Query psy4325
Match_columns 306
No_of_seqs 313 out of 2533
Neff 8.4
Searched_HMMs 46136
Date Fri Aug 16 22:44:29 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4325.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4325hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4577|consensus 100.0 7.1E-52 1.5E-56 354.5 2.7 216 69-284 32-247 (383)
2 KOG1701|consensus 99.9 2.2E-28 4.7E-33 221.0 0.4 173 17-192 276-464 (468)
3 KOG1701|consensus 99.9 2.9E-26 6.4E-31 207.3 -4.7 163 69-238 273-438 (468)
4 KOG2272|consensus 99.9 5.1E-25 1.1E-29 186.4 -0.1 169 17-189 139-311 (332)
5 KOG1044|consensus 99.9 8E-23 1.7E-27 190.8 2.9 170 19-191 69-251 (670)
6 KOG2272|consensus 99.9 5.2E-23 1.1E-27 174.2 -0.4 175 14-193 72-255 (332)
7 KOG1703|consensus 99.8 4.8E-22 1E-26 191.6 1.6 169 16-187 304-478 (479)
8 KOG0850|consensus 99.8 5.6E-19 1.2E-23 148.4 7.1 66 202-267 120-185 (245)
9 KOG0484|consensus 99.8 1.1E-19 2.4E-24 133.6 2.4 69 198-266 11-79 (125)
10 KOG2251|consensus 99.7 5.8E-18 1.3E-22 141.7 7.3 68 199-266 32-99 (228)
11 KOG0490|consensus 99.7 5.1E-18 1.1E-22 149.3 6.3 189 75-264 1-213 (235)
12 KOG0489|consensus 99.7 7.6E-18 1.6E-22 150.0 6.5 68 202-269 157-224 (261)
13 KOG0843|consensus 99.7 1E-17 2.2E-22 135.7 5.8 64 203-266 101-164 (197)
14 KOG1703|consensus 99.7 7.4E-18 1.6E-22 162.6 5.9 167 22-192 250-422 (479)
15 KOG0488|consensus 99.7 1.4E-17 3E-22 150.7 6.2 67 202-268 170-236 (309)
16 KOG0842|consensus 99.7 8.2E-17 1.8E-21 143.3 6.5 68 201-268 150-217 (307)
17 KOG0487|consensus 99.7 3E-17 6.5E-22 146.2 3.1 65 204-268 235-299 (308)
18 KOG0848|consensus 99.6 4.7E-17 1E-21 139.3 2.3 64 204-267 199-262 (317)
19 KOG0492|consensus 99.6 1.8E-16 3.8E-21 131.1 4.1 69 198-266 138-206 (246)
20 PF00046 Homeobox: Homeobox do 99.6 1.9E-16 4.2E-21 108.3 2.8 57 205-261 1-57 (57)
21 KOG0485|consensus 99.6 2.2E-16 4.8E-21 131.3 2.8 67 200-266 100-166 (268)
22 KOG0490|consensus 99.6 6.1E-16 1.3E-20 136.1 5.7 119 135-264 2-120 (235)
23 KOG0494|consensus 99.6 4.9E-16 1.1E-20 132.5 4.3 66 204-269 141-206 (332)
24 TIGR01565 homeo_ZF_HD homeobox 99.5 4.9E-15 1.1E-19 100.1 3.5 53 204-256 1-57 (58)
25 KOG0493|consensus 99.5 3.6E-15 7.7E-20 127.3 3.3 66 203-268 245-310 (342)
26 COG5576 Homeodomain-containing 99.5 1.2E-14 2.5E-19 118.7 5.5 73 196-268 43-115 (156)
27 KOG1044|consensus 99.5 1E-14 2.2E-19 137.0 4.3 161 17-192 18-192 (670)
28 smart00389 HOX Homeodomain. DN 99.5 1.5E-14 3.2E-19 98.4 2.5 55 206-260 2-56 (56)
29 KOG0483|consensus 99.5 1.7E-14 3.8E-19 121.6 3.2 62 204-265 50-111 (198)
30 cd00086 homeodomain Homeodomai 99.5 3.1E-14 6.7E-19 97.8 3.2 57 206-262 2-58 (59)
31 KOG0847|consensus 99.5 5.1E-14 1.1E-18 117.4 5.0 66 200-265 163-228 (288)
32 KOG0491|consensus 99.4 4.5E-14 9.8E-19 112.8 2.7 63 204-266 100-162 (194)
33 PF00412 LIM: LIM domain; Int 99.4 2.4E-13 5.2E-18 93.1 3.3 56 73-128 1-58 (58)
34 KOG3802|consensus 99.4 4.9E-13 1.1E-17 121.6 5.5 65 200-264 290-354 (398)
35 KOG0844|consensus 99.4 1.2E-13 2.6E-18 120.5 0.8 66 200-265 177-242 (408)
36 KOG0486|consensus 99.3 4.4E-13 9.5E-18 117.7 2.6 65 203-267 111-175 (351)
37 PF00412 LIM: LIM domain; Int 99.3 1.4E-12 3E-17 89.3 3.3 58 132-191 1-58 (58)
38 KOG1700|consensus 99.2 1.5E-12 3.3E-17 111.3 0.8 121 70-193 7-169 (200)
39 KOG0775|consensus 99.2 4.7E-11 1E-15 103.2 6.6 86 181-266 138-238 (304)
40 KOG1168|consensus 99.0 1.7E-10 3.6E-15 100.3 3.1 67 200-266 305-371 (385)
41 KOG0849|consensus 99.0 5.9E-10 1.3E-14 103.4 6.4 63 202-264 174-236 (354)
42 KOG4577|consensus 98.8 2.2E-10 4.8E-15 99.6 -3.8 113 20-132 38-158 (383)
43 PF05920 Homeobox_KN: Homeobox 98.7 3.6E-09 7.9E-14 66.2 1.2 34 225-258 7-40 (40)
44 smart00132 LIM Zinc-binding do 98.5 5.9E-08 1.3E-12 60.3 3.0 37 72-108 1-38 (39)
45 smart00132 LIM Zinc-binding do 98.5 8.1E-08 1.8E-12 59.7 2.7 38 131-168 1-38 (39)
46 KOG2252|consensus 98.5 2E-07 4.4E-12 88.4 6.3 60 200-259 416-475 (558)
47 KOG0774|consensus 98.5 1.2E-07 2.6E-12 81.7 4.4 60 204-263 188-250 (334)
48 KOG1146|consensus 97.6 5.7E-05 1.2E-09 78.5 4.5 63 204-266 903-965 (1406)
49 KOG1702|consensus 97.6 1E-05 2.2E-10 67.7 -1.1 60 70-129 4-64 (264)
50 KOG1700|consensus 97.4 4.2E-05 9E-10 65.6 0.6 60 69-128 107-167 (200)
51 KOG0773|consensus 96.9 0.00043 9.4E-09 64.4 2.1 58 204-261 239-299 (342)
52 PF11569 Homez: Homeodomain le 96.3 0.0007 1.5E-08 45.1 -0.6 42 216-257 10-51 (56)
53 KOG1702|consensus 95.9 0.0011 2.3E-08 55.8 -1.6 60 130-192 5-64 (264)
54 KOG3623|consensus 95.0 0.025 5.5E-07 56.1 4.0 48 216-263 568-615 (1007)
55 PF04218 CENP-B_N: CENP-B N-te 92.6 0.11 2.3E-06 34.5 2.4 47 205-256 1-47 (53)
56 PF08394 Arc_trans_TRASH: Arch 90.5 0.12 2.6E-06 31.5 0.8 33 132-167 1-33 (37)
57 PF10083 DUF2321: Uncharacteri 85.2 0.83 1.8E-05 37.1 2.8 28 116-144 27-54 (158)
58 PF14835 zf-RING_6: zf-RING of 83.2 1.4 3E-05 30.3 2.8 47 98-144 8-55 (65)
59 PF14446 Prok-RING_1: Prokaryo 82.8 0.78 1.7E-05 30.4 1.4 40 128-167 4-51 (54)
60 PF10367 Vps39_2: Vacuolar sor 82.3 1 2.2E-05 34.0 2.2 29 130-158 79-107 (109)
61 smart00504 Ubox Modified RING 81.2 0.99 2.1E-05 30.5 1.6 45 98-142 2-48 (63)
62 PF08394 Arc_trans_TRASH: Arch 80.7 1 2.2E-05 27.4 1.3 31 73-106 1-32 (37)
63 TIGR00270 conserved hypothetic 79.3 1.3 2.9E-05 36.2 2.0 24 234-257 85-108 (154)
64 PF04967 HTH_10: HTH DNA bindi 76.4 1.8 3.9E-05 28.7 1.6 40 211-250 1-42 (53)
65 PF04545 Sigma70_r4: Sigma-70, 75.6 2.3 5E-05 27.4 2.0 46 210-260 4-49 (50)
66 PF08281 Sigma70_r4_2: Sigma-7 74.8 2 4.4E-05 28.0 1.6 43 211-258 11-53 (54)
67 PF09943 DUF2175: Uncharacteri 72.6 0.82 1.8E-05 34.4 -0.8 35 158-193 3-37 (101)
68 PRK03975 tfx putative transcri 71.7 4.7 0.0001 32.5 3.3 52 208-265 4-55 (141)
69 COG1645 Uncharacterized Zn-fin 71.2 2.7 5.9E-05 33.3 1.8 22 99-124 30-51 (131)
70 PF13920 zf-C3HC4_3: Zinc fing 71.1 3 6.5E-05 26.9 1.7 42 99-140 4-48 (50)
71 cd06171 Sigma70_r4 Sigma70, re 69.0 2.5 5.4E-05 26.7 1.0 44 210-258 10-53 (55)
72 PF10668 Phage_terminase: Phag 68.9 2.4 5.2E-05 28.9 0.9 19 234-252 25-43 (60)
73 PF12773 DZR: Double zinc ribb 67.1 5.4 0.00012 25.6 2.3 9 131-139 31-39 (50)
74 KOG1813|consensus 66.7 3.4 7.3E-05 37.2 1.6 45 98-142 242-288 (313)
75 PRK04217 hypothetical protein; 65.5 9.5 0.00021 29.4 3.7 53 207-264 39-91 (110)
76 PF10235 Cript: Microtubule-as 64.4 4.3 9.3E-05 30.0 1.5 36 99-141 46-81 (90)
77 COG5152 Uncharacterized conser 62.6 1.5 3.3E-05 37.0 -1.3 49 97-145 196-246 (259)
78 KOG0978|consensus 60.1 2.2 4.7E-05 43.1 -0.9 46 99-144 645-693 (698)
79 PF06689 zf-C4_ClpX: ClpX C4-t 60.0 8.8 0.00019 23.8 2.2 33 159-191 3-35 (41)
80 TIGR03826 YvyF flagellar opero 59.9 4.2 9E-05 32.6 0.9 67 159-256 5-71 (137)
81 PF14634 zf-RING_5: zinc-RING 58.5 6.5 0.00014 24.6 1.4 38 100-137 2-44 (44)
82 PRK12526 RNA polymerase sigma 58.5 7.8 0.00017 33.0 2.4 32 233-264 171-202 (206)
83 PF13240 zinc_ribbon_2: zinc-r 57.7 8.5 0.00018 20.7 1.6 8 132-139 2-9 (23)
84 PF01527 HTH_Tnp_1: Transposas 57.7 3.5 7.6E-05 28.9 0.1 44 207-254 3-46 (76)
85 PF14471 DUF4428: Domain of un 57.1 4.2 9.1E-05 26.7 0.4 28 99-127 1-30 (51)
86 PRK00118 putative DNA-binding 56.2 8.4 0.00018 29.4 1.9 49 210-263 17-65 (104)
87 PRK06759 RNA polymerase factor 55.1 7.5 0.00016 31.1 1.6 47 210-261 106-152 (154)
88 PF13248 zf-ribbon_3: zinc-rib 54.8 9.3 0.0002 21.1 1.5 9 131-139 4-12 (26)
89 PRK14559 putative protein seri 54.8 14 0.0003 37.5 3.8 11 72-82 3-13 (645)
90 COG3413 Predicted DNA binding 54.6 7.7 0.00017 33.4 1.7 42 208-249 153-196 (215)
91 PF10367 Vps39_2: Vacuolar sor 54.6 9.9 0.00021 28.4 2.2 29 70-98 78-107 (109)
92 PRK09646 RNA polymerase sigma 53.9 9.4 0.0002 32.1 2.1 49 210-263 142-190 (194)
93 PF00196 GerE: Bacterial regul 53.8 7.8 0.00017 25.7 1.3 45 210-260 3-47 (58)
94 KOG2462|consensus 53.7 4.3 9.2E-05 36.2 -0.0 11 158-168 216-226 (279)
95 cd00569 HTH_Hin_like Helix-tur 53.4 14 0.0003 20.6 2.3 37 211-252 6-42 (42)
96 COG2191 Formylmethanofuran deh 53.2 6.7 0.00015 33.4 1.1 30 98-127 173-203 (206)
97 COG4847 Uncharacterized protei 53.1 3.2 7E-05 30.7 -0.7 33 158-191 7-39 (103)
98 PF11781 RRN7: RNA polymerase 52.8 9.4 0.0002 23.0 1.4 24 99-125 10-33 (36)
99 PRK08359 transcription factor; 52.7 7 0.00015 32.7 1.1 24 234-257 101-124 (176)
100 PF04570 DUF581: Protein of un 51.5 9.6 0.00021 25.7 1.4 26 160-185 19-44 (58)
101 KOG0320|consensus 50.5 5.1 0.00011 33.4 -0.1 47 96-142 130-180 (187)
102 PF12674 Zn_ribbon_2: Putative 50.4 6.7 0.00014 28.4 0.5 27 99-125 2-34 (81)
103 COG4357 Zinc finger domain con 50.4 2 4.4E-05 31.8 -2.1 39 72-110 37-75 (105)
104 PF13936 HTH_38: Helix-turn-he 50.2 7 0.00015 24.6 0.6 40 209-253 3-42 (44)
105 PLN03208 E3 ubiquitin-protein 49.9 13 0.00027 31.7 2.2 28 98-125 19-46 (193)
106 PRK10072 putative transcriptio 49.8 8 0.00017 29.0 0.9 41 210-257 32-72 (96)
107 COG1645 Uncharacterized Zn-fin 49.7 9 0.00019 30.4 1.2 21 160-187 31-51 (131)
108 PRK09642 RNA polymerase sigma 49.4 13 0.00027 30.0 2.1 30 234-263 125-154 (160)
109 PF06677 Auto_anti-p27: Sjogre 49.4 11 0.00023 23.6 1.3 10 177-186 31-40 (41)
110 PF06056 Terminase_5: Putative 48.8 9.3 0.0002 25.7 1.0 21 233-253 15-35 (58)
111 cd02249 ZZ Zinc finger, ZZ typ 48.3 11 0.00024 23.9 1.2 9 117-125 23-31 (46)
112 PF13443 HTH_26: Cro/C1-type H 48.2 7.9 0.00017 25.9 0.6 27 233-259 12-38 (63)
113 smart00291 ZnF_ZZ Zinc-binding 47.9 11 0.00024 23.6 1.3 10 117-126 27-36 (44)
114 PF09862 DUF2089: Protein of u 47.9 15 0.00032 28.4 2.1 11 158-168 13-23 (113)
115 PRK09652 RNA polymerase sigma 47.8 13 0.00028 30.4 2.0 48 210-262 128-175 (182)
116 PRK12515 RNA polymerase sigma 47.0 15 0.00032 30.6 2.3 51 210-265 131-181 (189)
117 PF00645 zf-PARP: Poly(ADP-rib 46.7 5.4 0.00012 28.7 -0.4 14 69-82 6-19 (82)
118 PRK14890 putative Zn-ribbon RN 46.2 19 0.00041 24.4 2.1 29 69-106 6-34 (59)
119 PRK12516 RNA polymerase sigma 45.5 19 0.00041 30.2 2.6 33 233-265 134-166 (187)
120 TIGR02999 Sig-70_X6 RNA polyme 45.4 15 0.00033 30.2 2.1 29 233-261 152-180 (183)
121 smart00421 HTH_LUXR helix_turn 44.8 20 0.00044 22.7 2.2 42 210-257 3-44 (58)
122 PF07191 zinc-ribbons_6: zinc- 44.3 10 0.00022 26.6 0.7 31 130-168 31-61 (70)
123 PRK12514 RNA polymerase sigma 44.1 17 0.00037 29.9 2.2 30 233-262 147-176 (179)
124 TIGR03830 CxxCG_CxxCG_HTH puta 44.0 21 0.00045 27.7 2.5 41 209-256 63-103 (127)
125 PF09943 DUF2175: Uncharacteri 43.9 13 0.00029 28.0 1.3 35 131-165 4-38 (101)
126 PRK12519 RNA polymerase sigma 43.8 15 0.00034 30.6 1.9 31 232-262 158-188 (194)
127 TIGR02959 SigZ RNA polymerase 43.8 17 0.00036 29.9 2.0 50 210-264 100-149 (170)
128 PRK06424 transcription factor; 43.5 11 0.00025 30.4 1.0 24 234-257 100-123 (144)
129 PRK09648 RNA polymerase sigma 42.9 17 0.00037 30.3 2.0 47 210-261 139-185 (189)
130 COG1813 Predicted transcriptio 42.9 32 0.00068 28.5 3.4 23 234-256 95-117 (165)
131 PF14255 Cys_rich_CPXG: Cystei 42.9 15 0.00033 24.2 1.3 29 72-100 2-30 (52)
132 PRK12530 RNA polymerase sigma 42.6 16 0.00034 30.6 1.7 30 233-262 152-181 (189)
133 cd04761 HTH_MerR-SF Helix-Turn 42.6 11 0.00024 23.7 0.6 21 234-254 3-23 (49)
134 PRK09639 RNA polymerase sigma 42.5 19 0.00042 29.0 2.2 47 211-263 113-159 (166)
135 KOG1146|consensus 42.4 31 0.00068 37.5 4.1 60 204-263 705-764 (1406)
136 COG4847 Uncharacterized protei 42.3 11 0.00025 27.9 0.7 31 131-164 8-38 (103)
137 TIGR02939 RpoE_Sigma70 RNA pol 42.1 17 0.00036 30.1 1.8 31 232-262 155-185 (190)
138 KOG3623|consensus 42.0 18 0.00039 36.8 2.2 60 206-265 628-687 (1007)
139 PF13518 HTH_28: Helix-turn-he 41.9 11 0.00024 24.0 0.6 25 233-257 14-38 (52)
140 PF13384 HTH_23: Homeodomain-l 41.8 12 0.00025 23.8 0.6 25 232-256 18-42 (50)
141 PRK12512 RNA polymerase sigma 41.8 18 0.00038 30.0 1.9 48 211-263 132-179 (184)
142 PRK09644 RNA polymerase sigma 41.5 19 0.0004 29.3 2.0 32 233-264 126-157 (165)
143 PRK12511 RNA polymerase sigma 41.4 33 0.00071 28.6 3.5 51 211-266 112-162 (182)
144 PRK12541 RNA polymerase sigma 41.2 17 0.00036 29.4 1.6 47 211-262 113-159 (161)
145 PRK05602 RNA polymerase sigma 41.0 22 0.00047 29.5 2.4 32 233-264 146-177 (186)
146 PRK12537 RNA polymerase sigma 40.9 20 0.00044 29.6 2.2 29 233-261 151-179 (182)
147 PRK11924 RNA polymerase sigma 40.6 18 0.0004 29.3 1.8 30 233-262 143-172 (179)
148 TIGR02948 SigW_bacill RNA poly 40.3 18 0.0004 29.8 1.8 30 233-262 154-183 (187)
149 TIGR02985 Sig70_bacteroi1 RNA 39.9 20 0.00043 28.5 1.9 29 233-261 131-159 (161)
150 TIGR02989 Sig-70_gvs1 RNA poly 39.8 20 0.00043 28.7 1.9 47 210-261 111-157 (159)
151 PRK14873 primosome assembly pr 39.5 26 0.00056 35.8 3.0 37 99-138 394-431 (665)
152 cd00162 RING RING-finger (Real 39.5 13 0.00028 22.3 0.6 9 116-124 19-27 (45)
153 cd01392 HTH_LacI Helix-turn-he 38.2 11 0.00024 24.1 0.1 21 236-256 2-22 (52)
154 PF13834 DUF4193: Domain of un 37.6 9.7 0.00021 28.6 -0.3 28 96-123 69-98 (99)
155 PRK06930 positive control sigm 37.4 23 0.0005 29.4 1.9 50 210-264 114-163 (170)
156 PRK00420 hypothetical protein; 37.1 21 0.00045 27.6 1.4 23 159-187 25-47 (112)
157 TIGR02937 sigma70-ECF RNA poly 37.1 24 0.00053 27.3 2.0 29 233-261 128-156 (158)
158 cd02340 ZZ_NBR1_like Zinc fing 37.1 23 0.0005 22.2 1.4 11 72-82 2-12 (43)
159 PRK12538 RNA polymerase sigma 37.0 20 0.00044 31.3 1.6 32 233-264 189-220 (233)
160 PRK12546 RNA polymerase sigma 36.9 22 0.00049 29.8 1.8 31 233-263 131-161 (188)
161 TIGR00721 tfx DNA-binding prot 36.9 44 0.00095 26.8 3.4 48 208-261 4-51 (137)
162 PF02069 Metallothio_Pro: Prok 36.8 22 0.00048 23.4 1.3 26 99-124 9-36 (52)
163 PF01258 zf-dskA_traR: Prokary 36.8 4.8 0.0001 24.1 -1.7 10 73-82 6-15 (36)
164 PF02796 HTH_7: Helix-turn-hel 36.7 22 0.00048 22.3 1.3 37 211-252 6-42 (45)
165 PF13411 MerR_1: MerR HTH fami 36.6 18 0.00038 24.7 0.9 18 234-251 3-20 (69)
166 PRK09637 RNA polymerase sigma 36.5 24 0.00052 29.3 1.9 32 233-264 124-155 (181)
167 PRK12547 RNA polymerase sigma 36.5 25 0.00054 28.5 2.0 30 233-262 130-159 (164)
168 KOG0773|consensus 36.2 22 0.00048 32.9 1.8 45 221-265 114-158 (342)
169 PRK09047 RNA polymerase factor 36.1 28 0.0006 27.9 2.2 30 234-263 125-154 (161)
170 PF01381 HTH_3: Helix-turn-hel 36.0 16 0.00035 23.5 0.6 23 234-256 12-34 (55)
171 KOG4739|consensus 35.8 25 0.00053 30.8 1.9 32 109-140 16-48 (233)
172 PF00376 MerR: MerR family reg 35.8 18 0.00039 22.0 0.8 18 234-251 2-19 (38)
173 PF11571 Med27: Mediator compl 35.3 15 0.00034 27.0 0.5 16 124-139 49-64 (90)
174 PRK06986 fliA flagellar biosyn 35.3 29 0.00063 30.2 2.3 47 211-262 185-231 (236)
175 PF07754 DUF1610: Domain of un 35.2 35 0.00076 18.6 1.7 11 132-142 1-11 (24)
176 PRK09413 IS2 repressor TnpA; R 35.0 28 0.00061 27.0 2.0 40 208-252 10-50 (121)
177 KOG3755|consensus 34.7 12 0.00026 37.0 -0.2 61 203-263 691-758 (769)
178 TIGR02983 SigE-fam_strep RNA p 34.7 26 0.00055 28.2 1.8 30 233-262 128-157 (162)
179 TIGR02947 SigH_actino RNA poly 34.6 20 0.00043 30.0 1.1 33 232-264 148-180 (193)
180 TIGR02954 Sig70_famx3 RNA poly 34.5 28 0.0006 28.3 2.0 46 211-261 120-165 (169)
181 cd00131 PAX Paired Box domain 34.2 83 0.0018 24.7 4.6 44 211-255 76-127 (128)
182 PRK12536 RNA polymerase sigma 33.9 28 0.00062 28.7 2.0 30 233-262 147-176 (181)
183 PRK12524 RNA polymerase sigma 33.8 36 0.00078 28.5 2.6 32 233-264 154-185 (196)
184 cd06170 LuxR_C_like C-terminal 33.7 36 0.00078 21.6 2.1 21 233-253 17-37 (57)
185 PF05502 Dynactin_p62: Dynacti 33.5 29 0.00063 34.0 2.2 82 54-136 1-93 (483)
186 PRK09649 RNA polymerase sigma 33.5 26 0.00056 29.2 1.7 29 233-261 148-176 (185)
187 PRK08301 sporulation sigma fac 33.4 33 0.00071 29.7 2.4 52 210-262 178-229 (234)
188 PRK06811 RNA polymerase factor 33.4 27 0.00058 29.1 1.7 50 210-264 131-180 (189)
189 PRK12543 RNA polymerase sigma 33.3 29 0.00063 28.6 1.9 31 233-263 135-165 (179)
190 KOG2893|consensus 33.2 10 0.00022 33.2 -0.9 36 69-107 9-44 (341)
191 TIGR03879 near_KaiC_dom probab 32.8 5.1 0.00011 28.4 -2.3 25 232-256 33-57 (73)
192 cd04762 HTH_MerR-trunc Helix-T 32.7 19 0.00041 22.1 0.6 24 234-257 3-26 (49)
193 PRK12540 RNA polymerase sigma 32.6 49 0.0011 27.5 3.2 33 233-265 129-161 (182)
194 cd02341 ZZ_ZZZ3 Zinc finger, Z 32.3 26 0.00057 22.6 1.1 10 117-126 26-35 (48)
195 PRK07037 extracytoplasmic-func 32.1 33 0.00071 27.6 2.0 29 233-261 127-155 (163)
196 TIGR03070 couple_hipB transcri 32.0 23 0.0005 22.7 0.9 23 234-256 18-40 (58)
197 PRK12518 RNA polymerase sigma 31.9 28 0.0006 28.4 1.6 35 231-265 136-170 (175)
198 cd02336 ZZ_RSC8 Zinc finger, Z 31.7 26 0.00057 22.3 1.1 28 99-126 2-32 (45)
199 PRK13919 putative RNA polymera 31.3 35 0.00076 28.1 2.1 29 233-261 153-181 (186)
200 PRK12513 RNA polymerase sigma 31.2 27 0.00058 29.2 1.4 32 232-263 156-187 (194)
201 PRK12545 RNA polymerase sigma 31.1 35 0.00075 28.8 2.1 32 233-264 157-188 (201)
202 TIGR03001 Sig-70_gmx1 RNA poly 31.1 34 0.00073 30.2 2.0 33 233-265 179-211 (244)
203 PRK09651 RNA polymerase sigma 31.0 41 0.0009 27.5 2.5 31 233-263 137-167 (172)
204 PRK04023 DNA polymerase II lar 30.6 73 0.0016 34.0 4.5 54 68-143 624-677 (1121)
205 PRK12532 RNA polymerase sigma 30.6 33 0.00072 28.7 1.8 32 233-264 154-185 (195)
206 TIGR02952 Sig70_famx2 RNA poly 30.5 37 0.0008 27.4 2.1 46 211-261 123-168 (170)
207 PRK12535 RNA polymerase sigma 30.5 34 0.00074 28.8 1.9 31 233-263 151-181 (196)
208 PRK12520 RNA polymerase sigma 30.3 35 0.00077 28.4 2.0 33 233-265 149-181 (191)
209 PRK09645 RNA polymerase sigma 30.3 41 0.0009 27.3 2.4 30 233-262 136-165 (173)
210 PRK12533 RNA polymerase sigma 30.1 34 0.00074 29.5 1.9 31 233-263 152-182 (216)
211 KOG2462|consensus 29.8 37 0.00081 30.4 2.0 70 95-168 128-198 (279)
212 PF10886 DUF2685: Protein of u 29.7 34 0.00074 22.7 1.3 12 131-142 3-14 (54)
213 PF09607 BrkDBD: Brinker DNA-b 29.6 32 0.00069 23.2 1.2 19 236-254 30-48 (58)
214 PRK12542 RNA polymerase sigma 29.5 36 0.00078 28.2 1.9 30 233-262 140-169 (185)
215 PF00130 C1_1: Phorbol esters/ 29.4 31 0.00067 22.2 1.2 13 69-81 10-22 (53)
216 PRK09647 RNA polymerase sigma 29.1 43 0.00093 28.5 2.3 31 234-264 157-187 (203)
217 PF12861 zf-Apc11: Anaphase-pr 29.0 24 0.00053 25.8 0.6 28 131-158 34-61 (85)
218 PF00569 ZZ: Zinc finger, ZZ t 28.9 19 0.00041 22.8 0.0 10 117-126 28-37 (46)
219 PRK12529 RNA polymerase sigma 28.6 39 0.00084 27.9 1.9 29 233-261 145-173 (178)
220 PRK12539 RNA polymerase sigma 28.2 44 0.00096 27.6 2.2 30 233-262 149-178 (184)
221 KOG2893|consensus 28.0 38 0.00081 29.7 1.7 49 130-188 11-59 (341)
222 PRK12523 RNA polymerase sigma 27.8 42 0.00092 27.3 2.0 29 233-261 137-165 (172)
223 KOG3576|consensus 27.8 4.4 9.5E-05 34.6 -3.9 73 92-168 112-184 (267)
224 PRK08295 RNA polymerase factor 27.4 55 0.0012 27.5 2.7 30 233-262 172-201 (208)
225 COG2191 Formylmethanofuran deh 27.3 23 0.0005 30.3 0.3 30 158-189 173-202 (206)
226 TIGR02943 Sig70_famx1 RNA poly 27.3 40 0.00087 28.1 1.8 48 211-263 132-179 (188)
227 TIGR02479 FliA_WhiG RNA polyme 27.2 46 0.001 28.6 2.2 47 210-261 175-221 (224)
228 PF04936 DUF658: Protein of un 26.7 19 0.00041 29.6 -0.3 33 232-264 15-47 (186)
229 TIGR02980 SigBFG RNA polymeras 26.5 45 0.00098 28.6 2.0 47 210-261 178-224 (227)
230 PRK12531 RNA polymerase sigma 26.4 43 0.00092 28.0 1.8 30 233-262 159-188 (194)
231 COG2888 Predicted Zn-ribbon RN 26.4 58 0.0013 22.1 2.0 29 70-107 9-37 (61)
232 cd00093 HTH_XRE Helix-turn-hel 26.4 32 0.0007 21.1 0.8 23 234-256 15-37 (58)
233 TIGR02859 spore_sigH RNA polym 26.3 56 0.0012 27.1 2.5 30 232-261 166-195 (198)
234 PHA02929 N1R/p28-like protein; 26.3 33 0.00072 30.2 1.1 39 130-168 175-227 (238)
235 COG0068 HypF Hydrogenase matur 26.3 26 0.00056 35.7 0.5 84 69-167 100-183 (750)
236 PF08280 HTH_Mga: M protein tr 26.3 36 0.00079 22.7 1.1 33 214-250 6-38 (59)
237 PF01286 XPA_N: XPA protein N- 26.1 31 0.00066 20.6 0.6 16 71-86 4-19 (34)
238 PRK09643 RNA polymerase sigma 26.1 61 0.0013 27.1 2.7 32 233-264 152-183 (192)
239 PF03672 UPF0154: Uncharacteri 25.9 84 0.0018 21.7 2.8 35 216-250 19-53 (64)
240 PRK12544 RNA polymerase sigma 25.9 45 0.00098 28.4 1.9 30 234-263 167-196 (206)
241 TIGR02941 Sigma_B RNA polymera 25.7 51 0.0011 29.0 2.3 47 210-261 205-251 (255)
242 PRK08583 RNA polymerase sigma 25.5 49 0.0011 29.1 2.1 48 210-262 205-252 (257)
243 PRK05657 RNA polymerase sigma 25.5 55 0.0012 30.2 2.5 54 210-264 262-315 (325)
244 cd04764 HTH_MlrA-like_sg1 Heli 25.5 35 0.00075 23.1 0.9 21 234-254 3-23 (67)
245 COG4367 Uncharacterized protei 25.2 42 0.00092 24.6 1.3 40 210-249 2-41 (97)
246 PRK09641 RNA polymerase sigma 25.0 46 0.001 27.3 1.7 31 232-262 153-183 (187)
247 PRK07670 RNA polymerase sigma 25.0 54 0.0012 28.8 2.2 46 211-261 202-247 (251)
248 cd02344 ZZ_HERC2 Zinc finger, 24.9 48 0.001 21.1 1.4 11 116-126 23-33 (45)
249 PHA01976 helix-turn-helix prot 24.9 37 0.00079 22.9 0.9 23 234-256 18-40 (67)
250 PRK00807 50S ribosomal protein 24.5 38 0.00082 22.3 0.9 24 131-154 3-28 (52)
251 cd04763 HTH_MlrA-like Helix-Tu 24.3 32 0.0007 23.4 0.5 20 234-253 3-22 (68)
252 cd02342 ZZ_UBA_plant Zinc fing 24.3 41 0.00088 21.2 0.9 9 117-125 24-32 (43)
253 COG1905 NuoE NADH:ubiquinone o 24.2 62 0.0014 26.7 2.3 36 214-249 26-61 (160)
254 PRK11923 algU RNA polymerase s 24.2 51 0.0011 27.3 1.9 31 233-263 156-186 (193)
255 cd01104 HTH_MlrA-CarA Helix-Tu 23.7 38 0.00083 22.8 0.9 20 234-253 3-22 (68)
256 PRK11552 putative DNA-binding 23.7 53 0.0011 28.3 1.9 43 216-260 19-61 (225)
257 PRK10403 transcriptional regul 23.6 39 0.00085 27.7 1.1 46 209-260 152-197 (215)
258 PF04810 zf-Sec23_Sec24: Sec23 23.6 46 0.001 20.4 1.1 30 71-105 3-32 (40)
259 PF08746 zf-RING-like: RING-li 23.4 29 0.00063 21.7 0.1 26 73-98 1-28 (43)
260 TIGR00599 rad18 DNA repair pro 23.4 36 0.00078 32.4 0.8 12 70-81 26-37 (397)
261 PF06971 Put_DNA-bind_N: Putat 23.4 40 0.00088 21.9 0.8 16 234-249 31-46 (50)
262 TIGR03020 EpsA transcriptional 23.3 60 0.0013 28.8 2.2 48 208-261 188-235 (247)
263 PRK12522 RNA polymerase sigma 23.1 58 0.0013 26.5 2.0 30 233-262 137-166 (173)
264 PRK11922 RNA polymerase sigma 23.1 49 0.0011 28.6 1.6 34 231-264 165-198 (231)
265 TIGR02607 antidote_HigA addict 23.0 41 0.00088 23.4 0.9 24 234-257 21-44 (78)
266 TIGR02950 SigM_subfam RNA poly 22.7 43 0.00094 26.5 1.1 33 229-261 119-151 (154)
267 PRK14714 DNA polymerase II lar 22.7 97 0.0021 33.9 3.8 24 218-241 857-880 (1337)
268 PF05269 Phage_CII: Bacterioph 22.7 45 0.00098 24.7 1.1 28 232-259 24-51 (91)
269 COG4306 Uncharacterized protei 22.6 57 0.0012 25.6 1.6 47 119-167 30-78 (160)
270 PF13730 HTH_36: Helix-turn-he 22.6 46 0.001 21.4 1.0 22 233-254 27-48 (55)
271 PRK15369 two component system 22.5 54 0.0012 26.5 1.7 46 209-260 148-193 (211)
272 KOG3476|consensus 22.3 4.8 0.0001 29.2 -4.0 38 98-142 55-92 (100)
273 cd02338 ZZ_PCMF_like Zinc fing 22.3 43 0.00093 21.6 0.8 10 117-126 24-33 (49)
274 PHA02955 hypothetical protein; 22.2 66 0.0014 27.7 2.1 45 214-258 61-106 (213)
275 PRK07408 RNA polymerase sigma 22.2 71 0.0015 28.2 2.5 49 210-263 203-251 (256)
276 PRK10100 DNA-binding transcrip 22.0 69 0.0015 27.6 2.3 46 209-260 154-199 (216)
277 KOG3816|consensus 22.0 31 0.00068 32.4 0.1 49 120-168 430-485 (526)
278 PRK12528 RNA polymerase sigma 22.0 56 0.0012 26.2 1.6 25 234-258 132-156 (161)
279 TIGR02957 SigX4 RNA polymerase 21.8 57 0.0012 29.2 1.8 29 234-262 127-155 (281)
280 PRK09415 RNA polymerase factor 21.8 55 0.0012 26.9 1.6 29 233-261 145-173 (179)
281 TIGR03541 reg_near_HchA LuxR f 21.7 65 0.0014 28.0 2.1 48 208-261 169-216 (232)
282 PF07638 Sigma70_ECF: ECF sigm 21.7 46 0.00099 27.8 1.1 29 233-261 153-181 (185)
283 PRK12527 RNA polymerase sigma 21.7 79 0.0017 25.2 2.5 30 233-262 123-152 (159)
284 PF06827 zf-FPG_IleRS: Zinc fi 21.6 24 0.00051 20.0 -0.5 10 72-81 3-12 (30)
285 PF13565 HTH_32: Homeodomain-l 21.5 1.9E+02 0.0042 19.8 4.2 40 212-251 32-76 (77)
286 PRK06704 RNA polymerase factor 21.2 69 0.0015 28.0 2.1 32 233-264 134-165 (228)
287 TIGR02835 spore_sigmaE RNA pol 21.1 87 0.0019 27.1 2.7 52 210-262 178-229 (234)
288 TIGR00595 priA primosomal prot 20.7 91 0.002 30.7 3.1 26 113-138 236-262 (505)
289 PRK12534 RNA polymerase sigma 20.5 78 0.0017 26.1 2.3 29 233-261 155-183 (187)
290 TIGR02846 spore_sigmaK RNA pol 20.4 91 0.002 26.9 2.7 52 209-261 173-224 (227)
291 PRK09636 RNA polymerase sigma 20.4 61 0.0013 29.2 1.7 29 234-262 134-162 (293)
292 PRK12495 hypothetical protein; 20.3 55 0.0012 28.4 1.2 10 98-107 43-52 (226)
293 smart00530 HTH_XRE Helix-turn- 20.3 52 0.0011 19.8 0.9 23 234-256 13-35 (56)
294 PRK05803 sporulation sigma fac 20.3 82 0.0018 27.2 2.4 52 210-262 175-226 (233)
295 TIGR02393 RpoD_Cterm RNA polym 20.2 89 0.0019 27.2 2.6 53 210-263 176-228 (238)
296 PF04564 U-box: U-box domain; 20.1 80 0.0017 22.0 1.9 47 96-142 3-52 (73)
No 1
>KOG4577|consensus
Probab=100.00 E-value=7.1e-52 Score=354.50 Aligned_cols=216 Identities=76% Similarity=1.313 Sum_probs=209.4
Q ss_pred CCCCCccCCCeeccceeeeecCccccccCcccCcCCCCCCCcceeeCCeeccccccccccCcCCCCCCCCCCCCCceecc
Q psy4325 69 SIPKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFARNGLLFCKEDFFKRFGTKCAGCEMGIPPTQVVRRA 148 (306)
Q Consensus 69 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f~~~g~~yC~~cy~~~~~~~C~~C~~~I~~~~~~~~~ 148 (306)
..++|++|.+.|.+++++.++++.||..|++|+.|..+|....|.++|.+||+.+|.++|+.+|.+|+..|....+|.+|
T Consensus 32 eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~drCFsR~~s~yCkedFfKrfGTKCsaC~~GIpPtqVVRkA 111 (383)
T KOG4577|consen 32 EIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLADRCFSREGSVYCKEDFFKRFGTKCSACQEGIPPTQVVRKA 111 (383)
T ss_pred ccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHHHHhhcCCceeehHHHHHHhCCcchhhcCCCChHHHHHHh
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999999888899
Q ss_pred cCccccCCCcccccCCCCCCCCCceeeccCCcccccchhHHHhhccCCCCCCCCCCCCCCcccchHhHHHHHhccccCCC
Q psy4325 149 QDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDYEAAKAKDGNCLDGDQPNKRPRTTITAKQLETLKMAYNTSPK 228 (306)
Q Consensus 149 ~~~~~H~~CF~C~~C~~~l~~g~~~~~~~~~~~~C~~c~~~~~~~~~~~~~~~~~~kr~rt~~s~~q~~~Le~~F~~~~~ 228 (306)
.+.+||.+||.|.+|++.|.+|++||++++++++|...|+.+..+.-..++++...||+||+++..|++.|+..|+..+.
