Query 045445
Match_columns 128
No_of_seqs 131 out of 1150
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 13:16:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045445.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045445hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0216 PrfA Protein chain rel 100.0 3.1E-36 6.8E-41 255.0 4.4 95 11-105 197-317 (363)
2 TIGR00019 prfA peptide chain r 100.0 1.3E-31 2.8E-36 227.8 4.3 97 9-105 194-315 (360)
3 KOG2726 Mitochondrial polypept 100.0 2.6E-31 5.6E-36 227.4 6.0 103 11-113 221-351 (386)
4 PRK05589 peptide chain release 100.0 4.2E-31 9E-36 222.2 5.1 96 10-105 169-290 (325)
5 PRK00591 prfA peptide chain re 100.0 7.1E-31 1.5E-35 223.1 6.0 98 8-105 193-315 (359)
6 TIGR03072 release_prfH putativ 100.0 9.9E-31 2.1E-35 207.7 5.3 94 10-104 84-198 (200)
7 PRK08787 peptide chain release 100.0 1E-30 2.2E-35 219.1 5.5 96 10-105 149-269 (313)
8 PRK06746 peptide chain release 100.0 1.2E-30 2.6E-35 219.6 4.3 96 9-105 169-291 (326)
9 PRK07342 peptide chain release 100.0 3.5E-30 7.6E-35 217.7 5.5 94 10-103 172-290 (339)
10 TIGR00020 prfB peptide chain r 100.0 1.1E-29 2.3E-34 216.2 4.9 96 10-105 208-329 (364)
11 PRK08179 prfH peptide chain re 100.0 1.9E-29 4.2E-34 200.3 4.8 92 10-102 85-197 (200)
12 PRK00578 prfB peptide chain re 100.0 1.7E-29 3.8E-34 215.1 4.0 96 9-105 207-329 (367)
13 COG1186 PrfB Protein chain rel 99.9 4.9E-28 1.1E-32 196.9 2.8 109 5-113 78-213 (239)
14 PF00472 RF-1: RF-1 domain; I 99.9 2.6E-27 5.6E-32 172.1 3.1 76 29-104 8-105 (113)
15 PRK09256 hypothetical protein; 99.8 6E-19 1.3E-23 133.3 4.4 55 30-84 10-92 (138)
16 KOG3429 Predicted peptidyl-tRN 99.3 1.2E-12 2.7E-17 102.3 4.7 59 26-84 33-120 (172)
17 PF02954 HTH_8: Bacterial regu 91.1 0.25 5.5E-06 29.7 2.6 23 106-128 9-31 (42)
18 PF13556 HTH_30: PucR C-termin 67.6 5.9 0.00013 25.1 2.5 22 106-127 3-24 (59)
19 PRK01905 DNA-binding protein F 62.9 8.5 0.00018 25.9 2.7 22 106-127 41-62 (77)
20 PRK00430 fis global DNA-bindin 60.4 9.7 0.00021 26.9 2.7 22 106-127 59-80 (95)
21 PF02815 MIR: MIR domain; Int 48.6 38 0.00082 25.7 4.5 38 37-74 121-158 (190)
22 PF06056 Terminase_5: Putative 43.4 21 0.00045 23.2 2.0 18 111-128 9-26 (58)
23 COG3284 AcoR Transcriptional a 40.8 24 0.00052 33.0 2.7 23 106-128 569-591 (606)
24 PF13384 HTH_23: Homeodomain-l 35.1 42 0.00091 19.8 2.3 21 107-128 10-30 (50)
25 TIGR02974 phageshock_pspF psp 34.2 38 0.00081 28.4 2.7 23 106-128 296-318 (329)
26 PF06972 DUF1296: Protein of u 33.9 46 0.001 22.4 2.5 24 102-125 19-42 (60)
27 TIGR01817 nifA Nif-specific re 33.6 37 0.0008 30.0 2.7 23 106-128 494-516 (534)
28 TIGR02915 PEP_resp_reg putativ 32.5 41 0.0009 28.3 2.7 22 106-127 409-430 (445)
29 PRK15115 response regulator Gl 32.0 43 0.00093 28.2 2.7 22 106-127 402-423 (444)
30 PRK11361 acetoacetate metaboli 31.9 43 0.00093 28.2 2.7 22 106-127 421-442 (457)
31 PRK11608 pspF phage shock prot 31.8 44 0.00095 27.8 2.7 23 106-128 290-312 (326)
32 TIGR01818 ntrC nitrogen regula 30.9 46 0.00099 28.1 2.7 22 106-127 430-451 (463)
33 smart00472 MIR Domain in ryano 30.8 49 0.0011 20.1 2.2 21 54-74 7-27 (57)
34 PF01527 HTH_Tnp_1: Transposas 30.7 22 0.00047 22.6 0.6 29 99-127 5-35 (76)
35 PF04545 Sigma70_r4: Sigma-70, 30.4 60 0.0013 19.3 2.5 23 106-128 11-33 (50)
36 cd06171 Sigma70_r4 Sigma70, re 29.4 61 0.0013 18.0 2.3 22 106-127 17-38 (55)
37 PRK05022 anaerobic nitric oxid 29.4 49 0.0011 29.3 2.7 22 106-127 472-493 (509)
38 PRK10365 transcriptional regul 29.2 51 0.0011 27.5 2.7 22 106-127 409-430 (441)
39 TIGR02607 antidote_HigA addict 29.0 70 0.0015 20.3 2.8 27 101-127 3-30 (78)
40 PRK11388 DNA-binding transcrip 28.6 50 0.0011 29.8 2.7 22 106-127 595-616 (638)
41 PRK10923 glnG nitrogen regulat 26.4 61 0.0013 27.6 2.7 22 106-127 433-454 (469)
42 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 25.1 68 0.0015 20.5 2.1 22 106-127 11-32 (50)
43 cd00194 UBA Ubiquitin Associat 24.8 90 0.002 17.5 2.5 20 106-125 17-36 (38)
44 smart00497 IENR1 Intron encode 24.5 49 0.0011 19.6 1.3 11 117-127 19-29 (53)
45 PF02796 HTH_7: Helix-turn-hel 22.9 74 0.0016 19.0 1.9 21 106-127 13-33 (45)
46 PF13744 HTH_37: Helix-turn-he 22.7 75 0.0016 21.1 2.1 22 106-127 22-43 (80)
47 PF09339 HTH_IclR: IclR helix- 22.3 60 0.0013 19.7 1.4 22 106-127 7-30 (52)
48 PF13014 KH_3: KH domain 21.8 33 0.00071 20.1 0.1 20 44-63 7-28 (43)
49 TIGR02329 propionate_PrpR prop 21.6 82 0.0018 28.5 2.7 22 106-127 494-515 (526)
50 COG2204 AtoC Response regulato 21.5 82 0.0018 28.5 2.7 22 106-127 421-442 (464)
51 PRK04217 hypothetical protein; 21.2 1.3E+02 0.0029 21.9 3.3 22 106-127 49-70 (110)
52 TIGR02040 PpsR-CrtJ transcript 20.7 89 0.0019 26.2 2.6 22 106-127 407-428 (442)
53 COG4567 Response regulator con 20.7 72 0.0016 25.7 1.9 22 106-127 146-167 (182)
54 PRK15424 propionate catabolism 20.7 88 0.0019 28.5 2.7 22 106-127 501-522 (538)
55 PF08281 Sigma70_r4_2: Sigma-7 20.4 1E+02 0.0023 18.3 2.3 22 106-127 17-38 (54)
No 1
>COG0216 PrfA Protein chain release factor A [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.1e-36 Score=255.01 Aligned_cols=95 Identities=27% Similarity=0.362 Sum_probs=90.0
Q ss_pred cccccccccceeeccCCcc----cccCceeEEEEeecCCCCcccccccccEEEEeeCCceEEEeeccC----ChhhHhhh
Q 045445 11 NCSSTSSSSKKNYFELTDD----EQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYL----PPPQLLQI 82 (128)
Q Consensus 11 ~~~~tS~a~v~v~p~l~~~----~~~~dl~~~~~RssGpGGQ~vNkt~saV~l~H~PtGi~v~~~~~R----Nr~~A~~~ 82 (128)
-+.|||+|+|.|+|+.++. ++++||+|+++||||+||||||+|+|||||+|+||||+|.||++| ||++||++
T Consensus 197 GRIHTStaTVaVlPE~ee~~ei~I~~~DlrIDt~RsSGaGGQhVNtTdSAVRiTHlPTGIvV~cQderSQ~kNk~kAmkv 276 (363)
T COG0216 197 GRIHTSAATVAVLPEVEEVEEIEINPKDLRIDTFRSSGAGGQHVNTTDSAVRITHLPTGIVVECQDERSQHKNKAKAMKV 276 (363)
T ss_pred CceeecceeEEeccCCCcccccccChHHceeeeeecCCCCCCCcCccchhheeeecCCceEEEecchhhhhhhHHHHHHH
Confidence 4689999999999999753 589999999999999999999999999999999999999999998 99999999
Q ss_pred CC------------------cccccccCCCCCCCCCCCCCh
Q 045445 83 LP------------------PKFTIRCSEVGPQIRPNNPKF 105 (128)
Q Consensus 83 L~------------------~~~q~~~~~r~~kIrtyn~~f 105 (128)
|+ ||+|+++++||++||||||..
T Consensus 277 L~ARl~~~~~~~~~~~~~~~RksqVGSGDRSErIRTYNfPQ 317 (363)
T COG0216 277 LRARLYDAERQKAQAEEASERKSQVGSGDRSERIRTYNFPQ 317 (363)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCCCchhhhhhccCCCC
Confidence 97 999999999999999999876
No 2
>TIGR00019 prfA peptide chain release factor 1. This model describes peptide chain release factor 1 (PrfA, RF-1), and excludes the related peptide chain release factor 2 (PrfB, RF-2). RF-1 helps recognize and terminate translation at UAA and UAG stop codons. The mitochondrial release factors are prfA-like, although not included above the trusted cutoff for this model. RF-1 does not have a translational frameshift.
