YRC Public Data Repository - Protein Structure Prediction

Protein:	NIF3
Organism:	Saccharomyces cerevisiae
Length:	288 amino acids
Reference:	Malmström L, et al. (2007) Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS Biol 5(4): e76. doi:10.1371/journal.pbio.0050076

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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 NIF3.

Description	E-value	Query Range	Subject Range
gi\|190407154 - gi\|190407154\|gb\|EDV10421.1\| NGG1-interacting factor 3 [Saccharomyces cerevisiae RM11-1a] gi\|151943598 - gi\|151943598\|gb\|EDN61908.1\| ngg1p-interacting factor [Saccharomyces cerevisiae YJM789] NIF3 - Protein of unknown function, similar to Listeria monocytogenes major sigma factor (rpoD gene product... NIF3_YEAST - NGG1-interacting factor 3 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=NIF3 PE=1 SV=1	5.0E-88	[1..288]	[1..288]
gi\|225861441, gi... - gi\|225861441\|ref\|YP_002742950.1\| hypothetical protein SPT_1550 [Streptococcus pneumoniae Taiwan19F-1... gi\|242244826, gi... - gi\|242244826\|ref\|ZP_04799263.1\| protein of hypothetical function DUF34 [Streptococcus pneumoniae TCH... gi\|116517031, gi... - gi\|116517031\|ref\|YP_816891.1\| hypothetical protein SPD_1434 [Streptococcus pneumoniae D39], gi\|11607... gi\|148988662, gi... - gi\|148988662\|ref\|ZP_01820095.1\| hypothetical protein CGSSp6BS73_09059 [Streptococcus pneumoniae SP6-... gi\|25509065 - pir\|\|E98054 conserved hypothetical protein spr1462 [imported] - Streptococcus pneumoniae (strain R6) gi\|15903505, gi\|... - gi\|15903505\|ref\|NP_359055.1\| hypothetical protein spr1462 [Streptococcus pneumoniae R6], gi\|15459119...	1.0E-69	[8..286]	[1..263]
gi\|145271396, gi... - gi\|145639605\|ref\|ZP_01795209.1\| hypothetical protein CGSHiII_10198 [Haemophilus influenzae PittII], ... gi\|145629013, gi... - gi\|145629013\|ref\|ZP_01784812.1\| seryl-tRNA synthetase [Haemophilus influenzae 22.1-21], gi\|144978516... Y105_HAEIN - UPF0135 protein HI_0105 OS=Haemophilus influenzae GN=HI_0105 PE=1 SV=2 GCH1L_HAEIN - GTP cyclohydrolase 1 type 2 homolog OS=Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 ... gi\|42632159 - gi\|42632159\|ref\|ZP_00157697.1\| COG0327: Uncharacterized conserved protein [Haemophilus influenzae R2...	3.0E-69	[5..284]	[1..250]
gi\|229351910, gi... - gi\|229511945\|ref\|ZP_04401424.1\| hypothetical protein VCE_003355 [Vibrio cholerae B33], gi\|229351910\|... gi\|229519081, gi... - gi\|229519081\|ref\|ZP_04408524.1\| hypothetical protein VCC_003109 [Vibrio cholerae RC9], gi\|229343770\|... gi\|116189056, gi... - gi\|75829407\|ref\|ZP_00758711.1\| COG0327: Uncharacterized conserved protein [Vibrio cholerae MO10], gi... gi\|229370018, gi... - gi\|229607363\|ref\|YP_002878011.1\| hypothetical protein VCD_002274 [Vibrio cholerae MJ-1236], gi\|22937... gi\|75814750, gi\|... - gi\|75814750\|ref\|ZP_00745303.1\| COG0327: Uncharacterized conserved protein [Vibrio cholerae V52], gi\|... gi\|227013990, gi... - gi\|75827400\|ref\|ZP_00756835.1\| COG0327: Uncharacterized conserved protein [Vibrio