Query 020677
Match_columns 323
No_of_seqs 136 out of 577
Neff 7.1
Searched_HMMs 46136
Date Fri Mar 29 04:17:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020677.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020677hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2869 Meiotic cell division 100.0 1.8E-94 3.9E-99 662.2 26.7 322 1-322 1-324 (379)
2 TIGR00111 pelota probable tran 100.0 2.3E-86 4.9E-91 637.4 39.2 301 1-316 1-304 (351)
3 COG1537 PelA Predicted RNA-bin 100.0 1.3E-81 2.8E-86 588.1 35.1 303 1-322 1-305 (352)
4 TIGR00108 eRF peptide chain re 100.0 2.8E-50 6.1E-55 393.7 17.6 270 29-316 27-319 (409)
5 TIGR03676 aRF1/eRF1 peptide ch 100.0 2E-45 4.3E-50 358.4 28.1 225 73-315 76-314 (403)
6 PRK04011 peptide chain release 100.0 9.2E-45 2E-49 355.1 27.9 229 73-317 83-324 (411)
7 PF03463 eRF1_1: eRF1 domain 1 100.0 6.9E-39 1.5E-43 268.3 7.4 128 1-128 1-131 (132)
8 COG1503 eRF1 Peptide chain rel 100.0 1.9E-33 4E-38 269.4 16.8 227 73-316 83-322 (411)
9 PF03464 eRF1_2: eRF1 domain 2 100.0 2E-29 4.4E-34 211.3 15.7 126 134-266 1-133 (133)
10 KOG0688 Peptide chain release 100.0 7.2E-29 1.6E-33 228.3 7.4 226 74-316 85-323 (431)
11 PF03465 eRF1_3: eRF1 domain 3 99.4 1.6E-13 3.5E-18 111.8 5.6 52 269-320 1-52 (113)
12 PF10116 Host_attach: Protein 95.2 0.074 1.6E-06 44.5 7.0 90 136-225 2-116 (138)
13 PF01248 Ribosomal_L7Ae: Ribos 67.8 12 0.00027 28.7 4.9 37 278-315 5-41 (95)
14 PRK07283 hypothetical protein; 65.9 7 0.00015 30.8 3.2 32 284-315 13-44 (98)
15 PRK07714 hypothetical protein; 65.1 7.1 0.00015 30.8 3.1 32 284-315 13-44 (100)
16 TIGR03677 rpl7ae 50S ribosomal 64.7 14 0.00031 30.0 4.9 30 286-315 23-52 (117)
17 PRK05583 ribosomal protein L7A 62.8 8.5 0.00018 30.7 3.1 32 284-315 12-43 (104)
18 TIGR01175 pilM type IV pilus a 62.1 1E+02 0.0022 29.3 11.1 90 135-224 190-307 (348)
19 PF08032 SpoU_sub_bind: RNA 2' 59.6 12 0.00027 27.1 3.4 24 291-314 2-26 (76)
20 PRK04175 rpl7ae 50S ribosomal 58.7 24 0.00052 28.9 5.2 40 276-316 18-57 (122)
21 PRK13602 putative ribosomal pr 58.7 19 0.0004 27.4 4.3 33 282-315 5-37 (82)
22 PTZ00106 60S ribosomal protein 58.7 21 0.00045 28.7 4.7 39 276-315 13-51 (108)
23 PF03485 Arg_tRNA_synt_N: Argi 57.8 12 0.00025 28.3 3.0 29 183-211 52-81 (85)
24 PRK01018 50S ribosomal protein 55.2 28 0.00062 27.3 4.9 29 287-315 14-42 (99)
25 PRK09190 hypothetical protein; 55.1 50 0.0011 30.1 7.1 32 284-315 106-137 (220)
26 PRK13601 putative L7Ae-like ri 50.4 25 0.00055 26.8 3.8 29 287-315 6-34 (82)
27 PRK06683 hypothetical protein; 49.7 33 0.00071 26.1 4.3 30 286-315 8-37 (82)
28 PRK13600 putative ribosomal pr 49.6 28 0.0006 26.8 3.9 26 290-315 14-39 (84)
29 PRK09557 fructokinase; Reviewe 48.1 66 0.0014 30.0 7.1 47 179-225 224-270 (301)
30 PRK05082 N-acetylmannosamine k 47.8 41 0.00089 31.2 5.6 46 180-225 214-259 (291)
31 COG1105 FruK Fructose-1-phosph 42.8 94 0.002 29.8 7.2 110 115-258 63-178 (310)
32 COG1855 ATPase (PilT family) [ 40.7 3.9E+02 0.0086 27.4 11.2 80 135-225 202-289 (604)
33 COG1358 RPL8A Ribosomal protei 38.6 61 0.0013 26.4 4.5 30 286-315 24-53 (116)
34 smart00536 AXH domain in Ataxi 37.2 1.3E+02 0.0028 24.6 6.1 78 13-122 12-92 (116)
35 PRK13310 N-acetyl-D-glucosamin 36.8 1.2E+02 0.0025 28.3 6.9 47 179-225 225-271 (303)
36 COG4972 PilM Tfp pilus assembl 34.3 66 0.0014 31.2 4.6 48 176-223 257-311 (354)
37 COG0018 ArgS Arginyl-tRNA synt 31.7 84 0.0018 32.8 5.3 61 185-245 57-126 (577)
38 PF11104 PilM_2: Type IV pilus 31.1 2.4E+02 0.0052 26.9 8.1 89 134-224 181-299 (340)
39 PF04628 Sedlin_N: Sedlin, N-t 30.4 2.9E+02 0.0064 22.5 7.5 71 118-195 35-106 (132)
40 PF07116 DUF1372: Protein of u 27.3 96 0.0021 24.7 3.7 38 78-118 55-92 (104)
41 PF08447 PAS_3: PAS fold; Int 27.0 2.4E+02 0.0052 20.2 6.2 59 18-85 31-91 (91)
42 COG1911 RPL30 Ribosomal protei 25.4 1.1E+02 0.0024 24.2 3.7 32 285-316 15-46 (100)
43 PF14213 DUF4325: Domain of un 23.8 87 0.0019 22.9 2.9 68 181-255 4-72 (74)
44 PRK15080 ethanolamine utilizat 23.6 1.8E+02 0.0038 26.9 5.5 87 135-223 137-245 (267)
45 PF09345 DUF1987: Domain of un 23.3 68 0.0015 25.4 2.3 21 70-90 3-23 (99)
46 TIGR00744 ROK_glcA_fam ROK fam 23.1 2.6E+02 0.0056 26.0 6.7 47 179-225 231-278 (318)
47 COG1940 NagC Transcriptional r 22.4 2E+02 0.0043 26.9 5.7 46 180-225 228-275 (314)
48 PF01336 tRNA_anti-codon: OB-f 22.4 1.2E+02 0.0025 21.3 3.3 33 10-43 23-55 (75)
49 PRK10439 enterobactin/ferric e 21.3 1.4E+02 0.003 29.7 4.5 49 212-260 262-312 (411)
50 PRK09698 D-allose kinase; Prov 20.9 3.1E+02 0.0067 25.4 6.7 47 179-225 216-263 (302)
51 PRK06851 hypothetical protein; 20.5 1.5E+02 0.0033 29.1 4.6 43 179-228 201-243 (367)
52 PF00158 Sigma54_activat: Sigm 20.5 3E+02 0.0065 23.5 6.0 57 178-247 6-62 (168)
No 1
>KOG2869 consensus Meiotic cell division protein Pelota/DOM34 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.8e-94 Score=662.22 Aligned_cols=322 Identities=57% Similarity=0.905 Sum_probs=317.7
Q ss_pred CeeeeeecccCCCceEEEeccCCchhhhHhhhcCCCCEEEEEeEEEEEeccCCCCccceEEEEEEEEEE--EEeecCCCe
Q 020677 1 MKILRRNLVENGPGSVKMEPVDSDDLWFAYNLIAPGDSVMAVTVRKVLRQMASGSRDAERVKLKLEIKV--VDYDKEGSV 78 (323)
Q Consensus 1 Mki~~~~~~~~~~g~v~l~~E~~dDlw~lynli~~GD~V~a~T~Rkv~~~~~~g~~~~~r~~~~L~i~V--vef~~~~~~ 78 (323)
||++++++.++|.|+|+++||+.|||||+||+|++||.|+|.|.|||+.+..+|+++++|+.++|+|+| ++||+.++.
T Consensus 1 MKli~K~~~rng~G~vtmvpEe~eDmw~~ynli~~gD~v~a~T~rkvq~e~a~G~~~s~rv~~~L~i~VesidfD~~~~~ 80 (379)
T KOG2869|consen 1 MKLIRKDIERNGSGSVTMVPEESEDLWHLYNLIQVGDSVIASTIRKVQKEEATGKTKSSRVLLKLKIKVESIDFDTKACV 80 (379)
T ss_pred CccchhhhhcCCCceEEECcCchhHHHHHHhhccCCceeEEEEEEEeeeccccCcccceEEEEEEEEEEEEeeccccccE
Confidence 999999999999999999999999999999999999999999999999998889888899999999999 999999999
Q ss_pred EEEEEEEeecCcccccccEEEEEEccCceeEEEEcccChhhHHHHHHhcCCCCCCcEEEEEEeCCeEEEEEEecceEEEE
Q 020677 79 LRIRGKNILENEHVKIGAFHTLEIELHRAFVLRKDLWDSLALDTLHQAADPTASADLAVVLMQEGLAHILLVGRSMTITR 158 (323)
Q Consensus 79 Lri~G~i~~~~e~v~~G~~HTi~i~~~~~~~i~K~~wd~~~~e~L~~a~~~~~~~~~~~vvid~g~A~i~ll~~~~~~~~ 158 (323)
||++|+++++|++|++|+|||++|+++++|++.|.+||++.+++|++||++..++++++|+++||.|+||+++.++|..+
T Consensus 81 L~~KGrti~eNe~Vk~GaYHTidlel~r~FtL~K~ewds~al~~l~~A~dp~~~ad~aaVvlqEGla~IcLvt~s~tilr 160 (379)
T KOG2869|consen 81 LRLKGRTIEENEYVKMGAYHTIDLELNRPFTLRKEEWDSMALKLLKEACDPAPSADVAAVVLQEGLAHICLVTKSSTILR 160 (379)
T ss_pred EEEeeeeeeecccccccceeEEEeccCCceEEEhhhchHHHHHHHHHhhCcccccceeeeehhcCceeEEEechhHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEEecCCCCCCCcchhhHHHHHHHHHHHHHHHhcccccCccEEEEECCcccHHHHHHHHHHHHHhccccccccccCcE
Q 020677 159 SRIETSIPRKHGPAIAGYESALNKFFENVLQAFLKHVDFNVVRCAVIASPGFTKDQFHRHLLLEAERRQLRPIIENKSRI 238 (323)
Q Consensus 159 ~~i~~~ip~K~~~~~s~~~~~~~~f~~~v~~~l~~~~~~~~v~~iIIaGPGf~kd~f~~~l~~~~~~~~~~~~~~~~~ki 238 (323)
++|+.++|+||+++.|++++.+++||++|.+++.++++|+.++|+|||||||+++.|++|+.+.+.+..++.++.|++||
T Consensus 161 ~kIe~siPrKr~~~~s~~e~~l~kfye~V~qA~~k~v~fd~vk~~vvASpgF~~~~~~d~~~q~A~~~~~k~il~nk~kf 240 (379)
T KOG2869|consen 161 AKIEVSIPRKRKGDVSQHEEGLEKFYENVVQAILKHVNFDVVKCVVVASPGFVKDQFMDYLFQQAVKLDLKLILENKSKF 240 (379)
T ss_pred HhhhcccccccCcchhHHHHHHHHHHHHHHHHHHHhcCcceEEEEEEcCCchhHHHHHHHHHHHHHHhchhhhhhcccce
Confidence 99999999998888889999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEcCCCccchHHHHhcChhHHHhhhhhhHHHHHHHHHHHHHHhhcCCCeEEEcHHHHHHHHhcCCccEEEEecCCccc
Q 020677 239 ILVHTSSGYKHSLREVLDAPNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHERMAVQTLLITDDLFRL 318 (323)
Q Consensus 239 ~~~~~s~~~~~gl~Evl~~~~v~~~l~d~k~~~e~~~le~f~~~l~~~~~~a~YG~~eV~~A~e~GAVetLLIsD~l~r~ 318 (323)
+.+|+|+|+.++|+|+|.+|.+.+.|+|+|++.|+++||+|+.+|+++|++||||++||.+|+|+|||++|||||++||+
T Consensus 241 ~~~h~ssg~~hslnevL~dp~v~~~l~dtK~~~EvkalddF~~~l~~~~drA~yG~khV~~A~e~~AI~tLLitD~lfr~ 320 (379)
T KOG2869|consen 241 PLVHASSGYKHSLNEVLKDPAVASKLQDTKAAKEVKALDDFYVMLSKDPDRACYGPKHVEKANEYGAIETLLITDELFRS 320 (379)
T ss_pred eEEecCCchHHHHHHHhcChHHHHHhhchhhHHHHHHHHHHHHHhccCccccccCHHHHHHHHhhcchhheehhhhhccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCC
Q 020677 319 VCSK 322 (323)
Q Consensus 319 ~d~~ 322 (323)
.|++
T Consensus 321 ~DV~ 324 (379)
T KOG2869|consen 321 QDVA 324 (379)
T ss_pred ccHH
Confidence 9985
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=100.00 E-value=2.3e-86 Score=637.38 Aligned_cols=301 Identities=28% Similarity=0.495 Sum_probs=285.3
Q ss_pred CeeeeeecccCCCceEEEeccCCchhhhHhhhcCCCCEEEEEeEEEEEeccCCCCccceEEEEEEEEEE--EEeecCCCe
Q 020677 1 MKILRRNLVENGPGSVKMEPVDSDDLWFAYNLIAPGDSVMAVTVRKVLRQMASGSRDAERVKLKLEIKV--VDYDKEGSV 78 (323)
Q Consensus 1 Mki~~~~~~~~~~g~v~l~~E~~dDlw~lynli~~GD~V~a~T~Rkv~~~~~~g~~~~~r~~~~L~i~V--vef~~~~~~ 78 (323)
|||++++. ++++|.|+|.||++||||||||||++||+|+|+|+|+|++++.+|+++ +|++++|+|+| ++|||++++
T Consensus 1 Mki~~~~~-~~~~g~v~l~pe~~dDlw~l~nli~~GD~V~~~T~Rkv~~~~~~g~~~-er~~~~l~i~Ve~ief~~~~~~ 78 (351)
T TIGR00111 1 MSIVEESF-NKGGAVIKLLPETLDDLWHLYQIIEKGDVEFAFTKRRTQDLDKIRSDK-SKDTVKLGIEVESVEFDMKTER 78 (351)
