Query 008193
Match_columns 574
No_of_seqs 443 out of 1771
Neff 5.0
Searched_HMMs 46136
Date Thu Mar 28 20:40:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008193.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008193hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4299 PHD Zn-finger protein 99.9 2E-23 4.4E-28 228.0 7.5 203 146-355 150-375 (613)
2 KOG1244 Predicted transcriptio 99.6 4.4E-17 9.5E-22 163.7 0.6 191 73-294 110-330 (336)
3 PF00046 Homeobox: Homeobox do 99.6 7.9E-16 1.7E-20 121.0 5.7 55 442-496 1-55 (57)
4 KOG0843 Transcription factor E 99.6 2.2E-15 4.9E-20 144.0 6.5 63 440-503 101-163 (197)
5 KOG0842 Transcription factor t 99.6 1.2E-15 2.6E-20 157.5 5.1 64 439-502 151-214 (307)
6 KOG0488 Transcription factor B 99.6 2.9E-15 6.3E-20 156.0 6.6 74 437-511 168-241 (309)
7 KOG0487 Transcription factor A 99.6 1.8E-15 3.8E-20 156.5 4.2 65 439-504 233-297 (308)
8 KOG0489 Transcription factor z 99.5 2.8E-15 6.2E-20 152.8 4.1 65 439-504 157-221 (261)
9 KOG0493 Transcription factor E 99.5 2.2E-14 4.7E-19 143.6 7.8 55 440-494 245-299 (342)
10 KOG0485 Transcription factor N 99.5 4E-14 8.6E-19 138.8 8.8 63 439-502 102-164 (268)
11 KOG0850 Transcription factor D 99.5 1.7E-14 3.6E-19 142.7 6.0 70 438-507 119-188 (245)
12 smart00389 HOX Homeodomain. DN 99.5 2.7E-14 5.8E-19 111.3 5.7 52 443-494 2-53 (56)
13 cd00086 homeodomain Homeodomai 99.5 3.4E-14 7.5E-19 111.3 5.8 54 443-496 2-55 (59)
14 TIGR01565 homeo_ZF_HD homeobox 99.5 5.6E-14 1.2E-18 112.8 5.2 53 442-494 2-58 (58)
15 KOG0484 Transcription factor P 99.5 3E-14 6.5E-19 125.6 3.8 64 440-503 16-79 (125)
16 KOG0492 Transcription factor M 99.4 5.3E-14 1.1E-18 137.2 4.8 65 439-503 142-206 (246)
17 KOG0483 Transcription factor H 99.4 1.2E-13 2.7E-18 135.5 4.8 58 446-504 55-112 (198)
18 KOG2251 Homeobox transcription 99.4 6.6E-13 1.4E-17 130.8 6.5 64 438-501 34-97 (228)
19 KOG0848 Transcription factor C 99.3 7.6E-13 1.6E-17 133.2 2.3 61 443-503 201-261 (317)
20 KOG0494 Transcription factor C 99.3 2.6E-12 5.6E-17 128.9 5.3 60 443-502 143-202 (332)
21 COG5576 Homeodomain-containing 99.3 3.2E-12 7E-17 121.5 5.0 56 441-496 51-106 (156)
22 KOG4577 Transcription factor L 99.3 3.2E-12 6.9E-17 129.8 4.4 65 440-504 166-230 (383)
23 KOG0491 Transcription factor B 99.3 2E-12 4.3E-17 122.4 2.7 62 439-500 98-159 (194)
24 KOG3802 Transcription factor O 99.2 1.3E-11 2.8E-16 130.7 4.0 58 439-496 292-349 (398)
25 KOG0844 Transcription factor E 99.2 8.6E-12 1.9E-16 127.5 2.4 65 439-503 179-243 (408)
26 KOG0847 Transcription factor, 99.0 1.6E-10 3.5E-15 113.8 3.4 64 440-503 166-229 (288)
27 KOG0486 Transcription factor P 98.9 7.2E-10 1.6E-14 114.2 3.0 61 439-500 110-170 (351)
28 KOG0490 Transcription factor, 98.8 1.9E-09 4.1E-14 105.9 2.6 61 439-500 58-118 (235)
29 KOG0775 Transcription factor S 98.8 7.4E-09 1.6E-13 105.1 5.3 55 446-503 181-235 (304)
30 PF00628 PHD: PHD-finger; Int 98.7 2.2E-09 4.8E-14 82.8 -0.7 50 240-294 1-50 (51)
31 KOG0849 Transcription factor P 98.7 1.8E-08 3.9E-13 107.3 4.6 61 440-500 175-235 (354)
32 KOG0825 PHD Zn-finger protein 98.6 1.3E-08 2.8E-13 114.4 1.6 52 236-294 213-265 (1134)
33 PF05920 Homeobox_KN: Homeobox 98.6 2.7E-08 5.9E-13 74.4 2.3 33 462-494 7-39 (40)
34 KOG0774 Transcription factor P 98.4 1.7E-07 3.7E-12 94.8 3.6 61 442-502 189-252 (334)
35 KOG2252 CCAAT displacement pro 98.4 5.9E-07 1.3E-11 98.8 7.1 58 438-495 417-474 (558)
36 KOG1168 Transcription factor A 98.4 1.1E-07 2.4E-12 97.3 1.2 60 439-498 307-366 (385)
37 KOG1512 PHD Zn-finger protein 98.3 1.8E-07 3.9E-12 95.7 0.8 72 213-293 284-361 (381)
38 smart00249 PHD PHD zinc finger 98.3 6.6E-07 1.4E-11 66.1 3.3 47 240-292 1-47 (47)
39 KOG4323 Polycomb-like PHD Zn-f 98.1 5.6E-07 1.2E-11 98.1 0.8 60 239-299 169-228 (464)
40 KOG0955 PHD finger protein BR1 98.1 1E-06 2.2E-11 104.0 2.7 77 235-318 216-296 (1051)
41 KOG1973 Chromatin remodeling p 98.0 4E-06 8.8E-11 86.6 3.0 52 235-296 216-269 (274)
42 KOG4443 Putative transcription 97.9 4.5E-06 9.8E-11 93.4 3.0 80 213-299 40-122 (694)
43 cd04718 BAH_plant_2 BAH, or Br 97.9 4.1E-06 8.9E-11 79.2 2.2 28 265-296 1-28 (148)
44 KOG0490 Transcription factor, 97.9 1.2E-05 2.6E-10 79.1 4.0 60 437-496 149-208 (235)
45 COG5141 PHD zinc finger-contai 97.8 6.7E-06 1.5E-10 89.4 1.8 57 232-295 187-243 (669)
46 KOG0954 PHD finger protein [Ge 97.8 1.4E-05 3E-10 90.4 3.8 52 236-294 269-320 (893)
47 KOG0773 Transcription factor M 97.8 9.2E-06 2E-10 85.7 2.2 64 440-503 238-304 (342)
48 KOG1245 Chromatin remodeling c 97.8 7.7E-06 1.7E-10 99.9 1.6 55 236-297 1106-1160(1404)
49 KOG0383 Predicted helicase [Ge 97.7 8.7E-06 1.9E-10 93.1 1.0 54 233-296 42-95 (696)
50 COG5034 TNG2 Chromatin remodel 97.7 2.5E-05 5.4E-10 79.3 3.4 49 236-294 219-269 (271)
51 KOG0956 PHD finger protein AF1 97.5 3E-05 6.5E-10 87.2 1.5 50 239-294 6-56 (900)
52 KOG1246 DNA-binding protein ju 97.4 0.00015 3.3E-09 86.0 5.7 216 236-463 153-383 (904)
53 KOG0957 PHD finger protein [Ge 97.3 7.5E-05 1.6E-09 81.6 1.3 53 237-294 543-597 (707)
54 KOG1146 Homeobox protein [Gene 96.9 0.00091 2E-08 80.3 4.5 62 439-500 901-962 (1406)
55 PF13831 PHD_2: PHD-finger; PD 96.4 0.00051 1.1E-08 50.4 -1.0 35 253-293 2-36 (36)
56 PF11569 Homez: Homeodomain le 96.1 0.0048 1E-07 49.7 3.0 42 453-494 10-51 (56)
57 KOG1473 Nucleosome remodeling 96.0 0.0021 4.6E-08 76.1 0.4 68 215-294 323-390 (1414)
58 KOG3623 Homeobox transcription 94.9 0.041 9E-07 63.2 6.0 48 453-503 568-615 (1007)
59 KOG0957 PHD finger protein [Ge 94.6 0.018 3.9E-07 63.6 2.1 56 239-296 120-180 (707)
60 PF15446 zf-PHD-like: PHD/FYVE 93.3 0.046 1E-06 53.1 1.9 56 240-296 1-61 (175)
61 PF04218 CENP-B_N: CENP-B N-te 93.0 0.18 3.9E-06 39.9 4.5 48 442-494 1-48 (53)
62 KOG4443 Putative transcription 91.5 0.05 1.1E-06 62.0 -0.4 58 236-297 16-73 (694)
63 KOG3612 PHD Zn-finger protein 87.4 0.44 9.4E-06 53.6 3.0 53 233-294 55-107 (588)
64 KOG4299 PHD Zn-finger protein 86.7 0.4 8.7E-06 54.6 2.3 51 238-297 47-97 (613)
65 PF14446 Prok-RING_1: Prokaryo 83.4 0.6 1.3E-05 37.5 1.3 35 238-274 5-39 (54)
66 KOG4628 Predicted E3 ubiquitin 81.6 0.73 1.6E-05 49.7 1.5 46 239-294 230-275 (348)
67 KOG1473 Nucleosome remodeling 78.0 0.34 7.4E-06 58.3 -2.5 52 239-297 429-481 (1414)
68 KOG3623 Homeobox transcription 78.0 1.7 3.8E-05 50.6 3.1 117 436-553 621-740 (1007)
69 PF01527 HTH_Tnp_1: Transposas 77.9 1.6 3.5E-05 35.7 2.1 46 444-493 3-48 (76)
70 PF04545 Sigma70_r4: Sigma-70, 74.5 4.4 9.6E-05 30.9 3.6 43 447-494 4-46 (50)
71 PF04967 HTH_10: HTH DNA bindi 74.4 4.6 9.9E-05 32.3 3.7 40 448-487 1-42 (53)
72 KOG4323 Polycomb-like PHD Zn-f 73.9 2.4 5.1E-05 47.4 2.7 59 235-300 80-138 (464)
73 cd06171 Sigma70_r4 Sigma70, re 72.1 3.3 7.1E-05 30.2 2.3 43 447-494 10-52 (55)
74 PF12861 zf-Apc11: Anaphase-pr 71.3 1.6 3.6E-05 38.2 0.6 35 254-295 46-80 (85)
75 cd00569 HTH_Hin_like Helix-tur 71.1 10 0.00022 24.6 4.5 39 446-489 4-42 (42)
76 PF13901 DUF4206: Domain of un 64.3 5.4 0.00012 39.8 2.7 43 239-295 153-198 (202)
77 KOG0383 Predicted helicase [Ge 57.8 2.7 5.8E-05 49.2 -0.8 53 235-297 503-556 (696)
78 PF08281 Sigma70_r4_2: Sigma-7 56.9 16 0.00034 28.0 3.6 43 447-494 10-52 (54)
79 KOG1512 PHD Zn-finger protein 56.6 2.5 5.3E-05 44.5 -1.2 62 237-301 257-323 (381)
80 PF13551 HTH_29: Winged helix- 54.8 26 0.00056 30.2 5.1 48 443-490 53-109 (112)
81 PF10668 Phage_terminase: Phag 54.1 8.7 0.00019 31.6 1.8 20 470-489 24-43 (60)
82 PF11793 FANCL_C: FANCL C-term 54.0 7.2 0.00016 32.5 1.4 55 239-296 3-65 (70)
83 TIGR01206 lysW lysine biosynth 52.6 7.8 0.00017 31.2 1.3 46 240-287 4-52 (54)
84 PRK03975 tfx putative transcri 52.4 14 0.00031 35.1 3.2 48 446-500 5-52 (141)
85 KOG2932 E3 ubiquitin ligase in 52.1 9.3 0.0002 40.9 2.1 50 238-302 90-139 (389)
86 PF13936 HTH_38: Helix-turn-he 51.7 15 0.00033 27.7 2.7 41 445-490 2-42 (44)
87 KOG1632 Uncharacterized PHD Zn 51.4 8.1 0.00018 41.8 1.6 42 253-298 73-116 (345)
88 KOG1734 Predicted RING-contain 51.1 12 0.00025 39.5 2.6 59 235-300 221-284 (328)
89 PF13832 zf-HC5HC2H_2: PHD-zin 51.1 7.2 0.00016 34.5 1.0 31 238-272 55-86 (110)
90 PRK10072 putative transcriptio 50.8 23 0.0005 31.6 4.1 41 447-494 32-72 (96)
91 smart00421 HTH_LUXR helix_turn 50.0 26 0.00056 26.0 3.8 42 447-494 3-44 (58)
92 PF10367 Vps39_2: Vacuolar sor 49.9 9.8 0.00021 32.9 1.6 32 237-272 77-108 (109)
93 PRK04217 hypothetical protein; 49.7 29 0.00062 31.8 4.6 51 446-502 41-91 (110)
94 PRK06759 RNA polymerase factor 49.5 18 0.00039 33.0 3.4 43 447-494 106-148 (154)
95 KOG0827 Predicted E3 ubiquitin 48.6 3.4 7.3E-05 45.2 -1.8 56 239-303 5-62 (465)
96 TIGR03879 near_KaiC_dom probab 48.1 8.3 0.00018 32.9 0.8 36 457-492 21-56 (73)
97 PHA02955 hypothetical protein; 48.0 18 0.0004 36.7 3.4 49 446-494 56-105 (213)
98 COG3413 Predicted DNA binding 47.8 20 0.00044 35.6 3.7 41 447-487 155-197 (215)
99 PF08280 HTH_Mga: M protein tr 45.3 28 0.00061 27.8 3.5 37 450-490 5-41 (59)
100 PF15446 zf-PHD-like: PHD/FYVE 45.1 15 0.00032 36.2 2.2 24 252-276 121-144 (175)
101 PF13639 zf-RING_2: Ring finge 44.5 1.6 3.5E-05 32.5 -3.6 43 240-293 2-44 (44)
102 PF13518 HTH_28: Helix-turn-he 43.8 17 0.00036 27.3 1.9 25 470-494 14-38 (52)
103 PF13443 HTH_26: Cro/C1-type H 43.6 30 0.00065 27.1 3.4 24 470-493 12-35 (63)
104 PRK09646 RNA polymerase sigma 43.6 27 0.00058 33.7 3.7 48 447-500 142-189 (194)
105 PRK12514 RNA polymerase sigma 41.6 23 0.00049 33.5 2.8 47 447-499 129-175 (179)
106 PF13771 zf-HC5HC2H: PHD-like 40.8 13 0.00028 31.5 1.0 31 238-272 36-67 (90)
107 PRK14559 putative protein seri 40.7 24 0.00052 41.4 3.4 50 239-297 2-52 (645)
108 PRK12526 RNA polymerase sigma 40.2 36 0.00078 33.3 4.1 48 447-500 153-200 (206)
109 TIGR02937 sigma70-ECF RNA poly 40.0 28 0.0006 30.5 3.0 43 447-494 110-152 (158)
110 cd04761 HTH_MerR-SF Helix-Turn 39.8 22 0.00047 26.3 1.9 24 471-494 3-26 (49)
111 cd06170 LuxR_C_like C-terminal 39.7 33 0.00073 25.5 3.0 37 448-490 1-37 (57)
112 PF12678 zf-rbx1: RING-H2 zinc 39.7 4.7 0.0001 33.8 -1.9 47 238-293 19-73 (73)
113 COG4367 Uncharacterized protei 39.5 39 0.00085 30.1 3.7 41 447-487 2-42 (97)
114 PRK09413 IS2 repressor TnpA; R 39.5 53 0.0012 29.8 4.8 43 446-493 11-54 (121)
115 PF13730 HTH_36: Helix-turn-he 38.7 79 0.0017 24.2 5.0 41 447-490 2-47 (55)
116 KOG1844 PHD Zn-finger proteins 38.1 18 0.0004 40.3 1.9 47 243-297 90-137 (508)
117 PF00196 GerE: Bacterial regul 37.6 44 0.00095 26.2 3.4 42 447-494 3-44 (58)
118 KOG2930 SCF ubiquitin ligase, 36.9 5.9 0.00013 36.0 -1.8 38 240-277 59-96 (114)
119 PRK11924 RNA polymerase sigma 36.6 44 0.00095 30.8 3.9 43 447-494 125-167 (179)
120 PRK12512 RNA polymerase sigma 36.5 35 0.00076 32.3 3.3 47 447-499 131-177 (184)
121 PHA02929 N1R/p28-like protein; 35.8 15 0.00033 37.8 0.7 49 238-296 174-226 (238)
122 cd00093 HTH_XRE Helix-turn-hel 35.6 31 0.00067 24.5 2.2 23 471-493 15-37 (58)
123 PF01381 HTH_3: Helix-turn-hel 35.3 31 0.00067 26.2 2.2 24 471-494 12-35 (55)
124 cd01392 HTH_LacI Helix-turn-he 35.3 24 0.00052 26.6 1.6 21 473-493 2-22 (52)
125 PF13411 MerR_1: MerR HTH fami 35.0 27 0.00059 27.8 1.9 20 471-490 3-22 (69)
126 TIGR03070 couple_hipB transcri 35.0 32 0.00069 25.9 2.3 24 471-494 18-41 (58)
127 PF02796 HTH_7: Helix-turn-hel 34.9 61 0.0013 24.4 3.7 38 447-489 5-42 (45)
128 KOG1081 Transcription factor N 34.5 26 0.00056 39.5 2.3 30 236-271 87-116 (463)
129 PF07227 DUF1423: Protein of u 34.5 33 0.00072 38.4 3.0 58 241-300 131-197 (446)
130 TIGR02948 SigW_bacill RNA poly 34.2 35 0.00077 32.1 2.9 47 447-499 136-182 (187)
131 PF12824 MRP-L20: Mitochondria 34.0 73 0.0016 31.1 5.0 45 445-491 83-127 (164)
132 PRK09652 RNA polymerase sigma 33.7 40 0.00088 31.2 3.2 43 447-494 128-170 (182)
133 PF06056 Terminase_5: Putative 33.5 29 0.00062 28.1 1.8 22 469-490 14-35 (58)
134 PRK12541 RNA polymerase sigma 32.7 45 0.00099 30.8 3.3 47 447-499 112-158 (161)
135 PRK09648 RNA polymerase sigma 32.5 53 0.0011 31.3 3.8 44 446-494 138-181 (189)
136 PF13384 HTH_23: Homeodomain-l 32.3 33 0.00072 25.7 1.9 26 468-493 17-42 (50)
137 PRK09642 RNA polymerase sigma 31.5 61 0.0013 29.8 3.9 49 447-501 106-154 (160)
138 TIGR02985 Sig70_bacteroi1 RNA 31.5 44 0.00095 30.2 2.9 43 447-494 113-155 (161)
139 KOG1146 Homeobox protein [Gene 31.3 42 0.0009 42.2 3.4 62 439-500 703-764 (1406)
140 PRK12519 RNA polymerase sigma 30.9 38 0.00082 32.3 2.5 47 447-499 141-187 (194)
141 TIGR02989 Sig-70_gvs1 RNA poly 30.9 48 0.001 30.3 3.1 43 447-494 111-153 (159)
142 PF00130 C1_1: Phorbol esters/ 30.8 31 0.00068 26.4 1.6 34 238-272 11-44 (53)
143 PF08274 PhnA_Zn_Ribbon: PhnA 30.8 16 0.00035 26.1 -0.0 23 240-263 4-26 (30)
144 PRK00118 putative DNA-binding 30.1 55 0.0012 29.7 3.2 43 447-494 17-59 (104)
145 PF01214 CK_II_beta: Casein ki 29.3 27 0.00059 34.6 1.2 34 261-294 101-135 (184)
146 TIGR02999 Sig-70_X6 RNA polyme 29.1 68 0.0015 30.2 3.9 47 447-499 134-180 (183)
147 PRK05602 RNA polymerase sigma 29.1 47 0.001 31.6 2.8 48 447-500 128-175 (186)
148 COG1773 Rubredoxin [Energy pro 28.8 40 0.00086 27.4 1.9 18 279-299 32-49 (55)
149 TIGR02954 Sig70_famx3 RNA poly 28.6 65 0.0014 30.0 3.6 47 447-499 119-165 (169)
150 smart00744 RINGv The RING-vari 28.5 12 0.00027 29.1 -1.0 44 240-292 1-48 (49)
151 PRK09047 RNA polymerase factor 28.3 1E+02 0.0023 28.1 4.9 48 447-500 106-153 (161)
152 cd04762 HTH_MerR-trunc Helix-T 28.1 45 0.00097 24.0 2.0 24 471-494 3-26 (49)
153 COG5432 RAD18 RING-finger-cont 28.0 17 0.00037 38.6 -0.4 44 239-296 26-69 (391)
154 KOG0956 PHD finger protein AF1 27.6 32 0.0007 40.4 1.6 59 238-296 117-181 (900)
155 PRK06811 RNA polymerase factor 27.5 68 0.0015 30.7 3.6 43 447-494 131-173 (189)
156 PTZ00396 Casein kinase II subu 27.5 45 0.00098 34.8 2.5 34 261-294 122-156 (251)
157 PRK09644 RNA polymerase sigma 27.4 76 0.0017 29.5 3.9 48 447-500 108-155 (165)
158 PRK09639 RNA polymerase sigma 27.3 84 0.0018 29.0 4.1 47 447-500 112-158 (166)
159 PRK06986 fliA flagellar biosyn 27.3 79 0.0017 31.6 4.2 48 447-500 184-231 (236)
160 PRK12516 RNA polymerase sigma 27.1 79 0.0017 30.5 4.0 50 447-502 116-165 (187)
161 TIGR02939 RpoE_Sigma70 RNA pol 27.1 57 0.0012 30.8 3.0 48 447-500 138-185 (190)
162 PF05502 Dynactin_p62: Dynacti 26.8 33 0.00071 38.9 1.4 25 328-352 82-106 (483)
163 KOG1829 Uncharacterized conser 26.7 21 0.00046 41.2 -0.1 46 239-296 512-560 (580)
164 cd04763 HTH_MlrA-like Helix-Tu 26.4 44 0.00095 26.9 1.8 20 472-491 4-23 (68)
165 KOG1080 Histone H3 (Lys4) meth 26.3 50 0.0011 40.7 2.9 51 238-294 573-623 (1005)
166 PHA01976 helix-turn-helix prot 26.0 58 0.0013 25.8 2.4 24 471-494 18-41 (67)
167 cd04764 HTH_MlrA-like_sg1 Heli 25.9 45 0.00098 26.7 1.8 22 472-493 4-25 (67)
168 PRK12537 RNA polymerase sigma 25.9 80 0.0017 30.0 3.8 46 447-498 133-178 (182)
169 PRK12530 RNA polymerase sigma 25.9 77 0.0017 30.5 3.7 48 447-500 134-181 (189)
170 PRK12524 RNA polymerase sigma 25.8 1.4E+02 0.003 28.7 5.5 49 447-501 136-184 (196)
171 PRK15369 two component system 25.8 83 0.0018 28.7 3.7 43 446-494 148-190 (211)
172 TIGR01562 FdhE formate dehydro 25.2 53 0.0012 35.1 2.6 32 236-268 182-222 (305)
173 KOG1632 Uncharacterized PHD Zn 25.2 12 0.00027 40.4 -2.1 58 235-294 236-294 (345)
174 COG2944 Predicted transcriptio 25.0 1E+02 0.0023 28.1 4.0 41 447-494 43-83 (104)
175 PRK12546 RNA polymerase sigma 24.9 73 0.0016 30.9 3.3 48 447-500 113-160 (188)
176 smart00530 HTH_XRE Helix-turn- 24.9 67 0.0015 22.5 2.4 24 471-494 13-36 (56)
177 PRK10403 transcriptional regul 24.4 67 0.0014 29.6 2.9 43 446-494 152-194 (215)
178 TIGR02959 SigZ RNA polymerase 24.2 90 0.002 29.4 3.7 49 447-501 100-148 (170)
179 PF10078 DUF2316: Uncharacteri 24.1 49 0.0011 29.3 1.8 44 447-490 2-45 (89)
180 PF10080 DUF2318: Predicted me 24.1 30 0.00064 31.3 0.4 42 230-272 27-68 (102)
181 TIGR02983 SigE-fam_strep RNA p 24.0 83 0.0018 28.9 3.4 47 447-499 110-156 (162)
182 COG5574 PEX10 RING-finger-cont 23.9 26 0.00056 36.7 0.0 52 233-296 210-261 (271)
183 KOG1244 Predicted transcriptio 23.9 15 0.00032 38.7 -1.8 61 236-299 222-288 (336)
184 COG1905 NuoE NADH:ubiquinone o 23.8 1.1E+02 0.0024 30.0 4.2 39 448-486 23-61 (160)
185 COG5194 APC11 Component of SCF 23.5 25 0.00055 30.7 -0.1 48 239-295 32-79 (88)
186 PRK05657 RNA polymerase sigma 23.5 97 0.0021 33.1 4.2 55 447-503 262-316 (325)
187 PF11212 DUF2999: Protein of u 23.4 1.2E+02 0.0027 26.1 3.9 37 446-486 11-47 (82)
188 PF00376 MerR: MerR family reg 23.4 56 0.0012 24.1 1.7 18 472-489 3-20 (38)
189 PRK12515 RNA polymerase sigma 23.4 1E+02 0.0022 29.4 4.0 48 447-500 131-178 (189)
190 smart00109 C1 Protein kinase C 23.0 39 0.00084 24.8 0.8 34 238-273 11-44 (49)
191 TIGR02941 Sigma_B RNA polymera 22.9 1E+02 0.0022 31.2 4.0 47 447-499 205-251 (255)
192 PRK11511 DNA-binding transcrip 22.9 91 0.002 28.4 3.4 40 452-492 10-49 (127)
193 PF02724 CDC45: CDC45-like pro 22.8 1.5E+02 0.0032 34.7 5.8 38 447-484 196-236 (622)
194 TIGR02479 FliA_WhiG RNA polyme 22.8 1.1E+02 0.0024 30.2 4.2 43 447-494 175-217 (224)
195 PRK13919 putative RNA polymera 22.6 79 0.0017 29.9 3.0 48 447-500 135-182 (186)
196 PRK08301 sporulation sigma fac 22.5 98 0.0021 30.7 3.8 52 447-500 178-229 (234)
197 TIGR00570 cdk7 CDK-activating 22.5 44 0.00095 35.9 1.3 50 238-295 3-52 (309)
198 PRK03564 formate dehydrogenase 22.3 69 0.0015 34.4 2.8 32 236-268 185-224 (309)
199 KOG1952 Transcription factor N 22.2 18 0.00039 43.3 -1.7 55 238-295 191-245 (950)
200 COG5047 SEC23 Vesicle coat com 22.1 38 0.00083 39.2 0.9 33 256-296 54-86 (755)
201 TIGR02393 RpoD_Cterm RNA polym 22.1 99 0.0021 31.0 3.7 52 447-500 176-227 (238)
202 KOG0773 Transcription factor M 21.9 63 0.0014 34.3 2.4 36 462-497 118-153 (342)
203 KOG2114 Vacuolar assembly/sort 21.9 38 0.00083 40.7 0.9 41 239-295 841-881 (933)
204 PRK09637 RNA polymerase sigma 21.8 96 0.0021 29.7 3.4 48 447-500 106-153 (181)
205 PRK05988 formate dehydrogenase 21.4 1.4E+02 0.0031 28.7 4.5 36 451-486 24-59 (156)
206 PRK10360 DNA-binding transcrip 21.3 84 0.0018 29.0 2.9 42 447-494 137-178 (196)
207 PRK09651 RNA polymerase sigma 21.3 91 0.002 29.4 3.1 50 447-502 119-168 (172)
208 TIGR00270 conserved hypothetic 21.2 71 0.0015 30.8 2.4 24 471-494 85-108 (154)
209 TIGR02607 antidote_HigA addict 21.1 69 0.0015 26.1 2.0 24 471-494 21-44 (78)
210 cd01104 HTH_MlrA-CarA Helix-Tu 21.1 63 0.0014 25.6 1.7 20 471-490 3-22 (68)
211 PRK12547 RNA polymerase sigma 20.8 1.1E+02 0.0024 28.5 3.6 43 447-494 112-154 (164)
212 PF07649 C1_3: C1-like domain; 20.8 33 0.00072 23.8 0.0 29 240-271 2-30 (30)
213 PRK06930 positive control sigm 20.7 1.1E+02 0.0025 29.6 3.7 47 447-499 114-160 (170)
214 TIGR00721 tfx DNA-binding prot 20.6 1.6E+02 0.0034 28.1 4.5 43 446-494 5-47 (137)
215 TIGR01958 nuoE_fam NADH-quinon 20.5 1.5E+02 0.0033 28.0 4.4 45 450-494 16-63 (148)
216 COG2963 Transposase and inacti 20.5 1.8E+02 0.004 25.7 4.8 46 445-494 5-51 (116)
217 TIGR00686 phnA alkylphosphonat 20.4 46 0.00099 30.6 0.8 27 240-267 4-30 (109)
218 TIGR03001 Sig-70_gmx1 RNA poly 20.2 81 0.0018 32.2 2.7 51 447-503 161-211 (244)
219 PF07638 Sigma70_ECF: ECF sigm 20.2 1.4E+02 0.003 28.9 4.2 43 447-494 135-177 (185)
220 KOG4215 Hepatocyte nuclear fac 20.2 44 0.00096 36.7 0.8 29 237-266 18-46 (432)
221 PRK08583 RNA polymerase sigma 20.1 1.3E+02 0.0028 30.4 4.2 46 447-498 205-250 (257)
No 1
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=99.88 E-value=2e-23 Score=228.03 Aligned_cols=203 Identities=37% Similarity=0.621 Sum_probs=162.6
Q ss_pred cchhHHHHHHHHHHHHHHHHHHhhhHhhhhcCcccccCccc---------CCChHHHHHHHHHHhhhhhhHHHHHhhhcc
Q 008193 146 ELDEASRLQRRTRYLLIKMKLEQNLIDAYSGEGWKGHSREK---------IRPEKELQRAKKQILKCKIGIRDAIRQLDS 216 (574)
Q Consensus 146 ~~~~~~ri~~r~r~~l~~~~~eq~l~dAy~~egWk~~sreK---------~rp~~Elerak~~ilk~k~~ir~~i~~~d~ 216 (574)
.+++.-|+..+++|++..+..+++++++|+.+||++.+.++ ++|.++...+..+|+.+++.++.+.++++.
