Citrus Sinensis ID: 026662

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-----
MVRNYNLWDDPTKSNEVLVKLADSLKVVNALKDLRYKAEEAKLIAQLAEMEAIDYGLFKRAYRASLDVSKLLDQYEMSKLLRGPNDVEGASVTIKAGSNGICPEIWAEQLLNMYVRWADKEGYRGRVVDKCCCKNGGVKSATIEFEFEYAFGYLSGETGAHCLINFPNGSFPHEATLACVDVVPLFLETSPDLQISDEDLLFSSPSLPGERQSIAKPAACIQHIPTGIAVQSLGA
ccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccEEEEEccccccHHHHHHHHHHHHHHHHHHcccccEEEEEccccccccccEEEEEEEEccccEEccccccEEEEEEcccccccccccccEEEEEEcccccccccccccccEEEEccccccccccccccEEEEccccccEEEEcccc
ccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccEEEEEcccccccHHHHHHHHHHHHHHHHHHHcccEEEEEEccccccccEEEEEEEEEccccEEEEEcccccEEEEEEEccccccccEEEEEEEcccEccccEEEEEcHHHEEEEEcccccccccccccEEEEEEccccEEEEEccc
mvrnynlwddptksnEVLVKLADSLKVVNALKDLRYKAEEAKLIAQLAEMEAIDYGLFKRAYRASLDVSKLLDQYEMSKllrgpndvegasvtikagsngicpeIWAEQLLNMYVRWadkegyrgrvvdkcccknggvksatIEFEFEYAfgylsgetgahclinfpngsfpheatlacVDVVplfletspdlqisdedllfsspslpgerqsiakpaaciqhiptgIAVQSLGA
mvrnynlwddptksnEVLVKLADSLKVVNALKDLRYKAEEAKLIAQLAEMEAIDYGLFKRAYRASLDVSKLLDQYEMSKLLRGPNDVEGASVTIKAGSNGICPEIWAEQLLNMYVRWADKEGYRGRVVDKCCCKNGGVKSATIEFEFEYAFGYLSGETGAHCLINFPNGSFPHEATLACVDVVPLFLETSPDLQISDEDLLFSSPSLPGERQSIAKPAACIQHIPTGIAVQSLGA
MVRNYNLWDDPTKSNEVLVKLADSLKVVNALKDLRYKAEEAKLIAQLAEMEAIDYGLFKRAYRASLDVSKLLDQYEMSKLLRGPNDVEGASVTIKAGSNGICPEIWAEQLLNMYVRWADKEGYRGRVVDKCCCKNGGVKSATIEFEFEYAFGYLSGETGAHCLINFPNGSFPHEATLACVDVVPLFLETSPDLQISDEDLLFSSPSLPGERQSIAKPAACIQHIPTGIAVQSLGA
******LWD****SNEVLVKLADSLKVVNALKDLRYKAEEAKLIAQLAEMEAIDYGLFKRAYRASLDVSKLLDQYEMSKLLRGPNDVEGASVTIKAGSNGICPEIWAEQLLNMYVRWADKEGYRGRVVDKCCCKNGGVKSATIEFEFEYAFGYLSGETGAHCLINFPNGSFPHEATLACVDVVPLFLETSPDLQI**********************AACIQHIPTGI*******
MVRNYNLWDDPTKS***********KVVNALKDLRYKAEEAKLIAQLAEMEAIDYGLFKRAYRASLDVSKLLDQYEMSKLLRGPNDVEGASVTIKAGSNGICPEIWAEQLLNMYVRWADKEGYRGRVVDKCCCKNGGVKSATIEFEFEYAFGYLSGETGAHCLINFPNGSFPHEATLACVDVVPLFLETSPDLQISDEDLLFSSPSLPGERQSIAKPAACIQHIPTGIAVQSLG*
MVRNYNLWDDPTKSNEVLVKLADSLKVVNALKDLRYKAEEAKLIAQLAEMEAIDYGLFKRAYRASLDVSKLLDQYEMSKLLRGPNDVEGASVTIKAGSNGICPEIWAEQLLNMYVRWADKEGYRGRVVDKCCCKNGGVKSATIEFEFEYAFGYLSGETGAHCLINFPNGSFPHEATLACVDVVPLFLETSPDLQISDEDLLFSSPSLPGERQSIAKPAACIQHIPTGIAVQSLGA
****YNLWDDPTKSNEVLVKLADSLKVVNALKDLRYKAEEAKLIAQLAEMEAIDYGLFKRAYRASLDVSKLLDQYEMSKLLRGPNDVEGASVTIKAGSNGICPEIWAEQLLNMYVRWADKEGYRGRVVDKCCCKNGGVKSATIEFEFEYAFGYLSGETGAHCLINFPNGSFPHEATLACVDVVPLFLETSPDLQISDEDLLFSSPSLPGERQSIAKPAACIQHIPTGIAVQS***
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ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MVRNYNLWDDPTKSNEVLVKLADSLKVVNAxxxxxxxxxxxxxxxxxxxxxAIDYGLFKRAYRASLDVSKLLDQYEMSKLLRGPNDVEGASVTIKAGSNGICPEIWAEQLLNMYVRWADKEGYRGRVVDKCCCKNGGVKSATIEFEFEYAFGYLSGETGAHCLINFPNGSFPHEATLACVDVVPLFLETSPDLQISDEDLLFSSPSLPGERQSIAKPAACIQHIPTGIAVQSLGA
no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST ?

Original result of BLAST against SWISS-PROT Database

ID ?Alignment graph ?Length ? Definition ? RBH(Q2H) ? RBH(H2Q) ? Q cover ? H cover ? Identity ? E-value ?
Query235 2.2.26 [Sep-21-2011]
P74476372 Peptide chain release fac N/A no 0.957 0.604 0.341 1e-32
B7K0A6365 Peptide chain release fac yes no 0.957 0.616 0.329 6e-30
B9L0E3 374 Peptide chain release fac yes no 0.940 0.590 0.313 7e-29
A9WPT6374 Peptide chain release fac yes no 0.948 0.596 0.326 3e-28
C5BYB6374 Peptide chain release fac yes no 0.948 0.596 0.326 7e-28
A4X3K6373 Peptide chain release fac yes no 0.948 0.597 0.326 2e-27
Q8NS78368 Peptide chain release fac yes no 0.940 0.600 0.313 6e-27
A4QCD3368 Peptide chain release fac yes no 0.940 0.600 0.313 6e-27
A8M3R1373 Peptide chain release fac yes no 0.948 0.597 0.313 2e-26
B8G607367 Peptide chain release fac yes no 0.923 0.591 0.333 2e-26
>sp|P74476|RF2_SYNY3 Peptide chain release factor 2 OS=Synechocystis sp. (strain PCC 6803 / Kazusa) GN=prfB PE=3 SV=2 Back     alignment and function desciption
 Score =  139 bits (351), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 79/231 (34%), Positives = 129/231 (55%), Gaps = 6/231 (2%)

Query: 6   NLWDDPTKSNEVLVKLADSLKVVNALKDLRYKAEEAKLIAQLAEMEAIDYGLFKRAYRAS 65
           + WDD  ++ ++L  L ++   +      + + ++++ I +L E+E  D  L   A    
Sbjct: 46  DFWDDTDQAQQILQTLNETKSQLEQWGIWQQQWQDSQAIVELLELED-DQALLTEAETTL 104