T ss_pred Cceeeeec-CCCcEEEEEEeCChHHHHHHHHhCCCCCEEEEEEEEEEeccccCCCcc-eEEEEEEEEEEEEEEecCCCCE
Confidence 99999997 777889999999999999999999999999999999999887788777 99999999999 999999999
Q ss_pred EEEEEEEeecC-cccccccEEEEEEccCceeEEEEcccChhhHHHHHHhcCCCCCCcEEEEEEeCCeEEEEEEecceEEE
Q 020677 79 LRIRGKNILEN-EHVKIGAFHTLEIELHRAFVLRKDLWDSLALDTLHQAADPTASADLAVVLMQEGLAHILLVGRSMTIT 157 (323)
Q Consensus 79 Lri~G~i~~~~-e~v~~G~~HTi~i~~~~~~~i~K~~wd~~~~e~L~~a~~~~~~~~~~~vvid~g~A~i~ll~~~~~~~ 157 (323)
|||+|+|+++| ++|++|+|||++|+||++|+|+|++||+|++++|++|++++.++.+++|+||+|+|+||+|+++++++
T Consensus 79 Lri~G~i~~~~e~~v~~G~~HTl~ie~~~~i~i~K~~w~~~~le~L~ea~~~~~~~~~~~vv~d~g~A~i~ll~~~~~~~ 158 (351)
T TIGR00111 79 LRYKGVIVTGPEDDVPVGSYHTLEIKYVYPLSIIKQNWKKWQLKRLREAVEISKRPKTAAVVMEEGIAHVGLVRQYSVEE 158 (351)
T ss_pred EEEEEEEecCCcccccccceEEEEEcCCCcEEEEEecCCHHHHHHHHHHhccccCCcEEEEEEeCCcEEEEEEcCCEEEE
Confidence 99999999998 79999999999999999999999999999999999999999888999999999999999999999999
Q ss_pred EEEEEEecCCCCCCCcchhhHHHHHHHHHHHHHHHhcccccCccEEEEECCcccHHHHHHHHHHHHHhccccccccccCc
Q 020677 158 RSRIETSIPRKHGPAIAGYESALNKFFENVLQAFLKHVDFNVVRCAVIASPGFTKDQFHRHLLLEAERRQLRPIIENKSR 237 (323)
Q Consensus 158 ~~~i~~~ip~K~~~~~s~~~~~~~~f~~~v~~~l~~~~~~~~v~~iIIaGPGf~kd~f~~~l~~~~~~~~~~~~~~~~~k 237 (323)
++++++++|+|+++ +.+++++++||++|++++.+ +++++|||||||||+|++|++||.+++++.. .+
T Consensus 159 ~~~i~~~iP~K~~~--~~~e~~~~~Ff~~v~~~l~~---~~~v~~iIiaGPGf~k~~f~~~l~~~~~~~~--------~k 225 (351)
T TIGR00111 159 IQKIEYHMPGKKRT--LKFGELRKEFYKEIAKKLLN---FDDLKTIIVAGPGFYKNDFYDFIFERYPEEA--------NK 225 (351)
T ss_pred EEEEEEeCCCCccc--chhHHHHHHHHHHHHHHHhh---hcccCEEEEECCHHHHHHHHHHHHHHhhhhh--------CC
Confidence 99999999999854 55888999999999999854 4689999999999999999999999987632 34
Q ss_pred EEEEEcCCCccchHHHHhcChhHHHhhhhhhHHHHHHHHHHHHHHhhcCCCeEEEcHHHHHHHHhcCCccEEEEecCCc
Q 020677 238 IILVHTSSGYKHSLREVLDAPNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHERMAVQTLLITDDLF 316 (323)
Q Consensus 238 i~~~~~s~~~~~gl~Evl~~~~v~~~l~d~k~~~e~~~le~f~~~l~~~~~~a~YG~~eV~~A~e~GAVetLLIsD~l~ 316 (323)
.++.++|+||.+||+|+|++|.++++|+|+++++|.++||+||++|++|+++||||++||.+|+++|||++|||||++|
T Consensus 226 ~ii~~~s~g~~~gl~EvL~~~~v~~~l~d~k~~~E~~~l~~f~~~l~kd~~~~~YG~~eV~~Ale~GAVetLLIsD~l~ 304 (351)
T TIGR00111 226 AVLENCSTGGRAGINEVLKRGLVARILQETRYAKEIMVIDEFLEHLAKDGDKAVYGEDEVVKAAEYGAIEYLLVTDKVL 304 (351)
T ss_pred cEEEecCCCchhHHHHHHhChHHHHHHhhhhHHHHHHHHHHHHHHHhcCCCeEEECHHHHHHHHHcCCceEEEEecchh
Confidence 5678999999999999999999999999999999999999999999999999999999999999999999999999996
No 3
>COG1537 PelA Predicted RNA-binding proteins [General function prediction only]
Probab=100.00 E-value=1.3e-81 Score=588.08 Aligned_cols=303 Identities=32% Similarity=0.523 Sum_probs=282.5
Q ss_pred CeeeeeecccCCCceEEEeccCCchhhhHhhhcCCCCEEEEEeEEEEEeccCCCCccceEEEEEEEEEE--EEeecCCCe
Q 020677 1 MKILRRNLVENGPGSVKMEPVDSDDLWFAYNLIAPGDSVMAVTVRKVLRQMASGSRDAERVKLKLEIKV--VDYDKEGSV 78 (323)
Q Consensus 1 Mki~~~~~~~~~~g~v~l~~E~~dDlw~lynli~~GD~V~a~T~Rkv~~~~~~g~~~~~r~~~~L~i~V--vef~~~~~~ 78 (323)
||+++++. ++|.++|+||++||||||||+|++||.|+|+|+|+.++....++++++|++|+|+|+| +|||+|+++
T Consensus 1 M~ile~~~---k~g~I~l~pE~lDDLw~L~~Ii~~GD~v~a~T~Rr~~~~d~~r~~~~eri~m~L~IkVe~ieF~~f~nr 77 (352)
T COG1537 1 MRILEEDK---KRGVIKLVPETLDDLWHLYNIIEKGDKVFAKTTRRDESSDVIRSKKGERIPMTLGIKVEKIEFDKFANR 77 (352)
T ss_pred Ccceeccc---cCceEEEecCChHHHHHHHHhcCCCCEEEEEEEEecccccccccCcceEEEEEEEEEEEEEEeeecccE
Confidence 99999996 5999999999999999999999999999999999933222334788899999999999 999999999
Q ss_pred EEEEEEEeecCcccccccEEEEEEccCceeEEEEcccChhhHHHHHHhcCCCCCCcEEEEEEeCCeEEEEEEecceEEEE
Q 020677 79 LRIRGKNILENEHVKIGAFHTLEIELHRAFVLRKDLWDSLALDTLHQAADPTASADLAVVLMQEGLAHILLVGRSMTITR 158 (323)
Q Consensus 79 Lri~G~i~~~~e~v~~G~~HTi~i~~~~~~~i~K~~wd~~~~e~L~~a~~~~~~~~~~~vvid~g~A~i~ll~~~~~~~~ 158 (323)
|||+|+++++|+.+++|+|||++|++|++|+|.|.+|+++++++|++|++++.++.+++|+||+|+|+||++++|++.++
T Consensus 78 LRi~G~i~~~~e~~~~G~yHTi~v~~g~~i~I~K~~W~~~~lerLkeA~~~~~~~~~~~v~~degea~i~iv~~ygi~~~ 157 (352)
T COG1537 78 LRIKGPIVEGPEEVVKGSYHTINVTIGTEIEIEKEEWNKDQLERLKEAVEASKRPEVAIVVVDEGEAAIAIVRDYGIIIL 157 (352)
T ss_pred EEEEEEEEEcCcccccccceEEEeccCceEEEEEccCCHHHHHHHHHHhhcccCCceEEEEEecCceEEEEEeccceEEE
Confidence 99999999999998899999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEEecCCCCCCCcchhhHHHHHHHHHHHHHHHhcccccCccEEEEECCcccHHHHHHHHHHHHHhccccccccccCcE
Q 020677 159 SRIETSIPRKHGPAIAGYESALNKFFENVLQAFLKHVDFNVVRCAVIASPGFTKDQFHRHLLLEAERRQLRPIIENKSRI 238 (323)
Q Consensus 159 ~~i~~~ip~K~~~~~s~~~~~~~~f~~~v~~~l~~~~~~~~v~~iIIaGPGf~kd~f~~~l~~~~~~~~~~~~~~~~~ki 238 (323)
.+++.+.|+|+.... + +..+||.+|++++.+.+ +++.||||||||+|++|++|+.+..++. .++
T Consensus 158 ~~i~~~~~gK~~~~~--~--~~~k~~~~i~~~~~~~~---~~~~iIvaGPGF~k~~~~~~~~~~~p~~---------~~~ 221 (352)
T COG1537 158 GKIRSGIPGKREGDI--R--AERKFFDEIAKALKEYA---NLDIIIVAGPGFAKEDFYDFLRERYPEL---------ANI 221 (352)
T ss_pred EEEeccCCCCcccch--h--hHHHHHHHHHHHHHHhh---CCCeEEEeCCchHHHHHHHHHHHhcccc---------cce
Confidence 999999998865433 2 22899999999999987 6889999999999999999999998753 237
Q ss_pred EEEEcCCCccchHHHHhcChhHHHhhhhhhHHHHHHHHHHHHHHhhcCCCeEEEcHHHHHHHHhcCCccEEEEecCCccc
Q 020677 239 ILVHTSSGYKHSLREVLDAPNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHERMAVQTLLITDDLFRL 318 (323)
Q Consensus 239 ~~~~~s~~~~~gl~Evl~~~~v~~~l~d~k~~~e~~~le~f~~~l~~~~~~a~YG~~eV~~A~e~GAVetLLIsD~l~r~ 318 (323)
++.|+|++|.+|++|+|++|.+.++++++++++|.++||+|++.|++++++||||++||.+|++||||++|||+|++||+
T Consensus 222 ~~~~~s~~g~~gi~EvLkr~~v~ki~~e~ria~e~~~~e~fl~~iak~~~~v~YG~~eV~~A~e~GAve~LLv~De~lr~ 301 (352)
T COG1537 222 VIEDTSTGGRAGINEVLKRGAVDKILSETRIAEEIELVEEFLERLAKDDDKVAYGLEEVEKAAEYGAVETLLVTDELLRS 301 (352)
T ss_pred EEEeccCcchHHHHHHHhhhhHHhHhhhhHHHHHHHHHHHHHHHHhcCCCceeEcHHHHHHHHhcCcceeEEeehhhhcc
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCC
Q 020677 319 VCSK 322 (323)
Q Consensus 319 ~d~~ 322 (323)
.|++
T Consensus 302 ~~~~ 305 (352)
T COG1537 302 DDVE 305 (352)
T ss_pred cchh
Confidence 7754
No 4
>TIGR00108 eRF peptide chain release factor eRF/aRF, subunit 1. Alternative names include eRF1, SUP45, omnipotent suppressor protein 1.
Probab=100.00 E-value=2.8e-50 Score=393.66 Aligned_cols=270 Identities=20% Similarity=0.283 Sum_probs=236.6
Q ss_pred HhhhcCCCCEE--EEEeEEEEEeccCCCCccceEEEEEEEEEE-------EEeecCCCeEEEEEEEeecCcccccccEEE
Q 020677 29 AYNLIAPGDSV--MAVTVRKVLRQMASGSRDAERVKLKLEIKV-------VDYDKEGSVLRIRGKNILENEHVKIGAFHT 99 (323)
Q Consensus 29 lynli~~GD~V--~a~T~Rkv~~~~~~g~~~~~r~~~~L~i~V-------vef~~~~~~Lri~G~i~~~~e~v~~G~~HT 99 (323)
++.+|.|||.| .+.|.|+-...++.-..++.|.+|...|++ ..--|.++.++++|.|..++.. |+|||
T Consensus 27 isl~ipp~~~i~~~~~~l~~e~~~a~niks~~~r~~v~~ai~~~~~~lk~~~~~p~nglv~~~G~v~~~~~~---~~~~t 103 (409)
T TIGR00108 27 ISLYIPPDRQISDVAKHLREELSQASNIKSKQTRKNVLSAIEAILQRLKLFNKPPENGLVIFCGMVPREGPT---EKMET 103 (409)
T ss_pred EEEEeCCCCcHHHHHHHHHHHHhhhhcccccchhhhHHHHHHHHHHHhhccCCCCCCcEEEEEeEeccCCCc---ccEEE
Confidence 46789999999 888888743322222233678888887777 2334678999999999988743 89999
Q ss_pred EEEccCceeEEEEcccC-hhhHHHHHHhcCCCCCCcEEEEEEeCCeEEEEEEecceEEEEEEEEEecCCCCCC-Ccch--
Q 020677 100 LEIELHRAFVLRKDLWD-SLALDTLHQAADPTASADLAVVLMQEGLAHILLVGRSMTITRSRIETSIPRKHGP-AIAG-- 175 (323)
Q Consensus 100 i~i~~~~~~~i~K~~wd-~~~~e~L~~a~~~~~~~~~~~vvid~g~A~i~ll~~~~~~~~~~i~~~ip~K~~~-~~s~-- 175 (323)
++|+|++||+++||.|| +|++++|++|++... .+++|+||+|+|+||+++++++++++++++++|+||+. |||+
T Consensus 104 ~~iep~~pi~~~~y~~d~~f~le~L~e~~~~~~--~~g~VvvD~~~A~i~~l~g~~~~~~~~i~~~vp~K~~~GGqS~~R 181 (409)
T TIGR00108 104 YVIEPPEPIKTYIYHCDSKFYLEPLSEMLEEKD--KYGLIVLDRQEATIGLVKGKRITVLKKLTSGVPGKHKAGGQSARR 181 (409)
T ss_pred EEEeCCCceEEEEEccCChhHHHHHHHHhcCCC--CEEEEEEecCCEEEEEEcCCEEEEEEEEeeeCCCcccCCCcchhh
Confidence 99999999999999654 799999999999765 99999999999999999999999999999999999876 7776
Q ss_pred ----hhHHHHHHHHHHHHHHHhcc---cccCccEEEEECCcccHHHHHH--HHHHHHHhccccccccccCcE-EEEEcCC
Q 020677 176 ----YESALNKFFENVLQAFLKHV---DFNVVRCAVIASPGFTKDQFHR--HLLLEAERRQLRPIIENKSRI-ILVHTSS 245 (323)
Q Consensus 176 ----~~~~~~~f~~~v~~~l~~~~---~~~~v~~iIIaGPGf~kd~f~~--~l~~~~~~~~~~~~~~~~~ki-~~~~~s~ 245 (323)
+++++++||++|++.+.++| +..++++||||||||+|++|++ ||.+++.+ ++ .++++|+
T Consensus 182 f~r~~e~~~~~f~~~Vae~~~~~f~~~~~~~v~~IIlaGpg~~K~~f~~~~~l~~~l~~-----------kvi~~vdvs~ 250 (409)
T TIGR00108 182 FERLRELAAHEFLKKVGEVANEAFLPNDDVKLKGIILGGPGHTKEEFAEGEYLHHELKK-----------KVISTVDVSY 250 (409)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhcccccceEEEEeccHHHHHHhhhhhhHHHHhhh-----------hEEEEEEcCC
Confidence 68889999999999999986 2337999999999999999998 99998864 33 4789999
Q ss_pred CccchHHHHhcChhHHHhhhhhhHHHHHHHHHHHHHHhhcCCCeEEEcHHHHHHHHhcCCccEEEEecCCc
Q 020677 246 GYKHSLREVLDAPNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHERMAVQTLLITDDLF 316 (323)
Q Consensus 246 ~~~~gl~Evl~~~~v~~~l~d~k~~~e~~~le~f~~~l~~~~~~a~YG~~eV~~A~e~GAVetLLIsD~l~ 316 (323)
||.+|++|++++. +++|+++++++|.++|++|++++++|+|+||||+++|.+|+++|||+||||+|++.
T Consensus 251 gg~~gl~E~l~~~--~~~L~~~k~~~E~~lle~F~~ei~~d~G~avyG~~eV~~ALe~GAVetLLV~d~l~ 319 (409)
T TIGR00108 251 TGEFGIRELIEKS--ADVLAEVDYMREKKLVQRFLKELIQEDGLACYGEDEVLKALDLGAVETLIVSEDLE 319 (409)
T ss_pred CcccCHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHhcCCCcEEeCHHHHHHHHHhCCCcEEEEecccc
Confidence 9999999999976 99999999999999999999999999999999999999999999999999999993
No 5
>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=100.00 E-value=2e-45 Score=358.42 Aligned_cols=225 Identities=24% Similarity=0.296 Sum_probs=206.7
Q ss_pred ecCCCeEEEEEEEeecCcccccccEEEEEEccCceeEEEEcccC-hhhHHHHHHhcCCCCCCcEEEEEEeCCeEEEEEEe
Q 020677 73 DKEGSVLRIRGKNILENEHVKIGAFHTLEIELHRAFVLRKDLWD-SLALDTLHQAADPTASADLAVVLMQEGLAHILLVG 151 (323)
Q Consensus 73 ~~~~~~Lri~G~i~~~~e~v~~G~~HTi~i~~~~~~~i~K~~wd-~~~~e~L~~a~~~~~~~~~~~vvid~g~A~i~ll~ 151 (323)
-|.++..-++|.+..+. ...+|||++|+||+||+++||.|| +||+++|++|++.. +.+++|+||+++|.||+++
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---GTEKMETYVIEPPEPINTYLYRCDSKFYLEPLEEMLEEK--DVYGLIVLDRREATIGLLK 150 (403)
T ss_pred CCCCeEEEEEeeecCCC---CceeEEEEEEeCCCceEEEEecCCChHHHHHHHHHhcCC--CCEEEEEEecCceEEEEEc
Confidence 47889999999998754 336999999999999999999765 69999999999975 4999999999999999999
Q ss_pred cceEEEEEEEEEecCCCCCC-Ccch------hhHHHHHHHHHHHHHHHhccc---ccCccEEEEECCcccHHHHHH--HH
Q 020677 152 RSMTITRSRIETSIPRKHGP-AIAG------YESALNKFFENVLQAFLKHVD---FNVVRCAVIASPGFTKDQFHR--HL 219 (323)
Q Consensus 152 ~~~~~~~~~i~~~ip~K~~~-~~s~------~~~~~~~f~~~v~~~l~~~~~---~~~v~~iIIaGPGf~kd~f~~--~l 219 (323)
++++++++++++++|+||+. |||+ +++++++||++|++++.++|. ..++++||||||||+|++|.+ ||
T Consensus 151 g~~~e~~~~i~~~vp~K~~~GGqS~~Rf~R~~e~~~~~f~~~Vae~~~~~f~~~~~~~v~~lILaGpg~~K~~f~~~~~L 230 (403)
T TIGR03676 151 GKRIEVLKELTSGVPGKHRAGGQSARRFERLIEIAAHEFYKRVGEAANEAFLPLKDKKLKGILIGGPGPTKEEFAEGDYL 230 (403)
T ss_pred CCEEEEEEEEEeeCCCCccCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccEEEEeCCHHHHHHHhhhhhh
Confidence 99999999999999999875 7887 788999999999999988763 226999999999999999999 99
Q ss_pred HHHHHhccccccccccCcE-EEEEcCCCccchHHHHhcChhHHHhhhhhhHHHHHHHHHHHHHHhhcCCCeEEEcHHHHH
Q 020677 220 LLEAERRQLRPIIENKSRI-ILVHTSSGYKHSLREVLDAPNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVE 298 (323)
Q Consensus 220 ~~~~~~~~~~~~~~~~~ki-~~~~~s~~~~~gl~Evl~~~~v~~~l~d~k~~~e~~~le~f~~~l~~~~~~a~YG~~eV~ 298 (323)
++++.+ ++ .++++|+++.+|++|++++. +++|++.++++|.++|++||++++++++++|||+++|.
T Consensus 231 ~~~l~~-----------kvi~~vd~s~~~~~Gl~Evl~~~--~~~L~~~k~~~E~~lle~f~~el~~d~g~avyG~~eV~ 297 (403)
T TIGR03676 231 HHELKK-----------KILGLFDVSYTGESGLRELVEKA--EDLLKDLELMKEKKLMERFFKELVKDGGLAAYGEEEVR 297 (403)
T ss_pred hHHHHh-----------hEEEEEecCCCCccCHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHhcCCCcEEEcHHHHH
Confidence 998764 34 68899999999999999985 99999999999999999999999999999999999999
Q ss_pred HHHhcCCccEEEEecCC
Q 020677 299 VAHERMAVQTLLITDDL 315 (323)
Q Consensus 299 ~A~e~GAVetLLIsD~l 315 (323)
+|+++|||+||||+|++
T Consensus 298 ~ALe~GAVetLLV~d~l 314 (403)
T TIGR03676 298 KALEMGAVDTLLISEDL 314 (403)
T ss_pred HHHHhCCCcEEEEEccc
Confidence 99999999999999999
No 6
>PRK04011 peptide chain release factor 1; Provisional
Probab=100.00 E-value=9.2e-45 Score=355.06 Aligned_cols=229 Identities=23% Similarity=0.282 Sum_probs=209.4
Q ss_pred ecCCCeEEEEEEEeecCcccccccEEEEEEccCceeEEEEcccCh-hhHHHHHHhcCCCCCCcEEEEEEeCCeEEEEEEe
Q 020677 73 DKEGSVLRIRGKNILENEHVKIGAFHTLEIELHRAFVLRKDLWDS-LALDTLHQAADPTASADLAVVLMQEGLAHILLVG 151 (323)
Q Consensus 73 ~~~~~~Lri~G~i~~~~e~v~~G~~HTi~i~~~~~~~i~K~~wd~-~~~e~L~~a~~~~~~~~~~~vvid~g~A~i~ll~ 151 (323)
-|.++..-++|.+..+.+ ..|.|||++|+||+||+++||.||+ |++++|++|++. ++.+++|+||+|+|.||+++
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 467888999999887642 2389999999999999999998776 999999999987 45999999999999999999
Q ss_pred cceEEEEEEEEEecCCCCCC-Ccch------hhHHHHHHHHHHHHHHHhccc---ccCccEEEEECCcccHHHHHH--HH
Q 020677 152 RSMTITRSRIETSIPRKHGP-AIAG------YESALNKFFENVLQAFLKHVD---FNVVRCAVIASPGFTKDQFHR--HL 219 (323)
Q Consensus 152 ~~~~~~~~~i~~~ip~K~~~-~~s~------~~~~~~~f~~~v~~~l~~~~~---~~~v~~iIIaGPGf~kd~f~~--~l 219 (323)
++++++++++++++|+||+. |||+ +++++++||++|++++.++|. +.++++||||||||+|++|.+ ||
T Consensus 159 g~~~~~~~~i~~~vp~K~~~GG~S~~Rf~r~~e~~~~~f~k~Vae~~~~~f~~~~~~~v~~IvlaGpg~~K~~f~~~~~L 238 (411)
T PRK04011 159 GKRIEVLKELTSFVPGKHRKGGQSARRFERLIEQAAHEFYKRVGEKANEAFLPLLEGKLKGILIGGPGPTKEEFLEGDYL 238 (411)
T ss_pred CCEEEEEEEEEeeCCCCccCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccEEEEECChhHHHHHhhhhhh
Confidence 99999999999999999885 7776 588999999999999998875 478999999999999999999 99
Q ss_pred HHHHHhccccccccccCcEEEEEcCCCccchHHHHhcChhHHHhhhhhhHHHHHHHHHHHHHHhhcCCCeEEEcHHHHHH
Q 020677 220 LLEAERRQLRPIIENKSRIILVHTSSGYKHSLREVLDAPNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEV 299 (323)
Q Consensus 220 ~~~~~~~~~~~~~~~~~ki~~~~~s~~~~~gl~Evl~~~~v~~~l~d~k~~~e~~~le~f~~~l~~~~~~a~YG~~eV~~ 299 (323)
++++.++ -+.++++|+++.+|++|++++. +++|+++++++|.++|++|+++++++++++|||+++|.+
T Consensus 239 ~~~l~~~----------vv~~~~~s~~~~~Gl~E~l~~~--~~~L~~~k~~~e~~lle~f~~~l~~d~g~avyG~~~V~~ 306 (411)
T PRK04011 239 HYELKKK----------ILGLFDVSYTGESGLRELVDKA--SDLLKEQELVKEKKLMEEFFKELAKDGGLAVYGEEEVRK 306 (411)
T ss_pred hHHHHhh----------eEEEEecCCCCccCHHHHHHHH--HHHHHHhHHHHHHHHHHHHHHHHhcCCCcEEEcHHHHHH
Confidence 9998642 2257899999999999999984 999999999999999999999999999999999999999
Q ss_pred HHhcCCccEEEEecCCcc
Q 020677 300 AHERMAVQTLLITDDLFR 317 (323)
Q Consensus 300 A~e~GAVetLLIsD~l~r 317 (323)
|+++|||+||||+|+++|
T Consensus 307 Ale~GAVetLLV~d~l~~ 324 (411)
T PRK04011 307 ALEMGAVDTLLISEDLRK 324 (411)
T ss_pred HHHcCCceEEEEeccccc
Confidence 999999999999999987
No 7
>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=100.00 E-value=6.9e-39 Score=268.25 Aligned_cols=128 Identities=49% Similarity=0.816 Sum_probs=120.5
Q ss_pred CeeeeeecccCCCceEEEeccCCchhhhHhhhcCCCCEEEEEeEEEEEec-cCCCCccceEEEEEEEEEE--EEeecCCC
Q 020677 1 MKILRRNLVENGPGSVKMEPVDSDDLWFAYNLIAPGDSVMAVTVRKVLRQ-MASGSRDAERVKLKLEIKV--VDYDKEGS 77 (323)
Q Consensus 1 Mki~~~~~~~~~~g~v~l~~E~~dDlw~lynli~~GD~V~a~T~Rkv~~~-~~~g~~~~~r~~~~L~i~V--vef~~~~~ 77 (323)
|||+++++.++++|.|+++||+.||||||||||.|||.|+|.|+|+|+.+ +.+|+..+++++++|+|+| ++|||+++
T Consensus 1 Mki~~~~~~~~~~~~i~ll~e~~dDlw~L~~li~~gD~v~~~t~Rkv~~~~~~~~~~~~~~v~~~L~i~ve~v~~~~~~~ 80 (132)
T PF03463_consen 1 MKIISKDIEKNGKGLIKLLPEEKDDLWHLYNLIIPGDEVISKTTRKVQEASNIKGSKTRERVQIALTIKVEKVEFDPENG 80 (132)
T ss_dssp -EEEEECHCHHHHHEEEEETTSHHHHHHHHHHEETTTEEEECCHCHHHHCTCESSHHHHHCEEEEEEEEEEEEEEETTTT
T ss_pred CccchhhhccccCceEEEcccccCCcEEEEEEEECCCEEEEEEEEeeeecccccCCcceEEEEEEEEEEEEEeEecCCCC
Confidence 99999999777899999999999999999999999999999999999543 4566778899999999999 99999999
Q ss_pred eEEEEEEEeecCcccccccEEEEEEccCceeEEEEcccChhhHHHHHHhcC
Q 020677 78 VLRIRGKNILENEHVKIGAFHTLEIELHRAFVLRKDLWDSLALDTLHQAAD 128 (323)
Q Consensus 78 ~Lri~G~i~~~~e~v~~G~~HTi~i~~~~~~~i~K~~wd~~~~e~L~~a~~ 128 (323)
.|||+|+|+++|+++++|+|||++|+||+||+++|+.||++++++|++|++
T Consensus 81 ~Lri~G~i~~~~~~~~~G~~hT~~i~~~~~~ti~K~~wd~~~~~~l~ea~~ 131 (132)
T PF03463_consen 81 LLRISGKIVEENEDVKLGKYHTLDIEPGRPFTIIKYRWDSYFLDRLKEAMD 131 (132)
T ss_dssp EEEEEEEEEEGSCGGGTTSEEEEEEETSSEEEEEEEEEEHHHHHHHHHHTS
T ss_pred EEEEEeEEccCCCCCCcceEEEEEEeCCCceEEEEecCCHHHHHHHHHHhc
Confidence 999999999999999999999999999999999999999999999999986
No 8
>COG1503 eRF1 Peptide chain release factor 1 (eRF1) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.9e-33 Score=269.39 Aligned_cols=227 Identities=24% Similarity=0.291 Sum_probs=206.9
Q ss_pred ecCCCeEEEEEEEeecCcccccccEEEEEEccCceeEEEEcccCh-hhHHHHHHhcCCCCCCcEEEEEEeCCeEEEEEEe
Q 020677 73 DKEGSVLRIRGKNILENEHVKIGAFHTLEIELHRAFVLRKDLWDS-LALDTLHQAADPTASADLAVVLMQEGLAHILLVG 151 (323)
Q Consensus 73 ~~~~~~Lri~G~i~~~~e~v~~G~~HTi~i~~~~~~~i~K~~wd~-~~~e~L~~a~~~~~~~~~~~vvid~g~A~i~ll~ 151 (323)
.|..+...++|.+..+-.. ...-|..++|+.|++.+.|.||+ |++++|++++.+.. .++++++|.++|+++++.
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 TPENGLVLFVGDVLGGGGK---TKKVTVVIEPPEPINTFLYRCDSKFYLEPLEEMLEDKD--LYGLIVLDRIEATIGLLK 157 (411)
T ss_pred CCCCCeEEEEeeeccCCCc---cceeeecccCCCCcceeeeccccHHHHHHHHHHhhhcc--cccEEEEecccceeeeec
Confidence 4678899999999876322 23467777999999999999998 99999999998877 999999999999999999
Q ss_pred cceEEEEEEEEEecCCCCCC-Ccch------hhHHHHHHHHHHHHHHHhccc---ccCccEEEEECCcccHHHHHH--HH
Q 020677 152 RSMTITRSRIETSIPRKHGP-AIAG------YESALNKFFENVLQAFLKHVD---FNVVRCAVIASPGFTKDQFHR--HL 219 (323)
Q Consensus 152 ~~~~~~~~~i~~~ip~K~~~-~~s~------~~~~~~~f~~~v~~~l~~~~~---~~~v~~iIIaGPGf~kd~f~~--~l 219 (323)
+..+.++.++++.+||||++ |||+ ++.+.++||+.|.+++.+.|. ..++++|||+|||.+|++|++ ||
T Consensus 158 g~r~evl~~~~s~vpgKh~~Ggqsa~rferl~ee~~h~f~k~vge~A~e~f~~~~~~~~kgIilgGp~~tk~ef~e~~yL 237 (411)
T COG1503 158 GKRIEVLKELTSDVPGKHRAGGQSARRFERLIEEAAHEFYKKVGEAASEAFLPIAKKELKGIILGGPGPTKEEFVEGDYL 237 (411)
T ss_pred cceeeHhhhhcccCcchhhcccchHHHHHHHHHHHHHHHHHHHHHHHHHHhcchhhhhhcceEeeCCcccchhhhccccc
Confidence 99999999999999999988 7887 788899999999999999985 226899999999999999997 99
Q ss_pred HHHHHhccccccccccCcEEEEEcCCCccchHHHHhcChhHHHhhhhhhHHHHHHHHHHHHHHhhcCCCeEEEcHHHHHH
Q 020677 220 LLEAERRQLRPIIENKSRIILVHTSSGYKHSLREVLDAPNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEV 299 (323)
Q Consensus 220 ~~~~~~~~~~~~~~~~~ki~~~~~s~~~~~gl~Evl~~~~v~~~l~d~k~~~e~~~le~f~~~l~~~~~~a~YG~~eV~~ 299 (323)
.++++.+.. .++++++++.+|++|++... .+.|++.++.+|.++|++|++.+.+++|+++||.++|.+
T Consensus 238 ~~~lk~kv~----------~lvDv~y~~esg~~eli~~A--~d~L~~~~~~~eK~l~e~f~~e~~~~~Gla~yG~~~vr~ 305 (411)
T COG1503 238 HHELKKKVL----------GLVDVSYTGESGLRELIEKA--EDALKDVDYVREKKLMEEFFKELAKDSGLAVYGEEEVRE 305 (411)
T ss_pred chHHHHHHH----------hhccccccccccHHHHHHHh--HHHHHhhhhhcchhHHHHHHHHhccCcceeecchHHHHH
Confidence 999875321 57999999999999999999 999999999999999999999999999999999999999
Q ss_pred HHhcCCccEEEEecCCc
Q 020677 300 AHERMAVQTLLITDDLF 316 (323)
Q Consensus 300 A~e~GAVetLLIsD~l~ 316 (323)
|+++|||++|||+.++-
T Consensus 306 aL~~gaVd~llv~Edl~ 322 (411)
T COG1503 306 ALEMGAVDTLLVSEDLE 322 (411)
T ss_pred HHHhcccceEEeecccc
Confidence 99999999999999875
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=99.97 E-value=2e-29 Score=211.28 Aligned_cols=126 Identities=42% Similarity=0.664 Sum_probs=114.8
Q ss_pred cEEEEEEeCCeEEEEEEecceEEEEEEEEEecCCCCCC-Ccchh----hHHHHHHHHHHHHHHHhc--ccccCccEEEEE
Q 020677 134 DLAVVLMQEGLAHILLVGRSMTITRSRIETSIPRKHGP-AIAGY----ESALNKFFENVLQAFLKH--VDFNVVRCAVIA 206 (323)
Q Consensus 134 ~~~~vvid~g~A~i~ll~~~~~~~~~~i~~~ip~K~~~-~~s~~----~~~~~~f~~~v~~~l~~~--~~~~~v~~iIIa 206 (323)
++++|+||+|+|+||+++++++++++++++++|+|+++ |+|+. ++++++||++|++++.++ .++.++++||||
T Consensus 1 ~v~~v~id~g~A~i~~l~~~~~~~~~~i~~~ip~K~~~Gg~s~~rf~r~~~~~~f~~~i~~~l~~~f~~~~~~~~~iIia 80 (133)
T PF03464_consen 1 KVGIVVIDEGEANICLLRGYGTEILQRIESNIPGKHKKGGQSQRRFEREKALEKFFKEIAEALKKYFLVNFDDVKCIIIA 80 (133)
T ss_dssp EEEEEEEETTEEEEEEEETTEEEEEEEEE-GHCCCSSTTCSHHHHHHHHHHHHHHHHHHHHHHHHHCCCHTTTCSEEEEE
T ss_pred CEEEEEEeCCCEEEEEEcCCEEEEEEEEEecCCCccCCCCcchhhHHHHHHHHHHHHHHHHHHHHHhhhccccccEEEEE
Confidence 48999999999999999999999999999999999986 67764 899999999999999999 679999999999
Q ss_pred CCcccHHHHHHHHHHHHHhccccccccccCcEEEEEcCCCccchHHHHhcChhHHHhhhh
Q 020677 207 SPGFTKDQFHRHLLLEAERRQLRPIIENKSRIILVHTSSGYKHSLREVLDAPNVMNMIKD 266 (323)
Q Consensus 207 GPGf~kd~f~~~l~~~~~~~~~~~~~~~~~ki~~~~~s~~~~~gl~Evl~~~~v~~~l~d 266 (323)
||||+|++|++|+..++..+. +.++.++++|+++++||+|+|++|+++++|+|
T Consensus 81 GPGf~k~~f~~~l~~~~~~~~-------~~~i~~~~~s~~~~~gl~Evl~~~~v~~~l~d 133 (133)
T PF03464_consen 81 GPGFTKEEFYKYLKAEARRKD-------KKKIVVVDTSSGGESGLNEVLKRPEVQKILKD 133 (133)
T ss_dssp ESTTHHHHHHHHHHHHHHHHT-------CCEEEEEE-SSSCHHHHHHHHHSHHHHHHHCT
T ss_pred CCHHHHHHHHHHHHHhhHhhc-------CCEEEEEECCCCCHHHHHHHHHhhhHHHHhcC
Confidence 999999999999999988642 25789999999999999999999999999976
No 10
>KOG0688 consensus Peptide chain release factor 1 (eRF1) [Translation, ribosomal structure and biogenesis]
Probab=99.95 E-value=7.2e-29 Score=228.28 Aligned_cols=226 Identities=14% Similarity=0.227 Sum_probs=201.8
Q ss_pred cCCCeEEEEEEEeecCcccccccEEEEEEccCceeEEEEcccCh-hhHHHHHHhcCCCCCCcEEEEEEeCCeEEEEEEec
Q 020677 74 KEGSVLRIRGKNILENEHVKIGAFHTLEIELHRAFVLRKDLWDS-LALDTLHQAADPTASADLAVVLMQEGLAHILLVGR 152 (323)
Q Consensus 74 ~~~~~Lri~G~i~~~~e~v~~G~~HTi~i~~~~~~~i~K~~wd~-~~~e~L~~a~~~~~~~~~~~vvid~g~A~i~ll~~ 152 (323)
|..+..-.+|.++.+. ...+..++++||.+||....|.||. ||++.|.+++.... .+|+++||...+.++++.+
T Consensus 85 Ppnglvly~gti~ted---gkekkv~idfepfkpintslyLcdNkfhte~l~~Ll~sd~--kfgfivmDg~~tlfgtl~g 159 (431)
T KOG0688|consen 85 PPNGLVLYTGTIVTED---GKEKKVNIDFEPFKPINTSLYLCDNKFHTEALKELLESDN--KFGFIVMDGNGTLFGTLQG 159 (431)
T ss_pred CCCceEEEeeeeEccC---CceeeeecccccccccccceEecCCccchHHHHHHHhhcc--cccEEEEcCCceeEEEecc
Confidence 5577888899999865 3346789999999999999999977 99999999999887 8999999999999999999
Q ss_pred ceEEEEEEEEEecCCCCCC-Ccch------hhHHHHHHHHHHHHHHHhccc---ccCccEEEEECCcccHHHHHH--HHH
Q 020677 153 SMTITRSRIETSIPRKHGP-AIAG------YESALNKFFENVLQAFLKHVD---FNVVRCAVIASPGFTKDQFHR--HLL 220 (323)
Q Consensus 153 ~~~~~~~~i~~~ip~K~~~-~~s~------~~~~~~~f~~~v~~~l~~~~~---~~~v~~iIIaGPGf~kd~f~~--~l~ 220 (323)
+...+++++.+.+|+||++ |||+ |.+.++.|.+.+++...+++. ..++.++|+||..-+|.++.+ .++
T Consensus 160 ntrevLhkftVdlPkkhgrggqSalrfarlR~ekRhnYVrkvae~a~q~fi~~~~~Nv~gLilaGsadfKtelsqSd~fd 239 (431)
T KOG0688|consen 160 NTREVLHKFTVDLPKKHGRGGQSALRFARLRMEKRHNYVRKVAELAVQRFITNDKPNVAGLILAGSADFKTELSQSDMFD 239 (431)
T ss_pred chHhhhheeeecCccccCccchhHHhhhhhhhhhhccceeeecccceeEEecCCCcceeEEEEecccccccccchhhhcc
Confidence 9999999999999999998 6775 778889999999999998884 678999999999988888765 566
Q ss_pred HHHHhccccccccccCcEEEEEcCCCccchHHHHhcChhHHHhhhhhhHHHHHHHHHHHHHHhhcCCCeEEEcHHHHHHH
Q 020677 221 LEAERRQLRPIIENKSRIILVHTSSGYKHSLREVLDAPNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVA 300 (323)
Q Consensus 221 ~~~~~~~~~~~~~~~~ki~~~~~s~~~~~gl~Evl~~~~v~~~l~d~k~~~e~~~le~f~~~l~~~~~~a~YG~~eV~~A 300 (323)
++++.+. +.++++||||.+|++++++-. .++|++.++++|.+++.+||++++.|.|+.|||++++.+|
T Consensus 240 ~rlqskv----------i~~vdvsyGGengfnQaIeL~--aevlsnvk~vqekkli~~yfdEisqdtgky~Fgv~dTl~a 307 (431)
T KOG0688|consen 240 PRLQSKV----------LKTVDVSYGGENGFNQAIELS--AEVLSNVKFVQEKKLIGKYFDEISQDTGKYCFGVEDTLLA 307 (431)
T ss_pred hHHhhhH----------HhhhcccccchhhHHHHHHHH--HhhhhcceeeehhhHHHHHhhhhhcccCcccccHHHHHHH
Confidence 6665322 257999999999999999988 8999999999999999999999999999999999999999
Q ss_pred HhcCCccEEEEecCCc
Q 020677 301 HERMAVQTLLITDDLF 316 (323)
Q Consensus 301 ~e~GAVetLLIsD~l~ 316 (323)
+++|||+||++...|=
T Consensus 308 Le~gavetli~~enLd 323 (431)
T KOG0688|consen 308 LEMGAVETLIVWENLD 323 (431)
T ss_pred HHcCCeeehhHhhhhh
Confidence 9999999999987663
No 11
>PF03465 eRF1_3: eRF1 domain 3; InterPro: IPR005142 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 but this awaits experimental verification.; PDB: 3OBY_A 3E1Y_D 1DT9_A 2KTU_A 2KTV_A 3IR9_A 3E20_H 3OBW_A 3AGJ_F 3MCA_B ....
Probab=99.43 E-value=1.6e-13 Score=111.81 Aligned_cols=52 Identities=44% Similarity=0.603 Sum_probs=48.9
Q ss_pred HHHHHHHHHHHHHHhhcCCCeEEEcHHHHHHHHhcCCccEEEEecCCcccCC
Q 020677 269 AAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHERMAVQTLLITDDLFRLVC 320 (323)
Q Consensus 269 ~~~e~~~le~f~~~l~~~~~~a~YG~~eV~~A~e~GAVetLLIsD~l~r~~d 320 (323)
+++|.++|++||++++++++++|||+++|.+|+++|||+||||+|+++|+.+
T Consensus 1 ~~~E~~~ve~f~~~l~k~~~~~~yG~~eV~~Al~~GaV~~LlI~d~l~~~~~ 52 (113)
T PF03465_consen 1 IIKEKKLVEEFFEELAKDPGLAVYGIEEVKKALEMGAVETLLISDDLFRSRD 52 (113)
T ss_dssp HHHHHHHHHHHHHHHHTTCSSEEESHHHHHHHHHTT-EEEEEEEHHHHTESC
T ss_pred CHHHHHHHHHHHHHHhhCCCcEEECHHHHHHHHHhCCCcEEEEecccccccc
Confidence 5789999999999999999999999999999999999999999999999865
No 12
>PF10116 Host_attach: Protein required for attachment to host cells; InterPro: IPR019291 Members of this family of bacterial proteins are required for the attachment of the bacterium to host cells [, ].
Probab=95.21 E-value=0.074 Score=44.51 Aligned_cols=90 Identities=14% Similarity=0.120 Sum_probs=59.5
Q ss_pred EEEEEeCCeEEEEEEecceE---EE------------EEEEEEecCCCCCC--Cc--c------hhhHHHHHHHHHHHHH
Q 020677 136 AVVLMQEGLAHILLVGRSMT---IT------------RSRIETSIPRKHGP--AI--A------GYESALNKFFENVLQA 190 (323)
Q Consensus 136 ~~vvid~g~A~i~ll~~~~~---~~------------~~~i~~~ip~K~~~--~~--s------~~~~~~~~f~~~v~~~ 190 (323)
.+||.|.+.|.|+...+... .. -+.+...-||.... |+ + ..+...++|.++|++.
T Consensus 2 wVvVaD~~~Ar~f~~~~~~~~~~~~~~~~~~~~~~~~~~dl~~d~~Gr~~~~~g~~~~~~~~~~~~~~~~~~Fa~~vA~~ 81 (138)
T PF10116_consen 2 WVVVADGSRARIFENEGDESEPLLELEELDHPESRLKDRDLVSDRPGRFHDSAGQRGSMEERTDPKEEEEERFAREVADR 81 (138)
T ss_pred EEEEEecceeEEEEecCCCCCcchhhhhhcccccccchhhhccCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHH
Confidence 47889999999998887743 11 13334445553222 11 1 1677788999999999
Q ss_pred HHhcccccCccEEEEECCcccHHHHHHHHHHHHHh
Q 020677 191 FLKHVDFNVVRCAVIASPGFTKDQFHRHLLLEAER 225 (323)
Q Consensus 191 l~~~~~~~~v~~iIIaGPGf~kd~f~~~l~~~~~~ 225 (323)
|.+.......+.+||++|--+--.+.+.|.....+
T Consensus 82 L~~~~~~~~~~~LvlvA~p~~LG~LR~~L~~~~~~ 116 (138)
T PF10116_consen 82 LEKARRAGKFDRLVLVAPPRFLGLLREHLSKAVRK 116 (138)
T ss_pred HHHHHHhCCCCeEEEEECHHHHHHHHHHhCHHHHH
Confidence 99998877777777777764444555555555544
No 13
>PF01248 Ribosomal_L7Ae: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; InterPro: IPR004038 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 family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, ribosomal protein L30 from eukaryotes and archaebacteria, Gadd45 and MyD118 [].; PDB: 2CZW_A 3V7E_B 2QEX_F 1YJ9_F 1VQ8_F 1YJN_F 3I56_F 1VQ6_F 2OTJ_F 1YIJ_F ....
Probab=67.75 E-value=12 Score=28.65 Aligned_cols=37 Identities=16% Similarity=0.260 Sum_probs=29.6
Q ss_pred HHHHHhhcCCCeEEEcHHHHHHHHhcCCccEEEEecCC
Q 020677 278 DFFNMLTNDPTRACYGPKHVEVAHERMAVQTLLITDDL 315 (323)
Q Consensus 278 ~f~~~l~~~~~~a~YG~~eV~~A~e~GAVetLLIsD~l 315 (323)
..+....+. ++.++|.++|.+|++.|-+.-++++.+.
T Consensus 5 ~~l~~a~~~-~~lv~G~~~v~k~l~~~~~~lvilA~d~ 41 (95)
T PF01248_consen 5 KLLKLARKA-GRLVKGIKEVLKALKKGKAKLVILAEDC 41 (95)
T ss_dssp HHHHHHHHH-SEEEESHHHHHHHHHTTCESEEEEETTS
T ss_pred HHHHHHHhc-CCEEEchHHHHHHHHcCCCcEEEEcCCC
Confidence 344443433 7899999999999999999999998765
No 14
>PRK07283 hypothetical protein; Provisional
Probab=65.95 E-value=7 Score=30.76 Aligned_cols=32 Identities=16% Similarity=0.184 Sum_probs=28.1
Q ss_pred hcCCCeEEEcHHHHHHHHhcCCccEEEEecCC
Q 020677 284 TNDPTRACYGPKHVEVAHERMAVQTLLITDDL 315 (323)
Q Consensus 284 ~~~~~~a~YG~~eV~~A~e~GAVetLLIsD~l 315 (323)
+...|+++.|.+.|.+|+..|.+.-++++.+.
T Consensus 13 A~raGklv~G~~~v~~aik~gk~~lVi~A~Da 44 (98)
T PRK07283 13 AQRAGRIISGEELVVKAIQSGQAKLVFLANDA 44 (98)
T ss_pred HHHhCCeeEcHHHHHHHHHcCCccEEEEeCCC
Confidence 44559999999999999999999999998764
No 15
>PRK07714 hypothetical protein; Provisional
Probab=65.08 E-value=7.1 Score=30.76 Aligned_cols=32 Identities=16% Similarity=0.202 Sum_probs=27.7
Q ss_pred hcCCCeEEEcHHHHHHHHhcCCccEEEEecCC
Q 020677 284 TNDPTRACYGPKHVEVAHERMAVQTLLITDDL 315 (323)
Q Consensus 284 ~~~~~~a~YG~~eV~~A~e~GAVetLLIsD~l 315 (323)
+...|++++|.+.|.+|+..|-+.-++++.+.
T Consensus 13 a~raGk~v~G~~~v~~al~~g~~~lViiA~D~ 44 (100)
T PRK07714 13 ANRARKVISGEELVLKEVRSGKAKLVLLSEDA 44 (100)
T ss_pred HHHhCCeeecHHHHHHHHHhCCceEEEEeCCC
Confidence 33449999999999999999999999998764
No 16
>TIGR03677 rpl7ae 50S ribosomal protein L7Ae. Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, box H/ACA, box C/D and box C'/D' sRNAs. Interacts with protein L15e.
Probab=64.71 E-value=14 Score=30.00 Aligned_cols=30 Identities=23% Similarity=0.338 Sum_probs=27.5
Q ss_pred CCCeEEEcHHHHHHHHhcCCccEEEEecCC
Q 020677 286 DPTRACYGPKHVEVAHERMAVQTLLITDDL 315 (323)
Q Consensus 286 ~~~~a~YG~~eV~~A~e~GAVetLLIsD~l 315 (323)
..++.++|.++|.+|+..|-+.-++|+.+.
T Consensus 23 ragkl~~G~~~v~kaikkgka~LVilA~D~ 52 (117)
T TIGR03677 23 ETGKIKKGTNEVTKAVERGIAKLVVIAEDV 52 (117)
T ss_pred HcCCEeEcHHHHHHHHHcCCccEEEEeCCC
Confidence 448999999999999999999999999876
No 17
>PRK05583 ribosomal protein L7Ae family protein; Provisional
Probab=62.75 E-value=8.5 Score=30.74 Aligned_cols=32 Identities=22% Similarity=0.318 Sum_probs=28.2
Q ss_pred hcCCCeEEEcHHHHHHHHhcCCccEEEEecCC
Q 020677 284 TNDPTRACYGPKHVEVAHERMAVQTLLITDDL 315 (323)
Q Consensus 284 ~~~~~~a~YG~~eV~~A~e~GAVetLLIsD~l 315 (323)
+...|++++|.+.|.+|+..|.+.-|+++.+.
T Consensus 12 A~rAGklv~G~~~v~~aik~gk~~lVI~A~D~ 43 (104)
T PRK05583 12 TKKAGKLLEGYNKCEEAIKKKKVYLIIISNDI 43 (104)
T ss_pred HHHhCCeeecHHHHHHHHHcCCceEEEEeCCC
Confidence 44559999999999999999999999998775
No 18
>TIGR01175 pilM type IV pilus assembly protein PilM. This protein is required for the assembly of the type IV fimbria in Pseudomonas aeruginosa responsible for twitching motility, and for a similar pilus-like structure in Synechocystis. It is also found in species such as Deinococcus described as having natural transformation (for which a type IV pilus-like structure is proposed) but not fimbria.
Probab=62.12 E-value=1e+02 Score=29.25 Aligned_cols=90 Identities=13% Similarity=0.162 Sum_probs=56.9
Q ss_pred EEEEEEeCCeEEEEEEecceEEEEEEEEEe-------------cCC------CCCCCcc--hhhHHHHHHHHHHHHHHHh
Q 020677 135 LAVVLMQEGLAHILLVGRSMTITRSRIETS-------------IPR------KHGPAIA--GYESALNKFFENVLQAFLK 193 (323)
Q Consensus 135 ~~~vvid~g~A~i~ll~~~~~~~~~~i~~~-------------ip~------K~~~~~s--~~~~~~~~f~~~v~~~l~~ 193 (323)
+++|-+..+...++++.+........+... +|- |...+.. .....++.++++++..+.+
T Consensus 190 ~~lvdiG~~~t~l~i~~~g~~~~~r~i~~G~~~i~~~i~~~~~~~~~~Ae~~k~~~~~~~~~~~~~~~~~~~~l~~eI~~ 269 (348)
T TIGR01175 190 AALVDIGATSSTLNLLHPGRMLFTREVPFGTRQLTSELSRAYGLNPEEAGEAKQQGGLPLLYDPEVLRRFKGELVDEIRR 269 (348)
T ss_pred EEEEEECCCcEEEEEEECCeEEEEEEeechHHHHHHHHHHHcCCCHHHHHHHHhcCCCCCchhHHHHHHHHHHHHHHHHH
Confidence 788888999999999988877777666532 110 0000100 0122334555555555555
Q ss_pred cccc-------cCccEEEEECCcccHHHHHHHHHHHHH
Q 020677 194 HVDF-------NVVRCAVIASPGFTKDQFHRHLLLEAE 224 (323)
Q Consensus 194 ~~~~-------~~v~~iIIaGPGf~kd~f~~~l~~~~~ 224 (323)
.+++ ..+..|+|+|-|.--..|.+++.+.+.
T Consensus 270 ~l~~~~~~~~~~~i~~I~LtGgga~~~gl~~~l~~~l~ 307 (348)
T TIGR01175 270 SLQFFTAQSGTNSLDGLVLAGGGATLSGLDAAIYQRLG 307 (348)
T ss_pred HHHhhcCCCCCcccceEEEECccccchhHHHHHHHHHC
Confidence 4432 258899999988777788888888763
No 19
>PF08032 SpoU_sub_bind: RNA 2'-O ribose methyltransferase substrate binding; InterPro: IPR013123 Most cellular RNAs undergo a number of post-transcriptional nucleoside modifications. While the biological role of many of these modifications is unknown, some have been shown to be necessary for cell growth or for resistance to antibiotics [, ]. One of the most common modifications is 2'O-ribose methylation catalysed by the RNA 2'O-ribose methyltransferases, a large enzyme family that transfer a methyl group from S-adenosyl-L-methionine (AdoMet) to the 2'-OH group of the backbone ribose []. This entry represents a substrate-binding domain found in a variety of bacterial and mitochondrial RNA 2'-O ribose methyltransferases. These include the bacterial enzyme RlmB, which specifically methylates the conserved nucleotide guanosine 2251 in 23S RNA, and PET56, which specifically methylates the equivalent guanosine in mitochondrial 21S RNA [, ]. This domain forms a four-stranded mixed beta sheet similar to that found in other RNA binding enzymes []. It shows considerable conformational flexibility which is thought to be important for its ability to bind RNA.; GO: 0008168 methyltransferase activity; PDB: 1GZ0_D 1IPA_A.
Probab=59.60 E-value=12 Score=27.14 Aligned_cols=24 Identities=25% Similarity=0.374 Sum_probs=22.8
Q ss_pred EEcHHHHHHHHhcCC-ccEEEEecC
Q 020677 291 CYGPKHVEVAHERMA-VQTLLITDD 314 (323)
Q Consensus 291 ~YG~~eV~~A~e~GA-VetLLIsD~ 314 (323)
.||...|..|++.|. +..|+++++
T Consensus 2 ieG~~~V~eaL~~~~~i~~l~~~~~ 26 (76)
T PF08032_consen 2 IEGRHAVEEALKSGPRIKKLFVTEE 26 (76)
T ss_dssp EESHHHHHHHHHCTGGEEEEEEETT
T ss_pred EEEHHHHHHHHcCCCCccEEEEEcC
Confidence 699999999999988 999999998
No 20
>PRK04175 rpl7ae 50S ribosomal protein L7Ae; Validated
Probab=58.67 E-value=24 Score=28.94 Aligned_cols=40 Identities=15% Similarity=0.145 Sum_probs=32.0
Q ss_pred HHHHHHHhhcCCCeEEEcHHHHHHHHhcCCccEEEEecCCc
Q 020677 276 LKDFFNMLTNDPTRACYGPKHVEVAHERMAVQTLLITDDLF 316 (323)
Q Consensus 276 le~f~~~l~~~~~~a~YG~~eV~~A~e~GAVetLLIsD~l~ 316 (323)
+-.++....+. ++...|.++|.+|++.|-+.-++|+.+.-
T Consensus 18 i~~lL~la~ra-gklv~G~~~v~kaikkgkakLVilA~D~s 57 (122)
T PRK04175 18 ALEAVEKARDT-GKIKKGTNETTKAVERGIAKLVVIAEDVD 57 (122)
T ss_pred HHHHHHHHHHc-CCEeEcHHHHHHHHHcCCccEEEEeCCCC
Confidence 33444444444 89999999999999999999999998863
No 21
>PRK13602 putative ribosomal protein L7Ae-like; Provisional
Probab=58.66 E-value=19 Score=27.40 Aligned_cols=33 Identities=18% Similarity=0.310 Sum_probs=28.0
Q ss_pred HhhcCCCeEEEcHHHHHHHHhcCCccEEEEecCC
Q 020677 282 MLTNDPTRACYGPKHVEVAHERMAVQTLLITDDL 315 (323)
Q Consensus 282 ~l~~~~~~a~YG~~eV~~A~e~GAVetLLIsD~l 315 (323)
.+.+. ++...|.++|.+|++.|-+.-++|..+.
T Consensus 5 ~~~ra-gkl~~G~~~v~kai~~gkaklViiA~D~ 37 (82)
T PRK13602 5 KVSQA-KSIVIGTKQTVKALKRGSVKEVVVAEDA 37 (82)
T ss_pred HHHhc-CCEEEcHHHHHHHHHcCCeeEEEEECCC
Confidence 34433 7899999999999999999999998764
No 22
>PTZ00106 60S ribosomal protein L30; Provisional
Probab=58.66 E-value=21 Score=28.73 Aligned_cols=39 Identities=10% Similarity=0.170 Sum_probs=31.4
Q ss_pred HHHHHHHhhcCCCeEEEcHHHHHHHHhcCCccEEEEecCC
Q 020677 276 LKDFFNMLTNDPTRACYGPKHVEVAHERMAVQTLLITDDL 315 (323)
Q Consensus 276 le~f~~~l~~~~~~a~YG~~eV~~A~e~GAVetLLIsD~l 315 (323)
++.++-. +...|+..+|.++|.+|+..|-+.-++|+.+.
T Consensus 13 i~~~Lgl-a~raGKlv~G~~~vlkalk~gkaklViiA~D~ 51 (108)
T PTZ00106 13 INSKLQL-VMKSGKYTLGTKSTLKALRNGKAKLVIISNNC 51 (108)
T ss_pred HHHHHHH-HHHhCCeeecHHHHHHHHHcCCeeEEEEeCCC
Confidence 3444444 44459999999999999999999999999875
No 23
>PF03485 Arg_tRNA_synt_N: Arginyl tRNA synthetase N terminal domain; InterPro: IPR005148 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This domain is found at the N terminus of Arginyl tRNA synthetase, also called additional domain 1 (Add-1). It is about 140 residues long and it has been suggested that this domain will be involved in tRNA recognition [].; GO: 0000166 nucleotide binding, 0004814 arginine-tRNA ligase activity, 0005524 ATP binding, 0006420 arginyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1F7V_A 1F7U_A 1BS2_A 2ZUE_A 2ZUF_A 1IQ0_A 3GDZ_B.
