Query 010241
Match_columns 514
No_of_seqs 77 out of 79
Neff 3.9
Searched_HMMs 46136
Date Thu Mar 28 22:41:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/010241.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/010241hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00550 Zalpha Z-DNA-bindin 91.5 0.33 7.1E-06 39.5 4.5 50 80-131 4-54 (68)
2 PRK13239 alkylmercury lyase; P 91.5 0.31 6.8E-06 48.3 5.2 56 81-143 21-76 (206)
3 PF09339 HTH_IclR: IclR helix- 90.4 0.3 6.4E-06 37.4 3.1 39 86-124 7-45 (52)
4 PF06163 DUF977: Bacterial pro 90.1 0.6 1.3E-05 43.4 5.3 56 81-143 11-67 (127)
5 COG3355 Predicted transcriptio 89.6 2.4 5.3E-05 39.3 8.9 84 85-172 30-118 (126)
6 smart00346 HTH_ICLR helix_turn 88.5 2.8 6.2E-05 34.3 7.9 77 85-164 8-88 (91)
7 PF12324 HTH_15: Helix-turn-he 87.3 0.71 1.5E-05 39.6 3.6 49 84-138 26-74 (77)
8 PRK06266 transcription initiat 86.6 3.8 8.3E-05 39.5 8.6 85 81-168 21-108 (178)
9 PF04703 FaeA: FaeA-like prote 84.7 1.2 2.5E-05 36.5 3.5 54 84-139 2-57 (62)
10 TIGR00373 conserved hypothetic 84.3 6.4 0.00014 37.2 8.8 80 86-168 18-100 (158)
11 PF13412 HTH_24: Winged helix- 84.3 2 4.3E-05 32.0 4.4 41 83-124 4-44 (48)
12 PF12840 HTH_20: Helix-turn-he 83.4 2.3 4.9E-05 33.4 4.6 53 80-135 8-60 (61)
13 PF04583 Baculo_p74: Baculovir 82.9 5.2 0.00011 41.0 8.0 87 143-258 62-153 (249)
14 PF08220 HTH_DeoR: DeoR-like h 81.3 3 6.6E-05 32.8 4.6 40 84-124 2-41 (57)
15 cd00090 HTH_ARSR Arsenical Res 80.6 9 0.0002 28.9 6.9 60 79-142 4-64 (78)
16 TIGR02844 spore_III_D sporulat 80.3 1.9 4.2E-05 36.9 3.4 34 83-118 7-40 (80)
17 smart00418 HTH_ARSR helix_turn 80.1 4.2 9.2E-05 30.0 4.8 50 87-140 2-51 (66)
18 PF09743 DUF2042: Uncharacteri 79.6 3.3 7.2E-05 42.5 5.4 57 80-138 53-109 (272)
19 smart00420 HTH_DEOR helix_turn 79.6 5.6 0.00012 28.8 5.2 47 84-133 2-48 (53)
20 PF08784 RPA_C: Replication pr 78.2 3.8 8.3E-05 35.2 4.6 44 81-124 46-92 (102)
21 PF08279 HTH_11: HTH domain; 77.4 7 0.00015 29.6 5.4 44 85-129 3-46 (55)
22 KOG3341 RNA polymerase II tran 76.6 6.1 0.00013 40.1 6.0 83 68-151 159-244 (249)
23 PF08221 HTH_9: RNA polymerase 73.1 6.3 0.00014 31.8 4.3 38 85-123 16-53 (62)
24 PRK15466 carboxysome structura 69.2 8.5 0.00018 37.4 4.9 41 84-124 111-151 (166)
25 PF12802 MarR_2: MarR family; 68.9 10 0.00022 28.9 4.6 41 84-124 7-48 (62)
26 PF01978 TrmB: Sugar-specific 68.5 12 0.00025 29.8 4.9 51 86-139 12-62 (68)
27 PF01726 LexA_DNA_bind: LexA D 67.9 7.7 0.00017 31.7 3.8 44 86-131 14-58 (65)
28 PF04539 Sigma70_r3: Sigma-70 66.1 7 0.00015 31.6 3.2 52 85-136 8-59 (78)
29 smart00753 PAM PCI/PINT associ 61.4 25 0.00053 28.9 5.7 66 81-146 8-73 (88)
30 smart00088 PINT motif in prote 61.4 25 0.00053 28.9 5.7 66 81-146 8-73 (88)
31 COG2512 Predicted membrane-ass 60.7 11 0.00023 38.6 4.2 46 77-123 191-236 (258)
32 cd07377 WHTH_GntR Winged helix 59.6 14 0.00031 27.9 3.8 48 82-131 5-57 (66)
33 TIGR02702 SufR_cyano iron-sulf 59.4 13 0.00028 35.7 4.3 46 83-131 2-47 (203)
34 PRK09802 DNA-binding transcrip 58.9 18 0.00039 36.7 5.4 53 80-135 15-67 (269)
35 smart00345 HTH_GNTR helix_turn 57.7 13 0.00029 27.5 3.3 38 94-133 16-54 (60)
36 PF13404 HTH_AsnC-type: AsnC-t 55.0 22 0.00047 26.8 3.9 38 83-121 4-41 (42)
37 PF06969 HemN_C: HemN C-termin 53.9 27 0.00059 27.4 4.6 52 83-135 7-64 (66)
38 cd00092 HTH_CRP helix_turn_hel 53.8 53 0.0011 25.2 6.1 39 96-136 24-62 (67)
39 PRK12423 LexA repressor; Provi 52.8 28 0.00061 33.6 5.4 52 82-135 6-62 (202)
40 PRK04424 fatty acid biosynthes 51.8 20 0.00043 34.5 4.2 46 82-130 7-52 (185)
41 PRK00888 ftsB cell division pr 51.7 64 0.0014 28.8 7.0 45 440-491 40-86 (105)
42 PRK10434 srlR DNA-bindng trans 51.5 65 0.0014 32.4 7.9 48 81-131 4-51 (256)
43 PF10717 ODV-E18: Occlusion-de 51.5 22 0.00048 31.2 3.9 7 177-183 27-33 (85)
44 PF03640 Lipoprotein_15: Secre 49.8 15 0.00032 28.6 2.4 22 124-145 6-27 (48)
45 PF01022 HTH_5: Bacterial regu 49.6 26 0.00056 26.2 3.7 39 83-123 3-41 (47)
46 cd07153 Fur_like Ferric uptake 48.7 54 0.0012 28.2 6.0 59 83-141 2-65 (116)
47 smart00347 HTH_MARR helix_turn 48.1 1.5E+02 0.0031 23.9 8.5 48 84-134 12-59 (101)
48 PF04405 ScdA_N: Domain of Unk 47.4 16 0.00035 29.3 2.3 38 84-121 12-55 (56)
49 PF02002 TFIIE_alpha: TFIIE al 47.2 25 0.00054 30.4 3.7 78 85-165 16-96 (105)
50 PF00356 LacI: Bacterial regul 47.0 14 0.0003 28.5 1.8 22 77-98 24-45 (46)
51 PF00392 GntR: Bacterial regul 46.8 15 0.00033 28.9 2.2 37 93-131 19-56 (64)
52 COG2345 Predicted transcriptio 46.7 37 0.0008 34.3 5.2 64 75-141 4-71 (218)
53 smart00344 HTH_ASNC helix_turn 46.0 33 0.00072 29.2 4.2 41 83-124 4-44 (108)
54 TIGR02431 pcaR_pcaU beta-ketoa 44.1 27 0.00058 34.4 3.8 44 86-131 13-56 (248)
55 PF00356 LacI: Bacterial regul 43.5 16 0.00036 28.1 1.8 21 99-119 1-21 (46)
56 PHA03242 envelope glycoprotein 43.5 1.5E+02 0.0032 33.0 9.5 31 411-444 325-355 (428)
57 COG1675 TFA1 Transcription ini 43.1 1.3E+02 0.0027 29.6 8.1 83 85-170 21-106 (176)
58 PRK10681 DNA-binding transcrip 43.0 35 0.00076 34.1 4.5 41 82-123 7-47 (252)
59 COG1349 GlpR Transcriptional r 40.4 1.2E+02 0.0025 30.6 7.7 57 80-137 3-65 (253)
60 PRK10906 DNA-binding transcrip 40.1 43 0.00093 33.7 4.6 42 82-124 5-46 (252)
61 PRK10411 DNA-binding transcrip 40.1 1.7E+02 0.0037 29.2 8.8 54 82-139 4-57 (240)
62 PRK10163 DNA-binding transcrip 40.0 36 0.00078 34.2 4.1 47 86-134 29-75 (271)
63 PRK11569 transcriptional repre 39.3 37 0.0008 34.1 4.0 46 86-133 32-77 (274)
64 PRK09480 slmA division inhibit 38.8 25 0.00054 32.1 2.5 33 80-112 8-45 (194)
65 smart00419 HTH_CRP helix_turn_ 38.1 32 0.0007 24.6 2.5 37 95-133 6-42 (48)
66 PRK15090 DNA-binding transcrip 37.9 1.4E+02 0.0031 29.5 7.8 45 86-133 18-62 (257)
67 PF01325 Fe_dep_repress: Iron 37.5 64 0.0014 25.8 4.4 32 93-124 18-49 (60)
68 PRK00135 scpB segregation and 37.3 76 0.0017 31.1 5.7 56 85-141 6-66 (188)
69 PHA01815 hypothetical protein 37.1 1.5E+02 0.0032 23.8 6.1 26 158-183 12-37 (55)
70 PRK13509 transcriptional repre 37.0 46 0.001 33.3 4.3 42 82-124 5-46 (251)
71 PHA02943 hypothetical protein; 36.7 2E+02 0.0042 28.2 8.1 60 83-144 9-69 (165)
72 PRK09834 DNA-binding transcrip 36.5 44 0.00096 33.3 4.1 48 86-135 15-63 (263)
73 PF08279 HTH_11: HTH domain; 36.4 17 0.00037 27.5 0.9 29 272-300 1-29 (55)
74 COG3695 Predicted methylated D 35.9 51 0.0011 30.0 3.9 60 81-140 5-70 (103)
75 PF13463 HTH_27: Winged helix 35.6 55 0.0012 25.3 3.7 45 85-131 6-50 (68)
76 PF01047 MarR: MarR family; I 35.1 72 0.0016 24.2 4.2 39 85-124 6-44 (59)
77 PF03297 Ribosomal_S25: S25 ri 34.8 61 0.0013 29.3 4.2 57 83-140 46-102 (105)
78 PRK10014 DNA-binding transcrip 34.6 26 0.00056 34.8 2.1 25 95-119 4-28 (342)
79 COG2846 Regulator of cell morp 34.4 29 0.00064 35.0 2.4 32 94-125 31-62 (221)
80 TIGR00498 lexA SOS regulatory 34.1 58 0.0013 30.9 4.3 48 82-131 6-58 (199)
81 COG1414 IclR Transcriptional r 34.0 51 0.0011 33.0 4.1 47 86-134 8-54 (246)
82 PLN03083 E3 UFM1-protein ligas 34.0 57 0.0012 38.7 4.9 62 80-147 58-119 (803)
83 PHA02701 ORF020 dsRNA-binding 33.9 52 0.0011 32.6 3.9 42 83-124 5-46 (183)
84 PRK11463 fxsA phage T7 F exclu 32.9 56 0.0012 30.9 3.9 39 412-450 80-119 (148)
85 PRK10992 iron-sulfur cluster r 32.7 39 0.00085 33.6 3.0 42 85-126 16-63 (220)
86 PF01316 Arg_repressor: Argini 32.2 1.1E+02 0.0025 25.6 5.2 46 83-144 21-67 (70)
87 cd06445 ATase The DNA repair p 32.1 70 0.0015 26.7 4.0 55 84-138 2-62 (79)
88 PF03640 Lipoprotein_15: Secre 31.6 23 0.00049 27.6 0.9 22 312-333 4-25 (48)
89 PF05331 DUF742: Protein of un 31.5 59 0.0013 29.7 3.7 48 84-135 42-91 (114)
90 PRK11014 transcriptional repre 31.2 52 0.0011 29.9 3.3 43 82-124 10-52 (141)
91 PRK07598 RNA polymerase sigma 30.9 1.9E+02 0.0042 31.8 8.0 87 92-178 273-364 (415)
92 TIGR00589 ogt O-6-methylguanin 30.5 97 0.0021 26.4 4.6 57 82-138 2-64 (80)
93 PF01035 DNA_binding_1: 6-O-me 30.4 62 0.0013 27.5 3.4 57 82-138 2-64 (85)
94 PF04157 EAP30: EAP30/Vps36 fa 30.3 63 0.0014 31.8 3.9 42 82-123 174-216 (223)
95 PRK11050 manganese transport r 29.8 3.5E+02 0.0076 25.1 8.6 55 85-143 40-94 (152)
96 PF06224 HTH_42: Winged helix 29.5 1E+02 0.0022 31.2 5.5 57 87-145 172-230 (327)
97 PF15145 DUF4577: Domain of un 29.3 24 0.00053 32.7 0.8 27 173-199 63-89 (128)
98 smart00874 B5 tRNA synthetase 28.7 65 0.0014 25.6 3.1 52 97-150 5-56 (71)
99 PRK11179 DNA-binding transcrip 28.7 93 0.002 28.7 4.6 41 83-124 10-50 (153)
100 PF11772 EpuA: DNA-directed RN 28.6 32 0.00068 27.1 1.2 25 258-282 22-46 (47)
101 smart00531 TFIIE Transcription 27.9 2.7E+02 0.0059 25.8 7.4 78 87-167 6-89 (147)
102 PTZ00326 phenylalanyl-tRNA syn 27.7 2E+02 0.0044 32.4 7.6 76 81-158 5-80 (494)
103 PRK09492 treR trehalose repres 27.5 36 0.00078 33.4 1.7 24 96-119 3-26 (315)
104 PRK13239 alkylmercury lyase; P 27.3 53 0.0011 32.9 2.8 56 269-332 20-75 (206)
105 PF03965 Penicillinase_R: Peni 27.3 2.1E+02 0.0046 25.1 6.3 79 83-168 4-86 (115)
106 PF10771 DUF2582: Protein of u 27.1 1E+02 0.0022 25.7 4.0 52 86-140 12-63 (65)
107 COG5232 SEC62 Preprotein trans 27.1 80 0.0017 32.3 4.0 58 374-432 145-212 (259)
108 PRK09526 lacI lac repressor; R 26.9 40 0.00086 33.5 1.9 24 96-119 4-27 (342)
109 PRK10141 DNA-binding transcrip 26.9 4.9E+02 0.011 23.7 9.2 60 79-141 13-72 (117)
110 PRK11552 putative DNA-binding 26.7 55 0.0012 31.8 2.8 33 82-114 13-49 (225)
111 COG1609 PurR Transcriptional r 26.7 1.4E+02 0.0031 30.8 6.0 59 78-136 26-98 (333)
112 PLN03238 probable histone acet 26.7 69 0.0015 33.8 3.6 52 84-140 210-261 (290)
113 PRK05472 redox-sensing transcr 26.6 91 0.002 30.2 4.3 40 82-121 16-56 (213)
114 PF01853 MOZ_SAS: MOZ/SAS fami 26.5 71 0.0015 31.7 3.5 38 84-121 135-174 (188)
115 PLN02853 Probable phenylalanyl 26.3 2.2E+02 0.0048 32.2 7.6 79 82-162 3-81 (492)
116 PRK03902 manganese transport t 25.8 4.7E+02 0.01 23.6 8.5 42 86-130 12-53 (142)
117 PF10025 DUF2267: Uncharacteri 25.3 39 0.00085 30.4 1.4 68 100-167 6-80 (125)
118 TIGR00540 hemY_coli hemY prote 25.3 2.8E+02 0.006 29.3 7.9 29 413-441 41-69 (409)
119 PRK15008 HTH-type transcriptio 25.2 52 0.0011 31.2 2.3 32 82-113 18-54 (212)
120 TIGR03826 YvyF flagellar opero 25.2 1.1E+02 0.0023 29.0 4.2 53 85-143 33-86 (137)
121 PRK14987 gluconate operon tran 25.2 42 0.00091 33.4 1.7 25 95-119 3-27 (331)
122 COG1321 TroR Mn-dependent tran 25.1 1.1E+02 0.0024 29.0 4.4 50 86-136 14-69 (154)
123 PRK14996 TetR family transcrip 25.0 48 0.001 30.6 2.0 29 84-112 10-43 (192)
124 TIGR02405 trehalos_R_Ecol treh 24.9 45 0.00098 33.0 1.9 23 97-119 1-23 (311)
125 PF00165 HTH_AraC: Bacterial r 24.8 55 0.0012 23.7 1.9 28 93-120 4-31 (42)
126 PRK10747 putative protoheme IX 24.8 3.3E+02 0.0073 28.7 8.4 28 412-439 40-67 (398)
127 TIGR02787 codY_Gpos GTP-sensin 24.5 83 0.0018 32.6 3.7 44 88-133 189-232 (251)
128 TIGR02944 suf_reg_Xantho FeS a 24.0 1.1E+02 0.0024 27.1 4.1 44 87-132 14-58 (130)
129 PF04967 HTH_10: HTH DNA bindi 23.2 1.5E+02 0.0033 23.7 4.2 36 85-120 6-46 (53)
130 PF10668 Phage_terminase: Phag 23.1 1E+02 0.0022 25.4 3.3 34 82-115 7-40 (60)
131 PF09012 FeoC: FeoC like trans 22.9 1.1E+02 0.0025 24.5 3.5 35 89-123 6-40 (69)
132 PRK09334 30S ribosomal protein 22.7 1.9E+02 0.004 25.5 5.0 59 79-140 24-84 (86)
133 PF07245 Phlebovirus_G2: Phleb 22.6 74 0.0016 35.8 3.2 18 134-151 421-438 (507)
134 PRK09975 DNA-binding transcrip 22.3 66 0.0014 30.0 2.4 32 82-113 11-47 (213)
135 KOG4251 Calcium binding protei 22.1 59 0.0013 34.1 2.1 58 265-322 275-335 (362)
136 PF10975 DUF2802: Protein of u 21.4 62 0.0013 27.1 1.7 29 88-116 35-63 (70)
137 PF09105 SelB-wing_1: Elongati 21.3 2.4E+02 0.0052 22.9 4.9 43 87-129 7-49 (61)
138 PF02796 HTH_7: Helix-turn-hel 21.2 74 0.0016 23.8 2.0 32 87-118 11-42 (45)
139 TIGR01884 cas_HTH CRISPR locus 21.2 2.9E+02 0.0063 26.6 6.5 47 84-133 145-191 (203)
140 PRK10344 DNA-binding transcrip 21.2 1.2E+02 0.0025 27.3 3.4 34 84-119 10-43 (92)
141 smart00421 HTH_LUXR helix_turn 21.1 1.7E+02 0.0037 21.0 3.9 46 78-127 3-48 (58)
142 PRK10703 DNA-binding transcrip 21.0 57 0.0012 32.5 1.8 22 98-119 2-23 (341)
143 PRK05441 murQ N-acetylmuramic 20.9 1.1E+02 0.0023 31.8 3.7 43 84-130 250-292 (299)
144 TIGR01481 ccpA catabolite cont 20.9 58 0.0013 32.1 1.8 22 98-119 2-23 (329)
145 PF14947 HTH_45: Winged helix- 20.8 1.3E+02 0.0028 24.9 3.5 38 87-124 8-46 (77)
146 PF12387 Peptidase_C74: Pestiv 20.6 57 0.0012 32.4 1.6 24 316-339 11-34 (200)
147 PF01316 Arg_repressor: Argini 20.4 75 0.0016 26.7 2.0 62 270-333 4-66 (70)
No 1
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=91.52 E-value=0.33 Score=39.54 Aligned_cols=50 Identities=16% Similarity=0.242 Sum_probs=43.0
Q ss_pred CchhhHHHHHHHHhcCC-ceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEe
Q 010241 80 PADVRNRAMDAVDACNR-RVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEV 131 (514)
Q Consensus 80 ~~~~~~~im~ave~~g~-rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqV 131 (514)
+....++|++.+.+.|. .+|+.|+|.+.|++...+.+.|..|..+ |-++-
T Consensus 4 ~~~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~--G~V~~ 54 (68)
T smart00550 4 QDSLEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKK--GKVCK 54 (68)
T ss_pred chHHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHC--CCEEe
Confidence 34567899999999988 6999999999999999999999999876 44443
No 2
>PRK13239 alkylmercury lyase; Provisional
Probab=91.46 E-value=0.31 Score=48.30 Aligned_cols=56 Identities=18% Similarity=0.284 Sum_probs=47.6
Q ss_pred chhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcCc
Q 010241 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPN 143 (514)
Q Consensus 81 ~~~~~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqVse~GeIlY~FP~ 143 (514)
..+.-.|++.+. .|.-||+.|+|+.+|.+.+++++.|.+|. ..+.+++|+|+- ||-
T Consensus 21 ~~~~~~llr~la-~G~pvt~~~lA~~~~~~~~~v~~~L~~l~-----~~~~d~~g~iv~-~pl 76 (206)
T PRK13239 21 ATLLVPLLRLLA-KGRPVSVTTLAAALGWPVEEVEAVLEAMP-----DTEYDEDGRIIG-YGL 76 (206)
T ss_pred hHHHHHHHHHHH-cCCCCCHHHHHHHhCCCHHHHHHHHHhCC-----CeEECCCCCEEe-ccc
Confidence 356677899988 99999999999999999999999999985 347899999975 543
No 3
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=90.38 E-value=0.3 Score=37.35 Aligned_cols=39 Identities=23% Similarity=0.434 Sum_probs=34.9
Q ss_pred HHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhh
Q 010241 86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (514)
Q Consensus 86 ~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd 124 (514)
+|++++.+.+...|+.|+|.++|++...+.+-|..|...
