Psyllid ID: psy2490

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60----
Protein Sequence
MSIFRRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTDS
Secondary Structure (PSIPRED)
ccccEEEcccccEEEEEccccccccccccccccEEEEEEEcccccccccccccEEEEEEccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHcccccHHcccccccccccccccHHHHHHHHcccccccccEEcccccEEEEEEccccc
Coil and Loop (DISEMBL)
MSIFRRHLSLASSLFrkydldyskvpkidekdiqerfvrgsgpggqavaktnncvvlthiptds
Flexible Loop (DISEMBL)
msifrrhlslasslfrkydldyskvpkidekdiQERFVRgsgpggqavaktnncvvlthiptds
Low Complexity Region (SEG)
MSIFRRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTDS
Disordered region (IsUnstruct)
*******LSLASSLFRKYDLDYSKVPKID*******FV********AVAKTNNCVVLTH*****
Disordered Region (DISOPRED)
***FRRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIP***
Disordered Region (DISEMBL)
MSIFRRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTDS
Disordered Region (DISPRO)
****RRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIP***
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiii
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSIFRRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTDS
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	64	2.2.26 [Sep-21-2011]
A5WUX7	156	Probable peptide chain re	yes	N/A	0.687	0.282	0.553	9e-10
Q9H3J6	166	Probable peptide chain re	yes	N/A	0.656	0.253	0.571	5e-09
Q80VP5	184	Probable peptide chain re	no	N/A	0.656	0.228	0.523	3e-08
A7I0P7	364	Peptide chain release fac	yes	N/A	0.906	0.159	0.474	5e-06
Q2GKS8	359	Peptide chain release fac	yes	N/A	0.562	0.100	0.583	3e-05
A0RQM7	369	Peptide chain release fac	yes	N/A	0.890	0.154	0.448	3e-05
Q5PAH2	359	Peptide chain release fac	yes	N/A	0.562	0.100	0.583	4e-05
B9KIV2	359	Peptide chain release fac	yes	N/A	0.562	0.100	0.583	4e-05
Q2GGM5	359	Peptide chain release fac	yes	N/A	0.562	0.100	0.555	8e-05
Q5HB80	359	Peptide chain release fac	yes	N/A	0.562	0.100	0.555	9e-05

>sp|A5WUX7|CL065_DANRE Probable peptide chain release factor C12orf65 homolog, mitochondrial OS=Danio rerio GN=si:ch211-275j6.5 PE=3 SV=1

 Score = 62.0 bits (149), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 26/47 (55%), Positives = 38/47 (80%), Gaps = 3/47 (6%)

Query: 16 RKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
          +KY ++   +P + E++++E+FVRGSGPGGQA  KT+NCVVL HIP+
Sbjct: 33 KKYQIE---LPVVHEEELEEQFVRGSGPGGQATNKTSNCVVLRHIPS 76

May act as a codon-independent translation release factor that has lost all stop codon specificity and directs the termination of translation in mitochondrion.
Danio rerio (taxid: 7955)

>sp|Q9H3J6|CL065_HUMAN Probable peptide chain release factor C12orf65, mitochondrial OS=Homo sapiens GN=C12orf65 PE=2 SV=1

 Score = 59.7 bits (143), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 24/42 (57%), Positives = 33/42 (78%)

Query: 21 DYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
          DY  +  +DE +++E+FV+G GPGGQA  KT+NCVVL HIP+
Sbjct: 48 DYPALLSLDENELEEQFVKGHGPGGQATNKTSNCVVLKHIPS 89

May act as a codon-independent translation release factor that has lost all stop codon specificity and directs the termination of translation in mitochondrion.

Homo sapiens (taxid: 9606)

>sp|Q80VP5|CL065_MOUSE Probable peptide chain release factor C12orf65 homolog, mitochondrial OS=Mus musculus PE=1 SV=1

 Score = 57.0 bits (136), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 22/42 (52%), Positives = 33/42 (78%)

Query: 21 DYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
          DY  +  ++E +++E+FV+G GPGGQA  KT+NCVVL H+P+
Sbjct: 51 DYPALLPLNESELEEQFVKGHGPGGQATNKTSNCVVLKHVPS 92

May act as a codon-independent translation release factor that has lost all stop codon specificity and directs the termination of translation in mitochondrion.

Mus musculus (taxid: 10090)

>sp|A7I0P7|RF2_CAMHC Peptide chain release factor 2 OS=Campylobacter hominis (strain ATCC BAA-381 / LMG 19568 / NCTC 13146 / CH001A) GN=prfB PE=3 SV=1

 Score = 50.1 bits (118), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 28/59 (47%), Positives = 36/59 (61%), Gaps = 1/59 (1%)

Query: 5   RRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTD 63
           RRH S AS +    +LD      IDEKD++  + R SG GGQ V KT + V +THIPT+
Sbjct: 211 RRHTSFASVVVSP-ELDDDIQINIDEKDLRIDYYRSSGAGGQHVNKTESAVRITHIPTN 268

Peptide chain release factor 2 directs the termination of translation in response to the peptide chain termination codons UGA and UAA.

Campylobacter hominis (strain ATCC BAA-381 / LMG 19568 / NCTC 13146 / CH001A) (taxid: 360107)

>sp|Q2GKS8|RF1_ANAPZ Peptide chain release factor 1 OS=Anaplasma phagocytophilum (strain HZ) GN=prfA PE=3 SV=1

 Score = 47.0 bits (110), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 21/36 (58%), Positives = 27/36 (75%)

Query: 27  KIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
           KIDEKD++    R SGPGGQ+V  T++ V +THIPT
Sbjct: 216 KIDEKDLRIDVYRSSGPGGQSVNTTDSAVRITHIPT 251

Peptide chain release factor 1 directs the termination of translation in response to the peptide chain termination codons UAG and UAA.

Anaplasma phagocytophilum (strain HZ) (taxid: 212042)

>sp|A0RQM7|RF2_CAMFF Peptide chain release factor 2 OS=Campylobacter fetus subsp. fetus (strain 82-40) GN=prfB PE=3 SV=1

 Score = 47.0 bits (110), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 26/58 (44%), Positives = 36/58 (62%), Gaps = 1/58 (1%)

Query: 5   RRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
           RRH S  SS+    ++D     +I+EKD++  + R SG GGQ V KT + V +THIPT
Sbjct: 211 RRHTSF-SSVMVSPEVDDDIAIEIEEKDLRLDYYRASGAGGQHVNKTESAVRITHIPT 267

Peptide chain release factor 2 directs the termination of translation in response to the peptide chain termination codons UGA and UAA.

Campylobacter fetus subsp. fetus (strain 82-40) (taxid: 360106)

>sp|Q5PAH2|RF1_ANAMM Peptide chain release factor 1 OS=Anaplasma marginale (strain St. Maries) GN=prfA PE=3 SV=1

 Score = 47.0 bits (110), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/36 (58%), Positives = 27/36 (75%)

Query: 27  KIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
           KIDEKD++    R SGPGGQ+V  T++ V +THIPT
Sbjct: 216 KIDEKDLRIDVYRSSGPGGQSVNTTDSAVRITHIPT 251

Peptide chain release factor 1 directs the termination of translation in response to the peptide chain termination codons UAG and UAA.

Anaplasma marginale (strain St. Maries) (taxid: 234826)

>sp|B9KIV2|RF1_ANAMF Peptide chain release factor 1 OS=Anaplasma marginale (strain Florida) GN=prfA PE=3 SV=1

 Score = 47.0 bits (110), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/36 (58%), Positives = 27/36 (75%)

Query: 27  KIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
           KIDEKD++    R SGPGGQ+V  T++ V +THIPT
Sbjct: 216 KIDEKDLRIDVYRSSGPGGQSVNTTDSAVRITHIPT 251

Peptide chain release factor 1 directs the termination of translation in response to the peptide chain termination codons UAG and UAA.

Anaplasma marginale (strain Florida) (taxid: 320483)

>sp|Q2GGM5|RF1_EHRCR Peptide chain release factor 1 OS=Ehrlichia chaffeensis (strain Arkansas) GN=prfA PE=3 SV=1

 Score = 45.8 bits (107), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 20/36 (55%), Positives = 27/36 (75%)

Query: 27  KIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
           KIDEKD++    R SGPGGQ+V  T++ V +THIP+
Sbjct: 216 KIDEKDLRIDVYRSSGPGGQSVNTTDSAVRITHIPS 251

Peptide chain release factor 1 directs the termination of translation in response to the peptide chain termination codons UAG and UAA.

Ehrlichia chaffeensis (strain Arkansas) (taxid: 205920)

>sp|Q5HB80|RF1_EHRRW Peptide chain release factor 1 OS=Ehrlichia ruminantium (strain Welgevonden) GN=prfA PE=3 SV=1

 Score = 45.8 bits (107), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 20/36 (55%), Positives = 27/36 (75%)

Query: 27  KIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
           KIDEKD++    R SGPGGQ+V  T++ V +THIP+
Sbjct: 216 KIDEKDLRIDVYRSSGPGGQSVNTTDSAVRITHIPS 251

Peptide chain release factor 1 directs the termination of translation in response to the peptide chain termination codons UAG and UAA.

Ehrlichia ruminantium (strain Welgevonden) (taxid: 254945)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	64
357624655	143	hypothetical protein KGM_09231 [Danaus p	0.718	0.321	0.717	2e-12
307170845	138	Uncharacterized protein C12orf65-like pr	0.718	0.333	0.695	9e-12
332030644	163	Uncharacterized protein C12orf65-like pr	0.734	0.288	0.666	1e-11
195334889	146	GM21684 [Drosophila sechellia] gi|194126	0.984	0.431	0.531	2e-11
195488245	146	GE11778 [Drosophila yakuba] gi|194178334	0.906	0.397	0.576	2e-11
24654113	146	CG30100 [Drosophila melanogaster] gi|216	0.906	0.397	0.576	3e-11
198456857	181	GA15649 [Drosophila pseudoobscura pseudo	0.703	0.248	0.644	3e-11
195121186	141	GI19248 [Drosophila mojavensis] gi|19391	0.843	0.382	0.596	3e-11
195150095	181	GL10726 [Drosophila persimilis] gi|19410	0.703	0.248	0.644	3e-11
194882555	148	GG20592 [Drosophila erecta] gi|190658563	0.906	0.391	0.576	3e-11

>gi|357624655|gb|EHJ75351.1| hypothetical protein KGM_09231 [Danaus plexippus]

 Score = 76.6 bits (187), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 33/46 (71%), Positives = 40/46 (86%)

Query: 17 KYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
          K+ +D+SKVPKI+E D+ E+FVRGSGPGG AV K +NCVVLTHIPT
Sbjct: 25 KHTIDFSKVPKINECDLTEQFVRGSGPGGSAVNKNSNCVVLTHIPT 70

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307170845|gb|EFN62956.1| Uncharacterized protein C12orf65-like protein [Camponotus floridanus]

 Score = 74.3 bits (181), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 32/46 (69%), Positives = 37/46 (80%)

Query: 17 KYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
          K  LDYSKVPK+DE D++E+F+RGSGPGGQA  KTNN V L H PT
Sbjct: 20 KRHLDYSKVPKLDEADLEEKFIRGSGPGGQATNKTNNAVSLKHKPT 65

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332030644|gb|EGI70332.1| Uncharacterized protein C12orf65-like protein [Acromyrmex echinatior]

