Query 029662
Match_columns 190
No_of_seqs 16 out of 18
Neff 2.2
Searched_HMMs 46136
Date Fri Mar 29 16:30:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029662.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029662hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF06784 UPF0240: Uncharacteri 97.7 0.00013 2.8E-09 60.2 7.5 106 66-178 54-162 (179)
2 PF02796 HTH_7: Helix-turn-hel 96.5 0.0035 7.7E-08 40.5 3.4 39 129-174 5-43 (45)
3 PF08784 RPA_C: Replication pr 94.8 0.036 7.8E-07 40.1 3.5 41 136-177 50-90 (102)
4 PF13936 HTH_38: Helix-turn-he 94.2 0.076 1.6E-06 34.4 3.7 39 129-174 4-42 (44)
5 PF04218 CENP-B_N: CENP-B N-te 94.1 0.056 1.2E-06 36.4 3.0 39 129-174 6-44 (53)
6 PF09012 FeoC: FeoC like trans 94.0 0.047 1E-06 37.5 2.5 36 134-177 4-39 (69)
7 PRK04217 hypothetical protein; 94.0 0.18 3.8E-06 39.3 5.9 59 108-174 22-80 (110)
8 PHA00675 hypothetical protein 93.6 0.19 4.2E-06 38.0 5.3 45 125-175 18-62 (78)
9 PF01047 MarR: MarR family; I 93.6 0.13 2.8E-06 33.2 3.9 41 130-176 1-41 (59)
10 PF13412 HTH_24: Winged helix- 92.7 0.44 9.5E-06 30.1 5.2 27 150-176 15-41 (48)
11 smart00346 HTH_ICLR helix_turn 92.5 0.33 7.2E-06 33.2 4.8 40 133-176 5-44 (91)
12 COG3355 Predicted transcriptio 92.5 0.14 3E-06 41.1 3.3 28 149-176 39-66 (126)
13 smart00421 HTH_LUXR helix_turn 92.5 0.49 1.1E-05 28.7 5.1 38 128-174 2-40 (58)
14 PF08765 Mor: Mor transcriptio 92.4 0.2 4.4E-06 37.4 3.9 44 124-175 50-95 (108)
15 PF06413 Neugrin: Neugrin; In 92.1 0.36 7.7E-06 41.5 5.5 56 123-182 4-59 (225)
16 PF02082 Rrf2: Transcriptional 92.0 0.33 7.1E-06 34.2 4.4 40 135-177 11-50 (83)
17 PF04545 Sigma70_r4: Sigma-70, 91.7 0.39 8.4E-06 30.7 4.2 38 130-174 5-42 (50)
18 PF13518 HTH_28: Helix-turn-he 91.7 0.39 8.5E-06 30.0 4.0 33 137-176 4-36 (52)
19 cd06171 Sigma70_r4 Sigma70, re 91.6 0.57 1.2E-05 27.6 4.6 39 129-175 10-49 (55)
20 PF08281 Sigma70_r4_2: Sigma-7 91.6 0.35 7.5E-06 31.0 3.8 35 134-174 14-48 (54)
21 PF08279 HTH_11: HTH domain; 91.5 0.22 4.8E-06 32.0 2.9 28 149-176 12-39 (55)
22 PF09339 HTH_IclR: IclR helix- 91.3 0.22 4.7E-06 32.4 2.7 29 148-176 14-42 (52)
23 PF10668 Phage_terminase: Phag 91.1 0.3 6.5E-06 34.9 3.5 31 137-171 11-41 (60)
24 COG4367 Uncharacterized protei 91.0 0.51 1.1E-05 37.1 4.8 49 129-179 2-50 (97)
25 cd00092 HTH_CRP helix_turn_hel 90.5 0.8 1.7E-05 29.5 4.8 40 138-177 9-50 (67)
26 TIGR00738 rrf2_super rrf2 fami 90.4 0.66 1.4E-05 34.1 4.8 30 148-177 21-50 (132)
27 PF04703 FaeA: FaeA-like prote 90.2 0.22 4.8E-06 35.3 2.0 28 150-177 13-40 (62)
28 smart00420 HTH_DEOR helix_turn 90.0 0.47 1E-05 28.9 3.2 27 151-177 13-39 (53)
29 TIGR02944 suf_reg_Xantho FeS a 89.6 0.79 1.7E-05 34.2 4.8 29 149-177 22-50 (130)
30 TIGR00180 parB_part ParB-like 89.0 0.33 7.1E-06 38.9 2.5 29 153-181 121-149 (187)
31 PF08100 Dimerisation: Dimeris 89.0 0.64 1.4E-05 31.8 3.5 26 151-176 21-50 (51)
32 PF13463 HTH_27: Winged helix 88.9 1.1 2.4E-05 29.2 4.5 42 130-176 1-42 (68)
33 cd00569 HTH_Hin_like Helix-tur 88.8 1.8 4E-05 22.5 4.6 36 130-172 6-41 (42)
34 PF12298 Bot1p: Eukaryotic mit 88.7 1.7 3.8E-05 36.0 6.6 58 104-178 2-59 (172)
35 PF01978 TrmB: Sugar-specific 88.3 0.25 5.5E-06 33.2 1.2 28 149-176 19-46 (68)
36 PF12802 MarR_2: MarR family; 88.2 1.3 2.8E-05 28.4 4.5 43 130-176 3-45 (62)
37 smart00351 PAX Paired Box doma 87.8 1.6 3.4E-05 33.4 5.4 43 125-174 13-55 (125)
38 smart00345 HTH_GNTR helix_turn 87.3 2.3 5E-05 26.4 5.1 26 152-177 19-45 (60)
39 TIGR02010 IscR iron-sulfur clu 87.3 1.2 2.7E-05 33.8 4.6 28 150-177 23-50 (135)
40 PRK11014 transcriptional repre 87.3 0.94 2E-05 34.6 4.0 27 151-177 24-50 (141)
41 PF04255 DUF433: Protein of un 86.9 1.4 3E-05 29.8 4.2 48 118-175 6-55 (56)
42 PF05225 HTH_psq: helix-turn-h 86.5 2.2 4.7E-05 28.0 4.8 36 133-174 3-38 (45)
43 cd06170 LuxR_C_like C-terminal 86.3 2.4 5.2E-05 25.9 4.7 22 153-174 16-37 (57)
44 PRK10857 DNA-binding transcrip 85.9 1.5 3.2E-05 35.4 4.6 28 150-177 23-50 (164)
45 cd00131 PAX Paired Box domain 85.9 2.2 4.7E-05 33.0 5.3 43 125-174 13-55 (128)
46 PRK10163 DNA-binding transcrip 85.7 3.2 6.9E-05 34.9 6.6 45 128-176 20-64 (271)
47 PF13384 HTH_23: Homeodomain-l 85.2 1.5 3.2E-05 27.6 3.5 22 153-174 18-39 (50)
48 PHA02943 hypothetical protein; 85.2 1.4 3.1E-05 37.3 4.3 37 134-176 12-48 (165)
49 PF08535 KorB: KorB domain; I 84.1 0.74 1.6E-05 33.2 1.9 29 153-181 4-32 (93)
50 smart00419 HTH_CRP helix_turn_ 84.0 1.5 3.1E-05 26.6 2.9 25 152-176 8-32 (48)
51 PRK11920 rirA iron-responsive 83.9 1.1 2.4E-05 35.4 3.0 29 149-177 21-49 (153)
52 PF14394 DUF4423: Domain of un 83.5 1.5 3.3E-05 35.6 3.7 37 134-177 28-66 (171)
53 PF14502 HTH_41: Helix-turn-he 83.5 1.2 2.6E-05 31.0 2.6 25 153-177 7-31 (48)
54 PRK15431 ferrous iron transpor 83.5 2.4 5.1E-05 31.9 4.4 37 132-176 4-40 (78)
55 TIGR02937 sigma70-ECF RNA poly 83.5 2 4.3E-05 29.7 3.8 23 153-175 127-149 (158)
56 PF13404 HTH_AsnC-type: AsnC-t 82.9 2.8 6.2E-05 27.2 4.1 35 136-175 6-40 (42)
57 TIGR02393 RpoD_Cterm RNA polym 82.5 2.5 5.5E-05 34.5 4.6 38 135-174 181-218 (238)
58 smart00347 HTH_MARR helix_turn 81.7 4.2 9.2E-05 27.2 4.8 42 129-176 7-48 (101)
59 smart00344 HTH_ASNC helix_turn 81.6 2.9 6.2E-05 29.8 4.1 35 137-176 7-41 (108)
60 TIGR02999 Sig-70_X6 RNA polyme 81.3 3 6.6E-05 31.6 4.4 31 136-174 140-172 (183)
61 PRK09834 DNA-binding transcrip 81.0 2.3 5.1E-05 35.4 4.0 29 148-176 22-50 (263)
62 PRK12542 RNA polymerase sigma 81.0 2.5 5.4E-05 32.5 3.9 30 136-173 128-159 (185)
63 TIGR01889 Staph_reg_Sar staphy 80.8 4.5 9.9E-05 29.6 5.0 46 129-176 22-67 (109)
64 PF01022 HTH_5: Bacterial regu 80.7 1.8 4E-05 27.7 2.6 26 151-176 14-39 (47)
65 PF04760 IF2_N: Translation in 80.5 0.99 2.2E-05 29.7 1.3 28 151-178 2-30 (54)
66 TIGR02392 rpoH_proteo alternat 80.4 2.9 6.3E-05 35.0 4.4 36 135-174 223-258 (270)
67 PF09286 Pro-kuma_activ: Pro-k 80.4 5.5 0.00012 30.2 5.5 47 131-177 25-72 (143)
68 PRK12547 RNA polymerase sigma 80.2 2.9 6.2E-05 31.7 3.9 22 153-174 129-150 (164)
69 PRK09652 RNA polymerase sigma 80.0 3 6.5E-05 30.8 3.9 23 152-174 144-166 (182)
70 TIGR02885 spore_sigF RNA polym 80.0 2.8 6.1E-05 33.7 4.0 33 136-174 189-221 (231)
71 PRK12543 RNA polymerase sigma 80.0 2.9 6.3E-05 32.1 3.9 20 153-172 134-153 (179)
72 PRK06759 RNA polymerase factor 79.9 3.3 7.1E-05 30.4 4.1 22 153-174 123-144 (154)
73 PF01726 LexA_DNA_bind: LexA D 79.9 1.3 2.8E-05 31.1 1.8 30 147-176 20-50 (65)
74 PRK00215 LexA repressor; Valid 79.9 3.1 6.6E-05 33.1 4.1 47 129-176 1-48 (205)
75 PF01710 HTH_Tnp_IS630: Transp 79.8 6 0.00013 29.8 5.5 42 129-178 56-97 (119)
76 smart00418 HTH_ARSR helix_turn 79.8 2.8 6.1E-05 25.5 3.2 28 150-177 8-35 (66)
77 TIGR02948 SigW_bacill RNA poly 79.8 2.6 5.7E-05 31.8 3.6 24 152-175 152-175 (187)
78 TIGR02997 Sig70-cyanoRpoD RNA 79.7 3.4 7.4E-05 35.2 4.6 37 136-174 255-291 (298)
79 TIGR00122 birA_repr_reg BirA b 79.7 2.3 5.1E-05 28.7 3.0 27 151-177 12-38 (69)
80 PRK06811 RNA polymerase factor 79.6 3 6.4E-05 32.4 3.9 22 153-174 148-169 (189)
81 PRK10870 transcriptional repre 79.2 5.1 0.00011 32.0 5.3 44 129-176 52-95 (176)
82 PRK12512 RNA polymerase sigma 79.1 3.2 6.9E-05 31.7 3.9 22 153-174 148-169 (184)
83 PF12840 HTH_20: Helix-turn-he 78.9 2.8 6.1E-05 27.8 3.1 34 136-174 13-46 (61)
84 PRK09047 RNA polymerase factor 78.8 4.1 8.8E-05 30.0 4.3 31 136-174 112-144 (161)
85 smart00342 HTH_ARAC helix_turn 78.3 2.8 6.1E-05 26.8 2.9 24 152-175 1-24 (84)
86 cd07377 WHTH_GntR Winged helix 78.2 10 0.00023 23.8 5.5 24 153-176 26-49 (66)
87 smart00550 Zalpha Z-DNA-bindin 78.2 3 6.4E-05 28.9 3.2 24 153-176 23-46 (68)
88 PRK12528 RNA polymerase sigma 78.0 3.8 8.2E-05 30.6 3.9 30 136-173 119-150 (161)
89 PRK10430 DNA-binding transcrip 77.8 6.5 0.00014 31.2 5.4 45 129-176 158-202 (239)
90 PF01325 Fe_dep_repress: Iron 77.4 6.4 0.00014 27.0 4.6 37 135-176 10-46 (60)
91 smart00342 HTH_ARAC helix_turn 77.0 7 0.00015 25.0 4.5 45 130-180 34-80 (84)
92 PRK07405 RNA polymerase sigma 76.7 4.5 9.8E-05 35.3 4.6 36 136-173 262-297 (317)
93 PRK09639 RNA polymerase sigma 76.7 4.6 0.0001 30.0 4.0 22 153-174 128-149 (166)
94 PRK08301 sporulation sigma fac 76.5 3.7 8E-05 33.0 3.8 36 136-173 184-219 (234)
95 PRK13919 putative RNA polymera 76.5 4.2 9.1E-05 31.0 3.9 22 153-174 152-173 (186)
96 PRK07037 extracytoplasmic-func 76.5 4.5 9.8E-05 30.1 4.0 21 153-173 126-146 (163)
97 PRK12530 RNA polymerase sigma 76.3 4.8 0.0001 31.5 4.2 31 135-173 139-171 (189)
98 PRK12523 RNA polymerase sigma 76.2 5.2 0.00011 30.4 4.3 31 135-173 124-156 (172)
99 PF00165 HTH_AraC: Bacterial r 76.1 4.3 9.2E-05 25.1 3.2 28 148-175 4-31 (42)
100 TIGR02943 Sig70_famx1 RNA poly 76.1 4.4 9.4E-05 31.8 4.0 21 153-173 148-168 (188)
101 TIGR02980 SigBFG RNA polymeras 76.0 4.4 9.5E-05 32.4 4.0 22 153-174 195-216 (227)
102 PRK12545 RNA polymerase sigma 76.0 4.3 9.2E-05 32.1 3.9 21 153-173 156-176 (201)
103 PRK12511 RNA polymerase sigma 75.9 5.1 0.00011 31.5 4.3 21 153-173 128-148 (182)
104 PRK12526 RNA polymerase sigma 75.9 4.3 9.2E-05 32.3 3.9 22 153-174 170-191 (206)
105 TIGR02431 pcaR_pcaU beta-ketoa 75.6 7.1 0.00015 32.0 5.2 40 133-176 9-48 (248)
106 PRK12529 RNA polymerase sigma 75.5 5.5 0.00012 30.7 4.3 30 136-173 133-164 (178)
107 PF08220 HTH_DeoR: DeoR-like h 75.3 3.2 6.9E-05 27.9 2.6 28 150-177 12-39 (57)
108 PRK12515 RNA polymerase sigma 75.2 4.7 0.0001 31.1 3.9 22 153-174 148-169 (189)
109 PF07638 Sigma70_ECF: ECF sigm 75.1 6.7 0.00015 31.0 4.8 24 153-176 152-175 (185)
110 PF04539 Sigma70_r3: Sigma-70 75.0 3.5 7.6E-05 28.0 2.8 27 151-177 19-45 (78)
111 PRK11924 RNA polymerase sigma 74.9 4.8 0.0001 29.6 3.7 22 153-174 142-163 (179)
112 PRK09637 RNA polymerase sigma 74.9 4.5 9.8E-05 31.6 3.8 22 153-174 123-144 (181)
113 PRK11923 algU RNA polymerase s 74.9 4.6 9.9E-05 31.1 3.7 23 152-174 154-176 (193)
114 PF13542 HTH_Tnp_ISL3: Helix-t 74.8 3.8 8.3E-05 25.9 2.8 22 153-174 28-49 (52)
115 PRK09642 RNA polymerase sigma 74.4 6.4 0.00014 29.3 4.3 21 153-173 123-143 (160)
116 PRK11512 DNA-binding transcrip 74.0 8 0.00017 29.2 4.8 42 129-176 37-78 (144)
117 PRK00118 putative DNA-binding 73.9 6.9 0.00015 30.2 4.5 34 135-174 22-55 (104)
118 TIGR02950 SigM_subfam RNA poly 73.7 2 4.3E-05 31.4 1.4 24 151-174 120-143 (154)
119 PRK09649 RNA polymerase sigma 73.6 5.3 0.00011 31.1 3.8 22 153-174 147-168 (185)
120 PRK12541 RNA polymerase sigma 73.5 5.2 0.00011 29.9 3.7 22 153-174 129-150 (161)
121 TIGR03209 P21_Cbot clostridium 73.5 4.1 8.8E-05 29.9 3.0 28 135-170 112-141 (142)
122 PRK11569 transcriptional repre 73.4 9.8 0.00021 32.0 5.6 41 132-176 27-67 (274)
123 PRK12536 RNA polymerase sigma 73.2 5.4 0.00012 30.7 3.8 21 153-173 146-166 (181)
124 PRK09651 RNA polymerase sigma 73.2 5 0.00011 30.7 3.6 32 136-173 125-156 (172)
125 PF06056 Terminase_5: Putative 73.2 6 0.00013 27.4 3.6 22 153-174 14-35 (58)
126 TIGR02983 SigE-fam_strep RNA p 73.1 5.5 0.00012 29.6 3.7 22 153-174 127-148 (162)
127 PRK12537 RNA polymerase sigma 72.5 5.6 0.00012 30.6 3.7 21 153-173 150-170 (182)
128 PRK12531 RNA polymerase sigma 72.3 6.1 0.00013 30.8 3.9 30 136-173 147-178 (194)
129 COG2442 Uncharacterized conser 71.5 12 0.00025 27.8 5.0 53 114-176 14-68 (79)
130 PRK12519 RNA polymerase sigma 71.5 5.5 0.00012 30.6 3.5 22 153-174 158-179 (194)
131 TIGR01884 cas_HTH CRISPR locus 71.4 8.1 0.00017 31.2 4.5 98 74-177 72-182 (203)
132 PRK06596 RNA polymerase factor 71.4 7 0.00015 33.4 4.4 35 136-174 236-270 (284)
133 PRK05572 sporulation sigma fac 71.3 6.7 0.00014 32.3 4.1 33 136-174 208-240 (252)
134 cd00090 HTH_ARSR Arsenical Res 71.0 14 0.00031 22.8 4.7 24 153-176 21-44 (78)
135 TIGR02147 Fsuc_second hypothet 70.7 5.3 0.00012 35.0 3.6 36 134-176 126-163 (271)
136 PRK12527 RNA polymerase sigma 70.6 7.4 0.00016 29.0 3.9 21 153-173 122-142 (159)
137 PRK12534 RNA polymerase sigma 70.5 8.2 0.00018 29.5 4.2 22 153-174 154-175 (187)
138 COG3415 Transposase and inacti 70.5 7.7 0.00017 31.4 4.2 36 132-175 9-44 (138)
139 PRK05803 sporulation sigma fac 70.5 6.3 0.00014 32.0 3.7 36 136-173 181-216 (233)
140 TIGR02952 Sig70_famx2 RNA poly 70.4 7.7 0.00017 28.7 3.9 22 153-174 139-160 (170)
141 PRK09643 RNA polymerase sigma 69.9 8.5 0.00018 30.1 4.3 30 136-173 140-171 (192)
142 PRK07500 rpoH2 RNA polymerase 69.3 8.3 0.00018 33.1 4.4 35 136-174 233-267 (289)
143 PRK13413 mpi multiple promoter 69.3 14 0.0003 29.5 5.4 35 133-174 160-194 (200)
144 TIGR02959 SigZ RNA polymerase 69.2 8.2 0.00018 29.6 4.0 31 136-174 106-138 (170)
145 TIGR02716 C20_methyl_CrtF C-20 69.1 4.7 0.0001 33.9 2.8 28 150-177 21-48 (306)
146 PRK05602 RNA polymerase sigma 69.1 7.4 0.00016 29.8 3.7 23 152-174 144-166 (186)
147 TIGR01764 excise DNA binding d 69.1 7.4 0.00016 23.3 3.0 28 153-180 2-29 (49)
148 cd00086 homeodomain Homeodomai 68.9 12 0.00026 23.5 4.1 45 128-174 5-49 (59)
149 PRK09646 RNA polymerase sigma 68.9 7.8 0.00017 30.2 3.9 21 153-173 159-179 (194)
150 PRK12546 RNA polymerase sigma 68.7 8.5 0.00019 30.5 4.1 21 153-173 130-150 (188)
151 PRK12513 RNA polymerase sigma 68.6 4.3 9.2E-05 31.4 2.3 23 151-173 154-176 (194)
152 PF12824 MRP-L20: Mitochondria 68.6 6.9 0.00015 32.3 3.6 59 104-173 67-125 (164)
153 TIGR02850 spore_sigG RNA polym 68.6 8.4 0.00018 31.8 4.2 33 136-174 212-244 (254)
154 PRK12538 RNA polymerase sigma 68.5 6.6 0.00014 32.5 3.6 22 153-174 188-209 (233)
155 PRK09645 RNA polymerase sigma 68.4 10 0.00022 28.6 4.3 31 135-173 123-155 (173)
156 PRK12533 RNA polymerase sigma 68.0 6.8 0.00015 32.1 3.5 22 153-174 151-172 (216)
157 PRK03573 transcriptional regul 67.9 15 0.00032 27.5 5.0 44 128-176 27-70 (144)
158 PRK12525 RNA polymerase sigma 67.9 9.2 0.0002 29.1 4.0 30 136-173 124-155 (168)
159 cd04761 HTH_MerR-SF Helix-Turn 67.9 9.7 0.00021 23.3 3.4 29 153-181 1-29 (49)
160 PRK07408 RNA polymerase sigma 67.8 8.3 0.00018 32.2 4.0 34 135-174 208-241 (256)
161 PRK06986 fliA flagellar biosyn 67.6 8.9 0.00019 31.1 4.1 23 152-174 200-222 (236)
162 COG1959 Predicted transcriptio 67.6 7.9 0.00017 30.7 3.7 26 152-177 25-50 (150)
163 TIGR02984 Sig-70_plancto1 RNA 67.2 10 0.00022 28.6 4.1 23 152-174 156-178 (189)
164 PF13551 HTH_29: Winged helix- 67.2 12 0.00026 26.0 4.2 22 154-175 14-35 (112)
165 TIGR02985 Sig70_bacteroi1 RNA 67.1 10 0.00022 27.3 3.9 23 153-175 130-152 (161)
166 TIGR02899 spore_safA spore coa 67.1 6.3 0.00014 23.1 2.4 21 154-174 6-26 (44)
167 PRK09641 RNA polymerase sigma 66.9 9 0.00019 28.9 3.7 24 151-174 151-174 (187)
168 PRK12514 RNA polymerase sigma 66.8 11 0.00024 28.6 4.2 22 153-174 146-167 (179)
169 PRK12516 RNA polymerase sigma 66.8 11 0.00025 29.6 4.4 31 135-173 121-153 (187)
170 PRK12540 RNA polymerase sigma 66.7 8.9 0.00019 30.0 3.8 21 153-173 128-148 (182)
171 PF00046 Homeobox: Homeobox do 66.4 8 0.00017 24.8 2.9 44 129-174 6-49 (57)
172 PRK11922 RNA polymerase sigma 66.3 5.8 0.00013 32.1 2.8 24 150-173 163-186 (231)
173 PRK12544 RNA polymerase sigma 66.3 12 0.00025 30.2 4.5 21 153-173 165-185 (206)
174 PRK06930 positive control sigm 66.2 12 0.00025 30.4 4.5 32 135-174 119-152 (170)
175 PRK09647 RNA polymerase sigma 66.1 9.4 0.0002 30.7 3.9 21 153-173 155-175 (203)
176 PRK07921 RNA polymerase sigma 66.0 11 0.00023 33.4 4.6 36 136-173 268-303 (324)
177 PRK05988 formate dehydrogenase 65.8 12 0.00026 30.2 4.4 48 131-178 7-67 (156)
178 PRK05911 RNA polymerase sigma 65.7 9.6 0.00021 31.9 4.0 33 136-174 211-243 (257)
179 TIGR02941 Sigma_B RNA polymera 65.5 11 0.00023 31.0 4.2 33 136-174 211-243 (255)
180 TIGR02337 HpaR homoprotocatech 65.5 16 0.00034 26.6 4.7 42 129-176 25-66 (118)
181 PRK10219 DNA-binding transcrip 65.2 7.8 0.00017 27.7 3.0 28 148-175 17-44 (107)
182 PF00392 GntR: Bacterial regul 65.2 18 0.00039 24.1 4.5 26 152-177 23-49 (64)
183 TIGR00721 tfx DNA-binding prot 65.2 15 0.00034 29.6 5.0 39 128-174 5-43 (137)
184 PRK05949 RNA polymerase sigma 65.1 12 0.00025 33.1 4.6 36 136-173 272-307 (327)
185 cd04762 HTH_MerR-trunc Helix-T 65.1 11 0.00023 22.3 3.1 29 153-181 1-29 (49)
186 PRK08241 RNA polymerase factor 65.0 7.8 0.00017 32.8 3.4 21 153-173 170-190 (339)
187 PRK08583 RNA polymerase sigma 64.8 10 0.00022 31.2 3.9 33 136-174 211-243 (257)
188 PF12728 HTH_17: Helix-turn-he 64.7 9.4 0.0002 24.2 3.0 29 153-181 2-30 (51)
189 PRK15090 DNA-binding transcrip 64.7 19 0.00041 29.8 5.5 41 131-176 12-52 (257)
190 TIGR02960 SigX5 RNA polymerase 64.6 8.7 0.00019 32.0 3.6 22 153-174 159-180 (324)
191 TIGR00498 lexA SOS regulatory 64.5 8 0.00017 30.7 3.2 28 149-176 22-50 (199)
192 TIGR02846 spore_sigmaK RNA pol 64.3 11 0.00023 30.6 3.9 22 153-174 195-216 (227)
193 TIGR02954 Sig70_famx3 RNA poly 64.2 10 0.00022 28.5 3.6 21 153-173 136-156 (169)
194 PRK07122 RNA polymerase sigma 64.1 11 0.00024 31.8 4.1 33 136-174 221-253 (264)
195 PRK12524 RNA polymerase sigma 64.0 12 0.00025 29.3 4.0 22 153-174 153-174 (196)
196 PRK09636 RNA polymerase sigma 64.0 10 0.00022 31.9 3.8 22 153-174 132-153 (293)
197 PRK12539 RNA polymerase sigma 63.9 10 0.00023 29.2 3.7 21 153-173 148-168 (184)
198 PRK09415 RNA polymerase factor 63.7 10 0.00022 29.2 3.6 21 153-173 144-164 (179)
199 PF08280 HTH_Mga: M protein tr 63.7 20 0.00044 24.1 4.6 44 134-183 7-52 (59)
200 PRK07571 bidirectional hydroge 63.1 11 0.00024 31.0 3.9 50 131-180 20-82 (169)
201 PRK12532 RNA polymerase sigma 62.8 11 0.00024 29.2 3.6 21 153-173 153-173 (195)
202 PRK09648 RNA polymerase sigma 62.3 13 0.00028 28.6 3.9 21 153-173 156-176 (189)
203 smart00027 EH Eps15 homology d 62.1 35 0.00075 24.2 5.8 49 130-178 4-55 (96)
204 TIGR02531 yecD_yerC TrpR-relat 62.0 16 0.00035 27.3 4.2 25 153-177 51-75 (88)
205 PRK12520 RNA polymerase sigma 61.9 13 0.00027 28.8 3.8 21 153-173 148-168 (191)
206 TIGR02947 SigH_actino RNA poly 61.7 8.1 0.00018 29.9 2.7 21 153-173 148-168 (193)
207 PRK09210 RNA polymerase sigma 61.4 14 0.00031 32.8 4.6 36 136-173 311-346 (367)
208 PRK08215 sporulation sigma fac 61.4 14 0.0003 30.6 4.1 38 130-174 210-247 (258)
209 PRK12522 RNA polymerase sigma 61.2 16 0.00035 27.7 4.2 21 153-173 136-156 (173)
210 TIGR03879 near_KaiC_dom probab 61.2 12 0.00026 27.6 3.3 35 135-174 20-54 (73)
211 PF03444 HrcA_DNA-bdg: Winged 61.0 18 0.0004 27.2 4.4 38 135-176 10-47 (78)
212 TIGR02939 RpoE_Sigma70 RNA pol 60.9 11 0.00025 28.4 3.3 23 151-173 153-175 (190)
213 cd07153 Fur_like Ferric uptake 60.7 20 0.00043 25.8 4.4 37 137-177 5-46 (116)
214 cd03073 PDI_b'_ERp72_ERp57 PDI 60.5 12 0.00026 28.1 3.3 28 155-182 40-75 (111)
215 PRK06288 RNA polymerase sigma 60.4 13 0.00029 30.9 4.0 32 136-173 218-249 (268)
216 PF04433 SWIRM: SWIRM domain; 60.4 8.6 0.00019 27.3 2.5 38 137-177 41-79 (86)
217 PF13551 HTH_29: Winged helix- 60.3 41 0.00089 23.3 5.8 45 130-174 58-109 (112)
218 PRK07598 RNA polymerase sigma 60.2 14 0.0003 34.5 4.3 36 136-173 356-391 (415)
219 PRK11169 leucine-responsive tr 60.2 18 0.00039 28.4 4.4 35 137-176 18-52 (164)
220 COG2345 Predicted transcriptio 59.8 15 0.00033 31.8 4.3 37 136-176 13-49 (218)
221 TIGR02479 FliA_WhiG RNA polyme 59.8 16 0.00034 29.4 4.1 23 152-174 191-213 (224)
222 PF13411 MerR_1: MerR HTH fami 59.2 12 0.00026 24.6 2.8 30 153-182 1-30 (69)
223 PRK05472 redox-sensing transcr 59.1 14 0.0003 30.0 3.7 49 123-176 5-56 (213)
224 PF00196 GerE: Bacterial regul 58.7 37 0.0008 22.1 5.1 35 130-172 4-38 (58)
225 PRK12535 RNA polymerase sigma 58.7 14 0.0003 29.4 3.6 21 153-173 150-170 (196)
226 COG1846 MarR Transcriptional r 58.6 25 0.00053 24.0 4.4 41 130-176 20-60 (126)
227 smart00422 HTH_MERR helix_turn 58.3 16 0.00034 23.9 3.3 29 153-181 1-29 (70)
228 PRK13239 alkylmercury lyase; P 58.3 19 0.00041 31.0 4.6 38 135-177 24-61 (206)
229 PF01476 LysM: LysM domain; I 58.2 11 0.00023 22.9 2.3 20 154-173 8-27 (44)
230 smart00389 HOX Homeodomain. DN 58.2 27 0.00059 21.9 4.3 45 128-174 5-49 (56)
231 PRK12427 flagellar biosynthesi 57.8 16 0.00035 30.2 4.0 33 136-174 189-221 (231)
232 PF00888 Cullin: Cullin family 57.5 8.8 0.00019 34.4 2.5 47 128-179 514-561 (588)
233 PF07180 DUF1401: Protein of u 57.5 10 0.00022 31.6 2.8 32 141-178 33-64 (146)
234 TIGR00426 competence protein C 57.0 26 0.00057 23.8 4.3 45 130-178 25-69 (69)
235 TIGR02957 SigX4 RNA polymerase 56.7 16 0.00036 30.7 3.9 22 153-174 125-146 (281)
236 cd01104 HTH_MlrA-CarA Helix-Tu 56.2 22 0.00048 23.2 3.7 27 153-179 1-27 (68)
237 PF12793 SgrR_N: Sugar transpo 55.4 24 0.00053 27.2 4.4 39 137-176 5-43 (115)
238 PRK09638 RNA polymerase sigma 54.8 13 0.00027 28.0 2.7 23 151-173 141-163 (176)
239 PRK08295 RNA polymerase factor 54.5 28 0.0006 26.9 4.6 22 153-174 171-192 (208)
240 TIGR03734 PRTRC_parB PRTRC sys 54.5 20 0.00043 35.0 4.5 29 153-181 110-138 (554)
241 PRK05901 RNA polymerase sigma 54.3 19 0.00041 34.5 4.3 36 136-173 453-488 (509)
242 TIGR02844 spore_III_D sporulat 53.4 14 0.00031 27.3 2.7 25 151-175 18-42 (80)
243 PF14493 HTH_40: Helix-turn-he 53.3 21 0.00046 25.5 3.5 33 137-176 5-38 (91)
244 PRK13832 plasmid partitioning 53.3 21 0.00045 34.9 4.4 29 153-181 119-147 (520)
245 cd00118 LysM Lysin domain, fou 53.0 16 0.00036 20.0 2.4 22 154-175 10-31 (46)
246 TIGR00373 conserved hypothetic 53.0 17 0.00036 29.2 3.2 27 150-176 26-52 (158)
247 COG4565 CitB Response regulato 52.7 51 0.0011 29.2 6.4 53 119-176 145-197 (224)
248 PRK11511 DNA-binding transcrip 52.5 37 0.00079 25.6 4.8 25 150-174 23-47 (127)
249 PRK09644 RNA polymerase sigma 52.4 27 0.00059 26.2 4.1 22 153-174 125-146 (165)
250 PRK07406 RNA polymerase sigma 51.8 26 0.00055 32.0 4.6 38 135-174 316-353 (373)
251 PRK06266 transcription initiat 51.5 18 0.00038 29.8 3.2 27 150-176 34-60 (178)
252 COG1595 RpoE DNA-directed RNA 51.4 29 0.00064 26.7 4.3 33 136-174 133-165 (182)
253 PF13994 PgaD: PgaD-like prote 51.2 18 0.00039 28.2 3.1 33 142-174 89-122 (138)
254 PF02022 Integrase_Zn: Integra 51.2 18 0.0004 23.8 2.7 22 154-175 11-32 (40)
255 PRK12517 RNA polymerase sigma 50.9 29 0.00063 27.3 4.2 21 153-173 145-165 (188)
256 PRK06704 RNA polymerase factor 50.4 25 0.00054 29.7 4.0 32 136-173 122-153 (228)
257 PF05361 PP1_inhibitor: PKC-ac 50.4 33 0.00071 28.6 4.6 100 76-181 1-104 (144)
258 PF13613 HTH_Tnp_4: Helix-turn 50.2 16 0.00036 24.0 2.3 24 153-176 20-43 (53)
259 PF09681 Phage_rep_org_N: N-te 50.1 31 0.00067 27.1 4.2 29 149-177 50-78 (121)
260 PRK11050 manganese transport r 50.0 20 0.00044 28.1 3.2 27 151-177 50-76 (152)
261 TIGR02989 Sig-70_gvs1 RNA poly 49.8 41 0.0009 24.6 4.7 21 153-173 128-148 (159)
262 PRK07670 RNA polymerase sigma 49.5 34 0.00074 28.1 4.6 33 135-173 206-238 (251)
263 TIGR02394 rpoS_proteo RNA poly 49.3 38 0.00082 28.6 4.9 37 136-174 228-264 (285)
264 PRK03902 manganese transport t 49.3 44 0.00096 25.4 4.9 41 132-176 6-46 (142)
265 cd05025 S-100A1 S-100A1: S-100 49.1 68 0.0015 22.5 5.5 49 131-181 7-66 (92)
266 TIGR02835 spore_sigmaE RNA pol 49.1 27 0.00059 28.4 4.0 23 152-174 198-220 (234)
267 TIGR03001 Sig-70_gmx1 RNA poly 49.1 31 0.00068 29.0 4.4 21 153-173 178-198 (244)
268 PRK05658 RNA polymerase sigma 49.0 25 0.00055 33.4 4.3 36 136-173 562-597 (619)
269 PF04297 UPF0122: Putative hel 48.8 28 0.0006 27.1 3.7 33 136-174 23-55 (101)
270 PF09171 DUF1886: Domain of un 47.9 7.4 0.00016 34.3 0.5 13 65-77 15-27 (246)
271 PF02002 TFIIE_alpha: TFIIE al 47.8 13 0.00028 27.1 1.7 28 150-177 25-52 (105)
272 PF03297 Ribosomal_S25: S25 ri 46.7 14 0.0003 28.8 1.8 27 151-177 58-84 (105)
273 PF04967 HTH_10: HTH DNA bindi 46.7 88 0.0019 21.6 5.6 41 133-173 4-44 (53)
274 PF13730 HTH_36: Helix-turn-he 46.3 75 0.0016 20.1 5.7 23 154-176 27-49 (55)
275 PRK09483 response regulator; P 45.7 53 0.0011 24.4 4.7 38 128-173 147-184 (217)
276 PF01257 2Fe-2S_thioredx: Thio 45.6 23 0.00051 27.7 3.0 27 154-180 33-59 (145)
277 TIGR01610 phage_O_Nterm phage 45.5 79 0.0017 23.0 5.5 47 129-176 22-71 (95)
278 PRK03975 tfx putative transcri 45.4 51 0.0011 26.7 4.9 38 129-174 6-43 (141)
279 PRK07539 NADH dehydrogenase su 45.3 25 0.00053 27.9 3.1 44 134-178 23-66 (154)
280 PF02186 TFIIE_beta: TFIIE bet 45.2 28 0.00061 24.8 3.1 40 132-177 4-43 (65)
281 TIGR02787 codY_Gpos GTP-sensin 44.8 47 0.001 29.9 5.0 48 125-176 172-222 (251)
282 PF03979 Sigma70_r1_1: Sigma-7 44.5 28 0.0006 24.9 2.9 43 130-177 4-49 (82)
283 PRK13777 transcriptional regul 43.9 55 0.0012 27.2 5.0 42 129-176 42-83 (185)
284 PF05402 PqqD: Coenzyme PQQ sy 43.6 29 0.00063 22.9 2.8 35 136-177 20-59 (68)
285 PRK14584 hmsS hemin storage sy 43.5 31 0.00066 28.8 3.5 33 142-174 88-120 (153)
286 PHA02591 hypothetical protein; 43.5 25 0.00054 27.2 2.7 22 153-174 60-81 (83)
287 PRK13698 plasmid-partitioning 43.5 20 0.00043 32.9 2.5 29 153-181 177-205 (323)
288 PRK12373 NADH dehydrogenase su 43.1 33 0.0007 32.4 3.9 50 131-180 19-83 (400)
289 cd04764 HTH_MlrA-like_sg1 Heli 42.9 47 0.001 22.0 3.7 28 153-180 1-28 (67)
290 smart00529 HTH_DTXR Helix-turn 42.5 26 0.00056 24.2 2.5 23 155-177 2-24 (96)
291 PF11268 DUF3071: Protein of u 41.6 56 0.0012 27.3 4.7 33 129-171 56-88 (170)
292 PRK09635 sigI RNA polymerase s 41.4 36 0.00078 29.3 3.7 33 136-174 124-156 (290)
293 PRK09393 ftrA transcriptional 41.2 37 0.00081 28.6 3.7 40 133-175 218-257 (322)
294 PF11035 SnAPC_2_like: Small n 40.8 1.1E+02 0.0023 29.0 6.8 60 116-177 10-70 (344)
295 PRK15435 bifunctional DNA-bind 40.6 51 0.0011 29.6 4.6 40 130-174 82-121 (353)
296 TIGR02859 spore_sigH RNA polym 40.3 55 0.0012 25.0 4.2 23 152-174 165-187 (198)
297 PF10078 DUF2316: Uncharacteri 40.0 28 0.00061 26.7 2.5 25 152-176 23-47 (89)
298 PRK14585 pgaD putative PGA bio 39.5 34 0.00073 28.4 3.1 34 142-175 79-112 (137)
299 COG5566 Uncharacterized conser 39.3 51 0.0011 27.5 4.1 79 76-174 46-124 (137)
300 TIGR02395 rpoN_sigma RNA polym 39.3 33 0.00072 31.7 3.4 28 147-174 313-340 (429)
301 PRK12518 RNA polymerase sigma 39.3 32 0.00069 25.8 2.7 25 150-174 134-158 (175)
302 PF01843 DIL: DIL domain; Int 39.1 12 0.00026 27.2 0.4 17 129-145 86-102 (105)
303 PF01527 HTH_Tnp_1: Transposas 38.9 56 0.0012 21.7 3.6 38 132-176 9-47 (76)
304 PRK04214 rbn ribonuclease BN/u 38.9 68 0.0015 29.0 5.2 28 149-176 307-334 (412)
305 cd04763 HTH_MlrA-like Helix-Tu 38.8 58 0.0013 21.7 3.7 27 153-179 1-27 (68)
306 PRK11179 DNA-binding transcrip 38.7 59 0.0013 25.1 4.2 33 137-174 13-45 (153)
307 smart00531 TFIIE Transcription 38.5 37 0.00081 26.6 3.1 27 151-177 14-40 (147)
308 PRK09334 30S ribosomal protein 38.4 33 0.00071 26.2 2.7 27 150-176 39-65 (86)
309 PF01399 PCI: PCI domain; Int 38.4 51 0.0011 22.4 3.4 27 149-175 57-83 (105)
310 PF13545 HTH_Crp_2: Crp-like h 37.9 38 0.00081 22.4 2.6 28 149-176 25-52 (76)
311 PF14947 HTH_45: Winged helix- 37.6 60 0.0013 22.8 3.8 36 135-176 8-43 (77)
312 PRK13502 transcriptional activ 37.5 73 0.0016 25.9 4.7 39 133-174 176-214 (282)
313 COG2963 Transposase and inacti 37.4 62 0.0013 23.6 3.9 29 136-171 14-44 (116)
314 PRK13503 transcriptional activ 37.3 42 0.0009 27.0 3.3 39 133-174 171-209 (278)
315 TIGR01958 nuoE_fam NADH-quinon 37.1 32 0.00069 27.0 2.5 44 134-178 17-60 (148)
316 PRK09191 two-component respons 37.1 49 0.0011 25.8 3.6 33 135-173 93-125 (261)
317 PRK10572 DNA-binding transcrip 37.0 46 0.00099 27.3 3.5 38 134-174 184-221 (290)
318 TIGR02297 HpaA 4-hydroxyphenyl 36.4 97 0.0021 25.1 5.3 40 132-174 185-224 (287)
319 PRK05590 hypothetical protein; 36.4 23 0.0005 30.0 1.7 27 147-173 40-68 (166)
320 smart00257 LysM Lysin motif. 36.3 43 0.00094 18.0 2.4 21 154-174 9-29 (44)
321 PF13413 HTH_25: Helix-turn-he 36.0 34 0.00073 23.7 2.2 29 153-181 11-41 (62)
322 PRK09640 RNA polymerase sigma 35.9 39 0.00084 26.1 2.8 24 150-173 148-171 (188)
323 COG1522 Lrp Transcriptional re 35.5 71 0.0015 23.7 4.1 35 137-176 12-46 (154)
324 PF08461 HTH_12: Ribonuclease 35.3 53 0.0012 22.9 3.2 29 148-176 9-42 (66)
325 PF01381 HTH_3: Helix-turn-hel 35.0 52 0.0011 20.6 2.8 27 153-179 10-36 (55)
326 PF00356 LacI: Bacterial regul 34.8 44 0.00096 22.2 2.6 21 154-174 1-21 (46)
327 PF01710 HTH_Tnp_IS630: Transp 34.6 73 0.0016 24.0 4.0 25 153-177 19-43 (119)
328 PRK10360 DNA-binding transcrip 34.4 1.1E+02 0.0024 22.3 4.8 37 129-173 137-173 (196)
329 PF00325 Crp: Bacterial regula 34.1 46 0.001 21.1 2.4 25 152-176 2-26 (32)
330 PF02001 DUF134: Protein of un 34.0 1.3E+02 0.0029 23.5 5.5 60 107-174 20-79 (106)
331 PTZ00183 centrin; Provisional 33.8 1.5E+02 0.0031 21.4 5.4 48 130-177 11-63 (158)
332 PRK09413 IS2 repressor TnpA; R 33.7 49 0.0011 24.9 3.0 24 152-175 29-52 (121)
333 PRK09802 DNA-binding transcrip 33.1 41 0.0009 28.7 2.8 40 132-176 16-55 (269)
334 PRK05932 RNA polymerase factor 32.6 51 0.0011 30.9 3.4 27 148-174 339-365 (455)
335 PRK09935 transcriptional regul 32.3 1.3E+02 0.0027 22.0 4.8 36 130-173 150-185 (210)
336 PRK09685 DNA-binding transcrip 32.3 97 0.0021 25.4 4.7 23 153-175 215-237 (302)
337 PRK13500 transcriptional activ 32.1 1.2E+02 0.0025 25.8 5.3 40 132-174 205-244 (312)
338 PRK15201 fimbriae regulatory p 32.0 1E+02 0.0023 27.0 5.0 37 129-173 133-169 (198)
339 PF13560 HTH_31: Helix-turn-he 31.9 50 0.0011 21.7 2.5 22 153-174 15-36 (64)
340 cd01106 HTH_TipAL-Mta Helix-Tu 31.8 76 0.0017 23.0 3.6 29 153-181 1-29 (103)
341 PF04963 Sigma54_CBD: Sigma-54 31.8 49 0.0011 27.0 2.9 28 149-176 47-76 (194)
342 PF06971 Put_DNA-bind_N: Putat 31.0 40 0.00088 23.1 1.9 19 153-171 29-47 (50)
343 PRK12423 LexA repressor; Provi 30.8 56 0.0012 26.6 3.0 26 149-174 22-48 (202)
344 KOG3062 RNA polymerase II elon 30.6 1.3E+02 0.0027 27.8 5.4 83 57-162 188-271 (281)
345 COG1321 TroR Mn-dependent tran 30.4 1.1E+02 0.0023 24.8 4.5 28 149-176 21-48 (154)
346 COG2207 AraC AraC-type DNA-bin 29.9 64 0.0014 22.0 2.8 26 149-174 33-58 (127)
347 cd04780 HTH_MerR-like_sg5 Heli 29.7 83 0.0018 23.1 3.6 29 153-181 1-29 (95)
348 smart00753 PAM PCI/PINT associ 29.7 51 0.0011 22.6 2.3 25 151-175 23-47 (88)
349 smart00088 PINT motif in prote 29.7 51 0.0011 22.6 2.3 25 151-175 23-47 (88)
350 PF05331 DUF742: Protein of un 29.6 62 0.0013 25.5 3.0 40 127-174 38-77 (114)
351 PRK10141 DNA-binding transcrip 29.2 91 0.002 24.3 3.9 27 150-176 28-54 (117)
352 PRK10046 dpiA two-component re 29.2 65 0.0014 25.4 3.1 40 136-180 165-205 (225)
353 COG4189 Predicted transcriptio 29.1 68 0.0015 29.6 3.6 30 137-171 27-56 (308)
354 PF12949 HeH: HeH/LEM domain; 28.9 39 0.00084 21.9 1.5 17 127-143 1-17 (35)
355 COG1961 PinR Site-specific rec 28.6 1.3E+02 0.0029 24.2 4.8 48 125-181 159-206 (222)
356 PF13443 HTH_26: Cro/C1-type H 28.6 1.2E+02 0.0025 19.5 3.8 22 153-174 11-32 (63)
357 PRK10100 DNA-binding transcrip 28.2 1.3E+02 0.0028 24.7 4.8 37 129-173 155-191 (216)
358 cd00213 S-100 S-100: S-100 dom 28.1 2E+02 0.0043 19.7 5.4 47 134-180 6-64 (88)
359 PRK07921 RNA polymerase sigma 28.0 79 0.0017 28.1 3.7 32 149-180 186-221 (324)
360 PF02319 E2F_TDP: E2F/DP famil 27.8 88 0.0019 22.0 3.3 26 136-164 11-39 (71)
361 PRK09210 RNA polymerase sigma 27.6 80 0.0017 28.2 3.7 27 150-176 230-256 (367)
362 COG2390 DeoR Transcriptional r 27.5 56 0.0012 29.5 2.8 38 133-176 13-50 (321)
363 PRK07408 RNA polymerase sigma 27.4 71 0.0015 26.7 3.2 26 148-173 125-150 (256)
364 PF06511 IpaD: Invasion plasmi 27.3 61 0.0013 30.1 3.0 49 129-177 254-323 (337)
365 TIGR02850 spore_sigG RNA polym 26.9 92 0.002 25.8 3.7 27 150-176 134-160 (254)
366 PRK10130 transcriptional regul 26.7 1.2E+02 0.0027 27.0 4.8 26 149-174 253-278 (350)
367 PRK13280 N-glycosylase/DNA lya 26.6 25 0.00054 31.5 0.4 33 66-99 25-58 (269)
368 PRK15320 transcriptional activ 26.5 1.1E+02 0.0024 27.6 4.4 87 74-170 98-197 (251)
369 PRK05657 RNA polymerase sigma 26.1 89 0.0019 27.5 3.7 23 152-174 282-304 (325)
370 PRK07122 RNA polymerase sigma 25.9 83 0.0018 26.6 3.3 31 150-180 141-177 (264)
371 TIGR02018 his_ut_repres histid 25.8 2.1E+02 0.0045 23.1 5.5 43 134-176 5-49 (230)
372 cd00592 HTH_MerR-like Helix-Tu 25.8 1E+02 0.0022 21.8 3.3 29 153-181 1-29 (100)
373 PRK15418 transcriptional regul 25.5 65 0.0014 28.4 2.7 35 135-175 18-52 (318)
374 PRK13501 transcriptional activ 25.5 77 0.0017 26.1 3.0 38 134-174 177-214 (290)
375 cd00093 HTH_XRE Helix-turn-hel 25.3 93 0.002 17.4 2.6 22 153-174 13-34 (58)
376 PRK13719 conjugal transfer tra 25.3 1.5E+02 0.0033 25.9 4.9 37 128-172 142-178 (217)
377 PHA01976 helix-turn-helix prot 24.7 98 0.0021 20.2 2.9 28 153-180 16-43 (67)
378 cd05022 S-100A13 S-100A13: S-1 24.5 98 0.0021 22.7 3.1 46 131-178 6-58 (89)
379 COG4901 Ribosomal protein S25 24.4 69 0.0015 25.8 2.5 28 150-177 57-84 (107)
380 PF12983 DUF3867: Protein of u 24.4 54 0.0012 28.5 2.0 57 125-181 32-90 (186)
381 TIGR03826 YvyF flagellar opero 24.3 1.3E+02 0.0028 24.4 4.1 26 149-174 43-68 (137)
382 PF12844 HTH_19: Helix-turn-he 24.2 81 0.0018 20.3 2.4 22 153-174 13-34 (64)
383 TIGR03454 partition_RepB plasm 24.2 61 0.0013 29.4 2.4 29 153-181 178-207 (325)
384 smart00453 WSN Worm-specific ( 24.1 1E+02 0.0022 22.1 3.0 40 133-175 14-54 (69)
385 TIGR03859 PQQ_PqqD coenzyme PQ 24.1 91 0.002 22.3 2.8 35 136-177 34-72 (81)
386 PRK09940 transcriptional regul 23.7 1.1E+02 0.0024 26.7 3.8 37 133-175 137-173 (253)
387 PF12833 HTH_18: Helix-turn-he 23.7 91 0.002 20.8 2.6 14 152-165 45-58 (81)
388 PF13591 MerR_2: MerR HTH fami 23.7 88 0.0019 22.5 2.7 29 153-181 1-29 (84)
389 TIGR02393 RpoD_Cterm RNA polym 23.7 1.1E+02 0.0024 25.0 3.6 27 150-176 101-127 (238)
390 smart00530 HTH_XRE Helix-turn- 23.6 1.1E+02 0.0024 17.0 2.6 21 153-173 11-31 (56)
391 PRK13626 transcriptional regul 23.6 1.2E+02 0.0025 28.1 4.1 41 135-176 7-47 (552)
392 PRK05932 RNA polymerase factor 23.5 91 0.002 29.2 3.4 30 148-177 132-163 (455)
393 PRK15044 transcriptional regul 23.4 1.5E+02 0.0033 26.9 4.7 29 147-175 203-231 (295)
394 TIGR02395 rpoN_sigma RNA polym 23.3 93 0.002 28.9 3.4 29 148-176 107-137 (429)
395 COG3413 Predicted DNA binding 23.2 2.5E+02 0.0054 22.8 5.5 46 129-174 155-200 (215)
396 PF04552 Sigma54_DBD: Sigma-54 23.2 27 0.00059 28.5 0.0 27 148-174 45-71 (160)
397 PRK06596 RNA polymerase factor 23.2 1.7E+02 0.0036 25.1 4.7 31 150-180 149-184 (284)
398 KOG4481 Uncharacterized conser 23.1 2.2E+02 0.0048 25.0 5.4 70 103-176 88-159 (194)
399 TIGR03070 couple_hipB transcri 23.1 95 0.0021 18.9 2.5 23 153-175 16-38 (58)
400 cd01392 HTH_LacI Helix-turn-he 23.1 55 0.0012 20.3 1.4 18 157-174 2-19 (52)
401 PF04157 EAP30: EAP30/Vps36 fa 22.9 72 0.0016 26.4 2.4 98 73-176 92-214 (223)
402 cd04777 HTH_MerR-like_sg1 Heli 22.8 69 0.0015 23.4 2.0 19 153-171 1-19 (107)
403 TIGR00635 ruvB Holliday juncti 22.6 1.1E+02 0.0024 25.3 3.4 25 150-174 253-277 (305)
404 COG1983 PspC Putative stress-r 22.6 64 0.0014 24.0 1.8 15 157-171 20-34 (70)
405 COG4567 Response regulator con 22.3 2.3E+02 0.005 24.7 5.3 47 119-174 131-177 (182)
406 PF10376 Mei5: Double-strand r 22.0 86 0.0019 27.1 2.8 39 131-169 168-218 (221)
407 PF01418 HTH_6: Helix-turn-hel 21.9 94 0.002 21.7 2.5 26 152-177 34-59 (77)
408 PRK15185 transcriptional regul 21.8 1.6E+02 0.0035 26.8 4.6 37 133-175 209-245 (309)
409 cd04766 HTH_HspR Helix-Turn-He 21.5 1.5E+02 0.0032 21.1 3.5 29 153-181 2-30 (91)
410 KOG3108 Single-stranded DNA-bi 21.3 1.3E+02 0.0029 26.8 3.9 30 149-178 218-248 (265)
411 cd02641 R3H_Smubp-2_like R3H d 21.3 52 0.0011 22.8 1.1 34 133-166 2-45 (60)
412 PRK06474 hypothetical protein; 21.2 1.2E+02 0.0026 24.7 3.3 37 136-176 14-51 (178)
413 PF02317 Octopine_DH: NAD/NADP 21.1 80 0.0017 24.8 2.2 24 154-177 124-147 (152)
414 PHA00542 putative Cro-like pro 21.1 1.6E+02 0.0035 21.0 3.6 24 153-176 32-55 (82)
415 PF05043 Mga: Mga helix-turn-h 21.1 82 0.0018 21.8 2.1 26 151-176 29-54 (87)
416 PF10493 Rod_C: Rough deal pro 20.9 1E+02 0.0023 29.6 3.3 41 138-178 192-245 (551)
417 COG2378 Predicted transcriptio 20.8 1.3E+02 0.0027 26.6 3.6 38 135-177 10-47 (311)
418 KOG2165 Anaphase-promoting com 20.7 1.2E+02 0.0026 31.3 3.8 36 136-176 605-640 (765)
419 PF09743 DUF2042: Uncharacteri 20.7 93 0.002 27.4 2.8 28 149-176 67-94 (272)
420 PF06738 DUF1212: Protein of u 20.7 1.2E+02 0.0027 23.8 3.2 39 121-162 53-91 (193)
421 TIGR02612 mob_myst_A mobile my 20.5 2.1E+02 0.0046 23.2 4.6 43 132-174 6-60 (150)
422 PRK10371 DNA-binding transcrip 20.4 1.6E+02 0.0034 25.1 4.0 39 134-175 192-230 (302)
423 PRK06986 fliA flagellar biosyn 20.2 1.6E+02 0.0034 23.9 3.8 29 148-176 107-135 (236)
424 COG5259 RSC8 RSC chromatin rem 20.1 65 0.0014 31.8 1.8 110 69-184 198-329 (531)
No 1
>PF06784 UPF0240: Uncharacterised protein family (UPF0240); InterPro: IPR009622 This is a group of proteins of unknown function.