T Consensus 150 ~~p~~~r~~n~lk~~t~~~~~~~~li~~~s~e~~~a~~~~k~~~r~~~~~~~~~~~sn~tt~~i~~r~~~~~s~~~hl~t 229 (613)
T KOG4299|consen 150 EVPDSFRDKNSLKYLTSLQNDVQELIDISSTEGWKASSDEKPPGRPFELLIRPAKESNVTTKEILNRKLTYRSLPRHLET 229 (613)
T ss_pred cCCCcchhhhhhhhhhccccccccccchhcccccccCCcccCcccchhhhcCcchhhccchhhhhhhhhhhhhhhhhhhh
Confidence 56788999999999999999999999999999999999999 999999999999999999999999999988
Q ss_pred CCCCCCCcCCcccCCCCcccccc--cccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccc
Q 008193 217 LSSVGCIEGSVIATDGSVHHEHI--ICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCEC 294 (574)
Q Consensus 217 l~~~~~l~~s~l~~dg~~~~ed~--~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~ 294 (574)
....+..++..+..|+....++. ||..|++.+.+ +++||||+ |+++|||+||.|||..+.+|.|. |||+.|.+
T Consensus 230 ~s~~~t~~e~r~~~D~~~~~~~~~~fCsaCn~~~~F--~~~i~CD~-Cp~sFH~~CLePPl~~eniP~g~--W~C~ec~~ 304 (613)
T KOG4299|consen 230 ESKEGTVEEKRRERDKNISVEDIEDFCSACNGSGLF--NDIICCDG-CPRSFHQTCLEPPLEPENIPPGS--WFCPECKI 304 (613)
T ss_pred hhhhccchhhhhhhccccccCCHHHHHHHhCCcccc--ccceeecC-CchHHHHhhcCCCCCcccCCCCc--cccCCCee
Confidence 88877788888888887766665 99999998766 78899996 99999999999999999999998 99999999
Q ss_pred hhhhhhhhh--------ccCCceec--ccCc--cccccccccCCCCCCccccCCCCCCCCCCCCCCCCCcccc
Q 008193 295 KMEIIESMN--------AHIGTSFS--VNSN--WQDIFKEEAAFPDGCSALLNQEEEWPSDDSEDDDYNPERR 355 (574)
Q Consensus 295 k~~~~~~~n--------~~~g~~f~--l~~~--~~~~F~e~a~~~~g~~~~~~~~~~~psddsEDeD~dp~~~ 355 (574)
+..+.+..+ ...++.|. |+.. |...|++.....-+... +....+++++..+.+|++...
T Consensus 305 k~~in~~~~t~~~~~~~~~i~t~~~~~IDs~np~q~~lPe~i~~~~~~v~--~g~~~~~sd~~~~~pl~~~~~ 375 (613)
T KOG4299|consen 305 KSVINPKMETLSNRGTVVDIFTQFVSKIDSHNPIQKILPENISESFGGVS--RGDDGQYSDTQDEKPLDPPAL 375 (613)
T ss_pred eeecccchhhhhhccchHHHHHHHHHhhhccchhhhhCCHHHHhhccccc--cCCCCccccccCCcCCChhhh
Confidence 876554443 23333333 3333 44445443322222211 334456688888888988443
No 2
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=99.63 E-value=4.4e-17 Score=163.65 Aligned_cols=191 Identities=21% Similarity=0.352 Sum_probs=133.3
Q ss_pred CCCC-chhhhhhhccccchhh--hccccccccccccccCCCc-cccccCCCCcccCCCchhhhhhcccchhhhcccc--c
Q 008193 73 GAGD-DFARSKSISQKNLHIK--IDRKGSKNWASSKHKGKNS-ALVISKGNGEVVDGDGETKKLRKGRSKKRRKEKV--E 146 (574)
Q Consensus 73 ~~~~-~~~~~~~~~~~~~~~~--~~~~~~~~~~s~~~~~~~~-~~~~~~~~~~~~~~~~~~~k~~~r~~~k~~~~~~--~ 146 (574)
++.+ ++++++||++++|+|+ ++.+++ .+|+..+. .-+..++|.+++|.+++++||++|-+.+.++-+. .
T Consensus 110 ~~~e~~~~leAll~seglekk~s~dar~e-----eti~d~qkq~~l~~p~dle~eD~eed~pkrknrsk~ka~~v~~~~~ 184 (336)
T KOG1244|consen 110 AASEHGACLEALLRSEGLEKKHSNDAREE-----ETINDDQKQSGLIFPTDLESEDLEEDIPKRKNRSKGKATGVGILRK 184 (336)
T ss_pred CcccccHHHHHHHhcccccccCCCCCCcc-----cchhhhhhccccccCcccchhhccccccccccCCcccceeeecccc
Confidence 5556 7999999999999999 888888 67886653 4677888889999999999999999999885543 4
Q ss_pred chhHHHHHHHHHHHHHHHHHHhhhHhhhhcCcccc-cCcccCCChHHHHHHHHH--HhhhhhhHH--------------H
Q 008193 147 LDEASRLQRRTRYLLIKMKLEQNLIDAYSGEGWKG-HSREKIRPEKELQRAKKQ--ILKCKIGIR--------------D 209 (574)
Q Consensus 147 ~~~~~ri~~r~r~~l~~~~~eq~l~dAy~~egWk~-~sreK~rp~~Elerak~~--ilk~k~~ir--------------~ 209 (574)
+.+.+.+.. |++ .--|.+-+|.. +...+ +++++. +...|..|+ +
T Consensus 185 l~~ss~l~~---~~~---------d~~~~~~~~~~ge~~vk-------qr~kkd~a~Pn~YCDFclgdsr~nkkt~~pee 245 (336)
T KOG1244|consen 185 LTDSSSLED---YVC---------DTGTKQTVFAPGEAKVK-------QRVKKDIAQPNPYCDFCLGDSRENKKTGMPEE 245 (336)
T ss_pred ccccccccc---hhh---------cccccccccCcchhhHH-------HhhhcccccCCcccceeccccccccccCCchh
Confidence 444444333 222 12234444444 23333 333332 222222222 2
Q ss_pred HHh--hhccCCCCCCCcCC--ccc---CCCCcccccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCC
Q 008193 210 AIR--QLDSLSSVGCIEGS--VIA---TDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPP 282 (574)
Q Consensus 210 ~i~--~~d~l~~~~~l~~s--~l~---~dg~~~~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~ 282 (574)
++. .|....|.+||... +++ ...|.+.++.+|.+|+..+ .+++||+||. |+++||+|||.||+- ..|+
T Consensus 246 lvscsdcgrsghpsclqft~nm~~avk~yrwqcieck~csicgtse--nddqllfcdd-cdrgyhmyclsppm~--eppe 320 (336)
T KOG1244|consen 246 LVSCSDCGRSGHPSCLQFTANMIAAVKTYRWQCIECKYCSICGTSE--NDDQLLFCDD-CDRGYHMYCLSPPMV--EPPE 320 (336)
T ss_pred hcchhhcCCCCCcchhhhhHHHHHHHHhheeeeeecceeccccCcC--CCceeEeecc-cCCceeeEecCCCcC--CCCC
Confidence 222 45556777777522 222 3568899999999999875 5689999995 999999999999998 6888
Q ss_pred CCCccccCcccc
Q 008193 283 GDQGWFCKFCEC 294 (574)
Q Consensus 283 gde~W~C~~C~~ 294 (574)
|. |.|..|..
T Consensus 321 gs--wsc~KOG~ 330 (336)
T KOG1244|consen 321 GS--WSCHLCLE 330 (336)
T ss_pred Cc--hhHHHHHH
Confidence 98 99999974
No 3
>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=99.61 E-value=7.9e-16 Score=121.03 Aligned_cols=55 Identities=35% Similarity=0.600 Sum_probs=52.2
Q ss_pred CCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHH
Q 008193 442 RRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLA 496 (574)
Q Consensus 442 kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~ 496 (574)
||+|+.||++|+.+|+.+|..++||+..++++||.+|||+..||++||||+|++.
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~ 55 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKE 55 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHh
Confidence 4678999999999999999999999999999999999999999999999999943
No 4
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.57 E-value=2.2e-15 Score=144.01 Aligned_cols=63 Identities=27% Similarity=0.425 Sum_probs=56.8
Q ss_pred ccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhhhh
Q 008193 440 KIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVE 503 (574)
Q Consensus 440 ~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~~e 503 (574)
+.||.||.||++|+..||.+|+.|.|....+|.+||+.|+|++.||+|||||||++. |+...+
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~-kr~~~e 163 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKH-KRMQQE 163 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHH-HHHHHH
Confidence 457888999999999999999999999999999999999999999999999999944 444444
No 5
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.57 E-value=1.2e-15 Score=157.54 Aligned_cols=64 Identities=28% Similarity=0.429 Sum_probs=58.2
Q ss_pred cccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhhh
Q 008193 439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKV 502 (574)
Q Consensus 439 ~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~~ 502 (574)
.++||+|.-||..|+-+||+-|....|++..+|++||..|+||+.||||||||||++-+|.++.
T Consensus 151 ~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~d 214 (307)
T KOG0842|consen 151 RKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKD 214 (307)
T ss_pred ccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhh
Confidence 4677788999999999999999999999999999999999999999999999999966555544
No 6
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.56 E-value=2.9e-15 Score=156.03 Aligned_cols=74 Identities=22% Similarity=0.319 Sum_probs=66.7
Q ss_pred CccccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhhhhccccCCCC
Q 008193 437 SNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVESARQVSGS 511 (574)
Q Consensus 437 ~~~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~~e~~~~~~~~ 511 (574)
.++++|+.|+.||..|+..||..|....|++..+|.+||..|||+..||++||||||+ +||+...++.+-++.-
T Consensus 168 ~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRt-KWKrq~a~g~~~~~~~ 241 (309)
T KOG0488|consen 168 TPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRT-KWKRQTAEGGELLYQA 241 (309)
T ss_pred CCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhH-HHHHHHHhhhcccccc
Confidence 3477888999999999999999999999999999999999999999999999999999 8888888765555533
No 7
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.56 E-value=1.8e-15 Score=156.46 Aligned_cols=65 Identities=23% Similarity=0.291 Sum_probs=57.2
Q ss_pred cccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhhhhc
Q 008193 439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVES 504 (574)
Q Consensus 439 ~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~~e~ 504 (574)
.+.||+|..+|+.|+.+||..|..|.|++.+.|.+||+.|+|+++||+|||||||+ ++|+..+|.
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRM-K~KK~~re~ 297 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRM-KEKKVNREN 297 (308)
T ss_pred cccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhh-HHhhhhhhh
Confidence 45567779999999999999999999999999999999999999999999999999 444444433
No 8
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.54 E-value=2.8e-15 Score=152.79 Aligned_cols=65 Identities=20% Similarity=0.334 Sum_probs=58.0
Q ss_pred cccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhhhhc
Q 008193 439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVES 504 (574)
Q Consensus 439 ~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~~e~ 504 (574)
...||.|+.||..|+.+||..|..|.|+++.+|.+||..|.|+++||+|||||||| +||+.....
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRM-K~Kk~~k~~ 221 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRM-KWKKENKAK 221 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHH-HHHHhhccc
Confidence 34678889999999999999999999999999999999999999999999999999 555444443
No 9
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.51 E-value=2.2e-14 Score=143.63 Aligned_cols=55 Identities=24% Similarity=0.500 Sum_probs=53.4
Q ss_pred ccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193 440 KIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 494 (574)
Q Consensus 440 ~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~ 494 (574)
..||+||.||.+|++.|...|.+|.|++...|++||.+|||.+.||+|||||+|+
T Consensus 245 eeKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRA 299 (342)
T KOG0493|consen 245 EEKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRA 299 (342)
T ss_pred hhcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhh
Confidence 4578999999999999999999999999999999999999999999999999999
No 10
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.51 E-value=4e-14 Score=138.79 Aligned_cols=63 Identities=21% Similarity=0.317 Sum_probs=58.2
Q ss_pred cccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhhh
Q 008193 439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKV 502 (574)
Q Consensus 439 ~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~~ 502 (574)
-++||+||.|+..||-.||..|....|++..+|..||+.|.|++.||+|||||||. +||...+
T Consensus 102 ~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRn-KwKRq~a 164 (268)
T KOG0485|consen 102 DRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRN-KWKRQYA 164 (268)
T ss_pred cccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhH-HHHHHHh
Confidence 46788999999999999999999999999999999999999999999999999999 5565544
No 11
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.50 E-value=1.7e-14 Score=142.65 Aligned_cols=70 Identities=21% Similarity=0.304 Sum_probs=62.4
Q ss_pred ccccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhhhhcccc
Q 008193 438 NAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVESARQ 507 (574)
Q Consensus 438 ~~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~~e~~~~ 507 (574)
+++.|++||.|+.-||+.|.+.|+.+.|+--.+|.+||..|||+..||+|||||||.+-+|..+..++.+
T Consensus 119 ~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~g~~~~ 188 (245)
T KOG0850|consen 119 GKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQGSGPV 188 (245)
T ss_pred cccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhcCCCcc
Confidence 4678899999999999999999999999999999999999999999999999999997766666443333
No 12
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.50 E-value=2.7e-14 Score=111.31 Aligned_cols=52 Identities=35% Similarity=0.622 Sum_probs=50.1
Q ss_pred CCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193 443 RSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 494 (574)
Q Consensus 443 r~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~ 494 (574)
+.|+.|+++|+.+|+.+|..|+||+..++.+||.+|||+..||++||+|+|+
T Consensus 2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~ 53 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRA 53 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhh
Confidence 4567899999999999999999999999999999999999999999999998
No 13
>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=99.49 E-value=3.4e-14 Score=111.33 Aligned_cols=54 Identities=39% Similarity=0.642 Sum_probs=50.9
Q ss_pred CCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHH
Q 008193 443 RSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLA 496 (574)
Q Consensus 443 r~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~ 496 (574)
+.+..|+++|+.+||.+|..|+||+..+++.||.+|||+..||++||+|+|++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~ 55 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKL 55 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 456789999999999999999999999999999999999999999999999943
No 14
>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=99.46 E-value=5.6e-14 Score=112.81 Aligned_cols=53 Identities=15% Similarity=0.292 Sum_probs=50.8
Q ss_pred CCCccCCCHHHHHHHHHHHHhCCC----CCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193 442 RRSFHRMPPNAVEKLRQVFAENEL----PSRIVKENLSKELSLEPEKVNKWFKNARY 494 (574)
Q Consensus 442 kr~r~r~t~~Q~~~Le~~F~~~~y----Ps~~~r~~LA~~LgL~~~qV~vWFQNrR~ 494 (574)
||.||.||++|++.||.+|..++| |+...|++||.+|||++++|+|||||-++
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k~ 58 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNKK 58 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCCC
Confidence 678899999999999999999999 99999999999999999999999999753
No 15
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.46 E-value=3e-14 Score=125.62 Aligned_cols=64 Identities=27% Similarity=0.466 Sum_probs=57.3
Q ss_pred ccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhhhh
Q 008193 440 KIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVE 503 (574)
Q Consensus 440 ~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~~e 503 (574)
+.||-|+.||..|+.+||.+|.+..||+.-+|++||..+.|++-.|+|||||||++-.|+.++.
T Consensus 16 KQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a 79 (125)
T KOG0484|consen 16 KQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAA 79 (125)
T ss_pred HhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHH
Confidence 4567789999999999999999999999999999999999999999999999999555555443
No 16
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.45 E-value=5.3e-14 Score=137.16 Aligned_cols=65 Identities=23% Similarity=0.338 Sum_probs=59.7
Q ss_pred cccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhhhh
Q 008193 439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVE 503 (574)
Q Consensus 439 ~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~~e 503 (574)
...|++|+.||.+|+..||..|.+..|++..+|.+++..|.|++.||+|||||||++++|-..+|
T Consensus 142 k~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae 206 (246)
T KOG0492|consen 142 KPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAE 206 (246)
T ss_pred CCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHH
Confidence 45678999999999999999999999999999999999999999999999999999777666553
No 17
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.41 E-value=1.2e-13 Score=135.47 Aligned_cols=58 Identities=31% Similarity=0.539 Sum_probs=55.0
Q ss_pred cCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhhhhc
Q 008193 446 HRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVES 504 (574)
Q Consensus 446 ~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~~e~ 504 (574)
.||+.+|+..||..|..+.|+++.+|..||++|||.++||.|||||||+ +||.+..|.
T Consensus 55 ~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRA-RwK~kqlE~ 112 (198)
T KOG0483|consen 55 RRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRA-RWKTKQLEK 112 (198)
T ss_pred ccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccc-cccchhhhh
Confidence 5899999999999999999999999999999999999999999999999 888887764
No 18
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.37 E-value=6.6e-13 Score=130.84 Aligned_cols=64 Identities=28% Similarity=0.494 Sum_probs=58.0
Q ss_pred ccccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhh
Q 008193 438 NAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK 501 (574)
Q Consensus 438 ~~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~ 501 (574)
+.+.||-||.|+-.|+++||..|.++.||+...|++||.+|+|++.+|+|||.|||++..++.+
T Consensus 34 pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~ 97 (228)
T KOG2251|consen 34 PRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQ 97 (228)
T ss_pred chhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhh
Confidence 4567888999999999999999999999999999999999999999999999999995444444
No 19
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.30 E-value=7.6e-13 Score=133.22 Aligned_cols=61 Identities=21% Similarity=0.246 Sum_probs=54.4
Q ss_pred CCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhhhh
Q 008193 443 RSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVE 503 (574)
Q Consensus 443 r~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~~e 503 (574)
|=|..+|+.|.-+||..|-.++|++..++-+||..|||++|||+|||||||++..|..+..
T Consensus 201 KYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk 261 (317)
T KOG0848|consen 201 KYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKK 261 (317)
T ss_pred ceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHH
Confidence 4467899999999999999999999999999999999999999999999999655544443
No 20
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.28 E-value=2.6e-12 Score=128.85 Aligned_cols=60 Identities=23% Similarity=0.373 Sum_probs=54.0
Q ss_pred CCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhhh
Q 008193 443 RSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKV 502 (574)
Q Consensus 443 r~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~~ 502 (574)
+-||.||..|+++||.+|.+-.||+-.-|+.||-.|.|++..|+|||||||++..|..+.
T Consensus 143 h~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~ 202 (332)
T KOG0494|consen 143 HFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKR 202 (332)
T ss_pred cccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhh
Confidence 348999999999999999999999999999999999999999999999999944444444
No 21
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.27 E-value=3.2e-12 Score=121.49 Aligned_cols=56 Identities=29% Similarity=0.427 Sum_probs=51.9
Q ss_pred cCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHH
Q 008193 441 IRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLA 496 (574)
Q Consensus 441 ~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~ 496 (574)
.+++|+|.|..|+.+|++.|..+|||+...|..||..|||+++-|++||||+|+..
T Consensus 51 ~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~ 106 (156)
T COG5576 51 PKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKE 106 (156)
T ss_pred CcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHH
Confidence 34556889999999999999999999999999999999999999999999999933
No 22
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.26 E-value=3.2e-12 Score=129.77 Aligned_cols=65 Identities=28% Similarity=0.452 Sum_probs=60.1
Q ss_pred ccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhhhhc
Q 008193 440 KIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVES 504 (574)
Q Consensus 440 ~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~~e~ 504 (574)
..||+||.||..|++.|..+|...|.|.+.+|++||.++||+.++|||||||||++.+|-++..+
T Consensus 166 ~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAG 230 (383)
T KOG4577|consen 166 SNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAG 230 (383)
T ss_pred ccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcc
Confidence 45789999999999999999999999999999999999999999999999999997777666554
No 23
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.26 E-value=2e-12 Score=122.38 Aligned_cols=62 Identities=23% Similarity=0.373 Sum_probs=56.6
Q ss_pred cccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhh
Q 008193 439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR 500 (574)
Q Consensus 439 ~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~ 500 (574)
-++++.|+.|+..|+..||..|+...|++..+|++||..|+|++.||++||||||++.+|.-
T Consensus 98 ~~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~ 159 (194)
T KOG0491|consen 98 CRRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQ 159 (194)
T ss_pred HHhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHH
Confidence 45677889999999999999999999999999999999999999999999999999554443
No 24
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=99.17 E-value=1.3e-11 Score=130.66 Aligned_cols=58 Identities=26% Similarity=0.378 Sum_probs=55.2
Q ss_pred cccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHH
Q 008193 439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLA 496 (574)
Q Consensus 439 ~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~ 496 (574)
.|+||+||.|...+..+||.+|..|+.|+.+++.+||.+|+|+.++|+|||+|||++.
T Consensus 292 ~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQke 349 (398)
T KOG3802|consen 292 SRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKE 349 (398)
T ss_pred ccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeecccccc
Confidence 4778889999999999999999999999999999999999999999999999999943
No 25
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.17 E-value=8.6e-12 Score=127.47 Aligned_cols=65 Identities=22% Similarity=0.362 Sum_probs=58.7
Q ss_pred cccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhhhh
Q 008193 439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVE 503 (574)
Q Consensus 439 ~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~~e 503 (574)
..-||=||.||.+||..||..|....|.++.+|-+||.+|+|++..|+|||||||++-+|+|-+.
T Consensus 179 dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRlam 243 (408)
T KOG0844|consen 179 DQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLAM 243 (408)
T ss_pred HHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhhc
Confidence 34567789999999999999999999999999999999999999999999999999777766553
No 26
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.01 E-value=1.6e-10 Score=113.84 Aligned_cols=64 Identities=20% Similarity=0.340 Sum_probs=55.3
Q ss_pred ccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhhhh
Q 008193 440 KIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVE 503 (574)
Q Consensus 440 ~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~~e 503 (574)
+++-.|..|+-.||..||..|....||-..+|.+||..|||++.||+|||||||++..|+..+|
T Consensus 166 ~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAaE 229 (288)
T KOG0847|consen 166 QRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAAE 229 (288)
T ss_pred cccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhccc
Confidence 4455666799999999999999999999999999999999999999999999999444444444
No 27
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=98.89 E-value=7.2e-10 Score=114.16 Aligned_cols=61 Identities=26% Similarity=0.468 Sum_probs=56.0
Q ss_pred cccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhh
Q 008193 439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR 500 (574)
Q Consensus 439 ~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~ 500 (574)
.+.||.|+-|+.+|+++||.+|..|.||+-.+|++||--++|++..|.|||.|||+ +||+|
T Consensus 110 ~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrra-kwrkr 170 (351)
T KOG0486|consen 110 SKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRA-KWRKR 170 (351)
T ss_pred hhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchh-hhhhh
Confidence 35678889999999999999999999999999999999999999999999999999 44444
No 28
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=98.80 E-value=1.9e-09 Score=105.90 Aligned_cols=61 Identities=21% Similarity=0.324 Sum_probs=55.4
Q ss_pred cccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhh
Q 008193 439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR 500 (574)
Q Consensus 439 ~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~ 500 (574)
.+.++.|+.|+..|+++||.+|..++||+...|+.||..++|++..|+|||||||+ ++++.
T Consensus 58 ~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrra-k~r~~ 118 (235)
T KOG0490|consen 58 FSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRA-KDRKE 118 (235)
T ss_pred ccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcH-hhhhh
Confidence 45577889999999999999999999999999999999999999999999999999 44433
No 29
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=98.76 E-value=7.4e-09 Score=105.14 Aligned_cols=55 Identities=27% Similarity=0.428 Sum_probs=49.6
Q ss_pred cCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhhhh
Q 008193 446 HRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVE 503 (574)
Q Consensus 446 ~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~~e 503 (574)
+.|.+.-...|..||..|+||+..++.+||+.+||+..||-+||.|||+ |.|.++
T Consensus 181 yCFKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQ---RDRa~~ 235 (304)
T KOG0775|consen 181 YCFKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQ---RDRAAA 235 (304)
T ss_pred eehhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhh---hhhhcc
Confidence 4567777899999999999999999999999999999999999999999 666443
No 30
>PF00628 PHD: PHD-finger; InterPro: IPR019787 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 the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=98.69 E-value=2.2e-09 Score=82.83 Aligned_cols=50 Identities=42% Similarity=1.097 Sum_probs=41.3
Q ss_pred cccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccc
Q 008193 240 ICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCEC 294 (574)
Q Consensus 240 ~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~ 294 (574)
+|.+|+..+ +++.||.||. |..+||+.|++|++....++.+. |+|+.|..
T Consensus 1 ~C~vC~~~~--~~~~~i~C~~-C~~~~H~~C~~~~~~~~~~~~~~--w~C~~C~~ 50 (51)
T PF00628_consen 1 YCPVCGQSD--DDGDMIQCDS-CNRWYHQECVGPPEKAEEIPSGD--WYCPNCRP 50 (51)
T ss_dssp EBTTTTSSC--TTSSEEEBST-TSCEEETTTSTSSHSHHSHHSSS--BSSHHHHH
T ss_pred eCcCCCCcC--CCCCeEEcCC-CChhhCcccCCCChhhccCCCCc--EECcCCcC
Confidence 588999843 5689999995 99999999999998754555555 99999974
No 31
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=98.65 E-value=1.8e-08 Score=107.32 Aligned_cols=61 Identities=28% Similarity=0.461 Sum_probs=54.9
Q ss_pred ccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhh
Q 008193 440 KIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR 500 (574)
Q Consensus 440 ~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~ 500 (574)
..+|.|+.|+.+|+..||.+|..++||+...|++||+++||++..|+|||+|||++..|..
T Consensus 175 ~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 175 GGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred cccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence 3445579999999999999999999999999999999999999999999999999554444
No 32
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=98.60 E-value=1.3e-08 Score=114.42 Aligned_cols=52 Identities=37% Similarity=1.049 Sum_probs=44.9
Q ss_pred cccccccccccCCCCCCCCccccCCCcCCc-ccccccCCCCCCCCCCCCCCccccCcccc
Q 008193 236 HEHIICAKCKLREAFPDNDIVLCDGTCNCA-FHQKCLDPPLDTESIPPGDQGWFCKFCEC 294 (574)
Q Consensus 236 ~ed~~C~vC~~~~~~~~g~lLlCDg~C~ra-fH~~Cl~PPL~~~~iP~gde~W~C~~C~~ 294 (574)
.+..-|.+|...+ ..+.||+||+ |+.+ ||+|||+|+|- ++|.+. |||+.|.-
T Consensus 213 ~E~~~C~IC~~~D--pEdVLLLCDs-CN~~~YH~YCLDPdl~--eiP~~e--WYC~NC~d 265 (1134)
T KOG0825|consen 213 QEEVKCDICTVHD--PEDVLLLCDS-CNKVYYHVYCLDPDLS--ESPVNE--WYCTNCSL 265 (1134)
T ss_pred cccccceeeccCC--hHHhheeecc-cccceeeccccCcccc--cccccc--eecCcchh
Confidence 3456799999986 4578999996 9999 99999999998 799988 99999974
No 33
>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=98.58 E-value=2.7e-08 Score=74.41 Aligned_cols=33 Identities=39% Similarity=0.681 Sum_probs=28.9
Q ss_pred hCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193 462 ENELPSRIVKENLSKELSLEPEKVNKWFKNARY 494 (574)
Q Consensus 462 ~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~ 494 (574)
.||||+.+++++||.++||+..||.+||-|.|.
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRr 39 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARR 39 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHc
Confidence 589999999999999999999999999999997
No 34
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=98.40 E-value=1.7e-07 Score=94.75 Aligned_cols=61 Identities=31% Similarity=0.428 Sum_probs=54.7
Q ss_pred CCCccCCCHHHHHHHHHHHH---hCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhhh
Q 008193 442 RRSFHRMPPNAVEKLRQVFA---ENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKV 502 (574)
Q Consensus 442 kr~r~r~t~~Q~~~Le~~F~---~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~~ 502 (574)
+|+|..|+....++|..+|- .||||+.+.+++||++.|++..||.+||-|+|.+.+|+...
T Consensus 189 rRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~k 252 (334)
T KOG0774|consen 189 RRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMGK 252 (334)
T ss_pred HHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhhh
Confidence 45567899999999999995 58999999999999999999999999999999977776543
No 35
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=98.37 E-value=5.9e-07 Score=98.83 Aligned_cols=58 Identities=29% Similarity=0.401 Sum_probs=54.7
Q ss_pred ccccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccH
Q 008193 438 NAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYL 495 (574)
Q Consensus 438 ~~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~ 495 (574)
....||+|+.||+.|...|..+|.++++|+.+..+.||.+|||..+.|.+||-|.|.|
T Consensus 417 ~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRR 474 (558)
T KOG2252|consen 417 MLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRR 474 (558)
T ss_pred cccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhh
Confidence 3456889999999999999999999999999999999999999999999999999993
No 36
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=98.36 E-value=1.1e-07 Score=97.28 Aligned_cols=60 Identities=22% Similarity=0.306 Sum_probs=55.3
Q ss_pred cccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHH
Q 008193 439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK 498 (574)
Q Consensus 439 ~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k 498 (574)
..+||+||.|-.-....||++|...|-|+.+....||..|.|-..+|+|||+|.|++.+|
T Consensus 307 ~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKR 366 (385)
T KOG1168|consen 307 GEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKR 366 (385)
T ss_pred cccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHH
Confidence 456778899999999999999999999999999999999999999999999999995544
No 37
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=98.29 E-value=1.8e-07 Score=95.70 Aligned_cols=72 Identities=21% Similarity=0.499 Sum_probs=57.4
Q ss_pred hhccCCCCCCCc-----CCcccCCCCcccccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCcc
Q 008193 213 QLDSLSSVGCIE-----GSVIATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGW 287 (574)
Q Consensus 213 ~~d~l~~~~~l~-----~s~l~~dg~~~~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W 287 (574)
.|...+|..|++ ..++....|.+.++..|.+|+++.. +.+||+|| .|+++||.+|++ |. .+|.|. |
T Consensus 284 ~C~~~~HP~Ci~M~~elv~~~KTY~W~C~~C~lC~IC~~P~~--E~E~~FCD-~CDRG~HT~CVG--L~--~lP~G~--W 354 (381)
T KOG1512|consen 284 PCATRPHPYCVAMIPELVGQYKTYFWKCSSCELCRICLGPVI--ESEHLFCD-VCDRGPHTLCVG--LQ--DLPRGE--W 354 (381)
T ss_pred ccccCCCCcchhcCHHHHhHHhhcchhhcccHhhhccCCccc--chheeccc-cccCCCCccccc--cc--cccCcc--c
Confidence 455667777765 3344456789999999999999863 58999999 699999999999 55 799999 9
Q ss_pred ccC-ccc
Q 008193 288 FCK-FCE 293 (574)
Q Consensus 288 ~C~-~C~ 293 (574)
.|. .|.
T Consensus 355 ICD~~C~ 361 (381)
T KOG1512|consen 355 ICDMRCR 361 (381)
T ss_pred hhhhHHH
Confidence 997 454
No 38
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=98.15 E-value=5.6e-07 Score=98.07 Aligned_cols=60 Identities=25% Similarity=0.584 Sum_probs=49.5
Q ss_pred ccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccchhhhh
Q 008193 239 IICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKMEII 299 (574)
Q Consensus 239 ~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k~~~~ 299 (574)
..|.||..+.....+.||.|++ |..+||+.|+.|++..+..-+-...|||..|...+..+
T Consensus 169 ~qc~vC~~g~~~~~NrmlqC~~-C~~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~~~~~~ 228 (464)
T KOG4323|consen 169 LQCSVCYCGGPGAGNRMLQCDK-CRQWYHQACHQPLIKDELAGDPFYEWFCDVCNRGPKKV 228 (464)
T ss_pred ceeeeeecCCcCccceeeeecc-cccHHHHHhccCCCCHhhccCccceEeehhhccchhhc
Confidence 4499999887777899999997 99999999999999865555544469999998876543
No 40
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=98.13 E-value=1e-06 Score=103.96 Aligned_cols=77 Identities=31% Similarity=0.640 Sum_probs=56.7
Q ss_pred ccccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccchhh----hhhhhhccCCcee
Q 008193 235 HHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKME----IIESMNAHIGTSF 310 (574)
Q Consensus 235 ~~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k~~----~~~~~n~~~g~~f 310 (574)
.+++.+|.+|..+++..-+.||+||+ |+.++|+.|++-| .+|+|. |+|..|..... |....+....+.-
T Consensus 216 ~~~D~~C~iC~~~~~~n~n~ivfCD~-Cnl~VHq~Cygi~----~ipeg~--WlCr~Cl~s~~~~v~c~~cp~~~gAFkq 288 (1051)
T KOG0955|consen 216 LEEDAVCCICLDGECQNSNVIVFCDG-CNLAVHQECYGIP----FIPEGQ--WLCRRCLQSPQRPVRCLLCPSKGGAFKQ 288 (1051)
T ss_pred cCCCccceeecccccCCCceEEEcCC-CcchhhhhccCCC----CCCCCc--EeehhhccCcCcccceEeccCCCCccee
Confidence 35678999999998877789999996 9999999999944 588998 99999987543 3333333333333
Q ss_pred cccCcccc
Q 008193 311 SVNSNWQD 318 (574)
Q Consensus 311 ~l~~~~~~ 318 (574)
+++-.|..
T Consensus 289 t~dgrw~H 296 (1051)
T KOG0955|consen 289 TDDGRWAH 296 (1051)
T ss_pred ccCCceee
Confidence 45455543
No 41
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=97.96 E-value=4e-06 Score=86.61 Aligned_cols=52 Identities=27% Similarity=0.703 Sum_probs=38.3
Q ss_pred ccccccccccccCCCCCCCCccccCC-CcC-CcccccccCCCCCCCCCCCCCCccccCcccchh
Q 008193 235 HHEHIICAKCKLREAFPDNDIVLCDG-TCN-CAFHQKCLDPPLDTESIPPGDQGWFCKFCECKM 296 (574)
Q Consensus 235 ~~ed~~C~vC~~~~~~~~g~lLlCDg-~C~-rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k~ 296 (574)
.++-.+|..+... -|.||.||+ .|+ .|||+.|++ |. ..|.|. |||+.|....
T Consensus 216 ~~e~~yC~Cnqvs----yg~Mi~CDn~~C~~eWFH~~CVG--L~--~~Pkgk--WyC~~C~~~~ 269 (274)
T KOG1973|consen 216 PDEPTYCICNQVS----YGKMIGCDNPGCPIEWFHFTCVG--LK--TKPKGK--WYCPRCKAEN 269 (274)
T ss_pred CCCCEEEEecccc----cccccccCCCCCCcceEEEeccc--cc--cCCCCc--ccchhhhhhh
Confidence 3445566444222 399999994 499 899999999 44 578888 9999998644
No 42
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=97.94 E-value=4.5e-06 Score=93.42 Aligned_cols=80 Identities=23% Similarity=0.571 Sum_probs=62.4
Q ss_pred hhccCCCCCCCc---CCcccCCCCcccccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCcccc
Q 008193 213 QLDSLSSVGCIE---GSVIATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFC 289 (574)
Q Consensus 213 ~~d~l~~~~~l~---~s~l~~dg~~~~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C 289 (574)
.|..++|..|+. .......+|.+..+.+|..|+.+. ++..+++|++ |+-.||.||..|+++ .||.|. |+|
T Consensus 40 ~c~~~yH~~cvt~~~~~~~l~~gWrC~~crvCe~c~~~g--D~~kf~~Ck~-cDvsyh~yc~~P~~~--~v~sg~--~~c 112 (694)
T KOG4443|consen 40 DCGQKYHPYCVTSWAQHAVLSGGWRCPSCRVCEACGTTG--DPKKFLLCKR-CDVSYHCYCQKPPND--KVPSGP--WLC 112 (694)
T ss_pred hhcccCCcchhhHHHhHHHhcCCcccCCceeeeeccccC--Cccccccccc-ccccccccccCCccc--cccCcc--ccc
Confidence 455666666654 111123568899999999999653 6688999996 999999999999999 799998 999
Q ss_pred Ccccchhhhh
Q 008193 290 KFCECKMEII 299 (574)
Q Consensus 290 ~~C~~k~~~~ 299 (574)
+.|...+.|-
T Consensus 113 kk~~~c~qc~ 122 (694)
T KOG4443|consen 113 KKCTRCRQCD 122 (694)
T ss_pred HHHHhhhhcc
Confidence 9998766543
No 43
>cd04718 BAH_plant_2 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=97.93 E-value=4.1e-06 Score=79.20 Aligned_cols=28 Identities=54% Similarity=1.351 Sum_probs=25.8
Q ss_pred cccccccCCCCCCCCCCCCCCccccCcccchh
Q 008193 265 AFHQKCLDPPLDTESIPPGDQGWFCKFCECKM 296 (574)
Q Consensus 265 afH~~Cl~PPL~~~~iP~gde~W~C~~C~~k~ 296 (574)
+||++||+|||. .+|+|+ |+||.|..+.
T Consensus 1 g~H~~CL~Ppl~--~~P~g~--W~Cp~C~~~~ 28 (148)
T cd04718 1 GFHLCCLRPPLK--EVPEGD--WICPFCEVEK 28 (148)
T ss_pred CcccccCCCCCC--CCCCCC--cCCCCCcCCC
Confidence 699999999998 899999 9999999764
No 44
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.85 E-value=1.2e-05 Score=79.06 Aligned_cols=60 Identities=32% Similarity=0.442 Sum_probs=55.4
Q ss_pred CccccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHH
Q 008193 437 SNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLA 496 (574)
Q Consensus 437 ~~~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~ 496 (574)
...+.++.++.|+..|+..|...|..++||+...+++|+..+|+++..|++||||+|+..
T Consensus 149 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~ 208 (235)
T KOG0490|consen 149 SNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKL 208 (235)
T ss_pred CccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHH
Confidence 345667888999999999999999999999999999999999999999999999999933
No 45
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=97.82 E-value=6.7e-06 Score=89.36 Aligned_cols=57 Identities=33% Similarity=0.732 Sum_probs=48.3
Q ss_pred CCcccccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccch
Q 008193 232 GSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECK 295 (574)
Q Consensus 232 g~~~~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k 295 (574)
+..+.-++.|.+|...++...+.||+||| |+-+.|+.|++.+ -+|+|- |+|..|...
T Consensus 187 ~~~d~~d~~C~~c~~t~~eN~naiVfCdg-C~i~VHq~CYGI~----f~peG~--WlCrkCi~~ 243 (669)
T COG5141 187 EPSDEFDDICTKCTSTHNENSNAIVFCDG-CEICVHQSCYGIQ----FLPEGF--WLCRKCIYG 243 (669)
T ss_pred CCchhhhhhhHhccccccCCcceEEEecC-cchhhhhhcccce----ecCcch--hhhhhhccc
Confidence 33345678999999998776788999997 9999999999987 589998 999999753
No 46
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=97.80 E-value=1.4e-05 Score=90.41 Aligned_cols=52 Identities=35% Similarity=0.919 Sum_probs=46.1
Q ss_pred cccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccc
Q 008193 236 HEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCEC 294 (574)
Q Consensus 236 ~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~ 294 (574)
.++.+|.||..+++...++||+||. |+...|+.|++. . .+|+|. |+|..|.-
T Consensus 269 dedviCDvCrspD~e~~neMVfCd~-Cn~cVHqaCyGI--l--e~p~gp--WlCr~Cal 320 (893)
T KOG0954|consen 269 DEDVICDVCRSPDSEEANEMVFCDK-CNICVHQACYGI--L--EVPEGP--WLCRTCAL 320 (893)
T ss_pred cccceeceecCCCccccceeEEecc-chhHHHHhhhce--e--ecCCCC--eeehhccc
Confidence 3678999999999888899999995 999999999994 3 699987 99999964
No 47
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=97.79 E-value=9.2e-06 Score=85.74 Aligned_cols=64 Identities=33% Similarity=0.364 Sum_probs=57.1
Q ss_pred ccCCCccCCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhhhh
Q 008193 440 KIRRSFHRMPPNAVEKLRQVFAE---NELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVE 503 (574)
Q Consensus 440 ~~kr~r~r~t~~Q~~~Le~~F~~---~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~~e 503 (574)
..+|++..|+...+.+|+.|+.+ +|||+..++..||+++||+..||.+||.|.|.+.|+....+
T Consensus 238 ~~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~~~~ 304 (342)
T KOG0773|consen 238 SKWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPMIEE 304 (342)
T ss_pred CCCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCchHHH
Confidence 35566779999999999999876 58999999999999999999999999999999888877654
No 48
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=97.78 E-value=7.7e-06 Score=99.86 Aligned_cols=55 Identities=38% Similarity=1.001 Sum_probs=48.3
Q ss_pred cccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccchhh
Q 008193 236 HEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKME 297 (574)
Q Consensus 236 ~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k~~ 297 (574)
.....|.+|.... .+..|++|++ |..+||++|+.|.+. .+|.|+ |+|+.|+....
T Consensus 1106 ~~~~~c~~cr~k~--~~~~m~lc~~-c~~~~h~~C~rp~~~--~~~~~d--W~C~~c~~e~~ 1160 (1404)
T KOG1245|consen 1106 AVNALCKVCRRKK--QDEKMLLCDE-CLSGFHLFCLRPALS--SVPPGD--WMCPSCRKEHR 1160 (1404)
T ss_pred cchhhhhhhhhcc--cchhhhhhHh-hhhhHHHHhhhhhhc--cCCcCC--ccCCccchhhh
Confidence 3468999999974 4578999996 999999999999998 799999 99999997765
No 49
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=97.74 E-value=8.7e-06 Score=93.06 Aligned_cols=54 Identities=35% Similarity=0.858 Sum_probs=47.6
Q ss_pred CcccccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccchh
Q 008193 233 SVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKM 296 (574)
Q Consensus 233 ~~~~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k~ 296 (574)
+...+..+|.+|+.+ +.+|+|| +|+.+||.+|++||+. .+|.++ |.|+.|.+..
T Consensus 42 ~~~~~~e~c~ic~~~-----g~~l~c~-tC~~s~h~~cl~~pl~--~~p~~~--~~c~Rc~~p~ 95 (696)
T KOG0383|consen 42 WDDAEQEACRICADG-----GELLWCD-TCPASFHASCLGPPLT--PQPNGE--FICPRCFCPK 95 (696)
T ss_pred cchhhhhhhhhhcCC-----CcEEEec-cccHHHHHHccCCCCC--cCCccc--eeeeeeccCC
Confidence 556777899999987 8999999 6999999999999998 799888 9999996544
No 50
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=97.69 E-value=2.5e-05 Score=79.27 Aligned_cols=49 Identities=33% Similarity=0.868 Sum_probs=39.0
Q ss_pred cccccccccccCCCCCCCCccccCC-CcCC-cccccccCCCCCCCCCCCCCCccccCcccc
Q 008193 236 HEHIICAKCKLREAFPDNDIVLCDG-TCNC-AFHQKCLDPPLDTESIPPGDQGWFCKFCEC 294 (574)
Q Consensus 236 ~ed~~C~vC~~~~~~~~g~lLlCDg-~C~r-afH~~Cl~PPL~~~~iP~gde~W~C~~C~~ 294 (574)
++..+| .|+..- =|+||-||+ .|.+ |||+-|++ |. ..|.|- |||+.|..
T Consensus 219 ~e~lYC-fCqqvS---yGqMVaCDn~nCkrEWFH~~CVG--Lk--~pPKG~--WYC~eCk~ 269 (271)
T COG5034 219 GEELYC-FCQQVS---YGQMVACDNANCKREWFHLECVG--LK--EPPKGK--WYCPECKK 269 (271)
T ss_pred CceeEE-Eecccc---cccceecCCCCCchhheeccccc--cC--CCCCCc--EeCHHhHh
Confidence 344556 687763 299999998 7986 89999999 44 688898 99999964
No 51
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=97.54 E-value=3e-05 Score=87.19 Aligned_cols=50 Identities=38% Similarity=0.959 Sum_probs=42.7
Q ss_pred ccccccccCCCCCCCCccccCC-CcCCcccccccCCCCCCCCCCCCCCccccCcccc
Q 008193 239 IICAKCKLREAFPDNDIVLCDG-TCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCEC 294 (574)
Q Consensus 239 ~~C~vC~~~~~~~~g~lLlCDg-~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~ 294 (574)
.-|+||.....-.++.||.||| .|.-+.||.|++.. .||.|. |||..|..
T Consensus 6 GGCCVCSDErGWaeNPLVYCDG~nCsVAVHQaCYGIv----qVPtGp--WfCrKCes 56 (900)
T KOG0956|consen 6 GGCCVCSDERGWAENPLVYCDGHNCSVAVHQACYGIV----QVPTGP--WFCRKCES 56 (900)
T ss_pred cceeeecCcCCCccCceeeecCCCceeeeehhcceeE----ecCCCc--hhhhhhhh
Confidence 4599998854445799999998 89999999999965 799998 99999954
No 52
>KOG1246 consensus DNA-binding protein jumonji/RBP2/SMCY, contains JmjC domain [General function prediction only]
Probab=97.43 E-value=0.00015 Score=85.96 Aligned_cols=216 Identities=20% Similarity=0.229 Sum_probs=142.4
Q ss_pred cccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccchhhhhhhhhccCCceecccCc
Q 008193 236 HEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKMEIIESMNAHIGTSFSVNSN 315 (574)
Q Consensus 236 ~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k~~~~~~~n~~~g~~f~l~~~ 315 (574)
.....|..|..+... ..+ +|++ |...||.+|..|++. .+|.++ |.|+.|..-... .....+|+.......
T Consensus 153 ~~~~~~~~~~k~~~~--~~~-~~~~-~~~~~~~~~~~~~~~--~~~~~~--~~~~~~~~~~~~--~~~~~~gf~~~~~~y 222 (904)
T KOG1246|consen 153 IDYPQCNTCSKGKEE--KLL-LCDS-CDDSYHTYCLRPPLT--RVPDGD--WRCPKCIPTPES--KPNYKFGFEQGSREY 222 (904)
T ss_pred ccchhhhccccCCCc--cce-eccc-ccCcccccccCCCCC--cCCcCc--ccCCcccccccC--CcccccCcCCCCCcc
Confidence 344679999987532 345 9996 999999999999998 799998 999999876221 112344555555555
Q ss_pred cccccccccCCCCCCccccCCCCCCCCCCCCCCCCCcccccCCcccCCCCCCCCCCCCCCCCCCCCCcCC-----ccccc
Q 008193 316 WQDIFKEEAAFPDGCSALLNQEEEWPSDDSEDDDYNPERRENSCSISRAGTDDDPSSSTSLSWFSDSETF-----SESMS 390 (574)
Q Consensus 316 ~~~~F~e~a~~~~g~~~~~~~~~~~psddsEDeD~dp~~~~~s~s~~~~G~dd~~s~S~s~S~Spn~e~~-----s~~~S 390 (574)
-...|...+......|+.......-..++.|-+.|+..........+.+|.+.. ...-+++.|..... ..+.+
T Consensus 223 t~~~f~~~~~~~~~~~~~~~~~~~~~~~~vE~e~w~~v~~~~~~~~~~~g~d~~--~~~~~s~~~~~~~~~~~~~~~~~y 300 (904)
T KOG1246|consen 223 TLPKFEEYADNFKKDYFPKSKNSPDSTEDVEKEFWRLVASNLESVEVLYGADLS--TKEFGSGFPKSASGPLLGSEAEKY 300 (904)
T ss_pred ccchhhhHhhhhhccccccccCCCCchHHHHHHHHHhhcccccceeeeeccchh--hccccccccccCCCCCCCcchhhh
Confidence 567777777777777765432221113477778888776665545556775433 33333344443333 35799
Q ss_pred cCCCCCccccccccccc----cccccchh---hccccccCCchhhhhhhccCCC---ccccCCCccCCCHHHHHHHHHHH
Q 008193 391 EDEDWGPAKRRRKEKES----DAVNSLMT---LYGSEEKYSKVKTAEVKKKLPS---NAKIRRSFHRMPPNAVEKLRQVF 460 (574)
Q Consensus 391 dDeDwgp~~RrrRe~eS----d~~~~~m~---~~es~~gs~~~~~~~~~~~~~~---~~~~kr~r~r~t~~Q~~~Le~~F 460 (574)
-+..|+.+...+....- +....+|+ +|.++..+...++-+....++- .-...+.++.++....++||.+-
T Consensus 301 ~~s~wnL~~i~~~~~svl~~~~~di~g~~~p~l~~gm~fs~~~wh~ed~~~~slny~h~g~pk~wy~v~~~~ae~~e~~~ 380 (904)
T KOG1246|consen 301 SNSGWNLNNIPRLEGSVLSHIDTDISGVTVPWLYIGMCFSTFCWHVEDHSLYSLNYLHLGEPKTWYSVPGSAAEKFEKAM 380 (904)
T ss_pred ccCcccccccccCCccccccccCCcCccccccccccccccccccccCCccccccchhhcCCceEEEecCcchHHHHHHHH
Confidence 99999999998644331 11123332 4888888888888776554443 23556788999999999999776
Q ss_pred HhC
Q 008193 461 AEN 463 (574)
Q Consensus 461 ~~~ 463 (574)
...
T Consensus 381 ~~~ 383 (904)
T KOG1246|consen 381 NKL 383 (904)
T ss_pred Hhh
Confidence 543
No 53
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=97.32 E-value=7.5e-05 Score=81.57 Aligned_cols=53 Identities=34% Similarity=0.852 Sum_probs=42.9
Q ss_pred ccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCC--CCccccCcccc
Q 008193 237 EHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPG--DQGWFCKFCEC 294 (574)
Q Consensus 237 ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~g--de~W~C~~C~~ 294 (574)
....|.+|.... +-.-++.|| +|...||+-||+|||+ .+|.. +.+|.|..|..
T Consensus 543 ~~ysCgiCkks~--dQHll~~CD-tC~lhYHlGCL~PPLT--R~Pkk~kn~gWqCsECdk 597 (707)
T KOG0957|consen 543 MNYSCGICKKST--DQHLLTQCD-TCHLHYHLGCLSPPLT--RLPKKNKNFGWQCSECDK 597 (707)
T ss_pred cceeeeeeccch--hhHHHhhcc-hhhceeeccccCCccc--cCcccccCcceeeccccc
Confidence 346799999873 345688899 7999999999999999 67753 45899999943
No 54
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=96.86 E-value=0.00091 Score=80.31 Aligned_cols=62 Identities=19% Similarity=0.282 Sum_probs=56.5
Q ss_pred cccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhh
Q 008193 439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR 500 (574)
Q Consensus 439 ~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~ 500 (574)
-.+++.|++++..|+..|..+|....||..++.+.|...++|+.+.|.+||||.|.+.+|..
