Query 006856
Match_columns 628
No_of_seqs 435 out of 2127
Neff 5.0
Searched_HMMs 46136
Date Thu Mar 28 15:28:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/006856.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/006856hhsearch_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 1.2E-24 2.7E-29 239.7 10.1 200 146-350 150-374 (613)
2 KOG0842 Transcription factor t 99.7 1.8E-18 3.9E-23 180.2 6.3 91 493-583 151-245 (307)
3 KOG0850 Transcription factor D 99.7 1.4E-17 3.1E-22 165.8 6.2 74 482-555 109-182 (245)
4 KOG1244 Predicted transcriptio 99.7 4E-18 8.7E-23 172.7 1.4 186 73-291 110-331 (336)
5 KOG0484 Transcription factor P 99.7 3.5E-17 7.6E-22 145.5 3.7 69 493-561 15-83 (125)
6 PF00046 Homeobox: Homeobox do 99.6 1.3E-15 2.9E-20 121.0 5.2 57 496-552 1-57 (57)
7 KOG0843 Transcription factor E 99.6 2E-15 4.4E-20 145.8 5.4 62 494-555 101-162 (197)
8 KOG0489 Transcription factor z 99.5 4.7E-15 1E-19 152.8 3.7 66 493-558 157-222 (261)
9 KOG0488 Transcription factor B 99.5 2.5E-14 5.4E-19 150.7 6.3 64 493-556 170-233 (309)
10 KOG0492 Transcription factor M 99.5 2.4E-14 5.3E-19 140.9 5.1 64 493-556 142-205 (246)
11 KOG2251 Homeobox transcription 99.5 4.3E-14 9.4E-19 140.5 6.5 68 490-557 32-99 (228)
12 KOG0485 Transcription factor N 99.5 7E-14 1.5E-18 138.5 7.0 66 492-557 101-166 (268)
13 KOG0493 Transcription factor E 99.5 4.6E-14 1E-18 142.7 5.4 62 493-554 244-305 (342)
14 smart00389 HOX Homeodomain. DN 99.5 6E-14 1.3E-18 110.5 4.8 53 497-549 2-54 (56)
15 KOG0487 Transcription factor A 99.4 4.3E-14 9.3E-19 147.8 4.6 63 493-555 233-295 (308)
16 cd00086 homeodomain Homeodomai 99.4 8.8E-14 1.9E-18 110.2 5.2 56 497-552 2-57 (59)
17 TIGR01565 homeo_ZF_HD homeobox 99.4 1.7E-13 3.7E-18 111.3 5.3 53 495-547 1-57 (58)
18 KOG0494 Transcription factor C 99.4 1.3E-13 2.8E-18 139.5 4.9 73 488-560 133-206 (332)
19 KOG0848 Transcription factor C 99.3 7.6E-13 1.6E-17 134.5 3.2 59 498-556 202-260 (317)
20 COG5576 Homeodomain-containing 99.3 2.4E-12 5.1E-17 123.7 5.6 63 494-556 50-112 (156)
21 KOG0483 Transcription factor H 99.3 1.5E-12 3.2E-17 129.2 3.9 56 496-551 51-106 (198)
22 KOG0486 Transcription factor P 99.3 2.3E-12 5E-17 133.6 3.5 65 493-557 110-174 (351)
23 KOG0491 Transcription factor B 99.1 2.3E-11 5E-16 116.4 1.9 60 495-554 100-159 (194)
24 KOG0847 Transcription factor, 99.1 4.2E-11 9.1E-16 119.0 3.1 66 493-558 165-230 (288)
25 KOG0844 Transcription factor E 99.0 7.3E-11 1.6E-15 122.0 2.9 66 491-556 177-242 (408)
26 KOG4577 Transcription factor L 99.0 1.2E-10 2.7E-15 119.6 4.2 62 495-556 167-228 (383)
27 KOG0490 Transcription factor, 99.0 3.9E-10 8.4E-15 112.0 5.8 64 492-555 57-120 (235)
28 KOG3802 Transcription factor O 98.9 5.6E-10 1.2E-14 119.6 4.4 61 494-554 293-353 (398)
29 KOG0849 Transcription factor P 98.7 8.6E-09 1.9E-13 110.9 4.5 62 493-554 174-235 (354)
30 KOG0775 Transcription factor S 98.7 9.5E-09 2.1E-13 105.5 4.2 48 502-549 183-230 (304)
31 KOG0825 PHD Zn-finger protein 98.6 7.7E-09 1.7E-13 117.2 1.7 52 236-290 213-265 (1134)
32 PF00628 PHD: PHD-finger; Int 98.6 9.1E-09 2E-13 80.3 1.0 48 240-290 1-50 (51)
33 KOG0774 Transcription factor P 98.6 3.4E-08 7.4E-13 100.7 5.2 60 495-554 188-250 (334)
34 PF05920 Homeobox_KN: Homeobox 98.5 3.4E-08 7.5E-13 74.7 1.7 33 516-548 7-39 (40)
35 KOG2252 CCAAT displacement pro 98.5 8.7E-08 1.9E-12 106.3 4.6 58 492-549 417-474 (558)
36 smart00249 PHD PHD zinc finger 98.3 4.4E-07 9.5E-12 67.9 3.3 46 240-288 1-47 (47)
37 KOG0955 PHD finger protein BR1 98.2 5.7E-07 1.2E-11 107.2 2.8 78 236-316 217-298 (1051)
38 KOG1512 PHD Zn-finger protein 98.2 3.9E-07 8.5E-12 94.2 1.1 72 213-289 284-361 (381)
39 KOG1168 Transcription factor A 98.2 7.1E-07 1.5E-11 92.4 1.9 60 494-553 308-367 (385)
40 KOG4443 Putative transcription 98.1 1.8E-06 4E-11 97.4 2.8 82 212-296 39-123 (694)
41 cd04718 BAH_plant_2 BAH, or Br 98.1 1.7E-06 3.7E-11 82.6 2.2 28 265-292 1-28 (148)
42 KOG1973 Chromatin remodeling p 98.0 2.3E-06 5E-11 89.4 2.9 51 236-292 217-269 (274)
43 KOG4323 Polycomb-like PHD Zn-f 98.0 1.4E-06 3E-11 96.1 0.8 57 239-296 169-229 (464)
44 COG5034 TNG2 Chromatin remodel 98.0 4.8E-06 1E-10 85.2 3.5 50 235-290 218-269 (271)
45 KOG0956 PHD finger protein AF1 97.9 3.4E-06 7.3E-11 95.5 1.7 50 239-290 6-56 (900)
46 KOG0954 PHD finger protein [Ge 97.9 3.6E-06 7.8E-11 95.9 1.4 51 237-290 270-320 (893)
47 COG5141 PHD zinc finger-contai 97.8 1.2E-05 2.6E-10 88.4 4.0 67 222-291 177-243 (669)
48 KOG0383 Predicted helicase [Ge 97.8 8.7E-06 1.9E-10 94.0 1.4 54 233-292 42-95 (696)
49 KOG0490 Transcription factor, 97.7 2.4E-05 5.1E-10 77.9 3.8 65 491-555 149-213 (235)
50 KOG0773 Transcription factor M 97.7 1.9E-05 4.1E-10 84.3 2.8 62 494-555 238-302 (342)
51 KOG1245 Chromatin remodeling c 97.6 1.4E-05 3E-10 98.8 -0.0 55 236-293 1106-1160(1404)
52 KOG0957 PHD finger protein [Ge 97.5 2.4E-05 5.1E-10 86.2 0.9 49 238-289 544-596 (707)
53 KOG1246 DNA-binding protein ju 97.2 0.00023 4.9E-09 85.5 4.2 163 237-408 154-326 (904)
54 KOG1146 Homeobox protein [Gene 97.0 0.00069 1.5E-08 82.1 4.5 63 493-555 901-963 (1406)
55 PF13831 PHD_2: PHD-finger; PD 96.6 0.00052 1.1E-08 51.0 -0.2 34 253-289 2-36 (36)
56 PF11569 Homez: Homeodomain le 96.0 0.005 1.1E-07 50.2 2.5 42 507-548 10-51 (56)
57 KOG1473 Nucleosome remodeling 95.4 0.0077 1.7E-07 72.2 2.2 47 237-289 343-389 (1414)
58 PF15446 zf-PHD-like: PHD/FYVE 94.5 0.02 4.3E-07 56.2 2.0 53 240-293 1-62 (175)
59 KOG0957 PHD finger protein [Ge 94.4 0.022 4.8E-07 63.6 2.3 52 239-292 120-180 (707)
60 KOG3623 Homeobox transcription 94.1 0.062 1.3E-06 62.5 5.1 46 507-552 568-613 (1007)
61 PF04218 CENP-B_N: CENP-B N-te 93.4 0.14 3E-06 41.0 4.5 48 496-548 1-48 (53)
62 KOG4443 Putative transcription 90.0 0.074 1.6E-06 61.3 -0.7 55 236-291 16-71 (694)
63 PF14446 Prok-RING_1: Prokaryo 88.9 0.23 4.9E-06 40.4 1.5 35 237-273 4-38 (54)
64 KOG1473 Nucleosome remodeling 82.6 0.27 5.9E-06 59.7 -1.3 48 239-291 429-479 (1414)
65 KOG4299 PHD Zn-finger protein 80.0 1 2.3E-05 52.0 2.1 48 238-291 47-95 (613)
66 PF01527 HTH_Tnp_1: Transposas 77.6 1.4 3E-05 36.5 1.7 47 497-547 2-48 (76)
67 KOG3612 PHD Zn-finger protein 76.0 1.9 4.1E-05 49.3 2.6 67 234-307 56-123 (588)
68 KOG4323 Polycomb-like PHD Zn-f 75.3 1.7 3.8E-05 49.0 2.1 56 235-293 80-135 (464)
69 KOG4628 Predicted E3 ubiquitin 75.3 1.5 3.2E-05 48.0 1.5 47 239-291 230-276 (348)
70 PF04545 Sigma70_r4: Sigma-70, 73.3 4.4 9.5E-05 31.3 3.4 44 501-549 4-47 (50)
71 PF04967 HTH_10: HTH DNA bindi 72.3 4.7 0.0001 32.6 3.4 40 502-541 1-42 (53)
72 KOG0383 Predicted helicase [Ge 67.9 1.2 2.7E-05 52.5 -1.1 52 236-293 504-556 (696)
73 PF12861 zf-Apc11: Anaphase-pr 67.6 2 4.2E-05 38.2 0.3 46 241-291 35-80 (85)
74 PF11793 FANCL_C: FANCL C-term 66.5 0.57 1.2E-05 39.6 -3.1 54 239-292 3-65 (70)
75 cd00569 HTH_Hin_like Helix-tur 66.0 12 0.00025 24.7 3.9 38 501-543 5-42 (42)
76 PF13639 zf-RING_2: Ring finge 65.5 0.7 1.5E-05 35.0 -2.6 43 240-289 2-44 (44)
77 cd06171 Sigma70_r4 Sigma70, re 65.4 4.9 0.00011 29.7 2.1 43 501-548 10-52 (55)
78 KOG1512 PHD Zn-finger protein 64.4 1.8 4E-05 46.0 -0.6 57 238-295 258-321 (381)
79 KOG2932 E3 ubiquitin ligase in 59.1 4.8 0.0001 43.4 1.4 50 238-298 90-139 (389)
80 KOG1734 Predicted RING-contain 56.1 8.5 0.00018 40.9 2.6 58 235-295 221-283 (328)
81 PF13901 DUF4206: Domain of un 56.0 8.6 0.00019 38.8 2.6 43 239-291 153-198 (202)
82 PF10668 Phage_terminase: Phag 54.9 6.7 0.00015 32.7 1.3 25 524-548 24-48 (60)
83 PRK03975 tfx putative transcri 50.9 18 0.00039 34.9 3.7 51 500-556 5-55 (141)
84 PF13551 HTH_29: Winged helix- 50.7 26 0.00057 30.5 4.5 49 496-544 52-109 (112)
85 PF13832 zf-HC5HC2H_2: PHD-zin 50.5 7.8 0.00017 34.8 1.1 31 238-272 55-86 (110)
86 COG3413 Predicted DNA binding 50.2 16 0.00034 36.8 3.4 41 501-541 155-197 (215)
87 PF10367 Vps39_2: Vacuolar sor 49.0 11 0.00025 32.9 1.9 31 238-272 78-108 (109)
88 PLN02638 cellulose synthase A 47.7 16 0.00034 45.4 3.4 51 237-291 16-68 (1079)
89 PF13443 HTH_26: Cro/C1-type H 47.4 17 0.00037 28.9 2.6 24 524-547 12-35 (63)
90 PF15446 zf-PHD-like: PHD/FYVE 47.1 14 0.0003 36.8 2.3 38 251-289 120-175 (175)
91 PF07227 DUF1423: Protein of u 46.8 13 0.00029 41.9 2.4 56 240-296 130-197 (446)
92 PF13936 HTH_38: Helix-turn-he 46.1 14 0.00031 28.2 1.8 40 500-544 3-42 (44)
93 smart00421 HTH_LUXR helix_turn 46.0 24 0.00052 26.5 3.1 42 501-548 3-44 (58)
94 PF12678 zf-rbx1: RING-H2 zinc 45.3 6.4 0.00014 33.4 -0.2 46 239-289 20-73 (73)
95 KOG1632 Uncharacterized PHD Zn 45.3 14 0.00031 40.4 2.4 39 254-293 74-115 (345)
96 PF00130 C1_1: Phorbol esters/ 44.9 18 0.0004 28.1 2.3 34 238-272 11-44 (53)
97 TIGR01206 lysW lysine biosynth 43.9 17 0.00036 29.7 2.0 43 240-283 4-52 (54)
98 KOG0773 Transcription factor M 43.5 15 0.00033 39.4 2.2 39 515-553 117-155 (342)
99 PHA02955 hypothetical protein; 42.4 27 0.00059 35.9 3.6 49 499-547 55-104 (213)
100 KOG0827 Predicted E3 ubiquitin 40.7 5.4 0.00012 44.2 -1.7 56 239-297 5-60 (465)
101 PRK10072 putative transcriptio 40.4 14 0.0003 33.4 1.1 40 502-548 33-72 (96)
102 TIGR02937 sigma70-ECF RNA poly 40.0 26 0.00056 31.2 2.8 46 501-551 110-155 (158)
103 TIGR03879 near_KaiC_dom probab 40.0 11 0.00024 32.6 0.4 37 511-547 21-57 (73)
104 KOG1080 Histone H3 (Lys4) meth 39.7 28 0.00061 43.2 3.9 51 238-290 573-623 (1005)
105 PRK06759 RNA polymerase factor 39.0 29 0.00063 32.1 3.1 46 501-551 106-151 (154)
106 smart00744 RINGv The RING-vari 38.9 6.1 0.00013 31.2 -1.3 44 240-288 1-48 (49)
107 PRK09413 IS2 repressor TnpA; R 38.6 43 0.00093 30.9 4.1 44 500-547 11-54 (121)
108 PRK04217 hypothetical protein; 38.5 40 0.00086 31.3 3.8 49 499-552 40-88 (110)
109 cd01392 HTH_LacI Helix-turn-he 38.4 14 0.0003 28.3 0.7 21 527-547 2-22 (52)
110 PF01381 HTH_3: Helix-turn-hel 38.4 18 0.00039 27.9 1.3 25 524-548 11-35 (55)
111 PF13771 zf-HC5HC2H: PHD-like 38.2 16 0.00035 31.3 1.2 30 239-272 37-67 (90)
112 PF13518 HTH_28: Helix-turn-he 36.4 19 0.00041 27.4 1.1 25 524-548 14-38 (52)
113 PHA02929 N1R/p28-like protein; 35.1 13 0.00029 38.7 0.2 48 238-291 174-225 (238)
114 PF10497 zf-4CXXC_R1: Zinc-fin 35.0 14 0.0003 33.9 0.2 49 238-290 7-69 (105)
115 KOG3970 Predicted E3 ubiquitin 34.8 14 0.0003 38.4 0.2 49 239-291 51-103 (299)
116 TIGR03070 couple_hipB transcri 34.3 24 0.00052 27.0 1.4 25 524-548 17-41 (58)
117 PF08280 HTH_Mga: M protein tr 33.4 39 0.00084 27.3 2.6 36 505-544 6-41 (59)
118 PRK09646 RNA polymerase sigma 33.3 43 0.00094 32.6 3.4 47 501-552 142-188 (194)
119 KOG1701 Focal adhesion adaptor 33.2 1.1E+02 0.0024 34.7 6.8 98 193-291 330-461 (468)
120 PLN02915 cellulose synthase A 32.7 35 0.00077 42.4 3.2 51 237-291 14-66 (1044)
121 PRK12514 RNA polymerase sigma 32.5 38 0.00082 32.3 2.8 47 501-552 129-175 (179)
122 KOG1146 Homeobox protein [Gene 32.1 11 0.00023 47.6 -1.3 58 496-553 445-502 (1406)
123 PRK09652 RNA polymerase sigma 31.5 42 0.00091 31.4 2.9 47 501-552 128-174 (182)
124 PRK11924 RNA polymerase sigma 31.1 41 0.00089 31.4 2.7 48 501-553 125-172 (179)
125 PF13384 HTH_23: Homeodomain-l 30.8 27 0.0006 26.6 1.3 26 522-547 17-42 (50)
126 PF07649 C1_3: C1-like domain; 30.8 21 0.00044 25.2 0.5 28 240-270 2-29 (30)
127 cd04761 HTH_MerR-SF Helix-Turn 30.2 27 0.00059 26.2 1.1 22 525-546 3-24 (49)
128 KOG1081 Transcription factor N 29.7 34 0.00073 39.0 2.2 46 236-290 87-132 (463)
129 PRK00118 putative DNA-binding 29.5 52 0.0011 30.2 3.0 44 502-550 18-61 (104)
130 PF06056 Terminase_5: Putative 28.9 30 0.00065 28.4 1.2 22 524-545 15-36 (58)
131 PF10080 DUF2318: Predicted me 28.9 28 0.00061 31.9 1.1 39 230-269 27-65 (102)
132 PRK12512 RNA polymerase sigma 28.8 56 0.0012 31.3 3.3 48 501-553 131-178 (184)
133 PHA01976 helix-turn-helix prot 28.6 29 0.00063 28.0 1.1 25 524-548 17-41 (67)
134 KOG0804 Cytoplasmic Zn-finger 28.5 26 0.00056 39.7 1.0 46 237-290 174-219 (493)
135 PF02796 HTH_7: Helix-turn-hel 28.5 63 0.0014 24.7 2.9 39 501-544 5-43 (45)
136 cd00162 RING RING-finger (Real 28.4 13 0.00029 26.5 -0.8 42 241-290 2-43 (45)
137 PF08281 Sigma70_r4_2: Sigma-7 28.2 27 0.00059 27.0 0.8 42 502-548 11-52 (54)
138 cd00093 HTH_XRE Helix-turn-hel 27.7 37 0.00079 24.4 1.4 23 525-547 15-37 (58)
139 KOG4218 Nuclear hormone recept 27.6 28 0.00061 38.3 1.1 55 236-291 13-76 (475)
140 PRK06811 RNA polymerase factor 27.5 62 0.0013 31.4 3.4 49 501-554 131-179 (189)
141 TIGR00595 priA primosomal prot 27.4 37 0.00081 38.9 2.1 43 238-291 213-262 (505)
142 cd06170 LuxR_C_like C-terminal 27.2 69 0.0015 24.1 3.0 39 502-546 1-39 (57)
143 KOG1952 Transcription factor N 27.2 13 0.00028 44.8 -1.6 50 239-290 192-244 (950)
144 PRK14559 putative protein seri 27.0 49 0.0011 39.4 2.9 49 239-292 2-51 (645)
145 cd00029 C1 Protein kinase C co 26.9 34 0.00074 25.8 1.1 33 239-272 12-44 (50)
146 PRK09648 RNA polymerase sigma 26.2 68 0.0015 30.9 3.4 48 500-552 138-185 (189)
147 PF00196 GerE: Bacterial regul 26.0 53 0.0012 26.0 2.2 43 501-549 3-45 (58)
148 PF13730 HTH_36: Helix-turn-he 25.4 1.3E+02 0.0028 23.3 4.2 42 501-545 2-48 (55)
149 KOG1829 Uncharacterized conser 25.2 23 0.00049 41.4 -0.1 46 240-293 513-561 (580)
150 TIGR02948 SigW_bacill RNA poly 25.0 58 0.0012 31.0 2.6 47 501-552 136-182 (187)
151 TIGR02985 Sig70_bacteroi1 RNA 24.8 61 0.0013 29.6 2.7 46 501-551 113-158 (161)
152 TIGR00270 conserved hypothetic 24.6 48 0.001 32.3 2.0 25 524-548 84-108 (154)
153 KOG2114 Vacuolar assembly/sort 24.4 82 0.0018 38.5 4.1 41 239-291 841-881 (933)
154 KOG3623 Homeobox transcription 24.3 61 0.0013 39.0 3.0 53 496-548 627-679 (1007)
155 PRK09639 RNA polymerase sigma 23.7 90 0.0019 29.2 3.6 47 500-552 111-157 (166)
156 PRK12519 RNA polymerase sigma 23.5 57 0.0012 31.6 2.3 47 501-552 141-187 (194)
157 PRK06986 fliA flagellar biosyn 23.3 82 0.0018 31.8 3.5 47 501-552 184-230 (236)
158 smart00109 C1 Protein kinase C 23.2 30 0.00066 25.8 0.3 33 238-272 11-43 (49)
159 PRK05988 formate dehydrogenase 23.2 1E+02 0.0022 30.0 4.0 36 505-540 24-59 (156)
160 KOG2930 SCF ubiquitin ligase, 23.2 16 0.00035 33.7 -1.4 27 260-290 79-105 (114)
161 TIGR02607 antidote_HigA addict 23.1 42 0.0009 27.8 1.1 24 525-548 21-44 (78)
162 PRK15369 two component system 23.1 84 0.0018 29.0 3.3 43 501-549 149-191 (211)
163 COG4367 Uncharacterized protei 23.0 90 0.0019 28.2 3.1 42 502-543 3-44 (97)
164 PRK14873 primosome assembly pr 22.9 58 0.0013 38.8 2.6 42 238-291 383-431 (665)
165 KOG4215 Hepatocyte nuclear fac 22.9 38 0.00083 37.6 1.0 29 237-266 18-46 (432)
166 KOG1844 PHD Zn-finger proteins 22.5 50 0.0011 37.3 1.9 46 243-292 90-136 (508)
167 PRK09644 RNA polymerase sigma 22.4 1.1E+02 0.0023 28.9 3.8 48 500-553 107-155 (165)
168 PF13411 MerR_1: MerR HTH fami 22.4 45 0.00097 26.9 1.1 18 526-543 4-21 (69)
169 PF13565 HTH_32: Homeodomain-l 22.3 2.2E+02 0.0047 23.4 5.3 40 503-542 32-76 (77)
170 TIGR00721 tfx DNA-binding prot 22.2 1E+02 0.0023 29.6 3.7 47 500-552 5-51 (137)
171 PRK03564 formate dehydrogenase 21.9 65 0.0014 35.0 2.5 32 237-269 186-225 (309)
172 PF08274 PhnA_Zn_Ribbon: PhnA 21.7 36 0.00079 24.6 0.4 23 240-263 4-26 (30)
173 PRK09706 transcriptional repre 21.6 44 0.00095 31.1 1.0 24 525-548 21-44 (135)
174 PRK07539 NADH dehydrogenase su 21.3 1.2E+02 0.0025 29.4 3.9 36 505-540 23-58 (154)
175 PF12844 HTH_19: Helix-turn-he 21.3 53 0.0011 26.2 1.3 25 524-548 14-38 (64)
176 PF05502 Dynactin_p62: Dynacti 21.3 78 0.0017 36.3 3.1 24 326-349 84-107 (483)
177 PRK05602 RNA polymerase sigma 21.3 73 0.0016 30.6 2.5 48 501-553 128-175 (186)
178 PRK12526 RNA polymerase sigma 21.0 65 0.0014 31.9 2.2 47 501-552 153-199 (206)
179 TIGR02954 Sig70_famx3 RNA poly 20.8 99 0.0021 29.2 3.3 46 501-551 119-164 (169)
180 COG2963 Transposase and inacti 20.7 1.5E+02 0.0032 26.7 4.2 46 499-548 5-51 (116)
181 TIGR01958 nuoE_fam NADH-quinon 20.6 1.2E+02 0.0027 28.9 3.9 36 505-540 17-52 (148)
182 PRK11511 DNA-binding transcrip 20.5 95 0.0021 28.7 3.0 41 505-546 9-49 (127)
183 PF02724 CDC45: CDC45-like pro 20.5 1.1E+02 0.0025 36.1 4.3 36 503-538 198-236 (622)
184 COG1905 NuoE NADH:ubiquinone o 20.4 1.2E+02 0.0027 30.0 3.8 38 503-540 24-61 (160)
185 PRK05657 RNA polymerase sigma 20.4 1E+02 0.0022 33.4 3.6 52 501-553 262-313 (325)
186 PF01726 LexA_DNA_bind: LexA D 20.2 1.2E+02 0.0027 25.2 3.3 38 502-541 4-45 (65)
187 PF13560 HTH_31: Helix-turn-he 20.1 58 0.0013 26.2 1.3 26 523-548 15-40 (64)
No 1
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=99.91 E-value=1.2e-24 Score=239.73 Aligned_cols=200 Identities=35% Similarity=0.567 Sum_probs=169.8
Q ss_pred cchhhHHHHHhhHHHHHHhhhhhhhhhhhhcCCCCcCCccc---------CCChHHHHHHHHHHHhhhhhHHHHHhhhhc
Q 006856 146 ELDEASRLQRRTRYLLIKMKLEQNLIDAYSGEGWKGHSREK---------IRPEKELQRAKKQILKCKIGIRDAIRQLDS 216 (628)
Q Consensus 146 ~~~~~~ri~~r~ry~l~~~~~Eq~l~~Ay~~egwkg~SreK---------~rP~kEl~rak~qi~k~K~~ird~l~~ld~ 216 (628)
.+++.-|+..+++|+...+..+|.++++|+.+||++.+.+| ++|.++..++..+|+.+++.++...+.++.