T Consensus 7 ~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~~ 45 (52)
T PF09339_consen 7 RILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVEE 45 (52)
T ss_dssp HHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 578999999999999999999999999999999998753
No 4
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=90.12 E-value=0.6 Score=43.38 Aligned_cols=56 Identities=30% Similarity=0.495 Sum_probs=46.5
Q ss_pred chhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccC-CcEEEEcCc
Q 010241 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDE-GDVLYVFPN 143 (514)
Q Consensus 81 ~~~~~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqVse~-GeIlY~FP~ 143 (514)
+.+..+|++.|.+. +|+|++|+++.+|++.+.++.-|..|.+ .|+|..+.. | +||.
T Consensus 11 ~eLk~rIvElVRe~-GRiTi~ql~~~TGasR~Tvk~~lreLVa--~G~l~~~G~~G----vF~s 67 (127)
T PF06163_consen 11 EELKARIVELVREH-GRITIKQLVAKTGASRNTVKRYLRELVA--RGDLYRHGRSG----VFPS 67 (127)
T ss_pred HHHHHHHHHHHHHc-CCccHHHHHHHHCCCHHHHHHHHHHHHH--cCCeEeCCCcc----cccc
Confidence 45667888888775 5899999999999999999999999985 688888776 6 5665
No 5
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=89.63 E-value=2.4 Score=39.29 Aligned_cols=84 Identities=21% Similarity=0.254 Sum_probs=67.2
Q ss_pred HHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceE---ec-cCCcEEEEc-CcchHHHHhhhhHHHhHH
Q 010241 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLE---VS-DEGDVLYVF-PNNYRAKLAAKSFRLKVE 159 (514)
Q Consensus 85 ~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~Lq---Vs-e~GeIlY~F-P~~fRs~l~~Ks~r~rl~ 159 (514)
-.++.++-+.++..|+-|+|..-+++...|+++|+.|... |-++ ++ +.|-..|.| |.++-.. .+-....++
T Consensus 30 v~v~~~LL~~~~~~tvdelae~lnr~rStv~rsl~~L~~~--GlV~Rek~~~~~Ggy~yiY~~i~~ee~--k~~i~~~l~ 105 (126)
T COG3355 30 VEVYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLEA--GLVEREKVNLKGGGYYYLYKPIDPEEI--KKKILKDLD 105 (126)
T ss_pred HHHHHHHHhhcCCcCHHHHHHHHCccHHHHHHHHHHHHHc--CCeeeeeeccCCCceeEEEecCCHHHH--HHHHHHHHH
Confidence 3566777778899999999999999999999999999875 3333 33 789999999 8887763 556777788
Q ss_pred HHHHHHhhhhHHH
Q 010241 160 PVIDKAKAAAEYS 172 (514)
Q Consensus 160 ~~~~k~w~v~~yl 172 (514)
.|.++++..+...
T Consensus 106 ~w~~~~~~~i~~~ 118 (126)
T COG3355 106 EWYDKMKQLIEEF 118 (126)
T ss_pred HHHHHHHHHHHHH
Confidence 8888887775543
No 6
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=88.54 E-value=2.8 Score=34.34 Aligned_cols=77 Identities=21% Similarity=0.379 Sum_probs=52.4
Q ss_pred HHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEc-CcchH---HHHhhhhHHHhHHH
Q 010241 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVF-PNNYR---AKLAAKSFRLKVEP 160 (514)
Q Consensus 85 ~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqVse~GeIlY~F-P~~fR---s~l~~Ks~r~rl~~ 160 (514)
-.|++.+.+.+..+|+.|+|...|++...+.+-|..|.+ .|.|+-...+. .|.. |+.++ ..+.+.++.....+
T Consensus 8 ~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~--~g~l~~~~~~~-~y~l~~~~~~~~~~~~~~~~l~~~~~~ 84 (91)
T smart00346 8 LAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQE--LGYVEQDGQNG-RYRLGPKVLELGQSYLSSLDLREVAKP 84 (91)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHH--CCCeeecCCCC-ceeecHHHHHHHHHHHhcCCHHHHHHH
Confidence 457888877766899999999999999999999999976 48887764333 3554 33222 22223345555555
Q ss_pred HHHH
Q 010241 161 VIDK 164 (514)
Q Consensus 161 ~~~k 164 (514)
.++.
T Consensus 85 ~l~~ 88 (91)
T smart00346 85 VLEE 88 (91)
T ss_pred HHHH
Confidence 5544
No 7
>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.
Probab=87.28 E-value=0.71 Score=39.57 Aligned_cols=49 Identities=22% Similarity=0.348 Sum_probs=35.5
Q ss_pred hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEE
Q 010241 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVL 138 (514)
Q Consensus 84 ~~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqVse~GeIl 138 (514)
--.+++.+.+ |.-||+.++|+.+|.+.+++.+.|.+.. ..|-+++|.||
T Consensus 26 ~r~LLr~LA~-G~PVt~~~LA~a~g~~~e~v~~~L~~~p-----~tEyD~~GrIV 74 (77)
T PF12324_consen 26 LRPLLRLLAK-GQPVTVEQLAAALGWPVEEVRAALAAMP-----DTEYDDQGRIV 74 (77)
T ss_dssp HHHHHHHHTT-TS-B-HHHHHHHHT--HHHHHHHHHH-T-----TSEEETTSEEE
T ss_pred HHHHHHHHHc-CCCcCHHHHHHHHCCCHHHHHHHHHhCC-----CceEcCCCCee
Confidence 3445666665 9999999999999999999988887775 37888888886
No 8
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=86.59 E-value=3.8 Score=39.53 Aligned_cols=85 Identities=19% Similarity=0.160 Sum_probs=61.1
Q ss_pred chhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhc--CC-ceEeccCCcEEEEcCcchHHHHhhhhHHHh
Q 010241 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT--DG-FLEVSDEGDVLYVFPNNYRAKLAAKSFRLK 157 (514)
Q Consensus 81 ~~~~~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~--~G-~LqVse~GeIlY~FP~~fRs~l~~Ks~r~r 157 (514)
.+..-.|++++...| .+|..|+|...|++.+++++-|..|..+- .. .....++|-+.|.+=-++..+ ....+.+
T Consensus 21 ~~~~~~Vl~~L~~~g-~~tdeeLA~~Lgi~~~~VRk~L~~L~e~gLv~~~r~r~~~~Gr~~y~w~l~~~~i--~d~ik~~ 97 (178)
T PRK06266 21 DEEGFEVLKALIKKG-EVTDEEIAEQTGIKLNTVRKILYKLYDARLADYKREKDEETNWYTYTWKPELEKL--PEIIKKK 97 (178)
T ss_pred CccHhHHHHHHHHcC-CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEeeeeccCCCcEEEEEEeCHHHH--HHHHHHH
Confidence 445678999999888 69999999999999999999999999885 11 223336888999775555553 2334444
Q ss_pred HHHHHHHHhhh
Q 010241 158 VEPVIDKAKAA 168 (514)
Q Consensus 158 l~~~~~k~w~v 168 (514)
+....++++.-
T Consensus 98 ~~~~~~klk~~ 108 (178)
T PRK06266 98 KMEELKKLKEQ 108 (178)
T ss_pred HHHHHHHHHHH
Confidence 55555555443
No 9
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=84.73 E-value=1.2 Score=36.53 Aligned_cols=54 Identities=22% Similarity=0.403 Sum_probs=41.3
Q ss_pred hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEecc--CCcEEE
Q 010241 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD--EGDVLY 139 (514)
Q Consensus 84 ~~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqVse--~GeIlY 139 (514)
.+.|++.+++....+|-.|||...|++..+|+.=|..|..+ |.++-++ .|-..|
T Consensus 2 ke~Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le~e--G~V~~~~~~rG~~~~ 57 (62)
T PF04703_consen 2 KEKILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLEKE--GKVERSPVRRGKSTY 57 (62)
T ss_dssp HHCHHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHHHC--TSEEEES-SSSSS-E
T ss_pred cHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHC--CCEEEecCCCCccee
Confidence 36799999998889999999999999999999999988765 5666544 354433
No 10
>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=84.32 E-value=6.4 Score=37.19 Aligned_cols=80 Identities=23% Similarity=0.230 Sum_probs=60.1
Q ss_pred HHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCC---ceEeccCCcEEEEcCcchHHHHhhhhHHHhHHHHH
Q 010241 86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDG---FLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEPVI 162 (514)
Q Consensus 86 ~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G---~LqVse~GeIlY~FP~~fRs~l~~Ks~r~rl~~~~ 162 (514)
.||+|+-..| -+|..|+|...|++++++++.|..|..+-=. +.+-.++|-+.|.+=-++..+ -...+.++....
T Consensus 18 ~Vl~aL~~~~-~~tdEeLa~~Lgi~~~~VRk~L~~L~e~~Lv~~~r~r~~~~gw~~Y~w~i~~~~i--~d~Ik~~~~~~~ 94 (158)
T TIGR00373 18 LVLFSLGIKG-EFTDEEISLELGIKLNEVRKALYALYDAGLADYKRRKDDETGWYEYTWRINYEKA--LDVLKRKLEETA 94 (158)
T ss_pred HHHHHHhccC-CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCceeeeeeecCCCcEEEEEEeCHHHH--HHHHHHHHHHHH
Confidence 4678887777 6999999999999999999999999988632 556677899999975567664 334555555555
Q ss_pred HHHhhh
Q 010241 163 DKAKAA 168 (514)
Q Consensus 163 ~k~w~v 168 (514)
++++.-
T Consensus 95 ~~lk~~ 100 (158)
T TIGR00373 95 KKLREK 100 (158)
T ss_pred HHHHHH
Confidence 555444
No 11
>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=84.31 E-value=2 Score=31.97 Aligned_cols=41 Identities=17% Similarity=0.324 Sum_probs=33.9
Q ss_pred hhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhh
Q 010241 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (514)
Q Consensus 83 ~~~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd 124 (514)
.+.+|++.+.+.+ ++|+.|+|...|++...+.+.|..|..+
T Consensus 4 ~~~~Il~~l~~~~-~~t~~ela~~~~is~~tv~~~l~~L~~~ 44 (48)
T PF13412_consen 4 TQRKILNYLRENP-RITQKELAEKLGISRSTVNRYLKKLEEK 44 (48)
T ss_dssp HHHHHHHHHHHCT-TS-HHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHcC-CCCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 4578999999955 5999999999999999999999998764
No 12
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=83.44 E-value=2.3 Score=33.40 Aligned_cols=53 Identities=26% Similarity=0.439 Sum_probs=44.2
Q ss_pred CchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCC
Q 010241 80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEG 135 (514)
Q Consensus 80 ~~~~~~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqVse~G 135 (514)
....|-+|++.+ ..+...|++++|...|++.+.+-.-|..|.. .|-+++..+|
T Consensus 8 ~~p~R~~Il~~L-~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~--aGli~~~~~g 60 (61)
T PF12840_consen 8 SDPTRLRILRLL-ASNGPMTVSELAEELGISQSTVSYHLKKLEE--AGLIEVEREG 60 (61)
T ss_dssp TSHHHHHHHHHH-HHCSTBEHHHHHHHHTS-HHHHHHHHHHHHH--TTSEEEEEET
T ss_pred CCHHHHHHHHHH-hcCCCCCHHHHHHHHCCCHHHHHHHHHHHHH--CCCeEEeccC
Confidence 345678888888 6788899999999999999999999999977 6778777766
No 13
>PF04583 Baculo_p74: Baculoviridae p74 conserved region; InterPro: IPR007663 Baculoviruses are distinct from other virus families in that there are two viral phenotypes: budded virus (BV) and occlusion-derived virus (ODV). BVs disseminate viral infection throughout the tissues of the host and ODVs transmit baculovirus between insect hosts. GFP tagging experiments implicate p74 as an ODV envelope protein [, ].; GO: 0019058 viral infectious cycle
Probab=82.89 E-value=5.2 Score=41.02 Aligned_cols=87 Identities=20% Similarity=0.421 Sum_probs=54.5
Q ss_pred cchHHHHhhhhHHHhHHH-----HHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCcCCCCce
Q 010241 143 NNYRAKLAAKSFRLKVEP-----VIDKAKAAAEYSIRVLFGTALIASIVIVFTAIIAILSSKSDDDDRGRRRRSFDSGFN 217 (514)
Q Consensus 143 ~~fRs~l~~Ks~r~rl~~-----~~~k~w~v~~yliRVsFG~~LIaSivlv~~aIiailss~s~~d~r~r~g~g~~~g~~ 217 (514)
+.+-.++.+..+|..+.. ..+-+-.++..+.|+...-+-|+-|++++++|+-++
T Consensus 62 ~~vt~rlLgetyKaav~h~~nr~aIkt~s~vAkal~r~~~~AaSVvgi~Li~~ti~Dlv--------------------- 120 (249)
T PF04583_consen 62 RRVTVRLLGETYKAAVVHQLNRIAIKTVSTVAKALTRIAIAAASVVGIVLIFLTIADLV--------------------- 120 (249)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------------
Confidence 445566666666554322 333447788888888888888888888888887662
Q ss_pred EeecCcccceeeCCccccccccccCCCccCCchhhhhhhcc
Q 010241 218 IFISPSDLFWYWDPYYYRRRRVQTDDDDKKMNFIKSVFSFV 258 (514)
Q Consensus 218 ~~~~p~DlFWy~dp~yyrrr~~~~~~~~~~mnFlEsVFSFv 258 (514)
+=+||||+|...=.+.=.++=-.+|+.|-|.=+
T Consensus 121 --------L~~WDPfGYnNMFPr~~ldDLs~sfl~A~~esl 153 (249)
T PF04583_consen 121 --------LMFWDPFGYNNMFPREYLDDLSRSFLSAYYESL 153 (249)
T ss_pred --------HHhcCcccccccCCCcchHHHHHHHHHHHHHHh
Confidence 236799998543221100111257777777655
No 14
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=81.34 E-value=3 Score=32.78 Aligned_cols=40 Identities=13% Similarity=0.298 Sum_probs=36.0
Q ss_pred hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhh
Q 010241 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (514)
Q Consensus 84 ~~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd 124 (514)
+..|++.+++. +.+|+.|+|..-|+|...+++.|..|+..
T Consensus 2 ~~~Il~~l~~~-~~~s~~ela~~~~VS~~TiRRDl~~L~~~ 41 (57)
T PF08220_consen 2 QQQILELLKEK-GKVSVKELAEEFGVSEMTIRRDLNKLEKQ 41 (57)
T ss_pred HHHHHHHHHHc-CCEEHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 46789999886 58999999999999999999999999875
No 15
>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=80.57 E-value=9 Score=28.85 Aligned_cols=60 Identities=25% Similarity=0.424 Sum_probs=46.5
Q ss_pred CCchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCC-cEEEEcC
Q 010241 79 LPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEG-DVLYVFP 142 (514)
Q Consensus 79 l~~~~~~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqVse~G-eIlY~FP 142 (514)
+....+..|++++.+.+ ++..|+|...|++...+.+.|..|.+. |.+....++ ...|.+.
T Consensus 4 ~~~~~~~~il~~l~~~~--~~~~ei~~~~~i~~~~i~~~l~~L~~~--g~i~~~~~~~~~~~~~~ 64 (78)
T cd00090 4 LSDPTRLRILRLLLEGP--LTVSELAERLGLSQSTVSRHLKKLEEA--GLVESRREGRRVYYSLT 64 (78)
T ss_pred ccChHHHHHHHHHHHCC--cCHHHHHHHHCcCHhHHHHHHHHHHHC--CCeEEEEeccEEEEEeC
Confidence 34456778899888866 999999999999999999999999764 677765544 4555554
No 16
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=80.27 E-value=1.9 Score=36.90 Aligned_cols=34 Identities=12% Similarity=0.081 Sum_probs=30.9
Q ss_pred hhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHH
Q 010241 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKAL 118 (514)
Q Consensus 83 ~~~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L 118 (514)
-+..|++.+.+ +.+|+.|||..+|+|...+.+.|
T Consensus 7 R~~~I~e~l~~--~~~ti~dvA~~~gvS~~TVsr~L 40 (80)
T TIGR02844 7 RVLEIGKYIVE--TKATVRETAKVFGVSKSTVHKDV 40 (80)
T ss_pred HHHHHHHHHHH--CCCCHHHHHHHhCCCHHHHHHHh
Confidence 45788999999 99999999999999999998866
No 17
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=80.12 E-value=4.2 Score=29.96 Aligned_cols=50 Identities=20% Similarity=0.376 Sum_probs=39.7
Q ss_pred HHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEE
Q 010241 87 AMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYV 140 (514)
Q Consensus 87 im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqVse~GeIlY~ 140 (514)
|+..+. ...+|+.|++...|++...+.+.|..|.++ |-+.....|...|.
T Consensus 2 il~~l~--~~~~~~~~i~~~l~is~~~v~~~l~~L~~~--g~i~~~~~~~~~~~ 51 (66)
T smart00418 2 ILKLLA--EGELCVCELAEILGLSQSTVSHHLKKLREA--GLVESRREGKRVYY 51 (66)
T ss_pred HHHHhh--cCCccHHHHHHHHCCCHHHHHHHHHHHHHC--CCeeeeecCCEEEE
Confidence 567776 667899999999999999999999999975 77776665554443
No 18
>PF09743 DUF2042: Uncharacterized conserved protein (DUF2042); InterPro: IPR018611 The ubiquitin fold modifier 1 (Ufm1) is the most recently discovered ubiquitin-like modifier whose conjugation (ufmylation) system is conserved in multicellular organisms. Ufm1 is known to covalently attach with cellular protein(s) via a specific E1-activating enzyme (Uba5), an E2-conjugating enzyme (Ufc1), and a E3-ligating enzyme []. This entry represents E3 UFM1-protein ligase 1.
Probab=79.59 E-value=3.3 Score=42.51 Aligned_cols=57 Identities=18% Similarity=0.367 Sum_probs=49.5
Q ss_pred CchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEE
Q 010241 80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVL 138 (514)
Q Consensus 80 ~~~~~~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqVse~GeIl 138 (514)
|.-++..|.+.+...|+|+++.|++..-|++.+..|+.+..+..+-. +++.. .||++
T Consensus 53 ~~~L~~EI~~el~~~gGRv~~~dL~~~LnVd~~~ie~~~~~i~~~~~-~~~l~-~geli 109 (272)
T PF09743_consen 53 PEQLEKEIKDELYVHGGRVNLVDLAQALNVDLDHIERRAQEIVKSDK-SLQLV-QGELI 109 (272)
T ss_pred HHHHHHHHHHHHHHcCCceEHHHHHHhcCcCHHHHHHHHHHHHhCCC-cEEEE-CCEEc
Confidence 45678899999999999999999999999999999999999998877 56544 68864
No 19
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=79.58 E-value=5.6 Score=28.84 Aligned_cols=47 Identities=15% Similarity=0.319 Sum_probs=38.3
Q ss_pred hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEecc
Q 010241 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD 133 (514)
Q Consensus 84 ~~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqVse 133 (514)
+..+++.+.+.+ .+|+.|++...|++...+.+.|..|..+ |.++-..
T Consensus 2 ~~~il~~l~~~~-~~s~~~l~~~l~~s~~tv~~~l~~L~~~--g~i~~~~ 48 (53)
T smart00420 2 QQQILELLAQQG-KVSVEELAELLGVSEMTIRRDLNKLEEQ--GLLTRVH 48 (53)
T ss_pred HHHHHHHHHHcC-CcCHHHHHHHHCCCHHHHHHHHHHHHHC--CCEEEee
Confidence 356788888765 5999999999999999999999998876 5565443
No 20
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=78.22 E-value=3.8 Score=35.17 Aligned_cols=44 Identities=20% Similarity=0.459 Sum_probs=37.6
Q ss_pred chhhHHHHHHHHh---cCCceeehhhhhhcCCCHHHHHHHHHHHHhh
Q 010241 81 ADVRNRAMDAVDA---CNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (514)
Q Consensus 81 ~~~~~~im~ave~---~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd 124 (514)
..++.+|+++++. ..-+|.+.+|+.+.|++.++++++|..|..+
T Consensus 46 ~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~e 92 (102)
T PF08784_consen 46 SPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSNE 92 (102)
T ss_dssp -HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHHT
T ss_pred CHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhC
Confidence 4578999999999 5667999999999999999999999999875
No 21
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=77.42 E-value=7 Score=29.64 Aligned_cols=44 Identities=9% Similarity=0.174 Sum_probs=34.7
Q ss_pred HHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCce
Q 010241 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFL 129 (514)
Q Consensus 85 ~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~L 129 (514)
.+|++.+.+.+..+|..++|...|+|...+++.|..| .+.+..+
T Consensus 3 ~~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L-~~~~~~I 46 (55)
T PF08279_consen 3 KQILKLLLESKEPITAKELAEELGVSRRTIRRDIKEL-REWGIPI 46 (55)
T ss_dssp HHHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHH-HHTT-EE
T ss_pred HHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHH-HHCCCeE
Confidence 5788889666666999999999999999999999999 4444333
No 22
>KOG3341 consensus RNA polymerase II transcription factor complex subunit [Transcription]
Probab=76.63 E-value=6.1 Score=40.15 Aligned_cols=83 Identities=17% Similarity=0.306 Sum_probs=69.3
Q ss_pred cCCCcccccCCCCchhh---HHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcCcc
Q 010241 68 VGPGRIVESDKLPADVR---NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNN 144 (514)
Q Consensus 68 ~~~~~~~~~~~l~~~~~---~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqVse~GeIlY~FP~~ 144 (514)
++.||.----++|..++ ..|+++++.+|| ||+.-+-+.-|-.-.-|.++|..|.++.=+-+.-...+|..|=||..
T Consensus 159 ~~iggK~~vrSVP~ELn~Dht~ILela~~~gy-vt~s~l~~~l~We~~Ra~qaLe~lv~egL~WiD~q~g~e~~YW~ps~ 237 (249)
T KOG3341|consen 159 IKIGGKKLVRSVPTELNMDHTVILELAEILGY-VTISLLKANLGWERSRAIQALEHLVKEGLAWIDLQAGDEAAYWFPSL 237 (249)
T ss_pred EEecCEEeeecCcchhcccHHHHHHHHHhcCc-eeHHHHHHhccchHHHHHHHHHHHHhccceeeeccCCcceeeechhh
Confidence 45566655566666654 579999999999 99999999999999999999999999988888888899999999999
Q ss_pred hHHHHhh
Q 010241 145 YRAKLAA 151 (514)
Q Consensus 145 fRs~l~~ 151 (514)
|-.....