T Consensus 901 ~~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~ 962 (1406)
T KOG1146|consen 901 MGRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAK 962 (1406)
T ss_pred hhhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhh
Confidence 35677889999999999999999999999999999999999999999999999999555444
No 55
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=96.43 E-value=0.00051 Score=50.43 Aligned_cols=35 Identities=46% Similarity=1.187 Sum_probs=19.6
Q ss_pred CCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCccc
Q 008193 253 NDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCE 293 (574)
Q Consensus 253 g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~ 293 (574)
+.||.|++ |.-.+|+.|++-. .+|.++ .|+|..|.
T Consensus 2 n~ll~C~~-C~v~VH~~CYGv~----~~~~~~-~W~C~~C~ 36 (36)
T PF13831_consen 2 NPLLFCDN-CNVAVHQSCYGVS----EVPDGD-DWLCDRCE 36 (36)
T ss_dssp CEEEE-SS-S--EEEHHHHT-S----S--SS------HHH-
T ss_pred CceEEeCC-CCCcCChhhCCcc----cCCCCC-cEECCcCC
Confidence 67999996 9999999999965 456652 29999884
No 56
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.12 E-value=0.0048 Score=49.67 Aligned_cols=42 Identities=12% Similarity=0.295 Sum_probs=32.1
Q ss_pred HHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193 453 VEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 494 (574)
Q Consensus 453 ~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~ 494 (574)
++-|+..|..+.++...+-..|..+.+|+..||+.||--++.
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 567999999999999999999999999999999999987765
No 57
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=95.97 E-value=0.0021 Score=76.07 Aligned_cols=68 Identities=22% Similarity=0.520 Sum_probs=50.8
Q ss_pred ccCCCCCCCcCCcccCCCCcccccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccc
Q 008193 215 DSLSSVGCIEGSVIATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCEC 294 (574)
Q Consensus 215 d~l~~~~~l~~s~l~~dg~~~~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~ 294 (574)
|.+....++++.+..+. ...-++.|.+|... ++++||. +|++.||+-|+.||+. .+|... |-|-.|..
T Consensus 323 Dq~l~~~s~R~e~~se~--~~~~ddhcrf~~d~-----~~~lc~E-t~prvvhlEcv~hP~~--~~~s~~--~e~evc~~ 390 (1414)
T KOG1473|consen 323 DQFLTVNSLRDEIDSEG--EIEYDDHCRFCHDL-----GDLLCCE-TCPRVVHLECVFHPRF--AVPSAF--WECEVCNI 390 (1414)
T ss_pred HHHHHHHHHHHHHhccc--ceeecccccccCcc-----cceeecc-cCCceEEeeecCCccc--cCCCcc--chhhhhhh
Confidence 34444444544443322 23446789999876 8999999 6999999999999998 789888 99999973
No 58
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=94.91 E-value=0.041 Score=63.22 Aligned_cols=48 Identities=25% Similarity=0.419 Sum_probs=44.2
Q ss_pred HHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhhhh
Q 008193 453 VEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVE 503 (574)
Q Consensus 453 ~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~~e 503 (574)
+..|..+|..|.+|+..+-..+|.+.||+...|++||+|+++ ..+..+
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a---~e~sv~ 615 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEA---EEMSVE 615 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhh---hhhhhc
Confidence 889999999999999999999999999999999999999999 445444
No 59
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=94.59 E-value=0.018 Score=63.61 Aligned_cols=56 Identities=32% Similarity=0.813 Sum_probs=44.0
Q ss_pred ccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCC-----CccccCcccchh
Q 008193 239 IICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGD-----QGWFCKFCECKM 296 (574)
Q Consensus 239 ~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gd-----e~W~C~~C~~k~ 296 (574)
.+|.||-...+.+.++||.||. |.-..|-.|++-. +...||.+. +.|||..|.+..
T Consensus 120 ~iCcVClg~rs~da~ei~qCd~-CGi~VHEgCYGv~-dn~si~s~~s~~stepWfCeaC~~Gv 180 (707)
T KOG0957|consen 120 VICCVCLGQRSVDAGEILQCDK-CGINVHEGCYGVL-DNVSIPSGSSDCSTEPWFCEACLYGV 180 (707)
T ss_pred eEEEEeecCccccccceeeccc-cCceecccccccc-cccccCCCCccCCCCchhhhhHhcCC
Confidence 3899999887777899999995 9999999999954 333566542 469999887643
No 60
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=93.27 E-value=0.046 Score=53.09 Aligned_cols=56 Identities=25% Similarity=0.627 Sum_probs=39.9
Q ss_pred ccccccc-CCCCCCCCccccCCCcCCcccccccCCCCCCCC----CCCCCCccccCcccchh
Q 008193 240 ICAKCKL-REAFPDNDIVLCDGTCNCAFHQKCLDPPLDTES----IPPGDQGWFCKFCECKM 296 (574)
Q Consensus 240 ~C~vC~~-~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~----iP~gde~W~C~~C~~k~ 296 (574)
.|.+|+. ++...-|.||.|-| |-.+||..||+|-...+. |-+++....|..|+--.
T Consensus 1 ~C~~C~~~g~~~~kG~Lv~CQG-Cs~sYHk~CLG~Rs~ReHlVTKVg~d~FVLQCr~Cig~~ 61 (175)
T PF15446_consen 1 TCDTCGYEGDDRNKGPLVYCQG-CSSSYHKACLGPRSQREHLVTKVGDDDFVLQCRRCIGIA 61 (175)
T ss_pred CcccccCCCCCccCCCeEEcCc-cChHHHhhhcCCccccceeeEEEcCCceEEechhhcChh
Confidence 4888865 34345689999998 999999999998764332 33444456788887543
No 61
>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=92.97 E-value=0.18 Score=39.88 Aligned_cols=48 Identities=17% Similarity=0.279 Sum_probs=36.5
Q ss_pred CCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193 442 RRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 494 (574)
Q Consensus 442 kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~ 494 (574)
||+|..||-++.-.+=..+...+ ...+||+++|++..+|..|..|+..
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k~~ 48 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNKDK 48 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCHHH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhHHH
Confidence 45678899999888888888776 5889999999999999999999753
No 62
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=91.46 E-value=0.05 Score=61.98 Aligned_cols=58 Identities=17% Similarity=0.490 Sum_probs=44.2
Q ss_pred cccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccchhh
Q 008193 236 HEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKME 297 (574)
Q Consensus 236 ~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k~~ 297 (574)
..+.+|.+|+.......+.|+.|.. |...||.+|+.-.+....+..+ |-|+.|+..-.
T Consensus 16 ~~~~mc~l~~s~G~~~ag~m~ac~~-c~~~yH~~cvt~~~~~~~l~~g---WrC~~crvCe~ 73 (694)
T KOG4443|consen 16 IVCLMCPLCGSSGKGRAGRLLACSD-CGQKYHPYCVTSWAQHAVLSGG---WRCPSCRVCEA 73 (694)
T ss_pred hhhhhhhhhccccccccCcchhhhh-hcccCCcchhhHHHhHHHhcCC---cccCCceeeee
Confidence 4567888998876666788999995 9999999999976653233333 99999987543
No 63
>KOG3612 consensus PHD Zn-finger protein [General function prediction only]
Probab=87.37 E-value=0.44 Score=53.63 Aligned_cols=53 Identities=17% Similarity=0.289 Sum_probs=43.0
Q ss_pred CcccccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccc
Q 008193 233 SVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCEC 294 (574)
Q Consensus 233 ~~~~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~ 294 (574)
.....+++|..|... +..|.|+ .|.+.||..|..|--. ++.....|.|+.|..
T Consensus 55 ~~~N~d~~cfechlp-----g~vl~c~-vc~Rs~h~~c~sp~~q---~r~~s~p~~~p~p~s 107 (588)
T KOG3612|consen 55 PSSNIDPFCFECHLP-----GAVLKCI-VCHRSFHENCQSPDPQ---KRNYSVPSDKPQPYS 107 (588)
T ss_pred cccCCCcccccccCC-----cceeeee-hhhccccccccCcchh---hccccccccCCcccc
Confidence 344567999999986 8889999 6999999999998643 666555799999974
No 64
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=86.66 E-value=0.4 Score=54.64 Aligned_cols=51 Identities=29% Similarity=0.707 Sum_probs=42.3
Q ss_pred cccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccchhh
Q 008193 238 HIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKME 297 (574)
Q Consensus 238 d~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k~~ 297 (574)
...|..|..+ +++++|+. |+.+||+.|.++++.. ..+... |.|..|-....
T Consensus 47 ~ts~~~~~~~-----gn~~~~~~-~~~s~h~~~~~~~~sp-~~~~~~--~~~~~~~~~~~ 97 (613)
T KOG4299|consen 47 ATSCGICKSG-----GNLLCCDH-CPASFHLECDKPPLSP-DLKGSE--INCSRCPKGRE 97 (613)
T ss_pred hhhcchhhhc-----CCcccccc-CccccchhccCcccCc-cccccc--ccccCCCcccc
Confidence 5679999987 88999995 9999999999999984 455555 99999977543
No 65
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=83.44 E-value=0.6 Score=37.54 Aligned_cols=35 Identities=26% Similarity=0.710 Sum_probs=28.6
Q ss_pred cccccccccCCCCCCCCccccCCCcCCcccccccCCC
Q 008193 238 HIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPP 274 (574)
Q Consensus 238 d~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PP 274 (574)
...|.+|+..- .+.+++|.|. .|...||-.|+...
T Consensus 5 ~~~C~~Cg~~~-~~~dDiVvCp-~CgapyHR~C~~~~ 39 (54)
T PF14446_consen 5 GCKCPVCGKKF-KDGDDIVVCP-ECGAPYHRDCWEKA 39 (54)
T ss_pred CccChhhCCcc-cCCCCEEECC-CCCCcccHHHHhhC
Confidence 46799999863 2468999999 59999999998743
No 66
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=81.58 E-value=0.73 Score=49.68 Aligned_cols=46 Identities=30% Similarity=0.593 Sum_probs=33.9
Q ss_pred ccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccc
Q 008193 239 IICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCEC 294 (574)
Q Consensus 239 ~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~ 294 (574)
+.|.+|-.... .|+.|--= .|...||..|.+|.|.. .+ =+||.|..
T Consensus 230 ~~CaIClEdY~--~GdklRiL-PC~H~FH~~CIDpWL~~----~r---~~CPvCK~ 275 (348)
T KOG4628|consen 230 DTCAICLEDYE--KGDKLRIL-PCSHKFHVNCIDPWLTQ----TR---TFCPVCKR 275 (348)
T ss_pred ceEEEeecccc--cCCeeeEe-cCCCchhhccchhhHhh----cC---ccCCCCCC
Confidence 68999998653 34444334 58899999999999872 11 37999986
No 67
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=78.02 E-value=0.34 Score=58.33 Aligned_cols=52 Identities=17% Similarity=0.208 Sum_probs=39.7
Q ss_pred ccccccccCCCCCCCCccccCCCcCCcccc-cccCCCCCCCCCCCCCCccccCcccchhh
Q 008193 239 IICAKCKLREAFPDNDIVLCDGTCNCAFHQ-KCLDPPLDTESIPPGDQGWFCKFCECKME 297 (574)
Q Consensus 239 ~~C~vC~~~~~~~~g~lLlCDg~C~rafH~-~Cl~PPL~~~~iP~gde~W~C~~C~~k~~ 297 (574)
..|.+|+. ++-+|+|+++|+.+||. .||+-..-...++++- |+|+.|..+..
T Consensus 429 rrl~Ie~~-----det~l~yysT~pqly~ll~cLd~~~~e~~L~d~i--~~~~ee~~rqM 481 (1414)
T KOG1473|consen 429 RRLRIEGM-----DETLLWYYSTCPQLYHLLRCLDRTYVEMYLCDGI--WERREEIIRQM 481 (1414)
T ss_pred eeeEEecC-----CCcEEEEecCcHHHHHHHHHhchHHHHHhhccch--hhhHHHHHHhc
Confidence 34666664 37789999889999999 9999443333688877 99999987654
No 68
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=77.97 E-value=1.7 Score=50.58 Aligned_cols=117 Identities=15% Similarity=0.173 Sum_probs=80.2
Q ss_pred CCccccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhhhhccccC-CCCCCC
Q 008193 436 PSNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVESARQV-SGSPRI 514 (574)
Q Consensus 436 ~~~~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~~e~~~~~-~~~~~~ 514 (574)
|++.+.-+-++.+..++-..|-+++.-+--|+..+=-..+.+|.+.+.+|.+||+||+. .-+..-...+.+. ...+.+
T Consensus 621 psg~~p~kv~sp~k~~dq~ql~~a~elq~s~~n~~~pl~~t~~~n~~pv~ev~dhsrss-tpsp~pl~ltss~n~~~p~y 699 (1007)
T KOG3623|consen 621 PSGERPVKVRSPIKEEDQQQLKQAYELQASPSNDEFPLIATRLQNDPPVVEVWDHSRSS-TPSPMPLFLTSSANGAAPPY 699 (1007)
T ss_pred CCCCCCccccCCCCccchhhhHhhhhcccCccCcccchhhhhccCCCcchhhcccCCCC-CCCCCcccccccccCCCCCC
Confidence 34444445557777788888888888888888877777788899999999999999998 2122211122222 134556
Q ss_pred CCCcchhh--ccccchhhhhccCccceeecCcchhcccCch
Q 008193 515 SKESSLET--EKKNADVLTLKNSLEETLICSPKSLKKIHPK 553 (574)
Q Consensus 515 ~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 553 (574)
+.|+...- +..+.||++.+.-..--++.+++.+.+-.+-
T Consensus 700 tpes~asee~Q~epLdlslprq~gepks~~~~~~~ekps~~ 740 (1007)
T KOG3623|consen 700 TPESQASEERQDEPLDLSLPRQPGEPKSESSPPYIEKPSGE 740 (1007)
T ss_pred CcchhccccccccccchhcccccCCCccccCcccccCCccc
Confidence 66663322 5559999999988777777777777665443
No 69
>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=77.94 E-value=1.6 Score=35.70 Aligned_cols=46 Identities=20% Similarity=0.339 Sum_probs=31.2
Q ss_pred CccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccc
Q 008193 444 SFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNAR 493 (574)
Q Consensus 444 ~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR 493 (574)
++.+||+++...+-..+ ..+.....+||+++||++.+|..|-.-.+
T Consensus 3 ~r~~ys~e~K~~~v~~~----~~~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 3 KRRRYSPEFKLQAVREY----LESGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp SS----HHHHHHHHHHH----HHHHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHH----HHCCCceEeeecccccccccccHHHHHHh
Confidence 44689999877766555 23457889999999999999999965443
No 70
>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=74.54 E-value=4.4 Score=30.87 Aligned_cols=43 Identities=21% Similarity=0.399 Sum_probs=33.7
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 494 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~ 494 (574)
.+++.+.++|...|. ....-.++|..||++...|+.+...-..
T Consensus 4 ~L~~~er~vi~~~y~-----~~~t~~eIa~~lg~s~~~V~~~~~~al~ 46 (50)
T PF04545_consen 4 QLPPREREVIRLRYF-----EGLTLEEIAERLGISRSTVRRILKRALK 46 (50)
T ss_dssp TS-HHHHHHHHHHHT-----ST-SHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhc-----CCCCHHHHHHHHCCcHHHHHHHHHHHHH
Confidence 589999999999992 3344678999999999999988765544
No 71
>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=74.39 E-value=4.6 Score=32.31 Aligned_cols=40 Identities=25% Similarity=0.429 Sum_probs=35.6
Q ss_pred CCHHHHHHHHHHHHhCCC--CCHHHHHHHHHHcCCChhhHHH
Q 008193 448 MPPNAVEKLRQVFAENEL--PSRIVKENLSKELSLEPEKVNK 487 (574)
Q Consensus 448 ~t~~Q~~~Le~~F~~~~y--Ps~~~r~~LA~~LgL~~~qV~v 487 (574)
+|+.|.++|..+|..-=| |-...-.+||++||++..-|..
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 689999999999988766 8888999999999999987764
No 72
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=73.88 E-value=2.4 Score=47.40 Aligned_cols=59 Identities=19% Similarity=0.304 Sum_probs=46.3
Q ss_pred ccccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccchhhhhh
Q 008193 235 HHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKMEIIE 300 (574)
Q Consensus 235 ~~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k~~~~~ 300 (574)
..+...|.+|......+.+.++.|+. |.++||+.|..|.... .+. |.|..|+......+
T Consensus 80 ~~~e~~~nv~~s~~~~p~~e~~~~~r-~~~~~~q~~~i~~~~~----~~~--~~~~~c~~~~~~~~ 138 (464)
T KOG4323|consen 80 PSSELNPNVLTSETVLPENEKVICGR-CKSGYHQGCNIPRFPS----LDI--GESTECVFPIFSQE 138 (464)
T ss_pred CccccCCcccccccccCchhhhhhhh-hccCcccccCccCcCc----CCc--cccccccccccccc
Confidence 45567899999987777889999995 9999999999987542 233 88999987665443
No 73
>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=72.06 E-value=3.3 Score=30.23 Aligned_cols=43 Identities=19% Similarity=0.306 Sum_probs=34.4
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 494 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~ 494 (574)
.+++.+..+|...|... ..-.++|.+||++..+|..|.+..+.
T Consensus 10 ~l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 10 KLPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALK 52 (55)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 57888888888777433 35678899999999999999876654
No 74
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=71.33 E-value=1.6 Score=38.16 Aligned_cols=35 Identities=26% Similarity=0.532 Sum_probs=24.8
Q ss_pred CccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccch
Q 008193 254 DIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECK 295 (574)
Q Consensus 254 ~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k 295 (574)
.+|++ .|...||+.|+.--|.+. ... =.||-|+..
T Consensus 46 plv~g--~C~H~FH~hCI~kWl~~~---~~~--~~CPmCR~~ 80 (85)
T PF12861_consen 46 PLVWG--KCSHNFHMHCILKWLSTQ---SSK--GQCPMCRQP 80 (85)
T ss_pred ceeec--cCccHHHHHHHHHHHccc---cCC--CCCCCcCCe
Confidence 35555 499999999999888742 112 369999854
No 75
>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=71.07 E-value=10 Score=24.62 Aligned_cols=39 Identities=13% Similarity=0.416 Sum_probs=29.8
Q ss_pred cCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhh
Q 008193 446 HRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWF 489 (574)
Q Consensus 446 ~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWF 489 (574)
..++.++...+...|.. .+ ...++|+++|++...|..|.
T Consensus 4 ~~~~~~~~~~i~~~~~~-~~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 4 PKLTPEQIEEARRLLAA-GE----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CcCCHHHHHHHHHHHHc-CC----CHHHHHHHHCCCHHHHHHhC
Confidence 34777777777777753 33 56789999999999999884
No 76
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=64.34 E-value=5.4 Score=39.81 Aligned_cols=43 Identities=26% Similarity=0.706 Sum_probs=31.2
Q ss_pred ccccccccCCCC---CCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccch
Q 008193 239 IICAKCKLREAF---PDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECK 295 (574)
Q Consensus 239 ~~C~vC~~~~~~---~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k 295 (574)
-+|.+|...+.. +.+..+.|.. |...||..|+.. . .||.|...
T Consensus 153 fiCe~C~~~~~IfPF~~~~~~~C~~-C~~v~H~~C~~~---------~----~CpkC~R~ 198 (202)
T PF13901_consen 153 FICEICNSDDIIFPFQIDTTVRCPK-CKSVFHKSCFRK---------K----SCPKCARR 198 (202)
T ss_pred CCCccCCCCCCCCCCCCCCeeeCCc-CccccchhhcCC---------C----CCCCcHhH
Confidence 468889875432 2346788995 999999999882 1 29999643
No 77
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=57.83 E-value=2.7 Score=49.24 Aligned_cols=53 Identities=23% Similarity=0.302 Sum_probs=44.2
Q ss_pred ccccccccccccCCCCCCCCccccCCCcCCcccccccCC-CCCCCCCCCCCCccccCcccchhh
Q 008193 235 HHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDP-PLDTESIPPGDQGWFCKFCECKME 297 (574)
Q Consensus 235 ~~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~P-PL~~~~iP~gde~W~C~~C~~k~~ 297 (574)
...++.|..|... ...++|. .|-+.||..|+.| |+.+ .+-+. |-|+.|..+..
T Consensus 503 ~~~d~~~~~~~~~-----l~~l~~p-~~lrr~k~d~l~~~P~Kt--e~i~~--~~~~~~Q~~~y 556 (696)
T KOG0383|consen 503 EFHDISCEEQIKK-----LHLLLCP-HMLRRLKLDVLKPMPLKT--ELIGR--VELSPCQKKYY 556 (696)
T ss_pred hcchhhHHHHHHh-----hccccCc-hhhhhhhhhhccCCCccc--eeEEE--EecCHHHHHHH
Confidence 3457889999986 6778899 6999999999999 8884 56677 99999987654
No 78
>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=56.92 E-value=16 Score=28.05 Aligned_cols=43 Identities=14% Similarity=0.268 Sum_probs=30.9
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 494 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~ 494 (574)
.+|+.+..++...|. ....-.++|..||+++..|++|.+.-|.
T Consensus 10 ~L~~~~r~i~~l~~~-----~g~s~~eIa~~l~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 10 QLPERQREIFLLRYF-----QGMSYAEIAEILGISESTVKRRLRRARK 52 (54)
T ss_dssp CS-HHHHHHHHHHHT-----S---HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHH-----HCcCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence 477888888876554 3456789999999999999999987664
No 79
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=56.58 E-value=2.5 Score=44.55 Aligned_cols=62 Identities=15% Similarity=0.183 Sum_probs=39.9
Q ss_pred ccccccccccCCC----CCCCCccccCCCcCCcccccccCCCCCCC-CCCCCCCccccCcccchhhhhhh
Q 008193 237 EHIICAKCKLREA----FPDNDIVLCDGTCNCAFHQKCLDPPLDTE-SIPPGDQGWFCKFCECKMEIIES 301 (574)
Q Consensus 237 ed~~C~vC~~~~~----~~~g~lLlCDg~C~rafH~~Cl~PPL~~~-~iP~gde~W~C~~C~~k~~~~~~ 301 (574)
....|..|-.+.. ...+.||+|- .|...||.+|+.-+..-. .+-.-. |.|-.|.-..-|..+
T Consensus 257 ~~~~~~~~~~~~~~~~~~r~~S~I~C~-~C~~~~HP~Ci~M~~elv~~~KTY~--W~C~~C~lC~IC~~P 323 (381)
T KOG1512|consen 257 RRNERKHFWDIQTNIIQSRRNSWIVCK-PCATRPHPYCVAMIPELVGQYKTYF--WKCSSCELCRICLGP 323 (381)
T ss_pred chhhhhhhhcchhhhhhhhhccceeec-ccccCCCCcchhcCHHHHhHHhhcc--hhhcccHhhhccCCc
Confidence 3456777766421 0135689998 699999999998654311 122334 999999866655433
No 80
>PF13551 HTH_29: Winged helix-turn helix
Probab=54.75 E-value=26 Score=30.16 Aligned_cols=48 Identities=23% Similarity=0.365 Sum_probs=32.9
Q ss_pred CCccCCCHHHHHHHHHHHHhCCCCC--HHHHHHHHHHc-------CCChhhHHHhhc
Q 008193 443 RSFHRMPPNAVEKLRQVFAENELPS--RIVKENLSKEL-------SLEPEKVNKWFK 490 (574)
Q Consensus 443 r~r~r~t~~Q~~~Le~~F~~~~yPs--~~~r~~LA~~L-------gL~~~qV~vWFQ 490 (574)
+++..+++++.+.|.+++..++.-. ......|+..| .+++..|..|++
T Consensus 53 ~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 53 RPRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 4444599999999999999988432 22333444432 488888888875
No 81
>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=54.13 E-value=8.7 Score=31.60 Aligned_cols=20 Identities=15% Similarity=0.494 Sum_probs=17.3
Q ss_pred HHHHHHHHcCCChhhHHHhh
Q 008193 470 VKENLSKELSLEPEKVNKWF 489 (574)
Q Consensus 470 ~r~~LA~~LgL~~~qV~vWF 489 (574)
.=.+||.+||+++.+|..|=
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHh
Confidence 34579999999999999994
No 82
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=53.98 E-value=7.2 Score=32.54 Aligned_cols=55 Identities=24% Similarity=0.434 Sum_probs=19.2
Q ss_pred ccccccccCCC-CCCCCccccCC-CcCCcccccccCCCCC------CCCCCCCCCccccCcccchh
Q 008193 239 IICAKCKLREA-FPDNDIVLCDG-TCNCAFHQKCLDPPLD------TESIPPGDQGWFCKFCECKM 296 (574)
Q Consensus 239 ~~C~vC~~~~~-~~~g~lLlCDg-~C~rafH~~Cl~PPL~------~~~iP~gde~W~C~~C~~k~ 296 (574)
..|.+|..... .+.-..+.|+. .|...||..||--.+. ..-+|. .+-||.|....
T Consensus 3 ~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~---~G~CP~C~~~i 65 (70)
T PF11793_consen 3 LECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPI---FGECPYCSSPI 65 (70)
T ss_dssp -S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT-----EEE-TTT-SEE
T ss_pred CCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeeccc---ccCCcCCCCee
Confidence 46888887532 11223578972 4999999999953322 001221 15699997543
No 83
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=52.64 E-value=7.8 Score=31.21 Aligned_cols=46 Identities=28% Similarity=0.714 Sum_probs=33.2
Q ss_pred cccccccCCCCC---CCCccccCCCcCCcccccccCCCCCCCCCCCCCCcc
Q 008193 240 ICAKCKLREAFP---DNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGW 287 (574)
Q Consensus 240 ~C~vC~~~~~~~---~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W 287 (574)
.|.+|+.....+ .|.+|-|. .|...|-...++| +.-+..|.-.+.|
T Consensus 4 ~CP~CG~~iev~~~~~GeiV~Cp-~CGaeleVv~~~p-~~L~~ap~~~eDw 52 (54)
T TIGR01206 4 ECPDCGAEIELENPELGELVICD-ECGAELEVVSLDP-LRLEAAPEEAEDW 52 (54)
T ss_pred CCCCCCCEEecCCCccCCEEeCC-CCCCEEEEEeCCC-CEEEeCccccccc
Confidence 599999853322 27899999 5999999999998 5544666544446
No 84
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=52.39 E-value=14 Score=35.14 Aligned_cols=48 Identities=17% Similarity=0.177 Sum_probs=38.0
Q ss_pred cCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhh
Q 008193 446 HRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR 500 (574)
Q Consensus 446 ~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~ 500 (574)
..+|+.|.++|+..+ ......++|..||++...|..|.++.+. .++..