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 45678899999999999999999999999999999999999 999999999999999999999999999988
Q ss_pred cCCCCCCCCCcccCCCCcccccc--ccccccccccCCCCCeeecCCccCccccccccCCC--CCCCCCCCcccccccchh
Q 006856 217 LSSVGCIEGSVIATDGSVHHEHI--ICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPP--LDTESNQGWFCKFCECKM 292 (628)
Q Consensus 217 l~~~~~i~~s~~~~dg~~~~e~~--~C~vC~~~~~~~~g~lllCDG~C~rayH~~CL~PP--L~~~P~g~W~Cp~C~~k~ 292 (628)
....+..++..+..++....+.. ||..|++.+.. ++|||||| |+++|||+||+|| ...+|.|.|||+.|.++.
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 87777777777777777666665 99999998775 78899996 9999999999999 456789999999999998
Q ss_pred hHHhhhh--------ccCCcccc--cCCc--cccccccccccCCCCccccCCCCCCCCCCCCCCCCCccc
Q 006856 293 EIIESMN--------AHIGTSFS--VNSN--WQDIFKEEAAFPDGCSALLNQEEEWPSDDSEDDDYNPER 350 (628)
Q Consensus 293 ~~~~~~n--------~~~gt~~~--l~~~--~~~vF~e~a~~~~g~~~~~n~e~~~psddseDed~dp~~ 350 (628)
..++..+ ..+++.|- |+.. |+.+||+.+...-++.. +...+|++|+..+.+|+|..
T Consensus 307 ~in~~~~t~~~~~~~~~i~t~~~~~IDs~np~q~~lPe~i~~~~~~v~--~g~~~~~sd~~~~~pl~~~~ 374 (613)
T KOG4299|consen 307 VINPKMETLSNRGTVVDIFTQFVSKIDSHNPIQKILPENISESFGGVS--RGDDGQYSDTQDEKPLDPPA 374 (613)
T ss_pred ecccchhhhhhccchHHHHHHHHHhhhccchhhhhCCHHHHhhccccc--cCCCCccccccCCcCCChhh
Confidence 7666555 45555554 5555 89999997665555543 66889999999999999943
No 2
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.74 E-value=1.8e-18 Score=180.19 Aligned_cols=91 Identities=25% Similarity=0.357 Sum_probs=75.7
Q ss_pred cccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhhhhhcc--ccCCCC--CC
Q 006856 493 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVESAR--QVSGSP--RI 568 (628)
Q Consensus 493 ~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~K~~~~~~~~--~l~~~~--~~ 568 (628)
.++||+|..||..|+-+||+.|.+++|+++.+|++||..|+||+.||||||||||||.+|..+....+ .+...+ ..
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 CCCchhhhhccchhh
Q 006856 569 SKESSLETEKKNADV 583 (628)
Q Consensus 569 s~~s~~~~~~~~~dl 583 (628)
.+.+.+++.++++-.
T Consensus 231 v~vpvlvrd~kp~~~ 245 (307)
T KOG0842|consen 231 VAVPVLVRDGKPCSG 245 (307)
T ss_pred cCCceeccCCCcccC
Confidence 888888888776654
No 3
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.70 E-value=1.4e-17 Score=165.76 Aligned_cols=74 Identities=19% Similarity=0.291 Sum_probs=69.7
Q ss_pred cchhhccCCCccccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhh
Q 006856 482 TAEVKKKLPSNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK 555 (628)
Q Consensus 482 ~~~~~~~~~~~~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~K~~~ 555 (628)
+....+.|+..+|.|++||.|+..||+.|.+.|++++|+...+|.+||..||||..||+|||||||.|++|..+
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 44556789999999999999999999999999999999999999999999999999999999999999988887
No 4
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=99.69 E-value=4e-18 Score=172.71 Aligned_cols=186 Identities=21% Similarity=0.331 Sum_probs=128.6
Q ss_pred CCCC-chhhhhhhcccccchh--hccccccccccccccCCcc-ceeccCCCCcccCCCccccccccccccccccc--ccc
Q 006856 73 GAGD-DFARSKSISQKNLHIK--IDRKGSKNWASSKHKGKNS-ALVISKGNGEVVDGDGETKKLRKGRSKKRRKE--KVE 146 (628)
Q Consensus 73 ~~~~-~~~~~~~~~~~~~~~~--~~~~~~~~~~s~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~k~k~~~~--~~~ 146 (628)
++.+ +++++|||++++|+++ ++.+++ ++|+..|- ..++++.|.+++|.+++++||+++-|.|.++- +-.
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 4555 7999999999999998 888888 78886663 46778888899999999999999999998844 335
Q ss_pred chhhHHHHHhhHHHHHHhhhhhhhhhhhhcCCCCcCCcccCCChHHHHHHHHHHHhhhhhHHHHHhhhhccC--------
Q 006856 147 LDEASRLQRRTRYLLIKMKLEQNLIDAYSGEGWKGHSREKIRPEKELQRAKKQILKCKIGIRDAIRQLDSLS-------- 218 (628)
Q Consensus 147 ~~~~~ri~~r~ry~l~~~~~Eq~l~~Ay~~egwkg~SreK~rP~kEl~rak~qi~k~K~~ird~l~~ld~l~-------- 218 (628)
+.+++-+.. |++. .-+..-+|... -.+.-+|+++. |......||+..
T Consensus 185 l~~ss~l~~---~~~d---------~~~~~~~~~~g------e~~vkqr~kkd-------~a~Pn~YCDFclgdsr~nkk 239 (336)
T KOG1244|consen 185 LTDSSSLED---YVCD---------TGTKQTVFAPG------EAKVKQRVKKD-------IAQPNPYCDFCLGDSRENKK 239 (336)
T ss_pred ccccccccc---hhhc---------ccccccccCcc------hhhHHHhhhcc-------cccCCcccceeccccccccc
Confidence 555544443 3331 11222233221 01223333331 111223344332
Q ss_pred -----------------CCCCCC--CCcc---cCCCCccccccccccccccccCCCCCeeecCCccCccccccccCCCCC
Q 006856 219 -----------------SVGCIE--GSVI---ATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLD 276 (628)
Q Consensus 219 -----------------~~~~i~--~s~~---~~dg~~~~e~~~C~vC~~~~~~~~g~lllCDG~C~rayH~~CL~PPL~ 276 (628)
|..|+. ..++ ....|.+.++.+|.+|+..++ +++||+|| .|+++||+|||.||+.
T Consensus 240 t~~peelvscsdcgrsghpsclqft~nm~~avk~yrwqcieck~csicgtsen--ddqllfcd-dcdrgyhmyclsppm~ 316 (336)
T KOG1244|consen 240 TGMPEELVSCSDCGRSGHPSCLQFTANMIAAVKTYRWQCIECKYCSICGTSEN--DDQLLFCD-DCDRGYHMYCLSPPMV 316 (336)
T ss_pred cCCchhhcchhhcCCCCCcchhhhhHHHHHHHHhheeeeeecceeccccCcCC--CceeEeec-ccCCceeeEecCCCcC
Confidence 233332 1222 246789999999999998765 78999999 7999999999999999
Q ss_pred CCCCCCcccccccch
Q 006856 277 TESNQGWFCKFCECK 291 (628)
Q Consensus 277 ~~P~g~W~Cp~C~~k 291 (628)
..|+|.|.|..|...
T Consensus 317 eppegswsc~KOG~~ 331 (336)
T KOG1244|consen 317 EPPEGSWSCHLCLEE 331 (336)
T ss_pred CCCCCchhHHHHHHH
Confidence 999999999999754
No 5
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.66 E-value=3.5e-17 Score=145.46 Aligned_cols=69 Identities=26% Similarity=0.440 Sum_probs=63.3
Q ss_pred cccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhhhhhccc
Q 006856 493 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVESARQ 561 (628)
Q Consensus 493 ~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~K~~~~~~~~~ 561 (628)
.|+||-|+.||..|+.+||++|.++.||+..+|++||-.|.||+.+|+|||||||+|++|+.++.....
T Consensus 15 rKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a~~~~ 83 (125)
T KOG0484|consen 15 RKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAAIAKM 83 (125)
T ss_pred HHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHHHHHh
Confidence 456888999999999999999999999999999999999999999999999999999999986654443
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=99.59 E-value=1.3e-15 Score=121.05 Aligned_cols=57 Identities=35% Similarity=0.585 Sum_probs=53.7
Q ss_pred CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHH
Q 006856 496 RRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK 552 (628)
Q Consensus 496 kR~r~rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~K 552 (628)
||++++||++|+..|+.+|..++||+..+++.||..|||++.||++||+|+|++.+|
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 577889999999999999999999999999999999999999999999999996554
No 7
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.57 E-value=2e-15 Score=145.81 Aligned_cols=62 Identities=24% Similarity=0.424 Sum_probs=57.7
Q ss_pred ccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhh
Q 006856 494 KIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK 555 (628)
Q Consensus 494 k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~K~~~ 555 (628)
+.||.||.||++|+..||..|+.++|....+|++||+.|+|++.||+|||||||+|.+|...
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 56888999999999999999999999999999999999999999999999999997666553
No 8
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.52 E-value=4.7e-15 Score=152.81 Aligned_cols=66 Identities=23% Similarity=0.335 Sum_probs=59.9
Q ss_pred cccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhhhhh
Q 006856 493 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVES 558 (628)
Q Consensus 493 ~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~K~~~~~~ 558 (628)
.+.||.|+.||..|+.+||..|.-|+|+++..|.+||..|.|+++||+|||||||.|.+|..+...
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 446888999999999999999999999999999999999999999999999999997776665444
No 9
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.49 E-value=2.5e-14 Score=150.67 Aligned_cols=64 Identities=22% Similarity=0.291 Sum_probs=59.4
Q ss_pred cccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhhh
Q 006856 493 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKV 556 (628)
Q Consensus 493 ~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~K~~~~ 556 (628)
+|.|+.|+.||..|+.+||..|+...|.+..+|.+||+.||||-.||++||||||+|++|....
T Consensus 170 kK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~ 233 (309)
T KOG0488|consen 170 KKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE 233 (309)
T ss_pred cccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence 6677889999999999999999999999999999999999999999999999999977766544
No 10
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.48 E-value=2.4e-14 Score=140.90 Aligned_cols=64 Identities=22% Similarity=0.325 Sum_probs=58.6
Q ss_pred cccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhhh
Q 006856 493 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKV 556 (628)
Q Consensus 493 ~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~K~~~~ 556 (628)
+..|++|+-||.+|+..||+.|.+.+|.++.+|.+++..|.||+.||+|||||||+|.+|...+
T Consensus 142 k~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQea 205 (246)
T KOG0492|consen 142 KPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEA 205 (246)
T ss_pred CCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHH
Confidence 4457789999999999999999999999999999999999999999999999999987776543
No 11
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.48 E-value=4.3e-14 Score=140.53 Aligned_cols=68 Identities=26% Similarity=0.470 Sum_probs=62.3
Q ss_pred CCccccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhhhh
Q 006856 490 PSNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVE 557 (628)
Q Consensus 490 ~~~~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~K~~~~~ 557 (628)
+...|.||.||+|+..|+.+||..|.+++||+...|++||.+|+|.+.+|+|||.|||+|.+++.+.+
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence 34466788999999999999999999999999999999999999999999999999999888877654
No 12
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.46 E-value=7e-14 Score=138.46 Aligned_cols=66 Identities=18% Similarity=0.285 Sum_probs=61.1
Q ss_pred ccccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhhhh
Q 006856 492 NAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVE 557 (628)
Q Consensus 492 ~~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~K~~~~~ 557 (628)
..++||.|+.|+..|+.+||..|....|++-.+|..||+.|.||+.||+|||||||.|++|+-+++
T Consensus 101 ~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad 166 (268)
T KOG0485|consen 101 DDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAAD 166 (268)
T ss_pred ccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhh
Confidence 346788899999999999999999999999999999999999999999999999999888887554
No 13
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.46 E-value=4.6e-14 Score=142.73 Aligned_cols=62 Identities=23% Similarity=0.437 Sum_probs=57.3
Q ss_pred cccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhh
Q 006856 493 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR 554 (628)
Q Consensus 493 ~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~K~~ 554 (628)
+.-||+|+.||.+|++.|...|++|.|.+...|.+||++|||.+.||+|||||+|+|.+|--
T Consensus 244 ~eeKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsT 305 (342)
T KOG0493|consen 244 KEEKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKST 305 (342)
T ss_pred chhcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhcc
Confidence 34589999999999999999999999999999999999999999999999999999766643
No 14
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.46 E-value=6e-14 Score=110.55 Aligned_cols=53 Identities=34% Similarity=0.597 Sum_probs=50.3
Q ss_pred CCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccH
Q 006856 497 RSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYL 549 (628)
Q Consensus 497 R~r~rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k 549 (628)
+.+++|+++|+..|+.+|..++||+..++..||..|||+..||++||+|+|++
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 15
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.45 E-value=4.3e-14 Score=147.75 Aligned_cols=63 Identities=22% Similarity=0.307 Sum_probs=56.7
Q ss_pred cccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhh
Q 006856 493 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK 555 (628)
Q Consensus 493 ~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~K~~~ 555 (628)
...|++|--||+.|+.+||+.|--|.|.+.+.|.+||+.|+||++||+|||||||.|.+|--+
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~r 295 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNR 295 (308)
T ss_pred cccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhh
Confidence 445666778999999999999999999999999999999999999999999999997666553
No 16
>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=8.8e-14 Score=110.21 Aligned_cols=56 Identities=38% Similarity=0.623 Sum_probs=51.8
Q ss_pred CCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHH
Q 006856 497 RSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK 552 (628)
Q Consensus 497 R~r~rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~K 552 (628)
+.+..|+..|+..|+.+|..++||+..++..||.+|||++.||++||+|+|++.++
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 45578999999999999999999999999999999999999999999999996543
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=1.7e-13 Score=111.27 Aligned_cols=53 Identities=15% Similarity=0.292 Sum_probs=50.9
Q ss_pred cCCCCCCCCHHHHHHHHHHHHhCCC----CCHHHHHHHHHHhCCCcchhhhccchhc
Q 006856 495 IRRSFHRMPPNAVEKLRQVFAENEL----PSRIVKENLSKELSLEPEKVNKWFKNAR 547 (628)
Q Consensus 495 ~kR~r~rft~~Q~~~Le~~F~~~~y----Ps~~~r~~LA~~lgLt~~QVkiWFqNrR 547 (628)
+||.|+.||++|++.|+.+|..++| |+..++++||..|||++.+|+|||||.+
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=99.41 E-value=1.3e-13 Score=139.50 Aligned_cols=73 Identities=23% Similarity=0.340 Sum_probs=62.7
Q ss_pred cCCCccccCCC-CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhhhhhcc
Q 006856 488 KLPSNAKIRRS-FHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVESAR 560 (628)
Q Consensus 488 ~~~~~~k~kR~-r~rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~K~~~~~~~~ 560 (628)
++.+.+++||. ||.||..|+.+||..|++-.||+...|+-||-.+.|++.+|+|||||||+|++|..+..+..
T Consensus 133 ~~~kkk~kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg~s 206 (332)
T KOG0494|consen 133 DNAKKKKKRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWGGS 206 (332)
T ss_pred cccccccccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcCcc
Confidence 34444445555 89999999999999999999999999999999999999999999999999888876655443
No 19
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.31 E-value=7.6e-13 Score=134.54 Aligned_cols=59 Identities=22% Similarity=0.232 Sum_probs=54.3
Q ss_pred CCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhhh
Q 006856 498 SFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKV 556 (628)
Q Consensus 498 ~r~rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~K~~~~ 556 (628)
=|..||+.|+.+||..|...+|.+...|-+||.-|||+++||+|||||||+|-+|..+.
T Consensus 202 YRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKK 260 (317)
T KOG0848|consen 202 YRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKK 260 (317)
T ss_pred eeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHH
Confidence 36779999999999999999999999999999999999999999999999987666543
No 20
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.30 E-value=2.4e-12 Score=123.72 Aligned_cols=63 Identities=29% Similarity=0.389 Sum_probs=56.3
Q ss_pred ccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhhh
Q 006856 494 KIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKV 556 (628)
Q Consensus 494 k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~K~~~~ 556 (628)
..+++|+|.|.+|+..|++.|..+|||+..+|..||..|||++.-|+|||||+|++.++.+..
