|ref\|ZP_03049196.1\| ribonucleoside-diphosphate reductase, beta subunit [Escherichia coli... gi\|56480071, gi\|... - gi\|56480071\|ref\|NP_708125.2\| ribonucleotide-diphosphate reductase beta subunit [Shigella flexneri 2a...	420.0	[0..1]	[376..14]
gi\|218559152, gi... - gi\|218559152\|ref\|YP_002392065.1\| ribonucleotide-diphosphate reductase subunit beta [Escherichia coli... gi\|218554798, gi... - gi\|218554798\|ref\|YP_002387711.1\| ribonucleotide-diphosphate reductase subunit beta [Escherichia coli... gi\|218370692, gi... - gi\|218700706\|ref\|YP_002408335.1\| ribonucleotide-diphosphate reductase subunit beta [Escherichia coli... gi\|218352573, gi... - gi\|218695841\|ref\|YP_002403508.1\| ribonucleotide-diphosphate reductase subunit beta [Escherichia coli... gi\|26248623, gi\|... - gi\|26248623\|ref\|NP_754663.1\| ribonucleotide-diphosphate reductase subunit beta [Escherichia coli CFT... gi\|227887293, gi... - gi\|227887293\|ref\|ZP_04005098.1\| ribonucleoside-diphosphate reductase, beta subunit [Escherichia coli... gi\|242377869, gi... - gi\|251785596\|ref\|YP_002999900.1\| hypothetical protein B21_02120 [Escherichia coli BL21], gi\|24237786... gi\|254289007, gi... - gi\|254289007\|ref\|YP_003054755.1\| ribonucleotide-diphosphate reductase beta subunit [Escherichia coli... gi\|253974147, gi... - gi\|254162246\|ref\|YP_003045354.1\| ribonucleotide-diphosphate reductase beta subunit [Escherichia coli... gi\|110642443, gi... - gi\|110642443\|ref\|YP_670173.1\| ribonucleotide-diphosphate reductase subunit beta [Escherichia coli 53... gi\|161485800 - gi\|161485800\|ref\|NP_708125.3\| ribonucleotide-diphosphate reductase subunit beta [Shigella flexneri 2... gi\|194418416, gi... - gi\|194433322\|ref\|ZP_03065602.1\| ribonucleoside-diphosphate reductase, beta subunit [Shigella dysente... gi\|161486465 - gi\|161486465\|ref\|NP_837840.2\| ribonucleotide-diphosphate reductase subunit beta [Shigella flexneri 2... gi\|215487452, gi... - gi\|215487452\|ref\|YP_002329883.1\| ribonucleotide-diphosphate reductase subunit beta [Escherichia coli... gi\|91211528, gi\|... - gi\|91211528\|ref\|YP_541514.1\| ribonucleotide-diphosphate reductase subunit beta [Escherichia coli UTI... gi\|209919687, gi... - gi\|209919687\|ref\|YP_002293771.1\| ribonucleotide-diphosphate reductase subunit beta [Escherichia coli... gi\|74312755, gi\|... - gi\|74312755\|ref\|YP_311174.1\| ribonucleotide-diphosphate reductase subunit beta [Shigella sonnei Ss04... gi\|75230375, gi\|... - gi\|75230375\|ref\|ZP_00716865.1\| COG0208: Ribonucleotide reductase, beta subunit [Escherichia coli B7A... gi\|75243050, gi\|... - gi\|75243050\|ref\|ZP_00726756.1\| COG0208: Ribonucleotide reductase, beta subunit [Escherichia coli F11... gi\|157157492, gi... - gi\|75187024\|ref\|ZP_00700291.1\| COG0208: Ribonucleotide reductase, beta subunit [Escherichia coli E24...	419.0	[0..1]	[376..1]
gi\|197361758, gi... - gi\|197361758\|ref\|YP_002141394.1\| ribonucleotide-diphosphate reductase subunit beta [Salmonella enter... gi\|56127082, gi\|... - gi\|56412825\|ref\|YP_149900.1\| ribonucleotide-diphosphate reductase subunit beta [Salmonella enterica ...	418.0	[0..1]	[376..1]
gi\|205344845, gi... - gi\|205344845\|gb\|EDZ31609.1\| ribonucleoside-diphosphate reductase, beta subunit [Salmonella enterica ... lcl\|NC_016856.1_... - [gene=nrdB] [protein=ribonucleotide-diphosphate reductase subunit beta] [protein_id=YP_005238349.1] ... gi\|168466025, gi... - gi\|195631367\|gb\|EDX49927.1\| ribonucleoside-diphosphate reductase, beta subunit [Salmonella enterica ... gi\|205349363, gi... - gi\|205349363\|gb\|EDZ35994.1\| ribonucleoside-diphosphate reductase, beta subunit [Salmonella enterica ... gi\|205338588, gi... - gi\|205338588\|gb\|EDZ25352.1\| ribonucleoside-diphosphate reductase, beta subunit [Salmonella enterica ... gi\|197211340, gi... - gi\|197247637\|ref\|YP_002147234.1\| ribonucleoside-diphosphate reductase, beta subunit [Salmonella ente... RIR2_SALTY - Ribonucleoside-diphosphate reductase 1 subunit beta OS=Salmonella typhimurium GN=nrdB PE=3 SV=3 gi\|194735273, gi... - gi\|194735273\|ref\|YP_002115349.1\| ribonucleoside-diphosphate reductase, beta subunit [Salmonella ente... gi\|194449379, gi... - gi\|194449379\|ref\|YP_002046332.1\| ribonucleotide-diphosphate reductase subunit beta [Salmonella enter... gi\|194401240, gi... - gi\|194442577\|ref\|YP_002041539.1\| ribonucleoside-diphosphate reductase, beta subunit [Salmonella ente... gi\|168237293, gi... - gi\|197289678\|gb\|EDY29041.1\| ribonucleoside-diphosphate reductase, beta subunit [Salmonella enterica ... gi\|167992612, gi... - gi\|205329222\|gb\|EDZ15986.1\| ribonucleoside-diphosphate reductase, beta subunit [Salmonella enterica ... gi\|205325266, gi... - gi\|205325266\|gb\|EDZ13105.1\| ribonucleoside-diphosphate reductase, beta subunit [Salmonella enterica ... gi\|161613001, gi... - gi\|161613001\|ref\|YP_001586966.1\| ribonucleotide-diphosphate reductase subunit beta [Salmonella enter... gi\|204929071, gi... - gi\|204929071\|ref\|ZP_03220214.1\| ribonucleoside-diphosphate reductase, beta subunit [Salmonella enter... gi\|200387602, gi... - gi\|200387602\|ref\|ZP_03214214.1\| ribonucleoside-diphosphate reductase, beta subunit [Salmonella enter... gi\|198242288, gi... - gi\|198242288\|ref\|YP_002216347.1\| ribonucleoside-diphosphate reductase, beta subunit [Salmonella ente... gi\|197240760, gi... - gi\|197262505\|ref\|ZP_03162579.1\| ribonucleoside-diphosphate reductase, beta subunit [Salmonella enter... RIR2_SALTY - Ribonucleoside-diphosphate reductase 1 subunit beta OS=Salmonella typhimurium (strain LT2 / SGSC1412... gi\|224583238, gi... - gi\|224583238\|ref\|YP_002637036.1\| ribonucleotide-diphosphate reductase beta subunit [Salmonella enter... RIR2_SALTY - Ribonucleoside-diphosphate reductase 1 subunit beta OS=Salmonella typhimurium GN=nrdB PE=3 SV=3 gi\|213161593 - gi\|213161593\|ref\|ZP_03347303.1\| ribonucleotide-diphosphate reductase subunit beta [Salmonella enteri... gi\|62128484, gi\|... - gi\|62180851\|ref\|YP_217268.1\| ribonucleotide-diphosphate reductase subunit beta [Salmonella enterica ... gi\|207857697, gi... - gi\|207857697\|ref\|YP_002244348.1\| ribonucleotide-diphosphate reductase subunit beta [Salmonella enter...	418.0	[0..1]	[376..1]
gi\|75259701, gi\|... - gi\|75259701\|ref\|ZP_00731003.1\| COG0208: Ribonucleotide reductase, beta subunit [Escherichia coli E22...	418.0	[0..1]	[376..18]
gi\|42543284, gi\|... - gi\|42543507\|pdb\|1R65\|B Chain B, Crystal Structure Of Ferrous Soaked Ribonucleotide Reductase R2 Subu...	418.0	[0..2]	[376..1]

