Query psy2492
Match_columns 162
No_of_seqs 159 out of 1185
Neff 5.0
Searched_HMMs 46136
Date Fri Aug 16 17:37:06 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2492.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2492hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0216 PrfA Protein chain rel 100.0 1.9E-42 4E-47 301.2 9.7 116 2-119 161-286 (363)
2 PRK08787 peptide chain release 100.0 1.4E-40 2.9E-45 287.8 12.8 116 2-119 114-239 (313)
3 KOG2726|consensus 100.0 5E-41 1.1E-45 295.9 9.6 121 2-124 185-316 (386)
4 PRK05589 peptide chain release 100.0 4.3E-40 9.4E-45 286.1 12.5 116 2-119 134-259 (325)
5 PRK07342 peptide chain release 100.0 1.1E-39 2.4E-44 284.7 13.7 116 2-119 137-262 (339)
6 PRK06746 peptide chain release 100.0 8.3E-40 1.8E-44 284.3 12.0 116 2-119 135-260 (326)
7 TIGR00019 prfA peptide chain r 100.0 3.7E-39 8.1E-44 283.4 14.7 116 2-119 160-284 (360)
8 PRK08179 prfH peptide chain re 100.0 1.9E-39 4.1E-44 266.1 11.5 116 2-119 50-170 (200)
9 TIGR03072 release_prfH putativ 100.0 3.6E-39 7.9E-44 264.4 12.3 116 2-119 49-169 (200)
10 TIGR00020 prfB peptide chain r 100.0 6.7E-39 1.4E-43 282.2 12.8 116 2-119 173-298 (364)
11 PRK00591 prfA peptide chain re 100.0 4.1E-38 8.9E-43 276.8 15.1 116 2-119 160-284 (359)
12 PRK00578 prfB peptide chain re 100.0 5.4E-38 1.2E-42 276.7 14.7 116 2-119 173-298 (367)
13 COG1186 PrfB Protein chain rel 100.0 1.6E-38 3.4E-43 266.1 9.9 116 2-119 48-173 (239)
14 PRK09256 hypothetical protein; 100.0 6E-31 1.3E-35 205.1 10.2 99 48-146 5-135 (138)
15 PF00472 RF-1: RF-1 domain; I 100.0 2E-29 4.3E-34 189.8 8.5 72 47-118 3-74 (113)
16 KOG3429|consensus 99.9 5.6E-22 1.2E-26 158.3 9.4 96 49-144 33-168 (172)
17 COG1186 PrfB Protein chain rel 55.8 2.4 5.2E-05 36.3 -1.2 50 89-138 168-225 (239)
18 PF10213 MRP-S28: Mitochondria 52.7 1E+02 0.0023 23.6 7.6 47 74-120 23-94 (127)
19 PF15290 Syntaphilin: Golgi-lo 52.1 49 0.0011 29.3 6.2 23 98-120 61-83 (305)
20 smart00322 KH K homology RNA-b 48.0 35 0.00076 21.0 3.6 45 67-114 19-68 (69)
21 PRK13763 putative RNA-processi 44.3 62 0.0013 26.0 5.3 60 67-136 111-172 (180)
22 cd00105 KH-I K homology RNA-bi 43.4 28 0.00062 21.9 2.7 41 67-110 16-63 (64)
23 cd02394 vigilin_like_KH K homo 41.1 39 0.00085 21.6 3.1 40 67-110 16-61 (62)
24 PF02815 MIR: MIR domain; Int 36.1 69 0.0015 25.2 4.4 39 60-98 121-159 (190)
25 COG0828 RpsU Ribosomal protein 35.7 1.4E+02 0.003 20.9 5.2 18 102-119 11-28 (67)
26 PF04149 DUF397: Domain of unk 29.3 1.1E+02 0.0023 20.2 3.7 20 78-97 16-35 (56)
27 PLN02757 sirohydrochlorine fer 28.5 2.9E+02 0.0063 21.6 7.0 45 87-133 14-69 (154)
28 COG0193 Pth Peptidyl-tRNA hydr 26.1 52 0.0011 27.3 2.2 24 47-72 91-114 (190)
29 smart00472 MIR Domain in ryano 24.4 80 0.0017 19.8 2.4 22 76-97 6-27 (57)
30 PRK00270 rpsU 30S ribosomal pr 22.5 2.6E+02 0.0056 19.0 5.0 18 102-119 11-28 (64)
31 PF14048 MBD_C: C-terminal dom 22.0 35 0.00076 25.2 0.4 27 88-114 70-96 (96)
32 TIGR03665 arCOG04150 arCOG0415 22.0 1.7E+02 0.0038 23.1 4.4 60 66-135 104-165 (172)
33 PF13014 KH_3: KH domain 21.5 33 0.00072 20.7 0.1 20 67-86 7-28 (43)
No 1
>COG0216 PrfA Protein chain release factor A [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.9e-42 Score=301.21 Aligned_cols=116 Identities=26% Similarity=0.327 Sum_probs=106.2
Q ss_pred ceeEEEEEeeccchhhhhhhhcccceeEEeecCCCccccc-------cccccCCC---CCCcCCCCeEEEEeecCCCCCc
Q psy2492 2 MIKIVMWPMRDRNLAGIRLLESQVTITRELRNDGYHRNLV-------SNIDIYST---IPKIDEKDIQERFVRGSGPGGQ 71 (162)
Q Consensus 2 ~ik~~~~~i~g~~ayg~~~l~~E~GvHR~~R~~~~~~~~~-------~~v~~~~~---~~~i~~~dl~i~~~RssGpGGQ 71 (162)
|+|.+.+.|.|.++|+ .|+||+|||||||+|.+.+.+. ..|-|..+ .+.|+|+||+|+++||||+|||
T Consensus 161 G~kEii~~I~G~gvys--~LKfEsGvHRVQRVP~TEsqGRIHTStaTVaVlPE~ee~~ei~I~~~DlrIDt~RsSGaGGQ 238 (363)
T COG0216 161 GYKEIIASISGKGVYS--RLKFESGVHRVQRVPATESQGRIHTSAATVAVLPEVEEVEEIEINPKDLRIDTFRSSGAGGQ 238 (363)
T ss_pred CceEEEEEEeccchhh--hhhhccCccceeccccccCCCceeecceeEEeccCCCcccccccChHHceeeeeecCCCCCC
Confidence 6899999999999999 9999999999999999965443 33445433 5899999999999999999999
Q ss_pred ccccccceEEEEecCceeEEEEcCcCCHHHHHHHHHHHHHHHHHHhhc
Q psy2492 72 AVAKTNNCVVLTHIPTGIVIKCHQSRSLSENRKTARELLVAQWDVQVN 119 (162)
Q Consensus 72 ~VNKt~s~V~l~h~Ptgi~v~~~~~RSq~~Nk~~A~~rL~~~L~~~~~ 119 (162)
|||+|+|+|||+|+||||+|.||++|||++||+.||..|+++|+++..