Query: 66  LDVSKLLDQYEMSKLLRGPNDVEGASVTIKAGSNGICPEIWAEQLLNMYVRWADKEGYRG 125
             + K LD++E+ +LL GP D +GA++TI AG+ G   + WAE LL MY RW++K+GY+ 
Sbjct: 105 EQLQKELDRWELQQLLSGPYDAKGATLTINAGAGGTDAQDWAEMLLRMYTRWSEKQGYKV 164

Query: 126 RVVDKCCCKNGGVKSATIEFEFEYAFGYLSGETGAHCLINFP--NGSFPHEATLACVDVV 183
            + +       G+KS T+E E  YA+GYL  E G H L+     N +   + + A V+V+
Sbjct: 165 HLAEISEGDEAGLKSVTLEIEGRYAYGYLKSEKGTHRLVRISPFNANGKRQTSFAGVEVM 224

Query: 184 PLFLETSPDLQISDEDLLFSSPSLPGE-RQSIAK--PAACIQHIPTGIAVQ 231
           PL  E +  L I D+DL  S+    G+  Q++ K   A  I H+PTG+AV+
Sbjct: 225 PLLGEEAISLDIPDKDLDISTSRAGGKGGQNVNKVETAVRIVHLPTGLAVR 275
Peptide chain release factor 2 directs the termination of translation in response to the peptide chain termination codons UGA and UAA.
Synechocystis sp. (strain PCC 6803 / Kazusa) (taxid: 1111708)
>sp|B7K0A6|RF2_CYAP8 Peptide chain release factor 2 OS=Cyanothece sp. (strain PCC 8801) GN=prfB PE=3 SV=1 Back     alignment and function description
>sp|B9L0E3|RF2_THERP Peptide chain release factor 2 OS=Thermomicrobium roseum (strain ATCC 27502 / DSM 5159 / P-2) GN=prfB PE=3 SV=1 Back     alignment and function description
>sp|A9WPT6|RF2_RENSM Peptide chain release factor 2 OS=Renibacterium salmoninarum (strain ATCC 33209 / DSM 20767 / JCM 11484 / NBRC 15589 / NCIMB 2235) GN=prfB PE=3 SV=1 Back     alignment and function description
>sp|C5BYB6|RF2_BEUC1 Peptide chain release factor 2 OS=Beutenbergia cavernae (strain ATCC BAA-8 / DSM 12333 / NBRC 16432) GN=prfB PE=3 SV=1 Back     alignment and function description
>sp|A4X3K6|RF2_SALTO Peptide chain release factor 2 OS=Salinispora tropica (strain ATCC BAA-916 / DSM 44818 / CNB-440) GN=prfB PE=3 SV=1 Back     alignment and function description
>sp|Q8NS78|RF2_CORGL Peptide chain release factor 2 OS=Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025) GN=prfB PE=3 SV=1 Back     alignment and function description
>sp|A4QCD3|RF2_CORGB Peptide chain release factor 2 OS=Corynebacterium glutamicum (strain R) GN=prfB PE=3 SV=1 Back     alignment and function description
>sp|A8M3R1|RF2_SALAI Peptide chain release factor 2 OS=Salinispora arenicola (strain CNS-205) GN=prfB PE=3 SV=1 Back     alignment and function description
>sp|B8G607|RF2_CHLAD Peptide chain release factor 2 OS=Chloroflexus aggregans (strain MD-66 / DSM 9485) GN=prfB PE=3 SV=1 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query235
225441347 417 PREDICTED: peptide chain release factor 0.995 0.561 0.672 4e-85
297739884 414 unnamed protein product [Vitis vinifera] 0.995 0.565 0.672 4e-85
147836146 450 hypothetical protein VITISV_041859 [Viti 0.995 0.52 0.673 4e-84
224086914 374 predicted protein [Populus trichocarpa] 0.995 0.625 0.651 2e-83
356504376 437 PREDICTED: peptide chain release factor 0.995 0.535 0.621 1e-81
356534710 427 PREDICTED: peptide chain release factor 0.995 0.548 0.612 7e-81
357439325 538 Peptide chain release factor [Medicago t 0.991 0.433 0.625 1e-78
356498639 385 PREDICTED: peptide chain release factor 0.995 0.607 0.6 3e-78
22135990 372 putative protein [Arabidopsis thaliana] 0.970 0.612 0.536 3e-65
30694592 406 putative peptide chain release factor [A 0.970 0.561 0.536 4e-65
>gi|225441347|ref|XP_002274658.1| PREDICTED: peptide chain release factor 2-like [Vitis vinifera] Back     alignment and taxonomy information
 Score =  320 bits (819), Expect = 4e-85,   Method: Compositional matrix adjust.
 Identities = 158/235 (67%), Positives = 182/235 (77%), Gaps = 1/235 (0%)

Query: 1   MVRNYNLWDDPTKSNEVLVKLADSLKVVNALKDLRYKAEEAKLIAQLAEMEAIDYGLFKR 60
           M+R YNLWDD TKSNE+L KLADS KVV+ LKDL YKAEEAKLI QL EM+AI++GLF++
Sbjct: 87  MIRKYNLWDDVTKSNEILGKLADSSKVVDTLKDLTYKAEEAKLITQLVEMDAINHGLFEQ 146

Query: 61  AYRASLDVSKLLDQYEMSKLLRGPNDVEGASVTIKAGSNGICPEIWAEQLLNMYVRWADK 120
           AY AS+DVSK L QYEMSKLLRG  D+EGA +TIKAG  GI  EIWAEQLL+MY +WA+K
Sbjct: 147 AYNASVDVSKFLYQYEMSKLLRGQFDMEGACLTIKAGPRGIYSEIWAEQLLSMYTKWAEK 206

Query: 121 EGYRGRVVDKCCCKNGGVKSATIEFEFEYAFGYLSGETGAHCLINFPNG-SFPHEATLAC 179
           +GY+GRVV+K   KNGG+KSATIEFE EY +GYLSGE G H +I   +  S  HE   A 
Sbjct: 207 QGYKGRVVEKYASKNGGIKSATIEFESEYGYGYLSGERGVHHMIRSSDDESILHETGSAV 266

Query: 180 VDVVPLFLETSPDLQISDEDLLFSSPSLPGERQSIAKPAACIQHIPTGIAVQSLG 234
           VDV+PLFLET+PDLQI D DL  SSPS  G  Q     A CIQHIPTGI+VQS G
Sbjct: 267 VDVIPLFLETAPDLQIDDGDLRISSPSCHGVEQGRTGHAVCIQHIPTGISVQSSG 321