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 345555667999999999999999999999999999999999999999999999977776644
No 21
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.29 E-value=1.5e-12 Score=129.23 Aligned_cols=56 Identities=29% Similarity=0.430 Sum_probs=51.1
Q ss_pred CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHH
Q 006856 496 RRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLAL 551 (628)
Q Consensus 496 kR~r~rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~ 551 (628)
.+++.||+.+|+..||..|..+.|....+|..||++|||.++||.||||||||+++
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 33446789999999999999999999999999999999999999999999999543
No 22
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.26 E-value=2.3e-12 Score=133.55 Aligned_cols=65 Identities=25% Similarity=0.395 Sum_probs=59.4
Q ss_pred cccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhhhh
Q 006856 493 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVE 557 (628)
Q Consensus 493 ~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~K~~~~~ 557 (628)
+|+||.|+.||.+|+++||.+|+.|.||++.+|++||-.++||+..|+|||+|||+|++|..+-+
T Consensus 110 ~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~ 174 (351)
T KOG0486|consen 110 SKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQ 174 (351)
T ss_pred hhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhH
Confidence 46788999999999999999999999999999999999999999999999999999766665433
No 23
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.10 E-value=2.3e-11 Score=116.42 Aligned_cols=60 Identities=23% Similarity=0.368 Sum_probs=54.9
Q ss_pred cCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhh
Q 006856 495 IRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR 554 (628)
Q Consensus 495 ~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~K~~ 554 (628)
+++-|+.|+..|+..|+..|+...|.+..+|.+||..|+|++.||+.||||||.|.+|.-
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=99.09 E-value=4.2e-11 Score=119.03 Aligned_cols=66 Identities=20% Similarity=0.326 Sum_probs=58.0
Q ss_pred cccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhhhhh
Q 006856 493 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVES 558 (628)
Q Consensus 493 ~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~K~~~~~~ 558 (628)
.+++-.+-.|+-.|++.||..|.+.+||-.++|.+||..||+++.||+|||||||+|++|+.+++-
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 334445566999999999999999999999999999999999999999999999998888766553
No 25
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.05 E-value=7.3e-11 Score=121.95 Aligned_cols=66 Identities=21% Similarity=0.384 Sum_probs=60.4
Q ss_pred CccccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhhh
Q 006856 491 SNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKV 556 (628)
Q Consensus 491 ~~~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~K~~~~ 556 (628)
.....||=|+.||.+|+..||+.|...+|.++..|-+||..|||++..|+|||||||.|-+|+|-+
T Consensus 177 a~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 177 ADDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred ccHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence 345568889999999999999999999999999999999999999999999999999988888743
No 26
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.04 E-value=1.2e-10 Score=119.55 Aligned_cols=62 Identities=29% Similarity=0.471 Sum_probs=57.3
Q ss_pred cCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhhh
Q 006856 495 IRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKV 556 (628)
Q Consensus 495 ~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~K~~~~ 556 (628)
.||+|+.+|.-|++.|..+|...+.|.+.+|++|+.++||..+.|||||||||+|.+|.++-
T Consensus 167 nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKD 228 (383)
T KOG4577|consen 167 NKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKD 228 (383)
T ss_pred cCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhh
Confidence 48899999999999999999999999999999999999999999999999999986655443
No 27
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.00 E-value=3.9e-10 Score=111.98 Aligned_cols=64 Identities=22% Similarity=0.331 Sum_probs=58.9
Q ss_pred ccccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhh
Q 006856 492 NAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK 555 (628)
Q Consensus 492 ~~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~K~~~ 555 (628)
..++||.|+.|+..|+++|++.|..++||+...|+.||..++|++..|+|||||+|++.++..+
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 4567888999999999999999999999999999999999999999999999999997666654
No 28
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=98.94 E-value=5.6e-10 Score=119.57 Aligned_cols=61 Identities=25% Similarity=0.351 Sum_probs=56.0
Q ss_pred ccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhh
Q 006856 494 KIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR 554 (628)
Q Consensus 494 k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~K~~ 554 (628)
|+||+||-|...+..+||.+|..|+.|+..+.-.||.+|+|....|+|||+|||.|.+|-.
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 6778889999999999999999999999999999999999999999999999999544433
No 29
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=98.72 E-value=8.6e-09 Score=110.92 Aligned_cols=62 Identities=27% Similarity=0.450 Sum_probs=57.3
Q ss_pred cccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhh
Q 006856 493 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR 554 (628)
Q Consensus 493 ~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~K~~ 554 (628)
.+.+|.|+.|+..|+..|+..|..++||+...|++||+++||++.+|++||+|||++.+|..
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 44566789999999999999999999999999999999999999999999999999776665
No 30
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=98.71 E-value=9.5e-09 Score=105.46 Aligned_cols=48 Identities=29% Similarity=0.459 Sum_probs=44.9
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccH
Q 006856 502 MPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYL 549 (628)
Q Consensus 502 ft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k 549 (628)
|..--...|.+||..++||+..+|.+||+.+||+..||.+||+|||.+
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQR 230 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQR 230 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhh
Confidence 566667899999999999999999999999999999999999999993
No 31
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=98.65 E-value=7.7e-09 Score=117.22 Aligned_cols=52 Identities=33% Similarity=0.944 Sum_probs=45.6
Q ss_pred ccccccccccccccCCCCCeeecCCccCcc-ccccccCCCCCCCCCCCcccccccc
Q 006856 236 HEHIICAKCKLREAFPDNDIVLCDGTCNCA-FHQKCLDPPLDTESNQGWFCKFCEC 290 (628)
Q Consensus 236 ~e~~~C~vC~~~~~~~~g~lllCDG~C~ra-yH~~CL~PPL~~~P~g~W~Cp~C~~ 290 (628)
.+...|.+|...+- .+.||+||+ |+.+ ||+|||+|+|..+|-+.|||+.|.-
T Consensus 213 ~E~~~C~IC~~~Dp--EdVLLLCDs-CN~~~YH~YCLDPdl~eiP~~eWYC~NC~d 265 (1134)
T KOG0825|consen 213 QEEVKCDICTVHDP--EDVLLLCDS-CNKVYYHVYCLDPDLSESPVNEWYCTNCSL 265 (1134)
T ss_pred cccccceeeccCCh--HHhheeecc-cccceeeccccCcccccccccceecCcchh
Confidence 34567999998764 679999995 9999 9999999999999999999999963
No 32
>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=98.62 E-value=9.1e-09 Score=80.31 Aligned_cols=48 Identities=35% Similarity=0.991 Sum_probs=40.5
Q ss_pred ccccccccccCCCCCeeecCCccCccccccccCCCCCCC--CCCCcccccccc
Q 006856 240 ICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTE--SNQGWFCKFCEC 290 (628)
Q Consensus 240 ~C~vC~~~~~~~~g~lllCDG~C~rayH~~CL~PPL~~~--P~g~W~Cp~C~~ 290 (628)
+|.+|+..+ +++.||.|| .|.++||+.|++|++... +...|+|+.|..
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 588999843 589999999 699999999999998744 356999999974
No 33
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=98.62 E-value=3.4e-08 Score=100.73 Aligned_cols=60 Identities=32% Similarity=0.447 Sum_probs=56.0
Q ss_pred cCCCCCCCCHHHHHHHHHHHH---hCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhh
Q 006856 495 IRRSFHRMPPNAVEKLRQVFA---ENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR 554 (628)
Q Consensus 495 ~kR~r~rft~~Q~~~Le~~F~---~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~K~~ 554 (628)
.+|+|+.|+...+.+|..+|. .||||+.+.+++||++.|++..||.+||.|+|.+.+|+.
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~ 250 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNM 250 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhh
Confidence 467778899999999999997 469999999999999999999999999999999998886
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=98.52 E-value=3.4e-08 Score=74.73 Aligned_cols=33 Identities=39% Similarity=0.681 Sum_probs=28.6
Q ss_pred hCCCCCHHHHHHHHHHhCCCcchhhhccchhcc
Q 006856 516 ENELPSRIVKENLSKELSLEPEKVNKWFKNARY 548 (628)
Q Consensus 516 ~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~ 548 (628)
.+|||+.+++++||+++||+..||..||-|.|.
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=98.49 E-value=8.7e-08 Score=106.27 Aligned_cols=58 Identities=29% Similarity=0.401 Sum_probs=55.0
Q ss_pred ccccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccH
Q 006856 492 NAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYL 549 (628)
Q Consensus 492 ~~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k 549 (628)
....||+|+.||+.|...|..+|++++||+.+..+.|+.+|||....|.+||.|.|.+
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 4567888999999999999999999999999999999999999999999999999984
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=98.21 E-value=5.7e-07 Score=107.19 Aligned_cols=78 Identities=26% Similarity=0.544 Sum_probs=59.0
Q ss_pred ccccccccccccccCCCCCeeecCCccCccccccccCCCCCCCCCCCcccccccchh----hHHhhhhccCCcccccCCc
Q 006856 236 HEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESNQGWFCKFCECKM----EIIESMNAHIGTSFSVNSN 311 (628)
Q Consensus 236 ~e~~~C~vC~~~~~~~~g~lllCDG~C~rayH~~CL~PPL~~~P~g~W~Cp~C~~k~----~~~~~~n~~~gt~~~l~~~ 311 (628)
.++.+|.+|...+...-+.||+||+ |+.++|+.|++ +..+|+|.|+|..|...+ .|+-..+....|.-++...
T Consensus 217 ~~D~~C~iC~~~~~~n~n~ivfCD~-Cnl~VHq~Cyg--i~~ipeg~WlCr~Cl~s~~~~v~c~~cp~~~gAFkqt~dgr 293 (1051)
T KOG0955|consen 217 EEDAVCCICLDGECQNSNVIVFCDG-CNLAVHQECYG--IPFIPEGQWLCRRCLQSPQRPVRCLLCPSKGGAFKQTDDGR 293 (1051)
T ss_pred CCCccceeecccccCCCceEEEcCC-CcchhhhhccC--CCCCCCCcEeehhhccCcCcccceEeccCCCCcceeccCCc
Confidence 4678999999988866699999995 99999999999 455889999999997643 3444445555555556666
Q ss_pred ccccc
Q 006856 312 WQDIF 316 (628)
Q Consensus 312 ~~~vF 316 (628)
|..+.
T Consensus 294 w~Hv~ 298 (1051)
T KOG0955|consen 294 WAHVV 298 (1051)
T ss_pred eeeee
Confidence 65443
No 38
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=98.21 E-value=3.9e-07 Score=94.18 Aligned_cols=72 Identities=18% Similarity=0.391 Sum_probs=58.2
Q ss_pred hhhccCCCCCCCC-----CcccCCCCccccccccccccccccCCCCCeeecCCccCccccccccCCCCCCCCCCCcccc-
Q 006856 213 QLDSLSSVGCIEG-----SVIATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESNQGWFCK- 286 (628)
Q Consensus 213 ~ld~l~~~~~i~~-----s~~~~dg~~~~e~~~C~vC~~~~~~~~g~lllCDG~C~rayH~~CL~PPL~~~P~g~W~Cp- 286 (628)
.|...+|..|++. .++....|.+.++..|.+|+++.- ...+|+|| .|+++||.+|++ |...|.|.|.|.
T Consensus 284 ~C~~~~HP~Ci~M~~elv~~~KTY~W~C~~C~lC~IC~~P~~--E~E~~FCD-~CDRG~HT~CVG--L~~lP~G~WICD~ 358 (381)
T KOG1512|consen 284 PCATRPHPYCVAMIPELVGQYKTYFWKCSSCELCRICLGPVI--ESEHLFCD-VCDRGPHTLCVG--LQDLPRGEWICDM 358 (381)
T ss_pred ccccCCCCcchhcCHHHHhHHhhcchhhcccHhhhccCCccc--chheeccc-cccCCCCccccc--cccccCccchhhh
Confidence 3555566666642 234567799999999999999875 67999999 899999999999 899999999997
Q ss_pred ccc
Q 006856 287 FCE 289 (628)
Q Consensus 287 ~C~ 289 (628)
.|.
T Consensus 359 ~C~ 361 (381)
T KOG1512|consen 359 RCR 361 (381)
T ss_pred HHH
Confidence 353
No 39
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=98.16 E-value=7.1e-07 Score=92.39 Aligned_cols=60 Identities=22% Similarity=0.300 Sum_probs=53.2
Q ss_pred ccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHh
Q 006856 494 KIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKA 553 (628)
Q Consensus 494 k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~K~ 553 (628)
.+||+|+-+-.-....||++|..+|.|+.+....||++|.|..+.|+|||+|.|.|.+|-
T Consensus 308 ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm 367 (385)
T KOG1168|consen 308 EKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRM 367 (385)
T ss_pred ccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHh
Confidence 456677777777788999999999999999999999999999999999999999965553
No 40
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=98.06 E-value=1.8e-06 Score=97.42 Aligned_cols=82 Identities=20% Similarity=0.484 Sum_probs=65.4
Q ss_pred hhhhccCCCCCCCC---CcccCCCCccccccccccccccccCCCCCeeecCCccCccccccccCCCCCCCCCCCcccccc
Q 006856 212 RQLDSLSSVGCIEG---SVIATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESNQGWFCKFC 288 (628)
Q Consensus 212 ~~ld~l~~~~~i~~---s~~~~dg~~~~e~~~C~vC~~~~~~~~g~lllCDG~C~rayH~~CL~PPL~~~P~g~W~Cp~C 288 (628)
..|-.++|..|+.. .+....||.+..+.+|..|+..+ +...+++|+ .|+.+||.||..||++.++.+.|+|+.|
T Consensus 39 ~~c~~~yH~~cvt~~~~~~~l~~gWrC~~crvCe~c~~~g--D~~kf~~Ck-~cDvsyh~yc~~P~~~~v~sg~~~ckk~ 115 (694)
T KOG4443|consen 39 SDCGQKYHPYCVTSWAQHAVLSGGWRCPSCRVCEACGTTG--DPKKFLLCK-RCDVSYHCYCQKPPNDKVPSGPWLCKKC 115 (694)
T ss_pred hhhcccCCcchhhHHHhHHHhcCCcccCCceeeeeccccC--Ccccccccc-cccccccccccCCccccccCcccccHHH
Confidence 34556677777642 22335679999999999999654 578999999 5999999999999999999999999999
Q ss_pred cchhhHHh
Q 006856 289 ECKMEIIE 296 (628)
Q Consensus 289 ~~k~~~~~ 296 (628)
.....|-.
T Consensus 116 ~~c~qc~~ 123 (694)
T KOG4443|consen 116 TRCRQCDS 123 (694)
T ss_pred Hhhhhccc
Confidence 76655443
No 41
>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=98.06 E-value=1.7e-06 Score=82.63 Aligned_cols=28 Identities=43% Similarity=1.075 Sum_probs=26.0
Q ss_pred cccccccCCCCCCCCCCCcccccccchh
Q 006856 265 AFHQKCLDPPLDTESNQGWFCKFCECKM 292 (628)
Q Consensus 265 ayH~~CL~PPL~~~P~g~W~Cp~C~~k~ 292 (628)
+||++||+|||..+|+|+|+||.|..+.
T Consensus 1 g~H~~CL~Ppl~~~P~g~W~Cp~C~~~~ 28 (148)
T cd04718 1 GFHLCCLRPPLKEVPEGDWICPFCEVEK 28 (148)
T ss_pred CcccccCCCCCCCCCCCCcCCCCCcCCC
Confidence 5999999999999999999999998663
No 42
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=98.04 E-value=2.3e-06 Score=89.39 Aligned_cols=51 Identities=25% Similarity=0.658 Sum_probs=40.8
Q ss_pred ccccccccccccccCCCCCeeecCC-ccC-ccccccccCCCCCCCCCCCcccccccchh
Q 006856 236 HEHIICAKCKLREAFPDNDIVLCDG-TCN-CAFHQKCLDPPLDTESNQGWFCKFCECKM 292 (628)
Q Consensus 236 ~e~~~C~vC~~~~~~~~g~lllCDG-~C~-rayH~~CL~PPL~~~P~g~W~Cp~C~~k~ 292 (628)
.+..||..+.. ..|.||-||+ .|+ .|||+.|++ |...|.|.|||+.|....
T Consensus 217 ~e~~yC~Cnqv----syg~Mi~CDn~~C~~eWFH~~CVG--L~~~PkgkWyC~~C~~~~ 269 (274)
T KOG1973|consen 217 DEPTYCICNQV----SYGKMIGCDNPGCPIEWFHFTCVG--LKTKPKGKWYCPRCKAEN 269 (274)
T ss_pred CCCEEEEeccc----ccccccccCCCCCCcceEEEeccc--cccCCCCcccchhhhhhh
Confidence 45567755432 3689999995 599 999999999 888899999999997553
No 43
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=98.02 E-value=1.4e-06 Score=96.08 Aligned_cols=57 Identities=26% Similarity=0.647 Sum_probs=47.9
Q ss_pred cccccccccccCCCCCeeecCCccCccccccccCCCCCCCC----CCCcccccccchhhHHh
Q 006856 239 IICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTES----NQGWFCKFCECKMEIIE 296 (628)
Q Consensus 239 ~~C~vC~~~~~~~~g~lllCDG~C~rayH~~CL~PPL~~~P----~g~W~Cp~C~~k~~~~~ 296 (628)
..|.||..+.....+.||.|++ |..+||+.|+.|++...- ...|||..|...+..+.
T Consensus 169 ~qc~vC~~g~~~~~NrmlqC~~-C~~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~~~~~~~ 229 (464)
T KOG4323|consen 169 LQCSVCYCGGPGAGNRMLQCDK-CRQWYHQACHQPLIKDELAGDPFYEWFCDVCNRGPKKVP 229 (464)
T ss_pred ceeeeeecCCcCccceeeeecc-cccHHHHHhccCCCCHhhccCccceEeehhhccchhhcc
Confidence 3499999888878899999995 999999999999986653 67899999988766443
No 44
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=97.97 E-value=4.8e-06 Score=85.22 Aligned_cols=50 Identities=28% Similarity=0.766 Sum_probs=41.0
Q ss_pred cccccccccccccccCCCCCeeecCC-ccCc-cccccccCCCCCCCCCCCcccccccc
Q 006856 235 HHEHIICAKCKLREAFPDNDIVLCDG-TCNC-AFHQKCLDPPLDTESNQGWFCKFCEC 290 (628)
Q Consensus 235 ~~e~~~C~vC~~~~~~~~g~lllCDG-~C~r-ayH~~CL~PPL~~~P~g~W~Cp~C~~ 290 (628)
.++..|| .|++.- -|+||-||| .|.+ |||+-|++ |...|.|.|||+.|..
T Consensus 218 e~e~lYC-fCqqvS---yGqMVaCDn~nCkrEWFH~~CVG--Lk~pPKG~WYC~eCk~ 269 (271)
T COG5034 218 EGEELYC-FCQQVS---YGQMVACDNANCKREWFHLECVG--LKEPPKGKWYCPECKK 269 (271)
T ss_pred cCceeEE-Eecccc---cccceecCCCCCchhheeccccc--cCCCCCCcEeCHHhHh
Confidence 3466788 576532 589999998 8985 79999999 8899999999999964
No 45
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=97.93 E-value=3.4e-06 Score=95.46 Aligned_cols=50 Identities=34% Similarity=0.852 Sum_probs=44.9
Q ss_pred cccccccccccCCCCCeeecCC-ccCccccccccCCCCCCCCCCCcccccccc
Q 006856 239 IICAKCKLREAFPDNDIVLCDG-TCNCAFHQKCLDPPLDTESNQGWFCKFCEC 290 (628)
Q Consensus 239 ~~C~vC~~~~~~~~g~lllCDG-~C~rayH~~CL~PPL~~~P~g~W~Cp~C~~ 290 (628)
.-|.||.+..-+.+|.||.||| .|-.+.|+.|+. +-.+|.|.|||..|..
T Consensus 6 GGCCVCSDErGWaeNPLVYCDG~nCsVAVHQaCYG--IvqVPtGpWfCrKCes 56 (900)
T KOG0956|consen 6 GGCCVCSDERGWAENPLVYCDGHNCSVAVHQACYG--IVQVPTGPWFCRKCES 56 (900)
T ss_pred cceeeecCcCCCccCceeeecCCCceeeeehhcce--eEecCCCchhhhhhhh
Confidence 3599999877778899999999 999999999999 7889999999999963
No 46
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=97.90 E-value=3.6e-06 Score=95.89 Aligned_cols=51 Identities=31% Similarity=0.849 Sum_probs=47.5
Q ss_pred cccccccccccccCCCCCeeecCCccCccccccccCCCCCCCCCCCcccccccc
Q 006856 237 EHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESNQGWFCKFCEC 290 (628)
Q Consensus 237 e~~~C~vC~~~~~~~~g~lllCDG~C~rayH~~CL~PPL~~~P~g~W~Cp~C~~ 290 (628)
++..|.||..++.+.+++||+|| .|+...|+.|++ +..+|++.|+|..|.-
T Consensus 270 edviCDvCrspD~e~~neMVfCd-~Cn~cVHqaCyG--Ile~p~gpWlCr~Cal 320 (893)
T KOG0954|consen 270 EDVICDVCRSPDSEEANEMVFCD-KCNICVHQACYG--ILEVPEGPWLCRTCAL 320 (893)
T ss_pred ccceeceecCCCccccceeEEec-cchhHHHHhhhc--eeecCCCCeeehhccc
Confidence 67899999999999999999999 799999999999 8899999999999963
No 47
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=97.84 E-value=1.2e-05 Score=88.35 Aligned_cols=67 Identities=25% Similarity=0.524 Sum_probs=51.5
Q ss_pred CCCCCcccCCCCccccccccccccccccCCCCCeeecCCccCccccccccCCCCCCCCCCCcccccccch
Q 006856 222 CIEGSVIATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESNQGWFCKFCECK 291 (628)
Q Consensus 222 ~i~~s~~~~dg~~~~e~~~C~vC~~~~~~~~g~lllCDG~C~rayH~~CL~PPL~~~P~g~W~Cp~C~~k 291 (628)
.+++..+..-+..+.-+..|.+|...++...+.||+||| |+-+.|+.|++. .-+|+|.|+|..|.-.
T Consensus 177 ~lp~k~vepi~~~d~~d~~C~~c~~t~~eN~naiVfCdg-C~i~VHq~CYGI--~f~peG~WlCrkCi~~ 243 (669)
T COG5141 177 GLPDKHVEPIEPSDEFDDICTKCTSTHNENSNAIVFCDG-CEICVHQSCYGI--QFLPEGFWLCRKCIYG 243 (669)
T ss_pred cCccccccccCCchhhhhhhHhccccccCCcceEEEecC-cchhhhhhcccc--eecCcchhhhhhhccc
Confidence 344333333333344578999999988877899999997 999999999995 4578999999999743
No 48
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=97.75 E-value=8.7e-06 Score=94.04 Aligned_cols=54 Identities=33% Similarity=0.802 Sum_probs=47.4
Q ss_pred CccccccccccccccccCCCCCeeecCCccCccccccccCCCCCCCCCCCcccccccchh
Q 006856 233 SVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESNQGWFCKFCECKM 292 (628)
Q Consensus 233 ~~~~e~~~C~vC~~~~~~~~g~lllCDG~C~rayH~~CL~PPL~~~P~g~W~Cp~C~~k~ 292 (628)
+...+..+|.+|+. ++.+|+|| .|+.+||.+|++||+...|.+.|.|+.|.+..
