Query psy14432
Match_columns 189
No_of_seqs 221 out of 1424
Neff 4.6
Searched_HMMs 46136
Date Fri Aug 16 19:43:37 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy14432.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/14432hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3429|consensus 100.0 1.2E-45 2.5E-50 302.4 10.0 141 22-189 4-145 (172)
2 PRK09256 hypothetical protein; 100.0 1.7E-36 3.7E-41 242.8 10.8 100 76-176 4-103 (138)
3 COG0216 PrfA Protein chain rel 100.0 4.1E-35 9E-40 262.7 9.3 132 10-173 151-286 (363)
4 PRK07342 peptide chain release 100.0 1.9E-29 4.2E-34 226.7 9.7 121 21-173 137-262 (339)
5 PRK05589 peptide chain release 100.0 3.8E-29 8.3E-34 223.8 10.1 120 21-172 134-258 (325)
6 TIGR00019 prfA peptide chain r 100.0 4.6E-29 1E-33 225.8 10.3 119 23-173 163-284 (360)
7 PRK08787 peptide chain release 100.0 3.9E-29 8.3E-34 222.7 9.3 120 22-173 115-239 (313)
8 PRK06746 peptide chain release 100.0 5.1E-29 1.1E-33 223.0 9.4 121 21-173 135-260 (326)
9 PRK00578 prfB peptide chain re 100.0 6.9E-29 1.5E-33 225.1 9.8 119 23-173 176-298 (367)
10 TIGR00020 prfB peptide chain r 100.0 1E-28 2.2E-33 223.8 9.6 121 21-173 173-298 (364)
11 KOG2726|consensus 100.0 1.7E-28 3.6E-33 222.9 10.3 120 22-173 187-311 (386)
12 PRK00591 prfA peptide chain re 100.0 2.9E-28 6.2E-33 220.6 9.6 119 23-173 163-284 (359)
13 PF00472 RF-1: RF-1 domain; I 99.9 6E-27 1.3E-31 181.0 7.9 70 78-172 5-74 (113)
14 TIGR03072 release_prfH putativ 99.9 1.7E-26 3.7E-31 195.0 10.0 116 22-173 50-169 (200)
15 PRK08179 prfH peptide chain re 99.9 1.1E-25 2.3E-30 190.1 9.6 116 22-173 51-170 (200)
16 COG1186 PrfB Protein chain rel 99.9 2.2E-26 4.8E-31 198.5 3.5 146 26-179 54-204 (239)
17 PF10213 MRP-S28: Mitochondria 98.2 2.1E-05 4.5E-10 62.6 10.3 84 85-173 9-93 (127)
18 KOG3933|consensus 97.0 0.0065 1.4E-07 54.6 10.4 87 84-173 148-235 (296)
19 COG1186 PrfB Protein chain rel 92.6 0.069 1.5E-06 47.0 1.9 32 142-173 142-173 (239)
20 cd02394 vigilin_like_KH K homo 65.6 6.8 0.00015 26.1 2.6 47 95-164 15-61 (62)
21 smart00322 KH K homology RNA-b 45.6 25 0.00055 22.3 2.7 50 96-168 19-68 (69)
22 cd00105 KH-I K homology RNA-bi 44.3 27 0.00058 22.8 2.7 21 95-115 15-37 (64)
23 PF14048 MBD_C: C-terminal dom 43.8 9.4 0.0002 29.1 0.5 26 143-168 71-96 (96)
24 cd02393 PNPase_KH Polynucleoti 32.5 28 0.00061 23.7 1.4 15 94-108 16-30 (61)
25 COG0193 Pth Peptidyl-tRNA hydr 29.3 46 0.001 28.5 2.5 23 77-101 92-114 (190)
26 PRK09374 rplB 50S ribosomal pr 28.2 75 0.0016 28.6 3.7 36 80-118 144-179 (276)
27 PF15128 T_cell_tran_alt: T-ce 26.7 32 0.00069 26.3 0.9 17 91-108 57-73 (92)
28 TIGR01171 rplB_bact ribosomal 25.4 90 0.002 28.1 3.7 37 79-118 141-177 (273)
29 cd02395 SF1_like-KH Splicing f 25.3 1.6E+02 0.0036 23.0 4.8 31 137-173 64-94 (120)
30 smart00878 Biotin_carb_C Bioti 24.2 1.1E+02 0.0024 23.4 3.5 19 156-174 60-78 (107)
31 PF07687 M20_dimer: Peptidase 23.6 94 0.002 22.0 2.9 24 94-117 64-87 (111)
32 cd02406 CRS2 Chloroplast RNA s 21.6 72 0.0016 27.1 2.2 38 76-115 90-135 (191)
33 cd00552 RaiA RaiA ("ribosome-a 21.2 3E+02 0.0066 19.3 7.8 57 85-171 34-90 (93)
34 PRK10470 ribosome hibernation 21.0 3.3E+02 0.0071 19.6 6.1 41 107-171 48-88 (95)
35 TIGR01891 amidohydrolases amid 20.0 1.5E+02 0.0032 26.2 4.0 73 98-170 227-301 (363)
No 1
>KOG3429|consensus
Probab=100.00 E-value=1.2e-45 Score=302.40 Aligned_cols=141 Identities=52% Similarity=0.838 Sum_probs=132.5
Q ss_pred eeeeeeccccCCCCCCCccCCCCCCCCCCCCCcccccccccCCCCcceeEEeecccCCCCcCCCCeEEEEeccCCCCccC
Q psy14432 22 YKSSISLDKLYPNSSMLLKTPTPDQVKAPDGLKFNGVIPVKAPDGLKFNGVIPVVIPRFSYITEELDITYSRSSGPGGQH 101 (189)
Q Consensus 22 ~~s~~sld~lyp~s~~~~~~~~~~~~~~~~~~~~~g~i~~~~~~~~~~~~v~p~~~~~~~i~~~~l~i~fsRSSGPGGQn 101 (189)
|+++++|+++|| ..+..++++.+ +.. +.+|.|.||+ +.++++|+|||||||||
T Consensus 4 ~k~~~~l~~n~~-~~~~~~t~~~~--~sg-~~~~~g~ipl-----------------------d~~~i~y~RSSGPGGQN 56 (172)
T KOG3429|consen 4 IKSSRSLDKNYP-KCLLTKTETRQ--PSG-AIHFKGKIPL-----------------------DQLEISYSRSSGPGGQN 56 (172)
T ss_pred cchhHhHHhhhh-hhhcccccccC--Ccc-ccccCCCCch-----------------------hheEEEEeecCCCCCcc
Confidence 899999999999 44446666655 566 8899999999 99999999999999999
Q ss_pred CCcccceEEEEEecCCCCccCHHHHHHHHHHhcccccCCceEEEEEcCcccHHHHHHHHHHHHHHHHHHhhCCCC-CCCh
Q psy14432 102 VNSVSTKVDIRFKVNAANWLNEDVKKQLIELNKNRLNKDGYLIIKSDRTRSQQLNLADAMTTLRNMIWKAAKPAP-QISE 180 (189)
Q Consensus 102 VNKv~SkV~Lrfhl~s~~wLp~~~r~~L~~~~~~ri~k~G~LvI~s~~~RSQ~~Nr~~Al~kL~~~I~~a~~~pk-~~S~ 180 (189)
|||+||||++||++..+.|||+++|+.|+..+.+||+++|+|+|.||++|||+.|.+|||+||+++|++++.+|+ +|++
T Consensus 57 VNKvNTKv~vrf~vs~a~Wipe~~R~~~~~~~~~rink~gelvI~Sd~TRsq~~NiaDcleKlr~~I~~~~~~~~~~~te 136 (172)
T KOG3429|consen 57 VNKVNTKVEVRFKVSNAEWIPEFLRNKLLTTEKNRINKDGELVIYSDKTRSQHKNIADCLEKLRDIIRAAEQTPPVDPTE 136 (172)
T ss_pred cccccceEEEEEecchhhhccHHHHHHHHHHHHHhhccCccEEEecchhHHhhccHHHHHHHHHHHHHHHhcCCCCCCCH
Confidence 999999999999999999999999999999999999999999999999999999999999999999999998888 9999
Q ss_pred hhHHHHhhC
Q psy14432 181 DTIDRIRIR 189 (189)
Q Consensus 181 Et~~~~r~~ 189 (189)
||.++|++|
T Consensus 137 E~~kk~r~~ 145 (172)
T KOG3429|consen 137 ETIKKIRIR 145 (172)
T ss_pred HHHHHHHHH
Confidence 999999875
No 2
>PRK09256 hypothetical protein; Provisional
Probab=100.00 E-value=1.7e-36 Score=242.77 Aligned_cols=100 Identities=41% Similarity=0.624 Sum_probs=95.5
Q ss_pred ccCCCCcCCCCeEEEEeccCCCCccCCCcccceEEEEEecCCCCccCHHHHHHHHHHhcccccCCceEEEEEcCcccHHH
Q psy14432 76 VIPRFSYITEELDITYSRSSGPGGQHVNSVSTKVDIRFKVNAANWLNEDVKKQLIELNKNRLNKDGYLIIKSDRTRSQQL 155 (189)
Q Consensus 76 ~~~~~~i~~~~l~i~fsRSSGPGGQnVNKv~SkV~Lrfhl~s~~wLp~~~r~~L~~~~~~ri~k~G~LvI~s~~~RSQ~~ 155 (189)