cholerae O395], gi... gi\|9656642, gi\|1... - gi\|9656642\|gb\|AAF95239.1\| conserved hypothetical protein [Vibrio cholerae O1 biovar El Tor str. N169... gi\|121548833, gi... - gi\|121586897\|ref\|ZP_01676677.1\| conserved hypothetical protein [Vibrio cholerae 2740-80], gi\|1215488... gi\|11280369 - gi\|11280369\|pir\|\|C82119 conserved hypothetical protein VC2093 [imported] - Vibrio cholerae (strain N... gi\|124119081, gi... - gi\|153222221\|ref\|ZP_01953000.1\| conserved hypothetical protein [Vibrio cholerae MAK 757], gi\|1241190... gi\|153818375, gi... - gi\|153818375\|ref\|ZP_01971042.1\| conserved hypothetical protein [Vibrio cholerae NCTC 8457], gi\|12651... gi\|227082219, gi... - gi\|227082219\|ref\|YP_002810770.1\| hypothetical protein VCM66_2017 [Vibrio cholerae M66-2], gi\|2270101... gi\|229355323, gi... - gi\|229507818\|ref\|ZP_04397323.1\| hypothetical protein VCF_003047 [Vibrio cholerae BX 330286], gi\|2293...	6.0E-69	[1..285]	[1..256]
GCH1L_PASMU - GTP cyclohydrolase 1 type 2 homolog OS=Pasteurella multocida (strain Pm70) GN=PM0183 PE=3 SV=1 Y183_PASMU - UPF0135 protein PM0183 OS=Pasteurella multocida GN=PM0183 PE=3 SV=1	9.0E-69	[8..284]	[1..250]
gi\|12847944 - gi\|12847944\|dbj\|BAB27769.1\| unnamed protein product [Mus musculus]	2.0E-68	[2..287]	[21..375]
YG09_STRPN, Y160... - (Q97PK0) Hypothetical UPF0135 protein SP1609, UPF0135 protein SP_1609 OS=Streptococcus pneumoniae GN... GCH1L_STRPN - GTP cyclohydrolase 1 type 2 homolog OS=Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TI...	3.0E-67	[8..285]	[1..262]
GCH1L_VIBCH - GTP cyclohydrolase 1 type 2 homolog OS=Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba... YK93_VIBCH, Y209... - (Q9KQA7) Hypothetical UPF0135 protein VC2093, UPF0135 protein VC_2093 OS=Vibrio cholerae GN=VC_2093 ...	3.0E-67	[5..285]	[1..252]
SPCC126.12 - NGG1p interacting factor 3 family NIF3_SCHPO - Protein NIF3 homolog OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPCC126.12 PE=3 SV=1	6.0E-66	[1..286]	[1..276]
gi\|15800413, gi\|... - gi\|15800413\|ref\|NP_286425.1\| putative hydrolase-oxidase [Escherichia coli O157:H7 EDL933], gi\|125136... YBGI_ECOLI - UPF0135 protein ybgI - Escherichia coli GCH1L_ECOL6 - GTP cyclohydrolase 1 type 2 homolog OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) G... EG13305 - NIF3 family metal-binding protein / Conserved metal-binding protein, NIF3 family, function unknown GCH1L_ECO57 - GTP cyclohydrolase 1 type 2 homolog OS=Escherichia coli O157:H7 GN=ybgI PE=3 SV=1 gi\|209162252, gi... - gi\|209400852\|ref\|YP_002269333.1\| NIF3 family protein [Escherichia coli O157:H7 str. EC4115], gi\|2091... gi\|209911219, gi... - gi\|209917960\|ref\|YP_002292044.1\| putative hydrolase-oxidase [Escherichia coli SE11], gi\|209911219\|db... gi\|215263805, gi... - gi\|215485733\|ref\|YP_002328164.1\| putative hydrolase-oxidase [Escherichia coli O127:H6 str. E2348/69]... EG13305 - NIF3 family metal-binding protein / Conserved metal-binding protein, NIF3 family, function unknown gi\|217325832, gi... - gi\|217325832\|ref\|ZP_03441916.1\| NIF3 family protein [Escherichia coli O157:H7 str. TW14588], gi\|2173... gi\|42543092\|pdb\|... - Chain D, Structural Genomics, Ybgi Protein, Unknown Function, Chain E, Structural Genomics, Ybgi Pro... gi\|218553237, gi... - gi\|218553237\|ref\|YP_002386150.1\| putative hydrolase-oxidase [Escherichia coli IAI1], gi\|218360005\|em... gi\|218364399, gi... - gi\|218557630\|ref\|YP_002390543.1\| putative hydrolase-oxidase [Escherichia coli S88], gi\|218364399\|emb... gi\|218426071, gi... - gi\|218688507\|ref\|YP_002396719.1\| putative hydrolase-oxidase [Escherichia coli ED1a], gi\|218426071\|em... gi\|218694133, gi... - gi\|218694133\|ref\|YP_002401800.1\| putative hydrolase-oxidase [Escherichia coli 55989], gi\|218350865\|e... gi\|168801382, gi... - gi\|189376484\|gb\|EDU94900.1\| NIF3 family protein [Escherichia coli O157:H7 str. EC508], gi\|168801382\|... gi\|170020945, gi... - gi\|170020945\|ref\|YP_001725899.1\| putative hydrolase-oxidase [Escherichia coli ATCC 8739], gi\|1697558... gi\|169888212, gi... - gi\|170080377\|ref\|YP_001729697.1\| metal-binding hydrolase-oxidase [Escherichia coli str. K-12 substr.... gi\|170520679, gi... - gi\|170682961\|ref\|YP_001742814.1\| NIF3 family protein [Escherichia coli SMS-3-5], gi\|170520679\|gb\|ACB... gi\|195939051 - gi\|195939051\|ref\|ZP_03084433.1\| putative hydrolase-oxidase [Escherichia coli O157:H7 str. EC4024] gi\|208728180, gi... - gi\|208808379\|ref\|ZP_03250716.1\| NIF3 family protein [Escherichia coli O157:H7 str. EC4206], gi\|20872... gi\|208815861, gi... - gi\|208815861\|ref\|ZP_03257040.1\| NIF3 family protein [Escherichia coli O157:H7 str. EC4045], gi\|20873... gi\|208737230, gi... - gi\|208823037\|ref\|ZP_03263355.1\| NIF3 family protein [Escherichia coli O157:H7 str. EC4042], gi\|20873... gi\|218704027, gi... - gi\|218704027\|ref\|YP_002411546.1\| putative hydrolase-oxidase [Escherichia coli UMN026], gi\|218431124\|... gi\|75209722, gi\|... - gi\|75209722\|ref\|ZP_00709930.1\| COG0327: Uncharacterized conserved protein [Escherichia coli B171], g... gi\|75229657, gi\|... - gi\|75229657\|ref\|ZP_00716194.1\| COG0327: Uncharacterized conserved protein [Escherichia coli B7A], gi... gi\|193070664, gi... - gi\|75234512\|ref\|ZP_00718859.1\| COG0327: Uncharacterized conserved protein [Escherichia coli E110019]... gi\|193065545, gi... - gi\|75256419\|ref\|ZP_00728077.1\| COG0327: Uncharacterized conserved protein [Escherichia coli E22], gi... gi\|188491915, gi... - gi\|75511597\|ref\|ZP_00734248.1\| COG0327: Uncharacterized conserved protein [Escherichia coli 53638], ... gi\|81244550, gi\|... - gi\|82543139\|ref\|YP_407086.1\| putative hydrolase-oxidase [Shigella boydii Sb227], gi\|81244550\|gb\|ABB6... gi\|89107568, gi\|... - gi\|89107568\|ref\|AP_001348.1\| conserved metal-binding protein [Escherichia coli str. K-12 substr. W31... gi\|91071320, gi\|... - gi\|91209746\|ref\|YP_539732.1\| putative hydrolase-oxidase [Escherichia coli UTI89], gi\|91071320\|gb\|ABE... gi\|187430792, gi... - gi\|75175909\|ref\|ZP_00696096.1\| COG0327: Uncharacterized conserved protein [Shigella boydii