YRC Public Data Repository - Protein Structure Prediction

Protein:	MRF1
Organism:	Saccharomyces cerevisiae
Length:	413 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 MRF1.

Description	E-value	Query Range	Subject Range
MRF1 - Mitochondrial translation release factor, involved in stop codon recognition and hydrolysis of the p... gi\|190407089 - gi\|190407089\|gb\|EDV10356.1\| mitochondrial polypeptide chain release factor [Saccharomyces cerevisiae... gi\|207345440 - gi\|207345440\|gb\|EDZ72262.1\| YGL143Cp-like protein [Saccharomyces cerevisiae AWRI1631] gi\|151943668 - gi\|151943668\|gb\|EDN61978.1\| mitochondrial translation release factor [Saccharomyces cerevisiae YJM78... RF1M_YEAST - Peptide chain release factor 1, mitochondrial OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288...	0.0	[1..413]	[1..413]
RF1_HAEIN - (P43917) Peptide chain release factor 1 (RF-1) gi\|148716243, gi... - gi\|148826083\|ref\|YP_001290836.1\| peptide chain release factor 1 [Haemophilus influenzae PittEE], gi\|... gi\|144982593, gi... - gi\|145642039\|ref\|ZP_01797610.1\| peptide chain release factor 1 [Haemophilus influenzae R3021], gi\|14... gi\|145637543, gi... - gi\|145637543\|ref\|ZP_01793200.1\| peptide chain release factor 1 [Haemophilus influenzae PittHH], gi\|1... gi\|145631803, gi... - gi\|145642039\|ref\|ZP_01797610.1\| peptide chain release factor 1 [Haemophilus influenzae R3021], gi\|14... gi\|16273461, gi\|... - gi\|16273461\|ref\|NP_439710.1\| peptide chain release factor 1 [Haemophilus influenzae Rd KW20], gi\|157... gi\|229809952, gi... - gi\|229847123\|ref\|ZP_04467228.1\| peptide chain release factor 1 [Haemophilus influenzae 7P49H1], gi\|2... gi\|229844233, gi... - gi\|229844233\|ref\|ZP_04464374.1\| peptide chain release factor 1 [Haemophilus influenzae 6P18H1], gi\|2...	0.0	[49..413]	[2..361]
RF1_PASMU - Peptide chain release factor 1 OS=Pasteurella multocida (strain Pm70) GN=prfA PE=3 SV=1 RF1_PASMU - Peptide chain release factor 1 OS=Pasteurella multocida GN=prfA PE=3 SV=1	0.0	[49..412]	[1..359]
RF1_VIBCM - Peptide chain release factor 1 OS=Vibrio cholerae serotype O1 (strain M66-2) GN=prfA PE=3 SV=1 gi\|116189311, gi... - gi\|75830361\|ref\|ZP_00759641.1\| COG0216: Protein chain release factor A [Vibrio cholerae MO10], gi\|25... gi\|229355248, gi... - gi\|229507743\|ref\|ZP_04397248.1\| peptide chain release factor 1 [Vibrio cholerae BX 330286], gi\|22935... RF1_VIBC3 - Peptide chain release factor 1 OS=Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 3... gi\|229513825, gi... - gi\|229513825\|ref\|ZP_04403287.1\| peptide chain release factor 1 [Vibrio cholerae TMA 21], gi\|22934900... gi\|229519157, gi... - gi\|229519157\|ref\|ZP_04408600.1\| peptide chain release factor 1 [Vibrio cholerae RC9], gi\|229343846\|g... gi\|229522130, gi... - gi\|229522130\|ref\|ZP_04411547.1\| peptide chain release factor 1 [Vibrio cholerae TM 11079-80], gi\|229... gi\|229337756, gi... - gi\|229524175\|ref\|ZP_04413580.1\| peptide chain release factor 1 [Vibrio cholerae bv. albensis VL426],... gi\|229332588, gi... - gi\|229528814\|ref\|ZP_04418204.1\| peptide chain release factor 1 [Vibrio cholerae 12129(1)], gi\|229332... gi\|229369943, gi... - gi\|229607288\|ref\|YP_002877936.1\| peptide chain release factor 1 [Vibrio cholerae MJ-1236], gi\|229369... gi\|197751315, gi... - gi\|254291410\|ref\|ZP_04962203.1\| peptide chain release factor 1 [Vibrio cholerae AM-19226], gi\|197751... gi\|148875897, gi... - gi\|153828626\|ref\|ZP_01981293.1\| peptide chain release factor 1 [Vibrio cholerae 623-39], gi\|14887589... gi\|149740734, gi... - gi\|153825583\|ref\|ZP_01978250.1\| peptide chain release factor 1 [Vibrio cholerae MZO-2], gi\|149740734... RF1_VIBCH - Peptide chain release factor 1 OS=Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N169... gi\|124116034, gi... - gi\|153213234\|ref\|ZP_01948646.1\| peptide chain release factor 1 [Vibrio cholerae 1587], gi\|124116034\|... gi\|153223504, gi... - gi\|153223504\|ref\|ZP_01953906.1\| peptide chain release factor 1 [Vibrio cholerae MAK 757], gi\|1241181... gi\|124122826, gi... - gi\|153801649\|ref\|ZP_01956235.1\| peptide chain release factor 1 [Vibrio cholerae MZO-3], gi\|124122826... RF1_VIBCH - Peptide chain release factor 1 OS=Vibrio cholerae GN=prfA PE=3 SV=1 gi\|153818801, gi... - gi\|153818801\|ref\|ZP_01971468.1\| peptide chain release factor 1 [Vibrio cholerae NCTC 8457], gi\|12651... gi\|126518907, gi... - gi\|229512021\|ref\|ZP_04401500.1\| peptide chain release factor 1 [Vibrio cholerae B33], gi\|229351986\|g...	0.0	[49..413]	[1..362]