T Consensus 5 ~~Lt~rqreVL~lr~------~GlTq~EIAe~LGiS~~tVs~ie~ra~k-kLr~~ 52 (141)
T PRK03975 5 SFLTERQIEVLRLRE------RGLTQQEIADILGTSRANVSSIEKRARE-NIEKA 52 (141)
T ss_pred cCCCHHHHHHHHHHH------cCCCHHHHHHHHCCCHHHHHHHHHHHHH-HHHHH
Confidence 579999999998732 2345679999999999999999998777 33433
No 85
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=52.06 E-value=9.3 Score=40.85 Aligned_cols=50 Identities=24% Similarity=0.612 Sum_probs=36.1
Q ss_pred cccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccchhhhhhhh
Q 008193 238 HIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKMEIIESM 302 (574)
Q Consensus 238 d~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k~~~~~~~ 302 (574)
.-||..|...... =|.||-|+ |.+||.-... +.+ -.|+.|..+...++.+
T Consensus 90 VHfCd~Cd~PI~I-YGRmIPCk-------HvFCl~CAr~-----~~d--K~Cp~C~d~VqrIeq~ 139 (389)
T KOG2932|consen 90 VHFCDRCDFPIAI-YGRMIPCK-------HVFCLECARS-----DSD--KICPLCDDRVQRIEQI 139 (389)
T ss_pred eEeecccCCccee-eecccccc-------hhhhhhhhhc-----Ccc--ccCcCcccHHHHHHHh
Confidence 4689999986543 37899888 8888886533 224 6899999887766554
No 86
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=51.72 E-value=15 Score=27.74 Aligned_cols=41 Identities=12% Similarity=0.343 Sum_probs=21.4
Q ss_pred ccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhc
Q 008193 445 FHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFK 490 (574)
Q Consensus 445 r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQ 490 (574)
+..||.+|...++..+. ......+||+.||.++..|..|..
T Consensus 2 ~~~Lt~~eR~~I~~l~~-----~G~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 2 YKHLTPEERNQIEALLE-----QGMSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp ----------HHHHHHC-----S---HHHHHHHTT--HHHHHHHHH
T ss_pred ccchhhhHHHHHHHHHH-----cCCCHHHHHHHHCcCcHHHHHHHh
Confidence 35689999999998865 345667799999999999988754
No 87
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=51.37 E-value=8.1 Score=41.79 Aligned_cols=42 Identities=21% Similarity=0.456 Sum_probs=33.4
Q ss_pred CCccccCCCcCCcccccc--cCCCCCCCCCCCCCCccccCcccchhhh
Q 008193 253 NDIVLCDGTCNCAFHQKC--LDPPLDTESIPPGDQGWFCKFCECKMEI 298 (574)
Q Consensus 253 g~lLlCDg~C~rafH~~C--l~PPL~~~~iP~gde~W~C~~C~~k~~~ 298 (574)
..|+.|++ |..+||..| ++++.. .+|..+ .|+|..|.....-
T Consensus 73 ~~~~~cd~-C~~~~~~ec~~v~~~~~--e~p~~~-~~~c~~c~~~~~~ 116 (345)
T KOG1632|consen 73 DLMEQCDL-CEDWYHGECWEVGTAEK--EAPKED-PKVCDECKEAQDG 116 (345)
T ss_pred hhhhcccc-ccccccccccccCchhh--cCCccc-cccccccchhhhh
Confidence 37899996 999999999 998877 555543 4999999876643
No 88
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=51.11 E-value=12 Score=39.47 Aligned_cols=59 Identities=22% Similarity=0.541 Sum_probs=34.9
Q ss_pred ccccccccccccCCCC--CCCCcc---ccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccchhhhhh
Q 008193 235 HHEHIICAKCKLREAF--PDNDIV---LCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKMEIIE 300 (574)
Q Consensus 235 ~~ed~~C~vC~~~~~~--~~g~lL---lCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k~~~~~ 300 (574)
..++.+|.+|+..-.. +++.+| .== .|+..||-.|...--- + |. .=+||.|..+.+...
T Consensus 221 hl~d~vCaVCg~~~~~s~~eegvienty~L-sCnHvFHEfCIrGWci---v--GK-kqtCPYCKekVdl~r 284 (328)
T KOG1734|consen 221 HLSDSVCAVCGQQIDVSVDEEGVIENTYKL-SCNHVFHEFCIRGWCI---V--GK-KQTCPYCKEKVDLKR 284 (328)
T ss_pred CCCcchhHhhcchheeecchhhhhhhheee-ecccchHHHhhhhhee---e--cC-CCCCchHHHHhhHhh
Confidence 3467899999985211 111111 001 5999999999874321 1 11 247999988776543
No 89
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=51.09 E-value=7.2 Score=34.54 Aligned_cols=31 Identities=26% Similarity=0.717 Sum_probs=25.3
Q ss_pred cccccccccCCCCCCCCccccCC-CcCCcccccccC
Q 008193 238 HIICAKCKLREAFPDNDIVLCDG-TCNCAFHQKCLD 272 (574)
Q Consensus 238 d~~C~vC~~~~~~~~g~lLlCDg-~C~rafH~~Cl~ 272 (574)
...|.+|+.. .|-+|-|.. .|...||..|..
T Consensus 55 ~~~C~iC~~~----~G~~i~C~~~~C~~~fH~~CA~ 86 (110)
T PF13832_consen 55 KLKCSICGKS----GGACIKCSHPGCSTAFHPTCAR 86 (110)
T ss_pred CCcCcCCCCC----CceeEEcCCCCCCcCCCHHHHH
Confidence 4689999986 377888882 399999999975
No 90
>PRK10072 putative transcriptional regulator; Provisional
Probab=50.79 E-value=23 Score=31.57 Aligned_cols=41 Identities=15% Similarity=0.213 Sum_probs=33.2
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 494 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~ 494 (574)
..+...+..|.....-+ ..+||+.||++...|..|.+.+|.
T Consensus 32 ~~~~~eik~LR~~~glT-------Q~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 32 TTSFTEFEQLRKGTGLK-------IDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred cCChHHHHHHHHHcCCC-------HHHHHHHhCCCHHHHHHHHcCCCC
Confidence 45777788876544333 789999999999999999999986
No 91
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=50.00 E-value=26 Score=25.97 Aligned_cols=42 Identities=17% Similarity=0.325 Sum_probs=32.0
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 494 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~ 494 (574)
.+++.+.+++..++. . ....++|..||++...|..|.+.-+.
T Consensus 3 ~l~~~e~~i~~~~~~--g----~s~~eia~~l~is~~tv~~~~~~~~~ 44 (58)
T smart00421 3 SLTPREREVLRLLAE--G----LTNKEIAERLGISEKTVKTHLSNIMR 44 (58)
T ss_pred CCCHHHHHHHHHHHc--C----CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 478889988866432 2 25589999999999999998875433
No 92
>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=49.91 E-value=9.8 Score=32.89 Aligned_cols=32 Identities=22% Similarity=0.546 Sum_probs=21.9
Q ss_pred ccccccccccCCCCCCCCccccCCCcCCcccccccC
Q 008193 237 EHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLD 272 (574)
Q Consensus 237 ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~ 272 (574)
+...|.+|+..-. .+.++.. .|+..||..|+.
T Consensus 77 ~~~~C~vC~k~l~--~~~f~~~--p~~~v~H~~C~~ 108 (109)
T PF10367_consen 77 ESTKCSVCGKPLG--NSVFVVF--PCGHVVHYSCIK 108 (109)
T ss_pred CCCCccCcCCcCC--CceEEEe--CCCeEEeccccc
Confidence 3567999999742 2333333 277899999975
No 93
>PRK04217 hypothetical protein; Provisional
Probab=49.72 E-value=29 Score=31.80 Aligned_cols=51 Identities=24% Similarity=0.164 Sum_probs=40.9
Q ss_pred cCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhhh
Q 008193 446 HRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKV 502 (574)
Q Consensus 446 ~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~~ 502 (574)
..++++|.+++...|.+.- .-.+||+.||++...|...++..+. .++..-.
T Consensus 41 ~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~RArk-kLre~L~ 91 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTSARK-KVAQMLV 91 (110)
T ss_pred ccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHH-HHHHHHH
Confidence 5799999999987775543 6678999999999999999988777 5555443
No 94
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=49.53 E-value=18 Score=33.03 Aligned_cols=43 Identities=9% Similarity=0.003 Sum_probs=36.2
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 494 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~ 494 (574)
.+++.|.+++...|-.+ ..-.++|..||+++..|++|...-|.
T Consensus 106 ~L~~~~r~ii~l~~~~~-----~s~~EIA~~l~is~~tV~~~~~ra~~ 148 (154)
T PRK06759 106 VLDEKEKYIIFERFFVG-----KTMGEIALETEMTYYQVRWIYRQALE 148 (154)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 69999999998776543 34789999999999999999887776
No 95
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=48.63 E-value=3.4 Score=45.20 Aligned_cols=56 Identities=25% Similarity=0.449 Sum_probs=35.5
Q ss_pred ccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCcc--ccCcccchhhhhhhhh
Q 008193 239 IICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGW--FCKFCECKMEIIESMN 303 (574)
Q Consensus 239 ~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W--~C~~C~~k~~~~~~~n 303 (574)
..|.+|-..- +.+.++---. +|...||..||.-... --| | -||.|..+..+.-..|
T Consensus 5 A~C~Ic~d~~-p~~~~l~~i~-~cGhifh~~cl~qwfe--~~P-----s~R~cpic~ik~~~r~~~N 62 (465)
T KOG0827|consen 5 AECHICIDGR-PNDHELGPIG-TCGHIFHTTCLTQWFE--GDP-----SNRGCPICQIKLQERHVAN 62 (465)
T ss_pred ceeeEeccCC-cccccccccc-chhhHHHHHHHHHHHc--cCC-----ccCCCCceeecccceeeec
Confidence 5699995542 2233444444 7999999999986544 223 5 5999996665544433
No 96
>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=48.10 E-value=8.3 Score=32.88 Aligned_cols=36 Identities=14% Similarity=0.136 Sum_probs=27.3
Q ss_pred HHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccc
Q 008193 457 RQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNA 492 (574)
Q Consensus 457 e~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNr 492 (574)
+.+|.-..|-..-...+||+.||+++..|++|+.+.
T Consensus 21 r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~~ 56 (73)
T TIGR03879 21 EAAAALAREEAGKTASEIAEELGRTEQTVRNHLKGE 56 (73)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcC
Confidence 344444455556677899999999999999998753
No 97
>PHA02955 hypothetical protein; Provisional
Probab=48.04 E-value=18 Score=36.67 Aligned_cols=49 Identities=8% Similarity=0.059 Sum_probs=40.6
Q ss_pred cCCCHHHHHHHHHHHHhC-CCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193 446 HRMPPNAVEKLRQVFAEN-ELPSRIVKENLSKELSLEPEKVNKWFKNARY 494 (574)
Q Consensus 446 ~r~t~~Q~~~Le~~F~~~-~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~ 494 (574)
..=...|+..|-++|.+. .-+++++|.++|++||+....|..||++.=-
T Consensus 56 ~sna~~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t~~~ 105 (213)
T PHA02955 56 NSDEEKNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKTDLQ 105 (213)
T ss_pred cCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccchhh
Confidence 334567788888888777 6789999999999999999889999998644
No 98
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=47.79 E-value=20 Score=35.58 Aligned_cols=41 Identities=22% Similarity=0.438 Sum_probs=36.0
Q ss_pred CCCHHHHHHHHHHHHhCCC--CCHHHHHHHHHHcCCChhhHHH
Q 008193 447 RMPPNAVEKLRQVFAENEL--PSRIVKENLSKELSLEPEKVNK 487 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~y--Ps~~~r~~LA~~LgL~~~qV~v 487 (574)
.||+.|+++|..+|..-=| |=.-.-.+||++||+++.-+.-
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~e 197 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSE 197 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHH
Confidence 6999999999999987655 8888999999999999976653
No 99
>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=45.26 E-value=28 Score=27.77 Aligned_cols=37 Identities=14% Similarity=0.228 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhc
Q 008193 450 PNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFK 490 (574)
Q Consensus 450 ~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQ 490 (574)
..|++.|+-.|. +...+.. +||..||++++.|+.-..
T Consensus 5 ~rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~~~i~ 41 (59)
T PF08280_consen 5 KRQLKLLELLLK-NKWITLK---ELAKKLNISERTIKNDIN 41 (59)
T ss_dssp HHHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHHHHHH
Confidence 358899999999 7777665 899999999999986543
No 100
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=45.06 E-value=15 Score=36.17 Aligned_cols=24 Identities=38% Similarity=0.772 Sum_probs=18.8
Q ss_pred CCCccccCCCcCCcccccccCCCCC
Q 008193 252 DNDIVLCDGTCNCAFHQKCLDPPLD 276 (574)
Q Consensus 252 ~g~lLlCDg~C~rafH~~Cl~PPL~ 276 (574)
++-|.=|. .|.++||+.-|-|+-.
T Consensus 121 ~nVLFRC~-~C~RawH~~HLP~~~~ 144 (175)
T PF15446_consen 121 DNVLFRCT-SCHRAWHFEHLPPPSG 144 (175)
T ss_pred hheEEecC-CccceeehhhCCCCcC
Confidence 35677799 4999999998877643
No 101
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=44.53 E-value=1.6 Score=32.50 Aligned_cols=43 Identities=23% Similarity=0.542 Sum_probs=28.1
Q ss_pred cccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCccc
Q 008193 240 ICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCE 293 (574)
Q Consensus 240 ~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~ 293 (574)
.|.+|...-. ++..++.. . |.-.||..|+...+.. . ..||.|+
T Consensus 2 ~C~IC~~~~~-~~~~~~~l-~-C~H~fh~~Ci~~~~~~------~--~~CP~CR 44 (44)
T PF13639_consen 2 ECPICLEEFE-DGEKVVKL-P-CGHVFHRSCIKEWLKR------N--NSCPVCR 44 (44)
T ss_dssp CETTTTCBHH-TTSCEEEE-T-TSEEEEHHHHHHHHHH------S--SB-TTTH
T ss_pred CCcCCChhhc-CCCeEEEc-c-CCCeeCHHHHHHHHHh------C--CcCCccC
Confidence 5888887642 12344444 3 9999999999977652 1 3688884
No 102
>PF13518 HTH_28: Helix-turn-helix domain
Probab=43.75 E-value=17 Score=27.32 Aligned_cols=25 Identities=20% Similarity=0.492 Sum_probs=21.3
Q ss_pred HHHHHHHHcCCChhhHHHhhccccc
Q 008193 470 VKENLSKELSLEPEKVNKWFKNARY 494 (574)
Q Consensus 470 ~r~~LA~~LgL~~~qV~vWFQNrR~ 494 (574)
...++|+++||+..+|..|.+.-+.
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHHh
Confidence 4567999999999999999876655
No 103
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=43.61 E-value=30 Score=27.14 Aligned_cols=24 Identities=4% Similarity=0.292 Sum_probs=17.2
Q ss_pred HHHHHHHHcCCChhhHHHhhcccc
Q 008193 470 VKENLSKELSLEPEKVNKWFKNAR 493 (574)
Q Consensus 470 ~r~~LA~~LgL~~~qV~vWFQNrR 493 (574)
...+||+.+|++..+|..||.++.
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~ 35 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKP 35 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT-
T ss_pred CHHHHHHHHCcCHHHHHHHHhccc
Confidence 567788999999999999988773
No 104
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=43.58 E-value=27 Score=33.68 Aligned_cols=48 Identities=8% Similarity=0.186 Sum_probs=38.4
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhh
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR 500 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~ 500 (574)
.|++.|..+|...|..+ ..-.++|+.||++...|++|...-|. ++|..
T Consensus 142 ~L~~~~r~vl~l~~~~~-----~s~~EIA~~Lgis~~tVk~~l~ra~~-~Lr~~ 189 (194)
T PRK09646 142 ALTDTQRESVTLAYYGG-----LTYREVAERLAVPLGTVKTRMRDGLI-RLRDC 189 (194)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHhCCChHhHHHHHHHHHH-HHHHH
Confidence 59999999998766443 44578999999999999999988777 44443
No 105
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=41.61 E-value=23 Score=33.45 Aligned_cols=47 Identities=11% Similarity=0.376 Sum_probs=37.5
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHh
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKA 499 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~ 499 (574)
.+++.+.++|...|... ..-+++|..||+++..|+++++.-|. .+|.
T Consensus 129 ~L~~~~r~i~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~Rar~-~Lr~ 175 (179)
T PRK12514 129 ELEKDRAAAVRRAYLEG-----LSYKELAERHDVPLNTMRTWLRRSLL-KLRE 175 (179)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCChHHHHHHHHHHHH-HHHH
Confidence 58889988888877432 23678999999999999999988777 5544
No 106
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=40.83 E-value=13 Score=31.55 Aligned_cols=31 Identities=26% Similarity=0.716 Sum_probs=24.6
Q ss_pred cccccccccCCCCCCCCccccCC-CcCCcccccccC
Q 008193 238 HIICAKCKLREAFPDNDIVLCDG-TCNCAFHQKCLD 272 (574)
Q Consensus 238 d~~C~vC~~~~~~~~g~lLlCDg-~C~rafH~~Cl~ 272 (574)
...|.+|+.. .|-.|-|.. .|...||..|..
T Consensus 36 ~~~C~~C~~~----~Ga~i~C~~~~C~~~fH~~CA~ 67 (90)
T PF13771_consen 36 KLKCSICKKK----GGACIGCSHPGCSRSFHVPCAR 67 (90)
T ss_pred CCCCcCCCCC----CCeEEEEeCCCCCcEEChHHHc
Confidence 3579999986 267777873 699999999976
No 107
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=40.71 E-value=24 Score=41.35 Aligned_cols=50 Identities=22% Similarity=0.685 Sum_probs=34.5
Q ss_pred ccccccccCCCCCCCCccccCCCcCCcc-cccccCCCCCCCCCCCCCCccccCcccchhh
Q 008193 239 IICAKCKLREAFPDNDIVLCDGTCNCAF-HQKCLDPPLDTESIPPGDQGWFCKFCECKME 297 (574)
Q Consensus 239 ~~C~vC~~~~~~~~g~lLlCDg~C~raf-H~~Cl~PPL~~~~iP~gde~W~C~~C~~k~~ 297 (574)
.+|..|+... .....+|.. |.... |..|....- .+|.+. =||+.|-.+..
T Consensus 2 ~~Cp~Cg~~n---~~~akFC~~-CG~~l~~~~Cp~CG~---~~~~~~--~fC~~CG~~~~ 52 (645)
T PRK14559 2 LICPQCQFEN---PNNNRFCQK-CGTSLTHKPCPQCGT---EVPVDE--AHCPNCGAETG 52 (645)
T ss_pred CcCCCCCCcC---CCCCccccc-cCCCCCCCcCCCCCC---CCCccc--ccccccCCccc
Confidence 4688888763 355668884 88764 356766553 477776 79999976543
No 108
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=40.20 E-value=36 Score=33.27 Aligned_cols=48 Identities=19% Similarity=0.356 Sum_probs=37.8
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhh
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR 500 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~ 500 (574)
.+++.|.++|...|..+ ..-.++|.+||+++..|++++...|. .++..
T Consensus 153 ~L~~~~r~vl~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Ra~~-~Lr~~ 200 (206)
T PRK12526 153 KLPEAQQTVVKGVYFQE-----LSQEQLAQQLNVPLGTVKSRLRLALA-KLKVQ 200 (206)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHH-HHHHH
Confidence 58999999998655333 35678999999999999999988777 44444
No 109
>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=39.97 E-value=28 Score=30.53 Aligned_cols=43 Identities=21% Similarity=0.332 Sum_probs=34.4
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 494 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~ 494 (574)
.+++.|..+|...|.. ...-.++|+.||+++..|..|.+.-+.
T Consensus 110 ~L~~~~~~ii~~~~~~-----g~s~~eIA~~l~~s~~~v~~~~~~~~~ 152 (158)
T TIGR02937 110 KLPEREREVLVLRYLE-----GLSYKEIAEILGISVGTVKRRLKRARK 152 (158)
T ss_pred hCCHHHHHHHhhHHhc-----CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 5789999998766543 234569999999999999999887766
No 110
>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=39.82 E-value=22 Score=26.35 Aligned_cols=24 Identities=13% Similarity=0.153 Sum_probs=19.9
Q ss_pred HHHHHHHcCCChhhHHHhhccccc
Q 008193 471 KENLSKELSLEPEKVNKWFKNARY 494 (574)
Q Consensus 471 r~~LA~~LgL~~~qV~vWFQNrR~ 494 (574)
..++|+.||+++..|..|.++---
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g~l 26 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIGLL 26 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCC
Confidence 358999999999999999765543
No 111
>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=39.73 E-value=33 Score=25.54 Aligned_cols=37 Identities=16% Similarity=0.328 Sum_probs=28.1
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhc
Q 008193 448 MPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFK 490 (574)
Q Consensus 448 ~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQ 490 (574)
+++.|.+++...+ +. ..-.++|+.||++...|..|..
T Consensus 1 l~~~e~~i~~~~~--~~----~s~~eia~~l~~s~~tv~~~~~ 37 (57)
T cd06170 1 LTPREREVLRLLA--EG----KTNKEIADILGISEKTVKTHLR 37 (57)
T ss_pred CCHHHHHHHHHHH--cC----CCHHHHHHHHCCCHHHHHHHHH
Confidence 4667777776543 22 3668899999999999999886
No 112
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 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 domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=39.72 E-value=4.7 Score=33.79 Aligned_cols=47 Identities=26% Similarity=0.542 Sum_probs=27.9
Q ss_pred cccccccccCCCCC--------CCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCccc
Q 008193 238 HIICAKCKLREAFP--------DNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCE 293 (574)
Q Consensus 238 d~~C~vC~~~~~~~--------~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~ 293 (574)
++.|.+|...-... ++-.+.-. .|.-.||..|+..-|.. . ..||.|+
T Consensus 19 ~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~-~C~H~FH~~Ci~~Wl~~------~--~~CP~CR 73 (73)
T PF12678_consen 19 DDNCAICREPLEDPCPECQAPQDECPIVWG-PCGHIFHFHCISQWLKQ------N--NTCPLCR 73 (73)
T ss_dssp CSBETTTTSBTTSTTCCHHHCTTTS-EEEE-TTSEEEEHHHHHHHHTT------S--SB-TTSS
T ss_pred CCcccccChhhhChhhhhcCCccccceEec-ccCCCEEHHHHHHHHhc------C--CcCCCCC
Confidence 34488888753111 11222223 59999999999877652 1 4699885
No 113
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=39.55 E-value=39 Score=30.07 Aligned_cols=41 Identities=17% Similarity=0.264 Sum_probs=35.7
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHH
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNK 487 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~v 487 (574)
.++++|.+.-.+.|+.|--...-..+++|++||.++..|..
T Consensus 2 SLn~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~lek 42 (97)
T COG4367 2 SLNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKLEK 42 (97)
T ss_pred CCCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHHHH
Confidence 47889999888888888888888899999999999987764
No 114
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=39.47 E-value=53 Score=29.84 Aligned_cols=43 Identities=12% Similarity=0.209 Sum_probs=29.3
Q ss_pred cCCCHHHHH-HHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccc
Q 008193 446 HRMPPNAVE-KLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNAR 493 (574)
Q Consensus 446 ~r~t~~Q~~-~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR 493 (574)
.+||.+... ++..++. +. ....+||+++|+++.+|..|.+--+
T Consensus 11 r~ys~EfK~~aV~~~~~-~g----~sv~evA~e~gIs~~tl~~W~r~y~ 54 (121)
T PRK09413 11 RRRTTQEKIAIVQQSFE-PG----MTVSLVARQHGVAASQLFLWRKQYQ 54 (121)
T ss_pred CCCCHHHHHHHHHHHHc-CC----CCHHHHHHHHCcCHHHHHHHHHHHh
Confidence 467777654 4444443 33 3456789999999999999965443
No 115
>PF13730 HTH_36: Helix-turn-helix domain
Probab=38.71 E-value=79 Score=24.17 Aligned_cols=41 Identities=24% Similarity=0.329 Sum_probs=30.2
Q ss_pred CCCHHHHHHHHHHHHhC-----CCCCHHHHHHHHHHcCCChhhHHHhhc
Q 008193 447 RMPPNAVEKLRQVFAEN-----ELPSRIVKENLSKELSLEPEKVNKWFK 490 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~-----~yPs~~~r~~LA~~LgL~~~qV~vWFQ 490 (574)
.+++.+..++-..+... .||+ ...||..+|++.+.|+.+..
T Consensus 2 ~Ls~~~~~v~~~l~~~~~~~~~~~pS---~~~la~~~g~s~~Tv~~~i~ 47 (55)
T PF13730_consen 2 NLSPTAKLVYLYLASYANKNGGCFPS---QETLAKDLGVSRRTVQRAIK 47 (55)
T ss_pred CCCHHHHHHHHHHHHhcCCCCCCCcC---HHHHHHHHCcCHHHHHHHHH
Confidence 46677777666555443 4564 77899999999999998765
No 116
>KOG1844 consensus PHD Zn-finger proteins [General function prediction only]
Probab=38.10 E-value=18 Score=40.28 Aligned_cols=47 Identities=23% Similarity=0.573 Sum_probs=35.8
Q ss_pred ccccCCCCC-CCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccchhh
Q 008193 243 KCKLREAFP-DNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKME 297 (574)
Q Consensus 243 vC~~~~~~~-~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k~~ 297 (574)
.|+..+ + ++.|+.|+. |..|-|..|+...-.+ .|+. ..|..|..+..
T Consensus 90 ~c~~~~--~~~g~~i~c~~-c~~Wqh~~C~g~~~~~--~p~~---y~c~~c~~~~~ 137 (508)
T KOG1844|consen 90 DCGLED--DMEGLMIQCDW-CGRWQHKICCGSFKST--KPDK---YVCEICTPRNK 137 (508)
T ss_pred cccccc--CCCceeeCCcc-cCcccCceeeeecCCC--Cchh---ceeeeeccccc
Confidence 566654 4 689999995 9999999999977553 3443 67999987653
No 117
>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=37.58 E-value=44 Score=26.16 Aligned_cols=42 Identities=14% Similarity=0.217 Sum_probs=33.9
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 494 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~ 494 (574)
.||+.++++|.-...-. ...++|.+||+++..|..+..|-+.
T Consensus 3 ~LT~~E~~vl~~l~~G~------~~~eIA~~l~is~~tV~~~~~~i~~ 44 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM------SNKEIAEELGISEKTVKSHRRRIMK 44 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-------HHHHHHHHTSHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHhcC------CcchhHHhcCcchhhHHHHHHHHHH
Confidence 68999999999666543 5688999999999999998887766
No 118
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=36.90 E-value=5.9 Score=36.02 Aligned_cols=38 Identities=29% Similarity=0.679 Sum_probs=22.0
Q ss_pred cccccccCCCCCCCCccccCCCcCCcccccccCCCCCC
Q 008193 240 ICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDT 277 (574)
Q Consensus 240 ~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~ 277 (574)
.|..|+...+...++...-=|.|+.+||+.|..--|.+
T Consensus 59 ~CieCQa~~~~~~~EC~VaWG~CNHaFH~hCisrWlkt 96 (114)
T KOG2930|consen 59 LCIECQANQSATSEECTVAWGVCNHAFHFHCISRWLKT 96 (114)
T ss_pred HHHhhccCCCCCCCceEEEeeecchHHHHHHHHHHHhh
Confidence 34555554321223322222469999999999877664
No 119
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=36.60 E-value=44 Score=30.85 Aligned_cols=43 Identities=16% Similarity=0.262 Sum_probs=35.4
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 494 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~ 494 (574)
.+++.+..+|...|... -.-.++|..||+++..|..|..--|.
