Query 021941
Match_columns 305
No_of_seqs 160 out of 283
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 06:49:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021941.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021941hhsearch_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 5.6E-38 1.2E-42 235.8 2.9 57 76-132 2-59 (60)
2 TIGR01566 ZF_HD_prot_N ZF-HD h 100.0 4.5E-38 9.8E-43 230.4 2.3 52 79-130 1-53 (53)
3 TIGR01565 homeo_ZF_HD homeobox 99.9 4.1E-27 8.9E-32 175.7 6.4 58 234-291 1-58 (58)
4 PF00046 Homeobox: Homeobox do 99.2 2.5E-12 5.4E-17 91.6 0.1 57 235-295 1-57 (57)
5 KOG4577 Transcription factor L 99.1 2E-11 4.4E-16 116.8 2.5 63 230-296 163-225 (383)
6 KOG0494 Transcription factor C 99.1 3.6E-11 7.8E-16 113.7 3.3 61 233-298 140-201 (332)
7 KOG2251 Homeobox transcription 99.1 1.4E-10 3E-15 106.9 4.6 64 230-297 33-96 (228)
8 KOG0843 Transcription factor E 99.0 7.4E-11 1.6E-15 106.4 1.8 64 232-299 100-163 (197)
9 KOG0484 Transcription factor P 99.0 3.5E-11 7.5E-16 101.2 -1.1 60 233-297 16-76 (125)
10 KOG0493 Transcription factor E 98.9 4.9E-10 1.1E-14 106.3 2.0 58 235-297 247-305 (342)
11 smart00389 HOX Homeodomain. DN 98.9 1.4E-09 3E-14 76.5 2.9 56 235-294 1-56 (56)
12 cd00086 homeodomain Homeodomai 98.8 1.6E-09 3.5E-14 76.3 2.1 58 235-296 1-58 (59)
13 KOG0844 Transcription factor E 98.6 2.4E-08 5.3E-13 96.6 3.8 61 233-298 180-241 (408)
14 KOG3802 Transcription factor O 98.6 7.6E-08 1.6E-12 94.9 6.5 63 232-298 292-354 (398)
15 KOG0490 Transcription factor, 98.5 3.7E-08 8E-13 85.6 2.4 63 231-297 57-119 (235)
16 KOG0485 Transcription factor N 98.3 2.1E-07 4.6E-12 86.7 2.5 64 230-297 100-163 (268)
17 KOG0488 Transcription factor B 98.3 3.6E-07 7.9E-12 87.3 3.0 61 232-296 170-230 (309)
18 KOG0489 Transcription factor z 98.3 1.7E-07 3.6E-12 87.0 0.0 65 232-300 157-221 (261)
19 KOG0850 Transcription factor D 98.3 8.9E-07 1.9E-11 82.6 4.4 58 235-296 123-180 (245)
20 COG5576 Homeodomain-containing 98.2 7.1E-07 1.5E-11 78.3 3.0 66 230-299 47-112 (156)
21 KOG0492 Transcription factor M 98.2 1.1E-06 2.5E-11 81.4 3.1 57 234-295 144-201 (246)
22 KOG0849 Transcription factor P 98.0 2E-06 4.4E-11 83.3 2.0 62 232-297 174-235 (354)
23 KOG0486 Transcription factor P 98.0 2.2E-06 4.7E-11 83.1 2.2 62 233-298 111-172 (351)
24 KOG0842 Transcription factor t 98.0 5.9E-06 1.3E-10 79.6 4.9 65 230-299 149-214 (307)
25 KOG1168 Transcription factor A 97.9 6.2E-06 1.3E-10 79.8 2.2 64 231-298 306-369 (385)
26 KOG0490 Transcription factor, 97.9 5.3E-06 1.2E-10 72.2 1.3 64 230-297 149-212 (235)
27 KOG0483 Transcription factor H 97.7 1.8E-05 3.8E-10 72.1 1.7 57 239-299 55-111 (198)
28 KOG1146 Homeobox protein [Gene 97.6 7.9E-05 1.7E-09 82.5 6.0 63 231-297 900-962 (1406)
29 KOG0847 Transcription factor, 97.5 3.9E-05 8.5E-10 72.1 1.0 63 231-297 164-226 (288)
30 KOG2252 CCAAT displacement pro 97.3 0.00016 3.5E-09 74.3 3.7 61 229-293 415-475 (558)
31 KOG0487 Transcription factor A 97.1 0.00042 9E-09 67.1 4.0 59 232-297 235-294 (308)
32 KOG0848 Transcription factor C 97.1 0.00015 3.3E-09 69.6 0.3 60 231-295 196-256 (317)
33 KOG0491 Transcription factor B 97.1 4.9E-05 1.1E-09 68.7 -2.9 61 232-296 98-158 (194)
34 PF01527 HTH_Tnp_1: Transposas 94.9 0.0076 1.7E-07 44.6 0.2 47 236-290 2-48 (76)
35 PF04218 CENP-B_N: CENP-B N-te 94.4 0.026 5.5E-07 41.2 1.9 47 235-290 1-47 (53)
36 cd00569 HTH_Hin_like Helix-tur 89.5 0.28 6E-06 28.8 1.9 39 239-286 4-42 (42)
37 PF05920 Homeobox_KN: Homeobox 88.6 0.065 1.4E-06 37.5 -1.5 33 259-291 7-39 (40)
38 COG2963 Transposase and inacti 81.6 0.84 1.8E-05 36.8 1.5 47 238-292 5-52 (116)
39 cd06171 Sigma70_r4 Sigma70, re 80.4 0.37 8E-06 31.6 -0.8 46 239-293 9-54 (55)
40 PF02796 HTH_7: Helix-turn-hel 78.7 0.5 1.1E-05 33.0 -0.6 39 239-286 4-42 (45)
41 PF06163 DUF977: Bacterial pro 76.4 0.89 1.9E-05 39.6 0.2 44 240-287 4-48 (127)
42 PF12651 RHH_3: Ribbon-helix-h 73.2 3.1 6.7E-05 29.5 2.2 40 234-273 2-41 (44)
43 KOG0774 Transcription factor P 71.0 4.7 0.0001 39.5 3.7 61 235-296 189-249 (334)
44 KOG0773 Transcription factor M 65.9 7.1 0.00015 37.3 3.7 63 232-296 237-300 (342)
45 KOG0775 Transcription factor S 65.7 6 0.00013 38.8 3.2 45 246-294 188-232 (304)
46 PRK09413 IS2 repressor TnpA; R 65.6 2.7 5.9E-05 34.7 0.8 43 238-288 10-52 (121)
47 KOG3623 Homeobox transcription 64.5 3.4 7.3E-05 45.3 1.4 52 240-296 563-614 (1007)
48 PRK09480 slmA division inhibit 62.5 4.7 0.0001 33.8 1.6 47 243-290 9-55 (194)
49 PF04967 HTH_10: HTH DNA bindi 62.5 6.3 0.00014 29.3 2.1 40 241-282 1-40 (53)
50 PF13022 HTH_Tnp_1_2: Helix-tu 60.4 2.3 5E-05 37.7 -0.6 56 234-290 4-59 (142)
51 PF08281 Sigma70_r4_2: Sigma-7 58.7 1.6 3.5E-05 30.5 -1.5 43 240-291 10-52 (54)
52 smart00421 HTH_LUXR helix_turn 56.6 2.7 5.8E-05 28.1 -0.7 45 240-294 3-47 (58)
53 PF13936 HTH_38: Helix-turn-he 56.0 1.6 3.5E-05 30.5 -1.9 42 238-288 2-43 (44)
54 TIGR00270 conserved hypothetic 55.8 2.5 5.3E-05 37.3 -1.2 51 234-289 53-106 (154)
55 TIGR02989 Sig-70_gvs1 RNA poly 54.7 2.2 4.7E-05 34.9 -1.6 47 239-295 110-157 (159)
56 PF05572 Peptidase_M43: Pregna 54.1 8.9 0.00019 33.4 2.0 18 237-254 137-154 (154)
57 PF13384 HTH_23: Homeodomain-l 53.5 4.2 9.2E-05 27.9 -0.1 38 243-289 4-41 (50)
58 PRK02220 4-oxalocrotonate taut 51.8 27 0.00058 24.9 3.9 34 242-289 13-46 (61)
59 PRK09646 RNA polymerase sigma 51.6 2.6 5.7E-05 36.3 -1.6 50 239-298 141-191 (194)
60 cd04762 HTH_MerR-trunc Helix-T 51.5 4 8.7E-05 26.7 -0.4 25 268-292 3-27 (49)
61 PHA02893 hypothetical protein; 51.1 5.6 0.00012 32.8 0.3 11 111-121 67-77 (88)
62 PRK00118 putative DNA-binding 50.7 2.4 5.2E-05 35.4 -2.0 46 240-294 17-62 (104)
63 PRK09644 RNA polymerase sigma 49.2 2.9 6.3E-05 34.9 -1.7 48 239-296 107-155 (165)
64 PF13698 DUF4156: Domain of un 48.0 7.6 0.00016 31.4 0.6 17 82-98 52-68 (93)
65 TIGR02607 antidote_HigA addict 48.0 7.3 0.00016 28.8 0.5 15 264-278 46-60 (78)
66 PF00249 Myb_DNA-binding: Myb- 47.9 51 0.0011 22.8 4.7 34 238-278 1-34 (48)
67 PRK04217 hypothetical protein; 47.7 3.4 7.3E-05 34.8 -1.5 47 240-295 42-88 (110)
68 PRK06424 transcription factor; 46.9 8.6 0.00019 33.7 0.8 55 234-290 68-122 (144)
69 PRK12512 RNA polymerase sigma 45.9 3.1 6.7E-05 35.2 -2.1 49 239-296 130-178 (184)
70 PRK12537 RNA polymerase sigma 45.0 4.4 9.5E-05 34.5 -1.3 47 240-296 133-180 (182)
71 cd08353 Glo_EDI_BRP_like_7 Thi 45.0 18 0.00038 28.8 2.3 44 243-286 11-54 (142)
72 PRK12539 RNA polymerase sigma 44.6 3.9 8.4E-05 34.9 -1.7 49 239-296 130-178 (184)
73 PF00196 GerE: Bacterial regul 44.2 2.9 6.2E-05 30.0 -2.2 45 240-294 3-47 (58)
74 TIGR03070 couple_hipB transcri 44.2 12 0.00025 25.5 1.0 34 248-289 6-39 (58)
75 TIGR02939 RpoE_Sigma70 RNA pol 44.0 2.7 5.8E-05 35.4 -2.7 32 265-296 154-185 (190)
76 PRK06759 RNA polymerase factor 44.0 4.9 0.00011 32.8 -1.1 48 239-296 105-153 (154)
77 COG3040 Blc Bacterial lipocali 43.7 22 0.00048 32.6 2.9 25 238-262 140-165 (174)
78 PRK12530 RNA polymerase sigma 43.6 3.7 8.1E-05 35.5 -2.0 48 239-295 133-180 (189)
79 PF04545 Sigma70_r4: Sigma-70, 43.4 3.4 7.4E-05 28.7 -1.8 44 240-292 4-47 (50)
80 PRK09652 RNA polymerase sigma 43.4 3.5 7.7E-05 33.9 -2.1 49 239-296 127-175 (182)
81 COG4802 FtrB Ferredoxin-thiore 42.6 26 0.00057 30.0 3.0 54 242-296 2-59 (110)
82 PF13518 HTH_28: Helix-turn-he 42.5 5.3 0.00011 27.2 -1.0 25 267-291 14-38 (52)
83 PRK12526 RNA polymerase sigma 42.4 4.1 8.8E-05 35.8 -1.9 48 240-296 153-200 (206)
84 PF06252 DUF1018: Protein of u 42.0 23 0.0005 29.2 2.6 25 237-261 18-42 (119)
85 PRK12541 RNA polymerase sigma 41.4 4.3 9.2E-05 33.7 -1.9 49 240-297 112-160 (161)
86 PRK10403 transcriptional regul 41.0 6.4 0.00014 32.0 -0.9 48 239-296 152-199 (215)
87 PRK12514 RNA polymerase sigma 40.9 5 0.00011 33.8 -1.6 49 239-296 128-176 (179)
88 TIGR02983 SigE-fam_strep RNA p 40.8 4.7 0.0001 33.3 -1.7 50 240-299 110-160 (162)
89 PRK09648 RNA polymerase sigma 40.5 4.5 9.8E-05 34.5 -1.9 51 236-296 135-186 (189)
90 TIGR02950 SigM_subfam RNA poly 40.3 5 0.00011 32.6 -1.6 34 262-295 118-151 (154)
91 PRK09726 antitoxin HipB; Provi 40.1 22 0.00047 27.7 2.0 19 269-287 29-47 (88)
92 COG0289 DapB Dihydrodipicolina 39.5 23 0.00051 34.3 2.5 22 239-260 101-122 (266)
93 PRK12533 RNA polymerase sigma 39.4 3.7 8.1E-05 37.0 -2.7 54 240-302 134-187 (216)
94 smart00351 PAX Paired Box doma 39.4 14 0.0003 30.9 0.9 41 241-290 18-58 (125)
95 PF13551 HTH_29: Winged helix- 39.1 22 0.00047 27.4 1.9 22 234-255 51-72 (112)
96 TIGR00290 MJ0570_dom MJ0570-re 38.9 50 0.0011 30.8 4.5 44 240-284 94-142 (223)
97 cd01994 Alpha_ANH_like_IV This 38.5 59 0.0013 29.2 4.8 45 239-284 96-145 (194)
98 PRK10072 putative transcriptio 38.4 16 0.00034 30.0 1.0 34 249-290 38-71 (96)
99 TIGR02959 SigZ RNA polymerase 38.3 5.1 0.00011 33.9 -1.9 49 238-295 98-146 (170)
100 PF13189 Cytidylate_kin2: Cyti 38.2 13 0.00029 32.2 0.6 40 249-290 16-55 (179)
101 PF08914 Myb_DNA-bind_2: Rap1 38.2 26 0.00056 27.0 2.1 47 238-285 2-49 (65)
102 cd00093 HTH_XRE Helix-turn-hel 38.1 10 0.00022 24.1 -0.1 20 270-289 17-36 (58)
103 TIGR01764 excise DNA binding d 37.4 7.1 0.00015 25.8 -0.9 23 268-290 4-26 (49)
104 PF13411 MerR_1: MerR HTH fami 37.1 6.9 0.00015 28.3 -1.1 23 268-290 3-25 (69)
105 TIGR02366 DHAK_reg probable di 37.1 21 0.00045 29.8 1.6 27 262-288 20-46 (176)
106 KOG0705 GTPase-activating prot 37.1 15 0.00033 39.6 0.9 36 93-129 514-550 (749)
107 TIGR02985 Sig70_bacteroi1 RNA 36.9 6.3 0.00014 31.7 -1.5 46 240-295 113-159 (161)
108 PF00356 LacI: Bacterial regul 36.9 40 0.00086 24.2 2.8 22 239-260 24-45 (46)
109 PRK09390 fixJ response regulat 36.5 8.8 0.00019 30.7 -0.7 47 240-296 141-187 (202)
110 PF01381 HTH_3: Helix-turn-hel 36.5 11 0.00024 26.0 -0.1 21 269-289 13-33 (55)
111 PF11569 Homez: Homeodomain le 36.1 9.3 0.0002 29.1 -0.6 37 249-289 13-49 (56)
112 PRK12547 RNA polymerase sigma 36.1 5.5 0.00012 33.4 -2.0 48 239-295 111-158 (164)
113 PRK11470 hypothetical protein; 35.8 17 0.00037 33.6 0.9 22 234-255 78-99 (200)
114 PF12844 HTH_19: Helix-turn-he 35.5 15 0.00032 26.3 0.4 17 263-279 39-55 (64)
115 cd06170 LuxR_C_like C-terminal 35.2 9.1 0.0002 25.8 -0.7 44 241-294 1-44 (57)
116 PF13443 HTH_26: Cro/C1-type H 34.9 7.1 0.00015 27.8 -1.3 24 267-290 12-35 (63)
117 cd04761 HTH_MerR-SF Helix-Turn 34.5 8.3 0.00018 25.9 -1.0 25 268-292 3-27 (49)
118 PRK09639 RNA polymerase sigma 34.5 8.7 0.00019 31.7 -1.1 47 239-295 111-157 (166)
119 PRK12546 RNA polymerase sigma 33.6 6.1 0.00013 34.5 -2.2 48 240-296 113-160 (188)
120 PRK09649 RNA polymerase sigma 33.4 7.3 0.00016 33.5 -1.7 48 239-295 129-176 (185)
121 TIGR02999 Sig-70_X6 RNA polyme 33.4 7 0.00015 32.9 -1.8 46 241-295 135-180 (183)
122 PRK12516 RNA polymerase sigma 33.4 6.8 0.00015 34.0 -2.0 48 240-296 116-163 (187)
123 PRK09642 RNA polymerase sigma 33.4 7.3 0.00016 32.2 -1.7 48 239-296 105-153 (160)
124 PRK13919 putative RNA polymera 33.4 7.3 0.00016 32.9 -1.7 53 237-298 132-184 (186)
125 PRK05602 RNA polymerase sigma 32.9 6.2 0.00013 33.6 -2.3 47 240-296 128-175 (186)
126 PRK12524 RNA polymerase sigma 32.9 6.8 0.00015 33.9 -2.0 48 239-296 135-183 (196)
127 PRK09047 RNA polymerase factor 32.8 7.7 0.00017 31.8 -1.6 48 239-295 105-152 (161)
128 PRK03975 tfx putative transcri 32.8 6.9 0.00015 34.3 -2.0 47 239-295 5-51 (141)
129 cd02259 Peptidase_C39_like Pep 32.7 83 0.0018 24.2 4.2 44 235-284 17-60 (122)
130 PF06252 DUF1018: Protein of u 32.6 1.3E+02 0.0028 24.8 5.5 40 239-278 53-95 (119)
131 PF00765 Autoind_synth: Autoin 32.2 4.1 8.9E-05 36.4 -3.6 42 243-288 7-53 (182)
132 PRK12522 RNA polymerase sigma 32.1 7.9 0.00017 32.5 -1.7 31 265-295 135-165 (173)
133 cd00029 C1 Protein kinase C co 32.0 19 0.00041 24.3 0.5 29 95-128 13-41 (50)
134 PRK15369 two component system 31.9 14 0.00031 29.6 -0.2 47 239-295 148-194 (211)
135 PF12728 HTH_17: Helix-turn-he 31.4 10 0.00022 26.3 -1.0 24 268-291 4-27 (51)
136 cd04275 ZnMc_pappalysin_like Z 31.3 28 0.00062 32.3 1.6 18 236-253 207-224 (225)
137 PRK06811 RNA polymerase factor 31.2 9.8 0.00021 32.7 -1.3 50 239-298 130-180 (189)
138 TIGR03879 near_KaiC_dom probab 31.1 12 0.00025 29.7 -0.8 28 264-291 31-58 (73)
139 PF01113 DapB_N: Dihydrodipico 31.0 18 0.00038 29.8 0.2 20 239-258 99-118 (124)
140 PF01902 ATP_bind_4: ATP-bindi 30.8 53 0.0011 30.4 3.3 44 240-284 94-142 (218)
141 PRK15008 HTH-type transcriptio 30.7 26 0.00057 30.6 1.2 56 234-290 8-63 (212)
142 PRK01964 4-oxalocrotonate taut 30.5 92 0.002 22.6 3.9 35 242-290 13-47 (64)
143 PRK11924 RNA polymerase sigma 30.2 8.2 0.00018 31.7 -1.9 47 240-295 125-171 (179)
144 TIGR02948 SigW_bacill RNA poly 30.2 7.5 0.00016 32.6 -2.2 47 239-295 135-182 (187)
145 PRK12536 RNA polymerase sigma 30.1 8.1 0.00018 32.9 -2.0 33 264-296 144-176 (181)
146 cd02425 Peptidase_C39F A sub-f 30.0 1.1E+02 0.0025 23.7 4.6 44 235-284 22-65 (126)
147 cd00491 4Oxalocrotonate_Tautom 29.9 1.2E+02 0.0025 21.1 4.3 35 242-290 12-46 (58)
148 PRK12520 RNA polymerase sigma 29.9 8.8 0.00019 32.8 -1.8 48 239-295 130-177 (191)
149 PTZ00397 macrophage migration 29.6 1.1E+02 0.0023 24.9 4.5 36 242-291 70-105 (116)
150 TIGR02937 sigma70-ECF RNA poly 29.4 8.8 0.00019 29.7 -1.7 47 240-295 110-156 (158)
151 cd08356 Glo_EDI_BRP_like_17 Th 29.3 38 0.00083 26.5 1.8 30 235-264 1-30 (113)
152 PRK11511 DNA-binding transcrip 28.9 22 0.00048 29.4 0.5 41 244-289 9-49 (127)
153 cd02986 DLP Dim1 family, Dim1- 28.3 45 0.00098 28.4 2.2 47 245-292 32-81 (114)
154 PF13223 DUF4031: Protein of u 28.3 29 0.00063 28.3 1.0 20 265-288 23-42 (83)
155 PF09607 BrkDBD: Brinker DNA-b 28.1 26 0.00057 26.9 0.7 45 238-287 3-47 (58)
156 KOG2767 Translation initiation 27.8 19 0.00041 36.6 -0.2 16 113-128 118-133 (400)
157 PF04492 Phage_rep_O: Bacterio 27.7 73 0.0016 26.3 3.3 46 235-281 24-70 (100)
158 PRK12540 RNA polymerase sigma 27.7 9.4 0.0002 33.0 -2.0 49 239-296 110-158 (182)
159 PRK12519 RNA polymerase sigma 27.6 7.5 0.00016 33.2 -2.6 31 265-295 157-187 (194)
160 smart00529 HTH_DTXR Helix-turn 27.5 1.1E+02 0.0025 23.2 4.2 31 240-276 66-96 (96)
161 PRK09645 RNA polymerase sigma 27.5 11 0.00023 31.6 -1.7 47 240-296 118-165 (173)
162 PRK07037 extracytoplasmic-func 27.3 9.6 0.00021 31.4 -2.0 47 240-296 109-156 (163)
163 TIGR02846 spore_sigmaK RNA pol 27.0 11 0.00024 33.7 -1.8 53 239-296 173-225 (227)
164 PRK12545 RNA polymerase sigma 26.9 10 0.00023 33.1 -1.9 48 240-296 139-186 (201)
165 smart00109 C1 Protein kinase C 26.8 36 0.00077 22.6 1.1 28 95-128 13-40 (49)
166 PF01710 HTH_Tnp_IS630: Transp 26.1 36 0.00077 28.1 1.2 55 236-300 52-106 (119)
167 PRK12531 RNA polymerase sigma 25.9 12 0.00025 32.4 -1.8 49 238-296 139-188 (194)
168 cd01104 HTH_MlrA-CarA Helix-Tu 25.7 15 0.00032 26.5 -1.0 21 268-288 3-23 (68)
169 PF12123 Amidase02_C: N-acetyl 25.4 67 0.0015 23.5 2.4 19 241-259 24-42 (45)
170 PRK12532 RNA polymerase sigma 25.4 12 0.00025 32.2 -1.9 48 240-296 136-183 (195)
171 PRK09636 RNA polymerase sigma 25.1 20 0.00044 33.2 -0.5 50 240-298 115-164 (293)
172 PRK12513 RNA polymerase sigma 25.1 7 0.00015 33.5 -3.3 34 263-296 153-186 (194)
173 PRK12535 RNA polymerase sigma 24.9 13 0.00027 32.7 -1.8 49 238-296 131-180 (196)
174 PF05419 GUN4: GUN4-like ; In 24.9 44 0.00094 28.9 1.5 18 245-262 80-97 (132)
175 PF02954 HTH_8: Bacterial regu 24.8 53 0.0012 22.5 1.7 31 245-283 6-36 (42)
176 PF09832 DUF2059: Uncharacteri 24.5 37 0.00079 24.8 0.9 21 235-255 11-31 (64)
177 TIGR02479 FliA_WhiG RNA polyme 24.5 13 0.00027 33.1 -1.9 49 239-296 174-222 (224)
178 PRK12511 RNA polymerase sigma 24.5 12 0.00026 32.4 -1.9 47 240-296 111-158 (182)
179 smart00857 Resolvase Resolvase 24.4 59 0.0013 26.4 2.2 19 243-261 18-36 (148)
180 PF11761 CbiG_mid: Cobalamin b 24.4 68 0.0015 24.2 2.4 34 251-287 6-39 (93)
181 PF05099 TerB: Tellurite resis 24.4 1.1E+02 0.0024 24.8 3.8 49 235-283 85-136 (140)
182 TIGR02957 SigX4 RNA polymerase 24.3 21 0.00045 33.1 -0.5 50 239-298 107-157 (281)
183 PF02943 FeThRed_B: Ferredoxin 24.3 1.4E+02 0.0029 25.4 4.3 25 247-272 8-32 (108)
184 PHA01976 helix-turn-helix prot 24.3 39 0.00084 24.3 1.0 18 263-280 42-59 (67)
185 PF05077 DUF678: Protein of un 24.3 30 0.00065 27.9 0.4 10 112-121 56-65 (74)
186 PRK12515 RNA polymerase sigma 24.2 13 0.00027 31.9 -1.9 51 236-296 127-178 (189)
187 PF11976 Rad60-SLD: Ubiquitin- 24.0 89 0.0019 22.8 2.9 27 265-291 24-51 (72)
188 PRK02289 4-oxalocrotonate taut 23.9 1.9E+02 0.0041 21.0 4.5 34 241-288 12-45 (60)
189 PRK08301 sporulation sigma fac 23.9 14 0.00031 32.8 -1.6 52 239-295 177-228 (234)
190 PF01870 Hjc: Archaeal hollida 23.9 38 0.00082 27.4 0.9 20 238-257 48-67 (88)
191 cd04763 HTH_MlrA-like Helix-Tu 23.8 17 0.00037 26.6 -1.0 21 268-288 3-23 (68)
192 cd02949 TRX_NTR TRX domain, no 23.7 55 0.0012 25.0 1.8 47 244-290 30-78 (97)
193 PRK09647 RNA polymerase sigma 23.5 13 0.00029 32.9 -1.9 47 240-296 138-185 (203)
194 PRK13858 type IV secretion sys 23.4 1.3E+02 0.0029 27.0 4.3 39 234-276 24-62 (147)
195 PRK10360 DNA-binding transcrip 23.3 24 0.00052 28.8 -0.3 48 239-296 136-183 (196)
196 TIGR03541 reg_near_HchA LuxR f 23.0 20 0.00044 32.4 -0.9 49 238-296 169-217 (232)
197 cd08577 PI-PLCc_GDPD_SF_unchar 23.0 1.4E+02 0.0029 27.7 4.5 40 239-278 177-222 (228)
198 PHA01623 hypothetical protein 23.0 18 0.00038 27.1 -1.1 27 232-258 11-37 (56)
199 TIGR02943 Sig70_famx1 RNA poly 22.8 14 0.00031 31.9 -1.8 47 240-295 131-177 (188)
200 PRK12543 RNA polymerase sigma 22.7 15 0.00032 31.2 -1.7 46 240-295 117-163 (179)
201 PF07813 LTXXQ: LTXXQ motif fa 22.6 50 0.0011 25.0 1.4 17 235-251 82-98 (100)
202 PRK09641 RNA polymerase sigma 22.5 13 0.00028 31.2 -2.1 31 265-295 152-182 (187)
203 TIGR00721 tfx DNA-binding prot 22.5 23 0.00049 31.0 -0.6 47 239-295 5-51 (137)
204 PRK09637 RNA polymerase sigma 22.4 14 0.0003 31.9 -2.0 47 240-295 106-152 (181)
205 PF05291 Bystin: Bystin; Inte 22.3 67 0.0014 31.8 2.4 21 235-255 253-273 (301)
206 PRK08942 D,D-heptose 1,7-bisph 22.3 2.4E+02 0.0051 24.0 5.5 43 237-279 58-120 (181)
207 cd02417 Peptidase_C39_likeA A 22.1 1.7E+02 0.0037 22.7 4.3 44 235-284 17-60 (121)
208 cd02423 Peptidase_C39G A sub-f 22.1 1.8E+02 0.0038 22.7 4.4 44 235-284 22-66 (129)
209 PRK09651 RNA polymerase sigma 22.1 9.9 0.00021 32.2 -2.9 48 237-293 116-163 (172)
210 cd01896 DRG The developmentall 21.8 1.9E+02 0.0041 26.2 5.1 43 243-285 91-158 (233)
211 PRK12544 RNA polymerase sigma 21.8 15 0.00032 32.7 -2.0 48 239-296 147-195 (206)
212 TIGR02954 Sig70_famx3 RNA poly 21.5 17 0.00037 30.3 -1.5 47 240-296 119-166 (169)
213 TIGR00013 taut 4-oxalocrotonat 21.4 2.1E+02 0.0045 20.3 4.3 34 242-289 13-46 (63)
214 PRK08295 RNA polymerase factor 21.4 16 0.00034 31.4 -1.8 48 239-296 154-201 (208)
215 cd02419 Peptidase_C39C A sub-f 21.3 1.9E+02 0.004 22.7 4.4 44 235-284 22-65 (127)
216 COG3916 LasI N-acyl-L-homoseri 21.2 47 0.001 31.3 1.1 28 245-272 19-48 (209)
217 PF10925 DUF2680: Protein of u 21.2 77 0.0017 24.1 2.1 15 241-255 1-15 (59)
218 PRK05657 RNA polymerase sigma 21.0 18 0.00039 34.8 -1.7 52 240-296 262-313 (325)
219 PRK06930 positive control sigm 20.9 14 0.00031 32.6 -2.2 47 239-295 113-160 (170)
220 PRK00745 4-oxalocrotonate taut 20.9 1.9E+02 0.0041 20.5 4.0 34 242-289 13-46 (62)
221 PF01873 eIF-5_eIF-2B: Domain 20.9 36 0.00078 29.2 0.3 13 111-123 112-124 (125)
222 PRK12542 RNA polymerase sigma 20.8 15 0.00033 31.2 -2.0 50 237-296 119-169 (185)
223 PRK11552 putative DNA-binding 20.7 47 0.001 29.7 1.0 47 243-291 12-58 (225)
224 PRK09975 DNA-binding transcrip 20.6 35 0.00076 29.2 0.1 47 243-290 10-56 (213)
225 COG3413 Predicted DNA binding 20.2 79 0.0017 28.3 2.3 42 240-283 155-196 (215)
226 PF12802 MarR_2: MarR family; 20.1 51 0.0011 23.1 0.9 36 241-282 3-38 (62)
227 PF13565 HTH_32: Homeodomain-l 20.0 34 0.00073 25.2 -0.1 37 236-278 28-65 (77)
228 TIGR01610 phage_O_Nterm phage 20.0 99 0.0021 24.6 2.6 43 239-282 21-64 (95)
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=5.6e-38 Score=235.82 Aligned_cols=57 Identities=79% Similarity=1.492 Sum_probs=54.4
Q ss_pred ceEeehhhhhhhhcccCCceeccccccccC-CCCCCcccccccccccccccccccccC
Q 021941 76 NVIRYRECLKNHAACIGGNIFDGCGEFMPS-GDEGTLEALKCAACECHRNFHRKEIDG 132 (305)
Q Consensus 76 ~~v~Y~EClkNHAa~~Gg~a~DGCgEFmp~-~~~gt~~al~CaACgCHRnFHrke~~~ 132 (305)
..|+||||||||||+||||+||||+||||+ +++|++++|+||||||||||||||+++
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 368999999999999999999999999999 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=4.5e-38 Score=230.38 Aligned_cols=52 Identities=75% Similarity=1.407 Sum_probs=50.1
Q ss_pred eehhhhhhhhcccCCceecccccccc-CCCCCCcccccccccccccccccccc
Q 021941 79 RYRECLKNHAACIGGNIFDGCGEFMP-SGDEGTLEALKCAACECHRNFHRKEI 130 (305)
Q Consensus 79 ~Y~EClkNHAa~~Gg~a~DGCgEFmp-~~~~gt~~al~CaACgCHRnFHrke~ 130 (305)
+||||||||||+|||||||||||||| +++++++++|+||||||||||||||+
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 68899999999999999999999984
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=4.1e-27 Score=175.73 Aligned_cols=58 Identities=62% Similarity=1.131 Sum_probs=56.8
Q ss_pred CCccCcCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccc
Q 021941 234 KKRFRTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKN 291 (305)
Q Consensus 234 kKR~RTkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~ 291 (305)
+||+||+||+||+++|++|||++||||+++|+.+|++||.+|||+++||||||||||.
