Query 026161
Match_columns 242
No_of_seqs 155 out of 276
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 04:29:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026161.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026161hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04770 ZF-HD_dimer: ZF-HD pr 100.0 2.9E-38 6.3E-43 230.8 3.0 57 47-103 2-59 (60)
2 TIGR01566 ZF_HD_prot_N ZF-HD h 100.0 2.3E-38 4.9E-43 225.6 2.3 52 50-101 1-53 (53)
3 TIGR01565 homeo_ZF_HD homeobox 99.9 5.5E-27 1.2E-31 170.1 6.3 58 179-236 1-58 (58)
4 PF00046 Homeobox: Homeobox do 99.2 1.5E-12 3.3E-17 90.0 0.1 56 180-239 1-56 (57)
5 KOG4577 Transcription factor L 99.2 3.7E-12 8.1E-17 118.5 2.3 60 176-239 164-223 (383)
6 KOG0494 Transcription factor C 99.1 1.3E-11 2.8E-16 113.6 2.1 59 178-241 140-199 (332)
7 KOG0484 Transcription factor P 99.1 5.4E-12 1.2E-16 103.1 -1.1 58 179-241 17-75 (125)
8 KOG2251 Homeobox transcription 99.1 9.5E-11 2.1E-15 104.9 3.9 61 176-240 34-94 (228)
9 KOG0843 Transcription factor E 99.0 9.2E-11 2E-15 102.8 2.3 60 178-241 101-160 (197)
10 KOG0493 Transcription factor E 99.0 8.4E-11 1.8E-15 108.4 2.1 57 179-240 246-303 (342)
11 smart00389 HOX Homeodomain. DN 98.9 5.6E-10 1.2E-14 76.2 2.8 55 180-238 1-55 (56)
12 cd00086 homeodomain Homeodomai 98.9 6.8E-10 1.5E-14 76.0 2.1 58 180-241 1-58 (59)
13 KOG0844 Transcription factor E 98.7 1.7E-08 3.8E-13 94.9 4.7 58 179-241 181-239 (408)
14 KOG0490 Transcription factor, 98.6 1.8E-08 3.8E-13 85.0 2.5 61 177-241 58-118 (235)
15 KOG3802 Transcription factor O 98.6 1.1E-07 2.3E-12 91.3 6.4 60 177-240 292-351 (398)
16 COG5576 Homeodomain-containing 98.4 2.3E-07 4.9E-12 79.0 3.1 62 176-241 48-109 (156)
17 KOG0489 Transcription factor z 98.3 6E-08 1.3E-12 87.3 -0.9 60 177-241 157-217 (261)
18 KOG0488 Transcription factor B 98.3 1.7E-07 3.7E-12 86.9 1.9 60 177-240 170-229 (309)
19 KOG0850 Transcription factor D 98.3 6E-07 1.3E-11 81.4 4.6 58 179-240 122-179 (245)
20 KOG0485 Transcription factor N 98.3 3.3E-07 7.2E-12 83.1 2.7 62 176-241 101-162 (268)
21 KOG0492 Transcription factor M 98.2 9.9E-07 2.1E-11 79.5 3.0 56 179-239 144-200 (246)
22 KOG0486 Transcription factor P 98.2 7.4E-07 1.6E-11 83.9 2.1 60 178-241 111-170 (351)
23 KOG0849 Transcription factor P 98.1 1.4E-06 3E-11 82.0 2.3 60 177-240 174-233 (354)
24 KOG0842 Transcription factor t 98.1 4.6E-06 1E-10 78.0 5.0 61 176-241 150-211 (307)
25 KOG0490 Transcription factor, 97.9 2.9E-06 6.2E-11 71.7 1.2 62 176-241 150-211 (235)
26 KOG1168 Transcription factor A 97.8 7.3E-06 1.6E-10 77.1 2.2 61 176-240 306-366 (385)
27 KOG0483 Transcription factor H 97.8 7.5E-06 1.6E-10 72.3 1.8 59 179-241 50-108 (198)
28 KOG0847 Transcription factor, 97.6 1.7E-05 3.7E-10 72.4 0.2 61 177-241 165-225 (288)
29 KOG2252 CCAAT displacement pro 97.5 4.3E-05 9.3E-10 76.2 2.0 57 178-238 419-475 (558)
30 KOG1146 Homeobox protein [Gene 97.4 5.4E-05 1.2E-09 81.4 1.8 60 177-240 901-960 (1406)
31 KOG0487 Transcription factor A 97.4 0.00016 3.5E-09 67.8 3.8 56 180-240 236-292 (308)
32 KOG0491 Transcription factor B 97.3 1.7E-05 3.7E-10 69.6 -2.7 60 177-240 98-157 (194)
33 KOG0848 Transcription factor C 97.2 7E-05 1.5E-09 69.8 -0.9 59 177-240 197-256 (317)
34 PF01527 HTH_Tnp_1: Transposas 95.1 0.0069 1.5E-07 43.5 0.5 46 181-234 2-47 (76)
35 PF04218 CENP-B_N: CENP-B N-te 94.6 0.023 5E-07 40.1 2.0 47 180-235 1-47 (53)
36 PF05920 Homeobox_KN: Homeobox 92.4 0.019 4E-07 39.0 -1.5 33 204-236 7-39 (40)
37 cd00569 HTH_Hin_like Helix-tur 88.7 0.32 6.9E-06 27.6 1.7 40 183-231 3-42 (42)
38 COG2963 Transposase and inacti 82.3 0.75 1.6E-05 35.9 1.4 48 180-236 3-51 (116)
39 cd06171 Sigma70_r4 Sigma70, re 82.1 0.28 6E-06 31.2 -0.9 46 184-238 9-54 (55)
40 PF02796 HTH_7: Helix-turn-hel 81.9 0.36 7.9E-06 32.6 -0.4 40 184-232 4-43 (45)
41 PF06163 DUF977: Bacterial pro 81.8 0.42 9.1E-06 40.3 -0.1 44 185-232 4-48 (127)
42 KOG0774 Transcription factor P 81.0 1.7 3.8E-05 41.2 3.6 60 180-241 189-249 (334)
43 KOG0773 Transcription factor M 77.1 2.2 4.8E-05 39.3 3.0 62 177-240 237-299 (342)
44 KOG0775 Transcription factor S 74.4 3 6.6E-05 39.6 3.1 45 191-239 188-232 (304)
45 KOG3623 Homeobox transcription 74.1 1.4 3.1E-05 46.6 1.1 48 185-237 563-610 (1007)
46 PRK09413 IS2 repressor TnpA; R 69.2 1.7 3.8E-05 34.7 0.3 43 183-233 10-52 (121)
47 PF04967 HTH_10: HTH DNA bindi 68.7 3.8 8.2E-05 29.5 1.9 41 186-228 1-41 (53)
48 PF08281 Sigma70_r4_2: Sigma-7 68.4 0.88 1.9E-05 30.8 -1.3 44 185-237 10-53 (54)
49 PF12651 RHH_3: Ribbon-helix-h 67.9 5.1 0.00011 27.4 2.4 39 179-217 2-40 (44)
50 smart00421 HTH_LUXR helix_turn 67.7 1.5 3.2E-05 28.5 -0.4 45 185-239 3-47 (58)
51 PF13022 HTH_Tnp_1_2: Helix-tu 67.1 1.4 3E-05 37.9 -0.7 55 180-235 5-59 (142)
52 PF12824 MRP-L20: Mitochondria 63.6 26 0.00057 30.3 6.4 39 183-227 83-121 (164)
53 PRK09480 slmA division inhibit 63.0 4.1 9E-05 33.0 1.4 47 188-235 9-55 (194)
54 PF13936 HTH_38: Helix-turn-he 63.0 1 2.2E-05 30.5 -1.8 42 183-233 2-43 (44)
55 TIGR02989 Sig-70_gvs1 RNA poly 62.7 1.6 3.4E-05 34.6 -1.1 47 184-240 110-157 (159)
56 cd04762 HTH_MerR-trunc Helix-T 61.1 2.1 4.5E-05 27.1 -0.6 23 213-235 3-25 (49)
57 PHA02893 hypothetical protein; 60.2 3.5 7.6E-05 32.9 0.4 20 73-92 58-77 (88)
58 PF00196 GerE: Bacterial regul 60.1 1.3 2.7E-05 30.8 -1.8 46 185-240 3-48 (58)
59 COG4802 FtrB Ferredoxin-thiore 59.8 9.2 0.0002 31.7 2.8 54 187-241 2-59 (110)
60 TIGR00270 conserved hypothetic 58.3 1.6 3.5E-05 37.2 -1.8 41 194-234 63-106 (154)
61 PRK10403 transcriptional regul 58.2 2.8 6E-05 33.1 -0.4 48 184-241 152-199 (215)
62 PF13384 HTH_23: Homeodomain-l 57.2 3.4 7.3E-05 27.5 -0.1 38 188-234 4-41 (50)
63 PF05572 Peptidase_M43: Pregna 54.5 8.9 0.00019 32.3 2.0 18 182-199 137-154 (154)
64 PRK02220 4-oxalocrotonate taut 53.5 25 0.00054 24.2 3.8 35 186-234 12-46 (61)
65 PRK00118 putative DNA-binding 53.4 1.8 3.9E-05 34.9 -2.2 45 185-238 17-61 (104)
66 PRK09644 RNA polymerase sigma 52.0 2.4 5.1E-05 34.3 -1.8 47 183-239 106-153 (165)
67 PRK12537 RNA polymerase sigma 51.7 3.2 6.9E-05 34.3 -1.1 47 184-240 132-179 (182)
68 PF13518 HTH_28: Helix-turn-he 51.3 3.1 6.8E-05 27.5 -1.0 24 212-235 14-37 (52)
69 PRK06424 transcription factor; 50.5 5.2 0.00011 33.9 0.0 55 180-235 68-122 (144)
70 TIGR02985 Sig70_bacteroi1 RNA 50.0 3 6.6E-05 32.4 -1.4 46 185-240 113-159 (161)
71 cd06170 LuxR_C_like C-terminal 49.9 4 8.6E-05 26.7 -0.7 44 186-239 1-44 (57)
72 PRK12512 RNA polymerase sigma 49.7 2.3 5E-05 34.8 -2.2 47 184-240 130-177 (184)
73 TIGR02607 antidote_HigA addict 49.4 6.8 0.00015 28.0 0.5 15 209-223 46-60 (78)
74 PRK04217 hypothetical protein; 49.2 3.3 7.2E-05 33.7 -1.3 44 185-238 42-86 (110)
75 PRK09652 RNA polymerase sigma 48.8 2.3 5.1E-05 33.9 -2.3 47 184-240 127-174 (182)
76 PRK09390 fixJ response regulat 48.3 4 8.7E-05 31.6 -0.9 47 185-241 141-187 (202)
77 PRK12541 RNA polymerase sigma 48.1 3.1 6.8E-05 33.3 -1.6 48 184-241 111-159 (161)
78 PF13551 HTH_29: Winged helix- 47.9 13 0.00027 27.7 1.8 22 179-200 51-72 (112)
79 PRK12530 RNA polymerase sigma 47.7 3.1 6.7E-05 34.8 -1.8 47 184-240 133-180 (189)
80 PRK09646 RNA polymerase sigma 47.3 3.2 6.9E-05 34.7 -1.8 47 184-240 141-188 (194)
81 TIGR01764 excise DNA binding d 47.2 4.1 8.8E-05 26.0 -0.9 23 213-235 4-26 (49)
82 TIGR02939 RpoE_Sigma70 RNA pol 46.5 2.1 4.5E-05 34.9 -3.0 46 185-240 138-184 (190)
83 PRK03975 tfx putative transcri 46.4 3.4 7.4E-05 35.0 -1.7 46 184-239 5-50 (141)
84 TIGR03070 couple_hipB transcri 46.1 11 0.00023 24.8 1.0 34 193-234 6-39 (58)
85 PF13698 DUF4156: Domain of un 45.9 7.2 0.00016 30.5 0.1 17 52-68 51-67 (93)
86 PRK12539 RNA polymerase sigma 45.2 3.5 7.5E-05 34.1 -1.8 48 184-240 130-177 (184)
87 PRK06759 RNA polymerase factor 45.0 4.1 9E-05 32.1 -1.4 48 184-241 105-153 (154)
88 PRK12526 RNA polymerase sigma 44.7 3.3 7.1E-05 35.2 -2.1 46 184-239 152-198 (206)
89 TIGR00290 MJ0570_dom MJ0570-re 44.6 37 0.0008 30.6 4.5 44 185-229 94-142 (223)
90 PF13411 MerR_1: MerR HTH fami 44.6 4.2 9.2E-05 28.5 -1.2 21 213-233 3-23 (69)
91 cd04761 HTH_MerR-SF Helix-Turn 44.2 4.8 0.0001 26.2 -0.9 23 213-235 3-25 (49)
92 PRK15369 two component system 44.0 7.9 0.00017 30.1 0.1 47 184-240 148-194 (211)
93 PF00249 Myb_DNA-binding: Myb- 43.9 68 0.0015 21.4 4.7 35 183-224 1-35 (48)
94 PRK09726 antitoxin HipB; Provi 43.8 17 0.00038 27.3 2.0 21 213-233 28-48 (88)
95 COG3040 Blc Bacterial lipocali 43.6 22 0.00049 31.6 2.9 26 182-207 139-165 (174)
96 cd08353 Glo_EDI_BRP_like_7 Thi 43.6 22 0.00048 27.3 2.5 45 187-231 10-54 (142)
97 PF04545 Sigma70_r4: Sigma-70, 43.5 2.8 6.1E-05 28.2 -2.2 43 185-236 4-46 (50)
98 PF13443 HTH_26: Cro/C1-type H 43.4 4.2 9.2E-05 28.1 -1.4 24 212-235 12-35 (63)
99 PF06252 DUF1018: Protein of u 42.4 20 0.00043 28.6 2.2 34 186-219 55-90 (119)
100 PRK12514 RNA polymerase sigma 42.3 4.3 9.4E-05 33.1 -1.7 47 184-240 128-175 (179)
101 PRK10072 putative transcriptio 41.7 12 0.00027 29.6 0.9 35 194-236 38-72 (96)
102 PRK10360 DNA-binding transcrip 41.7 7.9 0.00017 30.6 -0.2 48 184-241 136-183 (196)
103 PRK09648 RNA polymerase sigma 41.5 3.8 8.3E-05 33.8 -2.1 51 180-240 134-185 (189)
104 PF12728 HTH_17: Helix-turn-he 41.1 5.7 0.00012 26.6 -1.0 23 213-235 4-26 (51)
105 PRK13877 conjugal transfer rel 40.8 25 0.00055 28.8 2.6 55 179-237 10-85 (114)
106 cd00093 HTH_XRE Helix-turn-hel 40.7 8.7 0.00019 23.6 -0.1 16 208-223 39-54 (58)
107 PF01381 HTH_3: Helix-turn-hel 40.4 9 0.00019 25.6 -0.1 22 214-235 13-34 (55)
108 PF11569 Homez: Homeodomain le 39.8 6.8 0.00015 28.9 -0.8 37 194-234 13-49 (56)
109 PF13223 DUF4031: Protein of u 39.7 15 0.00031 29.0 1.0 18 210-227 23-40 (83)
110 TIGR02959 SigZ RNA polymerase 39.5 4.3 9.3E-05 33.3 -2.1 47 183-239 98-145 (170)
111 PRK05602 RNA polymerase sigma 39.4 4.4 9.5E-05 33.4 -2.1 47 184-240 127-174 (186)
112 cd01994 Alpha_ANH_like_IV This 38.8 58 0.0013 28.2 4.6 45 184-229 96-145 (194)
113 PF08914 Myb_DNA-bind_2: Rap1 38.6 24 0.00051 26.2 1.9 47 183-230 2-49 (65)
114 smart00351 PAX Paired Box doma 38.5 15 0.00032 29.7 0.9 41 185-234 17-57 (125)
115 TIGR02948 SigW_bacill RNA poly 38.4 4.9 0.00011 32.6 -1.9 46 184-239 135-181 (187)
116 PF12844 HTH_19: Helix-turn-he 38.3 13 0.00028 25.7 0.4 18 207-224 38-55 (64)
117 PRK09639 RNA polymerase sigma 38.3 6.4 0.00014 31.4 -1.2 46 184-239 111-156 (166)
118 PF13189 Cytidylate_kin2: Cyti 37.9 14 0.00029 31.1 0.6 40 194-235 16-55 (179)
119 TIGR02983 SigE-fam_strep RNA p 37.8 5 0.00011 32.0 -1.9 47 184-240 109-156 (162)
120 TIGR02937 sigma70-ECF RNA poly 37.8 5.3 0.00011 29.9 -1.7 47 185-240 110-156 (158)
121 TIGR03879 near_KaiC_dom probab 37.7 7.8 0.00017 29.7 -0.8 28 209-236 31-58 (73)
122 PRK15479 transcriptional regul 36.6 18 0.0004 28.8 1.1 50 185-240 148-202 (221)
123 TIGR03541 reg_near_HchA LuxR f 36.5 8.4 0.00018 33.8 -0.9 49 183-241 169-217 (232)
124 PRK09649 RNA polymerase sigma 36.3 6.6 0.00014 32.7 -1.5 47 184-240 129-176 (185)
125 TIGR02950 SigM_subfam RNA poly 36.2 6 0.00013 31.1 -1.7 32 209-240 120-151 (154)
126 COG0289 DapB Dihydrodipicolina 36.1 28 0.00062 32.7 2.4 20 184-203 101-120 (266)
127 KOG0705 GTPase-activating prot 35.9 14 0.00031 38.5 0.5 36 64-100 514-550 (749)
128 PRK12516 RNA polymerase sigma 35.8 6.1 0.00013 33.2 -1.8 45 185-239 116-161 (187)
129 PRK12547 RNA polymerase sigma 35.4 5.2 0.00011 32.4 -2.2 46 184-239 111-157 (164)
130 PF09607 BrkDBD: Brinker DNA-b 35.1 15 0.00033 27.3 0.4 46 183-233 3-48 (58)
131 PF00765 Autoind_synth: Autoin 35.1 3.4 7.4E-05 35.7 -3.5 22 197-218 21-42 (182)
132 cd00029 C1 Protein kinase C co 34.9 17 0.00036 23.8 0.5 30 66-100 13-42 (50)
133 smart00109 C1 Protein kinase C 34.8 18 0.0004 23.2 0.7 28 66-99 13-40 (49)
134 PRK09642 RNA polymerase sigma 34.4 6.4 0.00014 31.4 -1.8 47 184-240 105-152 (160)
135 PF01902 ATP_bind_4: ATP-bindi 34.4 51 0.0011 29.5 3.7 44 185-229 94-142 (218)
136 TIGR02999 Sig-70_X6 RNA polyme 34.3 6 0.00013 32.2 -2.0 45 186-240 135-180 (183)
137 PRK09645 RNA polymerase sigma 34.1 7.3 0.00016 31.5 -1.5 46 184-239 117-163 (173)
138 PRK09047 RNA polymerase factor 33.9 6.7 0.00015 31.1 -1.7 47 183-239 104-151 (161)
139 PRK15008 HTH-type transcriptio 33.9 23 0.0005 29.9 1.4 55 180-235 9-63 (212)
140 PRK12536 RNA polymerase sigma 33.9 5.3 0.00011 32.9 -2.4 30 211-240 146-175 (181)
141 PRK12546 RNA polymerase sigma 33.7 5.5 0.00012 33.7 -2.4 46 185-240 113-159 (188)
142 PRK12515 RNA polymerase sigma 33.7 7.1 0.00015 32.3 -1.7 50 181-240 127-177 (189)
143 PRK11511 DNA-binding transcrip 33.6 15 0.00032 29.4 0.1 40 190-234 10-49 (127)
144 PRK06811 RNA polymerase factor 33.5 8 0.00017 32.1 -1.4 48 184-241 130-178 (189)
145 PF05077 DUF678: Protein of un 33.5 17 0.00036 28.3 0.4 11 82-92 55-65 (74)
146 cd01104 HTH_MlrA-CarA Helix-Tu 33.2 8.1 0.00018 26.9 -1.3 21 213-233 3-23 (68)
147 PRK11924 RNA polymerase sigma 32.9 6.4 0.00014 31.3 -2.0 47 184-239 124-170 (179)
148 PRK12522 RNA polymerase sigma 32.8 7.2 0.00016 31.7 -1.8 29 212-240 137-165 (173)
149 PRK12519 RNA polymerase sigma 32.5 5.9 0.00013 32.7 -2.4 30 211-240 158-187 (194)
150 PRK12524 RNA polymerase sigma 32.3 6.4 0.00014 32.9 -2.2 47 183-239 134-181 (196)
151 PF02943 FeThRed_B: Ferredoxin 32.1 85 0.0018 25.7 4.3 26 191-217 7-32 (108)
152 PF06252 DUF1018: Protein of u 32.1 1.2E+02 0.0025 24.2 5.1 28 180-207 16-43 (119)
153 PRK13919 putative RNA polymera 32.1 6.7 0.00014 32.1 -2.1 50 181-240 131-181 (186)
154 PRK09975 DNA-binding transcrip 31.3 17 0.00036 30.2 0.1 44 190-234 12-55 (213)
155 cd02259 Peptidase_C39_like Pep 31.3 87 0.0019 23.2 4.0 44 180-229 17-60 (122)
156 TIGR00721 tfx DNA-binding prot 31.2 9.2 0.0002 32.3 -1.4 47 183-239 4-50 (137)
157 PF00356 LacI: Bacterial regul 31.2 64 0.0014 22.3 3.0 22 184-205 24-45 (46)
158 PRK12520 RNA polymerase sigma 31.2 7.2 0.00016 32.3 -2.1 46 184-239 130-176 (191)
159 PRK01964 4-oxalocrotonate taut 31.0 93 0.002 21.8 3.9 35 187-235 13-47 (64)
160 PF08688 ASD1: Apx/Shroom doma 30.7 2E+02 0.0043 25.7 6.7 16 178-193 122-137 (182)
161 PTZ00397 macrophage migration 30.7 1E+02 0.0022 24.1 4.5 37 186-236 69-105 (116)
162 cd04275 ZnMc_pappalysin_like Z 30.2 34 0.00074 30.7 1.9 17 181-197 207-223 (225)
163 cd04763 HTH_MlrA-like Helix-Tu 29.9 11 0.00024 26.7 -1.0 21 213-233 3-23 (68)
164 PRK10651 transcriptional regul 29.7 14 0.0003 29.2 -0.6 47 184-240 154-200 (216)
165 cd02425 Peptidase_C39F A sub-f 29.7 1.1E+02 0.0025 22.9 4.5 44 180-229 22-65 (126)
166 cd08356 Glo_EDI_BRP_like_17 Th 29.6 40 0.00087 25.5 1.9 30 180-209 1-30 (113)
167 PRK02289 4-oxalocrotonate taut 29.5 1.3E+02 0.0029 21.0 4.5 34 186-233 12-45 (60)
168 PRK09935 transcriptional regul 29.3 15 0.00032 29.1 -0.5 46 185-240 149-194 (210)
169 PRK09647 RNA polymerase sigma 29.3 9.5 0.00021 32.7 -1.7 47 184-240 137-184 (203)
170 PRK12544 RNA polymerase sigma 29.2 9.7 0.00021 32.7 -1.7 47 184-240 147-194 (206)
171 COG3413 Predicted DNA binding 29.2 40 0.00087 29.2 2.1 43 185-229 155-197 (215)
172 PRK12513 RNA polymerase sigma 29.2 5.1 0.00011 33.2 -3.3 32 209-240 154-185 (194)
173 KOG2767 Translation initiation 28.8 17 0.00038 35.7 -0.2 16 84-99 118-133 (400)
174 PRK08295 RNA polymerase factor 28.8 9.3 0.0002 31.8 -1.8 49 182-240 152-200 (208)
175 PF11761 CbiG_mid: Cobalamin b 28.7 82 0.0018 22.9 3.4 34 196-232 6-39 (93)
176 PRK12543 RNA polymerase sigma 28.6 10 0.00023 31.1 -1.5 46 184-239 116-162 (179)
177 PRK12528 RNA polymerase sigma 28.6 13 0.00027 29.8 -1.0 46 182-237 110-156 (161)
178 PRK06680 D-amino acid aminotra 28.4 1.4E+02 0.0031 26.9 5.5 47 186-232 45-94 (286)
179 smart00529 HTH_DTXR Helix-turn 28.2 1.1E+02 0.0024 22.4 4.1 31 185-221 66-96 (96)
180 PRK12535 RNA polymerase sigma 28.2 11 0.00023 32.0 -1.6 48 182-239 130-178 (196)
181 PF11976 Rad60-SLD: Ubiquitin- 28.2 71 0.0015 22.5 2.9 26 210-235 24-50 (72)
182 PRK12533 RNA polymerase sigma 28.1 8 0.00017 33.7 -2.4 47 184-240 133-180 (216)
183 PRK10336 DNA-binding transcrip 28.0 26 0.00057 27.9 0.7 51 184-240 148-203 (219)
184 PRK12540 RNA polymerase sigma 28.0 8.4 0.00018 32.2 -2.2 47 184-240 110-157 (182)
185 PRK09651 RNA polymerase sigma 28.0 9.8 0.00021 31.1 -1.8 47 181-237 115-162 (172)
186 PHA01976 helix-turn-helix prot 27.7 31 0.00068 23.9 1.0 19 207-225 41-59 (67)
187 TIGR03020 EpsA transcriptional 27.3 14 0.0003 33.7 -1.1 48 183-240 188-235 (247)
188 PF00376 MerR: MerR family reg 27.0 11 0.00024 25.0 -1.3 20 213-232 2-21 (38)
189 TIGR02846 spore_sigmaK RNA pol 26.9 10 0.00022 32.8 -1.9 52 184-240 173-224 (227)
190 PF08279 HTH_11: HTH domain; 26.5 20 0.00042 24.2 -0.2 18 211-228 16-33 (55)
191 PRK12531 RNA polymerase sigma 26.5 10 0.00023 31.6 -1.9 47 183-239 139-186 (194)
192 TIGR02479 FliA_WhiG RNA polyme 26.5 9.1 0.0002 32.8 -2.3 48 184-240 174-221 (224)
193 PRK06930 positive control sigm 26.3 11 0.00024 32.3 -1.9 46 184-239 113-159 (170)
194 KOG2146 Splicing coactivator S 26.3 31 0.00067 33.4 1.0 37 184-232 12-50 (354)
195 TIGR02954 Sig70_famx3 RNA poly 26.3 13 0.00029 29.9 -1.3 47 184-240 118-165 (169)
196 PRK12532 RNA polymerase sigma 26.0 10 0.00022 31.5 -2.1 47 184-240 135-182 (195)
197 cd00491 4Oxalocrotonate_Tautom 25.8 1.7E+02 0.0037 19.6 4.4 35 187-235 12-46 (58)
198 PF04492 Phage_rep_O: Bacterio 25.7 51 0.0011 26.3 2.0 44 182-226 26-70 (100)
199 PRK12545 RNA polymerase sigma 25.6 10 0.00022 32.0 -2.1 46 184-239 138-184 (201)
200 PF02954 HTH_8: Bacterial regu 25.5 48 0.001 21.9 1.6 32 190-229 6-37 (42)
201 PF01113 DapB_N: Dihydrodipico 25.5 24 0.00052 28.1 0.1 20 184-203 99-118 (124)
202 PRK09641 RNA polymerase sigma 25.4 9.8 0.00021 30.9 -2.2 46 185-240 136-182 (187)
203 PRK10668 DNA-binding transcrip 25.4 30 0.00065 28.8 0.6 47 187-234 9-55 (215)
204 PF09832 DUF2059: Uncharacteri 25.1 40 0.00086 23.8 1.1 21 180-200 11-31 (64)
205 PF13565 HTH_32: Homeodomain-l 25.1 21 0.00046 25.4 -0.3 38 180-223 27-65 (77)
206 PF05099 TerB: Tellurite resis 25.1 1.1E+02 0.0024 23.9 3.8 49 180-228 85-136 (140)
207 PRK12542 RNA polymerase sigma 25.1 12 0.00026 30.9 -1.8 48 182-239 119-167 (185)
208 PRK07037 extracytoplasmic-func 25.0 10 0.00022 30.3 -2.2 44 185-238 109-153 (163)
209 PRK06704 RNA polymerase factor 25.0 11 0.00025 33.6 -2.1 46 184-239 115-161 (228)
210 PF12123 Amidase02_C: N-acetyl 24.7 72 0.0016 22.5 2.3 19 186-204 24-42 (45)
211 PF01710 HTH_Tnp_IS630: Transp 24.7 36 0.00079 27.1 1.0 52 180-241 51-102 (119)
212 PRK12511 RNA polymerase sigma 24.7 11 0.00024 31.6 -2.1 45 185-239 111-156 (182)
213 PF07813 LTXXQ: LTXXQ motif fa 24.5 44 0.00095 24.5 1.3 17 180-196 82-98 (100)
214 PRK09637 RNA polymerase sigma 24.5 11 0.00024 31.4 -2.1 46 184-239 105-151 (181)
215 TIGR01610 phage_O_Nterm phage 24.4 68 0.0015 24.7 2.4 43 184-227 21-64 (95)
216 cd01276 PKCI_related Protein K 24.4 1.5E+02 0.0032 22.2 4.2 45 180-236 42-89 (104)
217 PRK00745 4-oxalocrotonate taut 24.3 1.5E+02 0.0032 20.3 3.9 35 186-234 12-46 (62)
218 PRK13558 bacterio-opsin activa 24.1 46 0.00099 32.8 1.7 44 183-228 605-648 (665)
219 PF11516 DUF3220: Protein of u 24.1 11 0.00024 30.3 -2.1 8 227-234 33-40 (106)
220 cd01763 Sumo Small ubiquitin-r 23.7 89 0.0019 23.5 2.9 27 211-237 36-62 (87)
221 TIGR02943 Sig70_famx1 RNA poly 23.7 12 0.00027 31.3 -2.0 47 184-240 130-177 (188)
222 PRK12529 RNA polymerase sigma 23.7 26 0.00057 28.8 0.0 43 184-236 126-169 (178)
223 cd02417 Peptidase_C39_likeA A 23.4 1.5E+02 0.0032 22.2 4.1 44 180-229 17-60 (121)
224 PF12802 MarR_2: MarR family; 23.4 34 0.00073 23.2 0.5 36 186-227 3-38 (62)
225 smart00422 HTH_MERR helix_turn 23.2 17 0.00037 25.3 -1.0 21 213-233 3-23 (70)
226 smart00857 Resolvase Resolvase 23.1 66 0.0014 25.2 2.2 19 188-206 18-36 (148)
227 PF10925 DUF2680: Protein of u 23.1 71 0.0015 23.4 2.1 28 186-217 1-28 (59)
228 PRK10100 DNA-binding transcrip 23.1 34 0.00074 29.9 0.6 47 184-240 154-200 (216)
229 PRK08301 sporulation sigma fac 23.0 14 0.0003 31.8 -1.8 52 184-240 177-228 (234)
230 PF05419 GUN4: GUN4-like ; In 22.8 50 0.0011 27.6 1.5 18 190-207 80-97 (132)
231 COG3916 LasI N-acyl-L-homoseri 22.7 40 0.00086 30.7 0.9 23 196-218 27-49 (209)
232 TIGR02952 Sig70_famx2 RNA poly 22.5 15 0.00032 29.3 -1.7 47 184-240 121-168 (170)
233 cd01559 ADCL_like ADCL_like: 4 22.4 1.8E+02 0.0039 25.4 4.9 48 186-234 23-73 (249)
234 PF05344 DUF746: Domain of Unk 22.3 29 0.00062 26.4 -0.0 34 192-231 1-34 (65)
235 cd04774 HTH_YfmP Helix-Turn-He 22.1 19 0.00042 27.9 -1.0 22 213-234 3-24 (96)
236 cd02986 DLP Dim1 family, Dim1- 22.1 70 0.0015 26.3 2.2 45 192-237 34-81 (114)
237 PF04719 TAFII28: hTAFII28-lik 22.0 1.4E+02 0.0031 23.7 3.8 31 184-220 6-36 (90)
238 PRK05657 RNA polymerase sigma 21.8 15 0.00033 34.2 -1.9 51 185-240 262-312 (325)
239 PF05121 GvpK: Gas vesicle pro 21.8 1.9E+02 0.004 23.3 4.4 35 184-226 40-74 (88)
240 KOG3755 SATB1 matrix attachmen 21.5 41 0.00089 35.5 0.9 57 177-236 645-704 (769)
241 cd01392 HTH_LacI Helix-turn-he 21.5 15 0.00032 24.3 -1.6 21 215-235 2-22 (52)
242 PF02042 RWP-RK: RWP-RK domain 21.4 2.9E+02 0.0064 19.9 5.0 35 185-224 4-43 (52)
243 cd02423 Peptidase_C39G A sub-f 21.3 1.9E+02 0.0042 21.7 4.4 40 184-229 27-66 (129)
244 PF01873 eIF-5_eIF-2B: Domain 21.2 33 0.00071 28.5 0.1 13 82-94 112-124 (125)
245 PRK09415 RNA polymerase factor 21.2 13 0.00029 30.6 -2.3 46 184-239 126-172 (179)
246 PF13011 LZ_Tnp_IS481: leucine 21.2 60 0.0013 25.6 1.5 42 185-234 8-49 (85)
247 TIGR00013 taut 4-oxalocrotonat 21.1 2.3E+02 0.0051 19.3 4.4 35 186-234 12-46 (63)
248 cd02421 Peptidase_C39_likeD A 21.0 1.3E+02 0.0029 22.6 3.4 44 180-229 17-60 (124)
249 PRK11552 putative DNA-binding 20.9 40 0.00086 29.2 0.5 40 189-235 13-57 (225)
250 cd00449 PLPDE_IV PyridoxaL 5'- 20.9 2.7E+02 0.0058 24.1 5.6 51 183-233 20-73 (256)
251 TIGR03613 RutR pyrimidine util 20.8 34 0.00074 28.1 0.1 46 188-234 7-52 (202)
252 cd02419 Peptidase_C39C A sub-f 20.8 1.9E+02 0.0042 21.8 4.3 44 180-229 22-65 (127)
253 cd02949 TRX_NTR TRX domain, no 20.7 65 0.0014 23.7 1.6 47 189-235 30-78 (97)
254 PF05930 Phage_AlpA: Prophage 20.6 13 0.00028 25.6 -2.1 22 213-234 6-27 (51)
255 PRK12525 RNA polymerase sigma 20.4 23 0.0005 28.8 -1.0 46 182-237 115-161 (168)
256 smart00661 RPOL9 RNA polymeras 20.4 61 0.0013 21.7 1.3 25 69-93 5-29 (52)
257 PRK12523 RNA polymerase sigma 20.4 21 0.00045 29.1 -1.3 48 181-238 115-163 (172)
258 PRK06986 fliA flagellar biosyn 20.3 12 0.00026 32.5 -2.8 47 185-240 184-230 (236)
259 PRK08942 D,D-heptose 1,7-bisph 20.3 2.8E+02 0.0061 22.7 5.5 44 182-225 58-121 (181)
260 PHA00542 putative Cro-like pro 20.3 64 0.0014 24.3 1.5 42 182-234 14-55 (82)
261 TIGR02531 yecD_yerC TrpR-relat 20.3 30 0.00066 27.1 -0.3 21 212-232 52-72 (88)
262 cd04768 HTH_BmrR-like Helix-Tu 20.2 24 0.00051 27.1 -0.9 21 213-233 3-23 (96)
263 PRK09483 response regulator; P 20.2 25 0.00055 28.2 -0.8 47 184-240 147-193 (217)
264 PRK09706 transcriptional repre 20.2 43 0.00094 26.9 0.6 18 208-225 45-62 (135)
265 PRK11083 DNA-binding response 20.1 40 0.00087 27.0 0.4 50 184-239 153-207 (228)
266 PF13730 HTH_36: Helix-turn-he 20.1 43 0.00093 22.5 0.5 44 184-232 1-47 (55)
No 1
>PF04770 ZF-HD_dimer: ZF-HD protein dimerisation region; InterPro: IPR006456 The homeodomain (HD) is a 60-amino acid DNA-binding domain found in many transcription factors. HD-containing proteins are found in diverse organisms such as humans, Drosophila, nematode worms, and plants, where they play important roles in development. Zinc-finger-homeodomain (ZF- HD) subfamily proteins have only been identified in plants, and likely play plant specific roles. ZF-HD proteins are expressed predominantly or exclusively in floral tissue, indicating a likely regulatory role during floral development []. The ZF-HD class of homeodomain proteins may also be involved in the photosynthesis-related mesophyll-specific gene expression of phosphoenolpyruvate carboxylase in C4 species [] and in pathogen signaling and plant defense mechanisms []. These proteins share three domains of high sequence similarity: the homeodomain (II) located at the carboxy-terminus, and two other segments (Ia and Ib) located in the amino-terminal part. These N-terminal domains contain five conserved cysteine residues and at least three conserved histidine residues whose spacing ressembles zinc-binding domains involved in dimerization of transcription factors. Although the two domains contain at least eight potential zinc-binding amino-acids, the unique spacing of the conserved cysteine and histidine residues within domain Ib suggests that both domains form one rather than two zinc finger structures. The two conserved motifs Ia and Ib constitute a dimerization domain which is sufficient for the formation of homo- and heterodimers []. This entry represents the N-terminal Cysteine/Histidine-rich dimerization domain. The companion ZF-HD homeobox domain is described in IPR006455 from INTERPRO.
Probab=100.00 E-value=2.9e-38 Score=230.83 Aligned_cols=57 Identities=72% Similarity=1.408 Sum_probs=54.5
Q ss_pred CceehHhhhhhhccccCccccccccccccc-CCCCCccccccccccccccccccccCC
Q 026161 47 RKARYRECLKNHAVGIGGHALDGCGEFMAA-GDEGTLDGLKCAACNCHRNFHRKEVDS 103 (242)
Q Consensus 47 ~~v~Y~eC~kNhaa~~Gg~a~DGCgEFm~~-~~~g~~~al~CaaCgCHRnFHr~e~~~ 103 (242)
..|+|+||||||||+||||+||||+||||+ ++++|+++|+||||||||||||||+++
T Consensus 2 ~~v~Y~EC~kNHAa~~Gg~a~DGCgEFm~~~g~eg~~~al~CaACgCHRnFHRre~~~ 59 (60)
T PF04770_consen 2 KVVRYRECLKNHAASIGGHAVDGCGEFMPSPGEEGTPEALKCAACGCHRNFHRREVEG 59 (60)
T ss_pred CceeHHHHHhhHhHhhCCcccccccccccCCCCCCCcccceecccCcchhcccCCcCC
Confidence 468999999999999999999999999999 889999999999999999999999865
No 2
>TIGR01566 ZF_HD_prot_N ZF-HD homeobox protein Cys/His-rich dimerization domain. This model describes a 54-residue domain found in the N-terminal region of plant proteins, the vast majority of which contain a ZF-HD class homeobox domain toward the C-terminus. The region between the two domains typically is rich in low complexity sequence. The companion ZF-HD homeobox domain is described in model TIGR01565.
Probab=100.00 E-value=2.3e-38 Score=225.56 Aligned_cols=52 Identities=73% Similarity=1.407 Sum_probs=50.0
Q ss_pred ehHhhhhhhccccCcccccccccccc-cCCCCCcccccccccccccccccccc
Q 026161 50 RYRECLKNHAVGIGGHALDGCGEFMA-AGDEGTLDGLKCAACNCHRNFHRKEV 101 (242)
Q Consensus 50 ~Y~eC~kNhaa~~Gg~a~DGCgEFm~-~~~~g~~~al~CaaCgCHRnFHr~e~ 101 (242)
+|+||||||||+|||||||||||||| +++++++++|+||||||||||||||+
T Consensus 1 ~Y~EC~kNHAa~~Gg~a~DGCgEFmps~g~~~~~~al~CaACgCHRnFHRre~ 53 (53)
T TIGR01566 1 LYKECLKNHAASIGGHALDGCGEFMPSSGEEGDPESLTCAACGCHRNFHRKEP 53 (53)
T ss_pred CHHHHHHhhHHHhCCcccccccccccCCCCCCCCcceeeeecCcccccccCCC
Confidence 69999999999999999999999999 78889999999999999999999984
No 3
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=99.94 E-value=5.5e-27 Score=170.14 Aligned_cols=58 Identities=57% Similarity=1.060 Sum_probs=56.8
Q ss_pred CCCcCccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccc
Q 026161 179 RKRFRTKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKH 236 (242)
Q Consensus 179 ~KR~RTkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~ 236 (242)
+||+||+||++|+++|++||+++||||+++|..++++||.+|||+++||||||||||.
T Consensus 1 ~kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k~ 58 (58)
T TIGR01565 1 KKRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNKK 58 (58)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCCC
Confidence 5999999999999999999999999999999999999999999999999999999984
No 4
>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=99.23 E-value=1.5e-12 Score=90.03 Aligned_cols=56 Identities=25% Similarity=0.388 Sum_probs=52.7
Q ss_pred CCcCccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccC
Q 026161 180 KRFRTKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLG 239 (242)
Q Consensus 180 KR~RTkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~g 239 (242)
||.||+||.+|++.|.++++. .++|+...+++++.++||+...|++||+|+|.+..
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~----~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~k 56 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQE----NPYPSKEEREELAKELGLTERQVKNWFQNRRRKEK 56 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHH----SSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHH----hccccccccccccccccccccccccCHHHhHHHhC
Confidence 789999999999999998887 79999999999999999999999999999998764
No 5
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.22 E-value=3.7e-12 Score=118.50 Aligned_cols=60 Identities=27% Similarity=0.414 Sum_probs=55.6
Q ss_pred CCCCCCcCccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccC
Q 026161 176 GGSRKRFRTKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLG 239 (242)
Q Consensus 176 ~~~~KR~RTkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~g 239 (242)
..+.||.||++|+.|+|.|+..+.. ..||-..++||+..|+||..||+||||||+|+|.+
T Consensus 164 d~~nKRPRTTItAKqLETLK~AYn~----SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEK 223 (383)
T KOG4577|consen 164 DASNKRPRTTITAKQLETLKQAYNT----SPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEK 223 (383)
T ss_pred ccccCCCcceeeHHHHHHHHHHhcC----CCchhHHHHHHhhhccCcceeehhhhhhhhhHHHH
Confidence 4567999999999999999998877 79999999999999999999999999999999864
No 6
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.15 E-value=1.3e-11 Score=113.60 Aligned_cols=59 Identities=24% Similarity=0.415 Sum_probs=54.5
Q ss_pred CCCCcCccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCCC
Q 026161 178 SRKRFRTKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGKK 241 (242)
Q Consensus 178 ~~KR~RTkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gkk 241 (242)
.+|+|||.||+.|+|.|++ |-|. ++||.-.++-++..+.|....|+|||||+|+||.|+
T Consensus 140 kRRh~RTiFT~~Qle~LEkaFkea-----HYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~ 199 (332)
T KOG0494|consen 140 KRRHFRTIFTSYQLEELEKAFKEA-----HYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKT 199 (332)
T ss_pred ccccccchhhHHHHHHHHHHHhhc-----cCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhh
Confidence 3566799999999999998 6666 999999999999999999999999999999999986
No 7
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.13 E-value=5.4e-12 Score=103.07 Aligned_cols=58 Identities=22% Similarity=0.400 Sum_probs=54.9
Q ss_pred CCCcCccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCCC
Q 026161 179 RKRFRTKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGKK 241 (242)
Q Consensus 179 ~KR~RTkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gkk 241 (242)
-+|.||.||.-|+..|+. |||. ++||--.+|+++..|.|+...+||||||+|+|+.|.
T Consensus 17 QRRIRTTFTS~QLkELErvF~ET-----HYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQ 75 (125)
T KOG0484|consen 17 QRRIRTTFTSAQLKELERVFAET-----HYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQ 75 (125)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhh-----cCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHH
Confidence 489999999999999988 9998 999999999999999999999999999999998764
No 8
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.06 E-value=9.5e-11 Score=104.94 Aligned_cols=61 Identities=21% Similarity=0.299 Sum_probs=55.5
Q ss_pred CCCCCCcCccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 176 GGSRKRFRTKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 176 ~~~~KR~RTkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
....+|-||.||-+|+|.|++++++ .|++|..++|+++..|.|...+|||||.|+|+|..+
T Consensus 34 pRkqRRERTtFtr~QlevLe~LF~k----TqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~ 94 (228)
T KOG2251|consen 34 PRKQRRERTTFTRKQLEVLEALFAK----TQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRR 94 (228)
T ss_pred chhcccccceecHHHHHHHHHHHHh----hcCccHHHHHHHHHHhCCchhhhhhhhccccchhhH
Confidence 3556899999999999999996665 599999999999999999999999999999999764
No 9
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.03 E-value=9.2e-11 Score=102.83 Aligned_cols=60 Identities=27% Similarity=0.335 Sum_probs=55.1
Q ss_pred CCCCcCccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCCC
Q 026161 178 SRKRFRTKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGKK 241 (242)
Q Consensus 178 ~~KR~RTkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gkk 241 (242)
..||.||.||.+|+.+|+..++. .++---++++++++.++|+..-+||||||+|-|++|+
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~----~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~ 160 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEG----NQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRM 160 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhc----CCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHH
Confidence 56999999999999999998888 5777788999999999999999999999999998763
No 10
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.03 E-value=8.4e-11 Score=108.39 Aligned_cols=57 Identities=30% Similarity=0.534 Sum_probs=53.1
Q ss_pred CCCcCccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 179 RKRFRTKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 179 ~KR~RTkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
.||.||-||.||+++|++ |-|. .+--|..+|+|++|+||+..-||+||||.|+|++|
T Consensus 246 eKRPRTAFtaeQL~RLK~EF~en-----RYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKK 303 (342)
T KOG0493|consen 246 EKRPRTAFTAEQLQRLKAEFQEN-----RYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKK 303 (342)
T ss_pred hcCccccccHHHHHHHHHHHhhh-----hhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhh
Confidence 489999999999999998 6665 78889999999999999999999999999999987
No 11
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=98.93 E-value=5.6e-10 Score=76.23 Aligned_cols=55 Identities=27% Similarity=0.454 Sum_probs=50.8
Q ss_pred CCcCccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccc
Q 026161 180 KRFRTKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTL 238 (242)
Q Consensus 180 KR~RTkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~ 238 (242)
|+.||.||++|++.|.+++++ .++|+.+.+++++.++||+...++.||+|.|.+.
T Consensus 1 ~k~r~~~~~~~~~~L~~~f~~----~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~ 55 (56)
T smart00389 1 RRKRTSFTPEQLEELEKEFQK----NPYPSREEREELAAKLGLSERQVKVWFQNRRAKW 55 (56)
T ss_pred CCCCCcCCHHHHHHHHHHHHh----CCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhcc
Confidence 577899999999999997777 5799999999999999999999999999999875
No 12
>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=98.89 E-value=6.8e-10 Score=75.95 Aligned_cols=58 Identities=28% Similarity=0.511 Sum_probs=53.7
Q ss_pred CCcCccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCCC
Q 026161 180 KRFRTKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGKK 241 (242)
Q Consensus 180 KR~RTkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gkk 241 (242)
++.|+.||.+|++.|+++++. .++|+...+++++.++||+...|++||+|.|.+..++
T Consensus 1 ~~~r~~~~~~~~~~Le~~f~~----~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 1 RRKRTRFTPEQLEELEKEFEK----NPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCCcCCHHHHHHHHHHHHh----CCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 567899999999999998888 7899999999999999999999999999999987764
No 13
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=98.68 E-value=1.7e-08 Score=94.93 Aligned_cols=58 Identities=21% Similarity=0.364 Sum_probs=50.4
Q ss_pred CCCcCccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCCC
Q 026161 179 RKRFRTKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGKK 241 (242)
Q Consensus 179 ~KR~RTkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gkk 241 (242)
-+|+||-||-||..+|+. |+.. ++-..-.+=+++..+.|..-+|||||||+|-|.+++
T Consensus 181 mRRYRTAFTReQIaRLEKEFyrE-----NYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQ 239 (408)
T KOG0844|consen 181 MRRYRTAFTREQIARLEKEFYRE-----NYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQ 239 (408)
T ss_pred HHHHHhhhhHHHHHHHHHHHHHh-----ccccCchhhhHHHhhCCCcceeehhhhhchhhhhhh
Confidence 499999999999999887 7766 566666788999999999999999999999887653
No 14
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=98.61 E-value=1.8e-08 Score=85.04 Aligned_cols=61 Identities=21% Similarity=0.171 Sum_probs=56.6
Q ss_pred CCCCCcCccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCCC
Q 026161 177 GSRKRFRTKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGKK 241 (242)
Q Consensus 177 ~~~KR~RTkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gkk 241 (242)
..+||.||+||..|++.++..+++ .+++|-...++++..+.++...|||||||.|+++.|.
T Consensus 58 ~~~rr~rt~~~~~ql~~ler~f~~----~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~ 118 (235)
T KOG0490|consen 58 FSKRCARCKFTISQLDELERAFEK----VHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKE 118 (235)
T ss_pred ccccccCCCCCcCHHHHHHHhhcC----CCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhh
Confidence 457999999999999999998888 4999999999999999999999999999999998764
No 15
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=98.56 E-value=1.1e-07 Score=91.26 Aligned_cols=60 Identities=13% Similarity=0.297 Sum_probs=56.5
Q ss_pred CCCCCcCccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 177 GSRKRFRTKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 177 ~~~KR~RTkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
.+|||.||.|+--.|..|+.++++ .+||..+++-++++++.+.|.|++|||=|+|+|.++
T Consensus 292 ~RkRKKRTSie~~vr~aLE~~F~~----npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR 351 (398)
T KOG3802|consen 292 SRKRKKRTSIEVNVRGALEKHFLK----NPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKR 351 (398)
T ss_pred ccccccccceeHHHHHHHHHHHHh----CCCCCHHHHHHHHHHhccccceEEEEeecccccccc
Confidence 457889999999999999999998 799999999999999999999999999999999864
No 16
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=98.37 E-value=2.3e-07 Score=78.99 Aligned_cols=62 Identities=16% Similarity=0.102 Sum_probs=56.4
Q ss_pred CCCCCCcCccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCCC
Q 026161 176 GGSRKRFRTKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGKK 241 (242)
Q Consensus 176 ~~~~KR~RTkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gkk 241 (242)
+...|+.|+.-|.+|+..|+..++. .++|+-....++...|+|+.+.+|+||||.|++.+++
T Consensus 48 s~~~~~~r~R~t~~Q~~vL~~~F~i----~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~ 109 (156)
T COG5576 48 SSPPKSKRRRTTDEQLMVLEREFEI----NPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKK 109 (156)
T ss_pred CCcCcccceechHHHHHHHHHHhcc----CCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHh
Confidence 3446888888899999999999998 7999999999999999999999999999999987764
No 17
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=98.35 E-value=6e-08 Score=87.32 Aligned_cols=60 Identities=20% Similarity=0.287 Sum_probs=52.4
Q ss_pred CCCCCcCccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCCC
Q 026161 177 GSRKRFRTKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGKK 241 (242)
Q Consensus 177 ~~~KR~RTkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gkk 241 (242)
+..||.||.||.+|+-.|+. |--+ .+--...+-|++.-+.|+.+=|||||||+|.|++|.
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhfN-----~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~ 217 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHFN-----KYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKE 217 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhccc-----cccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHh
Confidence 34699999999999999887 5444 577778899999999999999999999999999873
No 18
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=98.35 E-value=1.7e-07 Score=86.93 Aligned_cols=60 Identities=18% Similarity=0.264 Sum_probs=53.8
Q ss_pred CCCCCcCccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 177 GSRKRFRTKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 177 ~~~KR~RTkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
..+|+-||.||.-|+..|+.-+|+ -.+--...+.+++..+||+--=+|+||||+|.||++
T Consensus 170 kK~RksRTaFT~~Ql~~LEkrF~~----QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKr 229 (309)
T KOG0488|consen 170 KKRRKSRTAFSDHQLFELEKRFEK----QKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKR 229 (309)
T ss_pred cccccchhhhhHHHHHHHHHHHHH----hhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHH
Confidence 345778999999999999998888 356778889999999999999999999999999976
No 19
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=98.31 E-value=6e-07 Score=81.40 Aligned_cols=58 Identities=16% Similarity=0.268 Sum_probs=53.4
Q ss_pred CCCcCccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 179 RKRFRTKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 179 ~KR~RTkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
.|..||+|+.-|++.|..=+++ .|+----++.+|+..|||+.--||+||||+|-|++|
T Consensus 122 ~RKPRTIYSS~QLqaL~rRFQk----TQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KK 179 (245)
T KOG0850|consen 122 VRKPRTIYSSLQLQALNRRFQQ----TQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKK 179 (245)
T ss_pred ccCCcccccHHHHHHHHHHHhh----cchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHH
Confidence 4678999999999999998888 788888889999999999999999999999999876
No 20
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=98.30 E-value=3.3e-07 Score=83.07 Aligned_cols=62 Identities=15% Similarity=0.234 Sum_probs=54.4
Q ss_pred CCCCCCcCccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCCC
Q 026161 176 GGSRKRFRTKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGKK 241 (242)
Q Consensus 176 ~~~~KR~RTkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gkk 241 (242)
..+|||.||.|+.-|.-.|+.-+|. -.+-..+++.-|+..+-|+.--+|+||||+|+||+++
T Consensus 101 ~~RKKktRTvFSraQV~qLEs~Fe~----krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq 162 (268)
T KOG0485|consen 101 DDRKKKTRTVFSRAQVFQLESTFEL----KRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQ 162 (268)
T ss_pred ccccccchhhhhHHHHHHHHHHHHH----HhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHH
Confidence 4579999999999999999886655 2567778899999999999999999999999999865
No 21
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=98.18 E-value=9.9e-07 Score=79.49 Aligned_cols=56 Identities=21% Similarity=0.325 Sum_probs=52.2
Q ss_pred CCCcCccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccC
Q 026161 179 RKRFRTKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLG 239 (242)
Q Consensus 179 ~KR~RTkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~g 239 (242)
.|..||-||..|+..|+. |=|| |+-..+++.+|..-+-|+.--+|+||||+|+|-+
T Consensus 144 nRkPRtPFTtqQLlaLErkfrek-----qYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaK 200 (246)
T KOG0492|consen 144 NRKPRTPFTTQQLLALERKFREK-----QYLSIAERAEFSSSLELTETQVKIWFQNRRAKAK 200 (246)
T ss_pred CCCCCCCCCHHHHHHHHHHHhHh-----hhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHH
Confidence 477899999999999988 8888 9999999999999999999999999999999854
No 22
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=98.17 E-value=7.4e-07 Score=83.92 Aligned_cols=60 Identities=20% Similarity=0.332 Sum_probs=56.5
Q ss_pred CCCCcCccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCCC
Q 026161 178 SRKRFRTKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGKK 241 (242)
Q Consensus 178 ~~KR~RTkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gkk 241 (242)
.++|-||.||..|++.++..+.+ ..++|-..+|+++.=|.++...+.|||.|+|+||.|+
T Consensus 111 KqrrQrthFtSqqlqele~tF~r----NrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkr 170 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQR----NRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 170 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhh----ccCCccchhhHHHhhccccchhhhhhcccchhhhhhh
Confidence 35789999999999999998888 7899999999999999999999999999999999986
No 23
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=98.10 E-value=1.4e-06 Score=82.01 Aligned_cols=60 Identities=22% Similarity=0.391 Sum_probs=55.2
Q ss_pred CCCCCcCccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 177 GSRKRFRTKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 177 ~~~KR~RTkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
...+|-||+||++|++.+.+.+++ .+++|-..+++++++||+..-.|+|||+|.|+++.|
T Consensus 174 ~~~rr~rtsft~~Q~~~le~~f~r----t~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr 233 (354)
T KOG0849|consen 174 RGGRRNRTSFSPSQLEALEECFQR----TPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRR 233 (354)
T ss_pred ccccccccccccchHHHHHHHhcC----CCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhh
Confidence 445777999999999999999998 789999999999999999999999999999998765
No 24
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=98.06 E-value=4.6e-06 Score=77.96 Aligned_cols=61 Identities=10% Similarity=0.255 Sum_probs=53.9
Q ss_pred CCCCCCcCccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCCC
Q 026161 176 GGSRKRFRTKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGKK 241 (242)
Q Consensus 176 ~~~~KR~RTkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gkk 241 (242)
..+|||.|--||+-|-=.|++ |-.. .+--.-++|+|++.|.|+.-=+|+||||+|-|-+++
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQ-----RYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~ 211 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQ-----RYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQ 211 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhh-----hccccHhHHHHHHhcCCCchheeeeeecchhhhhhh
Confidence 456788889999999999888 7666 678889999999999999999999999999998764
No 25
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.95 E-value=2.9e-06 Score=71.69 Aligned_cols=62 Identities=27% Similarity=0.470 Sum_probs=55.3
Q ss_pred CCCCCCcCccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCCC
Q 026161 176 GGSRKRFRTKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGKK 241 (242)
Q Consensus 176 ~~~~KR~RTkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gkk 241 (242)
....+|.||.|+..|.+.+...+.. .++++...+++++..+|+..+|++|||+|.|.+..++
T Consensus 150 ~~~~~~~~~~~~~~~~~~~~~~~~~----~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~ 211 (235)
T KOG0490|consen 150 NKKPRRPRTTFTENQLEVLETVFRA----TPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKH 211 (235)
T ss_pred ccccCCCccccccchhHhhhhcccC----CCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhh
Confidence 3457999999999999999986655 6899999999999999999999999999999987653
No 26
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=97.84 E-value=7.3e-06 Score=77.12 Aligned_cols=61 Identities=21% Similarity=0.430 Sum_probs=53.7
Q ss_pred CCCCCCcCccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 176 GGSRKRFRTKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 176 ~~~~KR~RTkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
.+-|||.||.+-+-.|.-|++|+.- -.++..+-+..+++.+.|++.|++|||=|.|+|.++
T Consensus 306 ~~ekKRKRTSIAAPEKRsLEayFav----QPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKR 366 (385)
T KOG1168|consen 306 GGEKKRKRTSIAAPEKRSLEAYFAV----QPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKR 366 (385)
T ss_pred ccccccccccccCcccccHHHHhcc----CCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHH
Confidence 4558999999999999999996554 377888999999999999999999999999998654
No 27
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=97.82 E-value=7.5e-06 Score=72.34 Aligned_cols=59 Identities=20% Similarity=0.326 Sum_probs=48.6
Q ss_pred CCCcCccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCCC
Q 026161 179 RKRFRTKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGKK 241 (242)
Q Consensus 179 ~KR~RTkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gkk 241 (242)
.++.+-+||.||...|+.-++- -.+-.-....++++++||..|-++|||||+|++++.|
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~----~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~k 108 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFES----EKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTK 108 (198)
T ss_pred cccccccccHHHHHHhHHhhcc----ccccChHHHHHHHHhhCCChhHHHHHHhhccccccch
Confidence 3555557999999999884443 2566667799999999999999999999999999876
No 28
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=97.57 E-value=1.7e-05 Score=72.35 Aligned_cols=61 Identities=25% Similarity=0.343 Sum_probs=55.4
Q ss_pred CCCCCcCccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCCC
Q 026161 177 GSRKRFRTKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGKK 241 (242)
Q Consensus 177 ~~~KR~RTkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gkk 241 (242)
+.+|-.|-+|+-.|+..+..-+|. .++.--..+.+++..+|....-+||||||+|-||.||
T Consensus 165 G~rk~srPTf~g~qi~~le~~feq----tkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKk 225 (288)
T KOG0847|consen 165 GQRKQSRPTFTGHQIYQLERKFEQ----TKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKK 225 (288)
T ss_pred ccccccCCCccchhhhhhhhhhhh----hhcccchhHHHhhccccccHHHHHHHHhcchhhhhhh
Confidence 567889999999999999886666 5788888999999999999999999999999999987
No 29
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=97.51 E-value=4.3e-05 Score=76.16 Aligned_cols=57 Identities=14% Similarity=0.202 Sum_probs=52.5
Q ss_pred CCCCcCccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccc
Q 026161 178 SRKRFRTKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTL 238 (242)
Q Consensus 178 ~~KR~RTkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~ 238 (242)
..||.|+.||+.||+.|+++++. .++|+.++.+.+...++|+..++.=||+|.|-+.
T Consensus 419 ~~KKPRlVfTd~QkrTL~aiFke----~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 419 QTKKPRLVFTDIQKRTLQAIFKE----NKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred cCCCceeeecHHHHHHHHHHHhc----CCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 35899999999999999997777 6999999999999999999999999999998773
No 30
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=97.43 E-value=5.4e-05 Score=81.44 Aligned_cols=60 Identities=18% Similarity=0.280 Sum_probs=53.0
Q ss_pred CCCCCcCccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 177 GSRKRFRTKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 177 ~~~KR~RTkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
..+++.||.|+.+|+..|+.|.++ -..+-++..|.+-..|++..+|++|||+|+|++..|
T Consensus 901 ~~r~a~~~~~~d~qlk~i~~~~~~----q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k 960 (1406)
T KOG1146|consen 901 MGRRAYRTQESDLQLKIIKACYEA----QRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKK 960 (1406)
T ss_pred hhhhhhccchhHHHHHHHHHHHhh----ccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhh
Confidence 347999999999999999999999 344566788999999999999999999999998765
No 31
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=97.36 E-value=0.00016 Score=67.81 Aligned_cols=56 Identities=14% Similarity=0.240 Sum_probs=45.8
Q ss_pred CCcCccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 180 KRFRTKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 180 KR~RTkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
|..|--.|..|.-.|+. |+=. .+-..+-+-|+++.|.|+.|=|||||||+|-|.+|
T Consensus 236 RKKRcPYTK~QtlELEkEFlfN-----~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK 292 (308)
T KOG0487|consen 236 RKKRCPYTKHQTLELEKEFLFN-----MYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKK 292 (308)
T ss_pred ccccCCchHHHHHHHHHHHHHH-----HHHhHHHHHHHHHhcccchhheeeeehhhhhHHhh
Confidence 44455677888887776 6655 36677789999999999999999999999999887
No 32
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=97.34 E-value=1.7e-05 Score=69.57 Aligned_cols=60 Identities=20% Similarity=0.284 Sum_probs=52.1
Q ss_pred CCCCCcCccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 177 GSRKRFRTKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 177 ~~~KR~RTkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
-+++..||.|+.-|+.-+.+-+|+ -.+-.-.+++++++-++|+..-+|.||||+|-|++|
T Consensus 98 ~~r~K~Rtvfs~~ql~~l~~rFe~----QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk 157 (194)
T KOG0491|consen 98 CRRRKARTVFSDPQLSGLEKRFER----QRYLSTPERQELANALSLSETQVKTWFQNRRMKHKK 157 (194)
T ss_pred HHhhhhcccccCccccccHHHHhh----hhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHH
Confidence 346778999999999999997776 245667889999999999999999999999998876
No 33
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=97.16 E-value=7e-05 Score=69.81 Aligned_cols=59 Identities=14% Similarity=0.333 Sum_probs=45.3
Q ss_pred CCCCCcCccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 177 GSRKRFRTKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 177 ~~~KR~RTkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
..|-..|-..|+-|+=.|+. |--. .+.--...-||+..+||++|-+|+||||+|+|..|
T Consensus 197 RTkDKYRvVYTDhQRLELEKEfh~S-----ryITirRKSELA~~LgLsERQVKIWFQNRRAKERK 256 (317)
T KOG0848|consen 197 RTKDKYRVVYTDHQRLELEKEFHTS-----RYITIRRKSELAATLGLSERQVKIWFQNRRAKERK 256 (317)
T ss_pred ecccceeEEecchhhhhhhhhhccc-----cceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHH
Confidence 34567788899999887766 5444 33333445689999999999999999999998754
No 34
>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=95.14 E-value=0.0069 Score=43.47 Aligned_cols=46 Identities=22% Similarity=0.360 Sum_probs=33.4
Q ss_pred CcCccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccc
Q 026161 181 RFRTKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNN 234 (242)
Q Consensus 181 R~RTkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNn 234 (242)
+-|+.||+|+|..+...+.. +...|.++|.+.||++.+|.-|..--
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~--------~g~sv~~va~~~gi~~~~l~~W~~~~ 47 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLE--------SGESVSEVAREYGISPSTLYNWRKQY 47 (76)
T ss_dssp -SS----HHHHHHHHHHHHH--------HHCHHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHH--------CCCceEeeecccccccccccHHHHHH
Confidence 45789999999999887744 24689999999999999999997644
No 35
>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=94.59 E-value=0.023 Score=40.12 Aligned_cols=47 Identities=23% Similarity=0.349 Sum_probs=37.4
Q ss_pred CCcCccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccc
Q 026161 180 KRFRTKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNK 235 (242)
Q Consensus 180 KR~RTkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK 235 (242)
||.|+.+|-+||-.+...+|. .. .+.++|.+.||++.++.-|+.|..
T Consensus 1 krkR~~LTl~eK~~iI~~~e~------g~---s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEE------GE---SKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHC------TT----HHHHHHHHT--CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHc------CC---CHHHHHHHhCCCHHHHHHHHHhHH
Confidence 789999999999999999988 22 688999999999999999998854
No 36
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=92.44 E-value=0.019 Score=38.95 Aligned_cols=33 Identities=18% Similarity=0.401 Sum_probs=27.3
Q ss_pred ccCCCCHHHHHHHHHHhCCCCceEEEecccccc
Q 026161 204 RIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKH 236 (242)
Q Consensus 204 Riqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~ 236 (242)
...+|.+++.++||.++|+++.-|.-||-|.|.
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRr 39 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARR 39 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHc
Confidence 347899999999999999999999999999875
No 37
>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=88.73 E-value=0.32 Score=27.63 Aligned_cols=40 Identities=30% Similarity=0.414 Sum_probs=29.7
Q ss_pred CccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEec
Q 026161 183 RTKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWM 231 (242)
Q Consensus 183 RTkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWm 231 (242)
+..|+.+++..+....+. || .+.+++.++||++.+|..|+
T Consensus 3 ~~~~~~~~~~~i~~~~~~-~~--------s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 3 PPKLTPEQIEEARRLLAA-GE--------SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CCcCCHHHHHHHHHHHHc-CC--------CHHHHHHHHCCCHHHHHHhC
Confidence 345788888877775542 32 57889999999999887774
No 38
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=82.29 E-value=0.75 Score=35.90 Aligned_cols=48 Identities=23% Similarity=0.372 Sum_probs=39.0
Q ss_pred CCcCccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCC-CCceEEEecccccc
Q 026161 180 KRFRTKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGV-KRHVLKVWMHNNKH 236 (242)
Q Consensus 180 KR~RTkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv-~r~V~KVWmhNnK~ 236 (242)
+| |.+||.|-|..+-+++..- ...|.++|.+.|| +...|..|...-+.