RF1_RALSO - Peptide chain release factor 1 OS=Ralstonia solanacearum GN=prfA PE=3 SV=1 RF1_RALSO - Peptide chain release factor 1 OS=Ralstonia solanacearum (strain GMI1000) GN=prfA PE=3 SV=1	0.0	[49..412]	[1..359]
EG10761 - peptide chain release factor RF-1 / Peptide chain release factor 1, RF-1; translation termination fa... RF1_ECOLI - Peptide chain release factor 1 (RF-1) - Escherichia coli RF1_ECOL6 - Peptide chain release factor 1 OS=Escherichia coli O6 GN=prfA PE=3 SV=1 RF1_ECO55 - Peptide chain release factor 1 OS=Escherichia coli (strain 55989 / EAEC) GN=prfA PE=3 SV=1 RF1_ECO45 - Peptide chain release factor 1 OS=Escherichia coli O45:K1 (strain S88 / ExPEC) GN=prfA PE=3 SV=1 RF1_ECOLU - Peptide chain release factor 1 OS=Escherichia coli O17:K52:H18 (strain UMN026 / ExPEC) GN=prfA PE=3 ... RF1_ECO7I - Peptide chain release factor 1 OS=Escherichia coli O7:K1 (strain IAI39 / ExPEC) GN=prfA PE=3 SV=1 gi\|208816069, gi... - gi\|208816069\|ref\|ZP_03257248.1\| peptide chain release factor 1 [Escherichia coli O157:H7 str. EC4045... gi\|208727247, gi... - gi\|208807446\|ref\|ZP_03249783.1\| peptide chain release factor 1 [Escherichia coli O157:H7 str. EC4206... RF1_SHIDS - Peptide chain release factor 1 OS=Shigella dysenteriae serotype 1 (strain Sd197) GN=prfA PE=3 SV=1 RF1_ECO5E - Peptide chain release factor 1 OS=Escherichia coli O157:H7 (strain EC4115 / EHEC) GN=prfA PE=3 SV=1 gi\|208822717, gi... - gi\|208822717\|ref\|ZP_03263036.1\| peptide chain release factor 1 [Escherichia coli O157:H7 str. EC4042... gi\|217318645, gi... - gi\|217328218\|ref\|ZP_03444300.1\| peptide chain release factor 1 [Escherichia coli O157:H7 str. TW1458... RF1_ECOSE - Peptide chain release factor 1 OS=Escherichia coli (strain SE11) GN=prfA PE=3 SV=1 RF1_ECO8A - Peptide chain release factor 1 OS=Escherichia coli O8 (strain IAI1) GN=prfA PE=3 SV=1 RF1_ESCF3 - Peptide chain release factor 1 OS=Escherichia fergusonii (strain ATCC 35469 / DSM 13698 / CDC 0568-7... gi\|75212649, gi\|... - gi\|75212649\|ref\|ZP_00712647.1\| COG0216: Protein chain release factor A [Escherichia coli B171], gi\|1... gi\|193069953, gi... - gi\|75235277\|ref\|ZP_00719514.1\| COG0216: Protein chain release factor A [Escherichia coli E110019], g... RF1_ECO24 - Peptide chain release factor 1 OS=Escherichia coli O139:H28 (strain E24377A / ETEC) GN=prfA PE=3 SV=... RF1_ECOHS - Peptide chain release factor 1 OS=Escherichia coli O9:H4 (strain HS) GN=prfA PE=3 SV=1 gi\|188489481, gi... - gi\|75511753\|ref\|ZP_00734382.1\| COG0216: Protein chain release factor A [Escherichia coli 53638], gi\|... RF1_SHISS - Peptide chain release factor 1 OS=Shigella sonnei (strain Ss046) GN=prfA PE=3 SV=1 gi\|190908626, gi... - gi\|75242015\|ref\|ZP_00725809.1\| COG0216: Protein chain release factor A [Escherichia coli F11], gi\|19... gi\|193064852, gi... - gi\|75257119\|ref\|ZP_00728655.1\| COG0216: Protein chain release factor A [Escherichia coli E22], gi\|19... gi\|194434263, gi... - gi\|83569313\|ref\|ZP_00920769.1\| COG0216: Protein chain release factor A [Shigella dysenteriae 1012], ... gi\|194437123, gi... - gi\|83587355\|ref\|ZP_00925983.1\| COG0216: Protein chain release factor A [Escherichia coli 101-1], gi\|... gi\|227836571, gi... - gi\|227886367\|ref\|ZP_04004172.1\| peptide chain release factor 1 [Escherichia coli 83972], gi\|22783657... gi\|226899930, gi... - gi\|237705173\|ref\|ZP_04535654.1\| peptide chain release factor RF-1 [Escherichia sp. 3_2_53FAA], gi\|22... RF1_ECOBW - Peptide chain release factor 1 OS=Escherichia coli (strain K12 / MC4100 / BW2952) GN=prfA PE=3 SV=1 gi\|251784717, gi... - gi\|251784717\|ref\|YP_002999021.1\| hypothetical protein B21_01196 [Escherichia coli BL21], gi\|24237699... gi\|253977408, gi... - gi\|254288101\|ref\|YP_003053849.1\| peptide chain release factor 1 [Escherichia coli BL21(DE3)], gi\|253... gi\|254161293, gi... - gi\|254161293\|ref\|YP_003044401.1\| peptide chain release factor 1 [Escherichia coli B str. REL606], gi... gi\|254592081, gi... - gi\|254792681\|ref\|YP_003077518.1\| peptide chain release factor RF-1 [Escherichia coli O157:H7 str. TW... RF1_ECOL5 - Peptide chain release factor 1 OS=Escherichia coli O6:K15:H31 (strain 536 / UPEC) GN=prfA PE=3 SV=1 gi\|168776896, gi... - gi\|187767792\|gb\|EDU31636.1\| peptide chain release factor 1 [Escherichia coli O157:H7 str. EC4196], g... RF1_SHIF8 - Peptide chain release factor 1 OS=Shigella flexneri serotype 5b (strain 8401) GN=prfA PE=3 SV=1 gi\|189360046, gi... - gi\|189360046\|gb\|EDU78465.1\| peptide chain release factor 1 [Escherichia coli O157:H7 str. EC4486], g... gi\|168787715, gi... - gi\|189372547\|gb\|EDU90963.1\| peptide chain release factor 1 [Escherichia coli O157:H7 str. EC869], gi... gi\|188999995, gi... - gi\|188999995\|gb\|EDU68981.1\| peptide chain release factor 1 [Escherichia coli O157:H7 str. EC4076], g... RF1_ECODH - Peptide chain release factor 1 OS=Escherichia coli (strain K12 / DH10B) GN=prfA PE=3 SV=1 gi\|1651601, gi\|8... - gi\|89108056\|ref\|AP_001836.1\| peptide chain release factor RF-1 [Escherichia coli str. K-12 substr. W... gi\|189376326, gi... - gi\|189376326\|gb\|EDU94742.1\| peptide chain release factor 1 [Escherichia coli O157:H7 str. EC508], gi... RF1_ECOUT - Peptide chain release factor 1 OS=Escherichia coli (strain UTI89 / UPEC) GN=prfA PE=3 SV=1 gi\|195939099 - gi\|195939099\|ref\|ZP_03084481.1\| peptide chain release factor 1 [Escherichia coli O157:H7 str. EC4024... gi\|15830970, gi\|... - gi\|15830970\|ref\|NP_309743.1\| peptide chain release factor 1 [Escherichia coli O157:H7 str. Sakai], g... RF1_ECOSM - Peptide chain release factor 1 OS=Escherichia coli (strain SMS-3-5 / SECEC) GN=prfA PE=3 SV=1 gi\|168750771, gi... - gi\|188015105\|gb\|EDU53227.1\| peptide chain release factor 1 [Escherichia coli O157:H7 str. EC4113], g... gi\|168764382, gi... - gi\|189365613\|gb\|EDU84029.1\| peptide chain release factor 1 [Escherichia coli O157:H7 str. EC4501], g... RF1_ECOLC - Peptide chain release factor 1 OS=Escherichia coli (strain ATCC 8739 / DSM 1576 / Crooks) GN=prfA PE... gi\|189354981, gi... - gi\|189354981\|gb\|EDU73400.1\| peptide chain release factor 1 [Escherichia coli O157:H7 str. EC4401], g... RF1_SHIFL - Peptide chain release factor 1 OS=Shigella flexneri GN=prfA PE=3 SV=1 gi\|24112610, gi\|... - gi\|24112610\|ref\|NP_707120.1\| peptide chain release factor 1 [Shigella flexneri 2a str. 301], gi\|2405... RF1_ECO57 - Peptide chain release factor 1 OS=Escherichia coli O157:H7 GN=prfA PE=3 SV=1 EG10761 - peptide chain release factor RF-1 / Peptide chain release factor 1, RF-1; translation termination fa... RF1_ECOL6 - Peptide chain release factor 1 OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) GN=prf... gi\|30040983, gi\|... - gi\|30062735\|ref\|NP_836906.1\| peptide chain release factor 1 [Shigella flexneri 2a str. 2457T], gi\|30... RF1_ECOK1 - Peptide chain release factor 1 OS=Escherichia coli O1:K1 / APEC GN=prfA PE=3 SV=1 gi\|124500638, gi... - gi\|124528406\|ref\|ZP_01699716.1\| peptide chain release factor 1 [Escherichia coli B], gi\|124500638\|gb...	0.0	[49..412]	[1..359]
gi\|15801440, gi\|... - gi\|15801440\|ref\|NP_287457.1\| peptide chain release factor 1 [Escherichia coli O157:H7 EDL933], gi\|12... gi\|25299675 - pir\|\|A85701 peptide chain release factor RF-1 [imported] - Escherichia coli (strain O157:H7, substra...	0.0	[49..412]	[1..359]
RF1_PSEAE - Peptide chain release factor 1 OS=Pseudomonas aeruginosa GN=prfA PE=3 SV=2 gi\|107099668 - gi\|107099668\|ref\|ZP_01363586.1\| hypothetical protein PaerPA_01000686 [Pseudomonas aeruginosa PACS2] RF1_PSEAE - Peptide chain release factor 1 OS=Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / ...	0.0	[49..411]	[1..360]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	0.0	[49..412]	[1..359]
gi\|147567 - gi\|147567\|gb\|AAA24519.1\| peptide chain release factor 1	0.0	[49..412]	[1..359]

