Query 006832
Match_columns 629
No_of_seqs 423 out of 2067
Neff 5.0
Searched_HMMs 46136
Date Thu Mar 28 15:08:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/006832.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/006832hhsearch_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 3.1E-24 6.7E-29 236.7 9.7 193 146-351 150-374 (613)
2 KOG0842 Transcription factor t 99.7 2.1E-18 4.6E-23 179.7 6.4 91 494-584 151-245 (307)
3 KOG0850 Transcription factor D 99.7 1.8E-17 3.9E-22 165.0 6.1 74 483-556 109-182 (245)
4 KOG0484 Transcription factor P 99.7 4E-17 8.7E-22 145.0 3.7 70 494-563 15-84 (125)
5 KOG1244 Predicted transcriptio 99.6 2.3E-16 5E-21 160.0 4.4 192 73-292 110-331 (336)
6 PF00046 Homeobox: Homeobox do 99.6 1.4E-15 3E-20 121.0 5.1 57 497-553 1-57 (57)
7 KOG0843 Transcription factor E 99.6 2.4E-15 5.3E-20 145.2 5.4 62 495-556 101-162 (197)
8 KOG0489 Transcription factor z 99.5 6E-15 1.3E-19 152.1 3.6 66 494-559 157-222 (261)
9 KOG0492 Transcription factor M 99.5 2.3E-14 5.1E-19 141.0 5.1 65 494-558 142-206 (246)
10 KOG0488 Transcription factor B 99.5 3.4E-14 7.3E-19 149.7 6.3 65 493-557 169-233 (309)
11 KOG0485 Transcription factor N 99.5 6.5E-14 1.4E-18 138.6 6.2 66 493-558 101-166 (268)
12 smart00389 HOX Homeodomain. DN 99.5 5.8E-14 1.3E-18 110.7 4.7 53 498-550 2-54 (56)
13 KOG2251 Homeobox transcription 99.5 7.6E-14 1.6E-18 138.8 6.6 67 492-558 33-99 (228)
14 cd00086 homeodomain Homeodomai 99.4 8.2E-14 1.8E-18 110.5 5.0 56 498-553 2-57 (59)
15 KOG0493 Transcription factor E 99.4 7.3E-14 1.6E-18 141.3 5.3 62 494-555 244-305 (342)
16 KOG0487 Transcription factor A 99.4 7.9E-14 1.7E-18 145.8 4.6 63 494-556 233-295 (308)
17 TIGR01565 homeo_ZF_HD homeobox 99.4 1.9E-13 4.2E-18 110.9 5.3 53 496-548 1-57 (58)
18 KOG0494 Transcription factor C 99.4 2.3E-13 5.1E-18 137.6 4.9 72 489-560 133-205 (332)
19 KOG0848 Transcription factor C 99.3 8E-13 1.7E-17 134.3 2.3 59 499-557 202-260 (317)
20 KOG0483 Transcription factor H 99.3 1.7E-12 3.6E-17 128.9 3.8 56 497-552 51-106 (198)
21 COG5576 Homeodomain-containing 99.3 3.5E-12 7.5E-17 122.6 5.7 63 495-557 50-112 (156)
22 KOG0486 Transcription factor P 99.2 7E-12 1.5E-16 130.0 3.5 64 494-557 110-173 (351)
23 KOG0491 Transcription factor B 99.1 2.1E-11 4.5E-16 116.7 1.8 60 496-555 100-159 (194)
24 KOG0847 Transcription factor, 99.1 5.8E-11 1.3E-15 118.0 3.0 66 494-559 165-230 (288)
25 KOG4577 Transcription factor L 99.0 1.1E-10 2.3E-15 120.0 4.2 61 496-556 167-227 (383)
26 KOG0844 Transcription factor E 99.0 7.4E-11 1.6E-15 121.9 2.9 64 493-556 178-241 (408)
27 KOG0490 Transcription factor, 99.0 6.1E-10 1.3E-14 110.7 5.9 64 493-556 57-120 (235)
28 KOG3802 Transcription factor O 98.9 7.8E-10 1.7E-14 118.5 4.5 61 495-555 293-353 (398)
29 KOG0775 Transcription factor S 98.8 8.9E-09 1.9E-13 105.6 6.3 48 503-550 183-230 (304)
30 KOG0849 Transcription factor P 98.7 1.2E-08 2.7E-13 109.8 4.1 62 494-555 174-235 (354)
31 PF00628 PHD: PHD-finger; Int 98.6 4.8E-09 1E-13 81.9 -0.1 49 240-291 1-50 (51)
32 KOG0774 Transcription factor P 98.6 3.8E-08 8.3E-13 100.4 5.3 60 496-555 188-250 (334)
33 KOG0825 PHD Zn-finger protein 98.6 1.6E-08 3.5E-13 114.7 1.9 53 236-292 213-266 (1134)
34 PF05920 Homeobox_KN: Homeobox 98.5 2.6E-08 5.7E-13 75.3 1.5 33 517-549 7-39 (40)
35 KOG2252 CCAAT displacement pro 98.5 6.4E-08 1.4E-12 107.3 4.5 58 493-550 417-474 (558)
36 smart00249 PHD PHD zinc finger 98.3 5.9E-07 1.3E-11 67.2 3.7 46 240-289 1-47 (47)
37 KOG0955 PHD finger protein BR1 98.2 6E-07 1.3E-11 107.0 2.2 77 235-315 216-296 (1051)
38 KOG1168 Transcription factor A 98.2 7E-07 1.5E-11 92.4 2.0 62 494-555 307-368 (385)
39 KOG4323 Polycomb-like PHD Zn-f 98.2 5E-07 1.1E-11 99.5 1.0 54 240-294 170-226 (464)
40 KOG4443 Putative transcription 98.1 1.1E-06 2.3E-11 99.3 2.8 64 230-297 60-123 (694)
41 COG5034 TNG2 Chromatin remodel 98.0 3.3E-06 7.2E-11 86.4 3.8 50 235-291 218-269 (271)
42 KOG1512 PHD Zn-finger protein 98.0 1.9E-06 4.1E-11 89.2 1.6 53 229-287 305-357 (381)
43 KOG1973 Chromatin remodeling p 97.9 4.6E-06 1E-10 87.2 2.9 51 236-293 217-269 (274)
44 cd04718 BAH_plant_2 BAH, or Br 97.9 4.8E-06 1E-10 79.6 2.1 29 265-294 1-29 (148)
45 KOG0383 Predicted helicase [Ge 97.8 7.6E-06 1.7E-10 94.5 1.5 54 233-293 42-95 (696)
46 COG5141 PHD zinc finger-contai 97.8 1.2E-05 2.5E-10 88.4 2.2 53 235-291 190-242 (669)
47 KOG0773 Transcription factor M 97.7 1.4E-05 3E-10 85.4 2.7 62 495-556 238-302 (342)
48 KOG0490 Transcription factor, 97.7 2.4E-05 5.1E-10 78.0 3.8 64 492-555 149-212 (235)
49 KOG0954 PHD finger protein [Ge 97.6 1.9E-05 4E-10 90.3 1.8 51 237-291 270-320 (893)
50 KOG0957 PHD finger protein [Ge 97.6 1.8E-05 4E-10 87.0 1.2 51 237-290 543-596 (707)
51 KOG1245 Chromatin remodeling c 97.6 1.3E-05 2.8E-10 99.0 0.1 55 236-294 1106-1160(1404)
52 KOG0956 PHD finger protein AF1 97.5 3.4E-05 7.3E-10 87.6 1.8 50 239-291 6-56 (900)
53 KOG1146 Homeobox protein [Gene 96.9 0.00088 1.9E-08 81.2 4.6 63 494-556 901-963 (1406)
54 PF13831 PHD_2: PHD-finger; PD 96.3 0.00086 1.9E-08 49.8 -0.5 35 253-290 2-36 (36)
55 PF11569 Homez: Homeodomain le 96.2 0.0035 7.5E-08 51.0 2.4 42 508-549 10-51 (56)
56 PF15446 zf-PHD-like: PHD/FYVE 95.2 0.011 2.4E-07 57.9 2.3 53 240-293 1-61 (175)
57 KOG1473 Nucleosome remodeling 95.0 0.013 2.8E-07 70.5 2.2 49 236-291 342-390 (1414)
58 KOG3623 Homeobox transcription 94.2 0.062 1.3E-06 62.5 5.2 47 508-554 568-614 (1007)
59 KOG0957 PHD finger protein [Ge 93.3 0.043 9.4E-07 61.3 2.1 53 239-292 120-179 (707)
60 PF04218 CENP-B_N: CENP-B N-te 93.2 0.15 3.2E-06 40.9 4.4 48 497-549 1-48 (53)
61 KOG4443 Putative transcription 91.0 0.057 1.2E-06 62.2 -0.5 61 235-296 15-75 (694)
62 KOG1246 DNA-binding protein ju 88.4 0.31 6.7E-06 59.2 2.9 51 237-292 154-204 (904)
63 PF14446 Prok-RING_1: Prokaryo 87.0 0.35 7.7E-06 39.3 1.5 35 237-273 4-38 (54)
64 KOG4299 PHD Zn-finger protein 85.9 0.44 9.5E-06 55.0 2.1 49 238-292 47-95 (613)
65 KOG1512 PHD Zn-finger protein 80.3 0.43 9.3E-06 50.5 -0.7 59 237-296 257-321 (381)
66 KOG3612 PHD Zn-finger protein 80.3 1.1 2.5E-05 51.0 2.5 55 233-293 55-109 (588)
67 KOG1473 Nucleosome remodeling 79.9 0.33 7.2E-06 59.0 -1.8 50 238-293 428-480 (1414)
68 PF01527 HTH_Tnp_1: Transposas 76.8 1.4 3.1E-05 36.5 1.5 47 498-548 2-48 (76)
69 KOG4323 Polycomb-like PHD Zn-f 75.9 1.7 3.6E-05 49.1 2.2 56 235-294 80-135 (464)
70 KOG0383 Predicted helicase [Ge 74.0 0.94 2E-05 53.5 -0.3 53 235-294 503-556 (696)
71 PF04967 HTH_10: HTH DNA bindi 71.7 4.9 0.00011 32.5 3.4 40 503-542 1-42 (53)
72 PF04545 Sigma70_r4: Sigma-70, 70.9 5.1 0.00011 30.9 3.3 44 502-550 4-47 (50)
73 KOG1632 Uncharacterized PHD Zn 68.7 2.8 6E-05 45.8 1.8 40 254-294 74-115 (345)
74 PF12861 zf-Apc11: Anaphase-pr 68.5 1.8 3.9E-05 38.3 0.3 46 241-292 35-80 (85)
75 cd00569 HTH_Hin_like Helix-tur 65.6 12 0.00025 24.7 3.9 38 502-544 5-42 (42)
76 PF06524 NOA36: NOA36 protein; 65.5 11 0.00023 39.9 5.2 30 235-265 122-151 (314)
77 PF11793 FANCL_C: FANCL C-term 64.2 4.5 9.7E-05 34.2 1.8 53 239-293 3-65 (70)
78 cd06171 Sigma70_r4 Sigma70, re 63.7 5.3 0.00011 29.5 2.0 43 502-549 10-52 (55)
79 PF07227 DUF1423: Protein of u 56.3 9.9 0.00021 42.9 3.3 57 240-297 130-197 (446)
80 KOG4628 Predicted E3 ubiquitin 54.9 6.3 0.00014 43.2 1.5 47 239-292 230-276 (348)
81 PF13832 zf-HC5HC2H_2: PHD-zin 54.7 6.5 0.00014 35.3 1.3 30 238-272 55-86 (110)
82 PF10367 Vps39_2: Vacuolar sor 53.6 9.7 0.00021 33.3 2.2 31 238-272 78-108 (109)
83 PF13551 HTH_29: Winged helix- 53.2 21 0.00047 31.1 4.4 49 497-545 52-109 (112)
84 KOG1244 Predicted transcriptio 52.5 3 6.4E-05 44.2 -1.4 62 236-298 222-290 (336)
85 PF10668 Phage_terminase: Phag 52.5 7.5 0.00016 32.4 1.2 25 525-549 24-48 (60)
86 COG3413 Predicted DNA binding 51.2 15 0.00032 37.1 3.4 41 502-542 155-197 (215)
87 PF13901 DUF4206: Domain of un 50.2 13 0.00028 37.6 2.7 43 239-292 153-198 (202)
88 PF13639 zf-RING_2: Ring finge 49.6 1.5 3.3E-05 33.1 -3.1 43 240-290 2-44 (44)
89 PF15446 zf-PHD-like: PHD/FYVE 49.2 12 0.00026 37.2 2.3 23 252-275 121-143 (175)
90 KOG1832 HIV-1 Vpr-binding prot 49.0 25 0.00054 43.0 5.1 13 338-350 1402-1414(1516)
91 PRK03975 tfx putative transcri 47.4 20 0.00044 34.6 3.5 51 501-557 5-55 (141)
92 PF13771 zf-HC5HC2H: PHD-like 46.6 11 0.00024 32.5 1.4 32 238-273 36-68 (90)
93 PF13443 HTH_26: Cro/C1-type H 45.5 18 0.00039 28.8 2.4 24 525-548 12-35 (63)
94 smart00421 HTH_LUXR helix_turn 45.4 24 0.00052 26.5 3.0 42 502-549 3-44 (58)
95 PF13936 HTH_38: Helix-turn-he 45.2 14 0.00031 28.2 1.7 40 501-545 3-42 (44)
96 KOG0773 Transcription factor M 44.5 14 0.00031 39.7 2.2 39 517-555 118-156 (342)
97 KOG2932 E3 ubiquitin ligase in 44.2 13 0.00028 40.2 1.8 58 236-307 88-145 (389)
98 PRK10072 putative transcriptio 44.0 23 0.0005 32.0 3.1 41 502-549 32-72 (96)
99 KOG0827 Predicted E3 ubiquitin 42.8 4 8.7E-05 45.1 -2.3 56 239-300 5-62 (465)
100 PHA02955 hypothetical protein; 42.5 27 0.00058 36.0 3.6 46 503-548 58-104 (213)
101 COG5432 RAD18 RING-finger-cont 41.1 6.2 0.00013 42.2 -1.1 45 238-293 25-69 (391)
102 KOG1146 Homeobox protein [Gene 39.3 7 0.00015 49.1 -1.3 58 497-554 445-502 (1406)
103 KOG1189 Global transcriptional 39.0 32 0.00069 41.4 3.9 42 309-350 844-895 (960)
104 TIGR02937 sigma70-ECF RNA poly 38.7 27 0.00058 31.1 2.7 46 502-552 110-155 (158)
105 cd01392 HTH_LacI Helix-turn-he 38.7 13 0.00027 28.5 0.5 21 528-548 2-22 (52)
106 PF01381 HTH_3: Helix-turn-hel 37.1 18 0.00039 27.9 1.2 24 526-549 12-35 (55)
107 PRK09413 IS2 repressor TnpA; R 36.5 46 0.001 30.7 3.9 43 501-547 11-53 (121)
108 PRK04217 hypothetical protein; 36.3 44 0.00094 31.0 3.7 49 500-553 40-88 (110)
109 TIGR03879 near_KaiC_dom probab 35.9 13 0.00028 32.1 0.2 37 512-548 21-57 (73)
110 PRK06759 RNA polymerase factor 35.8 34 0.00073 31.6 3.0 46 502-552 106-151 (154)
111 PF13518 HTH_28: Helix-turn-he 35.1 19 0.00042 27.3 1.0 25 525-549 14-38 (52)
112 KOG1844 PHD Zn-finger proteins 34.7 22 0.00048 40.2 1.8 48 243-294 90-137 (508)
113 PF00130 C1_1: Phorbol esters/ 34.1 35 0.00075 26.5 2.3 35 238-273 11-45 (53)
114 KOG1829 Uncharacterized conser 33.7 16 0.00034 42.8 0.4 47 239-294 512-561 (580)
115 TIGR03070 couple_hipB transcri 33.3 24 0.00052 27.0 1.3 25 525-549 17-41 (58)
116 KOG3970 Predicted E3 ubiquitin 32.8 16 0.00036 37.9 0.4 87 239-335 51-140 (299)
117 PF08280 HTH_Mga: M protein tr 31.5 41 0.0009 27.2 2.4 36 506-545 6-41 (59)
118 PLN02638 cellulose synthase A 31.3 40 0.00088 42.1 3.3 53 237-294 16-70 (1079)
119 TIGR01206 lysW lysine biosynth 30.5 36 0.00078 27.8 1.9 34 240-274 4-40 (54)
120 KOG4215 Hepatocyte nuclear fac 30.4 23 0.0005 39.2 1.0 29 237-266 18-46 (432)
121 PRK09646 RNA polymerase sigma 30.4 53 0.0011 32.1 3.5 47 502-553 142-188 (194)
122 KOG1734 Predicted RING-contain 30.4 17 0.00037 38.7 0.0 61 235-299 221-286 (328)
123 PF12678 zf-rbx1: RING-H2 zinc 30.1 16 0.00035 30.9 -0.1 46 239-290 20-73 (73)
124 cd04761 HTH_MerR-SF Helix-Turn 29.9 26 0.00056 26.3 1.0 22 526-547 3-24 (49)
125 PRK12514 RNA polymerase sigma 29.6 44 0.00095 31.9 2.7 46 502-552 129-174 (179)
126 PRK09652 RNA polymerase sigma 29.5 48 0.001 31.1 2.9 47 502-553 128-174 (182)
127 PF13384 HTH_23: Homeodomain-l 29.4 26 0.00057 26.7 0.9 26 523-548 17-42 (50)
128 PHA02929 N1R/p28-like protein; 29.2 20 0.00042 37.5 0.2 48 238-292 174-225 (238)
129 KOG2114 Vacuolar assembly/sort 29.0 51 0.0011 40.1 3.5 41 239-292 841-881 (933)
130 PRK14559 putative protein seri 28.7 45 0.00097 39.7 3.0 50 239-294 2-52 (645)
131 PRK11924 RNA polymerase sigma 28.6 47 0.001 31.1 2.7 48 502-554 125-172 (179)
132 PF10497 zf-4CXXC_R1: Zinc-fin 28.6 26 0.00055 32.1 0.8 50 238-291 7-69 (105)
133 PF10080 DUF2318: Predicted me 28.2 29 0.00063 31.8 1.1 42 230-272 27-68 (102)
134 KOG2879 Predicted E3 ubiquitin 28.1 56 0.0012 35.0 3.3 55 231-293 232-286 (298)
135 PRK00118 putative DNA-binding 27.8 56 0.0012 30.0 2.9 45 503-552 18-62 (104)
136 PF06056 Terminase_5: Putative 27.6 31 0.00068 28.3 1.1 22 525-546 15-36 (58)
137 PHA01976 helix-turn-helix prot 27.5 30 0.00064 27.9 1.0 25 525-549 17-41 (67)
138 KOG3623 Homeobox transcription 27.4 50 0.0011 39.6 3.0 56 494-549 624-679 (1007)
139 cd06170 LuxR_C_like C-terminal 27.1 66 0.0014 24.2 2.8 39 503-547 1-39 (57)
140 PF08273 Prim_Zn_Ribbon: Zinc- 26.9 49 0.0011 25.4 2.0 10 281-290 24-33 (40)
141 PRK12512 RNA polymerase sigma 26.8 62 0.0013 31.0 3.2 48 502-554 131-178 (184)
142 PF02796 HTH_7: Helix-turn-hel 26.5 68 0.0015 24.5 2.7 39 502-545 5-43 (45)
143 PF08281 Sigma70_r4_2: Sigma-7 26.4 30 0.00064 26.8 0.8 42 503-549 11-52 (54)
144 cd00093 HTH_XRE Helix-turn-hel 26.4 38 0.00081 24.4 1.3 23 526-548 15-37 (58)
145 smart00744 RINGv The RING-vari 25.9 13 0.00029 29.3 -1.3 44 240-289 1-48 (49)
146 PRK06811 RNA polymerase factor 25.6 68 0.0015 31.1 3.3 49 502-555 131-179 (189)
147 PF00196 GerE: Bacterial regul 24.7 56 0.0012 25.9 2.1 43 502-550 3-45 (58)
148 KOG0956 PHD finger protein AF1 24.5 38 0.00081 40.3 1.4 57 238-294 117-182 (900)
149 PF13730 HTH_36: Helix-turn-he 24.3 1.3E+02 0.0028 23.2 4.1 42 502-546 2-48 (55)
150 PRK09648 RNA polymerase sigma 23.9 80 0.0017 30.5 3.4 48 501-553 138-185 (189)
151 TIGR00270 conserved hypothetic 23.9 47 0.001 32.4 1.8 26 524-549 83-108 (154)
152 KOG1080 Histone H3 (Lys4) meth 23.8 60 0.0013 40.5 3.0 51 238-291 573-623 (1005)
153 PRK05988 formate dehydrogenase 23.3 1E+02 0.0022 30.1 3.9 36 506-541 24-59 (156)
154 PF07649 C1_3: C1-like domain; 23.3 35 0.00076 24.0 0.6 28 240-270 2-29 (30)
155 KOG3241 Uncharacterized conser 23.2 55 0.0012 33.0 2.1 16 340-355 190-205 (227)
156 TIGR02948 SigW_bacill RNA poly 22.9 65 0.0014 30.7 2.5 47 502-553 136-182 (187)
157 PF08274 PhnA_Zn_Ribbon: PhnA 22.5 39 0.00084 24.5 0.7 24 240-264 4-27 (30)
158 PRK03564 formate dehydrogenase 22.4 68 0.0015 34.9 2.8 31 237-268 186-224 (309)
159 TIGR02607 antidote_HigA addict 22.4 42 0.00091 27.8 1.0 24 526-549 21-44 (78)
160 KOG4218 Nuclear hormone recept 22.3 40 0.00088 37.1 1.1 55 236-291 13-75 (475)
161 PRK09639 RNA polymerase sigma 22.3 97 0.0021 29.0 3.5 47 501-553 111-157 (166)
162 PF13411 MerR_1: MerR HTH fami 22.2 44 0.00095 27.0 1.0 18 527-544 4-21 (69)
163 TIGR02985 Sig70_bacteroi1 RNA 21.9 72 0.0016 29.1 2.6 46 502-552 113-158 (161)
164 PF12824 MRP-L20: Mitochondria 21.9 1.3E+02 0.0028 29.7 4.4 47 500-548 83-129 (164)
165 PRK15369 two component system 21.7 90 0.0019 28.8 3.2 43 502-550 149-191 (211)
166 PF04216 FdhE: Protein involve 21.7 41 0.00089 35.6 0.9 30 238-268 172-209 (290)
167 PRK11511 DNA-binding transcrip 21.6 83 0.0018 29.1 2.9 41 506-547 9-49 (127)
168 PF10446 DUF2457: Protein of u 21.5 1E+02 0.0023 35.0 4.0 18 266-288 2-19 (458)
169 PRK06986 fliA flagellar biosyn 21.5 92 0.002 31.5 3.4 47 502-553 184-230 (236)
170 PRK07539 NADH dehydrogenase su 21.4 1.1E+02 0.0025 29.4 3.9 36 506-541 23-58 (154)
171 PRK09706 transcriptional repre 21.0 44 0.00096 31.1 0.9 24 526-549 21-44 (135)
172 PRK12519 RNA polymerase sigma 20.9 67 0.0014 31.1 2.2 47 502-553 141-187 (194)
173 COG1905 NuoE NADH:ubiquinone o 20.8 1.2E+02 0.0025 30.1 3.8 38 504-541 24-61 (160)
174 PRK09644 RNA polymerase sigma 20.7 1.2E+02 0.0026 28.6 3.8 48 501-554 107-155 (165)
175 TIGR01958 nuoE_fam NADH-quinon 20.6 1.2E+02 0.0027 29.0 3.9 36 506-541 17-52 (148)
176 cd00162 RING RING-finger (Real 20.4 23 0.00051 25.2 -0.9 42 241-291 2-43 (45)
177 COG2963 Transposase and inacti 20.3 1.5E+02 0.0032 26.7 4.1 46 500-549 5-51 (116)
No 1
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=99.90 E-value=3.1e-24 Score=236.67 Aligned_cols=193 Identities=34% Similarity=0.565 Sum_probs=161.7
Q ss_pred cchhHHHHHHHHHHHHHHHHhhhhhHHhhhcCCCCCCCccc---------CCchHHHHHHHHhhhhhhhhHHHHhhhccc
Q 006832 146 ELDEASRLQRRTRYLLIKMKLEQNLIDAYSGEGWKGHSREK---------IRPEKELQRAKKQILKCKIGIRDAIRQLDS 216 (629)
Q Consensus 146 ~~~e~~ri~~r~r~~l~~~~~Eq~l~~Ay~~egwk~~sreK---------~rPekEl~Rak~~i~k~K~~ird~l~~ld~ 216 (629)
.+.+.-|...+++|+...+..++.++++|+.+||++.+.+| ++|.++..++..+|+.+++.++.+.+.++.
