Citrus Sinensis ID: 045445

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------13
Protein Sequence
PLFLSCNYNDNCSSTSSSSKKNYFELTDDEQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYLPPPQLLQILPPKFTIRCSEVGPQIRPNNPKFALLDLIFAVEGSVSEAAKFLSLL
Secondary Structure (PSIPRED)
ccccccccccccEEEEEEEEEEEcccccccccccccccEEEEccccccccccccccEEEcccccEEEEEccccccHHHHHHcccHHHHHHHHHHccccccccccHHHHHHHHHHcccHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
cEEEEEEccccccccccccccccccccHHHHHHHccEEEEEccccccccccccccEEEEEEccccEEEEEccccccHHHHHHccccccccccccccccccccccHHHHHHHHHHcccHHHHHHHHccc
Coil and Loop (DISEMBL)
plflscnyndncsstsssskknyfeltddeqfrecemdtykssgpggqhrnkresavrlkhvptassvnldaylpppqllqilppkftircsevgpqirpnnpkfALLDLIFAVEGSVSEAAKFLSLL
Flexible Loop (DISEMBL)
plflscnyndncsstsssskknyfELTDDEQFRECEMDtykssgpggqhrnkRESAVRLKHVPTASSVNLDAYLPPPQLLQILPPKFTIRCSEVGPQIRPNNPKFALLDLIFAVEGSVSEAAKFLSLL
Low Complexity Region (SEG)
PLFLscnyndncsstsssskknyFELTDDEQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYlpppqllqilppKFTIRCSEVGPQIRPNNPKFALLDLIFAVEGSVSEAAKFLSLL
Disordered region (IsUnstruct)
*******************************************************************VNLDAYLPPPQLLQILPPKFTIRCSEVGPQIRPNNPKFALLDLIFAVEGSV**********
Disordered Region (DISOPRED)
PLFLSC*YNDNCSSTSSSSKKNYFELTDDEQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYLPPPQ*LQ*************************LLDLIFAVEGSVSEAAKFLSLL
Disordered Region (DISEMBL)
PLFLSCNY************KNYFELTDDEQFRECEMDT*****************VRLKHVPTASSVNLDAYLPPPQLLQILPPKFTIRCSEVGPQIRPNNPKFALLDLIFAVEGSVSEAAKFLSLL
Disordered Region (DISPRO)
PLFLSCNYNDNCS***S*SKKNYFELTDDEQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYLPPPQLLQILPPKFTIRCSEVGPQIRPNNPKFALLDLIFAVEGSVSEAAK*****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
PLFLSCNYNDNCSSTSSSSKKNYFELTDDEQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYLPPPQLLQILPPKFTIRCSEVGPQIRPNNPKFALLDLIFAVEGSVSEAAKFLSLL
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	128	2.2.26 [Sep-21-2011]
Q2W3F8	371	Peptide chain release fac	yes	no	0.273	0.094	0.6	1e-07
A7I0P7	364	Peptide chain release fac	yes	no	0.312	0.109	0.545	1e-06
Q89AC4	366	Peptide chain release fac	yes	no	0.312	0.109	0.525	1e-06
A8EYR1	355	Peptide chain release fac	yes	no	0.562	0.202	0.355	2e-06
A8EWG5	365	Peptide chain release fac	yes	no	0.281	0.098	0.527	2e-06
Q1RJT5	357	Peptide chain release fac	yes	no	0.562	0.201	0.342	2e-06
A8GXI1	357	Peptide chain release fac	yes	no	0.562	0.201	0.342	2e-06
Q9PRE0	359	Peptide chain release fac	yes	no	0.25	0.089	0.593	2e-06
B1AHY9	359	Peptide chain release fac	yes	no	0.25	0.089	0.593	2e-06
Q30TP0	365	Peptide chain release fac	yes	no	0.281	0.098	0.555	2e-06

>sp|Q2W3F8|RF2_MAGSA Peptide chain release factor 2 OS=Magnetospirillum magneticum (strain AMB-1 / ATCC 700264) GN=prfB PE=3 SV=1

 Score = 55.1 bits (131), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 21/35 (60%), Positives = 28/35 (80%)

Query: 34  ECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSV 68
           EC +DTY++SG GGQH NK +SAVR+ H+PT  +V
Sbjct: 236 ECRIDTYRASGAGGQHINKTDSAVRITHIPTGIAV 270

Peptide chain release factor 2 directs the termination of translation in response to the peptide chain termination codons UGA and UAA.
Magnetospirillum magneticum (strain AMB-1 / ATCC 700264) (taxid: 342108)

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

 Score = 52.0 bits (123), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 24/44 (54%), Positives = 30/44 (68%), Gaps = 4/44 (9%)

Query: 25  ELTDDEQF----RECEMDTYKSSGPGGQHRNKRESAVRLKHVPT 64
           EL DD Q     ++  +D Y+SSG GGQH NK ESAVR+ H+PT
Sbjct: 224 ELDDDIQINIDEKDLRIDYYRSSGAGGQHVNKTESAVRITHIPT 267

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

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

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

 Score = 52.0 bits (123), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 21/40 (52%), Positives = 29/40 (72%)

Query: 29  DEQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSV 68
           D   R+ ++D Y++SG GGQH NK ESAVR++H+PT   V
Sbjct: 234 DINTRDLKIDVYRASGAGGQHVNKTESAVRIRHLPTGIVV 273

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|A8EYR1|RF1_RICCK Peptide chain release factor 1 OS=Rickettsia canadensis (strain McKiel) GN=prfA PE=3 SV=1

 Score = 51.6 bits (122), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 27/76 (35%), Positives = 39/76 (51%), Gaps = 4/76 (5%)

Query: 33  RECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLD----AYLPPPQLLQILPPKFT 88
           ++  +DTY+SSG GGQH N   SAVR+ H+PT  +V L      +    + L+IL  +  
Sbjct: 218 KDLRIDTYRSSGAGGQHVNTTNSAVRITHIPTGITVALQDEKSQHKNKAKALKILRARIY 277

Query: 89  IRCSEVGPQIRPNNPK 104
                   Q R NN +
Sbjct: 278 EEERRKKEQKRANNRR 293

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

Rickettsia canadensis (strain McKiel) (taxid: 293613)

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

 Score = 51.2 bits (121), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 19/36 (52%), Positives = 27/36 (75%)

Query: 33  RECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSV 68
           ++  +DTY++SG GGQH NK ESA+R+ H+PT   V
Sbjct: 236 KDIRIDTYRASGAGGQHVNKTESAIRITHIPTGIVV 271

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|Q1RJT5|RF1_RICBR Peptide chain release factor 1 OS=Rickettsia bellii (strain RML369-C) GN=prfA PE=3 SV=1

 Score = 51.2 bits (121), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 26/76 (34%), Positives = 40/76 (52%), Gaps = 4/76 (5%)

Query: 33  RECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLD----AYLPPPQLLQILPPKFT 88
           ++  +DTY++SG GGQH N  +SAVR+ H+PT  +V L      +    + L+IL  +  
Sbjct: 221 KDLRIDTYRASGAGGQHVNTTDSAVRITHIPTGITVALQDEKSQHKNKAKALKILRARIY 280

Query: 89  IRCSEVGPQIRPNNPK 104
                   Q R NN +
Sbjct: 281 EEERRKKDQERANNRR 296

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

Rickettsia bellii (strain RML369-C) (taxid: 336407)

>sp|A8GXI1|RF1_RICB8 Peptide chain release factor 1 OS=Rickettsia bellii (strain OSU 85-389) GN=prfA PE=3 SV=1

 Score = 51.2 bits (121), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 26/76 (34%), Positives = 40/76 (52%), Gaps = 4/76 (5%)

Query: 33  RECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLD----AYLPPPQLLQILPPKFT 88
           ++  +DTY++SG GGQH N  +SAVR+ H+PT  +V L      +    + L+IL  +  
Sbjct: 221 KDLRIDTYRASGAGGQHVNTTDSAVRITHIPTGITVALQDEKSQHKNKAKALKILRARIY 280

Query: 89  IRCSEVGPQIRPNNPK 104
                   Q R NN +
Sbjct: 281 EEERRKKDQERANNRR 296

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

Rickettsia bellii (strain OSU 85-389) (taxid: 391896)

>sp|Q9PRE0|RF1_UREPA Peptide chain release factor 1 OS=Ureaplasma parvum serovar 3 (strain ATCC 700970) GN=prfA PE=3 SV=1

 Score = 50.8 bits (120), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 19/32 (59%), Positives = 25/32 (78%)

Query: 34  ECEMDTYKSSGPGGQHRNKRESAVRLKHVPTA 65
           E  +DTY++SG GGQH N+ ESAVR+ H+PT 
Sbjct: 222 ELRIDTYRASGAGGQHVNRTESAVRITHIPTG 253

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

Ureaplasma parvum serovar 3 (strain ATCC 700970) (taxid: 273119)

>sp|B1AHY9|RF1_UREP2 Peptide chain release factor 1 OS=Ureaplasma parvum serovar 3 (strain ATCC 27815 / 27 / NCTC 11736) GN=prfA PE=3 SV=1

 Score = 50.8 bits (120), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 19/32 (59%), Positives = 25/32 (78%)

Query: 34  ECEMDTYKSSGPGGQHRNKRESAVRLKHVPTA 65
           E  +DTY++SG GGQH N+ ESAVR+ H+PT 
Sbjct: 222 ELRIDTYRASGAGGQHVNRTESAVRITHIPTG 253

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

Ureaplasma parvum serovar 3 (strain ATCC 27815 / 27 / NCTC 11736) (taxid: 505682)

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

 Score = 50.8 bits (120), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 20/36 (55%), Positives = 26/36 (72%)

Query: 33  RECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSV 68
           R+  +DTY+SSG GGQH NK ESA+R+ H+ T   V
Sbjct: 236 RDIRVDTYRSSGAGGQHVNKTESAIRITHIATGVVV 271

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)

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	128
356559945	250	PREDICTED: uncharacterized protein LOC10	0.968	0.496	0.518	8e-35
224127830	257	predicted protein [Populus trichocarpa]	0.921	0.459	0.522	1e-34
255556733	185	peptide chain release factor, putative [	0.75	0.518	0.590	1e-33
359493583	224	PREDICTED: peptide chain release factor	0.796	0.455	0.528	3e-31
326517198	170	predicted protein [Hordeum vulgare subsp	0.796	0.6	0.536	1e-29
413935468	543	hypothetical protein ZEAMMB73_426809 [Ze	0.796	0.187	0.558	1e-29
357126252	239	PREDICTED: uncharacterized protein LOC10	0.828	0.443	0.514	1e-29
242059479	259	hypothetical protein SORBIDRAFT_03g04217	0.828	0.409	0.507	3e-29
414879327	253	TPA: hypothetical protein ZEAMMB73_57118	0.867	0.438	0.489	4e-29
449447515	240	PREDICTED: peptide chain release factor	0.914	0.487	0.480	9e-29

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

 Score =  151 bits (382), Expect = 8e-35,   Method: Compositional matrix adjust.
 Identities = 83/160 (51%), Positives = 99/160 (61%), Gaps = 36/160 (22%)

Query: 4   LSCNYNDNCSSTSSSSKKNYFELTDDEQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVP 63
           L C+     S+    S+K Y  L+D+E  R+CEMDT+K+SGPGGQHRNKRESAVRLKH+P
Sbjct: 59  LWCSNYTTVSTIEEGSEKCYLNLSDEELMRQCEMDTFKASGPGGQHRNKRESAVRLKHLP 118

Query: 64  TA-------------------------------SSVNLDAYLPPPQLLQILPPKFTIRCS 92
           T                                 +V+L+AY PP +LLQILPPK +IR S
Sbjct: 119 TGIIAQASEDRSQHKNRASAINRLRSLIALKVRKTVDLEAYSPPRELLQILPPKSSIRGS 178

Query: 93  EVGPQIRPNNPKF-----ALLDLIFAVEGSVSEAAKFLSL 127
           + G QI PNNPKF     ALLDLIFAVEGSVSEAAK+L L
Sbjct: 179 DCGSQIGPNNPKFASGMQALLDLIFAVEGSVSEAAKYLGL 218

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  150 bits (379), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 82/157 (52%), Positives = 97/157 (61%), Gaps = 39/157 (24%)

Query: 7   NYNDNCSSTSSSSKKNYFELTDDEQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTA- 65
           NYN   +S S  +  NY ELTDDE  R+CEMDT+K+SGPGGQHRNKRESAVRLKH+PT  
Sbjct: 77  NYN---TSASHGNGTNYLELTDDELMRQCEMDTFKASGPGGQHRNKRESAVRLKHLPTGI 133

Query: 66  ------------------------------SSVNLDAYLPPPQLLQILPPKFTIRCSEVG 95
                                         +S+++D+Y P  +LLQILP K TIR S+ G
Sbjct: 134 IAQAVEDRSQHMNRASALKRLRALLAIRVRNSLDIDSYTPRLELLQILPLKSTIRGSDCG 193

Query: 96  PQIRPNNPKF-----ALLDLIFAVEGSVSEAAKFLSL 127
           PQI P NPKF     ALLDLIFAV+GS+SEA K L L
Sbjct: 194 PQIGPKNPKFILGMQALLDLIFAVDGSISEAGKLLGL 230

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255556733|ref|XP_002519400.1| peptide chain release factor, putative [Ricinus communis] gi|223541467|gb|EEF43017.1| peptide chain release factor, putative [Ricinus communis]

 Score =  147 bits (371), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 78/132 (59%), Positives = 87/132 (65%), Gaps = 36/132 (27%)

Query: 32  FRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTA-------------------------- 65
            R+CEMDTYK+SGPGGQHRNKRESAVR+KH+PT                           
Sbjct: 1   MRQCEMDTYKASGPGGQHRNKRESAVRIKHLPTGIISQAVEDRSQHKNRASALRRLRTLL 60

Query: 66  -----SSVNLDAYLPPPQLLQILPPKFTIRCSEVGPQIRPNNPKF-----ALLDLIFAVE 115
                ++V LDAY PPP+LLQILPPK TIR S+ GPQI PNNPKF     ALLDL+FAVE
Sbjct: 61  ALKVRNAVYLDAYSPPPELLQILPPKSTIRGSDCGPQIGPNNPKFVLGMQALLDLVFAVE 120

Query: 116 GSVSEAAKFLSL 127
           GSVSEAAKFL L
Sbjct: 121 GSVSEAAKFLGL 132

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359493583|ref|XP_002263666.2| PREDICTED: peptide chain release factor 1-like [Vitis vinifera] gi|297734721|emb|CBI16955.3| unnamed protein product [Vitis vinifera]

 Score =  139 bits (351), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 73/138 (52%), Positives = 88/138 (63%), Gaps = 36/138 (26%)

Query: 26  LTDDEQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTA-------------------- 65
           L+D++  ++CEM T+KSSGPGGQHRNKRESAVRLKH+PT                     
Sbjct: 55  LSDEQLMKQCEMSTFKSSGPGGQHRNKRESAVRLKHLPTGIIAQAVEDRSQHKNRASALA 114

Query: 66  -----------SSVNLDAYLPPPQLLQILPPKFTIRCSEVGPQIRPNNPKF-----ALLD 109
                      +S++LD Y PP +LLQILP K TIR S+ GPQI PNNPKF     ALLD
Sbjct: 115 RLRTLLALKVRNSIDLDTYSPPLELLQILPAKSTIRTSDCGPQIGPNNPKFALGMLALLD 174

Query: 110 LIFAVEGSVSEAAKFLSL 127
           LIFAVEGS+S+AAK + L
Sbjct: 175 LIFAVEGSISDAAKLMGL 192

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  134 bits (337), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 74/138 (53%), Positives = 83/138 (60%), Gaps = 36/138 (26%)

Query: 26  LTDDEQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTA-------------------- 65
           +TDDE   +C+M T+KSSGPGGQHRNKRESAVRL+H PT                     
Sbjct: 1   MTDDELMAQCDMGTFKSSGPGGQHRNKRESAVRLRHHPTGIVAQAVEDRSQHKNRSSALS 60

Query: 66  -----------SSVNLDAYLPPPQLLQILPPKFTIRCSEVGPQIRPNNPKF-----ALLD 109
                        +NLD Y PP +LLQILP K TIR  +VG QI PNNPKF     ALLD
Sbjct: 61  RLRTLIALKVRRPINLDNYTPPVELLQILPLKSTIRSKDVGNQIGPNNPKFSPGMQALLD 120

Query: 110 LIFAVEGSVSEAAKFLSL 127
           L+FAVEGSVSEAAK L L
Sbjct: 121 LLFAVEGSVSEAAKVLGL 138

Source: Hordeum vulgare subsp. vulgare

Species: Hordeum vulgare

Genus: Hordeum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|413935468|gb|AFW70019.1| hypothetical protein ZEAMMB73_426809 [Zea mays]

 Score =  134 bits (337), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 67/120 (55%), Positives = 84/120 (70%), Gaps = 18/120 (15%)

Query: 26  LTDDEQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTA-------------SSVNLDA 72
           ++D+E   +C+M T+K+SGPGGQHRNKRESAVRLKH+PT                +NL+ 
Sbjct: 121 MSDEELMEQCDMGTFKASGPGGQHRNKRESAVRLKHLPTGIIAQKRNYSASVRRPINLED 180

Query: 73  YLPPPQLLQILPPKFTIRCSEVGPQIRPNNPKF-----ALLDLIFAVEGSVSEAAKFLSL 127
           Y PP ++LQILP K ++R  +VGPQI PNN KF     ALLDL+FAVEGSVS+AAK L L
Sbjct: 181 YTPPVEILQILPLKSSVRGKDVGPQIGPNNSKFSPEMQALLDLLFAVEGSVSDAAKILGL 240

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357126252|ref|XP_003564802.1| PREDICTED: uncharacterized protein LOC100830192 [Brachypodium distachyon]

 Score =  134 bits (337), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 73/142 (51%), Positives = 85/142 (59%), Gaps = 36/142 (25%)

Query: 22  NYFELTDDEQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTA---------------- 65
           +Y  ++DDE   +C+M T+KSSGPGGQHRNKRESAVRL+H PT                 
Sbjct: 66  DYLGMSDDELMGQCDMGTFKSSGPGGQHRNKRESAVRLRHHPTGIVAQAVEDRSQHKNRS 125

Query: 66  ---------------SSVNLDAYLPPPQLLQILPPKFTIRCSEVGPQIRPNNPKF----- 105
                            +NL+ Y PP +LLQILP K TIR  +VG QI PNNPKF     
Sbjct: 126 SALSRLRTLIALKVRRPINLEDYTPPVELLQILPLKSTIRAKDVGNQIGPNNPKFSPGMQ 185

Query: 106 ALLDLIFAVEGSVSEAAKFLSL 127
           ALLDL+FAVEGSVSEAAK L L
Sbjct: 186 ALLDLLFAVEGSVSEAAKILGL 207

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

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 =  133 bits (334), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 72/142 (50%), Positives = 89/142 (62%), Gaps = 36/142 (25%)

Query: 22  NYFELTDDEQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPT----------------A 65
           +Y  ++D+E   +C+M T+K+SGPGGQHRNKRESAVRLKH+PT                A
Sbjct: 86  DYLGMSDEELMEQCDMGTFKASGPGGQHRNKRESAVRLKHLPTGIIAQAVEDRSQHKNRA 145

Query: 66  SS---------------VNLDAYLPPPQLLQILPPKFTIRCSEVGPQIRPNNPKF----- 105
           S+               +NLD Y PP +LLQILP K T+R  +VGPQI PNN KF     
Sbjct: 146 SALSRLRTLIALKVRRPINLDDYTPPVELLQILPLKSTVRGKDVGPQIGPNNSKFSPGMQ 205

Query: 106 ALLDLIFAVEGSVSEAAKFLSL 127
           ALLDL+FAVEGS+S+AAK L L
Sbjct: 206 ALLDLLFAVEGSISDAAKILGL 227

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 =  132 bits (332), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 72/147 (48%), Positives = 91/147 (61%), Gaps = 36/147 (24%)

Query: 17  SSSKKNYFELTDDEQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPT------------ 64
           S  + +Y  ++D+E   +C+M T+K+SGPGGQHRNKRESAVRLKH+PT            
Sbjct: 75  SGGRVDYLGMSDEELMEQCDMGTFKASGPGGQHRNKRESAVRLKHLPTGIIAQAVEDRSQ 134

Query: 65  ----ASS---------------VNLDAYLPPPQLLQILPPKFTIRCSEVGPQIRPNNPKF 105
               AS+               +NL+ Y PP +LLQILP K ++R  +VGPQI PNN KF
Sbjct: 135 HKNRASALSRLRTLIALKVRRPINLEDYTPPVELLQILPLKSSVRGKDVGPQIGPNNSKF 194

Query: 106 -----ALLDLIFAVEGSVSEAAKFLSL 127
                ALLDL+FAVEGSVS+AAK L L
Sbjct: 195 SPGMQALLDLLFAVEGSVSDAAKILGL 221

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449447515|ref|XP_004141513.1| PREDICTED: peptide chain release factor 1-like [Cucumis sativus] gi|449526225|ref|XP_004170114.1| PREDICTED: peptide chain release factor 1-like [Cucumis sativus]

 Score =  131 bits (329), Expect = 9e-29,   Method: Compositional matrix adjust.
 Identities = 75/156 (48%), Positives = 94/156 (60%), Gaps = 39/156 (25%)

Query: 11  NCSSTSSSS---KKNYFELTDDEQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTA-- 65
           NCSS++++S    K Y  L+D+E  ++CEM T+K+SGPGGQHRNKRESAVRLKH+PT   
Sbjct: 53  NCSSSNANSVCNGKQYLVLSDEELMKQCEMGTFKASGPGGQHRNKRESAVRLKHIPTGII 112

Query: 66  -----------------------------SSVNLDAYLPPPQLLQILPPKFTIRCSEVGP 96
                                        + V+L+ Y PPP+LLQILP K T+R  E GP
Sbjct: 113 AQAVEDRSQHKNRSSALARLRALLALKVRNPVDLEDYSPPPELLQILPLKSTVRPPECGP 172

Query: 97  QIRPNNPKF-----ALLDLIFAVEGSVSEAAKFLSL 127
           QI PNN KF     ALLDLI  ++GSVS+ AK L L
Sbjct: 173 QIGPNNSKFLPGMQALLDLISTLDGSVSDTAKLLGL 208

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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	128
TAIR|locus:2006897	257	AT1G33330 [Arabidopsis thalian	0.312	0.155	0.625	5.1e-11
UNIPROTKB|Q74EJ1	107	GSU0971 "Hydrolase, putative"	0.304	0.364	0.487	1e-06
TIGR_CMR|GSU_0971	107	GSU_0971 "peptidyl-tRNA hydrol	0.304	0.364	0.487	1e-06
TIGR_CMR|GSU_2278	372	GSU_2278 "peptide chain releas	0.312	0.107	0.522	1.4e-05
TIGR_CMR|APH_0479	376	APH_0479 "peptide chain releas	0.281	0.095	0.527	1.4e-05
TIGR_CMR|ECH_0705	366	ECH_0705 "peptide chain releas	0.25	0.087	0.562	1.7e-05
TIGR_CMR|GSU_3104	355	GSU_3104 "peptide chain releas	0.242	0.087	0.580	2.7e-05
DICTYBASE|DDB_G0288835	424	prfB "class I peptide chain re	0.281	0.084	0.555	2.8e-05
TIGR_CMR|SO_3833	363	SO_3833 "peptide chain release	0.242	0.085	0.548	2.8e-05
TIGR_CMR|NSE_0604	365	NSE_0604 "peptide chain releas	0.25	0.087	0.531	2.9e-05

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

 Score = 154 (59.3 bits), Expect = 5.1e-11, P = 5.1e-11
 Identities = 25/40 (62%), Positives = 35/40 (87%)

Query:    25 ELTDDEQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPT 64
             + TD+E  ++C ++T++ SGPGGQHRNKR+SAVRLKH+PT
Sbjct:    88 KFTDEELMKQCRLETFRVSGPGGQHRNKRDSAVRLKHLPT 127

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

 Score = 112 (44.5 bits), Expect = 1.0e-06, P = 1.0e-06
 Identities = 19/39 (48%), Positives = 31/39 (79%)

Query:    26 LTDDEQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPT 64
             +T D +  + +++ Y++SGPGGQHRN  +SAVR++H+PT
Sbjct:     1 MTVDIRDADIKVEYYRASGPGGQHRNTTDSAVRIRHLPT 39

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 = 112 (44.5 bits), Expect = 1.0e-06, P = 1.0e-06
 Identities = 19/39 (48%), Positives = 31/39 (79%)

Query:    26 LTDDEQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPT 64
             +T D +  + +++ Y++SGPGGQHRN  +SAVR++H+PT
Sbjct:     1 MTVDIRDADIKVEYYRASGPGGQHRNTTDSAVRIRHLPT 39

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

TIGR_CMR|GSU_2278 GSU_2278 "peptide chain release factor 2, programmed frameshift" [Geobacter sulfurreducens PCA (taxid:243231)]

 Score = 109 (43.4 bits), Expect = 1.4e-05, P = 1.4e-05
 Identities = 23/44 (52%), Positives = 30/44 (68%)

Query:    25 ELTDDEQFRECE----MDTYKSSGPGGQHRNKRESAVRLKHVPT 64
             E+ DD + +  E    +DTY+SSG GGQH N  +SAVRL H+PT
Sbjct:   223 EIEDDIEIKIAESDLRVDTYRSSGAGGQHVNTTDSAVRLTHLPT 266

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 = 109 (43.4 bits), Expect = 1.4e-05, P = 1.4e-05
 Identities = 19/36 (52%), Positives = 27/36 (75%)

Query:    33 RECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSV 68
             ++  +DTY++SG GGQH NK ESAVR+ H+P+   V
Sbjct:   238 KDLRIDTYRASGAGGQHVNKTESAVRITHIPSGMVV 273

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 = 108 (43.1 bits), Expect = 1.7e-05, P = 1.7e-05
 Identities = 18/32 (56%), Positives = 26/32 (81%)

Query:    33 RECEMDTYKSSGPGGQHRNKRESAVRLKHVPT 64
             ++  +DTY++SG GGQH NK ESAVR+ H+P+
Sbjct:   237 KDLRIDTYRASGAGGQHVNKTESAVRITHIPS 268

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

GO:0006415 "translational termination" evidence=ISS

TIGR_CMR|GSU_3104 GSU_3104 "peptide chain release factor 1" [Geobacter sulfurreducens PCA (taxid:243231)]

 Score = 106 (42.4 bits), Expect = 2.7e-05, P = 2.7e-05
 Identities = 18/31 (58%), Positives = 25/31 (80%)

Query:    34 ECEMDTYKSSGPGGQHRNKRESAVRLKHVPT 64
             + ++D Y++SG GGQH NK ESAVR+ H+PT
Sbjct:   216 DLKIDVYRASGAGGQHVNKTESAVRITHIPT 246

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

GO:0006415 "translational termination" evidence=ISS

DICTYBASE|DDB_G0288835 prfB "class I peptide chain release factor" [Dictyostelium discoideum (taxid:44689)]

 Score = 107 (42.7 bits), Expect = 2.8e-05, P = 2.8e-05
 Identities = 20/36 (55%), Positives = 26/36 (72%)

Query:    33 RECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSV 68
             ++   +T +SSG GGQH NK ESAVR+ H+PT  SV
Sbjct:   293 KDLHFETLRSSGAGGQHVNKTESAVRIVHIPTGISV 328

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

GO:0006415 "translational termination" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

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

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

 Score = 106 (42.4 bits), Expect = 2.8e-05, P = 2.8e-05
 Identities = 17/31 (54%), Positives = 26/31 (83%)

Query:    34 ECEMDTYKSSGPGGQHRNKRESAVRLKHVPT 64
             + ++DT++SSG GGQH NK +SA+R+ H+PT
Sbjct:   223 DLKVDTFRSSGAGGQHVNKTDSAIRITHIPT 253

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

GO:0006415 "translational termination" evidence=ISS

TIGR_CMR|NSE_0604 NSE_0604 "peptide chain release factor 2, programmed frameshift" [Neorickettsia sennetsu str. Miyayama (taxid:222891)]

 Score = 106 (42.4 bits), Expect = 2.9e-05, P = 2.9e-05
 Identities = 17/32 (53%), Positives = 27/32 (84%)

Query:    33 RECEMDTYKSSGPGGQHRNKRESAVRLKHVPT 64
             ++ ++DTY++SG GGQH NK ESA+R+ H+P+
Sbjct:   236 KDLKIDTYRASGAGGQHVNKTESAIRITHLPS 267

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

GO:0006415 "translational termination" evidence=ISS

---

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	128
pfam00472	114	pfam00472, RF-1, RF-1 domain	3e-13
COG1186	239	COG1186, PrfB, Protein chain release factor B [Tra	4e-13
PRK00578	367	PRK00578, prfB, peptide chain release factor 2; Va	2e-12
PRK00591	359	PRK00591, prfA, peptide chain release factor 1; Va	1e-11
TIGR03072	200	TIGR03072, release_prfH, putative peptide chain re	4e-11
PRK08179	200	PRK08179, prfH, peptide chain release factor-like	5e-11
PRK05589	325	PRK05589, PRK05589, peptide chain release factor 2	9e-11
COG0216	363	COG0216, PrfA, Protein chain release factor A [Tra	1e-10
TIGR00020	364	TIGR00020, prfB, peptide chain release factor 2	4e-10
TIGR00019	360	TIGR00019, prfA, peptide chain release factor 1	7e-10
PRK07342	339	PRK07342, PRK07342, peptide chain release factor 2	2e-09
PRK08787	313	PRK08787, PRK08787, peptide chain release factor 2	2e-08
PRK06746	326	PRK06746, PRK06746, peptide chain release factor 2	2e-06
PRK09256	138	PRK09256, PRK09256, hypothetical protein; Provisio	8e-04

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

 Score = 61.0 bits (149), Expect = 3e-13
 Identities = 21/35 (60%), Positives = 27/35 (77%)

Query: 34 ECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSV 68
          +  +DT++SSGPGGQ+ NK ESAVRL H+PT   V
Sbjct: 14 DLRIDTFRSSGPGGQNVNKTESAVRLTHLPTGIVV 48

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

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

 Score = 63.0 bits (154), Expect = 4e-13
 Identities = 20/36 (55%), Positives = 26/36 (72%)

Query: 34  ECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVN 69
           +  +DTY++SG GGQH NK +SAVRL H+PT   V 
Sbjct: 111 DLRIDTYRASGAGGQHVNKTDSAVRLTHLPTGIVVL 146

Length = 239

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

 Score = 62.2 bits (152), Expect = 2e-12
 Identities = 19/31 (61%), Positives = 25/31 (80%)

Query: 34  ECEMDTYKSSGPGGQHRNKRESAVRLKHVPT 64
           +  +DTY+SSG GGQH NK +SAVR+ H+PT
Sbjct: 236 DLRIDTYRSSGAGGQHVNKTDSAVRITHIPT 266

Length = 367

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

 Score = 59.7 bits (146), Expect = 1e-11
 Identities = 17/29 (58%), Positives = 23/29 (79%)

Query: 36  EMDTYKSSGPGGQHRNKRESAVRLKHVPT 64
            +DT++SSG GGQH N  +SAVR+ H+PT
Sbjct: 224 RIDTFRSSGAGGQHVNTTDSAVRITHLPT 252

Length = 359

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

 Score = 57.1 bits (138), Expect = 4e-11
 Identities = 27/60 (45%), Positives = 34/60 (56%), Gaps = 14/60 (23%)

Query: 20  KKNYF----------ELTDDEQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVN 69
           +KN+F          E T+DE  R    +T +SSGPGGQH NK ESAVR  H+ +  SV 
Sbjct: 87  RKNWFIGVQRFSASEEATEDE-IR---FETLRSSGPGGQHVNKTESAVRATHLASGISVK 142

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 = 57.0 bits (138), Expect = 5e-11
 Identities = 24/55 (43%), Positives = 35/55 (63%), Gaps = 6/55 (10%)

Query: 20  KKNYF----ELTDDEQFRECEM--DTYKSSGPGGQHRNKRESAVRLKHVPTASSV 68
           +KN+F      + DE+ +  E+  +T +SSGPGGQH NK +SAVR  H+ +  SV
Sbjct: 88  RKNWFVGIGRFSADEEEQSDEIRFETLRSSGPGGQHVNKTDSAVRATHLASGISV 142

Length = 200

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

 Score = 57.1 bits (138), Expect = 9e-11
 Identities = 28/62 (45%), Positives = 39/62 (62%), Gaps = 5/62 (8%)

Query: 8   YNDNCS-STSSSSKKNYFELTDDEQFR----ECEMDTYKSSGPGGQHRNKRESAVRLKHV 62
           +N N    TS +S +   ELTDD+       + ++DTY++ G GGQH NK ESAVR+ H+
Sbjct: 166 FNANGKRQTSFASVEVLPELTDDQDIEIRSEDLKIDTYRAGGAGGQHVNKTESAVRITHI 225

Query: 63  PT 64
           PT
Sbjct: 226 PT 227

Length = 325

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

 Score = 56.8 bits (138), Expect = 1e-10
 Identities = 17/29 (58%), Positives = 23/29 (79%)

Query: 36  EMDTYKSSGPGGQHRNKRESAVRLKHVPT 64
            +DT++SSG GGQH N  +SAVR+ H+PT
Sbjct: 226 RIDTFRSSGAGGQHVNTTDSAVRITHLPT 254

Length = 363

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

 Score = 55.6 bits (134), Expect = 4e-10
 Identities = 24/54 (44%), Positives = 33/54 (61%), Gaps = 4/54 (7%)

Query: 15  TSSSSKKNYFELTDDEQF----RECEMDTYKSSGPGGQHRNKRESAVRLKHVPT 64
           TS +S     E+ DD        +  +DTY++SG GGQH NK +SAVR+ H+PT
Sbjct: 213 TSFASVFVMPEVDDDIDIEIKPEDLRIDTYRASGAGGQHVNKTDSAVRITHIPT 266

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

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

 Score = 54.7 bits (132), Expect = 7e-10
 Identities = 18/35 (51%), Positives = 25/35 (71%)

Query: 34  ECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSV 68
           +  +DT++SSG GGQH N  +SAVR+ H+PT   V
Sbjct: 222 DLRIDTFRSSGAGGQHVNTTDSAVRITHLPTGIVV 256

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

 Score = 53.3 bits (128), Expect = 2e-09
 Identities = 19/35 (54%), Positives = 25/35 (71%)

Query: 34  ECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSV 68
           +  +DTY+SSG GGQH N  +SAVR+ H+PT   V
Sbjct: 200 DVRIDTYRSSGAGGQHVNTTDSAVRITHIPTGIVV 234

Length = 339

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

 Score = 50.8 bits (121), Expect = 2e-08
 Identities = 20/31 (64%), Positives = 24/31 (77%)

Query: 38  DTYKSSGPGGQHRNKRESAVRLKHVPTASSV 68
           D Y+SSG GGQH NK ESAVR+ H+PT + V
Sbjct: 181 DVYRSSGAGGQHVNKTESAVRITHIPTNTVV 211

Length = 313

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

 Score = 45.1 bits (106), Expect = 2e-06
 Identities = 18/35 (51%), Positives = 26/35 (74%)

Query: 34  ECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSV 68
           + ++DTY++SG GGQH N  +SAVR+ H PT + V
Sbjct: 198 DLKIDTYRASGAGGQHVNTTDSAVRITHTPTNTVV 232

Length = 326

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

 Score = 36.7 bits (86), Expect = 8e-04
 Identities = 17/43 (39%), Positives = 24/43 (55%), Gaps = 6/43 (13%)

Query: 41 KSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYLPPPQLLQIL 83
          ++SGPGGQ+ NK  +AV L+    ASS      LP     ++L
Sbjct: 21 RASGPGGQNVNKVSTAVELRFDIAASS------LPEFYKERLL 57

Length = 138

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	128
COG0216	363	PrfA Protein chain release factor A [Translation,	100.0
TIGR00019	360	prfA peptide chain release factor 1. This model de	99.97
KOG2726	386	consensus Mitochondrial polypeptide chain release	99.97
PRK05589	325	peptide chain release factor 2; Provisional	99.96
PRK00591	359	prfA peptide chain release factor 1; Validated	99.96
TIGR03072	200	release_prfH putative peptide chain release factor	99.96
PRK08787	313	peptide chain release factor 2; Provisional	99.96
PRK06746	326	peptide chain release factor 2; Provisional	99.96
PRK07342	339	peptide chain release factor 2; Provisional	99.96
TIGR00020	364	prfB peptide chain release factor 2. In many but n	99.96
PRK08179	200	prfH peptide chain release factor-like protein; Re	99.95
PRK00578	367	prfB peptide chain release factor 2; Validated	99.95
COG1186	239	PrfB Protein chain release factor B [Translation,	99.94
PF00472	113	RF-1: RF-1 domain; InterPro: IPR000352 Peptide cha	99.93
PRK09256	138	hypothetical protein; Provisional	99.75
KOG3429	172	consensus Predicted peptidyl-tRNA hydrolase [Trans	99.33
PF02954	42	HTH_8: Bacterial regulatory protein, Fis family; I	91.06

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

Probab=100.00  E-value=3.1e-36  Score=255.01  Aligned_cols=95  Identities=27%  Similarity=0.362  Sum_probs=90.0

Q ss_pred             cccccccccceeeccCCcc----cccCceeEEEEeecCCCCcccccccccEEEEeeCCceEEEeeccC----ChhhHhhh
Q 045445           11 NCSSTSSSSKKNYFELTDD----EQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYL----PPPQLLQI   82 (128)
Q Consensus        11 ~~~~tS~a~v~v~p~l~~~----~~~~dl~~~~~RssGpGGQ~vNkt~saV~l~H~PtGi~v~~~~~R----Nr~~A~~~   82 (128)
                      -+.|||+|+|.|+|+.++.    ++++||+|+++||||+||||||+|+|||||+|+||||+|.||++|    ||++||++
T Consensus       197 GRIHTStaTVaVlPE~ee~~ei~I~~~DlrIDt~RsSGaGGQhVNtTdSAVRiTHlPTGIvV~cQderSQ~kNk~kAmkv  276 (363)
T COG0216         197 GRIHTSAATVAVLPEVEEVEEIEINPKDLRIDTFRSSGAGGQHVNTTDSAVRITHLPTGIVVECQDERSQHKNKAKAMKV  276 (363)
T ss_pred             CceeecceeEEeccCCCcccccccChHHceeeeeecCCCCCCCcCccchhheeeecCCceEEEecchhhhhhhHHHHHHH
Confidence            4689999999999999753    589999999999999999999999999999999999999999998    99999999


Q ss_pred             CC------------------cccccccCCCCCCCCCCCCCh
Q 045445           83 LP------------------PKFTIRCSEVGPQIRPNNPKF  105 (128)
Q Consensus        83 L~------------------~~~q~~~~~r~~kIrtyn~~f  105 (128)
                      |+                  ||+|+++++||++||||||..
T Consensus       277 L~ARl~~~~~~~~~~~~~~~RksqVGSGDRSErIRTYNfPQ  317 (363)
T COG0216         277 LRARLYDAERQKAQAEEASERKSQVGSGDRSERIRTYNFPQ  317 (363)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhcCCCchhhhhhccCCCC
Confidence            97                  999999999999999999876

>TIGR00019 prfA peptide chain release factor 1

Probab=99.97  E-value=1.3e-31  Score=227.80  Aligned_cols=97  Identities=29%  Similarity=0.379  Sum_probs=89.9

Q ss_pred             CCcccccccccceeeccCCc---ccccCceeEEEEeecCCCCcccccccccEEEEeeCCceEEEeeccC----ChhhHhh
Q 045445            9 NDNCSSTSSSSKKNYFELTD---DEQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYL----PPPQLLQ   81 (128)
Q Consensus         9 ~d~~~~tS~a~v~v~p~l~~---~~~~~dl~~~~~RssGpGGQ~vNkt~saV~l~H~PtGi~v~~~~~R----Nr~~A~~   81 (128)
                      ...++||||++|.++|.+++   .++++||+++|+|||||||||||||+|||||+|+||||+|.|+++|    ||..||+
T Consensus       194 s~~R~hTsfa~V~v~P~~~~~~~~i~~~dl~~~~~RssG~GGQ~VNkt~SaVrl~h~ptgi~V~~~~eRSQ~~Nk~~A~~  273 (360)
T TIGR00019       194 SQGRIHTSAATVAVMPELEEVEVDINPADLRIDTFRSSGAGGQHVNTTDSAVRITHLPTGIVVECQDERSQHKNKDKAMK  273 (360)
T ss_pred             CCCCeecceeEEEEEcCCCccccccCcccEEEEEEECCCCCCCCcCceeeeEEEEECCCcEEEEECCccCHHHHHHHHHH
Confidence            44699999999999999875   4678999999999999999999999999999999999999999999    9999999


Q ss_pred             hCC------------------cccccccCCCCCCCCCCCCCh
Q 045445           82 ILP------------------PKFTIRCSEVGPQIRPNNPKF  105 (128)
Q Consensus        82 ~L~------------------~~~q~~~~~r~~kIrtyn~~f  105 (128)
                      +|+                  ++.+++.++||++|||||+..
T Consensus       274 ~L~~~L~~~~~~~~~~~~~~~r~~~~~~~~Rs~~IRtY~~~~  315 (360)
T TIGR00019       274 VLRARLYEAEQEKQQAAQASTRKSQVGSGDRSERIRTYNFPQ  315 (360)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhcceecccCCeEEEECCC
Confidence            987                  778888999999999999765

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.

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

Probab=99.97  E-value=2.6e-31  Score=227.39  Aligned_cols=103  Identities=29%  Similarity=0.342  Sum_probs=93.7

Q ss_pred             cccccccccceeeccCCc-----ccccCceeEEEEeecCCCCcccccccccEEEEeeCCceEEEeeccC----ChhhHhh
Q 045445           11 NCSSTSSSSKKNYFELTD-----DEQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYL----PPPQLLQ   81 (128)
Q Consensus        11 ~~~~tS~a~v~v~p~l~~-----~~~~~dl~~~~~RssGpGGQ~vNkt~saV~l~H~PtGi~v~~~~~R----Nr~~A~~   81 (128)
                      -++|||+++|.++|.+..     .++++||+++|+|+|||||||||||+|||||+|+||||+|+|+++|    ||+.|+.
T Consensus       221 gr~htstasV~ViP~~~~~~~~~~~~~~dl~i~~~R~~G~GGQhvNktdsaVrl~HiPTGIvv~cq~eRSq~~Nr~~A~~  300 (386)
T KOG2726|consen  221 GRRHTSTASVAVIPQPGRDEVDVEIDEKDLRIETFRASGPGGQHVNKTDSAVRLTHIPTGIVVECQEERSQHKNRALALK  300 (386)
T ss_pred             cccccccceEEEeccCCCCccceecCchheeEEecccCCCCcccccccccceEEEeecCceEEEeecHHhHHhhHHHHHH
Confidence            369999999999999842     2578999999999999999999999999999999999999999999    9999999


Q ss_pred             hCC------------------cccccccCCCCCCCCCCCCCh-hhHHHHHH
Q 045445           82 ILP------------------PKFTIRCSEVGPQIRPNNPKF-ALLDLIFA  113 (128)
Q Consensus        82 ~L~------------------~~~q~~~~~r~~kIrtyn~~f-~~lD~~~~  113 (128)
                      +|+                  ++.|+++.+|+++|||||+.. -|.|.++.
T Consensus       301 ~L~akL~~~~~~~~~~~~~~~r~~qv~s~~rsekiRTy~~~q~rv~D~r~~  351 (386)
T KOG2726|consen  301 RLRAKLAVIYREEKSEEEKKKRKAQVGSLKRSEKIRTYNFKQDRVTDHRIG  351 (386)
T ss_pred             HHHHHHHHHHHhhhhHHhhhhhHHhhcccCchhceeecccCccchhhhhhc
Confidence            986                  888899999999999999766 67777766

>PRK05589 peptide chain release factor 2; Provisional

Probab=99.96  E-value=4.2e-31  Score=222.25  Aligned_cols=96  Identities=32%  Similarity=0.409  Sum_probs=85.2

Q ss_pred             CcccccccccceeeccCCc----ccccCceeEEEEeecCCCCcccccccccEEEEeeCCceEEEeeccC----ChhhHhh
Q 045445           10 DNCSSTSSSSKKNYFELTD----DEQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYL----PPPQLLQ   81 (128)
Q Consensus        10 d~~~~tS~a~v~v~p~l~~----~~~~~dl~~~~~RssGpGGQ~vNkt~saV~l~H~PtGi~v~~~~~R----Nr~~A~~   81 (128)
                      ..++||||++|.++|.+++    .++++|++|+|+|||||||||||||+|||||+|+||||+|+|+++|    ||..|++
T Consensus       169 ~~rr~ts~a~V~VlP~~~~~~~~~i~~~dl~~~~~rssG~GGQ~VNkt~saVrl~H~ptgi~v~~q~eRSQ~~Nk~~A~~  248 (325)
T PRK05589        169 NGKRQTSFASVEVLPELTDDQDIEIRSEDLKIDTYRAGGAGGQHVNKTESAVRITHIPTGIVVQCQNERSQHSNKETAMK  248 (325)
T ss_pred             CCCeEeeeEEEEEecCcCccccccCCchheEEEEeeCCCCCCCcccceeeEEEEEECCCCEEEEECCccCHHHHHHHHHH
Confidence            3699999999999999865    4678999999999999999999999999999999999999999999    9999999


Q ss_pred             hCC-----------------cccccccCCCCCCCCCCCC-Ch
Q 045445           82 ILP-----------------PKFTIRCSEVGPQIRPNNP-KF  105 (128)
Q Consensus        82 ~L~-----------------~~~q~~~~~r~~kIrtyn~-~f  105 (128)
                      +|+                 .+.+....+||++|||||+ .+
T Consensus       249 ~L~~kL~~~~~~~~~~~~~~~r~~~~~~~~g~~IRtY~~~p~  290 (325)
T PRK05589        249 MLKSKLVELKERAHKEKIEDLTGELKDMGWGSQIRSYVFHPY  290 (325)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcccccccccCCceeeECCCC
Confidence            987                 2233344579999999998 54

>PRK00591 prfA peptide chain release factor 1; Validated

Probab=99.96  E-value=7.1e-31  Score=223.14  Aligned_cols=98  Identities=27%  Similarity=0.357  Sum_probs=90.6

Q ss_pred             cCCcccccccccceeeccCCc---ccccCceeEEEEeecCCCCcccccccccEEEEeeCCceEEEeeccC----ChhhHh
Q 045445            8 YNDNCSSTSSSSKKNYFELTD---DEQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYL----PPPQLL   80 (128)
Q Consensus         8 ~~d~~~~tS~a~v~v~p~l~~---~~~~~dl~~~~~RssGpGGQ~vNkt~saV~l~H~PtGi~v~~~~~R----Nr~~A~   80 (128)
                      ....++||||++|.++|.+++   .+.++||+++|+|||||||||||||+|+|+|+|+||||+|.|+++|    ||+.|+
T Consensus       193 ~s~~R~~tsfa~V~v~P~~~~~~~~i~~~dl~~~~~RssG~GGQ~VNkt~saVrl~H~ptGi~v~~~~eRSQ~~Nk~~Al  272 (359)
T PRK00591        193 ESQGRIHTSAATVAVLPEAEEVEVEINPKDLRIDTFRSSGAGGQHVNTTDSAVRITHLPTGIVVECQDERSQHKNKAKAM  272 (359)
T ss_pred             CCCCceecceEEEEEEcCCCccccccCcccEEEEEEECCCCCCCCccceeeeEEEEECCCcEEEEECCcCCHHHHHHHHH
Confidence            345799999999999999875   5688999999999999999999999999999999999999999999    999999


Q ss_pred             hhCC------------------cccccccCCCCCCCCCCCCCh
Q 045445           81 QILP------------------PKFTIRCSEVGPQIRPNNPKF  105 (128)
Q Consensus        81 ~~L~------------------~~~q~~~~~r~~kIrtyn~~f  105 (128)
                      ++|+                  ++.++..++||++|||||+..
T Consensus       273 ~~L~~~L~~~~~~~~~~~~~~~r~~~~~~~~Rse~IRtY~f~~  315 (359)
T PRK00591        273 KVLRARLYDAERQKAQAEEAATRKSQVGSGDRSERIRTYNFPQ  315 (359)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhcccccccCCeeeEECCC
Confidence            9987                  778899999999999999755

>TIGR03072 release_prfH putative peptide chain release factor H

Probab=99.96  E-value=9.9e-31  Score=207.70  Aligned_cols=94  Identities=26%  Similarity=0.313  Sum_probs=85.1

Q ss_pred             CcccccccccceeeccCCcccccCceeEEEEeecCCCCcccccccccEEEEeeCCceEEEeeccC----ChhhHhhhCC-
Q 045445           10 DNCSSTSSSSKKNYFELTDDEQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYL----PPPQLLQILP-   84 (128)
Q Consensus        10 d~~~~tS~a~v~v~p~l~~~~~~~dl~~~~~RssGpGGQ~vNkt~saV~l~H~PtGi~v~~~~~R----Nr~~A~~~L~-   84 (128)
                      ...|||||++|.++|. +.+++++||+++|+|||||||||||||+|+|+|+|+||||+|+|+++|    ||++|+++|+ 
T Consensus        84 ~~~R~ts~~~V~v~~~-~~~i~~~dl~~~~~RssGpGGQ~vNkt~saVrl~h~ptgi~v~~~~~RSQ~~Nk~~A~~~L~~  162 (200)
T TIGR03072        84 HHRRKNWFIGVQRFSA-SEEATEDEIRFETLRSSGPGGQHVNKTESAVRATHLASGISVKVQSERSQHANKRLATLLLAV  162 (200)
T ss_pred             CCCeeEEEEEEEEecC-ccccChhheEEEEEECCCCCcccccccceeEEEEECCCcEEEEECCccCHHHHHHHHHHHHHH
Confidence            4678999999999985 445788999999999999999999999999999999999999999999    9999999997 


Q ss_pred             ----------------cccccccCCCCCCCCCCCCC
Q 045445           85 ----------------PKFTIRCSEVGPQIRPNNPK  104 (128)
Q Consensus        85 ----------------~~~q~~~~~r~~kIrtyn~~  104 (128)
                                      ++.+....+||++|||||+.
T Consensus       163 ~l~~~~~~~~~~~~~~~r~~~~~~~Rg~~iRty~~~  198 (200)
T TIGR03072       163 RLADLQQEQAAALRAERRTAHHQIERGNPVRVFKGE  198 (200)
T ss_pred             HHHHHHHHHHHHHHHHHHhccccccccCceEeeeCC
Confidence                            56666777999999999953

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.

>PRK08787 peptide chain release factor 2; Provisional

Probab=99.96  E-value=1e-30  Score=219.10  Aligned_cols=96  Identities=35%  Similarity=0.358  Sum_probs=82.9

Q ss_pred             CcccccccccceeeccCCc----ccccCceeEEEEeecCCCCcccccccccEEEEeeCCceEEEeeccC----ChhhHhh
Q 045445           10 DNCSSTSSSSKKNYFELTD----DEQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYL----PPPQLLQ   81 (128)
Q Consensus        10 d~~~~tS~a~v~v~p~l~~----~~~~~dl~~~~~RssGpGGQ~vNkt~saV~l~H~PtGi~v~~~~~R----Nr~~A~~   81 (128)
                      ..++||||++|.++|.+++    .+.++||+|+|+|||||||||||||+|+|||+|+||||+|+|+++|    ||+.|++
T Consensus       149 ~~rrhTsfasV~V~P~~~~~~~i~i~~~dl~~~~~RssG~GGQ~VNkt~saVri~H~Ptgi~v~~q~eRSQ~~Nk~~A~~  228 (313)
T PRK08787        149 DNRRHTSFTSVFVSPEVDDNIEIDINPADLRTDVYRSSGAGGQHVNKTESAVRITHIPTNTVVACQTGRSQHQNRDNAMK  228 (313)
T ss_pred             CCCEEeeeEEEEEecCcCcccccccChhHeEEEEEECCCCCCCCcCCEeeEEEEEECCCcEEEEECCcccHHHHHHHHHH
Confidence            4689999999999999975    3578999999999999999999999999999999999999999999    9999999


Q ss_pred             hCC-----------------cccccccCCCCCCCCCCCCCh
Q 045445           82 ILP-----------------PKFTIRCSEVGPQIRPNNPKF  105 (128)
Q Consensus        82 ~L~-----------------~~~q~~~~~r~~kIrtyn~~f  105 (128)
                      +|+                 .+.+.....||+||||||+.-
T Consensus       229 ~L~~~L~~~~~e~~~~~~~~~~~~k~~i~~g~qIRtY~f~~  269 (313)
T PRK08787        229 MLAAKLYELEVQKRNAEKDALEATKSDIGWGSQIRNYVLDQ  269 (313)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhhhhCcccccccceeCCC
Confidence            987                 100111235889999998655

>PRK06746 peptide chain release factor 2; Provisional

Probab=99.96  E-value=1.2e-30  Score=219.62  Aligned_cols=96  Identities=29%  Similarity=0.373  Sum_probs=85.7

Q ss_pred             CCcccccccccceeeccCCc----ccccCceeEEEEeecCCCCcccccccccEEEEeeCCceEEEeeccC----ChhhHh
Q 045445            9 NDNCSSTSSSSKKNYFELTD----DEQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYL----PPPQLL   80 (128)
Q Consensus         9 ~d~~~~tS~a~v~v~p~l~~----~~~~~dl~~~~~RssGpGGQ~vNkt~saV~l~H~PtGi~v~~~~~R----Nr~~A~   80 (128)
                      ..-++||||++|.++|.+++    .++++||+++|+|||||||||||||+|||+|+|+||||+|+|+++|    ||+.|+
T Consensus       169 s~~rrhTsfa~V~v~P~~~~~~~i~i~~~dl~~~~~rssG~GGQ~vNkt~saVrl~h~ptgi~v~~q~~RSQ~~Nk~~A~  248 (326)
T PRK06746        169 SSGRRHTSFVSCEVVPEFNDEVEIEVRTEDLKIDTYRASGAGGQHVNTTDSAVRITHTPTNTVVTCQSERSQIKNREHAM  248 (326)
T ss_pred             CCCCeEeeEEEEEEecCcCCccccccChHHeEEEEEeCCCCCCCCccceeeEEEEEEeCCeEEEEECCCCCHHHHHHHHH
Confidence            34699999999999999864    3578999999999999999999999999999999999999999999    999999


Q ss_pred             hhCC------------------cccccccCCCCCCCCCCCC-Ch
Q 045445           81 QILP------------------PKFTIRCSEVGPQIRPNNP-KF  105 (128)
Q Consensus        81 ~~L~------------------~~~q~~~~~r~~kIrtyn~-~f  105 (128)
                      ++|+                  |+.++.. +|+++|||||+ .+
T Consensus       249 ~~L~akL~~~~~~~~~~~~~~~r~~~~~~-~rg~~IRtYnf~p~  291 (326)
T PRK06746        249 KMLKAKLYQKKLEEQQAELDEIRGEQKEI-GWGSQIRSYVFHPY  291 (326)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhccC-ccCCCeEEEECCCC
Confidence            9987                  5555544 68899999998 54

>PRK07342 peptide chain release factor 2; Provisional

Probab=99.96  E-value=3.5e-30  Score=217.73  Aligned_cols=94  Identities=32%  Similarity=0.360  Sum_probs=82.0

Q ss_pred             CcccccccccceeeccCCc----ccccCceeEEEEeecCCCCcccccccccEEEEeeCCceEEEeeccC----ChhhHhh
Q 045445           10 DNCSSTSSSSKKNYFELTD----DEQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYL----PPPQLLQ   81 (128)
Q Consensus        10 d~~~~tS~a~v~v~p~l~~----~~~~~dl~~~~~RssGpGGQ~vNkt~saV~l~H~PtGi~v~~~~~R----Nr~~A~~   81 (128)
                      ..++||||++|.++|.+++    .+.++||+++|+|||||||||||||+|||||+|+||||+|+|+++|    ||+.||+
T Consensus       172 ~~rrhTs~a~V~VlP~~~~~~~~~i~~~dl~~~~~RssG~GGQ~VNkt~saVrl~H~ptgi~v~~~~eRSQ~~Nk~~A~~  251 (339)
T PRK07342        172 NARRHTSFASIWVYPVIDDNIEVDVNESDVRIDTYRSSGAGGQHVNTTDSAVRITHIPTGIVVQCQQERSQHKNRAKAWS  251 (339)
T ss_pred             CCCeEeEEEEEEEEcCCCcccccccCcccEEEEEEECCCCCCCCccceeeeEEEEEcCCcEEEEECCcccHHHHHHHHHH
Confidence            4699999999999999975    3578999999999999999999999999999999999999999999    9999999


Q ss_pred             hCC--------------c---ccccccCCCCCCCCCCCC
Q 045445           82 ILP--------------P---KFTIRCSEVGPQIRPNNP  103 (128)
Q Consensus        82 ~L~--------------~---~~q~~~~~r~~kIrtyn~  103 (128)
                      +|+              .   +.+-..-.||++|||||+
T Consensus       252 ~L~~~L~~~~~~~~~~~~~~~~~~~~~i~~g~~IRtY~~  290 (339)
T PRK07342        252 MLRARLYEEELKKREEATNAAAASKTDIGWGHQIRSYVL  290 (339)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhhhccccCCcCCccC
Confidence            987              0   111112368899999987

>TIGR00020 prfB peptide chain release factor 2

Probab=99.96  E-value=1.1e-29  Score=216.24  Aligned_cols=96  Identities=30%  Similarity=0.363  Sum_probs=84.2

Q ss_pred             CcccccccccceeeccCCc----ccccCceeEEEEeecCCCCcccccccccEEEEeeCCceEEEeeccC----ChhhHhh
Q 045445           10 DNCSSTSSSSKKNYFELTD----DEQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYL----PPPQLLQ   81 (128)
Q Consensus        10 d~~~~tS~a~v~v~p~l~~----~~~~~dl~~~~~RssGpGGQ~vNkt~saV~l~H~PtGi~v~~~~~R----Nr~~A~~   81 (128)
                      ..++||||++|.++|..++    ++++.|++++|+|||||||||||||+|+|+|+|+||||+|.|+++|    ||..||+
T Consensus       208 ~~rrhts~a~V~vlP~~~~~~~~~i~~~d~~~~~~rssG~GGQ~VNkt~saVri~H~ptgi~v~~q~~RSQ~~Nk~~A~~  287 (364)
T TIGR00020       208 NGRRHTSFASVFVMPEVDDDIDIEIKPEDLRIDTYRASGAGGQHVNKTDSAVRITHIPTGIVVQCQNDRSQHKNKDSAMK  287 (364)
T ss_pred             CCCeEeeeEEEEEecCCCcccceecccccEEEEEeeCCCCCCccccccceEEEEEECCCcEEEEECCccCHHHHHHHHHH
Confidence            4699999999999999964    4678999999999999999999999999999999999999999999    9999999


Q ss_pred             hCC-----------------cccccccCCCCCCCCCCCC-Ch
Q 045445           82 ILP-----------------PKFTIRCSEVGPQIRPNNP-KF  105 (128)
Q Consensus        82 ~L~-----------------~~~q~~~~~r~~kIrtyn~-~f  105 (128)
                      +|+                 .+.+-...+||++|||||+ ++
T Consensus       288 ~L~~kL~~~~~~~~~~~~~~~r~~~~~~~rg~~IRtY~~~~~  329 (364)
T TIGR00020       288 VLKAKLYELEMEKEQAEKDAKEGEKSEIGWGSQIRSYVLHPY  329 (364)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhhccCccCCeEEEECCCC
Confidence            997                 1212233479999999998 54

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.

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

Probab=99.95  E-value=1.9e-29  Score=200.33  Aligned_cols=92  Identities=26%  Similarity=0.307  Sum_probs=83.0

Q ss_pred             CcccccccccceeeccCCcccccCceeEEEEeecCCCCcccccccccEEEEeeCCceEEEeeccC----ChhhHhhhCC-
Q 045445           10 DNCSSTSSSSKKNYFELTDDEQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYL----PPPQLLQILP-   84 (128)
Q Consensus        10 d~~~~tS~a~v~v~p~l~~~~~~~dl~~~~~RssGpGGQ~vNkt~saV~l~H~PtGi~v~~~~~R----Nr~~A~~~L~-   84 (128)
                      ..++||||++|.++|. +.+++++||+++|+|||||||||||||+|+|+|+|+||||+|+|+++|    ||+.|+++|+ 
T Consensus        85 ~~~R~~s~~~V~v~~~-~~~i~~~dl~~~~~RssGpGGQ~VNkt~saVrl~h~ptgi~v~~~~~RSQ~~Nk~~A~~~L~~  163 (200)
T PRK08179         85 HHGRKNWFVGIGRFSA-DEEEQSDEIRFETLRSSGPGGQHVNKTDSAVRATHLASGISVKVQSERSQHANKRLARLLIAW  163 (200)
T ss_pred             CCCceEEEEEEEEeCC-cCccCHHHeEEEEEEccCCcccccccccceEEEEEcCCcEEEEECCCCCHHHHHHHHHHHHHH
Confidence            3678999999999975 335788999999999999999999999999999999999999999999    9999999997 


Q ss_pred             ----------------cccccccCCCCCCCCCCC
Q 045445           85 ----------------PKFTIRCSEVGPQIRPNN  102 (128)
Q Consensus        85 ----------------~~~q~~~~~r~~kIrtyn  102 (128)
                                      ++.+..+.+||++||||-
T Consensus       164 ~L~~~~~~~~~~~~~~~~~~~~~~~Rg~~IRt~~  197 (200)
T PRK08179        164 KLEQQQQEQSAALKSQRRMFHHQIERGNPRRVFT  197 (200)
T ss_pred             HHHHHHHHHHHHHHHHHHhccccccccCceEeee
Confidence                            555666779999999995

>PRK00578 prfB peptide chain release factor 2; Validated

Probab=99.95  E-value=1.7e-29  Score=215.10  Aligned_cols=96  Identities=32%  Similarity=0.426  Sum_probs=84.9

Q ss_pred             CCcccccccccceeeccCCc----ccccCceeEEEEeecCCCCcccccccccEEEEeeCCceEEEeeccC----ChhhHh
Q 045445            9 NDNCSSTSSSSKKNYFELTD----DEQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYL----PPPQLL   80 (128)
Q Consensus         9 ~d~~~~tS~a~v~v~p~l~~----~~~~~dl~~~~~RssGpGGQ~vNkt~saV~l~H~PtGi~v~~~~~R----Nr~~A~   80 (128)
                      ...++||||++|.++|.+++    .+.++|++++|+|||||||||||||+|+|+|+|+||||+|.|+++|    ||+.|+
T Consensus       207 ~~~r~hts~~~V~vlP~~~~~~~~~i~~~dl~~~~~rssGpGGQ~vNkt~saVrl~h~ptgi~v~~~~~RSQ~~Nk~~A~  286 (367)
T PRK00578        207 SAGRRHTSFASVEVYPEVDDTIEIEINPKDLRIDTYRSSGAGGQHVNKTDSAVRITHIPTGIVVQCQNERSQHQNKASAM  286 (367)
T ss_pred             CCCceecceeeEEecCCCCCccccccChhhEEEEEeeCCCCCCCcccceeeEEEEEECCCcEEEEECCCCCHHHHHHHHH
Confidence            34799999999999999865    3678999999999999999999999999999999999999999999    999999


Q ss_pred             hhCC------------------cccccccCCCCCCCCCCCC-Ch
Q 045445           81 QILP------------------PKFTIRCSEVGPQIRPNNP-KF  105 (128)
Q Consensus        81 ~~L~------------------~~~q~~~~~r~~kIrtyn~-~f  105 (128)
                      ++|+                  |+.+ ...+||++|||||+ .+
T Consensus       287 ~~L~~kL~~~~~~~~~~~~~~~r~~~-~~~~rg~~IRtYn~~p~  329 (367)
T PRK00578        287 KMLKAKLYELELEKRAAEKDALKGEK-KEIGWGSQIRSYVLHPY  329 (367)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhh-ccccccCCeEEEECCCC
Confidence            9987                  2222 34589999999997 54

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

Probab=99.94  E-value=4.9e-28  Score=196.88  Aligned_cols=109  Identities=30%  Similarity=0.293  Sum_probs=90.7

Q ss_pred             eeecCCcccccccccceeeccCCcc----cccCceeEEEEeecCCCCcccccccccEEEEeeCCceEEEeeccC----Ch
Q 045445            5 SCNYNDNCSSTSSSSKKNYFELTDD----EQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYL----PP   76 (128)
Q Consensus         5 ~~~~~d~~~~tS~a~v~v~p~l~~~----~~~~dl~~~~~RssGpGGQ~vNkt~saV~l~H~PtGi~v~~~~~R----Nr   76 (128)
                      |-.+.+.++||||+++.++|.+++.    +.+.|++++|+|||||||||||||+|||+|+|+||||+|.||.+|    |+
T Consensus        78 Spf~~~~~R~tsf~~v~v~p~~~~~i~i~I~~~dl~idt~RASGaGGQhVNKt~SAVrlth~ptgivv~cq~eRSq~~n~  157 (239)
T COG1186          78 SPFDSNGRRHTSFASVEVFPELDISIEIEIPDDDLRIDTYRASGAGGQHVNKTDSAVRLTHLPTGIVVLCQNERSQHLNK  157 (239)
T ss_pred             cCCCcCcccccceeeeeecCCCCcccceecCccceEEEEEEcCCCCCCccccccccEEEEEcCCCCEecCHHHHHHHHHH
Confidence            4456779999999999999999752    467999999999999999999999999999999999999999999    99


Q ss_pred             hhHhhhCC-----------------cccccccCCCCCCCCCCCCC-h-hhHHHHHH
Q 045445           77 PQLLQILP-----------------PKFTIRCSEVGPQIRPNNPK-F-ALLDLIFA  113 (128)
Q Consensus        77 ~~A~~~L~-----------------~~~q~~~~~r~~kIrtyn~~-f-~~lD~~~~  113 (128)
                      ..||..|+                 ++..-+-.+|+.|||.|-++ + ++-|....
T Consensus       158 ~~a~~~l~~kL~~~~~~~Rsqe~n~~~a~~k~i~wg~qirsyv~~p~~~vKd~Rt~  213 (239)
T COG1186         158 ALARKMLKGKLYILAQEKRSQEKNRERALKKLIGWGNQIRSYVLDPYQPTKDLRTG  213 (239)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHhccccCCCccccccccccc
Confidence            99998876                 22223345899999999766 4 55554433

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

Probab=99.93  E-value=2.6e-27  Score=172.13  Aligned_cols=76  Identities=34%  Similarity=0.416  Sum_probs=69.4

Q ss_pred             ccccCceeEEEEeecCCCCcccccccccEEEEeeCCceEEEeeccC----ChhhHhhhCC------------------cc
Q 045445           29 DEQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYL----PPPQLLQILP------------------PK   86 (128)
Q Consensus        29 ~~~~~dl~~~~~RssGpGGQ~vNkt~saV~l~H~PtGi~v~~~~~R----Nr~~A~~~L~------------------~~   86 (128)
                      ++.++||+++|+|||||||||||||+|+|+|+|+||||+|+|+++|    |++.|+++|.                  ++
T Consensus         8 ~i~~~dl~~~~~RssGpGGQ~VNk~~s~V~l~h~ptgi~v~~~~~Rsq~~Nr~~A~~~L~~~l~~~~~~~~~~~~~~~~~   87 (113)
T PF00472_consen    8 DIPEKDLEISFSRSSGPGGQNVNKTNSKVRLRHIPTGIVVKCQESRSQHQNREDALEKLREKLDEAYREKRREKTREIRK   87 (113)
T ss_dssp             CC-GGGEEEEEEESSSSSSCHHHSSSEEEEEEETTTTEEEEEESSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTT
T ss_pred             ccCHHHeEEEEEecCCCCCCcccccCCEEEEEEecccEEEEEcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3678999999999999999999999999999999999999999999    9999999886                  66


Q ss_pred             cccccCCCCCCCCCCCCC
Q 045445           87 FTIRCSEVGPQIRPNNPK  104 (128)
Q Consensus        87 ~q~~~~~r~~kIrtyn~~  104 (128)
                      .+.+..+++++||+|++.
T Consensus        88 ~~~~~~~~~~~iR~y~~~  105 (113)
T PF00472_consen   88 SQVKRLERKKKIRTYNFP  105 (113)
T ss_dssp             TSCCCSSTTSEEEEEETT
T ss_pred             HHHhHHhhhcceecccCC
Confidence            677778999999999974

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

>PRK09256 hypothetical protein; Provisional

Probab=99.75  E-value=6e-19  Score=133.29  Aligned_cols=55  Identities=29%  Similarity=0.403  Sum_probs=50.5

Q ss_pred             cccCceeEEEEeecCCCCcccccccccEEEEe------eC-----------------Cc-eEEEeeccC----ChhhHhh
Q 045445           30 EQFRECEMDTYKSSGPGGQHRNKRESAVRLKH------VP-----------------TA-SSVNLDAYL----PPPQLLQ   81 (128)
Q Consensus        30 ~~~~dl~~~~~RssGpGGQ~vNkt~saV~l~H------~P-----------------tG-i~v~~~~~R----Nr~~A~~   81 (128)
                      +.++||+++|+|||||||||||||+|+|+|+|      +|                 .| |.|.|+++|    |++.|++
T Consensus        10 i~~~~l~~~~~RSSGPGGQ~VNKt~SkV~l~~~~~~~~lp~~~~~~l~~~~~~r~~~~g~l~i~~~~~RSQ~~Nr~~al~   89 (138)
T PRK09256         10 IPENELEWRFIRASGPGGQNVNKVSTAVELRFDIAASSLPEFYKERLLALAGHRITKDGVIVIKAQEFRSQERNREDALE   89 (138)
T ss_pred             cCHHHeEEEEEEcCCCCcccccccceeeEEEechhhccCCHHHHHHHHHHhcCcccCCCcEEEEECCcCCHHHHHHHHHH
Confidence            45689999999999999999999999999996      66                 35 999999999    9999999


Q ss_pred             hCC
Q 045445           82 ILP   84 (128)
Q Consensus        82 ~L~   84 (128)
                      +|.
T Consensus        90 kL~   92 (138)
T PRK09256         90 RLV   92 (138)
T ss_pred             HHH
Confidence            987

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

Probab=99.33  E-value=1.2e-12  Score=102.33  Aligned_cols=59  Identities=25%  Similarity=0.349  Sum_probs=49.2

Q ss_pred             CCcccccCceeEEEEeecCCCCcccccccccEEEEee-------CC------------------ceEEEeeccC----Ch
Q 045445           26 LTDDEQFRECEMDTYKSSGPGGQHRNKRESAVRLKHV-------PT------------------ASSVNLDAYL----PP   76 (128)
Q Consensus        26 l~~~~~~~dl~~~~~RssGpGGQ~vNkt~saV~l~H~-------Pt------------------Gi~v~~~~~R----Nr   76 (128)
                      ++..+....++++|.||||||||||||++|+|.|++.       |.                  .|.|.++.+|    |.
T Consensus        33 ~~g~ipld~~~i~y~RSSGPGGQNVNKvNTKv~vrf~vs~a~Wipe~~R~~~~~~~~~rink~gelvI~Sd~TRsq~~Ni  112 (172)
T KOG3429|consen   33 FKGKIPLDQLEISYSRSSGPGGQNVNKVNTKVEVRFKVSNAEWIPEFLRNKLLTTEKNRINKDGELVIYSDKTRSQHKNI  112 (172)
T ss_pred             cCCCCchhheEEEEeecCCCCCcccccccceEEEEEecchhhhccHHHHHHHHHHHHHhhccCccEEEecchhHHhhccH
Confidence            3334555789999999999999999999999999973       22                  2888888887    99


Q ss_pred             hhHhhhCC
Q 045445           77 PQLLQILP   84 (128)
Q Consensus        77 ~~A~~~L~   84 (128)
                      ..|+++|.
T Consensus       113 aDcleKlr  120 (172)
T KOG3429|consen  113 ADCLEKLR  120 (172)
T ss_pred             HHHHHHHH
Confidence            99999886

>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]

Probab=91.06  E-value=0.25  Score=29.73  Aligned_cols=23  Identities=26%  Similarity=0.371  Sum_probs=19.3

Q ss_pred             hhHHHHHHcCCChHHHHHHccCC
Q 045445          106 ALLDLIFAVEGSVSEAAKFLSLL  128 (128)
Q Consensus       106 ~~lD~~~~~~g~~~~aa~~l~l~  128 (128)
                      .+.+.|..++|+++.||+.||+.
T Consensus         9 ~i~~aL~~~~gn~~~aA~~Lgis   31 (42)
T PF02954_consen    9 LIRQALERCGGNVSKAARLLGIS   31 (42)
T ss_dssp             HHHHHHHHTTT-HHHHHHHHTS-
T ss_pred             HHHHHHHHhCCCHHHHHHHHCCC
Confidence            56789999999999999999973

It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	128
1ml5_Z	365	Structure Of The E. Coli Ribosomal Termination Comp		4e-06
1mi6_A	365	Docking Of The Modified Rf2 X-Ray Structure Into Th		4e-06
1gqe_A	365	Polypeptide Chain Release Factor 2 (Rf2) From Esche		5e-06
2b3t_B	360	Molecular Basis For Bacterial Class 1 Release Facto		6e-05
2fvo_A	333	Docking Of The Modified Rf1 X-ray Structure Into Th		9e-05
1rq0_A	342	Crystal Structure Of Peptide Releasing Factor 1 Len		9e-05
2wh1_Y	351	Insights Into Translational Termination From The St		3e-04
2ihr_1	365	Rf2 Of Thermus Thermophilus Length = 365		3e-04
3f1e_X	378	Crystal Structure Of A Translation Termination Comp		3e-04
2x9r_Y	351	Structure Of The 70s Ribosome Bound To Release Fact		3e-04
2b9m_Y	365	30s Ribosomal Subunit, Trnas, Mrna And Release Fact		3e-04
2b64_Y	354	30s Ribosomal Subunit, Trnas, Mrna And Release Fact		6e-04

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

Iteration: 1
 Score = 46.6 bits (109), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 17/29 (58%), Positives = 23/29 (79%)
Query: 37  MDTYKSSGPGGQHRNKRESAVRLKHVPTA 65
           +D Y++SG GGQH N+ ESAVR+ H+PT 
Sbjct: 241 IDVYRTSGAGGQHVNRTESAVRITHIPTG 269

>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 = 46.2 bits (108), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 17/29 (58%), Positives = 23/29 (79%)
Query: 37  MDTYKSSGPGGQHRNKRESAVRLKHVPTA 65
           +D Y++SG GGQH N+ ESAVR+ H+PT 
Sbjct: 241 IDVYRASGAGGQHVNRTESAVRITHIPTG 269

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

Iteration: 1
 Score = 46.2 bits (108), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 17/29 (58%), Positives = 23/29 (79%)
Query: 37  MDTYKSSGPGGQHRNKRESAVRLKHVPTA 65
           +D Y++SG GGQH N+ ESAVR+ H+PT 
Sbjct: 241 IDVYRASGAGGQHVNRTESAVRITHIPTG 269

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

Iteration: 1
 Score = 42.7 bits (99), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 16/29 (55%), Positives = 23/29 (79%)
Query: 37  MDTYKSSGPGGQHRNKRESAVRLKHVPTA 65
           +DT++SSG GGQH N  +SA+R+ H+PT 
Sbjct: 224 IDTFRSSGAGGQHVNTTDSAIRITHLPTG 252

>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 = 42.0 bits (97), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 17/36 (47%), Positives = 28/36 (77%)
Query: 34  ECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVN 69
           + +++T+++SG GGQ+ NK ESAVR+ H+PT   V+
Sbjct: 197 DLKIETFRASGHGGQYVNKTESAVRITHLPTGIVVS 232

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

Iteration: 1
 Score = 42.0 bits (97), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 17/36 (47%), Positives = 28/36 (77%)
Query: 34  ECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVN 69
           + +++T+++SG GGQ+ NK ESAVR+ H+PT   V+
Sbjct: 197 DLKIETFRASGHGGQYVNKTESAVRITHLPTGIVVS 232

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

Iteration: 1
 Score = 40.4 bits (93), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 17/36 (47%), Positives = 24/36 (66%)
Query: 34  ECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVN 69
           E  +D  ++SGPGGQ  N  +SAVR+ H+PT  +V 
Sbjct: 221 ELRIDVMRASGPGGQGVNTTDSAVRVVHLPTGITVT 256

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

Iteration: 1
 Score = 40.4 bits (93), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 17/36 (47%), Positives = 24/36 (66%)
Query: 34  ECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVN 69
           E  +D  ++SGPGGQ  N  +SAVR+ H+PT  +V 
Sbjct: 226 ELRIDVMRASGPGGQGVNTTDSAVRVVHLPTGITVT 261

>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 = 40.4 bits (93), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 17/36 (47%), Positives = 24/36 (66%)
Query: 34  ECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVN 69
           E  +D  ++SGPGGQ  N  +SAVR+ H+PT  +V 
Sbjct: 239 ELRIDVMRASGPGGQGVNTTDSAVRVVHLPTGITVT 274

>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 = 40.4 bits (93), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 17/36 (47%), Positives = 24/36 (66%)
Query: 34  ECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVN 69
           E  +D  ++SGPGGQ  N  +SAVR+ H+PT  +V 
Sbjct: 221 ELRIDVMRASGPGGQGVNTTDSAVRVVHLPTGITVT 256

>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 = 40.4 bits (93), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 17/36 (47%), Positives = 24/36 (66%)
Query: 34  ECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVN 69
           E  +D  ++SGPGGQ  N  +SAVR+ H+PT  +V 
Sbjct: 226 ELRIDVMRASGPGGQGVNTTDSAVRVVHLPTGITVT 261

>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 = 39.3 bits (90), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 17/36 (47%), Positives = 23/36 (63%)
Query: 34  ECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVN 69
           E  +D  ++SGPGGQ  N  +SAVR+ H+PT   V 
Sbjct: 216 EIRIDVMRASGPGGQGVNTTDSAVRVVHLPTGIMVT 251

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	128
2rsm_A	115	Probable peptide chain release factor C12ORF65 HO	1e-13
2ihr_1	365	Peptide chain release factor 2; mixed alpha-beta,	3e-13
1gqe_A	365	Release factor 2, RF2; protein synthesis, ribosome	9e-13
1zbt_A	371	RF-1, peptide chain release factor 1; peptide chai	5e-12
2b3t_B	360	RF-1, peptide chain release factor 1; translation	9e-12
3d5a_X	354	RF1, peptide chain release factor 1; ribosome, rib	9e-12
1rq0_A	342	RF-1, peptide chain release factor 1; X-RAY, cryst	1e-11
4dh9_Y	140	YAEJ; ribosome, YAEJ, ribosome stalling, ribosome	5e-11
2jva_A	108	Peptidyl-tRNA hydrolase domain protein; GFT hydrol	3e-10
1j26_A	112	Immature colon carcinoma transcript 1; peptide cha	1e-06

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

 Score = 61.6 bits (150), Expect = 1e-13
 Identities = 16/32 (50%), Positives = 18/32 (56%)

Query: 33 RECEMDTYKSSGPGGQHRNKRESAVRLKHVPT 64
           E E    K  GPGGQ  NK  + V LKHVP+
Sbjct: 46 SELEEQFVKGHGPGGQATNKTSNCVVLKHVPS 77

>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 = 63.4 bits (155), Expect = 3e-13
 Identities = 16/31 (51%), Positives = 22/31 (70%)

Query: 34  ECEMDTYKSSGPGGQHRNKRESAVRLKHVPT 64
           E  +D  ++SGPGGQ  N  +SAVR+ H+PT
Sbjct: 226 ELRIDVMRASGPGGQGVNTTDSAVRVVHLPT 256

>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 = 62.3 bits (152), Expect = 9e-13
 Identities = 25/54 (46%), Positives = 33/54 (61%), Gaps = 4/54 (7%)

Query: 15  TSSSSKKNYFELTDDEQF----RECEMDTYKSSGPGGQHRNKRESAVRLKHVPT 64
           TS SS   Y E+ DD        +  +D Y++SG GGQH N+ ESAVR+ H+PT
Sbjct: 215 TSFSSAFVYPEVDDDIDIEINPADLRIDVYRASGAGGQHVNRTESAVRITHIPT 268

>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 = 60.3 bits (147), Expect = 5e-12
 Identities = 15/31 (48%), Positives = 22/31 (70%)

Query: 34  ECEMDTYKSSGPGGQHRNKRESAVRLKHVPT 64
           +  +D Y +SG GGQ+ NK  +AVR+ H+PT
Sbjct: 234 DLRVDIYHASGAGGQNVNKVATAVRIIHLPT 264

>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 = 59.5 bits (145), Expect = 9e-12
 Identities = 16/31 (51%), Positives = 24/31 (77%)

Query: 34  ECEMDTYKSSGPGGQHRNKRESAVRLKHVPT 64
           +  +DT++SSG GGQH N  +SA+R+ H+PT
Sbjct: 221 DLRIDTFRSSGAGGQHVNTTDSAIRITHLPT 251

>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 = 59.5 bits (145), Expect = 9e-12
 Identities = 16/31 (51%), Positives = 22/31 (70%)

Query: 34  ECEMDTYKSSGPGGQHRNKRESAVRLKHVPT 64
           E  +D  ++SGPGGQ  N  +SAVR+ H+PT
Sbjct: 216 EIRIDVMRASGPGGQGVNTTDSAVRVVHLPT 246

>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 = 59.1 bits (144), Expect = 1e-11
 Identities = 16/28 (57%), Positives = 24/28 (85%)

Query: 37  MDTYKSSGPGGQHRNKRESAVRLKHVPT 64
           ++T+++SG GGQ+ NK ESAVR+ H+PT
Sbjct: 200 IETFRASGHGGQYVNKTESAVRITHLPT 227

>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 = 55.2 bits (133), Expect = 5e-11
 Identities = 17/50 (34%), Positives = 25/50 (50%), Gaps = 6/50 (12%)

Query: 34 ECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYLPPPQLLQIL 83
          E E+   ++ G GGQH NK  +A+ L+    ASS      LP     ++L
Sbjct: 14 ELEITAIRAQGAGGQHVNKTSTAIHLRFDIRASS------LPEYYKERLL 57

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

 Score = 52.6 bits (126), Expect = 3e-10
 Identities = 18/50 (36%), Positives = 26/50 (52%), Gaps = 6/50 (12%)

Query: 34 ECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYLPPPQLLQIL 83
          E E+   ++ G GGQ+ NK  SA+ L+    ASS      LPP    ++L
Sbjct: 14 EIELTAIRAQGAGGQNVNKVSSAMHLRFDINASS------LPPFYKERLL 57

>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 = 43.2 bits (101), Expect = 1e-06
 Identities = 12/50 (24%), Positives = 22/50 (44%), Gaps = 5/50 (10%)

Query: 34 ECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYLPPPQLLQIL 83
             +   +SSGPGGQ+ NK  S   ++    ++      ++  P   +I 
Sbjct: 21 RLSISYCRSSGPGGQNVNKVNSKAEVRFHLASAD-----WIEEPVRQKIA 65

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	128
1zbt_A	371	RF-1, peptide chain release factor 1; peptide chai	99.97
1rq0_A	342	RF-1, peptide chain release factor 1; X-RAY, cryst	99.97
2b3t_B	360	RF-1, peptide chain release factor 1; translation	99.97
3d5a_X	354	RF1, peptide chain release factor 1; ribosome, rib	99.97
1gqe_A	365	Release factor 2, RF2; protein synthesis, ribosome	99.96
2ihr_1	365	Peptide chain release factor 2; mixed alpha-beta,	99.96
2rsm_A	115	Probable peptide chain release factor C12ORF65 HO	99.94
1j26_A	112	Immature colon carcinoma transcript 1; peptide cha	99.85
2jva_A	108	Peptidyl-tRNA hydrolase domain protein; GFT hydrol	99.85
4dh9_Y	140	YAEJ; ribosome, YAEJ, ribosome stalling, ribosome	99.8
3e7l_A	63	Transcriptional regulator (NTRC family); sigma43 a	84.49

>1zbt_A RF-1, peptide chain release factor 1; peptide chain release factor 1 (RF-1), structural joint center for structural genomics, JCSG; 2.34A {Streptococcus mutans}

Probab=99.97  E-value=1.3e-32  Score=233.51  Aligned_cols=96  Identities=26%  Similarity=0.331  Sum_probs=78.2

Q ss_pred             CcccccccccceeeccCCcc---cccCceeEEEEeecCCCCcccccccccEEEEeeCCceEEEeeccC----ChhhHhhh
Q 045445           10 DNCSSTSSSSKKNYFELTDD---EQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYL----PPPQLLQI   82 (128)
Q Consensus        10 d~~~~tS~a~v~v~p~l~~~---~~~~dl~~~~~RssGpGGQ~vNkt~saV~l~H~PtGi~v~~~~~R----Nr~~A~~~   82 (128)
                      .-++|||||+|.++|.+++.   ++++||+++|+|||||||||||||+|+|+|+|+||||+|+|+++|    ||+.||++
T Consensus       207 ~gR~hTS~asV~V~Pe~~ev~i~I~~~dl~i~~~RssGpGGQ~VNkt~SaVrlthlPtGivV~~q~eRSQ~~Nr~~A~~~  286 (371)
T 1zbt_A          207 QGRVHTSTATVLVMPEVEEVEYEIDPKDLRVDIYHASGAGGQNVNKVATAVRIIHLPTNIKVEMQEERTQQKNRDKAMKI  286 (371)
T ss_dssp             SCCCEEEEEEEEEEECCCGGGSCCCGGGEEEEEECC---------CCCCEEEEEETTTTEEEEECSSSSHHHHHHHHHHH
T ss_pred             CCcccccceEEEEeccccccccccCcCcEEEEEecCCCCCCCcccccceeEEEEECCCeEEEEECCcCCHHHHHHHHHHH
Confidence            36899999999999999873   678999999999999999999999999999999999999999999    99999999


Q ss_pred             CC------------------cccccccCCCCCCCCCCCCCh
Q 045445           83 LP------------------PKFTIRCSEVGPQIRPNNPKF  105 (128)
Q Consensus        83 L~------------------~~~q~~~~~r~~kIrtyn~~f  105 (128)
                      |+                  ++.+++.++||++|||||+..
T Consensus       287 L~~~L~~~~~~~~~~~~~~~r~~~ig~g~Rse~IRtYnf~q  327 (371)
T 1zbt_A          287 IRARVADHFAQIAQDEQDAERKSTVGTGDRSERIRTYNFPQ  327 (371)
T ss_dssp             HHHHHHHHHHHHHHHHTCC----CCSCSCTTSEEEEEETTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhccccccCCCeeeEECCC
Confidence            86                  778899999999999999765

>1rq0_A RF-1, peptide chain release factor 1; X-RAY, crystal, peptide release factor 1, ribosome, structural genomics, BSGC structure funded by NIH; 2.65A {Thermotoga maritima} SCOP: e.38.1.1 PDB: 2fvo_A

Probab=99.97  E-value=2.1e-32  Score=230.22  Aligned_cols=95  Identities=31%  Similarity=0.351  Sum_probs=77.2

Q ss_pred             cccccccccceeeccCCcc---cccCceeEEEEeecCCCCcccccccccEEEEeeCCceEEEeeccC----ChhhHhhhC
Q 045445           11 NCSSTSSSSKKNYFELTDD---EQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYL----PPPQLLQIL   83 (128)
Q Consensus        11 ~~~~tS~a~v~v~p~l~~~---~~~~dl~~~~~RssGpGGQ~vNkt~saV~l~H~PtGi~v~~~~~R----Nr~~A~~~L   83 (128)
                      -++|||||+|.++|.+++.   ++++||+++|+|||||||||||||+|+|+|+|+||||+|+|+++|    ||+.||++|
T Consensus       171 gR~hTS~asV~V~Pe~~~~~i~i~~~dl~i~~~RssGpGGQ~VNKt~SaVrl~hlPtGivv~~q~~RSQ~~Nr~~A~~~L  250 (342)
T 1rq0_A          171 GRIHTSTATVAVLPEIEEKDIEIRPEDLKIETFRASGHGGQYVNKTESAVRITHLPTGIVVSCQNERSQYQNKQTALRIL  250 (342)
T ss_dssp             CCCEEEEEEEEEEECCCGGGSCCCGGGEEEEEECCCC----CCSSSSEEEEEEETTTCCEEEEEESSCHHHHHHHHHHHH
T ss_pred             CCCcccceEEEEeccccccccccChhHeEEEeecCCCCCCcccccccceEEEEECCCeEEEEECCCCCHHHHHHHHHHHH
Confidence            5899999999999999773   678999999999999999999999999999999999999999999    999999998


Q ss_pred             C------------------cccccccCCCCCCCCCCCCCh
Q 045445           84 P------------------PKFTIRCSEVGPQIRPNNPKF  105 (128)
Q Consensus        84 ~------------------~~~q~~~~~r~~kIrtyn~~f  105 (128)
                      +                  ++++++.++||++|||||+..
T Consensus       251 ~~~L~~~~~~~~~~~~~~~r~~~i~~g~Rse~IRtYnf~~  290 (342)
T 1rq0_A          251 RARLYQLQKEQKEREISQKRKSQIGTGERSEKIRTYNFPQ  290 (342)
T ss_dssp             HHHHHHHHHHHHHTTTCC----------CCCEEEEEETTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhcccccccCCeEEEECCC
Confidence            6                  778888899999999999765

>2b3t_B RF-1, peptide chain release factor 1; translation termination, methylation, conformational changes; HET: SAH; 3.10A {Escherichia coli} SCOP: e.38.1.1

Probab=99.97  E-value=2.3e-32  Score=231.18  Aligned_cols=95  Identities=27%  Similarity=0.337  Sum_probs=82.0

Q ss_pred             cccccccccceeeccCCcc----cccCceeEEEEeecCCCCcccccccccEEEEeeCCceEEEeeccC----ChhhHhhh
Q 045445           11 NCSSTSSSSKKNYFELTDD----EQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYL----PPPQLLQI   82 (128)
Q Consensus        11 ~~~~tS~a~v~v~p~l~~~----~~~~dl~~~~~RssGpGGQ~vNkt~saV~l~H~PtGi~v~~~~~R----Nr~~A~~~   82 (128)
                      -++|||||+|.++|.+++.    ++++||+++|+|||||||||||||+|+|+|+|+||||+|+|+++|    ||+.|+++
T Consensus       194 gR~hTS~asV~V~Pe~~~~e~i~i~~~dl~i~~~RssG~GGQ~VNkt~saVrl~hlPtGivv~~q~~RSQ~~Nr~~A~~~  273 (360)
T 2b3t_B          194 GRIHTSACTVAVMPELPDAELPDVNPADLRIDTFRSSGAGGQHVNTTDSAIRITHLPTGIVVECQDERSQHKNKAKALSV  273 (360)
T ss_dssp             CCCEEEEEEEECCBCCCTTTCCCCCSSSEEEEECCSSCCCTTTCCCSSEEEEEEETTTCCEEEEEESSCHHHHHHHHHHH
T ss_pred             CcCCccceEEEEecCcccccccccChhheEEeeecCCCCCCCccccccceEEEEECCCeEEEEECCCCCHHHHHHHHHHH
Confidence            6899999999999998763    568999999999999999999999999999999999999999999    99999998


Q ss_pred             CC------------------cccccccCCCCCCCCCCCCCh
Q 045445           83 LP------------------PKFTIRCSEVGPQIRPNNPKF  105 (128)
Q Consensus        83 L~------------------~~~q~~~~~r~~kIrtyn~~f  105 (128)
                      |+                  ++.+++.++||++|||||+..
T Consensus       274 L~~~L~~~~~~~~~~~~~~~r~~~i~~g~rse~IRtYnf~~  314 (360)
T 2b3t_B          274 LGARIHAAEMAKRQQAEASTRRNLLGSGDRSDRNRTYNFPQ  314 (360)
T ss_dssp             HHHHHTTTTTTSCC------CCC-------CCEEEEEETTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhcccccccCCeeeEECCC
Confidence            86                  778888899999999999765

>3d5a_X RF1, peptide chain release factor 1; ribosome, ribonucleoprotein, ribosomal protein, RNA-binding, binding, metal-binding, zinc-finger; 3.21A {Thermus thermophilus} PDB: 2b64_Y 3d5c_X 3mr8_V 3ms0_V

Probab=99.97  E-value=1.2e-32  Score=232.46  Aligned_cols=96  Identities=28%  Similarity=0.318  Sum_probs=89.4

Q ss_pred             CcccccccccceeeccCCcc---cccCceeEEEEeecCCCCcccccccccEEEEeeCCceEEEeeccC----ChhhHhhh
Q 045445           10 DNCSSTSSSSKKNYFELTDD---EQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYL----PPPQLLQI   82 (128)
Q Consensus        10 d~~~~tS~a~v~v~p~l~~~---~~~~dl~~~~~RssGpGGQ~vNkt~saV~l~H~PtGi~v~~~~~R----Nr~~A~~~   82 (128)
                      --++|||||+|.++|.+++.   ++++||+++|+|||||||||||||+|+|+|+|+||||+|+|+++|    ||+.||++
T Consensus       189 ~gR~hTS~asV~V~P~~~~~~i~i~~~dl~i~~~RssG~GGQ~VNkt~SaVrl~HlPtgivv~~q~~RSQ~~Nr~~A~~~  268 (354)
T 3d5a_X          189 QGRIHTSTATVAVLPKAEEEDFALNMDEIRIDVMRASGPGGQGVNTTDSAVRVVHLPTGIMVTCQDSRSQIKNREKALMI  268 (354)
T ss_dssp             SCCCEEEEEEEEEEECCCCCCCCCCGGGEEEEEECCCSCCHHHHHHCCCEEEEEETTTTEEEEECCSSCHHHHHHHHHHH
T ss_pred             CCcCccCceEEEEeccCcccccccCccceEEEeecCCCCCCcccccccceEEEEEcCCeEEEEECCCCCHHHHHHHHHHH
Confidence            35899999999999998763   678999999999999999999999999999999999999999999    99999999


Q ss_pred             CC------------------cccccccCCCCCCCCCCCCCh
Q 045445           83 LP------------------PKFTIRCSEVGPQIRPNNPKF  105 (128)
Q Consensus        83 L~------------------~~~q~~~~~r~~kIrtyn~~f  105 (128)
                      |+                  ++.+++.++||++|||||+..
T Consensus       269 L~~~L~~~~~~~~~~~~~~~r~~~i~~g~rse~IRtYnf~q  309 (354)
T 3d5a_X          269 LRSRLLEMKRAEEAERLRKTRLAQIGTGERSEKIRTYNFPQ  309 (354)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSCGGGGSCSSEEEETTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhcccccccCCeeeEECCC
Confidence            97                  677899999999999999765

>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=99.96  E-value=7.3e-31  Score=222.32  Aligned_cols=95  Identities=32%  Similarity=0.347  Sum_probs=83.0

Q ss_pred             CcccccccccceeeccCCcc----cccCceeEEEEeecCCCCcccccccccEEEEeeCCceEEEeeccC----ChhhHhh
Q 045445           10 DNCSSTSSSSKKNYFELTDD----EQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYL----PPPQLLQ   81 (128)
Q Consensus        10 d~~~~tS~a~v~v~p~l~~~----~~~~dl~~~~~RssGpGGQ~vNkt~saV~l~H~PtGi~v~~~~~R----Nr~~A~~   81 (128)
                      -.++|||||+|.++|.++++    +.++||+++|+|||||||||||||+|+|+|+|+||||+|+|+++|    ||..|++
T Consensus       210 ~gRrhTS~asV~V~Pe~~~~v~i~i~~~dl~~~~~RssG~GGQ~VNkt~saVrl~HiPtgivv~~q~~RSQ~~Nr~~A~~  289 (365)
T 1gqe_A          210 GGRRHTSFSSAFVYPEVDDDIDIEINPADLRIDVYRASGAGGQHVNRTESAVRITHIPTGIVTQCQNDRSQHKNKDQAMK  289 (365)
T ss_dssp             SCCEEEEEEEEEEEECCBTTBCCCCCGGGEEEEEECCCCSSCCSTTSSCCEEEEEETTTCCEEEECSSSCHHHHHHHHHH
T ss_pred             cCCCCcceeEEEEecCCCcccccccCHHHceEeeecCCCCCCCcccCccceEEEEECCCeEEEEECCCCCHHHHHHHHHH
Confidence            36899999999999999753    678999999999999999999999999999999999999999999    9999999


Q ss_pred             hCC------------------cccccccCCCCCCCCCCCCCh
Q 045445           82 ILP------------------PKFTIRCSEVGPQIRPNNPKF  105 (128)
Q Consensus        82 ~L~------------------~~~q~~~~~r~~kIrtyn~~f  105 (128)
                      +|+                  ++.+ ..-.||+||||||+..
T Consensus       290 ~L~~~L~~~~~~~~~~~~~~~r~~~-~~i~~G~~IRtY~f~~  330 (365)
T 1gqe_A          290 QMKAKLYEVEMQKKNAEKQAMEDNK-SDIGWGSQIRSYVLDD  330 (365)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCCSTTC-CCCCSCSEEEEEEGGG
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhh-cccCccCCeEeEECCC
Confidence            987                  2211 1236888999999644

>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=99.96  E-value=1.6e-30  Score=220.22  Aligned_cols=96  Identities=30%  Similarity=0.336  Sum_probs=83.2

Q ss_pred             CcccccccccceeeccCCcc----cccCceeEEEEeecCCCCcccccccccEEEEeeCCceEEEeeccC----ChhhHhh
Q 045445           10 DNCSSTSSSSKKNYFELTDD----EQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYL----PPPQLLQ   81 (128)
Q Consensus        10 d~~~~tS~a~v~v~p~l~~~----~~~~dl~~~~~RssGpGGQ~vNkt~saV~l~H~PtGi~v~~~~~R----Nr~~A~~   81 (128)
                      --++|||||+|.++|.+++.    ++++||+++|+|||||||||||||+|+|+|+|+||||+|+|+++|    ||..||+
T Consensus       198 ~gRrhTS~asV~V~P~~~~~~~i~i~~~dl~i~~~RssG~GGQ~VNkt~saVrl~h~Ptgivv~~q~~RSQ~~Nr~~A~~  277 (365)
T 2ihr_1          198 SGRRHTSFAGVEVIPEVDEEVEVVLKPEELRIDVMRASGPGGQGVNTTDSAVRVVHLPTGITVTCQTTRSQIKNKELALK  277 (365)
T ss_dssp             SCCEEEEEEEEEEEEECCSSSSCCCCGGGEEEEEECCCCSSCCSGGGSCSEEEEEETTTTEEEEECSSSCHHHHHHHHHH
T ss_pred             cCCccceeEEEEEecCCCcccccccCccceEEEEeecCCCCCceecccceEEEEEEcCCeEEEEECCCCCHHHHHHHHHH
Confidence            36899999999999999763    678999999999999999999999999999999999999999999    9999999


Q ss_pred             hCC-------------cccccc----cCCCCCCCCCCCCCh
Q 045445           82 ILP-------------PKFTIR----CSEVGPQIRPNNPKF  105 (128)
Q Consensus        82 ~L~-------------~~~q~~----~~~r~~kIrtyn~~f  105 (128)
                      +|+             ....++    .-.||++|||||+.-
T Consensus       278 ~L~~~L~~~~~~~~~~~~~~~r~~~~~i~~G~~IRtYnf~~  318 (365)
T 2ihr_1          278 ILKARLYELERKKREEELKALRGEVRPIEWGSQIRSYVLDK  318 (365)
T ss_dssp             HHHHHHHHHHHHHHHHHTTTTTCCSCCSCCCSCSEEEEGGG
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhhccCccCCeeeEECCC
Confidence            987             111111    236778999999765

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

Probab=99.94  E-value=8.4e-28  Score=176.49  Aligned_cols=70  Identities=27%  Similarity=0.243  Sum_probs=66.6

Q ss_pred             cccccceeeccCCcc----cccCceeEEEEeecCCCCcccccccccEEEEeeCCceEEEeeccC----ChhhHhhhCC
Q 045445           15 TSSSSKKNYFELTDD----EQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYL----PPPQLLQILP   84 (128)
Q Consensus        15 tS~a~v~v~p~l~~~----~~~~dl~~~~~RssGpGGQ~vNkt~saV~l~H~PtGi~v~~~~~R----Nr~~A~~~L~   84 (128)
                      ||+++|.++|+.++.    ++++||+|+|+|||||||||||||+|+|+|+|+||||+|+|+++|    ||+.||++|+
T Consensus        24 ts~~~v~v~p~~d~~~~l~I~~~dl~~~~~RssGpGGQ~VNKt~SaVrl~H~PTGivV~~q~~RSQ~~Nr~~A~~~L~  101 (115)
T 2rsm_A           24 MAASTVQVAGRKDYPALLPLNESELEEQFVKGHGPGGQATNKTSNCVVLKHVPSGIVVKCHQTRSVDQNRKIARKVLQ  101 (115)
T ss_dssp             CCCCCCCCCSCCCCCCSCCCCGGGCEEEECSCCCSCSSSCCCSCCCEEEECTTTCCEEEECCSSCHHHHHHHHHHHHH
T ss_pred             cceEEEEeccccCCCccCCcCHHHeEEEEeeCCCCCccccCccceeEEEecCCCCcEEEEcCCCCHHHHHHHHHHHHH
Confidence            999999999998753    678999999999999999999999999999999999999999999    9999999987

>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=99.85  E-value=3.6e-22  Score=145.41  Aligned_cols=59  Identities=24%  Similarity=0.330  Sum_probs=54.7

Q ss_pred             CCcccccCceeEEEEeecCCCCcccccccccEEEE-eeCCc------------------------eEEEeeccC----Ch
Q 045445           26 LTDDEQFRECEMDTYKSSGPGGQHRNKRESAVRLK-HVPTA------------------------SSVNLDAYL----PP   76 (128)
Q Consensus        26 l~~~~~~~dl~~~~~RssGpGGQ~vNkt~saV~l~-H~PtG------------------------i~v~~~~~R----Nr   76 (128)
                      |+-.+.++||+++|+|||||||||||||+|+|+|+ |+|+|                        |+|+|+++|    ||
T Consensus        13 ~~i~I~~~dl~~~~~RssGpGGQnVNKv~SaV~Lrf~i~t~~~Lp~~~k~rl~~~~~~ri~~~G~ivv~~q~~RSQ~~Nr   92 (112)
T 1j26_A           13 ASSYIPLDRLSISYCRSSGPGGQNVNKVNSKAEVRFHLASADWIEEPVRQKIALTHKNKINKAGELVLTSESSRYQFRNL   92 (112)
T ss_dssp             SCCCCCTTTSEEEEECCCCSSSSCCSSCCCEEEEEEEGGGCTTSCHHHHHHHHHHTTTTBCSSSEEEEEECCCSSHHHHH
T ss_pred             eEEecChHHeEEEEEECCCCCCCCccCCcceEEEEEeccccccCCHHHHHHHHHhhccccccCCeEEEEECCccCHHHHH
Confidence            44456789999999999999999999999999998 99998                        999999999    99


Q ss_pred             hhHhhhCC
Q 045445           77 PQLLQILP   84 (128)
Q Consensus        77 ~~A~~~L~   84 (128)
                      ++||++|.
T Consensus        93 ~~Al~rL~  100 (112)
T 1j26_A           93 AECLQKIR  100 (112)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99999986

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

Probab=99.85  E-value=3.4e-22  Score=144.80  Aligned_cols=56  Identities=27%  Similarity=0.377  Sum_probs=52.9

Q ss_pred             ccccCceeEEEEeecCCCCcccccccccEEEEe------eC-----------------Cc-eEEEeeccC----ChhhHh
Q 045445           29 DEQFRECEMDTYKSSGPGGQHRNKRESAVRLKH------VP-----------------TA-SSVNLDAYL----PPPQLL   80 (128)
Q Consensus        29 ~~~~~dl~~~~~RssGpGGQ~vNkt~saV~l~H------~P-----------------tG-i~v~~~~~R----Nr~~A~   80 (128)
                      .+.++||+++|+|||||||||||||+|+|+|+|      +|                 +| |.|+|+++|    ||+.|+
T Consensus         9 ~I~~~dl~~~~~RssGpGGQnVNKv~SaV~L~~d~~~s~lP~~~k~rl~~~~~~ri~~~G~ivv~~q~~RSQ~~Nr~~Al   88 (108)
T 2jva_A            9 HLPDAEIELTAIRAQGAGGQNVNKVSSAMHLRFDINASSLPPFYKERLLALNDSRITSDGVIVLKAQQYRTQEQNRADAL   88 (108)
T ss_dssp             EECGGGEEEEECCCTTCSSSSSCCCCCCEEEEEETTTSCCCHHHHHHHHTCSCTTBCTTCEEEEEECCSSSHHHHHHHHH
T ss_pred             ccChHHEEEEEEECCCCCCCCcCCCcceEEEEEEcccccCCHHHHHHHHHHhccccccCCcEEEEECCcCCHHHHHHHHH
Confidence            356789999999999999999999999999999      88                 88 999999999    999999


Q ss_pred             hhCC
Q 045445           81 QILP   84 (128)
Q Consensus        81 ~~L~   84 (128)
                      ++|.
T Consensus        89 ~rL~   92 (108)
T 2jva_A           89 LRLS   92 (108)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            9986

>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=99.80  E-value=1.2e-20  Score=141.87  Aligned_cols=55  Identities=27%  Similarity=0.409  Sum_probs=51.9

Q ss_pred             cccCceeEEEEeecCCCCcccccccccEEEE------eeCC------------------ceEEEeeccC----ChhhHhh
Q 045445           30 EQFRECEMDTYKSSGPGGQHRNKRESAVRLK------HVPT------------------ASSVNLDAYL----PPPQLLQ   81 (128)
Q Consensus        30 ~~~~dl~~~~~RssGpGGQ~vNkt~saV~l~------H~Pt------------------Gi~v~~~~~R----Nr~~A~~   81 (128)
                      +.++||+|+|+|||||||||||||+|+|+|+      |+|+                  +|+|+|+++|    ||+.|++
T Consensus        10 I~~~el~~~~~RssGpGGQnVNKv~SaV~L~~~~~~s~lp~~~k~rL~~~~~~rit~~G~ivv~~q~~RSQ~~Nr~~A~~   89 (140)
T 4dh9_Y           10 IPDGELEITAIRAQGAGGQHVNKTSTAIHLRFDIRASSLPEYYKERLLAASHHLISSDGVIVIKAQEYRSQELNREAALA   89 (140)
T ss_dssp             CCTTCSEEEEECCCSSSSHHHHTTCCCEEEEECCSSSSSCSHHHHHHHSCCCTTSCSSCCCCEEECCCSSHHHHHHHHHH
T ss_pred             cChHHeEEEEEECCCCCCCccccccceEEEEEecccccCCHHHHHHHHHHhccccccCCcEEEEEcCCcCHHHHHHHHHH
Confidence            5779999999999999999999999999999      6998                  5999999999    9999999


Q ss_pred             hCC
Q 045445           82 ILP   84 (128)
Q Consensus        82 ~L~   84 (128)
                      +|.
T Consensus        90 rL~   92 (140)
T 4dh9_Y           90 RLV   92 (140)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            987

>3e7l_A Transcriptional regulator (NTRC family); sigma43 activator, AAA+ ATPase, response regulator, transcriptional activator, ATP-binding; 2.25A {Aquifex aeolicus} PDB: 4fth_A

Probab=84.49  E-value=0.73  Score=28.54  Aligned_cols=22  Identities=5%  Similarity=0.072  Sum_probs=20.4

Q ss_pred             hhHHHHHHcCCChHHHHHHccC
Q 045445          106 ALLDLIFAVEGSVSEAAKFLSL  127 (128)
Q Consensus       106 ~~lD~~~~~~g~~~~aa~~l~l  127 (128)
                      .+...|..++|+.+.||+.||+
T Consensus        23 ~i~~aL~~~~gn~~~aA~~LGi   44 (63)
T 3e7l_A           23 FIEEKLREYDYDLKRTAEEIGI   44 (63)
T ss_dssp             HHHHHHHHTTTCHHHHHHHHTC
T ss_pred             HHHHHHHHhCCCHHHHHHHHCc
Confidence            6788999999999999999997

---

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	128
d1j26a_	112	d.50.4.1 (A:) Ict1 protein {Mouse (Mus musculus) [	2e-07
d1gqea_	362	e.38.1.1 (A:) Polypeptide chain release factor 2 (	9e-06
d1rq0a_	333	e.38.1.1 (A:) Peptide chain release factor 1, RF1	2e-04
d2b3tb1	344	e.38.1.1 (B:7-354) Peptide chain release factor 1,	3e-04

>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 = 43.8 bits (103), Expect = 2e-07
 Identities = 10/34 (29%), Positives = 17/34 (50%)

Query: 34 ECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASS 67
             +   +SSGPGGQ+ NK  S   ++    ++ 
Sbjct: 21 RLSISYCRSSGPGGQNVNKVNSKAEVRFHLASAD 54

>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 = 41.1 bits (96), Expect = 9e-06
 Identities = 25/55 (45%), Positives = 33/55 (60%), Gaps = 4/55 (7%)

Query: 14  STSSSSKKNYFELTDDEQF----RECEMDTYKSSGPGGQHRNKRESAVRLKHVPT 64
            TS SS   Y E+ DD        +  +D Y++SG GGQH N+ ESAVR+ H+PT
Sbjct: 211 HTSFSSAFVYPEVDDDIDIEINPADLRIDVYRASGAGGQHVNRTESAVRITHIPT 265

>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 = 37.4 bits (86), Expect = 2e-04
 Identities = 16/32 (50%), Positives = 26/32 (81%)

Query: 33  RECEMDTYKSSGPGGQHRNKRESAVRLKHVPT 64
            + +++T+++SG GGQ+ NK ESAVR+ H+PT
Sbjct: 196 EDLKIETFRASGHGGQYVNKTESAVRITHLPT 227

>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 = 36.6 bits (84), Expect = 3e-04
 Identities = 16/31 (51%), Positives = 24/31 (77%)

Query: 34  ECEMDTYKSSGPGGQHRNKRESAVRLKHVPT 64
           +  +DT++SSG GGQH N  +SA+R+ H+PT
Sbjct: 211 DLRIDTFRSSGAGGQHVNTTDSAIRITHLPT 241

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	128
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	99.97
d1j26a_	112	Ict1 protein {Mouse (Mus musculus) [TaxId: 10090]}	99.7
d1umqa_	60	Photosynthetic apparatus regulatory protein PprA (	90.26
d1ntca_	91	DNA-binding domain of NTRC {Salmonella typhimurium	80.56

>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=4.2e-35  Score=242.95  Aligned_cols=97  Identities=30%  Similarity=0.347  Sum_probs=78.1

Q ss_pred             CCcccccccccceeeccCCcc---cccCceeEEEEeecCCCCcccccccccEEEEeeCCceEEEeeccC----ChhhHhh
Q 045445            9 NDNCSSTSSSSKKNYFELTDD---EQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYL----PPPQLLQ   81 (128)
Q Consensus         9 ~d~~~~tS~a~v~v~p~l~~~---~~~~dl~~~~~RssGpGGQ~vNkt~saV~l~H~PtGi~v~~~~~R----Nr~~A~~   81 (128)
                      ...++||||++|.++|..++.   ++++||+|+|+|||||||||||||+|||||+|+||||+|+||++|    ||+.||+
T Consensus       169 ~~~r~hTs~~~V~v~p~~~~~~v~i~~~dl~i~~~RssG~GGQ~VNkt~sAVRitH~PTGi~v~~q~eRSQ~~Nk~~A~~  248 (333)
T d1rq0a_         169 SGGRIHTSTATVAVLPEIEEKDIEIRPEDLKIETFRASGHGGQYVNKTESAVRITHLPTGIVVSCQNERSQYQNKQTALR  248 (333)
T ss_dssp             CSCCCEEEEEEEEEEECCCGGGSCCCGGGEEEEEECCCC----CCSSSSEEEEEEETTTCCEEEEEESSCHHHHHHHHHH
T ss_pred             CCCceEEEEEEEEEecccccccccccccceeEEeecCCccccchhhhhhheeEEEEcCCccEEEcccccccHHHHHHHHH
Confidence            447999999999999997763   578999999999999999999999999999999999999999999    9999999


Q ss_pred             hCC------------------cccccccCCCCCCCCCCCCCh
Q 045445           82 ILP------------------PKFTIRCSEVGPQIRPNNPKF  105 (128)
Q Consensus        82 ~L~------------------~~~q~~~~~r~~kIrtyn~~f  105 (128)
                      +|+                  ++.|+++++||+||||||+.+
T Consensus       249 ~L~~kl~~~~~~~~~~~~~~~r~~~~~~~~r~~~iRtY~~p~  290 (333)
T d1rq0a_         249 ILRARLYQLQKEQKEREISQKRKSQIGTGERSEKIRTYNFPQ  290 (333)
T ss_dssp             HHHHHHHHHHHHHHHTTTCC----------CCCEEEEEETTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhccccccccCCCceeeeCCC
Confidence            986                  789999999999999999765

>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=4.9e-35  Score=242.95  Aligned_cols=98  Identities=27%  Similarity=0.324  Sum_probs=83.6

Q ss_pred             cCCcccccccccceeeccCCcc----cccCceeEEEEeecCCCCcccccccccEEEEeeCCceEEEeeccC----ChhhH
Q 045445            8 YNDNCSSTSSSSKKNYFELTDD----EQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYL----PPPQL   79 (128)
Q Consensus         8 ~~d~~~~tS~a~v~v~p~l~~~----~~~~dl~~~~~RssGpGGQ~vNkt~saV~l~H~PtGi~v~~~~~R----Nr~~A   79 (128)
                      ....++||||++|.++|.+.+.    ++++|++|+|+|||||||||||||+|||||+|+||||+|.||++|    ||+.|
T Consensus       181 ~~~~r~hts~~~v~v~p~~~~~~~~~i~~~dl~i~~~rssg~GGQ~vnkt~sAVRi~H~ptGi~v~~q~eRSq~~Nk~~A  260 (344)
T d2b3tb1         181 ESQGRIHTSACTVAVMPELPDAELPDVNPADLRIDTFRSSGAGGQHVNTTDSAIRITHLPTGIVVECQDERSQHKNKAKA  260 (344)
T ss_dssp             CSSCCCEEEEEEEECCBCCCTTTCCCCCSSSEEEEECCSSCCCTTTCCCSSEEEEEEETTTCCEEEEEESSCHHHHHHHH
T ss_pred             ccccccccceeeEeeecccccccccccCcccceEEEecCCCccccchhhhhceeEEEEcCCceEEEccCCCcchHHHHHH
Confidence            3446899999999999998653    577999999999999999999999999999999999999999999    99999


Q ss_pred             hhhCC------------------cccccccCCCCCCCCCCCCCh
Q 045445           80 LQILP------------------PKFTIRCSEVGPQIRPNNPKF  105 (128)
Q Consensus        80 ~~~L~------------------~~~q~~~~~r~~kIrtyn~~f  105 (128)
                      |++|+                  +++|+++++||+||||||+.+
T Consensus       261 ~~~L~~kl~~~~~~~~~~~~~~~r~~~~~~~~r~~~iRtY~~p~  304 (344)
T d2b3tb1         261 LSVLGARIHAAEMAKRQQAEASTRRNLLGSGDRSDRNRTYNFPQ  304 (344)
T ss_dssp             HHHHHHHHTTTTTTSCC------CCC-------CCEEEEEETTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhcccccccccCceEeeecCC
Confidence            99886                  789999999999999999766

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

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

Probab=99.97  E-value=8.8e-34  Score=236.66  Aligned_cols=97  Identities=31%  Similarity=0.328  Sum_probs=84.9

Q ss_pred             CCcccccccccceeeccCCcc----cccCceeEEEEeecCCCCcccccccccEEEEeeCCceEEEeeccC----ChhhHh
Q 045445            9 NDNCSSTSSSSKKNYFELTDD----EQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYL----PPPQLL   80 (128)
Q Consensus         9 ~d~~~~tS~a~v~v~p~l~~~----~~~~dl~~~~~RssGpGGQ~vNkt~saV~l~H~PtGi~v~~~~~R----Nr~~A~   80 (128)
                      ...++|||||+|.|+|.++++    ++++||+|+|+|||||||||||||+|||||+|+||||+|+||++|    ||..||
T Consensus       206 s~gr~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_         206 SGGRRHTSFSSAFVYPEVDDDIDIEINPADLRIDVYRASGAGGQHVNRTESAVRITHIPTGIVTQCQNDRSQHKNKDQAM  285 (362)
T ss_dssp             SSCCEEEEEEEEEEEECCBTTBCCCCCGGGEEEEEECCCCSSCCSTTSSCCEEEEEETTTCCEEEECSSSCHHHHHHHHH
T ss_pred             CCceEEEEEEEEEEeecCCCccceecChHHeEEEEeecCCCCccchhhhhceeEEEecCchhHHHhhhcchhhHHHHHHH
Confidence            347999999999999998654    578999999999999999999999999999999999999999999    999999


Q ss_pred             hhCC-----------------cccccccCCCCCCCCCCCCCh
Q 045445           81 QILP-----------------PKFTIRCSEVGPQIRPNNPKF  105 (128)
Q Consensus        81 ~~L~-----------------~~~q~~~~~r~~kIrtyn~~f  105 (128)
                      ++|+                 .+.+....+||+||||||+..
T Consensus       286 ~~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~g~~iRtY~~~~  327 (362)
T d1gqea_         286 KQMKAKLYEVEMQKKNAEKQAMEDNKSDIGWGSQIRSYVLDD  327 (362)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTCCSTTCCCCCSCSEEEEEEGGG
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhhcCcCcCCccCccCCC
Confidence            9887                 222333457999999999654

>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=99.70  E-value=5.4e-18  Score=121.55  Aligned_cols=56  Identities=21%  Similarity=0.256  Sum_probs=49.5

Q ss_pred             ccccCceeEEEEeecCCCCcccccccccEEEEee-------CC------------------ceEEEeeccC----ChhhH
Q 045445           29 DEQFRECEMDTYKSSGPGGQHRNKRESAVRLKHV-------PT------------------ASSVNLDAYL----PPPQL   79 (128)
Q Consensus        29 ~~~~~dl~~~~~RssGpGGQ~vNkt~saV~l~H~-------Pt------------------Gi~v~~~~~R----Nr~~A   79 (128)
                      .|..++++|+|+|||||||||||||+|+|.|++.       |.                  .|.|+|+++|    |+++|
T Consensus        16 ~Ip~~~i~~~f~RSsGPGGQ~VNKv~TkV~Lr~~v~~s~~l~~~~~~~l~~~~~~~i~~~g~l~I~s~~~RsQ~~Nr~~a   95 (112)
T d1j26a_          16 YIPLDRLSISYCRSSGPGGQNVNKVNSKAEVRFHLASADWIEEPVRQKIALTHKNKINKAGELVLTSESSRYQFRNLAEC   95 (112)
T ss_dssp             CCCTTTSEEEEECCCCSSSSCCSSCCCEEEEEEEGGGCTTSCHHHHHHHHHHTTTTBCSSSEEEEEECCCSSHHHHHHHH
T ss_pred             ccCHHHeEEEEEEcCCCCCCccceeccEEEEEEeccccccCCHHHHHHHHHHhhhcccCCCeEEEEEcccCCHHHHHHHH
Confidence            4667899999999999999999999999999853       21                  3999999999    99999


Q ss_pred             hhhCC
Q 045445           80 LQILP   84 (128)
Q Consensus        80 ~~~L~   84 (128)
                      +++|.
T Consensus        96 ~~kL~  100 (112)
T d1j26a_          96 LQKIR  100 (112)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            99986

>d1umqa_ a.4.1.12 (A:) Photosynthetic apparatus regulatory protein PprA (RegA), DNA-binding domain {Rhodobacter sphaeroides [TaxId: 1063]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: FIS-like
domain: Photosynthetic apparatus regulatory protein PprA (RegA), DNA-binding domain
species: Rhodobacter sphaeroides [TaxId: 1063]

Probab=90.26  E-value=0.095  Score=31.65  Aligned_cols=23  Identities=22%  Similarity=0.258  Sum_probs=21.3

Q ss_pred             hhHHHHHHcCCChHHHHHHccCC
Q 045445          106 ALLDLIFAVEGSVSEAAKFLSLL  128 (128)
Q Consensus       106 ~~lD~~~~~~g~~~~aa~~l~l~  128 (128)
                      .++..|..++|+++.||+.||+.
T Consensus        24 ~I~~aL~~~~gn~~~aA~~LGIs   46 (60)
T d1umqa_          24 HIQRIYEMCDRNVSETARRLNMH   46 (60)
T ss_dssp             HHHHHHHHTTSCHHHHHHHHTSC
T ss_pred             HHHHHHHHhcCcHHHHHHHHCCC
Confidence            78999999999999999999973

>d1ntca_ a.4.1.12 (A:) DNA-binding domain of NTRC {Salmonella typhimurium [TaxId: 90371]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: FIS-like
domain: DNA-binding domain of NTRC
species: Salmonella typhimurium [TaxId: 90371]

Probab=80.56  E-value=0.46  Score=29.97  Aligned_cols=22  Identities=27%  Similarity=0.342  Sum_probs=20.4

Q ss_pred             hhHHHHHHcCCChHHHHHHccC
Q 045445          106 ALLDLIFAVEGSVSEAAKFLSL  127 (128)
Q Consensus       106 ~~lD~~~~~~g~~~~aa~~l~l  127 (128)
                      .+-..|..++|+.+.||+.||+
T Consensus        55 lI~~aL~~~~Gn~~~AA~~LGI   76 (91)
T d1ntca_          55 LLTTALRHTQGHKQEAARLLGW   76 (91)
T ss_dssp             HHHHHHHHTTTCTTHHHHHTTC
T ss_pred             HHHHHHHHhCCcHHHHHHHHCC
Confidence            6788999999999999999997