YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|30042605, gi\|...
Organism:	Shigella flexneri 2a str. 2457T
Length:	164 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|30042605, gi|....

Description	E-value	Query Range	Subject Range
gi\|311538, gi\|628534 - pir\|\|S39401 hydrogenase maturation factor hupD [similarity] - Bradyrhizobium japonicum, gi\|311538\|em...	199.0	[0..2]	[161..9]
HUPD_BRAJA - Hydrogenase expression/formation protein hupD OS=Bradyrhizobium japonicum GN=hupD PE=3 SV=2 HUPD_BRADU - Hydrogenase expression/formation protein HupD OS=Bradyrhizobium diazoefficiens (strain JCM 10833 / I...	196.0	[0..2]	[161..9]
gi\|75240551, gi\|... - gi\|75240551\|ref\|ZP_00724479.1\| COG0680: Ni,Fe-hydrogenase maturation factor [Escherichia coli F11], ... gi\|218560068, gi... - gi\|218560068\|ref\|YP_002392981.1\| hydrogenase 2 maturation endopeptidase [Escherichia coli S88], gi\|2... gi\|170125102, gi... - gi\|170765956\|ref\|ZP_02900767.1\| hydrogenase 2 maturation peptidase [Escherichia albertii TW07627], g... gi\|26109969, gi\|... - gi\|26249561\|ref\|NP_755601.1\| hydrogenase 2 maturation endopeptidase [Escherichia coli CFT073], gi\|26... gi\|91212407, gi\|... - gi\|91212407\|ref\|YP_542393.1\| hydrogenase 2 maturation endopeptidase [Escherichia coli UTI89], gi\|910... gi\|218371753, gi... - gi\|218701767\|ref\|YP_002409396.1\| hydrogenase 2 maturation endopeptidase [Escherichia coli IAI39], gi... gi\|218691284, gi... - gi\|218691284\|ref\|YP_002399496.1\| hydrogenase 2 maturation endopeptidase [Escherichia coli ED1a], gi\|... gi\|115514422, gi... - gi\|117625298\|ref\|YP_854481.1\| hydrogenase 2 maturation endopeptidase [Escherichia coli APEC O1], gi\|... gi\|226899300, gi... - gi\|237706260\|ref\|ZP_04536741.1\| hydrogenase 2 maturation protease [Escherichia sp. 3_2_53FAA], gi\|22...	193.0	[0..1]	[164..1]
gi\|238902111, gi... - gi\|238902111\|ref\|YP_002927907.1\| putative maturation element for hydrogenase 2 [Escherichia coli BW2... gi\|89109768, gi\|... - gi\|89109768\|ref\|AP_003548.1\| predicted maturation element for hydrogenase 2 [Escherichia coli str. K... gi\|169890376, gi... - gi\|170082541\|ref\|YP_001731861.1\| hydrogenase 2 maturation protein [Escherichia coli str. K-12 substr... gi\|170018748, gi... - gi\|170018748\|ref\|YP_001723702.1\| hydrogenase 2 maturation endopeptidase [Escherichia coli ATCC 8739]... gi\|170518672, gi... - gi\|170680954\|ref\|YP_001745259.1\| hydrogenase 2 maturation peptidase [Escherichia coli SMS-3-5], gi\|1... gi\|124526087, gi... - gi\|124526087\|ref\|ZP_01698092.1\| hydrogenase expression/formation protein [Escherichia coli B], gi\|12... EG11802 - maturation protease for hydrogenase 2 / Maturation endoprotease for Ni-containing hydrogenase 2 gi\|194424360, gi... - gi\|83587560\|ref\|ZP_00926187.1\| COG0680: Ni,Fe-hydrogenase maturation factor [Escherichia coli 101-1]... HYBD_ECOLI - Hydrogenase 2 maturation protease (EC 3.4.24.-) - Escherichia coli gi\|157068153, gi... - gi\|75196957\|ref\|ZP_00707027.1\| COG0680: Ni,Fe-hydrogenase maturation factor [Escherichia coli HS], g... gi\|75515209, gi\|... - gi\|75515209\|ref\|ZP_00737393.1\| COG0680: Ni,Fe-hydrogenase maturation factor [Escherichia coli 53638]... gi\|110643233, gi... - gi\|110643233\|ref\|YP_670963.1\| hydrogenase 2 maturation endopeptidase [Escherichia coli 536], gi\|1103... EG11802 - maturation protease for hydrogenase 2 / Maturation endoprotease for Ni-containing hydrogenase 2	193.0	[0..1]	[164..1]
gi\|93354089, gi\|... - gi\|94310237\|ref\|YP_583447.1\| HyaD peptidase [Ralstonia metallidurans CH34], gi\|93354089\|gb\|ABF08178....	192.0	[0..2]	[161..20]