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 45677899999999999999999999999999999999999 999999999999999999999999999998
Q ss_pred cCCCCCCCCCcccCCCCcccccc--cccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCC-CCCceecccCchhh
Q 006832 217 LSSVGCIEGSVIATDGSVHHEHI--ICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTES-RDQGWFCKFCECKM 293 (629)
Q Consensus 217 l~~~g~le~s~~~~dg~~~~e~~--~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p-~dg~W~C~~C~~k~ 293 (629)
....+..++..+..++.....+. ||..|++.+.. +++||||| |+++|||.||.|||.... +.|.|||+.|.++.
T Consensus 230 ~s~~~t~~e~r~~~D~~~~~~~~~~fCsaCn~~~~F--~~~i~CD~-Cp~sFH~~CLePPl~~eniP~g~W~C~ec~~k~ 306 (613)
T KOG4299|consen 230 ESKEGTVEEKRRERDKNISVEDIEDFCSACNGSGLF--NDIICCDG-CPRSFHQTCLEPPLEPENIPPGSWFCPECKIKS 306 (613)
T ss_pred hhhhccchhhhhhhccccccCCHHHHHHHhCCcccc--ccceeecC-CchHHHHhhcCCCCCcccCCCCccccCCCeeee
Confidence 88777777777777776665555 99999999875 78999996 999999999999965544 47999999999986
Q ss_pred HHHH--------------------hhhccCCccccccchhhhhhccccccCCCCccccCCccCCCCCCCCCCCCCccc
Q 006832 294 EIIE--------------------SMNAHIGTSFSVNSNWQDIFKEEAAFPDGCSALLNQEEEWPSDDSEDDDYNPER 351 (629)
Q Consensus 294 ~~l~--------------------~~n~~~gtsf~lp~~~~d~F~eva~~~dG~~~~~~~e~~wpsddseD~dydP~~ 351 (629)
.++. .|..+++..|.||..+...|.+|..+ +.+|++|++.+.+|+|..
T Consensus 307 ~in~~~~t~~~~~~~~~i~t~~~~~IDs~np~q~~lPe~i~~~~~~v~~g----------~~~~~sd~~~~~pl~~~~ 374 (613)
T KOG4299|consen 307 VINPKMETLSNRGTVVDIFTQFVSKIDSHNPIQKILPENISESFGGVSRG----------DDGQYSDTQDEKPLDPPA 374 (613)
T ss_pred ecccchhhhhhccchHHHHHHHHHhhhccchhhhhCCHHHHhhccccccC----------CCCccccccCCcCCChhh
Confidence 5332 34555666666777777777776643 445778999999999944
No 2
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.73 E-value=2.1e-18 Score=179.71 Aligned_cols=91 Identities=25% Similarity=0.357 Sum_probs=75.9
Q ss_pred cccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhhhhhcc--ccCCCC--CC
Q 006832 494 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVESAR--QVSGSP--RI 569 (629)
Q Consensus 494 ~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~~~~~~--~l~~~~--~~ 569 (629)
.++||+|..||..||-+||+.|.++.|++..+|++||..|+||++||+|||||||||.+|+.+....+ .+...+ .-
T Consensus 151 ~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~~~~~~~~~~r~ 230 (307)
T KOG0842|consen 151 RKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEALLLASSPPPRR 230 (307)
T ss_pred ccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhcccCCCCCcccc
Confidence 45566788899999999999999999999999999999999999999999999999988887554433 333333 46
Q ss_pred CCCcchhhcccchhh
Q 006832 570 SKESSLETEKKNADV 584 (629)
Q Consensus 570 s~~~~~~~~~~~~dl 584 (629)
.+.+.++.+++++-.
T Consensus 231 v~vpvlvrd~kp~~~ 245 (307)
T KOG0842|consen 231 VAVPVLVRDGKPCSG 245 (307)
T ss_pred cCCceeccCCCcccC
Confidence 888899888876655
No 3
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.69 E-value=1.8e-17 Score=165.04 Aligned_cols=74 Identities=19% Similarity=0.291 Sum_probs=69.9
Q ss_pred cchhhccCCCccccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhh
Q 006832 483 TAEVKKKLPSNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK 556 (629)
Q Consensus 483 ~~~~~~~~~~~~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~ 556 (629)
+....+.|++.+|.|++||.|+..||+.|.+.|+.++|+-..+|.+||..||||.+||+|||||||.|++|..+
T Consensus 109 E~~e~~~Ngk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k 182 (245)
T KOG0850|consen 109 EPSERRPNGKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKK 182 (245)
T ss_pred CcceeccCCCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence 44556889999999999999999999999999999999999999999999999999999999999999888887
No 4
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.66 E-value=4e-17 Score=144.98 Aligned_cols=70 Identities=26% Similarity=0.434 Sum_probs=63.7
Q ss_pred cccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhhhhhcccc
Q 006832 494 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVESARQV 563 (629)
Q Consensus 494 ~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~~~~~~~l 563 (629)
.++||-|+.||..|+.+||++|.+++||+..+|++||-.|.||+..|+|||||||++++|+.++......
T Consensus 15 rKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a~~~~~ 84 (125)
T KOG0484|consen 15 RKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAAIAKMA 84 (125)
T ss_pred HHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHHHHHhh
Confidence 4567889999999999999999999999999999999999999999999999999999999876654433
No 5
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=99.62 E-value=2.3e-16 Score=160.05 Aligned_cols=192 Identities=22% Similarity=0.355 Sum_probs=129.6
Q ss_pred CCCC-chhhhhhhccccchhh--hccccccccccccccCCcc-ceeccCCCCcccCCcccchhcccccchhhccch--hc
Q 006832 73 GAGD-DFARSKSISQKNLHIK--IDRKGSKNWASSKHKGKNS-ALVISKGNGEVVDGDGETKKLRKGRSKKRRKEK--VE 146 (629)
Q Consensus 73 ~~~~-~~~~~~~~~~~~~~~~--~~~~~~~~~~s~~~~~~~~-~~~~~~~~~~~~d~~~~~~~~k~~rk~kr~~~~--~~ 146 (629)
++.+ ++++++||++++|+|+ ++.+++ .+|+..|- ..++++.|.+++|.++++++++.+-+.+.++-. -.
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 4556 7999999999999999 888888 78886663 467888889999999999999999999988543 34
Q ss_pred chhHHHHHHHHHHHHHHHHhhhhhHHh-hhcCCCCCCCcccCCchHHHHHHHHhhh---------------hhhhh-HHH
Q 006832 147 LDEASRLQRRTRYLLIKMKLEQNLIDA-YSGEGWKGHSREKIRPEKELQRAKKQIL---------------KCKIG-IRD 209 (629)
Q Consensus 147 ~~e~~ri~~r~r~~l~~~~~Eq~l~~A-y~~egwk~~sreK~rPekEl~Rak~~i~---------------k~K~~-ird 209 (629)
+...+-+.. |++ ++ +..-+|+.- ..+.-+|+++-|. .+|.+ ..+
T Consensus 185 l~~ss~l~~---~~~----------d~~~~~~~~~~g------e~~vkqr~kkd~a~Pn~YCDFclgdsr~nkkt~~pee 245 (336)
T KOG1244|consen 185 LTDSSSLED---YVC----------DTGTKQTVFAPG------EAKVKQRVKKDIAQPNPYCDFCLGDSRENKKTGMPEE 245 (336)
T ss_pred ccccccccc---hhh----------cccccccccCcc------hhhHHHhhhcccccCCcccceeccccccccccCCchh
Confidence 444444443 333 22 222233321 0122333333111 23333 223
Q ss_pred Hhhhcc--ccCCCCCCCC--Ccc---cCCCCcccccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCC
Q 006832 210 AIRQLD--SLSSVGCIEG--SVI---ATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQ 282 (629)
Q Consensus 210 ~l~~ld--~l~~~g~le~--s~~---~~dg~~~~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg 282 (629)
++...| ...+..++.. .++ ....|.+.++.+|.+|+..++ +++||+|| .|+++||||||.||+...| +|
T Consensus 246 lvscsdcgrsghpsclqft~nm~~avk~yrwqcieck~csicgtsen--ddqllfcd-dcdrgyhmyclsppm~epp-eg 321 (336)
T KOG1244|consen 246 LVSCSDCGRSGHPSCLQFTANMIAAVKTYRWQCIECKYCSICGTSEN--DDQLLFCD-DCDRGYHMYCLSPPMVEPP-EG 321 (336)
T ss_pred hcchhhcCCCCCcchhhhhHHHHHHHHhheeeeeecceeccccCcCC--CceeEeec-ccCCceeeEecCCCcCCCC-CC
Confidence 332221 2223333321 122 245699999999999998865 78999999 7999999999999999988 89
Q ss_pred ceecccCchh
Q 006832 283 GWFCKFCECK 292 (629)
Q Consensus 283 ~W~C~~C~~k 292 (629)
.|.|..|...
T Consensus 322 swsc~KOG~~ 331 (336)
T KOG1244|consen 322 SWSCHLCLEE 331 (336)
T ss_pred chhHHHHHHH
Confidence 9999999643
No 6
>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=99.58 E-value=1.4e-15 Score=121.04 Aligned_cols=57 Identities=35% Similarity=0.585 Sum_probs=53.6
Q ss_pred CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHH
Q 006832 497 RRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK 553 (629)
Q Consensus 497 kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K 553 (629)
||++++||++|+..|+.+|..++||+..+++.||..|||++.||++||+|+|++.+|
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence 567889999999999999999999999999999999999999999999999996553
No 7
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.56 E-value=2.4e-15 Score=145.20 Aligned_cols=62 Identities=24% Similarity=0.424 Sum_probs=57.6
Q ss_pred ccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhh
Q 006832 495 KIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK 556 (629)
Q Consensus 495 k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~ 556 (629)
+.||.||.||++|+..||..|+.++|....+|++||+.|+|++.||+|||||||.|.+|...
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~ 162 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQ 162 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHH
Confidence 56888999999999999999999999999999999999999999999999999997665553
No 8
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.51 E-value=6e-15 Score=152.11 Aligned_cols=66 Identities=23% Similarity=0.335 Sum_probs=59.9
Q ss_pred cccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhhhhh
Q 006832 494 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVES 559 (629)
Q Consensus 494 ~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~~~~ 559 (629)
.+.||.|+.||..|+.+||..|.-|.|+++..|.+||..|.|+++||+|||||||.|.+|..+...
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~ 222 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKS 222 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccc
Confidence 446888999999999999999999999999999999999999999999999999997776665443
No 9
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.48 E-value=2.3e-14 Score=140.96 Aligned_cols=65 Identities=23% Similarity=0.338 Sum_probs=59.2
Q ss_pred cccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhhhh
Q 006832 494 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVE 558 (629)
Q Consensus 494 ~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~~~ 558 (629)
+.-|++|+-||.+|+..||+.|.+.+|.++.+|.+++..|.||+.||+|||||||+|.+|...++
T Consensus 142 k~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae 206 (246)
T KOG0492|consen 142 KPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAE 206 (246)
T ss_pred CCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHH
Confidence 44578899999999999999999999999999999999999999999999999999877765443
No 10
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.48 E-value=3.4e-14 Score=149.71 Aligned_cols=65 Identities=22% Similarity=0.282 Sum_probs=59.8
Q ss_pred ccccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhhh
Q 006832 493 NAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKV 557 (629)
Q Consensus 493 ~~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~~ 557 (629)
.+|.|+.|+.||..|+.+||..|+...|.+..+|.+||+.||||-.||++||||||+|++|....
T Consensus 169 pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~ 233 (309)
T KOG0488|consen 169 PKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE 233 (309)
T ss_pred CcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence 36677889999999999999999999999999999999999999999999999999977766644
No 11
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.46 E-value=6.5e-14 Score=138.63 Aligned_cols=66 Identities=18% Similarity=0.285 Sum_probs=61.3
Q ss_pred ccccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhhhh
Q 006832 493 NAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVE 558 (629)
Q Consensus 493 ~~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~~~ 558 (629)
..++||.|+.|+..|+.+||..|....|++..+|..||+.|.||+.||+|||||||.|++|+-+++
T Consensus 101 ~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad 166 (268)
T KOG0485|consen 101 DDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAAD 166 (268)
T ss_pred ccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhh
Confidence 346788899999999999999999999999999999999999999999999999999888887655
No 12
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.46 E-value=5.8e-14 Score=110.68 Aligned_cols=53 Identities=34% Similarity=0.597 Sum_probs=50.3
Q ss_pred CCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccH
Q 006832 498 RSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYL 550 (629)
Q Consensus 498 R~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k 550 (629)
+.+++|+++|+..|+.+|..++||+..++..||..|||+..||++||+|+|++
T Consensus 2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~ 54 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAK 54 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhc
Confidence 45677999999999999999999999999999999999999999999999984
No 13
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.45 E-value=7.6e-14 Score=138.78 Aligned_cols=67 Identities=27% Similarity=0.475 Sum_probs=61.9
Q ss_pred CccccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhhhh
Q 006832 492 SNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVE 558 (629)
Q Consensus 492 ~~~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~~~ 558 (629)
...|.||.||+|+..|+.+||.+|.+++||+...|++||.+|+|.+.+|+|||.|||+|.+++.+.+
T Consensus 33 ~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 33 GPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred cchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence 3466788999999999999999999999999999999999999999999999999999888877654
No 14
>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=99.45 E-value=8.2e-14 Score=110.46 Aligned_cols=56 Identities=38% Similarity=0.623 Sum_probs=51.7
Q ss_pred CCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHH
Q 006832 498 RSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK 553 (629)
Q Consensus 498 R~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K 553 (629)
+.+..|+..|+..|+.+|..++||+..++..||.+|||+..||++||+|+|++.++
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~ 57 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKR 57 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence 45567999999999999999999999999999999999999999999999995543
No 15
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.44 E-value=7.3e-14 Score=141.26 Aligned_cols=62 Identities=23% Similarity=0.437 Sum_probs=57.2
Q ss_pred cccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhh
Q 006832 494 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR 555 (629)
Q Consensus 494 ~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~ 555 (629)
+.-||+|+.||.+|++.|...|++|.|.+...|.+||++|||.+.||+|||||+|+|.+|--
T Consensus 244 ~eeKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsT 305 (342)
T KOG0493|consen 244 KEEKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKST 305 (342)
T ss_pred chhcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhcc
Confidence 34589999999999999999999999999999999999999999999999999999666543
No 16
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.43 E-value=7.9e-14 Score=145.80 Aligned_cols=63 Identities=22% Similarity=0.307 Sum_probs=56.1
Q ss_pred cccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhh
Q 006832 494 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK 556 (629)
Q Consensus 494 ~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~ 556 (629)
.+.|++|--||+.|+.+||+.|--|.|.+.+.|.+||+.|+||++||+|||||||.|.+|--+
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~r 295 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNR 295 (308)
T ss_pred cccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhh
Confidence 344556677899999999999999999999999999999999999999999999997666553
No 17
>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=99.42 E-value=1.9e-13 Score=110.90 Aligned_cols=53 Identities=15% Similarity=0.292 Sum_probs=50.8
Q ss_pred cCCCCCCCCHHHHHHHHHHHHhCCC----CCHHHHHHHHHHhCCCcchhhhccchhc
Q 006832 496 IRRSFHRMPPNAVEKLRQVFAENEL----PSRIVKENLSKELSLEPEKVNKWFKNAR 548 (629)
Q Consensus 496 ~kR~r~rft~~Q~~~Le~~F~~~~y----Ps~~~re~LA~~lgLt~~QVkiWFQNrR 548 (629)
+||.|+.||++|+..|+.+|..++| |+..++++||..|||++.+|+|||||.+
T Consensus 1 ~kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 1 KKRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 3788999999999999999999999 9999999999999999999999999975
No 18
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.39 E-value=2.3e-13 Score=137.57 Aligned_cols=72 Identities=24% Similarity=0.346 Sum_probs=61.8
Q ss_pred cCCCccccCCC-CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhhhhhc
Q 006832 489 KLPSNAKIRRS-FHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVESA 560 (629)
Q Consensus 489 ~~~~~~k~kR~-r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~~~~~ 560 (629)
++.+.+++||. |+.||..|+.+||..|++-.||+...|+-||-++.|.+.+|+|||||||+|++|..+..+.
T Consensus 133 ~~~kkk~kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg~ 205 (332)
T KOG0494|consen 133 DNAKKKKKRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWGG 205 (332)
T ss_pred cccccccccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcCc
Confidence 33444445554 8899999999999999999999999999999999999999999999999988777665543
No 19
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.29 E-value=8e-13 Score=134.34 Aligned_cols=59 Identities=22% Similarity=0.232 Sum_probs=54.0
Q ss_pred CCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhhh
Q 006832 499 SFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKV 557 (629)
Q Consensus 499 ~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~~ 557 (629)
=|..||..|+.+||..|...+|.+...|-+||.-|||+++||+|||||||+|-+|..+.
T Consensus 202 YRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKK 260 (317)
T KOG0848|consen 202 YRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKK 260 (317)
T ss_pred eeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHH
Confidence 35679999999999999999999999999999999999999999999999986666543
No 20
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.28 E-value=1.7e-12 Score=128.90 Aligned_cols=56 Identities=29% Similarity=0.430 Sum_probs=51.2
Q ss_pred CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHH
Q 006832 497 RRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLAL 552 (629)
Q Consensus 497 kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~ 552 (629)
.+++.|||.+|+..||..|..+.|.....|..||++|||.++||.|||||||++++
T Consensus 51 ~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK 106 (198)
T KOG0483|consen 51 KGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWK 106 (198)
T ss_pred ccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhcccccc
Confidence 34446789999999999999999999999999999999999999999999999543
No 21
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.28 E-value=3.5e-12 Score=122.60 Aligned_cols=63 Identities=29% Similarity=0.389 Sum_probs=56.0
Q ss_pred ccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhhh
Q 006832 495 KIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKV 557 (629)
Q Consensus 495 k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~~ 557 (629)
..+++|+|.|.+|+..|++.|..+|||+..+|..||..|||+++-|+|||||+|++.++.+..