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 5999999999999999999999999999999999999999999999999999999985
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=99.20 E-value=2.5e-12 Score=91.60 Aligned_cols=57 Identities=26% Similarity=0.488 Sum_probs=53.7
Q ss_pred CccCcCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCC
Q 021941 235 KRFRTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVK 295 (305)
Q Consensus 235 KR~RTkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~k 295 (305)
||.||+||.+|++.|+++++. .++++.+.+++++.++||+...+++||+|+|.+.+|
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~----~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQE----NPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHH----SSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHH----hccccccccccccccccccccccccCHHHhHHHhCc
Confidence 789999999999999998887 799999999999999999999999999999988764
No 5
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.12 E-value=2e-11 Score=116.76 Aligned_cols=63 Identities=22% Similarity=0.310 Sum_probs=57.2
Q ss_pred CCCCCCccCcCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCC
Q 021941 230 FVLSKKRFRTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKN 296 (305)
Q Consensus 230 ~~~~kKR~RTkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK 296 (305)
+-.+.||.||++|+.|+|.|+..+.. ..|+-..++||+.+|+||..+|+||||||+|+|.|+-
T Consensus 163 gd~~nKRPRTTItAKqLETLK~AYn~----SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRL 225 (383)
T KOG4577|consen 163 GDASNKRPRTTITAKQLETLKQAYNT----SPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRL 225 (383)
T ss_pred cccccCCCcceeeHHHHHHHHHHhcC----CCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhh
Confidence 34467999999999999999998877 7999999999999999999999999999999997653
No 6
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.11 E-value=3.6e-11 Score=113.72 Aligned_cols=61 Identities=21% Similarity=0.396 Sum_probs=55.5
Q ss_pred CCCccCcCCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCCCC
Q 021941 233 SKKRFRTKFTQEQKDKMME-FAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKNKQ 298 (305)
Q Consensus 233 ~kKR~RTkFT~EQkekM~~-fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK~~ 298 (305)
.++||||.||..|+|+|++ |-|. +++|...+|-++..+.|.+..++|||||+|+||+|+..
T Consensus 140 kRRh~RTiFT~~Qle~LEkaFkea-----HYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek 201 (332)
T KOG0494|consen 140 KRRHFRTIFTSYQLEELEKAFKEA-----HYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEK 201 (332)
T ss_pred ccccccchhhHHHHHHHHHHHhhc-----cCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhh
Confidence 3466799999999999999 5555 99999999999999999999999999999999999854
No 7
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.05 E-value=1.4e-10 Score=106.93 Aligned_cols=64 Identities=19% Similarity=0.274 Sum_probs=57.5
Q ss_pred CCCCCCccCcCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCCC
Q 021941 230 FVLSKKRFRTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKNK 297 (305)
Q Consensus 230 ~~~~kKR~RTkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK~ 297 (305)
+..+.+|-||.||-+|+|.|+++++| .|++|..++|+++..|.|...++||||.|+|+|.++..
T Consensus 33 ~pRkqRRERTtFtr~QlevLe~LF~k----TqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq 96 (228)
T KOG2251|consen 33 GPRKQRRERTTFTRKQLEVLEALFAK----TQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQ 96 (228)
T ss_pred cchhcccccceecHHHHHHHHHHHHh----hcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhh
Confidence 34456899999999999999996666 69999999999999999999999999999999987653
No 8
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.03 E-value=7.4e-11 Score=106.36 Aligned_cols=64 Identities=27% Similarity=0.352 Sum_probs=58.9
Q ss_pred CCCCccCcCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCCCCC
Q 021941 232 LSKKRFRTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKNKQE 299 (305)
Q Consensus 232 ~~kKR~RTkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK~~~ 299 (305)
.+.||.||.||.||+.+|+..+|. .++---.+++++++.++|+..-+||||||+|-|+||..++
T Consensus 100 ~~~kr~RT~ft~~Ql~~LE~~F~~----~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e 163 (197)
T KOG0843|consen 100 MRPKRIRTAFTPEQLLKLEHAFEG----NQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQE 163 (197)
T ss_pred cCCCccccccCHHHHHHHHHHHhc----CCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHH
Confidence 367999999999999999999998 6888889999999999999999999999999999887655
No 9
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.01 E-value=3.5e-11 Score=101.16 Aligned_cols=60 Identities=23% Similarity=0.428 Sum_probs=56.2
Q ss_pred CCCccCcCCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCCC
Q 021941 233 SKKRFRTKFTQEQKDKMME-FAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKNK 297 (305)
Q Consensus 233 ~kKR~RTkFT~EQkekM~~-fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK~ 297 (305)
.-+|.||.||.-|+..|+. |||. +++|--.+|+++..|.|+...+||||||+|+|++|..
T Consensus 16 KQRRIRTTFTS~QLkELErvF~ET-----HYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQE 76 (125)
T KOG0484|consen 16 KQRRIRTTFTSAQLKELERVFAET-----HYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQE 76 (125)
T ss_pred HhhhhhhhhhHHHHHHHHHHHHhh-----cCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHH
Confidence 4589999999999999988 8888 9999999999999999999999999999999998864
No 10
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=98.90 E-value=4.9e-10 Score=106.27 Aligned_cols=58 Identities=28% Similarity=0.536 Sum_probs=53.3
Q ss_pred CccCcCCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCCC
Q 021941 235 KRFRTKFTQEQKDKMME-FAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKNK 297 (305)
Q Consensus 235 KR~RTkFT~EQkekM~~-fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK~ 297 (305)
||.||-||.||+++|++ |-|. .+--|..+|++++|+||...-+|+||||.|+|.||-.
T Consensus 247 KRPRTAFtaeQL~RLK~EF~en-----RYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsT 305 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQEN-----RYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKST 305 (342)
T ss_pred cCccccccHHHHHHHHHHHhhh-----hhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhcc
Confidence 89999999999999998 6555 7888999999999999999999999999999998853
No 11
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=98.86 E-value=1.4e-09 Score=76.52 Aligned_cols=56 Identities=25% Similarity=0.430 Sum_probs=51.4
Q ss_pred CccCcCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCC
Q 021941 235 KRFRTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTV 294 (305)
Q Consensus 235 KR~RTkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~ 294 (305)
|+.||.||.+|++.|+.++++ -.+++.+++++++.++|++...++.||+|.|.+.+
T Consensus 1 ~k~r~~~~~~~~~~L~~~f~~----~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 1 RRKRTSFTPEQLEELEKEFQK----NPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCCcCCHHHHHHHHHHHHh----CCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 577899999999999998887 67899999999999999999999999999998753
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=98.82 E-value=1.6e-09 Score=76.32 Aligned_cols=58 Identities=24% Similarity=0.471 Sum_probs=54.0
Q ss_pred CccCcCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCC
Q 021941 235 KRFRTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKN 296 (305)
Q Consensus 235 KR~RTkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK 296 (305)
++.|+.||.+|++.|+++++. ..+++..++++++.++||+...+++||.|.|.+.+++
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 467899999999999998888 7899999999999999999999999999999987764
No 13
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=98.62 E-value=2.4e-08 Score=96.55 Aligned_cols=61 Identities=21% Similarity=0.435 Sum_probs=53.6
Q ss_pred CCCccCcCCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCCCC
Q 021941 233 SKKRFRTKFTQEQKDKMME-FAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKNKQ 298 (305)
Q Consensus 233 ~kKR~RTkFT~EQkekM~~-fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK~~ 298 (305)
.-+|+||-||-||..+|+. |+.. .+-..-.+=|++..+.|.+-++||||||+|-|.|+...
T Consensus 180 qmRRYRTAFTReQIaRLEKEFyrE-----NYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRl 241 (408)
T KOG0844|consen 180 QMRRYRTAFTREQIARLEKEFYRE-----NYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRL 241 (408)
T ss_pred HHHHHHhhhhHHHHHHHHHHHHHh-----ccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhh
Confidence 3599999999999999987 7766 67777778899999999999999999999999888753
No 14
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=98.59 E-value=7.6e-08 Score=94.94 Aligned_cols=63 Identities=14% Similarity=0.303 Sum_probs=59.4
Q ss_pred CCCCccCcCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCCCC
Q 021941 232 LSKKRFRTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKNKQ 298 (305)
Q Consensus 232 ~~kKR~RTkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK~~ 298 (305)
++|||.||.|+.-.|..|+.+|++ .+|+.-++|-+++.++.+.|.|++|||=|+|+|.|+-.+
T Consensus 292 ~RkRKKRTSie~~vr~aLE~~F~~----npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 292 SRKRKKRTSIEVNVRGALEKHFLK----NPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred ccccccccceeHHHHHHHHHHHHh----CCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 378889999999999999999999 899999999999999999999999999999999988655
No 15
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=98.54 E-value=3.7e-08 Score=85.63 Aligned_cols=63 Identities=22% Similarity=0.228 Sum_probs=58.8
Q ss_pred CCCCCccCcCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCCC
Q 021941 231 VLSKKRFRTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKNK 297 (305)
Q Consensus 231 ~~~kKR~RTkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK~ 297 (305)
...+||.||+||.+|+|.++..+++ .+++|...+++++..+.++...|+|||+|.|++++|..
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~----~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEK----VHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcC----CCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 4567999999999999999999999 49999999999999999999999999999999998865
No 16
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=98.34 E-value=2.1e-07 Score=86.72 Aligned_cols=64 Identities=19% Similarity=0.194 Sum_probs=56.8
Q ss_pred CCCCCCccCcCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCCC
Q 021941 230 FVLSKKRFRTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKNK 297 (305)
Q Consensus 230 ~~~~kKR~RTkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK~ 297 (305)
+..+|||.||.|+.-|.-.|+.-+|. -.+-...++.-+++.+-|++--+|+||||+|+|||++-
T Consensus 100 g~~RKKktRTvFSraQV~qLEs~Fe~----krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~ 163 (268)
T KOG0485|consen 100 GDDRKKKTRTVFSRAQVFQLESTFEL----KRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQY 163 (268)
T ss_pred cccccccchhhhhHHHHHHHHHHHHH----HhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHH
Confidence 55689999999999999999987776 24567788999999999999999999999999999983
No 17
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=98.30 E-value=3.6e-07 Score=87.32 Aligned_cols=61 Identities=18% Similarity=0.268 Sum_probs=54.9
Q ss_pred CCCCccCcCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCC
Q 021941 232 LSKKRFRTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKN 296 (305)
Q Consensus 232 ~~kKR~RTkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK 296 (305)
..+|+-||.||..|+..|+.-||+ -.+--..++.+++..+||+--=+|+||||+|-||||.
T Consensus 170 kK~RksRTaFT~~Ql~~LEkrF~~----QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq 230 (309)
T KOG0488|consen 170 KKRRKSRTAFSDHQLFELEKRFEK----QKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQ 230 (309)
T ss_pred cccccchhhhhHHHHHHHHHHHHH----hhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHH
Confidence 445778999999999999999999 3447788899999999999999999999999999985
No 18
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=98.27 E-value=1.7e-07 Score=87.03 Aligned_cols=65 Identities=17% Similarity=0.170 Sum_probs=55.3
Q ss_pred CCCCccCcCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCCCCCC
Q 021941 232 LSKKRFRTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKNKQEP 300 (305)
Q Consensus 232 ~~kKR~RTkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK~~~~ 300 (305)
+..||-||.||-+|+-.|+.=|.- ..+--...+-|++.-+.|+.+=|||||||+|.|+||.....
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhf----N~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~ 221 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHF----NKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAK 221 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhcc----ccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhccc
Confidence 447999999999999999873333 36788889999999999999999999999999999765443
No 19
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=98.25 E-value=8.9e-07 Score=82.65 Aligned_cols=58 Identities=17% Similarity=0.267 Sum_probs=54.0
Q ss_pred CccCcCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCC
Q 021941 235 KRFRTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKN 296 (305)
Q Consensus 235 KR~RTkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK 296 (305)
+..||+|+.-|+..|..=|++ .|+---.++.+|+..|||+.--+|+||||+|-|+||-
T Consensus 123 RKPRTIYSS~QLqaL~rRFQk----TQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl 180 (245)
T KOG0850|consen 123 RKPRTIYSSLQLQALNRRFQQ----TQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKL 180 (245)
T ss_pred cCCcccccHHHHHHHHHHHhh----cchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHH
Confidence 668999999999999998888 7998888999999999999999999999999998874
No 20
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=98.23 E-value=7.1e-07 Score=78.29 Aligned_cols=66 Identities=15% Similarity=0.095 Sum_probs=59.0
Q ss_pred CCCCCCccCcCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCCCCC
Q 021941 230 FVLSKKRFRTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKNKQE 299 (305)
Q Consensus 230 ~~~~kKR~RTkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK~~~ 299 (305)
.++..|+.|+.-|.+|+..|+..++. -++|+-....++...++|+.+.+|+||||.|++.+++...
T Consensus 47 ~s~~~~~~r~R~t~~Q~~vL~~~F~i----~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 47 GSSPPKSKRRRTTDEQLMVLEREFEI----NPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred CCCcCcccceechHHHHHHHHHHhcc----CCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence 34456788888899999999999999 8999999999999999999999999999999998877543
No 21
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=98.16 E-value=1.1e-06 Score=81.36 Aligned_cols=57 Identities=23% Similarity=0.405 Sum_probs=53.1
Q ss_pred CCccCcCCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCC
Q 021941 234 KKRFRTKFTQEQKDKMME-FAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVK 295 (305)
Q Consensus 234 kKR~RTkFT~EQkekM~~-fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~k 295 (305)
.+..||-||..|+-.|+. |=|| |+-..+++.+|..-+-|+.--+|+||||+|+|.|+
T Consensus 144 nRkPRtPFTtqQLlaLErkfrek-----qYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKR 201 (246)
T KOG0492|consen 144 NRKPRTPFTTQQLLALERKFREK-----QYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKR 201 (246)
T ss_pred CCCCCCCCCHHHHHHHHHHHhHh-----hhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHH
Confidence 367899999999999988 8888 99999999999999999999999999999999775
No 22
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=98.03 E-value=2e-06 Score=83.35 Aligned_cols=62 Identities=19% Similarity=0.311 Sum_probs=57.2
Q ss_pred CCCCccCcCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCCC
Q 021941 232 LSKKRFRTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKNK 297 (305)
Q Consensus 232 ~~kKR~RTkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK~ 297 (305)
...+|-||+||++|.+.+.+.+++ .+++|-..+++++++||+..-.|+|||.|.|++++|..
T Consensus 174 ~~~rr~rtsft~~Q~~~le~~f~r----t~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 174 RGGRRNRTSFSPSQLEALEECFQR----TPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred ccccccccccccchHHHHHHHhcC----CCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence 345677999999999999999999 78999999999999999999999999999999988875
No 23
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=98.02 E-value=2.2e-06 Score=83.14 Aligned_cols=62 Identities=18% Similarity=0.308 Sum_probs=57.9
Q ss_pred CCCccCcCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCCCC
Q 021941 233 SKKRFRTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKNKQ 298 (305)
Q Consensus 233 ~kKR~RTkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK~~ 298 (305)
+++|-||-||..|+..++..+.+ ..++|-..+|+++.=+.++...+.|||.|+|+||+|+..
T Consensus 111 KqrrQrthFtSqqlqele~tF~r----NrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrEr 172 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQR----NRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRER 172 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhh----ccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhh
Confidence 45799999999999999999988 788999999999999999999999999999999999853
No 24
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=98.02 E-value=5.9e-06 Score=79.60 Aligned_cols=65 Identities=15% Similarity=0.330 Sum_probs=56.3
Q ss_pred CCCCCCccCcCCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCCCCC
Q 021941 230 FVLSKKRFRTKFTQEQKDKMME-FAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKNKQE 299 (305)
Q Consensus 230 ~~~~kKR~RTkFT~EQkekM~~-fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK~~~ 299 (305)
+..+|||-|--||+-|-=.|+. |-.. .+-..-++|++++.|.|+.-=+|+||||+|.|-||+...
T Consensus 149 ~~~~kRKrRVLFSqAQV~ELERRFrqQ-----RYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~d 214 (307)
T KOG0842|consen 149 GKRKKRKRRVLFSQAQVYELERRFRQQ-----RYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKD 214 (307)
T ss_pred ccccccccccccchhHHHHHHHHHHhh-----hccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhh
Confidence 4567888899999999999888 6554 568889999999999999999999999999999887543
No 25
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=97.87 E-value=6.2e-06 Score=79.81 Aligned_cols=64 Identities=19% Similarity=0.375 Sum_probs=56.4
Q ss_pred CCCCCccCcCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCCCC
Q 021941 231 VLSKKRFRTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKNKQ 298 (305)
Q Consensus 231 ~~~kKR~RTkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK~~ 298 (305)
.+-|||.||.+-+-.|..|++|+.- -.++..+-|..+++++.|++.|++|||=|.|+|.|+...
T Consensus 306 ~~ekKRKRTSIAAPEKRsLEayFav----QPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~ 369 (385)
T KOG1168|consen 306 GGEKKRKRTSIAAPEKRSLEAYFAV----QPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKR 369 (385)
T ss_pred ccccccccccccCcccccHHHHhcc----CCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhh
Confidence 4569999999999999999997665 367888999999999999999999999999999877543
No 26
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.85 E-value=5.3e-06 Score=72.20 Aligned_cols=64 Identities=27% Similarity=0.427 Sum_probs=57.5
Q ss_pred CCCCCCccCcCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCCC
Q 021941 230 FVLSKKRFRTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKNK 297 (305)
Q Consensus 230 ~~~~kKR~RTkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK~ 297 (305)
.....+|.||.|+..|.+.+...+.. ..+++...+++++.++|+..+|++|||+|.+.+.+++.
T Consensus 149 ~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~ 212 (235)
T KOG0490|consen 149 SNKKPRRPRTTFTENQLEVLETVFRA----TPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHK 212 (235)
T ss_pred CccccCCCccccccchhHhhhhcccC----CCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhc
Confidence 34567999999999999999997766 79999999999999999999999999999999987753
No 27
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=97.67 E-value=1.8e-05 Score=72.15 Aligned_cols=57 Identities=21% Similarity=0.345 Sum_probs=48.8
Q ss_pred cCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCCCCC
Q 021941 239 TKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKNKQE 299 (305)
Q Consensus 239 TkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK~~~ 299 (305)
-+||.||...|+.-++- -.+-.-....+++.++|+..+-++|||||+|+++|.|..+
T Consensus 55 ~Rlt~eQ~~~LE~~F~~----~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE 111 (198)
T KOG0483|consen 55 RRLTSEQVKFLEKSFES----EKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLE 111 (198)
T ss_pred ccccHHHHHHhHHhhcc----ccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhh
Confidence 46999999999885555 3666777899999999999999999999999999988643
No 28
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=97.61 E-value=7.9e-05 Score=82.50 Aligned_cols=63 Identities=17% Similarity=0.348 Sum_probs=55.0
Q ss_pred CCCCCccCcCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCCC
Q 021941 231 VLSKKRFRTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKNK 297 (305)
Q Consensus 231 ~~~kKR~RTkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK~ 297 (305)
...+++.||.|+.+|+..|+.|.++ --.+-+++.|.+-..|++..+|++|||+|+|.+.+|-.
T Consensus 900 ~~~r~a~~~~~~d~qlk~i~~~~~~----q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~ 962 (1406)
T KOG1146|consen 900 GMGRRAYRTQESDLQLKIIKACYEA----QRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAK 962 (1406)
T ss_pred hhhhhhhccchhHHHHHHHHHHHhh----ccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhh
Confidence 4567999999999999999999999 33455678888999999999999999999999987753
No 29
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=97.46 E-value=3.9e-05 Score=72.07 Aligned_cols=63 Identities=19% Similarity=0.248 Sum_probs=57.2
Q ss_pred CCCCCccCcCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCCC
Q 021941 231 VLSKKRFRTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKNK 297 (305)
Q Consensus 231 ~~~kKR~RTkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK~ 297 (305)
-++||--|-+|+-.|+..++.-+|. .++.-..++.+++.++|....-+||||||+|-||+||.
T Consensus 164 dG~rk~srPTf~g~qi~~le~~feq----tkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkh 226 (288)
T KOG0847|consen 164 NGQRKQSRPTFTGHQIYQLERKFEQ----TKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKH 226 (288)
T ss_pred CccccccCCCccchhhhhhhhhhhh----hhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhh
Confidence 4678889999999999999997777 67888889999999999999999999999999999984
No 30
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=97.33 E-value=0.00016 Score=74.31 Aligned_cols=61 Identities=13% Similarity=0.218 Sum_probs=55.2
Q ss_pred CCCCCCCccCcCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccC
Q 021941 229 PFVLSKKRFRTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNT 293 (305)
Q Consensus 229 ~~~~~kKR~RTkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~ 293 (305)
......||.|+.||++||+.|.++|+. .++++.++.+.+...+||+..++.=||+|.|-+.
T Consensus 415 d~~~~~KKPRlVfTd~QkrTL~aiFke----~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 415 DKMLQTKKPRLVFTDIQKRTLQAIFKE----NKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred cccccCCCceeeecHHHHHHHHHHHhc----CCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 334556999999999999999998887 6899999999999999999999999999998873
No 31
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=97.13 E-value=0.00042 Score=67.09 Aligned_cols=59 Identities=17% Similarity=0.275 Sum_probs=48.0
Q ss_pred CCCCccCcCCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCCC
Q 021941 232 LSKKRFRTKFTQEQKDKMME-FAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKNK 297 (305)
Q Consensus 232 ~~kKR~RTkFT~EQkekM~~-fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK~ 297 (305)
.+|| |=-.|..|.-.|+. |+=. .+-..+-+-|+.+.+.|+.|=+|+||||+|-|.||-.
T Consensus 235 ~RKK--RcPYTK~QtlELEkEFlfN-----~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~ 294 (308)
T KOG0487|consen 235 GRKK--RCPYTKHQTLELEKEFLFN-----MYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVN 294 (308)
T ss_pred cccc--cCCchHHHHHHHHHHHHHH-----HHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhh
Confidence 3444 46778888888776 5544 4777888999999999999999999999999988854
No 32
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=97.06 E-value=0.00015 Score=69.59 Aligned_cols=60 Identities=18% Similarity=0.417 Sum_probs=46.1
Q ss_pred CCCCCccCcCCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCC
Q 021941 231 VLSKKRFRTKFTQEQKDKMME-FAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVK 295 (305)
Q Consensus 231 ~~~kKR~RTkFT~EQkekM~~-fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~k 295 (305)
...|-++|-..|..|+=.|+. |--. .+.--..--||+..+||++|-+|+||||+|+|.+|
T Consensus 196 tRTkDKYRvVYTDhQRLELEKEfh~S-----ryITirRKSELA~~LgLsERQVKIWFQNRRAKERK 256 (317)
T KOG0848|consen 196 TRTKDKYRVVYTDHQRLELEKEFHTS-----RYITIRRKSELAATLGLSERQVKIWFQNRRAKERK 256 (317)
T ss_pred eecccceeEEecchhhhhhhhhhccc-----cceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHH
Confidence 345677888899999988776 5433 23333445689999999999999999999998654
No 33
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=97.05 E-value=4.9e-05 Score=68.69 Aligned_cols=61 Identities=15% Similarity=0.278 Sum_probs=52.8
Q ss_pred CCCCccCcCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCC
Q 021941 232 LSKKRFRTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKN 296 (305)
Q Consensus 232 ~~kKR~RTkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK 296 (305)
.+++..||.|+.-|+.-+.+-+|+ -.+-.-.+++|+++-++|+..-+|.||||+|-|+||-
T Consensus 98 ~~r~K~Rtvfs~~ql~~l~~rFe~----QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~ 158 (194)
T KOG0491|consen 98 CRRRKARTVFSDPQLSGLEKRFER----QRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQ 158 (194)
T ss_pred HHhhhhcccccCccccccHHHHhh----hhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHH
Confidence 345778999999999999998886 2346778999999999999999999999999988763
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=94.93 E-value=0.0076 Score=44.62 Aligned_cols=47 Identities=17% Similarity=0.306 Sum_probs=34.4
Q ss_pred ccCcCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccc
Q 021941 236 RFRTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNK 290 (305)
Q Consensus 236 R~RTkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK 290 (305)
|-|+.||+|+|..+...+.. +...|.++|.+.||++.+|--|..--+
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~--------~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLE--------SGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp -SS----HHHHHHHHHHHHH--------HHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHH--------CCCceEeeecccccccccccHHHHHHh
Confidence 45789999999999998844 246899999999999999999986554
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=94.40 E-value=0.026 Score=41.18 Aligned_cols=47 Identities=26% Similarity=0.357 Sum_probs=37.3
Q ss_pred CccCcCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccc
Q 021941 235 KRFRTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNK 290 (305)
Q Consensus 235 KR~RTkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK 290 (305)
||.|+.+|-+||-++...+|. .. .+.++|.+.||.+.++.-|+.|..
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 788999999999999999998 22 688999999999999999998854
No 36
>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=89.53 E-value=0.28 Score=28.82 Aligned_cols=39 Identities=23% Similarity=0.372 Sum_probs=29.9
Q ss_pred cCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEec
Q 021941 239 TKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWM 286 (305)
Q Consensus 239 TkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWm 286 (305)
.+|+.+++..+....+. || .+.++|.++||++.+|..|+
T Consensus 4 ~~~~~~~~~~i~~~~~~-~~--------s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 4 PKLTPEQIEEARRLLAA-GE--------SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CcCCHHHHHHHHHHHHc-CC--------CHHHHHHHHCCCHHHHHHhC
Confidence 45788888888776543 32 67789999999999888775
No 37
>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=88.65 E-value=0.065 Score=37.50 Aligned_cols=33 Identities=12% Similarity=0.382 Sum_probs=27.0
Q ss_pred ccCCCCHHHHHHHHHHhCCCCceEEEecccccc
Q 021941 259 RFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKN 291 (305)
Q Consensus 259 Riqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~ 291 (305)
.-.+|.+++.++||.++|+++.-+.-||-|.|.
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 346889999999999999999999999999874
No 38
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=81.56 E-value=0.84 Score=36.77 Aligned_cols=47 Identities=19% Similarity=0.307 Sum_probs=39.1
Q ss_pred CcCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCC-CCceEEEeccccccc
Q 021941 238 RTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGV-KRHVFKVWMHNNKNN 292 (305)
Q Consensus 238 RTkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV-~r~V~KVWmhNnK~~ 292 (305)
|.+||.|-|..+-+++..- ...|.+.|++.|| ....|..|+..-...
T Consensus 5 ~r~~s~EfK~~iv~~~~~~--------g~sv~~vAr~~gv~~~~~l~~W~~~~~~~ 52 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRG--------GDTVSEVAREFGIVSATQLYKWRIQLQKG 52 (116)
T ss_pred cccCCHHHHHHHHHHHHhc--------CccHHHHHHHhCCCChHHHHHHHHHHHHc
Confidence 8999999999999988761 1279999999995 999999999854443
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=80.36 E-value=0.37 Score=31.59 Aligned_cols=46 Identities=9% Similarity=0.226 Sum_probs=35.1
Q ss_pred cCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccC
Q 021941 239 TKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNT 293 (305)
Q Consensus 239 TkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~ 293 (305)
..++++|++.+..++.. +...+++|.++|++..+++.|.+.-+.++
T Consensus 9 ~~l~~~~~~~~~~~~~~---------~~~~~~ia~~~~~s~~~i~~~~~~~~~~l 54 (55)
T cd06171 9 DKLPEREREVILLRFGE---------GLSYEEIAEILGISRSTVRQRLHRALKKL 54 (55)
T ss_pred HhCCHHHHHHHHHHHhc---------CCCHHHHHHHHCcCHHHHHHHHHHHHHHc
Confidence 45788898888776632 23567889999999999999988766544
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=78.73 E-value=0.5 Score=33.00 Aligned_cols=39 Identities=18% Similarity=0.365 Sum_probs=28.7
Q ss_pred cCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEec
Q 021941 239 TKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWM 286 (305)
Q Consensus 239 TkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWm 286 (305)
.+++.+|.+.+.+..+. . .-+.++|.++||+|.+|.=|+
T Consensus 4 ~~~~~~~~~~i~~l~~~------G---~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 4 PKLSKEQIEEIKELYAE------G---MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSSSHCCHHHHHHHHHT------T-----HHHHHHHTTS-HHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHC------C---CCHHHHHHHHCcCHHHHHHHH
Confidence 46888888888887665 2 578999999999999876554
No 41
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=76.43 E-value=0.89 Score=39.62 Aligned_cols=44 Identities=18% Similarity=0.423 Sum_probs=34.7
Q ss_pred CCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecc
Q 021941 240 KFTQEQKDKMME-FAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMH 287 (305)
Q Consensus 240 kFT~EQkekM~~-fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmh 287 (305)
.||+||+++|.. .-|- +..+....+.+++.++|++|.++++.+.
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 599999999987 4444 3456677899999999999998876543
No 42
>PF12651 RHH_3: Ribbon-helix-helix domain
Probab=73.16 E-value=3.1 Score=29.50 Aligned_cols=40 Identities=23% Similarity=0.390 Sum_probs=32.4
Q ss_pred CCccCcCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHH
Q 021941 234 KKRFRTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCA 273 (305)
Q Consensus 234 kKR~RTkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~ 273 (305)
||||-+.++.|+.++|.++|++.|-.+.+-=+++|+.|-+
T Consensus 2 r~r~t~~l~~el~~~L~~ls~~t~i~~S~Ll~eAle~~l~ 41 (44)
T PF12651_consen 2 RKRFTFSLDKELYEKLKELSEETGIPKSKLLREALEDYLE 41 (44)
T ss_pred ceEEEEecCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 7899999999999999999999876665555566666644
No 43
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=70.99 E-value=4.7 Score=39.51 Aligned_cols=61 Identities=13% Similarity=0.277 Sum_probs=51.3
Q ss_pred CccCcCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCC
Q 021941 235 KRFRTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKN 296 (305)
Q Consensus 235 KR~RTkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK 296 (305)
+|.|-.|+..-.|.|.+++-. .-...++.|++-++++.+-||+..-+--||-|.|-.++|.
T Consensus 189 rRKRRNFsK~aTeiLneyF~~-h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~ 249 (334)
T KOG0774|consen 189 RRKRRNFSKQATEILNEYFYS-HLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKN 249 (334)
T ss_pred HHhhcccchhHHHHHHHHHHH-hcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhh
Confidence 677889999999999995543 1234568899999999999999999999999999888875
No 44
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=65.92 E-value=7.1 Score=37.25 Aligned_cols=63 Identities=19% Similarity=0.196 Sum_probs=51.8
Q ss_pred CCCCccCcCCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCC
Q 021941 232 LSKKRFRTKFTQEQKDKMME-FAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKN 296 (305)
Q Consensus 232 ~~kKR~RTkFT~EQkekM~~-fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK 296 (305)
..++|.+..|-.+...+|+. +++-+-|- ++.+.....++.++||++.=+.-||-|.|-+..|-
T Consensus 237 ~~~~r~~~~lP~~a~~ilr~Wl~~h~~~P--YPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p 300 (342)
T KOG0773|consen 237 QSKWRPQRGLPKEAVSILRAWLFEHLLHP--YPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKP 300 (342)
T ss_pred cCCCCCCCCCCHHHHHHHHHHHHHhccCC--CCcchhccccchhcCCCcccCCchhhhcccccCCc
Confidence 45788889999999999999 77776654 45555555999999999999999999999876653
No 45
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=65.75 E-value=6 Score=38.84 Aligned_cols=45 Identities=9% Similarity=0.207 Sum_probs=37.6
Q ss_pred HHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCC
Q 021941 246 KDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTV 294 (305)
Q Consensus 246 kekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~ 294 (305)
+..|++++-+ ..++...+-.++++.+||+.--+--||.|+|++-+
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 4456666665 68899999999999999998888889999998865
No 46
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=65.65 E-value=2.7 Score=34.73 Aligned_cols=43 Identities=16% Similarity=0.234 Sum_probs=33.9
Q ss_pred CcCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccc
Q 021941 238 RTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHN 288 (305)
Q Consensus 238 RTkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhN 288 (305)
|.+||.|+|..+...+-. +...|.++|.+.||+..+|--|..-
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 567999999877665444 2336788999999999999999654
No 47
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=64.46 E-value=3.4 Score=45.29 Aligned_cols=52 Identities=13% Similarity=0.351 Sum_probs=40.1
Q ss_pred CCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCC
Q 021941 240 KFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKN 296 (305)
Q Consensus 240 kFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK 296 (305)
-|++- .+.|++++.. .--+.++++..|+..|||...|+|+||.|.+.....-
T Consensus 563 ~~~~p-~sllkayyal----n~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv 614 (1007)
T KOG3623|consen 563 QFNHP-TSLLKAYYAL----NGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSV 614 (1007)
T ss_pred ccCCc-HHHHHHHHHh----cCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhh
Confidence 34444 5666665444 3568889999999999999999999999999875543
No 48
>PRK09480 slmA division inhibitor protein; Provisional
Probab=62.52 E-value=4.7 Score=33.76 Aligned_cols=47 Identities=13% Similarity=0.162 Sum_probs=37.7
Q ss_pred HHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccc
Q 021941 243 QEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNK 290 (305)
Q Consensus 243 ~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK 290 (305)
.+.++++.+-|.++=+.-.. +...++++|.+.||++.+|=-+|.|..
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 77788888877775444335 778999999999999999999998843
No 49
>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=62.51 E-value=6.3 Score=29.30 Aligned_cols=40 Identities=15% Similarity=0.321 Sum_probs=30.6
Q ss_pred CCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceE
Q 021941 241 FTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVF 282 (305)
Q Consensus 241 FT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~ 282 (305)
+|..|++.|....+. |+= ..|.+..+++++.++||++.+|
T Consensus 1 LT~~Q~e~L~~A~~~-GYf-d~PR~~tl~elA~~lgis~st~ 40 (53)
T PF04967_consen 1 LTDRQREILKAAYEL-GYF-DVPRRITLEELAEELGISKSTV 40 (53)
T ss_pred CCHHHHHHHHHHHHc-CCC-CCCCcCCHHHHHHHhCCCHHHH
Confidence 688999997765554 653 3455678999999999998765
No 50
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=60.42 E-value=2.3 Score=37.73 Aligned_cols=56 Identities=21% Similarity=0.340 Sum_probs=36.3
Q ss_pred CCccCcCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccc
Q 021941 234 KKRFRTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNK 290 (305)
Q Consensus 234 kKR~RTkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK 290 (305)
.|+.--++|.+|+..-+-+++.- .-+-..++...++++.++||++.+|--|++-++
T Consensus 4 ~~~le~~L~~~Q~kAa~ll~~ne-~~~~~~~r~T~~eiAee~Gis~~tLYrWr~~~~ 59 (142)
T PF13022_consen 4 LKELEAKLTLQQRKAAQLLVENE-LMPENGERRTQAEIAEEVGISRSTLYRWRQQNK 59 (142)
T ss_dssp HHHHHTTS-HHHHHHHHHHHHHH-HS------S-HHHHHHHHTS-HHHHHHHHHH-H
T ss_pred HHHHHHHcCHHHHHHHHHHHHHH-HhhhccccchHHHHHHHhCCCHHHHHHHHhcCH
Confidence 45566789999999777766650 001112445789999999999999999998666
No 51
>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=58.65 E-value=1.6 Score=30.49 Aligned_cols=43 Identities=7% Similarity=0.151 Sum_probs=29.3
Q ss_pred CCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccc
Q 021941 240 KFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKN 291 (305)
Q Consensus 240 kFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~ 291 (305)
+++++|++.+.-+.. +....+++|..+|++..++++|++.-|.
T Consensus 10 ~L~~~~r~i~~l~~~---------~g~s~~eIa~~l~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 10 QLPERQREIFLLRYF---------QGMSYAEIAEILGISESTVKRRLRRARK 52 (54)
T ss_dssp CS-HHHHHHHHHHHT---------S---HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHH---------HCcCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence 456777777665332 3457889999999999999999987654
No 52
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=56.58 E-value=2.7 Score=28.13 Aligned_cols=45 Identities=16% Similarity=0.280 Sum_probs=33.7
Q ss_pred CCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCC
Q 021941 240 KFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTV 294 (305)
Q Consensus 240 kFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~ 294 (305)
.+|.+|++.+..+++ |+ ..++.|.++||++.+++.|++.-+.+++
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 5688999999999999999887666554
No 53
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=56.01 E-value=1.6 Score=30.51 Aligned_cols=42 Identities=12% Similarity=0.257 Sum_probs=20.0
Q ss_pred CcCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccc
Q 021941 238 RTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHN 288 (305)
Q Consensus 238 RTkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhN 288 (305)
...||.+|+..+..+-+ ...-+.++|.++|+++.++--|+..
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 35799999999888743 2346778999999999887655543
No 54
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=55.76 E-value=2.5 Score=37.26 Aligned_cols=51 Identities=20% Similarity=0.270 Sum_probs=33.1
Q ss_pred CCccCcCCCHHHHHHHHHHHHHhCCccCCCCH---HHHHHHHHHhCCCCceEEEecccc
Q 021941 234 KKRFRTKFTQEQKDKMMEFAEKVGWRFQKQDD---DQVDKFCAEVGVKRHVFKVWMHNN 289 (305)
Q Consensus 234 kKR~RTkFT~EQkekM~~fAEklGWRiqk~de---~~ve~fC~eiGV~r~V~KVWmhNn 289 (305)
++|.|-.| +.|.++.+.+|++|..-.+ -..++|+..+||++.++.-|-.+.
T Consensus 53 ~~~~~~~~-----d~~~~l~~~~g~~Ir~~Re~~glSqeeLA~~lgvs~s~IsriE~G~ 106 (154)
T TIGR00270 53 VKRKRRKI-----DTTEELVEDYGIIIRREREKRGWSQEQLAKKIQEKESLIKKIENAE 106 (154)
T ss_pred CCCCCCcc-----chHHHHHHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCC
Confidence 34444567 2344555555555654322 357899999999999998887654
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=54.72 E-value=2.2 Score=34.92 Aligned_cols=47 Identities=6% Similarity=0.114 Sum_probs=38.0
Q ss_pred cCCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCC
Q 021941 239 TKFTQEQKDKMME-FAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVK 295 (305)
Q Consensus 239 TkFT~EQkekM~~-fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~k 295 (305)
.+++++|++.+.- |.+. ...+++|..+||++.+++++++.-|.++++
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 5688888888776 4433 356889999999999999999998888765
No 56
>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=54.10 E-value=8.9 Score=33.39 Aligned_cols=18 Identities=28% Similarity=0.254 Sum_probs=13.3
Q ss_pred cCcCCCHHHHHHHHHHHH
Q 021941 237 FRTKFTQEQKDKMMEFAE 254 (305)
Q Consensus 237 ~RTkFT~EQkekM~~fAE 254 (305)
.++.||+.|+++|+.+-|
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 789999999999998754
No 57
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=53.53 E-value=4.2 Score=27.94 Aligned_cols=38 Identities=18% Similarity=0.646 Sum_probs=21.8
Q ss_pred HHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccc
Q 021941 243 QEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNN 289 (305)
Q Consensus 243 ~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNn 289 (305)
.+++..+..+... || -+.++|..+||++.++.-|+..-
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 4555555555544 55 46899999999999999998653
No 58
>PRK02220 4-oxalocrotonate tautomerase; Provisional
Probab=51.83 E-value=27 Score=24.89 Aligned_cols=34 Identities=15% Similarity=0.223 Sum_probs=25.4
Q ss_pred CHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccc
Q 021941 242 TQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNN 289 (305)
Q Consensus 242 T~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNn 289 (305)
|.|||++|.+ . .-+.++..+|+++.-+.|++..+
T Consensus 13 s~eqk~~l~~---~-----------it~~l~~~~~~p~~~v~V~i~e~ 46 (61)
T PRK02220 13 TEEQLKALVK---D-----------VTAAVSKNTGAPAEHIHVIINEM 46 (61)
T ss_pred CHHHHHHHHH---H-----------HHHHHHHHhCcChhhEEEEEEEe
Confidence 7999988764 2 45568999999777777776544
No 59
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=51.61 E-value=2.6 Score=36.32 Aligned_cols=50 Identities=10% Similarity=0.052 Sum_probs=38.4
Q ss_pred cCCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCCCC
Q 021941 239 TKFTQEQKDKMME-FAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKNKQ 298 (305)
Q Consensus 239 TkFT~EQkekM~~-fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK~~ 298 (305)
.+++++|++.+.- |.+. ...+++++++||+..++|+|++.-|.++++.-.
T Consensus 141 ~~L~~~~r~vl~l~~~~~----------~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l~ 191 (194)
T PRK09646 141 DALTDTQRESVTLAYYGG----------LTYREVAERLAVPLGTVKTRMRDGLIRLRDCLG 191 (194)
T ss_pred HhCCHHHHHHHHHHHHcC----------CCHHHHHHHhCCChHhHHHHHHHHHHHHHHHhc
Confidence 3577777777654 3222 357899999999999999999999998877643
No 60
>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=51.51 E-value=4 Score=26.70 Aligned_cols=25 Identities=16% Similarity=0.392 Sum_probs=21.5
Q ss_pred HHHHHHHhCCCCceEEEeccccccc
Q 021941 268 VDKFCAEVGVKRHVFKVWMHNNKNN 292 (305)
Q Consensus 268 ve~fC~eiGV~r~V~KVWmhNnK~~ 292 (305)
++++|..+||++.+|.-|..+.+-.
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~~~ 27 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGKLK 27 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCCCC
Confidence 5789999999999999999876643
No 61
>PHA02893 hypothetical protein; Provisional
Probab=51.10 E-value=5.6 Score=32.82 Aligned_cols=11 Identities=36% Similarity=0.812 Sum_probs=8.8
Q ss_pred ccccccccccc
Q 021941 111 LEALKCAACEC 121 (305)
Q Consensus 111 ~~al~CaACgC 121 (305)
...|.|+|||-
T Consensus 67 ~~tL~CaACGS 77 (88)
T PHA02893 67 NSNIKCIACGS 77 (88)
T ss_pred CCceeehhhch
Confidence 35799999983
No 62
>PRK00118 putative DNA-binding protein; Validated
Probab=50.70 E-value=2.4 Score=35.39 Aligned_cols=46 Identities=15% Similarity=0.164 Sum_probs=34.3
Q ss_pred CCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCC
Q 021941 240 KFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTV 294 (305)
Q Consensus 240 kFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~ 294 (305)
++++.|++.+.-+... +..+.++|..+||++.+++.|++.-+.+.+
T Consensus 17 ~L~ekqRevl~L~y~e---------g~S~~EIAe~lGIS~~TV~r~L~RArkkLr 62 (104)
T PRK00118 17 LLTEKQRNYMELYYLD---------DYSLGEIAEEFNVSRQAVYDNIKRTEKLLE 62 (104)
T ss_pred cCCHHHHHHHHHHHHc---------CCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 4567788877654333 346788999999999999999987665543
No 63
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=49.17 E-value=2.9 Score=34.88 Aligned_cols=48 Identities=4% Similarity=0.062 Sum_probs=37.4
Q ss_pred cCCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCC
Q 021941 239 TKFTQEQKDKMME-FAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKN 296 (305)
Q Consensus 239 TkFT~EQkekM~~-fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK 296 (305)
-+++++|++.+.- +.+. ...+++|.++|++..++++|++--|.++++.