T Consensus 42 ~~~~~~e~c~ic~~-----~g~~l~c~-tC~~s~h~~cl~~pl~~~p~~~~~c~Rc~~p~ 95 (696)
T KOG0383|consen 42 WDDAEQEACRICAD-----GGELLWCD-TCPASFHASCLGPPLTPQPNGEFICPRCFCPK 95 (696)
T ss_pred cchhhhhhhhhhcC-----CCcEEEec-cccHHHHHHccCCCCCcCCccceeeeeeccCC
Confidence 45566789999995 68999999 89999999999999999998779999996654
No 49
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.73 E-value=2.4e-05 Score=77.87 Aligned_cols=65 Identities=31% Similarity=0.436 Sum_probs=58.4
Q ss_pred CccccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhh
Q 006856 491 SNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK 555 (628)
Q Consensus 491 ~~~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~K~~~ 555 (628)
...+.++.++.|+..|+..|...|..++||+...++.|+..+|++...|++||||+|++.++...
T Consensus 149 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 149 SNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred CccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 34667888899999999999999999999999999999999999999999999999996655443
No 50
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=97.70 E-value=1.9e-05 Score=84.31 Aligned_cols=62 Identities=32% Similarity=0.367 Sum_probs=55.2
Q ss_pred ccCCCCCCCCHHHHHHHHHHHHhC---CCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhh
Q 006856 494 KIRRSFHRMPPNAVEKLRQVFAEN---ELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK 555 (628)
Q Consensus 494 k~kR~r~rft~~Q~~~Le~~F~~~---~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~K~~~ 555 (628)
..+|++..|+...+.+|+.|+.++ |||+..++..||+++||+..||.+||.|.|.+.++...
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 51
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=97.60 E-value=1.4e-05 Score=98.77 Aligned_cols=55 Identities=29% Similarity=0.802 Sum_probs=48.5
Q ss_pred ccccccccccccccCCCCCeeecCCccCccccccccCCCCCCCCCCCcccccccchhh
Q 006856 236 HEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESNQGWFCKFCECKME 293 (628)
Q Consensus 236 ~e~~~C~vC~~~~~~~~g~lllCDG~C~rayH~~CL~PPL~~~P~g~W~Cp~C~~k~~ 293 (628)
.....|.+|..... ...|++|| .|..+||++|+.|.+..+|.++|+||.|.....
T Consensus 1106 ~~~~~c~~cr~k~~--~~~m~lc~-~c~~~~h~~C~rp~~~~~~~~dW~C~~c~~e~~ 1160 (1404)
T KOG1245|consen 1106 AVNALCKVCRRKKQ--DEKMLLCD-ECLSGFHLFCLRPALSSVPPGDWMCPSCRKEHR 1160 (1404)
T ss_pred cchhhhhhhhhccc--chhhhhhH-hhhhhHHHHhhhhhhccCCcCCccCCccchhhh
Confidence 45679999998763 67999999 599999999999999999999999999987654
No 52
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=97.55 E-value=2.4e-05 Score=86.23 Aligned_cols=49 Identities=37% Similarity=0.890 Sum_probs=42.7
Q ss_pred ccccccccccccCCCCCeeecCCccCccccccccCCCCCCCC----CCCccccccc
Q 006856 238 HIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTES----NQGWFCKFCE 289 (628)
Q Consensus 238 ~~~C~vC~~~~~~~~g~lllCDG~C~rayH~~CL~PPL~~~P----~g~W~Cp~C~ 289 (628)
...|.+|.+.. +..-+++|| +|..-||+.||+|||...| ...|.|..|.
T Consensus 544 ~ysCgiCkks~--dQHll~~CD-tC~lhYHlGCL~PPLTR~Pkk~kn~gWqCsECd 596 (707)
T KOG0957|consen 544 NYSCGICKKST--DQHLLTQCD-TCHLHYHLGCLSPPLTRLPKKNKNFGWQCSECD 596 (707)
T ss_pred ceeeeeeccch--hhHHHhhcc-hhhceeeccccCCccccCcccccCcceeecccc
Confidence 45799999854 467889999 8999999999999999999 4689999994
No 53
>KOG1246 consensus DNA-binding protein jumonji/RBP2/SMCY, contains JmjC domain [General function prediction only]
Probab=97.24 E-value=0.00023 Score=85.51 Aligned_cols=163 Identities=22% Similarity=0.284 Sum_probs=99.8
Q ss_pred cccccccccccccCCCCCeeecCCccCccccccccCCCCCCCCCCCcccccccchhhHHhhhhccCCcccccCCcccccc
Q 006856 237 EHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESNQGWFCKFCECKMEIIESMNAHIGTSFSVNSNWQDIF 316 (628)
Q Consensus 237 e~~~C~vC~~~~~~~~g~lllCDG~C~rayH~~CL~PPL~~~P~g~W~Cp~C~~k~~~~~~~n~~~gt~~~l~~~~~~vF 316 (628)
....|..|...... ..+ +|++ |...||.+|+.||+..++.+.|.|+.|..-.. ......+|+.......-...|
T Consensus 154 ~~~~~~~~~k~~~~--~~~-~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~gf~~~~~~yt~~~f 227 (904)
T KOG1246|consen 154 DYPQCNTCSKGKEE--KLL-LCDS-CDDSYHTYCLRPPLTRVPDGDWRCPKCIPTPE--SKPNYKFGFEQGSREYTLPKF 227 (904)
T ss_pred cchhhhccccCCCc--cce-eccc-ccCcccccccCCCCCcCCcCcccCCccccccc--CCcccccCcCCCCCccccchh
Confidence 34579999986542 344 9995 99999999999999999999999999986522 111233343333323333455
Q ss_pred ccccccCCCCccccCCCCCCCCCCCCCCCCCcccccCcccCCCC-CCCCCCCCCCCCCCCCCCcccc---------cccc
Q 006856 317 KEEAAFPDGCSALLNQEEEWPSDDSEDDDYNPERRENSCSISRA-GTDDDPSSSTSLSWFSDSETFS---------ESMR 386 (628)
Q Consensus 317 ~e~a~~~~g~~~~~n~e~~~psddseDed~dp~~~e~~~~~~~e-G~dd~~s~s~s~s~s~~~E~~~---------~s~~ 386 (628)
.+.+......|-.......=+-++.|-++|+....... .+.+. |+| .++..-+++++...... ....
T Consensus 228 ~~~~~~~~~~~~~~~~~~~~~~~~vE~e~w~~v~~~~~-~~~~~~g~d--~~~~~~~s~~~~~~~~~~~~~~~~~y~~s~ 304 (904)
T KOG1246|consen 228 EEYADNFKKDYFPKSKNSPDSTEDVEKEFWRLVASNLE-SVEVLYGAD--LSTKEFGSGFPKSASGPLLGSEAEKYSNSG 304 (904)
T ss_pred hhHhhhhhccccccccCCCCchHHHHHHHHHhhccccc-ceeeeeccc--hhhccccccccccCCCCCCCcchhhhccCc
Confidence 55555555544211101000134778888888765422 22222 444 23333333444332221 3668
Q ss_pred cccccCCCCCCCCCCCCCCCCC
Q 006856 387 WEMESNGYKNYSVDSSIGSDET 408 (628)
Q Consensus 387 ~~~~~~~~~~~s~~~~~~sd~~ 408 (628)
||++.+|....++.++++.|+.
T Consensus 305 wnL~~i~~~~~svl~~~~~di~ 326 (904)
T KOG1246|consen 305 WNLNNIPRLEGSVLSHIDTDIS 326 (904)
T ss_pred ccccccccCCccccccccCCcC
Confidence 9999999999999999986664
No 54
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=96.95 E-value=0.00069 Score=82.12 Aligned_cols=63 Identities=19% Similarity=0.267 Sum_probs=57.9
Q ss_pred cccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhh
Q 006856 493 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK 555 (628)
Q Consensus 493 ~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~K~~~ 555 (628)
-.+++.|++++..|+..|...|....||...+-|.|...++|..+.|.+||||.|.+.+|..-
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 345778999999999999999999999999999999999999999999999999997777664
No 55
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=96.56 E-value=0.00052 Score=50.98 Aligned_cols=34 Identities=38% Similarity=1.045 Sum_probs=19.2
Q ss_pred CCeeecCCccCccccccccCCCCCCCCCC-Cccccccc
Q 006856 253 NDIVLCDGTCNCAFHQKCLDPPLDTESNQ-GWFCKFCE 289 (628)
Q Consensus 253 g~lllCDG~C~rayH~~CL~PPL~~~P~g-~W~Cp~C~ 289 (628)
+.||.|+ .|....|+.|++ +...|.+ .|+|..|.
T Consensus 2 n~ll~C~-~C~v~VH~~CYG--v~~~~~~~~W~C~~C~ 36 (36)
T PF13831_consen 2 NPLLFCD-NCNVAVHQSCYG--VSEVPDGDDWLCDRCE 36 (36)
T ss_dssp CEEEE-S-SS--EEEHHHHT---SS--SS-----HHH-
T ss_pred CceEEeC-CCCCcCChhhCC--cccCCCCCcEECCcCC
Confidence 5899999 599999999999 4455544 79999884
No 56
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=95.98 E-value=0.005 Score=50.17 Aligned_cols=42 Identities=12% Similarity=0.295 Sum_probs=32.2
Q ss_pred HHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhcc
Q 006856 507 VEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 548 (628)
Q Consensus 507 ~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~ 548 (628)
++-|+.+|..++++....-..|..+.||+..||+.||--++.
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 567999999999999999999999999999999999987764
No 57
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=95.40 E-value=0.0077 Score=72.24 Aligned_cols=47 Identities=26% Similarity=0.576 Sum_probs=43.3
Q ss_pred cccccccccccccCCCCCeeecCCccCccccccccCCCCCCCCCCCccccccc
Q 006856 237 EHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESNQGWFCKFCE 289 (628)
Q Consensus 237 e~~~C~vC~~~~~~~~g~lllCDG~C~rayH~~CL~PPL~~~P~g~W~Cp~C~ 289 (628)
-++.|.+|.. .++++||. .|++.||+.|..||+..+|...|-|-.|.
T Consensus 343 ~ddhcrf~~d-----~~~~lc~E-t~prvvhlEcv~hP~~~~~s~~~e~evc~ 389 (1414)
T KOG1473|consen 343 YDDHCRFCHD-----LGDLLCCE-TCPRVVHLECVFHPRFAVPSAFWECEVCN 389 (1414)
T ss_pred ecccccccCc-----ccceeecc-cCCceEEeeecCCccccCCCccchhhhhh
Confidence 3578999995 68999999 79999999999999999999999999997
No 58
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=94.52 E-value=0.02 Score=56.21 Aligned_cols=53 Identities=25% Similarity=0.644 Sum_probs=38.8
Q ss_pred ccccccc-cccCCCCCeeecCCccCccccccccCCCCCCCC--------CCCcccccccchhh
Q 006856 240 ICAKCKL-REAFPDNDIVLCDGTCNCAFHQKCLDPPLDTES--------NQGWFCKFCECKME 293 (628)
Q Consensus 240 ~C~vC~~-~~~~~~g~lllCDG~C~rayH~~CL~PPL~~~P--------~g~W~Cp~C~~k~~ 293 (628)
.|.+|+. +++..-|.||+|-| |-.+||..||+|.-...- .....|..|+.-..
T Consensus 1 ~C~~C~~~g~~~~kG~Lv~CQG-Cs~sYHk~CLG~Rs~ReHlVTKVg~d~FVLQCr~Cig~~~ 62 (175)
T PF15446_consen 1 TCDTCGYEGDDRNKGPLVYCQG-CSSSYHKACLGPRSQREHLVTKVGDDDFVLQCRRCIGIAH 62 (175)
T ss_pred CcccccCCCCCccCCCeEEcCc-cChHHHhhhcCCccccceeeEEEcCCceEEechhhcChhh
Confidence 4888864 23445789999997 999999999998754332 34567888875443
No 59
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=94.41 E-value=0.022 Score=63.61 Aligned_cols=52 Identities=27% Similarity=0.747 Sum_probs=42.2
Q ss_pred cccccccccccCCCCCeeecCCccCccccccccCCCCCC--CC-------CCCcccccccchh
Q 006856 239 IICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDT--ES-------NQGWFCKFCECKM 292 (628)
Q Consensus 239 ~~C~vC~~~~~~~~g~lllCDG~C~rayH~~CL~PPL~~--~P-------~g~W~Cp~C~~k~ 292 (628)
.+|.||-...+.+.|+||.|| .|....|-.|++-- +. +| -..|||-.|.+..
T Consensus 120 ~iCcVClg~rs~da~ei~qCd-~CGi~VHEgCYGv~-dn~si~s~~s~~stepWfCeaC~~Gv 180 (707)
T KOG0957|consen 120 VICCVCLGQRSVDAGEILQCD-KCGINVHEGCYGVL-DNVSIPSGSSDCSTEPWFCEACLYGV 180 (707)
T ss_pred eEEEEeecCccccccceeecc-ccCceecccccccc-cccccCCCCccCCCCchhhhhHhcCC
Confidence 389999988888899999999 79999999999853 22 22 2689999998653
No 60
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=94.13 E-value=0.062 Score=62.49 Aligned_cols=46 Identities=22% Similarity=0.390 Sum_probs=42.9
Q ss_pred HHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHH
Q 006856 507 VEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK 552 (628)
Q Consensus 507 ~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~K 552 (628)
+..|..+|..|.+|+.++-..+|.++||+...|+.||+++++..+.
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~s 613 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMS 613 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhh
Confidence 7899999999999999999999999999999999999999994443
No 61
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=93.38 E-value=0.14 Score=41.03 Aligned_cols=48 Identities=17% Similarity=0.279 Sum_probs=36.8
Q ss_pred CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhcc
Q 006856 496 RRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 548 (628)
Q Consensus 496 kR~r~rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~ 548 (628)
||+|..||.++.-.+-..+...+ ...+||+++|++.++|..|..|+..
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 62
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=89.99 E-value=0.074 Score=61.31 Aligned_cols=55 Identities=18% Similarity=0.518 Sum_probs=44.2
Q ss_pred ccccccccccccccCCCCCeeecCCccCccccccccCCCCCCCC-CCCcccccccch
Q 006856 236 HEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTES-NQGWFCKFCECK 291 (628)
Q Consensus 236 ~e~~~C~vC~~~~~~~~g~lllCDG~C~rayH~~CL~PPL~~~P-~g~W~Cp~C~~k 291 (628)
..+..|.+|+..+....|.|+.|. .|...||.+|+.-.+.... .+.|.|+.|...
T Consensus 16 ~~~~mc~l~~s~G~~~ag~m~ac~-~c~~~yH~~cvt~~~~~~~l~~gWrC~~crvC 71 (694)
T KOG4443|consen 16 IVCLMCPLCGSSGKGRAGRLLACS-DCGQKYHPYCVTSWAQHAVLSGGWRCPSCRVC 71 (694)
T ss_pred hhhhhhhhhccccccccCcchhhh-hhcccCCcchhhHHHhHHHhcCCcccCCceee
Confidence 456789999988877789999999 7999999999996555443 456999999653
No 63
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=88.88 E-value=0.23 Score=40.42 Aligned_cols=35 Identities=29% Similarity=0.768 Sum_probs=29.0
Q ss_pred cccccccccccccCCCCCeeecCCccCccccccccCC
Q 006856 237 EHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDP 273 (628)
Q Consensus 237 e~~~C~vC~~~~~~~~g~lllCDG~C~rayH~~CL~P 273 (628)
....|.+|+..-. +++++|.|. .|...||..|+..
T Consensus 4 ~~~~C~~Cg~~~~-~~dDiVvCp-~CgapyHR~C~~~ 38 (54)
T PF14446_consen 4 EGCKCPVCGKKFK-DGDDIVVCP-ECGAPYHRDCWEK 38 (54)
T ss_pred cCccChhhCCccc-CCCCEEECC-CCCCcccHHHHhh
Confidence 3468999997543 578999999 8999999999964
No 64
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=82.63 E-value=0.27 Score=59.73 Aligned_cols=48 Identities=17% Similarity=0.186 Sum_probs=38.5
Q ss_pred cccccccccccCCCCCeeecCCccCccccc-cccCCC--CCCCCCCCcccccccch
Q 006856 239 IICAKCKLREAFPDNDIVLCDGTCNCAFHQ-KCLDPP--LDTESNQGWFCKFCECK 291 (628)
Q Consensus 239 ~~C~vC~~~~~~~~g~lllCDG~C~rayH~-~CL~PP--L~~~P~g~W~Cp~C~~k 291 (628)
..|.+|+. ++-+|+|+|+|+.+||+ .||+-. -...+++.|+|+.|..+
T Consensus 429 rrl~Ie~~-----det~l~yysT~pqly~ll~cLd~~~~e~~L~d~i~~~~ee~~r 479 (1414)
T KOG1473|consen 429 RRLRIEGM-----DETLLWYYSTCPQLYHLLRCLDRTYVEMYLCDGIWERREEIIR 479 (1414)
T ss_pred eeeEEecC-----CCcEEEEecCcHHHHHHHHHhchHHHHHhhccchhhhHHHHHH
Confidence 46888884 67899999889999999 999833 23456899999999755
No 65
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=79.97 E-value=1 Score=51.99 Aligned_cols=48 Identities=29% Similarity=0.726 Sum_probs=40.0
Q ss_pred ccccccccccccCCCCCeeecCCccCccccccccCCCCCCCC-CCCcccccccch
Q 006856 238 HIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTES-NQGWFCKFCECK 291 (628)
Q Consensus 238 ~~~C~vC~~~~~~~~g~lllCDG~C~rayH~~CL~PPL~~~P-~g~W~Cp~C~~k 291 (628)
...|..|.. +|.+++|+ .|+.+||+.|..+++.... ...|.|..|-..
T Consensus 47 ~ts~~~~~~-----~gn~~~~~-~~~~s~h~~~~~~~~sp~~~~~~~~~~~~~~~ 95 (613)
T KOG4299|consen 47 ATSCGICKS-----GGNLLCCD-HCPASFHLECDKPPLSPDLKGSEINCSRCPKG 95 (613)
T ss_pred hhhcchhhh-----cCCccccc-cCccccchhccCcccCcccccccccccCCCcc
Confidence 567999996 67899999 7999999999999988332 578999999763
No 66
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=77.55 E-value=1.4 Score=36.54 Aligned_cols=47 Identities=21% Similarity=0.365 Sum_probs=31.1
Q ss_pred CCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhc
Q 006856 497 RSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNAR 547 (628)
Q Consensus 497 R~r~rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR 547 (628)
+++.+||+++...+-..+ ..+.....+||+++||++.+|..|-.-.+
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 445679999987665555 22347889999999999999999965544
No 67
>KOG3612 consensus PHD Zn-finger protein [General function prediction only]
Probab=75.95 E-value=1.9 Score=49.29 Aligned_cols=67 Identities=18% Similarity=0.283 Sum_probs=47.4
Q ss_pred ccccccccccccccccCCCCCeeecCCccCccccccccCCCCCCCC-CCCcccccccchhhHHhhhhccCCcccc
Q 006856 234 VHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTES-NQGWFCKFCECKMEIIESMNAHIGTSFS 307 (628)
Q Consensus 234 ~~~e~~~C~vC~~~~~~~~g~lllCDG~C~rayH~~CL~PPL~~~P-~g~W~Cp~C~~k~~~~~~~n~~~gt~~~ 307 (628)
....+.+|..|.- ++..|.|+ .|.+.||..|+.|-..... ...|.|+.|..... ....|...|..+.
T Consensus 56 ~~N~d~~cfechl-----pg~vl~c~-vc~Rs~h~~c~sp~~q~r~~s~p~~~p~p~s~k~-~~~~nqp~gn~~~ 123 (588)
T KOG3612|consen 56 SSNIDPFCFECHL-----PGAVLKCI-VCHRSFHENCQSPDPQKRNYSVPSDKPQPYSFKV-NELDNQPLGNTQN 123 (588)
T ss_pred ccCCCcccccccC-----Ccceeeee-hhhccccccccCcchhhccccccccCCcccccCC-Cccccccccchhc
Confidence 3456789999995 67899999 7999999999998654443 56899999974321 2233444454443
No 68
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=75.32 E-value=1.7 Score=48.99 Aligned_cols=56 Identities=18% Similarity=0.322 Sum_probs=46.2
Q ss_pred cccccccccccccccCCCCCeeecCCccCccccccccCCCCCCCCCCCcccccccchhh
Q 006856 235 HHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESNQGWFCKFCECKME 293 (628)
Q Consensus 235 ~~e~~~C~vC~~~~~~~~g~lllCDG~C~rayH~~CL~PPL~~~P~g~W~Cp~C~~k~~ 293 (628)
..+...|.+|......+++.++.|+ .|.++||+.|..|+... .+.|.|..|+....
T Consensus 80 ~~~e~~~nv~~s~~~~p~~e~~~~~-r~~~~~~q~~~i~~~~~--~~~~~~~~c~~~~~ 135 (464)
T KOG4323|consen 80 PSSELNPNVLTSETVLPENEKVICG-RCKSGYHQGCNIPRFPS--LDIGESTECVFPIF 135 (464)
T ss_pred CccccCCcccccccccCchhhhhhh-hhccCcccccCccCcCc--CCcccccccccccc
Confidence 4456789999988887888999999 89999999999987533 47899999987644
No 69
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=75.32 E-value=1.5 Score=47.98 Aligned_cols=47 Identities=30% Similarity=0.583 Sum_probs=35.3
Q ss_pred cccccccccccCCCCCeeecCCccCccccccccCCCCCCCCCCCcccccccch
Q 006856 239 IICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESNQGWFCKFCECK 291 (628)
Q Consensus 239 ~~C~vC~~~~~~~~g~lllCDG~C~rayH~~CL~PPL~~~P~g~W~Cp~C~~k 291 (628)
+.|++|-.... .|+.|--= .|...||..|.+|.|..- .=+||.|.+.