Probab=97.73 E-value=0.00013 Score=60.17 Aligned_cols=106 Identities=26% Similarity=0.375 Sum_probs=77.4
Q ss_pred ccccCchHHHHHHHhhcccccCC-CCccccchhhhhhhhcCCCCCCCCCCCC--CCCCCCCCCCCCcccHHHHHHHHHHh
Q 029662 66 LEERDPQYDAMLNQMLGRVKTKA-GGKAEMGEAAVVERQTRPLPKLRNTTPV--SSRYEEKPSPPGTLNVAQLRRIMLLH 142 (190)
Q Consensus 66 l~erDp~ydaMl~qmvGrI~tkp-GGk~Emgea~vv~~ynRP~Pk~R~t~~~--sg~~eer~~p~GTLNva~l~~ii~L~ 142 (190)
+...|.+.+..|+++ .|+|+= =...+ =+.....+-.||+|-.|.+-++ -|-++..-||.|.|.+-|+-++|-.|
T Consensus 54 i~~Kd~~L~s~LK~V--yV~S~Dp~~~~~-~~~~~~~~~~r~l~l~r~~~~~~~fg~~ep~~vPkGkltl~qal~lL~~H 130 (179)
T PF06784_consen 54 ISRKDDKLLSRLKDV--YVTSKDPVPPQT-VKDAEPQQESRPLPLPRDTIPDFEFGFYEPEKVPKGKLTLRQALELLNNH 130 (179)
T ss_pred HHhhhHHHHHhhcee--EeecCCCCcccc-cccccccccCCCccCCCCCcccccccccCcccCCCCceeHHHHHHHHHHh
Confidence 456788889999988 666652 11111 1222334567888876665433 35567789999999999999999988
Q ss_pred hccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhhcC
Q 029662 143 QGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCLSL 178 (190)
Q Consensus 143 QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~Sl 178 (190)
|-.- --.++.-||++|.++...|.+||.|...
T Consensus 131 q~~P----~~WtaekIA~eY~L~~~dv~~iL~yF~~ 162 (179)
T PF06784_consen 131 QLDP----ETWTAEKIAQEYKLDEKDVKNILKYFKP 162 (179)
T ss_pred ccCc----cccCHHHHHHHhCCCHHHHHHHHHhcCC
Confidence 8332 2247999999999999999999999864
No 2
>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=96.50 E-value=0.0035 Score=40.47 Aligned_cols=39 Identities=26% Similarity=0.349 Sum_probs=30.5
Q ss_pred cccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 129 TLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 129 TLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
.++-.++.+|+.||+ .| |++.+||+.|+|-.+-|.++|.
T Consensus 5 ~~~~~~~~~i~~l~~------~G-~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 5 KLSKEQIEEIKELYA------EG-MSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp SSSHCCHHHHHHHHH------TT---HHHHHHHTTS-HHHHHHHHC
T ss_pred CCCHHHHHHHHHHHH------CC-CCHHHHHHHHCcCHHHHHHHHh
Confidence 456667999999996 35 9999999999999999999873
No 3
>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=94.83 E-value=0.036 Score=40.13 Aligned_cols=41 Identities=15% Similarity=0.281 Sum_probs=30.3
Q ss_pred HHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhhc
Q 029662 136 RRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCLS 177 (190)
Q Consensus 136 ~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~S 177 (190)
+.|+.+.+. ....+--|.|++||++|++....|..+|+||+
T Consensus 50 ~~Vl~~i~~-~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~ 90 (102)
T PF08784_consen 50 DKVLNFIKQ-QPNSEEGVHVDEIAQQLGMSENEVRKALDFLS 90 (102)
T ss_dssp HHHHHHHHC-----TTTEEHHHHHHHSTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHh-cCCCCCcccHHHHHHHhCcCHHHHHHHHHHHH
Confidence 456666666 33333349999999999999999999999986
No 4
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=94.25 E-value=0.076 Score=34.37 Aligned_cols=39 Identities=21% Similarity=0.290 Sum_probs=22.6
Q ss_pred cccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 129 TLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 129 TLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
.|+.++..+|..||+ .| |++.+||..|++..+-|-+.|+
T Consensus 4 ~Lt~~eR~~I~~l~~------~G-~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 4 HLTPEERNQIEALLE------QG-MSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp --------HHHHHHC------S----HHHHHHHTT--HHHHHHHHH
T ss_pred chhhhHHHHHHHHHH------cC-CCHHHHHHHHCcCcHHHHHHHh
Confidence 367788888888876 33 9999999999999999988764
No 5
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=94.15 E-value=0.056 Score=36.39 Aligned_cols=39 Identities=23% Similarity=0.379 Sum_probs=29.2
Q ss_pred cccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 129 TLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 129 TLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
+|.+.+=.+||.+|+ +|+ ++.+||.+|+|..++|..|+.
T Consensus 6 ~LTl~eK~~iI~~~e------~g~-s~~~ia~~fgv~~sTv~~I~K 44 (53)
T PF04218_consen 6 SLTLEEKLEIIKRLE------EGE-SKRDIAREFGVSRSTVSTILK 44 (53)
T ss_dssp S--HHHHHHHHHHHH------CTT--HHHHHHHHT--CCHHHHHHH
T ss_pred cCCHHHHHHHHHHHH------cCC-CHHHHHHHhCCCHHHHHHHHH
Confidence 577888889999985 344 899999999999999999985
No 6
>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=94.03 E-value=0.047 Score=37.54 Aligned_cols=36 Identities=22% Similarity=0.383 Sum_probs=26.9
Q ss_pred HHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhhc
Q 029662 134 QLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCLS 177 (190)
Q Consensus 134 ~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~S 177 (190)
+|+++|.. +|.+++.|||.+|+++...|+.+|.++-
T Consensus 4 ~i~~~l~~--------~~~~S~~eLa~~~~~s~~~ve~mL~~l~ 39 (69)
T PF09012_consen 4 EIRDYLRE--------RGRVSLAELAREFGISPEAVEAMLEQLI 39 (69)
T ss_dssp HHHHHHHH--------S-SEEHHHHHHHTT--HHHHHHHHHHHH
T ss_pred HHHHHHHH--------cCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 45555543 4568999999999999999999999873
No 7
>PRK04217 hypothetical protein; Provisional
Probab=94.02 E-value=0.18 Score=39.28 Aligned_cols=59 Identities=17% Similarity=0.252 Sum_probs=44.3
Q ss_pred CCCCCCCCCCCCCCCCCCCCCcccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 108 PKLRNTTPVSSRYEEKPSPPGTLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 108 Pk~R~t~~~sg~~eer~~p~GTLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
|.+|.-+|. +.--.+++|+.-|..++. +|+.|+.-.- |+++|||+.++|..+.|.++|.
T Consensus 22 ~~~~~~~~~-~~~~~~~~p~~~Lt~eer-eai~l~~~eG------lS~~EIAk~LGIS~sTV~r~L~ 80 (110)
T PRK04217 22 PQVRHFYPA-IPPVGPPKPPIFMTYEEF-EALRLVDYEG------LTQEEAGKRMGVSRGTVWRALT 80 (110)
T ss_pred CCcceEeCC-CCCccCCCCcccCCHHHH-HHHHHHHHcC------CCHHHHHHHHCcCHHHHHHHHH
Confidence 556666664 333457899999999995 6666554222 6999999999999999988875
No 8
>PHA00675 hypothetical protein
Probab=93.65 E-value=0.19 Score=38.05 Aligned_cols=45 Identities=27% Similarity=0.324 Sum_probs=38.6
Q ss_pred CCCCcccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHh
Q 029662 125 SPPGTLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQC 175 (190)
Q Consensus 125 ~p~GTLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf 175 (190)
-|.-+|+-+|+.+|..|+. --.++..+||.+|.|--+-|++|.++
T Consensus 18 h~~AKLt~~qV~~IR~l~~------r~G~s~~~IA~~fGVsrstV~~I~~g 62 (78)
T PHA00675 18 HPNAKLTDAEVERIRELHE------VEGMSYAVLAEKFEQSKGAIAKICRY 62 (78)
T ss_pred CCCcccCHHHHHHHHHHHH------hcCccHHHHHHHhCCCHHHHHHHHcc
Confidence 5677999999999999985 11258999999999999999999865
No 9
>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=93.60 E-value=0.13 Score=33.19 Aligned_cols=41 Identities=29% Similarity=0.460 Sum_probs=33.8
Q ss_pred ccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 130 LNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 130 LNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
||..|+.=+..||+ +|+|++.+||++++++.+-+-++++-|
T Consensus 1 lt~~q~~iL~~l~~------~~~~~~~~la~~~~~~~~~~t~~i~~L 41 (59)
T PF01047_consen 1 LTPSQFRILRILYE------NGGITQSELAEKLGISRSTVTRIIKRL 41 (59)
T ss_dssp STHHHHHHHHHHHH------HSSEEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHH------cCCCCHHHHHHHHCCChhHHHHHHHHH
Confidence 67788888888875 556999999999999999998888755
No 10
>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=92.66 E-value=0.44 Score=30.12 Aligned_cols=27 Identities=30% Similarity=0.378 Sum_probs=22.5
Q ss_pred CCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 150 NGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 150 ~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
++.|++.|||+++++...-|.++|+.|
T Consensus 15 ~~~~t~~ela~~~~is~~tv~~~l~~L 41 (48)
T PF13412_consen 15 NPRITQKELAEKLGISRSTVNRYLKKL 41 (48)
T ss_dssp CTTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred cCCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 556999999999999999999999865
No 11
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=92.54 E-value=0.33 Score=33.25 Aligned_cols=40 Identities=18% Similarity=0.230 Sum_probs=31.3
Q ss_pred HHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 133 AQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 133 a~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
+-...||.++.. +++++++.|||+.+++..+.|.++|+.|
T Consensus 5 ~r~~~Il~~l~~----~~~~~t~~~ia~~l~i~~~tv~r~l~~L 44 (91)
T smart00346 5 ERGLAVLRALAE----EPGGLTLAELAERLGLSKSTAHRLLNTL 44 (91)
T ss_pred HHHHHHHHHHHh----CCCCcCHHHHHHHhCCCHHHHHHHHHHH
Confidence 344555655532 3468999999999999999999999877
No 12
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=92.49 E-value=0.14 Score=41.14 Aligned_cols=28 Identities=36% Similarity=0.431 Sum_probs=26.2
Q ss_pred CCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 149 HNGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 149 h~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
-+||++|++|||+.+++-+.||+.||=|
T Consensus 39 ~~~~~tvdelae~lnr~rStv~rsl~~L 66 (126)
T COG3355 39 ENGPLTVDELAEILNRSRSTVYRSLQNL 66 (126)
T ss_pred hcCCcCHHHHHHHHCccHHHHHHHHHHH
Confidence 5899999999999999999999999865
No 13
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=92.48 E-value=0.49 Score=28.68 Aligned_cols=38 Identities=26% Similarity=0.415 Sum_probs=29.1
Q ss_pred CcccHHHHHHHHHHh-hccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 128 GTLNVAQLRRIMLLH-QGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 128 GTLNva~l~~ii~L~-QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
..|+-.+.+ |+.++ +| |+.++||+.++|....|.+.++
T Consensus 2 ~~l~~~e~~-i~~~~~~g--------~s~~eia~~l~is~~tv~~~~~ 40 (58)
T smart00421 2 ASLTPRERE-VLRLLAEG--------LTNKEIAERLGISEKTVKTHLS 40 (58)
T ss_pred CCCCHHHHH-HHHHHHcC--------CCHHHHHHHHCCCHHHHHHHHH
Confidence 457777776 66555 33 6899999999999998877655
No 14
>PF08765 Mor: Mor transcription activator family; InterPro: IPR014875 Mor (Middle operon regulator) is a sequence specific DNA binding protein. It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. The N-terminal region of Mor is the dimerisation region, and the C-terminal contains a helix-turn-helix motif which binds DNA []. ; PDB: 1RR7_A.
Probab=92.42 E-value=0.2 Score=37.39 Aligned_cols=44 Identities=23% Similarity=0.319 Sum_probs=27.4
Q ss_pred CCCCCcccHHHH--HHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHh
Q 029662 124 PSPPGTLNVAQL--RRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQC 175 (190)
Q Consensus 124 ~~p~GTLNva~l--~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf 175 (190)
-+|-+.--...+ ++|+..|.| |++.+||.||++-...|.+|+.-
T Consensus 50 yiP~~~~~~~~~R~~~I~~~f~G--------~n~~eLA~kyglS~r~I~~Ii~~ 95 (108)
T PF08765_consen 50 YIPKCDRLLRALRNREIRREFNG--------MNVRELARKYGLSERQIYRIIKR 95 (108)
T ss_dssp ----SHHHHHHHHHHHHHHH--S--------S-HHHHHHHHT--HHHHHHHHHH
T ss_pred EeeCccHHHHHHHHHHHHHHhCC--------CCHHHHHHHHCcCHHHHHHHHHH
Confidence 355565333444 478888885 77999999999999999999974
No 15
>PF06413 Neugrin: Neugrin; InterPro: IPR010487 This family contains mouse and human neugrin proteins. Neugrin and m-neugrin are mainly expressed in neurons in the nervous system, and are thought to play an important role in the process of neuronal differentiation []. Homologues of neugrin are found in fungi suggesting they have a alternative role or more than one function.
Probab=92.06 E-value=0.36 Score=41.50 Aligned_cols=56 Identities=23% Similarity=0.453 Sum_probs=46.8
Q ss_pred CCCCCCcccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhhcCCCCC
Q 029662 123 KPSPPGTLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCLSLPPES 182 (190)
Q Consensus 123 r~~p~GTLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~SlP~e~ 182 (190)
.-.|+-+|.-+++..|=.||+-..+ -+++..|||.|+|....|.+||.-=-.|.++
T Consensus 4 ~~~p~k~Ls~~~~~~ir~L~~~~p~----~~t~~~Lae~F~vspe~irrILkskw~p~~~ 59 (225)
T PF06413_consen 4 PGNPPKKLSREAMEQIRYLHKEDPE----EWTVERLAESFKVSPEAIRRILKSKWVPTEE 59 (225)
T ss_pred CCCCCCCCCHHHHHHHHHHHHhCcc----ccCHHHHHhhCCCCHHHHHHHHhcCCCCCHH
Confidence 3468889999999999999986543 3789999999999999999999876667553
No 16
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=92.00 E-value=0.33 Score=34.16 Aligned_cols=40 Identities=30% Similarity=0.471 Sum_probs=28.7
Q ss_pred HHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhhc
Q 029662 135 LRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCLS 177 (190)
Q Consensus 135 l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~S 177 (190)
|+-++.|.+. ...+++++++||+++++....|.+|++.|.
T Consensus 11 l~~l~~la~~---~~~~~~s~~eiA~~~~i~~~~l~kil~~L~ 50 (83)
T PF02082_consen 11 LRILLYLARH---PDGKPVSSKEIAERLGISPSYLRKILQKLK 50 (83)
T ss_dssp HHHHHHHHCT---TTSC-BEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHhC---CCCCCCCHHHHHHHHCcCHHHHHHHHHHHh
Confidence 4444555332 234569999999999999999999999874
No 17
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=91.74 E-value=0.39 Score=30.70 Aligned_cols=38 Identities=26% Similarity=0.340 Sum_probs=26.7
Q ss_pred ccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 130 LNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 130 LNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
|+-.+ ++||.++-. ..|+..|||+.+++....|.++..
T Consensus 5 L~~~e-r~vi~~~y~------~~~t~~eIa~~lg~s~~~V~~~~~ 42 (50)
T PF04545_consen 5 LPPRE-REVIRLRYF------EGLTLEEIAERLGISRSTVRRILK 42 (50)
T ss_dssp S-HHH-HHHHHHHHT------ST-SHHHHHHHHTSCHHHHHHHHH
T ss_pred CCHHH-HHHHHHHhc------CCCCHHHHHHHHCCcHHHHHHHHH
Confidence 44444 455655553 349999999999999999988864
No 18
>PF13518 HTH_28: Helix-turn-helix domain
Probab=91.67 E-value=0.39 Score=29.99 Aligned_cols=33 Identities=21% Similarity=0.275 Sum_probs=26.4
Q ss_pred HHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 137 RIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 137 ~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
+||++|.. | +++.+||++|+|..+.|.+.++-.
T Consensus 4 ~iv~~~~~------g-~s~~~~a~~~gis~~tv~~w~~~y 36 (52)
T PF13518_consen 4 QIVELYLE------G-ESVREIAREFGISRSTVYRWIKRY 36 (52)
T ss_pred HHHHHHHc------C-CCHHHHHHHHCCCHhHHHHHHHHH
Confidence 56777762 2 389999999999999999888643
No 19
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=91.64 E-value=0.57 Score=27.63 Aligned_cols=39 Identities=26% Similarity=0.292 Sum_probs=28.0
Q ss_pred cccHHHHHHHHHHh-hccCCCCCCCCCHHHHHHHhchhHHHHHHHHHh
Q 029662 129 TLNVAQLRRIMLLH-QGKADDHNGPLDAKQIAEKFRLDVLQVQAILQC 175 (190)
Q Consensus 129 TLNva~l~~ii~L~-QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf 175 (190)
+|+-.+.+-++++| +| |+..+||+.+++....|.++++-
T Consensus 10 ~l~~~~~~~~~~~~~~~--------~~~~~ia~~~~~s~~~i~~~~~~ 49 (55)
T cd06171 10 KLPEREREVILLRFGEG--------LSYEEIAEILGISRSTVRQRLHR 49 (55)
T ss_pred hCCHHHHHHHHHHHhcC--------CCHHHHHHHHCcCHHHHHHHHHH
Confidence 34445544444455 44 78999999999999999888753
No 20
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=91.59 E-value=0.35 Score=30.97 Aligned_cols=35 Identities=26% Similarity=0.309 Sum_probs=25.0
Q ss_pred HHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 134 QLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 134 ~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
.-++||.|+--.- |+.+|||+.+++..+.|+..+.
T Consensus 14 ~~r~i~~l~~~~g------~s~~eIa~~l~~s~~~v~~~l~ 48 (54)
T PF08281_consen 14 RQREIFLLRYFQG------MSYAEIAEILGISESTVKRRLR 48 (54)
T ss_dssp HHHHHHHHHHTS---------HHHHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHHHHHHHC------cCHHHHHHHHCcCHHHHHHHHH
Confidence 3477888865554 8999999999999999987664
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=91.52 E-value=0.22 Score=31.98 Aligned_cols=28 Identities=21% Similarity=0.383 Sum_probs=23.7
Q ss_pred CCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 149 HNGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 149 h~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
+++++++++||++|+|...-|++-++.|
T Consensus 12 ~~~~it~~eLa~~l~vS~rTi~~~i~~L 39 (55)
T PF08279_consen 12 SKEPITAKELAEELGVSRRTIRRDIKEL 39 (55)
T ss_dssp TTTSBEHHHHHHHCTS-HHHHHHHHHHH
T ss_pred cCCCcCHHHHHHHhCCCHHHHHHHHHHH
Confidence 3456999999999999999999988876
No 22
>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=91.27 E-value=0.22 Score=32.41 Aligned_cols=29 Identities=34% Similarity=0.525 Sum_probs=24.8
Q ss_pred CCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 148 DHNGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 148 ~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
.+.++|++.|||++.++..+-+.++|+-|
T Consensus 14 ~~~~~~t~~eia~~~gl~~stv~r~L~tL 42 (52)
T PF09339_consen 14 ESGGPLTLSEIARALGLPKSTVHRLLQTL 42 (52)
T ss_dssp CTBSCEEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred cCCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 45667999999999999999999999865
No 23
>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=91.14 E-value=0.3 Score=34.89 Aligned_cols=31 Identities=23% Similarity=0.410 Sum_probs=25.9
Q ss_pred HHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHH
Q 029662 137 RIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQA 171 (190)
Q Consensus 137 ~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~ 171 (190)
++..||+ +|+|-|..++||++++|..++|.+
T Consensus 11 kA~e~y~----~~~g~i~lkdIA~~Lgvs~~tIr~ 41 (60)
T PF10668_consen 11 KAFEIYK----ESNGKIKLKDIAEKLGVSESTIRK 41 (60)
T ss_pred HHHHHHH----HhCCCccHHHHHHHHCCCHHHHHH
Confidence 4666774 478889999999999999999864
No 24
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=90.98 E-value=0.51 Score=37.12 Aligned_cols=49 Identities=27% Similarity=0.306 Sum_probs=42.0
Q ss_pred cccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhhcCC
Q 029662 129 TLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCLSLP 179 (190)
Q Consensus 129 TLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~SlP 179 (190)
+||-+|++.--+-+|-.. ..-|+++.+||++.++.-.-||+|||..+-|
T Consensus 2 SLn~eq~~~Tk~elqan~--el~~LS~~~iA~~Ln~t~~~lekil~~tqr~ 50 (97)
T COG4367 2 SLNPEQKQRTKQELQANF--ELCPLSDEEIATALNWTEVKLEKILQVTQRP 50 (97)
T ss_pred CCCHHHHHHHHHHHHHhh--hhccccHHHHHHHhCCCHHHHHHHHHHhhcc
Confidence 689999988777777544 4678999999999999999999999988776
No 25
>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=90.48 E-value=0.8 Score=29.53 Aligned_cols=40 Identities=25% Similarity=0.233 Sum_probs=30.5
Q ss_pred HHHHhhcc--CCCCCCCCCHHHHHHHhchhHHHHHHHHHhhc
Q 029662 138 IMLLHQGK--ADDHNGPLDAKQIAEKFRLDVLQVQAILQCLS 177 (190)
Q Consensus 138 ii~L~QGk--~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~S 177 (190)
++.|++.- ....+++|+..+||+.+++...-|.++++-|.
T Consensus 9 l~~l~~~~~~~~~~~~~~s~~ela~~~g~s~~tv~r~l~~L~ 50 (67)
T cd00092 9 LLNLSLRYGAGDLVQLPLTRQEIADYLGLTRETVSRTLKELE 50 (67)
T ss_pred HHHHHHHcCCCccccCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 44455432 23467899999999999999999999987653
No 26
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=90.38 E-value=0.66 Score=34.15 Aligned_cols=30 Identities=30% Similarity=0.496 Sum_probs=26.4
Q ss_pred CCCCCCCHHHHHHHhchhHHHHHHHHHhhc
Q 029662 148 DHNGPLDAKQIAEKFRLDVLQVQAILQCLS 177 (190)
Q Consensus 148 ~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~S 177 (190)
+..+|+++.+||+.+++....|.+||+-|.
T Consensus 21 ~~~~~~s~~eia~~~~i~~~~v~~il~~L~ 50 (132)
T TIGR00738 21 PDEGPVSVKEIAERQGISRSYLEKILRTLR 50 (132)
T ss_pred CCCCcCcHHHHHHHHCcCHHHHHHHHHHHH
Confidence 334699999999999999999999998764
No 27
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=90.16 E-value=0.22 Score=35.35 Aligned_cols=28 Identities=36% Similarity=0.635 Sum_probs=24.6
Q ss_pred CCCCCHHHHHHHhchhHHHHHHHHHhhc
Q 029662 150 NGPLDAKQIAEKFRLDVLQVQAILQCLS 177 (190)
Q Consensus 150 ~gPM~v~~iAeKFrv~v~~vq~Ilqf~S 177 (190)
++|++..|||+.|++...++..+|++|-
T Consensus 13 ~~p~~T~eiA~~~gls~~~aR~yL~~Le 40 (62)
T PF04703_consen 13 NGPLKTREIADALGLSIYQARYYLEKLE 40 (62)
T ss_dssp TS-EEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 7899999999999999999999999984
No 28
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=90.01 E-value=0.47 Score=28.86 Aligned_cols=27 Identities=19% Similarity=0.353 Sum_probs=24.7
Q ss_pred CCCCHHHHHHHhchhHHHHHHHHHhhc
Q 029662 151 GPLDAKQIAEKFRLDVLQVQAILQCLS 177 (190)
Q Consensus 151 gPM~v~~iAeKFrv~v~~vq~Ilqf~S 177 (190)
+++++.+||+.|.+...-|.++|+.|.
T Consensus 13 ~~~s~~~l~~~l~~s~~tv~~~l~~L~ 39 (53)
T smart00420 13 GKVSVEELAELLGVSEMTIRRDLNKLE 39 (53)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 679999999999999999999998873
No 29
>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=89.62 E-value=0.79 Score=34.19 Aligned_cols=29 Identities=38% Similarity=0.471 Sum_probs=26.2
Q ss_pred CCCCCCHHHHHHHhchhHHHHHHHHHhhc
Q 029662 149 HNGPLDAKQIAEKFRLDVLQVQAILQCLS 177 (190)
Q Consensus 149 h~gPM~v~~iAeKFrv~v~~vq~Ilqf~S 177 (190)
.++++++++||+++++....|+++|+-|.
T Consensus 22 ~~~~~s~~eia~~l~is~~~v~~~l~~L~ 50 (130)
T TIGR02944 22 DSQPYSAAEIAEQTGLNAPTVSKILKQLS 50 (130)
T ss_pred CCCCccHHHHHHHHCcCHHHHHHHHHHHH
Confidence 35789999999999999999999998764
No 30
>TIGR00180 parB_part ParB-like partition proteins. This model represents the most well-conserved core of a set of chromosomal and plasmid partition proteins related to ParB, including Spo0J, RepB, and SopB. Spo0J has been shown to bind a specific DNA sequence that, when introduced into a plasmid, can serve as partition site. Study of RepB, which has nicking-closing activity, suggests that it forms a transient protein-DNA covalent intermediate during the strand transfer reaction.
Probab=89.01 E-value=0.33 Score=38.86 Aligned_cols=29 Identities=24% Similarity=0.461 Sum_probs=27.9
Q ss_pred CCHHHHHHHhchhHHHHHHHHHhhcCCCC
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQCLSLPPE 181 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilqf~SlP~e 181 (190)
|+.++||++|++..+.|.+.+.+..||++
T Consensus 121 ~s~~~iA~~lg~s~~~V~r~l~l~~lp~~ 149 (187)
T TIGR00180 121 MTQEDLAKKIGKSRAHITNLLRLLKLPSE 149 (187)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHcCCHH
Confidence 78999999999999999999999999986
No 31
>PF08100 Dimerisation: Dimerisation domain; InterPro: IPR012967 This domain is found at the N terminus of a variety of plant O-methyltransferases. It has been shown to mediate dimerisation of these proteins [].; GO: 0008168 methyltransferase activity, 0046983 protein dimerization activity; PDB: 1ZGJ_A 1ZG3_A 1ZHF_A 1ZGA_A 2QYO_A 1KYW_A 1KYZ_A 3REO_D 1FPX_A 1FP2_A ....
Probab=88.97 E-value=0.64 Score=31.79 Aligned_cols=26 Identities=27% Similarity=0.448 Sum_probs=23.3
Q ss_pred CCCCHHHHHHHhc----hhHHHHHHHHHhh
Q 029662 151 GPLDAKQIAEKFR----LDVLQVQAILQCL 176 (190)
Q Consensus 151 gPM~v~~iAeKFr----v~v~~vq~Ilqf~ 176 (190)
+|+++.|||.+.. -+...+++|+.||
T Consensus 21 ~~ls~~eia~~l~~~~p~~~~~L~RimR~L 50 (51)
T PF08100_consen 21 GPLSLSEIAARLPTSNPSAPPMLDRIMRLL 50 (51)
T ss_dssp S-BEHHHHHHTSTCT-TTHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHcCCCCcchHHHHHHHHHHh
Confidence 8999999999988 7788999999997
No 32
>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=88.88 E-value=1.1 Score=29.19 Aligned_cols=42 Identities=24% Similarity=0.415 Sum_probs=27.6
Q ss_pred ccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 130 LNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 130 LNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
|+..|+.=+..|+ ..+++|+..+||+.++++...|-++++=|
T Consensus 1 lt~~q~~vL~~l~-----~~~~~~t~~~l~~~~~~~~~~vs~~i~~L 42 (68)
T PF13463_consen 1 LTRPQWQVLRALA-----HSDGPMTQSDLAERLGISKSTVSRIIKKL 42 (68)
T ss_dssp --HHHHHHHHHHT-------TS-BEHHHHHHHTT--HHHHHHHHHHH
T ss_pred CCHHHHHHHHHHH-----ccCCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 4455665555565 56788999999999999999998888643
No 33
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=88.75 E-value=1.8 Score=22.50 Aligned_cols=36 Identities=14% Similarity=0.110 Sum_probs=27.1
Q ss_pred ccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHH
Q 029662 130 LNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAI 172 (190)
Q Consensus 130 LNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~I 172 (190)
++..+...|+.+|.. .+++.+||+.|++-...|-++
T Consensus 6 ~~~~~~~~i~~~~~~-------~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 6 LTPEQIEEARRLLAA-------GESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CCHHHHHHHHHHHHc-------CCCHHHHHHHHCCCHHHHHHh
Confidence 455667777777752 259999999999988877665
No 34
>PF12298 Bot1p: Eukaryotic mitochondrial regulator protein ; InterPro: IPR021036 This entry represents Ribosomal protein S35, which localises to the mitochondria in live cells and co-fractionates with purified mitochondrial ribosomes. This group of proteins have a novel function in the control of cell respiration by acting on the mitochondrial protein synthesis machinery and a role in mitochondrial integrity. Observations also indicate that in Schizosaccharomyces pombe (Fission yeast), alterations of mitochondrial function are linked to changes in cell cycle and cell morphology control mechanisms [].
Probab=88.66 E-value=1.7 Score=36.05 Aligned_cols=58 Identities=12% Similarity=0.161 Sum_probs=44.4
Q ss_pred cCCCCCCCCCCCCCCCCCCCCCCCCcccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhhcC
Q 029662 104 TRPLPKLRNTTPVSSRYEEKPSPPGTLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCLSL 178 (190)
Q Consensus 104 nRP~Pk~R~t~~~sg~~eer~~p~GTLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~Sl 178 (190)
.+|.|-+...++.+-=. =..=.+|+.+|+- ++++|.+||.+|+|+..-|..||+...+
T Consensus 2 ~~PFP~Np~f~~~~~ls-----------e~~r~~Iy~~~~~------~~~sv~~vS~~ygi~~~RV~AIvrLkei 59 (172)
T PF12298_consen 2 LQPFPLNPSFRSNPVLS-----------EELREQIYEDVMQ------DGKSVREVSQKYGIKIQRVEAIVRLKEI 59 (172)
T ss_pred CCCCCCCCCCCCCCcCC-----------HHHHHHHHHHHHh------CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 57888888887765433 3334567788864 3479999999999999999999987654
No 35
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=88.30 E-value=0.25 Score=33.20 Aligned_cols=28 Identities=36% Similarity=0.525 Sum_probs=25.5
Q ss_pred CCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 149 HNGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 149 h~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
.+|+|++.+||++.++.-+.|.++|+.|
T Consensus 19 ~~~~~t~~eIa~~l~i~~~~v~~~L~~L 46 (68)
T PF01978_consen 19 KNGPATAEEIAEELGISRSTVYRALKSL 46 (68)
T ss_dssp HHCHEEHHHHHHHHTSSHHHHHHHHHHH
T ss_pred HcCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 4577999999999999999999999876
No 36
>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=88.19 E-value=1.3 Score=28.43 Aligned_cols=43 Identities=26% Similarity=0.406 Sum_probs=32.0
Q ss_pred ccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 130 LNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 130 LNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
|+..|.+=++-|+..... .|++.|||+.+.++.+.|.++|+-|
T Consensus 3 lt~~q~~vL~~l~~~~~~----~~t~~~la~~l~~~~~~vs~~v~~L 45 (62)
T PF12802_consen 3 LTPSQFRVLMALARHPGE----ELTQSELAERLGISKSTVSRIVKRL 45 (62)
T ss_dssp STHHHHHHHHHHHHSTTS----GEEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred cCHHHHHHHHHHHHCCCC----CcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 566677666666553321 4999999999999999999998765
No 37
>smart00351 PAX Paired Box domain.
Probab=87.76 E-value=1.6 Score=33.42 Aligned_cols=43 Identities=21% Similarity=0.156 Sum_probs=35.3
Q ss_pred CCCCcccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 125 SPPGTLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 125 ~p~GTLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
+++.-|..+.=..|++||.+- ++..+||++|+|..+.|.++++
T Consensus 13 ~~~~~~s~~~R~riv~~~~~G-------~s~~~iA~~~gvs~~tV~kwi~ 55 (125)
T smart00351 13 VNGRPLPDEERQRIVELAQNG-------VRPCDISRQLCVSHGCVSKILG 55 (125)
T ss_pred cCCCCCCHHHHHHHHHHHHcC-------CCHHHHHHHHCcCHHHHHHHHH
Confidence 344447888888999998632 6899999999999999999887
No 38
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=87.35 E-value=2.3 Score=26.38 Aligned_cols=26 Identities=19% Similarity=0.326 Sum_probs=23.4
Q ss_pred CC-CHHHHHHHhchhHHHHHHHHHhhc
Q 029662 152 PL-DAKQIAEKFRLDVLQVQAILQCLS 177 (190)
Q Consensus 152 PM-~v~~iAeKFrv~v~~vq~Ilqf~S 177 (190)
.+ ++.+||+.|++...-|.+.|+.|.
T Consensus 19 ~l~s~~~la~~~~vs~~tv~~~l~~L~ 45 (60)
T smart00345 19 KLPSERELAAQLGVSRTTVREALSRLE 45 (60)
T ss_pred cCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 46 899999999999999999998774
No 39
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=87.34 E-value=1.2 Score=33.82 Aligned_cols=28 Identities=18% Similarity=0.404 Sum_probs=25.9
Q ss_pred CCCCCHHHHHHHhchhHHHHHHHHHhhc
Q 029662 150 NGPLDAKQIAEKFRLDVLQVQAILQCLS 177 (190)
Q Consensus 150 ~gPM~v~~iAeKFrv~v~~vq~Ilqf~S 177 (190)
.+++++++||+.+++....|.+||+-|.
T Consensus 23 ~~~~s~~~ia~~~~ip~~~l~kil~~L~ 50 (135)
T TIGR02010 23 TGPVTLADISERQGISLSYLEQLFAKLR 50 (135)
T ss_pred CCcCcHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4689999999999999999999999874
No 40
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=87.34 E-value=0.94 Score=34.63 Aligned_cols=27 Identities=15% Similarity=0.199 Sum_probs=24.8
Q ss_pred CCCCHHHHHHHhchhHHHHHHHHHhhc
Q 029662 151 GPLDAKQIAEKFRLDVLQVQAILQCLS 177 (190)
Q Consensus 151 gPM~v~~iAeKFrv~v~~vq~Ilqf~S 177 (190)
.++++.+||+.|+|....|.+|++-|.
T Consensus 24 ~~~s~~~ia~~~~is~~~vrk~l~~L~ 50 (141)
T PRK11014 24 RMTSISEVTEVYGVSRNHMVKIINQLS 50 (141)
T ss_pred CccCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 489999999999999999999999774
No 41
>PF04255 DUF433: Protein of unknown function (DUF433); InterPro: IPR007367 This is a family of uncharacterised proteins.; PDB: 2GA1_B.
Probab=86.93 E-value=1.4 Score=29.82 Aligned_cols=48 Identities=23% Similarity=0.392 Sum_probs=27.9
Q ss_pred CCCCCCCCCCCc-ccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhc-hhHHHHHHHHHh
Q 029662 118 SRYEEKPSPPGT-LNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFR-LDVLQVQAILQC 175 (190)
Q Consensus 118 g~~eer~~p~GT-LNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFr-v~v~~vq~Ilqf 175 (190)
+..+.+|+=.|| +-|..|-..+ .+| +++++|++.|. ++..+|+..|.|
T Consensus 6 ~~~~G~P~i~GTRI~v~~i~~~~--~~G--------~s~eeI~~~yp~Lt~~~i~aAl~y 55 (56)
T PF04255_consen 6 DILGGQPVIRGTRIPVRDILDLL--AAG--------ESPEEIAEDYPSLTLEDIRAALAY 55 (56)
T ss_dssp TSGGG--EETTSS-BHHHHHHHH--HTT----------HHHHHHHSTT--HHHHHHHHHH
T ss_pred cccCCcceEcCceecHHHHHHHH--HcC--------CCHHHHHHHCCCCCHHHHHHHHHh
Confidence 333445555554 4455443333 334 78999999998 999999999987
No 42
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=86.54 E-value=2.2 Score=28.04 Aligned_cols=36 Identities=17% Similarity=0.332 Sum_probs=26.1
Q ss_pred HHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 133 AQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 133 a~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
+.|+.+|.-+. +|-|++.+.|.+|+|.-+-+.+.+.
T Consensus 3 e~l~~Ai~~v~------~g~~S~r~AA~~ygVp~sTL~~r~~ 38 (45)
T PF05225_consen 3 EDLQKAIEAVK------NGKMSIRKAAKKYGVPRSTLRRRLR 38 (45)
T ss_dssp HHHHHHHHHHH------TTSS-HHHHHHHHT--HHHHHHHHH
T ss_pred HHHHHHHHHHH------hCCCCHHHHHHHHCcCHHHHHHHHc
Confidence 46777777776 4559999999999999998887653
No 43
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=86.33 E-value=2.4 Score=25.93 Aligned_cols=22 Identities=23% Similarity=0.283 Sum_probs=19.5
Q ss_pred CCHHHHHHHhchhHHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilq 174 (190)
|+.++||+.+++....|...+.
T Consensus 16 ~s~~eia~~l~~s~~tv~~~~~ 37 (57)
T cd06170 16 KTNKEIADILGISEKTVKTHLR 37 (57)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
Confidence 7999999999999998887654
No 44
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=85.93 E-value=1.5 Score=35.44 Aligned_cols=28 Identities=18% Similarity=0.398 Sum_probs=25.7
Q ss_pred CCCCCHHHHHHHhchhHHHHHHHHHhhc
Q 029662 150 NGPLDAKQIAEKFRLDVLQVQAILQCLS 177 (190)
Q Consensus 150 ~gPM~v~~iAeKFrv~v~~vq~Ilqf~S 177 (190)
.+|+++++||+++++....|.+||+-|.
T Consensus 23 ~~~vs~~eIA~~~~ip~~~l~kIl~~L~ 50 (164)
T PRK10857 23 AGPVPLADISERQGISLSYLEQLFSRLR 50 (164)
T ss_pred CCcCcHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4689999999999999999999999774
No 45
>cd00131 PAX Paired Box domain
Probab=85.85 E-value=2.2 Score=33.01 Aligned_cols=43 Identities=23% Similarity=0.211 Sum_probs=35.0
Q ss_pred CCCCcccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 125 SPPGTLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 125 ~p~GTLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
+.+-.|....=..||++|+.- |+..+||++|+|..+.|.++++
T Consensus 13 ~m~~~lS~d~R~rIv~~~~~G-------~s~~~iA~~~~Vs~~tV~r~i~ 55 (128)
T cd00131 13 VNGRPLPDSIRQRIVELAQSG-------IRPCDISRQLRVSHGCVSKILN 55 (128)
T ss_pred cCCCcCCHHHHHHHHHHHHcC-------CCHHHHHHHHCcCHHHHHHHHH
Confidence 344556677778899998632 8999999999999999999987
No 46
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=85.65 E-value=3.2 Score=34.90 Aligned_cols=45 Identities=16% Similarity=0.226 Sum_probs=36.0
Q ss_pred CcccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 128 GTLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 128 GTLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
|---++-.-.||.++. .+++++++.|||+..++.-+-|.+||+=|
T Consensus 20 ~~~sl~r~l~IL~~~~----~~~~~~tl~eIa~~lglpkStv~RlL~tL 64 (271)
T PRK10163 20 GAQALERGIAILQYLE----KSGGSSSVSDISLNLDLPLSTTFRLLKVL 64 (271)
T ss_pred cchHHHHHHHHHHHHH----hCCCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3334666777888873 46678999999999999999999999744
No 47
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=85.25 E-value=1.5 Score=27.59 Aligned_cols=22 Identities=14% Similarity=0.252 Sum_probs=18.1
Q ss_pred CCHHHHHHHhchhHHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilq 174 (190)
+++.+||+.|+|....|.++++
T Consensus 18 ~s~~~ia~~lgvs~~Tv~~w~k 39 (50)
T PF13384_consen 18 WSIREIAKRLGVSRSTVYRWIK 39 (50)
T ss_dssp --HHHHHHHHTS-HHHHHHHHT
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 6799999999999999999986
No 48
>PHA02943 hypothetical protein; Provisional
Probab=85.23 E-value=1.4 Score=37.32 Aligned_cols=37 Identities=19% Similarity=0.225 Sum_probs=32.0
Q ss_pred HHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 134 QLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 134 ~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
-+.+|+.+. +.|..+..|||+.+++..+++|.+|..|
T Consensus 12 R~~eILE~L------k~G~~TtseIAkaLGlS~~qa~~~LyvL 48 (165)
T PHA02943 12 RMIKTLRLL------ADGCKTTSRIANKLGVSHSMARNALYQL 48 (165)
T ss_pred HHHHHHHHH------hcCCccHHHHHHHHCCCHHHHHHHHHHH
Confidence 456777776 5788999999999999999999999876
No 49
>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This domain includes the DNA-binding HTH motif []. ; PDB: 1R71_C.
Probab=84.14 E-value=0.74 Score=33.19 Aligned_cols=29 Identities=28% Similarity=0.318 Sum_probs=22.0
Q ss_pred CCHHHHHHHhchhHHHHHHHHHhhcCCCC
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQCLSLPPE 181 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilqf~SlP~e 181 (190)
++-.|||.+++..-+.|.+.|.++.||++
T Consensus 4 ~tq~eIA~~lGks~s~Vs~~l~Ll~lP~~ 32 (93)
T PF08535_consen 4 WTQEEIAKRLGKSRSWVSNHLALLDLPEE 32 (93)
T ss_dssp --HHHHHHHTT--HHHHHHHHGGGS--HH
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHcCCHH
Confidence 67899999999999999999999999975
No 50
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=84.03 E-value=1.5 Score=26.64 Aligned_cols=25 Identities=36% Similarity=0.428 Sum_probs=22.9
Q ss_pred CCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 152 PLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 152 PM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
||++.+||+.+++...-|.++|+-|
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L 32 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRL 32 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHH
Confidence 6899999999999999999988765
No 51
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=83.88 E-value=1.1 Score=35.37 Aligned_cols=29 Identities=24% Similarity=0.197 Sum_probs=26.1
Q ss_pred CCCCCCHHHHHHHhchhHHHHHHHHHhhc
Q 029662 149 HNGPLDAKQIAEKFRLDVLQVQAILQCLS 177 (190)
Q Consensus 149 h~gPM~v~~iAeKFrv~v~~vq~Ilqf~S 177 (190)
+.+++++++||++++|....|.+|++-|.