T Consensus 112 qd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~k~~~~l~gd~~nKRPRTTItAKqLETLK~AYn~SpK 191 (383)
T KOG4577|consen 112 QDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAKQKHCNELEGDASNKRPRTTITAKQLETLKQAYNTSPK 191 (383)
T ss_pred hcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHHhccccccccccccCCCcceeeHHHHHHHHHHhcCCCc
Confidence 99999999999999999999999999999999999999999999977789999999999999999999999999999999
Q ss_pred CCHHHHHHHHHhhCCCccchhcccccchhHHHHhhhhcCCCCccccccCCCCCCCC
Q psy4325 229 PARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKKDAGRTRWSQYFRSMKGGTSP 284 (306)
Q Consensus 229 p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~~~~~~~~~~~~~~~~~~~~p 284 (306)
|....|++|+.++||..++|||||||||+|+||.++.+++..+.++++++.+..++
T Consensus 192 PARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAGR~RWgqyfrsmK~sgs~ 247 (383)
T KOG4577|consen 192 PARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGRTRWGQYFRSMKRSGSS 247 (383)
T ss_pred hhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcchhHHHHHHHHhhccCCc
Confidence 99999999999999999999999999999999999999999999999999887555
No 2
>KOG1701|consensus
Probab=99.94 E-value=2.2e-28 Score=221.01 Aligned_cols=173 Identities=27% Similarity=0.511 Sum_probs=148.6
Q ss_pred cccCCCCcccccch--hhhcccccccccC---CCccc-cCCccccCCcccccccCCCCCCCCCccCCCeeccceeeeecC
Q psy4325 17 AVQRGNGLTVGICA--SKLHDLLHEAHAG---SSSSF-SSSFNDVDYEGIMPVYMPIASIPKCGGCGDLILDRFILKVLE 90 (306)
Q Consensus 17 ~~~~~~~~~~~~~~--~~~~~~~~~~~~~---~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~~~~~~ 90 (306)
.+..|+..|.+... .+|++++|-.||+ |+..| .++|+..|+.+||..+|- ....+|..|++.|.+. |+.|+|
T Consensus 276 iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq-~tlekC~~Cg~~I~d~-iLrA~G 353 (468)
T KOG1701|consen 276 ICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQ-DTLEKCNKCGEPIMDR-ILRALG 353 (468)
T ss_pred hhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccccccccCCcccchHHHH-HHHHHHhhhhhHHHHH-HHHhcc
Confidence 57788888888764 4999999999994 55577 689999999999999986 4567999999999997 558999
Q ss_pred ccccccCcccCcCCCCCCCcce--eeCCeeccccccccccCcCCCCCCCCCCCCC-----ceecccCccccCCCcccccC
Q psy4325 91 RTWHARCLKCHECGAPLAEKCF--ARNGLLFCKEDFFKRFGTKCAGCEMGIPPTQ-----VVRRAQDLVYHLNCFACVMC 163 (306)
Q Consensus 91 ~~~H~~Cf~C~~C~~~l~~~~f--~~~g~~yC~~cy~~~~~~~C~~C~~~I~~~~-----~~~~~~~~~~H~~CF~C~~C 163 (306)
+.||+.||+|.+|++.|++..| ..++++||-.||+++|+++|+.|+++|...+ +-|.++++.||.+|++|..|
T Consensus 354 kayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAPrCs~C~~PI~P~~G~~etvRvvamdr~fHv~CY~CEDC 433 (468)
T KOG1701|consen 354 KAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAPRCSVCGNPILPRDGKDETVRVVAMDRDFHVNCYKCEDC 433 (468)
T ss_pred cccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcCcchhhccCCccCCCCCcceEEEEEccccccccceehhhc
Confidence 9999999999999999999998 4568999999999999999999999996554 22468999999999999999
Q ss_pred CCCCC---CCCceeeccCCcccccchhHHHhh
Q psy4325 164 ARQLN---TGDEFYLMEDRKLVCKPDYEAAKA 192 (306)
Q Consensus 164 ~~~l~---~g~~~~~~~~~~~~C~~c~~~~~~ 192 (306)
+..|+ ++...|- -|+.++|..|+.++..
T Consensus 434 g~~LS~e~e~qgCyP-ld~HllCk~Ch~~Rl~ 464 (468)
T KOG1701|consen 434 GLLLSSEEEGQGCYP-LDGHLLCKTCHLKRLQ 464 (468)
T ss_pred CccccccCCCCccee-ccCceeechhhhhhhc
Confidence 99997 3334555 4889999999876654
No 3
>KOG1701|consensus
Probab=99.90 E-value=2.9e-26 Score=207.26 Aligned_cols=163 Identities=23% Similarity=0.497 Sum_probs=133.2
Q ss_pred CCCCCccCCCeeccc-eeeeecCccccccCcccCcCCCCCCCcce-eeCCeeccccccccccCcCCCCCCCCCCCCCcee
Q psy4325 69 SIPKCGGCGDLILDR-FILKVLERTWHARCLKCHECGAPLAEKCF-ARNGLLFCKEDFFKRFGTKCAGCEMGIPPTQVVR 146 (306)
Q Consensus 69 ~~~~C~~C~~~I~~~-~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f-~~~g~~yC~~cy~~~~~~~C~~C~~~I~~~~~~~ 146 (306)
...+|++|+|.|+++ .-+.||++.||..||+|..|++.|.++.| .+|+++||+.||... ..||..|+++| .|.|+
T Consensus 273 ~~~iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~t-lekC~~Cg~~I--~d~iL 349 (468)
T KOG1701|consen 273 YFGICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDT-LEKCNKCGEPI--MDRIL 349 (468)
T ss_pred hhhhhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccccccccCCcccchHHHHHH-HHHHhhhhhHH--HHHHH
Confidence 344999999999874 44579999999999999999999998766 899999999999654 58999999999 56789
Q ss_pred cccCccccCCCcccccCCCCCCCCCceeeccCCcccccchhHHHhhcc-CCCCCCCCCCCCCCcccchHhHHHHHhcccc
Q psy4325 147 RAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDYEAAKAKD-GNCLDGDQPNKRPRTTITAKQLETLKMAYNT 225 (306)
Q Consensus 147 ~~~~~~~H~~CF~C~~C~~~l~~g~~~~~~~~~~~~C~~c~~~~~~~~-~~~~~~~~~~kr~rt~~s~~q~~~Le~~F~~ 225 (306)
+|.|+.||+.||+|.+|.+.| +|..|++..++++||.+||.+.|++. ..+....-+......+ --+..|-+.|+.
T Consensus 350 rA~GkayHp~CF~Cv~C~r~l-dgipFtvd~~n~v~Cv~dfh~kfAPrCs~C~~PI~P~~G~~et---vRvvamdr~fHv 425 (468)
T KOG1701|consen 350 RALGKAYHPGCFTCVVCARCL-DGIPFTVDSQNNVYCVPDFHKKFAPRCSVCGNPILPRDGKDET---VRVVAMDRDFHV 425 (468)
T ss_pred HhcccccCCCceEEEEecccc-CCccccccCCCceeeehhhhhhcCcchhhccCCccCCCCCcce---EEEEEccccccc
Confidence 999999999999999999999 68899999999999999999999984 2222222222222211 124467888999
Q ss_pred CCCCCHHHHHHHH
Q psy4325 226 SPKPARHVREQLS 238 (306)
Q Consensus 226 ~~~p~~~~r~~La 238 (306)
+-|-.+.-+..|+
T Consensus 426 ~CY~CEDCg~~LS 438 (468)
T KOG1701|consen 426 NCYKCEDCGLLLS 438 (468)
T ss_pred cceehhhcCcccc
Confidence 9998888888776
No 4
>KOG2272|consensus
Probab=99.89 E-value=5.1e-25 Score=186.38 Aligned_cols=169 Identities=25% Similarity=0.509 Sum_probs=149.4
Q ss_pred cccCCCCcccccchhhhccccccccc---CCCccccCCccccCCcccccccCCCCCCCCCccCCCeeccceeeeecCccc
Q psy4325 17 AVQRGNGLTVGICASKLHDLLHEAHA---GSSSSFSSSFNDVDYEGIMPVYMPIASIPKCGGCGDLILDRFILKVLERTW 93 (306)
Q Consensus 17 ~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~~~~~~~~~ 93 (306)
.++.|.+.|-.....--+..+|+.|| .|...|.+.-....++.||+.+.+....++|..|.++|.++. +.++|+.|
T Consensus 139 vC~KCh~~iD~~~l~fr~d~yH~yHFkCt~C~keL~sdaRevk~eLyClrChD~mgipiCgaC~rpIeerv-i~amgKhW 217 (332)
T KOG2272|consen 139 VCQKCHAHIDEQPLTFRGDPYHPYHFKCTTCGKELTSDAREVKGELYCLRCHDKMGIPICGACRRPIEERV-IFAMGKHW 217 (332)
T ss_pred ehhhhhhhcccccccccCCCCCccceecccccccccchhhhhccceeccccccccCCcccccccCchHHHH-HHHhcccc
Confidence 36677777777777777788888888 455688888888899999999999999999999999998764 46999999
Q ss_pred cccCcccCcCCCCCCC-cceeeCCeeccccccccccCcCCCCCCCCCCCCCceecccCccccCCCcccccCCCCCCCCCc
Q psy4325 94 HARCLKCHECGAPLAE-KCFARNGLLFCKEDFFKRFGTKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDE 172 (306)
Q Consensus 94 H~~Cf~C~~C~~~l~~-~~f~~~g~~yC~~cy~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~CF~C~~C~~~l~~g~~ 172 (306)
|.++|+|+.|.+|+-+ ..|++.|..||+.+|.++|+-.|..|+.+|.+. ++.+.++.|-++||.|+.|++.|...++
T Consensus 218 HveHFvCa~CekPFlGHrHYEkkGlaYCe~h~~qLfG~~CF~C~~~i~G~--vv~al~KawCv~cf~Cs~Cdkkl~~K~K 295 (332)
T KOG2272|consen 218 HVEHFVCAKCEKPFLGHRHYEKKGLAYCETHYHQLFGNLCFICNRVIGGD--VVSALNKAWCVECFSCSTCDKKLTQKNK 295 (332)
T ss_pred chhheeehhcCCcccchhhhhhcCchhHHHHHHHHhhhhheecCCccCcc--HHHHhhhhhccccccccccccccccccc
Confidence 9999999999999855 677999999999999999999999999999654 5689999999999999999999998899
Q ss_pred eeeccCCcccccchhHH
Q psy4325 173 FYLMEDRKLVCKPDYEA 189 (306)
Q Consensus 173 ~~~~~~~~~~C~~c~~~ 189 (306)
|+.. |-.|+|..||++
T Consensus 296 f~E~-DmkP~CKkCy~r 311 (332)
T KOG2272|consen 296 FYEF-DMKPVCKKCYDR 311 (332)
T ss_pred eeee-ccchHHHHHHhh
Confidence 9885 778999999963
No 5
>KOG1044|consensus
Probab=99.86 E-value=8e-23 Score=190.85 Aligned_cols=170 Identities=28% Similarity=0.577 Sum_probs=138.7
Q ss_pred cCCCCcccccchhhhcccccccccCCCc---cccC-CccccC-Cccccccc---CC-----CCCCCCCccCCCeecccee
Q psy4325 19 QRGNGLTVGICASKLHDLLHEAHAGSSS---SFSS-SFNDVD-YEGIMPVY---MP-----IASIPKCGGCGDLILDRFI 85 (306)
Q Consensus 19 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~-~~~~~~-~~~~~~~~---~~-----~~~~~~C~~C~~~I~~~~~ 85 (306)
+.|...+.+..+++|++.+|+.||.|+. ++.+ +-.... .+-.|..| .+ ......|++|++.|..+..
T Consensus 69 ~~c~~~~~gevvsa~gktyh~~cf~cs~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk~gq~ 148 (670)
T KOG1044|consen 69 DDCRAFVEGEVVSTLGKTYHPKCFSCSTCKSPFKSGDKVTFSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELKNGQA 148 (670)
T ss_pred cchhhhccceeEecccceeccccceecccCCCCCCCCeeeecchhhhhhhhcCcccCCcccccCCccccchhhhhhccce
Confidence 7889999999999999999999996655 4432 211111 11122222 12 2367799999999988777
Q ss_pred eeecCccccccCcccCcCCCCCCCcceeeCCeeccccccccccCcCCCCCCCCCCCCCceecccCccccCCCcccccCCC
Q psy4325 86 LKVLERTWHARCLKCHECGAPLAEKCFARNGLLFCKEDFFKRFGTKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCAR 165 (306)
Q Consensus 86 ~~~~~~~~H~~Cf~C~~C~~~l~~~~f~~~g~~yC~~cy~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~CF~C~~C~~ 165 (306)
+.|+++.||..||+|..|...|.++++.++|.+||+.||++.|+.+|..|.+.|.+. |+.|+|++||+.|-+|+.|+.
T Consensus 149 llald~qwhv~cfkc~~c~~vL~gey~skdg~pyce~dy~~~fgvkc~~c~~fisgk--vLqag~kh~HPtCARCsRCgq 226 (670)
T KOG1044|consen 149 LLALDKQWHVSCFKCKSCSAVLNGEYMSKDGVPYCEKDYQAKFGVKCEECEKFISGK--VLQAGDKHFHPTCARCSRCGQ 226 (670)
T ss_pred eeeeccceeeeeeehhhhcccccceeeccCCCcchhhhhhhhcCeehHHhhhhhhhh--hhhccCcccCcchhhhhhhcc
Confidence 789999999999999999999999999999999999999999999999999999765 789999999999999999999
Q ss_pred CCCCCCceeeccCCcccccchhHHHh
Q psy4325 166 QLNTGDEFYLMEDRKLVCKPDYEAAK 191 (306)
Q Consensus 166 ~l~~g~~~~~~~~~~~~C~~c~~~~~ 191 (306)
+|..|.+.|+ .+..++-..|-....
T Consensus 227 mF~eGEEMYl-QGs~iWHP~C~qa~~ 251 (670)
T KOG1044|consen 227 MFGEGEEMYL-QGSEIWHPDCKQATK 251 (670)
T ss_pred ccccchheee-ccccccCCccccccc
Confidence 9999999998 465666666654443
No 6
>KOG2272|consensus
Probab=99.85 E-value=5.2e-23 Score=174.24 Aligned_cols=175 Identities=18% Similarity=0.301 Sum_probs=152.0
Q ss_pred hcccccCCCCcccccchhhhcccccccccCCC---ccc-cCCccccCCcccccccCC-----CCCCCCCccCCCeeccce
Q psy4325 14 IGLAVQRGNGLTVGICASKLHDLLHEAHAGSS---SSF-SSSFNDVDYEGIMPVYMP-----IASIPKCGGCGDLILDRF 84 (306)
Q Consensus 14 ~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~-~~~~~~~~~~~~~~~~~~-----~~~~~~C~~C~~~I~~~~ 84 (306)
-+|.+..|+..|.|.-.++|+..||+.+|.|. ..| +..|....+...|..+.. ..+..+|.+|+..|.+.
T Consensus 72 faPcC~kC~EFiiGrVikamnnSwHp~CF~Cd~Cn~~Lad~gf~rnqgr~LC~~Cn~k~Ka~~~g~YvC~KCh~~iD~~- 150 (332)
T KOG2272|consen 72 FAPCCGKCGEFIIGRVIKAMNNSWHPACFRCDLCNKHLADQGFYRNQGRALCRECNQKEKAKGRGRYVCQKCHAHIDEQ- 150 (332)
T ss_pred hchhhcccccchhhHHHHhhccccCcccchhHHHHHHHhhhhhHhhcchHHhhhhhhhhcccccceeehhhhhhhcccc-
Confidence 36778999999999999999999999999654 466 677888888887876654 23567999999999774
Q ss_pred eeeecCccccccCcccCcCCCCCCCcceeeCCeeccccccccccCcCCCCCCCCCCCCCceecccCccccCCCcccccCC
Q psy4325 85 ILKVLERTWHARCLKCHECGAPLAEKCFARNGLLFCKEDFFKRFGTKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCA 164 (306)
Q Consensus 85 ~~~~~~~~~H~~Cf~C~~C~~~l~~~~f~~~g~~yC~~cy~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~CF~C~~C~ 164 (306)
.+...|..||+.+|+|..|++.|+...=...|.+||..|+.+.--|+|..|.+|| .+.++.++|++||.+.|+|+.|.
T Consensus 151 ~l~fr~d~yH~yHFkCt~C~keL~sdaRevk~eLyClrChD~mgipiCgaC~rpI--eervi~amgKhWHveHFvCa~Ce 228 (332)
T KOG2272|consen 151 PLTFRGDPYHPYHFKCTTCGKELTSDAREVKGELYCLRCHDKMGIPICGACRRPI--EERVIFAMGKHWHVEHFVCAKCE 228 (332)
T ss_pred cccccCCCCCccceecccccccccchhhhhccceeccccccccCCcccccccCch--HHHHHHHhccccchhheeehhcC
Confidence 5578999999999999999999988776788999999999998889999999999 46788999999999999999999
Q ss_pred CCCCCCCceeeccCCcccccchhHHHhhc
Q psy4325 165 RQLNTGDEFYLMEDRKLVCKPDYEAAKAK 193 (306)
Q Consensus 165 ~~l~~g~~~~~~~~~~~~C~~c~~~~~~~ 193 (306)
+++- |-+-|. ..|..||..+|.++++.
T Consensus 229 kPFl-GHrHYE-kkGlaYCe~h~~qLfG~ 255 (332)
T KOG2272|consen 229 KPFL-GHRHYE-KKGLAYCETHYHQLFGN 255 (332)
T ss_pred Cccc-chhhhh-hcCchhHHHHHHHHhhh
Confidence 9994 666666 68999999999999975
No 7
>KOG1703|consensus
Probab=99.84 E-value=4.8e-22 Score=191.58 Aligned_cols=169 Identities=23% Similarity=0.461 Sum_probs=147.9
Q ss_pred ccccCCCCcccc-cchhhhcccccccccCCCc---cc-cCCccccCCcccccccCCCCCCCCCccCCCeeccceeeeecC
Q psy4325 16 LAVQRGNGLTVG-ICASKLHDLLHEAHAGSSS---SF-SSSFNDVDYEGIMPVYMPIASIPKCGGCGDLILDRFILKVLE 90 (306)
Q Consensus 16 ~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~---~~-~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~~~~~~ 90 (306)
+.+..|++.|-+ ....++++.||..++.|.. .+ ...+...++..+|..++.....+.|.+|+++|.++.+ .+++
T Consensus 304 p~c~~c~~~i~~~~~i~~~~~~~h~~~~~c~~~~~~~~~~~~~~~~g~~~c~~~~~~~~~p~C~~C~~~i~~~~v-~a~~ 382 (479)
T KOG1703|consen 304 PLCLSCNQKIRSVKVIVALGKEWHPEHFSCEVCAIVILDGGPRELDGKILCHECFHAPFRPNCKRCLLPILEEGV-CALG 382 (479)
T ss_pred ccccccccCcccceeEeeccccccccceeeccccccccCCCccccCCCccHHHHHHHhhCccccccCCchHHhHh-hhcc
Confidence 457788899999 8889999999999996655 33 4667788899999999999999999999999999866 4779
Q ss_pred ccccccCcccCcCCCCCCCcce-eeCCeeccccccccccCcCCCCCCCCCCCCCceecccCccccCCCcccccCCCCCCC
Q psy4325 91 RTWHARCLKCHECGAPLAEKCF-ARNGLLFCKEDFFKRFGTKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNT 169 (306)
Q Consensus 91 ~~~H~~Cf~C~~C~~~l~~~~f-~~~g~~yC~~cy~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~CF~C~~C~~~l~~ 169 (306)
+.||+.||+|..|+++|.+..| ..+|.+||+.||++++.++|..|.++|...+..+++.+..||..||+|..|.+.|..
T Consensus 383 ~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~~~~~~~~~~~p~~~~~~~ie~~~~~~h~~~F~c~~c~~~l~~ 462 (479)
T KOG1703|consen 383 RLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKKLFTTKCDYCKKPVEFGSRQIEADGSPFHGDCFRCANCMKKLTK 462 (479)
T ss_pred CeechhceeeecccCCCCCCcccccCCccchhhhHhhhccccchhccchhHhhhhHhhccCccccccceehhhhhccccC
Confidence 9999999999999999987655 999999999999999999999999998766667799999999999999999999964
Q ss_pred CCceeeccCCcccccchh
Q psy4325 170 GDEFYLMEDRKLVCKPDY 187 (306)
Q Consensus 170 g~~~~~~~~~~~~C~~c~ 187 (306)
..|+ ...+.++|..|+
T Consensus 463 -~~~~-~~~~~p~c~~~~ 478 (479)
T KOG1703|consen 463 -KTFF-ETLDKPLCQKHF 478 (479)
T ss_pred -Ccee-ecCCccccccCC
Confidence 3444 468899999885
No 8
>KOG0850|consensus
Probab=99.77 E-value=5.6e-19 Score=148.44 Aligned_cols=66 Identities=35% Similarity=0.564 Sum_probs=61.8
Q ss_pred CCCCCCCcccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHhhhhcC
Q psy4325 202 QPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKKDAG 267 (306)
Q Consensus 202 ~~~kr~rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~~~~ 267 (306)
.+.|++||.++..||..|.+.|+++.|....+|++||..|||+..||+|||||||.|.||+.+...
T Consensus 120 KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~g~ 185 (245)
T KOG0850|consen 120 KKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQGS 185 (245)
T ss_pred ccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhcCC
Confidence 346789999999999999999999999999999999999999999999999999999999988443
No 9
>KOG0484|consensus
Probab=99.77 E-value=1.1e-19 Score=133.58 Aligned_cols=69 Identities=36% Similarity=0.537 Sum_probs=63.1
Q ss_pred CCCCCCCCCCCcccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHhhhhc
Q psy4325 198 LDGDQPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKKDA 266 (306)
Q Consensus 198 ~~~~~~~kr~rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~~~ 266 (306)
+...++++|.||+|+..|+.+||++|.+++||++..|++||.+++|++..|||||||||+|.||+.+..
T Consensus 11 l~ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a 79 (125)
T KOG0484|consen 11 LTEKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAA 79 (125)
T ss_pred hhHHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHH
Confidence 334456788999999999999999999999999999999999999999999999999999999987653
No 10
>KOG2251|consensus
Probab=99.73 E-value=5.8e-18 Score=141.74 Aligned_cols=68 Identities=40% Similarity=0.613 Sum_probs=63.8
Q ss_pred CCCCCCCCCCcccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHhhhhc
Q psy4325 199 DGDQPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKKDA 266 (306)
Q Consensus 199 ~~~~~~kr~rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~~~ 266 (306)
.+.++.+|.||+|+..|+++||..|.++.||+...|++||.+|+|.+.+|+|||+|||+|+|++++..
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence 45566789999999999999999999999999999999999999999999999999999999988765
No 11
>KOG0490|consensus
Probab=99.72 E-value=5.1e-18 Score=149.27 Aligned_cols=189 Identities=44% Similarity=0.850 Sum_probs=161.2
Q ss_pred cCCCeeccceeeeecCccccccCcccCcCCCCCC--CcceeeCCeecccccccc--ccCcCCCCCCCCCCCCCceecccC
Q psy4325 75 GCGDLILDRFILKVLERTWHARCLKCHECGAPLA--EKCFARNGLLFCKEDFFK--RFGTKCAGCEMGIPPTQVVRRAQD 150 (306)
Q Consensus 75 ~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~--~~~f~~~g~~yC~~cy~~--~~~~~C~~C~~~I~~~~~~~~~~~ 150 (306)
+|+..|.+.+.+.+.+..||..|..|..|...|. ...|..+|..||..+|.. .+..+|..|...|...+.+..+..
T Consensus 1 ~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~d~~~~~~~~~rr~rt~~~~~ql~~ler~f~ 80 (235)
T KOG0490|consen 1 GCGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSKDGSIYCKRDYQREFKFSKRCARCKFTISQLDELERAFE 80 (235)
T ss_pred CCCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccCCCcccccccchhhhhccccccCCCCCcCHHHHHHHhhc
Confidence 4788898888888889999999999999999997 677755999999999998 788899999999977778888888
Q ss_pred ccccCCCcccccCCCCCCCCCceeeccCCcccccchhHHH--hhcc------C------------CCCCCCCCCCCCCcc
Q psy4325 151 LVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDYEAA--KAKD------G------------NCLDGDQPNKRPRTT 210 (306)
Q Consensus 151 ~~~H~~CF~C~~C~~~l~~g~~~~~~~~~~~~C~~c~~~~--~~~~------~------------~~~~~~~~~kr~rt~ 210 (306)
++ |.-||.|..|...+..++++.+....+..|...+.+. .... . .......+.++.++.
T Consensus 81 ~~-h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 159 (235)
T KOG0490|consen 81 KV-HLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEERPLPEGENLPDLSGTAPPSASRDKLDKGPSNKKPRRPRTT 159 (235)
T ss_pred CC-CcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhccccccccCCCCCCCCCccccccccccCCCccccCCCccc
Confidence 88 9999999999999988998887655588888887554 2111 0 011122446678899
Q ss_pred cchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHhhh
Q psy4325 211 ITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKK 264 (306)
Q Consensus 211 ~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~ 264 (306)
+...|+..|...|...++|+...++.|+..+|++++.|++||||+|++.++...
T Consensus 160 ~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 160 FTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred cccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 999999999999999999999999999999999999999999999999998655
No 12
>KOG0489|consensus
Probab=99.72 E-value=7.6e-18 Score=149.97 Aligned_cols=68 Identities=31% Similarity=0.433 Sum_probs=63.0
Q ss_pred CCCCCCCcccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHhhhhcCCC
Q psy4325 202 QPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKKDAGRT 269 (306)
Q Consensus 202 ~~~kr~rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~~~~~~ 269 (306)
...+|.||.||..|+.+||+.|+.|.|.+...|.+||..|.|+++||+|||||||+||||..+.....
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~~ 224 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKSSQ 224 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccccc
Confidence 44789999999999999999999999999999999999999999999999999999999987765444
No 13
>KOG0843|consensus
Probab=99.71 E-value=1e-17 Score=135.74 Aligned_cols=64 Identities=39% Similarity=0.559 Sum_probs=60.9
Q ss_pred CCCCCCcccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHhhhhc
Q psy4325 203 PNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKKDA 266 (306)
Q Consensus 203 ~~kr~rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~~~ 266 (306)
+.||.||.|+.+|+..||..|+.++|....+|+.||+.|+|++.||+|||||||.|.||+....
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 5689999999999999999999999999999999999999999999999999999999987763
No 14
>KOG1703|consensus
Probab=99.71 E-value=7.4e-18 Score=162.59 Aligned_cols=167 Identities=20% Similarity=0.369 Sum_probs=137.5
Q ss_pred CCcccccchhhhcccccccccCCCc----cc-cCCccccCCcccccccCCCCCCCCCccCCCeeccceeeeecCcccccc
Q psy4325 22 NGLTVGICASKLHDLLHEAHAGSSS----SF-SSSFNDVDYEGIMPVYMPIASIPKCGGCGDLILDRFILKVLERTWHAR 96 (306)
Q Consensus 22 ~~~~~~~~~~~~~~~~~~~~~~~~~----~~-~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~ 96 (306)
..++.+....++...|+..++.+.. .+ .+.+........++..+.....+.|..|+..|.+..++.+++..||+.
T Consensus 250 ~~p~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~c~~c~~~i~~~~~i~~~~~~~h~~ 329 (479)
T KOG1703|consen 250 DSPECQPLVSAPRPASEGLHMKVEKELPLLLVESEALKKLREEEKPAEYHNVTRPLCLSCNQKIRSVKVIVALGKEWHPE 329 (479)
T ss_pred CCCccCcceecccccccccccccccccchhhcccccccccccccccccccccccccccccccCcccceeEeecccccccc
Confidence 3445555666888889999986654 22 344556667777777776667899999999999944557999999999
Q ss_pred CcccCcCCCCCCCcce-eeCCeeccccccccccCcCCCCCCCCCCCCCceecccCccccCCCcccccCCCCCCCCCceee
Q psy4325 97 CLKCHECGAPLAEKCF-ARNGLLFCKEDFFKRFGTKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYL 175 (306)
Q Consensus 97 Cf~C~~C~~~l~~~~f-~~~g~~yC~~cy~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~CF~C~~C~~~l~~g~~~~~ 175 (306)
+|.|..|+..+....| ..+|++||..||.+.+.+.|..|.++|.+. +|.+.+..||++||.|..|.+.|..+ .|+.
T Consensus 330 ~~~c~~~~~~~~~~~~~~~~g~~~c~~~~~~~~~p~C~~C~~~i~~~--~v~a~~~~wH~~cf~C~~C~~~~~~~-~~~~ 406 (479)
T KOG1703|consen 330 HFSCEVCAIVILDGGPRELDGKILCHECFHAPFRPNCKRCLLPILEE--GVCALGRLWHPECFVCADCGKPLKNS-SFFE 406 (479)
T ss_pred ceeeccccccccCCCccccCCCccHHHHHHHhhCccccccCCchHHh--HhhhccCeechhceeeecccCCCCCC-cccc
Confidence 9999999999977666 889999999999999999999999999765 56788999999999999999998644 3444
Q ss_pred ccCCcccccchhHHHhh
Q psy4325 176 MEDRKLVCKPDYEAAKA 192 (306)
Q Consensus 176 ~~~~~~~C~~c~~~~~~ 192 (306)
.++.+||..||.+++.
T Consensus 407 -~~~~pyce~~~~~~~~ 422 (479)
T KOG1703|consen 407 -SDGEPYCEDHYKKLFT 422 (479)
T ss_pred -cCCccchhhhHhhhcc
Confidence 7999999999999986
No 15
>KOG0488|consensus
Probab=99.70 E-value=1.4e-17 Score=150.73 Aligned_cols=67 Identities=30% Similarity=0.455 Sum_probs=62.0
Q ss_pred CCCCCCCcccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHhhhhcCC
Q psy4325 202 QPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKKDAGR 268 (306)
Q Consensus 202 ~~~kr~rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~~~~~ 268 (306)
++.++.||.||..|+..||+.|++..|.+..+|++||..|||+..||++||||||+||||+....+.
T Consensus 170 kK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~g~~ 236 (309)
T KOG0488|consen 170 KKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAEGGE 236 (309)
T ss_pred cccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHhhhc
Confidence 4456789999999999999999999999999999999999999999999999999999998877544
No 16
>KOG0842|consensus
Probab=99.67 E-value=8.2e-17 Score=143.33 Aligned_cols=68 Identities=28% Similarity=0.427 Sum_probs=63.0
Q ss_pred CCCCCCCCcccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHhhhhcCC
Q psy4325 201 DQPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKKDAGR 268 (306)
Q Consensus 201 ~~~~kr~rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~~~~~ 268 (306)
.+++|+.|.-|+..|+.+||+.|.+..|.+..||+.||..|.||+.||||||||||.|-||+.+....
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~ 217 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKAL 217 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhh
Confidence 45677888999999999999999999999999999999999999999999999999999998877644
No 17
>KOG0487|consensus
Probab=99.66 E-value=3e-17 Score=146.18 Aligned_cols=65 Identities=29% Similarity=0.446 Sum_probs=60.7
Q ss_pred CCCCCcccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHhhhhcCC
Q psy4325 204 NKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKKDAGR 268 (306)
Q Consensus 204 ~kr~rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~~~~~ 268 (306)
.+++|..+|..|+.+||+.|..|.|++.+.|.+|++.|+|+++||+|||||||+|+||+.++...
T Consensus 235 ~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~r~ 299 (308)
T KOG0487|consen 235 GRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRENRL 299 (308)
T ss_pred cccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhhhc
Confidence 46788999999999999999999999999999999999999999999999999999999875543
No 18
>KOG0848|consensus
Probab=99.64 E-value=4.7e-17 Score=139.31 Aligned_cols=64 Identities=33% Similarity=0.473 Sum_probs=59.4
Q ss_pred CCCCCcccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHhhhhcC
Q psy4325 204 NKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKKDAG 267 (306)
Q Consensus 204 ~kr~rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~~~~ 267 (306)
+.+-|..+|+.|+.+||+.|..+.|+++..+.+||..|||++|||+|||||||+|+||..++..
T Consensus 199 kDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk~ 262 (317)
T KOG0848|consen 199 KDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKKR 262 (317)
T ss_pred ccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHHH
Confidence 3466888999999999999999999999999999999999999999999999999999887763
No 19
>KOG0492|consensus
Probab=99.63 E-value=1.8e-16 Score=131.09 Aligned_cols=69 Identities=36% Similarity=0.584 Sum_probs=63.1
Q ss_pred CCCCCCCCCCCcccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHhhhhc
Q psy4325 198 LDGDQPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKKDA 266 (306)
Q Consensus 198 ~~~~~~~kr~rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~~~ 266 (306)
+....+.+++||.||..|+..||+.|.+.+|.++++|.+++..|.|++.||+|||||||+|.||.+...
T Consensus 138 LrKhk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae 206 (246)
T KOG0492|consen 138 LRKHKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAE 206 (246)
T ss_pred hcccCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHH
Confidence 344566789999999999999999999999999999999999999999999999999999999876543
No 20
>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=99.62 E-value=1.9e-16 Score=108.28 Aligned_cols=57 Identities=46% Similarity=0.767 Sum_probs=55.1
Q ss_pred CCCCcccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHH
Q psy4325 205 KRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261 (306)
Q Consensus 205 kr~rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~ 261 (306)
++.|+.|+..|+..|+..|..++||+..+++.||..+||+..+|++||+|+|+++||
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence 578999999999999999999999999999999999999999999999999999986
No 21
>KOG0485|consensus
Probab=99.61 E-value=2.2e-16 Score=131.33 Aligned_cols=67 Identities=30% Similarity=0.417 Sum_probs=62.1
Q ss_pred CCCCCCCCCcccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHhhhhc
Q psy4325 200 GDQPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKKDA 266 (306)
Q Consensus 200 ~~~~~kr~rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~~~ 266 (306)
++..+|+.||.|+..|+..||..|+...|.+..+|..||++|.|++.||+|||||||.||||+....
T Consensus 100 g~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad 166 (268)
T KOG0485|consen 100 GDDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAAD 166 (268)
T ss_pred cccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhh
Confidence 4456789999999999999999999999999999999999999999999999999999999986543
No 22
>KOG0490|consensus
Probab=99.61 E-value=6.1e-16 Score=136.06 Aligned_cols=119 Identities=32% Similarity=0.526 Sum_probs=102.1
Q ss_pred CCCCCCCCCceecccCccccCCCcccccCCCCCCCCCceeeccCCcccccchhHHHhhccCCCCCCCCCCCCCCcccchH
Q psy4325 135 CEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDYEAAKAKDGNCLDGDQPNKRPRTTITAK 214 (306)
Q Consensus 135 C~~~I~~~~~~~~~~~~~~H~~CF~C~~C~~~l~~g~~~~~~~~~~~~C~~c~~~~~~~~~~~~~~~~~~kr~rt~~s~~ 214 (306)
|+..|.+... +.+.+..||..|..|..|...+..+...+.. +|..||...+.. ....++++.|+.|+..
T Consensus 2 ~~~~~~~~~~-l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~---------~~~~~~rr~rt~~~~~ 70 (235)
T KOG0490|consen 2 CGRQILDRYL-LRVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQR---------EFKFSKRCARCKFTIS 70 (235)
T ss_pred CCccccchHH-hhcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchh---------hhhccccccCCCCCcC
Confidence 6677765543 3566889999999999999999644556665 999999998876 1223568899999999
Q ss_pred hHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHhhh
Q psy4325 215 QLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKK 264 (306)
Q Consensus 215 q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~ 264 (306)
|+++|++.|++++||+...|+.||..+++++..|+|||||||+||+++..
T Consensus 71 ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~ 120 (235)
T KOG0490|consen 71 QLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEER 120 (235)
T ss_pred HHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence 99999999999999999999999999999999999999999999998774
No 23
>KOG0494|consensus
Probab=99.60 E-value=4.9e-16 Score=132.46 Aligned_cols=66 Identities=39% Similarity=0.536 Sum_probs=60.9
Q ss_pred CCCCCcccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHhhhhcCCC
Q psy4325 204 NKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKKDAGRT 269 (306)
Q Consensus 204 ~kr~rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~~~~~~ 269 (306)
+++.||.||..|++.||+.|.+.+||+...|+.||.+++|.+..|+|||||||+||||..+..+..
T Consensus 141 RRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg~s 206 (332)
T KOG0494|consen 141 RRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWGGS 206 (332)
T ss_pred cccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcCcc
Confidence 344589999999999999999999999999999999999999999999999999999998876553
No 24
>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=99.53 E-value=4.9e-15 Score=100.06 Aligned_cols=53 Identities=26% Similarity=0.428 Sum_probs=50.9
Q ss_pred CCCCCcccchHhHHHHHhccccCCC----CCHHHHHHHHHhhCCCccchhcccccch
Q psy4325 204 NKRPRTTITAKQLETLKMAYNTSPK----PARHVREQLSQDTGLDMRVVQVWFQNRR 256 (306)
Q Consensus 204 ~kr~rt~~s~~q~~~Le~~F~~~~~----p~~~~r~~La~~~~l~~~~V~~WFqNrR 256 (306)
++|.||.||.+|++.|+..|+.++| |+..++++||..+||++++|+|||||.+
T Consensus 1 ~kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 1 KKRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 3789999999999999999999999 9999999999999999999999999975
No 25
>KOG0493|consensus
Probab=99.53 E-value=3.6e-15 Score=127.30 Aligned_cols=66 Identities=38% Similarity=0.642 Sum_probs=60.6
Q ss_pred CCCCCCcccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHhhhhcCC
Q psy4325 203 PNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKKDAGR 268 (306)
Q Consensus 203 ~~kr~rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~~~~~ 268 (306)
.-||+||.|+.+||..|+..|+.+.|.++..|.+||.+|||.+.||+|||||+|+|-||.......
T Consensus 245 eeKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTgskn~ 310 (342)
T KOG0493|consen 245 EEKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTGSKNR 310 (342)
T ss_pred hhcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccCCCCc
Confidence 357899999999999999999999999999999999999999999999999999999987655443
No 26
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.52 E-value=1.2e-14 Score=118.67 Aligned_cols=73 Identities=34% Similarity=0.512 Sum_probs=66.3
Q ss_pred CCCCCCCCCCCCCcccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHhhhhcCC
Q psy4325 196 NCLDGDQPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKKDAGR 268 (306)
Q Consensus 196 ~~~~~~~~~kr~rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~~~~~ 268 (306)
...++.++.++.|++.+..|+.+|++.|+.++||+..+|..|+..++|+++.|+|||||+|++.|+.......
T Consensus 43 ~~~~~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~~~~ 115 (156)
T COG5576 43 RKQDGSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGKVE 115 (156)
T ss_pred hcccCCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcccchh
Confidence 4566777888999999999999999999999999999999999999999999999999999999987765433
No 27
>KOG1044|consensus
Probab=99.50 E-value=1e-14 Score=136.98 Aligned_cols=161 Identities=20% Similarity=0.417 Sum_probs=119.2
Q ss_pred cccCCCCcccccchhhhcccccccccC---CCcccc-CCccccCCcccccccCCCCCCCCCccCCCeeccceeeeecCcc
Q psy4325 17 AVQRGNGLTVGICASKLHDLLHEAHAG---SSSSFS-SSFNDVDYEGIMPVYMPIASIPKCGGCGDLILDRFILKVLERT 92 (306)
Q Consensus 17 ~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~~~~~~~~ 92 (306)
-++.|...=.+.-...-+..+|..||+ |...|. .+|+..+++. .+. . ..|...|.+. ++.++|++
T Consensus 18 ~c~~c~~kc~gevlrv~d~~fhi~cf~c~~cg~~la~~gff~k~~~~----~yg---t---~~c~~~~~ge-vvsa~gkt 86 (670)
T KOG1044|consen 18 KCDKCRKKCSGEVLRVNDNHFHINCFQCKKCGRNLAEGGFFTKPENR----LYG---T---DDCRAFVEGE-VVSTLGKT 86 (670)
T ss_pred ehhhhCCccccceeEeeccccceeeeeccccCCCcccccceecccce----eec---c---cchhhhccce-eEecccce
Confidence 355555555555566677889999995 455774 6677766652 222 1 5677777665 56799999
Q ss_pred ccccCcccCcCCCCCC-Ccce-eeCCeeccccccccc--------cCcCCCCCCCCCCCCCceecccCccccCCCccccc
Q psy4325 93 WHARCLKCHECGAPLA-EKCF-ARNGLLFCKEDFFKR--------FGTKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVM 162 (306)
Q Consensus 93 ~H~~Cf~C~~C~~~l~-~~~f-~~~g~~yC~~cy~~~--------~~~~C~~C~~~I~~~~~~~~~~~~~~H~~CF~C~~ 162 (306)
||+.||.|+.|+.++. +... .......|..|..-. ....|++|+..|..... +.|.++.||+.||+|..
T Consensus 87 yh~~cf~cs~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk~gq~-llald~qwhv~cfkc~~ 165 (670)
T KOG1044|consen 87 YHPKCFSCSTCKSPFKSGDKVTFSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELKNGQA-LLALDKQWHVSCFKCKS 165 (670)
T ss_pred eccccceecccCCCCCCCCeeeecchhhhhhhhcCcccCCcccccCCccccchhhhhhccce-eeeeccceeeeeeehhh
Confidence 9999999999999994 3444 445568888886332 12369999999965544 46999999999999999
Q ss_pred CCCCCCCCCceeeccCCcccccchhHHHhh
Q psy4325 163 CARQLNTGDEFYLMEDRKLVCKPDYEAAKA 192 (306)
Q Consensus 163 C~~~l~~g~~~~~~~~~~~~C~~c~~~~~~ 192 (306)
|...|. |. |+.++|.+||..+|.+.|+
T Consensus 166 c~~vL~-ge--y~skdg~pyce~dy~~~fg 192 (670)
T KOG1044|consen 166 CSAVLN-GE--YMSKDGVPYCEKDYQAKFG 192 (670)
T ss_pred hccccc-ce--eeccCCCcchhhhhhhhcC
Confidence 999995 44 4558999999999998874
No 28
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.48 E-value=1.5e-14 Score=98.45 Aligned_cols=55 Identities=51% Similarity=0.802 Sum_probs=52.0
Q ss_pred CCCcccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHH
Q psy4325 206 RPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEK 260 (306)
Q Consensus 206 r~rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k 260 (306)
+.|+.++..|+..|+..|..++||+..++..||..+||+..+|++||+|||++.|
T Consensus 2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 5677899999999999999999999999999999999999999999999999853
No 29
>KOG0483|consensus
Probab=99.48 E-value=1.7e-14 Score=121.61 Aligned_cols=62 Identities=31% Similarity=0.533 Sum_probs=57.6
Q ss_pred CCCCCcccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHhhhh
Q psy4325 204 NKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKKD 265 (306)
Q Consensus 204 ~kr~rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~~ 265 (306)
..+.+.+|+.+|...||..|+.+.+..+.++..||++|||.++||.|||||||||||..+..
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE 111 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLE 111 (198)
T ss_pred cccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhh
Confidence 45678899999999999999999999999999999999999999999999999999976544
No 30
>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=99.46 E-value=3.1e-14 Score=97.84 Aligned_cols=57 Identities=49% Similarity=0.807 Sum_probs=54.1
Q ss_pred CCCcccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHh
Q psy4325 206 RPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRL 262 (306)
Q Consensus 206 r~rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~ 262 (306)
+.+..++..|+..|+.+|..++||+..++..||.++||++.+|++||+|+|++.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 567899999999999999999999999999999999999999999999999998863
No 31
>KOG0847|consensus
Probab=99.46 E-value=5.1e-14 Score=117.40 Aligned_cols=66 Identities=30% Similarity=0.426 Sum_probs=60.4
Q ss_pred CCCCCCCCCcccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHhhhh
Q psy4325 200 GDQPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKKD 265 (306)
Q Consensus 200 ~~~~~kr~rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~~ 265 (306)
-+.+++..|.+|+..|+..|+..|++..|+..++|.+||..+|+++.||+|||||||.||||+...
T Consensus 163 kdG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAa 228 (288)
T KOG0847|consen 163 LNGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAA 228 (288)
T ss_pred cCccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhcc
Confidence 345567788899999999999999999999999999999999999999999999999999987554
No 32
>KOG0491|consensus
Probab=99.43 E-value=4.5e-14 Score=112.75 Aligned_cols=63 Identities=27% Similarity=0.483 Sum_probs=59.1
Q ss_pred CCCCCcccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHhhhhc
Q psy4325 204 NKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKKDA 266 (306)
Q Consensus 204 ~kr~rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~~~ 266 (306)
+++.|+.|+..|+..|++.|+...|.+..+|.+||..|+|++.||+.||||||+|.||..+..
T Consensus 100 r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~ 162 (194)
T KOG0491|consen 100 RRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNN 162 (194)
T ss_pred hhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhcc
Confidence 457799999999999999999999999999999999999999999999999999999876654
No 33
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=99.38 E-value=2.4e-13 Score=93.13 Aligned_cols=56 Identities=38% Similarity=0.983 Sum_probs=49.9
Q ss_pred CccCCCeeccceee-eecCccccccCcccCcCCCCCCCcc-eeeCCeecccccccccc
Q psy4325 73 CGGCGDLILDRFIL-KVLERTWHARCLKCHECGAPLAEKC-FARNGLLFCKEDFFKRF 128 (306)
Q Consensus 73 C~~C~~~I~~~~~~-~~~~~~~H~~Cf~C~~C~~~l~~~~-f~~~g~~yC~~cy~~~~ 128 (306)
|.+|+++|.+..++ .++|+.||+.||+|..|+++|.+.. +..+|++||..||.++|
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~f 58 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLNDGDFYEKDGKPYCKDCYQKRF 58 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTTSSEEEETTEEEEHHHHHHHT
T ss_pred CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCCCeeEeECCEEECHHHHhhhC
Confidence 78999999987665 6999999999999999999998764 59999999999998765
No 34
>KOG3802|consensus
Probab=99.37 E-value=4.9e-13 Score=121.65 Aligned_cols=65 Identities=31% Similarity=0.559 Sum_probs=61.1
Q ss_pred CCCCCCCCCcccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHhhh
Q psy4325 200 GDQPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKK 264 (306)
Q Consensus 200 ~~~~~kr~rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~ 264 (306)
+..++|++||.+....+.+||+.|.+|+.|+.+++..||.+|+|...+|+|||+|||.|+||...
T Consensus 290 a~~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 290 AQSRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred ccccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 44467788999999999999999999999999999999999999999999999999999999877
No 35
>KOG0844|consensus
Probab=99.36 E-value=1.2e-13 Score=120.52 Aligned_cols=66 Identities=32% Similarity=0.484 Sum_probs=61.2
Q ss_pred CCCCCCCCCcccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHhhhh
Q psy4325 200 GDQPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKKD 265 (306)
Q Consensus 200 ~~~~~kr~rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~~ 265 (306)
++.+-+|-||.||.+|+..||+.|-+..|.+...|-+||.+|+|.+..|+|||||||+|+||++..
T Consensus 177 a~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 177 ADDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred ccHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence 444567889999999999999999999999999999999999999999999999999999998764
No 36
>KOG0486|consensus
Probab=99.33 E-value=4.4e-13 Score=117.71 Aligned_cols=65 Identities=32% Similarity=0.543 Sum_probs=60.7
Q ss_pred CCCCCCcccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHhhhhcC
Q psy4325 203 PNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKKDAG 267 (306)
Q Consensus 203 ~~kr~rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~~~~ 267 (306)
+++|.|+.|+..|+.+||..|.++.||+...|++||--++|++..|+|||+|||+||||++..+.
T Consensus 111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence 46688999999999999999999999999999999999999999999999999999999876543
No 37
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=99.30 E-value=1.4e-12 Score=89.33 Aligned_cols=58 Identities=40% Similarity=0.762 Sum_probs=51.4
Q ss_pred CCCCCCCCCCCCceecccCccccCCCcccccCCCCCCCCCceeeccCCcccccchhHHHh
Q psy4325 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDYEAAK 191 (306)
Q Consensus 132 C~~C~~~I~~~~~~~~~~~~~~H~~CF~C~~C~~~l~~g~~~~~~~~~~~~C~~c~~~~~ 191 (306)
|..|+++|.+.+.++.+.|+.||++||+|..|++.|..+. ++. .++++||..||.++|
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~-~~~-~~~~~~C~~c~~~~f 58 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLNDGD-FYE-KDGKPYCKDCYQKRF 58 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTTSS-EEE-ETTEEEEHHHHHHHT
T ss_pred CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCCCe-eEe-ECCEEECHHHHhhhC
Confidence 7899999998888878999999999999999999997655 554 688999999998875
No 38
>KOG1700|consensus
Probab=99.24 E-value=1.5e-12 Score=111.28 Aligned_cols=121 Identities=26% Similarity=0.635 Sum_probs=100.5
Q ss_pred CCCCccCCCeeccceeeeecCccccccCcccCcCCCCCCCcce-eeCCeeccccccccccCcC-----------------
Q psy4325 70 IPKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCF-ARNGLLFCKEDFFKRFGTK----------------- 131 (306)
Q Consensus 70 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f-~~~g~~yC~~cy~~~~~~~----------------- 131 (306)
...|..|++.++-.+.+...|..||+.||.|..|.+.|....+ ..++.+||+.||...++++
T Consensus 7 ~~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 86 (200)
T KOG1700|consen 7 TDKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVAQFGPKGGGFGKGFQKAGGLGKD 86 (200)
T ss_pred cchhhhccCcchHHHHHhccCcchhhhHHhccccccccccccccccccccccccchHhhhCcccccccccccccCCCCcc
Confidence 4589999999997767678899999999999999999977555 8899999999775555442
Q ss_pred ------------------------CCCCCCCCCCCCceecccCccccCCCcccccCCCCCCCCCceeeccCCcccccchh
Q psy4325 132 ------------------------CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187 (306)
Q Consensus 132 ------------------------C~~C~~~I~~~~~~~~~~~~~~H~~CF~C~~C~~~l~~g~~~~~~~~~~~~C~~c~ 187 (306)
|..|.+.+...+.+ ...+..||..||+|..|+..|..+. +....+.++|..++
T Consensus 87 ~~~~~~~~~~~~~~~~~~~g~~~~c~~c~k~vy~~Ek~-~~~~~~~hk~cfrc~~~~~~ls~~~--~~~~~g~l~~~~~~ 163 (200)
T KOG1700|consen 87 GKSLNESKPNQSAKFQVFAGEKEKCARCQKTVYPLEKV-TGNGLEFHKSCFRCTHCGKKLSPKN--YAALEGVLYCKHHF 163 (200)
T ss_pred cccccccccccchhHHhhhccccccccccceeeehHHH-hhhhhhhhhhheeecccccccCCcc--hhhcCCccccchhh
Confidence 99999999877665 5788899999999999999997655 45567889998888
Q ss_pred HHHhhc
Q psy4325 188 EAAKAK 193 (306)
Q Consensus 188 ~~~~~~ 193 (306)
.+.+-.
T Consensus 164 ~~~~~~ 169 (200)
T KOG1700|consen 164 AQLFKG 169 (200)
T ss_pred heeecC
Confidence 776654
No 39
>KOG0775|consensus
Probab=99.17 E-value=4.7e-11 Score=103.23 Aligned_cols=86 Identities=28% Similarity=0.449 Sum_probs=64.1
Q ss_pred ccccchhHHHhhccCCCCCCCCC------CCCCCcc---------cchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCc
Q psy4325 181 LVCKPDYEAAKAKDGNCLDGDQP------NKRPRTT---------ITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDM 245 (306)
Q Consensus 181 ~~C~~c~~~~~~~~~~~~~~~~~------~kr~rt~---------~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~ 245 (306)
++=..+|..+....|..+.+..+ -.-+||. |.+..+..|..+|.+++||++.++.+||+++||+.
T Consensus 138 lWl~AhY~EAek~RGR~LgaV~KYRvRrKfPlPrTIWDGEet~yCFKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~ 217 (304)
T KOG0775|consen 138 LWLKAHYKEAEKLRGRPLGAVDKYRVRRKFPLPRTIWDGEETVYCFKEKSRSLLREWYLQNPYPSPREKRELAEATGLTI 217 (304)
T ss_pred HHHHHHHHHHHHhcCCcCCccccceeeccCCCCCccccCceeeeehhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCch
Confidence 44455665554444444443322 2234555 55666889999999999999999999999999999
Q ss_pred cchhcccccchhHHHHhhhhc
Q psy4325 246 RVVQVWFQNRRAKEKRLKKDA 266 (306)
Q Consensus 246 ~~V~~WFqNrR~k~k~~~~~~ 266 (306)
.||-+||+|||+|+|....+.
T Consensus 218 tQVsNWFKNRRQRDRa~~ak~ 238 (304)
T KOG0775|consen 218 TQVSNWFKNRRQRDRAAAAKN 238 (304)
T ss_pred hhhhhhhhhhhhhhhhccccc
Confidence 999999999999999554433
No 40
>KOG1168|consensus
Probab=99.01 E-value=1.7e-10 Score=100.34 Aligned_cols=67 Identities=33% Similarity=0.578 Sum_probs=61.5
Q ss_pred CCCCCCCCCcccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHhhhhc
Q psy4325 200 GDQPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKKDA 266 (306)
Q Consensus 200 ~~~~~kr~rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~~~ 266 (306)
....+||+||.+.....+.||.+|...+.|+.+.+..||++|+|...+|+|||+|+|+|.||+....
T Consensus 305 ~~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~Sa 371 (385)
T KOG1168|consen 305 PGGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKRSA 371 (385)
T ss_pred CccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhhhh
Confidence 3345789999999999999999999999999999999999999999999999999999999976654
No 41
>KOG0849|consensus
Probab=98.99 E-value=5.9e-10 Score=103.40 Aligned_cols=63 Identities=43% Similarity=0.674 Sum_probs=58.6
Q ss_pred CCCCCCCcccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHhhh
Q psy4325 202 QPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKK 264 (306)
Q Consensus 202 ~~~kr~rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~ 264 (306)
+..++.|++|+..|++.|++.|+.++||+...|++||.++++++..|+|||+|||++++|...
T Consensus 174 ~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~ 236 (354)
T KOG0849|consen 174 RGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHR 236 (354)
T ss_pred ccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhccc
Confidence 345567899999999999999999999999999999999999999999999999999999873
No 42
>KOG4577|consensus
Probab=98.79 E-value=2.2e-10 Score=99.56 Aligned_cols=113 Identities=17% Similarity=0.278 Sum_probs=90.7
Q ss_pred CCCCcccccc-hhhhcccccccccCCCc---cccCCccccCCcccccccCCCCCCCCCccCCCeeccceee-eecCcccc
Q psy4325 20 RGNGLTVGIC-ASKLHDLLHEAHAGSSS---SFSSSFNDVDYEGIMPVYMPIASIPKCGGCGDLILDRFIL-KVLERTWH 94 (306)
Q Consensus 20 ~~~~~~~~~~-~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~~-~~~~~~~H 94 (306)
-|.+.|.... .+.+++.||..|-.|+. .|....+...+..||...+-..+..+|..|.+.|-...++ .|.+..||
T Consensus 38 gC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~drCFsR~~s~yCkedFfKrfGTKCsaC~~GIpPtqVVRkAqd~VYH 117 (383)
T KOG4577|consen 38 GCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLADRCFSREGSVYCKEDFFKRFGTKCSACQEGIPPTQVVRKAQDFVYH 117 (383)
T ss_pred chHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHHHHhhcCCceeehHHHHHHhCCcchhhcCCCChHHHHHHhhcceee
Confidence 3344444432 45889999999986655 8888888999999999988888899999999999876555 57788999
Q ss_pred ccCcccCcCCCCCC--Ccce-eeCCeeccccccccccCcCC
Q psy4325 95 ARCLKCHECGAPLA--EKCF-ARNGLLFCKEDFFKRFGTKC 132 (306)
Q Consensus 95 ~~Cf~C~~C~~~l~--~~~f-~~~g~~yC~~cy~~~~~~~C 132 (306)
..||.|.+|+..|. +++| +.|+++.|+.+|......-|
T Consensus 118 l~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~k~~ 158 (383)
T KOG4577|consen 118 LHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAKQKHC 158 (383)
T ss_pred hhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHHhccc
Confidence 99999999999994 3566 78899999999977554444
No 43
>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=98.73 E-value=3.6e-09 Score=66.21 Aligned_cols=34 Identities=32% Similarity=0.735 Sum_probs=29.4
Q ss_pred cCCCCCHHHHHHHHHhhCCCccchhcccccchhH
Q psy4325 225 TSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAK 258 (306)
Q Consensus 225 ~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k 258 (306)
.+|||+.++++.||.++||+..||..||-|.|.|
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 5799999999999999999999999999999976
No 44
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=98.55 E-value=5.9e-08 Score=60.29 Aligned_cols=37 Identities=46% Similarity=1.230 Sum_probs=33.1
Q ss_pred CCccCCCeeccc-eeeeecCccccccCcccCcCCCCCC
Q psy4325 72 KCGGCGDLILDR-FILKVLERTWHARCLKCHECGAPLA 108 (306)
Q Consensus 72 ~C~~C~~~I~~~-~~~~~~~~~~H~~Cf~C~~C~~~l~ 108 (306)
+|.+|+++|.+. ..+.+++..||+.||+|..|+.+|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 489999999986 6667899999999999999999885
No 45
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=98.50 E-value=8.1e-08 Score=59.66 Aligned_cols=38 Identities=42% Similarity=0.861 Sum_probs=33.9
Q ss_pred CCCCCCCCCCCCCceecccCccccCCCcccccCCCCCC
Q psy4325 131 KCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLN 168 (306)
Q Consensus 131 ~C~~C~~~I~~~~~~~~~~~~~~H~~CF~C~~C~~~l~ 168 (306)
+|..|+++|.+.+.++.+.++.||+.||+|..|+++|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 58899999988756678999999999999999999984
No 46
>KOG2252|consensus
Probab=98.49 E-value=2e-07 Score=88.41 Aligned_cols=60 Identities=28% Similarity=0.476 Sum_probs=56.2
Q ss_pred CCCCCCCCCcccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHH
Q psy4325 200 GDQPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKE 259 (306)
Q Consensus 200 ~~~~~kr~rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~ 259 (306)
.....|++|..|+..|++.|..+|+.+++|+.++.+.|+.+|+|..+.|.+||.|.|.|.
T Consensus 416 ~~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 416 KMLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred ccccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 334578899999999999999999999999999999999999999999999999999985
No 47
>KOG0774|consensus
Probab=98.49 E-value=1.2e-07 Score=81.66 Aligned_cols=60 Identities=23% Similarity=0.501 Sum_probs=54.9
Q ss_pred CCCCCcccchHhHHHHHhccc---cCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHhh
Q psy4325 204 NKRPRTTITAKQLETLKMAYN---TSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLK 263 (306)
Q Consensus 204 ~kr~rt~~s~~q~~~Le~~F~---~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~ 263 (306)
.+|+|+.|+....++|..+|. .+|||+.+.+++||++.+++..||.+||.|+|-+.||..
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~ 250 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNM 250 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhh
Confidence 457789999999999999984 789999999999999999999999999999999988753
No 48
>KOG1146|consensus
Probab=97.60 E-value=5.7e-05 Score=78.51 Aligned_cols=63 Identities=38% Similarity=0.566 Sum_probs=58.5
Q ss_pred CCCCCcccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHhhhhc
Q psy4325 204 NKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKKDA 266 (306)
Q Consensus 204 ~kr~rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~~~ 266 (306)
+++.|++++..|+..|...|....||..++.+.|.+.+++..++|++||||.|+|.|+.....
T Consensus 903 r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~n~ 965 (1406)
T KOG1146|consen 903 RRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKLNG 965 (1406)
T ss_pred hhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhhcc
Confidence 567899999999999999999999999999999999999999999999999999999876633
No 49
>KOG1702|consensus
Probab=97.57 E-value=1e-05 Score=67.68 Aligned_cols=60 Identities=25% Similarity=0.618 Sum_probs=52.7
Q ss_pred CCCCccCCCeeccceeeeecCccccccCcccCcCCCCCCCcce-eeCCeeccccccccccC
Q psy4325 70 IPKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCF-ARNGLLFCKEDFFKRFG 129 (306)
Q Consensus 70 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f-~~~g~~yC~~cy~~~~~ 129 (306)
...|..|++.++..+.+..+++.||..||+|..|+.+|..+.+ ..+.++||..+|-+..+
T Consensus 4 k~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq~a 64 (264)
T KOG1702|consen 4 KCNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQVA 64 (264)
T ss_pred cchhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCccccccee
Confidence 3468899999998777778999999999999999999999988 68999999999976553
No 50
>KOG1700|consensus
Probab=97.42 E-value=4.2e-05 Score=65.59 Aligned_cols=60 Identities=28% Similarity=0.657 Sum_probs=52.0
Q ss_pred CCCCCccCCCeeccceeeeecCccccccCcccCcCCCCCCCcce-eeCCeecccccccccc
Q psy4325 69 SIPKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCF-ARNGLLFCKEDFFKRF 128 (306)
Q Consensus 69 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f-~~~g~~yC~~cy~~~~ 128 (306)
....|..|.+.++..+.+...+..||..||+|..|+..|+...+ ..+|.+||+..+...+
T Consensus 107 ~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~~~g~l~~~~~~~~~~ 167 (200)
T KOG1700|consen 107 EKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYAALEGVLYCKHHFAQLF 167 (200)
T ss_pred cccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchhhcCCccccchhhheee
Confidence 45789999999998777778899999999999999999998877 7789999987765543
No 51
>KOG0773|consensus
Probab=96.92 E-value=0.00043 Score=64.43 Aligned_cols=58 Identities=24% Similarity=0.396 Sum_probs=49.7
Q ss_pred CCCCCcccchHhHHHHHhccc---cCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHH
Q psy4325 204 NKRPRTTITAKQLETLKMAYN---TSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261 (306)
Q Consensus 204 ~kr~rt~~s~~q~~~Le~~F~---~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~ 261 (306)
..+++..+......+|+.+.. ..+||+..++..||.++||+..||.+||-|.|.|..+
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~ 299 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWK 299 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCC
Confidence 556677888888888887743 3689999999999999999999999999999998554
No 52
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.33 E-value=0.0007 Score=45.13 Aligned_cols=42 Identities=17% Similarity=0.347 Sum_probs=31.1
Q ss_pred HHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchh
Q psy4325 216 LETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRA 257 (306)
Q Consensus 216 ~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~ 257 (306)
...|+.+|...+.+...+...|..+.+|+..||+.||--++.
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~ 51 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQ 51 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS-
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhcc
Confidence 456999999999999999999999999999999999976644
No 53
>KOG1702|consensus
Probab=95.94 E-value=0.0011 Score=55.81 Aligned_cols=60 Identities=32% Similarity=0.627 Sum_probs=47.2
Q ss_pred cCCCCCCCCCCCCCceecccCccccCCCcccccCCCCCCCCCceeeccCCcccccchhHHHhh
Q psy4325 130 TKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDYEAAKA 192 (306)
Q Consensus 130 ~~C~~C~~~I~~~~~~~~~~~~~~H~~CF~C~~C~~~l~~g~~~~~~~~~~~~C~~c~~~~~~ 192 (306)
+-|..|++.+.+.+.+ +..++.||..||.|..|+..|.- +-|-..+.++||.++|.+..+
T Consensus 5 ~n~~~cgk~vYPvE~v-~cldk~whk~cfkce~c~mtlnm--KnyKgy~kkpycn~hYpkq~a 64 (264)
T KOG1702|consen 5 CNREDCGKTVYPVEEV-KCLDKVWHKQCFKCEVCGMTLNM--KNYKGYDKKPYCNPHYPKQVA 64 (264)
T ss_pred chhhhhccccccHHHH-hhHHHHHHHHhheeeeccCChhh--hhccccccCCCcCccccccee
Confidence 3467788888777665 78899999999999999999853 234446889999999965544
No 54
>KOG3623|consensus
Probab=94.99 E-value=0.025 Score=56.06 Aligned_cols=48 Identities=27% Similarity=0.513 Sum_probs=44.4
Q ss_pred HHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHhh
Q psy4325 216 LETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLK 263 (306)
Q Consensus 216 ~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~ 263 (306)
+..|+..|..++.|+.++...+|.+.||+.+.|+.||++++++...-.
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~ 615 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVE 615 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhc
Confidence 678888999999999999999999999999999999999999987644
No 55
>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=92.63 E-value=0.11 Score=34.54 Aligned_cols=47 Identities=15% Similarity=0.302 Sum_probs=34.7
Q ss_pred CCCCcccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccch
Q psy4325 205 KRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRR 256 (306)
Q Consensus 205 kr~rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR 256 (306)
++.|..+|-++...+-..++..+ ....||+.+|++..+|..|..|+.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence 46788899888777777776665 578899999999999999999864
No 56
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=90.46 E-value=0.12 Score=31.50 Aligned_cols=33 Identities=30% Similarity=0.624 Sum_probs=25.7
Q ss_pred CCCCCCCCCCCCceecccCccccCCCcccccCCCCC
Q psy4325 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQL 167 (306)
Q Consensus 132 C~~C~~~I~~~~~~~~~~~~~~H~~CF~C~~C~~~l 167 (306)
|+-|+.+|.+...+++..++.|| |.|..|.+.|
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~---fCC~tC~~~f 33 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYY---FCCPTCLSQF 33 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEE---EECHHHHHHH
Confidence 77899999988888889999998 4455555444
No 57
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=85.21 E-value=0.83 Score=37.08 Aligned_cols=28 Identities=25% Similarity=0.350 Sum_probs=21.4
Q ss_pred CeeccccccccccCcCCCCCCCCCCCCCc
Q psy4325 116 GLLFCKEDFFKRFGTKCAGCEMGIPPTQV 144 (306)
Q Consensus 116 g~~yC~~cy~~~~~~~C~~C~~~I~~~~~ 144 (306)
..-||..|-.+.. ..|..|+.+|.+.+.
T Consensus 27 ~~~fC~kCG~~tI-~~Cp~C~~~IrG~y~ 54 (158)
T PF10083_consen 27 REKFCSKCGAKTI-TSCPNCSTPIRGDYH 54 (158)
T ss_pred HHHHHHHhhHHHH-HHCcCCCCCCCCcee
Confidence 4568888876544 589999999988643
No 58
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=83.22 E-value=1.4 Score=30.34 Aligned_cols=47 Identities=21% Similarity=0.413 Sum_probs=22.8
Q ss_pred cccCcCCCCCCCcce-eeCCeeccccccccccCcCCCCCCCCCCCCCc
Q psy4325 98 LKCHECGAPLAEKCF-ARNGLLFCKEDFFKRFGTKCAGCEMGIPPTQV 144 (306)
Q Consensus 98 f~C~~C~~~l~~~~f-~~~g~~yC~~cy~~~~~~~C~~C~~~I~~~~~ 144 (306)
.+|+.|..-|..... ..=..+||..|....++..|..|+.|-...+.