T Consensus 125 ~L~~~~r~i~~l~~~~~-----~~~~eIA~~lgis~~tv~~~~~ra~~ 167 (179)
T PRK11924 125 ALPVKQREVFLLRYVEG-----LSYREIAEILGVPVGTVKSRLRRARQ 167 (179)
T ss_pred hCCHHHHHHhhHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 58888999988776432 34478999999999999999988777
No 120
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=36.53 E-value=35 Score=32.29 Aligned_cols=47 Identities=19% Similarity=0.253 Sum_probs=38.1
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHh
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKA 499 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~ 499 (574)
.+|+.+.++|...|.. ...-.+||..||++...|.+++..-|. ++|.
T Consensus 131 ~L~~~~r~v~~l~~~~-----g~s~~eIA~~l~is~~tV~~~l~ra~~-~Lr~ 177 (184)
T PRK12512 131 TLPPRQRDVVQSISVE-----GASIKETAAKLSMSEGAVRVALHRGLA-ALAA 177 (184)
T ss_pred hCCHHHHHHHHHHHHc-----CCCHHHHHHHhCCCHHHHHHHHHHHHH-HHHH
Confidence 5899999999987544 234578999999999999999998888 4443
No 121
>PHA02929 N1R/p28-like protein; Provisional
Probab=35.77 E-value=15 Score=37.81 Aligned_cols=49 Identities=22% Similarity=0.362 Sum_probs=31.1
Q ss_pred cccccccccCCCCCCC---C-ccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccchh
Q 008193 238 HIICAKCKLREAFPDN---D-IVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKM 296 (574)
Q Consensus 238 d~~C~vC~~~~~~~~g---~-lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k~ 296 (574)
+..|++|...-..++. . .++. . |...||..|+...+. .. =.||.|+...
T Consensus 174 ~~eC~ICle~~~~~~~~~~~~~vl~-~-C~H~FC~~CI~~Wl~--~~------~tCPlCR~~~ 226 (238)
T PHA02929 174 DKECAICMEKVYDKEIKNMYFGILS-N-CNHVFCIECIDIWKK--EK------NTCPVCRTPF 226 (238)
T ss_pred CCCCccCCcccccCccccccceecC-C-CCCcccHHHHHHHHh--cC------CCCCCCCCEe
Confidence 4689999885221110 0 1333 2 999999999987665 11 2599998643
No 122
>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=35.64 E-value=31 Score=24.52 Aligned_cols=23 Identities=17% Similarity=0.375 Sum_probs=20.4
Q ss_pred HHHHHHHcCCChhhHHHhhcccc
Q 008193 471 KENLSKELSLEPEKVNKWFKNAR 493 (574)
Q Consensus 471 r~~LA~~LgL~~~qV~vWFQNrR 493 (574)
..+||+.+|+++..|..|..+.+
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~~ 37 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGKR 37 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCCC
Confidence 35899999999999999998874
No 123
>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=35.35 E-value=31 Score=26.23 Aligned_cols=24 Identities=13% Similarity=0.321 Sum_probs=20.7
Q ss_pred HHHHHHHcCCChhhHHHhhccccc
Q 008193 471 KENLSKELSLEPEKVNKWFKNARY 494 (574)
Q Consensus 471 r~~LA~~LgL~~~qV~vWFQNrR~ 494 (574)
..+||+.+|+++..|..|+.+.+.
T Consensus 12 ~~~la~~~gis~~~i~~~~~g~~~ 35 (55)
T PF01381_consen 12 QKELAEKLGISRSTISRIENGKRN 35 (55)
T ss_dssp HHHHHHHHTS-HHHHHHHHTTSST
T ss_pred HHHHHHHhCCCcchhHHHhcCCCC
Confidence 478999999999999999999764
No 124
>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=35.29 E-value=24 Score=26.59 Aligned_cols=21 Identities=5% Similarity=0.234 Sum_probs=19.7
Q ss_pred HHHHHcCCChhhHHHhhcccc
Q 008193 473 NLSKELSLEPEKVNKWFKNAR 493 (574)
Q Consensus 473 ~LA~~LgL~~~qV~vWFQNrR 493 (574)
+||+.+|++...|..|+.|..
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 699999999999999999985
No 125
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=35.05 E-value=27 Score=27.85 Aligned_cols=20 Identities=15% Similarity=0.343 Sum_probs=17.3
Q ss_pred HHHHHHHcCCChhhHHHhhc
Q 008193 471 KENLSKELSLEPEKVNKWFK 490 (574)
Q Consensus 471 r~~LA~~LgL~~~qV~vWFQ 490 (574)
..++|+.+|+++++|+.|=+
T Consensus 3 i~eva~~~gvs~~tlr~y~~ 22 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYER 22 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35899999999999999943
No 126
>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=35.04 E-value=32 Score=25.89 Aligned_cols=24 Identities=4% Similarity=-0.040 Sum_probs=21.6
Q ss_pred HHHHHHHcCCChhhHHHhhccccc
Q 008193 471 KENLSKELSLEPEKVNKWFKNARY 494 (574)
Q Consensus 471 r~~LA~~LgL~~~qV~vWFQNrR~ 494 (574)
..+||..+|++...|..|..+++.
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~~~ 41 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGKPT 41 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCCC
Confidence 578999999999999999988764
No 127
>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=34.89 E-value=61 Score=24.41 Aligned_cols=38 Identities=13% Similarity=0.510 Sum_probs=28.8
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhh
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWF 489 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWF 489 (574)
.++++|++.+...+... ....+||++||++...|.-|+
T Consensus 5 ~~~~~~~~~i~~l~~~G-----~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 5 KLSKEQIEEIKELYAEG-----MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHHHHHH
T ss_pred CCCHHHHHHHHHHHHCC-----CCHHHHHHHHCcCHHHHHHHH
Confidence 57887888877777765 347889999999999998765
No 128
>KOG1081 consensus Transcription factor NSD1 and related SET domain proteins [Transcription]
Probab=34.47 E-value=26 Score=39.46 Aligned_cols=30 Identities=30% Similarity=0.422 Sum_probs=21.7
Q ss_pred cccccccccccCCCCCCCCccccCCCcCCccccccc
Q 008193 236 HEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCL 271 (574)
Q Consensus 236 ~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl 271 (574)
.+...|.+|..+ +.+|+|+. |..++|-.|.
T Consensus 87 ~~~~~c~vc~~g-----gs~v~~~s-~~~~~~r~c~ 116 (463)
T KOG1081|consen 87 IEPSECFVCFKG-----GSLVTCKS-RIQAPHRKCK 116 (463)
T ss_pred CCcchhccccCC-----Cccceecc-ccccccccCc
Confidence 455789999987 78888983 6655566663
No 129
>PF07227 DUF1423: Protein of unknown function (DUF1423); InterPro: IPR004082 A total of 715 potential protein-coding genes have been identified in the nucleotide sequence of Arabidopsis thaliana chromosome 5, with an average gene density of 1 gene per 4001 bp []. Amongst the gene products is a well-conserved family of 130.7kDa proteins that share no sequence similarity with any other known proteins, other than in plants. The sequences are characterised by an N-terminal domain of variable length, a central cysteine-rich region and a relatively acidic C-terminal domain. The sequences may possess a PHD finger.
Probab=34.46 E-value=33 Score=38.42 Aligned_cols=58 Identities=22% Similarity=0.449 Sum_probs=33.5
Q ss_pred ccccccCCCC-CCCCccccCCCcCCcccccccCC--------CCCCCCCCCCCCccccCcccchhhhhh
Q 008193 241 CAKCKLREAF-PDNDIVLCDGTCNCAFHQKCLDP--------PLDTESIPPGDQGWFCKFCECKMEIIE 300 (574)
Q Consensus 241 C~vC~~~~~~-~~g~lLlCDg~C~rafH~~Cl~P--------PL~~~~iP~gde~W~C~~C~~k~~~~~ 300 (574)
|.+|..-+.. ++-..|-|| .|..+.|..|.-- ...- .+...+-.++|..|....+.+.
T Consensus 131 C~iC~kfD~~~n~~~Wi~Cd-~CgH~cH~dCALr~~~i~~G~s~~g-~~g~~d~~f~C~~C~~~seLlG 197 (446)
T PF07227_consen 131 CCICSKFDDNKNTCSWIGCD-VCGHWCHLDCALRHELIGTGPSVKG-SIGTLDMQFHCRACGKTSELLG 197 (446)
T ss_pred ccccCCcccCCCCeeEEecc-CCCceehhhhhcccccccCCccCCC-CCccCceEEEccCCCChhhHHH
Confidence 4455543221 123478899 6999999999532 1110 1111123499999988766543
No 130
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=34.21 E-value=35 Score=32.08 Aligned_cols=47 Identities=21% Similarity=0.300 Sum_probs=37.3
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHh
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKA 499 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~ 499 (574)
.+++.+.++|...|.. ...-.++|..||+++..|.++++.-|. +++.
T Consensus 136 ~L~~~~r~v~~l~~~~-----g~s~~eIA~~lgis~~~v~~~l~Rar~-~Lr~ 182 (187)
T TIGR02948 136 ALPPKYRMVIVLKYME-----DLSLKEISEILDLPVGTVKTRIHRGRE-ALRK 182 (187)
T ss_pred hCCHHHhHHhhhHHhc-----CCCHHHHHHHHCCCHHHHHHHHHHHHH-HHHH
Confidence 6899999999875443 345578999999999999999988777 4443
No 131
>PF12824 MRP-L20: Mitochondrial ribosomal protein subunit L20; InterPro: IPR024388 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents the essential mitochondrial ribosomal protein L20 family from fungi [].
Probab=33.99 E-value=73 Score=31.13 Aligned_cols=45 Identities=20% Similarity=0.380 Sum_probs=38.1
Q ss_pred ccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcc
Q 008193 445 FHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKN 491 (574)
Q Consensus 445 r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQN 491 (574)
.+.+|+++|+++.+.=.++ |....+..||+++|+++.-|.+=.+-
T Consensus 83 ~y~Lt~e~i~Eir~LR~~D--P~~wTr~~LAkkF~~S~~fV~~v~~~ 127 (164)
T PF12824_consen 83 KYHLTPEDIQEIRRLRAED--PEKWTRKKLAKKFNCSPLFVSMVAPA 127 (164)
T ss_pred cccCCHHHHHHHHHHHHcC--chHhhHHHHHHHhCCCHHHHHHhcCC
Confidence 3789999999999887766 78899999999999999888865543
No 132
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=33.70 E-value=40 Score=31.17 Aligned_cols=43 Identities=14% Similarity=0.113 Sum_probs=34.7
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 494 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~ 494 (574)
.+++.+.++|...|... -.-.++|..||+++..|..|.+.-+.
T Consensus 128 ~L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~ra~~ 170 (182)
T PRK09652 128 SLPEELRTAITLREIEG-----LSYEEIAEIMGCPIGTVRSRIFRARE 170 (182)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 59999999998775432 23458999999999999999986665
No 133
>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=33.49 E-value=29 Score=28.12 Aligned_cols=22 Identities=18% Similarity=0.373 Sum_probs=18.6
Q ss_pred HHHHHHHHHcCCChhhHHHhhc
Q 008193 469 IVKENLSKELSLEPEKVNKWFK 490 (574)
Q Consensus 469 ~~r~~LA~~LgL~~~qV~vWFQ 490 (574)
-.-.++|++||++...|..|-+
T Consensus 14 ~~~~eIA~~Lg~~~~TV~~W~~ 35 (58)
T PF06056_consen 14 WSIKEIAEELGVPRSTVYSWKD 35 (58)
T ss_pred CCHHHHHHHHCCChHHHHHHHH
Confidence 3456899999999999999954
No 134
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=32.73 E-value=45 Score=30.81 Aligned_cols=47 Identities=15% Similarity=0.064 Sum_probs=37.4
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHh
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKA 499 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~ 499 (574)
.+++.|..+|...|-.+ -.-.++|..||+++..|+++...-|. ++++
T Consensus 112 ~L~~~~r~v~~l~~~~~-----~s~~eIA~~lgis~~tv~~~l~Rar~-~L~~ 158 (161)
T PRK12541 112 SLPLERRNVLLLRDYYG-----FSYKEIAEMTGLSLAKVKIELHRGRK-ETKS 158 (161)
T ss_pred HCCHHHHHHhhhHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHH-HHHh
Confidence 58999999998765433 23478999999999999999988887 4444
No 135
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=32.48 E-value=53 Score=31.29 Aligned_cols=44 Identities=16% Similarity=0.115 Sum_probs=36.3
Q ss_pred cCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193 446 HRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 494 (574)
Q Consensus 446 ~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~ 494 (574)
..+++.|.+++...|... ..-.++|.+||++...|+.+...-|.
T Consensus 138 ~~L~~~~r~i~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Ra~~ 181 (189)
T PRK09648 138 DTLPEKQREILILRVVVG-----LSAEETAEAVGSTPGAVRVAQHRALA 181 (189)
T ss_pred HhCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 369999999999876553 34689999999999999998876666
No 136
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=32.33 E-value=33 Score=25.75 Aligned_cols=26 Identities=23% Similarity=0.445 Sum_probs=18.4
Q ss_pred HHHHHHHHHHcCCChhhHHHhhcccc
Q 008193 468 RIVKENLSKELSLEPEKVNKWFKNAR 493 (574)
Q Consensus 468 ~~~r~~LA~~LgL~~~qV~vWFQNrR 493 (574)
.....++|+.||++...|..|.+.-+
T Consensus 17 G~s~~~ia~~lgvs~~Tv~~w~kr~~ 42 (50)
T PF13384_consen 17 GWSIREIAKRLGVSRSTVYRWIKRYR 42 (50)
T ss_dssp T--HHHHHHHHTS-HHHHHHHHT---
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHcc
Confidence 55678999999999999999987644
No 137
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=31.50 E-value=61 Score=29.85 Aligned_cols=49 Identities=16% Similarity=0.169 Sum_probs=38.0
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhh
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK 501 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~ 501 (574)
.+|+.+.+++...|... -.-.++|..||+++..|++++..-|. .+|..-
T Consensus 106 ~Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Rar~-~Lr~~l 154 (160)
T PRK09642 106 ELPENYRDVVLAHYLEE-----KSYQEIALQEKIEVKTVEMKLYRARK-WIKKHW 154 (160)
T ss_pred hCCHHHHHHHHHHHHhC-----CCHHHHHHHHCCCHHHHHHHHHHHHH-HHHHHH
Confidence 58999999998765433 22368999999999999999988887 555543
No 138
>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=31.45 E-value=44 Score=30.20 Aligned_cols=43 Identities=14% Similarity=0.150 Sum_probs=33.7
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 494 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~ 494 (574)
.+++.+.++|...|-. .+ .-.++|..||+++..|+.+...-|.
T Consensus 113 ~L~~~~r~il~l~~~~-~~----~~~eIA~~lgis~~tv~~~~~ra~~ 155 (161)
T TIGR02985 113 KLPEQCRKIFILSRFE-GK----SYKEIAEELGISVKTVEYHISKALK 155 (161)
T ss_pred HCCHHHHHHHHHHHHc-CC----CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 5888999999876543 23 3456999999999999998877666
No 139
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=31.29 E-value=42 Score=42.18 Aligned_cols=62 Identities=18% Similarity=0.212 Sum_probs=55.3
Q ss_pred cccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhh
Q 008193 439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR 500 (574)
Q Consensus 439 ~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~ 500 (574)
.+.++.+..+-.++...|-++|..+.-|+.+.+.-|.-.-+.+.+++.+||+|-|.+.++-.
T Consensus 703 ~~~~~~~~~~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 703 PRDKLLRLTILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred cccccCcccccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc
Confidence 45667778888899999999999999999999999999999999999999999999554444
No 140
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=30.90 E-value=38 Score=32.35 Aligned_cols=47 Identities=15% Similarity=0.299 Sum_probs=37.3
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHh
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKA 499 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~ 499 (574)
.+++.+.++|...|.. ...-.++|..||+++..|++|++..|. +++.
T Consensus 141 ~L~~~~~~v~~l~~~~-----g~s~~EIA~~lgis~~tV~~~l~Ra~~-~Lr~ 187 (194)
T PRK12519 141 QLPESQRQVLELAYYE-----GLSQSEIAKRLGIPLGTVKARARQGLL-KLRE 187 (194)
T ss_pred hCCHHHhhhhhhhhhc-----CCCHHHHHHHhCCCHHHHHHHHHHHHH-HHHH
Confidence 5889999999876533 334578999999999999999988777 4444
No 141
>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=30.88 E-value=48 Score=30.28 Aligned_cols=43 Identities=19% Similarity=0.259 Sum_probs=34.8
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 494 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~ 494 (574)
.+|+.+.+++...|.. .-.-.++|..||++...|.++...-|.
T Consensus 111 ~L~~~~r~v~~l~~~~-----g~~~~eIA~~l~is~~tv~~~l~Rar~ 153 (159)
T TIGR02989 111 KLPERQRELLQLRYQR-----GVSLTALAEQLGRTVNAVYKALSRLRV 153 (159)
T ss_pred HCCHHHHHHHHHHHhc-----CCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 5899999999986543 234578999999999999998776666
No 142
>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=30.84 E-value=31 Score=26.40 Aligned_cols=34 Identities=24% Similarity=0.362 Sum_probs=24.6
Q ss_pred cccccccccCCCCCCCCccccCCCcCCcccccccC
Q 008193 238 HIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLD 272 (574)
Q Consensus 238 d~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~ 272 (574)
-.+|.+|+..-......-+.|.. |...+|..|+.
T Consensus 11 ~~~C~~C~~~i~g~~~~g~~C~~-C~~~~H~~C~~ 44 (53)
T PF00130_consen 11 PTYCDVCGKFIWGLGKQGYRCSW-CGLVCHKKCLS 44 (53)
T ss_dssp TEB-TTSSSBECSSSSCEEEETT-TT-EEETTGGC
T ss_pred CCCCcccCcccCCCCCCeEEECC-CCChHhhhhhh
Confidence 36899999865223466788995 99999999987
No 143
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=30.80 E-value=16 Score=26.06 Aligned_cols=23 Identities=22% Similarity=0.806 Sum_probs=12.1
Q ss_pred cccccccCCCCCCCCccccCCCcC
Q 008193 240 ICAKCKLREAFPDNDIVLCDGTCN 263 (574)
Q Consensus 240 ~C~vC~~~~~~~~g~lLlCDg~C~ 263 (574)
.|..|+......|+.++.|. .|.
T Consensus 4 ~Cp~C~se~~y~D~~~~vCp-~C~ 26 (30)
T PF08274_consen 4 KCPLCGSEYTYEDGELLVCP-ECG 26 (30)
T ss_dssp --TTT-----EE-SSSEEET-TTT
T ss_pred CCCCCCCcceeccCCEEeCC-ccc
Confidence 58888887776788888898 485
No 144
>PRK00118 putative DNA-binding protein; Validated
Probab=30.14 E-value=55 Score=29.69 Aligned_cols=43 Identities=7% Similarity=0.153 Sum_probs=35.1
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 494 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~ 494 (574)
.+++.|.+++...|... ..-.+||+.+|+++..|..|....|.
T Consensus 17 ~L~ekqRevl~L~y~eg-----~S~~EIAe~lGIS~~TV~r~L~RArk 59 (104)
T PRK00118 17 LLTEKQRNYMELYYLDD-----YSLGEIAEEFNVSRQAVYDNIKRTEK 59 (104)
T ss_pred cCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 57888999987776653 34567999999999999999987776
No 145
>PF01214 CK_II_beta: Casein kinase II regulatory subunit; InterPro: IPR000704 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. Casein kinase, a ubiquitous, well-conserved protein kinase involved in cell metabolism and differentiation, is characterised by its preference for Ser or Thr in acidic stretches of amino acids. The enzyme is a tetramer of 2 alpha- and 2 beta-subunits [, ]. However, some species (e.g., mammals) possess 2 related forms of the alpha-subunit (alpha and alpha'), while others (e.g., fungi) possess 2 related beta-subunits (beta and beta') []. The alpha-subunit is the catalytic unit and contains regions characteristic of serine/threonine protein kinases. The beta-subunit is believed to be regulatory, possessing an N-terminal auto-phosphorylation site, an internal acidic domain, and a potential metal-binding motif []. The beta subunit is a highly conserved protein of about 25kDa that contains, in its central section, a cysteine-rich motif, CX(n)C, that could be involved in binding a metal such as zinc []. The mammalian beta-subunit gene promoter shares common features with those of other mammalian protein kinases and is closely related to the promoter of the regulatory subunit of cAMP-dependent protein kinase [].; GO: 0019887 protein kinase regulator activity, 0005956 protein kinase CK2 complex; PDB: 2R6M_B 1RQF_K 1DS5_G 1QF8_B 3EED_A 4DGL_A 1JWH_D.
Probab=29.35 E-value=27 Score=34.64 Aligned_cols=34 Identities=15% Similarity=0.342 Sum_probs=15.2
Q ss_pred CcCCcccccccCCCCCCCCCCCCC-CccccCcccc
Q 008193 261 TCNCAFHQKCLDPPLDTESIPPGD-QGWFCKFCEC 294 (574)
Q Consensus 261 ~C~rafH~~Cl~PPL~~~~iP~gd-e~W~C~~C~~ 294 (574)
.|++.++..+..-|+...+.|... -.+|||.|..
T Consensus 101 ~CPRv~C~~~~lLPiGlsd~~g~~~vKlyCP~C~d 135 (184)
T PF01214_consen 101 RCPRVYCNGQPLLPIGLSDTPGESTVKLYCPRCKD 135 (184)
T ss_dssp B-SBGGGTT-B-EEEBS-SSTTS-BBEEEETTTTE
T ss_pred cCCcccCCCCceeCccCCCCCCccceeEECCCCcc
Confidence 355555443333333322344322 2599999974
No 146
>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=29.10 E-value=68 Score=30.16 Aligned_cols=47 Identities=19% Similarity=0.274 Sum_probs=37.5
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHh
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKA 499 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~ 499 (574)
.+|+.|..++...|... -.-.++|..||+++..|++..+.-|. ++++
T Consensus 134 ~Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tVk~~l~Rar~-~Lr~ 180 (183)
T TIGR02999 134 QVDPRQAEVVELRFFAG-----LTVEEIAELLGVSVRTVERDWRFARA-WLAD 180 (183)
T ss_pred cCCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHHHHHH-HHHH
Confidence 48999999998876443 34578999999999999999988777 4443
No 147
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=29.07 E-value=47 Score=31.58 Aligned_cols=48 Identities=13% Similarity=0.262 Sum_probs=37.6
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhh
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR 500 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~ 500 (574)
.+++.+.++|...|.+ ...-.++|+.||++...|+++...-|. .+|+.
T Consensus 128 ~L~~~~r~i~~l~~~~-----g~s~~EIA~~lgis~~tV~~~l~Rar~-~Lr~~ 175 (186)
T PRK05602 128 ALPERQREAIVLQYYQ-----GLSNIEAAAVMDISVDALESLLARGRR-ALRAQ 175 (186)
T ss_pred hCCHHHHHHhhHHHhc-----CCCHHHHHHHhCcCHHHHHHHHHHHHH-HHHHH
Confidence 5889999999876543 234578999999999999999988887 45544
No 148
>COG1773 Rubredoxin [Energy production and conversion]
Probab=28.83 E-value=40 Score=27.42 Aligned_cols=18 Identities=22% Similarity=0.708 Sum_probs=13.0
Q ss_pred CCCCCCCccccCcccchhhhh
Q 008193 279 SIPPGDQGWFCKFCECKMEII 299 (574)
Q Consensus 279 ~iP~gde~W~C~~C~~k~~~~ 299 (574)
.||+. |.||.|-.....+
T Consensus 32 dlPd~---w~CP~Cg~~K~~F 49 (55)
T COG1773 32 DLPDD---WVCPECGVGKKDF 49 (55)
T ss_pred hCCCc---cCCCCCCCCHhHe
Confidence 68864 9999998644333
No 149
>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=28.62 E-value=65 Score=30.02 Aligned_cols=47 Identities=9% Similarity=0.155 Sum_probs=36.8
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHh
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKA 499 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~ 499 (574)
.+++.+.++|...|... ..-.++|..||+++..|+++..--|. .+++
T Consensus 119 ~L~~~~r~i~~l~~~~g-----~s~~eiA~~lgis~~tv~~~l~Ra~~-~Lr~ 165 (169)
T TIGR02954 119 TLNDKYQTAIILRYYHD-----LTIKEIAEVMNKPEGTVKTYLHRALK-KLKK 165 (169)
T ss_pred hCCHHHhHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHH-HHHH
Confidence 58899999998876554 34578999999999999998877666 4443
No 150
>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class
Probab=28.53 E-value=12 Score=29.08 Aligned_cols=44 Identities=30% Similarity=0.724 Sum_probs=25.7
Q ss_pred cccccccCCCCCCCCccc-cCCCcC---CcccccccCCCCCCCCCCCCCCccccCcc
Q 008193 240 ICAKCKLREAFPDNDIVL-CDGTCN---CAFHQKCLDPPLDTESIPPGDQGWFCKFC 292 (574)
Q Consensus 240 ~C~vC~~~~~~~~g~lLl-CDg~C~---rafH~~Cl~PPL~~~~iP~gde~W~C~~C 292 (574)
+|.+|...+ .+++.++. |. |. ..+|..||..-+.. .+. ..|+.|
T Consensus 1 ~CrIC~~~~-~~~~~l~~PC~--C~G~~~~vH~~Cl~~W~~~----~~~--~~C~iC 48 (49)
T smart00744 1 ICRICHDEG-DEGDPLVSPCR--CKGSLKYVHQECLERWINE----SGN--KTCEIC 48 (49)
T ss_pred CccCCCCCC-CCCCeeEeccc--cCCchhHHHHHHHHHHHHH----cCC--CcCCCC
Confidence 477787622 12344443 43 55 56999999977652 112 468877
No 151
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=28.29 E-value=1e+02 Score=28.11 Aligned_cols=48 Identities=15% Similarity=0.177 Sum_probs=37.1
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhh
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR 500 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~ 500 (574)
.+|+.|.++|...|-+. -.-.++|..||+++..|++...--|. ++|..
T Consensus 106 ~Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~ra~~-~Lr~~ 153 (161)
T PRK09047 106 KLPARQREAFLLRYWED-----MDVAETAAAMGCSEGSVKTHCSRATH-ALAKA 153 (161)
T ss_pred hCCHHHHHHHHHHHHhc-----CCHHHHHHHHCCCHHHHHHHHHHHHH-HHHHH
Confidence 69999999999865432 22578999999999999998887766 44443
No 152
>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=28.12 E-value=45 Score=23.98 Aligned_cols=24 Identities=17% Similarity=0.573 Sum_probs=21.0
Q ss_pred HHHHHHHcCCChhhHHHhhccccc
Q 008193 471 KENLSKELSLEPEKVNKWFKNARY 494 (574)
Q Consensus 471 r~~LA~~LgL~~~qV~vWFQNrR~ 494 (574)
..++|+.||++...|..|.++-..
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~~ 26 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGKL 26 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCCC
Confidence 468999999999999999987655
No 153
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=28.05 E-value=17 Score=38.63 Aligned_cols=44 Identities=30% Similarity=0.674 Sum_probs=29.7
Q ss_pred ccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccchh
Q 008193 239 IICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKM 296 (574)
Q Consensus 239 ~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k~ 296 (574)
..|.+|..-- -|-|.-.|...|.-.|..--|.+ .-|||.|+...