Probab=99.97 E-value=1.3e-31 Score=227.80 Aligned_cols=97 Identities=29% Similarity=0.379 Sum_probs=89.9
Q ss_pred CCcccccccccceeeccCCc---ccccCceeEEEEeecCCCCcccccccccEEEEeeCCceEEEeeccC----ChhhHhh
Q 045445 9 NDNCSSTSSSSKKNYFELTD---DEQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYL----PPPQLLQ 81 (128)
Q Consensus 9 ~d~~~~tS~a~v~v~p~l~~---~~~~~dl~~~~~RssGpGGQ~vNkt~saV~l~H~PtGi~v~~~~~R----Nr~~A~~ 81 (128)
...++||||++|.++|.+++ .++++||+++|+|||||||||||||+|||||+|+||||+|.|+++| ||..||+
T Consensus 194 s~~R~hTsfa~V~v~P~~~~~~~~i~~~dl~~~~~RssG~GGQ~VNkt~SaVrl~h~ptgi~V~~~~eRSQ~~Nk~~A~~ 273 (360)
T TIGR00019 194 SQGRIHTSAATVAVMPELEEVEVDINPADLRIDTFRSSGAGGQHVNTTDSAVRITHLPTGIVVECQDERSQHKNKDKAMK 273 (360)
T ss_pred CCCCeecceeEEEEEcCCCccccccCcccEEEEEEECCCCCCCCcCceeeeEEEEECCCcEEEEECCccCHHHHHHHHHH
Confidence 44699999999999999875 4678999999999999999999999999999999999999999999 9999999
Q ss_pred hCC------------------cccccccCCCCCCCCCCCCCh
Q 045445 82 ILP------------------PKFTIRCSEVGPQIRPNNPKF 105 (128)
Q Consensus 82 ~L~------------------~~~q~~~~~r~~kIrtyn~~f 105 (128)
+|+ ++.+++.++||++|||||+..
T Consensus 274 ~L~~~L~~~~~~~~~~~~~~~r~~~~~~~~Rs~~IRtY~~~~ 315 (360)
T TIGR00019 274 VLRARLYEAEQEKQQAAQASTRKSQVGSGDRSERIRTYNFPQ 315 (360)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhcceecccCCeEEEECCC
Confidence 987 778888999999999999765
No 3
>KOG2726 consensus Mitochondrial polypeptide chain release factor [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=2.6e-31 Score=227.39 Aligned_cols=103 Identities=29% Similarity=0.342 Sum_probs=93.7
Q ss_pred cccccccccceeeccCCc-----ccccCceeEEEEeecCCCCcccccccccEEEEeeCCceEEEeeccC----ChhhHhh
Q 045445 11 NCSSTSSSSKKNYFELTD-----DEQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYL----PPPQLLQ 81 (128)
Q Consensus 11 ~~~~tS~a~v~v~p~l~~-----~~~~~dl~~~~~RssGpGGQ~vNkt~saV~l~H~PtGi~v~~~~~R----Nr~~A~~ 81 (128)
-++|||+++|.++|.+.. .++++||+++|+|+|||||||||||+|||||+|+||||+|+|+++| ||+.|+.
T Consensus 221 gr~htstasV~ViP~~~~~~~~~~~~~~dl~i~~~R~~G~GGQhvNktdsaVrl~HiPTGIvv~cq~eRSq~~Nr~~A~~ 300 (386)
T KOG2726|consen 221 GRRHTSTASVAVIPQPGRDEVDVEIDEKDLRIETFRASGPGGQHVNKTDSAVRLTHIPTGIVVECQEERSQHKNRALALK 300 (386)
T ss_pred cccccccceEEEeccCCCCccceecCchheeEEecccCCCCcccccccccceEEEeecCceEEEeecHHhHHhhHHHHHH
Confidence 369999999999999842 2578999999999999999999999999999999999999999999 9999999
Q ss_pred hCC------------------cccccccCCCCCCCCCCCCCh-hhHHHHHH
Q 045445 82 ILP------------------PKFTIRCSEVGPQIRPNNPKF-ALLDLIFA 113 (128)
Q Consensus 82 ~L~------------------~~~q~~~~~r~~kIrtyn~~f-~~lD~~~~ 113 (128)
+|+ ++.|+++.+|+++|||||+.. -|.|.++.
T Consensus 301 ~L~akL~~~~~~~~~~~~~~~r~~qv~s~~rsekiRTy~~~q~rv~D~r~~ 351 (386)
T KOG2726|consen 301 RLRAKLAVIYREEKSEEEKKKRKAQVGSLKRSEKIRTYNFKQDRVTDHRIG 351 (386)
T ss_pred HHHHHHHHHHHhhhhHHhhhhhHHhhcccCchhceeecccCccchhhhhhc
Confidence 986 888899999999999999766 67777766
No 4
>PRK05589 peptide chain release factor 2; Provisional
Probab=99.96 E-value=4.2e-31 Score=222.25 Aligned_cols=96 Identities=32% Similarity=0.409 Sum_probs=85.2
Q ss_pred CcccccccccceeeccCCc----ccccCceeEEEEeecCCCCcccccccccEEEEeeCCceEEEeeccC----ChhhHhh
Q 045445 10 DNCSSTSSSSKKNYFELTD----DEQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYL----PPPQLLQ 81 (128)
Q Consensus 10 d~~~~tS~a~v~v~p~l~~----~~~~~dl~~~~~RssGpGGQ~vNkt~saV~l~H~PtGi~v~~~~~R----Nr~~A~~ 81 (128)
..++||||++|.++|.+++ .++++|++|+|+|||||||||||||+|||||+|+||||+|+|+++| ||..|++
T Consensus 169 ~~rr~ts~a~V~VlP~~~~~~~~~i~~~dl~~~~~rssG~GGQ~VNkt~saVrl~H~ptgi~v~~q~eRSQ~~Nk~~A~~ 248 (325)
T PRK05589 169 NGKRQTSFASVEVLPELTDDQDIEIRSEDLKIDTYRAGGAGGQHVNKTESAVRITHIPTGIVVQCQNERSQHSNKETAMK 248 (325)
T ss_pred CCCeEeeeEEEEEecCcCccccccCCchheEEEEeeCCCCCCCcccceeeEEEEEECCCCEEEEECCccCHHHHHHHHHH
Confidence 3699999999999999865 4678999999999999999999999999999999999999999999 9999999
Q ss_pred hCC-----------------cccccccCCCCCCCCCCCC-Ch
Q 045445 82 ILP-----------------PKFTIRCSEVGPQIRPNNP-KF 105 (128)
Q Consensus 82 ~L~-----------------~~~q~~~~~r~~kIrtyn~-~f 105 (128)
+|+ .+.+....+||++|||||+ .+
T Consensus 249 ~L~~kL~~~~~~~~~~~~~~~r~~~~~~~~g~~IRtY~~~p~ 290 (325)
T PRK05589 249 MLKSKLVELKERAHKEKIEDLTGELKDMGWGSQIRSYVFHPY 290 (325)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcccccccccCCceeeECCCC
Confidence 987 2233344579999999998 54
No 5
>PRK00591 prfA peptide chain release factor 1; Validated
Probab=99.96 E-value=7.1e-31 Score=223.14 Aligned_cols=98 Identities=27% Similarity=0.357 Sum_probs=90.6
Q ss_pred cCCcccccccccceeeccCCc---ccccCceeEEEEeecCCCCcccccccccEEEEeeCCceEEEeeccC----ChhhHh
Q 045445 8 YNDNCSSTSSSSKKNYFELTD---DEQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYL----PPPQLL 80 (128)
Q Consensus 8 ~~d~~~~tS~a~v~v~p~l~~---~~~~~dl~~~~~RssGpGGQ~vNkt~saV~l~H~PtGi~v~~~~~R----Nr~~A~ 80 (128)
....++||||++|.++|.+++ .+.++||+++|+|||||||||||||+|+|+|+|+||||+|.|+++| ||+.|+
T Consensus 193 ~s~~R~~tsfa~V~v~P~~~~~~~~i~~~dl~~~~~RssG~GGQ~VNkt~saVrl~H~ptGi~v~~~~eRSQ~~Nk~~Al 272 (359)
T PRK00591 193 ESQGRIHTSAATVAVLPEAEEVEVEINPKDLRIDTFRSSGAGGQHVNTTDSAVRITHLPTGIVVECQDERSQHKNKAKAM 272 (359)
T ss_pred CCCCceecceEEEEEEcCCCccccccCcccEEEEEEECCCCCCCCccceeeeEEEEECCCcEEEEECCcCCHHHHHHHHH
Confidence 345799999999999999875 5688999999999999999999999999999999999999999999 999999
Q ss_pred hhCC------------------cccccccCCCCCCCCCCCCCh
Q 045445 81 QILP------------------PKFTIRCSEVGPQIRPNNPKF 105 (128)
Q Consensus 81 ~~L~------------------~~~q~~~~~r~~kIrtyn~~f 105 (128)
++|+ ++.++..++||++|||||+..
T Consensus 273 ~~L~~~L~~~~~~~~~~~~~~~r~~~~~~~~Rse~IRtY~f~~ 315 (359)
T PRK00591 273 KVLRARLYDAERQKAQAEEAATRKSQVGSGDRSERIRTYNFPQ 315 (359)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhcccccccCCeeeEECCC
Confidence 9987 778899999999999999755
No 6
>TIGR03072 release_prfH putative peptide chain release factor H. Members of this protein family are bacterial proteins homologous to peptide chain release factors 1 (RF-1, product of the prfA gene), and 2 (RF-2, product of the prfB gene). The member from Escherichia coli K-12, designated prfH, appears to be a pseudogene. This class I release factor is always found as the downstream gene of a two-gene operon.
Probab=99.96 E-value=9.9e-31 Score=207.70 Aligned_cols=94 Identities=26% Similarity=0.313 Sum_probs=85.1
Q ss_pred CcccccccccceeeccCCcccccCceeEEEEeecCCCCcccccccccEEEEeeCCceEEEeeccC----ChhhHhhhCC-
Q 045445 10 DNCSSTSSSSKKNYFELTDDEQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYL----PPPQLLQILP- 84 (128)
Q Consensus 10 d~~~~tS~a~v~v~p~l~~~~~~~dl~~~~~RssGpGGQ~vNkt~saV~l~H~PtGi~v~~~~~R----Nr~~A~~~L~- 84 (128)
...|||||++|.++|. +.+++++||+++|+|||||||||||||+|+|+|+|+||||+|+|+++| ||++|+++|+
T Consensus 84 ~~~R~ts~~~V~v~~~-~~~i~~~dl~~~~~RssGpGGQ~vNkt~saVrl~h~ptgi~v~~~~~RSQ~~Nk~~A~~~L~~ 162 (200)
T TIGR03072 84 HHRRKNWFIGVQRFSA-SEEATEDEIRFETLRSSGPGGQHVNKTESAVRATHLASGISVKVQSERSQHANKRLATLLLAV 162 (200)
T ss_pred CCCeeEEEEEEEEecC-ccccChhheEEEEEECCCCCcccccccceeEEEEECCCcEEEEECCccCHHHHHHHHHHHHHH
Confidence 4678999999999985 445788999999999999999999999999999999999999999999 9999999997
Q ss_pred ----------------cccccccCCCCCCCCCCCCC
Q 045445 85 ----------------PKFTIRCSEVGPQIRPNNPK 104 (128)
Q Consensus 85 ----------------~~~q~~~~~r~~kIrtyn~~ 104 (128)
++.+....+||++|||||+.
T Consensus 163 ~l~~~~~~~~~~~~~~~r~~~~~~~Rg~~iRty~~~ 198 (200)
T TIGR03072 163 RLADLQQEQAAALRAERRTAHHQIERGNPVRVFKGE 198 (200)
T ss_pred HHHHHHHHHHHHHHHHHHhccccccccCceEeeeCC
Confidence 56666777999999999953
No 7
>PRK08787 peptide chain release factor 2; Provisional
Probab=99.96 E-value=1e-30 Score=219.10 Aligned_cols=96 Identities=35% Similarity=0.358 Sum_probs=82.9
Q ss_pred CcccccccccceeeccCCc----ccccCceeEEEEeecCCCCcccccccccEEEEeeCCceEEEeeccC----ChhhHhh
Q 045445 10 DNCSSTSSSSKKNYFELTD----DEQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYL----PPPQLLQ 81 (128)
Q Consensus 10 d~~~~tS~a~v~v~p~l~~----~~~~~dl~~~~~RssGpGGQ~vNkt~saV~l~H~PtGi~v~~~~~R----Nr~~A~~ 81 (128)
..++||||++|.++|.+++ .+.++||+|+|+|||||||||||||+|+|||+|+||||+|+|+++| ||+.|++
T Consensus 149 ~~rrhTsfasV~V~P~~~~~~~i~i~~~dl~~~~~RssG~GGQ~VNkt~saVri~H~Ptgi~v~~q~eRSQ~~Nk~~A~~ 228 (313)
T PRK08787 149 DNRRHTSFTSVFVSPEVDDNIEIDINPADLRTDVYRSSGAGGQHVNKTESAVRITHIPTNTVVACQTGRSQHQNRDNAMK 228 (313)
T ss_pred CCCEEeeeEEEEEecCcCcccccccChhHeEEEEEECCCCCCCCcCCEeeEEEEEECCCcEEEEECCcccHHHHHHHHHH
Confidence 4689999999999999975 3578999999999999999999999999999999999999999999 9999999
Q ss_pred hCC-----------------cccccccCCCCCCCCCCCCCh
Q 045445 82 ILP-----------------PKFTIRCSEVGPQIRPNNPKF 105 (128)
Q Consensus 82 ~L~-----------------~~~q~~~~~r~~kIrtyn~~f 105 (128)
+|+ .+.+.....||+||||||+.-
T Consensus 229 ~L~~~L~~~~~e~~~~~~~~~~~~k~~i~~g~qIRtY~f~~ 269 (313)
T PRK08787 229 MLAAKLYELEVQKRNAEKDALEATKSDIGWGSQIRNYVLDQ 269 (313)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhhhCcccccccceeCCC
Confidence 987 100111235889999998655
No 8
>PRK06746 peptide chain release factor 2; Provisional
Probab=99.96 E-value=1.2e-30 Score=219.62 Aligned_cols=96 Identities=29% Similarity=0.373 Sum_probs=85.7
Q ss_pred CCcccccccccceeeccCCc----ccccCceeEEEEeecCCCCcccccccccEEEEeeCCceEEEeeccC----ChhhHh
Q 045445 9 NDNCSSTSSSSKKNYFELTD----DEQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYL----PPPQLL 80 (128)
Q Consensus 9 ~d~~~~tS~a~v~v~p~l~~----~~~~~dl~~~~~RssGpGGQ~vNkt~saV~l~H~PtGi~v~~~~~R----Nr~~A~ 80 (128)
..-++||||++|.++|.+++ .++++||+++|+|||||||||||||+|||+|+|+||||+|+|+++| ||+.|+
T Consensus 169 s~~rrhTsfa~V~v~P~~~~~~~i~i~~~dl~~~~~rssG~GGQ~vNkt~saVrl~h~ptgi~v~~q~~RSQ~~Nk~~A~ 248 (326)
T PRK06746 169 SSGRRHTSFVSCEVVPEFNDEVEIEVRTEDLKIDTYRASGAGGQHVNTTDSAVRITHTPTNTVVTCQSERSQIKNREHAM 248 (326)
T ss_pred CCCCeEeeEEEEEEecCcCCccccccChHHeEEEEEeCCCCCCCCccceeeEEEEEEeCCeEEEEECCCCCHHHHHHHHH
Confidence 34699999999999999864 3578999999999999999999999999999999999999999999 999999
Q ss_pred hhCC------------------cccccccCCCCCCCCCCCC-Ch
Q 045445 81 QILP------------------PKFTIRCSEVGPQIRPNNP-KF 105 (128)
Q Consensus 81 ~~L~------------------~~~q~~~~~r~~kIrtyn~-~f 105 (128)
++|+ |+.++.. +|+++|||||+ .+
T Consensus 249 ~~L~akL~~~~~~~~~~~~~~~r~~~~~~-~rg~~IRtYnf~p~ 291 (326)
T PRK06746 249 KMLKAKLYQKKLEEQQAELDEIRGEQKEI-GWGSQIRSYVFHPY 291 (326)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhccC-ccCCCeEEEECCCC
Confidence 9987 5555544 68899999998 54
No 9
>PRK07342 peptide chain release factor 2; Provisional
Probab=99.96 E-value=3.5e-30 Score=217.73 Aligned_cols=94 Identities=32% Similarity=0.360 Sum_probs=82.0
Q ss_pred CcccccccccceeeccCCc----ccccCceeEEEEeecCCCCcccccccccEEEEeeCCceEEEeeccC----ChhhHhh
Q 045445 10 DNCSSTSSSSKKNYFELTD----DEQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYL----PPPQLLQ 81 (128)
Q Consensus 10 d~~~~tS~a~v~v~p~l~~----~~~~~dl~~~~~RssGpGGQ~vNkt~saV~l~H~PtGi~v~~~~~R----Nr~~A~~ 81 (128)
..++||||++|.++|.+++ .+.++||+++|+|||||||||||||+|||||+|+||||+|+|+++| ||+.||+
T Consensus 172 ~~rrhTs~a~V~VlP~~~~~~~~~i~~~dl~~~~~RssG~GGQ~VNkt~saVrl~H~ptgi~v~~~~eRSQ~~Nk~~A~~ 251 (339)
T PRK07342 172 NARRHTSFASIWVYPVIDDNIEVDVNESDVRIDTYRSSGAGGQHVNTTDSAVRITHIPTGIVVQCQQERSQHKNRAKAWS 251 (339)
T ss_pred CCCeEeEEEEEEEEcCCCcccccccCcccEEEEEEECCCCCCCCccceeeeEEEEEcCCcEEEEECCcccHHHHHHHHHH
Confidence 4699999999999999975 3578999999999999999999999999999999999999999999 9999999
Q ss_pred hCC--------------c---ccccccCCCCCCCCCCCC
Q 045445 82 ILP--------------P---KFTIRCSEVGPQIRPNNP 103 (128)
Q Consensus 82 ~L~--------------~---~~q~~~~~r~~kIrtyn~ 103 (128)
+|+ . +.+-..-.||++|||||+
T Consensus 252 ~L~~~L~~~~~~~~~~~~~~~~~~~~~i~~g~~IRtY~~ 290 (339)
T PRK07342 252 MLRARLYEEELKKREEATNAAAASKTDIGWGHQIRSYVL 290 (339)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhhccccCCcCCccC
Confidence 987 0 111112368899999987
No 10
>TIGR00020 prfB peptide chain release factor 2. In many but not all taxa, there is a conserved real translational frameshift at a TGA codon. RF-2 helps terminate translation at TGA codons and can therefore regulate its own production by readthrough when RF-2 is insufficient. There is a Pfam model called "RF-1" for the superfamily of RF-1, RF-2, mitochondrial, RF-H, etc.
