Query psy6196
Match_columns 146
No_of_seqs 129 out of 461
Neff 6.1
Searched_HMMs 46136
Date Fri Aug 16 20:09:07 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6196.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6196hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2869|consensus 100.0 2.4E-34 5.2E-39 240.0 6.1 129 12-141 42-178 (379)
2 TIGR00111 pelota probable tran 100.0 3E-31 6.4E-36 224.8 12.7 109 27-135 60-172 (351)
3 COG1537 PelA Predicted RNA-bin 100.0 2.4E-31 5.2E-36 224.0 11.7 109 27-135 59-170 (352)
4 PF03463 eRF1_1: eRF1 domain 1 99.8 5.8E-19 1.3E-23 131.2 5.2 60 33-92 72-131 (132)
5 TIGR00108 eRF peptide chain re 99.6 6.3E-15 1.4E-19 127.5 13.1 100 35-139 78-178 (409)
6 PRK04011 peptide chain release 99.4 1.9E-12 4.1E-17 112.2 12.9 100 37-140 83-183 (411)
7 TIGR03676 aRF1/eRF1 peptide ch 99.4 3.3E-12 7.1E-17 110.5 13.3 99 37-140 76-175 (403)
8 KOG2869|consensus 98.9 8.2E-10 1.8E-14 93.3 3.7 43 1-43 96-138 (379)
9 PF03464 eRF1_2: eRF1 domain 2 98.7 2.4E-08 5.1E-13 74.0 5.7 43 98-140 1-43 (133)
10 TIGR00111 pelota probable tran 98.3 3.4E-07 7.4E-12 78.0 3.1 35 1-35 95-129 (351)
11 COG1537 PelA Predicted RNA-bin 98.0 3.9E-06 8.6E-11 71.6 2.9 36 1-36 93-128 (352)
12 TIGR00108 eRF peptide chain re 95.6 0.018 4E-07 50.2 4.6 35 2-36 99-134 (409)
13 TIGR03676 aRF1/eRF1 peptide ch 94.9 0.041 8.9E-07 48.0 4.6 33 3-35 96-129 (403)
14 KOG0688|consensus 92.0 0.48 1E-05 40.9 6.2 78 62-142 106-186 (431)
15 PRK04011 peptide chain release 91.8 0.22 4.8E-06 43.6 4.1 34 2-35 103-137 (411)
16 COG1503 eRF1 Peptide chain rel 82.7 4.9 0.00011 35.5 6.7 99 37-140 83-182 (411)
17 PF07683 CobW_C: Cobalamin syn 60.0 8.5 0.00018 25.7 2.3 53 4-67 1-56 (94)
18 PF07116 DUF1372: Protein of u 54.4 16 0.00035 26.4 3.0 38 43-83 56-93 (104)
19 PF14801 GCD14_N: tRNA methylt 38.6 19 0.00042 23.0 1.3 16 59-74 19-34 (54)
20 PF12894 Apc4_WD40: Anaphase-p 37.4 58 0.0013 19.8 3.3 24 94-117 20-43 (47)
21 PF08954 DUF1900: Domain of un 31.0 50 0.0011 24.7 2.6 36 104-142 73-108 (136)
22 PF10664 NdhM: Cyanobacterial 28.1 2E+02 0.0042 20.9 5.1 42 42-88 7-48 (108)
23 PF08366 LLGL: LLGL2; InterPr 27.1 44 0.00095 24.1 1.7 59 57-115 41-101 (105)
24 PF05420 BCSC_C: Cellulose syn 26.6 45 0.00097 28.8 1.9 35 40-74 165-201 (342)
25 TIGR03630 arch_S17P archaeal r 26.4 55 0.0012 23.5 2.1 17 37-53 17-33 (102)
26 PF14250 AbrB-like: AbrB-like 26.3 37 0.0008 22.9 1.1 24 52-75 37-62 (71)
27 PF09345 DUF1987: Domain of un 23.8 34 0.00074 24.2 0.6 21 33-53 2-22 (99)
28 KOG3069|consensus 23.6 1.4E+02 0.003 24.8 4.1 42 94-135 41-84 (246)
29 KOG1896|consensus 23.0 1.3E+02 0.0028 30.5 4.4 62 47-122 1052-1119(1366)
30 COG3081 Nucleoid-associated pr 22.8 42 0.0009 28.5 1.0 25 25-49 296-320 (335)
31 TIGR02571 ComEB ComE operon pr 22.6 1.3E+02 0.0027 22.7 3.5 33 77-109 3-37 (151)
32 PRK08572 rps17p 30S ribosomal 20.9 80 0.0017 22.9 2.0 17 37-53 19-35 (108)
33 cd01780 PLC_epsilon_RA Ubiquit 20.7 2E+02 0.0043 20.4 3.9 32 65-96 7-38 (93)
34 PF00240 ubiquitin: Ubiquitin 20.3 1.4E+02 0.0031 18.4 3.0 58 13-75 6-65 (69)
35 COG1188 Ribosome-associated he 20.2 1.5E+02 0.0033 21.2 3.3 36 39-76 32-67 (100)
No 1
>KOG2869|consensus
Probab=100.00 E-value=2.4e-34 Score=240.02 Aligned_cols=129 Identities=46% Similarity=0.693 Sum_probs=113.7
Q ss_pred CceEEEEcCCc---ChhHH--Hhccc---ccCCCCCceEEEEEeEEeeeCcccCCCceEEEEecCCCeEEEEcCCCChHH
Q psy6196 12 NRKFELSKPEW---DSLYT--ARIGL---KSPFTPAVGYYYYCGRNIQENQYVKMGAYHTLDLELNRKFELSKPEWDSIA 83 (146)
Q Consensus 12 ~~~ftl~K~~w---d~~~~--~~L~~---~vef~~~~~~LRI~G~i~~~~e~v~~G~yHTl~i~~~~~~tI~K~~Wd~~~ 83 (146)
.+.+++++++- .+-.. ..|++ .++||+.++.||++|+++++||+|++|+||||+|++|++|++.|++||+++
T Consensus 42 ~T~rkvq~e~a~G~~~s~rv~~~L~i~VesidfD~~~~~L~~KGrti~eNe~Vk~GaYHTidlel~r~FtL~K~ewds~a 121 (379)
T KOG2869|consen 42 STIRKVQKEEATGKTKSSRVLLKLKIKVESIDFDTKACVLRLKGRTIEENEYVKMGAYHTIDLELNRPFTLRKEEWDSMA 121 (379)
T ss_pred EEEEEeeeccccCcccceEEEEEEEEEEEEeeccccccEEEEeeeeeeecccccccceeEEEeccCCceEEEhhhchHHH
Confidence 34566666643 11122 23333 889999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhcccCCccEEEEEEecCeEEEEEEecceeEEEEEEEeeCCCccCCCCCcce
Q psy6196 84 LERIEVACNIEKTADVAAVMMQEGLANIMLITASMSLVRTKIETNIPRKRRGYFCATL 141 (146)
Q Consensus 84 le~L~eA~~~~~~~~v~~v~~~eG~A~i~lv~~~~~~~~~~i~~~ipkK~~~~~~~~~ 141 (146)
+++|++||++..++++|+|+|+||.|+|||++.++|..+++|+.+|||||++ +++|+
T Consensus 122 l~~l~~A~dp~~~ad~aaVvlqEGla~IcLvt~s~tilr~kIe~siPrKr~~-~~s~~ 178 (379)
T KOG2869|consen 122 LKLLKEACDPAPSADVAAVVLQEGLAHICLVTKSSTILRAKIEVSIPRKRKG-DVSQH 178 (379)
T ss_pred HHHHHHhhCcccccceeeeehhcCceeEEEechhHHHHHHhhhcccccccCc-chhHH
Confidence 9999999999999999999999999999999999999999999999999755 77765
No 2
>TIGR00111 pelota probable translation factor pelota. This model describes the Drosophila protein Pelota, the budding yeast protein DOM34 which it can replace, and a set of closely related archaeal proteins. Members contain a proposed RNA binding motif. The meiotic defect in pelota mutants may be a complex result of a protein translation defect, as suggested in yeast by ribosomal protein RPS30A being a multicopy suppressor and by an altered polyribosome profile in DOM34 mutants rescued by RPS30A. This family is homologous to a family of peptide chain release factors. Pelota is proposed to act in protein translation.
