Query psy5978
Match_columns 159
No_of_seqs 134 out of 245
Neff 3.8
Searched_HMMs 46136
Date Fri Aug 16 23:26:54 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5978.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5978hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3344|consensus 100.0 4.7E-75 1E-79 458.2 10.9 147 1-154 1-149 (150)
2 PTZ00034 40S ribosomal protein 100.0 3.1E-63 6.8E-68 383.4 11.5 98 1-98 2-99 (124)
3 PF03501 S10_plectin: Plectin/ 100.0 1.7E-62 3.7E-67 365.0 7.6 94 3-96 1-94 (95)
4 COG5045 Ribosomal protein S10E 100.0 2.2E-48 4.8E-53 290.7 7.3 102 1-103 1-102 (105)
5 cd00090 HTH_ARSR Arsenical Res 94.3 0.051 1.1E-06 34.5 2.9 69 4-78 5-75 (78)
6 PF03551 PadR: Transcriptional 93.5 0.11 2.4E-06 35.5 3.7 44 35-78 27-75 (75)
7 PF14947 HTH_45: Winged helix- 93.2 0.071 1.5E-06 37.3 2.4 40 36-79 30-69 (77)
8 PTZ00326 phenylalanyl-tRNA syn 93.1 0.054 1.2E-06 50.7 2.1 51 35-88 31-81 (494)
9 PLN02853 Probable phenylalanyl 93.0 0.058 1.2E-06 50.6 2.1 53 36-91 29-81 (492)
10 smart00347 HTH_MARR helix_turn 93.0 0.071 1.5E-06 36.3 2.0 69 6-79 10-81 (101)
11 PRK10141 DNA-binding transcrip 92.9 0.078 1.7E-06 40.7 2.3 71 3-79 13-84 (117)
12 PRK04172 pheS phenylalanyl-tRN 92.9 0.11 2.3E-06 47.6 3.6 67 6-78 6-72 (489)
13 PF13463 HTH_27: Winged helix 92.5 0.092 2E-06 34.3 2.0 37 36-72 29-68 (68)
14 PF13601 HTH_34: Winged helix 91.8 0.25 5.3E-06 35.1 3.6 69 8-81 2-74 (80)
15 PRK03902 manganese transport t 91.2 0.15 3.2E-06 38.8 2.1 72 7-87 9-94 (142)
16 PF02002 TFIIE_alpha: TFIIE al 91.0 0.091 2E-06 38.2 0.8 66 8-78 15-87 (105)
17 COG3432 Predicted transcriptio 90.4 0.22 4.8E-06 37.5 2.4 40 41-80 47-86 (95)
18 PRK05638 threonine synthase; V 89.3 0.32 6.9E-06 43.7 2.9 67 6-78 371-440 (442)
19 PF14338 Mrr_N: Mrr N-terminal 89.0 0.22 4.7E-06 35.6 1.4 36 41-79 56-91 (92)
20 PHA00738 putative HTH transcri 88.9 0.37 8.1E-06 37.2 2.6 66 5-75 11-76 (108)
21 PF09639 YjcQ: YjcQ protein; 88.5 0.22 4.8E-06 36.0 1.1 44 35-78 20-69 (88)
22 TIGR02647 DNA conserved hypoth 88.4 0.26 5.7E-06 36.1 1.4 33 38-75 32-64 (77)
23 PF01978 TrmB: Sugar-specific 88.4 0.27 5.9E-06 32.9 1.4 58 6-68 8-65 (68)
24 TIGR02702 SufR_cyano iron-sulf 88.2 0.24 5.1E-06 39.9 1.2 65 7-76 2-71 (203)
25 PF13814 Replic_Relax: Replica 87.8 0.76 1.6E-05 35.6 3.8 42 41-83 28-77 (191)
26 smart00418 HTH_ARSR helix_turn 86.9 1.1 2.3E-05 27.6 3.5 43 36-78 21-64 (66)
27 TIGR02337 HpaR homoprotocatech 86.9 0.79 1.7E-05 33.4 3.2 43 37-79 54-99 (118)
28 PRK14165 winged helix-turn-hel 86.1 0.84 1.8E-05 38.5 3.4 47 35-81 31-77 (217)
29 PRK09416 lstR lineage-specific 85.2 0.63 1.4E-05 37.0 2.1 46 37-84 75-123 (135)
30 smart00550 Zalpha Z-DNA-bindin 84.5 0.37 8E-06 33.1 0.5 65 1-71 1-67 (68)
31 PRK06266 transcription initiat 82.1 0.66 1.4E-05 37.7 1.1 70 7-81 23-99 (178)
32 PF10007 DUF2250: Uncharacteri 80.6 1.5 3.3E-05 32.6 2.5 65 9-78 10-91 (92)
33 COG1695 Predicted transcriptio 79.5 2.1 4.6E-05 32.1 3.0 47 37-83 42-93 (138)
34 PF09382 RQC: RQC domain; Int 79.2 3 6.5E-05 29.7 3.6 44 37-80 54-98 (106)
35 TIGR02719 repress_PhaQ poly-be 78.7 2.3 5E-05 33.6 3.1 49 37-85 55-108 (138)
36 TIGR03433 padR_acidobact trans 75.3 3.4 7.4E-05 29.9 3.0 45 36-80 36-85 (100)
37 TIGR01889 Staph_reg_Sar staphy 74.8 3.6 7.8E-05 30.0 3.1 43 36-78 54-99 (109)
38 PF03374 ANT: Phage antirepres 74.5 10 0.00022 27.4 5.3 60 7-81 37-106 (111)
39 COG1846 MarR Transcriptional r 74.1 3.6 7.7E-05 28.4 2.8 46 36-81 47-95 (126)
40 smart00529 HTH_DTXR Helix-turn 73.9 3.4 7.4E-05 28.6 2.6 43 35-80 9-51 (96)
41 COG1321 TroR Mn-dependent tran 73.5 1.7 3.6E-05 34.6 1.0 75 6-88 10-98 (154)
42 PF07381 DUF1495: Winged helix 71.8 2.5 5.5E-05 31.4 1.6 60 6-75 9-86 (90)
43 PF01638 HxlR: HxlR-like helix 71.1 5.6 0.00012 28.1 3.2 41 37-77 31-74 (90)
44 COG1497 Predicted transcriptio 70.7 4.2 9E-05 35.7 2.9 42 36-80 36-77 (260)
45 TIGR02277 PaaX_trns_reg phenyl 70.3 4.4 9.6E-05 34.9 3.0 43 36-78 31-73 (280)
46 PRK11512 DNA-binding transcrip 69.2 5.7 0.00012 30.0 3.1 43 36-78 65-110 (144)
47 PHA02943 hypothetical protein; 67.1 2.8 6.2E-05 34.6 1.1 60 6-71 11-70 (165)
48 TIGR00373 conserved hypothetic 66.9 4.8 0.0001 32.0 2.4 68 9-81 17-91 (158)
49 PF07848 PaaX: PaaX-like prote 65.8 6.3 0.00014 27.7 2.5 38 35-72 33-70 (70)
50 PRK03573 transcriptional regul 65.8 7.4 0.00016 29.1 3.1 44 37-80 58-104 (144)
51 TIGR01884 cas_HTH CRISPR locus 65.7 4.4 9.4E-05 32.6 1.9 61 6-72 143-203 (203)
52 KOG2784|consensus 65.2 7.1 0.00015 36.6 3.4 40 38-78 30-69 (483)
53 PF14531 Kinase-like: Kinase-l 64.3 1.8 3.8E-05 37.9 -0.6 41 40-82 152-192 (288)
54 TIGR02010 IscR iron-sulfur clu 64.1 3.2 6.9E-05 31.5 0.8 65 1-70 1-69 (135)
55 PRK10857 DNA-binding transcrip 62.6 3.1 6.8E-05 33.2 0.6 54 1-58 1-58 (164)
56 PRK10870 transcriptional repre 61.2 8.7 0.00019 30.5 2.9 44 36-79 82-128 (176)
57 COG0640 ArsR Predicted transcr 58.4 9.2 0.0002 24.8 2.2 68 5-78 24-92 (110)
58 COG1378 Predicted transcriptio 58.0 8.2 0.00018 32.8 2.4 63 6-73 16-78 (247)
59 PRK11014 transcriptional repre 56.7 6.8 0.00015 29.8 1.5 63 1-67 1-67 (141)
60 COG2345 Predicted transcriptio 56.5 7.6 0.00016 33.1 1.9 66 4-74 9-79 (218)
61 PRK13777 transcriptional regul 56.1 11 0.00024 30.8 2.8 44 37-80 71-117 (185)
62 COG5124 Protein predicted to b 55.1 9.4 0.0002 32.4 2.2 74 3-81 6-85 (209)
63 smart00346 HTH_ICLR helix_turn 48.5 15 0.00032 25.0 2.0 44 35-80 30-73 (91)
64 smart00531 TFIIE Transcription 47.9 19 0.0004 28.0 2.7 48 35-82 25-82 (147)
65 PRK11920 rirA iron-responsive 47.6 7.5 0.00016 30.5 0.5 63 1-69 1-67 (153)
66 PF01043 SecA_PP_bind: SecA pr 45.3 18 0.00039 27.5 2.2 21 67-87 34-54 (113)
67 KOG4412|consensus 43.6 16 0.00035 31.4 1.9 48 5-52 115-164 (226)
68 PRK04172 pheS phenylalanyl-tRN 41.5 26 0.00057 32.2 3.1 38 44-82 156-193 (489)
69 COG1542 Uncharacterized conser 39.0 20 0.00043 34.6 1.9 45 37-83 321-366 (593)
70 PF13412 HTH_24: Winged helix- 39.0 5 0.00011 24.9 -1.4 46 6-56 3-48 (48)
71 cd01223 PH_Vav Vav pleckstrin 38.4 14 0.00031 28.7 0.7 58 12-72 24-86 (116)
72 TIGR00738 rrf2_super rrf2 fami 37.0 14 0.00031 27.1 0.5 65 1-71 1-70 (132)
73 PF02082 Rrf2: Transcriptional 37.0 6.9 0.00015 27.2 -1.1 54 1-58 1-58 (83)
74 KOG3433|consensus 36.0 19 0.0004 30.7 1.1 74 3-81 5-84 (203)
75 PF13309 HTH_22: HTH domain 33.8 31 0.00067 23.5 1.7 25 2-26 20-44 (64)
76 KOG0921|consensus 32.6 58 0.0013 34.1 4.1 12 145-156 1250-1261(1282)
77 KOG3233|consensus 32.2 14 0.00031 33.0 -0.1 25 36-60 111-135 (297)
78 PF10662 PduV-EutP: Ethanolami 32.2 21 0.00045 28.4 0.8 38 39-81 105-142 (143)
79 cd03071 PDI_b'_NRX PDIb' famil 31.9 43 0.00093 26.4 2.4 30 57-86 52-81 (116)
80 PRK06474 hypothetical protein; 31.9 23 0.0005 28.5 1.0 67 3-74 8-81 (178)
81 PF06969 HemN_C: HemN C-termin 31.0 34 0.00073 22.3 1.5 27 43-73 39-65 (66)
82 PF01050 MannoseP_isomer: Mann 29.6 48 0.001 26.3 2.4 53 17-82 12-70 (151)
83 TIGR01689 EcbF-BcbF capsule bi 29.6 21 0.00045 27.6 0.4 48 36-91 23-70 (126)
84 PF03965 Penicillinase_R: Peni 28.2 39 0.00084 24.7 1.6 67 10-77 7-73 (115)
85 cd07153 Fur_like Ferric uptake 27.5 20 0.00044 25.7 -0.0 52 6-60 1-56 (116)
86 cd00092 HTH_CRP helix_turn_hel 27.1 45 0.00097 21.2 1.6 32 36-70 36-67 (67)
87 KOG1423|consensus 25.9 61 0.0013 30.0 2.7 29 53-81 234-267 (379)
88 PRK11050 manganese transport r 25.6 68 0.0015 24.9 2.6 40 35-77 61-100 (152)
89 PF09106 SelB-wing_2: Elongati 24.3 74 0.0016 20.8 2.3 25 3-27 32-56 (59)
90 cd07377 WHTH_GntR Winged helix 24.0 58 0.0013 20.3 1.7 23 36-58 36-58 (66)
91 PRK09249 coproporphyrinogen II 23.9 64 0.0014 29.2 2.5 33 42-78 401-433 (453)
92 PF14756 Pdase_C33_assoc: Pept 23.8 38 0.00083 27.2 0.9 23 71-93 14-36 (147)
93 PF13730 HTH_36: Helix-turn-he 23.6 35 0.00077 21.4 0.6 44 8-55 7-55 (55)
94 COG1959 Predicted transcriptio 23.4 38 0.00082 26.5 0.8 56 1-60 1-60 (150)
95 PF03962 Mnd1: Mnd1 family; I 22.4 93 0.002 25.4 3.0 45 36-80 26-71 (188)
96 PF06648 DUF1160: Protein of u 21.7 61 0.0013 25.4 1.7 31 37-80 81-111 (122)
97 PF11181 YflT: Heat induced st 21.5 90 0.0019 22.6 2.4 35 40-80 10-46 (103)
98 COG1905 NuoE NADH:ubiquinone o 21.4 38 0.00083 27.7 0.5 26 55-86 34-59 (160)
99 PF00961 LAGLIDADG_1: LAGLIDAD 21.3 1.6E+02 0.0035 20.3 3.6 45 37-81 37-83 (102)
100 PF01325 Fe_dep_repress: Iron 21.0 15 0.00033 24.7 -1.6 47 6-57 8-54 (60)
101 PF14277 DUF4364: Domain of un 20.8 1E+02 0.0022 24.8 2.8 42 37-78 31-73 (163)
102 PF13516 LRR_6: Leucine Rich r 20.7 58 0.0013 17.4 1.0 11 67-77 13-23 (24)
103 PHA00422 hypothetical protein 20.4 69 0.0015 23.1 1.6 36 44-79 28-65 (69)
104 KOG2175|consensus 20.1 27 0.00058 33.0 -0.7 25 59-83 200-225 (458)
105 KOG2383|consensus 20.1 70 0.0015 30.4 2.0 22 9-30 214-235 (467)
No 1
>KOG3344|consensus
Probab=100.00 E-value=4.7e-75 Score=458.18 Aligned_cols=147 Identities=61% Similarity=1.050 Sum_probs=130.7
Q ss_pred CccchhhHHHHHHHhhhcccEEEeeCCCCCCCCCccCCcHHHHHHHhcccccCccceeeeeceeEEEecchhHHHHHhhc
Q psy5978 1 MLMPKKNRYIIYEYLFKEGVLVAKKDFHAPKHPELDVPNLQVIKTLQSLKSKGWVNEQFAWRHYYWYITNDGIEKLRGVL 80 (159)
Q Consensus 1 Mlipk~~r~~IYe~LFkeGV~VakKD~~~~~Hpel~vpNL~Vik~mqSLkSrGyVke~FaWrh~Yw~LTneGI~yLR~yL 80 (159)
|||||+||++|||+||||||||||||+++++||||+||||||||+||||+|+|||||||||||||||||||||+|||+||
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 CCCCCCCccccccccCCCCCCCCCCCCCCCCCCCCCCCccccccCCCCCCCCccccCCCCc-cceecCCC-CcCCC
Q psy5978 81 NIPDEIVPSTLKRQARTTDASKVPRQMTQRPDGGRGADDRMSYRKGPQGVDKKADVGAGST-EVEFKGYG-GFGRG 154 (159)
Q Consensus 81 hLP~eiVPaTlk~~~r~~~~rpr~~~~g~~~~~~~~~~dr~~YRr~~~~~~k~~~~g~g~~-~~~fr~~g-gfGrG 154 (159)
|||+||||+||++ ++|++.||+++|.+.+......++||++||+.+-.. ++|||++ +|||| | |||++
T Consensus 81 hLP~EiVpaTl~~-~rP~~~rpr~~g~e~~~p~~~~r~dR~~yR~~~~~~----~~gA~s~~~~~fr--g~g~g~~ 149 (150)
T KOG3344|consen 81 HLPPEIVPATLKR-SRPETGRPRPPGLEGRGPADGTRGDRDGYRRGPVPP----EGGAGSGTEPQFR--GRGFGRP 149 (150)
T ss_pred cCCcccccchhhc-cCCCCCCCCCCCCCCCCcccccccchhhhccCCCCC----CCCCCcccccccc--ccCCCCC
Confidence 9999999999999 799999999987622222222348999999954322 6678887 99999 6 66664
No 2
>PTZ00034 40S ribosomal protein S10; Provisional
Probab=100.00 E-value=3.1e-63 Score=383.36 Aligned_cols=98 Identities=54% Similarity=0.986 Sum_probs=95.6
Q ss_pred CccchhhHHHHHHHhhhcccEEEeeCCCCCCCCCccCCcHHHHHHHhcccccCccceeeeeceeEEEecchhHHHHHhhc
Q psy5978 1 MLMPKKNRYIIYEYLFKEGVLVAKKDFHAPKHPELDVPNLQVIKTLQSLKSKGWVNEQFAWRHYYWYITNDGIEKLRGVL 80 (159)
Q Consensus 1 Mlipk~~r~~IYe~LFkeGV~VakKD~~~~~Hpel~vpNL~Vik~mqSLkSrGyVke~FaWrh~Yw~LTneGI~yLR~yL 80 (159)
|||||+||++||++||+|||||||||++.++||||+||||||||+||||+|||||+|||||||||||||||||+|||+||
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 psy5978 81 NIPDEIVPSTLKRQARTT 98 (159)
Q Consensus 81 hLP~eiVPaTlk~~~r~~ 98 (159)
|||+||||+||++++++.
T Consensus 82 ~LP~eivP~T~k~~~~~~ 99 (124)
T PTZ00034 82 HLPPDVFPATHKKKSVNF 99 (124)
T ss_pred CCCcccCchhhcccccCc
Confidence 999999999999976554
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=1.7e-62 Score=364.97 Aligned_cols=94 Identities=76% Similarity=1.304 Sum_probs=82.6
Q ss_pred cchhhHHHHHHHhhhcccEEEeeCCCCCCCCCccCCcHHHHHHHhcccccCccceeeeeceeEEEecchhHHHHHhhcCC
Q psy5978 3 MPKKNRYIIYEYLFKEGVLVAKKDFHAPKHPELDVPNLQVIKTLQSLKSKGWVNEQFAWRHYYWYITNDGIEKLRGVLNI 82 (159)
Q Consensus 3 ipk~~r~~IYe~LFkeGV~VakKD~~~~~Hpel~vpNL~Vik~mqSLkSrGyVke~FaWrh~Yw~LTneGI~yLR~yLhL 82 (159)
|||+||++|||+||||||||||||+++|+|||++||||||||+||||+|||||+|||||||||||||||||||||+||||
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 psy5978 83 PDEIVPSTLKRQAR 96 (159)
Q Consensus 83 P~eiVPaTlk~~~r 96 (159)
|+|||||||+++.+
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 99999999999643
No 4
>COG5045 Ribosomal protein S10E [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.2e-48 Score=290.74 Aligned_cols=102 Identities=50% Similarity=0.777 Sum_probs=97.3
Q ss_pred CccchhhHHHHHHHhhhcccEEEeeCCCCCCCCCccCCcHHHHHHHhcccccCccceeeeeceeEEEecchhHHHHHhhc
Q psy5978 1 MLMPKKNRYIIYEYLFKEGVLVAKKDFHAPKHPELDVPNLQVIKTLQSLKSKGWVNEQFAWRHYYWYITNDGIEKLRGVL 80 (159)
Q Consensus 1 Mlipk~~r~~IYe~LFkeGV~VakKD~~~~~Hpel~vpNL~Vik~mqSLkSrGyVke~FaWrh~Yw~LTneGI~yLR~yL 80 (159)
|||||+||.+|-++||++||.||||||++++|+||+||||||||+||||.|+||||.+|+|||+||+||+||++||||||
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 CCCCCCCccccccccCCCCCCCC
Q psy5978 81 NIPDEIVPSTLKRQARTTDASKV 103 (159)
Q Consensus 81 hLP~eiVPaTlk~~~r~~~~rpr 103 (159)
+||+|+||+|...+.+| +.||+
T Consensus 81 ~lp~e~Vp~t~~~~v~p-t~rp~ 102 (105)
T COG5045 81 VLPDEGVPSTEAPAVSP-TQRPQ 102 (105)
T ss_pred cCccccCccccccccCc-ccCCC
Confidence 99999999999986444 44654
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=94.29 E-value=0.051 Score=34.46 Aligned_cols=69 Identities=19% Similarity=0.302 Sum_probs=49.0
Q ss_pred chhhHHHHHHHhhhcccEEEeeCCCCCCCCCccCCcHHHHHHHhcccccCccceeeeeceeEEEec--chhHHHHHh
Q psy5978 4 PKKNRYIIYEYLFKEGVLVAKKDFHAPKHPELDVPNLQVIKTLQSLKSKGWVNEQFAWRHYYWYIT--NDGIEKLRG 78 (159)
Q Consensus 4 pk~~r~~IYe~LFkeGV~VakKD~~~~~Hpel~vpNL~Vik~mqSLkSrGyVke~FaWrh~Yw~LT--neGI~yLR~ 78 (159)
...++..|+.+|...+ +..+|.. ..+.++.=.|-++|..|++.|++...-.=+..||.|| .+.++.+++
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 3567889999998876 3334422 1335777778899999999999986433388999999 555555554
No 6
>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=93.53 E-value=0.11 Score=35.49 Aligned_cols=44 Identities=23% Similarity=0.415 Sum_probs=37.7
Q ss_pred ccCCcHHHHHHHhcccccCccceeeee-----ceeEEEecchhHHHHHh
Q psy5978 35 LDVPNLQVIKTLQSLKSKGWVNEQFAW-----RHYYWYITNDGIEKLRG 78 (159)
Q Consensus 35 l~vpNL~Vik~mqSLkSrGyVke~FaW-----rh~Yw~LTneGI~yLR~ 78 (159)
.+|..=.|.-+|+.|...|+|.....= .--||.||++|.++|+|
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 346777889999999999999988776 46689999999999986
No 7
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=93.24 E-value=0.071 Score=37.30 Aligned_cols=40 Identities=23% Similarity=0.352 Sum_probs=31.2
Q ss_pred cCCcHHHHHHHhcccccCccceeeeeceeEEEecchhHHHHHhh
Q psy5978 36 DVPNLQVIKTLQSLKSKGWVNEQFAWRHYYWYITNDGIEKLRGV 79 (159)
Q Consensus 36 ~vpNL~Vik~mqSLkSrGyVke~FaWrh~Yw~LTneGI~yLR~y 79 (159)
+++--.+.+.+..|.++|+|+. ..-.|.||++|.++|..+
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 3666788999999999999944 555679999999999875
No 8
>PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional
Probab=93.14 E-value=0.054 Score=50.67 Aligned_cols=51 Identities=20% Similarity=0.454 Sum_probs=40.5
Q ss_pred ccCCcHHHHHHHhcccccCccceeeeeceeEEEecchhHHHHHhhcCCCCCCCc
Q psy5978 35 LDVPNLQVIKTLQSLKSKGWVNEQFAWRHYYWYITNDGIEKLRGVLNIPDEIVP 88 (159)
Q Consensus 35 l~vpNL~Vik~mqSLkSrGyVke~FaWrh~Yw~LTneGI~yLR~yLhLP~eiVP 88 (159)
+.+.--.|+.++.||.|+|+|+-.-- ..-+|.||+||.+||+ -+||+..+=
T Consensus 31 ~~~~~~~v~~~~~~L~~kg~v~~~~~-~~~~~~LT~eG~~~~~--~G~PE~rl~ 81 (494)
T PTZ00326 31 LNIDHQKVVGAIKSLESANYITTEMK-KSNTWTLTEEGEDYLK--NGSPEYRLW 81 (494)
T ss_pred cCCCHHHHHHHHHHHHhCCCEEEEEE-EEEEEEECHHHHHHHH--cCCHHHHHH
Confidence 34677899999999999998875443 5678899999999999 467765543
No 9
>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain
Probab=93.05 E-value=0.058 Score=50.56 Aligned_cols=53 Identities=17% Similarity=0.292 Sum_probs=42.0
Q ss_pred cCCcHHHHHHHhcccccCccceeeeeceeEEEecchhHHHHHhhcCCCCCCCcccc
Q psy5978 36 DVPNLQVIKTLQSLKSKGWVNEQFAWRHYYWYITNDGIEKLRGVLNIPDEIVPSTL 91 (159)
Q Consensus 36 ~vpNL~Vik~mqSLkSrGyVke~FaWrh~Yw~LTneGI~yLR~yLhLP~eiVPaTl 91 (159)
.++--.|+.++.||.++|+|+-.- =..-+|.||+||.+||+ -+||+..|=+.+
T Consensus 29 g~~~~~v~~~~~~L~~kg~v~~~~-~~~~~~~LT~eG~~~l~--~G~PE~rl~~~l 81 (492)
T PLN02853 29 GLDHNEVVGVIKSLHGFRYVDAQD-IKRETWVLTEEGKKYAA--EGSPEVQLFAAV 81 (492)
T ss_pred CCCHHHHHHHHHHHHhCCCEEEEE-EEEEEEEECHHHHHHHH--cCCHHHHHHHHH
Confidence 467789999999999999887654 35678899999999999 467766554443
No 10
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=92.99 E-value=0.071 Score=36.26 Aligned_cols=69 Identities=23% Similarity=0.412 Sum_probs=48.8
Q ss_pred hhHHHHHHHhhhcccEEEeeCCCCCCCCCccCCcHHHHHHHhcccccCcccee---eeeceeEEEecchhHHHHHhh
Q psy5978 6 KNRYIIYEYLFKEGVLVAKKDFHAPKHPELDVPNLQVIKTLQSLKSKGWVNEQ---FAWRHYYWYITNDGIEKLRGV 79 (159)
Q Consensus 6 ~~r~~IYe~LFkeGV~VakKD~~~~~Hpel~vpNL~Vik~mqSLkSrGyVke~---FaWrh~Yw~LTneGI~yLR~y 79 (159)
.+...|+..|...|.+-. +|.. . .++++.=.|.++++.|.++|+|... ..=|..|+.||++|.+++.+.
T Consensus 10 ~~~~~il~~l~~~~~~~~-~~la--~--~~~~s~~~i~~~l~~L~~~g~v~~~~~~~~~r~~~~~lT~~g~~~~~~~ 81 (101)
T smart00347 10 PTQFLVLRILYEEGPLSV-SELA--K--RLGVSPSTVTRVLDRLEKKGLIRRLPSPEDRRSVLVSLTEEGRELIEEL 81 (101)
T ss_pred HHHHHHHHHHHHcCCcCH-HHHH--H--HHCCCchhHHHHHHHHHHCCCeEecCCCCCCCeEEEEECHhHHHHHHHH
Confidence 345678888887774332 2321 1 2346666788999999999999754 334678999999999888763
No 11
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=92.88 E-value=0.078 Score=40.66 Aligned_cols=71 Identities=15% Similarity=0.189 Sum_probs=55.6
Q ss_pred cchhhHHHHHHHhhhcc-cEEEeeCCCCCCCCCccCCcHHHHHHHhcccccCccceeeeeceeEEEecchhHHHHHhh
Q psy5978 3 MPKKNRYIIYEYLFKEG-VLVAKKDFHAPKHPELDVPNLQVIKTLQSLKSKGWVNEQFAWRHYYWYITNDGIEKLRGV 79 (159)
Q Consensus 3 ipk~~r~~IYe~LFkeG-V~VakKD~~~~~Hpel~vpNL~Vik~mqSLkSrGyVke~FaWrh~Yw~LTneGI~yLR~y 79 (159)
+...+|.+|...|.+.| +.|. |. ...++++.-.|-+.|+-|+.-|+|...--.|+.||.|+++..+++...
T Consensus 13 LadptRl~IL~~L~~~~~~~v~--el----a~~l~lsqstvS~HL~~L~~AGLV~~~r~Gr~~~Y~l~~~~~~~~~~~ 84 (117)
T PRK10141 13 LSDETRLGIVLLLRESGELCVC--DL----CTALDQSQPKISRHLALLRESGLLLDRKQGKWVHYRLSPHIPAWAAKI 84 (117)
T ss_pred hCCHHHHHHHHHHHHcCCcCHH--HH----HHHHCcCHHHHHHHHHHHHHCCceEEEEEcCEEEEEECchHHHHHHHH
Confidence 34578999999998754 3332 21 123467888899999999999999999999999999998877777753
No 12
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=92.88 E-value=0.11 Score=47.63 Aligned_cols=67 Identities=16% Similarity=0.194 Sum_probs=47.3
Q ss_pred hhHHHHHHHhhhcccEEEeeCCCCCCCCCccCCcHHHHHHHhcccccCccceeeeeceeEEEecchhHHHHHh
Q psy5978 6 KNRYIIYEYLFKEGVLVAKKDFHAPKHPELDVPNLQVIKTLQSLKSKGWVNEQFAWRHYYWYITNDGIEKLRG 78 (159)
Q Consensus 6 ~~r~~IYe~LFkeGV~VakKD~~~~~Hpel~vpNL~Vik~mqSLkSrGyVke~FaWrh~Yw~LTneGI~yLR~ 78 (159)
.+...|...|-.+|-+- -++. -..+.+..=.|+.++.+|.++|||...-. +..+|.||+||.+|+.+
T Consensus 6 ~~e~~vL~~L~~~~~~s-~~eL----A~~l~l~~~tVt~~i~~Le~kGlV~~~~~-~~~~i~LTeeG~~~~~~ 72 (489)
T PRK04172 6 PNEKKVLKALKELKEAT-LEEL----AEKLGLPPEAVMRAAEWLEEKGLVKVEER-VEEVYVLTEEGKKYAEE 72 (489)
T ss_pred HHHHHHHHHHHhCCCCC-HHHH----HHHhCcCHHHHHHHHHHHHhCCCEEEEee-eEEEEEECHHHHHHHHh
Confidence 34456777775444221 1111 11235788899999999999999997644 57899999999999984
No 13
>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=92.49 E-value=0.092 Score=34.33 Aligned_cols=37 Identities=22% Similarity=0.378 Sum_probs=28.8
Q ss_pred cCCcHHHHHHHhcccccCcccee---eeeceeEEEecchh
Q psy5978 36 DVPNLQVIKTLQSLKSKGWVNEQ---FAWRHYYWYITNDG 72 (159)
Q Consensus 36 ~vpNL~Vik~mqSLkSrGyVke~---FaWrh~Yw~LTneG 72 (159)
.++-=+|.+++++|..+|||..+ ..=|-.++.||++|
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 14
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=91.77 E-value=0.25 Score=35.09 Aligned_cols=69 Identities=22% Similarity=0.400 Sum_probs=44.8
Q ss_pred HHHHHHHhhhcccEEEeeCCCCCCCCCccCCcHHHHHHHhcccccCcccee--eeec--eeEEEecchhHHHHHhhcC
Q psy5978 8 RYIIYEYLFKEGVLVAKKDFHAPKHPELDVPNLQVIKTLQSLKSKGWVNEQ--FAWR--HYYWYITNDGIEKLRGVLN 81 (159)
Q Consensus 8 r~~IYe~LFkeGV~VakKD~~~~~Hpel~vpNL~Vik~mqSLkSrGyVke~--FaWr--h~Yw~LTneGI~yLR~yLh 81 (159)
|.+|..+|...+-+-. ++.. ..++++.=.+-+.|+.|...|||+-. |.=+ -.||.||++|.+.+.+|+.
T Consensus 2 Rl~Il~~L~~~~~~~f-~~L~----~~l~lt~g~Ls~hL~~Le~~GyV~~~k~~~~~~p~t~~~lT~~Gr~~~~~~~~ 74 (80)
T PF13601_consen 2 RLAILALLYANEEATF-SELK----EELGLTDGNLSKHLKKLEEAGYVEVEKEFEGRRPRTWYSLTDKGREAFERYVA 74 (80)
T ss_dssp HHHHHHHHHHHSEEEH-HHHH----HHTT--HHHHHHHHHHHHHTTSEEEEEE-SSS--EEEEEE-HHHHHHHHHHHH
T ss_pred HHHHHHHHhhcCCCCH-HHHH----HHhCcCHHHHHHHHHHHHHCCCEEEEEeccCCCCeEEEEECHHHHHHHHHHHH
Confidence 5667777776333321 1110 12457777788999999999999643 3333 6799999999999998874
No 15
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=91.16 E-value=0.15 Score=38.81 Aligned_cols=72 Identities=18% Similarity=0.210 Sum_probs=50.2
Q ss_pred hHHHHHHHhhhcccEEEeeCCCCCCCCCccCCcHHHHHHHhcccccCccceeeeeceeEEEecchh--------------
Q psy5978 7 NRYIIYEYLFKEGVLVAKKDFHAPKHPELDVPNLQVIKTLQSLKSKGWVNEQFAWRHYYWYITNDG-------------- 72 (159)
Q Consensus 7 ~r~~IYe~LFkeGV~VakKD~~~~~Hpel~vpNL~Vik~mqSLkSrGyVke~FaWrh~Yw~LTneG-------------- 72 (159)
...+||.++-..|.+-+ +|.. ..+.|..-.|...++.|..+|||.-. +...+.||++|
T Consensus 9 yL~~I~~l~~~~~~~~~-~ela----~~l~vs~~svs~~l~~L~~~Gli~~~---~~~~i~LT~~G~~~a~~~~~~h~~~ 80 (142)
T PRK03902 9 YIEQIYLLIEEKGYARV-SDIA----EALSVHPSSVTKMVQKLDKDEYLIYE---KYRGLVLTPKGKKIGKRLVYRHELL 80 (142)
T ss_pred HHHHHHHHHhcCCCcCH-HHHH----HHhCCChhHHHHHHHHHHHCCCEEEe---cCceEEECHHHHHHHHHHHHHHHHH
Confidence 35677877765564422 1111 12468888999999999999999733 45679999999
Q ss_pred HHHHHhhcCCCCCCC
Q psy5978 73 IEKLRGVLNIPDEIV 87 (159)
Q Consensus 73 I~yLR~yLhLP~eiV 87 (159)
..|| +.|+.+.+.+
T Consensus 81 e~~l-~~l~~~~~~~ 94 (142)
T PRK03902 81 EQFL-RIIGVDESKI 94 (142)
T ss_pred HHHH-HHhCcCHHHH
Confidence 4566 5678776654
No 16
>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=91.00 E-value=0.091 Score=38.20 Aligned_cols=66 Identities=30% Similarity=0.563 Sum_probs=37.6
Q ss_pred HHHHHHHhhhcccEEEeeCCCCCCCCCccCCcHHHHHHHhcccccCccce------eeeeceeEEEecchhH-HHHHh
Q psy5978 8 RYIIYEYLFKEGVLVAKKDFHAPKHPELDVPNLQVIKTLQSLKSKGWVNE------QFAWRHYYWYITNDGI-EKLRG 78 (159)
Q Consensus 8 r~~IYe~LFkeGV~VakKD~~~~~Hpel~vpNL~Vik~mqSLkSrGyVke------~FaWrh~Yw~LTneGI-~yLR~ 78 (159)
-..|.+.|..+|+|- .+|.. ..++++.=+|-++|..|...|+|+. +-+|..|||+++.+.| +.|+.
T Consensus 15 ~~~Il~~L~~~~~l~-de~la----~~~~l~~~~vRkiL~~L~~~~lv~~~~~~d~~~~~~~~yw~i~~~~~~~~ik~ 87 (105)
T PF02002_consen 15 AVRILDALLRKGELT-DEDLA----KKLGLKPKEVRKILYKLYEDGLVSYRRRKDDERGWTRYYWYIDYDQIIDVIKY 87 (105)
T ss_dssp THHHHHHHHHH--B--HHHHH----HTT-S-HHHHHHHHHHHHHHSS-EEEEE--------EEEEE-THHHH------
T ss_pred HHHHHHHHHHcCCcC-HHHHH----HHhCCCHHHHHHHHHHHHHCCCeEEEEEEcCCCcEEEEEEEEcHHHHHHHHHH
Confidence 356788888888752 33322 1345888899999999999999954 4589999999999887 44443
No 17
>COG3432 Predicted transcriptional regulator [Transcription]
Probab=90.39 E-value=0.22 Score=37.49 Aligned_cols=40 Identities=23% Similarity=0.194 Sum_probs=34.3
Q ss_pred HHHHHHhcccccCccceeeeeceeEEEecchhHHHHHhhc
Q psy5978 41 QVIKTLQSLKSKGWVNEQFAWRHYYWYITNDGIEKLRGVL 80 (159)
Q Consensus 41 ~Vik~mqSLkSrGyVke~FaWrh~Yw~LTneGI~yLR~yL 80 (159)
-.-+.++-|.++|+++.+=.=+--.|.||++|..+|++|=
T Consensus 47 ~~~~yi~~L~~~Gli~~~~~~~~~~y~lT~KG~~fle~y~ 86 (95)
T COG3432 47 RAQKYIEMLVEKGLIIKQDNGRRKVYELTEKGKRFLEKYS 86 (95)
T ss_pred HHHHHHHHHHhCCCEEeccCCccceEEEChhHHHHHHHHH
Confidence 3457889999999888888887878899999999999874
No 18
>PRK05638 threonine synthase; Validated
Probab=89.34 E-value=0.32 Score=43.74 Aligned_cols=67 Identities=18% Similarity=0.320 Sum_probs=45.2
Q ss_pred hhHHHHHHHhhhcccEEEeeCCCCCCCCCcc--CCcHHHHHHHhcccccCccceee-eeceeEEEecchhHHHHHh
Q psy5978 6 KNRYIIYEYLFKEGVLVAKKDFHAPKHPELD--VPNLQVIKTLQSLKSKGWVNEQF-AWRHYYWYITNDGIEKLRG 78 (159)
Q Consensus 6 ~~r~~IYe~LFkeGV~VakKD~~~~~Hpel~--vpNL~Vik~mqSLkSrGyVke~F-aWrh~Yw~LTneGI~yLR~ 78 (159)
..|..|...|.++- +.+ .+.. ..|+ ++.-.|.++|+.|+..|+|...+ -=+.-||.||++|.++|.+
T Consensus 371 ~~r~~IL~~L~~~~-~~~-~el~----~~l~~~~s~~~v~~hL~~Le~~GLV~~~~~~g~~~~Y~Lt~~g~~~l~~ 440 (442)
T PRK05638 371 GTKLEILKILSERE-MYG-YEIW----KALGKPLKYQAVYQHIKELEELGLIEEAYRKGRRVYYKLTEKGRRLLEN 440 (442)
T ss_pred chHHHHHHHHhhCC-ccH-HHHH----HHHcccCCcchHHHHHHHHHHCCCEEEeecCCCcEEEEECcHHHHHHHh
Confidence 34777887776432 211 1111 1222 66778999999999999997541 0167799999999999875
No 19
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=89.02 E-value=0.22 Score=35.64 Aligned_cols=36 Identities=25% Similarity=0.343 Sum_probs=28.4
Q ss_pred HHHHHHhcccccCccceeeeeceeEEEecchhHHHHHhh
Q psy5978 41 QVIKTLQSLKSKGWVNEQFAWRHYYWYITNDGIEKLRGV 79 (159)
Q Consensus 41 ~Vik~mqSLkSrGyVke~FaWrh~Yw~LTneGI~yLR~y 79 (159)
.|-=+++.|+.-|+|.. -. |- .|.||++|.++|.++
T Consensus 56 ri~Wa~~~L~~aGli~~-~~-rG-~~~iT~~G~~~l~~~ 91 (92)
T PF14338_consen 56 RIRWARSYLKKAGLIER-PK-RG-IWRITEKGRKALAEH 91 (92)
T ss_pred hHHHHHHHHHHCCCccC-CC-CC-ceEECHhHHHHHhhC
Confidence 45557899999999955 33 33 999999999999863
No 20
>PHA00738 putative HTH transcription regulator
Probab=88.90 E-value=0.37 Score=37.17 Aligned_cols=66 Identities=23% Similarity=0.222 Sum_probs=51.5
Q ss_pred hhhHHHHHHHhhhcccEEEeeCCCCCCCCCccCCcHHHHHHHhcccccCccceeeeeceeEEEecchhHHH
Q psy5978 5 KKNRYIIYEYLFKEGVLVAKKDFHAPKHPELDVPNLQVIKTLQSLKSKGWVNEQFAWRHYYWYITNDGIEK 75 (159)
Q Consensus 5 k~~r~~IYe~LFkeGV~VakKD~~~~~Hpel~vpNL~Vik~mqSLkSrGyVke~FaWrh~Yw~LTneGI~y 75 (159)
..+|++|.+.|.+.+-++| -|.. ..+++.--.|.+.|+-|+.-|+|...--=|+.||.|+++--+|
T Consensus 11 dptRr~IL~lL~~~e~~~V-~eLa----e~l~lSQptVS~HLKvLreAGLV~srK~Gr~vyY~Ln~~~~~~ 76 (108)
T PHA00738 11 KILRRKILELIAENYILSA-SLIS----HTLLLSYTTVLRHLKILNEQGYIELYKEGRTLYAKIRENSKEI 76 (108)
T ss_pred CHHHHHHHHHHHHcCCccH-HHHH----HhhCCCHHHHHHHHHHHHHCCceEEEEECCEEEEEECCCccHH
Confidence 5689999999998653333 2332 1235777789999999999999999999999999999876554
No 21
>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=88.50 E-value=0.22 Score=35.98 Aligned_cols=44 Identities=25% Similarity=0.220 Sum_probs=30.2
Q ss_pred ccCCcHHHHHHHhcccccCccceeeeec------eeEEEecchhHHHHHh
Q psy5978 35 LDVPNLQVIKTLQSLKSKGWVNEQFAWR------HYYWYITNDGIEKLRG 78 (159)
Q Consensus 35 l~vpNL~Vik~mqSLkSrGyVke~FaWr------h~Yw~LTneGI~yLR~ 78 (159)
.++.+-....+|+.|...||++-..-++ .--=.+|-+||+||.|
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 3467789999999999999997433322 2333478899999998
No 22
>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=88.43 E-value=0.26 Score=36.09 Aligned_cols=33 Identities=21% Similarity=0.315 Sum_probs=28.5
Q ss_pred CcHHHHHHHhcccccCccceeeeeceeEEEecchhHHH
Q psy5978 38 PNLQVIKTLQSLKSKGWVNEQFAWRHYYWYITNDGIEK 75 (159)
Q Consensus 38 pNL~Vik~mqSLkSrGyVke~FaWrh~Yw~LTneGI~y 75 (159)
-+-.++.+++.|..||++...-+= |||+||++-
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 23
>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=88.36 E-value=0.27 Score=32.87 Aligned_cols=58 Identities=28% Similarity=0.412 Sum_probs=45.2
Q ss_pred hhHHHHHHHhhhcccEEEeeCCCCCCCCCccCCcHHHHHHHhcccccCccceeeeeceeEEEe
Q psy5978 6 KNRYIIYEYLFKEGVLVAKKDFHAPKHPELDVPNLQVIKTLQSLKSKGWVNEQFAWRHYYWYI 68 (159)
Q Consensus 6 ~~r~~IYe~LFkeGV~VakKD~~~~~Hpel~vpNL~Vik~mqSLkSrGyVke~FaWrh~Yw~L 68 (159)
++-.+||.+|.++|-+-+. |.. ..+++|-=.|-+++++|.++|+|...-.-...|...
T Consensus 8 ~~E~~vy~~Ll~~~~~t~~-eIa----~~l~i~~~~v~~~L~~L~~~GlV~~~~~~~~~Y~a~ 65 (68)
T PF01978_consen 8 ENEAKVYLALLKNGPATAE-EIA----EELGISRSTVYRALKSLEEKGLVEREEGRPKVYRAV 65 (68)
T ss_dssp HHHHHHHHHHHHHCHEEHH-HHH----HHHTSSHHHHHHHHHHHHHTTSEEEEEECCEEEEEE
T ss_pred HHHHHHHHHHHHcCCCCHH-HHH----HHHCcCHHHHHHHHHHHHHCCCEEEEcCceEEEEEe
Confidence 4556899999988887763 321 245699999999999999999999988776666653
No 24
>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=88.18 E-value=0.24 Score=39.91 Aligned_cols=65 Identities=22% Similarity=0.403 Sum_probs=47.6
Q ss_pred hHHHHHHHhhhcccEEEeeCCCCCCCCCccCCcHHHHHHHhcccccCccceee-----eeceeEEEecchhHHHH
Q psy5978 7 NRYIIYEYLFKEGVLVAKKDFHAPKHPELDVPNLQVIKTLQSLKSKGWVNEQF-----AWRHYYWYITNDGIEKL 76 (159)
Q Consensus 7 ~r~~IYe~LFkeGV~VakKD~~~~~Hpel~vpNL~Vik~mqSLkSrGyVke~F-----aWrh~Yw~LTneGI~yL 76 (159)
+|.+|...|.+.|-+-+ .+.- ..+.|..-.|.+.|+.|.+.|+|...- .=+.++|+||++|.+.+
T Consensus 2 tr~~IL~~L~~~~~~t~-~eLA----~~lgis~~tV~~~L~~Le~~GlV~r~~~~~~~gRp~~~y~LT~~G~~~~ 71 (203)
T TIGR02702 2 TKEDILSYLLKQGQATA-AALA----EALAISPQAVRRHLKDLETEGLIEYEAVVQGMGRPQYHYQLSRQGREQF 71 (203)
T ss_pred HHHHHHHHHHHcCCCCH-HHHH----HHHCcCHHHHHHHHHHHHHCCCeEEeecccCCCCCceEEEECcchhhhc
Confidence 57889999987665322 2221 134578889999999999999997652 23678899999998654
No 25
>PF13814 Replic_Relax: Replication-relaxation
Probab=87.80 E-value=0.76 Score=35.61 Aligned_cols=42 Identities=26% Similarity=0.483 Sum_probs=34.8
Q ss_pred HHHHHHhcccccCccceeeee--------ceeEEEecchhHHHHHhhcCCC
Q psy5978 41 QVIKTLQSLKSKGWVNEQFAW--------RHYYWYITNDGIEKLRGVLNIP 83 (159)
Q Consensus 41 ~Vik~mqSLkSrGyVke~FaW--------rh~Yw~LTneGI~yLR~yLhLP 83 (159)
.+-..|+.|...|||+. |.. ..+.|+||.+|.++|.+-...+
T Consensus 28 ~~~rrL~~L~~~glv~~-~~~~~~~~~g~~~~vy~Lt~~G~~~l~~~~~~~ 77 (191)
T PF13814_consen 28 TARRRLKRLRELGLVDR-FRRRVGARGGSQPYVYYLTPAGARLLADLRGIR 77 (191)
T ss_pred HHHHHHHHHhhCCcEEe-ecccccccCCCcceEEEECHHHHHHHHhccCCc
Confidence 78899999999999955 444 4578999999999999876654
No 26
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=86.93 E-value=1.1 Score=27.57 Aligned_cols=43 Identities=19% Similarity=0.311 Sum_probs=34.8
Q ss_pred cCCcHHHHHHHhcccccCccceeeeeceeEEEecc-hhHHHHHh
Q psy5978 36 DVPNLQVIKTLQSLKSKGWVNEQFAWRHYYWYITN-DGIEKLRG 78 (159)
Q Consensus 36 ~vpNL~Vik~mqSLkSrGyVke~FaWrh~Yw~LTn-eGI~yLR~ 78 (159)
.++.-.|.++++.|.++|++...-.=+..||.||+ .|-+.+.+
T Consensus 21 ~is~~~v~~~l~~L~~~g~i~~~~~~~~~~~~~~~~~~~~~~~~ 64 (66)
T smart00418 21 GLSQSTVSHHLKKLREAGLVESRREGKRVYYSLTDEKVADLLEE 64 (66)
T ss_pred CCCHHHHHHHHHHHHHCCCeeeeecCCEEEEEEchHHHHHHHHh
Confidence 46667899999999999999977656788999999 66666553
No 27
>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=86.87 E-value=0.79 Score=33.43 Aligned_cols=43 Identities=19% Similarity=0.213 Sum_probs=36.9
Q ss_pred CCcHHHHHHHhcccccCccceee---eeceeEEEecchhHHHHHhh
Q psy5978 37 VPNLQVIKTLQSLKSKGWVNEQF---AWRHYYWYITNDGIEKLRGV 79 (159)
Q Consensus 37 vpNL~Vik~mqSLkSrGyVke~F---aWrh~Yw~LTneGI~yLR~y 79 (159)
+..=.|..+++.|..+|||..+- --|-.+++||++|.+.+.+-
T Consensus 54 ~~~~tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~LT~~G~~~~~~~ 99 (118)
T TIGR02337 54 ILRPSLTGILARLERDGLVTRLKASNDQRRVYISLTPKGQALYASL 99 (118)
T ss_pred CCchhHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHhHHHHHHHh
Confidence 56667899999999999999765 46889999999999998753
No 28
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=86.05 E-value=0.84 Score=38.45 Aligned_cols=47 Identities=17% Similarity=0.281 Sum_probs=40.2
Q ss_pred ccCCcHHHHHHHhcccccCccceeeeeceeEEEecchhHHHHHhhcC
Q psy5978 35 LDVPNLQVIKTLQSLKSKGWVNEQFAWRHYYWYITNDGIEKLRGVLN 81 (159)
Q Consensus 35 l~vpNL~Vik~mqSLkSrGyVke~FaWrh~Yw~LTneGI~yLR~yLh 81 (159)
+.+..-.|-+.++.|...|||.-+-.=+-.+|+||++|.+.|.+.+.
T Consensus 31 L~iS~~Tvsr~Lk~LEe~GlI~R~~~~r~~~v~LTekG~~ll~~~~~ 77 (217)
T PRK14165 31 TGTSSKTAARILKQLEDEGYITRTIVPRGQLITITEKGLDVLYNEYA 77 (217)
T ss_pred HCcCHHHHHHHHHHHHHCCCEEEEEcCCceEEEECHHHHHHHHHHHH
Confidence 35899999999999999999987766688999999999998765443
No 29
>PRK09416 lstR lineage-specific thermal regulator protein; Provisional
Probab=85.15 E-value=0.63 Score=37.02 Aligned_cols=46 Identities=17% Similarity=0.333 Sum_probs=37.5
Q ss_pred CCcHHHHHHHhcccccCccceeeee---ceeEEEecchhHHHHHhhcCCCC
Q psy5978 37 VPNLQVIKTLQSLKSKGWVNEQFAW---RHYYWYITNDGIEKLRGVLNIPD 84 (159)
Q Consensus 37 vpNL~Vik~mqSLkSrGyVke~FaW---rh~Yw~LTneGI~yLR~yLhLP~ 84 (159)
+..=.|.-+++.|...|+|... | +-=||.||++|.++|.+.+.-|.
T Consensus 75 ~s~GtIYp~L~RLE~~GlI~s~--~~~~~RK~Y~ITe~Gre~L~e~~~~~~ 123 (135)
T PRK09416 75 GNEGSLYTLLHRLEQNRFIQSS--WDHEGAKYYQLTDKGNKMLRKAEKNAT 123 (135)
T ss_pred CCCccHHHHHHHHHHCCCeEEe--ecCCCceEEEECHHHHHHHHHHHhCHH
Confidence 4555788899999999999764 5 34689999999999999887654
No 30
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=84.51 E-value=0.37 Score=33.05 Aligned_cols=65 Identities=28% Similarity=0.324 Sum_probs=45.9
Q ss_pred CccchhhHHHHHHHhhhccc--EEEeeCCCCCCCCCccCCcHHHHHHHhcccccCccceeeeeceeEEEecch
Q psy5978 1 MLMPKKNRYIIYEYLFKEGV--LVAKKDFHAPKHPELDVPNLQVIKTLQSLKSKGWVNEQFAWRHYYWYITND 71 (159)
Q Consensus 1 Mlipk~~r~~IYe~LFkeGV--~VakKD~~~~~Hpel~vpNL~Vik~mqSLkSrGyVke~FaWrh~Yw~LTne 71 (159)
|+.+..+...|+++|-+.|- +-+ +|. -..+.|+.-.|-++|.+|++.|+|.-.=. .--+|.|+.+
T Consensus 1 ~~~~~~~~~~IL~~L~~~g~~~~ta-~eL----a~~lgl~~~~v~r~L~~L~~~G~V~~~~~-~~~~W~i~~~ 67 (68)
T smart00550 1 SLTQDSLEEKILEFLENSGDETSTA-LQL----AKNLGLPKKEVNRVLYSLEKKGKVCKQGG-TPPLWKLTDK 67 (68)
T ss_pred CCCchHHHHHHHHHHHHCCCCCcCH-HHH----HHHHCCCHHHHHHHHHHHHHCCCEEecCC-CCCceEeecC
Confidence 46788889999999987754 322 222 12456888899999999999999965433 3247777653
No 31
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=82.14 E-value=0.66 Score=37.72 Aligned_cols=70 Identities=16% Similarity=0.286 Sum_probs=50.0
Q ss_pred hHHHHHHHhhhcccEEEeeCCCCCCCCCccCCcHHHHHHHhcccccCccc-----e-eeeeceeEEEecchhH-HHHHhh
Q psy5978 7 NRYIIYEYLFKEGVLVAKKDFHAPKHPELDVPNLQVIKTLQSLKSKGWVN-----E-QFAWRHYYWYITNDGI-EKLRGV 79 (159)
Q Consensus 7 ~r~~IYe~LFkeGV~VakKD~~~~~Hpel~vpNL~Vik~mqSLkSrGyVk-----e-~FaWrh~Yw~LTneGI-~yLR~y 79 (159)
....|...|...|++-+ .|.. ..|+|..=.|-++|..|...|+|. + .-+|=.|||.||.+-| +.|+..
T Consensus 23 ~~~~Vl~~L~~~g~~td-eeLA----~~Lgi~~~~VRk~L~~L~e~gLv~~~r~r~~~~Gr~~y~w~l~~~~i~d~ik~~ 97 (178)
T PRK06266 23 EGFEVLKALIKKGEVTD-EEIA----EQTGIKLNTVRKILYKLYDARLADYKREKDEETNWYTYTWKPELEKLPEIIKKK 97 (178)
T ss_pred cHhHHHHHHHHcCCcCH-HHHH----HHHCCCHHHHHHHHHHHHHCCCeEEeeeeccCCCcEEEEEEeCHHHHHHHHHHH
Confidence 45567777777675432 2211 134688889999999999999997 1 3589999999998776 666665
Q ss_pred cC
Q psy5978 80 LN 81 (159)
Q Consensus 80 Lh 81 (159)
+|
T Consensus 98 ~~ 99 (178)
T PRK06266 98 KM 99 (178)
T ss_pred HH
Confidence 54
No 32
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=80.56 E-value=1.5 Score=32.64 Aligned_cols=65 Identities=28% Similarity=0.319 Sum_probs=44.0
Q ss_pred HHHHHHhhhcccEEEeeCCCCCCCCCccCCcHHHHHHHhcccccCccceeeee-----------------ceeEEEecch
Q psy5978 9 YIIYEYLFKEGVLVAKKDFHAPKHPELDVPNLQVIKTLQSLKSKGWVNEQFAW-----------------RHYYWYITND 71 (159)
Q Consensus 9 ~~IYe~LFkeGV~VakKD~~~~~Hpel~vpNL~Vik~mqSLkSrGyVke~FaW-----------------rh~Yw~LTne 71 (159)
..|..+|.+-|+=-++-=. . .+.+|=-.|..++..|...|+|.+.-+= -|-||-||.+
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---R--RLKIPLEEVREALEKLEEMGLLERVEGKTIKRSEAKFKPKKEVHKHHTYYRLTRE 84 (92)
T ss_pred HHHHHHHHHHCCCcHHHHH---H--HHCCCHHHHHHHHHHHHHCCCeEEecCcccchhhhhcccchhhhcCCceeeecHh
Confidence 4566666655542221100 0 2346777888888888888888765432 4889999999
Q ss_pred hHHHHHh
Q psy5978 72 GIEKLRG 78 (159)
Q Consensus 72 GI~yLR~ 78 (159)
|-.+||+
T Consensus 85 G~~llR~ 91 (92)
T PF10007_consen 85 GELLLRE 91 (92)
T ss_pred HHHHHhc
Confidence 9999996
No 33
>COG1695 Predicted transcriptional regulators [Transcription]
Probab=79.52 E-value=2.1 Score=32.08 Aligned_cols=47 Identities=17% Similarity=0.259 Sum_probs=36.6
Q ss_pred CCcHHHHHHHhcccccCccceeeeec-----eeEEEecchhHHHHHhhcCCC
Q psy5978 37 VPNLQVIKTLQSLKSKGWVNEQFAWR-----HYYWYITNDGIEKLRGVLNIP 83 (159)
Q Consensus 37 vpNL~Vik~mqSLkSrGyVke~FaWr-----h~Yw~LTneGI~yLR~yLhLP 83 (159)
+.-=.+.-+|+.|.+.|||.....=+ ==||.||++|.++|.+.+...
T Consensus 42 ~s~gtiYp~L~~Le~~Gli~~~~~~~~~g~~rk~Y~lTe~G~~~l~~~~~~~ 93 (138)
T COG1695 42 PSPGTIYPLLKRLEKEGLIESRWEESGGGPPRKYYRLTEKGKEELAELREEW 93 (138)
T ss_pred CCCCcHHHHHHHHHHCCCeEEEecccCCCCCceEEEECHHHHHHHHHHHHHH
Confidence 34446778899999999998764444 368999999999999887443
No 34
>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=79.20 E-value=3 Score=29.73 Aligned_cols=44 Identities=20% Similarity=0.288 Sum_probs=38.0
Q ss_pred CCcHHHHHHHhcccccCccceeee-eceeEEEecchhHHHHHhhc
Q psy5978 37 VPNLQVIKTLQSLKSKGWVNEQFA-WRHYYWYITNDGIEKLRGVL 80 (159)
Q Consensus 37 vpNL~Vik~mqSLkSrGyVke~Fa-Wrh~Yw~LTneGI~yLR~yL 80 (159)
++.-.+..+++.|...||+.+.+. |.+-|-.||++|-++|+.-.
T Consensus 54 ~~~~~~~~li~~Li~~g~L~~~~~~~~~~~l~~~~~~~~~l~g~~ 98 (106)
T PF09382_consen 54 MSKDDWERLIRQLILEGYLSEDNGGFAYPYLKLTPKGKELLNGKQ 98 (106)
T ss_dssp S-HHHHHHHHHHHHHTTSEEEEECCCCTEEEEE-GGGHHHHCTTS
T ss_pred CCHHHHHHHHHHHHHcCCceecCCcccccEEEECHHHHHHHCCCc
Confidence 888999999999999999988875 89999999999999998643
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=78.67 E-value=2.3 Score=33.63 Aligned_cols=49 Identities=20% Similarity=0.240 Sum_probs=36.2
Q ss_pred CCcHHHHHHHhcccccCccceee----e-eceeEEEecchhHHHHHhhcCCCCC
Q psy5978 37 VPNLQVIKTLQSLKSKGWVNEQF----A-WRHYYWYITNDGIEKLRGVLNIPDE 85 (159)
Q Consensus 37 vpNL~Vik~mqSLkSrGyVke~F----a-Wrh~Yw~LTneGI~yLR~yLhLP~e 85 (159)
|..=.|.-+|+.|...|+|.... + =+--||.||++|.++|.+.+.--.+
T Consensus 55 v~~GtLYp~L~RLE~~GlI~~~~~~~~~gp~RK~Y~LTe~Gr~~L~~~~~~w~~ 108 (138)
T TIGR02719 55 VDQGNVYRTLRKLEKDNLISSQWDTSAEGPAKRIYSLTDAGEQYLSMCANSFEH 108 (138)
T ss_pred CCcChHHHHHHHHHHCCCEEEEeeecCCCCCcEEEEECHHHHHHHHHHHHHHHH
Confidence 45556788999999999998521 1 1148899999999999887654433
No 36
>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=75.31 E-value=3.4 Score=29.94 Aligned_cols=45 Identities=20% Similarity=0.472 Sum_probs=35.0
Q ss_pred cCCcHHHHHHHhcccccCccceeee-----eceeEEEecchhHHHHHhhc
Q psy5978 36 DVPNLQVIKTLQSLKSKGWVNEQFA-----WRHYYWYITNDGIEKLRGVL 80 (159)
Q Consensus 36 ~vpNL~Vik~mqSLkSrGyVke~Fa-----Wrh~Yw~LTneGI~yLR~yL 80 (159)
++..=.|..++..|..+|+|..... =+=-||.||++|.++|.+.+
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 4566678889999999999987421 12379999999999998754
No 37
>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=74.82 E-value=3.6 Score=29.97 Aligned_cols=43 Identities=16% Similarity=0.292 Sum_probs=38.0
Q ss_pred cCCcHHHHHHHhcccccCccceeeee---ceeEEEecchhHHHHHh
Q psy5978 36 DVPNLQVIKTLQSLKSKGWVNEQFAW---RHYYWYITNDGIEKLRG 78 (159)
Q Consensus 36 ~vpNL~Vik~mqSLkSrGyVke~FaW---rh~Yw~LTneGI~yLR~ 78 (159)
.+..=.|-+++..|..+|||+..=+. |-.|-+||++|.+-+-+
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 48888999999999999999987777 78999999999987754
No 38
>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=74.50 E-value=10 Score=27.42 Aligned_cols=60 Identities=23% Similarity=0.330 Sum_probs=39.0
Q ss_pred hHHHHHHHhhhcccEEE-eeCCCCCCCCCccCCcHHHHHHHhcccccCcccee-eeece--------eEEEecchhHHHH
Q psy5978 7 NRYIIYEYLFKEGVLVA-KKDFHAPKHPELDVPNLQVIKTLQSLKSKGWVNEQ-FAWRH--------YYWYITNDGIEKL 76 (159)
Q Consensus 7 ~r~~IYe~LFkeGV~Va-kKD~~~~~Hpel~vpNL~Vik~mqSLkSrGyVke~-FaWrh--------~Yw~LTneGI~yL 76 (159)
.+...++.|-++|+|.- .++.+.|. |...++||.... ..+.| ..=+.|.+|++||
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 36678999999999986 33444444 333455555443 22221 4567899999999
Q ss_pred HhhcC
Q psy5978 77 RGVLN 81 (159)
Q Consensus 77 R~yLh 81 (159)
.+.|.
T Consensus 102 ~~~l~ 106 (111)
T PF03374_consen 102 AKRLA 106 (111)
T ss_pred HHHHH
Confidence 98764
No 39
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=74.08 E-value=3.6 Score=28.42 Aligned_cols=46 Identities=24% Similarity=0.295 Sum_probs=39.6
Q ss_pred cCCcHHHHHHHhcccccCccceeee---eceeEEEecchhHHHHHhhcC
Q psy5978 36 DVPNLQVIKTLQSLKSKGWVNEQFA---WRHYYWYITNDGIEKLRGVLN 81 (159)
Q Consensus 36 ~vpNL~Vik~mqSLkSrGyVke~Fa---Wrh~Yw~LTneGI~yLR~yLh 81 (159)
.|..=.|..++++|..+|||+..-+ =|-.+..||++|-+.+.+..-
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 4777789999999999999998777 688999999999999886443
No 40
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=73.91 E-value=3.4 Score=28.65 Aligned_cols=43 Identities=26% Similarity=0.258 Sum_probs=34.0
Q ss_pred ccCCcHHHHHHHhcccccCccceeeeeceeEEEecchhHHHHHhhc
Q psy5978 35 LDVPNLQVIKTLQSLKSKGWVNEQFAWRHYYWYITNDGIEKLRGVL 80 (159)
Q Consensus 35 l~vpNL~Vik~mqSLkSrGyVke~FaWrh~Yw~LTneGI~yLR~yL 80 (159)
+.|+--.|.++++.|.++|||...=+ -.++||++|.+.+....
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 34777788999999999999987653 37899999998776543
No 41
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=73.46 E-value=1.7 Score=34.63 Aligned_cols=75 Identities=27% Similarity=0.221 Sum_probs=56.5
Q ss_pred hhHHHHHHHhhhcccEEEeeCCCCCCCCCccCCcHHHHHHHhcccccCccceeeeeceeEEEecchhH------------
Q psy5978 6 KNRYIIYEYLFKEGVLVAKKDFHAPKHPELDVPNLQVIKTLQSLKSKGWVNEQFAWRHYYWYITNDGI------------ 73 (159)
Q Consensus 6 ~~r~~IYe~LFkeGV~VakKD~~~~~Hpel~vpNL~Vik~mqSLkSrGyVke~FaWrh~Yw~LTneGI------------ 73 (159)
....+||+.+-+.|.+-. +|... .|+|.-=.|.+.++-|.+.|||+-. .+....||++|-
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 DYLETIYELLEEKGFART-KDIAE----RLKVSPPSVTEMLKRLERLGLVEYE---PYGGVTLTEKGREKAKELLRKHRL 81 (154)
T ss_pred HHHHHHHHHHhccCcccH-HHHHH----HhCCCcHHHHHHHHHHHHCCCeEEe---cCCCeEEChhhHHHHHHHHHHHHH
Confidence 345788887775565443 55431 4678888999999999999999753 345779999997
Q ss_pred --HHHHhhcCCCCCCCc
Q psy5978 74 --EKLRGVLNIPDEIVP 88 (159)
Q Consensus 74 --~yLR~yLhLP~eiVP 88 (159)
.||.+.|+++.+.+=
T Consensus 82 le~fL~~~lg~~~~~~~ 98 (154)
T COG1321 82 LERFLVDVLGLDWEEAH 98 (154)
T ss_pred HHHHHHHHhCCCHHHHH
Confidence 578888999977664
No 42
>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=71.79 E-value=2.5 Score=31.37 Aligned_cols=60 Identities=27% Similarity=0.308 Sum_probs=37.5
Q ss_pred hhHHHHHHHhhhcccEEEeeCCCCCCCCC---c----cCCcHHHHHHH----------hcccccCcc-ceeeeeceeEEE
Q psy5978 6 KNRYIIYEYLFKEGVLVAKKDFHAPKHPE---L----DVPNLQVIKTL----------QSLKSKGWV-NEQFAWRHYYWY 67 (159)
Q Consensus 6 ~~r~~IYe~LFkeGV~VakKD~~~~~Hpe---l----~vpNL~Vik~m----------qSLkSrGyV-ke~FaWrh~Yw~ 67 (159)
+.|.+|+.+|++- .|..-. | .+.-=+|.=+| .||.+.|+| .|.-.=..-||.
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 5688999999843 122222 2 12333444444 589999999 333323445999
Q ss_pred ecchhHHH
Q psy5978 68 ITNDGIEK 75 (159)
Q Consensus 68 LTneGI~y 75 (159)
||++|.++
T Consensus 79 lT~~G~~~ 86 (90)
T PF07381_consen 79 LTEKGKRI 86 (90)
T ss_pred eChhhhhH
Confidence 99999875
No 43
>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=71.06 E-value=5.6 Score=28.12 Aligned_cols=41 Identities=20% Similarity=0.245 Sum_probs=30.9
Q ss_pred CCcHHHHHHHhcccccCccceeee---eceeEEEecchhHHHHH
Q psy5978 37 VPNLQVIKTLQSLKSKGWVNEQFA---WRHYYWYITNDGIEKLR 77 (159)
Q Consensus 37 vpNL~Vik~mqSLkSrGyVke~Fa---Wrh~Yw~LTneGI~yLR 77 (159)
|++--+.+.|+.|...|+|..... =.+..|.||+.|.+.+.
T Consensus 31 is~~~L~~~L~~L~~~GLv~r~~~~~~p~~v~Y~LT~~G~~l~~ 74 (90)
T PF01638_consen 31 ISPKVLSQRLKELEEAGLVERRVYPEVPPRVEYSLTEKGKELLP 74 (90)
T ss_dssp S-HHHHHHHHHHHHHTTSEEEEEESSSSSEEEEEE-HHHHHHHH
T ss_pred hHHHHHHHHHHHHHHcchhhcccccCCCCCCccCCCcCHHHHHH
Confidence 677778899999999999976532 13578999999998764
No 44
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=70.68 E-value=4.2 Score=35.73 Aligned_cols=42 Identities=21% Similarity=0.253 Sum_probs=34.9
Q ss_pred cCCcHHHHHHHhcccccCccceeeeeceeEEEecchhHHHHHhhc
Q psy5978 36 DVPNLQVIKTLQSLKSKGWVNEQFAWRHYYWYITNDGIEKLRGVL 80 (159)
Q Consensus 36 ~vpNL~Vik~mqSLkSrGyVke~FaWrh~Yw~LTneGI~yLR~yL 80 (159)
.|.=.-|.-.|++|.+-|||++ - .--||-+|.||.++|-+.|
T Consensus 36 giT~QaVsehiK~Lv~eG~i~~--~-gR~~Y~iTkkG~e~l~~~~ 77 (260)
T COG1497 36 GITLQAVSEHIKELVKEGLIEK--E-GRGEYEITKKGAEWLLEQL 77 (260)
T ss_pred CCCHHHHHHHHHHHHhccceee--c-CCeeEEEehhHHHHHHHHH
Confidence 4888899999999999999999 2 2357799999999986543
No 45
>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=70.31 E-value=4.4 Score=34.86 Aligned_cols=43 Identities=16% Similarity=0.414 Sum_probs=33.9
Q ss_pred cCCcHHHHHHHhcccccCccceeeeeceeEEEecchhHHHHHh
Q psy5978 36 DVPNLQVIKTLQSLKSKGWVNEQFAWRHYYWYITNDGIEKLRG 78 (159)
Q Consensus 36 ~vpNL~Vik~mqSLkSrGyVke~FaWrh~Yw~LTneGI~yLR~ 78 (159)
.|..=.|..++.-|+++|++...=.=|--||.||++|.+.|.+
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 4677778899999999999977421123677999999999986
No 46
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=69.15 E-value=5.7 Score=29.96 Aligned_cols=43 Identities=23% Similarity=0.241 Sum_probs=37.3
Q ss_pred cCCcHHHHHHHhcccccCccceee---eeceeEEEecchhHHHHHh
Q psy5978 36 DVPNLQVIKTLQSLKSKGWVNEQF---AWRHYYWYITNDGIEKLRG 78 (159)
Q Consensus 36 ~vpNL~Vik~mqSLkSrGyVke~F---aWrh~Yw~LTneGI~yLR~ 78 (159)
.+..=.|.++++.|..+|||...- .=|-.+.+||++|.+.+.+
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 488888999999999999999764 4788999999999987765
No 47
>PHA02943 hypothetical protein; Provisional
Probab=67.12 E-value=2.8 Score=34.56 Aligned_cols=60 Identities=18% Similarity=0.256 Sum_probs=44.8
Q ss_pred hhHHHHHHHhhhcccEEEeeCCCCCCCCCccCCcHHHHHHHhcccccCccceeeeeceeEEEecch
Q psy5978 6 KNRYIIYEYLFKEGVLVAKKDFHAPKHPELDVPNLQVIKTLQSLKSKGWVNEQFAWRHYYWYITND 71 (159)
Q Consensus 6 ~~r~~IYe~LFkeGV~VakKD~~~~~Hpel~vpNL~Vik~mqSLkSrGyVke~FaWrh~Yw~LTne 71 (159)
.....|+|+| ++|+.-... . .+ .+.++-=+|-=+++-|.+-|+|++.=--+--||+|.+.
T Consensus 11 ~R~~eILE~L-k~G~~Ttse-I--Ak--aLGlS~~qa~~~LyvLErEG~VkrV~~G~~tyw~l~~d 70 (165)
T PHA02943 11 TRMIKTLRLL-ADGCKTTSR-I--AN--KLGVSHSMARNALYQLAKEGMVLKVEIGRAAIWCLDED 70 (165)
T ss_pred HHHHHHHHHH-hcCCccHHH-H--HH--HHCCCHHHHHHHHHHHHHcCceEEEeecceEEEEEChH
Confidence 4567899999 999863211 0 11 23477788888999999999999976667889999983
No 48
>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=66.94 E-value=4.8 Score=31.97 Aligned_cols=68 Identities=22% Similarity=0.362 Sum_probs=46.0
Q ss_pred HHHHHHhhhcccEEEeeCCCCCCCCCccCCcHHHHHHHhcccccCcc---c---eeeeeceeEEEecchhH-HHHHhhcC
Q psy5978 9 YIIYEYLFKEGVLVAKKDFHAPKHPELDVPNLQVIKTLQSLKSKGWV---N---EQFAWRHYYWYITNDGI-EKLRGVLN 81 (159)
Q Consensus 9 ~~IYe~LFkeGV~VakKD~~~~~Hpel~vpNL~Vik~mqSLkSrGyV---k---e~FaWrh~Yw~LTneGI-~yLR~yLh 81 (159)
+.|...|+..|+|- ..|.. ..|.+..=.|-|++..|...|+| + +.=+|.-|||+++-+-| +-|+..+|
T Consensus 17 v~Vl~aL~~~~~~t-dEeLa----~~Lgi~~~~VRk~L~~L~e~~Lv~~~r~r~~~~gw~~Y~w~i~~~~i~d~Ik~~~~ 91 (158)
T TIGR00373 17 GLVLFSLGIKGEFT-DEEIS----LELGIKLNEVRKALYALYDAGLADYKRRKDDETGWYEYTWRINYEKALDVLKRKLE 91 (158)
T ss_pred HHHHHHHhccCCCC-HHHHH----HHHCCCHHHHHHHHHHHHHCCCceeeeeeecCCCcEEEEEEeCHHHHHHHHHHHHH
Confidence 34555566555431 12211 13458888999999999999999 3 34489999999876655 67776655
No 49
>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=65.84 E-value=6.3 Score=27.67 Aligned_cols=38 Identities=26% Similarity=0.515 Sum_probs=31.0
Q ss_pred ccCCcHHHHHHHhcccccCccceeeeeceeEEEecchh
Q psy5978 35 LDVPNLQVIKTLQSLKSKGWVNEQFAWRHYYWYITNDG 72 (159)
Q Consensus 35 l~vpNL~Vik~mqSLkSrGyVke~FaWrh~Yw~LTneG 72 (159)
+.|..=-|--+|--|+++|++...=.=|.-||.||++|
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 34677778888999999999999999999999999987
No 50
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=65.76 E-value=7.4 Score=29.09 Aligned_cols=44 Identities=20% Similarity=0.268 Sum_probs=37.6
Q ss_pred CCcHHHHHHHhcccccCccceeee---eceeEEEecchhHHHHHhhc
Q psy5978 37 VPNLQVIKTLQSLKSKGWVNEQFA---WRHYYWYITNDGIEKLRGVL 80 (159)
Q Consensus 37 vpNL~Vik~mqSLkSrGyVke~Fa---Wrh~Yw~LTneGI~yLR~yL 80 (159)
+..=.|.+++..|..+|||...-+ =|..+-+||++|.+.+.+..
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 777789999999999999997744 47889999999999887643
No 51
>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=65.70 E-value=4.4 Score=32.61 Aligned_cols=61 Identities=21% Similarity=0.279 Sum_probs=43.3
Q ss_pred hhHHHHHHHhhhcccEEEeeCCCCCCCCCccCCcHHHHHHHhcccccCccceeeeeceeEEEecchh
Q psy5978 6 KNRYIIYEYLFKEGVLVAKKDFHAPKHPELDVPNLQVIKTLQSLKSKGWVNEQFAWRHYYWYITNDG 72 (159)
Q Consensus 6 ~~r~~IYe~LFkeGV~VakKD~~~~~Hpel~vpNL~Vik~mqSLkSrGyVke~FaWrh~Yw~LTneG 72 (159)
.....|..+|-+.|-+-. +|.. ..+.++-=.|-+.++.|...|+|...-. |.-+|.||++|
T Consensus 143 ~~~~~IL~~l~~~g~~s~-~eia----~~l~is~stv~r~L~~Le~~GlI~r~~~-r~~~~~lT~~G 203 (203)
T TIGR01884 143 REELKVLEVLKAEGEKSV-KNIA----KKLGKSLSTISRHLRELEKKGLVEQKGR-KGKRYSLTKLG 203 (203)
T ss_pred HHHHHHHHHHHHcCCcCH-HHHH----HHHCcCHHHHHHHHHHHHHCCCEEEEcC-CccEEEeCCCC
Confidence 445678888876543211 2211 1234666678899999999999998876 88899999987
No 52
>KOG2784|consensus
Probab=65.17 E-value=7.1 Score=36.59 Aligned_cols=40 Identities=25% Similarity=0.285 Sum_probs=31.1
Q ss_pred CcHHHHHHHhcccccCccceeeeeceeEEEecchhHHHHHh
Q psy5978 38 PNLQVIKTLQSLKSKGWVNEQFAWRHYYWYITNDGIEKLRG 78 (159)
Q Consensus 38 pNL~Vik~mqSLkSrGyVke~FaWrh~Yw~LTneGI~yLR~ 78 (159)
-.-+|+-+++||.+.|++.- --=-+.-|-||+||.++.++
T Consensus 30 ~h~~~v~al~SL~a~~~i~~-~~~~~~~~~LT~EG~~i~~e 69 (483)
T KOG2784|consen 30 DHQQVVGALKSLQAGGVIEV-KDVETKTYELTAEGEEIARE 69 (483)
T ss_pred hhHHHHHHHHHHhhcCceEE-EeeeeEEEeeChhHHHHHhc
Confidence 34456779999999777653 33467789999999999986
No 53
>PF14531 Kinase-like: Kinase-like; PDB: 3DZO_A 2W1Z_A 3BYV_A 3Q5Z_A 3Q60_A.
Probab=64.34 E-value=1.8 Score=37.89 Aligned_cols=41 Identities=22% Similarity=0.339 Sum_probs=31.8
Q ss_pred HHHHHHHhcccccCccceeeeeceeEEEecchhHHHHHhhcCC
Q psy5978 40 LQVIKTLQSLKSKGWVNEQFAWRHYYWYITNDGIEKLRGVLNI 82 (159)
Q Consensus 40 L~Vik~mqSLkSrGyVke~FaWrh~Yw~LTneGI~yLR~yLhL 82 (159)
+|+|++..+|.+.|+|.-.+.|..|+ |..+|.-||.++-++
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 788999999987544
No 54
>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=64.10 E-value=3.2 Score=31.45 Aligned_cols=65 Identities=14% Similarity=0.158 Sum_probs=44.9
Q ss_pred CccchhhHHHHHHHhhhcccEEEeeCCCCCCCCCc----cCCcHHHHHHHhcccccCccceeeeeceeEEEecc
Q psy5978 1 MLMPKKNRYIIYEYLFKEGVLVAKKDFHAPKHPEL----DVPNLQVIKTLQSLKSKGWVNEQFAWRHYYWYITN 70 (159)
Q Consensus 1 Mlipk~~r~~IYe~LFkeGV~VakKD~~~~~Hpel----~vpNL~Vik~mqSLkSrGyVke~FaWrh~Yw~LTn 70 (159)
|.|.++...+|.-.++ |....+-....-.+| +||-=+|-|+|+.|+..|+|..+=+ ..--|.|+.
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 8899999999988877 443333222233344 4999999999999999999986433 333455554
No 55
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=62.64 E-value=3.1 Score=33.21 Aligned_cols=54 Identities=15% Similarity=0.236 Sum_probs=38.0
Q ss_pred CccchhhHHHHHHHhhhcccEEEeeCCCCCCCCCc----cCCcHHHHHHHhcccccCcccee
Q psy5978 1 MLMPKKNRYIIYEYLFKEGVLVAKKDFHAPKHPEL----DVPNLQVIKTLQSLKSKGWVNEQ 58 (159)
Q Consensus 1 Mlipk~~r~~IYe~LFkeGV~VakKD~~~~~Hpel----~vpNL~Vik~mqSLkSrGyVke~ 58 (159)
|.|.++.+.++.-.++ |....+-....-.+| ++|.-+|-|+|+.|+..|+|..+
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 8888998888887765 222222111222334 49999999999999999999974
No 56
>PRK10870 transcriptional repressor MprA; Provisional
Probab=61.20 E-value=8.7 Score=30.53 Aligned_cols=44 Identities=23% Similarity=0.399 Sum_probs=37.4
Q ss_pred cCCcHHHHHHHhcccccCccceeee---eceeEEEecchhHHHHHhh
Q psy5978 36 DVPNLQVIKTLQSLKSKGWVNEQFA---WRHYYWYITNDGIEKLRGV 79 (159)
Q Consensus 36 ~vpNL~Vik~mqSLkSrGyVke~Fa---Wrh~Yw~LTneGI~yLR~y 79 (159)
.++.-.|..+++.|..+|||...-+ =|-.+-+||++|++.+.+.
T Consensus 82 ~l~~~tvsr~v~rLe~kGlV~R~~~~~DrR~~~v~LT~~G~~~~~~i 128 (176)
T PRK10870 82 GSSRTNATRIADELEKRGWIERRESDNDRRCLHLQLTEKGHEFLREV 128 (176)
T ss_pred CCCHHHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHHH
Confidence 3888899999999999999986543 4668999999999998864
No 57
>COG0640 ArsR Predicted transcriptional regulators [Transcription]
Probab=58.44 E-value=9.2 Score=24.80 Aligned_cols=68 Identities=18% Similarity=0.210 Sum_probs=47.8
Q ss_pred hhhHHHHHHHhhhc-ccEEEeeCCCCCCCCCccCCcHHHHHHHhcccccCccceeeeeceeEEEecchhHHHHHh
Q psy5978 5 KKNRYIIYEYLFKE-GVLVAKKDFHAPKHPELDVPNLQVIKTLQSLKSKGWVNEQFAWRHYYWYITNDGIEKLRG 78 (159)
Q Consensus 5 k~~r~~IYe~LFke-GV~VakKD~~~~~Hpel~vpNL~Vik~mqSLkSrGyVke~FaWrh~Yw~LTneGI~yLR~ 78 (159)
..+|.+|...|.+. .+.+..-.. .+++.--.|...+..|...|+|....-=++.||.|+++.|..+.+
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 45788899998875 333211111 114566778889999999999999888888999999887655443
No 58
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=57.95 E-value=8.2 Score=32.80 Aligned_cols=63 Identities=24% Similarity=0.236 Sum_probs=48.4
Q ss_pred hhHHHHHHHhhhcccEEEeeCCCCCCCCCccCCcHHHHHHHhcccccCccceeeeeceeEEEecchhH
Q psy5978 6 KNRYIIYEYLFKEGVLVAKKDFHAPKHPELDVPNLQVIKTLQSLKSKGWVNEQFAWRHYYWYITNDGI 73 (159)
Q Consensus 6 ~~r~~IYe~LFkeGV~VakKD~~~~~Hpel~vpNL~Vik~mqSLkSrGyVke~FaWrh~Yw~LTneGI 73 (159)
++=.+||-.|..-|.+-|+.=.. ..+||-=.|...|+||.+||||..+-+=--.|-..-.+=+
T Consensus 16 ~yEa~vY~aLl~~g~~tA~eis~-----~sgvP~~kvY~vl~sLe~kG~v~~~~g~P~~y~av~p~~~ 78 (247)
T COG1378 16 EYEAKVYLALLCLGEATAKEISE-----ASGVPRPKVYDVLRSLEKKGLVEVIEGRPKKYRAVPPEEL 78 (247)
T ss_pred HHHHHHHHHHHHhCCccHHHHHH-----HcCCCchhHHHHHHHHHHCCCEEeeCCCCceEEeCCHHHH
Confidence 44568999999999999843222 2349999999999999999999999776666666655443
No 59
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=56.65 E-value=6.8 Score=29.77 Aligned_cols=63 Identities=13% Similarity=0.158 Sum_probs=42.8
Q ss_pred CccchhhHHHHHHHhhhcccEEEeeCCCCCCCCCc----cCCcHHHHHHHhcccccCccceeeeeceeEEE
Q psy5978 1 MLMPKKNRYIIYEYLFKEGVLVAKKDFHAPKHPEL----DVPNLQVIKTLQSLKSKGWVNEQFAWRHYYWY 67 (159)
Q Consensus 1 Mlipk~~r~~IYe~LFkeGV~VakKD~~~~~Hpel----~vpNL~Vik~mqSLkSrGyVke~FaWrh~Yw~ 67 (159)
|-++++...+|...++- -...+-....-.+| +||--.|-|+|+.|+..|+|+..-+=.--|..
T Consensus 1 M~ls~~~~YAl~~~i~l----a~~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s~~G~~GG~~l 67 (141)
T PRK11014 1 MQLTSFTDYGLRALIYM----ASLPEGRMTSISEVTEVYGVSRNHMVKIINQLSRAGYVTAVRGKNGGIRL 67 (141)
T ss_pred CcCchHHhHHHHHHHHH----hcCCCCCccCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEEecCCCCCeee
Confidence 78899999998888762 11111112222333 59999999999999999999887653333443
No 60
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=56.52 E-value=7.6 Score=33.06 Aligned_cols=66 Identities=26% Similarity=0.350 Sum_probs=50.8
Q ss_pred chhhHHHHHHHhhhcccEEEeeCCCCCCCCCccCCcHHHHHHHhcccccCccceeeeec-----eeEEEecchhHH
Q psy5978 4 PKKNRYIIYEYLFKEGVLVAKKDFHAPKHPELDVPNLQVIKTLQSLKSKGWVNEQFAWR-----HYYWYITNDGIE 74 (159)
Q Consensus 4 pk~~r~~IYe~LFkeGV~VakKD~~~~~Hpel~vpNL~Vik~mqSLkSrGyVke~FaWr-----h~Yw~LTneGI~ 74 (159)
+-.+|..|.++|-+.|=+-| .|.- .+|.|++-.|-..|+.|..+|+|.-.+.=. .+-|.||..|++
T Consensus 9 ~~~tr~~il~lL~~~g~~sa-~elA----~~Lgis~~avR~HL~~Le~~Glv~~~~~~~g~GRP~~~y~Lt~~g~~ 79 (218)
T COG2345 9 SGSTRERILELLKKSGPVSA-DELA----EELGISPMAVRRHLDDLEAEGLVEVERQQGGRGRPAKLYRLTEKGRE 79 (218)
T ss_pred CccHHHHHHHHHhccCCccH-HHHH----HHhCCCHHHHHHHHHHHHhCcceeeeeccCCCCCCceeeeecccchh
Confidence 44578888888887776665 2221 256799999999999999999998884322 468999999996
No 61
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=56.14 E-value=11 Score=30.80 Aligned_cols=44 Identities=18% Similarity=0.221 Sum_probs=36.3
Q ss_pred CCcHHHHHHHhcccccCccceee---eeceeEEEecchhHHHHHhhc
Q psy5978 37 VPNLQVIKTLQSLKSKGWVNEQF---AWRHYYWYITNDGIEKLRGVL 80 (159)
Q Consensus 37 vpNL~Vik~mqSLkSrGyVke~F---aWrh~Yw~LTneGI~yLR~yL 80 (159)
+..=.|..+++.|..+|||.-.- -=|..+-+||++|.+.+.+..
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 45556889999999999999654 458999999999999987643
No 62
>COG5124 Protein predicted to be involved in meiotic recombination [Cell division and chromosome partitioning / General function prediction only]
Probab=55.11 E-value=9.4 Score=32.45 Aligned_cols=74 Identities=26% Similarity=0.388 Sum_probs=51.1
Q ss_pred cchhhHHHHHHHhhhcccEEEeeCCCCCCCCC-c---c-CCcHHHHHHHhcccccCccc-eeeeeceeEEEecchhHHHH
Q psy5978 3 MPKKNRYIIYEYLFKEGVLVAKKDFHAPKHPE-L---D-VPNLQVIKTLQSLKSKGWVN-EQFAWRHYYWYITNDGIEKL 76 (159)
Q Consensus 3 ipk~~r~~IYe~LFkeGV~VakKD~~~~~Hpe-l---~-vpNL~Vik~mqSLkSrGyVk-e~FaWrh~Yw~LTneGI~yL 76 (159)
|+-+..+.+.+.+|.+ .|||.--+.-| | + |-=..|--++|||..-|.|+ |..+=..+||+.-++|++-+
T Consensus 6 ls~~eKrr~L~aI~~~-----SKdFFqLkEvEkLGSKK~IVl~tVKd~lQqlVDDgvV~~EK~GtsN~YWsF~s~~~qk~ 80 (209)
T COG5124 6 LSLAEKRRRLEAIFHD-----SKDFFQLKEVEKLGSKKQIVLMTVKDLLQQLVDDGVVSVEKCGTSNIYWSFKSQTLQKL 80 (209)
T ss_pred ccHHHHHHHHHHHHhc-----cHHHHHHHHHHHhccccccHHHHHHHHHHHHhhcCceeeeeeccceeEEecchHHHHHH
Confidence 3446677888888865 46764322111 1 1 22234667899999999996 78899999999999999866
Q ss_pred HhhcC
Q psy5978 77 RGVLN 81 (159)
Q Consensus 77 R~yLh 81 (159)
-+-+.
T Consensus 81 ~~~~~ 85 (209)
T COG5124 81 YDSSE 85 (209)
T ss_pred HHHHH
Confidence 54443
No 63
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=48.46 E-value=15 Score=24.98 Aligned_cols=44 Identities=16% Similarity=0.226 Sum_probs=35.7
Q ss_pred ccCCcHHHHHHHhcccccCccceeeeeceeEEEecchhHHHHHhhc
Q psy5978 35 LDVPNLQVIKTLQSLKSKGWVNEQFAWRHYYWYITNDGIEKLRGVL 80 (159)
Q Consensus 35 l~vpNL~Vik~mqSLkSrGyVke~FaWrh~Yw~LTneGI~yLR~yL 80 (159)
++++-=.|-+.|+.|.+.||+... +..-.|.|+++.+++-..++
T Consensus 30 l~i~~~tv~r~l~~L~~~g~l~~~--~~~~~y~l~~~~~~~~~~~~ 73 (91)
T smart00346 30 LGLSKSTAHRLLNTLQELGYVEQD--GQNGRYRLGPKVLELGQSYL 73 (91)
T ss_pred hCCCHHHHHHHHHHHHHCCCeeec--CCCCceeecHHHHHHHHHHH
Confidence 458888999999999999999874 33456889999888877665
No 64
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=47.91 E-value=19 Score=28.00 Aligned_cols=48 Identities=27% Similarity=0.527 Sum_probs=33.9
Q ss_pred ccCCcHHHHHHHhcccccCcc-----c----eeeeeceeEEEec-chhHHHHHhhcCC
Q psy5978 35 LDVPNLQVIKTLQSLKSKGWV-----N----EQFAWRHYYWYIT-NDGIEKLRGVLNI 82 (159)
Q Consensus 35 l~vpNL~Vik~mqSLkSrGyV-----k----e~FaWrh~Yw~LT-neGI~yLR~yLhL 82 (159)
+.++.=+|-|+|..|..-+++ + ++=+|-.|||+|+ +.-|..|+..++.
T Consensus 25 l~i~~n~vRkiL~~L~ed~~~~~~~~~e~~~~~~~~~~~yw~i~y~~~~~vik~r~~~ 82 (147)
T smart00531 25 LGIKQKQLRKILYLLYDEKLIKIDYKREKDPETKTWYRYYWYINYDTLLDVVKYKLDK 82 (147)
T ss_pred hCCCHHHHHHHHHHHHhhhcchhheeeeeCCCCceEEEEEEEecHHHHHHHHHHHHHH
Confidence 457777888888888884442 2 1223999999999 5566777766654
No 65
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=47.58 E-value=7.5 Score=30.47 Aligned_cols=63 Identities=24% Similarity=0.287 Sum_probs=43.8
Q ss_pred CccchhhHHHHHHHhhhcccEEEeeCCCCCCCCCc----cCCcHHHHHHHhcccccCccceeeeeceeEEEec
Q psy5978 1 MLMPKKNRYIIYEYLFKEGVLVAKKDFHAPKHPEL----DVPNLQVIKTLQSLKSKGWVNEQFAWRHYYWYIT 69 (159)
Q Consensus 1 Mlipk~~r~~IYe~LFkeGV~VakKD~~~~~Hpel----~vpNL~Vik~mqSLkSrGyVke~FaWrh~Yw~LT 69 (159)
|.|.++...+|.-.++ |....+-.+ .=.+| +||--++.|+|+.|+..|+|+.+=+= +-=|.|+
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 8899999999988776 332222211 11244 49999999999999999999987763 3334443
No 66
>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=45.35 E-value=18 Score=27.55 Aligned_cols=21 Identities=38% Similarity=0.594 Sum_probs=17.8
Q ss_pred EecchhHHHHHhhcCCCCCCC
Q psy5978 67 YITNDGIEKLRGVLNIPDEIV 87 (159)
Q Consensus 67 ~LTneGI~yLR~yLhLP~eiV 87 (159)
.||++||+.+.++|++++++.
T Consensus 34 ~LT~~G~~~~e~~~~~~~~l~ 54 (113)
T PF01043_consen 34 ELTEKGIEKAEKLLGISDNLY 54 (113)
T ss_dssp EESHHHHHHHHHHHTSSSSTT
T ss_pred eEhHHHHHHHHHHhhhccccc
Confidence 799999999999999854443
No 67
>KOG4412|consensus
Probab=43.60 E-value=16 Score=31.41 Aligned_cols=48 Identities=33% Similarity=0.417 Sum_probs=41.7
Q ss_pred hhhHHHHHHHhhhcccEEEeeCCC--CCCCCCccCCcHHHHHHHhccccc
Q psy5978 5 KKNRYIIYEYLFKEGVLVAKKDFH--APKHPELDVPNLQVIKTLQSLKSK 52 (159)
Q Consensus 5 k~~r~~IYe~LFkeGV~VakKD~~--~~~Hpel~vpNL~Vik~mqSLkSr 52 (159)
-|+|..|-..|...|..+-.||-. .|.|---.|-||+||+.+-|+.+-
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 478899999999999999999964 478887789999999999998864
No 68
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=41.46 E-value=26 Score=32.25 Aligned_cols=38 Identities=26% Similarity=0.339 Sum_probs=31.6
Q ss_pred HHHhcccccCccceeeeeceeEEEecchhHHHHHhhcCC
Q psy5978 44 KTLQSLKSKGWVNEQFAWRHYYWYITNDGIEKLRGVLNI 82 (159)
Q Consensus 44 k~mqSLkSrGyVke~FaWrh~Yw~LTneGI~yLR~yLhL 82 (159)
+.++.|+.|++|++ -.+..++..||++|.+++.+.+.+
T Consensus 156 ~~l~~LkkRkL~~~-~~~~~~~~~~~~~~~~~~~~~~~~ 193 (489)
T PRK04172 156 KVLKELKKRKLVEE-KERTERSVELTDAGLELLKEGIEL 193 (489)
T ss_pred HHHHHHHhcCCeEE-EEEEEEEEEEccchhhhhhccccc
Confidence 46889999998877 678999999999999998765443
No 69
>COG1542 Uncharacterized conserved protein [Function unknown]
Probab=39.02 E-value=20 Score=34.60 Aligned_cols=45 Identities=22% Similarity=0.307 Sum_probs=36.1
Q ss_pred CCcHHHHHHHhcccccCccceeee-eceeEEEecchhHHHHHhhcCCC
Q psy5978 37 VPNLQVIKTLQSLKSKGWVNEQFA-WRHYYWYITNDGIEKLRGVLNIP 83 (159)
Q Consensus 37 vpNL~Vik~mqSLkSrGyVke~Fa-Wrh~Yw~LTneGI~yLR~yLhLP 83 (159)
+-.| |.-++.+|.|.|+++...+ -.-.||.||..|-.-|.+ |.-|
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 7788 9999999999999986554 334699999999998875 4443
No 70
>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=38.98 E-value=5 Score=24.92 Aligned_cols=46 Identities=22% Similarity=0.385 Sum_probs=31.3
Q ss_pred hhHHHHHHHhhhcccEEEeeCCCCCCCCCccCCcHHHHHHHhcccccCccc
Q psy5978 6 KNRYIIYEYLFKEGVLVAKKDFHAPKHPELDVPNLQVIKTLQSLKSKGWVN 56 (159)
Q Consensus 6 ~~r~~IYe~LFkeGV~VakKD~~~~~Hpel~vpNL~Vik~mqSLkSrGyVk 56 (159)
.+..+|+.+|.+++-+-. ++.. ..++++-=.|-+.++.|...|+|+
T Consensus 3 ~~~~~Il~~l~~~~~~t~-~ela----~~~~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 3 ETQRKILNYLRENPRITQ-KELA----EKLGISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHHHHCTTS-H-HHHH----HHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHHcCCCCH-HHHH----HHhCCCHHHHHHHHHHHHHCcCcC
Confidence 467789999997665332 2221 123477778999999999999985
No 71
>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=38.44 E-value=14 Score=28.72 Aligned_cols=58 Identities=17% Similarity=0.367 Sum_probs=34.4
Q ss_pred HHHhhhcccEEEeeCCCCCCCCCccCCcHHHHHHHh-----cccccCccceeeeeceeEEEecchh
Q psy5978 12 YEYLFKEGVLVAKKDFHAPKHPELDVPNLQVIKTLQ-----SLKSKGWVNEQFAWRHYYWYITNDG 72 (159)
Q Consensus 12 Ye~LFkeGV~VakKD~~~~~Hpel~vpNL~Vik~mq-----SLkSrGyVke~FaWrh~Yw~LTneG 72 (159)
|-+||...|||||.....+-+|+....+-++|...+ |.-+.|..+ -|+|++|....+|
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 456899999999977554335655544444443321 112223222 4998888877665
No 72
>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=37.01 E-value=14 Score=27.07 Aligned_cols=65 Identities=18% Similarity=0.183 Sum_probs=42.4
Q ss_pred CccchhhHHHHHHHhhhcccEEEeeCCC-CCCCCCc----cCCcHHHHHHHhcccccCccceeeeeceeEEEecch
Q psy5978 1 MLMPKKNRYIIYEYLFKEGVLVAKKDFH-APKHPEL----DVPNLQVIKTLQSLKSKGWVNEQFAWRHYYWYITND 71 (159)
Q Consensus 1 Mlipk~~r~~IYe~LFkeGV~VakKD~~-~~~Hpel----~vpNL~Vik~mqSLkSrGyVke~FaWrh~Yw~LTne 71 (159)
|.++++...+|.-.++ +. +.+-. ...-.+| .+|--.|-++|+.|++.|||...=+..- -|.|+..
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 7888888888887766 22 22211 2222333 5999999999999999999986433332 2445543
No 73
>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=37.00 E-value=6.9 Score=27.18 Aligned_cols=54 Identities=24% Similarity=0.363 Sum_probs=33.0
Q ss_pred CccchhhHHHHHHHhhhcccEEEeeCCCCCCCCCc----cCCcHHHHHHHhcccccCcccee
Q psy5978 1 MLMPKKNRYIIYEYLFKEGVLVAKKDFHAPKHPEL----DVPNLQVIKTLQSLKSKGWVNEQ 58 (159)
Q Consensus 1 Mlipk~~r~~IYe~LFkeGV~VakKD~~~~~Hpel----~vpNL~Vik~mqSLkSrGyVke~ 58 (159)
|-+.++...+|.-.++ |....|-....-.+| ++|--+|-++|+.|+..|+|+..
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 6777888888777766 322222211111233 58999999999999999999754
No 74
>KOG3433|consensus
Probab=36.03 E-value=19 Score=30.70 Aligned_cols=74 Identities=28% Similarity=0.450 Sum_probs=53.8
Q ss_pred cchhhHHHHHHHhhhcccEEEeeCCCCCC----CCCc-cCCcHHHHHHHhcccccCcc-ceeeeeceeEEEecchhHHHH
Q psy5978 3 MPKKNRYIIYEYLFKEGVLVAKKDFHAPK----HPEL-DVPNLQVIKTLQSLKSKGWV-NEQFAWRHYYWYITNDGIEKL 76 (159)
Q Consensus 3 ipk~~r~~IYe~LFkeGV~VakKD~~~~~----Hpel-~vpNL~Vik~mqSLkSrGyV-ke~FaWrh~Yw~LTneGI~yL 76 (159)
|+....+.|...||.| .|||..-+ -... .|---.|-.++|||..-|.| +|..+=..|||..-.+||.-+
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 3446677888888876 35654221 1111 25556788999999999998 578888899999999999888
Q ss_pred HhhcC
Q psy5978 77 RGVLN 81 (159)
Q Consensus 77 R~yLh 81 (159)
+.+|.
T Consensus 80 ks~~q 84 (203)
T KOG3433|consen 80 KSVLQ 84 (203)
T ss_pred HHHHH
Confidence 77664
No 75
>PF13309 HTH_22: HTH domain
Probab=33.75 E-value=31 Score=23.46 Aligned_cols=25 Identities=20% Similarity=0.420 Sum_probs=21.6
Q ss_pred ccchhhHHHHHHHhhhcccEEEeeC
Q psy5978 2 LMPKKNRYIIYEYLFKEGVLVAKKD 26 (159)
Q Consensus 2 lipk~~r~~IYe~LFkeGV~VakKD 26 (159)
.|++++++.|-+.|.+.|+.-.|.-
T Consensus 20 ~l~~~~k~~iV~~L~~~G~F~lKga 44 (64)
T PF13309_consen 20 RLSKEEKKEIVRQLYEKGIFLLKGA 44 (64)
T ss_pred hCCHHHHHHHHHHHHHCCCcccCcH
Confidence 4789999999999999999887553
No 76
>KOG0921|consensus
Probab=32.60 E-value=58 Score=34.08 Aligned_cols=12 Identities=58% Similarity=1.387 Sum_probs=8.2
Q ss_pred ecCCCCcCCCCC
Q psy5978 145 FKGYGGFGRGKA 156 (159)
Q Consensus 145 fr~~ggfGrG~~ 156 (159)
+|++||||||.+
T Consensus 1250 yrgsGGfgrggg 1261 (1282)
T KOG0921|consen 1250 YRGSGGFGRGGG 1261 (1282)
T ss_pred ccCCCCcCCCCC
Confidence 566677877664
No 77
>KOG3233|consensus
Probab=32.23 E-value=14 Score=32.99 Aligned_cols=25 Identities=32% Similarity=0.396 Sum_probs=21.5
Q ss_pred cCCcHHHHHHHhcccccCccceeee
Q psy5978 36 DVPNLQVIKTLQSLKSKGWVNEQFA 60 (159)
Q Consensus 36 ~vpNL~Vik~mqSLkSrGyVke~Fa 60 (159)
++|-..|.|+++||.|+.+||+.=+
T Consensus 111 nLp~~~v~K~LkSLEsKkLIKsVKs 135 (297)
T KOG3233|consen 111 NLPQTVVNKILKSLESKKLIKSVKS 135 (297)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 3788889999999999999998643
No 78
>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=32.17 E-value=21 Score=28.38 Aligned_cols=38 Identities=29% Similarity=0.433 Sum_probs=27.8
Q ss_pred cHHHHHHHhcccccCccceeeeeceeEEEecchhHHHHHhhcC
Q psy5978 39 NLQVIKTLQSLKSKGWVNEQFAWRHYYWYITNDGIEKLRGVLN 81 (159)
Q Consensus 39 NL~Vik~mqSLkSrGyVke~FaWrh~Yw~LTneGI~yLR~yLh 81 (159)
+-.+-++-+-|+..|. ++.|-= =.+|+|||+-|++||+
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 5566677778888776 444421 2579999999999996
No 79
>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=31.88 E-value=43 Score=26.36 Aligned_cols=30 Identities=23% Similarity=0.264 Sum_probs=24.1
Q ss_pred eeeeeceeEEEecchhHHHHHhhcCCCCCC
Q psy5978 57 EQFAWRHYYWYITNDGIEKLRGVLNIPDEI 86 (159)
Q Consensus 57 e~FaWrh~Yw~LTneGI~yLR~yLhLP~ei 86 (159)
+.=+=+.|++...+|=-+.||+|++||.+.
T Consensus 52 ~~dap~~f~~a~ede~tdsLRDf~nL~d~~ 81 (116)
T cd03071 52 EEEAPLLFFVAGEDDMTDSLRDYTNLPEAA 81 (116)
T ss_pred CCCcceeeeeeccchHHHHHHHhcCCCccC
Confidence 334457888889999999999999999553
No 80
>PRK06474 hypothetical protein; Provisional
Probab=31.87 E-value=23 Score=28.45 Aligned_cols=67 Identities=19% Similarity=0.300 Sum_probs=46.8
Q ss_pred cchhhHHHHHHHhhhccc-EEEeeCCCCCCCCCc-cCCcHHHHHHHhcccccCccceeee-----eceeEEEecchhHH
Q psy5978 3 MPKKNRYIIYEYLFKEGV-LVAKKDFHAPKHPEL-DVPNLQVIKTLQSLKSKGWVNEQFA-----WRHYYWYITNDGIE 74 (159)
Q Consensus 3 ipk~~r~~IYe~LFkeGV-~VakKD~~~~~Hpel-~vpNL~Vik~mqSLkSrGyVke~Fa-----Wrh~Yw~LTneGI~ 74 (159)
+....|.+|.+.|.+.+- +-+ ++.. ..+ +|+--.|...|+.|..-|+|+..-- =+.-||.|++++|.
T Consensus 8 La~p~R~~Il~~L~~~~~~~ta-~el~----~~l~~is~aTvYrhL~~L~e~GLI~~~~~~~~~~~~ek~y~~~~~~~~ 81 (178)
T PRK06474 8 LMHPVRMKICQVLMRNKEGLTP-LELV----KILKDVPQATLYRHLQTMVDSGILHVVKEKKVRSVSEKYYAINEEDAK 81 (178)
T ss_pred hCCHHHHHHHHHHHhCCCCCCH-HHHH----HHhcCCCHHHHHHHHHHHHHCCCEEEeecccccCceeEEEEeccceee
Confidence 456789999999987553 333 2221 122 3666678899999999999997432 23578999998865
No 81
>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=30.96 E-value=34 Score=22.32 Aligned_cols=27 Identities=22% Similarity=0.250 Sum_probs=20.2
Q ss_pred HHHHhcccccCccceeeeeceeEEEecchhH
Q psy5978 43 IKTLQSLKSKGWVNEQFAWRHYYWYITNDGI 73 (159)
Q Consensus 43 ik~mqSLkSrGyVke~FaWrh~Yw~LTneGI 73 (159)
.+.++.|...|+|.. ..-.+.||++|.
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 677899999999854 456889999985
No 82
>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=29.61 E-value=48 Score=26.30 Aligned_cols=53 Identities=25% Similarity=0.337 Sum_probs=32.8
Q ss_pred hcccEEEeeCCCCCCCCCccCCcHHHHHHHhcccccCccc------eeeeeceeEEEecchhHHHHHhhcCC
Q psy5978 17 KEGVLVAKKDFHAPKHPELDVPNLQVIKTLQSLKSKGWVN------EQFAWRHYYWYITNDGIEKLRGVLNI 82 (159)
Q Consensus 17 keGV~VakKD~~~~~Hpel~vpNL~Vik~mqSLkSrGyVk------e~FaWrh~Yw~LTneGI~yLR~yLhL 82 (159)
.|++|||.||.. -.|-+++..|++.+.-. +...|-+|.....+++ |.=..|.+
T Consensus 12 ~DaiLV~~k~~~-----------q~vK~~v~~lk~~~~~E~~~~~~~~rpWG~~~~l~~~~~--~~vkri~V 70 (151)
T PF01050_consen 12 PDAILVADKDRS-----------QDVKEVVEQLKQKGRYEAKEHRRVYRPWGSYEVLDEGEG--YKVKRITV 70 (151)
T ss_pred CCEEEEECcHHh-----------hhhHHHHHhhhcccccccccceeEecCCcEEEEEEccCC--EEEEEEEE
Confidence 478888888753 23445566666665433 3468998888776665 44444443
No 83
>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=29.60 E-value=21 Score=27.56 Aligned_cols=48 Identities=27% Similarity=0.261 Sum_probs=38.8
Q ss_pred cCCcHHHHHHHhcccccCccceeeeeceeEEEecchhHHHHHhhcCCCCCCCcccc
Q psy5978 36 DVPNLQVIKTLQSLKSKGWVNEQFAWRHYYWYITNDGIEKLRGVLNIPDEIVPSTL 91 (159)
Q Consensus 36 ~vpNL~Vik~mqSLkSrGyVke~FaWrh~Yw~LTneGI~yLR~yLhLP~eiVPaTl 91 (159)
..+|..++.+++.|++.|+.-=..+=|.+.++..|=|. +..+.+|.|+
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 46999999999999999998888888999999877666 4555556554
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=28.18 E-value=39 Score=24.73 Aligned_cols=67 Identities=22% Similarity=0.234 Sum_probs=40.8
Q ss_pred HHHHHhhhcccEEEeeCCCCCCCCCccCCcHHHHHHHhcccccCccceeeeeceeEEEecchhHHHHH
Q psy5978 10 IIYEYLFKEGVLVAKKDFHAPKHPELDVPNLQVIKTLQSLKSKGWVNEQFAWRHYYWYITNDGIEKLR 77 (159)
Q Consensus 10 ~IYe~LFkeGV~VakKD~~~~~Hpel~vpNL~Vik~mqSLkSrGyVke~FaWrh~Yw~LTneGI~yLR 77 (159)
.|.+.|-+.|= +.-+|++--.....+...=-|...|..|..||+|+-.=.=+.|+|+-+-.=-+|++
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 67777777776 33455432111112356678999999999999999876556665554433334444
No 85
>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=27.46 E-value=20 Score=25.66 Aligned_cols=52 Identities=29% Similarity=0.363 Sum_probs=33.7
Q ss_pred hhHHHHHHHhhhcc-cEEEeeCCCC---CCCCCccCCcHHHHHHHhcccccCccceeee
Q psy5978 6 KNRYIIYEYLFKEG-VLVAKKDFHA---PKHPELDVPNLQVIKTLQSLKSKGWVNEQFA 60 (159)
Q Consensus 6 ~~r~~IYe~LFkeG-V~VakKD~~~---~~Hpel~vpNL~Vik~mqSLkSrGyVke~Fa 60 (159)
+.|.+|++.|.+.. -+-| .|... ..+| +|.--.|..+|+.|...|+|++.-.
T Consensus 1 ~qR~~Il~~l~~~~~~~sa-~ei~~~l~~~~~--~i~~~TVYR~L~~L~~~Gli~~~~~ 56 (116)
T cd07153 1 PQRLAILEVLLESDGHLTA-EEIYERLRKKGP--SISLATVYRTLELLEEAGLVREIEL 56 (116)
T ss_pred CHHHHHHHHHHhCCCCCCH-HHHHHHHHhcCC--CCCHHHHHHHHHHHHhCCCEEEEEe
Confidence 36889999998642 2222 22211 1111 2555678999999999999998653
No 86
>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=27.10 E-value=45 Score=21.16 Aligned_cols=32 Identities=16% Similarity=0.259 Sum_probs=24.7
Q ss_pred cCCcHHHHHHHhcccccCccceeeeeceeEEEecc
Q psy5978 36 DVPNLQVIKTLQSLKSKGWVNEQFAWRHYYWYITN 70 (159)
Q Consensus 36 ~vpNL~Vik~mqSLkSrGyVke~FaWrh~Yw~LTn 70 (159)
.++--.|.++|+.|...|+|...- .=.|.|||
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 388889999999999999998754 12456654
No 87
>KOG1423|consensus
Probab=25.88 E-value=61 Score=29.95 Aligned_cols=29 Identities=21% Similarity=0.452 Sum_probs=21.1
Q ss_pred Cccceeeeecee--EE---EecchhHHHHHhhcC
Q psy5978 53 GWVNEQFAWRHY--YW---YITNDGIEKLRGVLN 81 (159)
Q Consensus 53 GyVke~FaWrh~--Yw---~LTneGI~yLR~yLh 81 (159)
-.-+...+|.|| |+ .|+-|||+=|++||-
T Consensus 234 ~~~~~~~gwshfe~vF~vSaL~G~GikdlkqyLm 267 (379)
T KOG1423|consen 234 EKWRTICGWSHFERVFMVSALYGEGIKDLKQYLM 267 (379)
T ss_pred cccccccCcccceeEEEEecccccCHHHHHHHHH
Confidence 333455668777 44 489999999999983
No 88
>PRK11050 manganese transport regulator MntR; Provisional
Probab=25.55 E-value=68 Score=24.88 Aligned_cols=40 Identities=25% Similarity=0.264 Sum_probs=31.4
Q ss_pred ccCCcHHHHHHHhcccccCccceeeeeceeEEEecchhHHHHH
Q psy5978 35 LDVPNLQVIKTLQSLKSKGWVNEQFAWRHYYWYITNDGIEKLR 77 (159)
Q Consensus 35 l~vpNL~Vik~mqSLkSrGyVke~FaWrh~Yw~LTneGI~yLR 77 (159)
+.|..-.|-++++.|.+.|+|...-. --.+||++|...+.