T Consensus 26 lrC~IC~~~i------~ip~~TtCgHtFCslCIR~hL~~--------qp~CP~Cr~~~ 69 (391)
T COG5432 26 LRCRICDCRI------SIPCETTCGHTFCSLCIRRHLGT--------QPFCPVCREDP 69 (391)
T ss_pred HHhhhhhhee------ecceecccccchhHHHHHHHhcC--------CCCCccccccH
Confidence 5688887642 12355468888888887766551 25899998754
No 154
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=27.55 E-value=32 Score=40.42 Aligned_cols=59 Identities=22% Similarity=0.479 Sum_probs=34.8
Q ss_pred cccccccccCCCCC---CCCccccCC-CcCCcccccccCCC-CCC-CCCCCCCCccccCcccchh
Q 008193 238 HIICAKCKLREAFP---DNDIVLCDG-TCNCAFHQKCLDPP-LDT-ESIPPGDQGWFCKFCECKM 296 (574)
Q Consensus 238 d~~C~vC~~~~~~~---~g~lLlCDg-~C~rafH~~Cl~PP-L~~-~~iP~gde~W~C~~C~~k~ 296 (574)
...|.+|.....+. -|-.+.|.. .|.++||..|..-. |.. +..-.-|..-||-.|..-.
T Consensus 117 nKtCYIC~E~GrpnkA~~GACMtCNKs~CkqaFHVTCAQ~~GLLCEE~gn~~dNVKYCGYCk~Hf 181 (900)
T KOG0956|consen 117 NKTCYICNEEGRPNKAAKGACMTCNKSGCKQAFHVTCAQRAGLLCEEEGNISDNVKYCGYCKYHF 181 (900)
T ss_pred cceeeeecccCCccccccccceecccccchhhhhhhHhhhhccceeccccccccceechhHHHHH
Confidence 45688888753322 245666763 59999999997632 111 1111112247899997543
No 155
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=27.54 E-value=68 Score=30.71 Aligned_cols=43 Identities=14% Similarity=0.170 Sum_probs=35.5
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 494 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~ 494 (574)
.+|+.+..+|...|-+. -.-.++|+.||++...|++..+--|.
T Consensus 131 ~L~~~~r~i~~l~~~~g-----~s~~EIAe~lgis~~~V~~~l~Ra~~ 173 (189)
T PRK06811 131 DLEKLDREIFIRRYLLG-----EKIEEIAKKLGLTRSAIDNRLSRGRK 173 (189)
T ss_pred hCCHHHHHHHHHHHHcc-----CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 69999999999766432 34578999999999999998887777
No 156
>PTZ00396 Casein kinase II subunit beta; Provisional
Probab=27.47 E-value=45 Score=34.77 Aligned_cols=34 Identities=12% Similarity=0.251 Sum_probs=17.8
Q ss_pred CcCCcccccccCCCCCCCCCCCC-CCccccCcccc
Q 008193 261 TCNCAFHQKCLDPPLDTESIPPG-DQGWFCKFCEC 294 (574)
Q Consensus 261 ~C~rafH~~Cl~PPL~~~~iP~g-de~W~C~~C~~ 294 (574)
.|+|.+.-.|...|+....+|.. .-.+|||.|..
T Consensus 122 ~CPRv~C~~q~~LPvGlSd~~g~~~VKlyCP~C~D 156 (251)
T PTZ00396 122 HCPRVLCEGQNVLPIGLSDVLKTSRVKVYCPRCQE 156 (251)
T ss_pred CCCCccCCCCcccccccCCCcCcCceeEeCCCchh
Confidence 45555443333333433355532 22589999964
No 157
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=27.38 E-value=76 Score=29.49 Aligned_cols=48 Identities=17% Similarity=0.158 Sum_probs=37.2
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhh
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR 500 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~ 500 (574)
.+|+.|.++|...|-.. ..-.++|..||+++..|++|.+--|. +++..
T Consensus 108 ~L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tv~~~l~Rar~-~Lr~~ 155 (165)
T PRK09644 108 TLPVIEAQAILLCDVHE-----LTYEEAASVLDLKLNTYKSHLFRGRK-RLKAL 155 (165)
T ss_pred hCCHHHHHHHHhHHHhc-----CCHHHHHHHHCCCHHHHHHHHHHHHH-HHHHH
Confidence 68999999988654322 34578999999999999999998887 44443
No 158
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=27.33 E-value=84 Score=28.97 Aligned_cols=47 Identities=13% Similarity=0.195 Sum_probs=37.3
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhh
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR 500 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~ 500 (574)
.+|+.|..+|...| ..+ .-.+||..||+++..|+++...-|. .+|..
T Consensus 112 ~L~~~~r~il~l~~--~g~----s~~eIA~~lgis~~tV~~~i~ra~~-~Lr~~ 158 (166)
T PRK09639 112 KMTERDRTVLLLRF--SGY----SYKEIAEALGIKESSVGTTLARAKK-KFRKI 158 (166)
T ss_pred cCCHHHHHHHHHHH--cCC----CHHHHHHHHCCCHHHHHHHHHHHHH-HHHHH
Confidence 58999999998877 333 4568999999999999999977777 44443
No 159
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=27.29 E-value=79 Score=31.58 Aligned_cols=48 Identities=19% Similarity=0.284 Sum_probs=39.2
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhh
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR 500 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~ 500 (574)
.+++.+.++|...|... ..-.++|..||++...|+.+...-|. .+|..
T Consensus 184 ~L~~~~r~vl~l~~~~g-----~s~~EIA~~lgis~~tV~~~~~ra~~-~Lr~~ 231 (236)
T PRK06986 184 SLPEREQLVLSLYYQEE-----LNLKEIGAVLGVSESRVSQIHSQAIK-RLRAR 231 (236)
T ss_pred hCCHHHHHHHHhHhccC-----CCHHHHHHHHCCCHHHHHHHHHHHHH-HHHHH
Confidence 58999999999887433 35689999999999999999998887 55543
No 160
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=27.11 E-value=79 Score=30.48 Aligned_cols=50 Identities=16% Similarity=0.129 Sum_probs=38.4
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhhh
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKV 502 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~~ 502 (574)
.+|+.|.++|...|.+. -.-.++|..||+++..|+++...-|. .++..-.
T Consensus 116 ~Lp~~~r~i~~L~~~~g-----~s~~EIA~~Lgis~~tVk~~l~Rar~-~Lr~~l~ 165 (187)
T PRK12516 116 QLPDDQREAIILVGASG-----FAYEEAAEICGCAVGTIKSRVNRARQ-RLQEILQ 165 (187)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHH-HHHHHHH
Confidence 58999999998765432 22468999999999999999998887 5555443
No 161
>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=27.08 E-value=57 Score=30.76 Aligned_cols=48 Identities=15% Similarity=0.158 Sum_probs=36.6
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhh
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR 500 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~ 500 (574)
.+++.+.++|...|. ....-.++|..||+++..|+++...-|. ++|+.
T Consensus 138 ~L~~~~r~v~~l~~~-----~~~s~~EIA~~lgis~~tv~~~l~rar~-~Lr~~ 185 (190)
T TIGR02939 138 ALPEDLRTAITLREL-----EGLSYEDIARIMDCPVGTVRSRIFRARE-AIAIR 185 (190)
T ss_pred cCCHHHhhhhhhhhh-----cCCCHHHHHHHHCcCHHHHHHHHHHHHH-HHHHH
Confidence 578888888876543 3334578999999999999999987777 44443
No 162
>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=26.78 E-value=33 Score=38.86 Aligned_cols=25 Identities=20% Similarity=0.045 Sum_probs=13.2
Q ss_pred CCCccccCCCCCCCCCCCCCCCCCc
Q 008193 328 DGCSALLNQEEEWPSDDSEDDDYNP 352 (574)
Q Consensus 328 ~g~~~~~~~~~~~psddsEDeD~dp 352 (574)
.+.|.+.=+-..|.+-+..-.|-.|
T Consensus 82 ~~~~~l~C~~C~Wss~~igi~Fdkp 106 (483)
T PF05502_consen 82 GKPYYLSCSYCRWSSRDIGIKFDKP 106 (483)
T ss_pred CCCEEEECCCceeeccccCccccCc
Confidence 3344433344567777666655444
No 163
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=26.69 E-value=21 Score=41.23 Aligned_cols=46 Identities=30% Similarity=0.674 Sum_probs=29.2
Q ss_pred ccccccccCCCCC---CCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccchh
Q 008193 239 IICAKCKLREAFP---DNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKM 296 (574)
Q Consensus 239 ~~C~vC~~~~~~~---~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k~ 296 (574)
.+|..|...+..- .....-|+ .|..+||..|+.-. . -.||.|...+
T Consensus 512 fiCe~Cq~~~iiyPF~~~~~~rC~-~C~avfH~~C~~r~-----s------~~CPrC~R~q 560 (580)
T KOG1829|consen 512 FICELCQHNDIIYPFETRNTRRCS-TCLAVFHKKCLRRK-----S------PCCPRCERRQ 560 (580)
T ss_pred eeeeeccCCCcccccccccceeHH-HHHHHHHHHHHhcc-----C------CCCCchHHHH
Confidence 4577775542211 23445688 59999999998732 1 1299997654
No 164
>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=26.38 E-value=44 Score=26.93 Aligned_cols=20 Identities=10% Similarity=0.386 Sum_probs=18.0
Q ss_pred HHHHHHcCCChhhHHHhhcc
Q 008193 472 ENLSKELSLEPEKVNKWFKN 491 (574)
Q Consensus 472 ~~LA~~LgL~~~qV~vWFQN 491 (574)
.++|+.+|+++..|+.|.+.
T Consensus 4 ~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 4 GEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred HHHHHHHCcCHHHHHHHHHh
Confidence 57999999999999999764
No 165
>KOG1080 consensus Histone H3 (Lys4) methyltransferase complex, subunit SET1 and related methyltransferases [Chromatin structure and dynamics; Transcription]
Probab=26.29 E-value=50 Score=40.71 Aligned_cols=51 Identities=29% Similarity=0.720 Sum_probs=38.8
Q ss_pred cccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccc
Q 008193 238 HIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCEC 294 (574)
Q Consensus 238 d~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~ 294 (574)
-.-|.+|........+.++.||. |....|..|+++. ..+.+ ..|+|..|..
T Consensus 573 t~~c~~~~~~~~~~~n~~~~~~~-~~~~~~s~~~g~~----~~~~~-~~~~~~~~~~ 623 (1005)
T KOG1080|consen 573 TERCAVCRDDEDWEKNVSIICDR-CTRSVHSECYGNL----KSYDG-TSWVCDSCET 623 (1005)
T ss_pred cccccccccccccccceeeeecc-ccccCCCcccccC----CCCCC-Ccchhhcccc
Confidence 35799999876555678999995 9999999999853 22222 2499999986
No 166
>PHA01976 helix-turn-helix protein
Probab=25.96 E-value=58 Score=25.81 Aligned_cols=24 Identities=13% Similarity=0.220 Sum_probs=21.3
Q ss_pred HHHHHHHcCCChhhHHHhhccccc
Q 008193 471 KENLSKELSLEPEKVNKWFKNARY 494 (574)
Q Consensus 471 r~~LA~~LgL~~~qV~vWFQNrR~ 494 (574)
..+||+.+|++...|..|...++.
T Consensus 18 ~~~lA~~~gvs~~~v~~~e~g~~~ 41 (67)
T PHA01976 18 APELSRRAGVRHSLIYDFEADKRL 41 (67)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCCC
Confidence 578999999999999999987764
No 167
>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=25.92 E-value=45 Score=26.71 Aligned_cols=22 Identities=14% Similarity=0.323 Sum_probs=18.8
Q ss_pred HHHHHHcCCChhhHHHhhcccc
Q 008193 472 ENLSKELSLEPEKVNKWFKNAR 493 (574)
Q Consensus 472 ~~LA~~LgL~~~qV~vWFQNrR 493 (574)
.++|+.||++++.|+.|-++-.
T Consensus 4 ~evA~~~gvs~~tlR~~~~~g~ 25 (67)
T cd04764 4 KEVSEIIGVKPHTLRYYEKEFN 25 (67)
T ss_pred HHHHHHHCcCHHHHHHHHHhcC
Confidence 5799999999999999977533
No 168
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=25.89 E-value=80 Score=29.98 Aligned_cols=46 Identities=15% Similarity=0.364 Sum_probs=36.1
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHH
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK 498 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k 498 (574)
.+|+.|.+++...|.++ ..-.++|..||++...|++|-..-|. ++|
T Consensus 133 ~L~~~~r~i~~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~ra~~-~Lr 178 (182)
T PRK12537 133 QLEPARRNCILHAYVDG-----CSHAEIAQRLGAPLGTVKAWIKRSLK-ALR 178 (182)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCChhhHHHHHHHHHH-HHH
Confidence 58899998888766433 34578999999999999999887776 444
No 169
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=25.88 E-value=77 Score=30.48 Aligned_cols=48 Identities=15% Similarity=0.214 Sum_probs=38.3
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhh
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR 500 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~ 500 (574)
.+|+.|.++|...|... -.-.++|..||+++..|+++...-|. ++|..
T Consensus 134 ~Lp~~~R~v~~L~~~~g-----~s~~EIA~~lgis~~tVk~~l~RAr~-~Lr~~ 181 (189)
T PRK12530 134 HLPAQQARVFMMREYLE-----LSSEQICQECDISTSNLHVLLYRARL-QLQAC 181 (189)
T ss_pred hCCHHHHHHHhHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHH-HHHHH
Confidence 58999999999876542 23678999999999999999988776 55543
No 170
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=25.80 E-value=1.4e+02 Score=28.73 Aligned_cols=49 Identities=16% Similarity=0.189 Sum_probs=38.3
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhh
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK 501 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~ 501 (574)
.+++.|.++|...|.. .| .-.++|+.||+++..|++++.--|. .+|..-
T Consensus 136 ~L~~~~r~i~~L~~~~-g~----s~~eIA~~lgis~~tV~~~l~Ra~~-~Lr~~l 184 (196)
T PRK12524 136 ALPERQRQAVVLRHIE-GL----SNPEIAEVMEIGVEAVESLTARGKR-ALAALL 184 (196)
T ss_pred hCCHHHHHHHHHHHHc-CC----CHHHHHHHHCcCHHHHHHHHHHHHH-HHHHHH
Confidence 5899999999886553 22 2578999999999999999998887 555543
No 171
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=25.78 E-value=83 Score=28.65 Aligned_cols=43 Identities=16% Similarity=0.248 Sum_probs=35.0
Q ss_pred cCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193 446 HRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 494 (574)
Q Consensus 446 ~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~ 494 (574)
..+|+.+.++|.- +..+ | ...++|+.|+++++.|++|.+|-|.
T Consensus 148 ~~lt~~e~~vl~l-~~~g-~----~~~~Ia~~l~~s~~tv~~~~~~~~~ 190 (211)
T PRK15369 148 PLLTPRERQILKL-ITEG-Y----TNRDIAEQLSISIKTVETHRLNMMR 190 (211)
T ss_pred cCCCHHHHHHHHH-HHCC-C----CHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3599999999986 4433 3 3679999999999999999998666
No 172
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=25.19 E-value=53 Score=35.14 Aligned_cols=32 Identities=16% Similarity=0.450 Sum_probs=22.5
Q ss_pred cccccccccccCCC---------CCCCCccccCCCcCCcccc
Q 008193 236 HEHIICAKCKLREA---------FPDNDIVLCDGTCNCAFHQ 268 (574)
Q Consensus 236 ~ed~~C~vC~~~~~---------~~~g~lLlCDg~C~rafH~ 268 (574)
....+|.|||.... ..+...+.|- .|...||+
T Consensus 182 ~~~~~CPvCGs~P~~s~~~~~~~~~G~RyL~Cs-lC~teW~~ 222 (305)
T TIGR01562 182 ESRTLCPACGSPPVASMVRQGGKETGLRYLSCS-LCATEWHY 222 (305)
T ss_pred CCCCcCCCCCChhhhhhhcccCCCCCceEEEcC-CCCCcccc
Confidence 44679999998631 1233588888 69988885
No 173
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=25.18 E-value=12 Score=40.40 Aligned_cols=58 Identities=22% Similarity=0.523 Sum_probs=39.6
Q ss_pred ccccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCC-CCCCccccCcccc
Q 008193 235 HHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIP-PGDQGWFCKFCEC 294 (574)
Q Consensus 235 ~~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP-~gde~W~C~~C~~ 294 (574)
+.+...|..|+..+... ..+++|+ .|-.+||..|+.+--...... ..++..+|+.|..
T Consensus 236 ~~~~~~~~~cg~~~~~~-~~~~~~~-~~e~w~~~~~v~~~~a~~~~~~~~~~~~~c~~~~~ 294 (345)
T KOG1632|consen 236 DYSKLICDPCGLSDANK-KFEICCD-LCESWFHGDCVQIFEARKRLNEIRNEVYKCPHCTV 294 (345)
T ss_pred ccccccccccCcchHHH-HHHHHHH-HHHHHhcccccccccchhhhhhhhccceecCceee
Confidence 34457899999875543 6788999 599999999998643321111 1223388999976
No 174
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=25.02 E-value=1e+02 Score=28.09 Aligned_cols=41 Identities=15% Similarity=0.400 Sum_probs=36.3
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 494 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~ 494 (574)
.+++.++..|.+.+.-. ....|+.||.+..-|+.|=|+|+.
T Consensus 43 ~ls~~eIk~iRe~~~lS-------Q~vFA~~L~vs~~Tv~~WEqGr~k 83 (104)
T COG2944 43 TLSPTEIKAIREKLGLS-------QPVFARYLGVSVSTVRKWEQGRKK 83 (104)
T ss_pred CCCHHHHHHHHHHhCCC-------HHHHHHHHCCCHHHHHHHHcCCcC
Confidence 49999999999887654 578999999999999999999986
No 175
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=24.92 E-value=73 Score=30.85 Aligned_cols=48 Identities=21% Similarity=0.149 Sum_probs=37.8
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhh
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR 500 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~ 500 (574)
.+|+.|.++|...|... ..-.++|..||+++..|+++++--|. .+|..
T Consensus 113 ~Lp~~~r~v~~L~~~~g-----~s~~EIA~~LgiS~~tVk~~l~Rar~-~Lr~~ 160 (188)
T PRK12546 113 QLPDEQREALILVGASG-----FSYEEAAEMCGVAVGTVKSRANRARA-RLAEL 160 (188)
T ss_pred hCCHHHhHHhhhHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHH-HHHHH
Confidence 58999999998765422 23568999999999999999998887 55543
No 176
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=24.87 E-value=67 Score=22.48 Aligned_cols=24 Identities=17% Similarity=0.313 Sum_probs=20.8
Q ss_pred HHHHHHHcCCChhhHHHhhccccc
Q 008193 471 KENLSKELSLEPEKVNKWFKNARY 494 (574)
Q Consensus 471 r~~LA~~LgL~~~qV~vWFQNrR~ 494 (574)
..+||+.+|++...|..|-.+++.
T Consensus 13 ~~~la~~~~i~~~~i~~~~~~~~~ 36 (56)
T smart00530 13 QEELAEKLGVSRSTLSRIENGKRK 36 (56)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCCC
Confidence 458999999999999999887754
No 177
>PRK10403 transcriptional regulator NarP; Provisional
Probab=24.42 E-value=67 Score=29.64 Aligned_cols=43 Identities=9% Similarity=0.218 Sum_probs=35.5
Q ss_pred cCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193 446 HRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 494 (574)
Q Consensus 446 ~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~ 494 (574)
..+|+.+.++|+..+.. -.+.+||+.|+++++.|++..+|=|.
T Consensus 152 ~~Lt~~e~~vl~~~~~g------~s~~~ia~~l~~s~~tv~~~~~~i~~ 194 (215)
T PRK10403 152 SVLTERELDVLHELAQG------LSNKQIASVLNISEQTVKVHIRNLLR 194 (215)
T ss_pred ccCCHHHHHHHHHHHCC------CCHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 46999999999865432 44678999999999999999988776
No 178
>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=24.18 E-value=90 Score=29.39 Aligned_cols=49 Identities=18% Similarity=0.269 Sum_probs=38.3
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhh
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK 501 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~ 501 (574)
.|++.+..+|...|-.+ -.-.++|.+||+++..|+++-+--|. +++..-
T Consensus 100 ~L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~Rar~-~Lr~~l 148 (170)
T TIGR02959 100 ELPDEYREAIRLTELEG-----LSQQEIAEKLGLSLSGAKSRVQRGRK-KLKELL 148 (170)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHH-HHHHHH
Confidence 68999999999876443 34578999999999999999877776 444443
No 179
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=24.12 E-value=49 Score=29.33 Aligned_cols=44 Identities=20% Similarity=0.302 Sum_probs=30.1
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhc
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFK 490 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQ 490 (574)
.++++|...-...++.|--.+.-..+++|..||+++..|..=|+
T Consensus 2 SLn~~Q~~~T~~ELq~nf~~~~ls~~~ia~dL~~s~~~le~vL~ 45 (89)
T PF10078_consen 2 SLNPEQRRATRQELQANFELSGLSLEQIAADLGTSPEHLEQVLN 45 (89)
T ss_pred CCCHHHHHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 36677766555555555444555678899999999999875443
No 180
>PF10080 DUF2318: Predicted membrane protein (DUF2318); InterPro: IPR018758 This domain of unknown function is found in hypothetical bacterial membrane proteins with no known function.
Probab=24.07 E-value=30 Score=31.33 Aligned_cols=42 Identities=21% Similarity=0.558 Sum_probs=30.5
Q ss_pred CCCCcccccccccccccCCCCCCCCccccCCCcCCcccccccC
Q 008193 230 TDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLD 272 (574)
Q Consensus 230 ~dg~~~~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~ 272 (574)
.++..-..-+.|.+|+.......++-|.|- .|+..|+..=++
T Consensus 27 ~dg~~~va~daCeiC~~~GY~q~g~~lvC~-~C~~~~~~~~ig 68 (102)
T PF10080_consen 27 PDGSYRVAFDACEICGPKGYYQEGDQLVCK-NCGVRFNLPTIG 68 (102)
T ss_pred CCCCEEEEEEeccccCCCceEEECCEEEEe-cCCCEEehhhcc
Confidence 345556667899999876555567888899 599999865443
No 181
>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=24.02 E-value=83 Score=28.94 Aligned_cols=47 Identities=15% Similarity=0.258 Sum_probs=37.0
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHh
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKA 499 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~ 499 (574)
.+++.+.++|...|.. .-.-.++|..||++...|+++-..-|. +++.
T Consensus 110 ~L~~~~r~i~~l~~~~-----g~s~~eIA~~lgis~~tV~~~l~ra~~-~Lr~ 156 (162)
T TIGR02983 110 RLPARQRAVVVLRYYE-----DLSEAQVAEALGISVGTVKSRLSRALA-RLRE 156 (162)
T ss_pred hCCHHHHHHhhhHHHh-----cCCHHHHHHHhCCCHHHHHHHHHHHHH-HHHH
Confidence 5889999999887743 233468999999999999999888777 4443
No 182
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=23.93 E-value=26 Score=36.74 Aligned_cols=52 Identities=21% Similarity=0.449 Sum_probs=36.5
Q ss_pred CcccccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccchh
Q 008193 233 SVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKM 296 (574)
Q Consensus 233 ~~~~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k~ 296 (574)
..+..+..|..|-.. -....|-. |...|.+.|+...+.. .-+ =|||.|+.+.
T Consensus 210 fip~~d~kC~lC~e~-----~~~ps~t~-CgHlFC~~Cl~~~~t~-~k~-----~~CplCRak~ 261 (271)
T COG5574 210 FIPLADYKCFLCLEE-----PEVPSCTP-CGHLFCLSCLLISWTK-KKY-----EFCPLCRAKV 261 (271)
T ss_pred cccccccceeeeecc-----cCCccccc-ccchhhHHHHHHHHHh-hcc-----ccCchhhhhc
Confidence 445567779999875 34456885 9999999998864442 111 4799998764
No 183
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=23.89 E-value=15 Score=38.74 Aligned_cols=61 Identities=18% Similarity=0.346 Sum_probs=40.4
Q ss_pred cccccccccccCCC-----CCCCCccccCCCcCCcccccccCCCCC-CCCCCCCCCccccCcccchhhhh
Q 008193 236 HEHIICAKCKLREA-----FPDNDIVLCDGTCNCAFHQKCLDPPLD-TESIPPGDQGWFCKFCECKMEII 299 (574)
Q Consensus 236 ~ed~~C~vC~~~~~-----~~~g~lLlCDg~C~rafH~~Cl~PPL~-~~~iP~gde~W~C~~C~~k~~~~ 299 (574)
....+|..|-+... .-+.+||.|.. |.+.=|..||.-... ...|-.-. |.|-.|....-|.
T Consensus 222 ~Pn~YCDFclgdsr~nkkt~~peelvscsd-cgrsghpsclqft~nm~~avk~yr--wqcieck~csicg 288 (336)
T KOG1244|consen 222 QPNPYCDFCLGDSRENKKTGMPEELVSCSD-CGRSGHPSCLQFTANMIAAVKTYR--WQCIECKYCSICG 288 (336)
T ss_pred cCCcccceeccccccccccCCchhhcchhh-cCCCCCcchhhhhHHHHHHHHhhe--eeeeecceecccc
Confidence 34568888876421 11467999994 999999999974321 01233445 9999998765443
No 184
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=23.79 E-value=1.1e+02 Score=29.95 Aligned_cols=39 Identities=10% Similarity=0.039 Sum_probs=34.8
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHH
Q 008193 448 MPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVN 486 (574)
Q Consensus 448 ~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~ 486 (574)
.-..-+..|..++.+..|.+......+|..|||+...|.
T Consensus 23 ~rsAlip~L~~aQ~~~G~l~~~ai~~iA~~L~i~~~~v~ 61 (160)
T COG1905 23 KRSALIPLLHIAQEQFGWLPPEAIEEIADMLGIPRARVY 61 (160)
T ss_pred chhHHHHHHHHHHHHhCCCCHHHHHHHHHHhCCCHHHhe
Confidence 445678899999999999999999999999999998864
No 185
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=23.54 E-value=25 Score=30.71 Aligned_cols=48 Identities=29% Similarity=0.587 Sum_probs=30.6
Q ss_pred ccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccch
Q 008193 239 IICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECK 295 (574)
Q Consensus 239 ~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k 295 (574)
+.|..|..+-. ++++..+-=|.|+.+||..|..--|.+ . =.||-|...
T Consensus 32 ~~C~eCq~~~~-~~~eC~v~wG~CnHaFH~HCI~rWL~T----k----~~CPld~q~ 79 (88)
T COG5194 32 GTCPECQFGMT-PGDECPVVWGVCNHAFHDHCIYRWLDT----K----GVCPLDRQT 79 (88)
T ss_pred CcCcccccCCC-CCCcceEEEEecchHHHHHHHHHHHhh----C----CCCCCCCce
Confidence 45777776432 234433333479999999999987764 2 248877654
No 186
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=23.51 E-value=97 Score=33.06 Aligned_cols=55 Identities=18% Similarity=0.134 Sum_probs=43.6
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhhhh
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVE 503 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~~e 503 (574)
.+++.|..+|...|.-. |-..-.-.+||..||++...|+.+....+. ++|..-..