T Consensus 21 ~~~~~s~~eIA~~~~is~~~L~kIl~~L~ 49 (153)
T PRK11920 21 DGKLSRIPEIARAYGVSELFLFKILQPLV 49 (153)
T ss_pred CCCcCcHHHHHHHHCcCHHHHHHHHHHHH
Confidence 34689999999999999999999999875
No 52
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=83.54 E-value=1.5 Score=35.56 Aligned_cols=37 Identities=22% Similarity=0.370 Sum_probs=33.3
Q ss_pred HHHHHHHHhhccCCCCCCCCCHHHHHHHh--chhHHHHHHHHHhhc
Q 029662 134 QLRRIMLLHQGKADDHNGPLDAKQIAEKF--RLDVLQVQAILQCLS 177 (190)
Q Consensus 134 ~l~~ii~L~QGk~~~h~gPM~v~~iAeKF--rv~v~~vq~Ilqf~S 177 (190)
-|++++.|..|+. |+.+||.++ .|.+.+|+..|+||-
T Consensus 28 ~ir~l~~l~~~~~-------d~~~iak~l~p~is~~ev~~sL~~L~ 66 (171)
T PF14394_consen 28 AIRELLPLMPFAP-------DPEWIAKRLRPKISAEEVRDSLEFLE 66 (171)
T ss_pred HHHHHhhcCCCCC-------CHHHHHHHhcCCCCHHHHHHHHHHHH
Confidence 4788999988876 899999999 999999999999983
No 53
>PF14502 HTH_41: Helix-turn-helix domain
Probab=83.48 E-value=1.2 Score=30.99 Aligned_cols=25 Identities=24% Similarity=0.287 Sum_probs=23.2
Q ss_pred CCHHHHHHHhchhHHHHHHHHHhhc
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQCLS 177 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilqf~S 177 (190)
..|++++++|.|-+..||+-|+||.
T Consensus 7 ~tI~e~~~~~~vs~GtiQ~Alk~Le 31 (48)
T PF14502_consen 7 PTISEYSEKFGVSRGTIQNALKFLE 31 (48)
T ss_pred CCHHHHHHHhCcchhHHHHHHHHHH
Confidence 5799999999999999999999984
No 54
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=83.47 E-value=2.4 Score=31.93 Aligned_cols=37 Identities=30% Similarity=0.489 Sum_probs=31.5
Q ss_pred HHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 132 VAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 132 va~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
.-|||..|.++ |.|++.|||.+|+.....|+..|..+
T Consensus 4 L~qlRd~l~~~--------gr~s~~~Ls~~~~~p~~~VeaMLe~l 40 (78)
T PRK15431 4 LIQVRDLLALR--------GRMEAAQISQTLNTPQPMINAMLQQL 40 (78)
T ss_pred HHHHHHHHHHc--------CcccHHHHHHHHCcCHHHHHHHHHHH
Confidence 34778888775 56999999999999999999999765
No 55
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=83.46 E-value=2 Score=29.69 Aligned_cols=23 Identities=35% Similarity=0.343 Sum_probs=20.3
Q ss_pred CCHHHHHHHhchhHHHHHHHHHh
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQC 175 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilqf 175 (190)
++..+||+++++....|.++++-
T Consensus 127 ~s~~eIA~~l~~s~~~v~~~~~~ 149 (158)
T TIGR02937 127 LSYKEIAEILGISVGTVKRRLKR 149 (158)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Confidence 78999999999999999887753
No 56
>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=82.93 E-value=2.8 Score=27.20 Aligned_cols=35 Identities=26% Similarity=0.336 Sum_probs=25.8
Q ss_pred HHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHh
Q 029662 136 RRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQC 175 (190)
Q Consensus 136 ~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf 175 (190)
+.||.+.|.. |.++..+||++.+|..+.|.+=++-
T Consensus 6 ~~Il~~Lq~d-----~r~s~~~la~~lglS~~~v~~Ri~r 40 (42)
T PF13404_consen 6 RKILRLLQED-----GRRSYAELAEELGLSESTVRRRIRR 40 (42)
T ss_dssp HHHHHHHHH------TTS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHHc-----CCccHHHHHHHHCcCHHHHHHHHHH
Confidence 4577777754 8899999999999999988775543
No 57
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=82.45 E-value=2.5 Score=34.46 Aligned_cols=38 Identities=13% Similarity=0.336 Sum_probs=29.7
Q ss_pred HHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 135 LRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 135 l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
-++||.|+-|-- ...+|+.+|||+.++|....|.+|.+
T Consensus 181 er~vl~l~ygl~--~~~~~t~~EIA~~lgis~~~V~q~~~ 218 (238)
T TIGR02393 181 ERKVLRMRYGLL--DGRPHTLEEVGKEFNVTRERIRQIES 218 (238)
T ss_pred HHHHHHHHhCCC--CCCCccHHHHHHHHCCCHHHHHHHHH
Confidence 366788876652 24679999999999999999988753
No 58
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=81.68 E-value=4.2 Score=27.23 Aligned_cols=42 Identities=24% Similarity=0.419 Sum_probs=33.0
Q ss_pred cccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 129 TLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 129 TLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
-|+..++.-+..|++ +++|++++||+.+++....|-++|+-|
T Consensus 7 ~l~~~~~~il~~l~~------~~~~~~~~la~~~~~s~~~i~~~l~~L 48 (101)
T smart00347 7 GLTPTQFLVLRILYE------EGPLSVSELAKRLGVSPSTVTRVLDRL 48 (101)
T ss_pred CCCHHHHHHHHHHHH------cCCcCHHHHHHHHCCCchhHHHHHHHH
Confidence 467777777777775 336999999999999988888877643
No 59
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=81.57 E-value=2.9 Score=29.77 Aligned_cols=35 Identities=20% Similarity=0.241 Sum_probs=27.7
Q ss_pred HHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 137 RIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 137 ~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
.|+.+.|- +++++..+||+++++....|.+.++-|
T Consensus 7 ~il~~L~~-----~~~~~~~~la~~l~~s~~tv~~~l~~L 41 (108)
T smart00344 7 KILEELQK-----DARISLAELAKKVGLSPSTVHNRVKRL 41 (108)
T ss_pred HHHHHHHH-----hCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 45555553 368999999999999999998887755
No 60
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=81.35 E-value=3 Score=31.56 Aligned_cols=31 Identities=26% Similarity=0.363 Sum_probs=24.7
Q ss_pred HHHHHHh--hccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 136 RRIMLLH--QGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 136 ~~ii~L~--QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
|+||.|+ +| |+.+|||+.+++.+..|...+.
T Consensus 140 r~v~~l~~~~g--------~s~~EIA~~lgis~~tVk~~l~ 172 (183)
T TIGR02999 140 AEVVELRFFAG--------LTVEEIAELLGVSVRTVERDWR 172 (183)
T ss_pred HHHHHHHHHcC--------CCHHHHHHHhCCCHHHHHHHHH
Confidence 5666664 44 8899999999999999987664
No 61
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=81.03 E-value=2.3 Score=35.35 Aligned_cols=29 Identities=24% Similarity=0.256 Sum_probs=26.1
Q ss_pred CCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 148 DHNGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 148 ~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
+|++++++.|||+++++.-+-|.++|+-|
T Consensus 22 ~~~~~ls~~eia~~lgl~kstv~RlL~tL 50 (263)
T PRK09834 22 RLDGGATVGLLAELTGLHRTTVRRLLETL 50 (263)
T ss_pred hcCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 45677999999999999999999999865
No 62
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=81.01 E-value=2.5 Score=32.52 Aligned_cols=30 Identities=13% Similarity=0.242 Sum_probs=23.9
Q ss_pred HHHHHH--hhccCCCCCCCCCHHHHHHHhchhHHHHHHHH
Q 029662 136 RRIMLL--HQGKADDHNGPLDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 136 ~~ii~L--~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Il 173 (190)
++||.| ++| |+.+|||+.+++....|..-+
T Consensus 128 r~i~~l~~~~g--------~s~~EIA~~lgis~~tVk~~l 159 (185)
T PRK12542 128 RQVFKYKVFYN--------LTYQEISSVMGITEANVRKQF 159 (185)
T ss_pred HHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHHH
Confidence 556666 355 889999999999999887654
No 63
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=80.82 E-value=4.5 Score=29.62 Aligned_cols=46 Identities=22% Similarity=0.360 Sum_probs=36.6
Q ss_pred cccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 129 TLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 129 TLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
-|+..|+.-+..|+ +-..++|+++.++||+.+.++.+-|-+++.-|
T Consensus 22 ~ls~~q~~vL~~l~--~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~L 67 (109)
T TIGR01889 22 NLSLEELLILYYLG--KLENNEGKLTLKEIIKEILIKQSALVKIIKKL 67 (109)
T ss_pred CCCHHHHHHHHHHH--hhhccCCcCcHHHHHHHHCCCHHHHHHHHHHH
Confidence 37888888777777 22334588999999999999999999888754
No 64
>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=80.67 E-value=1.8 Score=27.66 Aligned_cols=26 Identities=35% Similarity=0.505 Sum_probs=21.6
Q ss_pred CCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 151 GPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 151 gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
||+++.|||+.|++..+.|..=|..|
T Consensus 14 ~~~~~~el~~~l~~s~~~vs~hL~~L 39 (47)
T PF01022_consen 14 GPLTVSELAEELGLSQSTVSHHLKKL 39 (47)
T ss_dssp SSEEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCCchhhHHHhccccchHHHHHHHHH
Confidence 77999999999999999988766654
No 65
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=80.52 E-value=0.99 Score=29.69 Aligned_cols=28 Identities=11% Similarity=0.236 Sum_probs=22.1
Q ss_pred CCCCHHHHHHHhchhHHHHHHHH-HhhcC
Q 029662 151 GPLDAKQIAEKFRLDVLQVQAIL-QCLSL 178 (190)
Q Consensus 151 gPM~v~~iAeKFrv~v~~vq~Il-qf~Sl 178 (190)
.+|.|++||+++++.+..|-.+| +-+-+
T Consensus 2 ~~i~V~elAk~l~v~~~~ii~~l~~~~Gi 30 (54)
T PF04760_consen 2 EKIRVSELAKELGVPSKEIIKKLFKELGI 30 (54)
T ss_dssp -EE-TTHHHHHHSSSHHHHHHHH-HHHTS
T ss_pred CceEHHHHHHHHCcCHHHHHHHHHHhCCc
Confidence 46899999999999999999888 63443
No 66
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.
Probab=80.43 E-value=2.9 Score=35.03 Aligned_cols=36 Identities=17% Similarity=0.281 Sum_probs=28.2
Q ss_pred HHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 135 LRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 135 l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
=|+||.|+=+. ..+|+.+|||+.|+|....|.+|..
T Consensus 223 er~vl~l~y~~----~~~~t~~eIA~~lgvS~~~V~q~~~ 258 (270)
T TIGR02392 223 SRRIIEARWLD----DDKLTLQELAAEYGVSAERIRQIEK 258 (270)
T ss_pred HHHHHHHHhcC----CCCcCHHHHHHHHCCCHHHHHHHHH
Confidence 36677775553 3479999999999999999987754
No 67
>PF09286 Pro-kuma_activ: Pro-kumamolisin, activation domain ; InterPro: IPR015366 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This domain is found at the N terminus of peptidases belonging to MEROPS peptidase family S53 (sedolisin, clan SB). The domain adopts a ferredoxin-like fold, with an alpha+beta sandwich. Cleavage of the domain results in activation of the peptidase []. ; GO: 0008236 serine-type peptidase activity; PDB: 1T1E_A 3EDY_A 3EE6_A.
Probab=80.42 E-value=5.5 Score=30.22 Aligned_cols=47 Identities=17% Similarity=0.186 Sum_probs=32.9
Q ss_pred cHHHHHH-HHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhhc
Q 029662 131 NVAQLRR-IMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCLS 177 (190)
Q Consensus 131 Nva~l~~-ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~S 177 (190)
|.+.|.. +..+..=.+.+....|+-+||++.|.-....|+.|.+||.
T Consensus 25 n~~~L~~~l~~vsdP~s~~Ygk~Lt~~e~~~~~~p~~~~v~~V~~wL~ 72 (143)
T PF09286_consen 25 NLDALEQYLAEVSDPGSPNYGKYLTPEEFAALFAPSPEDVAAVKSWLK 72 (143)
T ss_dssp THHHHHHHHHHHHTTTSTTTT----HHHHHHHHS--HHHHHHHHHHHH
T ss_pred CHHHHHHHHHhCcCCCCcccccCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 5666665 4445666677778889999999999999999999999985
No 68
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=80.16 E-value=2.9 Score=31.68 Aligned_cols=22 Identities=9% Similarity=0.042 Sum_probs=19.2
Q ss_pred CCHHHHHHHhchhHHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilq 174 (190)
|+++|||+.+++....|...|.
T Consensus 129 ~s~~eIA~~lgis~~tV~~~l~ 150 (164)
T PRK12547 129 FSYEDAAAICGCAVGTIKSRVS 150 (164)
T ss_pred CCHHHHHHHhCCCHHHHHHHHH
Confidence 7899999999999998876653
No 69
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=80.03 E-value=3 Score=30.80 Aligned_cols=23 Identities=22% Similarity=0.182 Sum_probs=19.6
Q ss_pred CCCHHHHHHHhchhHHHHHHHHH
Q 029662 152 PLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 152 PM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
-|+.++||+++++.+..|...+.
T Consensus 144 ~~s~~eIA~~lgis~~tV~~~l~ 166 (182)
T PRK09652 144 GLSYEEIAEIMGCPIGTVRSRIF 166 (182)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHH
Confidence 38999999999999998876543
No 70
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=79.98 E-value=2.8 Score=33.66 Aligned_cols=33 Identities=18% Similarity=0.281 Sum_probs=25.6
Q ss_pred HHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 136 RRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 136 ~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
++||.|+-+ ..|+++|||++++|....|.+|..
T Consensus 189 ~~i~~~~~~------~~~t~~eIA~~lgis~~~V~~~~~ 221 (231)
T TIGR02885 189 RQIIMLRYF------KDKTQTEVANMLGISQVQVSRLEK 221 (231)
T ss_pred HHHHHHHHH------cCCCHHHHHHHHCcCHHHHHHHHH
Confidence 456666543 239999999999999999988753
No 71
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=79.95 E-value=2.9 Score=32.09 Aligned_cols=20 Identities=15% Similarity=0.287 Sum_probs=17.4
Q ss_pred CCHHHHHHHhchhHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAI 172 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~I 172 (190)
|+.+|||+.+++.+..|..-
T Consensus 134 ~s~~EIA~~lgis~~tV~~~ 153 (179)
T PRK12543 134 YSQEEIAQLLQIPIGTVKSR 153 (179)
T ss_pred CCHHHHHHHHCCCHHHHHHH
Confidence 78999999999999987643
No 72
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=79.94 E-value=3.3 Score=30.41 Aligned_cols=22 Identities=23% Similarity=0.184 Sum_probs=19.8
Q ss_pred CCHHHHHHHhchhHHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilq 174 (190)
|+..|||+.+++.+..|...+.
T Consensus 123 ~s~~EIA~~l~is~~tV~~~~~ 144 (154)
T PRK06759 123 KTMGEIALETEMTYYQVRWIYR 144 (154)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
Confidence 8899999999999999987764
No 73
>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=79.90 E-value=1.3 Score=31.12 Aligned_cols=30 Identities=30% Similarity=0.436 Sum_probs=22.4
Q ss_pred CCCCCCCCHHHHHHHhchh-HHHHHHHHHhh
Q 029662 147 DDHNGPLDAKQIAEKFRLD-VLQVQAILQCL 176 (190)
Q Consensus 147 ~~h~gPM~v~~iAeKFrv~-v~~vq~Ilqf~ 176 (190)
.+|.-|-++.|||+.|++. .+-|+..|+-|
T Consensus 20 ~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~L 50 (65)
T PF01726_consen 20 EENGYPPTVREIAEALGLKSTSTVQRHLKAL 50 (65)
T ss_dssp HHHSS---HHHHHHHHTSSSHHHHHHHHHHH
T ss_pred HHcCCCCCHHHHHHHhCCCChHHHHHHHHHH
Confidence 3444567999999999998 99999988765
No 74
>PRK00215 LexA repressor; Validated
Probab=79.87 E-value=3.1 Score=33.15 Aligned_cols=47 Identities=19% Similarity=0.273 Sum_probs=33.8
Q ss_pred cccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhch-hHHHHHHHHHhh
Q 029662 129 TLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRL-DVLQVQAILQCL 176 (190)
Q Consensus 129 TLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv-~v~~vq~Ilqf~ 176 (190)
+|+..|.+-+..|.+- ...+..++++.|||+.|++ .-+-|+++|+=|
T Consensus 1 ~lt~~q~~il~~i~~~-~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L 48 (205)
T PRK00215 1 MLTKRQQEILDFIRDH-IEETGYPPSRREIADALGLRSPSAVHEHLKAL 48 (205)
T ss_pred CCCHHHHHHHHHHHHH-HHHhCCCCCHHHHHHHhCCCChHHHHHHHHHH
Confidence 4666666666555531 2334557999999999999 889999988644
No 75
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=79.82 E-value=6 Score=29.83 Aligned_cols=42 Identities=12% Similarity=0.263 Sum_probs=34.8
Q ss_pred cccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhhcC
Q 029662 129 TLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCLSL 178 (190)
Q Consensus 129 TLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~Sl 178 (190)
.|+..+|+++|.-+-. +...|||++|+|..+-|...|+-+-+
T Consensus 56 Kid~~~L~~~v~~~pd--------~tl~Ela~~l~Vs~~ti~~~Lkrlg~ 97 (119)
T PF01710_consen 56 KIDRDELKALVEENPD--------ATLRELAERLGVSPSTIWRALKRLGI 97 (119)
T ss_pred cccHHHHHHHHHHCCC--------cCHHHHHHHcCCCHHHHHHHHHHcCc
Confidence 7888888888876433 77899999999999999999887654
No 76
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=79.82 E-value=2.8 Score=25.49 Aligned_cols=28 Identities=29% Similarity=0.269 Sum_probs=24.7
Q ss_pred CCCCCHHHHHHHhchhHHHHHHHHHhhc
Q 029662 150 NGPLDAKQIAEKFRLDVLQVQAILQCLS 177 (190)
Q Consensus 150 ~gPM~v~~iAeKFrv~v~~vq~Ilqf~S 177 (190)
++++++.+||+.|.+....|.++|+-|.
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~ 35 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLR 35 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4679999999999999999999987664
No 77
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=79.79 E-value=2.6 Score=31.82 Aligned_cols=24 Identities=29% Similarity=0.321 Sum_probs=20.7
Q ss_pred CCCHHHHHHHhchhHHHHHHHHHh
Q 029662 152 PLDAKQIAEKFRLDVLQVQAILQC 175 (190)
Q Consensus 152 PM~v~~iAeKFrv~v~~vq~Ilqf 175 (190)
-|+++|||+++++....|...+..
T Consensus 152 g~s~~eIA~~lgis~~~v~~~l~R 175 (187)
T TIGR02948 152 DLSLKEISEILDLPVGTVKTRIHR 175 (187)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHH
Confidence 389999999999999999877653
No 78
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=79.70 E-value=3.4 Score=35.18 Aligned_cols=37 Identities=24% Similarity=0.400 Sum_probs=30.3
Q ss_pred HHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 136 RRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 136 ~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
|+||.|+-|-.+ ..+++.+|||+.|+|...-|..|+.
T Consensus 255 r~Vi~lr~gl~~--~~~~Tl~EIa~~lgiS~erVrq~~~ 291 (298)
T TIGR02997 255 RQVLRLRFGLDG--GEPLTLAEIGRRLNLSRERVRQIEA 291 (298)
T ss_pred HHHHHHHhccCC--CCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 678888877632 3469999999999999999988864
No 79
>TIGR00122 birA_repr_reg BirA biotin operon repressor domain. This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.
Probab=79.69 E-value=2.3 Score=28.67 Aligned_cols=27 Identities=19% Similarity=0.388 Sum_probs=24.0
Q ss_pred CCCCHHHHHHHhchhHHHHHHHHHhhc
Q 029662 151 GPLDAKQIAEKFRLDVLQVQAILQCLS 177 (190)
Q Consensus 151 gPM~v~~iAeKFrv~v~~vq~Ilqf~S 177 (190)
+++++.+||+.|+|....|.+-++.+.
T Consensus 12 ~~~~~~eLa~~l~vS~~tv~~~l~~L~ 38 (69)
T TIGR00122 12 NPFSGEKLGEALGMSRTAVNKHIQTLR 38 (69)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 468999999999999999999888773
No 80
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=79.64 E-value=3 Score=32.42 Aligned_cols=22 Identities=23% Similarity=0.256 Sum_probs=19.6
Q ss_pred CCHHHHHHHhchhHHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilq 174 (190)
|+++|||+.+++....|...++
T Consensus 148 ~s~~EIAe~lgis~~~V~~~l~ 169 (189)
T PRK06811 148 EKIEEIAKKLGLTRSAIDNRLS 169 (189)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
Confidence 8899999999999998887664
No 81
>PRK10870 transcriptional repressor MprA; Provisional
Probab=79.23 E-value=5.1 Score=32.03 Aligned_cols=44 Identities=11% Similarity=0.171 Sum_probs=36.0
Q ss_pred cccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 129 TLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 129 TLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
-|+..|..-++.|+. .+++++++.+||+.+.++-+.|-++|+=|
T Consensus 52 gLt~~q~~iL~~L~~----~~~~~it~~eLa~~l~l~~~tvsr~v~rL 95 (176)
T PRK10870 52 GINETLFMALITLES----QENHSIQPSELSCALGSSRTNATRIADEL 95 (176)
T ss_pred CCCHHHHHHHHHHhc----CCCCCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 378888888888872 45678999999999999999998887643
No 82
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=79.07 E-value=3.2 Score=31.68 Aligned_cols=22 Identities=23% Similarity=0.250 Sum_probs=19.1
Q ss_pred CCHHHHHHHhchhHHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilq 174 (190)
|+.+|||+.|++.+..|..-+.
T Consensus 148 ~s~~eIA~~l~is~~tV~~~l~ 169 (184)
T PRK12512 148 ASIKETAAKLSMSEGAVRVALH 169 (184)
T ss_pred CCHHHHHHHhCCCHHHHHHHHH
Confidence 7899999999999998876553
No 83
>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=78.87 E-value=2.8 Score=27.80 Aligned_cols=34 Identities=29% Similarity=0.460 Sum_probs=24.7
Q ss_pred HHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 136 RRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 136 ~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
..|+.+. ..++||++.|||++|++..+.+..=|+
T Consensus 13 ~~Il~~L-----~~~~~~t~~ela~~l~~~~~t~s~hL~ 46 (61)
T PF12840_consen 13 LRILRLL-----ASNGPMTVSELAEELGISQSTVSYHLK 46 (61)
T ss_dssp HHHHHHH-----HHCSTBEHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHH-----hcCCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3455555 346789999999999999888766554
No 84
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=78.82 E-value=4.1 Score=30.04 Aligned_cols=31 Identities=19% Similarity=0.239 Sum_probs=24.2
Q ss_pred HHHHHHh--hccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 136 RRIMLLH--QGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 136 ~~ii~L~--QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
|+||.|+ +| |+++|||+.+++.+..|...+.
T Consensus 112 r~v~~l~~~~g--------~s~~EIA~~lgis~~tV~~~l~ 144 (161)
T PRK09047 112 REAFLLRYWED--------MDVAETAAAMGCSEGSVKTHCS 144 (161)
T ss_pred HHHHHHHHHhc--------CCHHHHHHHHCCCHHHHHHHHH
Confidence 5666663 55 7899999999999998876543
No 85
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=78.29 E-value=2.8 Score=26.84 Aligned_cols=24 Identities=21% Similarity=0.415 Sum_probs=21.1
Q ss_pred CCCHHHHHHHhchhHHHHHHHHHh
Q 029662 152 PLDAKQIAEKFRLDVLQVQAILQC 175 (190)
Q Consensus 152 PM~v~~iAeKFrv~v~~vq~Ilqf 175 (190)
++++++||+.|++....+.+++.-
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~~ 24 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFKK 24 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHH
Confidence 578999999999999999888764
No 86
>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=78.25 E-value=10 Score=23.81 Aligned_cols=24 Identities=21% Similarity=0.324 Sum_probs=21.0
Q ss_pred CCHHHHHHHhchhHHHHHHHHHhh
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
.++.+||+.|+|.-..|.+.|+-|
T Consensus 26 ~~~~~la~~~~is~~~v~~~l~~L 49 (66)
T cd07377 26 PSERELAEELGVSRTTVREALREL 49 (66)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHH
Confidence 359999999999999999888765
No 87
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=78.17 E-value=3 Score=28.95 Aligned_cols=24 Identities=29% Similarity=0.325 Sum_probs=22.2
Q ss_pred CCHHHHHHHhchhHHHHHHHHHhh
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
+++.|||++++|+.+-|.++|.-|
T Consensus 23 ~ta~eLa~~lgl~~~~v~r~L~~L 46 (68)
T smart00550 23 STALQLAKNLGLPKKEVNRVLYSL 46 (68)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHH
Confidence 999999999999999999998744
No 88
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=78.05 E-value=3.8 Score=30.63 Aligned_cols=30 Identities=30% Similarity=0.505 Sum_probs=23.7
Q ss_pred HHHHHHh--hccCCCCCCCCCHHHHHHHhchhHHHHHHHH
Q 029662 136 RRIMLLH--QGKADDHNGPLDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 136 ~~ii~L~--QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Il 173 (190)
|+||.|+ +| |+.+|||+.+++.+..|..-+
T Consensus 119 r~v~~L~~~~g--------~s~~EIA~~l~is~~tV~~~l 150 (161)
T PRK12528 119 KRAFLLAQVDG--------LGYGEIATELGISLATVKRYL 150 (161)
T ss_pred HHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHHH
Confidence 5566553 55 889999999999999987654
No 89
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=77.77 E-value=6.5 Score=31.15 Aligned_cols=45 Identities=13% Similarity=0.212 Sum_probs=36.4
Q ss_pred cccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 129 TLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 129 TLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
.|.-.++++++++.++. +..-++.++||+++++....|..-++|+
T Consensus 158 ~Lt~re~~~l~~~i~~~---~~~g~s~~eIA~~l~iS~~Tv~~~~~~~ 202 (239)
T PRK10430 158 GLTPQTLRTLCQWIDAH---QDYEFSTDELANAVNISRVSCRKYLIWL 202 (239)
T ss_pred CCCHHHHHHHHHHHHhC---CCCCcCHHHHHHHhCchHHHHHHHHHHH
Confidence 47778888887777544 3344899999999999999999988887
No 90
>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=77.42 E-value=6.4 Score=27.03 Aligned_cols=37 Identities=32% Similarity=0.531 Sum_probs=29.7
Q ss_pred HHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 135 LRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 135 l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
|+.|..|.+ ..+++...+||++++|..+-|-..|+-|
T Consensus 10 L~~Iy~l~~-----~~~~v~~~~iA~~L~vs~~tvt~ml~~L 46 (60)
T PF01325_consen 10 LKAIYELSE-----EGGPVRTKDIAERLGVSPPTVTEMLKRL 46 (60)
T ss_dssp HHHHHHHHH-----CTSSBBHHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHHc-----CCCCccHHHHHHHHCCChHHHHHHHHHH
Confidence 667777776 4678999999999999999888887755
No 91
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=77.02 E-value=7 Score=24.95 Aligned_cols=45 Identities=18% Similarity=0.236 Sum_probs=30.9
Q ss_pred ccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhch-hHHHHHHHH-HhhcCCC
Q 029662 130 LNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRL-DVLQVQAIL-QCLSLPP 180 (190)
Q Consensus 130 LNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv-~v~~vq~Il-qf~SlP~ 180 (190)
++...|+.++.+.+.. ++++++||+.+++ +.+.+.++. ++....|
T Consensus 34 ~~~~r~~~a~~~l~~~------~~~~~~ia~~~g~~s~~~f~r~Fk~~~g~sp 80 (84)
T smart00342 34 LRDRRLERARRLLRDT------DLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80 (84)
T ss_pred HHHHHHHHHHHHHHcC------CCCHHHHHHHhCCCChHHHHHHHHHHHCcCh
Confidence 3344455555554422 7999999999999 999888877 4544443
No 92
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=76.67 E-value=4.5 Score=35.27 Aligned_cols=36 Identities=25% Similarity=0.451 Sum_probs=29.9
Q ss_pred HHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHH
Q 029662 136 RRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 136 ~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Il 173 (190)
|+||.|+-|-.+ ..+|+.+|||+.|+|...-|..|.
T Consensus 262 r~Vi~lr~gl~~--~~~~Tl~EIa~~lgiS~erVRqi~ 297 (317)
T PRK07405 262 KEVIALRFGLED--GQPLTLAKIGERLNISRERVRQIE 297 (317)
T ss_pred HHHHHHHhhcCC--CCCcCHHHHHHHHCcCHHHHHHHH
Confidence 678888887643 356999999999999999998875
No 93
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=76.67 E-value=4.6 Score=30.01 Aligned_cols=22 Identities=27% Similarity=0.297 Sum_probs=19.7
Q ss_pred CCHHHHHHHhchhHHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilq 174 (190)
|+.+|||+.+++....|...+.
T Consensus 128 ~s~~eIA~~lgis~~tV~~~i~ 149 (166)
T PRK09639 128 YSYKEIAEALGIKESSVGTTLA 149 (166)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
Confidence 8999999999999999887664
No 94
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=76.52 E-value=3.7 Score=33.04 Aligned_cols=36 Identities=17% Similarity=0.244 Sum_probs=25.6
Q ss_pred HHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHH
Q 029662 136 RRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 136 ~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Il 173 (190)
|+||.|+-+-+. -.-|+.+|||+.++|.+.-|.+.+
T Consensus 184 R~v~~L~y~l~~--~eg~s~~EIA~~lgis~~tVk~~~ 219 (234)
T PRK08301 184 KQIMELRFGLNG--GEEKTQKEVADMLGISQSYISRLE 219 (234)
T ss_pred HHHHHHHhccCC--CCCCCHHHHHHHHCCCHHHHHHHH
Confidence 667777532110 123889999999999999987665
No 95
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=76.46 E-value=4.2 Score=30.98 Aligned_cols=22 Identities=9% Similarity=0.128 Sum_probs=19.2
Q ss_pred CCHHHHHHHhchhHHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilq 174 (190)
|+.+|||+.+++.+..|...+.
T Consensus 152 ~s~~eIA~~lgis~~~V~~~l~ 173 (186)
T PRK13919 152 YTHREAAQLLGLPLGTLKTRAR 173 (186)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 8899999999999999886543
No 96
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=76.45 E-value=4.5 Score=30.07 Aligned_cols=21 Identities=19% Similarity=0.237 Sum_probs=18.9
Q ss_pred CCHHHHHHHhchhHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Il 173 (190)
|+.+|||+.+++....|...+
T Consensus 126 ~s~~EIA~~lgis~~tV~~~l 146 (163)
T PRK07037 126 ETQKDIARELGVSPTLVNFMI 146 (163)
T ss_pred CCHHHHHHHHCCCHHHHHHHH
Confidence 789999999999999988764
No 97
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=76.33 E-value=4.8 Score=31.45 Aligned_cols=31 Identities=16% Similarity=0.416 Sum_probs=24.5
Q ss_pred HHHHHHHh--hccCCCCCCCCCHHHHHHHhchhHHHHHHHH
Q 029662 135 LRRIMLLH--QGKADDHNGPLDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 135 l~~ii~L~--QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Il 173 (190)
-|+|+.|+ +| |+++|||+.+++....|...|
T Consensus 139 ~R~v~~L~~~~g--------~s~~EIA~~lgis~~tVk~~l 171 (189)
T PRK12530 139 QARVFMMREYLE--------LSSEQICQECDISTSNLHVLL 171 (189)
T ss_pred HHHHHhHHHHcC--------CCHHHHHHHHCCCHHHHHHHH
Confidence 46677773 55 889999999999999886544
No 98
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=76.20 E-value=5.2 Score=30.41 Aligned_cols=31 Identities=29% Similarity=0.502 Sum_probs=24.5
Q ss_pred HHHHHHHh--hccCCCCCCCCCHHHHHHHhchhHHHHHHHH
Q 029662 135 LRRIMLLH--QGKADDHNGPLDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 135 l~~ii~L~--QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Il 173 (190)
-++||.|+ +| |+++|||+.+++.+.-|...|
T Consensus 124 ~r~v~~L~~~~g--------~s~~EIA~~lgis~~tV~~~l 156 (172)
T PRK12523 124 ARAAFLYNRLDG--------MGHAEIAERLGVSVSRVRQYL 156 (172)
T ss_pred HHHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHHH
Confidence 45666664 44 889999999999999887665
No 99
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=76.11 E-value=4.3 Score=25.14 Aligned_cols=28 Identities=14% Similarity=0.152 Sum_probs=20.1
Q ss_pred CCCCCCCHHHHHHHhchhHHHHHHHHHh
Q 029662 148 DHNGPLDAKQIAEKFRLDVLQVQAILQC 175 (190)
Q Consensus 148 ~h~gPM~v~~iAeKFrv~v~~vq~Ilqf 175 (190)
+-..+++|++||+.+++..+.+.++.+=
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 3455699999999999999999988763
No 100
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=76.06 E-value=4.4 Score=31.76 Aligned_cols=21 Identities=10% Similarity=0.442 Sum_probs=18.2
Q ss_pred CCHHHHHHHhchhHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Il 173 (190)
|+++|||+.+++.+.-|...|
T Consensus 148 ~s~~EIA~~lgis~~tvk~rl 168 (188)
T TIGR02943 148 FESDEICQELEISTSNCHVLL 168 (188)
T ss_pred CCHHHHHHHhCCCHHHHHHHH
Confidence 889999999999998876554
No 101
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=76.05 E-value=4.4 Score=32.38 Aligned_cols=22 Identities=23% Similarity=0.460 Sum_probs=20.0
Q ss_pred CCHHHHHHHhchhHHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilq 174 (190)
|+++|||+++++....|..++.
T Consensus 195 ~s~~eIA~~lgis~~~v~~~~~ 216 (227)
T TIGR02980 195 KTQSEIAERLGISQMHVSRLLR 216 (227)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 8999999999999999988764
No 102
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=75.99 E-value=4.3 Score=32.14 Aligned_cols=21 Identities=14% Similarity=0.352 Sum_probs=18.4
Q ss_pred CCHHHHHHHhchhHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Il 173 (190)
|+.+|||+.+++.+..|...|
T Consensus 156 ~s~~EIA~~lgis~~tVk~~l 176 (201)
T PRK12545 156 FEIDDICTELTLTANHCSVLL 176 (201)
T ss_pred CCHHHHHHHHCcCHHHHHHHH
Confidence 789999999999999887554
No 103
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=75.93 E-value=5.1 Score=31.50 Aligned_cols=21 Identities=10% Similarity=0.153 Sum_probs=18.4
Q ss_pred CCHHHHHHHhchhHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Il 173 (190)
|+.+|||+.+++...-|...+
T Consensus 128 ~s~~EIA~~lgis~~tV~~~l 148 (182)
T PRK12511 128 LSYQEAAAVLGIPIGTLMSRI 148 (182)
T ss_pred CCHHHHHHHhCcCHHHHHHHH
Confidence 889999999999998886654
No 104
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=75.91 E-value=4.3 Score=32.26 Aligned_cols=22 Identities=23% Similarity=0.403 Sum_probs=19.4
Q ss_pred CCHHHHHHHhchhHHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilq 174 (190)
|+.+|||+.+++.+..|...|.
T Consensus 170 ~s~~EIA~~lgis~~tV~~~l~ 191 (206)
T PRK12526 170 LSQEQLAQQLNVPLGTVKSRLR 191 (206)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
Confidence 8899999999999999877654
No 105
>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=75.57 E-value=7.1 Score=31.98 Aligned_cols=40 Identities=18% Similarity=0.110 Sum_probs=31.8
Q ss_pred HHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 133 AQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 133 a~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
.-.-.||.++. .+++||++.|||+..++.-+-+.+||+=|
T Consensus 9 ~ral~IL~~l~----~~~~~~~l~eia~~lglpksT~~RlL~tL 48 (248)
T TIGR02431 9 ARGLAVIEAFG----AERPRLTLTDVAEATGLTRAAARRFLLTL 48 (248)
T ss_pred HHHHHHHHHHh----cCCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 33445677763 35678999999999999999999999854
No 106
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=75.51 E-value=5.5 Score=30.74 Aligned_cols=30 Identities=20% Similarity=0.474 Sum_probs=23.7
Q ss_pred HHHHHH--hhccCCCCCCCCCHHHHHHHhchhHHHHHHHH
Q 029662 136 RRIMLL--HQGKADDHNGPLDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 136 ~~ii~L--~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Il 173 (190)
|+||.| ++| |+++|||+.+++.+.-|..-+
T Consensus 133 R~v~~L~~~~g--------~s~~EIA~~lgis~~tVk~~l 164 (178)
T PRK12529 133 KQAFLMATLDG--------MKQKDIAQALDIALPTVKKYI 164 (178)
T ss_pred HHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHHH
Confidence 566777 444 889999999999998887543
No 107
>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=75.34 E-value=3.2 Score=27.88 Aligned_cols=28 Identities=25% Similarity=0.472 Sum_probs=24.6
Q ss_pred CCCCCHHHHHHHhchhHHHHHHHHHhhc
Q 029662 150 NGPLDAKQIAEKFRLDVLQVQAILQCLS 177 (190)
Q Consensus 150 ~gPM~v~~iAeKFrv~v~~vq~Ilqf~S 177 (190)
+|.+++++||+.|+|-..-|.+=|+.|.
T Consensus 12 ~~~~s~~ela~~~~VS~~TiRRDl~~L~ 39 (57)
T PF08220_consen 12 KGKVSVKELAEEFGVSEMTIRRDLNKLE 39 (57)
T ss_pred cCCEEHHHHHHHHCcCHHHHHHHHHHHH
Confidence 5779999999999999999998887764
No 108
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=75.20 E-value=4.7 Score=31.13 Aligned_cols=22 Identities=9% Similarity=0.108 Sum_probs=19.6
Q ss_pred CCHHHHHHHhchhHHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilq 174 (190)
|+.+|||+.+++....|...|.
T Consensus 148 ~s~~eIA~~lgis~~tV~~~l~ 169 (189)
T PRK12515 148 KSVEEVGEIVGIPESTVKTRMF 169 (189)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 8999999999999999877653
No 109
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=75.13 E-value=6.7 Score=30.99 Aligned_cols=24 Identities=25% Similarity=0.340 Sum_probs=22.5
Q ss_pred CCHHHHHHHhchhHHHHHHHHHhh
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
++++|||+..+|....|++-|++.
T Consensus 152 ls~~EIA~~lgiS~~tV~r~l~~a 175 (185)
T PF07638_consen 152 LSVEEIAERLGISERTVRRRLRRA 175 (185)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHH
Confidence 899999999999999999998875
No 110
>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=74.95 E-value=3.5 Score=27.95 Aligned_cols=27 Identities=26% Similarity=0.362 Sum_probs=21.7
Q ss_pred CCCCHHHHHHHhchhHHHHHHHHHhhc
Q 029662 151 GPLDAKQIAEKFRLDVLQVQAILQCLS 177 (190)
Q Consensus 151 gPM~v~~iAeKFrv~v~~vq~Ilqf~S 177 (190)
-.-++.|||+..+|.+..|+.|+++..
T Consensus 19 r~Pt~eEiA~~lgis~~~v~~~l~~~~ 45 (78)
T PF04539_consen 19 REPTDEEIAEELGISVEEVRELLQASR 45 (78)
T ss_dssp S--BHHHHHHHHTS-HHHHHHHHHHHS
T ss_pred CCCCHHHHHHHHcccHHHHHHHHHhCC
Confidence 347899999999999999999998753
No 111
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=74.92 E-value=4.8 Score=29.64 Aligned_cols=22 Identities=32% Similarity=0.377 Sum_probs=20.0
Q ss_pred CCHHHHHHHhchhHHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilq 174 (190)
|+.+|||+.+++....|.+.+.
T Consensus 142 ~~~~eIA~~lgis~~tv~~~~~ 163 (179)
T PRK11924 142 LSYREIAEILGVPVGTVKSRLR 163 (179)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
Confidence 8999999999999999987764
No 112
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=74.90 E-value=4.5 Score=31.57 Aligned_cols=22 Identities=36% Similarity=0.477 Sum_probs=19.4
Q ss_pred CCHHHHHHHhchhHHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilq 174 (190)
|+++|||+.+++....|...+.
T Consensus 123 ~~~~EIA~~lgis~~tV~~~l~ 144 (181)
T PRK09637 123 LSQKEIAEKLGLSLSGAKSRVQ 144 (181)
T ss_pred CCHHHHHHHhCCCHHHHHHHHH
Confidence 8899999999999998877654
No 113
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=74.88 E-value=4.6 Score=31.06 Aligned_cols=23 Identities=22% Similarity=0.167 Sum_probs=19.3
Q ss_pred CCCHHHHHHHhchhHHHHHHHHH
Q 029662 152 PLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 152 PM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
-|+++|||+.+++....|...+.
T Consensus 154 g~s~~eIA~~lgis~~tv~~~l~ 176 (193)
T PRK11923 154 GLSYEDIASVMQCPVGTVRSRIF 176 (193)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHH
Confidence 38899999999999988876543
No 114
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=74.78 E-value=3.8 Score=25.92 Aligned_cols=22 Identities=18% Similarity=0.259 Sum_probs=20.4
Q ss_pred CCHHHHHHHhchhHHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilq 174 (190)
.++++||+.|+|...-|++|+.
T Consensus 28 ~s~~~vA~~~~vs~~TV~ri~~ 49 (52)
T PF13542_consen 28 RSFKDVARELGVSWSTVRRIFD 49 (52)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
Confidence 4899999999999999999985
No 115
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=74.38 E-value=6.4 Score=29.27 Aligned_cols=21 Identities=24% Similarity=0.262 Sum_probs=18.4
Q ss_pred CCHHHHHHHhchhHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Il 173 (190)
|+.+|||+.+++....|...|
T Consensus 123 ~s~~EIA~~lgis~~tV~~~l 143 (160)
T PRK09642 123 KSYQEIALQEKIEVKTVEMKL 143 (160)
T ss_pred CCHHHHHHHHCCCHHHHHHHH
Confidence 889999999999999986544
No 116
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=73.99 E-value=8 Score=29.22 Aligned_cols=42 Identities=12% Similarity=0.240 Sum_probs=34.9
Q ss_pred cccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 129 TLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 129 TLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
-|+..|..=+..|+. +++++..+||+.++++.+.|-++|+=|
T Consensus 37 glt~~q~~vL~~l~~------~~~~t~~eLa~~l~i~~~tvsr~l~~L 78 (144)
T PRK11512 37 DITAAQFKVLCSIRC------AACITPVELKKVLSVDLGALTRMLDRL 78 (144)
T ss_pred CCCHHHHHHHHHHHH------cCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 488888887777763 457999999999999999999888744
No 117
>PRK00118 putative DNA-binding protein; Validated
Probab=73.94 E-value=6.9 Score=30.24 Aligned_cols=34 Identities=24% Similarity=0.193 Sum_probs=25.5
Q ss_pred HHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 135 LRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 135 l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
-++++.|+... -|++++||+.|++....|.+.+.
T Consensus 22 qRevl~L~y~e------g~S~~EIAe~lGIS~~TV~r~L~ 55 (104)
T PRK00118 22 QRNYMELYYLD------DYSLGEIAEEFNVSRQAVYDNIK 55 (104)
T ss_pred HHHHHHHHHHc------CCCHHHHHHHHCcCHHHHHHHHH
Confidence 45556554332 28999999999999999887764
No 118
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=73.66 E-value=2 Score=31.44 Aligned_cols=24 Identities=29% Similarity=0.349 Sum_probs=20.7
Q ss_pred CCCCHHHHHHHhchhHHHHHHHHH
Q 029662 151 GPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 151 gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
.-|+.+|||+.+++.+..|...+.
T Consensus 120 ~g~s~~eIA~~lgis~~tv~~~l~ 143 (154)
T TIGR02950 120 KEFSYKEIAELLNLSLAKVKSNLF 143 (154)
T ss_pred ccCcHHHHHHHHCCCHHHHHHHHH
Confidence 448999999999999999887664
No 119
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=73.64 E-value=5.3 Score=31.13 Aligned_cols=22 Identities=14% Similarity=0.042 Sum_probs=19.4
Q ss_pred CCHHHHHHHhchhHHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilq 174 (190)
|+++|||+.+++....|...|.
T Consensus 147 ~s~~EIA~~lgis~~tVk~~l~ 168 (185)
T PRK09649 147 LSYADAAAVCGCPVGTIRSRVA 168 (185)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
Confidence 8999999999999998877654
No 120
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=73.54 E-value=5.2 Score=29.87 Aligned_cols=22 Identities=32% Similarity=0.362 Sum_probs=19.1
Q ss_pred CCHHHHHHHhchhHHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilq 174 (190)
++.+|||+.+++....|..-+.
T Consensus 129 ~s~~eIA~~lgis~~tv~~~l~ 150 (161)
T PRK12541 129 FSYKEIAEMTGLSLAKVKIELH 150 (161)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
Confidence 7899999999999998876553
No 121
>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR. Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo.
Probab=73.52 E-value=4.1 Score=29.94 Aligned_cols=28 Identities=18% Similarity=0.381 Sum_probs=21.8
Q ss_pred HHHHHHH--hhccCCCCCCCCCHHHHHHHhchhHHHHH
Q 029662 135 LRRIMLL--HQGKADDHNGPLDAKQIAEKFRLDVLQVQ 170 (190)
Q Consensus 135 l~~ii~L--~QGk~~~h~gPM~v~~iAeKFrv~v~~vq 170 (190)
-|+|+.| |+| |+.+|||+.+++.+.-|.
T Consensus 112 ~r~v~~l~~~~~--------~s~~EIA~~l~is~~tV~ 141 (142)
T TIGR03209 112 QKKIIYMKFFED--------MKEIDIAKKLHISRQSVY 141 (142)
T ss_pred HHHHHHHHHHcC--------CCHHHHHHHHCcCHHhhc
Confidence 4666777 455 789999999999887664
No 122
>PRK11569 transcriptional repressor IclR; Provisional
Probab=73.36 E-value=9.8 Score=31.99 Aligned_cols=41 Identities=12% Similarity=0.237 Sum_probs=32.0
Q ss_pred HHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 132 VAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 132 va~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
++.--.||.++. .++++|++.|||+..++.-+.|.+||+=|
T Consensus 27 l~ral~IL~~l~----~~~~~~~lseia~~lglpksTv~RlL~tL 67 (274)
T PRK11569 27 LTRGLKLLEWIA----ESNGSVALTELAQQAGLPNSTTHRLLTTM 67 (274)
T ss_pred HHHHHHHHHHHH----hCCCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 344445666653 36788999999999999999999999743
No 123
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=73.24 E-value=5.4 Score=30.66 Aligned_cols=21 Identities=19% Similarity=0.124 Sum_probs=19.1
Q ss_pred CCHHHHHHHhchhHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Il 173 (190)
|+.+|||+.+++....|...|
T Consensus 146 ~s~~EIA~~l~is~~tV~~~l 166 (181)
T PRK12536 146 LSVAETAQLTGLSESAVKVGI 166 (181)
T ss_pred CCHHHHHHHHCCCHHHHHHHH
Confidence 889999999999999988765
No 124
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=73.19 E-value=5 Score=30.70 Aligned_cols=32 Identities=31% Similarity=0.387 Sum_probs=23.4
Q ss_pred HHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHH
Q 029662 136 RRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 136 ~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Il 173 (190)
++|++|+-..- ++.+|||+.+++.+..|..-+
T Consensus 125 r~i~~l~~~~g------~s~~EIA~~lgis~~tV~~~l 156 (172)
T PRK09651 125 REAFLLSQLDG------LTYSEIAHKLGVSVSSVKKYV 156 (172)
T ss_pred hHHhhhhhccC------CCHHHHHHHhCCCHHHHHHHH
Confidence 45666643322 789999999999998887654
No 125
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=73.19 E-value=6 Score=27.44 Aligned_cols=22 Identities=23% Similarity=0.197 Sum_probs=19.4
Q ss_pred CCHHHHHHHhchhHHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilq 174 (190)
+++++||++++|..+.|++-.+
T Consensus 14 ~~~~eIA~~Lg~~~~TV~~W~~ 35 (58)
T PF06056_consen 14 WSIKEIAEELGVPRSTVYSWKD 35 (58)
T ss_pred CCHHHHHHHHCCChHHHHHHHH
Confidence 8899999999999999987554
No 126
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=73.06 E-value=5.5 Score=29.57 Aligned_cols=22 Identities=32% Similarity=0.404 Sum_probs=19.5
Q ss_pred CCHHHHHHHhchhHHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilq 174 (190)
|+.+|||+.+++....|...+.