T Consensus 3 ~r-~r~~s~EfK~~iv~~~~~~--------g~sv~~vAr~~gv~~~~~l~~W~~~~~~ 51 (116)
T COG2963 3 ER-RKKYSPEFKLEAVALYLRG--------GDTVSEVAREFGIVSATQLYKWRIQLQK 51 (116)
T ss_pred cc-cccCCHHHHHHHHHHHHhc--------CccHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 44 9999999999988887761 1279999999995 99999999874433
No 39
>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=82.07 E-value=0.28 Score=31.18 Aligned_cols=46 Identities=13% Similarity=0.234 Sum_probs=35.3
Q ss_pred ccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccc
Q 026161 184 TKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTL 238 (242)
Q Consensus 184 TkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~ 238 (242)
..++++|++.+..++.. +...+++|.++|++..+++.|.+..+.++
T Consensus 9 ~~l~~~~~~~~~~~~~~---------~~~~~~ia~~~~~s~~~i~~~~~~~~~~l 54 (55)
T cd06171 9 DKLPEREREVILLRFGE---------GLSYEEIAEILGISRSTVRQRLHRALKKL 54 (55)
T ss_pred HhCCHHHHHHHHHHHhc---------CCCHHHHHHHHCcCHHHHHHHHHHHHHHc
Confidence 45788898888776532 22477889999999999999998776554
No 40
>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=81.92 E-value=0.36 Score=32.60 Aligned_cols=40 Identities=20% Similarity=0.355 Sum_probs=29.1
Q ss_pred ccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecc
Q 026161 184 TKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMH 232 (242)
Q Consensus 184 TkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmh 232 (242)
.+++.+|.+.+.+..+. . ..+.++|.++||++.+|.-++.
T Consensus 4 ~~~~~~~~~~i~~l~~~------G---~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 4 PKLSKEQIEEIKELYAE------G---MSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp SSSSHCCHHHHHHHHHT------T-----HHHHHHHTTS-HHHHHHHHC
T ss_pred CCCCHHHHHHHHHHHHC------C---CCHHHHHHHHCcCHHHHHHHHh
Confidence 46888888888886655 1 5689999999999998865543
No 41
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=81.80 E-value=0.42 Score=40.32 Aligned_cols=44 Identities=25% Similarity=0.579 Sum_probs=35.5
Q ss_pred cCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecc
Q 026161 185 KFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMH 232 (242)
Q Consensus 185 kFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmh 232 (242)
.||+||+++|.. .-|- +..+....+.+++.++|++|.++++.+.
T Consensus 4 ~~T~eer~eLk~rIvEl----VRe~GRiTi~ql~~~TGasR~Tvk~~lr 48 (127)
T PF06163_consen 4 VFTPEEREELKARIVEL----VREHGRITIKQLVAKTGASRNTVKRYLR 48 (127)
T ss_pred cCCHHHHHHHHHHHHHH----HHHcCCccHHHHHHHHCCCHHHHHHHHH
Confidence 699999999887 4444 4556677899999999999999887654
No 42
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=80.98 E-value=1.7 Score=41.18 Aligned_cols=60 Identities=15% Similarity=0.286 Sum_probs=51.3
Q ss_pred CCcCccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCCC
Q 026161 180 KRFRTKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGKK 241 (242)
Q Consensus 180 KR~RTkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gkk 241 (242)
+|.|..|+..-.|.|.+ |... -...+|.+++.++++.+-+|+..-+--||-|.|-+++|.
T Consensus 189 rRKRRNFsK~aTeiLneyF~~h--~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~ 249 (334)
T KOG0774|consen 189 RRKRRNFSKQATEILNEYFYSH--LSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKN 249 (334)
T ss_pred HHhhcccchhHHHHHHHHHHHh--cCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhh
Confidence 78889999999999999 4444 235678899999999999999999999999999888763
No 43
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=77.14 E-value=2.2 Score=39.32 Aligned_cols=62 Identities=21% Similarity=0.232 Sum_probs=50.6
Q ss_pred CCCCCcCccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 177 GSRKRFRTKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 177 ~~~KR~RTkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
..++|.+..|..+...+|++ +++-+-|-. +.+.....++.++||++.=+.-||-|.|-+.-|
T Consensus 237 ~~~~r~~~~lP~~a~~ilr~Wl~~h~~~PY--Pse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~ 299 (342)
T KOG0773|consen 237 QSKWRPQRGLPKEAVSILRAWLFEHLLHPY--PSDDEKLMLAKQTGLSRPQVSNWFINARVRLWK 299 (342)
T ss_pred cCCCCCCCCCCHHHHHHHHHHHHHhccCCC--CcchhccccchhcCCCcccCCchhhhcccccCC
Confidence 34688888999999999988 777766654 444445599999999999999999999987654
No 44
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=74.40 E-value=3 Score=39.58 Aligned_cols=45 Identities=11% Similarity=0.177 Sum_probs=37.6
Q ss_pred HHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccC
Q 026161 191 KDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLG 239 (242)
Q Consensus 191 kekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~g 239 (242)
+..|++++-+ .++|......++++.+||+.--+--||.|+|++..
T Consensus 188 R~~LrewY~~----~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDR 232 (304)
T KOG0775|consen 188 RSLLREWYLQ----NPYPSPREKRELAEATGLTITQVSNWFKNRRQRDR 232 (304)
T ss_pred HHHHHHHHhc----CCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhh
Confidence 4447777665 78999999999999999998777889999998753
No 45
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=74.12 E-value=1.4 Score=46.62 Aligned_cols=48 Identities=15% Similarity=0.276 Sum_probs=37.5
Q ss_pred cCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccc
Q 026161 185 KFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHT 237 (242)
Q Consensus 185 kFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~ 237 (242)
.|++- .+.+++++.. .--+.++++..|+..|||+.+|+|+||.|.++.
T Consensus 563 ~~~~p-~sllkayyal----n~~ps~eelskia~qvglp~~vvk~wfE~~~a~ 610 (1007)
T KOG3623|consen 563 QFNHP-TSLLKAYYAL----NGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAE 610 (1007)
T ss_pred ccCCc-HHHHHHHHHh----cCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhh
Confidence 34444 5566664444 356888999999999999999999999998864
No 46
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=69.23 E-value=1.7 Score=34.72 Aligned_cols=43 Identities=19% Similarity=0.275 Sum_probs=33.5
Q ss_pred CccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccc
Q 026161 183 RTKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHN 233 (242)
Q Consensus 183 RTkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhN 233 (242)
|.+||.|+|..+...+-. +...|.++|.+.||+..+|--|..-
T Consensus 10 rr~ys~EfK~~aV~~~~~--------~g~sv~evA~e~gIs~~tl~~W~r~ 52 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFE--------PGMTVSLVARQHGVAASQLFLWRKQ 52 (121)
T ss_pred CCCCCHHHHHHHHHHHHc--------CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 567999998876665444 2235889999999999999999764
No 47
>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=68.70 E-value=3.8 Score=29.47 Aligned_cols=41 Identities=12% Similarity=0.323 Sum_probs=30.7
Q ss_pred CCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEE
Q 026161 186 FTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLK 228 (242)
Q Consensus 186 FT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~K 228 (242)
+|+.|++.|.... ..|+= ..|.+..++++++++||++.+|-
T Consensus 1 LT~~Q~e~L~~A~-~~GYf-d~PR~~tl~elA~~lgis~st~~ 41 (53)
T PF04967_consen 1 LTDRQREILKAAY-ELGYF-DVPRRITLEELAEELGISKSTVS 41 (53)
T ss_pred CCHHHHHHHHHHH-HcCCC-CCCCcCCHHHHHHHhCCCHHHHH
Confidence 6889999876644 44664 34556679999999999987763
No 48
>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=68.43 E-value=0.88 Score=30.84 Aligned_cols=44 Identities=9% Similarity=0.129 Sum_probs=30.1
Q ss_pred cCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccc
Q 026161 185 KFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHT 237 (242)
Q Consensus 185 kFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~ 237 (242)
+++++|++.+.-+.. +....+++|..+|++..++++|++.-|.+
T Consensus 10 ~L~~~~r~i~~l~~~---------~g~s~~eIa~~l~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 10 QLPERQREIFLLRYF---------QGMSYAEIAEILGISESTVKRRLRRARKK 53 (54)
T ss_dssp CS-HHHHHHHHHHHT---------S---HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHH---------HCcCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence 467777777665332 24468899999999999999999876654
No 49
>PF12651 RHH_3: Ribbon-helix-helix domain
Probab=67.92 E-value=5.1 Score=27.42 Aligned_cols=39 Identities=28% Similarity=0.414 Sum_probs=29.6
Q ss_pred CCCcCccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHH
Q 026161 179 RKRFRTKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFC 217 (242)
Q Consensus 179 ~KR~RTkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc 217 (242)
+|||-+.++.|+.++|.++|++.|=.+.+-=++.|+.|-
T Consensus 2 r~r~t~~l~~el~~~L~~ls~~t~i~~S~Ll~eAle~~l 40 (44)
T PF12651_consen 2 RKRFTFSLDKELYEKLKELSEETGIPKSKLLREALEDYL 40 (44)
T ss_pred ceEEEEecCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 689999999999999999999976544444445555543
No 50
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=67.66 E-value=1.5 Score=28.47 Aligned_cols=45 Identities=24% Similarity=0.458 Sum_probs=33.9
Q ss_pred cCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccC
Q 026161 185 KFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLG 239 (242)
Q Consensus 185 kFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~g 239 (242)
.+|++|++.+..+++ |+ ..++.|..+||++.+++.|++.-+.+++
T Consensus 3 ~l~~~e~~i~~~~~~--g~--------s~~eia~~l~is~~tv~~~~~~~~~kl~ 47 (58)
T smart00421 3 SLTPREREVLRLLAE--GL--------TNKEIAERLGISEKTVKTHLSNIMRKLG 47 (58)
T ss_pred CCCHHHHHHHHHHHc--CC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence 578888886654432 22 5688999999999999999887666654
No 51
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=67.09 E-value=1.4 Score=37.85 Aligned_cols=55 Identities=22% Similarity=0.364 Sum_probs=35.1
Q ss_pred CCcCccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccc
Q 026161 180 KRFRTKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNK 235 (242)
Q Consensus 180 KR~RTkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK 235 (242)
|+.-.++|.+|+..-+-+|+.- .-+-..+....+++++++||++.+|--|.+-|+
T Consensus 5 ~~le~~L~~~Q~kAa~ll~~ne-~~~~~~~r~T~~eiAee~Gis~~tLYrWr~~~~ 59 (142)
T PF13022_consen 5 KELEAKLTLQQRKAAQLLVENE-LMPENGERRTQAEIAEEVGISRSTLYRWRQQNK 59 (142)
T ss_dssp HHHHTTS-HHHHHHHHHHHHHH-HS------S-HHHHHHHHTS-HHHHHHHHHH-H
T ss_pred HHHHHHcCHHHHHHHHHHHHHH-HhhhccccchHHHHHHHhCCCHHHHHHHHhcCH
Confidence 5556789999999766666551 001111345789999999999999999997665
No 52
>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=63.57 E-value=26 Score=30.32 Aligned_cols=39 Identities=10% Similarity=0.205 Sum_probs=32.8
Q ss_pred CccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceE
Q 026161 183 RTKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVL 227 (242)
Q Consensus 183 RTkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~ 227 (242)
...+|+||.++|+.+=.. .|..-.+.+||.+.||++.-|
T Consensus 83 ~y~Lt~e~i~Eir~LR~~------DP~~wTr~~LAkkF~~S~~fV 121 (164)
T PF12824_consen 83 KYHLTPEDIQEIRRLRAE------DPEKWTRKKLAKKFNCSPLFV 121 (164)
T ss_pred cccCCHHHHHHHHHHHHc------CchHhhHHHHHHHhCCCHHHH
Confidence 468999999999997544 777889999999999987644
No 53
>PRK09480 slmA division inhibitor protein; Provisional
Probab=63.04 E-value=4.1 Score=32.99 Aligned_cols=47 Identities=11% Similarity=0.158 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccc
Q 026161 188 PEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNK 235 (242)
Q Consensus 188 ~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK 235 (242)
.+.++++.+-|.+|=+.-.. +...++++|++.||++.+|=-+|.|..
T Consensus 9 ~~~r~~Il~aa~~l~~~~~G-~~~ti~~Ia~~agvs~gt~Y~~F~~K~ 55 (194)
T PRK09480 9 GERREQILQALAQMLESPPG-ERITTAKLAARVGVSEAALYRHFPSKA 55 (194)
T ss_pred hhHHHHHHHHHHHHHHhcCC-CccCHHHHHHHhCCCHhHHHHHCCCHH
Confidence 56677777766665333234 778999999999999999999998843
No 54
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=63.01 E-value=1 Score=30.46 Aligned_cols=42 Identities=17% Similarity=0.330 Sum_probs=20.3
Q ss_pred CccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccc
Q 026161 183 RTKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHN 233 (242)
Q Consensus 183 RTkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhN 233 (242)
.+.||.+|+..+..+-+ ...-+.++|..+|+++.++--|+.+
T Consensus 2 ~~~Lt~~eR~~I~~l~~---------~G~s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 2 YKHLTPEERNQIEALLE---------QGMSIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp ----------HHHHHHC---------S---HHHHHHHTT--HHHHHHHHHH
T ss_pred ccchhhhHHHHHHHHHH---------cCCCHHHHHHHHCcCcHHHHHHHhc
Confidence 35799999999887743 2346788999999999887666544
No 55
>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=62.73 E-value=1.6 Score=34.60 Aligned_cols=47 Identities=9% Similarity=0.091 Sum_probs=38.4
Q ss_pred ccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 184 TKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 184 TkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
.+++++|++.+.- |.+. ...+++|..+||++.+++++++..|.++.+
T Consensus 110 ~~L~~~~r~v~~l~~~~g----------~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 110 EKLPERQRELLQLRYQRG----------VSLTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred HHCCHHHHHHHHHHHhcC----------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 6788888888666 5443 257889999999999999999999888765
No 56
>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=61.11 E-value=2.1 Score=27.15 Aligned_cols=23 Identities=22% Similarity=0.459 Sum_probs=20.2
Q ss_pred HHHHHHHhCCCCceEEEeccccc
Q 026161 213 VQQFCNDTGVKRHVLKVWMHNNK 235 (242)
Q Consensus 213 ve~fc~eiGv~r~V~KVWmhNnK 235 (242)
+.++|+.+||++.+|.-|..+.+
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~ 25 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGK 25 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCC
Confidence 57899999999999999987765
No 57
>PHA02893 hypothetical protein; Provisional
Probab=60.19 E-value=3.5 Score=32.93 Aligned_cols=20 Identities=25% Similarity=0.654 Sum_probs=12.9
Q ss_pred ccccCCCCCccccccccccc
Q 026161 73 FMAAGDEGTLDGLKCAACNC 92 (242)
Q Consensus 73 Fm~~~~~g~~~al~CaaCgC 92 (242)
|.+.|..+....|.|+|||-
T Consensus 58 ~~~~Gk~~~~~tL~CaACGS 77 (88)
T PHA02893 58 YLNIGKAFSNSNIKCIACGS 77 (88)
T ss_pred HHhccccCCCCceeehhhch
Confidence 44444433446899999983
No 58
>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=60.12 E-value=1.3 Score=30.80 Aligned_cols=46 Identities=15% Similarity=0.219 Sum_probs=36.8
Q ss_pred cCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 185 KFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 185 kFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
.||+.|++.|.-+++- ...++.+.++||+..+++.+..|-+.|++-
T Consensus 3 ~LT~~E~~vl~~l~~G----------~~~~eIA~~l~is~~tV~~~~~~i~~Kl~~ 48 (58)
T PF00196_consen 3 SLTERELEVLRLLAQG----------MSNKEIAEELGISEKTVKSHRRRIMKKLGV 48 (58)
T ss_dssp SS-HHHHHHHHHHHTT----------S-HHHHHHHHTSHHHHHHHHHHHHHHHHT-
T ss_pred ccCHHHHHHHHHHHhc----------CCcchhHHhcCcchhhHHHHHHHHHHHhCC
Confidence 5899999988888766 257889999999999999999988877663
No 59
>COG4802 FtrB Ferredoxin-thioredoxin reductase, catalytic subunit [Energy production and conversion]
Probab=59.84 E-value=9.2 Score=31.67 Aligned_cols=54 Identities=20% Similarity=0.285 Sum_probs=39.8
Q ss_pred CHHHHHHHHH----HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCCC
Q 026161 187 TPEQKDRMLE----LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGKK 241 (242)
Q Consensus 187 T~EQkekM~~----fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gkk 241 (242)
+.|.+++|.. +|+|-||++ ++|.+++..|..-+-..+..+-.|.=-+|.--+|+
T Consensus 2 ~~e~l~~my~~~eq~AeksG~~l-npD~e~~~~v~~gL~~~ke~yG~~~CPCRl~~g~e 59 (110)
T COG4802 2 SDEELNKMYRFTEQYAEKSGYRL-NPDREFTAEVLRGLASNKERYGYPSCPCRLVTGKE 59 (110)
T ss_pred cHHHHHHHHHHHHHHHHhcCcee-CCCHHHHHHHHHHHHHhHHHhCCCCCCeecccCCH
Confidence 3566777765 688999998 57888888888877777777777776666655553
No 60
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=58.31 E-value=1.6 Score=37.16 Aligned_cols=41 Identities=22% Similarity=0.230 Sum_probs=24.6
Q ss_pred HHHHHHHhCCccCCCCH---HHHHHHHHHhCCCCceEEEecccc
Q 026161 194 MLELAEKLGWRIQKHDE---EVVQQFCNDTGVKRHVLKVWMHNN 234 (242)
Q Consensus 194 M~~fAeklGWRiqk~d~---~~ve~fc~eiGv~r~V~KVWmhNn 234 (242)
|.++.+.+|++|..-.+ -..++|++.+||++.++.-|-++.
T Consensus 63 ~~~l~~~~g~~Ir~~Re~~glSqeeLA~~lgvs~s~IsriE~G~ 106 (154)
T TIGR00270 63 TEELVEDYGIIIRREREKRGWSQEQLAKKIQEKESLIKKIENAE 106 (154)
T ss_pred HHHHHHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCC
Confidence 33444444444444322 246788888888888887776654
No 61
>PRK10403 transcriptional regulator NarP; Provisional
Probab=58.24 E-value=2.8 Score=33.05 Aligned_cols=48 Identities=21% Similarity=0.245 Sum_probs=38.8
Q ss_pred ccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCCC
Q 026161 184 TKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGKK 241 (242)
Q Consensus 184 TkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gkk 241 (242)
..+|..+++.|..+++. ...+++++.++++.+++++.++|=+.|++.+
T Consensus 152 ~~Lt~~e~~vl~~~~~g----------~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~~ 199 (215)
T PRK10403 152 SVLTERELDVLHELAQG----------LSNKQIASVLNISEQTVKVHIRNLLRKLNVR 199 (215)
T ss_pred ccCCHHHHHHHHHHHCC----------CCHHHHHHHcCCCHHHHHHHHHHHHHHcCCC
Confidence 46999999988877654 2346778889999999999999988887754
No 62
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=57.22 E-value=3.4 Score=27.49 Aligned_cols=38 Identities=21% Similarity=0.649 Sum_probs=21.4
Q ss_pred HHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccc
Q 026161 188 PEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNN 234 (242)
Q Consensus 188 ~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNn 234 (242)
.+++..+..+... || .+.++|..+||++.++.-|+..-
T Consensus 4 ~~~R~~ii~l~~~-G~--------s~~~ia~~lgvs~~Tv~~w~kr~ 41 (50)
T PF13384_consen 4 EERRAQIIRLLRE-GW--------SIREIAKRLGVSRSTVYRWIKRY 41 (50)
T ss_dssp ------HHHHHHH-T----------HHHHHHHHTS-HHHHHHHHT--
T ss_pred hhHHHHHHHHHHC-CC--------CHHHHHHHHCcCHHHHHHHHHHc
Confidence 3444454444443 54 47899999999999999998764
No 63
>PF05572 Peptidase_M43: Pregnancy-associated plasma protein-A; InterPro: IPR008754 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. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase M43 (cytophagalysin family, clan MA(M)), subfamily M43. The predicted active site residues for members of this family and thermolysin, the type example for clan MA, occur in the motif HEXXH. The type example of this family is the pregnancy-associated plasma protein A (PAPP-A), which cleaves insulin-like growth factor (IGF) binding protein-4 (IGFBP-4), causing a dramatic reduction in its affinity for IGF-I and -II. Through this mechanism, PAPP-A is a regulator of IGF bioactivity in several systems, including the Homo sapiens ovary and the cardiovascular system [, , , ].; PDB: 3LUN_A 3LUM_B 2J83_A 2CKI_A.
Probab=54.54 E-value=8.9 Score=32.33 Aligned_cols=18 Identities=39% Similarity=0.457 Sum_probs=13.1
Q ss_pred cCccCCHHHHHHHHHHHH
Q 026161 182 FRTKFTPEQKDRMLELAE 199 (242)
Q Consensus 182 ~RTkFT~EQkekM~~fAe 199 (242)
.++.||+.|+++|+.+-|
T Consensus 137 c~~~FT~gQ~~RM~~~l~ 154 (154)
T PF05572_consen 137 CMNMFTPGQVARMRAVLE 154 (154)
T ss_dssp G--B-BHHHHHHHHHHHH
T ss_pred cccccCHHHHHHHHHHhC
Confidence 789999999999998654
No 64
>PRK02220 4-oxalocrotonate tautomerase; Provisional
Probab=53.48 E-value=25 Score=24.19 Aligned_cols=35 Identities=20% Similarity=0.280 Sum_probs=25.3
Q ss_pred CCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccc
Q 026161 186 FTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNN 234 (242)
Q Consensus 186 FT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNn 234 (242)
.|.|||++|.+ . +-+.++..+|+++.-+.|++..+
T Consensus 12 rs~eqk~~l~~---~-----------it~~l~~~~~~p~~~v~V~i~e~ 46 (61)
T PRK02220 12 RTEEQLKALVK---D-----------VTAAVSKNTGAPAEHIHVIINEM 46 (61)
T ss_pred CCHHHHHHHHH---H-----------HHHHHHHHhCcChhhEEEEEEEe
Confidence 38999988654 2 45668889999777777766543
No 65
>PRK00118 putative DNA-binding protein; Validated
Probab=53.41 E-value=1.8 Score=34.93 Aligned_cols=45 Identities=13% Similarity=0.143 Sum_probs=33.5
Q ss_pred cCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccc
Q 026161 185 KFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTL 238 (242)
Q Consensus 185 kFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~ 238 (242)
++++.|++.+.-+... +..+.++|..+||++.+++.|++.-+.++
T Consensus 17 ~L~ekqRevl~L~y~e---------g~S~~EIAe~lGIS~~TV~r~L~RArkkL 61 (104)
T PRK00118 17 LLTEKQRNYMELYYLD---------DYSLGEIAEEFNVSRQAVYDNIKRTEKLL 61 (104)
T ss_pred cCCHHHHHHHHHHHHc---------CCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 4677888886553322 33578899999999999999998766544
No 66
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=51.97 E-value=2.4 Score=34.29 Aligned_cols=47 Identities=9% Similarity=0.054 Sum_probs=36.6
Q ss_pred CccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccC
Q 026161 183 RTKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLG 239 (242)
Q Consensus 183 RTkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~g 239 (242)
--+++++|++.+.- +.+. ...+++|.++|++..++++|++.-|.++.
T Consensus 106 l~~L~~~~r~v~~l~~~~g----------~s~~eIA~~lgis~~tv~~~l~Rar~~Lr 153 (165)
T PRK09644 106 IHTLPVIEAQAILLCDVHE----------LTYEEAASVLDLKLNTYKSHLFRGRKRLK 153 (165)
T ss_pred HHhCCHHHHHHHHhHHHhc----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 35678888887654 4443 25789999999999999999998887764
No 67
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=51.67 E-value=3.2 Score=34.25 Aligned_cols=47 Identities=13% Similarity=0.350 Sum_probs=35.2
Q ss_pred ccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 184 TKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 184 TkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
.+++++|++.+.- |.+. ...+++|+++||+..++++|++.-+.++.+
T Consensus 132 ~~L~~~~r~i~~l~~~~~----------~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 179 (182)
T PRK12537 132 EQLEPARRNCILHAYVDG----------CSHAEIAQRLGAPLGTVKAWIKRSLKALRE 179 (182)
T ss_pred HhCCHHHHHHHHHHHHcC----------CCHHHHHHHHCCChhhHHHHHHHHHHHHHH
Confidence 3567777775333 4443 257889999999999999999988876643
No 68
>PF13518 HTH_28: Helix-turn-helix domain
Probab=51.32 E-value=3.1 Score=27.47 Aligned_cols=24 Identities=17% Similarity=0.540 Sum_probs=21.2
Q ss_pred HHHHHHHHhCCCCceEEEeccccc
Q 026161 212 VVQQFCNDTGVKRHVLKVWMHNNK 235 (242)
Q Consensus 212 ~ve~fc~eiGv~r~V~KVWmhNnK 235 (242)
.+.++|.++||++.+|.-|++.-+
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~ 37 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYR 37 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHH
Confidence 688899999999999999997644
No 69
>PRK06424 transcription factor; Provisional
Probab=50.52 E-value=5.2 Score=33.89 Aligned_cols=55 Identities=13% Similarity=0.137 Sum_probs=35.2
Q ss_pred CCcCccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccc
Q 026161 180 KRFRTKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNK 235 (242)
Q Consensus 180 KR~RTkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK 235 (242)
+|.|-.+.++..+.|.+|+++|=...... .-..++|+..+||++..|.-|..+.+
T Consensus 68 ~~~~~d~~~~~~~~~~~~g~~Ir~lRe~~-GLSQ~eLA~~iGvs~stIskiE~G~~ 122 (144)
T PRK06424 68 KKYKKKASDEDLDIVEDYAELVKNARERL-SMSQADLAAKIFERKNVIASIERGDL 122 (144)
T ss_pred CCccCcccHHHHHHHHHHHHHHHHHHHHc-CCCHHHHHHHhCCCHHHHHHHHCCCC
Confidence 33444455555577777777742111000 12468999999999999999988765
No 70
>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=49.99 E-value=3 Score=32.43 Aligned_cols=46 Identities=11% Similarity=0.201 Sum_probs=35.1
Q ss_pred cCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 185 KFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 185 kFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
+++.+|++.+.- +.+. ..++++|..+||++.+++++++..|.++.+
T Consensus 113 ~L~~~~r~il~l~~~~~----------~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 113 KLPEQCRKIFILSRFEG----------KSYKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred HCCHHHHHHHHHHHHcC----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 567777777655 3332 257789999999999999999998887754
No 71
>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=49.93 E-value=4 Score=26.67 Aligned_cols=44 Identities=25% Similarity=0.436 Sum_probs=30.7
Q ss_pred CCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccC
Q 026161 186 FTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLG 239 (242)
Q Consensus 186 FT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~g 239 (242)
++..|++.+.-+++ |+ ..+++|+.+||++.+++.|++.-+.+++
T Consensus 1 l~~~e~~i~~~~~~--~~--------s~~eia~~l~~s~~tv~~~~~~~~~~l~ 44 (57)
T cd06170 1 LTPREREVLRLLAE--GK--------TNKEIADILGISEKTVKTHLRNIMRKLG 44 (57)
T ss_pred CCHHHHHHHHHHHc--CC--------CHHHHHHHHCCCHHHHHHHHHHHHHHhC
Confidence 46677775433332 22 5688999999999999999886555544
No 72
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=49.74 E-value=2.3 Score=34.83 Aligned_cols=47 Identities=15% Similarity=0.307 Sum_probs=36.4
Q ss_pred ccCCHHHHHHHHHH-HHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 184 TKFTPEQKDRMLEL-AEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 184 TkFT~EQkekM~~f-AeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
.+++++|++.+.-+ .+. ...+++|..+||+..+++++++.-+.++.+
T Consensus 130 ~~L~~~~r~v~~l~~~~g----------~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~ 177 (184)
T PRK12512 130 ETLPPRQRDVVQSISVEG----------ASIKETAAKLSMSEGAVRVALHRGLAALAA 177 (184)
T ss_pred HhCCHHHHHHHHHHHHcC----------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 46777788776663 332 257899999999999999999998887654
No 73
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=49.41 E-value=6.8 Score=27.98 Aligned_cols=15 Identities=7% Similarity=0.284 Sum_probs=7.7
Q ss_pred CHHHHHHHHHHhCCC
Q 026161 209 DEEVVQQFCNDTGVK 223 (242)
Q Consensus 209 d~~~ve~fc~eiGv~ 223 (242)
....+.++|+-+||+
T Consensus 46 ~~~~~~~l~~~l~v~ 60 (78)
T TIGR02607 46 TADMALRLAKALGTS 60 (78)
T ss_pred CHHHHHHHHHHcCCC
Confidence 444555555555554
No 74
>PRK04217 hypothetical protein; Provisional
Probab=49.18 E-value=3.3 Score=33.74 Aligned_cols=44 Identities=14% Similarity=0.098 Sum_probs=33.7
Q ss_pred cCCHHHHHHHHHHH-HHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccc
Q 026161 185 KFTPEQKDRMLELA-EKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTL 238 (242)
Q Consensus 185 kFT~EQkekM~~fA-eklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~ 238 (242)
++|++|++.+.... +. ..++++|+.+||++.+|+..++.-+.++
T Consensus 42 ~Lt~eereai~l~~~eG----------lS~~EIAk~LGIS~sTV~r~L~RArkkL 86 (110)
T PRK04217 42 FMTYEEFEALRLVDYEG----------LTQEEAGKRMGVSRGTVWRALTSARKKV 86 (110)
T ss_pred cCCHHHHHHHHHHHHcC----------CCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 47889987765533 33 2688999999999999999888766654
No 75
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=48.75 E-value=2.3 Score=33.86 Aligned_cols=47 Identities=9% Similarity=0.096 Sum_probs=36.4
Q ss_pred ccCCHHHHHHHHHH-HHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 184 TKFTPEQKDRMLEL-AEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 184 TkFT~EQkekM~~f-AeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
..++++|++.+..+ .+ ....++++..+||++.+++.|++.-+.++.+
T Consensus 127 ~~L~~~~r~vl~l~~~~----------~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 174 (182)
T PRK09652 127 ESLPEELRTAITLREIE----------GLSYEEIAEIMGCPIGTVRSRIFRAREALRA 174 (182)
T ss_pred HhCCHHHHHHHHHHHHc----------CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46888888886553 32 2357789999999999999999988877654
No 76
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=48.31 E-value=4 Score=31.57 Aligned_cols=47 Identities=11% Similarity=0.157 Sum_probs=34.5
Q ss_pred cCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCCC
Q 026161 185 KFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGKK 241 (242)
Q Consensus 185 kFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gkk 241 (242)
+||+.|++.+..+++. + ..+++++++|++.+++++++++-+.|+++.
T Consensus 141 ~l~~~e~~vl~~~~~~--~--------~~~~ia~~l~~s~~tv~~~~~~~~~kl~~~ 187 (202)
T PRK09390 141 SLSERERQVMDGLVAG--L--------SNKVIARDLDISPRTVEVYRANVMTKMQAG 187 (202)
T ss_pred hhhhhHHHHHHHHHcc--C--------chHHHHHHcCCCHHHHHHHHHHHHHHHccc
Confidence 4666666666654442 1 256678899999999999999988887653
No 77
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=48.09 E-value=3.1 Score=33.34 Aligned_cols=48 Identities=13% Similarity=0.130 Sum_probs=37.3
Q ss_pred ccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCCC
Q 026161 184 TKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGKK 241 (242)
Q Consensus 184 TkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gkk 241 (242)
..++++|++.+.- +.+. -..+++|..+||+..+++++++..|.++.+.
T Consensus 111 ~~L~~~~r~v~~l~~~~~----------~s~~eIA~~lgis~~tv~~~l~Rar~~L~~~ 159 (161)
T PRK12541 111 SSLPLERRNVLLLRDYYG----------FSYKEIAEMTGLSLAKVKIELHRGRKETKSI 159 (161)
T ss_pred HHCCHHHHHHhhhHHhcC----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 3677778777554 3333 2578999999999999999999999887653
No 78
>PF13551 HTH_29: Winged helix-turn helix
Probab=47.94 E-value=13 Score=27.74 Aligned_cols=22 Identities=27% Similarity=0.502 Sum_probs=18.4
Q ss_pred CCCcCccCCHHHHHHHHHHHHH
Q 026161 179 RKRFRTKFTPEQKDRMLELAEK 200 (242)
Q Consensus 179 ~KR~RTkFT~EQkekM~~fAek 200 (242)
..|.++.+|++|++.+.+++..
T Consensus 51 ~g~~~~~l~~~~~~~l~~~~~~ 72 (112)
T PF13551_consen 51 GGRPRKRLSEEQRAQLIELLRE 72 (112)
T ss_pred CCCCCCCCCHHHHHHHHHHHHH
Confidence 3566666999999999998887
No 79
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=47.68 E-value=3.1 Score=34.79 Aligned_cols=47 Identities=13% Similarity=0.201 Sum_probs=36.4
Q ss_pred ccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 184 TKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 184 TkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
.+++++|++.+.- +.+. ..++++|..+||+..++|++++.-|.++.+
T Consensus 133 ~~Lp~~~R~v~~L~~~~g----------~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 180 (189)
T PRK12530 133 NHLPAQQARVFMMREYLE----------LSSEQICQECDISTSNLHVLLYRARLQLQA 180 (189)
T ss_pred HhCCHHHHHHHhHHHHcC----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4677888888655 3333 257899999999999999999988876643
No 80
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=47.26 E-value=3.2 Score=34.69 Aligned_cols=47 Identities=13% Similarity=0.097 Sum_probs=36.3
Q ss_pred ccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 184 TKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 184 TkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
.+++++|++.+.- +.+. -..+++++++||+..++|++++.-|.++.+
T Consensus 141 ~~L~~~~r~vl~l~~~~~----------~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~ 188 (194)
T PRK09646 141 DALTDTQRESVTLAYYGG----------LTYREVAERLAVPLGTVKTRMRDGLIRLRD 188 (194)
T ss_pred HhCCHHHHHHHHHHHHcC----------CCHHHHHHHhCCChHhHHHHHHHHHHHHHH
Confidence 4577888887644 3333 357899999999999999999998887653
No 81
>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=47.25 E-value=4.1 Score=26.04 Aligned_cols=23 Identities=17% Similarity=0.335 Sum_probs=19.4
Q ss_pred HHHHHHHhCCCCceEEEeccccc
Q 026161 213 VQQFCNDTGVKRHVLKVWMHNNK 235 (242)
Q Consensus 213 ve~fc~eiGv~r~V~KVWmhNnK 235 (242)
+++.|+.+||++.+|.-|..+.+
T Consensus 4 ~~e~a~~lgis~~ti~~~~~~g~ 26 (49)
T TIGR01764 4 VEEAAEYLGVSKDTVYRLIHEGE 26 (49)
T ss_pred HHHHHHHHCCCHHHHHHHHHcCC
Confidence 67889999999999998887664
No 82
>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=46.52 E-value=2.1 Score=34.94 Aligned_cols=46 Identities=2% Similarity=0.017 Sum_probs=33.9
Q ss_pred cCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 185 KFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 185 kFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
+++++|++.+.- |.+ ....+++|+.+|++..+++++++..|.++.+
T Consensus 138 ~L~~~~r~v~~l~~~~----------~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~ 184 (190)
T TIGR02939 138 ALPEDLRTAITLRELE----------GLSYEDIARIMDCPVGTVRSRIFRAREAIAI 184 (190)
T ss_pred cCCHHHhhhhhhhhhc----------CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 455666666443 222 2357899999999999999999998887754
No 83
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=46.40 E-value=3.4 Score=35.01 Aligned_cols=46 Identities=13% Similarity=0.121 Sum_probs=36.2
Q ss_pred ccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccC
Q 026161 184 TKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLG 239 (242)
Q Consensus 184 TkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~g 239 (242)
+.+|+.|++.+..++ -|| ..++++.++||++.+++.|.++-+.++.
T Consensus 5 ~~Lt~rqreVL~lr~--~Gl--------Tq~EIAe~LGiS~~tVs~ie~ra~kkLr 50 (141)
T PRK03975 5 SFLTERQIEVLRLRE--RGL--------TQQEIADILGTSRANVSSIEKRARENIE 50 (141)
T ss_pred cCCCHHHHHHHHHHH--cCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 568999999987643 233 4678999999999999999998776654
No 84
>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=46.14 E-value=11 Score=24.85 Aligned_cols=34 Identities=12% Similarity=0.132 Sum_probs=20.8
Q ss_pred HHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccc
Q 026161 193 RMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNN 234 (242)
Q Consensus 193 kM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNn 234 (242)
.+.++-++.||. .++|+..+||++.++.-|..+.
T Consensus 6 ~l~~~r~~~glt--------q~~lA~~~gvs~~~vs~~e~g~ 39 (58)
T TIGR03070 6 LVRARRKALGLT--------QADLADLAGVGLRFIRDVENGK 39 (58)
T ss_pred HHHHHHHHcCCC--------HHHHHHHhCCCHHHHHHHHCCC
Confidence 344455555553 4667777777777777776543
No 85
>PF13698 DUF4156: Domain of unknown function (DUF4156)
Probab=45.91 E-value=7.2 Score=30.52 Aligned_cols=17 Identities=35% Similarity=0.616 Sum_probs=14.3
Q ss_pred HhhhhhhccccCccccc
Q 026161 52 RECLKNHAVGIGGHALD 68 (242)
Q Consensus 52 ~eC~kNhaa~~Gg~a~D 68 (242)
.-=|||.||.|||.+|=
T Consensus 51 ~NdlrNeAa~lGgntV~ 67 (93)
T PF13698_consen 51 RNDLRNEAAKLGGNTVV 67 (93)
T ss_pred HHHHHHHHHHhCCCEEE
Confidence 34589999999998885
No 86
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=45.19 E-value=3.5 Score=34.08 Aligned_cols=48 Identities=13% Similarity=0.216 Sum_probs=35.7
Q ss_pred ccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 184 TKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 184 TkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
.+++++|++.+.-++- +.-.++++|+++||+..+++.+++..|.++.+
T Consensus 130 ~~L~~~~r~v~~l~~~---------~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 177 (184)
T PRK12539 130 ARLPEKMRLAIQAVKL---------EGLSVAEAATRSGMSESAVKVSVHRGLKALAA 177 (184)
T ss_pred HhCCHHHHHHHHHHHH---------cCCcHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4577777777654221 12357899999999999999999988877653
No 87
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=44.99 E-value=4.1 Score=32.12 Aligned_cols=48 Identities=6% Similarity=0.083 Sum_probs=36.7
Q ss_pred ccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCCC
Q 026161 184 TKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGKK 241 (242)
Q Consensus 184 TkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gkk 241 (242)
-++++.|++.+.- |.+. ...++++..+||+..++++|++.-+.++.+.
T Consensus 105 ~~L~~~~r~ii~l~~~~~----------~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~~ 153 (154)
T PRK06759 105 SVLDEKEKYIIFERFFVG----------KTMGEIALETEMTYYQVRWIYRQALEKMRNS 153 (154)
T ss_pred HhCCHHHHHHHHHHHhcC----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHhhc
Confidence 4677777777644 4332 3478999999999999999999988877653
No 88
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=44.66 E-value=3.3 Score=35.20 Aligned_cols=46 Identities=13% Similarity=0.077 Sum_probs=35.6
Q ss_pred ccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccC
Q 026161 184 TKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLG 239 (242)
Q Consensus 184 TkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~g 239 (242)
-+++++|++.+.. +.+. ...+++|+++||+..+++++++..+.++.
T Consensus 152 ~~L~~~~r~vl~l~~~~g----------~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr 198 (206)
T PRK12526 152 EKLPEAQQTVVKGVYFQE----------LSQEQLAQQLNVPLGTVKSRLRLALAKLK 198 (206)
T ss_pred HhCCHHHHHHHHHHHHcC----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 3577788888664 4333 25789999999999999999998887654
No 89
>TIGR00290 MJ0570_dom MJ0570-related uncharacterized domain. Proteins with this uncharacterized domain include two apparent ortholog families in the Archaea, one of which is universal among the first four completed archaeal genomes, and YLR143W, a much longer protein from Saccharomyces cerevisiae. The domain comprises the full length of the archaeal proteins and the first third of the yeast protein.
Probab=44.61 E-value=37 Score=30.64 Aligned_cols=44 Identities=18% Similarity=0.460 Sum_probs=36.7
Q ss_pred cCCHHHHHHHHHHHHHhCCcc-----CCCCHHHHHHHHHHhCCCCceEEE
Q 026161 185 KFTPEQKDRMLELAEKLGWRI-----QKHDEEVVQQFCNDTGVKRHVLKV 229 (242)
Q Consensus 185 kFT~EQkekM~~fAeklGWRi-----qk~d~~~ve~fc~eiGv~r~V~KV 229 (242)
.|+.+|+.+++..++++|++. +...++.+++|. +-|++-.+++|
T Consensus 94 I~s~~qr~~~e~v~~~lgl~~~~PLW~~~~~~ll~e~i-~~G~~aiIv~v 142 (223)
T TIGR00290 94 IYSEYQKTRIERVCRELGLKSFAPLWHRDPEKLMEEFV-EEKFEARIIAV 142 (223)
T ss_pred cccHHHHHHHHHHHHhcCCEEeccccCCCHHHHHHHHH-HcCCeEEEEEE
Confidence 478999999999999999876 455667888888 77888888777
No 90
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=44.56 E-value=4.2 Score=28.47 Aligned_cols=21 Identities=14% Similarity=0.328 Sum_probs=18.4
Q ss_pred HHHHHHHhCCCCceEEEeccc
Q 026161 213 VQQFCNDTGVKRHVLKVWMHN 233 (242)
Q Consensus 213 ve~fc~eiGv~r~V~KVWmhN 233 (242)
+.++|+.+||++++|+.|-..
T Consensus 3 i~eva~~~gvs~~tlr~y~~~ 23 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYERE 23 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHHHT
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 578999999999999999754
No 91
>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=44.25 E-value=4.8 Score=26.24 Aligned_cols=23 Identities=17% Similarity=0.268 Sum_probs=20.0
Q ss_pred HHHHHHHhCCCCceEEEeccccc
Q 026161 213 VQQFCNDTGVKRHVLKVWMHNNK 235 (242)
Q Consensus 213 ve~fc~eiGv~r~V~KVWmhNnK 235 (242)
+.++|+.+||+.++|+.|..+..
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g~ 25 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIGL 25 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCC
Confidence 67899999999999999977654
No 92
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=43.95 E-value=7.9 Score=30.05 Aligned_cols=47 Identities=11% Similarity=0.166 Sum_probs=37.5
Q ss_pred ccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 184 TKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 184 TkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
..||+.|++.+.-+++.. ..++++++++++.+++++|++|=+.|++-
T Consensus 148 ~~lt~~e~~vl~l~~~g~----------~~~~Ia~~l~~s~~tv~~~~~~~~~kl~~ 194 (211)
T PRK15369 148 PLLTPRERQILKLITEGY----------TNRDIAEQLSISIKTVETHRLNMMRKLDV 194 (211)
T ss_pred cCCCHHHHHHHHHHHCCC----------CHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 459999999887766541 25788889999999999999998887753
No 93
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=43.90 E-value=68 Score=21.35 Aligned_cols=35 Identities=23% Similarity=0.331 Sum_probs=25.2
Q ss_pred CccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCC
Q 026161 183 RTKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKR 224 (242)
Q Consensus 183 RTkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r 224 (242)
|-.||+|+-+++.+...+.|-. ....++..++..|
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~~-------~W~~Ia~~~~~~R 35 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGKD-------NWKKIAKRMPGGR 35 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTTT-------HHHHHHHHHSSSS
T ss_pred CCCCCHHHHHHHHHHHHHhCCc-------HHHHHHHHcCCCC
Confidence 5679999999999999996654 5666777776433
No 94
>PRK09726 antitoxin HipB; Provisional
Probab=43.85 E-value=17 Score=27.32 Aligned_cols=21 Identities=14% Similarity=0.390 Sum_probs=10.7
Q ss_pred HHHHHHHhCCCCceEEEeccc
Q 026161 213 VQQFCNDTGVKRHVLKVWMHN 233 (242)
Q Consensus 213 ve~fc~eiGv~r~V~KVWmhN 233 (242)
.++|+..+||++.+|.-|..+
T Consensus 28 q~elA~~~gvs~~tis~~e~g 48 (88)
T PRK09726 28 QSELAKKIGIKQATISNFENN 48 (88)
T ss_pred HHHHHHHHCcCHHHHHHHHCC
Confidence 345555555555555555443
No 95
>COG3040 Blc Bacterial lipocalin [Cell envelope biogenesis, outer membrane]
Probab=43.65 E-value=22 Score=31.56 Aligned_cols=26 Identities=38% Similarity=0.629 Sum_probs=22.9
Q ss_pred cCcc-CCHHHHHHHHHHHHHhCCccCC
Q 026161 182 FRTK-FTPEQKDRMLELAEKLGWRIQK 207 (242)
Q Consensus 182 ~RTk-FT~EQkekM~~fAeklGWRiqk 207 (242)
.||- .+++++++|++-|.++||-+.+
T Consensus 139 sRtP~~s~~~~~~ml~~ak~~Gfdv~~ 165 (174)
T COG3040 139 SRTPTLSQETLKRMLEIAKRRGFDVSK 165 (174)
T ss_pred ecCCCCCHHHHHHHHHHHHHcCCCcce
Confidence 3788 9999999999999999997654
No 96
>cd08353 Glo_EDI_BRP_like_7 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The structures of this family demonstrate domain swapping, which is shared by glyoxalase I and antibiotic resistance proteins.
Probab=43.63 E-value=22 Score=27.32 Aligned_cols=45 Identities=13% Similarity=0.102 Sum_probs=28.3
Q ss_pred CHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEec
Q 026161 187 TPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWM 231 (242)
Q Consensus 187 T~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWm 231 (242)
.-...++..+|+++|||++.......-..+-..+|++...+.+||
T Consensus 10 ~v~Dl~~s~~FY~~LG~~~~~~~~~~~~~~~~~~g~~~~~~~~~~ 54 (142)
T cd08353 10 VVRDLEAAIAFFLELGLELEGRAEIEGEWADRVTGLDGVRVEIAM 54 (142)
T ss_pred EeCCHHHHHHHHHHcCCEEccccccChHHHHHhcCCCCceEEEEE
Confidence 345688999999999998865432112233445677655555554
No 97
>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=43.55 E-value=2.8 Score=28.21 Aligned_cols=43 Identities=7% Similarity=0.247 Sum_probs=30.9
Q ss_pred cCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccc
Q 026161 185 KFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKH 236 (242)
Q Consensus 185 kFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~ 236 (242)
.++++|++.+...+ -.....++.++.+||++.+++.+.+.-..
T Consensus 4 ~L~~~er~vi~~~y---------~~~~t~~eIa~~lg~s~~~V~~~~~~al~ 46 (50)
T PF04545_consen 4 QLPPREREVIRLRY---------FEGLTLEEIAERLGISRSTVRRILKRALK 46 (50)
T ss_dssp TS-HHHHHHHHHHH---------TST-SHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHh---------cCCCCHHHHHHHHCCcHHHHHHHHHHHHH
Confidence 57889999987744 22346889999999999988877665433
No 98
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=43.44 E-value=4.2 Score=28.06 Aligned_cols=24 Identities=17% Similarity=0.361 Sum_probs=18.7
Q ss_pred HHHHHHHHhCCCCceEEEeccccc
Q 026161 212 VVQQFCNDTGVKRHVLKVWMHNNK 235 (242)
Q Consensus 212 ~ve~fc~eiGv~r~V~KVWmhNnK 235 (242)
.+.+|++++||++.+|.-|++++.
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~ 35 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKP 35 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT-
T ss_pred CHHHHHHHHCcCHHHHHHHHhccc
Confidence 478899999999999999999874
No 99
>PF06252 DUF1018: Protein of unknown function (DUF1018); InterPro: IPR009363 This family consists of several bacterial and phage proteins, related to Gp16 of phage Mu, of unknown function.
Probab=42.36 E-value=20 Score=28.62 Aligned_cols=34 Identities=21% Similarity=0.307 Sum_probs=21.4
Q ss_pred CCHHHHHHHHHHHHHhC--CccCCCCHHHHHHHHHH
Q 026161 186 FTPEQKDRMLELAEKLG--WRIQKHDEEVVQQFCND 219 (242)
Q Consensus 186 FT~EQkekM~~fAeklG--WRiqk~d~~~ve~fc~e 219 (242)
.|..|..|+.+....+| |-++.+.+..+..|+..
T Consensus 55 ~~~~q~~KI~aLw~~~~~~~~v~~~s~~aL~~fvkr 90 (119)
T PF06252_consen 55 ATSAQLRKIRALWKQLGKPGAVRDPSEAALDAFVKR 90 (119)
T ss_pred cchHHHHHHHHHHHHhhccCCccchHHHHHHHHHHH
Confidence 46667777777666666 34456666666666654
No 100
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=42.28 E-value=4.3 Score=33.11 Aligned_cols=47 Identities=9% Similarity=0.243 Sum_probs=35.2
Q ss_pred ccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 184 TKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 184 TkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
.+++++|++.+.- |.+. ...+++|+++||+..+++++++.-|.++.+
T Consensus 128 ~~L~~~~r~i~~l~~~~g----------~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 175 (179)
T PRK12514 128 EELEKDRAAAVRRAYLEG----------LSYKELAERHDVPLNTMRTWLRRSLLKLRE 175 (179)
T ss_pred HhCCHHHHHHHHHHHHcC----------CCHHHHHHHHCCChHHHHHHHHHHHHHHHH
Confidence 3567777776554 3322 247899999999999999999988877654
No 101
>PRK10072 putative transcriptional regulator; Provisional
Probab=41.73 E-value=12 Score=29.62 Aligned_cols=35 Identities=20% Similarity=0.414 Sum_probs=27.2
Q ss_pred HHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccc
Q 026161 194 MLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKH 236 (242)
Q Consensus 194 M~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~ 236 (242)
+..+.+++||. ..+||..+||+..+|.-|.+..+.
T Consensus 38 ik~LR~~~glT--------Q~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 38 FEQLRKGTGLK--------IDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred HHHHHHHcCCC--------HHHHHHHhCCCHHHHHHHHcCCCC
Confidence 45556777776 678999999999999999887653
No 102
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=41.67 E-value=7.9 Score=30.60 Aligned_cols=48 Identities=19% Similarity=0.303 Sum_probs=39.6
Q ss_pred ccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCCC
Q 026161 184 TKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGKK 241 (242)
Q Consensus 184 TkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gkk 241 (242)
..+|..+.+.+.-+++.+ ..++++++++++.+++++.++|=+.|++-+
T Consensus 136 ~~Lt~~E~~il~~l~~g~----------~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~~~ 183 (196)
T PRK10360 136 DPLTKRERQVAEKLAQGM----------AVKEIAAELGLSPKTVHVHRANLMEKLGVS 183 (196)
T ss_pred cCCCHHHHHHHHHHHCCC----------CHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence 369999999988888652 467788899999999999999988887754
No 103
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=41.54 E-value=3.8 Score=33.79 Aligned_cols=51 Identities=10% Similarity=0.160 Sum_probs=39.7
Q ss_pred CCcCccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 180 KRFRTKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 180 KR~RTkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
.+.-.++++.|++.+.- |.+- ...++++.++||+..+++++++.-+.++.+
T Consensus 134 ~~~l~~L~~~~r~i~~l~~~~g----------~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 185 (189)
T PRK09648 134 RELLDTLPEKQREILILRVVVG----------LSAEETAEAVGSTPGAVRVAQHRALARLRA 185 (189)
T ss_pred HHHHHhCCHHHHHHHHHHHHcC----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34556888888888765 4443 358899999999999999999988877654
No 104
>PF12728 HTH_17: Helix-turn-helix domain
Probab=41.12 E-value=5.7 Score=26.63 Aligned_cols=23 Identities=22% Similarity=0.494 Sum_probs=19.5
Q ss_pred HHHHHHHhCCCCceEEEeccccc
Q 026161 213 VQQFCNDTGVKRHVLKVWMHNNK 235 (242)
Q Consensus 213 ve~fc~eiGv~r~V~KVWmhNnK 235 (242)
++++|+.+||++.+|.-|.++.+
T Consensus 4 ~~e~a~~l~is~~tv~~~~~~g~ 26 (51)
T PF12728_consen 4 VKEAAELLGISRSTVYRWIRQGK 26 (51)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCC
Confidence 67899999999999999987654
No 105
>PRK13877 conjugal transfer relaxosome component TraJ; Provisional
Probab=40.78 E-value=25 Score=28.82 Aligned_cols=55 Identities=25% Similarity=0.501 Sum_probs=38.7
Q ss_pred CCCcCccCCHHHHHHHHHHHHHhC-------------CccC-CCCHHHHHHHH-------HHhCCCCceEEEeccccccc
Q 026161 179 RKRFRTKFTPEQKDRMLELAEKLG-------------WRIQ-KHDEEVVQQFC-------NDTGVKRHVLKVWMHNNKHT 237 (242)
Q Consensus 179 ~KR~RTkFT~EQkekM~~fAeklG-------------WRiq-k~d~~~ve~fc-------~eiGv~r~V~KVWmhNnK~~ 237 (242)
.+..++.+|+|.++.+.+-|+..| .+|+ .-|.+.+.++. .-=|| ||-||.+.+.+
T Consensus 10 ~~~I~vrvt~eE~~~I~~kA~~AGlS~SeYLR~~aLg~~I~s~~D~e~v~eL~~in~dlgRlGgL----lK~~l~~~~~~ 85 (114)
T PRK13877 10 GRHLRVPVLPDEKAEIEANAAAAGLSVARYLRDVGQGYQIKGVIDYEYVRELARINGDLGRLGGL----LKLWLTDDVRT 85 (114)
T ss_pred CceeEEEeCHHHHHHHHHHHHHhCCCHHHHHHHHHcCCCccccCCHHHHHHHHHhcccHHHHHHH----HHHHHhCCCCc
Confidence 355789999999999988777655 4443 46667777776 44444 78888886543
No 106
>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=40.74 E-value=8.7 Score=23.56 Aligned_cols=16 Identities=19% Similarity=0.356 Sum_probs=7.7
Q ss_pred CCHHHHHHHHHHhCCC
Q 026161 208 HDEEVVQQFCNDTGVK 223 (242)
Q Consensus 208 ~d~~~ve~fc~eiGv~ 223 (242)
+....+..+|+.+|++
T Consensus 39 ~~~~~~~~i~~~~~~~ 54 (58)
T cd00093 39 PSLETLEKLAKALGVS 54 (58)
T ss_pred CCHHHHHHHHHHhCCC
Confidence 4444455555555444
No 107
>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=40.37 E-value=9 Score=25.59 Aligned_cols=22 Identities=9% Similarity=0.339 Sum_probs=13.5
Q ss_pred HHHHHHhCCCCceEEEeccccc
Q 026161 214 QQFCNDTGVKRHVLKVWMHNNK 235 (242)
Q Consensus 214 e~fc~eiGv~r~V~KVWmhNnK 235 (242)
.+|+..+||++.++.-|+.+.+
T Consensus 13 ~~la~~~gis~~~i~~~~~g~~ 34 (55)
T PF01381_consen 13 KELAEKLGISRSTISRIENGKR 34 (55)
T ss_dssp HHHHHHHTS-HHHHHHHHTTSS
T ss_pred HHHHHHhCCCcchhHHHhcCCC
Confidence 5666666776666666666543
No 108
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=39.84 E-value=6.8 Score=28.89 Aligned_cols=37 Identities=14% Similarity=0.393 Sum_probs=26.0
Q ss_pred HHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccc
Q 026161 194 MLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNN 234 (242)
Q Consensus 194 M~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNn 234 (242)
|++|..+ -+.-.|..++.+|...|++-+=++.||--.
T Consensus 13 L~~Yy~~----h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~ 49 (56)
T PF11569_consen 13 LEDYYLK----HKQLQEEDLDELCDKSRMSYQQVRDWFAER 49 (56)
T ss_dssp HHHHHHH----T----TTHHHHHHHHTT--HHHHHHHHHHH
T ss_pred HHHHHHH----cCCccHhhHHHHHHHHCCCHHHHHHHHHHh
Confidence 7777766 345667889999999999999999999644
No 109
>PF13223 DUF4031: Protein of unknown function (DUF4031)
Probab=39.67 E-value=15 Score=29.02 Aligned_cols=18 Identities=22% Similarity=0.394 Sum_probs=13.5
Q ss_pred HHHHHHHHHHhCCCCceE
Q 026161 210 EEVVQQFCNDTGVKRHVL 227 (242)
Q Consensus 210 ~~~ve~fc~eiGv~r~V~ 227 (242)
-+++..|+..|||+|+-|
T Consensus 23 ~~ELHafA~riGv~rr~f 40 (83)
T PF13223_consen 23 LDELHAFAARIGVPRRWF 40 (83)
T ss_pred HHHHHHHHHHcCCCHHHH
Confidence 456788888899998633
No 110
>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=39.48 E-value=4.3 Score=33.29 Aligned_cols=47 Identities=13% Similarity=0.124 Sum_probs=35.4
Q ss_pred CccCCHHHHHHHHHH-HHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccC
Q 026161 183 RTKFTPEQKDRMLEL-AEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLG 239 (242)
Q Consensus 183 RTkFT~EQkekM~~f-AeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~g 239 (242)
-.+|+++|++.+.-+ .+. ...+++|.++||+..+++++++.-|.++.
T Consensus 98 l~~L~~~~r~v~~l~~~~g----------~s~~eIA~~lgis~~tV~~~l~Rar~~Lr 145 (170)
T TIGR02959 98 IKELPDEYREAIRLTELEG----------LSQQEIAEKLGLSLSGAKSRVQRGRKKLK 145 (170)
T ss_pred HHhCCHHHHHHHHHHHHcC----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 357788887776653 332 25789999999999999999988776653
No 111
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=39.44 E-value=4.4 Score=33.36 Aligned_cols=47 Identities=6% Similarity=0.090 Sum_probs=34.8
Q ss_pred ccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 184 TKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 184 TkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
.+++++|++.+.- |.+- ...+++|..+||++.+++++++..|.++.+
T Consensus 127 ~~L~~~~r~i~~l~~~~g----------~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 174 (186)
T PRK05602 127 AALPERQREAIVLQYYQG----------LSNIEAAAVMDISVDALESLLARGRRALRA 174 (186)
T ss_pred HhCCHHHHHHhhHHHhcC----------CCHHHHHHHhCcCHHHHHHHHHHHHHHHHH
Confidence 3466777776533 4333 357889999999999999999988877654
No 112
>cd01994 Alpha_ANH_like_IV This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases superfamily includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which binds to Adenosine group. This subfamily of proteins is predicted to bind ATP. This domainhas a strongly conserved motif SGGKD at the N terminus.
Probab=38.84 E-value=58 Score=28.24 Aligned_cols=45 Identities=24% Similarity=0.481 Sum_probs=35.8
Q ss_pred ccCCHHHHHHHHHHHHHhCCcc-----CCCCHHHHHHHHHHhCCCCceEEE
Q 026161 184 TKFTPEQKDRMLELAEKLGWRI-----QKHDEEVVQQFCNDTGVKRHVLKV 229 (242)
Q Consensus 184 TkFT~EQkekM~~fAeklGWRi-----qk~d~~~ve~fc~eiGv~r~V~KV 229 (242)
+.++..||.+++..++++|.+. ++..++.+++|. +-|++-.+++|
T Consensus 96 ~i~sd~~~~~~e~~~~~~gl~~~~PLW~~~~~~ll~e~~-~~g~~~~iv~v 145 (194)
T cd01994 96 AILSEYQRTRVERVCERLGLEPLAPLWGRDQEELLREMI-EAGFKAIIIKV 145 (194)
T ss_pred ccccHHHHHHHHHHHHHcCCEEEecccCCCHHHHHHHHH-HcCCeEEEEEe
Confidence 5688999999999999999654 345667888888 67887777766
No 113
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=38.56 E-value=24 Score=26.24 Aligned_cols=47 Identities=19% Similarity=0.353 Sum_probs=25.4
Q ss_pred CccCCHHHHHHHHHHHHHhCCc-cCCCCHHHHHHHHHHhCCCCceEEEe
Q 026161 183 RTKFTPEQKDRMLELAEKLGWR-IQKHDEEVVQQFCNDTGVKRHVLKVW 230 (242)
Q Consensus 183 RTkFT~EQkekM~~fAeklGWR-iqk~d~~~ve~fc~eiGv~r~V~KVW 230 (242)
||.||+|.=+.|.+|...-.+. ..-....+-++|..+ .+++++.|-|
T Consensus 2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~-~~t~HtwQSw 49 (65)
T PF08914_consen 2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEK-HPTRHTWQSW 49 (65)
T ss_dssp -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS--SSS--SHHH
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHH-cCCCCCHHHH
Confidence 8999999999999988553322 233445677777655 4667777666
No 114
>smart00351 PAX Paired Box domain.
Probab=38.48 E-value=15 Score=29.74 Aligned_cols=41 Identities=17% Similarity=0.248 Sum_probs=33.6
Q ss_pred cCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccc
Q 026161 185 KFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNN 234 (242)
Q Consensus 185 kFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNn 234 (242)
.++.++++++..+++. |+ ...++|.++||++.++.-|++.-
T Consensus 17 ~~s~~~R~riv~~~~~-G~--------s~~~iA~~~gvs~~tV~kwi~r~ 57 (125)
T smart00351 17 PLPDEERQRIVELAQN-GV--------RPCDISRQLCVSHGCVSKILGRY 57 (125)
T ss_pred CCCHHHHHHHHHHHHc-CC--------CHHHHHHHHCcCHHHHHHHHHHH
Confidence 3889999999987763 43 35688999999999999998753
No 115
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=38.43 E-value=4.9 Score=32.64 Aligned_cols=46 Identities=11% Similarity=0.195 Sum_probs=36.6
Q ss_pred ccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccC
Q 026161 184 TKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLG 239 (242)
Q Consensus 184 TkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~g 239 (242)
.+++++|++.+.- +.+. ..++++|+.+||+..+++++++.-|.++.
T Consensus 135 ~~L~~~~r~v~~l~~~~g----------~s~~eIA~~lgis~~~v~~~l~Rar~~Lr 181 (187)
T TIGR02948 135 QALPPKYRMVIVLKYMED----------LSLKEISEILDLPVGTVKTRIHRGREALR 181 (187)
T ss_pred HhCCHHHhHHhhhHHhcC----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4688888888554 4433 46889999999999999999998887764
No 116
>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=38.32 E-value=13 Score=25.69 Aligned_cols=18 Identities=17% Similarity=0.268 Sum_probs=7.5
Q ss_pred CCCHHHHHHHHHHhCCCC
Q 026161 207 KHDEEVVQQFCNDTGVKR 224 (242)
Q Consensus 207 k~d~~~ve~fc~eiGv~r 224 (242)
.+....+.++|..+||+.
T Consensus 38 ~~~~~~l~~i~~~~~v~~ 55 (64)
T PF12844_consen 38 KPSVSTLKKIAEALGVSL 55 (64)
T ss_dssp --BHHHHHHHHHHHTS-H
T ss_pred CCCHHHHHHHHHHhCCCH
Confidence 334445555555555543
No 117
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=38.29 E-value=6.4 Score=31.44 Aligned_cols=46 Identities=15% Similarity=0.260 Sum_probs=35.4
Q ss_pred ccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccC
Q 026161 184 TKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLG 239 (242)
Q Consensus 184 TkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~g 239 (242)
.+++++|++.+.-.. .|| ..++++..+||+..+++++++.-|.++.
T Consensus 111 ~~L~~~~r~il~l~~--~g~--------s~~eIA~~lgis~~tV~~~i~ra~~~Lr 156 (166)
T PRK09639 111 AKMTERDRTVLLLRF--SGY--------SYKEIAEALGIKESSVGTTLARAKKKFR 156 (166)
T ss_pred HcCCHHHHHHHHHHH--cCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 457778877765544 333 4788999999999999999988877654
No 118
>PF13189 Cytidylate_kin2: Cytidylate kinase-like family; PDB: 3FDI_A.
Probab=37.85 E-value=14 Score=31.12 Aligned_cols=40 Identities=23% Similarity=0.455 Sum_probs=19.0
Q ss_pred HHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccc
Q 026161 194 MLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNK 235 (242)
Q Consensus 194 M~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK 235 (242)
=+..|++||++. -|.+.+++.+.+.||+...|..|.....
T Consensus 16 a~~LA~~Lg~~~--~d~~ii~~~a~~~~~~~~~~~~~~e~~~ 55 (179)
T PF13189_consen 16 AERLAEKLGYPY--YDREIIEEAAKESGISEEEFEEFDEKKP 55 (179)
T ss_dssp HHHHHHHCT--E--E-HHHHHHCT------------SS-HHH
T ss_pred HHHHHHHcCCcc--CCHHHHHHHHHHccCCHHHHHHHhcccc
Confidence 356899999988 5668999999999999999988876543
No 119
>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=37.81 E-value=5 Score=32.01 Aligned_cols=47 Identities=13% Similarity=0.145 Sum_probs=35.1
Q ss_pred ccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 184 TKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 184 TkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
.+++++|++.+.- |.+. ...+++|..+||+..+++++.+..|.++.+
T Consensus 109 ~~L~~~~r~i~~l~~~~g----------~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 156 (162)
T TIGR02983 109 RRLPARQRAVVVLRYYED----------LSEAQVAEALGISVGTVKSRLSRALARLRE 156 (162)
T ss_pred HhCCHHHHHHhhhHHHhc----------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 3566777777544 3332 247789999999999999999998887654
No 120
>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=37.76 E-value=5.3 Score=29.95 Aligned_cols=47 Identities=11% Similarity=0.209 Sum_probs=35.4
Q ss_pred cCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 185 KFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 185 kFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
++++.|++.+..+.-. |+ ..+++|+++||++.+++.|++.-+.++.+
T Consensus 110 ~L~~~~~~ii~~~~~~-g~--------s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 110 KLPEREREVLVLRYLE-GL--------SYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred hCCHHHHHHHhhHHhc-CC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 6788888886553221 32 46699999999999999999888777654
No 121
>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=37.67 E-value=7.8 Score=29.71 Aligned_cols=28 Identities=4% Similarity=0.229 Sum_probs=23.4
Q ss_pred CHHHHHHHHHHhCCCCceEEEecccccc
Q 026161 209 DEEVVQQFCNDTGVKRHVLKVWMHNNKH 236 (242)
Q Consensus 209 d~~~ve~fc~eiGv~r~V~KVWmhNnK~ 236 (242)
+...+++++.++||+..++++|++++..
T Consensus 31 eGlS~kEIAe~LGIS~~TVk~~l~~~~~ 58 (73)
T TIGR03879 31 AGKTASEIAEELGRTEQTVRNHLKGETK 58 (73)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHhcCcc
Confidence 3446789999999999999999997643
No 122
>PRK15479 transcriptional regulatory protein TctD; Provisional
Probab=36.56 E-value=18 Score=28.81 Aligned_cols=50 Identities=16% Similarity=0.259 Sum_probs=38.1
Q ss_pred cCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhC-----CCCceEEEeccccccccCC
Q 026161 185 KFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTG-----VKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 185 kFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiG-----v~r~V~KVWmhNnK~~~gk 240 (242)
++|+.|.+.|.-++.. +......+++++++. ++.+++++++.+=|.|++.
T Consensus 148 ~Lt~~E~~il~~l~~~------~~~~~~~~~i~~~l~~~~~~~~~~tv~~~i~~ir~kl~~ 202 (221)
T PRK15479 148 ALTPREQALLTVLMYR------RTRPVSRQQLFEQVFSLNDEVSPESIELYIHRLRKKLQG 202 (221)
T ss_pred ecCHHHHHHHHHHHhC------CCCcCcHHHHHHHhcCCCCCCCcccHHHHHHHHHHhcCC
Confidence 5999999999988887 333344666776664 8899999998888877753
No 123
>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated. Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.