+.+++.|++++|+++|+|||||||||||||+|||+|+|++..+ |||++++++|.+++.++++++|.|+|+||++|||++
T Consensus 4 ~~~~~~i~~~~l~~~~~RSSGPGGQ~VNKt~SkV~l~~~~~~~-~lp~~~~~~l~~~~~~r~~~~g~l~i~~~~~RSQ~~ 82 (138)
T PRK09256 4 ITRRLVIPENELEWRFIRASGPGGQNVNKVSTAVELRFDIAAS-SLPEFYKERLLALAGHRITKDGVIVIKAQEFRSQER 82 (138)
T ss_pred cCccCccCHHHeEEEEEEcCCCCcccccccceeeEEEechhhc-cCCHHHHHHHHHHhcCcccCCCcEEEEECCcCCHHH
Confidence 5567889999999999999999999999999999999999988 999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhCCCC
Q psy14432 156 NLADAMTTLRNMIWKAAKPAP 176 (189)
Q Consensus 156 Nr~~Al~kL~~~I~~a~~~pk 176 (189)
|+++|+++|+++|.++..+|+
T Consensus 83 Nr~~al~kL~~~i~~~~~~p~ 103 (138)
T PRK09256 83 NREDALERLVALIREALKPPK 103 (138)
T ss_pred HHHHHHHHHHHHHHHHhhccc
Confidence 999999999999999977655
No 3
>COG0216 PrfA Protein chain release factor A [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.1e-35 Score=262.67 Aligned_cols=132 Identities=26% Similarity=0.358 Sum_probs=120.6
Q ss_pred hhhhcccceeeeeeeeeeccccCCCCCCCccCCCCCCC--CCCCCCcccccccccCCCCcceeEEeecccC--CCCcCCC
Q psy14432 10 LISNQRNVVKRFYKSSISLDKLYPNSSMLLKTPTPDQV--KAPDGLKFNGVIPVKAPDGLKFNGVIPVVIP--RFSYITE 85 (189)
Q Consensus 10 ~~~~~~~~~~~~~~s~~sld~lyp~s~~~~~~~~~~~~--~~~~~~~~~g~i~~~~~~~~~~~~v~p~~~~--~~~i~~~ 85 (189)
+++...+..|-.-+.+.++.- .+.|.+|+.++++|| +.| .+|++||||| |+|+|+|||++++ .+.|+++
T Consensus 151 i~s~se~~~GG~kEii~~I~G--~gvys~LKfEsGvHRVQRVP-~TEsqGRIHT----StaTVaVlPE~ee~~ei~I~~~ 223 (363)
T COG0216 151 ILSASESELGGYKEIIASISG--KGVYSRLKFESGVHRVQRVP-ATESQGRIHT----SAATVAVLPEVEEVEEIEINPK 223 (363)
T ss_pred EeecCcccCCCceEEEEEEec--cchhhhhhhccCccceeccc-cccCCCceee----cceeEEeccCCCcccccccChH
Confidence 566677777775567777777 788999999999999 889 9999999999 4699999999975 5899999
Q ss_pred CeEEEEeccCCCCccCCCcccceEEEEEecCCCCccCHHHHHHHHHHhcccccCCceEEEEEcCcccHHHHHHHHHHHHH
Q psy14432 86 ELDITYSRSSGPGGQHVNSVSTKVDIRFKVNAANWLNEDVKKQLIELNKNRLNKDGYLIIKSDRTRSQQLNLADAMTTLR 165 (189)
Q Consensus 86 ~l~i~fsRSSGPGGQnVNKv~SkV~Lrfhl~s~~wLp~~~r~~L~~~~~~ri~k~G~LvI~s~~~RSQ~~Nr~~Al~kL~ 165 (189)
||+|+++||||+||||||+|+|+|+|+ |+|++ |+|+||++|||++|++.||..|+
T Consensus 224 DlrIDt~RsSGaGGQhVNtTdSAVRiT-HlPTG------------------------IvV~cQderSQ~kNk~kAmkvL~ 278 (363)
T COG0216 224 DLRIDTFRSSGAGGQHVNTTDSAVRIT-HLPTG------------------------IVVECQDERSQHKNKAKAMKVLR 278 (363)
T ss_pred HceeeeeecCCCCCCCcCccchhheee-ecCCc------------------------eEEEecchhhhhhhHHHHHHHHH
Confidence 999999999999999999999999999 99999 99999999999999999999999
Q ss_pred HHHHHhhC
Q psy14432 166 NMIWKAAK 173 (189)
Q Consensus 166 ~~I~~a~~ 173 (189)
++|+++..
T Consensus 279 ARl~~~~~ 286 (363)
T COG0216 279 ARLYDAER 286 (363)
T ss_pred HHHHHHHH
Confidence 99999854
No 4
>PRK07342 peptide chain release factor 2; Provisional
Probab=99.96 E-value=1.9e-29 Score=226.70 Aligned_cols=121 Identities=26% Similarity=0.307 Sum_probs=109.3
Q ss_pred eeee-eeeccccCCCCCCCccCCCCCCC--CCCCCCcccccccccCCCCcceeEEeecccC--CCCcCCCCeEEEEeccC
Q psy14432 21 FYKS-SISLDKLYPNSSMLLKTPTPDQV--KAPDGLKFNGVIPVKAPDGLKFNGVIPVVIP--RFSYITEELDITYSRSS 95 (189)
Q Consensus 21 ~~~s-~~sld~lyp~s~~~~~~~~~~~~--~~~~~~~~~g~i~~~~~~~~~~~~v~p~~~~--~~~i~~~~l~i~fsRSS 95 (189)
.|+| .+.++- ++.++.|+.+.++|+ +.| ..+.+|++|| ++++|.|+|.+++ .+.|++++|+++|+|||
T Consensus 137 g~ksa~l~i~G--~~ay~~lk~E~GvHrv~rvs-p~~~~~rrhT----s~a~V~VlP~~~~~~~~~i~~~dl~~~~~Rss 209 (339)
T PRK07342 137 GIKSATILVKG--HNAYGWLKTESGVHRLVRIS-PYDSNARRHT----SFASIWVYPVIDDNIEVDVNESDVRIDTYRSS 209 (339)
T ss_pred ceEEEEEEEec--cCHHHHHhhccceeEEEecC-CCCCCCCeEe----EEEEEEEEcCCCcccccccCcccEEEEEEECC
Confidence 3454 567776 778888999999998 677 7899999999 4699999999875 58899999999999999
Q ss_pred CCCccCCCcccceEEEEEecCCCCccCHHHHHHHHHHhcccccCCceEEEEEcCcccHHHHHHHHHHHHHHHHHHhhC
Q psy14432 96 GPGGQHVNSVSTKVDIRFKVNAANWLNEDVKKQLIELNKNRLNKDGYLIIKSDRTRSQQLNLADAMTTLRNMIWKAAK 173 (189)
Q Consensus 96 GPGGQnVNKv~SkV~Lrfhl~s~~wLp~~~r~~L~~~~~~ri~k~G~LvI~s~~~RSQ~~Nr~~Al~kL~~~I~~a~~ 173 (189)
||||||||||+|+|+|+ |+|++ |+|+|+++|||++|++.||++|+++|++...
T Consensus 210 G~GGQ~VNkt~saVrl~-H~ptg------------------------i~v~~~~eRSQ~~Nk~~A~~~L~~~L~~~~~ 262 (339)
T PRK07342 210 GAGGQHVNTTDSAVRIT-HIPTG------------------------IVVQCQQERSQHKNRAKAWSMLRARLYEEEL 262 (339)
T ss_pred CCCCCCccceeeeEEEE-EcCCc------------------------EEEEECCcccHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999 99998 9999999999999999999999999998754
No 5
>PRK05589 peptide chain release factor 2; Provisional
Probab=99.96 E-value=3.8e-29 Score=223.78 Aligned_cols=120 Identities=23% Similarity=0.318 Sum_probs=108.7
Q ss_pred eeee-eeeccccCCCCCCCccCCCCCCC--CCCCCCcccccccccCCCCcceeEEeecccC--CCCcCCCCeEEEEeccC
Q psy14432 21 FYKS-SISLDKLYPNSSMLLKTPTPDQV--KAPDGLKFNGVIPVKAPDGLKFNGVIPVVIP--RFSYITEELDITYSRSS 95 (189)
Q Consensus 21 ~~~s-~~sld~lyp~s~~~~~~~~~~~~--~~~~~~~~~g~i~~~~~~~~~~~~v~p~~~~--~~~i~~~~l~i~fsRSS 95 (189)
.|+| .+.++- ++.++.|+.+.++|+ +.| ..+.+|++|| ++++|.|+|..++ ++.|+++||+|+|+|||
T Consensus 134 g~ks~~~~i~G--~~ay~~lk~E~GvHrv~r~s-~~~~~~rr~t----s~a~V~VlP~~~~~~~~~i~~~dl~~~~~rss 206 (325)
T PRK05589 134 GIKSVTLKITG--EFAYGYLKAEKGIHRLVRIS-PFNANGKRQT----SFASVEVLPELTDDQDIEIRSEDLKIDTYRAG 206 (325)
T ss_pred ceEEEEEEEec--cCHHHHHhhccceEEEEEcC-CCCCCCCeEe----eeEEEEEecCcCccccccCCchheEEEEeeCC
Confidence 4554 567776 778888999999998 677 7899999999 4699999999865 68999999999999999
Q ss_pred CCCccCCCcccceEEEEEecCCCCccCHHHHHHHHHHhcccccCCceEEEEEcCcccHHHHHHHHHHHHHHHHHHhh
Q psy14432 96 GPGGQHVNSVSTKVDIRFKVNAANWLNEDVKKQLIELNKNRLNKDGYLIIKSDRTRSQQLNLADAMTTLRNMIWKAA 172 (189)
Q Consensus 96 GPGGQnVNKv~SkV~Lrfhl~s~~wLp~~~r~~L~~~~~~ri~k~G~LvI~s~~~RSQ~~Nr~~Al~kL~~~I~~a~ 172 (189)
||||||||||+|+|+|+ |+|++ |+|+|+++|||++|++.|+++|+++|++..