T Consensus 238 ~~~~~~q 244 (249)
T KOG3341|consen 238 FTDQYAQ 244 (249)
T ss_pred hhHHHhh
Confidence 8765443
No 23
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.
Probab=73.13 E-value=6.3 Score=31.81 Aligned_cols=38 Identities=21% Similarity=0.366 Sum_probs=30.4
Q ss_pred HHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHh
Q 010241 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAA 123 (514)
Q Consensus 85 ~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAs 123 (514)
.+|.+.+-+.| +.|+.+++..++|+.++++++|..|..
T Consensus 16 ~~V~~~Ll~~G-~ltl~~i~~~t~l~~~~Vk~~L~~LiQ 53 (62)
T PF08221_consen 16 AKVGEVLLSRG-RLTLREIVRRTGLSPKQVKKALVVLIQ 53 (62)
T ss_dssp HHHHHHHHHC--SEEHHHHHHHHT--HHHHHHHHHHHHH
T ss_pred HHHHHHHHHcC-CcCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 46677776666 999999999999999999999999875
No 24
>PRK15466 carboxysome structural protein EutK; Provisional
Probab=69.24 E-value=8.5 Score=37.41 Aligned_cols=41 Identities=24% Similarity=0.404 Sum_probs=36.6
Q ss_pred hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhh
Q 010241 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (514)
Q Consensus 84 ~~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd 124 (514)
-+.++.-+-...++.|.|+||+.-|.++++|+.+|..|-+|
T Consensus 111 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 151 (166)
T PRK15466 111 ADELLALLTSVRQGMTAGEVAAHFGWPLEKARNALEQLFSA 151 (166)
T ss_pred HHHHHHHHHHHHccccHHHHHHHhCCcHHHHHHHHHHHHhc
Confidence 35667777788899999999999999999999999999886
No 25
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=68.87 E-value=10 Score=28.92 Aligned_cols=41 Identities=15% Similarity=0.255 Sum_probs=34.8
Q ss_pred hHHHHHHHHhcCCc-eeehhhhhhcCCCHHHHHHHHHHHHhh
Q 010241 84 RNRAMDAVDACNRR-VTIGDVAGKAGLKLNEAQKALQALAAD 124 (514)
Q Consensus 84 ~~~im~ave~~g~r-vTvgDVAa~aGL~l~~ae~~L~aLAsd 124 (514)
+=+++-+|...+.. +|+.|+|...|++...+.+.+..|...
T Consensus 7 q~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~ 48 (62)
T PF12802_consen 7 QFRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKK 48 (62)
T ss_dssp HHHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 34678888888887 999999999999999999999888764
No 26
>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=68.53 E-value=12 Score=29.77 Aligned_cols=51 Identities=22% Similarity=0.324 Sum_probs=40.4
Q ss_pred HHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEE
Q 010241 86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLY 139 (514)
Q Consensus 86 ~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqVse~GeIlY 139 (514)
++..++- ..+.+|+.|+|..+|++...+.+.|..|... |.++..+...-+|
T Consensus 12 ~vy~~Ll-~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~--GlV~~~~~~~~~Y 62 (68)
T PF01978_consen 12 KVYLALL-KNGPATAEEIAEELGISRSTVYRALKSLEEK--GLVEREEGRPKVY 62 (68)
T ss_dssp HHHHHHH-HHCHEEHHHHHHHHTSSHHHHHHHHHHHHHT--TSEEEEEECCEEE
T ss_pred HHHHHHH-HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC--CCEEEEcCceEEE
Confidence 4555555 5678999999999999999999999999875 7788777553333
No 27
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=67.86 E-value=7.7 Score=31.73 Aligned_cols=44 Identities=23% Similarity=0.363 Sum_probs=33.5
Q ss_pred HHHHHHHhcCCceeehhhhhhcCCC-HHHHHHHHHHHHhhcCCceEe
Q 010241 86 RAMDAVDACNRRVTIGDVAGKAGLK-LNEAQKALQALAADTDGFLEV 131 (514)
Q Consensus 86 ~im~ave~~g~rvTvgDVAa~aGL~-l~~ae~~L~aLAsd~~G~LqV 131 (514)
-|.+.+++.|+-.|+.|+|...|++ .+.+++-|.+|... |.|+-
T Consensus 14 ~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~k--G~I~r 58 (65)
T PF01726_consen 14 FIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKALERK--GYIRR 58 (65)
T ss_dssp HHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHHHHT--TSEEE
T ss_pred HHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHC--cCccC
Confidence 3455667799999999999999997 99999999999853 55553
No 28
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=66.08 E-value=7 Score=31.59 Aligned_cols=52 Identities=25% Similarity=0.258 Sum_probs=34.4
Q ss_pred HHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCc
Q 010241 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGD 136 (514)
Q Consensus 85 ~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqVse~Ge 136 (514)
+.+.+--.++|...|..+||...|+++++.+..|.....-..=++.+..+++
T Consensus 8 ~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~~~~~~Sl~~~~~~~~~ 59 (78)
T PF04539_consen 8 RARRELEQELGREPTDEEIAEELGISVEEVRELLQASRRPVSLDLPVGDEDD 59 (78)
T ss_dssp HHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHHHSCCEESSHCCSSSSS
T ss_pred HHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHhCCCCeEEeeeecCCCC
Confidence 3444455678999999999999999999998877765443344455555543
No 29
>smart00753 PAM PCI/PINT associated module.
Probab=61.44 E-value=25 Score=28.91 Aligned_cols=66 Identities=14% Similarity=0.164 Sum_probs=47.6
Q ss_pred chhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcCcchH
Q 010241 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYR 146 (514)
Q Consensus 81 ~~~~~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqVse~GeIlY~FP~~fR 146 (514)
...+.+.+..+-+--..+|..++|...+++.+++|..+..+..+..=+-.++....+++.-....|
T Consensus 8 ~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~~r 73 (88)
T smart00753 8 RKIRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVDPR 73 (88)
T ss_pred HHHHHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCchh
Confidence 345566666666667789999999999999999999999998885322245565556655544444
No 30
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=61.44 E-value=25 Score=28.91 Aligned_cols=66 Identities=14% Similarity=0.164 Sum_probs=47.6
Q ss_pred chhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcCcchH
Q 010241 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYR 146 (514)
Q Consensus 81 ~~~~~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqVse~GeIlY~FP~~fR 146 (514)
...+.+.+..+-+--..+|..++|...+++.+++|..+..+..+..=+-.++....+++.-....|
T Consensus 8 ~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~~r 73 (88)
T smart00088 8 RKIRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVDPR 73 (88)
T ss_pred HHHHHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCchh
Confidence 345566666666667789999999999999999999999998885322245565556655544444
No 31
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=60.68 E-value=11 Score=38.65 Aligned_cols=46 Identities=20% Similarity=0.293 Sum_probs=39.3
Q ss_pred CCCCchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHh
Q 010241 77 DKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAA 123 (514)
Q Consensus 77 ~~l~~~~~~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAs 123 (514)
..|+.+. ..||+++..+|+|+|+.|+..+.|+|...+=+.|+.|..
T Consensus 191 ~~L~~~e-~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LEk 236 (258)
T COG2512 191 YDLNEDE-KEILDLIRERGGRITQAELRRALGLSKTTVSRILRRLEK 236 (258)
T ss_pred CCCCHHH-HHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHHHHHHh
Confidence 3444443 468999999999999999999999999999999999865
No 32
>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=59.60 E-value=14 Score=27.90 Aligned_cols=48 Identities=21% Similarity=0.372 Sum_probs=35.3
Q ss_pred hhhHHHHHHHHhcC----Cc-eeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEe
Q 010241 82 DVRNRAMDAVDACN----RR-VTIGDVAGKAGLKLNEAQKALQALAADTDGFLEV 131 (514)
Q Consensus 82 ~~~~~im~ave~~g----~r-vTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqV 131 (514)
++.+.+.+.+.... .. .|+.|+|...|++...+.+.|..|+. .|.|+.
T Consensus 5 ~~~~~i~~~i~~~~~~~~~~~~~~~~la~~~~is~~~v~~~l~~L~~--~G~i~~ 57 (66)
T cd07377 5 QIADQLREAILSGELKPGDRLPSERELAEELGVSRTTVREALRELEA--EGLVER 57 (66)
T ss_pred HHHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH--CCCEEe
Confidence 45566666655432 22 45999999999999999999999987 455553
No 33
>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=59.43 E-value=13 Score=35.74 Aligned_cols=46 Identities=13% Similarity=0.263 Sum_probs=40.4
Q ss_pred hhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEe
Q 010241 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEV 131 (514)
Q Consensus 83 ~~~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqV 131 (514)
.|.+|+..+.+.|. +|+.|+|...|++...+.+.|..|.++ |-++-
T Consensus 2 tr~~IL~~L~~~~~-~t~~eLA~~lgis~~tV~~~L~~Le~~--GlV~r 47 (203)
T TIGR02702 2 TKEDILSYLLKQGQ-ATAAALAEALAISPQAVRRHLKDLETE--GLIEY 47 (203)
T ss_pred HHHHHHHHHHHcCC-CCHHHHHHHHCcCHHHHHHHHHHHHHC--CCeEE
Confidence 57899999998876 999999999999999999999999875 55653
No 34
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=58.93 E-value=18 Score=36.66 Aligned_cols=53 Identities=15% Similarity=0.250 Sum_probs=43.7
Q ss_pred CchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCC
Q 010241 80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEG 135 (514)
Q Consensus 80 ~~~~~~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqVse~G 135 (514)
..+-+.+|++.+++.|. +|+.|+|..-|+|...+++.|..|.+. |.++-..-|
T Consensus 15 ~~eR~~~Il~~L~~~~~-vtv~eLa~~l~VS~~TIRRDL~~Le~~--G~l~r~~GG 67 (269)
T PRK09802 15 TSERREQIIQRLRQQGS-VQVNDLSALYGVSTVTIRNDLAFLEKQ--GIAVRAYGG 67 (269)
T ss_pred HHHHHHHHHHHHHHcCC-EeHHHHHHHHCCCHHHHHHHHHHHHhC--CCeEEEeCC
Confidence 34667888999999876 999999999999999999999999664 666555544
No 35
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=57.71 E-value=13 Score=27.52 Aligned_cols=38 Identities=18% Similarity=0.359 Sum_probs=31.7
Q ss_pred cCCce-eehhhhhhcCCCHHHHHHHHHHHHhhcCCceEecc
Q 010241 94 CNRRV-TIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD 133 (514)
Q Consensus 94 ~g~rv-TvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqVse 133 (514)
-|.++ |+.|+|...|++...+.++|..|..+ |-|+...
T Consensus 16 ~~~~l~s~~~la~~~~vs~~tv~~~l~~L~~~--g~i~~~~ 54 (60)
T smart00345 16 PGDKLPSERELAAQLGVSRTTVREALSRLEAE--GLVQRRP 54 (60)
T ss_pred CCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHC--CCEEEec
Confidence 35677 89999999999999999999999975 5666543
No 36
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=55.03 E-value=22 Score=26.76 Aligned_cols=38 Identities=13% Similarity=0.297 Sum_probs=29.5
Q ss_pred hhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHH
Q 010241 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQAL 121 (514)
Q Consensus 83 ~~~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aL 121 (514)
+..+|++++.+- .|.+..++|...|++-.++.+-+..|
T Consensus 4 ~D~~Il~~Lq~d-~r~s~~~la~~lglS~~~v~~Ri~rL 41 (42)
T PF13404_consen 4 LDRKILRLLQED-GRRSYAELAEELGLSESTVRRRIRRL 41 (42)
T ss_dssp HHHHHHHHHHH--TTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHc-CCccHHHHHHHHCcCHHHHHHHHHHh
Confidence 446778887766 88999999999999999998888765
No 37
>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=53.86 E-value=27 Score=27.38 Aligned_cols=52 Identities=25% Similarity=0.490 Sum_probs=38.1
Q ss_pred hhHHHHHHHHhcCCceeehhhhhhcCCCHHHH-HHHHHHHHhh-----cCCceEeccCC
Q 010241 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEA-QKALQALAAD-----TDGFLEVSDEG 135 (514)
Q Consensus 83 ~~~~im~ave~~g~rvTvgDVAa~aGL~l~~a-e~~L~aLAsd-----~~G~LqVse~G 135 (514)
.++.+|..+.. ..++.+.++..+.|.+..+. .+.|..+.++ .+++|.+|+.|
T Consensus 7 ~~e~i~~~LR~-~~Gi~~~~~~~~~g~~~~~~~~~~l~~l~~~Gll~~~~~~l~lT~~G 64 (66)
T PF06969_consen 7 LREYIMLGLRC-NEGIDLSEFEQRFGIDFAEEFQKELEELQEDGLLEIDGGRLRLTEKG 64 (66)
T ss_dssp HHHHHHHHHHH-HSEEEHHHHHHHTT--THHH-HHHHHHHHHTTSEEE-SSEEEE-TTT
T ss_pred HHHHHHHHHHh-HCCcCHHHHHHHHCcCHHHHHHHHHHHHHHCCCEEEeCCEEEECccc
Confidence 45677777765 67899999999999987666 7778888876 47788888777
No 38
>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=53.78 E-value=53 Score=25.15 Aligned_cols=39 Identities=21% Similarity=0.385 Sum_probs=33.5
Q ss_pred CceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCc
Q 010241 96 RRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGD 136 (514)
Q Consensus 96 ~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqVse~Ge 136 (514)
..+|..|+|...|++...+.+.|..|..+ |-|+....|.
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~~L~~~--g~i~~~~~~~ 62 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLKELEEE--GLISRRGRGK 62 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHC--CCEEecCCCe
Confidence 56899999999999999999999999886 7787766453
No 39
>PRK12423 LexA repressor; Provisional
Probab=52.77 E-value=28 Score=33.65 Aligned_cols=52 Identities=23% Similarity=0.346 Sum_probs=41.1
Q ss_pred hhhHHHHHH----HHhcCCceeehhhhhhcCC-CHHHHHHHHHHHHhhcCCceEeccCC
Q 010241 82 DVRNRAMDA----VDACNRRVTIGDVAGKAGL-KLNEAQKALQALAADTDGFLEVSDEG 135 (514)
Q Consensus 82 ~~~~~im~a----ve~~g~rvTvgDVAa~aGL-~l~~ae~~L~aLAsd~~G~LqVse~G 135 (514)
..|.+|.+. +++.|+.-|+.++|...|+ +.+.+.+.|.+|+.. |+|+++..+
T Consensus 6 ~~q~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~~l~~L~~~--G~l~~~~~~ 62 (202)
T PRK12423 6 PKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARKHVQALAEA--GLIEVVPNQ 62 (202)
T ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHC--CCEEecCCC
Confidence 345555554 4556888899999999996 899999999999874 888887764
No 40
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=51.84 E-value=20 Score=34.48 Aligned_cols=46 Identities=13% Similarity=0.163 Sum_probs=39.4
Q ss_pred hhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceE
Q 010241 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLE 130 (514)
Q Consensus 82 ~~~~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~Lq 130 (514)
.-+..|++.+.+.| .+|+.|+|..-|.|...+++.|..|+.+ |.|+
T Consensus 7 ~R~~~Il~~l~~~~-~~~~~~La~~~~vS~~TiRRDl~~L~~~--g~~~ 52 (185)
T PRK04424 7 ERQKALQELIEENP-FITDEELAEKFGVSIQTIRLDRMELGIP--ELRE 52 (185)
T ss_pred HHHHHHHHHHHHCC-CEEHHHHHHHHCcCHHHHHHHHHHHhcc--hHHH
Confidence 55677888888854 6999999999999999999999999876 6655
No 41
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=51.65 E-value=64 Score=28.80 Aligned_cols=45 Identities=20% Similarity=0.200 Sum_probs=27.5
Q ss_pred HhhhhhHHHhhHHHHHHHHHhcCCChhHHHHHHHHHHHHhc--cccCCCceEEc
Q 010241 440 LQRNADIEKRNRTREKYARALKSPDISLRRKLLSARDMAQK--TFIGQDRIVYS 491 (514)
Q Consensus 440 q~rN~~I~~RN~~R~~~a~~l~~p~~~l~~Kl~~A~~~a~~--~vi~~~divYs 491 (514)
+.+|++.+.||.+=+.-...|+++ .+|....|.+ ..+.+.+|+|.
T Consensus 40 ~~e~~~l~~~n~~L~~eI~~L~~~-------~dyiEe~AR~~Lg~vk~gEivy~ 86 (105)
T PRK00888 40 QQTNAKLKARNDQLFAEIDDLKGG-------QEAIEERARNELGMVKPGETFYR 86 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhCc-------HHHHHHHHHHHcCCCCCCCEEEE
Confidence 344556666665555555555543 2455555554 77888899884
No 42
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=51.47 E-value=65 Score=32.39 Aligned_cols=48 Identities=10% Similarity=0.102 Sum_probs=40.2
Q ss_pred chhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEe
Q 010241 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEV 131 (514)
Q Consensus 81 ~~~~~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqV 131 (514)
..-+.+|++.+++.| ++|+.|+|...|+|...+++.|..|+.. |.|+-
T Consensus 4 ~eR~~~Il~~L~~~~-~v~v~eLa~~l~VS~~TIRRDL~~Le~~--g~l~r 51 (256)
T PRK10434 4 RQRQAAILEYLQKQG-KTSVEELAQYFDTTGTTIRKDLVILEHA--GTVIR 51 (256)
T ss_pred HHHHHHHHHHHHHcC-CEEHHHHHHHHCCCHHHHHHHHHHHHHC--CCEEE
Confidence 356778899888865 6999999999999999999999999876 44443
No 43
>PF10717 ODV-E18: Occlusion-derived virus envelope protein ODV-E18; InterPro: IPR019655 Baculovirus occlusion-derived virus (ODV) derives its envelope from an intranuclear membrane source. Occlusion-derived viral envelope proteins that are detected in viral-induced intranuclear microvesicles, but not detected in the plasma membrane, cytoplasmic membranes, or the nuclear envelope. This entry represents ODV-E18 protein which is encoded by baculovirus late genes with transcription initiating from a TAAG motif. ODV-E18 exists as a dimer in the ODV envelope, which contains a hydrophobic domain that putatively acts as a target or retention signal for intranuclear microvesicles []. ; GO: 0019031 viral envelope
Probab=51.45 E-value=22 Score=31.24 Aligned_cols=7 Identities=43% Similarity=0.396 Sum_probs=3.6
Q ss_pred HHHHHHH
Q 010241 177 FGTALIA 183 (514)
Q Consensus 177 FG~~LIa 183 (514)
++++||+
T Consensus 27 lMtILiv 33 (85)
T PF10717_consen 27 LMTILIV 33 (85)
T ss_pred HHHHHHH
Confidence 4555554
No 44
>PF03640 Lipoprotein_15: Secreted repeat of unknown function; InterPro: IPR005297 This repeat is found in tandem in a set of lipoproteins. The alignment contains a Y-X4-D motif.
Probab=49.76 E-value=15 Score=28.62 Aligned_cols=22 Identities=32% Similarity=0.543 Sum_probs=19.0
Q ss_pred hcCCceEeccCCcEEEEcCcch
Q 010241 124 DTDGFLEVSDEGDVLYVFPNNY 145 (514)
Q Consensus 124 d~~G~LqVse~GeIlY~FP~~f 145 (514)
...|..||+.+|-.||.|.+|=
T Consensus 6 ~~dG~~~~~~~G~~LY~f~~D~ 27 (48)
T PF03640_consen 6 RADGTIQVDYNGMPLYYFDKDS 27 (48)
T ss_pred eCCCCEEECCCCCEEEEECCCC
Confidence 3469999999999999998763
No 45
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=49.57 E-value=26 Score=26.23 Aligned_cols=39 Identities=21% Similarity=0.348 Sum_probs=33.7
Q ss_pred hhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHh
Q 010241 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAA 123 (514)
Q Consensus 83 ~~~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAs 123 (514)
.|-+|+.++.+ +..|+.|+|...|++...+.+-|..|-.
T Consensus 3 ~R~~Il~~L~~--~~~~~~el~~~l~~s~~~vs~hL~~L~~ 41 (47)
T PF01022_consen 3 TRLRILKLLSE--GPLTVSELAEELGLSQSTVSHHLKKLRE 41 (47)
T ss_dssp HHHHHHHHHTT--SSEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHh--CCCchhhHHHhccccchHHHHHHHHHHH
Confidence 57789999998 6799999999999999999999988754
No 46
>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=48.67 E-value=54 Score=28.23 Aligned_cols=59 Identities=12% Similarity=0.129 Sum_probs=45.1
Q ss_pred hhHHHHHHHHhcCCceeehhhhhhc-----CCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEc
Q 010241 83 VRNRAMDAVDACNRRVTIGDVAGKA-----GLKLNEAQKALQALAADTDGFLEVSDEGDVLYVF 141 (514)
Q Consensus 83 ~~~~im~ave~~g~rvTvgDVAa~a-----GL~l~~ae~~L~aLAsd~~G~LqVse~GeIlY~F 141 (514)
.|..|++++.+.+.-+|+.||..+. ++++..+=+.|..|+..-==+=-..++|...|..
T Consensus 2 qR~~Il~~l~~~~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~~~~~~~~~~y~~ 65 (116)
T cd07153 2 QRLAILEVLLESDGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREIELGDGKARYEL 65 (116)
T ss_pred HHHHHHHHHHhCCCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEEEEeCCCceEEEe
Confidence 4788999999999899999999876 6899999999999987632222233356677764
No 47
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=48.10 E-value=1.5e+02 Score=23.94 Aligned_cols=48 Identities=10% Similarity=0.232 Sum_probs=41.0
Q ss_pred hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccC
Q 010241 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDE 134 (514)
Q Consensus 84 ~~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqVse~ 134 (514)
.-.|+..+...+ .+|+.|+|...+++...+.+.|..|... |.++..++
T Consensus 12 ~~~il~~l~~~~-~~~~~~la~~~~~s~~~i~~~l~~L~~~--g~v~~~~~ 59 (101)
T smart00347 12 QFLVLRILYEEG-PLSVSELAKRLGVSPSTVTRVLDRLEKK--GLIRRLPS 59 (101)
T ss_pred HHHHHHHHHHcC-CcCHHHHHHHHCCCchhHHHHHHHHHHC--CCeEecCC
Confidence 456788888876 6999999999999999999999999986 77776654
No 48
>PF04405 ScdA_N: Domain of Unknown function (DUF542) ; InterPro: IPR007500 This is a domain of unknown function found at the N terminus of genes involved in cell wall development and nitrous oxide protection. ScdA is required for normal cell growth and development; mutants have an increased level of peptidoglycan cross-linking and aberrant cellular morphology suggesting a role for ScdA in cell wall metabolism []. NorA1, NorA2, and YtfE are involved in the nitrous oxide response. NorA1 and NorA2, which are similar to YtfE, are co-transcribed with the membrane-bound nitrous oxide (NO) reductases. The genes appear to be involved in NO protection but their function is unknown [, ].
Probab=47.38 E-value=16 Score=29.32 Aligned_cols=38 Identities=21% Similarity=0.287 Sum_probs=32.0
Q ss_pred hHHHHHHHHhc------CCceeehhhhhhcCCCHHHHHHHHHHH
Q 010241 84 RNRAMDAVDAC------NRRVTIGDVAGKAGLKLNEAQKALQAL 121 (514)
Q Consensus 84 ~~~im~ave~~------g~rvTvgDVAa~aGL~l~~ae~~L~aL 121 (514)
.|+..+.+++. |+..|+.+++.+.|+++++.-++|.+|
T Consensus 12 ~p~~a~vf~~~gIDfCCgG~~~L~eA~~~~~ld~~~vl~~L~~l 55 (56)
T PF04405_consen 12 DPRAARVFRKYGIDFCCGGNRSLEEACEEKGLDPEEVLEELNAL 55 (56)
T ss_pred ChHHHHHHHHcCCcccCCCCchHHHHHHHcCCCHHHHHHHHHHc
Confidence 46667777774 678999999999999999999988765
No 49
>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=47.23 E-value=25 Score=30.39 Aligned_cols=78 Identities=24% Similarity=0.235 Sum_probs=39.3
Q ss_pred HHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEec---cCCcEEEEcCcchHHHHhhhhHHHhHHHH
Q 010241 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVS---DEGDVLYVFPNNYRAKLAAKSFRLKVEPV 161 (514)
Q Consensus 85 ~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqVs---e~GeIlY~FP~~fRs~l~~Ks~r~rl~~~ 161 (514)
-.||+++-..| .+|=.|+|..+|++.+++++-|..|..+-=-+.+.. +.|-..|.+==|++.. -...+.++...
T Consensus 16 ~~Il~~L~~~~-~l~de~la~~~~l~~~~vRkiL~~L~~~~lv~~~~~~d~~~~~~~~yw~i~~~~~--~~~ik~r~~~~ 92 (105)
T PF02002_consen 16 VRILDALLRKG-ELTDEDLAKKLGLKPKEVRKILYKLYEDGLVSYRRRKDDERGWTRYYWYIDYDQI--IDVIKYRIYKM 92 (105)
T ss_dssp HHHHHHHHHH---B-HHHHHHTT-S-HHHHHHHHHHHHHHSS-EEEEE--------EEEEE-THHHH-------------
T ss_pred HHHHHHHHHcC-CcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeEEEEEEcCCCcEEEEEEEEcHHHH--HHHHHHHHHHH
Confidence 46899998776 489999999999999999999999998864444432 2344455554445443 12233444444
Q ss_pred HHHH
Q 010241 162 IDKA 165 (514)
Q Consensus 162 ~~k~ 165 (514)
.+++
T Consensus 93 ~~~l 96 (105)
T PF02002_consen 93 REKL 96 (105)
T ss_dssp ----
T ss_pred HHHH
Confidence 4443
No 50
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=47.03 E-value=14 Score=28.50 Aligned_cols=22 Identities=18% Similarity=0.412 Sum_probs=19.4
Q ss_pred CCCCchhhHHHHHHHHhcCCce
Q 010241 77 DKLPADVRNRAMDAVDACNRRV 98 (514)
Q Consensus 77 ~~l~~~~~~~im~ave~~g~rv 98 (514)
+++..+.+++|+++++++||+.
T Consensus 24 ~~vs~~tr~rI~~~a~~lgY~p 45 (46)
T PF00356_consen 24 PRVSEETRERILEAAEELGYRP 45 (46)
T ss_dssp SSSTHHHHHHHHHHHHHHTB-S
T ss_pred CCCCHHHHHHHHHHHHHHCCCC
Confidence 6889999999999999999973
No 51
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=46.84 E-value=15 Score=28.89 Aligned_cols=37 Identities=24% Similarity=0.425 Sum_probs=28.7
Q ss_pred hcCCce-eehhhhhhcCCCHHHHHHHHHHHHhhcCCceEe
Q 010241 93 ACNRRV-TIGDVAGKAGLKLNEAQKALQALAADTDGFLEV 131 (514)
Q Consensus 93 ~~g~rv-TvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqV 131 (514)
+.|.++ |..++|..-|+|...++++|..|+++ |.++.
T Consensus 19 ~~g~~lps~~~la~~~~vsr~tvr~al~~L~~~--g~i~~ 56 (64)
T PF00392_consen 19 PPGDRLPSERELAERYGVSRTTVREALRRLEAE--GLIER 56 (64)
T ss_dssp -TTSBE--HHHHHHHHTS-HHHHHHHHHHHHHT--TSEEE
T ss_pred CCCCEeCCHHHHHHHhccCCcHHHHHHHHHHHC--CcEEE
Confidence 356778 99999999999999999999999876 44443
No 52
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=46.71 E-value=37 Score=34.30 Aligned_cols=64 Identities=17% Similarity=0.322 Sum_probs=49.3
Q ss_pred ccCCCCchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEec----cCCcEEEEc
Q 010241 75 ESDKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVS----DEGDVLYVF 141 (514)
Q Consensus 75 ~~~~l~~~~~~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqVs----e~GeIlY~F 141 (514)
++.+.++..+.+|...+.+.| .+|++|+|.+-|++...|++-|..|.++. -+|+. .-|-+.+.|
T Consensus 4 ~~~~~~~~tr~~il~lL~~~g-~~sa~elA~~Lgis~~avR~HL~~Le~~G--lv~~~~~~~g~GRP~~~y 71 (218)
T COG2345 4 MLADPSGSTRERILELLKKSG-PVSADELAEELGISPMAVRRHLDDLEAEG--LVEVERQQGGRGRPAKLY 71 (218)
T ss_pred cccCCCccHHHHHHHHHhccC-CccHHHHHHHhCCCHHHHHHHHHHHHhCc--ceeeeeccCCCCCCceee
Confidence 456778888999988887766 58999999999999999999999998764 34433 235555544
No 53
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=46.04 E-value=33 Score=29.16 Aligned_cols=41 Identities=15% Similarity=0.414 Sum_probs=36.4
Q ss_pred hhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhh
Q 010241 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (514)
Q Consensus 83 ~~~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd 124 (514)
...+|+.++.+. .++|..++|...|++...+.+.+..|.++
T Consensus 4 ~D~~il~~L~~~-~~~~~~~la~~l~~s~~tv~~~l~~L~~~ 44 (108)
T smart00344 4 IDRKILEELQKD-ARISLAELAKKVGLSPSTVHNRVKRLEEE 44 (108)
T ss_pred HHHHHHHHHHHh-CCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 446788888886 48999999999999999999999999885
No 54
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=44.05 E-value=27 Score=34.35 Aligned_cols=44 Identities=30% Similarity=0.416 Sum_probs=36.4
Q ss_pred HHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEe
Q 010241 86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEV 131 (514)
Q Consensus 86 ~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqV 131 (514)
+|++++.+.+..+|+.|+|..+||+...+-+=|..|.+ -|.|+-
T Consensus 13 ~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~~--~G~l~~ 56 (248)
T TIGR02431 13 AVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLVE--LGYVTS 56 (248)
T ss_pred HHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEe
Confidence 45677777778899999999999999999998888865 467764
No 55
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=43.54 E-value=16 Score=28.07 Aligned_cols=21 Identities=33% Similarity=0.528 Sum_probs=18.5
Q ss_pred eehhhhhhcCCCHHHHHHHHH
Q 010241 99 TIGDVAGKAGLKLNEAQKALQ 119 (514)
Q Consensus 99 TvgDVAa~aGL~l~~ae~~L~ 119 (514)
|+.|||..+|+|...+-+.|.
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln 21 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLN 21 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHT
T ss_pred CHHHHHHHHCcCHHHHHHHHh
Confidence 788999999999999977764
No 56
>PHA03242 envelope glycoprotein M; Provisional
Probab=43.45 E-value=1.5e+02 Score=32.97 Aligned_cols=31 Identities=19% Similarity=0.323 Sum_probs=22.8
Q ss_pred hhhhHhhhhHHHHHHhHhhhhhHHHHHHHHhhhh
Q 010241 411 LKFVAYIFPLLQIYAGSFFAIPAVRWFLNLQRNA 444 (514)
Q Consensus 411 i~fv~~i~PlL~~Ya~~F~aIPl~R~f~iq~rN~ 444 (514)
+....+++|+ .+++++.+=++|+++--||++
T Consensus 325 i~~~Laviai---l~l~~~vvRlvRa~~yHr~~~ 355 (428)
T PHA03242 325 VRVALALVAL---FALAMAVLRLVRAYLYHRRHR 355 (428)
T ss_pred hhhHHHHHHH---HHHHHHHHHHHHHHHHHHHhh
Confidence 3445566666 689999999999998765543
No 57
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=43.09 E-value=1.3e+02 Score=29.64 Aligned_cols=83 Identities=25% Similarity=0.246 Sum_probs=61.0
Q ss_pred HHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhc--CCceEe-ccCCcEEEEcCcchHHHHhhhhHHHhHHHH
Q 010241 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT--DGFLEV-SDEGDVLYVFPNNYRAKLAAKSFRLKVEPV 161 (514)
Q Consensus 85 ~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~--~G~LqV-se~GeIlY~FP~~fRs~l~~Ks~r~rl~~~ 161 (514)
-.+.+++...| -+|=-++|...|+.++++.+.|.+|-.+- ..+=+. .++|...|..=-+++.++ -..+.+....
T Consensus 21 ~~v~~~l~~kg-e~tDeela~~l~i~~~~vrriL~~L~e~~li~~~k~rd~~~~~~~y~w~~~~~~v~--~~l~~~~~~~ 97 (176)
T COG1675 21 VLVVDALLEKG-ELTDEELAELLGIKKNEVRRILYALYEDGLISYRKKRDEESGWEEYTWYINYEKVL--EVLKGKKRKI 97 (176)
T ss_pred hHHHHHHHhcC-CcChHHHHHHhCccHHHHHHHHHHHHhCCceEEEeecccCCCcEEEEEEechHHHH--HHHHHHHHHH
Confidence 46788999988 99999999999999999999998887664 223333 458889998877777753 3345555556
Q ss_pred HHHHhhhhH
Q 010241 162 IDKAKAAAE 170 (514)
Q Consensus 162 ~~k~w~v~~ 170 (514)
+++++..+.
T Consensus 98 le~Lk~~le 106 (176)
T COG1675 98 LEKLKRKLE 106 (176)
T ss_pred HHHHHHHHH
Confidence 666665544
No 58
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=43.00 E-value=35 Score=34.12 Aligned_cols=41 Identities=17% Similarity=0.283 Sum_probs=36.2
Q ss_pred hhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHh
Q 010241 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAA 123 (514)
Q Consensus 82 ~~~~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAs 123 (514)
.-+.+|++-+++.| ++|+.|+|..-|+|...+++.|..|..
T Consensus 7 eR~~~I~~~l~~~~-~v~v~eLa~~~~VS~~TIRRDL~~Le~ 47 (252)
T PRK10681 7 ERIGQLLQALKRSD-KLHLKDAAALLGVSEMTIRRDLNAHSA 47 (252)
T ss_pred HHHHHHHHHHHHcC-CCcHHHHHHHhCCCHHHHHHHHHHhhc
Confidence 45678899888865 499999999999999999999999884
No 59
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=40.41 E-value=1.2e+02 Score=30.65 Aligned_cols=57 Identities=12% Similarity=0.267 Sum_probs=45.3
Q ss_pred CchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhh------cCCceEeccCCcE
Q 010241 80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD------TDGFLEVSDEGDV 137 (514)
Q Consensus 80 ~~~~~~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd------~~G~LqVse~GeI 137 (514)
+..-+.+|++-|++ .+.++|.|.|..-|.|..++++.|..|+.. +||-.-.+...+.
T Consensus 3 ~~eR~~~Il~~l~~-~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~g~l~R~hGGa~~~~~~~~~ 65 (253)
T COG1349 3 KEERHQKILELLKE-KGKVSVEELAELFGVSEMTIRRDLNELEEQGLLLRVHGGAVLPDSESEY 65 (253)
T ss_pred hHHHHHHHHHHHHH-cCcEEHHHHHHHhCCCHHHHHHhHHHHHHCCcEEEEeCCEecCCCcccc
Confidence 34467788999988 568999999999999999999999999986 4555555554444
No 60
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=40.12 E-value=43 Score=33.68 Aligned_cols=42 Identities=12% Similarity=0.202 Sum_probs=37.2
Q ss_pred hhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhh
Q 010241 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (514)
Q Consensus 82 ~~~~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd 124 (514)
.-+.+|++.+++.| .+|+.|+|..-|+|..++++.|..|..+
T Consensus 5 ~R~~~Il~~l~~~~-~~~~~ela~~l~vS~~TiRRdL~~Le~~ 46 (252)
T PRK10906 5 QRHDAIIELVKQQG-YVSTEELVEHFSVSPQTIRRDLNDLAEQ 46 (252)
T ss_pred HHHHHHHHHHHHcC-CEeHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 45778899997655 7999999999999999999999999985
No 61
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=40.11 E-value=1.7e+02 Score=29.25 Aligned_cols=54 Identities=15% Similarity=0.219 Sum_probs=42.6
Q ss_pred hhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEE
Q 010241 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLY 139 (514)
Q Consensus 82 ~~~~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqVse~GeIlY 139 (514)
+-+.+|++.+++.+ .+|+.|+|..-|+|...+++.|..|.. .|.|+-. .|-.+|
T Consensus 4 ~R~~~Il~~l~~~~-~~~~~eLa~~l~VS~~TiRRdL~~L~~--~~~l~r~-~Gga~~ 57 (240)
T PRK10411 4 ARQQAIVDLLLNHT-SLTTEALAEQLNVSKETIRRDLNELQT--QGKILRN-HGRAKY 57 (240)
T ss_pred HHHHHHHHHHHHcC-CCcHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEe-cCeEEE
Confidence 34577899998765 899999999999999999999999987 3667643 344333
No 62
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=39.99 E-value=36 Score=34.25 Aligned_cols=47 Identities=15% Similarity=0.273 Sum_probs=39.3
Q ss_pred HHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccC
Q 010241 86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDE 134 (514)
Q Consensus 86 ~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqVse~ 134 (514)
.|++++.+.+...|+.|+|..+|++...+-+=|..|.+. |.|+-+++
T Consensus 29 ~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~~--G~l~~~~~ 75 (271)
T PRK10163 29 AILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQAA--DFVYQDSQ 75 (271)
T ss_pred HHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC--CCEEEcCC
Confidence 567888888888999999999999999999888888764 77766543
No 63
>PRK11569 transcriptional repressor IclR; Provisional
Probab=39.28 E-value=37 Score=34.13 Aligned_cols=46 Identities=20% Similarity=0.413 Sum_probs=38.4
Q ss_pred HHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEecc
Q 010241 86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD 133 (514)
Q Consensus 86 ~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqVse 133 (514)
+|++++.+.+..+|+.|+|..+|++...+-+=|..|.. -|.|+-++
T Consensus 32 ~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~--~G~l~~~~ 77 (274)
T PRK11569 32 KLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQ--QGFVRQVG 77 (274)
T ss_pred HHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEcC
Confidence 56777777788899999999999999999998888875 47776544
No 64
>PRK09480 slmA division inhibitor protein; Provisional
Probab=38.81 E-value=25 Score=32.09 Aligned_cols=33 Identities=18% Similarity=0.396 Sum_probs=24.9
Q ss_pred CchhhHHHHHHH----H-hcCCceeehhhhhhcCCCHH
Q 010241 80 PADVRNRAMDAV----D-ACNRRVTIGDVAGKAGLKLN 112 (514)
Q Consensus 80 ~~~~~~~im~av----e-~~g~rvTvgDVAa~aGL~l~ 112 (514)
+.+.+++|++|. . +.|..+|+.|||.++|++..
T Consensus 8 ~~~~r~~Il~aa~~l~~~~~G~~~ti~~Ia~~agvs~g 45 (194)
T PRK09480 8 KGERREQILQALAQMLESPPGERITTAKLAARVGVSEA 45 (194)
T ss_pred chhHHHHHHHHHHHHHHhcCCCccCHHHHHHHhCCCHh
Confidence 345677887773 3 33689999999999999653
No 65
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=38.10 E-value=32 Score=24.64 Aligned_cols=37 Identities=19% Similarity=0.328 Sum_probs=30.6
Q ss_pred CCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEecc
Q 010241 95 NRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD 133 (514)
Q Consensus 95 g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqVse 133 (514)
...+|+.|+|...|++...+.+.|..|.+ .|.|+...
T Consensus 6 ~~~~s~~~la~~l~~s~~tv~~~l~~L~~--~g~l~~~~ 42 (48)
T smart00419 6 RLPLTRQEIAELLGLTRETVSRTLKRLEK--EGLISREG 42 (48)
T ss_pred EeccCHHHHHHHHCCCHHHHHHHHHHHHH--CCCEEEeC
Confidence 34678899999999999999999999987 46666543
No 66
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=37.90 E-value=1.4e+02 Score=29.53 Aligned_cols=45 Identities=13% Similarity=0.269 Sum_probs=35.0
Q ss_pred HHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEecc
Q 010241 86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD 133 (514)
Q Consensus 86 ~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqVse 133 (514)
+|++++.+. ..+|+.|+|..+|++...+-+=|..|.. -|.|+-++
T Consensus 18 ~IL~~l~~~-~~l~l~eia~~lgl~kstv~Rll~tL~~--~G~l~~~~ 62 (257)
T PRK15090 18 GILQALGEE-REIGITELSQRVMMSKSTVYRFLQTMKT--LGYVAQEG 62 (257)
T ss_pred HHHHHhhcC-CCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEcC
Confidence 456666554 4699999999999999999988888875 46776543
No 67
>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=37.49 E-value=64 Score=25.83 Aligned_cols=32 Identities=22% Similarity=0.267 Sum_probs=28.4
Q ss_pred hcCCceeehhhhhhcCCCHHHHHHHHHHHHhh
Q 010241 93 ACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (514)
Q Consensus 93 ~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd 124 (514)
+.+..|+..|+|...|++...|-..|..|+.+
T Consensus 18 ~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~ 49 (60)
T PF01325_consen 18 EEGGPVRTKDIAERLGVSPPTVTEMLKRLAEK 49 (60)
T ss_dssp HCTSSBBHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred cCCCCccHHHHHHHHCCChHHHHHHHHHHHHC
Confidence 37899999999999999999999999999864
No 68
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=37.29 E-value=76 Score=31.12 Aligned_cols=56 Identities=20% Similarity=0.261 Sum_probs=42.8
Q ss_pred HHHHHHHHhc-CC-ceeehhhhhhcCCCHHHHHHHHHHHHhhcC---CceEeccCCcEEEEc
Q 010241 85 NRAMDAVDAC-NR-RVTIGDVAGKAGLKLNEAQKALQALAADTD---GFLEVSDEGDVLYVF 141 (514)
Q Consensus 85 ~~im~ave~~-g~-rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~---G~LqVse~GeIlY~F 141 (514)
+++++|+-=. |- .+|+.++|...|++..+++..|..|..+|. .-+++.+.|+- |.|
T Consensus 6 ~~~iEA~LF~sg~pgls~~~La~~l~~~~~~v~~~l~~L~~~y~~~~~gi~i~~~~~~-y~l 66 (188)
T PRK00135 6 KSIIEALLFVSGEEGLSLEQLAEILELEPTEVQQLLEELQEKYEGDDRGLKLIEFNDV-YKL 66 (188)
T ss_pred HHHHHHHHHHcCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhhCCCCEEEEEECCE-EEE
Confidence 3445555444 55 499999999999999999999999999984 34777776654 665
No 69
>PHA01815 hypothetical protein
Probab=37.13 E-value=1.5e+02 Score=23.76 Aligned_cols=26 Identities=19% Similarity=0.215 Sum_probs=16.8
Q ss_pred HHHHHHHHhhhhHHHHHHHHHHHHHH
Q 010241 158 VEPVIDKAKAAAEYSIRVLFGTALIA 183 (514)
Q Consensus 158 l~~~~~k~w~v~~yliRVsFG~~LIa 183 (514)
+-+|+-.+--....-+|||||+....
T Consensus 12 llaflitliilmt~~irvsfgvlftt 37 (55)
T PHA01815 12 LLAFLITLIILMTLHIRVSFGVLFTT 37 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444445555667789999987644
No 70
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=36.96 E-value=46 Score=33.31 Aligned_cols=42 Identities=14% Similarity=0.219 Sum_probs=37.2
Q ss_pred hhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhh
Q 010241 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (514)
Q Consensus 82 ~~~~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd 124 (514)
.-+.+|++.+++ .+.+|+.|+|...|+|...+++.|..|...
T Consensus 5 ~R~~~Il~~l~~-~~~~~~~ela~~l~vS~~TirRdL~~Le~~ 46 (251)
T PRK13509 5 QRHQILLELLAQ-LGFVTVEKVIERLGISPATARRDINKLDES 46 (251)
T ss_pred HHHHHHHHHHHH-cCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 456788999986 678999999999999999999999999763
No 71
>PHA02943 hypothetical protein; Provisional
Probab=36.70 E-value=2e+02 Score=28.25 Aligned_cols=60 Identities=22% Similarity=0.279 Sum_probs=46.2
Q ss_pred hhHHHHHHHHh-cCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcCcc
Q 010241 83 VRNRAMDAVDA-CNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNN 144 (514)
Q Consensus 83 ~~~~im~ave~-~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqVse~GeIlY~FP~~ 144 (514)
+.+|+.+.+|= ..+-.|..+||-..|+|-.+|+-.|.-|..+ |.++--+-|-..|.+=.+
T Consensus 9 v~~R~~eILE~Lk~G~~TtseIAkaLGlS~~qa~~~LyvLErE--G~VkrV~~G~~tyw~l~~ 69 (165)
T PHA02943 9 VHTRMIKTLRLLADGCKTTSRIANKLGVSHSMARNALYQLAKE--GMVLKVEIGRAAIWCLDE 69 (165)
T ss_pred HHHHHHHHHHHHhcCCccHHHHHHHHCCCHHHHHHHHHHHHHc--CceEEEeecceEEEEECh
Confidence 44566666665 4555779999999999999999999888765 666666799888888543
No 72
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=36.54 E-value=44 Score=33.34 Aligned_cols=48 Identities=21% Similarity=0.401 Sum_probs=38.0
Q ss_pred HHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEecc-CC
Q 010241 86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD-EG 135 (514)
Q Consensus 86 ~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqVse-~G 135 (514)
+|++++...+..+|+.|+|...|++...+-+-|..|.. -|.|+-++ +|
T Consensus 15 ~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~~--~g~v~~~~~~~ 63 (263)
T PRK09834 15 MVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQE--EGYVRRSASDD 63 (263)
T ss_pred HHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEecCCC
Confidence 35666666677799999999999999999999999875 47776554 44
No 73
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=36.41 E-value=17 Score=27.47 Aligned_cols=29 Identities=34% Similarity=0.367 Sum_probs=23.6
Q ss_pred HHHHHHHHHHhcCCeEeeeeccCccCCCC
Q 010241 272 RWKLIGEYIASNGGVVTAEELAPYLDIDR 300 (514)
Q Consensus 272 RWk~Ig~~Ir~N~GvV~AEQLAPyLD~~~ 300 (514)
|++.|-.++.++++-|+++|||-.|+...
T Consensus 1 R~~~il~~L~~~~~~it~~eLa~~l~vS~ 29 (55)
T PF08279_consen 1 RQKQILKLLLESKEPITAKELAEELGVSR 29 (55)
T ss_dssp HHHHHHHHHHHTTTSBEHHHHHHHCTS-H
T ss_pred CHHHHHHHHHHcCCCcCHHHHHHHhCCCH
Confidence 67788888877777799999999999863
No 74
>COG3695 Predicted methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]
Probab=35.87 E-value=51 Score=29.98 Aligned_cols=60 Identities=25% Similarity=0.358 Sum_probs=46.4
Q ss_pred chhhHHHHHHHHhc--CCceeehhhhhhcCCC--HHHHHHHHHHHHhhc--CCceEeccCCcEEEE
Q 010241 81 ADVRNRAMDAVDAC--NRRVTIGDVAGKAGLK--LNEAQKALQALAADT--DGFLEVSDEGDVLYV 140 (514)
Q Consensus 81 ~~~~~~im~ave~~--g~rvTvgDVAa~aGL~--l~~ae~~L~aLAsd~--~G~LqVse~GeIlY~ 140 (514)
.+.++++.+.|.+. |+-.|-||||.-+|++ ..++-+.|..|-.++ .-|=-|+..|.|--.
T Consensus 5 def~~~v~~vv~~IP~GkV~TYGdIA~laG~p~~ARqVG~il~~l~~~s~lPWhRVvns~G~isl~ 70 (103)
T COG3695 5 DEFTQRVLDVVAAIPEGKVSTYGDIAKLAGLPRAARQVGRILKHLPEGSDLPWHRVVNSDGRISLP 70 (103)
T ss_pred hHHHHHHHHHHHhCCCCceeeHHHHHHHhCCChhHHHHHHHHhhCCCCCCCChhheecCCCcccCC
Confidence 35677888888875 6778999999999998 778877787665444 777778888887543
No 75
>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=35.63 E-value=55 Score=25.29 Aligned_cols=45 Identities=18% Similarity=0.352 Sum_probs=34.0
Q ss_pred HHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEe
Q 010241 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEV 131 (514)
Q Consensus 85 ~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqV 131 (514)
-.+|..+...+...|+.|+|...|++...+-+.|..|... |-|+-
T Consensus 6 ~~vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~--glv~~ 50 (68)
T PF13463_consen 6 WQVLRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLEEK--GLVEK 50 (68)
T ss_dssp HHHHHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHHHT--TSEEE
T ss_pred HHHHHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC--CCEEe
Confidence 3567888888899999999999999999999999999876 66643
No 76
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=35.13 E-value=72 Score=24.21 Aligned_cols=39 Identities=15% Similarity=0.251 Sum_probs=33.5
Q ss_pred HHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhh
Q 010241 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (514)
Q Consensus 85 ~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd 124 (514)
=.+|..+.+.|+ +|+.|+|...|++...+-+.+..|..+
T Consensus 6 ~~iL~~l~~~~~-~~~~~la~~~~~~~~~~t~~i~~L~~~ 44 (59)
T PF01047_consen 6 FRILRILYENGG-ITQSELAEKLGISRSTVTRIIKRLEKK 44 (59)
T ss_dssp HHHHHHHHHHSS-EEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHHHcCC-CCHHHHHHHHCCChhHHHHHHHHHHHC
Confidence 357888998888 999999999999999999999888764
No 77
>PF03297 Ribosomal_S25: S25 ribosomal protein; InterPro: IPR004977 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S25 ribosomal protein is a component of the 40S ribosomal subunit.; PDB: 2XZM_8 2XZN_8 3O30_Q 3U5G_Z 3IZB_V 3U5C_Z 3O2Z_Q 3IZ6_V.
Probab=34.80 E-value=61 Score=29.33 Aligned_cols=57 Identities=14% Similarity=0.115 Sum_probs=39.6
Q ss_pred hhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEE
Q 010241 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYV 140 (514)
Q Consensus 83 ~~~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqVse~GeIlY~ 140 (514)
.=+++.+-|-+. .-+|+.-||.+-+++...|+++|..|++.--=.+=+-..+-.||.
T Consensus 46 ~~~kl~kEV~~~-K~ITp~~lserlkI~~SlAr~~Lr~L~~kG~Ik~V~k~~~~~IYt 102 (105)
T PF03297_consen 46 TYDKLLKEVPKM-KLITPSVLSERLKINGSLARKALRELESKGLIKPVSKHHRQRIYT 102 (105)
T ss_dssp HHHHHHHHCTTS-SCECHHHHHHHHCCSCHHHHHHHHHHHHCCSSEEEECCTTCEEEE
T ss_pred HHHHHHHHhccC-cEeeHHHHHHhHhhHHHHHHHHHHHHHHCCCEEEEeccCCeEEEe
Confidence 334444433333 459999999999999999999999999864333334445666664
No 78
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=34.61 E-value=26 Score=34.82 Aligned_cols=25 Identities=32% Similarity=0.468 Sum_probs=22.5
Q ss_pred CCceeehhhhhhcCCCHHHHHHHHH
Q 010241 95 NRRVTIGDVAGKAGLKLNEAQKALQ 119 (514)
Q Consensus 95 g~rvTvgDVAa~aGL~l~~ae~~L~ 119 (514)
..++|+.|||..+|+|..++-++|.
T Consensus 4 ~~~~Ti~dIA~~agVS~~TVSr~Ln 28 (342)
T PRK10014 4 AKKITIHDVALAAGVSVSTVSLVLS 28 (342)
T ss_pred CCCCcHHHHHHHhCCCHHHHHHHHC
Confidence 4579999999999999999998885
No 79
>COG2846 Regulator of cell morphogenesis and NO signaling [Cell division and chromosome partitioning]
Probab=34.37 E-value=29 Score=35.00 Aligned_cols=32 Identities=31% Similarity=0.606 Sum_probs=29.9
Q ss_pred cCCceeehhhhhhcCCCHHHHHHHHHHHHhhc
Q 010241 94 CNRRVTIGDVAGKAGLKLNEAQKALQALAADT 125 (514)
Q Consensus 94 ~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~ 125 (514)
||+.+|+.+.|.+.|+.+++.++.|.+|....
T Consensus 31 CGG~~~L~~Aa~~k~l~~~~i~a~L~~l~~~~ 62 (221)
T COG2846 31 CGGKVTLERAAAEKGLDIDEIEARLNALQQEP 62 (221)
T ss_pred cCChHHHHHHHHHcCCCHHHHHHHHHHHHhcc
Confidence 79999999999999999999999999998754
No 80
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=34.11 E-value=58 Score=30.94 Aligned_cols=48 Identities=25% Similarity=0.439 Sum_probs=39.3
Q ss_pred hhhHHHHHHHHh----cCCceeehhhhhhcCCC-HHHHHHHHHHHHhhcCCceEe
Q 010241 82 DVRNRAMDAVDA----CNRRVTIGDVAGKAGLK-LNEAQKALQALAADTDGFLEV 131 (514)
Q Consensus 82 ~~~~~im~ave~----~g~rvTvgDVAa~aGL~-l~~ae~~L~aLAsd~~G~LqV 131 (514)
+.+.+|++.+.+ .|+..|+.|+|...|++ ...+...|..|..+ |.|+-
T Consensus 6 ~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~~--g~i~~ 58 (199)
T TIGR00498 6 ARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALERK--GYIER 58 (199)
T ss_pred HHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHHHC--CCEec
Confidence 456677777764 57779999999999998 99999999999876 66653
No 81
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=34.05 E-value=51 Score=32.96 Aligned_cols=47 Identities=21% Similarity=0.381 Sum_probs=38.3
Q ss_pred HHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccC
Q 010241 86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDE 134 (514)
Q Consensus 86 ~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqVse~ 134 (514)
+|++++.+.+..+|+.|+|.++|++.+.+-+=|..|.. -|-++-+++
T Consensus 8 ~iL~~l~~~~~~l~l~ela~~~glpksT~~RlL~tL~~--~G~v~~d~~ 54 (246)
T COG1414 8 AILDLLAEGPGGLSLAELAERLGLPKSTVHRLLQTLVE--LGYVEQDPE 54 (246)
T ss_pred HHHHHHHhCCCCCCHHHHHHHhCcCHHHHHHHHHHHHH--CCCEEEcCC
Confidence 57888888666689999999999999999998888865 466665553
No 82
>PLN03083 E3 UFM1-protein ligase 1 homolog; Provisional
Probab=34.04 E-value=57 Score=38.69 Aligned_cols=62 Identities=21% Similarity=0.358 Sum_probs=48.4
Q ss_pred CchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcCcchHH
Q 010241 80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRA 147 (514)
Q Consensus 80 ~~~~~~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqVse~GeIlY~FP~~fRs 147 (514)
|..++..|++-+. .|+||.+-|++..-|+.++-.|+.+..++.+- .++.. ..|||+ ..+|=.
T Consensus 58 ~~qL~~EI~~El~-~gGRvnlvdLa~~LnVD~~hiEr~~~~iv~~d-~~~~l-~~GeLi---t~~Yld 119 (803)
T PLN03083 58 QDQLRNEIEAEIK-KLGRVSLVDLADTIGVDLYHVERQAQQVVSDD-PGLML-VQGEII---SQSYWD 119 (803)
T ss_pred HHHHHHHHHHHHH-hCCCeeHHHHhhhcCCCHHHHHHHHHHHhcCC-CceEE-ecCEec---chHHHH
Confidence 4457788888885 58999999999999999999999999998885 44443 467764 445533
No 83
>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional
Probab=33.86 E-value=52 Score=32.56 Aligned_cols=42 Identities=14% Similarity=0.262 Sum_probs=37.7
Q ss_pred hhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhh
Q 010241 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (514)
Q Consensus 83 ~~~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd 124 (514)
--.+|.+.+.+.|-++|.-++|.+-|++..++.+.|-.|-..
T Consensus 5 ~~~~i~~~l~~~~~~~~a~~i~k~l~i~k~~vNr~LY~L~~~ 46 (183)
T PHA02701 5 CASLILTLLSSSGDKLPAKRIAKELGISKHEANRCLYRLLES 46 (183)
T ss_pred HHHHHHHHHHhcCCCCcHHHHHHHhCccHHHHHHHHHHHhhc
Confidence 346899999999977999999999999999999999998653
No 84
>PRK11463 fxsA phage T7 F exclusion suppressor FxsA; Reviewed
Probab=32.92 E-value=56 Score=30.90 Aligned_cols=39 Identities=15% Similarity=0.252 Sum_probs=25.1
Q ss_pred hhhHhhhhHHHHHH-hHhhhhhHHHHHHHHhhhhhHHHhh
Q 010241 412 KFVAYIFPLLQIYA-GSFFAIPAVRWFLNLQRNADIEKRN 450 (514)
Q Consensus 412 ~fv~~i~PlL~~Ya-~~F~aIPl~R~f~iq~rN~~I~~RN 450 (514)
+-++-++|-.++=. .+.+.+|..|.++.+.=++++.+|.
T Consensus 80 gg~LLi~PGf~tD~~Gllll~P~~R~~~~~~l~~~~~~~~ 119 (148)
T PRK11463 80 AGVLLLLPGFVTDILGLLLLLPPTRALLRPKLMKRLRRKR 119 (148)
T ss_pred HHHHHHccHHHHHHHHHHHHcchhHHHHHHHHHHHHHHHH
Confidence 33455566554433 3456789999999887776665555
No 85
>PRK10992 iron-sulfur cluster repair di-iron protein; Provisional
Probab=32.70 E-value=39 Score=33.62 Aligned_cols=42 Identities=21% Similarity=0.334 Sum_probs=35.0
Q ss_pred HHHHHHHHh------cCCceeehhhhhhcCCCHHHHHHHHHHHHhhcC
Q 010241 85 NRAMDAVDA------CNRRVTIGDVAGKAGLKLNEAQKALQALAADTD 126 (514)
Q Consensus 85 ~~im~ave~------~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~ 126 (514)
|+..+.+++ +|+..|+++++.+.|++.++.-.+|.++++...
T Consensus 16 p~~~~vf~~~~idfCcgG~~~l~ea~~~~~i~~~~~~~~l~~~~~~~~ 63 (220)
T PRK10992 16 PRATALFREYDLDFCCGGKQTLARAAARKNLDIDVIEARLAALQEQPI 63 (220)
T ss_pred ccHHHHHHHcCCcccCCCCchHHHHHHHcCCCHHHHHHHHHHHHhccc
Confidence 445556666 578999999999999999999999999986663
No 86
>PF01316 Arg_repressor: Arginine repressor, DNA binding domain; InterPro: IPR020900 The arginine dihydrolase (AD) pathway is found in many prokaryotes and some primitive eukaryotes, an example of the latter being Giardia lamblia (Giardia intestinalis) []. The three-enzyme anaerobic pathway breaks down L-arginine to form 1 mol of ATP, carbon dioxide and ammonia. In simpler bacteria, the first enzyme, arginine deiminase, can account for up to 10% of total cell protein []. Most prokaryotic arginine deiminase pathways are under the control of a repressor gene, termed ArgR []. This is a negative regulator, and will only release the arginine deiminase operon for expression in the presence of arginine []. The crystal structure of apo-ArgR from Bacillus stearothermophilus has been determined to 2.5A by means of X-ray crystallography []. The protein exists as a hexamer of identical subunits, and is shown to have six DNA-binding domains, clustered around a central oligomeric core when bound to arginine. It predominantly interacts with A.T residues in ARG boxes. This hexameric protein binds DNA at its N terminus to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbour-joining tree, some of these paralogous sequences show long branches and differ significantly from the well-conserved C-terminal region. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0006525 arginine metabolic process; PDB: 1AOY_A 3V4G_A 3LAJ_D 3FHZ_A 3LAP_B 3ERE_D 2P5L_C 1F9N_D 2P5K_A 1B4A_A ....
Probab=32.18 E-value=1.1e+02 Score=25.61 Aligned_cols=46 Identities=22% Similarity=0.455 Sum_probs=30.2
Q ss_pred hhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEec-cCCcEEEEcCcc
Q 010241 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVS-DEGDVLYVFPNN 144 (514)
Q Consensus 83 ~~~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqVs-e~GeIlY~FP~~ 144 (514)
.++.+++.+++.|..||.+-|+ +.|..| |-..|. ++|.-+|..|.+
T Consensus 21 sQ~eL~~~L~~~Gi~vTQaTiS-----------RDLkeL-----~~vKv~~~~g~~~Y~l~~~ 67 (70)
T PF01316_consen 21 SQEELVELLEEEGIEVTQATIS-----------RDLKEL-----GAVKVPDGNGKYRYVLPEE 67 (70)
T ss_dssp SHHHHHHHHHHTT-T--HHHHH-----------HHHHHH-----T-EEEECTTSSEEEE-TTS
T ss_pred CHHHHHHHHHHcCCCcchhHHH-----------HHHHHc-----CcEEeeCCCCCEEEEecCc
Confidence 4678888888888888877665 444444 445666 799999999974
No 87
>cd06445 ATase The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases are specific for repair of guanines with O6-alkyl adducts, however human ATase is not limited to O6-methylguanine, repairing many other adducts at the O6-position of guanine as well. ATase is widely distributed among species. Most ATases have N- and C-terminal domains. The C-terminal domain contains the conserved active-site cysteine motif (PCHR), the O6-alkylguanine binding channel, and the helix-turn-helix (HTH) DNA-binding motif. The active site is located near the recognition helix of the HTH motif. While the C-terminal domain of ATase contains residues that are necessary for DNA binding and alkyl transfer, the function of the N-terminal domain is still unknown. Removal of the N-terminal domain abolishes the activity of
Probab=32.15 E-value=70 Score=26.68 Aligned_cols=55 Identities=20% Similarity=0.175 Sum_probs=42.8
Q ss_pred hHHHHHHHHh--cCCceeehhhhhhcCC--CHHHHHHHHHHHHh--hcCCceEeccCCcEE
Q 010241 84 RNRAMDAVDA--CNRRVTIGDVAGKAGL--KLNEAQKALQALAA--DTDGFLEVSDEGDVL 138 (514)
Q Consensus 84 ~~~im~ave~--~g~rvTvgDVAa~aGL--~l~~ae~~L~aLAs--d~~G~LqVse~GeIl 138 (514)
+.++.++|.+ .|.-+|-||||...|. ....+-.+|.+.-. +..+|==|+.+|.+.
T Consensus 2 ~~~V~~~v~~IP~G~v~TYg~iA~~~g~p~~~R~Vg~al~~np~~~~vP~HRVv~~~g~~~ 62 (79)
T cd06445 2 QRRVWEALRQIPYGEVTTYGQIAKLAGTPKAARAVGSALARNPIPILIPCHRVVRSDGGLG 62 (79)
T ss_pred HHHHHHHHhcCCCCCcCcHHHHHHHHCCCCcHHHHHHHHHhCCCCCCCCceeEECCCCCcC
Confidence 4567777776 5677899999999999 46677777766654 678998899988876
No 88
>PF03640 Lipoprotein_15: Secreted repeat of unknown function; InterPro: IPR005297 This repeat is found in tandem in a set of lipoproteins. The alignment contains a Y-X4-D motif.
Probab=31.63 E-value=23 Score=27.57 Aligned_cols=22 Identities=36% Similarity=0.569 Sum_probs=19.2
Q ss_pred hhhcCCccccCCCCCEEEecCc
Q 010241 312 LLRFDGQPEIDEEGNILYRFPS 333 (514)
Q Consensus 312 L~rF~G~PeVse~G~IVY~FPe 333 (514)
..+-||...++.+|..||+|..
T Consensus 4 v~~~dG~~~~~~~G~~LY~f~~ 25 (48)
T PF03640_consen 4 VTRADGTIQVDYNGMPLYYFDK 25 (48)
T ss_pred EEeCCCCEEECCCCCEEEEECC
Confidence 4567899999999999999974
No 89
>PF05331 DUF742: Protein of unknown function (DUF742); InterPro: IPR007995 This family consists of several uncharacterised Streptomyces proteins as well as one from Mycobacterium tuberculosis. The function of these proteins is unknown.
Probab=31.52 E-value=59 Score=29.73 Aligned_cols=48 Identities=21% Similarity=0.467 Sum_probs=34.9
Q ss_pred hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhc--CCceEeccCC
Q 010241 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT--DGFLEVSDEG 135 (514)
Q Consensus 84 ~~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~--~G~LqVse~G 135 (514)
.+.--+.++-|....+|+|||+..+|++..++ -|++|- .|++.|....
T Consensus 42 ~pE~~~Il~lC~~~~SVAEiAA~L~lPlgVvr----VLvsDL~~~G~v~v~~p~ 91 (114)
T PF05331_consen 42 GPEHRAILELCRRPLSVAEIAARLGLPLGVVR----VLVSDLADAGLVRVRAPA 91 (114)
T ss_pred CHHHHHHHHHHCCCccHHHHHHhhCCCchhhh----hhHHHHHhCCCEEEeCCC
Confidence 34444445555669999999999999999984 444554 7899987654
No 90
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=31.22 E-value=52 Score=29.89 Aligned_cols=43 Identities=21% Similarity=0.190 Sum_probs=35.5
Q ss_pred hhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhh
Q 010241 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (514)
Q Consensus 82 ~~~~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd 124 (514)
+++..|+.+...-|..+++.++|...|+|..-+++.|..|..+
T Consensus 10 Al~~~i~la~~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~~ 52 (141)
T PRK11014 10 GLRALIYMASLPEGRMTSISEVTEVYGVSRNHMVKIINQLSRA 52 (141)
T ss_pred HHHHHHHHhcCCCCCccCHHHHHHHHCcCHHHHHHHHHHHHhC
Confidence 4556666666566778999999999999999999999999874
No 91
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=30.91 E-value=1.9e+02 Score=31.82 Aligned_cols=87 Identities=17% Similarity=0.202 Sum_probs=54.5
Q ss_pred HhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCc-----EEEEcCcchHHHHhhhhHHHhHHHHHHHHh
Q 010241 92 DACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGD-----VLYVFPNNYRAKLAAKSFRLKVEPVIDKAK 166 (514)
Q Consensus 92 e~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqVse~Ge-----IlY~FP~~fRs~l~~Ks~r~rl~~~~~k~w 166 (514)
.++|...|+.++|...|+++++.+..|.....-..-+..|.+++| ++-....+--..+.....+..++.+++.+.
T Consensus 273 ~~lgR~pt~~EiA~~l~is~~~vr~~l~~~~~~~SLd~~vg~~~d~~l~d~l~~~~~~pee~~~~~~l~~~L~~~L~~L~ 352 (415)
T PRK07598 273 QEKGRTPTIEDIAQELEMTPTQVREVLLRVPRSVSLETKVGKDKDTELGDLLETDDISPEEMLMRESLQRDLQHLLADLT 352 (415)
T ss_pred HHhCCCCCHHHHHHHhCCCHHHHHHHHHHccCCcccccccCCCccccHHHhccCCCCCHHHHHHHHHHHHHHHHHHHhCC
Confidence 457888999999999999999998776653322233333443433 221111122233334456667888888777
Q ss_pred hhhHHHHHHHHH
Q 010241 167 AAAEYSIRVLFG 178 (514)
Q Consensus 167 ~v~~yliRVsFG 178 (514)
.-=.-+|+..||
T Consensus 353 ~reR~VI~LRyg 364 (415)
T PRK07598 353 SRERDVIRMRFG 364 (415)
T ss_pred HHHHHHHHHHHh
Confidence 776777777776
No 92
>TIGR00589 ogt O-6-methylguanine DNA methyltransferase. All proteins in this family for which functions are known are involved alkyl-DNA transferases which remove alkyl groups from DNA as part of alkylation DNA repair. Some of the proteins in this family are also transcription regulators and have a distinct transcription regulatory domain. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=30.53 E-value=97 Score=26.38 Aligned_cols=57 Identities=14% Similarity=0.123 Sum_probs=41.9
Q ss_pred hhhHHHHHHHHhc--CCceeehhhhhhcCCCH--HHHHHHHHHH--HhhcCCceEeccCCcEE
Q 010241 82 DVRNRAMDAVDAC--NRRVTIGDVAGKAGLKL--NEAQKALQAL--AADTDGFLEVSDEGDVL 138 (514)
Q Consensus 82 ~~~~~im~ave~~--g~rvTvgDVAa~aGL~l--~~ae~~L~aL--Asd~~G~LqVse~GeIl 138 (514)
+.+.++.+++.+- |.-+|-||+|...|.+- ..+-.+|... .-...+|==|+.+|.+-
T Consensus 2 ~f~~~V~~~l~~IP~G~v~TYg~iA~~~g~p~~~RaVg~al~~np~~~~iPcHRVv~s~G~l~ 64 (80)
T TIGR00589 2 PFQQRVWQALRTIPYGETKSYGQLAARIGNPKAVRAVGGANGRNPLAILVPCHRVIGKNGSLT 64 (80)
T ss_pred hHHHHHHHHHhCCCCCCcCCHHHHHHHhCCCChHHHHHHHHHhCCCCCCCCCceeECCCCCCC
Confidence 4678899999987 66788899999999753 3333333332 22578999999999975
No 93
>PF01035 DNA_binding_1: 6-O-methylguanine DNA methyltransferase, DNA binding domain; InterPro: IPR014048 Synonym(s): 6-O-methylguanine-DNA methyltransferase, O-6-methylguanine-DNA-alkyltransferase This entry represents the DNA binding region of 6-O-methylguanine-DNA methyltransferases. The repair of DNA containing O6-alkylated guanine is carried out by DNA-[protein]-cysteine S-methyltransferase (2.1.1.63 from EC). The major mutagenic and carcinogenic effect of methylating agents in DNA is the formation of O6-alkylguanine. The alkyl group at the O-6 position is transferred to a cysteine residue in the enzyme []. This is a suicide reaction since the enzyme is irreversibly inactivated and the methylated protein accumulates as a dead-end product. Most, but not all of the methyltransferases are also able to repair O-4-methylthymine. DNA-[protein]-cysteine S-methyltransferases are widely distributed and are found in various prokaryotic and eukaryotic sources [].; GO: 0003824 catalytic activity, 0006281 DNA repair; PDB: 1SFE_A 1T39_B 1T38_A 1EH7_A 1EH6_A 1YFH_C 1EH8_A 1QNT_A 2KIM_A 2KIF_A ....
Probab=30.45 E-value=62 Score=27.52 Aligned_cols=57 Identities=19% Similarity=0.207 Sum_probs=44.5
Q ss_pred hhhHHHHHHHHhcC--CceeehhhhhhcC--CCHHHHHHHHHH--HHhhcCCceEeccCCcEE
Q 010241 82 DVRNRAMDAVDACN--RRVTIGDVAGKAG--LKLNEAQKALQA--LAADTDGFLEVSDEGDVL 138 (514)
Q Consensus 82 ~~~~~im~ave~~g--~rvTvgDVAa~aG--L~l~~ae~~L~a--LAsd~~G~LqVse~GeIl 138 (514)
+.+.++.+++.+.. .-+|-||||..+| -....+-.+|.. +.....+|==|+.+|.+-
T Consensus 2 ~f~~~V~~~v~~IP~G~v~TYg~iA~~~g~p~~ar~Vg~al~~np~~~~iP~HRVv~~~G~l~ 64 (85)
T PF01035_consen 2 PFQRRVWEAVRQIPYGKVTTYGEIARLLGRPKAARAVGSALARNPIPIIIPCHRVVNSDGSLG 64 (85)
T ss_dssp HHHHHHHHHHTTS-TT-BEEHHHHHHHTT-TTCHHHHHHHHHTSSCTTTSGGGGEEBTTSBEC
T ss_pred hHHHHHHHHHHcCCCCceEeHHHHHHHHhhcccHHHHHHHhccccccCCCCeEEEECCCCCcC
Confidence 46778888888865 5688899999999 666677777766 556779999999999975
No 94
>PF04157 EAP30: EAP30/Vps36 family; InterPro: IPR007286 EAP30 is a subunit of the ELL complex. The ELL is an 80kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity. ; PDB: 2ZME_A 3CUQ_A 1W7P_D 1U5T_B.
Probab=30.29 E-value=63 Score=31.79 Aligned_cols=42 Identities=24% Similarity=0.374 Sum_probs=35.5
Q ss_pred hhhHHHHHHH-HhcCCceeehhhhhhcCCCHHHHHHHHHHHHh
Q 010241 82 DVRNRAMDAV-DACNRRVTIGDVAGKAGLKLNEAQKALQALAA 123 (514)
Q Consensus 82 ~~~~~im~av-e~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAs 123 (514)
....+|++.+ +..++.+|+.++|...|.+..-|+..|..+..
T Consensus 174 ~~~~~il~~~~~~~~g~vt~~~l~~~~~ws~~~a~~~L~~~~~ 216 (223)
T PF04157_consen 174 KDQSRILELAEEENGGGVTASELAEKLGWSVERAKEALEELER 216 (223)
T ss_dssp HHHHHHHHHH--TTTSEEEHHHHHHHHTB-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHh
Confidence 6668889988 88899999999999999999999999988554
No 95
>PRK11050 manganese transport regulator MntR; Provisional
Probab=29.84 E-value=3.5e+02 Score=25.13 Aligned_cols=55 Identities=22% Similarity=0.329 Sum_probs=41.1
Q ss_pred HHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcCc
Q 010241 85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPN 143 (514)
Q Consensus 85 ~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqVse~GeIlY~FP~ 143 (514)
..|+.++.. +...|+.|+|...|++...+.+.|..|-++ |-++....+ -++.-+.
T Consensus 40 ~~I~~~l~~-~~~~t~~eLA~~l~is~stVsr~l~~Le~~--GlI~r~~~~-~v~LT~~ 94 (152)
T PRK11050 40 ELIADLIAE-VGEARQVDIAARLGVSQPTVAKMLKRLARD--GLVEMRPYR-GVFLTPE 94 (152)
T ss_pred HHHHHHHHh-cCCCCHHHHHHHHCCCHHHHHHHHHHHHHC--CCEEEecCC-ceEECch
Confidence 455666765 567999999999999999999999999986 677654432 3444444
No 96
>PF06224 HTH_42: Winged helix DNA-binding domain; InterPro: IPR009351 This is a family of conserved bacterial proteins with unknown function.
Probab=29.51 E-value=1e+02 Score=31.24 Aligned_cols=57 Identities=30% Similarity=0.411 Sum_probs=42.6
Q ss_pred HHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccC-CcE-EEEcCcch
Q 010241 87 AMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDE-GDV-LYVFPNNY 145 (514)
Q Consensus 87 im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqVse~-GeI-lY~FP~~f 145 (514)
+-..+...| -+|+.|+|.-+||+..+++++|..|.+ .|.=.+|+-+ |.- .|.-|.+-
T Consensus 172 v~Ryl~~~G-Pat~~d~a~w~gl~~~~~r~~l~~l~~-~~~L~~v~~~~G~~~~~~~~~~~ 230 (327)
T PF06224_consen 172 VRRYLRAYG-PATLADFAWWSGLPKTQARRALAQLVE-EGELVEVEVEGGKEPLYDLPEDL 230 (327)
T ss_pred HHHHHHHcC-CccHHHHHHHhccCHHHHHHHHHhhcc-CCcEEEEEEcCcceeEEechhhh
Confidence 344555555 899999999999999999998877764 3344566666 776 88888754
No 97
>PF15145 DUF4577: Domain of unknown function (DUF4577)
Probab=29.32 E-value=24 Score=32.66 Aligned_cols=27 Identities=26% Similarity=0.242 Sum_probs=21.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 010241 173 IRVLFGTALIASIVIVFTAIIAILSSK 199 (514)
Q Consensus 173 iRVsFG~~LIaSivlv~~aIiailss~ 199 (514)
|=|.+.++||+|+++|...|+.|+--+
T Consensus 63 ffvglii~LivSLaLVsFvIFLiiQTg 89 (128)
T PF15145_consen 63 FFVGLIIVLIVSLALVSFVIFLIIQTG 89 (128)
T ss_pred hHHHHHHHHHHHHHHHHHHHHheeecc
Confidence 337889999999999999998876443
No 98
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=28.69 E-value=65 Score=25.64 Aligned_cols=52 Identities=21% Similarity=0.260 Sum_probs=38.5
Q ss_pred ceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcCcchHHHHh
Q 010241 97 RVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLA 150 (514)
Q Consensus 97 rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqVse~GeIlY~FP~~fRs~l~ 150 (514)
.++..++..-.|+++.. .++..+....|...+.+++++.+.+.++-||.=+.
T Consensus 5 ~~~~~~i~~llG~~i~~--~ei~~~L~~lg~~~~~~~~~~~~~v~~P~~R~Di~ 56 (71)
T smart00874 5 TLRRERINRLLGLDLSA--EEIEEILKRLGFEVEVSGDDDTLEVTVPSYRFDIL 56 (71)
T ss_pred EecHHHHHHHHCCCCCH--HHHHHHHHHCCCeEEecCCCCeEEEECCCCccccC
Confidence 35667888889987763 45677777888888777667888888888886433
No 99
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=28.67 E-value=93 Score=28.67 Aligned_cols=41 Identities=10% Similarity=0.193 Sum_probs=35.2
Q ss_pred hhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhh
Q 010241 83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (514)
Q Consensus 83 ~~~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd 124 (514)
...+|++++.+- +|.+..++|.+.|+|...+.+-+..|-++
T Consensus 10 ~D~~Il~~Lq~d-~R~s~~eiA~~lglS~~tV~~Ri~rL~~~ 50 (153)
T PRK11179 10 LDRGILEALMEN-ARTPYAELAKQFGVSPGTIHVRVEKMKQA 50 (153)
T ss_pred HHHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 556677777665 89999999999999999999999999764
No 100
>PF11772 EpuA: DNA-directed RNA polymerase subunit beta; InterPro: IPR024596 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This entry represents the short 60-residue long bacterial family that is the beta subunit of the DNA-directed RNA polymerase, likely to be 2.7.7.6 from EC It is membrane-bound and is referred to by the name EpuA.
Probab=28.59 E-value=32 Score=27.08 Aligned_cols=25 Identities=24% Similarity=0.650 Sum_probs=21.7
Q ss_pred ccCCCCCCCchHHHHHHHHHHHHHh
Q 010241 258 VFGEGDPNQGIEEKRWKLIGEYIAS 282 (514)
Q Consensus 258 vFGDGDPN~~lEerRWk~Ig~~Ir~ 282 (514)
|.|||||-+=+..+-||.|-..+..
T Consensus 22 viG~G~p~~vf~~~tW~hi~d~~~g 46 (47)
T PF11772_consen 22 VIGDGNPFDVFSPDTWQHIIDFFTG 46 (47)
T ss_pred eeCCCCHHHhCCHHHHHHHHHHHcC
Confidence 4799999999999999999887753
No 101
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=27.85 E-value=2.7e+02 Score=25.83 Aligned_cols=78 Identities=22% Similarity=0.194 Sum_probs=52.1
Q ss_pred HHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcC----CceEec-cCC-cEEEEcCcchHHHHhhhhHHHhHHH
Q 010241 87 AMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTD----GFLEVS-DEG-DVLYVFPNNYRAKLAAKSFRLKVEP 160 (514)
Q Consensus 87 im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~----G~LqVs-e~G-eIlY~FP~~fRs~l~~Ks~r~rl~~ 160 (514)
||+++-..| -+|-.|+|...|++++++++.|..|-.|-- -.-+-+ ++| -..|.|==|++... -..+.++..
T Consensus 6 v~d~L~~~~-~~~dedLa~~l~i~~n~vRkiL~~L~ed~~~~~~~~~e~~~~~~~~~~~yw~i~y~~~~--~vik~r~~~ 82 (147)
T smart00531 6 VLDALMRNG-CVTEEDLAELLGIKQKQLRKILYLLYDEKLIKIDYKREKDPETKTWYRYYWYINYDTLL--DVVKYKLDK 82 (147)
T ss_pred ehHHHHhcC-CcCHHHHHHHhCCCHHHHHHHHHHHHhhhcchhheeeeeCCCCceEEEEEEEecHHHHH--HHHHHHHHH
Confidence 577777766 699999999999999999999999988542 122233 345 46777755565542 234445555
Q ss_pred HHHHHhh
Q 010241 161 VIDKAKA 167 (514)
Q Consensus 161 ~~~k~w~ 167 (514)
..+++..
T Consensus 83 ~~~~L~~ 89 (147)
T smart00531 83 MRKRLED 89 (147)
T ss_pred HHHHHHH
Confidence 5555543
No 102
>PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional
Probab=27.69 E-value=2e+02 Score=32.43 Aligned_cols=76 Identities=11% Similarity=0.125 Sum_probs=63.6
Q ss_pred chhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcCcchHHHHhhhhHHHhH
Q 010241 81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKV 158 (514)
Q Consensus 81 ~~~~~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqVse~GeIlY~FP~~fRs~l~~Ks~r~rl 158 (514)
+....+|++++++.+..++..++|...|++.+++.+++..|.+. |-++|.+.=...|+-...=+..+.+-+.=.++
T Consensus 5 ~~~e~~iL~~l~~~~~~~~~~~la~~~~~~~~~v~~~~~~L~~k--g~v~~~~~~~~~~~LT~eG~~~~~~G~PE~rl 80 (494)
T PTZ00326 5 ELEENTILSKLESENEIVNSLALAESLNIDHQKVVGAIKSLESA--NYITTEMKKSNTWTLTEEGEDYLKNGSPEYRL 80 (494)
T ss_pred hHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHHHhC--CCEEEEEEEEEEEEECHHHHHHHHcCCHHHHH
Confidence 45678899999986666899999999999999999999999997 79999999999999887777777775544443
No 103
>PRK09492 treR trehalose repressor; Provisional
Probab=27.46 E-value=36 Score=33.39 Aligned_cols=24 Identities=25% Similarity=0.448 Sum_probs=21.5
Q ss_pred CceeehhhhhhcCCCHHHHHHHHH
Q 010241 96 RRVTIGDVAGKAGLKLNEAQKALQ 119 (514)
Q Consensus 96 ~rvTvgDVAa~aGL~l~~ae~~L~ 119 (514)
.++|+.|||..+|+|..++-+.|.
T Consensus 3 ~~~ti~dIA~~agVS~~TVSrvLn 26 (315)
T PRK09492 3 NKLTIKDIARLSGVGKSTVSRVLN 26 (315)
T ss_pred CCCcHHHHHHHhCCCHHHHhHHhC
Confidence 468999999999999999988874
No 104
>PRK13239 alkylmercury lyase; Provisional
Probab=27.32 E-value=53 Score=32.93 Aligned_cols=56 Identities=25% Similarity=0.248 Sum_probs=45.4
Q ss_pred HHHHHHHHHHHHHhcCCeEeeeeccCccCCCCCCCCchhhhhHhhhcCCccccCCCCCEEEecC
Q 010241 269 EEKRWKLIGEYIASNGGVVTAEELAPYLDIDRTMSDESYVLPVLLRFDGQPEIDEEGNILYRFP 332 (514)
Q Consensus 269 EerRWk~Ig~~Ir~N~GvV~AEQLAPyLD~~~~~~~EsymLpvL~rF~G~PeVse~G~IVY~FP 332 (514)
+.+=|..|-+.+. +|..|+-++||--+++ +++.+..+|..+.. .+.+++|+||= ||
T Consensus 20 ~~~~~~~llr~la-~G~pvt~~~lA~~~~~-----~~~~v~~~L~~l~~-~~~d~~g~iv~-~p 75 (206)
T PRK13239 20 TATLLVPLLRLLA-KGRPVSVTTLAAALGW-----PVEEVEAVLEAMPD-TEYDEDGRIIG-YG 75 (206)
T ss_pred chHHHHHHHHHHH-cCCCCCHHHHHHHhCC-----CHHHHHHHHHhCCC-eEECCCCCEEe-cc
Confidence 3456788888888 9999999999998775 56778888888864 48999999986 55
No 105
>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=27.27 E-value=2.1e+02 Score=25.07 Aligned_cols=79 Identities=14% Similarity=0.195 Sum_probs=54.8
Q ss_pred hhHHHHHHHHhcCCceeehhhhhhc----CCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcCcchHHHHhhhhHHHhH
Q 010241 83 VRNRAMDAVDACNRRVTIGDVAGKA----GLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKV 158 (514)
Q Consensus 83 ~~~~im~ave~~g~rvTvgDVAa~a----GL~l~~ae~~L~aLAsd~~G~LqVse~GeIlY~FP~~fRs~l~~Ks~r~rl 158 (514)
.-..||+.+=++|. +|+.||.... +++.+.+..-|..|.. -|.|++...|---+-.|-- + +..+.+..+
T Consensus 4 ~E~~IM~~lW~~~~-~t~~eI~~~l~~~~~~~~sTv~t~L~rL~~--Kg~l~~~~~gr~~~Y~p~i--s--~~e~~~~~~ 76 (115)
T PF03965_consen 4 LELEIMEILWESGE-ATVREIHEALPEERSWAYSTVQTLLNRLVE--KGFLTREKIGRAYVYSPLI--S--REEYLAQEL 76 (115)
T ss_dssp HHHHHHHHHHHHSS-EEHHHHHHHHCTTSS--HHHHHHHHHHHHH--TTSEEEEEETTCEEEEESS--S--HHHHHHHHH
T ss_pred HHHHHHHHHHhCCC-CCHHHHHHHHHhccccchhHHHHHHHHHHh--CCceeEeecCCceEEEeCC--c--HHHHHHHHH
Confidence 34679999999999 9999999643 5668888777777776 6999999988744333441 1 233455667
Q ss_pred HHHHHHHhhh
Q 010241 159 EPVIDKAKAA 168 (514)
Q Consensus 159 ~~~~~k~w~v 168 (514)
+.+++++...
T Consensus 77 ~~~l~~~~~g 86 (115)
T PF03965_consen 77 RQFLDRLFDG 86 (115)
T ss_dssp HHHHHHHSTT
T ss_pred HHHHHHHhCC
Confidence 7777766443
No 106
>PF10771 DUF2582: Protein of unknown function (DUF2582); InterPro: IPR019707 This entry represents conserved proteins found in bacteria and archaea. The function is not known. ; PDB: 2L02_B 2L01_A.