Probab=99.97 E-value=3e-31 Score=224.78 Aligned_cols=109 Identities=29% Similarity=0.475 Sum_probs=102.8
Q ss_pred HHhccc---ccCCCCCceEEEEEeEEeeeC-cccCCCceEEEEecCCCeEEEEcCCCChHHHHHHHHHhcccCCccEEEE
Q psy6196 27 TARIGL---KSPFTPAVGYYYYCGRNIQEN-QYVKMGAYHTLDLELNRKFELSKPEWDSIALERIEVACNIEKTADVAAV 102 (146)
Q Consensus 27 ~~~L~~---~vef~~~~~~LRI~G~i~~~~-e~v~~G~yHTl~i~~~~~~tI~K~~Wd~~~le~L~eA~~~~~~~~v~~v 102 (146)
+++|++ +++|||++++|||+|+|+++| ++|++|+|||++|+||++|+|+|.+|+++++++|++||+++.++++++|
T Consensus 60 ~~~l~i~Ve~ief~~~~~~Lri~G~i~~~~e~~v~~G~~HTl~ie~~~~i~i~K~~w~~~~le~L~ea~~~~~~~~~~~v 139 (351)
T TIGR00111 60 TVKLGIEVESVEFDMKTERLRYKGVIVTGPEDDVPVGSYHTLEIKYVYPLSIIKQNWKKWQLKRLREAVEISKRPKTAAV 139 (351)
T ss_pred EEEEEEEEEEEEecCCCCEEEEEEEEecCCcccccccceEEEEEcCCCcEEEEEecCCHHHHHHHHHHhccccCCcEEEE
Confidence 344454 999999999999999999998 8999999999999999999999988999999999999999999999999
Q ss_pred EEecCeEEEEEEecceeEEEEEEEeeCCCccCC
Q psy6196 103 MMQEGLANIMLITASMSLVRTKIETNIPRKRRG 135 (146)
Q Consensus 103 ~~~eG~A~i~lv~~~~~~~~~~i~~~ipkK~~~ 135 (146)
+||+|+|+||+|++++++++++++.++|||+++
T Consensus 140 v~d~g~A~i~ll~~~~~~~~~~i~~~iP~K~~~ 172 (351)
T TIGR00111 140 VMEEGIAHVGLVRQYSVEEIQKIEYHMPGKKRT 172 (351)
T ss_pred EEeCCcEEEEEEcCCEEEEEEEEEEeCCCCccc
Confidence 999999999999999999999999999999753
No 3
>COG1537 PelA Predicted RNA-binding proteins [General function prediction only]
Probab=99.97 E-value=2.4e-31 Score=223.95 Aligned_cols=109 Identities=29% Similarity=0.492 Sum_probs=103.9
Q ss_pred HHhccc---ccCCCCCceEEEEEeEEeeeCcccCCCceEEEEecCCCeEEEEcCCCChHHHHHHHHHhcccCCccEEEEE
Q psy6196 27 TARIGL---KSPFTPAVGYYYYCGRNIQENQYVKMGAYHTLDLELNRKFELSKPEWDSIALERIEVACNIEKTADVAAVM 103 (146)
Q Consensus 27 ~~~L~~---~vef~~~~~~LRI~G~i~~~~e~v~~G~yHTl~i~~~~~~tI~K~~Wd~~~le~L~eA~~~~~~~~v~~v~ 103 (146)
++.|++ +++||.|+++|||+|+++++|+++++|+|||++|++|++|+|+|++|++++++||+|||++++++++++|+
T Consensus 59 ~m~L~IkVe~ieF~~f~nrLRi~G~i~~~~e~~~~G~yHTi~v~~g~~i~I~K~~W~~~~lerLkeA~~~~~~~~~~~v~ 138 (352)
T COG1537 59 PMTLGIKVEKIEFDKFANRLRIKGPIVEGPEEVVKGSYHTINVTIGTEIEIEKEEWNKDQLERLKEAVEASKRPEVAIVV 138 (352)
T ss_pred EEEEEEEEEEEEeeecccEEEEEEEEEEcCcccccccceEEEeccCceEEEEEccCCHHHHHHHHHHhhcccCCceEEEE
Confidence 445554 89999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EecCeEEEEEEecceeEEEEEEEeeCCCccCC
Q psy6196 104 MQEGLANIMLITASMSLVRTKIETNIPRKRRG 135 (146)
Q Consensus 104 ~~eG~A~i~lv~~~~~~~~~~i~~~ipkK~~~ 135 (146)
||||+|+||+|++||+.++++++.++|+|+.+
T Consensus 139 ~degea~i~iv~~ygi~~~~~i~~~~~gK~~~ 170 (352)
T COG1537 139 VDEGEAAIAIVRDYGIIILGKIRSGIPGKREG 170 (352)
T ss_pred EecCceEEEEEeccceEEEEEEeccCCCCccc
Confidence 99999999999999999999999999999755
No 4
>PF03463 eRF1_1: eRF1 domain 1; InterPro: IPR005140 This domain is found in the release factor eRF1 which terminates protein biosynthesis by recognizing stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known []. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site []. This domain is also found in other proteins for which the precise molecular function is unknown. Many of them are from Archaebacteria. These proteins may also be involved in translation termination but this awaits experimental verification.; PDB: 2VGN_A 2VGM_A 3J16_A 3IZQ 3AGK_A 3AGJ_B 3OBW_A 3E1Y_D 1DT9_A 2LLX_A ....
Probab=99.76 E-value=5.8e-19 Score=131.19 Aligned_cols=60 Identities=42% Similarity=0.716 Sum_probs=58.9
Q ss_pred ccCCCCCceEEEEEeEEeeeCcccCCCceEEEEecCCCeEEEEcCCCChHHHHHHHHHhc
Q psy6196 33 KSPFTPAVGYYYYCGRNIQENQYVKMGAYHTLDLELNRKFELSKPEWDSIALERIEVACN 92 (146)
Q Consensus 33 ~vef~~~~~~LRI~G~i~~~~e~v~~G~yHTl~i~~~~~~tI~K~~Wd~~~le~L~eA~~ 92 (146)
+++|+|+++.|||+|+|+++|+++++|+|||++|+||++|+|+|..||+.++++|+|||+
T Consensus 72 ~v~~~~~~~~Lri~G~i~~~~~~~~~G~~hT~~i~~~~~~ti~K~~wd~~~~~~l~ea~~ 131 (132)
T PF03463_consen 72 KVEFDPENGLLRISGKIVEENEDVKLGKYHTLDIEPGRPFTIIKYRWDSYFLDRLKEAMD 131 (132)
T ss_dssp EEEEETTTTEEEEEEEEEEGSCGGGTTSEEEEEEETSSEEEEEEEEEEHHHHHHHHHHTS
T ss_pred EeEecCCCCEEEEEeEEccCCCCCCcceEEEEEEeCCCceEEEEecCCHHHHHHHHHHhc
Confidence 899999999999999999999999999999999999999999999999999999999996
No 5
>TIGR00108 eRF peptide chain release factor eRF/aRF, subunit 1. Alternative names include eRF1, SUP45, omnipotent suppressor protein 1.