Probab=99.96 E-value=1.1e-29 Score=216.24 Aligned_cols=96 Identities=30% Similarity=0.363 Sum_probs=84.2
Q ss_pred CcccccccccceeeccCCc----ccccCceeEEEEeecCCCCcccccccccEEEEeeCCceEEEeeccC----ChhhHhh
Q 045445 10 DNCSSTSSSSKKNYFELTD----DEQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYL----PPPQLLQ 81 (128)
Q Consensus 10 d~~~~tS~a~v~v~p~l~~----~~~~~dl~~~~~RssGpGGQ~vNkt~saV~l~H~PtGi~v~~~~~R----Nr~~A~~ 81 (128)
..++||||++|.++|..++ ++++.|++++|+|||||||||||||+|+|+|+|+||||+|.|+++| ||..||+
T Consensus 208 ~~rrhts~a~V~vlP~~~~~~~~~i~~~d~~~~~~rssG~GGQ~VNkt~saVri~H~ptgi~v~~q~~RSQ~~Nk~~A~~ 287 (364)
T TIGR00020 208 NGRRHTSFASVFVMPEVDDDIDIEIKPEDLRIDTYRASGAGGQHVNKTDSAVRITHIPTGIVVQCQNDRSQHKNKDSAMK 287 (364)
T ss_pred CCCeEeeeEEEEEecCCCcccceecccccEEEEEeeCCCCCCccccccceEEEEEECCCcEEEEECCccCHHHHHHHHHH
Confidence 4699999999999999964 4678999999999999999999999999999999999999999999 9999999
Q ss_pred hCC-----------------cccccccCCCCCCCCCCCC-Ch
Q 045445 82 ILP-----------------PKFTIRCSEVGPQIRPNNP-KF 105 (128)
Q Consensus 82 ~L~-----------------~~~q~~~~~r~~kIrtyn~-~f 105 (128)
+|+ .+.+-...+||++|||||+ ++
T Consensus 288 ~L~~kL~~~~~~~~~~~~~~~r~~~~~~~rg~~IRtY~~~~~ 329 (364)
T TIGR00020 288 VLKAKLYELEMEKEQAEKDAKEGEKSEIGWGSQIRSYVLHPY 329 (364)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhccCccCCeEEEECCCC
Confidence 997 1212233479999999998 54
No 11
>PRK08179 prfH peptide chain release factor-like protein; Reviewed
Probab=99.95 E-value=1.9e-29 Score=200.33 Aligned_cols=92 Identities=26% Similarity=0.307 Sum_probs=83.0
Q ss_pred CcccccccccceeeccCCcccccCceeEEEEeecCCCCcccccccccEEEEeeCCceEEEeeccC----ChhhHhhhCC-
Q 045445 10 DNCSSTSSSSKKNYFELTDDEQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYL----PPPQLLQILP- 84 (128)
Q Consensus 10 d~~~~tS~a~v~v~p~l~~~~~~~dl~~~~~RssGpGGQ~vNkt~saV~l~H~PtGi~v~~~~~R----Nr~~A~~~L~- 84 (128)
..++||||++|.++|. +.+++++||+++|+|||||||||||||+|+|+|+|+||||+|+|+++| ||+.|+++|+
T Consensus 85 ~~~R~~s~~~V~v~~~-~~~i~~~dl~~~~~RssGpGGQ~VNkt~saVrl~h~ptgi~v~~~~~RSQ~~Nk~~A~~~L~~ 163 (200)
T PRK08179 85 HHGRKNWFVGIGRFSA-DEEEQSDEIRFETLRSSGPGGQHVNKTDSAVRATHLASGISVKVQSERSQHANKRLARLLIAW 163 (200)
T ss_pred CCCceEEEEEEEEeCC-cCccCHHHeEEEEEEccCCcccccccccceEEEEEcCCcEEEEECCCCCHHHHHHHHHHHHHH
Confidence 3678999999999975 335788999999999999999999999999999999999999999999 9999999997
Q ss_pred ----------------cccccccCCCCCCCCCCC
Q 045445 85 ----------------PKFTIRCSEVGPQIRPNN 102 (128)
Q Consensus 85 ----------------~~~q~~~~~r~~kIrtyn 102 (128)
++.+..+.+||++||||-
T Consensus 164 ~L~~~~~~~~~~~~~~~~~~~~~~~Rg~~IRt~~ 197 (200)
T PRK08179 164 KLEQQQQEQSAALKSQRRMFHHQIERGNPRRVFT 197 (200)
T ss_pred HHHHHHHHHHHHHHHHHHhccccccccCceEeee
Confidence 555666779999999995
No 12
>PRK00578 prfB peptide chain release factor 2; Validated
Probab=99.95 E-value=1.7e-29 Score=215.10 Aligned_cols=96 Identities=32% Similarity=0.426 Sum_probs=84.9
Q ss_pred CCcccccccccceeeccCCc----ccccCceeEEEEeecCCCCcccccccccEEEEeeCCceEEEeeccC----ChhhHh
Q 045445 9 NDNCSSTSSSSKKNYFELTD----DEQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYL----PPPQLL 80 (128)
Q Consensus 9 ~d~~~~tS~a~v~v~p~l~~----~~~~~dl~~~~~RssGpGGQ~vNkt~saV~l~H~PtGi~v~~~~~R----Nr~~A~ 80 (128)
...++||||++|.++|.+++ .+.++|++++|+|||||||||||||+|+|+|+|+||||+|.|+++| ||+.|+
T Consensus 207 ~~~r~hts~~~V~vlP~~~~~~~~~i~~~dl~~~~~rssGpGGQ~vNkt~saVrl~h~ptgi~v~~~~~RSQ~~Nk~~A~ 286 (367)
T PRK00578 207 SAGRRHTSFASVEVYPEVDDTIEIEINPKDLRIDTYRSSGAGGQHVNKTDSAVRITHIPTGIVVQCQNERSQHQNKASAM 286 (367)
T ss_pred CCCceecceeeEEecCCCCCccccccChhhEEEEEeeCCCCCCCcccceeeEEEEEECCCcEEEEECCCCCHHHHHHHHH
Confidence 34799999999999999865 3678999999999999999999999999999999999999999999 999999
Q ss_pred hhCC------------------cccccccCCCCCCCCCCCC-Ch
Q 045445 81 QILP------------------PKFTIRCSEVGPQIRPNNP-KF 105 (128)
Q Consensus 81 ~~L~------------------~~~q~~~~~r~~kIrtyn~-~f 105 (128)
++|+ |+.+ ...+||++|||||+ .+
T Consensus 287 ~~L~~kL~~~~~~~~~~~~~~~r~~~-~~~~rg~~IRtYn~~p~ 329 (367)
T PRK00578 287 KMLKAKLYELELEKRAAEKDALKGEK-KEIGWGSQIRSYVLHPY 329 (367)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhh-ccccccCCeEEEECCCC
Confidence 9987 2222 34589999999997 54
No 13
>COG1186 PrfB Protein chain release factor B [Translation, ribosomal structure and biogenesis]
Probab=99.94 E-value=4.9e-28 Score=196.88 Aligned_cols=109 Identities=30% Similarity=0.293 Sum_probs=90.7
Q ss_pred eeecCCcccccccccceeeccCCcc----cccCceeEEEEeecCCCCcccccccccEEEEeeCCceEEEeeccC----Ch
Q 045445 5 SCNYNDNCSSTSSSSKKNYFELTDD----EQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYL----PP 76 (128)
Q Consensus 5 ~~~~~d~~~~tS~a~v~v~p~l~~~----~~~~dl~~~~~RssGpGGQ~vNkt~saV~l~H~PtGi~v~~~~~R----Nr 76 (128)
|-.+.+.++||||+++.++|.+++. +.+.|++++|+|||||||||||||+|||+|+|+||||+|.||.+| |+
T Consensus 78 Spf~~~~~R~tsf~~v~v~p~~~~~i~i~I~~~dl~idt~RASGaGGQhVNKt~SAVrlth~ptgivv~cq~eRSq~~n~ 157 (239)
T COG1186 78 SPFDSNGRRHTSFASVEVFPELDISIEIEIPDDDLRIDTYRASGAGGQHVNKTDSAVRLTHLPTGIVVLCQNERSQHLNK 157 (239)
T ss_pred cCCCcCcccccceeeeeecCCCCcccceecCccceEEEEEEcCCCCCCccccccccEEEEEcCCCCEecCHHHHHHHHHH
Confidence 4456779999999999999999752 467999999999999999999999999999999999999999999 99
Q ss_pred hhHhhhCC-----------------cccccccCCCCCCCCCCCCC-h-hhHHHHHH
Q 045445 77 PQLLQILP-----------------PKFTIRCSEVGPQIRPNNPK-F-ALLDLIFA 113 (128)
Q Consensus 77 ~~A~~~L~-----------------~~~q~~~~~r~~kIrtyn~~-f-~~lD~~~~ 113 (128)
..||..|+ ++..-+-.+|+.|||.|-++ + ++-|....
T Consensus 158 ~~a~~~l~~kL~~~~~~~Rsqe~n~~~a~~k~i~wg~qirsyv~~p~~~vKd~Rt~ 213 (239)
T COG1186 158 ALARKMLKGKLYILAQEKRSQEKNRERALKKLIGWGNQIRSYVLDPYQPTKDLRTG 213 (239)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHhccccCCCccccccccccc
Confidence 99998876 22223345899999999766 4 55554433
No 14
>PF00472 RF-1: RF-1 domain; InterPro: IPR000352 Peptide chain release factors (RFs) are required for the termination of protein biosynthesis []. At present two classes of RFs can be distinguished. Class I RFs bind to ribosomes that have encountered a stop codon at their decoding site and induce release of the nascent polypeptide. Class II RFs are GTP-binding proteins that interact with class I RFs and enhance class I RF activity. In prokaryotes there are two class I RFs that act in a codon specific manner []: RF-1 (gene prfA) mediates UAA and UAG-dependent termination while RF-2 (gene prfB) mediates UAA and UGA-dependent termination. RF-1 and RF-2 are structurally and evolutionary related proteins which have been shown to be part of a larger family [].; GO: 0003747 translation release factor activity, 0006415 translational termination; PDB: 2JY9_A 1ZBT_A 1GQE_A 3F1G_X 3F1E_X 1RQ0_C 4DH9_Y 2JVA_A 1J26_A 3D5A_X ....