T Consensus 127 ~s~~eIA~~lgis~~tV~~~l~ 148 (162)
T TIGR02983 127 LSEAQVAEALGISVGTVKSRLS 148 (162)
T ss_pred CCHHHHHHHhCCCHHHHHHHHH
Confidence 8899999999999999887654
No 127
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=72.50 E-value=5.6 Score=30.59 Aligned_cols=21 Identities=19% Similarity=0.241 Sum_probs=18.7
Q ss_pred CCHHHHHHHhchhHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Il 173 (190)
|+.+|||+.++|.+..|..-+
T Consensus 150 ~s~~eIA~~lgis~~tV~~~l 170 (182)
T PRK12537 150 CSHAEIAQRLGAPLGTVKAWI 170 (182)
T ss_pred CCHHHHHHHHCCChhhHHHHH
Confidence 889999999999999887654
No 128
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=72.31 E-value=6.1 Score=30.79 Aligned_cols=30 Identities=27% Similarity=0.387 Sum_probs=23.2
Q ss_pred HHHHHH--hhccCCCCCCCCCHHHHHHHhchhHHHHHHHH
Q 029662 136 RRIMLL--HQGKADDHNGPLDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 136 ~~ii~L--~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Il 173 (190)
++||.| ++| |+.+|||+.+++.+..|..-+
T Consensus 147 r~v~~l~~~eg--------~s~~EIA~~lgis~~tVk~rl 178 (194)
T PRK12531 147 RDVLQAVYLEE--------LPHQQVAEMFDIPLGTVKSRL 178 (194)
T ss_pred HHHHHHHHHcC--------CCHHHHHHHhCcCHHHHHHHH
Confidence 446665 455 789999999999999887544
No 129
>COG2442 Uncharacterized conserved protein [Function unknown]
Probab=71.51 E-value=12 Score=27.82 Aligned_cols=53 Identities=19% Similarity=0.288 Sum_probs=40.6
Q ss_pred CCCCCCCCCCCCCCCc-ccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhc-hhHHHHHHHHHhh
Q 029662 114 TPVSSRYEEKPSPPGT-LNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFR-LDVLQVQAILQCL 176 (190)
Q Consensus 114 ~~~sg~~eer~~p~GT-LNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFr-v~v~~vq~Ilqf~ 176 (190)
+-.|+..+.||+=.|| +-|..|-+.+. +| ++++||++-|. ++..+|+..|.|-
T Consensus 14 ~~~P~i~gGkP~I~GtRI~V~~Il~~l~--~G--------~s~eeil~dyp~Lt~~dI~aal~ya 68 (79)
T COG2442 14 VITPGICGGKPCIRGTRIPVWDILEMLA--AG--------ESIEEILADYPDLTLEDIRAALRYA 68 (79)
T ss_pred EeCCcccCCcceEeCceecHHHHHHHHH--CC--------CCHHHHHHhCCCCCHHHHHHHHHHH
Confidence 3457788888888888 45554444333 33 78999999999 9999999999984
No 130
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=71.49 E-value=5.5 Score=30.65 Aligned_cols=22 Identities=23% Similarity=0.336 Sum_probs=19.4
Q ss_pred CCHHHHHHHhchhHHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilq 174 (190)
|+.+|||+.+++.++.|...+.
T Consensus 158 ~s~~EIA~~lgis~~tV~~~l~ 179 (194)
T PRK12519 158 LSQSEIAKRLGIPLGTVKARAR 179 (194)
T ss_pred CCHHHHHHHhCCCHHHHHHHHH
Confidence 8999999999999999886653
No 131
>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=71.44 E-value=8.1 Score=31.17 Aligned_cols=98 Identities=16% Similarity=0.135 Sum_probs=62.1
Q ss_pred HHHHHHhhcccccC---------CCCccccchhhhhhhhcCCC--CCCCCCCCC--CCCCCCCCCCCCcccHHHHHHHHH
Q 029662 74 DAMLNQMLGRVKTK---------AGGKAEMGEAAVVERQTRPL--PKLRNTTPV--SSRYEEKPSPPGTLNVAQLRRIML 140 (190)
Q Consensus 74 daMl~qmvGrI~tk---------pGGk~Emgea~vv~~ynRP~--Pk~R~t~~~--sg~~eer~~p~GTLNva~l~~ii~ 140 (190)
..++.|+..-|... .||-..++-+..+.-+-..- -++....-+ .-.......+...|+-.+++=+..
T Consensus 72 ~~~~~~v~~~i~~~~~~~v~vnlsgG~R~l~~~~~~a~~~~~~~~~~v~~~~e~~~~~~~~~~~~~~~~ls~~~~~IL~~ 151 (203)
T TIGR01884 72 PSILRQMSDIIKEEREPRVIINLSGGMRILILILLLLAILVKTRVFRVYYESEELIDFILLDLVPLLAGLSREELKVLEV 151 (203)
T ss_pred HHHHHHHHHHHHhcccCcEEEEcCCCchHHHHHHHHHHHhcccceEEEEEEeccccchhhhhhhhhhcCCCHHHHHHHHH
Confidence 46777777666554 67777777655544443321 123322222 233334455667888887654444
Q ss_pred HhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhhc
Q 029662 141 LHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCLS 177 (190)
Q Consensus 141 L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~S 177 (190)
|.+ +|++++.+||+++.+..+-|.+.|+-|.
T Consensus 152 l~~------~g~~s~~eia~~l~is~stv~r~L~~Le 182 (203)
T TIGR01884 152 LKA------EGEKSVKNIAKKLGKSLSTISRHLRELE 182 (203)
T ss_pred HHH------cCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 433 2679999999999999999999988763
No 132
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=71.40 E-value=7 Score=33.36 Aligned_cols=35 Identities=17% Similarity=0.230 Sum_probs=27.6
Q ss_pred HHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 136 RRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 136 ~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
++||.++=+. + .+|+.+|||+.|+|....|.+|..
T Consensus 236 r~VL~lry~~--~--~~~Tl~EIA~~lgvS~~rVrqi~~ 270 (284)
T PRK06596 236 RDIIEARWLD--D--DKSTLQELAAEYGVSAERVRQIEK 270 (284)
T ss_pred HHHHHHHhcC--C--CCcCHHHHHHHHCCCHHHHHHHHH
Confidence 4567765453 2 579999999999999999988864
No 133
>PRK05572 sporulation sigma factor SigF; Validated
Probab=71.29 E-value=6.7 Score=32.30 Aligned_cols=33 Identities=18% Similarity=0.251 Sum_probs=24.9
Q ss_pred HHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 136 RRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 136 ~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
++||.|+-. ..|+..|||++++|....|.++..
T Consensus 208 ~~v~~l~~~------~~~s~~eIA~~lgis~~~V~~~~~ 240 (252)
T PRK05572 208 RLIVYLRYF------KDKTQSEVAKRLGISQVQVSRLEK 240 (252)
T ss_pred HHHHHHHHh------CCCCHHHHHHHHCcCHHHHHHHHH
Confidence 455555542 239999999999999999987653
No 134
>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=71.00 E-value=14 Score=22.76 Aligned_cols=24 Identities=29% Similarity=0.373 Sum_probs=22.4
Q ss_pred CCHHHHHHHhchhHHHHHHHHHhh
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
+++.+||+.|++....|.++|.-|
T Consensus 21 ~~~~ei~~~~~i~~~~i~~~l~~L 44 (78)
T cd00090 21 LTVSELAERLGLSQSTVSRHLKKL 44 (78)
T ss_pred cCHHHHHHHHCcCHhHHHHHHHHH
Confidence 999999999999999999998876
No 135
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147. This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.
Probab=70.72 E-value=5.3 Score=34.98 Aligned_cols=36 Identities=19% Similarity=0.234 Sum_probs=31.1
Q ss_pred HHHHHHHHhhccCCCCCCCCCHHHHHHHhc--hhHHHHHHHHHhh
Q 029662 134 QLRRIMLLHQGKADDHNGPLDAKQIAEKFR--LDVLQVQAILQCL 176 (190)
Q Consensus 134 ~l~~ii~L~QGk~~~h~gPM~v~~iAeKFr--v~v~~vq~Ilqf~ 176 (190)
-||+++-+..|+ .++.+||++.+ |.+.+|+..|+||
T Consensus 126 virel~~~~~~~-------~~~~~ia~~l~p~is~~ev~~sL~~L 163 (271)
T TIGR02147 126 VIRELLGVMPFA-------DDPEELAKRCFPKISAEQVKESLDLL 163 (271)
T ss_pred HHHHHhhcCCCC-------CCHHHHHHHhCCCCCHHHHHHHHHHH
Confidence 478888887776 47899999999 8999999999997
No 136
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=70.60 E-value=7.4 Score=29.00 Aligned_cols=21 Identities=29% Similarity=0.357 Sum_probs=18.3
Q ss_pred CCHHHHHHHhchhHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Il 173 (190)
|+.+|||+.+++.+..|..-+
T Consensus 122 ~s~~eIA~~lgis~~tv~~~l 142 (159)
T PRK12527 122 LSHQQIAEHLGISRSLVEKHI 142 (159)
T ss_pred CCHHHHHHHhCCCHHHHHHHH
Confidence 889999999999998886544
No 137
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=70.51 E-value=8.2 Score=29.52 Aligned_cols=22 Identities=9% Similarity=0.215 Sum_probs=19.8
Q ss_pred CCHHHHHHHhchhHHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilq 174 (190)
|+++|||+.|++.+..|...|.
T Consensus 154 ~s~~eIA~~lgis~~~v~~~l~ 175 (187)
T PRK12534 154 ITYEELAARTDTPIGTVKSWIR 175 (187)
T ss_pred CCHHHHHHHhCCChhHHHHHHH
Confidence 8999999999999999987764
No 138
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=70.49 E-value=7.7 Score=31.36 Aligned_cols=36 Identities=14% Similarity=0.254 Sum_probs=27.6
Q ss_pred HHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHh
Q 029662 132 VAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQC 175 (190)
Q Consensus 132 va~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf 175 (190)
.-.+.-|..+++| ||+.|||++|+|-.+.|.+-+.=
T Consensus 9 ~R~~~~~~~~~~G--------~S~re~Ak~~gvs~sTvy~wv~r 44 (138)
T COG3415 9 LRERVVDAVVGEG--------LSCREAAKRFGVSISTVYRWVRR 44 (138)
T ss_pred HHHHHHHHHHHcC--------ccHHHHHHHhCccHHHHHHHHHH
Confidence 3344445556777 88999999999999999987764
No 139
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=70.48 E-value=6.3 Score=32.00 Aligned_cols=36 Identities=14% Similarity=0.239 Sum_probs=26.1
Q ss_pred HHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHH
Q 029662 136 RRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 136 ~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Il 173 (190)
|+||.|+-+-. + -..++.++||+.+++....|.+++
T Consensus 181 R~i~~l~y~~~-~-~e~~S~~EIA~~lgis~~tV~~~~ 216 (233)
T PRK05803 181 KEVIEMRYGLG-N-GKEKTQREIAKALGISRSYVSRIE 216 (233)
T ss_pred HHHHHHHhCCC-C-CCCcCHHHHHHHHCcCHHHHHHHH
Confidence 56777744211 0 133789999999999999998775
No 140
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=70.38 E-value=7.7 Score=28.74 Aligned_cols=22 Identities=14% Similarity=0.043 Sum_probs=19.7
Q ss_pred CCHHHHHHHhchhHHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilq 174 (190)
|+++|||+.+++....|...+.
T Consensus 139 ~s~~eIA~~l~is~~tv~~~l~ 160 (170)
T TIGR02952 139 LPIAEVARILGKTEGAVKILQF 160 (170)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
Confidence 8999999999999999887664
No 141
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=69.87 E-value=8.5 Score=30.14 Aligned_cols=30 Identities=17% Similarity=0.165 Sum_probs=23.6
Q ss_pred HHHHHH--hhccCCCCCCCCCHHHHHHHhchhHHHHHHHH
Q 029662 136 RRIMLL--HQGKADDHNGPLDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 136 ~~ii~L--~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Il 173 (190)
++|+.| ++| |+.+|||+.+++....|..-|
T Consensus 140 r~i~~l~~~~g--------~s~~EIA~~lg~s~~tV~~rl 171 (192)
T PRK09643 140 RAALVAVDMQG--------YSVADAARMLGVAEGTVKSRC 171 (192)
T ss_pred HHHHHHHHHcC--------CCHHHHHHHHCcCHHHHHHHH
Confidence 566655 355 789999999999999887654
No 142
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=69.28 E-value=8.3 Score=33.06 Aligned_cols=35 Identities=14% Similarity=0.149 Sum_probs=27.4
Q ss_pred HHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 136 RRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 136 ~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
++||.|+=+ +...|+.+|||+.|+|....|.+|+.
T Consensus 233 r~vl~lr~~----~~~~~t~~EIa~~lgvs~~~V~q~~~ 267 (289)
T PRK07500 233 LRIIRERRL----REDGATLEALGEELGISKERVRQIEA 267 (289)
T ss_pred HHHHHHHhc----CCCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 567777533 23568999999999999999988764
No 143
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=69.26 E-value=14 Score=29.52 Aligned_cols=35 Identities=17% Similarity=0.209 Sum_probs=28.6
Q ss_pred HHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 133 AQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 133 a~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
++.++|..|+... +++.+||.+++|-.+-|.+++.
T Consensus 160 ~~~~~i~~~~~~g-------~s~~~iak~lgis~~Tv~r~~k 194 (200)
T PRK13413 160 GKEEKIKKLLDKG-------TSKSEIARKLGVSRTTLARFLK 194 (200)
T ss_pred hhHHHHHHHHHCC-------CCHHHHHHHHCCCHHHHHHHHH
Confidence 3456777777532 7999999999999999999986
No 144
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=69.18 E-value=8.2 Score=29.58 Aligned_cols=31 Identities=32% Similarity=0.499 Sum_probs=24.1
Q ss_pred HHHHHHh--hccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 136 RRIMLLH--QGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 136 ~~ii~L~--QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
++|+.|+ +| ++.+|||+.+++....|...+.
T Consensus 106 r~v~~l~~~~g--------~s~~eIA~~lgis~~tV~~~l~ 138 (170)
T TIGR02959 106 REAIRLTELEG--------LSQQEIAEKLGLSLSGAKSRVQ 138 (170)
T ss_pred HHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHHHH
Confidence 5666663 54 7899999999999998876553
No 145
>TIGR02716 C20_methyl_CrtF C-20 methyltransferase BchU. Members of this protein family are the S-adenosylmethionine-depenedent C-20 methyltransferase BchU, part of the pathway of bacteriochlorophyll c production in photosynthetic green sulfur bacteria. The position modified by this enzyme represents the difference between bacteriochlorophylls c and d; strains lacking this protein can only produced bacteriochlorophyll d.
Probab=69.12 E-value=4.7 Score=33.86 Aligned_cols=28 Identities=21% Similarity=0.306 Sum_probs=25.6
Q ss_pred CCCCCHHHHHHHhchhHHHHHHHHHhhc
Q 029662 150 NGPLDAKQIAEKFRLDVLQVQAILQCLS 177 (190)
Q Consensus 150 ~gPM~v~~iAeKFrv~v~~vq~Ilqf~S 177 (190)
+||++++|||++.+++..-+.++|..|.
T Consensus 21 ~gp~t~~eLA~~~~~~~~~~~~lL~~L~ 48 (306)
T TIGR02716 21 EGPKDLATLAADTGSVPPRLEMLLETLR 48 (306)
T ss_pred cCCCCHHHHHHHcCCChHHHHHHHHHHH
Confidence 3799999999999999999999998874
No 146
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=69.11 E-value=7.4 Score=29.84 Aligned_cols=23 Identities=17% Similarity=0.250 Sum_probs=19.6
Q ss_pred CCCHHHHHHHhchhHHHHHHHHH
Q 029662 152 PLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 152 PM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
-|+.+|||+.+++....|...+.
T Consensus 144 g~s~~EIA~~lgis~~tV~~~l~ 166 (186)
T PRK05602 144 GLSNIEAAAVMDISVDALESLLA 166 (186)
T ss_pred CCCHHHHHHHhCcCHHHHHHHHH
Confidence 38899999999999998877653
No 147
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=69.09 E-value=7.4 Score=23.29 Aligned_cols=28 Identities=21% Similarity=0.243 Sum_probs=23.9
Q ss_pred CCHHHHHHHhchhHHHHHHHHHhhcCCC
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQCLSLPP 180 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilqf~SlP~ 180 (190)
|+++|+|+.|+|....|.+.++==.||.
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~~g~i~~ 29 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIHEGELPA 29 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHcCCCCe
Confidence 7899999999999999999887555554
No 148
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=68.93 E-value=12 Score=23.51 Aligned_cols=45 Identities=16% Similarity=0.162 Sum_probs=36.3
Q ss_pred CcccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 128 GTLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 128 GTLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
.++..+++..+-..|+- ..+...-.+.+||+.+++...+|+.-.+
T Consensus 5 ~~~~~~~~~~Le~~f~~--~~~P~~~~~~~la~~~~l~~~qV~~WF~ 49 (59)
T cd00086 5 TRFTPEQLEELEKEFEK--NPYPSREEREELAKELGLTERQVKIWFQ 49 (59)
T ss_pred CcCCHHHHHHHHHHHHh--CCCCCHHHHHHHHHHHCcCHHHHHHHHH
Confidence 45677788777778876 4477888899999999999999987543
No 149
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=68.92 E-value=7.8 Score=30.21 Aligned_cols=21 Identities=19% Similarity=0.379 Sum_probs=18.8
Q ss_pred CCHHHHHHHhchhHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Il 173 (190)
|+.+|||+.+++.+..|...+
T Consensus 159 ~s~~EIA~~Lgis~~tVk~~l 179 (194)
T PRK09646 159 LTYREVAERLAVPLGTVKTRM 179 (194)
T ss_pred CCHHHHHHHhCCChHhHHHHH
Confidence 899999999999999887654
No 150
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=68.73 E-value=8.5 Score=30.49 Aligned_cols=21 Identities=19% Similarity=0.131 Sum_probs=18.4
Q ss_pred CCHHHHHHHhchhHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Il 173 (190)
|+++|||+.+++.+..|...+
T Consensus 130 ~s~~EIA~~LgiS~~tVk~~l 150 (188)
T PRK12546 130 FSYEEAAEMCGVAVGTVKSRA 150 (188)
T ss_pred CCHHHHHHHHCCCHHHHHHHH
Confidence 789999999999999887654
No 151
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=68.63 E-value=4.3 Score=31.37 Aligned_cols=23 Identities=30% Similarity=0.335 Sum_probs=19.7
Q ss_pred CCCCHHHHHHHhchhHHHHHHHH
Q 029662 151 GPLDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 151 gPM~v~~iAeKFrv~v~~vq~Il 173 (190)
.-|+++|||+.+++.+..|...+
T Consensus 154 ~g~s~~EIA~~lgis~~tV~~~l 176 (194)
T PRK12513 154 GDLELEEIAELTGVPEETVKSRL 176 (194)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHH
Confidence 34899999999999999997654
No 152
>PF12824 MRP-L20: Mitochondrial ribosomal protein subunit L20; InterPro: IPR024388 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents the essential mitochondrial ribosomal protein L20 family from fungi [].
Probab=68.57 E-value=6.9 Score=32.27 Aligned_cols=59 Identities=22% Similarity=0.265 Sum_probs=40.6
Q ss_pred cCCCCCCCCCCCCCCCCCCCCCCCCcccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHH
Q 029662 104 TRPLPKLRNTTPVSSRYEEKPSPPGTLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 104 nRP~Pk~R~t~~~sg~~eer~~p~GTLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Il 173 (190)
...||-+...+..- ++ .=.|+-++|+||-+|....- .--++..||+||+|.-.-|.-|.
T Consensus 67 ~~~lPp~l~~~~~~----~k---~y~Lt~e~i~Eir~LR~~DP----~~wTr~~LAkkF~~S~~fV~~v~ 125 (164)
T PF12824_consen 67 SEDLPPILRYKSPH----EK---KYHLTPEDIQEIRRLRAEDP----EKWTRKKLAKKFNCSPLFVSMVA 125 (164)
T ss_pred hhhCCccccccccc----cc---cccCCHHHHHHHHHHHHcCc----hHhhHHHHHHHhCCCHHHHHHhc
Confidence 34566665555441 11 14799999999999986532 23689999999999876665443
No 153
>TIGR02850 spore_sigG RNA polymerase sigma-G factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.
Probab=68.56 E-value=8.4 Score=31.83 Aligned_cols=33 Identities=15% Similarity=0.144 Sum_probs=26.3
Q ss_pred HHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 136 RRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 136 ~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
++||.|+-+ ..|+.+|||+.|+|....|.++..
T Consensus 212 r~vi~~~~~------~~~t~~eIA~~lgis~~~V~~~~~ 244 (254)
T TIGR02850 212 KMILNMRFF------EGKTQMEVAEEIGISQAQVSRLEK 244 (254)
T ss_pred HHHHHHHHc------CCCCHHHHHHHHCcCHHHHHHHHH
Confidence 567777653 248999999999999999987753
No 154
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=68.55 E-value=6.6 Score=32.48 Aligned_cols=22 Identities=27% Similarity=0.431 Sum_probs=19.3
Q ss_pred CCHHHHHHHhchhHHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilq 174 (190)
|+.+|||+.+++.+..|...|.
T Consensus 188 ~s~~EIA~~Lgis~~tVk~~l~ 209 (233)
T PRK12538 188 MSNGEIAEVMDTTVAAVESLLK 209 (233)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 8899999999999998876654
No 155
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=68.43 E-value=10 Score=28.57 Aligned_cols=31 Identities=23% Similarity=0.320 Sum_probs=23.9
Q ss_pred HHHHHHHh--hccCCCCCCCCCHHHHHHHhchhHHHHHHHH
Q 029662 135 LRRIMLLH--QGKADDHNGPLDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 135 l~~ii~L~--QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Il 173 (190)
-|+||.|+ +| |+++|||+.+++....|...+
T Consensus 123 ~r~vl~L~~~~g--------~s~~EIA~~lgis~~tV~~~l 155 (173)
T PRK09645 123 HRAVLVRSYYRG--------WSTAQIAADLGIPEGTVKSRL 155 (173)
T ss_pred HHHHHHHHHHcC--------CCHHHHHHHHCcCHHHHHHHH
Confidence 35677664 44 789999999999999886543
No 156
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=67.99 E-value=6.8 Score=32.14 Aligned_cols=22 Identities=23% Similarity=0.187 Sum_probs=19.5
Q ss_pred CCHHHHHHHhchhHHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilq 174 (190)
|+.+|||+.++|.+..|...|.
T Consensus 151 ~s~~EIAe~LgiS~~tVk~~L~ 172 (216)
T PRK12533 151 MSYREIAAIADVPVGTVMSRLA 172 (216)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
Confidence 8899999999999999877653
No 157
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=67.92 E-value=15 Score=27.50 Aligned_cols=44 Identities=16% Similarity=0.099 Sum_probs=34.4
Q ss_pred CcccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 128 GTLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 128 GTLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
-.|+.+|..=++.|++. ++++++.+||+.+.++.+-|-++++=|
T Consensus 27 ~glt~~q~~vL~~l~~~-----~~~~t~~eLa~~l~~~~~tvt~~v~~L 70 (144)
T PRK03573 27 LELTQTHWVTLHNIHQL-----PPEQSQIQLAKAIGIEQPSLVRTLDQL 70 (144)
T ss_pred cCCCHHHHHHHHHHHHc-----CCCCCHHHHHHHhCCChhhHHHHHHHH
Confidence 35888888777777642 245889999999999999998888643
No 158
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=67.91 E-value=9.2 Score=29.06 Aligned_cols=30 Identities=20% Similarity=0.461 Sum_probs=23.6
Q ss_pred HHHHHH--hhccCCCCCCCCCHHHHHHHhchhHHHHHHHH
Q 029662 136 RRIMLL--HQGKADDHNGPLDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 136 ~~ii~L--~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Il 173 (190)
++|+.| |+| |+++|||+.+++....|..-+
T Consensus 124 r~v~~L~~~eg--------~s~~EIA~~l~is~~tV~~~l 155 (168)
T PRK12525 124 RAAFLMSQLEG--------LTYVEIGERLGVSLSRIHQYM 155 (168)
T ss_pred HHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHHH
Confidence 455655 455 779999999999999888765
No 159
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=67.88 E-value=9.7 Score=23.30 Aligned_cols=29 Identities=10% Similarity=0.035 Sum_probs=24.7
Q ss_pred CCHHHHHHHhchhHHHHHHHHHhhcCCCC
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQCLSLPPE 181 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilqf~SlP~e 181 (190)
|++.|+|+.++|....|....+---||++
T Consensus 1 ~~~~e~a~~~gv~~~tlr~~~~~g~l~~~ 29 (49)
T cd04761 1 YTIGELAKLTGVSPSTLRYYERIGLLSPA 29 (49)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHCCCCCCC
Confidence 78999999999999999988776667743
No 160
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=67.83 E-value=8.3 Score=32.18 Aligned_cols=34 Identities=18% Similarity=0.223 Sum_probs=26.5
Q ss_pred HHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 135 LRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 135 l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
-++||.|+-+ ..|+.+|||+.++|....|.+++.
T Consensus 208 ~r~vl~l~y~------~~~s~~eIA~~lgvs~~~V~~~~~ 241 (256)
T PRK07408 208 TREVLEFVFL------HDLTQKEAAERLGISPVTVSRRVK 241 (256)
T ss_pred HHHHHHHHHH------CCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3566666543 249999999999999999988764
No 161
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=67.63 E-value=8.9 Score=31.09 Aligned_cols=23 Identities=22% Similarity=0.273 Sum_probs=19.8
Q ss_pred CCCHHHHHHHhchhHHHHHHHHH
Q 029662 152 PLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 152 PM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
-|+.+|||+.++|.+..|...+.
T Consensus 200 g~s~~EIA~~lgis~~tV~~~~~ 222 (236)
T PRK06986 200 ELNLKEIGAVLGVSESRVSQIHS 222 (236)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHH
Confidence 48999999999999999886543
No 162
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=67.61 E-value=7.9 Score=30.70 Aligned_cols=26 Identities=27% Similarity=0.404 Sum_probs=24.1
Q ss_pred CCCHHHHHHHhchhHHHHHHHHHhhc
Q 029662 152 PLDAKQIAEKFRLDVLQVQAILQCLS 177 (190)
Q Consensus 152 PM~v~~iAeKFrv~v~~vq~Ilqf~S 177 (190)
++++++||++.+|.-+.+.+|+.-|.
T Consensus 25 ~~s~~~IA~~~~is~~~L~kil~~L~ 50 (150)
T COG1959 25 PVSSAEIAERQGISPSYLEKILSKLR 50 (150)
T ss_pred cccHHHHHHHhCcCHHHHHHHHHHHH
Confidence 89999999999999999999998663
No 163
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).
Probab=67.25 E-value=10 Score=28.59 Aligned_cols=23 Identities=17% Similarity=0.151 Sum_probs=19.9
Q ss_pred CCCHHHHHHHhchhHHHHHHHHH
Q 029662 152 PLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 152 PM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
-|+.+|||+.+++.+..|...+.
T Consensus 156 g~s~~eIA~~lgis~~~v~~~l~ 178 (189)
T TIGR02984 156 GLSFAEVAERMDRSEGAVSMLWV 178 (189)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHH
Confidence 38999999999999999887654
No 164
>PF13551 HTH_29: Winged helix-turn helix
Probab=67.25 E-value=12 Score=25.98 Aligned_cols=22 Identities=18% Similarity=0.194 Sum_probs=19.8
Q ss_pred CHHHHHHHhchhHHHHHHHHHh
Q 029662 154 DAKQIAEKFRLDVLQVQAILQC 175 (190)
Q Consensus 154 ~v~~iAeKFrv~v~~vq~Ilqf 175 (190)
++.+||..|++....|.++++-
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~ 35 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKR 35 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHH
Confidence 6999999999999999998864
No 165
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=67.15 E-value=10 Score=27.31 Aligned_cols=23 Identities=26% Similarity=0.274 Sum_probs=20.5
Q ss_pred CCHHHHHHHhchhHHHHHHHHHh
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQC 175 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilqf 175 (190)
+++.|||+.+++....|...+..
T Consensus 130 ~~~~eIA~~lgis~~tv~~~~~r 152 (161)
T TIGR02985 130 KSYKEIAEELGISVKTVEYHISK 152 (161)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Confidence 88999999999999999887754
No 166
>TIGR02899 spore_safA spore coat assembly protein SafA. in which one of which is found in most examples of endospore-forming bacteria. Lysin motifs are repeated in many proteins.
Probab=67.11 E-value=6.3 Score=23.08 Aligned_cols=21 Identities=19% Similarity=0.188 Sum_probs=17.1
Q ss_pred CHHHHHHHhchhHHHHHHHHH
Q 029662 154 DAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 154 ~v~~iAeKFrv~v~~vq~Ilq 174 (190)
++.+||++|++++..+..+=.
T Consensus 6 tl~~IA~~~~~~~~~l~~~N~ 26 (44)
T TIGR02899 6 TLWKIAKKYGVDFDELIQANP 26 (44)
T ss_pred CHHHHHHHHCcCHHHHHHHhh
Confidence 578999999999888776544
No 167
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=66.87 E-value=9 Score=28.92 Aligned_cols=24 Identities=29% Similarity=0.340 Sum_probs=20.3
Q ss_pred CCCCHHHHHHHhchhHHHHHHHHH
Q 029662 151 GPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 151 gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
..++.+|||+.++|.+..|...+.
T Consensus 151 ~~~s~~eIA~~lgis~~~v~~~l~ 174 (187)
T PRK09641 151 EDLSLKEISEILDLPVGTVKTRIH 174 (187)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHH
Confidence 348899999999999998877654
No 168
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=66.82 E-value=11 Score=28.63 Aligned_cols=22 Identities=23% Similarity=0.389 Sum_probs=19.5
Q ss_pred CCHHHHHHHhchhHHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilq 174 (190)
|+.+|||+.+++.+..|...+.
T Consensus 146 ~s~~eIA~~lgis~~tV~~~l~ 167 (179)
T PRK12514 146 LSYKELAERHDVPLNTMRTWLR 167 (179)
T ss_pred CCHHHHHHHHCCChHHHHHHHH
Confidence 8999999999999998876654
No 169
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=66.81 E-value=11 Score=29.59 Aligned_cols=31 Identities=19% Similarity=0.247 Sum_probs=24.1
Q ss_pred HHHHHHHh--hccCCCCCCCCCHHHHHHHhchhHHHHHHHH
Q 029662 135 LRRIMLLH--QGKADDHNGPLDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 135 l~~ii~L~--QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Il 173 (190)
-|+||.|+ +| |+.+|||+.+++....|..-|
T Consensus 121 ~r~i~~L~~~~g--------~s~~EIA~~Lgis~~tVk~~l 153 (187)
T PRK12516 121 QREAIILVGASG--------FAYEEAAEICGCAVGTIKSRV 153 (187)
T ss_pred HHHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHHH
Confidence 45677773 44 889999999999998886554
No 170
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=66.71 E-value=8.9 Score=30.05 Aligned_cols=21 Identities=10% Similarity=0.040 Sum_probs=18.1
Q ss_pred CCHHHHHHHhchhHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Il 173 (190)
|+++|||+.+++.+..|...|
T Consensus 128 ~s~~EIA~~Lgis~~tV~~~l 148 (182)
T PRK12540 128 FSYEDAAAICGCAVGTIKSRV 148 (182)
T ss_pred CCHHHHHHHHCCCHHHHHHHH
Confidence 789999999999998876554
No 171
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=66.37 E-value=8 Score=24.78 Aligned_cols=44 Identities=18% Similarity=0.206 Sum_probs=36.3
Q ss_pred cccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 129 TLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 129 TLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
.++..|+..+-..|+- +.+...-...+||++++|...+|+.-.+
T Consensus 6 ~~t~~q~~~L~~~f~~--~~~p~~~~~~~la~~l~l~~~~V~~WF~ 49 (57)
T PF00046_consen 6 RFTKEQLKVLEEYFQE--NPYPSKEEREELAKELGLTERQVKNWFQ 49 (57)
T ss_dssp SSSHHHHHHHHHHHHH--SSSCHHHHHHHHHHHHTSSHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHH--hccccccccccccccccccccccccCHH
Confidence 4678888888889984 6677777889999999999999987544
No 172
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=66.30 E-value=5.8 Score=32.13 Aligned_cols=24 Identities=21% Similarity=0.194 Sum_probs=20.3
Q ss_pred CCCCCHHHHHHHhchhHHHHHHHH
Q 029662 150 NGPLDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 150 ~gPM~v~~iAeKFrv~v~~vq~Il 173 (190)
-..|+.+|||+.+++..+.|...+
T Consensus 163 ~~g~s~~EIAe~lgis~~tVk~~l 186 (231)
T PRK11922 163 VEELSVEETAQALGLPEETVKTRL 186 (231)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHHH
Confidence 345899999999999999887665
No 173
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=66.29 E-value=12 Score=30.22 Aligned_cols=21 Identities=24% Similarity=0.477 Sum_probs=18.2
Q ss_pred CCHHHHHHHhchhHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Il 173 (190)
|++.|||+.+++.+..|..-+
T Consensus 165 ~s~~EIAe~lgis~~tV~~~l 185 (206)
T PRK12544 165 LETNEICHAVDLSVSNLNVLL 185 (206)
T ss_pred CCHHHHHHHHCcCHHHHHHHH
Confidence 889999999999998876554
No 174
>PRK06930 positive control sigma-like factor; Validated
Probab=66.18 E-value=12 Score=30.38 Aligned_cols=32 Identities=25% Similarity=0.501 Sum_probs=25.3
Q ss_pred HHHHHHHh--hccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 135 LRRIMLLH--QGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 135 l~~ii~L~--QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
-++|+.|+ +| |+.+|||+.|++.+..|+..+.
T Consensus 119 er~V~~L~~~eg--------~s~~EIA~~lgiS~~tVk~~l~ 152 (170)
T PRK06930 119 EKEVYLMHRGYG--------LSYSEIADYLNIKKSTVQSMIE 152 (170)
T ss_pred HHHHHHHHHHcC--------CCHHHHHHHHCcCHHHHHHHHH
Confidence 35666663 55 7799999999999999887764
No 175
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=66.05 E-value=9.4 Score=30.69 Aligned_cols=21 Identities=19% Similarity=0.300 Sum_probs=18.4
Q ss_pred CCHHHHHHHhchhHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Il 173 (190)
++++|||+.+++....|..-|
T Consensus 155 ~s~~EIA~~Lgis~~tV~~~l 175 (203)
T PRK09647 155 LSYEEIAATLGVKLGTVRSRI 175 (203)
T ss_pred CCHHHHHHHHCCCHHHHHHHH
Confidence 789999999999998887654
No 176
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=66.05 E-value=11 Score=33.45 Aligned_cols=36 Identities=28% Similarity=0.379 Sum_probs=27.8
Q ss_pred HHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHH
Q 029662 136 RRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 136 ~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Il 173 (190)
+.||.++=|--+ ..+|+.+|||+.|+|...-|.+|-
T Consensus 268 r~Vl~~rygl~~--~~~~Tl~eIa~~lgvS~eRVrQIe 303 (324)
T PRK07921 268 QQVIRLRFGLDD--GQPRTLDQIGKLFGLSRERVRQIE 303 (324)
T ss_pred HHHHHHHHhcCC--CCCcCHHHHHHHHCCCHHHHHHHH
Confidence 557777666532 357999999999999988888774
No 177
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=65.80 E-value=12 Score=30.23 Aligned_cols=48 Identities=21% Similarity=0.279 Sum_probs=33.5
Q ss_pred cHHHHHHHHHHhhccCC----------CCCCCCC---HHHHHHHhchhHHHHHHHHHhhcC
Q 029662 131 NVAQLRRIMLLHQGKAD----------DHNGPLD---AKQIAEKFRLDVLQVQAILQCLSL 178 (190)
Q Consensus 131 Nva~l~~ii~L~QGk~~----------~h~gPM~---v~~iAeKFrv~v~~vq~Ilqf~Sl 178 (190)
+.+.|++||.-|..+.+ ++.|-++ +++||+.++|..+.|..++-|-|.
T Consensus 7 ~~~~i~~ii~~y~~~~~~li~~L~~vQ~~~G~Ip~e~~~~iA~~l~v~~~~V~~vatFY~~ 67 (156)
T PRK05988 7 DAARIAAIIAEHKHLEGALLPILHAIQDEFGYVPEDAVPVIAEALNLSRAEVHGVITFYHD 67 (156)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHHHHHHHhhc
Confidence 34455555555543332 2455555 678999999999999999999775
No 178
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=65.70 E-value=9.6 Score=31.89 Aligned_cols=33 Identities=24% Similarity=0.237 Sum_probs=26.1
Q ss_pred HHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 136 RRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 136 ~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
|+||.|+-. ..|+.+|||+.++|....|..++.
T Consensus 211 r~vi~l~y~------e~~t~~EIA~~lgis~~~V~~~~~ 243 (257)
T PRK05911 211 RKVMALYYY------EELVLKEIGKILGVSESRVSQIHS 243 (257)
T ss_pred HHHHHHHHh------cCCCHHHHHHHHCcCHHHHHHHHH
Confidence 567777643 349999999999999999988754
No 179
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=65.51 E-value=11 Score=30.99 Aligned_cols=33 Identities=15% Similarity=0.285 Sum_probs=26.0
Q ss_pred HHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 136 RRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 136 ~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
|+||.|+-. .-|+.+|||+.++|....|..++.
T Consensus 211 r~ii~l~~~------~g~s~~eIA~~lgis~~~V~~~~~ 243 (255)
T TIGR02941 211 KSIIHCTFE------ENLSQKETGERLGISQMHVSRLQR 243 (255)
T ss_pred HHHHHHHHc------CCCCHHHHHHHHCcCHHHHHHHHH
Confidence 567777642 338999999999999999987764
No 180
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=65.49 E-value=16 Score=26.64 Aligned_cols=42 Identities=24% Similarity=0.302 Sum_probs=33.1
Q ss_pred cccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 129 TLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 129 TLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
.|+..|..=+..|++ ++++++.+||+.+.++-+.|-++|+-|
T Consensus 25 ~lt~~q~~iL~~l~~------~~~~t~~ela~~~~~~~~tvs~~l~~L 66 (118)
T TIGR02337 25 GLTEQQWRILRILAE------QGSMEFTQLANQACILRPSLTGILARL 66 (118)
T ss_pred CCCHHHHHHHHHHHH------cCCcCHHHHHHHhCCCchhHHHHHHHH
Confidence 367788776666654 457999999999999999998888744
No 181
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=65.22 E-value=7.8 Score=27.67 Aligned_cols=28 Identities=18% Similarity=0.279 Sum_probs=23.7
Q ss_pred CCCCCCCHHHHHHHhchhHHHHHHHHHh
Q 029662 148 DHNGPLDAKQIAEKFRLDVLQVQAILQC 175 (190)
Q Consensus 148 ~h~gPM~v~~iAeKFrv~v~~vq~Ilqf 175 (190)
+...++++.+||+++++....++++++-
T Consensus 17 ~~~~~~~~~~lA~~~~~S~~~l~r~f~~ 44 (107)
T PRK10219 17 HIDQPLNIDVVAKKSGYSKWYLQRMFRT 44 (107)
T ss_pred hcCCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 3455799999999999999999988764
No 182
>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=65.22 E-value=18 Score=24.07 Aligned_cols=26 Identities=23% Similarity=0.440 Sum_probs=21.6
Q ss_pred CC-CHHHHHHHhchhHHHHHHHHHhhc
Q 029662 152 PL-DAKQIAEKFRLDVLQVQAILQCLS 177 (190)
Q Consensus 152 PM-~v~~iAeKFrv~v~~vq~Ilqf~S 177 (190)
.+ +..+||++|+|....|.+.++.|.
T Consensus 23 ~lps~~~la~~~~vsr~tvr~al~~L~ 49 (64)
T PF00392_consen 23 RLPSERELAERYGVSRTTVREALRRLE 49 (64)
T ss_dssp BE--HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred EeCCHHHHHHHhccCCcHHHHHHHHHH
Confidence 57 999999999999999999998774
No 183
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=65.21 E-value=15 Score=29.55 Aligned_cols=39 Identities=28% Similarity=0.374 Sum_probs=29.1
Q ss_pred CcccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 128 GTLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 128 GTLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
+.|+-.|.+=+.+.++| |+.+|||+++++..+-|..+++
T Consensus 5 ~~Lte~qr~VL~Lr~~G--------lTq~EIAe~LgiS~stV~~~e~ 43 (137)
T TIGR00721 5 TFLTERQIKVLELREKG--------LSQKEIAKELKTTRANVSAIEK 43 (137)
T ss_pred CCCCHHHHHHHHHHHcC--------CCHHHHHHHHCcCHHHHHHHHH
Confidence 56777776555554455 6899999999999988886543
No 184
>PRK05949 RNA polymerase sigma factor; Validated
Probab=65.14 E-value=12 Score=33.13 Aligned_cols=36 Identities=22% Similarity=0.392 Sum_probs=28.8
Q ss_pred HHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHH
Q 029662 136 RRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 136 ~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Il 173 (190)
|+||.|+=|-.+ ..+|+.+|||+.|+|...-|..|+
T Consensus 272 r~Vi~lr~gl~~--~e~~Tl~EIa~~lgiS~erVrq~~ 307 (327)
T PRK05949 272 REVLTLRFGLED--GKELSLAKVGERLNLSRERVRQLE 307 (327)
T ss_pred HHHHHHHhccCC--CCCCCHHHHHHHHCcCHHHHHHHH
Confidence 677888766532 346999999999999999998875
No 185
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=65.12 E-value=11 Score=22.29 Aligned_cols=29 Identities=17% Similarity=0.116 Sum_probs=24.4
Q ss_pred CCHHHHHHHhchhHHHHHHHHHhhcCCCC
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQCLSLPPE 181 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilqf~SlP~e 181 (190)
|++.|+|+.++|....|.+.++---+|..
T Consensus 1 ~s~~e~a~~lgvs~~tl~~~~~~g~~~~~ 29 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKEGKLKAI 29 (49)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCCCce
Confidence 68999999999999999988876666653
No 186
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=65.02 E-value=7.8 Score=32.81 Aligned_cols=21 Identities=29% Similarity=0.347 Sum_probs=18.3
Q ss_pred CCHHHHHHHhchhHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Il 173 (190)
|+.+|||+.+++....|...|
T Consensus 170 ~s~~EIA~~lgis~~tVk~~l 190 (339)
T PRK08241 170 WSAAEVAELLDTSVAAVNSAL 190 (339)
T ss_pred CCHHHHHHHhCCCHHHHHHHH
Confidence 889999999999998876554
No 187
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=64.84 E-value=10 Score=31.17 Aligned_cols=33 Identities=15% Similarity=0.251 Sum_probs=24.8
Q ss_pred HHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 136 RRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 136 ~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
++||.|+-. .-++.+|||+.++|....|..++.
T Consensus 211 r~vl~l~~~------~g~s~~eIA~~l~is~~tV~~~~~ 243 (257)
T PRK08583 211 KSIIQCTFI------ENLSQKETGERLGISQMHVSRLQR 243 (257)
T ss_pred HHHHHHHHh------CCCCHHHHHHHHCCCHHHHHHHHH
Confidence 456666432 237899999999999999987754
No 188
>PF12728 HTH_17: Helix-turn-helix domain
Probab=64.74 E-value=9.4 Score=24.18 Aligned_cols=29 Identities=24% Similarity=0.269 Sum_probs=25.0
Q ss_pred CCHHHHHHHhchhHHHHHHHHHhhcCCCC
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQCLSLPPE 181 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilqf~SlP~e 181 (190)
|+++|+|+.++|..+.|.++++-=-||.-
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~~g~i~~~ 30 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIRQGKIPPF 30 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCCCeE
Confidence 78999999999999999999876666654
No 189
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=64.70 E-value=19 Score=29.77 Aligned_cols=41 Identities=12% Similarity=0.214 Sum_probs=31.8
Q ss_pred cHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 131 NVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 131 Nva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
.+.-.-.||.++. . + +++++.|||+..++..+.|.+||+-|
T Consensus 12 sl~r~l~IL~~l~---~-~-~~l~l~eia~~lgl~kstv~Rll~tL 52 (257)
T PRK15090 12 SVLKVFGILQALG---E-E-REIGITELSQRVMMSKSTVYRFLQTM 52 (257)
T ss_pred HHHHHHHHHHHhh---c-C-CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3445556666663 2 3 57999999999999999999999754
No 190
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=64.58 E-value=8.7 Score=32.03 Aligned_cols=22 Identities=27% Similarity=0.249 Sum_probs=19.3
Q ss_pred CCHHHHHHHhchhHHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilq 174 (190)
|+.+|||+.+++.+..|...|.
T Consensus 159 ~s~~EIA~~lgis~~tV~~~l~ 180 (324)
T TIGR02960 159 WRAAETAELLGTSTASVNSALQ 180 (324)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
Confidence 8899999999999998877654
No 191
>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=64.47 E-value=8 Score=30.65 Aligned_cols=28 Identities=21% Similarity=0.242 Sum_probs=23.6
Q ss_pred CCCCCCHHHHHHHhchh-HHHHHHHHHhh
Q 029662 149 HNGPLDAKQIAEKFRLD-VLQVQAILQCL 176 (190)
Q Consensus 149 h~gPM~v~~iAeKFrv~-v~~vq~Ilqf~ 176 (190)
+.-|.++.|||+.|++. .+-|++.|+-|
T Consensus 22 ~~~~~~~~ela~~~~~~s~~tv~~~l~~L 50 (199)
T TIGR00498 22 TGYPPSIREIARAVGLRSPSAAEEHLKAL 50 (199)
T ss_pred cCCCCcHHHHHHHhCCCChHHHHHHHHHH
Confidence 44568999999999999 88888888765
No 192
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor. The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.
Probab=64.32 E-value=11 Score=30.63 Aligned_cols=22 Identities=18% Similarity=0.181 Sum_probs=19.5
Q ss_pred CCHHHHHHHhchhHHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilq 174 (190)
|+.+|||+.+++.+..|..++.
T Consensus 195 ~S~~EIAe~lgis~~tV~~~~~ 216 (227)
T TIGR02846 195 KTQREIAKILGISRSYVSRIEK 216 (227)
T ss_pred cCHHHHHHHHCCCHHHHHHHHH
Confidence 8899999999999999977653
No 193
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=64.18 E-value=10 Score=28.53 Aligned_cols=21 Identities=33% Similarity=0.287 Sum_probs=18.9
Q ss_pred CCHHHHHHHhchhHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Il 173 (190)
|+.++||+.++|.+..|...+
T Consensus 136 ~s~~eiA~~lgis~~tv~~~l 156 (169)
T TIGR02954 136 LTIKEIAEVMNKPEGTVKTYL 156 (169)
T ss_pred CCHHHHHHHHCCCHHHHHHHH
Confidence 899999999999999887665
No 194
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=64.09 E-value=11 Score=31.82 Aligned_cols=33 Identities=24% Similarity=0.417 Sum_probs=26.0
Q ss_pred HHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 136 RRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 136 ~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
++||.|+-. ..|+.+|||+.++|....|.+++.
T Consensus 221 r~vl~l~y~------~~~t~~EIA~~lgis~~~V~~~~~ 253 (264)
T PRK07122 221 RTVLVLRFF------ESMTQTQIAERVGISQMHVSRLLA 253 (264)
T ss_pred HHHHHHHhc------CCCCHHHHHHHHCcCHHHHHHHHH
Confidence 456666543 259999999999999999998765
No 195
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=64.05 E-value=12 Score=29.28 Aligned_cols=22 Identities=27% Similarity=0.401 Sum_probs=19.4
Q ss_pred CCHHHHHHHhchhHHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilq 174 (190)
++.+|||+.++|....|...+.