gi\|75229320, gi\|... - gi\|75229320\|ref\|ZP_00715879.1\| COG0680: Ni,Fe-hydrogenase maturation factor [Escherichia coli B7A], ... gi\|194426400, gi... - gi\|75212361\|ref\|ZP_00712385.1\| COG0680: Ni,Fe-hydrogenase maturation factor [Escherichia coli B171],... gi\|75187816, gi\|... - gi\|75187816\|ref\|ZP_00701083.1\| COG0680: Ni,Fe-hydrogenase maturation factor [Escherichia coli E24377... gi\|209913728, gi... - gi\|209920469\|ref\|YP_002294553.1\| hydrogenase 2 maturation endopeptidase [Escherichia coli SE11], gi\|... gi\|217320037, gi... - gi\|217327670\|ref\|ZP_03443753.1\| hydrogenase expression/formation protein [Escherichia coli O157:H7 s... gi\|218353435, gi... - gi\|218696703\|ref\|YP_002404370.1\| hydrogenase 2 maturation endopeptidase [Escherichia coli 55989], gi... gi\|192932271, gi... - gi\|75259939\|ref\|ZP_00731217.1\| COG0680: Ni,Fe-hydrogenase maturation factor [Escherichia coli E22], ... gi\|254594350, gi... - gi\|254794950\|ref\|YP_003079787.1\| predicted maturation element for hydrogenase 2 [Escherichia coli O1... gi\|209759838, gi... - pir\|\|F91113 hydrogenase 2 maturation proteinase HybD [imported] - Escherichia coli (strain O157:H7, ... gi\|12517557, gi\|... - gi\|15803538\|ref\|NP_289571.1\| hydrogenase 2 maturation endopeptidase [Escherichia coli O157:H7 EDL933... gi\|13363350, gi\|... - gi\|15833132\|ref\|NP_311905.1\| HybD [Escherichia coli O157:H7], gi\|13363350\|dbj\|BAB37301.1\| hydrogenas... gi\|13363350, gi\|... - gi\|15833132\|ref\|NP_311905.1\| hydrogenase 2 maturation endopeptidase [Escherichia coli O157:H7 str. S... gi\|168781864, gi... - gi\|189000525\|gb\|EDU69511.1\| hydrogenase 2 maturation peptidase [Escherichia coli O157:H7 str. EC4076... gi\|189374025, gi... - gi\|189374025\|gb\|EDU92441.1\| hydrogenase 2 maturation peptidase [Escherichia coli O157:H7 str. EC869]... gi\|168797580, gi... - gi\|189379749\|gb\|EDU98165.1\| hydrogenase 2 maturation peptidase [Escherichia coli O157:H7 str. EC508]... gi\|195937139 - gi\|195937139\|ref\|ZP_03082521.1\| hydrogenase 2 maturation endopeptidase [Escherichia coli O157:H7 str... gi\|208807111, gi... - gi\|208807111\|ref\|ZP_03249448.1\| hydrogenase expression/formation protein [Escherichia coli O157:H7 s... gi\|208812501, gi... - gi\|208812501\|ref\|ZP_03253830.1\| hydrogenase expression/formation protein [Escherichia coli O157:H7 s... gi\|208820479, gi... - gi\|208820479\|ref\|ZP_03260799.1\| hydrogenase expression/formation protein [Escherichia coli O157:H7 s... gi\|209158674, gi... - gi\|209397274\|ref\|YP_002272472.1\| hydrogenase expression/formation protein [Escherichia coli O157:H7 ... gi\|188017917, gi... - gi\|188017917\|gb\|EDU56039.1\| hydrogenase 2 maturation peptidase [Escherichia coli O157:H7 str. EC4113... gi\|168753957, gi... - gi\|189358734\|gb\|EDU77153.1\| hydrogenase 2 maturation peptidase [Escherichia coli O157:H7 str. EC4401... gi\|189369230, gi... - gi\|189369230\|gb\|EDU87646.1\| hydrogenase 2 maturation peptidase [Escherichia coli O157:H7 str. EC4501... gi\|189363702, gi... - gi\|189363702\|gb\|EDU82121.1\| hydrogenase 2 maturation peptidase [Escherichia coli O157:H7 str. EC4486... gi\|168773355, gi... - gi\|187770988\|gb\|EDU34832.1\| hydrogenase 2 maturation peptidase [Escherichia coli O157:H7 str. EC4196...	192.0	[0..1]	[164..1]
gi\|81242386, gi\|... - gi\|82778238\|ref\|YP_404587.1\| hydrogenase 2 maturation endopeptidase [Shigella dysenteriae Sd197], gi...	191.0	[0..1]	[164..1]