Probab=99.62 E-value=6.3e-15 Score=127.51 Aligned_cols=100 Identities=16% Similarity=0.141 Sum_probs=88.3
Q ss_pred CCCCCceEEEEEeEEeeeCcccCCCceEEEEecCCCeEEEEcC-CCChHHHHHHHHHhcccCCccEEEEEEecCeEEEEE
Q psy6196 35 PFTPAVGYYYYCGRNIQENQYVKMGAYHTLDLELNRKFELSKP-EWDSIALERIEVACNIEKTADVAAVMMQEGLANIML 113 (146)
Q Consensus 35 ef~~~~~~LRI~G~i~~~~e~v~~G~yHTl~i~~~~~~tI~K~-~Wd~~~le~L~eA~~~~~~~~v~~v~~~eG~A~i~l 113 (146)
.--|..+.+++.|.+..++.. |+|||++|+|+++|+++|. +|++++++.|++|++. .+.+++|+||+|.|.||+
T Consensus 78 ~~~p~nglv~~~G~v~~~~~~---~~~~t~~iep~~pi~~~~y~~d~~f~le~L~e~~~~--~~~~g~VvvD~~~A~i~~ 152 (409)
T TIGR00108 78 NKPPENGLVIFCGMVPREGPT---EKMETYVIEPPEPIKTYIYHCDSKFYLEPLSEMLEE--KDKYGLIVLDRQEATIGL 152 (409)
T ss_pred CCCCCCcEEEEEeEeccCCCc---ccEEEEEEeCCCceEEEEEccCChhHHHHHHHHhcC--CCCEEEEEEecCCEEEEE
Confidence 445778999999999887743 8999999999999999996 5779999999999986 469999999999999999
Q ss_pred EecceeEEEEEEEeeCCCccCCCCCc
Q psy6196 114 ITASMSLVRTKIETNIPRKRRGYFCA 139 (146)
Q Consensus 114 v~~~~~~~~~~i~~~ipkK~~~~~~~ 139 (146)
+++++++++++++.++|||++..+.|
T Consensus 153 l~g~~~~~~~~i~~~vp~K~~~GGqS 178 (409)
T TIGR00108 153 VKGKRITVLKKLTSGVPGKHKAGGQS 178 (409)
T ss_pred EcCCEEEEEEEEeeeCCCcccCCCcc
Confidence 99999999999999999997533433
No 6
>PRK04011 peptide chain release factor 1; Provisional
Probab=99.43 E-value=1.9e-12 Score=112.25 Aligned_cols=100 Identities=15% Similarity=0.086 Sum_probs=84.5
Q ss_pred CCCceEEEEEeEEeeeCcccCCCceEEEEecCCCeEEEEcCC-CChHHHHHHHHHhcccCCccEEEEEEecCeEEEEEEe
Q psy6196 37 TPAVGYYYYCGRNIQENQYVKMGAYHTLDLELNRKFELSKPE-WDSIALERIEVACNIEKTADVAAVMMQEGLANIMLIT 115 (146)
Q Consensus 37 ~~~~~~LRI~G~i~~~~e~v~~G~yHTl~i~~~~~~tI~K~~-Wd~~~le~L~eA~~~~~~~~v~~v~~~eG~A~i~lv~ 115 (146)
-|..+..=+.|.+..+.+ +-|.|||++|+|+++|+++|.. |+.+++++|+++++. ++.+++|+||.|.|.||+++
T Consensus 83 ~p~nGl~~f~g~~~~~~~--~~~~~~t~~i~p~~~i~~~~y~~d~~f~le~L~e~~~~--~~~~~~VvvD~~~A~i~~l~ 158 (411)
T PRK04011 83 PPENGLVIFCGAVPIGGP--GTEDMETYVIEPPEPVPTFFYRCDSEFHTEPLEDMLED--KEVYGLIVVDRREATIGLLK 158 (411)
T ss_pred CCCCeEEEEEeecccCCC--CCceEEEEEEcCCCccEEEEecCCcHHHHHHHHHHhcC--CCCEEEEEEecCceEEEEEe
Confidence 456777778888776431 2389999999999999999975 555999999999985 88999999999999999999
Q ss_pred cceeEEEEEEEeeCCCccCCCCCcc
Q psy6196 116 ASMSLVRTKIETNIPRKRRGYFCAT 140 (146)
Q Consensus 116 ~~~~~~~~~i~~~ipkK~~~~~~~~ 140 (146)
+++++++++++.++|+|++..+.|+
T Consensus 159 g~~~~~~~~i~~~vp~K~~~GG~S~ 183 (411)
T PRK04011 159 GKRIEVLKELTSFVPGKHRKGGQSA 183 (411)
T ss_pred CCEEEEEEEEEeeCCCCccCCCcch
Confidence 9999999999999999976334444
No 7
>TIGR03676 aRF1/eRF1 peptide chain release factor 1, archaeal and eukaryotic forms. Directs the termination of nascent peptide synthesis (translation) in response to the termination codons UAA, UAG and UGA. This model identifies both archaeal (aRF1) and eukaryotic (eRF1) of the protein. Also known as translation termination factor 1.
Probab=99.42 E-value=3.3e-12 Score=110.55 Aligned_cols=99 Identities=15% Similarity=0.099 Sum_probs=83.2
Q ss_pred CCCceEEEEEeEEeeeCcccCCCceEEEEecCCCeEEEEcC-CCChHHHHHHHHHhcccCCccEEEEEEecCeEEEEEEe
Q psy6196 37 TPAVGYYYYCGRNIQENQYVKMGAYHTLDLELNRKFELSKP-EWDSIALERIEVACNIEKTADVAAVMMQEGLANIMLIT 115 (146)
Q Consensus 37 ~~~~~~LRI~G~i~~~~e~v~~G~yHTl~i~~~~~~tI~K~-~Wd~~~le~L~eA~~~~~~~~v~~v~~~eG~A~i~lv~ 115 (146)
-|..+-.-..|.+..+. +-.+|||++++|+++|+++|. +|++++++.|+++++. ++.+++|+||+|.|.||+++
T Consensus 76 ~p~nGlv~f~g~~~~~~---~~~~~~t~~iep~~pi~~~~y~cd~~f~lepL~e~l~~--~~~~g~VvvD~~~A~i~~l~ 150 (403)
T TIGR03676 76 PPENGLVLFAGMVPTGG---GTEKMETYVIEPPEPINTYLYRCDSKFYLEPLEEMLEE--KDVYGLIVLDRREATIGLLK 150 (403)
T ss_pred CCCCeEEEEEeeecCCC---CceeEEEEEEeCCCceEEEEecCCChHHHHHHHHHhcC--CCCEEEEEEecCceEEEEEc
Confidence 35666666678877643 225899999999999999996 5779999999999985 68999999999999999999
Q ss_pred cceeEEEEEEEeeCCCccCCCCCcc
Q psy6196 116 ASMSLVRTKIETNIPRKRRGYFCAT 140 (146)
Q Consensus 116 ~~~~~~~~~i~~~ipkK~~~~~~~~ 140 (146)
+++++++++++..+|||++..+.|+
T Consensus 151 g~~~e~~~~i~~~vp~K~~~GGqS~ 175 (403)
T TIGR03676 151 GKRIEVLKELTSGVPGKHRAGGQSA 175 (403)
T ss_pred CCEEEEEEEEEeeCCCCccCCCcch
Confidence 9999999999999999975334443
No 8
>KOG2869|consensus
Probab=98.91 E-value=8.2e-10 Score=93.28 Aligned_cols=43 Identities=47% Similarity=0.711 Sum_probs=38.9
Q ss_pred CCceEEEEeecCceEEEEcCCcChhHHHhcccccCCCCCceEE
Q psy6196 1 MGAYHTLDLELNRKFELSKPEWDSLYTARIGLKSPFTPAVGYY 43 (146)
Q Consensus 1 ~g~~ht~~~~~~~~ftl~K~~wd~~~~~~L~~~vef~~~~~~L 43 (146)
||+|||++|++|++|||+|++||+++.++|+++.+-.+.++.-
T Consensus 96 ~GaYHTidlel~r~FtL~K~ewds~al~~l~~A~dp~~~ad~a 138 (379)
T KOG2869|consen 96 MGAYHTIDLELNRPFTLRKEEWDSMALKLLKEACDPAPSADVA 138 (379)
T ss_pred ccceeEEEeccCCceEEEhhhchHHHHHHHHHhhCccccccee
Confidence 7999999999999999999999999999999988877666543
No 9
>PF03464 eRF1_2: eRF1 domain 2; InterPro: IPR005141 This domain is found in the release factor eRF1 which terminates protein biosynthesis by recognizing stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known []. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site []. This domain is also found in other proteins which may also be involved in translation termination ; PDB: 3AGK_A 2VGN_A 2VGM_A 3J16_A 3IZQ 3IR9_A 3OBW_A 3MCA_B 2QI2_A 3E1Y_D ....
Probab=98.72 E-value=2.4e-08 Score=73.98 Aligned_cols=43 Identities=33% Similarity=0.397 Sum_probs=37.2
Q ss_pred cEEEEEEecCeEEEEEEecceeEEEEEEEeeCCCccCCCCCcc
Q psy6196 98 DVAAVMMQEGLANIMLITASMSLVRTKIETNIPRKRRGYFCAT 140 (146)
Q Consensus 98 ~v~~v~~~eG~A~i~lv~~~~~~~~~~i~~~ipkK~~~~~~~~ 140 (146)
++++|+||+|+|+||++++++++++++|+.++|+|+...+.|+
T Consensus 1 ~v~~v~id~g~A~i~~l~~~~~~~~~~i~~~ip~K~~~Gg~s~ 43 (133)
T PF03464_consen 1 KVGIVVIDEGEANICLLRGYGTEILQRIESNIPGKHKKGGQSQ 43 (133)
T ss_dssp EEEEEEEETTEEEEEEEETTEEEEEEEEE-GHCCCSSTTCSHH
T ss_pred CEEEEEEeCCCEEEEEEcCCEEEEEEEEEecCCCccCCCCcch
Confidence 5899999999999999999999999999999999986434443
No 10
>TIGR00111 pelota probable translation factor pelota. This model describes the Drosophila protein Pelota, the budding yeast protein DOM34 which it can replace, and a set of closely related archaeal proteins. Members contain a proposed RNA binding motif. The meiotic defect in pelota mutants may be a complex result of a protein translation defect, as suggested in yeast by ribosomal protein RPS30A being a multicopy suppressor and by an altered polyribosome profile in DOM34 mutants rescued by RPS30A. This family is homologous to a family of peptide chain release factors. Pelota is proposed to act in protein translation.
Probab=98.32 E-value=3.4e-07 Score=78.03 Aligned_cols=35 Identities=23% Similarity=0.489 Sum_probs=32.8
Q ss_pred CCceEEEEeecCceEEEEcCCcChhHHHhcccccC
Q psy6196 1 MGAYHTLDLELNRKFELSKPEWDSLYTARIGLKSP 35 (146)
Q Consensus 1 ~g~~ht~~~~~~~~ftl~K~~wd~~~~~~L~~~ve 35 (146)
+|+|||++|+++++|+|+|.+||+++.++|+.+++
T Consensus 95 ~G~~HTl~ie~~~~i~i~K~~w~~~~le~L~ea~~ 129 (351)
T TIGR00111 95 VGSYHTLEIKYVYPLSIIKQNWKKWQLKRLREAVE 129 (351)
T ss_pred ccceEEEEEcCCCcEEEEEecCCHHHHHHHHHHhc
Confidence 69999999999999999999999999999997555
No 11
>COG1537 PelA Predicted RNA-binding proteins [General function prediction only]
Probab=97.99 E-value=3.9e-06 Score=71.62 Aligned_cols=36 Identities=25% Similarity=0.522 Sum_probs=33.1
Q ss_pred CCceEEEEeecCceEEEEcCCcChhHHHhcccccCC
Q psy6196 1 MGAYHTLDLELNRKFELSKPEWDSLYTARIGLKSPF 36 (146)
Q Consensus 1 ~g~~ht~~~~~~~~ftl~K~~wd~~~~~~L~~~vef 36 (146)
+|+|||++++++++|+|+|+.|+.+..++|+.+++=
T Consensus 93 ~G~yHTi~v~~g~~i~I~K~~W~~~~lerLkeA~~~ 128 (352)
T COG1537 93 KGSYHTINVTIGTEIEIEKEEWNKDQLERLKEAVEA 128 (352)
T ss_pred cccceEEEeccCceEEEEEccCCHHHHHHHHHHhhc
Confidence 699999999999999999999999999999974443
No 12
>TIGR00108 eRF peptide chain release factor eRF/aRF, subunit 1. Alternative names include eRF1, SUP45, omnipotent suppressor protein 1.
Probab=95.58 E-value=0.018 Score=50.22 Aligned_cols=35 Identities=9% Similarity=-0.093 Sum_probs=30.9
Q ss_pred CceEEEEeecCceEEEEc-CCcChhHHHhcccccCC
Q psy6196 2 GAYHTLDLELNRKFELSK-PEWDSLYTARIGLKSPF 36 (146)
Q Consensus 2 g~~ht~~~~~~~~ftl~K-~~wd~~~~~~L~~~vef 36 (146)
|+|||+++++++|+++.| .+|++++.+.|...++-
T Consensus 99 ~~~~t~~iep~~pi~~~~y~~d~~f~le~L~e~~~~ 134 (409)
T TIGR00108 99 EKMETYVIEPPEPIKTYIYHCDSKFYLEPLSEMLEE 134 (409)
T ss_pred ccEEEEEEeCCCceEEEEEccCChhHHHHHHHHhcC
Confidence 689999999999999999 57889999999975553
No 13
>TIGR03676 aRF1/eRF1 peptide chain release factor 1, archaeal and eukaryotic forms. Directs the termination of nascent peptide synthesis (translation) in response to the termination codons UAA, UAG and UGA. This model identifies both archaeal (aRF1) and eukaryotic (eRF1) of the protein. Also known as translation termination factor 1.
Probab=94.87 E-value=0.041 Score=48.03 Aligned_cols=33 Identities=9% Similarity=-0.065 Sum_probs=29.5
Q ss_pred ceEEEEeecCceEEEEc-CCcChhHHHhcccccC
Q psy6196 3 AYHTLDLELNRKFELSK-PEWDSLYTARIGLKSP 35 (146)
Q Consensus 3 ~~ht~~~~~~~~ftl~K-~~wd~~~~~~L~~~ve 35 (146)
+|||+++++++||+++| .||++++.+.|...++
T Consensus 96 ~~~t~~iep~~pi~~~~y~cd~~f~lepL~e~l~ 129 (403)
T TIGR03676 96 KMETYVIEPPEPINTYLYRCDSKFYLEPLEEMLE 129 (403)
T ss_pred eEEEEEEeCCCceEEEEecCCChHHHHHHHHHhc
Confidence 79999999999999999 5777999999997554
No 14
>KOG0688|consensus
Probab=92.05 E-value=0.48 Score=40.95 Aligned_cols=78 Identities=14% Similarity=0.127 Sum_probs=58.3
Q ss_pred EEEEecCCCeE--EEEcCCCChHHHHHHHHHhcccCCccEEEEEEecCeEEEEEEecceeEEEEEEEeeCCCccC-CCCC
Q psy6196 62 HTLDLELNRKF--ELSKPEWDSIALERIEVACNIEKTADVAAVMMQEGLANIMLITASMSLVRTKIETNIPRKRR-GYFC 138 (146)
Q Consensus 62 HTl~i~~~~~~--tI~K~~Wd~~~le~L~eA~~~~~~~~v~~v~~~eG~A~i~lv~~~~~~~~~~i~~~ipkK~~-~~~~ 138 (146)
-++++||-.+| +++= +=++++.+-|.+.... ....++++||..-+-++.+....-.++.++.+.+|||.. +..+
T Consensus 106 v~idfepfkpintslyL-cdNkfhte~l~~Ll~s--d~kfgfivmDg~~tlfgtl~gntrevLhkftVdlPkkhgrggqS 182 (431)
T KOG0688|consen 106 VNIDFEPFKPINTSLYL-CDNKFHTEALKELLES--DNKFGFIVMDGNGTLFGTLQGNTREVLHKFTVDLPKKHGRGGQS 182 (431)
T ss_pred eecccccccccccceEe-cCCccchHHHHHHHhh--cccccEEEEcCCceeEEEeccchHhhhheeeecCccccCccchh
Confidence 35666776665 3332 4567778888876644 447899999999999999999999999999999999953 4344
Q ss_pred ccee
Q psy6196 139 ATLY 142 (146)
Q Consensus 139 ~~~~ 142 (146)
+++|
T Consensus 183 alrf 186 (431)
T KOG0688|consen 183 ALRF 186 (431)
T ss_pred HHhh
Confidence 4443
No 15
>PRK04011 peptide chain release factor 1; Provisional
Probab=91.80 E-value=0.22 Score=43.57 Aligned_cols=34 Identities=9% Similarity=-0.206 Sum_probs=29.1
Q ss_pred CceEEEEeecCceEEEEcC-CcChhHHHhcccccC
Q psy6196 2 GAYHTLDLELNRKFELSKP-EWDSLYTARIGLKSP 35 (146)
Q Consensus 2 g~~ht~~~~~~~~ftl~K~-~wd~~~~~~L~~~ve 35 (146)
|.|||+++++++|++++|. +|+.++.+.|...++
T Consensus 103 ~~~~t~~i~p~~~i~~~~y~~d~~f~le~L~e~~~ 137 (411)
T PRK04011 103 EDMETYVIEPPEPVPTFFYRCDSEFHTEPLEDMLE 137 (411)
T ss_pred ceEEEEEEcCCCccEEEEecCCcHHHHHHHHHHhc
Confidence 6899999999999999996 555599999997444
No 16
>COG1503 eRF1 Peptide chain release factor 1 (eRF1) [Translation, ribosomal structure and biogenesis]
Probab=82.68 E-value=4.9 Score=35.51 Aligned_cols=99 Identities=16% Similarity=0.120 Sum_probs=74.7
Q ss_pred CCCceEEEEEeEEeeeCcccCCCceEEEEecCCCeEEEEc-CCCChHHHHHHHHHhcccCCccEEEEEEecCeEEEEEEe
Q psy6196 37 TPAVGYYYYCGRNIQENQYVKMGAYHTLDLELNRKFELSK-PEWDSIALERIEVACNIEKTADVAAVMMQEGLANIMLIT 115 (146)
Q Consensus 37 ~~~~~~LRI~G~i~~~~e~v~~G~yHTl~i~~~~~~tI~K-~~Wd~~~le~L~eA~~~~~~~~v~~v~~~eG~A~i~lv~ 115 (146)
.|..+--...|.+..+-... .-=|.-++|-.+++-.. .+=..+.++-|++... .+....+++|+-++|.++++.
T Consensus 83 ~P~nGlv~f~g~v~~~~~~t---~~~~~~~~PP~Pi~~~ly~cDs~F~~e~L~~~l~--~~~~ygliv~dr~ea~ig~l~ 157 (411)
T COG1503 83 TPENGLVLFVGDVLGGGGKT---KKVTVVIEPPEPINTFLYRCDSKFYLEPLEEMLE--DKDLYGLIVLDRIEATIGLLK 157 (411)
T ss_pred CCCCCeEEEEeeeccCCCcc---ceeeecccCCCCcceeeeccccHHHHHHHHHHhh--hcccccEEEEecccceeeeec
Confidence 35677777888887652222 22345558888876655 2677889999999764 466789999999999999999
Q ss_pred cceeEEEEEEEeeCCCccCCCCCcc
Q psy6196 116 ASMSLVRTKIETNIPRKRRGYFCAT 140 (146)
Q Consensus 116 ~~~~~~~~~i~~~ipkK~~~~~~~~ 140 (146)
+....+..+++...|||++..+.|+
T Consensus 158 g~r~evl~~~~s~vpgKh~~Ggqsa 182 (411)
T COG1503 158 GKRIEVLKELTSDVPGKHRAGGQSA 182 (411)
T ss_pred cceeeHhhhhcccCcchhhcccchH
Confidence 9999999999999999966434443
No 17
>PF07683 CobW_C: Cobalamin synthesis protein cobW C-terminal domain; InterPro: IPR011629 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase []. In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase []. There are at least two distinct cobalamin biosynthetic pathways in bacteria []: Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway []; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis []; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii subsp. shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) []. There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. CobW proteins are generally found proximal to the trimeric cobaltochelatase subunit CobN, which is essential for vitamin B12 (cobalamin) biosynthesis []. They contain a P-loop nucleotide-binding loop in the N-terminal domain and a histidine-rich region in the C-terminal portion suggesting a role in metal binding, possibly as an intermediary between the cobalt transport and chelation systems. CobW might be involved in cobalt reduction leading to cobalt(I) corrinoids. This entry represents the C-terminal domain found in CobW, as well as in P47K (P31521 from SWISSPROT), a Pseudomonas chlororaphis protein needed for nitrile hydratase expression [].; PDB: 1NIJ_A.
Probab=59.99 E-value=8.5 Score=25.72 Aligned_cols=53 Identities=15% Similarity=0.118 Sum_probs=27.6
Q ss_pred eEEEEeecCceEEEEcCCcChhHHHhcccccCCCCCceEEEEEeEEeeeCc--ccCC-CceEEEEec
Q psy6196 4 YHTLDLELNRKFELSKPEWDSLYTARIGLKSPFTPAVGYYYYCGRNIQENQ--YVKM-GAYHTLDLE 67 (146)
Q Consensus 4 ~ht~~~~~~~~ftl~K~~wd~~~~~~L~~~vef~~~~~~LRI~G~i~~~~e--~v~~-G~yHTl~i~ 67 (146)
+.|+.++..++|+. .+|..-++= ...+.||++|.+--+.. .+-+ |..+.+++.
T Consensus 1 i~s~~~~~~~p~~~----------~~l~~~l~~-~~~~vlR~KG~v~~~~~~~~~~~q~v~~~~~~~ 56 (94)
T PF07683_consen 1 ISSVTFEFDRPFDP----------ERLEAWLQE-LPGDVLRAKGIVWVADGPRRLVFQGVGGRYDIE 56 (94)
T ss_dssp EEEEEEEESS-B-H----------HHHHHHHHH-TTTTEEEEEEEE-BTT-SEEEEEEEETTEEEEE
T ss_pred CEEEEEEeCCCCCH----------HHHHHHHHh-CCCCEEEEEEEEEeCCcCeEEEEEeeCCEEEec
Confidence 46777777777654 222220000 55789999999986543 3333 444444444
No 18
>PF07116 DUF1372: Protein of unknown function (DUF1372); InterPro: IPR010779 This entry is represented by Streptococcus phage Sfi11, Gp93. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several Streptococcus bacteriophage sequences and related proteins from Streptococcus species. Members of this family are typically around 100 residues in length and their function is unknown.
Probab=54.38 E-value=16 Score=26.35 Aligned_cols=38 Identities=21% Similarity=0.349 Sum_probs=31.3
Q ss_pred EEEEeEEeeeCcccCCCceEEEEecCCCeEEEEcCCCChHH
Q psy6196 43 YYYCGRNIQENQYVKMGAYHTLDLELNRKFELSKPEWDSIA 83 (146)
Q Consensus 43 LRI~G~i~~~~e~v~~G~yHTl~i~~~~~~tI~K~~Wd~~~ 83 (146)
--+.|++++-. .+|..+|+++..--.|-+.|+..++..
T Consensus 56 ~ei~GkVt~K~---~ig~~yTvti~~YGkFlVtkeqY~~i~ 93 (104)
T PF07116_consen 56 AEIFGKVTEKE---IIGGLYTVTIGAYGKFLVTKEQYESIK 93 (104)
T ss_pred cEEEEEEeece---eECCEEEEEecCceEEEEehhhcceee
Confidence 56889998754 569999999999889999998776643
No 19
>PF14801 GCD14_N: tRNA methyltransferase complex GCD14 subunit N-term; PDB: 1I9G_A.
Probab=38.64 E-value=19 Score=23.00 Aligned_cols=16 Identities=38% Similarity=0.567 Sum_probs=9.8
Q ss_pred CceEEEEecCCCeEEE
Q psy6196 59 GAYHTLDLELNRKFEL 74 (146)
Q Consensus 59 G~yHTl~i~~~~~~tI 74 (146)
|..||+.|++|..|-=
T Consensus 19 gr~~Ti~L~~G~~fhT 34 (54)
T PF14801_consen 19 GRKHTITLEPGGEFHT 34 (54)
T ss_dssp --EEEEE--TT-EEEE
T ss_pred CCeeeEEECCCCeEEc
Confidence 9999999999999864
No 20
>PF12894 Apc4_WD40: Anaphase-promoting complex subunit 4 WD40 domain
Probab=37.41 E-value=58 Score=19.76 Aligned_cols=24 Identities=17% Similarity=0.140 Sum_probs=19.5
Q ss_pred cCCccEEEEEEecCeEEEEEEecc
Q psy6196 94 EKTADVAAVMMQEGLANIMLITAS 117 (146)
Q Consensus 94 ~~~~~v~~v~~~eG~A~i~lv~~~ 117 (146)
+++-|+.|+..++|+..+|.+..+
T Consensus 20 ~P~mdLiA~~t~~g~v~v~Rl~~q 43 (47)
T PF12894_consen 20 CPTMDLIALGTEDGEVLVYRLNWQ 43 (47)
T ss_pred CCCCCEEEEEECCCeEEEEECCCc
Confidence 456799999999999988887443
No 21
>PF08954 DUF1900: Domain of unknown function (DUF1900); InterPro: IPR015049 This domain is predominantly found in the structural protein coronin, and is duplicated in some sequences. It has no known function []. ; PDB: 2B4E_A 2AQ5_A.
Probab=30.95 E-value=50 Score=24.67 Aligned_cols=36 Identities=31% Similarity=0.486 Sum_probs=19.2
Q ss_pred EecCeEEEEEEecceeEEEEEEEeeCCCccCCCCCccee
Q psy6196 104 MQEGLANIMLITASMSLVRTKIETNIPRKRRGYFCATLY 142 (146)
Q Consensus 104 ~~eG~A~i~lv~~~~~~~~~~i~~~ipkK~~~~~~~~~~ 142 (146)
+....+.+..++..+ +..|...+|||+...+.++.|
T Consensus 73 ~~~Ei~R~lkl~~~~---iepisf~VPRk~~~~Fq~Dly 108 (136)
T PF08954_consen 73 MKCEIARFLKLTNDK---IEPISFIVPRKQSEYFQDDLY 108 (136)
T ss_dssp GGTEEEEEEEEETTE---EEEEEEE------SS--CCC-
T ss_pred hheeeeeeeeecCCc---EEEEEEEeeccccccccccCC
Confidence 344566778888888 788999999997555555555
No 22
>PF10664 NdhM: Cyanobacterial and plastid NDH-1 subunit M; InterPro: IPR018922 The NADH dehydrogenase I complex shuttles electrons from an unknown electron donor, via FMN and iron-sulphur (Fe-S) centres, to quinones in the respiratory and/or the photosynthetic chain. The immediate electron acceptor for the enzyme in plants is believed to be plastoquinone. The NADH dehydrogenase I complex couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient. This entry represents subunit M of the NADH dehydrogenase I complex in cyanobacteria and plant chloroplasts []. ; GO: 0016655 oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor, 0055114 oxidation-reduction process
Probab=28.09 E-value=2e+02 Score=20.86 Aligned_cols=42 Identities=24% Similarity=0.424 Sum_probs=33.4
Q ss_pred EEEEEeEEeeeCcccCCCceEEEEecCCCeEEEEcCCCChHHHHHHH
Q psy6196 42 YYYYCGRNIQENQYVKMGAYHTLDLELNRKFELSKPEWDSIALERIE 88 (146)
Q Consensus 42 ~LRI~G~i~~~~e~v~~G~yHTl~i~~~~~~tI~K~~Wd~~~le~L~ 88 (146)
-+||-.--++.++-++--..-||+|.|..+|. |+..+++.+-
T Consensus 7 HvrIftA~v~~~~lv~~~~~LTLdlDPdNEF~-----W~~~~l~kVy 48 (108)
T PF10664_consen 7 HVRIFTAEVENNELVPSDDKLTLDLDPDNEFN-----WNEEALQKVY 48 (108)
T ss_pred eEEEEEEEEecCceecCCCeeEEecCCCcccc-----cCHHHHHHHH
Confidence 46666666678888877889999999999984 9998887653
No 23
>PF08366 LLGL: LLGL2; InterPro: IPR013577 This domain is found in lethal giant larvae homologue 2 (LLGL2) proteins and syntaxin-binding proteins like tomosyn []. It has been identified in eukaryotes and tends to be found together with WD repeats (IPR001680 from INTERPRO).
Probab=27.05 E-value=44 Score=24.05 Aligned_cols=59 Identities=19% Similarity=0.102 Sum_probs=34.1
Q ss_pred CCCceEEEEecCCCeEEEEcCCCChHHHHHHHHH--hcccCCccEEEEEEecCeEEEEEEe
Q psy6196 57 KMGAYHTLDLELNRKFELSKPEWDSIALERIEVA--CNIEKTADVAAVMMQEGLANIMLIT 115 (146)
Q Consensus 57 ~~G~yHTl~i~~~~~~tI~K~~Wd~~~le~L~eA--~~~~~~~~v~~v~~~eG~A~i~lv~ 115 (146)
+-|..|++.|-.|+..+..-=.+.-++.-.+.+. .+....+..++|+++++.+.|=|-+
T Consensus 41 ~ygdr~~vTV~~g~~~~~ldf~s~VIDF~~i~~~~~~~e~~~P~alvVL~e~eLVvIDL~t 101 (105)
T PF08366_consen 41 SYGDRHCVTVMQGKTHVVLDFTSRVIDFFTICESPWPNEFQDPYALVVLLEEELVVIDLQT 101 (105)
T ss_pred ccCCCceEEEEeCCEEEEEEcCCceEEEEEEcCCCCccccCCCcEEEEEEcCcEEEEECCC
Confidence 3478899999888885544211111111111111 1234667888999999998765544
No 24
>PF05420 BCSC_C: Cellulose synthase operon protein C C-terminus (BCSC_C); InterPro: IPR008410 This entry contains the C-terminal regions of several bacterial cellulose synthase operon C (BCSC) proteins. BCSC is involved in cellulose synthesis although the exact function of this protein is unknown [].; GO: 0030244 cellulose biosynthetic process, 0019867 outer membrane
Probab=26.56 E-value=45 Score=28.76 Aligned_cols=35 Identities=37% Similarity=0.617 Sum_probs=29.5
Q ss_pred ceEEEEEeEEeeeCcccCC--CceEEEEecCCCeEEE
Q psy6196 40 VGYYYYCGRNIQENQYVKM--GAYHTLDLELNRKFEL 74 (146)
Q Consensus 40 ~~~LRI~G~i~~~~e~v~~--G~yHTl~i~~~~~~tI 74 (146)
.+-=+++|.+|+.|..+.+ |.|+.+--++++++++
T Consensus 165 ~~~~~ltG~nV~~N~~~~~~~G~y~~~~~~~~~~l~~ 201 (342)
T PF05420_consen 165 GGYHYLTGENVADNTRVEAMAGAYYRLINEPDRRLTV 201 (342)
T ss_pred eeeEEEeCcccCCCceEEEeeEEEEEcccCCCCEEEE
Confidence 3445789999999999988 9999998888888776
No 25
>TIGR03630 arch_S17P archaeal ribosomal protein S17P. This model describes exclusively the archaeal ribosomal protein S17P. It excludes homologous ribosomal proteins S11 from eukaryotes and S17 from bacteria.