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|297739884|emb|CBI30066.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|147836146|emb|CAN74766.1| hypothetical protein VITISV_041859 [Vitis vinifera] Back     alignment and taxonomy information
>gi|224086914|ref|XP_002308002.1| predicted protein [Populus trichocarpa] gi|222853978|gb|EEE91525.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|356504376|ref|XP_003520972.1| PREDICTED: peptide chain release factor 2-like [Glycine max] Back     alignment and taxonomy information
>gi|356534710|ref|XP_003535895.1| PREDICTED: peptide chain release factor 2-like [Glycine max] Back     alignment and taxonomy information
>gi|357439325|ref|XP_003589939.1| Peptide chain release factor [Medicago truncatula] gi|355478987|gb|AES60190.1| Peptide chain release factor [Medicago truncatula] Back     alignment and taxonomy information
>gi|356498639|ref|XP_003518157.1| PREDICTED: peptide chain release factor 2-like [Glycine max] Back     alignment and taxonomy information
>gi|22135990|gb|AAM91577.1| putative protein [Arabidopsis thaliana] gi|30725574|gb|AAP37809.1| At3g57190 [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|30694592|ref|NP_191278.2| putative peptide chain release factor [Arabidopsis thaliana] gi|332646104|gb|AEE79625.1| putative peptide chain release factor [Arabidopsis thaliana] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query235
TAIR|locus:2082563406 PrfB3 "peptide chain release f 0.970 0.561 0.536 1.6e-61
TAIR|locus:2158936456 HCF109 "high chlorophyll fluor 0.961 0.495 0.379 2.7e-36
TIGR_CMR|CHY_0163371 CHY_0163 "peptide chain releas 0.953 0.603 0.313 2.9e-25
UNIPROTKB|Q3Z8Y6362 prfB "Peptide chain release fa 0.948 0.616 0.301 3.3e-24
TIGR_CMR|DET_0570362 DET_0570 "peptide chain releas 0.948 0.616 0.301 3.3e-24
UNIPROTKB|P66026371 prfB "Peptide chain release fa 0.944 0.598 0.303 1.1e-23
TIGR_CMR|GSU_2278372 GSU_2278 "peptide chain releas 0.936 0.591 0.292 1.4e-23
UNIPROTKB|P07012365 prfB [Escherichia coli K-12 (t 0.940 0.605 0.307 4.8e-23
TAIR|locus:2010748482 AT1G56350 [Arabidopsis thalian 0.927 0.452 0.310 6.2e-22
TIGR_CMR|SPO_2585375 SPO_2585 "peptide chain releas 0.957 0.6 0.295 4.4e-21
TAIR|locus:2082563 PrfB3 "peptide chain release factor 3" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 629 (226.5 bits), Expect = 1.6e-61, P = 1.6e-61
 Identities = 126/235 (53%), Positives = 165/235 (70%)

Query:     2 VRNYNLWDDPTKSNEVLVKLADSLKVVNALKDLRYKAEEAKLIAQLAEMEAIDYGLFKRA 61
             +R ++LWDDP KS+E+L+KLAD  K V++LKDL+YKAEEAKLI QL EM+AIDY LF++A
Sbjct:    83 MRYFDLWDDPAKSDEILLKLADRAKAVDSLKDLKYKAEEAKLIIQLGEMDAIDYSLFEQA 142

Query:    62 YRASLDVSKLLDQYEMSKLLRGPNDVEGASVTIKAGSNGICPEIWAEQLLNMYVRWADKE 121
             Y +SLDVS+ L  YEMSKLLR   D EGA + IK+GS G   +IW EQ+++MY++WA++ 
Sbjct:   143 YDSSLDVSRSLHHYEMSKLLRDQYDAEGACMIIKSGSPGAKSQIWTEQVVSMYIKWAERL 202

Query:   122 GYRGRVVDKCCC--KNGGVKSATIEFEFEYAFGYLSGETGAHCLINFPNGSFPHEATLAC 179
             G   RV +KC       GV SATIEFEFE+A+GYL GE G H LI     S  +E   A 
Sbjct:   203 GQNARVAEKCSLLSNKSGVSSATIEFEFEFAYGYLLGERGVHRLII---SSTSNEECSAT 259

Query:   180 VDVVPLFLETSPDLQISDEDLLFSSPSLPGERQSIAKPAACIQHIPTGIAVQSLG 234
             VD++PLFL  SPD ++ + DL+ S P+   E   IA+   CI HIP+G+ +QS G
Sbjct:   260 VDIIPLFLRASPDFEVKEGDLIVSYPAK--EDHKIAENMVCIHHIPSGVTLQSSG 312
GO:0003747 "translation release factor activity" evidence=IEA;ISS
GO:0005737 "cytoplasm" evidence=IEA
GO:0006415 "translational termination" evidence=IEA;ISS
GO:0016149 "translation release factor activity, codon specific" evidence=IEA
GO:0003730 "mRNA 3'-UTR binding" evidence=IDA
GO:0009507 "chloroplast" evidence=IDA
GO:0009570 "chloroplast stroma" evidence=IDA
GO:0043488 "regulation of mRNA stability" evidence=IMP
GO:0043565 "sequence-specific DNA binding" evidence=IDA
GO:0009658 "chloroplast organization" evidence=IMP
GO:0009772 "photosynthetic electron transport in photosystem II" evidence=IMP
GO:0010190 "cytochrome b6f complex assembly" evidence=IMP
GO:0048255 "mRNA stabilization" evidence=IMP
GO:0016556 "mRNA modification" evidence=RCA
TAIR|locus:2158936 HCF109 "high chlorophyll fluorescent 109" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TIGR_CMR|CHY_0163 CHY_0163 "peptide chain release factor 2, programmed frameshift" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)] Back     alignment and assigned GO terms
UNIPROTKB|Q3Z8Y6 prfB "Peptide chain release factor 2" [Dehalococcoides ethenogenes 195 (taxid:243164)] Back     alignment and assigned GO terms
TIGR_CMR|DET_0570 DET_0570 "peptide chain release factor 2, programmed frameshift" [Dehalococcoides ethenogenes 195 (taxid:243164)] Back     alignment and assigned GO terms
UNIPROTKB|P66026 prfB "Peptide chain release factor 2" [Mycobacterium tuberculosis (taxid:1773)] Back     alignment and assigned GO terms
TIGR_CMR|GSU_2278 GSU_2278 "peptide chain release factor 2, programmed frameshift" [Geobacter sulfurreducens PCA (taxid:243231)] Back     alignment and assigned GO terms
UNIPROTKB|P07012 prfB [Escherichia coli K-12 (taxid:83333)] Back     alignment and assigned GO terms
TAIR|locus:2010748 AT1G56350 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TIGR_CMR|SPO_2585 SPO_2585 "peptide chain release factor 2" [Ruegeria pomeroyi DSS-3 (taxid:246200)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries ?

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query235
PRK00578367 PRK00578, prfB, peptide chain release factor 2; Va 1e-41
TIGR00020364 TIGR00020, prfB, peptide chain release factor 2 1e-33
PRK05589325 PRK05589, PRK05589, peptide chain release factor 2 2e-28
PRK08787313 PRK08787, PRK08787, peptide chain release factor 2 3e-21
PRK07342339 PRK07342, PRK07342, peptide chain release factor 2 4e-21
COG1186239 COG1186, PrfB, Protein chain release factor B [Tra 6e-21
PRK06746326 PRK06746, PRK06746, peptide chain release factor 2 9e-20
pfam03462115 pfam03462, PCRF, PCRF domain 4e-19
smart00937116 smart00937, PCRF, This domain is found in peptide 3e-18
TIGR00019360 TIGR00019, prfA, peptide chain release factor 1 1e-11
COG0216363 COG0216, PrfA, Protein chain release factor A [Tra 4e-07
PRK00591 359 PRK00591, prfA, peptide chain release factor 1; Va 4e-04
>gnl|CDD|234799 PRK00578, prfB, peptide chain release factor 2; Validated Back     alignment and domain information 
 Score =  145 bits (367), Expect = 1e-41
 Identities = 78/240 (32%), Positives = 125/240 (52%), Gaps = 23/240 (9%)

Query: 6   NLWDDPTKSNEVLVKLADSLKVVNALKDLRYKAEEAKLIAQLAEMEAIDYGLFKRAYRAS 65
           + W+D  ++ +V  +L+     ++ L++LR + ++ + + +LAE E  D      A    
Sbjct: 43  DFWNDQERAQKVTKELSSLKAKLDTLEELRQRLDDLEELLELAEEED-DEETLAEAEAEL 101