 Score = 73.9 bits (180), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 32/48 (66%), Positives = 40/48 (83%), Gaps = 1/48 (2%)

Query: 15 FRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
          F++Y LDYS VPK+DE D++E+F+RGSGPGGQA  KTNN V+L H PT
Sbjct: 44 FKRY-LDYSNVPKLDEIDLEEQFIRGSGPGGQATNKTNNAVLLKHKPT 90

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195334889|ref|XP_002034109.1| GM21684 [Drosophila sechellia] gi|194126079|gb|EDW48122.1| GM21684 [Drosophila sechellia]

 Score = 73.2 bits (178), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 34/64 (53%), Positives = 45/64 (70%), Gaps = 1/64 (1%)

Query: 1  MSIFRRHLSLASSLFR-KYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTH 59
          + +  R L+L     R K +LDYS+ P + E DI+E F+RGSGPGGQAV KT+NCV L H
Sbjct: 2  LRVLVRFLALPPPAVRCKSNLDYSRFPALQESDIEETFMRGSGPGGQAVNKTSNCVFLRH 61

Query: 60 IPTD 63
          +PT+
Sbjct: 62 LPTN 65

Source: Drosophila sechellia

Species: Drosophila sechellia

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195488245|ref|XP_002092233.1| GE11778 [Drosophila yakuba] gi|194178334|gb|EDW91945.1| GE11778 [Drosophila yakuba]

 Score = 72.8 bits (177), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 34/59 (57%), Positives = 43/59 (72%), Gaps = 1/59 (1%)

Query: 6  RHLSLASSLFR-KYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTD 63
          R L+L     R K +LDYS+ P + E DI+E F+RGSGPGGQAV KT+NCV L H+PT+
Sbjct: 7  RFLALPQPAVRCKSNLDYSRFPALQESDIEETFMRGSGPGGQAVNKTSNCVFLRHLPTN 65

Source: Drosophila yakuba

Species: Drosophila yakuba

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|24654113|ref|NP_725560.1| CG30100 [Drosophila melanogaster] gi|21627121|gb|AAM68513.1| CG30100 [Drosophila melanogaster] gi|157816290|gb|ABV82139.1| AT22563p2 [Drosophila melanogaster]

 Score = 72.8 bits (177), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 34/59 (57%), Positives = 44/59 (74%), Gaps = 1/59 (1%)

Query: 6  RHLSLASSLFR-KYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTD 63
          R L+L  +  R K +LDYS+ P + E DI+E F+RGSGPGGQAV KT+NCV L H+PT+
Sbjct: 7  RFLALPPTAVRCKSNLDYSRFPVLQESDIEETFMRGSGPGGQAVNKTSNCVFLRHLPTN 65

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|198456857|ref|XP_001360468.2| GA15649 [Drosophila pseudoobscura pseudoobscura] gi|198135777|gb|EAL25043.2| GA15649 [Drosophila pseudoobscura pseudoobscura]

 Score = 72.8 bits (177), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 29/45 (64%), Positives = 38/45 (84%)

Query: 19  DLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTD 63
           +LDYS+ PK+ E +I+E F+RGSGPGGQAV KT+NCV L H+PT+
Sbjct: 60  NLDYSRYPKLQESEIEETFMRGSGPGGQAVNKTSNCVFLRHLPTN 104

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195121186|ref|XP_002005101.1| GI19248 [Drosophila mojavensis] gi|193910169|gb|EDW09036.1| GI19248 [Drosophila mojavensis]

 Score = 72.8 bits (177), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 34/57 (59%), Positives = 41/57 (71%), Gaps = 3/57 (5%)

Query: 9  SLASSLFR---KYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
          SL+S+L R      LDYS+ P + E DI+E  +RGSGPGGQAV KTNNCV L H+PT
Sbjct: 10 SLSSNLCRLASNAHLDYSRYPTLQESDIEETLMRGSGPGGQAVNKTNNCVFLRHLPT 66

Source: Drosophila mojavensis

Species: Drosophila mojavensis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195150095|ref|XP_002015990.1| GL10726 [Drosophila persimilis] gi|194109837|gb|EDW31880.1| GL10726 [Drosophila persimilis]

 Score = 72.4 bits (176), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 29/45 (64%), Positives = 38/45 (84%)

Query: 19  DLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTD 63
           +LDYS+ PK+ E +I+E F+RGSGPGGQAV KT+NCV L H+PT+
Sbjct: 60  NLDYSRYPKLQESEIEETFMRGSGPGGQAVNKTSNCVFLRHLPTN 104

Source: Drosophila persimilis

Species: Drosophila persimilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194882555|ref|XP_001975376.1| GG20592 [Drosophila erecta] gi|190658563|gb|EDV55776.1| GG20592 [Drosophila erecta]

 Score = 72.4 bits (176), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 34/59 (57%), Positives = 43/59 (72%), Gaps = 1/59 (1%)

Query: 6  RHLSLASSLFR-KYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTD 63
          R L+L     R K +LDYS+ P + E DI+E F+RGSGPGGQAV KT+NCV L H+PT+
Sbjct: 7  RFLALPPPAVRCKSNLDYSRFPALQESDIEETFMRGSGPGGQAVNKTSNCVFLRHLPTN 65

Source: Drosophila erecta

Species: Drosophila erecta

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	64
FB|FBgn0050100	146	CG30100 [Drosophila melanogast	0.906	0.397	0.576	3.4e-13
UNIPROTKB|F5GWJ6	96	C12orf65 "Probable peptide cha	0.656	0.437	0.571	1.1e-09
UNIPROTKB|F5H4X5	138	C12orf65 "Probable peptide cha	0.656	0.304	0.571	1.1e-09
UNIPROTKB|Q9H3J6	166	C12orf65 "Probable peptide cha	0.656	0.253	0.571	1.1e-09
UNIPROTKB|E2QXR1	239	C12orf65 "Uncharacterized prot	0.656	0.175	0.571	2.1e-09
UNIPROTKB|F1RFL3	187	C12orf65 "Uncharacterized prot	0.546	0.187	0.628	5.9e-09
MGI|MGI:1919900	184	2810006K23Rik "RIKEN cDNA 2810	0.656	0.228	0.523	5.9e-09
UNIPROTKB|F1LWN5	127	RGD1563482 "Protein RGD1563482	0.656	0.330	0.523	5.9e-09
UNIPROTKB|F1M2Z8	183	RGD1563482 "Protein RGD1563482	0.656	0.229	0.523	5.9e-09
UNIPROTKB|F1MLX1	173	C17H12orf65 "Uncharacterized p	0.546	0.202	0.6	7.6e-09

FB|FBgn0050100 CG30100 [Drosophila melanogaster (taxid:7227)]

 Score = 173 (66.0 bits), Expect = 3.4e-13, P = 3.4e-13
 Identities = 34/59 (57%), Positives = 44/59 (74%)

Query:     6 RHLSLASSLFR-KYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTD 63
             R L+L  +  R K +LDYS+ P + E DI+E F+RGSGPGGQAV KT+NCV L H+PT+
Sbjct:     7 RFLALPPTAVRCKSNLDYSRFPVLQESDIEETFMRGSGPGGQAVNKTSNCVFLRHLPTN 65

GO:0003747 "translation release factor activity" evidence=IEA

GO:0006415 "translational termination" evidence=IEA

UNIPROTKB|F5GWJ6 C12orf65 "Probable peptide chain release factor C12orf65, mitochondrial" [Homo sapiens (taxid:9606)]

 Score = 140 (54.3 bits), Expect = 1.1e-09, P = 1.1e-09
 Identities = 24/42 (57%), Positives = 33/42 (78%)

Query:    21 DYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
             DY  +  +DE +++E+FV+G GPGGQA  KT+NCVVL HIP+
Sbjct:    48 DYPALLSLDENELEEQFVKGHGPGGQATNKTSNCVVLKHIPS 89

GO:0003747 "translation release factor activity" evidence=IEA

UNIPROTKB|F5H4X5 C12orf65 "Probable peptide chain release factor C12orf65, mitochondrial" [Homo sapiens (taxid:9606)]

 Score = 140 (54.3 bits), Expect = 1.1e-09, P = 1.1e-09
 Identities = 24/42 (57%), Positives = 33/42 (78%)

Query:    21 DYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
             DY  +  +DE +++E+FV+G GPGGQA  KT+NCVVL HIP+
Sbjct:    48 DYPALLSLDENELEEQFVKGHGPGGQATNKTSNCVVLKHIPS 89

GO:0003747 "translation release factor activity" evidence=IEA

UNIPROTKB|Q9H3J6 C12orf65 "Probable peptide chain release factor C12orf65, mitochondrial" [Homo sapiens (taxid:9606)]

 Score = 140 (54.3 bits), Expect = 1.1e-09, P = 1.1e-09
 Identities = 24/42 (57%), Positives = 33/42 (78%)

Query:    21 DYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
             DY  +  +DE +++E+FV+G GPGGQA  KT+NCVVL HIP+
Sbjct:    48 DYPALLSLDENELEEQFVKGHGPGGQATNKTSNCVVLKHIPS 89

GO:0003747 "translation release factor activity" evidence=IEA

GO:0005739 "mitochondrion" evidence=NAS

UNIPROTKB|E2QXR1 C12orf65 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 139 (54.0 bits), Expect = 2.1e-09, P = 2.1e-09
 Identities = 24/42 (57%), Positives = 33/42 (78%)

Query:    21 DYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
             D   +P +DE +++E+FV+G GPGGQA  KT+NCVVL HIP+
Sbjct:   121 DRPALPLLDESELEEQFVKGHGPGGQATNKTSNCVVLKHIPS 162

GO:0003747 "translation release factor activity" evidence=IEA

UNIPROTKB|F1RFL3 C12orf65 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 133 (51.9 bits), Expect = 5.9e-09, P = 5.9e-09
 Identities = 22/35 (62%), Positives = 31/35 (88%)

Query:    28 IDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
             +DE++++E+FV+G GPGGQA  KT+NCVVL HIP+
Sbjct:    58 LDERELEEQFVKGHGPGGQATNKTSNCVVLRHIPS 92

GO:0003747 "translation release factor activity" evidence=IEA

MGI|MGI:1919900 2810006K23Rik "RIKEN cDNA 2810006K23 gene" [Mus musculus (taxid:10090)]

 Score = 133 (51.9 bits), Expect = 5.9e-09, P = 5.9e-09
 Identities = 22/42 (52%), Positives = 33/42 (78%)

Query:    21 DYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
             DY  +  ++E +++E+FV+G GPGGQA  KT+NCVVL H+P+
Sbjct:    51 DYPALLPLNESELEEQFVKGHGPGGQATNKTSNCVVLKHVPS 92

GO:0003674 "molecular_function" evidence=ND

GO:0003747 "translation release factor activity" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0005739 "mitochondrion" evidence=IEA

GO:0006412 "translation" evidence=IEA

GO:0006415 "translational termination" evidence=IEA

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|F1LWN5 RGD1563482 "Protein RGD1563482" [Rattus norvegicus (taxid:10116)]

 Score = 133 (51.9 bits), Expect = 5.9e-09, P = 5.9e-09
 Identities = 22/42 (52%), Positives = 33/42 (78%)

Query:    21 DYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
             DY  +  ++E +++E+FV+G GPGGQA  KT+NCVVL H+P+
Sbjct:    50 DYPALLPLNESELEEQFVKGHGPGGQATNKTSNCVVLKHVPS 91

GO:0003747 "translation release factor activity" evidence=IEA

UNIPROTKB|F1M2Z8 RGD1563482 "Protein RGD1563482" [Rattus norvegicus (taxid:10116)]

 Score = 133 (51.9 bits), Expect = 5.9e-09, P = 5.9e-09
 Identities = 22/42 (52%), Positives = 33/42 (78%)

Query:    21 DYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
             DY  +  ++E +++E+FV+G GPGGQA  KT+NCVVL H+P+
Sbjct:    50 DYPALLPLNESELEEQFVKGHGPGGQATNKTSNCVVLKHVPS 91

GO:0003747 "translation release factor activity" evidence=IEA

UNIPROTKB|F1MLX1 C17H12orf65 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 132 (51.5 bits), Expect = 7.6e-09, P = 7.6e-09
 Identities = 21/35 (60%), Positives = 31/35 (88%)

Query:    28 IDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
             +DE++++E+FV+G GPGGQA  KT+NCVVL H+P+
Sbjct:    56 LDERELEEQFVKGHGPGGQATNKTSNCVVLRHVPS 90

GO:0003747 "translation release factor activity" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q53915	RF2_STRCO	No assigned EC number	0.5277	0.5625	0.0978	yes	N/A
C0ZXD0	RF2_RHOE4	No assigned EC number	0.5555	0.5625	0.0978	yes	N/A
Q5HB80	RF1_EHRRW	No assigned EC number	0.5555	0.5625	0.1002	yes	N/A
A5WUX7	CL065_DANRE	No assigned EC number	0.5531	0.6875	0.2820	yes	N/A
Q5NMC7	RF1_ZYMMO	No assigned EC number	0.5142	0.5468	0.0977	yes	N/A
B9KIV2	RF1_ANAMF	No assigned EC number	0.5833	0.5625	0.1002	yes	N/A
Q9H3J6	CL065_HUMAN	No assigned EC number	0.5714	0.6562	0.2530	yes	N/A
Q5PAH2	RF1_ANAMM	No assigned EC number	0.5833	0.5625	0.1002	yes	N/A
Q5GSS8	RF1_WOLTR	No assigned EC number	0.5135	0.5781	0.1030	yes	N/A
Q73IC2	RF1_WOLPM	No assigned EC number	0.5277	0.5625	0.1002	yes	N/A
Q2GKS8	RF1_ANAPZ	No assigned EC number	0.5833	0.5625	0.1002	yes	N/A
Q2GE03	RF1_NEOSM	No assigned EC number	0.5277	0.5625	0.0980	yes	N/A
Q5FGZ2	RF1_EHRRG	No assigned EC number	0.5555	0.5625	0.1002	yes	N/A
Q2GGM5	RF1_EHRCR	No assigned EC number	0.5555	0.5625	0.1002	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	64
pfam00472	114	pfam00472, RF-1, RF-1 domain	9e-14
COG1186	239	COG1186, PrfB, Protein chain release factor B [Tra	5e-11
TIGR00020	364	TIGR00020, prfB, peptide chain release factor 2	1e-08
PRK00578	367	PRK00578, prfB, peptide chain release factor 2; Va	4e-08
TIGR00019	360	TIGR00019, prfA, peptide chain release factor 1	2e-07
PRK00591	359	PRK00591, prfA, peptide chain release factor 1; Va	3e-07
COG0216	363	COG0216, PrfA, Protein chain release factor A [Tra	4e-07
PRK09256	138	PRK09256, PRK09256, hypothetical protein; Provisio	5e-07
PRK08787	313	PRK08787, PRK08787, peptide chain release factor 2	1e-06
PRK08179	200	PRK08179, prfH, peptide chain release factor-like	2e-06
TIGR03072	200	TIGR03072, release_prfH, putative peptide chain re	3e-06
PRK07342	339	PRK07342, PRK07342, peptide chain release factor 2	2e-05
PRK05589	325	PRK05589, PRK05589, peptide chain release factor 2	2e-04
PRK06746	326	PRK06746, PRK06746, peptide chain release factor 2	0.003

>gnl|CDD|201249 pfam00472, RF-1, RF-1 domain

 Score = 59.9 bits (146), Expect = 9e-14
 Identities = 21/44 (47%), Positives = 26/44 (59%)

Query: 19 DLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
           LD     +I E D++    R SGPGGQ V KT + V LTH+PT
Sbjct: 1  PLDEEVEIEIPESDLRIDTFRSSGPGGQNVNKTESAVRLTHLPT 44

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|224107 COG1186, PrfB, Protein chain release factor B [Translation, ribosomal structure and biogenesis]

 Score = 54.9 bits (133), Expect = 5e-11
 Identities = 27/61 (44%), Positives = 35/61 (57%), Gaps = 1/61 (1%)

Query: 2   SIFRRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIP 61
           S  RRH S AS      +LD S   +I + D++    R SG GGQ V KT++ V LTH+P
Sbjct: 82  SNGRRHTSFASV-EVFPELDISIEIEIPDDDLRIDTYRASGAGGQHVNKTDSAVRLTHLP 140

Query: 62  T 62
           T
Sbjct: 141 T 141

Length = 239

>gnl|CDD|232785 TIGR00020, prfB, peptide chain release factor 2

 Score = 48.6 bits (116), Expect = 1e-08
 Identities = 25/58 (43%), Positives = 35/58 (60%), Gaps = 1/58 (1%)

Query: 5   RRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
           RRH S AS +F   ++D     +I  +D++    R SG GGQ V KT++ V +THIPT
Sbjct: 210 RRHTSFAS-VFVMPEVDDDIDIEIKPEDLRIDTYRASGAGGQHVNKTDSAVRITHIPT 266

In many but not all taxa, there is a conserved real translational frameshift at a TGA codon. RF-2 helps terminate translation at TGA codons and can therefore regulate its own production by readthrough when RF-2 is insufficient. There is a PFAM model called "RF-1" for the superfamily of RF-1, RF-2, mitochondrial, RF-H, etc [Protein synthesis, Translation factors]. Length = 364

>gnl|CDD|234799 PRK00578, prfB, peptide chain release factor 2; Validated

 Score = 47.2 bits (113), Expect = 4e-08
 Identities = 25/66 (37%), Positives = 32/66 (48%), Gaps = 17/66 (25%)

Query: 5   RRHLSLASSLFRKYDLDYSKVPKID--------EKDIQERFVRGSGPGGQAVAKTNNCVV 56
           RRH S AS             P++D         KD++    R SG GGQ V KT++ V 
Sbjct: 210 RRHTSFASV---------EVYPEVDDTIEIEINPKDLRIDTYRSSGAGGQHVNKTDSAVR 260

Query: 57  LTHIPT 62
           +THIPT
Sbjct: 261 ITHIPT 266

Length = 367

>gnl|CDD|129130 TIGR00019, prfA, peptide chain release factor 1

 Score = 45.1 bits (107), Expect = 2e-07
 Identities = 15/37 (40%), Positives = 22/37 (59%)

Query: 26  PKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
             I+  D++    R SG GGQ V  T++ V +TH+PT
Sbjct: 216 VDINPADLRIDTFRSSGAGGQHVNTTDSAVRITHLPT 252

This model describes peptide chain release factor 1 (PrfA, RF-1), and excludes the related peptide chain release factor 2 (PrfB, RF-2). RF-1 helps recognize and terminate translation at UAA and UAG stop codons. The mitochondrial release factors are prfA-like, although not included above the trusted cutoff for this model. RF-1 does not have a translational frameshift [Protein synthesis, Translation factors]. Length = 360

>gnl|CDD|234801 PRK00591, prfA, peptide chain release factor 1; Validated

 Score = 44.3 bits (106), Expect = 3e-07
 Identities = 16/37 (43%), Positives = 24/37 (64%)

Query: 26  PKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
            +I+ KD++    R SG GGQ V  T++ V +TH+PT
Sbjct: 216 VEINPKDLRIDTFRSSGAGGQHVNTTDSAVRITHLPT 252

Length = 359

>gnl|CDD|223294 COG0216, PrfA, Protein chain release factor A [Translation, ribosomal structure and biogenesis]

 Score = 44.1 bits (105), Expect = 4e-07
 Identities = 16/37 (43%), Positives = 24/37 (64%)

Query: 26  PKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
            +I+ KD++    R SG GGQ V  T++ V +TH+PT
Sbjct: 218 IEINPKDLRIDTFRSSGAGGQHVNTTDSAVRITHLPT 254

Length = 363

>gnl|CDD|181730 PRK09256, PRK09256, hypothetical protein; Provisional

 Score = 42.8 bits (102), Expect = 5e-07
 Identities = 15/30 (50%), Positives = 20/30 (66%)

Query: 28 IDEKDIQERFVRGSGPGGQAVAKTNNCVVL 57
          I E +++ RF+R SGPGGQ V K +  V L
Sbjct: 10 IPENELEWRFIRASGPGGQNVNKVSTAVEL 39

Length = 138

>gnl|CDD|136970 PRK08787, PRK08787, peptide chain release factor 2; Provisional

 Score = 42.7 bits (100), Expect = 1e-06
 Identities = 24/59 (40%), Positives = 35/59 (59%), Gaps = 1/59 (1%)

Query: 5   RRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTD 63
           RRH S  +S+F   ++D +    I+  D++    R SG GGQ V KT + V +THIPT+
Sbjct: 151 RRHTSF-TSVFVSPEVDDNIEIDINPADLRTDVYRSSGAGGQHVNKTESAVRITHIPTN 208

Length = 313

>gnl|CDD|181271 PRK08179, prfH, peptide chain release factor-like protein; Reviewed

 Score = 42.0 bits (99), Expect = 2e-06
 Identities = 15/41 (36%), Positives = 24/41 (58%)

Query: 22  YSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
           +S   +    +I+   +R SGPGGQ V KT++ V  TH+ +
Sbjct: 98  FSADEEEQSDEIRFETLRSSGPGGQHVNKTDSAVRATHLAS 138

Length = 200

>gnl|CDD|213768 TIGR03072, release_prfH, putative peptide chain release factor H

 Score = 41.7 bits (98), Expect = 3e-06
 Identities = 16/41 (39%), Positives = 24/41 (58%)

Query: 22  YSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
           +S   +  E +I+   +R SGPGGQ V KT + V  TH+ +
Sbjct: 97  FSASEEATEDEIRFETLRSSGPGGQHVNKTESAVRATHLAS 137

Members of this protein family are bacterial proteins homologous to peptide chain release factors 1 (RF-1, product of the prfA gene), and 2 (RF-2, product of the prfB gene). The member from Escherichia coli K-12, designated prfH, appears to be a pseudogene. This class I release factor is always found as the downstream gene of a two-gene operon [Protein synthesis, Translation factors]. Length = 200

>gnl|CDD|235997 PRK07342, PRK07342, peptide chain release factor 2; Provisional

 Score = 39.5 bits (92), Expect = 2e-05
 Identities = 24/58 (41%), Positives = 32/58 (55%), Gaps = 1/58 (1%)

Query: 5   RRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
           RRH S AS        D  +V  ++E D++    R SG GGQ V  T++ V +THIPT
Sbjct: 174 RRHTSFASIWVYPVIDDNIEV-DVNESDVRIDTYRSSGAGGQHVNTTDSAVRITHIPT 230

Length = 339

>gnl|CDD|235520 PRK05589, PRK05589, peptide chain release factor 2; Provisional

 Score = 36.7 bits (85), Expect = 2e-04
 Identities = 16/35 (45%), Positives = 21/35 (60%)

Query: 28  IDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
           I  +D++    R  G GGQ V KT + V +THIPT
Sbjct: 193 IRSEDLKIDTYRAGGAGGQHVNKTESAVRITHIPT 227

Length = 325

>gnl|CDD|75726 PRK06746, PRK06746, peptide chain release factor 2; Provisional

 Score = 33.2 bits (75), Expect = 0.003
 Identities = 20/60 (33%), Positives = 32/60 (53%), Gaps = 1/60 (1%)

Query: 5   RRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTDS 64
           RRH S  S        D  ++ ++  +D++    R SG GGQ V  T++ V +TH PT++
Sbjct: 172 RRHTSFVSCEVVPEFNDEVEI-EVRTEDLKIDTYRASGAGGQHVNTTDSAVRITHTPTNT 230

Length = 326

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	64
COG0216	363	PrfA Protein chain release factor A [Translation,	99.94
COG1186	239	PrfB Protein chain release factor B [Translation,	99.93
PRK05589	325	peptide chain release factor 2; Provisional	99.93
PRK08787	313	peptide chain release factor 2; Provisional	99.93
PRK07342	339	peptide chain release factor 2; Provisional	99.92
PRK06746	326	peptide chain release factor 2; Provisional	99.92
TIGR00019	360	prfA peptide chain release factor 1. This model de	99.92
TIGR00020	364	prfB peptide chain release factor 2. In many but n	99.92
PRK00578	367	prfB peptide chain release factor 2; Validated	99.91
PRK00591	359	prfA peptide chain release factor 1; Validated	99.91
KOG2726|consensus	386		99.91
TIGR03072	200	release_prfH putative peptide chain release factor	99.9
PRK08179	200	prfH peptide chain release factor-like protein; Re	99.9
PF00472	113	RF-1: RF-1 domain; InterPro: IPR000352 Peptide cha	99.85
PRK09256	138	hypothetical protein; Provisional	99.67
KOG3429|consensus	172		99.32

>COG0216 PrfA Protein chain release factor A [Translation, ribosomal structure and biogenesis]

Probab=99.94  E-value=6e-28  Score=178.26  Aligned_cols=60  Identities=33%  Similarity=0.423  Sum_probs=57.1

Q ss_pred             eeeEeCceeEEEeecccCCCCCCccCCCCeEEEEEeecCCCcccccccCCeEEEEecCCCC
Q psy2490           4 FRRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTDS   64 (64)
Q Consensus         4 ~r~~tS~a~V~V~~~~l~~~~~~~i~~~dl~~~~~rssGpGGQ~vNk~~s~V~l~h~ptgi   64 (64)
                      .|+|||+|+|.|+ |+.+....++|+++||+|+++||||+||||||+|+|||||+|+||||
T Consensus       197 GRIHTStaTVaVl-PE~ee~~ei~I~~~DlrIDt~RsSGaGGQhVNtTdSAVRiTHlPTGI  256 (363)
T COG0216         197 GRIHTSAATVAVL-PEVEEVEEIEINPKDLRIDTFRSSGAGGQHVNTTDSAVRITHLPTGI  256 (363)
T ss_pred             CceeecceeEEec-cCCCcccccccChHHceeeeeecCCCCCCCcCccchhheeeecCCce
Confidence            4899999999999 88877777999999999999999999999999999999999999997

>COG1186 PrfB Protein chain release factor B [Translation, ribosomal structure and biogenesis]

Probab=99.93  E-value=6.1e-27  Score=165.82  Aligned_cols=62  Identities=44%  Similarity=0.489  Sum_probs=58.4

Q ss_pred             ceeeeEeCceeEEEeecccCCCCCCccCCCCeEEEEEeecCCCcccccccCCeEEEEecCCCC
Q psy2490           2 SIFRRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTDS   64 (64)
Q Consensus         2 ~~~r~~tS~a~V~V~~~~l~~~~~~~i~~~dl~~~~~rssGpGGQ~vNk~~s~V~l~h~ptgi   64 (64)
                      ++.||||||++|.|+ |.+++...++|+++||+++++|||||||||||||+|||+|+|+||||
T Consensus        82 ~~~~R~tsf~~v~v~-p~~~~~i~i~I~~~dl~idt~RASGaGGQhVNKt~SAVrlth~ptgi  143 (239)
T COG1186          82 SNGRRHTSFASVEVF-PELDISIEIEIPDDDLRIDTYRASGAGGQHVNKTDSAVRLTHLPTGI  143 (239)
T ss_pred             cCcccccceeeeeec-CCCCcccceecCccceEEEEEEcCCCCCCccccccccEEEEEcCCCC
Confidence            457999999999999 77778888999999999999999999999999999999999999996

>PRK05589 peptide chain release factor 2; Provisional

Probab=99.93  E-value=3e-26  Score=167.47  Aligned_cols=60  Identities=35%  Similarity=0.418  Sum_probs=55.7

Q ss_pred             eeeEeCceeEEEeecccCCCCCCccCCCCeEEEEEeecCCCcccccccCCeEEEEecCCCC
Q psy2490           4 FRRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTDS   64 (64)
Q Consensus         4 ~r~~tS~a~V~V~~~~l~~~~~~~i~~~dl~~~~~rssGpGGQ~vNk~~s~V~l~h~ptgi   64 (64)
                      .||||||++|+|+ |..+...++.|+++||+|+++|||||||||||||+|+|||+|+||||
T Consensus       170 ~rr~ts~a~V~Vl-P~~~~~~~~~i~~~dl~~~~~rssG~GGQ~VNkt~saVrl~H~ptgi  229 (325)
T PRK05589        170 GKRQTSFASVEVL-PELTDDQDIEIRSEDLKIDTYRAGGAGGQHVNKTESAVRITHIPTGI  229 (325)
T ss_pred             CCeEeeeEEEEEe-cCcCccccccCCchheEEEEeeCCCCCCCcccceeeEEEEEECCCCE
Confidence            5899999999999 66665557899999999999999999999999999999999999997

>PRK08787 peptide chain release factor 2; Provisional

Probab=99.93  E-value=2.6e-26  Score=167.33  Aligned_cols=60  Identities=38%  Similarity=0.561  Sum_probs=56.2

Q ss_pred             eeeEeCceeEEEeecccCCCCCCccCCCCeEEEEEeecCCCcccccccCCeEEEEecCCCC
Q psy2490           4 FRRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTDS   64 (64)
Q Consensus         4 ~r~~tS~a~V~V~~~~l~~~~~~~i~~~dl~~~~~rssGpGGQ~vNk~~s~V~l~h~ptgi   64 (64)
                      .|||||||+|+|+ |.++...+++|+++||+|+++|||||||||||||+|+|||+|+||||
T Consensus       150 ~rrhTsfasV~V~-P~~~~~~~i~i~~~dl~~~~~RssG~GGQ~VNkt~saVri~H~Ptgi  209 (313)
T PRK08787        150 NRRHTSFTSVFVS-PEVDDNIEIDINPADLRTDVYRSSGAGGQHVNKTESAVRITHIPTNT  209 (313)
T ss_pred             CCEEeeeEEEEEe-cCcCcccccccChhHeEEEEEECCCCCCCCcCCEeeEEEEEECCCcE
Confidence            5899999999999 67766667899999999999999999999999999999999999997

>PRK07342 peptide chain release factor 2; Provisional

Probab=99.92  E-value=5.8e-26  Score=166.79  Aligned_cols=60  Identities=38%  Similarity=0.481  Sum_probs=55.6

Q ss_pred             eeeEeCceeEEEeecccCCCCCCccCCCCeEEEEEeecCCCcccccccCCeEEEEecCCCC
Q psy2490           4 FRRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTDS   64 (64)
Q Consensus         4 ~r~~tS~a~V~V~~~~l~~~~~~~i~~~dl~~~~~rssGpGGQ~vNk~~s~V~l~h~ptgi   64 (64)
                      .|||||||+|+|+ |.++...+++|+++||+++++|||||||||||||+|+|||+|+||||
T Consensus       173 ~rrhTs~a~V~Vl-P~~~~~~~~~i~~~dl~~~~~RssG~GGQ~VNkt~saVrl~H~ptgi  232 (339)
T PRK07342        173 ARRHTSFASIWVY-PVIDDNIEVDVNESDVRIDTYRSSGAGGQHVNTTDSAVRITHIPTGI  232 (339)
T ss_pred             CCeEeEEEEEEEE-cCCCcccccccCcccEEEEEEECCCCCCCCccceeeeEEEEEcCCcE
Confidence            5899999999999 66665557889999999999999999999999999999999999996

>PRK06746 peptide chain release factor 2; Provisional

Probab=99.92  E-value=6.1e-26  Score=166.00  Aligned_cols=60  Identities=32%  Similarity=0.436  Sum_probs=56.2

Q ss_pred             eeeEeCceeEEEeecccCCCCCCccCCCCeEEEEEeecCCCcccccccCCeEEEEecCCCC
Q psy2490           4 FRRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTDS   64 (64)
Q Consensus         4 ~r~~tS~a~V~V~~~~l~~~~~~~i~~~dl~~~~~rssGpGGQ~vNk~~s~V~l~h~ptgi   64 (64)
                      .|||||||+|+|+ |.++...+++|+++||+++++|||||||||||||+|||||+|+||||
T Consensus       171 ~rrhTsfa~V~v~-P~~~~~~~i~i~~~dl~~~~~rssG~GGQ~vNkt~saVrl~h~ptgi  230 (326)
T PRK06746        171 GRRHTSFVSCEVV-PEFNDEVEIEVRTEDLKIDTYRASGAGGQHVNTTDSAVRITHTPTNT  230 (326)
T ss_pred             CCeEeeEEEEEEe-cCcCCccccccChHHeEEEEEeCCCCCCCCccceeeEEEEEEeCCeE
Confidence            6999999999999 67765677899999999999999999999999999999999999997

>TIGR00019 prfA peptide chain release factor 1

Probab=99.92  E-value=1.7e-25  Score=165.17  Aligned_cols=59  Identities=34%  Similarity=0.415  Sum_probs=54.2

Q ss_pred             eeeEeCceeEEEeecccCCCCCCccCCCCeEEEEEeecCCCcccccccCCeEEEEecCCCC
Q psy2490           4 FRRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTDS   64 (64)
Q Consensus         4 ~r~~tS~a~V~V~~~~l~~~~~~~i~~~dl~~~~~rssGpGGQ~vNk~~s~V~l~h~ptgi   64 (64)
                      .|+||||++|+|+ |.++. ..+.|+++||+|+++|||||||||||||+|||||+|+||||
T Consensus       196 ~R~hTsfa~V~v~-P~~~~-~~~~i~~~dl~~~~~RssG~GGQ~VNkt~SaVrl~h~ptgi  254 (360)
T TIGR00019       196 GRIHTSAATVAVM-PELEE-VEVDINPADLRIDTFRSSGAGGQHVNTTDSAVRITHLPTGI  254 (360)
T ss_pred             CCeecceeEEEEE-cCCCc-cccccCcccEEEEEEECCCCCCCCcCceeeeEEEEECCCcE
Confidence            5999999999999 56554 45789999999999999999999999999999999999997

This model describes peptide chain release factor 1 (PrfA, RF-1), and excludes the related peptide chain release factor 2 (PrfB, RF-2). RF-1 helps recognize and terminate translation at UAA and UAG stop codons. The mitochondrial release factors are prfA-like, although not included above the trusted cutoff for this model. RF-1 does not have a translational frameshift.

>TIGR00020 prfB peptide chain release factor 2

Probab=99.92  E-value=2.6e-25  Score=164.31  Aligned_cols=60  Identities=40%  Similarity=0.497  Sum_probs=55.6

Q ss_pred             eeeEeCceeEEEeecccCCCCCCccCCCCeEEEEEeecCCCcccccccCCeEEEEecCCCC
Q psy2490           4 FRRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTDS   64 (64)
Q Consensus         4 ~r~~tS~a~V~V~~~~l~~~~~~~i~~~dl~~~~~rssGpGGQ~vNk~~s~V~l~h~ptgi   64 (64)
                      .|+|||||+|+|+ |..+...+++|+++||+++++|||||||||||||+|+|||+|+||||
T Consensus       209 ~rrhts~a~V~vl-P~~~~~~~~~i~~~d~~~~~~rssG~GGQ~VNkt~saVri~H~ptgi  268 (364)
T TIGR00020       209 GRRHTSFASVFVM-PEVDDDIDIEIKPEDLRIDTYRASGAGGQHVNKTDSAVRITHIPTGI  268 (364)
T ss_pred             CCeEeeeEEEEEe-cCCCcccceecccccEEEEEeeCCCCCCccccccceEEEEEECCCcE
Confidence            5899999999999 66655567899999999999999999999999999999999999997

In many but not all taxa, there is a conserved real translational frameshift at a TGA codon. RF-2 helps terminate translation at TGA codons and can therefore regulate its own production by readthrough when RF-2 is insufficient. There is a Pfam model called "RF-1" for the superfamily of RF-1, RF-2, mitochondrial, RF-H, etc.

>PRK00578 prfB peptide chain release factor 2; Validated

Probab=99.91  E-value=3.7e-25  Score=163.51  Aligned_cols=60  Identities=42%  Similarity=0.501  Sum_probs=55.7

Q ss_pred             eeeEeCceeEEEeecccCCCCCCccCCCCeEEEEEeecCCCcccccccCCeEEEEecCCCC
Q psy2490           4 FRRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTDS   64 (64)
Q Consensus         4 ~r~~tS~a~V~V~~~~l~~~~~~~i~~~dl~~~~~rssGpGGQ~vNk~~s~V~l~h~ptgi   64 (64)
                      .|+||||++|+|+ |..+....+.|+++||+++++|||||||||||||+|+|||+|+||||
T Consensus       209 ~r~hts~~~V~vl-P~~~~~~~~~i~~~dl~~~~~rssGpGGQ~vNkt~saVrl~h~ptgi  268 (367)
T PRK00578        209 GRRHTSFASVEVY-PEVDDTIEIEINPKDLRIDTYRSSGAGGQHVNKTDSAVRITHIPTGI  268 (367)
T ss_pred             CceecceeeEEec-CCCCCccccccChhhEEEEEeeCCCCCCCcccceeeEEEEEECCCcE
Confidence            5899999999999 67665557789999999999999999999999999999999999997

>PRK00591 prfA peptide chain release factor 1; Validated

Probab=99.91  E-value=7e-25  Score=161.80  Aligned_cols=59  Identities=34%  Similarity=0.407  Sum_probs=54.3

Q ss_pred             eeeEeCceeEEEeecccCCCCCCccCCCCeEEEEEeecCCCcccccccCCeEEEEecCCCC
Q psy2490           4 FRRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTDS   64 (64)
Q Consensus         4 ~r~~tS~a~V~V~~~~l~~~~~~~i~~~dl~~~~~rssGpGGQ~vNk~~s~V~l~h~ptgi   64 (64)
                      .|+||||++|+|+ |.++. ..+.|+++||+++++|||||||||||||+|+|||+|+||||
T Consensus       196 ~R~~tsfa~V~v~-P~~~~-~~~~i~~~dl~~~~~RssG~GGQ~VNkt~saVrl~H~ptGi  254 (359)
T PRK00591        196 GRIHTSAATVAVL-PEAEE-VEVEINPKDLRIDTFRSSGAGGQHVNTTDSAVRITHLPTGI  254 (359)
T ss_pred             CceecceEEEEEE-cCCCc-cccccCcccEEEEEEECCCCCCCCccceeeeEEEEECCCcE
Confidence            5899999999999 56554 37889999999999999999999999999999999999997

>KOG2726|consensus

Probab=99.91  E-value=4.9e-25  Score=164.13  Aligned_cols=62  Identities=45%  Similarity=0.475  Sum_probs=55.9

Q ss_pred             eeeeEeCceeEEEeecccCCCCCCccCCCCeEEEEEeecCCCcccccccCCeEEEEecCCCC
Q psy2490           3 IFRRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTDS   64 (64)
Q Consensus         3 ~~r~~tS~a~V~V~~~~l~~~~~~~i~~~dl~~~~~rssGpGGQ~vNk~~s~V~l~h~ptgi   64 (64)
                      ..|+|||+|+|.|+|........+.++++||+++++||||||||||||++|||||+|+||||
T Consensus       220 ~gr~htstasV~ViP~~~~~~~~~~~~~~dl~i~~~R~~G~GGQhvNktdsaVrl~HiPTGI  281 (386)
T KOG2726|consen  220 SGRRHTSTASVAVIPQPGRDEVDVEIDEKDLRIETFRASGPGGQHVNKTDSAVRLTHIPTGI  281 (386)
T ss_pred             ccccccccceEEEeccCCCCccceecCchheeEEecccCCCCcccccccccceEEEeecCce
Confidence            35899999999999433446677889999999999999999999999999999999999997

>TIGR03072 release_prfH putative peptide chain release factor H

Probab=99.90  E-value=1.4e-24  Score=150.24  Aligned_cols=55  Identities=31%  Similarity=0.381  Sum_probs=50.3

Q ss_pred             eeeEeCceeEEEeecccCCCCCCccCCCCeEEEEEeecCCCcccccccCCeEEEEecCCCC
Q psy2490           4 FRRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTDS   64 (64)
Q Consensus         4 ~r~~tS~a~V~V~~~~l~~~~~~~i~~~dl~~~~~rssGpGGQ~vNk~~s~V~l~h~ptgi   64 (64)
                      .+|||||++|+|+| .     .++|+++||+++++|||||||||||||+|+|+|+|+||||
T Consensus        85 ~~R~ts~~~V~v~~-~-----~~~i~~~dl~~~~~RssGpGGQ~vNkt~saVrl~h~ptgi  139 (200)
T TIGR03072        85 HRRKNWFIGVQRFS-A-----SEEATEDEIRFETLRSSGPGGQHVNKTESAVRATHLASGI  139 (200)
T ss_pred             CCeeEEEEEEEEec-C-----ccccChhheEEEEEECCCCCcccccccceeEEEEECCCcE
Confidence            36899999999994 1     3579999999999999999999999999999999999997

Members of this protein family are bacterial proteins homologous to peptide chain release factors 1 (RF-1, product of the prfA gene), and 2 (RF-2, product of the prfB gene). The member from Escherichia coli K-12, designated prfH, appears to be a pseudogene. This class I release factor is always found as the downstream gene of a two-gene operon.

>PRK08179 prfH peptide chain release factor-like protein; Reviewed

Probab=99.90  E-value=1.4e-24  Score=150.14  Aligned_cols=55  Identities=27%  Similarity=0.300  Sum_probs=50.3

Q ss_pred             eeeEeCceeEEEeecccCCCCCCccCCCCeEEEEEeecCCCcccccccCCeEEEEecCCCC
Q psy2490           4 FRRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTDS   64 (64)
Q Consensus         4 ~r~~tS~a~V~V~~~~l~~~~~~~i~~~dl~~~~~rssGpGGQ~vNk~~s~V~l~h~ptgi   64 (64)
                      .+|||||++|+|++ .     +++|+++||+++|+|||||||||||||+|+|+|+|+||||
T Consensus        86 ~~R~~s~~~V~v~~-~-----~~~i~~~dl~~~~~RssGpGGQ~VNkt~saVrl~h~ptgi  140 (200)
T PRK08179         86 HGRKNWFVGIGRFS-A-----DEEEQSDEIRFETLRSSGPGGQHVNKTDSAVRATHLASGI  140 (200)
T ss_pred             CCceEEEEEEEEeC-C-----cCccCHHHeEEEEEEccCCcccccccccceEEEEEcCCcE
Confidence            46899999999994 2     3479999999999999999999999999999999999997

>PF00472 RF-1: RF-1 domain; InterPro: IPR000352 Peptide chain release factors (RFs) are required for the termination of protein biosynthesis []

Probab=99.85  E-value=4.5e-22  Score=126.32  Aligned_cols=43  Identities=53%  Similarity=0.706  Sum_probs=39.5

Q ss_pred             CCCCCccCCCCeEEEEEeecCCCcccccccCCeEEEEecCCCC
Q psy2490          22 YSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTDS   64 (64)
Q Consensus        22 ~~~~~~i~~~dl~~~~~rssGpGGQ~vNk~~s~V~l~h~ptgi   64 (64)
                      ....+.|+++||+++|+||||||||||||++|+|+|+|+||||
T Consensus         3 ~~~~~~i~~~dl~~~~~RssGpGGQ~VNk~~s~V~l~h~ptgi   45 (113)
T PF00472_consen    3 KEKEIDIPEKDLEISFSRSSGPGGQNVNKTNSKVRLRHIPTGI   45 (113)
T ss_dssp             TSSSSCC-GGGEEEEEEESSSSSSCHHHSSSEEEEEEETTTTE
T ss_pred             cccccccCHHHeEEEEEecCCCCCCcccccCCEEEEEEecccE
Confidence            4567899999999999999999999999999999999999995

At present two classes of RFs can be distinguished. Class I RFs bind to ribosomes that have encountered a stop codon at their decoding site and induce release of the nascent polypeptide. Class II RFs are GTP-binding proteins that interact with class I RFs and enhance class I RF activity. In prokaryotes there are two class I RFs that act in a codon specific manner []: RF-1 (gene prfA) mediates UAA and UAG-dependent termination while RF-2 (gene prfB) mediates UAA and UGA-dependent termination. RF-1 and RF-2 are structurally and evolutionary related proteins which have been shown to be part of a larger family [].; GO: 0003747 translation release factor activity, 0006415 translational termination; PDB: 2JY9_A 1ZBT_A 1GQE_A 3F1G_X 3F1E_X 1RQ0_C 4DH9_Y 2JVA_A 1J26_A 3D5A_X ....

>PRK09256 hypothetical protein; Provisional

Probab=99.67  E-value=3.6e-17  Score=107.82  Aligned_cols=38  Identities=39%  Similarity=0.645  Sum_probs=35.1

Q ss_pred             CCCCCccCCCCeEEEEEeecCCCcccccccCCeEEEEe
Q psy2490          22 YSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTH   59 (64)
Q Consensus        22 ~~~~~~i~~~dl~~~~~rssGpGGQ~vNk~~s~V~l~h   59 (64)
                      ...+++|+++||+++|+|||||||||||||+|+|+|+|
T Consensus         4 ~~~~~~i~~~~l~~~~~RSSGPGGQ~VNKt~SkV~l~~   41 (138)
T PRK09256          4 ITRRLVIPENELEWRFIRASGPGGQNVNKVSTAVELRF   41 (138)
T ss_pred             cCccCccCHHHeEEEEEEcCCCCcccccccceeeEEEe
Confidence            34567899999999999999999999999999999997

>KOG3429|consensus

Probab=99.32  E-value=1.3e-12  Score=89.25  Aligned_cols=36  Identities=36%  Similarity=0.494  Sum_probs=32.8

Q ss_pred             CCccCCCCeEEEEEeecCCCcccccccCCeEEEEec
Q psy2490          25 VPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHI   60 (64)
Q Consensus        25 ~~~i~~~dl~~~~~rssGpGGQ~vNk~~s~V~l~h~   60 (64)
                      ...|+.+.++++|.||||||||||||++|+|.+++.
T Consensus        34 ~g~ipld~~~i~y~RSSGPGGQNVNKvNTKv~vrf~   69 (172)
T KOG3429|consen   34 KGKIPLDQLEISYSRSSGPGGQNVNKVNTKVEVRFK   69 (172)
T ss_pred             CCCCchhheEEEEeecCCCCCcccccccceEEEEEe
Confidence            346888999999999999999999999999999963

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	64
2rsm_A	115	Solution Structure And Sirna-Mediated Knockdown Ana		2e-09
1mi6_A	365	Docking Of The Modified Rf2 X-Ray Structure Into Th		4e-04
1rq0_A	342	Crystal Structure Of Peptide Releasing Factor 1 Len		5e-04
1gqe_A	365	Polypeptide Chain Release Factor 2 (Rf2) From Esche		5e-04
2fvo_A	333	Docking Of The Modified Rf1 X-ray Structure Into Th		5e-04
1ml5_Z	365	Structure Of The E. Coli Ribosomal Termination Comp		7e-04

>pdb|2RSM|A Chain A, Solution Structure And Sirna-Mediated Knockdown Analysis Of The Mitochondrial Disease-Related Protein C12orf65 (Ict2) Length = 115

Iteration: 1
 Score = 57.0 bits (136), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 22/42 (52%), Positives = 33/42 (78%)
Query: 21 DYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
          DY  +  ++E +++E+FV+G GPGGQA  KT+NCVVL H+P+
Sbjct: 36 DYPALLPLNESELEEQFVKGHGPGGQATNKTSNCVVLKHVPS 77

>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

Iteration: 1
 Score = 39.7 bits (91), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 24/58 (41%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 5   RRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
           RRH S  SS F   ++D     +I+  D++    R SG GGQ V +T + V +THIPT
Sbjct: 212 RRHTSF-SSAFVYPEVDDDIDIEINPADLRIDVYRASGAGGQHVNRTESAVRITHIPT 268

>pdb|1RQ0|A Chain A, Crystal Structure Of Peptide Releasing Factor 1 Length = 342

Iteration: 1
 Score = 39.3 bits (90), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 21/45 (46%), Positives = 28/45 (62%), Gaps = 7/45 (15%)
Query: 25  VPKIDEKDIQER-------FVRGSGPGGQAVAKTNNCVVLTHIPT 62
           +P+I+EKDI+ R         R SG GGQ V KT + V +TH+PT
Sbjct: 183 LPEIEEKDIEIRPEDLKIETFRASGHGGQYVNKTESAVRITHLPT 227

>pdb|1GQE|A Chain A, Polypeptide Chain Release Factor 2 (Rf2) From Escherichia Coli Length = 365

Iteration: 1
 Score = 39.3 bits (90), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 24/58 (41%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 5   RRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
           RRH S  SS F   ++D     +I+  D++    R SG GGQ V +T + V +THIPT
Sbjct: 212 RRHTSF-SSAFVYPEVDDDIDIEINPADLRIDVYRASGAGGQHVNRTESAVRITHIPT 268

>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

Iteration: 1
 Score = 39.3 bits (90), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 21/45 (46%), Positives = 28/45 (62%), Gaps = 7/45 (15%)
Query: 25  VPKIDEKDIQER-------FVRGSGPGGQAVAKTNNCVVLTHIPT 62
           +P+I+EKDI+ R         R SG GGQ V KT + V +TH+PT
Sbjct: 183 LPEIEEKDIEIRPEDLKIETFRASGHGGQYVNKTESAVRITHLPT 227

>pdb|1ML5|Z Chain Z, Structure Of The E. Coli Ribosomal Termination Complex With Release Factor 2 Length = 365

Iteration: 1
 Score = 38.9 bits (89), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 24/58 (41%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 5   RRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
           RRH S  SS F   ++D     +I+  D++    R SG GGQ V +T + V +THIPT
Sbjct: 212 RRHTSF-SSAFVYPEVDDDIDIEINPADLRIDVYRTSGAGGQHVNRTESAVRITHIPT 268

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	64
2rsm_A	115	Probable peptide chain release factor C12ORF65 HO	4e-15
2jva_A	108	Peptidyl-tRNA hydrolase domain protein; GFT hydrol	3e-10
4dh9_Y	140	YAEJ; ribosome, YAEJ, ribosome stalling, ribosome	5e-09
1gqe_A	365	Release factor 2, RF2; protein synthesis, ribosome	2e-08
2b3t_B	360	RF-1, peptide chain release factor 1; translation	2e-08
2ihr_1	365	Peptide chain release factor 2; mixed alpha-beta,	4e-08
1rq0_A	342	RF-1, peptide chain release factor 1; X-RAY, cryst	9e-08
1zbt_A	371	RF-1, peptide chain release factor 1; peptide chai	9e-08
3d5a_X	354	RF1, peptide chain release factor 1; ribosome, rib	1e-07
1j26_A	112	Immature colon carcinoma transcript 1; peptide cha	3e-07

>2rsm_A Probable peptide chain release factor C12ORF65 HO mitochondrial; GGQ domain, translation; NMR {Mus musculus} Length = 115

 Score = 62.7 bits (153), Expect = 4e-15
 Identities = 22/42 (52%), Positives = 33/42 (78%)

Query: 21 DYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
          DY  +  ++E +++E+FV+G GPGGQA  KT+NCVVL H+P+
Sbjct: 36 DYPALLPLNESELEEQFVKGHGPGGQATNKTSNCVVLKHVPS 77

>2jva_A Peptidyl-tRNA hydrolase domain protein; GFT hydrolase, structural genomics, PSI-2, protein STRU initiative; NMR {Pseudomonas syringae PV} Length = 108

 Score = 50.3 bits (120), Expect = 3e-10
 Identities = 12/45 (26%), Positives = 20/45 (44%)

Query: 20 LDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTDS 64
          L  S    + + +I+   +R  G GGQ V K ++ + L      S
Sbjct: 2  LVISNNVHLPDAEIELTAIRAQGAGGQNVNKVSSAMHLRFDINAS 46

>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

 Score = 47.5 bits (113), Expect = 5e-09
 Identities = 12/45 (26%), Positives = 21/45 (46%)

Query: 20 LDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTDS 64
          +  S+   I + +++   +R  G GGQ V KT+  + L      S
Sbjct: 2  IVISRHVAIPDGELEITAIRAQGAGGQHVNKTSTAIHLRFDIRAS 46

>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

 Score = 47.7 bits (114), Expect = 2e-08
 Identities = 23/58 (39%), Positives = 33/58 (56%), Gaps = 1/58 (1%)

Query: 5   RRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
           RRH S +S  F   ++D     +I+  D++    R SG GGQ V +T + V +THIPT
Sbjct: 212 RRHTSFSS-AFVYPEVDDDIDIEINPADLRIDVYRASGAGGQHVNRTESAVRITHIPT 268

>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

 Score = 47.2 bits (113), Expect = 2e-08
 Identities = 14/38 (36%), Positives = 24/38 (63%)

Query: 25  VPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
           +P ++  D++    R SG GGQ V  T++ + +TH+PT
Sbjct: 214 LPDVNPADLRIDTFRSSGAGGQHVNTTDSAIRITHLPT 251

>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

 Score = 46.5 bits (111), Expect = 4e-08
 Identities = 19/58 (32%), Positives = 32/58 (55%), Gaps = 1/58 (1%)

Query: 5   RRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
           RRH S A  +    ++D      +  ++++   +R SGPGGQ V  T++ V + H+PT
Sbjct: 200 RRHTSFAG-VEVIPEVDEEVEVVLKPEELRIDVMRASGPGGQGVNTTDSAVRVVHLPT 256

>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

 Score = 45.7 bits (109), Expect = 9e-08
 Identities = 16/36 (44%), Positives = 23/36 (63%)

Query: 27  KIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
           +I  +D++    R SG GGQ V KT + V +TH+PT
Sbjct: 192 EIRPEDLKIETFRASGHGGQYVNKTESAVRITHLPT 227

>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

 Score = 45.3 bits (108), Expect = 9e-08
 Identities = 15/36 (41%), Positives = 20/36 (55%)

Query: 27  KIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
           +ID KD++      SG GGQ V K    V + H+PT
Sbjct: 229 EIDPKDLRVDIYHASGAGGQNVNKVATAVRIIHLPT 264

>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

 Score = 45.2 bits (108), Expect = 1e-07
 Identities = 14/36 (38%), Positives = 23/36 (63%)

Query: 27  KIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
            ++  +I+   +R SGPGGQ V  T++ V + H+PT
Sbjct: 211 ALNMDEIRIDVMRASGPGGQGVNTTDSAVRVVHLPT 246

>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

 Score = 42.8 bits (100), Expect = 3e-07
 Identities = 11/37 (29%), Positives = 16/37 (43%)

Query: 28 IDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTDS 64
          I    +   + R SGPGGQ V K N+   +      +
Sbjct: 17 IPLDRLSISYCRSSGPGGQNVNKVNSKAEVRFHLASA 53

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	64
1gqe_A	365	Release factor 2, RF2; protein synthesis, ribosome	99.93
2rsm_A	115	Probable peptide chain release factor C12ORF65 HO	99.93
2ihr_1	365	Peptide chain release factor 2; mixed alpha-beta,	99.93
2b3t_B	360	RF-1, peptide chain release factor 1; translation	99.92
1rq0_A	342	RF-1, peptide chain release factor 1; X-RAY, cryst	99.92
1zbt_A	371	RF-1, peptide chain release factor 1; peptide chai	99.92
3d5a_X	354	RF1, peptide chain release factor 1; ribosome, rib	99.92
2jva_A	108	Peptidyl-tRNA hydrolase domain protein; GFT hydrol	99.78
1j26_A	112	Immature colon carcinoma transcript 1; peptide cha	99.78
4dh9_Y	140	YAEJ; ribosome, YAEJ, ribosome stalling, ribosome	99.74

>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*

Probab=99.93  E-value=5.5e-27  Score=172.30  Aligned_cols=60  Identities=37%  Similarity=0.504  Sum_probs=56.4

Q ss_pred             eeeEeCceeEEEeecccCCCCCCccCCCCeEEEEEeecCCCcccccccCCeEEEEecCCCC
Q psy2490           4 FRRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTDS   64 (64)
Q Consensus         4 ~r~~tS~a~V~V~~~~l~~~~~~~i~~~dl~~~~~rssGpGGQ~vNk~~s~V~l~h~ptgi   64 (64)
                      .|||||||+|+|+ |+++....+.|+++||+++|+|||||||||||||+|+|+|+|+||||
T Consensus       211 gRrhTS~asV~V~-Pe~~~~v~i~i~~~dl~~~~~RssG~GGQ~VNkt~saVrl~HiPtgi  270 (365)
T 1gqe_A          211 GRRHTSFSSAFVY-PEVDDDIDIEINPADLRIDVYRASGAGGQHVNRTESAVRITHIPTGI  270 (365)
T ss_dssp             CCEEEEEEEEEEE-ECCBTTBCCCCCGGGEEEEEECCCCSSCCSTTSSCCEEEEEETTTCC
T ss_pred             CCCCcceeEEEEe-cCCCcccccccCHHHceEeeecCCCCCCCcccCccceEEEEECCCeE
Confidence            5899999999999 77776667899999999999999999999999999999999999997

>2rsm_A Probable peptide chain release factor C12ORF65 HO mitochondrial; GGQ domain, translation; NMR {Mus musculus}

Probab=99.93  E-value=3.6e-27  Score=151.45  Aligned_cols=57  Identities=39%  Similarity=0.747  Sum_probs=54.7

Q ss_pred             EeCceeEEEeecccCCCCCCccCCCCeEEEEEeecCCCcccccccCCeEEEEecCCCC
Q psy2490           7 HLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTDS   64 (64)
Q Consensus         7 ~tS~a~V~V~~~~l~~~~~~~i~~~dl~~~~~rssGpGGQ~vNk~~s~V~l~h~ptgi   64 (64)
                      -||+|+|.|+ |+.|....++|+++||+|+|+|||||||||||||+|+|+|+|+||||
T Consensus        23 gts~~~v~v~-p~~d~~~~l~I~~~dl~~~~~RssGpGGQ~VNKt~SaVrl~H~PTGi   79 (115)
T 2rsm_A           23 GMAASTVQVA-GRKDYPALLPLNESELEEQFVKGHGPGGQATNKTSNCVVLKHVPSGI   79 (115)
T ss_dssp             CCCCCCCCCC-SCCCCCCSCCCCGGGCEEEECSCCCSCSSSCCCSCCCEEEECTTTCC
T ss_pred             ccceEEEEec-cccCCCccCCcCHHHeEEEEeeCCCCCccccCccceeEEEecCCCCc
Confidence            3899999999 88888888999999999999999999999999999999999999997

>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

Probab=99.93  E-value=1.9e-26  Score=169.46  Aligned_cols=60  Identities=32%  Similarity=0.466  Sum_probs=56.4

Q ss_pred             eeeEeCceeEEEeecccCCCCCCccCCCCeEEEEEeecCCCcccccccCCeEEEEecCCCC
Q psy2490           4 FRRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTDS   64 (64)
Q Consensus         4 ~r~~tS~a~V~V~~~~l~~~~~~~i~~~dl~~~~~rssGpGGQ~vNk~~s~V~l~h~ptgi   64 (64)
                      .|||||||+|+|+ |+++....+.|+++||+++|+|||||||||||||+|+|+|+|+||||
T Consensus       199 gRrhTS~asV~V~-P~~~~~~~i~i~~~dl~i~~~RssG~GGQ~VNkt~saVrl~h~Ptgi  258 (365)
T 2ihr_1          199 GRRHTSFAGVEVI-PEVDEEVEVVLKPEELRIDVMRASGPGGQGVNTTDSAVRVVHLPTGI  258 (365)
T ss_dssp             CCEEEEEEEEEEE-EECCSSSSCCCCGGGEEEEEECCCCSSCCSGGGSCSEEEEEETTTTE
T ss_pred             CCccceeEEEEEe-cCCCcccccccCccceEEEEeecCCCCCceecccceEEEEEEcCCeE
Confidence            5899999999999 77776677899999999999999999999999999999999999996

>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

Probab=99.92  E-value=3.7e-26  Score=167.74  Aligned_cols=60  Identities=30%  Similarity=0.467  Sum_probs=54.8

Q ss_pred             eeeEeCceeEEEeecccCCCCCCccCCCCeEEEEEeecCCCcccccccCCeEEEEecCCCC
Q psy2490           4 FRRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTDS   64 (64)
Q Consensus         4 ~r~~tS~a~V~V~~~~l~~~~~~~i~~~dl~~~~~rssGpGGQ~vNk~~s~V~l~h~ptgi   64 (64)
                      .|+|||||+|+|+ |+++....+.|+++||+++|+|||||||||||||+|+|+|+|+||||
T Consensus       194 gR~hTS~asV~V~-Pe~~~~e~i~i~~~dl~i~~~RssG~GGQ~VNkt~saVrl~hlPtGi  253 (360)
T 2b3t_B          194 GRIHTSACTVAVM-PELPDAELPDVNPADLRIDTFRSSGAGGQHVNTTDSAIRITHLPTGI  253 (360)
T ss_dssp             CCCEEEEEEEECC-BCCCTTTCCCCCSSSEEEEECCSSCCCTTTCCCSSEEEEEEETTTCC
T ss_pred             CcCCccceEEEEe-cCcccccccccChhheEEeeecCCCCCCCccccccceEEEEECCCeE
Confidence            5899999999999 67665322789999999999999999999999999999999999997

>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

Probab=99.92  E-value=3.3e-26  Score=167.15  Aligned_cols=59  Identities=36%  Similarity=0.420  Sum_probs=50.8

Q ss_pred             eeeEeCceeEEEeecccCCCCCCccCCCCeEEEEEeecCCCcccccccCCeEEEEecCCCC
Q psy2490           4 FRRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTDS   64 (64)
Q Consensus         4 ~r~~tS~a~V~V~~~~l~~~~~~~i~~~dl~~~~~rssGpGGQ~vNk~~s~V~l~h~ptgi   64 (64)
                      .|+|||||+|+|+ |+++. .++.|+++||+++|+|||||||||||||+|+|+|+|+||||
T Consensus       171 gR~hTS~asV~V~-Pe~~~-~~i~i~~~dl~i~~~RssGpGGQ~VNKt~SaVrl~hlPtGi  229 (342)
T 1rq0_A          171 GRIHTSTATVAVL-PEIEE-KDIEIRPEDLKIETFRASGHGGQYVNKTESAVRITHLPTGI  229 (342)
T ss_dssp             CCCEEEEEEEEEE-ECCCG-GGSCCCGGGEEEEEECCCC----CCSSSSEEEEEEETTTCC
T ss_pred             CCCcccceEEEEe-ccccc-cccccChhHeEEEeecCCCCCCcccccccceEEEEECCCeE
Confidence            5899999999999 66665 45889999999999999999999999999999999999997

>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}

Probab=99.92  E-value=2.6e-26  Score=169.13  Aligned_cols=59  Identities=34%  Similarity=0.442  Sum_probs=45.8

Q ss_pred             eeeEeCceeEEEeecccCCCCCCccCCCCeEEEEEeecCCCcccccccCCeEEEEecCCCC
Q psy2490           4 FRRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTDS   64 (64)
Q Consensus         4 ~r~~tS~a~V~V~~~~l~~~~~~~i~~~dl~~~~~rssGpGGQ~vNk~~s~V~l~h~ptgi   64 (64)
                      .|+|||||+|+|+ |+++. ..+.|+++||+++|+|||||||||||||+|+|+|+|+||||
T Consensus       208 gR~hTS~asV~V~-Pe~~e-v~i~I~~~dl~i~~~RssGpGGQ~VNkt~SaVrlthlPtGi  266 (371)
T 1zbt_A          208 GRVHTSTATVLVM-PEVEE-VEYEIDPKDLRVDIYHASGAGGQNVNKVATAVRIIHLPTNI  266 (371)
T ss_dssp             CCCEEEEEEEEEE-ECCCG-GGSCCCGGGEEEEEECC---------CCCCEEEEEETTTTE
T ss_pred             CcccccceEEEEe-ccccc-cccccCcCcEEEEEecCCCCCCCcccccceeEEEEECCCeE
Confidence            5899999999999 67665 45889999999999999999999999999999999999996

>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

Probab=99.92  E-value=2.5e-26  Score=168.34  Aligned_cols=59  Identities=31%  Similarity=0.401  Sum_probs=54.8

Q ss_pred             eeeEeCceeEEEeecccCCCCCCccCCCCeEEEEEeecCCCcccccccCCeEEEEecCCCC
Q psy2490           4 FRRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTDS   64 (64)
Q Consensus         4 ~r~~tS~a~V~V~~~~l~~~~~~~i~~~dl~~~~~rssGpGGQ~vNk~~s~V~l~h~ptgi   64 (64)
                      .|+|||||+|+|+ |+++. ..++|+++||+++|+|||||||||||||+|+|+|+|+||||
T Consensus       190 gR~hTS~asV~V~-P~~~~-~~i~i~~~dl~i~~~RssG~GGQ~VNkt~SaVrl~HlPtgi  248 (354)
T 3d5a_X          190 GRIHTSTATVAVL-PKAEE-EDFALNMDEIRIDVMRASGPGGQGVNTTDSAVRVVHLPTGI  248 (354)
T ss_dssp             CCCEEEEEEEEEE-ECCCC-CCCCCCGGGEEEEEECCCSCCHHHHHHCCCEEEEEETTTTE
T ss_pred             CcCccCceEEEEe-ccCcc-cccccCccceEEEeecCCCCCCcccccccceEEEEEcCCeE
Confidence            5899999999999 66665 56889999999999999999999999999999999999996

>2jva_A Peptidyl-tRNA hydrolase domain protein; GFT hydrolase, structural genomics, PSI-2, protein STRU initiative; NMR {Pseudomonas syringae PV}

Probab=99.78  E-value=4.7e-20  Score=116.67  Aligned_cols=37  Identities=27%  Similarity=0.451  Sum_probs=34.9

Q ss_pred             CCCCccCCCCeEEEEEeecCCCcccccccCCeEEEEe
Q psy2490          23 SKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTH   59 (64)
Q Consensus        23 ~~~~~i~~~dl~~~~~rssGpGGQ~vNk~~s~V~l~h   59 (64)
                      ...+.|+++||+++|+|||||||||||||+|+|+|+|
T Consensus         5 ~~~i~I~~~dl~~~~~RssGpGGQnVNKv~SaV~L~~   41 (108)
T 2jva_A            5 SNNVHLPDAEIELTAIRAQGAGGQNVNKVSSAMHLRF   41 (108)
T ss_dssp             SSSCEECGGGEEEEECCCTTCSSSSSCCCCCCEEEEE
T ss_pred             ccccccChHHEEEEEEECCCCCCCCcCCCcceEEEEE
Confidence            4467899999999999999999999999999999999

>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

Probab=99.78  E-value=1.4e-19  Score=115.07  Aligned_cols=41  Identities=29%  Similarity=0.476  Sum_probs=37.9

Q ss_pred             CCCCccCCCCeEEEEEeecCCCcccccccCCeEEEE-ecCCC
Q psy2490          23 SKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLT-HIPTD   63 (64)
Q Consensus        23 ~~~~~i~~~dl~~~~~rssGpGGQ~vNk~~s~V~l~-h~ptg   63 (64)
                      ...+.|+++||+++|+|||||||||||||+|+|+|+ |+|+|
T Consensus        12 ~~~i~I~~~dl~~~~~RssGpGGQnVNKv~SaV~Lrf~i~t~   53 (112)
T 1j26_A           12 QASSYIPLDRLSISYCRSSGPGGQNVNKVNSKAEVRFHLASA   53 (112)
T ss_dssp             SSCCCCCTTTSEEEEECCCCSSSSCCSSCCCEEEEEEEGGGC
T ss_pred             ceEEecChHHeEEEEEECCCCCCCCccCCcceEEEEEecccc
Confidence            345679999999999999999999999999999998 99986

>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

Probab=99.74  E-value=1.2e-18  Score=114.23  Aligned_cols=42  Identities=29%  Similarity=0.479  Sum_probs=38.4

Q ss_pred             CCCCCCccCCCCeEEEEEeecCCCcccccccCCeEEEE------ecCC
Q psy2490          21 DYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLT------HIPT   62 (64)
Q Consensus        21 ~~~~~~~i~~~dl~~~~~rssGpGGQ~vNk~~s~V~l~------h~pt   62 (64)
                      .....+.|+++||+|+|+|||||||||||||+|+|+|+      |+|+
T Consensus         3 ~i~~~i~I~~~el~~~~~RssGpGGQnVNKv~SaV~L~~~~~~s~lp~   50 (140)
T 4dh9_Y            3 VISRHVAIPDGELEITAIRAQGAGGQHVNKTSTAIHLRFDIRASSLPE   50 (140)
T ss_dssp             CCCSSSCCCTTCSEEEEECCCSSSSHHHHTTCCCEEEEECCSSSSSCS
T ss_pred             cccCCCccChHHeEEEEEECCCCCCCccccccceEEEEEecccccCCH
Confidence            34566889999999999999999999999999999999      6887

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	64
d1j26a_	112	d.50.4.1 (A:) Ict1 protein {Mouse (Mus musculus) [	4e-11
d2b3tb1	344	e.38.1.1 (B:7-354) Peptide chain release factor 1,	1e-05
d1gqea_	362	e.38.1.1 (A:) Polypeptide chain release factor 2 (	3e-05
d1rq0a_	333	e.38.1.1 (A:) Peptide chain release factor 1, RF1	5e-05

>d1j26a_ d.50.4.1 (A:) Ict1 protein {Mouse (Mus musculus) [TaxId: 10090]} Length = 112

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: Peptidyl-tRNA hydrolase domain-like
family: Peptidyl-tRNA hydrolase domain
domain: Ict1 protein
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 51.5 bits (123), Expect = 4e-11
 Identities = 11/38 (28%), Positives = 16/38 (42%)

Query: 27 KIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTDS 64
           I    +   + R SGPGGQ V K N+   +      +
Sbjct: 16 YIPLDRLSISYCRSSGPGGQNVNKVNSKAEVRFHLASA 53

>d2b3tb1 e.38.1.1 (B:7-354) Peptide chain release factor 1, RF1 {Escherichia coli [TaxId: 562]} Length = 344

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]

 Score = 38.5 bits (89), Expect = 1e-05
 Identities = 15/45 (33%), Positives = 28/45 (62%)

Query: 18  YDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
            +L  +++P ++  D++    R SG GGQ V  T++ + +TH+PT
Sbjct: 197 PELPDAELPDVNPADLRIDTFRSSGAGGQHVNTTDSAIRITHLPT 241

>d1gqea_ e.38.1.1 (A:) Polypeptide chain release factor 2 (RF2) {Escherichia coli [TaxId: 562]} Length = 362

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 = 37.3 bits (86), Expect = 3e-05
 Identities = 23/59 (38%), Positives = 34/59 (57%), Gaps = 1/59 (1%)

Query: 5   RRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTD 63
           RRH S +S+ F   ++D     +I+  D++    R SG GGQ V +T + V +THIPT 
Sbjct: 209 RRHTSFSSA-FVYPEVDDDIDIEINPADLRIDVYRASGAGGQHVNRTESAVRITHIPTG 266

>d1rq0a_ e.38.1.1 (A:) Peptide chain release factor 1, RF1 {Thermotoga maritima [TaxId: 2336]} Length = 333

class: Multi-domain proteins (alpha and beta)
fold: Release factor
superfamily: Release factor
family: Release factor
domain: Peptide chain release factor 1, RF1
species: Thermotoga maritima [TaxId: 2336]

 Score = 36.6 bits (84), Expect = 5e-05
 Identities = 16/35 (45%), Positives = 22/35 (62%)

Query: 28  IDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
           I  +D++    R SG GGQ V KT + V +TH+PT
Sbjct: 193 IRPEDLKIETFRASGHGGQYVNKTESAVRITHLPT 227

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	64
d1gqea_	362	Polypeptide chain release factor 2 (RF2) {Escheric	99.95
d2b3tb1	344	Peptide chain release factor 1, RF1 {Escherichia c	99.94
d1rq0a_	333	Peptide chain release factor 1, RF1 {Thermotoga ma	99.94
d1j26a_	112	Ict1 protein {Mouse (Mus musculus) [TaxId: 10090]}	99.62

>d1gqea_ e.38.1.1 (A:) Polypeptide chain release factor 2 (RF2) {Escherichia coli [TaxId: 562]}

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=99.95  E-value=2.4e-29  Score=181.57  Aligned_cols=60  Identities=37%  Similarity=0.504  Sum_probs=56.9

Q ss_pred             eeeEeCceeEEEeecccCCCCCCccCCCCeEEEEEeecCCCcccccccCCeEEEEecCCCC
Q psy2490           4 FRRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTDS   64 (64)
Q Consensus         4 ~r~~tS~a~V~V~~~~l~~~~~~~i~~~dl~~~~~rssGpGGQ~vNk~~s~V~l~h~ptgi   64 (64)
                      .|+|||||+|.|+ |+++...+++|+++||+|+++|||||||||||||+|||||+|+||||
T Consensus       208 gr~hTS~a~V~v~-P~~~~~~~~~i~~~dl~i~~~rs~g~GGQ~vN~t~savri~H~ptgi  267 (362)
T d1gqea_         208 GRRHTSFSSAFVY-PEVDDDIDIEINPADLRIDVYRASGAGGQHVNRTESAVRITHIPTGI  267 (362)
T ss_dssp             CCEEEEEEEEEEE-ECCBTTBCCCCCGGGEEEEEECCCCSSCCSTTSSCCEEEEEETTTCC
T ss_pred             ceEEEEEEEEEEe-ecCCCccceecChHHeEEEEeecCCCCccchhhhhceeEEEecCchh
Confidence            5899999999999 77777778899999999999999999999999999999999999997

>d2b3tb1 e.38.1.1 (B:7-354) Peptide chain release factor 1, RF1 {Escherichia coli [TaxId: 562]}

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=99.94  E-value=6.1e-28  Score=173.27  Aligned_cols=60  Identities=30%  Similarity=0.467  Sum_probs=56.5

Q ss_pred             eeeEeCceeEEEeecccCCCCCCccCCCCeEEEEEeecCCCcccccccCCeEEEEecCCCC
Q psy2490           4 FRRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTDS   64 (64)
Q Consensus         4 ~r~~tS~a~V~V~~~~l~~~~~~~i~~~dl~~~~~rssGpGGQ~vNk~~s~V~l~h~ptgi   64 (64)
                      .|+|||||+|.|+ |+++....+.|+++||+|+++|||||||||||||+|||||+|+||||
T Consensus       184 ~r~hts~~~v~v~-p~~~~~~~~~i~~~dl~i~~~rssg~GGQ~vnkt~sAVRi~H~ptGi  243 (344)
T d2b3tb1         184 GRIHTSACTVAVM-PELPDAELPDVNPADLRIDTFRSSGAGGQHVNTTDSAIRITHLPTGI  243 (344)
T ss_dssp             CCCEEEEEEEECC-BCCCTTTCCCCCSSSEEEEECCSSCCCTTTCCCSSEEEEEEETTTCC
T ss_pred             cccccceeeEeee-cccccccccccCcccceEEEecCCCccccchhhhhceeEEEEcCCce
Confidence            4899999999999 77777777889999999999999999999999999999999999997

>d1rq0a_ e.38.1.1 (A:) Peptide chain release factor 1, RF1 {Thermotoga maritima [TaxId: 2336]}

class: Multi-domain proteins (alpha and beta)
fold: Release factor
superfamily: Release factor
family: Release factor
domain: Peptide chain release factor 1, RF1
species: Thermotoga maritima [TaxId: 2336]

Probab=99.94  E-value=5.7e-28  Score=173.27  Aligned_cols=59  Identities=36%  Similarity=0.437  Sum_probs=49.9

Q ss_pred             eeeEeCceeEEEeecccCCCCCCccCCCCeEEEEEeecCCCcccccccCCeEEEEecCCCC
Q psy2490           4 FRRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTDS   64 (64)
Q Consensus         4 ~r~~tS~a~V~V~~~~l~~~~~~~i~~~dl~~~~~rssGpGGQ~vNk~~s~V~l~h~ptgi   64 (64)
                      .|+|||||+|.|+ |..+ ..+++|+++||+|+++|||||||||||||+|||||+|+||||
T Consensus       171 ~r~hTs~~~V~v~-p~~~-~~~v~i~~~dl~i~~~RssG~GGQ~VNkt~sAVRitH~PTGi  229 (333)
T d1rq0a_         171 GRIHTSTATVAVL-PEIE-EKDIEIRPEDLKIETFRASGHGGQYVNKTESAVRITHLPTGI  229 (333)
T ss_dssp             CCCEEEEEEEEEE-ECCC-GGGSCCCGGGEEEEEECCCC----CCSSSSEEEEEEETTTCC
T ss_pred             CceEEEEEEEEEe-cccc-cccccccccceeEEeecCCccccchhhhhhheeEEEEcCCcc
Confidence            5899999999999 4443 346889999999999999999999999999999999999997

>d1j26a_ d.50.4.1 (A:) Ict1 protein {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: dsRBD-like
superfamily: Peptidyl-tRNA hydrolase domain-like
family: Peptidyl-tRNA hydrolase domain
domain: Ict1 protein
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.62  E-value=2e-16  Score=98.89  Aligned_cols=36  Identities=31%  Similarity=0.444  Sum_probs=33.2

Q ss_pred             CCCccCCCCeEEEEEeecCCCcccccccCCeEEEEe
Q psy2490          24 KVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTH   59 (64)
Q Consensus        24 ~~~~i~~~dl~~~~~rssGpGGQ~vNk~~s~V~l~h   59 (64)
                      ....|++++|+|+|+||||||||||||++++|.|++
T Consensus        13 ~~~~Ip~~~i~~~f~RSsGPGGQ~VNKv~TkV~Lr~   48 (112)
T d1j26a_          13 ASSYIPLDRLSISYCRSSGPGGQNVNKVNSKAEVRF   48 (112)
T ss_dssp             SCCCCCTTTSEEEEECCCCSSSSCCSSCCCEEEEEE
T ss_pred             hcCccCHHHeEEEEEEcCCCCCCccceeccEEEEEE
Confidence            345799999999999999999999999999999984