T Consensus 50 ~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 50 PPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred cCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence 345555667999999999999999999999999999999999999999999999977766643
No 22
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.20 E-value=7e-12 Score=130.05 Aligned_cols=64 Identities=25% Similarity=0.392 Sum_probs=58.8
Q ss_pred cccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhhh
Q 006832 494 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKV 557 (629)
Q Consensus 494 ~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~~ 557 (629)
+|+||.|+.||.+|+++||.+|+.|.||++.+|++||-.++||+..|+|||+|||++.+|..+-
T Consensus 110 ~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN 173 (351)
T KOG0486|consen 110 SKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERN 173 (351)
T ss_pred hhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhh
Confidence 4678889999999999999999999999999999999999999999999999999976665533
No 23
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.11 E-value=2.1e-11 Score=116.67 Aligned_cols=60 Identities=23% Similarity=0.368 Sum_probs=54.8
Q ss_pred cCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhh
Q 006832 496 IRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR 555 (629)
Q Consensus 496 ~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~ 555 (629)
+++-|+.|+..|+.-|+..|+...|.+..+|.+||..|+|++.||+.||||||.|.+|+-
T Consensus 100 r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~ 159 (194)
T KOG0491|consen 100 RRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQ 159 (194)
T ss_pred hhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHH
Confidence 455688999999999999999999999999999999999999999999999999655543
No 24
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.07 E-value=5.8e-11 Score=117.99 Aligned_cols=66 Identities=20% Similarity=0.326 Sum_probs=57.8
Q ss_pred cccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhhhhh
Q 006832 494 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVES 559 (629)
Q Consensus 494 ~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~~~~ 559 (629)
.+++-.+-.|+-.|++.|+..|.+.+||-..+|.+||..||+++.||+|||||||.|++|+.+++-
T Consensus 165 G~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAaEm 230 (288)
T KOG0847|consen 165 GQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAAEM 230 (288)
T ss_pred ccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhccch
Confidence 333444556899999999999999999999999999999999999999999999998877776653
No 25
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.05 E-value=1.1e-10 Score=119.98 Aligned_cols=61 Identities=30% Similarity=0.495 Sum_probs=56.9
Q ss_pred cCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhh
Q 006832 496 IRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK 556 (629)
Q Consensus 496 ~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~ 556 (629)
.||+|+.+|..|++.|..+|+..|.|.+.+|++|+.++||..+.|+|||||||+|-+|..+
T Consensus 167 nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKK 227 (383)
T KOG4577|consen 167 NKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKK 227 (383)
T ss_pred cCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhh
Confidence 4889999999999999999999999999999999999999999999999999998665543
No 26
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.05 E-value=7.4e-11 Score=121.85 Aligned_cols=64 Identities=22% Similarity=0.389 Sum_probs=59.5
Q ss_pred ccccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhh
Q 006832 493 NAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK 556 (629)
Q Consensus 493 ~~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~ 556 (629)
....||=|+.||-+|+..||+.|...+|.++..|-+||..|||++..|+|||||||.|-+|+|-
T Consensus 178 ~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRl 241 (408)
T KOG0844|consen 178 DDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRL 241 (408)
T ss_pred cHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhh
Confidence 3456788899999999999999999999999999999999999999999999999998888874
No 27
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=98.97 E-value=6.1e-10 Score=110.73 Aligned_cols=64 Identities=22% Similarity=0.331 Sum_probs=58.8
Q ss_pred ccccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhh
Q 006832 493 NAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK 556 (629)
Q Consensus 493 ~~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~ 556 (629)
..++||.|+.|+..|+.+|++.|..++||+...|+.||..++|++..|+|||||+|++.++..+
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~ 120 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEER 120 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence 4567888999999999999999999999999999999999999999999999999997666653
No 28
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=98.91 E-value=7.8e-10 Score=118.52 Aligned_cols=61 Identities=25% Similarity=0.351 Sum_probs=56.0
Q ss_pred ccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhh
Q 006832 495 KIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR 555 (629)
Q Consensus 495 k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~ 555 (629)
|+||+||-|...++.+||.+|..|+.|+..+.-.||.+|+|....|+|||+|||.|.+|-.
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~ 353 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRIT 353 (398)
T ss_pred cccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCC
Confidence 6777889999999999999999999999999999999999999999999999999544433
No 29
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=98.77 E-value=8.9e-09 Score=105.63 Aligned_cols=48 Identities=29% Similarity=0.459 Sum_probs=45.5
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccH
Q 006832 503 MPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYL 550 (629)
Q Consensus 503 ft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k 550 (629)
|..--...|.+||..++||+..+|.+||+.+||+..||.+||+|||++
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQR 230 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQR 230 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhh
Confidence 677778899999999999999999999999999999999999999994
No 30
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=98.67 E-value=1.2e-08 Score=109.82 Aligned_cols=62 Identities=27% Similarity=0.450 Sum_probs=57.1
Q ss_pred cccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhh
Q 006832 494 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR 555 (629)
Q Consensus 494 ~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~ 555 (629)
.+.+|.|+.|+..|+..|++.|..++||+...|++||.++||++..|++||+|+|++.+|..
T Consensus 174 ~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 174 RGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred ccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence 44566689999999999999999999999999999999999999999999999999776666
No 31
>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=98.64 E-value=4.8e-09 Score=81.89 Aligned_cols=49 Identities=35% Similarity=0.960 Sum_probs=40.8
Q ss_pred cccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCC-CCCceecccCch
Q 006832 240 ICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTES-RDQGWFCKFCEC 291 (629)
Q Consensus 240 ~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p-~dg~W~C~~C~~ 291 (629)
+|.+|+..+ .++.||.|| .|.++||+.|++|++.... ....|+|+.|..
T Consensus 1 ~C~vC~~~~--~~~~~i~C~-~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~~ 50 (51)
T PF00628_consen 1 YCPVCGQSD--DDGDMIQCD-SCNRWYHQECVGPPEKAEEIPSGDWYCPNCRP 50 (51)
T ss_dssp EBTTTTSSC--TTSSEEEBS-TTSCEEETTTSTSSHSHHSHHSSSBSSHHHHH
T ss_pred eCcCCCCcC--CCCCeEEcC-CCChhhCcccCCCChhhccCCCCcEECcCCcC
Confidence 589999854 478999999 5999999999999988544 235899999975
No 32
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=98.61 E-value=3.8e-08 Score=100.36 Aligned_cols=60 Identities=32% Similarity=0.447 Sum_probs=55.9
Q ss_pred cCCCCCCCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhh
Q 006832 496 IRRSFHRMPPNAVEKLRQVFAE---NELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR 555 (629)
Q Consensus 496 ~kR~r~rft~~Q~~~Le~~F~~---~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~ 555 (629)
.+|+|+.|+...+.+|..||.. ||||+.+.+++||++.|++..||.+||.|+|.+.+|+.
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~ 250 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNM 250 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhh
Confidence 4677788999999999999985 59999999999999999999999999999999988887
No 33
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=98.58 E-value=1.6e-08 Score=114.66 Aligned_cols=53 Identities=32% Similarity=0.909 Sum_probs=45.9
Q ss_pred cccccccccccCcCCCCCCceEeCCcCCcc-cccccCCCCCCCCCCCCceecccCchh
Q 006832 236 HEHIICAKCKLREAFPDNDIVLCDGTCNCA-FHQKCLDPPLDTESRDQGWFCKFCECK 292 (629)
Q Consensus 236 ~e~~~C~vC~~~g~~~~~~lLlCDG~C~ra-fH~~CL~PPL~~~p~dg~W~C~~C~~k 292 (629)
.+..-|.+|...+. .+.||+||+ |+.+ ||+|||+|+|..+| -+.|||++|.--
T Consensus 213 ~E~~~C~IC~~~Dp--EdVLLLCDs-CN~~~YH~YCLDPdl~eiP-~~eWYC~NC~dL 266 (1134)
T KOG0825|consen 213 QEEVKCDICTVHDP--EDVLLLCDS-CNKVYYHVYCLDPDLSESP-VNEWYCTNCSLL 266 (1134)
T ss_pred cccccceeeccCCh--HHhheeecc-cccceeeccccCccccccc-ccceecCcchhh
Confidence 34567999999864 679999996 9999 99999999999998 789999999753
No 34
>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=98.54 E-value=2.6e-08 Score=75.32 Aligned_cols=33 Identities=39% Similarity=0.681 Sum_probs=28.6
Q ss_pred hCCCCCHHHHHHHHHHhCCCcchhhhccchhcc
Q 006832 517 ENELPSRIVKENLSKELSLEPEKVNKWFKNARY 549 (629)
Q Consensus 517 ~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~ 549 (629)
.+|||+.++|+.||+++||+..||..||-|.|.
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 469999999999999999999999999999997
No 35
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=98.52 E-value=6.4e-08 Score=107.32 Aligned_cols=58 Identities=29% Similarity=0.401 Sum_probs=55.0
Q ss_pred ccccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccH
Q 006832 493 NAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYL 550 (629)
Q Consensus 493 ~~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k 550 (629)
....||+|+.||+.|...|..+|++++||+.+..+.|+++|||..+.|.+||.|.|.+
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 4567888999999999999999999999999999999999999999999999999995
No 36
>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 KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=98.18 E-value=6e-07 Score=107.00 Aligned_cols=77 Identities=26% Similarity=0.543 Sum_probs=55.6
Q ss_pred ccccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchhhH----HHHhhhccCCcccccc
Q 006832 235 HHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECKME----IIESMNAHIGTSFSVN 310 (629)
Q Consensus 235 ~~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k~~----~l~~~n~~~gtsf~lp 310 (629)
..++.+|.+|..++....+.+|+||+ |+.++|+.|++ +..+| +|.|+|..|...+. |+...+......-++.
T Consensus 216 ~~~D~~C~iC~~~~~~n~n~ivfCD~-Cnl~VHq~Cyg--i~~ip-eg~WlCr~Cl~s~~~~v~c~~cp~~~gAFkqt~d 291 (1051)
T KOG0955|consen 216 LEEDAVCCICLDGECQNSNVIVFCDG-CNLAVHQECYG--IPFIP-EGQWLCRRCLQSPQRPVRCLLCPSKGGAFKQTDD 291 (1051)
T ss_pred cCCCccceeecccccCCCceEEEcCC-CcchhhhhccC--CCCCC-CCcEeehhhccCcCcccceEeccCCCCcceeccC
Confidence 35678999999998876799999995 99999999999 33444 79999999987543 4444444333333444
Q ss_pred chhhh
Q 006832 311 SNWQD 315 (629)
Q Consensus 311 ~~~~d 315 (629)
..|.+
T Consensus 292 grw~H 296 (1051)
T KOG0955|consen 292 GRWAH 296 (1051)
T ss_pred Cceee
Confidence 44433
No 38
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=98.17 E-value=7e-07 Score=92.43 Aligned_cols=62 Identities=21% Similarity=0.307 Sum_probs=53.7
Q ss_pred cccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhh
Q 006832 494 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR 555 (629)
Q Consensus 494 ~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~ 555 (629)
..+||+|+-+-.-....||++|..+|.|+.+....||++|.|....|+|||+|.|.|.+|-.
T Consensus 307 ~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~ 368 (385)
T KOG1168|consen 307 GEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 368 (385)
T ss_pred cccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhh
Confidence 34566677667777889999999999999999999999999999999999999999665533
No 39
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=98.17 E-value=5e-07 Score=99.48 Aligned_cols=54 Identities=28% Similarity=0.648 Sum_probs=47.1
Q ss_pred cccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCC---CCCceecccCchhhH
Q 006832 240 ICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTES---RDQGWFCKFCECKME 294 (629)
Q Consensus 240 ~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p---~dg~W~C~~C~~k~~ 294 (629)
.|.||..++....|.||.|++ |..+||+.|+.|++...- +...|||..|...+.
T Consensus 170 qc~vC~~g~~~~~NrmlqC~~-C~~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~~~~ 226 (464)
T KOG4323|consen 170 QCSVCYCGGPGAGNRMLQCDK-CRQWYHQACHQPLIKDELAGDPFYEWFCDVCNRGPK 226 (464)
T ss_pred eeeeeecCCcCccceeeeecc-cccHHHHHhccCCCCHhhccCccceEeehhhccchh
Confidence 399999888777899999995 999999999999987765 457999999988765
No 40
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=98.14 E-value=1.1e-06 Score=99.34 Aligned_cols=64 Identities=23% Similarity=0.581 Sum_probs=57.0
Q ss_pred CCCCcccccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchhhHHHH
Q 006832 230 TDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECKMEIIE 297 (629)
Q Consensus 230 ~dg~~~~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k~~~l~ 297 (629)
..||.+..+.+|..|+.++ +...+++|++ |+-+||.||..|++..++ .+.|+|+.|..+..|-.
T Consensus 60 ~~gWrC~~crvCe~c~~~g--D~~kf~~Ck~-cDvsyh~yc~~P~~~~v~-sg~~~ckk~~~c~qc~~ 123 (694)
T KOG4443|consen 60 SGGWRCPSCRVCEACGTTG--DPKKFLLCKR-CDVSYHCYCQKPPNDKVP-SGPWLCKKCTRCRQCDS 123 (694)
T ss_pred cCCcccCCceeeeeccccC--Cccccccccc-ccccccccccCCcccccc-CcccccHHHHhhhhccc
Confidence 5679999999999999775 4789999995 999999999999999999 79999999998877554
No 41
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=98.04 E-value=3.3e-06 Score=86.37 Aligned_cols=50 Identities=28% Similarity=0.775 Sum_probs=40.6
Q ss_pred ccccccccccccCcCCCCCCceEeCC-cCCc-ccccccCCCCCCCCCCCCceecccCch
Q 006832 235 HHEHIICAKCKLREAFPDNDIVLCDG-TCNC-AFHQKCLDPPLDTESRDQGWFCKFCEC 291 (629)
Q Consensus 235 ~~e~~~C~vC~~~g~~~~~~lLlCDG-~C~r-afH~~CL~PPL~~~p~dg~W~C~~C~~ 291 (629)
..+..+|. |..... ++||-||+ .|.+ |||+-|++ |...| .|.|||+.|..
T Consensus 218 e~e~lYCf-CqqvSy---GqMVaCDn~nCkrEWFH~~CVG--Lk~pP-KG~WYC~eCk~ 269 (271)
T COG5034 218 EGEELYCF-CQQVSY---GQMVACDNANCKREWFHLECVG--LKEPP-KGKWYCPECKK 269 (271)
T ss_pred cCceeEEE-eccccc---ccceecCCCCCchhheeccccc--cCCCC-CCcEeCHHhHh
Confidence 44667885 766543 79999998 7986 99999999 77777 89999999964
No 42
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=98.01 E-value=1.9e-06 Score=89.19 Aligned_cols=53 Identities=21% Similarity=0.466 Sum_probs=47.1
Q ss_pred cCCCCcccccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecc
Q 006832 229 ATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCK 287 (629)
Q Consensus 229 ~~dg~~~~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~ 287 (629)
....|.+.++..|.+|+.+.. ...+|+|| .|+++||.+|++ |...| .|.|.|-
T Consensus 305 KTY~W~C~~C~lC~IC~~P~~--E~E~~FCD-~CDRG~HT~CVG--L~~lP-~G~WICD 357 (381)
T KOG1512|consen 305 KTYFWKCSSCELCRICLGPVI--ESEHLFCD-VCDRGPHTLCVG--LQDLP-RGEWICD 357 (381)
T ss_pred hhcchhhcccHhhhccCCccc--chheeccc-cccCCCCccccc--ccccc-Cccchhh
Confidence 345689999999999999865 67999999 799999999999 88888 7999997
No 43
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=97.94 E-value=4.6e-06 Score=87.18 Aligned_cols=51 Identities=25% Similarity=0.652 Sum_probs=38.4
Q ss_pred cccccccccccCcCCCCCCceEeCC-cCC-cccccccCCCCCCCCCCCCceecccCchhh
Q 006832 236 HEHIICAKCKLREAFPDNDIVLCDG-TCN-CAFHQKCLDPPLDTESRDQGWFCKFCECKM 293 (629)
Q Consensus 236 ~e~~~C~vC~~~g~~~~~~lLlCDG-~C~-rafH~~CL~PPL~~~p~dg~W~C~~C~~k~ 293 (629)
.+..+|..+... -+.||.||+ .|+ .|||+.|++ |...| .|.|||+.|....
T Consensus 217 ~e~~yC~Cnqvs----yg~Mi~CDn~~C~~eWFH~~CVG--L~~~P-kgkWyC~~C~~~~ 269 (274)
T KOG1973|consen 217 DEPTYCICNQVS----YGKMIGCDNPGCPIEWFHFTCVG--LKTKP-KGKWYCPRCKAEN 269 (274)
T ss_pred CCCEEEEecccc----cccccccCCCCCCcceEEEeccc--cccCC-CCcccchhhhhhh
Confidence 345666544222 369999995 499 999999999 66666 6889999997653
No 44
>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=97.91 E-value=4.8e-06 Score=79.64 Aligned_cols=29 Identities=41% Similarity=1.061 Sum_probs=26.2
Q ss_pred ccccccCCCCCCCCCCCCceecccCchhhH
Q 006832 265 AFHQKCLDPPLDTESRDQGWFCKFCECKME 294 (629)
Q Consensus 265 afH~~CL~PPL~~~p~dg~W~C~~C~~k~~ 294 (629)
+||++||+|||..+| +|+|+||.|.....
T Consensus 1 g~H~~CL~Ppl~~~P-~g~W~Cp~C~~~~~ 29 (148)
T cd04718 1 GFHLCCLRPPLKEVP-EGDWICPFCEVEKS 29 (148)
T ss_pred CcccccCCCCCCCCC-CCCcCCCCCcCCCC
Confidence 599999999999999 89999999987643
No 45
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=97.78 E-value=7.6e-06 Score=94.51 Aligned_cols=54 Identities=31% Similarity=0.778 Sum_probs=47.2
Q ss_pred CcccccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchhh
Q 006832 233 SVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECKM 293 (629)
Q Consensus 233 ~~~~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k~ 293 (629)
|...+..+|.+|+.++ .+|+|| +|+.+||.+|++||+...| .+.|.|+.|.+..
T Consensus 42 ~~~~~~e~c~ic~~~g-----~~l~c~-tC~~s~h~~cl~~pl~~~p-~~~~~c~Rc~~p~ 95 (696)
T KOG0383|consen 42 WDDAEQEACRICADGG-----ELLWCD-TCPASFHASCLGPPLTPQP-NGEFICPRCFCPK 95 (696)
T ss_pred cchhhhhhhhhhcCCC-----cEEEec-cccHHHHHHccCCCCCcCC-ccceeeeeeccCC
Confidence 5567788999999986 799999 7999999999999999999 5569999996654
No 46
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=97.75 E-value=1.2e-05 Score=88.38 Aligned_cols=53 Identities=32% Similarity=0.713 Sum_probs=45.7
Q ss_pred ccccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCch
Q 006832 235 HHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCEC 291 (629)
Q Consensus 235 ~~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~ 291 (629)
+.-++.|.+|.+.+....|.||+||| |+-+.|+.|++.+.. | +|.|+|..|.-
T Consensus 190 d~~d~~C~~c~~t~~eN~naiVfCdg-C~i~VHq~CYGI~f~--p-eG~WlCrkCi~ 242 (669)
T COG5141 190 DEFDDICTKCTSTHNENSNAIVFCDG-CEICVHQSCYGIQFL--P-EGFWLCRKCIY 242 (669)
T ss_pred hhhhhhhHhccccccCCcceEEEecC-cchhhhhhcccceec--C-cchhhhhhhcc
Confidence 34678999999998877899999997 999999999996644 4 68999999974
No 47
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=97.75 E-value=1.4e-05 Score=85.37 Aligned_cols=62 Identities=32% Similarity=0.367 Sum_probs=55.3
Q ss_pred ccCCCCCCCCHHHHHHHHHHHHhC---CCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhh
Q 006832 495 KIRRSFHRMPPNAVEKLRQVFAEN---ELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK 556 (629)
Q Consensus 495 k~kR~r~rft~~Q~~~Le~~F~~~---~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~ 556 (629)
..+|++..|+...+.+|+.|+.++ |||+..++..||+++||+..||.+||.|.|.+.++...
T Consensus 238 ~~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~~ 302 (342)
T KOG0773|consen 238 SKWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPMI 302 (342)
T ss_pred CCCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCchH
Confidence 356667789999999999998874 89999999999999999999999999999998777764
No 48
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.73 E-value=2.4e-05 Score=77.96 Aligned_cols=64 Identities=31% Similarity=0.429 Sum_probs=58.0
Q ss_pred CccccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhh
Q 006832 492 SNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR 555 (629)
Q Consensus 492 ~~~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~ 555 (629)
...+.++.++.|+..|+..|...|..++||+...++.|+..+|++...|++||||+|++.++..
T Consensus 149 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~ 212 (235)
T KOG0490|consen 149 SNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHK 212 (235)
T ss_pred CccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhc
Confidence 3456778889999999999999999999999999999999999999999999999999665544
No 49
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=97.64 E-value=1.9e-05 Score=90.28 Aligned_cols=51 Identities=31% Similarity=0.861 Sum_probs=46.2
Q ss_pred ccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCch
Q 006832 237 EHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCEC 291 (629)
Q Consensus 237 e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~ 291 (629)
++.+|.||..++.+..++||+|| .|+...|+.|++ +..+| ++.|+|..|.-
T Consensus 270 edviCDvCrspD~e~~neMVfCd-~Cn~cVHqaCyG--Ile~p-~gpWlCr~Cal 320 (893)
T KOG0954|consen 270 EDVICDVCRSPDSEEANEMVFCD-KCNICVHQACYG--ILEVP-EGPWLCRTCAL 320 (893)
T ss_pred ccceeceecCCCccccceeEEec-cchhHHHHhhhc--eeecC-CCCeeehhccc
Confidence 67899999999888889999999 799999999999 77888 79999999954
No 50
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=97.62 E-value=1.8e-05 Score=87.03 Aligned_cols=51 Identities=33% Similarity=0.849 Sum_probs=43.2
Q ss_pred ccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCC---CCCceecccCc
Q 006832 237 EHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTES---RDQGWFCKFCE 290 (629)
Q Consensus 237 e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p---~dg~W~C~~C~ 290 (629)
....|.+|.... +..-++.|| +|...||+.||+|||+..| ....|.|..|.
T Consensus 543 ~~ysCgiCkks~--dQHll~~CD-tC~lhYHlGCL~PPLTR~Pkk~kn~gWqCsECd 596 (707)
T KOG0957|consen 543 MNYSCGICKKST--DQHLLTQCD-TCHLHYHLGCLSPPLTRLPKKNKNFGWQCSECD 596 (707)
T ss_pred cceeeeeeccch--hhHHHhhcc-hhhceeeccccCCccccCcccccCcceeecccc
Confidence 345699999874 356899999 8999999999999999999 34689999994
No 51
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=97.61 E-value=1.3e-05 Score=98.97 Aligned_cols=55 Identities=29% Similarity=0.799 Sum_probs=48.4
Q ss_pred cccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchhhH
Q 006832 236 HEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECKME 294 (629)
Q Consensus 236 ~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k~~ 294 (629)
.....|.+|...+. ...|++||+ |..+||++|+.|.+..+| .++|+|+.|.....
T Consensus 1106 ~~~~~c~~cr~k~~--~~~m~lc~~-c~~~~h~~C~rp~~~~~~-~~dW~C~~c~~e~~ 1160 (1404)
T KOG1245|consen 1106 AVNALCKVCRRKKQ--DEKMLLCDE-CLSGFHLFCLRPALSSVP-PGDWMCPSCRKEHR 1160 (1404)
T ss_pred cchhhhhhhhhccc--chhhhhhHh-hhhhHHHHhhhhhhccCC-cCCccCCccchhhh
Confidence 44678999999864 579999995 999999999999999999 78999999998765
No 52
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=97.53 E-value=3.4e-05 Score=87.62 Aligned_cols=50 Identities=34% Similarity=0.848 Sum_probs=41.1
Q ss_pred ccccccccCcCCCCCCceEeCC-cCCcccccccCCCCCCCCCCCCceecccCch
Q 006832 239 IICAKCKLREAFPDNDIVLCDG-TCNCAFHQKCLDPPLDTESRDQGWFCKFCEC 291 (629)
Q Consensus 239 ~~C~vC~~~g~~~~~~lLlCDG-~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~ 291 (629)
.-|.||.+----.+|.||.||| .|.-+.|+.|++ +..+| .|.|||..|..
T Consensus 6 GGCCVCSDErGWaeNPLVYCDG~nCsVAVHQaCYG--IvqVP-tGpWfCrKCes 56 (900)
T KOG0956|consen 6 GGCCVCSDERGWAENPLVYCDGHNCSVAVHQACYG--IVQVP-TGPWFCRKCES 56 (900)
T ss_pred cceeeecCcCCCccCceeeecCCCceeeeehhcce--eEecC-CCchhhhhhhh
Confidence 4588887632235799999998 799999999999 66777 79999999954
No 53
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=96.88 E-value=0.00088 Score=81.24 Aligned_cols=63 Identities=19% Similarity=0.267 Sum_probs=57.7
Q ss_pred cccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhh
Q 006832 494 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK 556 (629)
Q Consensus 494 ~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~ 556 (629)
-.+++.|++++..|+..|..+|....||...+-|.|...++|..+.|.+||||.|.+.+|..-
T Consensus 901 ~~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 901 MGRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 345677899999999999999999999999999999999999999999999999997777663
No 54
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=96.27 E-value=0.00086 Score=49.79 Aligned_cols=35 Identities=37% Similarity=0.965 Sum_probs=18.9
Q ss_pred CCceEeCCcCCcccccccCCCCCCCCCCCCceecccCc
Q 006832 253 NDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCE 290 (629)
Q Consensus 253 ~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~ 290 (629)
+.||.|++ |....|+.|++...... ...|+|..|.
T Consensus 2 n~ll~C~~-C~v~VH~~CYGv~~~~~--~~~W~C~~C~ 36 (36)
T PF13831_consen 2 NPLLFCDN-CNVAVHQSCYGVSEVPD--GDDWLCDRCE 36 (36)
T ss_dssp CEEEE-SS-S--EEEHHHHT-SS--S--S-----HHH-
T ss_pred CceEEeCC-CCCcCChhhCCcccCCC--CCcEECCcCC
Confidence 57999995 99999999999654433 2479998883
No 55
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.16 E-value=0.0035 Score=51.05 Aligned_cols=42 Identities=12% Similarity=0.295 Sum_probs=32.3
Q ss_pred HHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhcc
Q 006832 508 VEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 549 (629)
Q Consensus 508 ~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~ 549 (629)
++-|+.+|..++++....-..|..+.||+..||+.||--++.
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 56
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=95.23 E-value=0.011 Score=57.91 Aligned_cols=53 Identities=26% Similarity=0.655 Sum_probs=38.6
Q ss_pred ccccccc-CcCCCCCCceEeCCcCCcccccccCCCCCCCCC-------CCCceecccCchhh
Q 006832 240 ICAKCKL-REAFPDNDIVLCDGTCNCAFHQKCLDPPLDTES-------RDQGWFCKFCECKM 293 (629)
Q Consensus 240 ~C~vC~~-~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p-------~dg~W~C~~C~~k~ 293 (629)
.|.+|+. ++...-+.||.|-| |..+||..||+|.....- ......|..|+...
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 23344689999997 999999999999865443 22456788887543
No 57
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=94.95 E-value=0.013 Score=70.45 Aligned_cols=49 Identities=24% Similarity=0.550 Sum_probs=43.3
Q ss_pred cccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCch
Q 006832 236 HEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCEC 291 (629)
Q Consensus 236 ~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~ 291 (629)
.-++.|.+|...+ +++||. +|++.||+.|+.||+...| ...|-|-.|..
T Consensus 342 ~~ddhcrf~~d~~-----~~lc~E-t~prvvhlEcv~hP~~~~~-s~~~e~evc~~ 390 (1414)
T KOG1473|consen 342 EYDDHCRFCHDLG-----DLLCCE-TCPRVVHLECVFHPRFAVP-SAFWECEVCNI 390 (1414)
T ss_pred eecccccccCccc-----ceeecc-cCCceEEeeecCCccccCC-Cccchhhhhhh
Confidence 3467899999874 899999 7999999999999999999 67899999974
No 58
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=94.16 E-value=0.062 Score=62.49 Aligned_cols=47 Identities=21% Similarity=0.383 Sum_probs=43.3
Q ss_pred HHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHh
Q 006832 508 VEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKA 554 (629)
Q Consensus 508 ~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~ 554 (629)
+..|..+|..|.+|+.++-..+|.++||+...|+.||+++++..+..
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv 614 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSV 614 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhh
Confidence 78999999999999999999999999999999999999999944443
No 59
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=93.33 E-value=0.043 Score=61.34 Aligned_cols=53 Identities=25% Similarity=0.653 Sum_probs=40.8
Q ss_pred ccccccccCcCCCCCCceEeCCcCCcccccccCCCCC-CCCC------CCCceecccCchh
Q 006832 239 IICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPL-DTES------RDQGWFCKFCECK 292 (629)
Q Consensus 239 ~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL-~~~p------~dg~W~C~~C~~k 292 (629)
.+|.||.+....+-++||.|| .|.-..|-.|++.-- ..+| ....|||-.|.+-
T Consensus 120 ~iCcVClg~rs~da~ei~qCd-~CGi~VHEgCYGv~dn~si~s~~s~~stepWfCeaC~~G 179 (707)
T KOG0957|consen 120 VICCVCLGQRSVDAGEILQCD-KCGINVHEGCYGVLDNVSIPSGSSDCSTEPWFCEACLYG 179 (707)
T ss_pred eEEEEeecCccccccceeecc-ccCceecccccccccccccCCCCccCCCCchhhhhHhcC
Confidence 389999987767779999999 699999999998641 1111 2257999999764
No 60
>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=93.21 E-value=0.15 Score=40.86 Aligned_cols=48 Identities=17% Similarity=0.279 Sum_probs=36.6
Q ss_pred CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhcc
Q 006832 497 RRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 549 (629)
Q Consensus 497 kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~ 549 (629)
||+|..||.++.-.+-..+...+ ...+||+++|++.++|..|..|+..
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 46677889999888888888776 6899999999999999999999753
No 61
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=90.98 E-value=0.057 Score=62.17 Aligned_cols=61 Identities=16% Similarity=0.400 Sum_probs=47.7
Q ss_pred ccccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchhhHHH
Q 006832 235 HHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECKMEII 296 (629)
Q Consensus 235 ~~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k~~~l 296 (629)
...+..|.+|+..|....+.|+.|. .|...||.+|+..-+.....-+.|-|+.|..+-.|.
T Consensus 15 ~~~~~mc~l~~s~G~~~ag~m~ac~-~c~~~yH~~cvt~~~~~~~l~~gWrC~~crvCe~c~ 75 (694)
T KOG4443|consen 15 IIVCLMCPLCGSSGKGRAGRLLACS-DCGQKYHPYCVTSWAQHAVLSGGWRCPSCRVCEACG 75 (694)
T ss_pred hhhhhhhhhhccccccccCcchhhh-hhcccCCcchhhHHHhHHHhcCCcccCCceeeeecc
Confidence 4557789999998887889999999 699999999999655444212569999998765443
No 62
>KOG1246 consensus DNA-binding protein jumonji/RBP2/SMCY, contains JmjC domain [General function prediction only]
Probab=88.41 E-value=0.31 Score=59.17 Aligned_cols=51 Identities=31% Similarity=0.829 Sum_probs=42.6
Q ss_pred ccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchh
Q 006832 237 EHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECK 292 (629)
Q Consensus 237 e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k 292 (629)
....|..|..+.. . .+++|++ |...||.+|+.||+..++ ++.|.|+.|..-
T Consensus 154 ~~~~~~~~~k~~~--~-~~~~~~~-~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~ 204 (904)
T KOG1246|consen 154 DYPQCNTCSKGKE--E-KLLLCDS-CDDSYHTYCLRPPLTRVP-DGDWRCPKCIPT 204 (904)
T ss_pred cchhhhccccCCC--c-cceeccc-ccCcccccccCCCCCcCC-cCcccCCccccc
Confidence 3456899988764 2 3449995 999999999999999999 899999999865
No 63
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=87.02 E-value=0.35 Score=39.30 Aligned_cols=35 Identities=29% Similarity=0.741 Sum_probs=28.9
Q ss_pred ccccccccccCcCCCCCCceEeCCcCCcccccccCCC
Q 006832 237 EHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDP 273 (629)
Q Consensus 237 e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~P 273 (629)
....|.+|+..- .+.+++|.|. .|...||..|+..
T Consensus 4 ~~~~C~~Cg~~~-~~~dDiVvCp-~CgapyHR~C~~~ 38 (54)
T PF14446_consen 4 EGCKCPVCGKKF-KDGDDIVVCP-ECGAPYHRDCWEK 38 (54)
T ss_pred cCccChhhCCcc-cCCCCEEECC-CCCCcccHHHHhh
Confidence 446799999863 3468999999 7999999999864
No 64
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=85.93 E-value=0.44 Score=54.96 Aligned_cols=49 Identities=29% Similarity=0.712 Sum_probs=41.1
Q ss_pred cccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchh
Q 006832 238 HIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECK 292 (629)
Q Consensus 238 ~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k 292 (629)
...|.+|..++ ++++|+ .|+.+||+.|..+++........|.|..|...
T Consensus 47 ~ts~~~~~~~g-----n~~~~~-~~~~s~h~~~~~~~~sp~~~~~~~~~~~~~~~ 95 (613)
T KOG4299|consen 47 ATSCGICKSGG-----NLLCCD-HCPASFHLECDKPPLSPDLKGSEINCSRCPKG 95 (613)
T ss_pred hhhcchhhhcC-----Cccccc-cCccccchhccCcccCcccccccccccCCCcc
Confidence 56799999875 799999 69999999999999984434578999999763
No 65
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=80.35 E-value=0.43 Score=50.49 Aligned_cols=59 Identities=15% Similarity=0.227 Sum_probs=41.6
Q ss_pred ccccccccccCcC----CCCCCceEeCCcCCcccccccCCCCCCCCC--CCCceecccCchhhHHH
Q 006832 237 EHIICAKCKLREA----FPDNDIVLCDGTCNCAFHQKCLDPPLDTES--RDQGWFCKFCECKMEII 296 (629)
Q Consensus 237 e~~~C~vC~~~g~----~~~~~lLlCDG~C~rafH~~CL~PPL~~~p--~dg~W~C~~C~~k~~~l 296 (629)
....|..|-.+-. ..-+.||+|- .|..+||.+|+..+..-+. ....|.|-.|.-+.-|+
T Consensus 257 ~~~~~~~~~~~~~~~~~~r~~S~I~C~-~C~~~~HP~Ci~M~~elv~~~KTY~W~C~~C~lC~IC~ 321 (381)
T KOG1512|consen 257 RRNERKHFWDIQTNIIQSRRNSWIVCK-PCATRPHPYCVAMIPELVGQYKTYFWKCSSCELCRICL 321 (381)
T ss_pred chhhhhhhhcchhhhhhhhhccceeec-ccccCCCCcchhcCHHHHhHHhhcchhhcccHhhhccC
Confidence 3456777765421 0136799999 7999999999987754433 34689999998776554
No 66
>KOG3612 consensus PHD Zn-finger protein [General function prediction only]
Probab=80.33 E-value=1.1 Score=51.00 Aligned_cols=55 Identities=16% Similarity=0.288 Sum_probs=42.8
Q ss_pred CcccccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchhh
Q 006832 233 SVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECKM 293 (629)
Q Consensus 233 ~~~~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k~ 293 (629)
.....+++|.-|.-.+ ..|.|+ .|.+.||..|+.|.-........|.|+.|....
T Consensus 55 ~~~N~d~~cfechlpg-----~vl~c~-vc~Rs~h~~c~sp~~q~r~~s~p~~~p~p~s~k 109 (588)
T KOG3612|consen 55 PSSNIDPFCFECHLPG-----AVLKCI-VCHRSFHENCQSPDPQKRNYSVPSDKPQPYSFK 109 (588)
T ss_pred cccCCCcccccccCCc-----ceeeee-hhhccccccccCcchhhccccccccCCcccccC
Confidence 3445679999999865 788999 699999999998865444434579999997643
No 67
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=79.89 E-value=0.33 Score=58.99 Aligned_cols=50 Identities=18% Similarity=0.206 Sum_probs=38.4
Q ss_pred cccccccccCcCCCCCCceEeCCcCCccccc-ccCCCCCC--CCCCCCceecccCchhh
Q 006832 238 HIICAKCKLREAFPDNDIVLCDGTCNCAFHQ-KCLDPPLD--TESRDQGWFCKFCECKM 293 (629)
Q Consensus 238 ~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~-~CL~PPL~--~~p~dg~W~C~~C~~k~ 293 (629)
...|.+|+. ++-+|||+|+|+.+||+ .||+-..- ..+ ++.|+|+.|..++
T Consensus 428 ~rrl~Ie~~-----det~l~yysT~pqly~ll~cLd~~~~e~~L~-d~i~~~~ee~~rq 480 (1414)
T KOG1473|consen 428 SRRLRIEGM-----DETLLWYYSTCPQLYHLLRCLDRTYVEMYLC-DGIWERREEIIRQ 480 (1414)
T ss_pred eeeeEEecC-----CCcEEEEecCcHHHHHHHHHhchHHHHHhhc-cchhhhHHHHHHh
Confidence 345777774 36899999889999999 99994432 333 7899999998754
No 68
>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=76.85 E-value=1.4 Score=36.47 Aligned_cols=47 Identities=21% Similarity=0.365 Sum_probs=30.9
Q ss_pred CCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhc
Q 006832 498 RSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNAR 548 (629)
Q Consensus 498 R~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR 548 (629)
+++.+||+++...+-..+ ..+.....+||.++||++.+|..|-.-.+
T Consensus 2 ~~r~~ys~e~K~~~v~~~----~~~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREY----LESGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp -SS----HHHHHHHHHHH----HHHHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHH----HHCCCceEeeecccccccccccHHHHHHh
Confidence 345678999977665555 22357888999999999999999965444
No 69
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=75.93 E-value=1.7 Score=49.11 Aligned_cols=56 Identities=18% Similarity=0.323 Sum_probs=46.5
Q ss_pred ccccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchhhH
Q 006832 235 HHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECKME 294 (629)
Q Consensus 235 ~~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k~~ 294 (629)
..+...|.+|......+++.++.|+ .|.++||+.|..|+.... +.|.|..|+..+.
T Consensus 80 ~~~e~~~nv~~s~~~~p~~e~~~~~-r~~~~~~q~~~i~~~~~~---~~~~~~~c~~~~~ 135 (464)
T KOG4323|consen 80 PSSELNPNVLTSETVLPENEKVICG-RCKSGYHQGCNIPRFPSL---DIGESTECVFPIF 135 (464)
T ss_pred CccccCCcccccccccCchhhhhhh-hhccCcccccCccCcCcC---Ccccccccccccc
Confidence 3455779999988777788999999 899999999999987664 6899999887653
No 70
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=74.05 E-value=0.94 Score=53.50 Aligned_cols=53 Identities=23% Similarity=0.285 Sum_probs=45.5
Q ss_pred ccccccccccccCcCCCCCCceEeCCcCCcccccccCCC-CCCCCCCCCceecccCchhhH
Q 006832 235 HHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDP-PLDTESRDQGWFCKFCECKME 294 (629)
Q Consensus 235 ~~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~P-PL~~~p~dg~W~C~~C~~k~~ 294 (629)
...+++|..|.... ..++|. .|.+.||..|+.| |+...+ -+.|-|+.|..+..
T Consensus 503 ~~~d~~~~~~~~~l-----~~l~~p-~~lrr~k~d~l~~~P~Kte~-i~~~~~~~~Q~~~y 556 (696)
T KOG0383|consen 503 EFHDISCEEQIKKL-----HLLLCP-HMLRRLKLDVLKPMPLKTEL-IGRVELSPCQKKYY 556 (696)
T ss_pred hcchhhHHHHHHhh-----ccccCc-hhhhhhhhhhccCCCcccee-EEEEecCHHHHHHH
Confidence 34578899999875 688899 8999999999999 888888 68999999987654
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=71.70 E-value=4.9 Score=32.54 Aligned_cols=40 Identities=25% Similarity=0.473 Sum_probs=36.1
Q ss_pred CCHHHHHHHHHHHHhC--CCCCHHHHHHHHHHhCCCcchhhh
Q 006832 503 MPPNAVEKLRQVFAEN--ELPSRIVKENLSKELSLEPEKVNK 542 (629)
Q Consensus 503 ft~~Q~~~Le~~F~~~--~yPs~~~re~LA~~lgLt~~QVki 542 (629)
+|+.|.+.|...|..- .+|-...-.+||++||++..-|..
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 5899999999999988 569999999999999999988765
No 72
>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=70.91 E-value=5.1 Score=30.93 Aligned_cols=44 Identities=20% Similarity=0.401 Sum_probs=33.7
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccH
Q 006832 502 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYL 550 (629)
Q Consensus 502 rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k 550 (629)
.+++.+.+.|...| |- ..+-.++|+.||++...|+.+......+
T Consensus 4 ~L~~~er~vi~~~y----~~-~~t~~eIa~~lg~s~~~V~~~~~~al~k 47 (50)
T PF04545_consen 4 QLPPREREVIRLRY----FE-GLTLEEIAERLGISRSTVRRILKRALKK 47 (50)
T ss_dssp TS-HHHHHHHHHHH----TS-T-SHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHh----cC-CCCHHHHHHHHCCcHHHHHHHHHHHHHH
Confidence 47899999999999 22 2336789999999999999987766553
No 73
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=68.71 E-value=2.8 Score=45.85 Aligned_cols=40 Identities=18% Similarity=0.467 Sum_probs=35.1
Q ss_pred CceEeCCcCCccccccc--CCCCCCCCCCCCceecccCchhhH
Q 006832 254 DIVLCDGTCNCAFHQKC--LDPPLDTESRDQGWFCKFCECKME 294 (629)
Q Consensus 254 ~lLlCDG~C~rafH~~C--L~PPL~~~p~dg~W~C~~C~~k~~ 294 (629)
.++.|++ |..+||-.| ++++....|....|+|..|.....