T Consensus 107 ~~L~~~~r~v~~l~~~~g----------~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~ 155 (165)
T PRK09644 107 HTLPVIEAQAILLCDVHE----------LTYEEAASVLDLKLNTYKSHLFRGRKRLKAL 155 (165)
T ss_pred HhCCHHHHHHHHhHHHhc----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 5667788877664 3333 2568899999999999999999998887654
No 64
>PF13698 DUF4156: Domain of unknown function (DUF4156)
Probab=48.04 E-value=7.6 Score=31.44 Aligned_cols=17 Identities=41% Similarity=0.444 Sum_probs=14.5
Q ss_pred hhhhhhhcccCCceecc
Q 021941 82 ECLKNHAACIGGNIFDG 98 (305)
Q Consensus 82 EClkNHAa~~Gg~a~DG 98 (305)
-=|||.||.|||.+|-.
T Consensus 52 NdlrNeAa~lGgntV~~ 68 (93)
T PF13698_consen 52 NDLRNEAAKLGGNTVVL 68 (93)
T ss_pred HHHHHHHHHhCCCEEEE
Confidence 45899999999998864
No 65
>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=48.01 E-value=7.3 Score=28.76 Aligned_cols=15 Identities=13% Similarity=0.286 Sum_probs=7.5
Q ss_pred CHHHHHHHHHHhCCC
Q 021941 264 DDDQVDKFCAEVGVK 278 (305)
Q Consensus 264 de~~ve~fC~eiGV~ 278 (305)
....+.++|+-+||+
T Consensus 46 ~~~~~~~l~~~l~v~ 60 (78)
T TIGR02607 46 TADMALRLAKALGTS 60 (78)
T ss_pred CHHHHHHHHHHcCCC
Confidence 344455555555554
No 66
>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=47.91 E-value=51 Score=22.78 Aligned_cols=34 Identities=24% Similarity=0.340 Sum_probs=25.0
Q ss_pred CcCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCC
Q 021941 238 RTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVK 278 (305)
Q Consensus 238 RTkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~ 278 (305)
|-.||+|+-++|++...+.|-. ....++..++..
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~~-------~W~~Ia~~~~~~ 34 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGKD-------NWKKIAKRMPGG 34 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTTT-------HHHHHHHHHSSS
T ss_pred CCCCCHHHHHHHHHHHHHhCCc-------HHHHHHHHcCCC
Confidence 5679999999999999997654 566677777633
No 67
>PRK04217 hypothetical protein; Provisional
Probab=47.75 E-value=3.4 Score=34.83 Aligned_cols=47 Identities=11% Similarity=0.068 Sum_probs=35.6
Q ss_pred CCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCC
Q 021941 240 KFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVK 295 (305)
Q Consensus 240 kFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~k 295 (305)
++|.+|++.+...... +..++++|+.+||++.+++..++.-+.+++.
T Consensus 42 ~Lt~eereai~l~~~e---------GlS~~EIAk~LGIS~sTV~r~L~RArkkLre 88 (110)
T PRK04217 42 FMTYEEFEALRLVDYE---------GLTQEEAGKRMGVSRGTVWRALTSARKKVAQ 88 (110)
T ss_pred cCCHHHHHHHHHHHHc---------CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4788998776554322 2378899999999999999999887766643
No 68
>PRK06424 transcription factor; Provisional
Probab=46.85 E-value=8.6 Score=33.68 Aligned_cols=55 Identities=16% Similarity=0.131 Sum_probs=35.8
Q ss_pred CCccCcCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccc
Q 021941 234 KKRFRTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNK 290 (305)
Q Consensus 234 kKR~RTkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK 290 (305)
++|.|..| .+-.+.|..|+++|=+..... .-..++|+..+||++..|.-|..+.+
T Consensus 68 ~~~~~d~~-~~~~~~~~~~g~~Ir~lRe~~-GLSQ~eLA~~iGvs~stIskiE~G~~ 122 (144)
T PRK06424 68 KKYKKKAS-DEDLDIVEDYAELVKNARERL-SMSQADLAAKIFERKNVIASIERGDL 122 (144)
T ss_pred CCccCccc-HHHHHHHHHHHHHHHHHHHHc-CCCHHHHHHHhCCCHHHHHHHHCCCC
Confidence 44555555 455577777877742111111 12467999999999999999988764
No 69
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=45.90 E-value=3.1 Score=35.23 Aligned_cols=49 Identities=10% Similarity=0.214 Sum_probs=37.4
Q ss_pred cCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCC
Q 021941 239 TKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKN 296 (305)
Q Consensus 239 TkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK 296 (305)
-+++++|++.+.-+.-. +...+++|.++||+..+++++++.-+.+++++
T Consensus 130 ~~L~~~~r~v~~l~~~~---------g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~ 178 (184)
T PRK12512 130 ETLPPRQRDVVQSISVE---------GASIKETAAKLSMSEGAVRVALHRGLAALAAK 178 (184)
T ss_pred HhCCHHHHHHHHHHHHc---------CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 35667777776663221 23568899999999999999999999888765
No 70
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=45.01 E-value=4.4 Score=34.55 Aligned_cols=47 Identities=6% Similarity=0.268 Sum_probs=34.8
Q ss_pred CCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCC
Q 021941 240 KFTQEQKDKMME-FAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKN 296 (305)
Q Consensus 240 kFT~EQkekM~~-fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK 296 (305)
+++++|++.+.- |.+. .-.++.|.++||+..++++|++.-+.++++.
T Consensus 133 ~L~~~~r~i~~l~~~~~----------~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 180 (182)
T PRK12537 133 QLEPARRNCILHAYVDG----------CSHAEIAQRLGAPLGTVKAWIKRSLKALREC 180 (182)
T ss_pred hCCHHHHHHHHHHHHcC----------CCHHHHHHHHCCChhhHHHHHHHHHHHHHHH
Confidence 566677764443 3333 3578899999999999999999988877653
No 71
>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=44.99 E-value=18 Score=28.81 Aligned_cols=44 Identities=9% Similarity=0.111 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEec
Q 021941 243 QEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWM 286 (305)
Q Consensus 243 ~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWm 286 (305)
-...+++.+|+++|||++.......-..+-..+|++...+.+||
T Consensus 11 v~Dl~~s~~FY~~LG~~~~~~~~~~~~~~~~~~g~~~~~~~~~~ 54 (142)
T cd08353 11 VRDLEAAIAFFLELGLELEGRAEIEGEWADRVTGLDGVRVEIAM 54 (142)
T ss_pred eCCHHHHHHHHHHcCCEEccccccChHHHHHhcCCCCceEEEEE
Confidence 34688999999999999865432111233445677665555554
No 72
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=44.64 E-value=3.9 Score=34.93 Aligned_cols=49 Identities=10% Similarity=0.135 Sum_probs=37.2
Q ss_pred cCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCC
Q 021941 239 TKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKN 296 (305)
Q Consensus 239 TkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK 296 (305)
.+++++|++.+.-++- +...+++.|.++||+..+++.+++.-|.++++.
T Consensus 130 ~~L~~~~r~v~~l~~~---------~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 178 (184)
T PRK12539 130 ARLPEKMRLAIQAVKL---------EGLSVAEAATRSGMSESAVKVSVHRGLKALAAL 178 (184)
T ss_pred HhCCHHHHHHHHHHHH---------cCCcHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4566777776654322 234678999999999999999999998887764
No 73
>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=44.24 E-value=2.9 Score=29.99 Aligned_cols=45 Identities=11% Similarity=0.139 Sum_probs=35.9
Q ss_pred CCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCC
Q 021941 240 KFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTV 294 (305)
Q Consensus 240 kFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~ 294 (305)
.||+.|++.|..+++- ...++.+.++||+..+++.+..|=+.|++
T Consensus 3 ~LT~~E~~vl~~l~~G----------~~~~eIA~~l~is~~tV~~~~~~i~~Kl~ 47 (58)
T PF00196_consen 3 SLTERELEVLRLLAQG----------MSNKEIAEELGISEKTVKSHRRRIMKKLG 47 (58)
T ss_dssp SS-HHHHHHHHHHHTT----------S-HHHHHHHHTSHHHHHHHHHHHHHHHHT
T ss_pred ccCHHHHHHHHHHHhc----------CCcchhHHhcCcchhhHHHHHHHHHHHhC
Confidence 5899999988888765 25678999999999999999888776654
No 74
>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=44.16 E-value=12 Score=25.49 Aligned_cols=34 Identities=9% Similarity=0.066 Sum_probs=22.0
Q ss_pred HHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccc
Q 021941 248 KMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNN 289 (305)
Q Consensus 248 kM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNn 289 (305)
.+.++-++.||. .++|+..+||++.++.-|..+.
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 445555665553 4677777777777777776543
No 75
>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=43.99 E-value=2.7 Score=35.41 Aligned_cols=32 Identities=0% Similarity=-0.019 Sum_probs=27.9
Q ss_pred HHHHHHHHHHhCCCCceEEEecccccccCCCC
Q 021941 265 DDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKN 296 (305)
Q Consensus 265 e~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK 296 (305)
....++.|..+|++..+++++++.-|.++++.
T Consensus 154 ~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~ 185 (190)
T TIGR02939 154 GLSYEDIARIMDCPVGTVRSRIFRAREAIAIR 185 (190)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 34678999999999999999999999887764
No 76
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=43.96 E-value=4.9 Score=32.77 Aligned_cols=48 Identities=8% Similarity=0.113 Sum_probs=36.3
Q ss_pred cCCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCC
Q 021941 239 TKFTQEQKDKMME-FAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKN 296 (305)
Q Consensus 239 TkFT~EQkekM~~-fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK 296 (305)
-++++.|++.+.- |.+ +...++++..+||+..++++|++.-+.++++.
T Consensus 105 ~~L~~~~r~ii~l~~~~----------~~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~~ 153 (154)
T PRK06759 105 SVLDEKEKYIIFERFFV----------GKTMGEIALETEMTYYQVRWIYRQALEKMRNS 153 (154)
T ss_pred HhCCHHHHHHHHHHHhc----------CCCHHHHHHHHCCCHHHHHHHHHHHHHHHhhc
Confidence 3566777776644 333 23578999999999999999999988887664
No 77
>COG3040 Blc Bacterial lipocalin [Cell envelope biogenesis, outer membrane]
Probab=43.67 E-value=22 Score=32.61 Aligned_cols=25 Identities=36% Similarity=0.626 Sum_probs=22.4
Q ss_pred CcC-CCHHHHHHHHHHHHHhCCccCC
Q 021941 238 RTK-FTQEQKDKMMEFAEKVGWRFQK 262 (305)
Q Consensus 238 RTk-FT~EQkekM~~fAEklGWRiqk 262 (305)
||- .++|++++|++-|+++||-+.+
T Consensus 140 RtP~~s~~~~~~ml~~ak~~Gfdv~~ 165 (174)
T COG3040 140 RTPTLSQETLKRMLEIAKRRGFDVSK 165 (174)
T ss_pred cCCCCCHHHHHHHHHHHHHcCCCcce
Confidence 787 9999999999999999997654
No 78
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=43.60 E-value=3.7 Score=35.45 Aligned_cols=48 Identities=10% Similarity=0.160 Sum_probs=36.3
Q ss_pred cCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCC
Q 021941 239 TKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVK 295 (305)
Q Consensus 239 TkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~k 295 (305)
.+++++|++.+.-+.-. +.-+++.|..+||+..++|++++.-|.++++
T Consensus 133 ~~Lp~~~R~v~~L~~~~---------g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 180 (189)
T PRK12530 133 NHLPAQQARVFMMREYL---------ELSSEQICQECDISTSNLHVLLYRARLQLQA 180 (189)
T ss_pred HhCCHHHHHHHhHHHHc---------CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45677777776663221 2357899999999999999999988877665
No 79
>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=43.45 E-value=3.4 Score=28.72 Aligned_cols=44 Identities=5% Similarity=0.181 Sum_probs=31.6
Q ss_pred CCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccccc
Q 021941 240 KFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNN 292 (305)
Q Consensus 240 kFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~ 292 (305)
.++++|++.+...+ -.+...++.+.++||++..++.+.+.-..+
T Consensus 4 ~L~~~er~vi~~~y---------~~~~t~~eIa~~lg~s~~~V~~~~~~al~k 47 (50)
T PF04545_consen 4 QLPPREREVIRLRY---------FEGLTLEEIAERLGISRSTVRRILKRALKK 47 (50)
T ss_dssp TS-HHHHHHHHHHH---------TST-SHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHh---------cCCCCHHHHHHHHCCcHHHHHHHHHHHHHH
Confidence 57889999888755 234467899999999999888776654433
No 80
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=43.38 E-value=3.5 Score=33.92 Aligned_cols=49 Identities=4% Similarity=0.062 Sum_probs=37.0
Q ss_pred cCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCC
Q 021941 239 TKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKN 296 (305)
Q Consensus 239 TkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK 296 (305)
-.++++|++.+.-+.- +..-.++++..+||++.+++.|++.-+.++++.
T Consensus 127 ~~L~~~~r~vl~l~~~---------~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 175 (182)
T PRK09652 127 ESLPEELRTAITLREI---------EGLSYEEIAEIMGCPIGTVRSRIFRAREALRAK 175 (182)
T ss_pred HhCCHHHHHHHHHHHH---------cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3577888887765321 233567899999999999999999888877653
No 81
>COG4802 FtrB Ferredoxin-thioredoxin reductase, catalytic subunit [Energy production and conversion]
Probab=42.57 E-value=26 Score=30.03 Aligned_cols=54 Identities=20% Similarity=0.285 Sum_probs=38.5
Q ss_pred CHHHHHHHHH----HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCC
Q 021941 242 TQEQKDKMME----FAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKN 296 (305)
Q Consensus 242 T~EQkekM~~----fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK 296 (305)
+.|.+++|.. +|||-||++ ++|.+.+..|..-+-..+..|-.|.=-.|.-..|+
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 3567778876 578999998 57888888888877777666666665555544443
No 82
>PF13518 HTH_28: Helix-turn-helix domain
Probab=42.53 E-value=5.3 Score=27.25 Aligned_cols=25 Identities=20% Similarity=0.523 Sum_probs=21.7
Q ss_pred HHHHHHHHhCCCCceEEEecccccc
Q 021941 267 QVDKFCAEVGVKRHVFKVWMHNNKN 291 (305)
Q Consensus 267 ~ve~fC~eiGV~r~V~KVWmhNnK~ 291 (305)
-+.++|.++||++.++.-|+..-+.
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHHh
Confidence 6788999999999999999976543
No 83
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=42.37 E-value=4.1 Score=35.77 Aligned_cols=48 Identities=8% Similarity=0.044 Sum_probs=36.4
Q ss_pred CCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCC
Q 021941 240 KFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKN 296 (305)
Q Consensus 240 kFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK 296 (305)
+++++|++.+..+.- +....+++|.++||+..+++++++.-+.++++.
T Consensus 153 ~L~~~~r~vl~l~~~---------~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 200 (206)
T PRK12526 153 KLPEAQQTVVKGVYF---------QELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQ 200 (206)
T ss_pred hCCHHHHHHHHHHHH---------cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 466777777665221 223678999999999999999999988877654
No 84
>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=42.02 E-value=23 Score=29.22 Aligned_cols=25 Identities=12% Similarity=0.347 Sum_probs=16.3
Q ss_pred cCcCCCHHHHHHHHHHHHHhCCccC
Q 021941 237 FRTKFTQEQKDKMMEFAEKVGWRFQ 261 (305)
Q Consensus 237 ~RTkFT~EQkekM~~fAEklGWRiq 261 (305)
-=+.+|..|++++++.++++||+.+
T Consensus 18 S~k~lt~~el~~vl~~l~~~G~k~~ 42 (119)
T PF06252_consen 18 SSKDLTEAELEKVLDELKRLGFKPP 42 (119)
T ss_pred hHHHCCHHHHHHHHHHHHHccCcCc
Confidence 3355677777777777777777543
No 85
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=41.38 E-value=4.3 Score=33.65 Aligned_cols=49 Identities=12% Similarity=0.143 Sum_probs=37.1
Q ss_pred CCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCCC
Q 021941 240 KFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKNK 297 (305)
Q Consensus 240 kFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK~ 297 (305)
.++.+|++.+.-.. -++...++.|..+||+..+++++++..|.++++..
T Consensus 112 ~L~~~~r~v~~l~~---------~~~~s~~eIA~~lgis~~tv~~~l~Rar~~L~~~~ 160 (161)
T PRK12541 112 SLPLERRNVLLLRD---------YYGFSYKEIAEMTGLSLAKVKIELHRGRKETKSIK 160 (161)
T ss_pred HCCHHHHHHhhhHH---------hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhc
Confidence 56777777665522 12235789999999999999999999999887643
No 86
>PRK10403 transcriptional regulator NarP; Provisional
Probab=40.97 E-value=6.4 Score=32.00 Aligned_cols=48 Identities=15% Similarity=0.187 Sum_probs=38.4
Q ss_pred cCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCC
Q 021941 239 TKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKN 296 (305)
Q Consensus 239 TkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK 296 (305)
..||..+++.|..+++. ...+++++.+|+++++++++++|=+.|++.+
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 2346778889999999999999988877654
No 87
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=40.88 E-value=5 Score=33.83 Aligned_cols=49 Identities=4% Similarity=0.124 Sum_probs=36.1
Q ss_pred cCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCC
Q 021941 239 TKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKN 296 (305)
Q Consensus 239 TkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK 296 (305)
.+++++|++.+.-.+- +..-.+++|.++||+..+++++++.-|.++++.
T Consensus 128 ~~L~~~~r~i~~l~~~---------~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 128 EELEKDRAAAVRRAYL---------EGLSYKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred HhCCHHHHHHHHHHHH---------cCCCHHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 3456777776555321 223578999999999999999999988887653
No 88
>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=40.75 E-value=4.7 Score=33.26 Aligned_cols=50 Identities=12% Similarity=0.159 Sum_probs=36.8
Q ss_pred CCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCCCCC
Q 021941 240 KFTQEQKDKMME-FAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKNKQE 299 (305)
Q Consensus 240 kFT~EQkekM~~-fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK~~~ 299 (305)
+++++|++.+.- |.+ ..-.++.|..+||++.+++++.+.-+.++++.-..
T Consensus 110 ~L~~~~r~i~~l~~~~----------g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~~ 160 (162)
T TIGR02983 110 RLPARQRAVVVLRYYE----------DLSEAQVAEALGISVGTVKSRLSRALARLRELLEE 160 (162)
T ss_pred hCCHHHHHHhhhHHHh----------cCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhcC
Confidence 455666666544 322 23467899999999999999999999988775443
No 89
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=40.48 E-value=4.5 Score=34.48 Aligned_cols=51 Identities=10% Similarity=0.135 Sum_probs=39.9
Q ss_pred ccCcCCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCC
Q 021941 236 RFRTKFTQEQKDKMME-FAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKN 296 (305)
Q Consensus 236 R~RTkFT~EQkekM~~-fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK 296 (305)
+.-.+++..|++.+.- |.+ ....++++.++||+..+++++++.-+.++++.
T Consensus 135 ~~l~~L~~~~r~i~~l~~~~----------g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 186 (189)
T PRK09648 135 ELLDTLPEKQREILILRVVV----------GLSAEETAEAVGSTPGAVRVAQHRALARLRAE 186 (189)
T ss_pred HHHHhCCHHHHHHHHHHHHc----------CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4456788888888776 333 23578999999999999999999988887654
No 90
>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=40.31 E-value=5 Score=32.61 Aligned_cols=34 Identities=6% Similarity=0.024 Sum_probs=28.3
Q ss_pred CCCHHHHHHHHHHhCCCCceEEEecccccccCCC
Q 021941 262 KQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVK 295 (305)
Q Consensus 262 k~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~k 295 (305)
.-++.-.++.|.++||+..+++++++--|.++++
T Consensus 118 ~~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 118 EFKEFSYKEIAELLNLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred hhccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3445678999999999999999999988877654
No 91
>PRK09726 antitoxin HipB; Provisional
Probab=40.09 E-value=22 Score=27.74 Aligned_cols=19 Identities=11% Similarity=0.412 Sum_probs=9.1
Q ss_pred HHHHHHhCCCCceEEEecc
Q 021941 269 DKFCAEVGVKRHVFKVWMH 287 (305)
Q Consensus 269 e~fC~eiGV~r~V~KVWmh 287 (305)
++|+..+||++.+|.-|..
T Consensus 29 ~elA~~~gvs~~tis~~e~ 47 (88)
T PRK09726 29 SELAKKIGIKQATISNFEN 47 (88)
T ss_pred HHHHHHHCcCHHHHHHHHC
Confidence 4444455555544444444
No 92
>COG0289 DapB Dihydrodipicolinate reductase [Amino acid transport and metabolism]
Probab=39.54 E-value=23 Score=34.29 Aligned_cols=22 Identities=50% Similarity=0.493 Sum_probs=19.1
Q ss_pred cCCCHHHHHHHHHHHHHhCCcc
Q 021941 239 TKFTQEQKDKMMEFAEKVGWRF 260 (305)
Q Consensus 239 TkFT~EQkekM~~fAEklGWRi 260 (305)
|=||.||+++|.+|+|+++-=+
T Consensus 101 TGf~~e~~~~l~~~a~~v~vv~ 122 (266)
T COG0289 101 TGFTEEQLEKLREAAEKVPVVI 122 (266)
T ss_pred CCCCHHHHHHHHHHHhhCCEEE
Confidence 8899999999999999965433
No 93
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=39.42 E-value=3.7 Score=36.98 Aligned_cols=54 Identities=11% Similarity=0.060 Sum_probs=39.0
Q ss_pred CCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCCCCCCCC
Q 021941 240 KFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKNKQEPAA 302 (305)
Q Consensus 240 kFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK~~~~~~ 302 (305)
++++.|++.+.-+ +-+..-.+++|..+||+..+++++++.-|.++++.-...++
T Consensus 134 ~Lp~~~R~v~~L~---------y~eg~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l~~~~~ 187 (216)
T PRK12533 134 KLPVEYREVLVLR---------ELEDMSYREIAAIADVPVGTVMSRLARARRRLAALLGGASA 187 (216)
T ss_pred cCCHHHHhHhhhH---------HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHcccch
Confidence 4555566655542 22234678999999999999999999999998886554443
No 94
>smart00351 PAX Paired Box domain.
Probab=39.42 E-value=14 Score=30.94 Aligned_cols=41 Identities=12% Similarity=0.244 Sum_probs=34.2
Q ss_pred CCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccc
Q 021941 241 FTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNK 290 (305)
Q Consensus 241 FT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK 290 (305)
++.|+++++..+++. |+ -..++|.++||++.++.-|++--+
T Consensus 18 ~s~~~R~riv~~~~~-G~--------s~~~iA~~~gvs~~tV~kwi~r~~ 58 (125)
T smart00351 18 LPDEERQRIVELAQN-GV--------RPCDISRQLCVSHGCVSKILGRYY 58 (125)
T ss_pred CCHHHHHHHHHHHHc-CC--------CHHHHHHHHCcCHHHHHHHHHHHH
Confidence 889999999998764 54 446889999999999999988644
No 95
>PF13551 HTH_29: Winged helix-turn helix
Probab=39.05 E-value=22 Score=27.39 Aligned_cols=22 Identities=23% Similarity=0.499 Sum_probs=18.6
Q ss_pred CCccCcCCCHHHHHHHHHHHHH
Q 021941 234 KKRFRTKFTQEQKDKMMEFAEK 255 (305)
Q Consensus 234 kKR~RTkFT~EQkekM~~fAEk 255 (305)
.+|.++.+|+||++.+.+++..