T Consensus 262 ~L~~~~R~vl~lrygL~-~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~-kLr~~l~~ 316 (325)
T PRK05657 262 ELNDKQREVLARRFGLL-GYEAATLEDVAREIGLTRERVRQIQVEALR-RLREILQT 316 (325)
T ss_pred cCCHHHHHHHHHHhccC-CCCCcCHHHHHHHHCcCHHHHHHHHHHHHH-HHHHHHHh
Confidence 69999999999888432 234556689999999999999999998888 55655443
No 187
>PF11212 DUF2999: Protein of unknown function (DUF2999); InterPro: IPR021376 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=23.44 E-value=1.2e+02 Score=26.09 Aligned_cols=37 Identities=22% Similarity=0.395 Sum_probs=28.1
Q ss_pred cCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHH
Q 008193 446 HRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVN 486 (574)
Q Consensus 446 ~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~ 486 (574)
+.++++|+..|.+.|.+||+-. ..+-.+|||++...+
T Consensus 11 hnvsd~qi~elFq~lT~NPl~A----Ma~i~qLGip~eKLQ 47 (82)
T PF11212_consen 11 HNVSDEQINELFQALTQNPLAA----MATIQQLGIPQEKLQ 47 (82)
T ss_pred cCCCHHHHHHHHHHHhhCHHHH----HHHHHHcCCCHHHHH
Confidence 5689999999999999998743 233456777777655
No 188
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=23.42 E-value=56 Score=24.14 Aligned_cols=18 Identities=17% Similarity=0.337 Sum_probs=15.3
Q ss_pred HHHHHHcCCChhhHHHhh
Q 008193 472 ENLSKELSLEPEKVNKWF 489 (574)
Q Consensus 472 ~~LA~~LgL~~~qV~vWF 489 (574)
-++|+.+|++.+.|..|=
T Consensus 3 ~e~A~~~gvs~~tlR~ye 20 (38)
T PF00376_consen 3 GEVAKLLGVSPRTLRYYE 20 (38)
T ss_dssp HHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHCCCHHHHHHHH
Confidence 479999999999999994
No 189
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=23.41 E-value=1e+02 Score=29.36 Aligned_cols=48 Identities=17% Similarity=0.215 Sum_probs=37.7
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhh
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR 500 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~ 500 (574)
.+++.+.++|+..|... -.-.++|..||+++..|++.+..-|. +++..
T Consensus 131 ~L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~Rar~-~Lr~~ 178 (189)
T PRK12515 131 KLSPAHREIIDLVYYHE-----KSVEEVGEIVGIPESTVKTRMFYARK-KLAEL 178 (189)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHH-HHHHH
Confidence 58999999998765433 23478999999999999998888877 44444
No 190
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=23.00 E-value=39 Score=24.82 Aligned_cols=34 Identities=21% Similarity=0.403 Sum_probs=24.9
Q ss_pred cccccccccCCCCCCCCccccCCCcCCcccccccCC
Q 008193 238 HIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDP 273 (574)
Q Consensus 238 d~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~P 273 (574)
..+|.+|+....... .-+-|.. |...+|..|+..
T Consensus 11 ~~~C~~C~~~i~~~~-~~~~C~~-C~~~~H~~C~~~ 44 (49)
T smart00109 11 PTKCCVCRKSIWGSF-QGLRCSW-CKVKCHKKCAEK 44 (49)
T ss_pred CCCccccccccCcCC-CCcCCCC-CCchHHHHHHhh
Confidence 357999998643211 3577995 999999999873
No 191
>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=22.95 E-value=1e+02 Score=31.18 Aligned_cols=47 Identities=17% Similarity=0.259 Sum_probs=37.9
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHh
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKA 499 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~ 499 (574)
.+++.|..+|...|... ..-.++|..||+++..|+.|...-+. ++|.
T Consensus 205 ~L~~~~r~ii~l~~~~g-----~s~~eIA~~lgis~~~V~~~~~ra~~-~Lr~ 251 (255)
T TIGR02941 205 ILSEREKSIIHCTFEEN-----LSQKETGERLGISQMHVSRLQRQAIS-KLKE 251 (255)
T ss_pred cCCHHHHHHHHHHHcCC-----CCHHHHHHHHCcCHHHHHHHHHHHHH-HHHH
Confidence 68999999999887543 24479999999999999999887776 4443
No 192
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=22.91 E-value=91 Score=28.41 Aligned_cols=40 Identities=18% Similarity=0.289 Sum_probs=28.8
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccc
Q 008193 452 AVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNA 492 (574)
Q Consensus 452 Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNr 492 (574)
-+..+..+...+ +-..-.-.+||+.+||+++++.-||+..
T Consensus 10 ~i~~~~~~I~~~-~~~~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 10 TIHSILDWIEDN-LESPLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred HHHHHHHHHHHh-cCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 344444444444 3344677899999999999999999865
No 193
>PF02724 CDC45: CDC45-like protein; InterPro: IPR003874 CDC45 is an essential gene required for initiation of DNA replication in Saccharomyces cerevisiae (cell division control protein 45), forming a complex with MCM5/CDC46. Homologs of CDC45 have been identified in human [], mouse and the smut fungus, Melampsora spp., (tsd2 protein) among others.; GO: 0006270 DNA-dependent DNA replication initiation
Probab=22.80 E-value=1.5e+02 Score=34.72 Aligned_cols=38 Identities=13% Similarity=0.261 Sum_probs=28.0
Q ss_pred CCCHHHHHHHHHHHHhCCC---CCHHHHHHHHHHcCCChhh
Q 008193 447 RMPPNAVEKLRQVFAENEL---PSRIVKENLSKELSLEPEK 484 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~y---Ps~~~r~~LA~~LgL~~~q 484 (574)
+.-.+..+.|+..|....| |+.-.-..||..||-+...
T Consensus 196 ~~~~~~~~~i~~yY~~gs~~g~ssa~~~y~La~~l~r~~~d 236 (622)
T PF02724_consen 196 REREEYREEIEKYYSQGSYYGKSSAVLMYELASSLGRDDND 236 (622)
T ss_pred HHHHHHHHHHHHHHhcCceecccHHHHHHHHHHHhCCCchH
Confidence 4445666777888877666 9999999999998744443
No 194
>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=22.79 E-value=1.1e+02 Score=30.19 Aligned_cols=43 Identities=14% Similarity=0.172 Sum_probs=36.0
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 494 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~ 494 (574)
.+++.+.++|...|... ..-.++|..||++...|+.|...-+.
T Consensus 175 ~L~~~~r~il~l~y~~~-----~s~~eIA~~lgis~~tV~~~~~ra~~ 217 (224)
T TIGR02479 175 SLSEREQLVLSLYYYEE-----LNLKEIGEVLGLTESRVSQIHSQALK 217 (224)
T ss_pred hCCHHHHHHHHHHHhCC-----CCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 58999999999988433 24589999999999999998877666
No 195
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=22.64 E-value=79 Score=29.88 Aligned_cols=48 Identities=13% Similarity=0.180 Sum_probs=37.4
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhh
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR 500 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~ 500 (574)
.+|+.+.++|...|-.. -.-.++|..||+++..|+++.+.-|. +++..
T Consensus 135 ~L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~~V~~~l~ra~~-~Lr~~ 182 (186)
T PRK13919 135 ALSPEERRVIEVLYYQG-----YTHREAAQLLGLPLGTLKTRARRALS-RLKEV 182 (186)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHH-HHHHH
Confidence 59999999998765333 34578999999999999998887776 44443
No 196
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=22.50 E-value=98 Score=30.74 Aligned_cols=52 Identities=10% Similarity=0.119 Sum_probs=39.2
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhh
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR 500 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~ 500 (574)
.+|+.|.+++...|.- .+-..-.-.++|..||++...|+++...-|. ++|+.
T Consensus 178 ~Lp~~~R~v~~L~y~l-~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~-~Lr~~ 229 (234)
T PRK08301 178 KLSDREKQIMELRFGL-NGGEEKTQKEVADMLGISQSYISRLEKRIIK-RLKKE 229 (234)
T ss_pred hCCHHHHHHHHHHhcc-CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH-HHHHH
Confidence 5899999999988732 1123344678999999999999999887777 55543
No 197
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=22.47 E-value=44 Score=35.86 Aligned_cols=50 Identities=18% Similarity=0.400 Sum_probs=29.6
Q ss_pred cccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccch
Q 008193 238 HIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECK 295 (574)
Q Consensus 238 d~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k 295 (574)
+..|++|.......+.--++--. |..-|...|+.--+. .+. -.||.|...
T Consensus 3 ~~~CP~Ck~~~y~np~~kl~i~~-CGH~~C~sCv~~l~~-----~~~--~~CP~C~~~ 52 (309)
T TIGR00570 3 DQGCPRCKTTKYRNPSLKLMVNV-CGHTLCESCVDLLFV-----RGS--GSCPECDTP 52 (309)
T ss_pred CCCCCcCCCCCccCcccccccCC-CCCcccHHHHHHHhc-----CCC--CCCCCCCCc
Confidence 46899999964433332222222 877777778775433 122 369999653
No 198
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=22.35 E-value=69 Score=34.40 Aligned_cols=32 Identities=16% Similarity=0.467 Sum_probs=22.4
Q ss_pred cccccccccccCCC--------CCCCCccccCCCcCCcccc
Q 008193 236 HEHIICAKCKLREA--------FPDNDIVLCDGTCNCAFHQ 268 (574)
Q Consensus 236 ~ed~~C~vC~~~~~--------~~~g~lLlCDg~C~rafH~ 268 (574)
+...+|.|||.... ..+...+.|. .|...||+
T Consensus 185 ~~~~~CPvCGs~P~~s~v~~~~~~G~RyL~Cs-lC~teW~~ 224 (309)
T PRK03564 185 EQRQFCPVCGSMPVSSVVQIGTTQGLRYLHCN-LCESEWHV 224 (309)
T ss_pred cCCCCCCCCCCcchhheeeccCCCCceEEEcC-CCCCcccc
Confidence 45689999998631 1234678888 58888875
No 199
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=22.25 E-value=18 Score=43.27 Aligned_cols=55 Identities=25% Similarity=0.617 Sum_probs=36.9
Q ss_pred cccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccch
Q 008193 238 HIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECK 295 (574)
Q Consensus 238 d~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k 295 (574)
-..|.+|..... ....|-.|- .|...||+.|..-.-.. .--.++..|-||.|..-
T Consensus 191 ~yeCmIC~e~I~-~t~~~WSC~-sCYhVFHl~CI~~WArs-~ek~~~~~WrCP~Cqsv 245 (950)
T KOG1952|consen 191 KYECMICTERIK-RTAPVWSCK-SCYHVFHLNCIKKWARS-SEKTGQDGWRCPACQSV 245 (950)
T ss_pred ceEEEEeeeecc-ccCCceecc-hhhhhhhHHHHHHHHHH-hhhccCccccCCcccch
Confidence 467999987543 235677898 59999999998643321 11123346999999843
No 200
>COG5047 SEC23 Vesicle coat complex COPII, subunit SEC23 [Intracellular trafficking and secretion]
Probab=22.07 E-value=38 Score=39.19 Aligned_cols=33 Identities=27% Similarity=0.805 Sum_probs=23.7
Q ss_pred cccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccchh
Q 008193 256 VLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKM 296 (574)
Q Consensus 256 LlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k~ 296 (574)
|-|-+.|...+..+|+- ..+...|.|+.|-.+.
T Consensus 54 v~C~~pC~avlnpyC~i--------d~r~~~W~CpfCnqrn 86 (755)
T COG5047 54 VKCTAPCKAVLNPYCHI--------DERNQSWICPFCNQRN 86 (755)
T ss_pred ceecccchhhcCcceee--------ccCCceEecceecCCC
Confidence 45664599999999965 2344459999997654
No 201
>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=22.05 E-value=99 Score=31.01 Aligned_cols=52 Identities=15% Similarity=0.162 Sum_probs=40.8
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhh
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR 500 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~ 500 (574)
.+++.+..+|...|.-..+ ....-.++|..||++...|+.+.+.-.. ++|..
T Consensus 176 ~L~~~er~vl~l~ygl~~~-~~~t~~EIA~~lgis~~~V~q~~~~al~-kLr~~ 227 (238)
T TIGR02393 176 TLTERERKVLRMRYGLLDG-RPHTLEEVGKEFNVTRERIRQIESKALR-KLRHP 227 (238)
T ss_pred hCCHHHHHHHHHHhCCCCC-CCccHHHHHHHHCCCHHHHHHHHHHHHH-HHhhh
Confidence 5899999999999853332 3345789999999999999999888777 44443
No 202
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=21.95 E-value=63 Score=34.34 Aligned_cols=36 Identities=33% Similarity=0.397 Sum_probs=32.3
Q ss_pred hCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHH
Q 008193 462 ENELPSRIVKENLSKELSLEPEKVNKWFKNARYLAL 497 (574)
Q Consensus 462 ~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~ 497 (574)
.++||+.-....|+-..+|+-.||.+||-|.|.+..
T Consensus 118 ~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~ 153 (342)
T KOG0773|consen 118 LNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLK 153 (342)
T ss_pred hccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHH
Confidence 468999999999999999999999999999999433
No 203
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=21.92 E-value=38 Score=40.65 Aligned_cols=41 Identities=27% Similarity=0.542 Sum_probs=28.9
Q ss_pred ccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccch
Q 008193 239 IICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECK 295 (574)
Q Consensus 239 ~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k 295 (574)
..|..|... -+=.+|.= .|...||+.|+.- ++ --||.|...
T Consensus 841 skCs~C~~~---LdlP~VhF--~CgHsyHqhC~e~---------~~--~~CP~C~~e 881 (933)
T KOG2114|consen 841 SKCSACEGT---LDLPFVHF--LCGHSYHQHCLED---------KE--DKCPKCLPE 881 (933)
T ss_pred eeecccCCc---cccceeee--ecccHHHHHhhcc---------Cc--ccCCccchh
Confidence 579999876 22334433 4999999999981 22 459999873
No 204
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=21.82 E-value=96 Score=29.70 Aligned_cols=48 Identities=21% Similarity=0.309 Sum_probs=37.4
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhh
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR 500 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~ 500 (574)
.+++.+.++|...|-.+ -.-.++|..||+++..|+..+..-|. +++..
T Consensus 106 ~L~~~~r~i~~l~~~~g-----~~~~EIA~~lgis~~tV~~~l~Rar~-~Lr~~ 153 (181)
T PRK09637 106 ALPEKYAEALRLTELEG-----LSQKEIAEKLGLSLSGAKSRVQRGRV-KLKEL 153 (181)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHhCCCHHHHHHHHHHHHH-HHHHH
Confidence 68999999998765332 34578999999999999999987776 45543
No 205
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=21.41 E-value=1.4e+02 Score=28.69 Aligned_cols=36 Identities=14% Similarity=0.113 Sum_probs=31.6
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHH
Q 008193 451 NAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVN 486 (574)
Q Consensus 451 ~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~ 486 (574)
.-+..|..+=....|.+.+.-..+|+.|||++.+|.
T Consensus 24 ~li~~L~~vQ~~~G~Ip~e~~~~iA~~l~v~~~~V~ 59 (156)
T PRK05988 24 ALLPILHAIQDEFGYVPEDAVPVIAEALNLSRAEVH 59 (156)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHH
Confidence 557777777778889999999999999999999975
No 206
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=21.33 E-value=84 Score=28.96 Aligned_cols=42 Identities=14% Similarity=0.188 Sum_probs=35.6
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 494 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~ 494 (574)
.+|+.+.++|+-.+.- | .+.+||.+|+++++.|++..+|=|.
T Consensus 137 ~Lt~~E~~il~~l~~g--~----~~~~Ia~~l~~s~~tv~~~~~~l~~ 178 (196)
T PRK10360 137 PLTKRERQVAEKLAQG--M----AVKEIAAELGLSPKTVHVHRANLME 178 (196)
T ss_pred CCCHHHHHHHHHHHCC--C----CHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 5999999999876643 2 6889999999999999998888776
No 207
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=21.29 E-value=91 Score=29.36 Aligned_cols=50 Identities=10% Similarity=0.113 Sum_probs=36.8
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhhh
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKV 502 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~~ 502 (574)
.+++.|.+++...|.+ ...-.++|+.||++...|+++...-+. .++....
T Consensus 119 ~L~~~~r~i~~l~~~~-----g~s~~EIA~~lgis~~tV~~~l~Ra~~-~~~~~~~ 168 (172)
T PRK09651 119 GLNGKTREAFLLSQLD-----GLTYSEIAHKLGVSVSSVKKYVAKATE-HCLLFRL 168 (172)
T ss_pred hCCHHHhHHhhhhhcc-----CCCHHHHHHHhCCCHHHHHHHHHHHHH-HHHHHHH
Confidence 5888888887765433 334688999999999999999876666 4444433
No 208
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=21.20 E-value=71 Score=30.80 Aligned_cols=24 Identities=17% Similarity=0.156 Sum_probs=17.9
Q ss_pred HHHHHHHcCCChhhHHHhhccccc
Q 008193 471 KENLSKELSLEPEKVNKWFKNARY 494 (574)
Q Consensus 471 r~~LA~~LgL~~~qV~vWFQNrR~ 494 (574)
.++||..+|++...|..|..+.+.
T Consensus 85 qeeLA~~lgvs~s~IsriE~G~~~ 108 (154)
T TIGR00270 85 QEQLAKKIQEKESLIKKIENAEIE 108 (154)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCCC
Confidence 567777777777777777777665
No 209
>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=21.10 E-value=69 Score=26.09 Aligned_cols=24 Identities=17% Similarity=0.239 Sum_probs=21.4
Q ss_pred HHHHHHHcCCChhhHHHhhccccc
Q 008193 471 KENLSKELSLEPEKVNKWFKNARY 494 (574)
Q Consensus 471 r~~LA~~LgL~~~qV~vWFQNrR~ 494 (574)
..+||+.+|++...|..|+.+++.
T Consensus 21 ~~~lA~~~gis~~tis~~~~g~~~ 44 (78)
T TIGR02607 21 IRALAKALGVSRSTLSRIVNGRRG 44 (78)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCCC
Confidence 468999999999999999988764
No 210
>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=21.05 E-value=63 Score=25.63 Aligned_cols=20 Identities=10% Similarity=0.431 Sum_probs=17.9
Q ss_pred HHHHHHHcCCChhhHHHhhc
Q 008193 471 KENLSKELSLEPEKVNKWFK 490 (574)
Q Consensus 471 r~~LA~~LgL~~~qV~vWFQ 490 (574)
..++|+.+|+++..|..|-+
T Consensus 3 ~~eva~~~gvs~~tlr~w~~ 22 (68)
T cd01104 3 IGAVARLTGVSPDTLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35799999999999999985
No 211
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=20.84 E-value=1.1e+02 Score=28.47 Aligned_cols=43 Identities=12% Similarity=0.066 Sum_probs=35.1
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 494 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~ 494 (574)
.+|+.+.++|...|.+. -.-.++|..||+++..|+++...-|.
T Consensus 112 ~L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~Rar~ 154 (164)
T PRK12547 112 LLSADQREAIILIGASG-----FSYEDAAAICGCAVGTIKSRVSRARN 154 (164)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 58999999998765432 23578999999999999999887777
No 212
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=20.80 E-value=33 Score=23.78 Aligned_cols=29 Identities=21% Similarity=0.593 Sum_probs=11.3
Q ss_pred cccccccCCCCCCCCccccCCCcCCccccccc
Q 008193 240 ICAKCKLREAFPDNDIVLCDGTCNCAFHQKCL 271 (574)
Q Consensus 240 ~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl 271 (574)
.|.+|+.... .+..-.|. .|+-..|..|.
T Consensus 2 ~C~~C~~~~~--~~~~Y~C~-~Cdf~lH~~Ca 30 (30)
T PF07649_consen 2 RCDACGKPID--GGWFYRCS-ECDFDLHEECA 30 (30)
T ss_dssp --TTTS------S--EEE-T-TT-----HHHH
T ss_pred cCCcCCCcCC--CCceEECc-cCCCccChhcC
Confidence 4888888642 13677798 59999998883
No 213
>PRK06930 positive control sigma-like factor; Validated
Probab=20.70 E-value=1.1e+02 Score=29.62 Aligned_cols=47 Identities=9% Similarity=0.070 Sum_probs=36.7
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHh
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKA 499 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~ 499 (574)
.||+.+.++|...|... ..-.++|..||+++..|++++..-|. +++.
T Consensus 114 ~L~~rer~V~~L~~~eg-----~s~~EIA~~lgiS~~tVk~~l~Ra~~-kLr~ 160 (170)
T PRK06930 114 VLTEREKEVYLMHRGYG-----LSYSEIADYLNIKKSTVQSMIERAEK-KIAR 160 (170)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHH-HHHH
Confidence 58999999888765333 23478999999999999999988777 4443
No 214
>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=20.64 E-value=1.6e+02 Score=28.06 Aligned_cols=43 Identities=16% Similarity=0.162 Sum_probs=35.7
Q ss_pred cCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193 446 HRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 494 (574)
Q Consensus 446 ~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~ 494 (574)
..+|+.|.++|+.. . . .....++|+.||++...|..|-+.-|.
T Consensus 5 ~~Lte~qr~VL~Lr-~-~----GlTq~EIAe~LgiS~stV~~~e~ra~k 47 (137)
T TIGR00721 5 TFLTERQIKVLELR-E-K----GLSQKEIAKELKTTRANVSAIEKRAME 47 (137)
T ss_pred CCCCHHHHHHHHHH-H-c----CCCHHHHHHHHCcCHHHHHHHHHhHHH
Confidence 57999999999873 2 2 236789999999999999999887777
No 215
>TIGR01958 nuoE_fam NADH-quinone oxidoreductase, E subunit. This model describes the E chain of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoB. This model does not identify proteins from chloroplast and cyanobacteria.
Probab=20.46 E-value=1.5e+02 Score=27.97 Aligned_cols=45 Identities=9% Similarity=0.061 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHH---Hhhccccc
Q 008193 450 PNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVN---KWFKNARY 494 (574)
Q Consensus 450 ~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~---vWFQNrR~ 494 (574)
..-+..|..+=....|.+.+..+.+|..|||++.+|. ..|.--+.
T Consensus 16 ~~li~~L~~vQ~~~G~i~~~~~~~iA~~l~~~~~~v~~v~tFY~~f~~ 63 (148)
T TIGR01958 16 SAIMPALMIAQEQKGWVTPEAIAAVAEMLGIPPVWVYEVATFYSMFDT 63 (148)
T ss_pred hHHHHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHHHHHHhHHhhcCc
Confidence 3556677666677789999999999999999998865 45555544
No 216
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=20.46 E-value=1.8e+02 Score=25.73 Aligned_cols=46 Identities=9% Similarity=0.209 Sum_probs=35.1
Q ss_pred ccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCC-ChhhHHHhhccccc
Q 008193 445 FHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSL-EPEKVNKWFKNARY 494 (574)
Q Consensus 445 r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL-~~~qV~vWFQNrR~ 494 (574)
+.+||++-...+-+...+..+ ...+||+++|+ .+.++..|-+..+.
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~----sv~~vAr~~gv~~~~~l~~W~~~~~~ 51 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGD----TVSEVAREFGIVSATQLYKWRIQLQK 51 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCc----cHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 457999987766666665555 77899999996 99999998654444
No 217
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=20.42 E-value=46 Score=30.59 Aligned_cols=27 Identities=22% Similarity=0.700 Sum_probs=19.6
Q ss_pred cccccccCCCCCCCCccccCCCcCCccc
Q 008193 240 ICAKCKLREAFPDNDIVLCDGTCNCAFH 267 (574)
Q Consensus 240 ~C~vC~~~~~~~~g~lLlCDg~C~rafH 267 (574)
.|+.|...+...++.++.|.. |...|.
T Consensus 4 ~CP~C~seytY~dg~~~iCpe-C~~EW~ 30 (109)
T TIGR00686 4 PCPKCNSEYTYHDGTQLICPS-CLYEWN 30 (109)
T ss_pred cCCcCCCcceEecCCeeECcc-cccccc
Confidence 588888877777778888884 766553
No 218
>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=20.22 E-value=81 Score=32.19 Aligned_cols=51 Identities=18% Similarity=0.332 Sum_probs=40.6
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhhhh
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVE 503 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~~e 503 (574)
.+++.|.+++...|.++ -.-.++|..||++...|+++...-|. .++..-..
T Consensus 161 ~Lp~~~R~v~~L~~~eg-----~S~~EIA~~Lgis~~TVk~rl~RAr~-~Lr~~l~~ 211 (244)
T TIGR03001 161 ALSERERHLLRLHFVDG-----LSMDRIGAMYQVHRSTVSRWVAQARE-RLLERTRR 211 (244)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHH-HHHHHHHH
Confidence 58999999998876543 23578999999999999999999998 55555443
No 219
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=20.19 E-value=1.4e+02 Score=28.85 Aligned_cols=43 Identities=21% Similarity=0.363 Sum_probs=35.5
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 494 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~ 494 (574)
.+.+.+.++++..|... | .-+++|..||++++.|...++.-|.
T Consensus 135 ~l~~~~~~~v~l~~~~G-l----s~~EIA~~lgiS~~tV~r~l~~aR~ 177 (185)
T PF07638_consen 135 ALDPRQRRVVELRFFEG-L----SVEEIAERLGISERTVRRRLRRARA 177 (185)
T ss_pred ccCHHHHHHHHHHHHCC-C----CHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 47888888888876543 2 6788999999999999998888886
No 220
>KOG4215 consensus Hepatocyte nuclear factor 4 and similar steroid hormone receptors [Transcription]
Probab=20.18 E-value=44 Score=36.71 Aligned_cols=29 Identities=28% Similarity=0.557 Sum_probs=19.8
Q ss_pred ccccccccccCCCCCCCCccccCCCcCCcc
Q 008193 237 EHIICAKCKLREAFPDNDIVLCDGTCNCAF 266 (574)
Q Consensus 237 ed~~C~vC~~~~~~~~g~lLlCDg~C~raf 266 (574)
...+|.+|+..-....=..+.||| |...|
T Consensus 18 ~~~~CaICGDkaTGKHYGA~SCdG-CKGFF 46 (432)
T KOG4215|consen 18 VAEFCAICGDKATGKHYGAISCDG-CKGFF 46 (432)
T ss_pred ccchhheeCCcccccccceeecCc-chHHH
Confidence 457999999853222224778998 97655
No 221
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=20.11 E-value=1.3e+02 Score=30.40 Aligned_cols=46 Identities=15% Similarity=0.262 Sum_probs=36.8
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHH
Q 008193 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK 498 (574)
Q Consensus 447 r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k 498 (574)
.+++.+.++|...|... ..-.++|..||++...|+.|...-+. ++|
T Consensus 205 ~L~~~~r~vl~l~~~~g-----~s~~eIA~~l~is~~tV~~~~~ra~~-kLr 250 (257)
T PRK08583 205 VLSDREKSIIQCTFIEN-----LSQKETGERLGISQMHVSRLQRQAIK-KLR 250 (257)
T ss_pred hCCHHHHHHHHHHHhCC-----CCHHHHHHHHCCCHHHHHHHHHHHHH-HHH
Confidence 58999999999877432 23489999999999999999877766 444
Done!