Probab=27.07 E-value=1e+02 Score=25.66 Aligned_cols=52 Identities=21% Similarity=0.337 Sum_probs=42.9
Q ss_pred HHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEE
Q 010241 86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYV 140 (514)
Q Consensus 86 ~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqVse~GeIlY~ 140 (514)
.|-+++.. .+..|+.+++..+|++-.++..|+==||.+ +.+++.+.++.+|+
T Consensus 12 ~Vw~~L~~-~~~~s~~el~k~~~l~~~~~~~AiGWLarE--~KI~~~~~~~~~~v 63 (65)
T PF10771_consen 12 KVWQLLNE-NGEWSVSELKKATGLSDKEVYLAIGWLARE--NKIEFEEKNGELYV 63 (65)
T ss_dssp HHHHHHCC-SSSEEHHHHHHHCT-SCHHHHHHHHHHHCT--TSEEEEEETTEEEE
T ss_pred HHHHHHhh-CCCcCHHHHHHHhCcCHHHHHHHHHHHhcc--CceeEEeeCCEEEE
Confidence 35667777 678999999999999999999999888875 78888888887776
No 107
>COG5232 SEC62 Preprotein translocase subunit Sec62 [Intracellular trafficking and secretion]
Probab=27.06 E-value=80 Score=32.34 Aligned_cols=58 Identities=17% Similarity=0.280 Sum_probs=34.7
Q ss_pred cCcccchhhhhhhhhHHHHHHHHHHHhH----H----hhhcCcchhh--hhHhhhhHHHHHHhHhhhhh
Q 010241 374 TNMSERGMAIGLGGLNLFGVIILGAMLQ----E----MAVTPNGFLK--FVAYIFPLLQIYAGSFFAIP 432 (514)
Q Consensus 374 a~~~q~~laigLG~~NL~g~lvLg~lL~----~----~a~~~gg~i~--fv~~i~PlL~~Ya~~F~aIP 432 (514)
.+...+.+++..+.+-.+.++||-.|-- + +....+|+|+ ||..|+-|. .|++..+..|
T Consensus 145 ep~~~~~~~l~~~fvlv~lalVlfplWPr~mr~g~~Y~s~g~~G~i~~ffvlaIlRli-Lf~it~~~y~ 212 (259)
T COG5232 145 EPTSNISLVLCGVFVLVTLALVLFPLWPRNMRQGLFYMSYGLGGFITFFFVLAILRLI-LFSITYLLYP 212 (259)
T ss_pred CCCccchhhHHHHHHHHHHHHHHHhcCchHhhcCeeeeeeccchHHHHHHHHHHHHHH-HHHhhheeec
Confidence 3444566777667777788888865432 1 3334677776 466666654 4666555444
No 108
>PRK09526 lacI lac repressor; Reviewed
Probab=26.94 E-value=40 Score=33.49 Aligned_cols=24 Identities=33% Similarity=0.462 Sum_probs=21.6
Q ss_pred CceeehhhhhhcCCCHHHHHHHHH
Q 010241 96 RRVTIGDVAGKAGLKLNEAQKALQ 119 (514)
Q Consensus 96 ~rvTvgDVAa~aGL~l~~ae~~L~ 119 (514)
.++|+.|||..||+|...+-+.|.
T Consensus 4 ~~~ti~dIA~~aGVS~~TVSrvLn 27 (342)
T PRK09526 4 KPVTLYDVARYAGVSYQTVSRVLN 27 (342)
T ss_pred CCCcHHHHHHHhCCCHHHHHHHhc
Confidence 468999999999999999988884
No 109
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=26.92 E-value=4.9e+02 Score=23.74 Aligned_cols=60 Identities=13% Similarity=0.139 Sum_probs=46.3
Q ss_pred CCchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEc
Q 010241 79 LPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVF 141 (514)
Q Consensus 79 l~~~~~~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqVse~GeIlY~F 141 (514)
|....|-+|+..+... +.+||+|+|...|++...+-+-|..|.. -|-+.....|.-+|-.
T Consensus 13 LadptRl~IL~~L~~~-~~~~v~ela~~l~lsqstvS~HL~~L~~--AGLV~~~r~Gr~~~Y~ 72 (117)
T PRK10141 13 LSDETRLGIVLLLRES-GELCVCDLCTALDQSQPKISRHLALLRE--SGLLLDRKQGKWVHYR 72 (117)
T ss_pred hCCHHHHHHHHHHHHc-CCcCHHHHHHHHCcCHHHHHHHHHHHHH--CCceEEEEEcCEEEEE
Confidence 4556788888888653 4699999999999999999999888864 4667777777655543
No 110
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=26.69 E-value=55 Score=31.78 Aligned_cols=33 Identities=18% Similarity=0.314 Sum_probs=25.9
Q ss_pred hhhHHHHHH----HHhcCCceeehhhhhhcCCCHHHH
Q 010241 82 DVRNRAMDA----VDACNRRVTIGDVAGKAGLKLNEA 114 (514)
Q Consensus 82 ~~~~~im~a----ve~~g~rvTvgDVAa~aGL~l~~a 114 (514)
+.|++|++| +-+.||.+|+.|||.+||++....
T Consensus 13 ~~r~~Il~aA~~lF~~~Gy~~s~~~IA~~AGvsk~ti 49 (225)
T PRK11552 13 QAKQQLIAAALAQFGEYGLHATTRDIAAQAGQNIAAI 49 (225)
T ss_pred HHHHHHHHHHHHHHHHhCccCCHHHHHHHhCCCHHHH
Confidence 556666655 556799999999999999987653
No 111
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=26.66 E-value=1.4e+02 Score=30.80 Aligned_cols=59 Identities=15% Similarity=0.195 Sum_probs=41.3
Q ss_pred CCCchhhHHHHHHHHhcCCceeehhhhhhcC--------------CCHHHHHHHHHHHHhhcCCceEeccCCc
Q 010241 78 KLPADVRNRAMDAVDACNRRVTIGDVAGKAG--------------LKLNEAQKALQALAADTDGFLEVSDEGD 136 (514)
Q Consensus 78 ~l~~~~~~~im~ave~~g~rvTvgDVAa~aG--------------L~l~~ae~~L~aLAsd~~G~LqVse~Ge 136 (514)
++..+.|+||+++++++||+....--+-+++ ---.+.-+++...+.+.|=++-+..+.+
T Consensus 26 ~Vs~eTr~kV~~a~~elgY~pN~~Ar~L~~~~s~~Ig~i~p~~~~~~~~~i~~gi~~~~~~~gy~~~l~~~~~ 98 (333)
T COG1609 26 YVSEETREKVLAAIKELGYRPNAVARSLRTGRTKTIGLVVPDITNPFFAEILKGIEEAAREAGYSLLLANTDD 98 (333)
T ss_pred CCCHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCCEEEEEeCCCCCchHHHHHHHHHHHHHHcCCEEEEECCCC
Confidence 7899999999999999999955543333332 2344555777777777777776665543
No 112
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=26.65 E-value=69 Score=33.81 Aligned_cols=52 Identities=17% Similarity=0.284 Sum_probs=40.1
Q ss_pred hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEE
Q 010241 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYV 140 (514)
Q Consensus 84 ~~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqVse~GeIlY~ 140 (514)
+..|++++.+.+..+|+.|++..||+..+++-.+|..| |.|.+-..+-+++.
T Consensus 210 ~~~il~~L~~~~~~isi~~is~~T~i~~~Dii~tL~~l-----~~l~~~~g~~~i~~ 261 (290)
T PLN03238 210 TRVLLEQLRDVKGDVSIKDLSLATGIRGEDIVSTLQSL-----NLIKYWKGQHVIHV 261 (290)
T ss_pred HHHHHHHHHhcCCCccHHHHHHHhCCCHHHHHHHHHHC-----CcEEEECCcEEEEe
Confidence 46788888888889999999999999999997777754 55655444444444
No 113
>PRK05472 redox-sensing transcriptional repressor Rex; Provisional
Probab=26.63 E-value=91 Score=30.19 Aligned_cols=40 Identities=18% Similarity=0.258 Sum_probs=36.2
Q ss_pred hhhHHHHHHHHhcC-CceeehhhhhhcCCCHHHHHHHHHHH
Q 010241 82 DVRNRAMDAVDACN-RRVTIGDVAGKAGLKLNEAQKALQAL 121 (514)
Q Consensus 82 ~~~~~im~ave~~g-~rvTvgDVAa~aGL~l~~ae~~L~aL 121 (514)
....+|++.+.+.| -+|++.+.|..+|++..++++.|..|
T Consensus 16 ~~~~~il~~l~~~~~~~vs~~~L~~~~~v~~~tirrDl~~l 56 (213)
T PRK05472 16 PLYYRYLKELKEEGVERVSSKELAEALGVDSAQIRKDLSYF 56 (213)
T ss_pred HHHHHHHHHHHHcCCcEEeHHHHHHHhCcCHHHHHHHHHHH
Confidence 34678899999987 69999999999999999999999999
No 114
>PF01853 MOZ_SAS: MOZ/SAS family; InterPro: IPR002717 Moz is a monocytic leukemia Zn_finger protein and the SAS protein from Saccharomyces cerevisiae (Baker's yeast) is involved in silencing the Hmr locus. These proteins were reported to be homologous to acetyltransferases [] but this similarity is not supported by standard sequence analysis.; GO: 0016747 transferase activity, transferring acyl groups other than amino-acyl groups, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3TO6_A 1MJA_A 1MJ9_A 3TO7_A 3TO9_A 1MJB_A 1FY7_A 2OZU_A 2RC4_A 2OU2_A ....
Probab=26.52 E-value=71 Score=31.71 Aligned_cols=38 Identities=18% Similarity=0.388 Sum_probs=33.3
Q ss_pred hHHHHHHHHhcCCc--eeehhhhhhcCCCHHHHHHHHHHH
Q 010241 84 RNRAMDAVDACNRR--VTIGDVAGKAGLKLNEAQKALQAL 121 (514)
Q Consensus 84 ~~~im~ave~~g~r--vTvgDVAa~aGL~l~~ae~~L~aL 121 (514)
+..|++.+.+.... +|+.|++..||+..++.-..|..|
T Consensus 135 ~~~i~~~L~~~~~~~~isi~~is~~Tgi~~~DIi~tL~~l 174 (188)
T PF01853_consen 135 RRVILEYLLEFKGKKSISIKDISQETGIRPEDIISTLQQL 174 (188)
T ss_dssp HHHHHHHHHHTSSE--EEHHHHHHHH-BTHHHHHHHHHHT
T ss_pred HHHHHHHHHhcCCCCeEEHHHHHHHHCCCHHHHHHHHHHC
Confidence 57889999999885 999999999999999998888876
No 115
>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain
Probab=26.33 E-value=2.2e+02 Score=32.15 Aligned_cols=79 Identities=15% Similarity=0.189 Sum_probs=64.5
Q ss_pred hhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcCcchHHHHhhhhHHHhHHHH
Q 010241 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEPV 161 (514)
Q Consensus 82 ~~~~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqVse~GeIlY~FP~~fRs~l~~Ks~r~rl~~~ 161 (514)
+...+|+++++..+..++..++|...|++.+++.+++..|.+. |-+++.+.=+..|+-...=+..+++-+.=.++-.+
T Consensus 3 ~~e~~iL~~l~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~k--g~v~~~~~~~~~~~LT~eG~~~l~~G~PE~rl~~~ 80 (492)
T PLN02853 3 MAEEALLGALSNNEEISDSGQFAASHGLDHNEVVGVIKSLHGF--RYVDAQDIKRETWVLTEEGKKYAAEGSPEVQLFAA 80 (492)
T ss_pred hHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHHHhC--CCEEEEEEEEEEEEECHHHHHHHHcCCHHHHHHHH
Confidence 4568899999987766899999999999999999999999997 69999999899999887777777765544444333
Q ss_pred H
Q 010241 162 I 162 (514)
Q Consensus 162 ~ 162 (514)
+
T Consensus 81 l 81 (492)
T PLN02853 81 V 81 (492)
T ss_pred H
Confidence 3
No 116
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=25.79 E-value=4.7e+02 Score=23.63 Aligned_cols=42 Identities=17% Similarity=0.158 Sum_probs=33.7
Q ss_pred HHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceE
Q 010241 86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLE 130 (514)
Q Consensus 86 ~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~Lq 130 (514)
.|... ...++.+|+.|+|...|++...+.+.|..|..+ |-++
T Consensus 12 ~I~~l-~~~~~~~~~~ela~~l~vs~~svs~~l~~L~~~--Gli~ 53 (142)
T PRK03902 12 QIYLL-IEEKGYARVSDIAEALSVHPSSVTKMVQKLDKD--EYLI 53 (142)
T ss_pred HHHHH-HhcCCCcCHHHHHHHhCCChhHHHHHHHHHHHC--CCEE
Confidence 33443 445667799999999999999999999999887 6665
No 117
>PF10025 DUF2267: Uncharacterized conserved protein (DUF2267); InterPro: IPR018727 This entry contains proteins that have no known function. ; PDB: 2YSK_A.
Probab=25.27 E-value=39 Score=30.35 Aligned_cols=68 Identities=21% Similarity=0.290 Sum_probs=52.1
Q ss_pred ehhhhhhcCC-CHHHHHHHHHHHHhhcCCceEeccCCcEEEEcCcchHHHHhh------hhHHHhHHHHHHHHhh
Q 010241 100 IGDVAGKAGL-KLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAA------KSFRLKVEPVIDKAKA 167 (514)
Q Consensus 100 vgDVAa~aGL-~l~~ae~~L~aLAsd~~G~LqVse~GeIlY~FP~~fRs~l~~------Ks~r~rl~~~~~k~w~ 167 (514)
+.+|+..+|+ +.++|++++++...--+-+|.+.+.-++.=..|.-.|..+.. ..-+...++|+..+..
T Consensus 6 l~~V~~~~~l~~~~~A~~a~~avL~~L~~rL~~~ea~~La~qLP~~l~~~l~~gw~~~~~~~~~~~~eF~~rVa~ 80 (125)
T PF10025_consen 6 LDEVRERAGLPDREEAYRATRAVLHTLRERLPPEEAADLAAQLPMELRGILYEGWRPSEGPGRFDLDEFLARVAE 80 (125)
T ss_dssp HHHHHHHHT---HHHHHHHHHHHHHHHHTTS-HHHHHHHHTTS-HHHHHHHHTT--TTS-----SHHHHHHHHHH
T ss_pred HHHHHHHhCCCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHhCCHHHHHHHHhcccCCCCCCCCCHHHHHHHHHH
Confidence 4688999999 999999999999999999999999999988899999999954 1233568888887765
No 118
>TIGR00540 hemY_coli hemY protein. This is an uncharacterized protein encoded next to a heme-biosynthetic enzyme in two gamma division proteobacteria (E. coli and H. influenzae). It is known in no other species. The gene symbol hemY is unfortunate in that an unrelated protein, protoporphyrinogen oxidase, is designated as HemG in E. coli but as HemY in Bacillus subtilis.
Probab=25.25 E-value=2.8e+02 Score=29.31 Aligned_cols=29 Identities=17% Similarity=0.100 Sum_probs=16.0
Q ss_pred hhHhhhhHHHHHHhHhhhhhHHHHHHHHh
Q 010241 413 FVAYIFPLLQIYAGSFFAIPAVRWFLNLQ 441 (514)
Q Consensus 413 fv~~i~PlL~~Ya~~F~aIPl~R~f~iq~ 441 (514)
++..++=++++|.++++..=++|++|...
T Consensus 41 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~p 69 (409)
T TIGR00540 41 ITGLAIFFIIALAIIFAFEWGLRRFFRLG 69 (409)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence 44444445555666666566666665433
No 119
>PRK15008 HTH-type transcriptional regulator RutR; Provisional
Probab=25.21 E-value=52 Score=31.24 Aligned_cols=32 Identities=9% Similarity=0.178 Sum_probs=24.4
Q ss_pred hhhHHHHH----HHHhcCCc-eeehhhhhhcCCCHHH
Q 010241 82 DVRNRAMD----AVDACNRR-VTIGDVAGKAGLKLNE 113 (514)
Q Consensus 82 ~~~~~im~----ave~~g~r-vTvgDVAa~aGL~l~~ 113 (514)
+.|++|++ .+.+.||. +|+.|||..+|++...
T Consensus 18 ~~r~~IL~AA~~lf~e~Gy~~~s~~dIA~~aGvs~gt 54 (212)
T PRK15008 18 AKKKAILSAALDTFSQFGFHGTRLEQIAELAGVSKTN 54 (212)
T ss_pred HHHHHHHHHHHHHHHHhCcccCCHHHHHHHhCcCHHH
Confidence 45666655 46678987 8999999999997643
No 120
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=25.19 E-value=1.1e+02 Score=28.98 Aligned_cols=53 Identities=13% Similarity=0.261 Sum_probs=40.7
Q ss_pred HHHHHHHHhcC-CceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcCc
Q 010241 85 NRAMDAVDACN-RRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPN 143 (514)
Q Consensus 85 ~~im~ave~~g-~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqVse~GeIlY~FP~ 143 (514)
.+|-+.+.... .++|+.+||..+|++..+..+=+. .|.|++++...+-|.=.+
T Consensus 33 ~kV~~yLr~~p~~~ati~eV~e~tgVs~~~I~~~Ir------eGRL~~~~~~nl~~~CE~ 86 (137)
T TIGR03826 33 EKVYKFLRKHENRQATVSEIVEETGVSEKLILKFIR------EGRLQLKHFPNLGYPCER 86 (137)
T ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCcCHHHHHHHHH------cCCeeccCCCCCcCcccc
Confidence 44556666544 369999999999999999866555 599999998888776544
No 121
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=25.16 E-value=42 Score=33.35 Aligned_cols=25 Identities=24% Similarity=0.426 Sum_probs=22.0
Q ss_pred CCceeehhhhhhcCCCHHHHHHHHH
Q 010241 95 NRRVTIGDVAGKAGLKLNEAQKALQ 119 (514)
Q Consensus 95 g~rvTvgDVAa~aGL~l~~ae~~L~ 119 (514)
..++|+.|||..+|+|..++-+.|.
T Consensus 3 ~~~~ti~dIA~~agVS~~TVSrvLn 27 (331)
T PRK14987 3 KKRPVLQDVADRVGVTKMTVSRFLR 27 (331)
T ss_pred CCCCcHHHHHHHhCCCHHHhhhhhC
Confidence 3479999999999999999988874
No 122
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=25.06 E-value=1.1e+02 Score=29.01 Aligned_cols=50 Identities=12% Similarity=0.155 Sum_probs=39.6
Q ss_pred HHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhc------CCceEeccCCc
Q 010241 86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT------DGFLEVSDEGD 136 (514)
Q Consensus 86 ~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~------~G~LqVse~Ge 136 (514)
.|-...+ .++.++++|+|..-+++...+.+.|..|+++- .|.++.|+.|+
T Consensus 14 ~Iy~l~~-~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~~GlV~~~~y~gi~LT~~G~ 69 (154)
T COG1321 14 TIYELLE-EKGFARTKDIAERLKVSPPSVTEMLKRLERLGLVEYEPYGGVTLTEKGR 69 (154)
T ss_pred HHHHHHh-ccCcccHHHHHHHhCCCcHHHHHHHHHHHHCCCeEEecCCCeEEChhhH
Confidence 3444444 77889999999999999999999999999863 55666666664
No 123
>PRK14996 TetR family transcriptional regulator; Provisional
Probab=25.02 E-value=48 Score=30.65 Aligned_cols=29 Identities=21% Similarity=0.186 Sum_probs=22.4
Q ss_pred hHHHHHH----HHhcCCc-eeehhhhhhcCCCHH
Q 010241 84 RNRAMDA----VDACNRR-VTIGDVAGKAGLKLN 112 (514)
Q Consensus 84 ~~~im~a----ve~~g~r-vTvgDVAa~aGL~l~ 112 (514)
|++|++| +.+.||. +|+.|||.++|++..
T Consensus 10 R~~Il~aA~~lf~e~G~~~tSi~~Ia~~aGvsk~ 43 (192)
T PRK14996 10 REVILQAAMRVALAEGFAAMTVRRIASEAQVAAG 43 (192)
T ss_pred HHHHHHHHHHHHHhcChhhccHHHHHHHhCCCcH
Confidence 5556555 5667887 899999999999654
No 124
>TIGR02405 trehalos_R_Ecol trehalose operon repressor, proteobacterial. This family consists of repressors of the LacI family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gammaproteobacteria and does not include the GntR family TreR of Bacillus subtilis
Probab=24.89 E-value=45 Score=32.96 Aligned_cols=23 Identities=30% Similarity=0.482 Sum_probs=20.8
Q ss_pred ceeehhhhhhcCCCHHHHHHHHH
Q 010241 97 RVTIGDVAGKAGLKLNEAQKALQ 119 (514)
Q Consensus 97 rvTvgDVAa~aGL~l~~ae~~L~ 119 (514)
++|+.|||..+|+|...+-++|.
T Consensus 1 ~~ti~dIA~~agVS~sTVSr~Ln 23 (311)
T TIGR02405 1 KLTIKDIARLAGVGKSTVSRVLN 23 (311)
T ss_pred CCcHHHHHHHhCCCHHHHHHHhC
Confidence 47999999999999999988883
No 125
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=24.83 E-value=55 Score=23.71 Aligned_cols=28 Identities=18% Similarity=0.356 Sum_probs=18.1
Q ss_pred hcCCceeehhhhhhcCCCHHHHHHHHHH
Q 010241 93 ACNRRVTIGDVAGKAGLKLNEAQKALQA 120 (514)
Q Consensus 93 ~~g~rvTvgDVAa~aGL~l~~ae~~L~a 120 (514)
.+....||.|||...|++..--.+....
T Consensus 4 ~~~~~~~l~~iA~~~g~S~~~f~r~Fk~ 31 (42)
T PF00165_consen 4 NLQQKLTLEDIAEQAGFSPSYFSRLFKK 31 (42)
T ss_dssp TT-SS--HHHHHHHHTS-HHHHHHHHHH
T ss_pred cccCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 3456789999999999988776655543
No 126
>PRK10747 putative protoheme IX biogenesis protein; Provisional
Probab=24.76 E-value=3.3e+02 Score=28.71 Aligned_cols=28 Identities=11% Similarity=0.007 Sum_probs=17.1
Q ss_pred hhhHhhhhHHHHHHhHhhhhhHHHHHHH
Q 010241 412 KFVAYIFPLLQIYAGSFFAIPAVRWFLN 439 (514)
Q Consensus 412 ~fv~~i~PlL~~Ya~~F~aIPl~R~f~i 439 (514)
.++..++=+++++.++++..=++|+.|.
T Consensus 40 sl~~~~~~~~~~~~~~~~~~~~~~~~~~ 67 (398)
T PRK10747 40 SVTGLAIILILAMVVLFAIEWLLRRIFR 67 (398)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3555555555566666666666766665
No 127
>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY. This model represents the full length of CodY, a pleiotropic repressor in Bacillus subtilis and other Firmicutes (low-GC Gram-positive bacteria) that responds to intracellular levels of GTP and branched chain amino acids. The C-terminal helix-turn-helix DNA-binding region is modeled by pfam08222 in Pfam.
Probab=24.54 E-value=83 Score=32.61 Aligned_cols=44 Identities=18% Similarity=0.357 Sum_probs=35.8
Q ss_pred HHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEecc
Q 010241 88 MDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD 133 (514)
Q Consensus 88 m~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqVse 133 (514)
++++.+..+|++-.++|.+.|+|......+++.|.++ |-+++-.
T Consensus 189 L~~L~~~egrlse~eLAerlGVSRs~ireAlrkLE~a--GvIe~r~ 232 (251)
T TIGR02787 189 FEELDGNEGLLVASKIADRVGITRSVIVNALRKLESA--GVIESRS 232 (251)
T ss_pred HHHhccccccccHHHHHHHHCCCHHHHHHHHHHHHHC--CCEEecc
Confidence 3333333579999999999999999999999999864 7777777
No 128
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=23.99 E-value=1.1e+02 Score=27.13 Aligned_cols=44 Identities=16% Similarity=0.329 Sum_probs=34.3
Q ss_pred HHHHHHhc-CCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEec
Q 010241 87 AMDAVDAC-NRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVS 132 (514)
Q Consensus 87 im~ave~~-g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqVs 132 (514)
+|..+-+. +.++|+.|+|.+.|+|...+++-|..|.. .|-++..
T Consensus 14 ~l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~~--~Gli~~~ 58 (130)
T TIGR02944 14 VLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLSL--AGIVTSK 58 (130)
T ss_pred HHHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHHH--CCcEEec
Confidence 44455443 56799999999999999999999999987 4566543
No 129
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=23.22 E-value=1.5e+02 Score=23.67 Aligned_cols=36 Identities=17% Similarity=0.300 Sum_probs=26.9
Q ss_pred HHHHHHHHhcCC-----ceeehhhhhhcCCCHHHHHHHHHH
Q 010241 85 NRAMDAVDACNR-----RVTIGDVAGKAGLKLNEAQKALQA 120 (514)
Q Consensus 85 ~~im~ave~~g~-----rvTvgDVAa~aGL~l~~ae~~L~a 120 (514)
.+++.+.=..|| ++|+.|+|..-|++...+..-|+.
T Consensus 6 ~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~LRr 46 (53)
T PF04967_consen 6 REILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHLRR 46 (53)
T ss_pred HHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHHHH
Confidence 344444444554 899999999999999988777664
No 130
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=23.07 E-value=1e+02 Score=25.40 Aligned_cols=34 Identities=21% Similarity=0.404 Sum_probs=29.9
Q ss_pred hhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHH
Q 010241 82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQ 115 (514)
Q Consensus 82 ~~~~~im~ave~~g~rvTvgDVAa~aGL~l~~ae 115 (514)
.-|+.+-+--..+++.+|+-|||.+-|++..+..
T Consensus 7 p~rdkA~e~y~~~~g~i~lkdIA~~Lgvs~~tIr 40 (60)
T PF10668_consen 7 PNRDKAFEIYKESNGKIKLKDIAEKLGVSESTIR 40 (60)
T ss_pred cCHHHHHHHHHHhCCCccHHHHHHHHCCCHHHHH
Confidence 3577888888899999999999999999998874
No 131
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=22.91 E-value=1.1e+02 Score=24.54 Aligned_cols=35 Identities=17% Similarity=0.236 Sum_probs=25.8
Q ss_pred HHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHh
Q 010241 89 DAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAA 123 (514)
Q Consensus 89 ~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAs 123 (514)
...-+.++++|++|+|...|++.+.++.-|..|-.
T Consensus 6 ~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~ 40 (69)
T PF09012_consen 6 RDYLRERGRVSLAELAREFGISPEAVEAMLEQLIR 40 (69)
T ss_dssp HHHHHHS-SEEHHHHHHHTT--HHHHHHHHHHHHC
T ss_pred HHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 33445678999999999999999999887777754
No 132
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=22.67 E-value=1.9e+02 Score=25.54 Aligned_cols=59 Identities=31% Similarity=0.409 Sum_probs=44.1
Q ss_pred CCchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCce-Eecc-CCcEEEE
Q 010241 79 LPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFL-EVSD-EGDVLYV 140 (514)
Q Consensus 79 l~~~~~~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~L-qVse-~GeIlY~ 140 (514)
++.+.-+++++-|-+ -.=+|+.-||.+-+++.+.|+++|..|... |.+ .|+. +.-.||+
T Consensus 24 ~dk~t~dkl~kEV~~-~K~ITps~lserlkI~~SlAr~~Lr~L~~k--G~Ik~V~~~~~q~IYt 84 (86)
T PRK09334 24 LDEELLKRVAKEVKK-EKIVTPYTLASKYGIKISVAKKVLRELEKR--GVLVLYSKNRRTPIYV 84 (86)
T ss_pred cCHHHHHHHHHHhcc-CcEEcHHHHHHHhcchHHHHHHHHHHHHHC--CCEEEEecCCCeEEec
Confidence 555667788877776 455899999999999999999999999864 444 2333 3555553
No 133
>PF07245 Phlebovirus_G2: Phlebovirus glycoprotein G2; InterPro: IPR009878 This domain is found in several Phlebovirus glycoprotein G2 sequences. Members of the Bunyaviridae family acquire an envelope by budding through the lipid bilayer of the Golgi complex. The budding compartment is thought to be determined by the accumulation of the two heterodimeric membrane glycoproteins G1 and G2 in the Golgi [].
Probab=22.60 E-value=74 Score=35.79 Aligned_cols=18 Identities=22% Similarity=0.421 Sum_probs=13.3
Q ss_pred CCcEEEEcCcchHHHHhh
Q 010241 134 EGDVLYVFPNNYRAKLAA 151 (514)
Q Consensus 134 ~GeIlY~FP~~fRs~l~~ 151 (514)
+|.++|.-+.+-|..-..
T Consensus 421 ~G~L~~~~~f~~r~~~~~ 438 (507)
T PF07245_consen 421 KGTLIYLGPFDDRNYTGG 438 (507)
T ss_pred EEEEEeccccccccccCc
Confidence 688999999887764333
No 134
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=22.33 E-value=66 Score=30.04 Aligned_cols=32 Identities=16% Similarity=0.257 Sum_probs=23.6
Q ss_pred hhhHHHHHH----HHhcCC-ceeehhhhhhcCCCHHH
Q 010241 82 DVRNRAMDA----VDACNR-RVTIGDVAGKAGLKLNE 113 (514)
Q Consensus 82 ~~~~~im~a----ve~~g~-rvTvgDVAa~aGL~l~~ 113 (514)
..|.+|++| +.+.|+ .+|+.|||..+|++...
T Consensus 11 ~~r~~Il~aa~~lf~~~G~~~~ti~~Ia~~agvsk~t 47 (213)
T PRK09975 11 KTRQELIETAIAQFALRGVSNTTLNDIADAANVTRGA 47 (213)
T ss_pred HHHHHHHHHHHHHHHHcCcccCCHHHHHHHcCCCHHH
Confidence 345555554 567886 69999999999997643
No 135
>KOG4251 consensus Calcium binding protein [General function prediction only]
Probab=22.15 E-value=59 Score=34.10 Aligned_cols=58 Identities=29% Similarity=0.361 Sum_probs=40.9
Q ss_pred CCchHHHHHHHHHHHHHhc-CCeEeeeeccCccCCCC--CCCCchhhhhHhhhcCCccccC
Q 010241 265 NQGIEEKRWKLIGEYIASN-GGVVTAEELAPYLDIDR--TMSDESYVLPVLLRFDGQPEID 322 (514)
Q Consensus 265 N~~lEerRWk~Ig~~Ir~N-~GvV~AEQLAPyLD~~~--~~~~EsymLpvL~rF~G~PeVs 322 (514)
..+|-++|-|..-..|-+| .|.||||||--|+|... ....|-...-+++.-|+....|
T Consensus 275 ddnwvkdRkkEFeElIDsNhDGivTaeELe~y~dP~n~~~alne~~~~ma~~d~n~~~~Ls 335 (362)
T KOG4251|consen 275 DDNWVKDRKKEFEELIDSNHDGIVTAEELEDYVDPQNFRLALNEVNDIMALTDANNDEKLS 335 (362)
T ss_pred HHHHHHHHHHHHHHHhhcCCccceeHHHHHhhcCchhhhhhHHHHHHHHhhhccCCCcccC
Confidence 3467889999999999765 79999999999999653 2234544445555555554444
No 136
>PF10975 DUF2802: Protein of unknown function (DUF2802); InterPro: IPR021244 This bacterial family of proteins has no known function.
Probab=21.42 E-value=62 Score=27.08 Aligned_cols=29 Identities=17% Similarity=0.318 Sum_probs=23.7
Q ss_pred HHHHHhcCCceeehhhhhhcCCCHHHHHH
Q 010241 88 MDAVDACNRRVTIGDVAGKAGLKLNEAQK 116 (514)
Q Consensus 88 m~ave~~g~rvTvgDVAa~aGL~l~~ae~ 116 (514)
-+|++-...++++.+|+...||+..||+-
T Consensus 35 ~~A~klv~~Ga~~~el~~~CgL~~aEAeL 63 (70)
T PF10975_consen 35 SQAIKLVRQGASVEELMEECGLSRAEAEL 63 (70)
T ss_pred HHHHHHHHcCCCHHHHHHHcCCCHHHHHH
Confidence 45666666779999999999999999953
No 137
>PF09105 SelB-wing_1: Elongation factor SelB, winged helix ; InterPro: IPR015189 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 1". 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 []. ; PDB: 2V9V_A 1LVA_A 2PLY_A.
Probab=21.27 E-value=2.4e+02 Score=22.92 Aligned_cols=43 Identities=26% Similarity=0.306 Sum_probs=31.6
Q ss_pred HHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCce
Q 010241 87 AMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFL 129 (514)
Q Consensus 87 im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~L 129 (514)
+-+.+....-+..-.+.|+++.|++++.++-|+..|+...-.|
T Consensus 7 laqiiqehregldwqeaatraslsleetrkllqsmaaagqvtl 49 (61)
T PF09105_consen 7 LAQIIQEHREGLDWQEAATRASLSLEETRKLLQSMAAAGQVTL 49 (61)
T ss_dssp HHHHHHC-TT-EEHHHHHHHHT--HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHccCcHHHHHHHhhccHHHHHHHHHHHHhcCceEE
Confidence 3566777788888899999999999999999999888654443
No 138
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=21.20 E-value=74 Score=23.78 Aligned_cols=32 Identities=13% Similarity=0.225 Sum_probs=20.5
Q ss_pred HHHHHHhcCCceeehhhhhhcCCCHHHHHHHH
Q 010241 87 AMDAVDACNRRVTIGDVAGKAGLKLNEAQKAL 118 (514)
Q Consensus 87 im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L 118 (514)
+-++++-+..+.|+.|||...|++.....+-|
T Consensus 11 ~~~i~~l~~~G~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 11 IEEIKELYAEGMSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp HHHHHHHHHTT--HHHHHHHTTS-HHHHHHHH
T ss_pred HHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHH
Confidence 33444444445999999999999998876544
No 139
>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=21.19 E-value=2.9e+02 Score=26.60 Aligned_cols=47 Identities=19% Similarity=0.368 Sum_probs=38.6
Q ss_pred hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEecc
Q 010241 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD 133 (514)
Q Consensus 84 ~~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~LqVse 133 (514)
.-+|+..+.+.| .+|+.|+|...|++...+.+.|..|... |-++...
T Consensus 145 ~~~IL~~l~~~g-~~s~~eia~~l~is~stv~r~L~~Le~~--GlI~r~~ 191 (203)
T TIGR01884 145 ELKVLEVLKAEG-EKSVKNIAKKLGKSLSTISRHLRELEKK--GLVEQKG 191 (203)
T ss_pred HHHHHHHHHHcC-CcCHHHHHHHHCcCHHHHHHHHHHHHHC--CCEEEEc
Confidence 447788887765 5899999999999999999999999865 6666554
No 140
>PRK10344 DNA-binding transcriptional regulator Nlp; Provisional
Probab=21.17 E-value=1.2e+02 Score=27.26 Aligned_cols=34 Identities=12% Similarity=0.191 Sum_probs=29.7
Q ss_pred hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHH
Q 010241 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQ 119 (514)
Q Consensus 84 ~~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~ 119 (514)
+..|+-|+++.| .|+..++.++||+-+....+|.
T Consensus 10 ~adI~AaL~KrG--~sLa~lsr~~Gls~~TL~nAL~ 43 (92)
T PRK10344 10 PADIIAGLRKKG--TSMAAESRRNGLSSSTLANALS 43 (92)
T ss_pred HHHHHHHHHHcC--CcHHHHHHHcCCChHHHHHHHc
Confidence 467899999988 7999999999999988888774
No 141
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=21.14 E-value=1.7e+02 Score=20.95 Aligned_cols=46 Identities=13% Similarity=0.213 Sum_probs=32.7
Q ss_pred CCCchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCC
Q 010241 78 KLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDG 127 (514)
Q Consensus 78 ~l~~~~~~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G 127 (514)
.|+..-+. ++..+ -.+.+..++|...|++...+.+-+..+-...+.
T Consensus 3 ~l~~~e~~-i~~~~---~~g~s~~eia~~l~is~~tv~~~~~~~~~kl~~ 48 (58)
T smart00421 3 SLTPRERE-VLRLL---AEGLTNKEIAERLGISEKTVKTHLSNIMRKLGV 48 (58)
T ss_pred CCCHHHHH-HHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Confidence 45554443 44443 234699999999999999999988887665543
No 142
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=20.97 E-value=57 Score=32.45 Aligned_cols=22 Identities=32% Similarity=0.487 Sum_probs=20.2
Q ss_pred eeehhhhhhcCCCHHHHHHHHH
Q 010241 98 VTIGDVAGKAGLKLNEAQKALQ 119 (514)
Q Consensus 98 vTvgDVAa~aGL~l~~ae~~L~ 119 (514)
+|+.|||..+|+|..++-+.|.
T Consensus 2 ~Ti~dIA~~agVS~~TVSrvLn 23 (341)
T PRK10703 2 ATIKDVAKRAGVSTTTVSHVIN 23 (341)
T ss_pred CCHHHHHHHhCCCHHHHHHHHc
Confidence 6999999999999999988884
No 143
>PRK05441 murQ N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=20.87 E-value=1.1e+02 Score=31.80 Aligned_cols=43 Identities=33% Similarity=0.415 Sum_probs=36.5
Q ss_pred hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceE
Q 010241 84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLE 130 (514)
Q Consensus 84 ~~~im~ave~~g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd~~G~Lq 130 (514)
.+...+++++.+|.|-++=+...+|++..+|++.|. +++|||.
T Consensus 250 ~~~a~~~l~~~~~~vk~a~~~~~~~~~~~~a~~~l~----~~~g~~~ 292 (299)
T PRK05441 250 REEAEAALEAADGSVKLAIVMILTGLDAAEAKALLA----RHGGFLR 292 (299)
T ss_pred HHHHHHHHHHhCCCcHHHHHHHHhCCCHHHHHHHHH----HcCCCHH
Confidence 456788999999999999999999999999976654 6888875
No 144
>TIGR01481 ccpA catabolite control protein A. Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.
Probab=20.85 E-value=58 Score=32.14 Aligned_cols=22 Identities=36% Similarity=0.539 Sum_probs=20.0
Q ss_pred eeehhhhhhcCCCHHHHHHHHH
Q 010241 98 VTIGDVAGKAGLKLNEAQKALQ 119 (514)
Q Consensus 98 vTvgDVAa~aGL~l~~ae~~L~ 119 (514)
+|+.|||..||+|...+-+.|.
T Consensus 2 ~ti~dIA~~agvS~~TVSrvLn 23 (329)
T TIGR01481 2 VTIYDVAREAGVSMATVSRVVN 23 (329)
T ss_pred CcHHHHHHHhCCCHHHHHHHhC
Confidence 6899999999999999988884
No 145
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=20.76 E-value=1.3e+02 Score=24.92 Aligned_cols=38 Identities=18% Similarity=0.217 Sum_probs=27.9
Q ss_pred HHHHHHhc-CCceeehhhhhhcCCCHHHHHHHHHHHHhh
Q 010241 87 AMDAVDAC-NRRVTIGDVAGKAGLKLNEAQKALQALAAD 124 (514)
Q Consensus 87 im~ave~~-g~rvTvgDVAa~aGL~l~~ae~~L~aLAsd 124 (514)
+++-++.+ ....+..+++..++|+-..+++-|..|...
T Consensus 8 i~~IL~~l~~~~~~~t~i~~~~~L~~~~~~~yL~~L~~~ 46 (77)
T PF14947_consen 8 IFDILKILSKGGAKKTEIMYKANLNYSTLKKYLKELEEK 46 (77)
T ss_dssp HHHHHHHH-TT-B-HHHHHTTST--HHHHHHHHHHHHHT
T ss_pred HHHHHHHHHcCCCCHHHHHHHhCcCHHHHHHHHHHHHHC
Confidence 34555555 788888999999999999999999999765
No 146
>PF12387 Peptidase_C74: Pestivirus NS2 peptidase; InterPro: IPR022120 The pestivirus NS2 peptidase is responsible for single cleavage between NS2 and NS3 of the Bovine viral diarrhea virus 1 polyprotein, a cleavage that is correlated with cytopathogenicity []. The peptidase is activated by its interaction with 'J-domain protein interacting with viral protein' - Jiv. ; GO: 0003968 RNA-directed RNA polymerase activity, 0004197 cysteine-type endopeptidase activity, 0004252 serine-type endopeptidase activity, 0016817 hydrolase activity, acting on acid anhydrides, 0017111 nucleoside-triphosphatase activity, 0070008 serine-type exopeptidase activity
Probab=20.64 E-value=57 Score=32.35 Aligned_cols=24 Identities=38% Similarity=0.594 Sum_probs=19.7
Q ss_pred CCccccCCCCCEEEecCcccchhh
Q 010241 316 DGQPEIDEEGNILYRFPSFQRTAA 339 (514)
Q Consensus 316 ~G~PeVse~G~IVY~FPeLQ~TA~ 339 (514)
|--=|+++.|+=||-||+.|.+.+
T Consensus 11 ~~iyd~~~~~EgVylfPS~qk~~~ 34 (200)
T PF12387_consen 11 NSIYDIDESGEGVYLFPSRQKGGS 34 (200)
T ss_pred cceeeecCCCceEEEccccccCCC
Confidence 444578999999999999998854
No 147
>PF01316 Arg_repressor: Arginine repressor, DNA binding domain; InterPro: IPR020900 The arginine dihydrolase (AD) pathway is found in many prokaryotes and some primitive eukaryotes, an example of the latter being Giardia lamblia (Giardia intestinalis) []. The three-enzyme anaerobic pathway breaks down L-arginine to form 1 mol of ATP, carbon dioxide and ammonia. In simpler bacteria, the first enzyme, arginine deiminase, can account for up to 10% of total cell protein []. Most prokaryotic arginine deiminase pathways are under the control of a repressor gene, termed ArgR []. This is a negative regulator, and will only release the arginine deiminase operon for expression in the presence of arginine []. The crystal structure of apo-ArgR from Bacillus stearothermophilus has been determined to 2.5A by means of X-ray crystallography []. The protein exists as a hexamer of identical subunits, and is shown to have six DNA-binding domains, clustered around a central oligomeric core when bound to arginine. It predominantly interacts with A.T residues in ARG boxes. This hexameric protein binds DNA at its N terminus to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbour-joining tree, some of these paralogous sequences show long branches and differ significantly from the well-conserved C-terminal region. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0006525 arginine metabolic process; PDB: 1AOY_A 3V4G_A 3LAJ_D 3FHZ_A 3LAP_B 3ERE_D 2P5L_C 1F9N_D 2P5K_A 1B4A_A ....
Probab=20.45 E-value=75 Score=26.67 Aligned_cols=62 Identities=24% Similarity=0.371 Sum_probs=40.4
Q ss_pred HHHHHHHHHHHHhcCCeEeeeeccCccCCCCCCCCchhhhhHhhhcCCcccc-CCCCCEEEecCc
Q 010241 270 EKRWKLIGEYIASNGGVVTAEELAPYLDIDRTMSDESYVLPVLLRFDGQPEI-DEEGNILYRFPS 333 (514)
Q Consensus 270 erRWk~Ig~~Ir~N~GvV~AEQLAPyLD~~~~~~~EsymLpvL~rF~G~PeV-se~G~IVY~FPe 333 (514)
+.|-++|.++|+++. +=+=|||.-+|....-.-...-+..-|-..+ -..| +++|.-+|..|+
T Consensus 4 ~~R~~~I~~li~~~~-i~sQ~eL~~~L~~~Gi~vTQaTiSRDLkeL~-~vKv~~~~g~~~Y~l~~ 66 (70)
T PF01316_consen 4 SKRQELIKELISEHE-ISSQEELVELLEEEGIEVTQATISRDLKELG-AVKVPDGNGKYRYVLPE 66 (70)
T ss_dssp HHHHHHHHHHHHHS----SHHHHHHHHHHTT-T--HHHHHHHHHHHT--EEEECTTSSEEEE-TT
T ss_pred HHHHHHHHHHHHHCC-cCCHHHHHHHHHHcCCCcchhHHHHHHHHcC-cEEeeCCCCCEEEEecC
Confidence 467889999999887 7888999998875432234455555565554 4455 589999999986
Done!