T Consensus 239 hVNtTdSAVRiTHlPTGIvV~cQderSQ~kNk~kAmkvL~ARl~~~~~ 286 (363)
T COG0216 239 HVNTTDSAVRITHLPTGIVVECQDERSQHKNKAKAMKVLRARLYDAER 286 (363)
T ss_pred CcCccchhheeeecCCceEEEecchhhhhhhHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999875
No 2
>PRK08787 peptide chain release factor 2; Provisional
Probab=100.00 E-value=1.4e-40 Score=287.76 Aligned_cols=116 Identities=28% Similarity=0.384 Sum_probs=105.7
Q ss_pred ceeEEEEEeeccchhhhhhhhcccceeEEeecCCCccccc---c--ccc--cCC---CCCCcCCCCeEEEEeecCCCCCc
Q psy2492 2 MIKIVMWPMRDRNLAGIRLLESQVTITRELRNDGYHRNLV---S--NID--IYS---TIPKIDEKDIQERFVRGSGPGGQ 71 (162)
Q Consensus 2 ~ik~~~~~i~g~~ayg~~~l~~E~GvHR~~R~~~~~~~~~---~--~v~--~~~---~~~~i~~~dl~i~~~RssGpGGQ 71 (162)
|||+|++.|+|++||| +|++|+|||||||+||+++.+. + .|+ |.. .++.|++.||+|+|+||||||||
T Consensus 114 Giksa~l~I~G~~ayg--~lk~E~GvHRv~R~sp~~s~~rrhTsfasV~V~P~~~~~~~i~i~~~dl~~~~~RssG~GGQ 191 (313)
T PRK08787 114 GIKSATVRIEGEYAYG--WLKTEIGVHRLVRKSPFDSDNRRHTSFTSVFVSPEVDDNIEIDINPADLRTDVYRSSGAGGQ 191 (313)
T ss_pred eeeEEEEEEecccHHH--HHhhccCeeEEEecCCCCCCCCEEeeeEEEEEecCcCcccccccChhHeEEEEEECCCCCCC
Confidence 7999999999999999 9999999999999999976553 2 232 433 25789999999999999999999
Q ss_pred ccccccceEEEEecCceeEEEEcCcCCHHHHHHHHHHHHHHHHHHhhc
Q psy2492 72 AVAKTNNCVVLTHIPTGIVIKCHQSRSLSENRKTARELLVAQWDVQVN 119 (162)
Q Consensus 72 ~VNKt~s~V~l~h~Ptgi~v~~~~~RSq~~Nk~~A~~rL~~~L~~~~~ 119 (162)
|||||+|+|+|+|+||||+|+||++|||++||+.|+++|+++|.+...
T Consensus 192 ~VNkt~saVri~H~Ptgi~v~~q~eRSQ~~Nk~~A~~~L~~~L~~~~~ 239 (313)
T PRK08787 192 HVNKTESAVRITHIPTNTVVACQTGRSQHQNRDNAMKMLAAKLYELEV 239 (313)
T ss_pred CcCCEeeEEEEEECCCcEEEEECCcccHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999864
No 3
>KOG2726|consensus
Probab=100.00 E-value=5e-41 Score=295.88 Aligned_cols=121 Identities=35% Similarity=0.439 Sum_probs=107.9
Q ss_pred ceeEEEEEeeccchhhhhhhhcccceeEEeecCCCcccc-----ccccc--cC----CCCCCcCCCCeEEEEeecCCCCC
Q psy2492 2 MIKIVMWPMRDRNLAGIRLLESQVTITRELRNDGYHRNL-----VSNID--IY----STIPKIDEKDIQERFVRGSGPGG 70 (162)
Q Consensus 2 ~ik~~~~~i~g~~ayg~~~l~~E~GvHR~~R~~~~~~~~-----~~~v~--~~----~~~~~i~~~dl~i~~~RssGpGG 70 (162)
||++|+++|+|+++|| +|++|.|||||||+|+++..+ ++.|. |. ..++.|+++||+|+|+|||||||
T Consensus 185 Gi~~At~~i~G~~ayg--~l~~E~GvHRv~r~p~~e~~gr~htstasV~ViP~~~~~~~~~~~~~~dl~i~~~R~~G~GG 262 (386)
T KOG2726|consen 185 GIKSATLEIEGESAYG--YLKFEAGVHRVQRVPSTETSGRRHTSTASVAVIPQPGRDEVDVEIDEKDLRIETFRASGPGG 262 (386)
T ss_pred cceeeeeEecccchhh--eeeccCcccceeecCCcccccccccccceEEEeccCCCCccceecCchheeEEecccCCCCc
Confidence 7999999999999999 999999999999999984332 22332 32 34688999999999999999999
Q ss_pred cccccccceEEEEecCceeEEEEcCcCCHHHHHHHHHHHHHHHHHHhhcCCCCH
Q psy2492 71 QAVAKTNNCVVLTHIPTGIVIKCHQSRSLSENRKTARELLVAQWDVQVNGEDSL 124 (162)
Q Consensus 71 Q~VNKt~s~V~l~h~Ptgi~v~~~~~RSq~~Nk~~A~~rL~~~L~~~~~~~ps~ 124 (162)
||||||+|+|+|+|+||||+|+||++|||++||+.|+.+|+++|++....+++.
T Consensus 263 QhvNktdsaVrl~HiPTGIvv~cq~eRSq~~Nr~~A~~~L~akL~~~~~~~~~~ 316 (386)
T KOG2726|consen 263 QHVNKTDSAVRLTHIPTGIVVECQEERSQHKNRALALKRLRAKLAVIYREEKSE 316 (386)
T ss_pred ccccccccceEEEeecCceEEEeecHHhHHhhHHHHHHHHHHHHHHHHHhhhhH
Confidence 999999999999999999999999999999999999999999999999855443
No 4
>PRK05589 peptide chain release factor 2; Provisional
Probab=100.00 E-value=4.3e-40 Score=286.08 Aligned_cols=116 Identities=32% Similarity=0.398 Sum_probs=105.5
Q ss_pred ceeEEEEEeeccchhhhhhhhcccceeEEeecCCCccccc---c----ccccCCC---CCCcCCCCeEEEEeecCCCCCc
Q psy2492 2 MIKIVMWPMRDRNLAGIRLLESQVTITRELRNDGYHRNLV---S----NIDIYST---IPKIDEKDIQERFVRGSGPGGQ 71 (162)
Q Consensus 2 ~ik~~~~~i~g~~ayg~~~l~~E~GvHR~~R~~~~~~~~~---~----~v~~~~~---~~~i~~~dl~i~~~RssGpGGQ 71 (162)
||+||++.|+|+++|| +|++|+|||||||+||+.+.+. + .|-|.+. ++.|+++||+|+|+||||||||
T Consensus 134 g~ks~~~~i~G~~ay~--~lk~E~GvHrv~r~s~~~~~~rr~ts~a~V~VlP~~~~~~~~~i~~~dl~~~~~rssG~GGQ 211 (325)
T PRK05589 134 GIKSVTLKITGEFAYG--YLKAEKGIHRLVRISPFNANGKRQTSFASVEVLPELTDDQDIEIRSEDLKIDTYRAGGAGGQ 211 (325)
T ss_pred ceEEEEEEEeccCHHH--HHhhccceEEEEEcCCCCCCCCeEeeeEEEEEecCcCccccccCCchheEEEEeeCCCCCCC
Confidence 7999999999999999 9999999999999999976543 2 2224432 5799999999999999999999
Q ss_pred ccccccceEEEEecCceeEEEEcCcCCHHHHHHHHHHHHHHHHHHhhc
Q psy2492 72 AVAKTNNCVVLTHIPTGIVIKCHQSRSLSENRKTARELLVAQWDVQVN 119 (162)
Q Consensus 72 ~VNKt~s~V~l~h~Ptgi~v~~~~~RSq~~Nk~~A~~rL~~~L~~~~~ 119 (162)
|||||+|+|+|+|+||||+|+||++|||++||+.|+.+|+++|++...