T Consensus 74 ~~~~cd~-C~~~~~~ec~~v~~~~~e~p~~~~~~c~~c~~~~~ 115 (345)
T KOG1632|consen 74 LMEQCDL-CEDWYHGECWEVGTAEKEAPKEDPKVCDECKEAQD 115 (345)
T ss_pred hhhcccc-ccccccccccccCchhhcCCccccccccccchhhh
Confidence 7899995 999999999 999998888557899999987654
No 74
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=68.53 E-value=1.8 Score=38.33 Aligned_cols=46 Identities=30% Similarity=0.624 Sum_probs=31.5
Q ss_pred ccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchh
Q 006832 241 CAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECK 292 (629)
Q Consensus 241 C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k 292 (629)
|..|.-+|. +-.+|++. |...||+.|+.--|.... ..=.||-|+..
T Consensus 35 Cp~Ck~Pgd--~Cplv~g~--C~H~FH~hCI~kWl~~~~--~~~~CPmCR~~ 80 (85)
T PF12861_consen 35 CPDCKFPGD--DCPLVWGK--CSHNFHMHCILKWLSTQS--SKGQCPMCRQP 80 (85)
T ss_pred CCCccCCCC--CCceeecc--CccHHHHHHHHHHHcccc--CCCCCCCcCCe
Confidence 555665543 34566664 999999999987776643 23389999864
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=65.60 E-value=12 Score=24.70 Aligned_cols=38 Identities=13% Similarity=0.434 Sum_probs=29.0
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhcc
Q 006832 502 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWF 544 (629)
Q Consensus 502 rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWF 544 (629)
.|+..+...+...|. +.+ ...++|+.+|++...|..|.
T Consensus 5 ~~~~~~~~~i~~~~~-~~~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 5 KLTPEQIEEARRLLA-AGE----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred cCCHHHHHHHHHHHH-cCC----CHHHHHHHHCCCHHHHHHhC
Confidence 467777777777775 333 56789999999999999884
No 76
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=65.54 E-value=11 Score=39.94 Aligned_cols=30 Identities=17% Similarity=0.371 Sum_probs=23.3
Q ss_pred ccccccccccccCcCCCCCCceEeCCcCCcc
Q 006832 235 HHEHIICAKCKLREAFPDNDIVLCDGTCNCA 265 (629)
Q Consensus 235 ~~e~~~C~vC~~~g~~~~~~lLlCDG~C~ra 265 (629)
+..+.+|..|..+-+..++.|..|. .|...
T Consensus 122 pl~da~C~EC~R~vw~hGGrif~Cs-fC~~f 151 (314)
T PF06524_consen 122 PLQDAVCIECERGVWDHGGRIFKCS-FCDNF 151 (314)
T ss_pred cCCCcEeeeeecccccCCCeEEEee-cCCCe
Confidence 3456678889887777789999998 78764
No 77
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=64.23 E-value=4.5 Score=34.21 Aligned_cols=53 Identities=21% Similarity=0.398 Sum_probs=18.8
Q ss_pred ccccccccCcC-CCCCCceEeCC-cCCcccccccCCCCC--------CCCCCCCceecccCchhh
Q 006832 239 IICAKCKLREA-FPDNDIVLCDG-TCNCAFHQKCLDPPL--------DTESRDQGWFCKFCECKM 293 (629)
Q Consensus 239 ~~C~vC~~~g~-~~~~~lLlCDG-~C~rafH~~CL~PPL--------~~~p~dg~W~C~~C~~k~ 293 (629)
..|.+|...-. ...-..+.|+. .|...||+.||---+ .-.| -.+-||.|....
T Consensus 3 ~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~--~~G~CP~C~~~i 65 (70)
T PF11793_consen 3 LECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIP--IFGECPYCSSPI 65 (70)
T ss_dssp -S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT----EEE-TTT-SEE
T ss_pred CCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecc--cccCCcCCCCee
Confidence 45888876532 11234588872 499999999993211 1112 346799997653
No 78
>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=63.70 E-value=5.3 Score=29.51 Aligned_cols=43 Identities=19% Similarity=0.306 Sum_probs=33.7
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhcc
Q 006832 502 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 549 (629)
Q Consensus 502 rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~ 549 (629)
.+++.+...|..+|... ..-.++|..+|++..+|..|....+.
T Consensus 10 ~l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 10 KLPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALK 52 (55)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 46788888888776422 35678899999999999999877655
No 79
>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=56.28 E-value=9.9 Score=42.87 Aligned_cols=57 Identities=19% Similarity=0.437 Sum_probs=37.0
Q ss_pred cccccccCcC-CCCCCceEeCCcCCcccccccCCCC--------CCCCC--CCCceecccCchhhHHHH
Q 006832 240 ICAKCKLREA-FPDNDIVLCDGTCNCAFHQKCLDPP--------LDTES--RDQGWFCKFCECKMEIIE 297 (629)
Q Consensus 240 ~C~vC~~~g~-~~~~~lLlCDG~C~rafH~~CL~PP--------L~~~p--~dg~W~C~~C~~k~~~l~ 297 (629)
.|.+|..-+. .++--.|.|| .|..|-|+.|---. ..... .++.++|..|....+++.
T Consensus 130 ~C~iC~kfD~~~n~~~Wi~Cd-~CgH~cH~dCALr~~~i~~G~s~~g~~g~~d~~f~C~~C~~~seLlG 197 (446)
T PF07227_consen 130 MCCICSKFDDNKNTCSWIGCD-VCGHWCHLDCALRHELIGTGPSVKGSIGTLDMQFHCRACGKTSELLG 197 (446)
T ss_pred CccccCCcccCCCCeeEEecc-CCCceehhhhhcccccccCCccCCCCCccCceEEEccCCCChhhHHH
Confidence 4566766432 2334688999 79999999986321 11111 357899999988766443
No 80
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=54.89 E-value=6.3 Score=43.18 Aligned_cols=47 Identities=30% Similarity=0.583 Sum_probs=35.1
Q ss_pred ccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchh
Q 006832 239 IICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECK 292 (629)
Q Consensus 239 ~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k 292 (629)
+.|++|-.... .|+.|--= .|...||..|.+|=|..- .=+||.|.+.
T Consensus 230 ~~CaIClEdY~--~GdklRiL-PC~H~FH~~CIDpWL~~~----r~~CPvCK~d 276 (348)
T KOG4628|consen 230 DTCAICLEDYE--KGDKLRIL-PCSHKFHVNCIDPWLTQT----RTFCPVCKRD 276 (348)
T ss_pred ceEEEeecccc--cCCeeeEe-cCCCchhhccchhhHhhc----CccCCCCCCc
Confidence 58999998653 44555445 699999999999876642 3489999863
No 81
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=54.70 E-value=6.5 Score=35.29 Aligned_cols=30 Identities=27% Similarity=0.755 Sum_probs=25.2
Q ss_pred cccccccccCcCCCCCCceEeCCc--CCcccccccCC
Q 006832 238 HIICAKCKLREAFPDNDIVLCDGT--CNCAFHQKCLD 272 (629)
Q Consensus 238 ~~~C~vC~~~g~~~~~~lLlCDG~--C~rafH~~CL~ 272 (629)
...|.+|+... +.+|.|. . |..+||..|..
T Consensus 55 ~~~C~iC~~~~----G~~i~C~-~~~C~~~fH~~CA~ 86 (110)
T PF13832_consen 55 KLKCSICGKSG----GACIKCS-HPGCSTAFHPTCAR 86 (110)
T ss_pred CCcCcCCCCCC----ceeEEcC-CCCCCcCCCHHHHH
Confidence 56899999863 5788998 6 99999999975
No 82
>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=53.60 E-value=9.7 Score=33.34 Aligned_cols=31 Identities=19% Similarity=0.525 Sum_probs=21.9
Q ss_pred cccccccccCcCCCCCCceEeCCcCCcccccccCC
Q 006832 238 HIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLD 272 (629)
Q Consensus 238 ~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~ 272 (629)
...|.+|+..=. ...++.. .|+..||..|+.
T Consensus 78 ~~~C~vC~k~l~--~~~f~~~--p~~~v~H~~C~~ 108 (109)
T PF10367_consen 78 STKCSVCGKPLG--NSVFVVF--PCGHVVHYSCIK 108 (109)
T ss_pred CCCccCcCCcCC--CceEEEe--CCCeEEeccccc
Confidence 467999998642 2344444 388999999975
No 83
>PF13551 HTH_29: Winged helix-turn helix
Probab=53.18 E-value=21 Score=31.09 Aligned_cols=49 Identities=22% Similarity=0.350 Sum_probs=33.2
Q ss_pred CCCCCCCCHHHHHHHHHHHHhCCCCC--HHHHHHHHHHh-------CCCcchhhhccc
Q 006832 497 RRSFHRMPPNAVEKLRQVFAENELPS--RIVKENLSKEL-------SLEPEKVNKWFK 545 (629)
Q Consensus 497 kR~r~rft~~Q~~~Le~~F~~~~yPs--~~~re~LA~~l-------gLt~~QVkiWFQ 545 (629)
.+++.++++++.+.|.+++.++|... ......|+..| .+++..|..|+.
T Consensus 52 g~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 52 GRPRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 34444489999999999999987432 23444555433 567777887764
No 84
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=52.50 E-value=3 Score=44.17 Aligned_cols=62 Identities=19% Similarity=0.346 Sum_probs=43.7
Q ss_pred cccccccccccCcC-----CCCCCceEeCCcCCcccccccCCCCCCCCC--CCCceecccCchhhHHHHh
Q 006832 236 HEHIICAKCKLREA-----FPDNDIVLCDGTCNCAFHQKCLDPPLDTES--RDQGWFCKFCECKMEIIES 298 (629)
Q Consensus 236 ~e~~~C~vC~~~g~-----~~~~~lLlCDG~C~rafH~~CL~PPL~~~p--~dg~W~C~~C~~k~~~l~~ 298 (629)
....+|..|.+... .-+.+||.|. .|.+.=|..||.-....+. ....|.|-.|..+.-|...
T Consensus 222 ~Pn~YCDFclgdsr~nkkt~~peelvscs-dcgrsghpsclqft~nm~~avk~yrwqcieck~csicgts 290 (336)
T KOG1244|consen 222 QPNPYCDFCLGDSRENKKTGMPEELVSCS-DCGRSGHPSCLQFTANMIAAVKTYRWQCIECKYCSICGTS 290 (336)
T ss_pred cCCcccceeccccccccccCCchhhcchh-hcCCCCCcchhhhhHHHHHHHHhheeeeeecceeccccCc
Confidence 44567888875431 1357899999 6999999999975433222 3468999999988665543
No 85
>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=52.49 E-value=7.5 Score=32.37 Aligned_cols=25 Identities=12% Similarity=0.488 Sum_probs=19.9
Q ss_pred HHHHHHHHhCCCcchhhhccchhcc
Q 006832 525 VKENLSKELSLEPEKVNKWFKNARY 549 (629)
Q Consensus 525 ~re~LA~~lgLt~~QVkiWFQNrR~ 549 (629)
.-.+||.+||+++.||..|=..-.+
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK~~dkW 48 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWKSRDKW 48 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHhhhcch
Confidence 4468999999999999999544443
No 86
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=51.25 E-value=15 Score=37.06 Aligned_cols=41 Identities=22% Similarity=0.465 Sum_probs=37.6
Q ss_pred CCCHHHHHHHHHHHHhC--CCCCHHHHHHHHHHhCCCcchhhh
Q 006832 502 RMPPNAVEKLRQVFAEN--ELPSRIVKENLSKELSLEPEKVNK 542 (629)
Q Consensus 502 rft~~Q~~~Le~~F~~~--~yPs~~~re~LA~~lgLt~~QVki 542 (629)
.||+-|++.|..+|..- .||-.-.-.+||++||+++.-+.-
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 68999999999999988 689999999999999999987764
No 87
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=50.23 E-value=13 Score=37.61 Aligned_cols=43 Identities=26% Similarity=0.733 Sum_probs=31.7
Q ss_pred ccccccccCcCC---CCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchh
Q 006832 239 IICAKCKLREAF---PDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECK 292 (629)
Q Consensus 239 ~~C~vC~~~g~~---~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k 292 (629)
-+|.+|...+.. .....+.|. .|...||..|+.. . .||.|...
T Consensus 153 fiCe~C~~~~~IfPF~~~~~~~C~-~C~~v~H~~C~~~----~------~CpkC~R~ 198 (202)
T PF13901_consen 153 FICEICNSDDIIFPFQIDTTVRCP-KCKSVFHKSCFRK----K------SCPKCARR 198 (202)
T ss_pred CCCccCCCCCCCCCCCCCCeeeCC-cCccccchhhcCC----C------CCCCcHhH
Confidence 468888875432 225788999 5999999999982 1 29999753
No 88
>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=49.59 E-value=1.5 Score=33.09 Aligned_cols=43 Identities=23% Similarity=0.539 Sum_probs=28.2
Q ss_pred cccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCc
Q 006832 240 ICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCE 290 (629)
Q Consensus 240 ~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~ 290 (629)
.|.+|...-. .+..++... |...||..|+..-+... -.||.|+
T Consensus 2 ~C~IC~~~~~-~~~~~~~l~--C~H~fh~~Ci~~~~~~~-----~~CP~CR 44 (44)
T PF13639_consen 2 ECPICLEEFE-DGEKVVKLP--CGHVFHRSCIKEWLKRN-----NSCPVCR 44 (44)
T ss_dssp CETTTTCBHH-TTSCEEEET--TSEEEEHHHHHHHHHHS-----SB-TTTH
T ss_pred CCcCCChhhc-CCCeEEEcc--CCCeeCHHHHHHHHHhC-----CcCCccC
Confidence 5888887642 234555554 99999999998654332 2788773
No 89
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=49.19 E-value=12 Score=37.20 Aligned_cols=23 Identities=39% Similarity=0.804 Sum_probs=19.5
Q ss_pred CCCceEeCCcCCcccccccCCCCC
Q 006832 252 DNDIVLCDGTCNCAFHQKCLDPPL 275 (629)
Q Consensus 252 ~~~lLlCDG~C~rafH~~CL~PPL 275 (629)
+|.|.-|. .|.++||+..|-|+-
T Consensus 121 ~nVLFRC~-~C~RawH~~HLP~~~ 143 (175)
T PF15446_consen 121 DNVLFRCT-SCHRAWHFEHLPPPS 143 (175)
T ss_pred hheEEecC-CccceeehhhCCCCc
Confidence 57888899 699999999987764
No 90
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=49.02 E-value=25 Score=42.97 Aligned_cols=13 Identities=38% Similarity=0.813 Sum_probs=6.2
Q ss_pred CCCCCCCCCCCcc
Q 006832 338 PSDDSEDDDYNPE 350 (629)
Q Consensus 338 psddseD~dydP~ 350 (629)
|.+|++|++-|.+
T Consensus 1402 ~~~dd~DeeeD~e 1414 (1516)
T KOG1832|consen 1402 PTDDDSDEEEDDE 1414 (1516)
T ss_pred CCccccCccccch
Confidence 4455555544443
No 91
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=47.38 E-value=20 Score=34.55 Aligned_cols=51 Identities=22% Similarity=0.181 Sum_probs=40.4
Q ss_pred CCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhhh
Q 006832 501 HRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKV 557 (629)
Q Consensus 501 ~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~~ 557 (629)
..+|+.|.+.|...+ ...+..+||+.||++...|+.|.++.|.+.++.+..
T Consensus 5 ~~Lt~rqreVL~lr~------~GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~t 55 (141)
T PRK03975 5 SFLTERQIEVLRLRE------RGLTQQEIADILGTSRANVSSIEKRARENIEKARET 55 (141)
T ss_pred cCCCHHHHHHHHHHH------cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 468999999998742 234567999999999999999999988866665543
No 92
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=46.58 E-value=11 Score=32.45 Aligned_cols=32 Identities=25% Similarity=0.678 Sum_probs=25.0
Q ss_pred cccccccccCcCCCCCCceEeCC-cCCcccccccCCC
Q 006832 238 HIICAKCKLREAFPDNDIVLCDG-TCNCAFHQKCLDP 273 (629)
Q Consensus 238 ~~~C~vC~~~g~~~~~~lLlCDG-~C~rafH~~CL~P 273 (629)
...|.+|+... |..|-|.- .|...||+.|..-
T Consensus 36 ~~~C~~C~~~~----Ga~i~C~~~~C~~~fH~~CA~~ 68 (90)
T PF13771_consen 36 KLKCSICKKKG----GACIGCSHPGCSRSFHVPCARK 68 (90)
T ss_pred CCCCcCCCCCC----CeEEEEeCCCCCcEEChHHHcc
Confidence 35799999871 46888873 5999999999854
No 93
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=45.45 E-value=18 Score=28.80 Aligned_cols=24 Identities=4% Similarity=0.292 Sum_probs=16.9
Q ss_pred HHHHHHHHhCCCcchhhhccchhc
Q 006832 525 VKENLSKELSLEPEKVNKWFKNAR 548 (629)
Q Consensus 525 ~re~LA~~lgLt~~QVkiWFQNrR 548 (629)
....||+.+|++..+|..||.++.
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 567788888888888888888773
No 94
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=45.41 E-value=24 Score=26.52 Aligned_cols=42 Identities=19% Similarity=0.335 Sum_probs=31.6
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhcc
Q 006832 502 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 549 (629)
Q Consensus 502 rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~ 549 (629)
.+++.+.+.+..++. .+ ...+||+.||++...|..|.+.-+.
T Consensus 3 ~l~~~e~~i~~~~~~--g~----s~~eia~~l~is~~tv~~~~~~~~~ 44 (58)
T smart00421 3 SLTPREREVLRLLAE--GL----TNKEIAERLGISEKTVKTHLSNIMR 44 (58)
T ss_pred CCCHHHHHHHHHHHc--CC----CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 368888887765432 22 5588999999999999998875544
No 95
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=45.20 E-value=14 Score=28.24 Aligned_cols=40 Identities=13% Similarity=0.333 Sum_probs=21.3
Q ss_pred CCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccc
Q 006832 501 HRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFK 545 (629)
Q Consensus 501 ~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQ 545 (629)
..||.+|...++..+.+. ....+||+.||.++..|..|..
T Consensus 3 ~~Lt~~eR~~I~~l~~~G-----~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQG-----MSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp ---------HHHHHHCS--------HHHHHHHTT--HHHHHHHHH
T ss_pred cchhhhHHHHHHHHHHcC-----CCHHHHHHHHCcCcHHHHHHHh
Confidence 468999999999887633 4556799999999999988754
No 96
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=44.49 E-value=14 Score=39.70 Aligned_cols=39 Identities=33% Similarity=0.375 Sum_probs=34.6
Q ss_pred hCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhh
Q 006832 517 ENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR 555 (629)
Q Consensus 517 ~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~ 555 (629)
.++||+...+.-|+...+|+..||.+||-|.|++..+..
T Consensus 118 ~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~ 156 (342)
T KOG0773|consen 118 LNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKEL 156 (342)
T ss_pred hccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhcc
Confidence 468999999999999999999999999999999655543
No 97
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=44.16 E-value=13 Score=40.20 Aligned_cols=58 Identities=22% Similarity=0.567 Sum_probs=40.0
Q ss_pred cccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchhhHHHHhhhccCCccc
Q 006832 236 HEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECKMEIIESMNAHIGTSF 307 (629)
Q Consensus 236 ~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k~~~l~~~n~~~gtsf 307 (629)
...-||..|...-... +.||-|+ |.+||.=.... .+-.|+.|..+...++++ ..++-|
T Consensus 88 p~VHfCd~Cd~PI~IY-GRmIPCk-------HvFCl~CAr~~----~dK~Cp~C~d~VqrIeq~--~~g~iF 145 (389)
T KOG2932|consen 88 PRVHFCDRCDFPIAIY-GRMIPCK-------HVFCLECARSD----SDKICPLCDDRVQRIEQI--MMGGIF 145 (389)
T ss_pred cceEeecccCCcceee-ecccccc-------hhhhhhhhhcC----ccccCcCcccHHHHHHHh--cccceE
Confidence 3357899998764332 6788887 88888754333 356899999998877766 344444
No 98
>PRK10072 putative transcriptional regulator; Provisional
Probab=44.04 E-value=23 Score=31.97 Aligned_cols=41 Identities=15% Similarity=0.193 Sum_probs=32.1
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhcc
Q 006832 502 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 549 (629)
Q Consensus 502 rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~ 549 (629)
+.+...+..|...... +..+||+.||++...|..|.+.+|.