gi\|16421700, gi\|... - gi\|16766446\|ref\|NP_462061.1\| hydrogenase 2 maturation endopeptidase [Salmonella typhimurium LT2], gi... lcl\|NC_016856.1_... - [gene=hybD] [protein=hydrogenase 2 maturation endopeptidase] [protein_id=YP_005239309.1] [location=c... gi\|224584942, gi... - gi\|224584942\|ref\|YP_002638741.1\| hydrogenase-2 component protein [Salmonella enterica subsp. enteric... gi\|197262619, gi... - gi\|197262619\|ref\|ZP_03162693.1\| hydrogenase expression/formation protein [Salmonella enterica subsp.... gi\|199604401, gi... - gi\|200387303\|ref\|ZP_03213915.1\| hydrogenase expression/formation protein [Salmonella enterica subsp.... gi\|194736032, gi... - gi\|194736032\|ref\|YP_002116101.1\| hydrogenase expression/formation protein [Salmonella enterica subsp... gi\|197212220, gi... - gi\|197248517\|ref\|YP_002148067.1\| hydrogenase expression/formation protein [Salmonella enterica subsp... gi\|195633252, gi... - gi\|195633252\|gb\|EDX51666.1\| hydrogenase expression/formation protein [Salmonella enterica subsp. ent... gi\|194403241, gi... - gi\|194444578\|ref\|YP_002042410.1\| hydrogenase expression/formation protein [Salmonella enterica subsp... gi\|205331071, gi... - gi\|205331071\|gb\|EDZ17835.1\| hydrogenase expression/formation protein [Salmonella enterica subsp. ent... gi\|197289030, gi... - gi\|197289030\|gb\|EDY28401.1\| hydrogenase expression/formation protein [Salmonella enterica subsp. ent... gi\|161365490, gi... - gi\|161616126\|ref\|YP_001590091.1\| hydrogenase 2 maturation endopeptidase [Salmonella enterica subsp. ... gi\|205323275, gi... - gi\|205323275\|gb\|EDZ11114.1\| hydrogenase expression/formation protein [Salmonella enterica subsp. ent... gi\|62181657, gi\|... - gi\|62181657\|ref\|YP_218074.1\| hydrogenase 2 maturation endopeptidase [Salmonella enterica subsp. ente...	191.0	[0..1]	[163..1]
gi\|83376049 - gi\|83376049\|gb\|ABC17830.1\| HupD [Bradyrhizobium sp. UPM1029]	190.0	[0..2]	[160..10]
gi\|194448917, gi... - gi\|194448917\|ref\|YP_002047141.1\| hydrogenase 2 maturation endopeptidase [Salmonella enterica subsp. ... gi\|205343443, gi... - gi\|205343443\|gb\|EDZ30207.1\| hydrogenase expression/formation protein [Salmonella enterica subsp. ent... gi\|205348455, gi... - gi\|205348455\|gb\|EDZ35086.1\| hydrogenase expression/formation protein [Salmonella enterica subsp. ent... gi\|168242965, gi... - gi\|205337770\|gb\|EDZ24534.1\| hydrogenase expression/formation protein [Salmonella enterica subsp. ent... gi\|168231738, gi... - gi\|205333909\|gb\|EDZ20673.1\| hydrogenase expression/formation protein [Salmonella enterica subsp. ent... gi\|160867630, gi... - gi\|161506283\|ref\|YP_001573395.1\| hydrogenase 2 maturation endopeptidase [Salmonella enterica subsp. ... gi\|56129344, gi\|... - gi\|56415087\|ref\|YP_152162.1\| hydrogenase 2 maturation endopeptidase [Salmonella enterica subsp. ente... gi\|238909946 - gi\|238909946\|ref\|ZP_04653783.1\| hydrogenase 2 maturation endopeptidase [Salmonella enterica subsp. e... gi\|206710208, gi... - gi\|207858405\|ref\|YP_002245056.1\| hydrogenase 2 maturation endopeptidase [Salmonella enterica subsp. ... gi\|205273845, gi... - gi\|205354064\|ref\|YP_002227865.1\| hydrogenase 2 maturation endopeptidase [Salmonella enterica subsp. ... gi\|204928109, gi... - gi\|204928109\|ref\|ZP_03219309.1\| hydrogenase expression/formation protein [Salmonella enterica subsp.... gi\|197938422, gi... - gi\|198243906\|ref\|YP_002217123.1\| hydrogenase expression/formation protein [Salmonella enterica subsp... gi\|197095493, gi... - gi\|197364016\|ref\|YP_002143653.1\| hydrogenase 2 maturation endopeptidase [Salmonella enterica subsp. ... gi\|194469608, gi... - gi\|194469608\|ref\|ZP_03075592.1\| hydrogenase expression/formation protein [Salmonella enterica subsp....	190.0	[0..1]	[163..1]

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Predicted Domain #1

Region A:
Residues: [1-164]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MRILVLGVGN ILLTDEAIGV RIVEALEQRY ILPDYVEILD GGTAGMELLG DMANRDHLII  60
   61 ADAIVSKKNT PGTMMILRDE EVPALFTNKI SPHQLGLADV LSALRFTGEF PKKLTLVGVI 120
  121 PESLEPHIGL TPTVEAMIEP ALEQVLAALR ESGVEAIPRE AIHD

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	48.0
Match:	1cfzA
Description:	Hydrogenase maturating endopeptidase HybD
Matching Structure (courtesy of the PDB):

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