Query 036979
Match_columns 212
No_of_seqs 234 out of 1088
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 07:21:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036979.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036979hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0216 PrfA Protein chain rel 100.0 1.9E-52 4E-57 380.8 9.6 164 3-185 167-338 (363)
2 TIGR00019 prfA peptide chain r 100.0 2.7E-45 5.9E-50 337.1 10.6 174 3-197 166-346 (360)
3 PRK08787 peptide chain release 100.0 3.8E-44 8.2E-49 324.3 13.9 183 3-205 120-311 (313)
4 PRK05589 peptide chain release 100.0 2.8E-44 6.1E-49 326.7 11.8 173 3-196 140-320 (325)
5 PRK06746 peptide chain release 100.0 2.4E-44 5.3E-49 327.2 11.3 174 3-197 141-322 (326)
6 PRK07342 peptide chain release 100.0 7E-44 1.5E-48 325.6 12.7 175 3-198 143-325 (339)
7 PRK00591 prfA peptide chain re 100.0 3.9E-44 8.5E-49 329.4 10.1 174 3-197 166-346 (359)
8 KOG2726 Mitochondrial polypept 100.0 3.7E-43 8.1E-48 323.9 11.0 165 3-185 191-363 (386)
9 TIGR00020 prfB peptide chain r 100.0 3.4E-43 7.4E-48 323.7 10.4 174 3-197 179-360 (364)
10 PRK00578 prfB peptide chain re 100.0 5.2E-43 1.1E-47 322.8 11.1 175 3-198 179-361 (367)
11 TIGR03072 release_prfH putativ 100.0 9.7E-39 2.1E-43 274.0 9.7 138 3-158 55-197 (200)
12 PRK08179 prfH peptide chain re 100.0 1.1E-37 2.4E-42 267.5 9.8 139 3-157 56-197 (200)
13 COG1186 PrfB Protein chain rel 100.0 5.6E-36 1.2E-40 262.5 7.3 170 3-191 54-231 (239)
14 PF00472 RF-1: RF-1 domain; I 100.0 1.4E-31 3.1E-36 210.5 7.9 101 45-158 4-104 (113)
15 PRK09256 hypothetical protein; 99.9 4E-23 8.6E-28 168.7 8.8 73 46-122 6-102 (138)
16 KOG3429 Predicted peptidyl-tRN 99.7 7.8E-18 1.7E-22 141.2 6.2 70 49-122 36-130 (172)
17 PF10213 MRP-S28: Mitochondria 61.1 61 0.0013 26.3 7.8 34 88-121 60-94 (127)
18 cd02164 PPAT_CoAS phosphopante 60.8 5.3 0.00011 32.7 1.6 17 190-206 103-119 (143)
19 PF07035 Mic1: Colon cancer-as 56.2 21 0.00046 30.3 4.6 43 160-202 74-118 (167)
20 PF00356 LacI: Bacterial regul 51.9 40 0.00086 22.7 4.5 36 167-202 4-43 (46)
21 PF14974 DUF4511: Domain of un 47.9 14 0.0003 29.5 2.0 83 103-199 3-96 (105)
22 PLN02388 phosphopantetheine ad 47.8 11 0.00024 32.2 1.6 27 179-205 110-138 (177)
23 PRK10219 DNA-binding transcrip 47.5 25 0.00054 26.2 3.3 44 167-210 26-71 (107)
24 PRK13502 transcriptional activ 46.5 23 0.0005 30.5 3.4 42 170-211 200-243 (282)
25 PRK13503 transcriptional activ 40.1 29 0.00062 29.6 3.0 42 170-211 195-238 (278)
26 COG3077 RelB DNA-damage-induci 40.0 29 0.00063 26.9 2.7 20 165-184 19-38 (88)
27 COG1019 Predicted nucleotidylt 38.9 18 0.00039 30.9 1.5 17 190-206 106-122 (158)
28 PRK10371 DNA-binding transcrip 36.7 39 0.00084 30.2 3.3 42 170-211 215-258 (302)
29 PF12623 Hen1_L: RNA repair, l 33.8 33 0.00073 31.1 2.4 50 21-80 24-85 (245)
30 PRK10572 DNA-binding transcrip 33.5 49 0.0011 28.7 3.4 42 170-211 207-250 (290)
31 smart00342 HTH_ARAC helix_turn 33.5 50 0.0011 22.2 2.8 41 167-207 6-48 (84)
32 TIGR02297 HpaA 4-hydroxyphenyl 33.4 49 0.0011 28.4 3.4 42 170-211 210-253 (287)
33 PF02815 MIR: MIR domain; Int 32.5 81 0.0018 26.1 4.4 39 61-99 121-159 (190)
34 PRK13500 transcriptional activ 32.3 51 0.0011 29.4 3.4 42 170-211 230-273 (312)
35 PRK11511 DNA-binding transcrip 31.2 53 0.0012 25.7 3.0 44 167-210 30-75 (127)
36 PF02787 CPSase_L_D3: Carbamoy 29.9 70 0.0015 25.6 3.5 36 169-207 68-103 (123)
37 cd01392 HTH_LacI Helix-turn-he 29.9 1.2E+02 0.0026 19.4 4.0 21 167-187 2-22 (52)
38 PRK10296 DNA-binding transcrip 29.1 53 0.0011 28.3 2.9 43 169-211 195-239 (278)
39 PF12833 HTH_18: Helix-turn-he 26.1 68 0.0015 22.4 2.5 37 170-206 3-41 (81)
40 PF01418 HTH_6: Helix-turn-hel 26.1 54 0.0012 23.6 2.0 20 166-185 38-57 (77)
41 smart00354 HTH_LACI helix_turn 25.7 1.6E+02 0.0035 20.6 4.4 22 167-188 5-26 (70)
42 COG2207 AraC AraC-type DNA-bin 25.7 98 0.0021 22.4 3.4 44 167-210 41-86 (127)
43 PRK13501 transcriptional activ 25.3 80 0.0017 27.5 3.3 42 170-211 200-243 (290)
44 cd02394 vigilin_like_KH K homo 24.9 73 0.0016 21.4 2.4 29 67-95 15-50 (62)
45 smart00472 MIR Domain in ryano 24.0 83 0.0018 20.8 2.5 23 77-99 6-28 (57)
46 PF00440 TetR_N: Bacterial reg 23.9 83 0.0018 20.3 2.4 27 167-193 21-47 (47)
47 PRK09393 ftrA transcriptional 23.8 87 0.0019 27.9 3.3 42 170-211 242-285 (322)
48 COG2340 Uncharacterized protei 23.3 55 0.0012 28.0 1.9 27 182-208 77-103 (207)
49 COG2522 Predicted transcriptio 23.3 81 0.0018 25.6 2.7 23 166-188 26-48 (119)
50 PRK15186 AraC family transcrip 22.3 95 0.0021 28.2 3.3 46 166-211 200-247 (291)
51 PF00165 HTH_AraC: Bacterial r 21.7 86 0.0019 19.7 2.1 19 167-185 13-31 (42)
52 PRK07394 hypothetical protein; 20.6 1.3E+02 0.0028 28.0 3.9 43 166-208 132-189 (342)
No 1
>COG0216 PrfA Protein chain release factor A [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.9e-52 Score=380.78 Aligned_cols=164 Identities=26% Similarity=0.364 Sum_probs=143.4
Q ss_pred ceeechhhhHhhhhhccccceeecCCccccceeEee-----eCCCCCC-CccccChhhhhccceEEEEeeCCCCCCCCCc
Q 036979 3 REFKNNKIITLLTCWTGLDWADWAGPSIRMGFHHCS-----CPASKKK-NYLELTDDELLRECEMHTYKSSGPGGQHRNK 76 (212)
Q Consensus 3 ~~~~g~~~~~~l~~e~Gvhrvqrvp~~~~~~~~~~s-----~~~~~~~-~~i~i~~~~L~~~~~i~~~RsSGPGGQ~VNK 76 (212)
..|+|.++|+.|+||+|||||||||.|+..|+.|+| |+|..+. ..+.|+++|| +|++|||||+||||||+
T Consensus 167 ~~I~G~gvys~LKfEsGvHRVQRVP~TEsqGRIHTStaTVaVlPE~ee~~ei~I~~~Dl----rIDt~RsSGaGGQhVNt 242 (363)
T COG0216 167 ASISGKGVYSRLKFESGVHRVQRVPATESQGRIHTSAATVAVLPEVEEVEEIEINPKDL----RIDTFRSSGAGGQHVNT 242 (363)
T ss_pred EEEeccchhhhhhhccCccceeccccccCCCceeecceeEEeccCCCcccccccChHHc----eeeeeecCCCCCCCcCc
Confidence 468999999999999999999999999999988886 5666654 4799999999 99999999999999999
Q ss_pred cCceEEEEEecCCcEEEEcccccHHHHHHHHHHHHHHHHHHHHHhhhccCCCCChhhhhhcCCCCCcccCCCCCCCcCCC
Q 036979 77 CETAVRLKHVPTGVIAQAAEDRSQHKNRALALSRLPTFLALKVRSSVNLGAYSPPLQLLQILPPKSTIRSSEVGPQIGPN 156 (212)
Q Consensus 77 t~saVrl~HlPtGIvv~~~e~RSq~~Nk~~Al~~L~~~l~~~~~e~~~~~~~s~~~e~~q~~~rKsqir~~drs~qIRtY 156 (212)
|+||||||||||||+|+||++|||++||+.||+.|+++|....+++.+. .++..||+|+++||||++||||
T Consensus 243 TdSAVRiTHlPTGIvV~cQderSQ~kNk~kAmkvL~ARl~~~~~~~~~~---------~~~~~RksqVGSGDRSErIRTY 313 (363)
T COG0216 243 TDSAVRITHLPTGIVVECQDERSQHKNKAKAMKVLRARLYDAERQKAQA---------EEASERKSQVGSGDRSERIRTY 313 (363)
T ss_pred cchhheeeecCCceEEEecchhhhhhhHHHHHHHHHHHHHHHHHHHHHH---------HHHHHHHHhcCCCchhhhhhcc
Confidence 9999999999999999999999999999999999999888766655442 2356899999999999999999
Q ss_pred CcchHHHHHHHHH--HHhcCChhHHHHHhhc
Q 036979 157 NPKFALVLLYSLL--LRLLLSTGALSRLILS 185 (212)
Q Consensus 157 N~~fp~~~~ldl~--~~lg~sts~l~k~l~~ 185 (212)
|| | =.-+ -|.||+-=.|..+|.+
T Consensus 314 Nf--P----QnRVTDHRI~lTl~kLd~vm~g 338 (363)
T COG0216 314 NF--P----QNRVTDHRINLTLYKLDEVMEG 338 (363)
T ss_pred CC--C----CCcccchhcccccccHHHHhcc
Confidence 94 5 3344 3778888788888874
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=100.00 E-value=2.7e-45 Score=337.12 Aligned_cols=174 Identities=24% Similarity=0.338 Sum_probs=146.7
Q ss_pred ceeechhhhHhhhhhccccceeecCCccc-----cceeEeeeCCCCCCCccccChhhhhccceEEEEeeCCCCCCCCCcc
Q 036979 3 REFKNNKIITLLTCWTGLDWADWAGPSIR-----MGFHHCSCPASKKKNYLELTDDELLRECEMHTYKSSGPGGQHRNKC 77 (212)
Q Consensus 3 ~~~~g~~~~~~l~~e~Gvhrvqrvp~~~~-----~~~~~~s~~~~~~~~~i~i~~~~L~~~~~i~~~RsSGPGGQ~VNKt 77 (212)
+.|+|.++|++|++|.|||||||+|+++. |+|..+.+.|......+.|++.|| +|+|+|||||||||||||
T Consensus 166 l~i~G~~ay~~lk~E~GvHrv~Rvp~~~s~~R~hTsfa~V~v~P~~~~~~~~i~~~dl----~~~~~RssG~GGQ~VNkt 241 (360)
T TIGR00019 166 AEIKGDGVYSRLKFESGVHRVQRVPVTESQGRIHTSAATVAVMPELEEVEVDINPADL----RIDTFRSSGAGGQHVNTT 241 (360)
T ss_pred EEEecccHHHHHhhcCeeEEEECCCCCCCCCCeecceeEEEEEcCCCccccccCcccE----EEEEEECCCCCCCCcCce
Confidence 57899999999999999999999999986 444455566655545578887777 999999999999999999
Q ss_pred CceEEEEEecCCcEEEEcccccHHHHHHHHHHHHHHHHHHHHHhhhccCCCCChhhhhhcCCCCCcccCCCCCCCcCCCC
Q 036979 78 ETAVRLKHVPTGVIAQAAEDRSQHKNRALALSRLPTFLALKVRSSVNLGAYSPPLQLLQILPPKSTIRSSEVGPQIGPNN 157 (212)
Q Consensus 78 ~saVrl~HlPtGIvv~~~e~RSq~~Nk~~Al~~L~~~l~~~~~e~~~~~~~s~~~e~~q~~~rKsqir~~drs~qIRtYN 157 (212)
+|||||+|+||||+|.|+++|||++||+.||++|+++|.....++...+ +...++++++.++||++|||||
T Consensus 242 ~SaVrl~h~ptgi~V~~~~eRSQ~~Nk~~A~~~L~~~L~~~~~~~~~~~---------~~~~r~~~~~~~~Rs~~IRtY~ 312 (360)
T TIGR00019 242 DSAVRITHLPTGIVVECQDERSQHKNKDKAMKVLRARLYEAEQEKQQAA---------QASTRKSQVGSGDRSERIRTYN 312 (360)
T ss_pred eeeEEEEECCCcEEEEECCccCHHHHHHHHHHHHHHHHHHHHHHHHHHH---------HHHHHhhhcceecccCCeEEEE
Confidence 9999999999999999999999999999999999998877665433221 1245799999999999999999
Q ss_pred cchHHHHHHHHHH--HhcCChhHHHHHhhcChhHHHHHHHHH
Q 036979 158 PKFALVLLYSLLL--RLLLSTGALSRLILSDDSLRMAVNEFR 197 (212)
Q Consensus 158 ~~fp~~~~ldl~~--~lg~sts~l~k~l~~~~~~~~~vn~~r 197 (212)
| | .+.|+ |+|+++++|..||.++ +=.++..+.
T Consensus 313 ~--~----~~rV~DhRtg~~~~~l~~vl~G~--Ld~~I~~~l 346 (360)
T TIGR00019 313 F--P----QNRVTDHRINLTLYKLDEVLEGD--LDELIEALI 346 (360)
T ss_pred C--C----CCeeeeeccCCeEcChHHHhCCc--hHHHHHHHH
Confidence 7 6 78896 9999999999999886 444444443
No 3
>PRK08787 peptide chain release factor 2; Provisional
Probab=100.00 E-value=3.8e-44 Score=324.31 Aligned_cols=183 Identities=23% Similarity=0.234 Sum_probs=144.8
Q ss_pred ceeechhhhHhhhhhccccceeecCCccccc-----eeEeeeCCCCC-CCccccChhhhhccceEEEEeeCCCCCCCCCc
Q 036979 3 REFKNNKIITLLTCWTGLDWADWAGPSIRMG-----FHHCSCPASKK-KNYLELTDDELLRECEMHTYKSSGPGGQHRNK 76 (212)
Q Consensus 3 ~~~~g~~~~~~l~~e~Gvhrvqrvp~~~~~~-----~~~~s~~~~~~-~~~i~i~~~~L~~~~~i~~~RsSGPGGQ~VNK 76 (212)
+.|+|.++|++|++|+|||||||+|+++..+ |..+.+.|..+ ...+.|+++|| +|+|+||||||||||||
T Consensus 120 l~I~G~~ayg~lk~E~GvHRv~R~sp~~s~~rrhTsfasV~V~P~~~~~~~i~i~~~dl----~~~~~RssG~GGQ~VNk 195 (313)
T PRK08787 120 VRIEGEYAYGWLKTEIGVHRLVRKSPFDSDNRRHTSFTSVFVSPEVDDNIEIDINPADL----RTDVYRSSGAGGQHVNK 195 (313)
T ss_pred EEEecccHHHHHhhccCeeEEEecCCCCCCCCEEeeeEEEEEecCcCcccccccChhHe----EEEEEECCCCCCCCcCC
Confidence 5789999999999999999999999987544 44444555443 34678888888 99999999999999999
Q ss_pred cCceEEEEEecCCcEEEEcccccHHHHHHHHHHHHHHHHHHHHHhhhccCCCCChhhhhhcCCCCCcccCCCCCCCcCCC
Q 036979 77 CETAVRLKHVPTGVIAQAAEDRSQHKNRALALSRLPTFLALKVRSSVNLGAYSPPLQLLQILPPKSTIRSSEVGPQIGPN 156 (212)
Q Consensus 77 t~saVrl~HlPtGIvv~~~e~RSq~~Nk~~Al~~L~~~l~~~~~e~~~~~~~s~~~e~~q~~~rKsqir~~drs~qIRtY 156 (212)
|+|||||+|+||||+|+||++|||++||+.|+++|+++|.....++.+.+ .......|+++ .||+|||||
T Consensus 196 t~saVri~H~Ptgi~v~~q~eRSQ~~Nk~~A~~~L~~~L~~~~~e~~~~~-------~~~~~~~k~~i---~~g~qIRtY 265 (313)
T PRK08787 196 TESAVRITHIPTNTVVACQTGRSQHQNRDNAMKMLAAKLYELEVQKRNAE-------KDALEATKSDI---GWGSQIRNY 265 (313)
T ss_pred EeeEEEEEECCCcEEEEECCcccHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHhhhhhhC---cccccccce
Confidence 99999999999999999999999999999999999998876555443321 11112346665 588899999
Q ss_pred CcchHHHHHHHHHH--HhcCChhHHHHHhhcC-hhHHHHHHHHHHhcccccc
Q 036979 157 NPKFALVLLYSLLL--RLLLSTGALSRLILSD-DSLRMAVNEFRTSKCLMAY 205 (212)
Q Consensus 157 N~~fp~~~~ldl~~--~lg~sts~l~k~l~~~-~~~~~~vn~~r~~~gl~~~ 205 (212)
||. | +.|+ |+|+++++|..||.+| +.+-.++=..+.++|-|.|
T Consensus 266 ~f~-~-----~~V~DhRtg~~~~~l~~vldG~ld~fI~a~l~~~~~~~~~~~ 311 (313)
T PRK08787 266 VLD-Q-----SRIKDLRTGIERSDTQKVLDGDLDEFVEASLKAGLAAGSKRL 311 (313)
T ss_pred eCC-C-----CcceeeccCceEcChhHhhCCChHHHHHHHHHHHHhcccccc
Confidence 987 6 5676 9999999999999997 3344444445566665543
No 4
>PRK05589 peptide chain release factor 2; Provisional
Probab=100.00 E-value=2.8e-44 Score=326.73 Aligned_cols=173 Identities=24% Similarity=0.369 Sum_probs=141.2
Q ss_pred ceeechhhhHhhhhhccccceeecCCccccc-----eeEeeeCCCCC-CCccccChhhhhccceEEEEeeCCCCCCCCCc
Q 036979 3 REFKNNKIITLLTCWTGLDWADWAGPSIRMG-----FHHCSCPASKK-KNYLELTDDELLRECEMHTYKSSGPGGQHRNK 76 (212)
Q Consensus 3 ~~~~g~~~~~~l~~e~Gvhrvqrvp~~~~~~-----~~~~s~~~~~~-~~~i~i~~~~L~~~~~i~~~RsSGPGGQ~VNK 76 (212)
+.|+|.++|++|++|+|+|||||+|+++..+ |..+.+.|... ...+.|+++|| +|+++||||||||||||
T Consensus 140 ~~i~G~~ay~~lk~E~GvHrv~r~s~~~~~~rr~ts~a~V~VlP~~~~~~~~~i~~~dl----~~~~~rssG~GGQ~VNk 215 (325)
T PRK05589 140 LKITGEFAYGYLKAEKGIHRLVRISPFNANGKRQTSFASVEVLPELTDDQDIEIRSEDL----KIDTYRAGGAGGQHVNK 215 (325)
T ss_pred EEEeccCHHHHHhhccceEEEEEcCCCCCCCCeEeeeEEEEEecCcCccccccCCchhe----EEEEeeCCCCCCCcccc
Confidence 5789999999999999999999999997544 44444555553 34688888888 99999999999999999
Q ss_pred cCceEEEEEecCCcEEEEcccccHHHHHHHHHHHHHHHHHHHHHhhhccCCCCChhhhhhcCCCCCcccCCCCCCCcCCC
Q 036979 77 CETAVRLKHVPTGVIAQAAEDRSQHKNRALALSRLPTFLALKVRSSVNLGAYSPPLQLLQILPPKSTIRSSEVGPQIGPN 156 (212)
Q Consensus 77 t~saVrl~HlPtGIvv~~~e~RSq~~Nk~~Al~~L~~~l~~~~~e~~~~~~~s~~~e~~q~~~rKsqir~~drs~qIRtY 156 (212)
|+|||||+|+||||+|+|+++|||++||+.|+++|+++|.....++.+.+ ....+++....+||++||||
T Consensus 216 t~saVrl~H~ptgi~v~~q~eRSQ~~Nk~~A~~~L~~kL~~~~~~~~~~~----------~~~~r~~~~~~~~g~~IRtY 285 (325)
T PRK05589 216 TESAVRITHIPTGIVVQCQNERSQHSNKETAMKMLKSKLVELKERAHKEK----------IEDLTGELKDMGWGSQIRSY 285 (325)
T ss_pred eeeEEEEEECCCCEEEEECCccCHHHHHHHHHHHHHHHHHHHHHHHHHHH----------HHHHhcccccccccCCceee
Confidence 99999999999999999999999999999999999998876544433321 12234555556899999999
Q ss_pred CcchHHHHHHHHHH--HhcCChhHHHHHhhcChhHHHHHHHH
Q 036979 157 NPKFALVLLYSLLL--RLLLSTGALSRLILSDDSLRMAVNEF 196 (212)
Q Consensus 157 N~~fp~~~~ldl~~--~lg~sts~l~k~l~~~~~~~~~vn~~ 196 (212)
||. | +++|+ |+|+++++|..+|.++ +=.++..+
T Consensus 286 ~~~-p----~~rVtDhR~g~~~~~l~~vl~G~--Ld~~I~a~ 320 (325)
T PRK05589 286 VFH-P----YNLVKDHRTGVETSNVDSVMDGD--IDNFITQY 320 (325)
T ss_pred ECC-C----CceeeeeccCceecChHHhhCCC--HHHHHHHH
Confidence 985 6 88896 9999999999999887 44444443
No 5
>PRK06746 peptide chain release factor 2; Provisional
Probab=100.00 E-value=2.4e-44 Score=327.15 Aligned_cols=174 Identities=24% Similarity=0.307 Sum_probs=144.7
Q ss_pred ceeechhhhHhhhhhccccceeecCCccccc-----eeEeeeCCCC-CCCccccChhhhhccceEEEEeeCCCCCCCCCc
Q 036979 3 REFKNNKIITLLTCWTGLDWADWAGPSIRMG-----FHHCSCPASK-KKNYLELTDDELLRECEMHTYKSSGPGGQHRNK 76 (212)
Q Consensus 3 ~~~~g~~~~~~l~~e~Gvhrvqrvp~~~~~~-----~~~~s~~~~~-~~~~i~i~~~~L~~~~~i~~~RsSGPGGQ~VNK 76 (212)
+.|+|.++|++|++|+|||||||+|+++..+ |..|.+.|.. ....+.|+++|| +|+|+||||||||||||
T Consensus 141 l~i~G~~ay~~lk~E~GvHrv~Rvsp~~s~~rrhTsfa~V~v~P~~~~~~~i~i~~~dl----~~~~~rssG~GGQ~vNk 216 (326)
T PRK06746 141 LLIKGHNAYGYLKAEKGVHRLVRISPFDSSGRRHTSFVSCEVVPEFNDEVEIEVRTEDL----KIDTYRASGAGGQHVNT 216 (326)
T ss_pred EEEeccCHHHHHhhccceEEEEecCCCCCCCCeEeeEEEEEEecCcCCccccccChHHe----EEEEEeCCCCCCCCccc
Confidence 5789999999999999999999999998544 4444455554 356788888888 99999999999999999
Q ss_pred cCceEEEEEecCCcEEEEcccccHHHHHHHHHHHHHHHHHHHHHhhhccCCCCChhhhhhcCCCCCcccCCCCCCCcCCC
Q 036979 77 CETAVRLKHVPTGVIAQAAEDRSQHKNRALALSRLPTFLALKVRSSVNLGAYSPPLQLLQILPPKSTIRSSEVGPQIGPN 156 (212)
Q Consensus 77 t~saVrl~HlPtGIvv~~~e~RSq~~Nk~~Al~~L~~~l~~~~~e~~~~~~~s~~~e~~q~~~rKsqir~~drs~qIRtY 156 (212)
|+|||||+|+||||+|+||++|||++||+.|+++|+++|.....++.+.+ ....|++++.. +||++||||
T Consensus 217 t~saVrl~h~ptgi~v~~q~~RSQ~~Nk~~A~~~L~akL~~~~~~~~~~~---------~~~~r~~~~~~-~rg~~IRtY 286 (326)
T PRK06746 217 TDSAVRITHTPTNTVVTCQSERSQIKNREHAMKMLKAKLYQKKLEEQQAE---------LDEIRGEQKEI-GWGSQIRSY 286 (326)
T ss_pred eeeEEEEEEeCCeEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH---------HHHHHhhhccC-ccCCCeEEE
Confidence 99999999999999999999999999999999999998876655554321 12456777655 688999999
Q ss_pred CcchHHHHHHHHHH--HhcCChhHHHHHhhcChhHHHHHHHHH
Q 036979 157 NPKFALVLLYSLLL--RLLLSTGALSRLILSDDSLRMAVNEFR 197 (212)
Q Consensus 157 N~~fp~~~~ldl~~--~lg~sts~l~k~l~~~~~~~~~vn~~r 197 (212)
||. | +++|+ |+|+++++|..||.++ +=.++..+.
T Consensus 287 nf~-p----~~rVtDhR~~~~~~~l~~vl~G~--ld~~I~~~~ 322 (326)
T PRK06746 287 VFH-P----YSLVKDHRTNTEVGNVQAVMDGE--IDPFIDAYL 322 (326)
T ss_pred ECC-C----CceeeeeecCceecChHHhhCCC--HHHHHHHHH
Confidence 985 6 78886 9999999999999887 555555544
No 6
>PRK07342 peptide chain release factor 2; Provisional
Probab=100.00 E-value=7e-44 Score=325.55 Aligned_cols=175 Identities=26% Similarity=0.302 Sum_probs=142.2
Q ss_pred ceeechhhhHhhhhhccccceeecCCccccc-----eeEeeeCCCCCC-CccccChhhhhccceEEEEeeCCCCCCCCCc
Q 036979 3 REFKNNKIITLLTCWTGLDWADWAGPSIRMG-----FHHCSCPASKKK-NYLELTDDELLRECEMHTYKSSGPGGQHRNK 76 (212)
Q Consensus 3 ~~~~g~~~~~~l~~e~Gvhrvqrvp~~~~~~-----~~~~s~~~~~~~-~~i~i~~~~L~~~~~i~~~RsSGPGGQ~VNK 76 (212)
+.|+|.++|++|++|+|||||||+|+++..+ |..+.+.|.... ..+.|+++|| +|+++||||||||||||
T Consensus 143 l~i~G~~ay~~lk~E~GvHrv~rvsp~~~~~rrhTs~a~V~VlP~~~~~~~~~i~~~dl----~~~~~RssG~GGQ~VNk 218 (339)
T PRK07342 143 ILVKGHNAYGWLKTESGVHRLVRISPYDSNARRHTSFASIWVYPVIDDNIEVDVNESDV----RIDTYRSSGAGGQHVNT 218 (339)
T ss_pred EEEeccCHHHHHhhccceeEEEecCCCCCCCCeEeEEEEEEEEcCCCcccccccCcccE----EEEEEECCCCCCCCccc
Confidence 5799999999999999999999999998544 444445555543 3677887776 99999999999999999
Q ss_pred cCceEEEEEecCCcEEEEcccccHHHHHHHHHHHHHHHHHHHHHhhhccCCCCChhhhhhcCCCCCcccCCCCCCCcCCC
Q 036979 77 CETAVRLKHVPTGVIAQAAEDRSQHKNRALALSRLPTFLALKVRSSVNLGAYSPPLQLLQILPPKSTIRSSEVGPQIGPN 156 (212)
Q Consensus 77 t~saVrl~HlPtGIvv~~~e~RSq~~Nk~~Al~~L~~~l~~~~~e~~~~~~~s~~~e~~q~~~rKsqir~~drs~qIRtY 156 (212)
|+|||||+|+||||+|+|+++|||++||+.|+++|+++|.....++.+.+ ......+++++ .||++||||
T Consensus 219 t~saVrl~H~ptgi~v~~~~eRSQ~~Nk~~A~~~L~~~L~~~~~~~~~~~-------~~~~~~~~~~i---~~g~~IRtY 288 (339)
T PRK07342 219 TDSAVRITHIPTGIVVQCQQERSQHKNRAKAWSMLRARLYEEELKKREEA-------TNAAAASKTDI---GWGHQIRSY 288 (339)
T ss_pred eeeeEEEEEcCCcEEEEECCcccHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHhhhhhc---cccCCcCCc
Confidence 99999999999999999999999999999999999998876655544321 11112346666 578899999
Q ss_pred CcchHHHHHHHHHH--HhcCChhHHHHHhhcChhHHHHHHHHHH
Q 036979 157 NPKFALVLLYSLLL--RLLLSTGALSRLILSDDSLRMAVNEFRT 198 (212)
Q Consensus 157 N~~fp~~~~ldl~~--~lg~sts~l~k~l~~~~~~~~~vn~~r~ 198 (212)
||. | +++|+ |+|+++++|..||.++ +=.++..+..
T Consensus 289 ~~~-p----~~rVtDhRtg~~~~~l~~vl~G~--Ld~~I~a~l~ 325 (339)
T PRK07342 289 VLQ-P----YQLVKDLRTGVESTNPQDVLDGD--LNEFMEAALA 325 (339)
T ss_pred cCC-C----CceeeeeccCceecChHHhhCCC--HHHHHHHHHH
Confidence 986 7 89996 9999999999999987 5455555544
No 7
>PRK00591 prfA peptide chain release factor 1; Validated
Probab=100.00 E-value=3.9e-44 Score=329.41 Aligned_cols=174 Identities=24% Similarity=0.354 Sum_probs=146.7
Q ss_pred ceeechhhhHhhhhhccccceeecCCccc-----cceeEeeeCCCCCCCccccChhhhhccceEEEEeeCCCCCCCCCcc
Q 036979 3 REFKNNKIITLLTCWTGLDWADWAGPSIR-----MGFHHCSCPASKKKNYLELTDDELLRECEMHTYKSSGPGGQHRNKC 77 (212)
Q Consensus 3 ~~~~g~~~~~~l~~e~Gvhrvqrvp~~~~-----~~~~~~s~~~~~~~~~i~i~~~~L~~~~~i~~~RsSGPGGQ~VNKt 77 (212)
+.|+|.++|++|++|.|||||||+|+++. |+|..+.+.|......+.|++.|| +|+|+|||||||||||||
T Consensus 166 l~i~G~~ay~~Lk~E~GvHrv~R~p~~~s~~R~~tsfa~V~v~P~~~~~~~~i~~~dl----~~~~~RssG~GGQ~VNkt 241 (359)
T PRK00591 166 AEISGDGVYSKLKFESGVHRVQRVPATESQGRIHTSAATVAVLPEAEEVEVEINPKDL----RIDTFRSSGAGGQHVNTT 241 (359)
T ss_pred EEEecccHHHHHhhcCeeEEEEeeCCCCCCCceecceEEEEEEcCCCccccccCcccE----EEEEEECCCCCCCCccce
Confidence 57899999999999999999999999975 445455566666555778887777 999999999999999999
Q ss_pred CceEEEEEecCCcEEEEcccccHHHHHHHHHHHHHHHHHHHHHhhhccCCCCChhhhhhcCCCCCcccCCCCCCCcCCCC
Q 036979 78 ETAVRLKHVPTGVIAQAAEDRSQHKNRALALSRLPTFLALKVRSSVNLGAYSPPLQLLQILPPKSTIRSSEVGPQIGPNN 157 (212)
Q Consensus 78 ~saVrl~HlPtGIvv~~~e~RSq~~Nk~~Al~~L~~~l~~~~~e~~~~~~~s~~~e~~q~~~rKsqir~~drs~qIRtYN 157 (212)
+|||||+|+||||+|+|+++|||++||+.|+++|+++|.....++.+.+ ....+++++++++||++|||||
T Consensus 242 ~saVrl~H~ptGi~v~~~~eRSQ~~Nk~~Al~~L~~~L~~~~~~~~~~~---------~~~~r~~~~~~~~Rse~IRtY~ 312 (359)
T PRK00591 242 DSAVRITHLPTGIVVECQDERSQHKNKAKAMKVLRARLYDAERQKAQAE---------EAATRKSQVGSGDRSERIRTYN 312 (359)
T ss_pred eeeEEEEECCCcEEEEECCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHH---------HHHHHHhhcccccccCCeeeEE
Confidence 9999999999999999999999999999999999998877666554431 1235689999999999999999
Q ss_pred cchHHHHHHHHHH--HhcCChhHHHHHhhcChhHHHHHHHHH
Q 036979 158 PKFALVLLYSLLL--RLLLSTGALSRLILSDDSLRMAVNEFR 197 (212)
Q Consensus 158 ~~fp~~~~ldl~~--~lg~sts~l~k~l~~~~~~~~~vn~~r 197 (212)
| | -+.|+ |+|+++++|..||.++ +=.++..+.
T Consensus 313 f--~----~~~V~DhRtg~~~~~l~~vl~G~--Ld~fI~~~l 346 (359)
T PRK00591 313 F--P----QGRVTDHRINLTLYKLDEVMEGD--LDELIDALI 346 (359)
T ss_pred C--C----CCeeeeeccCCEEcChHHHhCCC--hHHHHHHHH
Confidence 7 4 47786 9999999999999886 444444443
No 8
>KOG2726 consensus Mitochondrial polypeptide chain release factor [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.7e-43 Score=323.88 Aligned_cols=165 Identities=30% Similarity=0.412 Sum_probs=140.6
Q ss_pred ceeechhhhHhhhhhccccceeecCCcccccee-----EeeeCCCC--CCCccccChhhhhccceEEEEeeCCCCCCCCC
Q 036979 3 REFKNNKIITLLTCWTGLDWADWAGPSIRMGFH-----HCSCPASK--KKNYLELTDDELLRECEMHTYKSSGPGGQHRN 75 (212)
Q Consensus 3 ~~~~g~~~~~~l~~e~Gvhrvqrvp~~~~~~~~-----~~s~~~~~--~~~~i~i~~~~L~~~~~i~~~RsSGPGGQ~VN 75 (212)
++|.|+++|++|++|.|||||||+|.++..|+. .++|.|.+ ....+.+++.|| +|+++|+|||||||||
T Consensus 191 ~~i~G~~ayg~l~~E~GvHRv~r~p~~e~~gr~htstasV~ViP~~~~~~~~~~~~~~dl----~i~~~R~~G~GGQhvN 266 (386)
T KOG2726|consen 191 LEIEGESAYGYLKFEAGVHRVQRVPSTETSGRRHTSTASVAVIPQPGRDEVDVEIDEKDL----RIETFRASGPGGQHVN 266 (386)
T ss_pred eEecccchhheeeccCcccceeecCCcccccccccccceEEEeccCCCCccceecCchhe----eEEecccCCCCccccc
Confidence 689999999999999999999999999754443 44466655 455666776666 9999999999999999
Q ss_pred ccCceEEEEEecCCcEEEEcccccHHHHHHHHHHHHHHHHHHHHHhhhccCCCCChhhhhhcCCCCCcccCCCCCCCcCC
Q 036979 76 KCETAVRLKHVPTGVIAQAAEDRSQHKNRALALSRLPTFLALKVRSSVNLGAYSPPLQLLQILPPKSTIRSSEVGPQIGP 155 (212)
Q Consensus 76 Kt~saVrl~HlPtGIvv~~~e~RSq~~Nk~~Al~~L~~~l~~~~~e~~~~~~~s~~~e~~q~~~rKsqir~~drs~qIRt 155 (212)
||+|||||+|+||||+|+||++|||++||+.|+.+|+++|+....++...+. ...++.++++.+|+++|||
T Consensus 267 ktdsaVrl~HiPTGIvv~cq~eRSq~~Nr~~A~~~L~akL~~~~~~~~~~~~---------~~~r~~qv~s~~rsekiRT 337 (386)
T KOG2726|consen 267 KTDSAVRLTHIPTGIVVECQEERSQHKNRALALKRLRAKLAVIYREEKSEEE---------KKKRKAQVGSLKRSEKIRT 337 (386)
T ss_pred ccccceEEEeecCceEEEeecHHhHHhhHHHHHHHHHHHHHHHHHhhhhHHh---------hhhhHHhhcccCchhceee
Confidence 9999999999999999999999999999999999999999888777765422 2568999999999999999
Q ss_pred CCcchHHHHHHHHH-HHhcCChhHHHHHhhc
Q 036979 156 NNPKFALVLLYSLL-LRLLLSTGALSRLILS 185 (212)
Q Consensus 156 YN~~fp~~~~ldl~-~~lg~sts~l~k~l~~ 185 (212)
|||. + .-+. -++|++..++.-||.+
T Consensus 338 y~~~-q----~rv~D~r~~~~~~d~~~~l~G 363 (386)
T KOG2726|consen 338 YNFK-Q----DRVTDHRIGLESHDLESFLDG 363 (386)
T ss_pred cccC-c----cchhhhhhcccccchHHHHhc
Confidence 9987 4 3333 3888888888888877
No 9
>TIGR00020 prfB peptide chain release factor 2. In many but not all taxa, there is a conserved real translational frameshift at a TGA codon. RF-2 helps terminate translation at TGA codons and can therefore regulate its own production by readthrough when RF-2 is insufficient. There is a Pfam model called "RF-1" for the superfamily of RF-1, RF-2, mitochondrial, RF-H, etc.
Probab=100.00 E-value=3.4e-43 Score=323.66 Aligned_cols=174 Identities=26% Similarity=0.325 Sum_probs=140.8
Q ss_pred ceeechhhhHhhhhhccccceeecCCccccc-----eeEeeeCCCC-CCCccccChhhhhccceEEEEeeCCCCCCCCCc
Q 036979 3 REFKNNKIITLLTCWTGLDWADWAGPSIRMG-----FHHCSCPASK-KKNYLELTDDELLRECEMHTYKSSGPGGQHRNK 76 (212)
Q Consensus 3 ~~~~g~~~~~~l~~e~Gvhrvqrvp~~~~~~-----~~~~s~~~~~-~~~~i~i~~~~L~~~~~i~~~RsSGPGGQ~VNK 76 (212)
+.|+|.++|++|++|+|||||||+|+++..+ |..+.+.|.. +...+.|++.|| +|+++||||||||||||
T Consensus 179 ~~i~G~~ay~~lk~E~GvHrv~rvs~~~~~~rrhts~a~V~vlP~~~~~~~~~i~~~d~----~~~~~rssG~GGQ~VNk 254 (364)
T TIGR00020 179 ILIKGPYAYGYLKSEQGVHRLVRISPFDANGRRHTSFASVFVMPEVDDDIDIEIKPEDL----RIDTYRASGAGGQHVNK 254 (364)
T ss_pred EEEeccCHHHHHhhccceEEEEecCCCCCCCCeEeeeEEEEEecCCCcccceecccccE----EEEEeeCCCCCCccccc
Confidence 5789999999999999999999999997544 4444455544 455678887777 99999999999999999
Q ss_pred cCceEEEEEecCCcEEEEcccccHHHHHHHHHHHHHHHHHHHHHhhhccCCCCChhhhhhcCCCCCcccCCCCCCCcCCC
Q 036979 77 CETAVRLKHVPTGVIAQAAEDRSQHKNRALALSRLPTFLALKVRSSVNLGAYSPPLQLLQILPPKSTIRSSEVGPQIGPN 156 (212)
Q Consensus 77 t~saVrl~HlPtGIvv~~~e~RSq~~Nk~~Al~~L~~~l~~~~~e~~~~~~~s~~~e~~q~~~rKsqir~~drs~qIRtY 156 (212)
|+|||||+|+||||+|+|+++|||++||+.||++|+++|.....++.+.+ . ...|+++ ...+||++||||
T Consensus 255 t~saVri~H~ptgi~v~~q~~RSQ~~Nk~~A~~~L~~kL~~~~~~~~~~~-------~--~~~r~~~-~~~~rg~~IRtY 324 (364)
T TIGR00020 255 TDSAVRITHIPTGIVVQCQNDRSQHKNKDSAMKVLKAKLYELEMEKEQAE-------K--DAKEGEK-SEIGWGSQIRSY 324 (364)
T ss_pred cceEEEEEECCCcEEEEECCccCHHHHHHHHHHHHHHHHHHHHHHHHHHH-------H--HHHHhhh-hccCccCCeEEE
Confidence 99999999999999999999999999999999999998876655544321 1 1233233 333799999999
Q ss_pred CcchHHHHHHHHHH--HhcCChhHHHHHhhcChhHHHHHHHHH
Q 036979 157 NPKFALVLLYSLLL--RLLLSTGALSRLILSDDSLRMAVNEFR 197 (212)
Q Consensus 157 N~~fp~~~~ldl~~--~lg~sts~l~k~l~~~~~~~~~vn~~r 197 (212)
||. | ++.|+ |+|+++++|..||.++ +=.+++.+.
T Consensus 325 ~~~-~----~~rVtDhR~g~~~~~l~~vl~G~--Ld~~I~a~~ 360 (364)
T TIGR00020 325 VLH-P----YSMVKDLRTGYETGNVQAVLDGD--IDQFIEAYL 360 (364)
T ss_pred ECC-C----CCcccccccCCeecChHHHhCCC--hHHHHHHHH
Confidence 985 5 78885 9999999999999886 555555554
No 10
>PRK00578 prfB peptide chain release factor 2; Validated
Probab=100.00 E-value=5.2e-43 Score=322.76 Aligned_cols=175 Identities=26% Similarity=0.309 Sum_probs=142.4
Q ss_pred ceeechhhhHhhhhhccccceeecCCcccccee-----EeeeCCCCCC-CccccChhhhhccceEEEEeeCCCCCCCCCc
Q 036979 3 REFKNNKIITLLTCWTGLDWADWAGPSIRMGFH-----HCSCPASKKK-NYLELTDDELLRECEMHTYKSSGPGGQHRNK 76 (212)
Q Consensus 3 ~~~~g~~~~~~l~~e~Gvhrvqrvp~~~~~~~~-----~~s~~~~~~~-~~i~i~~~~L~~~~~i~~~RsSGPGGQ~VNK 76 (212)
+.|+|.++|++|++|+|||||||+|+++..+.. .+.+.|.... ..+.|+++|| +|+|+||||||||||||
T Consensus 179 ~~i~G~~a~~~lk~E~GvHrvqrvs~~~~~~r~hts~~~V~vlP~~~~~~~~~i~~~dl----~~~~~rssGpGGQ~vNk 254 (367)
T PRK00578 179 FKIKGPYAYGYLKSETGVHRLVRISPFDSAGRRHTSFASVEVYPEVDDTIEIEINPKDL----RIDTYRSSGAGGQHVNK 254 (367)
T ss_pred EEEeccCHHHHHhhccceEEEEecCCCCCCCceecceeeEEecCCCCCccccccChhhE----EEEEeeCCCCCCCcccc
Confidence 578999999999999999999999999864444 4445555543 3678888777 99999999999999999
Q ss_pred cCceEEEEEecCCcEEEEcccccHHHHHHHHHHHHHHHHHHHHHhhhccCCCCChhhhhhcCCCCCcccCCCCCCCcCCC
Q 036979 77 CETAVRLKHVPTGVIAQAAEDRSQHKNRALALSRLPTFLALKVRSSVNLGAYSPPLQLLQILPPKSTIRSSEVGPQIGPN 156 (212)
Q Consensus 77 t~saVrl~HlPtGIvv~~~e~RSq~~Nk~~Al~~L~~~l~~~~~e~~~~~~~s~~~e~~q~~~rKsqir~~drs~qIRtY 156 (212)
|+|||||+|+||||+|+|+++|||++||+.|+++|+++|.....++.+.+ . ...|+.+ ...+||++||||
T Consensus 255 t~saVrl~h~ptgi~v~~~~~RSQ~~Nk~~A~~~L~~kL~~~~~~~~~~~-------~--~~~r~~~-~~~~rg~~IRtY 324 (367)
T PRK00578 255 TDSAVRITHIPTGIVVQCQNERSQHQNKASAMKMLKAKLYELELEKRAAE-------K--DALKGEK-KEIGWGSQIRSY 324 (367)
T ss_pred eeeEEEEEECCCcEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-------H--HHHHhhh-ccccccCCeEEE
Confidence 99999999999999999999999999999999999998877655554321 1 1233333 455899999999
Q ss_pred CcchHHHHHHHHHH--HhcCChhHHHHHhhcChhHHHHHHHHHH
Q 036979 157 NPKFALVLLYSLLL--RLLLSTGALSRLILSDDSLRMAVNEFRT 198 (212)
Q Consensus 157 N~~fp~~~~ldl~~--~lg~sts~l~k~l~~~~~~~~~vn~~r~ 198 (212)
||. | ++.|+ |+|++..+|..||.++ +=.++..+..
T Consensus 325 n~~-p----~~rVtDhR~g~~~~~l~~vl~G~--ld~~I~~l~~ 361 (367)
T PRK00578 325 VLH-P----YQMVKDLRTGYETGNTQAVLDGD--LDGFIEAYLR 361 (367)
T ss_pred ECC-C----CceeeeeccCceecCHHHhhCCC--hHHHHHHHHH
Confidence 985 5 78885 9999999999999886 5555555443
No 11
>TIGR03072 release_prfH putative peptide chain release factor H. Members of this protein family are bacterial proteins homologous to peptide chain release factors 1 (RF-1, product of the prfA gene), and 2 (RF-2, product of the prfB gene). The member from Escherichia coli K-12, designated prfH, appears to be a pseudogene. This class I release factor is always found as the downstream gene of a two-gene operon.
Probab=100.00 E-value=9.7e-39 Score=274.04 Aligned_cols=138 Identities=27% Similarity=0.293 Sum_probs=111.8
Q ss_pred ceeechhhhHhhhhhccccceeec-CCccccc----eeEeeeCCCCCCCccccChhhhhccceEEEEeeCCCCCCCCCcc
Q 036979 3 REFKNNKIITLLTCWTGLDWADWA-GPSIRMG----FHHCSCPASKKKNYLELTDDELLRECEMHTYKSSGPGGQHRNKC 77 (212)
Q Consensus 3 ~~~~g~~~~~~l~~e~Gvhrvqrv-p~~~~~~----~~~~s~~~~~~~~~i~i~~~~L~~~~~i~~~RsSGPGGQ~VNKt 77 (212)
++|+|+++|++|+.|.|+|+.++. |....++ |..+.+.| ..++|+++|| +|+|+|||||||||||||
T Consensus 55 ~~i~G~~ay~~l~~~~G~h~~v~~sp~r~~~~R~ts~~~V~v~~----~~~~i~~~dl----~~~~~RssGpGGQ~vNkt 126 (200)
T TIGR03072 55 VSLDGEAAAALADRWEGTLLWICPSPYRPHHRRKNWFIGVQRFS----ASEEATEDEI----RFETLRSSGPGGQHVNKT 126 (200)
T ss_pred EEEEccCHHHHhhcccceEEEEEcCCCCCCCCeeEEEEEEEEec----CccccChhhe----EEEEEECCCCCccccccc
Confidence 679999999999888888754444 5443333 34444443 3456777777 999999999999999999
Q ss_pred CceEEEEEecCCcEEEEcccccHHHHHHHHHHHHHHHHHHHHHhhhccCCCCChhhhhhcCCCCCcccCCCCCCCcCCCC
Q 036979 78 ETAVRLKHVPTGVIAQAAEDRSQHKNRALALSRLPTFLALKVRSSVNLGAYSPPLQLLQILPPKSTIRSSEVGPQIGPNN 157 (212)
Q Consensus 78 ~saVrl~HlPtGIvv~~~e~RSq~~Nk~~Al~~L~~~l~~~~~e~~~~~~~s~~~e~~q~~~rKsqir~~drs~qIRtYN 157 (212)
+|||+|+|+||||+|+|+++|||++||+.|+++|+++|.....++.+. +...++++..+.+||++|||||
T Consensus 127 ~saVrl~h~ptgi~v~~~~~RSQ~~Nk~~A~~~L~~~l~~~~~~~~~~----------~~~~~r~~~~~~~Rg~~iRty~ 196 (200)
T TIGR03072 127 ESAVRATHLASGISVKVQSERSQHANKRLATLLLAVRLADLQQEQAAA----------LRAERRTAHHQIERGNPVRVFK 196 (200)
T ss_pred ceeEEEEECCCcEEEEECCccCHHHHHHHHHHHHHHHHHHHHHHHHHH----------HHHHHHhccccccccCceEeee
Confidence 999999999999999999999999999999999999988765555432 1345777888889999999999
Q ss_pred c
Q 036979 158 P 158 (212)
Q Consensus 158 ~ 158 (212)
.
T Consensus 197 ~ 197 (200)
T TIGR03072 197 G 197 (200)
T ss_pred C
Confidence 4
No 12
>PRK08179 prfH peptide chain release factor-like protein; Reviewed
Probab=100.00 E-value=1.1e-37 Score=267.54 Aligned_cols=139 Identities=24% Similarity=0.277 Sum_probs=109.8
Q ss_pred ceeechhhhHhhhhhcccc-ceeecCCccccceeEee--eCCCCCCCccccChhhhhccceEEEEeeCCCCCCCCCccCc
Q 036979 3 REFKNNKIITLLTCWTGLD-WADWAGPSIRMGFHHCS--CPASKKKNYLELTDDELLRECEMHTYKSSGPGGQHRNKCET 79 (212)
Q Consensus 3 ~~~~g~~~~~~l~~e~Gvh-rvqrvp~~~~~~~~~~s--~~~~~~~~~i~i~~~~L~~~~~i~~~RsSGPGGQ~VNKt~s 79 (212)
++|+|+++|++|+.|.|+| |||+.|.....++++.+ |.+. +..+.|+++|| +|+|+|||||||||||||+|
T Consensus 56 ~~i~G~~a~~~l~~~~G~~~~V~~sp~~~~~~R~~s~~~V~v~--~~~~~i~~~dl----~~~~~RssGpGGQ~VNkt~s 129 (200)
T PRK08179 56 VSLDGDNAEALAESWCGTIQWICPSPYRPHHGRKNWFVGIGRF--SADEEEQSDEI----RFETLRSSGPGGQHVNKTDS 129 (200)
T ss_pred EEEEccCHHHHhhcccCeeEEEecCCCCCCCCceEEEEEEEEe--CCcCccCHHHe----EEEEEEccCCcccccccccc
Confidence 5789999999999666654 55555555444433332 2222 23457888877 99999999999999999999
Q ss_pred eEEEEEecCCcEEEEcccccHHHHHHHHHHHHHHHHHHHHHhhhccCCCCChhhhhhcCCCCCcccCCCCCCCcCCCC
Q 036979 80 AVRLKHVPTGVIAQAAEDRSQHKNRALALSRLPTFLALKVRSSVNLGAYSPPLQLLQILPPKSTIRSSEVGPQIGPNN 157 (212)
Q Consensus 80 aVrl~HlPtGIvv~~~e~RSq~~Nk~~Al~~L~~~l~~~~~e~~~~~~~s~~~e~~q~~~rKsqir~~drs~qIRtYN 157 (212)
||+|+|+||||+|+|+++|||++||+.|+++|+++|.....++.+. +...++++..+.+||++||||-
T Consensus 130 aVrl~h~ptgi~v~~~~~RSQ~~Nk~~A~~~L~~~L~~~~~~~~~~----------~~~~~~~~~~~~~Rg~~IRt~~ 197 (200)
T PRK08179 130 AVRATHLASGISVKVQSERSQHANKRLARLLIAWKLEQQQQEQSAA----------LKSQRRMFHHQIERGNPRRVFT 197 (200)
T ss_pred eEEEEEcCCcEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH----------HHHHHHhccccccccCceEeee
Confidence 9999999999999999999999999999999999888765555432 1345677778889999999984
No 13
>COG1186 PrfB Protein chain release factor B [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.6e-36 Score=262.53 Aligned_cols=170 Identities=28% Similarity=0.323 Sum_probs=137.7
Q ss_pred ceeechhhhHhhhhhccccceeecCCccccceeE-----eeeCCCC-CCCccccChhhhhccceEEEEeeCCCCCCCCCc
Q 036979 3 REFKNNKIITLLTCWTGLDWADWAGPSIRMGFHH-----CSCPASK-KKNYLELTDDELLRECEMHTYKSSGPGGQHRNK 76 (212)
Q Consensus 3 ~~~~g~~~~~~l~~e~Gvhrvqrvp~~~~~~~~~-----~s~~~~~-~~~~i~i~~~~L~~~~~i~~~RsSGPGGQ~VNK 76 (212)
+.|+|.+.|++|+.|.||||.-|+.|.+..+.-| +.++|.. ....+.|+++|| +|+|+||||||||||||
T Consensus 54 ~~~~g~~a~g~~~~e~g~hrlvr~Spf~~~~~R~tsf~~v~v~p~~~~~i~i~I~~~dl----~idt~RASGaGGQhVNK 129 (239)
T COG1186 54 LKIKGENAYGYLKTETGVHRLVRISPFDSNGRRHTSFASVEVFPELDISIEIEIPDDDL----RIDTYRASGAGGQHVNK 129 (239)
T ss_pred EEEechHHHHHHHhhcceeEEEeecCCCcCcccccceeeeeecCCCCcccceecCccce----EEEEEEcCCCCCCcccc
Confidence 5689999999999999999999998887544333 3344443 555888888888 99999999999999999
Q ss_pred cCceEEEEEecCCcEEEEcccccHHHHHHHHHHHHHHHHHHHHHhhhccCCCCChhhhhhcCCCCCcccCCCCCCCcCCC
Q 036979 77 CETAVRLKHVPTGVIAQAAEDRSQHKNRALALSRLPTFLALKVRSSVNLGAYSPPLQLLQILPPKSTIRSSEVGPQIGPN 156 (212)
Q Consensus 77 t~saVrl~HlPtGIvv~~~e~RSq~~Nk~~Al~~L~~~l~~~~~e~~~~~~~s~~~e~~q~~~rKsqir~~drs~qIRtY 156 (212)
|+|||||||+||||+|.||.+|||++|++.|+..|+..|.....+..+. |.++....+..+ +|+.|||+|
T Consensus 130 t~SAVrlth~ptgivv~cq~eRSq~~n~~~a~~~l~~kL~~~~~~~Rsq-------e~n~~~a~~k~i---~wg~qirsy 199 (239)
T COG1186 130 TDSAVRLTHLPTGIVVLCQNERSQHLNKALARKMLKGKLYILAQEKRSQ-------EKNRERALKKLI---GWGNQIRSY 199 (239)
T ss_pred ccccEEEEEcCCCCEecCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHhhhH---HHHHhcccc
Confidence 9999999999999999999999999999999999999665443333221 122233334444 899999999
Q ss_pred CcchHHHHHHHHHH--HhcCChhHHHHHhhcChhHHH
Q 036979 157 NPKFALVLLYSLLL--RLLLSTGALSRLILSDDSLRM 191 (212)
Q Consensus 157 N~~fp~~~~ldl~~--~lg~sts~l~k~l~~~~~~~~ 191 (212)
.++ | +..+| +++.++++..++++++-..|.
T Consensus 200 v~~-p----~~~vKd~Rt~~E~~~~~~v~dg~~~~~~ 231 (239)
T COG1186 200 VLD-P----YQPTKDLRTGVERRNKSKVLDGDKDGFI 231 (239)
T ss_pred CCC-c----cccccccccceeeccHHHhhhhhHHHHH
Confidence 998 7 77785 999999999999999666553
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=99.97 E-value=1.4e-31 Score=210.46 Aligned_cols=101 Identities=35% Similarity=0.495 Sum_probs=87.5
Q ss_pred CCccccChhhhhccceEEEEeeCCCCCCCCCccCceEEEEEecCCcEEEEcccccHHHHHHHHHHHHHHHHHHHHHhhhc
Q 036979 45 KNYLELTDDELLRECEMHTYKSSGPGGQHRNKCETAVRLKHVPTGVIAQAAEDRSQHKNRALALSRLPTFLALKVRSSVN 124 (212)
Q Consensus 45 ~~~i~i~~~~L~~~~~i~~~RsSGPGGQ~VNKt~saVrl~HlPtGIvv~~~e~RSq~~Nk~~Al~~L~~~l~~~~~e~~~ 124 (212)
...+.|+++|| +|+|+|||||||||||||+|+|+|+|+||||+|+|+++|||++|++.|+++|+++|..+..++..
T Consensus 4 ~~~~~i~~~dl----~~~~~RssGpGGQ~VNk~~s~V~l~h~ptgi~v~~~~~Rsq~~Nr~~A~~~L~~~l~~~~~~~~~ 79 (113)
T PF00472_consen 4 EKEIDIPEKDL----EISFSRSSGPGGQNVNKTNSKVRLRHIPTGIVVKCQESRSQHQNREDALEKLREKLDEAYREKRR 79 (113)
T ss_dssp SSSSCC-GGGE----EEEEEESSSSSSCHHHSSSEEEEEEETTTTEEEEEESSSSHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred ccccccCHHHe----EEEEEecCCCCCCcccccCCEEEEEEecccEEEEEcccCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44678888887 99999999999999999999999999999999999999999999999999999999888754433
Q ss_pred cCCCCChhhhhhcCCCCCcccCCCCCCCcCCCCc
Q 036979 125 LGAYSPPLQLLQILPPKSTIRSSEVGPQIGPNNP 158 (212)
Q Consensus 125 ~~~~s~~~e~~q~~~rKsqir~~drs~qIRtYN~ 158 (212)
.+ ....++++.+..+++++||+||+
T Consensus 80 ~~---------~~~~~~~~~~~~~~~~~iR~y~~ 104 (113)
T PF00472_consen 80 EK---------TREIRKSQVKRLERKKKIRTYNF 104 (113)
T ss_dssp HH---------TTTTTTTSCCCSSTTSEEEEEET
T ss_pred HH---------HHHHHHHHHhHHhhhcceecccC
Confidence 21 12457788888899999999997
No 15
>PRK09256 hypothetical protein; Provisional
Probab=99.89 E-value=4e-23 Score=168.65 Aligned_cols=73 Identities=40% Similarity=0.621 Sum_probs=65.5
Q ss_pred CccccChhhhhccceEEEEeeCCCCCCCCCccCceEEEEE------ec-----------------CC-cEEEEcccccHH
Q 036979 46 NYLELTDDELLRECEMHTYKSSGPGGQHRNKCETAVRLKH------VP-----------------TG-VIAQAAEDRSQH 101 (212)
Q Consensus 46 ~~i~i~~~~L~~~~~i~~~RsSGPGGQ~VNKt~saVrl~H------lP-----------------tG-Ivv~~~e~RSq~ 101 (212)
+.+.|+.++| +++|+|||||||||||||+|+|+|+| +| +| |+|+|+++|||+
T Consensus 6 ~~~~i~~~~l----~~~~~RSSGPGGQ~VNKt~SkV~l~~~~~~~~lp~~~~~~l~~~~~~r~~~~g~l~i~~~~~RSQ~ 81 (138)
T PRK09256 6 RRLVIPENEL----EWRFIRASGPGGQNVNKVSTAVELRFDIAASSLPEFYKERLLALAGHRITKDGVIVIKAQEFRSQE 81 (138)
T ss_pred ccCccCHHHe----EEEEEEcCCCCcccccccceeeEEEechhhccCCHHHHHHHHHHhcCcccCCCcEEEEECCcCCHH
Confidence 3567887777 99999999999999999999999996 77 36 999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHhh
Q 036979 102 KNRALALSRLPTFLALKVRSS 122 (212)
Q Consensus 102 ~Nk~~Al~~L~~~l~~~~~e~ 122 (212)
+|++.|+++|.++|..+...+
T Consensus 82 ~Nr~~al~kL~~~i~~~~~~p 102 (138)
T PRK09256 82 RNREDALERLVALIREALKPP 102 (138)
T ss_pred HHHHHHHHHHHHHHHHHhhcc
Confidence 999999999999998877643
No 16
>KOG3429 consensus Predicted peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis]
Probab=99.72 E-value=7.8e-18 Score=141.20 Aligned_cols=70 Identities=36% Similarity=0.577 Sum_probs=61.5
Q ss_pred ccChhhhhccceEEEEeeCCCCCCCCCccCceEEEEE-------ec-----------------CC-cEEEEcccccHHHH
Q 036979 49 ELTDDELLRECEMHTYKSSGPGGQHRNKCETAVRLKH-------VP-----------------TG-VIAQAAEDRSQHKN 103 (212)
Q Consensus 49 ~i~~~~L~~~~~i~~~RsSGPGGQ~VNKt~saVrl~H-------lP-----------------tG-Ivv~~~e~RSq~~N 103 (212)
.||.+.+ ++.|.||||||||||||++|+|.|++ || .| |+|.++.+|||+.|
T Consensus 36 ~ipld~~----~i~y~RSSGPGGQNVNKvNTKv~vrf~vs~a~Wipe~~R~~~~~~~~~rink~gelvI~Sd~TRsq~~N 111 (172)
T KOG3429|consen 36 KIPLDQL----EISYSRSSGPGGQNVNKVNTKVEVRFKVSNAEWIPEFLRNKLLTTEKNRINKDGELVIYSDKTRSQHKN 111 (172)
T ss_pred CCchhhe----EEEEeecCCCCCcccccccceEEEEEecchhhhccHHHHHHHHHHHHHhhccCccEEEecchhHHhhcc
Confidence 3565666 99999999999999999999999994 55 25 99999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhh
Q 036979 104 RALALSRLPTFLALKVRSS 122 (212)
Q Consensus 104 k~~Al~~L~~~l~~~~~e~ 122 (212)
.++|+++|+++|..+...+
T Consensus 112 iaDcleKlr~~I~~~~~~~ 130 (172)
T KOG3429|consen 112 IADCLEKLRDIIRAAEQTP 130 (172)
T ss_pred HHHHHHHHHHHHHHHhcCC
Confidence 9999999999998876654
No 17
>PF10213 MRP-S28: Mitochondrial ribosomal subunit protein ; InterPro: IPR019349 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents a conserved region of approx. 125 residues of one of the proteins that makes up the small subunit of the mitochondrial ribosome. In Saccharomyces cerevisiae (Baker's yeast) it is mitochondrial ribosomal protein S24 whereas in humans it is S35.
Probab=61.14 E-value=61 Score=26.30 Aligned_cols=34 Identities=9% Similarity=0.031 Sum_probs=31.1
Q ss_pred CC-cEEEEcccccHHHHHHHHHHHHHHHHHHHHHh
Q 036979 88 TG-VIAQAAEDRSQHKNRALALSRLPTFLALKVRS 121 (212)
Q Consensus 88 tG-Ivv~~~e~RSq~~Nk~~Al~~L~~~l~~~~~e 121 (212)
+| |.++|...-++.+|+.-|...|..++.++.+.