T Consensus 32 ~~~~~eik~LR~~~gl-------TQ~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 32 TTSFTEFEQLRKGTGL-------KIDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred cCChHHHHHHHHHcCC-------CHHHHHHHhCCCHHHHHHHHcCCCC
Confidence 3466667777654433 3789999999999999999999886
No 99
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=42.76 E-value=4 Score=45.10 Aligned_cols=56 Identities=23% Similarity=0.430 Sum_probs=36.8
Q ss_pred ccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCce--ecccCchhhHHHHhhh
Q 006832 239 IICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGW--FCKFCECKMEIIESMN 300 (629)
Q Consensus 239 ~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W--~C~~C~~k~~~l~~~n 300 (629)
..|.+|-.+ ...+.++---. +|...||..||.--....| | -||.|.-+..+...+|
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 AECHICIDG-RPNDHELGPIG-TCGHIFHTTCLTQWFEGDP----SNRGCPICQIKLQERHVAN 62 (465)
T ss_pred ceeeEeccC-Ccccccccccc-chhhHHHHHHHHHHHccCC----ccCCCCceeecccceeeec
Confidence 469999554 22334444444 7999999999985444444 5 6999986655554443
No 100
>PHA02955 hypothetical protein; Provisional
Probab=42.53 E-value=27 Score=35.97 Aligned_cols=46 Identities=9% Similarity=0.068 Sum_probs=40.0
Q ss_pred CCHHHHHHHHHHHHhC-CCCCHHHHHHHHHHhCCCcchhhhccchhc
Q 006832 503 MPPNAVEKLRQVFAEN-ELPSRIVKENLSKELSLEPEKVNKWFKNAR 548 (629)
Q Consensus 503 ft~~Q~~~Le~~F~~~-~yPs~~~re~LA~~lgLt~~QVkiWFQNrR 548 (629)
=...|+..|-+.|.+. .-.+..+|.++|.+||+....|..||++.=
T Consensus 58 na~~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t~~ 104 (213)
T PHA02955 58 DEEKNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKTDL 104 (213)
T ss_pred CHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccchh
Confidence 3567888888899888 778899999999999999988999999853
No 101
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=41.15 E-value=6.2 Score=42.22 Aligned_cols=45 Identities=29% Similarity=0.709 Sum_probs=33.1
Q ss_pred cccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchhh
Q 006832 238 HIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECKM 293 (629)
Q Consensus 238 ~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k~ 293 (629)
-..|.+|...- -|-|.-.|...|-..|..--|...| |||.|....
T Consensus 25 ~lrC~IC~~~i------~ip~~TtCgHtFCslCIR~hL~~qp-----~CP~Cr~~~ 69 (391)
T COG5432 25 MLRCRICDCRI------SIPCETTCGHTFCSLCIRRHLGTQP-----FCPVCREDP 69 (391)
T ss_pred HHHhhhhhhee------ecceecccccchhHHHHHHHhcCCC-----CCccccccH
Confidence 46799998753 2334436888888889887777766 899998765
No 102
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=39.32 E-value=7 Score=49.05 Aligned_cols=58 Identities=14% Similarity=0.004 Sum_probs=50.2
Q ss_pred CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHh
Q 006832 497 RRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKA 554 (629)
Q Consensus 497 kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~ 554 (629)
+-.+++++..|+..|..+|....||.-...+.||+-|++-.+.+..||+|++.++.++
T Consensus 445 ~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~ 502 (1406)
T KOG1146|consen 445 LLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQN 502 (1406)
T ss_pred hhhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccc
Confidence 3357788999999999999999999999999999999999999888888866644433
No 103
>KOG1189 consensus Global transcriptional regulator, cell division control protein [Amino acid transport and metabolism]
Probab=39.04 E-value=32 Score=41.36 Aligned_cols=42 Identities=40% Similarity=0.613 Sum_probs=24.5
Q ss_pred ccchhhhhhccccccC-----CCCccccCCcc---CCCCCCCC--CCCCCcc
Q 006832 309 VNSNWQDIFKEEAAFP-----DGCSALLNQEE---EWPSDDSE--DDDYNPE 350 (629)
Q Consensus 309 lp~~~~d~F~eva~~~-----dG~~~~~~~e~---~wpsddse--D~dydP~ 350 (629)
+.-.|..+.+-+...| +|+..+++.+. +-.+++|+ |+-|.|.
T Consensus 844 ~sLNW~~ImKTI~dDP~~Ffe~GgW~fL~~~~sdsee~~~ese~e~~~y~ps 895 (960)
T KOG1189|consen 844 QSLNWTKIMKTITDDPIAFFEDGGWSFLNVESSDSEEGGDESEEEDSAYEPS 895 (960)
T ss_pred ccccHHHHhhhhccCHHHHHhcCCeeeecCCCCcccccccccccccccCCcc
Confidence 3446777776655554 77777776555 22233443 6667776
No 104
>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=38.73 E-value=27 Score=31.07 Aligned_cols=46 Identities=22% Similarity=0.281 Sum_probs=34.9
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHH
Q 006832 502 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLAL 552 (629)
Q Consensus 502 rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~ 552 (629)
.+++.+.+.|...|-. .+ .-.+||+.+|+++..|..|.+.-+.+.+
T Consensus 110 ~L~~~~~~ii~~~~~~-g~----s~~eIA~~l~~s~~~v~~~~~~~~~kl~ 155 (158)
T TIGR02937 110 KLPEREREVLVLRYLE-GL----SYKEIAEILGISVGTVKRRLKRARKKLR 155 (158)
T ss_pred hCCHHHHHHHhhHHhc-CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4678888887766542 23 4558999999999999999988777443
No 105
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=38.72 E-value=13 Score=28.51 Aligned_cols=21 Identities=5% Similarity=0.234 Sum_probs=19.7
Q ss_pred HHHHHhCCCcchhhhccchhc
Q 006832 528 NLSKELSLEPEKVNKWFKNAR 548 (629)
Q Consensus 528 ~LA~~lgLt~~QVkiWFQNrR 548 (629)
+||+.+|++...|..|+.|.+
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 699999999999999999985
No 106
>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=37.11 E-value=18 Score=27.92 Aligned_cols=24 Identities=13% Similarity=0.321 Sum_probs=20.9
Q ss_pred HHHHHHHhCCCcchhhhccchhcc
Q 006832 526 KENLSKELSLEPEKVNKWFKNARY 549 (629)
Q Consensus 526 re~LA~~lgLt~~QVkiWFQNrR~ 549 (629)
..+||+.+|+++..|..|+.+.|.
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 488999999999999999999774
No 107
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=36.50 E-value=46 Score=30.65 Aligned_cols=43 Identities=12% Similarity=0.124 Sum_probs=28.8
Q ss_pred CCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchh
Q 006832 501 HRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNA 547 (629)
Q Consensus 501 ~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNr 547 (629)
.+||.+.....-.....+.+ .-.+||+++|+++.+|..|.+--
T Consensus 11 r~ys~EfK~~aV~~~~~~g~----sv~evA~e~gIs~~tl~~W~r~y 53 (121)
T PRK09413 11 RRRTTQEKIAIVQQSFEPGM----TVSLVARQHGVAASQLFLWRKQY 53 (121)
T ss_pred CCCCHHHHHHHHHHHHcCCC----CHHHHHHHHCcCHHHHHHHHHHH
Confidence 45677775543333333433 34578999999999999995543
No 108
>PRK04217 hypothetical protein; Provisional
Probab=36.31 E-value=44 Score=31.00 Aligned_cols=49 Identities=22% Similarity=0.131 Sum_probs=38.3
Q ss_pred CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHH
Q 006832 500 FHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK 553 (629)
Q Consensus 500 r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K 553 (629)
-..++.+|.++|...|.+.- .-.+||+.||++...|...+...|.+.+.
T Consensus 40 ~~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~RArkkLre 88 (110)
T PRK04217 40 PIFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTSARKKVAQ 88 (110)
T ss_pred cccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 34679999888877765433 66789999999999999999888874433
No 109
>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=35.87 E-value=13 Score=32.11 Aligned_cols=37 Identities=14% Similarity=0.131 Sum_probs=27.4
Q ss_pred HHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhc
Q 006832 512 RQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNAR 548 (629)
Q Consensus 512 e~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR 548 (629)
+..|....|-..-...+||+.||+++..|+.|+.+.-
T Consensus 21 r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~~~ 57 (73)
T TIGR03879 21 EAAAALAREEAGKTASEIAEELGRTEQTVRNHLKGET 57 (73)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcCc
Confidence 3344444444555678999999999999999987633
No 110
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=35.80 E-value=34 Score=31.63 Aligned_cols=46 Identities=9% Similarity=-0.033 Sum_probs=35.2
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHH
Q 006832 502 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLAL 552 (629)
Q Consensus 502 rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~ 552 (629)
.+++.+.+.+...|-+. -.-.+||+.||+++..|+.|....|.+.+
T Consensus 106 ~L~~~~r~ii~l~~~~~-----~s~~EIA~~l~is~~tV~~~~~ra~~~Lr 151 (154)
T PRK06759 106 VLDEKEKYIIFERFFVG-----KTMGEIALETEMTYYQVRWIYRQALEKMR 151 (154)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence 57888888877665432 33678999999999999999887777443
No 111
>PF13518 HTH_28: Helix-turn-helix domain
Probab=35.10 E-value=19 Score=27.34 Aligned_cols=25 Identities=20% Similarity=0.492 Sum_probs=21.3
Q ss_pred HHHHHHHHhCCCcchhhhccchhcc
Q 006832 525 VKENLSKELSLEPEKVNKWFKNARY 549 (629)
Q Consensus 525 ~re~LA~~lgLt~~QVkiWFQNrR~ 549 (629)
...++|+++||+..+|..|.+.-+.
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHHh
Confidence 4566999999999999999887655
No 112
>KOG1844 consensus PHD Zn-finger proteins [General function prediction only]
Probab=34.75 E-value=22 Score=40.18 Aligned_cols=48 Identities=21% Similarity=0.535 Sum_probs=37.2
Q ss_pred ccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchhhH
Q 006832 243 KCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECKME 294 (629)
Q Consensus 243 vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k~~ 294 (629)
.|+..+. .++.++.|+ .|.+|-|.+|+...-...| ....|..|..+..
T Consensus 90 ~c~~~~~-~~g~~i~c~-~c~~Wqh~~C~g~~~~~~p--~~y~c~~c~~~~~ 137 (508)
T KOG1844|consen 90 DCGLEDD-MEGLMIQCD-WCGRWQHKICCGSFKSTKP--DKYVCEICTPRNK 137 (508)
T ss_pred ccccccC-CCceeeCCc-ccCcccCceeeeecCCCCc--hhceeeeeccccc
Confidence 3655432 268999999 5999999999998877665 5788999987643
No 113
>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=34.07 E-value=35 Score=26.53 Aligned_cols=35 Identities=23% Similarity=0.351 Sum_probs=25.2
Q ss_pred cccccccccCcCCCCCCceEeCCcCCcccccccCCC
Q 006832 238 HIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDP 273 (629)
Q Consensus 238 ~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~P 273 (629)
-.+|.+|+..-......-+.|. .|...+|..|+.-
T Consensus 11 ~~~C~~C~~~i~g~~~~g~~C~-~C~~~~H~~C~~~ 45 (53)
T PF00130_consen 11 PTYCDVCGKFIWGLGKQGYRCS-WCGLVCHKKCLSK 45 (53)
T ss_dssp TEB-TTSSSBECSSSSCEEEET-TTT-EEETTGGCT
T ss_pred CCCCcccCcccCCCCCCeEEEC-CCCChHhhhhhhh
Confidence 3579999886422346789999 6999999999873
No 114
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=33.66 E-value=16 Score=42.76 Aligned_cols=47 Identities=30% Similarity=0.684 Sum_probs=30.6
Q ss_pred ccccccccCcCCC---CCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchhhH
Q 006832 239 IICAKCKLREAFP---DNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECKME 294 (629)
Q Consensus 239 ~~C~vC~~~g~~~---~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k~~ 294 (629)
.+|..|...+..- .....-|+ .|..+||..|+.-- .-.||.|...+.
T Consensus 512 fiCe~Cq~~~iiyPF~~~~~~rC~-~C~avfH~~C~~r~--------s~~CPrC~R~q~ 561 (580)
T KOG1829|consen 512 FICELCQHNDIIYPFETRNTRRCS-TCLAVFHKKCLRRK--------SPCCPRCERRQK 561 (580)
T ss_pred eeeeeccCCCcccccccccceeHH-HHHHHHHHHHHhcc--------CCCCCchHHHHH
Confidence 4577785443211 23456788 69999999998732 223999986554
No 115
>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=33.31 E-value=24 Score=26.97 Aligned_cols=25 Identities=4% Similarity=-0.039 Sum_probs=22.0
Q ss_pred HHHHHHHHhCCCcchhhhccchhcc
Q 006832 525 VKENLSKELSLEPEKVNKWFKNARY 549 (629)
Q Consensus 525 ~re~LA~~lgLt~~QVkiWFQNrR~ 549 (629)
...+||..+|++...|..|+..++.
T Consensus 17 tq~~lA~~~gvs~~~vs~~e~g~~~ 41 (58)
T TIGR03070 17 TQADLADLAGVGLRFIRDVENGKPT 41 (58)
T ss_pred CHHHHHHHhCCCHHHHHHHHCCCCC
Confidence 3688999999999999999988764
No 116
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=32.81 E-value=16 Score=37.86 Aligned_cols=87 Identities=21% Similarity=0.314 Sum_probs=48.5
Q ss_pred ccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCC---CCCceecccCchhhHHHHhhhccCCccccccchhhh
Q 006832 239 IICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTES---RDQGWFCKFCECKMEIIESMNAHIGTSFSVNSNWQD 315 (629)
Q Consensus 239 ~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p---~dg~W~C~~C~~k~~~l~~~n~~~gtsf~lp~~~~d 315 (629)
-.|..|+..= ..++.+-=. |...||+.|++-.-...| .-....||.|.... +..+|..- .|..-.++
T Consensus 51 pNC~LC~t~L--a~gdt~RLv--CyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~ei--FPp~Nlvs----Pva~aLre 120 (299)
T KOG3970|consen 51 PNCRLCNTPL--ASGDTTRLV--CYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEI--FPPINLVS----PVAEALRE 120 (299)
T ss_pred CCCceeCCcc--ccCcceeeh--hhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCcc--CCCccccc----hhHHHHHH
Confidence 4588887653 234444333 888999999975433333 11578999997643 22222111 23344566
Q ss_pred hhccccccCCCCccccCCcc
Q 006832 316 IFKEEAAFPDGCSALLNQEE 335 (629)
Q Consensus 316 ~F~eva~~~dG~~~~~~~e~ 335 (629)
.+..+..+..|=+-.+-+|.
T Consensus 121 ~L~qvNWaRagLGLpll~E~ 140 (299)
T KOG3970|consen 121 QLKQVNWARAGLGLPLLPEL 140 (299)
T ss_pred HHHhhhHHhhccCCccchhh
Confidence 66666666666444333333
No 117
>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=31.47 E-value=41 Score=27.16 Aligned_cols=36 Identities=14% Similarity=0.240 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccc
Q 006832 506 NAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFK 545 (629)
Q Consensus 506 ~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQ 545 (629)
-|++.|+-.|. +++.+.. +||..||++++.|+.-..
T Consensus 6 rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~~~i~ 41 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITLK---ELAKKLNISERTIKNDIN 41 (59)
T ss_dssp HHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHHHHHH
Confidence 46778888888 7777665 899999999999876443
No 118
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=31.28 E-value=40 Score=42.05 Aligned_cols=53 Identities=21% Similarity=0.550 Sum_probs=35.1
Q ss_pred ccccccccccC--cCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchhhH
Q 006832 237 EHIICAKCKLR--EAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECKME 294 (629)
Q Consensus 237 e~~~C~vC~~~--g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k~~ 294 (629)
+..+|.+|+.. -..+++..|-|. .|.=..--.|+. .+.. +|.=.||.|..+..
T Consensus 16 ~~qiCqICGD~vg~~~~Ge~FVAC~-eC~FPVCrpCYE--YEr~--eG~q~CPqCktrYk 70 (1079)
T PLN02638 16 GGQVCQICGDNVGKTVDGEPFVACD-VCAFPVCRPCYE--YERK--DGNQSCPQCKTKYK 70 (1079)
T ss_pred CCceeeecccccCcCCCCCEEEEec-cCCCccccchhh--hhhh--cCCccCCccCCchh
Confidence 45689999973 223456788999 686555556664 2222 47789999987644
No 119
>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=30.48 E-value=36 Score=27.80 Aligned_cols=34 Identities=26% Similarity=0.666 Sum_probs=26.1
Q ss_pred cccccccCcCCC---CCCceEeCCcCCcccccccCCCC
Q 006832 240 ICAKCKLREAFP---DNDIVLCDGTCNCAFHQKCLDPP 274 (629)
Q Consensus 240 ~C~vC~~~g~~~---~~~lLlCDG~C~rafH~~CL~PP 274 (629)
.|.+|+..-..+ .+.+|-|. .|...|-...++|.
T Consensus 4 ~CP~CG~~iev~~~~~GeiV~Cp-~CGaeleVv~~~p~ 40 (54)
T TIGR01206 4 ECPDCGAEIELENPELGELVICD-ECGAELEVVSLDPL 40 (54)
T ss_pred CCCCCCCEEecCCCccCCEEeCC-CCCCEEEEEeCCCC
Confidence 588898643221 27899999 69999999999985
No 120
>KOG4215 consensus Hepatocyte nuclear factor 4 and similar steroid hormone receptors [Transcription]
Probab=30.42 E-value=23 Score=39.22 Aligned_cols=29 Identities=28% Similarity=0.557 Sum_probs=21.6
Q ss_pred ccccccccccCcCCCCCCceEeCCcCCccc
Q 006832 237 EHIICAKCKLREAFPDNDIVLCDGTCNCAF 266 (629)
Q Consensus 237 e~~~C~vC~~~g~~~~~~lLlCDG~C~raf 266 (629)
...+|.+|+.......--.+-||| |...|
T Consensus 18 ~~~~CaICGDkaTGKHYGA~SCdG-CKGFF 46 (432)
T KOG4215|consen 18 VAEFCAICGDKATGKHYGAISCDG-CKGFF 46 (432)
T ss_pred ccchhheeCCcccccccceeecCc-chHHH
Confidence 457999999865444456889997 98766
No 121
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=30.42 E-value=53 Score=32.05 Aligned_cols=47 Identities=6% Similarity=0.128 Sum_probs=35.7
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHH
Q 006832 502 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK 553 (629)
Q Consensus 502 rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K 553 (629)
.+++.+...|.-.|-++ -.-.+||+.||++...|+++....|.+.++
T Consensus 142 ~L~~~~r~vl~l~~~~~-----~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~ 188 (194)
T PRK09646 142 ALTDTQRESVTLAYYGG-----LTYREVAERLAVPLGTVKTRMRDGLIRLRD 188 (194)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHhCCChHhHHHHHHHHHHHHHH
Confidence 47888888887655333 344789999999999999999887774443
No 122
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=30.36 E-value=17 Score=38.68 Aligned_cols=61 Identities=20% Similarity=0.453 Sum_probs=36.4
Q ss_pred ccccccccccccCcCCCC--CCce---EeCCcCCcccccccCCCCCCCCCCCCceecccCchhhHHHHhh
Q 006832 235 HHEHIICAKCKLREAFPD--NDIV---LCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECKMEIIESM 299 (629)
Q Consensus 235 ~~e~~~C~vC~~~g~~~~--~~lL---lCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k~~~l~~~ 299 (629)
..++.+|+||+..-.... +.+| .== .|+..||-.|...=..- .-.=+||.|..+.++..+.