T Consensus 207 G~GGQ~VNkt~saVrl~-H~ptg------------------------i~v~~q~eRSQ~~Nk~~A~~~L~~kL~~~~ 258 (325)
T PRK05589 207 GAGGQHVNKTESAVRIT-HIPTG------------------------IVVQCQNERSQHSNKETAMKMLKSKLVELK 258 (325)
T ss_pred CCCCCcccceeeEEEEE-ECCCC------------------------EEEEECCccCHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999 99998 999999999999999999999999999864
No 6
>TIGR00019 prfA peptide chain release factor 1. 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.
Probab=99.96 E-value=4.6e-29 Score=225.79 Aligned_cols=119 Identities=25% Similarity=0.336 Sum_probs=107.5
Q ss_pred eeeeeccccCCCCCCCccCCCCCCC--CCCCCCcccccccccCCCCcceeEEeecccC-CCCcCCCCeEEEEeccCCCCc
Q psy14432 23 KSSISLDKLYPNSSMLLKTPTPDQV--KAPDGLKFNGVIPVKAPDGLKFNGVIPVVIP-RFSYITEELDITYSRSSGPGG 99 (189)
Q Consensus 23 ~s~~sld~lyp~s~~~~~~~~~~~~--~~~~~~~~~g~i~~~~~~~~~~~~v~p~~~~-~~~i~~~~l~i~fsRSSGPGG 99 (189)
...+.++- ++.++.|+.+.++|+ +.| ..+++||+|| ++++|.|+|.+++ .+.|+++||+|+|+|||||||
T Consensus 163 sa~l~i~G--~~ay~~lk~E~GvHrv~Rvp-~~~s~~R~hT----sfa~V~v~P~~~~~~~~i~~~dl~~~~~RssG~GG 235 (360)
T TIGR00019 163 EVIAEIKG--DGVYSRLKFESGVHRVQRVP-VTESQGRIHT----SAATVAVMPELEEVEVDINPADLRIDTFRSSGAGG 235 (360)
T ss_pred EEEEEEec--ccHHHHHhhcCeeEEEECCC-CCCCCCCeec----ceeEEEEEcCCCccccccCcccEEEEEEECCCCCC
Confidence 34556666 566888899999998 788 8999999999 4699999999864 688999999999999999999
Q ss_pred cCCCcccceEEEEEecCCCCccCHHHHHHHHHHhcccccCCceEEEEEcCcccHHHHHHHHHHHHHHHHHHhhC
Q psy14432 100 QHVNSVSTKVDIRFKVNAANWLNEDVKKQLIELNKNRLNKDGYLIIKSDRTRSQQLNLADAMTTLRNMIWKAAK 173 (189)
Q Consensus 100 QnVNKv~SkV~Lrfhl~s~~wLp~~~r~~L~~~~~~ri~k~G~LvI~s~~~RSQ~~Nr~~Al~kL~~~I~~a~~ 173 (189)
||||||+|+|+|+ |+|++ |+|.|+++|||++|++.||++|+++|++...
T Consensus 236 Q~VNkt~SaVrl~-h~ptg------------------------i~V~~~~eRSQ~~Nk~~A~~~L~~~L~~~~~ 284 (360)
T TIGR00019 236 QHVNTTDSAVRIT-HLPTG------------------------IVVECQDERSQHKNKDKAMKVLRARLYEAEQ 284 (360)
T ss_pred CCcCceeeeEEEE-ECCCc------------------------EEEEECCccCHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999 99998 9999999999999999999999999998763
No 7
>PRK08787 peptide chain release factor 2; Provisional
Probab=99.96 E-value=3.9e-29 Score=222.69 Aligned_cols=120 Identities=23% Similarity=0.263 Sum_probs=107.8
Q ss_pred eee-eeeccccCCCCCCCccCCCCCCC--CCCCCCcccccccccCCCCcceeEEeecccC--CCCcCCCCeEEEEeccCC
Q psy14432 22 YKS-SISLDKLYPNSSMLLKTPTPDQV--KAPDGLKFNGVIPVKAPDGLKFNGVIPVVIP--RFSYITEELDITYSRSSG 96 (189)
Q Consensus 22 ~~s-~~sld~lyp~s~~~~~~~~~~~~--~~~~~~~~~g~i~~~~~~~~~~~~v~p~~~~--~~~i~~~~l~i~fsRSSG 96 (189)
|+| .+.++- ++.|+.|+.+.++|+ +.| ....+|++|| ++++|.|+|.+++ ++.|+++||+|+|+||||
T Consensus 115 iksa~l~I~G--~~ayg~lk~E~GvHRv~R~s-p~~s~~rrhT----sfasV~V~P~~~~~~~i~i~~~dl~~~~~RssG 187 (313)
T PRK08787 115 IKSATVRIEG--EYAYGWLKTEIGVHRLVRKS-PFDSDNRRHT----SFTSVFVSPEVDDNIEIDINPADLRTDVYRSSG 187 (313)
T ss_pred eeEEEEEEec--ccHHHHHhhccCeeEEEecC-CCCCCCCEEe----eeEEEEEecCcCcccccccChhHeEEEEEECCC
Confidence 444 566766 667888999999998 666 7889999999 4699999999865 688999999999999999
Q ss_pred CCccCCCcccceEEEEEecCCCCccCHHHHHHHHHHhcccccCCceEEEEEcCcccHHHHHHHHHHHHHHHHHHhhC
Q psy14432 97 PGGQHVNSVSTKVDIRFKVNAANWLNEDVKKQLIELNKNRLNKDGYLIIKSDRTRSQQLNLADAMTTLRNMIWKAAK 173 (189)
Q Consensus 97 PGGQnVNKv~SkV~Lrfhl~s~~wLp~~~r~~L~~~~~~ri~k~G~LvI~s~~~RSQ~~Nr~~Al~kL~~~I~~a~~ 173 (189)
|||||||||+|+|+|+ |+|++ |+|+|+++|||++|++.|+++|+++|++...
T Consensus 188 ~GGQ~VNkt~saVri~-H~Ptg------------------------i~v~~q~eRSQ~~Nk~~A~~~L~~~L~~~~~ 239 (313)
T PRK08787 188 AGGQHVNKTESAVRIT-HIPTN------------------------TVVACQTGRSQHQNRDNAMKMLAAKLYELEV 239 (313)
T ss_pred CCCCCcCCEeeEEEEE-ECCCc------------------------EEEEECCcccHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999 99998 9999999999999999999999999998643
No 8
>PRK06746 peptide chain release factor 2; Provisional
Probab=99.96 E-value=5.1e-29 Score=223.02 Aligned_cols=121 Identities=25% Similarity=0.295 Sum_probs=109.0
Q ss_pred eeee-eeeccccCCCCCCCccCCCCCCC--CCCCCCcccccccccCCCCcceeEEeecccC--CCCcCCCCeEEEEeccC
Q psy14432 21 FYKS-SISLDKLYPNSSMLLKTPTPDQV--KAPDGLKFNGVIPVKAPDGLKFNGVIPVVIP--RFSYITEELDITYSRSS 95 (189)
Q Consensus 21 ~~~s-~~sld~lyp~s~~~~~~~~~~~~--~~~~~~~~~g~i~~~~~~~~~~~~v~p~~~~--~~~i~~~~l~i~fsRSS 95 (189)
.|+| .+.++- ++.|+.|+.+.++|+ +.| ..+.+|++|| ++++|.|+|.+++ ++.|+++||+++|+|||
T Consensus 135 g~ksa~l~i~G--~~ay~~lk~E~GvHrv~Rvs-p~~s~~rrhT----sfa~V~v~P~~~~~~~i~i~~~dl~~~~~rss 207 (326)
T PRK06746 135 GIKSVTLLIKG--HNAYGYLKAEKGVHRLVRIS-PFDSSGRRHT----SFVSCEVVPEFNDEVEIEVRTEDLKIDTYRAS 207 (326)
T ss_pred ceEEEEEEEec--cCHHHHHhhccceEEEEecC-CCCCCCCeEe----eEEEEEEecCcCCccccccChHHeEEEEEeCC
Confidence 4555 567776 778888999999998 777 8899999999 4699999999853 68889999999999999
Q ss_pred CCCccCCCcccceEEEEEecCCCCccCHHHHHHHHHHhcccccCCceEEEEEcCcccHHHHHHHHHHHHHHHHHHhhC
Q psy14432 96 GPGGQHVNSVSTKVDIRFKVNAANWLNEDVKKQLIELNKNRLNKDGYLIIKSDRTRSQQLNLADAMTTLRNMIWKAAK 173 (189)
Q Consensus 96 GPGGQnVNKv~SkV~Lrfhl~s~~wLp~~~r~~L~~~~~~ri~k~G~LvI~s~~~RSQ~~Nr~~Al~kL~~~I~~a~~ 173 (189)
||||||||||+|+|+|+ |+|++ |+|+|+++|||++|++.|+++|+++|++...