T Consensus 153 ~s~~eIA~~lgis~~tV~~~l~ 174 (196)
T PRK12524 153 LSNPEIAEVMEIGVEAVESLTA 174 (196)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 8899999999999998877654
No 196
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=63.97 E-value=10 Score=31.85 Aligned_cols=22 Identities=9% Similarity=0.107 Sum_probs=19.5
Q ss_pred CCHHHHHHHhchhHHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilq 174 (190)
|+.+|||+.+++....|...|+
T Consensus 132 ~s~~EIA~~lg~s~~tVk~~l~ 153 (293)
T PRK09636 132 VPFDEIASTLGRSPAACRQLAS 153 (293)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
Confidence 8999999999999998887664
No 197
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=63.87 E-value=10 Score=29.16 Aligned_cols=21 Identities=14% Similarity=0.167 Sum_probs=19.0
Q ss_pred CCHHHHHHHhchhHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Il 173 (190)
|+++|||+.+++.+..|...+
T Consensus 148 ~s~~eIA~~lgis~~tV~~~l 168 (184)
T PRK12539 148 LSVAEAATRSGMSESAVKVSV 168 (184)
T ss_pred CcHHHHHHHHCcCHHHHHHHH
Confidence 889999999999999988765
No 198
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=63.74 E-value=10 Score=29.16 Aligned_cols=21 Identities=33% Similarity=0.317 Sum_probs=18.2
Q ss_pred CCHHHHHHHhchhHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Il 173 (190)
|+.+|||+.+++....|..-+
T Consensus 144 ~s~~EIA~~l~is~~tv~~~l 164 (179)
T PRK09415 144 LSIKEIAEVTGVNENTVKTRL 164 (179)
T ss_pred CCHHHHHHHHCCCHHHHHHHH
Confidence 789999999999998886554
No 199
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=63.66 E-value=20 Score=24.05 Aligned_cols=44 Identities=23% Similarity=0.333 Sum_probs=30.9
Q ss_pred HHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhhc--CCCCCC
Q 029662 134 QLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCLS--LPPESS 183 (190)
Q Consensus 134 ~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~S--lP~e~~ 183 (190)
|++=+-+|++. +.|++++||+++++-...|++-+..+. +|+.-.
T Consensus 7 q~~Ll~~L~~~------~~~~~~ela~~l~~S~rti~~~i~~L~~~f~~~~~ 52 (59)
T PF08280_consen 7 QLKLLELLLKN------KWITLKELAKKLNISERTIKNDINELNEFFPENIS 52 (59)
T ss_dssp HHHHHHHHHHH------TSBBHHHHHHHCTS-HHHHHHHHHHHHTT--TCCC
T ss_pred HHHHHHHHHcC------CCCcHHHHHHHHCCCHHHHHHHHHHHHHHhhhhce
Confidence 34444455653 349999999999999999999998886 666543
No 200
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=63.14 E-value=11 Score=31.05 Aligned_cols=50 Identities=20% Similarity=0.215 Sum_probs=37.4
Q ss_pred cHHHHHHHHHHhhccCC----------CCCCCCC---HHHHHHHhchhHHHHHHHHHhhcCCC
Q 029662 131 NVAQLRRIMLLHQGKAD----------DHNGPLD---AKQIAEKFRLDVLQVQAILQCLSLPP 180 (190)
Q Consensus 131 Nva~l~~ii~L~QGk~~----------~h~gPM~---v~~iAeKFrv~v~~vq~Ilqf~SlP~ 180 (190)
+++.|.+||.-|..+.. ++.|-++ +..||+.++|..+.|..|+.|-+.-.
T Consensus 20 ~~~~i~~ii~~~~~~~~~li~~L~~iQ~~~GyIp~e~~~~iA~~l~v~~a~V~gVatFY~~f~ 82 (169)
T PRK07571 20 RFKVLEATMKRNQYRQDALIEVLHKAQELFGYLERDLLLYVARQLKLPLSRVYGVATFYHLFS 82 (169)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHHHHHHHHccccC
Confidence 45667777777755443 2556665 56799999999999999999987653
No 201
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=62.80 E-value=11 Score=29.21 Aligned_cols=21 Identities=10% Similarity=0.279 Sum_probs=18.5
Q ss_pred CCHHHHHHHhchhHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Il 173 (190)
|+.+|||+.+++.+..|...+
T Consensus 153 ~s~~EIA~~lgis~~tVk~~l 173 (195)
T PRK12532 153 FSSDEIQQMCGISTSNYHTIM 173 (195)
T ss_pred CCHHHHHHHHCCCHHHHHHHH
Confidence 889999999999999887654
No 202
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=62.34 E-value=13 Score=28.57 Aligned_cols=21 Identities=24% Similarity=0.129 Sum_probs=18.4
Q ss_pred CCHHHHHHHhchhHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Il 173 (190)
++.+|||+.+++.+.-|...+
T Consensus 156 ~s~~EIA~~lgis~~tV~~~l 176 (189)
T PRK09648 156 LSAEETAEAVGSTPGAVRVAQ 176 (189)
T ss_pred CCHHHHHHHHCCCHHHHHHHH
Confidence 889999999999998887654
No 203
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=62.07 E-value=35 Score=24.19 Aligned_cols=49 Identities=8% Similarity=0.138 Sum_probs=36.9
Q ss_pred ccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHh---chhHHHHHHHHHhhcC
Q 029662 130 LNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKF---RLDVLQVQAILQCLSL 178 (190)
Q Consensus 130 LNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKF---rv~v~~vq~Ilqf~Sl 178 (190)
|+-+++.++...|+---.++.|-++.+++.+-| ++.-..|+.|+.-+..
T Consensus 4 ls~~~~~~l~~~F~~~D~d~~G~Is~~el~~~l~~~~~~~~ev~~i~~~~d~ 55 (96)
T smart00027 4 ISPEDKAKYEQIFRSLDKNQDGTVTGAQAKPILLKSGLPQTLLAKIWNLADI 55 (96)
T ss_pred CCHHHHHHHHHHHHHhCCCCCCeEeHHHHHHHHHHcCCCHHHHHHHHHHhcC
Confidence 567788888888877667899999999998866 4556677777765543
No 204
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=61.97 E-value=16 Score=27.32 Aligned_cols=25 Identities=12% Similarity=0.247 Sum_probs=22.7
Q ss_pred CCHHHHHHHhchhHHHHHHHHHhhc
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQCLS 177 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilqf~S 177 (190)
+++.|||++|+|..+-|.+|.+++.
T Consensus 51 ~S~~eIA~~LgISrsTIyRi~R~~n 75 (88)
T TIGR02531 51 KTYSDIEAETGASTATISRVKRCLN 75 (88)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHhcc
Confidence 6899999999999999999988744
No 205
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=61.92 E-value=13 Score=28.81 Aligned_cols=21 Identities=14% Similarity=0.441 Sum_probs=18.5
Q ss_pred CCHHHHHHHhchhHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Il 173 (190)
|+.+|||+.+++...-|..-|
T Consensus 148 ~s~~EIA~~lgis~~tV~~~l 168 (191)
T PRK12520 148 LETEEICQELQITATNAWVLL 168 (191)
T ss_pred CCHHHHHHHHCCCHHHHHHHH
Confidence 889999999999998887654
No 206
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=61.68 E-value=8.1 Score=29.89 Aligned_cols=21 Identities=29% Similarity=0.235 Sum_probs=18.7
Q ss_pred CCHHHHHHHhchhHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Il 173 (190)
|+.+|||+.+++.+..|...|
T Consensus 148 ~s~~EIA~~lgis~~tVk~~l 168 (193)
T TIGR02947 148 FAYKEIAEIMGTPIGTVMSRL 168 (193)
T ss_pred CCHHHHHHHHCCCHHHHHHHH
Confidence 899999999999999887654
No 207
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=61.45 E-value=14 Score=32.82 Aligned_cols=36 Identities=14% Similarity=0.256 Sum_probs=28.6
Q ss_pred HHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHH
Q 029662 136 RRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 136 ~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Il 173 (190)
++||.|+-|-.+ ..+++.+|||+.|+|.-.-|.+|-
T Consensus 311 r~Vl~lrygl~~--~~~~tl~EIa~~lgvs~erVrQi~ 346 (367)
T PRK09210 311 ENVLRLRFGLDD--GRTRTLEEVGKVFGVTRERIRQIE 346 (367)
T ss_pred HHHHHHHhccCC--CCCccHHHHHHHHCCCHHHHHHHH
Confidence 568888877643 247999999999999988887773
No 208
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=61.37 E-value=14 Score=30.59 Aligned_cols=38 Identities=21% Similarity=0.204 Sum_probs=26.5
Q ss_pred ccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 130 LNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 130 LNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
|+-.+ ++||.|+-.. .|+.+|||++++|....|.++..
T Consensus 210 L~~~e-r~vi~~~~~~------~~t~~eIA~~lgis~~~V~~~~~ 247 (258)
T PRK08215 210 LNDRE-KLILNLRFFQ------GKTQMEVAEEIGISQAQVSRLEK 247 (258)
T ss_pred CCHHH-HHHHHHHHhc------CCCHHHHHHHHCcCHHHHHHHHH
Confidence 44444 4555554321 38999999999999999987753
No 209
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=61.20 E-value=16 Score=27.68 Aligned_cols=21 Identities=19% Similarity=0.251 Sum_probs=18.0
Q ss_pred CCHHHHHHHhchhHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Il 173 (190)
|+.+|||+.+++.+..|..-+
T Consensus 136 ~s~~EIA~~lgis~~tV~~~l 156 (173)
T PRK12522 136 YSYKEMSEILNIPIGTVKYRL 156 (173)
T ss_pred CCHHHHHHHhCCCHHHHHHHH
Confidence 789999999999998876554
No 210
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=61.16 E-value=12 Score=27.62 Aligned_cols=35 Identities=20% Similarity=0.167 Sum_probs=26.2
Q ss_pred HHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 135 LRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 135 l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
.++++.|+. ...-|+++|||+.+++...-|..++.
T Consensus 20 ~r~af~L~R-----~~eGlS~kEIAe~LGIS~~TVk~~l~ 54 (73)
T TIGR03879 20 AEAAAALAR-----EEAGKTASEIAEELGRTEQTVRNHLK 54 (73)
T ss_pred HHHHHHHHH-----HHcCCCHHHHHHHHCcCHHHHHHHHh
Confidence 456666651 11228999999999999999998875
No 211
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=61.03 E-value=18 Score=27.18 Aligned_cols=38 Identities=21% Similarity=0.289 Sum_probs=33.0
Q ss_pred HHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 135 LRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 135 l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
|+.|+.+|.-. ..|+.-++||+++.++..-|.++++.|
T Consensus 10 L~alV~~Y~~~----~~PVgSk~ia~~l~~s~aTIRN~M~~L 47 (78)
T PF03444_consen 10 LKALVELYIET----GEPVGSKTIAEELGRSPATIRNEMADL 47 (78)
T ss_pred HHHHHHHHHhc----CCCcCHHHHHHHHCCChHHHHHHHHHH
Confidence 67889999754 579999999999999999999998765
No 212
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=60.85 E-value=11 Score=28.43 Aligned_cols=23 Identities=22% Similarity=0.164 Sum_probs=19.7
Q ss_pred CCCCHHHHHHHhchhHHHHHHHH
Q 029662 151 GPLDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 151 gPM~v~~iAeKFrv~v~~vq~Il 173 (190)
.-|+.+|||+.+++....|...+
T Consensus 153 ~~~s~~EIA~~lgis~~tv~~~l 175 (190)
T TIGR02939 153 EGLSYEDIARIMDCPVGTVRSRI 175 (190)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHH
Confidence 44899999999999999887655
No 213
>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=60.68 E-value=20 Score=25.75 Aligned_cols=37 Identities=24% Similarity=0.365 Sum_probs=28.6
Q ss_pred HHHHHhhccCCCCCCCCCHHHHHHHh-----chhHHHHHHHHHhhc
Q 029662 137 RIMLLHQGKADDHNGPLDAKQIAEKF-----RLDVLQVQAILQCLS 177 (190)
Q Consensus 137 ~ii~L~QGk~~~h~gPM~v~~iAeKF-----rv~v~~vq~Ilqf~S 177 (190)
.|+.+... +++++++++|.++. ++..+-|-++|++|.
T Consensus 5 ~Il~~l~~----~~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~ 46 (116)
T cd07153 5 AILEVLLE----SDGHLTAEEIYERLRKKGPSISLATVYRTLELLE 46 (116)
T ss_pred HHHHHHHh----CCCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHH
Confidence 45555543 25789999999998 688999999998873
No 214
>cd03073 PDI_b'_ERp72_ERp57 PDIb' family, ERp72 and ERp57 subfamily, second redox inactive TRX-like domain b'; ERp72 and ER57 are involved in oxidative protein folding in the ER, like PDI. They exhibit both disulfide oxidase and reductase functions, by catalyzing the formation of disulfide bonds of newly synthesized polypeptides and acting as isomerases to correct any non-native disulfide bonds. They also display chaperone activity to prevent protein aggregation and facilitate the folding of newly synthesized proteins. ERp57 contains two redox-active TRX (a) domains and two redox inactive TRX-like (b) domains. It shares the same domain arrangement of abb'a' as PDI, but lacks the C-terminal acid-rich region (c domain) that is present in PDI. ERp72 contains one additional redox-active TRX (a) domain at the N-terminus with a molecular structure of a"abb'a'. ERp57 interacts with the lectin chaperones, calnexin and calreticulin, and specifically promotes the oxidative folding of glycoprotei
Probab=60.47 E-value=12 Score=28.13 Aligned_cols=28 Identities=18% Similarity=0.177 Sum_probs=23.5
Q ss_pred HHHHHHHhc--------hhHHHHHHHHHhhcCCCCC
Q 029662 155 AKQIAEKFR--------LDVLQVQAILQCLSLPPES 182 (190)
Q Consensus 155 v~~iAeKFr--------v~v~~vq~Ilqf~SlP~e~ 182 (190)
+++||++|| +|+..-+++++|+.|..++
T Consensus 40 ~~~vAk~fk~gki~Fv~~D~~~~~~~l~~fgl~~~~ 75 (111)
T cd03073 40 VLKVAKDFPDRKLNFAVADKEDFSHELEEFGLDFSG 75 (111)
T ss_pred HHHHHHHCcCCeEEEEEEcHHHHHHHHHHcCCCccc
Confidence 678899998 7888888899999998753
No 215
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=60.45 E-value=13 Score=30.88 Aligned_cols=32 Identities=13% Similarity=0.259 Sum_probs=24.1
Q ss_pred HHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHH
Q 029662 136 RRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 136 ~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Il 173 (190)
|+||.|+-. .-|+.+|||+.+++....|..++
T Consensus 218 r~vl~l~~~------~~~s~~eIA~~lgis~~tV~~~~ 249 (268)
T PRK06288 218 KKVLILYYY------EDLTLKEIGKVLGVTESRISQLH 249 (268)
T ss_pred HHHHHHHHH------cCCCHHHHHHHHCcCHHHHHHHH
Confidence 556666422 23899999999999999998655
No 216
>PF04433 SWIRM: SWIRM domain; InterPro: IPR007526 The SWIRM domain is a small alpha-helical domain of about 85 amino acid residues found in eukaryotic chromosomal proteins. It is named after the proteins SWI3, RSC8 and MOIRA in which it was first recognised. This domain is predicted to mediate protein-protein interactions in the assembly of chromatin-protein complexes. The SWIRM domain can be linked to different domains, such as the ZZ-type zinc finger (IPR000433 from INTERPRO), the Myb DNA-binding domain (IPR001005 from INTERPRO), the HORMA domain (IPR003511 from INTERPRO), the amino-oxidase domain, the chromo domain (IPR000953 from INTERPRO), and the JAB1/PAD1 domain.; GO: 0005515 protein binding; PDB: 2Z3Y_A 2UXN_A 2Y48_A 2HKO_A 2XAF_A 2X0L_A 2XAJ_A 2UXX_A 2V1D_A 2L3D_A ....
Probab=60.44 E-value=8.6 Score=27.28 Aligned_cols=38 Identities=18% Similarity=0.266 Sum_probs=29.0
Q ss_pred HHHHHhhccCCCCCCCCCHHHHHHHhc-hhHHHHHHHHHhhc
Q 029662 137 RIMLLHQGKADDHNGPLDAKQIAEKFR-LDVLQVQAILQCLS 177 (190)
Q Consensus 137 ~ii~L~QGk~~~h~gPM~v~~iAeKFr-v~v~~vq~Ilqf~S 177 (190)
.||.+| ..+..+.+++.+--+-++ +|+..+.+|.+||.
T Consensus 41 ~il~~w---~~n~~~~lt~~~~~~~i~~~d~~~~~ri~~FL~ 79 (86)
T PF04433_consen 41 TILAEW---RKNPNKYLTKTDARKLIKGIDVNKIRRIYDFLE 79 (86)
T ss_dssp HHHHHH---HHHTTS---HHHHHHHTTSSSHHHHHHHHHHHH
T ss_pred HHHHHH---HHCCCCcccHHHHHHHccccCHHHHHHHHHHHH
Confidence 456777 345677899999999999 99999999999985
No 217
>PF13551 HTH_29: Winged helix-turn helix
Probab=60.31 E-value=41 Score=23.27 Aligned_cols=45 Identities=16% Similarity=0.232 Sum_probs=33.9
Q ss_pred ccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHh-------chhHHHHHHHHH
Q 029662 130 LNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKF-------RLDVLQVQAILQ 174 (190)
Q Consensus 130 LNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKF-------rv~v~~vq~Ilq 174 (190)
|+-++...|+.++.-+..+-....+.++||+.. .+-.+-|.+||+
T Consensus 58 l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 58 LSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 889999999999987665522468889998854 456667887775
No 218
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=60.21 E-value=14 Score=34.55 Aligned_cols=36 Identities=22% Similarity=0.309 Sum_probs=29.0
Q ss_pred HHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHH
Q 029662 136 RRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 136 ~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Il 173 (190)
++||.|+-|-.+ ..+|+.+|||+.|+|...-|..|+
T Consensus 356 R~VI~LRygl~d--~~~~Tl~EIA~~LGvS~erVRqie 391 (415)
T PRK07598 356 RDVIRMRFGLAD--GHTYSLAEIGRALDLSRERVRQIE 391 (415)
T ss_pred HHHHHHHHhcCC--CCCCCHHHHHHHHCcCHHHHHHHH
Confidence 568888777543 347999999999999999888774
No 219
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=60.17 E-value=18 Score=28.39 Aligned_cols=35 Identities=14% Similarity=0.219 Sum_probs=27.6
Q ss_pred HHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 137 RIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 137 ~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
.||.+.| .+|.++..+||++.++..+-|.+=++=|
T Consensus 18 ~IL~~Lq-----~d~R~s~~eiA~~lglS~~tv~~Ri~rL 52 (164)
T PRK11169 18 NILNELQ-----KDGRISNVELSKRVGLSPTPCLERVRRL 52 (164)
T ss_pred HHHHHhc-----cCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 4555555 5778999999999999999888766543
No 220
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=59.81 E-value=15 Score=31.83 Aligned_cols=37 Identities=30% Similarity=0.451 Sum_probs=30.0
Q ss_pred HHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 136 RRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 136 ~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
++.|+++.=+ .|||+++|||++.+|....|.+=|++|
T Consensus 13 r~~il~lL~~----~g~~sa~elA~~Lgis~~avR~HL~~L 49 (218)
T COG2345 13 RERILELLKK----SGPVSADELAEELGISPMAVRRHLDDL 49 (218)
T ss_pred HHHHHHHHhc----cCCccHHHHHHHhCCCHHHHHHHHHHH
Confidence 4555555544 489999999999999999999888876
No 221
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=59.78 E-value=16 Score=29.35 Aligned_cols=23 Identities=30% Similarity=0.349 Sum_probs=19.8
Q ss_pred CCCHHHHHHHhchhHHHHHHHHH
Q 029662 152 PLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 152 PM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
.|+.+|||+.+++....|..++.
T Consensus 191 ~~s~~eIA~~lgis~~tV~~~~~ 213 (224)
T TIGR02479 191 ELNLKEIGEVLGLTESRVSQIHS 213 (224)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHH
Confidence 38999999999999999987653
No 222
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=59.21 E-value=12 Score=24.60 Aligned_cols=30 Identities=17% Similarity=0.182 Sum_probs=25.4
Q ss_pred CCHHHHHHHhchhHHHHHHHHHhhcCCCCC
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQCLSLPPES 182 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilqf~SlP~e~ 182 (190)
|++.|+|+.++|....|..-.+---|++..
T Consensus 1 yti~eva~~~gvs~~tlr~y~~~gll~~~~ 30 (69)
T PF13411_consen 1 YTIKEVAKLLGVSPSTLRYYEREGLLPPPR 30 (69)
T ss_dssp EEHHHHHHHTTTTHHHHHHHHHTTSSTTBE
T ss_pred CcHHHHHHHHCcCHHHHHHHHHhcCccccc
Confidence 689999999999999999877655577775
No 223
>PRK05472 redox-sensing transcriptional repressor Rex; Provisional
Probab=59.10 E-value=14 Score=29.99 Aligned_cols=49 Identities=22% Similarity=0.323 Sum_probs=35.3
Q ss_pred CCCCCCcccHH-HHHHHHHHhhccCCCCCC--CCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 123 KPSPPGTLNVA-QLRRIMLLHQGKADDHNG--PLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 123 r~~p~GTLNva-~l~~ii~L~QGk~~~h~g--PM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
+-+|..|++-. -.++|+.+.. .+| .+++++||++|+|+..+|.+=|.++
T Consensus 5 ~~~~~~~~~r~~~~~~il~~l~-----~~~~~~vs~~~L~~~~~v~~~tirrDl~~l 56 (213)
T PRK05472 5 KKIPEATIKRLPLYYRYLKELK-----EEGVERVSSKELAEALGVDSAQIRKDLSYF 56 (213)
T ss_pred ccCCHHHHHHhHHHHHHHHHHH-----HcCCcEEeHHHHHHHhCcCHHHHHHHHHHH
Confidence 45777788733 3344444332 245 7999999999999999999877776
No 224
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=58.66 E-value=37 Score=22.11 Aligned_cols=35 Identities=31% Similarity=0.448 Sum_probs=26.3
Q ss_pred ccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHH
Q 029662 130 LNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAI 172 (190)
Q Consensus 130 LNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~I 172 (190)
|.-.+++=+..|.+| ++.+|||+..+|...-|...
T Consensus 4 LT~~E~~vl~~l~~G--------~~~~eIA~~l~is~~tV~~~ 38 (58)
T PF00196_consen 4 LTERELEVLRLLAQG--------MSNKEIAEELGISEKTVKSH 38 (58)
T ss_dssp S-HHHHHHHHHHHTT--------S-HHHHHHHHTSHHHHHHHH
T ss_pred cCHHHHHHHHHHHhc--------CCcchhHHhcCcchhhHHHH
Confidence 556677777788888 56999999999998876543
No 225
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=58.66 E-value=14 Score=29.39 Aligned_cols=21 Identities=10% Similarity=0.072 Sum_probs=18.7
Q ss_pred CCHHHHHHHhchhHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Il 173 (190)
|+++|||+.+++.+..|..-|
T Consensus 150 ~s~~EIAe~lgis~~tV~~~l 170 (196)
T PRK12535 150 YTYEEAAKIADVRVGTIRSRV 170 (196)
T ss_pred CCHHHHHHHhCCCHHHHHHHH
Confidence 889999999999999887655
No 226
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=58.57 E-value=25 Score=23.96 Aligned_cols=41 Identities=27% Similarity=0.414 Sum_probs=33.7
Q ss_pred ccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 130 LNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 130 LNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
|+..|++-++.|++... ++..+||++..++.+-|-++|+=|
T Consensus 20 lt~~q~~~L~~l~~~~~------~~~~~la~~l~i~~~~vt~~l~~L 60 (126)
T COG1846 20 LTPPQYQVLLALYEAGG------ITVKELAERLGLDRSTVTRLLKRL 60 (126)
T ss_pred CCHHHHHHHHHHHHhCC------CcHHHHHHHHCCCHHHHHHHHHHH
Confidence 88899998888887554 333999999999999999998754
No 227
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=58.35 E-value=16 Score=23.91 Aligned_cols=29 Identities=17% Similarity=0.172 Sum_probs=25.3
Q ss_pred CCHHHHHHHhchhHHHHHHHHHhhcCCCC
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQCLSLPPE 181 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilqf~SlP~e 181 (190)
|++.|+|++++|....|....+.--+|++
T Consensus 1 ~s~~eva~~~gvs~~tlr~~~~~gli~~~ 29 (70)
T smart00422 1 YTIGEVAKLAGVSVRTLRYYERIGLLPPP 29 (70)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCCCC
Confidence 68999999999999999998887777764
No 228
>PRK13239 alkylmercury lyase; Provisional
Probab=58.34 E-value=19 Score=31.01 Aligned_cols=38 Identities=21% Similarity=0.380 Sum_probs=30.4
Q ss_pred HHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhhc
Q 029662 135 LRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCLS 177 (190)
Q Consensus 135 l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~S 177 (190)
++-|++++- |..|.++.+||+.++..+..|+.+|+-+.
T Consensus 24 ~~~llr~la-----~G~pvt~~~lA~~~~~~~~~v~~~L~~l~ 61 (206)
T PRK13239 24 LVPLLRLLA-----KGRPVSVTTLAAALGWPVEEVEAVLEAMP 61 (206)
T ss_pred HHHHHHHHH-----cCCCCCHHHHHHHhCCCHHHHHHHHHhCC
Confidence 445555542 56689999999999999999999999853
No 229
>PF01476 LysM: LysM domain; InterPro: IPR018392 This domain is about 40 residues long and is found in a variety of enzymes involved in bacterial cell wall degradation []. This domain may have a general peptidoglycan binding function.; GO: 0016998 cell wall macromolecule catabolic process; PDB: 2DJP_A 3ZQD_A 1Y7M_B 4A52_A 2L9Y_A 1E0G_A.
Probab=58.25 E-value=11 Score=22.85 Aligned_cols=20 Identities=15% Similarity=0.250 Sum_probs=15.3
Q ss_pred CHHHHHHHhchhHHHHHHHH
Q 029662 154 DAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 154 ~v~~iAeKFrv~v~~vq~Il 173 (190)
++..||.+|++.+..+.+.=
T Consensus 8 tl~~IA~~~~~~~~~l~~~N 27 (44)
T PF01476_consen 8 TLWSIAKRYGISVDELMELN 27 (44)
T ss_dssp -HHHHHHHTTS-HHHHHHHC
T ss_pred cHHHHHhhhhhhHhHHHHhc
Confidence 57899999999999887653
No 230
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=58.23 E-value=27 Score=21.86 Aligned_cols=45 Identities=20% Similarity=0.195 Sum_probs=35.8
Q ss_pred CcccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 128 GTLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 128 GTLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
+.++..|+..+-..|+=.. +...-...+||+..++...+|+.-.+
T Consensus 5 ~~~~~~~~~~L~~~f~~~~--~P~~~~~~~la~~~~l~~~qV~~WF~ 49 (56)
T smart00389 5 TSFTPEQLEELEKEFQKNP--YPSREEREELAAKLGLSERQVKVWFQ 49 (56)
T ss_pred CcCCHHHHHHHHHHHHhCC--CCCHHHHHHHHHHHCcCHHHHHHhHH
Confidence 4578888888888886433 67778899999999999999987543
No 231
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=57.79 E-value=16 Score=30.16 Aligned_cols=33 Identities=18% Similarity=0.166 Sum_probs=25.7
Q ss_pred HHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 136 RRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 136 ~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
|+||.|+-. ..|+.++||+.++|..+.|.+|.+
T Consensus 189 r~vi~l~~~------~~~t~~EIA~~lgis~~~V~q~~~ 221 (231)
T PRK12427 189 QLILHLYYQ------HEMSLKEIALVLDLTEARICQLNK 221 (231)
T ss_pred HHHHHHHHH------cCCCHHHHHHHHCcCHHHHHHHHH
Confidence 556666542 358999999999999999987764
No 232
>PF00888 Cullin: Cullin family; InterPro: IPR001373 Cullins are a family of hydrophobic proteins that act as scaffolds for ubiquitin ligases (E3). Cullins are found throughout eukaryotes. Humans express seven cullins (Cul1, 2, 3, 4A, 4B, 5 and 7), each forming part of a multi-subunit ubiquitin complex. Cullin-RING ubiquitin ligases (CRLs), such as Cul1 (SCF) [], play an essential role in targeting proteins for ubiquitin-mediated destruction; as such, they are diverse in terms of composition and function, regulating many different processes from glucose sensing and DNA replication to limb patterning and circadian rhythms. The catalytic core of CRLs consists of a RING protein and a cullin family member. For Cul1, the C-terminal cullin-homology domain binds the RING protein. The RING protein appears to function as a docking site for ubiquitin-conjugating enzymes (E2s). Other proteins contain a cullin-homology domain, such as the APC2 subunit of the anaphase-promoting complex/cyclosome and the p53 cytoplasmic anchor PARC; both APC2 and PARC have ubiquitin ligase activity. The N-terminal region of cullins is more variable, and is used to interact with specific adaptor proteins [, , ]. This entry represents the N-terminal region of cullin proteins, which consists of several domains, including cullin repeat domain, a 4-helical bundle domain, an alpha+beta domain, and a winged helix-like domain.; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 2WZK_A 3DQV_D 3DPL_C 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_A 1U6G_A 4A0K_A ....
Probab=57.54 E-value=8.8 Score=34.37 Aligned_cols=47 Identities=26% Similarity=0.351 Sum_probs=34.5
Q ss_pred CcccHHHHHHHHHH-hhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhhcCC
Q 029662 128 GTLNVAQLRRIMLL-HQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCLSLP 179 (190)
Q Consensus 128 GTLNva~l~~ii~L-~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~SlP 179 (190)
-+|.|.-+|-+|+| |+- ...+++++|+++.+++-..++++|+++.--
T Consensus 514 ~~l~~s~~q~~iLl~Fn~-----~~~~t~~ei~~~~~~~~~~l~~~L~~l~~~ 561 (588)
T PF00888_consen 514 YELTVSTLQAAILLLFND-----NDSLTVEEISEKTGISEEELKRALKSLVKS 561 (588)
T ss_dssp EEEEEEHHHHHHHHGGGS-----SSEEEHHHHHHHC---HHHHHHHHHCCCTT
T ss_pred eeEEeeHHHHHHHHHHcc-----CCCccHHHHHHHHCcCHHHHHHHHHHHHhC
Confidence 56777777766654 444 556999999999999999999999987643
No 233
>PF07180 DUF1401: Protein of unknown function (DUF1401); InterPro: IPR020357 This entry represents CaiF, a specific carnitine-sensitive transcription regulator. CaiF and CRP a cyclic AMP receptor protein, are required to activate the cai and fix operons, which are involved in anaerobic carnitine metabolism [].; GO: 0006351 transcription, DNA-dependent
Probab=57.51 E-value=10 Score=31.60 Aligned_cols=32 Identities=22% Similarity=0.357 Sum_probs=27.7
Q ss_pred HhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhhcC
Q 029662 141 LHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCLSL 178 (190)
Q Consensus 141 L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~Sl 178 (190)
|.||.- ++.+|||+.|.|..-..-.||-|++-
T Consensus 33 l~q~rw------itr~dIS~aF~I~~rrA~~ilsYI~s 64 (146)
T PF07180_consen 33 LQQNRW------ITRNDISEAFHITQRRASNILSYILS 64 (146)
T ss_pred HHhcCc------ccHHHHHHhcCCchhhHHHHHHHHHh
Confidence 456655 99999999999999999999999873
No 234
>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region. Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model.
Probab=57.00 E-value=26 Score=23.76 Aligned_cols=45 Identities=9% Similarity=0.078 Sum_probs=33.7
Q ss_pred ccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhhcC
Q 029662 130 LNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCLSL 178 (190)
Q Consensus 130 LNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~Sl 178 (190)
|+....+.||...+- +.+-=++++|....+|.-...++|++|+.+
T Consensus 25 ig~~~a~~Il~~R~~----~g~~~s~~dL~~v~gi~~~~~~~i~~~~~~ 69 (69)
T TIGR00426 25 VGLKKAEAIVSYREE----YGPFKTVEDLKQVPGIGNSLVEKNLAVITL 69 (69)
T ss_pred CCHHHHHHHHHHHHH----cCCcCCHHHHHcCCCCCHHHHHHHHhhccC
Confidence 777777777776531 111229999999999999999999999863
No 235
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=56.65 E-value=16 Score=30.68 Aligned_cols=22 Identities=9% Similarity=0.089 Sum_probs=19.1
Q ss_pred CCHHHHHHHhchhHHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilq 174 (190)
|+.+|||+.+++....|...+.
T Consensus 125 ~s~~EIA~~lg~s~~tVr~~l~ 146 (281)
T TIGR02957 125 YPYEEIASIVGKSEANCRQLVS 146 (281)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
Confidence 8899999999999988876653
No 236
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=56.18 E-value=22 Score=23.24 Aligned_cols=27 Identities=15% Similarity=0.094 Sum_probs=22.3
Q ss_pred CCHHHHHHHhchhHHHHHHHHHhhcCC
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQCLSLP 179 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilqf~SlP 179 (190)
|++.|+|++++|....|.+..+-..++
T Consensus 1 ~s~~eva~~~gvs~~tlr~w~~~~g~~ 27 (68)
T cd01104 1 YTIGAVARLTGVSPDTLRAWERRYGLP 27 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHhCCCC
Confidence 578999999999999999988743343
No 237
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=55.41 E-value=24 Score=27.18 Aligned_cols=39 Identities=13% Similarity=0.100 Sum_probs=30.2
Q ss_pred HHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 137 RIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 137 ~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
+-.+||+--. ++.-+++++|||+.|..---.++.||+=+
T Consensus 5 ~y~~L~~~~~-~~~~~vtl~elA~~l~cS~Rn~r~lLkkm 43 (115)
T PF12793_consen 5 QYQRLWQHYG-GQPVEVTLDELAELLFCSRRNARTLLKKM 43 (115)
T ss_pred HHHHHHHHcC-CCCcceeHHHHHHHhCCCHHHHHHHHHHH
Confidence 3444554433 77888999999999999999999888754
No 238
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=54.76 E-value=13 Score=28.02 Aligned_cols=23 Identities=13% Similarity=0.072 Sum_probs=18.7
Q ss_pred CCCCHHHHHHHhchhHHHHHHHH
Q 029662 151 GPLDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 151 gPM~v~~iAeKFrv~v~~vq~Il 173 (190)
.-|+.+|||+.|++.++-|...+
T Consensus 141 ~g~s~~eIA~~l~is~~~V~~~l 163 (176)
T PRK09638 141 YGYTYEEIAKMLNIPEGTVKSRV 163 (176)
T ss_pred cCCCHHHHHHHHCCChhHHHHHH
Confidence 34999999999999999775443
No 239
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=54.54 E-value=28 Score=26.92 Aligned_cols=22 Identities=27% Similarity=0.338 Sum_probs=19.7
Q ss_pred CCHHHHHHHhchhHHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilq 174 (190)
++.+|||+.+++....|...+.
T Consensus 171 ~s~~EIA~~lgis~~tV~~~l~ 192 (208)
T PRK08295 171 KSYQEIAEELNRHVKSIDNALQ 192 (208)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
Confidence 8999999999999999987664
No 240
>TIGR03734 PRTRC_parB PRTRC system ParB family protein. A novel genetic system characterized by six major proteins, included a ParB homolog and a ThiF homolog, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. It is often found on plasmids. This protein family the member related to ParB, and is designated PRTRC system ParB family protein.
Probab=54.51 E-value=20 Score=35.00 Aligned_cols=29 Identities=14% Similarity=0.143 Sum_probs=27.4
Q ss_pred CCHHHHHHHhchhHHHHHHHHHhhcCCCC
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQCLSLPPE 181 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilqf~SlP~e 181 (190)
.+.++||++|++....|++.|..+.|+++
T Consensus 110 ~t~eeIA~~lG~S~~~V~rrLkL~~L~p~ 138 (554)
T TIGR03734 110 GDREEAARRLGWSPATLDRRLALMNCTDE 138 (554)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHcCCCHH
Confidence 48999999999999999999999999986
No 241
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=54.28 E-value=19 Score=34.53 Aligned_cols=36 Identities=14% Similarity=0.289 Sum_probs=28.3
Q ss_pred HHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHH
Q 029662 136 RRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 136 ~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Il 173 (190)
|.||.|+=|--+ ..+|+.+|||+.|+|--..|.+|-
T Consensus 453 r~VI~lRyGL~~--~e~~TL~EIa~~lGVSrERVRQIe 488 (509)
T PRK05901 453 AGVIRMRFGLTD--GQPKTLDEIGQVYGVTRERIRQIE 488 (509)
T ss_pred HHHHHHHhhccC--CCCCCHHHHHHHHCCCHHHHHHHH
Confidence 567778767632 367999999999999988887774
No 242
>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=53.38 E-value=14 Score=27.33 Aligned_cols=25 Identities=12% Similarity=0.090 Sum_probs=22.0
Q ss_pred CCCCHHHHHHHhchhHHHHHHHHHh
Q 029662 151 GPLDAKQIAEKFRLDVLQVQAILQC 175 (190)
Q Consensus 151 gPM~v~~iAeKFrv~v~~vq~Ilqf 175 (190)
|.+++++||+.|+|-.+-|-+.|..
T Consensus 18 ~~~ti~dvA~~~gvS~~TVsr~L~~ 42 (80)
T TIGR02844 18 TKATVRETAKVFGVSKSTVHKDVTE 42 (80)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHhcC
Confidence 4589999999999999999997753
No 243
>PF14493 HTH_40: Helix-turn-helix domain
Probab=53.29 E-value=21 Score=25.51 Aligned_cols=33 Identities=21% Similarity=0.196 Sum_probs=23.8
Q ss_pred HHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHH-HHHhh
Q 029662 137 RIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQA-ILQCL 176 (190)
Q Consensus 137 ~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~-Ilqf~ 176 (190)
.-+.||| +- |++++||++-++..+-|.. +++|+
T Consensus 5 ~T~~l~~-~G------~si~eIA~~R~L~~sTI~~HL~~~~ 38 (91)
T PF14493_consen 5 ITYELFQ-KG------LSIEEIAKIRGLKESTIYGHLAELI 38 (91)
T ss_pred HHHHHHH-cC------CCHHHHHHHcCCCHHHHHHHHHHHH
Confidence 4456676 22 8999999999999988765 44444
No 244
>PRK13832 plasmid partitioning protein; Provisional
Probab=53.29 E-value=21 Score=34.90 Aligned_cols=29 Identities=21% Similarity=0.249 Sum_probs=27.4
Q ss_pred CCHHHHHHHhchhHHHHHHHHHhhcCCCC
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQCLSLPPE 181 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilqf~SlP~e 181 (190)
++.++||.+|++....|++++.+..|||+
T Consensus 119 ~T~EeIA~~lG~S~~~V~rlllLA~L~P~ 147 (520)
T PRK13832 119 WTEEAIAVALALPVRQIRKLRLLANVLPA 147 (520)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHcCCCHH
Confidence 99999999999999999999998899875
No 245
>cd00118 LysM Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function.
Probab=53.04 E-value=16 Score=20.01 Aligned_cols=22 Identities=14% Similarity=0.255 Sum_probs=17.5
Q ss_pred CHHHHHHHhchhHHHHHHHHHh
Q 029662 154 DAKQIAEKFRLDVLQVQAILQC 175 (190)
Q Consensus 154 ~v~~iAeKFrv~v~~vq~Ilqf 175 (190)
++.+||++|++....+..+-..
T Consensus 10 t~~~ia~~~~~~~~~~~~~N~~ 31 (46)
T cd00118 10 TLSSIAQRYGISVEELLKLNGL 31 (46)
T ss_pred CHHHHHHHHCcCHHHHHHHcCC
Confidence 6889999999998877665443
No 246
>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=52.97 E-value=17 Score=29.25 Aligned_cols=27 Identities=19% Similarity=0.375 Sum_probs=24.6
Q ss_pred CCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 150 NGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 150 ~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
+|.|+.++||+..++....|-+||..|
T Consensus 26 ~~~~tdEeLa~~Lgi~~~~VRk~L~~L 52 (158)
T TIGR00373 26 KGEFTDEEISLELGIKLNEVRKALYAL 52 (158)
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 456999999999999999999999876
No 247
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=52.69 E-value=51 Score=29.24 Aligned_cols=53 Identities=17% Similarity=0.310 Sum_probs=44.2
Q ss_pred CCCCCCCCCCcccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 119 RYEEKPSPPGTLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 119 ~~eer~~p~GTLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
.-...++|-| |+-.-++.|+++++ ...-+.+.+++|++-++.-+-+.+-|.|+
T Consensus 145 ~~~~~~LPkG-i~~~Tl~~i~~~~~----~~~~~~Taeela~~~giSRvTaRRYLeyl 197 (224)
T COG4565 145 EQPPDDLPKG-LDELTLQKVREALK----EPDQELTAEELAQALGISRVTARRYLEYL 197 (224)
T ss_pred ccCcccCCCC-cCHHHHHHHHHHHh----CcCCccCHHHHHHHhCccHHHHHHHHHHH
Confidence 4455778855 78888899999988 34567999999999999999999999987
No 248
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=52.50 E-value=37 Score=25.58 Aligned_cols=25 Identities=16% Similarity=0.412 Sum_probs=22.4
Q ss_pred CCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 150 NGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 150 ~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
..++++++||+.+++....++++++
T Consensus 23 ~~~~sl~~lA~~~g~S~~~l~r~Fk 47 (127)
T PRK11511 23 ESPLSLEKVSERSGYSKWHLQRMFK 47 (127)
T ss_pred CCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3569999999999999999999876
No 249
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=52.40 E-value=27 Score=26.23 Aligned_cols=22 Identities=18% Similarity=0.161 Sum_probs=18.7
Q ss_pred CCHHHHHHHhchhHHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilq 174 (190)
++..|||+.|++.+..|...++
T Consensus 125 ~s~~eIA~~lgis~~tv~~~l~ 146 (165)
T PRK09644 125 LTYEEAASVLDLKLNTYKSHLF 146 (165)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
Confidence 7899999999999998876553
No 250
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=51.82 E-value=26 Score=32.03 Aligned_cols=38 Identities=18% Similarity=0.256 Sum_probs=29.1
Q ss_pred HHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 135 LRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 135 l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
-|+||.|+=|--+ ..+++.++||+.|+|...-|.+|..
T Consensus 316 Er~IL~lrygl~~--~~~~Tl~EIA~~lgiS~eRVRQie~ 353 (373)
T PRK07406 316 ERDVLRLRYGLDD--GRMKTLEEIGQIFNVTRERIRQIEA 353 (373)
T ss_pred HHHHHHHHHhcCC--CCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3668888666522 2369999999999999998888754
No 251
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=51.50 E-value=18 Score=29.82 Aligned_cols=27 Identities=30% Similarity=0.417 Sum_probs=24.8
Q ss_pred CCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 150 NGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 150 ~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
+|+++.++||+..++....|.++|+.|
T Consensus 34 ~g~~tdeeLA~~Lgi~~~~VRk~L~~L 60 (178)
T PRK06266 34 KGEVTDEEIAEQTGIKLNTVRKILYKL 60 (178)
T ss_pred cCCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 457999999999999999999999876
No 252
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=51.39 E-value=29 Score=26.73 Aligned_cols=33 Identities=30% Similarity=0.358 Sum_probs=25.5
Q ss_pred HHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 136 RRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 136 ~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
|+++.|+.-.- ++..|||+.++|.+.-|+.-+.
T Consensus 133 R~~~~l~~~~g------ls~~EIA~~l~i~~~tVks~l~ 165 (182)
T COG1595 133 REAFLLRYLEG------LSYEEIAEILGISVGTVKSRLH 165 (182)
T ss_pred hHHhhhHhhcC------CCHHHHHHHHCCCHHHHHHHHH
Confidence 45555555443 8999999999999999987664
No 253
>PF13994 PgaD: PgaD-like protein
Probab=51.21 E-value=18 Score=28.24 Aligned_cols=33 Identities=24% Similarity=0.437 Sum_probs=25.3
Q ss_pred hhccCCCCC-CCCCHHHHHHHhchhHHHHHHHHH
Q 029662 142 HQGKADDHN-GPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 142 ~QGk~~~h~-gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
|+|+..-+. .+.+.+|+|+.|.|+..++|++-|
T Consensus 89 f~~~~rr~~~~~~~~~elA~~f~l~~~~l~~lr~ 122 (138)
T PF13994_consen 89 FRGRRRRRRPPPVSDEELARSFGLSPEQLQQLRQ 122 (138)
T ss_pred hcchhhccCCCCCCHHHHHHHcCCCHHHHHHHHh
Confidence 455554433 349999999999999999998755
No 254
>PF02022 Integrase_Zn: Integrase Zinc binding domain The structure of the N-terminal zinc binding domain.; InterPro: IPR003308 Retroviral integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains: an N-terminal zinc binding domain, a central catalytic core and a C-terminal DNA-binding domain [, ]. Often found as part of the POL polyprotein.; GO: 0008270 zinc ion binding; PDB: 1E0E_A 3F9K_F 1E27_C 1K6Y_B 1WJD_A 1WJB_A 1WJF_A 1WJE_B 3HPG_B 3HPH_C ....
Probab=51.20 E-value=18 Score=23.82 Aligned_cols=22 Identities=27% Similarity=0.418 Sum_probs=17.4
Q ss_pred CHHHHHHHhchhHHHHHHHHHh
Q 029662 154 DAKQIAEKFRLDVLQVQAILQC 175 (190)
Q Consensus 154 ~v~~iAeKFrv~v~~vq~Ilqf 175 (190)
+++.|+.+|+|--.+...||+-
T Consensus 11 n~~~L~~~f~ip~~vAk~IV~~ 32 (40)
T PF02022_consen 11 NAKALRHKFGIPRLVAKQIVNQ 32 (40)
T ss_dssp -HHHHHHHHT--HHHHHHHHHH
T ss_pred CHHHHHHHHccCHHHHHHHHHH
Confidence 6789999999999999999973
No 255
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=50.94 E-value=29 Score=27.26 Aligned_cols=21 Identities=29% Similarity=0.344 Sum_probs=18.4
Q ss_pred CCHHHHHHHhchhHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Il 173 (190)
++.+|||+.+++.+..|...+
T Consensus 145 ~s~~EIA~~lgis~~tV~~~l 165 (188)
T PRK12517 145 FSGEEIAEILDLNKNTVMTRL 165 (188)
T ss_pred CCHHHHHHHHCCCHHHHHHHH
Confidence 889999999999999887654
No 256
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=50.40 E-value=25 Score=29.70 Aligned_cols=32 Identities=25% Similarity=0.192 Sum_probs=23.3
Q ss_pred HHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHH
Q 029662 136 RRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 136 ~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Il 173 (190)
|+|+.|.--. | |+.+|||+..++....|...|
T Consensus 122 R~v~lL~~~e-----g-~S~~EIAe~LgiS~~tVksrL 153 (228)
T PRK06704 122 SAILLLKDVF-----Q-YSIADIAKVCSVSEGAVKASL 153 (228)
T ss_pred hhHhhhHHhh-----C-CCHHHHHHHHCcCHHHHHHHH
Confidence 5666663211 2 899999999999998887543
No 257
>PF05361 PP1_inhibitor: PKC-activated protein phosphatase-1 inhibitor; InterPro: IPR008025 Contractility of vascular smooth muscle depends on phosphorylation of myosin light chains, and is modulated by hormonal control of myosin phosphatase activity. Signaling pathways activate kinases such as PKC or Rho-dependent kinases that phosphorylate the myosin phosphatase inhibitor protein called CPI-17. Phosphorylation of CPI-17 at Thr-38 enhances its inhibitory potency 1000-fold, creating a molecular switch for regulating contraction [].; GO: 0042325 regulation of phosphorylation, 0005737 cytoplasm; PDB: 2RLT_A 1J2M_A 1K5O_A 1J2N_A.
Probab=50.39 E-value=33 Score=28.63 Aligned_cols=100 Identities=19% Similarity=0.256 Sum_probs=52.1
Q ss_pred HHHHhhcccccCCCCccccchhhhhhhhcCCCCCCCCCCCCCCCCCCCCCCCCcccHHHH--HHHHHHhhccCCCCCCCC
Q 029662 76 MLNQMLGRVKTKAGGKAEMGEAAVVERQTRPLPKLRNTTPVSSRYEEKPSPPGTLNVAQL--RRIMLLHQGKADDHNGPL 153 (190)
Q Consensus 76 Ml~qmvGrI~tkpGGk~Emgea~vv~~ynRP~Pk~R~t~~~sg~~eer~~p~GTLNva~l--~~ii~L~QGk~~~h~gPM 153 (190)
|..+-|||-.+.-++.++-..+. .-+.++-|...--+..|.-+++ .=-|+|+.. -++-.||++..++..--+
T Consensus 1 m~~~~~g~r~~~~~~s~~~~~~~-----~~~~~~~rR~~~lTvKYdRkeL-qkRL~vE~WId~qL~eLy~~~e~~~p~EI 74 (144)
T PF05361_consen 1 MAANRVGRRRTSSTHSPSRAHFP-----DSGEPKSRRQGRLTVKYDRKEL-QKRLDVEEWIDEQLQELYDCQEDEMPEEI 74 (144)
T ss_dssp ----------------------------SSSSSS-S-SSSSSSSS-SSSS-CHHHHHHHHHHHHHHHCSSSSSTTS-SSS
T ss_pred CcchhhcceeccCCCCcccccCC-----CCccccccccceeEEEECHHHH-HHHHHHHHHHHHHHHHHhcCCCCCCCCcc
Confidence 66777888888777777544433 4567777888888889999998 558888764 356679999999988889
Q ss_pred CHHHHHHHhchh--HHHHHHHHHhhcCCCC
Q 029662 154 DAKQIAEKFRLD--VLQVQAILQCLSLPPE 181 (190)
Q Consensus 154 ~v~~iAeKFrv~--v~~vq~Ilqf~SlP~e 181 (190)
||++|=+-=.-+ ..-+|.||+=.+-|.|
T Consensus 75 DIDeLLDl~sdeeR~~~LqelL~~C~~ptE 104 (144)
T PF05361_consen 75 DIDELLDLESDEERRRKLQELLQDCPKPTE 104 (144)
T ss_dssp HHHHHHCTSSTTHHHHHHHHHHTTCSSTTH
T ss_pred cHHHHhcCCchHHHHHHHHHHHhhcCCCHH
Confidence 999996533222 2337778875555543
No 258
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=50.15 E-value=16 Score=24.01 Aligned_cols=24 Identities=21% Similarity=0.300 Sum_probs=21.2
Q ss_pred CCHHHHHHHhchhHHHHHHHHHhh
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
.+..+||..|+|..+.|.+|+..+
T Consensus 20 ~~~~~La~~FgIs~stvsri~~~~ 43 (53)
T PF13613_consen 20 LTFQDLAYRFGISQSTVSRIFHEW 43 (53)
T ss_pred CcHhHHhhheeecHHHHHHHHHHH
Confidence 567899999999999999998764
No 259
>PF09681 Phage_rep_org_N: N-terminal phage replisome organiser (Phage_rep_org_N); InterPro: IPR010056 This entry is represented by the N-terminal domain of Bacteriophage A500, Gp45. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. The proteins in this entry contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The low-complexity region is adjacent to this N-terminal domain.
Probab=50.13 E-value=31 Score=27.08 Aligned_cols=29 Identities=28% Similarity=0.275 Sum_probs=26.4
Q ss_pred CCCCCCHHHHHHHhchhHHHHHHHHHhhc
Q 029662 149 HNGPLDAKQIAEKFRLDVLQVQAILQCLS 177 (190)
Q Consensus 149 h~gPM~v~~iAeKFrv~v~~vq~Ilqf~S 177 (190)
-+-|.+.+.||..|+.++..|+..|+++.
T Consensus 50 ~~ipy~~e~LA~~~~~~~~~V~~AL~~f~ 78 (121)
T PF09681_consen 50 GNIPYTAEMLALEFDRPVDTVRLALAVFQ 78 (121)
T ss_pred CCCCCcHHHHHHHHCCCHHHHHHHHHHHH
Confidence 45699999999999999999999999875
No 260
>PRK11050 manganese transport regulator MntR; Provisional
Probab=49.95 E-value=20 Score=28.08 Aligned_cols=27 Identities=22% Similarity=0.321 Sum_probs=24.2
Q ss_pred CCCCHHHHHHHhchhHHHHHHHHHhhc
Q 029662 151 GPLDAKQIAEKFRLDVLQVQAILQCLS 177 (190)
Q Consensus 151 gPM~v~~iAeKFrv~v~~vq~Ilqf~S 177 (190)
|++.+.+||+.|+|..+-|.++|+.|.
T Consensus 50 ~~~t~~eLA~~l~is~stVsr~l~~Le 76 (152)
T PRK11050 50 GEARQVDIAARLGVSQPTVAKMLKRLA 76 (152)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 679999999999999999999987664
No 261
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=49.80 E-value=41 Score=24.64 Aligned_cols=21 Identities=24% Similarity=0.237 Sum_probs=18.6
Q ss_pred CCHHHHHHHhchhHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Il 173 (190)
|+.+|||+.+++....|..-+
T Consensus 128 ~~~~eIA~~l~is~~tv~~~l 148 (159)
T TIGR02989 128 VSLTALAEQLGRTVNAVYKAL 148 (159)
T ss_pred CCHHHHHHHhCCCHHHHHHHH
Confidence 899999999999999887654
No 262
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=49.48 E-value=34 Score=28.14 Aligned_cols=33 Identities=15% Similarity=0.226 Sum_probs=25.1
Q ss_pred HHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHH
Q 029662 135 LRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 135 l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Il 173 (190)
-|+||.|+- -.-|+.+|||+.++|....|...+
T Consensus 206 ~r~vl~l~~------~~~~s~~EIA~~lgis~~tV~~~~ 238 (251)
T PRK07670 206 EQLVISLFY------KEELTLTEIGQVLNLSTSRISQIH 238 (251)
T ss_pred HHHHHHHHH------hcCCCHHHHHHHHCcCHHHHHHHH
Confidence 466777642 234889999999999999887654
No 263
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=49.32 E-value=38 Score=28.59 Aligned_cols=37 Identities=19% Similarity=0.245 Sum_probs=26.1
Q ss_pred HHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 136 RRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 136 ~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
|+||.|+-|-.. -..|+.+|||+.+++...-|..++.
T Consensus 228 R~Vl~l~ygL~~--~e~~s~~EIA~~Lgis~~tVk~~l~ 264 (285)
T TIGR02394 228 REVLARRFGLLG--YEPATLEEVAAEVGLTRERVRQIQV 264 (285)
T ss_pred HHHHHHHhCCCC--CCCccHHHHHHHHCCCHHHHHHHHH
Confidence 567776543221 1228999999999999998887653
No 264
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=49.30 E-value=44 Score=25.37 Aligned_cols=41 Identities=20% Similarity=0.241 Sum_probs=29.7
Q ss_pred HHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 132 VAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 132 va~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
+.+.-+.|..+. ..+|++.+.+||+.++|...-|-++|+-|
T Consensus 6 ~edyL~~I~~l~----~~~~~~~~~ela~~l~vs~~svs~~l~~L 46 (142)
T PRK03902 6 MEDYIEQIYLLI----EEKGYARVSDIAEALSVHPSSVTKMVQKL 46 (142)
T ss_pred HHHHHHHHHHHH----hcCCCcCHHHHHHHhCCChhHHHHHHHHH
Confidence 344444444332 35578899999999999999998888755
No 265
>cd05025 S-100A1 S-100A1: S-100A1 domain found in proteins similar to S100A1. S100A1 is a calcium-binding protein belonging to a large S100 vertebrate-specific protein family within the EF-hand superfamily of calcium-binding proteins. Note that the S-100 hierarchy, to which this S-100A1 group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. As is the case with many other members of S100 protein family, S100A1 is implicated in intracellular and extracellular regulatory activities, including interaction with myosin-associated twitchin kinase, actin-capping protein CapZ, sinapsin I, and tubulin. Structural data suggests that S100A1 proteins exist within cells as antiparallel homodimers, while heterodimers with S100A4 and S100B also has been reported. Upon binding calcium S100A1 changes conformation to expose a hydrophobic cleft which is the interaction site of S100A1 with its more that 20 known target proteins.
Probab=49.10 E-value=68 Score=22.52 Aligned_cols=49 Identities=16% Similarity=0.272 Sum_probs=34.7
Q ss_pred cHHHHHHHHHHhhccCCCCCC-CCCHHHHHHHhch----------hHHHHHHHHHhhcCCCC
Q 029662 131 NVAQLRRIMLLHQGKADDHNG-PLDAKQIAEKFRL----------DVLQVQAILQCLSLPPE 181 (190)
Q Consensus 131 Nva~l~~ii~L~QGk~~~h~g-PM~v~~iAeKFrv----------~v~~vq~Ilqf~SlP~e 181 (190)
.+..|++++.+|. ..+++| -++.++|..-++- .-..|+.|++.+....+
T Consensus 7 ~~~~l~~~F~~fD--d~dg~G~~Is~~El~~~l~~~lg~~~~~~~s~~~v~~i~~~~D~d~~ 66 (92)
T cd05025 7 AMETLINVFHAHS--GKEGDKYKLSKKELKDLLQTELSDFLDAQKDADAVDKIMKELDENGD 66 (92)
T ss_pred HHHHHHHHHHHHh--cccCCCCeECHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHCCCCC
Confidence 3566777777775 245688 5999999988863 34668899888755443
No 266
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active.
Probab=49.08 E-value=27 Score=28.40 Aligned_cols=23 Identities=9% Similarity=0.177 Sum_probs=19.9
Q ss_pred CCCHHHHHHHhchhHHHHHHHHH
Q 029662 152 PLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 152 PM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
-|+.+|||+..++...-|...+.
T Consensus 198 g~s~~EIA~~Lgis~~tV~~~l~ 220 (234)
T TIGR02835 198 EKTQKEVADMLGISQSYISRLEK 220 (234)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHH
Confidence 48999999999999998877653
No 267
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=49.07 E-value=31 Score=28.97 Aligned_cols=21 Identities=14% Similarity=0.265 Sum_probs=18.5
Q ss_pred CCHHHHHHHhchhHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Il 173 (190)
|+.+|||+.+++.+.-|..-|
T Consensus 178 ~S~~EIA~~Lgis~~TVk~rl 198 (244)
T TIGR03001 178 LSMDRIGAMYQVHRSTVSRWV 198 (244)
T ss_pred CCHHHHHHHHCcCHHHHHHHH
Confidence 889999999999999887654
No 268
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=49.03 E-value=25 Score=33.41 Aligned_cols=36 Identities=11% Similarity=0.265 Sum_probs=28.9
Q ss_pred HHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHH
Q 029662 136 RRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 136 ~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Il 173 (190)
+.||.|+=|.- ...+++.++||+.|+|.-..|.+|-
T Consensus 562 ~~Vl~~r~g~~--~~~~~tl~ei~~~lgvs~eRVrQie 597 (619)
T PRK05658 562 AKVLRMRFGID--MNTDHTLEEVGKQFDVTRERIRQIE 597 (619)
T ss_pred HHHHHHhcCCC--CCCCccHHHHHHHhCCCHHHHHHHH
Confidence 56888877763 2467999999999999988887764
No 269
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=48.85 E-value=28 Score=27.06 Aligned_cols=33 Identities=24% Similarity=0.300 Sum_probs=22.0
Q ss_pred HHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 136 RRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 136 ~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
++++.||--- -+|+.|||+.++|.-.-|...++
T Consensus 23 ~~~l~lyy~e------DlSlsEIAe~~~iSRqaV~d~ik 55 (101)
T PF04297_consen 23 REILELYYEE------DLSLSEIAEELGISRQAVYDSIK 55 (101)
T ss_dssp HHHHHHHCTS---------HHHHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHHHcc------CCCHHHHHHHHCCCHHHHHHHHH
Confidence 5667777443 49999999999998877766554
No 270
>PF09171 DUF1886: Domain of unknown function (DUF1886); InterPro: IPR015254 This entry represents a set of known and suspected archaeal N-glycosylase/DNA lyases. These DNA repair enzymes are part of the base excision repair (BER) pathway; they protect from oxidative damage by removing the major product of DNA oxidation, 8-oxoguanine (GO), from single- and double-stranded DNA substrates [].Cleavage of the N-glycosidic bond between the aberrant base and the sugar-phosphate backbone generates an apurinic (AP) site. Subsequently, the phosphodiester bond 3' from the AP site is cleaved by an elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate. The protein contains two alpha-helical subdomains, with the 8-oxoguanine binding site located in a cleft at their interface. A helix-hairpin-helix (HhH) structural motif and a Gly/Pro-rich sequence followed by a conserved Asp (HhH-GPD motif) are present [].; GO: 0003906 DNA-(apurinic or apyrimidinic site) lyase activity, 0016799 hydrolase activity, hydrolyzing N-glycosyl compounds; PDB: 1XQP_A 1XQO_A 1XG7_A.
Probab=47.85 E-value=7.4 Score=34.29 Aligned_cols=13 Identities=62% Similarity=0.994 Sum_probs=11.1
Q ss_pred cccccCchHHHHH
Q 029662 65 VLEERDPQYDAML 77 (190)
Q Consensus 65 vl~erDp~ydaMl 77 (190)
.+||+||||+||-
T Consensus 15 ~iEe~DpQy~av~ 27 (246)
T PF09171_consen 15 YIEERDPQYKAVK 27 (246)
T ss_dssp HHHCCSHHHHHHH
T ss_pred HHHHhChHHHHHH
Confidence 4789999999974
No 271
>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=47.79 E-value=13 Score=27.07 Aligned_cols=28 Identities=32% Similarity=0.426 Sum_probs=20.4
Q ss_pred CCCCCHHHHHHHhchhHHHHHHHHHhhc
Q 029662 150 NGPLDAKQIAEKFRLDVLQVQAILQCLS 177 (190)
Q Consensus 150 ~gPM~v~~iAeKFrv~v~~vq~Ilqf~S 177 (190)
+|-|+=++||++.+++...|.+||.-|.
T Consensus 25 ~~~l~de~la~~~~l~~~~vRkiL~~L~ 52 (105)
T PF02002_consen 25 KGELTDEDLAKKLGLKPKEVRKILYKLY 52 (105)
T ss_dssp H--B-HHHHHHTT-S-HHHHHHHHHHHH
T ss_pred cCCcCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 3568889999999999999999998763
No 272
>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=46.74 E-value=14 Score=28.84 Aligned_cols=27 Identities=11% Similarity=0.228 Sum_probs=23.9
Q ss_pred CCCCHHHHHHHhchhHHHHHHHHHhhc
Q 029662 151 GPLDAKQIAEKFRLDVLQVQAILQCLS 177 (190)
Q Consensus 151 gPM~v~~iAeKFrv~v~~vq~Ilqf~S 177 (190)
.-+++-.|||||+|..++..++|+.|.
T Consensus 58 K~ITp~~lserlkI~~SlAr~~Lr~L~ 84 (105)
T PF03297_consen 58 KLITPSVLSERLKINGSLARKALRELE 84 (105)
T ss_dssp SCECHHHHHHHHCCSCHHHHHHHHHHH
T ss_pred cEeeHHHHHHhHhhHHHHHHHHHHHHH
Confidence 348899999999999999999999873
No 273
>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=46.73 E-value=88 Score=21.59 Aligned_cols=41 Identities=15% Similarity=0.039 Sum_probs=31.8
Q ss_pred HHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHH
Q 029662 133 AQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 133 a~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Il 173 (190)
.|..-+..-|..---|.+--.++.+||+.|+|.-+-+...|
T Consensus 4 ~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~L 44 (53)
T PF04967_consen 4 RQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHL 44 (53)
T ss_pred HHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHH
Confidence 45555566676667778888999999999999988776655
No 274
>PF13730 HTH_36: Helix-turn-helix domain
Probab=46.28 E-value=75 Score=20.13 Aligned_cols=23 Identities=17% Similarity=0.255 Sum_probs=21.4
Q ss_pred CHHHHHHHhchhHHHHHHHHHhh
Q 029662 154 DAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 154 ~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
+.+.||+.+++...-|++.++-|
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L 49 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKEL 49 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHH
Confidence 99999999999999999998765
No 275
>PRK09483 response regulator; Provisional
Probab=45.75 E-value=53 Score=24.36 Aligned_cols=38 Identities=18% Similarity=0.394 Sum_probs=27.9
Q ss_pred CcccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHH
Q 029662 128 GTLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 128 GTLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Il 173 (190)
..|.-.+.+-+-++.+| ++.+|||+++.+...-|...+
T Consensus 147 ~~Lt~rE~~vl~~~~~G--------~~~~~Ia~~l~is~~TV~~~~ 184 (217)
T PRK09483 147 ASLSERELQIMLMITKG--------QKVNEISEQLNLSPKTVNSYR 184 (217)
T ss_pred cccCHHHHHHHHHHHCC--------CCHHHHHHHhCCCHHHHHHHH
Confidence 34777777666666666 568899999999888776544
No 276
>PF01257 2Fe-2S_thioredx: Thioredoxin-like [2Fe-2S] ferredoxin; InterPro: IPR002023 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. Among the many polypeptide subunits that make up complex I, there is one with a molecular weight of 24 kDa (in mammals), which is a component of the iron-sulphur (IP) fragment of the enzyme. It seems to bind a 2Fe-2S iron-sulphur cluster. The 24 kDa subunit is nuclear encoded, as a precursor form with a transit peptide in mammals and in Neurospora crassa. There is a highly conserved region located in the central section of this subunit that contains two conserved cysteines, that are probably involved in the binding of the 2Fe-2S centre. The 24 kDa subunit is highly similar to [, ]: Subunit E of Escherichia coli NADH-ubiquinone oxidoreductase (gene nuoE) Subunit NQO2 of Paracoccus denitrificans NADH-ubiquinone oxidoreductase ; GO: 0016491 oxidoreductase activity, 0051287 NAD binding, 0055114 oxidation-reduction process; PDB: 1M2D_A 1M2A_B 1F37_B 1M2B_B 2FUG_B 3M9S_B 3IAM_B 3IAS_K 2YBB_2 3I9V_B ....
Probab=45.57 E-value=23 Score=27.66 Aligned_cols=27 Identities=19% Similarity=0.204 Sum_probs=22.6
Q ss_pred CHHHHHHHhchhHHHHHHHHHhhcCCC
Q 029662 154 DAKQIAEKFRLDVLQVQAILQCLSLPP 180 (190)
Q Consensus 154 ~v~~iAeKFrv~v~~vq~Ilqf~SlP~ 180 (190)
.+++||+.++|..+.|..++.|-+.=.
T Consensus 33 ~~~~iA~~l~i~~~~v~~v~tFY~~f~ 59 (145)
T PF01257_consen 33 ALEEIAEALGIPPAEVYGVATFYSMFR 59 (145)
T ss_dssp HHHHHHHHHTS-HHHHHHHHHHSSSS-
T ss_pred HHHHHHHHHCCCHHHHHHHHHHHHHcc
Confidence 478999999999999999999987643
No 277
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=45.47 E-value=79 Score=23.03 Aligned_cols=47 Identities=21% Similarity=0.275 Sum_probs=34.3
Q ss_pred cccHHHHHHHHHHhh---ccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 129 TLNVAQLRRIMLLHQ---GKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 129 TLNva~l~~ii~L~Q---Gk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
.|+..+.+-++.|.+ |.. ....+++-.|||+..+++-.-|.++|.-|
T Consensus 22 ~l~~r~~~vLl~L~~~~~G~~-~~~~~is~~eLa~~~g~sr~tVsr~L~~L 71 (95)
T TIGR01610 22 DLSGREFRVLLAIIRLTYGWN-KKQDRVTATVIAELTGLSRTHVSDAIKSL 71 (95)
T ss_pred CCCHHHHHHHHHHHHHHhCcc-ccCCccCHHHHHHHHCcCHHHHHHHHHHH
Confidence 355556665555542 533 36678999999999999999999988654
No 278
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=45.37 E-value=51 Score=26.72 Aligned_cols=38 Identities=21% Similarity=0.239 Sum_probs=26.6
Q ss_pred cccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 129 TLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 129 TLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
.|+-.| ++||+|+. .-|+.+|||+.+++..+.|..+.+
T Consensus 6 ~Lt~rq-reVL~lr~-------~GlTq~EIAe~LGiS~~tVs~ie~ 43 (141)
T PRK03975 6 FLTERQ-IEVLRLRE-------RGLTQQEIADILGTSRANVSSIEK 43 (141)
T ss_pred CCCHHH-HHHHHHHH-------cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 344444 45566652 228899999999999988877764
No 279
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=45.27 E-value=25 Score=27.88 Aligned_cols=44 Identities=9% Similarity=0.140 Sum_probs=29.8
Q ss_pred HHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhhcC
Q 029662 134 QLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCLSL 178 (190)
Q Consensus 134 ~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~Sl 178 (190)
.|-.||++-|-. -++=-+=.+.+||+.++|..+.|..++-|-+.
T Consensus 23 ~ll~~L~~vQ~~-~g~ip~~~~~~iA~~l~v~~~~v~~v~tFY~~ 66 (154)
T PRK07539 23 AVIPALKIVQEQ-RGWVPDEAIEAVADYLGMPAIDVEEVATFYSM 66 (154)
T ss_pred HHHHHHHHHHHH-hCCCCHHHHHHHHHHhCcCHHHHHHHHHHHhh
Confidence 344444444422 12222334789999999999999999999875
No 280
>PF02186 TFIIE_beta: TFIIE beta subunit core domain; InterPro: IPR003166 Initiation of eukaryotic mRNA transcription requires melting of promoter DNA with the help of the general transcription factors TFIIE and TFIIH. In higher eukaryotes, the general transcription factor TFIIE consists of two subunits: the large alpha subunit (IPR002853 from INTERPRO) and the small beta (IPR003166 from INTERPRO). TFIIE beta has been found to bind to the region where the promoter starts to open to be single-stranded upon transcription initiation by RNA polymerase II. The approximately 120-residue central core domain of TFIIE beta plays a role in double-stranded DNA binding of TFIIE []. The TFIIE beta central core DNA-binding domain consists of three helices with a beta hairpin at the C terminus, resembling the winged helix proteins. It shows a novel double-stranded DNA-binding activity where the DNA-binding surface locates on the opposite side to the previously reported winged helix motif by forming a positively charged furrow []. This entry represents the beta subunit of the transcription factor TFIIE.; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005673 transcription factor TFIIE complex; PDB: 1D8K_A 1D8J_A.
Probab=45.21 E-value=28 Score=24.76 Aligned_cols=40 Identities=23% Similarity=0.365 Sum_probs=26.4
Q ss_pred HHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhhc
Q 029662 132 VAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCLS 177 (190)
Q Consensus 132 va~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~S 177 (190)
..||..|+..-+.+ +.|.+++||.+...+++. +.++++|-
T Consensus 4 ~tql~~~VeymK~r----~~Plt~~eI~d~l~~d~~--~~~~~~Lk 43 (65)
T PF02186_consen 4 FTQLAKAVEYMKKR----DHPLTLEEILDYLSLDIG--KKLKQWLK 43 (65)
T ss_dssp HHHHHHHHHHHHHH-----S-B-HHHHHHHHTSSS---HHHHHHHH
T ss_pred hhHHHHHHHHHHhc----CCCcCHHHHHHHHcCCCC--HHHHHHHH
Confidence 45677777766665 789999999999998876 35566553
No 281
>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=44.77 E-value=47 Score=29.90 Aligned_cols=48 Identities=23% Similarity=0.270 Sum_probs=37.1
Q ss_pred CCCCcccHH---HHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 125 SPPGTLNVA---QLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 125 ~p~GTLNva---~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
++=+||... -+.+|+...||. +|.++-.+||++|+|..+.|.+-++-|
T Consensus 172 ~Ai~tLSySEleAv~~IL~~L~~~----egrlse~eLAerlGVSRs~ireAlrkL 222 (251)
T TIGR02787 172 MAINTLSYSELEAVEHIFEELDGN----EGLLVASKIADRVGITRSVIVNALRKL 222 (251)
T ss_pred HHHHhccHhHHHHHHHHHHHhccc----cccccHHHHHHHHCCCHHHHHHHHHHH
Confidence 455677655 567888888774 577999999999999999887766543
No 282
>PF03979 Sigma70_r1_1: Sigma-70 factor, region 1.1; InterPro: IPR007127 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 [, ]. This entry represents Region 1.1 which modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase [, ]. Region 1.1 is also involved in promoter binding.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2K6X_A.
Probab=44.50 E-value=28 Score=24.94 Aligned_cols=43 Identities=23% Similarity=0.371 Sum_probs=30.2
Q ss_pred ccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhc---hhHHHHHHHHHhhc
Q 029662 130 LNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFR---LDVLQVQAILQCLS 177 (190)
Q Consensus 130 LNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFr---v~v~~vq~Ilqf~S 177 (190)
++...|+.+|.+ ||. .|-++.++|.+.|- ++..++..|+++|.
T Consensus 4 ~~~~~i~~Li~~--gK~---~G~lT~~eI~~~L~~~~~~~e~id~i~~~L~ 49 (82)
T PF03979_consen 4 QYEEAIKKLIEK--GKK---KGYLTYDEINDALPEDDLDPEQIDEIYDTLE 49 (82)
T ss_dssp HHHHHHHHHHHH--HHH---HSS-BHHHHHHH-S-S---HHHHHHHHHHHH
T ss_pred hhHHHHHHHHHH--Hhh---cCcCCHHHHHHHcCccCCCHHHHHHHHHHHH
Confidence 466788885554 775 45599999999876 88999999999874
No 283
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=43.86 E-value=55 Score=27.21 Aligned_cols=42 Identities=14% Similarity=0.039 Sum_probs=33.9
Q ss_pred cccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 129 TLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 129 TLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
.|+..|..=+..|++. ++++.++||+.+.++.+-|-++|+-|
T Consensus 42 gLt~~q~~iL~~L~~~------~~itq~eLa~~l~l~~sTvtr~l~rL 83 (185)
T PRK13777 42 DLNINEHHILWIAYHL------KGASISEIAKFGVMHVSTAFNFSKKL 83 (185)
T ss_pred CCCHHHHHHHHHHHhC------CCcCHHHHHHHHCCCHhhHHHHHHHH
Confidence 4888888877777753 35999999999999988888877644
No 284
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=43.65 E-value=29 Score=22.90 Aligned_cols=35 Identities=26% Similarity=0.391 Sum_probs=18.9
Q ss_pred HHHHHHhhccCCCCCCCCCHHHH----HHHhchhHHHH-HHHHHhhc
Q 029662 136 RRIMLLHQGKADDHNGPLDAKQI----AEKFRLDVLQV-QAILQCLS 177 (190)
Q Consensus 136 ~~ii~L~QGk~~~h~gPM~v~~i----AeKFrv~v~~v-q~Ilqf~S 177 (190)
..|..+.+| +.++.+| +++|.++...+ +.|.+||.
T Consensus 20 ~~Iw~~~~g-------~~t~~ei~~~l~~~y~~~~~~~~~dv~~fl~ 59 (68)
T PF05402_consen 20 AFIWELLDG-------PRTVEEIVDALAEEYDVDPEEAEEDVEEFLE 59 (68)
T ss_dssp HHHHHH--S-------SS-HHHHHHHHHHHTT--HHHHHHHHHHHHH
T ss_pred HHHHHHccC-------CCCHHHHHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 346666654 4577665 67899998855 45666763
No 285
>PRK14584 hmsS hemin storage system protein; Provisional
Probab=43.52 E-value=31 Score=28.82 Aligned_cols=33 Identities=21% Similarity=0.285 Sum_probs=28.6
Q ss_pred hhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 142 HQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 142 ~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
|+|..-.+.-+.|.+|+|+-|+|+..+++.+-+
T Consensus 88 F~~eRR~~~~~l~~dElA~sF~l~~e~i~qLr~ 120 (153)
T PRK14584 88 FQVERRGHRPDLDDDELASSFALSPELIAQLKS 120 (153)
T ss_pred hcccccCCCCCCChHHHHHHcCCCHHHHHHHHh
Confidence 677777788889999999999999999988755
No 286
>PHA02591 hypothetical protein; Provisional
Probab=43.48 E-value=25 Score=27.20 Aligned_cols=22 Identities=23% Similarity=0.374 Sum_probs=20.3
Q ss_pred CCHHHHHHHhchhHHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilq 174 (190)
|++.|||+..+|++..|.++|.
T Consensus 60 lSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 60 FTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred CCHHHHHHHhCCCHHHHHHHHh
Confidence 8899999999999999998774
No 287
>PRK13698 plasmid-partitioning protein; Provisional
Probab=43.45 E-value=20 Score=32.90 Aligned_cols=29 Identities=10% Similarity=0.147 Sum_probs=27.7
Q ss_pred CCHHHHHHHhchhHHHHHHHHHhhcCCCC
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQCLSLPPE 181 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilqf~SlP~e 181 (190)
++-++||+++++.-+.|-+.|+.++||++
T Consensus 177 ~tQeeLA~~lG~SRs~Vsn~Lrla~LP~~ 205 (323)
T PRK13698 177 GNISALADAENISRKIITRCINTAKLPKS 205 (323)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHcCCHH
Confidence 89999999999999999999999999875
No 288
>PRK12373 NADH dehydrogenase subunit E; Provisional
Probab=43.13 E-value=33 Score=32.40 Aligned_cols=50 Identities=12% Similarity=0.181 Sum_probs=38.5
Q ss_pred cHHHHHHHHHHhh--ccCC----------CCCCCCC---HHHHHHHhchhHHHHHHHHHhhcCCC
Q 029662 131 NVAQLRRIMLLHQ--GKAD----------DHNGPLD---AKQIAEKFRLDVLQVQAILQCLSLPP 180 (190)
Q Consensus 131 Nva~l~~ii~L~Q--Gk~~----------~h~gPM~---v~~iAeKFrv~v~~vq~Ilqf~SlP~ 180 (190)
|.+.|.+||.-|. .+.+ ++.|-++ +.+||+.++|....|..|+-|.++=.
T Consensus 19 ~~~~i~~ii~~yp~~~~~salIplL~~~Qe~~GyIp~~ai~~VAe~Lgvp~~~V~eVATFYtmF~ 83 (400)
T PRK12373 19 NAAWAEKQITKYPEGRQASAVIPLLMRAQEQEGWVTRAAIEKVADMLDMAYIRVLEVATFYTQFQ 83 (400)
T ss_pred HHHHHHHHHHHCCCccCHHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHHHHHHHhhccc
Confidence 6777888888884 3333 4667776 57799999999999999999987643
No 289
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=42.95 E-value=47 Score=22.00 Aligned_cols=28 Identities=11% Similarity=0.070 Sum_probs=22.7
Q ss_pred CCHHHHHHHhchhHHHHHHHHHhhcCCC
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQCLSLPP 180 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilqf~SlP~ 180 (190)
|++.|+|+.++|....|...-+-.-|+.
T Consensus 1 ~~i~evA~~~gvs~~tlR~~~~~g~l~~ 28 (67)
T cd04764 1 YTIKEVSEIIGVKPHTLRYYEKEFNLYI 28 (67)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHhcCCCC
Confidence 6789999999999999998876433543
No 290
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=42.45 E-value=26 Score=24.24 Aligned_cols=23 Identities=26% Similarity=0.410 Sum_probs=20.6
Q ss_pred HHHHHHHhchhHHHHHHHHHhhc
Q 029662 155 AKQIAEKFRLDVLQVQAILQCLS 177 (190)
Q Consensus 155 v~~iAeKFrv~v~~vq~Ilqf~S 177 (190)
+.+||+.|+|+-+-|.++|+.|-
T Consensus 2 ~~ela~~l~is~stvs~~l~~L~ 24 (96)
T smart00529 2 TSEIAERLNVSPPTVTQMLKKLE 24 (96)
T ss_pred HHHHHHHhCCChHHHHHHHHHHH
Confidence 57999999999999999998763
No 291
>PF11268 DUF3071: Protein of unknown function (DUF3071); InterPro: IPR021421 Some members in this family of proteins are annotated as DNA-binding proteins however this cannot be confirmed. Currently no function is known.
Probab=41.63 E-value=56 Score=27.32 Aligned_cols=33 Identities=21% Similarity=0.317 Sum_probs=29.3
Q ss_pred cccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHH
Q 029662 129 TLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQA 171 (190)
Q Consensus 129 TLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~ 171 (190)
+|..-+||.-|+- | +++.|||+.++++++.|++
T Consensus 56 ~L~PReIQarIRa--G--------as~eeVA~~~G~~~~rV~r 88 (170)
T PF11268_consen 56 SLRPREIQARIRA--G--------ASAEEVAEEAGVPVERVRR 88 (170)
T ss_pred CCCHHHHHHHHHC--C--------CCHHHHHHHhCCCHHHhhh
Confidence 8999999998872 3 8899999999999999986
No 292
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=41.36 E-value=36 Score=29.33 Aligned_cols=33 Identities=21% Similarity=0.266 Sum_probs=24.6
Q ss_pred HHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 136 RRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 136 ~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
|+++.|+.-.- |+.+|||+.+++...-|...++
T Consensus 124 R~vf~L~~~~g------~s~~EIA~~Lgis~~tVr~~l~ 156 (290)
T PRK09635 124 RVVFVLHEIFG------LPYQQIATTIGSQASTCRQLAH 156 (290)
T ss_pred HHHhhHHHHhC------CCHHHHHHHHCcCHHHHHHHHH
Confidence 45556653333 8999999999999988876654
No 293
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=41.16 E-value=37 Score=28.64 Aligned_cols=40 Identities=8% Similarity=0.099 Sum_probs=29.6
Q ss_pred HHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHh
Q 029662 133 AQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQC 175 (190)
Q Consensus 133 a~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf 175 (190)
..|++++.+.+. +...++++++||+.+++....++++++-
T Consensus 218 ~~~~~~~~~i~~---~~~~~~sl~~lA~~~~~S~~~l~r~fk~ 257 (322)
T PRK09393 218 DRLGPLIDWMRA---HLAEPHTVASLAARAAMSPRTFLRRFEA 257 (322)
T ss_pred HHHHHHHHHHHh---ccCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 345555554443 3456799999999999999999998763
No 294
>PF11035 SnAPC_2_like: Small nuclear RNA activating complex subunit 2-like; InterPro: IPR021281 This family of proteins is SnAPC subunit 2-like. SnAPC allows the transcription of human small nuclear RNA genes to occur by recognition of the proximal sequence element [].
Probab=40.80 E-value=1.1e+02 Score=28.96 Aligned_cols=60 Identities=20% Similarity=0.317 Sum_probs=45.9
Q ss_pred CCCCCCCCCCCCCcccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhch-hHHHHHHHHHhhc
Q 029662 116 VSSRYEEKPSPPGTLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRL-DVLQVQAILQCLS 177 (190)
Q Consensus 116 ~sg~~eer~~p~GTLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv-~v~~vq~Ilqf~S 177 (190)
.+.||..-...+-..+.-+-+++++|.|.-.. .--.|+.+||.+.+= ....|+++||+|-
T Consensus 10 ~PaRy~g~~~gp~~Ws~rEkr~Llr~Lqar~g--~~epd~ael~~~l~~Rs~aEI~~fl~~LK 70 (344)
T PF11035_consen 10 APARYLGEVTGPAAWSAREKRQLLRLLQARRG--QPEPDAAELAKELPGRSEAEIRDFLQQLK 70 (344)
T ss_pred CCccccCCCCCcccCcHHHHHHHHHHHHHhcC--CCCcCHHHHHhhccCcCHHHHHHHHHHHH
Confidence 55788776666667788899999999997543 345789999987655 6778888888874
No 295
>PRK15435 bifunctional DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase; Provisional
Probab=40.61 E-value=51 Score=29.63 Aligned_cols=40 Identities=8% Similarity=0.291 Sum_probs=30.9
Q ss_pred ccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 130 LNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 130 LNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
-....|.+++.+-+- +.++++++||+.+++....++++.+
T Consensus 82 ~~~~~i~~a~~~I~~-----~~~lsl~eLA~~lG~S~~~L~R~Fk 121 (353)
T PRK15435 82 HRLDKITHACRLLEQ-----ETPVTLEALADQVAMSPFHLHRLFK 121 (353)
T ss_pred hHHHHHHHHHHHHHh-----CCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 345567777776533 2579999999999999999998875
No 296
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=40.33 E-value=55 Score=24.97 Aligned_cols=23 Identities=22% Similarity=0.195 Sum_probs=19.3
Q ss_pred CCCHHHHHHHhchhHHHHHHHHH
Q 029662 152 PLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 152 PM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
-++.+|||+.+++.++.|..-+.
T Consensus 165 ~~s~~eIA~~l~~s~~tV~~~l~ 187 (198)
T TIGR02859 165 GKSYQEIACDLNRHVKSIDNALQ 187 (198)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHH
Confidence 48999999999999998875543
No 297
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=39.98 E-value=28 Score=26.68 Aligned_cols=25 Identities=20% Similarity=0.226 Sum_probs=22.9
Q ss_pred CCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 152 PLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 152 PM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
.++.++||..+++....|++||+--
T Consensus 23 ~ls~~~ia~dL~~s~~~le~vL~l~ 47 (89)
T PF10078_consen 23 GLSLEQIAADLGTSPEHLEQVLNLK 47 (89)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHcCC
Confidence 4899999999999999999999754
No 298
>PRK14585 pgaD putative PGA biosynthesis protein; Provisional
Probab=39.54 E-value=34 Score=28.38 Aligned_cols=34 Identities=12% Similarity=0.077 Sum_probs=29.6
Q ss_pred hhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHh
Q 029662 142 HQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQC 175 (190)
Q Consensus 142 ~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf 175 (190)
|||+.-.|.-..+.+|+|+-|+++-..++.+-+.
T Consensus 79 F~~~~R~~~~~~~~~eLA~Sf~is~el~~qL~~~ 112 (137)
T PRK14585 79 FQKQQHHAAYQYTPQEYAESLAIPDELYQQLQKS 112 (137)
T ss_pred hhhhccCCCCCCChHHHHHHcCCCHHHHHHHhcC
Confidence 7888877778899999999999999999887653
No 299
>COG5566 Uncharacterized conserved protein [Function unknown]
Probab=39.31 E-value=51 Score=27.50 Aligned_cols=79 Identities=16% Similarity=0.174 Sum_probs=55.3
Q ss_pred HHHHhhcccccCCCCccccchhhhhhhhcCCCCCCCCCCCCCCCCCCCCCCCCcccHHHHHHHHHHhhccCCCCCCCCCH
Q 029662 76 MLNQMLGRVKTKAGGKAEMGEAAVVERQTRPLPKLRNTTPVSSRYEEKPSPPGTLNVAQLRRIMLLHQGKADDHNGPLDA 155 (190)
Q Consensus 76 Ml~qmvGrI~tkpGGk~Emgea~vv~~ynRP~Pk~R~t~~~sg~~eer~~p~GTLNva~l~~ii~L~QGk~~~h~gPM~v 155 (190)
|+...--.|.-+-|+++..--+.+..+|-- |+. =-+|.|+-=.+.+|.+. +| ++|+ -|++
T Consensus 46 ~~ael~~a~ie~~gk~~alk~v~~l~~y~G------------Grs--fYlP~G~s~r~t~Rn~~-if----sd~d-G~n~ 105 (137)
T COG5566 46 FLAELEDAGIEDNGKPLALKLVFKLMEYGG------------GRS--FYLPKGDSIRATLRNKQ-IF----SDFD-GSNY 105 (137)
T ss_pred HHHHHHHHhhhhccCchHHHHHHHHHHHcC------------Cee--EEeeCchHHHHHHHHHH-HH----HhcC-CccH
Confidence 333333445666676776666666666631 222 35889998888888764 33 3566 4899
Q ss_pred HHHHHHhchhHHHHHHHHH
Q 029662 156 KQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 156 ~~iAeKFrv~v~~vq~Ilq 174 (190)
-|+|.|||+.-..|-+|+.
T Consensus 106 ~eLaKkYrlS~~~Iy~VIr 124 (137)
T COG5566 106 VELAKKYRLSENHIYRVIR 124 (137)
T ss_pred HHHHHHhcccHHHHHHHHH
Confidence 9999999999999999886
No 300
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=39.29 E-value=33 Score=31.75 Aligned_cols=28 Identities=18% Similarity=0.311 Sum_probs=25.1
Q ss_pred CCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 147 DDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 147 ~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
..+-.||..++||++.+|..|-|-|++.
T Consensus 313 ~~~LkPLtlkdiA~~lglheSTVSRav~ 340 (429)
T TIGR02395 313 PAALKPLTLREVAEELGLHESTISRAIN 340 (429)
T ss_pred cccCcCCcHHHHHHHhCCCccchhhhhc
Confidence 3467999999999999999999999974
No 301
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=39.27 E-value=32 Score=25.84 Aligned_cols=25 Identities=32% Similarity=0.266 Sum_probs=20.6
Q ss_pred CCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 150 NGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 150 ~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
-.-|+.+|||+.+++....|...+.
T Consensus 134 ~~g~s~~eIA~~lg~s~~tv~~~l~ 158 (175)
T PRK12518 134 LEDLPQKEIAEILNIPVGTVKSRLF 158 (175)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3448999999999999998876653
No 302
>PF01843 DIL: DIL domain; InterPro: IPR018444 Dilute encodes a novel type of myosin heavy chain, with a tail, or C-terminal, region that has elements of both type II (alpha-helical coiled-coil) and type I (non-coiled-coil) myosin heavy chains. The DIL non alpha-helical domain is found in dilute myosin heavy chain proteins and other myosins. In mouse the dilute protein may play a role in the elaboration, maintenance, or function of cellular processes of melanocytes and neurons []. The MYO2 protein of Saccharomyces cerevisiae is implicated in vectorial vesicle transport and is homologous to the dilute protein over practically its entire length [].; PDB: 3MMI_B 2F6H_X.
Probab=39.15 E-value=12 Score=27.21 Aligned_cols=17 Identities=41% Similarity=0.470 Sum_probs=12.4
Q ss_pred cccHHHHHHHHHHhhcc
Q 029662 129 TLNVAQLRRIMLLHQGK 145 (190)
Q Consensus 129 TLNva~l~~ii~L~QGk 145 (190)
.||..||++|+..|+=.
T Consensus 86 ~Ln~~Qi~~iL~~Y~~~ 102 (105)
T PF01843_consen 86 SLNPAQIRKILSNYQPD 102 (105)
T ss_dssp TS-HHHHHHHHCCB---
T ss_pred cCCHHHHHHHHHhCCCc
Confidence 79999999999999743
No 303
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=38.92 E-value=56 Score=21.67 Aligned_cols=38 Identities=3% Similarity=-0.063 Sum_probs=27.2
Q ss_pred HHHHHHHHHHh-hccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 132 VAQLRRIMLLH-QGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 132 va~l~~ii~L~-QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
...-..||.+| ++. ++|.+||..|+|..++|-+-++-.
T Consensus 9 ~e~K~~~v~~~~~~g-------~sv~~va~~~gi~~~~l~~W~~~~ 47 (76)
T PF01527_consen 9 PEFKLQAVREYLESG-------ESVSEVAREYGISPSTLYNWRKQY 47 (76)
T ss_dssp HHHHHHHHHHHHHHH-------CHHHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHCC-------CceEeeecccccccccccHHHHHH
Confidence 44556677776 332 789999999999999998766543
No 304
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=38.88 E-value=68 Score=28.95 Aligned_cols=28 Identities=21% Similarity=0.230 Sum_probs=25.2
Q ss_pred CCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 149 HNGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 149 h~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
+..|++.+|||++.+++..+|++|+.-|
T Consensus 307 ~g~~~t~~~La~~l~~~~~~v~~iL~~L 334 (412)
T PRK04214 307 HGKALDVDEIRRLEPMGYDELGELLCEL 334 (412)
T ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 4469999999999999999999999765
No 305
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=38.81 E-value=58 Score=21.67 Aligned_cols=27 Identities=11% Similarity=-0.010 Sum_probs=21.8
Q ss_pred CCHHHHHHHhchhHHHHHHHHHhhcCC
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQCLSLP 179 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilqf~SlP 179 (190)
|++.|+|++++|..+.|..--+-.-|+
T Consensus 1 ~~i~e~A~~~gVs~~tlr~ye~~~gl~ 27 (68)
T cd04763 1 YTIGEVALLTGIKPHVLRAWEREFGLL 27 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHhcCCC
Confidence 578999999999999999876633444
No 306
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=38.68 E-value=59 Score=25.14 Aligned_cols=33 Identities=12% Similarity=0.144 Sum_probs=25.9
Q ss_pred HHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 137 RIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 137 ~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
.||.+.|- +|.++..+||++.++..+.|++=++
T Consensus 13 ~Il~~Lq~-----d~R~s~~eiA~~lglS~~tV~~Ri~ 45 (153)
T PRK11179 13 GILEALME-----NARTPYAELAKQFGVSPGTIHVRVE 45 (153)
T ss_pred HHHHHHHH-----cCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 45555553 3889999999999999998887655
No 307
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=38.47 E-value=37 Score=26.59 Aligned_cols=27 Identities=26% Similarity=0.338 Sum_probs=24.5
Q ss_pred CCCCHHHHHHHhchhHHHHHHHHHhhc
Q 029662 151 GPLDAKQIAEKFRLDVLQVQAILQCLS 177 (190)
Q Consensus 151 gPM~v~~iAeKFrv~v~~vq~Ilqf~S 177 (190)
|-|+-++||+..+++...|.+||..|-
T Consensus 14 ~~~~dedLa~~l~i~~n~vRkiL~~L~ 40 (147)
T smart00531 14 GCVTEEDLAELLGIKQKQLRKILYLLY 40 (147)
T ss_pred CCcCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 459999999999999999999998874
No 308
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=38.44 E-value=33 Score=26.18 Aligned_cols=27 Identities=15% Similarity=0.292 Sum_probs=23.9
Q ss_pred CCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 150 NGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 150 ~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
..-++.-.|||||+|.+++..++|.-|
T Consensus 39 ~K~ITps~lserlkI~~SlAr~~Lr~L 65 (86)
T PRK09334 39 EKIVTPYTLASKYGIKISVAKKVLREL 65 (86)
T ss_pred CcEEcHHHHHHHhcchHHHHHHHHHHH
Confidence 445789999999999999999999876
No 309
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=38.40 E-value=51 Score=22.37 Aligned_cols=27 Identities=22% Similarity=0.297 Sum_probs=22.3
Q ss_pred CCCCCCHHHHHHHhchhHHHHHHHHHh
Q 029662 149 HNGPLDAKQIAEKFRLDVLQVQAILQC 175 (190)
Q Consensus 149 h~gPM~v~~iAeKFrv~v~~vq~Ilqf 175 (190)
-...+++.+||+.|.++...|+.+|.-
T Consensus 57 ~y~~i~~~~ia~~l~~~~~~vE~~l~~ 83 (105)
T PF01399_consen 57 PYSSISISEIAKALQLSEEEVESILID 83 (105)
T ss_dssp C-SEEEHHHHHHHHTCCHHHHHHHHHH
T ss_pred HhcccchHHHHHHhccchHHHHHHHHH
Confidence 344589999999999999999998753
No 310
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=37.86 E-value=38 Score=22.43 Aligned_cols=28 Identities=29% Similarity=0.326 Sum_probs=25.1
Q ss_pred CCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 149 HNGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 149 h~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
..-+++-++||+..++....|.++|+.+
T Consensus 25 ~~~~lt~~~iA~~~g~sr~tv~r~l~~l 52 (76)
T PF13545_consen 25 IPLPLTQEEIADMLGVSRETVSRILKRL 52 (76)
T ss_dssp EEEESSHHHHHHHHTSCHHHHHHHHHHH
T ss_pred EEecCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 4567999999999999999999999876
No 311
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=37.62 E-value=60 Score=22.80 Aligned_cols=36 Identities=19% Similarity=0.234 Sum_probs=25.4
Q ss_pred HHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 135 LRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 135 l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
|.+|+.... +|+.+..+|+.+-+++-..++++|.+|
T Consensus 8 i~~IL~~l~------~~~~~~t~i~~~~~L~~~~~~~yL~~L 43 (77)
T PF14947_consen 8 IFDILKILS------KGGAKKTEIMYKANLNYSTLKKYLKEL 43 (77)
T ss_dssp HHHHHHHH-------TT-B-HHHHHTTST--HHHHHHHHHHH
T ss_pred HHHHHHHHH------cCCCCHHHHHHHhCcCHHHHHHHHHHH
Confidence 345555543 577899999999999999999999987
No 312
>PRK13502 transcriptional activator RhaR; Provisional
Probab=37.54 E-value=73 Score=25.90 Aligned_cols=39 Identities=5% Similarity=0.108 Sum_probs=30.3
Q ss_pred HHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 133 AQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 133 a~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
..+++|+++.+-. ..-++++++||+.|++...-+.++++
T Consensus 176 ~~~~~~~~~I~~~---~~~~~~~~~lA~~~~iS~~~L~r~fk 214 (282)
T PRK13502 176 TLLDKLITALANS---LECPFALDAFCQQEQCSERVLRQQFR 214 (282)
T ss_pred HHHHHHHHHHHhc---ccCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 4566777765533 34469999999999999999999886
No 313
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=37.43 E-value=62 Score=23.58 Aligned_cols=29 Identities=17% Similarity=0.263 Sum_probs=21.7
Q ss_pred HHHHHHhh-ccCCCCCCCCCHHHHHHHhch-hHHHHHH
Q 029662 136 RRIMLLHQ-GKADDHNGPLDAKQIAEKFRL-DVLQVQA 171 (190)
Q Consensus 136 ~~ii~L~Q-Gk~~~h~gPM~v~~iAeKFrv-~v~~vq~ 171 (190)
.+|+.+|- +.. +|.+||.+|+| +.+++-+
T Consensus 14 ~~iv~~~~~~g~-------sv~~vAr~~gv~~~~~l~~ 44 (116)
T COG2963 14 LEAVALYLRGGD-------TVSEVAREFGIVSATQLYK 44 (116)
T ss_pred HHHHHHHHhcCc-------cHHHHHHHhCCCChHHHHH
Confidence 45666664 332 89999999996 9998875
No 314
>PRK13503 transcriptional activator RhaS; Provisional
Probab=37.32 E-value=42 Score=26.97 Aligned_cols=39 Identities=18% Similarity=0.365 Sum_probs=29.2
Q ss_pred HHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 133 AQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 133 a~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
+.|++++.+- ..+...++++++||++|++..+.+.++.+
T Consensus 171 ~~i~~~~~~I---~~~~~~~~tl~~lA~~~~lS~~~l~r~Fk 209 (278)
T PRK13503 171 ARLNQLLAWL---EDHFAEEVNWEALADQFSLSLRTLHRQLK 209 (278)
T ss_pred HHHHHHHHHH---HHhhcCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3466666543 33445689999999999999999988875
No 315
>TIGR01958 nuoE_fam NADH-quinone oxidoreductase, E subunit. This model describes the E chain of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoB. This model does not identify proteins from chloroplast and cyanobacteria.