T Consensus 60 ~d~l~i~sdr~~~~~qN~~~l~~~l~~L~~EA~~~ 94 (127)
T PF10213_consen 60 TDILKISSDRFPTRAQNKKYLSDLLTRLIHEAKDL 94 (127)
T ss_pred CCEEEEecccCCCHHHHHHHHHHHHHHHHHHHhhc
Confidence 67 88999999999999999999999999988774
No 18
>cd02164 PPAT_CoAS phosphopantetheine adenylyltransferase domain of eukaryotic and archaeal bifunctional enzymes. The PPAT domain of the bifunctional enzyme with PPAT and DPCK functions. The final two steps of the CoA biosynthesis pathway are catalyzed by phosphopantetheine adenylyltransferase (PPAT) and dephospho-CoA (dPCoA) kinase (DPCK). The PPAT reaction involves the reversible adenylation of 4'-phosphopantetheine to form 3'-dPCoA and PPi, and DPCK catalyses phosphorylation of the 3'-hydroxy group of the ribose moiety of dPCoA. In eukaryotes the two enzymes are part of a large multienzyme complex . Studies in Corynebacterium ammoniagenes suggested that separate enzymes were present, and this was confirmed through identification of the bacterial PPAT/CoAD.
Probab=60.78 E-value=5.3 Score=32.67 Aligned_cols=17 Identities=18% Similarity=0.167 Sum_probs=14.8
Q ss_pred HHHHHHHHHhccccccc
Q 036979 190 RMAVNEFRTSKCLMAYF 206 (212)
Q Consensus 190 ~~~vn~~r~~~gl~~~~ 206 (212)
..++|+.|.++||+||-
T Consensus 103 ~~~iN~~R~~~gl~pl~ 119 (143)
T cd02164 103 ALKINRKREENGLSPLE 119 (143)
T ss_pred HHHHHHHHHHCCCCcee
Confidence 46799999999999973
No 19
>PF07035 Mic1: Colon cancer-associated protein Mic1-like; InterPro: IPR009755 This entry represents the C terminus (approximately 160 residues) of a number of proteins that resemble colon cancer-associated protein Mic1.
Probab=56.20 E-value=21 Score=30.26 Aligned_cols=43 Identities=16% Similarity=0.162 Sum_probs=36.0
Q ss_pred hHHHHH--HHHHHHhcCChhHHHHHhhcChhHHHHHHHHHHhccc
Q 036979 160 FALVLL--YSLLLRLLLSTGALSRLILSDDSLRMAVNEFRTSKCL 202 (212)
Q Consensus 160 fp~~~~--ldl~~~lg~sts~l~k~l~~~~~~~~~vn~~r~~~gl 202 (212)
+|.+.+ +|+++||+.....++.+|.++-....|+.=.|..++.
T Consensus 74 ~~~~~Ql~lDMLkRL~~~~~~iievLL~~g~vl~ALr~ar~~~~~ 118 (167)
T PF07035_consen 74 YPPAYQLGLDMLKRLGTAYEEIIEVLLSKGQVLEALRYARQYHKV 118 (167)
T ss_pred ChHHHHHHHHHHHHhhhhHHHHHHHHHhCCCHHHHHHHHHHcCCc
Confidence 455555 9999999999999999999999888888888876554
No 20
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=51.89 E-value=40 Score=22.65 Aligned_cols=36 Identities=14% Similarity=0.063 Sum_probs=25.4
Q ss_pred HHHHHhcCChhHHHHHhhcChh----HHHHHHHHHHhccc
Q 036979 167 SLLLRLLLSTGALSRLILSDDS----LRMAVNEFRTSKCL 202 (212)
Q Consensus 167 dl~~~lg~sts~l~k~l~~~~~----~~~~vn~~r~~~gl 202 (212)
|+-+.+|+|++.++++|...+. .+..|.+.=.+.|-
T Consensus 4 dIA~~agvS~~TVSr~ln~~~~vs~~tr~rI~~~a~~lgY 43 (46)
T PF00356_consen 4 DIAREAGVSKSTVSRVLNGPPRVSEETRERILEAAEELGY 43 (46)
T ss_dssp HHHHHHTSSHHHHHHHHTTCSSSTHHHHHHHHHHHHHHTB
T ss_pred HHHHHHCcCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHCC
Confidence 5668999999999999998653 44455544444443
No 21
>PF14974 DUF4511: Domain of unknown function (DUF4511)
Probab=47.95 E-value=14 Score=29.55 Aligned_cols=83 Identities=11% Similarity=0.085 Sum_probs=51.4
Q ss_pred HHHHHHHHHHHHHHHHHHhhhccCCCCChhhhhhcCCCCCcccCCCCCCCcCCCCcchHHHHH--HHHHHHhcCChh---
Q 036979 103 NRALALSRLPTFLALKVRSSVNLGAYSPPLQLLQILPPKSTIRSSEVGPQIGPNNPKFALVLL--YSLLLRLLLSTG--- 177 (212)
Q Consensus 103 Nk~~Al~~L~~~l~~~~~e~~~~~~~s~~~e~~q~~~rKsqir~~drs~qIRtYN~~fp~~~~--ldl~~~lg~sts--- 177 (212)
+++.|-..|.+.|+..-..+.. ++...-|+..+ +|.... -++-||..++ .+++++.|.+-+
T Consensus 3 t~e~ak~~l~eil~a~~~peN~----------~kl~eAk~~ag-ndm~k~---mq~v~Pva~qiq~~VIk~yGF~~~~eG 68 (105)
T PF14974_consen 3 TKEQAKAILTEILDAFNQPENA----------AKLEEAKANAG-NDMLKM---MQFVFPVATQIQMEVIKKYGFPESREG 68 (105)
T ss_pred CHHHHHHHHHHHHHHHcCchHH----------HHHHHHHHhcc-chHHHH---HHHHHHHHHHHHHHHHHHcCCCCCcch
Confidence 4667777777777654333221 11122233332 233222 2667898887 899999998863
Q ss_pred -----HHHHHh-hcChhHHHHHHHHHHh
Q 036979 178 -----ALSRLI-LSDDSLRMAVNEFRTS 199 (212)
Q Consensus 178 -----~l~k~l-~~~~~~~~~vn~~r~~ 199 (212)
++++-+ +.||.+.++-+++|+-
T Consensus 69 ~~~f~~~i~~~e~~D~eva~l~~~iRs~ 96 (105)
T PF14974_consen 69 VMQFAQLIRELEKDDPEVARLHSQIRSL 96 (105)
T ss_pred HHHHHHHHHHHHccCHHHHHHHHHHHHH
Confidence 456666 7888888888888864
No 22
>PLN02388 phosphopantetheine adenylyltransferase
Probab=47.80 E-value=11 Score=32.22 Aligned_cols=27 Identities=26% Similarity=0.480 Sum_probs=19.6
Q ss_pred HHHHhhcChhH--HHHHHHHHHhcccccc
Q 036979 179 LSRLILSDDSL--RMAVNEFRTSKCLMAY 205 (212)
Q Consensus 179 l~k~l~~~~~~--~~~vn~~r~~~gl~~~ 205 (212)
+..++-|.-++ ...+|+.|.++||+||
T Consensus 110 ~d~LVVS~ET~~g~~~IN~~R~e~Gl~pL 138 (177)
T PLN02388 110 LEAIVVSKETLPGGLSVNKKRAERGLSQL 138 (177)
T ss_pred CCEEEEcHhHhhhHHHHHHHHHHCCCCCe
Confidence 44455555444 3579999999999997
No 23
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=47.54 E-value=25 Score=26.22 Aligned_cols=44 Identities=11% Similarity=-0.008 Sum_probs=34.6
Q ss_pred HHHHHhcCChhHHHHHhhcC--hhHHHHHHHHHHhcccccccccCC
Q 036979 167 SLLLRLLLSTGALSRLILSD--DSLRMAVNEFRTSKCLMAYFNSNL 210 (212)
Q Consensus 167 dl~~~lg~sts~l~k~l~~~--~~~~~~vn~~r~~~gl~~~~~~~~ 210 (212)
|+.+.+|+|...|.++++.. -+....++++|.++....|-+++.
T Consensus 26 ~lA~~~~~S~~~l~r~f~~~~g~s~~~~i~~~Rl~~a~~~L~~~~~ 71 (107)
T PRK10219 26 VVAKKSGYSKWYLQRMFRTVTHQTLGDYIRQRRLLLAAVELRTTER 71 (107)
T ss_pred HHHHHHCCCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHccCC
Confidence 44579999999999999874 667788899998887777766554
No 24
>PRK13502 transcriptional activator RhaR; Provisional
Probab=46.50 E-value=23 Score=30.51 Aligned_cols=42 Identities=12% Similarity=0.042 Sum_probs=38.3
Q ss_pred HHhcCChhHHHHHhhc--ChhHHHHHHHHHHhcccccccccCCC
Q 036979 170 LRLLLSTGALSRLILS--DDSLRMAVNEFRTSKCLMAYFNSNLP 211 (212)
Q Consensus 170 ~~lg~sts~l~k~l~~--~~~~~~~vn~~r~~~gl~~~~~~~~~ 211 (212)
+.+|+|++-|.+++++ .-+.-..+++.|-++-...|-++++|
T Consensus 200 ~~~~iS~~~L~r~fk~~~G~t~~~yi~~~Rl~~A~~lL~~t~~s 243 (282)
T PRK13502 200 QQEQCSERVLRQQFRAQTGMTINQYLRQVRICHAQYLLQHSPLM 243 (282)
T ss_pred HHHCcCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHcCCCC
Confidence 6899999999999997 78999999999999999888888765
No 25
>PRK13503 transcriptional activator RhaS; Provisional
Probab=40.13 E-value=29 Score=29.62 Aligned_cols=42 Identities=19% Similarity=0.108 Sum_probs=36.7
Q ss_pred HHhcCChhHHHHHhhcC--hhHHHHHHHHHHhcccccccccCCC
Q 036979 170 LRLLLSTGALSRLILSD--DSLRMAVNEFRTSKCLMAYFNSNLP 211 (212)
Q Consensus 170 ~~lg~sts~l~k~l~~~--~~~~~~vn~~r~~~gl~~~~~~~~~ 211 (212)
+.+|+|++.|.+++++. -+...-+|+.|-.+-...|-+++++
T Consensus 195 ~~~~lS~~~l~r~Fk~~~G~S~~~yi~~~Rl~~A~~LL~~~~~s 238 (278)
T PRK13503 195 DQFSLSLRTLHRQLKQQTGLTPQRYLNRLRLLKARHLLRHSDAS 238 (278)
T ss_pred HHHCCCHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHHHcCCCC
Confidence 79999999999999875 6888999999999888888777654
No 26
>COG3077 RelB DNA-damage-inducible protein J [DNA replication, recombination, and repair]
Probab=40.04 E-value=29 Score=26.90 Aligned_cols=20 Identities=20% Similarity=0.240 Sum_probs=17.7
Q ss_pred HHHHHHHhcCChhHHHHHhh
Q 036979 165 LYSLLLRLLLSTGALSRLIL 184 (212)
Q Consensus 165 ~ldl~~~lg~sts~l~k~l~ 184 (212)
++++++.+|+++|+.++++.
T Consensus 19 A~~Vl~~mGlt~S~airm~L 38 (88)
T COG3077 19 ATAVLEEMGLTISDAIRMFL 38 (88)
T ss_pred HHHHHHHhCCCHHHHHHHHH
Confidence 38999999999999999864
No 27
>COG1019 Predicted nucleotidyltransferase [General function prediction only]
Probab=38.92 E-value=18 Score=30.87 Aligned_cols=17 Identities=24% Similarity=0.329 Sum_probs=14.5
Q ss_pred HHHHHHHHHhccccccc
Q 036979 190 RMAVNEFRTSKCLMAYF 206 (212)
Q Consensus 190 ~~~vn~~r~~~gl~~~~ 206 (212)
...+|+.|.++||+||-
T Consensus 106 Al~IN~~R~~~Gl~pL~ 122 (158)
T COG1019 106 ALKINEIREKRGLPPLE 122 (158)
T ss_pred HHHHHHHHHHCCCCCeE
Confidence 34699999999999983
No 28
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=36.70 E-value=39 Score=30.20 Aligned_cols=42 Identities=5% Similarity=0.069 Sum_probs=36.6
Q ss_pred HHhcCChhHHHHHhhc--ChhHHHHHHHHHHhcccccccccCCC
Q 036979 170 LRLLLSTGALSRLILS--DDSLRMAVNEFRTSKCLMAYFNSNLP 211 (212)
Q Consensus 170 ~~lg~sts~l~k~l~~--~~~~~~~vn~~r~~~gl~~~~~~~~~ 211 (212)
..+|+|.+.|.++++. .-+....+|++|-++-...|-+++.+
T Consensus 215 ~~~~~S~~~l~r~Fk~~~G~t~~~~l~~~Rl~~A~~lL~~~~~s 258 (302)
T PRK10371 215 EHVKLNANYAMGIFQRVMQLTMKQYITAMRINHVRALLSDTDKS 258 (302)
T ss_pred HHHCcCHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHhcCCCC
Confidence 6999999999999998 57899999999999988888776543
No 29
>PF12623 Hen1_L: RNA repair, ligase-Pnkp-associating, region of Hen1; InterPro: IPR024740 This entry represents the N-terminal domain of the bacterial Hen1 protein, which is a 3' terminal RNA ribose 2'-O-methyltransferase that is involved in bacterial RNA repair []. Hen1 forms a heterotetramer with Pnkp. The heterotetramer has been shown to repair transfer RNAs cleaved by ribotoxins in vitro []. The N-terminal domain of Hen1 contributes to the ligase activity of the heterotetramer.
Probab=33.81 E-value=33 Score=31.11 Aligned_cols=50 Identities=22% Similarity=0.242 Sum_probs=32.2
Q ss_pred cceeecCCccccceeEeeeCCCCCCC-----ccccChhhhhccceEEEEeeC-CC---C---CCCCCccCce
Q 036979 21 DWADWAGPSIRMGFHHCSCPASKKKN-----YLELTDDELLRECEMHTYKSS-GP---G---GQHRNKCETA 80 (212)
Q Consensus 21 hrvqrvp~~~~~~~~~~s~~~~~~~~-----~i~i~~~~L~~~~~i~~~RsS-GP---G---GQ~VNKt~sa 80 (212)
+|||.++.+ .|+.|++-|+..... .+++++-+| .|++ |+ + +|.||...-+
T Consensus 24 dr~q~f~~~--~G~AhVfYPeat~erCtaaLlldvDpv~L--------vR~~~g~~~~~~~L~qYVNDRPYa 85 (245)
T PF12623_consen 24 DRVQSFDLS--FGTAHVFYPEATDERCTAALLLDVDPVAL--------VRGRRGSSADDFALAQYVNDRPYA 85 (245)
T ss_pred ccceeeecC--CceEEEEcccCChhHEEEEEEEecCcHHh--------ccCCCCCCCCCcccccccccchhH
Confidence 578877655 678888877765533 456777777 4533 22 2 8999975443
No 30
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=33.53 E-value=49 Score=28.68 Aligned_cols=42 Identities=19% Similarity=0.207 Sum_probs=36.5
Q ss_pred HHhcCChhHHHHHhhcC--hhHHHHHHHHHHhcccccccccCCC
Q 036979 170 LRLLLSTGALSRLILSD--DSLRMAVNEFRTSKCLMAYFNSNLP 211 (212)
Q Consensus 170 ~~lg~sts~l~k~l~~~--~~~~~~vn~~r~~~gl~~~~~~~~~ 211 (212)
+.+|+|++.|.|+++.. -+....+|+.|-.+-...|-.+++|
T Consensus 207 ~~~~lS~~~l~r~Fk~~~G~tp~~~l~~~Rl~~A~~lL~~t~~s 250 (290)
T PRK10572 207 QHVCLSPSRLAHLFRQQLGISVLRWREDQRISRAKLLLQTTRMP 250 (290)
T ss_pred HHHCCCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHcCCCC
Confidence 69999999999999985 6788899999999988888777664
No 31
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=33.49 E-value=50 Score=22.16 Aligned_cols=41 Identities=17% Similarity=0.152 Sum_probs=29.1
Q ss_pred HHHHHhcCChhHHHHHhhcC--hhHHHHHHHHHHhcccccccc
Q 036979 167 SLLLRLLLSTGALSRLILSD--DSLRMAVNEFRTSKCLMAYFN 207 (212)
Q Consensus 167 dl~~~lg~sts~l~k~l~~~--~~~~~~vn~~r~~~gl~~~~~ 207 (212)
++.+.+|+|.+.|.++++.. .+....++..|..+-+.-|.+
T Consensus 6 ~la~~~~~s~~~l~~~f~~~~~~s~~~~~~~~r~~~a~~~l~~ 48 (84)
T smart00342 6 DLAEALGMSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRD 48 (84)
T ss_pred HHHHHhCCCHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHHHc
Confidence 44479999999999999854 356667777777665555443
No 32
>TIGR02297 HpaA 4-hydroxyphenylacetate catabolism regulatory protein HpaA. This putative transcriptional regulator, which contains both the substrate-binding, dimerization domain (pfam02311) and the helix-turn-helix DNA-binding domain (pfam00165) of the AraC famil, is located proximal to genes of the 4-hydroxyphenylacetate catabolism pathway.
Probab=33.42 E-value=49 Score=28.41 Aligned_cols=42 Identities=14% Similarity=-0.007 Sum_probs=35.5
Q ss_pred HHhcCChhHHHHHhhc--ChhHHHHHHHHHHhcccccccccCCC
Q 036979 170 LRLLLSTGALSRLILS--DDSLRMAVNEFRTSKCLMAYFNSNLP 211 (212)
Q Consensus 170 ~~lg~sts~l~k~l~~--~~~~~~~vn~~r~~~gl~~~~~~~~~ 211 (212)
+.+|+|++.|.|+++. .-+....+++.|-++-...|-++++|
T Consensus 210 ~~~~~S~~~l~r~Fk~~~G~t~~~yi~~~Rl~~A~~lL~~t~~s 253 (287)
T TIGR02297 210 DRLGISESRLNDICRRFSALSPKRLIIERVMQEARRLLLFTQHS 253 (287)
T ss_pred HHHCCCHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHcCCCC
Confidence 6999999999999998 45788889999988887777777765
No 33
>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=32.53 E-value=81 Score=26.10 Aligned_cols=39 Identities=23% Similarity=0.370 Sum_probs=30.6
Q ss_pred EEEEeeCCCCCCCCCccCceEEEEEecCCcEEEEccccc
Q 036979 61 MHTYKSSGPGGQHRNKCETAVRLKHVPTGVIAQAAEDRS 99 (212)
Q Consensus 61 i~~~RsSGPGGQ~VNKt~saVrl~HlPtGIvv~~~e~RS 99 (212)
++..-..|.++..+=..+|.|||+|..||..+.+++.+.
T Consensus 121 ~~~~~~~~~~~~~~~~~~s~frL~H~~t~~~L~~~~~~l 159 (190)
T PF02815_consen 121 FEEKSSTGMGEDEIKTLDSYFRLRHVATGCWLHSHDVKL 159 (190)
T ss_dssp EEEEESSSCSSSSBBBTTSEEEEEETTTTEEEEEEEEES
T ss_pred EEecccCCccCCcEEecccEEEEEECCcCEEEecCCccc
Confidence 444556677788888889999999999998887776554
No 34
>PRK13500 transcriptional activator RhaR; Provisional
Probab=32.34 E-value=51 Score=29.41 Aligned_cols=42 Identities=12% Similarity=0.031 Sum_probs=38.1
Q ss_pred HHhcCChhHHHHHhhc--ChhHHHHHHHHHHhcccccccccCCC
Q 036979 170 LRLLLSTGALSRLILS--DDSLRMAVNEFRTSKCLMAYFNSNLP 211 (212)
Q Consensus 170 ~~lg~sts~l~k~l~~--~~~~~~~vn~~r~~~gl~~~~~~~~~ 211 (212)
+.+|+|++.|.++++. .-+...-+++.|-.+....|-+++++
T Consensus 230 ~~~~iS~~~L~r~FK~~tG~T~~~yi~~~RL~~A~~LL~~t~~s 273 (312)
T PRK13500 230 DEASCSERVLRQQFRQQTGMTINQYLRQVRVCHAQYLLQHSRLL 273 (312)
T ss_pred HHHCcCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHcCCCC
Confidence 6999999999999997 58999999999999999888888765
No 35
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=31.17 E-value=53 Score=25.68 Aligned_cols=44 Identities=18% Similarity=0.084 Sum_probs=29.3
Q ss_pred HHHHHhcCChhHHHHHhhcC--hhHHHHHHHHHHhcccccccccCC
Q 036979 167 SLLLRLLLSTGALSRLILSD--DSLRMAVNEFRTSKCLMAYFNSNL 210 (212)
Q Consensus 167 dl~~~lg~sts~l~k~l~~~--~~~~~~vn~~r~~~gl~~~~~~~~ 210 (212)
|+.+.+|+|+..|.++++.. -+....++..|.+.-...|.++++
T Consensus 30 ~lA~~~g~S~~~l~r~Fk~~~G~s~~~~l~~~Rl~~A~~~L~~t~~ 75 (127)
T PRK11511 30 KVSERSGYSKWHLQRMFKKETGHSLGQYIRSRKMTEIAQKLKESNE 75 (127)
T ss_pred HHHHHHCcCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHcCCC
Confidence 33468899999998888876 456667777776544444444443
No 36
>PF02787 CPSase_L_D3: Carbamoyl-phosphate synthetase large chain, oligomerisation domain; InterPro: IPR005480 Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates [, ]. CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate []. The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC). Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain []. CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites []. The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain. Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein []. The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP []. There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia []. CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains []. This entry represents the oligomerisation domain found in the large subunit of carbamoyl phosphate synthases as well as in certain other carboxy phsophate domain-containing enzymes.; GO: 0006807 nitrogen compound metabolic process; PDB: 1M6V_C 1CS0_C 1C30_E 1C3O_G 1BXR_A 1T36_E 1A9X_A 1KEE_G 1CE8_A 1JDB_H ....
Probab=29.95 E-value=70 Score=25.61 Aligned_cols=36 Identities=22% Similarity=0.307 Sum_probs=25.6
Q ss_pred HHHhcCChhHHHHHhhcChhHHHHHHHHHHhcccccccc
Q 036979 169 LLRLLLSTGALSRLILSDDSLRMAVNEFRTSKCLMAYFN 207 (212)
Q Consensus 169 ~~~lg~sts~l~k~l~~~~~~~~~vn~~r~~~gl~~~~~ 207 (212)
.|++|.|-.++.++...+. ..|-++|.+.|+.|-|.
T Consensus 68 aK~~GFsD~~IA~l~~~~e---~~vr~~R~~~~i~p~yk 103 (123)
T PF02787_consen 68 AKRLGFSDRQIARLWGVSE---EEVRELRKEHGIVPVYK 103 (123)
T ss_dssp HHHTT--HHHHHHHHTS-H---HHHHHHHHHHT---EEE
T ss_pred HHHcCCCHHHHHhccCCCH---HHHHHHHHHcCCceeee
Confidence 3899999999999997765 46889999999999874
No 37
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=29.86 E-value=1.2e+02 Score=19.41 Aligned_cols=21 Identities=14% Similarity=0.150 Sum_probs=17.7
Q ss_pred HHHHHhcCChhHHHHHhhcCh
Q 036979 167 SLLLRLLLSTGALSRLILSDD 187 (212)
Q Consensus 167 dl~~~lg~sts~l~k~l~~~~ 187 (212)
|+-+++|+|.+.+++++...+
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 345789999999999999874
No 38
>PRK10296 DNA-binding transcriptional regulator ChbR; Provisional
Probab=29.09 E-value=53 Score=28.27 Aligned_cols=43 Identities=16% Similarity=-0.021 Sum_probs=37.3
Q ss_pred HHHhcCChhHHHHHhhcC--hhHHHHHHHHHHhcccccccccCCC
Q 036979 169 LLRLLLSTGALSRLILSD--DSLRMAVNEFRTSKCLMAYFNSNLP 211 (212)
Q Consensus 169 ~~~lg~sts~l~k~l~~~--~~~~~~vn~~r~~~gl~~~~~~~~~ 211 (212)
...+|+|+..|.++++.. -+.-..+|+.|-.+-...|-++|++
T Consensus 195 A~~~~~s~~~l~r~fk~~~G~t~~~yi~~~Rl~~A~~lL~~t~~s 239 (278)
T PRK10296 195 VRLSGKSQEYLTRATRRYYGKTPMQIINEIRINFAKKQLEMTNYS 239 (278)
T ss_pred HHHhCCCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHcCCCC
Confidence 358899999999999987 8889999999999988888888765
No 39
>PF12833 HTH_18: Helix-turn-helix domain; PDB: 2K9S_A 3LSG_C 3OIO_A 1D5Y_B 3GBG_A 3OOU_A 1BL0_A 1XS9_A 3MN2_B 3MKL_B ....