Probab=57.76 E-value=12 Score=28.31 Aligned_cols=29 Identities=14% Similarity=0.348 Sum_probs=21.0
Q ss_pred HHHHHHHHHHhccccc-CccEEEEECCccc
Q 020677 183 FFENVLQAFLKHVDFN-VVRCAVIASPGFT 211 (323)
Q Consensus 183 f~~~v~~~l~~~~~~~-~v~~iIIaGPGf~ 211 (323)
==.+|++.+.+.+... .++.+=++||||+
T Consensus 52 ~P~~iA~~i~~~l~~~~~i~~vev~gpGFi 81 (85)
T PF03485_consen 52 NPREIAEEIAEKLEKSPIIEKVEVAGPGFI 81 (85)
T ss_dssp -HHHHHHHHHHCHCTTTTEEEEEEETTTEE
T ss_pred CHHHHHHHHHHhcCCCCCEEEEEEcCCcEE
Confidence 3346777777777533 3889999999996
No 24
>PRK01018 50S ribosomal protein L30e; Reviewed
Probab=55.23 E-value=28 Score=27.34 Aligned_cols=29 Identities=10% Similarity=0.142 Sum_probs=27.0
Q ss_pred CCeEEEcHHHHHHHHhcCCccEEEEecCC
Q 020677 287 PTRACYGPKHVEVAHERMAVQTLLITDDL 315 (323)
Q Consensus 287 ~~~a~YG~~eV~~A~e~GAVetLLIsD~l 315 (323)
.++...|.++|.+|++.|-+.-++|+++.
T Consensus 14 agkl~~G~~~v~kai~~gkaklViiA~D~ 42 (99)
T PRK01018 14 TGKVILGSKRTIKAIKLGKAKLVIVASNC 42 (99)
T ss_pred cCCEEEcHHHHHHHHHcCCceEEEEeCCC
Confidence 48999999999999999999999999874
No 25
>PRK09190 hypothetical protein; Provisional
Probab=55.14 E-value=50 Score=30.07 Aligned_cols=32 Identities=16% Similarity=0.156 Sum_probs=27.8
Q ss_pred hcCCCeEEEcHHHHHHHHhcCCccEEEEecCC
Q 020677 284 TNDPTRACYGPKHVEVAHERMAVQTLLITDDL 315 (323)
Q Consensus 284 ~~~~~~a~YG~~eV~~A~e~GAVetLLIsD~l 315 (323)
++..|++++|.+.|..|+..|-+.-||++.+.
T Consensus 106 ArRAGklVsG~~~V~~alk~gk~~Lvi~A~Da 137 (220)
T PRK09190 106 ARKAGQVVSGFEKVDAALRSGEAAALIHASDG 137 (220)
T ss_pred HhhhCCEeecHHHHHHHHHcCCceEEEEeccC
Confidence 44559999999999999999999999888764
No 26
>PRK13601 putative L7Ae-like ribosomal protein; Provisional
Probab=50.42 E-value=25 Score=26.80 Aligned_cols=29 Identities=24% Similarity=0.327 Sum_probs=26.5
Q ss_pred CCeEEEcHHHHHHHHhcCCccEEEEecCC
Q 020677 287 PTRACYGPKHVEVAHERMAVQTLLITDDL 315 (323)
Q Consensus 287 ~~~a~YG~~eV~~A~e~GAVetLLIsD~l 315 (323)
+|+...|.++|.+|+..|-+.-++|..+.
T Consensus 6 ~GKlv~G~~~vlkaIk~gkakLViiA~Da 34 (82)
T PRK13601 6 PSKRVVGAKQTLKAITNCNVLQVYIAKDA 34 (82)
T ss_pred CccEEEchHHHHHHHHcCCeeEEEEeCCC
Confidence 47899999999999999999999998764
No 27
>PRK06683 hypothetical protein; Provisional
Probab=49.73 E-value=33 Score=26.09 Aligned_cols=30 Identities=20% Similarity=0.256 Sum_probs=27.0
Q ss_pred CCCeEEEcHHHHHHHHhcCCccEEEEecCC
Q 020677 286 DPTRACYGPKHVEVAHERMAVQTLLITDDL 315 (323)
Q Consensus 286 ~~~~a~YG~~eV~~A~e~GAVetLLIsD~l 315 (323)
+.++.+.|.++|.+|++.|-+.-++|..+.
T Consensus 8 ~agk~v~G~~~v~kaik~gkaklViiA~Da 37 (82)
T PRK06683 8 NAENVVVGHKRTLEAIKNGIVKEVVIAEDA 37 (82)
T ss_pred hCCCEEEcHHHHHHHHHcCCeeEEEEECCC
Confidence 448899999999999999999999998764
No 28
>PRK13600 putative ribosomal protein L7Ae-like; Provisional
Probab=49.56 E-value=28 Score=26.79 Aligned_cols=26 Identities=27% Similarity=0.344 Sum_probs=23.7
Q ss_pred EEEcHHHHHHHHhcCCccEEEEecCC
Q 020677 290 ACYGPKHVEVAHERMAVQTLLITDDL 315 (323)
Q Consensus 290 a~YG~~eV~~A~e~GAVetLLIsD~l 315 (323)
..+|.+++.+|++.|-+..++|..|.
T Consensus 14 ~vvG~kqt~Kai~kg~~~~v~iA~Da 39 (84)
T PRK13600 14 FVVGLKETLKALKKDQVTSLIIAEDV 39 (84)
T ss_pred ceeeHHHHHHHHhcCCceEEEEeCCC
Confidence 48999999999999999999998764
No 29
>PRK09557 fructokinase; Reviewed
Probab=48.07 E-value=66 Score=29.97 Aligned_cols=47 Identities=9% Similarity=0.099 Sum_probs=32.9
Q ss_pred HHHHHHHHHHHHHHhcccccCccEEEEECCcccHHHHHHHHHHHHHh
Q 020677 179 ALNKFFENVLQAFLKHVDFNVVRCAVIASPGFTKDQFHRHLLLEAER 225 (323)
Q Consensus 179 ~~~~f~~~v~~~l~~~~~~~~v~~iIIaGPGf~kd~f~~~l~~~~~~ 225 (323)
.+++|.+.++.++....+..++..|||+|.-...+.|.+.+.+...+
T Consensus 224 ~l~~~~~~La~~l~~l~~~ldP~~IvlgG~~~~~~~~~~~l~~~~~~ 270 (301)
T PRK09557 224 AFRRYEDRLAKSLAHVINILDPDVIVLGGGMSNVDRLYPTLPALLKQ 270 (301)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCEEEEcCcccchHHHHHHHHHHHHH
Confidence 35566666666777777777899999999866556676666655544
No 30
>PRK05082 N-acetylmannosamine kinase; Provisional
Probab=47.77 E-value=41 Score=31.17 Aligned_cols=46 Identities=7% Similarity=0.049 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHHHhcccccCccEEEEECCcccHHHHHHHHHHHHHh
Q 020677 180 LNKFFENVLQAFLKHVDFNVVRCAVIASPGFTKDQFHRHLLLEAER 225 (323)
Q Consensus 180 ~~~f~~~v~~~l~~~~~~~~v~~iIIaGPGf~kd~f~~~l~~~~~~ 225 (323)
+++|...++..+....+..+++.|||+|+....+.|.+.+.+.+.+
T Consensus 214 ~~~~~~~la~~l~~l~~~~dpe~IvlgG~~~~~~~~~~~i~~~l~~ 259 (291)
T PRK05082 214 INRSAQAIARLIADLKATLDCQCVVLGGSVGLAEGYLELVQAYLAQ 259 (291)
T ss_pred HHHHHHHHHHHHHHHHHHhCCCEEEEcCccccHHHHHHHHHHHHHh
Confidence 3355555666666666667899999999987777777766666544
No 31
>COG1105 FruK Fructose-1-phosphate kinase and related fructose-6-phosphate kinase (PfkB) [Carbohydrate transport and metabolism]
Probab=42.84 E-value=94 Score=29.81 Aligned_cols=110 Identities=15% Similarity=0.161 Sum_probs=57.6
Q ss_pred cChhhHHHHHHhcCCCCCCcEEEEEE-eCCeEEEEEEecc---eEEEEEEEEEecCCCCCCCcchhhHHHHHHHHHHHHH
Q 020677 115 WDSLALDTLHQAADPTASADLAVVLM-QEGLAHILLVGRS---MTITRSRIETSIPRKHGPAIAGYESALNKFFENVLQA 190 (323)
Q Consensus 115 wd~~~~e~L~~a~~~~~~~~~~~vvi-d~g~A~i~ll~~~---~~~~~~~i~~~ip~K~~~~~s~~~~~~~~f~~~v~~~ 190 (323)
+-.+..+.|++.- -...++-+ .+-..++-++.+. .|+ -+-|+= .-.+...+.|.+.+...
T Consensus 63 tg~~~~~~l~~~g-----i~~~fv~v~g~TRinvki~~~~~~~~Te------in~~Gp-----~is~~~~~~~l~~~~~~ 126 (310)
T COG1105 63 TGEFFVALLKDEG-----IPDAFVEVKGDTRINVKILDEEDGEETE------INFPGP-----EISEAELEQFLEQLKAL 126 (310)
T ss_pred cHHHHHHHHHhcC-----CCceEEEccCCCeeeEEEEecCCCcEEE------ecCCCC-----CCCHHHHHHHHHHHHHh
Confidence 4446666666531 23345544 4445555555552 222 222321 11345667777665444
Q ss_pred HHhcccccCccEEEEEC--CcccHHHHHHHHHHHHHhccccccccccCcEEEEEcCCCccchHHHHhcCh
Q 020677 191 FLKHVDFNVVRCAVIAS--PGFTKDQFHRHLLLEAERRQLRPIIENKSRIILVHTSSGYKHSLREVLDAP 258 (323)
Q Consensus 191 l~~~~~~~~v~~iIIaG--PGf~kd~f~~~l~~~~~~~~~~~~~~~~~ki~~~~~s~~~~~gl~Evl~~~ 258 (323)
+.. .+.||++| |.-+..++|.-|-+.+++ .+..+++|+|.. .|.++|+-+
T Consensus 127 l~~------~d~VvlsGSlP~g~~~d~y~~li~~~~~---------~g~~vilD~Sg~---~L~~~L~~~ 178 (310)
T COG1105 127 LES------DDIVVLSGSLPPGVPPDAYAELIRILRQ---------QGAKVILDTSGE---ALLAALEAK 178 (310)
T ss_pred ccc------CCEEEEeCCCCCCCCHHHHHHHHHHHHh---------cCCeEEEECChH---HHHHHHccC
Confidence 443 44699999 333444555545555543 245578888863 456666654
No 32
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=40.65 E-value=3.9e+02 Score=27.43 Aligned_cols=80 Identities=14% Similarity=0.072 Sum_probs=47.7
Q ss_pred EEEEEEeCCeEEEEEEecceEEEE-------EEEEEecCCCCCCCcchhhHHHHHHHHHHHHHHHhcccccCccEEEEEC
Q 020677 135 LAVVLMQEGLAHILLVGRSMTITR-------SRIETSIPRKHGPAIAGYESALNKFFENVLQAFLKHVDFNVVRCAVIAS 207 (323)
Q Consensus 135 ~~~vvid~g~A~i~ll~~~~~~~~-------~~i~~~ip~K~~~~~s~~~~~~~~f~~~v~~~l~~~~~~~~v~~iIIaG 207 (323)
=.++=|+...|++.-++.+.+.+- -+++.--|=-+.. - ..-..-++.. +-|.+ .-.+|+|||
T Consensus 202 ~sfIEi~r~GatVvQlrn~RIvIarPPfSd~~EITavRPvvk~~-l-edY~L~dkl~----eRL~e-----raeGILIAG 270 (604)
T COG1855 202 DSFIEIDRPGATVVQLRNYRIVIARPPFSDRWEITAVRPVVKLS-L-EDYGLSDKLK----ERLEE-----RAEGILIAG 270 (604)
T ss_pred CceEEEccCCceEEEeccEEEEEecCCCCCceEEEEEeeeEEec-h-hhcCCCHHHH----HHHHh-----hhcceEEec
Confidence 478999999999999998887762 2344433321100 0 0000111122 22222 456899988
Q ss_pred -CcccHHHHHHHHHHHHHh
Q 020677 208 -PGFTKDQFHRHLLLEAER 225 (323)
Q Consensus 208 -PGf~kd~f~~~l~~~~~~ 225 (323)
||.=|..|.+-|.+-+.+
T Consensus 271 ~PGaGKsTFaqAlAefy~~ 289 (604)
T COG1855 271 APGAGKSTFAQALAEFYAS 289 (604)
T ss_pred CCCCChhHHHHHHHHHHHh
Confidence 688899999877666654
No 33
>COG1358 RPL8A Ribosomal protein HS6-type (S12/L30/L7a) [Translation, ribosomal structure and biogenesis]
Probab=38.62 E-value=61 Score=26.44 Aligned_cols=30 Identities=23% Similarity=0.305 Sum_probs=26.6
Q ss_pred CCCeEEEcHHHHHHHHhcCCccEEEEecCC
Q 020677 286 DPTRACYGPKHVEVAHERMAVQTLLITDDL 315 (323)
Q Consensus 286 ~~~~a~YG~~eV~~A~e~GAVetLLIsD~l 315 (323)
..++..+|.++|.+|++.|-..-++|+.|.
T Consensus 24 ~~~ki~~G~~e~~Kai~~g~a~LVviA~Dv 53 (116)
T COG1358 24 RAGKLKKGTNEVTKAIERGKAKLVVIAEDV 53 (116)
T ss_pred hcCCchhhHHHHHHHHHcCCCcEEEEecCC
Confidence 347899999999999999999999998764
No 34
>smart00536 AXH domain in Ataxins and HMG containing proteins. unknown function
Probab=37.22 E-value=1.3e+02 Score=24.59 Aligned_cols=78 Identities=21% Similarity=0.286 Sum_probs=50.9
Q ss_pred CceEEEeccCC--chhhhHhhhcCCCCEEEEEeEEEEEeccCCCCccceEEEEEEEEEE-EEeecCCCeEEEEEEEeecC
Q 020677 13 PGSVKMEPVDS--DDLWFAYNLIAPGDSVMAVTVRKVLRQMASGSRDAERVKLKLEIKV-VDYDKEGSVLRIRGKNILEN 89 (323)
Q Consensus 13 ~g~v~l~~E~~--dDlw~lynli~~GD~V~a~T~Rkv~~~~~~g~~~~~r~~~~L~i~V-vef~~~~~~Lri~G~i~~~~ 89 (323)
+|..+ ..||. ||+-.- -...++-.+.+.|.-+|... +.... | +.|++....
T Consensus 12 ~G~~k-rvEDl~teDfi~s-a~~s~~~~l~~stv~~i~~~---~~~~~----------v~itF~~g~~~----------- 65 (116)
T smart00536 12 NGSNK-KVEDLKTEDFIRS-AECSNDEEIQMSTVKRIGSS---GLPSV----------VTLTFDPGVED----------- 65 (116)
T ss_pred CCCee-eeeccchhhhHhh-hccCCcccccceeEEEeCCC---CCcce----------EEEEEEecCcc-----------
Confidence 34544 67887 887666 66677888999999888642 21111 3 667654322
Q ss_pred cccccccEEEEEEccCceeEEEEcccChhhHHH
Q 020677 90 EHVKIGAFHTLEIELHRAFVLRKDLWDSLALDT 122 (323)
Q Consensus 90 e~v~~G~~HTi~i~~~~~~~i~K~~wd~~~~e~ 122 (323)
+--|++..+..||=++-..|.++.=++
T Consensus 66 ------~~v~~ev~~eHPfFV~gqGWsSc~P~l 92 (116)
T smart00536 66 ------ALLTVECQVEHPFFVKGKGWSSCYPSL 92 (116)
T ss_pred ------ceEEEEEecCCCeEEcCccccccChhh
Confidence 335677778888888777999865444
No 35
>PRK13310 N-acetyl-D-glucosamine kinase; Provisional
Probab=36.82 E-value=1.2e+02 Score=28.30 Aligned_cols=47 Identities=9% Similarity=0.040 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHHHHhcccccCccEEEEECCcccHHHHHHHHHHHHHh
Q 020677 179 ALNKFFENVLQAFLKHVDFNVVRCAVIASPGFTKDQFHRHLLLEAER 225 (323)
Q Consensus 179 ~~~~f~~~v~~~l~~~~~~~~v~~iIIaGPGf~kd~f~~~l~~~~~~ 225 (323)
.+++|.+.++..+....+..++..|||+|+-...+.|.+.+.+.+.+
T Consensus 225 ~~~~~~~~la~~l~n~~~~ldP~~IvlgG~~~~~~~~~~~l~~~~~~ 271 (303)
T PRK13310 225 HVERYLDLLAICLGNILTIVDPHLVVLGGGLSNFDAIYEQLPKRLPR 271 (303)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCCEEEECCcccChHHHHHHHHHHHHH
Confidence 34455556666666666677899999999754445666666666544
No 36
>COG4972 PilM Tfp pilus assembly protein, ATPase PilM [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=34.35 E-value=66 Score=31.19 Aligned_cols=48 Identities=13% Similarity=0.195 Sum_probs=39.0
Q ss_pred hhHHHHHHHHHHHHHHHhcccc-------cCccEEEEECCcccHHHHHHHHHHHH
Q 020677 176 YESALNKFFENVLQAFLKHVDF-------NVVRCAVIASPGFTKDQFHRHLLLEA 223 (323)
Q Consensus 176 ~~~~~~~f~~~v~~~l~~~~~~-------~~v~~iIIaGPGf~kd~f~~~l~~~~ 223 (323)
.......|..++.+.+.+.+.| .++++|+++|||-.-..+-+++.+++
T Consensus 257 ~~~vl~~f~~~l~~ei~Rslqfy~~~s~~~~id~i~LaGggA~l~gL~~~i~qrl 311 (354)
T COG4972 257 GSEVLRPFLGELTQEIRRSLQFYLSQSEMVDIDQILLAGGGASLEGLAAAIQQRL 311 (354)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhccccceeeEEEEecCCcchhhHHHHHHHHh
Confidence 3445678999999999877653 47999999999988888888887776
No 37
>COG0018 ArgS Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=31.72 E-value=84 Score=32.79 Aligned_cols=61 Identities=18% Similarity=0.354 Sum_probs=33.0
Q ss_pred HHHHHHHHhccccc-CccEEEEECCcccH----HH-HHHHHHHHHHhccc---cccccccCcEEEEEcCC
Q 020677 185 ENVLQAFLKHVDFN-VVRCAVIASPGFTK----DQ-FHRHLLLEAERRQL---RPIIENKSRIILVHTSS 245 (323)
Q Consensus 185 ~~v~~~l~~~~~~~-~v~~iIIaGPGf~k----d~-f~~~l~~~~~~~~~---~~~~~~~~ki~~~~~s~ 245 (323)
++||+.+...+..+ .+..|-+|||||+. .. +.+.+.+-+.+... ......-.+|++.++|.
T Consensus 57 ~eiA~~i~~~l~~~~~~~~veiaGpgfINf~l~~~~~~~~~~~~l~~~~~~~G~~~~~~~~kV~iE~sSa 126 (577)
T COG0018 57 REIAEEIAEKLDTDEIIEKVEIAGPGFINFFLSPEFLAELLLEILEKGDDRYGRSKLGKGKKVVIEYSSA 126 (577)
T ss_pred HHHHHHHHHhccccCcEeEEEEcCCCEEEEEECHHHHHHHHHHHHHhcccccCccccCCCCEEEEEEeCC
Confidence 45666666666543 47889999999763 22 22344343332111 11111123777888774
No 38
>PF11104 PilM_2: Type IV pilus assembly protein PilM;; PDB: 2YCH_A.
Probab=31.14 E-value=2.4e+02 Score=26.86 Aligned_cols=89 Identities=16% Similarity=0.178 Sum_probs=57.4
Q ss_pred cEEEEEEeCCeEEEEEEecceEEEEEEEEEecCCCCC---------------------CC--cchhhHHHHHHHHHHHHH
Q 020677 134 DLAVVLMQEGLAHILLVGRSMTITRSRIETSIPRKHG---------------------PA--IAGYESALNKFFENVLQA 190 (323)
Q Consensus 134 ~~~~vvid~g~A~i~ll~~~~~~~~~~i~~~ip~K~~---------------------~~--~s~~~~~~~~f~~~v~~~ 190 (323)
.+++|-+.....+++++.+........+ ++++..- .+ .......+..|++++++.
T Consensus 181 ~~~lvdiG~~~t~~~i~~~g~~~f~R~i--~~G~~~l~~~i~~~~~i~~~~Ae~~k~~~~l~~~~~~~~l~~~~~~l~~E 258 (340)
T PF11104_consen 181 TVALVDIGASSTTVIIFQNGKPIFSRSI--PIGGNDLTEAIARELGIDFEEAEELKRSGGLPEEYDQDALRPFLEELARE 258 (340)
T ss_dssp EEEEEEE-SS-EEEEEEETTEEEEEEEE--S-SHHHHHHHHHHHTT--HHHHHHHHHHT------HHHHHHHHHHHHHHH
T ss_pred eEEEEEecCCeEEEEEEECCEEEEEEEE--eeCHHHHHHHHHHhcCCCHHHHHHHHhcCCCCcchHHHHHHHHHHHHHHH
Confidence 5788999999999999988877665554 3332100 00 000134466788888888
Q ss_pred HHhcccc-------cCccEEEEECCcccHHHHHHHHHHHHH
Q 020677 191 FLKHVDF-------NVVRCAVIASPGFTKDQFHRHLLLEAE 224 (323)
Q Consensus 191 l~~~~~~-------~~v~~iIIaGPGf~kd~f~~~l~~~~~ 224 (323)
+.+.+++ ..++.|+++|.|---..+.+||.+++.
T Consensus 259 I~rsl~~y~~~~~~~~i~~I~L~Ggga~l~gL~~~l~~~l~ 299 (340)
T PF11104_consen 259 IRRSLDFYQSQSGGESIERIYLSGGGARLPGLAEYLSEELG 299 (340)
T ss_dssp HHHHHHHHHHH------SEEEEESGGGGSTTHHHHHHHHHT
T ss_pred HHHHHHHHHhcCCCCCCCEEEEECCccchhhHHHHHHHHHC
Confidence 8776652 368999999999887888889988863
No 39
>PF04628 Sedlin_N: Sedlin, N-terminal conserved region; InterPro: IPR006722 Sedlin is a 140 amino-acid protein with a putative role in endoplasmic reticulum-to-Golgi transport. Several missense mutations and deletion mutations in the SEDL gene, which result in protein truncation by frame shift, are responsible for spondyloepiphyseal dysplasia tarda, a progressive skeletal disorder (OMIM:313400). [].; GO: 0006888 ER to Golgi vesicle-mediated transport, 0005622 intracellular; PDB: 3PR6_A 2J3W_A 1H3Q_A.
Probab=30.42 E-value=2.9e+02 Score=22.54 Aligned_cols=71 Identities=14% Similarity=0.098 Sum_probs=52.2
Q ss_pred hhHHHHHHhcCC-CCCCcEEEEEEeCCeEEEEEEecceEEEEEEEEEecCCCCCCCcchhhHHHHHHHHHHHHHHHhcc
Q 020677 118 LALDTLHQAADP-TASADLAVVLMQEGLAHILLVGRSMTITRSRIETSIPRKHGPAIAGYESALNKFFENVLQAFLKHV 195 (323)
Q Consensus 118 ~~~e~L~~a~~~-~~~~~~~~vvid~g~A~i~ll~~~~~~~~~~i~~~ip~K~~~~~s~~~~~~~~f~~~v~~~l~~~~ 195 (323)
-.|+.+++.+.. ....-+|.|---++-..-+.++..+++.+--.... .....+..+..||++|.+.-.+.+
T Consensus 35 ~sLD~iee~~~~~~~~~yLg~l~~~~~~~vygyvT~t~~Kfvl~~~~~-------~~~~~d~~ik~fF~~vh~~Y~~~~ 106 (132)
T PF04628_consen 35 SSLDVIEEKLWKSSSDMYLGLLDPFEDYKVYGYVTNTGIKFVLVHDMS-------DNSIRDEDIKQFFKEVHELYVKAL 106 (132)
T ss_dssp HHHHHHHHCCHCSSSCSEEEEEEEETTEEEEEEETTT--EEEEEECGG-------G-S--HHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhhcccccccCceehhhhHHHHhhhccCceeEEEEEecc-------cCCcchHHHHHHHHHHHHHHHHHc
Confidence 368888888777 66667888888899999999999998887655421 111257899999999999888766
No 40
>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=27.25 E-value=96 Score=24.73 Aligned_cols=38 Identities=26% Similarity=0.360 Sum_probs=31.0
Q ss_pred eEEEEEEEeecCcccccccEEEEEEccCceeEEEEcccChh
Q 020677 78 VLRIRGKNILENEHVKIGAFHTLEIELHRAFVLRKDLWDSL 118 (323)
Q Consensus 78 ~Lri~G~i~~~~e~v~~G~~HTi~i~~~~~~~i~K~~wd~~ 118 (323)
---+.|++++-. ..|.++|+++..--.|-+.|+..++.
T Consensus 55 G~ei~GkVt~K~---~ig~~yTvti~~YGkFlVtkeqY~~i 92 (104)
T PF07116_consen 55 GAEIFGKVTEKE---IIGGLYTVTIGAYGKFLVTKEQYESI 92 (104)
T ss_pred CcEEEEEEeece---eECCEEEEEecCceEEEEehhhccee
Confidence 356889998865 67999999999988999998776653
No 41
>PF08447 PAS_3: PAS fold; InterPro: IPR013655 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []. The PAS fold appears in archaea, eubacteria and eukarya. The PAS domain contains a sensory box, or S-box domain that occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include haem in the oxygen sensor FixL [], FAD in the redox potential sensor NifL [], and a 4-hydroxycinnamyl chromophore in photoactive yellow protein []. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator. This domain has been found in the gene product of the madA gene of the filamentous zygomycete fungus Phycomyces blakesleeanus. It has been shown that MadA encodes a blue-light photoreceptor for phototropism and other light responses. The gene is involved in the phototropic responses associated with sporangiophore growth; they exhibit phototropism by bending toward near-UV and blue wavelengths and away from far-UV wavelengths in a manner that is physiologically similar to plant phototropic responses [].; GO: 0005515 protein binding; PDB: 3NJA_D 3H9W_A 3GDI_B 3ICY_A 3EEH_A 3MR0_B.
Probab=26.98 E-value=2.4e+02 Score=20.19 Aligned_cols=59 Identities=20% Similarity=0.278 Sum_probs=36.8
Q ss_pred EeccCCchhhhHhhh-cCCCCEEEEEeEEEEEeccCCCCccceEEEEEEEEEE-EEeecCCCeEEEEEEE
Q 020677 18 MEPVDSDDLWFAYNL-IAPGDSVMAVTVRKVLRQMASGSRDAERVKLKLEIKV-VDYDKEGSVLRIRGKN 85 (323)
Q Consensus 18 l~~E~~dDlw~lynl-i~~GD~V~a~T~Rkv~~~~~~g~~~~~r~~~~L~i~V-vef~~~~~~Lri~G~i 85 (323)
+.||+.+-++....- ...++.......|-..+ .| +-+ .+..+. +-||+.++..++.|++
T Consensus 31 ihpdD~~~~~~~~~~~~~~~~~~~~~e~R~~~~---~G----~~~--wi~~~~~~~~d~~g~~~~~~Gv~ 91 (91)
T PF08447_consen 31 IHPDDRERVRQAIQQAALQNGEPFEIEYRIRRK---DG----EYR--WIEVRGRPIFDENGKPIRIIGVI 91 (91)
T ss_dssp B-TTTHHHHHHHHHHHHHHTT-EEEEEEEEEGT---TS----TEE--EEEEEEEEEETTTS-EEEEEEEE
T ss_pred cCHHHHHHHHHHHHHHhhccCcceEEEEEEECC---CC----CEE--EEEEEEEEEECCCCCEEEEEEEC
Confidence 567888877777666 45556566667777643 22 333 344444 5559999999999986
No 42
>COG1911 RPL30 Ribosomal protein L30E [Translation, ribosomal structure and biogenesis]
Probab=25.41 E-value=1.1e+02 Score=24.24 Aligned_cols=32 Identities=9% Similarity=0.081 Sum_probs=28.1
Q ss_pred cCCCeEEEcHHHHHHHHhcCCccEEEEecCCc
Q 020677 285 NDPTRACYGPKHVEVAHERMAVQTLLITDDLF 316 (323)
Q Consensus 285 ~~~~~a~YG~~eV~~A~e~GAVetLLIsD~l~ 316 (323)
.+.|++..|.+.+.+++.+|..+-++|..+..