T Consensus 8 LrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~~~CPvC~~Paw~qD~ 55 (65)
T PF14835_consen 8 LRCSICFDILKEPVCLGGCEHIFCSSCIRDCIGSECPVCHTPAWIQDI 55 (65)
T ss_dssp TS-SSS-S--SS-B---SSS--B-TTTGGGGTTTB-SSS--B-S-SS-
T ss_pred cCCcHHHHHhcCCceeccCccHHHHHHhHHhcCCCCCCcCChHHHHHH
Confidence 367777766644322 33367899999988888999999988765554
No 59
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=82.76 E-value=0.78 Score=30.43 Aligned_cols=40 Identities=25% Similarity=0.621 Sum_probs=27.0
Q ss_pred cCcCCCCCCCCCCCCC-cee-cccCccccCCCc----cccc--CCCCC
Q psy4325 128 FGTKCAGCEMGIPPTQ-VVR-RAQDLVYHLNCF----ACVM--CARQL 167 (306)
Q Consensus 128 ~~~~C~~C~~~I~~~~-~~~-~~~~~~~H~~CF----~C~~--C~~~l 167 (306)
.+.+|..|+++|...+ .|+ ..-+-.||.+|+ .|.. |+..+
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~g~C~~~~c~~~~ 51 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKAGGCINYSCGTGF 51 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCCCcccHHHHhhCCceEeccCCCCc
Confidence 4578999999996444 332 456778999988 3655 55444
No 60
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=82.27 E-value=1 Score=33.99 Aligned_cols=29 Identities=28% Similarity=0.450 Sum_probs=18.2
Q ss_pred cCCCCCCCCCCCCCceecccCccccCCCc
Q psy4325 130 TKCAGCEMGIPPTQVVRRAQDLVYHLNCF 158 (306)
Q Consensus 130 ~~C~~C~~~I~~~~~~~~~~~~~~H~~CF 158 (306)
..|..|+++|.....++--.|..+|..|+
T Consensus 79 ~~C~vC~k~l~~~~f~~~p~~~v~H~~C~ 107 (109)
T PF10367_consen 79 TKCSVCGKPLGNSVFVVFPCGHVVHYSCI 107 (109)
T ss_pred CCccCcCCcCCCceEEEeCCCeEEecccc
Confidence 46777888776544444344566777765
No 61
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=81.19 E-value=0.99 Score=30.51 Aligned_cols=45 Identities=7% Similarity=0.034 Sum_probs=30.2
Q ss_pred cccCcCCCCCCCcceeeCCeecccccccccc--CcCCCCCCCCCCCC
Q psy4325 98 LKCHECGAPLAEKCFARNGLLFCKEDFFKRF--GTKCAGCEMGIPPT 142 (306)
Q Consensus 98 f~C~~C~~~l~~~~f~~~g~~yC~~cy~~~~--~~~C~~C~~~I~~~ 142 (306)
|.|..|+..+........|..||..|..+.+ ...|..|++++...
T Consensus 2 ~~Cpi~~~~~~~Pv~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~~ 48 (63)
T smart00504 2 FLCPISLEVMKDPVILPSGQTYERRAIEKWLLSHGTDPVTGQPLTHE 48 (63)
T ss_pred cCCcCCCCcCCCCEECCCCCEEeHHHHHHHHHHCCCCCCCcCCCChh
Confidence 5688888877665445568889988875433 24677777766443
No 62
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=80.73 E-value=1 Score=27.43 Aligned_cols=31 Identities=26% Similarity=0.572 Sum_probs=21.4
Q ss_pred CccCCCeecccee-eeecCccccccCcccCcCCCC
Q psy4325 73 CGGCGDLILDRFI-LKVLERTWHARCLKCHECGAP 106 (306)
Q Consensus 73 C~~C~~~I~~~~~-~~~~~~~~H~~Cf~C~~C~~~ 106 (306)
|.-||.+|.++.+ +...++.|| |.|..|...
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~---fCC~tC~~~ 32 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYY---FCCPTCLSQ 32 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEE---EECHHHHHH
Confidence 6789999987654 456788888 455555443
No 63
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=79.32 E-value=1.3 Score=36.24 Aligned_cols=24 Identities=13% Similarity=0.088 Sum_probs=21.0
Q ss_pred HHHHHHhhCCCccchhcccccchh
Q psy4325 234 REQLSQDTGLDMRVVQVWFQNRRA 257 (306)
Q Consensus 234 r~~La~~~~l~~~~V~~WFqNrR~ 257 (306)
.++||..+|++...|..|-.+.+.
T Consensus 85 qeeLA~~lgvs~s~IsriE~G~~~ 108 (154)
T TIGR00270 85 QEQLAKKIQEKESLIKKIENAEIE 108 (154)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCCC
Confidence 668999999999999999987754
No 64
>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=76.42 E-value=1.8 Score=28.71 Aligned_cols=40 Identities=33% Similarity=0.450 Sum_probs=32.2
Q ss_pred cchHhHHHHHhccccCC--CCCHHHHHHHHHhhCCCccchhc
Q psy4325 211 ITAKQLETLKMAYNTSP--KPARHVREQLSQDTGLDMRVVQV 250 (306)
Q Consensus 211 ~s~~q~~~Le~~F~~~~--~p~~~~r~~La~~~~l~~~~V~~ 250 (306)
+|+.|+++|...++.-= +|-.....+||..+|+++..|.-
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~ 42 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSE 42 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHH
Confidence 47889999999887553 47777888999999999877654
No 65
>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=75.60 E-value=2.3 Score=27.36 Aligned_cols=46 Identities=13% Similarity=0.289 Sum_probs=33.5
Q ss_pred ccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHH
Q psy4325 210 TITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEK 260 (306)
Q Consensus 210 ~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k 260 (306)
.+++.+..++...|-.. ..-.++|..+|++...|+.+...-..|-|
T Consensus 4 ~L~~~er~vi~~~y~~~-----~t~~eIa~~lg~s~~~V~~~~~~al~kLR 49 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG-----LTLEEIAERLGISRSTVRRILKRALKKLR 49 (50)
T ss_dssp TS-HHHHHHHHHHHTST------SHHHHHHHHTSCHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCC-----CCHHHHHHHHCCcHHHHHHHHHHHHHHhc
Confidence 46788888888887322 35678999999999999887766555544
No 66
>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=74.80 E-value=2 Score=28.02 Aligned_cols=43 Identities=16% Similarity=0.255 Sum_probs=28.3
Q ss_pred cchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhH
Q psy4325 211 ITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAK 258 (306)
Q Consensus 211 ~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k 258 (306)
+++.+..++...|-. .....++|..+|+++..|+.|.+.-|.+
T Consensus 11 L~~~~r~i~~l~~~~-----g~s~~eIa~~l~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 11 LPERQREIFLLRYFQ-----GMSYAEIAEILGISESTVKRRLRRARKK 53 (54)
T ss_dssp S-HHHHHHHHHHHTS--------HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHH-----CcCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence 456666666664332 3467889999999999999998766554
No 67
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=72.56 E-value=0.82 Score=34.44 Aligned_cols=35 Identities=17% Similarity=0.446 Sum_probs=26.2
Q ss_pred cccccCCCCCCCCCceeeccCCcccccchhHHHhhc
Q psy4325 158 FACVMCARQLNTGDEFYLMEDRKLVCKPDYEAAKAK 193 (306)
Q Consensus 158 F~C~~C~~~l~~g~~~~~~~~~~~~C~~c~~~~~~~ 193 (306)
++|..|+..+..|..|++... -+.--.||....++
T Consensus 3 WkC~iCg~~I~~gqlFTF~~k-G~VH~~C~~~~~~~ 37 (101)
T PF09943_consen 3 WKCYICGKPIYEGQLFTFTKK-GPVHYECFREKASK 37 (101)
T ss_pred eEEEecCCeeeecceEEEecC-CcEeHHHHHHHHhh
Confidence 468888888888888887655 57777788766554
No 68
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=71.71 E-value=4.7 Score=32.51 Aligned_cols=52 Identities=13% Similarity=0.215 Sum_probs=40.6
Q ss_pred CcccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHhhhh
Q psy4325 208 RTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKKD 265 (306)
Q Consensus 208 rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~~ 265 (306)
...+++.|+++|...++ . ....++|..+|++...|..|-++.+.+.|+....
T Consensus 4 ~~~Lt~rqreVL~lr~~--G----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~t 55 (141)
T PRK03975 4 ESFLTERQIEVLRLRER--G----LTQQEIADILGTSRANVSSIEKRARENIEKARET 55 (141)
T ss_pred ccCCCHHHHHHHHHHHc--C----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 45678889999887422 2 2467899999999999999999988887765544
No 69
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=71.24 E-value=2.7 Score=33.25 Aligned_cols=22 Identities=41% Similarity=1.014 Sum_probs=17.6
Q ss_pred ccCcCCCCCCCcceeeCCeecccccc
Q psy4325 99 KCHECGAPLAEKCFARNGLLFCKEDF 124 (306)
Q Consensus 99 ~C~~C~~~l~~~~f~~~g~~yC~~cy 124 (306)
.|..|+.|| |.++|.+||..|-
T Consensus 30 hCp~Cg~PL----F~KdG~v~CPvC~ 51 (131)
T COG1645 30 HCPKCGTPL----FRKDGEVFCPVCG 51 (131)
T ss_pred hCcccCCcc----eeeCCeEECCCCC
Confidence 478888888 6688999987775
No 70
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=71.09 E-value=3 Score=26.90 Aligned_cols=42 Identities=26% Similarity=0.419 Sum_probs=27.6
Q ss_pred ccCcCCCCCCCcceeeCCee-ccccccccc--cCcCCCCCCCCCC
Q psy4325 99 KCHECGAPLAEKCFARNGLL-FCKEDFFKR--FGTKCAGCEMGIP 140 (306)
Q Consensus 99 ~C~~C~~~l~~~~f~~~g~~-yC~~cy~~~--~~~~C~~C~~~I~ 140 (306)
.|..|........+..=|.. +|..|..+. ...+|..|..+|.
T Consensus 4 ~C~iC~~~~~~~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 4 ECPICFENPRDVVLLPCGHLCFCEECAERLLKRKKKCPICRQPIE 48 (50)
T ss_dssp B-TTTSSSBSSEEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred CCccCCccCCceEEeCCCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence 46666666544444444676 999998776 3578999998884
No 71
>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=68.99 E-value=2.5 Score=26.73 Aligned_cols=44 Identities=11% Similarity=0.243 Sum_probs=30.9
Q ss_pred ccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhH
Q psy4325 210 TITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAK 258 (306)
Q Consensus 210 ~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k 258 (306)
.++..+...+...+... .....+|..+|++..+|..|....+.+
T Consensus 10 ~l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 10 KLPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALKK 53 (55)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 35666777776665322 246678999999999999988665543
No 72
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=68.86 E-value=2.4 Score=28.88 Aligned_cols=19 Identities=11% Similarity=0.443 Sum_probs=16.6
Q ss_pred HHHHHHhhCCCccchhccc
Q psy4325 234 REQLSQDTGLDMRVVQVWF 252 (306)
Q Consensus 234 r~~La~~~~l~~~~V~~WF 252 (306)
-..||.+||+++.+|+.|=
T Consensus 25 lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 25 LKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred HHHHHHHHCCCHHHHHHHh
Confidence 4578999999999999883
No 73
>PF12773 DZR: Double zinc ribbon
Probab=67.08 E-value=5.4 Score=25.65 Aligned_cols=9 Identities=22% Similarity=0.612 Sum_probs=4.0
Q ss_pred CCCCCCCCC
Q psy4325 131 KCAGCEMGI 139 (306)
Q Consensus 131 ~C~~C~~~I 139 (306)
.|..|+..+
T Consensus 31 ~C~~Cg~~~ 39 (50)
T PF12773_consen 31 ICPNCGAEN 39 (50)
T ss_pred CCcCCcCCC
Confidence 344444443
No 74
>KOG1813|consensus
Probab=66.67 E-value=3.4 Score=37.20 Aligned_cols=45 Identities=22% Similarity=0.479 Sum_probs=33.1
Q ss_pred cccCcCCCCCCCcceeeCCeeccccccccccC--cCCCCCCCCCCCC
Q psy4325 98 LKCHECGAPLAEKCFARNGLLFCKEDFFKRFG--TKCAGCEMGIPPT 142 (306)
Q Consensus 98 f~C~~C~~~l~~~~f~~~g~~yC~~cy~~~~~--~~C~~C~~~I~~~ 142 (306)
|.|..|.+.+.......-+..+|+.|..+.+- ++|..|++.+.+.
T Consensus 242 f~c~icr~~f~~pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g~ 288 (313)
T KOG1813|consen 242 FKCFICRKYFYRPVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHGS 288 (313)
T ss_pred ccccccccccccchhhcCCceeehhhhccccccCCcceecccccccc
Confidence 77888887765544455578889999877663 6899998888664
No 75
>PRK04217 hypothetical protein; Provisional
Probab=65.48 E-value=9.5 Score=29.38 Aligned_cols=53 Identities=17% Similarity=0.223 Sum_probs=39.5
Q ss_pred CCcccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHhhh
Q psy4325 207 PRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKK 264 (306)
Q Consensus 207 ~rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~ 264 (306)
+-..++..+++++...+...- ..++||+.+|++...|...+...+.+.|..-.
T Consensus 39 p~~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~RArkkLre~L~ 91 (110)
T PRK04217 39 PPIFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTSARKKVAQMLV 91 (110)
T ss_pred CcccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 355677778777776653222 57789999999999999998888887776543
No 76
>PF10235 Cript: Microtubule-associated protein CRIPT; InterPro: IPR019367 The CRIPT protein is a cytoskeletal protein involved in microtubule production. This C-terminal domain is essential for binding to the PDZ3 domain of the SAP90 protein, one of a super-family of PDZ-containing proteins that play an important role in coupling the membrane ion channels with their signalling partners [].
Probab=64.39 E-value=4.3 Score=30.01 Aligned_cols=36 Identities=28% Similarity=0.628 Sum_probs=24.9
Q ss_pred ccCcCCCCCCCcceeeCCeeccccccccccCcCCCCCCCCCCC
Q psy4325 99 KCHECGAPLAEKCFARNGLLFCKEDFFKRFGTKCAGCEMGIPP 141 (306)
Q Consensus 99 ~C~~C~~~l~~~~f~~~g~~yC~~cy~~~~~~~C~~C~~~I~~ 141 (306)
.|..|+..+ +..|.-||..|.++. -+|+-|++.|.+
T Consensus 46 ~C~~CK~~v-----~q~g~~YCq~CAYkk--GiCamCGKki~d 81 (90)
T PF10235_consen 46 KCKICKTKV-----HQPGAKYCQTCAYKK--GICAMCGKKILD 81 (90)
T ss_pred ccccccccc-----ccCCCccChhhhccc--CcccccCCeecc
Confidence 677777655 223667899887654 378889888844
No 77
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=62.64 E-value=1.5 Score=37.02 Aligned_cols=49 Identities=18% Similarity=0.381 Sum_probs=34.2
Q ss_pred CcccCcCCCCCCCcceeeCCeecccccccccc--CcCCCCCCCCCCCCCce
Q psy4325 97 CLKCHECGAPLAEKCFARNGLLFCKEDFFKRF--GTKCAGCEMGIPPTQVV 145 (306)
Q Consensus 97 Cf~C~~C~~~l~~~~f~~~g~~yC~~cy~~~~--~~~C~~C~~~I~~~~~~ 145 (306)
=|.|..|++-........=|..||..|+.+.+ ++.|..|++.-.+..+|
T Consensus 196 PF~C~iCKkdy~spvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~G~f~V 246 (259)
T COG5152 196 PFLCGICKKDYESPVVTECGHSFCSLCAIRKYQKGDECGVCGKATYGRFWV 246 (259)
T ss_pred ceeehhchhhccchhhhhcchhHHHHHHHHHhccCCcceecchhhccceeH
Confidence 47888888766544434457888999987655 47888888877665443
No 78
>KOG0978|consensus
Probab=60.12 E-value=2.2 Score=43.15 Aligned_cols=46 Identities=26% Similarity=0.663 Sum_probs=27.5
Q ss_pred ccCcCCCCCCCcceeeCCeeccccccccccC---cCCCCCCCCCCCCCc
Q psy4325 99 KCHECGAPLAEKCFARNGLLFCKEDFFKRFG---TKCAGCEMGIPPTQV 144 (306)
Q Consensus 99 ~C~~C~~~l~~~~f~~~g~~yC~~cy~~~~~---~~C~~C~~~I~~~~~ 144 (306)
+|..|+...-+.....=+..||..|...++. -+|+.|+..+...|+
T Consensus 645 kCs~Cn~R~Kd~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganDv 693 (698)
T KOG0978|consen 645 KCSVCNTRWKDAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGANDV 693 (698)
T ss_pred eCCCccCchhhHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCcccc
Confidence 5555554333322233355677777766554 479999888866654
No 79
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=60.05 E-value=8.8 Score=23.84 Aligned_cols=33 Identities=18% Similarity=0.337 Sum_probs=20.0
Q ss_pred ccccCCCCCCCCCceeeccCCcccccchhHHHh
Q psy4325 159 ACVMCARQLNTGDEFYLMEDRKLVCKPDYEAAK 191 (306)
Q Consensus 159 ~C~~C~~~l~~g~~~~~~~~~~~~C~~c~~~~~ 191 (306)
.|+.|++............++...|..|.....
T Consensus 3 ~CSFCgr~~~~v~~li~g~~~~~IC~~Cv~~~~ 35 (41)
T PF06689_consen 3 RCSFCGRPESEVGRLISGPNGAYICDECVEQAY 35 (41)
T ss_dssp B-TTT--BTTTSSSEEEES-SEEEEHHHHHHHH
T ss_pred CccCCCCCHHHHhceecCCCCcEECHHHHHHHH
Confidence 588888888655555444447789999976554
No 80
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=59.90 E-value=4.2 Score=32.64 Aligned_cols=67 Identities=16% Similarity=0.394 Sum_probs=39.0
Q ss_pred ccccCCCCCCCCCceeeccCCcccccchhHHHhhccCCCCCCCCCCCCCCcccchHhHHHHHhccccCCCCCHHHHHHHH
Q psy4325 159 ACVMCARQLNTGDEFYLMEDRKLVCKPDYEAAKAKDGNCLDGDQPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLS 238 (306)
Q Consensus 159 ~C~~C~~~l~~g~~~~~~~~~~~~C~~c~~~~~~~~~~~~~~~~~~kr~rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La 238 (306)
.|..|++.+. ..+..+|..|+.+.... ......+...++.+ .....+++
T Consensus 5 nC~~CgklF~--------~~~~~iCp~C~~~~e~~----------------------f~kV~~yLr~~p~~-~ati~eV~ 53 (137)
T TIGR03826 5 NCPKCGRLFV--------KTGRDVCPSCYEEEERE----------------------FEKVYKFLRKHENR-QATVSEIV 53 (137)
T ss_pred cccccchhhh--------hcCCccCHHHhHHHHHH----------------------HHHHHHHHHHCCCC-CCCHHHHH
Confidence 4788888773 13567899998443221 01111111223321 13466788
Q ss_pred HhhCCCccchhcccccch
Q psy4325 239 QDTGLDMRVVQVWFQNRR 256 (306)
Q Consensus 239 ~~~~l~~~~V~~WFqNrR 256 (306)
..+|++..+|..|..--|
T Consensus 54 e~tgVs~~~I~~~IreGR 71 (137)
T TIGR03826 54 EETGVSEKLILKFIREGR 71 (137)
T ss_pred HHHCcCHHHHHHHHHcCC
Confidence 889999999988865443
No 81
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=58.55 E-value=6.5 Score=24.59 Aligned_cols=38 Identities=26% Similarity=0.523 Sum_probs=23.1
Q ss_pred cCcCCCCCC-Ccce-eeC-Ceecccccccccc--CcCCCCCCC
Q psy4325 100 CHECGAPLA-EKCF-ARN-GLLFCKEDFFKRF--GTKCAGCEM 137 (306)
Q Consensus 100 C~~C~~~l~-~~~f-~~~-g~~yC~~cy~~~~--~~~C~~C~~ 137 (306)
|..|...+. ...+ ... |.++|..|..+.. ...|..|++
T Consensus 2 C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~~~~~~CP~C~k 44 (44)
T PF14634_consen 2 CNICFEKYSEERRPRLTSCGHIFCEKCLKKLKGKSVKCPICRK 44 (44)
T ss_pred CcCcCccccCCCCeEEcccCCHHHHHHHHhhcCCCCCCcCCCC
Confidence 556666662 2222 333 7888888887766 456777753
No 82
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=58.49 E-value=7.8 Score=33.03 Aligned_cols=32 Identities=25% Similarity=0.183 Sum_probs=26.5
Q ss_pred HHHHHHHhhCCCccchhcccccchhHHHHhhh
Q psy4325 233 VREQLSQDTGLDMRVVQVWFQNRRAKEKRLKK 264 (306)
Q Consensus 233 ~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~ 264 (306)
..+++|..+|++...|+++....|.+.|+.-.
T Consensus 171 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 202 (206)
T PRK12526 171 SQEQLAQQLNVPLGTVKSRLRLALAKLKVQMG 202 (206)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 46789999999999999999888877776543
No 83
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=57.75 E-value=8.5 Score=20.72 Aligned_cols=8 Identities=38% Similarity=1.057 Sum_probs=3.7
Q ss_pred CCCCCCCC
Q psy4325 132 CAGCEMGI 139 (306)
Q Consensus 132 C~~C~~~I 139 (306)
|..|+..|
T Consensus 2 Cp~CG~~~ 9 (23)
T PF13240_consen 2 CPNCGAEI 9 (23)
T ss_pred CcccCCCC
Confidence 44444444
No 84
>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=57.66 E-value=3.5 Score=28.86 Aligned_cols=44 Identities=9% Similarity=0.163 Sum_probs=27.0
Q ss_pred CCcccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhccccc
Q psy4325 207 PRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQN 254 (306)
Q Consensus 207 ~rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqN 254 (306)
.+..|+.++...+-.... ........+|.++|+++.++..|-.-
T Consensus 3 ~r~~ys~e~K~~~v~~~~----~~g~sv~~va~~~gi~~~~l~~W~~~ 46 (76)
T PF01527_consen 3 KRRRYSPEFKLQAVREYL----ESGESVSEVAREYGISPSTLYNWRKQ 46 (76)
T ss_dssp SS----HHHHHHHHHHHH----HHHCHHHHHHHHHTS-HHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHHH----HCCCceEeeecccccccccccHHHHH
Confidence 467788877665554431 12246788999999999999988543
No 85
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=57.06 E-value=4.2 Score=26.67 Aligned_cols=28 Identities=36% Similarity=0.743 Sum_probs=19.9
Q ss_pred ccCcCCCCCCC-cce-eeCCeeccccccccc
Q psy4325 99 KCHECGAPLAE-KCF-ARNGLLFCKEDFFKR 127 (306)
Q Consensus 99 ~C~~C~~~l~~-~~f-~~~g~~yC~~cy~~~ 127 (306)
.|..|+..++- ..| ..|| ..|.+|+.+.
T Consensus 1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDG-YICKDCLKKL 30 (51)
T ss_pred CCCccccccccccceeccCc-cchHHHHHHh
Confidence 47888888765 336 5566 6899998664
No 86
>PRK00118 putative DNA-binding protein; Validated
Probab=56.16 E-value=8.4 Score=29.35 Aligned_cols=49 Identities=10% Similarity=0.104 Sum_probs=35.5
Q ss_pred ccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHhh
Q psy4325 210 TITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLK 263 (306)
Q Consensus 210 ~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~ 263 (306)
.+++.|..++...|.... ...+||+.+|+++..|..|....|.+.|+..
T Consensus 17 ~L~ekqRevl~L~y~eg~-----S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~ 65 (104)
T PRK00118 17 LLTEKQRNYMELYYLDDY-----SLGEIAEEFNVSRQAVYDNIKRTEKLLEDYE 65 (104)
T ss_pred cCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 345666666665544322 4677999999999999999988777776543
No 87
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=55.08 E-value=7.5 Score=31.06 Aligned_cols=47 Identities=9% Similarity=0.120 Sum_probs=32.4
Q ss_pred ccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHH
Q psy4325 210 TITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261 (306)
Q Consensus 210 ~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~ 261 (306)
.+++.++.++...|-.. ...+++|..+|++...|+.|...-|.+-|+
T Consensus 106 ~L~~~~r~ii~l~~~~~-----~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 106 VLDEKEKYIIFERFFVG-----KTMGEIALETEMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 34555555554433222 246789999999999999998877777665
No 88
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=54.85 E-value=9.3 Score=21.10 Aligned_cols=9 Identities=33% Similarity=0.818 Sum_probs=4.4
Q ss_pred CCCCCCCCC
Q psy4325 131 KCAGCEMGI 139 (306)
Q Consensus 131 ~C~~C~~~I 139 (306)
.|..|+..|
T Consensus 4 ~Cp~Cg~~~ 12 (26)
T PF13248_consen 4 FCPNCGAEI 12 (26)
T ss_pred CCcccCCcC
Confidence 355555544
No 89
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=54.78 E-value=14 Score=37.51 Aligned_cols=11 Identities=18% Similarity=0.217 Sum_probs=7.0
Q ss_pred CCccCCCeecc
Q psy4325 72 KCGGCGDLILD 82 (306)
Q Consensus 72 ~C~~C~~~I~~ 82 (306)
+|..|+..+.+
T Consensus 3 ~Cp~Cg~~n~~ 13 (645)
T PRK14559 3 ICPQCQFENPN 13 (645)
T ss_pred cCCCCCCcCCC
Confidence 57777766544
No 90
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=54.63 E-value=7.7 Score=33.44 Aligned_cols=42 Identities=26% Similarity=0.521 Sum_probs=34.8
Q ss_pred CcccchHhHHHHHhccccC--CCCCHHHHHHHHHhhCCCccchh
Q psy4325 208 RTTITAKQLETLKMAYNTS--PKPARHVREQLSQDTGLDMRVVQ 249 (306)
Q Consensus 208 rt~~s~~q~~~Le~~F~~~--~~p~~~~r~~La~~~~l~~~~V~ 249 (306)
...+|+.|+++|...|..- -||-......||+++|+++..+.
T Consensus 153 ~~~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ 196 (215)
T COG3413 153 KNDLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLS 196 (215)
T ss_pred cccCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHH
Confidence 3379999999999998765 35777888899999999986654
No 91
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=54.60 E-value=9.9 Score=28.44 Aligned_cols=29 Identities=21% Similarity=0.480 Sum_probs=18.0
Q ss_pred CCCCccCCCeeccceeeee-cCccccccCc
Q psy4325 70 IPKCGGCGDLILDRFILKV-LERTWHARCL 98 (306)
Q Consensus 70 ~~~C~~C~~~I~~~~~~~~-~~~~~H~~Cf 98 (306)
...|..|+++|.....+.. .|..+|..|+
T Consensus 78 ~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~ 107 (109)
T PF10367_consen 78 STKCSVCGKPLGNSVFVVFPCGHVVHYSCI 107 (109)
T ss_pred CCCccCcCCcCCCceEEEeCCCeEEecccc
Confidence 4578888888876544323 3455666654
No 92
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=53.89 E-value=9.4 Score=32.07 Aligned_cols=49 Identities=12% Similarity=0.221 Sum_probs=34.3
Q ss_pred ccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHhh
Q psy4325 210 TITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLK 263 (306)
Q Consensus 210 ~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~ 263 (306)
.++..++.+|...|-.. ...+++|+.+|++...|+++...-|.+-|+.-
T Consensus 142 ~L~~~~r~vl~l~~~~~-----~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l 190 (194)
T PRK09646 142 ALTDTQRESVTLAYYGG-----LTYREVAERLAVPLGTVKTRMRDGLIRLRDCL 190 (194)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHhCCChHhHHHHHHHHHHHHHHHh
Confidence 35556666665433222 24678999999999999999988777777643
No 93
>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=53.82 E-value=7.8 Score=25.71 Aligned_cols=45 Identities=16% Similarity=0.293 Sum_probs=33.1
Q ss_pred ccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHH
Q psy4325 210 TITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEK 260 (306)
Q Consensus 210 ~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k 260 (306)
.+|+.+++.|.....-. ...++|..+++++..|..+..+-+.|..
T Consensus 3 ~LT~~E~~vl~~l~~G~------~~~eIA~~l~is~~tV~~~~~~i~~Kl~ 47 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM------SNKEIAEELGISEKTVKSHRRRIMKKLG 47 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-------HHHHHHHHTSHHHHHHHHHHHHHHHHT
T ss_pred ccCHHHHHHHHHHHhcC------CcchhHHhcCcchhhHHHHHHHHHHHhC
Confidence 56777777777654433 3678999999999999998877776644
No 94
>KOG2462|consensus
Probab=53.70 E-value=4.3 Score=36.23 Aligned_cols=11 Identities=27% Similarity=0.990 Sum_probs=7.5
Q ss_pred cccccCCCCCC
Q psy4325 158 FACVMCARQLN 168 (306)
Q Consensus 158 F~C~~C~~~l~ 168 (306)
|.|..|++.|.
T Consensus 216 F~C~hC~kAFA 226 (279)
T KOG2462|consen 216 FSCPHCGKAFA 226 (279)
T ss_pred ccCCcccchhc
Confidence 66777777764
No 95
>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=53.44 E-value=14 Score=20.64 Aligned_cols=37 Identities=11% Similarity=0.254 Sum_probs=23.9
Q ss_pred cchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhccc
Q psy4325 211 ITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWF 252 (306)
Q Consensus 211 ~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WF 252 (306)
++..+...+...+.. .+ ....+|..+|++...|..|.
T Consensus 6 ~~~~~~~~i~~~~~~-~~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 6 LTPEQIEEARRLLAA-GE----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CCHHHHHHHHHHHHc-CC----CHHHHHHHHCCCHHHHHHhC
Confidence 445555555444432 22 46678899999998888874
No 96
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=53.20 E-value=6.7 Score=33.43 Aligned_cols=30 Identities=30% Similarity=0.526 Sum_probs=21.4
Q ss_pred cccCcCCCCCCCcce-eeCCeeccccccccc
Q psy4325 98 LKCHECGAPLAEKCF-ARNGLLFCKEDFFKR 127 (306)
Q Consensus 98 f~C~~C~~~l~~~~f-~~~g~~yC~~cy~~~ 127 (306)
-+|..|+..+....- ..+|++.|..||.+.
T Consensus 173 v~C~kCGE~~~e~~~~~~ng~~vC~~C~~~~ 203 (206)
T COG2191 173 VRCSKCGELFMEPRAVVLNGKPVCKPCAEKK 203 (206)
T ss_pred eeccccCcccccchhhhcCCceecccccccc
Confidence 367777776655433 778999999999753
No 97
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=53.08 E-value=3.2 Score=30.69 Aligned_cols=33 Identities=18% Similarity=0.410 Sum_probs=22.9
Q ss_pred cccccCCCCCCCCCceeeccCCcccccchhHHHh
Q psy4325 158 FACVMCARQLNTGDEFYLMEDRKLVCKPDYEAAK 191 (306)
Q Consensus 158 F~C~~C~~~l~~g~~~~~~~~~~~~C~~c~~~~~ 191 (306)
|+|.+|+..+..|..|++...| +.--+|+....
T Consensus 7 wkC~VCg~~iieGqkFTF~~kG-sVH~eCl~~s~ 39 (103)
T COG4847 7 WKCYVCGGTIIEGQKFTFTKKG-SVHYECLAESK 39 (103)
T ss_pred eeEeeeCCEeeeccEEEEeeCC-cchHHHHHHHH
Confidence 6788888888888888776544 45556764443
No 98
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=52.80 E-value=9.4 Score=23.04 Aligned_cols=24 Identities=21% Similarity=0.661 Sum_probs=14.5
Q ss_pred ccCcCCCCCCCcceeeCCeeccccccc
Q psy4325 99 KCHECGAPLAEKCFARNGLLFCKEDFF 125 (306)
Q Consensus 99 ~C~~C~~~l~~~~f~~~g~~yC~~cy~ 125 (306)
.|..|+.. .+...+|..||..|-.
T Consensus 10 ~C~~C~~~---~~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 10 PCPVCGSR---WFYSDDGFYYCDRCGH 33 (36)
T ss_pred cCCCCCCe---EeEccCCEEEhhhCce
Confidence 46666643 2226678888876643
No 99
>PRK08359 transcription factor; Validated
Probab=52.66 E-value=7 Score=32.75 Aligned_cols=24 Identities=21% Similarity=0.295 Sum_probs=20.4
Q ss_pred HHHHHHhhCCCccchhcccccchh
Q psy4325 234 REQLSQDTGLDMRVVQVWFQNRRA 257 (306)
Q Consensus 234 r~~La~~~~l~~~~V~~WFqNrR~ 257 (306)
.++||..+|++...|..|=.+++.
T Consensus 101 QeeLA~~lgvs~stI~~iE~G~~~ 124 (176)
T PRK08359 101 YEELSHEVGLSVNDLRRIAHGEYE 124 (176)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCcC
Confidence 568999999999999988877774
No 100
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=51.53 E-value=9.6 Score=25.75 Aligned_cols=26 Identities=27% Similarity=0.889 Sum_probs=20.9
Q ss_pred cccCCCCCCCCCceeeccCCcccccc
Q psy4325 160 CVMCARQLNTGDEFYLMEDRKLVCKP 185 (306)
Q Consensus 160 C~~C~~~l~~g~~~~~~~~~~~~C~~ 185 (306)
|..|++.|..+..+|...+.+.+|..
T Consensus 19 C~~C~k~L~~~~DiymYrGd~aFCS~ 44 (58)
T PF04570_consen 19 CYLCKKKLDPGKDIYMYRGDKAFCSE 44 (58)
T ss_pred HHccCCCCCCCCCeeeeccccccccH
Confidence 77889999877777777788889954
No 101
>KOG0320|consensus
Probab=50.53 E-value=5.1 Score=33.41 Aligned_cols=47 Identities=26% Similarity=0.546 Sum_probs=35.4
Q ss_pred cCcccCcCCCCCCCcc-e-eeCCeecccccccccc--CcCCCCCCCCCCCC
Q psy4325 96 RCLKCHECGAPLAEKC-F-ARNGLLFCKEDFFKRF--GTKCAGCEMGIPPT 142 (306)
Q Consensus 96 ~Cf~C~~C~~~l~~~~-f-~~~g~~yC~~cy~~~~--~~~C~~C~~~I~~~ 142 (306)
.++.|-.|-.....+. + ..=|.+||+.|..... +-+|..|++.|...
T Consensus 130 ~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~k 180 (187)
T KOG0320|consen 130 GTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITHK 180 (187)
T ss_pred cccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCcccccchh
Confidence 5688888887776654 5 4559999999986543 46899999988544
No 102
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=50.40 E-value=6.7 Score=28.43 Aligned_cols=27 Identities=26% Similarity=0.666 Sum_probs=19.2
Q ss_pred ccCcCCCCCCCcc-e--eeC---Ceeccccccc
Q psy4325 99 KCHECGAPLAEKC-F--ARN---GLLFCKEDFF 125 (306)
Q Consensus 99 ~C~~C~~~l~~~~-f--~~~---g~~yC~~cy~ 125 (306)
.|..|+.||.... + ..| +.-||..||.
T Consensus 2 ~CQSCGMPl~~~~~~Gte~dGs~s~~YC~yCy~ 34 (81)
T PF12674_consen 2 FCQSCGMPLSKDEDFGTEADGSKSEDYCSYCYQ 34 (81)
T ss_pred cCCcCcCccCCccccccccCCCCchhHHHHHhc
Confidence 4889999997644 4 333 4579999985
No 103
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=50.36 E-value=2 Score=31.85 Aligned_cols=39 Identities=18% Similarity=0.326 Sum_probs=26.9
Q ss_pred CCccCCCeeccceeeeecCccccccCcccCcCCCCCCCc
Q psy4325 72 KCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEK 110 (306)
Q Consensus 72 ~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~ 110 (306)
.|..|+..+.+.....+.-..+++.+..|.+|.+.|+-.
T Consensus 37 aCy~CHdel~~Hpf~p~~~~~~~~~~iiCGvC~~~LT~~ 75 (105)
T COG4357 37 ACYHCHDELEDHPFEPWGLQEFNPKAIICGVCRKLLTRA 75 (105)
T ss_pred hHHHHHhHHhcCCCccCChhhcCCccEEhhhhhhhhhHH
Confidence 467777777665555555577777788888888777543
No 104
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=50.17 E-value=7 Score=24.56 Aligned_cols=40 Identities=8% Similarity=0.130 Sum_probs=19.9
Q ss_pred cccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccc
Q psy4325 209 TTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQ 253 (306)
Q Consensus 209 t~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFq 253 (306)
..+|..++..++..++.. ....+||+.+|.++..|..|.+
T Consensus 3 ~~Lt~~eR~~I~~l~~~G-----~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQG-----MSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp ---------HHHHHHCS--------HHHHHHHTT--HHHHHHHHH
T ss_pred cchhhhHHHHHHHHHHcC-----CCHHHHHHHHCcCcHHHHHHHh
Confidence 456777777777765533 3567799999999999877643
No 105
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=49.89 E-value=13 Score=31.68 Aligned_cols=28 Identities=21% Similarity=0.477 Sum_probs=14.1
Q ss_pred cccCcCCCCCCCcceeeCCeeccccccc
Q psy4325 98 LKCHECGAPLAEKCFARNGLLFCKEDFF 125 (306)
Q Consensus 98 f~C~~C~~~l~~~~f~~~g~~yC~~cy~ 125 (306)
|.|..|...+.......=|..||..|..