Probab=26.14 E-value=68 Score=22.39 Aligned_cols=37 Identities=22% Similarity=0.157 Sum_probs=24.1
Q ss_pred HHhcCChhHHHHHhhc--ChhHHHHHHHHHHhccccccc
Q 036979 170 LRLLLSTGALSRLILS--DDSLRMAVNEFRTSKCLMAYF 206 (212)
Q Consensus 170 ~~lg~sts~l~k~l~~--~~~~~~~vn~~r~~~gl~~~~ 206 (212)
+.+|+|.+.|.++++. ..+....+++.|...-+..|.
T Consensus 3 ~~~~~s~~~l~~~f~~~~g~s~~~~~~~~R~~~a~~~L~ 41 (81)
T PF12833_consen 3 DELGMSERYLSRIFKKETGMSFKQYLRELRLQRAKELLR 41 (81)
T ss_dssp HHCTS-HHHHHHHHHHHHSS-HHHHHHHHHHHHHHHHHH
T ss_pred HHhCcCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4677788888877776 556666777777766665553
No 40
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=26.13 E-value=54 Score=23.59 Aligned_cols=20 Identities=15% Similarity=0.101 Sum_probs=15.8
Q ss_pred HHHHHHhcCChhHHHHHhhc
Q 036979 166 YSLLLRLLLSTGALSRLILS 185 (212)
Q Consensus 166 ldl~~~lg~sts~l~k~l~~ 185 (212)
-++.+.+|+|++.++||.++
T Consensus 38 ~elA~~~~vS~sti~Rf~kk 57 (77)
T PF01418_consen 38 SELAEKAGVSPSTIVRFCKK 57 (77)
T ss_dssp HHHHHHCTS-HHHHHHHHHH
T ss_pred HHHHHHcCCCHHHHHHHHHH
Confidence 45558999999999999874
No 41
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=25.74 E-value=1.6e+02 Score=20.65 Aligned_cols=22 Identities=14% Similarity=0.140 Sum_probs=18.7
Q ss_pred HHHHHhcCChhHHHHHhhcChh
Q 036979 167 SLLLRLLLSTGALSRLILSDDS 188 (212)
Q Consensus 167 dl~~~lg~sts~l~k~l~~~~~ 188 (212)
|+-+++|+|.+.++++|...+.
T Consensus 5 ~iA~~~gvS~~TVSr~ln~~~~ 26 (70)
T smart00354 5 DVARLAGVSKATVSRVLNGNGR 26 (70)
T ss_pred HHHHHHCCCHHHHHHHHCCCCC
Confidence 5668999999999999988764
No 42
>COG2207 AraC AraC-type DNA-binding domain-containing proteins [Transcription]
Probab=25.72 E-value=98 Score=22.41 Aligned_cols=44 Identities=25% Similarity=0.261 Sum_probs=33.1
Q ss_pred HHHHHhcCChhHHHHHhhcC--hhHHHHHHHHHHhcccccccccCC
Q 036979 167 SLLLRLLLSTGALSRLILSD--DSLRMAVNEFRTSKCLMAYFNSNL 210 (212)
Q Consensus 167 dl~~~lg~sts~l~k~l~~~--~~~~~~vn~~r~~~gl~~~~~~~~ 210 (212)
++...+|+|.+.|.+.++.. -+....+++.|-......|-+++.
T Consensus 41 ~la~~~g~S~~~l~r~f~~~~g~s~~~~~~~~Rl~~A~~lL~~~~~ 86 (127)
T COG2207 41 DLARRLGMSRRTLSRLFKKETGTSPSQYLRQLRLEEARRLLRSTDL 86 (127)
T ss_pred HHHHHHCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHcCCC
Confidence 33469999999999999843 344468899998888777766654
No 43
>PRK13501 transcriptional activator RhaR; Provisional
Probab=25.29 E-value=80 Score=27.45 Aligned_cols=42 Identities=14% Similarity=0.079 Sum_probs=37.0
Q ss_pred HHhcCChhHHHHHhhcC--hhHHHHHHHHHHhcccccccccCCC
Q 036979 170 LRLLLSTGALSRLILSD--DSLRMAVNEFRTSKCLMAYFNSNLP 211 (212)
Q Consensus 170 ~~lg~sts~l~k~l~~~--~~~~~~vn~~r~~~gl~~~~~~~~~ 211 (212)
+.+|+|++.|.+++++. -+....+|+.|-.+-...|-++++|
T Consensus 200 ~~~~lS~~~l~r~Fk~~~G~T~~qyi~~~Ri~~A~~LL~~t~~s 243 (290)
T PRK13501 200 HKNQLVERSLKQLFRQQTGMSISHYLRQIRLCHAKCLLRGSEHR 243 (290)
T ss_pred HHHCcCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHcCCCC
Confidence 69999999999999974 5788999999999988888888765
No 44
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=24.87 E-value=73 Score=21.40 Aligned_cols=29 Identities=21% Similarity=0.334 Sum_probs=18.6
Q ss_pred CCCCCCCCCc--cCceEEEEEec----CC-cEEEEc
Q 036979 67 SGPGGQHRNK--CETAVRLKHVP----TG-VIAQAA 95 (212)
Q Consensus 67 SGPGGQ~VNK--t~saVrl~HlP----tG-Ivv~~~ 95 (212)
=|+||.++++ .++.|.|..-+ .+ +.+...
T Consensus 15 IG~~G~~i~~i~~~~g~~I~i~~~~~~~~~v~I~G~ 50 (62)
T cd02394 15 IGKKGSNIRKIMEETGVKIRFPDPGSKSDTITITGP 50 (62)
T ss_pred cCCCCCcHHHHHHHhCCEEEcCCCCCCCCEEEEEcC
Confidence 3899999995 34677766544 34 445444
No 45
>smart00472 MIR Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases.
Probab=24.02 E-value=83 Score=20.76 Aligned_cols=23 Identities=35% Similarity=0.518 Sum_probs=18.2
Q ss_pred cCceEEEEEecCCcEEEEccccc
Q 036979 77 CETAVRLKHVPTGVIAQAAEDRS 99 (212)
Q Consensus 77 t~saVrl~HlPtGIvv~~~e~RS 99 (212)
..+.|||+|.-||--+.+++.+.
T Consensus 6 ~g~~vrL~H~~tg~yL~s~~~~~ 28 (57)
T smart00472 6 WGDVVRLRHVTTGRYLHSHENKL 28 (57)
T ss_pred cCCEEEEEEhhhCcEeecCCCCC
Confidence 35899999999997777777653
No 46
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=23.86 E-value=83 Score=20.31 Aligned_cols=27 Identities=33% Similarity=0.348 Sum_probs=21.9
Q ss_pred HHHHHhcCChhHHHHHhhcChhHHHHH
Q 036979 167 SLLLRLLLSTGALSRLILSDDSLRMAV 193 (212)
Q Consensus 167 dl~~~lg~sts~l~k~l~~~~~~~~~v 193 (212)
|+.+++|+|.+.+-+-+.+-+.++.+|
T Consensus 21 ~Ia~~~gvs~~~~y~~f~~k~~l~~a~ 47 (47)
T PF00440_consen 21 DIARRAGVSKGSFYRYFPSKDDLLRAV 47 (47)
T ss_dssp HHHHHHTSCHHHHHHHCSSHHHHHHHH
T ss_pred HHHHHHccchhhHHHHcCCHHHHHhhC
Confidence 444799999999999988888777654
No 47
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=23.82 E-value=87 Score=27.87 Aligned_cols=42 Identities=14% Similarity=-0.020 Sum_probs=36.4
Q ss_pred HHhcCChhHHHHHhhcC--hhHHHHHHHHHHhcccccccccCCC
Q 036979 170 LRLLLSTGALSRLILSD--DSLRMAVNEFRTSKCLMAYFNSNLP 211 (212)
Q Consensus 170 ~~lg~sts~l~k~l~~~--~~~~~~vn~~r~~~gl~~~~~~~~~ 211 (212)
+.+|+|.+.|.++++.. -+....+++.|-++-...|.++++|
T Consensus 242 ~~~~~S~~~l~r~fk~~~g~s~~~~~~~~Rl~~A~~lL~~~~~~ 285 (322)
T PRK09393 242 ARAAMSPRTFLRRFEAATGMTPAEWLLRERLARARDLLESSALS 285 (322)
T ss_pred HHHCcCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHcCCCC
Confidence 69999999999999984 6778999999999988888777665
No 48
>COG2340 Uncharacterized protein with SCP/PR1 domains [Function unknown]
Probab=23.26 E-value=55 Score=28.00 Aligned_cols=27 Identities=15% Similarity=0.060 Sum_probs=21.9
Q ss_pred HhhcChhHHHHHHHHHHhccccccccc
Q 036979 182 LILSDDSLRMAVNEFRTSKCLMAYFNS 208 (212)
Q Consensus 182 ~l~~~~~~~~~vn~~r~~~gl~~~~~~ 208 (212)
+-.....+...+|+.|+.+||.||-.+
T Consensus 77 ~~~~~~~~~~~~N~~R~~~~l~~L~~n 103 (207)
T COG2340 77 LAQFEKAVVAETNQERAKHGLPPLAWN 103 (207)
T ss_pred cchhHHHHHHHHHHHHhhcCCCCcccC
Confidence 445566789999999999999998643
No 49
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=23.26 E-value=81 Score=25.57 Aligned_cols=23 Identities=22% Similarity=0.293 Sum_probs=20.6
Q ss_pred HHHHHHhcCChhHHHHHhhcChh
Q 036979 166 YSLLLRLLLSTGALSRLILSDDS 188 (212)
Q Consensus 166 ldl~~~lg~sts~l~k~l~~~~~ 188 (212)
+++.+.||+|.+||++-|+++..
T Consensus 26 ~~iA~LLGltqaAVS~Yls~krg 48 (119)
T COG2522 26 YRIAKLLGLTQAAVSQYLSGKRG 48 (119)
T ss_pred HHHHHHhCCCHHHHHHHHccCCc
Confidence 66778999999999999999876
No 50
>PRK15186 AraC family transcriptional regulator; Provisional
Probab=22.32 E-value=95 Score=28.18 Aligned_cols=46 Identities=20% Similarity=0.138 Sum_probs=35.9
Q ss_pred HHHH-HHhcCChhHHHHHhhcC-hhHHHHHHHHHHhcccccccccCCC
Q 036979 166 YSLL-LRLLLSTGALSRLILSD-DSLRMAVNEFRTSKCLMAYFNSNLP 211 (212)
Q Consensus 166 ldl~-~~lg~sts~l~k~l~~~-~~~~~~vn~~r~~~gl~~~~~~~~~ 211 (212)
++.+ +.+|+|.+.|.+.++.. -+....+++.|-.+.+..|-+++.|
T Consensus 200 l~~lA~~~gmS~stl~R~Fk~~g~s~~~~~~~~Rl~~A~~lL~~~~~s 247 (291)
T PRK15186 200 LKDISDSLYMSCSTLKRKLKQENTSFSEVYLNARMNKATKLLRNSEYN 247 (291)
T ss_pred HHHHHHHHCcCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHcCCCC
Confidence 4444 69999999999999986 4455567889999888888776654
No 51
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=21.71 E-value=86 Score=19.68 Aligned_cols=19 Identities=21% Similarity=0.170 Sum_probs=14.4
Q ss_pred HHHHHhcCChhHHHHHhhc
Q 036979 167 SLLLRLLLSTGALSRLILS 185 (212)
Q Consensus 167 dl~~~lg~sts~l~k~l~~ 185 (212)
|+...+|+|.+.+.|+++.
T Consensus 13 ~iA~~~g~S~~~f~r~Fk~ 31 (42)
T PF00165_consen 13 DIAEQAGFSPSYFSRLFKK 31 (42)
T ss_dssp HHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHCCCHHHHHHHHHH
Confidence 4447999999999998865
No 52
>PRK07394 hypothetical protein; Provisional
Probab=20.63 E-value=1.3e+02 Score=28.02 Aligned_cols=43 Identities=12% Similarity=-0.021 Sum_probs=33.8
Q ss_pred HHHHHHhcC-----ChhHHHHHhhcC----------hhHHHHHHHHHHhccccccccc
Q 036979 166 YSLLLRLLL-----STGALSRLILSD----------DSLRMAVNEFRTSKCLMAYFNS 208 (212)
Q Consensus 166 ldl~~~lg~-----sts~l~k~l~~~----------~~~~~~vn~~r~~~gl~~~~~~ 208 (212)
-|+++.||+ ++.++.+.|... -++++.+-..|.+-|++.+||.
T Consensus 132 aDvLe~LGv~~~~~~~~~~~~~l~~~g~~Fl~ap~~hP~m~~~~~vR~~Lg~RT~fN~ 189 (342)
T PRK07394 132 VELWQGLGVDLTGLSLEQVQEGFEQTGLAFIYQPDHFPLAESLIPYRDEIGKRPPLAT 189 (342)
T ss_pred HHHHHHCCCCCCCCCHHHHHHHHHHcCceeeechhhCHHHHHHHHHHHHhCCCCHHHH
Confidence 477789997 667788888873 2345678889999999999984
Done!