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 68999997543 45555445 699999999999988653 2379999863
No 70
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=73.27 E-value=4.4 Score=31.31 Aligned_cols=44 Identities=20% Similarity=0.406 Sum_probs=33.8
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccH
Q 006856 501 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYL 549 (628)
Q Consensus 501 rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k 549 (628)
.+++.+.+.|...| | ...+-.++|+.||++...|+.+......+
T Consensus 4 ~L~~~er~vi~~~y----~-~~~t~~eIa~~lg~s~~~V~~~~~~al~k 47 (50)
T PF04545_consen 4 QLPPREREVIRLRY----F-EGLTLEEIAERLGISRSTVRRILKRALKK 47 (50)
T ss_dssp TS-HHHHHHHHHHH----T-ST-SHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHh----c-CCCCHHHHHHHHCCcHHHHHHHHHHHHHH
Confidence 47899999999999 2 22346789999999999999987766553
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=72.28 E-value=4.7 Score=32.64 Aligned_cols=40 Identities=25% Similarity=0.473 Sum_probs=35.9
Q ss_pred CCHHHHHHHHHHHHhC--CCCCHHHHHHHHHHhCCCcchhhh
Q 006856 502 MPPNAVEKLRQVFAEN--ELPSRIVKENLSKELSLEPEKVNK 541 (628)
Q Consensus 502 ft~~Q~~~Le~~F~~~--~yPs~~~r~~LA~~lgLt~~QVki 541 (628)
+|+.|.+.|..+|..- .+|-...-.+||++||++..-|..
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
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=67.86 E-value=1.2 Score=52.52 Aligned_cols=52 Identities=23% Similarity=0.278 Sum_probs=45.2
Q ss_pred ccccccccccccccCCCCCeeecCCccCccccccccCC-CCCCCCCCCcccccccchhh
Q 006856 236 HEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDP-PLDTESNQGWFCKFCECKME 293 (628)
Q Consensus 236 ~e~~~C~vC~~~~~~~~g~lllCDG~C~rayH~~CL~P-PL~~~P~g~W~Cp~C~~k~~ 293 (628)
..++.|..|.. ....++|. .|-+.||..|+.| |+...+-+.|-|+.|..+..
T Consensus 504 ~~d~~~~~~~~-----~l~~l~~p-~~lrr~k~d~l~~~P~Kte~i~~~~~~~~Q~~~y 556 (696)
T KOG0383|consen 504 FHDISCEEQIK-----KLHLLLCP-HMLRRLKLDVLKPMPLKTELIGRVELSPCQKKYY 556 (696)
T ss_pred cchhhHHHHHH-----hhccccCc-hhhhhhhhhhccCCCccceeEEEEecCHHHHHHH
Confidence 45688999996 45788899 7999999999999 99999999999999987643
No 73
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=67.60 E-value=2 Score=38.16 Aligned_cols=46 Identities=30% Similarity=0.624 Sum_probs=30.8
Q ss_pred cccccccccCCCCCeeecCCccCccccccccCCCCCCCCCCCcccccccch
Q 006856 241 CAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESNQGWFCKFCECK 291 (628)
Q Consensus 241 C~vC~~~~~~~~g~lllCDG~C~rayH~~CL~PPL~~~P~g~W~Cp~C~~k 291 (628)
|..|.-++ ++-.+|++ .|...||+.|+.-.|..... .=.||-|+..
T Consensus 35 Cp~Ck~Pg--d~Cplv~g--~C~H~FH~hCI~kWl~~~~~-~~~CPmCR~~ 80 (85)
T PF12861_consen 35 CPDCKFPG--DDCPLVWG--KCSHNFHMHCILKWLSTQSS-KGQCPMCRQP 80 (85)
T ss_pred CCCccCCC--CCCceeec--cCccHHHHHHHHHHHccccC-CCCCCCcCCe
Confidence 44455433 23355655 49999999999887776432 3389999854
No 74
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=66.52 E-value=0.57 Score=39.60 Aligned_cols=54 Identities=20% Similarity=0.378 Sum_probs=20.3
Q ss_pred ccccccccccc-CCCCCeeecCC-ccCccccccccCCCCCCCC-------CCCcccccccchh
Q 006856 239 IICAKCKLREA-FPDNDIVLCDG-TCNCAFHQKCLDPPLDTES-------NQGWFCKFCECKM 292 (628)
Q Consensus 239 ~~C~vC~~~~~-~~~g~lllCDG-~C~rayH~~CL~PPL~~~P-------~g~W~Cp~C~~k~ 292 (628)
..|.+|..... .+.-..+.|+. .|...||+.||.-.+...+ .-.+-||.|..+.
T Consensus 3 ~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i 65 (70)
T PF11793_consen 3 LECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPI 65 (70)
T ss_dssp -S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEE
T ss_pred CCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCee
Confidence 45888886432 11224588973 5999999999964443222 2235699997653
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=65.97 E-value=12 Score=24.69 Aligned_cols=38 Identities=13% Similarity=0.434 Sum_probs=29.1
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhcc
Q 006856 501 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWF 543 (628)
Q Consensus 501 rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWF 543 (628)
.|+..+...+...|. +.+ ...++|+.+|++...|..|.
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
>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=65.45 E-value=0.7 Score=34.95 Aligned_cols=43 Identities=23% Similarity=0.539 Sum_probs=29.3
Q ss_pred ccccccccccCCCCCeeecCCccCccccccccCCCCCCCCCCCccccccc
Q 006856 240 ICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESNQGWFCKFCE 289 (628)
Q Consensus 240 ~C~vC~~~~~~~~g~lllCDG~C~rayH~~CL~PPL~~~P~g~W~Cp~C~ 289 (628)
.|.+|...-. .+..++... |...||..|+...+... -.||.|+
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 5888886543 244555553 99999999998766543 3888884
No 77
>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=65.40 E-value=4.9 Score=29.66 Aligned_cols=43 Identities=19% Similarity=0.306 Sum_probs=33.6
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhcc
Q 006856 501 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 548 (628)
Q Consensus 501 rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~ 548 (628)
.+++.+...|..+|... ..-.++|..+|++..+|..|....+.
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 78
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=64.44 E-value=1.8 Score=45.96 Aligned_cols=57 Identities=16% Similarity=0.219 Sum_probs=38.6
Q ss_pred cccccccccccc----CCCCCeeecCCccCccccccccCCCCCCCC---CCCcccccccchhhHH
Q 006856 238 HIICAKCKLREA----FPDNDIVLCDGTCNCAFHQKCLDPPLDTES---NQGWFCKFCECKMEII 295 (628)
Q Consensus 238 ~~~C~vC~~~~~----~~~g~lllCDG~C~rayH~~CL~PPL~~~P---~g~W~Cp~C~~k~~~~ 295 (628)
+..|..|-.... .-.+.||+|. .|..+||.+|+.-+..-+. --.|.|-.|.-..-|.
T Consensus 258 ~~~~~~~~~~~~~~~~~r~~S~I~C~-~C~~~~HP~Ci~M~~elv~~~KTY~W~C~~C~lC~IC~ 321 (381)
T KOG1512|consen 258 RNERKHFWDIQTNIIQSRRNSWIVCK-PCATRPHPYCVAMIPELVGQYKTYFWKCSSCELCRICL 321 (381)
T ss_pred hhhhhhhhcchhhhhhhhhccceeec-ccccCCCCcchhcCHHHHhHHhhcchhhcccHhhhccC
Confidence 446777753221 1246799999 7999999999986543322 4689999997554443
No 79
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=59.10 E-value=4.8 Score=43.38 Aligned_cols=50 Identities=24% Similarity=0.626 Sum_probs=36.2
Q ss_pred ccccccccccccCCCCCeeecCCccCccccccccCCCCCCCCCCCcccccccchhhHHhhh
Q 006856 238 HIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESNQGWFCKFCECKMEIIESM 298 (628)
Q Consensus 238 ~~~C~vC~~~~~~~~g~lllCDG~C~rayH~~CL~PPL~~~P~g~W~Cp~C~~k~~~~~~~ 298 (628)
.-+|..|....... |.||-|+ |.+||+=. +-+.+-.|+.|..+...++++
T Consensus 90 VHfCd~Cd~PI~IY-GRmIPCk-------HvFCl~CA---r~~~dK~Cp~C~d~VqrIeq~ 139 (389)
T KOG2932|consen 90 VHFCDRCDFPIAIY-GRMIPCK-------HVFCLECA---RSDSDKICPLCDDRVQRIEQI 139 (389)
T ss_pred eEeecccCCcceee-ecccccc-------hhhhhhhh---hcCccccCcCcccHHHHHHHh
Confidence 45899999776544 6888888 88888733 223467899998887766655
No 80
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=56.09 E-value=8.5 Score=40.89 Aligned_cols=58 Identities=21% Similarity=0.463 Sum_probs=35.9
Q ss_pred cccccccccccccccCCC--CCe---eecCCccCccccccccCCCCCCCCCCCcccccccchhhHH
Q 006856 235 HHEHIICAKCKLREAFPD--NDI---VLCDGTCNCAFHQKCLDPPLDTESNQGWFCKFCECKMEII 295 (628)
Q Consensus 235 ~~e~~~C~vC~~~~~~~~--g~l---llCDG~C~rayH~~CL~PPL~~~P~g~W~Cp~C~~k~~~~ 295 (628)
..++.+|.+|++.-.... +-+ +.=- .|+..||-+|.... .+-.-.=.||.|..+.+..
T Consensus 221 hl~d~vCaVCg~~~~~s~~eegvienty~L-sCnHvFHEfCIrGW--civGKkqtCPYCKekVdl~ 283 (328)
T KOG1734|consen 221 HLSDSVCAVCGQQIDVSVDEEGVIENTYKL-SCNHVFHEFCIRGW--CIVGKKQTCPYCKEKVDLK 283 (328)
T ss_pred CCCcchhHhhcchheeecchhhhhhhheee-ecccchHHHhhhhh--eeecCCCCCchHHHHhhHh
Confidence 356789999997542111 000 0111 59999999998743 2333455899998886643
No 81
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=56.05 E-value=8.6 Score=38.83 Aligned_cols=43 Identities=26% Similarity=0.733 Sum_probs=31.3
Q ss_pred cccccccccccC---CCCCeeecCCccCccccccccCCCCCCCCCCCcccccccch
Q 006856 239 IICAKCKLREAF---PDNDIVLCDGTCNCAFHQKCLDPPLDTESNQGWFCKFCECK 291 (628)
Q Consensus 239 ~~C~vC~~~~~~---~~g~lllCDG~C~rayH~~CL~PPL~~~P~g~W~Cp~C~~k 291 (628)
-+|.+|...+.. +....+.|. .|...||..|+.. . .||.|...
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 368888865432 234678999 6999999999983 1 39999743
No 82
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=54.88 E-value=6.7 Score=32.66 Aligned_cols=25 Identities=12% Similarity=0.488 Sum_probs=19.8
Q ss_pred HHHHHHHHhCCCcchhhhccchhcc
Q 006856 524 VKENLSKELSLEPEKVNKWFKNARY 548 (628)
Q Consensus 524 ~r~~LA~~lgLt~~QVkiWFqNrR~ 548 (628)
.-.+||.+||+++.||..|=..-+.
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK~~dkW 48 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWKSRDKW 48 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHhhhcch
Confidence 4568999999999999999544333
No 83
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=50.89 E-value=18 Score=34.93 Aligned_cols=51 Identities=22% Similarity=0.181 Sum_probs=40.7
Q ss_pred CCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhhh
Q 006856 500 HRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKV 556 (628)
Q Consensus 500 ~rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~K~~~~ 556 (628)
..+|+.|.+.|...+ ..-+..+||+.||++...|+.|.++.|.+.++.+..
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 234567999999999999999999988866666544
No 84
>PF13551 HTH_29: Winged helix-turn helix
Probab=50.65 E-value=26 Score=30.52 Aligned_cols=49 Identities=22% Similarity=0.350 Sum_probs=32.8
Q ss_pred CCCCCCCCHHHHHHHHHHHHhCCCCC--HHHHHHHHHHh-------CCCcchhhhccc
Q 006856 496 RRSFHRMPPNAVEKLRQVFAENELPS--RIVKENLSKEL-------SLEPEKVNKWFK 544 (628)
Q Consensus 496 kR~r~rft~~Q~~~Le~~F~~~~yPs--~~~r~~LA~~l-------gLt~~QVkiWFq 544 (628)
.+++.++++++.+.|.+++.+++... .-+...|+..| .+++..|..|+.
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 34444489999999999999887432 23344444433 567777887764
No 85
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=50.54 E-value=7.8 Score=34.76 Aligned_cols=31 Identities=26% Similarity=0.717 Sum_probs=25.2
Q ss_pred ccccccccccccCCCCCeeecCC-ccCccccccccC
Q 006856 238 HIICAKCKLREAFPDNDIVLCDG-TCNCAFHQKCLD 272 (628)
Q Consensus 238 ~~~C~vC~~~~~~~~g~lllCDG-~C~rayH~~CL~ 272 (628)
...|.+|+.. .|.+|.|.. .|..+||..|..
T Consensus 55 ~~~C~iC~~~----~G~~i~C~~~~C~~~fH~~CA~ 86 (110)
T PF13832_consen 55 KLKCSICGKS----GGACIKCSHPGCSTAFHPTCAR 86 (110)
T ss_pred CCcCcCCCCC----CceeEEcCCCCCCcCCCHHHHH
Confidence 4689999974 578899982 399999999975
No 86
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=50.25 E-value=16 Score=36.81 Aligned_cols=41 Identities=22% Similarity=0.465 Sum_probs=37.4
Q ss_pred CCCHHHHHHHHHHHHhC--CCCCHHHHHHHHHHhCCCcchhhh
Q 006856 501 RMPPNAVEKLRQVFAEN--ELPSRIVKENLSKELSLEPEKVNK 541 (628)
Q Consensus 501 rft~~Q~~~Le~~F~~~--~yPs~~~r~~LA~~lgLt~~QVki 541 (628)
.||+-|++.|..+|..- .||-.-.-.+||++||++..-+.-
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 689999999999999999987654
No 87
>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=48.95 E-value=11 Score=32.89 Aligned_cols=31 Identities=19% Similarity=0.525 Sum_probs=22.3
Q ss_pred ccccccccccccCCCCCeeecCCccCccccccccC
Q 006856 238 HIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLD 272 (628)
Q Consensus 238 ~~~C~vC~~~~~~~~g~lllCDG~C~rayH~~CL~ 272 (628)
...|.+|++.-. .+.++.. .|...||..|+.
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 467999998653 3444444 378999999974
No 88
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=47.67 E-value=16 Score=45.43 Aligned_cols=51 Identities=20% Similarity=0.489 Sum_probs=36.4
Q ss_pred cccccccccccc--cCCCCCeeecCCccCccccccccCCCCCCCCCCCcccccccch
Q 006856 237 EHIICAKCKLRE--AFPDNDIVLCDGTCNCAFHQKCLDPPLDTESNQGWFCKFCECK 291 (628)
Q Consensus 237 e~~~C~vC~~~~--~~~~g~lllCDG~C~rayH~~CL~PPL~~~P~g~W~Cp~C~~k 291 (628)
...+|.+|+..- ..+++..|-|. .|.-..-..|+. -+..+|.=.||.|..+
T Consensus 16 ~~qiCqICGD~vg~~~~Ge~FVAC~-eC~FPVCrpCYE---YEr~eG~q~CPqCktr 68 (1079)
T PLN02638 16 GGQVCQICGDNVGKTVDGEPFVACD-VCAFPVCRPCYE---YERKDGNQSCPQCKTK 68 (1079)
T ss_pred CCceeeecccccCcCCCCCEEEEec-cCCCccccchhh---hhhhcCCccCCccCCc
Confidence 346899999631 13466789999 797777677775 3445788899999754
No 89
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=47.37 E-value=17 Score=28.93 Aligned_cols=24 Identities=4% Similarity=0.292 Sum_probs=17.6
Q ss_pred HHHHHHHHhCCCcchhhhccchhc
Q 006856 524 VKENLSKELSLEPEKVNKWFKNAR 547 (628)
Q Consensus 524 ~r~~LA~~lgLt~~QVkiWFqNrR 547 (628)
....||+.+|++..+|..||.++.
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 567889999999999999998874
No 90
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=47.08 E-value=14 Score=36.84 Aligned_cols=38 Identities=42% Similarity=0.878 Sum_probs=27.9
Q ss_pred CCCCeeecCCccCccccccccCCCCCCCC------------------CCCccccccc
Q 006856 251 PDNDIVLCDGTCNCAFHQKCLDPPLDTES------------------NQGWFCKFCE 289 (628)
Q Consensus 251 ~~g~lllCDG~C~rayH~~CL~PPL~~~P------------------~g~W~Cp~C~ 289 (628)
.++.|.-|. .|.++||+..|-|+-...+ ...|.|..|.
T Consensus 120 ~~nVLFRC~-~C~RawH~~HLP~~~~~~~~~~~~~~~~~~~~R~~EYs~~W~C~dC~ 175 (175)
T PF15446_consen 120 PDNVLFRCT-SCHRAWHFEHLPPPSGTTSDDDDDDDTDLRSQRLKEYSIDWQCKDCA 175 (175)
T ss_pred hhheEEecC-CccceeehhhCCCCcCCCCCcccccchhHHHHHHHHhCCccccCCCC
Confidence 357788899 6999999999976532211 3579998883
No 91
>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=46.77 E-value=13 Score=41.90 Aligned_cols=56 Identities=18% Similarity=0.452 Sum_probs=36.8
Q ss_pred ccccccccccC-CCCCeeecCCccCccccccccCC--------CCCCC---CCCCcccccccchhhHHh
Q 006856 240 ICAKCKLREAF-PDNDIVLCDGTCNCAFHQKCLDP--------PLDTE---SNQGWFCKFCECKMEIIE 296 (628)
Q Consensus 240 ~C~vC~~~~~~-~~g~lllCDG~C~rayH~~CL~P--------PL~~~---P~g~W~Cp~C~~k~~~~~ 296 (628)
.|.+|...+.. ++--.|.|| .|..+-|..|--- -.... .+..++|..|....+.+.
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 46667765432 345678999 7999999998621 11111 256899999987655443
No 92
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=46.13 E-value=14 Score=28.24 Aligned_cols=40 Identities=13% Similarity=0.333 Sum_probs=21.3
Q ss_pred CCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccc
Q 006856 500 HRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFK 544 (628)
Q Consensus 500 ~rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFq 544 (628)
..||.+|...++..+.+. ....+||+.||.++..|..|..
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 468999999999886533 4566799999999999988754
No 93
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=46.04 E-value=24 Score=26.50 Aligned_cols=42 Identities=19% Similarity=0.335 Sum_probs=31.6
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhcc
Q 006856 501 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 548 (628)
Q Consensus 501 rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~ 548 (628)
.+++.+.+.+..++. .+ ...+||+.||++...|..|.+.-+.
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 5589999999999999998875544
No 94
>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=45.35 E-value=6.4 Score=33.41 Aligned_cols=46 Identities=26% Similarity=0.542 Sum_probs=27.6
Q ss_pred cccccccccccCC--------CCCeeecCCccCccccccccCCCCCCCCCCCccccccc
Q 006856 239 IICAKCKLREAFP--------DNDIVLCDGTCNCAFHQKCLDPPLDTESNQGWFCKFCE 289 (628)
Q Consensus 239 ~~C~vC~~~~~~~--------~g~lllCDG~C~rayH~~CL~PPL~~~P~g~W~Cp~C~ 289 (628)
+.|.+|...-... .+-.+.-. .|...||..|+...|... ..||.|.
T Consensus 20 d~C~IC~~~l~~~~~~~~~~~~~~~i~~~-~C~H~FH~~Ci~~Wl~~~----~~CP~CR 73 (73)
T PF12678_consen 20 DNCAICREPLEDPCPECQAPQDECPIVWG-PCGHIFHFHCISQWLKQN----NTCPLCR 73 (73)
T ss_dssp SBETTTTSBTTSTTCCHHHCTTTS-EEEE-TTSEEEEHHHHHHHHTTS----SB-TTSS
T ss_pred CcccccChhhhChhhhhcCCccccceEec-ccCCCEEHHHHHHHHhcC----CcCCCCC
Confidence 3488887543111 12223333 699999999998766544 3899884
No 95
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=45.30 E-value=14 Score=40.37 Aligned_cols=39 Identities=18% Similarity=0.467 Sum_probs=34.0
Q ss_pred CeeecCCccCccccccc--cCCCCCCCC-CCCcccccccchhh
Q 006856 254 DIVLCDGTCNCAFHQKC--LDPPLDTES-NQGWFCKFCECKME 293 (628)
Q Consensus 254 ~lllCDG~C~rayH~~C--L~PPL~~~P-~g~W~Cp~C~~k~~ 293 (628)
.++.|+ .|..+||..| ++.+....| ...|+|..|....+
T Consensus 74 ~~~~cd-~C~~~~~~ec~~v~~~~~e~p~~~~~~c~~c~~~~~ 115 (345)
T KOG1632|consen 74 LMEQCD-LCEDWYHGECWEVGTAEKEAPKEDPKVCDECKEAQD 115 (345)
T ss_pred hhhccc-cccccccccccccCchhhcCCccccccccccchhhh
Confidence 789999 5999999999 999888887 57899999987654
No 96
>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=44.94 E-value=18 Score=28.10 Aligned_cols=34 Identities=24% Similarity=0.367 Sum_probs=26.2
Q ss_pred ccccccccccccCCCCCeeecCCccCccccccccC
Q 006856 238 HIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLD 272 (628)
Q Consensus 238 ~~~C~vC~~~~~~~~g~lllCDG~C~rayH~~CL~ 272 (628)
-.+|.+|+..-+.....-+.|. .|...+|..|+.