T Consensus 212 ~VNkt~saVrl~H~ptgi~v~~q~eRSQ~~Nk~~A~~~L~~kL~~~~~ 259 (325)
T PRK05589 212 HVNKTESAVRITHIPTGIVVQCQNERSQHSNKETAMKMLKSKLVELKE 259 (325)
T ss_pred cccceeeEEEEEECCCCEEEEECCccCHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999864
No 5
>PRK07342 peptide chain release factor 2; Provisional
Probab=100.00 E-value=1.1e-39 Score=284.70 Aligned_cols=116 Identities=33% Similarity=0.425 Sum_probs=105.6
Q ss_pred ceeEEEEEeeccchhhhhhhhcccceeEEeecCCCccccc---c----ccccCCC---CCCcCCCCeEEEEeecCCCCCc
Q psy2492 2 MIKIVMWPMRDRNLAGIRLLESQVTITRELRNDGYHRNLV---S----NIDIYST---IPKIDEKDIQERFVRGSGPGGQ 71 (162)
Q Consensus 2 ~ik~~~~~i~g~~ayg~~~l~~E~GvHR~~R~~~~~~~~~---~----~v~~~~~---~~~i~~~dl~i~~~RssGpGGQ 71 (162)
||++|++.|+|++||| +|++|+|||||||+||+.+.+. + .|-|.+. ++.|+++||+|+|+||||||||
T Consensus 137 g~ksa~l~i~G~~ay~--~lk~E~GvHrv~rvsp~~~~~rrhTs~a~V~VlP~~~~~~~~~i~~~dl~~~~~RssG~GGQ 214 (339)
T PRK07342 137 GIKSATILVKGHNAYG--WLKTESGVHRLVRISPYDSNARRHTSFASIWVYPVIDDNIEVDVNESDVRIDTYRSSGAGGQ 214 (339)
T ss_pred ceEEEEEEEeccCHHH--HHhhccceeEEEecCCCCCCCCeEeEEEEEEEEcCCCcccccccCcccEEEEEEECCCCCCC
Confidence 7999999999999999 9999999999999999976553 2 2224332 4789999999999999999999
Q ss_pred ccccccceEEEEecCceeEEEEcCcCCHHHHHHHHHHHHHHHHHHhhc
Q psy2492 72 AVAKTNNCVVLTHIPTGIVIKCHQSRSLSENRKTARELLVAQWDVQVN 119 (162)
Q Consensus 72 ~VNKt~s~V~l~h~Ptgi~v~~~~~RSq~~Nk~~A~~rL~~~L~~~~~ 119 (162)
|||||+|+|+|+|+||||+|+|+++|||++||+.|+++|+++|++...
T Consensus 215 ~VNkt~saVrl~H~ptgi~v~~~~eRSQ~~Nk~~A~~~L~~~L~~~~~ 262 (339)
T PRK07342 215 HVNTTDSAVRITHIPTGIVVQCQQERSQHKNRAKAWSMLRARLYEEEL 262 (339)
T ss_pred CccceeeeEEEEEcCCcEEEEECCcccHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999998874
No 6
>PRK06746 peptide chain release factor 2; Provisional
Probab=100.00 E-value=8.3e-40 Score=284.32 Aligned_cols=116 Identities=28% Similarity=0.339 Sum_probs=105.8
Q ss_pred ceeEEEEEeeccchhhhhhhhcccceeEEeecCCCccccc---c--cc--ccCC---CCCCcCCCCeEEEEeecCCCCCc
Q psy2492 2 MIKIVMWPMRDRNLAGIRLLESQVTITRELRNDGYHRNLV---S--NI--DIYS---TIPKIDEKDIQERFVRGSGPGGQ 71 (162)
Q Consensus 2 ~ik~~~~~i~g~~ayg~~~l~~E~GvHR~~R~~~~~~~~~---~--~v--~~~~---~~~~i~~~dl~i~~~RssGpGGQ 71 (162)
|||+|++.|+|+++|| +|++|+|||||||+||+++.+. + .| .|.. .++.|+++||+|+|+||||||||
T Consensus 135 g~ksa~l~i~G~~ay~--~lk~E~GvHrv~Rvsp~~s~~rrhTsfa~V~v~P~~~~~~~i~i~~~dl~~~~~rssG~GGQ 212 (326)
T PRK06746 135 GIKSVTLLIKGHNAYG--YLKAEKGVHRLVRISPFDSSGRRHTSFVSCEVVPEFNDEVEIEVRTEDLKIDTYRASGAGGQ 212 (326)
T ss_pred ceEEEEEEEeccCHHH--HHhhccceEEEEecCCCCCCCCeEeeEEEEEEecCcCCccccccChHHeEEEEEeCCCCCCC
Confidence 7999999999999999 9999999999999999976553 1 22 2332 35889999999999999999999
Q ss_pred ccccccceEEEEecCceeEEEEcCcCCHHHHHHHHHHHHHHHHHHhhc
Q psy2492 72 AVAKTNNCVVLTHIPTGIVIKCHQSRSLSENRKTARELLVAQWDVQVN 119 (162)
Q Consensus 72 ~VNKt~s~V~l~h~Ptgi~v~~~~~RSq~~Nk~~A~~rL~~~L~~~~~ 119 (162)
|||||+|+|+|+|+||||+|.||++|||++||+.|+.+|+++|++...
T Consensus 213 ~vNkt~saVrl~h~ptgi~v~~q~~RSQ~~Nk~~A~~~L~akL~~~~~ 260 (326)
T PRK06746 213 HVNTTDSAVRITHTPTNTVVTCQSERSQIKNREHAMKMLKAKLYQKKL 260 (326)
T ss_pred CccceeeEEEEEEeCCeEEEEECCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999875
No 7
>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=100.00 E-value=3.7e-39 Score=283.42 Aligned_cols=116 Identities=27% Similarity=0.322 Sum_probs=105.2
Q ss_pred ceeEEEEEeeccchhhhhhhhcccceeEEeecCCCccccc---c--cc--ccCC--CCCCcCCCCeEEEEeecCCCCCcc
Q psy2492 2 MIKIVMWPMRDRNLAGIRLLESQVTITRELRNDGYHRNLV---S--NI--DIYS--TIPKIDEKDIQERFVRGSGPGGQA 72 (162)
Q Consensus 2 ~ik~~~~~i~g~~ayg~~~l~~E~GvHR~~R~~~~~~~~~---~--~v--~~~~--~~~~i~~~dl~i~~~RssGpGGQ~ 72 (162)
|||||++.|+|+++|| +|++|.|||||||+|++++... + .| -|.+ ..+.|+++||+|+|+|||||||||
T Consensus 160 g~ksa~l~i~G~~ay~--~lk~E~GvHrv~Rvp~~~s~~R~hTsfa~V~v~P~~~~~~~~i~~~dl~~~~~RssG~GGQ~ 237 (360)
T TIGR00019 160 GYKEVIAEIKGDGVYS--RLKFESGVHRVQRVPVTESQGRIHTSAATVAVMPELEEVEVDINPADLRIDTFRSSGAGGQH 237 (360)
T ss_pred cceEEEEEEecccHHH--HHhhcCeeEEEECCCCCCCCCCeecceeEEEEEcCCCccccccCcccEEEEEEECCCCCCCC
Confidence 7999999999999999 9999999999999999966443 2 22 2433 247899999999999999999999
Q ss_pred cccccceEEEEecCceeEEEEcCcCCHHHHHHHHHHHHHHHHHHhhc
Q psy2492 73 VAKTNNCVVLTHIPTGIVIKCHQSRSLSENRKTARELLVAQWDVQVN 119 (162)
Q Consensus 73 VNKt~s~V~l~h~Ptgi~v~~~~~RSq~~Nk~~A~~rL~~~L~~~~~ 119 (162)
||||+|+|+|+|+||||+|.||++|||++||+.|+++|+++|.....
T Consensus 238 VNkt~SaVrl~h~ptgi~V~~~~eRSQ~~Nk~~A~~~L~~~L~~~~~ 284 (360)
T TIGR00019 238 VNTTDSAVRITHLPTGIVVECQDERSQHKNKDKAMKVLRARLYEAEQ 284 (360)
T ss_pred cCceeeeEEEEECCCcEEEEECCccCHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999874
No 8
>PRK08179 prfH peptide chain release factor-like protein; Reviewed
Probab=100.00 E-value=1.9e-39 Score=266.10 Aligned_cols=116 Identities=27% Similarity=0.362 Sum_probs=107.1
Q ss_pred ceeEEEEEeeccchhhhhhhhcccceeEEeecCCCccccc-----cccccCCCCCCcCCCCeEEEEeecCCCCCcccccc
Q psy2492 2 MIKIVMWPMRDRNLAGIRLLESQVTITRELRNDGYHRNLV-----SNIDIYSTIPKIDEKDIQERFVRGSGPGGQAVAKT 76 (162)
Q Consensus 2 ~ik~~~~~i~g~~ayg~~~l~~E~GvHR~~R~~~~~~~~~-----~~v~~~~~~~~i~~~dl~i~~~RssGpGGQ~VNKt 76 (162)
|||+|++.|+|+++|| +|++|.|+|++++.||++..+. +.|++.+.++.|+++||+++|+|||||||||||||
T Consensus 50 g~ksa~~~i~G~~a~~--~l~~~~G~~~~V~~sp~~~~~~R~~s~~~V~v~~~~~~i~~~dl~~~~~RssGpGGQ~VNkt 127 (200)
T PRK08179 50 TLRSALVSLDGDNAEA--LAESWCGTIQWICPSPYRPHHGRKNWFVGIGRFSADEEEQSDEIRFETLRSSGPGGQHVNKT 127 (200)
T ss_pred ceEEEEEEEEccCHHH--HhhcccCeeEEEecCCCCCCCCceEEEEEEEEeCCcCccCHHHeEEEEEEccCCcccccccc
Confidence 5999999999999999 9999999999999999865443 34566677889999999999999999999999999
Q ss_pred cceEEEEecCceeEEEEcCcCCHHHHHHHHHHHHHHHHHHhhc
Q psy2492 77 NNCVVLTHIPTGIVIKCHQSRSLSENRKTARELLVAQWDVQVN 119 (162)
Q Consensus 77 ~s~V~l~h~Ptgi~v~~~~~RSq~~Nk~~A~~rL~~~L~~~~~ 119 (162)
+|+|+|+|+||||+|+||++|||++||+.|+++|+++|.+...
