Query 030302
Match_columns 179
No_of_seqs 140 out of 245
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 11:40:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030302.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030302hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3344 40s ribosomal protein 100.0 4.5E-74 9.9E-79 460.6 11.1 148 1-165 1-149 (150)
2 PTZ00034 40S ribosomal protein 100.0 1.1E-62 2.3E-67 387.0 12.0 98 1-98 2-99 (124)
3 PF03501 S10_plectin: Plectin/ 100.0 2E-62 4.4E-67 370.9 7.5 94 3-96 1-94 (95)
4 COG5045 Ribosomal protein S10E 100.0 2.5E-48 5.4E-53 295.7 7.5 102 1-102 1-102 (105)
5 cd00090 HTH_ARSR Arsenical Res 95.1 0.028 6E-07 36.3 3.2 69 4-78 5-75 (78)
6 smart00347 HTH_MARR helix_turn 93.8 0.054 1.2E-06 37.5 2.5 70 6-80 10-82 (101)
7 PRK10141 DNA-binding transcrip 93.7 0.065 1.4E-06 41.9 3.1 73 3-80 13-85 (117)
8 PRK03902 manganese transport t 93.7 0.038 8.2E-07 42.8 1.7 72 7-87 9-94 (142)
9 PF03551 PadR: Transcriptional 93.6 0.12 2.6E-06 36.0 4.0 44 35-78 27-75 (75)
10 PF14947 HTH_45: Winged helix- 93.5 0.073 1.6E-06 37.9 2.8 40 36-79 30-69 (77)
11 PLN02853 Probable phenylalanyl 93.1 0.065 1.4E-06 51.1 2.7 54 35-91 28-81 (492)
12 PRK04172 pheS phenylalanyl-tRN 93.0 0.1 2.2E-06 48.7 3.7 67 6-78 6-72 (489)
13 PTZ00326 phenylalanyl-tRNA syn 92.9 0.074 1.6E-06 50.7 2.6 77 5-88 5-81 (494)
14 PF02002 TFIIE_alpha: TFIIE al 92.6 0.053 1.2E-06 40.1 1.0 66 8-78 15-87 (105)
15 PF13601 HTH_34: Winged helix 92.6 0.16 3.6E-06 36.7 3.5 70 8-82 2-75 (80)
16 PF13463 HTH_27: Winged helix 92.3 0.11 2.4E-06 34.6 2.2 37 36-72 29-68 (68)
17 PF01978 TrmB: Sugar-specific 91.2 0.13 2.9E-06 35.0 1.7 58 6-68 8-65 (68)
18 COG3432 Predicted transcriptio 90.2 0.26 5.7E-06 37.8 2.7 41 41-81 47-87 (95)
19 PRK05638 threonine synthase; V 89.5 0.3 6.6E-06 44.7 3.0 67 6-78 371-440 (442)
20 TIGR02702 SufR_cyano iron-sulf 89.0 0.19 4.1E-06 41.2 1.2 65 7-76 2-71 (203)
21 TIGR02647 DNA conserved hypoth 88.5 0.3 6.4E-06 36.5 1.8 33 38-75 32-64 (77)
22 PHA00738 putative HTH transcri 88.2 0.42 9.1E-06 37.6 2.6 67 4-75 10-76 (108)
23 smart00418 HTH_ARSR helix_turn 88.2 0.86 1.9E-05 28.5 3.6 43 36-78 21-64 (66)
24 PF13814 Replic_Relax: Replica 88.0 0.77 1.7E-05 36.2 4.0 43 41-84 28-78 (191)
25 TIGR02337 HpaR homoprotocatech 87.9 0.69 1.5E-05 34.3 3.5 44 36-79 53-99 (118)
26 PRK14165 winged helix-turn-hel 87.0 0.71 1.5E-05 39.6 3.5 48 35-82 31-78 (217)
27 PF14338 Mrr_N: Mrr N-terminal 86.7 0.41 8.9E-06 34.8 1.6 36 41-79 56-91 (92)
28 PF09639 YjcQ: YjcQ protein; 85.6 0.69 1.5E-05 34.0 2.4 44 35-78 20-69 (88)
29 PRK09416 lstR lineage-specific 85.3 0.68 1.5E-05 37.5 2.4 47 36-84 74-123 (135)
30 PRK06266 transcription initiat 85.0 0.52 1.1E-05 39.0 1.6 71 7-82 23-100 (178)
31 smart00550 Zalpha Z-DNA-bindin 83.9 0.43 9.4E-06 33.3 0.6 64 1-70 1-66 (68)
32 TIGR00373 conserved hypothetic 81.3 0.95 2.1E-05 36.6 1.8 69 9-82 17-92 (158)
33 COG1695 Predicted transcriptio 79.9 2.3 5.1E-05 32.4 3.4 50 37-86 42-96 (138)
34 PF03374 ANT: Phage antirepres 79.1 6.4 0.00014 29.0 5.4 60 7-81 37-106 (111)
35 TIGR02719 repress_PhaQ poly-be 79.0 2.6 5.6E-05 34.0 3.5 52 36-87 54-110 (138)
36 PF10007 DUF2250: Uncharacteri 78.6 2 4.3E-05 32.7 2.6 65 9-78 10-91 (92)
37 smart00529 HTH_DTXR Helix-turn 77.0 2.9 6.3E-05 29.5 3.0 43 35-80 9-51 (96)
38 COG1321 TroR Mn-dependent tran 76.4 1.7 3.8E-05 35.2 1.9 74 6-87 10-97 (154)
39 TIGR03433 padR_acidobact trans 76.4 3.7 7.9E-05 30.3 3.5 45 36-80 36-85 (100)
40 TIGR01889 Staph_reg_Sar staphy 76.2 3.4 7.4E-05 30.7 3.3 43 36-78 54-99 (109)
41 PF09382 RQC: RQC domain; Int 76.0 3.8 8.2E-05 29.7 3.4 45 36-80 53-98 (106)
42 TIGR01884 cas_HTH CRISPR locus 75.7 1.3 2.7E-05 36.4 0.9 61 6-72 143-203 (203)
43 COG1497 Predicted transcriptio 73.2 3.6 7.8E-05 36.8 3.2 43 35-80 35-77 (260)
44 TIGR02277 PaaX_trns_reg phenyl 72.2 4.2 9.1E-05 35.7 3.3 43 36-78 31-73 (280)
45 PHA02943 hypothetical protein; 71.3 2.4 5.1E-05 35.7 1.5 60 6-71 11-70 (165)
46 COG1846 MarR Transcriptional r 70.9 5.3 0.00011 28.0 3.1 46 36-81 47-95 (126)
47 PRK11512 DNA-binding transcrip 70.6 5.3 0.00011 30.7 3.2 43 36-78 65-110 (144)
48 PF01638 HxlR: HxlR-like helix 70.3 6.3 0.00014 28.4 3.4 68 4-77 3-74 (90)
49 PRK10857 DNA-binding transcrip 68.4 2.4 5.2E-05 34.5 1.0 54 1-58 1-58 (164)
50 PF07381 DUF1495: Winged helix 68.3 3.4 7.4E-05 31.3 1.7 61 6-76 9-87 (90)
51 PRK03573 transcriptional regul 67.6 7 0.00015 29.8 3.3 44 37-80 58-104 (144)
52 TIGR02010 IscR iron-sulfur clu 67.5 2.8 6.1E-05 32.3 1.2 65 1-70 1-69 (135)
53 COG1378 Predicted transcriptio 67.2 5.4 0.00012 34.5 2.9 69 6-79 16-85 (247)
54 COG0640 ArsR Predicted transcr 66.5 6.3 0.00014 26.1 2.6 68 5-78 24-92 (110)
55 KOG2784 Phenylalanyl-tRNA synt 65.8 6.9 0.00015 37.4 3.5 41 37-78 29-69 (483)
56 PF07848 PaaX: PaaX-like prote 65.3 6.2 0.00013 28.3 2.5 38 35-72 33-70 (70)
57 PRK10870 transcriptional repre 63.6 8.1 0.00017 31.3 3.1 45 36-80 82-129 (176)
58 COG5124 Protein predicted to b 63.4 6.4 0.00014 34.1 2.6 72 3-81 6-85 (209)
59 PF14531 Kinase-like: Kinase-l 63.4 1.5 3.3E-05 39.0 -1.2 41 40-82 152-192 (288)
60 PRK11014 transcriptional repre 59.8 5.5 0.00012 30.9 1.5 65 1-69 1-69 (141)
61 smart00346 HTH_ICLR helix_turn 58.5 10 0.00022 26.3 2.5 45 35-81 30-74 (91)
62 smart00531 TFIIE Transcription 58.4 11 0.00025 29.8 3.1 67 11-82 6-82 (147)
63 COG2345 Predicted transcriptio 57.6 6.9 0.00015 33.9 1.9 66 4-74 9-79 (218)
64 KOG3973 Uncharacterized conser 57.4 32 0.0007 32.8 6.3 9 124-132 337-345 (465)
65 PRK13777 transcriptional regul 56.1 13 0.00027 31.1 3.1 44 37-80 71-117 (185)
66 cd01223 PH_Vav Vav pleckstrin 53.7 6.3 0.00014 31.3 0.9 58 12-72 24-86 (116)
67 PRK11920 rirA iron-responsive 53.6 6.1 0.00013 31.6 0.8 63 1-69 1-67 (153)
68 KOG4412 26S proteasome regulat 52.4 9.4 0.0002 33.5 1.8 48 5-52 115-164 (226)
69 PF03962 Mnd1: Mnd1 family; I 50.3 13 0.00029 31.0 2.4 49 30-80 22-71 (188)
70 KOG0921 Dosage compensation co 49.7 19 0.00042 38.0 3.8 9 159-167 1253-1261(1282)
71 PF13412 HTH_24: Winged helix- 48.4 3.6 7.7E-05 26.1 -1.0 46 6-56 3-48 (48)
72 KOG3233 RNA polymerase III, su 44.6 9.1 0.0002 34.9 0.6 25 36-60 111-135 (297)
73 PF01043 SecA_PP_bind: SecA pr 43.8 21 0.00046 27.7 2.5 40 42-87 11-54 (113)
74 PRK04172 pheS phenylalanyl-tRN 42.2 24 0.00052 33.1 3.0 39 44-83 156-194 (489)
75 PF02082 Rrf2: Transcriptional 41.4 5.6 0.00012 28.2 -1.0 54 1-58 1-58 (83)
76 PRK06474 hypothetical protein; 37.6 16 0.00035 29.9 1.0 67 3-74 8-81 (178)
77 TIGR00738 rrf2_super rrf2 fami 37.2 15 0.00033 27.4 0.7 65 1-71 1-70 (132)
78 PF13309 HTH_22: HTH domain 36.8 25 0.00054 24.4 1.7 26 2-27 20-45 (64)
79 KOG1423 Ras-like GTPase ERA [C 36.4 31 0.00067 32.4 2.7 35 47-81 228-267 (379)
80 KOG3433 Protein involved in me 35.8 22 0.00048 30.8 1.6 74 3-81 5-84 (203)
81 cd00092 HTH_CRP helix_turn_hel 35.4 23 0.0005 23.0 1.3 32 36-70 36-67 (67)
82 PF10662 PduV-EutP: Ethanolami 34.3 19 0.00042 29.1 0.9 38 39-81 105-142 (143)
83 COG1542 Uncharacterized conser 33.8 27 0.0006 34.3 2.0 45 37-83 321-366 (593)
84 PF03965 Penicillinase_R: Peni 33.0 26 0.00056 26.2 1.4 67 10-77 7-73 (115)
85 KOG0921 Dosage compensation co 32.7 95 0.0021 33.2 5.6 10 125-134 1178-1187(1282)
86 TIGR01689 EcbF-BcbF capsule bi 32.6 18 0.00039 28.5 0.5 48 36-91 23-70 (126)
87 PF01050 MannoseP_isomer: Mann 30.7 43 0.00093 27.1 2.4 45 17-72 12-62 (151)
88 PF06969 HemN_C: HemN C-termin 30.6 30 0.00064 23.0 1.2 27 43-73 39-65 (66)
89 COG1733 Predicted transcriptio 29.4 43 0.00092 26.1 2.1 69 3-77 20-92 (120)
90 cd07377 WHTH_GntR Winged helix 28.7 42 0.0009 21.4 1.7 23 36-58 36-58 (66)
91 cd07153 Fur_like Ferric uptake 28.5 19 0.00041 26.3 -0.0 52 7-60 2-56 (116)
92 PRK11050 manganese transport r 28.3 54 0.0012 25.9 2.5 40 35-77 61-100 (152)
93 COG1959 Predicted transcriptio 27.6 28 0.0006 27.8 0.8 61 1-65 1-65 (150)
94 PF07106 TBPIP: Tat binding pr 27.6 22 0.00047 28.4 0.2 58 9-68 4-62 (169)
95 cd03071 PDI_b'_NRX PDIb' famil 27.6 58 0.0013 26.2 2.6 31 56-86 51-81 (116)
96 PF01325 Fe_dep_repress: Iron 27.4 10 0.00023 26.0 -1.5 46 7-57 9-54 (60)
97 PRK09249 coproporphyrinogen II 26.5 57 0.0012 30.1 2.7 34 42-79 401-434 (453)
98 PF12840 HTH_20: Helix-turn-he 25.8 22 0.00047 23.7 -0.1 51 3-58 7-57 (61)
99 PF14756 Pdase_C33_assoc: Pept 25.4 44 0.00095 27.5 1.6 24 70-93 13-36 (147)
100 PF06648 DUF1160: Protein of u 25.3 55 0.0012 26.2 2.1 31 37-80 81-111 (122)
101 PF06992 Phage_lambda_P: Repli 23.9 18 0.0004 31.8 -0.9 40 35-74 118-163 (233)
102 KOG3973 Uncharacterized conser 23.2 59 0.0013 31.1 2.1 14 158-171 443-456 (465)
103 PF00961 LAGLIDADG_1: LAGLIDAD 22.9 1.4E+02 0.003 21.1 3.6 45 37-81 37-83 (102)
104 PF13730 HTH_36: Helix-turn-he 22.8 39 0.00085 21.6 0.7 44 8-55 7-55 (55)
105 PF09106 SelB-wing_2: Elongati 22.7 78 0.0017 21.2 2.2 25 3-27 32-56 (59)
106 TIGR00635 ruvB Holliday juncti 22.1 44 0.00096 28.2 1.0 38 36-77 266-304 (305)
107 PF02099 Josephin: Josephin; 22.1 64 0.0014 26.4 1.9 27 33-62 130-156 (157)
108 PF11181 YflT: Heat induced st 21.9 89 0.0019 23.1 2.5 36 40-81 10-47 (103)
109 PF13545 HTH_Crp_2: Crp-like h 21.8 94 0.002 20.7 2.5 31 36-70 39-69 (76)
110 COG1339 Transcriptional regula 21.7 95 0.0021 27.3 3.0 47 32-78 26-72 (214)
111 PF14277 DUF4364: Domain of un 21.1 1.1E+02 0.0023 25.2 3.0 42 37-78 31-73 (163)
112 KOG2175 Protein predicted to b 20.6 30 0.00066 33.3 -0.3 25 59-83 200-225 (458)
113 PF05158 RNA_pol_Rpc34: RNA po 20.2 50 0.0011 29.9 1.0 26 38-63 113-138 (327)
No 1
>KOG3344 consensus 40s ribosomal protein s10 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.5e-74 Score=460.58 Aligned_cols=148 Identities=64% Similarity=1.125 Sum_probs=129.2
Q ss_pred CccchhhHHHHHHHhhhcccEEEeecCCCCCCCccccCCHHHHHHhhhcccccccceeeeceeeeeeechhhHHHHHHhh
Q 030302 1 MIIPEKNRKEICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEFLRTYL 80 (179)
Q Consensus 1 MlipK~nr~~IYe~LFkEGV~VakKD~~~p~Hpel~VpNL~ViK~mqSLkSrGyVkEqFaWrh~Yw~LTneGI~YLR~yL 80 (179)
|||||+||++|||+||||||||||||+++++||||+||||||||+||||+|||||||||||||||||||||||+|||+||
T Consensus 1 Mlipk~nr~~I~e~Lfkegv~vakkD~~~~kH~el~vpNL~vikaMQSl~SrgYvkeqfaWrH~Yw~LTneGi~yLR~YL 80 (150)
T KOG3344|consen 1 MLIPKANRKAIYEYLFKEGVLVAKKDFNLPKHPELEVPNLHVIKAMQSLKSRGYVKEQFAWRHFYWYLTNEGIEYLREYL 80 (150)
T ss_pred CCcchHHHHHHHHHHHHhcceeeccccCCccCcccCCccHHHHHHHHHHhhhhhHHhhhhhheeeeeechhHHHHHHHHh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCccccccccCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCccccCCCCCCCCCCCCCCCCCCCCCcccccCCCC
Q 030302 81 NLPSEIVPATLKKSAKPAGRPMG-GPGGDRPRGPPRFDGDRPRFGDREGYRGGPRGGDFGGEKGGAPADFQPSFRGSGGR 159 (179)
Q Consensus 81 hLP~eiVPaTlk~~~~~~~rp~~-~~~g~r~~~~~r~~~~~~~~~dR~~YRr~~~~~~~~~~k~gag~~~~~~Fr~~~~r 159 (179)
|||+||||+||+++++++.||++ +.++.+|. ++. .+||++||++++++ ++|||++++|||||
T Consensus 81 hLP~EiVpaTl~~~rP~~~rpr~~g~e~~~p~-----~~~---r~dR~~yR~~~~~~-----~~gA~s~~~~~frg---- 143 (150)
T KOG3344|consen 81 HLPPEIVPATLKRSRPETGRPRPPGLEGRGPA-----DGT---RGDRDGYRRGPVPP-----EGGAGSGTEPQFRG---- 143 (150)
T ss_pred cCCcccccchhhccCCCCCCCCCCCCCCCCcc-----ccc---ccchhhhccCCCCC-----CCCCCccccccccc----
Confidence 99999999999998777788865 33332221 222 27999999988754 56899999999982
Q ss_pred CCcCCC
Q 030302 160 PGFGRG 165 (179)
Q Consensus 160 ggfGrG 165 (179)
-|||++
T Consensus 144 ~g~g~~ 149 (150)
T KOG3344|consen 144 RGFGRP 149 (150)
T ss_pred cCCCCC
Confidence 255554
No 2
>PTZ00034 40S ribosomal protein S10; Provisional
Probab=100.00 E-value=1.1e-62 Score=387.01 Aligned_cols=98 Identities=55% Similarity=0.971 Sum_probs=95.6
Q ss_pred CccchhhHHHHHHHhhhcccEEEeecCCCCCCCccccCCHHHHHHhhhcccccccceeeeceeeeeeechhhHHHHHHhh
Q 030302 1 MIIPEKNRKEICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEFLRTYL 80 (179)
Q Consensus 1 MlipK~nr~~IYe~LFkEGV~VakKD~~~p~Hpel~VpNL~ViK~mqSLkSrGyVkEqFaWrh~Yw~LTneGI~YLR~yL 80 (179)
|||||+||++|||+||||||||||||+++++||||+||||||||+||||+|||||+|||||||||||||||||+|||+||
T Consensus 2 m~ipK~~r~~Iye~LfkeGVlvakKd~~~~~h~el~vpNL~Vik~mqSL~Srg~Vke~f~WrhyYw~LT~eGieyLR~yL 81 (124)
T PTZ00034 2 VYVPKANRKAIYRYLFKEGVIVCKKDPKGPWHPELNVPNLHVMMLMRSLKSRGLVKEQFAWQHYYYYLTDEGIEYLRTYL 81 (124)
T ss_pred CccchHHHHHHHHHHhhCceEEEecCCCCCCCCccCCccHHHHHHHHccccCCceEEEEeeEEEEEEEchHHHHHHHHHh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCccccccccCCCC
Q 030302 81 NLPSEIVPATLKKSAKPA 98 (179)
Q Consensus 81 hLP~eiVPaTlk~~~~~~ 98 (179)
|||+||||+||+++.++.
T Consensus 82 ~LP~eivP~T~k~~~~~~ 99 (124)
T PTZ00034 82 HLPPDVFPATHKKKSVNF 99 (124)
T ss_pred CCCcccCchhhcccccCc
Confidence 999999999999976654
No 3
>PF03501 S10_plectin: Plectin/S10 domain; InterPro: IPR005326 This presumed domain is found at the N terminus of some isoforms of the cytoskeletal muscle protein plectin as well as the ribosomal S10 protein. This domain may be involved in RNA binding.; PDB: 2XZM_7 2XZN_7 3U5C_K 3U5G_K.
