Citrus Sinensis ID: 043121

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-------17
TNDNCSSSSSSKKKNYLELTDDELLRECEMDTYKLSGPGSQHRNKRESAVRLKHVPTGVIAHAAEDRSQHKNHASSVNLDAYSPPPQLLQILPPKSTITSSEVGPQIGPNNPKFSLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLILSDDSHQIAVNELRTSKVC
cccccccccccccccccccccHHHHcccccccEEcccccccccccccccEEEcccccccEEEccccHHHHHHHHHHHcccccccHHHHHccccccccccccccccccccccccccccHHHHHHHHHHHcccHHHHHHHccccccHHHHHHHccHHHHHHHHHHHHcccc
ccccccccEEcccccHccccHHHccHHccEEEEEccccccccccccccEEEEEcccccEEEEEcccHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccHHHHHHHHHHHHccHHHHHHHHcccHHHHHHHHHccHHHHHHHHHHHHHccc
tndncsssssskkknylelTDDELLRECemdtyklsgpgsqhrnkresavrlkhvptgviahaaedrsqhknhassvnldayspppqllqilppkstitssevgpqigpnnpkfsLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLILSDDSHQIAVNELRTSKVC
tndncsssssskkknylelTDDELLRECEMDTyklsgpgsqhrnkresavrlkHVPTGVIAHAAEDRSQHKNHASSVNLDAYSPPPQLLQILPPKSTITSSEVGPQIGPNNPKFSLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLilsddshqiavnelrtskvc
TNDNCsssssskkkNYLELTDDELLRECEMDTYKLSGPGSQHRNKRESAVRLKHVPTGVIAHAAEDRSQHKNHASSVNLDAYSpppqllqilppKSTITSSEVGPQIGPNNPKFSLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLILSDDSHQIAVNELRTSKVC
*****************************************************************************************************************FSLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLILSDD***************
****CSS*SSSKKKNYLELTDDELLRECEMDTYKLSGPGSQHRNKRESAVRLKHVPTGVIAHAAED****KNHASSVNLDA****************************NNPKFSLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLILSDDSHQ*****L******
*************KNYLELTDDELLRECEMDTYKL**************VRLKHVPTGVIAHAAE**********SVNLDAYSPPPQLLQILPPKSTITSSEVGPQIGPNNPKFSLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLILSDDSHQIAVNELRTSKVC
****CSSSSSSKKKNYLELTDDELLRECEMDTYKLSG****HRNKRESAVRLKHVPTGVIAHAAEDRSQHKNHASSVNLDAYSPPPQLLQILPPKSTIT**EVGPQIGPNNPKFSLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLILSDDSHQIAVNELRTSK*C
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiii
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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TNDNCSSSSSSKKKNYLELTDDELLRECEMDTYKLSGPGSQHRNKRESAVRLKHVPTGVIAHAAEDRSQHKNHASSVNLDAYSPPPQLLQILPPKSTITSSEVGPQIGPNNPKFSLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLILSDDSHQIAVNELRTSKVC
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 ?
Query169 2.2.26 [Sep-21-2011]
A7ZE19366 Peptide chain release fac yes no 0.467 0.215 0.387 5e-12
A0RQM7369 Peptide chain release fac yes no 0.502 0.230 0.395 7e-12
Q7MAP4368 Peptide chain release fac yes no 0.319 0.146 0.481 3e-11
A6SUF6360 Peptide chain release fac yes no 0.313 0.147 0.509 4e-11
Q30TP0365 Peptide chain release fac yes no 0.319 0.147 0.5 5e-11
A8EWG5365 Peptide chain release fac yes no 0.319 0.147 0.481 5e-11
Q7VIE6366 Peptide chain release fac yes no 0.319 0.147 0.481 6e-11
A6Q582368 Peptide chain release fac yes no 0.319 0.146 0.462 6e-11
Q12F86373 Peptide chain release fac yes no 0.313 0.142 0.490 7e-11
A6W1C2362 Peptide chain release fac yes no 0.295 0.138 0.54 7e-11
>sp|A7ZE19|RF2_CAMC1 Peptide chain release factor 2 OS=Campylobacter concisus (strain 13826) GN=prfB PE=3 SV=1 Back     alignment and function desciption
 Score = 70.5 bits (171), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 31/80 (38%), Positives = 52/80 (65%), Gaps = 1/80 (1%)

Query: 26  RECEMDTYKLSGPGSQHRNKRESAVRLKHVPTGVIAHAAEDRSQHKNHASSVN-LDAYSP 84
           ++ ++DTY+ SG G QH NK ESA+R+ H+PTG++     DRSQHKN A+++  L +   
Sbjct: 236 KDLKIDTYRASGAGGQHVNKTESAIRITHIPTGIVVQCQNDRSQHKNRATAMKMLKSRLY 295

Query: 85  PPQLLQILPPKSTITSSEVG 104
             +L++     +++  SE+G
Sbjct: 296 ELELMKQQEASNSVEKSEIG 315
Peptide chain release factor 2 directs the termination of translation in response to the peptide chain termination codons UGA and UAA.
Campylobacter concisus (strain 13826) (taxid: 360104)
>sp|A0RQM7|RF2_CAMFF Peptide chain release factor 2 OS=Campylobacter fetus subsp. fetus (strain 82-40) GN=prfB PE=3 SV=1 Back     alignment and function description
>sp|Q7MAP4|RF2_WOLSU Peptide chain release factor 2 OS=Wolinella succinogenes (strain ATCC 29543 / DSM 1740 / LMG 7466 / NCTC 11488 / FDC 602W) GN=prfB PE=3 SV=1 Back     alignment and function description
>sp|A6SUF6|RF1_JANMA Peptide chain release factor 1 OS=Janthinobacterium sp. (strain Marseille) GN=prfA PE=3 SV=1 Back     alignment and function description
>sp|Q30TP0|RF2_SULDN Peptide chain release factor 2 OS=Sulfurimonas denitrificans (strain ATCC 33889 / DSM 1251) GN=prfB PE=3 SV=1 Back     alignment and function description
>sp|A8EWG5|RF2_ARCB4 Peptide chain release factor 2 OS=Arcobacter butzleri (strain RM4018) GN=prfB PE=3 SV=1 Back     alignment and function description
>sp|Q7VIE6|RF2_HELHP Peptide chain release factor 2 OS=Helicobacter hepaticus (strain ATCC 51449 / 3B1) GN=prfB PE=3 SV=1 Back     alignment and function description
>sp|A6Q582|RF2_NITSB Peptide chain release factor 2 OS=Nitratiruptor sp. (strain SB155-2) GN=prfB PE=3 SV=1 Back     alignment and function description
>sp|Q12F86|RF1_POLSJ Peptide chain release factor 1 OS=Polaromonas sp. (strain JS666 / ATCC BAA-500) GN=prfA PE=3 SV=1 Back     alignment and function description
>sp|A6W1C2|RF1_MARMS Peptide chain release factor 1 OS=Marinomonas sp. (strain MWYL1) GN=prfA 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 ?
Query169
224127830257 predicted protein [Populus trichocarpa] 0.964 0.634 0.679 5e-62
255556733185 peptide chain release factor, putative [ 0.846 0.772 0.746 2e-61
356559945250 PREDICTED: uncharacterized protein LOC10 0.917 0.62 0.694 5e-60
359493583224 PREDICTED: peptide chain release factor 0.893 0.674 0.692 6e-60
242059479259 hypothetical protein SORBIDRAFT_03g04217 0.905 0.590 0.660 3e-57
414879327253 TPA: hypothetical protein ZEAMMB73_57118 0.946 0.632 0.634 8e-57
326517198170 predicted protein [Hordeum vulgare subsp 0.881 0.876 0.682 2e-56
357126252239 PREDICTED: uncharacterized protein LOC10 0.905 0.640 0.660 3e-56
449447515240 PREDICTED: peptide chain release factor 0.970 0.683 0.620 8e-55
125528646246 hypothetical protein OsI_04716 [Oryza sa 0.881 0.605 0.658 8e-55
>gi|224127830|ref|XP_002329188.1| predicted protein [Populus trichocarpa] gi|222870969|gb|EEF08100.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
 Score =  242 bits (617), Expect = 5e-62,   Method: Compositional matrix adjust.
 Identities = 121/178 (67%), Positives = 140/178 (78%), Gaps = 15/178 (8%)

Query: 6   SSSSSSKKKNYLELTDDELLRECEMDTYKLSGPGSQHRNKRESAVRLKHVPTGVIAHAAE 65
           +S+S     NYLELTDDEL+R+CEMDT+K SGPG QHRNKRESAVRLKH+PTG+IA A E
Sbjct: 80  TSASHGNGTNYLELTDDELMRQCEMDTFKASGPGGQHRNKRESAVRLKHLPTGIIAQAVE 139

Query: 66  DRSQHKNHAS---------------SVNLDAYSPPPQLLQILPPKSTITSSEVGPQIGPN 110
           DRSQH N AS               S+++D+Y+P  +LLQILP KSTI  S+ GPQIGP 
Sbjct: 140 DRSQHMNRASALKRLRALLAIRVRNSLDIDSYTPRLELLQILPLKSTIRGSDCGPQIGPK 199

Query: 111 NPKFSLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLILSDDSHQIAVNELRTSKV 168
           NPKF LGMQALLDLIFAV+GS+SEA KLL LSTGALSRLILSDDS ++AVN+LR SKV
Sbjct: 200 NPKFILGMQALLDLIFAVDGSISEAGKLLGLSTGALSRLILSDDSLRMAVNDLRNSKV 257

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|255556733|ref|XP_002519400.1| peptide chain release factor, putative [Ricinus communis] gi|223541467|gb|EEF43017.1| peptide chain release factor, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|356559945|ref|XP_003548256.1| PREDICTED: uncharacterized protein LOC100793467 [Glycine max] Back     alignment and taxonomy information
>gi|359493583|ref|XP_002263666.2| PREDICTED: peptide chain release factor 1-like [Vitis vinifera] gi|297734721|emb|CBI16955.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|242059479|ref|XP_002458885.1| hypothetical protein SORBIDRAFT_03g042170 [Sorghum bicolor] gi|241930860|gb|EES04005.1| hypothetical protein SORBIDRAFT_03g042170 [Sorghum bicolor] Back     alignment and taxonomy information
>gi|414879327|tpg|DAA56458.1| TPA: hypothetical protein ZEAMMB73_571187 [Zea mays] Back     alignment and taxonomy information
>gi|326517198|dbj|BAJ99965.1| predicted protein [Hordeum vulgare subsp. vulgare] Back     alignment and taxonomy information
>gi|357126252|ref|XP_003564802.1| PREDICTED: uncharacterized protein LOC100830192 [Brachypodium distachyon] Back     alignment and taxonomy information
>gi|449447515|ref|XP_004141513.1| PREDICTED: peptide chain release factor 1-like [Cucumis sativus] gi|449526225|ref|XP_004170114.1| PREDICTED: peptide chain release factor 1-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|125528646|gb|EAY76760.1| hypothetical protein OsI_04716 [Oryza sativa Indica Group] 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 ?
Query169
TAIR|locus:2006897257 AT1G33330 [Arabidopsis thalian 0.976 0.642 0.513 1.4e-41
TIGR_CMR|ECH_0705366 ECH_0705 "peptide chain releas 0.366 0.169 0.476 1e-10
TIGR_CMR|CPS_3552362 CPS_3552 "peptide chain releas 0.313 0.146 0.471 2.1e-10
TIGR_CMR|CJE_1628365 CJE_1628 "peptide chain releas 0.366 0.169 0.469 3.5e-10
TIGR_CMR|CBU_1965361 CBU_1965 "peptide chain releas 0.313 0.146 0.471 4.4e-10
UNIPROTKB|Q74EJ1107 GSU0971 "Hydrolase, putative" 0.301 0.476 0.450 6.6e-10
TIGR_CMR|GSU_0971107 GSU_0971 "peptidyl-tRNA hydrol 0.301 0.476 0.450 6.6e-10
TIGR_CMR|SO_3833363 SO_3833 "peptide chain release 0.313 0.146 0.433 7.4e-10
TIGR_CMR|APH_0479376 APH_0479 "peptide chain releas 0.331 0.148 0.464 1e-09
UNIPROTKB|P07012365 prfB [Escherichia coli K-12 (t 0.337 0.156 0.475 1.2e-09
TAIR|locus:2006897 AT1G33330 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 441 (160.3 bits), Expect = 1.4e-41, P = 1.4e-41
 Identities = 93/181 (51%), Positives = 124/181 (68%)

Query:     2 NDNCXXXXXXXXXNYLELTDDELLRECEMDTYKLSGPGSQHRNKRESAVRLKHVPTGVIA 61
             ND+          NYL+ TD+EL+++C ++T+++SGPG QHRNKR+SAVRLKH+PTG++A
Sbjct:    72 NDSVSVVSDVQSPNYLKFTDEELMKQCRLETFRVSGPGGQHRNKRDSAVRLKHLPTGIVA 131

Query:    62 HAAEDRSQHKNHASSVN---------------LDAYSXXXXXXXXXXXKSTITSSEVGPQ 106
              A EDRSQHKN AS++N               ++AY+           KSTI +S  G Q
Sbjct:   132 QAVEDRSQHKNRASALNRLRTLLAIKVRNKVDIEAYAPPPELLQILPPKSTIRTSS-GSQ 190

Query:   107 IGPNNPKFSLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLILSDDSHQIAVNELRTS 166
             IGPNNPKF  GMQALLD+I A +GS++++AKLL LSTG LSRLILS D  ++AVN +R +
Sbjct:   191 IGPNNPKFVPGMQALLDVISASDGSIADSAKLLGLSTGGLSRLILSHDGLRMAVNSMRAA 250

Query:   167 K 167
             K
Sbjct:   251 K 251
GO:0003747 "translation release factor activity" evidence=IEA;ISS
GO:0006415 "translational termination" evidence=IEA;ISS
GO:0009507 "chloroplast" evidence=IDA
GO:0006783 "heme biosynthetic process" evidence=RCA
TIGR_CMR|ECH_0705 ECH_0705 "peptide chain release factor 2, programmed frameshift" [Ehrlichia chaffeensis str. Arkansas (taxid:205920)] Back     alignment and assigned GO terms
TIGR_CMR|CPS_3552 CPS_3552 "peptide chain release factor 1" [Colwellia psychrerythraea 34H (taxid:167879)] Back     alignment and assigned GO terms
TIGR_CMR|CJE_1628 CJE_1628 "peptide chain release factor 2" [Campylobacter jejuni RM1221 (taxid:195099)] Back     alignment and assigned GO terms
TIGR_CMR|CBU_1965 CBU_1965 "peptide chain release factor 1" [Coxiella burnetii RSA 493 (taxid:227377)] Back     alignment and assigned GO terms
UNIPROTKB|Q74EJ1 GSU0971 "Hydrolase, putative" [Geobacter sulfurreducens PCA (taxid:243231)] Back     alignment and assigned GO terms
TIGR_CMR|GSU_0971 GSU_0971 "peptidyl-tRNA hydrolase domain protein" [Geobacter sulfurreducens PCA (taxid:243231)] Back     alignment and assigned GO terms
TIGR_CMR|SO_3833 SO_3833 "peptide chain release factor 1" [Shewanella oneidensis MR-1 (taxid:211586)] Back     alignment and assigned GO terms
TIGR_CMR|APH_0479 APH_0479 "peptide chain release factor 2, programmed frameshift" [Anaplasma phagocytophilum HZ (taxid:212042)] Back     alignment and assigned GO terms
UNIPROTKB|P07012 prfB [Escherichia coli K-12 (taxid:83333)] 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 ?
Query169
pfam00472114 pfam00472, RF-1, RF-1 domain 7e-17
PRK00578367 PRK00578, prfB, peptide chain release factor 2; Va 2e-15
PRK00591359 PRK00591, prfA, peptide chain release factor 1; Va 3e-14
TIGR00020364 TIGR00020, prfB, peptide chain release factor 2 3e-14
COG0216363 COG0216, PrfA, Protein chain release factor A [Tra 8e-14
PRK05589325 PRK05589, PRK05589, peptide chain release factor 2 3e-13
COG1186239 COG1186, PrfB, Protein chain release factor B [Tra 6e-13
PRK07342339 PRK07342, PRK07342, peptide chain release factor 2 6e-13
TIGR00019360 TIGR00019, prfA, peptide chain release factor 1 8e-13
TIGR03072200 TIGR03072, release_prfH, putative peptide chain re 4e-12
PRK08179200 PRK08179, prfH, peptide chain release factor-like 5e-11
PRK08787313 PRK08787, PRK08787, peptide chain release factor 2 6e-10
PRK06746326 PRK06746, PRK06746, peptide chain release factor 2 2e-07
>gnl|CDD|201249 pfam00472, RF-1, RF-1 domain Back     alignment and domain information 
 Score = 71.8 bits (177), Expect = 7e-17
 Identities = 26/46 (56%), Positives = 35/46 (76%)

Query: 27 ECEMDTYKLSGPGSQHRNKRESAVRLKHVPTGVIAHAAEDRSQHKN 72
          +  +DT++ SGPG Q+ NK ESAVRL H+PTG++    E+RSQHKN
Sbjct: 14 DLRIDTFRSSGPGGQNVNKTESAVRLTHLPTGIVVKCQEERSQHKN 59

This domain is found in peptide chain release factors such as RF-1 and RF-2, and a number of smaller proteins of unknown function. This domain contains the peptidyl-tRNA hydrolase activity. The domain contains a highly conserved motif GGQ, where the glutamine is thought to coordinate the water that mediates the hydrolysis. Length = 114
>gnl|CDD|234799 PRK00578, prfB, peptide chain release factor 2; Validated Back     alignment and domain information
>gnl|CDD|234801 PRK00591, prfA, peptide chain release factor 1; Validated Back     alignment and domain information
>gnl|CDD|232785 TIGR00020, prfB, peptide chain release factor 2 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|235520 PRK05589, PRK05589, 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|235997 PRK07342, PRK07342, peptide chain release factor 2; Provisional Back     alignment and domain information
>gnl|CDD|129130 TIGR00019, prfA, peptide chain release factor 1 Back     alignment and domain information
>gnl|CDD|213768 TIGR03072, release_prfH, putative peptide chain release factor H Back     alignment and domain information
>gnl|CDD|181271 PRK08179, prfH, peptide chain release factor-like protein; Reviewed Back     alignment and domain information
>gnl|CDD|136970 PRK08787, PRK08787, peptide chain release factor 2; Provisional Back     alignment and domain information
>gnl|CDD|75726 PRK06746, PRK06746, peptide chain release factor 2; Provisional Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 169
COG0216363 PrfA Protein chain release factor A [Translation, 100.0
KOG2726386 consensus Mitochondrial polypeptide chain release 99.97
PF00472113 RF-1: RF-1 domain; InterPro: IPR000352 Peptide cha 99.97
PRK08787313 peptide chain release factor 2; Provisional 99.97
TIGR03072200 release_prfH putative peptide chain release factor 99.97
PRK05589325 peptide chain release factor 2; Provisional 99.97
PRK06746326 peptide chain release factor 2; Provisional 99.96
PRK08179200 prfH peptide chain release factor-like protein; Re 99.96
TIGR00019360 prfA peptide chain release factor 1. This model de 99.96
PRK07342339 peptide chain release factor 2; Provisional 99.96
PRK00591359 prfA peptide chain release factor 1; Validated 99.96
TIGR00020364 prfB peptide chain release factor 2. In many but n 99.96
PRK00578367 prfB peptide chain release factor 2; Validated 99.96
COG1186239 PrfB Protein chain release factor B [Translation, 99.94
PRK09256138 hypothetical protein; Provisional 99.86
KOG3429172 consensus Predicted peptidyl-tRNA hydrolase [Trans 99.6
PF0295442 HTH_8: Bacterial regulatory protein, Fis family; I 95.49
PRK0190577 DNA-binding protein Fis; Provisional 88.39
smart0034284 HTH_ARAC helix_turn_helix, arabinose operon contro 87.83
PRK0043095 fis global DNA-binding transcriptional dual regula 86.4
PF1374480 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_ 86.01
PF1272851 HTH_17: Helix-turn-helix domain 81.99
PF0279645 HTH_7: Helix-turn-helix domain of resolvase; Inter 81.68
PF1354252 HTH_Tnp_ISL3: Helix-turn-helix domain of transposa 80.97
PF1338450 HTH_23: Homeodomain-like domain; PDB: 2X48_C. 80.25
PF0016542 HTH_AraC: Bacterial regulatory helix-turn-helix pr 80.13
>COG0216 PrfA Protein chain release factor A [Translation, ribosomal structure and biogenesis] Back     alignment and domain information 
Probab=100.00  E-value=3.1e-36  Score=265.42  Aligned_cols=97  Identities=32%  Similarity=0.473  Sum_probs=88.5

Q ss_pred             CcccChhhhhcceeEEEEeecCCCCCcCCccCceEEEEeeCCceEEEEcccCCHHHHHHHHHHHH-hCCChhhhhh----
Q 043121           16 YLELTDDELLRECEMDTYKLSGPGSQHRNKRESAVRLKHVPTGVIAHAAEDRSQHKNHASSVNLD-AYSPPPQLLQ----   90 (169)
Q Consensus        16 ~~~i~~~~l~~dl~i~~~RssGpGGQ~vNk~~saVrl~H~ptGi~v~~~~~RSq~~Nr~~Al~~L-~~L~~~el~~----   90 (169)
                      -+.|+++||    +|++|||||+||||||+|+|||||||+||||+|.||++|||++||++||+.| ++|++.+.++    
T Consensus       217 ei~I~~~Dl----rIDt~RsSGaGGQhVNtTdSAVRiTHlPTGIvV~cQderSQ~kNk~kAmkvL~ARl~~~~~~~~~~~  292 (363)
T COG0216         217 EIEINPKDL----RIDTFRSSGAGGQHVNTTDSAVRITHLPTGIVVECQDERSQHKNKAKAMKVLRARLYDAERQKAQAE  292 (363)
T ss_pred             ccccChHHc----eeeeeecCCCCCCCcCccchhheeeecCCceEEEecchhhhhhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            477887755    9999999999999999999999999999999999999999999999999999 7999877654    


Q ss_pred             -cCCCCCcccCCCCCCCCCCCCCCchh
Q 043121           91 -ILPPKSTITSSEVGPQIGPNNPKFSL  116 (169)
Q Consensus        91 -~~~~ksqir~~~rg~qIRtYn~~f~~  116 (169)
                       ...+++|+++||||++||||||.-+.
T Consensus       293 ~~~~RksqVGSGDRSErIRTYNfPQnR  319 (363)
T COG0216         293 EASERKSQVGSGDRSERIRTYNFPQNR  319 (363)
T ss_pred             HHHHHHHhcCCCchhhhhhccCCCCCc
Confidence             37899999999999999999996654

>KOG2726 consensus Mitochondrial polypeptide chain release factor [Translation, ribosomal structure and biogenesis] 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
>PRK08787 peptide chain release factor 2; Provisional Back     alignment and domain information
>TIGR03072 release_prfH putative peptide chain release factor H Back     alignment and domain information
>PRK05589 peptide chain release factor 2; Provisional Back     alignment and domain information
>PRK06746 peptide chain release factor 2; Provisional Back     alignment and domain information
>PRK08179 prfH peptide chain release factor-like protein; Reviewed Back     alignment and domain information
>TIGR00019 prfA peptide chain release factor 1 Back     alignment and domain information
>PRK07342 peptide chain release factor 2; Provisional Back     alignment and domain information
>PRK00591 prfA peptide chain release factor 1; Validated 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
>COG1186 PrfB Protein chain release factor B [Translation, ribosomal structure and biogenesis] 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
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,] Back     alignment and domain information
>PRK01905 DNA-binding protein Fis; Provisional Back     alignment and domain information
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein Back     alignment and domain information
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional Back     alignment and domain information
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A Back     alignment and domain information
>PF12728 HTH_17: Helix-turn-helix domain Back     alignment and domain information
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms Back     alignment and domain information
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3 Back     alignment and domain information
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C Back     alignment and domain information
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A 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 ?
Query169
1ml5_Z365 Structure Of The E. Coli Ribosomal Termination Comp 3e-10
1mi6_A365 Docking Of The Modified Rf2 X-Ray Structure Into Th 3e-10
1gqe_A365 Polypeptide Chain Release Factor 2 (Rf2) From Esche 3e-10
2b3t_B360 Molecular Basis For Bacterial Class 1 Release Facto 6e-09
1rq0_A342 Crystal Structure Of Peptide Releasing Factor 1 Len 1e-07
2fvo_A333 Docking Of The Modified Rf1 X-ray Structure Into Th 1e-07
2b64_Y354 30s Ribosomal Subunit, Trnas, Mrna And Release Fact 7e-06
3f1e_X378 Crystal Structure Of A Translation Termination Comp 4e-05
2ihr_1365 Rf2 Of Thermus Thermophilus Length = 365 4e-05
2x9r_Y351 Structure Of The 70s Ribosome Bound To Release Fact 4e-05
2wh1_Y351 Insights Into Translational Termination From The St 4e-05
2b9m_Y365 30s Ribosomal Subunit, Trnas, Mrna And Release Fact 4e-05
1zbt_A371 Crystal Structure Of Peptide Chain Release Factor 1 4e-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 = 61.2 bits (147), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 24/43 (55%), Positives = 31/43 (72%)
Query: 30  MDTYKLSGPGSQHRNKRESAVRLKHVPTGVIAHAAEDRSQHKN 72
           +D Y+ SG G QH N+ ESAVR+ H+PTG++     DRSQHKN
Sbjct: 241 IDVYRTSGAGGQHVNRTESAVRITHIPTGIVTQCQNDRSQHKN 283
>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|2B3T|B Chain B, Molecular Basis For Bacterial Class 1 Release Factor Methylation By Prmc Length = 360 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|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|2IHR|1 Chain 1, Rf2 Of Thermus Thermophilus Length = 365 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|2WH1|Y Chain Y, Insights Into Translational Termination From The Structure Of Rf2 Bound To The Ribosome Length = 351 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|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 ?
Query169
2rsm_A115 Probable peptide chain release factor C12ORF65 HO 2e-17
2ihr_1365 Peptide chain release factor 2; mixed alpha-beta, 8e-16
1gqe_A365 Release factor 2, RF2; protein synthesis, ribosome 1e-15
1zbt_A371 RF-1, peptide chain release factor 1; peptide chai 2e-15
2b3t_B360 RF-1, peptide chain release factor 1; translation 3e-15
3d5a_X354 RF1, peptide chain release factor 1; ribosome, rib 3e-15
1rq0_A342 RF-1, peptide chain release factor 1; X-RAY, cryst 5e-15
4dh9_Y140 YAEJ; ribosome, YAEJ, ribosome stalling, ribosome 2e-06
2jva_A108 Peptidyl-tRNA hydrolase domain protein; GFT hydrol 2e-06
1j26_A112 Immature colon carcinoma transcript 1; peptide cha 2e-04
>2rsm_A Probable peptide chain release factor C12ORF65 HO mitochondrial; GGQ domain, translation; NMR {Mus musculus} Length = 115 Back     alignment and structure
 Score = 72.4 bits (178), Expect = 2e-17
 Identities = 22/58 (37%), Positives = 29/58 (50%), Gaps = 4/58 (6%)

Query: 17 LELTDDELLRECEMDTYKLSGPGSQHRNKRESAVRLKHVPTGVIAHAAEDRSQHKNHA 74
          L L + EL    E    K  GPG Q  NK  + V LKHVP+G++    + RS  +N  
Sbjct: 41 LPLNESEL----EEQFVKGHGPGGQATNKTSNCVVLKHVPSGIVVKCHQTRSVDQNRK 94
>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
>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
>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
>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
>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
>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 Length = 140 Back     alignment and structure
>2jva_A Peptidyl-tRNA hydrolase domain protein; GFT hydrolase, structural genomics, PSI-2, protein STRU initiative; NMR {Pseudomonas syringae PV} Length = 108 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 Length = 112 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query169
1zbt_A371 RF-1, peptide chain release factor 1; peptide chai 99.97
1rq0_A342 RF-1, peptide chain release factor 1; X-RAY, cryst 99.96
2b3t_B360 RF-1, peptide chain release factor 1; translation 99.96
3d5a_X354 RF1, peptide chain release factor 1; ribosome, rib 99.96
1gqe_A365 Release factor 2, RF2; protein synthesis, ribosome 99.96
2ihr_1365 Peptide chain release factor 2; mixed alpha-beta, 99.96
2rsm_A115 Probable peptide chain release factor C12ORF65 HO 99.95
1j26_A112 Immature colon carcinoma transcript 1; peptide cha 99.92
2jva_A108 Peptidyl-tRNA hydrolase domain protein; GFT hydrol 99.92
4dh9_Y140 YAEJ; ribosome, YAEJ, ribosome stalling, ribosome 99.89
3e7l_A63 Transcriptional regulator (NTRC family); sigma43 a 93.5
1umq_A81 Photosynthetic apparatus regulatory protein; DNA-b 92.3
1g2h_A61 Transcriptional regulatory protein TYRR homolog; p 91.35
1ntc_A91 Protein (nitrogen regulation protein (NTRC)); heli 90.69
3oou_A108 LIN2118 protein; protein structure initiative, PSI 90.34
1eto_A98 FIS, factor for inversion stimulation; transcripti 90.16
3mn2_A108 Probable ARAC family transcriptional regulator; st 88.37
3oio_A113 Transcriptional regulator (ARAC-type DNA-binding c 87.87
2k9s_A107 Arabinose operon regulatory protein; activator, ar 87.15
3lsg_A103 Two-component response regulator YESN; structural 85.54
1bl0_A129 Protein (multiple antibiotic resistance protein), 84.59
2pij_A67 Prophage PFL 6 CRO; transcription factor, helix-tu 82.02
3mkl_A120 HTH-type transcriptional regulator GADX; PSI2, MCS 81.59
>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
Probab=99.97  E-value=1.7e-31  Score=236.80  Aligned_cols=94  Identities=28%  Similarity=0.350  Sum_probs=71.0

Q ss_pred             cccChhhhhcceeEEEEeecCCCCCcCCccCceEEEEeeCCceEEEEcccCCHHHHHHHHHHHH-hCCChhhhhh-----
Q 043121           17 LELTDDELLRECEMDTYKLSGPGSQHRNKRESAVRLKHVPTGVIAHAAEDRSQHKNHASSVNLD-AYSPPPQLLQ-----   90 (169)
Q Consensus        17 ~~i~~~~l~~dl~i~~~RssGpGGQ~vNk~~saVrl~H~ptGi~v~~~~~RSq~~Nr~~Al~~L-~~L~~~el~~-----   90 (169)
                      +.|+++    ||+|+|+|||||||||||||+|+|||+|+||||+|+|+++|||++||+.||++| ++|++.+.++     
T Consensus       228 i~I~~~----dl~i~~~RssGpGGQ~VNkt~SaVrlthlPtGivV~~q~eRSQ~~Nr~~A~~~L~~~L~~~~~~~~~~~~  303 (371)
T 1zbt_A          228 YEIDPK----DLRVDIYHASGAGGQNVNKVATAVRIIHLPTNIKVEMQEERTQQKNRDKAMKIIRARVADHFAQIAQDEQ  303 (371)
T ss_dssp             SCCCGG----GEEEEEECC---------CCCCEEEEEETTTTEEEEECSSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             cccCcC----cEEEEEecCCCCCCCcccccceeEEEEECCCeEEEEECCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            455555    669999999999999999999999999999999999999999999999999999 6787776544     


Q ss_pred             cCCCCCcccCCCCCCCCCCCCCCc
Q 043121           91 ILPPKSTITSSEVGPQIGPNNPKF  114 (169)
Q Consensus        91 ~~~~ksqir~~~rg~qIRtYn~~f  114 (169)
                      ...++++++.++||++||||||.-
T Consensus       304 ~~~r~~~ig~g~Rse~IRtYnf~q  327 (371)
T 1zbt_A          304 DAERKSTVGTGDRSERIRTYNFPQ  327 (371)
T ss_dssp             CC----CCSCSCTTSEEEEEETTT
T ss_pred             HHHHHhhccccccCCCeeeEECCC
Confidence            356688899999999999999844
>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
>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
>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
>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
>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
>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
>3e7l_A Transcriptional regulator (NTRC family); sigma43 activator, AAA+ ATPase, response regulator, transcriptional activator, ATP-binding; 2.25A {Aquifex aeolicus} PDB: 4fth_A Back     alignment and structure
>1g2h_A Transcriptional regulatory protein TYRR homolog; protein structure, , DNA-binding domain, helix- turn-helix motif; NMR {Haemophilus influenzae} SCOP: a.4.1.12 Back     alignment and structure
>1ntc_A Protein (nitrogen regulation protein (NTRC)); helix-turn-helix, FIS, four-helix bundle, transcription regulation; NMR {Salmonella typhimurium} SCOP: a.4.1.12 Back     alignment and structure
>3oou_A LIN2118 protein; protein structure initiative, PSI-2, structural genomics, MI center for structural genomics, MCSG, unknown function; HET: BTB; 1.57A {Listeria innocua} Back     alignment and structure
>1eto_A FIS, factor for inversion stimulation; transcriptional activation region, DNA-binding protein, transcription activator; 1.90A {Escherichia coli} SCOP: a.4.1.12 PDB: 1etq_A 1ety_A 1fia_A 3fis_A 3iv5_A* 3jr9_A* 3jra_A* 3jrb_A* 3jrc_A* 3jrd_A* 3jre_A* 3jrf_A* 3jrg_A* 3jrh_A* 3jri_A* 1f36_A 1etv_A 1etk_A 1etx_A 1fip_A ... Back     alignment and structure
>3mn2_A Probable ARAC family transcriptional regulator; structural genomics, PSI-2, protein structure initiative; 1.80A {Rhodopseudomonas palustris} Back     alignment and structure
>3oio_A Transcriptional regulator (ARAC-type DNA-binding containing proteins); PSI-2, midwest center for structural genomics; 1.65A {Chromobacterium violaceum} Back     alignment and structure
>2k9s_A Arabinose operon regulatory protein; activator, arabinose catabolism, carbohydrate metabolism, cytoplasm, DNA-binding, repressor, transcription; NMR {Escherichia coli} Back     alignment and structure
>3lsg_A Two-component response regulator YESN; structural genomics, PSI-2, protein structure initiative, MCSG; 2.05A {Fusobacterium nucleatum} Back     alignment and structure
>1bl0_A Protein (multiple antibiotic resistance protein), DNA (5'- D(*CP*CP*GP*AP*TP*GP*CP*CP*AP*CP*GP*TP*TP*TP*TP*GP*CP*TP*AP *AP*AP*TP* CP*C)-3')...; transcriptional activator; HET: DNA; 2.30A {Escherichia coli} SCOP: a.4.1.8 a.4.1.8 PDB: 1xs9_A Back     alignment and structure
>2pij_A Prophage PFL 6 CRO; transcription factor, helix-turn-helix, structural evolution, transcription; 1.70A {Pseudomonas fluorescens} Back     alignment and structure
>3mkl_A HTH-type transcriptional regulator GADX; PSI2, MCSG, structural genomics, protein structure initiativ midwest center for structural genomics; 2.15A {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 169
d1gqea_362 e.38.1.1 (A:) Polypeptide chain release factor 2 ( 1e-06
d1rq0a_333 e.38.1.1 (A:) Peptide chain release factor 1, RF1 1e-06
d1j26a_112 d.50.4.1 (A:) Ict1 protein {Mouse (Mus musculus) [ 3e-06
d2b3tb1344 e.38.1.1 (B:7-354) Peptide chain release factor 1, 4e-06
>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 = 45.0 bits (106), Expect = 1e-06
 Identities = 24/55 (43%), Positives = 34/55 (61%)

Query: 27  ECEMDTYKLSGPGSQHRNKRESAVRLKHVPTGVIAHAAEDRSQHKNHASSVNLDA 81
           +  +D Y+ SG G QH N+ ESAVR+ H+PTG++     DRSQHKN   ++    
Sbjct: 235 DLRIDVYRASGAGGQHVNRTESAVRITHIPTGIVTQCQNDRSQHKNKDQAMKQMK 289
>d1rq0a_ e.38.1.1 (A:) Peptide chain release factor 1, RF1 {Thermotoga maritima [TaxId: 2336]} Length = 333 Back     information, alignment and structure
>d1j26a_ d.50.4.1 (A:) Ict1 protein {Mouse (Mus musculus) [TaxId: 10090]} Length = 112 Back     information, alignment and structure
>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

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query169
d2b3tb1344 Peptide chain release factor 1, RF1 {Escherichia c 100.0
d1rq0a_333 Peptide chain release factor 1, RF1 {Thermotoga ma 100.0
d1gqea_362 Polypeptide chain release factor 2 (RF2) {Escheric 99.97
d1j26a_112 Ict1 protein {Mouse (Mus musculus) [TaxId: 10090]} 99.83
d1umqa_60 Photosynthetic apparatus regulatory protein PprA ( 95.0
d1etxa_89 FIS protein {Escherichia coli [TaxId: 562]} 89.38
d1g2ha_61 Transcriptional regulator TyrR, C-terminal domain 87.87
d1ntca_91 DNA-binding domain of NTRC {Salmonella typhimurium 87.53
>d2b3tb1 e.38.1.1 (B:7-354) Peptide chain release factor 1, RF1 {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: Peptide chain release factor 1, RF1
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=3.2e-35  Score=255.80  Aligned_cols=91  Identities=27%  Similarity=0.445  Sum_probs=75.6

Q ss_pred             cceeEEEEeecCCCCCcCCccCceEEEEeeCCceEEEEcccCCHHHHHHHHHHHH-hCCChhhhhhc-----CCCCCccc
Q 043121           26 RECEMDTYKLSGPGSQHRNKRESAVRLKHVPTGVIAHAAEDRSQHKNHASSVNLD-AYSPPPQLLQI-----LPPKSTIT   99 (169)
Q Consensus        26 ~dl~i~~~RssGpGGQ~vNk~~saVrl~H~ptGi~v~~~~~RSq~~Nr~~Al~~L-~~L~~~el~~~-----~~~ksqir   99 (169)
                      +||+|+|+|||||||||||||+|||||+|+||||+|.||++|||++||+.||++| ++|++.+++++     ..++++++
T Consensus       210 ~dl~i~~~rssg~GGQ~vnkt~sAVRi~H~ptGi~v~~q~eRSq~~Nk~~A~~~L~~kl~~~~~~~~~~~~~~~r~~~~~  289 (344)
T d2b3tb1         210 ADLRIDTFRSSGAGGQHVNTTDSAIRITHLPTGIVVECQDERSQHKNKAKALSVLGARIHAAEMAKRQQAEASTRRNLLG  289 (344)
T ss_dssp             SSEEEEECCSSCCCTTTCCCSSEEEEEEETTTCCEEEEEESSCHHHHHHHHHHHHHHHHTTTTTTSCC------CCC---
T ss_pred             ccceEEEecCCCccccchhhhhceeEEEEcCCceEEEccCCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence            4779999999999999999999999999999999999999999999999999999 79998877653     56778899


Q ss_pred             CCCCCCCCCCCCCCchh
Q 043121          100 SSEVGPQIGPNNPKFSL  116 (169)
Q Consensus       100 ~~~rg~qIRtYn~~f~~  116 (169)
                      +++||+|||||||.+..
T Consensus       290 ~~~r~~~iRtY~~p~~~  306 (344)
T d2b3tb1         290 SGDRSDRNRTYNFPQGR  306 (344)
T ss_dssp             ----CCEEEEEETTTTE
T ss_pred             cccccCceEeeecCCCc
Confidence            99999999999996654
>d1rq0a_ e.38.1.1 (A:) Peptide chain release factor 1, RF1 {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d1gqea_ e.38.1.1 (A:) Polypeptide chain release factor 2 (RF2) {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1j26a_ d.50.4.1 (A:) Ict1 protein {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1umqa_ a.4.1.12 (A:) Photosynthetic apparatus regulatory protein PprA (RegA), DNA-binding domain {Rhodobacter sphaeroides [TaxId: 1063]} Back     information, alignment and structure
>d1etxa_ a.4.1.12 (A:) FIS protein {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1g2ha_ a.4.1.12 (A:) Transcriptional regulator TyrR, C-terminal domain {Haemophilus influenzae [TaxId: 727]} Back     information, alignment and structure
>d1ntca_ a.4.1.12 (A:) DNA-binding domain of NTRC {Salmonella typhimurium [TaxId: 90371]} Back     information, alignment and structure