T Consensus 19 ~~CpICld~~~dPVvT~CGH~FC~~CI~ 46 (193)
T PLN03208 19 FDCNICLDQVRDPVVTLCGHLFCWPCIH 46 (193)
T ss_pred cCCccCCCcCCCcEEcCCCchhHHHHHH
Confidence 4555555544332223335666666653
No 106
>PRK10072 putative transcriptional regulator; Provisional
Probab=49.78 E-value=8 Score=29.00 Aligned_cols=41 Identities=17% Similarity=0.319 Sum_probs=30.1
Q ss_pred ccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchh
Q psy4325 210 TITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRA 257 (306)
Q Consensus 210 ~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~ 257 (306)
..+...+..|...... ...+||+.+|++...|..|.+.+|.
T Consensus 32 ~~~~~eik~LR~~~gl-------TQ~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 32 TTSFTEFEQLRKGTGL-------KIDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred cCChHHHHHHHHHcCC-------CHHHHHHHhCCCHHHHHHHHcCCCC
Confidence 3355556666543322 3678999999999999999998875
No 107
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=49.74 E-value=9 Score=30.38 Aligned_cols=21 Identities=24% Similarity=0.583 Sum_probs=17.6
Q ss_pred cccCCCCCCCCCceeeccCCcccccchh
Q psy4325 160 CVMCARQLNTGDEFYLMEDRKLVCKPDY 187 (306)
Q Consensus 160 C~~C~~~l~~g~~~~~~~~~~~~C~~c~ 187 (306)
|..|+.+| |- ++|.+||..|-
T Consensus 31 Cp~Cg~PL------F~-KdG~v~CPvC~ 51 (131)
T COG1645 31 CPKCGTPL------FR-KDGEVFCPVCG 51 (131)
T ss_pred CcccCCcc------ee-eCCeEECCCCC
Confidence 88888888 44 79999999995
No 108
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=49.45 E-value=13 Score=30.02 Aligned_cols=30 Identities=10% Similarity=0.171 Sum_probs=25.3
Q ss_pred HHHHHHhhCCCccchhcccccchhHHHHhh
Q psy4325 234 REQLSQDTGLDMRVVQVWFQNRRAKEKRLK 263 (306)
Q Consensus 234 r~~La~~~~l~~~~V~~WFqNrR~k~k~~~ 263 (306)
.+++|..+|+++..|+++....|.+-|+.-
T Consensus 125 ~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (160)
T PRK09642 125 YQEIALQEKIEVKTVEMKLYRARKWIKKHW 154 (160)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 458999999999999999988887777643
No 109
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=49.35 E-value=11 Score=23.58 Aligned_cols=10 Identities=30% Similarity=0.561 Sum_probs=5.7
Q ss_pred cCCcccccch
Q psy4325 177 EDRKLVCKPD 186 (306)
Q Consensus 177 ~~~~~~C~~c 186 (306)
++|+.||..|
T Consensus 31 k~g~~~Cv~C 40 (41)
T PF06677_consen 31 KDGKIYCVSC 40 (41)
T ss_pred cCCCEECCCC
Confidence 4556666554
No 110
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=48.83 E-value=9.3 Score=25.74 Aligned_cols=21 Identities=14% Similarity=0.395 Sum_probs=17.8
Q ss_pred HHHHHHHhhCCCccchhcccc
Q psy4325 233 VREQLSQDTGLDMRVVQVWFQ 253 (306)
Q Consensus 233 ~r~~La~~~~l~~~~V~~WFq 253 (306)
...+||..||++.++|..|-+
T Consensus 15 ~~~eIA~~Lg~~~~TV~~W~~ 35 (58)
T PF06056_consen 15 SIKEIAEELGVPRSTVYSWKD 35 (58)
T ss_pred CHHHHHHHHCCChHHHHHHHH
Confidence 356899999999999999954
No 111
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=48.28 E-value=11 Score=23.92 Aligned_cols=9 Identities=11% Similarity=0.423 Sum_probs=5.3
Q ss_pred eeccccccc
Q psy4325 117 LLFCKEDFF 125 (306)
Q Consensus 117 ~~yC~~cy~ 125 (306)
--+|..||.
T Consensus 23 ~dLC~~Cf~ 31 (46)
T cd02249 23 FDLCSSCYA 31 (46)
T ss_pred CcCHHHHHC
Confidence 446666664
No 112
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=48.22 E-value=7.9 Score=25.94 Aligned_cols=27 Identities=11% Similarity=0.319 Sum_probs=18.6
Q ss_pred HHHHHHHhhCCCccchhcccccchhHH
Q psy4325 233 VREQLSQDTGLDMRVVQVWFQNRRAKE 259 (306)
Q Consensus 233 ~r~~La~~~~l~~~~V~~WFqNrR~k~ 259 (306)
....||+.+|++..+|..|+.++....
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~~~ 38 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPSNP 38 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT----
T ss_pred CHHHHHHHHCcCHHHHHHHHhcccccc
Confidence 467899999999999999999885443
No 113
>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
Probab=47.94 E-value=11 Score=23.64 Aligned_cols=10 Identities=30% Similarity=0.530 Sum_probs=6.1
Q ss_pred eecccccccc
Q psy4325 117 LLFCKEDFFK 126 (306)
Q Consensus 117 ~~yC~~cy~~ 126 (306)
.-+|..||.+
T Consensus 27 ~dlC~~Cf~~ 36 (44)
T smart00291 27 YDLCQSCFAK 36 (44)
T ss_pred ccchHHHHhC
Confidence 4467777754
No 114
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=47.88 E-value=15 Score=28.43 Aligned_cols=11 Identities=18% Similarity=0.821 Sum_probs=8.4
Q ss_pred cccccCCCCCC
Q psy4325 158 FACVMCARQLN 168 (306)
Q Consensus 158 F~C~~C~~~l~ 168 (306)
..|..|++.+.
T Consensus 13 l~C~~C~t~i~ 23 (113)
T PF09862_consen 13 LKCPSCGTEIE 23 (113)
T ss_pred EEcCCCCCEEE
Confidence 56888888883
No 115
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=47.83 E-value=13 Score=30.38 Aligned_cols=48 Identities=8% Similarity=0.075 Sum_probs=33.2
Q ss_pred ccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHh
Q psy4325 210 TITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRL 262 (306)
Q Consensus 210 ~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~ 262 (306)
.+++.++.++...|-. .....++|..+|++...|+.|...-+.+-|+.
T Consensus 128 ~L~~~~r~vl~l~~~~-----~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 175 (182)
T PRK09652 128 SLPEELRTAITLREIE-----GLSYEEIAEIMGCPIGTVRSRIFRAREALRAK 175 (182)
T ss_pred hCCHHHHHHHHHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3555666666554321 12356889999999999999998777766653
No 116
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=46.97 E-value=15 Score=30.64 Aligned_cols=51 Identities=18% Similarity=0.252 Sum_probs=35.1
Q ss_pred ccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHhhhh
Q psy4325 210 TITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKKD 265 (306)
Q Consensus 210 ~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~~ 265 (306)
.++..++.+|+..+-. ....+++|..+|+++..|++....-|.+.|+.-..
T Consensus 131 ~L~~~~r~vl~l~~~~-----~~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 181 (189)
T PRK12515 131 KLSPAHREIIDLVYYH-----EKSVEEVGEIVGIPESTVKTRMFYARKKLAELLKA 181 (189)
T ss_pred hCCHHHHHHHHHHHHc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 3455555555443221 12466899999999999999998888888876443
No 117
>PF00645 zf-PARP: Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region; InterPro: IPR001510 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents PARP (Poly(ADP) polymerase) type zinc finger domains. NAD(+) ADP-ribosyltransferase(2.4.2.30 from EC) [, ] is a eukaryotic enzyme that catalyses the covalent attachment of ADP-ribose units from NAD(+) to various nuclear acceptor proteins. This post-translational modification of nuclear proteins is dependent on DNA. It appears to be involved in the regulation of various important cellular processes such as differentiation, proliferation and tumour transformation as well as in the regulation of the molecular events involved in the recovery of the cell from DNA damage. Structurally, NAD(+) ADP-ribosyltransferase consists of three distinct domains: an N-terminal zinc-dependent DNA-binding domain, a central automodification domain and a C-terminal NAD-binding domain. The DNA-binding region contains a pair of PARP-type zinc finger domains which have been shown to bind DNA in a zinc-dependent manner. The PARP-type zinc finger domains seem to bind specifically to single-stranded DNA and to act as a DNA nick sensor. DNA ligase III [] contains, in its N-terminal section, a single copy of a zinc finger highly similar to those of PARP. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding; PDB: 1UW0_A 3OD8_D 3ODA_A 4AV1_A 2DMJ_A 4DQY_D 2L30_A 2CS2_A 2L31_A 3ODE_B ....
Probab=46.66 E-value=5.4 Score=28.66 Aligned_cols=14 Identities=36% Similarity=0.729 Sum_probs=10.3
Q ss_pred CCCCCccCCCeecc
Q psy4325 69 SIPKCGGCGDLILD 82 (306)
Q Consensus 69 ~~~~C~~C~~~I~~ 82 (306)
+-..|.+|++.|..
T Consensus 6 ~Ra~Ck~C~~~I~k 19 (82)
T PF00645_consen 6 GRAKCKGCKKKIAK 19 (82)
T ss_dssp STEBETTTSCBE-T
T ss_pred CCccCcccCCcCCC
Confidence 34589999999964
No 118
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=46.19 E-value=19 Score=24.35 Aligned_cols=29 Identities=34% Similarity=0.610 Sum_probs=17.6
Q ss_pred CCCCCccCCCeeccceeeeecCccccccCcccCcCCCC
Q psy4325 69 SIPKCGGCGDLILDRFILKVLERTWHARCLKCHECGAP 106 (306)
Q Consensus 69 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~ 106 (306)
..+.|..|+..|.+.... --|.|-.|+..
T Consensus 6 ~~~~CtSCg~~i~~~~~~---------~~F~CPnCG~~ 34 (59)
T PRK14890 6 EPPKCTSCGIEIAPREKA---------VKFLCPNCGEV 34 (59)
T ss_pred cCccccCCCCcccCCCcc---------CEeeCCCCCCe
Confidence 345788888887643311 12677777765
No 119
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=45.51 E-value=19 Score=30.18 Aligned_cols=33 Identities=9% Similarity=0.139 Sum_probs=27.1
Q ss_pred HHHHHHHhhCCCccchhcccccchhHHHHhhhh
Q psy4325 233 VREQLSQDTGLDMRVVQVWFQNRRAKEKRLKKD 265 (306)
Q Consensus 233 ~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~~ 265 (306)
.-+++|..+|+++..|+++...-|.+.|+.-..
T Consensus 134 s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~~ 166 (187)
T PRK12516 134 AYEEAAEICGCAVGTIKSRVNRARQRLQEILQI 166 (187)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 356889999999999999998888887775443
No 120
>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=45.36 E-value=15 Score=30.23 Aligned_cols=29 Identities=21% Similarity=0.211 Sum_probs=24.4
Q ss_pred HHHHHHHhhCCCccchhcccccchhHHHH
Q psy4325 233 VREQLSQDTGLDMRVVQVWFQNRRAKEKR 261 (306)
Q Consensus 233 ~r~~La~~~~l~~~~V~~WFqNrR~k~k~ 261 (306)
..+++|..+|+++..|++....-|.+-|+
T Consensus 152 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 180 (183)
T TIGR02999 152 TVEEIAELLGVSVRTVERDWRFARAWLAD 180 (183)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 35688999999999999998887777665
No 121
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=44.78 E-value=20 Score=22.75 Aligned_cols=42 Identities=14% Similarity=0.320 Sum_probs=28.7
Q ss_pred ccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchh
Q psy4325 210 TITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRA 257 (306)
Q Consensus 210 ~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~ 257 (306)
.++..+...+...+.. ....++|+.+|++...|..|.+.-+.
T Consensus 3 ~l~~~e~~i~~~~~~g------~s~~eia~~l~is~~tv~~~~~~~~~ 44 (58)
T smart00421 3 SLTPREREVLRLLAEG------LTNKEIAERLGISEKTVKTHLSNIMR 44 (58)
T ss_pred CCCHHHHHHHHHHHcC------CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3566676666554322 24578899999999999988774433
No 122
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=44.33 E-value=10 Score=26.60 Aligned_cols=31 Identities=23% Similarity=0.472 Sum_probs=14.1
Q ss_pred cCCCCCCCCCCCCCceecccCccccCCCcccccCCCCCC
Q psy4325 130 TKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLN 168 (306)
Q Consensus 130 ~~C~~C~~~I~~~~~~~~~~~~~~H~~CF~C~~C~~~l~ 168 (306)
+.|..|++++ .++++-|-. =|.|..|+..++
T Consensus 31 a~CPdC~~~L----e~LkACGAv----dYFC~~c~gLiS 61 (70)
T PF07191_consen 31 AFCPDCGQPL----EVLKACGAV----DYFCNHCHGLIS 61 (70)
T ss_dssp EE-TTT-SB-----EEEEETTEE----EEE-TTTT-EE-
T ss_pred ccCCCcccHH----HHHHHhccc----ceeeccCCceee
Confidence 4577777776 244665532 134777777664
No 123
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=44.09 E-value=17 Score=29.91 Aligned_cols=30 Identities=10% Similarity=0.336 Sum_probs=25.2
Q ss_pred HHHHHHHhhCCCccchhcccccchhHHHHh
Q psy4325 233 VREQLSQDTGLDMRVVQVWFQNRRAKEKRL 262 (306)
Q Consensus 233 ~r~~La~~~~l~~~~V~~WFqNrR~k~k~~ 262 (306)
..+++|..+|+++..|+++...-|.+.|+.
T Consensus 147 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 147 SYKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred CHHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 467899999999999999988877777653
No 124
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=44.03 E-value=21 Score=27.65 Aligned_cols=41 Identities=5% Similarity=0.101 Sum_probs=28.3
Q ss_pred cccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccch
Q psy4325 209 TTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRR 256 (306)
Q Consensus 209 t~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR 256 (306)
..++..++..+...... ...+||..+|+++..|..|-..+.
T Consensus 63 ~~~~~~~i~~~r~~~gl-------tq~~lA~~lg~~~~tis~~e~g~~ 103 (127)
T TIGR03830 63 GLLTPPEIRRIRKKLGL-------SQREAAELLGGGVNAFSRYERGEV 103 (127)
T ss_pred CCcCHHHHHHHHHHcCC-------CHHHHHHHhCCCHHHHHHHHCCCC
Confidence 34555566666554322 345789999999999999987665
No 125
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=43.91 E-value=13 Score=28.04 Aligned_cols=35 Identities=23% Similarity=0.318 Sum_probs=25.9
Q ss_pred CCCCCCCCCCCCCceecccCccccCCCcccccCCC
Q psy4325 131 KCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCAR 165 (306)
Q Consensus 131 ~C~~C~~~I~~~~~~~~~~~~~~H~~CF~C~~C~~ 165 (306)
+|..|+++|..++.+.-..+..-|.+||+=..=.+
T Consensus 4 kC~iCg~~I~~gqlFTF~~kG~VH~~C~~~~~~~k 38 (101)
T PF09943_consen 4 KCYICGKPIYEGQLFTFTKKGPVHYECFREKASKK 38 (101)
T ss_pred EEEecCCeeeecceEEEecCCcEeHHHHHHHHhhh
Confidence 69999999988876644556678999987544333
No 126
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=43.82 E-value=15 Score=30.60 Aligned_cols=31 Identities=13% Similarity=0.230 Sum_probs=25.8
Q ss_pred HHHHHHHHhhCCCccchhcccccchhHHHHh
Q psy4325 232 HVREQLSQDTGLDMRVVQVWFQNRRAKEKRL 262 (306)
Q Consensus 232 ~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~ 262 (306)
....++|..+|++...|+.|+...|.+-|+.
T Consensus 158 ~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 188 (194)
T PRK12519 158 LSQSEIAKRLGIPLGTVKARARQGLLKLREL 188 (194)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 3467899999999999999998777776653
No 127
>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=43.75 E-value=17 Score=29.86 Aligned_cols=50 Identities=16% Similarity=0.250 Sum_probs=34.1
Q ss_pred ccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHhhh
Q psy4325 210 TITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKK 264 (306)
Q Consensus 210 ~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~ 264 (306)
.+++.++.++...|-.. ...+++|..+|+++..|+++.+.-|.+.|+.-.
T Consensus 100 ~L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 149 (170)
T TIGR02959 100 ELPDEYREAIRLTELEG-----LSQQEIAEKLGLSLSGAKSRVQRGRKKLKELLE 149 (170)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 34445555555433221 246689999999999999999888877776544
No 128
>PRK06424 transcription factor; Provisional
Probab=43.53 E-value=11 Score=30.43 Aligned_cols=24 Identities=8% Similarity=-0.058 Sum_probs=21.2
Q ss_pred HHHHHHhhCCCccchhcccccchh
Q psy4325 234 REQLSQDTGLDMRVVQVWFQNRRA 257 (306)
Q Consensus 234 r~~La~~~~l~~~~V~~WFqNrR~ 257 (306)
.++||+.+|++...|..|..+++.
T Consensus 100 Q~eLA~~iGvs~stIskiE~G~~~ 123 (144)
T PRK06424 100 QADLAAKIFERKNVIASIERGDLL 123 (144)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCCC
Confidence 568999999999999999998875
No 129
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=42.88 E-value=17 Score=30.26 Aligned_cols=47 Identities=21% Similarity=0.153 Sum_probs=31.7
Q ss_pred ccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHH
Q psy4325 210 TITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261 (306)
Q Consensus 210 ~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~ 261 (306)
.++..++.++...|-. ....+++|..+|++...|+.+...-|.+-|+
T Consensus 139 ~L~~~~r~i~~l~~~~-----g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 185 (189)
T PRK09648 139 TLPEKQREILILRVVV-----GLSAEETAEAVGSTPGAVRVAQHRALARLRA 185 (189)
T ss_pred hCCHHHHHHHHHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3445555555543222 2346789999999999999988766666655
No 130
>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]
Probab=42.85 E-value=32 Score=28.48 Aligned_cols=23 Identities=13% Similarity=0.149 Sum_probs=18.3
Q ss_pred HHHHHHhhCCCccchhcccccch
Q psy4325 234 REQLSQDTGLDMRVVQVWFQNRR 256 (306)
Q Consensus 234 r~~La~~~~l~~~~V~~WFqNrR 256 (306)
++.||++++.....|+.|=+.+-
T Consensus 95 qedLA~ki~ek~svI~~iE~g~~ 117 (165)
T COG1813 95 QEDLAAKLKEKVSVIRRIERGEA 117 (165)
T ss_pred HHHHHHHhcccHHHHHHHHhccc
Confidence 56899999999999988855443
No 131
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=42.85 E-value=15 Score=24.17 Aligned_cols=29 Identities=21% Similarity=0.429 Sum_probs=16.4
Q ss_pred CCccCCCeeccceeeeecCccccccCccc
Q psy4325 72 KCGGCGDLILDRFILKVLERTWHARCLKC 100 (306)
Q Consensus 72 ~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C 100 (306)
.|..||+.|.-..-.+..++.|-.+|-.|
T Consensus 2 ~CPyCge~~~~~iD~s~~~Q~yiEDC~vC 30 (52)
T PF14255_consen 2 QCPYCGEPIEILIDPSAGDQEYIEDCQVC 30 (52)
T ss_pred CCCCCCCeeEEEEecCCCCeeEEeehhhc
Confidence 47888887753222234456666665333
No 132
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=42.62 E-value=16 Score=30.64 Aligned_cols=30 Identities=17% Similarity=0.231 Sum_probs=25.3
Q ss_pred HHHHHHHhhCCCccchhcccccchhHHHHh
Q psy4325 233 VREQLSQDTGLDMRVVQVWFQNRRAKEKRL 262 (306)
Q Consensus 233 ~r~~La~~~~l~~~~V~~WFqNrR~k~k~~ 262 (306)
..+++|..+|+++..|+++....|.+-|+.
T Consensus 152 s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~ 181 (189)
T PRK12530 152 SSEQICQECDISTSNLHVLLYRARLQLQAC 181 (189)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 467899999999999999988777777654
No 133
>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=42.61 E-value=11 Score=23.66 Aligned_cols=21 Identities=14% Similarity=0.176 Sum_probs=17.6
Q ss_pred HHHHHHhhCCCccchhccccc
Q psy4325 234 REQLSQDTGLDMRVVQVWFQN 254 (306)
Q Consensus 234 r~~La~~~~l~~~~V~~WFqN 254 (306)
..++|+.+|++++.|+.|.+.
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~ 23 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERI 23 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 467899999999999999543
No 134
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=42.54 E-value=19 Score=29.03 Aligned_cols=47 Identities=11% Similarity=0.229 Sum_probs=33.8
Q ss_pred cchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHhh
Q psy4325 211 ITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLK 263 (306)
Q Consensus 211 ~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~ 263 (306)
++..+..+|...+ . . ...++||..+|++...|+.+...-|.+.|+.-
T Consensus 113 L~~~~r~il~l~~-~-g----~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l 159 (166)
T PRK09639 113 MTERDRTVLLLRF-S-G----YSYKEIAEALGIKESSVGTTLARAKKKFRKIY 159 (166)
T ss_pred CCHHHHHHHHHHH-c-C----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4555666666555 2 2 24678999999999999999987777777643
No 135
>KOG1146|consensus
Probab=42.41 E-value=31 Score=37.50 Aligned_cols=60 Identities=27% Similarity=0.352 Sum_probs=53.8
Q ss_pred CCCCCcccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHhh
Q psy4325 204 NKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLK 263 (306)
Q Consensus 204 ~kr~rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~ 263 (306)
.++.+...-..++..|-++|-.+..|+...+.-|....+.+.+++.+||+|-|.|.++..
T Consensus 705 ~~~~~~~~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 705 DKLLRLTILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred cccCcccccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc
Confidence 345666777789999999999999999999999999999999999999999999998866
No 136
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=42.30 E-value=11 Score=27.86 Aligned_cols=31 Identities=23% Similarity=0.331 Sum_probs=19.2
Q ss_pred CCCCCCCCCCCCCceecccCccccCCCcccccCC
Q psy4325 131 KCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCA 164 (306)
Q Consensus 131 ~C~~C~~~I~~~~~~~~~~~~~~H~~CF~C~~C~ 164 (306)
+|..|+.+|..++.+.-.....-| |-|..=.
T Consensus 8 kC~VCg~~iieGqkFTF~~kGsVH---~eCl~~s 38 (103)
T COG4847 8 KCYVCGGTIIEGQKFTFTKKGSVH---YECLAES 38 (103)
T ss_pred eEeeeCCEeeeccEEEEeeCCcch---HHHHHHH
Confidence 799999999766654222233334 7776543
No 137
>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=42.07 E-value=17 Score=30.15 Aligned_cols=31 Identities=10% Similarity=-0.037 Sum_probs=25.4
Q ss_pred HHHHHHHHhhCCCccchhcccccchhHHHHh
Q psy4325 232 HVREQLSQDTGLDMRVVQVWFQNRRAKEKRL 262 (306)
Q Consensus 232 ~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~ 262 (306)
..-+++|..+|+++..|+++...-|.+-|+.
T Consensus 155 ~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~ 185 (190)
T TIGR02939 155 LSYEDIARIMDCPVGTVRSRIFRAREAIAIR 185 (190)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3467899999999999999988777776654
No 138
>KOG3623|consensus
Probab=41.97 E-value=18 Score=36.79 Aligned_cols=60 Identities=22% Similarity=0.311 Sum_probs=40.4
Q ss_pred CCCcccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHhhhh
Q psy4325 206 RPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKKD 265 (306)
Q Consensus 206 r~rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~~ 265 (306)
+.++.....+...|...++-+..+...+-..++..+-..+.+|.+||++|+..-+++...
T Consensus 628 kv~sp~k~~dq~ql~~a~elq~s~~n~~~pl~~t~~~n~~pv~ev~dhsrsstpsp~pl~ 687 (1007)
T KOG3623|consen 628 KVRSPIKEEDQQQLKQAYELQASPSNDEFPLIATRLQNDPPVVEVWDHSRSSTPSPMPLF 687 (1007)
T ss_pred cccCCCCccchhhhHhhhhcccCccCcccchhhhhccCCCcchhhcccCCCCCCCCCccc
Confidence 445556666666677776655555544444444456778889999999999988876543
No 139
>PF13518 HTH_28: Helix-turn-helix domain
Probab=41.90 E-value=11 Score=23.96 Aligned_cols=25 Identities=16% Similarity=0.436 Sum_probs=20.2
Q ss_pred HHHHHHHhhCCCccchhcccccchh
Q psy4325 233 VREQLSQDTGLDMRVVQVWFQNRRA 257 (306)
Q Consensus 233 ~r~~La~~~~l~~~~V~~WFqNrR~ 257 (306)
...++|.++|++..+|..|.+.-+.
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHHh
Confidence 4567999999999999999765443
No 140
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=41.83 E-value=12 Score=23.82 Aligned_cols=25 Identities=16% Similarity=0.379 Sum_probs=17.3
Q ss_pred HHHHHHHHhhCCCccchhcccccch
Q psy4325 232 HVREQLSQDTGLDMRVVQVWFQNRR 256 (306)
Q Consensus 232 ~~r~~La~~~~l~~~~V~~WFqNrR 256 (306)
....++|+.+|++..+|..|.+.-+
T Consensus 18 ~s~~~ia~~lgvs~~Tv~~w~kr~~ 42 (50)
T PF13384_consen 18 WSIREIAKRLGVSRSTVYRWIKRYR 42 (50)
T ss_dssp --HHHHHHHHTS-HHHHHHHHT---
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHcc
Confidence 3567899999999999999976533
No 141
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=41.80 E-value=18 Score=29.97 Aligned_cols=48 Identities=8% Similarity=0.010 Sum_probs=33.3
Q ss_pred cchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHhh
Q psy4325 211 ITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLK 263 (306)
Q Consensus 211 ~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~ 263 (306)
+++.++.++...|-. ...-++||..+|++...|+.++..-|.+-|+.-
T Consensus 132 L~~~~r~v~~l~~~~-----g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12512 132 LPPRQRDVVQSISVE-----GASIKETAAKLSMSEGAVRVALHRGLAALAAKF 179 (184)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 444455555553222 224668999999999999999988888877643
No 142
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=41.52 E-value=19 Score=29.25 Aligned_cols=32 Identities=19% Similarity=0.172 Sum_probs=27.0
Q ss_pred HHHHHHHhhCCCccchhcccccchhHHHHhhh
Q psy4325 233 VREQLSQDTGLDMRVVQVWFQNRRAKEKRLKK 264 (306)
Q Consensus 233 ~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~ 264 (306)
..+++|..+|++...|++|.+.-|.+-|+.-.
T Consensus 126 s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~ 157 (165)
T PRK09644 126 TYEEAASVLDLKLNTYKSHLFRGRKRLKALLK 157 (165)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 46689999999999999999988888776544
No 143
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=41.41 E-value=33 Score=28.58 Aligned_cols=51 Identities=10% Similarity=0.133 Sum_probs=34.3
Q ss_pred cchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHhhhhc
Q psy4325 211 ITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKKDA 266 (306)
Q Consensus 211 ~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~~~ 266 (306)
++..++.++...|-. ....+++|..+|++...|+++..--|.+-|+.-...
T Consensus 112 Lp~~~R~v~~L~~~e-----g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~~~~ 162 (182)
T PRK12511 112 LPEEQRAALHLVAIE-----GLSYQEAAAVLGIPIGTLMSRIGRARAALRAFEEGT 162 (182)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHhc
Confidence 444555555443221 123668999999999999999887777777665543
No 144
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=41.16 E-value=17 Score=29.38 Aligned_cols=47 Identities=15% Similarity=0.244 Sum_probs=31.7
Q ss_pred cchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHh
Q psy4325 211 ITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRL 262 (306)
Q Consensus 211 ~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~ 262 (306)
++..|+.++...|-. ....+++|..+|++...|+.+...-|.+-|+.
T Consensus 113 L~~~~r~v~~l~~~~-----~~s~~eIA~~lgis~~tv~~~l~Rar~~L~~~ 159 (161)
T PRK12541 113 LPLERRNVLLLRDYY-----GFSYKEIAEMTGLSLAKVKIELHRGRKETKSI 159 (161)
T ss_pred CCHHHHHHhhhHHhc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 445555555443211 12457899999999999999888777776653
No 145
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=41.00 E-value=22 Score=29.49 Aligned_cols=32 Identities=3% Similarity=0.014 Sum_probs=26.4
Q ss_pred HHHHHHHhhCCCccchhcccccchhHHHHhhh
Q psy4325 233 VREQLSQDTGLDMRVVQVWFQNRRAKEKRLKK 264 (306)
Q Consensus 233 ~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~ 264 (306)
.-+++|+.+|++...|+.+...-|.+-|+.-.
T Consensus 146 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 177 (186)
T PRK05602 146 SNIEAAAVMDISVDALESLLARGRRALRAQLA 177 (186)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 35689999999999999999888877776544
No 146
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=40.86 E-value=20 Score=29.62 Aligned_cols=29 Identities=14% Similarity=0.368 Sum_probs=24.2
Q ss_pred HHHHHHHhhCCCccchhcccccchhHHHH
Q psy4325 233 VREQLSQDTGLDMRVVQVWFQNRRAKEKR 261 (306)
Q Consensus 233 ~r~~La~~~~l~~~~V~~WFqNrR~k~k~ 261 (306)
..+++|+.+|++...|++|....|.+-|+
T Consensus 151 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 179 (182)
T PRK12537 151 SHAEIAQRLGAPLGTVKAWIKRSLKALRE 179 (182)
T ss_pred CHHHHHHHHCCChhhHHHHHHHHHHHHHH
Confidence 36689999999999999998877776665
No 147
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=40.63 E-value=18 Score=29.34 Aligned_cols=30 Identities=10% Similarity=0.167 Sum_probs=25.6
Q ss_pred HHHHHHHhhCCCccchhcccccchhHHHHh
Q psy4325 233 VREQLSQDTGLDMRVVQVWFQNRRAKEKRL 262 (306)
Q Consensus 233 ~r~~La~~~~l~~~~V~~WFqNrR~k~k~~ 262 (306)
...++|..+|+++..|..|..--|.+.|+.
T Consensus 143 ~~~eIA~~lgis~~tv~~~~~ra~~~lr~~ 172 (179)
T PRK11924 143 SYREIAEILGVPVGTVKSRLRRARQLLREC 172 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 456899999999999999998888887754
No 148
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=40.29 E-value=18 Score=29.77 Aligned_cols=30 Identities=13% Similarity=0.173 Sum_probs=25.2
Q ss_pred HHHHHHHhhCCCccchhcccccchhHHHHh
Q psy4325 233 VREQLSQDTGLDMRVVQVWFQNRRAKEKRL 262 (306)
Q Consensus 233 ~r~~La~~~~l~~~~V~~WFqNrR~k~k~~ 262 (306)
..+++|..+|+++..|+++++.-|.+-|+.
T Consensus 154 s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 154 SLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 467899999999999999998777776653
No 149
>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=39.86 E-value=20 Score=28.48 Aligned_cols=29 Identities=7% Similarity=0.313 Sum_probs=23.4
Q ss_pred HHHHHHHhhCCCccchhcccccchhHHHH
Q psy4325 233 VREQLSQDTGLDMRVVQVWFQNRRAKEKR 261 (306)
Q Consensus 233 ~r~~La~~~~l~~~~V~~WFqNrR~k~k~ 261 (306)
...++|..+|+++..|+.+...-|.+.|+
T Consensus 131 ~~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 131 SYKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 35678999999999999988777776654
No 150
>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=39.83 E-value=20 Score=28.68 Aligned_cols=47 Identities=17% Similarity=0.244 Sum_probs=30.6
Q ss_pred ccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHH
Q psy4325 210 TITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261 (306)
Q Consensus 210 ~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~ 261 (306)
.+++.+..++...|- .....+++|..+|++..+|.++...-|.+.|.
T Consensus 111 ~L~~~~r~v~~l~~~-----~g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 111 KLPERQRELLQLRYQ-----RGVSLTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred HCCHHHHHHHHHHHh-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 345555555555222 22346789999999999999887666665543
No 151
>PRK14873 primosome assembly protein PriA; Provisional
Probab=39.52 E-value=26 Score=35.83 Aligned_cols=37 Identities=22% Similarity=0.479 Sum_probs=25.5
Q ss_pred ccCcCCCCCCCccee-eCCeeccccccccccCcCCCCCCCC
Q psy4325 99 KCHECGAPLAEKCFA-RNGLLFCKEDFFKRFGTKCAGCEMG 138 (306)
Q Consensus 99 ~C~~C~~~l~~~~f~-~~g~~yC~~cy~~~~~~~C~~C~~~ 138 (306)
+|..|+.+|. |+ ..+.+.|..|-.......|..|+..
T Consensus 394 ~C~~C~~~L~---~h~~~~~l~Ch~CG~~~~p~~Cp~Cgs~ 431 (665)
T PRK14873 394 RCRHCTGPLG---LPSAGGTPRCRWCGRAAPDWRCPRCGSD 431 (665)
T ss_pred ECCCCCCcee---EecCCCeeECCCCcCCCcCccCCCCcCC
Confidence 4455555553 33 3568889999776666789999876
No 152
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=39.51 E-value=13 Score=22.28 Aligned_cols=9 Identities=33% Similarity=0.951 Sum_probs=4.3
Q ss_pred Ceecccccc
Q psy4325 116 GLLFCKEDF 124 (306)
Q Consensus 116 g~~yC~~cy 124 (306)
|..||..|.
T Consensus 19 ~H~~c~~C~ 27 (45)
T cd00162 19 GHVFCRSCI 27 (45)
T ss_pred CChhcHHHH
Confidence 444555554
No 153
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=38.18 E-value=11 Score=24.06 Aligned_cols=21 Identities=10% Similarity=0.325 Sum_probs=19.3
Q ss_pred HHHHhhCCCccchhcccccch
Q psy4325 236 QLSQDTGLDMRVVQVWFQNRR 256 (306)
Q Consensus 236 ~La~~~~l~~~~V~~WFqNrR 256 (306)
+||+.+|++..+|..|+.+++
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 589999999999999999984
No 154
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=37.62 E-value=9.7 Score=28.57 Aligned_cols=28 Identities=14% Similarity=0.344 Sum_probs=18.7
Q ss_pred cCcccCcCCCCCCC--cceeeCCeeccccc
Q psy4325 96 RCLKCHECGAPLAE--KCFARNGLLFCKED 123 (306)
Q Consensus 96 ~Cf~C~~C~~~l~~--~~f~~~g~~yC~~c 123 (306)
+=|+|..|-..--. .....+|.+||..|
T Consensus 69 DEFTCssCFLV~HRSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 69 DEFTCSSCFLVHHRSQLAREKDGQPICRDC 98 (99)
T ss_pred CceeeeeeeeEechhhhccccCCCEecccc
Confidence 45888888753322 22266799999888
No 155
>PRK06930 positive control sigma-like factor; Validated
Probab=37.42 E-value=23 Score=29.41 Aligned_cols=50 Identities=14% Similarity=0.123 Sum_probs=35.0
Q ss_pred ccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHhhh
Q psy4325 210 TITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKK 264 (306)
Q Consensus 210 ~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~ 264 (306)
.+++.++.++...|... ..-.++|..+|++...|+.+....|.+-++.-.