Probab=100.00 E-value=2e-62 Score=370.93 Aligned_cols=94 Identities=70% Similarity=1.220 Sum_probs=82.6
Q ss_pred cchhhHHHHHHHhhhcccEEEeecCCCCCCCccccCCHHHHHHhhhcccccccceeeeceeeeeeechhhHHHHHHhhCC
Q 030302 3 IPEKNRKEICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEFLRTYLNL 82 (179)
Q Consensus 3 ipK~nr~~IYe~LFkEGV~VakKD~~~p~Hpel~VpNL~ViK~mqSLkSrGyVkEqFaWrh~Yw~LTneGI~YLR~yLhL 82 (179)
|||+||++|||+||||||||||||+++|+|||++||||||||+||||+|||||||||||||||||||||||||||+||||
T Consensus 1 ipk~~r~~Iye~LFkeGVlvakKD~~~~~H~el~vpNL~V~k~mqSL~SrgyVke~faWrh~Yw~LT~eGIeyLR~yL~L 80 (95)
T PF03501_consen 1 IPKKNRIAIYEYLFKEGVLVAKKDFHMPKHPELNVPNLHVIKAMQSLKSRGYVKEQFAWRHYYWYLTNEGIEYLREYLHL 80 (95)
T ss_dssp --HHHHHHHHHHHHHHSEEEEES-TTSCS-TTTSSBHHHHHHHHHHHHHCTSEEEEECTTEEEEEE-HHHHHHHHHHC-S
T ss_pred CCchHHHHHHHHHhhcceEEEEccCCCCCCCccCCCcHHHHHHHhcccchhhhcCeecceEEEEEEcchhHHHHHHHhCC
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCccccccccCC
Q 030302 83 PSEIVPATLKKSAK 96 (179)
Q Consensus 83 P~eiVPaTlk~~~~ 96 (179)
|+||||+||+++.+
T Consensus 81 P~eivPaTlk~~~~ 94 (95)
T PF03501_consen 81 PAEIVPATLKKSRR 94 (95)
T ss_dssp STT--TCCCS-S--
T ss_pred ChhhCcHHhccccC
Confidence 99999999999754
No 4
>COG5045 Ribosomal protein S10E [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.5e-48 Score=295.71 Aligned_cols=102 Identities=50% Similarity=0.859 Sum_probs=98.9
Q ss_pred CccchhhHHHHHHHhhhcccEEEeecCCCCCCCccccCCHHHHHHhhhcccccccceeeeceeeeeeechhhHHHHHHhh
Q 030302 1 MIIPEKNRKEICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEFLRTYL 80 (179)
Q Consensus 1 MlipK~nr~~IYe~LFkEGV~VakKD~~~p~Hpel~VpNL~ViK~mqSLkSrGyVkEqFaWrh~Yw~LTneGI~YLR~yL 80 (179)
|||||+||.+|.++||++||+||||||++++|+||+||||||||+||||.|+||||.+|+|||+||+||+||++|||+||
T Consensus 1 MLvPk~nr~kIhq~Lf~~gv~vakkDfnl~kH~el~ipNL~vika~qsl~S~GYvkt~~~W~~~YytLT~eGveyLREyL 80 (105)
T COG5045 1 MLVPKENRYKIHQRLFQKGVAVAKKDFNLGKHRELEIPNLHVIKAMQSLISYGYVKTIHVWRHSYYTLTPEGVEYLREYL 80 (105)
T ss_pred CCcchHHHHHHHHHHHHhhhhHhhhhccccCCcccCCCchHHHHHHHHHhhcceeEEEeeeeeeEEEecHHHHHHHHHHh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCccccccccCCCCCCCC
Q 030302 81 NLPSEIVPATLKKSAKPAGRPM 102 (179)
Q Consensus 81 hLP~eiVPaTlk~~~~~~~rp~ 102 (179)
+||+|+||+|.+....++.||.
T Consensus 81 ~lp~e~Vp~t~~~~v~pt~rp~ 102 (105)
T COG5045 81 VLPDEGVPSTEAPAVSPTQRPQ 102 (105)
T ss_pred cCccccCccccccccCcccCCC
Confidence 9999999999998877777773
No 5
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=95.11 E-value=0.028 Score=36.29 Aligned_cols=69 Identities=13% Similarity=0.234 Sum_probs=49.6
Q ss_pred chhhHHHHHHHhhhcccEEEeecCCCCCCCccccCCHHHHHHhhhcccccccceeeeceeeeeeec--hhhHHHHHH
Q 030302 4 PEKNRKEICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLT--NDGIEFLRT 78 (179)
Q Consensus 4 pK~nr~~IYe~LFkEGV~VakKD~~~p~Hpel~VpNL~ViK~mqSLkSrGyVkEqFaWrh~Yw~LT--neGI~YLR~ 78 (179)
...++..|+.+|...+ +..+|.. ..++++.=.|-++|..|++.|++...-.=+..||.|| .+.++.+++
T Consensus 5 ~~~~~~~il~~l~~~~--~~~~ei~----~~~~i~~~~i~~~l~~L~~~g~i~~~~~~~~~~~~~~~g~~~~~~~~~ 75 (78)
T cd00090 5 SDPTRLRILRLLLEGP--LTVSELA----ERLGLSQSTVSRHLKKLEEAGLVESRREGRRVYYSLTDAERLLALLES 75 (78)
T ss_pred cChHHHHHHHHHHHCC--cCHHHHH----HHHCcCHhHHHHHHHHHHHCCCeEEEEeccEEEEEeCCchHHHHHHHH
Confidence 4567889999998876 3344432 2345777788899999999999885433388999999 566666554
No 6
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=93.79 E-value=0.054 Score=37.49 Aligned_cols=70 Identities=16% Similarity=0.266 Sum_probs=49.7
Q ss_pred hhHHHHHHHhhhcccEEEeecCCCCCCCccccCCHHHHHHhhhccccccccee---eeceeeeeeechhhHHHHHHhh
Q 030302 6 KNRKEICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVRET---FAWMHYYWYLTNDGIEFLRTYL 80 (179)
Q Consensus 6 ~nr~~IYe~LFkEGV~VakKD~~~p~Hpel~VpNL~ViK~mqSLkSrGyVkEq---FaWrh~Yw~LTneGI~YLR~yL 80 (179)
.+...|+..|...+.+- .+|.. ..++++.=.|.++++.|.++|+|... ..=|..|+.||++|.+++.+..
T Consensus 10 ~~~~~il~~l~~~~~~~-~~~la----~~~~~s~~~i~~~l~~L~~~g~v~~~~~~~~~r~~~~~lT~~g~~~~~~~~ 82 (101)
T smart00347 10 PTQFLVLRILYEEGPLS-VSELA----KRLGVSPSTVTRVLDRLEKKGLIRRLPSPEDRRSVLVSLTEEGRELIEELL 82 (101)
T ss_pred HHHHHHHHHHHHcCCcC-HHHHH----HHHCCCchhHHHHHHHHHHCCCeEecCCCCCCCeEEEEECHhHHHHHHHHH
Confidence 35668888888777432 22221 12456667788999999999999654 3346789999999998887643
No 7
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=93.75 E-value=0.065 Score=41.86 Aligned_cols=73 Identities=10% Similarity=0.110 Sum_probs=56.0
Q ss_pred cchhhHHHHHHHhhhcccEEEeecCCCCCCCccccCCHHHHHHhhhcccccccceeeeceeeeeeechhhHHHHHHhh
Q 030302 3 IPEKNRKEICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEFLRTYL 80 (179)
Q Consensus 3 ipK~nr~~IYe~LFkEGV~VakKD~~~p~Hpel~VpNL~ViK~mqSLkSrGyVkEqFaWrh~Yw~LTneGI~YLR~yL 80 (179)
+...+|.+|...|.+.|-+.+. +. ...++++.-.|-+.|+-|+.-|+|...--.|+.||.|+++..++|...+
T Consensus 13 LadptRl~IL~~L~~~~~~~v~-el----a~~l~lsqstvS~HL~~L~~AGLV~~~r~Gr~~~Y~l~~~~~~~~~~~~ 85 (117)
T PRK10141 13 LSDETRLGIVLLLRESGELCVC-DL----CTALDQSQPKISRHLALLRESGLLLDRKQGKWVHYRLSPHIPAWAAKII 85 (117)
T ss_pred hCCHHHHHHHHHHHHcCCcCHH-HH----HHHHCcCHHHHHHHHHHHHHCCceEEEEEcCEEEEEECchHHHHHHHHH
Confidence 3457899999999875422111 11 1235678888999999999999999999999999999998777777633
No 8
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=93.70 E-value=0.038 Score=42.82 Aligned_cols=72 Identities=19% Similarity=0.242 Sum_probs=50.1
Q ss_pred hHHHHHHHhhhcccEEEeecCCCCCCCccccCCHHHHHHhhhcccccccceeeeceeeeeeechhh--------------
Q 030302 7 NRKEICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDG-------------- 72 (179)
Q Consensus 7 nr~~IYe~LFkEGV~VakKD~~~p~Hpel~VpNL~ViK~mqSLkSrGyVkEqFaWrh~Yw~LTneG-------------- 72 (179)
...+||.++-..|.+-+ +|. -..++|..-.|...++.|..+|||.-. +...|.||++|
T Consensus 9 yL~~I~~l~~~~~~~~~-~el----a~~l~vs~~svs~~l~~L~~~Gli~~~---~~~~i~LT~~G~~~a~~~~~~h~~~ 80 (142)
T PRK03902 9 YIEQIYLLIEEKGYARV-SDI----AEALSVHPSSVTKMVQKLDKDEYLIYE---KYRGLVLTPKGKKIGKRLVYRHELL 80 (142)
T ss_pred HHHHHHHHHhcCCCcCH-HHH----HHHhCCChhHHHHHHHHHHHCCCEEEe---cCceEEECHHHHHHHHHHHHHHHHH
Confidence 34577877765554421 111 113568889999999999999999733 45679999999
Q ss_pred HHHHHHhhCCCCCCc
Q 030302 73 IEFLRTYLNLPSEIV 87 (179)
Q Consensus 73 I~YLR~yLhLP~eiV 87 (179)
.+|| +.|+.+.+.+
T Consensus 81 e~~l-~~l~~~~~~~ 94 (142)
T PRK03902 81 EQFL-RIIGVDESKI 94 (142)
T ss_pred HHHH-HHhCcCHHHH
Confidence 4566 5678876654
No 9
>PF03551 PadR: Transcriptional regulator PadR-like family; InterPro: IPR005149 Phenolic acids, also called substituted hydroxycinnamic acids, are abundant in the plant kingdom because they are involved in the structure of plant cell walls and are present in some vacuoles. In plant-soil ecosystems they are released as free acids by hemicellulases produced by several fungi and bacteria. Of these weak acids, the most abundant are p-coumaric, ferulic, and caffeic acids, considered to be natural toxins that inhibit the growth of microorganisms, especially at low pHs. In spite of this chemical stress, some bacteria can use phenolic acids as a sole source of carbon. For other microorganisms, these compounds induce a specific response by which the organism adapts to its environment. The ubiquitous lactic acid bacterium Lactobacillus plantarum exhibits an inducible phenolic acid decarboxylase (PAD) activity which converts these substrates into less-toxic vinyl phenol derivatives. PadR acts as a repressor of padA gene expression in the phenolic acid stress response [].; PDB: 1XMA_B 2ESH_A 2DQL_B 3L9F_C 3ELK_B 4EJO_B 3L7W_A 3HHH_A 1YG2_A 3F8B_A ....
Probab=93.64 E-value=0.12 Score=36.01 Aligned_cols=44 Identities=14% Similarity=0.242 Sum_probs=37.8
Q ss_pred cccCCHHHHHHhhhcccccccceeeec-----eeeeeeechhhHHHHHH
Q 030302 35 IDVPNLQVIKLMQSFKSREYVRETFAW-----MHYYWYLTNDGIEFLRT 78 (179)
Q Consensus 35 l~VpNL~ViK~mqSLkSrGyVkEqFaW-----rh~Yw~LTneGI~YLR~ 78 (179)
.+|..=.|..+|+.|...|+|+....= .--||.||++|.++|++
T Consensus 27 ~~i~~g~lY~~L~~Le~~gli~~~~~~~~~~~~rk~Y~iT~~G~~~l~E 75 (75)
T PF03551_consen 27 WKISPGSLYPALKRLEEEGLIESRWEEEGNGRPRKYYRITEKGREELRE 75 (75)
T ss_dssp EETTHHHHHHHHHHHHHTTSEEEEEEEETTSSEEEEEEESHHHHHHHHH
T ss_pred cccChhHHHHHHHHHHhCCCEEEeeeccCCCCCCEEEEECHHHHHHhcC
Confidence 356777899999999999999987776 46689999999999986
No 10
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=93.52 E-value=0.073 Score=37.93 Aligned_cols=40 Identities=18% Similarity=0.350 Sum_probs=31.5
Q ss_pred ccCCHHHHHHhhhcccccccceeeeceeeeeeechhhHHHHHHh
Q 030302 36 DVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEFLRTY 79 (179)
Q Consensus 36 ~VpNL~ViK~mqSLkSrGyVkEqFaWrh~Yw~LTneGI~YLR~y 79 (179)
+++--.+.+.+..|.++|+|+. ..-.|.||++|.+||..+
T Consensus 30 ~L~~~~~~~yL~~L~~~gLI~~----~~~~Y~lTekG~~~l~~l 69 (77)
T PF14947_consen 30 NLNYSTLKKYLKELEEKGLIKK----KDGKYRLTEKGKEFLEEL 69 (77)
T ss_dssp T--HHHHHHHHHHHHHTTSEEE----ETTEEEE-HHHHHHHHHH
T ss_pred CcCHHHHHHHHHHHHHCcCeeC----CCCEEEECccHHHHHHHH
Confidence 4666788999999999999944 556779999999999875
No 11
>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain
Probab=93.13 E-value=0.065 Score=51.13 Aligned_cols=54 Identities=19% Similarity=0.287 Sum_probs=42.1
Q ss_pred cccCCHHHHHHhhhcccccccceeeeceeeeeeechhhHHHHHHhhCCCCCCccccc
Q 030302 35 IDVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEFLRTYLNLPSEIVPATL 91 (179)
Q Consensus 35 l~VpNL~ViK~mqSLkSrGyVkEqFaWrh~Yw~LTneGI~YLR~yLhLP~eiVPaTl 91 (179)
+.+.--.|+.++.||.++|+|+-.- =..-+|.||+||.+||+ -+||+..|=+.+
T Consensus 28 ~g~~~~~v~~~~~~L~~kg~v~~~~-~~~~~~~LT~eG~~~l~--~G~PE~rl~~~l 81 (492)
T PLN02853 28 HGLDHNEVVGVIKSLHGFRYVDAQD-IKRETWVLTEEGKKYAA--EGSPEVQLFAAV 81 (492)
T ss_pred cCCCHHHHHHHHHHHHhCCCEEEEE-EEEEEEEECHHHHHHHH--cCCHHHHHHHHH
Confidence 3467789999999999999887553 36678899999999999 467766554333
No 12
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=93.01 E-value=0.1 Score=48.67 Aligned_cols=67 Identities=15% Similarity=0.248 Sum_probs=47.7
Q ss_pred hhHHHHHHHhhhcccEEEeecCCCCCCCccccCCHHHHHHhhhcccccccceeeeceeeeeeechhhHHHHHH
Q 030302 6 KNRKEICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEFLRT 78 (179)
Q Consensus 6 ~nr~~IYe~LFkEGV~VakKD~~~p~Hpel~VpNL~ViK~mqSLkSrGyVkEqFaWrh~Yw~LTneGI~YLR~ 78 (179)
.+...|...|-.++.+ ..++. -..+.+..=.|+.++.+|.++|||...-. +..+|.||+||.+|+.+
T Consensus 6 ~~e~~vL~~L~~~~~~-s~~eL----A~~l~l~~~tVt~~i~~Le~kGlV~~~~~-~~~~i~LTeeG~~~~~~ 72 (489)
T PRK04172 6 PNEKKVLKALKELKEA-TLEEL----AEKLGLPPEAVMRAAEWLEEKGLVKVEER-VEEVYVLTEEGKKYAEE 72 (489)
T ss_pred HHHHHHHHHHHhCCCC-CHHHH----HHHhCcCHHHHHHHHHHHHhCCCEEEEee-eEEEEEECHHHHHHHHh
Confidence 4456777777544422 11111 11335788899999999999999987644 57899999999999984
No 13
>PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional
Probab=92.90 E-value=0.074 Score=50.73 Aligned_cols=77 Identities=19% Similarity=0.295 Sum_probs=50.3
Q ss_pred hhhHHHHHHHhhhcccEEEeecCCCCCCCccccCCHHHHHHhhhcccccccceeeeceeeeeeechhhHHHHHHhhCCCC
Q 030302 5 EKNRKEICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEFLRTYLNLPS 84 (179)
Q Consensus 5 K~nr~~IYe~LFkEGV~VakKD~~~p~Hpel~VpNL~ViK~mqSLkSrGyVkEqFaWrh~Yw~LTneGI~YLR~yLhLP~ 84 (179)
..+-++|.+.|-+++-.+ |.. ..-..+++.--.|+.++.||.|+|+|+-.-- ..-+|.||+||.+||+ -+||+
T Consensus 5 ~~~e~~iL~~l~~~~~~~---~~~-~la~~~~~~~~~v~~~~~~L~~kg~v~~~~~-~~~~~~LT~eG~~~~~--~G~PE 77 (494)
T PTZ00326 5 ELEENTILSKLESENEIV---NSL-ALAESLNIDHQKVVGAIKSLESANYITTEMK-KSNTWTLTEEGEDYLK--NGSPE 77 (494)
T ss_pred hHHHHHHHHHHHhcCCCC---CHH-HHHHHcCCCHHHHHHHHHHHHhCCCEEEEEE-EEEEEEECHHHHHHHH--cCCHH
Confidence 344567777776521111 110 0011334677899999999999998765443 5678899999999999 46666
Q ss_pred CCcc
Q 030302 85 EIVP 88 (179)
Q Consensus 85 eiVP 88 (179)
..|=
T Consensus 78 ~rl~ 81 (494)
T PTZ00326 78 YRLW 81 (494)
T ss_pred HHHH
Confidence 5543
No 14
>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024550 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation, together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits, TFIIE-alpha and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF []. This entry represents a helix-turn-helix (HTH) domain found in eukaryotic TFIIE-alpha []. It is also found in proteins from archaebacteria that are presumed to be TFIIE-alpha subunits [], the transcriptional regulator SarR, and also DNA-directed RNA polymerase III subunit Rpc3.; PDB: 1VD4_A 1Q1H_A.
Probab=92.61 E-value=0.053 Score=40.14 Aligned_cols=66 Identities=21% Similarity=0.471 Sum_probs=38.0
Q ss_pred HHHHHHHhhhcccEEEeecCCCCCCCccccCCHHHHHHhhhcccccccce------eeeceeeeeeechhhH-HHHHH
Q 030302 8 RKEICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVRE------TFAWMHYYWYLTNDGI-EFLRT 78 (179)
Q Consensus 8 r~~IYe~LFkEGV~VakKD~~~p~Hpel~VpNL~ViK~mqSLkSrGyVkE------qFaWrh~Yw~LTneGI-~YLR~ 78 (179)
-..|.+.|..+|+| ..+|.. ..++++.=+|-++|..|...++|+. +-+|..|||+++.+.| +.|+.
T Consensus 15 ~~~Il~~L~~~~~l-~de~la----~~~~l~~~~vRkiL~~L~~~~lv~~~~~~d~~~~~~~~yw~i~~~~~~~~ik~ 87 (105)
T PF02002_consen 15 AVRILDALLRKGEL-TDEDLA----KKLGLKPKEVRKILYKLYEDGLVSYRRRKDDERGWTRYYWYIDYDQIIDVIKY 87 (105)
T ss_dssp THHHHHHHHHH--B--HHHHH----HTT-S-HHHHHHHHHHHHHHSS-EEEEE--------EEEEE-THHHH------
T ss_pred HHHHHHHHHHcCCc-CHHHHH----HHhCCCHHHHHHHHHHHHHCCCeEEEEEEcCCCcEEEEEEEEcHHHHHHHHHH
Confidence 45788888888876 233322 1345888899999999999999954 4589999999999887 44443
No 15
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=92.56 E-value=0.16 Score=36.66 Aligned_cols=70 Identities=19% Similarity=0.330 Sum_probs=46.6
Q ss_pred HHHHHHHhhhcccEEEeecCCCCCCCccccCCHHHHHHhhhcccccccce--eeece--eeeeeechhhHHHHHHhhCC
Q 030302 8 RKEICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVRE--TFAWM--HYYWYLTNDGIEFLRTYLNL 82 (179)
Q Consensus 8 r~~IYe~LFkEGV~VakKD~~~p~Hpel~VpNL~ViK~mqSLkSrGyVkE--qFaWr--h~Yw~LTneGI~YLR~yLhL 82 (179)
|.+|..+|...+-+ +|.- .-..++++.=.+-+.|+.|...|||+- .|.=+ -.||.||++|.+.+.+|+..
T Consensus 2 Rl~Il~~L~~~~~~----~f~~-L~~~l~lt~g~Ls~hL~~Le~~GyV~~~k~~~~~~p~t~~~lT~~Gr~~~~~~~~~ 75 (80)
T PF13601_consen 2 RLAILALLYANEEA----TFSE-LKEELGLTDGNLSKHLKKLEEAGYVEVEKEFEGRRPRTWYSLTDKGREAFERYVAA 75 (80)
T ss_dssp HHHHHHHHHHHSEE----EHHH-HHHHTT--HHHHHHHHHHHHHTTSEEEEEE-SSS--EEEEEE-HHHHHHHHHHHHH
T ss_pred HHHHHHHHhhcCCC----CHHH-HHHHhCcCHHHHHHHHHHHHHCCCEEEEEeccCCCCeEEEEECHHHHHHHHHHHHH
Confidence 66777888764443 3320 011345777778899999999999753 34334 67999999999999998753
No 16
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=92.33 E-value=0.11 Score=34.59 Aligned_cols=37 Identities=14% Similarity=0.256 Sum_probs=28.9
Q ss_pred ccCCHHHHHHhhhccccccccee---eeceeeeeeechhh
Q 030302 36 DVPNLQVIKLMQSFKSREYVRET---FAWMHYYWYLTNDG 72 (179)
Q Consensus 36 ~VpNL~ViK~mqSLkSrGyVkEq---FaWrh~Yw~LTneG 72 (179)
++.--+|.+++++|..+|||..+ ..=|-.|+.||++|
T Consensus 29 ~~~~~~vs~~i~~L~~~glv~~~~~~~d~R~~~~~LT~~G 68 (68)
T PF13463_consen 29 GISKSTVSRIIKKLEEKGLVEKERDPHDKRSKRYRLTPAG 68 (68)
T ss_dssp T--HHHHHHHHHHHHHTTSEEEEEESSCTTSEEEEE-HHH
T ss_pred CcCHHHHHHHHHHHHHCCCEEecCCCCcCCeeEEEeCCCC
Confidence 46777889999999999999766 34577999999998
No 17
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=91.24 E-value=0.13 Score=35.01 Aligned_cols=58 Identities=16% Similarity=0.265 Sum_probs=45.3
Q ss_pred hhHHHHHHHhhhcccEEEeecCCCCCCCccccCCHHHHHHhhhcccccccceeeeceeeeeee
Q 030302 6 KNRKEICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVRETFAWMHYYWYL 68 (179)
Q Consensus 6 ~nr~~IYe~LFkEGV~VakKD~~~p~Hpel~VpNL~ViK~mqSLkSrGyVkEqFaWrh~Yw~L 68 (179)
++-.+||.+|.++|-+-+.. .. ..+++|-=.|.++|++|.++|+|+..-.-...|+..