BS512], g... gi\|157160190, gi... - gi\|75194869\|ref\|ZP_00704939.1\| COG0327: Uncharacterized conserved protein [Escherichia coli HS], gi\|... gi\|188015211, gi... - gi\|188015211\|gb\|EDU53333.1\| NIF3 family protein [Escherichia coli O157:H7 str. EC4113], gi\|168750640... gi\|254591256, gi... - gi\|254791856\|ref\|YP_003076693.1\| metal-binding predicted hydrolase-oxidase [Escherichia coli O157:H7... gi\|168757161, gi... - gi\|189355794\|gb\|EDU74213.1\| NIF3 family protein [Escherichia coli O157:H7 str. EC4401], gi\|168757161... gi\|238860257, gi... - gi\|238899975\|ref\|YP_002925771.1\| conserved metal-binding protein [Escherichia coli BW2952], gi\|23886... gi\|189365925, gi... - gi\|189365925\|gb\|EDU84341.1\| NIF3 family protein [Escherichia coli O157:H7 str. EC4501], gi\|168763989... gi\|226898536, gi... - gi\|237707326\|ref\|ZP_04537807.1\| NIF3 family protein [Escherichia sp. 3_2_53FAA], gi\|226898536\|gb\|EEH... gi\|13360193, gi\|... - gi\|15829989\|ref\|NP_308762.1\| putative hydrolase-oxidase [Escherichia coli O157:H7 str. Sakai], gi\|13... gi\|168767149, gi... - gi\|189363426\|gb\|EDU81845.1\| NIF3 family protein [Escherichia coli O157:H7 str. EC4486], gi\|168767149... gi\|227838407, gi... - gi\|227884321\|ref\|ZP_04002126.1\| hydrolase-oxidase [Escherichia coli 83972], gi\|227838407\|gb\|EEJ48873... gi\|168777034, gi... - gi\|187767664\|gb\|EDU31508.1\| NIF3 family protein [Escherichia coli O157:H7 str. EC4196], gi\|168777034... gi\|189002799, gi... - gi\|189002799\|gb\|EDU71785.1\| NIF3 family protein [Escherichia coli O157:H7 str. EC4076], gi\|168779192... gi\|168786862, gi... - gi\|189373117\|gb\|EDU91533.1\| NIF3 family protein [Escherichia coli O157:H7 str. EC869], gi\|168786862\|... gi\|115512031, gi... - gi\|117622907\|ref\|YP_851820.1\| putative hydrolase-oxidase [Escherichia coli APEC O1], gi\|115512031\|gb... gi\|124501528, gi... - gi\|124526834\|ref\|ZP_01698716.1\| protein of unknown function DUF34 [Escherichia coli B], gi\|124501528... YBGI_ECOL6 - UPF0135 protein ybgI OS=Escherichia coli O6 GN=ybgI PE=3 SV=1	2.0E-65	[8..284]	[1..246]

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Predicted Domain #1

Region A:
Residues: [1-288]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSRAITRAQL DKLVRSITKF YPQKYADKSW DNTGLLIDCS TAQVTTADAN AKTKVLLTVD  60
   61 LTKSVAQEAV DANCNVIVAY HPFIFPSWNR LSPHTNPQHE TAIKLIQYGI SVYCPHTAVD 120
  121 AARGGVNDWL VRGLNNGENV AKSYALETVS GETDDLIGYG RFVEFNKDIS LEQIVKNVKR 180
  181 VLRVPYVQVA SLAAPSAWNQ LKIKKVAVCA GSGSGVFKQL KEDVDLYYTG EMSHHEVLKW 240
  241 KEMGKTVIVC NHSNTERGFL QDVMKGLLQD EGHEVVVSKM DCDPLTVA

[Run NCBI BLAST on this sequence.]

Detection Method:	Pfam
Confidence:	105.026872
Match:	PF01784
Description:	NIF3 (NGG1p interacting factor 3)

Shown below is our most confident prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted functions:

Term	Confidence	Notes
binding	2.36275821588531	bayes_pls_golite062009
transcription factor binding	0.8197800099048	bayes_pls_golite062009
protein binding	0.188326419539465	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: