254780874

254780874

peptide chain release factor 1

GeneID in NCBI database:8209889Locus tag:CLIBASIA_03855
Protein GI in NCBI database:254780874Protein Accession:YP_003065287.1
Gene range:+(846202, 847275)Protein Length:357aa
Gene description:peptide chain release factor 1
COG prediction:[J] Protein chain release factor A
KEGG prediction:prfA; peptide chain release factor 1; K02835 peptide chain release factor RF-1
SEED prediction:Peptide chain release factor 1
Pathway involved in KEGG:not defined
Subsystem involved in SEED:Translation termination factors bacterial;
Glutaredoxins;
sequencesequence profile

Prediction of Local Sequence Properties

SourceSummaryResult
scaler
NCBI Databasesequence
PSIPREDsecondary structure
SSPROsecondary structure
DISEMBLcoil and loop
DISEMBLflexible loop
SEGlow complexity
DISOPREDdisordered
DISEMBLmissing residues
DISPROdisordered
TMHMMnone TM-Helix
TOPPREDnone TM-Helix
HMMTOPnone TM-Helix
MEMSATnone TM-Helix
MEMSAT_SVMnone TM-Helix
PHOBIUSnone TM-Helix
SignalP_HMMno
SignalP_NNno
COILScoiled coil
70% MSAconservation map
90% MSAconservation map
  
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------
MVFLSHKQICDLKNRFAEIELRMSESPSVDAYIKLTEEYAAISPIISKISIYDQKKQEEQDLHTVIGDHNSDSEIRDLAQIEVLAIEKEIRELENEINYLLLPKDTDDDKSCILEIRAGTGGSEAALFVGDLFRMYERYAALRKWKVEVLSSSDNDDGGYKEIVATISGRGVFSRMKFESGVHRVQRVPATEASGRVHTSAATVAVLPEAAEIDVDIPLEDIRIDTMRASGSGGQHVNTTDSAVRITHIPTGIMVTSSEKSQHQNRLRAMKVLRARLYDVERKRMANERSANRKLQIGSGDRSERIRTYNFSQGRITDHRINLTLYKLEYVLQGYIDDIINPLLTAHQAKMIGSASE
ccccHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccEEEEEcccccHHHHHHHHHHHHHHHHHHHHHcccEEEEEEccccccccEEEEEEEEEcccHHHHHHHcccccEEEEEcccccccccccccEEEEEccccccccccccccccEEEEEEcccccccccccccEEEEEEEcccEEEEEEccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccEEEEEcccccEEEEEccccccccHHHHcccHHHHHHHHHHHHHHHHHHHHcc
cccccHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccEEEEEEcccccHHHHHHHHHHHHHHHHHHHHcccEEEEEEcccccccccEEEEEEEcccccEEEEEEccccEEEEEcccccccccEEccccEEEEccccccEEEEEcHHHcEEEEEEccccccccccccccEEEEEcccccEEEEcccHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHEEEEccccccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHcc
MVFLSHKQICDLKNRFAEIELrmsespsvDAYIKLTEEYAAISPIISKISIYDQKKQEEQDLHTVigdhnsdseiRDLAQIEVLAIEKEIRELENEINYlllpkdtdddkscileiragtggseaALFVGDLFRMYERYAALRKWKVEVLsssdnddggyKEIVATISgrgvfsrmkfesgvhrvqrvpateasgrvhtsaATVAvlpeaaeidvdiplediridtmrasgsggqhvnttdsavrithiptgimvtsseksQHQNRLRAMKVLRARLYDVERKRMANersanrklqigsgdrserirtynfsqgritdhriNLTLYKLEYVLQGYIDDIINPLLTAHQAKMIGSASE
MVFLSHKQICDLKNRFAEIELRMSESPSVDAYIKLTEEYAAISPIISKISIYDQKKQEEQDLHTVigdhnsdseiRDLAQIEVLAIEKEIRELENEINYLllpkdtdddKSCILEiragtggseaaLFVGDLFRMYERYAALRKWKVEVlsssdnddggyKEIVAtisgrgvfsRMKFESGVHRVQrvpateasgrvhtsaatvavlpeaaeidvdipLEDIRIDTmrasgsggqhvnttdsavRITHIPTGimvtsseksqhqnrLRAMKVLRARLYDVerkrmanersanrklqigsgdrserirtynfsqgritdhriNLTLYKLEYVLQGYIDDIINPLLTAHQAKMIGSASE
MVFLSHKQICDLKNRFAEIELRMSESPSVDAYIKLTEEYAAispiiskisiYDQKKQEEQDLHTVIGDHNSDSEIRDLAQIEVLAIEKEIRELENEINYLLLPKDTDDDKSCILEIRAGTGGSEAALFVGDLFRMYERYAALRKWKVEVLSSSDNDDGGYKEIVATISGRGVFSRMKFESGVHRVQRVPATEASGRVHTSAATVAVLPEAAEIDVDIPLEDIRIDTMRASGSGGQHVNTTDSAVRITHIPTGIMVTSSEKSQHQNRLRAMKVLRARLYDVERKRMANERSANRKLQIGSGDRSERIRTYNFSQGRITDHRINLTLYKLEYVLQGYIDDIINPLLTAHQAKMIGSASE
******K**CDLKNRFAEIELRMSESPSVDAYIKLTEEYAAISPIISKISIYDQKKQEEQDLHTVIGDHNSDSEIRDLAQI************ENEINYLLLPKDTDDDKSCILEIRAGTGGSEAALFVGDLFRMYERYAALRKWKVEVLSSSDNDDGGYKEIVATISGRGVFSRMKFESGVHRVQRVPATEASGRVHTSAATVAVLPEAAEIDVDIPLEDIRIDTMRASGSGGQHVNTTDSAVRITHIPTGIMVTSSEKSQ*QNRLRAMKVLRARLY***********************RSERIRTYNFSQGRITDHRINLTLYKLEYVLQGYIDDIINPLLTAHQAKMIG****
MVFLSHKQICDLKNRFAEIELRMSESPSVDAYIKLTEEYAAISPIISKISIYDQKKQEEQDLHTVIGDHNSDSEIRDLAQIEVLAIEKEIRELENEINYLLLPKDTDDDKSCILEIRAGTGGSEAALFVGDLFRMYERYAALRKWKVEVLSSSDNDDGGYKEIVATISGRGVFSRMKFESGVHRVQRVPATEASGRVHTSAATVAVLPEAAEIDVDIPLEDIRIDTMRASGSGGQHVNTTDSAVRITHIPTGIMV**********RLRAMKVLRARLYDVERKRMANERSANRKLQIGSGDRSERIRTYNFSQGRITDHRINLTLYKLEYVLQGYIDDIINPLLTAHQAKMIGSASE
*VFLSHKQICDLKNRFAEIELRMSESPSVDAYIKLTEEYAAISPIISKISIYDQKKQEEQDLHTVIGDHNSDSEIRDLAQIEVLAIEKEIRELENEINYLLLPKDTDDDKSCILEIRAGTGGSEAALFVGDLFRMYERYAALRKWKVEVLSSSDNDDGGYKEIVATISGRGVFSRMKFESGVHRVQRVPATEASGRVHTSAATVAVLPEAAEIDVDIPLEDIRIDTMRASGSGGQHVNTTDSAVRITHIPTGIMVTSSEKSQHQNRLRAMKVLRARLYDVERKRMAN*********IGSGDRSERIRTYNFSQGRITDHRINLTLYKLEYVLQGYIDDIINPLLTAHQAKMIGS***
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MVFLSHKQICDLKNRFAEIELRMSESPSVDAYIKLTEEYAAISPIISKISIYDQKKQEEQDLHTVIGDHNSDSEIxxxxxxxxxxxxxxxxxxxxxINYLLLPKDTDDDKSCILEIRAGTGGSEAALFVGDLFRMYERYAALRKWKVEVLSSSDNDDGGYKEIVATISGRGVFSRMKFESGVHRVQRVPATEASGRVHTSAATVAVLPEAAEIDVDIPLEDIRIDTMRASGSGGQHVNTTDSAVRITHIPTGIMVTSSEKSQHQNRLRAMKVLRARLYDVERKRMANERSANRKLQIGSGDRSERIRTYNFSQGRITDHRINLTLYKLEYVLQGYIDDIINPLLTAHQAKMIGSASE
MVFLSHKQICDLKNRFAEIELRMSESPSVDAYIKLTEEYAAISPIISKISIYDQKKQEEQDLHTVIGDHNSDSEIRDLAQIEVLAIEKEIRELENEINYLLLPKDTDDDKSCILEIRAGTGGSEAALFVGDLFRMYERYAALRKWKVEVLSSSDNDDGGYKEIVATISGRGVFSRMKFESGVHRVQRVPATEASGRVHTSAATVAVLPEAAEIDVDIPLEDIRIDTMRASGSGGQHVNTTDSAVRITHIPTGIMVTSSEKSQHQNRLRAMKVLRARLYDVERKRMANERSANRKLQIGSGDRSERIRTYNFSQGRITDHRINLTLYKLEYVLQGYIDDIINPLLTAHQAKMIGSASE
MVFLSHKQICDLKNRFAEIELRMSESPSVDAYIKLTEEYAAISPIISKISIYDQKKQEEQDLHTVIGDHNSDSEIRDLAQIEVLAIEKEIRELENEINYLLLPKDTDDDKSCILEIRAGTGGSEAALFVGDLFRMYERYAALRKWKVEVLSSSDNDDGGYKEIVATISGRGVFSRMKFESGVHRVQRVPATEASGRVHTSAATVAVLPEAAEIDVDIPLEDIRIDTMRASGSGGQHVNTTDSAVRITHIPTGIMVTSSEKSQHQNRLRAMKVLRARLYDVERKRMANERSANRKLQIGSGDRSERIRTYNFSQGRITDHRINLTLYKLEYVLQGYIDDIINPLLTAHQAKMIGSASE

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

IdentityAlignment graphLength Definition E-value
Target357 peptide chain release factor 1 [Candidatus Liberibacter
254780753355 peptide chain release factor 2 [Candidatus Liberib 1e-44
>gi|254780753|ref|YP_003065166.1| peptide chain release factor 2 [Candidatus Liberibacter asiaticus str. psy62] Length = 355 Back     alignment
 Score =  172 bits (435), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 105/270 (38%), Positives = 160/270 (59%), Gaps = 16/270 (5%)

Query: 81  IEVLAIEKEIRELENEINYLLLPKDTDDDKSCILEIRAGTGGSEAALFVGDLFRMYERYA 140
           ++ + +E E ++ E+     LL  + D + +  LE+ AG GG+E+  +   L RMY R+A
Sbjct: 92  LQRIKLEVEYKQFES-----LLSGEADSNDA-YLEVHAGAGGTESQDWANMLLRMYTRWA 145

Query: 141 ALRKWKVEVLSSSDNDDGGYKEIVATISGRGVFSRMKFESGVHRVQRVPATEASGRVHTS 200
             RK+K E L   D ++ G K     I G   +  +K E GVHR+ R+   +++ R HTS
Sbjct: 146 EKRKFKTEALEIHDGEEAGIKSATLLIKGPNAYGWLKGEQGVHRLVRISPYDSNSRRHTS 205

Query: 201 AATVAVLPEAAE-IDVDIPLEDIRIDTMRASGSGGQHVNTTDSAVRITHIPTGIMV-TSS 258
            +++ V P   + I+++I   D RIDT RASG+GGQHVNTTDSAVRITHIPTG++V    
Sbjct: 206 FSSIWVYPVVDDSIEIEISESDCRIDTYRASGAGGQHVNTTDSAVRITHIPTGVVVQCQQ 265

Query: 259 EKSQHQNRLRAMKVLRARLYDVE---RKRMANERSANRKLQIGSGDRSERIRTYNFSQGR 315
           E+SQH+N+ +A  +LRA+LY++E   R+ +AN   ++ K +IG G    +IR+Y     +
Sbjct: 266 ERSQHKNKAQAWNMLRAKLYELELQKREEIANIGESS-KTEIGWG---RQIRSYVLQPYQ 321

Query: 316 -ITDHRINLTLYKLEYVLQGYIDDIINPLL 344
            + D R N+       VL G +DD +   L
Sbjct: 322 MVKDLRTNIEKTSPSDVLDGDLDDFMKATL 351

Close Homologs Detected BLAST or PSI-BLAST in the First 2 Iterations

IdentityAlignment graphLength Definition Round E-value
Target357 peptide chain release factor 1 [Candidatus Liberibacter
315122704357 peptide chain release factor 1 [Candidatus Liberibacter 1 0.0
15966364360 peptide chain release factor 1 [Sinorhizobium meliloti 1 1e-139
307321056360 peptide chain release factor 1 [Sinorhizobium meliloti 1 1e-138
15890803360 peptide chain release factor 1 [Agrobacterium tumefacie 1 1e-138
332716892360 peptide chain release factor 1 [Agrobacterium sp. H13-3 1 1e-137
150397700360 peptide chain release factor 1 [Sinorhizobium medicae W 1 1e-136
116254019359 peptide chain release factor 1 [Rhizobium leguminosarum 1 1e-136
241206502359 peptide chain release factor 1 [Rhizobium leguminosarum 1 1e-136
209551100359 peptide chain release factor 1 [Rhizobium leguminosarum 1 1e-135
119361587359 RecName: Full=Peptide chain release factor 1; Short=RF- 1 1e-135
>gi|315122704|ref|YP_004063193.1| peptide chain release factor 1 [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 357 Back     alignment and organism information
 Score =  639 bits (1648), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 311/357 (87%), Positives = 331/357 (92%)

Query: 1   MVFLSHKQICDLKNRFAEIELRMSESPSVDAYIKLTEEYAAISPIISKISIYDQKKQEEQ 60
           MVFLSHKQ+C+LKNRF+EIELRMSESPSVD YIKLTEEYAAISPIISKI IY++KK EEQ
Sbjct: 1   MVFLSHKQVCNLKNRFSEIELRMSESPSVDVYIKLTEEYAAISPIISKIDIYEKKKGEEQ 60

Query: 61  DLHTVIGDHNSDSEIRDLAQIEVLAIEKEIRELENEINYLLLPKDTDDDKSCILEIRAGT 120
           DL T+I D +SD  IRDLA+ E+  +EKEI+ LE EI+ LLLPKDTDDDKSCILEIRAGT
Sbjct: 61  DLRTIIDDQDSDLGIRDLAKAEIGEVEKEIKALEYEISCLLLPKDTDDDKSCILEIRAGT 120

Query: 121 GGSEAALFVGDLFRMYERYAALRKWKVEVLSSSDNDDGGYKEIVATISGRGVFSRMKFES 180
           GGSEAALFVGDLFRMYERYA  +KWKVE+LSSSDNDDGGYKEIVATISG GVF RMKFES
Sbjct: 121 GGSEAALFVGDLFRMYERYATYQKWKVEILSSSDNDDGGYKEIVATISGNGVFYRMKFES 180

Query: 181 GVHRVQRVPATEASGRVHTSAATVAVLPEAAEIDVDIPLEDIRIDTMRASGSGGQHVNTT 240
           GVHRVQRVPATEASGRVHTSAATVAVLPEA EIDV I  EDIRIDTMRASGSGGQHVNTT
Sbjct: 181 GVHRVQRVPATEASGRVHTSAATVAVLPEAEEIDVAIATEDIRIDTMRASGSGGQHVNTT 240

Query: 241 DSAVRITHIPTGIMVTSSEKSQHQNRLRAMKVLRARLYDVERKRMANERSANRKLQIGSG 300
           DSAVRITHIPTGIMVTSSEKSQHQNRL+AMKVLRARLYD+ERKRMA+ERS NRK QIGSG
Sbjct: 241 DSAVRITHIPTGIMVTSSEKSQHQNRLQAMKVLRARLYDIERKRMAHERSENRKAQIGSG 300

Query: 301 DRSERIRTYNFSQGRITDHRINLTLYKLEYVLQGYIDDIINPLLTAHQAKMIGSASE 357
           DRSERIRTYNF QGRITDHRINLTLYKLEYVLQGY+D+I+N LLTAHQAKMIGSASE
Sbjct: 301 DRSERIRTYNFPQGRITDHRINLTLYKLEYVLQGYLDEIVNALLTAHQAKMIGSASE 357


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|15966364|ref|NP_386717.1| peptide chain release factor 1 [Sinorhizobium meliloti 1021] Length = 360 Back     alignment and organism information
>gi|307321056|ref|ZP_07600462.1| peptide chain release factor 1 [Sinorhizobium meliloti AK83] Length = 360 Back     alignment and organism information
>gi|15890803|ref|NP_356475.1| peptide chain release factor 1 [Agrobacterium tumefaciens str. C58] Length = 360 Back     alignment and organism information
>gi|332716892|ref|YP_004444358.1| peptide chain release factor 1 [Agrobacterium sp. H13-3] Length = 360 Back     alignment and organism information
>gi|150397700|ref|YP_001328167.1| peptide chain release factor 1 [Sinorhizobium medicae WSM419] Length = 360 Back     alignment and organism information
>gi|116254019|ref|YP_769857.1| peptide chain release factor 1 [Rhizobium leguminosarum bv. viciae 3841] Length = 359 Back     alignment and organism information
>gi|241206502|ref|YP_002977598.1| peptide chain release factor 1 [Rhizobium leguminosarum bv. trifolii WSM1325] Length = 359 Back     alignment and organism information
>gi|209551100|ref|YP_002283017.1| peptide chain release factor 1 [Rhizobium leguminosarum bv. trifolii WSM2304] Length = 359 Back     alignment and organism information
>gi|119361587|sp|Q2K3T1|RF1_RHIEC RecName: Full=Peptide chain release factor 1; Short=RF-1 Length = 359 Back     alignment and organism information