T Consensus 8 ~~E~~vy~~Ll~~~~~t~~e-Ia----~~l~i~~~~v~~~L~~L~~~GlV~~~~~~~~~Y~a~ 65 (68)
T PF01978_consen 8 ENEAKVYLALLKNGPATAEE-IA----EELGISRSTVYRALKSLEEKGLVEREEGRPKVYRAV 65 (68)
T ss_dssp HHHHHHHHHHHHHCHEEHHH-HH----HHHTSSHHHHHHHHHHHHHTTSEEEEEECCEEEEEE
T ss_pred HHHHHHHHHHHHcCCCCHHH-HH----HHHCcCHHHHHHHHHHHHHCCCEEEEcCceEEEEEe
Confidence 45678999999888775432 21 245689999999999999999999988877777654
No 18
>COG3432 Predicted transcriptional regulator [Transcription]
Probab=90.23 E-value=0.26 Score=37.85 Aligned_cols=41 Identities=17% Similarity=0.239 Sum_probs=34.8
Q ss_pred HHHHHhhhcccccccceeeeceeeeeeechhhHHHHHHhhC
Q 030302 41 QVIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEFLRTYLN 81 (179)
Q Consensus 41 ~ViK~mqSLkSrGyVkEqFaWrh~Yw~LTneGI~YLR~yLh 81 (179)
-.-+.++-|.++|+++.+=.=+--+|.||++|..+|++|=-
T Consensus 47 ~~~~yi~~L~~~Gli~~~~~~~~~~y~lT~KG~~fle~y~~ 87 (95)
T COG3432 47 RAQKYIEMLVEKGLIIKQDNGRRKVYELTEKGKRFLEKYSE 87 (95)
T ss_pred HHHHHHHHHHhCCCEEeccCCccceEEEChhHHHHHHHHHH
Confidence 34578899999998888888877788999999999998743
No 19
>PRK05638 threonine synthase; Validated
Probab=89.52 E-value=0.3 Score=44.68 Aligned_cols=67 Identities=18% Similarity=0.279 Sum_probs=44.9
Q ss_pred hhHHHHHHHhhhcccEEEeecCCCCCCCccc--cCCHHHHHHhhhcccccccceee-eceeeeeeechhhHHHHHH
Q 030302 6 KNRKEICKYLFQEGVCYAKKDYNLAKHPEID--VPNLQVIKLMQSFKSREYVRETF-AWMHYYWYLTNDGIEFLRT 78 (179)
Q Consensus 6 ~nr~~IYe~LFkEGV~VakKD~~~p~Hpel~--VpNL~ViK~mqSLkSrGyVkEqF-aWrh~Yw~LTneGI~YLR~ 78 (179)
..|..|...|.++- +. -.+.. ..|+ ++.-.|.++|+.|+..|+|...+ -=+.-||.||++|.++|.+
T Consensus 371 ~~r~~IL~~L~~~~-~~-~~el~----~~l~~~~s~~~v~~hL~~Le~~GLV~~~~~~g~~~~Y~Lt~~g~~~l~~ 440 (442)
T PRK05638 371 GTKLEILKILSERE-MY-GYEIW----KALGKPLKYQAVYQHIKELEELGLIEEAYRKGRRVYYKLTEKGRRLLEN 440 (442)
T ss_pred chHHHHHHHHhhCC-cc-HHHHH----HHHcccCCcchHHHHHHHHHHCCCEEEeecCCCcEEEEECcHHHHHHHh
Confidence 34777888776432 21 01111 1222 66778999999999999997541 0167799999999999875
No 20
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=89.02 E-value=0.19 Score=41.20 Aligned_cols=65 Identities=14% Similarity=0.326 Sum_probs=47.6
Q ss_pred hHHHHHHHhhhcccEEEeecCCCCCCCccccCCHHHHHHhhhcccccccceee-----eceeeeeeechhhHHHH
Q 030302 7 NRKEICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVRETF-----AWMHYYWYLTNDGIEFL 76 (179)
Q Consensus 7 nr~~IYe~LFkEGV~VakKD~~~p~Hpel~VpNL~ViK~mqSLkSrGyVkEqF-----aWrh~Yw~LTneGI~YL 76 (179)
+|.+|..+|.+.|-+ .-.+.- ..+.|..-.|.+.|+.|.+.|+|...- .=+.++|+||++|.+.+
T Consensus 2 tr~~IL~~L~~~~~~-t~~eLA----~~lgis~~tV~~~L~~Le~~GlV~r~~~~~~~gRp~~~y~LT~~G~~~~ 71 (203)
T TIGR02702 2 TKEDILSYLLKQGQA-TAAALA----EALAISPQAVRRHLKDLETEGLIEYEAVVQGMGRPQYHYQLSRQGREQF 71 (203)
T ss_pred HHHHHHHHHHHcCCC-CHHHHH----HHHCcCHHHHHHHHHHHHHCCCeEEeecccCCCCCceEEEECcchhhhc
Confidence 578899999876653 222211 134578889999999999999997652 23678899999998654
No 21
>TIGR02647 DNA conserved hypothetical protein TIGR02647. Members of this family are found, so far, only in the Gammaproteobacteria. The function is unknown. The location on the chromosome usually is not far from housekeeping genes rather than in what is clearly, say, a prophage region. Some members have been annotated in public databases as DNA-binding protein inhibitor Id-2-related protein, putative transcriptional regulator, or hypothetical DNA binding protein.
Probab=88.51 E-value=0.3 Score=36.55 Aligned_cols=33 Identities=15% Similarity=0.198 Sum_probs=28.5
Q ss_pred CCHHHHHHhhhcccccccceeeeceeeeeeechhhHHH
Q 030302 38 PNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEF 75 (179)
Q Consensus 38 pNL~ViK~mqSLkSrGyVkEqFaWrh~Yw~LTneGI~Y 75 (179)
-+-.++.+++.|..||++...-+= |||+||++-
T Consensus 32 A~p~~i~a~~RLheKGLI~~pdGg-----yLT~~G~~~ 64 (77)
T TIGR02647 32 ASPAAVAAAARLHEKGLTTQPDGG-----YLTSLGLEA 64 (77)
T ss_pred CCHHHHHHHHHHHHcCCccCCCCC-----EecHHHHHH
Confidence 456789999999999999987765 999999963
No 22
>PHA00738 putative HTH transcription regulator
Probab=88.23 E-value=0.42 Score=37.61 Aligned_cols=67 Identities=10% Similarity=0.124 Sum_probs=51.4
Q ss_pred chhhHHHHHHHhhhcccEEEeecCCCCCCCccccCCHHHHHHhhhcccccccceeeeceeeeeeechhhHHH
Q 030302 4 PEKNRKEICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEF 75 (179)
Q Consensus 4 pK~nr~~IYe~LFkEGV~VakKD~~~p~Hpel~VpNL~ViK~mqSLkSrGyVkEqFaWrh~Yw~LTneGI~Y 75 (179)
-..+|++|.++|.+.+.++|- |.. ..+++.--.|.+.|+-|+.-|+|...--=||.||.|+++=-+|
T Consensus 10 ~dptRr~IL~lL~~~e~~~V~-eLa----e~l~lSQptVS~HLKvLreAGLV~srK~Gr~vyY~Ln~~~~~~ 76 (108)
T PHA00738 10 AKILRRKILELIAENYILSAS-LIS----HTLLLSYTTVLRHLKILNEQGYIELYKEGRTLYAKIRENSKEI 76 (108)
T ss_pred CCHHHHHHHHHHHHcCCccHH-HHH----HhhCCCHHHHHHHHHHHHHCCceEEEEECCEEEEEECCCccHH
Confidence 356899999999986533322 322 1235777789999999999999999999999999999875544
No 23
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=88.21 E-value=0.86 Score=28.52 Aligned_cols=43 Identities=14% Similarity=0.218 Sum_probs=34.8
Q ss_pred ccCCHHHHHHhhhcccccccceeeeceeeeeeech-hhHHHHHH
Q 030302 36 DVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTN-DGIEFLRT 78 (179)
Q Consensus 36 ~VpNL~ViK~mqSLkSrGyVkEqFaWrh~Yw~LTn-eGI~YLR~ 78 (179)
.|..-.|.++++.|.++|++...-.=+..||.||+ .+.+.+.+
T Consensus 21 ~is~~~v~~~l~~L~~~g~i~~~~~~~~~~~~~~~~~~~~~~~~ 64 (66)
T smart00418 21 GLSQSTVSHHLKKLREAGLVESRREGKRVYYSLTDEKVADLLEE 64 (66)
T ss_pred CCCHHHHHHHHHHHHHCCCeeeeecCCEEEEEEchHHHHHHHHh
Confidence 46677899999999999999977656788999999 66666553
No 24
>PF13814 Replic_Relax: Replication-relaxation
Probab=87.98 E-value=0.77 Score=36.22 Aligned_cols=43 Identities=19% Similarity=0.361 Sum_probs=35.0
Q ss_pred HHHHHhhhcccccccceeeec--------eeeeeeechhhHHHHHHhhCCCC
Q 030302 41 QVIKLMQSFKSREYVRETFAW--------MHYYWYLTNDGIEFLRTYLNLPS 84 (179)
Q Consensus 41 ~ViK~mqSLkSrGyVkEqFaW--------rh~Yw~LTneGI~YLR~yLhLP~ 84 (179)
.+-..|+.|...|||+. +.. .-+.|+||.+|.++|.+-...++
T Consensus 28 ~~~rrL~~L~~~glv~~-~~~~~~~~~g~~~~vy~Lt~~G~~~l~~~~~~~~ 78 (191)
T PF13814_consen 28 TARRRLKRLRELGLVDR-FRRRVGARGGSQPYVYYLTPAGARLLADLRGIRP 78 (191)
T ss_pred HHHHHHHHHhhCCcEEe-ecccccccCCCcceEEEECHHHHHHHHhccCCcc
Confidence 78899999999999954 444 45789999999999998766543
No 25
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=87.88 E-value=0.69 Score=34.34 Aligned_cols=44 Identities=11% Similarity=0.113 Sum_probs=37.3
Q ss_pred ccCCHHHHHHhhhcccccccceee---eceeeeeeechhhHHHHHHh
Q 030302 36 DVPNLQVIKLMQSFKSREYVRETF---AWMHYYWYLTNDGIEFLRTY 79 (179)
Q Consensus 36 ~VpNL~ViK~mqSLkSrGyVkEqF---aWrh~Yw~LTneGI~YLR~y 79 (179)
.+..=.|..+++.|..+|||..+- .-|-.+++||++|.+.+.+.
T Consensus 53 ~~~~~tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~LT~~G~~~~~~~ 99 (118)
T TIGR02337 53 CILRPSLTGILARLERDGLVTRLKASNDQRRVYISLTPKGQALYASL 99 (118)
T ss_pred CCCchhHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHhHHHHHHHh
Confidence 356667899999999999998765 56889999999999998764
No 26
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=87.04 E-value=0.71 Score=39.63 Aligned_cols=48 Identities=10% Similarity=0.190 Sum_probs=40.6
Q ss_pred cccCCHHHHHHhhhcccccccceeeeceeeeeeechhhHHHHHHhhCC
Q 030302 35 IDVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEFLRTYLNL 82 (179)
Q Consensus 35 l~VpNL~ViK~mqSLkSrGyVkEqFaWrh~Yw~LTneGI~YLR~yLhL 82 (179)
+++..-.|-+.++.|..+|||.-+-.=+-.+|+||++|.+.|.+-+.-
T Consensus 31 L~iS~~Tvsr~Lk~LEe~GlI~R~~~~r~~~v~LTekG~~ll~~~~~d 78 (217)
T PRK14165 31 TGTSSKTAARILKQLEDEGYITRTIVPRGQLITITEKGLDVLYNEYAD 78 (217)
T ss_pred HCcCHHHHHHHHHHHHHCCCEEEEEcCCceEEEECHHHHHHHHHHHHH
Confidence 468999999999999999999876666889999999999987654433
No 27
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=86.71 E-value=0.41 Score=34.83 Aligned_cols=36 Identities=14% Similarity=0.158 Sum_probs=28.5
Q ss_pred HHHHHhhhcccccccceeeeceeeeeeechhhHHHHHHh
Q 030302 41 QVIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEFLRTY 79 (179)
Q Consensus 41 ~ViK~mqSLkSrGyVkEqFaWrh~Yw~LTneGI~YLR~y 79 (179)
.|-=+++.|+.-|+|.. -. .-+|.||++|.++|.++
T Consensus 56 ri~Wa~~~L~~aGli~~-~~--rG~~~iT~~G~~~l~~~ 91 (92)
T PF14338_consen 56 RIRWARSYLKKAGLIER-PK--RGIWRITEKGRKALAEH 91 (92)
T ss_pred hHHHHHHHHHHCCCccC-CC--CCceEECHhHHHHHhhC
Confidence 45557899999999955 33 34999999999999863
No 28
>PF09639 YjcQ: YjcQ protein; InterPro: IPR018597 YjcQ is a protein of approx. 100 residues containing four alpha helices and three beta strands. It is found in bacteria and also in the Lactococcus phage Tuc2009. In bacteria it appears to be under the regulation of SigD RNA polymerase which is responsible for the expression of many genes encoding cell-surface proteins related to flagellar assembly, motility, chemotaxis and autolysis in the late exponential growth phase. The exact function of YjcQ is unknown []. However, it is thought to be the major head protein in viruses [] and is found in prophage in bacteria. ; PDB: 2HGC_A.
Probab=85.60 E-value=0.69 Score=34.03 Aligned_cols=44 Identities=16% Similarity=0.213 Sum_probs=30.3
Q ss_pred cccCCHHHHHHhhhcccccccceeeece------eeeeeechhhHHHHHH
Q 030302 35 IDVPNLQVIKLMQSFKSREYVRETFAWM------HYYWYLTNDGIEFLRT 78 (179)
Q Consensus 35 l~VpNL~ViK~mqSLkSrGyVkEqFaWr------h~Yw~LTneGI~YLR~ 78 (179)
.++.+-....+|+.|...||++-..-|+ .--=.+|-+||+||.+
T Consensus 20 ~~~~~~~~~~il~~L~d~GyI~G~~~~~~~~~~~~~~~~IT~~Gi~YL~E 69 (88)
T PF09639_consen 20 PDITDSYWSDILRMLQDEGYIKGVSVVRYSPYVALSDPRITLKGIEYLEE 69 (88)
T ss_dssp HTS-HHHHHHHHHHHHHHTSEE--EESSSSEE--SS--EE-HHHHHHHHH
T ss_pred cchhHHHHHHHHHHHHHCCCccceEEEeccceeecCCceEcHHHHHHHHH
Confidence 3466789999999999999998433332 2333478999999998
No 29
>PRK09416 lstR lineage-specific thermal regulator protein; Provisional
Probab=85.31 E-value=0.68 Score=37.52 Aligned_cols=47 Identities=17% Similarity=0.405 Sum_probs=38.2
Q ss_pred ccCCHHHHHHhhhcccccccceeeec---eeeeeeechhhHHHHHHhhCCCC
Q 030302 36 DVPNLQVIKLMQSFKSREYVRETFAW---MHYYWYLTNDGIEFLRTYLNLPS 84 (179)
Q Consensus 36 ~VpNL~ViK~mqSLkSrGyVkEqFaW---rh~Yw~LTneGI~YLR~yLhLP~ 84 (179)
++..=.|.-+++.|...|+|... | +-=||.||++|.++|.+.+.-|.
T Consensus 74 ~~s~GtIYp~L~RLE~~GlI~s~--~~~~~RK~Y~ITe~Gre~L~e~~~~~~ 123 (135)
T PRK09416 74 EGNEGSLYTLLHRLEQNRFIQSS--WDHEGAKYYQLTDKGNKMLRKAEKNAT 123 (135)
T ss_pred cCCCccHHHHHHHHHHCCCeEEe--ecCCCceEEEECHHHHHHHHHHHhCHH
Confidence 34556788899999999999763 5 34689999999999999988654
No 30
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=85.01 E-value=0.52 Score=39.04 Aligned_cols=71 Identities=17% Similarity=0.277 Sum_probs=50.4
Q ss_pred hHHHHHHHhhhcccEEEeecCCCCCCCccccCCHHHHHHhhhcccccccc-----e-eeeceeeeeeechhhH-HHHHHh
Q 030302 7 NRKEICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVR-----E-TFAWMHYYWYLTNDGI-EFLRTY 79 (179)
Q Consensus 7 nr~~IYe~LFkEGV~VakKD~~~p~Hpel~VpNL~ViK~mqSLkSrGyVk-----E-qFaWrh~Yw~LTneGI-~YLR~y 79 (179)
..+.|...|...|++- |-.+. ..|+|..=.|-++|+.|...|+|. + .-.|=.|||+||.+=| +.|+..
T Consensus 23 ~~~~Vl~~L~~~g~~t---deeLA--~~Lgi~~~~VRk~L~~L~e~gLv~~~r~r~~~~Gr~~y~w~l~~~~i~d~ik~~ 97 (178)
T PRK06266 23 EGFEVLKALIKKGEVT---DEEIA--EQTGIKLNTVRKILYKLYDARLADYKREKDEETNWYTYTWKPELEKLPEIIKKK 97 (178)
T ss_pred cHhHHHHHHHHcCCcC---HHHHH--HHHCCCHHHHHHHHHHHHHCCCeEEeeeeccCCCcEEEEEEeCHHHHHHHHHHH
Confidence 4566777777767542 21111 134688889999999999999987 1 4689999999998776 666666
Q ss_pred hCC
Q 030302 80 LNL 82 (179)
Q Consensus 80 LhL 82 (179)
+|-
T Consensus 98 ~~~ 100 (178)
T PRK06266 98 KME 100 (178)
T ss_pred HHH
Confidence 553
No 31
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=83.87 E-value=0.43 Score=33.33 Aligned_cols=64 Identities=16% Similarity=0.266 Sum_probs=45.0
Q ss_pred CccchhhHHHHHHHhhhccc--EEEeecCCCCCCCccccCCHHHHHHhhhcccccccceeeeceeeeeeech
Q 030302 1 MIIPEKNRKEICKYLFQEGV--CYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTN 70 (179)
Q Consensus 1 MlipK~nr~~IYe~LFkEGV--~VakKD~~~p~Hpel~VpNL~ViK~mqSLkSrGyVkEqFaWrh~Yw~LTn 70 (179)
|+.+..+...|+++|-+.|- +- -+|. -.+++|+.-.|-++|.+|++.|+|.-.=. .--+|.|+.
T Consensus 1 ~~~~~~~~~~IL~~L~~~g~~~~t-a~eL----a~~lgl~~~~v~r~L~~L~~~G~V~~~~~-~~~~W~i~~ 66 (68)
T smart00550 1 SLTQDSLEEKILEFLENSGDETST-ALQL----AKNLGLPKKEVNRVLYSLEKKGKVCKQGG-TPPLWKLTD 66 (68)
T ss_pred CCCchHHHHHHHHHHHHCCCCCcC-HHHH----HHHHCCCHHHHHHHHHHHHHCCCEEecCC-CCCceEeec
Confidence 46778889999999987654 21 1121 12456888899999999999999965433 224777764
No 32
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=81.33 E-value=0.95 Score=36.63 Aligned_cols=69 Identities=16% Similarity=0.275 Sum_probs=47.8
Q ss_pred HHHHHHhhhcccEEEeecCCCCCCCccccCCHHHHHHhhhccccccc---c---eeeeceeeeeeechhhH-HHHHHhhC
Q 030302 9 KEICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYV---R---ETFAWMHYYWYLTNDGI-EFLRTYLN 81 (179)
Q Consensus 9 ~~IYe~LFkEGV~VakKD~~~p~Hpel~VpNL~ViK~mqSLkSrGyV---k---EqFaWrh~Yw~LTneGI-~YLR~yLh 81 (179)
+.|...|+..|+| ...|.. ..|.+..=.|-|++..|...|+| + +.-.|.-|||+++-+=| +-|+..+|
T Consensus 17 v~Vl~aL~~~~~~-tdEeLa----~~Lgi~~~~VRk~L~~L~e~~Lv~~~r~r~~~~gw~~Y~w~i~~~~i~d~Ik~~~~ 91 (158)
T TIGR00373 17 GLVLFSLGIKGEF-TDEEIS----LELGIKLNEVRKALYALYDAGLADYKRRKDDETGWYEYTWRINYEKALDVLKRKLE 91 (158)
T ss_pred HHHHHHHhccCCC-CHHHHH----HHHCCCHHHHHHHHHHHHHCCCceeeeeeecCCCcEEEEEEeCHHHHHHHHHHHHH
Confidence 4566666666653 222211 13458888999999999999999 3 34489999999877665 77776665
Q ss_pred C
Q 030302 82 L 82 (179)
Q Consensus 82 L 82 (179)
-
T Consensus 92 ~ 92 (158)
T TIGR00373 92 E 92 (158)
T ss_pred H
Confidence 3
No 33
>COG1695 Predicted transcriptional regulators [Transcription]
Probab=79.85 E-value=2.3 Score=32.43 Aligned_cols=50 Identities=14% Similarity=0.173 Sum_probs=38.1
Q ss_pred cCCHHHHHHhhhcccccccceeeece-----eeeeeechhhHHHHHHhhCCCCCC
Q 030302 37 VPNLQVIKLMQSFKSREYVRETFAWM-----HYYWYLTNDGIEFLRTYLNLPSEI 86 (179)
Q Consensus 37 VpNL~ViK~mqSLkSrGyVkEqFaWr-----h~Yw~LTneGI~YLR~yLhLP~ei 86 (179)
+.-=.+..+|+.|.+.|||.....=+ ==||.||++|.++|.+.+....++
T Consensus 42 ~s~gtiYp~L~~Le~~Gli~~~~~~~~~g~~rk~Y~lTe~G~~~l~~~~~~~~~~ 96 (138)
T COG1695 42 PSPGTIYPLLKRLEKEGLIESRWEESGGGPPRKYYRLTEKGKEELAELREEWGAL 96 (138)
T ss_pred CCCCcHHHHHHHHHHCCCeEEEecccCCCCCceEEEECHHHHHHHHHHHHHHHHH
Confidence 44446788899999999998764444 268999999999999888544333
No 34
>PF03374 ANT: Phage antirepressor protein KilAC domain; InterPro: IPR005039 This entry is represented by Bacteriophage P1, Ant1 C-terminal domain, which represents the processed Ant2 chain. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Prophages P1 and P7 exist as unit copy DNA plasmids in the bacterial cell. Maintenance of the prophage state requires the continuous expression of two repressors: (i) C1 is a protein which negatively regulates the expression of lytic genes including the C1 inactivator gene coi, and (ii) C4 is an antisense RNA which specifically inhibits the synthesis of an anti-repressor Ant.; GO: 0003677 DNA binding
Probab=79.11 E-value=6.4 Score=28.99 Aligned_cols=60 Identities=23% Similarity=0.393 Sum_probs=39.5
Q ss_pred hHHHHHHHhhhcccEEE-eecCCCCCCCccccCCHHHHHHhhhccccccccee-eecee--------eeeeechhhHHHH
Q 030302 7 NRKEICKYLFQEGVCYA-KKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVRET-FAWMH--------YYWYLTNDGIEFL 76 (179)
Q Consensus 7 nr~~IYe~LFkEGV~Va-kKD~~~p~Hpel~VpNL~ViK~mqSLkSrGyVkEq-FaWrh--------~Yw~LTneGI~YL 76 (179)
.+...++.|-++|+|.- .++.+.|. |...++||.... ..|.| ..=+.|.+|++||
T Consensus 37 ~~~~l~~~Lr~~g~l~~~~~~~~~p~---------------q~~~~~G~~~~k~~~~~~~~g~~~~~~~~~iT~kG~~~i 101 (111)
T PF03374_consen 37 GRNKLFQWLREKGWLYRRGKGRNLPY---------------QKYIDAGYFEVKETTYTHSDGEGKTSSQTRITPKGLEWI 101 (111)
T ss_pred CHHHHHHHHHhCCceEECCCCCcccC---------------hhhhccceEEEeeeEeecCCCCcEEEEEEEEehhHHHHH
Confidence 46788999999999976 34444444 333455664333 22222 5567899999999
Q ss_pred HHhhC
Q 030302 77 RTYLN 81 (179)
Q Consensus 77 R~yLh 81 (179)
.+.|+
T Consensus 102 ~~~l~ 106 (111)
T PF03374_consen 102 AKRLA 106 (111)
T ss_pred HHHHH
Confidence 98764
No 35
>TIGR02719 repress_PhaQ poly-beta-hydroxybutyrate-responsive repressor. Members of this family are transcriptional regulatory proteins found in the vicinity of poly-beta-hydroxybutyrate (PHB) operons in several species of Bacillus. This protein appears to have repressor activity modulated by PHB itself. This protein belongs to the larger PadR family (see pfam03551).
Probab=78.96 E-value=2.6 Score=33.99 Aligned_cols=52 Identities=13% Similarity=0.199 Sum_probs=37.9
Q ss_pred ccCCHHHHHHhhhcccccccceee----e-ceeeeeeechhhHHHHHHhhCCCCCCc
Q 030302 36 DVPNLQVIKLMQSFKSREYVRETF----A-WMHYYWYLTNDGIEFLRTYLNLPSEIV 87 (179)
Q Consensus 36 ~VpNL~ViK~mqSLkSrGyVkEqF----a-Wrh~Yw~LTneGI~YLR~yLhLP~eiV 87 (179)
+|..=.|.-+|+.|...|+|.... + =+--||.||++|.++|.+.+.--.++.
T Consensus 54 ~v~~GtLYp~L~RLE~~GlI~~~~~~~~~gp~RK~Y~LTe~Gr~~L~~~~~~w~~~~ 110 (138)
T TIGR02719 54 SVDQGNVYRTLRKLEKDNLISSQWDTSAEGPAKRIYSLTDAGEQYLSMCANSFEHYQ 110 (138)
T ss_pred CCCcChHHHHHHHHHHCCCEEEEeeecCCCCCcEEEEECHHHHHHHHHHHHHHHHHH
Confidence 355556888999999999998521 1 114789999999999988775544443
No 36
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=78.60 E-value=2 Score=32.67 Aligned_cols=65 Identities=23% Similarity=0.298 Sum_probs=43.6
Q ss_pred HHHHHHhhhcccEEEeecCCCCCCCccccCCHHHHHHhhhcccccccceeeec-----------------eeeeeeechh
Q 030302 9 KEICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVRETFAW-----------------MHYYWYLTND 71 (179)
Q Consensus 9 ~~IYe~LFkEGV~VakKD~~~p~Hpel~VpNL~ViK~mqSLkSrGyVkEqFaW-----------------rh~Yw~LTne 71 (179)
..|..+|.+-|+=-++-=. -.+.+|=-.|..++..|...|+|.+.-+= -|-||-||.+
T Consensus 10 ~~IL~hl~~~~~Dy~k~ia-----~~l~~~~~~v~~~l~~Le~~GLler~~g~~iK~~~~k~K~~~e~~~hHtYY~LTr~ 84 (92)
T PF10007_consen 10 LKILQHLKKAGPDYAKSIA-----RRLKIPLEEVREALEKLEEMGLLERVEGKTIKRSEAKFKPKKEVHKHHTYYRLTRE 84 (92)
T ss_pred HHHHHHHHHHCCCcHHHHH-----HHHCCCHHHHHHHHHHHHHCCCeEEecCcccchhhhhcccchhhhcCCceeeecHh
Confidence 4666677665542111100 02346667788888888888888765432 4899999999
Q ss_pred hHHHHHH
Q 030302 72 GIEFLRT 78 (179)
Q Consensus 72 GI~YLR~ 78 (179)
|-.+||+
T Consensus 85 G~~llR~ 91 (92)
T PF10007_consen 85 GELLLRE 91 (92)
T ss_pred HHHHHhc
Confidence 9999996
No 37
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=77.00 E-value=2.9 Score=29.54 Aligned_cols=43 Identities=19% Similarity=0.208 Sum_probs=34.2
Q ss_pred cccCCHHHHHHhhhcccccccceeeeceeeeeeechhhHHHHHHhh
Q 030302 35 IDVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEFLRTYL 80 (179)
Q Consensus 35 l~VpNL~ViK~mqSLkSrGyVkEqFaWrh~Yw~LTneGI~YLR~yL 80 (179)
+.|+--.|.++++.|.++|||...=+ -+++||++|.+.+...+
T Consensus 9 l~is~stvs~~l~~L~~~glI~r~~~---~~~~lT~~g~~~~~~~~ 51 (96)
T smart00529 9 LNVSPPTVTQMLKKLEKDGLVEYEPY---RGITLTEKGRRLARRLL 51 (96)
T ss_pred hCCChHHHHHHHHHHHHCCCEEEcCC---CceEechhHHHHHHHHH
Confidence 35777889999999999999877543 37899999998776544
No 38
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=76.43 E-value=1.7 Score=35.17 Aligned_cols=74 Identities=22% Similarity=0.189 Sum_probs=55.9
Q ss_pred hhHHHHHHHhhhcccEEEeecCCCCCCCccccCCHHHHHHhhhcccccccceeeeceeeeeeechhhH------------
Q 030302 6 KNRKEICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDGI------------ 73 (179)
Q Consensus 6 ~nr~~IYe~LFkEGV~VakKD~~~p~Hpel~VpNL~ViK~mqSLkSrGyVkEqFaWrh~Yw~LTneGI------------ 73 (179)
....+||+.+-+.|.+ --+|... .|+|.--.|.+.++-|.+.|||+-. .+....||++|-
T Consensus 10 dYL~~Iy~l~~~~~~~-~~~diA~----~L~Vsp~sVt~ml~rL~~~GlV~~~---~y~gi~LT~~G~~~a~~~~r~hrl 81 (154)
T COG1321 10 DYLETIYELLEEKGFA-RTKDIAE----RLKVSPPSVTEMLKRLERLGLVEYE---PYGGVTLTEKGREKAKELLRKHRL 81 (154)
T ss_pred HHHHHHHHHHhccCcc-cHHHHHH----HhCCCcHHHHHHHHHHHHCCCeEEe---cCCCeEEChhhHHHHHHHHHHHHH
Confidence 3456888877655544 4455431 4678888999999999999999753 345779999997
Q ss_pred --HHHHHhhCCCCCCc
Q 030302 74 --EFLRTYLNLPSEIV 87 (179)
Q Consensus 74 --~YLR~yLhLP~eiV 87 (179)
.||.+.|+++.+.+
T Consensus 82 le~fL~~~lg~~~~~~ 97 (154)
T COG1321 82 LERFLVDVLGLDWEEA 97 (154)
T ss_pred HHHHHHHHhCCCHHHH
Confidence 57888899997775
No 39
>TIGR03433 padR_acidobact transcriptional regulator, Acidobacterial, PadR-family. Members of this protein family are putative transcriptional regulators of the PadR family, as found in species of the Acidobacteria. This family of proteins has expanded greatly in this lineage, and where it regularly is found in the vicinity of a putative transporter protein
Probab=76.37 E-value=3.7 Score=30.34 Aligned_cols=45 Identities=13% Similarity=0.225 Sum_probs=35.3
Q ss_pred ccCCHHHHHHhhhcccccccceee-----eceeeeeeechhhHHHHHHhh
Q 030302 36 DVPNLQVIKLMQSFKSREYVRETF-----AWMHYYWYLTNDGIEFLRTYL 80 (179)
Q Consensus 36 ~VpNL~ViK~mqSLkSrGyVkEqF-----aWrh~Yw~LTneGI~YLR~yL 80 (179)
+|..=.|..++..|..+|+|.... .=+=-||.||++|.++|.+.+
T Consensus 36 ~i~~gtlY~~L~rLe~~GlI~~~~~~~~~~~~rk~y~iT~~Gr~~l~~~~ 85 (100)
T TIGR03433 36 QVEEGSLYPALHRLERRGWIAAEWGESENNRRAKFYRLTAAGRKQLAAET 85 (100)
T ss_pred ccCCCcHHHHHHHHHHCCCeEEEeeecCCCCCceEEEECHHHHHHHHHHH
Confidence 466667889999999999998742 112379999999999998754
No 40
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=76.24 E-value=3.4 Score=30.67 Aligned_cols=43 Identities=5% Similarity=0.145 Sum_probs=38.0
Q ss_pred ccCCHHHHHHhhhcccccccceeeec---eeeeeeechhhHHHHHH
Q 030302 36 DVPNLQVIKLMQSFKSREYVRETFAW---MHYYWYLTNDGIEFLRT 78 (179)
Q Consensus 36 ~VpNL~ViK~mqSLkSrGyVkEqFaW---rh~Yw~LTneGI~YLR~ 78 (179)
++..=.|.+++..|..+|||+..=+. |-.|-+||++|.+.+.+
T Consensus 54 ~~~~stvs~~i~~Le~kg~I~r~~~~~D~R~~~i~lT~~G~~~~~~ 99 (109)
T TIGR01889 54 LIKQSALVKIIKKLSKKGYLSKERSEDDERKVIISINKEQRSKIES 99 (109)
T ss_pred CCCHHHHHHHHHHHHHCCCEeccCCcccCCeEEEEECHHHHHHHHH
Confidence 57888899999999999999987777 78999999999987764
No 41
>PF09382 RQC: RQC domain; InterPro: IPR018982 This entry represents the RQC domain, which is a DNA-binding domain found only in RecQ family enzymes. RecQ family helicases can unwind G4 DNA, and play important roles at G-rich domains of the genome, including the telomeres, rDNA, and immunoglobulin switch regions. This domain has a helix-turn-helix structure and acts as a high affinity G4 DNA binding domain []. Binding of RecQ to Holliday junctions involves both the RQC and the HRDC domains.; GO: 0043140 ATP-dependent 3'-5' DNA helicase activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1OYW_A 1OYY_A 3AAF_A 2AXL_A 2V1X_B 2WWY_B.
Probab=76.02 E-value=3.8 Score=29.73 Aligned_cols=45 Identities=22% Similarity=0.269 Sum_probs=38.2
Q ss_pred ccCCHHHHHHhhhcccccccceeee-ceeeeeeechhhHHHHHHhh
Q 030302 36 DVPNLQVIKLMQSFKSREYVRETFA-WMHYYWYLTNDGIEFLRTYL 80 (179)
Q Consensus 36 ~VpNL~ViK~mqSLkSrGyVkEqFa-Wrh~Yw~LTneGI~YLR~yL 80 (179)
+++.-.+..+++.|...||+.+... |.+-|-.||++|-++|+.-.
T Consensus 53 ~~~~~~~~~li~~Li~~g~L~~~~~~~~~~~l~~~~~~~~~l~g~~ 98 (106)
T PF09382_consen 53 DMSKDDWERLIRQLILEGYLSEDNGGFAYPYLKLTPKGKELLNGKQ 98 (106)
T ss_dssp TS-HHHHHHHHHHHHHTTSEEEEECCCCTEEEEE-GGGHHHHCTTS
T ss_pred cCCHHHHHHHHHHHHHcCCceecCCcccccEEEECHHHHHHHCCCc
Confidence 3788899999999999999988775 89999999999999998643
No 42
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein. Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.
Probab=75.73 E-value=1.3 Score=36.39 Aligned_cols=61 Identities=13% Similarity=0.159 Sum_probs=43.6
Q ss_pred hhHHHHHHHhhhcccEEEeecCCCCCCCccccCCHHHHHHhhhcccccccceeeeceeeeeeechhh
Q 030302 6 KNRKEICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDG 72 (179)
Q Consensus 6 ~nr~~IYe~LFkEGV~VakKD~~~p~Hpel~VpNL~ViK~mqSLkSrGyVkEqFaWrh~Yw~LTneG 72 (179)
.....|+.+|-+.|-+ .-+|.. ..++++--.|.+.++.|...|+|...-. |.-+|.||++|
T Consensus 143 ~~~~~IL~~l~~~g~~-s~~eia----~~l~is~stv~r~L~~Le~~GlI~r~~~-r~~~~~lT~~G 203 (203)
T TIGR01884 143 REELKVLEVLKAEGEK-SVKNIA----KKLGKSLSTISRHLRELEKKGLVEQKGR-KGKRYSLTKLG 203 (203)
T ss_pred HHHHHHHHHHHHcCCc-CHHHHH----HHHCcCHHHHHHHHHHHHHCCCEEEEcC-CccEEEeCCCC
Confidence 4456888888765432 112211 1235666778899999999999998876 88899999987
No 43
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=73.15 E-value=3.6 Score=36.82 Aligned_cols=43 Identities=14% Similarity=0.207 Sum_probs=35.4
Q ss_pred cccCCHHHHHHhhhcccccccceeeeceeeeeeechhhHHHHHHhh
Q 030302 35 IDVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEFLRTYL 80 (179)
Q Consensus 35 l~VpNL~ViK~mqSLkSrGyVkEqFaWrh~Yw~LTneGI~YLR~yL 80 (179)
|.|.=.-|.-.|++|.+-|||++ - .--||-+|.||.++|-+.|
T Consensus 35 lgiT~QaVsehiK~Lv~eG~i~~--~-gR~~Y~iTkkG~e~l~~~~ 77 (260)
T COG1497 35 LGITLQAVSEHIKELVKEGLIEK--E-GRGEYEITKKGAEWLLEQL 77 (260)
T ss_pred cCCCHHHHHHHHHHHHhccceee--c-CCeeEEEehhHHHHHHHHH
Confidence 45888889999999999999999 2 2357799999999986544
No 44
>TIGR02277 PaaX_trns_reg phenylacetic acid degradation operon negative regulatory protein PaaX. This transcriptional regulator is always found in association with operons believed to be involved in the degradation of phenylacetic acid. The gene product has been shown to bind to the promoter sites and repress their transcription.
Probab=72.18 E-value=4.2 Score=35.68 Aligned_cols=43 Identities=9% Similarity=0.155 Sum_probs=33.9
Q ss_pred ccCCHHHHHHhhhcccccccceeeeceeeeeeechhhHHHHHH
Q 030302 36 DVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEFLRT 78 (179)
Q Consensus 36 ~VpNL~ViK~mqSLkSrGyVkEqFaWrh~Yw~LTneGI~YLR~ 78 (179)
.|..=.|..++.-|+++|++...=.=+--||.||++|.+.|.+
T Consensus 31 gi~~~~vr~al~RL~~~G~l~~~~~grr~~Y~LT~~g~~~l~~ 73 (280)
T TIGR02277 31 GINERLVRTAVSRLVAQGWLQSERKGRRSFYSLTDKGRRRFAA 73 (280)
T ss_pred CCCcchHHHHHHHHHHCCCEEeeecCCCCEEEECHHHHHHHHH
Confidence 4677788999999999999977411123677999999999986
No 45
>PHA02943 hypothetical protein; Provisional
Probab=71.27 E-value=2.4 Score=35.72 Aligned_cols=60 Identities=13% Similarity=0.188 Sum_probs=44.4
Q ss_pred hhHHHHHHHhhhcccEEEeecCCCCCCCccccCCHHHHHHhhhcccccccceeeeceeeeeeechh
Q 030302 6 KNRKEICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTND 71 (179)
Q Consensus 6 ~nr~~IYe~LFkEGV~VakKD~~~p~Hpel~VpNL~ViK~mqSLkSrGyVkEqFaWrh~Yw~LTne 71 (179)
...+.|+|+| +.|+.-... +.+ .+.++-=+|-=+++-|.+-|+|++.===+--||+|.+.
T Consensus 11 ~R~~eILE~L-k~G~~Ttse---IAk--aLGlS~~qa~~~LyvLErEG~VkrV~~G~~tyw~l~~d 70 (165)
T PHA02943 11 TRMIKTLRLL-ADGCKTTSR---IAN--KLGVSHSMARNALYQLAKEGMVLKVEIGRAAIWCLDED 70 (165)
T ss_pred HHHHHHHHHH-hcCCccHHH---HHH--HHCCCHHHHHHHHHHHHHcCceEEEeecceEEEEEChH
Confidence 4567899999 999862111 111 23577788888999999999999966556789999983
No 46
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=70.91 E-value=5.3 Score=28.05 Aligned_cols=46 Identities=17% Similarity=0.243 Sum_probs=39.7
Q ss_pred ccCCHHHHHHhhhcccccccceeee---ceeeeeeechhhHHHHHHhhC
Q 030302 36 DVPNLQVIKLMQSFKSREYVRETFA---WMHYYWYLTNDGIEFLRTYLN 81 (179)
Q Consensus 36 ~VpNL~ViK~mqSLkSrGyVkEqFa---Wrh~Yw~LTneGI~YLR~yLh 81 (179)
.|..=.|..++++|..+|||+..-. =|-.+..||++|-+.+.+..-
T Consensus 47 ~i~~~~vt~~l~~Le~~glv~r~~~~~DrR~~~l~lT~~G~~~~~~~~~ 95 (126)
T COG1846 47 GLDRSTVTRLLKRLEDKGLIERLRDPEDRRAVLVRLTEKGRELLEQLLP 95 (126)
T ss_pred CCCHHHHHHHHHHHHHCCCeeecCCccccceeeEEECccHHHHHHHhcc
Confidence 4777789999999999999988776 688999999999999886543
No 47
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=70.56 E-value=5.3 Score=30.69 Aligned_cols=43 Identities=12% Similarity=0.094 Sum_probs=37.2
Q ss_pred ccCCHHHHHHhhhcccccccceee---eceeeeeeechhhHHHHHH
Q 030302 36 DVPNLQVIKLMQSFKSREYVRETF---AWMHYYWYLTNDGIEFLRT 78 (179)
Q Consensus 36 ~VpNL~ViK~mqSLkSrGyVkEqF---aWrh~Yw~LTneGI~YLR~ 78 (179)
.|..=.|.++++.|..+|||...- .=|-.+.+||++|.+.+.+
T Consensus 65 ~i~~~tvsr~l~~Le~~GlI~R~~~~~DrR~~~l~LT~~G~~~~~~ 110 (144)
T PRK11512 65 SVDLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTSGAAICEQ 110 (144)
T ss_pred CCCHHHHHHHHHHHHHCCCEEeccCcccCCeeEeEEChhHHHHHHH
Confidence 478888999999999999998764 4788999999999988765
No 48
>PF01638 HxlR: HxlR-like helix-turn-helix; InterPro: IPR002577 The hxlR-type HTH domain is a domain of ~90-100 amino acids present in putative transcription regulators with a winged helix-turn-helix (wHTH) structure. The domain is named after Bacillus subtilis hxlR, a transcription activator of the hxlAB operon involved in the detoxification of formaldehyde []. The hxlR-type domain forms the core of putative transcription regulators and of hypothetical proteins occurring in eubacteria as well as in archaea. The sequence and structure of hxlR-type proteins show similarities with the marR-type wHTH []. The crystal structure of ytfH resembles the DNA-binding domains of winged helix proteins, containing a three helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-H2-B1-H3-H4-B2-B3-H5-H6. This topology corresponds with that of the marR-type DNA-binding domain, wherein helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. ; PDB: 2F2E_B 3DF8_A 1Z7U_B 1YYV_A 4A5M_D 4A5N_B 2FSW_A 2HZT_D.
Probab=70.35 E-value=6.3 Score=28.38 Aligned_cols=68 Identities=18% Similarity=0.181 Sum_probs=42.8
Q ss_pred chhhHHHHHHHhhhcccEEEeecCCCCCCCcc-ccCCHHHHHHhhhcccccccceeee---ceeeeeeechhhHHHHH
Q 030302 4 PEKNRKEICKYLFQEGVCYAKKDYNLAKHPEI-DVPNLQVIKLMQSFKSREYVRETFA---WMHYYWYLTNDGIEFLR 77 (179)
Q Consensus 4 pK~nr~~IYe~LFkEGV~VakKD~~~p~Hpel-~VpNL~ViK~mqSLkSrGyVkEqFa---Wrh~Yw~LTneGI~YLR 77 (179)
.++=...|...|++ |.+ -|+- .+..+ +|++--+.+.|+.|...|+|..+.. =.+..|.||++|.+.+.
T Consensus 3 g~kW~~~IL~~l~~-g~~----rf~e-l~~~l~~is~~~L~~~L~~L~~~GLv~r~~~~~~p~~v~Y~LT~~G~~l~~ 74 (90)
T PF01638_consen 3 GGKWTLLILRALFQ-GPM----RFSE-LQRRLPGISPKVLSQRLKELEEAGLVERRVYPEVPPRVEYSLTEKGKELLP 74 (90)
T ss_dssp HSTTHHHHHHHHTT-SSE----EHHH-HHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSSSEEEEEE-HHHHHHHH
T ss_pred CCCCHHHHHHHHHh-CCC----cHHH-HHHhcchhHHHHHHHHHHHHHHcchhhcccccCCCCCCccCCCcCHHHHHH
Confidence 34445567777776 433 2220 01123 3666778899999999999966532 13578999999998764
No 49
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=68.43 E-value=2.4 Score=34.52 Aligned_cols=54 Identities=13% Similarity=0.151 Sum_probs=37.8
Q ss_pred CccchhhHHHHHHHhhhcccEEEeecCCCCCCCcc----ccCCHHHHHHhhhccccccccee
Q 030302 1 MIIPEKNRKEICKYLFQEGVCYAKKDYNLAKHPEI----DVPNLQVIKLMQSFKSREYVRET 58 (179)
Q Consensus 1 MlipK~nr~~IYe~LFkEGV~VakKD~~~p~Hpel----~VpNL~ViK~mqSLkSrGyVkEq 58 (179)
|.|.++.+.++.-.++ |....+-....-.+| +||.-+|-|+|+.|+..|+|..+
T Consensus 1 M~ls~~~~yAl~~l~~----lA~~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s~ 58 (164)
T PRK10857 1 MRLTSKGRYAVTAMLD----VALNSEAGPVPLADISERQGISLSYLEQLFSRLRKNGLVSSV 58 (164)
T ss_pred CcCCcHHHHHHHHHHH----HHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeC
Confidence 8888988888887765 322222111223334 58999999999999999999974
No 50
>PF07381 DUF1495: Winged helix DNA-binding domain (DUF1495); InterPro: IPR010863 This family consists of several hypothetical archaeal proteins of around 110 residues in length. The function of this family is unknown, although one sequence (Q8U3W1 from SWISSPROT) is described as a putative HTH transcription regulator.
Probab=68.25 E-value=3.4 Score=31.32 Aligned_cols=61 Identities=23% Similarity=0.234 Sum_probs=38.0
Q ss_pred hhHHHHHHHhhhcccEEEeecCCCCCCCc---c----ccCCHHHHHHh----------hhccccccc-ceeeeceeeeee
Q 030302 6 KNRKEICKYLFQEGVCYAKKDYNLAKHPE---I----DVPNLQVIKLM----------QSFKSREYV-RETFAWMHYYWY 67 (179)
Q Consensus 6 ~nr~~IYe~LFkEGV~VakKD~~~p~Hpe---l----~VpNL~ViK~m----------qSLkSrGyV-kEqFaWrh~Yw~ 67 (179)
+.|+.|+.+|++- .|..-. | .+.-=+|+-+| .||.+-|+| .|.-.=..-||.
T Consensus 9 ~~R~~vl~~L~~~----------yp~~~~~~eIar~v~~~~snV~GaL~G~g~rY~~e~SLv~lGLV~~~~~~~g~k~Y~ 78 (90)
T PF07381_consen 9 KVRKKVLEYLCSI----------YPEPAYPSEIARSVGSDYSNVLGALRGDGKRYNKEDSLVGLGLVEEEEEKGGFKYYR 78 (90)
T ss_pred HHHHHHHHHHHHc----------CCCcCCHHHHHHHHCCCHHHHHHHHhcCCCCcCcchhHHHcCCeeEeeecCCeeEEE
Confidence 5688999999842 122222 2 12222344444 589999999 333333445999
Q ss_pred echhhHHHH
Q 030302 68 LTNDGIEFL 76 (179)
Q Consensus 68 LTneGI~YL 76 (179)
||++|+++.
T Consensus 79 lT~~G~~~~ 87 (90)
T PF07381_consen 79 LTEKGKRIA 87 (90)
T ss_pred eChhhhhHH
Confidence 999999763
No 51
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=67.62 E-value=7 Score=29.77 Aligned_cols=44 Identities=5% Similarity=0.095 Sum_probs=37.5
Q ss_pred cCCHHHHHHhhhcccccccceeee---ceeeeeeechhhHHHHHHhh
Q 030302 37 VPNLQVIKLMQSFKSREYVRETFA---WMHYYWYLTNDGIEFLRTYL 80 (179)
Q Consensus 37 VpNL~ViK~mqSLkSrGyVkEqFa---Wrh~Yw~LTneGI~YLR~yL 80 (179)
+..=.|.+++..|..+|||.-.-+ =|..+-+||++|.+.+.+..
T Consensus 58 ~~~~tvt~~v~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~~~~~ 104 (144)
T PRK03573 58 IEQPSLVRTLDQLEEKGLISRQTCASDRRAKRIKLTEKAEPLISEVE 104 (144)
T ss_pred CChhhHHHHHHHHHHCCCEeeecCCCCcCeeeeEEChHHHHHHHHHH
Confidence 677789999999999999987744 47899999999999887644
No 52
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=67.49 E-value=2.8 Score=32.32 Aligned_cols=65 Identities=12% Similarity=0.083 Sum_probs=45.0
Q ss_pred CccchhhHHHHHHHhhhcccEEEeecCCCCCCCcc----ccCCHHHHHHhhhcccccccceeeeceeeeeeech
Q 030302 1 MIIPEKNRKEICKYLFQEGVCYAKKDYNLAKHPEI----DVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTN 70 (179)
Q Consensus 1 MlipK~nr~~IYe~LFkEGV~VakKD~~~p~Hpel----~VpNL~ViK~mqSLkSrGyVkEqFaWrh~Yw~LTn 70 (179)
|.|.++...+|.-.++ |....+-....-.+| +||-=+|-|+|+.|+..|+|..+=+ ..--|.|+.
T Consensus 1 M~ls~~~~YAl~~l~~----La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s~~G-~~Ggy~l~~ 69 (135)
T TIGR02010 1 MRLTTKGRYAVTAMLD----LALNAETGPVTLADISERQGISLSYLEQLFAKLRKAGLVKSVRG-PGGGYQLGR 69 (135)
T ss_pred CcCCcHHHHHHHHHHH----HHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEeC-CCCCEeccC
Confidence 8899999999888877 443333222233344 5999999999999999999987433 333455554
No 53
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=67.19 E-value=5.4 Score=34.55 Aligned_cols=69 Identities=16% Similarity=0.176 Sum_probs=52.1
Q ss_pred hhHHHHHHHhhhcccEEEeecCCCCCCCccccCCHHHHHHhhhcccccccceeeeceeeeeeechhhH-HHHHHh
Q 030302 6 KNRKEICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDGI-EFLRTY 79 (179)
Q Consensus 6 ~nr~~IYe~LFkEGV~VakKD~~~p~Hpel~VpNL~ViK~mqSLkSrGyVkEqFaWrh~Yw~LTneGI-~YLR~y 79 (179)
++=.+||-.|..-|.+-|+.=.. ..+||-=.|..+|+||.+||||..+-+=--.|-..-.+=+ +..++.
T Consensus 16 ~yEa~vY~aLl~~g~~tA~eis~-----~sgvP~~kvY~vl~sLe~kG~v~~~~g~P~~y~av~p~~~i~~~~~~ 85 (247)
T COG1378 16 EYEAKVYLALLCLGEATAKEISE-----ASGVPRPKVYDVLRSLEKKGLVEVIEGRPKKYRAVPPEELIERIKEE 85 (247)
T ss_pred HHHHHHHHHHHHhCCccHHHHHH-----HcCCCchhHHHHHHHHHHCCCEEeeCCCCceEEeCCHHHHHHHHHHH
Confidence 45568999999999998765433 2359999999999999999999999776667777666544 433333
No 54
>COG0640 ArsR Predicted transcriptional regulators [Transcription]
Probab=66.54 E-value=6.3 Score=26.06 Aligned_cols=68 Identities=12% Similarity=0.103 Sum_probs=47.8
Q ss_pred hhhHHHHHHHhhhc-ccEEEeecCCCCCCCccccCCHHHHHHhhhcccccccceeeeceeeeeeechhhHHHHHH
Q 030302 5 EKNRKEICKYLFQE-GVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEFLRT 78 (179)
Q Consensus 5 K~nr~~IYe~LFkE-GV~VakKD~~~p~Hpel~VpNL~ViK~mqSLkSrGyVkEqFaWrh~Yw~LTneGI~YLR~ 78 (179)
..+|.+|+..|.+. .+.+..-.. .+++.--.|...+..|...|+|....-=++.||.|+++.|..+..
T Consensus 24 ~~~r~~il~~l~~~~~~~~~~l~~------~~~~~~~~v~~hL~~L~~~glv~~~~~~~~~~~~l~~~~~~~~~~ 92 (110)
T COG0640 24 DPTRLEILSLLAEGGELTVGELAE------ALGLSQSTVSHHLKVLREAGLVELRREGRLRLYRLADEKVAELLE 92 (110)
T ss_pred CHHHHHHHHHHHhcCCccHHHHHH------HHCCChhHHHHHHHHHHHCCCeEEEecccEEEEecCcHHHHHHHH
Confidence 45788999999875 232111111 114566778889999999999999888888999999887655443
No 55
>KOG2784 consensus Phenylalanyl-tRNA synthetase, beta subunit [Translation, ribosomal structure and biogenesis]
Probab=65.83 E-value=6.9 Score=37.37 Aligned_cols=41 Identities=20% Similarity=0.192 Sum_probs=31.5
Q ss_pred cCCHHHHHHhhhcccccccceeeeceeeeeeechhhHHHHHH
Q 030302 37 VPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEFLRT 78 (179)
Q Consensus 37 VpNL~ViK~mqSLkSrGyVkEqFaWrh~Yw~LTneGI~YLR~ 78 (179)
.-.-+|+-+++||.+.+++.- --=-+.-|-||+||.++.++
T Consensus 29 ~~h~~~v~al~SL~a~~~i~~-~~~~~~~~~LT~EG~~i~~e 69 (483)
T KOG2784|consen 29 EDHQQVVGALKSLQAGGVIEV-KDVETKTYELTAEGEEIARE 69 (483)
T ss_pred hhhHHHHHHHHHHhhcCceEE-EeeeeEEEeeChhHHHHHhc
Confidence 334557779999999777643 33467789999999999986
No 56
>PF07848 PaaX: PaaX-like protein; InterPro: IPR012906 This entry describes the N-terminal region of proteins that are similar to, and nclude, the product of the paaX gene of Escherichia coli (P76086 from SWISSPROT). PaaX is a transcriptional regulator that is always found in association with operons believed to be involved in the degradation of phenylacetic acid []. The gene product has been shown to bind to the promoter sites and repress their transcription []. ; PDB: 3KFW_X 3L09_B.
Probab=65.29 E-value=6.2 Score=28.27 Aligned_cols=38 Identities=18% Similarity=0.261 Sum_probs=31.0
Q ss_pred cccCCHHHHHHhhhcccccccceeeeceeeeeeechhh
Q 030302 35 IDVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDG 72 (179)
Q Consensus 35 l~VpNL~ViK~mqSLkSrGyVkEqFaWrh~Yw~LTneG 72 (179)
+.|..=-|--+|--|+++|++...=.=|.-||.||++|
T Consensus 33 ~Gv~e~avR~alsRl~~~G~L~~~r~Gr~~~Y~Lt~~g 70 (70)
T PF07848_consen 33 FGVSESAVRTALSRLVRRGWLESERRGRRSYYRLTERG 70 (70)
T ss_dssp TT--HHHHHHHHHHHHHTTSEEEECCCTEEEEEE-HHH
T ss_pred cCCChHHHHHHHHHHHHcCceeeeecCccceEeeCCCC
Confidence 45677778889999999999999988999999999987
No 57
>PRK10870 transcriptional repressor MprA; Provisional
Probab=63.63 E-value=8.1 Score=31.30 Aligned_cols=45 Identities=20% Similarity=0.313 Sum_probs=37.7
Q ss_pred ccCCHHHHHHhhhcccccccceeee---ceeeeeeechhhHHHHHHhh
Q 030302 36 DVPNLQVIKLMQSFKSREYVRETFA---WMHYYWYLTNDGIEFLRTYL 80 (179)
Q Consensus 36 ~VpNL~ViK~mqSLkSrGyVkEqFa---Wrh~Yw~LTneGI~YLR~yL 80 (179)
.++.-.|..+++.|..+|||...-+ =|-.+-+||++|++.+.+..
T Consensus 82 ~l~~~tvsr~v~rLe~kGlV~R~~~~~DrR~~~v~LT~~G~~~~~~i~ 129 (176)
T PRK10870 82 GSSRTNATRIADELEKRGWIERRESDNDRRCLHLQLTEKGHEFLREVL 129 (176)
T ss_pred CCCHHHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHHHH
Confidence 4788889999999999999986543 46689999999999988643
No 58
>COG5124 Protein predicted to be involved in meiotic recombination [Cell division and chromosome partitioning / General function prediction only]
Probab=63.41 E-value=6.4 Score=34.12 Aligned_cols=72 Identities=18% Similarity=0.334 Sum_probs=51.1
Q ss_pred cchhhHHHHHHHhhhcccEEEeecCCCCCCCccc-------cCCHHHHHHhhhcccccccc-eeeeceeeeeeechhhHH
Q 030302 3 IPEKNRKEICKYLFQEGVCYAKKDYNLAKHPEID-------VPNLQVIKLMQSFKSREYVR-ETFAWMHYYWYLTNDGIE 74 (179)
Q Consensus 3 ipK~nr~~IYe~LFkEGV~VakKD~~~p~Hpel~-------VpNL~ViK~mqSLkSrGyVk-EqFaWrh~Yw~LTneGI~ 74 (179)
|+-+.++.|.+.+|.+ .|||.--+ |++ |-=..|-.++|||..-|.|+ |..+=..+||+.-+++|+
T Consensus 6 ls~~eKrr~L~aI~~~-----SKdFFqLk--EvEkLGSKK~IVl~tVKd~lQqlVDDgvV~~EK~GtsN~YWsF~s~~~q 78 (209)
T COG5124 6 LSLAEKRRRLEAIFHD-----SKDFFQLK--EVEKLGSKKQIVLMTVKDLLQQLVDDGVVSVEKCGTSNIYWSFKSQTLQ 78 (209)
T ss_pred ccHHHHHHHHHHHHhc-----cHHHHHHH--HHHHhccccccHHHHHHHHHHHHhhcCceeeeeeccceeEEecchHHHH
Confidence 3446677888888864 56765211 221 22234667899999999986 789999999999999998
Q ss_pred HHHHhhC
Q 030302 75 FLRTYLN 81 (179)
Q Consensus 75 YLR~yLh 81 (179)
-+-+-+.
T Consensus 79 k~~~~~~ 85 (209)
T COG5124 79 KLYDSSE 85 (209)
T ss_pred HHHHHHH
Confidence 7655444
No 59
>PF14531 Kinase-like: Kinase-like; PDB: 3DZO_A 2W1Z_A 3BYV_A 3Q5Z_A 3Q60_A.
Probab=63.39 E-value=1.5 Score=39.01 Aligned_cols=41 Identities=27% Similarity=0.423 Sum_probs=31.8
Q ss_pred HHHHHHhhhcccccccceeeeceeeeeeechhhHHHHHHhhCC
Q 030302 40 LQVIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEFLRTYLNL 82 (179)
Q Consensus 40 L~ViK~mqSLkSrGyVkEqFaWrh~Yw~LTneGI~YLR~yLhL 82 (179)
+|+|++..+|.+.|+|.-.+.|.+++ |..+|.-||.++-++
T Consensus 152 ~Q~I~lvA~Lh~~GlVHgdi~~~nfl--l~~~G~v~Lg~F~~~ 192 (288)
T PF14531_consen 152 VQMIRLVANLHSYGLVHGDIKPENFL--LDQDGGVFLGDFSSL 192 (288)
T ss_dssp HHHHHHHHHHHHTTEEEST-SGGGEE--E-TTS-EEE--GGGE
T ss_pred HHHHHHHHHHhhcceEecccceeeEE--EcCCCCEEEcChHHH
Confidence 56699999999999999999999987 788999999987554
No 60
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=59.84 E-value=5.5 Score=30.86 Aligned_cols=65 Identities=9% Similarity=0.094 Sum_probs=43.8
Q ss_pred CccchhhHHHHHHHhhhcccEEEeecCCCCCCCcc----ccCCHHHHHHhhhcccccccceeeeceeeeeeec
Q 030302 1 MIIPEKNRKEICKYLFQEGVCYAKKDYNLAKHPEI----DVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLT 69 (179)
Q Consensus 1 MlipK~nr~~IYe~LFkEGV~VakKD~~~p~Hpel----~VpNL~ViK~mqSLkSrGyVkEqFaWrh~Yw~LT 69 (179)
|-++++...+|...++. -...+-....-.+| +||--.|-|+|+.|+..|+|+..-+=.-.|....
T Consensus 1 M~ls~~~~YAl~~~i~l----a~~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s~~G~~GG~~l~~ 69 (141)
T PRK11014 1 MQLTSFTDYGLRALIYM----ASLPEGRMTSISEVTEVYGVSRNHMVKIINQLSRAGYVTAVRGKNGGIRLGK 69 (141)
T ss_pred CcCchHHhHHHHHHHHH----hcCCCCCccCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEEecCCCCCeeecC
Confidence 78899999888888762 11111112222333 5999999999999999999988765433444433
No 61
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=58.54 E-value=10 Score=26.32 Aligned_cols=45 Identities=16% Similarity=0.290 Sum_probs=36.4
Q ss_pred cccCCHHHHHHhhhcccccccceeeeceeeeeeechhhHHHHHHhhC
Q 030302 35 IDVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEFLRTYLN 81 (179)
Q Consensus 35 l~VpNL~ViK~mqSLkSrGyVkEqFaWrh~Yw~LTneGI~YLR~yLh 81 (179)
++|+-=.|-+.|+.|.+.|||... +..-.|.|+++.+++-..++.
T Consensus 30 l~i~~~tv~r~l~~L~~~g~l~~~--~~~~~y~l~~~~~~~~~~~~~ 74 (91)
T smart00346 30 LGLSKSTAHRLLNTLQELGYVEQD--GQNGRYRLGPKVLELGQSYLS 74 (91)
T ss_pred hCCCHHHHHHHHHHHHHCCCeeec--CCCCceeecHHHHHHHHHHHh
Confidence 468888999999999999999764 344568999999888777653
No 62
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=58.40 E-value=11 Score=29.76 Aligned_cols=67 Identities=21% Similarity=0.530 Sum_probs=42.2
Q ss_pred HHHHhhhcccEEEeecCCCCCCCccccCCHHHHHHhhhccccccc-----c----eeeeceeeeeeec-hhhHHHHHHhh
Q 030302 11 ICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYV-----R----ETFAWMHYYWYLT-NDGIEFLRTYL 80 (179)
Q Consensus 11 IYe~LFkEGV~VakKD~~~p~Hpel~VpNL~ViK~mqSLkSrGyV-----k----EqFaWrh~Yw~LT-neGI~YLR~yL 80 (179)
|...|+..|++ ...|.. ..+.++.=+|-|+|..|..-+++ + ++=+|-.|||+|+ +.-|..|+..+
T Consensus 6 v~d~L~~~~~~-~dedLa----~~l~i~~n~vRkiL~~L~ed~~~~~~~~~e~~~~~~~~~~~yw~i~y~~~~~vik~r~ 80 (147)
T smart00531 6 VLDALMRNGCV-TEEDLA----ELLGIKQKQLRKILYLLYDEKLIKIDYKREKDPETKTWYRYYWYINYDTLLDVVKYKL 80 (147)
T ss_pred ehHHHHhcCCc-CHHHHH----HHhCCCHHHHHHHHHHHHhhhcchhheeeeeCCCCceEEEEEEEecHHHHHHHHHHHH
Confidence 44556666653 222211 13457777888999988884442 2 2223999999999 56667777766
Q ss_pred CC
Q 030302 81 NL 82 (179)
Q Consensus 81 hL 82 (179)
+.
T Consensus 81 ~~ 82 (147)
T smart00531 81 DK 82 (147)
T ss_pred HH
Confidence 65
No 63
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=57.61 E-value=6.9 Score=33.94 Aligned_cols=66 Identities=18% Similarity=0.240 Sum_probs=49.5
Q ss_pred chhhHHHHHHHhhhcccEEEeecCCCCCCCccccCCHHHHHHhhhcccccccceeeece-----eeeeeechhhHH
Q 030302 4 PEKNRKEICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVRETFAWM-----HYYWYLTNDGIE 74 (179)
Q Consensus 4 pK~nr~~IYe~LFkEGV~VakKD~~~p~Hpel~VpNL~ViK~mqSLkSrGyVkEqFaWr-----h~Yw~LTneGI~ 74 (179)
+-.+|..|.++|-+.|=+-|.. . =.+|.|++-.|-+.|+.|.-+|+|.-.+.=. .+-|.||..|++
T Consensus 9 ~~~tr~~il~lL~~~g~~sa~e-l----A~~Lgis~~avR~HL~~Le~~Glv~~~~~~~g~GRP~~~y~Lt~~g~~ 79 (218)
T COG2345 9 SGSTRERILELLKKSGPVSADE-L----AEELGISPMAVRRHLDDLEAEGLVEVERQQGGRGRPAKLYRLTEKGRE 79 (218)
T ss_pred CccHHHHHHHHHhccCCccHHH-H----HHHhCCCHHHHHHHHHHHHhCcceeeeeccCCCCCCceeeeecccchh
Confidence 3457788888888776554322 1 1256799999999999999999998873322 468999999995
No 64
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=57.37 E-value=32 Score=32.75 Aligned_cols=9 Identities=11% Similarity=0.361 Sum_probs=5.5
Q ss_pred CCccccCCC
Q 030302 124 GDREGYRGG 132 (179)
Q Consensus 124 ~dR~~YRr~ 132 (179)
..+++|+++
T Consensus 337 ggkg~f~~~ 345 (465)
T KOG3973|consen 337 GGKGTFDRP 345 (465)
T ss_pred CCCCCCcCc
Confidence 345677764
No 65
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=56.06 E-value=13 Score=31.12 Aligned_cols=44 Identities=18% Similarity=0.217 Sum_probs=36.2
Q ss_pred cCCHHHHHHhhhcccccccceee---eceeeeeeechhhHHHHHHhh
Q 030302 37 VPNLQVIKLMQSFKSREYVRETF---AWMHYYWYLTNDGIEFLRTYL 80 (179)
Q Consensus 37 VpNL~ViK~mqSLkSrGyVkEqF---aWrh~Yw~LTneGI~YLR~yL 80 (179)
+..=.|..+++.|..+|||.-.- -=|..+=+||++|.+.+.+..
T Consensus 71 l~~sTvtr~l~rLE~kGlI~R~~~~~DrR~~~I~LTekG~~l~~~l~ 117 (185)
T PRK13777 71 MHVSTAFNFSKKLEERGYLTFSKKEDDKRNTYIELTEKGEELLLETM 117 (185)
T ss_pred CCHhhHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHHHH
Confidence 44456889999999999998654 458999999999999987643
No 66
>cd01223 PH_Vav Vav pleckstrin homology (PH) domain. Vav pleckstrin homology (PH) domain. Vav acts as a guanosine nucleotide exchange factor(GEF) for Rho/Rac proteins. Mammalian Vav proteins consist of a calponin homology (CH) domain, an acidic region, a rho-GEF (DH)domain, a PH domain, a Zinc finger region and an SH2 domain, flanked by two SH3 domains. In invertebrates such as Drosophila and C.elegans, Vav is missing the N-terminal SH3 domain . PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=53.71 E-value=6.3 Score=31.29 Aligned_cols=58 Identities=10% Similarity=0.147 Sum_probs=36.0
Q ss_pred HHHhhhcccEEEeecCCCCCCCccccCCHHHHHHhhh-----cccccccceeeeceeeeeeechhh
Q 030302 12 CKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQS-----FKSREYVRETFAWMHYYWYLTNDG 72 (179)
Q Consensus 12 Ye~LFkEGV~VakKD~~~p~Hpel~VpNL~ViK~mqS-----LkSrGyVkEqFaWrh~Yw~LTneG 72 (179)
|-+||...|||||.....+-+|+....+-++|...+- .-+.|..+ -|+|++|....+|
T Consensus 24 yiFLFDk~lI~CK~~~~~~~~~~Y~~Ke~~~l~~~~I~~~~~~d~~~~~~---~~~~~f~L~~~~~ 86 (116)
T cd01223 24 YIFLFDKAVIVCKALGDNTGDMQYTYKDIHDLADYKIENNPSRDTEGRDT---RWKYGFYLAHKQG 86 (116)
T ss_pred EEEEecceEEEEEecCCCCCCccEEhHHhhhhheeeeEecCccCcccCCc---ceEEEEEEEecCC
Confidence 5579999999999876644466666555555444221 11222222 4999888877655
No 67
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=53.62 E-value=6.1 Score=31.59 Aligned_cols=63 Identities=21% Similarity=0.251 Sum_probs=43.9
Q ss_pred CccchhhHHHHHHHhhhcccEEEeecCCCCCCCcc----ccCCHHHHHHhhhcccccccceeeeceeeeeeec
Q 030302 1 MIIPEKNRKEICKYLFQEGVCYAKKDYNLAKHPEI----DVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLT 69 (179)
Q Consensus 1 MlipK~nr~~IYe~LFkEGV~VakKD~~~p~Hpel----~VpNL~ViK~mqSLkSrGyVkEqFaWrh~Yw~LT 69 (179)
|.|.++...+|.-.++ |....+-.+ .=.+| +||--++.|+|+.|+..|+|+.+=+= +-=|.|+
T Consensus 1 M~ls~~~~YAlr~L~~----LA~~~~~~~-s~~eIA~~~~is~~~L~kIl~~L~~aGlv~S~rG~-~GGy~La 67 (153)
T PRK11920 1 MRLTKQTNYAIRMLMY----CAANDGKLS-RIPEIARAYGVSELFLFKILQPLVEAGLVETVRGR-NGGVRLG 67 (153)
T ss_pred CcCchHHhHHHHHHHH----HHhCCCCcC-cHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeecCC-CCCeeec
Confidence 8899999999887766 332222211 12244 59999999999999999999987764 3344443
No 68
>KOG4412 consensus 26S proteasome regulatory complex, subunit PSMD10 [Posttranslational modification, protein turnover, chaperones]
Probab=52.40 E-value=9.4 Score=33.47 Aligned_cols=48 Identities=29% Similarity=0.344 Sum_probs=42.1
Q ss_pred hhhHHHHHHHhhhcccEEEeecCC--CCCCCccccCCHHHHHHhhhcccc
Q 030302 5 EKNRKEICKYLFQEGVCYAKKDYN--LAKHPEIDVPNLQVIKLMQSFKSR 52 (179)
Q Consensus 5 K~nr~~IYe~LFkEGV~VakKD~~--~p~Hpel~VpNL~ViK~mqSLkSr 52 (179)
-|+|..|-..|...|..|-.||-. .|.|---.|-||+||+.+-|+.+-
T Consensus 115 gK~r~eIaqlLle~ga~i~~kD~~~qtplHRAAavGklkvie~Li~~~a~ 164 (226)
T KOG4412|consen 115 GKGRLEIAQLLLEKGALIRIKDKQGQTPLHRAAAVGKLKVIEYLISQGAP 164 (226)
T ss_pred cCChhhHHHHHHhcCCCCcccccccCchhHHHHhccchhhHHHHHhcCCC
Confidence 367999999999999999999965 577877789999999999998864
No 69
>PF03962 Mnd1: Mnd1 family; InterPro: IPR005647 This family of proteins includes meiotic nuclear division protein 1 (MND1) from Saccharomyces cerevisiae (Baker's yeast). The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair [].
Probab=50.34 E-value=13 Score=30.95 Aligned_cols=49 Identities=20% Similarity=0.379 Sum_probs=39.3
Q ss_pred CCCCccccCCHHHHHHhhhcccccccc-eeeeceeeeeeechhhHHHHHHhh
Q 030302 30 AKHPEIDVPNLQVIKLMQSFKSREYVR-ETFAWMHYYWYLTNDGIEFLRTYL 80 (179)
Q Consensus 30 p~Hpel~VpNL~ViK~mqSLkSrGyVk-EqFaWrh~Yw~LTneGI~YLR~yL 80 (179)
|++. .|.-..|--++|||.+-|+|. |..+=..|||++-++-..=+++.+
T Consensus 22 pK~~--gI~~~~VKdvlq~LvDDglV~~EKiGssn~YWsFps~~~~~~~~~~ 71 (188)
T PF03962_consen 22 PKEK--GIVSMSVKDVLQSLVDDGLVHVEKIGSSNYYWSFPSQAKQKRQNKL 71 (188)
T ss_pred cccc--CCchhhHHHHHHHHhccccchhhhccCeeEEEecChHHHHHHHHHH
Confidence 5533 466789999999999999975 788889999999998877666543
No 70
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=49.69 E-value=19 Score=38.03 Aligned_cols=9 Identities=78% Similarity=1.586 Sum_probs=5.6
Q ss_pred CCCcCCCCC
Q 030302 159 RPGFGRGGG 167 (179)
Q Consensus 159 rggfGrG~g 167 (179)
+||||||+|
T Consensus 1253 sGGfgrggg 1261 (1282)
T KOG0921|consen 1253 SGGFGRGGG 1261 (1282)
T ss_pred CCCcCCCCC
Confidence 567776654
No 71
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=48.37 E-value=3.6 Score=26.11 Aligned_cols=46 Identities=11% Similarity=0.338 Sum_probs=32.0
Q ss_pred hhHHHHHHHhhhcccEEEeecCCCCCCCccccCCHHHHHHhhhcccccccc
Q 030302 6 KNRKEICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVR 56 (179)
Q Consensus 6 ~nr~~IYe~LFkEGV~VakKD~~~p~Hpel~VpNL~ViK~mqSLkSrGyVk 56 (179)
.+..+|+.+|.+++-+ ..++.. ..++++-=.|-+.++.|+..|+|+
T Consensus 3 ~~~~~Il~~l~~~~~~-t~~ela----~~~~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 3 ETQRKILNYLRENPRI-TQKELA----EKLGISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHHHHCTTS--HHHHH----HHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHHcCCC-CHHHHH----HHhCCCHHHHHHHHHHHHHCcCcC
Confidence 5677999999987664 222221 123577778999999999999985
No 72
>KOG3233 consensus RNA polymerase III, subunit C34 [Transcription]
Probab=44.60 E-value=9.1 Score=34.91 Aligned_cols=25 Identities=20% Similarity=0.477 Sum_probs=21.4
Q ss_pred ccCCHHHHHHhhhcccccccceeee
Q 030302 36 DVPNLQVIKLMQSFKSREYVRETFA 60 (179)
Q Consensus 36 ~VpNL~ViK~mqSLkSrGyVkEqFa 60 (179)
++|-..|.|+++||.|+.+||++=+
T Consensus 111 nLp~~~v~K~LkSLEsKkLIKsVKs 135 (297)
T KOG3233|consen 111 NLPQTVVNKILKSLESKKLIKSVKS 135 (297)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 4677889999999999999998643
No 73
>PF01043 SecA_PP_bind: SecA preprotein cross-linking domain; InterPro: IPR011130 The SecA ATPase is involved in the insertion and retraction of preproteins through the plasma membrane. This domain has been found to cross-link to preproteins, thought to indicate a role in preprotein binding. The pre-protein cross-linking domain is comprised of two sub domains that are inserted within the ATPase domain [].; GO: 0017038 protein import, 0016020 membrane; PDB: 3DIN_B 3JUX_A 3IQY_A 2IBM_A 3DL8_A 3JV2_B 3IQM_A 1TF2_A 1TF5_A 1M74_A ....
Probab=43.78 E-value=21 Score=27.67 Aligned_cols=40 Identities=23% Similarity=0.349 Sum_probs=26.3
Q ss_pred HHHHhhhcccc-ccc---ceeeeceeeeeeechhhHHHHHHhhCCCCCCc
Q 030302 42 VIKLMQSFKSR-EYV---RETFAWMHYYWYLTNDGIEFLRTYLNLPSEIV 87 (179)
Q Consensus 42 ViK~mqSLkSr-GyV---kEqFaWrh~Yw~LTneGI~YLR~yLhLP~eiV 87 (179)
+.++.++|+.- -|. ++.- ..||++||+.+.++|++++++.
T Consensus 11 a~~~~~~L~~~~dy~vde~~~~------v~LT~~G~~~~e~~~~~~~~l~ 54 (113)
T PF01043_consen 11 ADKFAKQLKEDEDYEVDEKQRT------VELTEKGIEKAEKLLGISDNLY 54 (113)
T ss_dssp HHHHHHHSHTTTSECECTSTTE------EEESHHHHHHHHHHHTSSSSTT
T ss_pred HHHHHHhCCCCCCEEEeCCCCe------eeEhHHHHHHHHHHhhhccccc
Confidence 44556666654 343 2222 3799999999999999854443
No 74
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=42.17 E-value=24 Score=33.10 Aligned_cols=39 Identities=28% Similarity=0.404 Sum_probs=32.1
Q ss_pred HHhhhcccccccceeeeceeeeeeechhhHHHHHHhhCCC
Q 030302 44 KLMQSFKSREYVRETFAWMHYYWYLTNDGIEFLRTYLNLP 83 (179)
Q Consensus 44 K~mqSLkSrGyVkEqFaWrh~Yw~LTneGI~YLR~yLhLP 83 (179)
+.++.|+.|++|++ -.+..++..||++|.+++.+.+.+-
T Consensus 156 ~~l~~LkkRkL~~~-~~~~~~~~~~~~~~~~~~~~~~~~~ 194 (489)
T PRK04172 156 KVLKELKKRKLVEE-KERTERSVELTDAGLELLKEGIELK 194 (489)
T ss_pred HHHHHHHhcCCeEE-EEEEEEEEEEccchhhhhhcccccc
Confidence 46889999998877 6789999999999999997754433
No 75
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=41.44 E-value=5.6 Score=28.20 Aligned_cols=54 Identities=13% Similarity=0.216 Sum_probs=32.7
Q ss_pred CccchhhHHHHHHHhhhcccEEEeecCCCCCCCc----cccCCHHHHHHhhhccccccccee
Q 030302 1 MIIPEKNRKEICKYLFQEGVCYAKKDYNLAKHPE----IDVPNLQVIKLMQSFKSREYVRET 58 (179)
Q Consensus 1 MlipK~nr~~IYe~LFkEGV~VakKD~~~p~Hpe----l~VpNL~ViK~mqSLkSrGyVkEq 58 (179)
|-+.++...+|.-.++ |....+-....-.| ++||--+|-|+|+.|+..|+|+..
T Consensus 1 M~~s~~~~~Al~~l~~----la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~ 58 (83)
T PF02082_consen 1 MKLSKRTDYALRILLY----LARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKAGLIESS 58 (83)
T ss_dssp S---HHHHHHHHHHHH----HHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred CCCCcHHHHHHHHHHH----HHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEec
Confidence 6777888877776665 32222221111123 358899999999999999998654
No 76
>PRK06474 hypothetical protein; Provisional
Probab=37.62 E-value=16 Score=29.91 Aligned_cols=67 Identities=13% Similarity=0.248 Sum_probs=45.9
Q ss_pred cchhhHHHHHHHhhhccc-EEEeecCCCCCCCcc-ccCCHHHHHHhhhcccccccceeee-----ceeeeeeechhhHH
Q 030302 3 IPEKNRKEICKYLFQEGV-CYAKKDYNLAKHPEI-DVPNLQVIKLMQSFKSREYVRETFA-----WMHYYWYLTNDGIE 74 (179)
Q Consensus 3 ipK~nr~~IYe~LFkEGV-~VakKD~~~p~Hpel-~VpNL~ViK~mqSLkSrGyVkEqFa-----Wrh~Yw~LTneGI~ 74 (179)
+....|.+|.+.|.+.+- +-+. +.. ..+ +|+---|...|+.|..-|+|+..-- =+.-||.|++++|.
T Consensus 8 La~p~R~~Il~~L~~~~~~~ta~-el~----~~l~~is~aTvYrhL~~L~e~GLI~~~~~~~~~~~~ek~y~~~~~~~~ 81 (178)
T PRK06474 8 LMHPVRMKICQVLMRNKEGLTPL-ELV----KILKDVPQATLYRHLQTMVDSGILHVVKEKKVRSVSEKYYAINEEDAK 81 (178)
T ss_pred hCCHHHHHHHHHHHhCCCCCCHH-HHH----HHhcCCCHHHHHHHHHHHHHCCCEEEeecccccCceeEEEEeccceee
Confidence 456789999999986543 2221 111 112 3666678899999999999987432 23578999998764
No 77
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=37.23 E-value=15 Score=27.42 Aligned_cols=65 Identities=12% Similarity=0.060 Sum_probs=42.2
Q ss_pred CccchhhHHHHHHHhhhcccEEEeecCC-CCCCCcc----ccCCHHHHHHhhhcccccccceeeeceeeeeeechh
Q 030302 1 MIIPEKNRKEICKYLFQEGVCYAKKDYN-LAKHPEI----DVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTND 71 (179)
Q Consensus 1 MlipK~nr~~IYe~LFkEGV~VakKD~~-~p~Hpel----~VpNL~ViK~mqSLkSrGyVkEqFaWrh~Yw~LTne 71 (179)
|.++++...+|.-.++ |. +.+-. ...-.+| ++|--.|-++|+.|++.|||...=+..- -|.|+..
T Consensus 1 M~ls~~~~~al~~l~~----la-~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~~~gli~~~~g~~g-gy~l~~~ 70 (132)
T TIGR00738 1 MKLTKKTEYALRALLD----LA-LNPDEGPVSVKEIAERQGISRSYLEKILRTLRRAGLVESVRGPGG-GYRLARP 70 (132)
T ss_pred CcCccHHHHHHHHHHH----HH-hCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEEeccCCCC-CccCCCC
Confidence 7888888888877765 22 22211 2222233 5899999999999999999987534333 3455543
No 78
>PF13309 HTH_22: HTH domain
Probab=36.83 E-value=25 Score=24.43 Aligned_cols=26 Identities=23% Similarity=0.501 Sum_probs=22.2
Q ss_pred ccchhhHHHHHHHhhhcccEEEeecC
Q 030302 2 IIPEKNRKEICKYLFQEGVCYAKKDY 27 (179)
Q Consensus 2 lipK~nr~~IYe~LFkEGV~VakKD~ 27 (179)
.|++++++.|-+.|.++|+.-.|.-.
T Consensus 20 ~l~~~~k~~iV~~L~~~G~F~lKgav 45 (64)
T PF13309_consen 20 RLSKEEKKEIVRQLYEKGIFLLKGAV 45 (64)
T ss_pred hCCHHHHHHHHHHHHHCCCcccCcHH
Confidence 47889999999999999999776644
No 79
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=36.44 E-value=31 Score=32.44 Aligned_cols=35 Identities=31% Similarity=0.548 Sum_probs=23.8
Q ss_pred hhcccccccceeeeceee--ee---eechhhHHHHHHhhC
Q 030302 47 QSFKSREYVRETFAWMHY--YW---YLTNDGIEFLRTYLN 81 (179)
Q Consensus 47 qSLkSrGyVkEqFaWrh~--Yw---~LTneGI~YLR~yLh 81 (179)
++..|--.-+...+|.|| |+ .|+-|||+=|++||-
T Consensus 228 ~~~p~~~~~~~~~gwshfe~vF~vSaL~G~GikdlkqyLm 267 (379)
T KOG1423|consen 228 TDVPSDEKWRTICGWSHFERVFMVSALYGEGIKDLKQYLM 267 (379)
T ss_pred ccCCcccccccccCcccceeEEEEecccccCHHHHHHHHH
Confidence 333333344556678777 44 489999999999983
No 80
>KOG3433 consensus Protein involved in meiotic recombination/predicted coiled-coil protein [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=35.79 E-value=22 Score=30.84 Aligned_cols=74 Identities=23% Similarity=0.377 Sum_probs=54.4
Q ss_pred cchhhHHHHHHHhhhcccEEEeecCCCCCC-----CccccCCHHHHHHhhhccccccc-ceeeeceeeeeeechhhHHHH
Q 030302 3 IPEKNRKEICKYLFQEGVCYAKKDYNLAKH-----PEIDVPNLQVIKLMQSFKSREYV-RETFAWMHYYWYLTNDGIEFL 76 (179)
Q Consensus 3 ipK~nr~~IYe~LFkEGV~VakKD~~~p~H-----pel~VpNL~ViK~mqSLkSrGyV-kEqFaWrh~Yw~LTneGI~YL 76 (179)
|+...++.|...||.| .|||..-+. |--.|---.|-.++|||..-|.| +|...=..|||..-.|+|.=+
T Consensus 5 ls~~ekr~~l~eIf~e-----skDff~LkelEKlG~kKgIv~~tvKdvLQsLvDD~lV~~eKIgtSnyywsfps~a~~~~ 79 (203)
T KOG3433|consen 5 LSSDEKRMILLEIFQE-----SKDFFQLKELEKLGSKKGIVWQTVKDVLQSLVDDGLVIKEKIGTSNYYWSFPSEAICDR 79 (203)
T ss_pred cchHHHHHHHHHHHHh-----hHhHHHHHHHHHhCCccceehhHHHHHHHHHhccchHHHHHhcccccccccchHHHHHH
Confidence 3445677888888876 356542110 11124556788999999999996 688888999999999999988
Q ss_pred HHhhC
Q 030302 77 RTYLN 81 (179)
Q Consensus 77 R~yLh 81 (179)
+.+|.