T Consensus 221 hl~d~vCaVCg~~~~~s~~eegvienty~L-sCnHvFHEfCIrGWciv---GKkqtCPYCKekVdl~rmf 286 (328)
T KOG1734|consen 221 HLSDSVCAVCGQQIDVSVDEEGVIENTYKL-SCNHVFHEFCIRGWCIV---GKKQTCPYCKEKVDLKRMF 286 (328)
T ss_pred CCCcchhHhhcchheeecchhhhhhhheee-ecccchHHHhhhhheee---cCCCCCchHHHHhhHhhhc
Confidence 356789999997532110 0010 111 49999999997642111 1244899999988754443
No 123
>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=30.14 E-value=16 Score=30.94 Aligned_cols=46 Identities=26% Similarity=0.538 Sum_probs=26.3
Q ss_pred ccccccccCcCCC--------CCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCc
Q 006832 239 IICAKCKLREAFP--------DNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCE 290 (629)
Q Consensus 239 ~~C~vC~~~g~~~--------~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~ 290 (629)
+.|.+|...-... +.-.|.-. .|...||..|+..=|.. ...||.|+
T Consensus 20 d~C~IC~~~l~~~~~~~~~~~~~~~i~~~-~C~H~FH~~Ci~~Wl~~-----~~~CP~CR 73 (73)
T PF12678_consen 20 DNCAICREPLEDPCPECQAPQDECPIVWG-PCGHIFHFHCISQWLKQ-----NNTCPLCR 73 (73)
T ss_dssp SBETTTTSBTTSTTCCHHHCTTTS-EEEE-TTSEEEEHHHHHHHHTT-----SSB-TTSS
T ss_pred CcccccChhhhChhhhhcCCccccceEec-ccCCCEEHHHHHHHHhc-----CCcCCCCC
Confidence 4488887653111 12233333 69999999999643332 23788884
No 124
>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=29.87 E-value=26 Score=26.27 Aligned_cols=22 Identities=14% Similarity=0.200 Sum_probs=18.3
Q ss_pred HHHHHHHhCCCcchhhhccchh
Q 006832 526 KENLSKELSLEPEKVNKWFKNA 547 (629)
Q Consensus 526 re~LA~~lgLt~~QVkiWFQNr 547 (629)
..++|+.||+++..|..|.++-
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g 24 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIG 24 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 3578999999999999996543
No 125
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=29.63 E-value=44 Score=31.90 Aligned_cols=46 Identities=9% Similarity=0.299 Sum_probs=34.4
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHH
Q 006832 502 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLAL 552 (629)
Q Consensus 502 rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~ 552 (629)
.+++.+.+.|...|-+. ..-.+||+.||+++..|++++...|.+.+
T Consensus 129 ~L~~~~r~i~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr 174 (179)
T PRK12514 129 ELEKDRAAAVRRAYLEG-----LSYKELAERHDVPLNTMRTWLRRSLLKLR 174 (179)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCChHHHHHHHHHHHHHHH
Confidence 46777777777665322 23578999999999999999988887443
No 126
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=29.49 E-value=48 Score=31.09 Aligned_cols=47 Identities=13% Similarity=0.058 Sum_probs=35.3
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHH
Q 006832 502 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK 553 (629)
Q Consensus 502 rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K 553 (629)
.+++.+.+.|...|-. .-.-.+||+.||+++..|..|....|.+.++
T Consensus 128 ~L~~~~r~vl~l~~~~-----~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 174 (182)
T PRK09652 128 SLPEELRTAITLREIE-----GLSYEEIAEIMGCPIGTVRSRIFRAREALRA 174 (182)
T ss_pred hCCHHHHHHHHHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4788888888776532 2234589999999999999999877765444
No 127
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=29.38 E-value=26 Score=26.69 Aligned_cols=26 Identities=23% Similarity=0.445 Sum_probs=18.3
Q ss_pred HHHHHHHHHHhCCCcchhhhccchhc
Q 006832 523 RIVKENLSKELSLEPEKVNKWFKNAR 548 (629)
Q Consensus 523 ~~~re~LA~~lgLt~~QVkiWFQNrR 548 (629)
.....++|+.||++...|..|.+.-+
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 45678899999999999999987644
No 128
>PHA02929 N1R/p28-like protein; Provisional
Probab=29.22 E-value=20 Score=37.52 Aligned_cols=48 Identities=23% Similarity=0.411 Sum_probs=30.8
Q ss_pred cccccccccCcCCCCC---C-ceEeCCcCCcccccccCCCCCCCCCCCCceecccCchh
Q 006832 238 HIICAKCKLREAFPDN---D-IVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECK 292 (629)
Q Consensus 238 ~~~C~vC~~~g~~~~~---~-lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k 292 (629)
+..|++|...-..++. . .++. .|...||..|+.+-+...+ .||.|+..
T Consensus 174 ~~eC~ICle~~~~~~~~~~~~~vl~--~C~H~FC~~CI~~Wl~~~~-----tCPlCR~~ 225 (238)
T PHA02929 174 DKECAICMEKVYDKEIKNMYFGILS--NCNHVFCIECIDIWKKEKN-----TCPVCRTP 225 (238)
T ss_pred CCCCccCCcccccCccccccceecC--CCCCcccHHHHHHHHhcCC-----CCCCCCCE
Confidence 4679999875321110 0 2333 3999999999987544332 69999865
No 129
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=29.00 E-value=51 Score=40.13 Aligned_cols=41 Identities=29% Similarity=0.575 Sum_probs=30.7
Q ss_pred ccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchh
Q 006832 239 IICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECK 292 (629)
Q Consensus 239 ~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k 292 (629)
..|..|...= +=.+|.= .|..+||+.|+. ++.--||.|...
T Consensus 841 skCs~C~~~L---dlP~VhF--~CgHsyHqhC~e--------~~~~~CP~C~~e 881 (933)
T KOG2114|consen 841 SKCSACEGTL---DLPFVHF--LCGHSYHQHCLE--------DKEDKCPKCLPE 881 (933)
T ss_pred eeecccCCcc---ccceeee--ecccHHHHHhhc--------cCcccCCccchh
Confidence 5799998753 2345544 499999999999 355679999873
No 130
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=28.71 E-value=45 Score=39.67 Aligned_cols=50 Identities=18% Similarity=0.574 Sum_probs=29.5
Q ss_pred ccccccccCcCCCCCCceEeCCcCCcccc-cccCCCCCCCCCCCCceecccCchhhH
Q 006832 239 IICAKCKLREAFPDNDIVLCDGTCNCAFH-QKCLDPPLDTESRDQGWFCKFCECKME 294 (629)
Q Consensus 239 ~~C~vC~~~g~~~~~~lLlCDG~C~rafH-~~CL~PPL~~~p~dg~W~C~~C~~k~~ 294 (629)
.+|..|+... +....+|. .|..... ..|....-.. | .+.=||+.|-.+..
T Consensus 2 ~~Cp~Cg~~n---~~~akFC~-~CG~~l~~~~Cp~CG~~~-~-~~~~fC~~CG~~~~ 52 (645)
T PRK14559 2 LICPQCQFEN---PNNNRFCQ-KCGTSLTHKPCPQCGTEV-P-VDEAHCPNCGAETG 52 (645)
T ss_pred CcCCCCCCcC---CCCCcccc-ccCCCCCCCcCCCCCCCC-C-cccccccccCCccc
Confidence 3577776653 34566777 5765533 4565443332 2 35669999977653
No 131
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=28.61 E-value=47 Score=31.08 Aligned_cols=48 Identities=17% Similarity=0.241 Sum_probs=35.5
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHh
Q 006832 502 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKA 554 (629)
Q Consensus 502 rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~ 554 (629)
.+++.+.+.|...|-. .-.-.+||+.||+++..|..|..-.|.+.++.
T Consensus 125 ~L~~~~r~i~~l~~~~-----~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~ 172 (179)
T PRK11924 125 ALPVKQREVFLLRYVE-----GLSYREIAEILGVPVGTVKSRLRRARQLLREC 172 (179)
T ss_pred hCCHHHHHHhhHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3677777777665533 23347899999999999999998888855443
No 132
>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type [].
Probab=28.60 E-value=26 Score=32.12 Aligned_cols=50 Identities=22% Similarity=0.627 Sum_probs=31.2
Q ss_pred cccccccccCcCCCCCCceEe------CCcC---CcccccccCCCCCCCCC----CCCceecccCch
Q 006832 238 HIICAKCKLREAFPDNDIVLC------DGTC---NCAFHQKCLDPPLDTES----RDQGWFCKFCEC 291 (629)
Q Consensus 238 ~~~C~vC~~~g~~~~~~lLlC------DG~C---~rafH~~CL~PPL~~~p----~dg~W~C~~C~~ 291 (629)
...|..|..... +..+.| . .| ...|=..||.-.....+ .+..|.||.|..
T Consensus 7 g~~CHqCrqKt~---~~~~~C~~~~~~~-~C~~~~~~fC~~CL~~ryge~~~ev~~~~~W~CP~Crg 69 (105)
T PF10497_consen 7 GKTCHQCRQKTL---DFKTICTGHWKNS-SCRGCRGKFCGGCLRNRYGENVEEVLEDPNWKCPKCRG 69 (105)
T ss_pred CCCchhhcCCCC---CCceEcCCCCCCC-CCccCcceehHhHHHHHHhhhHHHHhcCCceECCCCCC
Confidence 456888877542 344556 4 35 66676677654443322 357899999975
No 133
>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=28.25 E-value=29 Score=31.77 Aligned_cols=42 Identities=21% Similarity=0.558 Sum_probs=31.7
Q ss_pred CCCCcccccccccccccCcCCCCCCceEeCCcCCcccccccCC
Q 006832 230 TDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLD 272 (629)
Q Consensus 230 ~dg~~~~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~ 272 (629)
++|..-..-+.|.+|+..+....++.|.|- .|+.-|++.=++
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 456556667889999887766668888899 799999864333
No 134
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=28.07 E-value=56 Score=34.99 Aligned_cols=55 Identities=16% Similarity=0.323 Sum_probs=30.4
Q ss_pred CCCcccccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchhh
Q 006832 231 DGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECKM 293 (629)
Q Consensus 231 dg~~~~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k~ 293 (629)
..........|.+|+..-. -+-.+.+ |...|-.+|+.-.... +-...||.|-...
T Consensus 232 sss~~t~~~~C~~Cg~~Pt-iP~~~~~----C~HiyCY~Ci~ts~~~---~asf~Cp~Cg~~~ 286 (298)
T KOG2879|consen 232 SSSTGTSDTECPVCGEPPT-IPHVIGK----CGHIYCYYCIATSRLW---DASFTCPLCGENV 286 (298)
T ss_pred ccccccCCceeeccCCCCC-CCeeecc----ccceeehhhhhhhhcc---hhhcccCccCCCC
Confidence 3344556788999998643 2233333 3334444454433222 3457899997654
No 135
>PRK00118 putative DNA-binding protein; Validated
Probab=27.76 E-value=56 Score=30.00 Aligned_cols=45 Identities=9% Similarity=0.144 Sum_probs=34.1
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHH
Q 006832 503 MPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLAL 552 (629)
Q Consensus 503 ft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~ 552 (629)
+++.|.+.+..+|.+ ...-.+||+.+|+++..|..|....|.+.+
T Consensus 18 L~ekqRevl~L~y~e-----g~S~~EIAe~lGIS~~TV~r~L~RArkkLr 62 (104)
T PRK00118 18 LTEKQRNYMELYYLD-----DYSLGEIAEEFNVSRQAVYDNIKRTEKLLE 62 (104)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 577787777666554 233466999999999999999988777433
No 136
>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=27.63 E-value=31 Score=28.26 Aligned_cols=22 Identities=18% Similarity=0.404 Sum_probs=18.7
Q ss_pred HHHHHHHHhCCCcchhhhccch
Q 006832 525 VKENLSKELSLEPEKVNKWFKN 546 (629)
Q Consensus 525 ~re~LA~~lgLt~~QVkiWFQN 546 (629)
.-.+||+.||++...|..|-+-
T Consensus 15 ~~~eIA~~Lg~~~~TV~~W~~r 36 (58)
T PF06056_consen 15 SIKEIAEELGVPRSTVYSWKDR 36 (58)
T ss_pred CHHHHHHHHCCChHHHHHHHHh
Confidence 3568999999999999999653
No 137
>PHA01976 helix-turn-helix protein
Probab=27.50 E-value=30 Score=27.90 Aligned_cols=25 Identities=12% Similarity=0.198 Sum_probs=21.7
Q ss_pred HHHHHHHHhCCCcchhhhccchhcc
Q 006832 525 VKENLSKELSLEPEKVNKWFKNARY 549 (629)
Q Consensus 525 ~re~LA~~lgLt~~QVkiWFQNrR~ 549 (629)
...+||+.+|++...|..|...++.
T Consensus 17 t~~~lA~~~gvs~~~v~~~e~g~~~ 41 (67)
T PHA01976 17 SAPELSRRAGVRHSLIYDFEADKRL 41 (67)
T ss_pred CHHHHHHHhCCCHHHHHHHHcCCCC
Confidence 3578999999999999999987764
No 138
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=27.37 E-value=50 Score=39.65 Aligned_cols=56 Identities=14% Similarity=0.192 Sum_probs=43.5
Q ss_pred cccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhcc
Q 006832 494 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 549 (629)
Q Consensus 494 ~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~ 549 (629)
...-+-+.-...++-+.|-.++.-+.-|+..+-.-++..|.+.+..|.+||++|+.
T Consensus 624 ~~p~kv~sp~k~~dq~ql~~a~elq~s~~n~~~pl~~t~~~n~~pv~ev~dhsrss 679 (1007)
T KOG3623|consen 624 ERPVKVRSPIKEEDQQQLKQAYELQASPSNDEFPLIATRLQNDPPVVEVWDHSRSS 679 (1007)
T ss_pred CCCccccCCCCccchhhhHhhhhcccCccCcccchhhhhccCCCcchhhcccCCCC
Confidence 33334445556677778889999888887777777777799999999999999998
No 139
>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=27.12 E-value=66 Score=24.23 Aligned_cols=39 Identities=18% Similarity=0.337 Sum_probs=28.1
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchh
Q 006832 503 MPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNA 547 (629)
Q Consensus 503 ft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNr 547 (629)
+++.|.+.+..++ +. ..-.++|+.+|++...|..|...-
T Consensus 1 l~~~e~~i~~~~~--~~----~s~~eia~~l~~s~~tv~~~~~~~ 39 (57)
T cd06170 1 LTPREREVLRLLA--EG----KTNKEIADILGISEKTVKTHLRNI 39 (57)
T ss_pred CCHHHHHHHHHHH--cC----CCHHHHHHHHCCCHHHHHHHHHHH
Confidence 3566677665543 22 256889999999999999988643
No 140
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=26.91 E-value=49 Score=25.42 Aligned_cols=10 Identities=30% Similarity=1.169 Sum_probs=7.0
Q ss_pred CCceecccCc
Q 006832 281 DQGWFCKFCE 290 (629)
Q Consensus 281 dg~W~C~~C~ 290 (629)
.+.|+|..|.
T Consensus 24 ~G~~~C~~C~ 33 (40)
T PF08273_consen 24 RGTWICRQCG 33 (40)
T ss_dssp -S-EEETTTT
T ss_pred CCCEECCCCC
Confidence 4899999993
No 141
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=26.81 E-value=62 Score=31.03 Aligned_cols=48 Identities=13% Similarity=0.160 Sum_probs=36.4
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHh
Q 006832 502 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKA 554 (629)
Q Consensus 502 rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~ 554 (629)
.+++.+.+.|...|-+ .-.-.+||+.||++...|..++...|.+.++.
T Consensus 131 ~L~~~~r~v~~l~~~~-----g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~ 178 (184)
T PRK12512 131 TLPPRQRDVVQSISVE-----GASIKETAAKLSMSEGAVRVALHRGLAALAAK 178 (184)
T ss_pred hCCHHHHHHHHHHHHc-----CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 4677788877776433 23347899999999999999999988855443
No 142
>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=26.49 E-value=68 Score=24.49 Aligned_cols=39 Identities=13% Similarity=0.507 Sum_probs=28.8
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccc
Q 006832 502 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFK 545 (629)
Q Consensus 502 rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQ 545 (629)
.++++|++.+.+.+... + ...+||+.+|++...|..++.
T Consensus 5 ~~~~~~~~~i~~l~~~G-~----si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 5 KLSKEQIEEIKELYAEG-M----SIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp SSSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHHHHHHC
T ss_pred CCCHHHHHHHHHHHHCC-C----CHHHHHHHHCcCHHHHHHHHh
Confidence 36887788777777765 3 477899999999999987663
No 143
>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=26.43 E-value=30 Score=26.83 Aligned_cols=42 Identities=14% Similarity=0.263 Sum_probs=28.4
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhcc
Q 006832 503 MPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 549 (629)
Q Consensus 503 ft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~ 549 (629)
+++.+...+.-.|- ..-.-.++|+.+|+++..|+.|.+..|.
T Consensus 11 L~~~~r~i~~l~~~-----~g~s~~eIa~~l~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 11 LPERQREIFLLRYF-----QGMSYAEIAEILGISESTVKRRLRRARK 52 (54)
T ss_dssp S-HHHHHHHHHHHT-----S---HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHH-----HCcCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence 46666666665443 3345678999999999999999987765
No 144
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=26.43 E-value=38 Score=24.40 Aligned_cols=23 Identities=17% Similarity=0.375 Sum_probs=20.4
Q ss_pred HHHHHHHhCCCcchhhhccchhc
Q 006832 526 KENLSKELSLEPEKVNKWFKNAR 548 (629)
Q Consensus 526 re~LA~~lgLt~~QVkiWFQNrR 548 (629)
...||..+|+++..|..|..+.+
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~~ 37 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGKR 37 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCCC
Confidence 45899999999999999998875
No 145
>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=25.85 E-value=13 Score=29.32 Aligned_cols=44 Identities=27% Similarity=0.652 Sum_probs=25.4
Q ss_pred cccccccCcCCCCCCceE-eCCcCC---cccccccCCCCCCCCCCCCceecccC
Q 006832 240 ICAKCKLREAFPDNDIVL-CDGTCN---CAFHQKCLDPPLDTESRDQGWFCKFC 289 (629)
Q Consensus 240 ~C~vC~~~g~~~~~~lLl-CDG~C~---rafH~~CL~PPL~~~p~dg~W~C~~C 289 (629)
+|.+|...+ .+++.++. |. |. ..+|..||..=+... +...|+.|
T Consensus 1 ~CrIC~~~~-~~~~~l~~PC~--C~G~~~~vH~~Cl~~W~~~~---~~~~C~iC 48 (49)
T smart00744 1 ICRICHDEG-DEGDPLVSPCR--CKGSLKYVHQECLERWINES---GNKTCEIC 48 (49)
T ss_pred CccCCCCCC-CCCCeeEeccc--cCCchhHHHHHHHHHHHHHc---CCCcCCCC
Confidence 477887622 22334433 32 54 579999998544432 23467776
No 146
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=25.56 E-value=68 Score=31.12 Aligned_cols=49 Identities=14% Similarity=0.154 Sum_probs=37.0
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhh
Q 006832 502 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR 555 (629)
Q Consensus 502 rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~ 555 (629)
.+++.+...|.-.|-+. -.-.+||+.||++...|++..+-.|.+.+++.
T Consensus 131 ~L~~~~r~i~~l~~~~g-----~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~~ 179 (189)
T PRK06811 131 DLEKLDREIFIRRYLLG-----EKIEEIAKKLGLTRSAIDNRLSRGRKKLQKNK 179 (189)
T ss_pred hCCHHHHHHHHHHHHcc-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHcc
Confidence 57888888887655332 33478999999999999998887777555554
No 147
>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=24.71 E-value=56 Score=25.91 Aligned_cols=43 Identities=14% Similarity=0.196 Sum_probs=33.7
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccH
Q 006832 502 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYL 550 (629)
Q Consensus 502 rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k 550 (629)
.||+.+++.|.-...-. ...++|..||+++..|..+..|-+.|
T Consensus 3 ~LT~~E~~vl~~l~~G~------~~~eIA~~l~is~~tV~~~~~~i~~K 45 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM------SNKEIAEELGISEKTVKSHRRRIMKK 45 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-------HHHHHHHHTSHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHhcC------CcchhHHhcCcchhhHHHHHHHHHHH
Confidence 57888888888766543 45789999999999999988887763
No 148
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=24.47 E-value=38 Score=40.34 Aligned_cols=57 Identities=23% Similarity=0.540 Sum_probs=37.5
Q ss_pred cccccccccCcCCCC---CCceEeCC-cCCcccccccCCCC-CCCCC----CCCceecccCchhhH
Q 006832 238 HIICAKCKLREAFPD---NDIVLCDG-TCNCAFHQKCLDPP-LDTES----RDQGWFCKFCECKME 294 (629)
Q Consensus 238 ~~~C~vC~~~g~~~~---~~lLlCDG-~C~rafH~~CL~PP-L~~~p----~dg~W~C~~C~~k~~ 294 (629)
...|.+|...|.... +..+.|.- .|.++||..|..-. |..+. .+..-||-.|...+.
T Consensus 117 nKtCYIC~E~GrpnkA~~GACMtCNKs~CkqaFHVTCAQ~~GLLCEE~gn~~dNVKYCGYCk~Hfs 182 (900)
T KOG0956|consen 117 NKTCYICNEEGRPNKAAKGACMTCNKSGCKQAFHVTCAQRAGLLCEEEGNISDNVKYCGYCKYHFS 182 (900)
T ss_pred cceeeeecccCCccccccccceecccccchhhhhhhHhhhhccceeccccccccceechhHHHHHH
Confidence 456999988765432 44566652 48999999997543 22222 345789999987653
No 149
>PF13730 HTH_36: Helix-turn-helix domain
Probab=24.30 E-value=1.3e+02 Score=23.24 Aligned_cols=42 Identities=24% Similarity=0.335 Sum_probs=29.0
Q ss_pred CCCHHHHHHHHHHHHh---C--CCCCHHHHHHHHHHhCCCcchhhhccch
Q 006832 502 RMPPNAVEKLRQVFAE---N--ELPSRIVKENLSKELSLEPEKVNKWFKN 546 (629)
Q Consensus 502 rft~~Q~~~Le~~F~~---~--~yPs~~~re~LA~~lgLt~~QVkiWFQN 546 (629)
.+++.+...+-..+.. + -|| ....||..+|++.+.|+.+.+.