T Consensus 11 ~~~C~~C~~~i~g~~~~g~~C~-~C~~~~H~~C~~ 44 (53)
T PF00130_consen 11 PTYCDVCGKFIWGLGKQGYRCS-WCGLVCHKKCLS 44 (53)
T ss_dssp TEB-TTSSSBECSSSSCEEEET-TTT-EEETTGGC
T ss_pred CCCCcccCcccCCCCCCeEEEC-CCCChHhhhhhh
Confidence 3689999987744467789999 699999999986
No 97
>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=43.87 E-value=17 Score=29.71 Aligned_cols=43 Identities=23% Similarity=0.660 Sum_probs=30.0
Q ss_pred ccccccccccCC---CCCeeecCCccCccccccccCCCC-CCCC--CCCc
Q 006856 240 ICAKCKLREAFP---DNDIVLCDGTCNCAFHQKCLDPPL-DTES--NQGW 283 (628)
Q Consensus 240 ~C~vC~~~~~~~---~g~lllCDG~C~rayH~~CL~PPL-~~~P--~g~W 283 (628)
.|.+|+..-..+ .|.+|-|. .|...|-...++|.- ...| ..+|
T Consensus 4 ~CP~CG~~iev~~~~~GeiV~Cp-~CGaeleVv~~~p~~L~~ap~~~eDw 52 (54)
T TIGR01206 4 ECPDCGAEIELENPELGELVICD-ECGAELEVVSLDPLRLEAAPEEAEDW 52 (54)
T ss_pred CCCCCCCEEecCCCccCCEEeCC-CCCCEEEEEeCCCCEEEeCccccccc
Confidence 588888543322 27899999 799999999999852 2233 4566
No 98
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=43.52 E-value=15 Score=39.43 Aligned_cols=39 Identities=33% Similarity=0.388 Sum_probs=34.6
Q ss_pred HhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHh
Q 006856 515 AENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKA 553 (628)
Q Consensus 515 ~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~K~ 553 (628)
..++||+.....-|+...+|+..||.+||-|.|+...+.
T Consensus 117 ~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~ 155 (342)
T KOG0773|consen 117 RLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKE 155 (342)
T ss_pred hhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhc
Confidence 356899999999999999999999999999999965544
No 99
>PHA02955 hypothetical protein; Provisional
Probab=42.38 E-value=27 Score=35.91 Aligned_cols=49 Identities=8% Similarity=0.065 Sum_probs=41.3
Q ss_pred CCCCCHHHHHHHHHHHHhC-CCCCHHHHHHHHHHhCCCcchhhhccchhc
Q 006856 499 FHRMPPNAVEKLRQVFAEN-ELPSRIVKENLSKELSLEPEKVNKWFKNAR 547 (628)
Q Consensus 499 r~rft~~Q~~~Le~~F~~~-~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR 547 (628)
+.-=...|+..|-+.|.+. .-.+.++|.++|.+||+....|..||++.=
T Consensus 55 C~sna~~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t~~ 104 (213)
T PHA02955 55 CNSDEEKNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKTDL 104 (213)
T ss_pred hcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccchh
Confidence 3333667888999999988 778899999999999999988999999853
No 100
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=40.73 E-value=5.4 Score=44.17 Aligned_cols=56 Identities=21% Similarity=0.437 Sum_probs=34.8
Q ss_pred cccccccccccCCCCCeeecCCccCccccccccCCCCCCCCCCCcccccccchhhHHhh
Q 006856 239 IICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESNQGWFCKFCECKMEIIES 297 (628)
Q Consensus 239 ~~C~vC~~~~~~~~g~lllCDG~C~rayH~~CL~PPL~~~P~g~W~Cp~C~~k~~~~~~ 297 (628)
..|.+|-..- ....++---. +|...||..||.-.....|.. --||.|..+..+...
T Consensus 5 A~C~Ic~d~~-p~~~~l~~i~-~cGhifh~~cl~qwfe~~Ps~-R~cpic~ik~~~r~~ 60 (465)
T KOG0827|consen 5 AECHICIDGR-PNDHELGPIG-TCGHIFHTTCLTQWFEGDPSN-RGCPICQIKLQERHV 60 (465)
T ss_pred ceeeEeccCC-cccccccccc-chhhHHHHHHHHHHHccCCcc-CCCCceeecccceee
Confidence 5789995432 1223343333 799999999998765555421 269999855444333
No 101
>PRK10072 putative transcriptional regulator; Provisional
Probab=40.39 E-value=14 Score=33.38 Aligned_cols=40 Identities=15% Similarity=0.199 Sum_probs=31.6
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhcc
Q 006856 502 MPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 548 (628)
Q Consensus 502 ft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~ 548 (628)
.+...+..|...... ++.+||+.||++...|..|.+.+|.
T Consensus 33 ~~~~eik~LR~~~gl-------TQ~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 33 TSFTEFEQLRKGTGL-------KIDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred CChHHHHHHHHHcCC-------CHHHHHHHhCCCHHHHHHHHcCCCC
Confidence 366667777544433 3789999999999999999999886
No 102
>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=40.04 E-value=26 Score=31.15 Aligned_cols=46 Identities=22% Similarity=0.281 Sum_probs=34.8
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHH
Q 006856 501 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLAL 551 (628)
Q Consensus 501 rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~ 551 (628)
.+++.|.+.|...|-. .+ .-.+||+.+|+++..|..|.+.-+.+.+
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 4569999999999999999988777543
No 103
>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=40.02 E-value=11 Score=32.56 Aligned_cols=37 Identities=14% Similarity=0.131 Sum_probs=28.0
Q ss_pred HHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhc
Q 006856 511 RQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNAR 547 (628)
Q Consensus 511 e~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR 547 (628)
++.|....|-..-...+||+.||+++..|+.|+.+..
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 3445544555566778999999999999999988643
No 104
>KOG1080 consensus Histone H3 (Lys4) methyltransferase complex, subunit SET1 and related methyltransferases [Chromatin structure and dynamics; Transcription]
Probab=39.69 E-value=28 Score=43.19 Aligned_cols=51 Identities=29% Similarity=0.761 Sum_probs=42.7
Q ss_pred ccccccccccccCCCCCeeecCCccCccccccccCCCCCCCCCCCcccccccc
Q 006856 238 HIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESNQGWFCKFCEC 290 (628)
Q Consensus 238 ~~~C~vC~~~~~~~~g~lllCDG~C~rayH~~CL~PPL~~~P~g~W~Cp~C~~ 290 (628)
-..|.+|........+.++.|| .|....|..|+.+ +.......|.|..|..
T Consensus 573 t~~c~~~~~~~~~~~n~~~~~~-~~~~~~~s~~~g~-~~~~~~~~~~~~~~~~ 623 (1005)
T KOG1080|consen 573 TERCAVCRDDEDWEKNVSIICD-RCTRSVHSECYGN-LKSYDGTSWVCDSCET 623 (1005)
T ss_pred cccccccccccccccceeeeec-cccccCCCccccc-CCCCCCCcchhhcccc
Confidence 3579999987777789999999 7999999999974 4555567899999986
No 105
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=39.04 E-value=29 Score=32.06 Aligned_cols=46 Identities=9% Similarity=-0.033 Sum_probs=35.4
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHH
Q 006856 501 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLAL 551 (628)
Q Consensus 501 rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~ 551 (628)
.+++.+.+.+...|-+. -.-.+||+.||+++..|+.|....|.+.+
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 56888888877665432 34678999999999999999887777443
No 106
>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=38.91 E-value=6.1 Score=31.22 Aligned_cols=44 Identities=27% Similarity=0.684 Sum_probs=26.0
Q ss_pred ccccccccccCCCCCeee-cCCccC---ccccccccCCCCCCCCCCCcccccc
Q 006856 240 ICAKCKLREAFPDNDIVL-CDGTCN---CAFHQKCLDPPLDTESNQGWFCKFC 288 (628)
Q Consensus 240 ~C~vC~~~~~~~~g~lll-CDG~C~---rayH~~CL~PPL~~~P~g~W~Cp~C 288 (628)
+|.+|...+. +++.++. |. |. ..+|..||...+... +...|+.|
T Consensus 1 ~CrIC~~~~~-~~~~l~~PC~--C~G~~~~vH~~Cl~~W~~~~--~~~~C~iC 48 (49)
T smart00744 1 ICRICHDEGD-EGDPLVSPCR--CKGSLKYVHQECLERWINES--GNKTCEIC 48 (49)
T ss_pred CccCCCCCCC-CCCeeEeccc--cCCchhHHHHHHHHHHHHHc--CCCcCCCC
Confidence 4777776222 3344432 33 55 579999998766443 23478777
No 107
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=38.60 E-value=43 Score=30.86 Aligned_cols=44 Identities=11% Similarity=0.132 Sum_probs=29.7
Q ss_pred CCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhc
Q 006856 500 HRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNAR 547 (628)
Q Consensus 500 ~rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR 547 (628)
.+||.+.....-....++.+ .-.+||+++|+++.+|..|.+-.|
T Consensus 11 r~ys~EfK~~aV~~~~~~g~----sv~evA~e~gIs~~tl~~W~r~y~ 54 (121)
T PRK09413 11 RRRTTQEKIAIVQQSFEPGM----TVSLVARQHGVAASQLFLWRKQYQ 54 (121)
T ss_pred CCCCHHHHHHHHHHHHcCCC----CHHHHHHHHCcCHHHHHHHHHHHh
Confidence 45788775544333344433 345789999999999999955443
No 108
>PRK04217 hypothetical protein; Provisional
Probab=38.51 E-value=40 Score=31.28 Aligned_cols=49 Identities=22% Similarity=0.131 Sum_probs=38.3
Q ss_pred CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHH
Q 006856 499 FHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK 552 (628)
Q Consensus 499 r~rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~K 552 (628)
-..++.+|.+++...|.+.- .-.+||+.||++...|...+...|.+.+.
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 66789999999999999999888774433
No 109
>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=38.43 E-value=14 Score=28.33 Aligned_cols=21 Identities=5% Similarity=0.234 Sum_probs=19.7
Q ss_pred HHHHHhCCCcchhhhccchhc
Q 006856 527 NLSKELSLEPEKVNKWFKNAR 547 (628)
Q Consensus 527 ~LA~~lgLt~~QVkiWFqNrR 547 (628)
+||+.+|++...|..|+.|++
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 699999999999999999985
No 110
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=38.37 E-value=18 Score=27.94 Aligned_cols=25 Identities=12% Similarity=0.295 Sum_probs=20.9
Q ss_pred HHHHHHHHhCCCcchhhhccchhcc
Q 006856 524 VKENLSKELSLEPEKVNKWFKNARY 548 (628)
Q Consensus 524 ~r~~LA~~lgLt~~QVkiWFqNrR~ 548 (628)
...+||+.+|+++..|..|+.+.|.
T Consensus 11 s~~~la~~~gis~~~i~~~~~g~~~ 35 (55)
T PF01381_consen 11 SQKELAEKLGISRSTISRIENGKRN 35 (55)
T ss_dssp -HHHHHHHHTS-HHHHHHHHTTSST
T ss_pred CHHHHHHHhCCCcchhHHHhcCCCC
Confidence 3488999999999999999999774
No 111
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=38.17 E-value=16 Score=31.34 Aligned_cols=30 Identities=27% Similarity=0.733 Sum_probs=24.4
Q ss_pred cccccccccccCCCCCeeecCC-ccCccccccccC
Q 006856 239 IICAKCKLREAFPDNDIVLCDG-TCNCAFHQKCLD 272 (628)
Q Consensus 239 ~~C~vC~~~~~~~~g~lllCDG-~C~rayH~~CL~ 272 (628)
..|.+|+.. .|-.|-|.- .|...||..|..
T Consensus 37 ~~C~~C~~~----~Ga~i~C~~~~C~~~fH~~CA~ 67 (90)
T PF13771_consen 37 LKCSICKKK----GGACIGCSHPGCSRSFHVPCAR 67 (90)
T ss_pred CCCcCCCCC----CCeEEEEeCCCCCcEEChHHHc
Confidence 579999963 367888873 599999999985
No 112
>PF13518 HTH_28: Helix-turn-helix domain
Probab=36.41 E-value=19 Score=27.42 Aligned_cols=25 Identities=20% Similarity=0.492 Sum_probs=21.5
Q ss_pred HHHHHHHHhCCCcchhhhccchhcc
Q 006856 524 VKENLSKELSLEPEKVNKWFKNARY 548 (628)
Q Consensus 524 ~r~~LA~~lgLt~~QVkiWFqNrR~ 548 (628)
...++|+++|++..+|..|.+..+.
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHHh
Confidence 4566999999999999999887665
No 113
>PHA02929 N1R/p28-like protein; Provisional
Probab=35.14 E-value=13 Score=38.73 Aligned_cols=48 Identities=23% Similarity=0.411 Sum_probs=31.3
Q ss_pred ccccccccccccCCCC---C-eeecCCccCccccccccCCCCCCCCCCCcccccccch
Q 006856 238 HIICAKCKLREAFPDN---D-IVLCDGTCNCAFHQKCLDPPLDTESNQGWFCKFCECK 291 (628)
Q Consensus 238 ~~~C~vC~~~~~~~~g---~-lllCDG~C~rayH~~CL~PPL~~~P~g~W~Cp~C~~k 291 (628)
...|.+|...-...+. . .++. .|...||..|+.+.+...+ .||.|...
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 4679999864221110 0 1333 3999999999987665432 79999855
No 114
>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=34.98 E-value=14 Score=33.89 Aligned_cols=49 Identities=20% Similarity=0.628 Sum_probs=31.6
Q ss_pred ccccccccccccCCCCCeeec------CCcc---CccccccccCCCCCCC-----CCCCcccccccc
Q 006856 238 HIICAKCKLREAFPDNDIVLC------DGTC---NCAFHQKCLDPPLDTE-----SNQGWFCKFCEC 290 (628)
Q Consensus 238 ~~~C~vC~~~~~~~~g~lllC------DG~C---~rayH~~CL~PPL~~~-----P~g~W~Cp~C~~ 290 (628)
...|..|+.... +..+.| . .| ...|=..||.-..... .+..|.||.|..
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 357888987653 344566 4 46 6667667765443332 367899999964
No 115
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=34.84 E-value=14 Score=38.43 Aligned_cols=49 Identities=27% Similarity=0.518 Sum_probs=33.0
Q ss_pred cccccccccccCCCCCeeecCCccCccccccccCCCCCCCC----CCCcccccccch
Q 006856 239 IICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTES----NQGWFCKFCECK 291 (628)
Q Consensus 239 ~~C~vC~~~~~~~~g~lllCDG~C~rayH~~CL~PPL~~~P----~g~W~Cp~C~~k 291 (628)
--|..|+..-. .++.+-- .|...||+.|++-.-...| .....||-|...
T Consensus 51 pNC~LC~t~La--~gdt~RL--vCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~e 103 (299)
T KOG3970|consen 51 PNCRLCNTPLA--SGDTTRL--VCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQE 103 (299)
T ss_pred CCCceeCCccc--cCcceee--hhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCc
Confidence 45888885433 4444433 3889999999985544444 356799999754
No 116
>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=34.28 E-value=24 Score=26.97 Aligned_cols=25 Identities=4% Similarity=-0.039 Sum_probs=22.1
Q ss_pred HHHHHHHHhCCCcchhhhccchhcc
Q 006856 524 VKENLSKELSLEPEKVNKWFKNARY 548 (628)
Q Consensus 524 ~r~~LA~~lgLt~~QVkiWFqNrR~ 548 (628)
...+||+.+|++...|..|+..++.
T Consensus 17 tq~~lA~~~gvs~~~vs~~e~g~~~ 41 (58)
T TIGR03070 17 TQADLADLAGVGLRFIRDVENGKPT 41 (58)
T ss_pred CHHHHHHHhCCCHHHHHHHHCCCCC
Confidence 3688999999999999999988764
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=33.44 E-value=39 Score=27.32 Aligned_cols=36 Identities=14% Similarity=0.240 Sum_probs=27.9
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccc
Q 006856 505 NAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFK 544 (628)
Q Consensus 505 ~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFq 544 (628)
.|++.|+-.|. +++.+.. +||+.||++++.|+.=..
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
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=33.28 E-value=43 Score=32.61 Aligned_cols=47 Identities=6% Similarity=0.128 Sum_probs=35.6
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHH
Q 006856 501 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK 552 (628)
Q Consensus 501 rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~K 552 (628)
.+++.+.+.|.-.|-++ -.-.+||+.||++...|+++....|.+.++
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 345789999999999999999887774443
No 119
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=33.24 E-value=1.1e+02 Score=34.68 Aligned_cols=98 Identities=24% Similarity=0.375 Sum_probs=52.9
Q ss_pred HHHHHHHHHhhhhhHHHHH-hhhhccCCCCCCCCC-----------cccCCCCcc-cc---c---cccccccccccCCCC
Q 006856 193 LQRAKKQILKCKIGIRDAI-RQLDSLSSVGCIEGS-----------VIATDGSVH-HE---H---IICAKCKLREAFPDN 253 (628)
Q Consensus 193 l~rak~qi~k~K~~ird~l-~~ld~l~~~~~i~~s-----------~~~~dg~~~-~e---~---~~C~vC~~~~~~~~g 253 (628)
.+..-.+...|-..|+|.| +.+...+|.+||.=. +++.+..+. .. . -.|.+|+......+|
T Consensus 330 yq~tlekC~~Cg~~I~d~iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAPrCs~C~~PI~P~~G 409 (468)
T KOG1701|consen 330 YQDTLEKCNKCGEPIMDRILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAPRCSVCGNPILPRDG 409 (468)
T ss_pred HHHHHHHHhhhhhHHHHHHHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcCcchhhccCCccCCCC
Confidence 5555555677777788765 778888887776411 112222211 11 1 258889865543322
Q ss_pred --CeeecCCccCccccccccC-----CCCCCCC--------CCCcccccccch
Q 006856 254 --DIVLCDGTCNCAFHQKCLD-----PPLDTES--------NQGWFCKFCECK 291 (628)
Q Consensus 254 --~lllCDG~C~rayH~~CL~-----PPL~~~P--------~g~W~Cp~C~~k 291 (628)
+.|--. .-++-||..|+. -.|.... ++.-+|..|..+
T Consensus 410 ~~etvRvv-amdr~fHv~CY~CEDCg~~LS~e~e~qgCyPld~HllCk~Ch~~ 461 (468)
T KOG1701|consen 410 KDETVRVV-AMDRDFHVNCYKCEDCGLLLSSEEEGQGCYPLDGHLLCKTCHLK 461 (468)
T ss_pred CcceEEEE-EccccccccceehhhcCccccccCCCCcceeccCceeechhhhh
Confidence 123333 347889998873 2222111 556777777543
No 120
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=32.72 E-value=35 Score=42.39 Aligned_cols=51 Identities=18% Similarity=0.447 Sum_probs=36.8
Q ss_pred cccccccccccc--cCCCCCeeecCCccCccccccccCCCCCCCCCCCcccccccch
Q 006856 237 EHIICAKCKLRE--AFPDNDIVLCDGTCNCAFHQKCLDPPLDTESNQGWFCKFCECK 291 (628)
Q Consensus 237 e~~~C~vC~~~~--~~~~g~lllCDG~C~rayH~~CL~PPL~~~P~g~W~Cp~C~~k 291 (628)
...+|.+|+..- ..+++..|-|. .|.-..--.|+. .+..+|.=.||+|..+
T Consensus 14 ~~~~c~iCGd~vg~~~~Ge~FVAC~-eC~fpvCr~cye---ye~~~g~~~cp~c~t~ 66 (1044)
T PLN02915 14 DAKTCRVCGDEVGVKEDGQPFVACH-VCGFPVCKPCYE---YERSEGNQCCPQCNTR 66 (1044)
T ss_pred CcchhhccccccCcCCCCCEEEEec-cCCCccccchhh---hhhhcCCccCCccCCc
Confidence 457899999642 13466789999 798777777875 3445788899999755
No 121
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=32.54 E-value=38 Score=32.35 Aligned_cols=47 Identities=9% Similarity=0.292 Sum_probs=34.9
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHH
Q 006856 501 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK 552 (628)
Q Consensus 501 rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~K 552 (628)
.+++.+.+.|...|-+ ...-.+||+.||+++..|++++...|.+.++
T Consensus 129 ~L~~~~r~i~~l~~~~-----g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 175 (179)
T PRK12514 129 ELEKDRAAAVRRAYLE-----GLSYKELAERHDVPLNTMRTWLRRSLLKLRE 175 (179)
T ss_pred hCCHHHHHHHHHHHHc-----CCCHHHHHHHHCCChHHHHHHHHHHHHHHHH
Confidence 4677777777766532 2235789999999999999999888874443
No 122
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=32.14 E-value=11 Score=47.55 Aligned_cols=58 Identities=14% Similarity=0.004 Sum_probs=50.2
Q ss_pred CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHh
Q 006856 496 RRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKA 553 (628)
Q Consensus 496 kR~r~rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~K~ 553 (628)
+-.+++++..|+..|..+|+...||.-...+.||+-|++-.+.+-.||+|++.++.++
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 3357788999999999999999999999999999999999999888888866644444
No 123
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=31.47 E-value=42 Score=31.45 Aligned_cols=47 Identities=13% Similarity=0.058 Sum_probs=35.3
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHH
Q 006856 501 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK 552 (628)
Q Consensus 501 rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~K 552 (628)
.+++.+.+.|...|-. .-.-.+||+.||+++..|+.|....|.+.++
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 2234589999999999999999877665444
No 124
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=31.09 E-value=41 Score=31.44 Aligned_cols=48 Identities=17% Similarity=0.241 Sum_probs=35.7
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHh
Q 006856 501 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKA 553 (628)
Q Consensus 501 rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~K~ 553 (628)
.+++.+.+.|...|-. .-.-.+||+.||+++..|..|..-.|.+.++.