T Consensus 208 G~GGQ~vNkt~saVrl~-h~ptg------------------------i~v~~q~~RSQ~~Nk~~A~~~L~akL~~~~~ 260 (326)
T PRK06746 208 GAGGQHVNTTDSAVRIT-HTPTN------------------------TVVTCQSERSQIKNREHAMKMLKAKLYQKKL 260 (326)
T ss_pred CCCCCCccceeeEEEEE-EeCCe------------------------EEEEECCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999 99998 9999999999999999999999999998753
No 9
>PRK00578 prfB peptide chain release factor 2; Validated
Probab=99.95 E-value=6.9e-29 Score=225.14 Aligned_cols=119 Identities=25% Similarity=0.346 Sum_probs=108.4
Q ss_pred eeeeeccccCCCCCCCccCCCCCCC--CCCCCCcccccccccCCCCcceeEEeecccC--CCCcCCCCeEEEEeccCCCC
Q psy14432 23 KSSISLDKLYPNSSMLLKTPTPDQV--KAPDGLKFNGVIPVKAPDGLKFNGVIPVVIP--RFSYITEELDITYSRSSGPG 98 (189)
Q Consensus 23 ~s~~sld~lyp~s~~~~~~~~~~~~--~~~~~~~~~g~i~~~~~~~~~~~~v~p~~~~--~~~i~~~~l~i~fsRSSGPG 98 (189)
...+.++- ++.+..|+.+.|+|+ +.| .++.+|++|| ++++|+|+|..++ .+.|+++|++++|+||||||
T Consensus 176 s~~~~i~G--~~a~~~lk~E~GvHrvqrvs-~~~~~~r~ht----s~~~V~vlP~~~~~~~~~i~~~dl~~~~~rssGpG 248 (367)
T PRK00578 176 SATFKIKG--PYAYGYLKSETGVHRLVRIS-PFDSAGRRHT----SFASVEVYPEVDDTIEIEINPKDLRIDTYRSSGAG 248 (367)
T ss_pred EEEEEEec--cCHHHHHhhccceEEEEecC-CCCCCCceec----ceeeEEecCCCCCccccccChhhEEEEEeeCCCCC
Confidence 34556766 778889999999998 677 8999999999 4699999999875 68899999999999999999
Q ss_pred ccCCCcccceEEEEEecCCCCccCHHHHHHHHHHhcccccCCceEEEEEcCcccHHHHHHHHHHHHHHHHHHhhC
Q psy14432 99 GQHVNSVSTKVDIRFKVNAANWLNEDVKKQLIELNKNRLNKDGYLIIKSDRTRSQQLNLADAMTTLRNMIWKAAK 173 (189)
Q Consensus 99 GQnVNKv~SkV~Lrfhl~s~~wLp~~~r~~L~~~~~~ri~k~G~LvI~s~~~RSQ~~Nr~~Al~kL~~~I~~a~~ 173 (189)
|||||||+|+|+|+ |+|++ |+|+|+++|||++|++.|+++|+++|++...
T Consensus 249 GQ~vNkt~saVrl~-h~ptg------------------------i~v~~~~~RSQ~~Nk~~A~~~L~~kL~~~~~ 298 (367)
T PRK00578 249 GQHVNKTDSAVRIT-HIPTG------------------------IVVQCQNERSQHQNKASAMKMLKAKLYELEL 298 (367)
T ss_pred CCcccceeeEEEEE-ECCCc------------------------EEEEECCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999 99998 9999999999999999999999999998753
No 10
>TIGR00020 prfB peptide chain release factor 2. 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.
Probab=99.95 E-value=1e-28 Score=223.82 Aligned_cols=121 Identities=26% Similarity=0.339 Sum_probs=109.2
Q ss_pred eeee-eeeccccCCCCCCCccCCCCCCC--CCCCCCcccccccccCCCCcceeEEeecccC--CCCcCCCCeEEEEeccC
Q psy14432 21 FYKS-SISLDKLYPNSSMLLKTPTPDQV--KAPDGLKFNGVIPVKAPDGLKFNGVIPVVIP--RFSYITEELDITYSRSS 95 (189)
Q Consensus 21 ~~~s-~~sld~lyp~s~~~~~~~~~~~~--~~~~~~~~~g~i~~~~~~~~~~~~v~p~~~~--~~~i~~~~l~i~fsRSS 95 (189)
.|+| .+.++- ++.++.|+.+.|+|+ +.| ..+.+|++|| ++++|.|+|..++ ++.|+++|++|+|+|||
T Consensus 173 g~ks~~~~i~G--~~ay~~lk~E~GvHrv~rvs-~~~~~~rrht----s~a~V~vlP~~~~~~~~~i~~~d~~~~~~rss 245 (364)
T TIGR00020 173 GIKSVTILIKG--PYAYGYLKSEQGVHRLVRIS-PFDANGRRHT----SFASVFVMPEVDDDIDIEIKPEDLRIDTYRAS 245 (364)
T ss_pred ceEEEEEEEec--cCHHHHHhhccceEEEEecC-CCCCCCCeEe----eeEEEEEecCCCcccceecccccEEEEEeeCC
Confidence 3554 567776 788889999999998 677 8999999999 4699999999853 68889999999999999
Q ss_pred CCCccCCCcccceEEEEEecCCCCccCHHHHHHHHHHhcccccCCceEEEEEcCcccHHHHHHHHHHHHHHHHHHhhC
Q psy14432 96 GPGGQHVNSVSTKVDIRFKVNAANWLNEDVKKQLIELNKNRLNKDGYLIIKSDRTRSQQLNLADAMTTLRNMIWKAAK 173 (189)
Q Consensus 96 GPGGQnVNKv~SkV~Lrfhl~s~~wLp~~~r~~L~~~~~~ri~k~G~LvI~s~~~RSQ~~Nr~~Al~kL~~~I~~a~~ 173 (189)
||||||||||+|+|+|+ |+|++ |+|+|+++|||++|++.|+++|+++|++...
T Consensus 246 G~GGQ~VNkt~saVri~-H~ptg------------------------i~v~~q~~RSQ~~Nk~~A~~~L~~kL~~~~~ 298 (364)
T TIGR00020 246 GAGGQHVNKTDSAVRIT-HIPTG------------------------IVVQCQNDRSQHKNKDSAMKVLKAKLYELEM 298 (364)
T ss_pred CCCCccccccceEEEEE-ECCCc------------------------EEEEECCccCHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999 99998 9999999999999999999999999998753
No 11
>KOG2726|consensus
Probab=99.95 E-value=1.7e-28 Score=222.89 Aligned_cols=120 Identities=23% Similarity=0.308 Sum_probs=108.1
Q ss_pred eeeeeeccccCCCCCCCccCCCCCCC--CCCCCCcccccccccCCCCcceeEEeecc--cC-CCCcCCCCeEEEEeccCC
Q psy14432 22 YKSSISLDKLYPNSSMLLKTPTPDQV--KAPDGLKFNGVIPVKAPDGLKFNGVIPVV--IP-RFSYITEELDITYSRSSG 96 (189)
Q Consensus 22 ~~s~~sld~lyp~s~~~~~~~~~~~~--~~~~~~~~~g~i~~~~~~~~~~~~v~p~~--~~-~~~i~~~~l~i~fsRSSG 96 (189)
-.+.++++- -..|+.+..+.++|| +.| .++.+|++|| ++++|+|+|.. ++ ++.++++||+++|.|+||
T Consensus 187 ~~At~~i~G--~~ayg~l~~E~GvHRv~r~p-~~e~~gr~ht----stasV~ViP~~~~~~~~~~~~~~dl~i~~~R~~G 259 (386)
T KOG2726|consen 187 KSATLEIEG--ESAYGYLKFEAGVHRVQRVP-STETSGRRHT----STASVAVIPQPGRDEVDVEIDEKDLRIETFRASG 259 (386)
T ss_pred eeeeeEecc--cchhheeeccCcccceeecC-Cccccccccc----ccceEEEeccCCCCccceecCchheeEEecccCC
Confidence 345677777 456788899999999 788 8889999999 57999999998 33 688899999999999999
Q ss_pred CCccCCCcccceEEEEEecCCCCccCHHHHHHHHHHhcccccCCceEEEEEcCcccHHHHHHHHHHHHHHHHHHhhC
Q psy14432 97 PGGQHVNSVSTKVDIRFKVNAANWLNEDVKKQLIELNKNRLNKDGYLIIKSDRTRSQQLNLADAMTTLRNMIWKAAK 173 (189)
Q Consensus 97 PGGQnVNKv~SkV~Lrfhl~s~~wLp~~~r~~L~~~~~~ri~k~G~LvI~s~~~RSQ~~Nr~~Al~kL~~~I~~a~~ 173 (189)
|||||||||+|+|+|+ |+|+| |+|+|+++|||++|++.|+.+|+++|+....
T Consensus 260 ~GGQhvNktdsaVrl~-HiPTG------------------------Ivv~cq~eRSq~~Nr~~A~~~L~akL~~~~~ 311 (386)
T KOG2726|consen 260 PGGQHVNKTDSAVRLT-HIPTG------------------------IVVECQEERSQHKNRALALKRLRAKLAVIYR 311 (386)
T ss_pred CCcccccccccceEEE-eecCc------------------------eEEEeecHHhHHhhHHHHHHHHHHHHHHHHH
Confidence 9999999999999999 99999 9999999999999999999999999998643
No 12
>PRK00591 prfA peptide chain release factor 1; Validated
Probab=99.95 E-value=2.9e-28 Score=220.59 Aligned_cols=119 Identities=26% Similarity=0.354 Sum_probs=107.4
Q ss_pred eeeeeccccCCCCCCCccCCCCCCC--CCCCCCcccccccccCCCCcceeEEeecccC-CCCcCCCCeEEEEeccCCCCc
Q psy14432 23 KSSISLDKLYPNSSMLLKTPTPDQV--KAPDGLKFNGVIPVKAPDGLKFNGVIPVVIP-RFSYITEELDITYSRSSGPGG 99 (189)
Q Consensus 23 ~s~~sld~lyp~s~~~~~~~~~~~~--~~~~~~~~~g~i~~~~~~~~~~~~v~p~~~~-~~~i~~~~l~i~fsRSSGPGG 99 (189)
.+.+.++- ++.|+.|+.+.++|+ +.| ..+.+||+|| ++++|.|+|..++ ++.|+++||+|+|+|||||||
T Consensus 163 sa~l~i~G--~~ay~~Lk~E~GvHrv~R~p-~~~s~~R~~t----sfa~V~v~P~~~~~~~~i~~~dl~~~~~RssG~GG 235 (359)
T PRK00591 163 EVIAEISG--DGVYSKLKFESGVHRVQRVP-ATESQGRIHT----SAATVAVLPEAEEVEVEINPKDLRIDTFRSSGAGG 235 (359)
T ss_pred EEEEEEec--ccHHHHHhhcCeeEEEEeeC-CCCCCCceec----ceEEEEEEcCCCccccccCcccEEEEEEECCCCCC
Confidence 34456665 677788899999998 677 8899999999 4699999999864 788999999999999999999
Q ss_pred cCCCcccceEEEEEecCCCCccCHHHHHHHHHHhcccccCCceEEEEEcCcccHHHHHHHHHHHHHHHHHHhhC
Q psy14432 100 QHVNSVSTKVDIRFKVNAANWLNEDVKKQLIELNKNRLNKDGYLIIKSDRTRSQQLNLADAMTTLRNMIWKAAK 173 (189)
Q Consensus 100 QnVNKv~SkV~Lrfhl~s~~wLp~~~r~~L~~~~~~ri~k~G~LvI~s~~~RSQ~~Nr~~Al~kL~~~I~~a~~ 173 (189)
||||||+|+|+|+ |+|++ |+|+|+++|||++|++.|+++|+++|.++..
T Consensus 236 Q~VNkt~saVrl~-H~ptG------------------------i~v~~~~eRSQ~~Nk~~Al~~L~~~L~~~~~ 284 (359)
T PRK00591 236 QHVNTTDSAVRIT-HLPTG------------------------IVVECQDERSQHKNKAKAMKVLRARLYDAER 284 (359)
T ss_pred CCccceeeeEEEE-ECCCc------------------------EEEEECCcCCHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999 99998 9999999999999999999999999998753
No 13
>PF00472 RF-1: RF-1 domain; InterPro: IPR000352 Peptide chain release factors (RFs) are required for the termination of protein biosynthesis []. 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 ....
Probab=99.94 E-value=6e-27 Score=181.04 Aligned_cols=70 Identities=37% Similarity=0.629 Sum_probs=65.7
Q ss_pred CCCCcCCCCeEEEEeccCCCCccCCCcccceEEEEEecCCCCccCHHHHHHHHHHhcccccCCceEEEEEcCcccHHHHH
Q psy14432 78 PRFSYITEELDITYSRSSGPGGQHVNSVSTKVDIRFKVNAANWLNEDVKKQLIELNKNRLNKDGYLIIKSDRTRSQQLNL 157 (189)
Q Consensus 78 ~~~~i~~~~l~i~fsRSSGPGGQnVNKv~SkV~Lrfhl~s~~wLp~~~r~~L~~~~~~ri~k~G~LvI~s~~~RSQ~~Nr 157 (189)
..+.|++++|+++|+|||||||||||||+|+|+|+ |.|++ |+|+|+++|||..|+
T Consensus 5 ~~~~i~~~dl~~~~~RssGpGGQ~VNk~~s~V~l~-h~ptg------------------------i~v~~~~~Rsq~~Nr 59 (113)
T PF00472_consen 5 KEIDIPEKDLEISFSRSSGPGGQNVNKTNSKVRLR-HIPTG------------------------IVVKCQESRSQHQNR 59 (113)
T ss_dssp SSSCC-GGGEEEEEEESSSSSSCHHHSSSEEEEEE-ETTTT------------------------EEEEEESSSSHHHHH
T ss_pred cccccCHHHeEEEEEecCCCCCCcccccCCEEEEE-Eeccc------------------------EEEEEcccCCHHHHH
Confidence 46788999999999999999999999999999999 77888 999999999999999
Q ss_pred HHHHHHHHHHHHHhh
Q psy14432 158 ADAMTTLRNMIWKAA 172 (189)
Q Consensus 158 ~~Al~kL~~~I~~a~ 172 (189)
++|+++|+++|.++.
T Consensus 60 ~~A~~~L~~~l~~~~ 74 (113)
T PF00472_consen 60 EDALEKLREKLDEAY 74 (113)
T ss_dssp HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHH
Confidence 999999999999986
No 14
>TIGR03072 release_prfH putative peptide chain release factor H. 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.
Probab=99.94 E-value=1.7e-26 Score=194.96 Aligned_cols=116 Identities=22% Similarity=0.191 Sum_probs=94.3
Q ss_pred eee-eeeccccCCCCCCCccCCCCCCC---CCCCCCcccccccccCCCCcceeEEeecccCCCCcCCCCeEEEEeccCCC
Q psy14432 22 YKS-SISLDKLYPNSSMLLKTPTPDQV---KAPDGLKFNGVIPVKAPDGLKFNGVIPVVIPRFSYITEELDITYSRSSGP 97 (189)
Q Consensus 22 ~~s-~~sld~lyp~s~~~~~~~~~~~~---~~~~~~~~~g~i~~~~~~~~~~~~v~p~~~~~~~i~~~~l~i~fsRSSGP 97 (189)
|+| .+.++- ++.++.+..+.++|. +.| .....+|. + ++++|.|+|. .++|+++||+++|+|||||
T Consensus 50 ~ksa~~~i~G--~~ay~~l~~~~G~h~~v~~sp-~r~~~~R~-t----s~~~V~v~~~---~~~i~~~dl~~~~~RssGp 118 (200)
T TIGR03072 50 LRSALVSLDG--EAAAALADRWEGTLLWICPSP-YRPHHRRK-N----WFIGVQRFSA---SEEATEDEIRFETLRSSGP 118 (200)
T ss_pred eEEEEEEEEc--cCHHHHhhcccceEEEEEcCC-CCCCCCee-E----EEEEEEEecC---ccccChhheEEEEEECCCC
Confidence 555 677777 667766667777665 344 33333333 5 3577778873 5678999999999999999
Q ss_pred CccCCCcccceEEEEEecCCCCccCHHHHHHHHHHhcccccCCceEEEEEcCcccHHHHHHHHHHHHHHHHHHhhC
Q psy14432 98 GGQHVNSVSTKVDIRFKVNAANWLNEDVKKQLIELNKNRLNKDGYLIIKSDRTRSQQLNLADAMTTLRNMIWKAAK 173 (189)
Q Consensus 98 GGQnVNKv~SkV~Lrfhl~s~~wLp~~~r~~L~~~~~~ri~k~G~LvI~s~~~RSQ~~Nr~~Al~kL~~~I~~a~~ 173 (189)
||||||||+|+|+|+ |+|++ |+|+|+++|||++|++.|+++|+++|.+...
T Consensus 119 GGQ~vNkt~saVrl~-h~ptg------------------------i~v~~~~~RSQ~~Nk~~A~~~L~~~l~~~~~ 169 (200)
T TIGR03072 119 GGQHVNKTESAVRAT-HLASG------------------------ISVKVQSERSQHANKRLATLLLAVRLADLQQ 169 (200)
T ss_pred CcccccccceeEEEE-ECCCc------------------------EEEEECCccCHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999 99998 9999999999999999999999999998753
No 15
>PRK08179 prfH peptide chain release factor-like protein; Reviewed
Probab=99.93 E-value=1.1e-25 Score=190.10 Aligned_cols=116 Identities=24% Similarity=0.232 Sum_probs=91.5
Q ss_pred eee-eeeccccCCCCCCCccCCCCCCC---CCCCCCcccccccccCCCCcceeEEeecccCCCCcCCCCeEEEEeccCCC
Q psy14432 22 YKS-SISLDKLYPNSSMLLKTPTPDQV---KAPDGLKFNGVIPVKAPDGLKFNGVIPVVIPRFSYITEELDITYSRSSGP 97 (189)
Q Consensus 22 ~~s-~~sld~lyp~s~~~~~~~~~~~~---~~~~~~~~~g~i~~~~~~~~~~~~v~p~~~~~~~i~~~~l~i~fsRSSGP 97 (189)
||| .++++- ++.+..+....+.|. +.| .....+|. + ++++|.|+| ..+.|+++||+++|+|||||
T Consensus 51 ~ksa~~~i~G--~~a~~~l~~~~G~~~~V~~sp-~~~~~~R~-~----s~~~V~v~~---~~~~i~~~dl~~~~~RssGp 119 (200)
T PRK08179 51 LRSALVSLDG--DNAEALAESWCGTIQWICPSP-YRPHHGRK-N----WFVGIGRFS---ADEEEQSDEIRFETLRSSGP 119 (200)
T ss_pred eEEEEEEEEc--cCHHHHhhcccCeeEEEecCC-CCCCCCce-E----EEEEEEEeC---CcCccCHHHeEEEEEEccCC
Confidence 555 577776 555555565656554 344 33333343 4 246666765 35688999999999999999
Q ss_pred CccCCCcccceEEEEEecCCCCccCHHHHHHHHHHhcccccCCceEEEEEcCcccHHHHHHHHHHHHHHHHHHhhC
Q psy14432 98 GGQHVNSVSTKVDIRFKVNAANWLNEDVKKQLIELNKNRLNKDGYLIIKSDRTRSQQLNLADAMTTLRNMIWKAAK 173 (189)
Q Consensus 98 GGQnVNKv~SkV~Lrfhl~s~~wLp~~~r~~L~~~~~~ri~k~G~LvI~s~~~RSQ~~Nr~~Al~kL~~~I~~a~~ 173 (189)
||||||||+|+|+|+ |+|++ |+|+|+++|||++|++.|+++|+++|.+...
T Consensus 120 GGQ~VNkt~saVrl~-h~ptg------------------------i~v~~~~~RSQ~~Nk~~A~~~L~~~L~~~~~ 170 (200)
T PRK08179 120 GGQHVNKTDSAVRAT-HLASG------------------------ISVKVQSERSQHANKRLARLLIAWKLEQQQQ 170 (200)
T ss_pred cccccccccceEEEE-EcCCc------------------------EEEEECCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999 99998 9999999999999999999999999998753
No 16
>COG1186 PrfB Protein chain release factor B [Translation, ribosomal structure and biogenesis]
Probab=99.92 E-value=2.2e-26 Score=198.47 Aligned_cols=146 Identities=23% Similarity=0.212 Sum_probs=125.5
Q ss_pred eeccccCCCCCCCccCCCCCCC--CCCCCCcccccccccCCCCcceeEEeecccC--CCCcCCCCeEEEEeccCCCCccC
Q psy14432 26 ISLDKLYPNSSMLLKTPTPDQV--KAPDGLKFNGVIPVKAPDGLKFNGVIPVVIP--RFSYITEELDITYSRSSGPGGQH 101 (189)
Q Consensus 26 ~sld~lyp~s~~~~~~~~~~~~--~~~~~~~~~g~i~~~~~~~~~~~~v~p~~~~--~~~i~~~~l~i~fsRSSGPGGQn 101 (189)
+.|+- ++.++-++++.++|+ +.+ .-...|+-|+ +++.+.|+|.+++ .+.|+++||+++|+|||||||||
T Consensus 54 ~~~~g--~~a~g~~~~e~g~hrlvr~S-pf~~~~~R~t----sf~~v~v~p~~~~~i~i~I~~~dl~idt~RASGaGGQh 126 (239)
T COG1186 54 LKIKG--ENAYGYLKTETGVHRLVRIS-PFDSNGRRHT----SFASVEVFPELDISIEIEIPDDDLRIDTYRASGAGGQH 126 (239)
T ss_pred EEEec--hHHHHHHHhhcceeEEEeec-CCCcCccccc----ceeeeeecCCCCcccceecCccceEEEEEEcCCCCCCc
Confidence 45555 566778899999997 444 4667899999 5688999999865 67889999999999999999999
Q ss_pred CCcccceEEEEEecCCC-CccCHHHHHHHHHHhcccccCCceEEEEEcCcccHHHHHHHHHHHHHHHHHHhhCCCCCCC
Q psy14432 102 VNSVSTKVDIRFKVNAA-NWLNEDVKKQLIELNKNRLNKDGYLIIKSDRTRSQQLNLADAMTTLRNMIWKAAKPAPQIS 179 (189)
Q Consensus 102 VNKv~SkV~Lrfhl~s~-~wLp~~~r~~L~~~~~~ri~k~G~LvI~s~~~RSQ~~Nr~~Al~kL~~~I~~a~~~pk~~S 179 (189)
||||+|+|+|+ |++++ ...++..|.+++.+...+...+|.|++..+++|+|..|+.+|++++.+.+.++...+..|-
T Consensus 127 VNKt~SAVrlt-h~ptgivv~cq~eRSq~~n~~~a~~~l~~kL~~~~~~~Rsqe~n~~~a~~k~i~wg~qirsyv~~p~ 204 (239)
T COG1186 127 VNKTDSAVRLT-HLPTGIVVLCQNERSQHLNKALARKMLKGKLYILAQEKRSQEKNRERALKKLIGWGNQIRSYVLDPY 204 (239)
T ss_pred cccccccEEEE-EcCCCCEecCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHhccccCCCcc
Confidence 99999999999 88888 7789999999999999999999999999999999999999999999999999865555433
No 17
>PF10213 MRP-S28: Mitochondrial ribosomal subunit protein ; InterPro: IPR019349 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents a conserved region of approx. 125 residues of one of the proteins that makes up the small subunit of the mitochondrial ribosome. In Saccharomyces cerevisiae (Baker's yeast) it is mitochondrial ribosomal protein S24 whereas in humans it is S35.
Probab=98.18 E-value=2.1e-05 Score=62.62 Aligned_cols=84 Identities=24% Similarity=0.270 Sum_probs=73.5
Q ss_pred CCeEEEEeccCCCCccCCCcccceEEEEEecCCCCccCHHHHHHHHHHhcccccC-CceEEEEEcCcccHHHHHHHHHHH
Q psy14432 85 EELDITYSRSSGPGGQHVNSVSTKVDIRFKVNAANWLNEDVKKQLIELNKNRLNK-DGYLIIKSDRTRSQQLNLADAMTT 163 (189)
Q Consensus 85 ~~l~i~fsRSSGPGGQnVNKv~SkV~Lrfhl~s~~wLp~~~r~~L~~~~~~ri~k-~G~LvI~s~~~RSQ~~Nr~~Al~k 163 (189)
.-|+++|.-=-|.| |..+.||.|+|++... .|++.++.+|+...+.|++. .|.|.|+|+..-++.+|++-|.+.
T Consensus 9 ~pl~~~~~~y~~~~----~p~~rkV~l~v~l~dL-~L~~~a~~Kl~~LaG~Ryd~~~d~l~i~sdr~~~~~qN~~~l~~~ 83 (127)
T PF10213_consen 9 FPLRFRYTDYMGES----HPANRKVVLQVKLSDL-GLSEKARHKLKLLAGPRYDPETDILKISSDRFPTRAQNKKYLSDL 83 (127)
T ss_pred CCEEEEEEeecCCC----CCccCEEEEEEEHHhc-CCCHHHHHHHHHHhhcccCCCCCEEEEecccCCCHHHHHHHHHHH
Confidence 34566666555555 7789999999999765 78999999999999999994 789999999999999999999999
Q ss_pred HHHHHHHhhC
Q psy14432 164 LRNMIWKAAK 173 (189)
Q Consensus 164 L~~~I~~a~~ 173 (189)
|..+|.+|..
T Consensus 84 l~~L~~EA~~ 93 (127)
T PF10213_consen 84 LTRLIHEAKD 93 (127)
T ss_pred HHHHHHHHhh
Confidence 9999999965
No 18
>KOG3933|consensus
Probab=97.04 E-value=0.0065 Score=54.63 Aligned_cols=87 Identities=31% Similarity=0.318 Sum_probs=73.6
Q ss_pred CCCeEEEEeccCCCCccCCCcccceEEEEEecCCCCccCHHHHHHHHHHhcccccC-CceEEEEEcCcccHHHHHHHHHH
Q psy14432 84 TEELDITYSRSSGPGGQHVNSVSTKVDIRFKVNAANWLNEDVKKQLIELNKNRLNK-DGYLIIKSDRTRSQQLNLADAMT 162 (189)
Q Consensus 84 ~~~l~i~fsRSSGPGGQnVNKv~SkV~Lrfhl~s~~wLp~~~r~~L~~~~~~ri~k-~G~LvI~s~~~RSQ~~Nr~~Al~ 162 (189)
+..+..+++-+||||=-|-| +-+|.+++++.. ..|++.++.+|+...+.|+++ .+.+.|+||..-...+|+..|+.
T Consensus 148 p~~i~~t~~~~sg~s~~~p~--~RvVvmsvk~~e-L~L~ehq~~klr~Lvg~RY~~~tD~~tissDR~~~r~QN~~y~~~ 224 (296)
T KOG3933|consen 148 PISIQSTDYFASGPSIRHPN--SRVVVMSVKVKE-LGLSEHQRKKLRRLVGKRYNKTTDLLTISSDRCEHREQNYDYALY 224 (296)
T ss_pred cccceeEEEeccCCcccCCC--CceEEEEEEecc-cCccHHHHHHHHHHhhhccCCCCCeEEEeccccchhhHhHHHHHH
Confidence 44667777788888877654 567888877754 589999999999999999997 45899999999999999999999
Q ss_pred HHHHHHHHhhC
Q psy14432 163 TLRNMIWKAAK 173 (189)
Q Consensus 163 kL~~~I~~a~~ 173 (189)
.|..++.++..
T Consensus 225 lLt~L~~ES~k 235 (296)
T KOG3933|consen 225 LLTVLYHESGK 235 (296)
T ss_pred HHHHHHHHhcc
Confidence 99999999844
No 19
>COG1186 PrfB Protein chain release factor B [Translation, ribosomal structure and biogenesis]
Probab=92.61 E-value=0.069 Score=46.96 Aligned_cols=32 Identities=28% Similarity=0.339 Sum_probs=29.0
Q ss_pred eEEEEEcCcccHHHHHHHHHHHHHHHHHHhhC
Q psy14432 142 YLIIKSDRTRSQQLNLADAMTTLRNMIWKAAK 173 (189)
Q Consensus 142 ~LvI~s~~~RSQ~~Nr~~Al~kL~~~I~~a~~ 173 (189)
.|++.||.+|||+.|++.|+..|+..|++...
T Consensus 142 givv~cq~eRSq~~n~~~a~~~l~~kL~~~~~ 173 (239)
T COG1186 142 GIVVLCQNERSQHLNKALARKMLKGKLYILAQ 173 (239)
T ss_pred CCEecCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 38999999999999999999999999987643
No 20
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=65.56 E-value=6.8 Score=26.10 Aligned_cols=47 Identities=13% Similarity=0.312 Sum_probs=27.9
Q ss_pred CCCCccCCCcccceEEEEEecCCCCccCHHHHHHHHHHhcccccCCceEEEEEcCcccHHHHHHHHHHHH
Q psy14432 95 SGPGGQHVNSVSTKVDIRFKVNAANWLNEDVKKQLIELNKNRLNKDGYLIIKSDRTRSQQLNLADAMTTL 164 (189)
Q Consensus 95 SGPGGQnVNKv~SkV~Lrfhl~s~~wLp~~~r~~L~~~~~~ri~k~G~LvI~s~~~RSQ~~Nr~~Al~kL 164 (189)
=|+||.|+++...+--..+.++... +.++.+.|... ..+.+.|.+.|
T Consensus 15 IG~~G~~i~~i~~~~g~~I~i~~~~------------------~~~~~v~I~G~-----~~~v~~A~~~i 61 (62)
T cd02394 15 IGKKGSNIRKIMEETGVKIRFPDPG------------------SKSDTITITGP-----KENVEKAKEEI 61 (62)
T ss_pred cCCCCCcHHHHHHHhCCEEEcCCCC------------------CCCCEEEEEcC-----HHHHHHHHHHh
Confidence 5999999997653333333454430 34566777776 34555665544
No 21
>smart00322 KH K homology RNA-binding domain.
Probab=45.57 E-value=25 Score=22.28 Aligned_cols=50 Identities=12% Similarity=0.327 Sum_probs=29.5
Q ss_pred CCCccCCCcccceEEEEEecCCCCccCHHHHHHHHHHhcccccCCceEEEEEcCcccHHHHHHHHHHHHHHHH
Q psy14432 96 GPGGQHVNSVSTKVDIRFKVNAANWLNEDVKKQLIELNKNRLNKDGYLIIKSDRTRSQQLNLADAMTTLRNMI 168 (189)
Q Consensus 96 GPGGQnVNKv~SkV~Lrfhl~s~~wLp~~~r~~L~~~~~~ri~k~G~LvI~s~~~RSQ~~Nr~~Al~kL~~~I 168 (189)
|++|.++..........++++...- ....+.|... ..+.+.|.+.|.+.+
T Consensus 19 G~~G~~i~~i~~~~~~~i~~~~~~~------------------~~~~v~i~g~-----~~~v~~a~~~i~~~~ 68 (69)
T smart00322 19 GKGGSTIKKIEEETGVKIDIPEDGS------------------EERVVEITGP-----PENVEKAAELILEIL 68 (69)
T ss_pred CCCchHHHHHHHHHCCEEEECCCCC------------------CccEEEEEcC-----HHHHHHHHHHHHHHh
Confidence 8899988876554444444433200 2233555554 577778877777654
No 22
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=44.25 E-value=27 Score=22.76 Aligned_cols=21 Identities=19% Similarity=0.480 Sum_probs=16.1
Q ss_pred CCCCccCCCcccce--EEEEEec
Q psy14432 95 SGPGGQHVNSVSTK--VDIRFKV 115 (189)
Q Consensus 95 SGPGGQnVNKv~Sk--V~Lrfhl 115 (189)
=||||.+++....+ |.+.|+-
T Consensus 15 IG~~G~~i~~I~~~s~~~I~i~~ 37 (64)
T cd00105 15 IGKGGSTIKEIREETGAKIKIPD 37 (64)
T ss_pred ECCCCHHHHHHHHHHCCEEEEcC
Confidence 59999999987644 7777654
No 23
>PF14048 MBD_C: C-terminal domain of methyl-CpG binding protein 2 and 3; PDB: 2L2L_B.
Probab=43.84 E-value=9.4 Score=29.15 Aligned_cols=26 Identities=15% Similarity=0.337 Sum_probs=20.1
Q ss_pred EEEEEcCcccHHHHHHHHHHHHHHHH
Q psy14432 143 LIIKSDRTRSQQLNLADAMTTLRNMI 168 (189)
Q Consensus 143 LvI~s~~~RSQ~~Nr~~Al~kL~~~I 168 (189)
++|+.++=|.|..-..+|.+||.+.|
T Consensus 71 ~~VT~eDIr~QE~rVk~aR~RLaeAL 96 (96)
T PF14048_consen 71 FVVTEEDIRRQERRVKKARKRLAEAL 96 (96)
T ss_dssp ----HHHHHHHHHHHHHHHHHHHHHH
T ss_pred CccCHHHHHHHHHHHHHHHHHHHHHC
Confidence 67888999999999999999998764
No 24
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=32.51 E-value=28 Score=23.68 Aligned_cols=15 Identities=27% Similarity=0.716 Sum_probs=11.0
Q ss_pred cCCCCccCCCcccce
Q psy14432 94 SSGPGGQHVNSVSTK 108 (189)
Q Consensus 94 SSGPGGQnVNKv~Sk 108 (189)
==|+||.+++.....
T Consensus 16 iIGkgG~~ik~I~~~ 30 (61)
T cd02393 16 VIGPGGKTIKKIIEE 30 (61)
T ss_pred eECCCchHHHHHHHH
Confidence 359999999875443
No 25
>COG0193 Pth Peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis]
Probab=29.26 E-value=46 Score=28.51 Aligned_cols=23 Identities=13% Similarity=0.352 Sum_probs=18.5
Q ss_pred cCCCCcCCCCeEEEEeccCCCCccC
Q psy14432 77 IPRFSYITEELDITYSRSSGPGGQH 101 (189)
Q Consensus 77 ~~~~~i~~~~l~i~fsRSSGPGGQn 101 (189)
-++++++...++++. ++|.||+|
T Consensus 92 hDdLdl~~G~vrlk~--~Gg~gGHN 114 (190)
T COG0193 92 HDELDLPLGKVRLKL--GGGAGGHN 114 (190)
T ss_pred eeccCCCCceEEEEc--CCCCCCcc
Confidence 356788888777777 89999987
No 26
>PRK09374 rplB 50S ribosomal protein L2; Validated
Probab=28.22 E-value=75 Score=28.64 Aligned_cols=36 Identities=17% Similarity=0.210 Sum_probs=28.4
Q ss_pred CCcCCCCeEEEEeccCCCCccCCCcccceEEEEEecCCC
Q psy14432 80 FSYITEELDITYSRSSGPGGQHVNSVSTKVDIRFKVNAA 118 (189)
Q Consensus 80 ~~i~~~~l~i~fsRSSGPGGQnVNKv~SkV~Lrfhl~s~ 118 (189)
+++.+.+ --.|+||+|--+|=|.+.+..|.|+ ||++
T Consensus 144 IE~~pG~-Ggkl~RsAGt~A~ii~k~~~~~~vk--LPSG 179 (276)
T PRK09374 144 IELKPGK-GGQLARSAGTSAQLVAKEGKYATLR--LPSG 179 (276)
T ss_pred EEecCCC-CceeEeecCCeEEEEEecCCEEEEE--CCCC
Confidence 3444443 3569999999999999999999987 8876
No 27
>PF15128 T_cell_tran_alt: T-cell leukemia translocation-altered
Probab=26.67 E-value=32 Score=26.28 Aligned_cols=17 Identities=41% Similarity=0.677 Sum_probs=12.3
Q ss_pred EeccCCCCccCCCcccce
Q psy14432 91 YSRSSGPGGQHVNSVSTK 108 (189)
Q Consensus 91 fsRSSGPGGQnVNKv~Sk 108 (189)
|.|. |+||||=-+.++.
T Consensus 57 yyRq-G~ggqNggTPd~~ 73 (92)
T PF15128_consen 57 YYRQ-GTGGQNGGTPDTS 73 (92)
T ss_pred eeCC-CCCccCCCCCCCc
Confidence 5555 9999997766554
No 28
>TIGR01171 rplB_bact ribosomal protein L2, bacterial/organellar. This model distinguishes bacterial and organellar ribosomal protein L2 from its counterparts in the archaea nad in the eukaryotic cytosol. Plant mitochondrial examples tend to have long, variable inserts.
Probab=25.37 E-value=90 Score=28.08 Aligned_cols=37 Identities=16% Similarity=0.209 Sum_probs=29.1
Q ss_pred CCCcCCCCeEEEEeccCCCCccCCCcccceEEEEEecCCC
Q psy14432 79 RFSYITEELDITYSRSSGPGGQHVNSVSTKVDIRFKVNAA 118 (189)
Q Consensus 79 ~~~i~~~~l~i~fsRSSGPGGQnVNKv~SkV~Lrfhl~s~ 118 (189)
.+++.+.+ --.|+||+|--+|-+.+.+..|.|+ ||++
T Consensus 141 NIE~~pg~-Ggkl~RsAGt~A~ii~k~~~~~~vk--LPSG 177 (273)
T TIGR01171 141 NIELKPGK-GGQLARSAGTSAQILAKEGGYVTLR--LPSG 177 (273)
T ss_pred EEEecCCC-CceEEEecCCeEEEEEecCCEEEEE--CCCC
Confidence 34444444 3479999999999999999999987 7876
No 29
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=25.28 E-value=1.6e+02 Score=22.96 Aligned_cols=31 Identities=19% Similarity=0.207 Sum_probs=17.8
Q ss_pred ccCCceEEEEEcCcccHHHHHHHHHHHHHHHHHHhhC
Q psy14432 137 LNKDGYLIIKSDRTRSQQLNLADAMTTLRNMIWKAAK 173 (189)
Q Consensus 137 i~k~G~LvI~s~~~RSQ~~Nr~~Al~kL~~~I~~a~~ 173 (189)
.+..+.+.|++... -++|+++-.++|.....
T Consensus 64 ~~eplhV~I~a~~~------~~e~~~~A~~~I~~ll~ 94 (120)
T cd02395 64 LNEPLHVLITAETP------PEEALAKAVEAIEELLK 94 (120)
T ss_pred CCCCcEEEEEeCCc------HHHHHHHHHHHHHHHhc
Confidence 34567889998864 23444444444444433
No 30
>smart00878 Biotin_carb_C Biotin carboxylase C-terminal domain. Biotin carboxylase is a component of the acetyl-CoA carboxylase multi-component enzyme which catalyses the first committed step in fatty acid synthesis in animals, plants and bacteria. Most of the active site residues reported in reference are in this C-terminal domain.
Probab=24.16 E-value=1.1e+02 Score=23.38 Aligned_cols=19 Identities=16% Similarity=0.141 Sum_probs=15.8
Q ss_pred HHHHHHHHHHHHHHHhhCC
Q psy14432 156 NLADAMTTLRNMIWKAAKP 174 (189)
Q Consensus 156 Nr~~Al~kL~~~I~~a~~~ 174 (189)
++++|+++|+..|.+....
T Consensus 60 ~R~~A~~rl~~aL~e~~i~ 78 (107)
T smart00878 60 TREEAIARLRRALDEFRIE 78 (107)
T ss_pred CHHHHHHHHHHHHHhCEEE
Confidence 6889999999999987543
No 31
>PF07687 M20_dimer: Peptidase dimerisation domain This family only corresponds to M20 family; InterPro: IPR011650 This domain consists of 4 beta strands and two alpha helices which make up the dimerisation surface of members of the MEROPS peptidase family M20 []. This family includes a range of zinc exopeptidases: carboxypeptidases, dipeptidases and specialised aminopeptidases [].; GO: 0016787 hydrolase activity; PDB: 3GB0_A 2F7V_A 1R3N_C 2VL1_D 2V8V_C 1R43_B 2V8G_B 2V8H_D 2V8D_A 3PFE_A ....
Probab=23.60 E-value=94 Score=22.05 Aligned_cols=24 Identities=17% Similarity=0.282 Sum_probs=18.5
Q ss_pred cCCCCccCCCcccceEEEEEecCC
Q psy14432 94 SSGPGGQHVNSVSTKVDIRFKVNA 117 (189)
Q Consensus 94 SSGPGGQnVNKv~SkV~Lrfhl~s 117 (189)
...-||...|-+...+++.+++..
T Consensus 64 ~~i~gG~~~n~ip~~a~~~~~~R~ 87 (111)
T PF07687_consen 64 GSIEGGTAPNVIPDEATLTVDIRY 87 (111)
T ss_dssp EEEEEESSTTEESSEEEEEEEEEE
T ss_pred eecccCCcCCEECCEEEEEEEEEC
Confidence 344566799999999999988653
No 32
>cd02406 CRS2 Chloroplast RNA splicing 2 (CRS2) is a nuclear-encoded protein required for the splicing of group II introns in the chloroplast. CRS2 forms stable complexes with two CRS2-associated factors, CAF1 and CAF2, which are required for the splicing of distinct subsets of CRS2-dependent introns. CRS2 is closely related to bacterial peptidyl-tRNA hydrolases (PTH).
Probab=21.59 E-value=72 Score=27.08 Aligned_cols=38 Identities=11% Similarity=0.245 Sum_probs=25.4
Q ss_pred ccCCCCcCCCCeEEEEeccCCCCccC-----CCcc-cc--eEEEEEec
Q psy14432 76 VIPRFSYITEELDITYSRSSGPGGQH-----VNSV-ST--KVDIRFKV 115 (189)
Q Consensus 76 ~~~~~~i~~~~l~i~fsRSSGPGGQn-----VNKv-~S--kV~Lrfhl 115 (189)
+-++++++...++++ ..+|+||+| .... .| =.+||+=+
T Consensus 90 ihDdldl~~G~irlk--~gGs~gGHNGlkSI~~~Lggt~~f~RlrIGI 135 (191)
T cd02406 90 IYDDMSLPNGVLRLQ--PKGGHGRHNGLQSVIEHLDGSREFPRLSIGI 135 (191)
T ss_pred EEECCCCCCCeEEEc--CCCCCCCcCCHHHHHHHhCCCCCeEEEEEEe
Confidence 346788888888877 678899998 4444 32 45555543
No 33
>cd00552 RaiA RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal A site. RaiA is also thought to counteract miscoding at the A site thus reducing translation errors. The RaiA fold structurally resembles the double-stranded RNA-binding domain (dsRBD).
Probab=21.16 E-value=3e+02 Score=19.29 Aligned_cols=57 Identities=16% Similarity=0.197 Sum_probs=38.5
Q ss_pred CCeEEEEeccCCCCccCCCcccceEEEEEecCCCCccCHHHHHHHHHHhcccccCCceEEEEEcCcccHHHHHHHHHHHH
Q psy14432 85 EELDITYSRSSGPGGQHVNSVSTKVDIRFKVNAANWLNEDVKKQLIELNKNRLNKDGYLIIKSDRTRSQQLNLADAMTTL 164 (189)
Q Consensus 85 ~~l~i~fsRSSGPGGQnVNKv~SkV~Lrfhl~s~~wLp~~~r~~L~~~~~~ri~k~G~LvI~s~~~RSQ~~Nr~~Al~kL 164 (189)
..+++.+..-.++|+ .-.|+++++++.. .++...+.-+-..=...|+++|
T Consensus 34 ~~~~V~l~~~~~~~~------~~~v~i~v~~~g~------------------------~~~a~~~~~d~~~Aid~a~~kl 83 (93)
T cd00552 34 ISVDVVLSVEKNHGK------RFKVEITIHLPGG------------------------VLRAEASAEDLYAAIDLAVDKL 83 (93)
T ss_pred ceEEEEEEEecCCCC------ceEEEEEEEeCCC------------------------EEEEEEccCCHHHHHHHHHHHH
Confidence 346777776666532 3478888887633 4555566667777788888888
Q ss_pred HHHHHHh
Q psy14432 165 RNMIWKA 171 (189)
Q Consensus 165 ~~~I~~a 171 (189)
...|...
T Consensus 84 ~rqL~k~ 90 (93)
T cd00552 84 ERQLRKY 90 (93)
T ss_pred HHHHHHh
Confidence 8887754
No 34
>PRK10470 ribosome hibernation promoting factor HPF; Provisional
Probab=21.03 E-value=3.3e+02 Score=19.62 Aligned_cols=41 Identities=12% Similarity=0.112 Sum_probs=27.6
Q ss_pred ceEEEEEecCCCCccCHHHHHHHHHHhcccccCCceEEEEEcCcccHHHHHHHHHHHHHHHHHHh
Q psy14432 107 TKVDIRFKVNAANWLNEDVKKQLIELNKNRLNKDGYLIIKSDRTRSQQLNLADAMTTLRNMIWKA 171 (189)
Q Consensus 107 SkV~Lrfhl~s~~wLp~~~r~~L~~~~~~ri~k~G~LvI~s~~~RSQ~~Nr~~Al~kL~~~I~~a 171 (189)
-.|+++++++.. .|+++ ...-.-..=.+.|+++|...|...
T Consensus 48 ~~~ei~~~~~g~-----------------------~l~a~-~~~~d~y~Aid~a~~klerqL~k~ 88 (95)
T PRK10470 48 HISDATLHVNGG-----------------------EIHAS-AEGQDMYAAIDGLIDKLARQLTKH 88 (95)
T ss_pred eEEEEEEEeCCC-----------------------EEEEE-EecCcHHHHHHHHHHHHHHHHHHH
Confidence 468888888643 34444 445566667778888888877764
No 35
>TIGR01891 amidohydrolases amidohydrolase. This model represents a subfamily of amidohydrolases which are a subset of those sequences detected by pfam01546. Included within this group are hydrolases of hippurate (N-benzylglycine), indoleacetic acid (IAA) N-conjugates of amino acids, N-acetyl-L-amino acids and aminobenzoylglutamate. These hydrolases are of the carboxypeptidase-type, most likely utilizing a zinc ion in the active site.
Probab=20.04 E-value=1.5e+02 Score=26.20 Aligned_cols=73 Identities=11% Similarity=0.105 Sum_probs=37.5
Q ss_pred CccCCCcccceEEEEEecCCCCcc-CHHHHHHHHHHhcccccC-CceEEEEEcCcccHHHHHHHHHHHHHHHHHH
Q psy14432 98 GGQHVNSVSTKVDIRFKVNAANWL-NEDVKKQLIELNKNRLNK-DGYLIIKSDRTRSQQLNLADAMTTLRNMIWK 170 (189)
Q Consensus 98 GGQnVNKv~SkV~Lrfhl~s~~wL-p~~~r~~L~~~~~~ri~k-~G~LvI~s~~~RSQ~~Nr~~Al~kL~~~I~~ 170 (189)
||..+|.+...++++|++.....- .+++.+.|.+.+...-.. ...+.+.....+--..+-..+.+.|++.+.+
T Consensus 227 gG~~~nvvP~~~~~~~diR~~~~~~~e~~~~~i~~~~~~~~~~~~~~ve~~~~~~~p~~~~~~~l~~~l~~a~~~ 301 (363)
T TIGR01891 227 AGGAPNVIPDKASMSGTVRSLDPEVRDQIIDRIERIVEGAAAMYGAKVELNYDRGLPAVTNDPALTQILKEVARH 301 (363)
T ss_pred cCCCCcEECCeeEEEEEEEeCCHHHHHHHHHHHHHHHHHHHHHhCCeEEEEEecCCCCccCCHHHHHHHHHHHHH
Confidence 345889999999999987654322 233444444433322111 1245555443322222224455666666655
Done!