T Consensus 2 ~Ls~~~~~v~~~l~~~~~~~~~~~p---S~~~la~~~g~s~~Tv~~~i~~ 48 (55)
T PF13730_consen 2 NLSPTAKLVYLYLASYANKNGGCFP---SQETLAKDLGVSRRTVQRAIKE 48 (55)
T ss_pred CCCHHHHHHHHHHHHhcCCCCCCCc---CHHHHHHHHCcCHHHHHHHHHH
Confidence 3566666655444433 2 455 4788999999999999987654
No 150
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=23.94 E-value=80 Score=30.47 Aligned_cols=48 Identities=15% Similarity=0.064 Sum_probs=36.3
Q ss_pred CCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHH
Q 006832 501 HRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK 553 (629)
Q Consensus 501 ~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K 553 (629)
..+++.|...+...|-+. ..-.+||+.||+++..|+.+....|.+.++
T Consensus 138 ~~L~~~~r~i~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 185 (189)
T PRK09648 138 DTLPEKQREILILRVVVG-----LSAEETAEAVGSTPGAVRVAQHRALARLRA 185 (189)
T ss_pred HhCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 357888888888765542 346789999999999999988777664443
No 151
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=23.89 E-value=47 Score=32.39 Aligned_cols=26 Identities=15% Similarity=0.109 Sum_probs=23.2
Q ss_pred HHHHHHHHHhCCCcchhhhccchhcc
Q 006832 524 IVKENLSKELSLEPEKVNKWFKNARY 549 (629)
Q Consensus 524 ~~re~LA~~lgLt~~QVkiWFQNrR~ 549 (629)
.++++||+.+|++...|..|..+.+.
T Consensus 83 lSqeeLA~~lgvs~s~IsriE~G~~~ 108 (154)
T TIGR00270 83 WSQEQLAKKIQEKESLIKKIENAEIE 108 (154)
T ss_pred CCHHHHHHHhCCCHHHHHHHHCCCCC
Confidence 34789999999999999999998876
No 152
>KOG1080 consensus Histone H3 (Lys4) methyltransferase complex, subunit SET1 and related methyltransferases [Chromatin structure and dynamics; Transcription]
Probab=23.79 E-value=60 Score=40.48 Aligned_cols=51 Identities=27% Similarity=0.718 Sum_probs=40.4
Q ss_pred cccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCch
Q 006832 238 HIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCEC 291 (629)
Q Consensus 238 ~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~ 291 (629)
-.-|.+|........+.++.|+ .|...-|..|+++. .... .-.|+|..|..
T Consensus 573 t~~c~~~~~~~~~~~n~~~~~~-~~~~~~~s~~~g~~-~~~~-~~~~~~~~~~~ 623 (1005)
T KOG1080|consen 573 TERCAVCRDDEDWEKNVSIICD-RCTRSVHSECYGNL-KSYD-GTSWVCDSCET 623 (1005)
T ss_pred cccccccccccccccceeeeec-cccccCCCcccccC-CCCC-CCcchhhcccc
Confidence 4569999886655678999999 69999999999853 3332 46899999986
No 153
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=23.32 E-value=1e+02 Score=30.10 Aligned_cols=36 Identities=14% Similarity=0.113 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhh
Q 006832 506 NAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVN 541 (629)
Q Consensus 506 ~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVk 541 (629)
.-+..|..+=.+..|.+.+....||+.||+++.+|.
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 456677777777789999999999999999999975
No 154
>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=23.29 E-value=35 Score=23.96 Aligned_cols=28 Identities=21% Similarity=0.628 Sum_probs=11.5
Q ss_pred cccccccCcCCCCCCceEeCCcCCccccccc
Q 006832 240 ICAKCKLREAFPDNDIVLCDGTCNCAFHQKC 270 (629)
Q Consensus 240 ~C~vC~~~g~~~~~~lLlCDG~C~rafH~~C 270 (629)
.|.+|+.... .+..-.|. .|+=..|+.|
T Consensus 2 ~C~~C~~~~~--~~~~Y~C~-~Cdf~lH~~C 29 (30)
T PF07649_consen 2 RCDACGKPID--GGWFYRCS-ECDFDLHEEC 29 (30)
T ss_dssp --TTTS------S--EEE-T-TT-----HHH
T ss_pred cCCcCCCcCC--CCceEECc-cCCCccChhc
Confidence 4888988763 23788899 6999999887
No 155
>KOG3241 consensus Uncharacterized conserved protein [Function unknown]
Probab=23.16 E-value=55 Score=33.03 Aligned_cols=16 Identities=38% Similarity=0.794 Sum_probs=11.1
Q ss_pred CCCCCCCCCccccccc
Q 006832 340 DDSEDDDYNPERRENS 355 (629)
Q Consensus 340 ddseD~dydP~~~~~~ 355 (629)
|..+||||||+..+++
T Consensus 190 de~~DDd~d~d~D~eD 205 (227)
T KOG3241|consen 190 DEAHDDDSDPDSDEED 205 (227)
T ss_pred ccccccccCCcccccc
Confidence 4555669999876664
No 156
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=22.94 E-value=65 Score=30.70 Aligned_cols=47 Identities=19% Similarity=0.229 Sum_probs=35.4
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHH
Q 006832 502 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK 553 (629)
Q Consensus 502 rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K 553 (629)
.+++.+.+.|.-.|-+ .-.-.++|+.||+++..|.++++..|.+.++
T Consensus 136 ~L~~~~r~v~~l~~~~-----g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 182 (187)
T TIGR02948 136 ALPPKYRMVIVLKYME-----DLSLKEISEILDLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred hCCHHHhHHhhhHHhc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4688888887764432 3345789999999999999999888875443
No 157
>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=22.54 E-value=39 Score=24.47 Aligned_cols=24 Identities=21% Similarity=0.754 Sum_probs=11.9
Q ss_pred cccccccCcCCCCCCceEeCCcCCc
Q 006832 240 ICAKCKLREAFPDNDIVLCDGTCNC 264 (629)
Q Consensus 240 ~C~vC~~~g~~~~~~lLlCDG~C~r 264 (629)
.|..|+......++.++.|. .|..
T Consensus 4 ~Cp~C~se~~y~D~~~~vCp-~C~~ 27 (30)
T PF08274_consen 4 KCPLCGSEYTYEDGELLVCP-ECGH 27 (30)
T ss_dssp --TTT-----EE-SSSEEET-TTTE
T ss_pred CCCCCCCcceeccCCEEeCC-cccc
Confidence 48888876666677888888 5853
No 158
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=22.44 E-value=68 Score=34.87 Aligned_cols=31 Identities=16% Similarity=0.483 Sum_probs=23.0
Q ss_pred ccccccccccCc--------CCCCCCceEeCCcCCccccc
Q 006832 237 EHIICAKCKLRE--------AFPDNDIVLCDGTCNCAFHQ 268 (629)
Q Consensus 237 e~~~C~vC~~~g--------~~~~~~lLlCDG~C~rafH~ 268 (629)
...+|.||+..- ...+...+.|. .|...||+
T Consensus 186 ~~~~CPvCGs~P~~s~v~~~~~~G~RyL~Cs-lC~teW~~ 224 (309)
T PRK03564 186 QRQFCPVCGSMPVSSVVQIGTTQGLRYLHCN-LCESEWHV 224 (309)
T ss_pred CCCCCCCCCCcchhheeeccCCCCceEEEcC-CCCCcccc
Confidence 467899999752 11345789998 79999986
No 159
>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=22.36 E-value=42 Score=27.75 Aligned_cols=24 Identities=17% Similarity=0.239 Sum_probs=21.5
Q ss_pred HHHHHHHhCCCcchhhhccchhcc
Q 006832 526 KENLSKELSLEPEKVNKWFKNARY 549 (629)
Q Consensus 526 re~LA~~lgLt~~QVkiWFQNrR~ 549 (629)
..+||+.+|++...|..|+.++|.
T Consensus 21 ~~~lA~~~gis~~tis~~~~g~~~ 44 (78)
T TIGR02607 21 IRALAKALGVSRSTLSRIVNGRRG 44 (78)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCCC
Confidence 468999999999999999988764
No 160
>KOG4218 consensus Nuclear hormone receptor betaFTZ-F1 [Transcription]
Probab=22.33 E-value=40 Score=37.09 Aligned_cols=55 Identities=16% Similarity=0.357 Sum_probs=35.0
Q ss_pred cccccccccccCcCCCCCCceEeCCcCCccc--------ccccCCCCCCCCCCCCceecccCch
Q 006832 236 HEHIICAKCKLREAFPDNDIVLCDGTCNCAF--------HQKCLDPPLDTESRDQGWFCKFCEC 291 (629)
Q Consensus 236 ~e~~~C~vC~~~g~~~~~~lLlCDG~C~raf--------H~~CL~PPL~~~p~dg~W~C~~C~~ 291 (629)
+....|.||+..-....--+|.|. .|...| |..|..-.--.+.....=-||.|+.
T Consensus 13 dl~ElCPVCGDkVSGYHYGLLTCE-SCKGFFKRTVQNnK~YtC~e~qnC~iDkTqRKRCP~CRF 75 (475)
T KOG4218|consen 13 DLGELCPVCGDKVSGYHYGLLTCE-SCKGFFKRTVQNNKQYTCSEEQNCHIDKTQRKRCPSCRF 75 (475)
T ss_pred ccccccccccCccccceeeeeehh-hhhhHHHHHhhcCcceecccccccccchHhhccCCchhH
Confidence 445789999986544445799999 498766 3456544333333224557999965
No 161
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=22.30 E-value=97 Score=28.96 Aligned_cols=47 Identities=15% Similarity=0.155 Sum_probs=36.0
Q ss_pred CCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHH
Q 006832 501 HRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK 553 (629)
Q Consensus 501 ~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K 553 (629)
..+++.+...|.-.| ..+ .-.+||+.||+++..|+.+....|.+.++
T Consensus 111 ~~L~~~~r~il~l~~--~g~----s~~eIA~~lgis~~tV~~~i~ra~~~Lr~ 157 (166)
T PRK09639 111 AKMTERDRTVLLLRF--SGY----SYKEIAEALGIKESSVGTTLARAKKKFRK 157 (166)
T ss_pred HcCCHHHHHHHHHHH--cCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 346888888888777 444 34689999999999999999877775443
No 162
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=22.19 E-value=44 Score=27.00 Aligned_cols=18 Identities=17% Similarity=0.370 Sum_probs=16.3
Q ss_pred HHHHHHhCCCcchhhhcc
Q 006832 527 ENLSKELSLEPEKVNKWF 544 (629)
Q Consensus 527 e~LA~~lgLt~~QVkiWF 544 (629)
.++|+.+|+++.+|+.|=
T Consensus 4 ~eva~~~gvs~~tlr~y~ 21 (69)
T PF13411_consen 4 KEVAKLLGVSPSTLRYYE 21 (69)
T ss_dssp HHHHHHTTTTHHHHHHHH
T ss_pred HHHHHHHCcCHHHHHHHH
Confidence 479999999999999993
No 163
>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=21.95 E-value=72 Score=29.15 Aligned_cols=46 Identities=11% Similarity=0.076 Sum_probs=33.1
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHH
Q 006832 502 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLAL 552 (629)
Q Consensus 502 rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~ 552 (629)
.+++.+.+.|.-.|- ..+ .-.+||+.||+++..|+.+...-|.+.+
T Consensus 113 ~L~~~~r~il~l~~~-~~~----~~~eIA~~lgis~~tv~~~~~ra~~~Lr 158 (161)
T TIGR02985 113 KLPEQCRKIFILSRF-EGK----SYKEIAEELGISVKTVEYHISKALKELR 158 (161)
T ss_pred HCCHHHHHHHHHHHH-cCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 457777777776553 233 3456999999999999998887776443
No 164
>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=21.93 E-value=1.3e+02 Score=29.75 Aligned_cols=47 Identities=19% Similarity=0.385 Sum_probs=39.3
Q ss_pred CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhc
Q 006832 500 FHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNAR 548 (629)
Q Consensus 500 r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR 548 (629)
.+.+|+++++++.+.=.++ |...++..||+++|+++.-|.+-..--.
T Consensus 83 ~y~Lt~e~i~Eir~LR~~D--P~~wTr~~LAkkF~~S~~fV~~v~~~~~ 129 (164)
T PF12824_consen 83 KYHLTPEDIQEIRRLRAED--PEKWTRKKLAKKFNCSPLFVSMVAPAPK 129 (164)
T ss_pred cccCCHHHHHHHHHHHHcC--chHhhHHHHHHHhCCCHHHHHHhcCCCH
Confidence 4679999999999887776 6788999999999999998887665443
No 165
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=21.75 E-value=90 Score=28.82 Aligned_cols=43 Identities=16% Similarity=0.231 Sum_probs=34.5
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccH
Q 006832 502 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYL 550 (629)
Q Consensus 502 rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k 550 (629)
.+|+.+.+.|.- +.+ .| ...++|+.|++++..|+.|.+|-|.|
T Consensus 149 ~lt~~e~~vl~l-~~~-g~----~~~~Ia~~l~~s~~tv~~~~~~~~~k 191 (211)
T PRK15369 149 LLTPRERQILKL-ITE-GY----TNRDIAEQLSISIKTVETHRLNMMRK 191 (211)
T ss_pred CCCHHHHHHHHH-HHC-CC----CHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 479999888886 443 33 36799999999999999999987774
No 166
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=21.68 E-value=41 Score=35.59 Aligned_cols=30 Identities=13% Similarity=0.338 Sum_probs=15.0
Q ss_pred cccccccccCcC------CC--CCCceEeCCcCCccccc
Q 006832 238 HIICAKCKLREA------FP--DNDIVLCDGTCNCAFHQ 268 (629)
Q Consensus 238 ~~~C~vC~~~g~------~~--~~~lLlCDG~C~rafH~ 268 (629)
..+|.|||..-. .. +...+.|. .|...||+
T Consensus 172 ~g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs-~C~t~W~~ 209 (290)
T PF04216_consen 172 RGYCPVCGSPPVLSVLRGGEREGKRYLHCS-LCGTEWRF 209 (290)
T ss_dssp -SS-TTT---EEEEEEE------EEEEEET-TT--EEE-
T ss_pred CCcCCCCCCcCceEEEecCCCCccEEEEcC-CCCCeeee
Confidence 469999996310 01 24889998 79999984
No 167
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=21.63 E-value=83 Score=29.08 Aligned_cols=41 Identities=17% Similarity=0.259 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchh
Q 006832 506 NAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNA 547 (629)
Q Consensus 506 ~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNr 547 (629)
.-+..+..+...+ |.....-.+||+.+|+++.++..+|+..
T Consensus 9 ~~i~~~~~~I~~~-~~~~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 9 ITIHSILDWIEDN-LESPLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred HHHHHHHHHHHHh-cCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3445565555555 3445777999999999999999999876
No 168
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=21.51 E-value=1e+02 Score=35.01 Aligned_cols=18 Identities=22% Similarity=0.584 Sum_probs=9.9
Q ss_pred cccccCCCCCCCCCCCCceeccc
Q 006832 266 FHQKCLDPPLDTESRDQGWFCKF 288 (629)
Q Consensus 266 fH~~CL~PPL~~~p~dg~W~C~~ 288 (629)
||-++-..+ .+.+|+=..
T Consensus 2 FHEFaSs~~-----e~ddWi~~~ 19 (458)
T PF10446_consen 2 FHEFASSEP-----EEDDWIRQD 19 (458)
T ss_pred ccccccCcc-----chhhhhhcc
Confidence 676665532 135786555
No 169
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=21.47 E-value=92 Score=31.51 Aligned_cols=47 Identities=13% Similarity=0.154 Sum_probs=37.2
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHH
Q 006832 502 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK 553 (629)
Q Consensus 502 rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K 553 (629)
.+++.+...|...|-+. -.-.+||+.||++...|+.+....|.+.++
T Consensus 184 ~L~~~~r~vl~l~~~~g-----~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 230 (236)
T PRK06986 184 SLPEREQLVLSLYYQEE-----LNLKEIGAVLGVSESRVSQIHSQAIKRLRA 230 (236)
T ss_pred hCCHHHHHHHHhHhccC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46888888888776432 356899999999999999999988885444
No 170
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=21.36 E-value=1.1e+02 Score=29.42 Aligned_cols=36 Identities=14% Similarity=0.139 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhh
Q 006832 506 NAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVN 541 (629)
Q Consensus 506 ~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVk 541 (629)
.-+..|...=....|.+.+....+|+.|||++.+|.
T Consensus 23 ~ll~~L~~vQ~~~g~ip~~~~~~iA~~l~v~~~~v~ 58 (154)
T PRK07539 23 AVIPALKIVQEQRGWVPDEAIEAVADYLGMPAIDVE 58 (154)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHHH
Confidence 346677766677789999999999999999999975
No 171
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=20.96 E-value=44 Score=31.12 Aligned_cols=24 Identities=13% Similarity=0.416 Sum_probs=22.0
Q ss_pred HHHHHHHhCCCcchhhhccchhcc
Q 006832 526 KENLSKELSLEPEKVNKWFKNARY 549 (629)
Q Consensus 526 re~LA~~lgLt~~QVkiWFQNrR~ 549 (629)
..+||..+|+++..|..|..+.+.
T Consensus 21 q~~lA~~~gvs~~~is~~E~g~~~ 44 (135)
T PRK09706 21 QRSLAKAVKVSHVSISQWERDETE 44 (135)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCCC
Confidence 579999999999999999999874
No 172
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=20.92 E-value=67 Score=31.09 Aligned_cols=47 Identities=11% Similarity=0.200 Sum_probs=33.8
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHH
Q 006832 502 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK 553 (629)
Q Consensus 502 rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K 553 (629)
.+++.+...|...|- ..-.-.+||+.||++...|+.|+...|.+.++
T Consensus 141 ~L~~~~~~v~~l~~~-----~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 187 (194)
T PRK12519 141 QLPESQRQVLELAYY-----EGLSQSEIAKRLGIPLGTVKARARQGLLKLRE 187 (194)
T ss_pred hCCHHHhhhhhhhhh-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 356667666665442 22345789999999999999999887774443
No 173
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=20.83 E-value=1.2e+02 Score=30.11 Aligned_cols=38 Identities=11% Similarity=0.053 Sum_probs=33.9
Q ss_pred CHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhh
Q 006832 504 PPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVN 541 (629)
Q Consensus 504 t~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVk 541 (629)
-..-+..|...+.+.-|.+.+..+.+|..||++...|.
T Consensus 24 rsAlip~L~~aQ~~~G~l~~~ai~~iA~~L~i~~~~v~ 61 (160)
T COG1905 24 RSALIPLLHIAQEQFGWLPPEAIEEIADMLGIPRARVY 61 (160)
T ss_pred hhHHHHHHHHHHHHhCCCCHHHHHHHHHHhCCCHHHhe
Confidence 34567899999999999999999999999999998864
No 174
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=20.70 E-value=1.2e+02 Score=28.60 Aligned_cols=48 Identities=15% Similarity=0.104 Sum_probs=36.0
Q ss_pred CCCCHHHHHHHHHH-HHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHh
Q 006832 501 HRMPPNAVEKLRQV-FAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKA 554 (629)
Q Consensus 501 ~rft~~Q~~~Le~~-F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~ 554 (629)
..+++.+.+.|.-. |..-+ -++||..||+++..|+.|.+--|.+.++.
T Consensus 107 ~~L~~~~r~v~~l~~~~g~s------~~eIA~~lgis~~tv~~~l~Rar~~Lr~~ 155 (165)
T PRK09644 107 HTLPVIEAQAILLCDVHELT------YEEAASVLDLKLNTYKSHLFRGRKRLKAL 155 (165)
T ss_pred HhCCHHHHHHHHhHHHhcCC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 34678888877754 34333 47899999999999999998888855443
No 175
>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=20.57 E-value=1.2e+02 Score=28.97 Aligned_cols=36 Identities=11% Similarity=0.052 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhh
Q 006832 506 NAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVN 541 (629)
Q Consensus 506 ~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVk 541 (629)
.-+..|...=.+..|.+.+..+.+|+.|||++.+|.
T Consensus 17 ~li~~L~~vQ~~~G~i~~~~~~~iA~~l~~~~~~v~ 52 (148)
T TIGR01958 17 AIMPALMIAQEQKGWVTPEAIAAVAEMLGIPPVWVY 52 (148)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHHH
Confidence 445666666667789999999999999999998865
No 176
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=20.44 E-value=23 Score=25.22 Aligned_cols=42 Identities=24% Similarity=0.531 Sum_probs=27.6
Q ss_pred ccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCch
Q 006832 241 CAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCEC 291 (629)
Q Consensus 241 C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~ 291 (629)
|.+|...- ...+... .|...||..|+..-+.. +...||.|..
T Consensus 2 C~iC~~~~----~~~~~~~-~C~H~~c~~C~~~~~~~----~~~~Cp~C~~ 43 (45)
T cd00162 2 CPICLEEF----REPVVLL-PCGHVFCRSCIDKWLKS----GKNTCPLCRT 43 (45)
T ss_pred CCcCchhh----hCceEec-CCCChhcHHHHHHHHHh----CcCCCCCCCC
Confidence 77887653 2344445 38899999998754443 2456888864
No 177
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=20.26 E-value=1.5e+02 Score=26.71 Aligned_cols=46 Identities=9% Similarity=0.209 Sum_probs=36.0
Q ss_pred CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCC-Ccchhhhccchhcc
Q 006832 500 FHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSL-EPEKVNKWFKNARY 549 (629)
Q Consensus 500 r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgL-t~~QVkiWFQNrR~ 549 (629)
+.+||.+-...+-+.+.+..+ .-..||+++|+ ...++..|-...+.
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 567899988777777766666 77889999996 99999998654443
Done!