Query: 66  LDVSKLLDQYEMSKLLRGPNDVEGASVTIKAGSNGICPEIWAEQLLNMYVRWADKEGYRG 125
             + K L   E+ +LL G  D   A +TI AG+ G   + WA  LL MY+RWA++ G++ 
Sbjct: 102 KALEKKLAALELERLLSGEYDANNAILTIHAGAGGTEAQDWASMLLRMYLRWAERHGFKV 161

Query: 126 RVVDKCCCKNGGVKSATIEFEFEYAFGYLSGETGAHCLIN---FPNG-----SFPHEATL 177
            V+D    +  G+KSAT + +  YA+GYL  ETG H L+    F +      SF      
Sbjct: 162 EVLDYSEGEEAGIKSATFKIKGPYAYGYLKSETGVHRLVRISPFDSAGRRHTSF------ 215

Query: 178 ACVDVVPLFLETSPDLQISDEDL---LFSSPSLPGERQSIAK--PAACIQHIPTGIAVQS 232
           A V+V P  ++ + +++I+ +DL    + S S  G  Q + K   A  I HIPTGI VQ 
Sbjct: 216 ASVEVYPE-VDDTIEIEINPKDLRIDTYRS-SGAGG-QHVNKTDSAVRITHIPTGIVVQC 272

Length = 367
>gnl|CDD|232785 TIGR00020, prfB, peptide chain release factor 2 Back     alignment and domain information
>gnl|CDD|235520 PRK05589, PRK05589, peptide chain release factor 2; Provisional Back     alignment and domain information
>gnl|CDD|136970 PRK08787, PRK08787, peptide chain release factor 2; Provisional Back     alignment and domain information
>gnl|CDD|235997 PRK07342, PRK07342, peptide chain release factor 2; Provisional Back     alignment and domain information
>gnl|CDD|224107 COG1186, PrfB, Protein chain release factor B [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|75726 PRK06746, PRK06746, peptide chain release factor 2; Provisional Back     alignment and domain information
>gnl|CDD|217573 pfam03462, PCRF, PCRF domain Back     alignment and domain information
>gnl|CDD|214923 smart00937, PCRF, This domain is found in peptide chain release factors Back     alignment and domain information
>gnl|CDD|129130 TIGR00019, prfA, peptide chain release factor 1 Back     alignment and domain information
>gnl|CDD|223294 COG0216, PrfA, Protein chain release factor A [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|234801 PRK00591, prfA, peptide chain release factor 1; Validated Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 235
COG0216363 PrfA Protein chain release factor A [Translation, 100.0
PRK05589325 peptide chain release factor 2; Provisional 100.0
PRK06746326 peptide chain release factor 2; Provisional 100.0
PRK07342339 peptide chain release factor 2; Provisional 100.0
TIGR00020364 prfB peptide chain release factor 2. In many but n 100.0
PRK00578367 prfB peptide chain release factor 2; Validated 100.0
TIGR00019360 prfA peptide chain release factor 1. This model de 100.0
PRK00591359 prfA peptide chain release factor 1; Validated 100.0
PRK08787313 peptide chain release factor 2; Provisional 100.0
KOG2726386 consensus Mitochondrial polypeptide chain release 100.0
COG1186239 PrfB Protein chain release factor B [Translation, 100.0
PRK08179200 prfH peptide chain release factor-like protein; Re 100.0
TIGR03072200 release_prfH putative peptide chain release factor 100.0
PF03462115 PCRF: PCRF domain; InterPro: IPR005139 This domain 100.0
PF00472113 RF-1: RF-1 domain; InterPro: IPR000352 Peptide cha 99.68
PRK09256138 hypothetical protein; Provisional 99.26
KOG3429172 consensus Predicted peptidyl-tRNA hydrolase [Trans 97.19
COG0216 363 PrfA Protein chain release factor A [Translation, 82.81
>COG0216 PrfA Protein chain release factor A [Translation, ribosomal structure and biogenesis] Back     alignment and domain information 
Probab=100.00  E-value=5.8e-81  Score=563.71  Aligned_cols=232  Identities=21%  Similarity=0.316  Sum_probs=221.4

Q ss_pred             CCCCCcCCCCHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHHHHHHHHHHHHHHH----H
Q 026662            1 MVRNYNLWDDPTKSNEVLVKLADSLKVVNALKDLRYKAEEAKLIAQLAEMEAIDYGLFKRAYRASLDVSKLLDQY----E   76 (235)
Q Consensus         1 ~msdP~~WdD~~ka~~~~~el~~l~~~~~~~~~~~~~~~e~~~l~el~~~~~~D~el~~~a~ee~~~l~~~l~~l----e   76 (235)
                      +|+||++.+|++++++++++++.|..+++.|+++++..++++...+|+.+. .|+||++||++|+..++..+..|    +
T Consensus        22 ~L~~p~v~~d~~~~~~lske~a~l~~iv~~~~~~~~~~~~l~~a~~~l~~~-~D~em~ema~~Ei~~~~~~~~~le~~L~  100 (363)
T COG0216          22 LLSDPEVISDPDEYRKLSKEYAELEPIVEKYREYKKAQEDLEDAKEMLAEE-KDPEMREMAEEEIKELEAKIEELEEELK  100 (363)
T ss_pred             HhcCcccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc-CCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            589999999999999999999999999999999999999999999998764 69999999999999999888655    4


Q ss_pred             HHhcCCCCCCcCCceEEEecCCCchHHHHHHHHHHHHHHHHHHhcCCeEEEEecccCCCCceeEEEEEEeeccccccccc
Q 026662           77 MSKLLRGPNDVEGASVTIKAGSNGICPEIWAEQLLNMYVRWADKEGYRGRVVDKCCCKNGGVKSATIEFEFEYAFGYLSG  156 (235)
Q Consensus        77 ~~~l~~~~~D~~~~~leI~aG~GG~Ea~~~a~~L~~my~~~a~~~g~~~~~~~~~~~~~~g~k~~~~~i~g~~a~~~l~~  156 (235)
                      ..+||+||+|.++|+||||||+||+||++||++||+||.+||+.+||++++++.++++.||||++++.|+|.+||+.|||
T Consensus       101 ~lLlPkDpnd~knvilEIRagtGGdEAalFagDLfrMY~rYAe~kgWk~ei~s~se~~~GG~kEii~~I~G~gvys~LKf  180 (363)
T COG0216         101 ILLLPKDPNDDKNIILEIRAGTGGDEAALFAGDLFRMYSRYAESKGWKVEILSASESELGGYKEIIASISGKGVYSRLKF  180 (363)
T ss_pred             HhcCCCCCCCCcCeEEEEecCCCchHHHHHHHHHHHHHHHHHHhCCCEEEEeecCcccCCCceEEEEEEeccchhhhhhh
Confidence            77899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccceeEE-cCCCCCCCCcccc-eeEEeeeCCCCCCCCCcCCCCCeEEec--CCCC-CCcccCCCCeeEEEeecCceEEE
Q 026662          157 ETGAHCLI-NFPNGSFPHEATL-ACVDVVPLFLETSPDLQISDEDLLFSS--PSLP-GERQSIAKPAACIQHIPTGIAVQ  231 (235)
Q Consensus       157 e~Gvhrv~-~~~~~~~~r~~ts-~~V~v~P~~~~~~~~~~i~~~dl~i~t--~sG~-GQhVNkteSAVRi~H~PTGi~V~  231 (235)
                      |+|||||| +|.|+++||+||| |+|+|||+++ +..+++|+|+||||||  |||+ |||||||+|||||||+||||+|+
T Consensus       181 EsGvHRVQRVP~TEsqGRIHTStaTVaVlPE~e-e~~ei~I~~~DlrIDt~RsSGaGGQhVNtTdSAVRiTHlPTGIvV~  259 (363)
T COG0216         181 ESGVHRVQRVPATESQGRIHTSAATVAVLPEVE-EVEEIEINPKDLRIDTFRSSGAGGQHVNTTDSAVRITHLPTGIVVE  259 (363)
T ss_pred             ccCccceeccccccCCCceeecceeEEeccCCC-cccccccChHHceeeeeecCCCCCCCcCccchhheeeecCCceEEE
Confidence            99999999 9999999999999 9999999983 3457999999999999  9999 99999999999999999999999