T Consensus 15 vkTGkvilG~k~tiK~lk~gkaKliiiAsN~P 46 (100)
T COG1911 15 VKTGKVILGSKRTIKSLKLGKAKLIIIASNCP 46 (100)
T ss_pred HhcCCEEEehHHHHHHHHcCCCcEEEEecCCC
Confidence 34589999999999999999999999987654
No 43
>PF14213 DUF4325: Domain of unknown function (DUF4325)
Probab=23.81 E-value=87 Score=22.94 Aligned_cols=68 Identities=12% Similarity=0.161 Sum_probs=38.9
Q ss_pred HHHHHHHHHHHHhccc-ccCccEEEEECCcccHHHHHHHHHHHHHhccccccccccCcEEEEEcCCCccchHHHHh
Q 020677 181 NKFFENVLQAFLKHVD-FNVVRCAVIASPGFTKDQFHRHLLLEAERRQLRPIIENKSRIILVHTSSGYKHSLREVL 255 (323)
Q Consensus 181 ~~f~~~v~~~l~~~~~-~~~v~~iIIaGPGf~kd~f~~~l~~~~~~~~~~~~~~~~~ki~~~~~s~~~~~gl~Evl 255 (323)
+++|+.+..++..--. .-+..+|-..||+|+-+-|-..+....... .+.++.+.+.+.....-|+.++
T Consensus 4 ~~~~~~i~~~l~~~~~V~lDF~gv~~~~ssFl~eafg~l~~~~~~~~-------~~~~l~~~~~~~~~~~~I~~vi 72 (74)
T PF14213_consen 4 ERLRDEIEPALKEGEKVVLDFEGVESITSSFLNEAFGQLVREFGEEE-------IKKRLKFKNANESIKEMIKRVI 72 (74)
T ss_pred HHHHHHHHHHHhcCCeEEEECCCcccccHHHHHHHHHHHHHHcCHHH-------HhheeEEecCCHHHHHHHHHHH
Confidence 5677887777764211 123455677899999999987665543221 1235556665554444444433
No 44
>PRK15080 ethanolamine utilization protein EutJ; Provisional
Probab=23.64 E-value=1.8e+02 Score=26.93 Aligned_cols=87 Identities=13% Similarity=0.100 Sum_probs=51.3
Q ss_pred EEEEEEeCCeEEEEEEecceEEEEEEEEEecCCCCCC-------Ccc---------------hhhHHHHHHHHHHHHHHH
Q 020677 135 LAVVLMQEGLAHILLVGRSMTITRSRIETSIPRKHGP-------AIA---------------GYESALNKFFENVLQAFL 192 (323)
Q Consensus 135 ~~~vvid~g~A~i~ll~~~~~~~~~~i~~~ip~K~~~-------~~s---------------~~~~~~~~f~~~v~~~l~ 192 (323)
..++-|..|...++++........ ...++.+.+-. +-+ .-...++.+++++.+.+.
T Consensus 137 ~~vvDIGggtt~i~v~~~g~~~~~--~~~~~GG~~it~~Ia~~l~i~~~eAE~lK~~~~~~~~~~~ii~~~~~~i~~~i~ 214 (267)
T PRK15080 137 GAVVDIGGGTTGISILKDGKVVYS--ADEPTGGTHMSLVLAGAYGISFEEAEQYKRDPKHHKEIFPVVKPVVEKMASIVA 214 (267)
T ss_pred cEEEEeCCCcEEEEEEECCeEEEE--ecccCchHHHHHHHHHHhCCCHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHH
Confidence 467777788888888876654432 22233322100 000 011233456777777777
Q ss_pred hcccccCccEEEEECCcccHHHHHHHHHHHH
Q 020677 193 KHVDFNVVRCAVIASPGFTKDQFHRHLLLEA 223 (323)
Q Consensus 193 ~~~~~~~v~~iIIaGPGf~kd~f~~~l~~~~ 223 (323)
+.+....+..|+++|-|---..+.+++.+.+
T Consensus 215 ~~l~~~~~~~IvLtGG~s~lpgl~e~l~~~l 245 (267)
T PRK15080 215 RHIEGQDVEDIYLVGGTCCLPGFEEVFEKQT 245 (267)
T ss_pred HHHhcCCCCEEEEECCcccchhHHHHHHHHh
Confidence 7766667888888888866666666666665
No 45
>PF09345 DUF1987: Domain of unknown function (DUF1987); InterPro: IPR018530 This family of proteins are functionally uncharacterised.
Probab=23.29 E-value=68 Score=25.38 Aligned_cols=21 Identities=38% Similarity=0.570 Sum_probs=18.5
Q ss_pred EEeecCCCeEEEEEEEeecCc
Q 020677 70 VDYDKEGSVLRIRGKNILENE 90 (323)
Q Consensus 70 vef~~~~~~Lri~G~i~~~~e 90 (323)
|.||+.+++|+|+|.-..++.
T Consensus 3 V~Fd~~~g~l~i~GeSypEn~ 23 (99)
T PF09345_consen 3 VDFDFDTGRLEISGESYPENA 23 (99)
T ss_pred EEEEccCCEEEEecccCccCH
Confidence 689999999999999987773
No 46
>TIGR00744 ROK_glcA_fam ROK family protein (putative glucokinase). This alignment models one branch of the ROK superfamily of proteins. The three members of the seed alignment for this model all have experimental evidence for activity as glucokinase, but the set of related proteins is crowded with paralogs of different or unknown function. Proteins scoring above the trusted_cutoff will show strong similarity to at least one known glucokinase and may be designated as putative glucokinases. However, definitive identification of glucokinases should be done only with extreme caution.
Probab=23.13 E-value=2.6e+02 Score=26.04 Aligned_cols=47 Identities=6% Similarity=-0.075 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHHHHhcccccCccEEEEECCccc-HHHHHHHHHHHHHh
Q 020677 179 ALNKFFENVLQAFLKHVDFNVVRCAVIASPGFT-KDQFHRHLLLEAER 225 (323)
Q Consensus 179 ~~~~f~~~v~~~l~~~~~~~~v~~iIIaGPGf~-kd~f~~~l~~~~~~ 225 (323)
.++++.+.++.++....+..+++.|||+|+-+. .+.|.+.+.+...+
T Consensus 231 i~~~~~~~L~~~i~~~~~~~dP~~IvlgG~~~~~~~~~~~~i~~~~~~ 278 (318)
T TIGR00744 231 SYREVARWAGAGLADLASLFNPSAIVLGGGLSDAGDLLLDPIRKSYKR 278 (318)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCEEEECChhhhCcHHHHHHHHHHHHH
Confidence 344555555555666656668899999997543 24566666665543
No 47
>COG1940 NagC Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]
Probab=22.41 E-value=2e+02 Score=26.86 Aligned_cols=46 Identities=9% Similarity=0.061 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHHHhcccccCccEEEEEC--CcccHHHHHHHHHHHHHh
Q 020677 180 LNKFFENVLQAFLKHVDFNVVRCAVIAS--PGFTKDQFHRHLLLEAER 225 (323)
Q Consensus 180 ~~~f~~~v~~~l~~~~~~~~v~~iIIaG--PGf~kd~f~~~l~~~~~~ 225 (323)
++++.+.++..+....+..++..|||+| +.-..+.|.+.+......
T Consensus 228 ~~~~~~~la~~ianl~~~~~P~~IvigG~g~~~~~~~~~~~l~~~~~~ 275 (314)
T COG1940 228 IERAADYLARGLANLINLLDPEVIVIGGGGVSALGDLLLPRLRKLLAK 275 (314)
T ss_pred HHHHHHHHHHHHHHHHHhcCCCeEEEECcccccchhHHHHHHHHHHHH
Confidence 4555666666666666677889999987 555667777777766654
No 48
>PF01336 tRNA_anti-codon: OB-fold nucleic acid binding domain; InterPro: IPR004365 The OB-fold (oligonucleotide/oligosaccharide-binding fold) is found in all three kingdoms and its common architecture presents a binding face that has adapted to bind different ligands. The OB-fold is a five/six-stranded closed beta-barrel formed by 70-80 amino acid residues. The strands are connected by loops of varying length which form the functional appendages of the protein. The majority of OB-fold proteins use the same face for ligand binding or as an active site. Different OB-fold proteins use this 'fold-related binding face' to, variously, bind oligosaccharides, oligonucleotides, proteins, metal ions and catalytic substrates. This entry contains OB-fold domains that bind to nucleic acids []. It includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl-tRNA synthetases (See IPR004364 from INTERPRO). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule 6.1.1 from EC. This domain is found in RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family [, ]. This domain is also found at the C terminus of bacterial DNA polymerase III alpha chain.; GO: 0003676 nucleic acid binding; PDB: 1BBU_A 1KRS_A 1BBW_A 1KRT_A 1EQR_B 1IL2_B 1C0A_A 3KFU_A 1EOV_A 1ASY_A ....
Probab=22.36 E-value=1.2e+02 Score=21.34 Aligned_cols=33 Identities=21% Similarity=0.272 Sum_probs=26.1
Q ss_pred cCCCceEEEeccCCchhhhHhhhcCCCCEEEEEe
Q 020677 10 ENGPGSVKMEPVDSDDLWFAYNLIAPGDSVMAVT 43 (323)
Q Consensus 10 ~~~~g~v~l~~E~~dDlw~lynli~~GD~V~a~T 43 (323)
.|+.|.+.+..-+ ++.-..+..|.+||.|...-
T Consensus 23 ~D~tg~i~~~~~~-~~~~~~~~~l~~g~~v~v~G 55 (75)
T PF01336_consen 23 EDGTGSIQVVFFN-EEYERFREKLKEGDIVRVRG 55 (75)
T ss_dssp EETTEEEEEEEET-HHHHHHHHTS-TTSEEEEEE
T ss_pred EECCccEEEEEcc-HHhhHHhhcCCCCeEEEEEE
Confidence 4577888888777 77778888999999999884
No 49
>PRK10439 enterobactin/ferric enterobactin esterase; Provisional
Probab=21.28 E-value=1.4e+02 Score=29.66 Aligned_cols=49 Identities=16% Similarity=0.103 Sum_probs=34.3
Q ss_pred HHHHHHHHHHHHHhccccc--cccccCcEEEEEcCCCccchHHHHhcChhH
Q 020677 212 KDQFHRHLLLEAERRQLRP--IIENKSRIILVHTSSGYKHSLREVLDAPNV 260 (323)
Q Consensus 212 kd~f~~~l~~~~~~~~~~~--~~~~~~ki~~~~~s~~~~~gl~Evl~~~~v 260 (323)
...|.+||.+++.....+. ....+++.++...|+||..+++=.|+.|+.
T Consensus 262 ~~~f~~~l~~eLlP~I~~~y~~~~d~~~~~IaG~S~GGl~AL~~al~~Pd~ 312 (411)
T PRK10439 262 NADFWLAVQQELLPQVRAIAPFSDDADRTVVAGQSFGGLAALYAGLHWPER 312 (411)
T ss_pred hHHHHHHHHHHHHHHHHHhCCCCCCccceEEEEEChHHHHHHHHHHhCccc
Confidence 3467777777765432221 223445678999999999999999999854
No 50
>PRK09698 D-allose kinase; Provisional
Probab=20.87 E-value=3.1e+02 Score=25.36 Aligned_cols=47 Identities=9% Similarity=0.135 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHHHHhcccccCccEEEEECCcccHH-HHHHHHHHHHHh
Q 020677 179 ALNKFFENVLQAFLKHVDFNVVRCAVIASPGFTKD-QFHRHLLLEAER 225 (323)
Q Consensus 179 ~~~~f~~~v~~~l~~~~~~~~v~~iIIaGPGf~kd-~f~~~l~~~~~~ 225 (323)
.+++|.+.++..+....+..++..|||+|...-.. .|.+++.+.+.+
T Consensus 216 ~~~~~~~~la~~l~~li~~ldP~~IvlgG~~~~~~~~~~~~l~~~~~~ 263 (302)
T PRK09698 216 FIQSLLENLARAIATSINLFDPDAIILGGGVMDMPAFPRETLIAMIQK 263 (302)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCEEEEcCccccCchhHHHHHHHHHHH
Confidence 45666777777777777777899999999754333 345566665544
No 51
>PRK06851 hypothetical protein; Provisional
Probab=20.49 E-value=1.5e+02 Score=29.07 Aligned_cols=43 Identities=16% Similarity=0.262 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHHHHhcccccCccEEEEECCcccHHHHHHHHHHHHHhccc
Q 020677 179 ALNKFFENVLQAFLKHVDFNVVRCAVIASPGFTKDQFHRHLLLEAERRQL 228 (323)
Q Consensus 179 ~~~~f~~~v~~~l~~~~~~~~v~~iIIaGPGf~kd~f~~~l~~~~~~~~~ 228 (323)
..-.||..+.+.+.+. -+|-++||--|..+...+...+.+++.
T Consensus 201 G~~s~~~~l~~~~~~~-------~~i~G~pG~GKstl~~~i~~~a~~~G~ 243 (367)
T PRK06851 201 GAVDFVPSLTEGVKNR-------YFLKGRPGTGKSTMLKKIAKAAEERGF 243 (367)
T ss_pred cHHhhHHhHhcccceE-------EEEeCCCCCcHHHHHHHHHHHHHhCCC
Confidence 4556888877555443 377788999999999998888876554
No 52
>PF00158 Sigma54_activat: Sigma-54 interaction domain; InterPro: IPR002078 Some bacterial regulatory proteins activate the expression of genes from promoters recognised by core RNA polymerase associated with the alternative sigma-54 factor. These have a conserved domain of about 230 residues involved in the ATP-dependent [, ] interaction with sigma-54. About half of the proteins in which this domain is found (algB, dcdT, flbD, hoxA, hupR1, hydG, ntrC, pgtA and pilR) belong to signal transduction two-component systems [] and possess a domain that can be phosphorylated by a sensor-kinase protein in their N-terminal section. Almost all of these proteins possess a helix-turn-helix DNA-binding domain in their C-terminal section. The domain which interacts with the sigma-54 factor has an ATPase activity. This may be required to promote a conformational change necessary for the interaction []. The domain contains an atypical ATP-binding motif A (P-loop) as well as a form of motif B. The two ATP-binding motifs are located in the N-terminal section of the domain.; GO: 0005524 ATP binding, 0008134 transcription factor binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1NY6_K 3M0E_G 1NY5_A 1OJL_A 3DZD_B 2C9C_A 2C98_A 2C96_A 2BJV_A 2C99_A ....
Probab=20.45 E-value=3e+02 Score=23.52 Aligned_cols=57 Identities=14% Similarity=0.208 Sum_probs=35.3
Q ss_pred HHHHHHHHHHHHHHHhcccccCccEEEEECCcccHHHHHHHHHHHHHhccccccccccCcEEEEEcCCCc
Q 020677 178 SALNKFFENVLQAFLKHVDFNVVRCAVIASPGFTKDQFHRHLLLEAERRQLRPIIENKSRIILVHTSSGY 247 (323)
Q Consensus 178 ~~~~~f~~~v~~~l~~~~~~~~v~~iIIaGPGf~kd~f~~~l~~~~~~~~~~~~~~~~~ki~~~~~s~~~ 247 (323)
.++.+..+++ .+... .+...+|.+-||-=|+.|.+.+.+...+. ...|+.++++.-.
T Consensus 6 ~~m~~~~~~~----~~~a~-~~~pVlI~GE~GtGK~~lA~~IH~~s~r~--------~~pfi~vnc~~~~ 62 (168)
T PF00158_consen 6 PAMKRLREQA----KRAAS-SDLPVLITGETGTGKELLARAIHNNSPRK--------NGPFISVNCAALP 62 (168)
T ss_dssp HHHHHHHHHH----HHHTT-STS-EEEECSTTSSHHHHHHHHHHCSTTT--------TS-EEEEETTTS-
T ss_pred HHHHHHHHHH----HHHhC-CCCCEEEEcCCCCcHHHHHHHHHHhhhcc--------cCCeEEEehhhhh
Confidence 3455555444 44333 23556777778888999999888865542 2478899988643
Done!