Probab=37.13 E-value=32 Score=27.02 Aligned_cols=44 Identities=14% Similarity=0.190 Sum_probs=30.2
Q ss_pred HHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhhcC
Q 029662 134 QLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCLSL 178 (190)
Q Consensus 134 ~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~Sl 178 (190)
.|-.||+.-|-.- ++=-+=.+.+||+.++|..+.|..++.|-+.
T Consensus 17 ~li~~L~~vQ~~~-G~i~~~~~~~iA~~l~~~~~~v~~v~tFY~~ 60 (148)
T TIGR01958 17 AIMPALMIAQEQK-GWVTPEAIAAVAEMLGIPPVWVYEVATFYSM 60 (148)
T ss_pred HHHHHHHHHHHHh-CCCCHHHHHHHHHHhCcCHHHHHHHHhHHhh
Confidence 4445555555221 1222334788999999999999999999775
No 316
>PRK09191 two-component response regulator; Provisional
Probab=37.08 E-value=49 Score=25.84 Aligned_cols=33 Identities=24% Similarity=0.331 Sum_probs=23.0
Q ss_pred HHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHH
Q 029662 135 LRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 135 l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Il 173 (190)
-|+|++|+- -..|+.+|||+..++...-|...+
T Consensus 93 ~r~v~~l~~------~~~~s~~eIA~~l~~s~~tV~~~l 125 (261)
T PRK09191 93 PRQAFLLTA------LEGFSVEEAAEILGVDPAEAEALL 125 (261)
T ss_pred HhHHHHHHH------HhcCCHHHHHHHHCCCHHHHHHHH
Confidence 355666632 122889999999999987766554
No 317
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=37.00 E-value=46 Score=27.25 Aligned_cols=38 Identities=13% Similarity=0.248 Sum_probs=28.6
Q ss_pred HHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 134 QLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 134 ~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
.|++++++-+ .+...+++|++||+++++..+.+.++.+
T Consensus 184 ~i~~~~~~i~---~~~~~~isl~~lA~~~~lS~~~l~r~Fk 221 (290)
T PRK10572 184 RVREACQYIS---DHLASEFDIESVAQHVCLSPSRLAHLFR 221 (290)
T ss_pred HHHHHHHHHH---hcccCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3555555442 3344789999999999999999988875
No 318
>TIGR02297 HpaA 4-hydroxyphenylacetate catabolism regulatory protein HpaA. This putative transcriptional regulator, which contains both the substrate-binding, dimerization domain (pfam02311) and the helix-turn-helix DNA-binding domain (pfam00165) of the AraC famil, is located proximal to genes of the 4-hydroxyphenylacetate catabolism pathway.
Probab=36.42 E-value=97 Score=25.09 Aligned_cols=40 Identities=13% Similarity=0.247 Sum_probs=28.0
Q ss_pred HHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 132 VAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 132 va~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
...++.++.+-. ++...+.++++||+++++...-+.++.+
T Consensus 185 ~~~~~~~~~~I~---~~~~~~~sl~~lA~~~~~S~~~l~r~Fk 224 (287)
T TIGR02297 185 LYLFNRFNFLIE---ENYKQHLRLPEYADRLGISESRLNDICR 224 (287)
T ss_pred HHHHHHHHHHHH---HhhccCCCHHHHHHHHCCCHHHHHHHHH
Confidence 344455554332 2333468999999999999999988765
No 319
>PRK05590 hypothetical protein; Provisional
Probab=36.40 E-value=23 Score=30.02 Aligned_cols=27 Identities=30% Similarity=0.461 Sum_probs=18.4
Q ss_pred CCCCCCC--CHHHHHHHhchhHHHHHHHH
Q 029662 147 DDHNGPL--DAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 147 ~~h~gPM--~v~~iAeKFrv~v~~vq~Il 173 (190)
.+|.... +|++|||||.+++.-.-..|
T Consensus 40 ~~~~~~~~gtv~ela~k~~~~~~~~~Gfl 68 (166)
T PRK05590 40 ANHKEVVEGTVKELAEKFGTSVVFFMGFL 68 (166)
T ss_pred cCCCceeeeeHHHHHHHhCCChhhhhhhh
Confidence 3444433 69999999999976544433
No 320
>smart00257 LysM Lysin motif.
Probab=36.34 E-value=43 Score=17.96 Aligned_cols=21 Identities=14% Similarity=0.302 Sum_probs=16.4
Q ss_pred CHHHHHHHhchhHHHHHHHHH
Q 029662 154 DAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 154 ~v~~iAeKFrv~v~~vq~Ilq 174 (190)
++.+||.+|+++...+..+-.
T Consensus 9 t~~~ia~~~~~~~~~~~~~N~ 29 (44)
T smart00257 9 TLSSIARRYGISVSDLLELNN 29 (44)
T ss_pred CHHHHHHHhCCCHHHHHHHcC
Confidence 688999999999866665543
No 321
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=35.97 E-value=34 Score=23.67 Aligned_cols=29 Identities=31% Similarity=0.415 Sum_probs=20.3
Q ss_pred CCHHHHHHHhchhHHHHHHHH--HhhcCCCC
Q 029662 153 LDAKQIAEKFRLDVLQVQAIL--QCLSLPPE 181 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Il--qf~SlP~e 181 (190)
+++++||++-+|.+..|+.|= +|-.||.+
T Consensus 11 lsl~~va~~t~I~~~~l~aiE~~~~~~lp~~ 41 (62)
T PF13413_consen 11 LSLEDVAEETKISVSYLEAIENGDFDSLPSP 41 (62)
T ss_dssp --HHHHHHHCS--HHHHHHHHCT-GCCSSSH
T ss_pred CCHHHHHHHhCCCHHHHHHHHCcChhhCCcH
Confidence 899999999999999999984 46666643
No 322
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=35.85 E-value=39 Score=26.11 Aligned_cols=24 Identities=13% Similarity=0.216 Sum_probs=20.2
Q ss_pred CCCCCHHHHHHHhchhHHHHHHHH
Q 029662 150 NGPLDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 150 ~gPM~v~~iAeKFrv~v~~vq~Il 173 (190)
-.-|+.+|||+.++|....|..-+
T Consensus 148 ~~g~s~~EIA~~lgis~~tV~~~l 171 (188)
T PRK09640 148 VAELEFQEIADIMHMGLSATKMRY 171 (188)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHH
Confidence 345899999999999999887654
No 323
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=35.54 E-value=71 Score=23.70 Aligned_cols=35 Identities=26% Similarity=0.339 Sum_probs=26.9
Q ss_pred HHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 137 RIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 137 ~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
.|+.+.|. +++++..+||++-++...-|.+.++=|
T Consensus 12 ~IL~~L~~-----d~r~~~~eia~~lglS~~~v~~Ri~~L 46 (154)
T COG1522 12 RILRLLQE-----DARISNAELAERVGLSPSTVLRRIKRL 46 (154)
T ss_pred HHHHHHHH-----hCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 45555554 446999999999999999988877643
No 324
>PF08461 HTH_12: Ribonuclease R winged-helix domain; InterPro: IPR013668 This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaea.
Probab=35.25 E-value=53 Score=22.95 Aligned_cols=29 Identities=28% Similarity=0.515 Sum_probs=22.1
Q ss_pred CCCCCCCHHHHHHHhc---hhH--HHHHHHHHhh
Q 029662 148 DHNGPLDAKQIAEKFR---LDV--LQVQAILQCL 176 (190)
Q Consensus 148 ~h~gPM~v~~iAeKFr---v~v--~~vq~Ilqf~ 176 (190)
++++||+-++||+.|. .++ ..|.+-|..+
T Consensus 9 ~~~~P~g~~~l~~~L~~~g~~~se~avRrrLr~m 42 (66)
T PF08461_consen 9 ESDKPLGRKQLAEELKLRGEELSEEAVRRRLRAM 42 (66)
T ss_pred HcCCCCCHHHHHHHHHhcChhhhHHHHHHHHHHH
Confidence 4778999999999985 555 6667776654
No 325
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=35.00 E-value=52 Score=20.55 Aligned_cols=27 Identities=26% Similarity=0.326 Sum_probs=20.5
Q ss_pred CCHHHHHHHhchhHHHHHHHHHhhcCC
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQCLSLP 179 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilqf~SlP 179 (190)
|+.+|+|++.+|....|.+++.=-..|
T Consensus 10 ls~~~la~~~gis~~~i~~~~~g~~~~ 36 (55)
T PF01381_consen 10 LSQKELAEKLGISRSTISRIENGKRNP 36 (55)
T ss_dssp S-HHHHHHHHTS-HHHHHHHHTTSSTS
T ss_pred CCHHHHHHHhCCCcchhHHHhcCCCCC
Confidence 889999999999999999887654443
No 326
>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=34.82 E-value=44 Score=22.18 Aligned_cols=21 Identities=24% Similarity=0.276 Sum_probs=18.6
Q ss_pred CHHHHHHHhchhHHHHHHHHH
Q 029662 154 DAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 154 ~v~~iAeKFrv~v~~vq~Ilq 174 (190)
++++||+..+|..+-|-++|.
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 478999999999999998874
No 327
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=34.60 E-value=73 Score=23.98 Aligned_cols=25 Identities=16% Similarity=0.155 Sum_probs=22.1
Q ss_pred CCHHHHHHHhchhHHHHHHHHHhhc
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQCLS 177 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilqf~S 177 (190)
+++.++|..|+|...-|.+.++.-.
T Consensus 19 ~s~~eaa~~F~VS~~Tv~~W~k~~~ 43 (119)
T PF01710_consen 19 KSIREAAKRFGVSRNTVYRWLKRKE 43 (119)
T ss_pred chHHHHHHHhCcHHHHHHHHHHhcc
Confidence 6899999999999999999998433
No 328
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=34.35 E-value=1.1e+02 Score=22.28 Aligned_cols=37 Identities=24% Similarity=0.235 Sum_probs=26.4
Q ss_pred cccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHH
Q 029662 129 TLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 129 TLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Il 173 (190)
.|.-.+..=+-+|.+| ++.++||+++.+....|...+
T Consensus 137 ~Lt~~E~~il~~l~~g--------~~~~~Ia~~l~~s~~tv~~~~ 173 (196)
T PRK10360 137 PLTKRERQVAEKLAQG--------MAVKEIAAELGLSPKTVHVHR 173 (196)
T ss_pred CCCHHHHHHHHHHHCC--------CCHHHHHHHhCCCHHHHHHHH
Confidence 4666666444456677 689999999999877766544
No 329
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 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. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=34.09 E-value=46 Score=21.15 Aligned_cols=25 Identities=32% Similarity=0.442 Sum_probs=20.0
Q ss_pred CCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 152 PLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 152 PM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
||+-.|||.-.++-...|-++|..+
T Consensus 2 ~mtr~diA~~lG~t~ETVSR~l~~l 26 (32)
T PF00325_consen 2 PMTRQDIADYLGLTRETVSRILKKL 26 (32)
T ss_dssp E--HHHHHHHHTS-HHHHHHHHHHH
T ss_pred CcCHHHHHHHhCCcHHHHHHHHHHH
Confidence 6899999999999999999998765
No 330
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=34.03 E-value=1.3e+02 Score=23.52 Aligned_cols=60 Identities=28% Similarity=0.377 Sum_probs=41.0
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCcccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 107 LPKLRNTTPVSSRYEEKPSPPGTLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 107 ~Pk~R~t~~~sg~~eer~~p~GTLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
+|..+.-+|.. ...+-...+=+|.+.++.-|=|.+ .+| |+-.|-|++.+|.-.-+++||.
T Consensus 20 ~P~~~~F~P~g-~~~~~~~~~V~L~~dElEAiRL~D------~eg-l~QeeaA~~MgVSR~T~~ril~ 79 (106)
T PF02001_consen 20 EPEYRCFKPAG-PGSELEKEPVVLTVDELEAIRLVD------YEG-LSQEEAAERMGVSRPTFQRILE 79 (106)
T ss_pred CcCCCEEeCCC-CCCCCCcceEEeeHHHHHHHHHHH------HcC-CCHHHHHHHcCCcHHHHHHHHH
Confidence 45566666654 222223344589999986554432 233 8899999999999999999985
No 331
>PTZ00183 centrin; Provisional
Probab=33.83 E-value=1.5e+02 Score=21.41 Aligned_cols=48 Identities=17% Similarity=0.218 Sum_probs=30.0
Q ss_pred ccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhc-----hhHHHHHHHHHhhc
Q 029662 130 LNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFR-----LDVLQVQAILQCLS 177 (190)
Q Consensus 130 LNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFr-----v~v~~vq~Ilqf~S 177 (190)
+|-.++.+|..+|.--..+.+|-++..|+..-++ +.-..++.+++.+.
T Consensus 11 ~~~~~~~~~~~~F~~~D~~~~G~i~~~e~~~~l~~~g~~~~~~~~~~l~~~~d 63 (158)
T PTZ00183 11 LTEDQKKEIREAFDLFDTDGSGTIDPKELKVAMRSLGFEPKKEEIKQMIADVD 63 (158)
T ss_pred CCHHHHHHHHHHHHHhCCCCCCcccHHHHHHHHHHhCCCCCHHHHHHHHHHhC
Confidence 5566666666666554556788888888865443 44455666665543
No 332
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=33.72 E-value=49 Score=24.92 Aligned_cols=24 Identities=8% Similarity=0.022 Sum_probs=20.6
Q ss_pred CCCHHHHHHHhchhHHHHHHHHHh
Q 029662 152 PLDAKQIAEKFRLDVLQVQAILQC 175 (190)
Q Consensus 152 PM~v~~iAeKFrv~v~~vq~Ilqf 175 (190)
-++|.+||.+|+|..++|-+-++-
T Consensus 29 g~sv~evA~e~gIs~~tl~~W~r~ 52 (121)
T PRK09413 29 GMTVSLVARQHGVAASQLFLWRKQ 52 (121)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHH
Confidence 379999999999999999886653
No 333
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=33.07 E-value=41 Score=28.71 Aligned_cols=40 Identities=10% Similarity=0.262 Sum_probs=31.1
Q ss_pred HHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 132 VAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 132 va~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
.+-+..|+.+.+- +|.++++|||+.|+|...-|.+=|.+|
T Consensus 16 ~eR~~~Il~~L~~-----~~~vtv~eLa~~l~VS~~TIRRDL~~L 55 (269)
T PRK09802 16 SERREQIIQRLRQ-----QGSVQVNDLSALYGVSTVTIRNDLAFL 55 (269)
T ss_pred HHHHHHHHHHHHH-----cCCEeHHHHHHHHCCCHHHHHHHHHHH
Confidence 4556677766543 334999999999999999999888776
No 334
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=32.57 E-value=51 Score=30.88 Aligned_cols=27 Identities=22% Similarity=0.266 Sum_probs=24.8
Q ss_pred CCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 148 DHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 148 ~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
.+-.||..++||++.+|..|-|-|++.
T Consensus 339 ~~LkPLtlkdvAe~lglheSTVSRav~ 365 (455)
T PRK05932 339 EALKPLVLKDIAEELGMHESTISRATT 365 (455)
T ss_pred ccCcCccHHHHHHHhCCCccchhhhhc
Confidence 378999999999999999999999984
No 335
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=32.31 E-value=1.3e+02 Score=21.97 Aligned_cols=36 Identities=28% Similarity=0.319 Sum_probs=26.4
Q ss_pred ccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHH
Q 029662 130 LNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 130 LNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Il 173 (190)
|.-.++.-+-.|.+| ++.+|||++..+...-|..-+
T Consensus 150 lt~re~~vl~~l~~g--------~s~~eIa~~l~~s~~tv~~~~ 185 (210)
T PRK09935 150 LSNREVTILRYLVSG--------LSNKEIADQLLLSNKTVSAHK 185 (210)
T ss_pred CCHHHHHHHHHHHcC--------CCHHHHHHHhCCCHHHHHHHH
Confidence 666666555555577 889999999999887665544
No 336
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=32.29 E-value=97 Score=25.37 Aligned_cols=23 Identities=17% Similarity=0.235 Sum_probs=21.5
Q ss_pred CCHHHHHHHhchhHHHHHHHHHh
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQC 175 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilqf 175 (190)
+++.+||++++|....++++.+-
T Consensus 215 ls~~~lA~~~giS~r~L~r~Fk~ 237 (302)
T PRK09685 215 LRPEWIAGELGISVRSLYRLFAE 237 (302)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Confidence 89999999999999999998874
No 337
>PRK13500 transcriptional activator RhaR; Provisional
Probab=32.13 E-value=1.2e+02 Score=25.82 Aligned_cols=40 Identities=5% Similarity=0.126 Sum_probs=30.1
Q ss_pred HHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 132 VAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 132 va~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
...++.|+.+-+-.- .-++++++||++|.+....+.++.+
T Consensus 205 ~~~l~~i~~yI~~~~---~e~isl~~lA~~~~iS~~~L~r~FK 244 (312)
T PRK13500 205 ETLLDKLITRLAASL---KSPFALDKFCDEASCSERVLRQQFR 244 (312)
T ss_pred HHHHHHHHHHHHHcc---cCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 355666766554432 3459999999999999999998875
No 338
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=32.02 E-value=1e+02 Score=27.02 Aligned_cols=37 Identities=16% Similarity=0.225 Sum_probs=30.9
Q ss_pred cccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHH
Q 029662 129 TLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 129 TLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Il 173 (190)
.|.-.+++=+.++-||+ +.+|||++..+....|..-+
T Consensus 133 ~LSpRErEVLrLLAqGk--------TnKEIAe~L~IS~rTVkth~ 169 (198)
T PRK15201 133 HFSVTERHLLKLIASGY--------HLSETAALLSLSEEQTKSLR 169 (198)
T ss_pred CCCHHHHHHHHHHHCCC--------CHHHHHHHhCCCHHHHHHHH
Confidence 38889988888889995 58999999999998876544
No 339
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=31.95 E-value=50 Score=21.73 Aligned_cols=22 Identities=23% Similarity=0.344 Sum_probs=17.5
Q ss_pred CCHHHHHHHhchhHHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilq 174 (190)
|+..|+|++.++..+-|.+|-+
T Consensus 15 ls~~~lA~~~g~s~s~v~~iE~ 36 (64)
T PF13560_consen 15 LSQAQLADRLGVSQSTVSRIER 36 (64)
T ss_dssp S-HHHHHHHHTS-HHHHHHHHT
T ss_pred CCHHHHHHHHCcCHHHHHHHHC
Confidence 8899999999999888888765
No 340
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=31.83 E-value=76 Score=23.02 Aligned_cols=29 Identities=14% Similarity=0.083 Sum_probs=23.9
Q ss_pred CCHHHHHHHhchhHHHHHHHHHhhcCCCC
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQCLSLPPE 181 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilqf~SlP~e 181 (190)
|+++|+|++|+|....|..-.+.==||+.
T Consensus 1 ~ti~eva~~~gvs~~tlR~ye~~Gll~~~ 29 (103)
T cd01106 1 YTVGEVAKLTGVSVRTLHYYDEIGLLKPS 29 (103)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCCCC
Confidence 68899999999999999987776556653
No 341
>PF04963 Sigma54_CBD: Sigma-54 factor, core binding domain; InterPro: IPR007046 This domain makes a direct interaction with the core RNA polymerase, to form an enhancer dependent holoenzyme []. The centre of this domain contains a very weak similarity to a helix-turn-helix motif, which may represent a DNA binding domain.; GO: 0003677 DNA binding, 0006352 transcription initiation, DNA-dependent; PDB: 2K9L_A 2K9M_A.
Probab=31.76 E-value=49 Score=27.03 Aligned_cols=28 Identities=25% Similarity=0.348 Sum_probs=21.5
Q ss_pred CCCC--CCHHHHHHHhchhHHHHHHHHHhh
Q 029662 149 HNGP--LDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 149 h~gP--M~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
.+|= .++++||++|.|+...|+.+|+.|
T Consensus 47 ~~GyL~~~~~eia~~l~~~~~~v~~~l~~l 76 (194)
T PF04963_consen 47 DDGYLTESLEEIAEELGVSEEEVEKALELL 76 (194)
T ss_dssp TTSTCSS-HHHHHHHCTS-HHHHHHHHHHH
T ss_pred CCCccCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 4553 578899999999999999988766
No 342
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=31.05 E-value=40 Score=23.07 Aligned_cols=19 Identities=21% Similarity=0.405 Sum_probs=15.7
Q ss_pred CCHHHHHHHhchhHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQA 171 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~ 171 (190)
++-.+|||.++|+.+||-+
T Consensus 29 vSS~~La~~~gi~~~qVRK 47 (50)
T PF06971_consen 29 VSSQELAEALGITPAQVRK 47 (50)
T ss_dssp E-HHHHHHHHTS-HHHHHH
T ss_pred ECHHHHHHHHCCCHHHhcc
Confidence 7889999999999999975
No 343
>PRK12423 LexA repressor; Provisional
Probab=30.82 E-value=56 Score=26.57 Aligned_cols=26 Identities=19% Similarity=0.240 Sum_probs=18.3
Q ss_pred CCCCCCHHHHHHHhch-hHHHHHHHHH
Q 029662 149 HNGPLDAKQIAEKFRL-DVLQVQAILQ 174 (190)
Q Consensus 149 h~gPM~v~~iAeKFrv-~v~~vq~Ilq 174 (190)
+.-+.++.|||+.|++ --+.|..-|+
T Consensus 22 ~g~~Ps~~eia~~~g~~s~~~v~~~l~ 48 (202)
T PRK12423 22 AGQPPSLAEIAQAFGFASRSVARKHVQ 48 (202)
T ss_pred cCCCCCHHHHHHHhCCCChHHHHHHHH
Confidence 3445899999999995 5555555444
No 344
>KOG3062 consensus RNA polymerase II elongator associated protein [General function prediction only]
Probab=30.56 E-value=1.3e+02 Score=27.77 Aligned_cols=83 Identities=19% Similarity=0.276 Sum_probs=64.1
Q ss_pred CCccCCCCcccccCchHHHHHHHhhcccccCCCCccccchhhhhhhhcCCCCCCCCCCCCCCCCCCCCCCC-CcccHHHH
Q 029662 57 NRPVNTGNVLEERDPQYDAMLNQMLGRVKTKAGGKAEMGEAAVVERQTRPLPKLRNTTPVSSRYEEKPSPP-GTLNVAQL 135 (190)
Q Consensus 57 ~~r~n~~nvl~erDp~ydaMl~qmvGrI~tkpGGk~Emgea~vv~~ynRP~Pk~R~t~~~sg~~eer~~p~-GTLNva~l 135 (190)
..+...-|.|-|=|---.+.++-+++-+++++++-.- .+| .+.-++|- -+++.++|
T Consensus 188 ~~p~s~~N~L~eLDk~tq~II~~Im~~~ks~~~~~l~----------------------vpg-t~~~~l~i~~~v~l~eL 244 (281)
T KOG3062|consen 188 AAPLSEANFLYELDKATQEIIKAIMEAQKSNGTALLR----------------------VPG-TELPPLPICRPVTLPEL 244 (281)
T ss_pred cCCcccccHHHHHHHHHHHHHHHHHHhhhccCceeEE----------------------ecC-CcCCCccccccccHHHH
Confidence 3466778999999999999999999999988766432 123 23333666 46899999
Q ss_pred HHHHHHhhccCCCCCCCCCHHHHHHHh
Q 029662 136 RRIMLLHQGKADDHNGPLDAKQIAEKF 162 (190)
Q Consensus 136 ~~ii~L~QGk~~~h~gPM~v~~iAeKF 162 (190)
+.+=+-|=---..|.-|-+++||+..|
T Consensus 245 ~RLRrqFI~~~~~~~~~t~~~q~~~lF 271 (281)
T KOG3062|consen 245 QRLRRQFIKLTKGQPLPTDLDQLKRLF 271 (281)
T ss_pred HHHHHHHHHhhcCCCCCCCHHHHHHHH
Confidence 988776655557788999999999988
No 345
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=30.40 E-value=1.1e+02 Score=24.76 Aligned_cols=28 Identities=29% Similarity=0.432 Sum_probs=24.5
Q ss_pred CCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 149 HNGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 149 h~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
..|++.+.+||++.+|...-|..+|+=|
T Consensus 21 ~~~~~~~~diA~~L~Vsp~sVt~ml~rL 48 (154)
T COG1321 21 EKGFARTKDIAERLKVSPPSVTEMLKRL 48 (154)
T ss_pred ccCcccHHHHHHHhCCCcHHHHHHHHHH
Confidence 5688999999999999999998887754
No 346
>COG2207 AraC AraC-type DNA-binding domain-containing proteins [Transcription]
Probab=29.93 E-value=64 Score=22.01 Aligned_cols=26 Identities=12% Similarity=0.330 Sum_probs=22.7
Q ss_pred CCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 149 HNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 149 h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
...+.++++||+.+++....++++++
T Consensus 33 ~~~~~~l~~la~~~g~S~~~l~r~f~ 58 (127)
T COG2207 33 LAEPLTLEDLARRLGMSRRTLSRLFK 58 (127)
T ss_pred hcCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 34449999999999999999999887
No 347
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=29.75 E-value=83 Score=23.13 Aligned_cols=29 Identities=14% Similarity=0.233 Sum_probs=23.9
Q ss_pred CCHHHHHHHhchhHHHHHHHHHhhcCCCC
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQCLSLPPE 181 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilqf~SlP~e 181 (190)
|++.|+|++++|.+..|..-.+-=-||++
T Consensus 1 m~I~eva~~~gvs~~tlR~Ye~~GLl~p~ 29 (95)
T cd04780 1 MRMSELSKRSGVSVATIKYYLREGLLPEG 29 (95)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCCCC
Confidence 78999999999999998877665556664
No 348
>smart00753 PAM PCI/PINT associated module.
Probab=29.67 E-value=51 Score=22.58 Aligned_cols=25 Identities=16% Similarity=0.311 Sum_probs=21.1
Q ss_pred CCCCHHHHHHHhchhHHHHHHHHHh
Q 029662 151 GPLDAKQIAEKFRLDVLQVQAILQC 175 (190)
Q Consensus 151 gPM~v~~iAeKFrv~v~~vq~Ilqf 175 (190)
.-++++.||+.|.++...|+.++--
T Consensus 23 ~~i~~~~i~~~~~l~~~~vE~~i~~ 47 (88)
T smart00753 23 SSISLSDLAKLLGLSVPEVEKLVSK 47 (88)
T ss_pred ceeeHHHHHHHhCcCHHHHHHHHHH
Confidence 4589999999999999988877653
No 349
>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=29.67 E-value=51 Score=22.58 Aligned_cols=25 Identities=16% Similarity=0.311 Sum_probs=21.1
Q ss_pred CCCCHHHHHHHhchhHHHHHHHHHh
Q 029662 151 GPLDAKQIAEKFRLDVLQVQAILQC 175 (190)
Q Consensus 151 gPM~v~~iAeKFrv~v~~vq~Ilqf 175 (190)
.-++++.||+.|.++...|+.++--
T Consensus 23 ~~i~~~~i~~~~~l~~~~vE~~i~~ 47 (88)
T smart00088 23 SSISLSDLAKLLGLSVPEVEKLVSK 47 (88)
T ss_pred ceeeHHHHHHHhCcCHHHHHHHHHH
Confidence 4589999999999999988877653
No 350
>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=29.64 E-value=62 Score=25.50 Aligned_cols=40 Identities=28% Similarity=0.457 Sum_probs=32.3
Q ss_pred CCcccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 127 PGTLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 127 ~GTLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
+..|+-+| +.|+.|.++ |.+|-|||...++-+.+|+=+|-
T Consensus 38 ~~~l~pE~-~~Il~lC~~-------~~SVAEiAA~L~lPlgVvrVLvs 77 (114)
T PF05331_consen 38 PAGLGPEH-RAILELCRR-------PLSVAEIAARLGLPLGVVRVLVS 77 (114)
T ss_pred CCCCCHHH-HHHHHHHCC-------CccHHHHHHhhCCCchhhhhhHH
Confidence 35566555 789999876 79999999999999999886654
No 351
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=29.21 E-value=91 Score=24.29 Aligned_cols=27 Identities=15% Similarity=0.173 Sum_probs=21.6
Q ss_pred CCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 150 NGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 150 ~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
.|+++|.+||+.|.+.-+.|-.=|+.|
T Consensus 28 ~~~~~v~ela~~l~lsqstvS~HL~~L 54 (117)
T PRK10141 28 SGELCVCDLCTALDQSQPKISRHLALL 54 (117)
T ss_pred cCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 368999999999999888776655544
No 352
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=29.21 E-value=65 Score=25.36 Aligned_cols=40 Identities=10% Similarity=0.096 Sum_probs=30.3
Q ss_pred HHHHHHh-hccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhhcCCC
Q 029662 136 RRIMLLH-QGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCLSLPP 180 (190)
Q Consensus 136 ~~ii~L~-QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~SlP~ 180 (190)
++|++|. +| .+.++.+|||++..|-..-|.+-+.|+-...
T Consensus 165 r~Vl~~~~~g-----~~g~s~~eIa~~l~iS~~Tv~~~~~~~~~~~ 205 (225)
T PRK10046 165 NAVRKLFKEP-----GVQHTAETVAQALTISRTTARRYLEYCASRH 205 (225)
T ss_pred HHHHHHHHcC-----CCCcCHHHHHHHhCccHHHHHHHHHHHHhCC
Confidence 4666555 22 2247899999999999999999999986543
No 353
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=29.09 E-value=68 Score=29.61 Aligned_cols=30 Identities=33% Similarity=0.503 Sum_probs=21.8
Q ss_pred HHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHH
Q 029662 137 RIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQA 171 (190)
Q Consensus 137 ~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~ 171 (190)
+||+|..- .|||+|.||||..++.-+-+-.
T Consensus 27 ~Il~lL~~-----k~plNvneiAe~lgLpqst~s~ 56 (308)
T COG4189 27 AILQLLHR-----KGPLNVNEIAEALGLPQSTMSA 56 (308)
T ss_pred HHHHHHHH-----hCCCCHHHHHHHhCCchhhhhh
Confidence 45555443 3699999999999987766543
No 354
>PF12949 HeH: HeH/LEM domain; PDB: 2OUT_A.
Probab=28.88 E-value=39 Score=21.92 Aligned_cols=17 Identities=53% Similarity=0.733 Sum_probs=11.5
Q ss_pred CCcccHHHHHHHHHHhh
Q 029662 127 PGTLNVAQLRRIMLLHQ 143 (190)
Q Consensus 127 ~GTLNva~l~~ii~L~Q 143 (190)
|-+|.|+||+.|+.-|.
T Consensus 1 p~sltV~~Lk~iL~~~~ 17 (35)
T PF12949_consen 1 PKSLTVAQLKRILDEHG 17 (35)
T ss_dssp STT--SHHHHHHHHHHT
T ss_pred CCcCcHHHHHHHHHHcC
Confidence 34789999999987653
No 355
>COG1961 PinR Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]
Probab=28.59 E-value=1.3e+02 Score=24.20 Aligned_cols=48 Identities=19% Similarity=0.112 Sum_probs=38.0
Q ss_pred CCCCcccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhhcCCCC
Q 029662 125 SPPGTLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCLSLPPE 181 (190)
Q Consensus 125 ~p~GTLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~SlP~e 181 (190)
.+......+.++.++..+- ++..+||..|++....|-+++++.....+
T Consensus 159 ~~~~~~~~~~v~~l~~~~~---------~~~~~~a~~~~i~~~t~~r~~~~~~~~~~ 206 (222)
T COG1961 159 RKKAEEQAAAVRRLLADGL---------GSYSEIARALGISRSTVYRILNKLKKRGG 206 (222)
T ss_pred ccccchhHHHHHHHHHhcc---------chHHHHHHHcCccHHHHHHhhhhhhcccc
Confidence 5566667777777766554 88999999999999999999998765544
No 356
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=28.56 E-value=1.2e+02 Score=19.52 Aligned_cols=22 Identities=23% Similarity=0.329 Sum_probs=12.4
Q ss_pred CCHHHHHHHhchhHHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilq 174 (190)
|+..+||++-+|..+.|.+++.
T Consensus 11 it~~~La~~~gis~~tl~~~~~ 32 (63)
T PF13443_consen 11 ITQKDLARKTGISRSTLSRILN 32 (63)
T ss_dssp --HHHHHHHHT--HHHHHHHHT
T ss_pred CCHHHHHHHHCcCHHHHHHHHh
Confidence 5677777777777766666654
No 357
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=28.16 E-value=1.3e+02 Score=24.74 Aligned_cols=37 Identities=19% Similarity=0.172 Sum_probs=29.7
Q ss_pred cccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHH
Q 029662 129 TLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 129 TLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Il 173 (190)
.|.-.+.+=+-+++|| ++.+|||+++.+....|..-+
T Consensus 155 ~Lt~rE~~Vl~l~~~G--------~s~~eIA~~L~iS~~TVk~~~ 191 (216)
T PRK10100 155 LLTHREKEILNKLRIG--------ASNNEIARSLFISENTVKTHL 191 (216)
T ss_pred CCCHHHHHHHHHHHcC--------CCHHHHHHHhCCCHHHHHHHH
Confidence 3777787777788998 568999999999988776544
No 358
>cd00213 S-100 S-100: S-100 domain, which represents the largest family within the superfamily of proteins carrying the Ca-binding EF-hand motif. Note that this S-100 hierarchy contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100 proteins are expressed exclusively in vertebrates, and are implicated in intracellular and extracellular regulatory activities. Intracellularly, S100 proteins act as Ca-signaling or Ca-buffering proteins. The most unusual characteristic of certain S100 proteins is their occurrence in extracellular space, where they act in a cytokine-like manner through RAGE, the receptor for advanced glycation products. Structural data suggest that many S100 members exist within cells as homo- or heterodimers and even oligomers; oligomerization contributes to their functional diversification. Upon binding calcium, most S100 proteins change conformation to a more open structure exposing a hydrophobic cleft. This hydrophobic surface represents th
Probab=28.12 E-value=2e+02 Score=19.66 Aligned_cols=47 Identities=17% Similarity=0.253 Sum_probs=28.6
Q ss_pred HHHHHHHHhhccCC--CCCCCCCHHHHHHHhch----------hHHHHHHHHHhhcCCC
Q 029662 134 QLRRIMLLHQGKAD--DHNGPLDAKQIAEKFRL----------DVLQVQAILQCLSLPP 180 (190)
Q Consensus 134 ~l~~ii~L~QGk~~--~h~gPM~v~~iAeKFrv----------~v~~vq~Ilqf~SlP~ 180 (190)
+|.++..+|.--.. +++|-++.+++.+-++- .-..|..|+..+....
T Consensus 6 ~~~~l~~~F~~~D~~~~~~G~Is~~el~~~l~~~~g~~~~~~~~~~ei~~i~~~~d~~~ 64 (88)
T cd00213 6 AIETIIDVFHKYSGKEGDKDTLSKKELKELLETELPNFLKNQKDPEAVDKIMKDLDVNK 64 (88)
T ss_pred HHHHHHHHHHHHhhccCCCCcCcHHHHHHHHHHHhhhhccCCCCHHHHHHHHHHhccCC
Confidence 34445444554455 67888888888776642 2456777776654443
No 359
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=28.04 E-value=79 Score=28.08 Aligned_cols=32 Identities=16% Similarity=0.192 Sum_probs=25.5
Q ss_pred CCCCCCHHHHHHHhchhHHHHHHHHHh----hcCCC
Q 029662 149 HNGPLDAKQIAEKFRLDVLQVQAILQC----LSLPP 180 (190)
Q Consensus 149 h~gPM~v~~iAeKFrv~v~~vq~Ilqf----~SlP~ 180 (190)
+...-+++|||+.+++.+..|+.++++ +||-.
T Consensus 186 lgr~pt~~EiA~~lgi~~~~v~~~~~~~~~~~SLd~ 221 (324)
T PRK07921 186 LGREATDEELAEESGIPEEKIADLLEHSRDPVSLDM 221 (324)
T ss_pred hCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCceecC
Confidence 445567999999999999999999765 46643
No 360
>PF02319 E2F_TDP: E2F/DP family winged-helix DNA-binding domain; InterPro: IPR003316 The mammalian transcription factor E2F plays an important role in regulating the expression of genes that are required for passage through the cell cycle. Multiple E2F family members have been identified that bind to DNA as heterodimers, interacting with proteins known as DP - the dimerisation partners [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005667 transcription factor complex; PDB: 1CF7_B.
Probab=27.84 E-value=88 Score=21.95 Aligned_cols=26 Identities=19% Similarity=0.475 Sum_probs=19.2
Q ss_pred HHHHHHhhccCCCCCCCCCHHHHHHHh---ch
Q 029662 136 RRIMLLHQGKADDHNGPLDAKQIAEKF---RL 164 (190)
Q Consensus 136 ~~ii~L~QGk~~~h~gPM~v~~iAeKF---rv 164 (190)
+.+|.+|+... ++.+++++||+++ ++
T Consensus 11 ~~fi~~~~~~~---~~~i~l~~ia~~l~~~~~ 39 (71)
T PF02319_consen 11 QRFIQLFESSP---DKSISLNEIADKLISENV 39 (71)
T ss_dssp HHHHHHHHHCC---CTEEEHHHHHHHCHHHCC
T ss_pred HHHHHHHHHCC---CCcccHHHHHHHHccccc
Confidence 34566666522 3889999999999 77
No 361
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=27.58 E-value=80 Score=28.22 Aligned_cols=27 Identities=22% Similarity=0.291 Sum_probs=22.9
Q ss_pred CCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 150 NGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 150 ~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
...-++.|||+..++.+..|..++++.
T Consensus 230 gr~pt~~EiA~~l~~~~~~v~~~~~~~ 256 (367)
T PRK09210 230 GREPTPEEIAEEMDMPPEKVREILKIA 256 (367)
T ss_pred CCCCCHHHHHHHhCcCHHHHHHHHHHh
Confidence 344589999999999999999988763
No 362
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=27.46 E-value=56 Score=29.49 Aligned_cols=38 Identities=24% Similarity=0.210 Sum_probs=30.4
Q ss_pred HHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 133 AQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 133 a~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
..+..|-.|| +..+|+=.|||+|++|--..|.+.|++.
T Consensus 13 ~l~~~~A~lY------Y~~gltQ~eIA~~LgiSR~~v~rlL~~A 50 (321)
T COG2390 13 RLLARAAWLY------YVEGLTQSEIAERLGISRATVSRLLAKA 50 (321)
T ss_pred HHHHHHHHHH------HhcCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 4455666666 3455999999999999999999999974
No 363
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=27.45 E-value=71 Score=26.70 Aligned_cols=26 Identities=15% Similarity=0.207 Sum_probs=22.2
Q ss_pred CCCCCCCHHHHHHHhchhHHHHHHHH
Q 029662 148 DHNGPLDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 148 ~h~gPM~v~~iAeKFrv~v~~vq~Il 173 (190)
.+..+-+..+||+..++++..|+.|.
T Consensus 125 ~lgr~pt~~elA~~lgi~~~~v~~~~ 150 (256)
T PRK07408 125 ELGRQPTDQEIAQALDISLEEWQEIK 150 (256)
T ss_pred HhCCCCCHHHHHHHcCCCHHHHHHHH
Confidence 34566779999999999999999886
No 364
>PF06511 IpaD: Invasion plasmid antigen IpaD; InterPro: IPR009483 This family consists of several invasion plasmid antigen IpaD proteins. Entry of Shigella flexneri into epithelial cells and lysis of the phagosome involve the IpaB, IpaC, and IpaD proteins, which are secreted by type III secretion machinery, and appear to form a multi-protein complex capable of inducing the phagocytic event which internalizes the bacterium [].; GO: 0009405 pathogenesis; PDB: 3R9V_B 2JAA_B 2J0O_A 2J0N_B 2P7N_A 2YM9_A 3NZZ_A 3O02_A 3O00_A 2YM0_B ....
Probab=27.34 E-value=61 Score=30.12 Aligned_cols=49 Identities=12% Similarity=0.288 Sum_probs=39.7
Q ss_pred cccHHHHHHHHHHhhccCCCCCCCCC---------------------HHHHHHHhchhHHHHHHHHHhhc
Q 029662 129 TLNVAQLRRIMLLHQGKADDHNGPLD---------------------AKQIAEKFRLDVLQVQAILQCLS 177 (190)
Q Consensus 129 TLNva~l~~ii~L~QGk~~~h~gPM~---------------------v~~iAeKFrv~v~~vq~Ilqf~S 177 (190)
++|..-|..|+..+.|..++-.+.|+ +.+|++||+=.-+-..+++|-||
T Consensus 254 ~~D~spL~~m~~sl~~~~~~~~~~~~~a~~qaw~~~f~~~~~~~~~~~q~~~~kys~ans~~dnl~k~ls 323 (337)
T PF06511_consen 254 SPDMSPLDKMIKSLDGLGSNGDVELSTAEYQAWQAGFDAQKNNIQSNVQSLTQKYSQANSTFDNLIKVLS 323 (337)
T ss_dssp EE-THHHHHHHHHHHHTTSTSCEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred EeCchHHHHHHHhccCCCCCCcccccHHHHHHHHHHHhHHHHHHHHHHHHHHHHHhhccchHHHHHHHHH
Confidence 68999999999999998776555543 67899999999888888888876
No 365
>TIGR02850 spore_sigG RNA polymerase sigma-G factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.
Probab=26.85 E-value=92 Score=25.77 Aligned_cols=27 Identities=15% Similarity=0.223 Sum_probs=23.3
Q ss_pred CCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 150 NGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 150 ~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
...-++++||++.++++..|..+++..
T Consensus 134 ~~~pt~~elA~~l~~~~e~v~~~~~~~ 160 (254)
T TIGR02850 134 SKEPTVSEIAKELKVPQEEVVFALDAI 160 (254)
T ss_pred CCCCCHHHHHHHHCcCHHHHHHHHHhc
Confidence 344589999999999999999988876
No 366
>PRK10130 transcriptional regulator EutR; Provisional
Probab=26.74 E-value=1.2e+02 Score=27.02 Aligned_cols=26 Identities=8% Similarity=0.259 Sum_probs=22.7
Q ss_pred CCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 149 HNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 149 h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
..-|++|++||+.++|....+++..+
T Consensus 253 ~~~~ltv~~lA~~~gvS~r~L~r~Fk 278 (350)
T PRK10130 253 MSEPVTVLDLCNQLHVSRRTLQNAFH 278 (350)
T ss_pred hcCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 34579999999999999999998873
No 367
>PRK13280 N-glycosylase/DNA lyase; Provisional
Probab=26.57 E-value=25 Score=31.50 Aligned_cols=33 Identities=33% Similarity=0.516 Sum_probs=19.2
Q ss_pred cccc-CchHHHHHHHhhcccccCCCCccccchhhh
Q 029662 66 LEER-DPQYDAMLNQMLGRVKTKAGGKAEMGEAAV 99 (190)
Q Consensus 66 l~er-Dp~ydaMl~qmvGrI~tkpGGk~Emgea~v 99 (190)
+||+ ||||+|| +.++..+-.-...+.-+++|.|
T Consensus 25 iee~~DpQy~av-~~L~~~~g~~~~~~Lvi~NaLv 58 (269)
T PRK13280 25 IEERVDPQYKAV-ENLVESLGEDLFAKLVIANALV 58 (269)
T ss_pred HHhccCHHHHHH-HHHHHHcCccHHHHHHHHHHHH
Confidence 4566 9999986 3334433333455555655554
No 368
>PRK15320 transcriptional activator SprB; Provisional
Probab=26.45 E-value=1.1e+02 Score=27.65 Aligned_cols=87 Identities=28% Similarity=0.312 Sum_probs=57.7
Q ss_pred HHHHHHhhcccccCCCCccccchhhhhhhhcCCCCCCCCC--------CCC-----CCCCCCCCCCCCcccHHHHHHHHH
Q 029662 74 DAMLNQMLGRVKTKAGGKAEMGEAAVVERQTRPLPKLRNT--------TPV-----SSRYEEKPSPPGTLNVAQLRRIML 140 (190)
Q Consensus 74 daMl~qmvGrI~tkpGGk~Emgea~vv~~ynRP~Pk~R~t--------~~~-----sg~~eer~~p~GTLNva~l~~ii~ 140 (190)
|+.|+|-+.-|-.----|+.+-||..- --.||--|--.+ +|| -.+|.---+|| +|+-.++.=+.+
T Consensus 98 ~~~l~~el~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~LSdREIEVL~L 175 (251)
T PRK15320 98 DYVLKDELSCAIRSEREKLRLPEAWLR-FCHRPQKKTVAATYAFNAGETPEEVLFNINQYAWWNLPP-GVTQAKYALLIL 175 (251)
T ss_pred hHHHHHHHHHHhcccccccCCcHHHHH-HhcCccccccceeeeccCCCChHHHhhhccceeeecCCC-CCCHHHHHHHHH
Confidence 677777777666655667777777542 235665443222 222 12344444666 588888888889
Q ss_pred HhhccCCCCCCCCCHHHHHHHhchhHHHHH
Q 029662 141 LHQGKADDHNGPLDAKQIAEKFRLDVLQVQ 170 (190)
Q Consensus 141 L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq 170 (190)
|-+|. +.+|||++|.+..+-|.
T Consensus 176 LAkG~--------SNKEIAekL~LS~KTVS 197 (251)
T PRK15320 176 LSSGH--------PAIELAKKFGLGTKTVS 197 (251)
T ss_pred HHcCC--------CHHHHHHHhccchhhHH
Confidence 99995 58999999999888775
No 369
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=26.07 E-value=89 Score=27.52 Aligned_cols=23 Identities=17% Similarity=0.196 Sum_probs=20.4
Q ss_pred CCCHHHHHHHhchhHHHHHHHHH
Q 029662 152 PLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 152 PM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
.|+.+|||+.++|....|..++.
T Consensus 282 ~~s~~EIA~~Lgis~~tV~~~~~ 304 (325)
T PRK05657 282 AATLEDVAREIGLTRERVRQIQV 304 (325)
T ss_pred CcCHHHHHHHHCcCHHHHHHHHH
Confidence 49999999999999999988764
No 370
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=25.88 E-value=83 Score=26.63 Aligned_cols=31 Identities=23% Similarity=0.233 Sum_probs=24.4
Q ss_pred CCCCCHHHHHHHhchhHHHHHHHHH------hhcCCC
Q 029662 150 NGPLDAKQIAEKFRLDVLQVQAILQ------CLSLPP 180 (190)
Q Consensus 150 ~gPM~v~~iAeKFrv~v~~vq~Ilq------f~SlP~ 180 (190)
...-++.+||++.+|++..|+.+++ .+||-.
T Consensus 141 g~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~ 177 (264)
T PRK07122 141 GRAPTASELAAELGMDREEVVEGLVAGSAYNTLSIDS 177 (264)
T ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHhhcCCCCcccc
Confidence 3334799999999999999999875 456654
No 371
>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial. This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.
Probab=25.82 E-value=2.1e+02 Score=23.08 Aligned_cols=43 Identities=12% Similarity=0.248 Sum_probs=30.3
Q ss_pred HHHHHHH--HhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 134 QLRRIML--LHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 134 ~l~~ii~--L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
||.+.|+ +.+|.-.....=-+-.+||++|+|.-.-|.+.|+-|
T Consensus 5 qi~~~l~~~I~~g~~~~g~~LPsE~eLa~~~~VSR~TVR~Al~~L 49 (230)
T TIGR02018 5 RIKQDILERIRSGEWPPGHRIPSEHELVAQYGCSRMTVNRALREL 49 (230)
T ss_pred HHHHHHHHHHHhCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 4444443 345665444444489999999999999999888755
No 372
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=25.79 E-value=1e+02 Score=21.80 Aligned_cols=29 Identities=21% Similarity=0.251 Sum_probs=23.8
Q ss_pred CCHHHHHHHhchhHHHHHHHHHhhcCCCC
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQCLSLPPE 181 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilqf~SlP~e 181 (190)
|++.|+|++++|....|....+.-=||+.
T Consensus 1 ~~~~eva~~~gi~~~tlr~~~~~Gll~~~ 29 (100)
T cd00592 1 YTIGEVAKLLGVSVRTLRYYEEKGLLPPE 29 (100)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCcCCC
Confidence 78999999999999999988776555543
No 373
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=25.52 E-value=65 Score=28.41 Aligned_cols=35 Identities=26% Similarity=0.357 Sum_probs=28.2
Q ss_pred HHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHh
Q 029662 135 LRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQC 175 (190)
Q Consensus 135 l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf 175 (190)
+-+|-.||=- .-|+-.|||+|++|--..|.++|+.
T Consensus 18 ~~~vA~lYY~------~g~tQ~eIA~~lgiSR~~VsRlL~~ 52 (318)
T PRK15418 18 VARIAWFYYH------DGLTQSEIGERLGLTRLKVSRLLEK 52 (318)
T ss_pred HHHHHHHHHh------cCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 5566667633 3399999999999999999999874
No 374
>PRK13501 transcriptional activator RhaR; Provisional
Probab=25.50 E-value=77 Score=26.10 Aligned_cols=38 Identities=21% Similarity=0.195 Sum_probs=27.1
Q ss_pred HHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 134 QLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 134 ~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
.++.++..-+- +...++++++||+++++..+.+.++++
T Consensus 177 ~~~~i~~~I~~---~~~e~~sl~~lA~~~~lS~~~l~r~Fk 214 (290)
T PRK13501 177 QLDLIMSALQQ---SLGAYFDMADFCHKNQLVERSLKQLFR 214 (290)
T ss_pred HHHHHHHHHHH---hhccCCCHHHHHHHHCcCHHHHHHHHH
Confidence 34444443332 334569999999999999999988765
No 375
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=25.30 E-value=93 Score=17.40 Aligned_cols=22 Identities=23% Similarity=0.342 Sum_probs=17.1
Q ss_pred CCHHHHHHHhchhHHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilq 174 (190)
++..+||..+++....|.+++.