Probab=99.93 E-value=2.6e-27 Score=172.13 Aligned_cols=76 Identities=34% Similarity=0.416 Sum_probs=69.4
Q ss_pred ccccCceeEEEEeecCCCCcccccccccEEEEeeCCceEEEeeccC----ChhhHhhhCC------------------cc
Q 045445 29 DEQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYL----PPPQLLQILP------------------PK 86 (128)
Q Consensus 29 ~~~~~dl~~~~~RssGpGGQ~vNkt~saV~l~H~PtGi~v~~~~~R----Nr~~A~~~L~------------------~~ 86 (128)
++.++||+++|+|||||||||||||+|+|+|+|+||||+|+|+++| |++.|+++|. ++
T Consensus 8 ~i~~~dl~~~~~RssGpGGQ~VNk~~s~V~l~h~ptgi~v~~~~~Rsq~~Nr~~A~~~L~~~l~~~~~~~~~~~~~~~~~ 87 (113)
T PF00472_consen 8 DIPEKDLEISFSRSSGPGGQNVNKTNSKVRLRHIPTGIVVKCQESRSQHQNREDALEKLREKLDEAYREKRREKTREIRK 87 (113)
T ss_dssp CC-GGGEEEEEEESSSSSSCHHHSSSEEEEEEETTTTEEEEEESSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTT
T ss_pred ccCHHHeEEEEEecCCCCCCcccccCCEEEEEEecccEEEEEcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3678999999999999999999999999999999999999999999 9999999886 66
Q ss_pred cccccCCCCCCCCCCCCC
Q 045445 87 FTIRCSEVGPQIRPNNPK 104 (128)
Q Consensus 87 ~q~~~~~r~~kIrtyn~~ 104 (128)
.+.+..+++++||+|++.
T Consensus 88 ~~~~~~~~~~~iR~y~~~ 105 (113)
T PF00472_consen 88 SQVKRLERKKKIRTYNFP 105 (113)
T ss_dssp TSCCCSSTTSEEEEEETT
T ss_pred HHHhHHhhhcceecccCC
Confidence 677778999999999974
No 15
>PRK09256 hypothetical protein; Provisional
Probab=99.75 E-value=6e-19 Score=133.29 Aligned_cols=55 Identities=29% Similarity=0.403 Sum_probs=50.5
Q ss_pred cccCceeEEEEeecCCCCcccccccccEEEEe------eC-----------------Cc-eEEEeeccC----ChhhHhh
Q 045445 30 EQFRECEMDTYKSSGPGGQHRNKRESAVRLKH------VP-----------------TA-SSVNLDAYL----PPPQLLQ 81 (128)
Q Consensus 30 ~~~~dl~~~~~RssGpGGQ~vNkt~saV~l~H------~P-----------------tG-i~v~~~~~R----Nr~~A~~ 81 (128)
+.++||+++|+|||||||||||||+|+|+|+| +| .| |.|.|+++| |++.|++
T Consensus 10 i~~~~l~~~~~RSSGPGGQ~VNKt~SkV~l~~~~~~~~lp~~~~~~l~~~~~~r~~~~g~l~i~~~~~RSQ~~Nr~~al~ 89 (138)
T PRK09256 10 IPENELEWRFIRASGPGGQNVNKVSTAVELRFDIAASSLPEFYKERLLALAGHRITKDGVIVIKAQEFRSQERNREDALE 89 (138)
T ss_pred cCHHHeEEEEEEcCCCCcccccccceeeEEEechhhccCCHHHHHHHHHHhcCcccCCCcEEEEECCcCCHHHHHHHHHH
Confidence 45689999999999999999999999999996 66 35 999999999 9999999
Q ss_pred hCC
Q 045445 82 ILP 84 (128)
Q Consensus 82 ~L~ 84 (128)
+|.
T Consensus 90 kL~ 92 (138)
T PRK09256 90 RLV 92 (138)
T ss_pred HHH
Confidence 987
No 16
>KOG3429 consensus Predicted peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis]
Probab=99.33 E-value=1.2e-12 Score=102.33 Aligned_cols=59 Identities=25% Similarity=0.349 Sum_probs=49.2
Q ss_pred CCcccccCceeEEEEeecCCCCcccccccccEEEEee-------CC------------------ceEEEeeccC----Ch
Q 045445 26 LTDDEQFRECEMDTYKSSGPGGQHRNKRESAVRLKHV-------PT------------------ASSVNLDAYL----PP 76 (128)
Q Consensus 26 l~~~~~~~dl~~~~~RssGpGGQ~vNkt~saV~l~H~-------Pt------------------Gi~v~~~~~R----Nr 76 (128)
++..+....++++|.||||||||||||++|+|.|++. |. .|.|.++.+| |.
T Consensus 33 ~~g~ipld~~~i~y~RSSGPGGQNVNKvNTKv~vrf~vs~a~Wipe~~R~~~~~~~~~rink~gelvI~Sd~TRsq~~Ni 112 (172)
T KOG3429|consen 33 FKGKIPLDQLEISYSRSSGPGGQNVNKVNTKVEVRFKVSNAEWIPEFLRNKLLTTEKNRINKDGELVIYSDKTRSQHKNI 112 (172)
T ss_pred cCCCCchhheEEEEeecCCCCCcccccccceEEEEEecchhhhccHHHHHHHHHHHHHhhccCccEEEecchhHHhhccH
Confidence 3334555789999999999999999999999999973 22 2888888887 99
Q ss_pred hhHhhhCC
Q 045445 77 PQLLQILP 84 (128)
Q Consensus 77 ~~A~~~L~ 84 (128)
..|+++|.
T Consensus 113 aDcleKlr 120 (172)
T KOG3429|consen 113 ADCLEKLR 120 (172)
T ss_pred HHHHHHHH
Confidence 99999886
No 17
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=91.06 E-value=0.25 Score=29.73 Aligned_cols=23 Identities=26% Similarity=0.371 Sum_probs=19.3
Q ss_pred hhHHHHHHcCCChHHHHHHccCC
Q 045445 106 ALLDLIFAVEGSVSEAAKFLSLL 128 (128)
Q Consensus 106 ~~lD~~~~~~g~~~~aa~~l~l~ 128 (128)
.+.+.|..++|+++.||+.||+.
T Consensus 9 ~i~~aL~~~~gn~~~aA~~Lgis 31 (42)
T PF02954_consen 9 LIRQALERCGGNVSKAARLLGIS 31 (42)
T ss_dssp HHHHHHHHTTT-HHHHHHHHTS-
T ss_pred HHHHHHHHhCCCHHHHHHHHCCC
Confidence 56789999999999999999973
No 18
>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B.
Probab=67.61 E-value=5.9 Score=25.14 Aligned_cols=22 Identities=23% Similarity=0.383 Sum_probs=17.8
Q ss_pred hhHHHHHHcCCChHHHHHHccC
Q 045445 106 ALLDLIFAVEGSVSEAAKFLSL 127 (128)
Q Consensus 106 ~~lD~~~~~~g~~~~aa~~l~l 127 (128)
+.|+....++|+++.||+.|++
T Consensus 3 ~TL~~yl~~~~n~~~tA~~L~i 24 (59)
T PF13556_consen 3 ETLRAYLENNGNISKTARALHI 24 (59)
T ss_dssp -HHHHHHHTTT-HHHHHHHHTS
T ss_pred hHHHHHHHcCCCHHHHHHHHCC
Confidence 3578888999999999999986
No 19
>PRK01905 DNA-binding protein Fis; Provisional
Probab=62.93 E-value=8.5 Score=25.86 Aligned_cols=22 Identities=27% Similarity=0.309 Sum_probs=20.2
Q ss_pred hhHHHHHHcCCChHHHHHHccC
Q 045445 106 ALLDLIFAVEGSVSEAAKFLSL 127 (128)
Q Consensus 106 ~~lD~~~~~~g~~~~aa~~l~l 127 (128)
.+...+..++|+.+.||+.||+
T Consensus 41 ~i~~aL~~~~gn~s~aAr~LGI 62 (77)
T PRK01905 41 LLEVVMEQAGGNQSLAAEYLGI 62 (77)
T ss_pred HHHHHHHHcCCCHHHHHHHHCC
Confidence 5788999999999999999996
No 20
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=60.42 E-value=9.7 Score=26.92 Aligned_cols=22 Identities=23% Similarity=0.231 Sum_probs=20.2
Q ss_pred hhHHHHHHcCCChHHHHHHccC
Q 045445 106 ALLDLIFAVEGSVSEAAKFLSL 127 (128)
Q Consensus 106 ~~lD~~~~~~g~~~~aa~~l~l 127 (128)
.+...+..++|+.+.||+.||+
T Consensus 59 ~i~~aL~~~~gn~s~AAr~LGI 80 (95)
T PRK00430 59 LLDMVMQYTRGNQTRAALMLGI 80 (95)
T ss_pred HHHHHHHHcCCCHHHHHHHhCC
Confidence 5678999999999999999997
No 21
>PF02815 MIR: MIR domain; InterPro: IPR003608 The MIR domain is named after three of the proteins in which it occurs: protein Mannosyltransferase (2.4.1.109 from EC), Inositol 1,4,5-trisphosphate receptor (IP3R) and Ryanodine receptor (RyR). MIR domains have also been found in eukaryotic stromal cell-derived factor 2 (SDF-2) and in Chlamydia trachomatis protein CT153. The MIR domain may have a ligand transferase function. This domain has a closed beta-barrel structure with a hairpin triplet, and has an internal pseudo-threefold symmetry. The MIR motifs that make up the MIR domain consist of ~50 residues and are often found in multiple copies. Inositol 1,4,5-trisphosphate (InsP3) is an intracellular second messenger that transduces growth factor and neurotransmitter signals. InsP3 mediates the release of Ca2+ from intracellular stores by binding to specific Ca2+ channel-coupled receptors. Ryanodine receptors are involved in communication between transverse-tubules and the sarcoplamic reticulum of cardiac and skeletal muscle. The proteins function as a Ca2+-release channels following depolarisation of transverse-tubules []. The function is modulated by Ca2+, Mg2+, ATP and calmodulin. Deficiency in the ryanodine receptor may be the cause of malignant hyperthermia (MH) and of central core disease of muscle (CCD) []. protein O-mannosyltransferases transfer mannose from DOL-P-mannose to ser or thr residues on proteins.; GO: 0016020 membrane; PDB: 1T9F_A 3UJ4_B 3UJ0_B 3T8S_B 3MAL_B 2XOA_A 1N4K_A.
Probab=48.56 E-value=38 Score=25.71 Aligned_cols=38 Identities=24% Similarity=0.308 Sum_probs=29.8
Q ss_pred EEEEeecCCCCcccccccccEEEEeeCCceEEEeeccC
Q 045445 37 MDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYL 74 (128)
Q Consensus 37 ~~~~RssGpGGQ~vNkt~saV~l~H~PtGi~v~~~~~R 74 (128)
++..-..|.++..+-..++.|+|+|..||.-+..+..+
T Consensus 121 ~~~~~~~~~~~~~~~~~~s~frL~H~~t~~~L~~~~~~ 158 (190)
T PF02815_consen 121 FEEKSSTGMGEDEIKTLDSYFRLRHVATGCWLHSHDVK 158 (190)
T ss_dssp EEEEESSSCSSSSBBBTTSEEEEEETTTTEEEEEEEEE
T ss_pred EEecccCCccCCcEEecccEEEEEECCcCEEEecCCcc
Confidence 34444557778888888999999999999888777655
No 22
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=43.40 E-value=21 Score=23.15 Aligned_cols=18 Identities=22% Similarity=0.228 Sum_probs=15.1
Q ss_pred HHHcCCChHHHHHHccCC
Q 045445 111 IFAVEGSVSEAAKFLSLL 128 (128)
Q Consensus 111 ~~~~~g~~~~aa~~l~l~ 128 (128)
|.-.|+.++++|+.||+.
T Consensus 9 LY~~G~~~~eIA~~Lg~~ 26 (58)
T PF06056_consen 9 LYLQGWSIKEIAEELGVP 26 (58)
T ss_pred HHHcCCCHHHHHHHHCCC
Confidence 445799999999999973
No 23
>COG3284 AcoR Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]
Probab=40.81 E-value=24 Score=33.04 Aligned_cols=23 Identities=43% Similarity=0.629 Sum_probs=21.3
Q ss_pred hhHHHHHHcCCChHHHHHHccCC
Q 045445 106 ALLDLIFAVEGSVSEAAKFLSLL 128 (128)
Q Consensus 106 ~~lD~~~~~~g~~~~aa~~l~l~ 128 (128)
.+++-+.+++|.+++||+.||+.
T Consensus 569 ~l~~al~~~~~~is~aa~~lgi~ 591 (606)
T COG3284 569 ALLAALQATNGNISEAARLLGIS 591 (606)
T ss_pred HHHHHHHHcCCCHHHHHHHhCCC
Confidence 67999999999999999999973
No 24
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=35.07 E-value=42 Score=19.79 Aligned_cols=21 Identities=29% Similarity=0.295 Sum_probs=13.4
Q ss_pred hHHHHHHcCCChHHHHHHccCC
Q 045445 107 LLDLIFAVEGSVSEAAKFLSLL 128 (128)
Q Consensus 107 ~lD~~~~~~g~~~~aa~~l~l~ 128 (128)
++-++.. |++++++|+.||+.
T Consensus 10 ii~l~~~-G~s~~~ia~~lgvs 30 (50)
T PF13384_consen 10 IIRLLRE-GWSIREIAKRLGVS 30 (50)
T ss_dssp HHHHHHH-T--HHHHHHHHTS-
T ss_pred HHHHHHC-CCCHHHHHHHHCcC
Confidence 3444444 99999999999973
No 25
>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF. Members of this protein family are PspF, the sigma-54-dependent transcriptional activator of the phage shock protein (psp) operon, in Escherichia coli and numerous other species. The psp operon is induced by a number of stress conditions, including heat shock, ethanol, and filamentous phage infection. Changed com_name to adhere to TIGR role notes conventions. 09/15/06 - DMH
Probab=34.19 E-value=38 Score=28.42 Aligned_cols=23 Identities=22% Similarity=0.198 Sum_probs=20.3
Q ss_pred hhHHHHHHcCCChHHHHHHccCC
Q 045445 106 ALLDLIFAVEGSVSEAAKFLSLL 128 (128)
Q Consensus 106 ~~lD~~~~~~g~~~~aa~~l~l~ 128 (128)
.+...|..++|+.+.||+.||+.
T Consensus 296 ~I~~aL~~~~gn~~~aA~~LGis 318 (329)
T TIGR02974 296 LLQQALAEAQFNQRKAAELLGLT 318 (329)
T ss_pred HHHHHHHHhCCCHHHHHHHhCCC
Confidence 56778899999999999999973
No 26
>PF06972 DUF1296: Protein of unknown function (DUF1296); InterPro: IPR009719 This family represents a conserved region approximately 60 residues long within a number of plant proteins of unknown function.
Probab=33.93 E-value=46 Score=22.40 Aligned_cols=24 Identities=13% Similarity=0.128 Sum_probs=21.0
Q ss_pred CCChhhHHHHHHcCCChHHHHHHc
Q 045445 102 NPKFALLDLIFAVEGSVSEAAKFL 125 (128)
Q Consensus 102 n~~f~~lD~~~~~~g~~~~aa~~l 125 (128)
|.+-.+...|..|++|+-+|++.|
T Consensus 19 hse~eIya~L~ecnMDpnea~qrL 42 (60)
T PF06972_consen 19 HSEEEIYAMLKECNMDPNEAVQRL 42 (60)
T ss_pred CCHHHHHHHHHHhCCCHHHHHHHH
Confidence 455588999999999999999987
No 27
>TIGR01817 nifA Nif-specific regulatory protein. This model represents NifA, a DNA-binding regulatory protein for nitrogen fixation. The model produces scores between the trusted and noise cutoffs for a well-described NifA homolog in Aquifex aeolicus (which lacks nitrogenase), for transcriptional activators of alternative nitrogenases (VFe or FeFe instead of MoFe), and truncated forms.
Probab=33.63 E-value=37 Score=29.96 Aligned_cols=23 Identities=17% Similarity=0.203 Sum_probs=21.0
Q ss_pred hhHHHHHHcCCChHHHHHHccCC
Q 045445 106 ALLDLIFAVEGSVSEAAKFLSLL 128 (128)
Q Consensus 106 ~~lD~~~~~~g~~~~aa~~l~l~ 128 (128)
.+.+.|..++|+.+.||+.||+.
T Consensus 494 ~i~~aL~~~~gn~~~aA~~LGis 516 (534)
T TIGR01817 494 RLIAALEQAGWVQAKAARLLGMT 516 (534)
T ss_pred HHHHHHHHhCCCHHHHHHHHCCC
Confidence 67899999999999999999973
No 28
>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator. Members of this protein family share full-length homology with (but do not include) the acetoacetate metabolism regulatory protein AtoC. These proteins have a Fis family DNA binding sequence (pfam02954), a response regulator receiver domain (pfam00072), and sigma-54 interaction domain (pfam00158).
Probab=32.49 E-value=41 Score=28.32 Aligned_cols=22 Identities=32% Similarity=0.543 Sum_probs=20.2
Q ss_pred hhHHHHHHcCCChHHHHHHccC
Q 045445 106 ALLDLIFAVEGSVSEAAKFLSL 127 (128)
Q Consensus 106 ~~lD~~~~~~g~~~~aa~~l~l 127 (128)
.+...|..++|+.+.||+.||+
T Consensus 409 ~i~~al~~~~gn~~~aA~~Lgi 430 (445)
T TIGR02915 409 AVRKAIARVDGNIARAAELLGI 430 (445)
T ss_pred HHHHHHHHhCCCHHHHHHHhCC
Confidence 5678899999999999999997
No 29
>PRK15115 response regulator GlrR; Provisional
Probab=32.04 E-value=43 Score=28.23 Aligned_cols=22 Identities=27% Similarity=0.359 Sum_probs=20.1
Q ss_pred hhHHHHHHcCCChHHHHHHccC
Q 045445 106 ALLDLIFAVEGSVSEAAKFLSL 127 (128)
Q Consensus 106 ~~lD~~~~~~g~~~~aa~~l~l 127 (128)
.+...|..++|+.+.||+.||+
T Consensus 402 ~i~~al~~~~gn~~~aA~~Lgi 423 (444)
T PRK15115 402 YLRKLLQITKGNVTHAARMAGR 423 (444)
T ss_pred HHHHHHHHhCCCHHHHHHHhCC
Confidence 5678899999999999999997
No 30
>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional
Probab=31.85 E-value=43 Score=28.20 Aligned_cols=22 Identities=18% Similarity=0.413 Sum_probs=19.9
Q ss_pred hhHHHHHHcCCChHHHHHHccC
Q 045445 106 ALLDLIFAVEGSVSEAAKFLSL 127 (128)
Q Consensus 106 ~~lD~~~~~~g~~~~aa~~l~l 127 (128)
.+...|..++|+.+.||+.||+
T Consensus 421 ~i~~al~~~~gn~~~aA~~LGi 442 (457)
T PRK11361 421 IIMEVLEQQEGNRTRTALMLGI 442 (457)
T ss_pred HHHHHHHHhCCCHHHHHHHHCC
Confidence 5677899999999999999997
No 31
>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional
Probab=31.83 E-value=44 Score=27.83 Aligned_cols=23 Identities=22% Similarity=0.146 Sum_probs=20.3
Q ss_pred hhHHHHHHcCCChHHHHHHccCC
Q 045445 106 ALLDLIFAVEGSVSEAAKFLSLL 128 (128)
Q Consensus 106 ~~lD~~~~~~g~~~~aa~~l~l~ 128 (128)
.+...|..++|+.+.||+.||+.