T Consensus 80 ks~~q 84 (203)
T KOG3433|consen 80 KSVLQ 84 (203)
T ss_pred HHHHH
Confidence 87775
No 81
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=35.37 E-value=23 Score=22.98 Aligned_cols=32 Identities=3% Similarity=0.066 Sum_probs=24.9
Q ss_pred ccCCHHHHHHhhhcccccccceeeeceeeeeeech
Q 030302 36 DVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTN 70 (179)
Q Consensus 36 ~VpNL~ViK~mqSLkSrGyVkEqFaWrh~Yw~LTn 70 (179)
+++--.|.++|+.|...|+|...- .-.|.|||
T Consensus 36 g~s~~tv~r~l~~L~~~g~i~~~~---~~~~~l~~ 67 (67)
T cd00092 36 GLTRETVSRTLKELEEEGLISRRG---RGKYRVNP 67 (67)
T ss_pred CCCHHHHHHHHHHHHHCCCEEecC---CCeEEeCC
Confidence 478889999999999999998754 22466654
No 82
>PF10662 PduV-EutP: Ethanolamine utilisation - propanediol utilisation; InterPro: IPR012381 Members of this family function in ethanolamine [] and propanediol [] degradation pathways. Both pathways require coenzyme B12 (adenosylcobalamin, AdoCbl). Bacteria that harbour these pathways can use ethanolamine as a source of carbon and nitrogen, or propanediol as a sole carbon and energy source, respectively. The exact roles of the EutP and PduV proteins in these respective pathways are not yet determined. Members of this family contain P-loop consensus motifs in the N-terminal part, and are distantly related to various GTPases and ATPases, including ATPase components of transport systems. Propanediol degradation is thought to be important for the natural Salmonella populations, since propanediol is produced by the fermentation of the common plant sugars rhamnose and fucose [, ]. More than 1% of the Salmonella enterica genome is devoted to the utilisation of propanediol and cobalamin biosynthesis. In vivo expression technology has indicated that propanediol utilisation (pdu) genes may be important for growth in host tissues, and competitive index studies with mice have shown that pdu mutations confer a virulence defect [, ]. The pdu operon is contiguous and co-regulated with the cobalamin (B12) biosynthesis cob operon, indicating that propanediol catabolism may be the primary reason for de novo B12 synthesis in Salmonella [, , ]. Please see IPR003207 from INTERPRO, IPR003208 from INTERPRO, IPR009204 from INTERPRO, IPR009191 from INTERPRO, IPR009192 from INTERPRO for more details on the propanediol utilisation pathway and the pdu operon.; GO: 0005524 ATP binding, 0006576 cellular biogenic amine metabolic process
Probab=34.32 E-value=19 Score=29.12 Aligned_cols=38 Identities=26% Similarity=0.402 Sum_probs=27.9
Q ss_pred CHHHHHHhhhcccccccceeeeceeeeeeechhhHHHHHHhhC
Q 030302 39 NLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEFLRTYLN 81 (179)
Q Consensus 39 NL~ViK~mqSLkSrGyVkEqFaWrh~Yw~LTneGI~YLR~yLh 81 (179)
+-.+-++-+-|+..|. ++.|-= =.+|+|||+-|++||+
T Consensus 105 ~~~i~~a~~~L~~aG~-~~if~v----S~~~~eGi~eL~~~L~ 142 (143)
T PF10662_consen 105 DANIERAKKWLKNAGV-KEIFEV----SAVTGEGIEELKDYLE 142 (143)
T ss_pred hhhHHHHHHHHHHcCC-CCeEEE----ECCCCcCHHHHHHHHh
Confidence 5566677777888776 455421 2589999999999996
No 83
>COG1542 Uncharacterized conserved protein [Function unknown]
Probab=33.83 E-value=27 Score=34.30 Aligned_cols=45 Identities=18% Similarity=0.225 Sum_probs=35.7
Q ss_pred cCCHHHHHHhhhcccccccceeee-ceeeeeeechhhHHHHHHhhCCC
Q 030302 37 VPNLQVIKLMQSFKSREYVRETFA-WMHYYWYLTNDGIEFLRTYLNLP 83 (179)
Q Consensus 37 VpNL~ViK~mqSLkSrGyVkEqFa-Wrh~Yw~LTneGI~YLR~yLhLP 83 (179)
+-.| |.-++.+|.|.|+++...+ -.-.||.||..|-.-|-+ |.-|
T Consensus 321 ~~Dl-vt~aL~~LEs~glik~ev~k~g~l~yvlTe~Gekvle~-l~k~ 366 (593)
T COG1542 321 IDDL-VTAALYTLESFGLIKREVVKNGDLTYVLTEFGEKVLED-LEKS 366 (593)
T ss_pred ccch-HHHHHHhhhhccchhhhhhhcCceEEEehhhhHHHHhc-ccCc
Confidence 5778 9999999999999986554 344699999999998765 4444
No 84
>PF03965 Penicillinase_R: Penicillinase repressor; InterPro: IPR005650 Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea. Many are BlaI/MecI proteins which regulate resistance to penicillins (beta-lactams), though at least one protein (Q47839 from SWISSPROT) appears to be involved in the regulation of copper homeostasis []. BlaI regulators repress the expression of penicillin-degrading enzymes (penicillinases) until the cell encounters the antiobiotic, at which point repression ceases and penicillinase expression occurs, allowing cell growth []. MecI regulators repress the expression of MecA, a cell-wall biosynthetic enzyme not inhibited by penicillins at clinically achievable concentrations, until the presence of the antibiotic is detected []. At this point repression ends and MecA expression occurs which, together with the switching off of the penicillin-sensitive enzymes, allows the cell to grow despite the presence of antibiotic.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G9W_A 2K4B_A 1XSD_A 1SD4_A 1SD7_A 1SD6_A 2P7C_B 1P6R_A 1OKR_B 2D45_B ....
Probab=32.99 E-value=26 Score=26.19 Aligned_cols=67 Identities=16% Similarity=0.176 Sum_probs=39.9
Q ss_pred HHHHHhhhcccEEEeecCCCCCCCccccCCHHHHHHhhhcccccccceeeeceeeeeeechhhHHHHH
Q 030302 10 EICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEFLR 77 (179)
Q Consensus 10 ~IYe~LFkEGV~VakKD~~~p~Hpel~VpNL~ViK~mqSLkSrGyVkEqFaWrh~Yw~LTneGI~YLR 77 (179)
.|.+.|-+.|= +.-+|++--.....+...=-|...|..|..||||+-.=.=+.|+|+-+-.=-+|++
T Consensus 7 ~IM~~lW~~~~-~t~~eI~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~~~~~gr~~~Y~p~is~~e~~~ 73 (115)
T PF03965_consen 7 EIMEILWESGE-ATVREIHEALPEERSWAYSTVQTLLNRLVEKGFLTREKIGRAYVYSPLISREEYLA 73 (115)
T ss_dssp HHHHHHHHHSS-EEHHHHHHHHCTTSS--HHHHHHHHHHHHHTTSEEEEEETTCEEEEESSSHHHHHH
T ss_pred HHHHHHHhCCC-CCHHHHHHHHHhccccchhHHHHHHHHHHhCCceeEeecCCceEEEeCCcHHHHHH
Confidence 67777777777 45555441111112356678999999999999998775555555543322234443
No 85
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=32.68 E-value=95 Score=33.21 Aligned_cols=10 Identities=40% Similarity=0.853 Sum_probs=6.1
Q ss_pred CccccCCCCC
Q 030302 125 DREGYRGGPR 134 (179)
Q Consensus 125 dR~~YRr~~~ 134 (179)
..+.|||...
T Consensus 1178 n~SgyRRGgs 1187 (1282)
T KOG0921|consen 1178 NNSGYRRGGS 1187 (1282)
T ss_pred CccccccCCC
Confidence 3467887544
No 86
>TIGR01689 EcbF-BcbF capsule biosynthesis phosphatase. Due to the likelihood that the substrates of these enzymes are different depending on the nature of the particular polysaccharides associated with each species, this model has been classified as a subfamily despite the close homology.
Probab=32.56 E-value=18 Score=28.46 Aligned_cols=48 Identities=19% Similarity=0.211 Sum_probs=39.3
Q ss_pred ccCCHHHHHHhhhcccccccceeeeceeeeeeechhhHHHHHHhhCCCCCCccccc
Q 030302 36 DVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEFLRTYLNLPSEIVPATL 91 (179)
Q Consensus 36 ~VpNL~ViK~mqSLkSrGyVkEqFaWrh~Yw~LTneGI~YLR~yLhLP~eiVPaTl 91 (179)
+.+|..++++++.|+++|+.-=..+=|.+.+++.|=|+ +..+.+|.|+
T Consensus 23 ~~~~~~~ie~L~~l~~~G~~IiiaTGR~~~~~~~n~~~--------i~~~~~~~t~ 70 (126)
T TIGR01689 23 VAPILAVIEKLRHYKALGFEIVISSSRNMRTYEGNVGK--------INIHTLPIII 70 (126)
T ss_pred cccCHHHHHHHHHHHHCCCEEEEECCCCchhhhccccc--------cchhhHHHHH
Confidence 46999999999999999998777888999999877666 5556666665
No 87
>PF01050 MannoseP_isomer: Mannose-6-phosphate isomerase; InterPro: IPR001538 Mannose-6-phosphate isomerase or phosphomannose isomerase (5.3.1.8 from EC) (PMI) is the enzyme that catalyses the interconversion of mannose-6-phosphate and fructose-6-phosphate. In eukaryotes PMI is involved in the synthesis of GDP-mannose, a constituent of N- and O-linked glycans and GPI anchors and in prokaryotes it participates in a variety of pathways, including capsular polysaccharide biosynthesis and D-mannose metabolism. PMI's belong to the cupin superfamily whose functions range from isomerase and epimerase activities involved in the modification of cell wall carbohydrates in bacteria and plants, to non-enzymatic storage proteins in plant seeds, and transcription factors linked to congenital baldness in mammals []. Three classes of PMI have been defined []. The type II phosphomannose isomerases are bifunctional enzymes 5.3.1.8 from EC. This entry covers the isomerase region of the protein []. The guanosine diphospho-D-mannose pyrophosphorylase region is described in another InterPro entry (see IPR005836 from INTERPRO).; GO: 0016779 nucleotidyltransferase activity, 0005976 polysaccharide metabolic process
Probab=30.73 E-value=43 Score=27.09 Aligned_cols=45 Identities=18% Similarity=0.277 Sum_probs=29.7
Q ss_pred hcccEEEeecCCCCCCCccccCCHHHHHHhhhcccccccc------eeeeceeeeeeechhh
Q 030302 17 QEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVR------ETFAWMHYYWYLTNDG 72 (179)
Q Consensus 17 kEGV~VakKD~~~p~Hpel~VpNL~ViK~mqSLkSrGyVk------EqFaWrh~Yw~LTneG 72 (179)
.|++|||.||.. -.|-+++..|++++.-. +.-.|-+|.....+++
T Consensus 12 ~DaiLV~~k~~~-----------q~vK~~v~~lk~~~~~E~~~~~~~~rpWG~~~~l~~~~~ 62 (151)
T PF01050_consen 12 PDAILVADKDRS-----------QDVKEVVEQLKQKGRYEAKEHRRVYRPWGSYEVLDEGEG 62 (151)
T ss_pred CCEEEEECcHHh-----------hhhHHHHHhhhcccccccccceeEecCCcEEEEEEccCC
Confidence 478888888854 23445566666665433 3468998888877665
No 88
>PF06969 HemN_C: HemN C-terminal domain; InterPro: IPR010723 Proteins containing this domain are all oxygen-independent coproporphyrinogen-III oxidases (HemN). This enzyme catalyses the oxygen-independent conversion of coproporphyrinogen-III to protoporphyrinogen-IX [], one of the last steps in haem biosynthesis. The function of this domain is unclear, but comparison to other proteins containing a radical SAM domain suggest it may be a substrate binding domain.; GO: 0004109 coproporphyrinogen oxidase activity, 0006779 porphyrin-containing compound biosynthetic process, 0055114 oxidation-reduction process, 0005737 cytoplasm; PDB: 1OLT_A.
Probab=30.60 E-value=30 Score=23.04 Aligned_cols=27 Identities=15% Similarity=0.060 Sum_probs=20.1
Q ss_pred HHHhhhcccccccceeeeceeeeeeechhhH
Q 030302 43 IKLMQSFKSREYVRETFAWMHYYWYLTNDGI 73 (179)
Q Consensus 43 iK~mqSLkSrGyVkEqFaWrh~Yw~LTneGI 73 (179)
.+.++.|...|+|+. ..-++.||++|.
T Consensus 39 ~~~l~~l~~~Gll~~----~~~~l~lT~~G~ 65 (66)
T PF06969_consen 39 QKELEELQEDGLLEI----DGGRLRLTEKGR 65 (66)
T ss_dssp HHHHHHHHHTTSEEE-----SSEEEE-TTTG
T ss_pred HHHHHHHHHCCCEEE----eCCEEEECcccC
Confidence 677899999999843 456889999984
No 89
>COG1733 Predicted transcriptional regulators [Transcription]
Probab=29.40 E-value=43 Score=26.06 Aligned_cols=69 Identities=19% Similarity=0.198 Sum_probs=44.0
Q ss_pred cchhhHHHHHHHhhhcccEEEeecCCCCCCCccc-cCCHHHHHHhhhcccccccceeeec---eeeeeeechhhHHHHH
Q 030302 3 IPEKNRKEICKYLFQEGVCYAKKDYNLAKHPEID-VPNLQVIKLMQSFKSREYVRETFAW---MHYYWYLTNDGIEFLR 77 (179)
Q Consensus 3 ipK~nr~~IYe~LFkEGV~VakKD~~~p~Hpel~-VpNL~ViK~mqSLkSrGyVkEqFaW---rh~Yw~LTneGI~YLR 77 (179)
|-++-...|-..||+ |++ -|+- ..-.+. |..--....|+.|...|+|.-+.-= =+.+|.||+.|-.-+-
T Consensus 20 ig~kW~~lIl~~L~~-g~~----RF~e-L~r~i~~Is~k~Ls~~Lk~Le~~Glv~R~~~~~~PprveY~LT~~G~~L~~ 92 (120)
T COG1733 20 IGGKWTLLILRDLFD-GPK----RFNE-LRRSIGGISPKMLSRRLKELEEDGLVERVVYPEEPPRVEYRLTEKGRDLLP 92 (120)
T ss_pred HcCccHHHHHHHHhc-CCC----cHHH-HHHHccccCHHHHHHHHHHHHHCCCEEeeecCCCCceeEEEEhhhHHHHHH
Confidence 456667788888886 543 3331 111222 5555567788888999997654321 2778999999976543
No 90
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=28.66 E-value=42 Score=21.36 Aligned_cols=23 Identities=13% Similarity=0.238 Sum_probs=19.6
Q ss_pred ccCCHHHHHHhhhccccccccee
Q 030302 36 DVPNLQVIKLMQSFKSREYVRET 58 (179)
Q Consensus 36 ~VpNL~ViK~mqSLkSrGyVkEq 58 (179)
+|+--.|-++|+.|...|+|...
T Consensus 36 ~is~~~v~~~l~~L~~~G~i~~~ 58 (66)
T cd07377 36 GVSRTTVREALRELEAEGLVERR 58 (66)
T ss_pred CCCHHHHHHHHHHHHHCCCEEec
Confidence 47778899999999999998654
No 91
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=28.46 E-value=19 Score=26.32 Aligned_cols=52 Identities=19% Similarity=0.249 Sum_probs=32.7
Q ss_pred hHHHHHHHhhhcccEEEeecCC--C-CCCCccccCCHHHHHHhhhcccccccceeee
Q 030302 7 NRKEICKYLFQEGVCYAKKDYN--L-AKHPEIDVPNLQVIKLMQSFKSREYVRETFA 60 (179)
Q Consensus 7 nr~~IYe~LFkEGV~VakKD~~--~-p~Hpel~VpNL~ViK~mqSLkSrGyVkEqFa 60 (179)
.|.+|++.|.+..--+.-.|.. + ..+| +|.--.|...|+.|...|+|++.-.
T Consensus 2 qR~~Il~~l~~~~~~~sa~ei~~~l~~~~~--~i~~~TVYR~L~~L~~~Gli~~~~~ 56 (116)
T cd07153 2 QRLAILEVLLESDGHLTAEEIYERLRKKGP--SISLATVYRTLELLEEAGLVREIEL 56 (116)
T ss_pred HHHHHHHHHHhCCCCCCHHHHHHHHHhcCC--CCCHHHHHHHHHHHHhCCCEEEEEe
Confidence 6889999998642211111211 0 1112 2455678999999999999998653
No 92
>PRK11050 manganese transport regulator MntR; Provisional
Probab=28.29 E-value=54 Score=25.95 Aligned_cols=40 Identities=18% Similarity=0.219 Sum_probs=31.3
Q ss_pred cccCCHHHHHHhhhcccccccceeeeceeeeeeechhhHHHHH
Q 030302 35 IDVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEFLR 77 (179)
Q Consensus 35 l~VpNL~ViK~mqSLkSrGyVkEqFaWrh~Yw~LTneGI~YLR 77 (179)
++|..-.|-++++.|.+.|+|...-. --.+||++|...+.
T Consensus 61 l~is~stVsr~l~~Le~~GlI~r~~~---~~v~LT~~G~~l~~ 100 (152)
T PRK11050 61 LGVSQPTVAKMLKRLARDGLVEMRPY---RGVFLTPEGEKLAQ 100 (152)
T ss_pred HCCCHHHHHHHHHHHHHCCCEEEecC---CceEECchHHHHHH
Confidence 35888899999999999999975432 24689999987644
No 93
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=27.59 E-value=28 Score=27.83 Aligned_cols=61 Identities=13% Similarity=0.114 Sum_probs=41.2
Q ss_pred CccchhhHHHHHHHhhhcccEEEeecCCCCCCCcc----ccCCHHHHHHhhhcccccccceeeeceeee
Q 030302 1 MIIPEKNRKEICKYLFQEGVCYAKKDYNLAKHPEI----DVPNLQVIKLMQSFKSREYVRETFAWMHYY 65 (179)
Q Consensus 1 MlipK~nr~~IYe~LFkEGV~VakKD~~~p~Hpel----~VpNL~ViK~mqSLkSrGyVkEqFaWrh~Y 65 (179)
|-+.++.+.++.-.++ |....+.....-.+| +||-.++.|+|..|+..|+|+.+=+=.--|
T Consensus 1 Mklt~~~~yal~~L~~----LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~kaGlV~S~rG~~GGy 65 (150)
T COG1959 1 MKLTSKGEYALRALLY----LALLPGGGPVSSAEIAERQGISPSYLEKILSKLRKAGLVKSVRGKGGGY 65 (150)
T ss_pred CccchhHhHHHHHHHH----HHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHHcCCEEeecCCCCCc
Confidence 7778888888877766 332333222112233 599999999999999999999876533333
No 94
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=27.59 E-value=22 Score=28.45 Aligned_cols=58 Identities=17% Similarity=0.221 Sum_probs=35.5
Q ss_pred HHHHHHhhhcccEEEeecCCCCCCCccccCCHHHHHHhhhcccccccc-eeeeceeeeeee
Q 030302 9 KEICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVR-ETFAWMHYYWYL 68 (179)
Q Consensus 9 ~~IYe~LFkEGV~VakKD~~~p~Hpel~VpNL~ViK~mqSLkSrGyVk-EqFaWrh~Yw~L 68 (179)
.+|++||-+..==..-.|+..-.|. .|+.-.|.|+|-+|.+.|-+. ..|+=+-+||++
T Consensus 4 ~~Il~y~~~qNRPys~~di~~nL~~--~~~K~~v~k~Ld~L~~~g~i~~K~~GKqkiY~~~ 62 (169)
T PF07106_consen 4 DAILEYMKEQNRPYSAQDIFDNLHN--KVGKTAVQKALDSLVEEGKIVEKEYGKQKIYFAN 62 (169)
T ss_pred HHHHHHHHHcCCCCcHHHHHHHHHh--hccHHHHHHHHHHHHhCCCeeeeeecceEEEeeC
Confidence 4677777643211111122111232 356667999999999999854 467778888875
No 95
>cd03071 PDI_b'_NRX PDIb' family, NRX subgroup, redox inactive TRX-like domain b'; composed of vertebrate nucleoredoxins (NRX). NRX is a 400-amino acid nuclear protein with one redox active TRX domain followed by one redox inactive TRX-like domain homologous to the b' domain of PDI. In vitro studies show that NRX has thiol oxidoreductase activity and that it may be involved in the redox regulation of transcription, in a manner different from that of TRX or glutaredoxin. NRX enhances the activation of NF-kB by TNFalpha, as well as PMA-1 induced AP-1 and FK-induced CREB activation. Mouse NRX transcripts are expressed in all adult tissues but is restricted to the nervous system and limb buds in embryos. The mouse NRX gene is implicated in streptozotocin-induced diabetes. Similar to PDI, the b' domain of NRX is likely involved in substrate recognition.
Probab=27.58 E-value=58 Score=26.15 Aligned_cols=31 Identities=29% Similarity=0.369 Sum_probs=24.8
Q ss_pred ceeeeceeeeeeechhhHHHHHHhhCCCCCC
Q 030302 56 RETFAWMHYYWYLTNDGIEFLRTYLNLPSEI 86 (179)
Q Consensus 56 kEqFaWrh~Yw~LTneGI~YLR~yLhLP~ei 86 (179)
|+.=+=+.|++-..+|=-+.||+|++||.+.