T Consensus 13 ~s~~~~a~~~~~~~~~v~~~~~ 34 (58)
T cd00093 13 LTQEELAEKLGVSRSTISRIEN 34 (58)
T ss_pred CCHHHHHHHHCCCHHHHHHHHc
Confidence 7788999998888777766554
No 376
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=25.26 E-value=1.5e+02 Score=25.88 Aligned_cols=37 Identities=16% Similarity=0.157 Sum_probs=29.8
Q ss_pred CcccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHH
Q 029662 128 GTLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAI 172 (190)
Q Consensus 128 GTLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~I 172 (190)
..|.-.+++=+-++-|| |+.+|||+++.+.+..|++-
T Consensus 142 ~~LS~RE~eVL~Lia~G--------~SnkEIA~~L~IS~~TVk~h 178 (217)
T PRK13719 142 NKVTKYQNDVFILYSFG--------FSHEYIAQLLNITVGSSKNK 178 (217)
T ss_pred CCCCHHHHHHHHHHHCC--------CCHHHHHHHhCCCHHHHHHH
Confidence 46888887777777788 56999999999999877653
No 377
>PHA01976 helix-turn-helix protein
Probab=24.65 E-value=98 Score=20.15 Aligned_cols=28 Identities=11% Similarity=0.087 Sum_probs=21.6
Q ss_pred CCHHHHHHHhchhHHHHHHHHHhhcCCC
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQCLSLPP 180 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilqf~SlP~ 180 (190)
|+.+|+|++.+|..+.|.++..=.+.|.
T Consensus 16 lt~~~lA~~~gvs~~~v~~~e~g~~~p~ 43 (67)
T PHA01976 16 WSAPELSRRAGVRHSLIYDFEADKRLPN 43 (67)
T ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCCC
Confidence 7889999999998888887765555554
No 378
>cd05022 S-100A13 S-100A13: S-100A13 domain found in proteins similar to S100A13. S100A13 is a calcium-binding protein belonging to a large S100 vertebrate-specific protein family within the EF-hand superfamily of calcium-binding proteins. Note that the S-100 hierarchy, to which this S-100A13 group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100A13 is involved in the cellular export of interleukin-1 (IL-1) and of fibroblast growth factor-1 (FGF-1), which plays an important role in angiogenesis and tissue regeneration. Export is based on the CuII-dependent formation of multiprotein complexes containing the S100A13 protein. Assembly of these complexes occurs near the inner surface of the plasma membrane. Binding of two Ca(II) ions per monomer triggers key conformational changes leading to the creation of two identical and symmetrical Cu(II)-binding sites on the surface of the protein, close to the interface between the two monomers. These Cu
Probab=24.48 E-value=98 Score=22.73 Aligned_cols=46 Identities=13% Similarity=0.093 Sum_probs=28.9
Q ss_pred cHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhch------hH-HHHHHHHHhhcC
Q 029662 131 NVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRL------DV-LQVQAILQCLSL 178 (190)
Q Consensus 131 Nva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv------~v-~~vq~Ilqf~Sl 178 (190)
.+..|++++..|.++ +.+|-|+.+++-.-+.- .. .-|+.+++.+-.
T Consensus 6 ai~~l~~~F~~fd~~--~~~g~i~~~ELk~ll~~elg~~ls~~~~v~~mi~~~D~ 58 (89)
T cd05022 6 AIETLVSNFHKASVK--GGKESLTASEFQELLTQQLPHLLKDVEGLEEKMKNLDV 58 (89)
T ss_pred HHHHHHHHHHHHhCC--CCCCeECHHHHHHHHHHHhhhhccCHHHHHHHHHHhCC
Confidence 467788888888777 77888887776543322 12 346666655443
No 379
>COG4901 Ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=24.42 E-value=69 Score=25.77 Aligned_cols=28 Identities=11% Similarity=0.230 Sum_probs=24.5
Q ss_pred CCCCCHHHHHHHhchhHHHHHHHHHhhc
Q 029662 150 NGPLDAKQIAEKFRLDVLQVQAILQCLS 177 (190)
Q Consensus 150 ~gPM~v~~iAeKFrv~v~~vq~Ilqf~S 177 (190)
.--+++..||.|++|+.++...+|.-|+
T Consensus 57 ~r~VTpy~la~r~gI~~SvAr~vLR~Le 84 (107)
T COG4901 57 ERVVTPYVLASRYGINGSVARIVLRHLE 84 (107)
T ss_pred ceeecHHHHHHHhccchHHHHHHHHHHH
Confidence 3457899999999999999999998775
No 380
>PF12983 DUF3867: Protein of unknown function (DUF3867); InterPro: IPR024218 This entry represents a family of functionally uncharacterised proteins that are found in bacteria. Proteins in this family are approximately 190 amino acids in length.
Probab=24.38 E-value=54 Score=28.54 Aligned_cols=57 Identities=12% Similarity=0.282 Sum_probs=45.1
Q ss_pred CCCCcccHHHHHHHHHHhhccCCC-CCCCCCH-HHHHHHhchhHHHHHHHHHhhcCCCC
Q 029662 125 SPPGTLNVAQLRRIMLLHQGKADD-HNGPLDA-KQIAEKFRLDVLQVQAILQCLSLPPE 181 (190)
Q Consensus 125 ~p~GTLNva~l~~ii~L~QGk~~~-h~gPM~v-~~iAeKFrv~v~~vq~Ilqf~SlP~e 181 (190)
|..|+||+++.-.=|.-|+.+--= |+.-|++ +++-|+|++|.+.|+..++-+-+-..
T Consensus 32 ~a~Gklsm~dFsk~I~~YmeeNNISqeKf~niQkk~mERYGfd~~~iE~q~K~~Gid~~ 90 (186)
T PF12983_consen 32 VAEGKLSMADFSKKIMEYMEENNISQEKFLNIQKKFMERYGFDPSEIEKQMKSMGIDMS 90 (186)
T ss_pred HhcCcccHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHhCCCHHHHHHHHHHcCCCcc
Confidence 578999999999999999876432 4455555 47899999999999999887766544
No 381
>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=24.34 E-value=1.3e+02 Score=24.38 Aligned_cols=26 Identities=12% Similarity=0.162 Sum_probs=20.9
Q ss_pred CCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 149 HNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 149 h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
.+..-++.||||..+|++.+|++.+.
T Consensus 43 p~~~ati~eV~e~tgVs~~~I~~~Ir 68 (137)
T TIGR03826 43 ENRQATVSEIVEETGVSEKLILKFIR 68 (137)
T ss_pred CCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 33356899999999999998887654
No 382
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=24.23 E-value=81 Score=20.34 Aligned_cols=22 Identities=27% Similarity=0.379 Sum_probs=16.3
Q ss_pred CCHHHHHHHhchhHHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilq 174 (190)
|+..++|++.++..+.+.+|..
T Consensus 13 lt~~~~a~~~~i~~~~i~~~e~ 34 (64)
T PF12844_consen 13 LTQKDLAEKLGISRSTISKIEN 34 (64)
T ss_dssp --HHHHHHHHTS-HHHHHHHHT
T ss_pred CCHHHHHHHHCcCHHHHHHHHC
Confidence 7899999999998888877764
No 383
>TIGR03454 partition_RepB plasmid partitioning protein RepB. Members of this family are the RepB protein involved in replicon partitioning. RepB is found, in general, as part of a repABC operon in plasmids and small chromosomes, separate from the main chromosome, in various bacteria. This model describes a rather narrow clade of proteins; it should be noted that additional homologs scoring below the trusted cutoff have very similar functions, although they may be named differently.
Probab=24.22 E-value=61 Score=29.37 Aligned_cols=29 Identities=17% Similarity=0.409 Sum_probs=26.5
Q ss_pred CCHHHHHHHhchhHHHHHHHHHhh-cCCCC
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQCL-SLPPE 181 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilqf~-SlP~e 181 (190)
++-++||++++++-+.|.++|.++ .||++
T Consensus 178 ~~~~~ia~~Lg~~ks~vSr~lsl~~~lP~~ 207 (325)
T TIGR03454 178 FDRDTIMAALSVDKTELSRMISVARRIPEE 207 (325)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHhCCHH
Confidence 577899999999999999999998 79875
No 384
>smart00453 WSN Worm-specific (usually) N-terminal domain.
Probab=24.11 E-value=1e+02 Score=22.11 Aligned_cols=40 Identities=25% Similarity=0.442 Sum_probs=27.8
Q ss_pred HHHHHHHHHhhccCCCCCCCCCHHH-HHHHhchhHHHHHHHHHh
Q 029662 133 AQLRRIMLLHQGKADDHNGPLDAKQ-IAEKFRLDVLQVQAILQC 175 (190)
Q Consensus 133 a~l~~ii~L~QGk~~~h~gPM~v~~-iAeKFrv~v~~vq~Ilqf 175 (190)
|.|--.|-|.+|-. +|-+.+++ |||-++++.+.++.|..|
T Consensus 14 aRv~N~I~LQ~~l~---~gsi~~~~vI~ELL~~~~~~~~~i~~~ 54 (69)
T smart00453 14 ARVTNAISLQAGLI---NGSIPIDDVIAELLNIDSSKLSDIINV 54 (69)
T ss_pred HHHHHHHHHHHHHH---cCCCCHHHHHHHHHcCCCccHHHHHhc
Confidence 44444555555544 56677766 799999988888888776
No 385
>TIGR03859 PQQ_PqqD coenzyme PQQ biosynthesis protein PqqD. This model identifies PqqD, a protein involved in the final steps of the biosynthesis of pyrroloquinoline quinone, coenzyme PQQ.
Probab=24.06 E-value=91 Score=22.28 Aligned_cols=35 Identities=20% Similarity=0.283 Sum_probs=24.5
Q ss_pred HHHHHHhhccCCCCCCCCCHHHHH----HHhchhHHHHHHHHHhhc
Q 029662 136 RRIMLLHQGKADDHNGPLDAKQIA----EKFRLDVLQVQAILQCLS 177 (190)
Q Consensus 136 ~~ii~L~QGk~~~h~gPM~v~~iA----eKFrv~v~~vq~Ilqf~S 177 (190)
-.|..|-+|+ .+|.+|+ ++|.+....-+.+++||+
T Consensus 34 ~~Iw~lldg~-------~tv~eI~~~L~~~Y~~~e~~~~dV~~fL~ 72 (81)
T TIGR03859 34 GEILELCDGK-------RSLAEIIQELAQRFPAAEEIEDDVIAFLA 72 (81)
T ss_pred HHHHHHccCC-------CcHHHHHHHHHHHcCChhhHHHHHHHHHH
Confidence 4677787775 4787765 566883344588999986
No 386
>PRK09940 transcriptional regulator YdeO; Provisional
Probab=23.71 E-value=1.1e+02 Score=26.75 Aligned_cols=37 Identities=16% Similarity=0.198 Sum_probs=28.7
Q ss_pred HHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHh
Q 029662 133 AQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQC 175 (190)
Q Consensus 133 a~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf 175 (190)
..++.+|. ++...+.++++||+.+++..+.++++++-
T Consensus 137 ~kv~~~I~------~~~~~~~tl~~LA~~~gmS~s~l~R~FK~ 173 (253)
T PRK09940 137 GKVRNIVN------MKLAHPWKLKDICDCLYISESLLKKKLKQ 173 (253)
T ss_pred HHHHHHHH------HhhcCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 45566653 33456799999999999999999998864
No 387
>PF12833 HTH_18: Helix-turn-helix domain; PDB: 2K9S_A 3LSG_C 3OIO_A 1D5Y_B 3GBG_A 3OOU_A 1BL0_A 1XS9_A 3MN2_B 3MKL_B ....
Probab=23.71 E-value=91 Score=20.82 Aligned_cols=14 Identities=29% Similarity=0.387 Sum_probs=8.8
Q ss_pred CCCHHHHHHHhchh
Q 029662 152 PLDAKQIAEKFRLD 165 (190)
Q Consensus 152 PM~v~~iAeKFrv~ 165 (190)
-+++.+||.+++..
T Consensus 45 ~~~i~~ia~~~Gf~ 58 (81)
T PF12833_consen 45 DLSIAEIAEECGFS 58 (81)
T ss_dssp T--HHHHHHHTT-S
T ss_pred cccHHHHHHHcCCC
Confidence 48899999888765
No 388
>PF13591 MerR_2: MerR HTH family regulatory protein
Probab=23.69 E-value=88 Score=22.50 Aligned_cols=29 Identities=10% Similarity=0.229 Sum_probs=24.2
Q ss_pred CCHHHHHHHhchhHHHHHHHHHhhcCCCC
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQCLSLPPE 181 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilqf~SlP~e 181 (190)
++++|+++.++++.+.|..++++==+.+.
T Consensus 1 is~~e~~~~~~i~~~~l~~lve~Gli~p~ 29 (84)
T PF13591_consen 1 ISLEEFCEACGIEPEFLRELVEEGLIEPE 29 (84)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCeeec
Confidence 47899999999999999999987555444
No 389
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=23.66 E-value=1.1e+02 Score=24.96 Aligned_cols=27 Identities=15% Similarity=0.227 Sum_probs=22.6
Q ss_pred CCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 150 NGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 150 ~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
...-++.+||+..++++..|+.++.+.
T Consensus 101 g~~pt~~eia~~l~~~~~~v~~~~~~~ 127 (238)
T TIGR02393 101 GREPTDEELAERMGMPAEKVREIKKIA 127 (238)
T ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHh
Confidence 345679999999999999999987654
No 390
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=23.63 E-value=1.1e+02 Score=16.95 Aligned_cols=21 Identities=24% Similarity=0.327 Sum_probs=15.6
Q ss_pred CCHHHHHHHhchhHHHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQAIL 173 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Il 173 (190)
|+..+||+..++....|.+++
T Consensus 11 ~s~~~la~~~~i~~~~i~~~~ 31 (56)
T smart00530 11 LTQEELAEKLGVSRSTLSRIE 31 (56)
T ss_pred CCHHHHHHHhCCCHHHHHHHH
Confidence 778888888888776665544
No 391
>PRK13626 transcriptional regulator SgrR; Provisional
Probab=23.60 E-value=1.2e+02 Score=28.12 Aligned_cols=41 Identities=12% Similarity=0.233 Sum_probs=32.1
Q ss_pred HHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 135 LRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 135 l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
.++-++||+. ..++...++++|||+.|-.---.++.||+-+
T Consensus 7 ~~~~~~L~~~-~~~~~~~~~l~~la~~l~cs~R~~~~~l~~~ 47 (552)
T PRK13626 7 QQQFIRLWQC-CEGKSQETTLNELAELLNCSRRHMRTLLNTM 47 (552)
T ss_pred HHHHHHHHHh-cCCCcceeeHHHHHHHhcCChhHHHHHHHHH
Confidence 3567778777 4466668999999999999888888887644
No 392
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=23.54 E-value=91 Score=29.24 Aligned_cols=30 Identities=33% Similarity=0.577 Sum_probs=25.5
Q ss_pred CCCCCC--CHHHHHHHhchhHHHHHHHHHhhc
Q 029662 148 DHNGPL--DAKQIAEKFRLDVLQVQAILQCLS 177 (190)
Q Consensus 148 ~h~gPM--~v~~iAeKFrv~v~~vq~Ilqf~S 177 (190)
|.+|-+ ++++||+.|+++...|+++|+.|-
T Consensus 132 D~~GyL~~~~~eia~~l~~~~~~v~~~l~~lQ 163 (455)
T PRK05932 132 DDEGYLTEDLEEIAESLGVELDEVEAVLKRIQ 163 (455)
T ss_pred CCCCCCCCCHHHHHHHcCCCHHHHHHHHHHHh
Confidence 467765 889999999999999999988763
No 393
>PRK15044 transcriptional regulator SirC; Provisional
Probab=23.37 E-value=1.5e+02 Score=26.88 Aligned_cols=29 Identities=17% Similarity=0.226 Sum_probs=25.6
Q ss_pred CCCCCCCCHHHHHHHhchhHHHHHHHHHh
Q 029662 147 DDHNGPLDAKQIAEKFRLDVLQVQAILQC 175 (190)
Q Consensus 147 ~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf 175 (190)
++...++++++||+++++....+.+.++.
T Consensus 203 ~nl~~~~SLeeLA~~lgmS~~tL~R~Fk~ 231 (295)
T PRK15044 203 SDLTRKWSQAEVAGKLFMSVSSLKRKLAA 231 (295)
T ss_pred hCcccCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 56677899999999999999999998764
No 394
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=23.27 E-value=93 Score=28.88 Aligned_cols=29 Identities=28% Similarity=0.552 Sum_probs=24.4
Q ss_pred CCCCCC--CHHHHHHHhchhHHHHHHHHHhh
Q 029662 148 DHNGPL--DAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 148 ~h~gPM--~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
|++|-+ ++++||+.|+++...|+.+++.+
T Consensus 107 D~~GyL~~~~~eia~~l~~~~~~ve~~l~~i 137 (429)
T TIGR02395 107 DEDGYLEIDLEEIADELEVSEEEVEKVLELI 137 (429)
T ss_pred CCCCCCCCCHHHHHHHcCCCHHHHHHHHHHH
Confidence 466654 58999999999999999988776
No 395
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=23.18 E-value=2.5e+02 Score=22.83 Aligned_cols=46 Identities=17% Similarity=0.120 Sum_probs=36.9
Q ss_pred cccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 129 TLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 129 TLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
-|.-.|++-+..-|.=--=|.+--.+.++||+.|+|--+-++..|.
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLR 200 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLR 200 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHH
Confidence 5777888877777765566778889999999999999888776653
No 396
>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore, this region contains a putative helix-turn-helix motif. At the C terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins [].; PDB: 2AHQ_A 2O9L_A 2O8K_A.
Probab=23.17 E-value=27 Score=28.52 Aligned_cols=27 Identities=26% Similarity=0.340 Sum_probs=0.0
Q ss_pred CCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 148 DHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 148 ~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
.+-.||..++||+..+|.+|-|-+++.
T Consensus 45 ~~l~PLt~~~iA~~lgl~~STVSRav~ 71 (160)
T PF04552_consen 45 GALKPLTMKDIADELGLHESTVSRAVK 71 (160)
T ss_dssp ---------------------------
T ss_pred ccCcCCCHHHHHHHhCCCHhHHHHHHc
Confidence 478899999999999999999999874
No 397
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=23.17 E-value=1.7e+02 Score=25.09 Aligned_cols=31 Identities=19% Similarity=0.238 Sum_probs=25.2
Q ss_pred CCCCCHHHHHHHhchhHHHHHHHHH-----hhcCCC
Q 029662 150 NGPLDAKQIAEKFRLDVLQVQAILQ-----CLSLPP 180 (190)
Q Consensus 150 ~gPM~v~~iAeKFrv~v~~vq~Ilq-----f~SlP~ 180 (190)
..+-++.+||+..+++...|+.++. .+||-.
T Consensus 149 ~~~~t~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~ 184 (284)
T PRK06596 149 LNPEEVEMVAEELGVSEEEVREMESRLSGQDASLDA 184 (284)
T ss_pred CCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCcCcCC
Confidence 3556799999999999999999976 566644
No 398
>KOG4481 consensus Uncharacterized conserved protein [Function unknown]
Probab=23.15 E-value=2.2e+02 Score=25.02 Aligned_cols=70 Identities=20% Similarity=0.231 Sum_probs=50.8
Q ss_pred hcCCCCCCCCCCCCCCCCC--CCCCCCCcccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 103 QTRPLPKLRNTTPVSSRYE--EKPSPPGTLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 103 ynRP~Pk~R~t~~~sg~~e--er~~p~GTLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
--+|+|+-+.+--+-+-|+ -+-+|.|.|-+-+--+.|.-|+= + ..--..+-||..+-++...|..|+.|.
T Consensus 88 ~q~~fp~e~r~p~~~~f~~~~i~rIpkgkit~~eAL~~ln~hkL--~--petw~AekIA~ey~l~~~~v~~il~YF 159 (194)
T KOG4481|consen 88 RQEEFPKEFRLPKDYHFDEINIKRIPKGKITIVEALTFLNNHKL--L--PETWTAEKIAQEYHLEQEDVNDILKYF 159 (194)
T ss_pred hcccchhhcCCcccccCCCcCcccCCCCceeHHHHHHHHhhhhc--C--hhhhHHHHHHHHHhhchhhHHHHHHHh
Confidence 4578888776655555443 47799999998766665544321 1 334578889999999999999999986
No 399
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=23.09 E-value=95 Score=18.91 Aligned_cols=23 Identities=9% Similarity=0.133 Sum_probs=19.8
Q ss_pred CCHHHHHHHhchhHHHHHHHHHh
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQC 175 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilqf 175 (190)
|+..++|++.+|..+.|-++..=
T Consensus 16 ltq~~lA~~~gvs~~~vs~~e~g 38 (58)
T TIGR03070 16 LTQADLADLAGVGLRFIRDVENG 38 (58)
T ss_pred CCHHHHHHHhCCCHHHHHHHHCC
Confidence 88999999999999888887653
No 400
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=23.05 E-value=55 Score=20.29 Aligned_cols=18 Identities=28% Similarity=0.359 Sum_probs=14.7
Q ss_pred HHHHHhchhHHHHHHHHH
Q 029662 157 QIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 157 ~iAeKFrv~v~~vq~Ilq 174 (190)
+||++.+|..+.|.+++.
T Consensus 2 ~lA~~~gvs~~tvs~~l~ 19 (52)
T cd01392 2 DIARAAGVSVATVSRVLN 19 (52)
T ss_pred cHHHHHCcCHHHHHHHHc
Confidence 688999988888887764
No 401
>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=22.88 E-value=72 Score=26.40 Aligned_cols=98 Identities=23% Similarity=0.272 Sum_probs=53.7
Q ss_pred HHHHHHHhhcccc---cCCCCccccchhhhhhhhcCCCCC----------------------CCCCCCCCCCCCCCCCCC
Q 029662 73 YDAMLNQMLGRVK---TKAGGKAEMGEAAVVERQTRPLPK----------------------LRNTTPVSSRYEEKPSPP 127 (190)
Q Consensus 73 ydaMl~qmvGrI~---tkpGGk~Emgea~vv~~ynRP~Pk----------------------~R~t~~~sg~~eer~~p~ 127 (190)
|.+.-.|++.-.. .+-||--+| ..|...|||=+.. ++--+-.+|..--+-+|.
T Consensus 92 ~~ELa~qi~e~c~~~~~~~GGii~L--~dl~~~~nr~R~g~~lISp~Di~~A~~~l~~lg~g~~l~~~~sg~~vv~s~~~ 169 (223)
T PF04157_consen 92 YYELAVQIAEVCLATRSKNGGIISL--SDLYCRYNRARGGSELISPEDILRACKLLEVLGLGFRLRKFGSGVKVVQSVPY 169 (223)
T ss_dssp HHHHHHHHHHHHHHHCCTTTSEEEH--HHHHHHHHHCTTTSST--HHHHHHHHHHHCCCTSSEEEEEETTTEEEEECST-
T ss_pred HHHHHHHHHHHHHHHHhcCCCEEEH--HHHHHHHHHhcccCCCcCHHHHHHHHHHHHHcCCCeEEEEeCCCcEEEEeCCc
Confidence 4555556555443 367775555 4567889983311 111111122222223333
Q ss_pred CcccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 128 GTLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 128 GTLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
..+|.-+ ..|+.+-+ +...|.+++.+||++|++.....+..|..+
T Consensus 170 ~e~~~~~-~~il~~~~---~~~~g~vt~~~l~~~~~ws~~~a~~~L~~~ 214 (223)
T PF04157_consen 170 SELSKDQ-SRILELAE---EENGGGVTASELAEKLGWSVERAKEALEEL 214 (223)
T ss_dssp CHH-HHH-HHHHHHH-----TTTSEEEHHHHHHHHTB-HHHHHHHHHHH
T ss_pred hhhhHHH-HHHHHHHH---hhcCCCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 4553332 23333332 667889999999999999999999988764
No 402
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=22.79 E-value=69 Score=23.41 Aligned_cols=19 Identities=16% Similarity=0.246 Sum_probs=16.6
Q ss_pred CCHHHHHHHhchhHHHHHH
Q 029662 153 LDAKQIAEKFRLDVLQVQA 171 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~ 171 (190)
|.+.|+|++++|.+..|.-
T Consensus 1 m~Ige~a~~~gvs~~tlRy 19 (107)
T cd04777 1 MKIGKFAKKNNITIDTVRH 19 (107)
T ss_pred CCHHHHHHHHCcCHHHHHH
Confidence 7899999999999988753
No 403
>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=22.62 E-value=1.1e+02 Score=25.27 Aligned_cols=25 Identities=20% Similarity=0.422 Sum_probs=22.0
Q ss_pred CCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 150 NGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 150 ~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
.++.++++||+..+++...+.++++
T Consensus 253 ~~~~~~~~ia~~lg~~~~~~~~~~e 277 (305)
T TIGR00635 253 GGPVGLKTLAAALGEDADTIEDVYE 277 (305)
T ss_pred CCcccHHHHHHHhCCCcchHHHhhh
Confidence 3468999999999999999999877
No 404
>COG1983 PspC Putative stress-responsive transcriptional regulator [Transcription / Signal transduction mechanisms]
Probab=22.61 E-value=64 Score=23.96 Aligned_cols=15 Identities=33% Similarity=0.406 Sum_probs=12.6
Q ss_pred HHHHHhchhHHHHHH
Q 029662 157 QIAEKFRLDVLQVQA 171 (190)
Q Consensus 157 ~iAeKFrv~v~~vq~ 171 (190)
=|||.|++|+..|.=
T Consensus 20 Gla~yf~id~tlVRl 34 (70)
T COG1983 20 GLAEYFGIDPTLVRL 34 (70)
T ss_pred hHHHHhCCChHHHHH
Confidence 489999999988764
No 405
>COG4567 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]
Probab=22.29 E-value=2.3e+02 Score=24.70 Aligned_cols=47 Identities=17% Similarity=0.294 Sum_probs=39.8
Q ss_pred CCCCCCCCCCcccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662 119 RYEEKPSPPGTLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 119 ~~eer~~p~GTLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
--.|++.+.-.|-.+|||+.+..+.| +|.+-|.+.+.----+|+||+
T Consensus 131 ~~~~~pmS~~rl~WEhIqrvl~e~~~---------NiSeTARrL~MHRRTLqRkL~ 177 (182)
T COG4567 131 APPENPMSADRLRWEHIQRVLEECEG---------NISETARRLNMHRRTLQRKLA 177 (182)
T ss_pred CCCCCCCchhHhhHHHHHHHHHHhCC---------CHHHHHHHhhhhHHHHHHHHh
Confidence 33467788888999999999998887 478899999999999999986
No 406
>PF10376 Mei5: Double-strand recombination repair protein ; InterPro: IPR018468 Mei5 is one of a pair of meiosis-specific proteins which facilitate the loading of Dmc1 on to Rad51 on DNA at double-strand breaks during recombination. Recombination is carried out by a large protein complex based around the two RecA homologues, Rad51 and Dmc1 []. This complex may play both a catalytic and a structural role in the interaction between homologous chromosomes during meiosis. Mei5 is seen to contain a coiled-coli region.
Probab=22.01 E-value=86 Score=27.09 Aligned_cols=39 Identities=10% Similarity=0.312 Sum_probs=29.1
Q ss_pred cHHHHHHHH------------HHhhccCCCCCCCCCHHHHHHHhchhHHHH
Q 029662 131 NVAQLRRIM------------LLHQGKADDHNGPLDAKQIAEKFRLDVLQV 169 (190)
Q Consensus 131 Nva~l~~ii------------~L~QGk~~~h~gPM~v~~iAeKFrv~v~~v 169 (190)
|..+|+..| .|+..-+.+.+..|+..||+..|+||..+|
T Consensus 168 ~~~~Lq~lI~Kwr~~~q~~l~eL~~~~~~~e~~~~TM~eL~~~l~ID~~LI 218 (221)
T PF10376_consen 168 DLEQLQSLIKKWRSASQEALYELQSEMSEEEGEKFTMGELIKRLGIDYDLI 218 (221)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCccHHHHHHHhCCCcccc
Confidence 456777766 455444444778899999999999998766
No 407
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=21.88 E-value=94 Score=21.66 Aligned_cols=26 Identities=15% Similarity=0.146 Sum_probs=20.0
Q ss_pred CCCHHHHHHHhchhHHHHHHHHHhhc
Q 029662 152 PLDAKQIAEKFRLDVLQVQAILQCLS 177 (190)
Q Consensus 152 PM~v~~iAeKFrv~v~~vq~Ilqf~S 177 (190)
-|++.+||++-.|-.+-|-+..+-|-
T Consensus 34 ~~si~elA~~~~vS~sti~Rf~kkLG 59 (77)
T PF01418_consen 34 FMSISELAEKAGVSPSTIVRFCKKLG 59 (77)
T ss_dssp T--HHHHHHHCTS-HHHHHHHHHHCT
T ss_pred HccHHHHHHHcCCCHHHHHHHHHHhC
Confidence 49999999999999999988887654
No 408
>PRK15185 transcriptional regulator HilD; Provisional
Probab=21.79 E-value=1.6e+02 Score=26.77 Aligned_cols=37 Identities=8% Similarity=0.134 Sum_probs=28.3
Q ss_pred HHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHh
Q 029662 133 AQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQC 175 (190)
Q Consensus 133 a~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf 175 (190)
.+++++|. ++...+.++++||+.+++....+.+.++.
T Consensus 209 erV~~~I~------~n~~~~~SledLA~~lgmS~~tL~R~FK~ 245 (309)
T PRK15185 209 ERVYNIIS------SSPSRQWKLTDVADHIFMSTSTLKRKLAE 245 (309)
T ss_pred HHHHHHHH------hCccCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 34555554 23456799999999999999999999764
No 409
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=21.46 E-value=1.5e+02 Score=21.08 Aligned_cols=29 Identities=14% Similarity=-0.017 Sum_probs=24.2
Q ss_pred CCHHHHHHHhchhHHHHHHHHHhhcCCCC
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQCLSLPPE 181 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilqf~SlP~e 181 (190)
|++.++|+.++|.+..|..-.+.=-+++.
T Consensus 2 ~~i~e~A~~~gvs~~tLr~ye~~Gli~p~ 30 (91)
T cd04766 2 YVISVAAELSGMHPQTLRLYERLGLLSPS 30 (91)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHCCCcCCC
Confidence 78999999999999999988876555553
No 410
>KOG3108 consensus Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [Replication, recombination and repair]
Probab=21.30 E-value=1.3e+02 Score=26.81 Aligned_cols=30 Identities=23% Similarity=0.287 Sum_probs=24.4
Q ss_pred CCCCCCHHHHHHHhch-hHHHHHHHHHhhcC
Q 029662 149 HNGPLDAKQIAEKFRL-DVLQVQAILQCLSL 178 (190)
Q Consensus 149 h~gPM~v~~iAeKFrv-~v~~vq~Ilqf~Sl 178 (190)
|.--..+++||++++. .++.+..+++||++
T Consensus 218 h~eGv~~~~i~~~l~~~~~~~~~~~~~~l~~ 248 (265)
T KOG3108|consen 218 HIEGVHIKEIAAQLREPSVSELREAVDFLLN 248 (265)
T ss_pred ccccccHHHHHHHhcccchhhHHHHHHHHhc
Confidence 3355889999999998 47888888998875
No 411
>cd02641 R3H_Smubp-2_like R3H domain of Smubp-2_like proteins. Smubp-2_like proteins also contain a helicase_like and an AN1-like Zinc finger domain and have been shown to bind single-stranded DNA. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA.
Probab=21.25 E-value=52 Score=22.80 Aligned_cols=34 Identities=18% Similarity=0.319 Sum_probs=21.0
Q ss_pred HHHHHHHHHhhccCC--C-CCCC-CC------HHHHHHHhchhH
Q 029662 133 AQLRRIMLLHQGKAD--D-HNGP-LD------AKQIAEKFRLDV 166 (190)
Q Consensus 133 a~l~~ii~L~QGk~~--~-h~gP-M~------v~~iAeKFrv~v 166 (190)
.+++++|..|---.. . +=-| |+ ||+||++|++..
T Consensus 2 ~~~~~~i~~F~~~~~~~~l~F~p~ls~~eR~~vH~lA~~~gL~s 45 (60)
T cd02641 2 KHLKAMVKAFMKDPKATELEFPPTLSSHDRLLVHELAEELGLRH 45 (60)
T ss_pred hhHHHHHHHHHcCCCcCcEECCCCCCHHHHHHHHHHHHHcCCce
Confidence 356666666644322 1 3345 65 789999999853
No 412
>PRK06474 hypothetical protein; Provisional
Probab=21.22 E-value=1.2e+02 Score=24.66 Aligned_cols=37 Identities=11% Similarity=0.113 Sum_probs=25.4
Q ss_pred HHHHHHhhccCCCCCCCCCHHHHHHHh-chhHHHHHHHHHhh
Q 029662 136 RRIMLLHQGKADDHNGPLDAKQIAEKF-RLDVLQVQAILQCL 176 (190)
Q Consensus 136 ~~ii~L~QGk~~~h~gPM~v~~iAeKF-rv~v~~vq~Ilqf~ 176 (190)
..||.+..+ ++++|++.|||+.+ .+..+-|-+.|+.|
T Consensus 14 ~~Il~~L~~----~~~~~ta~el~~~l~~is~aTvYrhL~~L 51 (178)
T PRK06474 14 MKICQVLMR----NKEGLTPLELVKILKDVPQATLYRHLQTM 51 (178)
T ss_pred HHHHHHHHh----CCCCCCHHHHHHHhcCCCHHHHHHHHHHH
Confidence 345554432 23359999999999 67777777777655
No 413
>PF02317 Octopine_DH: NAD/NADP octopine/nopaline dehydrogenase, alpha-helical domain; InterPro: IPR003421 This group of enzymes act on the CH-NH substrate bond using NAD(+) or NADP(+) as an acceptor. This domain is found primarily in octopine dehydrogenase (1.5.1.11 from EC), nopaline dehydrogenase (1.5.1.19 from EC), and lysopine dehydrogenase (1.5.1.16 from EC). NADPH is the preferred cofactor, but NADH is also used. Octopine dehydrogenase is involved in the reductive condensation of arginine and pyruvic acid to D-octopine []. Opine dehydrogenases can be found in both bacteria and marine cephalopods. In bacteria, some of these opine dehydrogenases are involved in crown gall tumours that are produced by Agrobacterium spp., and which encode for the opine dehydrogenases on a Ti-plasmid. These bacteria can transfer a portion of this plasmid (T-DNA) to a susceptible plant cell; the T-DNA then integrates into the plant nuclear genome, where its genes can be expressed. Some of these genes direct the synthesis and secretion of unusual amino acid and sugar derivatives called opines - these opines are used as a carbon and sometimes a nitrogen source by the infecting bacteria. Opine dehydrogenases are also found in the marine invertebrate cephalopods (octopuses, squid, and cuttlefish). For example in marine cephalopods, octopine dehydrogenase activity in mantle muscle is significantly correlated with a species' ability to buffer the acidic end products of anaerobic metabolism, with activity declining strongly with a species' habitat depth [].; GO: 0016491 oxidoreductase activity, 0050662 coenzyme binding, 0055114 oxidation-reduction process; PDB: 3IQD_B 3C7D_B 3C7A_A 3C7C_B 1BG6_A.
Probab=21.15 E-value=80 Score=24.76 Aligned_cols=24 Identities=17% Similarity=0.207 Sum_probs=18.0
Q ss_pred CHHHHHHHhchhHHHHHHHHHhhc
Q 029662 154 DAKQIAEKFRLDVLQVQAILQCLS 177 (190)
Q Consensus 154 ~v~~iAeKFrv~v~~vq~Ilqf~S 177 (190)
-+.+|||+++|+.-.+..|+.+-|
T Consensus 124 ~~~~la~~~GV~tP~id~~I~~a~ 147 (152)
T PF02317_consen 124 PLASLAELLGVPTPVIDSIITWAS 147 (152)
T ss_dssp HHHHHHHHCT---HHHHHHHHHHH
T ss_pred HHHHHHHHhCCCchHHHHHHHHHH
Confidence 468999999999999999998754
No 414
>PHA00542 putative Cro-like protein
Probab=21.10 E-value=1.6e+02 Score=20.98 Aligned_cols=24 Identities=17% Similarity=0.117 Sum_probs=22.0
Q ss_pred CCHHHHHHHhchhHHHHHHHHHhh
Q 029662 153 LDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 153 M~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
|+..++|+.++|.-+.|.+|+.--
T Consensus 32 lTq~elA~~lgIs~~tIsr~e~g~ 55 (82)
T PHA00542 32 WSQEQIADATDVSQPTICRIYSGR 55 (82)
T ss_pred CCHHHHHHHHCcCHHHHHHHHcCC
Confidence 899999999999999999998665
No 415
>PF05043 Mga: Mga helix-turn-helix domain; InterPro: IPR007737 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions []. The family also contains VirR like proteins which match only at the C terminus of the alignment.; PDB: 3SQN_A.
Probab=21.07 E-value=82 Score=21.80 Aligned_cols=26 Identities=12% Similarity=0.133 Sum_probs=19.8
Q ss_pred CCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 151 GPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 151 gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
...++.++|+++.|..+-+.+.++-+
T Consensus 29 ~~~s~~~la~~~~iS~sti~~~i~~l 54 (87)
T PF05043_consen 29 EYVSIEDLAEELFISRSTIYRDIKKL 54 (87)
T ss_dssp SEEEHHHHHHHHT--HHHHHHHHHHH
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 34899999999999999888877643
No 416
>PF10493 Rod_C: Rough deal protein C-terminal region; InterPro: IPR019527 Rod, the Rough deal protein (also known as Kinetochore-associated protein 1) displays a dynamic intracellular staining pattern, localising first to kinetochores in pro-metaphase, but moving to kinetochore microtubules at metaphase. Early in anaphase the protein is once again restricted to the kinetochores, where it persists until the end of telophase. This behaviour is in all respects similar to that described for ZW10 [], and indeed the two proteins function together, localisation of each depending upon the other []. These two proteins are found at the kinetochore in complex with a third, Zwilch, in both flies and humans. The C- terminus is the most conserved part of the protein. During pro-metaphase, the ZW10-Rod complex, dynein/dynactin, and Mad2 all accumulate on unattached kinetochores; microtubule capture leads to Mad2 depletion as it is carried off by dynein/dynactin; ZW10-Rod complex accumulation continues, replenishing kinetochore dynein. The continuing recruitment of the ZW10-Rod complex during metaphase may serve to maintain adequate dynein/dynactin complex on kinetochores for assisting chromatid movement during anaphase[]. The ZW10-Rod complex acts as a bridge whose association with Zwint-1 links Mad1 and Mad2, components that are directly responsible for generating the diffusible 'wait anaphase' signal, to a structural, inner kinetochore complex containing Mis12 and KNL-1AF15q14, the last of which has been proved to be essential for kinetochore assembly in Caenorhabditis elegans. Removal of ZW10 or Rod inactivates the mitotic checkpoint [].
Probab=20.86 E-value=1e+02 Score=29.60 Aligned_cols=41 Identities=29% Similarity=0.266 Sum_probs=28.9
Q ss_pred HHHHhhccCCC--------CCCCC---CHHHHHHHhchhHHHHHHHH--HhhcC
Q 029662 138 IMLLHQGKADD--------HNGPL---DAKQIAEKFRLDVLQVQAIL--QCLSL 178 (190)
Q Consensus 138 ii~L~QGk~~~--------h~gPM---~v~~iAeKFrv~v~~vq~Il--qf~Sl 178 (190)
|..||+.-+.. |..|+ =|+|||+.|++|...|+.-| ++|..
T Consensus 192 I~~LY~h~~i~~r~~~~~~~~~~DIh~~v~eIAein~Ldl~kIr~~LlekWL~~ 245 (551)
T PF10493_consen 192 IVELYEHESIWQRYRNPTGHDYPDIHAAVKEIAEINNLDLDKIRDQLLEKWLCP 245 (551)
T ss_pred HHHHHcCcchhhhhhcccccCcccHHHHHHHHHHHhCCCHHHHHHHHHHHHhCc
Confidence 66788877763 33442 25899999999999888755 55554
No 417
>COG2378 Predicted transcriptional regulator [Transcription]
Probab=20.75 E-value=1.3e+02 Score=26.56 Aligned_cols=38 Identities=21% Similarity=0.366 Sum_probs=29.9
Q ss_pred HHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhhc
Q 029662 135 LRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCLS 177 (190)
Q Consensus 135 l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~S 177 (190)
|-.||++.+++. . +++.++|+.|.|....|.+=+..|+
T Consensus 10 L~~ii~~L~~~~----~-vta~~lA~~~~VS~RTi~RDi~~L~ 47 (311)
T COG2378 10 LLQIIQILRAKE----T-VTAAELADEFEVSVRTIYRDIATLR 47 (311)
T ss_pred HHHHHHHHHhCc----c-chHHHHHHhcCCCHHHHHHHHHHHH
Confidence 456777777654 4 8999999999999999998766554
No 418
>KOG2165 consensus Anaphase-promoting complex (APC), subunit 2 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=20.72 E-value=1.2e+02 Score=31.29 Aligned_cols=36 Identities=19% Similarity=0.248 Sum_probs=32.7
Q ss_pred HHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 136 RRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 136 ~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
--||.+||-|.+ .+.+|+||+.++-+..+.+-|.|.
T Consensus 605 A~iI~~Fqek~t-----wt~eelse~l~ip~~~lrrrL~fW 640 (765)
T KOG2165|consen 605 AAIINLFQEKNT-----WTLEELSESLGIPVPALRRRLSFW 640 (765)
T ss_pred HHHHHHhcCccc-----ccHHHHHHHhCCCHHHHHHHHHHH
Confidence 357889999987 899999999999999999999985
No 419
>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=20.67 E-value=93 Score=27.40 Aligned_cols=28 Identities=18% Similarity=0.376 Sum_probs=25.7
Q ss_pred CCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 149 HNGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 149 h~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
|.|.+++-+||.-.+||...|++.++.+
T Consensus 67 ~gGRv~~~dL~~~LnVd~~~ie~~~~~i 94 (272)
T PF09743_consen 67 HGGRVNLVDLAQALNVDLDHIERRAQEI 94 (272)
T ss_pred cCCceEHHHHHHhcCcCHHHHHHHHHHH
Confidence 6688999999999999999999998875
No 420
>PF06738 DUF1212: Protein of unknown function (DUF1212); InterPro: IPR010619 This entry represents a predicted domain found within a number of hypothetical proteins of unknown function found in eukaryotes, bacteria and archaea. Some of these sequences are predicted to be membrane proteins.
Probab=20.66 E-value=1.2e+02 Score=23.76 Aligned_cols=39 Identities=21% Similarity=0.376 Sum_probs=29.5
Q ss_pred CCCCCCCCcccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHh
Q 029662 121 EEKPSPPGTLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKF 162 (190)
Q Consensus 121 eer~~p~GTLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKF 162 (190)
.-+.++++++|...|.++-+|..--. .|.|+++|.-+++
T Consensus 53 ~~~~v~~~~~nl~~l~~v~~l~~~~~---~~~~~~~ea~~~L 91 (193)
T PF06738_consen 53 RVRRVPPRGVNLDKLAAVNRLSRRIV---AGQLSLEEAIERL 91 (193)
T ss_pred EEEEeCCCCcCHHHHHHHHHHHHHHh---cCCCCHHHHHHHH
Confidence 34667999999999999888876554 3778998876543
No 421
>TIGR02612 mob_myst_A mobile mystery protein A. Members of this protein family are found in mobization-related contexts more often than not, including within a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and on plasmids in Agrobacterium tumefaciens and Coxiella burnetii, always together with mobile mystery protein B, a member of the Fic protein family (pfam02661). This protein is encoded by the upstream member of the gene pair and belongs to a family of helix-turn-helix DNA binding proteins (pfam01381).
Probab=20.55 E-value=2.1e+02 Score=23.21 Aligned_cols=43 Identities=16% Similarity=0.251 Sum_probs=28.6
Q ss_pred HHHHHHHHHHhhccCCCCCC------------CCCHHHHHHHhchhHHHHHHHHH
Q 029662 132 VAQLRRIMLLHQGKADDHNG------------PLDAKQIAEKFRLDVLQVQAILQ 174 (190)
Q Consensus 132 va~l~~ii~L~QGk~~~h~g------------PM~v~~iAeKFrv~v~~vq~Ilq 174 (190)
..|+++.+.-|.+-..-... -|+..|+|++.+|....|.+|.+
T Consensus 6 ~~q~~~~l~~~~~~~~~~~p~~~~Ir~~R~~lGmTq~eLAerlGVS~~tIs~iE~ 60 (150)
T TIGR02612 6 LRQLDQRLVALAGAGAIQTPKEGWVRAIRKALGMSGAQLAGRLGVTPQRVEALEK 60 (150)
T ss_pred HHHHHHHHHHHhhccccccCcHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 45566666555444433322 28899999999998887777765
No 422
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=20.41 E-value=1.6e+02 Score=25.10 Aligned_cols=39 Identities=15% Similarity=0.226 Sum_probs=28.9
Q ss_pred HHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHh
Q 029662 134 QLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQC 175 (190)
Q Consensus 134 ~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf 175 (190)
.|++|+..-.-. ...++++++||+.+++....+.++.+-
T Consensus 192 ~i~~~~~~i~~~---~~~~~tl~~lA~~~~~S~~~l~r~Fk~ 230 (302)
T PRK10371 192 YVSQMLGFIAEN---YDQALTINDVAEHVKLNANYAMGIFQR 230 (302)
T ss_pred HHHHHHHHHHHh---hcCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 456665544333 334699999999999999999988764
No 423
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=20.24 E-value=1.6e+02 Score=23.94 Aligned_cols=29 Identities=17% Similarity=0.211 Sum_probs=24.1
Q ss_pred CCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662 148 DHNGPLDAKQIAEKFRLDVLQVQAILQCL 176 (190)
Q Consensus 148 ~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~ 176 (190)
.+...-++.+||+..+|+...|+.+++..
T Consensus 107 ~~~~~~~~~ela~~l~i~~~~v~~~~~~~ 135 (236)
T PRK06986 107 ELGREPTDTEVAEKLGLSLEEYREMLLDT 135 (236)
T ss_pred HHCCCCCHHHHHHHcCCCHHHHHHHHHHH
Confidence 35556789999999999999999888753
No 424
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=20.06 E-value=65 Score=31.81 Aligned_cols=110 Identities=19% Similarity=0.214 Sum_probs=62.0
Q ss_pred cCchHHHHHHHhhccc---ccCCC----CccccchhhhhhhhcCCCCCCCCCCCCCCCCCCCCCCCCccc----------
Q 029662 69 RDPQYDAMLNQMLGRV---KTKAG----GKAEMGEAAVVERQTRPLPKLRNTTPVSSRYEEKPSPPGTLN---------- 131 (190)
Q Consensus 69 rDp~ydaMl~qmvGrI---~tkpG----Gk~Emgea~vv~~ynRP~Pk~R~t~~~sg~~eer~~p~GTLN---------- 131 (190)
-+|.|++|++.=-|.. +..+- ---+-|.++..-+|.-=.-+.-|..+ --|.....|.+++-
T Consensus 198 ~sps~~~~~k~s~~k~~el~~~~~~~~~~C~~cG~~~~~t~y~nlra~~~n~C~--~C~~qg~f~s~~~ssDf~~v~~~~ 275 (531)
T COG5259 198 YSPSLKSPKKESQGKVDELKDHSEKHPSSCSCCGNKSFNTRYHNLRAEKYNSCS--ECYDQGRFPSEFTSSDFKPVTISL 275 (531)
T ss_pred CCchhhhhhhhcCCCccccccccccCCceeeccCccccchhhhhhhhhhcccch--HHHhcCcCCCccccccchhhhhhc
Confidence 4788888887433332 22221 11245777777777543222223332 23334445555432
Q ss_pred --HH---HHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhhcCCCCCCc
Q 029662 132 --VA---QLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCLSLPPESSN 184 (190)
Q Consensus 132 --va---~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~SlP~e~~~ 184 (190)
+. -=+|.++|-.|+---- =|.++||.--+ .-+.=|=|+.||+||-++.-
T Consensus 276 ~~~dk~WS~qE~~LLLEGIe~yg---DdW~kVA~HVg-tKt~EqCIl~FL~LPieD~~ 329 (531)
T COG5259 276 LIRDKNWSRQELLLLLEGIEMYG---DDWDKVARHVG-TKTKEQCILHFLQLPIEDNY 329 (531)
T ss_pred ccccccccHHHHHHHHHHHHHhh---hhHHHHHHHhC-CCCHHHHHHHHHcCCcchhh
Confidence 11 1256777777764110 15778887776 55667889999999998754
Done!