Q ss_pred             eec
Q 026662          232 SLG  234 (235)
Q Consensus       232 ~q~  234 (235)
                      ||+
T Consensus       260 cQd  262 (363)
T COG0216         260 CQD  262 (363)
T ss_pred             ecc
Confidence            996

>PRK05589 peptide chain release factor 2; Provisional Back     alignment and domain information
>PRK06746 peptide chain release factor 2; Provisional Back     alignment and domain information
>PRK07342 peptide chain release factor 2; Provisional Back     alignment and domain information
>TIGR00020 prfB peptide chain release factor 2 Back     alignment and domain information
>PRK00578 prfB peptide chain release factor 2; Validated Back     alignment and domain information
>TIGR00019 prfA peptide chain release factor 1 Back     alignment and domain information
>PRK00591 prfA peptide chain release factor 1; Validated Back     alignment and domain information
>PRK08787 peptide chain release factor 2; Provisional Back     alignment and domain information
>KOG2726 consensus Mitochondrial polypeptide chain release factor [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>COG1186 PrfB Protein chain release factor B [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK08179 prfH peptide chain release factor-like protein; Reviewed Back     alignment and domain information
>TIGR03072 release_prfH putative peptide chain release factor H Back     alignment and domain information
>PF03462 PCRF: PCRF domain; InterPro: IPR005139 This domain is found in peptide chain release factors Back     alignment and domain information
>PF00472 RF-1: RF-1 domain; InterPro: IPR000352 Peptide chain release factors (RFs) are required for the termination of protein biosynthesis [] Back     alignment and domain information
>PRK09256 hypothetical protein; Provisional Back     alignment and domain information
>KOG3429 consensus Predicted peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>COG0216 PrfA Protein chain release factor A [Translation, ribosomal structure and biogenesis] Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query235
1ml5_Z365 Structure Of The E. Coli Ribosomal Termination Comp 3e-22
1mi6_A365 Docking Of The Modified Rf2 X-Ray Structure Into Th 3e-22
1gqe_A365 Polypeptide Chain Release Factor 2 (Rf2) From Esche 1e-20
2wh1_Y351 Insights Into Translational Termination From The St 2e-13
2x9r_Y351 Structure Of The 70s Ribosome Bound To Release Fact 2e-13
2ihr_1365 Rf2 Of Thermus Thermophilus Length = 365 2e-13
2b9m_Y365 30s Ribosomal Subunit, Trnas, Mrna And Release Fact 2e-13
3f1e_X378 Crystal Structure Of A Translation Termination Comp 2e-13
1rq0_A 342 Crystal Structure Of Peptide Releasing Factor 1 Len 6e-12
2fvo_A333 Docking Of The Modified Rf1 X-ray Structure Into Th 6e-12
2b64_Y354 30s Ribosomal Subunit, Trnas, Mrna And Release Fact 6e-10
2b3t_B360 Molecular Basis For Bacterial Class 1 Release Facto 3e-09
1zbt_A371 Crystal Structure Of Peptide Chain Release Factor 1 1e-05
>pdb|1ML5|Z Chain Z, Structure Of The E. Coli Ribosomal Termination Complex With Release Factor 2 Length = 365 Back     alignment and structure 
Iteration: 1

 Score =  102 bits (253), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 72/234 (30%), Positives = 123/234 (52%), Gaps = 13/234 (5%)
Query: 6   NLWDDPTKSNEVLVKLADSLK-VVNALKDLRYKAEEAKLIAQLAEMEAIDYGLFKRAYRA 64
           ++W++P ++ + L K   SL+ VV+ L  ++   E+   + +LA +EA D   F  A  A
Sbjct: 45  DVWNEPERA-QALGKERSSLEAVVDTLDQMKQGLEDVSGLLELA-VEADDEETFNEAV-A 101
Query: 65  SLD-VSKLLDQYEMSKLLRGPNDVEGASVTIKAGSNGICPEIWAEQLLNMYVRWADKEGY 123
            LD + + L Q E  ++  G  D     + I+AGS G   + WA  L  MY+RWA+  G+
Sbjct: 102 ELDALEEKLAQLEFRRMFSGEYDSADCYLDIQAGSGGTEAQDWASMLERMYLRWAESRGF 161
Query: 124 RGRVVDKCCCKNGGVKSATIEFEFEYAFGYLSGETGAHCLIN---FPNGSFPHEATLACV 180
           +  ++++   +  G+KS TI+   +YA+G+L  ETG H L+    F +G   H  + +  
Sbjct: 162 KTEIIEESEGEVAGIKSVTIKISGDYAYGWLRTETGVHRLVRKSPFDSGGRRH-TSFSSA 220
Query: 181 DVVPLFLETSPDLQISDEDL---LFSSPSLPGERQSIAKPAACIQHIPTGIAVQ 231
            V P  ++   D++I+  DL   ++ +    G+  +  + A  I HIPTGI  Q
Sbjct: 221 FVYPE-VDDDIDIEINPADLRIDVYRTSGAGGQHVNRTESAVRITHIPTGIVTQ 273
>pdb|1MI6|A Chain A, Docking Of The Modified Rf2 X-Ray Structure Into The Low Resolution Cryo-Em Map Of Rf2 E.Coli 70s Ribosome Length = 365 Back     alignment and structure
>pdb|1GQE|A Chain A, Polypeptide Chain Release Factor 2 (Rf2) From Escherichia Coli Length = 365 Back     alignment and structure
>pdb|2WH1|Y Chain Y, Insights Into Translational Termination From The Structure Of Rf2 Bound To The Ribosome Length = 351 Back     alignment and structure
>pdb|2X9R|Y Chain Y, Structure Of The 70s Ribosome Bound To Release Factor 2 And A Substrate Analog Provides Insights Into Catalysis Of Peptide Release Length = 351 Back     alignment and structure
>pdb|2IHR|1 Chain 1, Rf2 Of Thermus Thermophilus Length = 365 Back     alignment and structure
>pdb|2B9M|Y Chain Y, 30s Ribosomal Subunit, Trnas, Mrna And Release Factor Rf2 From A Crystal Structure Of The Whole Ribosomal Complex. This File Contains The 30s Ribosomal Subunit, Trnas, Mrna And Release Factor Rf2 From A Crystal Structure Of The Whole Ribosomal Complex". The Entire Crystal Structure Contains One 70s Ribosome, Trnas, Mrna And Release Factor Rf2 And Is Described In Remark 400 Length = 365 Back     alignment and structure
>pdb|3F1E|X Chain X, Crystal Structure Of A Translation Termination Complex Formed With Release Factor Rf2. This File Contains The 30s Subunit, Rf2, Two Trna, And Mrna Molecules Of One 70s Ribosome. The Entire Crystal Structure Contains Two 70s Ribosomes As Described In Remark 400. Length = 378 Back     alignment and structure
>pdb|1RQ0|A Chain A, Crystal Structure Of Peptide Releasing Factor 1 Length = 342 Back     alignment and structure
>pdb|2FVO|A Chain A, Docking Of The Modified Rf1 X-ray Structure Into The Low Resolution Cryo-em Map Of E.coli 70s Ribosome Bound With Rf1 Length = 333 Back     alignment and structure
>pdb|2B64|Y Chain Y, 30s Ribosomal Subunit, Trnas, Mrna And Release Factor Rf1 From A Crystal Structure Of The Whole Ribosomal Complex. This File Contains The 30s Subunit, Trnas, Mrna And Release Factor Rf1 From A Crystal Structure Of The Whole Ribosomal Complex". The Entire Crystal Structure Contains One 70s Ribosome, Trnas, Mrna And Release Factor Rf1 And Is Described In Remark 400. Length = 354 Back     alignment and structure
>pdb|2B3T|B Chain B, Molecular Basis For Bacterial Class 1 Release Factor Methylation By Prmc Length = 360 Back     alignment and structure
>pdb|1ZBT|A Chain A, Crystal Structure Of Peptide Chain Release Factor 1 (rf-1) (smu.1085) From Streptococcus Mutans At 2.34 A Resolution Length = 371 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query235
2ihr_1365 Peptide chain release factor 2; mixed alpha-beta, 2e-39
1gqe_A365 Release factor 2, RF2; protein synthesis, ribosome 3e-39
1rq0_A 342 RF-1, peptide chain release factor 1; X-RAY, cryst 2e-10
3d5a_X354 RF1, peptide chain release factor 1; ribosome, rib 1e-09
1zbt_A371 RF-1, peptide chain release factor 1; peptide chai 2e-08
2b3t_B360 RF-1, peptide chain release factor 1; translation 4e-07
>2ihr_1 Peptide chain release factor 2; mixed alpha-beta, translation; 2.50A {Thermus thermophilus} PDB: 2b9m_Y* 3f1e_X 3f1g_X 2x9r_Y* 2x9t_Y* 2jl5_Y 2jl7_Y 2wh1_Y 2wh3_Y Length = 365 Back     alignment and structure
 Score =  138 bits (350), Expect = 2e-39
 Identities = 66/240 (27%), Positives = 108/240 (45%), Gaps = 27/240 (11%)