T Consensus 51 ~g~~~~~l~~~~~~~l~~~~~~ 72 (112)
T PF13551_consen 51 GGRPRKRLSEEQRAQLIELLRE 72 (112)
T ss_pred CCCCCCCCCHHHHHHHHHHHHH
Confidence 4566666999999999999888
No 96
>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=38.89 E-value=50 Score=30.83 Aligned_cols=44 Identities=14% Similarity=0.380 Sum_probs=36.9
Q ss_pred CCCHHHHHHHHHHHHHhCCcc-----CCCCHHHHHHHHHHhCCCCceEEE
Q 021941 240 KFTQEQKDKMMEFAEKVGWRF-----QKQDDDQVDKFCAEVGVKRHVFKV 284 (305)
Q Consensus 240 kFT~EQkekM~~fAEklGWRi-----qk~de~~ve~fC~eiGV~r~V~KV 284 (305)
.|+.+|+..++..++++|++. ++..++.+++|. +-|++-.+++|
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 478999999999999999886 455567888888 78888888887
No 97
>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=38.50 E-value=59 Score=29.17 Aligned_cols=45 Identities=18% Similarity=0.389 Sum_probs=36.6
Q ss_pred cCCCHHHHHHHHHHHHHhCCcc-----CCCCHHHHHHHHHHhCCCCceEEE
Q 021941 239 TKFTQEQKDKMMEFAEKVGWRF-----QKQDDDQVDKFCAEVGVKRHVFKV 284 (305)
Q Consensus 239 TkFT~EQkekM~~fAEklGWRi-----qk~de~~ve~fC~eiGV~r~V~KV 284 (305)
+.++.+||..++..++++|.+. ++..++.+++|. +-|++-.+.+|
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 5678999999999999999665 345567888888 77888777777
No 98
>PRK10072 putative transcriptional regulator; Provisional
Probab=38.42 E-value=16 Score=30.02 Aligned_cols=34 Identities=21% Similarity=0.469 Sum_probs=26.8
Q ss_pred HHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccc
Q 021941 249 MMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNK 290 (305)
Q Consensus 249 M~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK 290 (305)
+..+.+++||. ..+||..+||+..++.-|....+
T Consensus 38 ik~LR~~~glT--------Q~elA~~lGvS~~TVs~WE~G~r 71 (96)
T PRK10072 38 FEQLRKGTGLK--------IDDFARVLGVSVAMVKEWESRRV 71 (96)
T ss_pred HHHHHHHcCCC--------HHHHHHHhCCCHHHHHHHHcCCC
Confidence 55566787776 57889999999999999987654
No 99
>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=38.33 E-value=5.1 Score=33.94 Aligned_cols=49 Identities=6% Similarity=0.081 Sum_probs=36.3
Q ss_pred CcCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCC
Q 021941 238 RTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVK 295 (305)
Q Consensus 238 RTkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~k 295 (305)
--+|+++|++.+.-+... ....+++|.++||+..+++++++.-|.++++
T Consensus 98 l~~L~~~~r~v~~l~~~~---------g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 146 (170)
T TIGR02959 98 IKELPDEYREAIRLTELE---------GLSQQEIAEKLGLSLSGAKSRVQRGRKKLKE 146 (170)
T ss_pred HHhCCHHHHHHHHHHHHc---------CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 346777777776653322 2356889999999999999999988877654
No 100
>PF13189 Cytidylate_kin2: Cytidylate kinase-like family; PDB: 3FDI_A.
Probab=38.23 E-value=13 Score=32.25 Aligned_cols=40 Identities=20% Similarity=0.447 Sum_probs=19.5
Q ss_pred HHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccc
Q 021941 249 MMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNK 290 (305)
Q Consensus 249 M~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK 290 (305)
=+..||+||++. -|.+.+++.+.+.||+...|..|.....
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 5668999999999999999988877655
No 101
>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=38.17 E-value=26 Score=26.97 Aligned_cols=47 Identities=17% Similarity=0.388 Sum_probs=25.7
Q ss_pred CcCCCHHHHHHHHHHHHHhCCc-cCCCCHHHHHHHHHHhCCCCceEEEe
Q 021941 238 RTKFTQEQKDKMMEFAEKVGWR-FQKQDDDQVDKFCAEVGVKRHVFKVW 285 (305)
Q Consensus 238 RTkFT~EQkekM~~fAEklGWR-iqk~de~~ve~fC~eiGV~r~V~KVW 285 (305)
||.||.|.=+.|..|..+-.+. ..-....+-++|..+ .+++++.|-|
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 8999999999999998553332 233345677777655 4678877766
No 102
>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=38.07 E-value=10 Score=24.08 Aligned_cols=20 Identities=15% Similarity=0.318 Sum_probs=10.1
Q ss_pred HHHHHhCCCCceEEEecccc
Q 021941 270 KFCAEVGVKRHVFKVWMHNN 289 (305)
Q Consensus 270 ~fC~eiGV~r~V~KVWmhNn 289 (305)
+|+..+|+++..+.-|+.+.
T Consensus 17 ~~a~~~~~~~~~v~~~~~g~ 36 (58)
T cd00093 17 ELAEKLGVSRSTISRIENGK 36 (58)
T ss_pred HHHHHHCCCHHHHHHHHcCC
Confidence 45555555555555554443
No 103
>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=37.43 E-value=7.1 Score=25.75 Aligned_cols=23 Identities=17% Similarity=0.351 Sum_probs=19.7
Q ss_pred HHHHHHHhCCCCceEEEeccccc
Q 021941 268 VDKFCAEVGVKRHVFKVWMHNNK 290 (305)
Q Consensus 268 ve~fC~eiGV~r~V~KVWmhNnK 290 (305)
+++.|..+||++.+|.-|+.+.+
T Consensus 4 ~~e~a~~lgis~~ti~~~~~~g~ 26 (49)
T TIGR01764 4 VEEAAEYLGVSKDTVYRLIHEGE 26 (49)
T ss_pred HHHHHHHHCCCHHHHHHHHHcCC
Confidence 67889999999999999987765
No 104
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=37.14 E-value=6.9 Score=28.32 Aligned_cols=23 Identities=9% Similarity=0.270 Sum_probs=19.5
Q ss_pred HHHHHHHhCCCCceEEEeccccc
Q 021941 268 VDKFCAEVGVKRHVFKVWMHNNK 290 (305)
Q Consensus 268 ve~fC~eiGV~r~V~KVWmhNnK 290 (305)
+.++|+.+||++++|+.|-..--
T Consensus 3 i~eva~~~gvs~~tlr~y~~~gl 25 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYEREGL 25 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHHHTTS
T ss_pred HHHHHHHHCcCHHHHHHHHHhcC
Confidence 57899999999999999976543
No 105
>TIGR02366 DHAK_reg probable dihydroxyacetone kinase regulator. The seed alignment for this family was built from a set of closely related uncharacterized proteins associated with operons for the type of bacterial dihydroxyacetone kinase that transfers PEP-derived phosphate from a phosphoprotein, as in phosphotransferase system transport, rather than from ATP. Members have a TetR transcriptional regulator domain (pfam00440) at the N-terminus and sequence homology throughout.
Probab=37.14 E-value=21 Score=29.82 Aligned_cols=27 Identities=11% Similarity=0.219 Sum_probs=21.9
Q ss_pred CCCHHHHHHHHHHhCCCCceEEEeccc
Q 021941 262 KQDDDQVDKFCAEVGVKRHVFKVWMHN 288 (305)
Q Consensus 262 k~de~~ve~fC~eiGV~r~V~KVWmhN 288 (305)
.-++-.|+++|++.||+|.+|=.-|.+
T Consensus 20 ~~~~ITV~~I~~~AgvsR~TFY~hF~d 46 (176)
T TIGR02366 20 AFSKISVSDIMSTAQIRRQTFYNHFQD 46 (176)
T ss_pred CCccCCHHHHHHHhCCCHHHHHHHCCC
Confidence 456678999999999999998655544
No 106
>KOG0705 consensus GTPase-activating protein Centaurin gamma (contains Ras-like GTPase, PH and ankyrin repeat domains) [Signal transduction mechanisms]
Probab=37.13 E-value=15 Score=39.55 Aligned_cols=36 Identities=31% Similarity=0.518 Sum_probs=27.0
Q ss_pred CceeccccccccCCCCCCccccccccc-cccccccccc
Q 021941 93 GNIFDGCGEFMPSGDEGTLEALKCAAC-ECHRNFHRKE 129 (305)
Q Consensus 93 g~a~DGCgEFmp~~~~gt~~al~CaAC-gCHRnFHrke 129 (305)
+|++| |+---|.-..-.+.+|.|--| |||||++...
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 46777 776655544455679999999 8999999754
No 107
>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=36.95 E-value=6.3 Score=31.68 Aligned_cols=46 Identities=11% Similarity=0.185 Sum_probs=34.1
Q ss_pred CCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCC
Q 021941 240 KFTQEQKDKMME-FAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVK 295 (305)
Q Consensus 240 kFT~EQkekM~~-fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~k 295 (305)
+++.+|++.+.- |.+ +..+++.|..+||++.+++.+++.-|.++++
T Consensus 113 ~L~~~~r~il~l~~~~----------~~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 113 KLPEQCRKIFILSRFE----------GKSYKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred HCCHHHHHHHHHHHHc----------CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 456666666554 322 2356789999999999999999988887764
No 108
>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=36.92 E-value=40 Score=24.17 Aligned_cols=22 Identities=27% Similarity=0.682 Sum_probs=18.8
Q ss_pred cCCCHHHHHHHHHHHHHhCCcc
Q 021941 239 TKFTQEQKDKMMEFAEKVGWRF 260 (305)
Q Consensus 239 TkFT~EQkekM~~fAEklGWRi 260 (305)
-.+++|=+++.++.|+++||+.
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 3678999999999999999974
No 109
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=36.49 E-value=8.8 Score=30.65 Aligned_cols=47 Identities=6% Similarity=0.151 Sum_probs=34.5
Q ss_pred CCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCC
Q 021941 240 KFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKN 296 (305)
Q Consensus 240 kFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK 296 (305)
+||..+++.|..+++. + ..+++++++|++..++++++++-+.|+++.
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 4666676666654442 1 255678899999999999999988887654
No 110
>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=36.47 E-value=11 Score=25.98 Aligned_cols=21 Identities=10% Similarity=0.306 Sum_probs=14.0
Q ss_pred HHHHHHhCCCCceEEEecccc
Q 021941 269 DKFCAEVGVKRHVFKVWMHNN 289 (305)
Q Consensus 269 e~fC~eiGV~r~V~KVWmhNn 289 (305)
.+|+..+||++.++.-|+.+.
T Consensus 13 ~~la~~~gis~~~i~~~~~g~ 33 (55)
T PF01381_consen 13 KELAEKLGISRSTISRIENGK 33 (55)
T ss_dssp HHHHHHHTS-HHHHHHHHTTS
T ss_pred HHHHHHhCCCcchhHHHhcCC
Confidence 667777777777777776663
No 111
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=36.12 E-value=9.3 Score=29.15 Aligned_cols=37 Identities=11% Similarity=0.461 Sum_probs=26.0
Q ss_pred HHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccc
Q 021941 249 MMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNN 289 (305)
Q Consensus 249 M~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNn 289 (305)
|++|..+ -+--.|..++.+|.+.|++-+=++.||--.
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 6777776 344677899999999999999999999543
No 112
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=36.12 E-value=5.5 Score=33.39 Aligned_cols=48 Identities=10% Similarity=0.161 Sum_probs=34.8
Q ss_pred cCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCC
Q 021941 239 TKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVK 295 (305)
Q Consensus 239 TkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~k 295 (305)
-+++++|++.+.-+. -++..++++|.++||+..+++++++.-|.++++
T Consensus 111 ~~L~~~~r~v~~l~~---------~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 158 (164)
T PRK12547 111 NLLSADQREAIILIG---------ASGFSYEDAAAICGCAVGTIKSRVSRARNRLQE 158 (164)
T ss_pred HhCCHHHHHHHHHHH---------HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 355666666554422 223467899999999999999999988877654
No 113
>PRK11470 hypothetical protein; Provisional
Probab=35.78 E-value=17 Score=33.63 Aligned_cols=22 Identities=27% Similarity=0.444 Sum_probs=20.3
Q ss_pred CCccCcCCCHHHHHHHHHHHHH
Q 021941 234 KKRFRTKFTQEQKDKMMEFAEK 255 (305)
Q Consensus 234 kKR~RTkFT~EQkekM~~fAEk 255 (305)
-+|.++.+|.+|+++|.++|++
T Consensus 78 v~Rl~~~l~~~~~~~~~~~A~~ 99 (200)
T PRK11470 78 IKRLDAGLTEQQKQRIVEQVPS 99 (200)
T ss_pred EEEecCCCCHHHHHHHHHHHHH
Confidence 4899999999999999999988
No 114
>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=35.52 E-value=15 Score=26.25 Aligned_cols=17 Identities=18% Similarity=0.288 Sum_probs=7.3
Q ss_pred CCHHHHHHHHHHhCCCC
Q 021941 263 QDDDQVDKFCAEVGVKR 279 (305)
Q Consensus 263 ~de~~ve~fC~eiGV~r 279 (305)
+....+..+|..+||+.
T Consensus 39 ~~~~~l~~i~~~~~v~~ 55 (64)
T PF12844_consen 39 PSVSTLKKIAEALGVSL 55 (64)
T ss_dssp -BHHHHHHHHHHHTS-H
T ss_pred CCHHHHHHHHHHhCCCH
Confidence 33444555555555543
No 115
>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=35.18 E-value=9.1 Score=25.78 Aligned_cols=44 Identities=14% Similarity=0.203 Sum_probs=30.3
Q ss_pred CCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCC
Q 021941 241 FTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTV 294 (305)
Q Consensus 241 FT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~ 294 (305)
++..|++.+..++ -|+ ..++.|..+||++.+++.|++--+.+.+
T Consensus 1 l~~~e~~i~~~~~--~~~--------s~~eia~~l~~s~~tv~~~~~~~~~~l~ 44 (57)
T cd06170 1 LTPREREVLRLLA--EGK--------TNKEIADILGISEKTVKTHLRNIMRKLG 44 (57)
T ss_pred CCHHHHHHHHHHH--cCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHhC
Confidence 4667777543332 122 5688999999999999999886554443
No 116
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=34.93 E-value=7.1 Score=27.83 Aligned_cols=24 Identities=8% Similarity=0.277 Sum_probs=18.5
Q ss_pred HHHHHHHHhCCCCceEEEeccccc
Q 021941 267 QVDKFCAEVGVKRHVFKVWMHNNK 290 (305)
Q Consensus 267 ~ve~fC~eiGV~r~V~KVWmhNnK 290 (305)
-+.+|++++||++.+|.-|++++.
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 467899999999999999999773
No 117
>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=34.51 E-value=8.3 Score=25.94 Aligned_cols=25 Identities=8% Similarity=0.167 Sum_probs=21.0
Q ss_pred HHHHHHHhCCCCceEEEeccccccc
Q 021941 268 VDKFCAEVGVKRHVFKVWMHNNKNN 292 (305)
Q Consensus 268 ve~fC~eiGV~r~V~KVWmhNnK~~ 292 (305)
+.++|+.+||+..+|+-|..+..-.
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g~l~ 27 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIGLLS 27 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCCC
Confidence 5789999999999999998766543
No 118
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=34.49 E-value=8.7 Score=31.69 Aligned_cols=47 Identities=15% Similarity=0.260 Sum_probs=36.2
Q ss_pred cCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCC
Q 021941 239 TKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVK 295 (305)
Q Consensus 239 TkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~k 295 (305)
.+++.+|++.+.-+. .|| ..++++..+||+..+++++++.-+.++++
T Consensus 111 ~~L~~~~r~il~l~~--~g~--------s~~eIA~~lgis~~tV~~~i~ra~~~Lr~ 157 (166)
T PRK09639 111 AKMTERDRTVLLLRF--SGY--------SYKEIAEALGIKESSVGTTLARAKKKFRK 157 (166)
T ss_pred HcCCHHHHHHHHHHH--cCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 456777777765544 344 56789999999999999999988877664
No 119
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=33.56 E-value=6.1 Score=34.49 Aligned_cols=48 Identities=10% Similarity=0.138 Sum_probs=34.9
Q ss_pred CCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCC
Q 021941 240 KFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKN 296 (305)
Q Consensus 240 kFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK 296 (305)
+++++|++.+.-. +-++.-+++.|..+||+..+++++++--|.++++.
T Consensus 113 ~Lp~~~r~v~~L~---------~~~g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~ 160 (188)
T PRK12546 113 QLPDEQREALILV---------GASGFSYEEAAEMCGVAVGTVKSRANRARARLAEL 160 (188)
T ss_pred hCCHHHhHHhhhH---------HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4555666555432 12234578999999999999999999999887764
No 120
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=33.41 E-value=7.3 Score=33.53 Aligned_cols=48 Identities=8% Similarity=0.100 Sum_probs=36.1
Q ss_pred cCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCC
Q 021941 239 TKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVK 295 (305)
Q Consensus 239 TkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~k 295 (305)
.+++++|++.+.-.. -++.-+++++..+||+..++|++++--|.++++
T Consensus 129 ~~Lp~~~r~v~~L~~---------~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 129 ADLTTDQREALLLTQ---------LLGLSYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred HhCCHHHhHHhhhHH---------HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 456666666654421 122357899999999999999999999988887
No 121
>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=33.41 E-value=7 Score=32.86 Aligned_cols=46 Identities=9% Similarity=-0.057 Sum_probs=34.7
Q ss_pred CCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCC
Q 021941 241 FTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVK 295 (305)
Q Consensus 241 FT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~k 295 (305)
+.++|++.+.-... ++.-.++.+..+||+..++|+.++.-|.++++
T Consensus 135 Lp~~~r~v~~l~~~---------~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 180 (183)
T TIGR02999 135 VDPRQAEVVELRFF---------AGLTVEEIAELLGVSVRTVERDWRFARAWLAD 180 (183)
T ss_pred CCHHHHHHHHHHHH---------cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 66667766655322 23467889999999999999999998887765
No 122
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=33.40 E-value=6.8 Score=34.04 Aligned_cols=48 Identities=6% Similarity=0.129 Sum_probs=34.9
Q ss_pred CCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCC
Q 021941 240 KFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKN 296 (305)
Q Consensus 240 kFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK 296 (305)
+++++|++.+.-.. -++.-.++++..+||+..++|++++.-|.++++.
T Consensus 116 ~Lp~~~r~i~~L~~---------~~g~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~ 163 (187)
T PRK12516 116 QLPDDQREAIILVG---------ASGFAYEEAAEICGCAVGTIKSRVNRARQRLQEI 163 (187)
T ss_pred hCCHHHHHHHHHHH---------HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 45566666654421 2233567899999999999999999998887653
No 123
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=33.38 E-value=7.3 Score=32.15 Aligned_cols=48 Identities=6% Similarity=0.199 Sum_probs=35.8
Q ss_pred cCCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCC
Q 021941 239 TKFTQEQKDKMME-FAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKN 296 (305)
Q Consensus 239 TkFT~EQkekM~~-fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK 296 (305)
.+++++|++.+.- +.+. .-.++++..+||+..++|++++.-|.++++.
T Consensus 105 ~~Lp~~~r~v~~l~~~~g----------~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 153 (160)
T PRK09642 105 RELPENYRDVVLAHYLEE----------KSYQEIALQEKIEVKTVEMKLYRARKWIKKH 153 (160)
T ss_pred HhCCHHHHHHHHHHHHhC----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3466777776654 3332 3567899999999999999999888877654
No 124
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=33.36 E-value=7.3 Score=32.94 Aligned_cols=53 Identities=6% Similarity=-0.013 Sum_probs=38.1
Q ss_pred cCcCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCCCC
Q 021941 237 FRTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKNKQ 298 (305)
Q Consensus 237 ~RTkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK~~ 298 (305)
.-.+++..|++.+.-+. -++.-.++.|+++||+..+++++++.-|.+++++-.
T Consensus 132 ~l~~L~~~~r~vl~l~~---------~~~~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~l~ 184 (186)
T PRK13919 132 ALKALSPEERRVIEVLY---------YQGYTHREAAQLLGLPLGTLKTRARRALSRLKEVLR 184 (186)
T ss_pred HHHhCCHHHHHHHHHHH---------HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhc
Confidence 33456677777665422 122356889999999999999999998888776543
No 125
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=32.94 E-value=6.2 Score=33.57 Aligned_cols=47 Identities=4% Similarity=0.108 Sum_probs=35.1
Q ss_pred CCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCC
Q 021941 240 KFTQEQKDKMME-FAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKN 296 (305)
Q Consensus 240 kFT~EQkekM~~-fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK 296 (305)
+++++|++.+.- |.+ ..-.+++|..+||++.+++++++.-|.++++.
T Consensus 128 ~L~~~~r~i~~l~~~~----------g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 175 (186)
T PRK05602 128 ALPERQREAIVLQYYQ----------GLSNIEAAAVMDISVDALESLLARGRRALRAQ 175 (186)
T ss_pred hCCHHHHHHhhHHHhc----------CCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 456666665543 333 23568899999999999999999999887764
No 126
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=32.92 E-value=6.8 Score=33.87 Aligned_cols=48 Identities=6% Similarity=0.017 Sum_probs=36.8
Q ss_pred cCCCHHHHHHHHHH-HHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCC
Q 021941 239 TKFTQEQKDKMMEF-AEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKN 296 (305)
Q Consensus 239 TkFT~EQkekM~~f-AEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK 296 (305)
-+++++|++.+.-. .+. --.+++|+.+||+..+++++++--|.++++.
T Consensus 135 ~~L~~~~r~i~~L~~~~g----------~s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~ 183 (196)
T PRK12524 135 AALPERQRQAVVLRHIEG----------LSNPEIAEVMEIGVEAVESLTARGKRALAAL 183 (196)
T ss_pred HhCCHHHHHHHHHHHHcC----------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 46777777776653 332 2468899999999999999999988887653
No 127
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=32.84 E-value=7.7 Score=31.76 Aligned_cols=48 Identities=17% Similarity=0.173 Sum_probs=35.9
Q ss_pred cCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCC
Q 021941 239 TKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVK 295 (305)
Q Consensus 239 TkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~k 295 (305)
-+++++|++.+.-+.-. +.-+++.|..+||+..++|++++.-+.++++
T Consensus 105 ~~Lp~~~r~v~~l~~~~---------g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 152 (161)
T PRK09047 105 QKLPARQREAFLLRYWE---------DMDVAETAAAMGCSEGSVKTHCSRATHALAK 152 (161)
T ss_pred HhCCHHHHHHHHHHHHh---------cCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46677777777663221 2247899999999999999999988877654
No 128
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=32.78 E-value=6.9 Score=34.30 Aligned_cols=47 Identities=15% Similarity=0.136 Sum_probs=37.3
Q ss_pred cCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCC
Q 021941 239 TKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVK 295 (305)
Q Consensus 239 TkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~k 295 (305)
+.+|+.|++.|..++ -|| ..++++.++|+++.+++.|+++-+.++++
T Consensus 5 ~~Lt~rqreVL~lr~--~Gl--------Tq~EIAe~LGiS~~tVs~ie~ra~kkLr~ 51 (141)
T PRK03975 5 SFLTERQIEVLRLRE--RGL--------TQQEIADILGTSRANVSSIEKRARENIEK 51 (141)
T ss_pred cCCCHHHHHHHHHHH--cCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 578999999987642 344 45789999999999999999987777654
No 129
>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=32.66 E-value=83 Score=24.17 Aligned_cols=44 Identities=11% Similarity=0.121 Sum_probs=34.5
Q ss_pred CccCcCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEE
Q 021941 235 KRFRTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKV 284 (305)
Q Consensus 235 KR~RTkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KV 284 (305)
+.+...++.++. .+.++|.-...+...+.++++..|++-+.+++
T Consensus 17 ~~~g~~~~~~~l------~~~~~~~~~~~~~~~l~~~a~~~gl~~~~~~~ 60 (122)
T cd02259 17 RYFGIPVRRDVL------LNAQQRRQQGLSLADLVSLANKLGLTAQGVKL 60 (122)
T ss_pred HHcCCCCCHHHH------HHHHhhccCCCCHHHHHHHHHHcCCeeeEEEc
Confidence 566777888877 34556666778889999999999999888765
No 130
>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=32.55 E-value=1.3e+02 Score=24.83 Aligned_cols=40 Identities=20% Similarity=0.287 Sum_probs=32.1
Q ss_pred cCCCHHHHHHHHHHHHHhCC--ccCCCCHHHHHHHHHHh-CCC
Q 021941 239 TKFTQEQKDKMMEFAEKVGW--RFQKQDDDQVDKFCAEV-GVK 278 (305)
Q Consensus 239 TkFT~EQkekM~~fAEklGW--Riqk~de~~ve~fC~ei-GV~ 278 (305)
...+..|..|+.++...+|| -+....+.....|+..+ ||.
T Consensus 53 ~~~~~~q~~KI~aLw~~~~~~~~v~~~s~~aL~~fvkr~~gv~ 95 (119)
T PF06252_consen 53 GMATSAQLRKIRALWKQLGKPGAVRDPSEAALDAFVKRQFGVD 95 (119)
T ss_pred CCcchHHHHHHHHHHHHhhccCCccchHHHHHHHHHHHHHCCC
Confidence 34599999999999999994 56788888999998764 454
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=32.21 E-value=4.1 Score=36.41 Aligned_cols=42 Identities=19% Similarity=0.528 Sum_probs=26.1
Q ss_pred HHHHHHHHH-----HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccc
Q 021941 243 QEQKDKMME-----FAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHN 288 (305)
Q Consensus 243 ~EQkekM~~-----fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhN 288 (305)
.+.+++|.. |.++|||.+...|..++++|=.. .-+.-|++.+
T Consensus 7 ~~~l~~~~rlR~~vFv~rlgW~v~~~dg~E~DqyD~~----~~~ylv~~~~ 53 (182)
T PF00765_consen 7 RRLLEEMFRLRHRVFVDRLGWDVPCEDGMEIDQYDDP----DAVYLVALDD 53 (182)
T ss_dssp HHHHHHHHHHHHHHHTTCSCCCHHCCTSEE--TTGCT----T-EEEEEEET
T ss_pred HHHHHHHHHHHHHHHHHhhCCCCcCCCCcEeeecCCC----CCeEEEEEEC
Confidence 444555543 99999999999998888888432 3334445544
No 132
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=32.11 E-value=7.9 Score=32.54 Aligned_cols=31 Identities=6% Similarity=0.056 Sum_probs=26.3
Q ss_pred HHHHHHHHHHhCCCCceEEEecccccccCCC
Q 021941 265 DDQVDKFCAEVGVKRHVFKVWMHNNKNNTVK 295 (305)
Q Consensus 265 e~~ve~fC~eiGV~r~V~KVWmhNnK~~~~k 295 (305)
+.-.++.|+.+||+..+++++++.-|.++++
T Consensus 135 ~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 165 (173)
T PRK12522 135 QYSYKEMSEILNIPIGTVKYRLNYAKKQMRE 165 (173)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 3456889999999999999999988887764
No 133
>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=31.96 E-value=19 Score=24.34 Aligned_cols=29 Identities=24% Similarity=0.456 Sum_probs=20.6
Q ss_pred eeccccccccCCCCCCcccccccccccccccccc
Q 021941 95 IFDGCGEFMPSGDEGTLEALKCAACECHRNFHRK 128 (305)
Q Consensus 95 a~DGCgEFmp~~~~gt~~al~CaACgCHRnFHrk 128 (305)
.=+-|+++|... ...+++|..| ..+.|++
T Consensus 13 ~C~~C~~~i~~~---~~~~~~C~~C--~~~~H~~ 41 (50)
T cd00029 13 FCDVCRKSIWGL---FKQGLRCSWC--KVKCHKK 41 (50)
T ss_pred Chhhcchhhhcc---ccceeEcCCC--CCchhhh
Confidence 357799999864 3468999887 5555654
No 134
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=31.89 E-value=14 Score=29.57 Aligned_cols=47 Identities=6% Similarity=0.035 Sum_probs=37.0
Q ss_pred cCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCC
Q 021941 239 TKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVK 295 (305)
Q Consensus 239 TkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~k 295 (305)
..||..|++.|.-+++.. ..++++++++++.++++.|+.|=+.|++-
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 359999999887766541 25688889999999999999997777653
No 135
>PF12728 HTH_17: Helix-turn-helix domain
Probab=31.39 E-value=10 Score=26.29 Aligned_cols=24 Identities=21% Similarity=0.437 Sum_probs=20.2
Q ss_pred HHHHHHHhCCCCceEEEecccccc
Q 021941 268 VDKFCAEVGVKRHVFKVWMHNNKN 291 (305)
Q Consensus 268 ve~fC~eiGV~r~V~KVWmhNnK~ 291 (305)
++|.|+.+||++.+|.-|.++.+-
T Consensus 4 ~~e~a~~l~is~~tv~~~~~~g~i 27 (51)
T PF12728_consen 4 VKEAAELLGISRSTVYRWIRQGKI 27 (51)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCCC
Confidence 678999999999999999876654
No 136
>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=31.35 E-value=28 Score=32.26 Aligned_cols=18 Identities=22% Similarity=0.333 Sum_probs=15.4
Q ss_pred ccCcCCCHHHHHHHHHHH
Q 021941 236 RFRTKFTQEQKDKMMEFA 253 (305)
Q Consensus 236 R~RTkFT~EQkekM~~fA 253 (305)
..+..||+.|+++|++..
T Consensus 207 ~C~~~FT~~Q~~RM~~~~ 224 (225)
T cd04275 207 SCMNEFTPGQVTRMRSYL 224 (225)
T ss_pred chhcccCHHHHHHHHHHh
Confidence 467899999999999853
No 137
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=31.19 E-value=9.8 Score=32.69 Aligned_cols=50 Identities=10% Similarity=0.333 Sum_probs=38.8
Q ss_pred cCCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCCCC
Q 021941 239 TKFTQEQKDKMME-FAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKNKQ 298 (305)
Q Consensus 239 TkFT~EQkekM~~-fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK~~ 298 (305)
-+++++|++.+.- |.+- .-.+++|+.+||++.++++.++--|.+++|...
T Consensus 130 ~~L~~~~r~i~~l~~~~g----------~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~~~ 180 (189)
T PRK06811 130 NDLEKLDREIFIRRYLLG----------EKIEEIAKKLGLTRSAIDNRLSRGRKKLQKNKL 180 (189)
T ss_pred HhCCHHHHHHHHHHHHcc----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHccc
Confidence 4677777777654 3332 357899999999999999999999988887654
No 138
>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=31.13 E-value=12 Score=29.74 Aligned_cols=28 Identities=7% Similarity=0.248 Sum_probs=23.6
Q ss_pred CHHHHHHHHHHhCCCCceEEEecccccc
Q 021941 264 DDDQVDKFCAEVGVKRHVFKVWMHNNKN 291 (305)
Q Consensus 264 de~~ve~fC~eiGV~r~V~KVWmhNnK~ 291 (305)
++..+++++.++||+..++++|+++...
T Consensus 31 eGlS~kEIAe~LGIS~~TVk~~l~~~~~ 58 (73)
T TIGR03879 31 AGKTASEIAEELGRTEQTVRNHLKGETK 58 (73)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHhcCcc
Confidence 4456789999999999999999997543
No 139
>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=31.02 E-value=18 Score=29.83 Aligned_cols=20 Identities=40% Similarity=0.551 Sum_probs=17.8
Q ss_pred cCCCHHHHHHHHHHHHHhCC
Q 021941 239 TKFTQEQKDKMMEFAEKVGW 258 (305)
Q Consensus 239 TkFT~EQkekM~~fAEklGW 258 (305)
|=|+.||+++|.+++++++|
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 67899999999999999765
No 140
>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=30.81 E-value=53 Score=30.42 Aligned_cols=44 Identities=16% Similarity=0.259 Sum_probs=32.0
Q ss_pred CCCHHHHHHHHHHHHHhCCccCC-----CCHHHHHHHHHHhCCCCceEEE
Q 021941 240 KFTQEQKDKMMEFAEKVGWRFQK-----QDDDQVDKFCAEVGVKRHVFKV 284 (305)
Q Consensus 240 kFT~EQkekM~~fAEklGWRiqk-----~de~~ve~fC~eiGV~r~V~KV 284 (305)
.|+.+|+..++..++++|++..- ..++.+++|.+. |++-.+++|
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 37899999999999999988743 334677888754 988888877
No 141
>PRK15008 HTH-type transcriptional regulator RutR; Provisional
Probab=30.74 E-value=26 Score=30.55 Aligned_cols=56 Identities=11% Similarity=0.183 Sum_probs=38.3
Q ss_pred CCccCcCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccc
Q 021941 234 KKRFRTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNK 290 (305)
Q Consensus 234 kKR~RTkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK 290 (305)
+++.|+.=-.+.++++++-|..+=|+- .-+..-+.++|.+.||++.+|-..|.|..
T Consensus 8 ~~~~~~~~~~~~r~~IL~AA~~lf~e~-Gy~~~s~~dIA~~aGvs~gtiY~hF~sKe 63 (212)
T PRK15008 8 TTGKRSRAVSAKKKAILSAALDTFSQF-GFHGTRLEQIAELAGVSKTNLLYYFPSKE 63 (212)
T ss_pred CCCCcchhhHHHHHHHHHHHHHHHHHh-CcccCCHHHHHHHhCcCHHHHHHHCCCHH
Confidence 444444434567888877555543332 45566899999999999999988886643
No 142
>PRK01964 4-oxalocrotonate tautomerase; Provisional
Probab=30.52 E-value=92 Score=22.57 Aligned_cols=35 Identities=11% Similarity=0.271 Sum_probs=26.6
Q ss_pred CHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccc
Q 021941 242 TQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNK 290 (305)
Q Consensus 242 T~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK 290 (305)
|.|||++|.+ . +-+.++..+|++...+-|.+..+.
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 7899988764 2 445678889999998888876553
No 143
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=30.20 E-value=8.2 Score=31.66 Aligned_cols=47 Identities=9% Similarity=0.075 Sum_probs=34.2
Q ss_pred CCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCC
Q 021941 240 KFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVK 295 (305)
Q Consensus 240 kFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~k 295 (305)
++++++++.+..+. -++...++.|.++|+++.+++.|++--+.++++
T Consensus 125 ~L~~~~r~i~~l~~---------~~~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~ 171 (179)
T PRK11924 125 ALPVKQREVFLLRY---------VEGLSYREIAEILGVPVGTVKSRLRRARQLLRE 171 (179)
T ss_pred hCCHHHHHHhhHHH---------HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35566666554422 223456899999999999999999988877665
No 144
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=30.17 E-value=7.5 Score=32.63 Aligned_cols=47 Identities=11% Similarity=0.179 Sum_probs=36.9
Q ss_pred cCCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCC
Q 021941 239 TKFTQEQKDKMME-FAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVK 295 (305)
Q Consensus 239 TkFT~EQkekM~~-fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~k 295 (305)
.+++++|++.+.- |.+ ..-+++.|+.+||+..+++++++.-|.++++
T Consensus 135 ~~L~~~~r~v~~l~~~~----------g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 182 (187)
T TIGR02948 135 QALPPKYRMVIVLKYME----------DLSLKEISEILDLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred HhCCHHHhHHhhhHHhc----------CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4677778777655 333 3467899999999999999999998887765
No 145
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=30.11 E-value=8.1 Score=32.88 Aligned_cols=33 Identities=15% Similarity=0.173 Sum_probs=28.1
Q ss_pred CHHHHHHHHHHhCCCCceEEEecccccccCCCC
Q 021941 264 DDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKN 296 (305)
Q Consensus 264 de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK 296 (305)
+....+++|.++||++.++++.++.-|.++++.
T Consensus 144 ~g~s~~EIA~~l~is~~tV~~~l~rar~~Lr~~ 176 (181)
T PRK12536 144 EGLSVAETAQLTGLSESAVKVGIHRGLKALAAK 176 (181)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 334678999999999999999999998887764
No 146
>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=29.96 E-value=1.1e+02 Score=23.70 Aligned_cols=44 Identities=18% Similarity=0.210 Sum_probs=35.8
Q ss_pred CccCcCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEE
Q 021941 235 KRFRTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKV 284 (305)
Q Consensus 235 KR~RTkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KV 284 (305)
+++...++.++... .++|.-+..+...+.+++++.|++-++.++
T Consensus 22 ~~~~~~~~~~~l~~------~~~~~~~~~~~~~l~~~a~~~gl~~~~~~~ 65 (126)
T cd02425 22 NYFGYKVSLNELRE------KYELGRDGLSLSYLKQLLEEYGFKCKVYKI 65 (126)
T ss_pred HHhCCCCCHHHHHH------hccCCCCCcCHHHHHHHHHHCCCcceEEEE
Confidence 56777788887643 457777788899999999999999988876
No 147
>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=29.95 E-value=1.2e+02 Score=21.12 Aligned_cols=35 Identities=20% Similarity=0.288 Sum_probs=26.6
Q ss_pred CHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccc
Q 021941 242 TQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNK 290 (305)
Q Consensus 242 T~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK 290 (305)
|.|||++|.+ ++.+.+...+|+++..+-|.++...
T Consensus 12 t~eqk~~l~~--------------~i~~~l~~~~g~~~~~v~V~i~e~~ 46 (58)
T cd00491 12 TDEQKRELIE--------------RVTEAVSEILGAPEATIVVIIDEMP 46 (58)
T ss_pred CHHHHHHHHH--------------HHHHHHHHHhCcCcccEEEEEEEeC
Confidence 5899988754 2455678889999999999887643
No 148
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=29.90 E-value=8.8 Score=32.85 Aligned_cols=48 Identities=8% Similarity=0.094 Sum_probs=35.7
Q ss_pred cCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCC
Q 021941 239 TKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVK 295 (305)
Q Consensus 239 TkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~k 295 (305)
.+++++|++.+.-.. -++.-.++++..+|++..++++.++.-|.++++
T Consensus 130 ~~Lp~~~r~v~~l~~---------~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 177 (191)
T PRK12520 130 DRLPPRTGRVFMMRE---------WLELETEEICQELQITATNAWVLLYRARMRLRE 177 (191)
T ss_pred HhCCHHHHHHHHHHH---------HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 456677777665422 123467899999999999999999998887755
No 149
>PTZ00397 macrophage migration inhibition factor-like protein; Provisional
Probab=29.61 E-value=1.1e+02 Score=24.89 Aligned_cols=36 Identities=6% Similarity=0.112 Sum_probs=28.3
Q ss_pred CHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccc
Q 021941 242 TQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKN 291 (305)
Q Consensus 242 T~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~ 291 (305)
+.|||++|-+ + .-+.+.+++||+...+-|.|+++..
T Consensus 70 ~~e~k~~l~~---~-----------i~~~l~~~lgi~~~rv~I~f~~~~~ 105 (116)
T PTZ00397 70 SRSNNSSIAA---A-----------ITKILASHLKVKSERVYIEFKDCSA 105 (116)
T ss_pred CHHHHHHHHH---H-----------HHHHHHHHhCcCcccEEEEEEECCh
Confidence 5799987644 3 4456778899999999999998764
No 150
>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=29.38 E-value=8.8 Score=29.68 Aligned_cols=47 Identities=9% Similarity=0.189 Sum_probs=34.8
Q ss_pred CCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCC
Q 021941 240 KFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVK 295 (305)
Q Consensus 240 kFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~k 295 (305)
+++..|++.+..+.-. |+ ..++.|+++||++.+++.|++.-+.++++
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 6678888876553221 33 45699999999999999998887776654
No 151
>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=29.32 E-value=38 Score=26.46 Aligned_cols=30 Identities=13% Similarity=0.308 Sum_probs=25.4
Q ss_pred CccCcCCCHHHHHHHHHHHHHhCCccCCCC
Q 021941 235 KRFRTKFTQEQKDKMMEFAEKVGWRFQKQD 264 (305)
Q Consensus 235 KR~RTkFT~EQkekM~~fAEklGWRiqk~d 264 (305)
|+..+.+.-...++..+|++.|||+....+
T Consensus 1 ~~~~~~l~v~Dl~~s~~FY~~LGf~~~~~~ 30 (113)
T cd08356 1 KSIRPFIPAKDFAESKQFYQALGFELEWEN 30 (113)
T ss_pred CcceeccccccHHHHHHHHHHhCCeeEecC
Confidence 566788888899999999999999987654
No 152
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=28.88 E-value=22 Score=29.37 Aligned_cols=41 Identities=7% Similarity=0.198 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccc
Q 021941 244 EQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNN 289 (305)
Q Consensus 244 EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNn 289 (305)
.-.+++.+|-+. +..+.-.|+++|.++||+++.|.-||...
T Consensus 9 ~~i~~~~~~I~~-----~~~~~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 9 ITIHSILDWIED-----NLESPLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred HHHHHHHHHHHH-----hcCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 344677777776 44455789999999999999988877643
No 153
>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=28.31 E-value=45 Score=28.37 Aligned_cols=47 Identities=11% Similarity=0.095 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHhC--CccCCCCHHHHHHHHHHhCCC-CceEEEeccccccc
Q 021941 245 QKDKMMEFAEKVG--WRFQKQDDDQVDKFCAEVGVK-RHVFKVWMHNNKNN 292 (305)
Q Consensus 245 QkekM~~fAEklG--WRiqk~de~~ve~fC~eiGV~-r~V~KVWmhNnK~~ 292 (305)
.-+.+.++|+++- =.+-+-|.+++.+|+++.+|+ .-+|- .|.|+||-
T Consensus 32 mdp~l~ela~~~~~~~~f~kVDVDev~dva~~y~I~amPtfv-ffkngkh~ 81 (114)
T cd02986 32 LDDILSKTSHDLSKMASIYLVDVDKVPVYTQYFDISYIPSTI-FFFNGQHM 81 (114)
T ss_pred HHHHHHHHHHHccCceEEEEEeccccHHHHHhcCceeCcEEE-EEECCcEE
Confidence 3456667888752 124567889999999999998 77776 67777763
No 154
>PF13223 DUF4031: Protein of unknown function (DUF4031)
Probab=28.26 E-value=29 Score=28.28 Aligned_cols=20 Identities=35% Similarity=0.826 Sum_probs=14.6
Q ss_pred HHHHHHHHHHhCCCCceEEEeccc
Q 021941 265 DDQVDKFCAEVGVKRHVFKVWMHN 288 (305)
Q Consensus 265 e~~ve~fC~eiGV~r~V~KVWmhN 288 (305)
.+++.+|+..|||+|+ |||.
T Consensus 23 ~~ELHafA~riGv~rr----~fq~ 42 (83)
T PF13223_consen 23 LDELHAFAARIGVPRR----WFQR 42 (83)
T ss_pred HHHHHHHHHHcCCCHH----HHcC
Confidence 4567777777899986 5555
No 155
>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=28.10 E-value=26 Score=26.94 Aligned_cols=45 Identities=27% Similarity=0.413 Sum_probs=31.0
Q ss_pred CcCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecc
Q 021941 238 RTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMH 287 (305)
Q Consensus 238 RTkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmh 287 (305)
|-.||.+=|-+..++|++ ...-......-+.+.||.|+-++-|.+
T Consensus 3 rrsy~~~FKL~Vv~~a~~-----~~nc~~~~RAaarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEK-----DNNCKGNQRAAARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHHHHH------TTTTT-HHHHHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHHHHH-----ccchhhhHHHHHHHhCccHHHHHHHHH
Confidence 457999999999999998 455444556778999999999999975
No 156
>KOG2767 consensus Translation initiation factor 5 (eIF-5) [Translation, ribosomal structure and biogenesis]
Probab=27.84 E-value=19 Score=36.60 Aligned_cols=16 Identities=31% Similarity=0.767 Sum_probs=12.7
Q ss_pred cccccccccccccccc
Q 021941 113 ALKCAACECHRNFHRK 128 (305)
Q Consensus 113 al~CaACgCHRnFHrk 128 (305)
+++|+||||+-+---|
T Consensus 118 ~~~CkACG~r~~~d~r 133 (400)
T KOG2767|consen 118 SLKCKACGFRSDMDLR 133 (400)
T ss_pred hhHHHHcCCcccccch
Confidence 7899999998765443
No 157
>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=27.71 E-value=73 Score=26.35 Aligned_cols=46 Identities=20% Similarity=0.377 Sum_probs=35.9
Q ss_pred CccCcCCCHHHHHHHHHHHHH-hCCccCCCCHHHHHHHHHHhCCCCce
Q 021941 235 KRFRTKFTQEQKDKMMEFAEK-VGWRFQKQDDDQVDKFCAEVGVKRHV 281 (305)
Q Consensus 235 KR~RTkFT~EQkekM~~fAEk-lGWRiqk~de~~ve~fC~eiGV~r~V 281 (305)
.=.|..||.-|+..+++...+ .||. ++.|.-...+|+..+|+++..
T Consensus 24 ~l~~~dls~rq~ki~~ai~RkTyG~n-Kk~d~Is~sq~~e~tg~~~~~ 70 (100)
T PF04492_consen 24 ALLRADLSGRQLKILLAIIRKTYGWN-KKMDRISNSQIAEMTGLSRDH 70 (100)
T ss_pred HHHhccccHHHHHHHHHHHHHccCCC-CccceeeHHHHHHHHCcCHHH
Confidence 334678999999887775544 7887 677778899999999988764
No 158
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=27.69 E-value=9.4 Score=33.01 Aligned_cols=49 Identities=12% Similarity=0.162 Sum_probs=36.0
Q ss_pred cCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCC
Q 021941 239 TKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKN 296 (305)
Q Consensus 239 TkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK 296 (305)
.+++++|++.+.-.. -++..+++.|+++||+..++++.++--|.++++.
T Consensus 110 ~~Lp~~~R~v~~L~~---------~~g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~ 158 (182)
T PRK12540 110 DKLPQDQREALILVG---------ASGFSYEDAAAICGCAVGTIKSRVNRARSKLSAL 158 (182)
T ss_pred HhCCHHHHHHhhHHH---------HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 355666666654422 1234578999999999999999999988887665
No 159
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=27.62 E-value=7.5 Score=33.18 Aligned_cols=31 Identities=6% Similarity=0.021 Sum_probs=26.6
Q ss_pred HHHHHHHHHHhCCCCceEEEecccccccCCC
Q 021941 265 DDQVDKFCAEVGVKRHVFKVWMHNNKNNTVK 295 (305)
Q Consensus 265 e~~ve~fC~eiGV~r~V~KVWmhNnK~~~~k 295 (305)
..-.+++|..+||+..++++|++.-+.++++
T Consensus 157 g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 187 (194)
T PRK12519 157 GLSQSEIAKRLGIPLGTVKARARQGLLKLRE 187 (194)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 3467899999999999999999988877665
No 160
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=27.53 E-value=1.1e+02 Score=23.19 Aligned_cols=31 Identities=19% Similarity=0.193 Sum_probs=24.4
Q ss_pred CCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhC
Q 021941 240 KFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVG 276 (305)
Q Consensus 240 kFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiG 276 (305)
.|+.|+.+.+....++ --+++..+.+|+-+|
T Consensus 66 ~~~~~e~~~l~~~l~~------~~~~~~~~~~~~~~~ 96 (96)
T smart00529 66 GVDEEEVHEEAERLEH------VLSDELEDRLDRFLG 96 (96)
T ss_pred CCCHHHHHHHHHHHHc------cCCHHHHHHHHHHhC
Confidence 6888888888776666 567788889998776
No 161
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=27.53 E-value=11 Score=31.59 Aligned_cols=47 Identities=11% Similarity=0.215 Sum_probs=36.6
Q ss_pred CCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCC
Q 021941 240 KFTQEQKDKMME-FAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKN 296 (305)
Q Consensus 240 kFT~EQkekM~~-fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK 296 (305)
+++++|++.+.- +.|. .-++++|..+||+..+++++++.-+.++++.
T Consensus 118 ~L~~~~r~vl~L~~~~g----------~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 165 (173)
T PRK09645 118 QLSPEHRAVLVRSYYRG----------WSTAQIAADLGIPEGTVKSRLHYALRALRLA 165 (173)
T ss_pred hCCHHHHHHHHHHHHcC----------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 467777777665 3332 3578999999999999999999988877664
No 162
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=27.30 E-value=9.6 Score=31.45 Aligned_cols=47 Identities=9% Similarity=0.112 Sum_probs=33.6
Q ss_pred CCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCC
Q 021941 240 KFTQEQKDKMME-FAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKN 296 (305)
Q Consensus 240 kFT~EQkekM~~-fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK 296 (305)
+++++|++.+.- |.+- .-.++.|+++||+..+++++++--+.++++.
T Consensus 109 ~L~~~~r~v~~l~~~~~----------~s~~EIA~~lgis~~tV~~~l~ra~~~lr~~ 156 (163)
T PRK07037 109 ELPARTRYAFEMYRLHG----------ETQKDIARELGVSPTLVNFMIRDALVHCRKC 156 (163)
T ss_pred hCCHHHHHHHHHHHHcC----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 556666666644 3332 2467899999999999999988777666543
No 163
>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=27.04 E-value=11 Score=33.71 Aligned_cols=53 Identities=6% Similarity=0.010 Sum_probs=39.0
Q ss_pred cCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCC
Q 021941 239 TKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKN 296 (305)
Q Consensus 239 TkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK 296 (305)
.+|++.|++.+.-..-- .+-++.-.+++|+++||+..+++++++.-+.+++++
T Consensus 173 ~~L~~~~r~il~l~y~~-----~~~e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~~ 225 (227)
T TIGR02846 173 SVLDGREREVIEMRYGL-----GDGRRKTQREIAKILGISRSYVSRIEKRALMKLYKE 225 (227)
T ss_pred HhCCHHHHHHHHHHHcC-----CCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 57788888887764310 012445789999999999999999998877776653
No 164
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=26.85 E-value=10 Score=33.08 Aligned_cols=48 Identities=13% Similarity=0.180 Sum_probs=34.8
Q ss_pred CCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCC
Q 021941 240 KFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKN 296 (305)
Q Consensus 240 kFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK 296 (305)
+++++|++.+.-. +-++.-.++.|..+||+..++|+.++.-|.++++.