T Consensus 290 ~I~~aL~~~~gn~~~aA~~LGIs 312 (326)
T PRK11608 290 LLQRSLQQAKFNQKRAAELLGLT 312 (326)
T ss_pred HHHHHHHHhCCCHHHHHHHhCCC
Confidence 46788899999999999999973
No 32
>TIGR01818 ntrC nitrogen regulation protein NR(I). This model represents NtrC, a DNA-binding response regulator that is phosphorylated by NtrB and interacts with sigma-54. NtrC usually controls the expression of glutamine synthase, GlnA, and may be called GlnL, GlnG, etc.
Probab=30.91 E-value=46 Score=28.15 Aligned_cols=22 Identities=27% Similarity=0.258 Sum_probs=19.7
Q ss_pred hhHHHHHHcCCChHHHHHHccC
Q 045445 106 ALLDLIFAVEGSVSEAAKFLSL 127 (128)
Q Consensus 106 ~~lD~~~~~~g~~~~aa~~l~l 127 (128)
.+...|..++|+.+.||+.||+
T Consensus 430 ~i~~al~~~~gn~~~aA~~Lgi 451 (463)
T TIGR01818 430 LLEAALQHTRGHKQEAAALLGW 451 (463)
T ss_pred HHHHHHHHcCCCHHHHHHHhCC
Confidence 5677888999999999999997
No 33
>smart00472 MIR Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases.
Probab=30.77 E-value=49 Score=20.06 Aligned_cols=21 Identities=29% Similarity=0.363 Sum_probs=16.3
Q ss_pred cccEEEEeeCCceEEEeeccC
Q 045445 54 ESAVRLKHVPTASSVNLDAYL 74 (128)
Q Consensus 54 ~saV~l~H~PtGi~v~~~~~R 74 (128)
.+.|||+|.-||--+.++..+
T Consensus 7 g~~vrL~H~~tg~yL~s~~~~ 27 (57)
T smart00472 7 GDVVRLRHVTTGRYLHSHENK 27 (57)
T ss_pred CCEEEEEEhhhCcEeecCCCC
Confidence 578999999999766666544
No 34
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=30.71 E-value=22 Score=22.65 Aligned_cols=29 Identities=28% Similarity=0.358 Sum_probs=21.4
Q ss_pred CCCCCCh--hhHHHHHHcCCChHHHHHHccC
Q 045445 99 RPNNPKF--ALLDLIFAVEGSVSEAAKFLSL 127 (128)
Q Consensus 99 rtyn~~f--~~lD~~~~~~g~~~~aa~~l~l 127 (128)
+.|.++| .++......|.++++.|..+|+
T Consensus 5 ~~ys~e~K~~~v~~~~~~g~sv~~va~~~gi 35 (76)
T PF01527_consen 5 RRYSPEFKLQAVREYLESGESVSEVAREYGI 35 (76)
T ss_dssp ----HHHHHHHHHHHHHHHCHHHHHHHHHTS
T ss_pred CCCCHHHHHHHHHHHHHCCCceEeeeccccc
Confidence 5677888 7777777889999999999987
No 35
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=30.39 E-value=60 Score=19.32 Aligned_cols=23 Identities=17% Similarity=0.196 Sum_probs=19.6
Q ss_pred hhHHHHHHcCCChHHHHHHccCC
Q 045445 106 ALLDLIFAVEGSVSEAAKFLSLL 128 (128)
Q Consensus 106 ~~lD~~~~~~g~~~~aa~~l~l~ 128 (128)
.+|.+.+-.+.+.+++|+.||+.
T Consensus 11 ~vi~~~y~~~~t~~eIa~~lg~s 33 (50)
T PF04545_consen 11 EVIRLRYFEGLTLEEIAERLGIS 33 (50)
T ss_dssp HHHHHHHTST-SHHHHHHHHTSC
T ss_pred HHHHHHhcCCCCHHHHHHHHCCc
Confidence 68888999999999999999973
No 36
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=29.43 E-value=61 Score=17.96 Aligned_cols=22 Identities=27% Similarity=0.282 Sum_probs=18.9
Q ss_pred hhHHHHHHcCCChHHHHHHccC
Q 045445 106 ALLDLIFAVEGSVSEAAKFLSL 127 (128)
Q Consensus 106 ~~lD~~~~~~g~~~~aa~~l~l 127 (128)
.++.++...|.+.+++|+.+|+
T Consensus 17 ~~~~~~~~~~~~~~~ia~~~~~ 38 (55)
T cd06171 17 EVILLRFGEGLSYEEIAEILGI 38 (55)
T ss_pred HHHHHHHhcCCCHHHHHHHHCc
Confidence 6677777899999999999986
No 37
>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional
Probab=29.43 E-value=49 Score=29.26 Aligned_cols=22 Identities=23% Similarity=0.282 Sum_probs=20.6
Q ss_pred hhHHHHHHcCCChHHHHHHccC
Q 045445 106 ALLDLIFAVEGSVSEAAKFLSL 127 (128)
Q Consensus 106 ~~lD~~~~~~g~~~~aa~~l~l 127 (128)
.+.+.|..++|+.+.||+.||+
T Consensus 472 ~I~~aL~~~~gn~~~aA~~LGi 493 (509)
T PRK05022 472 LIRQALAQHQGNWAAAARALEL 493 (509)
T ss_pred HHHHHHHHcCCCHHHHHHHhCC
Confidence 6789999999999999999997
No 38
>PRK10365 transcriptional regulatory protein ZraR; Provisional
Probab=29.20 E-value=51 Score=27.52 Aligned_cols=22 Identities=27% Similarity=0.397 Sum_probs=19.9
Q ss_pred hhHHHHHHcCCChHHHHHHccC
Q 045445 106 ALLDLIFAVEGSVSEAAKFLSL 127 (128)
Q Consensus 106 ~~lD~~~~~~g~~~~aa~~l~l 127 (128)
.+...|..++|+.+.||+.||+
T Consensus 409 ~i~~~l~~~~gn~~~aa~~Lgi 430 (441)
T PRK10365 409 VILAALEKTGGNKTEAARQLGI 430 (441)
T ss_pred HHHHHHHHhCCCHHHHHHHhCC
Confidence 5677899999999999999997
No 39
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=29.02 E-value=70 Score=20.33 Aligned_cols=27 Identities=22% Similarity=0.229 Sum_probs=20.9
Q ss_pred CCCChhhH-HHHHHcCCChHHHHHHccC
Q 045445 101 NNPKFALL-DLIFAVEGSVSEAAKFLSL 127 (128)
Q Consensus 101 yn~~f~~l-D~~~~~~g~~~~aa~~l~l 127 (128)
++|..-+. .++...+....+.|+.+|+
T Consensus 3 ~~~g~~i~~~~~~~~~~t~~~lA~~~gi 30 (78)
T TIGR02607 3 AHPGEILREEFLEPLGLSIRALAKALGV 30 (78)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHhCC
Confidence 34444455 7899999999999999986
No 40
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=28.64 E-value=50 Score=29.79 Aligned_cols=22 Identities=23% Similarity=0.436 Sum_probs=20.4
Q ss_pred hhHHHHHHcCCChHHHHHHccC
Q 045445 106 ALLDLIFAVEGSVSEAAKFLSL 127 (128)
Q Consensus 106 ~~lD~~~~~~g~~~~aa~~l~l 127 (128)
.+...|..++|+.+.||+.||+
T Consensus 595 ~i~~al~~~~gn~~~aA~~LGi 616 (638)
T PRK11388 595 AIINAAQVCGGRIQEMAALLGI 616 (638)
T ss_pred HHHHHHHHhCCCHHHHHHHHCC
Confidence 6788999999999999999997
No 41
>PRK10923 glnG nitrogen regulation protein NR(I); Provisional
Probab=26.45 E-value=61 Score=27.60 Aligned_cols=22 Identities=27% Similarity=0.342 Sum_probs=19.5
Q ss_pred hhHHHHHHcCCChHHHHHHccC
Q 045445 106 ALLDLIFAVEGSVSEAAKFLSL 127 (128)
Q Consensus 106 ~~lD~~~~~~g~~~~aa~~l~l 127 (128)
.+...|..++|+.+.||+.||+
T Consensus 433 ~i~~aL~~~~gn~~~aA~~Lgi 454 (469)
T PRK10923 433 LLTTALRHTQGHKQEAARLLGW 454 (469)
T ss_pred HHHHHHHHhCCCHHHHHHHhCC
Confidence 4567888899999999999997
No 42
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=25.12 E-value=68 Score=20.49 Aligned_cols=22 Identities=18% Similarity=0.274 Sum_probs=17.6
Q ss_pred hhHHHHHHcCCChHHHHHHccC
Q 045445 106 ALLDLIFAVEGSVSEAAKFLSL 127 (128)
Q Consensus 106 ~~lD~~~~~~g~~~~aa~~l~l 127 (128)
.-+|++...|.+..+.|.++|-
T Consensus 11 aqid~m~qlG~s~~~isr~i~R 32 (50)
T PF11427_consen 11 AQIDVMHQLGMSLREISRRIGR 32 (50)
T ss_dssp HHHHHHHHTT--HHHHHHHHT-
T ss_pred HHHHHHHHhchhHHHHHHHhCc
Confidence 6799999999999999999873
No 43
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=24.84 E-value=90 Score=17.47 Aligned_cols=20 Identities=20% Similarity=0.258 Sum_probs=17.6
Q ss_pred hhHHHHHHcCCChHHHHHHc
Q 045445 106 ALLDLIFAVEGSVSEAAKFL 125 (128)
Q Consensus 106 ~~lD~~~~~~g~~~~aa~~l 125 (128)
.+...|..++|++..|+..|
T Consensus 17 ~~~~AL~~~~~d~~~A~~~L 36 (38)
T cd00194 17 EARKALRATNNNVERAVEWL 36 (38)
T ss_pred HHHHHHHHhCCCHHHHHHHH
Confidence 77889999999999998875
No 44