T Consensus 128 ~saVrl~h~ptgi~v~~~~~RSQ~~Nk~~A~~~L~~~L~~~~~ 170 (200)
T PRK08179 128 DSAVRATHLASGISVKVQSERSQHANKRLARLLIAWKLEQQQQ 170 (200)
T ss_pred cceEEEEEcCCcEEEEECCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999998864
No 9
>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=100.00 E-value=3.6e-39 Score=264.44 Aligned_cols=116 Identities=24% Similarity=0.322 Sum_probs=106.9
Q ss_pred ceeEEEEEeeccchhhhhhhhcccceeEEeecCCCccccc-----cccccCCCCCCcCCCCeEEEEeecCCCCCcccccc
Q psy2492 2 MIKIVMWPMRDRNLAGIRLLESQVTITRELRNDGYHRNLV-----SNIDIYSTIPKIDEKDIQERFVRGSGPGGQAVAKT 76 (162)
Q Consensus 2 ~ik~~~~~i~g~~ayg~~~l~~E~GvHR~~R~~~~~~~~~-----~~v~~~~~~~~i~~~dl~i~~~RssGpGGQ~VNKt 76 (162)
||++|++.|+|+++|| +|..|.|+|++++.||+...+. +.|++.+.++.|+++||+++|+|||||||||||||
T Consensus 49 g~ksa~~~i~G~~ay~--~l~~~~G~h~~v~~sp~r~~~~R~ts~~~V~v~~~~~~i~~~dl~~~~~RssGpGGQ~vNkt 126 (200)
T TIGR03072 49 TLRSALVSLDGEAAAA--LADRWEGTLLWICPSPYRPHHRRKNWFIGVQRFSASEEATEDEIRFETLRSSGPGGQHVNKT 126 (200)
T ss_pred ceEEEEEEEEccCHHH--HhhcccceEEEEEcCCCCCCCCeeEEEEEEEEecCccccChhheEEEEEECCCCCccccccc
Confidence 5999999999999999 9999999999999999865443 34555667788999999999999999999999999
Q ss_pred cceEEEEecCceeEEEEcCcCCHHHHHHHHHHHHHHHHHHhhc
Q psy2492 77 NNCVVLTHIPTGIVIKCHQSRSLSENRKTARELLVAQWDVQVN 119 (162)
Q Consensus 77 ~s~V~l~h~Ptgi~v~~~~~RSq~~Nk~~A~~rL~~~L~~~~~ 119 (162)
+|+|+|+|+||||+|+||++|||++||++|+++|+++|.+...
T Consensus 127 ~saVrl~h~ptgi~v~~~~~RSQ~~Nk~~A~~~L~~~l~~~~~ 169 (200)
T TIGR03072 127 ESAVRATHLASGISVKVQSERSQHANKRLATLLLAVRLADLQQ 169 (200)
T ss_pred ceeEEEEECCCcEEEEECCccCHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999998864
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=100.00 E-value=6.7e-39 Score=282.20 Aligned_cols=116 Identities=32% Similarity=0.394 Sum_probs=105.7
Q ss_pred ceeEEEEEeeccchhhhhhhhcccceeEEeecCCCccccc---c--cc--ccCC---CCCCcCCCCeEEEEeecCCCCCc
Q psy2492 2 MIKIVMWPMRDRNLAGIRLLESQVTITRELRNDGYHRNLV---S--NI--DIYS---TIPKIDEKDIQERFVRGSGPGGQ 71 (162)
Q Consensus 2 ~ik~~~~~i~g~~ayg~~~l~~E~GvHR~~R~~~~~~~~~---~--~v--~~~~---~~~~i~~~dl~i~~~RssGpGGQ 71 (162)
||++|++.|+|+++|| +|++|+|||||||+||+.+.+. + .| -|.+ .++.|++.||+|+|+||||||||
T Consensus 173 g~ks~~~~i~G~~ay~--~lk~E~GvHrv~rvs~~~~~~rrhts~a~V~vlP~~~~~~~~~i~~~d~~~~~~rssG~GGQ 250 (364)
T TIGR00020 173 GIKSVTILIKGPYAYG--YLKSEQGVHRLVRISPFDANGRRHTSFASVFVMPEVDDDIDIEIKPEDLRIDTYRASGAGGQ 250 (364)
T ss_pred ceEEEEEEEeccCHHH--HHhhccceEEEEecCCCCCCCCeEeeeEEEEEecCCCcccceecccccEEEEEeeCCCCCCc
Confidence 7999999999999999 9999999999999999976553 2 22 2433 25799999999999999999999
Q ss_pred ccccccceEEEEecCceeEEEEcCcCCHHHHHHHHHHHHHHHHHHhhc
Q psy2492 72 AVAKTNNCVVLTHIPTGIVIKCHQSRSLSENRKTARELLVAQWDVQVN 119 (162)
Q Consensus 72 ~VNKt~s~V~l~h~Ptgi~v~~~~~RSq~~Nk~~A~~rL~~~L~~~~~ 119 (162)
|||||+|+|+|+|+||||+|.||++|||++||+.|+.+|+++|++...
T Consensus 251 ~VNkt~saVri~H~ptgi~v~~q~~RSQ~~Nk~~A~~~L~~kL~~~~~ 298 (364)
T TIGR00020 251 HVNKTDSAVRITHIPTGIVVQCQNDRSQHKNKDSAMKVLKAKLYELEM 298 (364)
T ss_pred cccccceEEEEEECCCcEEEEECCccCHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999874
No 11
>PRK00591 prfA peptide chain release factor 1; Validated
Probab=100.00 E-value=4.1e-38 Score=276.78 Aligned_cols=116 Identities=28% Similarity=0.347 Sum_probs=105.1
Q ss_pred ceeEEEEEeeccchhhhhhhhcccceeEEeecCCCccccc---c--ccc--cCC--CCCCcCCCCeEEEEeecCCCCCcc
Q psy2492 2 MIKIVMWPMRDRNLAGIRLLESQVTITRELRNDGYHRNLV---S--NID--IYS--TIPKIDEKDIQERFVRGSGPGGQA 72 (162)
Q Consensus 2 ~ik~~~~~i~g~~ayg~~~l~~E~GvHR~~R~~~~~~~~~---~--~v~--~~~--~~~~i~~~dl~i~~~RssGpGGQ~ 72 (162)
||++|++.|+|++||| +|++|.|||||||+|++.+... + .|+ |.+ .++.|+++||+|+|+|||||||||
T Consensus 160 g~ksa~l~i~G~~ay~--~Lk~E~GvHrv~R~p~~~s~~R~~tsfa~V~v~P~~~~~~~~i~~~dl~~~~~RssG~GGQ~ 237 (359)
T PRK00591 160 GYKEVIAEISGDGVYS--KLKFESGVHRVQRVPATESQGRIHTSAATVAVLPEAEEVEVEINPKDLRIDTFRSSGAGGQH 237 (359)
T ss_pred ceeEEEEEEecccHHH--HHhhcCeeEEEEeeCCCCCCCceecceEEEEEEcCCCccccccCcccEEEEEEECCCCCCCC
Confidence 7999999999999999 9999999999999999965432 1 232 433 247899999999999999999999
Q ss_pred cccccceEEEEecCceeEEEEcCcCCHHHHHHHHHHHHHHHHHHhhc
Q psy2492 73 VAKTNNCVVLTHIPTGIVIKCHQSRSLSENRKTARELLVAQWDVQVN 119 (162)
Q Consensus 73 VNKt~s~V~l~h~Ptgi~v~~~~~RSq~~Nk~~A~~rL~~~L~~~~~ 119 (162)
||||+|+|+|+|+||||+|.|+++|||++||+.|+++|+++|.....
T Consensus 238 VNkt~saVrl~H~ptGi~v~~~~eRSQ~~Nk~~Al~~L~~~L~~~~~ 284 (359)
T PRK00591 238 VNTTDSAVRITHLPTGIVVECQDERSQHKNKAKAMKVLRARLYDAER 284 (359)
T ss_pred ccceeeeEEEEECCCcEEEEECCcCCHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999875
No 12
>PRK00578 prfB peptide chain release factor 2; Validated
Probab=100.00 E-value=5.4e-38 Score=276.70 Aligned_cols=116 Identities=31% Similarity=0.413 Sum_probs=105.6
Q ss_pred ceeEEEEEeeccchhhhhhhhcccceeEEeecCCCccccc---c----ccccCCC---CCCcCCCCeEEEEeecCCCCCc
Q psy2492 2 MIKIVMWPMRDRNLAGIRLLESQVTITRELRNDGYHRNLV---S----NIDIYST---IPKIDEKDIQERFVRGSGPGGQ 71 (162)
Q Consensus 2 ~ik~~~~~i~g~~ayg~~~l~~E~GvHR~~R~~~~~~~~~---~----~v~~~~~---~~~i~~~dl~i~~~RssGpGGQ 71 (162)
|+++|++.|+|+++|| +|++|+|||||||+||+.+.+. + .|-|.+. ++.|+++||+++|+||||||||
T Consensus 173 g~ks~~~~i~G~~a~~--~lk~E~GvHrvqrvs~~~~~~r~hts~~~V~vlP~~~~~~~~~i~~~dl~~~~~rssGpGGQ 250 (367)
T PRK00578 173 GIKSATFKIKGPYAYG--YLKSETGVHRLVRISPFDSAGRRHTSFASVEVYPEVDDTIEIEINPKDLRIDTYRSSGAGGQ 250 (367)
T ss_pred CeeEEEEEEeccCHHH--HHhhccceEEEEecCCCCCCCceecceeeEEecCCCCCccccccChhhEEEEEeeCCCCCCC
Confidence 7999999999999999 9999999999999999976553 1 2234433 5789999999999999999999
Q ss_pred ccccccceEEEEecCceeEEEEcCcCCHHHHHHHHHHHHHHHHHHhhc
Q psy2492 72 AVAKTNNCVVLTHIPTGIVIKCHQSRSLSENRKTARELLVAQWDVQVN 119 (162)
Q Consensus 72 ~VNKt~s~V~l~h~Ptgi~v~~~~~RSq~~Nk~~A~~rL~~~L~~~~~ 119 (162)
|||||+|+|+|+|+||||+|.|+++|||++||+.|+.+|+++|.+...
T Consensus 251 ~vNkt~saVrl~h~ptgi~v~~~~~RSQ~~Nk~~A~~~L~~kL~~~~~ 298 (367)
T PRK00578 251 HVNKTDSAVRITHIPTGIVVQCQNERSQHQNKASAMKMLKAKLYELEL 298 (367)
T ss_pred cccceeeEEEEEECCCcEEEEECCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999875
No 13
>COG1186 PrfB Protein chain release factor B [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.6e-38 Score=266.07 Aligned_cols=116 Identities=31% Similarity=0.430 Sum_probs=106.2
Q ss_pred ceeEEEEEeeccchhhhhhhhcccceeEEeecCCCcccccc-------ccccC---CCCCCcCCCCeEEEEeecCCCCCc
Q psy2492 2 MIKIVMWPMRDRNLAGIRLLESQVTITRELRNDGYHRNLVS-------NIDIY---STIPKIDEKDIQERFVRGSGPGGQ 71 (162)
Q Consensus 2 ~ik~~~~~i~g~~ayg~~~l~~E~GvHR~~R~~~~~~~~~~-------~v~~~---~~~~~i~~~dl~i~~~RssGpGGQ 71 (162)
|||||++.|+|++||| +|+.|.||||++|+|||++.... .+.|. ...+.|+++||+|+|+||||||||
T Consensus 48 g~ks~~~~~~g~~a~g--~~~~e~g~hrlvr~Spf~~~~~R~tsf~~v~v~p~~~~~i~i~I~~~dl~idt~RASGaGGQ 125 (239)
T COG1186 48 GIKSATLKIKGENAYG--YLKTETGVHRLVRISPFDSNGRRHTSFASVEVFPELDISIEIEIPDDDLRIDTYRASGAGGQ 125 (239)
T ss_pred ccceEEEEEechHHHH--HHHhhcceeEEEeecCCCcCcccccceeeeeecCCCCcccceecCccceEEEEEEcCCCCCC
Confidence 7999999999999999 99999999999999999775542 23343 347889999999999999999999
Q ss_pred ccccccceEEEEecCceeEEEEcCcCCHHHHHHHHHHHHHHHHHHhhc
Q psy2492 72 AVAKTNNCVVLTHIPTGIVIKCHQSRSLSENRKTARELLVAQWDVQVN 119 (162)
Q Consensus 72 ~VNKt~s~V~l~h~Ptgi~v~~~~~RSq~~Nk~~A~~rL~~~L~~~~~ 119 (162)
|||||+|||+|+|+||||+|.||.+|||+.|++.|+..|+.+|+....
T Consensus 126 hVNKt~SAVrlth~ptgivv~cq~eRSq~~n~~~a~~~l~~kL~~~~~ 173 (239)
T COG1186 126 HVNKTDSAVRLTHLPTGIVVLCQNERSQHLNKALARKMLKGKLYILAQ 173 (239)
T ss_pred ccccccccEEEEEcCCCCEecCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999988765
No 14
>PRK09256 hypothetical protein; Provisional
Probab=99.97 E-value=6e-31 Score=205.07 Aligned_cols=99 Identities=34% Similarity=0.507 Sum_probs=90.8
Q ss_pred CCCCCcCCCCeEEEEeecCCCCCcccccccceEEEEe------cC-----------------ce-eEEEEcCcCCHHHHH
Q psy2492 48 STIPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTH------IP-----------------TG-IVIKCHQSRSLSENR 103 (162)
Q Consensus 48 ~~~~~i~~~dl~i~~~RssGpGGQ~VNKt~s~V~l~h------~P-----------------tg-i~v~~~~~RSq~~Nk 103 (162)
..++.|+++||+++|+|||||||||||||+|+|+|+| +| +| |+|+|+++|||++|+
T Consensus 5 ~~~~~i~~~~l~~~~~RSSGPGGQ~VNKt~SkV~l~~~~~~~~lp~~~~~~l~~~~~~r~~~~g~l~i~~~~~RSQ~~Nr 84 (138)
T PRK09256 5 TRRLVIPENELEWRFIRASGPGGQNVNKVSTAVELRFDIAASSLPEFYKERLLALAGHRITKDGVIVIKAQEFRSQERNR 84 (138)
T ss_pred CccCccCHHHeEEEEEEcCCCCcccccccceeeEEEechhhccCCHHHHHHHHHHhcCcccCCCcEEEEECCcCCHHHHH
Confidence 3568899999999999999999999999999999996 66 24 999999999999999
Q ss_pred HHHHHHHHHHHHHhhcC-------CCCHHHHHHHHHHHHHhh-HHHHhhhh
Q psy2492 104 KTARELLVAQWDVQVNG-------EDSLNAQIRRIDEKRRAT-QEQKKRKL 146 (162)
Q Consensus 104 ~~A~~rL~~~L~~~~~~-------~ps~~a~~kRl~~Kk~~~-~K~~r~k~ 146 (162)
++|+++|.++|..++.. +|+++++++||+.|+++| +|++|++.
T Consensus 85 ~~al~kL~~~i~~~~~~p~~r~~tk~~~~~~~rRl~~Kk~~S~~K~~R~~~ 135 (138)
T PRK09256 85 EDALERLVALIREALKPPKKRRATKPTRGSKERRLESKKQRGEVKALRGKV 135 (138)
T ss_pred HHHHHHHHHHHHHHhhccccccCCcccHHHHHHHHHHHHHHhHHHHhhCCC
Confidence 99999999999998865 589999999999999999 99988664
No 15
>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=99.96 E-value=2e-29 Score=189.77 Aligned_cols=72 Identities=50% Similarity=0.687 Sum_probs=68.4
Q ss_pred CCCCCCcCCCCeEEEEeecCCCCCcccccccceEEEEecCceeEEEEcCcCCHHHHHHHHHHHHHHHHHHhh
Q psy2492 47 YSTIPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTGIVIKCHQSRSLSENRKTARELLVAQWDVQV 118 (162)
Q Consensus 47 ~~~~~~i~~~dl~i~~~RssGpGGQ~VNKt~s~V~l~h~Ptgi~v~~~~~RSq~~Nk~~A~~rL~~~L~~~~ 118 (162)
....+.|+++||+|+|+|||||||||||||+|+|+|+|+||||+|+|+++|||+.|+++|+++|.++|..+.
T Consensus 3 ~~~~~~i~~~dl~~~~~RssGpGGQ~VNk~~s~V~l~h~ptgi~v~~~~~Rsq~~Nr~~A~~~L~~~l~~~~ 74 (113)
T PF00472_consen 3 KEKEIDIPEKDLEISFSRSSGPGGQNVNKTNSKVRLRHIPTGIVVKCQESRSQHQNREDALEKLREKLDEAY 74 (113)
T ss_dssp TSSSSCC-GGGEEEEEEESSSSSSCHHHSSSEEEEEEETTTTEEEEEESSSSHHHHHHHHHHHHHHHHHHHH
T ss_pred cccccccCHHHeEEEEEecCCCCCCcccccCCEEEEEEecccEEEEEcccCCHHHHHHHHHHHHHHHHHHHH
Confidence 345789999999999999999999999999999999999999999999999999999999999999999987
No 16
>KOG3429|consensus
Probab=99.87 E-value=5.6e-22 Score=158.35 Aligned_cols=96 Identities=28% Similarity=0.369 Sum_probs=81.8
Q ss_pred CCCCcCCCCeEEEEeecCCCCCcccccccceEEEEe-------cC------------------ceeEEEEcCcCCHHHHH
Q psy2492 49 TIPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTH-------IP------------------TGIVIKCHQSRSLSENR 103 (162)
Q Consensus 49 ~~~~i~~~dl~i~~~RssGpGGQ~VNKt~s~V~l~h-------~P------------------tgi~v~~~~~RSq~~Nk 103 (162)
....||-+.|+++|.||||||||||||++|+|.|++ || ..|++.++.+|||+.|.
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 346789999999999999999999999999999997 44 25999999999999999
Q ss_pred HHHHHHHHHHHHHhhcC---CCCHH-----------HHHHHHHHHHHhh-HHHHhh
Q psy2492 104 KTARELLVAQWDVQVNG---EDSLN-----------AQIRRIDEKRRAT-QEQKKR 144 (162)
Q Consensus 104 ~~A~~rL~~~L~~~~~~---~ps~~-----------a~~kRl~~Kk~~~-~K~~r~ 144 (162)
++||++|.++|..++.. +||.+ +..+||..||..+ +|.+|+
T Consensus 113 aDcleKlr~~I~~~~~~~~~~~teE~~kk~r~~~e~an~eRL~~Kk~~s~kK~~Rr 168 (172)
T KOG3429|consen 113 ADCLEKLRDIIRAAEQTPPVDPTEETIKKIRIRKEKANRERLQEKKVHSDKKTSRR 168 (172)
T ss_pred HHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhhHHhhhhc
Confidence 99999999999999875 34432 4467888888888 777664
No 17
>COG1186 PrfB Protein chain release factor B [Translation, ribosomal structure and biogenesis]
Probab=55.76 E-value=2.4 Score=36.31 Aligned_cols=50 Identities=22% Similarity=0.139 Sum_probs=39.8
Q ss_pred eEEEEcCcCCHHHHHHHHHHHHHHHHHHhhcC--------CCCHHHHHHHHHHHHHhh
Q psy2492 89 IVIKCHQSRSLSENRKTARELLVAQWDVQVNG--------EDSLNAQIRRIDEKRRAT 138 (162)
Q Consensus 89 i~v~~~~~RSq~~Nk~~A~~rL~~~L~~~~~~--------~ps~~a~~kRl~~Kk~~~ 138 (162)
|.+..+++|+|..|++.|+.++.+.+.++... +|.+.+.+.++..+-..+
T Consensus 168 L~~~~~~~Rsqe~n~~~a~~k~i~wg~qirsyv~~p~~~vKd~Rt~~E~~~~~~v~dg 225 (239)
T COG1186 168 LYILAQEKRSQEKNRERALKKLIGWGNQIRSYVLDPYQPTKDLRTGVERRNKSKVLDG 225 (239)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhHHHHHhccccCCCccccccccccceeeccHHHhhhh
Confidence 88899999999999999999999999998654 355556666665555555
No 18
>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=52.68 E-value=1e+02 Score=23.64 Aligned_cols=47 Identities=21% Similarity=0.116 Sum_probs=40.3
Q ss_pred ccccceEEEEecC------------------------c-eeEEEEcCcCCHHHHHHHHHHHHHHHHHHhhcC
Q psy2492 74 AKTNNCVVLTHIP------------------------T-GIVIKCHQSRSLSENRKTARELLVAQWDVQVNG 120 (162)
Q Consensus 74 NKt~s~V~l~h~P------------------------t-gi~v~~~~~RSq~~Nk~~A~~rL~~~L~~~~~~ 120 (162)
|..+.+|.|.... + -|.+.|...-++.+|+.-+...|..+|.++...
T Consensus 23 ~p~~rkV~l~v~l~dL~L~~~a~~Kl~~LaG~Ryd~~~d~l~i~sdr~~~~~qN~~~l~~~l~~L~~EA~~~ 94 (127)
T PF10213_consen 23 HPANRKVVLQVKLSDLGLSEKARHKLKLLAGPRYDPETDILKISSDRFPTRAQNKKYLSDLLTRLIHEAKDL 94 (127)
T ss_pred CCccCEEEEEEEHHhcCCCHHHHHHHHHHhhcccCCCCCEEEEecccCCCHHHHHHHHHHHHHHHHHHHhhc
Confidence 6678899988732 2 389999999999999999999999999999874
No 19
>PF15290 Syntaphilin: Golgi-localised syntaxin-1-binding clamp
Probab=52.09 E-value=49 Score=29.33 Aligned_cols=23 Identities=13% Similarity=0.078 Sum_probs=18.9
Q ss_pred CHHHHHHHHHHHHHHHHHHhhcC
Q psy2492 98 SLSENRKTARELLVAQWDVQVNG 120 (162)
Q Consensus 98 Sq~~Nk~~A~~rL~~~L~~~~~~ 120 (162)
+.++-|+-|++.|+++|.+..+.
T Consensus 61 TPLQQKEV~iRHLkakLkes~~~ 83 (305)
T PF15290_consen 61 TPLQQKEVCIRHLKAKLKESENR 83 (305)
T ss_pred ChHHHHHHHHHHHHHHHHHHHHH
Confidence 56788999999999999887653
No 20
>smart00322 KH K homology RNA-binding domain.
Probab=48.00 E-value=35 Score=20.95 Aligned_cols=45 Identities=27% Similarity=0.389 Sum_probs=28.8
Q ss_pred CCCCccccccc--ceEEEEecCce---eEEEEcCcCCHHHHHHHHHHHHHHHH
Q psy2492 67 GPGGQAVAKTN--NCVVLTHIPTG---IVIKCHQSRSLSENRKTARELLVAQW 114 (162)
Q Consensus 67 GpGGQ~VNKt~--s~V~l~h~Ptg---i~v~~~~~RSq~~Nk~~A~~rL~~~L 114 (162)
|++|.+++... +.+.+...+.+ -++....+ ..|...|...|...+
T Consensus 19 G~~G~~i~~i~~~~~~~i~~~~~~~~~~~v~i~g~---~~~v~~a~~~i~~~~ 68 (69)
T smart00322 19 GKGGSTIKKIEEETGVKIDIPEDGSEERVVEITGP---PENVEKAAELILEIL 68 (69)
T ss_pred CCCchHHHHHHHHHCCEEEECCCCCCccEEEEEcC---HHHHHHHHHHHHHHh
Confidence 88898887443 45555554432 44555544 578888888887765
No 21
>PRK13763 putative RNA-processing protein; Provisional
Probab=44.27 E-value=62 Score=25.95 Aligned_cols=60 Identities=18% Similarity=0.209 Sum_probs=38.8
Q ss_pred CCCCccccccc--ceEEEEecCceeEEEEcCcCCHHHHHHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHH
Q psy2492 67 GPGGQAVAKTN--NCVVLTHIPTGIVIKCHQSRSLSENRKTARELLVAQWDVQVNGEDSLNAQIRRIDEKRR 136 (162)
Q Consensus 67 GpGGQ~VNKt~--s~V~l~h~Ptgi~v~~~~~RSq~~Nk~~A~~rL~~~L~~~~~~~ps~~a~~kRl~~Kk~ 136 (162)
|+||+.....+ |.|+|......+.+ .. ...|.+.|.+.+..++.... | ....+.|+...+
T Consensus 111 G~~G~~~k~ie~~t~~~i~i~~~~v~i--~G---~~~~~~~A~~~I~~li~g~~---~--~~~~~~l~~~~~ 172 (180)
T PRK13763 111 GEGGKTRRIIEELTGVDISVYGKTVAI--IG---DPEQVEIAREAIEMLIEGAP---H--GTVYKFLERKKR 172 (180)
T ss_pred CCCcHHHHHHHHHHCcEEEEcCCEEEE--Ee---CHHHHHHHHHHHHHHHcCCC---c--HHHHHHHHHHHH
Confidence 89999988554 77777765444443 33 67789999998888773332 2 344666665544
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=43.39 E-value=28 Score=21.95 Aligned_cols=41 Identities=17% Similarity=0.328 Sum_probs=26.6
Q ss_pred CCCCccccccc--ceEEEEecCc-----eeEEEEcCcCCHHHHHHHHHHHH
Q psy2492 67 GPGGQAVAKTN--NCVVLTHIPT-----GIVIKCHQSRSLSENRKTARELL 110 (162)
Q Consensus 67 GpGGQ~VNKt~--s~V~l~h~Pt-----gi~v~~~~~RSq~~Nk~~A~~rL 110 (162)
|+||.+++... |.|.|...|. .-.|.+... ..|...|...|
T Consensus 16 G~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~---~~~v~~a~~~i 63 (64)
T cd00105 16 GKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGT---PEAVEKAKELI 63 (64)
T ss_pred CCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcC---HHHHHHHHHHh
Confidence 89999999665 4588777663 344455444 45666666554
No 23
>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=41.11 E-value=39 Score=21.61 Aligned_cols=40 Identities=23% Similarity=0.271 Sum_probs=24.0
Q ss_pred CCCCccccccc--ceEEEEecC----ceeEEEEcCcCCHHHHHHHHHHHH
Q psy2492 67 GPGGQAVAKTN--NCVVLTHIP----TGIVIKCHQSRSLSENRKTARELL 110 (162)
Q Consensus 67 GpGGQ~VNKt~--s~V~l~h~P----tgi~v~~~~~RSq~~Nk~~A~~rL 110 (162)
|+||.++++.. +.|.|...+ .+. |..... ..+-..|...|
T Consensus 16 G~~G~~i~~i~~~~g~~I~i~~~~~~~~~-v~I~G~---~~~v~~A~~~i 61 (62)
T cd02394 16 GKKGSNIRKIMEETGVKIRFPDPGSKSDT-ITITGP---KENVEKAKEEI 61 (62)
T ss_pred CCCCCcHHHHHHHhCCEEEcCCCCCCCCE-EEEEcC---HHHHHHHHHHh
Confidence 89999999544 777777765 333 233333 34555565544
No 24
>PF02815 MIR: MIR domain; InterPro: IPR003608 The MIR domain is named after three of the proteins in which it occurs: protein Mannosyltransferase (2.4.1.109 from EC), Inositol 1,4,5-trisphosphate receptor (IP3R) and Ryanodine receptor (RyR). MIR domains have also been found in eukaryotic stromal cell-derived factor 2 (SDF-2) and in Chlamydia trachomatis protein CT153. The MIR domain may have a ligand transferase function. This domain has a closed beta-barrel structure with a hairpin triplet, and has an internal pseudo-threefold symmetry. The MIR motifs that make up the MIR domain consist of ~50 residues and are often found in multiple copies. Inositol 1,4,5-trisphosphate (InsP3) is an intracellular second messenger that transduces growth factor and neurotransmitter signals. InsP3 mediates the release of Ca2+ from intracellular stores by binding to specific Ca2+ channel-coupled receptors. Ryanodine receptors are involved in communication between transverse-tubules and the sarcoplamic reticulum of cardiac and skeletal muscle. The proteins function as a Ca2+-release channels following depolarisation of transverse-tubules []. The function is modulated by Ca2+, Mg2+, ATP and calmodulin. Deficiency in the ryanodine receptor may be the cause of malignant hyperthermia (MH) and of central core disease of muscle (CCD) []. protein O-mannosyltransferases transfer mannose from DOL-P-mannose to ser or thr residues on proteins.; GO: 0016020 membrane; PDB: 1T9F_A 3UJ4_B 3UJ0_B 3T8S_B 3MAL_B 2XOA_A 1N4K_A.
Probab=36.06 E-value=69 Score=25.22 Aligned_cols=39 Identities=18% Similarity=0.295 Sum_probs=30.5
Q ss_pred EEEeecCCCCCcccccccceEEEEecCceeEEEEcCcCC
Q psy2492 60 ERFVRGSGPGGQAVAKTNNCVVLTHIPTGIVIKCHQSRS 98 (162)
Q Consensus 60 i~~~RssGpGGQ~VNKt~s~V~l~h~Ptgi~v~~~~~RS 98 (162)
+...-..|.++..+-..+|.|+|+|..||..+.+++.+.
T Consensus 121 ~~~~~~~~~~~~~~~~~~s~frL~H~~t~~~L~~~~~~l 159 (190)
T PF02815_consen 121 FEEKSSTGMGEDEIKTLDSYFRLRHVATGCWLHSHDVKL 159 (190)
T ss_dssp EEEEESSSCSSSSBBBTTSEEEEEETTTTEEEEEEEEES
T ss_pred EEecccCCccCCcEEecccEEEEEECCcCEEEecCCccc
Confidence 334445677788888889999999999998888876544
No 25
>COG0828 RpsU Ribosomal protein S21 [Translation, ribosomal structure and biogenesis]
Probab=35.70 E-value=1.4e+02 Score=20.93 Aligned_cols=18 Identities=6% Similarity=-0.162 Sum_probs=14.8
Q ss_pred HHHHHHHHHHHHHHHhhc
Q psy2492 102 NRKTARELLVAQWDVQVN 119 (162)
Q Consensus 102 Nk~~A~~rL~~~L~~~~~ 119 (162)
+.+.||.+|+..+.....
T Consensus 11 ~~d~ALrrFKr~~~k~gi 28 (67)
T COG0828 11 PLDKALRRFKRKVEKEGI 28 (67)
T ss_pred hHHHHHHHHHHHHHHHHH
Confidence 589999999998887643
No 26
>PF04149 DUF397: Domain of unknown function (DUF397); InterPro: IPR007278 The function of this family is unknown. It has been suggested that some members of this family are regulators of transcription.
Probab=29.35 E-value=1.1e+02 Score=20.22 Aligned_cols=20 Identities=25% Similarity=0.707 Sum_probs=15.3
Q ss_pred ceEEEEecCceeEEEEcCcC
Q psy2492 78 NCVVLTHIPTGIVIKCHQSR 97 (162)
Q Consensus 78 s~V~l~h~Ptgi~v~~~~~R 97 (162)
++|++...|.++.|..+...
T Consensus 16 ~CVEva~~~~~v~vRDSk~p 35 (56)
T PF04149_consen 16 NCVEVARLPGGVAVRDSKDP 35 (56)
T ss_pred CcEEEEeecceEEEecCCCC
Confidence 58899898888777776543
No 27
>PLN02757 sirohydrochlorine ferrochelatase
Probab=28.53 E-value=2.9e+02 Score=21.62 Aligned_cols=45 Identities=31% Similarity=0.338 Sum_probs=33.5
Q ss_pred ceeEEEEcCcCCHHHHHHHHHHHHHHHHHHhhcC-----------CCCHHHHHHHHHH
Q psy2492 87 TGIVIKCHQSRSLSENRKTARELLVAQWDVQVNG-----------EDSLNAQIRRIDE 133 (162)
Q Consensus 87 tgi~v~~~~~RSq~~Nk~~A~~rL~~~L~~~~~~-----------~ps~~a~~kRl~~ 133 (162)
++|++-.+.+|....| .+++.|...|.+.... +|+.......+..
T Consensus 14 ~~lllvgHGSrd~~a~--~~~~~la~~l~~~~~~~~V~~aFle~~~Psl~eal~~l~~ 69 (154)
T PLN02757 14 DGVVIVDHGSRRKESN--LMLEEFVAMYKQKTGHPIVEPAHMELAEPSIKDAFGRCVE 69 (154)
T ss_pred cEEEEEeCCCCCHHHH--HHHHHHHHHHHhhCCCCcEEEEEEecCCCCHHHHHHHHHH
Confidence 5899999999999888 5678888888653221 6888877766643
No 28
>COG0193 Pth Peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis]
Probab=26.15 E-value=52 Score=27.30 Aligned_cols=24 Identities=17% Similarity=0.382 Sum_probs=19.9
Q ss_pred CCCCCCcCCCCeEEEEeecCCCCCcc
Q psy2492 47 YSTIPKIDEKDIQERFVRGSGPGGQA 72 (162)
Q Consensus 47 ~~~~~~i~~~dl~i~~~RssGpGGQ~ 72 (162)
..++++++...+++.. +||.||+|
T Consensus 91 vhDdLdl~~G~vrlk~--~Gg~gGHN 114 (190)
T COG0193 91 VHDELDLPLGKVRLKL--GGGAGGHN 114 (190)
T ss_pred EeeccCCCCceEEEEc--CCCCCCcc
Confidence 3667888888888887 89999987
No 29
>smart00472 MIR Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases.
Probab=24.40 E-value=80 Score=19.75 Aligned_cols=22 Identities=27% Similarity=0.514 Sum_probs=17.7
Q ss_pred ccceEEEEecCceeEEEEcCcC
Q psy2492 76 TNNCVVLTHIPTGIVIKCHQSR 97 (162)
Q Consensus 76 t~s~V~l~h~Ptgi~v~~~~~R 97 (162)
..+.|+|+|.-||--+.+++..
T Consensus 6 ~g~~vrL~H~~tg~yL~s~~~~ 27 (57)
T smart00472 6 WGDVVRLRHVTTGRYLHSHENK 27 (57)
T ss_pred cCCEEEEEEhhhCcEeecCCCC
Confidence 3589999999998777777665
No 30
>PRK00270 rpsU 30S ribosomal protein S21; Reviewed
Probab=22.45 E-value=2.6e+02 Score=19.00 Aligned_cols=18 Identities=6% Similarity=-0.167 Sum_probs=15.0
Q ss_pred HHHHHHHHHHHHHHHhhc
Q psy2492 102 NRKTARELLVAQWDVQVN 119 (162)
Q Consensus 102 Nk~~A~~rL~~~L~~~~~ 119 (162)
|-+.||.+|..++...-.
T Consensus 11 ~ie~Alrrfkr~~~k~gi 28 (64)
T PRK00270 11 SIDKALRRFKRKVEKAGI 28 (64)
T ss_pred hHHHHHHHHHHHHHHcch
Confidence 689999999999887643
No 31
>PF14048 MBD_C: C-terminal domain of methyl-CpG binding protein 2 and 3; PDB: 2L2L_B.
Probab=21.99 E-value=35 Score=25.21 Aligned_cols=27 Identities=22% Similarity=0.218 Sum_probs=18.2
Q ss_pred eeEEEEcCcCCHHHHHHHHHHHHHHHH
Q psy2492 88 GIVIKCHQSRSLSENRKTARELLVAQW 114 (162)
Q Consensus 88 gi~v~~~~~RSq~~Nk~~A~~rL~~~L 114 (162)
.++|+..+=|.|..--..|++||++.|
T Consensus 70 ~~~VT~eDIr~QE~rVk~aR~RLaeAL 96 (96)
T PF14048_consen 70 QFVVTEEDIRRQERRVKKARKRLAEAL 96 (96)
T ss_dssp -----HHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCccCHHHHHHHHHHHHHHHHHHHHHC
Confidence 466777888888888888888888754
No 32
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=21.95 E-value=1.7e+02 Score=23.13 Aligned_cols=60 Identities=17% Similarity=0.165 Sum_probs=36.9
Q ss_pred CCCCCccccccc--ceEEEEecCceeEEEEcCcCCHHHHHHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHH
Q psy2492 66 SGPGGQAVAKTN--NCVVLTHIPTGIVIKCHQSRSLSENRKTARELLVAQWDVQVNGEDSLNAQIRRIDEKR 135 (162)
Q Consensus 66 sGpGGQ~VNKt~--s~V~l~h~Ptgi~v~~~~~RSq~~Nk~~A~~rL~~~L~~~~~~~ps~~a~~kRl~~Kk 135 (162)
=|+||+.+..-+ |.|.|..... .|.... ...|.+.|.+.+..+|.... .+ .....|+..+
T Consensus 104 IG~~G~t~~~ie~~t~~~i~i~~~--~v~i~G---~~~~~~~A~~~i~~li~~~~--~~---~vy~~l~~~~ 165 (172)
T TIGR03665 104 IGEGGKTRRIIEELTGVSISVYGK--TVGIIG---DPEQVQIAREAIEMLIEGAP--HG---TVYKFLERKR 165 (172)
T ss_pred cCCCcHHHHHHHHHHCCeEEEcCC--EEEEEC---CHHHHHHHHHHHHHHHcCCC--Ch---hHHHHHHHHH
Confidence 389999888443 6777765543 344444 56788888888877763332 22 3356664443
No 33
>PF13014 KH_3: KH domain
Probab=21.55 E-value=33 Score=20.72 Aligned_cols=20 Identities=20% Similarity=0.454 Sum_probs=15.6
Q ss_pred CCCCccccc--ccceEEEEecC
Q psy2492 67 GPGGQAVAK--TNNCVVLTHIP 86 (162)
Q Consensus 67 GpGGQ~VNK--t~s~V~l~h~P 86 (162)
|+||+++|. .+|.|+|...+
T Consensus 7 G~~G~~I~~I~~~tg~~I~i~~ 28 (43)
T PF13014_consen 7 GKGGSTIKEIREETGAKIQIPP 28 (43)
T ss_pred CCCChHHHHHHHHhCcEEEECC
Confidence 889999994 45788887766
Done!