T Consensus 51 k~~dap~~f~~a~ede~tdsLRDf~nL~d~~ 81 (116)
T cd03071 51 KEEEAPLLFFVAGEDDMTDSLRDYTNLPEAA 81 (116)
T ss_pred cCCCcceeeeeeccchHHHHHHHhcCCCccC
Confidence 3444557888889999999999999999653
No 96
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=27.39 E-value=10 Score=26.00 Aligned_cols=46 Identities=20% Similarity=0.194 Sum_probs=33.6
Q ss_pred hHHHHHHHhhhcccEEEeecCCCCCCCccccCCHHHHHHhhhcccccccce
Q 030302 7 NRKEICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVRE 57 (179)
Q Consensus 7 nr~~IYe~LFkEGV~VakKD~~~p~Hpel~VpNL~ViK~mqSLkSrGyVkE 57 (179)
..++||+..- ++-.|--+|.- ..|+|..-.|.+.++.|...|||.-
T Consensus 9 YL~~Iy~l~~-~~~~v~~~~iA----~~L~vs~~tvt~ml~~L~~~GlV~~ 54 (60)
T PF01325_consen 9 YLKAIYELSE-EGGPVRTKDIA----ERLGVSPPTVTEMLKRLAEKGLVEY 54 (60)
T ss_dssp HHHHHHHHHH-CTSSBBHHHHH----HHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHc-CCCCccHHHHH----HHHCCChHHHHHHHHHHHHCCCEEe
Confidence 4578999886 54445555543 1457899999999999999999874
No 97
>PRK09249 coproporphyrinogen III oxidase; Provisional
Probab=26.48 E-value=57 Score=30.06 Aligned_cols=34 Identities=12% Similarity=0.090 Sum_probs=26.8
Q ss_pred HHHHhhhcccccccceeeeceeeeeeechhhHHHHHHh
Q 030302 42 VIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEFLRTY 79 (179)
Q Consensus 42 ViK~mqSLkSrGyVkEqFaWrh~Yw~LTneGI~YLR~y 79 (179)
++++++.|+.+|+|.. ..-+|.||++|.-++...
T Consensus 401 ~~~~l~~l~~~gll~~----~~~~~~lT~~G~~~~d~i 434 (453)
T PRK09249 401 ELERLAPLEADGLVEL----DENGITVTPKGRLLVRNI 434 (453)
T ss_pred HHHHHHHHHHCCCEEE----ECCEEEECccchHHHHHH
Confidence 4567889999999874 345899999999887643
No 98
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=25.78 E-value=22 Score=23.70 Aligned_cols=51 Identities=12% Similarity=0.217 Sum_probs=33.4
Q ss_pred cchhhHHHHHHHhhhcccEEEeecCCCCCCCccccCCHHHHHHhhhccccccccee
Q 030302 3 IPEKNRKEICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVRET 58 (179)
Q Consensus 3 ipK~nr~~IYe~LFkEGV~VakKD~~~p~Hpel~VpNL~ViK~mqSLkSrGyVkEq 58 (179)
+...+|.+|+++|..++-+.+.. . -..++++.=.|-..|+-|..-|+|+..
T Consensus 7 L~~p~R~~Il~~L~~~~~~t~~e-l----a~~l~~~~~t~s~hL~~L~~aGli~~~ 57 (61)
T PF12840_consen 7 LSDPTRLRILRLLASNGPMTVSE-L----AEELGISQSTVSYHLKKLEEAGLIEVE 57 (61)
T ss_dssp HTSHHHHHHHHHHHHCSTBEHHH-H----HHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred hCCHHHHHHHHHHhcCCCCCHHH-H----HHHHCCCHHHHHHHHHHHHHCCCeEEe
Confidence 34578999999993333222111 0 113357777899999999999999864
No 99
>PF14756 Pdase_C33_assoc: Peptidase_C33-associated domain
Probab=25.45 E-value=44 Score=27.46 Aligned_cols=24 Identities=29% Similarity=0.569 Sum_probs=20.3
Q ss_pred hhhHHHHHHhhCCCCCCccccccc
Q 030302 70 NDGIEFLRTYLNLPSEIVPATLKK 93 (179)
Q Consensus 70 neGI~YLR~yLhLP~eiVPaTlk~ 93 (179)
..-+..|-+..|||+.++|+.|..
T Consensus 13 pacldrla~vmhlps~~ipaalae 36 (147)
T PF14756_consen 13 PACLDRLAEVMHLPSSVIPAALAE 36 (147)
T ss_pred hHHHHHHHHHhcCccchhHHHHHH
Confidence 344678999999999999999976
No 100
>PF06648 DUF1160: Protein of unknown function (DUF1160); InterPro: IPR010594 This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf75; it is a family of uncharacterised viral proteins.
Probab=25.27 E-value=55 Score=26.22 Aligned_cols=31 Identities=32% Similarity=0.503 Sum_probs=26.1
Q ss_pred cCCHHHHHHhhhcccccccceeeeceeeeeeechhhHHHHHHhh
Q 030302 37 VPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEFLRTYL 80 (179)
Q Consensus 37 VpNL~ViK~mqSLkSrGyVkEqFaWrh~Yw~LTneGI~YLR~yL 80 (179)
.-|-+||.++|.... +.-||++.|.||.++|
T Consensus 81 ~~n~~I~~Il~~~vd-------------~~~l~dddi~~ls~FL 111 (122)
T PF06648_consen 81 YNNRYIINILQKFVD-------------GQHLTDDDISYLSEFL 111 (122)
T ss_pred HccHHHHHHHHHHhc-------------CccCCcccHHHHHHHH
Confidence 478899999998764 3458999999999988
No 101
>PF06992 Phage_lambda_P: Replication protein P; InterPro: IPR009731 This family consists of several Bacteriophage lambda replication protein P like proteins. The bacteriophage lambda P protein promoters replication of the phage chromosome by recruiting a key component of the cellular replication machinery to the viral origin. Specifically, P protein delivers one or more molecules of Escherichia coli DnaB helicase to a nucleoprotein structure formed by the lambda O initiator at the lambda replication origin [].; GO: 0006270 DNA-dependent DNA replication initiation
Probab=23.93 E-value=18 Score=31.81 Aligned_cols=40 Identities=20% Similarity=0.502 Sum_probs=27.8
Q ss_pred cccCCHH-HHHHhh-hcccccc--cceeeecee--eeeeechhhHH
Q 030302 35 IDVPNLQ-VIKLMQ-SFKSREY--VRETFAWMH--YYWYLTNDGIE 74 (179)
Q Consensus 35 l~VpNL~-ViK~mq-SLkSrGy--VkEqFaWrh--~Yw~LTneGI~ 74 (179)
+.+||.. ++..+. -..-+|+ --|+|.|+| .||.+|+-.-+
T Consensus 118 lGLP~~del~~~~~~y~~~rg~y~~~e~f~w~s~v~YwlvtdLy~~ 163 (233)
T PF06992_consen 118 LGLPSVDELYQRYKRYCRYRGFYPSIEEFPWRSNVEYWLVTDLYRR 163 (233)
T ss_pred cCCCCHHHHHHHHHHHHHHhCCCCChhhCCCcchhHHHHHHHHHHH
Confidence 4689984 666554 3444675 247999998 69999986653
No 102
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=23.20 E-value=59 Score=31.09 Aligned_cols=14 Identities=64% Similarity=1.075 Sum_probs=6.9
Q ss_pred CCCCcCCCCCCCCC
Q 030302 158 GRPGFGRGGGGYGA 171 (179)
Q Consensus 158 ~rggfGrG~g~~~~ 171 (179)
+|+|-|||+|+.|+
T Consensus 443 gr~gggrgrggggg 456 (465)
T KOG3973|consen 443 GRDGGGRGRGGGGG 456 (465)
T ss_pred CCCCCCCCCCCCCC
Confidence 34555555554333
No 103
>PF00961 LAGLIDADG_1: LAGLIDADG endonuclease; InterPro: IPR001982 The LAGLIDADG and HNH domains of site-specific DNA endonucleases encoded by viruses, bacteriophages as well as archaeal, eukaryotic nuclear and organellar genomes are characterised by the sequence motifs 'LAGLIDADG' and 'HNH', respectively [, ]. Phylogenetic analysis of the two domains indicates a lack of exchange of endonucleases between different mobile elements (environments) and between hosts from different phylogenetic kingdoms. However, there does appear to have been considerable exchange of endonuclease domains amongst elements of the same type. Such events are suggested to be important for the formation of elements of new specficity []. 'Homing' is the lateral transfer of an intervening genetic sequence, either an intron or an intein, to a cognate allele that lacks that element. The end result of homing is the duplication of the intervening sequence. The process is initiated by site-specific endonucleases that are encoded by open reading frames within the mobile elements. These endonucleases may be contrasted with a variety of enzymes involved in nucleic acid strand breakage and rearrangement, particularly restriction endonucleases. They are encoded within the intervening sequence and there are interesting limitations on the position and length of their open reading frames, and therefore on their structures. These enzymes display a unique strategy of flexible recognition of very long DNA target sites. This strategy allows these sequences to minimize nonspecific cleavage within the host genome, while maximizing the ability of the endonuclease to cleave closely related variants of the homing site [].; GO: 0003677 DNA binding, 0004519 endonuclease activity, 0006314 intron homing; PDB: 2EX5_B 3R7P_A 4EFJ_A 3E54_B 2QOJ_Z 3EH8_A 1P8K_Z 3QQY_A 2VBO_B 4AAB_A ....
Probab=22.92 E-value=1.4e+02 Score=21.07 Aligned_cols=45 Identities=9% Similarity=0.226 Sum_probs=37.1
Q ss_pred cCCHHHHHHhhhcccccccceeeeceeeeeeech--hhHHHHHHhhC
Q 030302 37 VPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTN--DGIEFLRTYLN 81 (179)
Q Consensus 37 VpNL~ViK~mqSLkSrGyVkEqFaWrh~Yw~LTn--eGI~YLR~yLh 81 (179)
.-|+.++..++++-.-|.|...-.-..++|.+|+ +.++.|-.||.
T Consensus 37 ~~~~~lL~~I~~~l~~g~i~~~~~~~~~~~~i~~~~~~~~~ii~~f~ 83 (102)
T PF00961_consen 37 IKDKELLEKIKEYLGIGNIYKNKKKKTYRYRISSNKKIINKIIPYFN 83 (102)
T ss_dssp GGGHHHHHHHHHHHTSSEEEEESSSTEEEEEEESHHHHHHHHHHHHH
T ss_pred cchHHHHHHHHHHhCCceEEEeccCcEEEEEEeehHHHHHHHHHHhh
Confidence 4699999999999988888888887789999997 66677776664
No 104
>PF13730 HTH_36: Helix-turn-helix domain
Probab=22.77 E-value=39 Score=21.61 Aligned_cols=44 Identities=18% Similarity=0.351 Sum_probs=27.5
Q ss_pred HHHHHHHhhhcccEEEeecCC-CCCCCcc----ccCCHHHHHHhhhccccccc
Q 030302 8 RKEICKYLFQEGVCYAKKDYN-LAKHPEI----DVPNLQVIKLMQSFKSREYV 55 (179)
Q Consensus 8 r~~IYe~LFkEGV~VakKD~~-~p~Hpel----~VpNL~ViK~mqSLkSrGyV 55 (179)
-+.||-+|.. .+.++-. -|....| .+.-=.|.++++.|+.+||+
T Consensus 7 ~~~v~~~l~~----~~~~~~~~~pS~~~la~~~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 7 AKLVYLYLAS----YANKNGGCFPSQETLAKDLGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred HHHHHHHHHH----hcCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCcCC
Confidence 4577777763 1222222 2333344 36667899999999999985
No 105
>PF09106 SelB-wing_2: Elongation factor SelB, winged helix ; InterPro: IPR015190 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing []. Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 2". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity []. ; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0005525 GTP binding, 0001514 selenocysteine incorporation, 0005737 cytoplasm; PDB: 2V9V_A 1LVA_A 2PLY_A 2UWM_A.
Probab=22.72 E-value=78 Score=21.17 Aligned_cols=25 Identities=24% Similarity=0.341 Sum_probs=19.8
Q ss_pred cchhhHHHHHHHhhhcccEEEeecC
Q 030302 3 IPEKNRKEICKYLFQEGVCYAKKDY 27 (179)
Q Consensus 3 ipK~nr~~IYe~LFkEGV~VakKD~ 27 (179)
+|.+.-.++-+.|.++|+|+...|+
T Consensus 32 l~~k~~~~ll~~l~~~g~l~~~g~~ 56 (59)
T PF09106_consen 32 LPPKLFNALLEALVAEGRLKVEGDW 56 (59)
T ss_dssp S-HCCHHHHHHHHHHTTSEEEESSE
T ss_pred CCHHHHHHHHHHHHHCCCeeeECCE
Confidence 4666777899999999999987764
No 106
>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=22.10 E-value=44 Score=28.15 Aligned_cols=38 Identities=8% Similarity=-0.058 Sum_probs=27.7
Q ss_pred ccCCHHHHHHhh-hcccccccceeeeceeeeeeechhhHHHHH
Q 030302 36 DVPNLQVIKLMQ-SFKSREYVRETFAWMHYYWYLTNDGIEFLR 77 (179)
Q Consensus 36 ~VpNL~ViK~mq-SLkSrGyVkEqFaWrh~Yw~LTneGI~YLR 77 (179)
+++...+...+. .|..+|++. +=.|- -+.|++||+||-
T Consensus 266 g~~~~~~~~~~e~~Li~~~li~---~~~~g-~~~~~~~~~~~~ 304 (305)
T TIGR00635 266 GEDADTIEDVYEPYLLQIGFLQ---RTPRG-RIATELAYEHLG 304 (305)
T ss_pred CCCcchHHHhhhHHHHHcCCcc---cCCch-hhhhHHHHHHhC
Confidence 467777888788 599999984 22233 268999999984
No 107
>PF02099 Josephin: Josephin; InterPro: IPR006155 Human genes containing triplet repeats can markedly expand in length, leading to neuropsychiatric disease. Expansion of triplet repeats explains the phenomenon of anticipation, i.e. the increasing severity or earlier age of onset in successive generations in a pedigree []. A novel gene containing CAG repeats has been identified and mapped to chromosome 14q32.1, the genetic locus for Machado-Joseph disease (MJD). Normally, the gene contains 13-36 CAG repeats, but most clinically diagnosed patients and all affected members of a family with the clinical and pathological diagnosis of MJD show expansion of the repeat number, from 68-79 []. Similar abnormalities in related genes may give rise to diseases similar to MJD. MJD is a neurodegenerative disorder characterised by cerebellar ataxia, pyramidal and extra-pyramidal signs, peripheral nerve palsy, external ophtalmoplegia, facial and lingual fasciculation and bulging. The disease is autosomal dominant, with late onset of symptoms, generally after the fourth decade.; GO: 0008242 omega peptidase activity; PDB: 3O65_G 1YZB_A 2JRI_A 2DOS_A 2AGA_A.
Probab=22.08 E-value=64 Score=26.36 Aligned_cols=27 Identities=22% Similarity=0.529 Sum_probs=21.0
Q ss_pred CccccCCHHHHHHhhhcccccccceeeece
Q 030302 33 PEIDVPNLQVIKLMQSFKSREYVRETFAWM 62 (179)
Q Consensus 33 pel~VpNL~ViK~mqSLkSrGyVkEqFaWr 62 (179)
|++ |.+.++.+.|++|++.|| +.|.++
T Consensus 130 P~~-i~~~~l~~fL~~l~~~g~--~ifvV~ 156 (157)
T PF02099_consen 130 PEL-ISDFYLSAFLQQLQSEGY--SIFVVR 156 (157)
T ss_dssp -EE-E-HHHHHHHHHHHHCCTE--EEEEEE
T ss_pred Ccc-cCHHHHHHHHHHHHhCCc--EEEEEe
Confidence 554 678899999999999999 777764
No 108
>PF11181 YflT: Heat induced stress protein YflT
Probab=21.93 E-value=89 Score=23.10 Aligned_cols=36 Identities=14% Similarity=0.270 Sum_probs=28.7
Q ss_pred HHHHHHhhhcccccccceeeeceeeeeeec--hhhHHHHHHhhC
Q 030302 40 LQVIKLMQSFKSREYVRETFAWMHYYWYLT--NDGIEFLRTYLN 81 (179)
Q Consensus 40 L~ViK~mqSLkSrGyVkEqFaWrh~Yw~LT--neGI~YLR~yLh 81 (179)
-+++.++++|++.||-++... .|| ++-++.|.+..+
T Consensus 10 ~E~~~~I~~L~~~Gy~~ddI~------Vva~d~~~~~~l~~~t~ 47 (103)
T PF11181_consen 10 EEALSAIEELKAQGYSEDDIY------VVAKDKDRTERLADQTD 47 (103)
T ss_pred HHHHHHHHHHHHcCCCcccEE------EEEcCchHHHHHHHhcC
Confidence 368999999999999999873 777 455788887663
No 109
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=21.79 E-value=94 Score=20.74 Aligned_cols=31 Identities=10% Similarity=0.135 Sum_probs=25.0
Q ss_pred ccCCHHHHHHhhhcccccccceeeeceeeeeeech
Q 030302 36 DVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTN 70 (179)
Q Consensus 36 ~VpNL~ViK~mqSLkSrGyVkEqFaWrh~Yw~LTn 70 (179)
.+.--+|.+.|+-|+..|++. +.+-+|.++|
T Consensus 39 g~sr~tv~r~l~~l~~~g~I~----~~~~~i~I~d 69 (76)
T PF13545_consen 39 GVSRETVSRILKRLKDEGIIE----VKRGKIIILD 69 (76)
T ss_dssp TSCHHHHHHHHHHHHHTTSEE----EETTEEEESS
T ss_pred CCCHHHHHHHHHHHHHCCCEE----EcCCEEEECC
Confidence 377788999999999999987 4555777776
No 110
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=21.68 E-value=95 Score=27.30 Aligned_cols=47 Identities=15% Similarity=0.290 Sum_probs=39.7
Q ss_pred CCccccCCHHHHHHhhhcccccccceeeeceeeeeeechhhHHHHHH
Q 030302 32 HPEIDVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEFLRT 78 (179)
Q Consensus 32 Hpel~VpNL~ViK~mqSLkSrGyVkEqFaWrh~Yw~LTneGI~YLR~ 78 (179)
+..+.+........++.|..-||+....+=+--.-.+|++|++.|-.
T Consensus 26 a~~l~~S~qta~R~l~~le~~~~I~R~~~~~Gq~i~iTekG~~~L~~ 72 (214)
T COG1339 26 AKRLGVSSQTAARKLKELEDEGYITRTISKRGQLITITEKGIDLLYK 72 (214)
T ss_pred HHHhCcCcHHHHHHHHhhccCCcEEEEecCCCcEEEehHhHHHHHHH
Confidence 45567888999999999999999998887777777999999988753
No 111
>PF14277 DUF4364: Domain of unknown function (DUF4364)
Probab=21.07 E-value=1.1e+02 Score=25.19 Aligned_cols=42 Identities=10% Similarity=0.066 Sum_probs=31.0
Q ss_pred cCCHHHHHHhhhcccccccceee-eceeeeeeechhhHHHHHH
Q 030302 37 VPNLQVIKLMQSFKSREYVRETF-AWMHYYWYLTNDGIEFLRT 78 (179)
Q Consensus 37 VpNL~ViK~mqSLkSrGyVkEqF-aWrh~Yw~LTneGI~YLR~ 78 (179)
+--+.+-.++.-|.+.|+|...- .=-..+|.||++|.+=|--
T Consensus 31 ~nYF~lqq~l~eL~es~~i~~~~~~~~~~~y~iTe~G~~tl~~ 73 (163)
T PF14277_consen 31 TNYFTLQQALSELVESGLITLETDSDNKTRYSITEKGKETLEF 73 (163)
T ss_pred ccHHHHHHHHHHHHHCCCEEEeeccCCCcEEEECHhhHHHHHH
Confidence 34567788899999999998542 3234688999999876543
No 112
>KOG2175 consensus Protein predicted to be involved in carbohydrate metabolism [Carbohydrate transport and metabolism]
Probab=20.57 E-value=30 Score=33.29 Aligned_cols=25 Identities=28% Similarity=0.452 Sum_probs=21.9
Q ss_pred eeceeeeeeechhhH-HHHHHhhCCC
Q 030302 59 FAWMHYYWYLTNDGI-EFLRTYLNLP 83 (179)
Q Consensus 59 FaWrh~Yw~LTneGI-~YLR~yLhLP 83 (179)
..|.-+||+|+++|| ..|-.+++.|
T Consensus 200 ~~~~~~fkTlv~~~i~~~le~~~~~~ 225 (458)
T KOG2175|consen 200 QSRDAFFKTLVNKGILDALEYVLKMP 225 (458)
T ss_pred chhhHHHHHHHHhhhHHHHHHHhcCC
Confidence 568889999999999 7888888988
No 113
>PF05158 RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; InterPro: IPR007832 The family comprises a subunit specific to RNA Pol III, the tRNA specific polymerase. The C34 subunit of Saccharomyces cerevisiae RNA Pol III is part of a subcomplex of three subunits which have no counterpart in the other two nuclear RNA polymerases. This subunit interacts with TFIIIB70 and therefore participates in Pol III recruitment [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2DK8_A 2DK5_A 2YU3_A.
Probab=20.23 E-value=50 Score=29.89 Aligned_cols=26 Identities=15% Similarity=0.322 Sum_probs=19.5
Q ss_pred CCHHHHHHhhhcccccccceeeecee
Q 030302 38 PNLQVIKLMQSFKSREYVRETFAWMH 63 (179)
Q Consensus 38 pNL~ViK~mqSLkSrGyVkEqFaWrh 63 (179)
+--.|.|++++|.+|+++|+.-+=.|
T Consensus 113 ~~~~~~k~lk~Le~k~lIK~vksv~~ 138 (327)
T PF05158_consen 113 HQTQLTKILKSLESKKLIKSVKSVKN 138 (327)
T ss_dssp -HHHHHHHHHHHHHTTSEEEE--SS-
T ss_pred CHHHHHHHHHHHHhCCCEEEecCcCC
Confidence 44568999999999999999888666
Done!