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=24.52 E-value=49 Score=19.62 Aligned_cols=11 Identities=55% Similarity=0.878 Sum_probs=9.3
Q ss_pred ChHHHHHHccC
Q 045445 117 SVSEAAKFLSL 127 (128)
Q Consensus 117 ~~~~aa~~l~l 127 (128)
++.+||+.||+
T Consensus 19 S~~eAa~~lg~ 29 (53)
T smart00497 19 SIREAAKYLGI 29 (53)
T ss_pred CHHHHHHHhCC
Confidence 67899999886
No 45
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=22.94 E-value=74 Score=18.97 Aligned_cols=21 Identities=29% Similarity=0.308 Sum_probs=14.4
Q ss_pred hhHHHHHHcCCChHHHHHHccC
Q 045445 106 ALLDLIFAVEGSVSEAAKFLSL 127 (128)
Q Consensus 106 ~~lD~~~~~~g~~~~aa~~l~l 127 (128)
.++-++ ..|.++++.|+.+|+
T Consensus 13 ~i~~l~-~~G~si~~IA~~~gv 33 (45)
T PF02796_consen 13 EIKELY-AEGMSIAEIAKQFGV 33 (45)
T ss_dssp HHHHHH-HTT--HHHHHHHTTS
T ss_pred HHHHHH-HCCCCHHHHHHHHCc
Confidence 555544 555999999999997
No 46
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=22.67 E-value=75 Score=21.08 Aligned_cols=22 Identities=23% Similarity=0.113 Sum_probs=18.0
Q ss_pred hhHHHHHHcCCChHHHHHHccC
Q 045445 106 ALLDLIFAVEGSVSEAAKFLSL 127 (128)
Q Consensus 106 ~~lD~~~~~~g~~~~aa~~l~l 127 (128)
.+-+++.+.+++-+++|+.+|+
T Consensus 22 ~i~~~~~~~~ltQ~e~A~~lgi 43 (80)
T PF13744_consen 22 AIRELREERGLTQAELAERLGI 43 (80)
T ss_dssp HHHHHHHCCT--HHHHHHHHTS
T ss_pred HHHHHHHHcCCCHHHHHHHHCC
Confidence 5678999999999999999996
No 47
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=22.26 E-value=60 Score=19.67 Aligned_cols=22 Identities=32% Similarity=0.477 Sum_probs=17.6
Q ss_pred hhHHHHHHcCCC--hHHHHHHccC
Q 045445 106 ALLDLIFAVEGS--VSEAAKFLSL 127 (128)
Q Consensus 106 ~~lD~~~~~~g~--~~~aa~~l~l 127 (128)
.+||.+...++. +++.|+.+|+
T Consensus 7 ~iL~~l~~~~~~~t~~eia~~~gl 30 (52)
T PF09339_consen 7 RILEALAESGGPLTLSEIARALGL 30 (52)
T ss_dssp HHHHCHHCTBSCEEHHHHHHHHTS
T ss_pred HHHHHHHcCCCCCCHHHHHHHHCc
Confidence 467888887774 8899999886
No 48
>PF13014 KH_3: KH domain
Probab=21.82 E-value=33 Score=20.10 Aligned_cols=20 Identities=25% Similarity=0.615 Sum_probs=15.2
Q ss_pred CCCCcccc--cccccEEEEeeC
Q 045445 44 GPGGQHRN--KRESAVRLKHVP 63 (128)
Q Consensus 44 GpGGQ~vN--kt~saV~l~H~P 63 (128)
|+||++++ ..+|.|+|...+
T Consensus 7 G~~G~~I~~I~~~tg~~I~i~~ 28 (43)
T PF13014_consen 7 GKGGSTIKEIREETGAKIQIPP 28 (43)
T ss_pred CCCChHHHHHHHHhCcEEEECC
Confidence 88999998 455777877655
No 49
>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR. At least five distinct pathways exists for the catabolism of propionate by way of propionyl-CoA. Members of this family represent the transcriptional regulatory protein PrpR, whose gene is found in most cases divergently transcribed from an operon for the methylcitric acid cycle of propionate catabolism. 2-methylcitric acid, a catabolite by this pathway, is a coactivator of PrpR.
Probab=21.64 E-value=82 Score=28.52 Aligned_cols=22 Identities=27% Similarity=0.253 Sum_probs=20.4
Q ss_pred hhHHHHHHcCCChHHHHHHccC
Q 045445 106 ALLDLIFAVEGSVSEAAKFLSL 127 (128)
Q Consensus 106 ~~lD~~~~~~g~~~~aa~~l~l 127 (128)
.+...|..++|+.+.||+.||+
T Consensus 494 ~I~~aL~~~~Gn~~~aA~~LGI 515 (526)
T TIGR02329 494 AVRAALERFGGDRDAAAKALGI 515 (526)
T ss_pred HHHHHHHHcCCCHHHHHHHhCC
Confidence 5788999999999999999997
No 50
>COG2204 AtoC Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]
Probab=21.51 E-value=82 Score=28.49 Aligned_cols=22 Identities=32% Similarity=0.371 Sum_probs=20.5
Q ss_pred hhHHHHHHcCCChHHHHHHccC
Q 045445 106 ALLDLIFAVEGSVSEAAKFLSL 127 (128)
Q Consensus 106 ~~lD~~~~~~g~~~~aa~~l~l 127 (128)
.+.+-|..++|+.+.||+.||+
T Consensus 421 ~I~~aL~~~~g~~~~aA~~LGi 442 (464)
T COG2204 421 LILQALERTGGNKSEAAERLGI 442 (464)
T ss_pred HHHHHHHHhCCCHHHHHHHHCC
Confidence 5789999999999999999997
No 51
>PRK04217 hypothetical protein; Provisional
Probab=21.22 E-value=1.3e+02 Score=21.94 Aligned_cols=22 Identities=23% Similarity=0.116 Sum_probs=18.9
Q ss_pred hhHHHHHHcCCChHHHHHHccC
Q 045445 106 ALLDLIFAVEGSVSEAAKFLSL 127 (128)
Q Consensus 106 ~~lD~~~~~~g~~~~aa~~l~l 127 (128)
.++-++...+-+++++|+.||+
T Consensus 49 eai~l~~~eGlS~~EIAk~LGI 70 (110)
T PRK04217 49 EALRLVDYEGLTQEEAGKRMGV 70 (110)
T ss_pred HHHHHHHHcCCCHHHHHHHHCc
Confidence 5677777788999999999997
No 52
>TIGR02040 PpsR-CrtJ transcriptional regulator PpsR. This model represents the transcriptional regulator PpsR which is strictly associated with photosynthetic proteobacteria and found in photosynthetic operons. PpsR has been reported to be a repressor. These proteins contain a Helix-Turn_Helix motif of the "fis" type (pfam02954).
Probab=20.72 E-value=89 Score=26.24 Aligned_cols=22 Identities=18% Similarity=0.196 Sum_probs=20.0
Q ss_pred hhHHHHHHcCCChHHHHHHccC
Q 045445 106 ALLDLIFAVEGSVSEAAKFLSL 127 (128)
Q Consensus 106 ~~lD~~~~~~g~~~~aa~~l~l 127 (128)
.+...|..++|+.+.||+.||+
T Consensus 407 ~i~~~l~~~~~n~~~aa~~lgi 428 (442)
T TIGR02040 407 CIEAALELTRDNRASAAEILGL 428 (442)
T ss_pred HHHHHHHHcCCCHHHHHHHhCC
Confidence 4678899999999999999997
No 53
>COG4567 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]
Probab=20.69 E-value=72 Score=25.67 Aligned_cols=22 Identities=27% Similarity=0.471 Sum_probs=20.2
Q ss_pred hhHHHHHHcCCChHHHHHHccC
Q 045445 106 ALLDLIFAVEGSVSEAAKFLSL 127 (128)
Q Consensus 106 ~~lD~~~~~~g~~~~aa~~l~l 127 (128)
+.=-++..|+|++|+.|..||.
T Consensus 146 hIqrvl~e~~~NiSeTARrL~M 167 (182)
T COG4567 146 HIQRVLEECEGNISETARRLNM 167 (182)
T ss_pred HHHHHHHHhCCCHHHHHHHhhh
Confidence 7788999999999999999985
No 54
>PRK15424 propionate catabolism operon regulatory protein PrpR; Provisional
Probab=20.66 E-value=88 Score=28.52 Aligned_cols=22 Identities=23% Similarity=0.407 Sum_probs=20.5
Q ss_pred hhHHHHHHcCCChHHHHHHccC
Q 045445 106 ALLDLIFAVEGSVSEAAKFLSL 127 (128)
Q Consensus 106 ~~lD~~~~~~g~~~~aa~~l~l 127 (128)
.+...|..++|+.+.||+.||+
T Consensus 501 ~I~~~L~~~~Gn~~~aA~~LGI 522 (538)
T PRK15424 501 TLQQALERFNGDKTAAANYLGI 522 (538)
T ss_pred HHHHHHHHhCCCHHHHHHHhCC
Confidence 5788999999999999999997
No 55
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=20.45 E-value=1e+02 Score=18.31 Aligned_cols=22 Identities=23% Similarity=0.247 Sum_probs=16.5
Q ss_pred hhHHHHHHcCCChHHHHHHccC
Q 045445 106 ALLDLIFAVEGSVSEAAKFLSL 127 (128)
Q Consensus 106 ~~lD~~~~~~g~~~~aa~~l~l 127 (128)
.++-+..-.|.+++++|+.||+
T Consensus 17 ~i~~l~~~~g~s~~eIa~~l~~ 38 (54)
T PF08281_consen 17 EIFLLRYFQGMSYAEIAEILGI 38 (54)
T ss_dssp HHHHHHHTS---HHHHHHHCTS
T ss_pred HHHHHHHHHCcCHHHHHHHHCc
Confidence 6777888899999999999986
Done!