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 3677777777665532 23448999999999999999999888855543
No 125
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=30.83 E-value=27 Score=26.58 Aligned_cols=26 Identities=23% Similarity=0.445 Sum_probs=18.3
Q ss_pred HHHHHHHHHHhCCCcchhhhccchhc
Q 006856 522 RIVKENLSKELSLEPEKVNKWFKNAR 547 (628)
Q Consensus 522 ~~~r~~LA~~lgLt~~QVkiWFqNrR 547 (628)
.....++|+.||++...|..|.+.-+
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 45678899999999999999987654
No 126
>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=30.81 E-value=21 Score=25.17 Aligned_cols=28 Identities=21% Similarity=0.628 Sum_probs=11.7
Q ss_pred ccccccccccCCCCCeeecCCccCccccccc
Q 006856 240 ICAKCKLREAFPDNDIVLCDGTCNCAFHQKC 270 (628)
Q Consensus 240 ~C~vC~~~~~~~~g~lllCDG~C~rayH~~C 270 (628)
.|.+|+.... ++..-.|. .|+-..|..|
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 5889997653 34788899 7999999887
No 127
>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=30.15 E-value=27 Score=26.17 Aligned_cols=22 Identities=14% Similarity=0.200 Sum_probs=18.4
Q ss_pred HHHHHHHhCCCcchhhhccchh
Q 006856 525 KENLSKELSLEPEKVNKWFKNA 546 (628)
Q Consensus 525 r~~LA~~lgLt~~QVkiWFqNr 546 (628)
..++|+.+|+++..|..|.++-
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g 24 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIG 24 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 3578999999999999996543
No 128
>KOG1081 consensus Transcription factor NSD1 and related SET domain proteins [Transcription]
Probab=29.69 E-value=34 Score=39.03 Aligned_cols=46 Identities=24% Similarity=0.350 Sum_probs=31.5
Q ss_pred ccccccccccccccCCCCCeeecCCccCccccccccCCCCCCCCCCCcccccccc
Q 006856 236 HEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESNQGWFCKFCEC 290 (628)
Q Consensus 236 ~e~~~C~vC~~~~~~~~g~lllCDG~C~rayH~~CL~PPL~~~P~g~W~Cp~C~~ 290 (628)
.+...|.+|.. ++.+|+|+ .|..++|-.|.. ...|...|.|..|..
T Consensus 87 ~~~~~c~vc~~-----ggs~v~~~-s~~~~~~r~c~~---~~~~~c~~~~~d~~~ 132 (463)
T KOG1081|consen 87 IEPSECFVCFK-----GGSLVTCK-SRIQAPHRKCKP---AQLEKCSKRCTDCRA 132 (463)
T ss_pred CCcchhccccC-----CCccceec-cccccccccCcC---ccCcccccCCcceee
Confidence 34568999995 67899999 577777777754 334456666665543
No 129
>PRK00118 putative DNA-binding protein; Validated
Probab=29.53 E-value=52 Score=30.23 Aligned_cols=44 Identities=9% Similarity=0.169 Sum_probs=33.7
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHH
Q 006856 502 MPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLA 550 (628)
Q Consensus 502 ft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~ 550 (628)
+++.|.+.+..+|.+ ...-.+||+.+|+++..|..|....|.+.
T Consensus 18 L~ekqRevl~L~y~e-----g~S~~EIAe~lGIS~~TV~r~L~RArkkL 61 (104)
T PRK00118 18 LTEKQRNYMELYYLD-----DYSLGEIAEEFNVSRQAVYDNIKRTEKLL 61 (104)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 577777777666554 23446799999999999999998877743
No 130
>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=28.90 E-value=30 Score=28.40 Aligned_cols=22 Identities=18% Similarity=0.404 Sum_probs=18.6
Q ss_pred HHHHHHHHhCCCcchhhhccch
Q 006856 524 VKENLSKELSLEPEKVNKWFKN 545 (628)
Q Consensus 524 ~r~~LA~~lgLt~~QVkiWFqN 545 (628)
.-.+||+.||++...|..|-+-
T Consensus 15 ~~~eIA~~Lg~~~~TV~~W~~r 36 (58)
T PF06056_consen 15 SIKEIAEELGVPRSTVYSWKDR 36 (58)
T ss_pred CHHHHHHHHCCChHHHHHHHHh
Confidence 3568999999999999999653
No 131
>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=28.86 E-value=28 Score=31.89 Aligned_cols=39 Identities=23% Similarity=0.580 Sum_probs=30.8
Q ss_pred CCCCccccccccccccccccCCCCCeeecCCccCcccccc
Q 006856 230 TDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQK 269 (628)
Q Consensus 230 ~dg~~~~e~~~C~vC~~~~~~~~g~lllCDG~C~rayH~~ 269 (628)
.+|.....-+.|.+|+..+-...++.|.|- .|+..|++.
T Consensus 27 ~dg~~~va~daCeiC~~~GY~q~g~~lvC~-~C~~~~~~~ 65 (102)
T PF10080_consen 27 PDGSYRVAFDACEICGPKGYYQEGDQLVCK-NCGVRFNLP 65 (102)
T ss_pred CCCCEEEEEEeccccCCCceEEECCEEEEe-cCCCEEehh
Confidence 456666677899999877666678888999 799998864
No 132
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=28.81 E-value=56 Score=31.33 Aligned_cols=48 Identities=13% Similarity=0.160 Sum_probs=36.3
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHh
Q 006856 501 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKA 553 (628)
Q Consensus 501 rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~K~ 553 (628)
.+++.+.+.|...|-+ ...-.+||+.||++...|+.++...|.+.++.
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 4677777777776433 23457899999999999999999988855443
No 133
>PHA01976 helix-turn-helix protein
Probab=28.64 E-value=29 Score=27.95 Aligned_cols=25 Identities=12% Similarity=0.198 Sum_probs=21.8
Q ss_pred HHHHHHHHhCCCcchhhhccchhcc
Q 006856 524 VKENLSKELSLEPEKVNKWFKNARY 548 (628)
Q Consensus 524 ~r~~LA~~lgLt~~QVkiWFqNrR~ 548 (628)
+..+||+.+|++...|..|...++.
T Consensus 17 t~~~lA~~~gvs~~~v~~~e~g~~~ 41 (67)
T PHA01976 17 SAPELSRRAGVRHSLIYDFEADKRL 41 (67)
T ss_pred CHHHHHHHhCCCHHHHHHHHcCCCC
Confidence 4678999999999999999987764
No 134
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=28.48 E-value=26 Score=39.70 Aligned_cols=46 Identities=30% Similarity=0.515 Sum_probs=30.1
Q ss_pred cccccccccccccCCCCCeeecCCccCccccccccCCCCCCCCCCCcccccccc
Q 006856 237 EHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESNQGWFCKFCEC 290 (628)
Q Consensus 237 e~~~C~vC~~~~~~~~g~lllCDG~C~rayH~~CL~PPL~~~P~g~W~Cp~C~~ 290 (628)
+-..|.||-..-..+.+-|+-- -|+..||..|+.-... -.||.|+.
T Consensus 174 ELPTCpVCLERMD~s~~gi~t~--~c~Hsfh~~cl~~w~~------~scpvcR~ 219 (493)
T KOG0804|consen 174 ELPTCPVCLERMDSSTTGILTI--LCNHSFHCSCLMKWWD------SSCPVCRY 219 (493)
T ss_pred cCCCcchhHhhcCccccceeee--ecccccchHHHhhccc------CcChhhhh
Confidence 4458999997654444444444 4999999999985432 24666653
No 135
>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=28.45 E-value=63 Score=24.70 Aligned_cols=39 Identities=13% Similarity=0.507 Sum_probs=28.9
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccc
Q 006856 501 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFK 544 (628)
Q Consensus 501 rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFq 544 (628)
.++++|.+.+.+.+... + ...+||+.+|++...|..++.
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 36887888777777765 3 477899999999999987763
No 136
>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=28.39 E-value=13 Score=26.52 Aligned_cols=42 Identities=24% Similarity=0.531 Sum_probs=27.5
Q ss_pred cccccccccCCCCCeeecCCccCccccccccCCCCCCCCCCCcccccccc
Q 006856 241 CAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESNQGWFCKFCEC 290 (628)
Q Consensus 241 C~vC~~~~~~~~g~lllCDG~C~rayH~~CL~PPL~~~P~g~W~Cp~C~~ 290 (628)
|.+|...- ...+... .|...||..|+...+.. +...||.|..
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 77787532 2333444 48888999999865443 4567998863
No 137
>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=28.24 E-value=27 Score=27.04 Aligned_cols=42 Identities=14% Similarity=0.263 Sum_probs=28.5
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhcc
Q 006856 502 MPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 548 (628)
Q Consensus 502 ft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~ 548 (628)
+++.+...+.-.|- ..-.-.++|+.+|+++..|+.|.+..|.
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 56666666665443 3445688999999999999999987765
No 138
>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=27.74 E-value=37 Score=24.44 Aligned_cols=23 Identities=17% Similarity=0.375 Sum_probs=20.5
Q ss_pred HHHHHHHhCCCcchhhhccchhc
Q 006856 525 KENLSKELSLEPEKVNKWFKNAR 547 (628)
Q Consensus 525 r~~LA~~lgLt~~QVkiWFqNrR 547 (628)
..+||+.+|+++..|..|..+.+
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~~ 37 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGKR 37 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCCC
Confidence 45899999999999999998875
No 139
>KOG4218 consensus Nuclear hormone receptor betaFTZ-F1 [Transcription]
Probab=27.59 E-value=28 Score=38.26 Aligned_cols=55 Identities=16% Similarity=0.353 Sum_probs=35.2
Q ss_pred ccccccccccccccCCCCCeeecCCccCccc--------cccccCCCCCCCC-CCCcccccccch
Q 006856 236 HEHIICAKCKLREAFPDNDIVLCDGTCNCAF--------HQKCLDPPLDTES-NQGWFCKFCECK 291 (628)
Q Consensus 236 ~e~~~C~vC~~~~~~~~g~lllCDG~C~ray--------H~~CL~PPL~~~P-~g~W~Cp~C~~k 291 (628)
+....|.||+..-+..---+|-|. .|...| |..|..-.-=.+. -..-.||.|+..
T Consensus 13 dl~ElCPVCGDkVSGYHYGLLTCE-SCKGFFKRTVQNnK~YtC~e~qnC~iDkTqRKRCP~CRFQ 76 (475)
T KOG4218|consen 13 DLGELCPVCGDKVSGYHYGLLTCE-SCKGFFKRTVQNNKQYTCSEEQNCHIDKTQRKRCPSCRFQ 76 (475)
T ss_pred ccccccccccCccccceeeeeehh-hhhhHHHHHhhcCcceecccccccccchHhhccCCchhHH
Confidence 345789999987664445689999 698766 3456543222222 245679999753
No 140
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=27.50 E-value=62 Score=31.39 Aligned_cols=49 Identities=14% Similarity=0.154 Sum_probs=37.1
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhh
Q 006856 501 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR 554 (628)
Q Consensus 501 rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~K~~ 554 (628)
.+++.+...|.-.|-+. -.-.+||+.||++...|+...+-.|.+.+++.
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 33578999999999999998887777655554
No 141
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=27.42 E-value=37 Score=38.89 Aligned_cols=43 Identities=21% Similarity=0.653 Sum_probs=24.3
Q ss_pred ccccccccccccCCCCCeeecCCccC--ccccc-----cccCCCCCCCCCCCcccccccch
Q 006856 238 HIICAKCKLREAFPDNDIVLCDGTCN--CAFHQ-----KCLDPPLDTESNQGWFCKFCECK 291 (628)
Q Consensus 238 ~~~C~vC~~~~~~~~g~lllCDG~C~--rayH~-----~CL~PPL~~~P~g~W~Cp~C~~k 291 (628)
..+|..|+. .+.|. .|+ ..||. .|+-=. ....-.|.||.|...
T Consensus 213 ~~~C~~Cg~--------~~~C~-~C~~~l~~h~~~~~l~Ch~Cg--~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 213 NLLCRSCGY--------ILCCP-NCDVSLTYHKKEGKLRCHYCG--YQEPIPKTCPQCGSE 262 (505)
T ss_pred eeEhhhCcC--------ccCCC-CCCCceEEecCCCeEEcCCCc--CcCCCCCCCCCCCCC
Confidence 367888883 34566 466 34663 344311 112345999999653
No 142
>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=27.23 E-value=69 Score=24.11 Aligned_cols=39 Identities=18% Similarity=0.337 Sum_probs=28.1
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchh
Q 006856 502 MPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNA 546 (628)
Q Consensus 502 ft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNr 546 (628)
+++.|.+.+...+ +. ..-.++|+.+|++...|..|...-
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 143
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=27.21 E-value=13 Score=44.83 Aligned_cols=50 Identities=24% Similarity=0.650 Sum_probs=36.0
Q ss_pred cccccccccccCCCCCeeecCCccCccccccccCCCCCCCC---CCCcccccccc
Q 006856 239 IICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTES---NQGWFCKFCEC 290 (628)
Q Consensus 239 ~~C~vC~~~~~~~~g~lllCDG~C~rayH~~CL~PPL~~~P---~g~W~Cp~C~~ 290 (628)
..|.+|-.... ....|--|- .|...||+.|..-.-.... ...|-||.|..
T Consensus 192 yeCmIC~e~I~-~t~~~WSC~-sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqs 244 (950)
T KOG1952|consen 192 YECMICTERIK-RTAPVWSCK-SCYHVFHLNCIKKWARSSEKTGQDGWRCPACQS 244 (950)
T ss_pred eEEEEeeeecc-ccCCceecc-hhhhhhhHHHHHHHHHHhhhccCccccCCcccc
Confidence 46888886544 345677898 7999999999854322222 46899999973
No 144
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=27.00 E-value=49 Score=39.36 Aligned_cols=49 Identities=18% Similarity=0.573 Sum_probs=30.1
Q ss_pred cccccccccccCCCCCeeecCCccCcccc-ccccCCCCCCCCCCCcccccccchh
Q 006856 239 IICAKCKLREAFPDNDIVLCDGTCNCAFH-QKCLDPPLDTESNQGWFCKFCECKM 292 (628)
Q Consensus 239 ~~C~vC~~~~~~~~g~lllCDG~C~rayH-~~CL~PPL~~~P~g~W~Cp~C~~k~ 292 (628)
.+|..|+... +....+|. .|..... ..|.... ...|.+.=||+.|-.+.
T Consensus 2 ~~Cp~Cg~~n---~~~akFC~-~CG~~l~~~~Cp~CG-~~~~~~~~fC~~CG~~~ 51 (645)
T PRK14559 2 LICPQCQFEN---PNNNRFCQ-KCGTSLTHKPCPQCG-TEVPVDEAHCPNCGAET 51 (645)
T ss_pred CcCCCCCCcC---CCCCcccc-ccCCCCCCCcCCCCC-CCCCcccccccccCCcc
Confidence 3577777543 34556777 5766533 4565543 33556777999997653
No 145
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=26.91 E-value=34 Score=25.81 Aligned_cols=33 Identities=24% Similarity=0.462 Sum_probs=25.5
Q ss_pred cccccccccccCCCCCeeecCCccCccccccccC
Q 006856 239 IICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLD 272 (628)
Q Consensus 239 ~~C~vC~~~~~~~~g~lllCDG~C~rayH~~CL~ 272 (628)
.+|.+|+..-......-+.|. .|....|..|..
T Consensus 12 ~~C~~C~~~i~~~~~~~~~C~-~C~~~~H~~C~~ 44 (50)
T cd00029 12 TFCDVCRKSIWGLFKQGLRCS-WCKVKCHKKCAD 44 (50)
T ss_pred CChhhcchhhhccccceeEcC-CCCCchhhhhhc
Confidence 579999976642224678899 699999999986
No 146
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=26.21 E-value=68 Score=30.94 Aligned_cols=48 Identities=15% Similarity=0.064 Sum_probs=36.2
Q ss_pred CCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHH
Q 006856 500 HRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK 552 (628)
Q Consensus 500 ~rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~K 552 (628)
..+++.|...+...|-+. ..-.+||+.||+++..|+.+....|.+.++
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 457888888888765442 346789999999999999988776664443
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=25.99 E-value=53 Score=26.02 Aligned_cols=43 Identities=14% Similarity=0.196 Sum_probs=33.7
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccH
Q 006856 501 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYL 549 (628)
Q Consensus 501 rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k 549 (628)
.||+.+++.|.-...-. ...++|..||+++..|..+..|-+.|
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 57888988888766533 46789999999999999988887763
No 148
>PF13730 HTH_36: Helix-turn-helix domain
Probab=25.44 E-value=1.3e+02 Score=23.30 Aligned_cols=42 Identities=24% Similarity=0.335 Sum_probs=29.3
Q ss_pred CCCHHHHHHHHHHHHh---C--CCCCHHHHHHHHHHhCCCcchhhhccch
Q 006856 501 RMPPNAVEKLRQVFAE---N--ELPSRIVKENLSKELSLEPEKVNKWFKN 545 (628)
Q Consensus 501 rft~~Q~~~Le~~F~~---~--~yPs~~~r~~LA~~lgLt~~QVkiWFqN 545 (628)
.+++.+...+-..+.. + -|| ....||+.+|++.+.|+.+.+.
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 3566666655544433 2 455 5788999999999999987654
No 149
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=25.22 E-value=23 Score=41.45 Aligned_cols=46 Identities=30% Similarity=0.729 Sum_probs=28.9
Q ss_pred ccccccccccCC---CCCeeecCCccCccccccccCCCCCCCCCCCcccccccchhh
Q 006856 240 ICAKCKLREAFP---DNDIVLCDGTCNCAFHQKCLDPPLDTESNQGWFCKFCECKME 293 (628)
Q Consensus 240 ~C~vC~~~~~~~---~g~lllCDG~C~rayH~~CL~PPL~~~P~g~W~Cp~C~~k~~ 293 (628)
+|..|...+..- .....-|+ .|..+||..|+.-- .+ .||.|.....
T Consensus 513 iCe~Cq~~~iiyPF~~~~~~rC~-~C~avfH~~C~~r~---s~----~CPrC~R~q~ 561 (580)
T KOG1829|consen 513 ICELCQHNDIIYPFETRNTRRCS-TCLAVFHKKCLRRK---SP----CCPRCERRQK 561 (580)
T ss_pred eeeeccCCCcccccccccceeHH-HHHHHHHHHHHhcc---CC----CCCchHHHHH
Confidence 577775332211 23346788 69999999999722 11 2999975543
No 150
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=25.04 E-value=58 Score=31.03 Aligned_cols=47 Identities=19% Similarity=0.229 Sum_probs=35.4
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHH
Q 006856 501 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK 552 (628)
Q Consensus 501 rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~K 552 (628)
.+++.+.+.|.-.|-+ ...-.++|+.||+++..|+++++..|.+.++
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 3445789999999999999999888875443
No 151
>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=24.84 E-value=61 Score=29.63 Aligned_cols=46 Identities=13% Similarity=0.096 Sum_probs=33.2
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHH
Q 006856 501 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLAL 551 (628)
Q Consensus 501 rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~ 551 (628)
.+++.+.+.|.-.|-+ .+ .-.+||+.||+++..|+.+...-|.+.+
T Consensus 113 ~L~~~~r~il~l~~~~-~~----~~~eIA~~lgis~~tv~~~~~ra~~~Lr 158 (161)
T TIGR02985 113 KLPEQCRKIFILSRFE-GK----SYKEIAEELGISVKTVEYHISKALKELR 158 (161)
T ss_pred HCCHHHHHHHHHHHHc-CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4577777777764432 23 3456999999999999998887776443
No 152
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=24.61 E-value=48 Score=32.33 Aligned_cols=25 Identities=16% Similarity=0.137 Sum_probs=22.9
Q ss_pred HHHHHHHHhCCCcchhhhccchhcc
Q 006856 524 VKENLSKELSLEPEKVNKWFKNARY 548 (628)
Q Consensus 524 ~r~~LA~~lgLt~~QVkiWFqNrR~ 548 (628)
++++||+.+|++...|..|..+.+.
T Consensus 84 SqeeLA~~lgvs~s~IsriE~G~~~ 108 (154)
T TIGR00270 84 SQEQLAKKIQEKESLIKKIENAEIE 108 (154)
T ss_pred CHHHHHHHhCCCHHHHHHHHCCCCC
Confidence 4789999999999999999998876
No 153
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=24.42 E-value=82 Score=38.47 Aligned_cols=41 Identities=27% Similarity=0.554 Sum_probs=30.3
Q ss_pred cccccccccccCCCCCeeecCCccCccccccccCCCCCCCCCCCcccccccch
Q 006856 239 IICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESNQGWFCKFCECK 291 (628)
Q Consensus 239 ~~C~vC~~~~~~~~g~lllCDG~C~rayH~~CL~PPL~~~P~g~W~Cp~C~~k 291 (628)
..|..|...- +=++|.= .|...||+.|+. ++.--||.|...
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 5799999632 2344544 499999999998 456689999873
No 154
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=24.30 E-value=61 Score=38.99 Aligned_cols=53 Identities=15% Similarity=0.202 Sum_probs=41.4
Q ss_pred CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhcc
Q 006856 496 RRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 548 (628)
Q Consensus 496 kR~r~rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~ 548 (628)
-+-+.-...++-..|..++.-+.-|+..+-.-++.+|.+.+..|.+||++|+.
T Consensus 627 ~kv~sp~k~~dq~ql~~a~elq~s~~n~~~pl~~t~~~n~~pv~ev~dhsrss 679 (1007)
T KOG3623|consen 627 VKVRSPIKEEDQQQLKQAYELQASPSNDEFPLIATRLQNDPPVVEVWDHSRSS 679 (1007)
T ss_pred ccccCCCCccchhhhHhhhhcccCccCcccchhhhhccCCCcchhhcccCCCC
Confidence 33345556677778888898887777766666677788999999999999998
No 155
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=23.74 E-value=90 Score=29.16 Aligned_cols=47 Identities=15% Similarity=0.155 Sum_probs=36.0
Q ss_pred CCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHH
Q 006856 500 HRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK 552 (628)
Q Consensus 500 ~rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~K 552 (628)
..+++.+...|.-.| ..+ .-.+||+.||+++..|+.+....|.+.++
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 346888888887777 334 35689999999999999999877775443
No 156
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=23.48 E-value=57 Score=31.55 Aligned_cols=47 Identities=11% Similarity=0.200 Sum_probs=33.7
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHH
Q 006856 501 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK 552 (628)
Q Consensus 501 rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~K 552 (628)
.+++.+...|.-.|- ....-.+||+.||+++..|+.|+...|.+.++
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 356666666655432 23345789999999999999999887774443
No 157
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=23.32 E-value=82 Score=31.84 Aligned_cols=47 Identities=13% Similarity=0.154 Sum_probs=37.2
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHH
Q 006856 501 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK 552 (628)
Q Consensus 501 rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~K 552 (628)
.+++.+.+.|...|-+. -.-.+||+.||++...|+.+....|.+.++
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 356899999999999999999988885544
No 158
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=23.24 E-value=30 Score=25.76 Aligned_cols=33 Identities=21% Similarity=0.426 Sum_probs=24.9
Q ss_pred ccccccccccccCCCCCeeecCCccCccccccccC
Q 006856 238 HIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLD 272 (628)
Q Consensus 238 ~~~C~vC~~~~~~~~g~lllCDG~C~rayH~~CL~ 272 (628)
..+|.+|+..-.... .-+.|. .|....|..|+.