Probab=36.45 E-value=8.4 Score=33.76 Aligned_cols=49 Identities=8% Similarity=0.138 Sum_probs=40.0
Q ss_pred CccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCCC
Q 026161 183 RTKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGKK 241 (242)
Q Consensus 183 RTkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gkk 241 (242)
..+||+.|+|.+.-.|+- ...++.+..+||+.++++.+++|-+.|++-+
T Consensus 169 ~~~Lt~re~evl~~~a~G----------~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~~ 217 (232)
T TIGR03541 169 AGVLSEREREVLAWTALG----------RRQADIAAILGISERTVENHLRSARRKLGVA 217 (232)
T ss_pred hccCCHHHHHHHHHHHCC----------CCHHHHHHHHCcCHHHHHHHHHHHHHHHCCC
Confidence 458999999998776532 3467788999999999999999999888753
No 124
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=36.30 E-value=6.6 Score=32.71 Aligned_cols=47 Identities=11% Similarity=0.092 Sum_probs=35.3
Q ss_pred ccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 184 TKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 184 TkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
.+++++|++.+.- +.+. ...+++|..+||+..++|++++.-|.++.|
T Consensus 129 ~~Lp~~~r~v~~L~~~~g----------~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 129 ADLTTDQREALLLTQLLG----------LSYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred HhCCHHHhHHhhhHHHcC----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 4667777777543 3333 257899999999999999999988877653
No 125
>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=36.17 E-value=6 Score=31.12 Aligned_cols=32 Identities=13% Similarity=0.090 Sum_probs=26.7
Q ss_pred CHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 209 DEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 209 d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
+....+++|+.+||+..+++++++--|.++.+
T Consensus 120 ~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 120 KEFSYKEIAELLNLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred ccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34568999999999999999999988777643
No 126
>COG0289 DapB Dihydrodipicolinate reductase [Amino acid transport and metabolism]
Probab=36.10 E-value=28 Score=32.65 Aligned_cols=20 Identities=45% Similarity=0.498 Sum_probs=18.1
Q ss_pred ccCCHHHHHHHHHHHHHhCC
Q 026161 184 TKFTPEQKDRMLELAEKLGW 203 (242)
Q Consensus 184 TkFT~EQkekM~~fAeklGW 203 (242)
|=||+||+++|.+++++++-
T Consensus 101 TGf~~e~~~~l~~~a~~v~v 120 (266)
T COG0289 101 TGFTEEQLEKLREAAEKVPV 120 (266)
T ss_pred CCCCHHHHHHHHHHHhhCCE
Confidence 88999999999999999653
No 127
>KOG0705 consensus GTPase-activating protein Centaurin gamma (contains Ras-like GTPase, PH and ankyrin repeat domains) [Signal transduction mechanisms]
Probab=35.94 E-value=14 Score=38.55 Aligned_cols=36 Identities=31% Similarity=0.509 Sum_probs=26.2
Q ss_pred cccccccccccccCCCCCccccccccc-cccccccccc
Q 026161 64 GHALDGCGEFMAAGDEGTLDGLKCAAC-NCHRNFHRKE 100 (242)
Q Consensus 64 g~a~DGCgEFm~~~~~g~~~al~CaaC-gCHRnFHr~e 100 (242)
+|.+| |+---|.=..-.+++|.|.-| |||||++...
T Consensus 514 ~~c~d-c~~~n~~wAslnlg~l~cieCsgihr~lgt~l 550 (749)
T KOG0705|consen 514 SHCVD-CGTPNPKWASLNLGVLMCIECSGIHRNLGTHL 550 (749)
T ss_pred ceeee-cCCCCcccccccCCeEEEEEchhhhhhhhhhh
Confidence 46676 775555434445679999999 8999999764
No 128
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=35.81 E-value=6.1 Score=33.20 Aligned_cols=45 Identities=11% Similarity=0.163 Sum_probs=33.9
Q ss_pred cCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccC
Q 026161 185 KFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLG 239 (242)
Q Consensus 185 kFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~g 239 (242)
+++++|++.+.- +.+. ...++++..+||+..++|++++.-|.++.
T Consensus 116 ~Lp~~~r~i~~L~~~~g----------~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr 161 (187)
T PRK12516 116 QLPDDQREAIILVGASG----------FAYEEAAEICGCAVGTIKSRVNRARQRLQ 161 (187)
T ss_pred hCCHHHHHHHHHHHHcC----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 566777777544 3333 25778999999999999999998887664
No 129
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=35.41 E-value=5.2 Score=32.45 Aligned_cols=46 Identities=11% Similarity=0.122 Sum_probs=34.5
Q ss_pred ccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccC
Q 026161 184 TKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLG 239 (242)
Q Consensus 184 TkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~g 239 (242)
-++++.|++.+.- +.+. ...+++|..+||+..+++++++.-|.++.
T Consensus 111 ~~L~~~~r~v~~l~~~~g----------~s~~eIA~~lgis~~tV~~~l~Rar~~Lr 157 (164)
T PRK12547 111 NLLSADQREAIILIGASG----------FSYEDAAAICGCAVGTIKSRVSRARNRLQ 157 (164)
T ss_pred HhCCHHHHHHHHHHHHcC----------CCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 4667777776444 3333 35789999999999999999998877654
No 130
>PF09607 BrkDBD: Brinker DNA-binding domain; InterPro: IPR018586 This DNA-binding domain is the first approx. 100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway []. ; PDB: 2GLO_A.
Probab=35.15 E-value=15 Score=27.27 Aligned_cols=46 Identities=24% Similarity=0.367 Sum_probs=30.5
Q ss_pred CccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccc
Q 026161 183 RTKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHN 233 (242)
Q Consensus 183 RTkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhN 233 (242)
|-.||.+=|-+..++|++ ...-......-+.+.||+|+-++-|.+-
T Consensus 3 rrsy~~~FKL~Vv~~a~~-----~~nc~~~~RAaarkf~V~r~~Vr~W~kq 48 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEK-----DNNCKGNQRAAARKFNVSRRQVRKWRKQ 48 (58)
T ss_dssp -----HHHHHHHHHHHHH------TTTTT-HHHHHHHTTS-HHHHHHHHTT
T ss_pred ccccChHHHHHHHHHHHH-----ccchhhhHHHHHHHhCccHHHHHHHHHH
Confidence 667999999999999988 3443434566788999999999999763
No 131
>PF00765 Autoind_synth: Autoinducer synthetase; InterPro: IPR001690 Bacterial species have many methods of controlling gene expression and cell growth. Regulation of gene expression in response to changes in cell density is termed quorum sensing [, ]. Quorum-sensing bacteria produce, release and respond to hormone-like molecules (autoinducers) that accumulate in the external environment as the cell population grows. Once a threshold of these molecules is reached, a signal transduction cascade is triggered that ultimately leads to behavioural changes in the bacterium []. Autoinducers are thus clearly important mediators of molecular communication. Conjugal transfer of Agrobacterium octopine-type Ti plasmids is activated by octopine, a metabolite released from plant tumours []. Octopine causes conjugal donors to secrete a pheromone, Agrobacterium autoinducer (AAI), and exogenous AAI further stimulates conjugation. The putative AAI synthase and an AAI-responsive transcriptional regulator have been found to be encoded by the Ti plasmid traI and traR genes, respectively. TraR and TraI are similar to the LuxR and LuxI regulatory proteins of Vibrio fischeri, and AAI is similar in structure to the diffusable V. fischeri autoinducer, the inducing ligand of LuxR. TraR activates target genes in the presence of AAI and also activates traR and traI themselves, creating two positive-feedback loops. TraR-AAI-mediated activation in wild-type Agrobacterium strains is enhanced by culturing on solid media, suggesting a possible role in cell density sensing []. Production of light by the marine bacterium V. fischeri and by recombinant hosts containing cloned lux genes is controlled by the density of the culture []. Density-dependent regulation of lux gene expression has been shown to require a locus consisting of the luxR and luxI genes. In these and other Gram-negative bacteria, N-(3-oxohexanoyl)-L-homoserine lactone (OHHL) acts as the autoinducer by binding to transcriptional regulatory proteins and activating them []. OHHL and related molecules, such as N-butanoyl- (BHL), N-hexanoyl- (HHL) and N-oxododecanoyl- (PAI) homoserine lactones, are produced by a family of proteins that share a high level of sequence similarity. Proteins which currently members of this family include: luxI from V. fischeri. ahyI and asaI from Aeromonas species, which synthesize BHL and whose targets are ahyR and asaR respectively. carI from Erwinia carotovora. The target of OHHL is carR which activates genes involved in the biosynthesis of carbapenem antibiotics. eagI from Enterobacter agglomerans. The target of OHHL is not yet known. esaI from Erwinia stewartii. expI from Erwinia carotovora. lasI from Pseudomonas aeruginosa, which synthesizes PAI and whose target is lasR which activates the transcription of the elastase gene. rhlI (or vsmI) from P. aeruginosa, which synthesizes BHL and HHL and whose target is rhlR. swrI from Serratia liquefaciens, which synthesizes BHL. yenI from Yersinia enterocolitica. ; GO: 0007165 signal transduction; PDB: 3P2H_A 3P2F_A 1KZF_A 1K4J_A 1RO5_A.
Probab=35.07 E-value=3.4 Score=35.71 Aligned_cols=22 Identities=23% Similarity=0.656 Sum_probs=17.7
Q ss_pred HHHHhCCccCCCCHHHHHHHHH
Q 026161 197 LAEKLGWRIQKHDEEVVQQFCN 218 (242)
Q Consensus 197 fAeklGWRiqk~d~~~ve~fc~ 218 (242)
|.++|||.++..|..+++||=+
T Consensus 21 Fv~rlgW~v~~~dg~E~DqyD~ 42 (182)
T PF00765_consen 21 FVDRLGWDVPCEDGMEIDQYDD 42 (182)
T ss_dssp HTTCSCCCHHCCTSEE--TTGC
T ss_pred HHHhhCCCCcCCCCcEeeecCC
Confidence 9999999999999888888744
No 132
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=34.88 E-value=17 Score=23.79 Aligned_cols=30 Identities=27% Similarity=0.439 Sum_probs=21.4
Q ss_pred cccccccccccCCCCCccccccccccccccccccc
Q 026161 66 ALDGCGEFMAAGDEGTLDGLKCAACNCHRNFHRKE 100 (242)
Q Consensus 66 a~DGCgEFm~~~~~g~~~al~CaaCgCHRnFHr~e 100 (242)
.=+-|.++|... ...+|+|..| ..+.|++=
T Consensus 13 ~C~~C~~~i~~~---~~~~~~C~~C--~~~~H~~C 42 (50)
T cd00029 13 FCDVCRKSIWGL---FKQGLRCSWC--KVKCHKKC 42 (50)
T ss_pred Chhhcchhhhcc---ccceeEcCCC--CCchhhhh
Confidence 356799999864 3478999887 56666653
No 133
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=34.83 E-value=18 Score=23.24 Aligned_cols=28 Identities=25% Similarity=0.489 Sum_probs=20.0
Q ss_pred cccccccccccCCCCCcccccccccccccccccc
Q 026161 66 ALDGCGEFMAAGDEGTLDGLKCAACNCHRNFHRK 99 (242)
Q Consensus 66 a~DGCgEFm~~~~~g~~~al~CaaCgCHRnFHr~ 99 (242)
.=+-|+++|.... .+++|..| ....|.+
T Consensus 13 ~C~~C~~~i~~~~----~~~~C~~C--~~~~H~~ 40 (49)
T smart00109 13 KCCVCRKSIWGSF----QGLRCSWC--KVKCHKK 40 (49)
T ss_pred CccccccccCcCC----CCcCCCCC--CchHHHH
Confidence 4578999998643 47999977 4555554
No 134
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=34.38 E-value=6.4 Score=31.43 Aligned_cols=47 Identities=11% Similarity=0.196 Sum_probs=35.3
Q ss_pred ccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 184 TKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 184 TkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
.+++++|++.+.- +.+. ...++++..+||+..+++++++.-|.++.+
T Consensus 105 ~~Lp~~~r~v~~l~~~~g----------~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 152 (160)
T PRK09642 105 RELPENYRDVVLAHYLEE----------KSYQEIALQEKIEVKTVEMKLYRARKWIKK 152 (160)
T ss_pred HhCCHHHHHHHHHHHHhC----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4577777777544 3333 257899999999999999999988876643
No 135
>PF01902 ATP_bind_4: ATP-binding region; InterPro: IPR002761 This domain is about 200 amino acids long with a strongly conserved motif SGGKD at the N-terminal. The structure of Q8U2K6 from SWISSPROT from Pyrococcus furiosus has been resolved to 2.7A and is suggested to be a putative N-type pytophosphatase. In some members of the family e.g. Q12429 from SWISSPROT, this domain is associated with IPR006175 from INTERPRO, another domain of unknown function. Proteins with this uncharacterised domain include two apparent ortholog families in the archaea, one of which is universal among the first four completed archaeal genomes. The domain comprises the full length of the archaeal proteins and the first third of fungal proteins.; PDB: 3RK0_A 3RK1_A 3RJZ_A 2D13_D.
Probab=34.38 E-value=51 Score=29.52 Aligned_cols=44 Identities=23% Similarity=0.367 Sum_probs=32.1
Q ss_pred cCCHHHHHHHHHHHHHhCCccCC-----CCHHHHHHHHHHhCCCCceEEE
Q 026161 185 KFTPEQKDRMLELAEKLGWRIQK-----HDEEVVQQFCNDTGVKRHVLKV 229 (242)
Q Consensus 185 kFT~EQkekM~~fAeklGWRiqk-----~d~~~ve~fc~eiGv~r~V~KV 229 (242)
.++.+|+.+++..++++|++.-. ..++.+++|.+. |++-.+++|
T Consensus 94 I~~~~~r~~~e~vc~~lGl~~~~PLW~~d~~~ll~e~i~~-Gf~aiIv~V 142 (218)
T PF01902_consen 94 IDSEYQRNWVERVCERLGLEAVFPLWGRDREELLREFIES-GFEAIIVKV 142 (218)
T ss_dssp TS-HHHHHHHHHHHHHCT-EEE-TTTT--HHHHHHHHHHT-T-EEEEEEE
T ss_pred CCcHHHHHHHHHHHHHcCCEEEecccCCCHHHHHHHHHHC-CCeEEEEEE
Confidence 47899999999999999988643 345777888864 888888777
No 136
>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=34.29 E-value=6 Score=32.19 Aligned_cols=45 Identities=13% Similarity=0.052 Sum_probs=34.6
Q ss_pred CCHHHHHHHHHH-HHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 186 FTPEQKDRMLEL-AEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 186 FT~EQkekM~~f-AeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
+++.|++.+.-. .+. ...++.+..+||+..++|+.++.-|.++.+
T Consensus 135 Lp~~~r~v~~l~~~~g----------~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 180 (183)
T TIGR02999 135 VDPRQAEVVELRFFAG----------LTVEEIAELLGVSVRTVERDWRFARAWLAD 180 (183)
T ss_pred CCHHHHHHHHHHHHcC----------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 777777775543 332 357889999999999999999988877653
No 137
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=34.12 E-value=7.3 Score=31.49 Aligned_cols=46 Identities=17% Similarity=0.306 Sum_probs=35.4
Q ss_pred ccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccC
Q 026161 184 TKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLG 239 (242)
Q Consensus 184 TkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~g 239 (242)
.++++.|++.+.- +.+. ...+++|..+||+..++++.++.-|.++.
T Consensus 117 ~~L~~~~r~vl~L~~~~g----------~s~~EIA~~lgis~~tV~~~l~ra~~~Lr 163 (173)
T PRK09645 117 AQLSPEHRAVLVRSYYRG----------WSTAQIAADLGIPEGTVKSRLHYALRALR 163 (173)
T ss_pred HhCCHHHHHHHHHHHHcC----------CCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 3577888887655 4443 24789999999999999999988776654
No 138
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=33.95 E-value=6.7 Score=31.05 Aligned_cols=47 Identities=19% Similarity=0.218 Sum_probs=35.7
Q ss_pred CccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccC
Q 026161 183 RTKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLG 239 (242)
Q Consensus 183 RTkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~g 239 (242)
=-+++++|++.+.- +.+. -..+++|+.+||+..++|+.++.-+.++.
T Consensus 104 l~~Lp~~~r~v~~l~~~~g----------~s~~EIA~~lgis~~tV~~~l~ra~~~Lr 151 (161)
T PRK09047 104 IQKLPARQREAFLLRYWED----------MDVAETAAAMGCSEGSVKTHCSRATHALA 151 (161)
T ss_pred HHhCCHHHHHHHHHHHHhc----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 35678888888655 4333 24789999999999999999988776654
No 139
>PRK15008 HTH-type transcriptional regulator RutR; Provisional
Probab=33.91 E-value=23 Score=29.89 Aligned_cols=55 Identities=15% Similarity=0.158 Sum_probs=35.5
Q ss_pred CCcCccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccc
Q 026161 180 KRFRTKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNK 235 (242)
Q Consensus 180 KR~RTkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK 235 (242)
++.|+.=-.+.++++++-|..+=|+- .-+...+.++|.+.||++.+|-..|.|..
T Consensus 9 ~~~~~~~~~~~r~~IL~AA~~lf~e~-Gy~~~s~~dIA~~aGvs~gtiY~hF~sKe 63 (212)
T PRK15008 9 TGKRSRAVSAKKKAILSAALDTFSQF-GFHGTRLEQIAELAGVSKTNLLYYFPSKE 63 (212)
T ss_pred CCCcchhhHHHHHHHHHHHHHHHHHh-CcccCCHHHHHHHhCcCHHHHHHHCCCHH
Confidence 33333333456666666444432222 45566899999999999999988886643
No 140
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=33.91 E-value=5.3 Score=32.90 Aligned_cols=30 Identities=23% Similarity=0.271 Sum_probs=26.0
Q ss_pred HHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 211 EVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 211 ~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
...+++|.++||++.++++.++.-|.++.+
T Consensus 146 ~s~~EIA~~l~is~~tV~~~l~rar~~Lr~ 175 (181)
T PRK12536 146 LSVAETAQLTGLSESAVKVGIHRGLKALAA 175 (181)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 357899999999999999999998887654
No 141
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=33.73 E-value=5.5 Score=33.67 Aligned_cols=46 Identities=15% Similarity=0.172 Sum_probs=33.7
Q ss_pred cCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 185 KFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 185 kFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
+++++|++.+.- +.+. ...++.|..+||+..+++++++.-|.++.+
T Consensus 113 ~Lp~~~r~v~~L~~~~g----------~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~ 159 (188)
T PRK12546 113 QLPDEQREALILVGASG----------FSYEEAAEMCGVAVGTVKSRANRARARLAE 159 (188)
T ss_pred hCCHHHhHHhhhHHhcC----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 456666666443 2222 357899999999999999999988877653
No 142
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=33.70 E-value=7.1 Score=32.30 Aligned_cols=50 Identities=14% Similarity=0.249 Sum_probs=38.3
Q ss_pred CcCccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 181 RFRTKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 181 R~RTkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
+.-..++++|++.+.- +.+. ...+++|..+||+..++++.++.-|.++.+
T Consensus 127 ~~l~~L~~~~r~vl~l~~~~~----------~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 177 (189)
T PRK12515 127 ACLAKLSPAHREIIDLVYYHE----------KSVEEVGEIVGIPESTVKTRMFYARKKLAE 177 (189)
T ss_pred HHHHhCCHHHHHHHHHHHHcC----------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 3345788888888644 5554 257899999999999999999988877643
No 143
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=33.64 E-value=15 Score=29.45 Aligned_cols=40 Identities=10% Similarity=0.204 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccc
Q 026161 190 QKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNN 234 (242)
Q Consensus 190 QkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNn 234 (242)
-.+++.+|.+. +..+.-.++++|.++||+++.|+-+|+..
T Consensus 10 ~i~~~~~~I~~-----~~~~~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 10 TIHSILDWIED-----NLESPLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred HHHHHHHHHHH-----hcCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 34566776666 34455689999999999999998887643
No 144
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=33.55 E-value=8 Score=32.15 Aligned_cols=48 Identities=10% Similarity=0.275 Sum_probs=37.1
Q ss_pred ccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCCC
Q 026161 184 TKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGKK 241 (242)
Q Consensus 184 TkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gkk 241 (242)
.+++++|++.+.- |.+- .-.+++|+.+||++.++++.++-.|+++.|.
T Consensus 130 ~~L~~~~r~i~~l~~~~g----------~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~ 178 (189)
T PRK06811 130 NDLEKLDREIFIRRYLLG----------EKIEEIAKKLGLTRSAIDNRLSRGRKKLQKN 178 (189)
T ss_pred HhCCHHHHHHHHHHHHcc----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHc
Confidence 5677888887654 4433 2578999999999999999999888777653
No 145
>PF05077 DUF678: Protein of unknown function (DUF678); InterPro: IPR007769 This family contains poxvirus proteins belonging to the A19 family. The proteins are of unknown function.
Probab=33.53 E-value=17 Score=28.35 Aligned_cols=11 Identities=36% Similarity=0.842 Sum_probs=8.9
Q ss_pred ccccccccccc
Q 026161 82 LDGLKCAACNC 92 (242)
Q Consensus 82 ~~al~CaaCgC 92 (242)
.+.|.|+|||-
T Consensus 55 ~~tLsCsACGS 65 (74)
T PF05077_consen 55 GNTLSCSACGS 65 (74)
T ss_pred CCeEeehhccc
Confidence 35799999983
No 146
>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=33.17 E-value=8.1 Score=26.94 Aligned_cols=21 Identities=24% Similarity=0.490 Sum_probs=18.5
Q ss_pred HHHHHHHhCCCCceEEEeccc
Q 026161 213 VQQFCNDTGVKRHVLKVWMHN 233 (242)
Q Consensus 213 ve~fc~eiGv~r~V~KVWmhN 233 (242)
+.++|+.+||+..+|+-|.+.
T Consensus 3 ~~eva~~~gvs~~tlr~w~~~ 23 (68)
T cd01104 3 IGAVARLTGVSPDTLRAWERR 23 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 568999999999999999864
No 147
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=32.92 E-value=6.4 Score=31.26 Aligned_cols=47 Identities=13% Similarity=0.134 Sum_probs=34.0
Q ss_pred ccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccC
Q 026161 184 TKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLG 239 (242)
Q Consensus 184 TkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~g 239 (242)
.++++.+++.+..+.. +....+++|.++|+++.+++.|++--|.++.
T Consensus 124 ~~L~~~~r~i~~l~~~---------~~~~~~eIA~~lgis~~tv~~~~~ra~~~lr 170 (179)
T PRK11924 124 DALPVKQREVFLLRYV---------EGLSYREIAEILGVPVGTVKSRLRRARQLLR 170 (179)
T ss_pred HhCCHHHHHHhhHHHH---------cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4466777776544221 2235789999999999999999998777654
No 148
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=32.79 E-value=7.2 Score=31.72 Aligned_cols=29 Identities=7% Similarity=0.107 Sum_probs=24.8
Q ss_pred HHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 212 VVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 212 ~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
-.++.|+.+||+..+++++++.-|.++.+
T Consensus 137 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 165 (173)
T PRK12522 137 SYKEMSEILNIPIGTVKYRLNYAKKQMRE 165 (173)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 46889999999999999999988877643
No 149
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=32.47 E-value=5.9 Score=32.72 Aligned_cols=30 Identities=10% Similarity=0.087 Sum_probs=25.6
Q ss_pred HHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 211 EVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 211 ~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
...+++|..+||+..++++|++..+.++.+
T Consensus 158 ~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 187 (194)
T PRK12519 158 LSQSEIAKRLGIPLGTVKARARQGLLKLRE 187 (194)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 357899999999999999999988877653
No 150
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=32.27 E-value=6.4 Score=32.93 Aligned_cols=47 Identities=9% Similarity=0.071 Sum_probs=35.9
Q ss_pred CccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccC
Q 026161 183 RTKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLG 239 (242)
Q Consensus 183 RTkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~g 239 (242)
-..++++|++.+.- +.+. -..+++|+.+||+..+++++++--|.++.
T Consensus 134 l~~L~~~~r~i~~L~~~~g----------~s~~eIA~~lgis~~tV~~~l~Ra~~~Lr 181 (196)
T PRK12524 134 LAALPERQRQAVVLRHIEG----------LSNPEIAEVMEIGVEAVESLTARGKRALA 181 (196)
T ss_pred HHhCCHHHHHHHHHHHHcC----------CCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 34678888877555 3433 24788999999999999999998877664
No 151
>PF02943 FeThRed_B: Ferredoxin thioredoxin reductase catalytic beta chain; InterPro: IPR004209 Ferredoxin thioredoxin reductase is a [4FE-4S] protein present in organisms performing oxygenic photosynthesis, and plays an important role in the ferredoxin/thioredoxin regulatory chain. It converts an electron signal (photoreduced ferredoxin) to a thiol signal (reduced thioredoxin), regulating enzymes by reduction of specific disulphide groups. It catalyses the light-dependent activation of several photosynthetis enzymes. Ferredoxin thioredoxin reductase is a heterodimer of subunit alpha and subunit beta. Subunit alpha is the variable subunit, and beta is the catalytic chain []. The structure of the beta subunit has been determined and found to fold around the FeS cluster [].; GO: 0008937 ferredoxin-NAD(P) reductase activity, 0055114 oxidation-reduction process; PDB: 2PUK_E 2PVD_A 2PVG_A 2PUO_A 2PU9_A 1DJ7_A 2PVO_A.
Probab=32.11 E-value=85 Score=25.68 Aligned_cols=26 Identities=31% Similarity=0.450 Sum_probs=15.9
Q ss_pred HHHHHHHHHHhCCccCCCCHHHHHHHH
Q 026161 191 KDRMLELAEKLGWRIQKHDEEVVQQFC 217 (242)
Q Consensus 191 kekM~~fAeklGWRiqk~d~~~ve~fc 217 (242)
++.+..+|++.||++. +|++++..+-
T Consensus 7 ~~~~~~~a~~~G~~~N-pD~~~~~~v~ 32 (108)
T PF02943_consen 7 YKFLEKYAEKSGYKLN-PDEEVTDDVL 32 (108)
T ss_dssp HHHHHHHHHHTT-B-B-SSHHHHHHHH
T ss_pred HHHHHHHHHHhCCEEC-CCHHHHHHHH
Confidence 3445568999999985 6666665543
No 152
>PF06252 DUF1018: Protein of unknown function (DUF1018); InterPro: IPR009363 This family consists of several bacterial and phage proteins, related to Gp16 of phage Mu, of unknown function.
Probab=32.10 E-value=1.2e+02 Score=24.20 Aligned_cols=28 Identities=21% Similarity=0.419 Sum_probs=24.2
Q ss_pred CCcCccCCHHHHHHHHHHHHHhCCccCC
Q 026161 180 KRFRTKFTPEQKDRMLELAEKLGWRIQK 207 (242)
Q Consensus 180 KR~RTkFT~EQkekM~~fAeklGWRiqk 207 (242)
|+.-+.+|..|++++.+..+++||+.++
T Consensus 16 k~S~k~lt~~el~~vl~~l~~~G~k~~~ 43 (119)
T PF06252_consen 16 KSSSKDLTEAELEKVLDELKRLGFKPPK 43 (119)
T ss_pred hhhHHHCCHHHHHHHHHHHHHccCcCcc
Confidence 5666789999999999999999997554
No 153
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=32.07 E-value=6.7 Score=32.10 Aligned_cols=50 Identities=14% Similarity=0.111 Sum_probs=37.1
Q ss_pred CcCccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 181 RFRTKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 181 R~RTkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
+.-..+++.|++.+.- +.+. ...+++|+.+||+..+++++++..|.++.+
T Consensus 131 ~~l~~L~~~~r~vl~l~~~~~----------~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~ 181 (186)
T PRK13919 131 RALKALSPEERRVIEVLYYQG----------YTHREAAQLLGLPLGTLKTRARRALSRLKE 181 (186)
T ss_pred HHHHhCCHHHHHHHHHHHHcC----------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 3445677778877554 4333 257889999999999999999988877653
No 154
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=31.34 E-value=17 Score=30.19 Aligned_cols=44 Identities=11% Similarity=0.191 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccc
Q 026161 190 QKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNN 234 (242)
Q Consensus 190 QkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNn 234 (242)
-++++.+-|.++= .-+.-+...++++|++.||++.+|-.+|.|.
T Consensus 12 ~r~~Il~aa~~lf-~~~G~~~~ti~~Ia~~agvsk~t~Y~~F~sK 55 (213)
T PRK09975 12 TRQELIETAIAQF-ALRGVSNTTLNDIADAANVTRGAIYWHFENK 55 (213)
T ss_pred HHHHHHHHHHHHH-HHcCcccCCHHHHHHHcCCCHHHHHHHcCCH
Confidence 3455555333331 1124567789999999999999999888764
No 155
>cd02259 Peptidase_C39_like Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is not conserved in all sub-families.
Probab=31.28 E-value=87 Score=23.24 Aligned_cols=44 Identities=14% Similarity=0.114 Sum_probs=32.3
Q ss_pred CCcCccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEE
Q 026161 180 KRFRTKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKV 229 (242)
Q Consensus 180 KR~RTkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KV 229 (242)
+.+...++.+|. .+.++|.-...+...+.++++..|++-+.+++
T Consensus 17 ~~~g~~~~~~~l------~~~~~~~~~~~~~~~l~~~a~~~gl~~~~~~~ 60 (122)
T cd02259 17 RYFGIPVRRDVL------LNAQQRRQQGLSLADLVSLANKLGLTAQGVKL 60 (122)
T ss_pred HHcCCCCCHHHH------HHHHhhccCCCCHHHHHHHHHHcCCeeeEEEc
Confidence 556667777776 34455666677888899999999998887764
No 156
>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=31.23 E-value=9.2 Score=32.30 Aligned_cols=47 Identities=11% Similarity=0.070 Sum_probs=37.3
Q ss_pred CccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccC
Q 026161 183 RTKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLG 239 (242)
Q Consensus 183 RTkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~g 239 (242)
.|.+|+.|++.+.-++ -|| ..++++..+|+++.+++.|.+.-+.++.
T Consensus 4 ~~~Lte~qr~VL~Lr~--~Gl--------Tq~EIAe~LgiS~stV~~~e~ra~kkLr 50 (137)
T TIGR00721 4 KTFLTERQIKVLELRE--KGL--------SQKEIAKELKTTRANVSAIEKRAMENIE 50 (137)
T ss_pred cCCCCHHHHHHHHHHH--cCC--------CHHHHHHHHCcCHHHHHHHHHhHHHHHH
Confidence 3678999999877653 333 5788999999999999999888776654
No 157
>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=31.17 E-value=64 Score=22.31 Aligned_cols=22 Identities=41% Similarity=0.765 Sum_probs=19.0
Q ss_pred ccCCHHHHHHHHHHHHHhCCcc
Q 026161 184 TKFTPEQKDRMLELAEKLGWRI 205 (242)
Q Consensus 184 TkFT~EQkekM~~fAeklGWRi 205 (242)
-.++++=+++.++.|+++||+.
T Consensus 24 ~~vs~~tr~rI~~~a~~lgY~p 45 (46)
T PF00356_consen 24 PRVSEETRERILEAAEELGYRP 45 (46)
T ss_dssp SSSTHHHHHHHHHHHHHHTB-S
T ss_pred CCCCHHHHHHHHHHHHHHCCCC
Confidence 4789999999999999999974
No 158
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=31.15 E-value=7.2 Score=32.32 Aligned_cols=46 Identities=9% Similarity=0.140 Sum_probs=35.0
Q ss_pred ccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccC
Q 026161 184 TKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLG 239 (242)
Q Consensus 184 TkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~g 239 (242)
.+++++|++.+.- +.+. ...++++..+|++..++++.++.-|.++.
T Consensus 130 ~~Lp~~~r~v~~l~~~~g----------~s~~EIA~~lgis~~tV~~~l~Rar~~Lr 176 (191)
T PRK12520 130 DRLPPRTGRVFMMREWLE----------LETEEICQELQITATNAWVLLYRARMRLR 176 (191)
T ss_pred HhCCHHHHHHHHHHHHcC----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4577777777544 3332 35789999999999999999998877664
No 159
>PRK01964 4-oxalocrotonate tautomerase; Provisional
Probab=30.97 E-value=93 Score=21.77 Aligned_cols=35 Identities=11% Similarity=0.249 Sum_probs=26.2
Q ss_pred CHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccc
Q 026161 187 TPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNK 235 (242)
Q Consensus 187 T~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK 235 (242)
|.|||++|.+ . +-+.++..+|++...+-|.+..+.
T Consensus 13 t~eqk~~l~~---~-----------it~~l~~~lg~p~~~v~V~i~e~~ 47 (64)
T PRK01964 13 PEEKIKNLIR---E-----------VTEAISATLDVPKERVRVIVNEVP 47 (64)
T ss_pred CHHHHHHHHH---H-----------HHHHHHHHhCcChhhEEEEEEEcC
Confidence 8899988654 2 455678889999998888876543
No 160
>PF08688 ASD1: Apx/Shroom domain ASD1; InterPro: IPR014800 Cell shape changes require the coordination of actin and microtubule cytoskeletons. The Shroom family is a small group of related proteins that are defined by sequence similarity and in most cases by some link to the actin cytoskeleton. The Shroom (Shrm) protein family is found only in animals. Proteins of this family are predicted to be utilised in multiple morphogenic and developmental processes across animal phyla to regulate cells shape or intracellular architecture in an actin and myosin-dependent manner []. While the founding member of the Shrm family is Shrm1 (formerly Apx), it appears that this protein is found only in Xenopus []. In mice and humans, the Shrm family of proteins consists of: Shrm2 (formerly Apxl), a protein involved in the morphogenesis, maintenance, and/or function of vascular endothelial cells. Shrm3 (formerly Shroom), a protein necessary for neural tube closure in vertebrate development as deficiency in Shrm results in spina bifida. Shrm3 is also conserved in some invertebrates, as orthologues can be found in sea urchins. Shrm4, a regulator of cyto-skeletal architecture that may play an important role in vertebrate development. It is implicated in X-linked mental retardation in humans. This protein family is based on the conservation of a specific arrangement of an N-terminal PDZ domain, a centrally positioned sequence motif termed ASD1 (Apx/Shrm Domain 1) and a C-terminal motif termed ASD2 [, , ]. Shrm2 and Shrm3 contain all three domains, while Shrm4 contains the PDZ and ASD2 domains, but lacks a discernible ASD1 element. To date, the ASD1 and ASD2 elements have only been found in Shrm-related proteins and do not appear in combination with other conserved domains. ASD1 is required for targeting actin, while ASD2 is capable of eliciting an actomyosin based constriction event [, ]. ASD2 is the most highly conserved sequence element shared by Shrm1, Shrm2, Shrm3, and Shrm4. It possesses a well conserved series of leucine residues that exhibit spacing consistent with that of a leucine zipper motif []. This region is found in the actin binding protein Shroom. ASD1 has been implicated directly in F-actin binding.
Probab=30.70 E-value=2e+02 Score=25.73 Aligned_cols=16 Identities=50% Similarity=0.534 Sum_probs=11.6
Q ss_pred CCCCcCccCCHHHHHH
Q 026161 178 SRKRFRTKFTPEQKDR 193 (242)
Q Consensus 178 ~~KR~RTkFT~EQkek 193 (242)
.+--.|-.||+|||.+
T Consensus 122 ~RiGgRkRlTaEQKkr 137 (182)
T PF08688_consen 122 SRIGGRKRLTAEQKKR 137 (182)
T ss_pred ccccccccCCHHHhhh
Confidence 4455666799999964
No 161
>PTZ00397 macrophage migration inhibition factor-like protein; Provisional
Probab=30.68 E-value=1e+02 Score=24.13 Aligned_cols=37 Identities=5% Similarity=0.127 Sum_probs=28.5
Q ss_pred CCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccc
Q 026161 186 FTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKH 236 (242)
Q Consensus 186 FT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~ 236 (242)
.|.|||++|-+ + +-+.+.+.+||+...+-|-|+++..
T Consensus 69 ~~~e~k~~l~~---~-----------i~~~l~~~lgi~~~rv~I~f~~~~~ 105 (116)
T PTZ00397 69 ISRSNNSSIAA---A-----------ITKILASHLKVKSERVYIEFKDCSA 105 (116)
T ss_pred CCHHHHHHHHH---H-----------HHHHHHHHhCcCcccEEEEEEECCh
Confidence 36788887543 3 4556778899999999999998754
No 162
>cd04275 ZnMc_pappalysin_like Zinc-dependent metalloprotease, pappalysin_like subfamily. The pregnancy-associated plasma protein A (PAPP-A or pappalysin-1) cleaves insulin-like growth factor-binding proteins 4 and 5, thereby promoting cell growth by releasing bound growth factor. This model includes pappalysins and related metalloprotease domains from all three kingdoms of life. The three-dimensional structure of an archaeal representative, ulilysin, has been solved.
Probab=30.19 E-value=34 Score=30.72 Aligned_cols=17 Identities=35% Similarity=0.458 Sum_probs=14.7
Q ss_pred CcCccCCHHHHHHHHHH
Q 026161 181 RFRTKFTPEQKDRMLEL 197 (242)
Q Consensus 181 R~RTkFT~EQkekM~~f 197 (242)
..++.||+.|+++|+..
T Consensus 207 ~C~~~FT~~Q~~RM~~~ 223 (225)
T cd04275 207 SCMNEFTPGQVTRMRSY 223 (225)
T ss_pred chhcccCHHHHHHHHHH
Confidence 45789999999999975
No 163
>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=29.91 E-value=11 Score=26.72 Aligned_cols=21 Identities=33% Similarity=0.664 Sum_probs=17.9
Q ss_pred HHHHHHHhCCCCceEEEeccc
Q 026161 213 VQQFCNDTGVKRHVLKVWMHN 233 (242)
Q Consensus 213 ve~fc~eiGv~r~V~KVWmhN 233 (242)
+.++|+.+||+.++|+.|...
T Consensus 3 i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 568899999999999999753
No 164
>PRK10651 transcriptional regulator NarL; Provisional
Probab=29.70 E-value=14 Score=29.21 Aligned_cols=47 Identities=13% Similarity=0.215 Sum_probs=36.6
Q ss_pred ccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 184 TKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 184 TkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
..||+.|++.|.-+++- + ..++++.+++|+.+++++...|=+.|++-
T Consensus 154 ~~Lt~rE~~vl~~l~~g------~----~~~~ia~~l~is~~tV~~~~~~l~~Kl~~ 200 (216)
T PRK10651 154 NQLTPRERDILKLIAQG------L----PNKMIARRLDITESTVKVHVKHMLKKMKL 200 (216)
T ss_pred ccCCHHHHHHHHHHHcC------C----CHHHHHHHcCCCHHHHHHHHHHHHHHcCC
Confidence 35999999988777653 1 35667888999999999999887777653
No 165
>cd02425 Peptidase_C39F A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family.
Probab=29.67 E-value=1.1e+02 Score=22.87 Aligned_cols=44 Identities=18% Similarity=0.194 Sum_probs=34.7
Q ss_pred CCcCccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEE
Q 026161 180 KRFRTKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKV 229 (242)
Q Consensus 180 KR~RTkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KV 229 (242)
+++...++.++... .++|.-+..+...+.++++..|++-++.++
T Consensus 22 ~~~~~~~~~~~l~~------~~~~~~~~~~~~~l~~~a~~~gl~~~~~~~ 65 (126)
T cd02425 22 NYFGYKVSLNELRE------KYELGRDGLSLSYLKQLLEEYGFKCKVYKI 65 (126)
T ss_pred HHhCCCCCHHHHHH------hccCCCCCcCHHHHHHHHHHCCCcceEEEE
Confidence 56677788777543 457777788889999999999999888876
No 166
>cd08356 Glo_EDI_BRP_like_17 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping.
Probab=29.56 E-value=40 Score=25.46 Aligned_cols=30 Identities=13% Similarity=0.261 Sum_probs=25.4
Q ss_pred CCcCccCCHHHHHHHHHHHHHhCCccCCCC
Q 026161 180 KRFRTKFTPEQKDRMLELAEKLGWRIQKHD 209 (242)
Q Consensus 180 KR~RTkFT~EQkekM~~fAeklGWRiqk~d 209 (242)
|+..+.+.-...++-.+|++.|||+....+
T Consensus 1 ~~~~~~l~v~Dl~~s~~FY~~LGf~~~~~~ 30 (113)
T cd08356 1 KSIRPFIPAKDFAESKQFYQALGFELEWEN 30 (113)
T ss_pred CcceeccccccHHHHHHHHHHhCCeeEecC
Confidence 566788888899999999999999987654
No 167
>PRK02289 4-oxalocrotonate tautomerase; Provisional
Probab=29.48 E-value=1.3e+02 Score=21.01 Aligned_cols=34 Identities=15% Similarity=0.307 Sum_probs=26.5
Q ss_pred CCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccc
Q 026161 186 FTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHN 233 (242)
Q Consensus 186 FT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhN 233 (242)
.|.|||++|.+ . +-+.++..+|++...+.|.+..
T Consensus 12 rs~EqK~~L~~---~-----------it~a~~~~~~~p~~~v~V~i~e 45 (60)
T PRK02289 12 RSQEQKNALAR---E-----------VTEVVSRIAKAPKEAIHVFIND 45 (60)
T ss_pred CCHHHHHHHHH---H-----------HHHHHHHHhCcCcceEEEEEEE
Confidence 48999988643 2 5566788899999999998764
No 168
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=29.27 E-value=15 Score=29.09 Aligned_cols=46 Identities=9% Similarity=0.036 Sum_probs=37.0
Q ss_pred cCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 185 KFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 185 kFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
.+|..+.+.|.-+++- ...++++.+++++.+++++++.+=+.|++-
T Consensus 149 ~lt~re~~vl~~l~~g----------~s~~eIa~~l~~s~~tv~~~~~~~~~kl~~ 194 (210)
T PRK09935 149 VLSNREVTILRYLVSG----------LSNKEIADQLLLSNKTVSAHKSNIYGKLGL 194 (210)
T ss_pred cCCHHHHHHHHHHHcC----------CCHHHHHHHhCCCHHHHHHHHHHHHHHcCC
Confidence 4788888887766654 357788889999999999999998888763
No 169
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=29.26 E-value=9.5 Score=32.68 Aligned_cols=47 Identities=17% Similarity=0.261 Sum_probs=34.5
Q ss_pred ccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 184 TKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 184 TkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
-+++++|++.+.- |.+- .-.+++++.+||+..+++++++..|.++.+
T Consensus 137 ~~L~~~~r~v~~L~~~~g----------~s~~EIA~~Lgis~~tV~~~l~RArk~Lr~ 184 (203)
T PRK09647 137 DSLPPEFRAAVVLCDIEG----------LSYEEIAATLGVKLGTVRSRIHRGRQQLRA 184 (203)
T ss_pred HhCCHHHHHHHHHHHHcC----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3567777776433 3333 247889999999999999999988877643
No 170
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=29.21 E-value=9.7 Score=32.70 Aligned_cols=47 Identities=9% Similarity=0.112 Sum_probs=36.2
Q ss_pred ccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 184 TKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 184 TkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
.+++++|++.+.- |.+. ...+++|..+||+..+++++++.-|+++++
T Consensus 147 ~~L~~~~r~v~~L~~~~g----------~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~ 194 (206)
T PRK12544 147 DGLPAKYARVFMMREFIE----------LETNEICHAVDLSVSNLNVLLYRARLRLRE 194 (206)
T ss_pred HhCCHHHHHHHHHHHHcC----------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4677778877544 4443 247899999999999999999988887654
No 171
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=29.16 E-value=40 Score=29.18 Aligned_cols=43 Identities=16% Similarity=0.275 Sum_probs=32.9
Q ss_pred cCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEE
Q 026161 185 KFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKV 229 (242)
Q Consensus 185 kFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KV 229 (242)
-||+.|++.+.. |=++|+= ..|.....+++++++||++.+|.-
T Consensus 155 ~LTdrQ~~vL~~-A~~~GYF-d~PR~~~l~dLA~~lGISkst~~e 197 (215)
T COG3413 155 DLTDRQLEVLRL-AYKMGYF-DYPRRVSLKDLAKELGISKSTLSE 197 (215)
T ss_pred cCCHHHHHHHHH-HHHcCCC-CCCccCCHHHHHHHhCCCHHHHHH
Confidence 799999999655 4455764 345556799999999999887643
No 172
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=29.15 E-value=5.1 Score=33.18 Aligned_cols=32 Identities=16% Similarity=0.230 Sum_probs=27.3
Q ss_pred CHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 209 DEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 209 d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
+...++++|.++||++.+++++++..|.++.+
T Consensus 154 ~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 185 (194)
T PRK12513 154 GDLELEEIAELTGVPEETVKSRLRYALQKLRE 185 (194)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34468999999999999999999998887654
No 173
>KOG2767 consensus Translation initiation factor 5 (eIF-5) [Translation, ribosomal structure and biogenesis]
Probab=28.84 E-value=17 Score=35.72 Aligned_cols=16 Identities=31% Similarity=0.777 Sum_probs=12.6
Q ss_pred cccccccccccccccc
Q 026161 84 GLKCAACNCHRNFHRK 99 (242)
Q Consensus 84 al~CaaCgCHRnFHr~ 99 (242)
+++|+||||+-+---|
T Consensus 118 ~~~CkACG~r~~~d~r 133 (400)
T KOG2767|consen 118 SLKCKACGFRSDMDLR 133 (400)
T ss_pred hhHHHHcCCcccccch
Confidence 7899999998765443
No 174
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=28.82 E-value=9.3 Score=31.75 Aligned_cols=49 Identities=10% Similarity=0.114 Sum_probs=36.9
Q ss_pred cCccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 182 FRTKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 182 ~RTkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
.-.++++.+++.+.-+.+. ...+++|+.+||+..++++.++.-|.++.+
T Consensus 152 ~~~~L~~~~r~vl~l~~e~----------~s~~EIA~~lgis~~tV~~~l~rar~~Lr~ 200 (208)
T PRK08295 152 IEELLSELEKEVLELYLDG----------KSYQEIAEELNRHVKSIDNALQRVKRKLEK 200 (208)
T ss_pred HHHhCCHHHHHHHHHHHcc----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3456777777776545443 357889999999999999999988877653
No 175
>PF11761 CbiG_mid: Cobalamin biosynthesis central region; InterPro: IPR021745 Members of this family are involved in cobalamin synthesis. The gene encoded by P72862 from SWISSPROT has been designated cbiH but in fact represents a fusion between cbiH and cbiG. As other multi-functional proteins involved in cobalamin biosynthesis catalyse adjacent steps in the pathway, including CysG, CobL (CbiET), CobIJ and CobA-HemD, it is therefore possible that CbiG catalyses a reaction step adjacent to CbiH. In the anaerobic pathway such a step could be the formation of a gamma lactone, which is thought to help to mediate the anaerobic ring contraction process [].
Probab=28.66 E-value=82 Score=22.94 Aligned_cols=34 Identities=29% Similarity=0.575 Sum_probs=22.5
Q ss_pred HHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecc
Q 026161 196 ELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMH 232 (242)
Q Consensus 196 ~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmh 232 (242)
.||.++||+| .+...+.++...+ |..+.+.+|-.
T Consensus 6 ~la~~~g~~i--~~~~~~k~vsaal-v~g~~V~~~~~ 39 (93)
T PF11761_consen 6 LLARELGWRI--ENREAVKRVSAAL-VNGEPVALYQD 39 (93)
T ss_pred hhhhhCCCEE--cCHHHHHHHHHHH-HCCCEEEEEEe
Confidence 4899999999 4445566666665 45555555544
No 176
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=28.58 E-value=10 Score=31.11 Aligned_cols=46 Identities=9% Similarity=0.075 Sum_probs=34.5
Q ss_pred ccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccC
Q 026161 184 TKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLG 239 (242)
Q Consensus 184 TkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~g 239 (242)
.++++.|++.+.- +.+- ...++++..+||+..++++.++.-++++.
T Consensus 116 ~~Lp~~~r~i~~l~~~e~----------~s~~EIA~~lgis~~tV~~~l~ra~~~Lr 162 (179)
T PRK12543 116 HKLPYKLRQVIILRYLHD----------YSQEEIAQLLQIPIGTVKSRIHAALKKLR 162 (179)
T ss_pred HhCCHHHHHHHHHHHHcc----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 3566777766544 3333 25788999999999999999998887764
No 177
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=28.58 E-value=13 Score=29.84 Aligned_cols=46 Identities=11% Similarity=0.166 Sum_probs=33.9
Q ss_pred cCccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccc
Q 026161 182 FRTKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHT 237 (242)
Q Consensus 182 ~RTkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~ 237 (242)
.=.+++++|++.+.- +.+- ...++++..+||+..+++++++.-+.+
T Consensus 110 ~l~~L~~~~r~v~~L~~~~g----------~s~~EIA~~l~is~~tV~~~l~ra~~~ 156 (161)
T PRK12528 110 LLDGLPPLVKRAFLLAQVDG----------LGYGEIATELGISLATVKRYLNKAAMR 156 (161)
T ss_pred HHHHCCHHHHHHHHHHHHcC----------CCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 345677788887544 4443 257889999999999999999876543
No 178
>PRK06680 D-amino acid aminotransferase; Reviewed
Probab=28.36 E-value=1.4e+02 Score=26.86 Aligned_cols=47 Identities=9% Similarity=0.099 Sum_probs=37.8
Q ss_pred CCHHHHHHHHHHHHHhCCccCCCCH---HHHHHHHHHhCCCCceEEEecc
Q 026161 186 FTPEQKDRMLELAEKLGWRIQKHDE---EVVQQFCNDTGVKRHVLKVWMH 232 (242)
Q Consensus 186 FT~EQkekM~~fAeklGWRiqk~d~---~~ve~fc~eiGv~r~V~KVWmh 232 (242)
+=.+..++|..-|+.||+.+....+ +.++++++..++....+++|+.
T Consensus 45 ~l~~Hl~RL~~Sa~~L~i~~~~~~~~l~~~i~~~~~~~~~~~~~lr~~vt 94 (286)
T PRK06680 45 DLDRHLARLFRSLGEIRIAPPMTRAELVEVLRELIRRNRVREGLVYLQVT 94 (286)
T ss_pred chHHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHcCCCceEEEEEEE
Confidence 5588999999999999999775543 5666777767888888998886
No 179
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=28.18 E-value=1.1e+02 Score=22.44 Aligned_cols=31 Identities=16% Similarity=0.104 Sum_probs=24.0
Q ss_pred cCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhC
Q 026161 185 KFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTG 221 (242)
Q Consensus 185 kFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiG 221 (242)
.|+.++.+.+....++ .-.++..+.+|+.+|
T Consensus 66 ~~~~~e~~~l~~~l~~------~~~~~~~~~~~~~~~ 96 (96)
T smart00529 66 GVDEEEVHEEAERLEH------VLSDELEDRLDRFLG 96 (96)
T ss_pred CCCHHHHHHHHHHHHc------cCCHHHHHHHHHHhC
Confidence 6888888887776666 567778899998776
No 180
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=28.16 E-value=11 Score=32.03 Aligned_cols=48 Identities=8% Similarity=0.138 Sum_probs=36.0
Q ss_pred cCccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccC
Q 026161 182 FRTKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLG 239 (242)
Q Consensus 182 ~RTkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~g 239 (242)
.-.++++.|++.+.- +.+- ..++++|..+||+..+++++++.-|.++.
T Consensus 130 ~l~~Lp~~~r~v~~l~~~~g----------~s~~EIAe~lgis~~tV~~~l~Rar~~Lr 178 (196)
T PRK12535 130 LIDALPPERREALILTQVLG----------YTYEEAAKIADVRVGTIRSRVARARADLI 178 (196)
T ss_pred HHHcCCHHHHHHhhhHHHhC----------CCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 345677777777543 4443 25889999999999999999998777653
No 181
>PF11976 Rad60-SLD: Ubiquitin-2 like Rad60 SUMO-like; InterPro: IPR022617 This entry includes small ubiquitin-related modifier (SUMO) proteins. SUMOs are small proteins that are covalently attached to lysines as post-translational modifications and are used to control multiple cellular process including signal transduction, nuclear transport and DNA replication and repair []. Unlike ubiquitin, they are not involved in protein degradation. This entry also contains the C-terminal Rad60 DNA repair protein SUMO-like domain.; PDB: 3RD2_A 2JXX_A 3RCZ_A 3GOE_A 3A4S_D 3A4R_B 2IO1_D 1U4A_A 2K1F_A 1WZ0_A ....
Probab=28.15 E-value=71 Score=22.50 Aligned_cols=26 Identities=8% Similarity=0.598 Sum_probs=22.7
Q ss_pred HHHHHHHHHHhCCCC-ceEEEeccccc
Q 026161 210 EEVVQQFCNDTGVKR-HVLKVWMHNNK 235 (242)
Q Consensus 210 ~~~ve~fc~eiGv~r-~V~KVWmhNnK 235 (242)
..+.+.||.+.|++. ..++.+|...+
T Consensus 24 ~~l~~~~~~~~~i~~~~~~~l~fdG~~ 50 (72)
T PF11976_consen 24 SKLIEKYCEKKGIPPEESIRLIFDGKR 50 (72)
T ss_dssp HHHHHHHHHHHTTTT-TTEEEEETTEE
T ss_pred HHHHHHHHHhhCCCccceEEEEECCEE
Confidence 467899999999999 99999998765
No 182
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=28.08 E-value=8 Score=33.74 Aligned_cols=47 Identities=11% Similarity=0.108 Sum_probs=34.9
Q ss_pred ccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 184 TKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 184 TkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
..+++.|++.+.- |.+. .-.+++|..+||+..+++++++.-|.++.+
T Consensus 133 ~~Lp~~~R~v~~L~y~eg----------~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~ 180 (216)
T PRK12533 133 AKLPVEYREVLVLRELED----------MSYREIAAIADVPVGTVMSRLARARRRLAA 180 (216)
T ss_pred HcCCHHHHhHhhhHHhcC----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3566667776544 3333 357899999999999999999988877643
No 183
>PRK10336 DNA-binding transcriptional regulator QseB; Provisional
Probab=27.97 E-value=26 Score=27.94 Aligned_cols=51 Identities=14% Similarity=0.138 Sum_probs=38.7
Q ss_pred ccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhC-----CCCceEEEeccccccccCC
Q 026161 184 TKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTG-----VKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 184 TkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiG-----v~r~V~KVWmhNnK~~~gk 240 (242)
.+||..+.+.|.-+++. .......++++.++. ++.+++++.+.|=|.|++.
T Consensus 148 ~~Lt~~E~~il~~l~~~------~~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~lr~Kl~~ 203 (219)
T PRK10336 148 LTLKPKEFALLELLMRN------AGRVLPRKLIEEKLYTWDEEVTSNAVEVHVHHLRRKLGS 203 (219)
T ss_pred EecCHHHHHHHHHHHhC------CCccCcHHHHHHHhcCCCCCCCccCHHHHHHHHHHhcCC
Confidence 46999999999888886 222234557777775 8999999999888888763
No 184
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=27.96 E-value=8.4 Score=32.24 Aligned_cols=47 Identities=13% Similarity=0.151 Sum_probs=34.7
Q ss_pred ccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 184 TKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 184 TkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
.++++.|++.+.- +.+- ...+++|..+||+..++++.++--|.++.+
T Consensus 110 ~~Lp~~~R~v~~L~~~~g----------~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~ 157 (182)
T PRK12540 110 DKLPQDQREALILVGASG----------FSYEDAAAICGCAVGTIKSRVNRARSKLSA 157 (182)
T ss_pred HhCCHHHHHHhhHHHHcC----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4566777777444 3332 357899999999999999999988776643
No 185
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=27.95 E-value=9.8 Score=31.14 Aligned_cols=47 Identities=9% Similarity=0.160 Sum_probs=34.0
Q ss_pred CcCccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccc
Q 026161 181 RFRTKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHT 237 (242)
Q Consensus 181 R~RTkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~ 237 (242)
+.-.+++++|++.+.- +.+. ...++++..+||+..+++++++.-+.+
T Consensus 115 ~~l~~L~~~~r~i~~l~~~~g----------~s~~EIA~~lgis~~tV~~~l~Ra~~~ 162 (172)
T PRK09651 115 SMLDGLNGKTREAFLLSQLDG----------LTYSEIAHKLGVSVSSVKKYVAKATEH 162 (172)
T ss_pred HHHHhCCHHHhHHhhhhhccC----------CCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 3445677777777443 3333 357899999999999999999876654
No 186
>PHA01976 helix-turn-helix protein
Probab=27.72 E-value=31 Score=23.94 Aligned_cols=19 Identities=11% Similarity=0.186 Sum_probs=13.0
Q ss_pred CCCHHHHHHHHHHhCCCCc
Q 026161 207 KHDEEVVQQFCNDTGVKRH 225 (242)
Q Consensus 207 k~d~~~ve~fc~eiGv~r~ 225 (242)
.|+...+.++|+-+||+..
T Consensus 41 ~p~~~~l~~ia~~l~v~~~ 59 (67)
T PHA01976 41 LPNLKTLLRLADALGVTLD 59 (67)
T ss_pred CCCHHHHHHHHHHHCcCHH
Confidence 4566777777777777654
No 187
>TIGR03020 EpsA transcriptional regulator EpsA. Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.
Probab=27.34 E-value=14 Score=33.67 Aligned_cols=48 Identities=10% Similarity=0.103 Sum_probs=38.6
Q ss_pred CccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 183 RTKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 183 RTkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
...+|+.|++.|.-.++- + ..+++++.+||+.+++|.++.|-+.|++-
T Consensus 188 ~~~LT~RE~evl~l~a~G------~----s~~eIA~~L~IS~~TVk~hl~~i~~KL~v 235 (247)
T TIGR03020 188 AGLITAREAEILAWVRDG------K----TNEEIAAILGISSLTVKNHLQHIFKKLDV 235 (247)
T ss_pred ccCCCHHHHHHHHHHHCC------C----CHHHHHHHHCcCHHHHHHHHHHHHHHhCC
Confidence 457999999998876543 2 35678899999999999999998888764
No 188
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 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 is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. 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; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=27.01 E-value=11 Score=25.01 Aligned_cols=20 Identities=15% Similarity=0.302 Sum_probs=16.2
Q ss_pred HHHHHHHhCCCCceEEEecc
Q 026161 213 VQQFCNDTGVKRHVLKVWMH 232 (242)
Q Consensus 213 ve~fc~eiGv~r~V~KVWmh 232 (242)
+-++++.+||+.++|+.|-.
T Consensus 2 i~e~A~~~gvs~~tlR~ye~ 21 (38)
T PF00376_consen 2 IGEVAKLLGVSPRTLRYYER 21 (38)
T ss_dssp HHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHCCCHHHHHHHHH
Confidence 46889999999999999854
No 189
>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=26.88 E-value=10 Score=32.81 Aligned_cols=52 Identities=8% Similarity=0.029 Sum_probs=38.1
Q ss_pred ccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 184 TKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 184 TkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
..+++.|++.+.-..-- .+-++-..+++|+++||+..+++++++.-+.++.+
T Consensus 173 ~~L~~~~r~il~l~y~~-----~~~e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~ 224 (227)
T TIGR02846 173 SVLDGREREVIEMRYGL-----GDGRRKTQREIAKILGISRSYVSRIEKRALMKLYK 224 (227)
T ss_pred HhCCHHHHHHHHHHHcC-----CCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 57888888887664310 01234468999999999999999998887776654
No 190
>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=26.54 E-value=20 Score=24.22 Aligned_cols=18 Identities=17% Similarity=0.488 Sum_probs=14.5
Q ss_pred HHHHHHHHHhCCCCceEE
Q 026161 211 EVVQQFCNDTGVKRHVLK 228 (242)
Q Consensus 211 ~~ve~fc~eiGv~r~V~K 228 (242)
-..+++++++||++++++
T Consensus 16 it~~eLa~~l~vS~rTi~ 33 (55)
T PF08279_consen 16 ITAKELAEELGVSRRTIR 33 (55)
T ss_dssp BEHHHHHHHCTS-HHHHH
T ss_pred cCHHHHHHHhCCCHHHHH
Confidence 568999999999998864
No 191
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=26.53 E-value=10 Score=31.60 Aligned_cols=47 Identities=15% Similarity=0.097 Sum_probs=35.7
Q ss_pred CccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccC
Q 026161 183 RTKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLG 239 (242)
Q Consensus 183 RTkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~g 239 (242)
-.+++++|++.+.- +.+. ...+++|+.+||+..++++.++.-|.++.
T Consensus 139 l~~Lp~~~r~v~~l~~~eg----------~s~~EIA~~lgis~~tVk~rl~ra~~~Lr 186 (194)
T PRK12531 139 LDRLPKAQRDVLQAVYLEE----------LPHQQVAEMFDIPLGTVKSRLRLAVEKLR 186 (194)
T ss_pred HHhCCHHHHHHHHHHHHcC----------CCHHHHHHHhCcCHHHHHHHHHHHHHHHH
Confidence 35677778887654 4433 25789999999999999999998877654
No 192
>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=26.45 E-value=9.1 Score=32.83 Aligned_cols=48 Identities=6% Similarity=0.009 Sum_probs=37.0
Q ss_pred ccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 184 TKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 184 TkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
.++++.|++.+..++. ++...+++|..+||+..+++.+++..+.++.+
T Consensus 174 ~~L~~~~r~il~l~y~---------~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~ 221 (224)
T TIGR02479 174 ESLSEREQLVLSLYYY---------EELNLKEIGEVLGLTESRVSQIHSQALKKLRA 221 (224)
T ss_pred HhCCHHHHHHHHHHHh---------CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 4678888888766432 12357899999999999999999988777654
No 193
>PRK06930 positive control sigma-like factor; Validated
Probab=26.34 E-value=11 Score=32.30 Aligned_cols=46 Identities=9% Similarity=0.156 Sum_probs=36.1
Q ss_pred ccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccC
Q 026161 184 TKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLG 239 (242)
Q Consensus 184 TkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~g 239 (242)
.++|+.+++.+.- |++- ....++|..+||+..+++++++.-+.++.
T Consensus 113 ~~L~~rer~V~~L~~~eg----------~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr 159 (170)
T PRK06930 113 SVLTEREKEVYLMHRGYG----------LSYSEIADYLNIKKSTVQSMIERAEKKIA 159 (170)
T ss_pred HhCCHHHHHHHHHHHHcC----------CCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 4688888887655 4444 25788999999999999999998887764
No 194
>KOG2146 consensus Splicing coactivator SRm160/300, subunit SRm160 (contains PWI domain) [RNA processing and modification; General function prediction only]
Probab=26.30 E-value=31 Score=33.39 Aligned_cols=37 Identities=27% Similarity=0.469 Sum_probs=23.8
Q ss_pred ccCCHHHHHHHHH--HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecc
Q 026161 184 TKFTPEQKDRMLE--LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMH 232 (242)
Q Consensus 184 TkFT~EQkekM~~--fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmh 232 (242)
|.||..||..|.. |++-| ++-..+--|+-.|||-|+-
T Consensus 12 trFSdkeKKLmkqmKF~~~l------------ekkVDmsKvnleVlkPWIt 50 (354)
T KOG2146|consen 12 TRFSDKEKKLMKQMKFPACL------------EKKVDMSKVNLEVLKPWIT 50 (354)
T ss_pred cccchHHHHHHHhcccHHHH------------hhhcchhhcchhhhhHHHH
Confidence 6799999999887 77664 2222333455566666653
No 195
>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=26.29 E-value=13 Score=29.95 Aligned_cols=47 Identities=9% Similarity=0.183 Sum_probs=35.1
Q ss_pred ccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 184 TKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 184 TkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
.+++.+|++.+.. |.+. ...++.|+.+||+..+++++++-.|.++.+
T Consensus 118 ~~L~~~~r~i~~l~~~~g----------~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~ 165 (169)
T TIGR02954 118 DTLNDKYQTAIILRYYHD----------LTIKEIAEVMNKPEGTVKTYLHRALKKLKK 165 (169)
T ss_pred HhCCHHHhHHHHHHHHcC----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3677778877644 4443 246789999999999999999887776543
No 196
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=26.00 E-value=10 Score=31.52 Aligned_cols=47 Identities=9% Similarity=0.049 Sum_probs=34.6
Q ss_pred ccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 184 TKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 184 TkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
.+++++|++.+.- +.+. ...+++|..+||+..+++++++.-|.++.+
T Consensus 135 ~~L~~~~r~i~~L~~~~g----------~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 182 (195)
T PRK12532 135 YNLPENTARVFTLKEILG----------FSSDEIQQMCGISTSNYHTIMHRARESLRQ 182 (195)
T ss_pred HhCCHHHHHHhhhHHHhC----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3567777777543 3333 357899999999999999999987776543
No 197
>cd00491 4Oxalocrotonate_Tautomerase 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one dimer and the third from a neighboring monomer. Each monomer is a beta-alpha-beta fold with two small beta strands at the C-terminus that fold back on themselves. A pair of monomers form a dimer with two-fold symmetry, consisting of a 4-stranded beta sheet with two helices on one side and two additional small beta strands at each end. The dimers are assembled around a 3-fold axis of rotation to form a hexamer, with the short beta strands from each dimer contacting the neighboring dimers.
Probab=25.84 E-value=1.7e+02 Score=19.56 Aligned_cols=35 Identities=23% Similarity=0.322 Sum_probs=26.2
Q ss_pred CHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccc
Q 026161 187 TPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNK 235 (242)
Q Consensus 187 T~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK 235 (242)
|.|||++|.+ . +.+.+...+|+++..+-|.++...
T Consensus 12 t~eqk~~l~~---~-----------i~~~l~~~~g~~~~~v~V~i~e~~ 46 (58)
T cd00491 12 TDEQKRELIE---R-----------VTEAVSEILGAPEATIVVIIDEMP 46 (58)
T ss_pred CHHHHHHHHH---H-----------HHHHHHHHhCcCcccEEEEEEEeC
Confidence 5899988643 2 456677888999999999887643
No 198
>PF04492 Phage_rep_O: Bacteriophage replication protein O ; InterPro: IPR006497 This entry is represented by the N-terminal domain of Bacteriophage lambda, GpO. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; GO: 0006260 DNA replication
Probab=25.73 E-value=51 Score=26.35 Aligned_cols=44 Identities=25% Similarity=0.448 Sum_probs=34.7
Q ss_pred cCccCCHHHHHHHHHHH-HHhCCccCCCCHHHHHHHHHHhCCCCce
Q 026161 182 FRTKFTPEQKDRMLELA-EKLGWRIQKHDEEVVQQFCNDTGVKRHV 226 (242)
Q Consensus 182 ~RTkFT~EQkekM~~fA-eklGWRiqk~d~~~ve~fc~eiGv~r~V 226 (242)
.+..||.-|+..+++.. .-.||. ++-|.-...+|+..+|+++..
T Consensus 26 ~~~dls~rq~ki~~ai~RkTyG~n-Kk~d~Is~sq~~e~tg~~~~~ 70 (100)
T PF04492_consen 26 LRADLSGRQLKILLAIIRKTYGWN-KKMDRISNSQIAEMTGLSRDH 70 (100)
T ss_pred HhccccHHHHHHHHHHHHHccCCC-CccceeeHHHHHHHHCcCHHH
Confidence 46789999998777744 347897 677778899999999998764
No 199
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=25.64 E-value=10 Score=32.04 Aligned_cols=46 Identities=7% Similarity=0.101 Sum_probs=33.9
Q ss_pred ccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccC
Q 026161 184 TKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLG 239 (242)
Q Consensus 184 TkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~g 239 (242)
.+++++|++.+.- +.+. ...+++|..+||+..++|+.++.-|.++.
T Consensus 138 ~~Lp~~~r~v~~L~~~eg----------~s~~EIA~~lgis~~tVk~~l~RAr~~Lr 184 (201)
T PRK12545 138 DHLPEQIGRVFMMREFLD----------FEIDDICTELTLTANHCSVLLYRARTRLR 184 (201)
T ss_pred HhCCHHHHHHHHHHHHcC----------CCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 3566677776554 2332 35789999999999999999998777654
No 200
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=25.54 E-value=48 Score=21.89 Aligned_cols=32 Identities=22% Similarity=0.254 Sum_probs=21.6
Q ss_pred HHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEE
Q 026161 190 QKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKV 229 (242)
Q Consensus 190 QkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KV 229 (242)
+++.+.+.-++-+|. +.+.|+.+||+|.+|.-
T Consensus 6 E~~~i~~aL~~~~gn--------~~~aA~~Lgisr~tL~~ 37 (42)
T PF02954_consen 6 EKQLIRQALERCGGN--------VSKAARLLGISRRTLYR 37 (42)
T ss_dssp HHHHHHHHHHHTTT---------HHHHHHHHTS-HHHHHH
T ss_pred HHHHHHHHHHHhCCC--------HHHHHHHHCCCHHHHHH
Confidence 344466677776665 46889999999988743
No 201
>PF01113 DapB_N: Dihydrodipicolinate reductase, N-terminus; InterPro: IPR000846 Dihydrodipicolinate reductase catalyzes the second step in the biosynthesis of diaminopimelic acid and lysine, the NAD or NADP-dependent reduction of 2,3-dihydrodipicolinate into 2,3,4,5-tetrahydrodipicolinate [, , ]. In Escherichia coli and Mycobacterium tuberculosis, dihydrodipicolinate reductase has equal specificity for NADH and NADPH, however in Thermotoga maritima there it has a greater affinity for NADPH []. In addition, the enzyme is inhibited by high concentrations of its substrate, which consequently acts as a feedback control on the lysine biosynthesis pathway. In T. maritima, the enzyme also lacks N-terminal and C-terminal loops which are present in enzyme of the former two organisms. This entry represents the N-terminal domain of dihydrodipicolinate reductase which binds the dinucleotide NAD(P)H.; GO: 0008839 dihydrodipicolinate reductase activity, 0009089 lysine biosynthetic process via diaminopimelate, 0055114 oxidation-reduction process; PDB: 3QY9_D 1VM6_C 1ARZ_A 1DIH_A 1DRW_A 1DRV_A 1DRU_A 2DAP_A 1DAP_B 3DAP_A ....
Probab=25.51 E-value=24 Score=28.09 Aligned_cols=20 Identities=45% Similarity=0.526 Sum_probs=17.3
Q ss_pred ccCCHHHHHHHHHHHHHhCC
Q 026161 184 TKFTPEQKDRMLELAEKLGW 203 (242)
Q Consensus 184 TkFT~EQkekM~~fAeklGW 203 (242)
|=||+||++++.++|++++|
T Consensus 99 TG~~~~~~~~l~~~a~~~~v 118 (124)
T PF01113_consen 99 TGFSDEQIDELEELAKKIPV 118 (124)
T ss_dssp SSSHHHHHHHHHHHTTTSEE
T ss_pred CCCCHHHHHHHHHHhccCCE
Confidence 66899999999999998665
No 202
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=25.45 E-value=9.8 Score=30.88 Aligned_cols=46 Identities=9% Similarity=0.204 Sum_probs=33.4
Q ss_pred cCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 185 KFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 185 kFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
+++++|++.+.- +. ++...+++|..+||+..+++++++.-|.++.+
T Consensus 136 ~L~~~~r~il~l~~~----------~~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 182 (187)
T PRK09641 136 QLPEKYRTVIVLKYI----------EDLSLKEISEILDLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred hCCHHHHHHhhhHHh----------hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 456666666432 22 22357899999999999999999998887653
No 203
>PRK10668 DNA-binding transcriptional repressor AcrR; Provisional
Probab=25.45 E-value=30 Score=28.79 Aligned_cols=47 Identities=19% Similarity=0.266 Sum_probs=33.0
Q ss_pred CHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccc
Q 026161 187 TPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNN 234 (242)
Q Consensus 187 T~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNn 234 (242)
.++-++++.+-|.++=|+ +.-+...++++|.+.||++.+|--+|-|.
T Consensus 9 ~~~~R~~Il~AA~~lf~e-~G~~~~t~~~Ia~~agvs~~tlY~~F~sK 55 (215)
T PRK10668 9 AQETRQHILDAALRLFSQ-QGVSATSLADIAKAAGVTRGAIYWHFKNK 55 (215)
T ss_pred HHHHHHHHHHHHHHHHHH-cCcccCCHHHHHHHhCCChHHHHHHCCCH
Confidence 355666666644443222 25556689999999999999999888654
No 204
>PF09832 DUF2059: Uncharacterized protein conserved in bacteria (DUF2059); InterPro: IPR018637 This entry contains proteins that have no known function. ; PDB: 2X3O_B 3OAO_A.
Probab=25.11 E-value=40 Score=23.75 Aligned_cols=21 Identities=29% Similarity=0.450 Sum_probs=16.9
Q ss_pred CCcCccCCHHHHHHHHHHHHH
Q 026161 180 KRFRTKFTPEQKDRMLELAEK 200 (242)
Q Consensus 180 KR~RTkFT~EQkekM~~fAek 200 (242)
..+...||.++++.|.+|++.
T Consensus 11 ~~y~~~ft~~El~~i~~FY~S 31 (64)
T PF09832_consen 11 PIYAEHFTEEELDAILAFYES 31 (64)
T ss_dssp HHHHHHS-HHHHHHHHHHHHS
T ss_pred HHHHHHCCHHHHHHHHHHHCC
Confidence 346788999999999999875
No 205
>PF13565 HTH_32: Homeodomain-like domain
Probab=25.07 E-value=21 Score=25.41 Aligned_cols=38 Identities=29% Similarity=0.592 Sum_probs=24.6
Q ss_pred CCcCccCCHHHHHHHHHHHHH-hCCccCCCCHHHHHHHHHHhCCC
Q 026161 180 KRFRTKFTPEQKDRMLELAEK-LGWRIQKHDEEVVQQFCNDTGVK 223 (242)
Q Consensus 180 KR~RTkFT~EQkekM~~fAek-lGWRiqk~d~~~ve~fc~eiGv~ 223 (242)
-|.|+ ++||.+.+.++... -.|.. +.+.+.+..+.|++
T Consensus 27 Grp~~--~~e~~~~i~~~~~~~p~wt~----~~i~~~L~~~~g~~ 65 (77)
T PF13565_consen 27 GRPRK--DPEQRERIIALIEEHPRWTP----REIAEYLEEEFGIS 65 (77)
T ss_pred CCCCC--cHHHHHHHHHHHHhCCCCCH----HHHHHHHHHHhCCC
Confidence 34455 89998999987665 23433 45667777776653
No 206
>PF05099 TerB: Tellurite resistance protein TerB; InterPro: IPR007791 The prokaryotic heat shock protein DnaJ interacts with the chaperone hsp70-like DnaK protein []. Structurally, the DnaJ protein consists of an N-terminal conserved domain (called 'J' domain) of about 70 amino acids, a glycine-rich region ('G' domain') of about 30 residues, a central domain containing four repeats of a CXXCXGXG motif ('CRR' domain) and a C-terminal region of 120 to 170 residues. Direct interaction between DnaK and djlA is needed for the induction of the wcaABCDE operon which is involved in the synthesis of a colanic acid polysaccharide capsule. The colanic acid capsule may help the bacterium survive conditions outside the host [, ]; PDB: 2H5N_D 2JXU_A.
Probab=25.07 E-value=1.1e+02 Score=23.89 Aligned_cols=49 Identities=14% Similarity=0.503 Sum_probs=33.6
Q ss_pred CCcCccCCHHHHHHHHHHHHHhCC---ccCCCCHHHHHHHHHHhCCCCceEE
Q 026161 180 KRFRTKFTPEQKDRMLELAEKLGW---RIQKHDEEVVQQFCNDTGVKRHVLK 228 (242)
Q Consensus 180 KR~RTkFT~EQkekM~~fAeklGW---Riqk~d~~~ve~fc~eiGv~r~V~K 228 (242)
+.+++.|+.+++..+...+..+-- .+.......+.+++..+||+..-|+
T Consensus 85 ~~l~~~~~~~~r~~ll~~l~~ia~ADG~~~~~E~~~l~~ia~~L~i~~~~~~ 136 (140)
T PF05099_consen 85 RELRDSLSPEEREDLLRMLIAIAYADGEISPEEQEFLRRIAEALGISEEDFQ 136 (140)
T ss_dssp HHHCTS--HHHHHHHHHHHHHHCTCTTC-SCCHHHHHHHHHHHCTS-SS---
T ss_pred HHHHHhhchHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHcCCCHHHHh
Confidence 567888899999998887776532 3555666899999999999987764
No 207
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=25.06 E-value=12 Score=30.87 Aligned_cols=48 Identities=4% Similarity=0.087 Sum_probs=36.3
Q ss_pred cCccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccC
Q 026161 182 FRTKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLG 239 (242)
Q Consensus 182 ~RTkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~g 239 (242)
.=.+++++|++.+.- +.+. -..+++|+.+||+..++++.++.-|.++.
T Consensus 119 ~l~~L~~~~r~i~~l~~~~g----------~s~~EIA~~lgis~~tVk~~l~Rar~~Lr 167 (185)
T PRK12542 119 LLKELNESNRQVFKYKVFYN----------LTYQEISSVMGITEANVRKQFERARKRVQ 167 (185)
T ss_pred HHHhCCHHHHHHHHHHHHcC----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 345677888887554 4443 25789999999999999999988877654
No 208
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=24.99 E-value=10 Score=30.28 Aligned_cols=44 Identities=7% Similarity=0.117 Sum_probs=32.1
Q ss_pred cCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccc
Q 026161 185 KFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTL 238 (242)
Q Consensus 185 kFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~ 238 (242)
+++++|++.+.- |.+- ...++.|+++||+..+++++++--+.++
T Consensus 109 ~L~~~~r~v~~l~~~~~----------~s~~EIA~~lgis~~tV~~~l~ra~~~l 153 (163)
T PRK07037 109 ELPARTRYAFEMYRLHG----------ETQKDIARELGVSPTLVNFMIRDALVHC 153 (163)
T ss_pred hCCHHHHHHHHHHHHcC----------CCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 567777777644 4333 2467899999999999999887666554
No 209
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=24.97 E-value=11 Score=33.57 Aligned_cols=46 Identities=11% Similarity=0.119 Sum_probs=33.9
Q ss_pred ccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccC
Q 026161 184 TKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLG 239 (242)
Q Consensus 184 TkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~g 239 (242)
.+++++|++.+.- +.+. ...+++++.+|++..++|++++..|+++.
T Consensus 115 ~~Lp~~~R~v~lL~~~eg----------~S~~EIAe~LgiS~~tVksrL~Rark~Lr 161 (228)
T PRK06704 115 SSLNVQQSAILLLKDVFQ----------YSIADIAKVCSVSEGAVKASLFRSRNRLK 161 (228)
T ss_pred HhCCHHHhhHhhhHHhhC----------CCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 4566666666433 3332 24689999999999999999998887764
No 210
>PF12123 Amidase02_C: N-acetylmuramoyl-l-alanine amidase; InterPro: IPR021976 This domain is found in bacteria and viruses. This domain is about 50 amino acids in length. This domain is classified with the enzyme classification code 3.5.1.28 from EC. This domain is the C-terminal of the enzyme which hydrolyses the link between N-acetylmuramoyl residues and L-amino acid residues in certain cell-wall glycopeptides. ; PDB: 2L48_B.
Probab=24.75 E-value=72 Score=22.51 Aligned_cols=19 Identities=16% Similarity=0.512 Sum_probs=13.8
Q ss_pred CCHHHHHHHHHHHHHhCCc
Q 026161 186 FTPEQKDRMLELAEKLGWR 204 (242)
Q Consensus 186 FT~EQkekM~~fAeklGWR 204 (242)
++..|+++|.++.++-||-
T Consensus 24 ~s~~~L~k~~~wld~rgWw 42 (45)
T PF12123_consen 24 LSDAELDKFTAWLDERGWW 42 (45)
T ss_dssp --HHHHHHHHHHHHHTT--
T ss_pred CCHHHHHHHHHHHHhcCcE
Confidence 5678999999999888994
No 211
>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=24.67 E-value=36 Score=27.11 Aligned_cols=52 Identities=23% Similarity=0.272 Sum_probs=32.6
Q ss_pred CCcCccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCCC
Q 026161 180 KRFRTKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGKK 241 (242)
Q Consensus 180 KR~RTkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gkk 241 (242)
.|.|.|+. .+.|.++.+. ++|. .+.++|..+||+..+|--.++--.-+++|+
T Consensus 51 ~r~~~Kid---~~~L~~~v~~------~pd~-tl~Ela~~l~Vs~~ti~~~Lkrlg~t~KK~ 102 (119)
T PF01710_consen 51 PRGRKKID---RDELKALVEE------NPDA-TLRELAERLGVSPSTIWRALKRLGITRKKK 102 (119)
T ss_pred cccccccc---HHHHHHHHHH------CCCc-CHHHHHHHcCCCHHHHHHHHHHcCchhccC
Confidence 34444663 4556777666 6666 456788899998887766655544444443
No 212
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=24.66 E-value=11 Score=31.59 Aligned_cols=45 Identities=16% Similarity=0.105 Sum_probs=34.7
Q ss_pred cCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccC
Q 026161 185 KFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLG 239 (242)
Q Consensus 185 kFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~g 239 (242)
++++.|++.+.- +.+. ...+++|..+||+..+++++++--|.++.
T Consensus 111 ~Lp~~~R~v~~L~~~eg----------~s~~EIA~~lgis~~tV~~~l~Rar~~Lr 156 (182)
T PRK12511 111 DLPEEQRAALHLVAIEG----------LSYQEAAAVLGIPIGTLMSRIGRARAALR 156 (182)
T ss_pred hCCHHHHHHHHHHHHcC----------CCHHHHHHHhCcCHHHHHHHHHHHHHHHH
Confidence 677888887554 3333 35789999999999999999988776654
No 213
>PF07813 LTXXQ: LTXXQ motif family protein; InterPro: IPR012899 This five residue motif is found in a number of bacterial proteins bearing similarity to the protein CpxP (P32158 from SWISSPROT). This is a periplasmic protein that aids in combating extracytoplasmic protein-mediated toxicity, and may also be involved in the response to alkaline pH []. Another member of this family, Spy (P77754 from SWISSPROT) is also a periplasmic protein that may be involved in the response to stress []. The homology between CpxP and Spy may indicate that these two proteins are functionally related []. The motif is found repeated twice in many members of this entry. ; GO: 0042597 periplasmic space; PDB: 3ITF_B 3QZC_B 3OEO_D 3O39_A.
Probab=24.53 E-value=44 Score=24.51 Aligned_cols=17 Identities=29% Similarity=0.499 Sum_probs=13.2
Q ss_pred CCcCccCCHHHHHHHHH
Q 026161 180 KRFRTKFTPEQKDRMLE 196 (242)
Q Consensus 180 KR~RTkFT~EQkekM~~ 196 (242)
..++..||+||++++.+
T Consensus 82 ~~~~~vLt~eQk~~~~~ 98 (100)
T PF07813_consen 82 HALYAVLTPEQKEKFDQ 98 (100)
T ss_dssp HHHHTTS-HHHHHHHHH
T ss_pred HHHHhcCCHHHHHHHHH
Confidence 56789999999999764
No 214
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=24.49 E-value=11 Score=31.39 Aligned_cols=46 Identities=9% Similarity=0.058 Sum_probs=33.4
Q ss_pred ccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccC
Q 026161 184 TKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLG 239 (242)
Q Consensus 184 TkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~g 239 (242)
.+++++|++.+.- +.+. .-++++|..+||+..+++..++.-|+++.
T Consensus 105 ~~L~~~~r~i~~l~~~~g----------~~~~EIA~~lgis~~tV~~~l~Rar~~Lr 151 (181)
T PRK09637 105 DALPEKYAEALRLTELEG----------LSQKEIAEKLGLSLSGAKSRVQRGRVKLK 151 (181)
T ss_pred HhCCHHHHHHHHHHHhcC----------CCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 3566667666543 3333 25788999999999999999988777654
No 215
>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=24.43 E-value=68 Score=24.67 Aligned_cols=43 Identities=19% Similarity=0.353 Sum_probs=31.1
Q ss_pred ccCCHHHHHHHHHHHHH-hCCccCCCCHHHHHHHHHHhCCCCceE
Q 026161 184 TKFTPEQKDRMLELAEK-LGWRIQKHDEEVVQQFCNDTGVKRHVL 227 (242)
Q Consensus 184 TkFT~EQkekM~~fAek-lGWRiqk~d~~~ve~fc~eiGv~r~V~ 227 (242)
..++..|...|...+++ -||.. ..+.-..++||+.+|++|.++
T Consensus 21 ~~l~~r~~~vLl~L~~~~~G~~~-~~~~is~~eLa~~~g~sr~tV 64 (95)
T TIGR01610 21 ADLSGREFRVLLAIIRLTYGWNK-KQDRVTATVIAELTGLSRTHV 64 (95)
T ss_pred CCCCHHHHHHHHHHHHHHhCccc-cCCccCHHHHHHHHCcCHHHH
Confidence 45677788888888763 47763 344556789999999998754
No 216
>cd01276 PKCI_related Protein Kinase C Interacting protein related (PKCI): PKCI and related proteins belong to the ubiquitous HIT family of hydrolases that act on alpha-phosphates of ribonucleotides. The members of this subgroup have a conserved HxHxHxx motif (x is a hydrophobic residue) that is a signature for this family. No enzymatic activity has been reported however, for PKCI and its related members.
Probab=24.36 E-value=1.5e+02 Score=22.21 Aligned_cols=45 Identities=13% Similarity=0.263 Sum_probs=28.8
Q ss_pred CCcCccCCH---HHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccc
Q 026161 180 KRFRTKFTP---EQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKH 236 (242)
Q Consensus 180 KR~RTkFT~---EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~ 236 (242)
||..+.|.. +.++.+.++... ++++.+.++.+..-|.+|+||...
T Consensus 42 k~H~~~~~dl~~~~~~~l~~~~~~------------~~~~~~~~~~~~~~~n~~~~~g~~ 89 (104)
T cd01276 42 KKHIASLSDATEEDEELLGHLLSA------------AAKVAKDLGIAEDGYRLVINCGKD 89 (104)
T ss_pred cceeCChHHcccccHHHHHHHHHH------------HHHHHHHhCCCCCCEEEEEeCCCC
Confidence 666666655 555555554444 355566666556779999998764
No 217
>PRK00745 4-oxalocrotonate tautomerase; Provisional
Probab=24.25 E-value=1.5e+02 Score=20.31 Aligned_cols=35 Identities=17% Similarity=0.284 Sum_probs=26.6
Q ss_pred CCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccc
Q 026161 186 FTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNN 234 (242)
Q Consensus 186 FT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNn 234 (242)
.|.|||+.|.+ . +.+.++..+|++...+.|.|...
T Consensus 12 rs~eqk~~l~~---~-----------it~~l~~~~~~p~~~v~V~i~e~ 46 (62)
T PRK00745 12 RTVEQKRKLVE---E-----------ITRVTVETLGCPPESVDIIITDV 46 (62)
T ss_pred CCHHHHHHHHH---H-----------HHHHHHHHcCCChhHEEEEEEEc
Confidence 38899987543 3 45668888999999999888754
No 218
>PRK13558 bacterio-opsin activator; Provisional
Probab=24.11 E-value=46 Score=32.78 Aligned_cols=44 Identities=11% Similarity=0.184 Sum_probs=34.0
Q ss_pred CccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEE
Q 026161 183 RTKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLK 228 (242)
Q Consensus 183 RTkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~K 228 (242)
+..+|..|+|.|+.-.+. |+= .-|.+...++++.++||++.+|.
T Consensus 605 ~~~lt~~q~e~l~~a~~~-gyf-~~pr~~~~~e~a~~l~is~~t~~ 648 (665)
T PRK13558 605 ENDLTDRQLTALQKAYVS-GYF-EWPRRVEGEELAESMGISRSTFH 648 (665)
T ss_pred hhhCCHHHHHHHHHHHHc-CCC-CCCccCCHHHHHHHhCCCHHHHH
Confidence 358999999997765554 653 34666789999999999998763
No 219
>PF11516 DUF3220: Protein of unknown function (DUF3120); InterPro: IPR021597 This family of proteins with unknown function appears to be restricted to Bordetella. ; PDB: 2JPF_A.
Probab=24.10 E-value=11 Score=30.32 Aligned_cols=8 Identities=63% Similarity=1.203 Sum_probs=5.7
Q ss_pred EEEecccc
Q 026161 227 LKVWMHNN 234 (242)
Q Consensus 227 ~KVWmhNn 234 (242)
+||||||-
T Consensus 33 vkvwmqnl 40 (106)
T PF11516_consen 33 VKVWMQNL 40 (106)
T ss_dssp HHHHHHHH
T ss_pred HHHHHHHH
Confidence 57788774
No 220
>cd01763 Sumo Small ubiquitin-related modifier (SUMO). Small ubiquitin-related modifier (SUMO) proteins are conjugated to numerous intracellular targets and serve to modulate protein interaction, localization, activity or stability. SUMO (also known as "Smt3" and "sentrin" in other organisms) is linked to several different pathways, including nucleocytoplasmic transport. Attachment of SUMO to targets proteins is stimulated by PIAS (Protein inhibitor of activated STATs) proteins which serve as E3-like ligases.
Probab=23.75 E-value=89 Score=23.51 Aligned_cols=27 Identities=7% Similarity=0.463 Sum_probs=20.8
Q ss_pred HHHHHHHHHhCCCCceEEEeccccccc
Q 026161 211 EVVQQFCNDTGVKRHVLKVWMHNNKHT 237 (242)
Q Consensus 211 ~~ve~fc~eiGv~r~V~KVWmhNnK~~ 237 (242)
.+.++||...||+...++.||...+=.
T Consensus 36 ~l~~~y~~~~gi~~~~~rf~f~G~~L~ 62 (87)
T cd01763 36 KLMEAYCQRQGLSMNSVRFLFDGQRIR 62 (87)
T ss_pred HHHHHHHHHhCCCccceEEEECCeECC
Confidence 356778888889999999999876543
No 221
>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=23.72 E-value=12 Score=31.25 Aligned_cols=47 Identities=6% Similarity=0.092 Sum_probs=35.4
Q ss_pred ccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 184 TKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 184 TkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
.++++.|++.+.- |.+. ...+++++++|++..+++++++.-|.++.+
T Consensus 130 ~~L~~~~r~v~~l~~~~g----------~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~ 177 (188)
T TIGR02943 130 YHLPEQTARVFMMREVLG----------FESDEICQELEISTSNCHVLLYRARLSLRA 177 (188)
T ss_pred HhCCHHHHHHHHHHHHhC----------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 4677777777544 3333 357899999999999999999888777643
No 222
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=23.68 E-value=26 Score=28.84 Aligned_cols=43 Identities=12% Similarity=0.189 Sum_probs=32.3
Q ss_pred ccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccc
Q 026161 184 TKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKH 236 (242)
Q Consensus 184 TkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~ 236 (242)
.+++++|++.+.- +.+- -..++++..+||+..++|+.++.-..
T Consensus 126 ~~Lp~~~R~v~~L~~~~g----------~s~~EIA~~lgis~~tVk~~l~rAl~ 169 (178)
T PRK12529 126 DTLRPRVKQAFLMATLDG----------MKQKDIAQALDIALPTVKKYIHQAYV 169 (178)
T ss_pred HhCCHHHHHHHHHHHHcC----------CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4677888887544 3333 25789999999999999999986543
No 223
>cd02417 Peptidase_C39_likeA A sub-family of peptidase C39 which contains Cyclolysin and Hemolysin processing peptidases. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is not conserved in this
Probab=23.38 E-value=1.5e+02 Score=22.24 Aligned_cols=44 Identities=14% Similarity=0.195 Sum_probs=32.5
Q ss_pred CCcCccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEE
Q 026161 180 KRFRTKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKV 229 (242)
Q Consensus 180 KR~RTkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KV 229 (242)
+.+.-.++.+++.. .++|.....+...+.+.++.+|++-+..++
T Consensus 17 ~~~g~~~~~~~l~~------~~~~~~~~~~~~~l~~~a~~~Gl~~~~~~~ 60 (121)
T cd02417 17 RYHGIAADPEQLRH------EFGLAGEPFNSTELLLAAKSLGLKAKAVRQ 60 (121)
T ss_pred HHcCCCCCHHHHHH------HhcCCCCCCCHHHHHHHHHHcCCeeEEEec
Confidence 44555677777664 456666677888899999999998888765
No 224
>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=23.36 E-value=34 Score=23.16 Aligned_cols=36 Identities=19% Similarity=0.373 Sum_probs=26.3
Q ss_pred CCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceE
Q 026161 186 FTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVL 227 (242)
Q Consensus 186 FT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~ 227 (242)
||..|...|..++.. ..++-.+.++|..+++++.++
T Consensus 3 lt~~q~~vL~~l~~~------~~~~~t~~~la~~l~~~~~~v 38 (62)
T PF12802_consen 3 LTPSQFRVLMALARH------PGEELTQSELAERLGISKSTV 38 (62)
T ss_dssp STHHHHHHHHHHHHS------TTSGEEHHHHHHHHTS-HHHH
T ss_pred cCHHHHHHHHHHHHC------CCCCcCHHHHHHHHCcCHHHH
Confidence 688888888887776 333457889999999987654
No 225
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=23.20 E-value=17 Score=25.25 Aligned_cols=21 Identities=14% Similarity=0.256 Sum_probs=17.9
Q ss_pred HHHHHHHhCCCCceEEEeccc
Q 026161 213 VQQFCNDTGVKRHVLKVWMHN 233 (242)
Q Consensus 213 ve~fc~eiGv~r~V~KVWmhN 233 (242)
+.++|+.+||+.++|+.|...
T Consensus 3 ~~eva~~~gvs~~tlr~~~~~ 23 (70)
T smart00422 3 IGEVAKLAGVSVRTLRYYERI 23 (70)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 578999999999999999653
No 226
>smart00857 Resolvase Resolvase, N terminal domain. The N-terminal domain of the resolvase family contains the active site and the dimer interface. The extended arm at the C-terminus of this domain connects to the C-terminal helix-turn-helix domain of resolvase.
Probab=23.10 E-value=66 Score=25.23 Aligned_cols=19 Identities=21% Similarity=0.461 Sum_probs=16.8
Q ss_pred HHHHHHHHHHHHHhCCccC
Q 026161 188 PEQKDRMLELAEKLGWRIQ 206 (242)
Q Consensus 188 ~EQkekM~~fAeklGWRiq 206 (242)
+.|++.+.+||.+.||.+-
T Consensus 18 ~~Q~~~~~~~a~~~g~~i~ 36 (148)
T smart00857 18 ERQLEALRAYAKANGWEVV 36 (148)
T ss_pred HHHHHHHHHHHHHCCCEEE
Confidence 5799999999999999863
No 227
>PF10925 DUF2680: Protein of unknown function (DUF2680); InterPro: IPR024485 Members in this family of proteins are annotated as YckD however currently no function is known.
Probab=23.08 E-value=71 Score=23.42 Aligned_cols=28 Identities=14% Similarity=0.415 Sum_probs=17.6
Q ss_pred CCHHHHHHHHHHHHHhCCccCCCCHHHHHHHH
Q 026161 186 FTPEQKDRMLELAEKLGWRIQKHDEEVVQQFC 217 (242)
Q Consensus 186 FT~EQkekM~~fAeklGWRiqk~d~~~ve~fc 217 (242)
+|.+|+..+.+|... |-....+.|++..
T Consensus 1 lT~~Qk~el~~l~~q----m~e~kK~~idk~V 28 (59)
T PF10925_consen 1 LTDQQKKELKALYKQ----MLELKKQIIDKYV 28 (59)
T ss_pred CCHHHHHHHHHHHHH----HHHHHHHHHHHHH
Confidence 688999999887666 3333344444443
No 228
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=23.07 E-value=34 Score=29.89 Aligned_cols=47 Identities=13% Similarity=0.126 Sum_probs=37.9
Q ss_pred ccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 184 TKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 184 TkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
..||+-|++.+.-.++ ||. .++.+++++|+.+++|.++.|-..|++-
T Consensus 154 ~~Lt~rE~~Vl~l~~~--G~s--------~~eIA~~L~iS~~TVk~~~~~i~~Kl~v 200 (216)
T PRK10100 154 ALLTHREKEILNKLRI--GAS--------NNEIARSLFISENTVKTHLYNLFKKIAV 200 (216)
T ss_pred CCCCHHHHHHHHHHHc--CCC--------HHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 3599999999888777 543 4678899999999999999887777654
No 229
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=22.98 E-value=14 Score=31.84 Aligned_cols=52 Identities=13% Similarity=0.125 Sum_probs=37.1
Q ss_pred ccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 184 TKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 184 TkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
.+++++|++.+.-... + ..-++...++++..+||+..+++++++.-+.++.+
T Consensus 177 ~~Lp~~~R~v~~L~y~---l--~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~ 228 (234)
T PRK08301 177 KKLSDREKQIMELRFG---L--NGGEEKTQKEVADMLGISQSYISRLEKRIIKRLKK 228 (234)
T ss_pred HhCCHHHHHHHHHHhc---c--CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4677888887655320 0 11234468899999999999999999988776643
No 230
>PF05419 GUN4: GUN4-like ; InterPro: IPR008629 In Arabidopsis, GUN4 is required for the functioning of the plastid mediated repression of nuclear transcription that is involved in controlling the levels of magnesium- protoporphyrin IX. GUN4 binds the product and substrate of Mg-chelatase, an enzyme that produces Mg-Proto, and activates Mg-chelatase. GUN4 is thought to participate in plastid-to-nucleus signalling by regulating magnesium-protoporphyrin IX synthesis or trafficking.; PDB: 1Y6I_A 1Z3X_A 1Z3Y_A.
Probab=22.81 E-value=50 Score=27.62 Aligned_cols=18 Identities=17% Similarity=0.599 Sum_probs=10.2
Q ss_pred HHHHHHHHHHHhCCccCC
Q 026161 190 QKDRMLELAEKLGWRIQK 207 (242)
Q Consensus 190 QkekM~~fAeklGWRiqk 207 (242)
..+....|+++||||.+.
T Consensus 80 ~~~~~~~F~~~VGW~~~~ 97 (132)
T PF05419_consen 80 DREIWEKFGDRVGWRKGG 97 (132)
T ss_dssp ----HHHHHHHCT--CTT
T ss_pred hHHHHHHHHHhcCCCCCC
Confidence 344578899999999764
No 231
>COG3916 LasI N-acyl-L-homoserine lactone synthetase [Signal transduction mechanisms / Secondary metabolites biosynthesis, transport, and catabolism]
Probab=22.71 E-value=40 Score=30.74 Aligned_cols=23 Identities=30% Similarity=0.546 Sum_probs=19.8
Q ss_pred HHHHHhCCccCCCCHHHHHHHHH
Q 026161 196 ELAEKLGWRIQKHDEEVVQQFCN 218 (242)
Q Consensus 196 ~fAeklGWRiqk~d~~~ve~fc~ 218 (242)
-|-|+|||.+.-.+..+++||=+
T Consensus 27 vF~erL~W~v~~~~g~E~DqyD~ 49 (209)
T COG3916 27 VFKERLGWDVVCIDGFEIDQYDN 49 (209)
T ss_pred HHHHhcCCceeccCCccccccCC
Confidence 39999999999999988888743
No 232
>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=22.54 E-value=15 Score=29.31 Aligned_cols=47 Identities=13% Similarity=0.210 Sum_probs=35.8
Q ss_pred ccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 184 TKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 184 TkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
.++++.|++.+.- |.+. ...+++|..+||+..++++.++--|.++.+
T Consensus 121 ~~L~~~~r~vl~l~~~~g----------~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 121 KILTPKQQHVIALRFGQN----------LPIAEVARILGKTEGAVKILQFRAIKKLAR 168 (170)
T ss_pred HhCCHHHHHHHHHHHhcC----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4677788887655 3433 357899999999999999999877777654
No 233
>cd01559 ADCL_like ADCL_like: 4-Amino-4-deoxychorismate lyase: is a member of the fold-type IV of PLP dependent enzymes that converts 4-amino-4-deoxychorismate (ADC) to p-aminobenzoate and pyruvate. Based on the information available from the crystal structure, most members of this subgroup are likely to function as dimers. The enzyme from E.Coli, the structure of which is available, is a homodimer that is folded into a small and a larger domain. The coenzyme pyridoxal 5; -phosphate resides at the interface of the two domains that is linked by a flexible loop. Members of this subgroup are found in Eukaryotes and bacteria.
Probab=22.43 E-value=1.8e+02 Score=25.42 Aligned_cols=48 Identities=8% Similarity=0.182 Sum_probs=35.7
Q ss_pred CCHHHHHHHHHHHHHhCCccCCCCH---HHHHHHHHHhCCCCceEEEecccc
Q 026161 186 FTPEQKDRMLELAEKLGWRIQKHDE---EVVQQFCNDTGVKRHVLKVWMHNN 234 (242)
Q Consensus 186 FT~EQkekM~~fAeklGWRiqk~d~---~~ve~fc~eiGv~r~V~KVWmhNn 234 (242)
+=.+..++|..-|+.||.. ....+ +.++++++..+++..++++|+.-.
T Consensus 23 ~l~~Hl~RL~~Sa~~l~~~-~~~~~~l~~~i~~~i~~~~~~~~~ir~~v~rg 73 (249)
T cd01559 23 LLDAHLARLERSARRLGIP-EPDLPRLRAALESLLAANDIDEGRIRLILSRG 73 (249)
T ss_pred cHHHHHHHHHHHHHhcCcC-CCCHHHHHHHHHHHHHhCCCCceEEEEEEecC
Confidence 4578999999999999998 32222 345566666677788999998743
No 234
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=22.27 E-value=29 Score=26.39 Aligned_cols=34 Identities=18% Similarity=0.366 Sum_probs=28.6
Q ss_pred HHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEec
Q 026161 192 DRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWM 231 (242)
Q Consensus 192 ekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWm 231 (242)
|+|.+|.--|||.+. +.+.+.++|++..++.-|.
T Consensus 1 ~~~~~fIrlLs~~~s------~~~Aa~~lG~~~~~v~~wv 34 (65)
T PF05344_consen 1 EKARAFIRLLSQQIS------VAQAADRLGTDPGTVRRWV 34 (65)
T ss_pred CcHHHHHHHhccccc------HHHHHHHHCcCHHHHHHHH
Confidence 478889999999885 7788899999998887775
No 235
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. 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 winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=22.14 E-value=19 Score=27.89 Aligned_cols=22 Identities=18% Similarity=0.362 Sum_probs=18.9
Q ss_pred HHHHHHHhCCCCceEEEecccc
Q 026161 213 VQQFCNDTGVKRHVLKVWMHNN 234 (242)
Q Consensus 213 ve~fc~eiGv~r~V~KVWmhNn 234 (242)
+.++|+.+||+.++|+.|....
T Consensus 3 I~e~a~~~gvs~~tLR~ye~~G 24 (96)
T cd04774 3 VDEVAKRLGLTKRTLKYYEEIG 24 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 5789999999999999997643
No 236
>cd02986 DLP Dim1 family, Dim1-like protein (DLP) subfamily; DLP is a novel protein which shares 38% sequence identity to Dim1. Like Dim1, it is also implicated in pre-mRNA splicing and cell cycle progression. DLP is located in the nucleus and has been shown to interact with the U5 small nuclear ribonucleoprotein particle (snRNP)-specific 102kD protein (or Prp6). Dim1 protein, also known as U5 snRNP-specific 15kD protein is a component of U5 snRNP, which pre-assembles with U4/U6 snRNPs to form a [U4/U6:U5] tri-snRNP complex required for pre-mRNA splicing. Dim1 adopts a thioredoxin fold but does not contain the redox active CXXC motif.
Probab=22.10 E-value=70 Score=26.33 Aligned_cols=45 Identities=16% Similarity=0.158 Sum_probs=32.4
Q ss_pred HHHHHHHHHhC--CccCCCCHHHHHHHHHHhCCC-CceEEEeccccccc
Q 026161 192 DRMLELAEKLG--WRIQKHDEEVVQQFCNDTGVK-RHVLKVWMHNNKHT 237 (242)
Q Consensus 192 ekM~~fAeklG--WRiqk~d~~~ve~fc~eiGv~-r~V~KVWmhNnK~~ 237 (242)
+.+.++|+++- =.+-+-|.+++.+|+++.+|+ .-+|- .|.|+||-
T Consensus 34 p~l~ela~~~~~~~~f~kVDVDev~dva~~y~I~amPtfv-ffkngkh~ 81 (114)
T cd02986 34 DILSKTSHDLSKMASIYLVDVDKVPVYTQYFDISYIPSTI-FFFNGQHM 81 (114)
T ss_pred HHHHHHHHHccCceEEEEEeccccHHHHHhcCceeCcEEE-EEECCcEE
Confidence 45666887751 124456888999999999998 77776 67777663
No 237
>PF04719 TAFII28: hTAFII28-like protein conserved region; InterPro: IPR006809 The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex. The conserved region is found at the C terminus of most member proteins. The crystal structure of hTAFII28 with hTAFII18 shows that this region is involved in the binding of these two subunits. The conserved region contains four alpha helices and three loops arranged as in histone H3 [, ].; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005634 nucleus; PDB: 1BH9_B 1BH8_B.
Probab=21.96 E-value=1.4e+02 Score=23.67 Aligned_cols=31 Identities=19% Similarity=0.394 Sum_probs=16.8
Q ss_pred ccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHh
Q 026161 184 TKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDT 220 (242)
Q Consensus 184 TkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~ei 220 (242)
..||+||.++-..|=.. +-....|.++++.+
T Consensus 6 ~~f~~eQ~~Rye~fRRs------~~~k~~ikkli~~~ 36 (90)
T PF04719_consen 6 SNFDEEQLDRYEAFRRS------SFNKAAIKKLINQV 36 (90)
T ss_dssp ----HHHHHHHHHHHH----------HHHHHHHHHHH
T ss_pred HcCCHHHHHHHHHHHHc------cCCHHHHHHHHHHH
Confidence 46999999996665444 45556777777763
No 238
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=21.84 E-value=15 Score=34.19 Aligned_cols=51 Identities=10% Similarity=0.210 Sum_probs=36.9
Q ss_pred cCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 185 KFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 185 kFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
++++.|++.+...+ |+ ..-+....++++..+||++.+++++++.-+.++.+
T Consensus 262 ~L~~~~R~vl~lry---gL--~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~ 312 (325)
T PRK05657 262 ELNDKQREVLARRF---GL--LGYEAATLEDVAREIGLTRERVRQIQVEALRRLRE 312 (325)
T ss_pred cCCHHHHHHHHHHh---cc--CCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 66777777765422 22 12345578999999999999999999988777643
No 239
>PF05121 GvpK: Gas vesicle protein K ; InterPro: IPR007805 Gas vesicles are intracellular, protein-coated, and hollow organelles found in cyanobacteria and halophilic archaea. They are permeable to ambient gases by diffusion and provide buoyancy, enabling cells to move upwards in liquid to access oxygen and/or light. Proteins containing this domain are involved in the formation of gas vesicles [].; GO: 0031412 gas vesicle organization
Probab=21.79 E-value=1.9e+02 Score=23.26 Aligned_cols=35 Identities=29% Similarity=0.454 Sum_probs=28.1
Q ss_pred ccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCce
Q 026161 184 TKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHV 226 (242)
Q Consensus 184 TkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V 226 (242)
-.+|++|.|++-.-..++ ++.++++|...||+..=
T Consensus 40 G~Lse~qiErlG~tLm~L--------e~~~~~l~~~~gl~~~d 74 (88)
T PF05121_consen 40 GSLSEEQIERLGETLMKL--------EEAMEELCERFGLTPED 74 (88)
T ss_pred CCCCHHHHHHHHHHHHHH--------HHHHHHHHHHcCCCHHH
Confidence 468999999988866663 56799999999998653
No 240
>KOG3755 consensus SATB1 matrix attachment region binding protein [Transcription]
Probab=21.51 E-value=41 Score=35.45 Aligned_cols=57 Identities=16% Similarity=0.281 Sum_probs=48.4
Q ss_pred CCCCCcCccCCHHHHHHHHHHHHHhCCccCCCCHHH---HHHHHHHhCCCCceEEEecccccc
Q 026161 177 GSRKRFRTKFTPEQKDRMLELAEKLGWRIQKHDEEV---VQQFCNDTGVKRHVLKVWMHNNKH 236 (242)
Q Consensus 177 ~~~KR~RTkFT~EQkekM~~fAeklGWRiqk~d~~~---ve~fc~eiGv~r~V~KVWmhNnK~ 236 (242)
.-++|+||+++-|-...+++|+..+|- .+|+.+ +.-+...+.+.++++--.|+|.+-
T Consensus 645 ~~~p~~~~~isge~~~~~qs~i~~~gl---~pd~~a~~~~~~LSa~~~~pk~~~~k~f~~~~~ 704 (769)
T KOG3755|consen 645 WHKPRKRTKISGEALGILQSFITDVGL---YPDKEAPYFIKTLSAQLDLPKKTIIKFFQNQRY 704 (769)
T ss_pred ccCccccceecccchHHHHHHHHHhcc---CchhhcccccchhhhhhcccHHHHHHhhhccee
Confidence 447999999999999999999999874 567766 888999999999988888888753
No 241
>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=21.47 E-value=15 Score=24.32 Aligned_cols=21 Identities=10% Similarity=0.196 Sum_probs=18.2
Q ss_pred HHHHHhCCCCceEEEeccccc
Q 026161 215 QFCNDTGVKRHVLKVWMHNNK 235 (242)
Q Consensus 215 ~fc~eiGv~r~V~KVWmhNnK 235 (242)
+|++.+||++.++.-|++|+.
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 588899999999999998874
No 242
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=21.35 E-value=2.9e+02 Score=19.91 Aligned_cols=35 Identities=26% Similarity=0.449 Sum_probs=24.8
Q ss_pred cCCHHHHHH-----HHHHHHHhCCccCCCCHHHHHHHHHHhCCCC
Q 026161 185 KFTPEQKDR-----MLELAEKLGWRIQKHDEEVVQQFCNDTGVKR 224 (242)
Q Consensus 185 kFT~EQkek-----M~~fAeklGWRiqk~d~~~ve~fc~eiGv~r 224 (242)
.+|-|+++. +.+.|..|| -...++.+.|.+.||+|
T Consensus 4 ~lt~~~L~~~fhlp~~eAA~~Lg-----v~~T~LKr~CR~~GI~R 43 (52)
T PF02042_consen 4 SLTLEDLSQYFHLPIKEAAKELG-----VSVTTLKRRCRRLGIPR 43 (52)
T ss_pred ccCHHHHHHHhCCCHHHHHHHhC-----CCHHHHHHHHHHcCCCC
Confidence 456666655 345677764 45678999999999986
No 243
>cd02423 Peptidase_C39G A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family of proteins with a single peptidase domain, which are
Probab=21.25 E-value=1.9e+02 Score=21.70 Aligned_cols=40 Identities=10% Similarity=0.135 Sum_probs=22.2
Q ss_pred ccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEE
Q 026161 184 TKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKV 229 (242)
Q Consensus 184 TkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KV 229 (242)
-.++.+|+. +.++|.-+..+...+.++++..|++-+.+++
T Consensus 27 ~~~~~~~l~------~~~~~~~~~~s~~~l~~~a~~~Gl~~~~~~~ 66 (129)
T cd02423 27 INITEQEVL------KLMLIRSEGFSMLDLKRYAEALGLKANGYRL 66 (129)
T ss_pred CCCCHHHHH------HHhCcccCCcCHHHHHHHHHHCCCcceEEEc
Confidence 445555443 2334444455666666666666666666554
No 244
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=21.20 E-value=33 Score=28.46 Aligned_cols=13 Identities=54% Similarity=0.836 Sum_probs=10.8
Q ss_pred ccccccccccccc
Q 026161 82 LDGLKCAACNCHR 94 (242)
Q Consensus 82 ~~al~CaaCgCHR 94 (242)
.-.|+|.|||..|
T Consensus 112 ~~~l~C~aCGa~~ 124 (125)
T PF01873_consen 112 LIFLKCKACGASR 124 (125)
T ss_dssp CCEEEETTTSCEE
T ss_pred EEEEEecccCCcC
Confidence 4589999999876
No 245
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=21.18 E-value=13 Score=30.58 Aligned_cols=46 Identities=15% Similarity=0.245 Sum_probs=35.1
Q ss_pred ccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccC
Q 026161 184 TKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLG 239 (242)
Q Consensus 184 TkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~g 239 (242)
.+++++|++.+.- +.+. ...++.|..+||+..+++.+++-.|+++.
T Consensus 126 ~~L~~~~r~v~~l~~~~g----------~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr 172 (179)
T PRK09415 126 MSLPIKYREVIYLFYYEE----------LSIKEIAEVTGVNENTVKTRLKKAKELLK 172 (179)
T ss_pred HhCCHHHhhHhHhHHhcC----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4677778777544 4444 25789999999999999999988777654
No 246
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=21.18 E-value=60 Score=25.64 Aligned_cols=42 Identities=24% Similarity=0.528 Sum_probs=31.8
Q ss_pred cCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccc
Q 026161 185 KFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNN 234 (242)
Q Consensus 185 kFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNn 234 (242)
.+|+..+..|-.-.-.-||. +.++|++.||++.+..-|+.--
T Consensus 8 ~Lt~~gR~~lv~~vv~~g~~--------~a~aA~~~gVS~~Ta~kW~~Ry 49 (85)
T PF13011_consen 8 RLTPRGRLRLVRRVVEQGWP--------VAHAAAEFGVSRRTAYKWLARY 49 (85)
T ss_pred CCCHHHHHHHHHHHHHcCCc--------HHHHHHHhCCCHHHHHHHHHHH
Confidence 47888888876644443554 6789999999999999998543
No 247
>TIGR00013 taut 4-oxalocrotonate tautomerase family enzyme. 4-oxalocrotonate tautomerase is a homohexamer in which each monomer is very small, at about 62 amino acids. Pro-1 of the mature protein serves as a general base. The enzyme functions in meta-cleavage pathways of aromatic hydrocarbon catabolism. Because several Arg residues located near the active site in the crystal structure of Pseudomonas putida are not conserved among all members of this family, because the literature describes a general role in the isomerization of beta,gamma-unsaturated enones to their alpha,beta-isomers, and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.
Probab=21.14 E-value=2.3e+02 Score=19.31 Aligned_cols=35 Identities=23% Similarity=0.316 Sum_probs=26.4
Q ss_pred CCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccc
Q 026161 186 FTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNN 234 (242)
Q Consensus 186 FT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNn 234 (242)
.|.|||++|.+ . +-+.++..+|++...+-|.+...
T Consensus 12 rt~eqK~~l~~---~-----------it~~l~~~lg~~~~~v~V~i~e~ 46 (63)
T TIGR00013 12 RTDEQKRQLIE---G-----------VTEAMAETLGANLESIVVIIDEM 46 (63)
T ss_pred CCHHHHHHHHH---H-----------HHHHHHHHhCCCcccEEEEEEEc
Confidence 38899988643 2 45667888999998888887654
No 248
>cd02421 Peptidase_C39_likeD A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is not conserved in this sub-family.
Probab=20.97 E-value=1.3e+02 Score=22.64 Aligned_cols=44 Identities=9% Similarity=0.138 Sum_probs=32.6
Q ss_pred CCcCccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEE
Q 026161 180 KRFRTKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKV 229 (242)
Q Consensus 180 KR~RTkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KV 229 (242)
+.++-.++.+|.. ..+||.-...+...+.+.++.+|++-+..++
T Consensus 17 ~~~g~~~~~~~l~------~~~~~~~~~~~~~~l~~~a~~~Gl~~~~~~~ 60 (124)
T cd02421 17 RQFGKPASRDSLV------AGLPLDDGRLSPALFPRAAARAGLSARVVRR 60 (124)
T ss_pred HHhCCCCCHHHHH------hcCCCCCCCcCHHHHHHHHHHCCCcceeeeC
Confidence 4445566666665 3567776678888899999999998888765
No 249
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=20.93 E-value=40 Score=29.17 Aligned_cols=40 Identities=8% Similarity=0.260 Sum_probs=29.9
Q ss_pred HHHHHHHH-----HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccc
Q 026161 189 EQKDRMLE-----LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNK 235 (242)
Q Consensus 189 EQkekM~~-----fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK 235 (242)
+-++++.+ |+++ .-+ ..++++|++.||++.+|-.+|-|..
T Consensus 13 ~~r~~Il~aA~~lF~~~------Gy~-~s~~~IA~~AGvsk~tiy~~F~sKe 57 (225)
T PRK11552 13 QAKQQLIAAALAQFGEY------GLH-ATTRDIAAQAGQNIAAITYYFGSKE 57 (225)
T ss_pred HHHHHHHHHHHHHHHHh------Ccc-CCHHHHHHHhCCCHHHHHHHcCCHH
Confidence 44555444 6665 344 6899999999999999999997743
No 250
>cd00449 PLPDE_IV PyridoxaL 5'-Phosphate Dependent Enzymes class IV (PLPDE_IV). This D-amino acid superfamily, one of five classes of PLPDE, consists of branched-chain amino acid aminotransferases (BCAT), D-amino acid transferases (DAAT), and 4-amino-4-deoxychorismate lyases (ADCL). BCAT catalyzes the reversible transamination reaction between the L-branched-chain amino and alpha-keto acids. DAAT catalyzes the synthesis of D-glutamic acid and D-alanine, and ADCL converts 4-amino-4-deoxychorismate to p-aminobenzoate and pyruvate. Except for a few enzymes, i. e., Escherichia coli and Salmonella BCATs, which are homohexamers arranged as a double trimer, the class IV PLPDEs are homodimers. Homodimer formation is required for catalytic activity.
Probab=20.85 E-value=2.7e+02 Score=24.05 Aligned_cols=51 Identities=20% Similarity=0.235 Sum_probs=38.1
Q ss_pred CccCCHHHHHHHHHHHHHhCCccCCCCH---HHHHHHHHHhCCCCceEEEeccc
Q 026161 183 RTKFTPEQKDRMLELAEKLGWRIQKHDE---EVVQQFCNDTGVKRHVLKVWMHN 233 (242)
Q Consensus 183 RTkFT~EQkekM~~fAeklGWRiqk~d~---~~ve~fc~eiGv~r~V~KVWmhN 233 (242)
|=-+-.+.+++|..-|+.+|+.+.-..+ +.+++++...++...++++++.-
T Consensus 20 ~~~~l~~Hl~RL~~sa~~l~~~~~~~~~~~~~~i~~~~~~~~~~~~~ir~~v~~ 73 (256)
T cd00449 20 RLFRLDEHLDRLNRSAKRLGLPIPYDREELREALKELVAANNGASLYIRPLLTR 73 (256)
T ss_pred EEEChHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHhCCCCCEEEEEEEEe
Confidence 3446678999999999999998653333 35666666668888889998853
No 251
>TIGR03613 RutR pyrimidine utilization regulatory protein R. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the TetR family of transcriptional regulators defined by the N-teminal model pfam00440 and the C-terminal model pfam08362 (YcdC-like protein, C-terminal region).
Probab=20.78 E-value=34 Score=28.05 Aligned_cols=46 Identities=15% Similarity=0.157 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccc
Q 026161 188 PEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNN 234 (242)
Q Consensus 188 ~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNn 234 (242)
.+.++++.+-|..+=|+ +.-+...++++|++.||++..|--.|.|.
T Consensus 7 ~~~r~~Il~aA~~lf~e-~G~~~~s~~~IA~~agvs~~~lY~hF~sK 52 (202)
T TIGR03613 7 EAKRKAILSAALDTFSR-FGFHGTSLEQIAELAGVSKTNLLYYFPSK 52 (202)
T ss_pred HHHHHHHHHHHHHHHHH-hCcccCCHHHHHHHhCCCHHHHHHHcCCH
Confidence 45666665533332111 14455689999999999999988877764
No 252
>cd02419 Peptidase_C39C A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family.
Probab=20.77 E-value=1.9e+02 Score=21.82 Aligned_cols=44 Identities=5% Similarity=0.091 Sum_probs=32.5
Q ss_pred CCcCccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEE
Q 026161 180 KRFRTKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKV 229 (242)
Q Consensus 180 KR~RTkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KV 229 (242)
+.+...++.++... .++|.....+...+.++++..|++-+++++
T Consensus 22 ~~~g~~~~~~~l~~------~~~~~~~~~~~~~l~~~a~~~Gl~~~~~~~ 65 (127)
T cd02419 22 SYHGHHVDLASLRQ------RFPVSLKGATLADLIDIAQQLGLSTRALRL 65 (127)
T ss_pred HHcCCCCCHHHHHH------HcCCCCCCcCHHHHHHHHHHCCCceeEEEc
Confidence 55667777777653 456666667888888888899988888775
No 253
>cd02949 TRX_NTR TRX domain, novel NADPH thioredoxin reductase (NTR) family; composed of fusion proteins found only in oxygenic photosynthetic organisms containing both TRX and NTR domains. The TRX domain functions as a protein disulfide reductase via the reversible oxidation of an active center dithiol present in a CXXC motif, while the NTR domain functions as a reductant to oxidized TRX. The fusion protein is bifunctional, showing both TRX and NTR activities, but it is not an independent NTR/TRX system. In plants, the protein is found exclusively in shoots and mature leaves and is localized in the chloroplast. It is involved in plant protection against oxidative stress.
Probab=20.67 E-value=65 Score=23.74 Aligned_cols=47 Identities=9% Similarity=0.148 Sum_probs=33.6
Q ss_pred HHHHHHHHHHHHhC--CccCCCCHHHHHHHHHHhCCCCceEEEeccccc
Q 026161 189 EQKDRMLELAEKLG--WRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNK 235 (242)
Q Consensus 189 EQkekM~~fAeklG--WRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK 235 (242)
+.+..|.+++++++ +++-+-|.+.-.+++++.+|..--.-+++.|.+
T Consensus 30 ~~~~~l~~l~~~~~~~v~~~~id~d~~~~l~~~~~v~~vPt~~i~~~g~ 78 (97)
T cd02949 30 TLKPILNKVIDEFDGAVHFVEIDIDEDQEIAEAAGIMGTPTVQFFKDKE 78 (97)
T ss_pred HHHHHHHHHHHHhCCceEEEEEECCCCHHHHHHCCCeeccEEEEEECCe
Confidence 34556667777765 666677766677899999998777777776654
No 254
>PF05930 Phage_AlpA: Prophage CP4-57 regulatory protein (AlpA); InterPro: IPR010260 This entry is represents phage P4, Orf88. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. In Escherichia coli phage P4 Orf 88 is similar to AlpA of the CP4-57 cryptic prophage []. AlpA acts as a positive transcriptional regulator of slpA, a gene linked to alpA and necessary for suppression of lon mutants [, ]. The sequence of slpA suggests that it encodes an integrase gene closely related to phage P4 int and that both alpA and slpA are part of a cryptic P4-like prophage. Increase in alpA expression increases SlpA synthesis. Increased SlpA leads, in turn, to the excision and loss of the cryptic prophage. ; PDB: 1Z4H_A.
Probab=20.63 E-value=13 Score=25.57 Aligned_cols=22 Identities=14% Similarity=0.317 Sum_probs=17.9
Q ss_pred HHHHHHHhCCCCceEEEecccc
Q 026161 213 VQQFCNDTGVKRHVLKVWMHNN 234 (242)
Q Consensus 213 ve~fc~eiGv~r~V~KVWmhNn 234 (242)
++++|+.+||++.+|--|+.+.
T Consensus 6 ~~ev~~~~g~s~~ti~~~~k~g 27 (51)
T PF05930_consen 6 IKEVAELLGVSRSTIYRLIKDG 27 (51)
T ss_dssp HHHHHHHHSS-HHHHHHHHHHH
T ss_pred HHHHHHHHCCCHHHHHHHHhcc
Confidence 5788999999999998888764
No 255
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=20.42 E-value=23 Score=28.79 Aligned_cols=46 Identities=11% Similarity=0.094 Sum_probs=34.2
Q ss_pred cCccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccc
Q 026161 182 FRTKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHT 237 (242)
Q Consensus 182 ~RTkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~ 237 (242)
.-.++++.|++.+.- +.+- ...++.|..+|++..+++.++.+.+..
T Consensus 115 ~l~~L~~~~r~v~~L~~~eg----------~s~~EIA~~l~is~~tV~~~l~ra~~~ 161 (168)
T PRK12525 115 LLDGLSGKARAAFLMSQLEG----------LTYVEIGERLGVSLSRIHQYMVEAFKC 161 (168)
T ss_pred HHHhCCHHHHHHHHHHHHcC----------CCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 345688888887544 3333 257899999999999999999876643
No 256
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=20.39 E-value=61 Score=21.69 Aligned_cols=25 Identities=16% Similarity=0.542 Sum_probs=15.6
Q ss_pred ccccccccCCCCCcccccccccccc
Q 026161 69 GCGEFMAAGDEGTLDGLKCAACNCH 93 (242)
Q Consensus 69 GCgEFm~~~~~g~~~al~CaaCgCH 93 (242)
-||..|...+.....-+.|..||-|
T Consensus 5 ~Cg~~l~~~~~~~~~~~vC~~Cg~~ 29 (52)
T smart00661 5 KCGNMLIPKEGKEKRRFVCRKCGYE 29 (52)
T ss_pred CCCCccccccCCCCCEEECCcCCCe
Confidence 3777776543222236889999954
No 257
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=20.38 E-value=21 Score=29.08 Aligned_cols=48 Identities=10% Similarity=0.158 Sum_probs=34.6
Q ss_pred CcCccCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccc
Q 026161 181 RFRTKFTPEQKDRMLE-LAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTL 238 (242)
Q Consensus 181 R~RTkFT~EQkekM~~-fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~ 238 (242)
+.=.+++++|++.+.- +.+- ...+++|+.+||+..++++++++-+.+.
T Consensus 115 ~~l~~Lp~~~r~v~~L~~~~g----------~s~~EIA~~lgis~~tV~~~l~ra~~~~ 163 (172)
T PRK12523 115 RLLGKLSSKARAAFLYNRLDG----------MGHAEIAERLGVSVSRVRQYLAQGLRQC 163 (172)
T ss_pred HHHHhCCHHHHHHHHHHHHcC----------CCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 3345677777777544 3332 3578999999999999999998766543
No 258
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=20.35 E-value=12 Score=32.46 Aligned_cols=47 Identities=9% Similarity=0.029 Sum_probs=33.9
Q ss_pred cCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 185 KFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 185 kFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
++++.|++.+.... -+....+++|..+||+..+++++++.-+.++.+
T Consensus 184 ~L~~~~r~vl~l~~---------~~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 230 (236)
T PRK06986 184 SLPEREQLVLSLYY---------QEELNLKEIGAVLGVSESRVSQIHSQAIKRLRA 230 (236)
T ss_pred hCCHHHHHHHHhHh---------ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45666666654421 223468899999999999999999988776643
No 259
>PRK08942 D,D-heptose 1,7-bisphosphate phosphatase; Validated
Probab=20.27 E-value=2.8e+02 Score=22.73 Aligned_cols=44 Identities=14% Similarity=0.061 Sum_probs=31.0
Q ss_pred cCccCCHHHHHHH----HHHHHHhCC----------------ccCCCCHHHHHHHHHHhCCCCc
Q 026161 182 FRTKFTPEQKDRM----LELAEKLGW----------------RIQKHDEEVVQQFCNDTGVKRH 225 (242)
Q Consensus 182 ~RTkFT~EQkekM----~~fAeklGW----------------Riqk~d~~~ve~fc~eiGv~r~ 225 (242)
.|..|+..|.+++ ....+++|+ ...||+....+..++.+|++..
T Consensus 58 ~~~~~~~~~~~~~~~~~~~~l~~~g~~f~~i~~~~~~~~~~~~~~KP~p~~~~~~~~~l~~~~~ 121 (181)
T PRK08942 58 ARGLFTEAQLNALHEKMDWSLADRGGRLDGIYYCPHHPEDGCDCRKPKPGMLLSIAERLNIDLA 121 (181)
T ss_pred cCCcCCHHHHHHHHHHHHHHHHHcCCccceEEECCCCCCCCCcCCCCCHHHHHHHHHHcCCChh
Confidence 4667888876654 334445554 2358999999999999999743
No 260
>PHA00542 putative Cro-like protein
Probab=20.26 E-value=64 Score=24.29 Aligned_cols=42 Identities=14% Similarity=0.177 Sum_probs=28.6
Q ss_pred cCccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccc
Q 026161 182 FRTKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNN 234 (242)
Q Consensus 182 ~RTkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNn 234 (242)
.+.++.+.+.. .+.+..|| ...++|+.+||++.+|.-|..+.
T Consensus 14 ~~~~~~~~~l~---~~l~~~gl--------Tq~elA~~lgIs~~tIsr~e~g~ 55 (82)
T PHA00542 14 AAYTQRPDELV---CALIRAGW--------SQEQIADATDVSQPTICRIYSGR 55 (82)
T ss_pred cccCcCHHHHH---HHHHHCCC--------CHHHHHHHHCcCHHHHHHHHcCC
Confidence 34455544433 33455555 46789999999999999988765
No 261
>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=20.26 E-value=30 Score=27.06 Aligned_cols=21 Identities=10% Similarity=0.101 Sum_probs=19.0
Q ss_pred HHHHHHHHhCCCCceEEEecc
Q 026161 212 VVQQFCNDTGVKRHVLKVWMH 232 (242)
Q Consensus 212 ~ve~fc~eiGv~r~V~KVWmh 232 (242)
.+.++|.++||++.+|.-|..
T Consensus 52 S~~eIA~~LgISrsTIyRi~R 72 (88)
T TIGR02531 52 TYSDIEAETGASTATISRVKR 72 (88)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 678899999999999999776
No 262
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. 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.
Probab=20.23 E-value=24 Score=27.15 Aligned_cols=21 Identities=19% Similarity=0.325 Sum_probs=18.6
Q ss_pred HHHHHHHhCCCCceEEEeccc
Q 026161 213 VQQFCNDTGVKRHVLKVWMHN 233 (242)
Q Consensus 213 ve~fc~eiGv~r~V~KVWmhN 233 (242)
+.++|..+||+.++|+.|-..
T Consensus 3 i~eva~~~gvs~~tLRyye~~ 23 (96)
T cd04768 3 IGEFAKLAGVSIRTLRHYDDI 23 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 578999999999999999764
No 263
>PRK09483 response regulator; Provisional
Probab=20.20 E-value=25 Score=28.21 Aligned_cols=47 Identities=9% Similarity=0.114 Sum_probs=36.6
Q ss_pred ccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccccCC
Q 026161 184 TKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMHNNKHTLGK 240 (242)
Q Consensus 184 TkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmhNnK~~~gk 240 (242)
..||+-++|.|.-+++- + ...+++++++|+.++++.-.+|=+.|++-
T Consensus 147 ~~Lt~rE~~vl~~~~~G--~--------~~~~Ia~~l~is~~TV~~~~~~i~~Kl~v 193 (217)
T PRK09483 147 ASLSERELQIMLMITKG--Q--------KVNEISEQLNLSPKTVNSYRYRMFSKLNI 193 (217)
T ss_pred cccCHHHHHHHHHHHCC--C--------CHHHHHHHhCCCHHHHHHHHHHHHHHcCC
Confidence 56999999998766532 2 34488899999999999988887777764
No 264
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=20.19 E-value=43 Score=26.87 Aligned_cols=18 Identities=0% Similarity=-0.077 Sum_probs=10.2
Q ss_pred CCHHHHHHHHHHhCCCCc
Q 026161 208 HDEEVVQQFCNDTGVKRH 225 (242)
Q Consensus 208 ~d~~~ve~fc~eiGv~r~ 225 (242)
++...+.++|.-+||+..
T Consensus 45 p~~~~l~~la~~l~vs~~ 62 (135)
T PRK09706 45 PTGKNLFALAKALQCSPT 62 (135)
T ss_pred CCHHHHHHHHHHHCcCHH
Confidence 455556666666666543
No 265
>PRK11083 DNA-binding response regulator CreB; Provisional
Probab=20.15 E-value=40 Score=27.00 Aligned_cols=50 Identities=10% Similarity=-0.075 Sum_probs=38.7
Q ss_pred ccCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCC-----CceEEEeccccccccC
Q 026161 184 TKFTPEQKDRMLELAEKLGWRIQKHDEEVVQQFCNDTGVK-----RHVLKVWMHNNKHTLG 239 (242)
Q Consensus 184 TkFT~EQkekM~~fAeklGWRiqk~d~~~ve~fc~eiGv~-----r~V~KVWmhNnK~~~g 239 (242)
-.||.-+.+.|.-+++. +...-..+++++.+..+ .+++++..++=|.|++
T Consensus 153 ~~Lt~~E~~il~~l~~~------~~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~l~~Kl~ 207 (228)
T PRK11083 153 LTLTRYEFLLLKTLLLS------PGRVFSRQQLMDIVWEDAQDSYDRTVDTHIKTLRAKLR 207 (228)
T ss_pred eecCHHHHHHHHHHHhC------CCceECHHHHHHHhcCCCCCCCccCHHHHHHHHHHHhc
Confidence 36999999999999986 22234567788888775 7899999988888875
No 266
>PF13730 HTH_36: Helix-turn-helix domain
Probab=20.07 E-value=43 Score=22.52 Aligned_cols=44 Identities=25% Similarity=0.265 Sum_probs=28.6
Q ss_pred ccCCHHHHHHHHHHHH---HhCCccCCCCHHHHHHHHHHhCCCCceEEEecc
Q 026161 184 TKFTPEQKDRMLELAE---KLGWRIQKHDEEVVQQFCNDTGVKRHVLKVWMH 232 (242)
Q Consensus 184 TkFT~EQkekM~~fAe---klGWRiqk~d~~~ve~fc~eiGv~r~V~KVWmh 232 (242)
|.+|+.++-.+..++. +-|| -.| -++.+|.++|+++++++-++.
T Consensus 1 ~~Ls~~~~~v~~~l~~~~~~~~~--~~p---S~~~la~~~g~s~~Tv~~~i~ 47 (55)
T PF13730_consen 1 KNLSPTAKLVYLYLASYANKNGG--CFP---SQETLAKDLGVSRRTVQRAIK 47 (55)
T ss_pred CCCCHHHHHHHHHHHHhcCCCCC--CCc---CHHHHHHHHCcCHHHHHHHHH
Confidence 3567777776555333 3333 222 478999999999998876553
Done!