Conserved Domains in CDD Database
Detected by RPS-BLAST and HHsearch

Conserved Domains in CDD Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target357 peptide chain release factor 1 [Candidatus Liberibacter
PRK00591359 PRK00591, prfA, peptide chain release factor 1; Validat 1e-159
TIGR00019360 TIGR00019, prfA, peptide chain release factor 1 1e-125
KOG2726386 KOG2726, KOG2726, KOG2726, Mitochondrial polypeptide ch 8e-83
PRK00578367 PRK00578, prfB, peptide chain release factor 2; Validat 9e-67
TIGR00020364 TIGR00020, prfB, peptide chain release factor 2 9e-61
PRK06746326 PRK06746, PRK06746, peptide chain release factor 2; Pro 1e-43
COG0216363 COG0216, PrfA, Protein chain release factor A [Translat 1e-132
COG1186239 COG1186, PrfB, Protein chain release factor B [Translat 2e-49
PRK05589325 PRK05589, PRK05589, peptide chain release factor 2; Pro 3e-46
PRK08787313 PRK08787, PRK08787, peptide chain release factor 2; Pro 7e-42
PRK07342339 PRK07342, PRK07342, peptide chain release factor 2; Pro 7e-47
pfam00472114 pfam00472, RF-1, RF-1 domain 5e-43
pfam03462115 pfam03462, PCRF, PCRF domain 1e-38
TIGR03072200 TIGR03072, release_prfH, putative peptide chain release 1e-21
PRK08179200 PRK08179, prfH, peptide chain release factor-like prote 3e-19
PRK09256138 PRK09256, PRK09256, hypothetical protein; Provisional 3e-05
>gnl|CDD|179074 PRK00591, prfA, peptide chain release factor 1; Validated Back     alignment and domain information
>gnl|CDD|129130 TIGR00019, prfA, peptide chain release factor 1 Back     alignment and domain information
>gnl|CDD|37937 KOG2726, KOG2726, KOG2726, Mitochondrial polypeptide chain release factor [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|179072 PRK00578, prfB, peptide chain release factor 2; Validated Back     alignment and domain information
>gnl|CDD|161667 TIGR00020, prfB, peptide chain release factor 2 Back     alignment and domain information
>gnl|CDD|75726 PRK06746, PRK06746, peptide chain release factor 2; Provisional Back     alignment and domain information
>gnl|CDD|30565 COG0216, PrfA, Protein chain release factor A [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|31379 COG1186, PrfB, Protein chain release factor B [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|180152 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|168914 PRK07342, PRK07342, peptide chain release factor 2; Provisional Back     alignment and domain information
>gnl|CDD|144168 pfam00472, RF-1, RF-1 domain Back     alignment and domain information
>gnl|CDD|146218 pfam03462, PCRF, PCRF domain Back     alignment and domain information
>gnl|CDD|132116 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|181730 PRK09256, PRK09256, hypothetical protein; Provisional Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 357 peptide chain release factor 1 [Candidatus Liberibacter
TIGR00019373 prfA peptide chain release factor 1; InterPro: IPR00437 100.0
TIGR00020373 prfB peptide chain release factor 2; InterPro: IPR00437 100.0
PRK00591360 prfA peptide chain release factor 1; Validated 100.0
COG0216363 PrfA Protein chain release factor A [Translation, ribos 100.0
PRK07245337 consensus 100.0
PRK00578367 prfB peptide chain release factor 2; Validated 100.0
PRK05589325 peptide chain release factor 2; Provisional 100.0
PRK06746326 peptide chain release factor 2; Provisional 100.0
KOG2726386 consensus 100.0
PRK07342322 peptide chain release factor 2; Provisional 100.0
PRK08787313 peptide chain release factor 2; Provisional 100.0
COG1186239 PrfB Protein chain release factor B [Translation, ribos 100.0
TIGR03072200 release_prfH putative peptide chain release factor H. M 100.0
PRK08179204 prfH peptide chain release factor-like protein; Reviewe 100.0
pfam00472114 RF-1 RF-1 domain. This domain is found in peptide chain 100.0
pfam03462115 PCRF PCRF domain. This domain is found in peptide chain 100.0
PRK09256138 hypothetical protein; Provisional 99.67
KOG3429172 consensus 98.94
PRK07245337 consensus 95.4
PRK11147 632 ABC transporter ATPase component; Reviewed 93.15
>TIGR00019 prfA peptide chain release factor 1; InterPro: IPR004373 This family describes peptide chain release factor 1 (PrfA, RF-1), and excludes the related peptide chain release factor 2 (PrfB, RF-2) Back     alignment and domain information
>TIGR00020 prfB peptide chain release factor 2; InterPro: IPR004374 In many but not all taxa, there is a conserved real translational frameshift at a TGA codon Back     alignment and domain information
>PRK00591 prfA peptide chain release factor 1; Validated Back     alignment and domain information
>COG0216 PrfA Protein chain release factor A [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK07245 consensus Back     alignment and domain information
>PRK00578 prfB peptide chain release factor 2; Validated 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
>KOG2726 consensus Back     alignment and domain information
>PRK07342 peptide chain release factor 2; Provisional Back     alignment and domain information
>PRK08787 peptide chain release factor 2; Provisional Back     alignment and domain information
>COG1186 PrfB Protein chain release factor B [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>TIGR03072 release_prfH putative peptide chain release factor H Back     alignment and domain information
>PRK08179 prfH peptide chain release factor-like protein; Reviewed Back     alignment and domain information
>pfam00472 RF-1 RF-1 domain Back     alignment and domain information
>pfam03462 PCRF PCRF domain Back     alignment and domain information
>PRK09256 hypothetical protein; Provisional Back     alignment and domain information
>KOG3429 consensus Back     alignment and domain information
>PRK07245 consensus Back     alignment and domain information
>PRK11147 ABC transporter ATPase component; Reviewed Back     alignment and domain information

Homologous Structures in PDB Database
Detected by PSI-BLAST, RPS-BLAST and HHsearch

Homologous Structures Detected by PSI-BLAST against Nonredundant Database

IdentityAlignment graphLength Definition E-value
Target357 peptide chain release factor 1 [Candidatus Liberibacter
2b3t_B360 Molecular Basis For Bacterial Class 1 Release Facto 2e-72
1zbt_A371 Crystal Structure Of Peptide Chain Release Factor 1 1e-69
2b64_Y354 30s Ribosomal Subunit, Trnas, Mrna And Release Fact 9e-67
1mi6_A365 Docking Of The Modified Rf2 X-Ray Structure Into Th 7e-60
1gqe_A365 Polypeptide Chain Release Factor 2 (Rf2) From Esche 7e-60
1ml5_Z365 Structure Of The E. Coli Ribosomal Termination Comp 7e-60
1rq0_A342 Crystal Structure Of Peptide Releasing Factor 1 Len 7e-58
2fvo_A333 Docking Of The Modified Rf1 X-Ray Structure Into Th 9e-58
2x9r_Y351 Structure Of The 70s Ribosome Bound To Release Fact 5e-51
2jl7_Y351 Insights Into Translational Termination From The St 9e-51
3f1e_X378 Crystal Structure Of A Translation Termination Comp 1e-50
2ihr_1365 Rf2 Of Thermus Thermophilus Length = 365 2e-50
2b9m_Y365 30s Ribosomal Subunit, Trnas, Mrna And Release Fact 4e-50
>gi|88192214|pdb|2B3T|B Chain B, Molecular Basis For Bacterial Class 1 Release Factor Methylation By Prmc Length = 360 Back     alignment and structure
 Score =  277 bits (708), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 171/355 (48%), Positives = 252/355 (70%), Gaps = 9/355 (2%)

Query: 8   QICDLKNRFAEIELRMSESPSVDA---YIKLTEEYAAISPIISKISIYDQKKQEEQDLHT 64
           ++  L  R  E++  + ++ ++     +  L+ EYA +S +    + + Q +++ +    
Sbjct: 8   KLEALHERHEEVQALLGDAQTIADQERFRALSREYAQLSDVSRCFTDWQQVQEDIETAQM 67

Query: 65  VIGDHNSDSEIRDLAQIEVLAIEKEIRELENEINYLLLPKDTDDDKSCILEIRAGTGGSE 124
           ++     D E+R++AQ E+   +++  +LE ++  LLLPKD DD+++  LE+RAGTGG E
Sbjct: 68  ML----DDPEMREMAQDELREAKEKSEQLEQQLQVLLLPKDPDDERNAFLEVRAGTGGDE 123

Query: 125 AALFVGDLFRMYERYAALRKWKVEVLSSSDNDDGGYKEIVATISGRGVFSRMKFESGVHR 184
           AALF GDLFRMY RYA  R+W+VE++S+S+ + GGYKEI+A ISG GV+ R+KFESG HR
Sbjct: 124 AALFAGDLFRMYSRYAEARRWRVEIMSASEGEHGGYKEIIAKISGDGVYGRLKFESGGHR 183

Query: 185 VQRVPATEASGRVHTSAATVAVLPEAAEID-VDIPLEDIRIDTMRASGSGGQHVNTTDSA 243
           VQRVPATE+ GR+HTSA TVAV+PE  + +  D+   D+RIDT R+SG+GGQHVNTTDSA
Sbjct: 184 VQRVPATESQGRIHTSACTVAVMPELPDAELPDVNPADLRIDTFRSSGAGGQHVNTTDSA 243

Query: 244 VRITHIPTGIMV-TSSEKSQHQNRLRAMKVLRARLYDVERKRMANERSANRKLQIGSGDR 302
           +RITH+PTGI+V    E+SQH+N+ +A+ VL AR++  E  +     ++ R+  +GSGDR
Sbjct: 244 IRITHLPTGIVVECQDERSQHKNKAKALSVLGARIHAAEMAKRQQAEASTRRNLLGSGDR 303

Query: 303 SERIRTYNFSQGRITDHRINLTLYKLEYVLQGYIDDIINPLLTAHQAKMIGSASE 357
           S+R RTYNF QGR+TDHRINLTLY+L+ V++G +D +I P++  HQA  + + SE
Sbjct: 304 SDRNRTYNFPQGRVTDHRINLTLYRLDEVMEGKLDMLIEPIIQEHQADQLAALSE 358


>gi|66361428|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
gi|88192257|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
>gi|28373662|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
>gi|20663625|pdb|1GQE|A Chain A, Polypeptide Chain Release Factor 2 (Rf2) From Escherichia Coli Length = 365 Back     alignment and structure
gi|28373696|pdb|1ML5|Z Chain Z, Structure Of The E. Coli Ribosomal Termination Complex With Release Factor 2 Length = 365 Back     alignment and structure
gi|52695394|pdb|1RQ0|A Chain A, Crystal Structure Of Peptide Releasing Factor 1 Length = 342 Back     alignment and structure
>gi|93279782|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
>gi|295982099|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
gi|218766794|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
>gi|134104518|pdb|2IHR|1 Chain 1, Rf2 Of Thermus Thermophilus Length = 365 Back     alignment and structure
>gi|88192320|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

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target357 peptide chain release factor 1 [Candidatus Liberibacter
1gqe_A365 Release factor 2, RF2; protein synthesis, ribosome, mac 4e-89
1zbt_A371 RF-1, peptide chain release factor 1; peptide chain rel 3e-69
3d5a_X354 RF1, peptide chain release factor 1; ribosome, coiled c 3e-65
2b3t_B360 RF-1, peptide chain release factor 1; translation termi 3e-63
1rq0_A342 RF-1, peptide chain release factor 1; X-RAY, crystal, p 1e-60
2ihr_1365 Peptide chain release factor 2; mixed alpha-beta, trans 9e-58
1j26_A112 Immature colon carcinoma transcript 1; peptide chain re 1e-14
2jy9_A148 Putative tRNA hydrolase domain; GFT protein structure, 3e-14
2jva_A108 Peptidyl-tRNA hydrolase domain protein; GFT hydrolase, 9e-13
>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
 Score =  323 bits (829), Expect = 4e-89
 Identities = 118/344 (34%), Positives = 190/344 (55%), Gaps = 17/344 (4%)

Query: 11  DLKNRFAEIELRMSESPSV----DAYIKLTEEYAAISPIISKISIYDQKKQEEQDLHTVI 66
             K R  E+   + + P V    +    L +E +++  ++  +    Q  ++   L  + 
Sbjct: 29  AKKERLEEVNAELEQ-PDVWNEPERAQALGKERSSLEAVVDTLDQMKQGLEDVSGLLELA 87

Query: 67  GDHNSDSEIRDLAQIEVLAIEKEIRELENEINYLLLPKDTDDDKSCILEIRAGTGGSEAA 126
            + + D E  + A  E+ A+E+++ +LE    +  +     D   C L+I+AG+GG+EA 
Sbjct: 88  VEAD-DEETFNEAVAELDALEEKLAQLE----FRRMFSGEYDSADCYLDIQAGSGGTEAQ 142

Query: 127 LFVGDLFRMYERYAALRKWKVEVLSSSDNDDGGYKEIVATISGRGVFSRMKFESGVHRVQ 186
            +   L RMY R+A  R +K E++  S+ +  G K +   ISG   +  ++ E+GVHR+ 
Sbjct: 143 DWASMLERMYLRWAESRGFKTEIIEESEGEVAGIKSVTIKISGDYAYGWLRTETGVHRLV 202

Query: 187 RVPATEASGRVHTSAATVAVLPEAAE-IDVDIPLEDIRIDTMRASGSGGQHVNTTDSAVR 245
           R    ++ GR HTS ++  V PE  + ID++I   D+RID  RASG+GGQHVN T+SAVR
Sbjct: 203 RKSPFDSGGRRHTSFSSAFVYPEVDDDIDIEINPADLRIDVYRASGAGGQHVNRTESAVR 262

Query: 246 ITHIPTGIMVT-SSEKSQHQNRLRAMKVLRARLYDVERKRMANERSA--NRKLQIGSGDR 302
           ITHIPTGI+    +++SQH+N+ +AMK ++A+LY+VE ++   E+ A  + K  IG G  
Sbjct: 263 ITHIPTGIVTQCQNDRSQHKNKDQAMKQMKAKLYEVEMQKKNAEKQAMEDNKSDIGWG-- 320

Query: 303 SERIRTYNFSQGRITDHRINLTLYKLEYVLQGYIDDIINPLLTA 346
             +IR+Y     RI D R  +     + VL G +D  I   L A
Sbjct: 321 -SQIRSYVLDDSRIKDLRTGVETRNTQAVLDGSLDQFIEASLKA 363


>1zbt_A RF-1, peptide chain release factor 1; peptide chain release factor 1 (RF-1), structural genomics, joint center for structural genomics, JCSG; 2.34A {Streptococcus mutans} Length = 371 Back     alignment and structure
>3d5a_X RF1, peptide chain release factor 1; ribosome, coiled coil, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding; 3.21A {Thermus thermophilus HB27} PDB: 2b64_Y 3d5c_X Length = 354 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
>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
>2ihr_1 Peptide chain release factor 2; mixed alpha-beta, translation; 2.50A {Thermus thermophilus} PDB: 2b9m_Y* 3f1e_X 3f1g_X 2jl5_Y 2jl7_Y 2wh1_Y 2wh3_Y Length = 365 Back     alignment and structure
>1j26_A Immature colon carcinoma transcript 1; peptide chain release factors, RF-1, the GGQ motif, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.50.4.1 Length = 112 Back     alignment and structure
>2jy9_A Putative tRNA hydrolase domain; GFT protein structure, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium LT2} Length = 148 Back     alignment and structure
>2jva_A Peptidyl-tRNA hydrolase domain protein; GFT hydrolase, structural genomics, PSI-2, protein structure initiative; NMR {Pseudomonas syringae PV} Length = 108 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target357 peptide chain release factor 1 [Candidatus Liberibacter
1zbt_A371 RF-1, peptide chain release factor 1; peptide chain rel 100.0
3d5a_X354 RF1, peptide chain release factor 1; ribosome, coiled c 100.0
1gqe_A365 Release factor 2, RF2; protein synthesis, ribosome, mac 100.0
2b3t_B360 RF-1, peptide chain release factor 1; translation termi 100.0
2ihr_1365 Peptide chain release factor 2; mixed alpha-beta, trans 100.0
1rq0_A342 RF-1, peptide chain release factor 1; X-RAY, crystal, p 100.0
2jva_A108 Peptidyl-tRNA hydrolase domain protein; GFT hydrolase, 99.71
2jy9_A148 Putative tRNA hydrolase domain; GFT protein structure, 99.7
1j26_A112 Immature colon carcinoma transcript 1; peptide chain re 99.65
1gqe_A365 Release factor 2, RF2; protein synthesis, ribosome, mac 94.48
3ghg_A 562 Fibrinogen alpha chain; triple-stranded coiled coil, be 91.44
>1zbt_A RF-1, peptide chain release factor 1; peptide chain release factor 1 (RF-1), structural genomics, joint center for structural genomics, JCSG; 2.34A {Streptococcus mutans} Back     alignment and structure
Probab=100.00  E-value=0  Score=969.53  Aligned_cols=355  Identities=44%  Similarity=0.712  Sum_probs=346.2

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHCCCCCHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHH
Q ss_conf             786898999999999999985385315799---99999998799999999999999998999999972037853566543
Q gi|254780874|r    3 FLSHKQICDLKNRFAEIELRMSESPSVDAY---IKLTEEYAAISPIISKISIYDQKKQEEQDLHTVIGDHNSDSEIRDLA   79 (357)
Q Consensus         3 mi~~~kL~~l~~rl~ELE~~Lsdp~~w~d~---~klsKe~s~L~~iv~~~~~~~~~~~ei~el~eLl~e~e~D~El~elA   79 (357)
                      |-+-+||+.+..|+.+|+.+|++|+||+|+   ++++|+++.|+++++.|+.|....+++.++.+|+.+.++|++|.+++
T Consensus        13 M~ifdkLe~i~~r~~eLe~~lsdp~~w~D~~ka~~l~kE~s~L~~~v~~~~~l~~~~~dl~el~eLl~e~~~D~el~ela   92 (371)
T 1zbt_A           13 MNIYDQLQAVEDRYEELGELLSDPDVVSDTKRFMELSREEANSRETVAVYREYKQVVQNIADAQEMIKDASGDPELEEMA   92 (371)
T ss_dssp             CCHHHHHHHHHHHHHHC--------------------CCHHHHHHHHHHHHHHHHHHHHHHHHHHC-------CHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCCHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHH
T ss_conf             12999999999999999998709841229999999999999899999999999999987999999985136885799999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCCCCC
Q ss_conf             32223320005778889998640001135540378862268852178899999999999987649840013211354477
Q gi|254780874|r   80 QIEVLAIEKEIRELENEINYLLLPKDTDDDKSCILEIRAGTGGSEAALFVGDLFRMYERYAALRKWKVEVLSSSDNDDGG  159 (357)
Q Consensus        80 eeEl~~l~~~l~~le~eL~~~LLpsde~D~~nailEI~aGaGG~EA~dwA~~L~rMY~r~ae~~gwk~eii~~~~ge~aG  159 (357)
                      ++|+..+..+++.++++|+..|||+||+|.+||||||||||||+||||||+||||||+|||+++||++++++.++|++||
T Consensus        93 ~eEl~~~~~~l~~l~~~le~~lL~~d~~D~~nailEIrAGaGG~EA~dwA~~L~RMY~r~Ae~~g~k~eiid~~~g~~gG  172 (371)
T 1zbt_A           93 KEELKNSKVAKEEYEEKLRFLLLPKDPNDDKNIILEIRGAAGGDEAALFAGDLLNMYQKYAENQGWKFEVMEASANGVGG  172 (371)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTTSCCCTTTTSCEEEEEEECTTTHHHHHHHHHHHHHHHHHHHHHTCEEEEEEEEECSSSC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCEEECCCCCCCCCC
T ss_conf             99998755458999999999851589776668699996488853799999999999999999769834761435777677


Q ss_pred             CCEEEEEEECCCHHHHHHCCCCCEEEEEECCCCCCCCCCEEEEEEEEEECCCCCCCCCCCCEEEEEEECCCCCCCCCCCC
Q ss_conf             21113777503111210002465026761254567851101688885303343322245434799985288875200063
Q gi|254780874|r  160 YKEIVATISGRGVFSRMKFESGVHRVQRVPATEASGRVHTSAATVAVLPEAAEIDVDIPLEDIRIDTMRASGSGGQHVNT  239 (357)
Q Consensus       160 ik~v~~~I~G~~aYg~Lk~E~GvHRvqRip~~es~gR~hTS~a~V~V~P~~~~~~~~i~~~dl~i~~~rssG~GGQ~vN~  239 (357)
                      ||+|++.|+|++|||+||+|+|||||||||||+++||+|||||+|+|+|++++++++|+|+||+||||||||||||||||
T Consensus       173 iKsa~~~I~G~~ayg~Lk~E~GvHRv~Rip~~~s~~r~hts~~~v~v~p~~~~~~~~i~~~dl~idt~RssG~GGQ~VNk  252 (371)
T 1zbt_A          173 LKEVVAMVSGQSVYSKLKYESGAHRVQRVPVTESQGRVHTSTATVLVMPEVEEVEYEIDPKDLRVDIYHASGAGGQNVNK  252 (371)
T ss_dssp             EEEEEEEEESTTHHHHHGGGCEEEEEEECCTTCSSCCCEEEEEEEEEEECCCGGGSCCCGGGEEEEEECC---------C
T ss_pred             CCEEEEEEEECEEHHCCEEECEEEEEEEECCCCCCCCEEEEEEEEEEECCCCCCCCCCCCCCEEEEEECCCCCCCCCCCC
T ss_conf             12169999502121021340514799997887888870688789998056776544057775069983388887777776


Q ss_pred             CCCEEEEEECCCCEEE-EECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEECCCCCCCEEE
Q ss_conf             2121588964984488-843654135899999999999999999999999987446522467423822104489981124
Q gi|254780874|r  240 TDSAVRITHIPTGIMV-TSSEKSQHQNRLRAMKVLRARLYDVERKRMANERSANRKLQIGSGDRSERIRTYNFSQGRITD  318 (357)
Q Consensus       240 t~savri~H~ptgi~v-~~~eRsQ~~Nk~~A~~~L~~~l~~~~~~~~~~~~~~~r~~~~g~~~rs~~iRtY~~~~~rv~D  318 (357)
                      |+|||||||+||||+| ||+|||||+||++||++|++|||+++.+++.++..+.||+|||+|+||+|||||||||+||||
T Consensus       253 t~sAVRitH~pTGi~v~~q~eRSQ~~Nk~~A~~~L~~kl~~~~~~~~~~~~~~~rk~~~~~~~rs~~IRtY~~p~~~V~D  332 (371)
T 1zbt_A          253 VATAVRIIHLPTNIKVEMQEERTQQKNRDKAMKIIRARVADHFAQIAQDEQDAERKSTVGTGDRSERIRTYNFPQNRVTD  332 (371)
T ss_dssp             CCCEEEEEETTTTEEEEECSSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHTCC----CCSCSCTTSEEEEEETTTTEEEE
T ss_pred             CCCEEEEEEECCCCEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHH
T ss_conf             55158999934885899426514387999999999999999999999999999887304026643575081079775066


Q ss_pred             EECCCEECCHHHHHCCCHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             321644178778728866999999999999999874059
Q gi|254780874|r  319 HRINLTLYKLEYVLQGYIDDIINPLLTAHQAKMIGSASE  357 (357)
Q Consensus       319 hR~~~~~~~~~~~l~G~l~~~i~~~~~~~~~~~l~~~~e  357 (357)
                      ||||++++|+++||||+||+||++|+.|+.+++|+++++
T Consensus       333 hR~~~~~~~~~~vldG~ld~~i~a~~~~~~~~~l~~~~~  371 (371)
T 1zbt_A          333 HRIGLTLQKLDSILSGKLDEVIDALILYDQTQKLEELNK  371 (371)
T ss_dssp             TTTTEEESCHHHHHTTCCHHHHHHHHHHHHHHHHHHCC-
T ss_pred             HCCCCEECCHHHHHCCCHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             324886368357619866999999999999999996069



>3d5a_X RF1, peptide chain release factor 1; ribosome, coiled coil, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding; 3.21A {Thermus thermophilus HB27} 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
>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
>2jva_A Peptidyl-tRNA hydrolase domain protein; GFT hydrolase, structural genomics, PSI-2, protein structure initiative; NMR {Pseudomonas syringae PV} Back     alignment and structure
>2jy9_A Putative tRNA hydrolase domain; GFT protein structure, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium LT2} Back     alignment and structure
>1j26_A Immature colon carcinoma transcript 1; peptide chain release factors, RF-1, the GGQ motif, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.50.4.1 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
>3ghg_A Fibrinogen alpha chain; triple-stranded coiled coil, beta sheets, alpha helices, alternative splicing, amyloid, amyloidosis, blood coagulation, coiled coil; HET: NAG NDG BMA MAN GAL SIA; 2.90A {Homo sapiens} PDB: 3h32_A* 2a45_G* Back     alignment and structure

Homologous Domains in SCOP and MMDB Database
Detected by RPS-BLAST and HHsearch

Homologous Domains in SCOP70 (Version1.75) Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 357 peptide chain release factor 1 [Candidatus Liberibacter
d1gqea_362 e.38.1.1 (A:) Polypeptide chain release factor 2 (RF2) 1e-69
d2b3tb1344 e.38.1.1 (B:7-354) Peptide chain release factor 1, RF1 1e-64
d1rq0a_333 e.38.1.1 (A:) Peptide chain release factor 1, RF1 {Ther 1e-60
d1j26a_112 d.50.4.1 (A:) Ict1 protein {Mouse (Mus musculus) [TaxId 2e-14
>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 =  256 bits (656), Expect = 1e-69
 Identities = 112/345 (32%), Positives = 181/345 (52%), Gaps = 19/345 (5%)

Query: 11  DLKNRFAEIELRMSESPSV----DAYIKLTEEYAAISPIISKISIYDQKKQEEQDLHTVI 66
             K R  E+   + + P V    +    L +E +++  ++  +    Q  ++   L  + 
Sbjct: 26  AKKERLEEVNAELEQ-PDVWNEPERAQALGKERSSLEAVVDTLDQMKQGLEDVSGLLELA 84

Query: 67  GDHNSDSEIRDLA-QIEVLAIEKEIRELENEINYLLLPKDTDDDKSCILEIRAGTGGSEA 125
            + + +    +   +++ L  +    E         +     D   C L+I+AG+GG+EA
Sbjct: 85  VEADDEETFNEAVAELDALEEKLAQLEFR------RMFSGEYDSADCYLDIQAGSGGTEA 138

Query: 126 ALFVGDLFRMYERYAALRKWKVEVLSSSDNDDGGYKEIVATISGRGVFSRMKFESGVHRV 185
             +   L RMY R+A  R +K E++  S+ +  G K +   ISG   +  ++ E+GVHR+
Sbjct: 139 QDWASMLERMYLRWAESRGFKTEIIEESEGEVAGIKSVTIKISGDYAYGWLRTETGVHRL 198

Query: 186 QRVPATEASGRVHTSAATVAVLPEAAE-IDVDIPLEDIRIDTMRASGSGGQHVNTTDSAV 244
            R    ++ GR HTS ++  V PE  + ID++I   D+RID  RASG+GGQHVN T+SAV
Sbjct: 199 VRKSPFDSGGRRHTSFSSAFVYPEVDDDIDIEINPADLRIDVYRASGAGGQHVNRTESAV 258

Query: 245 RITHIPTGIMVTSS-EKSQHQNRLRAMKVLRARLYDVERKRMANERSA--NRKLQIGSGD 301
           RITHIPTGI+     ++SQH+N+ +AMK ++A+LY+VE ++   E+ A  + K  IG G 
Sbjct: 259 RITHIPTGIVTQCQNDRSQHKNKDQAMKQMKAKLYEVEMQKKNAEKQAMEDNKSDIGWG- 317

Query: 302 RSERIRTYNFSQGRITDHRINLTLYKLEYVLQGYIDDIINPLLTA 346
              +IR+Y     RI D R  +     + VL G +D  I   L A
Sbjct: 318 --SQIRSYVLDDSRIKDLRTGVETRNTQAVLDGSLDQFIEASLKA 360


>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
>d1j26a_ d.50.4.1 (A:) Ict1 protein {Mouse (Mus musculus) [TaxId: 10090]} Length = 112 Back     information, alignment and structure

Homologous Domains in SCOP70 (Version 1.75) Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target357 peptide chain release factor 1 [Candidatus Liberibacter
d1gqea_362 Polypeptide chain release factor 2 (RF2) {Escherichia c 100.0
d2b3tb1344 Peptide chain release factor 1, RF1 {Escherichia coli [ 100.0
d1rq0a_333 Peptide chain release factor 1, RF1 {Thermotoga maritim 100.0
d1j26a_112 Ict1 protein {Mouse (Mus musculus) [TaxId: 10090]} 99.61
d1gqea_362 Polypeptide chain release factor 2 (RF2) {Escherichia c 94.23
>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=0  Score=933.05  Aligned_cols=331  Identities=34%  Similarity=0.549  Sum_probs=307.6

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHH
Q ss_conf             899999999999998538531579---99999999879999999999999999899999997203785356654332223
Q gi|254780874|r    8 QICDLKNRFAEIELRMSESPSVDA---YIKLTEEYAAISPIISKISIYDQKKQEEQDLHTVIGDHNSDSEIRDLAQIEVL   84 (357)
Q Consensus         8 kL~~l~~rl~ELE~~Lsdp~~w~d---~~klsKe~s~L~~iv~~~~~~~~~~~ei~el~eLl~e~e~D~El~elAeeEl~   84 (357)
                      .++.++.|+.+|+.+|++|+||+|   +++++|+++.|+++++.|+.|.+...++.++.+++.+ ++|+++.++++.++.
T Consensus        23 Dld~kk~Rl~ELE~~lsdP~fW~D~~kAqkl~KE~s~L~~iVe~~~~l~~~leDl~eL~Ela~e-e~deel~~e~~~~l~  101 (362)
T d1gqea_          23 DYDAKKERLEEVNAELEQPDVWNEPERAQALGKERSSLEAVVDTLDQMKQGLEDVSGLLELAVE-ADDEETFNEAVAELD  101 (362)
T ss_dssp             THHHHHHHHHHHHHHHHSGGGGGSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HTCHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHCCCHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHH
T ss_conf             9798999999999986397144499999999999999999999999999999988877877641-105888888999999


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCCCCCCCEEE
Q ss_conf             32000577888999864000113554037886226885217889999999999998764984001321135447721113
Q gi|254780874|r   85 AIEKEIRELENEINYLLLPKDTDDDKSCILEIRAGTGGSEAALFVGDLFRMYERYAALRKWKVEVLSSSDNDDGGYKEIV  164 (357)
Q Consensus        85 ~l~~~l~~le~eL~~~LLpsde~D~~nailEI~aGaGG~EA~dwA~~L~rMY~r~ae~~gwk~eii~~~~ge~aGik~v~  164 (357)
                      .+...+++    |+..+||+||+|.+||||||||||||+||||||+||||||+|||+++||+++++++++|++||||+|+
T Consensus       102 ~l~~~l~~----le~~ll~~~~~D~~nailEIrAGaGG~EA~dfA~~L~RMY~r~ae~~gwk~eiid~~~~e~gG~K~v~  177 (362)
T d1gqea_         102 ALEEKLAQ----LEFRRMFSGEYDSADCYLDIQAGSGGTEAQDWASMLERMYLRWAESRGFKTEIIEESEGEVAGIKSVT  177 (362)
T ss_dssp             HHHHHHHH----HGGGGGCCSTTTTSCEEEEEEECSSHHHHHHHHHHHHHHHHHHHHHTTCEEEEEEEEECSSSSEEEEE
T ss_pred             HHHHHHHH----HHHHHCCCCCCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCEEEEECCCCCCCCCEEEEE
T ss_conf             98622467----78752136754545437999825760668899999999999999975985899414567766546999


Q ss_pred             EEEECCCHHHHHHCCCCCEEEEEECCCCCCCCCCEEEEEEEEEECC-CCCCCCCCCCEEEEEEECCCCCCCCCCCCCCCE
Q ss_conf             7775031112100024650267612545678511016888853033-433222454347999852888752000632121
Q gi|254780874|r  165 ATISGRGVFSRMKFESGVHRVQRVPATEASGRVHTSAATVAVLPEA-AEIDVDIPLEDIRIDTMRASGSGGQHVNTTDSA  243 (357)
Q Consensus       165 ~~I~G~~aYg~Lk~E~GvHRvqRip~~es~gR~hTS~a~V~V~P~~-~~~~~~i~~~dl~i~~~rssG~GGQ~vN~t~sa  243 (357)
                      |.|+|+||||+||+|+|||||||||||+++||||||||+|+|+|++ ++++++|+|+||+|||||||||||||||||+||
T Consensus       178 ~~I~G~~ayg~Lk~EsGvHRvqRvp~~es~gr~hTS~a~V~v~P~~~~~~~~~i~~~dl~i~~~rs~g~GGQ~vN~t~sa  257 (362)
T d1gqea_         178 IKISGDYAYGWLRTETGVHRLVRKSPFDSGGRRHTSFSSAFVYPEVDDDIDIEINPADLRIDVYRASGAGGQHVNRTESA  257 (362)
T ss_dssp             EEEESTTHHHHHGGGCEEEEEEEECTTSSSCCEEEEEEEEEEEECCBTTBCCCCCGGGEEEEEECCCCSSCCSTTSSCCE
T ss_pred             EEEECCCHHHHHHHHCCCEEEEEECCCCCCCEEEEEEEEEEEEECCCCCCCEECCHHHEEEEEEECCCCCCCCHHHHHCE
T ss_conf             99977668899987237504888404677734799877889962478763111176782799752699886512033141


Q ss_pred             EEEEECCCCEEE-EECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHCCCCCCCCCEEECCCCCCCEEEEE
Q ss_conf             588964984488-8436541358999999999999999999999999874--4652246742382210448998112432
Q gi|254780874|r  244 VRITHIPTGIMV-TSSEKSQHQNRLRAMKVLRARLYDVERKRMANERSAN--RKLQIGSGDRSERIRTYNFSQGRITDHR  320 (357)
Q Consensus       244 vri~H~ptgi~v-~~~eRsQ~~Nk~~A~~~L~~~l~~~~~~~~~~~~~~~--r~~~~g~~~rs~~iRtY~~~~~rv~DhR  320 (357)
                      |||||+||||+| ||+|||||+||++||++|++|||+++.+++.++....  ++.++|   ||+||||||||||||||||
T Consensus       258 vri~H~ptgi~v~~q~ersq~~Nk~~A~~~L~~~l~~~~~~~~~~~~~~~~~~~~~~~---~g~~iRtY~~~~~rv~DhR  334 (362)
T d1gqea_         258 VRITHIPTGIVTQCQNDRSQHKNKDQAMKQMKAKLYEVEMQKKNAEKQAMEDNKSDIG---WGSQIRSYVLDDSRIKDLR  334 (362)
T ss_dssp             EEEEETTTCCEEEECSSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSTTCCCCC---SCSEEEEEEGGGTEEEETT
T ss_pred             EEEEECCCHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC---CCCCCCCCCCCCCCCCCCC
T ss_conf             6887447336777642210147899999999999999999999999998874231275---7698467658998150005


Q ss_pred             CCCEECCHHHHHCCCHHHHHHHHHHH
Q ss_conf             16441787787288669999999999
Q gi|254780874|r  321 INLTLYKLEYVLQGYIDDIINPLLTA  346 (357)
Q Consensus       321 ~~~~~~~~~~~l~G~l~~~i~~~~~~  346 (357)
                      ||++++|+++||+|+||+||++|++.
T Consensus       335 ~~~~~~~~~~vl~G~ld~~i~a~l~~  360 (362)
T d1gqea_         335 TGVETRNTQAVLDGSLDQFIEASLKA  360 (362)
T ss_dssp             TCCEESCHHHHHTTCCHHHHHHHHHT
T ss_pred             CCCEECCHHHHHCCCHHHHHHHHHHC
T ss_conf             39725784687588779999999877



>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
>d1gqea_ e.38.1.1 (A:) Polypeptide chain release factor 2 (RF2) {Escherichia coli [TaxId: 562]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 357 peptide chain release factor 1 [Candidatus Liberib
2b3t_B_84-214_295-336173 (B:84-214,B:295-336) RF-1, peptide chain release f 3e-40
1zbt_A_117-228_312-349150 (A:117-228,A:312-349) RF-1, peptide chain release 2e-36
2ihr_1_111-220_304-365172 (1:111-220,1:304-365) Peptide chain release factor 5e-35
3d5a_X_100-210_297-331146 (X:100-210,X:297-331) RF1, peptide chain release f 8e-35
1gqe_A_121-231_315-365162 (A:121-231,A:315-365) Release factor 2, RF2; prote 1e-34
1rq0_A_84-191_274-312147 (A:84-191,A:274-312) RF-1, peptide chain release f 3e-33
2b3t_B_84-214_295-336173 (B:84-214,B:295-336) RF-1, peptide chain release f 2e-16
1zbt_A_117-228_312-349150 (A:117-228,A:312-349) RF-1, peptide chain release 2e-15
2ihr_1_111-220_304-365172 (1:111-220,1:304-365) Peptide chain release factor 3e-15
3d5a_X_100-210_297-331146 (X:100-210,X:297-331) RF1, peptide chain release f 8e-13
1gqe_A_121-231_315-365162 (A:121-231,A:315-365) Release factor 2, RF2; prote 5e-13
1rq0_A_84-191_274-312147 (A:84-191,A:274-312) RF-1, peptide chain release f 6e-15
2jy9_A_148 (A:) Putative tRNA hydrolase domain; GFT protein s 2e-23
3d5a_X_211-29686 (X:211-296) RF1, peptide chain release factor 1; r 3e-23
1zbt_A_229-31183 (A:229-311) RF-1, peptide chain release factor 1; 5e-22
2ihr_1_221-30383 (1:221-303) Peptide chain release factor 2; mixed 1e-21
1rq0_A_192-27382 (A:192-273) RF-1, peptide chain release factor 1; 1e-21
2b3t_B_215-29480 (B:215-294) RF-1, peptide chain release factor 1; 3e-21
1gqe_A_232-31483 (A:232-314) Release factor 2, RF2; protein synthes 9e-21
1j26_A_112 (A:) Immature colon carcinoma transcript 1; peptid 5e-21
2jva_A_14-10895 (A:14-108) Peptidyl-tRNA hydrolase domain protein; 2e-16
1zbt_A_1-116116 (A:1-116) RF-1, peptide chain release factor 1; pe 5e-11
3d5a_X_1-99_332-354122 (X:1-99,X:332-354) RF1, peptide chain release fact 4e-10
1gqe_A_1-120120 (A:1-120) Release factor 2, RF2; protein synthesis 7e-06
2ihr_1_1-110110 (1:1-110) Peptide chain release factor 2; mixed al 1e-05
>2b3t_B (B:84-214,B:295-336) RF-1, peptide chain release factor 1; translation termination, methylation, conformational changes; HET: SAH; 3.10A {Escherichia coli}Length = 173 Back     alignment and structure
 Score =  160 bits (406), Expect = 3e-40
 Identities = 79/130 (60%), Positives = 105/130 (80%)

Query: 86  IEKEIRELENEINYLLLPKDTDDDKSCILEIRAGTGGSEAALFVGDLFRMYERYAALRKW 145
            +++  +LE ++  LLLPKD DD+++  LE+RAGTGG EAALF GDLFRMY RYA  R+W
Sbjct: 2   AKEKSEQLEQQLQVLLLPKDPDDERNAFLEVRAGTGGDEAALFAGDLFRMYSRYAEARRW 61

Query: 146 KVEVLSSSDNDDGGYKEIVATISGRGVFSRMKFESGVHRVQRVPATEASGRVHTSAATVA 205
           +VE++S+S+ + GGYKEI+A ISG GV+ R+KFESG HRVQRVPATE+ GR+HTSA TVA
Sbjct: 62  RVEIMSASEGEHGGYKEIIAKISGDGVYGRLKFESGGHRVQRVPATESQGRIHTSACTVA 121

Query: 206 VLPEAAEIDV 215
           V+PE  + ++
Sbjct: 122 VMPELPDAEL 131


>1zbt_A (A:117-228,A:312-349) RF-1, peptide chain release factor 1; peptide chain release factor 1 (RF-1), structural genomics, joint center for structural genomics, JCSG; 2.34A {Streptococcus mutans}Length = 150 Back     alignment and structure
>2ihr_1 (1:111-220,1:304-365) Peptide chain release factor 2; mixed alpha-beta, translation; 2.50A {Thermus thermophilus} PDB: 2b9m_Y* 3f1e_X 3f1g_X 2jl5_Y 2jl7_Y 2wh1_Y 2wh3_YLength = 172 Back     alignment and structure
>3d5a_X (X:100-210,X:297-331) RF1, peptide chain release factor 1; ribosome, coiled coil, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding; 3.21A {Thermus thermophilus HB27} PDB: 2b64_Y 3d5c_XLength = 146 Back     alignment and structure
>1gqe_A (A:121-231,A:315-365) Release factor 2, RF2; protein synthesis, ribosome, macromolecular mimicry, translation; 1.81A {Escherichia coli}Length = 162 Back     alignment and structure
>1rq0_A (A:84-191,A:274-312) 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}Length = 147 Back     alignment and structure
>2b3t_B (B:84-214,B:295-336) RF-1, peptide chain release factor 1; translation termination, methylation, conformational changes; HET: SAH; 3.10A {Escherichia coli}Length = 173 Back     alignment and structure
>1zbt_A (A:117-228,A:312-349) RF-1, peptide chain release factor 1; peptide chain release factor 1 (RF-1), structural genomics, joint center for structural genomics, JCSG; 2.34A {Streptococcus mutans}Length = 150 Back     alignment and structure
>2ihr_1 (1:111-220,1:304-365) Peptide chain release factor 2; mixed alpha-beta, translation; 2.50A {Thermus thermophilus} PDB: 2b9m_Y* 3f1e_X 3f1g_X 2jl5_Y 2jl7_Y 2wh1_Y 2wh3_YLength = 172 Back     alignment and structure
>3d5a_X (X:100-210,X:297-331) RF1, peptide chain release factor 1; ribosome, coiled coil, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding; 3.21A {Thermus thermophilus HB27} PDB: 2b64_Y 3d5c_XLength = 146 Back     alignment and structure
>1gqe_A (A:121-231,A:315-365) Release factor 2, RF2; protein synthesis, ribosome, macromolecular mimicry, translation; 1.81A {Escherichia coli}Length = 162 Back     alignment and structure
>1rq0_A (A:84-191,A:274-312) 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}Length = 147 Back     alignment and structure
>2jy9_A (A:) Putative tRNA hydrolase domain; GFT protein structure, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium LT2}Length = 148 Back     alignment and structure
>3d5a_X (X:211-296) RF1, peptide chain release factor 1; ribosome, coiled coil, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding; 3.21A {Thermus thermophilus HB27} PDB: 2b64_Y 3d5c_XLength = 86 Back     alignment and structure
>1zbt_A (A:229-311) RF-1, peptide chain release factor 1; peptide chain release factor 1 (RF-1), structural genomics, joint center for structural genomics, JCSG; 2.34A {Streptococcus mutans}Length = 83 Back     alignment and structure
>2ihr_1 (1:221-303) Peptide chain release factor 2; mixed alpha-beta, translation; 2.50A {Thermus thermophilus} PDB: 2b9m_Y* 3f1e_X 3f1g_X 2jl5_Y 2jl7_Y 2wh1_Y 2wh3_YLength = 83 Back     alignment and structure
>1rq0_A (A:192-273) 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}Length = 82 Back     alignment and structure
>2b3t_B (B:215-294) RF-1, peptide chain release factor 1; translation termination, methylation, conformational changes; HET: SAH; 3.10A {Escherichia coli}Length = 80 Back     alignment and structure
>1gqe_A (A:232-314) Release factor 2, RF2; protein synthesis, ribosome, macromolecular mimicry, translation; 1.81A {Escherichia coli}Length = 83 Back     alignment and structure
>1j26_A (A:) Immature colon carcinoma transcript 1; peptide chain release factors, RF-1, the GGQ motif, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus}Length = 112 Back     alignment and structure
>2jva_A (A:14-108) Peptidyl-tRNA hydrolase domain protein; GFT hydrolase, structural genomics, PSI-2, protein structure initiative; NMR {Pseudomonas syringae PV}Length = 95 Back     alignment and structure
>1zbt_A (A:1-116) RF-1, peptide chain release factor 1; peptide chain release factor 1 (RF-1), structural genomics, joint center for structural genomics, JCSG; 2.34A {Streptococcus mutans}Length = 116 Back     alignment and structure
>3d5a_X (X:1-99,X:332-354) RF1, peptide chain release factor 1; ribosome, coiled coil, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding; 3.21A {Thermus thermophilus HB27} PDB: 2b64_Y 3d5c_XLength = 122 Back     alignment and structure
>1gqe_A (A:1-120) Release factor 2, RF2; protein synthesis, ribosome, macromolecular mimicry, translation; 1.81A {Escherichia coli}Length = 120 Back     alignment and structure
>2ihr_1 (1:1-110) Peptide chain release factor 2; mixed alpha-beta, translation; 2.50A {Thermus thermophilus} PDB: 2b9m_Y* 3f1e_X 3f1g_X 2jl5_Y 2jl7_Y 2wh1_Y 2wh3_YLength = 110 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target357 peptide chain release factor 1 [Candidatus Liberibacter
2b3t_B_84-214_295-336173 RF-1, peptide chain release factor 1; translation 100.0
1zbt_A_117-228_312-349150 RF-1, peptide chain release factor 1; peptide chai 100.0
2ihr_1_111-220_304-365172 Peptide chain release factor 2; mixed alpha-beta, 100.0
1gqe_A_121-231_315-365162 Release factor 2, RF2; protein synthesis, ribosome 100.0
1rq0_A_84-191_274-312147 RF-1, peptide chain release factor 1; X-RAY, cryst 100.0
2jy9_A_148 Putative tRNA hydrolase domain; GFT protein struct 99.95
3d5a_X_211-29686 RF1, peptide chain release factor 1; ribosome, coi 99.93
1zbt_A_229-31183 RF-1, peptide chain release factor 1; peptide chai 99.93
2ihr_1_221-30383 Peptide chain release factor 2; mixed alpha-beta, 99.93
1gqe_A_232-31483 Release factor 2, RF2; protein synthesis, ribosome 99.93
1rq0_A_192-27382 RF-1, peptide chain release factor 1; X-RAY, cryst 99.92
2b3t_B_215-29480 RF-1, peptide chain release factor 1; translation 99.91
1j26_A_112 Immature colon carcinoma transcript 1; peptide cha 99.85
2jva_A_14-10895 Peptidyl-tRNA hydrolase domain protein; GFT hydrol 99.8
3d5a_X_1-99_332-354122 RF1, peptide chain release factor 1; ribosome, coi 99.25
1zbt_A_1-116116 RF-1, peptide chain release factor 1; peptide chai 99.24
1gqe_A_1-120120 Release factor 2, RF2; protein synthesis, ribosome 99.03
2ihr_1_1-110110 Peptide chain release factor 2; mixed alpha-beta, 98.7
1rq0_A_1-83_313-342113 RF-1, peptide chain release factor 1; X-RAY, cryst 91.8
>2b3t_B (B:84-214,B:295-336) RF-1, peptide chain release factor 1; translation termination, methylation, conformational changes; HET: SAH; 3.10A {Escherichia coli} Back     alignment and structure
Probab=100.00  E-value=0  Score=508.46  Aligned_cols=172  Identities=62%  Similarity=1.074  Sum_probs=166.1

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCCCCCCCEEEE
Q ss_conf             20005778889998640001135540378862268852178899999999999987649840013211354477211137
Q gi|254780874|r   86 IEKEIRELENEINYLLLPKDTDDDKSCILEIRAGTGGSEAALFVGDLFRMYERYAALRKWKVEVLSSSDNDDGGYKEIVA  165 (357)
Q Consensus        86 l~~~l~~le~eL~~~LLpsde~D~~nailEI~aGaGG~EA~dwA~~L~rMY~r~ae~~gwk~eii~~~~ge~aGik~v~~  165 (357)
                      ++.+++.++++|+.+|+|++|+|.+||+|||+||+||+||||||+||||||.+||+++||++++++.++++.||||+|++
T Consensus         2 ~~~~~~~l~~~l~~~ll~~~~~D~~~a~leI~aG~GG~EA~~fa~~L~~MY~~~a~~~g~k~ev~~~~~~~~~G~k~~~~   81 (173)
T 2b3t_B            2 AKEKSEQLEQQLQVLLLPKDPDDERNAFLEVRAGTGGDEAALFAGDLFRMYSRYAEARRWRVEIMSASEGEHGGYKEIIA   81 (173)
T ss_dssp             ----------CCCCCCCSCCSGGGSCEEEEEEECSSSHHHHHHHHHHHHHHHHHHHHTTCCCCEEEEEECTTSSEEEEEE
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCCCCCCCEEEEEE
T ss_conf             66545589999999862344355455489996267767899999999999999998749851002225656777148999


Q ss_pred             EEECCCHHHHHHCCCCCEEEEEECCCCCCCCCCEEEEEEEEEECCCCCCCCCCCCEEEEEEECCCCCCCCCCCCCCCEEE
Q ss_conf             77503111210002465026761254567851101688885303343322245434799985288875200063212158
Q gi|254780874|r  166 TISGRGVFSRMKFESGVHRVQRVPATEASGRVHTSAATVAVLPEAAEIDVDIPLEDIRIDTMRASGSGGQHVNTTDSAVR  245 (357)
Q Consensus       166 ~I~G~~aYg~Lk~E~GvHRvqRip~~es~gR~hTS~a~V~V~P~~~~~~~~i~~~dl~i~~~rssG~GGQ~vN~t~savr  245 (357)
                      .|+|++|||+||+|+|||||||||||+++||+|||||+|+|+|+++|+++                              
T Consensus        82 ~I~G~~aY~~Lk~E~GvHRvqRvp~te~~gR~hTStasV~VlP~~~d~~~------------------------------  131 (173)
T 2b3t_B           82 KISGDGVYGRLKFESGGHRVQRVPATESQGRIHTSACTVAVMPELPDAEL------------------------------  131 (173)
T ss_dssp             EECSSSCHHHHGGGCEEEEEEECCTTCSSCCCEEEEEEEECCBCCCTTTC------------------------------
T ss_pred             EEECCCCCCEEEEEECCEEEEEECCCCCCCCCCEEEEEEEECCCCCCCCC------------------------------
T ss_conf             99767744234664123389972476434530202456621001332123------------------------------


Q ss_pred             EEECCCCEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEECCCCCCCEEEEECCCEE
Q ss_conf             89649844888436541358999999999999999999999999874465224674238221044899811243216441
Q gi|254780874|r  246 ITHIPTGIMVTSSEKSQHQNRLRAMKVLRARLYDVERKRMANERSANRKLQIGSGDRSERIRTYNFSQGRITDHRINLTL  325 (357)
Q Consensus       246 i~H~ptgi~v~~~eRsQ~~Nk~~A~~~L~~~l~~~~~~~~~~~~~~~r~~~~g~~~rs~~iRtY~~~~~rv~DhR~~~~~  325 (357)
                                                                      |+||||||||||||||||||+||||||+|+++
T Consensus       132 ------------------------------------------------k~qvgs~dRsekIRTYNf~q~rvtDHRi~~~~  163 (173)
T 2b3t_B          132 ------------------------------------------------RNLLGSGDRSDRNRTYNFPQGRVTDHRINLTL  163 (173)
T ss_dssp             ------------------------------------------------CC-------CCEEEEEETTTTEEEEGGGTEEE
T ss_pred             ------------------------------------------------HHHCCCCCCCCCEEEEECCCCCCCEECCCCEE
T ss_conf             ------------------------------------------------60041001438547661698862100458867


Q ss_pred             CCHHHHHCCC
Q ss_conf             7877872886
Q gi|254780874|r  326 YKLEYVLQGY  335 (357)
Q Consensus       326 ~~~~~~l~G~  335 (357)
                      ++|+.||+|+
T Consensus       164 ~~l~~~l~Ge  173 (173)
T 2b3t_B          164 YRLDEVMEGK  173 (173)
T ss_dssp             SCHHHHHHTC
T ss_pred             CCHHHHHCCC
T ss_conf             7844764987



>1zbt_A (A:117-228,A:312-349) RF-1, peptide chain release factor 1; peptide chain release factor 1 (RF-1), structural genomics, joint center for structural genomics, JCSG; 2.34A {Streptococcus mutans} Back     alignment and structure
>2ihr_1 (1:111-220,1:304-365) Peptide chain release factor 2; mixed alpha-beta, translation; 2.50A {Thermus thermophilus} PDB: 2b9m_Y* 3f1e_X 3f1g_X 2jl5_Y 2jl7_Y 2wh1_Y 2wh3_Y Back     alignment and structure
>1gqe_A (A:121-231,A:315-365) Release factor 2, RF2; protein synthesis, ribosome, macromolecular mimicry, translation; 1.81A {Escherichia coli} Back     alignment and structure
>1rq0_A (A:84-191,A:274-312) 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} Back     alignment and structure
>2jy9_A (A:) Putative tRNA hydrolase domain; GFT protein structure, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium LT2} Back     alignment and structure
>3d5a_X (X:211-296) RF1, peptide chain release factor 1; ribosome, coiled coil, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding; 3.21A {Thermus thermophilus HB27} PDB: 2b64_Y 3d5c_X Back     alignment and structure
>1zbt_A (A:229-311) RF-1, peptide chain release factor 1; peptide chain release factor 1 (RF-1), structural genomics, joint center for structural genomics, JCSG; 2.34A {Streptococcus mutans} Back     alignment and structure
>2ihr_1 (1:221-303) Peptide chain release factor 2; mixed alpha-beta, translation; 2.50A {Thermus thermophilus} PDB: 2b9m_Y* 3f1e_X 3f1g_X 2jl5_Y 2jl7_Y 2wh1_Y 2wh3_Y Back     alignment and structure
>1gqe_A (A:232-314) Release factor 2, RF2; protein synthesis, ribosome, macromolecular mimicry, translation; 1.81A {Escherichia coli} Back     alignment and structure
>1rq0_A (A:192-273) 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} Back     alignment and structure
>2b3t_B (B:215-294) RF-1, peptide chain release factor 1; translation termination, methylation, conformational changes; HET: SAH; 3.10A {Escherichia coli} Back     alignment and structure
>1j26_A (A:) Immature colon carcinoma transcript 1; peptide chain release factors, RF-1, the GGQ motif, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} Back     alignment and structure
>2jva_A (A:14-108) Peptidyl-tRNA hydrolase domain protein; GFT hydrolase, structural genomics, PSI-2, protein structure initiative; NMR {Pseudomonas syringae PV} Back     alignment and structure
>3d5a_X (X:1-99,X:332-354) RF1, peptide chain release factor 1; ribosome, coiled coil, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding; 3.21A {Thermus thermophilus HB27} PDB: 2b64_Y 3d5c_X Back     alignment and structure
>1zbt_A (A:1-116) RF-1, peptide chain release factor 1; peptide chain release factor 1 (RF-1), structural genomics, joint center for structural genomics, JCSG; 2.34A {Streptococcus mutans} Back     alignment and structure
>1gqe_A (A:1-120) Release factor 2, RF2; protein synthesis, ribosome, macromolecular mimicry, translation; 1.81A {Escherichia coli} Back     alignment and structure
>2ihr_1 (1:1-110) Peptide chain release factor 2; mixed alpha-beta, translation; 2.50A {Thermus thermophilus} PDB: 2b9m_Y* 3f1e_X 3f1g_X 2jl5_Y 2jl7_Y 2wh1_Y 2wh3_Y Back     alignment and structure
>1rq0_A (A:1-83,A:313-342) 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} Back     alignment and structure