T Consensus 11 ~~~C~~C~~~i~~~~-~~~~C~-~C~~~~H~~C~~ 43 (49)
T smart00109 11 PTKCCVCRKSIWGSF-QGLRCS-WCKVKCHKKCAE 43 (49)
T ss_pred CCCccccccccCcCC-CCcCCC-CCCchHHHHHHh
Confidence 357999998664221 467899 699999999986
No 159
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=23.21 E-value=1e+02 Score=30.04 Aligned_cols=36 Identities=14% Similarity=0.113 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhh
Q 006856 505 NAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVN 540 (628)
Q Consensus 505 ~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVk 540 (628)
.-+..|..+=.+..|.+.+....||+.||+++.+|.
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 160
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=23.20 E-value=16 Score=33.69 Aligned_cols=27 Identities=37% Similarity=0.730 Sum_probs=19.8
Q ss_pred CccCccccccccCCCCCCCCCCCcccccccc
Q 006856 260 GTCNCAFHQKCLDPPLDTESNQGWFCKFCEC 290 (628)
Q Consensus 260 G~C~rayH~~CL~PPL~~~P~g~W~Cp~C~~ 290 (628)
|.|+.+||+.|..--|.... .||.|..
T Consensus 79 G~CNHaFH~hCisrWlktr~----vCPLdn~ 105 (114)
T KOG2930|consen 79 GVCNHAFHFHCISRWLKTRN----VCPLDNK 105 (114)
T ss_pred eecchHHHHHHHHHHHhhcC----cCCCcCc
Confidence 47999999999986665542 5776653
No 161
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=23.14 E-value=42 Score=27.76 Aligned_cols=24 Identities=17% Similarity=0.239 Sum_probs=21.6
Q ss_pred HHHHHHHhCCCcchhhhccchhcc
Q 006856 525 KENLSKELSLEPEKVNKWFKNARY 548 (628)
Q Consensus 525 r~~LA~~lgLt~~QVkiWFqNrR~ 548 (628)
..+||+.+|++...|..|+.++|.
T Consensus 21 ~~~lA~~~gis~~tis~~~~g~~~ 44 (78)
T TIGR02607 21 IRALAKALGVSRSTLSRIVNGRRG 44 (78)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCCC
Confidence 568999999999999999988764
No 162
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=23.08 E-value=84 Score=28.98 Aligned_cols=43 Identities=16% Similarity=0.231 Sum_probs=34.6
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccH
Q 006856 501 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYL 549 (628)
Q Consensus 501 rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k 549 (628)
.+|+.+.+.|.- +.+ .| ...++|+.|++++..|+.|.+|-|.|
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 479999988886 443 33 36799999999999999999987774
No 163
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.03 E-value=90 Score=28.24 Aligned_cols=42 Identities=17% Similarity=0.261 Sum_probs=33.3
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhcc
Q 006856 502 MPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWF 543 (628)
Q Consensus 502 ft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWF 543 (628)
++++|.+.-.+.|+.|--...-..+++|..||.++-.|..=.
T Consensus 3 Ln~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~lekil 44 (97)
T COG4367 3 LNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKLEKIL 44 (97)
T ss_pred CCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHHHHHH
Confidence 578888877777777777777788999999999998776433
No 164
>PRK14873 primosome assembly protein PriA; Provisional
Probab=22.91 E-value=58 Score=38.83 Aligned_cols=42 Identities=21% Similarity=0.633 Sum_probs=24.7
Q ss_pred ccccccccccccCCCCCeeecCCccC--ccccc-----cccCCCCCCCCCCCcccccccch
Q 006856 238 HIICAKCKLREAFPDNDIVLCDGTCN--CAFHQ-----KCLDPPLDTESNQGWFCKFCECK 291 (628)
Q Consensus 238 ~~~C~vC~~~~~~~~g~lllCDG~C~--rayH~-----~CL~PPL~~~P~g~W~Cp~C~~k 291 (628)
..+|..|+. .+.|. .|+ ..||. .|+-=-... ..|.||.|-..
T Consensus 383 ~l~C~~Cg~--------~~~C~-~C~~~L~~h~~~~~l~Ch~CG~~~---~p~~Cp~Cgs~ 431 (665)
T PRK14873 383 SLACARCRT--------PARCR-HCTGPLGLPSAGGTPRCRWCGRAA---PDWRCPRCGSD 431 (665)
T ss_pred eeEhhhCcC--------eeECC-CCCCceeEecCCCeeECCCCcCCC---cCccCCCCcCC
Confidence 467888883 45666 566 34664 254322211 36999999654
No 165
>KOG4215 consensus Hepatocyte nuclear factor 4 and similar steroid hormone receptors [Transcription]
Probab=22.91 E-value=38 Score=37.59 Aligned_cols=29 Identities=28% Similarity=0.557 Sum_probs=19.8
Q ss_pred cccccccccccccCCCCCeeecCCccCccc
Q 006856 237 EHIICAKCKLREAFPDNDIVLCDGTCNCAF 266 (628)
Q Consensus 237 e~~~C~vC~~~~~~~~g~lllCDG~C~ray 266 (628)
...+|.+|+..-..----.+-||| |...|
T Consensus 18 ~~~~CaICGDkaTGKHYGA~SCdG-CKGFF 46 (432)
T KOG4215|consen 18 VAEFCAICGDKATGKHYGAISCDG-CKGFF 46 (432)
T ss_pred ccchhheeCCcccccccceeecCc-chHHH
Confidence 457999999754322224678997 98765
No 166
>KOG1844 consensus PHD Zn-finger proteins [General function prediction only]
Probab=22.46 E-value=50 Score=37.30 Aligned_cols=46 Identities=22% Similarity=0.554 Sum_probs=35.0
Q ss_pred cccccccCC-CCCeeecCCccCccccccccCCCCCCCCCCCcccccccchh
Q 006856 243 KCKLREAFP-DNDIVLCDGTCNCAFHQKCLDPPLDTESNQGWFCKFCECKM 292 (628)
Q Consensus 243 vC~~~~~~~-~g~lllCDG~C~rayH~~CL~PPL~~~P~g~W~Cp~C~~k~ 292 (628)
.|+..+ + ++.++.|+ .|.+|-|.+|+...-... .....|..|..+.
T Consensus 90 ~c~~~~--~~~g~~i~c~-~c~~Wqh~~C~g~~~~~~-p~~y~c~~c~~~~ 136 (508)
T KOG1844|consen 90 DCGLED--DMEGLMIQCD-WCGRWQHKICCGSFKSTK-PDKYVCEICTPRN 136 (508)
T ss_pred cccccc--CCCceeeCCc-ccCcccCceeeeecCCCC-chhceeeeecccc
Confidence 566543 4 78999999 699999999998765444 3567799997653
No 167
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=22.39 E-value=1.1e+02 Score=28.89 Aligned_cols=48 Identities=15% Similarity=0.104 Sum_probs=36.0
Q ss_pred CCCCHHHHHHHHHH-HHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHh
Q 006856 500 HRMPPNAVEKLRQV-FAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKA 553 (628)
Q Consensus 500 ~rft~~Q~~~Le~~-F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~K~ 553 (628)
..+++.+.+.|.-. |..-+ -++||..||+++..|+.|.+--|.+.++.
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 168
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=22.38 E-value=45 Score=26.95 Aligned_cols=18 Identities=17% Similarity=0.370 Sum_probs=16.3
Q ss_pred HHHHHHhCCCcchhhhcc
Q 006856 526 ENLSKELSLEPEKVNKWF 543 (628)
Q Consensus 526 ~~LA~~lgLt~~QVkiWF 543 (628)
.++|+.+|+++.+|+.|=
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 169
>PF13565 HTH_32: Homeodomain-like domain
Probab=22.35 E-value=2.2e+02 Score=23.38 Aligned_cols=40 Identities=20% Similarity=0.356 Sum_probs=28.8
Q ss_pred CHHHHHHHHHHHHhCC-CCCHHHHHHHHHHhCC----Ccchhhhc
Q 006856 503 PPNAVEKLRQVFAENE-LPSRIVKENLSKELSL----EPEKVNKW 542 (628)
Q Consensus 503 t~~Q~~~Le~~F~~~~-yPs~~~r~~LA~~lgL----t~~QVkiW 542 (628)
++++.+.|.+.+.++| +-.......|++++|+ +...|..|
T Consensus 32 ~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~~~S~~tv~R~ 76 (77)
T PF13565_consen 32 DPEQRERIIALIEEHPRWTPREIAEYLEEEFGISVRVSRSTVYRI 76 (77)
T ss_pred cHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCCccHhHHHHh
Confidence 7888899999999997 4455666777887775 44555444
No 170
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=22.24 E-value=1e+02 Score=29.60 Aligned_cols=47 Identities=17% Similarity=0.098 Sum_probs=37.5
Q ss_pred CCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHH
Q 006856 500 HRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK 552 (628)
Q Consensus 500 ~rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~K 552 (628)
..+|+.|.+.|.-.+ .. -+..+||+.||++...|+.|-+..|.+.++
T Consensus 5 ~~Lte~qr~VL~Lr~--~G----lTq~EIAe~LgiS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 5 TFLTERQIKVLELRE--KG----LSQKEIAKELKTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred CCCCHHHHHHHHHHH--cC----CCHHHHHHHHCcCHHHHHHHHHhHHHHHHH
Confidence 457999999998742 22 277899999999999999998888875543
No 171
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=21.90 E-value=65 Score=35.00 Aligned_cols=32 Identities=16% Similarity=0.450 Sum_probs=23.5
Q ss_pred cccccccccccc--------cCCCCCeeecCCccCcccccc
Q 006856 237 EHIICAKCKLRE--------AFPDNDIVLCDGTCNCAFHQK 269 (628)
Q Consensus 237 e~~~C~vC~~~~--------~~~~g~lllCDG~C~rayH~~ 269 (628)
...+|.||+..- ...+...+.|. .|...||+.
T Consensus 186 ~~~~CPvCGs~P~~s~v~~~~~~G~RyL~Cs-lC~teW~~~ 225 (309)
T PRK03564 186 QRQFCPVCGSMPVSSVVQIGTTQGLRYLHCN-LCESEWHVV 225 (309)
T ss_pred CCCCCCCCCCcchhheeeccCCCCceEEEcC-CCCCccccc
Confidence 457999999652 12356889998 799988864
No 172
>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=21.71 E-value=36 Score=24.64 Aligned_cols=23 Identities=22% Similarity=0.806 Sum_probs=11.1
Q ss_pred ccccccccccCCCCCeeecCCccC
Q 006856 240 ICAKCKLREAFPDNDIVLCDGTCN 263 (628)
Q Consensus 240 ~C~vC~~~~~~~~g~lllCDG~C~ 263 (628)
.|..|+....-.++.++.|. .|.
T Consensus 4 ~Cp~C~se~~y~D~~~~vCp-~C~ 26 (30)
T PF08274_consen 4 KCPLCGSEYTYEDGELLVCP-ECG 26 (30)
T ss_dssp --TTT-----EE-SSSEEET-TTT
T ss_pred CCCCCCCcceeccCCEEeCC-ccc
Confidence 47778876665677788888 674
No 173
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=21.64 E-value=44 Score=31.12 Aligned_cols=24 Identities=13% Similarity=0.416 Sum_probs=22.0
Q ss_pred HHHHHHHhCCCcchhhhccchhcc
Q 006856 525 KENLSKELSLEPEKVNKWFKNARY 548 (628)
Q Consensus 525 r~~LA~~lgLt~~QVkiWFqNrR~ 548 (628)
..+||..+|++...|..|..+++.
T Consensus 21 q~~lA~~~gvs~~~is~~E~g~~~ 44 (135)
T PRK09706 21 QRSLAKAVKVSHVSISQWERDETE 44 (135)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCCC
Confidence 579999999999999999999874
No 174
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=21.33 E-value=1.2e+02 Score=29.36 Aligned_cols=36 Identities=14% Similarity=0.139 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhh
Q 006856 505 NAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVN 540 (628)
Q Consensus 505 ~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVk 540 (628)
.-+..|...=.+..|.+.+....+|+.|||++.+|.
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 345667666677789999999999999999999975
No 175
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=21.32 E-value=53 Score=26.16 Aligned_cols=25 Identities=16% Similarity=0.323 Sum_probs=20.8
Q ss_pred HHHHHHHHhCCCcchhhhccchhcc
Q 006856 524 VKENLSKELSLEPEKVNKWFKNARY 548 (628)
Q Consensus 524 ~r~~LA~~lgLt~~QVkiWFqNrR~ 548 (628)
+..++|+.+|++..+|..|-.++|.
T Consensus 14 t~~~~a~~~~i~~~~i~~~e~g~~~ 38 (64)
T PF12844_consen 14 TQKDLAEKLGISRSTISKIENGKRK 38 (64)
T ss_dssp -HHHHHHHHTS-HHHHHHHHTTSS-
T ss_pred CHHHHHHHHCcCHHHHHHHHCCCcC
Confidence 5788999999999999999999874
No 176
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=21.31 E-value=78 Score=36.31 Aligned_cols=24 Identities=21% Similarity=0.059 Sum_probs=15.0
Q ss_pred CccccCCCCCCCCCCCCCCCCCcc
Q 006856 326 CSALLNQEEEWPSDDSEDDDYNPE 349 (628)
Q Consensus 326 ~~~~~n~e~~~psddseDed~dp~ 349 (628)
.|.+.=...-|.+-|..=.|..|.
T Consensus 84 ~~~l~C~~C~Wss~~igi~Fdkpt 107 (483)
T PF05502_consen 84 PYYLSCSYCRWSSRDIGIKFDKPT 107 (483)
T ss_pred CEEEECCCceeeccccCccccCch
Confidence 343333446688888877766664
No 177
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=21.27 E-value=73 Score=30.62 Aligned_cols=48 Identities=6% Similarity=0.136 Sum_probs=34.5
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHh
Q 006856 501 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKA 553 (628)
Q Consensus 501 rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~K~ 553 (628)
.+++.+...|...|-+ .-.-.+||+.||++...|+.+....|.+.++.
T Consensus 128 ~L~~~~r~i~~l~~~~-----g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 175 (186)
T PRK05602 128 ALPERQREAIVLQYYQ-----GLSNIEAAAVMDISVDALESLLARGRRALRAQ 175 (186)
T ss_pred hCCHHHHHHhhHHHhc-----CCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 3577777777664432 22347899999999999999998888754443
No 178
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=20.99 E-value=65 Score=31.87 Aligned_cols=47 Identities=15% Similarity=0.239 Sum_probs=34.2
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHH
Q 006856 501 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK 552 (628)
Q Consensus 501 rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~K 552 (628)
.+++.+...|...|- ..-.-.+||+.||+++..|+++....|.+.++
T Consensus 153 ~L~~~~r~vl~l~~~-----~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 199 (206)
T PRK12526 153 KLPEAQQTVVKGVYF-----QELSQEQLAQQLNVPLGTVKSRLRLALAKLKV 199 (206)
T ss_pred hCCHHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 367777777765432 23345789999999999999999877774443
No 179
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=20.82 E-value=99 Score=29.15 Aligned_cols=46 Identities=4% Similarity=0.073 Sum_probs=33.8
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHH
Q 006856 501 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLAL 551 (628)
Q Consensus 501 rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~ 551 (628)
.+++.+.+.|...|-+. ..-.++|+.||+++..|+++..-.|.+.+
T Consensus 119 ~L~~~~r~i~~l~~~~g-----~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr 164 (169)
T TIGR02954 119 TLNDKYQTAIILRYYHD-----LTIKEIAEVMNKPEGTVKTYLHRALKKLK 164 (169)
T ss_pred hCCHHHhHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 46777888776655433 33468999999999999998777666433
No 180
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=20.68 E-value=1.5e+02 Score=26.73 Aligned_cols=46 Identities=9% Similarity=0.209 Sum_probs=36.2
Q ss_pred CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCC-Ccchhhhccchhcc
Q 006856 499 FHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSL-EPEKVNKWFKNARY 548 (628)
Q Consensus 499 r~rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgL-t~~QVkiWFqNrR~ 548 (628)
+.+||.+-...+-+.+.+..+ .-.+||+++|+ ...++..|-...+.
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 567899988877777776666 77899999996 99999988654443
No 181
>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=20.59 E-value=1.2e+02 Score=28.94 Aligned_cols=36 Identities=11% Similarity=0.052 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhh
Q 006856 505 NAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVN 540 (628)
Q Consensus 505 ~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVk 540 (628)
.-+..|...=.+..|.+.+..+.+|+.|||++.+|.
T Consensus 17 ~li~~L~~vQ~~~G~i~~~~~~~iA~~l~~~~~~v~ 52 (148)
T TIGR01958 17 AIMPALMIAQEQKGWVTPEAIAAVAEMLGIPPVWVY 52 (148)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHHH
Confidence 445566666666789999999999999999998865
No 182
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=20.52 E-value=95 Score=28.68 Aligned_cols=41 Identities=17% Similarity=0.259 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchh
Q 006856 505 NAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNA 546 (628)
Q Consensus 505 ~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNr 546 (628)
.-+..+..+...+ |.....-.+||+.+|+++.++..+|+..
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 3345555555555 4445777999999999999999999876
No 183
>PF02724 CDC45: CDC45-like protein; InterPro: IPR003874 CDC45 is an essential gene required for initiation of DNA replication in Saccharomyces cerevisiae (cell division control protein 45), forming a complex with MCM5/CDC46. Homologs of CDC45 have been identified in human [], mouse and the smut fungus, Melampsora spp., (tsd2 protein) among others.; GO: 0006270 DNA-dependent DNA replication initiation
Probab=20.47 E-value=1.1e+02 Score=36.09 Aligned_cols=36 Identities=11% Similarity=0.251 Sum_probs=25.9
Q ss_pred CHHHHHHHHHHHHhCCC---CCHHHHHHHHHHhCCCcch
Q 006856 503 PPNAVEKLRQVFAENEL---PSRIVKENLSKELSLEPEK 538 (628)
Q Consensus 503 t~~Q~~~Le~~F~~~~y---Ps~~~r~~LA~~lgLt~~Q 538 (628)
-......|+.+|.+.-| |..-+-..||..||=+-..
T Consensus 198 ~~~~~~~i~~yY~~gs~~g~ssa~~~y~La~~l~r~~~d 236 (622)
T PF02724_consen 198 REEYREEIEKYYSQGSYYGKSSAVLMYELASSLGRDDND 236 (622)
T ss_pred HHHHHHHHHHHHhcCceecccHHHHHHHHHHHhCCCchH
Confidence 34555678888877654 8899999999986654443
No 184
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=20.38 E-value=1.2e+02 Score=29.99 Aligned_cols=38 Identities=11% Similarity=0.053 Sum_probs=33.8
Q ss_pred CHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhh
Q 006856 503 PPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVN 540 (628)
Q Consensus 503 t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVk 540 (628)
-..-+..|..++.+..|.+.+..+.+|..||++...|.
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 35567899999999999999999999999999998764
No 185
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=20.36 E-value=1e+02 Score=33.36 Aligned_cols=52 Identities=17% Similarity=0.109 Sum_probs=41.0
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHh
Q 006856 501 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKA 553 (628)
Q Consensus 501 rft~~Q~~~Le~~F~~~~yPs~~~r~~LA~~lgLt~~QVkiWFqNrR~k~~K~ 553 (628)
.+++.|...|...|.-. |-..-+-.+||+.||++...|+.+....+.+.++.
T Consensus 262 ~L~~~~R~vl~lrygL~-~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~ 313 (325)
T PRK05657 262 ELNDKQREVLARRFGLL-GYEAATLEDVAREIGLTRERVRQIQVEALRRLREI 313 (325)
T ss_pred cCCHHHHHHHHHHhccC-CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 57999999999888433 23445668999999999999999999888855443
No 186
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=20.20 E-value=1.2e+02 Score=25.23 Aligned_cols=38 Identities=21% Similarity=0.421 Sum_probs=25.1
Q ss_pred CCHHHHHH---HHHHHHhCCCCCHHHHHHHHHHhCCC-cchhhh
Q 006856 502 MPPNAVEK---LRQVFAENELPSRIVKENLSKELSLE-PEKVNK 541 (628)
Q Consensus 502 ft~~Q~~~---Le~~F~~~~yPs~~~r~~LA~~lgLt-~~QVki 541 (628)
+|+-|.+. |..+..++.||. +-.+||+.+|+. ...|+.
T Consensus 4 LT~rQ~~vL~~I~~~~~~~G~~P--t~rEIa~~~g~~S~~tv~~ 45 (65)
T PF01726_consen 4 LTERQKEVLEFIREYIEENGYPP--TVREIAEALGLKSTSTVQR 45 (65)
T ss_dssp --HHHHHHHHHHHHHHHHHSS-----HHHHHHHHTSSSHHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHcCCCC--CHHHHHHHhCCCChHHHHH
Confidence 56666554 456677889984 788999999997 776754
No 187
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=20.07 E-value=58 Score=26.22 Aligned_cols=26 Identities=15% Similarity=0.282 Sum_probs=22.1
Q ss_pred HHHHHHHHHhCCCcchhhhccchhcc
Q 006856 523 IVKENLSKELSLEPEKVNKWFKNARY 548 (628)
Q Consensus 523 ~~r~~LA~~lgLt~~QVkiWFqNrR~ 548 (628)
-+..+||+.+|++...|..|.+.++.
T Consensus 15 ls~~~lA~~~g~s~s~v~~iE~G~~~ 40 (64)
T PF13560_consen 15 LSQAQLADRLGVSQSTVSRIERGRRP 40 (64)
T ss_dssp S-HHHHHHHHTS-HHHHHHHHTTSSS
T ss_pred CCHHHHHHHHCcCHHHHHHHHCCCCC
Confidence 36789999999999999999999985
Done!