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 35888899999999999999976432 24689999987644
No 89
>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=24.31 E-value=74 Score=20.84 Aligned_cols=25 Identities=32% Similarity=0.421 Sum_probs=20.0
Q ss_pred cchhhHHHHHHHhhhcccEEEeeCC
Q psy5978 3 MPKKNRYIIYEYLFKEGVLVAKKDF 27 (159)
Q Consensus 3 ipk~~r~~IYe~LFkeGV~VakKD~ 27 (159)
+|.+.-.++-+.|.++|+++...|+
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 4667778899999999999987664
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=24.01 E-value=58 Score=20.25 Aligned_cols=23 Identities=26% Similarity=0.450 Sum_probs=19.5
Q ss_pred cCCcHHHHHHHhcccccCcccee
Q psy5978 36 DVPNLQVIKTLQSLKSKGWVNEQ 58 (159)
Q Consensus 36 ~vpNL~Vik~mqSLkSrGyVke~ 58 (159)
+|+--.|-++++.|...|+|...
T Consensus 36 ~is~~~v~~~l~~L~~~G~i~~~ 58 (66)
T cd07377 36 GVSRTTVREALRELEAEGLVERR 58 (66)
T ss_pred CCCHHHHHHHHHHHHHCCCEEec
Confidence 47777899999999999999643
No 91
>PRK09249 coproporphyrinogen III oxidase; Provisional
Probab=23.91 E-value=64 Score=29.16 Aligned_cols=33 Identities=21% Similarity=0.243 Sum_probs=26.2
Q ss_pred HHHHHhcccccCccceeeeeceeEEEecchhHHHHHh
Q psy5978 42 VIKTLQSLKSKGWVNEQFAWRHYYWYITNDGIEKLRG 78 (159)
Q Consensus 42 Vik~mqSLkSrGyVke~FaWrh~Yw~LTneGI~yLR~ 78 (159)
++++++.|..+|++... .-.|.||++|.-++..
T Consensus 401 ~~~~l~~l~~~gll~~~----~~~~~lT~~G~~~~d~ 433 (453)
T PRK09249 401 ELERLAPLEADGLVELD----ENGITVTPKGRLLVRN 433 (453)
T ss_pred HHHHHHHHHHCCCEEEE----CCEEEECccchHHHHH
Confidence 45668899999998753 4579999999988754
No 92
>PF14756 Pdase_C33_assoc: Peptidase_C33-associated domain
Probab=23.80 E-value=38 Score=27.24 Aligned_cols=23 Identities=22% Similarity=0.674 Sum_probs=19.6
Q ss_pred hhHHHHHhhcCCCCCCCcccccc
Q psy5978 71 DGIEKLRGVLNIPDEIVPSTLKR 93 (159)
Q Consensus 71 eGI~yLR~yLhLP~eiVPaTlk~ 93 (159)
.-+..|-+..|||+.++|+.|..
T Consensus 14 acldrla~vmhlps~~ipaalae 36 (147)
T PF14756_consen 14 ACLDRLAEVMHLPSSVIPAALAE 36 (147)
T ss_pred HHHHHHHHHhcCccchhHHHHHH
Confidence 34678899999999999999875
No 93
>PF13730 HTH_36: Helix-turn-helix domain
Probab=23.57 E-value=35 Score=21.40 Aligned_cols=44 Identities=27% Similarity=0.437 Sum_probs=27.2
Q ss_pred HHHHHHHhhhcccEEEeeCCC-CCCCCCc----cCCcHHHHHHHhcccccCcc
Q psy5978 8 RYIIYEYLFKEGVLVAKKDFH-APKHPEL----DVPNLQVIKTLQSLKSKGWV 55 (159)
Q Consensus 8 r~~IYe~LFkeGV~VakKD~~-~~~Hpel----~vpNL~Vik~mqSLkSrGyV 55 (159)
-+.||-+|.. .+.++-. -|....| .+.-=.|.++++.|+.+||+
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 3467777762 2222222 1333334 37777899999999999985
No 94
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=23.37 E-value=38 Score=26.55 Aligned_cols=56 Identities=20% Similarity=0.255 Sum_probs=39.1
Q ss_pred CccchhhHHHHHHHhhhcccEEEeeCCCCCCCCCc----cCCcHHHHHHHhcccccCccceeee
Q psy5978 1 MLMPKKNRYIIYEYLFKEGVLVAKKDFHAPKHPEL----DVPNLQVIKTLQSLKSKGWVNEQFA 60 (159)
Q Consensus 1 Mlipk~~r~~IYe~LFkeGV~VakKD~~~~~Hpel----~vpNL~Vik~mqSLkSrGyVke~Fa 60 (159)
|-+.++.+.++.-.++ |....+-....-.+| +||-.++.|+|..|+..|+|+.+=+
T Consensus 1 Mklt~~~~yal~~L~~----LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~kaGlV~S~rG 60 (150)
T COG1959 1 MKLTSKGEYALRALLY----LALLPGGGPVSSAEIAERQGISPSYLEKILSKLRKAGLVKSVRG 60 (150)
T ss_pred CccchhHhHHHHHHHH----HHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHHcCCEEeecC
Confidence 7788888888877776 332222211112233 4999999999999999999998654
No 95
>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=22.37 E-value=93 Score=25.42 Aligned_cols=45 Identities=29% Similarity=0.521 Sum_probs=37.2
Q ss_pred cCCcHHHHHHHhcccccCccc-eeeeeceeEEEecchhHHHHHhhc
Q psy5978 36 DVPNLQVIKTLQSLKSKGWVN-EQFAWRHYYWYITNDGIEKLRGVL 80 (159)
Q Consensus 36 ~vpNL~Vik~mqSLkSrGyVk-e~FaWrh~Yw~LTneGI~yLR~yL 80 (159)
.|.-..|--++|||.+-|+|. |..+=..|||+..++-..=+.+.+
T Consensus 26 gI~~~~VKdvlq~LvDDglV~~EKiGssn~YWsFps~~~~~~~~~~ 71 (188)
T PF03962_consen 26 GIVSMSVKDVLQSLVDDGLVHVEKIGSSNYYWSFPSQAKQKRQNKL 71 (188)
T ss_pred CCchhhHHHHHHHHhccccchhhhccCeeEEEecChHHHHHHHHHH
Confidence 467789999999999999996 678888999999988876665443
No 96
>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=21.66 E-value=61 Score=25.44 Aligned_cols=31 Identities=29% Similarity=0.275 Sum_probs=25.8
Q ss_pred CCcHHHHHHHhcccccCccceeeeeceeEEEecchhHHHHHhhc
Q psy5978 37 VPNLQVIKTLQSLKSKGWVNEQFAWRHYYWYITNDGIEKLRGVL 80 (159)
Q Consensus 37 vpNL~Vik~mqSLkSrGyVke~FaWrh~Yw~LTneGI~yLR~yL 80 (159)
.-|-+||.++|.... +.-||++.|.||.++|
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 578899999998664 3358999999999987
No 97
>PF11181 YflT: Heat induced stress protein YflT
Probab=21.50 E-value=90 Score=22.63 Aligned_cols=35 Identities=17% Similarity=0.416 Sum_probs=28.4
Q ss_pred HHHHHHHhcccccCccceeeeeceeEEEec--chhHHHHHhhc
Q psy5978 40 LQVIKTLQSLKSKGWVNEQFAWRHYYWYIT--NDGIEKLRGVL 80 (159)
Q Consensus 40 L~Vik~mqSLkSrGyVke~FaWrh~Yw~LT--neGI~yLR~yL 80 (159)
-+++.++++|++.||-++... .|| ++-++.|.+.-
T Consensus 10 ~E~~~~I~~L~~~Gy~~ddI~------Vva~d~~~~~~l~~~t 46 (103)
T PF11181_consen 10 EEALSAIEELKAQGYSEDDIY------VVAKDKDRTERLADQT 46 (103)
T ss_pred HHHHHHHHHHHHcCCCcccEE------EEEcCchHHHHHHHhc
Confidence 368999999999999999883 777 45578888765
No 98
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=21.37 E-value=38 Score=27.66 Aligned_cols=26 Identities=31% Similarity=0.640 Sum_probs=20.9
Q ss_pred cceeeeeceeEEEecchhHHHHHhhcCCCCCC
Q psy5978 55 VNEQFAWRHYYWYITNDGIEKLRGVLNIPDEI 86 (159)
Q Consensus 55 Vke~FaWrh~Yw~LTneGI~yLR~yLhLP~ei 86 (159)
+.++|+ +|+++.|+|+-++|++|..=
T Consensus 34 aQ~~~G------~l~~~ai~~iA~~L~i~~~~ 59 (160)
T COG1905 34 AQEQFG------WLPPEAIEEIADMLGIPRAR 59 (160)
T ss_pred HHHHhC------CCCHHHHHHHHHHhCCCHHH
Confidence 345666 58999999999999999543
No 99
>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=21.26 E-value=1.6e+02 Score=20.29 Aligned_cols=45 Identities=13% Similarity=0.261 Sum_probs=37.2
Q ss_pred CCcHHHHHHHhcccccCccceeeeeceeEEEecc--hhHHHHHhhcC
Q psy5978 37 VPNLQVIKTLQSLKSKGWVNEQFAWRHYYWYITN--DGIEKLRGVLN 81 (159)
Q Consensus 37 vpNL~Vik~mqSLkSrGyVke~FaWrh~Yw~LTn--eGI~yLR~yLh 81 (159)
.-|+.++..++++-.-|.|...-.-..++|.+|+ +.++.|-.||.
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 4699999999999998999888888889999998 55666666654
No 100
>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=21.03 E-value=15 Score=24.68 Aligned_cols=47 Identities=34% Similarity=0.333 Sum_probs=33.4
Q ss_pred hhHHHHHHHhhhcccEEEeeCCCCCCCCCccCCcHHHHHHHhcccccCccce
Q psy5978 6 KNRYIIYEYLFKEGVLVAKKDFHAPKHPELDVPNLQVIKTLQSLKSKGWVNE 57 (159)
Q Consensus 6 ~~r~~IYe~LFkeGV~VakKD~~~~~Hpel~vpNL~Vik~mqSLkSrGyVke 57 (159)
....+||+..- ++-.|--+|.- ..|+|..-.|.+.++.|...|||.-
T Consensus 8 ~YL~~Iy~l~~-~~~~v~~~~iA----~~L~vs~~tvt~ml~~L~~~GlV~~ 54 (60)
T PF01325_consen 8 DYLKAIYELSE-EGGPVRTKDIA----ERLGVSPPTVTEMLKRLAEKGLVEY 54 (60)
T ss_dssp HHHHHHHHHHH-CTSSBBHHHHH----HHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHHc-CCCCccHHHHH----HHHCCChHHHHHHHHHHHHCCCEEe
Confidence 34578999886 44444445542 1356889999999999999999974
No 101
>PF14277 DUF4364: Domain of unknown function (DUF4364)
Probab=20.75 E-value=1e+02 Score=24.79 Aligned_cols=42 Identities=19% Similarity=0.204 Sum_probs=30.9
Q ss_pred CCcHHHHHHHhcccccCccceee-eeceeEEEecchhHHHHHh
Q psy5978 37 VPNLQVIKTLQSLKSKGWVNEQF-AWRHYYWYITNDGIEKLRG 78 (159)
Q Consensus 37 vpNL~Vik~mqSLkSrGyVke~F-aWrh~Yw~LTneGI~yLR~ 78 (159)
+--+.+-.++..|.+.|+|...- .=-.-+|.||++|.+=|.-
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 44567778888999999999542 3334688999999876543
No 102
>PF13516 LRR_6: Leucine Rich repeat; PDB: 3RGZ_A 3RJ0_A 3RIZ_A 3RGX_A 1DFJ_I 2BNH_A 3VQ1_A 3VQ2_A 2Z64_A 2OMX_A ....
Probab=20.70 E-value=58 Score=17.40 Aligned_cols=11 Identities=36% Similarity=0.567 Sum_probs=8.9
Q ss_pred EecchhHHHHH
Q psy5978 67 YITNDGIEKLR 77 (159)
Q Consensus 67 ~LTneGI~yLR 77 (159)
-||++|+++|-
T Consensus 13 ~i~~~g~~~l~ 23 (24)
T PF13516_consen 13 QITDEGASALA 23 (24)
T ss_dssp BEHHHHHHHHH
T ss_pred cCCHHHHHHhC
Confidence 48899999885
No 103
>PHA00422 hypothetical protein
Probab=20.43 E-value=69 Score=23.10 Aligned_cols=36 Identities=19% Similarity=0.286 Sum_probs=24.9
Q ss_pred HHHhcccccCccce--eeeeceeEEEecchhHHHHHhh
Q psy5978 44 KTLQSLKSKGWVNE--QFAWRHYYWYITNDGIEKLRGV 79 (159)
Q Consensus 44 k~mqSLkSrGyVke--~FaWrh~Yw~LTneGI~yLR~y 79 (159)
.+.-++.|||.+.- .-+=--.-|-+|-.|.+||+.+
T Consensus 28 alvaeaAsrGhiScL~~~Grn~g~W~vT~~G~~fL~~~ 65 (69)
T PHA00422 28 SLVAEAASRGHISCLSTDGRNAGAWEITASGVRFLKQM 65 (69)
T ss_pred HHHHHHHhcCChhhhhccCcccceEEEeccHHHHHHHh
Confidence 34556778887642 2233346799999999999976
No 104
>KOG2175|consensus
Probab=20.14 E-value=27 Score=33.01 Aligned_cols=25 Identities=28% Similarity=0.525 Sum_probs=21.7
Q ss_pred eeeceeEEEecchhH-HHHHhhcCCC
Q psy5978 59 FAWRHYYWYITNDGI-EKLRGVLNIP 83 (159)
Q Consensus 59 FaWrh~Yw~LTneGI-~yLR~yLhLP 83 (159)
.+|.-+||+|+++|| ..|-.+++.|
T Consensus 200 ~~~~~~fkTlv~~~i~~~le~~~~~~ 225 (458)
T KOG2175|consen 200 QSRDAFFKTLVNKGILDALEYVLKMP 225 (458)
T ss_pred chhhHHHHHHHHhhhHHHHHHHhcCC
Confidence 568889999999999 7777788888
No 105
>KOG2383|consensus
Probab=20.10 E-value=70 Score=30.38 Aligned_cols=22 Identities=36% Similarity=0.626 Sum_probs=15.3
Q ss_pred HHHHHHhhhcccEEEeeCCCCC
Q psy5978 9 YIIYEYLFKEGVLVAKKDFHAP 30 (159)
Q Consensus 9 ~~IYe~LFkeGV~VakKD~~~~ 30 (159)
+.++++||+.||+++---...|
T Consensus 214 ~rLf~~Lf~~GvVlvATSNR~P 235 (467)
T KOG2383|consen 214 KRLFEHLFKNGVVLVATSNRAP 235 (467)
T ss_pred HHHHHHHHhCCeEEEEeCCCCh
Confidence 5689999999976654444333
Done!