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Predicted Domain #1

Region A:
Residues: [1-376]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MAYTTFSQTK NDQLKEPMFF GQPVNVARYD QQKYDIFEKL IEKQLSFFWR PEEVDVSRDR  60
   61 IDYQALPEHE KHIFISNLKY QTLLDSIQGR SPNVALLPLI SIPELETWVE TWAFSETIHS 120
  121 RSYTHIIRNI VNDPSVVFDD IVTNEQIQKR AEGISSYYDE LIEMTSYWHL LGEGTHTVNG 180
  181 KTVTVSLREL KKKLYLCLMS VNALEAIRFY VSFACSFAFA ERELMEGNAK IIRLIARDEA 240
  241 LHLTGTQHML NLLRSGADDP EMAEIAEECK QECYDLFVQA AQQEKDWADY LFRDGSMIGL 300
  301 NKDILCQYVE YITNIRMQAV GLDLPFQTRS NPIPWINTWL VSDNVQVAPQ EVEVSSYLVG 360
  361 QIDSEVDTDD LSNFQL

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	117.0
Match:	1piyA
Description:	RIBONUCLEOTIDE REDUCTASE R2 SOAKED WITH FERROUS ION AT NEUTRAL PH
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
oxidoreductase activity, acting on CH or CH2 groups, disulfide as acceptor	12.7205287868529	bayes_pls_golite062009
ribonucleoside-diphosphate reductase activity	12.6679910771829	bayes_pls_golite062009
oxidoreductase activity, acting on CH or CH2 groups	12.0783326936172	bayes_pls_golite062009
class I ribonucleotide reductase activity	7.27682621818194	bayes_pls_golite062009
binding	2.38747290927526	bayes_pls_golite062009
nucleic acid binding	1.75581372355926	bayes_pls_golite062009
DNA binding	1.75528223979795	bayes_pls_golite062009
protein binding	0.30514049100341	bayes_pls_golite062009
catalytic activity	0.197328811494233	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: