Citrus Sinensis ID: 043141

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-----
Protein Sequence
MCYHTNDNCSSSSSSSKKNYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSRLRTLLALNVRSSVKLDAYSPPPQLLQILPPKSTIRSSEVGPQIGPNNPKFAL
Secondary Structure (PSIPRED)
cccccccccEEEcccccEEccccccccccccccEEEEEcccccccccccccccEEccccccccEEEccccHHHHHHHHHHHHHHHHHHHHHHHccHHHHcccccccEEEEccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccEEEEEEEcccccccccccHHHcEEEEEEEcccccccccccccEEEEEcccccEEEEEcccHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccEEEEcccccccccccccccc
Coil and Loop (DISEMBL)
mcyhtndncssssssskknyleltddeLFREcemdtykssgpggqhinkresavrikhvptgvIAQAAEDRSQHKNRVSALSRLRTLLALNVrssvkldayspppqllqilppkstirssevgpqigpnnpkfal
Flexible Loop (DISEMBL)
mcyhtndncssssssskknYLELTDDELFRECEMDtykssgpggqhinKRESAVRIKHVPTGVIaqaaedrsqhknrVSALSRLRTLLALNVRSSvkldayspppqlLQILPPKSTIRssevgpqigpnnpkfal
Low Complexity Region (SEG)
MCYHTNDNCsssssssKKNYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVsalsrlrtllalNVRSSVKLDAYSpppqllqilppKSTIRSSEVGPQIGPNNPKFAL
Disordered region (IsUnstruct)
**************************************************************V******************SRLRTLLALNVRSSVKL*************************************
Disordered Region (DISOPRED)
MCYHTNDNCSSSSSSSKKNYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSRLRTLLA************************KSTIRSSEVGPQIGP******L
Disordered Region (DISEMBL)
*******************YLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQA**********VSALSRLRTLLALNVRSSVKLDAYSPPPQLLQILPPKSTIRSSEVGPQIGPNNPKFAL
Disordered Region (DISPRO)
*C**TNDNCSSSSSSSKKNYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSRLRTLLALNVRSSVKL**************PKSTIRSSEVGPQIGPNNPK***
Transmembrane Helix (TMHMM)
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Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MCYHTNDNCSSSSSSSKKNYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSRLRTLLALNVRSSVKLDAYSPPPQLLQILPPKSTIRSSEVGPQIGPNNPKFAL
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	135	2.2.26 [Sep-21-2011]
A7ZE19	366	Peptide chain release fac	yes	no	0.437	0.161	0.542	8e-16
Q30TP0	365	Peptide chain release fac	yes	no	0.437	0.161	0.576	1e-15
A8EWG5	365	Peptide chain release fac	yes	no	0.437	0.161	0.542	3e-15
A6Q582	368	Peptide chain release fac	yes	no	0.437	0.160	0.525	4e-15
A5IED7	362	Peptide chain release fac	yes	no	0.407	0.151	0.6	4e-15
Q5WUB1	362	Peptide chain release fac	yes	no	0.407	0.151	0.6	4e-15
Q5ZT29	362	Peptide chain release fac	yes	no	0.407	0.151	0.6	4e-15
Q5X2V3	362	Peptide chain release fac	yes	no	0.407	0.151	0.6	4e-15
Q89AC4	366	Peptide chain release fac	yes	no	0.437	0.161	0.542	4e-15
A0RQM7	369	Peptide chain release fac	yes	no	0.481	0.176	0.5	5e-15

>sp|A7ZE19|RF2_CAMC1 Peptide chain release factor 2 OS=Campylobacter concisus (strain 13826) GN=prfB PE=3 SV=1

 Score = 82.4 bits (202), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 32/59 (54%), Positives = 47/59 (79%)

Query: 30  RECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSRLRTLL 88
           ++ ++DTY++SG GGQH+NK ESA+RI H+PTG++ Q   DRSQHKNR +A+  L++ L
Sbjct: 236 KDLKIDTYRASGAGGQHVNKTESAIRITHIPTGIVVQCQNDRSQHKNRATAMKMLKSRL 294

Peptide chain release factor 2 directs the termination of translation in response to the peptide chain termination codons UGA and UAA.
Campylobacter concisus (strain 13826) (taxid: 360104)

>sp|Q30TP0|RF2_SULDN Peptide chain release factor 2 OS=Sulfurimonas denitrificans (strain ATCC 33889 / DSM 1251) GN=prfB PE=3 SV=1

 Score = 82.0 bits (201), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 34/59 (57%), Positives = 45/59 (76%)

Query: 30  RECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSRLRTLL 88
           R+  +DTY+SSG GGQH+NK ESA+RI H+ TGV+ Q   DRSQHKNR +A+  L++ L
Sbjct: 236 RDIRVDTYRSSGAGGQHVNKTESAIRITHIATGVVVQCQNDRSQHKNRATAMKMLKSRL 294

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

Sulfurimonas denitrificans (strain ATCC 33889 / DSM 1251) (taxid: 326298)

>sp|A8EWG5|RF2_ARCB4 Peptide chain release factor 2 OS=Arcobacter butzleri (strain RM4018) GN=prfB PE=3 SV=1

 Score = 80.5 bits (197), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 32/59 (54%), Positives = 45/59 (76%)

Query: 30  RECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSRLRTLL 88
           ++  +DTY++SG GGQH+NK ESA+RI H+PTG++ Q   DRSQHKN+ SA   L++ L
Sbjct: 236 KDIRIDTYRASGAGGQHVNKTESAIRITHIPTGIVVQCQNDRSQHKNKDSAFKMLKSRL 294

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

Arcobacter butzleri (strain RM4018) (taxid: 367737)

>sp|A6Q582|RF2_NITSB Peptide chain release factor 2 OS=Nitratiruptor sp. (strain SB155-2) GN=prfB PE=3 SV=1

 Score = 80.1 bits (196), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 31/59 (52%), Positives = 46/59 (77%)

Query: 30  RECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSRLRTLL 88
           ++  +DTY++SG GGQH+NK +SA+RI H+PTG++ Q   DRSQHKNR +A+  L++ L
Sbjct: 236 KDIRVDTYRASGAGGQHVNKTDSAIRITHIPTGIVVQCQNDRSQHKNRATAMKMLKSRL 294

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

Nitratiruptor sp. (strain SB155-2) (taxid: 387092)

>sp|A5IED7|RF1_LEGPC Peptide chain release factor 1 OS=Legionella pneumophila (strain Corby) GN=prfA PE=3 SV=1

 Score = 80.1 bits (196), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 45/55 (81%)

Query: 34  MDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSRLRTLL 88
           +DTY+SSG GGQH+NK +SA+RI H+PTGV+ +  ++RSQHKNR  A+S L+T L
Sbjct: 226 IDTYRSSGAGGQHVNKTDSAIRITHIPTGVVVECQDERSQHKNRAKAMSLLKTRL 280

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

Legionella pneumophila (strain Corby) (taxid: 400673)

>sp|Q5WUB1|RF1_LEGPL Peptide chain release factor 1 OS=Legionella pneumophila (strain Lens) GN=prfA PE=3 SV=1

 Score = 80.1 bits (196), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 45/55 (81%)

Query: 34  MDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSRLRTLL 88
           +DTY+SSG GGQH+NK +SA+RI H+PTGV+ +  ++RSQHKNR  A+S L+T L
Sbjct: 226 IDTYRSSGAGGQHVNKTDSAIRITHIPTGVVVECQDERSQHKNRAKAMSLLKTRL 280

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

Legionella pneumophila (strain Lens) (taxid: 297245)

>sp|Q5ZT29|RF1_LEGPH Peptide chain release factor 1 OS=Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) GN=prfA PE=3 SV=1

 Score = 80.1 bits (196), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 45/55 (81%)

Query: 34  MDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSRLRTLL 88
           +DTY+SSG GGQH+NK +SA+RI H+PTGV+ +  ++RSQHKNR  A+S L+T L
Sbjct: 226 IDTYRSSGAGGQHVNKTDSAIRITHIPTGVVVECQDERSQHKNRAKAMSLLKTRL 280

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

Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (taxid: 272624)

>sp|Q5X2V3|RF1_LEGPA Peptide chain release factor 1 OS=Legionella pneumophila (strain Paris) GN=prfA PE=3 SV=1

 Score = 80.1 bits (196), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 45/55 (81%)

Query: 34  MDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSRLRTLL 88
           +DTY+SSG GGQH+NK +SA+RI H+PTGV+ +  ++RSQHKNR  A+S L+T L
Sbjct: 226 IDTYRSSGAGGQHVNKTDSAIRITHIPTGVVVECQDERSQHKNRAKAMSLLKTRL 280

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

Legionella pneumophila (strain Paris) (taxid: 297246)

>sp|Q89AC4|RF2_BUCBP Peptide chain release factor 2 OS=Buchnera aphidicola subsp. Baizongia pistaciae (strain Bp) GN=prfB PE=3 SV=2

 Score = 79.7 bits (195), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 32/59 (54%), Positives = 46/59 (77%)

Query: 30  RECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSRLRTLL 88
           R+ ++D Y++SG GGQH+NK ESAVRI+H+PTG++ Q   DRSQHKN+  A+ +L+  L
Sbjct: 238 RDLKIDVYRASGAGGQHVNKTESAVRIRHLPTGIVVQCQNDRSQHKNKDQAMKQLKAKL 296

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

Buchnera aphidicola subsp. Baizongia pistaciae (strain Bp) (taxid: 224915)

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

 Score = 79.7 bits (195), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 35/70 (50%), Positives = 49/70 (70%), Gaps = 5/70 (7%)

Query: 24  TDDELFRECE-----MDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRV 78
            DD++  E E     +D Y++SG GGQH+NK ESAVRI H+PTG++ Q   DRSQHKN+ 
Sbjct: 225 VDDDIAIEIEEKDLRLDYYRASGAGGQHVNKTESAVRITHIPTGIVVQCQNDRSQHKNKA 284

Query: 79  SALSRLRTLL 88
           +A+  L++ L
Sbjct: 285 TAMKMLKSRL 294

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)

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	135
224127830	257	predicted protein [Populus trichocarpa]	0.977	0.513	0.674	8e-48
356559945	250	PREDICTED: uncharacterized protein LOC10	0.933	0.504	0.706	4e-47
297851766	256	hypothetical protein ARALYDRAFT_473511 [	0.851	0.449	0.715	8e-45
30692851	257	Class I peptide chain release factor [Ar	0.851	0.447	0.698	5e-44
12322377	255	peptide chain release factor, putative;	0.851	0.450	0.698	6e-44
242059479	259	hypothetical protein SORBIDRAFT_03g04217	0.925	0.482	0.656	3e-43
414879327	253	TPA: hypothetical protein ZEAMMB73_57118	0.911	0.486	0.650	9e-43
414879328	220	TPA: hypothetical protein ZEAMMB73_57118	0.911	0.559	0.650	1e-42
326517198	170	predicted protein [Hordeum vulgare subsp	0.829	0.658	0.732	2e-42
414873877	507	TPA: hypothetical protein ZEAMMB73_69586	0.911	0.242	0.650	3e-42

>gi|224127830|ref|XP_002329188.1| predicted protein [Populus trichocarpa] gi|222870969|gb|EEF08100.1| predicted protein [Populus trichocarpa]

 Score =  194 bits (494), Expect = 8e-48,   Method: Compositional matrix adjust.
 Identities = 91/135 (67%), Positives = 111/135 (82%), Gaps = 3/135 (2%)

Query: 1   MCYHTNDNCSSSSSSSKKNYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVP 60
           +C++ N   +S+S  +  NYLELTDDEL R+CEMDT+K+SGPGGQH NKRESAVR+KH+P
Sbjct: 74  ICFNYN---TSASHGNGTNYLELTDDELMRQCEMDTFKASGPGGQHRNKRESAVRLKHLP 130

Query: 61  TGVIAQAAEDRSQHKNRVSALSRLRTLLALNVRSSVKLDAYSPPPQLLQILPPKSTIRSS 120
           TG+IAQA EDRSQH NR SAL RLR LLA+ VR+S+ +D+Y+P  +LLQILP KSTIR S
Sbjct: 131 TGIIAQAVEDRSQHMNRASALKRLRALLAIRVRNSLDIDSYTPRLELLQILPLKSTIRGS 190

Query: 121 EVGPQIGPNNPKFAL 135
           + GPQIGP NPKF L
Sbjct: 191 DCGPQIGPKNPKFIL 205

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356559945|ref|XP_003548256.1| PREDICTED: uncharacterized protein LOC100793467 [Glycine max]

 Score =  192 bits (488), Expect = 4e-47,   Method: Compositional matrix adjust.
 Identities = 89/126 (70%), Positives = 109/126 (86%)

Query: 9   CSSSSSSSKKNYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAA 68
            S+    S+K YL L+D+EL R+CEMDT+K+SGPGGQH NKRESAVR+KH+PTG+IAQA+
Sbjct: 67  VSTIEEGSEKCYLNLSDEELMRQCEMDTFKASGPGGQHRNKRESAVRLKHLPTGIIAQAS 126

Query: 69  EDRSQHKNRVSALSRLRTLLALNVRSSVKLDAYSPPPQLLQILPPKSTIRSSEVGPQIGP 128
           EDRSQHKNR SA++RLR+L+AL VR +V L+AYSPP +LLQILPPKS+IR S+ G QIGP
Sbjct: 127 EDRSQHKNRASAINRLRSLIALKVRKTVDLEAYSPPRELLQILPPKSSIRGSDCGSQIGP 186

Query: 129 NNPKFA 134
           NNPKFA
Sbjct: 187 NNPKFA 192

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297851766|ref|XP_002893764.1| hypothetical protein ARALYDRAFT_473511 [Arabidopsis lyrata subsp. lyrata] gi|297339606|gb|EFH70023.1| hypothetical protein ARALYDRAFT_473511 [Arabidopsis lyrata subsp. lyrata]

 Score =  184 bits (468), Expect = 8e-45,   Method: Compositional matrix adjust.
 Identities = 83/116 (71%), Positives = 102/116 (87%), Gaps = 1/116 (0%)

Query: 19  NYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRV 78
           NYL+ TDDEL ++C ++T++ SGPGGQH NKR+SAVR+KH+PTG++AQA EDRSQHKNR 
Sbjct: 84  NYLKFTDDELMKQCRLETFRVSGPGGQHRNKRDSAVRLKHLPTGIVAQAVEDRSQHKNRA 143

Query: 79  SALSRLRTLLALNVRSSVKLDAYSPPPQLLQILPPKSTIRSSEVGPQIGPNNPKFA 134
           SAL+RLRTLLA+ VR+ V L+AY+PPP+LLQILPPKSTIR+S  G QIGPNNPKF 
Sbjct: 144 SALNRLRTLLAIKVRNKVDLEAYAPPPELLQILPPKSTIRTSS-GSQIGPNNPKFV 198

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|30692851|ref|NP_174601.2| Class I peptide chain release factor [Arabidopsis thaliana] gi|12322576|gb|AAG51290.1|AC027035_13 unknown protein [Arabidopsis thaliana] gi|26450075|dbj|BAC42157.1| putative peptide chain release factor [Arabidopsis thaliana] gi|29824307|gb|AAP04114.1| putative peptide chain release factor [Arabidopsis thaliana] gi|332193463|gb|AEE31584.1| Class I peptide chain release factor [Arabidopsis thaliana]

 Score =  182 bits (461), Expect = 5e-44,   Method: Compositional matrix adjust.
 Identities = 81/116 (69%), Positives = 102/116 (87%), Gaps = 1/116 (0%)

Query: 19  NYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRV 78
           NYL+ TD+EL ++C ++T++ SGPGGQH NKR+SAVR+KH+PTG++AQA EDRSQHKNR 
Sbjct: 85  NYLKFTDEELMKQCRLETFRVSGPGGQHRNKRDSAVRLKHLPTGIVAQAVEDRSQHKNRA 144

Query: 79  SALSRLRTLLALNVRSSVKLDAYSPPPQLLQILPPKSTIRSSEVGPQIGPNNPKFA 134
           SAL+RLRTLLA+ VR+ V ++AY+PPP+LLQILPPKSTIR+S  G QIGPNNPKF 
Sbjct: 145 SALNRLRTLLAIKVRNKVDIEAYAPPPELLQILPPKSTIRTSS-GSQIGPNNPKFV 199

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|12322377|gb|AAG51209.1|AC051630_6 peptide chain release factor, putative; 8726-9996 [Arabidopsis thaliana]

 Score =  181 bits (460), Expect = 6e-44,   Method: Compositional matrix adjust.
 Identities = 81/116 (69%), Positives = 102/116 (87%), Gaps = 1/116 (0%)

Query: 19  NYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRV 78
           NYL+ TD+EL ++C ++T++ SGPGGQH NKR+SAVR+KH+PTG++AQA EDRSQHKNR 
Sbjct: 85  NYLKFTDEELMKQCRLETFRVSGPGGQHRNKRDSAVRLKHLPTGIVAQAVEDRSQHKNRA 144

Query: 79  SALSRLRTLLALNVRSSVKLDAYSPPPQLLQILPPKSTIRSSEVGPQIGPNNPKFA 134
           SAL+RLRTLLA+ VR+ V ++AY+PPP+LLQILPPKSTIR+S  G QIGPNNPKF 
Sbjct: 145 SALNRLRTLLAIKVRNKVDIEAYAPPPELLQILPPKSTIRTSS-GSQIGPNNPKFV 199

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242059479|ref|XP_002458885.1| hypothetical protein SORBIDRAFT_03g042170 [Sorghum bicolor] gi|241930860|gb|EES04005.1| hypothetical protein SORBIDRAFT_03g042170 [Sorghum bicolor]

 Score =  179 bits (455), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 82/125 (65%), Positives = 101/125 (80%)

Query: 10  SSSSSSSKKNYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAE 69
           + S      +YL ++D+EL  +C+M T+K+SGPGGQH NKRESAVR+KH+PTG+IAQA E
Sbjct: 77  AKSGGGGHVDYLGMSDEELMEQCDMGTFKASGPGGQHRNKRESAVRLKHLPTGIIAQAVE 136

Query: 70  DRSQHKNRVSALSRLRTLLALNVRSSVKLDAYSPPPQLLQILPPKSTIRSSEVGPQIGPN 129
           DRSQHKNR SALSRLRTL+AL VR  + LD Y+PP +LLQILP KST+R  +VGPQIGPN
Sbjct: 137 DRSQHKNRASALSRLRTLIALKVRRPINLDDYTPPVELLQILPLKSTVRGKDVGPQIGPN 196

Query: 130 NPKFA 134
           N KF+
Sbjct: 197 NSKFS 201

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|414879327|tpg|DAA56458.1| TPA: hypothetical protein ZEAMMB73_571187 [Zea mays]

 Score =  177 bits (450), Expect = 9e-43,   Method: Compositional matrix adjust.
 Identities = 80/123 (65%), Positives = 102/123 (82%)

Query: 12  SSSSSKKNYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDR 71
           + S  + +YL ++D+EL  +C+M T+K+SGPGGQH NKRESAVR+KH+PTG+IAQA EDR
Sbjct: 73  AKSGGRVDYLGMSDEELMEQCDMGTFKASGPGGQHRNKRESAVRLKHLPTGIIAQAVEDR 132

Query: 72  SQHKNRVSALSRLRTLLALNVRSSVKLDAYSPPPQLLQILPPKSTIRSSEVGPQIGPNNP 131
           SQHKNR SALSRLRTL+AL VR  + L+ Y+PP +LLQILP KS++R  +VGPQIGPNN 
Sbjct: 133 SQHKNRASALSRLRTLIALKVRRPINLEDYTPPVELLQILPLKSSVRGKDVGPQIGPNNS 192

Query: 132 KFA 134
           KF+
Sbjct: 193 KFS 195

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|414879328|tpg|DAA56459.1| TPA: hypothetical protein ZEAMMB73_571187 [Zea mays]

 Score =  177 bits (449), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 80/123 (65%), Positives = 102/123 (82%)

Query: 12  SSSSSKKNYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDR 71
           + S  + +YL ++D+EL  +C+M T+K+SGPGGQH NKRESAVR+KH+PTG+IAQA EDR
Sbjct: 73  AKSGGRVDYLGMSDEELMEQCDMGTFKASGPGGQHRNKRESAVRLKHLPTGIIAQAVEDR 132

Query: 72  SQHKNRVSALSRLRTLLALNVRSSVKLDAYSPPPQLLQILPPKSTIRSSEVGPQIGPNNP 131
           SQHKNR SALSRLRTL+AL VR  + L+ Y+PP +LLQILP KS++R  +VGPQIGPNN 
Sbjct: 133 SQHKNRASALSRLRTLIALKVRRPINLEDYTPPVELLQILPLKSSVRGKDVGPQIGPNNS 192

Query: 132 KFA 134
           KF+
Sbjct: 193 KFS 195

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|326517198|dbj|BAJ99965.1| predicted protein [Hordeum vulgare subsp. vulgare]

 Score =  177 bits (448), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 82/112 (73%), Positives = 96/112 (85%)

Query: 23  LTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALS 82
           +TDDEL  +C+M T+KSSGPGGQH NKRESAVR++H PTG++AQA EDRSQHKNR SALS
Sbjct: 1   MTDDELMAQCDMGTFKSSGPGGQHRNKRESAVRLRHHPTGIVAQAVEDRSQHKNRSSALS 60

Query: 83  RLRTLLALNVRSSVKLDAYSPPPQLLQILPPKSTIRSSEVGPQIGPNNPKFA 134
           RLRTL+AL VR  + LD Y+PP +LLQILP KSTIRS +VG QIGPNNPKF+
Sbjct: 61  RLRTLIALKVRRPINLDNYTPPVELLQILPLKSTIRSKDVGNQIGPNNPKFS 112

Source: Hordeum vulgare subsp. vulgare

Species: Hordeum vulgare

Genus: Hordeum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|414873877|tpg|DAA52434.1| TPA: hypothetical protein ZEAMMB73_695866 [Zea mays]

 Score =  176 bits (446), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 80/123 (65%), Positives = 102/123 (82%)

Query: 12  SSSSSKKNYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDR 71
           + S S  +YL ++D+EL  +C+M T+K+SGPGGQH NKRESAVR+KH+P G+IAQA EDR
Sbjct: 74  AKSGSHVDYLGMSDEELMEQCDMGTFKASGPGGQHCNKRESAVRLKHLPIGIIAQAVEDR 133

Query: 72  SQHKNRVSALSRLRTLLALNVRSSVKLDAYSPPPQLLQILPPKSTIRSSEVGPQIGPNNP 131
           SQHKNR SALSRLRTL+AL VR  + L+ Y+PP +LLQILP KS++R ++VGPQIGPNN 
Sbjct: 134 SQHKNRASALSRLRTLIALKVRRPINLEDYTPPVELLQILPLKSSVRGNDVGPQIGPNNS 193

Query: 132 KFA 134
           KF+
Sbjct: 194 KFS 196

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

---

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	135
TAIR|locus:2006897	257	AT1G33330 [Arabidopsis thalian	0.940	0.494	0.492	1.3e-29
UNIPROTKB|P07012	365	prfB [Escherichia coli K-12 (t	0.429	0.158	0.516	3.7e-12
TIGR_CMR|CPS_3552	362	CPS_3552 "peptide chain releas	0.348	0.129	0.574	4.7e-12
TIGR_CMR|CJE_1628	365	CJE_1628 "peptide chain releas	0.414	0.153	0.55	4.8e-12
TIGR_CMR|SO_3833	363	SO_3833 "peptide chain release	0.348	0.129	0.553	6.1e-12
TIGR_CMR|ECH_0705	366	ECH_0705 "peptide chain releas	0.407	0.150	0.517	1.3e-11
TIGR_CMR|APH_0479	376	APH_0479 "peptide chain releas	0.370	0.132	0.56	1.4e-11
TIGR_CMR|CBU_1965	361	CBU_1965 "peptide chain releas	0.348	0.130	0.531	2.7e-11
UNIPROTKB|Q74EJ1	107	GSU0971 "Hydrolase, putative"	0.407	0.514	0.509	3.5e-11
TIGR_CMR|GSU_0971	107	GSU_0971 "peptidyl-tRNA hydrol	0.407	0.514	0.509	3.5e-11

TAIR|locus:2006897 AT1G33330 [Arabidopsis thaliana (taxid:3702)]

 Score = 328 (120.5 bits), Expect = 1.3e-29, P = 1.3e-29
 Identities = 63/128 (49%), Positives = 82/128 (64%)

Query:     6 NDNCXXXXXXXKKNYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIA 65
             ND+          NYL+ TD+EL ++C ++T++ SGPGGQH NKR+SAVR+KH+PTG++A
Sbjct:    72 NDSVSVVSDVQSPNYLKFTDEELMKQCRLETFRVSGPGGQHRNKRDSAVRLKHLPTGIVA 131

Query:    66 QAAEDRSQHKNRVXXXXXXXXXXXXNVRSSVKLDAYSXXXXXXXXXXXKSTIRSSEVGPQ 125
             QA EDRSQHKNR              VR+ V ++AY+           KSTIR+S  G Q
Sbjct:   132 QAVEDRSQHKNRASALNRLRTLLAIKVRNKVDIEAYAPPPELLQILPPKSTIRTSS-GSQ 190

Query:   126 IGPNNPKF 133
             IGPNNPKF
Sbjct:   191 IGPNNPKF 198

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

GO:0006415 "translational termination" evidence=IEA;ISS

GO:0009507 "chloroplast" evidence=IDA

GO:0006783 "heme biosynthetic process" evidence=RCA

UNIPROTKB|P07012 prfB [Escherichia coli K-12 (taxid:83333)]

 Score = 169 (64.5 bits), Expect = 3.7e-12, P = 3.7e-12
 Identities = 32/62 (51%), Positives = 44/62 (70%)

Query:    20 YLELTDD---ELF-RECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHK 75
             Y E+ DD   E+   +  +D Y++SG GGQH+N+ ESAVRI H+PTG++ Q   DRSQHK
Sbjct:   223 YPEVDDDIDIEINPADLRIDVYRTSGAGGQHVNRTESAVRITHIPTGIVTQCQNDRSQHK 282

Query:    76 NR 77
             N+
Sbjct:   283 NK 284

GO:0015858 "nucleoside transport" evidence=IMP

GO:0015864 "pyrimidine nucleoside transport" evidence=IMP

GO:0015862 "uridine transport" evidence=IMP

GO:0006412 "translation" evidence=IEA

GO:0016149 "translation release factor activity, codon specific" evidence=IEA;IDA

GO:0006415 "translational termination" evidence=IEA;IDA

GO:0005737 "cytoplasm" evidence=IEA

TIGR_CMR|CPS_3552 CPS_3552 "peptide chain release factor 1" [Colwellia psychrerythraea 34H (taxid:167879)]

 Score = 168 (64.2 bits), Expect = 4.7e-12, P = 4.7e-12
 Identities = 27/47 (57%), Positives = 39/47 (82%)

Query:    31 ECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNR 77
             + ++DT+++SG GGQH+NK +SA+RI H+PTGV+ +  E RSQHKNR
Sbjct:   223 DLKVDTFRASGAGGQHVNKTDSAIRITHIPTGVVVECQEQRSQHKNR 269

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

GO:0006415 "translational termination" evidence=ISS

TIGR_CMR|CJE_1628 CJE_1628 "peptide chain release factor 2" [Campylobacter jejuni RM1221 (taxid:195099)]

 Score = 168 (64.2 bits), Expect = 4.8e-12, P = 4.8e-12
 Identities = 33/60 (55%), Positives = 43/60 (71%)

Query:    22 ELTDD-ELF---RECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNR 77
             EL DD E+    ++  +D Y++SG GGQH+NK ESAVRI H PTG++ Q   DRSQHKN+
Sbjct:   224 ELDDDIEIEIEEKDIRIDYYRASGAGGQHVNKTESAVRITHFPTGIVVQCQNDRSQHKNK 283

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

GO:0006415 "translational termination" evidence=ISS

TIGR_CMR|SO_3833 SO_3833 "peptide chain release factor 1" [Shewanella oneidensis MR-1 (taxid:211586)]

 Score = 167 (63.8 bits), Expect = 6.1e-12, P = 6.1e-12
 Identities = 26/47 (55%), Positives = 39/47 (82%)

Query:    31 ECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNR 77
             + ++DT++SSG GGQH+NK +SA+RI H+PTG++ +  + RSQHKNR
Sbjct:   223 DLKVDTFRSSGAGGQHVNKTDSAIRITHIPTGIVVECQDQRSQHKNR 269

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

GO:0006415 "translational termination" evidence=ISS

TIGR_CMR|ECH_0705 ECH_0705 "peptide chain release factor 2, programmed frameshift" [Ehrlichia chaffeensis str. Arkansas (taxid:205920)]

 Score = 164 (62.8 bits), Expect = 1.3e-11, P = 1.3e-11
 Identities = 29/56 (51%), Positives = 43/56 (76%)

Query:    22 ELTDDELF-RECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKN 76
             E T+ E+  ++  +DTY++SG GGQH+NK ESAVRI H+P+G++ Q   +RSQH+N
Sbjct:   228 EDTNIEILDKDLRIDTYRASGAGGQHVNKTESAVRITHIPSGIVVQCQNNRSQHQN 283

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

GO:0006415 "translational termination" evidence=ISS

TIGR_CMR|APH_0479 APH_0479 "peptide chain release factor 2, programmed frameshift" [Anaplasma phagocytophilum HZ (taxid:212042)]

 Score = 164 (62.8 bits), Expect = 1.4e-11, P = 1.4e-11
 Identities = 28/50 (56%), Positives = 39/50 (78%)

Query:    28 LFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNR 77
             L ++  +DTY++SG GGQH+NK ESAVRI H+P+G++ Q    RSQH+NR
Sbjct:   236 LEKDLRIDTYRASGAGGQHVNKTESAVRITHIPSGMVVQCQTSRSQHQNR 285

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

GO:0006415 "translational termination" evidence=ISS

TIGR_CMR|CBU_1965 CBU_1965 "peptide chain release factor 1" [Coxiella burnetii RSA 493 (taxid:227377)]

 Score = 161 (61.7 bits), Expect = 2.7e-11, P = 2.7e-11
 Identities = 25/47 (53%), Positives = 39/47 (82%)

Query:    31 ECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNR 77
             E  +DT+++SG GGQH+N+ +SA+RI H+PTGV+ +  ++RSQHKN+
Sbjct:   223 ELRIDTFRASGAGGQHVNRTDSAIRITHLPTGVVVECQDERSQHKNK 269

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

GO:0006415 "translational termination" evidence=ISS

UNIPROTKB|Q74EJ1 GSU0971 "Hydrolase, putative" [Geobacter sulfurreducens PCA (taxid:243231)]

 Score = 154 (59.3 bits), Expect = 3.5e-11, P = 3.5e-11
 Identities = 28/55 (50%), Positives = 42/55 (76%)

Query:    23 LTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNR 77
             +T D    + +++ Y++SGPGGQH N  +SAVRI+H+PTG++ QA+E RSQ +NR
Sbjct:     1 MTVDIRDADIKVEYYRASGPGGQHRNTTDSAVRIRHLPTGIVVQASESRSQAQNR 55

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

TIGR_CMR|GSU_0971 GSU_0971 "peptidyl-tRNA hydrolase domain protein" [Geobacter sulfurreducens PCA (taxid:243231)]

 Score = 154 (59.3 bits), Expect = 3.5e-11, P = 3.5e-11
 Identities = 28/55 (50%), Positives = 42/55 (76%)

Query:    23 LTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNR 77
             +T D    + +++ Y++SGPGGQH N  +SAVRI+H+PTG++ QA+E RSQ +NR
Sbjct:     1 MTVDIRDADIKVEYYRASGPGGQHRNTTDSAVRIRHLPTGIVVQASESRSQAQNR 55

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	135
pfam00472	114	pfam00472, RF-1, RF-1 domain	3e-26
PRK00578	367	PRK00578, prfB, peptide chain release factor 2; Va	3e-24
PRK00591	359	PRK00591, prfA, peptide chain release factor 1; Va	5e-24
COG0216	363	COG0216, PrfA, Protein chain release factor A [Tra	3e-22
TIGR00020	364	TIGR00020, prfB, peptide chain release factor 2	2e-21
PRK07342	339	PRK07342, PRK07342, peptide chain release factor 2	2e-20
PRK05589	325	PRK05589, PRK05589, peptide chain release factor 2	2e-20
COG1186	239	COG1186, PrfB, Protein chain release factor B [Tra	4e-20
TIGR00019	360	TIGR00019, prfA, peptide chain release factor 1	4e-20
TIGR03072	200	TIGR03072, release_prfH, putative peptide chain re	1e-16
PRK08179	200	PRK08179, prfH, peptide chain release factor-like	2e-15
PRK08787	313	PRK08787, PRK08787, peptide chain release factor 2	2e-15
PRK06746	326	PRK06746, PRK06746, peptide chain release factor 2	4e-12
PRK09256	138	PRK09256, PRK09256, hypothetical protein; Provisio	8e-08

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

 Score = 94.6 bits (236), Expect = 3e-26
 Identities = 33/59 (55%), Positives = 46/59 (77%)

Query: 31 ECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSRLRTLLA 89
          +  +DT++SSGPGGQ++NK ESAVR+ H+PTG++ +  E+RSQHKNR  AL RL+  L 
Sbjct: 14 DLRIDTFRSSGPGGQNVNKTESAVRLTHLPTGIVVKCQEERSQHKNREKALERLKAKLY 72

This domain is found in peptide chain release factors such as RF-1 and RF-2, and a number of smaller proteins of unknown function. This domain contains the peptidyl-tRNA hydrolase activity. The domain contains a highly conserved motif GGQ, where the glutamine is thought to coordinate the water that mediates the hydrolysis. Length = 114

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

 Score = 95.0 bits (237), Expect = 3e-24
 Identities = 33/68 (48%), Positives = 48/68 (70%), Gaps = 4/68 (5%)

Query: 21  LELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSA 80
           +E+   +L     +DTY+SSG GGQH+NK +SAVRI H+PTG++ Q   +RSQH+N+ SA
Sbjct: 230 IEINPKDL----RIDTYRSSGAGGQHVNKTDSAVRITHIPTGIVVQCQNERSQHQNKASA 285

Query: 81  LSRLRTLL 88
           +  L+  L
Sbjct: 286 MKMLKAKL 293

Length = 367

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

 Score = 94.0 bits (235), Expect = 5e-24
 Identities = 28/54 (51%), Positives = 41/54 (75%)

Query: 33  EMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSRLRT 86
            +DT++SSG GGQH+N  +SAVRI H+PTG++ +  ++RSQHKN+  A+  LR 
Sbjct: 224 RIDTFRSSGAGGQHVNTTDSAVRITHLPTGIVVECQDERSQHKNKAKAMKVLRA 277

Length = 359

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

 Score = 89.6 bits (223), Expect = 3e-22
 Identities = 29/57 (50%), Positives = 42/57 (73%)

Query: 33  EMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSRLRTLLA 89
            +DT++SSG GGQH+N  +SAVRI H+PTG++ +  ++RSQHKN+  A+  LR  L 
Sbjct: 226 RIDTFRSSGAGGQHVNTTDSAVRITHLPTGIVVECQDERSQHKNKAKAMKVLRARLY 282

Length = 363

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

 Score = 87.1 bits (216), Expect = 2e-21
 Identities = 32/54 (59%), Positives = 42/54 (77%)

Query: 35  DTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSRLRTLL 88
           DTY++SG GGQH+NK +SAVRI H+PTG++ Q   DRSQHKN+ SA+  L+  L
Sbjct: 240 DTYRASGAGGQHVNKTDSAVRITHIPTGIVVQCQNDRSQHKNKDSAMKVLKAKL 293

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|235997 PRK07342, PRK07342, peptide chain release factor 2; Provisional

 Score = 84.5 bits (209), Expect = 2e-20
 Identities = 33/58 (56%), Positives = 43/58 (74%)

Query: 31  ECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSRLRTLL 88
           +  +DTY+SSG GGQH+N  +SAVRI H+PTG++ Q  ++RSQHKNR  A S LR  L
Sbjct: 200 DVRIDTYRSSGAGGQHVNTTDSAVRITHIPTGIVVQCQQERSQHKNRAKAWSMLRARL 257

Length = 339

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

 Score = 84.1 bits (208), Expect = 2e-20
 Identities = 34/71 (47%), Positives = 50/71 (70%), Gaps = 4/71 (5%)

Query: 22  ELTDDELFR----ECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNR 77
           ELTDD+       + ++DTY++ G GGQH+NK ESAVRI H+PTG++ Q   +RSQH N+
Sbjct: 184 ELTDDQDIEIRSEDLKIDTYRAGGAGGQHVNKTESAVRITHIPTGIVVQCQNERSQHSNK 243

Query: 78  VSALSRLRTLL 88
            +A+  L++ L
Sbjct: 244 ETAMKMLKSKL 254

Length = 325

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

 Score = 81.9 bits (203), Expect = 4e-20
 Identities = 30/65 (46%), Positives = 45/65 (69%), Gaps = 4/65 (6%)

Query: 21  LELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSA 80
           +E+ DD+L     +DTY++SG GGQH+NK +SAVR+ H+PTG++     +RSQH N+  A
Sbjct: 105 IEIPDDDL----RIDTYRASGAGGQHVNKTDSAVRLTHLPTGIVVLCQNERSQHLNKALA 160

Query: 81  LSRLR 85
              L+
Sbjct: 161 RKMLK 165

Length = 239

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

 Score = 83.6 bits (207), Expect = 4e-20
 Identities = 29/58 (50%), Positives = 43/58 (74%)

Query: 31  ECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSRLRTLL 88
           +  +DT++SSG GGQH+N  +SAVRI H+PTG++ +  ++RSQHKN+  A+  LR  L
Sbjct: 222 DLRIDTFRSSGAGGQHVNTTDSAVRITHLPTGIVVECQDERSQHKNKDKAMKVLRARL 279

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|213768 TIGR03072, release_prfH, putative peptide chain release factor H

 Score = 72.1 bits (177), Expect = 1e-16
 Identities = 32/68 (47%), Positives = 42/68 (61%), Gaps = 4/68 (5%)

Query: 22  ELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSAL 81
           E T+DE+  E    T +SSGPGGQH+NK ESAVR  H+ +G+  +   +RSQH N+  A 
Sbjct: 102 EATEDEIRFE----TLRSSGPGGQHVNKTESAVRATHLASGISVKVQSERSQHANKRLAT 157

Query: 82  SRLRTLLA 89
             L   LA
Sbjct: 158 LLLAVRLA 165

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

 Score = 68.9 bits (169), Expect = 2e-15
 Identities = 25/60 (41%), Positives = 36/60 (60%)

Query: 30  RECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSRLRTLLA 89
            E   +T +SSGPGGQH+NK +SAVR  H+ +G+  +   +RSQH N+  A   +   L 
Sbjct: 107 DEIRFETLRSSGPGGQHVNKTDSAVRATHLASGISVKVQSERSQHANKRLARLLIAWKLE 166

Length = 200

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

 Score = 70.5 bits (172), Expect = 2e-15
 Identities = 28/50 (56%), Positives = 35/50 (70%)

Query: 35  DTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSRL 84
           D Y+SSG GGQH+NK ESAVRI H+PT  +      RSQH+NR +A+  L
Sbjct: 181 DVYRSSGAGGQHVNKTESAVRITHIPTNTVVACQTGRSQHQNRDNAMKML 230

Length = 313

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

 Score = 61.3 bits (148), Expect = 4e-12
 Identities = 27/58 (46%), Positives = 38/58 (65%)

Query: 31  ECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSRLRTLL 88
           + ++DTY++SG GGQH+N  +SAVRI H PT  +     +RSQ KNR  A+  L+  L
Sbjct: 198 DLKIDTYRASGAGGQHVNTTDSAVRITHTPTNTVVTCQSERSQIKNREHAMKMLKAKL 255

Length = 326

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

 Score = 47.5 bits (114), Expect = 8e-08
 Identities = 31/95 (32%), Positives = 42/95 (44%), Gaps = 32/95 (33%)

Query: 21 LELTDDELFRECEMDTYKSSGPGGQHINKRESAV-------------------------R 55
          L + ++EL    E    ++SGPGGQ++NK  +AV                         R
Sbjct: 8  LVIPENEL----EWRFIRASGPGGQNVNKVSTAVELRFDIAASSLPEFYKERLLALAGHR 63

Query: 56 IKHVPTGVIA-QAAEDRSQHKNRVSALSRLRTLLA 89
          I     GVI  +A E RSQ +NR  AL RL  L+ 
Sbjct: 64 I--TKDGVIVIKAQEFRSQERNREDALERLVALIR 96

Length = 138

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	135
COG0216	363	PrfA Protein chain release factor A [Translation,	100.0
TIGR00019	360	prfA peptide chain release factor 1. This model de	99.98
TIGR03072	200	release_prfH putative peptide chain release factor	99.98
KOG2726	386	consensus Mitochondrial polypeptide chain release	99.98
PRK00591	359	prfA peptide chain release factor 1; Validated	99.98
PF00472	113	RF-1: RF-1 domain; InterPro: IPR000352 Peptide cha	99.97
PRK08179	200	prfH peptide chain release factor-like protein; Re	99.97
PRK05589	325	peptide chain release factor 2; Provisional	99.97
PRK06746	326	peptide chain release factor 2; Provisional	99.97
PRK08787	313	peptide chain release factor 2; Provisional	99.97
PRK07342	339	peptide chain release factor 2; Provisional	99.97
PRK00578	367	prfB peptide chain release factor 2; Validated	99.97
TIGR00020	364	prfB peptide chain release factor 2. In many but n	99.96
PRK09256	138	hypothetical protein; Provisional	99.93
COG1186	239	PrfB Protein chain release factor B [Translation,	99.91
KOG3429	172	consensus Predicted peptidyl-tRNA hydrolase [Trans	99.81
PF10213	127	MRP-S28: Mitochondrial ribosomal subunit protein ;	92.87

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

Probab=100.00  E-value=5.3e-39  Score=272.45  Aligned_cols=116  Identities=34%  Similarity=0.520  Sum_probs=104.6

Q ss_pred             ccccCcceeccCCCCCcC-CcccChhhhhccceEEEEeccCCCccCCCccCceEEEEEcCCeeEEEeccccCHHHHHHHH
Q 043141            2 CYHTNDNCSSSSSSSKKN-YLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSA   80 (135)
Q Consensus         2 ~~ht~~~~~~~~~~~~~~-~~~i~~~~L~~~~~~~~~RsSGPGGQ~VNK~~t~V~l~h~ptGi~v~~~e~RSq~~Nk~~A   80 (135)
                      -+|||||+|.++|..... -+.|+++||    +|+++||||+||||||+|+|+||||||||||+|+||++|||++||+.|
T Consensus       198 RIHTStaTVaVlPE~ee~~ei~I~~~Dl----rIDt~RsSGaGGQhVNtTdSAVRiTHlPTGIvV~cQderSQ~kNk~kA  273 (363)
T COG0216         198 RIHTSAATVAVLPEVEEVEEIEINPKDL----RIDTFRSSGAGGQHVNTTDSAVRITHLPTGIVVECQDERSQHKNKAKA  273 (363)
T ss_pred             ceeecceeEEeccCCCcccccccChHHc----eeeeeecCCCCCCCcCccchhheeeecCCceEEEecchhhhhhhHHHH
Confidence            389999999999987543 589999999    999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhHhcccccCCCCCCccccccCCCCcccccCCCCCCCCCCC
Q 043141           81 LSRLRTLLALNVRSSVKLDAYSPPPQLLQILPPKSTIRSSEVGPQIGPNN  130 (135)
Q Consensus        81 ~~rL~~~l~~~~~~~~~~~~~~~~~~~~~~~~~k~q~~~g~~~~kIr~~n  130 (135)
                      |+.|++.|....+..-..         ++...||+|+++|||||+|||||
T Consensus       274 mkvL~ARl~~~~~~~~~~---------~~~~~RksqVGSGDRSErIRTYN  314 (363)
T COG0216         274 MKVLRARLYDAERQKAQA---------EEASERKSQVGSGDRSERIRTYN  314 (363)
T ss_pred             HHHHHHHHHHHHHHHHHH---------HHHHHHHHhcCCCchhhhhhccC
Confidence            999999988766554222         33468999999999999999999

>TIGR00019 prfA peptide chain release factor 1

Probab=99.98  E-value=2.4e-33  Score=239.65  Aligned_cols=115  Identities=33%  Similarity=0.512  Sum_probs=100.6

Q ss_pred             cccCcceeccCCCCCcCCcccChhhhhccceEEEEeccCCCccCCCccCceEEEEEcCCeeEEEeccccCHHHHHHHHHH
Q 043141            3 YHTNDNCSSSSSSSKKNYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALS   82 (135)
Q Consensus         3 ~ht~~~~~~~~~~~~~~~~~i~~~~L~~~~~~~~~RsSGPGGQ~VNK~~t~V~l~h~ptGi~v~~~e~RSq~~Nk~~A~~   82 (135)
                      .|||++.|.+.|......+.|++.||    +|+|+|||||||||||||+|+|+|+|+||||+|.|+++|||++||+.||+
T Consensus       198 ~hTsfa~V~v~P~~~~~~~~i~~~dl----~~~~~RssG~GGQ~VNkt~SaVrl~h~ptgi~V~~~~eRSQ~~Nk~~A~~  273 (360)
T TIGR00019       198 IHTSAATVAVMPELEEVEVDINPADL----RIDTFRSSGAGGQHVNTTDSAVRITHLPTGIVVECQDERSQHKNKDKAMK  273 (360)
T ss_pred             eecceeEEEEEcCCCccccccCcccE----EEEEEECCCCCCCCcCceeeeEEEEECCCcEEEEECCccCHHHHHHHHHH
Confidence            69999999998866555577888888    99999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhHhcccccCCCCCCccccccCCCCcccccCCCCCCCCCCC
Q 043141           83 RLRTLLALNVRSSVKLDAYSPPPQLLQILPPKSTIRSSEVGPQIGPNN  130 (135)
Q Consensus        83 rL~~~l~~~~~~~~~~~~~~~~~~~~~~~~~k~q~~~g~~~~kIr~~n  130 (135)
                      +|+++|.....+....         ++...+|+++++|+||++||+||
T Consensus       274 ~L~~~L~~~~~~~~~~---------~~~~~r~~~~~~~~Rs~~IRtY~  312 (360)
T TIGR00019       274 VLRARLYEAEQEKQQA---------AQASTRKSQVGSGDRSERIRTYN  312 (360)
T ss_pred             HHHHHHHHHHHHHHHH---------HHHHHHhhhcceecccCCeEEEE
Confidence            9999988776542221         12346799999999999999999

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.

>TIGR03072 release_prfH putative peptide chain release factor H

Probab=99.98  E-value=3.5e-33  Score=222.77  Aligned_cols=112  Identities=31%  Similarity=0.348  Sum_probs=97.0

Q ss_pred             ccCcceeccCCCCCcCCcccChhhhhccceEEEEeccCCCccCCCccCceEEEEEcCCeeEEEeccccCHHHHHHHHHHH
Q 043141            4 HTNDNCSSSSSSSKKNYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSR   83 (135)
Q Consensus         4 ht~~~~~~~~~~~~~~~~~i~~~~L~~~~~~~~~RsSGPGGQ~VNK~~t~V~l~h~ptGi~v~~~e~RSq~~Nk~~A~~r   83 (135)
                      |||+++|.+.+    ..++|+++||    +|+|+|||||||||||||+|+|+|+|+||||+|+|+++|||++||+.|+++
T Consensus        88 ~ts~~~V~v~~----~~~~i~~~dl----~~~~~RssGpGGQ~vNkt~saVrl~h~ptgi~v~~~~~RSQ~~Nk~~A~~~  159 (200)
T TIGR03072        88 KNWFIGVQRFS----ASEEATEDEI----RFETLRSSGPGGQHVNKTESAVRATHLASGISVKVQSERSQHANKRLATLL  159 (200)
T ss_pred             eEEEEEEEEec----CccccChhhe----EEEEEECCCCCcccccccceeEEEEECCCcEEEEECCccCHHHHHHHHHHH
Confidence            67888888865    3466888888    999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhHhcccccCCCCCCccccccCCCCcccccCCCCCCCCCCC-CCC
Q 043141           84 LRTLLALNVRSSVKLDAYSPPPQLLQILPPKSTIRSSEVGPQIGPNN-PKF  133 (135)
Q Consensus        84 L~~~l~~~~~~~~~~~~~~~~~~~~~~~~~k~q~~~g~~~~kIr~~n-~~~  133 (135)
                      |+++|.....+...          ++...++++...++||++||+|| ++|
T Consensus       160 L~~~l~~~~~~~~~----------~~~~~~r~~~~~~~Rg~~iRty~~~~f  200 (200)
T TIGR03072       160 LAVRLADLQQEQAA----------ALRAERRTAHHQIERGNPVRVFKGELF  200 (200)
T ss_pred             HHHHHHHHHHHHHH----------HHHHHHHhccccccccCceEeeeCCcC
Confidence            99998876555432          23456788888889999999999 766

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.

>KOG2726 consensus Mitochondrial polypeptide chain release factor [Translation, ribosomal structure and biogenesis]

Probab=99.98  E-value=4.2e-33  Score=239.19  Aligned_cols=115  Identities=37%  Similarity=0.593  Sum_probs=103.3

Q ss_pred             cccCcceeccCCCC--CcCCcccChhhhhccceEEEEeccCCCccCCCccCceEEEEEcCCeeEEEeccccCHHHHHHHH
Q 043141            3 YHTNDNCSSSSSSS--KKNYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSA   80 (135)
Q Consensus         3 ~ht~~~~~~~~~~~--~~~~~~i~~~~L~~~~~~~~~RsSGPGGQ~VNK~~t~V~l~h~ptGi~v~~~e~RSq~~Nk~~A   80 (135)
                      .|||+..|++.|..  ....+.+++.||    +++|+|+||||||||||++|+|+|+|+||||+|+|+++|||++||+.|
T Consensus       223 ~htstasV~ViP~~~~~~~~~~~~~~dl----~i~~~R~~G~GGQhvNktdsaVrl~HiPTGIvv~cq~eRSq~~Nr~~A  298 (386)
T KOG2726|consen  223 RHTSTASVAVIPQPGRDEVDVEIDEKDL----RIETFRASGPGGQHVNKTDSAVRLTHIPTGIVVECQEERSQHKNRALA  298 (386)
T ss_pred             cccccceEEEeccCCCCccceecCchhe----eEEecccCCCCcccccccccceEEEeecCceEEEeecHHhHHhhHHHH
Confidence            79999999999887  555566887777    999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhHhcccccCCCCCCccccccCCCCcccccCCCCCCCCCCC
Q 043141           81 LSRLRTLLALNVRSSVKLDAYSPPPQLLQILPPKSTIRSSEVGPQIGPNN  130 (135)
Q Consensus        81 ~~rL~~~l~~~~~~~~~~~~~~~~~~~~~~~~~k~q~~~g~~~~kIr~~n  130 (135)
                      +.+|+++|..........+         ..+.++.|+++++++++||+||
T Consensus       299 ~~~L~akL~~~~~~~~~~~---------~~~~r~~qv~s~~rsekiRTy~  339 (386)
T KOG2726|consen  299 LKRLRAKLAVIYREEKSEE---------EKKKRKAQVGSLKRSEKIRTYN  339 (386)
T ss_pred             HHHHHHHHHHHHHhhhhHH---------hhhhhHHhhcccCchhceeecc
Confidence            9999999998877764433         2367999999999999999998

>PRK00591 prfA peptide chain release factor 1; Validated

Probab=99.98  E-value=5.4e-33  Score=237.38  Aligned_cols=115  Identities=34%  Similarity=0.554  Sum_probs=101.5

Q ss_pred             cccCcceeccCCCCCcCCcccChhhhhccceEEEEeccCCCccCCCccCceEEEEEcCCeeEEEeccccCHHHHHHHHHH
Q 043141            3 YHTNDNCSSSSSSSKKNYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALS   82 (135)
Q Consensus         3 ~ht~~~~~~~~~~~~~~~~~i~~~~L~~~~~~~~~RsSGPGGQ~VNK~~t~V~l~h~ptGi~v~~~e~RSq~~Nk~~A~~   82 (135)
                      .|||+++|.+.|......+.|++.||    +|+|+|||||||||||||+|+|+|+|+||||+|.|+++|||++||+.|++
T Consensus       198 ~~tsfa~V~v~P~~~~~~~~i~~~dl----~~~~~RssG~GGQ~VNkt~saVrl~H~ptGi~v~~~~eRSQ~~Nk~~Al~  273 (359)
T PRK00591        198 IHTSAATVAVLPEAEEVEVEINPKDL----RIDTFRSSGAGGQHVNTTDSAVRITHLPTGIVVECQDERSQHKNKAKAMK  273 (359)
T ss_pred             eecceEEEEEEcCCCccccccCcccE----EEEEEECCCCCCCCccceeeeEEEEECCCcEEEEECCcCCHHHHHHHHHH
Confidence            69999999998876665677888887    99999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhHhcccccCCCCCCccccccCCCCcccccCCCCCCCCCCC
Q 043141           83 RLRTLLALNVRSSVKLDAYSPPPQLLQILPPKSTIRSSEVGPQIGPNN  130 (135)
Q Consensus        83 rL~~~l~~~~~~~~~~~~~~~~~~~~~~~~~k~q~~~g~~~~kIr~~n  130 (135)
                      +|+.+|.....+....+         ..+.+|+++.+|+||++||+||
T Consensus       274 ~L~~~L~~~~~~~~~~~---------~~~~r~~~~~~~~Rse~IRtY~  312 (359)
T PRK00591        274 VLRARLYDAERQKAQAE---------EAATRKSQVGSGDRSERIRTYN  312 (359)
T ss_pred             HHHHHHHHHHHHHHHHH---------HHHHHHhhcccccccCCeeeEE
Confidence            99999887665543322         2236699999999999999998

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

Probab=99.97  E-value=2.1e-32  Score=200.10  Aligned_cols=101  Identities=36%  Similarity=0.558  Sum_probs=87.6

Q ss_pred             cCCcccChhhhhccceEEEEeccCCCccCCCccCceEEEEEcCCeeEEEeccccCHHHHHHHHHHHHHHHHHHhHhcccc
Q 043141           18 KNYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSRLRTLLALNVRSSVK   97 (135)
Q Consensus        18 ~~~~~i~~~~L~~~~~~~~~RsSGPGGQ~VNK~~t~V~l~h~ptGi~v~~~e~RSq~~Nk~~A~~rL~~~l~~~~~~~~~   97 (135)
                      ...+.|+++||    +|+|+|||||||||||||+|+|+|+|+|+||+|+|+++|||.+|++.|+++|+++|..+..+...
T Consensus         4 ~~~~~i~~~dl----~~~~~RssGpGGQ~VNk~~s~V~l~h~ptgi~v~~~~~Rsq~~Nr~~A~~~L~~~l~~~~~~~~~   79 (113)
T PF00472_consen    4 EKEIDIPEKDL----EISFSRSSGPGGQNVNKTNSKVRLRHIPTGIVVKCQESRSQHQNREDALEKLREKLDEAYREKRR   79 (113)
T ss_dssp             SSSSCC-GGGE----EEEEEESSSSSSCHHHSSSEEEEEEETTTTEEEEEESSSSHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccccccCHHHe----EEEEEecCCCCCCcccccCCEEEEEEecccEEEEEcccCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34578888888    99999999999999999999999999999999999999999999999999999999988744333


Q ss_pred             cCCCCCCccccccCCCCcccccCCCCCCCCCCCC
Q 043141           98 LDAYSPPPQLLQILPPKSTIRSSEVGPQIGPNNP  131 (135)
Q Consensus        98 ~~~~~~~~~~~~~~~~k~q~~~g~~~~kIr~~n~  131 (135)
                      ..         ....++++.+.++++++||+||-
T Consensus        80 ~~---------~~~~~~~~~~~~~~~~~iR~y~~  104 (113)
T PF00472_consen   80 EK---------TREIRKSQVKRLERKKKIRTYNF  104 (113)
T ss_dssp             HH---------TTTTTTTSCCCSSTTSEEEEEET
T ss_pred             HH---------HHHHHHHHHhHHhhhcceecccC
Confidence            22         23568888888999999999984

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 ....

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

Probab=99.97  E-value=8.6e-32  Score=214.79  Aligned_cols=109  Identities=28%  Similarity=0.275  Sum_probs=93.6

Q ss_pred             ccCcceeccCCCCCcCCcccChhhhhccceEEEEeccCCCccCCCccCceEEEEEcCCeeEEEeccccCHHHHHHHHHHH
Q 043141            4 HTNDNCSSSSSSSKKNYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSR   83 (135)
Q Consensus         4 ht~~~~~~~~~~~~~~~~~i~~~~L~~~~~~~~~RsSGPGGQ~VNK~~t~V~l~h~ptGi~v~~~e~RSq~~Nk~~A~~r   83 (135)
                      |||+++|.+.+    ..+.|+++||    +|+|+|||||||||||||+|+|+|+|+||||+|+|+++|||++||+.|+++
T Consensus        89 ~~s~~~V~v~~----~~~~i~~~dl----~~~~~RssGpGGQ~VNkt~saVrl~h~ptgi~v~~~~~RSQ~~Nk~~A~~~  160 (200)
T PRK08179         89 KNWFVGIGRFS----ADEEEQSDEI----RFETLRSSGPGGQHVNKTDSAVRATHLASGISVKVQSERSQHANKRLARLL  160 (200)
T ss_pred             eEEEEEEEEeC----CcCccCHHHe----EEEEEEccCCcccccccccceEEEEEcCCcEEEEECCCCCHHHHHHHHHHH
Confidence            67788888764    3467888888    999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhHhcccccCCCCCCccccccCCCCcccccCCCCCCCCCCC
Q 043141           84 LRTLLALNVRSSVKLDAYSPPPQLLQILPPKSTIRSSEVGPQIGPNN  130 (135)
Q Consensus        84 L~~~l~~~~~~~~~~~~~~~~~~~~~~~~~k~q~~~g~~~~kIr~~n  130 (135)
                      |+++|.....++...          +...++++...++||++||+|-
T Consensus       161 L~~~L~~~~~~~~~~----------~~~~~~~~~~~~~Rg~~IRt~~  197 (200)
T PRK08179        161 IAWKLEQQQQEQSAA----------LKSQRRMFHHQIERGNPRRVFT  197 (200)
T ss_pred             HHHHHHHHHHHHHHH----------HHHHHHhccccccccCceEeee
Confidence            999988765554332          2356777778888999999984

>PRK05589 peptide chain release factor 2; Provisional

Probab=99.97  E-value=1e-31  Score=227.15  Aligned_cols=115  Identities=32%  Similarity=0.481  Sum_probs=94.5

Q ss_pred             cccCcceeccCCCCCc-CCcccChhhhhccceEEEEeccCCCccCCCccCceEEEEEcCCeeEEEeccccCHHHHHHHHH
Q 043141            3 YHTNDNCSSSSSSSKK-NYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSAL   81 (135)
Q Consensus         3 ~ht~~~~~~~~~~~~~-~~~~i~~~~L~~~~~~~~~RsSGPGGQ~VNK~~t~V~l~h~ptGi~v~~~e~RSq~~Nk~~A~   81 (135)
                      .|||+++|.+.|.... ..+.|+++||    +|+|+|||||||||||||+|+|+|+|+||||+|+|+++|||++||+.|+
T Consensus       172 r~ts~a~V~VlP~~~~~~~~~i~~~dl----~~~~~rssG~GGQ~VNkt~saVrl~H~ptgi~v~~q~eRSQ~~Nk~~A~  247 (325)
T PRK05589        172 RQTSFASVEVLPELTDDQDIEIRSEDL----KIDTYRAGGAGGQHVNKTESAVRITHIPTGIVVQCQNERSQHSNKETAM  247 (325)
T ss_pred             eEeeeEEEEEecCcCccccccCCchhe----EEEEeeCCCCCCCcccceeeEEEEEECCCCEEEEECCccCHHHHHHHHH
Confidence            6999999999987643 2578888888    9999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhHhcccccCCCCCCccccccCCCCcccccCCCCCCCCCCCC
Q 043141           82 SRLRTLLALNVRSSVKLDAYSPPPQLLQILPPKSTIRSSEVGPQIGPNNP  131 (135)
Q Consensus        82 ~rL~~~l~~~~~~~~~~~~~~~~~~~~~~~~~k~q~~~g~~~~kIr~~n~  131 (135)
                      ++|+++|..........          +...++.+.....||++||+||=
T Consensus       248 ~~L~~kL~~~~~~~~~~----------~~~~~r~~~~~~~~g~~IRtY~~  287 (325)
T PRK05589        248 KMLKSKLVELKERAHKE----------KIEDLTGELKDMGWGSQIRSYVF  287 (325)
T ss_pred             HHHHHHHHHHHHHHHHH----------HHHHHhcccccccccCCceeeEC
Confidence            99999888654332221          11223344445567789999984

>PRK06746 peptide chain release factor 2; Provisional

Probab=99.97  E-value=2.9e-31  Score=224.42  Aligned_cols=115  Identities=30%  Similarity=0.368  Sum_probs=97.1

Q ss_pred             cccCcceeccCCCCC-cCCcccChhhhhccceEEEEeccCCCccCCCccCceEEEEEcCCeeEEEeccccCHHHHHHHHH
Q 043141            3 YHTNDNCSSSSSSSK-KNYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSAL   81 (135)
Q Consensus         3 ~ht~~~~~~~~~~~~-~~~~~i~~~~L~~~~~~~~~RsSGPGGQ~VNK~~t~V~l~h~ptGi~v~~~e~RSq~~Nk~~A~   81 (135)
                      .|||++.|.+.|... ...+.|+++||    +|+|+|||||||||||||+|+|+|+|+||||+|+|+++|||++||+.|+
T Consensus       173 rhTsfa~V~v~P~~~~~~~i~i~~~dl----~~~~~rssG~GGQ~vNkt~saVrl~h~ptgi~v~~q~~RSQ~~Nk~~A~  248 (326)
T PRK06746        173 RHTSFVSCEVVPEFNDEVEIEVRTEDL----KIDTYRASGAGGQHVNTTDSAVRITHTPTNTVVTCQSERSQIKNREHAM  248 (326)
T ss_pred             eEeeEEEEEEecCcCCccccccChHHe----EEEEEeCCCCCCCCccceeeEEEEEEeCCeEEEEECCCCCHHHHHHHHH
Confidence            699999999987652 45677888888    9999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhHhcccccCCCCCCccccccCCCCcccccCCCCCCCCCCCC
Q 043141           82 SRLRTLLALNVRSSVKLDAYSPPPQLLQILPPKSTIRSSEVGPQIGPNNP  131 (135)
Q Consensus        82 ~rL~~~l~~~~~~~~~~~~~~~~~~~~~~~~~k~q~~~g~~~~kIr~~n~  131 (135)
                      ++|+++|.....+....+         ....|++++..+ ||++||+||=
T Consensus       249 ~~L~akL~~~~~~~~~~~---------~~~~r~~~~~~~-rg~~IRtYnf  288 (326)
T PRK06746        249 KMLKAKLYQKKLEEQQAE---------LDEIRGEQKEIG-WGSQIRSYVF  288 (326)
T ss_pred             HHHHHHHHHHHHHHHHHH---------HHHHHhhhccCc-cCCCeEEEEC
Confidence            999998886655543322         235677777664 6789999984

>PRK08787 peptide chain release factor 2; Provisional

Probab=99.97  E-value=4.5e-31  Score=222.25  Aligned_cols=114  Identities=33%  Similarity=0.405  Sum_probs=92.5

Q ss_pred             cccCcceeccCCCCCc-CCcccChhhhhccceEEEEeccCCCccCCCccCceEEEEEcCCeeEEEeccccCHHHHHHHHH
Q 043141            3 YHTNDNCSSSSSSSKK-NYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSAL   81 (135)
Q Consensus         3 ~ht~~~~~~~~~~~~~-~~~~i~~~~L~~~~~~~~~RsSGPGGQ~VNK~~t~V~l~h~ptGi~v~~~e~RSq~~Nk~~A~   81 (135)
                      .|||++.|.+.|.... ..+.|++.||    +|+|+|||||||||||||+|+|+|+|+||||+|+|+++|||++||+.|+
T Consensus       152 rhTsfasV~V~P~~~~~~~i~i~~~dl----~~~~~RssG~GGQ~VNkt~saVri~H~Ptgi~v~~q~eRSQ~~Nk~~A~  227 (313)
T PRK08787        152 RHTSFTSVFVSPEVDDNIEIDINPADL----RTDVYRSSGAGGQHVNKTESAVRITHIPTNTVVACQTGRSQHQNRDNAM  227 (313)
T ss_pred             EEeeeEEEEEecCcCcccccccChhHe----EEEEEECCCCCCCCcCCEeeEEEEEECCCcEEEEECCcccHHHHHHHHH
Confidence            6999999999876643 3577888888    9999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhHhcccccCCCCCCccccccCCCCcccccCCCCCCCCCCC
Q 043141           82 SRLRTLLALNVRSSVKLDAYSPPPQLLQILPPKSTIRSSEVGPQIGPNN  130 (135)
Q Consensus        82 ~rL~~~l~~~~~~~~~~~~~~~~~~~~~~~~~k~q~~~g~~~~kIr~~n  130 (135)
                      ++|+++|.....+....+..       .....|+++++|   +|||+||
T Consensus       228 ~~L~~~L~~~~~e~~~~~~~-------~~~~~k~~i~~g---~qIRtY~  266 (313)
T PRK08787        228 KMLAAKLYELEVQKRNAEKD-------ALEATKSDIGWG---SQIRNYV  266 (313)
T ss_pred             HHHHHHHHHHHHHHHHHHHH-------HHhhhhhhCccc---cccccee
Confidence            99999888654443222100       011236666544   5899998

>PRK07342 peptide chain release factor 2; Provisional

Probab=99.97  E-value=6.9e-31  Score=223.09  Aligned_cols=115  Identities=34%  Similarity=0.448  Sum_probs=93.2

Q ss_pred             cccCcceeccCCCCCc-CCcccChhhhhccceEEEEeccCCCccCCCccCceEEEEEcCCeeEEEeccccCHHHHHHHHH
Q 043141            3 YHTNDNCSSSSSSSKK-NYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSAL   81 (135)
Q Consensus         3 ~ht~~~~~~~~~~~~~-~~~~i~~~~L~~~~~~~~~RsSGPGGQ~VNK~~t~V~l~h~ptGi~v~~~e~RSq~~Nk~~A~   81 (135)
                      .|||+++|.+.|.... ..+.|++.||    +|+|+|||||||||||||+|+|+|+|+||||+|+|+++|||++||+.|+
T Consensus       175 rhTs~a~V~VlP~~~~~~~~~i~~~dl----~~~~~RssG~GGQ~VNkt~saVrl~H~ptgi~v~~~~eRSQ~~Nk~~A~  250 (339)
T PRK07342        175 RHTSFASIWVYPVIDDNIEVDVNESDV----RIDTYRSSGAGGQHVNTTDSAVRITHIPTGIVVQCQQERSQHKNRAKAW  250 (339)
T ss_pred             eEeEEEEEEEEcCCCcccccccCcccE----EEEEEECCCCCCCCccceeeeEEEEEcCCcEEEEECCcccHHHHHHHHH
Confidence            6999999999886643 2467777777    9999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhHhcccccCCCCCCccccccCCCCcccccCCCCCCCCCCCC
Q 043141           82 SRLRTLLALNVRSSVKLDAYSPPPQLLQILPPKSTIRSSEVGPQIGPNNP  131 (135)
Q Consensus        82 ~rL~~~l~~~~~~~~~~~~~~~~~~~~~~~~~k~q~~~g~~~~kIr~~n~  131 (135)
                      ++|+++|.....+....+..       ....+++++++|+   +||+||=
T Consensus       251 ~~L~~~L~~~~~~~~~~~~~-------~~~~~~~~i~~g~---~IRtY~~  290 (339)
T PRK07342        251 SMLRARLYEEELKKREEATN-------AAAASKTDIGWGH---QIRSYVL  290 (339)
T ss_pred             HHHHHHHHHHHHHHHHHHHH-------HHHhhhhhccccC---CcCCccC
Confidence            99999888665544332110       1123466666554   8999983

>PRK00578 prfB peptide chain release factor 2; Validated

Probab=99.97  E-value=8.8e-31  Score=224.31  Aligned_cols=114  Identities=33%  Similarity=0.474  Sum_probs=95.4

Q ss_pred             cccCcceeccCCCCCcC-CcccChhhhhccceEEEEeccCCCccCCCccCceEEEEEcCCeeEEEeccccCHHHHHHHHH
Q 043141            3 YHTNDNCSSSSSSSKKN-YLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSAL   81 (135)
Q Consensus         3 ~ht~~~~~~~~~~~~~~-~~~i~~~~L~~~~~~~~~RsSGPGGQ~VNK~~t~V~l~h~ptGi~v~~~e~RSq~~Nk~~A~   81 (135)
                      .|||+++|.+.|..... .+.|+++||    +|+|+|||||||||||||+|+|+|+|+||||+|.|+++|||++||+.|+
T Consensus       211 ~hts~~~V~vlP~~~~~~~~~i~~~dl----~~~~~rssGpGGQ~vNkt~saVrl~h~ptgi~v~~~~~RSQ~~Nk~~A~  286 (367)
T PRK00578        211 RHTSFASVEVYPEVDDTIEIEINPKDL----RIDTYRSSGAGGQHVNKTDSAVRITHIPTGIVVQCQNERSQHQNKASAM  286 (367)
T ss_pred             eecceeeEEecCCCCCccccccChhhE----EEEEeeCCCCCCCcccceeeEEEEEECCCcEEEEECCCCCHHHHHHHHH
Confidence            69999999999876432 567888888    9999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhHhcccccCCCCCCccccccCCCCcccccCCCCCCCCCCC
Q 043141           82 SRLRTLLALNVRSSVKLDAYSPPPQLLQILPPKSTIRSSEVGPQIGPNN  130 (135)
Q Consensus        82 ~rL~~~l~~~~~~~~~~~~~~~~~~~~~~~~~k~q~~~g~~~~kIr~~n  130 (135)
                      ++|+++|..........+         ..+.|+.+ ...+||++||+||
T Consensus       287 ~~L~~kL~~~~~~~~~~~---------~~~~r~~~-~~~~rg~~IRtYn  325 (367)
T PRK00578        287 KMLKAKLYELELEKRAAE---------KDALKGEK-KEIGWGSQIRSYV  325 (367)
T ss_pred             HHHHHHHHHHHHHHHHHH---------HHHHHhhh-ccccccCCeEEEE
Confidence            999998887665543322         12344444 4556778999999

>TIGR00020 prfB peptide chain release factor 2

Probab=99.96  E-value=1.3e-30  Score=223.16  Aligned_cols=115  Identities=34%  Similarity=0.449  Sum_probs=94.2

Q ss_pred             cccCcceeccCCCC-CcCCcccChhhhhccceEEEEeccCCCccCCCccCceEEEEEcCCeeEEEeccccCHHHHHHHHH
Q 043141            3 YHTNDNCSSSSSSS-KKNYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSAL   81 (135)
Q Consensus         3 ~ht~~~~~~~~~~~-~~~~~~i~~~~L~~~~~~~~~RsSGPGGQ~VNK~~t~V~l~h~ptGi~v~~~e~RSq~~Nk~~A~   81 (135)
                      .|||++.|.+.|.. ....+.|++.||    +|+|+||||||||||||++|+|+|+|+||||+|+|+++|||++||+.|+
T Consensus       211 rhts~a~V~vlP~~~~~~~~~i~~~d~----~~~~~rssG~GGQ~VNkt~saVri~H~ptgi~v~~q~~RSQ~~Nk~~A~  286 (364)
T TIGR00020       211 RHTSFASVFVMPEVDDDIDIEIKPEDL----RIDTYRASGAGGQHVNKTDSAVRITHIPTGIVVQCQNDRSQHKNKDSAM  286 (364)
T ss_pred             eEeeeEEEEEecCCCcccceecccccE----EEEEeeCCCCCCccccccceEEEEEECCCcEEEEECCccCHHHHHHHHH
Confidence            69999999998866 344567777777    9999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhHhcccccCCCCCCccccccCCCCcccccCCCCCCCCCCCC
Q 043141           82 SRLRTLLALNVRSSVKLDAYSPPPQLLQILPPKSTIRSSEVGPQIGPNNP  131 (135)
Q Consensus        82 ~rL~~~l~~~~~~~~~~~~~~~~~~~~~~~~~k~q~~~g~~~~kIr~~n~  131 (135)
                      ++|+++|.....+....+         ....|+++... +||++||+||=
T Consensus       287 ~~L~~kL~~~~~~~~~~~---------~~~~r~~~~~~-~rg~~IRtY~~  326 (364)
T TIGR00020       287 KVLKAKLYELEMEKEQAE---------KDAKEGEKSEI-GWGSQIRSYVL  326 (364)
T ss_pred             HHHHHHHHHHHHHHHHHH---------HHHHHhhhhcc-CccCCeEEEEC
Confidence            999998886655443321         12345333333 57789999984

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.

>PRK09256 hypothetical protein; Provisional

Probab=99.93  E-value=1.1e-25  Score=170.81  Aligned_cols=83  Identities=37%  Similarity=0.585  Sum_probs=72.4

Q ss_pred             CcCCcccChhhhhccceEEEEeccCCCccCCCccCceEEEEE------cC-----------------Ce-eEEEeccccC
Q 043141           17 KKNYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKH------VP-----------------TG-VIAQAAEDRS   72 (135)
Q Consensus        17 ~~~~~~i~~~~L~~~~~~~~~RsSGPGGQ~VNK~~t~V~l~h------~p-----------------tG-i~v~~~e~RS   72 (135)
                      .+..+.|+.++|    +|+|+|||||||||||||+|+|+|+|      +|                 +| |+|+|+++||
T Consensus         4 ~~~~~~i~~~~l----~~~~~RSSGPGGQ~VNKt~SkV~l~~~~~~~~lp~~~~~~l~~~~~~r~~~~g~l~i~~~~~RS   79 (138)
T PRK09256          4 ITRRLVIPENEL----EWRFIRASGPGGQNVNKVSTAVELRFDIAASSLPEFYKERLLALAGHRITKDGVIVIKAQEFRS   79 (138)
T ss_pred             cCccCccCHHHe----EEEEEEcCCCCcccccccceeeEEEechhhccCCHHHHHHHHHHhcCcccCCCcEEEEECCcCC
Confidence            445688998888    99999999999999999999999996      66                 46 9999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhHhcccccCCCCC
Q 043141           73 QHKNRVSALSRLRTLLALNVRSSVKLDAYSP  103 (135)
Q Consensus        73 q~~Nk~~A~~rL~~~l~~~~~~~~~~~~~~~  103 (135)
                      |.+|+++|+++|.++|..++..+....+..|
T Consensus        80 Q~~Nr~~al~kL~~~i~~~~~~p~~r~~tk~  110 (138)
T PRK09256         80 QERNREDALERLVALIREALKPPKKRRATKP  110 (138)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhccccccCCcc
Confidence            9999999999999999998886555444443

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

Probab=99.91  E-value=1.3e-25  Score=183.40  Aligned_cols=115  Identities=32%  Similarity=0.426  Sum_probs=84.7

Q ss_pred             ccCcceeccCCCC-CcCCcccChhhhhccceEEEEeccCCCccCCCccCceEEEEEcCCeeEEEeccccCHHHHHHHHHH
Q 043141            4 HTNDNCSSSSSSS-KKNYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALS   82 (135)
Q Consensus         4 ht~~~~~~~~~~~-~~~~~~i~~~~L~~~~~~~~~RsSGPGGQ~VNK~~t~V~l~h~ptGi~v~~~e~RSq~~Nk~~A~~   82 (135)
                      |||=.-+.+.|.- ....+.|+++||    +++|+|||||||||||||+|+|+|+|+|+||+|.|+.+|||+.|++.|+.
T Consensus        87 ~tsf~~v~v~p~~~~~i~i~I~~~dl----~idt~RASGaGGQhVNKt~SAVrlth~ptgivv~cq~eRSq~~n~~~a~~  162 (239)
T COG1186          87 HTSFASVEVFPELDISIEIEIPDDDL----RIDTYRASGAGGQHVNKTDSAVRLTHLPTGIVVLCQNERSQHLNKALARK  162 (239)
T ss_pred             ccceeeeeecCCCCcccceecCccce----EEEEEEcCCCCCCccccccccEEEEEcCCCCEecCHHHHHHHHHHHHHHH
Confidence            5665444444322 455677888888    99999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhHhcccccCCCCCCccccccCCCCcccccCCCCCCCCCCCCC
Q 043141           83 RLRTLLALNVRSSVKLDAYSPPPQLLQILPPKSTIRSSEVGPQIGPNNPK  132 (135)
Q Consensus        83 rL~~~l~~~~~~~~~~~~~~~~~~~~~~~~~k~q~~~g~~~~kIr~~n~~  132 (135)
                      .|+..|.....+....+       ..++...+..+.+|.   +||.|-.+
T Consensus       163 ~l~~kL~~~~~~~Rsqe-------~n~~~a~~k~i~wg~---qirsyv~~  202 (239)
T COG1186         163 MLKGKLYILAQEKRSQE-------KNRERALKKLIGWGN---QIRSYVLD  202 (239)
T ss_pred             HHHHHHHHHHHHHHHHH-------HHHHHHHhhhHHHHH---hccccCCC
Confidence            99997664443322211       011223344454443   78877654

>KOG3429 consensus Predicted peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis]

Probab=99.81  E-value=3.4e-20  Score=144.59  Aligned_cols=70  Identities=34%  Similarity=0.643  Sum_probs=62.7

Q ss_pred             ccChhhhhccceEEEEeccCCCccCCCccCceEEEEE-------cC-----------------Ce-eEEEeccccCHHHH
Q 043141           22 ELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKH-------VP-----------------TG-VIAQAAEDRSQHKN   76 (135)
Q Consensus        22 ~i~~~~L~~~~~~~~~RsSGPGGQ~VNK~~t~V~l~h-------~p-----------------tG-i~v~~~e~RSq~~N   76 (135)
                      .|+.+.|    ++.|+||||||||||||++|+|.|++       ||                 .| |+|.++.+|||+.|
T Consensus        36 ~ipld~~----~i~y~RSSGPGGQNVNKvNTKv~vrf~vs~a~Wipe~~R~~~~~~~~~rink~gelvI~Sd~TRsq~~N  111 (172)
T KOG3429|consen   36 KIPLDQL----EISYSRSSGPGGQNVNKVNTKVEVRFKVSNAEWIPEFLRNKLLTTEKNRINKDGELVIYSDKTRSQHKN  111 (172)
T ss_pred             CCchhhe----EEEEeecCCCCCcccccccceEEEEEecchhhhccHHHHHHHHHHHHHhhccCccEEEecchhHHhhcc
Confidence            3666777    99999999999999999999999996       44                 45 99999999999999


Q ss_pred             HHHHHHHHHHHHHHhHhcc
Q 043141           77 RVSALSRLRTLLALNVRSS   95 (135)
Q Consensus        77 k~~A~~rL~~~l~~~~~~~   95 (135)
                      .++||++|+++|..+...+
T Consensus       112 iaDcleKlr~~I~~~~~~~  130 (172)
T KOG3429|consen  112 IADCLEKLRDIIRAAEQTP  130 (172)
T ss_pred             HHHHHHHHHHHHHHHhcCC
Confidence            9999999999999877654

>PF10213 MRP-S28: Mitochondrial ribosomal subunit protein ; InterPro: IPR019349 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=92.87  E-value=0.74  Score=34.58  Aligned_cols=34  Identities=12%  Similarity=0.017  Sum_probs=31.5

Q ss_pred             Ce-eEEEeccccCHHHHHHHHHHHHHHHHHHhHhc
Q 043141           61 TG-VIAQAAEDRSQHKNRVSALSRLRTLLALNVRS   94 (135)
Q Consensus        61 tG-i~v~~~e~RSq~~Nk~~A~~rL~~~l~~~~~~   94 (135)
                      +| |.+.|+..-++.+|+.-|...|..+|.++.+.
T Consensus        60 ~d~l~i~sdr~~~~~qN~~~l~~~l~~L~~EA~~~   94 (127)
T PF10213_consen   60 TDILKISSDRFPTRAQNKKYLSDLLTRLIHEAKDL   94 (127)
T ss_pred             CCEEEEecccCCCHHHHHHHHHHHHHHHHHHHhhc
Confidence            67 99999999999999999999999999988774

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents a conserved region of approx. 125 residues of one of the proteins that makes up the small subunit of the mitochondrial ribosome. In Saccharomyces cerevisiae (Baker's yeast) it is mitochondrial ribosomal protein S24 whereas in humans it is S35.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	135
1ml5_Z	365	Structure Of The E. Coli Ribosomal Termination Comp		4e-13
1mi6_A	365	Docking Of The Modified Rf2 X-Ray Structure Into Th		4e-13
1gqe_A	365	Polypeptide Chain Release Factor 2 (Rf2) From Esche		5e-13
2b3t_B	360	Molecular Basis For Bacterial Class 1 Release Facto		2e-11
2fvo_A	333	Docking Of The Modified Rf1 X-ray Structure Into Th		1e-09
1rq0_A	342	Crystal Structure Of Peptide Releasing Factor 1 Len		1e-09
2b64_Y	354	30s Ribosomal Subunit, Trnas, Mrna And Release Fact		9e-09
1zbt_A	371	Crystal Structure Of Peptide Chain Release Factor 1		4e-08
3f1e_X	378	Crystal Structure Of A Translation Termination Comp		9e-08
2x9r_Y	351	Structure Of The 70s Ribosome Bound To Release Fact		1e-07
2wh1_Y	351	Insights Into Translational Termination From The St		1e-07
2ihr_1	365	Rf2 Of Thermus Thermophilus Length = 365		1e-07
2b9m_Y	365	30s Ribosomal Subunit, Trnas, Mrna And Release Fact		1e-07
2rsm_A	115	Solution Structure And Sirna-Mediated Knockdown Ana		4e-05

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

Iteration: 1
 Score = 70.1 bits (170), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 27/47 (57%), Positives = 37/47 (78%)
Query: 31  ECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNR 77
           +  +D Y++SG GGQH+N+ ESAVRI H+PTG++ Q   DRSQHKN+
Sbjct: 238 DLRIDVYRTSGAGGQHVNRTESAVRITHIPTGIVTQCQNDRSQHKNK 284

>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 = 69.7 bits (169), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 27/47 (57%), Positives = 37/47 (78%)
Query: 31  ECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNR 77
           +  +D Y++SG GGQH+N+ ESAVRI H+PTG++ Q   DRSQHKN+
Sbjct: 238 DLRIDVYRASGAGGQHVNRTESAVRITHIPTGIVTQCQNDRSQHKNK 284

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

Iteration: 1
 Score = 69.7 bits (169), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 27/47 (57%), Positives = 37/47 (78%)
Query: 31  ECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNR 77
           +  +D Y++SG GGQH+N+ ESAVRI H+PTG++ Q   DRSQHKN+
Sbjct: 238 DLRIDVYRASGAGGQHVNRTESAVRITHIPTGIVTQCQNDRSQHKNK 284

>pdb|2B3T|B Chain B, Molecular Basis For Bacterial Class 1 Release Factor Methylation By Prmc Length = 360

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 24/48 (50%), Positives = 38/48 (79%)
Query: 31  ECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRV 78
           +  +DT++SSG GGQH+N  +SA+RI H+PTG++ +  ++RSQHKN+ 
Sbjct: 221 DLRIDTFRSSGAGGQHVNTTDSAIRITHLPTGIVVECQDERSQHKNKA 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 = 58.2 bits (139), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 22/47 (46%), Positives = 38/47 (80%)
Query: 31  ECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNR 77
           + +++T+++SG GGQ++NK ESAVRI H+PTG++     +RSQ++N+
Sbjct: 197 DLKIETFRASGHGGQYVNKTESAVRITHLPTGIVVSCQNERSQYQNK 243

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

Iteration: 1
 Score = 58.2 bits (139), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 22/47 (46%), Positives = 38/47 (80%)
Query: 31  ECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNR 77
           + +++T+++SG GGQ++NK ESAVRI H+PTG++     +RSQ++N+
Sbjct: 197 DLKIETFRASGHGGQYVNKTESAVRITHLPTGIVVSCQNERSQYQNK 243

>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

Iteration: 1
 Score = 55.5 bits (132), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 23/47 (48%), Positives = 33/47 (70%)
Query: 31  ECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNR 77
           E  +D  ++SGPGGQ +N  +SAVR+ H+PTG++    + RSQ KNR
Sbjct: 216 EIRIDVMRASGPGGQGVNTTDSAVRVVHLPTGIMVTCQDSRSQIKNR 262

>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

Iteration: 1
 Score = 53.1 bits (126), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 34/48 (70%)
Query: 30  RECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNR 77
           ++  +D Y +SG GGQ++NK  +AVRI H+PT +  +  E+R+Q KNR
Sbjct: 233 KDLRVDIYHASGAGGQNVNKVATAVRIIHLPTNIKVEXQEERTQQKNR 280

>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

Iteration: 1
 Score = 52.0 bits (123), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 22/47 (46%), Positives = 31/47 (65%)
Query: 31  ECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNR 77
           E  +D  ++SGPGGQ +N  +SAVR+ H+PTG+       RSQ KN+
Sbjct: 239 ELRIDVMRASGPGGQGVNTTDSAVRVVHLPTGITVTCQTTRSQIKNK 285

>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

Iteration: 1
 Score = 52.0 bits (123), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 22/47 (46%), Positives = 31/47 (65%)
Query: 31  ECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNR 77
           E  +D  ++SGPGGQ +N  +SAVR+ H+PTG+       RSQ KN+
Sbjct: 221 ELRIDVMRASGPGGQGVNTTDSAVRVVHLPTGITVTCQTTRSQIKNK 267

>pdb|2WH1|Y Chain Y, Insights Into Translational Termination From The Structure Of Rf2 Bound To The Ribosome Length = 351

Iteration: 1
 Score = 52.0 bits (123), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 22/47 (46%), Positives = 31/47 (65%)
Query: 31  ECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNR 77
           E  +D  ++SGPGGQ +N  +SAVR+ H+PTG+       RSQ KN+
Sbjct: 221 ELRIDVMRASGPGGQGVNTTDSAVRVVHLPTGITVTCQTTRSQIKNK 267

>pdb|2IHR|1 Chain 1, Rf2 Of Thermus Thermophilus Length = 365

Iteration: 1
 Score = 52.0 bits (123), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 22/47 (46%), Positives = 31/47 (65%)
Query: 31  ECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNR 77
           E  +D  ++SGPGGQ +N  +SAVR+ H+PTG+       RSQ KN+
Sbjct: 226 ELRIDVMRASGPGGQGVNTTDSAVRVVHLPTGITVTCQTTRSQIKNK 272

>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

Iteration: 1
 Score = 51.6 bits (122), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 22/47 (46%), Positives = 31/47 (65%)
Query: 31  ECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNR 77
           E  +D  ++SGPGGQ +N  +SAVR+ H+PTG+       RSQ KN+
Sbjct: 226 ELRIDVMRASGPGGQGVNTTDSAVRVVHLPTGITVTCQTTRSQIKNK 272

>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 = 43.5 bits (101), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 25/64 (39%), Positives = 36/64 (56%), Gaps = 7/64 (10%)
Query: 17 KKNY---LELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQ 73
          +K+Y   L L + EL    E    K  GPGGQ  NK  + V +KHVP+G++ +  + RS 
Sbjct: 34 RKDYPALLPLNESEL----EEQFVKGHGPGGQATNKTSNCVVLKHVPSGIVVKCHQTRSV 89
Query: 74 HKNR 77
           +NR
Sbjct: 90 DQNR 93

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	135
2ihr_1	365	Peptide chain release factor 2; mixed alpha-beta,	3e-25
2rsm_A	115	Probable peptide chain release factor C12ORF65 HO	5e-25
1gqe_A	365	Release factor 2, RF2; protein synthesis, ribosome	8e-25
1zbt_A	371	RF-1, peptide chain release factor 1; peptide chai	2e-24
3d5a_X	354	RF1, peptide chain release factor 1; ribosome, rib	3e-24
2b3t_B	360	RF-1, peptide chain release factor 1; translation	4e-24
1rq0_A	342	RF-1, peptide chain release factor 1; X-RAY, cryst	1e-23
4dh9_Y	140	YAEJ; ribosome, YAEJ, ribosome stalling, ribosome	2e-14
2jva_A	108	Peptidyl-tRNA hydrolase domain protein; GFT hydrol	5e-14
1j26_A	112	Immature colon carcinoma transcript 1; peptide cha	7e-11

>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 = 97.3 bits (243), Expect = 3e-25
 Identities = 25/55 (45%), Positives = 35/55 (63%)

Query: 31  ECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSRLR 85
           E  +D  ++SGPGGQ +N  +SAVR+ H+PTG+       RSQ KN+  AL  L+
Sbjct: 226 ELRIDVMRASGPGGQGVNTTDSAVRVVHLPTGITVTCQTTRSQIKNKELALKILK 280

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

 Score = 90.9 bits (226), Expect = 5e-25
 Identities = 25/68 (36%), Positives = 36/68 (52%), Gaps = 4/68 (5%)

Query: 21  LELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSA 80
           L L + EL    E    K  GPGGQ  NK  + V +KHVP+G++ +  + RS  +NR  A
Sbjct: 41  LPLNESEL----EEQFVKGHGPGGQATNKTSNCVVLKHVPSGIVVKCHQTRSVDQNRKIA 96

Query: 81  LSRLRTLL 88
              L+  +
Sbjct: 97  RKVLQEKV 104

>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 = 96.2 bits (240), Expect = 8e-25
 Identities = 29/58 (50%), Positives = 43/58 (74%)

Query: 31  ECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSRLRTLL 88
           +  +D Y++SG GGQH+N+ ESAVRI H+PTG++ Q   DRSQHKN+  A+ +++  L
Sbjct: 238 DLRIDVYRASGAGGQHVNRTESAVRITHIPTGIVTQCQNDRSQHKNKDQAMKQMKAKL 295

>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 = 94.6 bits (236), Expect = 2e-24
 Identities = 24/58 (41%), Positives = 38/58 (65%)

Query: 31  ECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSRLRTLL 88
           +  +D Y +SG GGQ++NK  +AVRI H+PT +  +  E+R+Q KNR  A+  +R  +
Sbjct: 234 DLRVDIYHASGAGGQNVNKVATAVRIIHLPTNIKVEMQEERTQQKNRDKAMKIIRARV 291

>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 = 94.2 bits (235), Expect = 3e-24
 Identities = 28/58 (48%), Positives = 39/58 (67%)

Query: 31  ECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSRLRTLL 88
           E  +D  ++SGPGGQ +N  +SAVR+ H+PTG++    + RSQ KNR  AL  LR+ L
Sbjct: 216 EIRIDVMRASGPGGQGVNTTDSAVRVVHLPTGIMVTCQDSRSQIKNREKALMILRSRL 273

>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 = 93.8 bits (234), Expect = 4e-24
 Identities = 28/58 (48%), Positives = 43/58 (74%)

Query: 31  ECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSRLRTLL 88
           +  +DT++SSG GGQH+N  +SA+RI H+PTG++ +  ++RSQHKN+  ALS L   +
Sbjct: 221 DLRIDTFRSSGAGGQHVNTTDSAIRITHLPTGIVVECQDERSQHKNKAKALSVLGARI 278

>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 = 92.7 bits (231), Expect = 1e-23
 Identities = 27/55 (49%), Positives = 42/55 (76%)

Query: 34  MDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSRLRTLL 88
           ++T+++SG GGQ++NK ESAVRI H+PTG++     +RSQ++N+ +AL  LR  L
Sbjct: 200 IETFRASGHGGQYVNKTESAVRITHLPTGIVVSCQNERSQYQNKQTALRILRARL 254

>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 = 64.0 bits (156), Expect = 2e-14
 Identities = 21/83 (25%), Positives = 36/83 (43%), Gaps = 24/83 (28%)

Query: 31 ECEMDTYKSSGPGGQHINKRESAVRIK------------------------HVPTGVIAQ 66
          E E+   ++ G GGQH+NK  +A+ ++                             ++ +
Sbjct: 14 ELEITAIRAQGAGGQHVNKTSTAIHLRFDIRASSLPEYYKERLLAASHHLISSDGVIVIK 73

Query: 67 AAEDRSQHKNRVSALSRLRTLLA 89
          A E RSQ  NR +AL+RL  ++ 
Sbjct: 74 AQEYRSQELNREAALARLVAMIK 96

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

 Score = 62.6 bits (152), Expect = 5e-14
 Identities = 20/83 (24%), Positives = 35/83 (42%), Gaps = 24/83 (28%)

Query: 31 ECEMDTYKSSGPGGQHINKRESAVRIKHVPTG------------------------VIAQ 66
          E E+   ++ G GGQ++NK  SA+ ++                             ++ +
Sbjct: 14 EIELTAIRAQGAGGQNVNKVSSAMHLRFDINASSLPPFYKERLLALNDSRITSDGVIVLK 73

Query: 67 AAEDRSQHKNRVSALSRLRTLLA 89
          A + R+Q +NR  AL RL  L+ 
Sbjct: 74 AQQYRTQEQNRADALLRLSELIV 96

>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 = 54.4 bits (130), Expect = 7e-11
 Identities = 16/84 (19%), Positives = 30/84 (35%), Gaps = 25/84 (29%)

Query: 31  ECEMDTYKSSGPGGQHINKRESAVRIKHVPTG-------------------------VIA 65
              +   +SSGPGGQ++NK  S   ++                              ++ 
Sbjct: 21  RLSISYCRSSGPGGQNVNKVNSKAEVRFHLASADWIEEPVRQKIALTHKNKINKAGELVL 80

Query: 66  QAAEDRSQHKNRVSALSRLRTLLA 89
            +   R Q +N    L ++R ++A
Sbjct: 81  TSESSRYQFRNLAECLQKIRDMIA 104

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	135
1zbt_A	371	RF-1, peptide chain release factor 1; peptide chai	100.0
1rq0_A	342	RF-1, peptide chain release factor 1; X-RAY, cryst	100.0
2b3t_B	360	RF-1, peptide chain release factor 1; translation	100.0
3d5a_X	354	RF1, peptide chain release factor 1; ribosome, rib	100.0
2rsm_A	115	Probable peptide chain release factor C12ORF65 HO	99.97
1gqe_A	365	Release factor 2, RF2; protein synthesis, ribosome	99.97
2ihr_1	365	Peptide chain release factor 2; mixed alpha-beta,	99.97
2jva_A	108	Peptidyl-tRNA hydrolase domain protein; GFT hydrol	99.95
1j26_A	112	Immature colon carcinoma transcript 1; peptide cha	99.95
4dh9_Y	140	YAEJ; ribosome, YAEJ, ribosome stalling, ribosome	99.94

>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=100.00  E-value=4.4e-35  Score=249.86  Aligned_cols=116  Identities=30%  Similarity=0.408  Sum_probs=90.9

Q ss_pred             cccCcceeccCCCCCcCCcccChhhhhccceEEEEeccCCCccCCCccCceEEEEEcCCeeEEEeccccCHHHHHHHHHH
Q 043141            3 YHTNDNCSSSSSSSKKNYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALS   82 (135)
Q Consensus         3 ~ht~~~~~~~~~~~~~~~~~i~~~~L~~~~~~~~~RsSGPGGQ~VNK~~t~V~l~h~ptGi~v~~~e~RSq~~Nk~~A~~   82 (135)
                      +|||+++|.+.|......+.|+++||    +|+|+|||||||||||||+|+|+|+|+||||+|+|+++|||++||+.|++
T Consensus       210 ~hTS~asV~V~Pe~~ev~i~I~~~dl----~i~~~RssGpGGQ~VNkt~SaVrlthlPtGivV~~q~eRSQ~~Nr~~A~~  285 (371)
T 1zbt_A          210 VHTSTATVLVMPEVEEVEYEIDPKDL----RVDIYHASGAGGQNVNKVATAVRIIHLPTNIKVEMQEERTQQKNRDKAMK  285 (371)
T ss_dssp             CEEEEEEEEEEECCCGGGSCCCGGGE----EEEEECC---------CCCCEEEEEETTTTEEEEECSSSSHHHHHHHHHH
T ss_pred             ccccceEEEEeccccccccccCcCcE----EEEEecCCCCCCCcccccceeEEEEECCCeEEEEECCcCCHHHHHHHHHH
Confidence            79999999999877665677888888    99999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhHhcccccCCCCCCccccccCCCCcccccCCCCCCCCCCCC
Q 043141           83 RLRTLLALNVRSSVKLDAYSPPPQLLQILPPKSTIRSSEVGPQIGPNNP  131 (135)
Q Consensus        83 rL~~~l~~~~~~~~~~~~~~~~~~~~~~~~~k~q~~~g~~~~kIr~~n~  131 (135)
                      +|+++|..........+         ....+|+++++|+||++||+||=
T Consensus       286 ~L~~~L~~~~~~~~~~~---------~~~~r~~~ig~g~Rse~IRtYnf  325 (371)
T 1zbt_A          286 IIRARVADHFAQIAQDE---------QDAERKSTVGTGDRSERIRTYNF  325 (371)
T ss_dssp             HHHHHHHHHHHHHHHHH---------TCC----CCSCSCTTSEEEEEET
T ss_pred             HHHHHHHHHHHHHHHHH---------HHHHHHhhccccccCCCeeeEEC
Confidence            99999887766543332         23467899999999999999983

>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=100.00  E-value=6.3e-35  Score=246.75  Aligned_cols=115  Identities=32%  Similarity=0.474  Sum_probs=89.9

Q ss_pred             cccCcceeccCCCCCcCCcccChhhhhccceEEEEeccCCCccCCCccCceEEEEEcCCeeEEEeccccCHHHHHHHHHH
Q 043141            3 YHTNDNCSSSSSSSKKNYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALS   82 (135)
Q Consensus         3 ~ht~~~~~~~~~~~~~~~~~i~~~~L~~~~~~~~~RsSGPGGQ~VNK~~t~V~l~h~ptGi~v~~~e~RSq~~Nk~~A~~   82 (135)
                      +|||+++|.+.|......+.|+++||    +|+|+|||||||||||||+|+|+|+|+||||+|+|+++|||++||+.|++
T Consensus       173 ~hTS~asV~V~Pe~~~~~i~i~~~dl----~i~~~RssGpGGQ~VNKt~SaVrl~hlPtGivv~~q~~RSQ~~Nr~~A~~  248 (342)
T 1rq0_A          173 IHTSTATVAVLPEIEEKDIEIRPEDL----KIETFRASGHGGQYVNKTESAVRITHLPTGIVVSCQNERSQYQNKQTALR  248 (342)
T ss_dssp             CEEEEEEEEEEECCCGGGSCCCGGGE----EEEEECCCC----CCSSSSEEEEEEETTTCCEEEEEESSCHHHHHHHHHH
T ss_pred             CcccceEEEEeccccccccccChhHe----EEEeecCCCCCCcccccccceEEEEECCCeEEEEECCCCCHHHHHHHHHH
Confidence            79999999999877665677888888    99999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhHhcccccCCCCCCccccccCCCCcccccCCCCCCCCCCC
Q 043141           83 RLRTLLALNVRSSVKLDAYSPPPQLLQILPPKSTIRSSEVGPQIGPNN  130 (135)
Q Consensus        83 rL~~~l~~~~~~~~~~~~~~~~~~~~~~~~~k~q~~~g~~~~kIr~~n  130 (135)
                      +|+++|..........+         ....+++++++|+||++||+||
T Consensus       249 ~L~~~L~~~~~~~~~~~---------~~~~r~~~i~~g~Rse~IRtYn  287 (342)
T 1rq0_A          249 ILRARLYQLQKEQKERE---------ISQKRKSQIGTGERSEKIRTYN  287 (342)
T ss_dssp             HHHHHHHHHHHHHHHTT---------TCC----------CCCEEEEEE
T ss_pred             HHHHHHHHHHHHHHHHH---------HHHHHHhhcccccccCCeEEEE
Confidence            99999987766653332         2246789999999999999998

>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=100.00  E-value=6.4e-35  Score=248.10  Aligned_cols=115  Identities=29%  Similarity=0.457  Sum_probs=92.9

Q ss_pred             cccCcceeccCCCCCcCC-cccChhhhhccceEEEEeccCCCccCCCccCceEEEEEcCCeeEEEeccccCHHHHHHHHH
Q 043141            3 YHTNDNCSSSSSSSKKNY-LELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSAL   81 (135)
Q Consensus         3 ~ht~~~~~~~~~~~~~~~-~~i~~~~L~~~~~~~~~RsSGPGGQ~VNK~~t~V~l~h~ptGi~v~~~e~RSq~~Nk~~A~   81 (135)
                      +|||+++|.+.|.....- +.|+++||    +|+|+|||||||||||||+|+|+|+|+||||+|+|+++|||++||+.|+
T Consensus       196 ~hTS~asV~V~Pe~~~~e~i~i~~~dl----~i~~~RssG~GGQ~VNkt~saVrl~hlPtGivv~~q~~RSQ~~Nr~~A~  271 (360)
T 2b3t_B          196 IHTSACTVAVMPELPDAELPDVNPADL----RIDTFRSSGAGGQHVNTTDSAIRITHLPTGIVVECQDERSQHKNKAKAL  271 (360)
T ss_dssp             CEEEEEEEECCBCCCTTTCCCCCSSSE----EEEECCSSCCCTTTCCCSSEEEEEEETTTCCEEEEEESSCHHHHHHHHH
T ss_pred             CCccceEEEEecCcccccccccChhhe----EEeeecCCCCCCCccccccceEEEEECCCeEEEEECCCCCHHHHHHHHH
Confidence            799999999998766544 66888887    9999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhHhcccccCCCCCCccccccCCCCcccccCCCCCCCCCCC
Q 043141           82 SRLRTLLALNVRSSVKLDAYSPPPQLLQILPPKSTIRSSEVGPQIGPNN  130 (135)
Q Consensus        82 ~rL~~~l~~~~~~~~~~~~~~~~~~~~~~~~~k~q~~~g~~~~kIr~~n  130 (135)
                      ++|+++|.....+....+         ....+|+++++|+||++||+||
T Consensus       272 ~~L~~~L~~~~~~~~~~~---------~~~~r~~~i~~g~rse~IRtYn  311 (360)
T 2b3t_B          272 SVLGARIHAAEMAKRQQA---------EASTRRNLLGSGDRSDRNRTYN  311 (360)
T ss_dssp             HHHHHHHTTTTTTSCC---------------CCC-------CCEEEEEE
T ss_pred             HHHHHHHHHHHHHHHHHH---------HHHHHHHhcccccccCCeeeEE
Confidence            999999988776654332         2346789999999999999998

>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=100.00  E-value=4.2e-35  Score=248.74  Aligned_cols=115  Identities=32%  Similarity=0.439  Sum_probs=102.1

Q ss_pred             cccCcceeccCCCCCcCCcccChhhhhccceEEEEeccCCCccCCCccCceEEEEEcCCeeEEEeccccCHHHHHHHHHH
Q 043141            3 YHTNDNCSSSSSSSKKNYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALS   82 (135)
Q Consensus         3 ~ht~~~~~~~~~~~~~~~~~i~~~~L~~~~~~~~~RsSGPGGQ~VNK~~t~V~l~h~ptGi~v~~~e~RSq~~Nk~~A~~   82 (135)
                      +|||+++|.+.|......+.|+++||    +|+|+|||||||||||||+|+|+|+|+||||+|+|+++|||++||+.|++
T Consensus       192 ~hTS~asV~V~P~~~~~~i~i~~~dl----~i~~~RssG~GGQ~VNkt~SaVrl~HlPtgivv~~q~~RSQ~~Nr~~A~~  267 (354)
T 3d5a_X          192 IHTSTATVAVLPKAEEEDFALNMDEI----RIDVMRASGPGGQGVNTTDSAVRVVHLPTGIMVTCQDSRSQIKNREKALM  267 (354)
T ss_dssp             CEEEEEEEEEEECCCCCCCCCCGGGE----EEEEECCCSCCHHHHHHCCCEEEEEETTTTEEEEECCSSCHHHHHHHHHH
T ss_pred             CccCceEEEEeccCcccccccCccce----EEEeecCCCCCCcccccccceEEEEEcCCeEEEEECCCCCHHHHHHHHHH
Confidence            79999999999877666677888888    99999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhHhcccccCCCCCCccccccCCCCcccccCCCCCCCCCCC
Q 043141           83 RLRTLLALNVRSSVKLDAYSPPPQLLQILPPKSTIRSSEVGPQIGPNN  130 (135)
Q Consensus        83 rL~~~l~~~~~~~~~~~~~~~~~~~~~~~~~k~q~~~g~~~~kIr~~n  130 (135)
                      +|+++|..........+         ....+|+++++|+||++||+||
T Consensus       268 ~L~~~L~~~~~~~~~~~---------~~~~r~~~i~~g~rse~IRtYn  306 (354)
T 3d5a_X          268 ILRSRLLEMKRAEEAER---------LRKTRLAQIGTGERSEKIRTYN  306 (354)
T ss_dssp             HHHHHHHHHHHHHHHHH---------HHHHHHHHSCGGGGSCSSEEEE
T ss_pred             HHHHHHHHHHHHHHHHH---------HHHHHHhhcccccccCCeeeEE
Confidence            99999887765543321         2245689999999999999998

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

Probab=99.97  E-value=1.2e-31  Score=197.20  Aligned_cols=87  Identities=30%  Similarity=0.440  Sum_probs=79.4

Q ss_pred             cCcceeccCCCCC-cCCcccChhhhhccceEEEEeccCCCccCCCccCceEEEEEcCCeeEEEeccccCHHHHHHHHHHH
Q 043141            5 TNDNCSSSSSSSK-KNYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSR   83 (135)
Q Consensus         5 t~~~~~~~~~~~~-~~~~~i~~~~L~~~~~~~~~RsSGPGGQ~VNK~~t~V~l~h~ptGi~v~~~e~RSq~~Nk~~A~~r   83 (135)
                      ||.|+|.+++... ...+.|+++||    +|+|+|||||||||||||+|+|+|+|+||||+|+|+++|||++||+.||++
T Consensus        24 ts~~~v~v~p~~d~~~~l~I~~~dl----~~~~~RssGpGGQ~VNKt~SaVrl~H~PTGivV~~q~~RSQ~~Nr~~A~~~   99 (115)
T 2rsm_A           24 MAASTVQVAGRKDYPALLPLNESEL----EEQFVKGHGPGGQATNKTSNCVVLKHVPSGIVVKCHQTRSVDQNRKIARKV   99 (115)
T ss_dssp             CCCCCCCCCSCCCCCCSCCCCGGGC----EEEECSCCCSCSSSCCCSCCCEEEECTTTCCEEEECCSSCHHHHHHHHHHH
T ss_pred             cceEEEEeccccCCCccCCcCHHHe----EEEEeeCCCCCccccCccceeEEEecCCCCcEEEEcCCCCHHHHHHHHHHH
Confidence            7888888886554 34588999999    999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhHhcc
Q 043141           84 LRTLLALNVRSS   95 (135)
Q Consensus        84 L~~~l~~~~~~~   95 (135)
                      |+++|.+.+...
T Consensus       100 L~~kL~e~~~~~  111 (115)
T 2rsm_A          100 LQEKVDVFYNSG  111 (115)
T ss_dssp             HHHHHHHHHHSC
T ss_pred             HHHHHHHHhccc
Confidence            999999887653

>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=99.97  E-value=4.5e-32  Score=230.99  Aligned_cols=112  Identities=33%  Similarity=0.476  Sum_probs=94.7

Q ss_pred             cccCcceeccCCCCC-cCCcccChhhhhccceEEEEeccCCCccCCCccCceEEEEEcCCeeEEEeccccCHHHHHHHHH
Q 043141            3 YHTNDNCSSSSSSSK-KNYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSAL   81 (135)
Q Consensus         3 ~ht~~~~~~~~~~~~-~~~~~i~~~~L~~~~~~~~~RsSGPGGQ~VNK~~t~V~l~h~ptGi~v~~~e~RSq~~Nk~~A~   81 (135)
                      +|||+++|.+.|... ...+.|+++||    +|+|+|||||||||||||+|+|+|+|+||||+|+|+++|||++||+.|+
T Consensus       213 rhTS~asV~V~Pe~~~~v~i~i~~~dl----~~~~~RssG~GGQ~VNkt~saVrl~HiPtgivv~~q~~RSQ~~Nr~~A~  288 (365)
T 1gqe_A          213 RHTSFSSAFVYPEVDDDIDIEINPADL----RIDVYRASGAGGQHVNRTESAVRITHIPTGIVTQCQNDRSQHKNKDQAM  288 (365)
T ss_dssp             EEEEEEEEEEEECCBTTBCCCCCGGGE----EEEEECCCCSSCCSTTSSCCEEEEEETTTCCEEEECSSSCHHHHHHHHH
T ss_pred             CCcceeEEEEecCCCcccccccCHHHc----eEeeecCCCCCCCcccCccceEEEEECCCeEEEEECCCCCHHHHHHHHH
Confidence            799999999998764 35677888888    9999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhHhcccccCCCCCCccccccCCCC--cccccCCCCCCCCCCC
Q 043141           82 SRLRTLLALNVRSSVKLDAYSPPPQLLQILPPK--STIRSSEVGPQIGPNN  130 (135)
Q Consensus        82 ~rL~~~l~~~~~~~~~~~~~~~~~~~~~~~~~k--~q~~~g~~~~kIr~~n  130 (135)
                      ++|+++|.....+....+         ..+.|+  .++++|+   +||+||
T Consensus       289 ~~L~~~L~~~~~~~~~~~---------~~~~r~~~~~i~~G~---~IRtY~  327 (365)
T 1gqe_A          289 KQMKAKLYEVEMQKKNAE---------KQAMEDNKSDIGWGS---QIRSYV  327 (365)
T ss_dssp             HHHHHHHHHHHHHHHHHH---------TTCCSTTCCCCCSCS---EEEEEE
T ss_pred             HHHHHHHHHHHHHHHHHH---------HHHHhhhhcccCccC---CeEeEE
Confidence            999999887665544432         123444  5565554   899998

>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=99.97  E-value=1e-31  Score=228.78  Aligned_cols=112  Identities=30%  Similarity=0.343  Sum_probs=95.8

Q ss_pred             cccCcceeccCCCCC-cCCcccChhhhhccceEEEEeccCCCccCCCccCceEEEEEcCCeeEEEeccccCHHHHHHHHH
Q 043141            3 YHTNDNCSSSSSSSK-KNYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSAL   81 (135)
Q Consensus         3 ~ht~~~~~~~~~~~~-~~~~~i~~~~L~~~~~~~~~RsSGPGGQ~VNK~~t~V~l~h~ptGi~v~~~e~RSq~~Nk~~A~   81 (135)
                      +|||+++|.+.|... ...+.|+++||    +|+|+|||||||||||||+|+|+|+|+||||+|+|+++|||++||+.|+
T Consensus       201 rhTS~asV~V~P~~~~~~~i~i~~~dl----~i~~~RssG~GGQ~VNkt~saVrl~h~Ptgivv~~q~~RSQ~~Nr~~A~  276 (365)
T 2ihr_1          201 RHTSFAGVEVIPEVDEEVEVVLKPEEL----RIDVMRASGPGGQGVNTTDSAVRVVHLPTGITVTCQTTRSQIKNKELAL  276 (365)
T ss_dssp             EEEEEEEEEEEEECCSSSSCCCCGGGE----EEEEECCCCSSCCSGGGSCSEEEEEETTTTEEEEECSSSCHHHHHHHHH
T ss_pred             ccceeEEEEEecCCCcccccccCccce----EEEEeecCCCCCceecccceEEEEEEcCCeEEEEECCCCCHHHHHHHHH
Confidence            699999999998654 35677888888    9999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhHhcccccCCCCCCccccccCCC--CcccccCCCCCCCCCCC
Q 043141           82 SRLRTLLALNVRSSVKLDAYSPPPQLLQILPP--KSTIRSSEVGPQIGPNN  130 (135)
Q Consensus        82 ~rL~~~l~~~~~~~~~~~~~~~~~~~~~~~~~--k~q~~~g~~~~kIr~~n  130 (135)
                      ++|+++|.....+....+         ....|  +.++++|+   +||+||
T Consensus       277 ~~L~~~L~~~~~~~~~~~---------~~~~r~~~~~i~~G~---~IRtYn  315 (365)
T 2ihr_1          277 KILKARLYELERKKREEE---------LKALRGEVRPIEWGS---QIRSYV  315 (365)
T ss_dssp             HHHHHHHHHHHHHHHHHH---------TTTTTCCSCCSCCCS---CSEEEE
T ss_pred             HHHHHHHHHHHHHHHHHH---------HHHHHhhhhccCccC---CeeeEE
Confidence            999999887655543332         22345  67777776   699998

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

Probab=99.95  E-value=1.5e-28  Score=178.80  Aligned_cols=75  Identities=33%  Similarity=0.592  Sum_probs=69.4

Q ss_pred             CcCCcccChhhhhccceEEEEeccCCCccCCCccCceEEEEE------cC-----------------Ce-eEEEeccccC
Q 043141           17 KKNYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKH------VP-----------------TG-VIAQAAEDRS   72 (135)
Q Consensus        17 ~~~~~~i~~~~L~~~~~~~~~RsSGPGGQ~VNK~~t~V~l~h------~p-----------------tG-i~v~~~e~RS   72 (135)
                      .+..+.|+++||    +|+|+|||||||||||||+|+|+|+|      +|                 +| |+|+|+++||
T Consensus         4 i~~~i~I~~~dl----~~~~~RssGpGGQnVNKv~SaV~L~~d~~~s~lP~~~k~rl~~~~~~ri~~~G~ivv~~q~~RS   79 (108)
T 2jva_A            4 ISNNVHLPDAEI----ELTAIRAQGAGGQNVNKVSSAMHLRFDINASSLPPFYKERLLALNDSRITSDGVIVLKAQQYRT   79 (108)
T ss_dssp             CSSSCEECGGGE----EEEECCCTTCSSSSSCCCCCCEEEEEETTTSCCCHHHHHHHHTCSCTTBCTTCEEEEEECCSSS
T ss_pred             cccccccChHHE----EEEEEECCCCCCCCcCCCcceEEEEEEcccccCCHHHHHHHHHHhccccccCCcEEEEECCcCC
Confidence            345688999988    99999999999999999999999999      88                 88 9999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhHhcc
Q 043141           73 QHKNRVSALSRLRTLLALNVRSS   95 (135)
Q Consensus        73 q~~Nk~~A~~rL~~~l~~~~~~~   95 (135)
                      |.+||++|+++|+++|..++..+
T Consensus        80 Q~~Nr~~Al~rL~~~l~~a~~~~  102 (108)
T 2jva_A           80 QEQNRADALLRLSELIVNAAKLE  102 (108)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHSS
T ss_pred             HHHHHHHHHHHHHHHHHHHccCc
Confidence            99999999999999999887653

>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=99.95  E-value=3.9e-28  Score=177.67  Aligned_cols=74  Identities=27%  Similarity=0.478  Sum_probs=67.4

Q ss_pred             CcCCcccChhhhhccceEEEEeccCCCccCCCccCceEEEE-EcCCe------------------------eEEEecccc
Q 043141           17 KKNYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIK-HVPTG------------------------VIAQAAEDR   71 (135)
Q Consensus        17 ~~~~~~i~~~~L~~~~~~~~~RsSGPGGQ~VNK~~t~V~l~-h~ptG------------------------i~v~~~e~R   71 (135)
                      ..-.+.|+++||    +|+|+|||||||||||||+|+|+|+ |+|+|                        |+|+|+++|
T Consensus        11 ~~~~i~I~~~dl----~~~~~RssGpGGQnVNKv~SaV~Lrf~i~t~~~Lp~~~k~rl~~~~~~ri~~~G~ivv~~q~~R   86 (112)
T 1j26_A           11 KQASSYIPLDRL----SISYCRSSGPGGQNVNKVNSKAEVRFHLASADWIEEPVRQKIALTHKNKINKAGELVLTSESSR   86 (112)
T ss_dssp             CSSCCCCCTTTS----EEEEECCCCSSSSCCSSCCCEEEEEEEGGGCTTSCHHHHHHHHHHTTTTBCSSSEEEEEECCCS
T ss_pred             cceEEecChHHe----EEEEEECCCCCCCCccCCcceEEEEEeccccccCCHHHHHHHHHhhccccccCCeEEEEECCcc
Confidence            333466888888    9999999999999999999999998 99986                        999999999


Q ss_pred             CHHHHHHHHHHHHHHHHHHhHhc
Q 043141           72 SQHKNRVSALSRLRTLLALNVRS   94 (135)
Q Consensus        72 Sq~~Nk~~A~~rL~~~l~~~~~~   94 (135)
                      ||++||++||++|+++|..++..
T Consensus        87 SQ~~Nr~~Al~rL~~~l~~a~~~  109 (112)
T 1j26_A           87 YQFRNLAECLQKIRDMIAEASGP  109 (112)
T ss_dssp             SHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             CHHHHHHHHHHHHHHHHHHhhcC
Confidence            99999999999999999988753

>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=99.94  E-value=2.9e-27  Score=178.74  Aligned_cols=84  Identities=31%  Similarity=0.525  Sum_probs=74.9

Q ss_pred             CcCCcccChhhhhccceEEEEeccCCCccCCCccCceEEEE------EcCC-----------------e-eEEEeccccC
Q 043141           17 KKNYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIK------HVPT-----------------G-VIAQAAEDRS   72 (135)
Q Consensus        17 ~~~~~~i~~~~L~~~~~~~~~RsSGPGGQ~VNK~~t~V~l~------h~pt-----------------G-i~v~~~e~RS   72 (135)
                      ++..+.|+++||    +|+|+|||||||||||||+|+|+|+      |||+                 | |+|+|+++||
T Consensus         4 i~~~i~I~~~el----~~~~~RssGpGGQnVNKv~SaV~L~~~~~~s~lp~~~k~rL~~~~~~rit~~G~ivv~~q~~RS   79 (140)
T 4dh9_Y            4 ISRHVAIPDGEL----EITAIRAQGAGGQHVNKTSTAIHLRFDIRASSLPEYYKERLLAASHHLISSDGVIVIKAQEYRS   79 (140)
T ss_dssp             CCSSSCCCTTCS----EEEEECCCSSSSHHHHTTCCCEEEEECCSSSSSCSHHHHHHHSCCCTTSCSSCCCCEEECCCSS
T ss_pred             ccCCCccChHHe----EEEEEECCCCCCCccccccceEEEEEecccccCCHHHHHHHHHHhccccccCCcEEEEEcCCcC
Confidence            455688999998    9999999999999999999999999      6997                 5 9999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhHhcccccCCCCCC
Q 043141           73 QHKNRVSALSRLRTLLALNVRSSVKLDAYSPP  104 (135)
Q Consensus        73 q~~Nk~~A~~rL~~~l~~~~~~~~~~~~~~~~  104 (135)
                      |++|+++|+++|.++|..++..+.+..+..|.
T Consensus        80 Q~~Nr~~A~~rL~~~l~~a~~~pk~R~~tkpt  111 (140)
T 4dh9_Y           80 QELNREAALARLVAMIKELTTEKKARRPTRPT  111 (140)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHSCCCCCCCCCCS
T ss_pred             HHHHHHHHHHHHHHHHHHhccCCCCCcCCCCc
Confidence            99999999999999999998877666555443

---

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	135
d1j26a_	112	d.50.4.1 (A:) Ict1 protein {Mouse (Mus musculus) [	3e-13
d1gqea_	362	e.38.1.1 (A:) Polypeptide chain release factor 2 (	3e-09
d1rq0a_	333	e.38.1.1 (A:) Peptide chain release factor 1, RF1	3e-08
d2b3tb1	344	e.38.1.1 (B:7-354) Peptide chain release factor 1,	7e-08

>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 = 59.6 bits (144), Expect = 3e-13
 Identities = 16/84 (19%), Positives = 30/84 (35%), Gaps = 25/84 (29%)

Query: 31  ECEMDTYKSSGPGGQHINKRESAVRIKH-------------------------VPTGVIA 65
              +   +SSGPGGQ++NK  S   ++                              ++ 
Sbjct: 21  RLSISYCRSSGPGGQNVNKVNSKAEVRFHLASADWIEEPVRQKIALTHKNKINKAGELVL 80

Query: 66  QAAEDRSQHKNRVSALSRLRTLLA 89
            +   R Q +N    L ++R ++A
Sbjct: 81  TSESSRYQFRNLAECLQKIRDMIA 104

>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 = 51.2 bits (122), Expect = 3e-09
 Identities = 29/58 (50%), Positives = 43/58 (74%)

Query: 31  ECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSRLRTLL 88
           +  +D Y++SG GGQH+N+ ESAVRI H+PTG++ Q   DRSQHKN+  A+ +++  L
Sbjct: 235 DLRIDVYRASGAGGQHVNRTESAVRITHIPTGIVTQCQNDRSQHKNKDQAMKQMKAKL 292

>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 = 48.6 bits (115), Expect = 3e-08
 Identities = 26/56 (46%), Positives = 43/56 (76%)

Query: 30  RECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSRLR 85
            + +++T+++SG GGQ++NK ESAVRI H+PTG++     +RSQ++N+ +AL  LR
Sbjct: 196 EDLKIETFRASGHGGQYVNKTESAVRITHLPTGIVVSCQNERSQYQNKQTALRILR 251

>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 = 47.4 bits (112), Expect = 7e-08
 Identities = 28/58 (48%), Positives = 43/58 (74%)

Query: 31  ECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSRLRTLL 88
           +  +DT++SSG GGQH+N  +SA+RI H+PTG++ +  ++RSQHKN+  ALS L   +
Sbjct: 211 DLRIDTFRSSGAGGQHVNTTDSAIRITHLPTGIVVECQDERSQHKNKAKALSVLGARI 268

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	135
d1rq0a_	333	Peptide chain release factor 1, RF1 {Thermotoga ma	100.0
d2b3tb1	344	Peptide chain release factor 1, RF1 {Escherichia c	100.0
d1gqea_	362	Polypeptide chain release factor 2 (RF2) {Escheric	100.0
d1j26a_	112	Ict1 protein {Mouse (Mus musculus) [TaxId: 10090]}	99.92

>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=100.00  E-value=3.2e-37  Score=257.57  Aligned_cols=117  Identities=32%  Similarity=0.487  Sum_probs=91.4

Q ss_pred             cccCcceeccCCCCCcCCcccChhhhhccceEEEEeccCCCccCCCccCceEEEEEcCCeeEEEeccccCHHHHHHHHHH
Q 043141            3 YHTNDNCSSSSSSSKKNYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALS   82 (135)
Q Consensus         3 ~ht~~~~~~~~~~~~~~~~~i~~~~L~~~~~~~~~RsSGPGGQ~VNK~~t~V~l~h~ptGi~v~~~e~RSq~~Nk~~A~~   82 (135)
                      +|||+++|.+.|......+.|+++||    +|+|+|||||||||||||+|+|||+|+||||+|.|+++|||++||+.||+
T Consensus       173 ~hTs~~~V~v~p~~~~~~v~i~~~dl----~i~~~RssG~GGQ~VNkt~sAVRitH~PTGi~v~~q~eRSQ~~Nk~~A~~  248 (333)
T d1rq0a_         173 IHTSTATVAVLPEIEEKDIEIRPEDL----KIETFRASGHGGQYVNKTESAVRITHLPTGIVVSCQNERSQYQNKQTALR  248 (333)
T ss_dssp             CEEEEEEEEEEECCCGGGSCCCGGGE----EEEEECCCC----CCSSSSEEEEEEETTTCCEEEEEESSCHHHHHHHHHH
T ss_pred             eEEEEEEEEEecccccccccccccce----eEEeecCCccccchhhhhhheeEEEEcCCccEEEcccccccHHHHHHHHH
Confidence            79999999998877777788998888    99999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhHhcccccCCCCCCccccccCCCCcccccCCCCCCCCCCCCCCC
Q 043141           83 RLRTLLALNVRSSVKLDAYSPPPQLLQILPPKSTIRSSEVGPQIGPNNPKFA  134 (135)
Q Consensus        83 rL~~~l~~~~~~~~~~~~~~~~~~~~~~~~~k~q~~~g~~~~kIr~~n~~~~  134 (135)
                      +|+++|.....+....+         ..+.||+|+++|+||++|||||  ||
T Consensus       249 ~L~~kl~~~~~~~~~~~---------~~~~r~~~~~~~~r~~~iRtY~--~p  289 (333)
T d1rq0a_         249 ILRARLYQLQKEQKERE---------ISQKRKSQIGTGERSEKIRTYN--FP  289 (333)
T ss_dssp             HHHHHHHHHHHHHHHTT---------TCC----------CCCEEEEEE--TT
T ss_pred             HHHHHHHHHHHHHHHHH---------HHHHHhccccccccCCCceeee--CC
Confidence            99998886665554432         2357899999999999999999  55

>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=100.00  E-value=2e-36  Score=253.21  Aligned_cols=117  Identities=29%  Similarity=0.481  Sum_probs=91.9

Q ss_pred             cccCcceeccCCCCCc-CCcccChhhhhccceEEEEeccCCCccCCCccCceEEEEEcCCeeEEEeccccCHHHHHHHHH
Q 043141            3 YHTNDNCSSSSSSSKK-NYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSAL   81 (135)
Q Consensus         3 ~ht~~~~~~~~~~~~~-~~~~i~~~~L~~~~~~~~~RsSGPGGQ~VNK~~t~V~l~h~ptGi~v~~~e~RSq~~Nk~~A~   81 (135)
                      +|||++.|.+.|.... ..+.|+++||    +|+++|||||||||||||+|+|||+|+||||+|.|+++|||++||+.||
T Consensus       186 ~hts~~~v~v~p~~~~~~~~~i~~~dl----~i~~~rssg~GGQ~vnkt~sAVRi~H~ptGi~v~~q~eRSq~~Nk~~A~  261 (344)
T d2b3tb1         186 IHTSACTVAVMPELPDAELPDVNPADL----RIDTFRSSGAGGQHVNTTDSAIRITHLPTGIVVECQDERSQHKNKAKAL  261 (344)
T ss_dssp             CEEEEEEEECCBCCCTTTCCCCCSSSE----EEEECCSSCCCTTTCCCSSEEEEEEETTTCCEEEEEESSCHHHHHHHHH
T ss_pred             cccceeeEeeecccccccccccCcccc----eEEEecCCCccccchhhhhceeEEEEcCCceEEEccCCCcchHHHHHHH
Confidence            7999999999876543 4457888888    9999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhHhcccccCCCCCCccccccCCCCcccccCCCCCCCCCCCCCCC
Q 043141           82 SRLRTLLALNVRSSVKLDAYSPPPQLLQILPPKSTIRSSEVGPQIGPNNPKFA  134 (135)
Q Consensus        82 ~rL~~~l~~~~~~~~~~~~~~~~~~~~~~~~~k~q~~~g~~~~kIr~~n~~~~  134 (135)
                      ++|+.+|.....+....+         ....||+++++|+||+|||+||  ||
T Consensus       262 ~~L~~kl~~~~~~~~~~~---------~~~~r~~~~~~~~r~~~iRtY~--~p  303 (344)
T d2b3tb1         262 SVLGARIHAAEMAKRQQA---------EASTRRNLLGSGDRSDRNRTYN--FP  303 (344)
T ss_dssp             HHHHHHHTTTTTTSCC---------------CCC-------CCEEEEEE--TT
T ss_pred             HHHHHHHHHHHHHHHHHH---------HHHHHhcccccccccCceEeee--cC
Confidence            999998876655433322         2357899999999999999999  55

>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=100.00  E-value=8.4e-34  Score=238.59  Aligned_cols=114  Identities=34%  Similarity=0.497  Sum_probs=93.0

Q ss_pred             cccCcceeccCCCC-CcCCcccChhhhhccceEEEEeccCCCccCCCccCceEEEEEcCCeeEEEeccccCHHHHHHHHH
Q 043141            3 YHTNDNCSSSSSSS-KKNYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSAL   81 (135)
Q Consensus         3 ~ht~~~~~~~~~~~-~~~~~~i~~~~L~~~~~~~~~RsSGPGGQ~VNK~~t~V~l~h~ptGi~v~~~e~RSq~~Nk~~A~   81 (135)
                      +|||+++|.+.|.. ....+.|++.||    +|+++|||||||||||||+|+|||+|+||||+|.|+++|||++||+.||
T Consensus       210 ~hTS~a~V~v~P~~~~~~~~~i~~~dl----~i~~~rs~g~GGQ~vN~t~savri~H~ptgi~v~~q~ersq~~Nk~~A~  285 (362)
T d1gqea_         210 RHTSFSSAFVYPEVDDDIDIEINPADL----RIDVYRASGAGGQHVNRTESAVRITHIPTGIVTQCQNDRSQHKNKDQAM  285 (362)
T ss_dssp             EEEEEEEEEEEECCBTTBCCCCCGGGE----EEEEECCCCSSCCSTTSSCCEEEEEETTTCCEEEECSSSCHHHHHHHHH
T ss_pred             EEEEEEEEEEeecCCCccceecChHHe----EEEEeecCCCCccchhhhhceeEEEecCchhHHHhhhcchhhHHHHHHH
Confidence            79999999998764 445678898888    9999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhHhcccccCCCCCCccccccCCCCcccccCCCCCCCCCCC
Q 043141           82 SRLRTLLALNVRSSVKLDAYSPPPQLLQILPPKSTIRSSEVGPQIGPNN  130 (135)
Q Consensus        82 ~rL~~~l~~~~~~~~~~~~~~~~~~~~~~~~~k~q~~~g~~~~kIr~~n  130 (135)
                      .+|+++|.....+....+.       .....+|.+++   ||+||||||
T Consensus       286 ~~L~~~l~~~~~~~~~~~~-------~~~~~~~~~~~---~g~~iRtY~  324 (362)
T d1gqea_         286 KQMKAKLYEVEMQKKNAEK-------QAMEDNKSDIG---WGSQIRSYV  324 (362)
T ss_dssp             HHHHHHHHHHHHHHHHHHT-------TCCSTTCCCCC---SCSEEEEEE
T ss_pred             HHHHHHHHHHHHHHHHHHH-------HHHHhhhhcCc---CcCCccCcc
Confidence            9999988654333322211       11223455555   556899998

>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=99.92  E-value=3.1e-25  Score=160.47  Aligned_cols=74  Identities=27%  Similarity=0.476  Sum_probs=64.7

Q ss_pred             CcCCcccChhhhhccceEEEEeccCCCccCCCccCceEEEEE-------cC-----------------Ce-eEEEecccc
Q 043141           17 KKNYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKH-------VP-----------------TG-VIAQAAEDR   71 (135)
Q Consensus        17 ~~~~~~i~~~~L~~~~~~~~~RsSGPGGQ~VNK~~t~V~l~h-------~p-----------------tG-i~v~~~e~R   71 (135)
                      ......||.++|    +|+|+|||||||||||||+|+|+|++       +|                 .| |+|+|+++|
T Consensus        11 ~~~~~~Ip~~~i----~~~f~RSsGPGGQ~VNKv~TkV~Lr~~v~~s~~l~~~~~~~l~~~~~~~i~~~g~l~I~s~~~R   86 (112)
T d1j26a_          11 KQASSYIPLDRL----SISYCRSSGPGGQNVNKVNSKAEVRFHLASADWIEEPVRQKIALTHKNKINKAGELVLTSESSR   86 (112)
T ss_dssp             CSSCCCCCTTTS----EEEEECCCCSSSSCCSSCCCEEEEEEEGGGCTTSCHHHHHHHHHHTTTTBCSSSEEEEEECCCS
T ss_pred             hhhcCccCHHHe----EEEEEEcCCCCCCccceeccEEEEEEeccccccCCHHHHHHHHHHhhhcccCCCeEEEEEcccC
Confidence            334456888888    99999999999999999999999995       22                 35 999999999


Q ss_pred             CHHHHHHHHHHHHHHHHHHhHhc
Q 043141           72 SQHKNRVSALSRLRTLLALNVRS   94 (135)
Q Consensus        72 Sq~~Nk~~A~~rL~~~l~~~~~~   94 (135)
                      ||.+|+++|+++|.++|.++.++
T Consensus        87 sQ~~Nr~~a~~kL~~li~~A~kP  109 (112)
T d1j26a_          87 YQFRNLAECLQKIRDMIAEASGP  109 (112)
T ss_dssp             SHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             CHHHHHHHHHHHHHHHHHHHhCC
Confidence            99999999999999999887654