T Consensus 139 ~Lp~~~r~v~~L~---------~~eg~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~ 186 (201)
T PRK12545 139 HLPEQIGRVFMMR---------EFLDFEIDDICTELTLTANHCSVLLYRARTRLRTC 186 (201)
T ss_pred hCCHHHHHHHHHH---------HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4555666655542 22234678999999999999999999988877653
No 165
>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=26.75 E-value=36 Score=22.64 Aligned_cols=28 Identities=21% Similarity=0.396 Sum_probs=19.6
Q ss_pred eeccccccccCCCCCCcccccccccccccccccc
Q 021941 95 IFDGCGEFMPSGDEGTLEALKCAACECHRNFHRK 128 (305)
Q Consensus 95 a~DGCgEFmp~~~~gt~~al~CaACgCHRnFHrk 128 (305)
.=+.|+++|.... .+++|..| ....|.+
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 47999877 4444543
No 166
>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=26.10 E-value=36 Score=28.10 Aligned_cols=55 Identities=16% Similarity=0.229 Sum_probs=38.8
Q ss_pred ccCcCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCCCCCC
Q 021941 236 RFRTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKNKQEP 300 (305)
Q Consensus 236 R~RTkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK~~~~ 300 (305)
|.|.|+. .+.|.++.+. .+|. .+.|+|.++||+..++--.++--.-++||+...+
T Consensus 52 r~~~Kid---~~~L~~~v~~------~pd~-tl~Ela~~l~Vs~~ti~~~Lkrlg~t~KK~~~~~ 106 (119)
T PF01710_consen 52 RGRKKID---RDELKALVEE------NPDA-TLRELAERLGVSPSTIWRALKRLGITRKKKTLHS 106 (119)
T ss_pred ccccccc---HHHHHHHHHH------CCCc-CHHHHHHHcCCCHHHHHHHHHHcCchhccCcccc
Confidence 3333663 4556777666 5665 5567899999999998888887777777776543
No 167
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=25.94 E-value=12 Score=32.37 Aligned_cols=49 Identities=8% Similarity=0.110 Sum_probs=36.9
Q ss_pred CcCCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCC
Q 021941 238 RTKFTQEQKDKMME-FAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKN 296 (305)
Q Consensus 238 RTkFT~EQkekM~~-fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK 296 (305)
--+++++|++.|.- +.+. ...++.|..+||+..++++.++.-+.++++.
T Consensus 139 l~~Lp~~~r~v~~l~~~eg----------~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~ 188 (194)
T PRK12531 139 LDRLPKAQRDVLQAVYLEE----------LPHQQVAEMFDIPLGTVKSRLRLAVEKLRHS 188 (194)
T ss_pred HHhCCHHHHHHHHHHHHcC----------CCHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 34566777777665 3332 3568899999999999999999988887654
No 168
>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=25.74 E-value=15 Score=26.48 Aligned_cols=21 Identities=14% Similarity=0.438 Sum_probs=18.7
Q ss_pred HHHHHHHhCCCCceEEEeccc
Q 021941 268 VDKFCAEVGVKRHVFKVWMHN 288 (305)
Q Consensus 268 ve~fC~eiGV~r~V~KVWmhN 288 (305)
+.++|+.+||+..+|.-|.+.
T Consensus 3 ~~eva~~~gvs~~tlr~w~~~ 23 (68)
T cd01104 3 IGAVARLTGVSPDTLRAWERR 23 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 578999999999999999864
No 169
>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=25.38 E-value=67 Score=23.47 Aligned_cols=19 Identities=21% Similarity=0.639 Sum_probs=14.1
Q ss_pred CCHHHHHHHHHHHHHhCCc
Q 021941 241 FTQEQKDKMMEFAEKVGWR 259 (305)
Q Consensus 241 FT~EQkekM~~fAEklGWR 259 (305)
++..|++||.++.++-||-
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 4578999999999998994
No 170
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=25.38 E-value=12 Score=32.24 Aligned_cols=48 Identities=8% Similarity=0.090 Sum_probs=34.2
Q ss_pred CCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCC
Q 021941 240 KFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKN 296 (305)
Q Consensus 240 kFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK 296 (305)
+++++|++.+.-. +-+..-.++.|..+||+..+++++++.-|.++++.
T Consensus 136 ~L~~~~r~i~~L~---------~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 183 (195)
T PRK12532 136 NLPENTARVFTLK---------EILGFSSDEIQQMCGISTSNYHTIMHRARESLRQC 183 (195)
T ss_pred hCCHHHHHHhhhH---------HHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4556666655431 12234578999999999999999999888776653
No 171
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=25.09 E-value=20 Score=33.24 Aligned_cols=50 Identities=4% Similarity=0.105 Sum_probs=38.2
Q ss_pred CCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCCCC
Q 021941 240 KFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKNKQ 298 (305)
Q Consensus 240 kFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK~~ 298 (305)
+++++|++.+.-..- ++...++.|+.+|++..++|+.++.-|.++++..+
T Consensus 115 ~L~~~~R~v~~L~~~---------~g~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~~ 164 (293)
T PRK09636 115 RLSPLERAAFLLHDV---------FGVPFDEIASTLGRSPAACRQLASRARKHVRAARP 164 (293)
T ss_pred hCCHHHHHHHHHHHH---------hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC
Confidence 577777776554211 12356889999999999999999999999888654
No 172
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=25.06 E-value=7 Score=33.46 Aligned_cols=34 Identities=12% Similarity=0.149 Sum_probs=29.3
Q ss_pred CCHHHHHHHHHHhCCCCceEEEecccccccCCCC
Q 021941 263 QDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKN 296 (305)
Q Consensus 263 ~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK 296 (305)
-+..-+++.|.++||++.+++++++.-|.++++.
T Consensus 153 ~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 186 (194)
T PRK12513 153 HGDLELEEIAELTGVPEETVKSRLRYALQKLREL 186 (194)
T ss_pred ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3455789999999999999999999999887764
No 173
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=24.93 E-value=13 Score=32.67 Aligned_cols=49 Identities=4% Similarity=0.085 Sum_probs=36.6
Q ss_pred CcCCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCC
Q 021941 238 RTKFTQEQKDKMME-FAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKN 296 (305)
Q Consensus 238 RTkFT~EQkekM~~-fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK 296 (305)
-.++++.|++.+.- +.+ ...+++.|..+||+..+++++++.-|.++++.
T Consensus 131 l~~Lp~~~r~v~~l~~~~----------g~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~ 180 (196)
T PRK12535 131 IDALPPERREALILTQVL----------GYTYEEAAKIADVRVGTIRSRVARARADLIAA 180 (196)
T ss_pred HHcCCHHHHHHhhhHHHh----------CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 34566667666543 222 23578999999999999999999988887664
No 174
>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=24.89 E-value=44 Score=28.94 Aligned_cols=18 Identities=28% Similarity=0.719 Sum_probs=10.2
Q ss_pred HHHHHHHHHHHhCCccCC
Q 021941 245 QKDKMMEFAEKVGWRFQK 262 (305)
Q Consensus 245 QkekM~~fAEklGWRiqk 262 (305)
-.+....|+++||||.+.
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 175
>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=24.81 E-value=53 Score=22.48 Aligned_cols=31 Identities=23% Similarity=0.330 Sum_probs=21.9
Q ss_pred HHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEE
Q 021941 245 QKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFK 283 (305)
Q Consensus 245 QkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~K 283 (305)
+++.+...-++-||. +.+-|+.+||+|.+|.
T Consensus 6 E~~~i~~aL~~~~gn--------~~~aA~~Lgisr~tL~ 36 (42)
T PF02954_consen 6 EKQLIRQALERCGGN--------VSKAARLLGISRRTLY 36 (42)
T ss_dssp HHHHHHHHHHHTTT---------HHHHHHHHTS-HHHHH
T ss_pred HHHHHHHHHHHhCCC--------HHHHHHHHCCCHHHHH
Confidence 455666777776665 4688999999998874
No 176
>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=24.52 E-value=37 Score=24.77 Aligned_cols=21 Identities=29% Similarity=0.548 Sum_probs=16.9
Q ss_pred CccCcCCCHHHHHHHHHHHHH
Q 021941 235 KRFRTKFTQEQKDKMMEFAEK 255 (305)
Q Consensus 235 KR~RTkFT~EQkekM~~fAEk 255 (305)
..+...||.++++.|.+|++.
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 356678999999999999875
No 177
>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=24.50 E-value=13 Score=33.07 Aligned_cols=49 Identities=2% Similarity=0.040 Sum_probs=37.6
Q ss_pred cCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCC
Q 021941 239 TKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKN 296 (305)
Q Consensus 239 TkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK 296 (305)
.++++.|++.+..++. ++...+++|..+||+..+++.+++.-+.+++++
T Consensus 174 ~~L~~~~r~il~l~y~---------~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 222 (224)
T TIGR02479 174 ESLSEREQLVLSLYYY---------EELNLKEIGEVLGLTESRVSQIHSQALKKLRAK 222 (224)
T ss_pred HhCCHHHHHHHHHHHh---------CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 4577778777776432 223578999999999999999999888777653
No 178
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=24.46 E-value=12 Score=32.40 Aligned_cols=47 Identities=11% Similarity=0.068 Sum_probs=35.7
Q ss_pred CCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCC
Q 021941 240 KFTQEQKDKMME-FAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKN 296 (305)
Q Consensus 240 kFT~EQkekM~~-fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK 296 (305)
++++.|++.+.- |.+ +...+++|..+||+..+++++++--|.++++.
T Consensus 111 ~Lp~~~R~v~~L~~~e----------g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 158 (182)
T PRK12511 111 DLPEEQRAALHLVAIE----------GLSYQEAAAVLGIPIGTLMSRIGRARAALRAF 158 (182)
T ss_pred hCCHHHHHHHHHHHHc----------CCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 577777776655 222 33578999999999999999999888776553
No 179
>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=24.43 E-value=59 Score=26.38 Aligned_cols=19 Identities=21% Similarity=0.562 Sum_probs=17.1
Q ss_pred HHHHHHHHHHHHHhCCccC
Q 021941 243 QEQKDKMMEFAEKVGWRFQ 261 (305)
Q Consensus 243 ~EQkekM~~fAEklGWRiq 261 (305)
..|++.+++||++.||.+-
T Consensus 18 ~~Q~~~~~~~a~~~g~~i~ 36 (148)
T smart00857 18 ERQLEALRAYAKANGWEVV 36 (148)
T ss_pred HHHHHHHHHHHHHCCCEEE
Confidence 6899999999999999863
No 180
>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=24.42 E-value=68 Score=24.20 Aligned_cols=34 Identities=21% Similarity=0.544 Sum_probs=25.2
Q ss_pred HHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecc
Q 021941 251 EFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMH 287 (305)
Q Consensus 251 ~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmh 287 (305)
.||.++||+| .+.+.+..+...+ |..+.+.+|-.
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 5566778877776 55566666655
No 181
>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=24.40 E-value=1.1e+02 Score=24.78 Aligned_cols=49 Identities=8% Similarity=0.447 Sum_probs=34.0
Q ss_pred CccCcCCCHHHHHHHHHHHHHhCC---ccCCCCHHHHHHHHHHhCCCCceEE
Q 021941 235 KRFRTKFTQEQKDKMMEFAEKVGW---RFQKQDDDQVDKFCAEVGVKRHVFK 283 (305)
Q Consensus 235 KR~RTkFT~EQkekM~~fAEklGW---Riqk~de~~ve~fC~eiGV~r~V~K 283 (305)
+.+++.|+.++|+.++..+..+-- .+.......+.+++..+||+..-|+
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 667888999999999998877532 3455556899999999999987764
No 182
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=24.34 E-value=21 Score=33.15 Aligned_cols=50 Identities=4% Similarity=0.054 Sum_probs=38.2
Q ss_pred cCCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCCCC
Q 021941 239 TKFTQEQKDKMME-FAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKNKQ 298 (305)
Q Consensus 239 TkFT~EQkekM~~-fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK~~ 298 (305)
-++++.|++.+.- +.+. ...++.|..+|++..+++++++.-|.++++..+
T Consensus 107 ~~L~~~~R~v~~L~~~~g----------~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~~~ 157 (281)
T TIGR02957 107 ERLSPLERAVFVLREVFD----------YPYEEIASIVGKSEANCRQLVSRARRHLDARRP 157 (281)
T ss_pred hhCCHHHHHHHHHHHHcC----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC
Confidence 3567777776544 2222 256889999999999999999999999887654
No 183
>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=24.30 E-value=1.4e+02 Score=25.39 Aligned_cols=25 Identities=24% Similarity=0.545 Sum_probs=14.8
Q ss_pred HHHHHHHHHhCCccCCCCHHHHHHHH
Q 021941 247 DKMMEFAEKVGWRFQKQDDDQVDKFC 272 (305)
Q Consensus 247 ekM~~fAEklGWRiqk~de~~ve~fC 272 (305)
+.+..+|++.||++. +|++++..+-
T Consensus 8 ~~~~~~a~~~G~~~N-pD~~~~~~v~ 32 (108)
T PF02943_consen 8 KFLEKYAEKSGYKLN-PDEEVTDDVL 32 (108)
T ss_dssp HHHHHHHHHTT-B-B-SSHHHHHHHH
T ss_pred HHHHHHHHHhCCEEC-CCHHHHHHHH
Confidence 344457889999985 6666655543
No 184
>PHA01976 helix-turn-helix protein
Probab=24.28 E-value=39 Score=24.28 Aligned_cols=18 Identities=11% Similarity=0.211 Sum_probs=12.0
Q ss_pred CCHHHHHHHHHHhCCCCc
Q 021941 263 QDDDQVDKFCAEVGVKRH 280 (305)
Q Consensus 263 ~de~~ve~fC~eiGV~r~ 280 (305)
++.+.+.++|.-+||+..
T Consensus 42 p~~~~l~~ia~~l~v~~~ 59 (67)
T PHA01976 42 PNLKTLLRLADALGVTLD 59 (67)
T ss_pred CCHHHHHHHHHHHCcCHH
Confidence 556667777777777654
No 185
>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=24.27 E-value=30 Score=27.91 Aligned_cols=10 Identities=40% Similarity=1.046 Sum_probs=8.3
Q ss_pred cccccccccc
Q 021941 112 EALKCAACEC 121 (305)
Q Consensus 112 ~al~CaACgC 121 (305)
..|.|+|||-
T Consensus 56 ~tLsCsACGS 65 (74)
T PF05077_consen 56 NTLSCSACGS 65 (74)
T ss_pred CeEeehhccc
Confidence 4799999983
No 186
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=24.20 E-value=13 Score=31.87 Aligned_cols=51 Identities=12% Similarity=0.203 Sum_probs=39.1
Q ss_pred ccCcCCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCC
Q 021941 236 RFRTKFTQEQKDKMME-FAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKN 296 (305)
Q Consensus 236 R~RTkFT~EQkekM~~-fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK 296 (305)
+.-..++++|++.+.- +.+. ...++.|..+||+..++++.++.-|.++++.
T Consensus 127 ~~l~~L~~~~r~vl~l~~~~~----------~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 178 (189)
T PRK12515 127 ACLAKLSPAHREIIDLVYYHE----------KSVEEVGEIVGIPESTVKTRMFYARKKLAEL 178 (189)
T ss_pred HHHHhCCHHHHHHHHHHHHcC----------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3345778888888754 4443 3578899999999999999999988887653
No 187
>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=24.01 E-value=89 Score=22.76 Aligned_cols=27 Identities=11% Similarity=0.479 Sum_probs=23.3
Q ss_pred HHHHHHHHHHhCCCC-ceEEEecccccc
Q 021941 265 DDQVDKFCAEVGVKR-HVFKVWMHNNKN 291 (305)
Q Consensus 265 e~~ve~fC~eiGV~r-~V~KVWmhNnK~ 291 (305)
..+.+.||.+.|++. ..++.+|...+-
T Consensus 24 ~~l~~~~~~~~~i~~~~~~~l~fdG~~L 51 (72)
T PF11976_consen 24 SKLIEKYCEKKGIPPEESIRLIFDGKRL 51 (72)
T ss_dssp HHHHHHHHHHHTTTT-TTEEEEETTEEE
T ss_pred HHHHHHHHHhhCCCccceEEEEECCEEc
Confidence 468899999999999 999999987654
No 188
>PRK02289 4-oxalocrotonate tautomerase; Provisional
Probab=23.88 E-value=1.9e+02 Score=20.97 Aligned_cols=34 Identities=15% Similarity=0.282 Sum_probs=26.7
Q ss_pred CCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccc
Q 021941 241 FTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHN 288 (305)
Q Consensus 241 FT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhN 288 (305)
.|.|||++|.+ . +-+.++..+|++...+.|.+..
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 37999988754 2 5566788899999999998764
No 189
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=23.88 E-value=14 Score=32.83 Aligned_cols=52 Identities=10% Similarity=0.084 Sum_probs=38.0
Q ss_pred cCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCC
Q 021941 239 TKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVK 295 (305)
Q Consensus 239 TkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~k 295 (305)
.+++++|++.+.-... + ..-++.-.++.+..+||+..+++++++.-+.++++
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 4566777777665321 0 12345568899999999999999999988887765
No 190
>PF01870 Hjc: Archaeal holliday junction resolvase (hjc); InterPro: IPR002732 This entry represents Holliday junction resolvases (hjc gene) and related proteins, primarily from archaeal species []. The Holliday junction is an essential intermediate of homologous recombination. Holliday junctions are four-stranded DNA complexes that are formed during recombination and related DNA repair events. In the presence of divalent cations, these junctions exist predominantly as the stacked-X form in which the double-helical segments are coaxially stacked and twisted by 60 degrees in a right-handed direction across the junction cross-over. In this structure, the stacked arms resemble two adjacent double-helices, but are linked at the junction by two common strands that cross-over between the duplexes []. During homologous recombination, genetic information is physically exchanged between parental DNAs via crossing single strands of the same polarity within the four-way Holliday structure. This process is terminated by the endonucleolytic activity of resolvases, which convert the four-way DNA back to two double strands.; PDB: 2WJ0_A 2WIZ_B 2WIW_B 2WCW_C 2WCZ_A 1HH1_A 1GEF_D 1IPI_B 2EO0_B 1OB9_A ....
Probab=23.86 E-value=38 Score=27.44 Aligned_cols=20 Identities=30% Similarity=0.627 Sum_probs=17.8
Q ss_pred CcCCCHHHHHHHHHHHHHhC
Q 021941 238 RTKFTQEQKDKMMEFAEKVG 257 (305)
Q Consensus 238 RTkFT~EQkekM~~fAEklG 257 (305)
+-.+..||-++|.+|+++.|
T Consensus 48 ~~~l~~eqve~L~~f~~~fg 67 (88)
T PF01870_consen 48 KIYLEKEQVEKLKEFSKRFG 67 (88)
T ss_dssp EEEEEHHHHHHHHHHHHHHT
T ss_pred ceeECHHHHHHHHHHHHHhC
Confidence 67789999999999999964
No 191
>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=23.81 E-value=17 Score=26.60 Aligned_cols=21 Identities=24% Similarity=0.650 Sum_probs=18.2
Q ss_pred HHHHHHHhCCCCceEEEeccc
Q 021941 268 VDKFCAEVGVKRHVFKVWMHN 288 (305)
Q Consensus 268 ve~fC~eiGV~r~V~KVWmhN 288 (305)
+.++|+.+||+..+|+.|...
T Consensus 3 i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 568999999999999999754
No 192
>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=23.67 E-value=55 Score=25.00 Aligned_cols=47 Identities=11% Similarity=0.177 Sum_probs=34.9
Q ss_pred HHHHHHHHHHHHhC--CccCCCCHHHHHHHHHHhCCCCceEEEeccccc
Q 021941 244 EQKDKMMEFAEKVG--WRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNK 290 (305)
Q Consensus 244 EQkekM~~fAEklG--WRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK 290 (305)
+.+..|.+++++++ |++-+-|.+.-.+++.+.||..--.=+++.|.+
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 44556777887775 667777777777899999998777777776654
No 193
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=23.53 E-value=13 Score=32.85 Aligned_cols=47 Identities=15% Similarity=0.188 Sum_probs=34.5
Q ss_pred CCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCC
Q 021941 240 KFTQEQKDKMME-FAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKN 296 (305)
Q Consensus 240 kFT~EQkekM~~-fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK 296 (305)
+++.+|++.+.- |.+- .-+++.++.+||+..+++++++.-|.++++.
T Consensus 138 ~L~~~~r~v~~L~~~~g----------~s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~ 185 (203)
T PRK09647 138 SLPPEFRAAVVLCDIEG----------LSYEEIAATLGVKLGTVRSRIHRGRQQLRAA 185 (203)
T ss_pred hCCHHHHHHHHHHHHcC----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 455666665433 2222 3568899999999999999999998887653
No 194
>PRK13858 type IV secretion system T-DNA border endonuclease VirD1; Provisional
Probab=23.42 E-value=1.3e+02 Score=26.97 Aligned_cols=39 Identities=15% Similarity=0.203 Sum_probs=32.0
Q ss_pred CCccCcCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhC
Q 021941 234 KKRFRTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVG 276 (305)
Q Consensus 234 kKR~RTkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiG 276 (305)
.|.+.|+||.+.++.+..-|+.+|+. .-+.|.+.+.++|
T Consensus 24 ~kvVsvRLTe~Ey~~L~~rA~~aGlS----~SEfIRqAi~~~~ 62 (147)
T PRK13858 24 FKVVSTRLRSAEYESFSAQARLLGLS----DSMAIRVAVRRIG 62 (147)
T ss_pred CeEEEEecCHHHHHHHHHHHHHcCCC----HHHHHHHHHHhcC
Confidence 48899999999999999999998873 3456777777766
No 195
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=23.26 E-value=24 Score=28.79 Aligned_cols=48 Identities=17% Similarity=0.234 Sum_probs=38.8
Q ss_pred cCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCC
Q 021941 239 TKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKN 296 (305)
Q Consensus 239 TkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK 296 (305)
..||..+.+.+.-+++-+ ..++++++++++.+++++.+.|=+.|++-+
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 369999999988888641 466788899999999999998888776644
No 196
>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=22.98 E-value=20 Score=32.43 Aligned_cols=49 Identities=8% Similarity=0.156 Sum_probs=39.8
Q ss_pred CcCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCC
Q 021941 238 RTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKN 296 (305)
Q Consensus 238 RTkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK 296 (305)
..+||..|+|.+.-.|+ | ...++.+..+||+.++++.++.|-+.|++-+
T Consensus 169 ~~~Lt~re~evl~~~a~--G--------~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~~ 217 (232)
T TIGR03541 169 AGVLSEREREVLAWTAL--G--------RRQADIAAILGISERTVENHLRSARRKLGVA 217 (232)
T ss_pred hccCCHHHHHHHHHHHC--C--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHCCC
Confidence 45899999999877652 2 3456788999999999999999998887754
No 197
>cd08577 PI-PLCc_GDPD_SF_unchar3 Uncharacterized hypothetical proteins similar to the catalytic domains of Phosphoinositide-specific phospholipaseand Glycerophosphodiester phosphodiesterases. This subfamily corresponds to a group of uncharacterized hypothetical proteins similar to the catalytic domains of Phosphoinositide-specific phospholipase C (PI-PLC), and glycerophosphodiester phosphodiesterases (GP-GDE), and also sphingomyelinases D (SMases D) and similar proteins. They hydrolyze the 3'-5' phosphodiester bonds in different substrates, utilizing a similar mechanism of general base and acid catalysis involving two conserved histidine residues.
Probab=22.97 E-value=1.4e+02 Score=27.75 Aligned_cols=40 Identities=25% Similarity=0.307 Sum_probs=25.7
Q ss_pred cCCCHHHHHHHHHH---HHHhCCccCC---CCHHHHHHHHHHhCCC
Q 021941 239 TKFTQEQKDKMMEF---AEKVGWRFQK---QDDDQVDKFCAEVGVK 278 (305)
Q Consensus 239 TkFT~EQkekM~~f---AEklGWRiqk---~de~~ve~fC~eiGV~ 278 (305)
-.|+.+|+++|.++ |.+.|+++.- ++...+=+.+.+.||.
T Consensus 177 g~~~~~q~~~l~~~v~~a~~~Gl~vr~Wtv~~~~~~~~~l~~~GVd 222 (228)
T cd08577 177 GDTPEDEKEKLKSIIDKAHARGKKVRFWGTPDRPNVWKTLMELGVD 222 (228)
T ss_pred CCCCHHHHHHHHHHHHHHHHCCCEEEEEccCChHHHHHHHHHhCCC
Confidence 45999999999997 5566766643 2223333455566764
No 198
>PHA01623 hypothetical protein
Probab=22.96 E-value=18 Score=27.06 Aligned_cols=27 Identities=15% Similarity=0.225 Sum_probs=22.5
Q ss_pred CCCCccCcCCCHHHHHHHHHHHHHhCC
Q 021941 232 LSKKRFRTKFTQEQKDKMMEFAEKVGW 258 (305)
Q Consensus 232 ~~kKR~RTkFT~EQkekM~~fAEklGW 258 (305)
-.++||--++..+..++|..++++.|-
T Consensus 11 ~k~~r~sVrldeel~~~Ld~y~~~~g~ 37 (56)
T PHA01623 11 KQKAVFGIYMDKDLKTRLKVYCAKNNL 37 (56)
T ss_pred ccceeEEEEeCHHHHHHHHHHHHHcCC
Confidence 456888889999999999999999554
No 199
>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=22.79 E-value=14 Score=31.90 Aligned_cols=47 Identities=11% Similarity=0.134 Sum_probs=34.5
Q ss_pred CCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCC
Q 021941 240 KFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVK 295 (305)
Q Consensus 240 kFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~k 295 (305)
+++++|++.+.-.+ -+..-+++++.++|++..++|++++.-|.++++
T Consensus 131 ~L~~~~r~v~~l~~---------~~g~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~ 177 (188)
T TIGR02943 131 HLPEQTARVFMMRE---------VLGFESDEICQELEISTSNCHVLLYRARLSLRA 177 (188)
T ss_pred hCCHHHHHHHHHHH---------HhCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 55666666654422 123467899999999999999999988877665
No 200
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=22.69 E-value=15 Score=31.21 Aligned_cols=46 Identities=9% Similarity=0.150 Sum_probs=33.8
Q ss_pred CCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCC
Q 021941 240 KFTQEQKDKMME-FAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVK 295 (305)
Q Consensus 240 kFT~EQkekM~~-fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~k 295 (305)
++++.|++.+.- +.+ +.-.++++..+||+..++++.++.-+.++++
T Consensus 117 ~Lp~~~r~i~~l~~~e----------~~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 163 (179)
T PRK12543 117 KLPYKLRQVIILRYLH----------DYSQEEIAQLLQIPIGTVKSRIHAALKKLRQ 163 (179)
T ss_pred hCCHHHHHHHHHHHHc----------cCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 455666655554 223 2357889999999999999999998887664
No 201
>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=22.64 E-value=50 Score=25.04 Aligned_cols=17 Identities=29% Similarity=0.376 Sum_probs=13.6
Q ss_pred CccCcCCCHHHHHHHHH
Q 021941 235 KRFRTKFTQEQKDKMME 251 (305)
Q Consensus 235 KR~RTkFT~EQkekM~~ 251 (305)
..++..||+||++++.+
T Consensus 82 ~~~~~vLt~eQk~~~~~ 98 (100)
T PF07813_consen 82 HALYAVLTPEQKEKFDQ 98 (100)
T ss_dssp HHHHTTS-HHHHHHHHH
T ss_pred HHHHhcCCHHHHHHHHH
Confidence 66889999999999765
No 202
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=22.55 E-value=13 Score=31.20 Aligned_cols=31 Identities=13% Similarity=0.181 Sum_probs=26.9
Q ss_pred HHHHHHHHHHhCCCCceEEEecccccccCCC
Q 021941 265 DDQVDKFCAEVGVKRHVFKVWMHNNKNNTVK 295 (305)
Q Consensus 265 e~~ve~fC~eiGV~r~V~KVWmhNnK~~~~k 295 (305)
+.-.++.|.++||+..+++++++.-|.++++
T Consensus 152 ~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 182 (187)
T PRK09641 152 DLSLKEISEILDLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3467899999999999999999998888765
No 203
>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=22.46 E-value=23 Score=30.97 Aligned_cols=47 Identities=17% Similarity=0.094 Sum_probs=38.6
Q ss_pred cCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCC
Q 021941 239 TKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVK 295 (305)
Q Consensus 239 TkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~k 295 (305)
|.+|..|++.+.-++ -|| ..++++.++|+++..++.|.+.-+.++++
T Consensus 5 ~~Lte~qr~VL~Lr~--~Gl--------Tq~EIAe~LgiS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 5 TFLTERQIKVLELRE--KGL--------SQKEIAKELKTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred CCCCHHHHHHHHHHH--cCC--------CHHHHHHHHCcCHHHHHHHHHhHHHHHHH
Confidence 788999999887753 344 56789999999999999999988877764
No 204
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=22.42 E-value=14 Score=31.86 Aligned_cols=47 Identities=4% Similarity=0.053 Sum_probs=33.5
Q ss_pred CCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCC
Q 021941 240 KFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVK 295 (305)
Q Consensus 240 kFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~k 295 (305)
+++++|++.+.-+. -++.-+++.|..+||+..+++.+++.-|.++++
T Consensus 106 ~L~~~~r~i~~l~~---------~~g~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 152 (181)
T PRK09637 106 ALPEKYAEALRLTE---------LEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKE 152 (181)
T ss_pred hCCHHHHHHHHHHH---------hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 55666666653321 122357889999999999999999988877664
No 205
>PF05291 Bystin: Bystin; InterPro: IPR007955 Trophinin and tastin form a cell adhesion molecule complex that potentially mediates an initial attachment of the blastocyst to uterine epithelial cells at the time of implantation. Trophinin and tastin bind to an intermediary cytoplasmic protein called bystin. Bystin may be involved in implantation and trophoblast invasion because bystin is found with trophinin and tastin in the cells at human implantation sites and also in the intermediate trophoblasts at invasion front in the placenta from early pregnancy []. This family also includes the Saccharomyces cerevisiae protein ENP1. ENP1 is an essential protein in S. cerevisiae and is localised in the nucleus []. It is thought that ENP1 plays a direct role in the early steps of rRNA processing as enp1 defective S. cerevisiae cannot synthesise 20S pre-rRNA and hence 18S rRNA, which leads to reduced formation of 40S ribosomal subunits [].
Probab=22.30 E-value=67 Score=31.81 Aligned_cols=21 Identities=33% Similarity=0.724 Sum_probs=20.0
Q ss_pred CccCcCCCHHHHHHHHHHHHH
Q 021941 235 KRFRTKFTQEQKDKMMEFAEK 255 (305)
Q Consensus 235 KR~RTkFT~EQkekM~~fAEk 255 (305)
+|+|+.+|.|||+.|++...+
T Consensus 253 qrYk~di~~eqk~~L~~ll~~ 273 (301)
T PF05291_consen 253 QRYKNDITEEQKEALLELLRK 273 (301)
T ss_pred HHHHHhCCHHHHHHHHHHHHh
Confidence 899999999999999999888
No 206
>PRK08942 D,D-heptose 1,7-bisphosphate phosphatase; Validated
Probab=22.27 E-value=2.4e+02 Score=24.03 Aligned_cols=43 Identities=16% Similarity=0.127 Sum_probs=30.8
Q ss_pred cCcCCCHHHHHHH----HHHHHHhCCc----------------cCCCCHHHHHHHHHHhCCCC
Q 021941 237 FRTKFTQEQKDKM----MEFAEKVGWR----------------FQKQDDDQVDKFCAEVGVKR 279 (305)
Q Consensus 237 ~RTkFT~EQkekM----~~fAEklGWR----------------iqk~de~~ve~fC~eiGV~r 279 (305)
.|..|+..|.+++ ....+++|+. ..||+....+..++.+|++.
T Consensus 58 ~~~~~~~~~~~~~~~~~~~~l~~~g~~f~~i~~~~~~~~~~~~~~KP~p~~~~~~~~~l~~~~ 120 (181)
T PRK08942 58 ARGLFTEAQLNALHEKMDWSLADRGGRLDGIYYCPHHPEDGCDCRKPKPGMLLSIAERLNIDL 120 (181)
T ss_pred cCCcCCHHHHHHHHHHHHHHHHHcCCccceEEECCCCCCCCCcCCCCCHHHHHHHHHHcCCCh
Confidence 4668888886654 3344555642 35889999999999999974
No 207
>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=22.13 E-value=1.7e+02 Score=22.71 Aligned_cols=44 Identities=11% Similarity=0.105 Sum_probs=34.0
Q ss_pred CccCcCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEE
Q 021941 235 KRFRTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKV 284 (305)
Q Consensus 235 KR~RTkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KV 284 (305)
+.+.-.++.++... .++|.....+...+.+.++++|++-+..++
T Consensus 17 ~~~g~~~~~~~l~~------~~~~~~~~~~~~~l~~~a~~~Gl~~~~~~~ 60 (121)
T cd02417 17 RYHGIAADPEQLRH------EFGLAGEPFNSTELLLAAKSLGLKAKAVRQ 60 (121)
T ss_pred HHcCCCCCHHHHHH------HhcCCCCCCCHHHHHHHHHHcCCeeEEEec
Confidence 45566677777764 456766678889999999999999888876
No 208
>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=22.12 E-value=1.8e+02 Score=22.71 Aligned_cols=44 Identities=9% Similarity=0.212 Sum_probs=28.6
Q ss_pred CccC-cCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEE
Q 021941 235 KRFR-TKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKV 284 (305)
Q Consensus 235 KR~R-TkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KV 284 (305)
+.++ -.++.+|.. +.++|.-...+...+.+++++.|++-+.+++
T Consensus 22 ~~~g~~~~~~~~l~------~~~~~~~~~~s~~~l~~~a~~~Gl~~~~~~~ 66 (129)
T cd02423 22 RYYGGINITEQEVL------KLMLIRSEGFSMLDLKRYAEALGLKANGYRL 66 (129)
T ss_pred HhcCCCCCCHHHHH------HHhCcccCCcCHHHHHHHHHHCCCcceEEEc
Confidence 4444 556666553 3445655667777778888888887777765
No 209
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=22.11 E-value=9.9 Score=32.17 Aligned_cols=48 Identities=8% Similarity=0.178 Sum_probs=33.8
Q ss_pred cCcCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccC
Q 021941 237 FRTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNT 293 (305)
Q Consensus 237 ~RTkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~ 293 (305)
.-.+++++|++.+.-. .-++.-.++++..+||+..+++++++.-+...
T Consensus 116 ~l~~L~~~~r~i~~l~---------~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~ 163 (172)
T PRK09651 116 MLDGLNGKTREAFLLS---------QLDGLTYSEIAHKLGVSVSSVKKYVAKATEHC 163 (172)
T ss_pred HHHhCCHHHhHHhhhh---------hccCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 3456677777664431 22233578999999999999999998776554
No 210
>cd01896 DRG The developmentally regulated GTP-binding protein (DRG) subfamily is an uncharacterized member of the Obg family, an evolutionary branch of GTPase superfamily proteins. GTPases act as molecular switches regulating diverse cellular processes. DRG2 and DRG1 comprise the DRG subfamily in eukaryotes. In view of their widespread expression in various tissues and high conservation among distantly related species in eukaryotes and archaea, DRG proteins may regulate fundamental cellular processes. It is proposed that the DRG subfamily proteins play their physiological roles through RNA binding.
Probab=21.82 E-value=1.9e+02 Score=26.23 Aligned_cols=43 Identities=16% Similarity=0.253 Sum_probs=35.6
Q ss_pred HHHHHHHHHHHHHhCCccCC-------------------------CCHHHHHHHHHHhCCCCceEEEe
Q 021941 243 QEQKDKMMEFAEKVGWRFQK-------------------------QDDDQVDKFCAEVGVKRHVFKVW 285 (305)
Q Consensus 243 ~EQkekM~~fAEklGWRiqk-------------------------~de~~ve~fC~eiGV~r~V~KVW 285 (305)
.+|++.+.++++++|=++.+ -|++.|.++.+|.||-...+..|
T Consensus 91 ~~~~~~~~~~l~~~gi~l~~~~~~v~~~~~~~ggi~~~~~~~~~~~~~~~v~~~l~~~~i~~~~v~~~ 158 (233)
T cd01896 91 EGHREILERELEGVGIRLNKRPPNITIKKKKKGGINITSTVPLTKLDEKTIKAILREYKIHNADVLIR 158 (233)
T ss_pred hhHHHHHHHHHHHcCceecCCCCeEEEEEEecCCEEEeccCCCCCCCHHHHHHHHHHhCeeeEEEEEc
Confidence 45999999999999887543 56799999999999988877664
No 211
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=21.75 E-value=15 Score=32.69 Aligned_cols=48 Identities=8% Similarity=0.083 Sum_probs=35.5
Q ss_pred cCCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCC
Q 021941 239 TKFTQEQKDKMME-FAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKN 296 (305)
Q Consensus 239 TkFT~EQkekM~~-fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK 296 (305)
.+++++|++.+.- |.+ ..-+++.+..+||+..+++++++.-|+++++.
T Consensus 147 ~~L~~~~r~v~~L~~~~----------g~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~ 195 (206)
T PRK12544 147 DGLPAKYARVFMMREFI----------ELETNEICHAVDLSVSNLNVLLYRARLRLREC 195 (206)
T ss_pred HhCCHHHHHHHHHHHHc----------CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3556666666554 222 23568899999999999999999988887764
No 212
>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=21.51 E-value=17 Score=30.29 Aligned_cols=47 Identities=6% Similarity=0.182 Sum_probs=35.0
Q ss_pred CCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCC
Q 021941 240 KFTQEQKDKMME-FAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKN 296 (305)
Q Consensus 240 kFT~EQkekM~~-fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK 296 (305)
+++.+|++.+.. |.+. .-.++.|+.+||+..+++++++--+.++++.
T Consensus 119 ~L~~~~r~i~~l~~~~g----------~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~ 166 (169)
T TIGR02954 119 TLNDKYQTAIILRYYHD----------LTIKEIAEVMNKPEGTVKTYLHRALKKLKKR 166 (169)
T ss_pred hCCHHHhHHHHHHHHcC----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 566777777644 3332 2467899999999999999999888777653
No 213
>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=21.41 E-value=2.1e+02 Score=20.33 Aligned_cols=34 Identities=21% Similarity=0.332 Sum_probs=26.3
Q ss_pred CHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccc
Q 021941 242 TQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNN 289 (305)
Q Consensus 242 T~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNn 289 (305)
|.|||++|.+ . +-+.++..+|+....+-|.+...
T Consensus 13 t~eqK~~l~~---~-----------it~~l~~~lg~~~~~v~V~i~e~ 46 (63)
T TIGR00013 13 TDEQKRQLIE---G-----------VTEAMAETLGANLESIVVIIDEM 46 (63)
T ss_pred CHHHHHHHHH---H-----------HHHHHHHHhCCCcccEEEEEEEc
Confidence 7999988654 2 55668888999999888887654
No 214
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=21.39 E-value=16 Score=31.38 Aligned_cols=48 Identities=8% Similarity=0.110 Sum_probs=36.3
Q ss_pred cCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCC
Q 021941 239 TKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKN 296 (305)
Q Consensus 239 TkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK 296 (305)
.++++.+++.+.-+.+. .-.+++|..+||+..++++.++.-|.++++.
T Consensus 154 ~~L~~~~r~vl~l~~e~----------~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~ 201 (208)
T PRK08295 154 ELLSELEKEVLELYLDG----------KSYQEIAEELNRHVKSIDNALQRVKRKLEKY 201 (208)
T ss_pred HhCCHHHHHHHHHHHcc----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 45667777776554443 3568899999999999999999888877653
No 215
>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=21.34 E-value=1.9e+02 Score=22.67 Aligned_cols=44 Identities=2% Similarity=0.088 Sum_probs=34.9
Q ss_pred CccCcCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEE
Q 021941 235 KRFRTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKV 284 (305)
Q Consensus 235 KR~RTkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KV 284 (305)
+.+...++.++... .++|.....+...+.++++..|++-+++++
T Consensus 22 ~~~g~~~~~~~l~~------~~~~~~~~~~~~~l~~~a~~~Gl~~~~~~~ 65 (127)
T cd02419 22 SYHGHHVDLASLRQ------RFPVSLKGATLADLIDIAQQLGLSTRALRL 65 (127)
T ss_pred HHcCCCCCHHHHHH------HcCCCCCCcCHHHHHHHHHHCCCceeEEEc
Confidence 56777888887754 456766678888999999999999888875
No 216
>COG3916 LasI N-acyl-L-homoserine lactone synthetase [Signal transduction mechanisms / Secondary metabolites biosynthesis, transport, and catabolism]
Probab=21.23 E-value=47 Score=31.31 Aligned_cols=28 Identities=21% Similarity=0.526 Sum_probs=22.3
Q ss_pred HHHHHHH--HHHHhCCccCCCCHHHHHHHH
Q 021941 245 QKDKMME--FAEKVGWRFQKQDDDQVDKFC 272 (305)
Q Consensus 245 QkekM~~--fAEklGWRiqk~de~~ve~fC 272 (305)
+.-+++. |-|++||...-.++.++++|=
T Consensus 19 em~rlR~~vF~erL~W~v~~~~g~E~DqyD 48 (209)
T COG3916 19 EMHRLRYQVFKERLGWDVVCIDGFEIDQYD 48 (209)
T ss_pred HHHHHHHHHHHHhcCCceeccCCccccccC
Confidence 4444444 999999999999988988874
No 217
>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=21.20 E-value=77 Score=24.06 Aligned_cols=15 Identities=20% Similarity=0.414 Sum_probs=12.6
Q ss_pred CCHHHHHHHHHHHHH
Q 021941 241 FTQEQKDKMMEFAEK 255 (305)
Q Consensus 241 FT~EQkekM~~fAEk 255 (305)
+|.+||.+|.+|...
T Consensus 1 lT~~Qk~el~~l~~q 15 (59)
T PF10925_consen 1 LTDQQKKELKALYKQ 15 (59)
T ss_pred CCHHHHHHHHHHHHH
Confidence 689999999997766
No 218
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=20.98 E-value=18 Score=34.84 Aligned_cols=52 Identities=10% Similarity=0.174 Sum_probs=38.0
Q ss_pred CCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCC
Q 021941 240 KFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKN 296 (305)
Q Consensus 240 kFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK 296 (305)
++++.|++.+...+ |+ ..-+....++++..+||++.+++++++.-+.++++.
T Consensus 262 ~L~~~~R~vl~lry---gL--~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~ 313 (325)
T PRK05657 262 ELNDKQREVLARRF---GL--LGYEAATLEDVAREIGLTRERVRQIQVEALRRLREI 313 (325)
T ss_pred cCCHHHHHHHHHHh---cc--CCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 56666666655432 22 233556789999999999999999999988887653
No 219
>PRK06930 positive control sigma-like factor; Validated
Probab=20.90 E-value=14 Score=32.61 Aligned_cols=47 Identities=6% Similarity=0.145 Sum_probs=36.5
Q ss_pred cCCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCC
Q 021941 239 TKFTQEQKDKMME-FAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVK 295 (305)
Q Consensus 239 TkFT~EQkekM~~-fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~k 295 (305)
.+|++.+++.+.- |++- ....++|..+||+..+++++++.-+.++++
T Consensus 113 ~~L~~rer~V~~L~~~eg----------~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~ 160 (170)
T PRK06930 113 SVLTEREKEVYLMHRGYG----------LSYSEIADYLNIKKSTVQSMIERAEKKIAR 160 (170)
T ss_pred HhCCHHHHHHHHHHHHcC----------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4577777777665 4333 356789999999999999999988887664
No 220
>PRK00745 4-oxalocrotonate tautomerase; Provisional
Probab=20.89 E-value=1.9e+02 Score=20.54 Aligned_cols=34 Identities=21% Similarity=0.264 Sum_probs=26.5
Q ss_pred CHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccc
Q 021941 242 TQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNN 289 (305)
Q Consensus 242 T~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNn 289 (305)
|.|||+.|.+ . ..+.++..+|++...+-|.|...
T Consensus 13 s~eqk~~l~~---~-----------it~~l~~~~~~p~~~v~V~i~e~ 46 (62)
T PRK00745 13 TVEQKRKLVE---E-----------ITRVTVETLGCPPESVDIIITDV 46 (62)
T ss_pred CHHHHHHHHH---H-----------HHHHHHHHcCCChhHEEEEEEEc
Confidence 7999987654 3 55668889999999999888654
No 221
>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=20.88 E-value=36 Score=29.18 Aligned_cols=13 Identities=54% Similarity=0.907 Sum_probs=10.8
Q ss_pred ccccccccccccc
Q 021941 111 LEALKCAACECHR 123 (305)
Q Consensus 111 ~~al~CaACgCHR 123 (305)
.-.|+|.|||..|
T Consensus 112 ~~~l~C~aCGa~~ 124 (125)
T PF01873_consen 112 LIFLKCKACGASR 124 (125)
T ss_dssp CCEEEETTTSCEE
T ss_pred EEEEEecccCCcC
Confidence 3489999999876
No 222
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=20.84 E-value=15 Score=31.22 Aligned_cols=50 Identities=2% Similarity=0.062 Sum_probs=37.6
Q ss_pred cCcCCCHHHHHHHHH-HHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCC
Q 021941 237 FRTKFTQEQKDKMME-FAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKN 296 (305)
Q Consensus 237 ~RTkFT~EQkekM~~-fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK 296 (305)
.=.+++++|++.+.- +.+. .-.+++|..+||+..++++.++.-|.++++.
T Consensus 119 ~l~~L~~~~r~i~~l~~~~g----------~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 169 (185)
T PRK12542 119 LLKELNESNRQVFKYKVFYN----------LTYQEISSVMGITEANVRKQFERARKRVQNM 169 (185)
T ss_pred HHHhCCHHHHHHHHHHHHcC----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 345677777777654 3333 3578999999999999999999888877653
No 223
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=20.66 E-value=47 Score=29.67 Aligned_cols=47 Identities=9% Similarity=0.105 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccc
Q 021941 243 QEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKN 291 (305)
Q Consensus 243 ~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~ 291 (305)
.+-++++++-|..|=+. +.-+ ..++++|++.||++.+|-.+|-|...
T Consensus 12 ~~~r~~Il~aA~~lF~~-~Gy~-~s~~~IA~~AGvsk~tiy~~F~sKe~ 58 (225)
T PRK11552 12 EQAKQQLIAAALAQFGE-YGLH-ATTRDIAAQAGQNIAAITYYFGSKED 58 (225)
T ss_pred HHHHHHHHHHHHHHHHH-hCcc-CCHHHHHHHhCCCHHHHHHHcCCHHH
Confidence 45566666533322111 1344 68999999999999999999976443
No 224
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=20.63 E-value=35 Score=29.21 Aligned_cols=47 Identities=11% Similarity=0.107 Sum_probs=32.9
Q ss_pred HHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEeccccc
Q 021941 243 QEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNK 290 (305)
Q Consensus 243 ~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK 290 (305)
.+-|+++.+-|.++=++ +.-+.-.++++|++.||++.+|-.+|.|..
T Consensus 10 ~~~r~~Il~aa~~lf~~-~G~~~~ti~~Ia~~agvsk~t~Y~~F~sKe 56 (213)
T PRK09975 10 LKTRQELIETAIAQFAL-RGVSNTTLNDIADAANVTRGAIYWHFENKT 56 (213)
T ss_pred HHHHHHHHHHHHHHHHH-cCcccCCHHHHHHHcCCCHHHHHHHcCCHH
Confidence 34456666644443111 355677999999999999999998887643
No 225
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=20.15 E-value=79 Score=28.30 Aligned_cols=42 Identities=14% Similarity=0.268 Sum_probs=32.5
Q ss_pred CCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEE
Q 021941 240 KFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFK 283 (305)
Q Consensus 240 kFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~K 283 (305)
.||..|++.+... =+.|+= ..|..-..+++++++||++.+|.
T Consensus 155 ~LTdrQ~~vL~~A-~~~GYF-d~PR~~~l~dLA~~lGISkst~~ 196 (215)
T COG3413 155 DLTDRQLEVLRLA-YKMGYF-DYPRRVSLKDLAKELGISKSTLS 196 (215)
T ss_pred cCCHHHHHHHHHH-HHcCCC-CCCccCCHHHHHHHhCCCHHHHH
Confidence 8999999996654 445663 34666789999999999988764
No 226
>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=20.10 E-value=51 Score=23.08 Aligned_cols=36 Identities=14% Similarity=0.293 Sum_probs=26.7
Q ss_pred CCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceE
Q 021941 241 FTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVF 282 (305)
Q Consensus 241 FT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~ 282 (305)
||..|...|..+++. ..++-.+.++|..+|+++.++
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 227
>PF13565 HTH_32: Homeodomain-like domain
Probab=20.03 E-value=34 Score=25.21 Aligned_cols=37 Identities=22% Similarity=0.469 Sum_probs=24.5
Q ss_pred ccCcCCCHHHHHHHHHHHHH-hCCccCCCCHHHHHHHHHHhCCC
Q 021941 236 RFRTKFTQEQKDKMMEFAEK-VGWRFQKQDDDQVDKFCAEVGVK 278 (305)
Q Consensus 236 R~RTkFT~EQkekM~~fAEk-lGWRiqk~de~~ve~fC~eiGV~ 278 (305)
|.|+ +.||.+.|.++.+. -.|.. +.+.+.+..+.|++
T Consensus 28 rp~~--~~e~~~~i~~~~~~~p~wt~----~~i~~~L~~~~g~~ 65 (77)
T PF13565_consen 28 RPRK--DPEQRERIIALIEEHPRWTP----REIAEYLEEEFGIS 65 (77)
T ss_pred CCCC--cHHHHHHHHHHHHhCCCCCH----HHHHHHHHHHhCCC
Confidence 3455 89998999997665 23333 45666777776754
No 228
>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=20.01 E-value=99 Score=24.62 Aligned_cols=43 Identities=16% Similarity=0.286 Sum_probs=31.4
Q ss_pred cCCCHHHHHHHHHHHHH-hCCccCCCCHHHHHHHHHHhCCCCceE
Q 021941 239 TKFTQEQKDKMMEFAEK-VGWRFQKQDDDQVDKFCAEVGVKRHVF 282 (305)
Q Consensus 239 TkFT~EQkekM~~fAEk-lGWRiqk~de~~ve~fC~eiGV~r~V~ 282 (305)
..++..|...|+..+++ -||.. ..+.-..++||+.+|++|.++
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 45677788888888863 47763 344556789999999998754
Done!