Query: 6   NLWDDPTKSNEVLVKLADSLKVVNALKDLRYKAEEAKLIAQLAEMEAIDYGLFKRAYRAS 65
           +LW+DP  + +V  + A   + V+  + L    +    + +    E     L        
Sbjct: 37  SLWNDPEAARKVSQEAARLRRTVDTFRSLESDLQGLLELMEELPAEE-REALKPEL---- 91

Query: 66  LDVSKLLDQYEMSKLLRGPNDVEGASVTIKAGSNGICPEIWAEQLLNMYVRWADKEGYRG 125
            + +K LD+     LL  P+  + A +TI+ G+ G     WAE LL MY R+A+++G++ 
Sbjct: 92  EEAAKKLDELYHQTLLNFPHAEKNAILTIQPGAGGTEACDWAEMLLRMYTRFAERQGFQV 151

Query: 126 RVVDKCCCKNGGVKSATIEFEFEYAFGYLSGETGAHCLIN---FPNG-----SFPHEATL 177
            VVD       G+  A I  + E A+G LS E G H L+    F        SF      
Sbjct: 152 EVVDLTPGPEAGIDYAQILVKGENAYGLLSPEAGVHRLVRPSPFDASGRRHTSF------ 205

Query: 178 ACVDVVPLFLETSPDLQISDEDL---LFSSPSLPGERQSIAK--PAACIQHIPTGIAVQS 232
           A V+V+P  ++   ++ +  E+L   +  + S PG  Q +     A  + H+PTGI V  
Sbjct: 206 AGVEVIPE-VDEEVEVVLKPEELRIDVMRA-SGPGG-QGVNTTDSAVRVVHLPTGITVTC 262
>1gqe_A Release factor 2, RF2; protein synthesis, ribosome, macromolecular mimicry, translation; 1.81A {Escherichia coli} SCOP: e.38.1.1 PDB: 1mi6_A 1ml5_Z* Length = 365 Back     alignment and structure
>1rq0_A RF-1, peptide chain release factor 1; X-RAY, crystal, peptide release factor 1, ribosome, structural genomics, BSGC structure funded by NIH; 2.65A {Thermotoga maritima} SCOP: e.38.1.1 PDB: 2fvo_A Length = 342 Back     alignment and structure
>3d5a_X RF1, peptide chain release factor 1; ribosome, ribonucleoprotein, ribosomal protein, RNA-binding, binding, metal-binding, zinc-finger; 3.21A {Thermus thermophilus} PDB: 2b64_Y 3d5c_X 3mr8_V 3ms0_V Length = 354 Back     alignment and structure
>1zbt_A RF-1, peptide chain release factor 1; peptide chain release factor 1 (RF-1), structural joint center for structural genomics, JCSG; 2.34A {Streptococcus mutans} Length = 371 Back     alignment and structure
>2b3t_B RF-1, peptide chain release factor 1; translation termination, methylation, conformational changes; HET: SAH; 3.10A {Escherichia coli} SCOP: e.38.1.1 Length = 360 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query235
1gqe_A365 Release factor 2, RF2; protein synthesis, ribosome 100.0
1zbt_A371 RF-1, peptide chain release factor 1; peptide chai 100.0
3d5a_X354 RF1, peptide chain release factor 1; ribosome, rib 100.0
2b3t_B360 RF-1, peptide chain release factor 1; translation 100.0
2ihr_1365 Peptide chain release factor 2; mixed alpha-beta, 100.0
1rq0_A 342 RF-1, peptide chain release factor 1; X-RAY, cryst 100.0
2rsm_A115 Probable peptide chain release factor C12ORF65 HO 99.94
1j26_A112 Immature colon carcinoma transcript 1; peptide cha 99.62
2jva_A108 Peptidyl-tRNA hydrolase domain protein; GFT hydrol 99.58
4dh9_Y140 YAEJ; ribosome, YAEJ, ribosome stalling, ribosome 99.47
2lw1_A89 ABC transporter ATP-binding protein UUP; ABC REG s 89.96
>1gqe_A Release factor 2, RF2; protein synthesis, ribosome, macromolecular mimicry, translation; 1.81A {Escherichia coli} SCOP: e.38.1.1 PDB: 1mi6_A 1ml5_Z* Back     alignment and structure
Probab=100.00  E-value=8.6e-80  Score=566.71  Aligned_cols=231  Identities=28%  Similarity=0.440  Sum_probs=224.6

Q ss_pred             CCCCcCCCCHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 026662            2 VRNYNLWDDPTKSNEVLVKLADSLKVVNALKDLRYKAEEAKLIAQLAEMEAIDYGLFKRAYRASLDVSKLLDQYEMSKLL   81 (235)
Q Consensus         2 msdP~~WdD~~ka~~~~~el~~l~~~~~~~~~~~~~~~e~~~l~el~~~~~~D~el~~~a~ee~~~l~~~l~~le~~~l~   81 (235)
                      |++|+||+||+++++++++++.|+.+++.|+++++.+++++++.+|++++ .|++|+++|.+++..+++.+++++..+||
T Consensus        41 ~~~p~~w~d~~~~~~~~ke~~~l~~~v~~~~~~~~~~~d~~~~~el~~~e-~D~e~~~~a~~e~~~l~~~l~~le~~~ll  119 (365)
T 1gqe_A           41 LEQPDVWNEPERAQALGKERSSLEAVVDTLDQMKQGLEDVSGLLELAVEA-DDEETFNEAVAELDALEEKLAQLEFRRMF  119 (365)
T ss_dssp             HHSGGGGGSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-TCHHHHHHHHHHHHHHHHHHHHHGGGGGC
T ss_pred             hcCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc-CCHHHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence            68999999999999999999999999999999999999999999999763 69999999999999999999999999999


Q ss_pred             CCCCCcCCceEEEecCCCchHHHHHHHHHHHHHHHHHHhcCCeEEEEecccCCCCceeEEEEEEeeccccccccccccce
Q 026662           82 RGPNDVEGASVTIKAGSNGICPEIWAEQLLNMYVRWADKEGYRGRVVDKCCCKNGGVKSATIEFEFEYAFGYLSGETGAH  161 (235)
Q Consensus        82 ~~~~D~~~~~leI~aG~GG~Ea~~~a~~L~~my~~~a~~~g~~~~~~~~~~~~~~g~k~~~~~i~g~~a~~~l~~e~Gvh  161 (235)
                      +||+|.++|+|||+||+||+||++||++||+||.+||+++||++++++..+++.+|||+|++.|+|++||++||+|+|||
T Consensus       120 ~~~~D~~naileI~aGaGG~Ea~~fa~~L~rMY~r~Ae~~g~k~evl~~~~~e~~G~Ks~~~~I~G~~ayg~Lk~EsGvH  199 (365)
T 1gqe_A          120 SGEYDSADCYLDIQAGSGGTEAQDWASMLERMYLRWAESRGFKTEIIEESEGEVAGIKSVTIKISGDYAYGWLRTETGVH  199 (365)
T ss_dssp             CSTTTTSCEEEEEEECSSHHHHHHHHHHHHHHHHHHHHHTTCEEEEEEEEECSSSSEEEEEEEEESTTHHHHHGGGCEEE
T ss_pred             CCcccccceEEEEEcCCCcHHHHHHHHHHHHHHHHHHHHCCCeEEEEecCCCCCCceeEEEEEEECcCHHHHhhhccceE
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eEE-cCCCCCCCCcccc-eeEEeeeCCCCCCCCCcCCCCCeEEec--CCCC-CCcccCCCCeeEEEeecCceEEEeec
Q 026662          162 CLI-NFPNGSFPHEATL-ACVDVVPLFLETSPDLQISDEDLLFSS--PSLP-GERQSIAKPAACIQHIPTGIAVQSLG  234 (235)
Q Consensus       162 rv~-~~~~~~~~r~~ts-~~V~v~P~~~~~~~~~~i~~~dl~i~t--~sG~-GQhVNkteSAVRi~H~PTGi~V~~q~  234 (235)
                      ||| +|||+++|||||| |+|+|+|+++ +++++.|+++||+|+|  |||| |||||||+|||||||+||||+|+||+
T Consensus       200 RvqRvs~~es~gRrhTS~asV~V~Pe~~-~~v~i~i~~~dl~~~~~RssG~GGQ~VNkt~saVrl~HiPtgivv~~q~  276 (365)
T 1gqe_A          200 RLVRKSPFDSGGRRHTSFSSAFVYPEVD-DDIDIEINPADLRIDVYRASGAGGQHVNRTESAVRITHIPTGIVTQCQN  276 (365)
T ss_dssp             EEEEECTTSSSCCEEEEEEEEEEEECCB-TTBCCCCCGGGEEEEEECCCCSSCCSTTSSCCEEEEEETTTCCEEEECS
T ss_pred             EEEEeCCCCCcCCCCcceeEEEEecCCC-cccccccCHHHceEeeecCCCCCCCcccCccceEEEEECCCeEEEEECC
Confidence            999 9999999999999 9999999984 4578999999999999  8999 99999999999999999999999996
>1zbt_A RF-1, peptide chain release factor 1; peptide chain release factor 1 (RF-1), structural joint center for structural genomics, JCSG; 2.34A {Streptococcus mutans} Back     alignment and structure
>3d5a_X RF1, peptide chain release factor 1; ribosome, ribonucleoprotein, ribosomal protein, RNA-binding, binding, metal-binding, zinc-finger; 3.21A {Thermus thermophilus} PDB: 2b64_Y 3d5c_X 3mr8_V 3ms0_V Back     alignment and structure
>2b3t_B RF-1, peptide chain release factor 1; translation termination, methylation, conformational changes; HET: SAH; 3.10A {Escherichia coli} SCOP: e.38.1.1 Back     alignment and structure
>2ihr_1 Peptide chain release factor 2; mixed alpha-beta, translation; 2.50A {Thermus thermophilus} PDB: 2b9m_Y* 3f1e_X 3f1g_X 2x9r_Y* 2x9t_Y* 2jl5_Y 2jl7_Y 2wh1_Y 2wh3_Y Back     alignment and structure
>1rq0_A RF-1, peptide chain release factor 1; X-RAY, crystal, peptide release factor 1, ribosome, structural genomics, BSGC structure funded by NIH; 2.65A {Thermotoga maritima} SCOP: e.38.1.1 PDB: 2fvo_A Back     alignment and structure
>2rsm_A Probable peptide chain release factor C12ORF65 HO mitochondrial; GGQ domain, translation; NMR {Mus musculus} Back     alignment and structure
>1j26_A Immature colon carcinoma transcript 1; peptide chain release factors, RF-1, the GGQ motif, immature carcinoma transcript 1; NMR {Mus musculus} SCOP: d.50.4.1 Back     alignment and structure
>2jva_A Peptidyl-tRNA hydrolase domain protein; GFT hydrolase, structural genomics, PSI-2, protein STRU initiative; NMR {Pseudomonas syringae PV} Back     alignment and structure
>4dh9_Y YAEJ; ribosome, YAEJ, ribosome stalling, ribosome rescue, rescue F alternative rescue factor, ARFB, release factor, rescue of ribosomes; 3.20A {Escherichia coli} PDB: 2jy9_A Back     alignment and structure
>2lw1_A ABC transporter ATP-binding protein UUP; ABC REG subfamily, DNA binding protein; NMR {Escherichia coli} Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 235
d1gqea_362 e.38.1.1 (A:) Polypeptide chain release factor 2 ( 1e-26
d2b3tb1344 e.38.1.1 (B:7-354) Peptide chain release factor 1, 2e-19
d1rq0a_333 e.38.1.1 (A:) Peptide chain release factor 1, RF1 1e-13
>d1gqea_ e.38.1.1 (A:) Polypeptide chain release factor 2 (RF2) {Escherichia coli [TaxId: 562]} Length = 362 Back     information, alignment and structure

class: Multi-domain proteins (alpha and beta)
fold: Release factor
superfamily: Release factor
family: Release factor
domain: Polypeptide chain release factor 2 (RF2)
species: Escherichia coli [TaxId: 562]

 Score =  103 bits (258), Expect = 1e-26
 Identities = 61/231 (26%), Positives = 110/231 (47%), Gaps = 5/231 (2%)

Query: 6   NLWDDPTKSNEVLVKLADSLKVVNALKDLRYKAEEAKLIAQLAEMEAIDYGLFKRAYRAS 65
           ++W++P ++  +  + +    VV+ L  ++   E+   + +LA     +   F  A    
Sbjct: 42  DVWNEPERAQALGKERSSLEAVVDTLDQMKQGLEDVSGLLELAVEADDEE-TFNEAVAEL 100

Query: 66  LDVSKLLDQYEMSKLLRGPNDVEGASVTIKAGSNGICPEIWAEQLLNMYVRWADKEGYRG 125
             + + L Q E  ++  G  D     + I+AGS G   + WA  L  MY+RWA+  G++ 
Sbjct: 101 DALEEKLAQLEFRRMFSGEYDSADCYLDIQAGSGGTEAQDWASMLERMYLRWAESRGFKT 160

Query: 126 RVVDKCCCKNGGVKSATIEFEFEYAFGYLSGETGAHCLIN-FPNGSFPHEATLACVDVVP 184
            ++++   +  G+KS TI+   +YA+G+L  ETG H L+   P  S     T      V 
Sbjct: 161 EIIEESEGEVAGIKSVTIKISGDYAYGWLRTETGVHRLVRKSPFDSGGRRHTSFSSAFVY 220

Query: 185 LFLETSPDLQISDEDL---LFSSPSLPGERQSIAKPAACIQHIPTGIAVQS 232
             ++   D++I+  DL   ++ +    G+  +  + A  I HIPTGI  Q 
Sbjct: 221 PEVDDDIDIEINPADLRIDVYRASGAGGQHVNRTESAVRITHIPTGIVTQC 271
>d2b3tb1 e.38.1.1 (B:7-354) Peptide chain release factor 1, RF1 {Escherichia coli [TaxId: 562]} Length = 344 Back     information, alignment and structure
>d1rq0a_ e.38.1.1 (A:) Peptide chain release factor 1, RF1 {Thermotoga maritima [TaxId: 2336]} Length = 333 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

Original result of HHsearch against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query235
d1gqea_362 Polypeptide chain release factor 2 (RF2) {Escheric 100.0
d2b3tb1344 Peptide chain release factor 1, RF1 {Escherichia c 100.0
d1rq0a_333 Peptide chain release factor 1, RF1 {Thermotoga ma 100.0
d1j26a_112 Ict1 protein {Mouse (Mus musculus) [TaxId: 10090]} 98.85
d1seta1110 Seryl-tRNA synthetase (SerRS) {Thermus thermophilu 82.13
>d1gqea_ e.38.1.1 (A:) Polypeptide chain release factor 2 (RF2) {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
class: Multi-domain proteins (alpha and beta)
fold: Release factor
superfamily: Release factor
family: Release factor
domain: Polypeptide chain release factor 2 (RF2)
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=4.9e-84  Score=595.58  Aligned_cols=231  Identities=28%  Similarity=0.440  Sum_probs=224.6

Q ss_pred             CCCCcCCCCHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 026662            2 VRNYNLWDDPTKSNEVLVKLADSLKVVNALKDLRYKAEEAKLIAQLAEMEAIDYGLFKRAYRASLDVSKLLDQYEMSKLL   81 (235)
Q Consensus         2 msdP~~WdD~~ka~~~~~el~~l~~~~~~~~~~~~~~~e~~~l~el~~~~~~D~el~~~a~ee~~~l~~~l~~le~~~l~   81 (235)
                      |+||+||+||++|++++++++.|+.+++.|+++++.++|++++++|+.++ +|++|.+++..++..+++.++++++.+||
T Consensus        38 lsdP~fW~D~~kAqkl~KE~s~L~~iVe~~~~l~~~leDl~eL~Ela~ee-~deel~~e~~~~l~~l~~~l~~le~~ll~  116 (362)
T d1gqea_          38 LEQPDVWNEPERAQALGKERSSLEAVVDTLDQMKQGLEDVSGLLELAVEA-DDEETFNEAVAELDALEEKLAQLEFRRMF  116 (362)
T ss_dssp             HHSGGGGGSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-TCHHHHHHHHHHHHHHHHHHHHHGGGGGC
T ss_pred             hcCChhhhCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh-hhHHHHHHHHHHHHHHhhhhhHHHHhhcc
Confidence            68999999999999999999999999999999999999999999998763 68999999999999999999999999999


Q ss_pred             CCCCCcCCceEEEecCCCchHHHHHHHHHHHHHHHHHHhcCCeEEEEecccCCCCceeEEEEEEeeccccccccccccce
Q 026662           82 RGPNDVEGASVTIKAGSNGICPEIWAEQLLNMYVRWADKEGYRGRVVDKCCCKNGGVKSATIEFEFEYAFGYLSGETGAH  161 (235)
Q Consensus        82 ~~~~D~~~~~leI~aG~GG~Ea~~~a~~L~~my~~~a~~~g~~~~~~~~~~~~~~g~k~~~~~i~g~~a~~~l~~e~Gvh  161 (235)
                      ++|+|.++|+|||+||+||+||++||+|||+||.|||+++||++++++.++++.+|||+|++.|+|++||++||+|+|||
T Consensus       117 ~~~~D~~nailEIrAGaGG~EA~dfA~~L~RMY~r~ae~~gwk~eiid~~~~e~gG~K~v~~~I~G~~ayg~Lk~EsGvH  196 (362)
T d1gqea_         117 SGEYDSADCYLDIQAGSGGTEAQDWASMLERMYLRWAESRGFKTEIIEESEGEVAGIKSVTIKISGDYAYGWLRTETGVH  196 (362)
T ss_dssp             CSTTTTSCEEEEEEECSSHHHHHHHHHHHHHHHHHHHHHTTCEEEEEEEEECSSSSEEEEEEEEESTTHHHHHGGGCEEE
T ss_pred             cCcccccceEEEEEecCchhhHHHHHHHHHHHHHHHHHHcCCeEEEeccccCCccceeEEEEEEECccHHHHHHHhcCce
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eEE-cCCCCCCCCcccc-eeEEeeeCCCCCCCCCcCCCCCeEEec--CCCC-CCcccCCCCeeEEEeecCceEEEeec
Q 026662          162 CLI-NFPNGSFPHEATL-ACVDVVPLFLETSPDLQISDEDLLFSS--PSLP-GERQSIAKPAACIQHIPTGIAVQSLG  234 (235)
Q Consensus       162 rv~-~~~~~~~~r~~ts-~~V~v~P~~~~~~~~~~i~~~dl~i~t--~sG~-GQhVNkteSAVRi~H~PTGi~V~~q~  234 (235)
                      ||| +|||+++|||||| |+|+|+|.++ ++++++|+|+||+|+|  |||| |||||||+|||||||+||||+|.||+
T Consensus       197 RvqRvp~~es~gr~hTS~a~V~v~P~~~-~~~~~~i~~~dl~i~~~rs~g~GGQ~vN~t~savri~H~ptgi~v~~q~  273 (362)
T d1gqea_         197 RLVRKSPFDSGGRRHTSFSSAFVYPEVD-DDIDIEINPADLRIDVYRASGAGGQHVNRTESAVRITHIPTGIVTQCQN  273 (362)
T ss_dssp             EEEEECTTSSSCCEEEEEEEEEEEECCB-TTBCCCCCGGGEEEEEECCCCSSCCSTTSSCCEEEEEETTTCCEEEECS
T ss_pred             eEEEecccCCCceEEEEEEEEEEeecCC-CccceecChHHeEEEEeecCCCCccchhhhhceeEEEecCchhHHHhhh
Confidence            999 9999999999999 9999999984 4578999999999999  9999 99999999999999999999999997
>d2b3tb1 e.38.1.1 (B:7-354) Peptide chain release factor 1, RF1 {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1rq0a_ e.38.1.1 (A:) Peptide chain release factor 1, RF1 {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d1j26a_ d.50.4.1 (A:) Ict1 protein {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1seta1 a.2.7.1 (A:1-110) Seryl-tRNA synthetase (SerRS) {Thermus thermophilus, strain hb27 [TaxId: 274]} Back     information, alignment and structure