T Consensus 114 ~L~~rer~V~~L~~~eg-----~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~ 163 (170)
T PRK06930 114 VLTEREKEVYLMHRGYG-----LSYSEIADYLNIKKSTVQSMIERAEKKIARQIN 163 (170)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 45556666655533211 235688999999999999999988888776543
No 156
>PRK00420 hypothetical protein; Validated
Probab=37.15 E-value=21 Score=27.62 Aligned_cols=23 Identities=26% Similarity=0.667 Sum_probs=14.4
Q ss_pred ccccCCCCCCCCCceeeccCCcccccchh
Q psy4325 159 ACVMCARQLNTGDEFYLMEDRKLVCKPDY 187 (306)
Q Consensus 159 ~C~~C~~~l~~g~~~~~~~~~~~~C~~c~ 187 (306)
.|..|+.+| +-..+|..+|..|-
T Consensus 25 ~CP~Cg~pL------f~lk~g~~~Cp~Cg 47 (112)
T PRK00420 25 HCPVCGLPL------FELKDGEVVCPVHG 47 (112)
T ss_pred CCCCCCCcc------eecCCCceECCCCC
Confidence 366666666 23357777777773
No 157
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=37.13 E-value=24 Score=27.31 Aligned_cols=29 Identities=14% Similarity=0.271 Sum_probs=23.8
Q ss_pred HHHHHHHhhCCCccchhcccccchhHHHH
Q psy4325 233 VREQLSQDTGLDMRVVQVWFQNRRAKEKR 261 (306)
Q Consensus 233 ~r~~La~~~~l~~~~V~~WFqNrR~k~k~ 261 (306)
...++|+.+|+++..|..|...-+.|-|+
T Consensus 128 s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 128 SYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 45689999999999999988877776654
No 158
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=37.09 E-value=23 Score=22.20 Aligned_cols=11 Identities=36% Similarity=0.918 Sum_probs=6.1
Q ss_pred CCccCCCeecc
Q psy4325 72 KCGGCGDLILD 82 (306)
Q Consensus 72 ~C~~C~~~I~~ 82 (306)
.|.+|+++|.+
T Consensus 2 ~Cd~C~~~i~G 12 (43)
T cd02340 2 ICDGCQGPIVG 12 (43)
T ss_pred CCCCCCCcCcC
Confidence 46666665543
No 159
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=37.04 E-value=20 Score=31.28 Aligned_cols=32 Identities=9% Similarity=0.196 Sum_probs=26.7
Q ss_pred HHHHHHHhhCCCccchhcccccchhHHHHhhh
Q psy4325 233 VREQLSQDTGLDMRVVQVWFQNRRAKEKRLKK 264 (306)
Q Consensus 233 ~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~ 264 (306)
..++||..+|++...|+++.+.-|.+.|+.-.
T Consensus 189 s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l~ 220 (233)
T PRK12538 189 SNGEIAEVMDTTVAAVESLLKRGRQQLRDLLR 220 (233)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 45689999999999999999888888776543
No 160
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=36.94 E-value=22 Score=29.77 Aligned_cols=31 Identities=19% Similarity=0.202 Sum_probs=26.0
Q ss_pred HHHHHHHhhCCCccchhcccccchhHHHHhh
Q psy4325 233 VREQLSQDTGLDMRVVQVWFQNRRAKEKRLK 263 (306)
Q Consensus 233 ~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~ 263 (306)
..+++|..+|++...|++++..-|.+-|+.-
T Consensus 131 s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l 161 (188)
T PRK12546 131 SYEEAAEMCGVAVGTVKSRANRARARLAELL 161 (188)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3568999999999999999998888877643
No 161
>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=36.88 E-value=44 Score=26.80 Aligned_cols=48 Identities=10% Similarity=0.153 Sum_probs=37.8
Q ss_pred CcccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHH
Q psy4325 208 RTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261 (306)
Q Consensus 208 rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~ 261 (306)
.+.++..|+.+|+... .. ...+++|..+|++...|..|-+..|.+-++
T Consensus 4 ~~~Lte~qr~VL~Lr~--~G----lTq~EIAe~LgiS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 4 KTFLTERQIKVLELRE--KG----LSQKEIAKELKTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred cCCCCHHHHHHHHHHH--cC----CCHHHHHHHHCcCHHHHHHHHHhHHHHHHH
Confidence 4567888988887742 22 257789999999999999998888888775
No 162
>PF02069 Metallothio_Pro: Prokaryotic metallothionein; InterPro: IPR000518 Metallothioneins (MT) are small proteins that bind heavy metals, such as zinc, copper, cadmium and nickel. They have a high content of cysteine residues that bind the metal ions through clusters of thiolate bonds [, , ]. An empirical classification into three classes was proposed by Kojima [], with class III MTs including atypical polypeptides composed of gamma-glutamylcysteinyl units. Class I and class II MTs (the proteinaceous sequences) have now been grouped into families of phylogenetically-related and thus alignable sequences. The MT superfamily is subdivided into families, subfamilies, subgroups, and isolated isoforms and alleles. The metallothionein superfamily comprises all polypeptides that resemble equine renal metallothionein in several respects [], e.g., low molecular weight; high metal content; amino acid composition with high Cys and low aromatic residue content; unique sequence with characteristic distribution of cysteines, and spectroscopic manifestations indicative of metal thiolate clusters. A MT family subsumes MTs that share particular sequence-specific features and are thought to be evolutionarily related. Fifteen MT families have been characterised, each family being identified by its number and its taxonomic range. Family 14 consists of prokaryota MTs. Its members are recognised by the sequence pattern K-C-A-C-x(2)-C-L-C.The taxonomic range of the members extends to cyanobacteria. Known characteristics are: 53 to 56 AAs; 9 conserved Cys; one conserved tyrosine residue; one conserved histidine residue; contain other unusual residues. ; GO: 0046872 metal ion binding; PDB: 1JJD_A.
Probab=36.77 E-value=22 Score=23.41 Aligned_cols=26 Identities=19% Similarity=0.646 Sum_probs=14.4
Q ss_pred ccCcCCCCCC-CcceeeCCeeccc-ccc
Q psy4325 99 KCHECGAPLA-EKCFARNGLLFCK-EDF 124 (306)
Q Consensus 99 ~C~~C~~~l~-~~~f~~~g~~yC~-~cy 124 (306)
-|..|.-.++ ...+.+||+.||. .|.
T Consensus 9 aC~~C~C~V~~~~Ai~~dGk~YCS~aCA 36 (52)
T PF02069_consen 9 ACPSCSCVVSEEEAIQKDGKYYCSEACA 36 (52)
T ss_dssp SSTT----B-TTTSEESSS-EESSHHHH
T ss_pred cCCCCEeEECchHhHHhCCEeeecHHHh
Confidence 3567777776 5677899999996 454
No 163
>PF01258 zf-dskA_traR: Prokaryotic dksA/traR C4-type zinc finger; InterPro: IPR000962 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents domains identified in zinc finger-containing members of the DksA/TraR family. DksA is a critical component of the rRNA transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. In delta-dksA mutants, rRNA promoters are unresponsive to changes in amino acid availability, growth rate, or growth phase. In vitro, DksA binds to RNAP, reduces open complex lifetime, inhibits rRNA promoter activity, and amplifies effects of ppGpp and the initiating NTP on rRNA transcription [, ]. The dksA gene product suppresses the temperature-sensitive growth and filamentation of a dnaK deletion mutant of Escherichia coli. Gene knockout [] and deletion [] experiments have shown the gene to be non-essential, mutations causing a mild sensitivity to UV light, but not affecting DNA recombination []. In Pseudomonas aeruginosa, dksA is a novel regulator involved in the post-transcriptional control of extracellular virulence factor production []. The proteins contain a C-terminal region thought to fold into a 4-cysteine zinc finger. Other proteins found to contain a similar zinc finger domain include: the traR gene products encoded on the E. coli F and R100 plasmids [, ] the traR gene products encoded on Salmonella spp. plasmids pED208 and pSLT the dnaK suppressor hypothetical proteins from bacteria and bacteriophage FHL4, LIM proteins from Homo sapiens (Human) and Mus musculus (Mouse) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2GVI_A 2KQ9_A 2KGO_A 1TJL_I.
Probab=36.75 E-value=4.8 Score=24.14 Aligned_cols=10 Identities=40% Similarity=1.122 Sum_probs=5.1
Q ss_pred CccCCCeecc
Q psy4325 73 CGGCGDLILD 82 (306)
Q Consensus 73 C~~C~~~I~~ 82 (306)
|..|+++|..
T Consensus 6 C~~CGe~I~~ 15 (36)
T PF01258_consen 6 CEDCGEPIPE 15 (36)
T ss_dssp -TTTSSBEEH
T ss_pred ccccCChHHH
Confidence 5566665544
No 164
>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=36.68 E-value=22 Score=22.29 Aligned_cols=37 Identities=16% Similarity=0.349 Sum_probs=22.3
Q ss_pred cchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhccc
Q psy4325 211 ITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWF 252 (306)
Q Consensus 211 ~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WF 252 (306)
++.++.+.+...+... ....+||+.+|++...|..++
T Consensus 6 ~~~~~~~~i~~l~~~G-----~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 6 LSKEQIEEIKELYAEG-----MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHHHHHH
T ss_pred CCHHHHHHHHHHHHCC-----CCHHHHHHHHCcCHHHHHHHH
Confidence 4444444444444333 357889999999998887654
No 165
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=36.61 E-value=18 Score=24.66 Aligned_cols=18 Identities=6% Similarity=0.228 Sum_probs=16.3
Q ss_pred HHHHHHhhCCCccchhcc
Q psy4325 234 REQLSQDTGLDMRVVQVW 251 (306)
Q Consensus 234 r~~La~~~~l~~~~V~~W 251 (306)
..++|+.+|++.++|+.|
T Consensus 3 i~eva~~~gvs~~tlr~y 20 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYY 20 (69)
T ss_dssp HHHHHHHTTTTHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHH
Confidence 467899999999999999
No 166
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=36.53 E-value=24 Score=29.33 Aligned_cols=32 Identities=22% Similarity=0.331 Sum_probs=25.7
Q ss_pred HHHHHHHhhCCCccchhcccccchhHHHHhhh
Q psy4325 233 VREQLSQDTGLDMRVVQVWFQNRRAKEKRLKK 264 (306)
Q Consensus 233 ~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~ 264 (306)
..+++|..+|++...|+..+..-|.+.|+.-.
T Consensus 124 ~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 155 (181)
T PRK09637 124 SQKEIAEKLGLSLSGAKSRVQRGRVKLKELLE 155 (181)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 35689999999999999999877777665443
No 167
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=36.48 E-value=25 Score=28.54 Aligned_cols=30 Identities=13% Similarity=0.165 Sum_probs=24.8
Q ss_pred HHHHHHHhhCCCccchhcccccchhHHHHh
Q psy4325 233 VREQLSQDTGLDMRVVQVWFQNRRAKEKRL 262 (306)
Q Consensus 233 ~r~~La~~~~l~~~~V~~WFqNrR~k~k~~ 262 (306)
..+++|..+|+++..|+++...-|.+-|..
T Consensus 130 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 159 (164)
T PRK12547 130 SYEDAAAICGCAVGTIKSRVSRARNRLQEL 159 (164)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 466899999999999999988777776653
No 168
>KOG0773|consensus
Probab=36.25 E-value=22 Score=32.94 Aligned_cols=45 Identities=27% Similarity=0.346 Sum_probs=38.0
Q ss_pred hccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHhhhh
Q psy4325 221 MAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKKD 265 (306)
Q Consensus 221 ~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~~ 265 (306)
..-..++||+..+...|+....|+..+|.+||-|.|.+.++..+.
T Consensus 114 ~~~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~~~ 158 (342)
T KOG0773|consen 114 EEHRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKELKM 158 (342)
T ss_pred hhhhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhccCC
Confidence 334568999999999999999999999999999999997764433
No 169
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=36.07 E-value=28 Score=27.89 Aligned_cols=30 Identities=7% Similarity=-0.020 Sum_probs=24.5
Q ss_pred HHHHHHhhCCCccchhcccccchhHHHHhh
Q psy4325 234 REQLSQDTGLDMRVVQVWFQNRRAKEKRLK 263 (306)
Q Consensus 234 r~~La~~~~l~~~~V~~WFqNrR~k~k~~~ 263 (306)
.+++|..+|++...|++....-|.+.|+.-
T Consensus 125 ~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 154 (161)
T PRK09047 125 VAETAAAMGCSEGSVKTHCSRATHALAKAL 154 (161)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 568999999999999998887777766543
No 170
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=35.98 E-value=16 Score=23.54 Aligned_cols=23 Identities=13% Similarity=0.328 Sum_probs=19.6
Q ss_pred HHHHHHhhCCCccchhcccccch
Q psy4325 234 REQLSQDTGLDMRVVQVWFQNRR 256 (306)
Q Consensus 234 r~~La~~~~l~~~~V~~WFqNrR 256 (306)
..+||+.+|+++..|..|..+++
T Consensus 12 ~~~la~~~gis~~~i~~~~~g~~ 34 (55)
T PF01381_consen 12 QKELAEKLGISRSTISRIENGKR 34 (55)
T ss_dssp HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred HHHHHHHhCCCcchhHHHhcCCC
Confidence 47899999999999999999865
No 171
>KOG4739|consensus
Probab=35.84 E-value=25 Score=30.84 Aligned_cols=32 Identities=19% Similarity=0.357 Sum_probs=24.1
Q ss_pred Ccceee-CCeeccccccccccCcCCCCCCCCCC
Q psy4325 109 EKCFAR-NGLLFCKEDFFKRFGTKCAGCEMGIP 140 (306)
Q Consensus 109 ~~~f~~-~g~~yC~~cy~~~~~~~C~~C~~~I~ 140 (306)
..+|.. =..++|..|.....++.|..|.++|.
T Consensus 16 ~~f~LTaC~HvfC~~C~k~~~~~~C~lCkk~ir 48 (233)
T KOG4739|consen 16 DPFFLTACRHVFCEPCLKASSPDVCPLCKKSIR 48 (233)
T ss_pred CceeeeechhhhhhhhcccCCccccccccceee
Confidence 345543 37889999987777778999998873
No 172
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=35.78 E-value=18 Score=21.99 Aligned_cols=18 Identities=11% Similarity=0.281 Sum_probs=14.4
Q ss_pred HHHHHHhhCCCccchhcc
Q psy4325 234 REQLSQDTGLDMRVVQVW 251 (306)
Q Consensus 234 r~~La~~~~l~~~~V~~W 251 (306)
+.++|+.+|++.+.|+-|
T Consensus 2 i~e~A~~~gvs~~tlR~y 19 (38)
T PF00376_consen 2 IGEVAKLLGVSPRTLRYY 19 (38)
T ss_dssp HHHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHHCCCHHHHHHH
Confidence 457899999999999877
No 173
>PF11571 Med27: Mediator complex subunit 27; InterPro: IPR021627 Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function []. Mediator exists in two major forms in human cells: a smaller form that interacts strongly with pol II and activates transcription, and a large form that does not interact strongly with pol II and does not directly activate transcription. The ubiquitous expression of Med27 mRNA suggests a universal requirement for Med27 in transcriptional initiation. Loss of Crsp34/Med27 decreases amacrine cell number, but increases the number of rod photoreceptor cells [].
Probab=35.34 E-value=15 Score=27.01 Aligned_cols=16 Identities=25% Similarity=0.573 Sum_probs=12.5
Q ss_pred cccccCcCCCCCCCCC
Q psy4325 124 FFKRFGTKCAGCEMGI 139 (306)
Q Consensus 124 y~~~~~~~C~~C~~~I 139 (306)
|...|...|..|++.+
T Consensus 49 Y~~lfs~pC~~C~klL 64 (90)
T PF11571_consen 49 YRNLFSTPCKKCGKLL 64 (90)
T ss_pred HhhhccchhhHHHhHh
Confidence 4567778888888887
No 174
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=35.31 E-value=29 Score=30.17 Aligned_cols=47 Identities=9% Similarity=0.100 Sum_probs=34.6
Q ss_pred cchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHh
Q psy4325 211 ITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRL 262 (306)
Q Consensus 211 ~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~ 262 (306)
+++.++.++...|-.. ....++|..+|++...|+.+...-|.+-|+.
T Consensus 185 L~~~~r~vl~l~~~~g-----~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 231 (236)
T PRK06986 185 LPEREQLVLSLYYQEE-----LNLKEIGAVLGVSESRVSQIHSQAIKRLRAR 231 (236)
T ss_pred CCHHHHHHHHhHhccC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4555666665554222 2467899999999999999999888887764
No 175
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=35.16 E-value=35 Score=18.64 Aligned_cols=11 Identities=36% Similarity=0.957 Sum_probs=5.8
Q ss_pred CCCCCCCCCCC
Q psy4325 132 CAGCEMGIPPT 142 (306)
Q Consensus 132 C~~C~~~I~~~ 142 (306)
|.+|+..|.+.
T Consensus 1 C~sC~~~i~~r 11 (24)
T PF07754_consen 1 CTSCGRPIAPR 11 (24)
T ss_pred CccCCCcccCc
Confidence 45566555443
No 176
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=35.04 E-value=28 Score=27.02 Aligned_cols=40 Identities=10% Similarity=0.243 Sum_probs=26.2
Q ss_pred CcccchHhHH-HHHhccccCCCCCHHHHHHHHHhhCCCccchhccc
Q psy4325 208 RTTITAKQLE-TLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWF 252 (306)
Q Consensus 208 rt~~s~~q~~-~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WF 252 (306)
+.+++.+... ++...+. .. ....++|..+|+++.+|..|.
T Consensus 10 rr~ys~EfK~~aV~~~~~-~g----~sv~evA~e~gIs~~tl~~W~ 50 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFE-PG----MTVSLVARQHGVAASQLFLWR 50 (121)
T ss_pred CCCCCHHHHHHHHHHHHc-CC----CCHHHHHHHHCcCHHHHHHHH
Confidence 4556666544 3333333 22 246678999999999999993
No 177
>KOG3755|consensus
Probab=34.74 E-value=12 Score=37.04 Aligned_cols=61 Identities=25% Similarity=0.245 Sum_probs=0.0
Q ss_pred CCCCCCcccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccc-------hhcccccchhHHHHhh
Q psy4325 203 PNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRV-------VQVWFQNRRAKEKRLK 263 (306)
Q Consensus 203 ~~kr~rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~-------V~~WFqNrR~k~k~~~ 263 (306)
+++..-..|.+.-.++-+.+|.++..+......+-.+.+.|.+-. |+.||.|||.+.++.+
T Consensus 691 pk~~~~k~f~~~~~ev~~~w~~k~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k 758 (769)
T KOG3755|consen 691 PKKTIIKFFQNQRYEVKHHWKLKTRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLK 758 (769)
T ss_pred cHHHHHHhhhcceeecchhheecccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhh
No 178
>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=34.68 E-value=26 Score=28.20 Aligned_cols=30 Identities=17% Similarity=0.302 Sum_probs=25.2
Q ss_pred HHHHHHHhhCCCccchhcccccchhHHHHh
Q psy4325 233 VREQLSQDTGLDMRVVQVWFQNRRAKEKRL 262 (306)
Q Consensus 233 ~r~~La~~~~l~~~~V~~WFqNrR~k~k~~ 262 (306)
.-+++|..+|++...|+.+...-|.+-|+.
T Consensus 128 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 157 (162)
T TIGR02983 128 SEAQVAEALGISVGTVKSRLSRALARLREL 157 (162)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 356789999999999999988888877764
No 179
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=34.63 E-value=20 Score=29.97 Aligned_cols=33 Identities=9% Similarity=0.141 Sum_probs=27.4
Q ss_pred HHHHHHHHhhCCCccchhcccccchhHHHHhhh
Q psy4325 232 HVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKK 264 (306)
Q Consensus 232 ~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~ 264 (306)
....++|..+|++...|+++...-|.+.|+.-.
T Consensus 148 ~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 180 (193)
T TIGR02947 148 FAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLV 180 (193)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 346789999999999999999988888776543
No 180
>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=34.49 E-value=28 Score=28.28 Aligned_cols=46 Identities=11% Similarity=0.174 Sum_probs=31.0
Q ss_pred cchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHH
Q psy4325 211 ITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261 (306)
Q Consensus 211 ~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~ 261 (306)
++..+.+++...|-.. ...+++|..+|++...|+++..--|.+-|+
T Consensus 120 L~~~~r~i~~l~~~~g-----~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~ 165 (169)
T TIGR02954 120 LNDKYQTAIILRYYHD-----LTIKEIAEVMNKPEGTVKTYLHRALKKLKK 165 (169)
T ss_pred CCHHHhHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4455555554433222 246789999999999999887777766665
No 181
>cd00131 PAX Paired Box domain
Probab=34.22 E-value=83 Score=24.71 Aligned_cols=44 Identities=11% Similarity=0.213 Sum_probs=27.3
Q ss_pred cchHhHHHHHhccccCCCCCHHHHHH-HHHhhCC-------Cccchhcccccc
Q psy4325 211 ITAKQLETLKMAYNTSPKPARHVREQ-LSQDTGL-------DMRVVQVWFQNR 255 (306)
Q Consensus 211 ~s~~q~~~Le~~F~~~~~p~~~~r~~-La~~~~l-------~~~~V~~WFqNr 255 (306)
.+..+...++.....+|..+..+..+ |+ .-|+ +.++|-.||+++
T Consensus 76 ~~~~~~~~i~~~v~~~p~~Tl~El~~~L~-~~gv~~~~~~~s~stI~R~L~~~ 127 (128)
T cd00131 76 ATPEVVKKIEIYKQENPGMFAWEIRDRLL-QEGVCDKSNVPSVSSINRILRNK 127 (128)
T ss_pred CCHHHHHHHHHHHHHCCCCCHHHHHHHHH-HcCCcccCCCCCHHHHHHHHHhc
Confidence 45556566666667777777665554 45 3365 677777776653
No 182
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=33.93 E-value=28 Score=28.70 Aligned_cols=30 Identities=20% Similarity=0.065 Sum_probs=25.2
Q ss_pred HHHHHHHhhCCCccchhcccccchhHHHHh
Q psy4325 233 VREQLSQDTGLDMRVVQVWFQNRRAKEKRL 262 (306)
Q Consensus 233 ~r~~La~~~~l~~~~V~~WFqNrR~k~k~~ 262 (306)
..+++|+.+|++...|++.....|.+.|+.
T Consensus 147 s~~EIA~~l~is~~tV~~~l~rar~~Lr~~ 176 (181)
T PRK12536 147 SVAETAQLTGLSESAVKVGIHRGLKALAAK 176 (181)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 456899999999999999998877777663
No 183
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=33.78 E-value=36 Score=28.53 Aligned_cols=32 Identities=6% Similarity=0.070 Sum_probs=26.8
Q ss_pred HHHHHHHhhCCCccchhcccccchhHHHHhhh
Q psy4325 233 VREQLSQDTGLDMRVVQVWFQNRRAKEKRLKK 264 (306)
Q Consensus 233 ~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~ 264 (306)
.-++||+.+|++...|++++.-.|.+-|+.-.
T Consensus 154 s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 185 (196)
T PRK12524 154 SNPEIAEVMEIGVEAVESLTARGKRALAALLA 185 (196)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 35689999999999999999988888777544
No 184
>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=33.67 E-value=36 Score=21.58 Aligned_cols=21 Identities=10% Similarity=0.336 Sum_probs=18.1
Q ss_pred HHHHHHHhhCCCccchhcccc
Q psy4325 233 VREQLSQDTGLDMRVVQVWFQ 253 (306)
Q Consensus 233 ~r~~La~~~~l~~~~V~~WFq 253 (306)
...++|+.++++...|..|..
T Consensus 17 s~~eia~~l~~s~~tv~~~~~ 37 (57)
T cd06170 17 TNKEIADILGISEKTVKTHLR 37 (57)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 467889999999999998876
No 185
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=33.51 E-value=29 Score=33.97 Aligned_cols=82 Identities=12% Similarity=0.121 Sum_probs=0.0
Q ss_pred ccCCcccccccCC---------CCCCCCCccCCCeeccceeeeecCccccccCcccCcCCCCCCCcce--eeCCeecccc
Q psy4325 54 DVDYEGIMPVYMP---------IASIPKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCF--ARNGLLFCKE 122 (306)
Q Consensus 54 ~~~~~~~~~~~~~---------~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f--~~~g~~yC~~ 122 (306)
+.....||..|.. +.....|..|-..+...++ ...+..-...||.|-.|..+|.-... ......-...
T Consensus 1 pl~~L~fC~~C~~irc~~c~~~Ei~~~yCp~CL~~~p~~e~-~~~~nrC~r~Cf~CP~C~~~L~~~~~~~~~~~~~~~~~ 79 (483)
T PF05502_consen 1 PLEELYFCEHCHKIRCPRCVSEEIDSYYCPNCLFEVPSSEA-RSEKNRCSRNCFDCPICFSPLSVRASDTPPSPPDPSSD 79 (483)
T ss_pred CcccceecccccccCChhhcccccceeECccccccCChhhh-eeccceeccccccCCCCCCcceeEeccccccccccccc
Q ss_pred ccccccCcCCCCCC
Q psy4325 123 DFFKRFGTKCAGCE 136 (306)
Q Consensus 123 cy~~~~~~~C~~C~ 136 (306)
--.+.|.-.|..|.
T Consensus 80 ~~~~~~~l~C~~C~ 93 (483)
T PF05502_consen 80 SGGKPYYLSCSYCR 93 (483)
T ss_pred CCCCCEEEECCCce
No 186
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=33.51 E-value=26 Score=29.15 Aligned_cols=29 Identities=7% Similarity=-0.003 Sum_probs=23.6
Q ss_pred HHHHHHHhhCCCccchhcccccchhHHHH
Q psy4325 233 VREQLSQDTGLDMRVVQVWFQNRRAKEKR 261 (306)
Q Consensus 233 ~r~~La~~~~l~~~~V~~WFqNrR~k~k~ 261 (306)
..++||..+|+++..|+++...-|.+-|+
T Consensus 148 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 148 SYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 35689999999999999988766666655
No 187
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=33.43 E-value=33 Score=29.72 Aligned_cols=52 Identities=4% Similarity=0.150 Sum_probs=34.9
Q ss_pred ccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHh
Q psy4325 210 TITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRL 262 (306)
Q Consensus 210 ~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~ 262 (306)
.+++.++.++...|.. .+-.....+++|..+|++...|+.+....|.+-|+.
T Consensus 178 ~Lp~~~R~v~~L~y~l-~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~ 229 (234)
T PRK08301 178 KLSDREKQIMELRFGL-NGGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKE 229 (234)
T ss_pred hCCHHHHHHHHHHhcc-CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3556666666655410 001223467889999999999999988888777764
No 188
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=33.37 E-value=27 Score=29.11 Aligned_cols=50 Identities=16% Similarity=0.173 Sum_probs=33.7
Q ss_pred ccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHhhh
Q psy4325 210 TITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKK 264 (306)
Q Consensus 210 ~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~ 264 (306)
.+++.+..++...|-. ....+++|+.+|++...|++..+.-|.+-|++..
T Consensus 131 ~L~~~~r~i~~l~~~~-----g~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~~~ 180 (189)
T PRK06811 131 DLEKLDREIFIRRYLL-----GEKIEEIAKKLGLTRSAIDNRLSRGRKKLQKNKL 180 (189)
T ss_pred hCCHHHHHHHHHHHHc-----cCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHccc
Confidence 3455555555543211 1246789999999999999988877777776543
No 189
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=33.33 E-value=29 Score=28.59 Aligned_cols=31 Identities=13% Similarity=0.157 Sum_probs=26.2
Q ss_pred HHHHHHHhhCCCccchhcccccchhHHHHhh
Q psy4325 233 VREQLSQDTGLDMRVVQVWFQNRRAKEKRLK 263 (306)
Q Consensus 233 ~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~ 263 (306)
..+++|..+|++...|++....-|.+-|+.-
T Consensus 135 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 165 (179)
T PRK12543 135 SQEEIAQLLQIPIGTVKSRIHAALKKLRQKE 165 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3568999999999999999998888877643
No 190
>KOG2893|consensus
Probab=33.24 E-value=10 Score=33.18 Aligned_cols=36 Identities=33% Similarity=0.515 Sum_probs=26.8
Q ss_pred CCCCCccCCCeeccceeeeecCccccccCcccCcCCCCC
Q psy4325 69 SIPKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPL 107 (306)
Q Consensus 69 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l 107 (306)
..+-|..|++.+.++.++. ++-...+|+|.+|.+.|
T Consensus 9 ~kpwcwycnrefddekili---qhqkakhfkchichkkl 44 (341)
T KOG2893|consen 9 DKPWCWYCNREFDDEKILI---QHQKAKHFKCHICHKKL 44 (341)
T ss_pred CCceeeecccccchhhhhh---hhhhhccceeeeehhhh
Confidence 4567999999998876653 33344679999999877
No 191
>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=32.81 E-value=5.1 Score=28.42 Aligned_cols=25 Identities=8% Similarity=0.252 Sum_probs=21.0
Q ss_pred HHHHHHHHhhCCCccchhcccccch
Q psy4325 232 HVREQLSQDTGLDMRVVQVWFQNRR 256 (306)
Q Consensus 232 ~~r~~La~~~~l~~~~V~~WFqNrR 256 (306)
-...+||..+|+++..|+.|+.+..
T Consensus 33 lS~kEIAe~LGIS~~TVk~~l~~~~ 57 (73)
T TIGR03879 33 KTASEIAEELGRTEQTVRNHLKGET 57 (73)
T ss_pred CCHHHHHHHHCcCHHHHHHHHhcCc
Confidence 3577899999999999999987543
No 192
>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=32.71 E-value=19 Score=22.08 Aligned_cols=24 Identities=8% Similarity=0.332 Sum_probs=19.7
Q ss_pred HHHHHHhhCCCccchhcccccchh
Q psy4325 234 REQLSQDTGLDMRVVQVWFQNRRA 257 (306)
Q Consensus 234 r~~La~~~~l~~~~V~~WFqNrR~ 257 (306)
..++|+.+|++.+.|..|.++-+-
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~~ 26 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGKL 26 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCCC
Confidence 467899999999999999776543
No 193
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=32.57 E-value=49 Score=27.49 Aligned_cols=33 Identities=15% Similarity=0.079 Sum_probs=26.5
Q ss_pred HHHHHHHhhCCCccchhcccccchhHHHHhhhh
Q psy4325 233 VREQLSQDTGLDMRVVQVWFQNRRAKEKRLKKD 265 (306)
Q Consensus 233 ~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~~ 265 (306)
..+++|..+|++...|+....--|.+-|+.-..
T Consensus 129 s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~~ 161 (182)
T PRK12540 129 SYEDAAAICGCAVGTIKSRVNRARSKLSALLYV 161 (182)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 456899999999999999888777777765443
No 194
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=32.32 E-value=26 Score=22.60 Aligned_cols=10 Identities=20% Similarity=0.530 Sum_probs=6.4
Q ss_pred eecccccccc
Q psy4325 117 LLFCKEDFFK 126 (306)
Q Consensus 117 ~~yC~~cy~~ 126 (306)
--+|..||..
T Consensus 26 ~DlC~~C~~~ 35 (48)
T cd02341 26 FDLCQDCVVK 35 (48)
T ss_pred CccCHHHHhC
Confidence 4467777754
No 195
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=32.10 E-value=33 Score=27.59 Aligned_cols=29 Identities=7% Similarity=0.308 Sum_probs=22.7
Q ss_pred HHHHHHHhhCCCccchhcccccchhHHHH
Q psy4325 233 VREQLSQDTGLDMRVVQVWFQNRRAKEKR 261 (306)
Q Consensus 233 ~r~~La~~~~l~~~~V~~WFqNrR~k~k~ 261 (306)
..+++|+.+|++...|+....-.|.+-|+
T Consensus 127 s~~EIA~~lgis~~tV~~~l~ra~~~lr~ 155 (163)
T PRK07037 127 TQKDIARELGVSPTLVNFMIRDALVHCRK 155 (163)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 36789999999999999976655555554
No 196
>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=31.98 E-value=23 Score=22.72 Aligned_cols=23 Identities=13% Similarity=0.280 Sum_probs=20.4
Q ss_pred HHHHHHhhCCCccchhcccccch
Q psy4325 234 REQLSQDTGLDMRVVQVWFQNRR 256 (306)
Q Consensus 234 r~~La~~~~l~~~~V~~WFqNrR 256 (306)
..+||..+|++...|..|..+++
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 57899999999999999998775
No 197
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=31.88 E-value=28 Score=28.40 Aligned_cols=35 Identities=6% Similarity=0.137 Sum_probs=28.3
Q ss_pred HHHHHHHHHhhCCCccchhcccccchhHHHHhhhh
Q psy4325 231 RHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKKD 265 (306)
Q Consensus 231 ~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~~ 265 (306)
...-+++|..+|+++..|++.+..-|.+-|+.-+.
T Consensus 136 g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l~~ 170 (175)
T PRK12518 136 DLPQKEIAEILNIPVGTVKSRLFYARRQLRKFLQQ 170 (175)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 33467899999999999999998888887775443
No 198
>cd02336 ZZ_RSC8 Zinc finger, ZZ type. Zinc finger present in RSC8 and related proteins. RSC8 is a component of the RSC complex, which is closely related to the SWI/SNF complex and is involved in remodeling chromatin structure. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=31.70 E-value=26 Score=22.26 Aligned_cols=28 Identities=14% Similarity=0.483 Sum_probs=17.4
Q ss_pred ccCcCCCCCCCcce--ee-CCeecccccccc
Q psy4325 99 KCHECGAPLAEKCF--AR-NGLLFCKEDFFK 126 (306)
Q Consensus 99 ~C~~C~~~l~~~~f--~~-~g~~yC~~cy~~ 126 (306)
.|..|+..++..+| .+ .+..+|..||.+
T Consensus 2 ~C~~Cg~D~t~vryh~~~~~~~dLC~~CF~~ 32 (45)
T cd02336 2 HCFTCGNDCTRVRYHNLKAKKYDLCPSCYQE 32 (45)
T ss_pred cccCCCCccCceEEEecCCCccccChHHHhC
Confidence 46677776665444 12 246788888854
No 199
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=31.33 E-value=35 Score=28.15 Aligned_cols=29 Identities=14% Similarity=0.171 Sum_probs=23.6
Q ss_pred HHHHHHHhhCCCccchhcccccchhHHHH
Q psy4325 233 VREQLSQDTGLDMRVVQVWFQNRRAKEKR 261 (306)
Q Consensus 233 ~r~~La~~~~l~~~~V~~WFqNrR~k~k~ 261 (306)
.-+++|..+|++...|+.+...-|.+-|+
T Consensus 153 s~~eIA~~lgis~~~V~~~l~ra~~~Lr~ 181 (186)
T PRK13919 153 THREAAQLLGLPLGTLKTRARRALSRLKE 181 (186)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 35688999999999999988777766665
No 200
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=31.24 E-value=27 Score=29.15 Aligned_cols=32 Identities=19% Similarity=0.172 Sum_probs=26.6
Q ss_pred HHHHHHHHhhCCCccchhcccccchhHHHHhh
Q psy4325 232 HVREQLSQDTGLDMRVVQVWFQNRRAKEKRLK 263 (306)
Q Consensus 232 ~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~ 263 (306)
...+++|..+|++...|+++...-|.+.|+.-
T Consensus 156 ~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 187 (194)
T PRK12513 156 LELEEIAELTGVPEETVKSRLRYALQKLRELL 187 (194)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 45678999999999999999888888777643
No 201
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=31.08 E-value=35 Score=28.84 Aligned_cols=32 Identities=9% Similarity=0.119 Sum_probs=26.3
Q ss_pred HHHHHHHhhCCCccchhcccccchhHHHHhhh
Q psy4325 233 VREQLSQDTGLDMRVVQVWFQNRRAKEKRLKK 264 (306)
Q Consensus 233 ~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~ 264 (306)
..+++|..+|++...|++.....|.+-|+.-.
T Consensus 157 s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~ 188 (201)
T PRK12545 157 EIDDICTELTLTANHCSVLLYRARTRLRTCLS 188 (201)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 35689999999999999998888887776543
No 202
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=31.06 E-value=34 Score=30.17 Aligned_cols=33 Identities=9% Similarity=0.183 Sum_probs=27.4
Q ss_pred HHHHHHHhhCCCccchhcccccchhHHHHhhhh
Q psy4325 233 VREQLSQDTGLDMRVVQVWFQNRRAKEKRLKKD 265 (306)
Q Consensus 233 ~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~~ 265 (306)
..+++|..+|++...|+++...-|.+-|+.-..
T Consensus 179 S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l~~ 211 (244)
T TIGR03001 179 SMDRIGAMYQVHRSTVSRWVAQARERLLERTRR 211 (244)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 356899999999999999999988887765433
No 203
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=31.00 E-value=41 Score=27.46 Aligned_cols=31 Identities=6% Similarity=0.205 Sum_probs=24.5
Q ss_pred HHHHHHHhhCCCccchhcccccchhHHHHhh
Q psy4325 233 VREQLSQDTGLDMRVVQVWFQNRRAKEKRLK 263 (306)
Q Consensus 233 ~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~ 263 (306)
..+++|..+|++...|+++....+.+.+...
T Consensus 137 s~~EIA~~lgis~~tV~~~l~Ra~~~~~~~~ 167 (172)
T PRK09651 137 TYSEIAHKLGVSVSSVKKYVAKATEHCLLFR 167 (172)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 4678999999999999998876666655543
No 204
>PRK04023 DNA polymerase II large subunit; Validated
Probab=30.64 E-value=73 Score=33.97 Aligned_cols=54 Identities=20% Similarity=0.404 Sum_probs=37.4
Q ss_pred CCCCCCccCCCeeccceeeeecCccccccCcccCcCCCCCCCcceeeCCeeccccccccccCcCCCCCCCCCCCCC
Q psy4325 68 ASIPKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFARNGLLFCKEDFFKRFGTKCAGCEMGIPPTQ 143 (306)
Q Consensus 68 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f~~~g~~yC~~cy~~~~~~~C~~C~~~I~~~~ 143 (306)
.....|..|+... .=|+|..|+.. .....+|..|-...-...|..|+..+....
T Consensus 624 Vg~RfCpsCG~~t---------------~~frCP~CG~~-------Te~i~fCP~CG~~~~~y~CPKCG~El~~~s 677 (1121)
T PRK04023 624 IGRRKCPSCGKET---------------FYRRCPFCGTH-------TEPVYRCPRCGIEVEEDECEKCGREPTPYS 677 (1121)
T ss_pred ccCccCCCCCCcC---------------CcccCCCCCCC-------CCcceeCccccCcCCCCcCCCCCCCCCccc
Confidence 4567888888863 11688888875 233457888866665677999998886554
No 205
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=30.56 E-value=33 Score=28.66 Aligned_cols=32 Identities=9% Similarity=0.181 Sum_probs=26.4
Q ss_pred HHHHHHHhhCCCccchhcccccchhHHHHhhh
Q psy4325 233 VREQLSQDTGLDMRVVQVWFQNRRAKEKRLKK 264 (306)
Q Consensus 233 ~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~ 264 (306)
..+++|..+|++...|+.+....|.+.|+.-.
T Consensus 154 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 185 (195)
T PRK12532 154 SSDEIQQMCGISTSNYHTIMHRARESLRQCLQ 185 (195)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 35689999999999999999888888776543
No 206
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=30.53 E-value=37 Score=27.37 Aligned_cols=46 Identities=15% Similarity=0.152 Sum_probs=28.6
Q ss_pred cchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHH
Q psy4325 211 ITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261 (306)
Q Consensus 211 ~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~ 261 (306)
+++.++.++...|- .....+++|+.+|++...|+....--|.+-|+
T Consensus 123 L~~~~r~vl~l~~~-----~g~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 123 LTPKQQHVIALRFG-----QNLPIAEVARILGKTEGAVKILQFRAIKKLAR 168 (170)
T ss_pred CCHHHHHHHHHHHh-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 44455555554321 11235688999999999999876555555443
No 207
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=30.51 E-value=34 Score=28.83 Aligned_cols=31 Identities=10% Similarity=0.072 Sum_probs=25.2
Q ss_pred HHHHHHHhhCCCccchhcccccchhHHHHhh
Q psy4325 233 VREQLSQDTGLDMRVVQVWFQNRRAKEKRLK 263 (306)
Q Consensus 233 ~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~ 263 (306)
..+++|..+|++...|+++...-|.+-|+.-
T Consensus 151 s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l 181 (196)
T PRK12535 151 TYEEAAKIADVRVGTIRSRVARARADLIAAT 181 (196)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 4568999999999999999877777766543
No 208
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=30.28 E-value=35 Score=28.36 Aligned_cols=33 Identities=12% Similarity=0.092 Sum_probs=27.1
Q ss_pred HHHHHHHhhCCCccchhcccccchhHHHHhhhh
Q psy4325 233 VREQLSQDTGLDMRVVQVWFQNRRAKEKRLKKD 265 (306)
Q Consensus 233 ~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~~ 265 (306)
..+++|..+|++...|++....-|.+-|+.-..
T Consensus 149 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 181 (191)
T PRK12520 149 ETEEICQELQITATNAWVLLYRARMRLRECLDL 181 (191)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 356899999999999999998888887765443
No 209
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=30.26 E-value=41 Score=27.32 Aligned_cols=30 Identities=13% Similarity=0.126 Sum_probs=24.4
Q ss_pred HHHHHHHhhCCCccchhcccccchhHHHHh
Q psy4325 233 VREQLSQDTGLDMRVVQVWFQNRRAKEKRL 262 (306)
Q Consensus 233 ~r~~La~~~~l~~~~V~~WFqNrR~k~k~~ 262 (306)
..+++|..+|+++..|+.....-|.+-|+.
T Consensus 136 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 165 (173)
T PRK09645 136 STAQIAADLGIPEGTVKSRLHYALRALRLA 165 (173)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 356899999999999999887777766654
No 210
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=30.07 E-value=34 Score=29.49 Aligned_cols=31 Identities=10% Similarity=0.086 Sum_probs=25.9
Q ss_pred HHHHHHHhhCCCccchhcccccchhHHHHhh
Q psy4325 233 VREQLSQDTGLDMRVVQVWFQNRRAKEKRLK 263 (306)
Q Consensus 233 ~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~ 263 (306)
..+++|..+|+++..|+++...-|.+.|+.-
T Consensus 152 s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l 182 (216)
T PRK12533 152 SYREIAAIADVPVGTVMSRLARARRRLAALL 182 (216)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4568999999999999999988887777654
No 211
>KOG2462|consensus
Probab=29.82 E-value=37 Score=30.41 Aligned_cols=70 Identities=17% Similarity=0.298 Sum_probs=46.1
Q ss_pred ccCcccCcCCCCCCC-cceeeCCeeccccccccccCcCCCCCCCCCCCCCceecccCccccCCCcccccCCCCCC
Q psy4325 95 ARCLKCHECGAPLAE-KCFARNGLLFCKEDFFKRFGTKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLN 168 (306)
Q Consensus 95 ~~Cf~C~~C~~~l~~-~~f~~~g~~yC~~cy~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~CF~C~~C~~~l~ 168 (306)
...++|..|++.+.. ....+..+.-|..+- ..+-.|..|++.-+...- ..+-..-|--=+.|.+|++.|.
T Consensus 128 ~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s--~ka~~C~~C~K~YvSmpA--LkMHirTH~l~c~C~iCGKaFS 198 (279)
T KOG2462|consen 128 HPRYKCPECGKSYSTSSNLSRHKQTHRSLDS--KKAFSCKYCGKVYVSMPA--LKMHIRTHTLPCECGICGKAFS 198 (279)
T ss_pred CCceeccccccccccccccchhhcccccccc--cccccCCCCCceeeehHH--HhhHhhccCCCccccccccccc
Confidence 467899999998865 445667777777664 344589999987643211 1122223544467999999985
No 212
>PF10886 DUF2685: Protein of unknown function (DUF2685); InterPro: IPR024362 This is a family of uncharacterised bacteriophage proteins. Their function in unknown.
Probab=29.69 E-value=34 Score=22.67 Aligned_cols=12 Identities=25% Similarity=0.542 Sum_probs=6.4
Q ss_pred CCCCCCCCCCCC
Q psy4325 131 KCAGCEMGIPPT 142 (306)
Q Consensus 131 ~C~~C~~~I~~~ 142 (306)
+|..|.+||...
T Consensus 3 ~CvVCKqpi~~a 14 (54)
T PF10886_consen 3 ICVVCKQPIDDA 14 (54)
T ss_pred eeeeeCCccCcc
Confidence 455555555443
No 213
>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=29.62 E-value=32 Score=23.23 Aligned_cols=19 Identities=16% Similarity=0.354 Sum_probs=14.9
Q ss_pred HHHHhhCCCccchhccccc
Q psy4325 236 QLSQDTGLDMRVVQVWFQN 254 (306)
Q Consensus 236 ~La~~~~l~~~~V~~WFqN 254 (306)
.-|.+.|+++++|+-|-+-
T Consensus 30 Aaarkf~V~r~~Vr~W~kq 48 (58)
T PF09607_consen 30 AAARKFNVSRRQVRKWRKQ 48 (58)
T ss_dssp HHHHHTTS-HHHHHHHHTT
T ss_pred HHHHHhCccHHHHHHHHHH
Confidence 3499999999999999654
No 214
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=29.51 E-value=36 Score=28.16 Aligned_cols=30 Identities=17% Similarity=0.296 Sum_probs=24.4
Q ss_pred HHHHHHHhhCCCccchhcccccchhHHHHh
Q psy4325 233 VREQLSQDTGLDMRVVQVWFQNRRAKEKRL 262 (306)
Q Consensus 233 ~r~~La~~~~l~~~~V~~WFqNrR~k~k~~ 262 (306)
..+++|..+|+++..|++....-|.+-|+.
T Consensus 140 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 169 (185)
T PRK12542 140 TYQEISSVMGITEANVRKQFERARKRVQNM 169 (185)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 356899999999999999887777776654
No 215
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=29.42 E-value=31 Score=22.18 Aligned_cols=13 Identities=31% Similarity=0.710 Sum_probs=9.1
Q ss_pred CCCCCccCCCeec
Q psy4325 69 SIPKCGGCGDLIL 81 (306)
Q Consensus 69 ~~~~C~~C~~~I~ 81 (306)
....|..|++.|.
T Consensus 10 ~~~~C~~C~~~i~ 22 (53)
T PF00130_consen 10 KPTYCDVCGKFIW 22 (53)
T ss_dssp STEB-TTSSSBEC
T ss_pred CCCCCcccCcccC
Confidence 3458999999983
No 216
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=29.07 E-value=43 Score=28.46 Aligned_cols=31 Identities=13% Similarity=0.238 Sum_probs=25.9
Q ss_pred HHHHHHhhCCCccchhcccccchhHHHHhhh
Q psy4325 234 REQLSQDTGLDMRVVQVWFQNRRAKEKRLKK 264 (306)
Q Consensus 234 r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~ 264 (306)
.+++|+.+|+++..|+++...-|.+-|+.-.
T Consensus 157 ~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l~ 187 (203)
T PRK09647 157 YEEIAATLGVKLGTVRSRIHRGRQQLRAALA 187 (203)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 5688999999999999999888888776443
No 217
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=29.01 E-value=24 Score=25.76 Aligned_cols=28 Identities=18% Similarity=0.465 Sum_probs=16.6
Q ss_pred CCCCCCCCCCCCCceecccCccccCCCc
Q psy4325 131 KCAGCEMGIPPTQVVRRAQDLVYHLNCF 158 (306)
Q Consensus 131 ~C~~C~~~I~~~~~~~~~~~~~~H~~CF 158 (306)
.|..|..|-.+-..+.-.-+..||..|.
T Consensus 34 ~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI 61 (85)
T PF12861_consen 34 CCPDCKFPGDDCPLVWGKCSHNFHMHCI 61 (85)
T ss_pred CCCCccCCCCCCceeeccCccHHHHHHH
Confidence 4556665543333444557778888875
No 218
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=28.87 E-value=19 Score=22.84 Aligned_cols=10 Identities=30% Similarity=0.587 Sum_probs=6.3
Q ss_pred eecccccccc
Q psy4325 117 LLFCKEDFFK 126 (306)
Q Consensus 117 ~~yC~~cy~~ 126 (306)
.-+|..||.+
T Consensus 28 ~dLC~~C~~~ 37 (46)
T PF00569_consen 28 YDLCEDCFSK 37 (46)
T ss_dssp -EEEHHHHHH
T ss_pred CchhhHHHhC
Confidence 4578888754
No 219
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=28.58 E-value=39 Score=27.85 Aligned_cols=29 Identities=7% Similarity=0.164 Sum_probs=23.0
Q ss_pred HHHHHHHhhCCCccchhcccccchhHHHH
Q psy4325 233 VREQLSQDTGLDMRVVQVWFQNRRAKEKR 261 (306)
Q Consensus 233 ~r~~La~~~~l~~~~V~~WFqNrR~k~k~ 261 (306)
..+++|..+|+++..|+......+.+-+.
T Consensus 145 s~~EIA~~lgis~~tVk~~l~rAl~~~~~ 173 (178)
T PRK12529 145 KQKDIAQALDIALPTVKKYIHQAYVTCLS 173 (178)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35689999999999999988866665543
No 220
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=28.16 E-value=44 Score=27.59 Aligned_cols=30 Identities=13% Similarity=0.118 Sum_probs=24.4
Q ss_pred HHHHHHHhhCCCccchhcccccchhHHHHh
Q psy4325 233 VREQLSQDTGLDMRVVQVWFQNRRAKEKRL 262 (306)
Q Consensus 233 ~r~~La~~~~l~~~~V~~WFqNrR~k~k~~ 262 (306)
..+++|..+|++...|+.+...-|.+-|+.
T Consensus 149 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 178 (184)
T PRK12539 149 SVAEAATRSGMSESAVKVSVHRGLKALAAL 178 (184)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 467899999999999999887766666653
No 221
>KOG2893|consensus
Probab=27.95 E-value=38 Score=29.71 Aligned_cols=49 Identities=16% Similarity=0.379 Sum_probs=27.7
Q ss_pred cCCCCCCCCCCCCCceecccCccccCCCcccccCCCCCCCCCceeeccCCcccccchhH
Q psy4325 130 TKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDYE 188 (306)
Q Consensus 130 ~~C~~C~~~I~~~~~~~~~~~~~~H~~CF~C~~C~~~l~~g~~~~~~~~~~~~C~~c~~ 188 (306)
+-|..|+..+.++..+| - +-...+|+|.+|.+.|-+|- +-.+.|..-+.
T Consensus 11 pwcwycnrefddekili-q---hqkakhfkchichkkl~sgp------glsihcmqvhk 59 (341)
T KOG2893|consen 11 PWCWYCNREFDDEKILI-Q---HQKAKHFKCHICHKKLFSGP------GLSIHCMQVHK 59 (341)
T ss_pred ceeeecccccchhhhhh-h---hhhhccceeeeehhhhccCC------Cceeehhhhhh
Confidence 44666777664432222 1 12235699999999985443 33456655443
No 222
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=27.78 E-value=42 Score=27.34 Aligned_cols=29 Identities=7% Similarity=0.134 Sum_probs=23.8
Q ss_pred HHHHHHHhhCCCccchhcccccchhHHHH
Q psy4325 233 VREQLSQDTGLDMRVVQVWFQNRRAKEKR 261 (306)
Q Consensus 233 ~r~~La~~~~l~~~~V~~WFqNrR~k~k~ 261 (306)
..+++|..+|++...|+++....+.+-+.
T Consensus 137 s~~EIA~~lgis~~tV~~~l~ra~~~~~~ 165 (172)
T PRK12523 137 GHAEIAERLGVSVSRVRQYLAQGLRQCYI 165 (172)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35688999999999999998777776654
No 223
>KOG3576|consensus
Probab=27.78 E-value=4.4 Score=34.59 Aligned_cols=73 Identities=19% Similarity=0.428 Sum_probs=41.7
Q ss_pred cccccCcccCcCCCCCCCcceeeCCeeccccccccccCcCCCCCCCCCCCCCceecccCccccCCCcccccCCCCCC
Q psy4325 92 TWHARCLKCHECGAPLAEKCFARNGLLFCKEDFFKRFGTKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLN 168 (306)
Q Consensus 92 ~~H~~Cf~C~~C~~~l~~~~f~~~g~~yC~~cy~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~CF~C~~C~~~l~ 168 (306)
.--.+=|+|.+|++.++-.. ..+..+-|..+..+ -.|..|++.+.+..-+.+...-+--..=|+|..|++.++
T Consensus 112 ssd~d~ftCrvCgK~F~lQR-mlnrh~kch~~vkr---~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaft 184 (267)
T KOG3576|consen 112 SSDQDSFTCRVCGKKFGLQR-MLNRHLKCHSDVKR---HLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFT 184 (267)
T ss_pred CCCCCeeeeehhhhhhhHHH-HHHHHhhhccHHHH---HHHhhccCcccchhhhhhhhccccCccccchhhhhHHHH
Confidence 33356689999998775332 22334455555433 258899998855432211111111234578999999885
No 224
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=27.41 E-value=55 Score=27.46 Aligned_cols=30 Identities=7% Similarity=0.192 Sum_probs=23.9
Q ss_pred HHHHHHHhhCCCccchhcccccchhHHHHh
Q psy4325 233 VREQLSQDTGLDMRVVQVWFQNRRAKEKRL 262 (306)
Q Consensus 233 ~r~~La~~~~l~~~~V~~WFqNrR~k~k~~ 262 (306)
.-.++|..+|+++..|++.....|.+.|+.
T Consensus 172 s~~EIA~~lgis~~tV~~~l~rar~~Lr~~ 201 (208)
T PRK08295 172 SYQEIAEELNRHVKSIDNALQRVKRKLEKY 201 (208)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 467899999999999998777766666653
No 225
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=27.28 E-value=23 Score=30.27 Aligned_cols=30 Identities=27% Similarity=0.459 Sum_probs=21.7
Q ss_pred cccccCCCCCCCCCceeeccCCcccccchhHH
Q psy4325 158 FACVMCARQLNTGDEFYLMEDRKLVCKPDYEA 189 (306)
Q Consensus 158 F~C~~C~~~l~~g~~~~~~~~~~~~C~~c~~~ 189 (306)
-+|..|+-.+-... ..+.+|+++|.+|+..
T Consensus 173 v~C~kCGE~~~e~~--~~~~ng~~vC~~C~~~ 202 (206)
T COG2191 173 VRCSKCGELFMEPR--AVVLNGKPVCKPCAEK 202 (206)
T ss_pred eeccccCcccccch--hhhcCCceeccccccc
Confidence 46888888875433 2346899999999854
No 226
>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=27.28 E-value=40 Score=28.11 Aligned_cols=48 Identities=8% Similarity=0.090 Sum_probs=32.7
Q ss_pred cchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHhh
Q psy4325 211 ITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLK 263 (306)
Q Consensus 211 ~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~ 263 (306)
+++.+++++...|-. ....++||..+|++...|++....-|.+-|+.-
T Consensus 132 L~~~~r~v~~l~~~~-----g~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l 179 (188)
T TIGR02943 132 LPEQTARVFMMREVL-----GFESDEICQELEISTSNCHVLLYRARLSLRACL 179 (188)
T ss_pred CCHHHHHHHHHHHHh-----CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 444555555543221 224678999999999999998887777776643
No 227
>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=27.15 E-value=46 Score=28.58 Aligned_cols=47 Identities=13% Similarity=0.152 Sum_probs=33.9
Q ss_pred ccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHH
Q psy4325 210 TITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261 (306)
Q Consensus 210 ~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~ 261 (306)
.+++.++.+|...|-.. ...+++|..+|++...|+.+....+.+-|+
T Consensus 175 ~L~~~~r~il~l~y~~~-----~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~ 221 (224)
T TIGR02479 175 SLSEREQLVLSLYYYEE-----LNLKEIGEVLGLTESRVSQIHSQALKKLRA 221 (224)
T ss_pred hCCHHHHHHHHHHHhCC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 35666777776655322 246789999999999999988777766654
No 228
>PF04936 DUF658: Protein of unknown function (DUF658); InterPro: IPR007020 This entry is represented by Bacteriophage r1t, Orf18. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. These are proteins of unknown function found in Lactococcus lactis and in their associated bacteriophage.
Probab=26.75 E-value=19 Score=29.59 Aligned_cols=33 Identities=18% Similarity=0.337 Sum_probs=28.4
Q ss_pred HHHHHHHHhhCCCccchhcccccchhHHHHhhh
Q psy4325 232 HVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKK 264 (306)
Q Consensus 232 ~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~ 264 (306)
.++++|+..++++..+|-+|..|=+...++..+
T Consensus 15 gt~~e~~~~~~VS~~sv~~WiKNG~~~~~a~~~ 47 (186)
T PF04936_consen 15 GTIDELADYFDVSRTSVSVWIKNGKDPKRAKPK 47 (186)
T ss_pred ccHHHHHHHHccCHHHHHHHHHcCCCcccccch
Confidence 468899999999999999999999888775543
No 229
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=26.52 E-value=45 Score=28.63 Aligned_cols=47 Identities=9% Similarity=0.210 Sum_probs=34.1
Q ss_pred ccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHH
Q psy4325 210 TITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261 (306)
Q Consensus 210 ~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~ 261 (306)
.+++.+...+...|-. .....++|+.+|++...|..|...-+.+-|+
T Consensus 178 ~L~~~~r~vl~l~y~~-----~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~ 224 (227)
T TIGR02980 178 ALPERERRILLLRFFE-----DKTQSEIAERLGISQMHVSRLLRRALKKLRE 224 (227)
T ss_pred cCCHHHHHHHHHHHhc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4666677777665432 2257789999999999999988776666554
No 230
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=26.44 E-value=43 Score=28.01 Aligned_cols=30 Identities=10% Similarity=0.096 Sum_probs=23.7
Q ss_pred HHHHHHHhhCCCccchhcccccchhHHHHh
Q psy4325 233 VREQLSQDTGLDMRVVQVWFQNRRAKEKRL 262 (306)
Q Consensus 233 ~r~~La~~~~l~~~~V~~WFqNrR~k~k~~ 262 (306)
.-+++|..+|++...|++.....|.+-|+.
T Consensus 159 s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~ 188 (194)
T PRK12531 159 PHQQVAEMFDIPLGTVKSRLRLAVEKLRHS 188 (194)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 356899999999999998877666666653
No 231
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=26.43 E-value=58 Score=22.07 Aligned_cols=29 Identities=28% Similarity=0.528 Sum_probs=17.1
Q ss_pred CCCCccCCCeeccceeeeecCccccccCcccCcCCCCC
Q psy4325 70 IPKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPL 107 (306)
Q Consensus 70 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l 107 (306)
.+.|..|+..|...+.. --|-|-.|+..+
T Consensus 9 ~~~CtSCg~~i~p~e~~---------v~F~CPnCGe~~ 37 (61)
T COG2888 9 PPVCTSCGREIAPGETA---------VKFPCPNCGEVE 37 (61)
T ss_pred CceeccCCCEeccCCce---------eEeeCCCCCcee
Confidence 46888888888432211 126777777544
No 232
>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=26.41 E-value=32 Score=21.06 Aligned_cols=23 Identities=17% Similarity=0.348 Sum_probs=19.7
Q ss_pred HHHHHHhhCCCccchhcccccch
Q psy4325 234 REQLSQDTGLDMRVVQVWFQNRR 256 (306)
Q Consensus 234 r~~La~~~~l~~~~V~~WFqNrR 256 (306)
...+|..+|+++..|..|..+.+
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~~ 37 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGKR 37 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCCC
Confidence 45789999999999999988764
No 233
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=26.35 E-value=56 Score=27.14 Aligned_cols=30 Identities=10% Similarity=0.175 Sum_probs=23.8
Q ss_pred HHHHHHHHhhCCCccchhcccccchhHHHH
Q psy4325 232 HVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261 (306)
Q Consensus 232 ~~r~~La~~~~l~~~~V~~WFqNrR~k~k~ 261 (306)
....++|..+|++..+|++++.--|.+-|+
T Consensus 166 ~s~~eIA~~l~~s~~tV~~~l~r~r~~L~~ 195 (198)
T TIGR02859 166 KSYQEIACDLNRHVKSIDNALQRVKRKLEK 195 (198)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 346789999999999999877766666554
No 234
>PHA02929 N1R/p28-like protein; Provisional
Probab=26.33 E-value=33 Score=30.22 Aligned_cols=39 Identities=18% Similarity=0.498 Sum_probs=24.4
Q ss_pred cCCCCCCCCCCCCC------ceecccCccccCCCc--------ccccCCCCCC
Q psy4325 130 TKCAGCEMGIPPTQ------VVRRAQDLVYHLNCF--------ACVMCARQLN 168 (306)
Q Consensus 130 ~~C~~C~~~I~~~~------~~~~~~~~~~H~~CF--------~C~~C~~~l~ 168 (306)
..|..|...+...+ .++...+..||..|+ .|..|...+.
T Consensus 175 ~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~ 227 (238)
T PHA02929 175 KECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFI 227 (238)
T ss_pred CCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEee
Confidence 46788877664332 133456777777777 5777777663
No 235
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=26.26 E-value=26 Score=35.67 Aligned_cols=84 Identities=20% Similarity=0.417 Sum_probs=58.7
Q ss_pred CCCCCccCCCeeccceeeeecCccccccCcccCcCCCCCCCcceeeCCeeccccccccccCcCCCCCCCCCCCCCceecc
Q psy4325 69 SIPKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFARNGLLFCKEDFFKRFGTKCAGCEMGIPPTQVVRRA 148 (306)
Q Consensus 69 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f~~~g~~yC~~cy~~~~~~~C~~C~~~I~~~~~~~~~ 148 (306)
...+|..|-+.|.+. .++.||-.--.|..|+=.+ ......||=.......--+.|..|.+.- ...
T Consensus 100 D~a~C~~Cl~Ei~dp-----~~rrY~YPF~~CT~CGPRf----TIi~alPYDR~nTsM~~F~lC~~C~~EY------~dP 164 (750)
T COG0068 100 DAATCEDCLEEIFDP-----NSRRYLYPFINCTNCGPRF----TIIEALPYDRENTSMADFPLCPFCDKEY------KDP 164 (750)
T ss_pred chhhhHHHHHHhcCC-----CCcceeccccccCCCCcce----eeeccCCCCcccCccccCcCCHHHHHHh------cCc
Confidence 346899998877653 4788888888999998433 2555666654443333336788886533 146
Q ss_pred cCccccCCCcccccCCCCC
Q psy4325 149 QDLVYHLNCFACVMCARQL 167 (306)
Q Consensus 149 ~~~~~H~~CF~C~~C~~~l 167 (306)
.++.||..=..|..|+=.+
T Consensus 165 ~nRRfHAQp~aCp~CGP~~ 183 (750)
T COG0068 165 LNRRFHAQPIACPKCGPHL 183 (750)
T ss_pred cccccccccccCcccCCCe
Confidence 7889999988899998766
No 236
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=26.26 E-value=36 Score=22.68 Aligned_cols=33 Identities=15% Similarity=0.274 Sum_probs=23.3
Q ss_pred HhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhc
Q psy4325 214 KQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQV 250 (306)
Q Consensus 214 ~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~ 250 (306)
.|+..|+-.+. +++.+. .+||..+|+++++|+.
T Consensus 6 rq~~Ll~~L~~-~~~~~~---~ela~~l~~S~rti~~ 38 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITL---KELAKKLNISERTIKN 38 (59)
T ss_dssp HHHHHHHHHHH-HTSBBH---HHHHHHCTS-HHHHHH
T ss_pred HHHHHHHHHHc-CCCCcH---HHHHHHHCCCHHHHHH
Confidence 45666666666 666654 4899999999998874
No 237
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=26.14 E-value=31 Score=20.60 Aligned_cols=16 Identities=44% Similarity=1.209 Sum_probs=8.0
Q ss_pred CCCccCCCeeccceee
Q psy4325 71 PKCGGCGDLILDRFIL 86 (306)
Q Consensus 71 ~~C~~C~~~I~~~~~~ 86 (306)
+.|..|++++.+.++.
T Consensus 4 ~~C~eC~~~f~dSyL~ 19 (34)
T PF01286_consen 4 PKCDECGKPFMDSYLL 19 (34)
T ss_dssp EE-TTT--EES-SSCC
T ss_pred chHhHhCCHHHHHHHH
Confidence 4688888877766553
No 238
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=26.07 E-value=61 Score=27.08 Aligned_cols=32 Identities=16% Similarity=0.091 Sum_probs=23.3
Q ss_pred HHHHHHHhhCCCccchhcccccchhHHHHhhh
Q psy4325 233 VREQLSQDTGLDMRVVQVWFQNRRAKEKRLKK 264 (306)
Q Consensus 233 ~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~ 264 (306)
..++||..+|++..+|++=...-|.+.|+.-.
T Consensus 152 s~~EIA~~lg~s~~tV~~rl~rar~~Lr~~l~ 183 (192)
T PRK09643 152 SVADAARMLGVAEGTVKSRCARGRARLAELLG 183 (192)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 45688999999999998766555555555433
No 239
>PF03672 UPF0154: Uncharacterised protein family (UPF0154); InterPro: IPR005359 The proteins in this entry are functionally uncharacterised.
Probab=25.90 E-value=84 Score=21.66 Aligned_cols=35 Identities=9% Similarity=0.105 Sum_probs=28.3
Q ss_pred HHHHHhccccCCCCCHHHHHHHHHhhCCCccchhc
Q psy4325 216 LETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQV 250 (306)
Q Consensus 216 ~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~ 250 (306)
+..+++.+.+||-.+++....+..+.|-.+++-++
T Consensus 19 r~~~~k~l~~NPpine~mir~M~~QMG~kpSekqi 53 (64)
T PF03672_consen 19 RKYMEKQLKENPPINEKMIRAMMMQMGRKPSEKQI 53 (64)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHhCCCccHHHH
Confidence 45678888899999999999999999987654443
No 240
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=25.87 E-value=45 Score=28.38 Aligned_cols=30 Identities=10% Similarity=0.203 Sum_probs=25.6
Q ss_pred HHHHHHhhCCCccchhcccccchhHHHHhh
Q psy4325 234 REQLSQDTGLDMRVVQVWFQNRRAKEKRLK 263 (306)
Q Consensus 234 r~~La~~~~l~~~~V~~WFqNrR~k~k~~~ 263 (306)
..++|..+|++...|+++.+.-|.+-|+.-
T Consensus 167 ~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l 196 (206)
T PRK12544 167 TNEICHAVDLSVSNLNVLLYRARLRLRECL 196 (206)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 578999999999999999888888777643
No 241
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=25.70 E-value=51 Score=28.96 Aligned_cols=47 Identities=9% Similarity=0.172 Sum_probs=34.2
Q ss_pred ccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHH
Q psy4325 210 TITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261 (306)
Q Consensus 210 ~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~ 261 (306)
.+++.++.++...|... ....++|..+|++...|+.+....+.+-|+
T Consensus 205 ~L~~~~r~ii~l~~~~g-----~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~ 251 (255)
T TIGR02941 205 ILSEREKSIIHCTFEEN-----LSQKETGERLGISQMHVSRLQRQAISKLKE 251 (255)
T ss_pred cCCHHHHHHHHHHHcCC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 45666677776665322 235789999999999999988877777665
No 242
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=25.54 E-value=49 Score=29.11 Aligned_cols=48 Identities=6% Similarity=0.129 Sum_probs=34.1
Q ss_pred ccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHh
Q psy4325 210 TITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRL 262 (306)
Q Consensus 210 ~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~ 262 (306)
.+++.++.+|...|-.. ....++|..+|++...|+.|...-+.+-|+.
T Consensus 205 ~L~~~~r~vl~l~~~~g-----~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~ 252 (257)
T PRK08583 205 VLSDREKSIIQCTFIEN-----LSQKETGERLGISQMHVSRLQRQAIKKLREA 252 (257)
T ss_pred hCCHHHHHHHHHHHhCC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 35666666666654221 2357899999999999999988777776653
No 243
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=25.51 E-value=55 Score=30.23 Aligned_cols=54 Identities=15% Similarity=0.151 Sum_probs=38.7
Q ss_pred ccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHhhh
Q psy4325 210 TITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKK 264 (306)
Q Consensus 210 ~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~ 264 (306)
.++..++.+|...|.- .+......++||..+|++...|+.+....+.+-|+.-.
T Consensus 262 ~L~~~~R~vl~lrygL-~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l~ 315 (325)
T PRK05657 262 ELNDKQREVLARRFGL-LGYEAATLEDVAREIGLTRERVRQIQVEALRRLREILQ 315 (325)
T ss_pred cCCHHHHHHHHHHhcc-CCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 4666777777765421 11223456889999999999999999988888876544
No 244
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=25.48 E-value=35 Score=23.13 Aligned_cols=21 Identities=10% Similarity=0.219 Sum_probs=17.6
Q ss_pred HHHHHHhhCCCccchhccccc
Q psy4325 234 REQLSQDTGLDMRVVQVWFQN 254 (306)
Q Consensus 234 r~~La~~~~l~~~~V~~WFqN 254 (306)
..++|+.+|+++++++-|-+.
T Consensus 3 i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 467899999999999988653
No 245
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.18 E-value=42 Score=24.62 Aligned_cols=40 Identities=8% Similarity=0.070 Sum_probs=27.3
Q ss_pred ccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchh
Q psy4325 210 TITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQ 249 (306)
Q Consensus 210 ~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~ 249 (306)
.++.+|+..-...|+.+--...-..+++|.+|+.++..|+
T Consensus 2 SLn~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~le 41 (97)
T COG4367 2 SLNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKLE 41 (97)
T ss_pred CCCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHHH
Confidence 3556676666666655555555678889999999876543
No 246
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=25.03 E-value=46 Score=27.33 Aligned_cols=31 Identities=13% Similarity=0.147 Sum_probs=25.2
Q ss_pred HHHHHHHHhhCCCccchhcccccchhHHHHh
Q psy4325 232 HVREQLSQDTGLDMRVVQVWFQNRRAKEKRL 262 (306)
Q Consensus 232 ~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~ 262 (306)
...+++|..+|++...|+++...-|.+.|+.
T Consensus 153 ~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T PRK09641 153 LSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3467899999999999999888777776653
No 247
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=25.01 E-value=54 Score=28.81 Aligned_cols=46 Identities=13% Similarity=0.151 Sum_probs=32.3
Q ss_pred cchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHH
Q psy4325 211 ITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261 (306)
Q Consensus 211 ~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~ 261 (306)
+++.++.++...|- .....+++|..+|++...|+.++..-|.+-|+
T Consensus 202 L~~~~r~vl~l~~~-----~~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 247 (251)
T PRK07670 202 LSEKEQLVISLFYK-----EELTLTEIGQVLNLSTSRISQIHSKALFKLKK 247 (251)
T ss_pred CCHHHHHHHHHHHh-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 45555555555432 22246789999999999999988877777665
No 248
>cd02344 ZZ_HERC2 Zinc finger, ZZ type. Zinc finger present in HERC2 and related proteins. HERC2 is a potential E3 ubiquitin protein ligase and/or guanine nucleotide exchange factor. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=24.94 E-value=48 Score=21.11 Aligned_cols=11 Identities=27% Similarity=0.585 Sum_probs=7.0
Q ss_pred Ceecccccccc
Q psy4325 116 GLLFCKEDFFK 126 (306)
Q Consensus 116 g~~yC~~cy~~ 126 (306)
+.-+|..||..
T Consensus 23 dyDLC~~Cf~~ 33 (45)
T cd02344 23 DFDFCENCFKT 33 (45)
T ss_pred CccchHHhhCC
Confidence 34577777754
No 249
>PHA01976 helix-turn-helix protein
Probab=24.93 E-value=37 Score=22.88 Aligned_cols=23 Identities=17% Similarity=0.358 Sum_probs=20.1
Q ss_pred HHHHHHhhCCCccchhcccccch
Q psy4325 234 REQLSQDTGLDMRVVQVWFQNRR 256 (306)
Q Consensus 234 r~~La~~~~l~~~~V~~WFqNrR 256 (306)
..+||+.+|++...|..|-..++
T Consensus 18 ~~~lA~~~gvs~~~v~~~e~g~~ 40 (67)
T PHA01976 18 APELSRRAGVRHSLIYDFEADKR 40 (67)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 56899999999999999987765
No 250
>PRK00807 50S ribosomal protein L24e; Validated
Probab=24.49 E-value=38 Score=22.26 Aligned_cols=24 Identities=17% Similarity=0.306 Sum_probs=12.9
Q ss_pred CCCCCCCCCCCCCce--ecccCcccc
Q psy4325 131 KCAGCEMGIPPTQVV--RRAQDLVYH 154 (306)
Q Consensus 131 ~C~~C~~~I~~~~~~--~~~~~~~~H 154 (306)
.|+.|+..|.+.... +...|++|.
T Consensus 3 ~C~fcG~~I~pg~G~~~vr~Dgkv~~ 28 (52)
T PRK00807 3 TCSFCGKEIEPGTGKMYVKKDGTILY 28 (52)
T ss_pred ccCCCCCeEcCCCCeEEEEeCCcEEE
Confidence 577777777643322 234455554
No 251
>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=24.29 E-value=32 Score=23.41 Aligned_cols=20 Identities=20% Similarity=0.418 Sum_probs=17.2
Q ss_pred HHHHHHhhCCCccchhcccc
Q psy4325 234 REQLSQDTGLDMRVVQVWFQ 253 (306)
Q Consensus 234 r~~La~~~~l~~~~V~~WFq 253 (306)
..++|+.+|++++.++.|.+
T Consensus 3 i~e~A~~~gVs~~tlr~ye~ 22 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 46789999999999998854
No 252
>cd02342 ZZ_UBA_plant Zinc finger, ZZ type. Zinc finger present in plant ubiquitin-associated (UBA) proteins. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=24.25 E-value=41 Score=21.23 Aligned_cols=9 Identities=22% Similarity=0.294 Sum_probs=4.9
Q ss_pred eeccccccc
Q psy4325 117 LLFCKEDFF 125 (306)
Q Consensus 117 ~~yC~~cy~ 125 (306)
.-+|..||.
T Consensus 24 yDLC~~C~~ 32 (43)
T cd02342 24 YDLCTICFS 32 (43)
T ss_pred CccHHHHhh
Confidence 345666654
No 253
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=24.23 E-value=62 Score=26.66 Aligned_cols=36 Identities=14% Similarity=0.066 Sum_probs=31.0
Q ss_pred HhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchh
Q psy4325 214 KQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQ 249 (306)
Q Consensus 214 ~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~ 249 (306)
.-+..|+...++..|........+|..||++...|.
T Consensus 26 Alip~L~~aQ~~~G~l~~~ai~~iA~~L~i~~~~v~ 61 (160)
T COG1905 26 ALIPLLHIAQEQFGWLPPEAIEEIADMLGIPRARVY 61 (160)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHHHhCCCHHHhe
Confidence 457788888888899999999999999999987654
No 254
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=24.18 E-value=51 Score=27.35 Aligned_cols=31 Identities=10% Similarity=0.020 Sum_probs=26.0
Q ss_pred HHHHHHHhhCCCccchhcccccchhHHHHhh
Q psy4325 233 VREQLSQDTGLDMRVVQVWFQNRRAKEKRLK 263 (306)
Q Consensus 233 ~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~ 263 (306)
..+++|..+|+++..|++..+.-|.+-|+.-
T Consensus 156 s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 186 (193)
T PRK11923 156 SYEDIASVMQCPVGTVRSRIFRAREAIDKAL 186 (193)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3568999999999999999888888877643
No 255
>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=23.74 E-value=38 Score=22.81 Aligned_cols=20 Identities=15% Similarity=0.350 Sum_probs=17.3
Q ss_pred HHHHHHhhCCCccchhcccc
Q psy4325 234 REQLSQDTGLDMRVVQVWFQ 253 (306)
Q Consensus 234 r~~La~~~~l~~~~V~~WFq 253 (306)
..++|+.+|++..+++.|-+
T Consensus 3 ~~eva~~~gvs~~tlr~w~~ 22 (68)
T cd01104 3 IGAVARLTGVSPDTLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 46789999999999999864
No 256
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=23.71 E-value=53 Score=28.33 Aligned_cols=43 Identities=5% Similarity=0.169 Sum_probs=35.4
Q ss_pred HHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHH
Q psy4325 216 LETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEK 260 (306)
Q Consensus 216 ~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k 260 (306)
+.+-...|....|- ...+.||+..|++...|-.+|.|+..-..
T Consensus 19 l~aA~~lF~~~Gy~--~s~~~IA~~AGvsk~tiy~~F~sKe~L~~ 61 (225)
T PRK11552 19 IAAALAQFGEYGLH--ATTRDIAAQAGQNIAAITYYFGSKEDLYL 61 (225)
T ss_pred HHHHHHHHHHhCcc--CCHHHHHHHhCCCHHHHHHHcCCHHHHHH
Confidence 44455568888887 57889999999999999999999988654
No 257
>PRK10403 transcriptional regulator NarP; Provisional
Probab=23.64 E-value=39 Score=27.66 Aligned_cols=46 Identities=17% Similarity=0.227 Sum_probs=35.2
Q ss_pred cccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHH
Q psy4325 209 TTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEK 260 (306)
Q Consensus 209 t~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k 260 (306)
..++..+.+.|...... ..+++||+.++++++.|++...|-|.|-.
T Consensus 152 ~~Lt~~e~~vl~~~~~g------~s~~~ia~~l~~s~~tv~~~~~~i~~kl~ 197 (215)
T PRK10403 152 SVLTERELDVLHELAQG------LSNKQIASVLNISEQTVKVHIRNLLRKLN 197 (215)
T ss_pred ccCCHHHHHHHHHHHCC------CCHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence 35788888888765443 34678899999999999998888777743
No 258
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=23.61 E-value=46 Score=20.36 Aligned_cols=30 Identities=23% Similarity=0.589 Sum_probs=11.3
Q ss_pred CCCccCCCeeccceeeeecCccccccCcccCcCCC
Q psy4325 71 PKCGGCGDLILDRFILKVLERTWHARCLKCHECGA 105 (306)
Q Consensus 71 ~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~ 105 (306)
.+|..|+--|..-..+...++.| +|..|+.
T Consensus 3 ~rC~~C~aylNp~~~~~~~~~~w-----~C~~C~~ 32 (40)
T PF04810_consen 3 VRCRRCRAYLNPFCQFDDGGKTW-----ICNFCGT 32 (40)
T ss_dssp -B-TTT--BS-TTSEEETTTTEE-----EETTT--
T ss_pred cccCCCCCEECCcceEcCCCCEE-----ECcCCCC
Confidence 46777776665432222233444 5666654
No 259
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=23.40 E-value=29 Score=21.73 Aligned_cols=26 Identities=15% Similarity=0.448 Sum_probs=9.9
Q ss_pred CccCCCeeccceeee--ecCccccccCc
Q psy4325 73 CGGCGDLILDRFILK--VLERTWHARCL 98 (306)
Q Consensus 73 C~~C~~~I~~~~~~~--~~~~~~H~~Cf 98 (306)
|..|++.+.-+.... --+..||..|+
T Consensus 1 C~~C~~iv~~G~~C~~~~C~~r~H~~C~ 28 (43)
T PF08746_consen 1 CEACKEIVTQGQRCSNRDCNVRLHDDCF 28 (43)
T ss_dssp -TTT-SB-SSSEE-SS--S--EE-HHHH
T ss_pred CcccchhHeeeccCCCCccCchHHHHHH
Confidence 566777666554432 12334666553
No 260
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=23.37 E-value=36 Score=32.39 Aligned_cols=12 Identities=25% Similarity=0.509 Sum_probs=6.6
Q ss_pred CCCCccCCCeec
Q psy4325 70 IPKCGGCGDLIL 81 (306)
Q Consensus 70 ~~~C~~C~~~I~ 81 (306)
...|..|...+.
T Consensus 26 ~l~C~IC~d~~~ 37 (397)
T TIGR00599 26 SLRCHICKDFFD 37 (397)
T ss_pred ccCCCcCchhhh
Confidence 346666665543
No 261
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=23.37 E-value=40 Score=21.94 Aligned_cols=16 Identities=19% Similarity=0.380 Sum_probs=12.7
Q ss_pred HHHHHHhhCCCccchh
Q psy4325 234 REQLSQDTGLDMRVVQ 249 (306)
Q Consensus 234 r~~La~~~~l~~~~V~ 249 (306)
-.+||+.+|+++.||+
T Consensus 31 S~~La~~~gi~~~qVR 46 (50)
T PF06971_consen 31 SQELAEALGITPAQVR 46 (50)
T ss_dssp HHHHHHHHTS-HHHHH
T ss_pred HHHHHHHHCCCHHHhc
Confidence 4578999999999986
No 262
>TIGR03020 EpsA transcriptional regulator EpsA. Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.
Probab=23.28 E-value=60 Score=28.75 Aligned_cols=48 Identities=21% Similarity=0.182 Sum_probs=37.6
Q ss_pred CcccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHH
Q psy4325 208 RTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261 (306)
Q Consensus 208 rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~ 261 (306)
...+|+.+.++|....+- ....++|..|++++..|+.+.+|-+.|..-
T Consensus 188 ~~~LT~RE~evl~l~a~G------~s~~eIA~~L~IS~~TVk~hl~~i~~KL~v 235 (247)
T TIGR03020 188 AGLITAREAEILAWVRDG------KTNEEIAAILGISSLTVKNHLQHIFKKLDV 235 (247)
T ss_pred ccCCCHHHHHHHHHHHCC------CCHHHHHHHHCcCHHHHHHHHHHHHHHhCC
Confidence 457899999999875422 246678999999999999999888877553
No 263
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=23.10 E-value=58 Score=26.49 Aligned_cols=30 Identities=7% Similarity=0.131 Sum_probs=24.7
Q ss_pred HHHHHHHhhCCCccchhcccccchhHHHHh
Q psy4325 233 VREQLSQDTGLDMRVVQVWFQNRRAKEKRL 262 (306)
Q Consensus 233 ~r~~La~~~~l~~~~V~~WFqNrR~k~k~~ 262 (306)
.-+++|..+|++...|+++...-|.+-|+.
T Consensus 137 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 166 (173)
T PRK12522 137 SYKEMSEILNIPIGTVKYRLNYAKKQMREH 166 (173)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 356889999999999999888777776654
No 264
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=23.06 E-value=49 Score=28.63 Aligned_cols=34 Identities=18% Similarity=0.138 Sum_probs=27.7
Q ss_pred HHHHHHHHHhhCCCccchhcccccchhHHHHhhh
Q psy4325 231 RHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKK 264 (306)
Q Consensus 231 ~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~ 264 (306)
....+++|..+|++..+|++....-|.+.|+.-.
T Consensus 165 g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l~ 198 (231)
T PRK11922 165 ELSVEETAQALGLPEETVKTRLHRARRLLRESLA 198 (231)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 3457789999999999999988877777777554
No 265
>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=23.04 E-value=41 Score=23.38 Aligned_cols=24 Identities=17% Similarity=0.267 Sum_probs=20.8
Q ss_pred HHHHHHhhCCCccchhcccccchh
Q psy4325 234 REQLSQDTGLDMRVVQVWFQNRRA 257 (306)
Q Consensus 234 r~~La~~~~l~~~~V~~WFqNrR~ 257 (306)
...||+.+|++...|..|..+++.
T Consensus 21 ~~~lA~~~gis~~tis~~~~g~~~ 44 (78)
T TIGR02607 21 IRALAKALGVSRSTLSRIVNGRRG 44 (78)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCCC
Confidence 468999999999999999987753
No 266
>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=22.69 E-value=43 Score=26.48 Aligned_cols=33 Identities=12% Similarity=0.102 Sum_probs=26.0
Q ss_pred CCHHHHHHHHHhhCCCccchhcccccchhHHHH
Q psy4325 229 PARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261 (306)
Q Consensus 229 p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~ 261 (306)
......+++|..+|+++..|+++..-.|.+.|+
T Consensus 119 ~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 119 FKEFSYKEIAELLNLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred hccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 344467789999999999999988777766654
No 267
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=22.66 E-value=97 Score=33.93 Aligned_cols=24 Identities=21% Similarity=0.098 Sum_probs=18.1
Q ss_pred HHHhccccCCCCCHHHHHHHHHhh
Q psy4325 218 TLKMAYNTSPKPARHVREQLSQDT 241 (306)
Q Consensus 218 ~Le~~F~~~~~p~~~~r~~La~~~ 241 (306)
.|+++|...+|-+...++.|...|
T Consensus 857 LL~k~Ygl~~fYn~~~~eDLiGhL 880 (1337)
T PRK14714 857 LLEKFYGLPRFYNVEKREDLVGHL 880 (1337)
T ss_pred HHHHhhCCCcccCCCChhhcccee
Confidence 577778888888877777776555
No 268
>PF05269 Phage_CII: Bacteriophage CII protein; InterPro: IPR007933 The CII protein is a transcription activator, conserved in bacteriophage lambda and related phages, that plays a key role in the decision between lytic or lysogenic phage development. CII is regulated at multiple levels including transcription, translation initiation, mRNA stability, and proteolysis []. Conditions that stabilise cII favour lysogenic development. The lambda CII protein activates three specific promoters, binding to direct repeat sequences rather than the more usual inverted repeats. Structurally, CII is a homotetramer where each monomer is composed of four alpha helices and a disordered C terminus [, ]. The alpha helical region is responsible for DNA binding and multimerisation. The homotetramer has an unusual spatial arrangement that allows recognition of the direct repeat sequences.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1ZS4_C 1ZPQ_C 1XWR_A.
Probab=22.66 E-value=45 Score=24.73 Aligned_cols=28 Identities=14% Similarity=0.290 Sum_probs=21.5
Q ss_pred HHHHHHHHhhCCCccchhcccccchhHH
Q psy4325 232 HVREQLSQDTGLDMRVVQVWFQNRRAKE 259 (306)
Q Consensus 232 ~~r~~La~~~~l~~~~V~~WFqNrR~k~ 259 (306)
.....+|+.+|+++.+|..|..+.+.++
T Consensus 24 ~gq~~vA~~~Gv~eStISR~k~~~~~~~ 51 (91)
T PF05269_consen 24 VGQKKVAEAMGVDESTISRWKNDFIEKM 51 (91)
T ss_dssp HHHHHHHHHHTSSTTTHHHHHHHHHHHH
T ss_pred HhhHHHHHHhCCCHHHHHHHHhhHHHHH
Confidence 3456789999999999999966544443
No 269
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.61 E-value=57 Score=25.62 Aligned_cols=47 Identities=23% Similarity=0.416 Sum_probs=25.0
Q ss_pred ccccccccccCcCCCCCCCCCCCCCceec--ccCccccCCCcccccCCCCC
Q psy4325 119 FCKEDFFKRFGTKCAGCEMGIPPTQVVRR--AQDLVYHLNCFACVMCARQL 167 (306)
Q Consensus 119 yC~~cy~~~~~~~C~~C~~~I~~~~~~~~--~~~~~~H~~CF~C~~C~~~l 167 (306)
||..|-.... ..|..|+-+|.+.+.+-- ..|.-|-+--| |..|++.+
T Consensus 30 fcskcgeati-~qcp~csasirgd~~vegvlglg~dye~psf-chncgs~f 78 (160)
T COG4306 30 FCSKCGEATI-TQCPICSASIRGDYYVEGVLGLGGDYEPPSF-CHNCGSRF 78 (160)
T ss_pred HHhhhchHHH-hcCCccCCcccccceeeeeeccCCCCCCcch-hhcCCCCC
Confidence 4444433222 468889999988765422 23334444333 55555555
No 270
>PF13730 HTH_36: Helix-turn-helix domain
Probab=22.58 E-value=46 Score=21.43 Aligned_cols=22 Identities=32% Similarity=0.454 Sum_probs=17.9
Q ss_pred HHHHHHHhhCCCccchhccccc
Q psy4325 233 VREQLSQDTGLDMRVVQVWFQN 254 (306)
Q Consensus 233 ~r~~La~~~~l~~~~V~~WFqN 254 (306)
..+.||+.+|++.+.|+.+...
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~ 48 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKE 48 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHH
Confidence 4778999999999999876543
No 271
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=22.47 E-value=54 Score=26.52 Aligned_cols=46 Identities=13% Similarity=0.230 Sum_probs=34.0
Q ss_pred cccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHH
Q psy4325 209 TTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEK 260 (306)
Q Consensus 209 t~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k 260 (306)
..++..+...|... ... + ..+++|+.++++++.|+.+.+|-|.|..
T Consensus 148 ~~lt~~e~~vl~l~-~~g-~----~~~~Ia~~l~~s~~tv~~~~~~~~~kl~ 193 (211)
T PRK15369 148 PLLTPRERQILKLI-TEG-Y----TNRDIAEQLSISIKTVETHRLNMMRKLD 193 (211)
T ss_pred cCCCHHHHHHHHHH-HCC-C----CHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 34777777777663 322 2 2578899999999999999888777653
No 272
>KOG3476|consensus
Probab=22.32 E-value=4.8 Score=29.24 Aligned_cols=38 Identities=29% Similarity=0.577 Sum_probs=26.0
Q ss_pred cccCcCCCCCCCcceeeCCeeccccccccccCcCCCCCCCCCCCC
Q psy4325 98 LKCHECGAPLAEKCFARNGLLFCKEDFFKRFGTKCAGCEMGIPPT 142 (306)
Q Consensus 98 f~C~~C~~~l~~~~f~~~g~~yC~~cy~~~~~~~C~~C~~~I~~~ 142 (306)
-.|..|+..+ +..|.-||..|.+++ -+|+-|++.|...
T Consensus 55 ~kC~iCk~~v-----HQ~GshYC~tCAY~K--giCAMCGKki~nT 92 (100)
T KOG3476|consen 55 AKCRICKQLV-----HQPGSHYCQTCAYKK--GICAMCGKKILNT 92 (100)
T ss_pred chhHHHHHHh-----cCCcchhHhHhhhhh--hHHHHhhhHhhcc
Confidence 3667776543 345677999987654 4788898888543
No 273
>cd02338 ZZ_PCMF_like Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel modulatory factor 1 or FIGC has been shown to possess intrinsic E3 ubiquitin ligase activity and to promote ubiquitination.
Probab=22.26 E-value=43 Score=21.56 Aligned_cols=10 Identities=10% Similarity=0.311 Sum_probs=6.1
Q ss_pred eecccccccc
Q psy4325 117 LLFCKEDFFK 126 (306)
Q Consensus 117 ~~yC~~cy~~ 126 (306)
.-+|..||..
T Consensus 24 ~dlC~~Cf~~ 33 (49)
T cd02338 24 YDLCADCYDS 33 (49)
T ss_pred CccchhHHhC
Confidence 3467777753
No 274
>PHA02955 hypothetical protein; Provisional
Probab=22.17 E-value=66 Score=27.74 Aligned_cols=45 Identities=11% Similarity=0.125 Sum_probs=32.2
Q ss_pred HhHHHHHhccccC-CCCCHHHHHHHHHhhCCCccchhcccccchhH
Q psy4325 214 KQLETLKMAYNTS-PKPARHVREQLSQDTGLDMRVVQVWFQNRRAK 258 (306)
Q Consensus 214 ~q~~~Le~~F~~~-~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k 258 (306)
.++..|.+.|.+. .-..+++|+++|+++|+....|..||.+.-.+
T Consensus 61 ~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t~~~q 106 (213)
T PHA02955 61 KNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKTDLQL 106 (213)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccchhhh
Confidence 3455555555443 45667889999999999988789999876543
No 275
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=22.17 E-value=71 Score=28.23 Aligned_cols=49 Identities=12% Similarity=0.196 Sum_probs=35.1
Q ss_pred ccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHhh
Q psy4325 210 TITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLK 263 (306)
Q Consensus 210 ~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~ 263 (306)
.+++.+..+|...|-. .....++|..+|++...|+.+..--+.|.|+.-
T Consensus 203 ~L~~~~r~vl~l~y~~-----~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~l 251 (256)
T PRK07408 203 QLEERTREVLEFVFLH-----DLTQKEAAERLGISPVTVSRRVKKGLDQLKKLL 251 (256)
T ss_pred cCCHHHHHHHHHHHHC-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 3555666666665532 235678999999999999999887777777643
No 276
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=22.03 E-value=69 Score=27.60 Aligned_cols=46 Identities=13% Similarity=0.090 Sum_probs=35.9
Q ss_pred cccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHH
Q psy4325 209 TTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEK 260 (306)
Q Consensus 209 t~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k 260 (306)
..+|+.++++|+...+-. ...++|+.++++++.|+.+..+-..|..
T Consensus 154 ~~Lt~rE~~Vl~l~~~G~------s~~eIA~~L~iS~~TVk~~~~~i~~Kl~ 199 (216)
T PRK10100 154 ALLTHREKEILNKLRIGA------SNNEIARSLFISENTVKTHLYNLFKKIA 199 (216)
T ss_pred CCCCHHHHHHHHHHHcCC------CHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 358899999998876522 3567899999999999999887766644
No 277
>KOG3816|consensus
Probab=22.00 E-value=31 Score=32.40 Aligned_cols=49 Identities=16% Similarity=0.362 Sum_probs=30.4
Q ss_pred cccccccccCcCCCCCCCCCCCCCceeccc---C----ccccCCCcccccCCCCCC
Q psy4325 120 CKEDFFKRFGTKCAGCEMGIPPTQVVRRAQ---D----LVYHLNCFACVMCARQLN 168 (306)
Q Consensus 120 C~~cy~~~~~~~C~~C~~~I~~~~~~~~~~---~----~~~H~~CF~C~~C~~~l~ 168 (306)
|-.|.+-.....|..|.++..+...++-.+ + ..--+.=|+|..|.++|.
T Consensus 430 C~~CL~g~~sI~C~~Ck~~wDGss~vLGTmY~YDI~aa~pCC~~R~~C~~C~k~l~ 485 (526)
T KOG3816|consen 430 CARCLWGDWSIICKNCKKDWDGSSFVLGTMYYYDIVAAGPCCPVRLVCQSCRKSLG 485 (526)
T ss_pred HHHHhcccchHHHhhcCCCCCCcceeechhhhhhhhhcCCcchhhhhhhhhccccc
Confidence 566766666677999998877665443211 0 011234467888998885
No 278
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=21.95 E-value=56 Score=26.18 Aligned_cols=25 Identities=8% Similarity=0.372 Sum_probs=20.1
Q ss_pred HHHHHHhhCCCccchhcccccchhH
Q psy4325 234 REQLSQDTGLDMRVVQVWFQNRRAK 258 (306)
Q Consensus 234 r~~La~~~~l~~~~V~~WFqNrR~k 258 (306)
-+++|..+|++...|+++...-+.+
T Consensus 132 ~~EIA~~l~is~~tV~~~l~ra~~~ 156 (161)
T PRK12528 132 YGEIATELGISLATVKRYLNKAAMR 156 (161)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 5688999999999999887655544
No 279
>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=21.83 E-value=57 Score=29.24 Aligned_cols=29 Identities=10% Similarity=0.036 Sum_probs=24.7
Q ss_pred HHHHHHhhCCCccchhcccccchhHHHHh
Q psy4325 234 REQLSQDTGLDMRVVQVWFQNRRAKEKRL 262 (306)
Q Consensus 234 r~~La~~~~l~~~~V~~WFqNrR~k~k~~ 262 (306)
-+++|..+|+++..|+..++.-|.+-|..
T Consensus 127 ~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~ 155 (281)
T TIGR02957 127 YEEIASIVGKSEANCRQLVSRARRHLDAR 155 (281)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 45789999999999999998888877653
No 280
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=21.82 E-value=55 Score=26.93 Aligned_cols=29 Identities=14% Similarity=0.281 Sum_probs=23.7
Q ss_pred HHHHHHHhhCCCccchhcccccchhHHHH
Q psy4325 233 VREQLSQDTGLDMRVVQVWFQNRRAKEKR 261 (306)
Q Consensus 233 ~r~~La~~~~l~~~~V~~WFqNrR~k~k~ 261 (306)
..+++|..+|++...|+.+..--|.+-|+
T Consensus 145 s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~ 173 (179)
T PRK09415 145 SIKEIAEVTGVNENTVKTRLKKAKELLKK 173 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35689999999999999988777766665
No 281
>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=21.74 E-value=65 Score=28.02 Aligned_cols=48 Identities=15% Similarity=0.174 Sum_probs=38.1
Q ss_pred CcccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHH
Q psy4325 208 RTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261 (306)
Q Consensus 208 rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~ 261 (306)
...++..+++.|.-...- ..-.++|..+|++++.|+.+..|-+.|.+-
T Consensus 169 ~~~Lt~re~evl~~~a~G------~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~ 216 (232)
T TIGR03541 169 AGVLSEREREVLAWTALG------RRQADIAAILGISERTVENHLRSARRKLGV 216 (232)
T ss_pred hccCCHHHHHHHHHHHCC------CCHHHHHHHHCcCHHHHHHHHHHHHHHHCC
Confidence 457899999999875322 346778999999999999999998888664
No 282
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=21.73 E-value=46 Score=27.78 Aligned_cols=29 Identities=24% Similarity=0.365 Sum_probs=23.8
Q ss_pred HHHHHHHhhCCCccchhcccccchhHHHH
Q psy4325 233 VREQLSQDTGLDMRVVQVWFQNRRAKEKR 261 (306)
Q Consensus 233 ~r~~La~~~~l~~~~V~~WFqNrR~k~k~ 261 (306)
..+++|..+|++++.|+..++.-|++-++
T Consensus 153 s~~EIA~~lgiS~~tV~r~l~~aR~~l~~ 181 (185)
T PF07638_consen 153 SVEEIAERLGISERTVRRRLRRARAWLRR 181 (185)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 45689999999999999988888866554
No 283
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=21.67 E-value=79 Score=25.25 Aligned_cols=30 Identities=13% Similarity=0.200 Sum_probs=23.8
Q ss_pred HHHHHHHhhCCCccchhcccccchhHHHHh
Q psy4325 233 VREQLSQDTGLDMRVVQVWFQNRRAKEKRL 262 (306)
Q Consensus 233 ~r~~La~~~~l~~~~V~~WFqNrR~k~k~~ 262 (306)
..+++|..+|++...|++.....|.+-|+.
T Consensus 123 s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~ 152 (159)
T PRK12527 123 SHQQIAEHLGISRSLVEKHIVNAMKHCRVR 152 (159)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 356899999999999998887666666554
No 284
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=21.65 E-value=24 Score=20.02 Aligned_cols=10 Identities=40% Similarity=0.766 Sum_probs=4.1
Q ss_pred CCccCCCeec
Q psy4325 72 KCGGCGDLIL 81 (306)
Q Consensus 72 ~C~~C~~~I~ 81 (306)
.|..|+..|.
T Consensus 3 ~C~rC~~~~~ 12 (30)
T PF06827_consen 3 KCPRCWNYIE 12 (30)
T ss_dssp B-TTT--BBE
T ss_pred cCccCCCcce
Confidence 4666666654
No 285
>PF13565 HTH_32: Homeodomain-like domain
Probab=21.45 E-value=1.9e+02 Score=19.78 Aligned_cols=40 Identities=15% Similarity=0.135 Sum_probs=26.5
Q ss_pred chHhHHHHHhccccCCCCCHHHHH-HHHHhhCC----Cccchhcc
Q psy4325 212 TAKQLETLKMAYNTSPKPARHVRE-QLSQDTGL----DMRVVQVW 251 (306)
Q Consensus 212 s~~q~~~Le~~F~~~~~p~~~~r~-~La~~~~l----~~~~V~~W 251 (306)
+.++...+...+..++..+..+.. .|+.+.|. +.+.|..|
T Consensus 32 ~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~~~S~~tv~R~ 76 (77)
T PF13565_consen 32 DPEQRERIIALIEEHPRWTPREIAEYLEEEFGISVRVSRSTVYRI 76 (77)
T ss_pred cHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCCccHhHHHHh
Confidence 677768888888888766655544 57777664 55555544
No 286
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=21.24 E-value=69 Score=27.95 Aligned_cols=32 Identities=9% Similarity=0.116 Sum_probs=26.2
Q ss_pred HHHHHHHhhCCCccchhcccccchhHHHHhhh
Q psy4325 233 VREQLSQDTGLDMRVVQVWFQNRRAKEKRLKK 264 (306)
Q Consensus 233 ~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~~ 264 (306)
..+++|+.+|+++..|+++...-|.+-|+.-.
T Consensus 134 S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l~ 165 (228)
T PRK06704 134 SIADIAKVCSVSEGAVKASLFRSRNRLKTVSE 165 (228)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 35689999999999999998888887776543
No 287
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active.
Probab=21.07 E-value=87 Score=27.15 Aligned_cols=52 Identities=4% Similarity=0.142 Sum_probs=33.9
Q ss_pred ccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHh
Q psy4325 210 TITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRL 262 (306)
Q Consensus 210 ~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~ 262 (306)
.++..++.++...|-... -.....+++|+.+|++...|+++...-|.+-|+.
T Consensus 178 ~Lp~~~R~ii~L~~~l~~-~eg~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~ 229 (234)
T TIGR02835 178 KLNDREKKIMELRFGLVG-GTEKTQKEVADMLGISQSYISRLEKRILKRLKKE 229 (234)
T ss_pred hCCHHHHHHHHHHHccCC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 455666666665441000 0112467889999999999999887777776664
No 288
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=20.72 E-value=91 Score=30.73 Aligned_cols=26 Identities=19% Similarity=0.393 Sum_probs=19.0
Q ss_pred eeCCeecccccccccc-CcCCCCCCCC
Q psy4325 113 ARNGLLFCKEDFFKRF-GTKCAGCEMG 138 (306)
Q Consensus 113 ~~~g~~yC~~cy~~~~-~~~C~~C~~~ 138 (306)
..++.+.|..|-...- ...|..|+..
T Consensus 236 ~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 236 KKEGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred cCCCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 3467889998875543 4689999864
No 289
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=20.49 E-value=78 Score=26.07 Aligned_cols=29 Identities=28% Similarity=0.384 Sum_probs=22.8
Q ss_pred HHHHHHHhhCCCccchhcccccchhHHHH
Q psy4325 233 VREQLSQDTGLDMRVVQVWFQNRRAKEKR 261 (306)
Q Consensus 233 ~r~~La~~~~l~~~~V~~WFqNrR~k~k~ 261 (306)
..+++|..+|++...|++....-|.+-|+
T Consensus 155 s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 183 (187)
T PRK12534 155 TYEELAARTDTPIGTVKSWIRRGLAKLKA 183 (187)
T ss_pred CHHHHHHHhCCChhHHHHHHHHHHHHHHH
Confidence 46689999999999999877666666554
No 290
>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=20.43 E-value=91 Score=26.86 Aligned_cols=52 Identities=13% Similarity=0.223 Sum_probs=32.9
Q ss_pred cccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHH
Q psy4325 209 TTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261 (306)
Q Consensus 209 t~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~ 261 (306)
..+++.++.++...|-...+ .....+++|+.+|+++..|..+....+.+-|+
T Consensus 173 ~~L~~~~r~il~l~y~~~~~-e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~ 224 (227)
T TIGR02846 173 SVLDGREREVIEMRYGLGDG-RRKTQREIAKILGISRSYVSRIEKRALMKLYK 224 (227)
T ss_pred HhCCHHHHHHHHHHHcCCCC-CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34566677777665421000 11246789999999999998876655655554
No 291
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=20.41 E-value=61 Score=29.18 Aligned_cols=29 Identities=7% Similarity=0.080 Sum_probs=24.5
Q ss_pred HHHHHHhhCCCccchhcccccchhHHHHh
Q psy4325 234 REQLSQDTGLDMRVVQVWFQNRRAKEKRL 262 (306)
Q Consensus 234 r~~La~~~~l~~~~V~~WFqNrR~k~k~~ 262 (306)
.+++|+.+|+++..|+...+..|.+-|+.
T Consensus 134 ~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~ 162 (293)
T PRK09636 134 FDEIASTLGRSPAACRQLASRARKHVRAA 162 (293)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 45789999999999999998777777764
No 292
>PRK12495 hypothetical protein; Provisional
Probab=20.31 E-value=55 Score=28.38 Aligned_cols=10 Identities=50% Similarity=1.434 Sum_probs=5.3
Q ss_pred cccCcCCCCC
Q psy4325 98 LKCHECGAPL 107 (306)
Q Consensus 98 f~C~~C~~~l 107 (306)
+.|..|+.||
T Consensus 43 ~hC~~CG~PI 52 (226)
T PRK12495 43 AHCDECGDPI 52 (226)
T ss_pred hhcccccCcc
Confidence 4455555555
No 293
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=20.31 E-value=52 Score=19.85 Aligned_cols=23 Identities=17% Similarity=0.329 Sum_probs=19.5
Q ss_pred HHHHHHhhCCCccchhcccccch
Q psy4325 234 REQLSQDTGLDMRVVQVWFQNRR 256 (306)
Q Consensus 234 r~~La~~~~l~~~~V~~WFqNrR 256 (306)
...||+.+|++...|..|-.+++
T Consensus 13 ~~~la~~~~i~~~~i~~~~~~~~ 35 (56)
T smart00530 13 QEELAEKLGVSRSTLSRIENGKR 35 (56)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 55889999999999999987764
No 294
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=20.31 E-value=82 Score=27.24 Aligned_cols=52 Identities=12% Similarity=0.175 Sum_probs=33.1
Q ss_pred ccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHh
Q psy4325 210 TITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRL 262 (306)
Q Consensus 210 ~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~ 262 (306)
.+++.++.++...|--.. -.....+++|..+|++...|+.+-...+.+-|+.
T Consensus 175 ~Lp~~~R~i~~l~y~~~~-~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~ 226 (233)
T PRK05803 175 ILDEREKEVIEMRYGLGN-GKEKTQREIAKALGISRSYVSRIEKRALKKLFKE 226 (233)
T ss_pred hCCHHHHHHHHHHhCCCC-CCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 455666677766541100 1123467899999999999988866555555543
No 295
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=20.17 E-value=89 Score=27.16 Aligned_cols=53 Identities=15% Similarity=0.202 Sum_probs=39.2
Q ss_pred ccchHhHHHHHhccccCCCCCHHHHHHHHHhhCCCccchhcccccchhHHHHhh
Q psy4325 210 TITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLK 263 (306)
Q Consensus 210 ~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~~~l~~~~V~~WFqNrR~k~k~~~ 263 (306)
.+++.+..+|...|....+ ......++|..+|++...|+.+....+.|.|...
T Consensus 176 ~L~~~er~vl~l~ygl~~~-~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~~~ 228 (238)
T TIGR02393 176 TLTERERKVLRMRYGLLDG-RPHTLEEVGKEFNVTRERIRQIESKALRKLRHPS 228 (238)
T ss_pred hCCHHHHHHHHHHhCCCCC-CCccHHHHHHHHCCCHHHHHHHHHHHHHHHhhhH
Confidence 5677788888877732222 2235788999999999999999888888877653
No 296
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=20.09 E-value=80 Score=21.99 Aligned_cols=47 Identities=9% Similarity=0.140 Sum_probs=27.2
Q ss_pred cCcccCcCCCCCCCcceeeCCeecccccccccc---CcCCCCCCCCCCCC
Q psy4325 96 RCLKCHECGAPLAEKCFARNGLLFCKEDFFKRF---GTKCAGCEMGIPPT 142 (306)
Q Consensus 96 ~Cf~C~~C~~~l~~~~f~~~g~~yC~~cy~~~~---~~~C~~C~~~I~~~ 142 (306)
+-|.|..++..+.+-...-+|..|+..+..+-+ +..|..++.++...
T Consensus 3 ~~f~CpIt~~lM~dPVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~ 52 (73)
T PF04564_consen 3 DEFLCPITGELMRDPVILPSGHTYERSAIERWLEQNGGTDPFTRQPLSES 52 (73)
T ss_dssp GGGB-TTTSSB-SSEEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SGG
T ss_pred cccCCcCcCcHhhCceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCcc
Confidence 457888888777665556678888887664332 45677776666543
Done!