Probab=26.36 E-value=55 Score=23.50 Aligned_cols=17 Identities=18% Similarity=0.170 Sum_probs=14.0
Q ss_pred CCCceEEEEEeEEeeeC
Q psy6196 37 TPAVGYYYYCGRNIQEN 53 (146)
Q Consensus 37 ~~~~~~LRI~G~i~~~~ 53 (146)
-||.+.|+|+|++..|-
T Consensus 17 cpf~g~l~irgk~l~G~ 33 (102)
T TIGR03630 17 CPFHGHLKVRGQILEGV 33 (102)
T ss_pred CCccceeeeeeEEEEEE
Confidence 36789999999998763
No 26
>PF14250 AbrB-like: AbrB-like transcriptional regulator
Probab=26.30 E-value=37 Score=22.89 Aligned_cols=24 Identities=25% Similarity=0.407 Sum_probs=15.6
Q ss_pred eCcccCCCceEE--EEecCCCeEEEE
Q psy6196 52 ENQYVKMGAYHT--LDLELNRKFELS 75 (146)
Q Consensus 52 ~~e~v~~G~yHT--l~i~~~~~~tI~ 75 (146)
.|-..=+|+-=| ++++||++|.|.
T Consensus 37 ~NGnLLIG~AYT~~m~L~PGdEFeI~ 62 (71)
T PF14250_consen 37 GNGNLLIGSAYTKQMGLKPGDEFEIK 62 (71)
T ss_pred cCCCEEEcHHHHHHhCCCCCCEEEEE
Confidence 343343454333 789999999985
No 27
>PF09345 DUF1987: Domain of unknown function (DUF1987); InterPro: IPR018530 This family of proteins are functionally uncharacterised.
Probab=23.80 E-value=34 Score=24.21 Aligned_cols=21 Identities=24% Similarity=0.292 Sum_probs=18.0
Q ss_pred ccCCCCCceEEEEEeEEeeeC
Q psy6196 33 KSPFTPAVGYYYYCGRNIQEN 53 (146)
Q Consensus 33 ~vef~~~~~~LRI~G~i~~~~ 53 (146)
.|.||+..++|+|+|.-..++
T Consensus 2 ~V~Fd~~~g~l~i~GeSypEn 22 (99)
T PF09345_consen 2 EVDFDFDTGRLEISGESYPEN 22 (99)
T ss_pred eEEEEccCCEEEEecccCccC
Confidence 478999999999999987655
No 28
>KOG3069|consensus
Probab=23.58 E-value=1.4e+02 Score=24.75 Aligned_cols=42 Identities=26% Similarity=0.317 Sum_probs=35.2
Q ss_pred cCCccEEEEEEec--CeEEEEEEecceeEEEEEEEeeCCCccCC
Q psy6196 94 EKTADVAAVMMQE--GLANIMLITASMSLVRTKIETNIPRKRRG 135 (146)
Q Consensus 94 ~~~~~v~~v~~~e--G~A~i~lv~~~~~~~~~~i~~~ipkK~~~ 135 (146)
.+++.|++.++++ |++.+-|-.++.+.-...-++..||-|+.
T Consensus 41 ~~~~aVlI~L~~~~~~~l~vLltkRSr~LrshsGev~fPGG~~d 84 (246)
T KOG3069|consen 41 NRKAAVLIPLVQVGSGELSVLLTKRSRTLRSHSGEVCFPGGRRD 84 (246)
T ss_pred CCCccEEEEEEEcCCCceEEEEEeccccccccCCceeCCCCcCC
Confidence 4578888888887 88888888889998899999999987654
No 29
>KOG1896|consensus
Probab=23.03 E-value=1.3e+02 Score=30.53 Aligned_cols=62 Identities=23% Similarity=0.315 Sum_probs=42.2
Q ss_pred eEEeeeCcccCC-CceEEEEe-----cCCCeEEEEcCCCChHHHHHHHHHhcccCCccEEEEEEecCeEEEEEEecceeE
Q psy6196 47 GRNIQENQYVKM-GAYHTLDL-----ELNRKFELSKPEWDSIALERIEVACNIEKTADVAAVMMQEGLANIMLITASMSL 120 (146)
Q Consensus 47 G~i~~~~e~v~~-G~yHTl~i-----~~~~~~tI~K~~Wd~~~le~L~eA~~~~~~~~v~~v~~~eG~A~i~lv~~~~~~ 120 (146)
|......|++.. |+.|-++| +||+++|=.| |++....+.++.|.+|-==.| .++..+|.+
T Consensus 1052 GT~~~~gEDv~~RGr~hi~diIeVVPepgkP~t~~K----------lKel~~eE~KGtVsavceV~G----~l~~~~GqK 1117 (1366)
T KOG1896|consen 1052 GTAFIQGEDVPARGRIHIFDIIEVVPEPGKPFTKNK----------LKELYIEEQKGTVSAVCEVRG----HLLSSQGQK 1117 (1366)
T ss_pred EEeecccccccCcccEEEEEEEEecCCCCCCcccce----------eeeeehhhcccceEEEEEecc----EEEEccCcE
Confidence 444446788888 99999998 7888888655 455555667777777732234 566777766
Q ss_pred EE
Q psy6196 121 VR 122 (146)
Q Consensus 121 ~~ 122 (146)
+.
T Consensus 1118 I~ 1119 (1366)
T KOG1896|consen 1118 II 1119 (1366)
T ss_pred EE
Confidence 64
No 30
>COG3081 Nucleoid-associated protein [General function prediction only]
Probab=22.78 E-value=42 Score=28.54 Aligned_cols=25 Identities=16% Similarity=0.179 Sum_probs=21.4
Q ss_pred hHHHhcccccCCCCCceEEEEEeEE
Q psy6196 25 LYTARIGLKSPFTPAVGYYYYCGRN 49 (146)
Q Consensus 25 ~~~~~L~~~vef~~~~~~LRI~G~i 49 (146)
+.-+.|+..|.|||.++.|-|+|.-
T Consensus 296 FdA~LLg~rvfwD~~tDtLtIkg~P 320 (335)
T COG3081 296 FDAMLLGERVFWDPATDTLTIKGTP 320 (335)
T ss_pred ehhhhhCCeeeeccccceeEecCCC
Confidence 4557888899999999999999963
No 31
>TIGR02571 ComEB ComE operon protein 2. This protein is found in the ComE operon for "late competence" as characterized in B. subtilis. Proteins in this family contain homology to a cytidine/deoxycytidine deaminase domain family (pfam00383), and may carry out this activity.
Probab=22.59 E-value=1.3e+02 Score=22.75 Aligned_cols=33 Identities=12% Similarity=0.236 Sum_probs=21.9
Q ss_pred CCCChHHHHHHHHHhccc--CCccEEEEEEecCeE
Q psy6196 77 PEWDSIALERIEVACNIE--KTADVAAVMMQEGLA 109 (146)
Q Consensus 77 ~~Wd~~~le~L~eA~~~~--~~~~v~~v~~~eG~A 109 (146)
..||...+++..+....+ .+..|++|++.+|+.
T Consensus 3 ~~~d~~fM~~A~~~A~rs~~~~~~VGAVIV~d~~I 37 (151)
T TIGR02571 3 IKWDQYFMAQSHLLALRSTCTRLSVGATIVRDKRI 37 (151)
T ss_pred CcHHHHHHHHHHHHHHhcCCCCCCEEEEEEECCEE
Confidence 368877666655544332 356899999988874
No 32
>PRK08572 rps17p 30S ribosomal protein S17P; Reviewed
Probab=20.86 E-value=80 Score=22.87 Aligned_cols=17 Identities=18% Similarity=0.221 Sum_probs=13.9
Q ss_pred CCCceEEEEEeEEeeeC
Q psy6196 37 TPAVGYYYYCGRNIQEN 53 (146)
Q Consensus 37 ~~~~~~LRI~G~i~~~~ 53 (146)
-||.+.|+|+|++..|-
T Consensus 19 cP~~g~l~irgk~l~G~ 35 (108)
T PRK08572 19 CPFHGTLPVRGQVLEGT 35 (108)
T ss_pred CCCcceeeeeeEEEEEE
Confidence 46779999999998763
No 33
>cd01780 PLC_epsilon_RA Ubiquitin-like domain of Phosphatidylinositide-specific phospholipase. PLC_epsilon_RA Phosphatidylinositide-specific phospholipase C (PLC) is a signaling enzyme that hydrolyzes membrane phospholipids to generate inositol triphosphate. PLC-epsilon represents a novel forth class of PLC that has a PLC catalytic core domain, a CDC25 guanine nucleotide exchange factor domain and two RA (Ras-association) domains of which the second is critical for Ras activation of the enzyme.
Probab=20.75 E-value=2e+02 Score=20.40 Aligned_cols=32 Identities=9% Similarity=0.146 Sum_probs=26.9
Q ss_pred EecCCCeEEEEcCCCChHHHHHHHHHhcccCC
Q psy6196 65 DLELNRKFELSKPEWDSIALERIEVACNIEKT 96 (146)
Q Consensus 65 ~i~~~~~~tI~K~~Wd~~~le~L~eA~~~~~~ 96 (146)
++.++.+++|.|-.=-+-+.+.|.+|.-..++
T Consensus 7 ~vs~dqP~~il~a~~~STa~Dvi~Qal~KA~r 38 (93)
T cd01780 7 NVSPDQPYAILRAPRVSTAQDVIQQTLCKARR 38 (93)
T ss_pred cCCCCCCeeEEEccccccHHHHHHHHHHHhcc
Confidence 67789999999988888999999998765544
No 34
>PF00240 ubiquitin: Ubiquitin family; InterPro: IPR000626 Ubiquitinylation is an ATP-dependent process that involves the action of at least three enzymes: a ubiquitin-activating enzyme (E1, IPR000011 from INTERPRO), a ubiquitin-conjugating enzyme (E2, IPR000608 from INTERPRO), and a ubiquitin ligase (E3, IPR000569 from INTERPRO, IPR003613 from INTERPRO), which work sequentially in a cascade. There are many different E3 ligases, which are responsible for the type of ubiquitin chain formed, the specificity of the target protein, and the regulation of the ubiquitinylation process []. Ubiquitinylation is an important regulatory tool that controls the concentration of key signalling proteins, such as those involved in cell cycle control, as well as removing misfolded, damaged or mutant proteins that could be harmful to the cell. Several ubiquitin-like molecules have been discovered, such as Ufm1 (IPR005375 from INTERPRO), SUMO1 (IPR003653 from INTERPRO), NEDD8, Rad23 (IPR004806 from INTERPRO), Elongin B and Parkin (IPR003977 from INTERPRO), the latter being involved in Parkinson's disease []. Ubiquitin is a protein of 76 amino acid residues, found in all eukaryotic cells and whose sequence is extremely well conserved from protozoan to vertebrates. Ubiquitin acts through its post-translational attachment (ubiquitinylation) to other proteins, where these modifications alter the function, location or trafficking of the protein, or targets it for destruction by the 26S proteasome []. The terminal glycine in the C-terminal 4-residue tail of ubiquitin can form an isopeptide bond with a lysine residue in the target protein, or with a lysine in another ubiquitin molecule to form a ubiquitin chain that attaches itself to a target protein. Ubiquitin has seven lysine residues, any one of which can be used to link ubiquitin molecules together, resulting in different structures that alter the target protein in different ways. It appears that Lys(11)-, Lys(29) and Lys(48)-linked poly-ubiquitin chains target the protein to the proteasome for degradation, while mono-ubiquitinylated and Lys(6)- or Lys(63)-linked poly-ubiquitin chains signal reversible modifications in protein activity, location or trafficking []. For example, Lys(63)-linked poly-ubiquitinylation is known to be involved in DNA damage tolerance, inflammatory response, protein trafficking and signal transduction through kinase activation []. In addition, the length of the ubiquitin chain alters the fate of the target protein. Regulatory proteins such as transcription factors and histones are frequent targets of ubquitinylation [].; GO: 0005515 protein binding; PDB: 2DZI_A 2XEW_E 3NOB_E 2KWU_B 2Y5B_F 3PHD_G 2KWV_B 2KOX_A 2XK5_B 3NHE_B ....
Probab=20.32 E-value=1.4e+02 Score=18.40 Aligned_cols=58 Identities=14% Similarity=0.297 Sum_probs=38.1
Q ss_pred ceEEEEcCCcChhHHHhccc--ccCCCCCceEEEEEeEEeeeCcccCCCceEEEEecCCCeEEEE
Q psy6196 13 RKFELSKPEWDSLYTARIGL--KSPFTPAVGYYYYCGRNIQENQYVKMGAYHTLDLELNRKFELS 75 (146)
Q Consensus 13 ~~ftl~K~~wd~~~~~~L~~--~vef~~~~~~LRI~G~i~~~~e~v~~G~yHTl~i~~~~~~tI~ 75 (146)
+.|++.-++++.+....-.+ .....+..-+|-..|+..+. .-.++.| .|..|+.+.+.
T Consensus 6 ~~~~~~v~~~~tV~~lK~~i~~~~~~~~~~~~L~~~G~~L~d--~~tL~~~---~i~~~~~I~l~ 65 (69)
T PF00240_consen 6 KTFTLEVDPDDTVADLKQKIAEETGIPPEQQRLIYNGKELDD--DKTLSDY---GIKDGSTIHLV 65 (69)
T ss_dssp EEEEEEEETTSBHHHHHHHHHHHHTSTGGGEEEEETTEEEST--TSBTGGG---TTSTTEEEEEE
T ss_pred cEEEEEECCCCCHHHhhhhcccccccccccceeeeeeecccC--cCcHHHc---CCCCCCEEEEE
Confidence 45666666667666554443 55678888999999999943 3345655 56666665544
No 35
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=20.19 E-value=1.5e+02 Score=21.22 Aligned_cols=36 Identities=22% Similarity=0.221 Sum_probs=28.9
Q ss_pred CceEEEEEeEEeeeCcccCCCceEEEEecCCCeEEEEc
Q psy6196 39 AVGYYYYCGRNIQENQYVKMGAYHTLDLELNRKFELSK 76 (146)
Q Consensus 39 ~~~~LRI~G~i~~~~e~v~~G~yHTl~i~~~~~~tI~K 76 (146)
.+++.+|.|..+..+..|+.|-- |+|..|...-.+|
T Consensus 32 ~~GrV~vNG~~aKpS~~VK~GD~--l~i~~~~~~~~v~ 67 (100)
T COG1188 32 EGGRVKVNGQRAKPSKEVKVGDI--LTIRFGNKEFTVK 67 (100)
T ss_pred HCCeEEECCEEcccccccCCCCE--EEEEeCCcEEEEE
Confidence 37999999999999999999987 6666676655544
Done!