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Predicted Domain #1

Region A:
Residues: [1-143]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MWLSKFQFPS RSIFKGVFLG HKLPLLVRLT STTTNSKSNG SIPTQYTELS PLLVKQAEKY  60
   61 EAELKDLDKD LSCGIHFDVN KQKHYAKLSA LTDTFIEYKE KLNELKSLQE MIVSDPSLRA 120
  121 EAEQEYAELV PQYETTSSRL VNK

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	502.0
Match:	1gqeA_
Description:	Polypeptide chain release factor 2 (RF2)
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
translation release factor activity	8.49824253851587	bayes_pls_golite062009
translation termination factor activity	8.4944923601206	bayes_pls_golite062009
translation regulator activity	5.08132283479856	bayes_pls_golite062009
translation factor activity, nucleic acid binding	5.06589285641735	bayes_pls_golite062009
nucleic acid binding	4.97313255824207	bayes_pls_golite062009
binding	3.98889300462019	bayes_pls_golite062009
translation release factor activity, codon specific	0.183484956864194	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [144-265]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LLPPHPFADK PSLLELRPGV GGIEAMIFTQ NLLDMYIGYA NYRKWKYRII SKNENESGSG  60
   61 IIDAILSIEE AGSYDRLRFE AGVHRVQRIP STETKGRTHT STAAVVVLPQ IGDESAKSID 120
  121 AY

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [354-413]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NRSDKIRTYN FPQNRITDHR CGFTLLDLPG VLSGERLDEV IEAMSKYDST ERAKELLESN  60
   61

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	502.0
Match:	1gqeA_
Description:	Polypeptide chain release factor 2 (RF2)
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [266-353]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 ERTFKPGEIR VDIMRASGKG GQHVNTTDSA VRLTHIPSGI VVSMQDERSQ HKNKAKAFTI  60
   61 LRARLAEKER LEKEEKERKA RKSQVSST

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	502.0
Match:	1gqeA_
Description:	Polypeptide chain release factor 2 (RF2)
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

Predicted functions: