Query psy4272
Match_columns 575
No_of_seqs 749 out of 4295
Neff 7.7
Searched_HMMs 46136
Date Fri Aug 16 21:20:24 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4272.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4272hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.9 2.2E-23 4.9E-28 201.9 9.3 133 59-217 129-264 (279)
2 KOG2462|consensus 99.8 1.5E-20 3.2E-25 182.4 8.1 125 86-236 128-255 (279)
3 KOG0484|consensus 99.8 9.8E-21 2.1E-25 155.5 5.3 69 319-387 13-81 (125)
4 KOG2251|consensus 99.8 2.3E-19 4.9E-24 168.4 8.4 68 318-385 32-99 (228)
5 KOG3623|consensus 99.7 3.3E-17 7.2E-22 174.9 10.9 110 89-222 211-335 (1007)
6 KOG3576|consensus 99.7 1.4E-17 3.1E-22 153.7 6.7 124 83-219 112-235 (267)
7 KOG0850|consensus 99.7 3.3E-17 7.2E-22 154.4 8.5 71 315-385 114-184 (245)
8 KOG0494|consensus 99.7 1.7E-17 3.7E-22 157.8 6.6 65 322-386 140-204 (332)
9 KOG0489|consensus 99.7 1.3E-17 2.8E-22 167.5 4.0 67 320-386 156-222 (261)
10 KOG0488|consensus 99.7 7E-17 1.5E-21 164.8 7.4 67 318-384 167-233 (309)
11 KOG0843|consensus 99.7 5.1E-17 1.1E-21 147.4 4.9 64 321-384 100-163 (197)
12 KOG0485|consensus 99.6 2.6E-15 5.6E-20 139.7 10.2 65 320-384 101-165 (268)
13 KOG0487|consensus 99.6 3.4E-16 7.4E-21 156.8 4.4 69 318-386 230-298 (308)
14 KOG0842|consensus 99.6 1.5E-15 3.2E-20 152.2 8.6 70 320-389 150-219 (307)
15 KOG0486|consensus 99.6 1.6E-15 3.4E-20 148.8 6.6 71 319-389 108-178 (351)
16 KOG0492|consensus 99.6 1.1E-15 2.4E-20 141.3 4.1 66 320-385 141-206 (246)
17 KOG0848|consensus 99.6 1.4E-15 3E-20 145.8 4.4 66 321-386 197-262 (317)
18 KOG0493|consensus 99.6 4E-15 8.7E-20 141.8 7.0 94 288-382 212-305 (342)
19 PF00046 Homeobox: Homeobox do 99.6 3.6E-15 7.7E-20 114.6 5.3 57 324-380 1-57 (57)
20 KOG4577|consensus 99.5 1.4E-14 3E-19 140.1 7.6 66 322-387 166-231 (383)
21 KOG0844|consensus 99.5 6.5E-15 1.4E-19 143.3 3.5 68 318-385 176-243 (408)
22 KOG1074|consensus 99.5 1.8E-14 3.8E-19 157.0 6.8 55 86-141 351-405 (958)
23 TIGR01565 homeo_ZF_HD homeobox 99.5 2.5E-14 5.5E-19 108.5 5.3 53 323-375 1-57 (58)
24 KOG3623|consensus 99.5 1.1E-14 2.4E-19 155.8 2.9 83 84-168 890-972 (1007)
25 KOG0491|consensus 99.5 1.7E-14 3.6E-19 128.9 2.7 67 320-386 97-163 (194)
26 KOG1074|consensus 99.5 3.8E-14 8.2E-19 154.5 4.5 84 118-220 606-692 (958)
27 smart00389 HOX Homeodomain. DN 99.4 5.1E-13 1.1E-17 102.1 5.3 56 324-379 1-56 (56)
28 KOG0483|consensus 99.4 2.8E-13 6E-18 128.7 4.3 72 323-394 50-121 (198)
29 cd00086 homeodomain Homeodomai 99.4 9.1E-13 2E-17 101.7 5.9 58 324-381 1-58 (59)
30 COG5576 Homeodomain-containing 99.4 7.2E-13 1.6E-17 121.8 5.9 67 321-387 49-115 (156)
31 KOG0847|consensus 99.3 1.5E-12 3.3E-17 121.4 4.9 66 321-386 165-230 (288)
32 KOG3802|consensus 99.3 1.2E-12 2.5E-17 133.8 4.1 62 322-383 293-354 (398)
33 KOG3576|consensus 99.2 8.9E-12 1.9E-16 115.6 4.9 114 58-173 115-239 (267)
34 KOG3608|consensus 99.2 3.7E-12 8E-17 126.9 1.8 131 66-221 185-317 (467)
35 KOG0490|consensus 99.2 5.2E-12 1.1E-16 125.5 2.4 64 320-383 57-120 (235)
36 KOG3608|consensus 99.1 1.8E-11 3.8E-16 122.1 1.5 150 62-217 209-373 (467)
37 KOG0849|consensus 99.1 3.2E-10 6.9E-15 118.7 8.8 69 317-385 170-238 (354)
38 KOG1146|consensus 98.9 4E-09 8.7E-14 121.2 11.4 64 320-383 900-963 (1406)
39 PHA00733 hypothetical protein 98.9 1.2E-09 2.6E-14 97.9 3.2 84 83-171 35-124 (128)
40 PHA02768 hypothetical protein; 98.8 1.4E-09 3E-14 81.0 2.2 44 117-163 5-48 (55)
41 KOG1168|consensus 98.8 2.1E-09 4.6E-14 104.6 1.9 64 320-383 306-369 (385)
42 PLN03086 PRLI-interacting fact 98.7 1.6E-08 3.5E-13 110.2 6.6 101 86-217 451-561 (567)
43 KOG0775|consensus 98.6 7E-08 1.5E-12 93.9 7.7 51 330-380 183-233 (304)
44 PHA00733 hypothetical protein 98.6 3.7E-08 8E-13 88.3 3.7 94 104-222 27-125 (128)
45 PHA02768 hypothetical protein; 98.5 7E-08 1.5E-12 72.0 1.9 44 88-134 5-48 (55)
46 PLN03086 PRLI-interacting fact 98.4 1.2E-07 2.6E-12 103.5 3.2 101 62-171 455-565 (567)
47 PF13465 zf-H2C2_2: Zinc-finge 98.4 1.7E-07 3.6E-12 59.7 1.7 24 133-157 2-25 (26)
48 PF13465 zf-H2C2_2: Zinc-finge 98.3 2.7E-07 6E-12 58.7 2.0 26 104-129 1-26 (26)
49 KOG3993|consensus 98.3 1.3E-07 2.9E-12 96.9 -0.3 85 89-175 268-385 (500)
50 KOG0774|consensus 98.2 4.3E-06 9.4E-11 80.7 7.3 60 323-382 188-250 (334)
51 KOG3993|consensus 98.2 6.8E-07 1.5E-11 91.9 1.5 108 118-226 268-386 (500)
52 PHA00616 hypothetical protein 98.1 1.4E-06 3.1E-11 61.9 1.6 36 117-153 1-36 (44)
53 KOG0490|consensus 98.1 3.4E-06 7.3E-11 83.7 4.4 65 319-383 149-213 (235)
54 KOG1146|consensus 98.0 1.4E-05 3E-10 92.9 9.3 274 91-382 439-764 (1406)
55 PHA00732 hypothetical protein 98.0 4E-06 8.7E-11 68.4 2.6 45 117-168 1-46 (79)
56 PF05920 Homeobox_KN: Homeobox 98.0 4.1E-06 8.8E-11 59.0 2.2 34 344-377 7-40 (40)
57 KOG2252|consensus 97.9 9.2E-06 2E-10 86.8 5.2 58 321-378 418-475 (558)
58 PHA00732 hypothetical protein 97.6 3.4E-05 7.4E-10 63.0 2.9 48 88-142 1-49 (79)
59 PHA00616 hypothetical protein 97.5 4.9E-05 1.1E-09 54.2 1.7 39 88-127 1-39 (44)
60 PF05605 zf-Di19: Drought indu 97.4 0.00018 3.8E-09 54.4 4.0 49 118-170 3-53 (54)
61 PF00096 zf-C2H2: Zinc finger, 97.3 0.0001 2.3E-09 45.2 1.7 23 118-140 1-23 (23)
62 COG5189 SFP1 Putative transcri 97.2 0.00011 2.4E-09 73.2 0.7 53 114-167 346-419 (423)
63 PF00096 zf-C2H2: Zinc finger, 97.0 0.00031 6.7E-09 43.1 1.3 22 147-168 1-22 (23)
64 PF13894 zf-C2H2_4: C2H2-type 96.8 0.00057 1.2E-08 41.9 1.5 23 147-169 1-23 (24)
65 PF05605 zf-Di19: Drought indu 96.7 0.0018 4E-08 48.8 3.7 50 88-141 2-53 (54)
66 PF13912 zf-C2H2_6: C2H2-type 96.5 0.0013 2.8E-08 42.0 1.6 23 118-140 2-24 (27)
67 PF13894 zf-C2H2_4: C2H2-type 96.5 0.0016 3.4E-08 39.9 1.9 23 118-140 1-23 (24)
68 PF13912 zf-C2H2_6: C2H2-type 96.4 0.0012 2.6E-08 42.1 0.9 24 147-170 2-25 (27)
69 PRK04860 hypothetical protein; 96.3 0.0017 3.6E-08 60.5 1.5 39 117-160 119-157 (160)
70 PF09237 GAGA: GAGA factor; I 95.9 0.006 1.3E-07 44.6 2.5 32 114-145 21-52 (54)
71 PF12756 zf-C2H2_2: C2H2 type 95.9 0.0046 9.9E-08 52.3 2.1 74 90-170 1-74 (100)
72 smart00355 ZnF_C2H2 zinc finge 95.7 0.0079 1.7E-07 37.2 2.2 22 119-140 2-23 (26)
73 PF12756 zf-C2H2_2: C2H2 type 95.5 0.0053 1.1E-07 51.9 0.9 26 197-222 51-76 (100)
74 COG5189 SFP1 Putative transcri 95.3 0.0073 1.6E-07 60.6 1.5 71 142-216 346-418 (423)
75 PRK04860 hypothetical protein; 95.3 0.0066 1.4E-07 56.5 1.1 40 87-131 118-157 (160)
76 PF11569 Homez: Homeodomain le 95.2 0.014 3.1E-07 43.9 2.4 41 335-375 10-50 (56)
77 smart00355 ZnF_C2H2 zinc finge 95.1 0.015 3.2E-07 35.9 2.0 22 147-168 1-22 (26)
78 COG5048 FOG: Zn-finger [Genera 94.9 0.0084 1.8E-07 64.1 0.5 72 87-160 288-367 (467)
79 PF09237 GAGA: GAGA factor; I 94.8 0.015 3.3E-07 42.5 1.5 38 134-172 12-50 (54)
80 PF12874 zf-met: Zinc-finger o 93.8 0.036 7.7E-07 34.5 1.5 22 118-139 1-22 (25)
81 KOG0773|consensus 93.4 0.11 2.4E-06 54.7 5.3 60 322-381 238-300 (342)
82 PF13909 zf-H2C2_5: C2H2-type 93.1 0.052 1.1E-06 33.4 1.4 23 147-170 1-23 (24)
83 PF12874 zf-met: Zinc-finger o 92.6 0.054 1.2E-06 33.6 0.9 22 147-168 1-22 (25)
84 PF04218 CENP-B_N: CENP-B N-te 92.6 0.17 3.7E-06 37.9 3.8 46 324-374 1-46 (53)
85 PF13909 zf-H2C2_5: C2H2-type 92.3 0.1 2.2E-06 32.1 1.9 23 118-141 1-23 (24)
86 PF12171 zf-C2H2_jaz: Zinc-fin 91.8 0.069 1.5E-06 34.0 0.7 22 118-139 2-23 (27)
87 KOG2482|consensus 90.4 0.19 4.1E-06 51.3 2.6 127 88-219 144-357 (423)
88 PF12171 zf-C2H2_jaz: Zinc-fin 89.9 0.084 1.8E-06 33.6 -0.2 22 147-168 2-23 (27)
89 COG5048 FOG: Zn-finger [Genera 89.8 0.096 2.1E-06 55.9 0.0 59 116-176 288-352 (467)
90 KOG2231|consensus 89.2 0.46 1E-05 53.5 4.7 22 148-169 184-205 (669)
91 KOG2893|consensus 88.9 0.13 2.8E-06 49.8 0.1 47 120-171 13-59 (341)
92 PF13913 zf-C2HC_2: zinc-finge 87.5 0.42 9E-06 30.0 1.7 19 148-167 4-22 (25)
93 KOG2231|consensus 87.1 0.7 1.5E-05 52.1 4.5 86 119-228 184-275 (669)
94 PF13913 zf-C2HC_2: zinc-finge 86.6 0.51 1.1E-05 29.6 1.8 20 118-138 3-22 (25)
95 smart00451 ZnF_U1 U1-like zinc 82.3 0.87 1.9E-05 30.5 1.6 21 118-138 4-24 (35)
96 PF09538 FYDLN_acid: Protein o 81.6 1 2.2E-05 39.1 2.2 30 118-159 10-39 (108)
97 TIGR00622 ssl1 transcription f 80.3 1.8 3.9E-05 37.7 3.2 91 89-219 2-104 (112)
98 KOG2893|consensus 80.0 0.58 1.3E-05 45.4 0.1 47 90-141 12-59 (341)
99 smart00451 ZnF_U1 U1-like zinc 79.7 1.1 2.3E-05 30.1 1.3 22 147-168 4-25 (35)
100 COG4049 Uncharacterized protei 78.3 0.9 1.9E-05 34.0 0.6 31 140-171 12-42 (65)
101 cd00350 rubredoxin_like Rubred 78.2 1.3 2.8E-05 29.7 1.4 24 118-154 2-25 (33)
102 KOG2186|consensus 74.0 1.8 3.9E-05 42.7 1.6 47 118-168 4-50 (276)
103 TIGR02300 FYDLN_acid conserved 73.7 2.4 5.2E-05 37.5 2.2 33 118-162 10-42 (129)
104 PF09986 DUF2225: Uncharacteri 72.0 1 2.2E-05 44.2 -0.6 44 116-159 4-61 (214)
105 KOG2186|consensus 71.1 1.6 3.6E-05 43.0 0.6 49 89-141 4-52 (276)
106 PF04545 Sigma70_r4: Sigma-70, 70.8 7 0.00015 28.5 3.8 46 329-379 4-49 (50)
107 COG4049 Uncharacterized protei 70.7 1.9 4E-05 32.3 0.7 31 111-141 11-41 (65)
108 cd00729 rubredoxin_SM Rubredox 69.6 2.4 5.1E-05 28.7 1.0 25 117-154 2-26 (34)
109 PF09538 FYDLN_acid: Protein o 69.4 2.9 6.2E-05 36.3 1.7 33 86-130 7-39 (108)
110 PF04967 HTH_10: HTH DNA bindi 69.4 7.9 0.00017 29.0 3.8 42 330-371 1-44 (53)
111 TIGR00373 conserved hypothetic 68.8 4.2 9E-05 37.9 2.8 39 111-159 103-141 (158)
112 PRK06266 transcription initiat 66.1 4.4 9.5E-05 38.5 2.4 36 114-159 114-149 (178)
113 COG1198 PriA Primosomal protei 65.8 2.4 5.3E-05 48.8 0.7 48 90-155 437-484 (730)
114 COG1997 RPL43A Ribosomal prote 65.6 2.3 5.1E-05 35.0 0.4 33 116-159 34-66 (89)
115 KOG4173|consensus 65.5 3 6.6E-05 39.8 1.1 79 88-171 79-171 (253)
116 PRK00464 nrdR transcriptional 65.0 1.8 3.8E-05 40.2 -0.5 13 147-159 29-41 (154)
117 COG5236 Uncharacterized conser 64.7 5.3 0.00012 41.1 2.8 66 103-170 167-244 (493)
118 COG1592 Rubrerythrin [Energy p 64.3 3.5 7.5E-05 38.6 1.3 24 117-154 134-157 (166)
119 TIGR02098 MJ0042_CXXC MJ0042 f 63.4 3.4 7.4E-05 28.4 0.8 33 118-156 3-35 (38)
120 PF08456 Vmethyltransf_C: Vira 63.3 7.4 0.00016 37.5 3.3 50 502-551 86-135 (212)
121 COG5236 Uncharacterized conser 60.8 8.8 0.00019 39.6 3.5 90 73-172 201-307 (493)
122 cd06171 Sigma70_r4 Sigma70, re 60.0 13 0.00028 26.4 3.5 44 329-377 10-53 (55)
123 PF08281 Sigma70_r4_2: Sigma-7 59.7 13 0.00028 27.4 3.5 42 330-376 11-52 (54)
124 PF12013 DUF3505: Protein of u 59.7 10 0.00022 32.7 3.4 25 147-171 81-109 (109)
125 KOG2785|consensus 59.1 10 0.00022 39.8 3.7 50 118-168 167-242 (390)
126 PF13719 zinc_ribbon_5: zinc-r 58.5 5.3 0.00012 27.5 1.1 32 119-156 4-35 (37)
127 smart00531 TFIIE Transcription 58.3 7 0.00015 35.9 2.2 40 114-158 96-135 (147)
128 KOG2071|consensus 58.3 7.1 0.00015 43.3 2.5 14 143-157 511-524 (579)
129 PF05443 ROS_MUCR: ROS/MUCR tr 58.2 4.4 9.6E-05 36.5 0.8 26 117-145 72-97 (132)
130 KOG2593|consensus 57.5 7.3 0.00016 41.6 2.4 39 113-155 124-162 (436)
131 TIGR02300 FYDLN_acid conserved 57.0 6.9 0.00015 34.7 1.8 37 86-134 7-43 (129)
132 PF02892 zf-BED: BED zinc fing 56.8 7.4 0.00016 27.7 1.7 23 115-137 14-40 (45)
133 PRK03975 tfx putative transcri 55.9 17 0.00036 33.2 4.1 50 328-383 5-54 (141)
134 PRK00464 nrdR transcriptional 55.2 3.7 8.1E-05 38.0 -0.2 43 90-133 2-44 (154)
135 PF09845 DUF2072: Zn-ribbon co 54.3 7.9 0.00017 34.6 1.7 31 117-158 1-32 (131)
136 PRK00398 rpoP DNA-directed RNA 54.3 3.8 8.2E-05 29.6 -0.2 29 117-156 3-31 (46)
137 smart00614 ZnF_BED BED zinc fi 53.7 8.6 0.00019 28.2 1.6 23 118-140 19-47 (50)
138 TIGR02605 CxxC_CxxC_SSSS putat 53.6 4.6 9.9E-05 29.8 0.1 13 118-130 6-18 (52)
139 smart00834 CxxC_CXXC_SSSS Puta 53.4 4.6 9.9E-05 28.0 0.1 13 118-130 6-18 (41)
140 PF02892 zf-BED: BED zinc fing 53.4 8.3 0.00018 27.4 1.5 28 142-170 13-44 (45)
141 COG4957 Predicted transcriptio 53.4 6 0.00013 35.3 0.8 25 118-145 77-101 (148)
142 COG4530 Uncharacterized protei 53.0 7.6 0.00016 33.4 1.3 27 119-157 11-37 (129)
143 KOG4173|consensus 52.2 14 0.00031 35.4 3.2 86 116-217 78-167 (253)
144 COG1996 RPC10 DNA-directed RNA 51.9 6.7 0.00014 28.9 0.7 11 117-127 6-16 (49)
145 smart00659 RPOLCX RNA polymera 51.5 8.3 0.00018 27.7 1.2 26 118-155 3-28 (44)
146 PF01527 HTH_Tnp_1: Transposas 50.9 11 0.00024 29.8 2.0 44 325-373 2-46 (76)
147 PF13717 zinc_ribbon_4: zinc-r 49.9 9.2 0.0002 26.2 1.1 33 118-156 3-35 (36)
148 TIGR00622 ssl1 transcription f 49.7 21 0.00045 31.2 3.6 79 86-168 13-103 (112)
149 COG2888 Predicted Zn-ribbon RN 49.6 10 0.00023 28.9 1.5 30 118-153 28-57 (61)
150 KOG3755|consensus 49.2 5.3 0.00012 44.1 -0.2 60 324-383 692-759 (769)
151 PF14353 CpXC: CpXC protein 49.1 12 0.00026 33.3 2.1 26 141-166 33-58 (128)
152 PF00196 GerE: Bacterial regul 48.7 26 0.00056 26.3 3.7 46 329-380 3-48 (58)
153 PRK09678 DNA-binding transcrip 45.7 7 0.00015 31.3 0.0 40 118-160 2-43 (72)
154 PF09110 HAND: HAND; InterPro 45.6 30 0.00064 30.4 3.9 46 509-559 43-88 (113)
155 cd00569 HTH_Hin_like Helix-tur 45.5 53 0.0011 20.6 4.6 38 329-371 5-42 (42)
156 PF05443 ROS_MUCR: ROS/MUCR tr 45.3 11 0.00024 33.9 1.3 22 147-171 73-94 (132)
157 PF09986 DUF2225: Uncharacteri 45.1 4 8.7E-05 40.0 -1.7 25 143-168 3-27 (214)
158 PF04959 ARS2: Arsenite-resist 44.4 7.3 0.00016 38.1 -0.0 31 142-173 74-104 (214)
159 PRK10072 putative transcriptio 43.9 30 0.00065 29.4 3.6 41 329-376 32-72 (96)
160 COG5152 Uncharacterized conser 43.8 13 0.00028 35.4 1.5 57 85-165 193-253 (259)
161 PF07295 DUF1451: Protein of u 43.5 12 0.00027 34.3 1.3 44 104-158 95-143 (146)
162 PF04959 ARS2: Arsenite-resist 43.3 9.9 0.00021 37.2 0.7 30 114-143 74-103 (214)
163 COG5151 SSL1 RNA polymerase II 42.5 16 0.00036 37.1 2.1 27 195-221 387-413 (421)
164 PF10668 Phage_terminase: Phag 42.3 18 0.00038 27.9 1.8 27 352-380 24-50 (60)
165 TIGR00595 priA primosomal prot 42.3 9 0.00019 42.7 0.3 10 144-154 252-261 (505)
166 PRK14873 primosome assembly pr 42.0 8.2 0.00018 44.4 -0.1 47 90-155 385-431 (665)
167 COG1997 RPL43A Ribosomal prote 41.9 16 0.00035 30.2 1.6 34 87-131 34-67 (89)
168 PTZ00303 phosphatidylinositol 40.5 18 0.0004 41.3 2.3 36 118-161 461-496 (1374)
169 PRK00118 putative DNA-binding 40.2 45 0.00098 28.7 4.2 49 329-382 17-65 (104)
170 PF10571 UPF0547: Uncharacteri 40.2 18 0.0004 22.9 1.3 10 119-128 16-25 (26)
171 PF09723 Zn-ribbon_8: Zinc rib 40.2 11 0.00025 26.6 0.4 13 118-130 6-18 (42)
172 KOG4167|consensus 39.7 7.5 0.00016 43.9 -0.8 26 117-142 792-817 (907)
173 TIGR03879 near_KaiC_dom probab 39.0 14 0.00031 29.6 0.9 35 339-373 21-55 (73)
174 KOG1280|consensus 38.4 14 0.0003 38.3 0.9 29 143-172 77-105 (381)
175 KOG0782|consensus 38.3 17 0.00037 40.0 1.5 34 128-162 236-269 (1004)
176 PRK06759 RNA polymerase factor 38.3 44 0.00095 30.1 4.2 47 329-380 106-152 (154)
177 COG1592 Rubrerythrin [Energy p 36.8 19 0.0004 33.8 1.4 24 88-125 134-157 (166)
178 COG3413 Predicted DNA binding 36.7 41 0.0009 32.7 3.9 47 329-377 155-203 (215)
179 PF09607 BrkDBD: Brinker DNA-b 35.8 68 0.0015 24.6 4.0 44 327-372 3-47 (58)
180 KOG4167|consensus 35.6 9.6 0.00021 43.1 -0.8 23 147-169 793-815 (907)
181 PRK04217 hypothetical protein; 35.6 58 0.0012 28.4 4.1 48 329-381 42-89 (110)
182 PRK14890 putative Zn-ribbon RN 35.5 19 0.00042 27.5 1.0 30 118-154 26-56 (59)
183 PF13936 HTH_38: Helix-turn-he 35.2 29 0.00064 24.7 1.9 40 328-372 3-42 (44)
184 KOG4124|consensus 35.1 8.3 0.00018 39.8 -1.3 50 116-166 348-418 (442)
185 PRK09646 RNA polymerase sigma 34.9 49 0.0011 31.4 4.1 48 329-381 142-189 (194)
186 PRK09652 RNA polymerase sigma 34.8 48 0.001 30.5 3.9 47 329-380 128-174 (182)
187 PHA00626 hypothetical protein 34.7 14 0.00029 27.9 0.1 12 147-158 24-35 (59)
188 COG3091 SprT Zn-dependent meta 34.4 15 0.00033 33.7 0.3 34 116-155 116-149 (156)
189 PRK12526 RNA polymerase sigma 34.1 49 0.0011 31.8 3.9 49 329-382 153-201 (206)
190 COG4306 Uncharacterized protei 34.0 14 0.0003 32.6 0.1 42 118-160 40-82 (160)
191 smart00531 TFIIE Transcription 34.0 16 0.00035 33.4 0.5 40 85-129 96-135 (147)
192 COG2331 Uncharacterized protei 33.3 16 0.00035 29.3 0.3 31 118-156 13-43 (82)
193 PF08649 DASH_Dad1: DASH compl 33.2 29 0.00064 26.5 1.7 22 514-536 3-24 (58)
194 KOG2785|consensus 32.6 39 0.00084 35.7 3.0 52 86-138 164-241 (390)
195 PF05527 DUF758: Domain of unk 32.1 43 0.00093 32.0 3.0 38 504-541 39-81 (186)
196 PTZ00255 60S ribosomal protein 31.1 24 0.00051 29.5 1.0 33 116-159 35-67 (90)
197 smart00421 HTH_LUXR helix_turn 30.9 76 0.0016 22.7 3.7 43 329-377 3-45 (58)
198 PRK12512 RNA polymerase sigma 30.9 63 0.0014 30.2 4.0 50 329-383 131-180 (184)
199 COG4888 Uncharacterized Zn rib 30.8 9.1 0.0002 32.4 -1.5 39 115-158 20-58 (104)
200 COG3091 SprT Zn-dependent meta 30.7 18 0.0004 33.1 0.3 38 85-128 114-151 (156)
201 smart00734 ZnF_Rad18 Rad18-lik 30.6 37 0.00081 21.4 1.6 19 148-167 3-21 (26)
202 PRK12519 RNA polymerase sigma 30.5 52 0.0011 31.1 3.4 46 330-380 142-187 (194)
203 KOG3362|consensus 30.4 18 0.00038 32.8 0.1 20 118-137 130-149 (156)
204 COG2944 Predicted transcriptio 30.1 70 0.0015 27.6 3.7 39 330-375 44-82 (104)
205 cd04761 HTH_MerR-SF Helix-Turn 30.0 34 0.00074 24.2 1.6 22 353-374 3-24 (49)
206 PF10083 DUF2321: Uncharacteri 30.0 11 0.00023 34.8 -1.4 43 119-162 41-84 (158)
207 TIGR01206 lysW lysine biosynth 29.8 17 0.00037 27.4 -0.1 30 118-156 3-32 (54)
208 smart00426 TEA TEA domain. 29.7 35 0.00077 26.9 1.6 26 517-542 39-64 (68)
209 PRK09642 RNA polymerase sigma 29.4 67 0.0015 29.2 3.9 48 330-382 107-154 (160)
210 PRK05580 primosome assembly pr 29.3 19 0.00041 41.7 0.1 18 358-375 574-593 (679)
211 TIGR02937 sigma70-ECF RNA poly 29.1 68 0.0015 28.1 3.8 47 329-380 110-156 (158)
212 PF13443 HTH_26: Cro/C1-type H 29.0 36 0.00078 25.7 1.7 26 352-377 12-37 (63)
213 PF06056 Terminase_5: Putative 29.0 22 0.00047 27.2 0.4 31 351-383 14-44 (58)
214 KOG0320|consensus 28.9 22 0.00048 33.5 0.5 52 86-159 129-180 (187)
215 KOG0696|consensus 28.9 22 0.00048 38.1 0.5 46 113-168 69-114 (683)
216 PRK06930 positive control sigm 28.6 75 0.0016 29.9 4.0 49 329-382 114-162 (170)
217 PF09416 UPF1_Zn_bind: RNA hel 28.5 43 0.00093 30.9 2.3 37 118-155 15-69 (152)
218 TIGR02999 Sig-70_X6 RNA polyme 28.5 75 0.0016 29.6 4.1 46 330-380 135-180 (183)
219 PF01363 FYVE: FYVE zinc finge 28.1 23 0.00051 27.6 0.4 10 119-128 11-20 (69)
220 PF09845 DUF2072: Zn-ribbon co 28.0 37 0.0008 30.4 1.7 27 88-125 1-27 (131)
221 PRK11924 RNA polymerase sigma 28.0 72 0.0016 29.2 3.9 47 330-381 126-172 (179)
222 TIGR00280 L37a ribosomal prote 27.9 26 0.00057 29.4 0.7 33 116-159 34-66 (91)
223 KOG2461|consensus 27.8 1.1E+02 0.0025 32.8 5.7 62 106-168 320-381 (396)
224 COG1571 Predicted DNA-binding 27.8 34 0.00074 36.8 1.7 30 119-160 352-381 (421)
225 TIGR02985 Sig70_bacteroi1 RNA 27.7 83 0.0018 28.2 4.2 47 329-380 113-159 (161)
226 PRK03824 hypA hydrogenase nick 27.3 25 0.00055 31.8 0.6 15 116-130 69-83 (135)
227 PRK09648 RNA polymerase sigma 27.2 80 0.0017 29.6 4.1 48 328-380 138-185 (189)
228 PF15269 zf-C2H2_7: Zinc-finge 27.2 36 0.00079 24.4 1.2 22 147-168 21-42 (54)
229 TIGR00373 conserved hypothetic 27.1 30 0.00065 32.2 1.1 35 85-129 106-140 (158)
230 KOG0782|consensus 27.0 13 0.00028 40.8 -1.5 52 103-160 239-290 (1004)
231 PRK12514 RNA polymerase sigma 26.9 83 0.0018 29.2 4.1 47 330-381 130-176 (179)
232 TIGR02989 Sig-70_gvs1 RNA poly 26.7 86 0.0019 28.3 4.1 47 328-379 110-156 (159)
233 KOG2593|consensus 26.5 40 0.00087 36.2 1.9 52 71-126 111-162 (436)
234 PF08280 HTH_Mga: M protein tr 26.2 76 0.0016 24.0 3.0 35 333-371 6-40 (59)
235 KOG0978|consensus 26.2 25 0.00053 40.3 0.4 19 147-165 679-697 (698)
236 PRK06266 transcription initiat 26.1 32 0.00069 32.7 1.0 34 86-129 115-148 (178)
237 PRK12515 RNA polymerase sigma 25.8 89 0.0019 29.4 4.1 49 329-382 131-179 (189)
238 COG1198 PriA Primosomal protei 25.6 23 0.0005 41.1 0.0 36 498-533 674-712 (730)
239 KOG4141|consensus 25.6 57 0.0012 31.6 2.6 31 515-545 32-62 (222)
240 TIGR02959 SigZ RNA polymerase 25.4 95 0.0021 28.7 4.2 48 329-381 100-147 (170)
241 PRK09644 RNA polymerase sigma 25.4 89 0.0019 28.6 3.9 49 329-382 108-156 (165)
242 COG3677 Transposase and inacti 25.3 26 0.00057 31.4 0.3 13 147-159 54-66 (129)
243 PRK12530 RNA polymerase sigma 24.1 1E+02 0.0022 29.2 4.1 47 329-380 134-180 (189)
244 KOG2807|consensus 24.1 79 0.0017 32.7 3.4 28 193-220 342-369 (378)
245 PF03604 DNA_RNApol_7kD: DNA d 24.0 49 0.0011 22.1 1.3 11 118-128 1-11 (32)
246 PRK05602 RNA polymerase sigma 24.0 89 0.0019 29.2 3.7 48 330-382 129-176 (186)
247 PRK03976 rpl37ae 50S ribosomal 24.0 33 0.00072 28.7 0.6 32 116-158 35-66 (90)
248 TIGR00100 hypA hydrogenase nic 24.0 36 0.00077 29.9 0.9 24 118-154 71-94 (115)
249 PRK09637 RNA polymerase sigma 24.0 98 0.0021 29.0 4.0 47 329-380 106-152 (181)
250 PRK09639 RNA polymerase sigma 23.9 1E+02 0.0022 28.1 4.0 47 329-381 112-158 (166)
251 TIGR00721 tfx DNA-binding prot 23.7 1.3E+02 0.0028 27.4 4.4 48 327-380 4-51 (137)
252 PRK12380 hydrogenase nickel in 23.7 38 0.00083 29.6 1.0 24 118-154 71-94 (113)
253 TIGR02948 SigW_bacill RNA poly 23.6 86 0.0019 29.2 3.5 48 329-381 136-183 (187)
254 COG5432 RAD18 RING-finger-cont 23.5 36 0.00079 34.4 0.9 43 89-156 26-69 (391)
255 PF01780 Ribosomal_L37ae: Ribo 23.3 24 0.00052 29.5 -0.3 32 116-158 34-65 (90)
256 PRK12541 RNA polymerase sigma 23.2 1E+02 0.0023 27.9 4.0 48 329-381 112-159 (161)
257 PF10263 SprT-like: SprT-like 23.2 22 0.00047 32.6 -0.7 32 117-157 123-154 (157)
258 COG3357 Predicted transcriptio 23.2 45 0.00098 27.8 1.3 27 116-153 57-83 (97)
259 cd04762 HTH_MerR-trunc Helix-T 22.9 43 0.00094 23.3 1.0 25 353-377 3-27 (49)
260 KOG1813|consensus 22.7 51 0.0011 33.6 1.8 59 86-168 239-301 (313)
261 cd00924 Cyt_c_Oxidase_Vb Cytoc 22.4 33 0.00072 29.2 0.4 23 107-130 70-92 (97)
262 PF12013 DUF3505: Protein of u 22.4 57 0.0012 28.1 1.8 25 118-142 81-109 (109)
263 cd00065 FYVE FYVE domain; Zinc 22.3 48 0.0011 24.6 1.2 11 118-128 19-29 (57)
264 PRK12537 RNA polymerase sigma 22.3 1.1E+02 0.0025 28.4 4.1 47 329-380 133-179 (182)
265 TIGR02939 RpoE_Sigma70 RNA pol 22.1 90 0.0019 29.1 3.4 47 330-381 139-185 (190)
266 KOG2461|consensus 22.1 1.3E+02 0.0028 32.4 4.8 50 104-154 346-395 (396)
267 PF13384 HTH_23: Homeodomain-l 21.9 61 0.0013 23.2 1.7 22 351-372 18-39 (50)
268 cd06170 LuxR_C_like C-terminal 21.9 1.1E+02 0.0024 21.9 3.2 36 331-372 2-37 (57)
269 PRK07037 extracytoplasmic-func 21.4 1.3E+02 0.0027 27.4 4.1 48 329-381 109-156 (163)
270 COG0068 HypF Hydrogenase matur 21.3 14 0.0003 42.1 -2.8 72 91-203 104-180 (750)
271 PRK05978 hypothetical protein; 21.3 41 0.00089 30.9 0.7 32 118-159 34-65 (148)
272 PRK09047 RNA polymerase factor 21.2 1.3E+02 0.0028 27.2 4.1 47 329-380 106-152 (161)
273 COG4957 Predicted transcriptio 21.1 55 0.0012 29.4 1.4 24 90-117 78-101 (148)
274 smart00064 FYVE Protein presen 21.0 52 0.0011 25.5 1.2 10 119-128 12-21 (68)
275 PRK12529 RNA polymerase sigma 21.0 1.3E+02 0.0028 28.0 4.2 48 329-381 127-174 (178)
276 PRK09413 IS2 repressor TnpA; R 21.0 1.7E+02 0.0036 25.7 4.6 40 327-371 10-50 (121)
277 PRK12543 RNA polymerase sigma 20.9 1.3E+02 0.0028 28.0 4.1 50 329-383 117-166 (179)
278 COG1656 Uncharacterized conser 20.9 70 0.0015 29.9 2.1 47 118-167 98-151 (165)
279 PRK06986 fliA flagellar biosyn 20.9 1.1E+02 0.0024 30.0 3.9 48 329-381 184-231 (236)
280 PF13518 HTH_28: Helix-turn-he 20.8 63 0.0014 23.2 1.6 22 352-373 14-35 (52)
281 PRK12538 RNA polymerase sigma 20.8 1E+02 0.0022 30.4 3.5 48 330-382 172-219 (233)
282 TIGR02983 SigE-fam_strep RNA p 20.8 1.2E+02 0.0026 27.5 3.8 48 329-381 110-157 (162)
283 PF01927 Mut7-C: Mut7-C RNAse 20.7 58 0.0013 29.8 1.6 48 118-166 92-144 (147)
284 COG5151 SSL1 RNA polymerase II 20.4 73 0.0016 32.6 2.3 47 119-168 364-410 (421)
285 PF02796 HTH_7: Helix-turn-hel 20.0 1.2E+02 0.0025 21.6 2.7 38 329-371 5-42 (45)
No 1
>KOG2462|consensus
Probab=99.89 E-value=2.2e-23 Score=201.91 Aligned_cols=133 Identities=17% Similarity=0.243 Sum_probs=122.9
Q ss_pred hccccccCchHHHhhhccCCCCCCCCC---CCCCCCCCCcchhhcchhHHHHHhhhcCCCCcccccccCccccChhhHHH
Q psy4272 59 IADVATKTLPVIQELLSQRDGKPVGKA---TLPSPLKAKLSDYENKMKNVRESIRQKRLAQGLTCLQCGRSYCRPYNLKR 135 (575)
Q Consensus 59 ~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~p~~C~~C~~~f~~~~~~L~~H~r~H~~~kp~~C~~Cgk~F~~~~~L~~ 135 (575)
..-+|..|.+.+.+.+.+.+|+..|-. ...+.|.+|+|.|... ..|+.|+|+|+ -+++|.+|||.|.+..-|+.
T Consensus 129 ~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSm-pALkMHirTH~--l~c~C~iCGKaFSRPWLLQG 205 (279)
T KOG2462|consen 129 PRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSM-PALKMHIRTHT--LPCECGICGKAFSRPWLLQG 205 (279)
T ss_pred CceeccccccccccccccchhhcccccccccccccCCCCCceeeeh-HHHhhHhhccC--CCcccccccccccchHHhhc
Confidence 345788999999999988888877755 5668999999999998 69999999998 68999999999999999999
Q ss_pred HhhhhhCCCCCcccccccccccChhhHHHHHHhhccCcccchhhhhhhhhcccccCCCCCCCcchhhhhhccChhhhHhh
Q psy4272 136 HIQYECGKAPQFPCLYCSYRARHKHDLKKHVTFKHAAYLDHFQAVQEELEVTTKELSPGPKAENRHRFREFLNEHRNLER 215 (575)
Q Consensus 136 H~r~H~gekp~~~C~~Cgk~F~~~~~L~~H~r~~H~~~~~~~~~~~~~~~~~t~e~sp~p~~~C~~C~k~F~~~~~l~~H 215 (575)
|+|+|||||| |.|.+|+|.|..+++|+.||++ |.+.++| +|..|+|+|...+.|.+|
T Consensus 206 HiRTHTGEKP-F~C~hC~kAFADRSNLRAHmQT-HS~~K~~---------------------qC~~C~KsFsl~SyLnKH 262 (279)
T KOG2462|consen 206 HIRTHTGEKP-FSCPHCGKAFADRSNLRAHMQT-HSDVKKH---------------------QCPRCGKSFALKSYLNKH 262 (279)
T ss_pred ccccccCCCC-ccCCcccchhcchHHHHHHHHh-hcCCccc---------------------cCcchhhHHHHHHHHHHh
Confidence 9999999999 9999999999999999999999 8888888 999999999999999999
Q ss_pred hh
Q psy4272 216 NV 217 (575)
Q Consensus 216 ~~ 217 (575)
..
T Consensus 263 ~E 264 (279)
T KOG2462|consen 263 SE 264 (279)
T ss_pred hh
Confidence 64
No 2
>KOG2462|consensus
Probab=99.82 E-value=1.5e-20 Score=182.44 Aligned_cols=125 Identities=17% Similarity=0.244 Sum_probs=115.3
Q ss_pred CCCCCCCCCcchhhcchhHHHHHhhhcC---CCCcccccccCccccChhhHHHHhhhhhCCCCCcccccccccccChhhH
Q psy4272 86 TLPSPLKAKLSDYENKMKNVRESIRQKR---LAQGLTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSYRARHKHDL 162 (575)
Q Consensus 86 ~~p~~C~~C~~~f~~~~~~L~~H~r~H~---~~kp~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk~F~~~~~L 162 (575)
..-|.|..||+.|.+. ++|.+|+.+|. ..+.|.|++|||.|.....|+.|+|+|+ -+ ++|.+|||.|.+..-|
T Consensus 128 ~~r~~c~eCgk~ysT~-snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~--l~-c~C~iCGKaFSRPWLL 203 (279)
T KOG2462|consen 128 HPRYKCPECGKSYSTS-SNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT--LP-CECGICGKAFSRPWLL 203 (279)
T ss_pred CCceeccccccccccc-cccchhhcccccccccccccCCCCCceeeehHHHhhHhhccC--CC-cccccccccccchHHh
Confidence 3458999999999988 79999999996 3577999999999999999999999998 56 9999999999999999
Q ss_pred HHHHHhhccCcccchhhhhhhhhcccccCCCCCCCcchhhhhhccChhhhHhhhhhhhhhhccccCCCCCCCCC
Q psy4272 163 KKHVTFKHAAYLDHFQAVQEELEVTTKELSPGPKAENRHRFREFLNEHRNLERNVSHEEIRTHKKHEQPRKESS 236 (575)
Q Consensus 163 ~~H~r~~H~~~~~~~~~~~~~~~~~t~e~sp~p~~~C~~C~k~F~~~~~l~~H~~th~~~~~~~~~~~~~~~ss 236 (575)
+-|+|+ |+||+|| .|.+|+|.|..+++|+.|+.||.+.+.|.+..+.+.++.
T Consensus 204 QGHiRT-HTGEKPF---------------------~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl 255 (279)
T KOG2462|consen 204 QGHIRT-HTGEKPF---------------------SCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFAL 255 (279)
T ss_pred hccccc-ccCCCCc---------------------cCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHH
Confidence 999999 9999999 999999999999999999999999999999888665554
No 3
>KOG0484|consensus
Probab=99.82 E-value=9.8e-21 Score=155.49 Aligned_cols=69 Identities=30% Similarity=0.557 Sum_probs=64.3
Q ss_pred cCCCCCCCcccCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhcCCcchh
Q psy4272 319 LQCNTGRFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTHPDMVV 387 (575)
Q Consensus 319 ~~~~~rr~Rt~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~~~~~~~ 387 (575)
..+|+||-||+||..||.+||+.|.+++||++..|++||.++.|++.+|||||||||||+||+.+....
T Consensus 13 ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a~~ 81 (125)
T KOG0484|consen 13 EKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAAIA 81 (125)
T ss_pred HHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHHHH
Confidence 357899999999999999999999999999999999999999999999999999999999998765443
No 4
>KOG2251|consensus
Probab=99.79 E-value=2.3e-19 Score=168.37 Aligned_cols=68 Identities=29% Similarity=0.438 Sum_probs=64.6
Q ss_pred ccCCCCCCCcccCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhcCCcc
Q psy4272 318 LLQCNTGRFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTHPDM 385 (575)
Q Consensus 318 ~~~~~~rr~Rt~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~~~~~ 385 (575)
...+|+||.||+|+..||++||.+|.+++||++..|++||.+|+|++.+|||||+|||||+|++++.+
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 45689999999999999999999999999999999999999999999999999999999999988765
No 5
>KOG3623|consensus
Probab=99.71 E-value=3.3e-17 Score=174.86 Aligned_cols=110 Identities=20% Similarity=0.318 Sum_probs=77.2
Q ss_pred CCCCCCcchhhcchhHHHHHhhh-c-CCCCcccccccCccccChhhHHHHhhhhh-------------CCCCCccccccc
Q psy4272 89 SPLKAKLSDYENKMKNVRESIRQ-K-RLAQGLTCLQCGRSYCRPYNLKRHIQYEC-------------GKAPQFPCLYCS 153 (575)
Q Consensus 89 ~~C~~C~~~f~~~~~~L~~H~r~-H-~~~kp~~C~~Cgk~F~~~~~L~~H~r~H~-------------gekp~~~C~~Cg 153 (575)
..|.+|.+.|.+. ..|+.|+.. | ..+..|.|..|...|..+..|.+|+.+|. +.+. |+|..||
T Consensus 211 ltcpycdrgykrl-tslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRK-FKCtECg 288 (1007)
T KOG3623|consen 211 LTCPYCDRGYKRL-TSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRK-FKCTECG 288 (1007)
T ss_pred hcchhHHHHHHHH-HHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhcc-ccccccc
Confidence 3577777777766 466666653 2 23445778778877877777777777763 2355 7788888
Q ss_pred ccccChhhHHHHHHhhccCcccchhhhhhhhhcccccCCCCCCCcchhhhhhccChhhhHhhhhhhhhh
Q psy4272 154 YRARHKHDLKKHVTFKHAAYLDHFQAVQEELEVTTKELSPGPKAENRHRFREFLNEHRNLERNVSHEEI 222 (575)
Q Consensus 154 k~F~~~~~L~~H~r~~H~~~~~~~~~~~~~~~~~t~e~sp~p~~~C~~C~k~F~~~~~l~~H~~th~~~ 222 (575)
|.|..+.+|+.|+|+ |.|+++| +|..|.|.|........|+-+...|
T Consensus 289 KAFKfKHHLKEHlRI-HSGEKPf---------------------eCpnCkKRFSHSGSySSHmSSKKCI 335 (1007)
T KOG3623|consen 289 KAFKFKHHLKEHLRI-HSGEKPF---------------------ECPNCKKRFSHSGSYSSHMSSKKCI 335 (1007)
T ss_pred hhhhhHHHHHhhhee-ecCCCCc---------------------CCcccccccccCCcccccccccchh
Confidence 888888888888777 7777777 7777877777777777776544333
No 6
>KOG3576|consensus
Probab=99.70 E-value=1.4e-17 Score=153.66 Aligned_cols=124 Identities=12% Similarity=0.162 Sum_probs=104.6
Q ss_pred CCCCCCCCCCCCcchhhcchhHHHHHhhhcCCCCcccccccCccccChhhHHHHhhhhhCCCCCcccccccccccChhhH
Q psy4272 83 GKATLPSPLKAKLSDYENKMKNVRESIRQKRLAQGLTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSYRARHKHDL 162 (575)
Q Consensus 83 ~~~~~p~~C~~C~~~f~~~~~~L~~H~r~H~~~kp~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk~F~~~~~L 162 (575)
.+....+.|.+|+|.|.-+ ..|.+|++.|...|.|-|..|||.|.....|++|+|+|+|.+| |+|..|+|.|.++..|
T Consensus 112 ssd~d~ftCrvCgK~F~lQ-Rmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrp-ykc~~c~kaftqrcsl 189 (267)
T KOG3576|consen 112 SSDQDSFTCRVCGKKFGLQ-RMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRP-YKCSLCEKAFTQRCSL 189 (267)
T ss_pred CCCCCeeeeehhhhhhhHH-HHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccc-cchhhhhHHHHhhccH
Confidence 3446779999999999888 5999999999999999999999999999999999999999999 9999999999999999
Q ss_pred HHHHHhhccCcccchhhhhhhhhcccccCCCCCCCcchhhhhhccChhhhHhhhhhh
Q psy4272 163 KKHVTFKHAAYLDHFQAVQEELEVTTKELSPGPKAENRHRFREFLNEHRNLERNVSH 219 (575)
Q Consensus 163 ~~H~r~~H~~~~~~~~~~~~~~~~~t~e~sp~p~~~C~~C~k~F~~~~~l~~H~~th 219 (575)
..|.+..|+..-.|..+... .-.+.|+.|+.+-........|...|
T Consensus 190 eshl~kvhgv~~~yaykerr-----------~kl~vcedcg~t~~~~e~~~~h~~~~ 235 (267)
T KOG3576|consen 190 ESHLKKVHGVQHQYAYKERR-----------AKLYVCEDCGYTSERPEVYYLHLKLH 235 (267)
T ss_pred HHHHHHHcCchHHHHHHHhh-----------hheeeecccCCCCCChhHHHHHHHhc
Confidence 99999878765544332211 11237999998877777777787655
No 7
>KOG0850|consensus
Probab=99.70 E-value=3.3e-17 Score=154.42 Aligned_cols=71 Identities=39% Similarity=0.582 Sum_probs=65.9
Q ss_pred cccccCCCCCCCcccCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhcCCcc
Q psy4272 315 HKNLLQCNTGRFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTHPDM 385 (575)
Q Consensus 315 ~~~~~~~~~rr~Rt~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~~~~~ 385 (575)
.-+..++|.|+.||.|+..||..|.+.|++++|....+|.+||..|||+..||||||||||.|.||..+..
T Consensus 114 ~~Ngk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~g 184 (245)
T KOG0850|consen 114 RPNGKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQG 184 (245)
T ss_pred ccCCCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhcC
Confidence 34566788899999999999999999999999999999999999999999999999999999999988743
No 8
>KOG0494|consensus
Probab=99.70 E-value=1.7e-17 Score=157.83 Aligned_cols=65 Identities=35% Similarity=0.618 Sum_probs=59.7
Q ss_pred CCCCCcccCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhcCCcch
Q psy4272 322 NTGRFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTHPDMV 386 (575)
Q Consensus 322 ~~rr~Rt~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~~~~~~ 386 (575)
++|+.||.||..|+..||+.|.+.+||+...|+.||.++.|++.+||||||||||||||..+...
T Consensus 140 kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg 204 (332)
T KOG0494|consen 140 KRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWG 204 (332)
T ss_pred ccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcC
Confidence 44445999999999999999999999999999999999999999999999999999999876543
No 9
>KOG0489|consensus
Probab=99.68 E-value=1.3e-17 Score=167.52 Aligned_cols=67 Identities=46% Similarity=0.735 Sum_probs=62.9
Q ss_pred CCCCCCCcccCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhcCCcch
Q psy4272 320 QCNTGRFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTHPDMV 386 (575)
Q Consensus 320 ~~~~rr~Rt~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~~~~~~ 386 (575)
..+.||.||.||..||.+||+.|..|+|.++..|.|||..|.|+|+||||||||||+||||..+...
T Consensus 156 ~~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~ 222 (261)
T KOG0489|consen 156 GGKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKS 222 (261)
T ss_pred cCCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccc
Confidence 3457999999999999999999999999999999999999999999999999999999999877654
No 10
>KOG0488|consensus
Probab=99.67 E-value=7e-17 Score=164.81 Aligned_cols=67 Identities=42% Similarity=0.655 Sum_probs=63.0
Q ss_pred ccCCCCCCCcccCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhcCCc
Q psy4272 318 LLQCNTGRFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTHPD 384 (575)
Q Consensus 318 ~~~~~~rr~Rt~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~~~~ 384 (575)
..++|+|+.||.||..||..||+.|++..|.+..+|.+||..|||+..||++||||||+||||+...
T Consensus 167 ~~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~ 233 (309)
T KOG0488|consen 167 STPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE 233 (309)
T ss_pred CCCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence 3448889999999999999999999999999999999999999999999999999999999997654
No 11
>KOG0843|consensus
Probab=99.66 E-value=5.1e-17 Score=147.45 Aligned_cols=64 Identities=38% Similarity=0.692 Sum_probs=61.1
Q ss_pred CCCCCCcccCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhcCCc
Q psy4272 321 CNTGRFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTHPD 384 (575)
Q Consensus 321 ~~~rr~Rt~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~~~~ 384 (575)
.+.||.||.||.+||..||..|+.++|....+|+.||+.|+|++.||||||||||.|.||.+..
T Consensus 100 ~~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e 163 (197)
T KOG0843|consen 100 MRPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQE 163 (197)
T ss_pred cCCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHH
Confidence 4889999999999999999999999999999999999999999999999999999999997654
No 12
>KOG0485|consensus
Probab=99.61 E-value=2.6e-15 Score=139.72 Aligned_cols=65 Identities=45% Similarity=0.658 Sum_probs=61.2
Q ss_pred CCCCCCCcccCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhcCCc
Q psy4272 320 QCNTGRFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTHPD 384 (575)
Q Consensus 320 ~~~~rr~Rt~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~~~~ 384 (575)
..++||.||+|+..|+..||..|+..+|.+..+|..||.+|.|++.||||||||||-||||+...
T Consensus 101 ~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aa 165 (268)
T KOG0485|consen 101 DDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAA 165 (268)
T ss_pred ccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhh
Confidence 45788899999999999999999999999999999999999999999999999999999997643
No 13
>KOG0487|consensus
Probab=99.61 E-value=3.4e-16 Score=156.79 Aligned_cols=69 Identities=45% Similarity=0.668 Sum_probs=63.6
Q ss_pred ccCCCCCCCcccCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhcCCcch
Q psy4272 318 LLQCNTGRFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTHPDMV 386 (575)
Q Consensus 318 ~~~~~~rr~Rt~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~~~~~~ 386 (575)
...+..|++|.-+|..|+.+||+.|..|.|.+...|.+|++.|+|++|||||||||||+|+||..+...
T Consensus 230 ~~~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~r 298 (308)
T KOG0487|consen 230 SSARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRENR 298 (308)
T ss_pred ccccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhhh
Confidence 334678889999999999999999999999999999999999999999999999999999999886443
No 14
>KOG0842|consensus
Probab=99.60 E-value=1.5e-15 Score=152.17 Aligned_cols=70 Identities=41% Similarity=0.656 Sum_probs=64.2
Q ss_pred CCCCCCCcccCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhcCCcchhhh
Q psy4272 320 QCNTGRFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTHPDMVVEY 389 (575)
Q Consensus 320 ~~~~rr~Rt~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~~~~~~~~~ 389 (575)
.+++||.|..|+..|+.+||+.|..++|.+..+|+.||..|+|++.||||||||||-|.||+++......
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~ 219 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEA 219 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhc
Confidence 4567788999999999999999999999999999999999999999999999999999999887665443
No 15
>KOG0486|consensus
Probab=99.58 E-value=1.6e-15 Score=148.80 Aligned_cols=71 Identities=28% Similarity=0.484 Sum_probs=65.9
Q ss_pred cCCCCCCCcccCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhcCCcchhhh
Q psy4272 319 LQCNTGRFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTHPDMVVEY 389 (575)
Q Consensus 319 ~~~~~rr~Rt~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~~~~~~~~~ 389 (575)
+-.|+||.||.||..||.+||..|.+|+||++..|++||..++|++.+|+|||+||||||||+.+.++.+.
T Consensus 108 ki~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ae~ 178 (351)
T KOG0486|consen 108 KISKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQAEL 178 (351)
T ss_pred hhhhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHHHHh
Confidence 33588999999999999999999999999999999999999999999999999999999999998877443
No 16
>KOG0492|consensus
Probab=99.57 E-value=1.1e-15 Score=141.33 Aligned_cols=66 Identities=39% Similarity=0.624 Sum_probs=61.3
Q ss_pred CCCCCCCcccCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhcCCcc
Q psy4272 320 QCNTGRFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTHPDM 385 (575)
Q Consensus 320 ~~~~rr~Rt~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~~~~~ 385 (575)
.+..|+.||-||..||..||+.|...+|.++.+|.+++..|.|++.||||||||||||.||.+...
T Consensus 141 hk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae 206 (246)
T KOG0492|consen 141 HKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAE 206 (246)
T ss_pred cCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHH
Confidence 345678899999999999999999999999999999999999999999999999999999977543
No 17
>KOG0848|consensus
Probab=99.57 E-value=1.4e-15 Score=145.82 Aligned_cols=66 Identities=44% Similarity=0.773 Sum_probs=61.0
Q ss_pred CCCCCCcccCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhcCCcch
Q psy4272 321 CNTGRFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTHPDMV 386 (575)
Q Consensus 321 ~~~rr~Rt~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~~~~~~ 386 (575)
+.+-+.|.++|..|+.+||+.|..++|.++..+.|||.-|||+||||||||||||||+||.++...
T Consensus 197 RTkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk~ 262 (317)
T KOG0848|consen 197 RTKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKKR 262 (317)
T ss_pred ecccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHHH
Confidence 344567899999999999999999999999999999999999999999999999999999887664
No 18
>KOG0493|consensus
Probab=99.56 E-value=4e-15 Score=141.84 Aligned_cols=94 Identities=33% Similarity=0.527 Sum_probs=72.6
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCcccccccccCCCCCCCcccCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhh
Q psy4272 288 KDIPSNLDLSQIPKPPPSSSHTYSNQIHKNLLQCNTGRFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQI 367 (575)
Q Consensus 288 ~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~rr~Rt~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V 367 (575)
...|.++.+.-+...+.+ +.-+...++.....+.-||.||.||.+||..|+..|..|+|.+...|.+||.+|||.+.||
T Consensus 212 ~mwPAWVycTRYSDRPSs-GPR~Rk~kkkk~~~~eeKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQI 290 (342)
T KOG0493|consen 212 SMWPAWVYCTRYSDRPSS-GPRHRKPKKKKSSSKEEKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQI 290 (342)
T ss_pred cccceeeeeecccCCCCC-CcccccccccCCccchhcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHh
Confidence 555666666555444333 3222222222223455689999999999999999999999999999999999999999999
Q ss_pred hhcccchhhhhhhcC
Q psy4272 368 KIWFQNRRMKLKRTH 382 (575)
Q Consensus 368 ~vWFqNrRak~kk~~ 382 (575)
||||||+|||-||..
T Consensus 291 KIWFQNKRAKiKKsT 305 (342)
T KOG0493|consen 291 KIWFQNKRAKIKKST 305 (342)
T ss_pred hHHhhhhhhhhhhcc
Confidence 999999999999854
No 19
>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=99.56 E-value=3.6e-15 Score=114.63 Aligned_cols=57 Identities=47% Similarity=0.712 Sum_probs=55.5
Q ss_pred CCCcccCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhh
Q psy4272 324 GRFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKR 380 (575)
Q Consensus 324 rr~Rt~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk 380 (575)
||.|+.||..|+.+|+..|..++||+..+++.||..+||+..+|++||+|||+|+||
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 678999999999999999999999999999999999999999999999999999986
No 20
>KOG4577|consensus
Probab=99.53 E-value=1.4e-14 Score=140.06 Aligned_cols=66 Identities=32% Similarity=0.466 Sum_probs=62.0
Q ss_pred CCCCCcccCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhcCCcchh
Q psy4272 322 NTGRFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTHPDMVV 387 (575)
Q Consensus 322 ~~rr~Rt~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~~~~~~~ 387 (575)
..||+||++|..||+.|+.+|...+.|.+..|+.|+.++||..|+|||||||||||+||.++....
T Consensus 166 ~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAGR 231 (383)
T KOG4577|consen 166 SNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGR 231 (383)
T ss_pred ccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcch
Confidence 358999999999999999999999999999999999999999999999999999999998876543
No 21
>KOG0844|consensus
Probab=99.51 E-value=6.5e-15 Score=143.27 Aligned_cols=68 Identities=44% Similarity=0.661 Sum_probs=62.5
Q ss_pred ccCCCCCCCcccCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhcCCcc
Q psy4272 318 LLQCNTGRFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTHPDM 385 (575)
Q Consensus 318 ~~~~~~rr~Rt~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~~~~~ 385 (575)
......||.||.||.+|+..||+.|.+-.|.++..|.|||..|+|++..|||||||||+|+||++-.+
T Consensus 176 sa~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRlam 243 (408)
T KOG0844|consen 176 SADDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLAM 243 (408)
T ss_pred CccHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhhc
Confidence 34456799999999999999999999999999999999999999999999999999999999977543
No 22
>KOG1074|consensus
Probab=99.50 E-value=1.8e-14 Score=157.05 Aligned_cols=55 Identities=16% Similarity=0.260 Sum_probs=50.7
Q ss_pred CCCCCCCCCcchhhcchhHHHHHhhhcCCCCcccccccCccccChhhHHHHhhhhh
Q psy4272 86 TLPSPLKAKLSDYENKMKNVRESIRQKRLAQGLTCLQCGRSYCRPYNLKRHIQYEC 141 (575)
Q Consensus 86 ~~p~~C~~C~~~f~~~~~~L~~H~r~H~~~kp~~C~~Cgk~F~~~~~L~~H~r~H~ 141 (575)
..++.|.+|.|.|... +.|+.|.|.|||++||+|.+||.+|..+.+|+-|...|+
T Consensus 351 ~~khkCr~CakvfgS~-SaLqiHlRSHTGERPfqCnvCG~~FSTkGNLKvH~~rH~ 405 (958)
T KOG1074|consen 351 FFKHKCRFCAKVFGSD-SALQIHLRSHTGERPFQCNVCGNRFSTKGNLKVHFQRHR 405 (958)
T ss_pred cccchhhhhHhhcCch-hhhhhhhhccCCCCCeeecccccccccccceeeeeeecc
Confidence 4567899999999988 899999999999999999999999999999999987664
No 23
>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=99.50 E-value=2.5e-14 Score=108.49 Aligned_cols=53 Identities=17% Similarity=0.394 Sum_probs=50.9
Q ss_pred CCCCcccCCHHHHHHHHHHhhhCCC----CCHHHHHHHHHHhCCChhhhhhcccchh
Q psy4272 323 TGRFRQVYSSHQIVELEKEFRLTNY----LPSDRRKVLSKELGLTERQIKIWFQNRR 375 (575)
Q Consensus 323 ~rr~Rt~~t~~ql~~L~~~F~~~~~----p~~~~r~~la~~l~l~~~~V~vWFqNrR 375 (575)
+||.||.||.+|+..|+..|+.+.| |+..+|++||..|||++++|||||||.+
T Consensus 1 ~kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 1 KKRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 3789999999999999999999999 9999999999999999999999999964
No 24
>KOG3623|consensus
Probab=99.48 E-value=1.1e-14 Score=155.81 Aligned_cols=83 Identities=14% Similarity=0.316 Sum_probs=78.4
Q ss_pred CCCCCCCCCCCcchhhcchhHHHHHhhhcCCCCcccccccCccccChhhHHHHhhhhhCCCCCcccccccccccChhhHH
Q psy4272 84 KATLPSPLKAKLSDYENKMKNVRESIRQKRLAQGLTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSYRARHKHDLK 163 (575)
Q Consensus 84 ~~~~p~~C~~C~~~f~~~~~~L~~H~r~H~~~kp~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk~F~~~~~L~ 163 (575)
....+|.|..|+|.|... +.|.+|.--|+|.+||+|.+|.|.|+.+.+|..|+|.|.|||| |.|+.|+|+|++...+.
T Consensus 890 te~gmyaCDqCDK~FqKq-SSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKP-fQCdKClKRFSHSGSYS 967 (1007)
T KOG3623|consen 890 TEDGMYACDQCDKAFQKQ-SSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKP-FQCDKCLKRFSHSGSYS 967 (1007)
T ss_pred CccccchHHHHHHHHHhh-HHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCc-chhhhhhhhcccccchH
Confidence 346789999999999887 7899999999999999999999999999999999999999999 99999999999999999
Q ss_pred HHHHh
Q psy4272 164 KHVTF 168 (575)
Q Consensus 164 ~H~r~ 168 (575)
.||.-
T Consensus 968 QHMNH 972 (1007)
T KOG3623|consen 968 QHMNH 972 (1007)
T ss_pred hhhcc
Confidence 99963
No 25
>KOG0491|consensus
Probab=99.47 E-value=1.7e-14 Score=128.87 Aligned_cols=67 Identities=40% Similarity=0.697 Sum_probs=62.4
Q ss_pred CCCCCCCcccCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhcCCcch
Q psy4272 320 QCNTGRFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTHPDMV 386 (575)
Q Consensus 320 ~~~~rr~Rt~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~~~~~~ 386 (575)
..++++.||+|+..|+..|++.|+..+|.+..+|.|||..|+|++.|||.||||||+|.||.++...
T Consensus 97 ~~~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~ 163 (194)
T KOG0491|consen 97 HCRRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQ 163 (194)
T ss_pred HHHhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccC
Confidence 4567888999999999999999999999999999999999999999999999999999999876544
No 26
>KOG1074|consensus
Probab=99.45 E-value=3.8e-14 Score=154.49 Aligned_cols=84 Identities=24% Similarity=0.320 Sum_probs=74.6
Q ss_pred ccccccCccccChhhHHHHhhhhhCCCCCcccccccccccChhhHHHHHHhhccCcccchhhhhhhhhcccccCCCCCCC
Q psy4272 118 LTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSYRARHKHDLKKHVTFKHAAYLDHFQAVQEELEVTTKELSPGPKA 197 (575)
Q Consensus 118 ~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk~F~~~~~L~~H~r~~H~~~~~~~~~~~~~~~~~t~e~sp~p~~ 197 (575)
-.|-+|-++...++.|+.|.|+|+|||| |+|.+||+.|.++.+|+.||-+ |...-++. ..+
T Consensus 606 NqCiiC~rVlSC~saLqmHyrtHtGERP-FkCKiCgRAFtTkGNLkaH~~v-Hka~p~~R-----------------~q~ 666 (958)
T KOG1074|consen 606 NQCIICLRVLSCPSALQMHYRTHTGERP-FKCKICGRAFTTKGNLKAHMSV-HKAKPPAR-----------------VQF 666 (958)
T ss_pred cceeeeeecccchhhhhhhhhcccCcCc-cccccccchhccccchhhcccc-cccCcccc-----------------ccc
Confidence 3899999999999999999999999999 9999999999999999999998 66554441 123
Q ss_pred cch---hhhhhccChhhhHhhhhhhh
Q psy4272 198 ENR---HRFREFLNEHRNLERNVSHE 220 (575)
Q Consensus 198 ~C~---~C~k~F~~~~~l~~H~~th~ 220 (575)
.|. .|.+.|.+.-.|.+|.+.|.
T Consensus 667 ScP~~~ic~~kftn~V~lpQhIriH~ 692 (958)
T KOG1074|consen 667 SCPSTFICQKKFTNAVTLPQHIRIHL 692 (958)
T ss_pred cCCchhhhcccccccccccceEEeec
Confidence 888 99999999999999988876
No 27
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.38 E-value=5.1e-13 Score=102.11 Aligned_cols=56 Identities=48% Similarity=0.812 Sum_probs=52.9
Q ss_pred CCCcccCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhh
Q psy4272 324 GRFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLK 379 (575)
Q Consensus 324 rr~Rt~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~k 379 (575)
++.|+.|+..|+.+|++.|..++||+..++..||..+||+..+|++||+|||++.|
T Consensus 1 ~k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 1 RRKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 35678899999999999999999999999999999999999999999999999864
No 28
>KOG0483|consensus
Probab=99.37 E-value=2.8e-13 Score=128.66 Aligned_cols=72 Identities=36% Similarity=0.522 Sum_probs=63.4
Q ss_pred CCCCcccCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhcCCcchhhhhhhch
Q psy4272 323 TGRFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTHPDMVVEYVKESS 394 (575)
Q Consensus 323 ~rr~Rt~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~~~~~~~~~~~~~~ 394 (575)
..+++.+|+.+|+..||..|+...|.....+..||..|||.+|||.|||||||||||.++.......++...
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~~~Lk~~~ 121 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDYESLKRQL 121 (198)
T ss_pred cccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhHHHHHHHH
Confidence 445556899999999999999999999999999999999999999999999999999988776666655443
No 29
>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=99.36 E-value=9.1e-13 Score=101.72 Aligned_cols=58 Identities=57% Similarity=0.879 Sum_probs=54.9
Q ss_pred CCCcccCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhc
Q psy4272 324 GRFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRT 381 (575)
Q Consensus 324 rr~Rt~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~ 381 (575)
++.|+.|+..|+.+|++.|..++||+..++..||..+||+..+|++||+|||++.++.
T Consensus 1 ~~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 1 RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 3568899999999999999999999999999999999999999999999999998874
No 30
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.36 E-value=7.2e-13 Score=121.76 Aligned_cols=67 Identities=31% Similarity=0.473 Sum_probs=61.3
Q ss_pred CCCCCCcccCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhcCCcchh
Q psy4272 321 CNTGRFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTHPDMVV 387 (575)
Q Consensus 321 ~~~rr~Rt~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~~~~~~~ 387 (575)
...+++|++.|..|+.+|++.|..++||+...|..|+..|+|+++-|||||||||+|.|+.......
T Consensus 49 ~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~~~~ 115 (156)
T COG5576 49 SPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGKVE 115 (156)
T ss_pred CcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcccchh
Confidence 4567788889999999999999999999999999999999999999999999999999998766543
No 31
>KOG0847|consensus
Probab=99.31 E-value=1.5e-12 Score=121.39 Aligned_cols=66 Identities=39% Similarity=0.716 Sum_probs=60.8
Q ss_pred CCCCCCcccCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhcCCcch
Q psy4272 321 CNTGRFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTHPDMV 386 (575)
Q Consensus 321 ~~~rr~Rt~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~~~~~~ 386 (575)
.+++-.|.+|+-.|+..|+..|+.++|+-..+|.+||..+|+++.+|+|||||||.||||+.....
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 466677899999999999999999999999999999999999999999999999999999875443
No 32
>KOG3802|consensus
Probab=99.30 E-value=1.2e-12 Score=133.83 Aligned_cols=62 Identities=27% Similarity=0.381 Sum_probs=59.8
Q ss_pred CCCCCcccCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhcCC
Q psy4272 322 NTGRFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTHP 383 (575)
Q Consensus 322 ~~rr~Rt~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~~~ 383 (575)
|+||+||.|.......||++|.+|+.|+..++..||.+|+|.+.||+|||.|||.|.||...
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred cccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 78889999999999999999999999999999999999999999999999999999999765
No 33
>KOG3576|consensus
Probab=99.22 E-value=8.9e-12 Score=115.60 Aligned_cols=114 Identities=9% Similarity=0.123 Sum_probs=99.3
Q ss_pred hhccccccCchHHHhhhccCCCCCCCCCCCCCCCCCCcchhhcchhHHHHHhhhcCCCCcccccccCccccChhhHHHHh
Q psy4272 58 TIADVATKTLPVIQELLSQRDGKPVGKATLPSPLKAKLSDYENKMKNVRESIRQKRLAQGLTCLQCGRSYCRPYNLKRHI 137 (575)
Q Consensus 58 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~C~~C~~~f~~~~~~L~~H~r~H~~~kp~~C~~Cgk~F~~~~~L~~H~ 137 (575)
...-.|..|.+.|....-+..|..-|...+-|.|..||+.|.... .|++|+|+|+|.+||+|..|+|.|.++..|..|.
T Consensus 115 ~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtf-dlkrh~rthtgvrpykc~~c~kaftqrcsleshl 193 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTF-DLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHL 193 (267)
T ss_pred CCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchh-hhhhhhccccCccccchhhhhHHHHhhccHHHHH
Confidence 344568899999988888888888888899999999999999984 8999999999999999999999999999999998
Q ss_pred hh-hh----------CCCCCcccccccccccChhhHHHHHHhhccCc
Q psy4272 138 QY-EC----------GKAPQFPCLYCSYRARHKHDLKKHVTFKHAAY 173 (575)
Q Consensus 138 r~-H~----------gekp~~~C~~Cgk~F~~~~~L~~H~r~~H~~~ 173 (575)
+. |- ..|- |.|+.||..-.....+..|++.||...
T Consensus 194 ~kvhgv~~~yaykerr~kl-~vcedcg~t~~~~e~~~~h~~~~hp~S 239 (267)
T KOG3576|consen 194 KKVHGVQHQYAYKERRAKL-YVCEDCGYTSERPEVYYLHLKLHHPFS 239 (267)
T ss_pred HHHcCchHHHHHHHhhhhe-eeecccCCCCCChhHHHHHHHhcCCCC
Confidence 64 42 3466 999999999999999999999977643
No 34
>KOG3608|consensus
Probab=99.21 E-value=3.7e-12 Score=126.92 Aligned_cols=131 Identities=12% Similarity=0.195 Sum_probs=97.4
Q ss_pred CchHHHhhhccCCCCCCCCCCCCCCCCCCcchhhcchhHHHHHhhhcC--CCCcccccccCccccChhhHHHHhhhhhCC
Q psy4272 66 TLPVIQELLSQRDGKPVGKATLPSPLKAKLSDYENKMKNVRESIRQKR--LAQGLTCLQCGRSYCRPYNLKRHIQYECGK 143 (575)
Q Consensus 66 ~~~~~~~~~~~~~~~~~~~~~~p~~C~~C~~~f~~~~~~L~~H~r~H~--~~kp~~C~~Cgk~F~~~~~L~~H~r~H~ge 143 (575)
|...+.....++.|.+.|+.++--.|..||.-|.++ ..|-.|.+.-+ ...+|.|..|.|.|.....|+.|++.|..
T Consensus 185 Ct~~~~~k~~LreH~r~Hs~eKvvACp~Cg~~F~~~-tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn- 262 (467)
T KOG3608|consen 185 CTKHMGNKYRLREHIRTHSNEKVVACPHCGELFRTK-TKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVN- 262 (467)
T ss_pred hhhhhccHHHHHHHHHhcCCCeEEecchHHHHhccc-cHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhh-
Confidence 444555566666666777777777777777777776 45555555433 34567777777777777777777777753
Q ss_pred CCCcccccccccccChhhHHHHHHhhccCcccchhhhhhhhhcccccCCCCCCCcchhhhhhccChhhhHhhhhhhhh
Q psy4272 144 APQFPCLYCSYRARHKHDLKKHVTFKHAAYLDHFQAVQEELEVTTKELSPGPKAENRHRFREFLNEHRNLERNVSHEE 221 (575)
Q Consensus 144 kp~~~C~~Cgk~F~~~~~L~~H~r~~H~~~~~~~~~~~~~~~~~t~e~sp~p~~~C~~C~k~F~~~~~l~~H~~th~~ 221 (575)
- |+|+.|+......+.|.+|++..|...+++ +|+.|.+.|.+.++|.+|..+|.+
T Consensus 263 -~-ykCplCdmtc~~~ssL~~H~r~rHs~dkpf---------------------KCd~Cd~~c~~esdL~kH~~~HS~ 317 (467)
T KOG3608|consen 263 -C-YKCPLCDMTCSSASSLTTHIRYRHSKDKPF---------------------KCDECDTRCVRESDLAKHVQVHSK 317 (467)
T ss_pred -c-ccccccccCCCChHHHHHHHHhhhccCCCc---------------------cccchhhhhccHHHHHHHHHhccc
Confidence 3 778888877777888888888777777777 999999999999999999998873
No 35
>KOG0490|consensus
Probab=99.20 E-value=5.2e-12 Score=125.48 Aligned_cols=64 Identities=27% Similarity=0.357 Sum_probs=61.3
Q ss_pred CCCCCCCcccCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhcCC
Q psy4272 320 QCNTGRFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTHP 383 (575)
Q Consensus 320 ~~~~rr~Rt~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~~~ 383 (575)
..++||.||.|+..|+++|++.|+.++||+...|+.||..+++++.+|||||||||+||++..+
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 4678999999999999999999999999999999999999999999999999999999999775
No 36
>KOG3608|consensus
Probab=99.11 E-value=1.8e-11 Score=122.11 Aligned_cols=150 Identities=15% Similarity=0.147 Sum_probs=106.6
Q ss_pred ccccCchHHHhhhccCCCCCCC--CCCCCCCCCCCcchhhcchhHHHHHhhhcCCCCcccccccCccccChhhHHHHhhh
Q psy4272 62 VATKTLPVIQELLSQRDGKPVG--KATLPSPLKAKLSDYENKMKNVRESIRQKRLAQGLTCLQCGRSYCRPYNLKRHIQY 139 (575)
Q Consensus 62 ~~~~~~~~~~~~~~~~~~~~~~--~~~~p~~C~~C~~~f~~~~~~L~~H~r~H~~~kp~~C~~Cgk~F~~~~~L~~H~r~ 139 (575)
.|+.|..-|.+..++-+|-+.. ....+|.|..|.|.|.+. ..|+.|++.|-. -|+|+.|+......+.|.+|++.
T Consensus 209 ACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTe-klL~~Hv~rHvn--~ykCplCdmtc~~~ssL~~H~r~ 285 (467)
T KOG3608|consen 209 ACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATE-KLLKSHVVRHVN--CYKCPLCDMTCSSASSLTTHIRY 285 (467)
T ss_pred ecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHH-HHHHHHHHHhhh--cccccccccCCCChHHHHHHHHh
Confidence 4667777666555444433222 346699999999999988 689999998864 59999999999999999999985
Q ss_pred -hhCCCCCcccccccccccChhhHHHHHHhhccCcccc---------hhhhhhhhh---cccccCCCCCCCcchhhhhhc
Q psy4272 140 -ECGKAPQFPCLYCSYRARHKHDLKKHVTFKHAAYLDH---------FQAVQEELE---VTTKELSPGPKAENRHRFREF 206 (575)
Q Consensus 140 -H~gekp~~~C~~Cgk~F~~~~~L~~H~r~~H~~~~~~---------~~~~~~~~~---~~t~e~sp~p~~~C~~C~k~F 206 (575)
|...|| |+|+.|++.|.+.+.|.+|..+ |. +..| ..+....+. ....|..-.+.+.|..|.|.|
T Consensus 286 rHs~dkp-fKCd~Cd~~c~~esdL~kH~~~-HS-~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~Y~CH~Cdr~f 362 (467)
T KOG3608|consen 286 RHSKDKP-FKCDECDTRCVRESDLAKHVQV-HS-KTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPILYACHCCDRFF 362 (467)
T ss_pred hhccCCC-ccccchhhhhccHHHHHHHHHh-cc-ccceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCceeeecchhhh
Confidence 888999 9999999999999999999998 54 2222 111111111 112233334455677777777
Q ss_pred cChhhhHhhhh
Q psy4272 207 LNEHRNLERNV 217 (575)
Q Consensus 207 ~~~~~l~~H~~ 217 (575)
..-..|..|..
T Consensus 363 t~G~~L~~HL~ 373 (467)
T KOG3608|consen 363 TSGKSLSAHLM 373 (467)
T ss_pred ccchhHHHHHH
Confidence 76666666654
No 37
>KOG0849|consensus
Probab=99.07 E-value=3.2e-10 Score=118.71 Aligned_cols=69 Identities=41% Similarity=0.598 Sum_probs=63.6
Q ss_pred cccCCCCCCCcccCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhcCCcc
Q psy4272 317 NLLQCNTGRFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTHPDM 385 (575)
Q Consensus 317 ~~~~~~~rr~Rt~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~~~~~ 385 (575)
....++.+|.||+|+..|+..|++.|+.++||++..|++||.+++|++.+|+|||+|||+||+|.....
T Consensus 170 ~~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~~~ 238 (354)
T KOG0849|consen 170 YALQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHRDC 238 (354)
T ss_pred ccccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhccccc
Confidence 344577888899999999999999999999999999999999999999999999999999999987543
No 38
>KOG1146|consensus
Probab=98.93 E-value=4e-09 Score=121.17 Aligned_cols=64 Identities=25% Similarity=0.397 Sum_probs=60.2
Q ss_pred CCCCCCCcccCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhcCC
Q psy4272 320 QCNTGRFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTHP 383 (575)
Q Consensus 320 ~~~~rr~Rt~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~~~ 383 (575)
...+|+.||.++..||..|...|....||...+.|.|...++|..++|+|||||.|+|.||...
T Consensus 900 ~~~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 900 GMGRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhhhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 4567889999999999999999999999999999999999999999999999999999998654
No 39
>PHA00733 hypothetical protein
Probab=98.86 E-value=1.2e-09 Score=97.87 Aligned_cols=84 Identities=18% Similarity=0.235 Sum_probs=68.9
Q ss_pred CCCCCCCCCCCCcchhhcchhHH------HHHhhhcCCCCcccccccCccccChhhHHHHhhhhhCCCCCcccccccccc
Q psy4272 83 GKATLPSPLKAKLSDYENKMKNV------RESIRQKRLAQGLTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSYRA 156 (575)
Q Consensus 83 ~~~~~p~~C~~C~~~f~~~~~~L------~~H~r~H~~~kp~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk~F 156 (575)
....+.+.|.+|.+.|... ..| .+|+.+ .+.++|.|..||+.|.....|..|++.| +.+ |.|.+|++.|
T Consensus 35 ~~~~~~~~~~~~~~~~~~~-~~l~~~~~l~~~~~~-~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~-~~C~~CgK~F 109 (128)
T PHA00733 35 TPEQKRLIRAVVKTLIYNP-QLLDESSYLYKLLTS-KAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHS-KVCPVCGKEF 109 (128)
T ss_pred ChhhhhHHHHHHhhhccCh-hhhcchHHHHhhccc-CCCCCccCCCCCCcCCCHHHHHHHHhcC--CcC-ccCCCCCCcc
Confidence 3345678899999888765 344 344444 4588999999999999999999999987 467 9999999999
Q ss_pred cChhhHHHHHHhhcc
Q psy4272 157 RHKHDLKKHVTFKHA 171 (575)
Q Consensus 157 ~~~~~L~~H~r~~H~ 171 (575)
.....|..|+...|.
T Consensus 110 ~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 110 RNTDSTLDHVCKKHN 124 (128)
T ss_pred CCHHHHHHHHHHhcC
Confidence 999999999998664
No 40
>PHA02768 hypothetical protein; Provisional
Probab=98.84 E-value=1.4e-09 Score=81.03 Aligned_cols=44 Identities=16% Similarity=0.360 Sum_probs=39.8
Q ss_pred cccccccCccccChhhHHHHhhhhhCCCCCcccccccccccChhhHH
Q psy4272 117 GLTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSYRARHKHDLK 163 (575)
Q Consensus 117 p~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk~F~~~~~L~ 163 (575)
.|.|++||+.|.+..+|.+|+++|+ ++ |+|..|++.|.+.+.|.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~-~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TN-LKLSNCKRISLRTGEYI 48 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--Cc-ccCCcccceecccceeE
Confidence 3899999999999999999999999 67 99999999999887764
No 41
>KOG1168|consensus
Probab=98.78 E-value=2.1e-09 Score=104.57 Aligned_cols=64 Identities=22% Similarity=0.372 Sum_probs=59.7
Q ss_pred CCCCCCCcccCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhcCC
Q psy4272 320 QCNTGRFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTHP 383 (575)
Q Consensus 320 ~~~~rr~Rt~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~~~ 383 (575)
...+||+||.+..-..+.||++|...+.|+.+....+|++|.|.+.+|+|||.|.|.|.||...
T Consensus 306 ~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~ 369 (385)
T KOG1168|consen 306 GGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKR 369 (385)
T ss_pred ccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhh
Confidence 3467899999999999999999999999999999999999999999999999999999998554
No 42
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.72 E-value=1.6e-08 Score=110.24 Aligned_cols=101 Identities=10% Similarity=0.176 Sum_probs=81.9
Q ss_pred CCCCCCCCCcchhhcchhHHHHHhhhcCCCCcccccccCccccChhhHHHHhhhhhCCCCCcccccccccccC-------
Q psy4272 86 TLPSPLKAKLSDYENKMKNVRESIRQKRLAQGLTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSYRARH------- 158 (575)
Q Consensus 86 ~~p~~C~~C~~~f~~~~~~L~~H~r~H~~~kp~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk~F~~------- 158 (575)
...+.|..|++.|. . ..|..|+.+|+ ++|.|+ ||+.| .+..|..|+++|.++++ +.|.+|++.|..
T Consensus 451 ~~H~~C~~Cgk~f~-~-s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kp-i~C~fC~~~v~~g~~~~d~ 523 (567)
T PLN03086 451 KNHVHCEKCGQAFQ-Q-GEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRL-ITCRFCGDMVQAGGSAMDV 523 (567)
T ss_pred ccCccCCCCCCccc-h-HHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCc-eeCCCCCCccccCccccch
Confidence 45578999999995 3 68999999985 899999 99765 66899999999999999 999999999952
Q ss_pred ---hhhHHHHHHhhccCcccchhhhhhhhhcccccCCCCCCCcchhhhhhccChhhhHhhhh
Q psy4272 159 ---KHDLKKHVTFKHAAYLDHFQAVQEELEVTTKELSPGPKAENRHRFREFLNEHRNLERNV 217 (575)
Q Consensus 159 ---~~~L~~H~r~~H~~~~~~~~~~~~~~~~~t~e~sp~p~~~C~~C~k~F~~~~~l~~H~~ 217 (575)
...|..|... + +.+++ .|..|++.|..+ .+..|.+
T Consensus 524 ~d~~s~Lt~HE~~-C-G~rt~---------------------~C~~Cgk~Vrlr-dm~~H~~ 561 (567)
T PLN03086 524 RDRLRGMSEHESI-C-GSRTA---------------------PCDSCGRSVMLK-EMDIHQI 561 (567)
T ss_pred hhhhhhHHHHHHh-c-CCcce---------------------EccccCCeeeeh-hHHHHHH
Confidence 3478899887 3 66666 999999888654 4555543
No 43
>KOG0775|consensus
Probab=98.64 E-value=7e-08 Score=93.87 Aligned_cols=51 Identities=24% Similarity=0.433 Sum_probs=47.2
Q ss_pred CCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhh
Q psy4272 330 YSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKR 380 (575)
Q Consensus 330 ~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk 380 (575)
|...-..+|+++|..++||+..++.+||+.+||+..||-.||+|||.++|-
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa 233 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRA 233 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhh
Confidence 445567899999999999999999999999999999999999999999993
No 44
>PHA00733 hypothetical protein
Probab=98.58 E-value=3.7e-08 Score=88.30 Aligned_cols=94 Identities=15% Similarity=0.191 Sum_probs=72.6
Q ss_pred HHHHHhhhcCCCCcccccccCccccChhhHHHH--hh---hhhCCCCCcccccccccccChhhHHHHHHhhccCcccchh
Q psy4272 104 NVRESIRQKRLAQGLTCLQCGRSYCRPYNLKRH--IQ---YECGKAPQFPCLYCSYRARHKHDLKKHVTFKHAAYLDHFQ 178 (575)
Q Consensus 104 ~L~~H~r~H~~~kp~~C~~Cgk~F~~~~~L~~H--~r---~H~gekp~~~C~~Cgk~F~~~~~L~~H~r~~H~~~~~~~~ 178 (575)
.|..+-..-...+++.|.+|.+.|.....|..| ++ .+.+.++ |.|..||+.|.....|..|++. |. .++
T Consensus 27 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kP-y~C~~Cgk~Fss~s~L~~H~r~-h~--~~~-- 100 (128)
T PHA00733 27 ELKRYHSLTPEQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSP-YVCPLCLMPFSSSVSLKQHIRY-TE--HSK-- 100 (128)
T ss_pred HhhhhhcCChhhhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCC-ccCCCCCCcCCCHHHHHHHHhc-CC--cCc--
Confidence 343333333456789999999999888777666 22 2345788 9999999999999999999987 32 234
Q ss_pred hhhhhhhcccccCCCCCCCcchhhhhhccChhhhHhhhhhhhhh
Q psy4272 179 AVQEELEVTTKELSPGPKAENRHRFREFLNEHRNLERNVSHEEI 222 (575)
Q Consensus 179 ~~~~~~~~~t~e~sp~p~~~C~~C~k~F~~~~~l~~H~~th~~~ 222 (575)
.|..|++.|.....|..|+.....+
T Consensus 101 -------------------~C~~CgK~F~~~~sL~~H~~~~h~~ 125 (128)
T PHA00733 101 -------------------VCPVCGKEFRNTDSTLDHVCKKHNI 125 (128)
T ss_pred -------------------cCCCCCCccCCHHHHHHHHHHhcCc
Confidence 9999999999999999998765443
No 45
>PHA02768 hypothetical protein; Provisional
Probab=98.46 E-value=7e-08 Score=72.01 Aligned_cols=44 Identities=16% Similarity=0.115 Sum_probs=40.3
Q ss_pred CCCCCCCcchhhcchhHHHHHhhhcCCCCcccccccCccccChhhHH
Q psy4272 88 PSPLKAKLSDYENKMKNVRESIRQKRLAQGLTCLQCGRSYCRPYNLK 134 (575)
Q Consensus 88 p~~C~~C~~~f~~~~~~L~~H~r~H~~~kp~~C~~Cgk~F~~~~~L~ 134 (575)
.|.|.+||+.|... ++|..|+++|+ ++|+|..|++.|.+.+.|.
T Consensus 5 ~y~C~~CGK~Fs~~-~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPICGEIYIKR-KSMITHLRKHN--TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred ccCcchhCCeeccH-HHHHHHHHhcC--CcccCCcccceecccceeE
Confidence 58999999999988 79999999999 7999999999999887764
No 46
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.42 E-value=1.2e-07 Score=103.52 Aligned_cols=101 Identities=18% Similarity=0.125 Sum_probs=79.6
Q ss_pred ccccCchHHHhhhccCCCCCCCCCCCCCCCCCCcchhhcchhHHHHHhhhcCCCCcccccccCccccC----------hh
Q psy4272 62 VATKTLPVIQELLSQRDGKPVGKATLPSPLKAKLSDYENKMKNVRESIRQKRLAQGLTCLQCGRSYCR----------PY 131 (575)
Q Consensus 62 ~~~~~~~~~~~~~~~~~~~~~~~~~~p~~C~~C~~~f~~~~~~L~~H~r~H~~~kp~~C~~Cgk~F~~----------~~ 131 (575)
+|..|.+.+. ...+..|...+ ..++.|. |++.+. + ..|..|+++|.+++++.|.+|++.|.. ..
T Consensus 455 ~C~~Cgk~f~-~s~LekH~~~~--Hkpv~Cp-Cg~~~~-R-~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s 528 (567)
T PLN03086 455 HCEKCGQAFQ-QGEMEKHMKVF--HEPLQCP-CGVVLE-K-EQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLR 528 (567)
T ss_pred cCCCCCCccc-hHHHHHHHHhc--CCCccCC-CCCCcc-h-hHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhh
Confidence 5677777664 34445565554 2789999 997663 3 699999999999999999999999952 35
Q ss_pred hHHHHhhhhhCCCCCcccccccccccChhhHHHHHHhhcc
Q psy4272 132 NLKRHIQYECGKAPQFPCLYCSYRARHKHDLKKHVTFKHA 171 (575)
Q Consensus 132 ~L~~H~r~H~gekp~~~C~~Cgk~F~~~~~L~~H~r~~H~ 171 (575)
.|..|..++ |.++ +.|..||+.|..+ .|..|+...|.
T Consensus 529 ~Lt~HE~~C-G~rt-~~C~~Cgk~Vrlr-dm~~H~~~~h~ 565 (567)
T PLN03086 529 GMSEHESIC-GSRT-APCDSCGRSVMLK-EMDIHQIAVHQ 565 (567)
T ss_pred hHHHHHHhc-CCcc-eEccccCCeeeeh-hHHHHHHHhhc
Confidence 799999885 9999 9999999998876 58888877664
No 47
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.36 E-value=1.7e-07 Score=59.72 Aligned_cols=24 Identities=33% Similarity=0.874 Sum_probs=13.5
Q ss_pred HHHHhhhhhCCCCCccccccccccc
Q psy4272 133 LKRHIQYECGKAPQFPCLYCSYRAR 157 (575)
Q Consensus 133 L~~H~r~H~gekp~~~C~~Cgk~F~ 157 (575)
|.+|+++|+|++| |.|++|++.|.
T Consensus 2 l~~H~~~H~~~k~-~~C~~C~k~F~ 25 (26)
T PF13465_consen 2 LRRHMRTHTGEKP-YKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHSSSSS-EEESSSSEEES
T ss_pred HHHHhhhcCCCCC-CCCCCCcCeeC
Confidence 4555555555555 55555555554
No 48
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.33 E-value=2.7e-07 Score=58.73 Aligned_cols=26 Identities=27% Similarity=0.637 Sum_probs=24.0
Q ss_pred HHHHHhhhcCCCCcccccccCccccC
Q psy4272 104 NVRESIRQKRLAQGLTCLQCGRSYCR 129 (575)
Q Consensus 104 ~L~~H~r~H~~~kp~~C~~Cgk~F~~ 129 (575)
+|..|+++|+|++||.|++|++.|..
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEESS
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeCc
Confidence 47899999999999999999999974
No 49
>KOG3993|consensus
Probab=98.28 E-value=1.3e-07 Score=96.94 Aligned_cols=85 Identities=21% Similarity=0.377 Sum_probs=71.0
Q ss_pred CCCCCCcchhhcchhHHHHHhhhcCCCCcccccccCccccChhhHHHHhhhhh--------CCC----------------
Q psy4272 89 SPLKAKLSDYENKMKNVRESIRQKRLAQGLTCLQCGRSYCRPYNLKRHIQYEC--------GKA---------------- 144 (575)
Q Consensus 89 ~~C~~C~~~f~~~~~~L~~H~r~H~~~kp~~C~~Cgk~F~~~~~L~~H~r~H~--------gek---------------- 144 (575)
|-|..|...|..-. .|.+|.-.....--|+|..|+|.|....+|..|+|+|. |..
T Consensus 268 yiCqLCK~kYeD~F-~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~ 346 (500)
T KOG3993|consen 268 YICQLCKEKYEDAF-ALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAE 346 (500)
T ss_pred HHHHHHHHhhhhHH-HHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhcc
Confidence 78999999999884 78888755444455999999999999999999999994 111
Q ss_pred ---------CCcccccccccccChhhHHHHHHhhccCccc
Q psy4272 145 ---------PQFPCLYCSYRARHKHDLKKHVTFKHAAYLD 175 (575)
Q Consensus 145 ---------p~~~C~~Cgk~F~~~~~L~~H~r~~H~~~~~ 175 (575)
- |.|.+|+|.|.+...|++|+-+||.....
T Consensus 347 rsg~dss~gi-~~C~~C~KkFrRqAYLrKHqlthq~~~~~ 385 (500)
T KOG3993|consen 347 RSGDDSSSGI-FSCHTCGKKFRRQAYLRKHQLTHQRAPLA 385 (500)
T ss_pred ccCCcccCce-eecHHhhhhhHHHHHHHHhHHhhhccccc
Confidence 2 88999999999999999999997765543
No 50
>KOG0774|consensus
Probab=98.17 E-value=4.3e-06 Score=80.73 Aligned_cols=60 Identities=25% Similarity=0.453 Sum_probs=55.6
Q ss_pred CCCCcccCCHHHHHHHHHHhh---hCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhcC
Q psy4272 323 TGRFRQVYSSHQIVELEKEFR---LTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTH 382 (575)
Q Consensus 323 ~rr~Rt~~t~~ql~~L~~~F~---~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~~ 382 (575)
.||+|..|+..-.++|..+|. .++||+...+++||.+.|++..||-.||.|.|-+.||.-
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~ 250 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNM 250 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhh
Confidence 467888999999999999997 578999999999999999999999999999999998854
No 51
>KOG3993|consensus
Probab=98.15 E-value=6.8e-07 Score=91.88 Aligned_cols=108 Identities=14% Similarity=0.160 Sum_probs=75.1
Q ss_pred ccccccCccccChhhHHHHhhhhhCCCCCcccccccccccChhhHHHHHHhhccC-------cccchhh----hhhhhhc
Q psy4272 118 LTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSYRARHKHDLKKHVTFKHAA-------YLDHFQA----VQEELEV 186 (575)
Q Consensus 118 ~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk~F~~~~~L~~H~r~~H~~-------~~~~~~~----~~~~~~~ 186 (575)
|.|..|...|.....|.+|.-.-.-..- |+|..|+|.|+-..+|..|.|.|... ..+-... .......
T Consensus 268 yiCqLCK~kYeD~F~LAQHrC~RIV~vE-YrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~ 346 (500)
T KOG3993|consen 268 YICQLCKEKYEDAFALAQHRCPRIVHVE-YRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAE 346 (500)
T ss_pred HHHHHHHHhhhhHHHHhhccCCeeEEee-ecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhcc
Confidence 9999999999999999999732111123 99999999999999999999994321 1111000 0000011
Q ss_pred ccccCCCCCCCcchhhhhhccChhhhHhhhhhhhhhhccc
Q psy4272 187 TTKELSPGPKAENRHRFREFLNEHRNLERNVSHEEIRTHK 226 (575)
Q Consensus 187 ~t~e~sp~p~~~C~~C~k~F~~~~~l~~H~~th~~~~~~~ 226 (575)
.....+.+..+.|.+|+|.|.+...|..|+.+|......+
T Consensus 347 rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~~~~k 386 (500)
T KOG3993|consen 347 RSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRAPLAK 386 (500)
T ss_pred ccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhccccch
Confidence 1122233457899999999999999999999997754433
No 52
>PHA00616 hypothetical protein
Probab=98.08 E-value=1.4e-06 Score=61.89 Aligned_cols=36 Identities=17% Similarity=0.346 Sum_probs=31.0
Q ss_pred cccccccCccccChhhHHHHhhhhhCCCCCccccccc
Q psy4272 117 GLTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCS 153 (575)
Q Consensus 117 p~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cg 153 (575)
||+|..||+.|..+..|.+|++.|+|+++ +.|+.--
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~-~~~~~~y 36 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNK-LTLEYFY 36 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCc-cceeEEE
Confidence 58899999999999999999999999998 8887643
No 53
>KOG0490|consensus
Probab=98.06 E-value=3.4e-06 Score=83.71 Aligned_cols=65 Identities=38% Similarity=0.607 Sum_probs=61.0
Q ss_pred cCCCCCCCcccCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhcCC
Q psy4272 319 LQCNTGRFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTHP 383 (575)
Q Consensus 319 ~~~~~rr~Rt~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~~~ 383 (575)
...+.++.|+.+...|+..|...|..+.+|+...++.|+..+|+++++|+|||||+|++.++...
T Consensus 149 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 149 SNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred CccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 34678899999999999999999999999999999999999999999999999999999998665
No 54
>KOG1146|consensus
Probab=98.04 E-value=1.4e-05 Score=92.90 Aligned_cols=274 Identities=15% Similarity=0.134 Sum_probs=146.9
Q ss_pred CCCCcchhhcchhHHHHHhh-hcCCCCcccccccCccccChhhHHHHhhh-hh------------------------CCC
Q psy4272 91 LKAKLSDYENKMKNVRESIR-QKRLAQGLTCLQCGRSYCRPYNLKRHIQY-EC------------------------GKA 144 (575)
Q Consensus 91 C~~C~~~f~~~~~~L~~H~r-~H~~~kp~~C~~Cgk~F~~~~~L~~H~r~-H~------------------------gek 144 (575)
|..|+..+...+ .+-.|+. .|.-.|-|+|+.|+..|+....|..|+|. |. +.+
T Consensus 439 ~~~~e~~~~s~r-~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~ 517 (1406)
T KOG1146|consen 439 LTKAEPLLESKR-SLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGK 517 (1406)
T ss_pred ccchhhhhhhhc-ccccceeeeecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCC
Confidence 444444444442 3333333 36666889999999999999999999987 21 336
Q ss_pred CCcccccccccccChhhHHHHHHhh-ccCcccchh-------hhh----hhhh---------cccccCCCCCCCcchhhh
Q psy4272 145 PQFPCLYCSYRARHKHDLKKHVTFK-HAAYLDHFQ-------AVQ----EELE---------VTTKELSPGPKAENRHRF 203 (575)
Q Consensus 145 p~~~C~~Cgk~F~~~~~L~~H~r~~-H~~~~~~~~-------~~~----~~~~---------~~t~e~sp~p~~~C~~C~ 203 (575)
+ |.|..|...|..+.+|..|+..- |..+..... +.. .... ..+.+..+.+...|+.|.
T Consensus 518 p-~~C~~C~~stttng~LsihlqS~~h~~~lee~~~~~g~~v~~~~~~v~s~~P~~ag~~~~ags~~pktkP~~~C~vc~ 596 (1406)
T KOG1146|consen 518 P-YPCRACNYSTTTNGNLSIHLQSDLHRNELEEAEENAGEQVRLLPASVTSAVPEEAGLGPSAGSSGPKTKPSWRCEVCS 596 (1406)
T ss_pred c-ccceeeeeeeecchHHHHHHHHHhhHHHHHHHHhccccchhhhhhhhcccCcccccCCCCCCCCCCCCCCCcchhhhc
Confidence 7 99999999999999999998752 222110000 000 0000 001112335667899998
Q ss_pred hhccChhhhHhhhhhhhhhhc-cccCCCCCCCCCcc-ccccccCCCCCcccccccCCCcchHHHHHHHHHHhhhcCCCCC
Q psy4272 204 REFLNEHRNLERNVSHEEIRT-HKKHEQPRKESSYK-ETENTQFNSETNDLSKLEEPNKTSSILLAHLQQVQKDLGLGAS 281 (575)
Q Consensus 204 k~F~~~~~l~~H~~th~~~~~-~~~~~~~~~~ss~~-~~~~~~~~s~~~~~s~~e~p~~tss~~lsh~~e~q~~~g~g~S 281 (575)
..-.-..+|..|+..-..... +..-.+....+... .......+. +...... .. ..+...+. .-+..+...
T Consensus 597 yetniarnlrihmtss~~s~~p~~~Lq~~it~~l~~~~~~~~~lp~-tps~~~~----s~-~~l~qkl~--l~~~~~e~~ 668 (1406)
T KOG1146|consen 597 YETNIARNLRIHMTASPSSSPPSLVLQQNITSSLASLLGGQGRLPF-TPSSPPS----SD-YELSQKLE--LPDLSLEVA 668 (1406)
T ss_pred chhhhhhccccccccCCCCCChHHHhhhcchhhccccccCcCCCCC-CCCCCcc----cc-chhhhhhc--ccccccccc
Confidence 776666677777643211111 11000100000000 000111110 0000000 00 00000000 000000000
Q ss_pred CCCCCCCCCC---CCCCCCCCCCCCCCCCCCCcccccccccCCCCCCCcccCCHHHHHHHHHHhhhCCCCCHHHHHHHHH
Q psy4272 282 DSLSSEKDIP---SNLDLSQIPKPPPSSSHTYSNQIHKNLLQCNTGRFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSK 358 (575)
Q Consensus 282 ~s~ss~~~~~---~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~rr~Rt~~t~~ql~~L~~~F~~~~~p~~~~r~~la~ 358 (575)
....+..+.. ...|....|....+.+ ......+.++-|+.+-..++..|-++|..+.-|+...+..|..
T Consensus 669 a~~as~~~~~~~~~~~~~~~aPt~s~~g~--------~~~~~~~~~~~~~~~~~~aa~~l~~a~~~~~sps~k~~~civc 740 (1406)
T KOG1146|consen 669 AKPASGLDGQLQLIRADPFLAPTGSEVGG--------GESLSPRDKLLRLTILPEAAMILGRAYMQDNSPSLKVFDCIVC 740 (1406)
T ss_pred ccccccccchhhhccCCcccCCCCCCCCC--------CCCCCcccccCcccccHHHHhhhhhcccCCCCHHHHHHHHhhh
Confidence 0011110000 1222222222222222 1122345678889999999999999999999999999999999
Q ss_pred HhCCChhhhhhcccchhhhhhhcC
Q psy4272 359 ELGLTERQIKIWFQNRRMKLKRTH 382 (575)
Q Consensus 359 ~l~l~~~~V~vWFqNrRak~kk~~ 382 (575)
....+.+++++||+|-|.+.+|..
T Consensus 741 d~~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 741 DVFSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred hhhhhhhHHHHhhcchhhhhhhhc
Confidence 999999999999999999988866
No 55
>PHA00732 hypothetical protein
Probab=97.98 E-value=4e-06 Score=68.42 Aligned_cols=45 Identities=24% Similarity=0.439 Sum_probs=32.5
Q ss_pred cccccccCccccChhhHHHHhhh-hhCCCCCcccccccccccChhhHHHHHHh
Q psy4272 117 GLTCLQCGRSYCRPYNLKRHIQY-ECGKAPQFPCLYCSYRARHKHDLKKHVTF 168 (575)
Q Consensus 117 p~~C~~Cgk~F~~~~~L~~H~r~-H~gekp~~~C~~Cgk~F~~~~~L~~H~r~ 168 (575)
||.|..||+.|.....|+.|++. |. + +.|+.||+.|. .|..|.++
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~-~~C~~CgKsF~---~l~~H~~~ 46 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---L-TKCPVCNKSYR---RLNQHFYS 46 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---C-CccCCCCCEeC---Chhhhhcc
Confidence 47788888888888888888774 54 4 67888888776 46777755
No 56
>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=97.97 E-value=4.1e-06 Score=59.01 Aligned_cols=34 Identities=32% Similarity=0.637 Sum_probs=28.8
Q ss_pred hCCCCCHHHHHHHHHHhCCChhhhhhcccchhhh
Q psy4272 344 LTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMK 377 (575)
Q Consensus 344 ~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak 377 (575)
.++||+..++++||..+||+..||..||-|.|.+
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 4789999999999999999999999999999864
No 57
>KOG2252|consensus
Probab=97.94 E-value=9.2e-06 Score=86.79 Aligned_cols=58 Identities=21% Similarity=0.278 Sum_probs=54.3
Q ss_pred CCCCCCcccCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhh
Q psy4272 321 CNTGRFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKL 378 (575)
Q Consensus 321 ~~~rr~Rt~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~ 378 (575)
...||.|.+||..|.+.|...|..+++|+....+.|+.+|||..+.|..||-|-|.+.
T Consensus 418 ~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 418 LQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred ccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 3567889999999999999999999999999999999999999999999999987664
No 58
>PHA00732 hypothetical protein
Probab=97.64 E-value=3.4e-05 Score=62.96 Aligned_cols=48 Identities=17% Similarity=0.198 Sum_probs=40.4
Q ss_pred CCCCCCCcchhhcchhHHHHHhhh-cCCCCcccccccCccccChhhHHHHhhhhhC
Q psy4272 88 PSPLKAKLSDYENKMKNVRESIRQ-KRLAQGLTCLQCGRSYCRPYNLKRHIQYECG 142 (575)
Q Consensus 88 p~~C~~C~~~f~~~~~~L~~H~r~-H~~~kp~~C~~Cgk~F~~~~~L~~H~r~H~g 142 (575)
||.|..|++.|... ..|+.|++. |.+ +.|..||+.|. .|..|.+++..
T Consensus 1 py~C~~Cgk~F~s~-s~Lk~H~r~~H~~---~~C~~CgKsF~---~l~~H~~~~~~ 49 (79)
T PHA00732 1 MFKCPICGFTTVTL-FALKQHARRNHTL---TKCPVCNKSYR---RLNQHFYSQYD 49 (79)
T ss_pred CccCCCCCCccCCH-HHHHHHhhcccCC---CccCCCCCEeC---ChhhhhcccCC
Confidence 68999999999988 799999984 654 68999999998 58889876554
No 59
>PHA00616 hypothetical protein
Probab=97.51 E-value=4.9e-05 Score=54.15 Aligned_cols=39 Identities=15% Similarity=-0.064 Sum_probs=34.1
Q ss_pred CCCCCCCcchhhcchhHHHHHhhhcCCCCcccccccCccc
Q psy4272 88 PSPLKAKLSDYENKMKNVRESIRQKRLAQGLTCLQCGRSY 127 (575)
Q Consensus 88 p~~C~~C~~~f~~~~~~L~~H~r~H~~~kp~~C~~Cgk~F 127 (575)
||.|..||+.|... +.|..|++.|+|++++.|+.--..|
T Consensus 1 pYqC~~CG~~F~~~-s~l~~H~r~~hg~~~~~~~~~y~~f 39 (44)
T PHA00616 1 MYQCLRCGGIFRKK-KEVIEHLLSVHKQNKLTLEYFYIYF 39 (44)
T ss_pred CCccchhhHHHhhH-HHHHHHHHHhcCCCccceeEEEEEE
Confidence 68999999999988 7999999999999999998643333
No 60
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=97.42 E-value=0.00018 Score=54.44 Aligned_cols=49 Identities=27% Similarity=0.579 Sum_probs=34.5
Q ss_pred ccccccCccccChhhHHHHhhh-hhCC-CCCcccccccccccChhhHHHHHHhhc
Q psy4272 118 LTCLQCGRSYCRPYNLKRHIQY-ECGK-APQFPCLYCSYRARHKHDLKKHVTFKH 170 (575)
Q Consensus 118 ~~C~~Cgk~F~~~~~L~~H~r~-H~ge-kp~~~C~~Cgk~F~~~~~L~~H~r~~H 170 (575)
|.|++|++.| ....|..|... |..+ +. +.|++|...+. .+|..|+..+|
T Consensus 3 f~CP~C~~~~-~~~~L~~H~~~~H~~~~~~-v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 3 FTCPYCGKGF-SESSLVEHCEDEHRSESKN-VVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred cCCCCCCCcc-CHHHHHHHHHhHCcCCCCC-ccCCCchhhhh--hHHHHHHHHhc
Confidence 7888888844 45678888654 6554 45 88888887654 37888887765
No 61
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.35 E-value=0.0001 Score=45.20 Aligned_cols=23 Identities=39% Similarity=0.829 Sum_probs=13.0
Q ss_pred ccccccCccccChhhHHHHhhhh
Q psy4272 118 LTCLQCGRSYCRPYNLKRHIQYE 140 (575)
Q Consensus 118 ~~C~~Cgk~F~~~~~L~~H~r~H 140 (575)
|.|.+|++.|..+..|.+|++.|
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhHC
Confidence 45555555555555555555543
No 62
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.18 E-value=0.00011 Score=73.20 Aligned_cols=53 Identities=25% Similarity=0.468 Sum_probs=44.9
Q ss_pred CCCcccccc--cCccccChhhHHHHhhh-hh------------------CCCCCcccccccccccChhhHHHHHH
Q psy4272 114 LAQGLTCLQ--CGRSYCRPYNLKRHIQY-EC------------------GKAPQFPCLYCSYRARHKHDLKKHVT 167 (575)
Q Consensus 114 ~~kp~~C~~--Cgk~F~~~~~L~~H~r~-H~------------------gekp~~~C~~Cgk~F~~~~~L~~H~r 167 (575)
++|||+|++ |.|.++....|+-|+.- |. ..|| |+|++|+|+|.....|+.|+.
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KP-YrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKP-YRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCc-eeccccchhhccCccceeccc
Confidence 359999988 99999999999999863 31 2388 999999999999999998864
No 63
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.02 E-value=0.00031 Score=43.05 Aligned_cols=22 Identities=27% Similarity=0.594 Sum_probs=21.1
Q ss_pred cccccccccccChhhHHHHHHh
Q psy4272 147 FPCLYCSYRARHKHDLKKHVTF 168 (575)
Q Consensus 147 ~~C~~Cgk~F~~~~~L~~H~r~ 168 (575)
|.|..|++.|..+..|..|++.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 7899999999999999999987
No 64
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=96.85 E-value=0.00057 Score=41.90 Aligned_cols=23 Identities=30% Similarity=0.678 Sum_probs=11.1
Q ss_pred cccccccccccChhhHHHHHHhh
Q psy4272 147 FPCLYCSYRARHKHDLKKHVTFK 169 (575)
Q Consensus 147 ~~C~~Cgk~F~~~~~L~~H~r~~ 169 (575)
|.|++|++.|.....|..|++++
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHhh
Confidence 34555555555555555555543
No 65
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=96.71 E-value=0.0018 Score=48.85 Aligned_cols=50 Identities=16% Similarity=0.268 Sum_probs=38.1
Q ss_pred CCCCCCCcchhhcchhHHHHHhh-hcCCC-CcccccccCccccChhhHHHHhhhhh
Q psy4272 88 PSPLKAKLSDYENKMKNVRESIR-QKRLA-QGLTCLQCGRSYCRPYNLKRHIQYEC 141 (575)
Q Consensus 88 p~~C~~C~~~f~~~~~~L~~H~r-~H~~~-kp~~C~~Cgk~F~~~~~L~~H~r~H~ 141 (575)
.|.|++|++.|.. ..|..|.. .|..+ +.+.|++|...+.. +|.+|+..+.
T Consensus 2 ~f~CP~C~~~~~~--~~L~~H~~~~H~~~~~~v~CPiC~~~~~~--~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGKGFSE--SSLVEHCEDEHRSESKNVVCPICSSRVTD--NLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCCccCH--HHHHHHHHhHCcCCCCCccCCCchhhhhh--HHHHHHHHhc
Confidence 4899999996553 47877765 46654 57999999987664 8999998754
No 66
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=96.53 E-value=0.0013 Score=41.96 Aligned_cols=23 Identities=22% Similarity=0.651 Sum_probs=11.2
Q ss_pred ccccccCccccChhhHHHHhhhh
Q psy4272 118 LTCLQCGRSYCRPYNLKRHIQYE 140 (575)
Q Consensus 118 ~~C~~Cgk~F~~~~~L~~H~r~H 140 (575)
|.|..|++.|.....|..|++.|
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~~h 24 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKRSH 24 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHCTT
T ss_pred CCCCccCCccCChhHHHHHhHHh
Confidence 44455555555555555554443
No 67
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=96.52 E-value=0.0016 Score=39.86 Aligned_cols=23 Identities=26% Similarity=0.726 Sum_probs=19.1
Q ss_pred ccccccCccccChhhHHHHhhhh
Q psy4272 118 LTCLQCGRSYCRPYNLKRHIQYE 140 (575)
Q Consensus 118 ~~C~~Cgk~F~~~~~L~~H~r~H 140 (575)
|.|.+|++.|.....|..|+++|
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHhh
Confidence 68999999999999999999876
No 68
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=96.43 E-value=0.0012 Score=42.15 Aligned_cols=24 Identities=21% Similarity=0.336 Sum_probs=22.5
Q ss_pred cccccccccccChhhHHHHHHhhc
Q psy4272 147 FPCLYCSYRARHKHDLKKHVTFKH 170 (575)
Q Consensus 147 ~~C~~Cgk~F~~~~~L~~H~r~~H 170 (575)
|.|..|++.|.....|..|++.|+
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCccCCccCChhHHHHHhHHhc
Confidence 899999999999999999998854
No 69
>PRK04860 hypothetical protein; Provisional
Probab=96.31 E-value=0.0017 Score=60.47 Aligned_cols=39 Identities=23% Similarity=0.477 Sum_probs=33.9
Q ss_pred cccccccCccccChhhHHHHhhhhhCCCCCcccccccccccChh
Q psy4272 117 GLTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSYRARHKH 160 (575)
Q Consensus 117 p~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk~F~~~~ 160 (575)
+|.|. |++ ....+++|.++|+|+++ |.|..|++.|....
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~-YrC~~C~~~l~~~~ 157 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAV-YRCRRCGETLVFKG 157 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCcc-EECCCCCceeEEec
Confidence 59998 997 67788999999999999 99999999887654
No 70
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 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. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=95.94 E-value=0.006 Score=44.57 Aligned_cols=32 Identities=34% Similarity=0.528 Sum_probs=17.1
Q ss_pred CCCcccccccCccccChhhHHHHhhhhhCCCC
Q psy4272 114 LAQGLTCLQCGRSYCRPYNLKRHIQYECGKAP 145 (575)
Q Consensus 114 ~~kp~~C~~Cgk~F~~~~~L~~H~r~H~gekp 145 (575)
.+.|..|++|+..+.+..+|++|+.++++.||
T Consensus 21 S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 21 SEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred cCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 45566677777777666677777666665554
No 71
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=95.90 E-value=0.0046 Score=52.30 Aligned_cols=74 Identities=16% Similarity=0.279 Sum_probs=22.1
Q ss_pred CCCCCcchhhcchhHHHHHhhhcCCCCcccccccCccccChhhHHHHhhhhhCCCCCcccccccccccChhhHHHHHHhh
Q psy4272 90 PLKAKLSDYENKMKNVRESIRQKRLAQGLTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSYRARHKHDLKKHVTFK 169 (575)
Q Consensus 90 ~C~~C~~~f~~~~~~L~~H~r~H~~~kp~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk~F~~~~~L~~H~r~~ 169 (575)
.|.+|+..|... ..|..|+....+-. .. ....+.....+..+.+.-.. .. +.|..|++.|.....|..|++.+
T Consensus 1 ~C~~C~~~f~~~-~~l~~H~~~~H~~~---~~-~~~~l~~~~~~~~~~~~~~~-~~-~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 1 QCLFCDESFSSV-DDLLQHMKKKHGFD---IP-DQKYLVDPNRLLNYLRKKVK-ES-FRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp ------------------------------------------------------SS-EEBSSSS-EESSHHHHHHHHHHT
T ss_pred Cccccccccccc-cccccccccccccc---cc-cccccccccccccccccccC-CC-CCCCccCCCCcCHHHHHHHHcCc
Confidence 489999999886 67888886533321 11 11222233444444443222 25 89999999999999999999975
Q ss_pred c
Q psy4272 170 H 170 (575)
Q Consensus 170 H 170 (575)
+
T Consensus 74 ~ 74 (100)
T PF12756_consen 74 H 74 (100)
T ss_dssp T
T ss_pred c
Confidence 3
No 72
>smart00355 ZnF_C2H2 zinc finger.
Probab=95.73 E-value=0.0079 Score=37.21 Aligned_cols=22 Identities=27% Similarity=0.696 Sum_probs=10.7
Q ss_pred cccccCccccChhhHHHHhhhh
Q psy4272 119 TCLQCGRSYCRPYNLKRHIQYE 140 (575)
Q Consensus 119 ~C~~Cgk~F~~~~~L~~H~r~H 140 (575)
.|..|++.|.....|..|++.|
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 2 RCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCcchhCCHHHHHHHHHHh
Confidence 4444555555555555554443
No 73
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=95.48 E-value=0.0053 Score=51.91 Aligned_cols=26 Identities=12% Similarity=-0.083 Sum_probs=21.5
Q ss_pred CcchhhhhhccChhhhHhhhhhhhhh
Q psy4272 197 AENRHRFREFLNEHRNLERNVSHEEI 222 (575)
Q Consensus 197 ~~C~~C~k~F~~~~~l~~H~~th~~~ 222 (575)
..|..|++.|.....|..|+..+...
T Consensus 51 ~~C~~C~~~f~s~~~l~~Hm~~~~H~ 76 (100)
T PF12756_consen 51 FRCPYCNKTFRSREALQEHMRSKHHK 76 (100)
T ss_dssp EEBSSSS-EESSHHHHHHHHHHTTTT
T ss_pred CCCCccCCCCcCHHHHHHHHcCccCC
Confidence 48999999999999999999876443
No 74
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=95.34 E-value=0.0073 Score=60.59 Aligned_cols=71 Identities=14% Similarity=0.195 Sum_probs=46.6
Q ss_pred CCCCCccccc--ccccccChhhHHHHHHhhccCcccchhhhhhhhhcccccCCCCCCCcchhhhhhccChhhhHhhh
Q psy4272 142 GKAPQFPCLY--CSYRARHKHDLKKHVTFKHAAYLDHFQAVQEELEVTTKELSPGPKAENRHRFREFLNEHRNLERN 216 (575)
Q Consensus 142 gekp~~~C~~--Cgk~F~~~~~L~~H~r~~H~~~~~~~~~~~~~~~~~t~e~sp~p~~~C~~C~k~F~~~~~l~~H~ 216 (575)
++|| |+|++ |.|.|.....|+.|+.--|...+....-.....+....+. -.+.|+.|+|.|.+-..|..|.
T Consensus 346 d~Kp-ykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~---KPYrCevC~KRYKNlNGLKYHr 418 (423)
T COG5189 346 DGKP-YKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKD---KPYRCEVCDKRYKNLNGLKYHR 418 (423)
T ss_pred cCce-ecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccC---CceeccccchhhccCccceecc
Confidence 4589 99987 9999999999999986434332221111111111222222 2348999999999999998884
No 75
>PRK04860 hypothetical protein; Provisional
Probab=95.33 E-value=0.0066 Score=56.51 Aligned_cols=40 Identities=23% Similarity=0.242 Sum_probs=34.2
Q ss_pred CCCCCCCCcchhhcchhHHHHHhhhcCCCCcccccccCccccChh
Q psy4272 87 LPSPLKAKLSDYENKMKNVRESIRQKRLAQGLTCLQCGRSYCRPY 131 (575)
Q Consensus 87 ~p~~C~~C~~~f~~~~~~L~~H~r~H~~~kp~~C~~Cgk~F~~~~ 131 (575)
-+|.|. |++ ....+++|.++|+++++|.|..|++.|....
T Consensus 118 ~~Y~C~-C~~----~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 118 FPYRCK-CQE----HQLTVRRHNRVVRGEAVYRCRRCGETLVFKG 157 (160)
T ss_pred EEEEcC-CCC----eeCHHHHHHHHhcCCccEECCCCCceeEEec
Confidence 479998 987 3357899999999999999999999987654
No 76
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=95.23 E-value=0.014 Score=43.85 Aligned_cols=41 Identities=22% Similarity=0.369 Sum_probs=30.8
Q ss_pred HHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchh
Q psy4272 335 IVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRR 375 (575)
Q Consensus 335 l~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrR 375 (575)
+..|+++|....++.......|..+.+|+..+|+.||-.|+
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~ 50 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERM 50 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhc
Confidence 45699999999999999999999999999999999996543
No 77
>smart00355 ZnF_C2H2 zinc finger.
Probab=95.14 E-value=0.015 Score=35.91 Aligned_cols=22 Identities=27% Similarity=0.531 Sum_probs=20.8
Q ss_pred cccccccccccChhhHHHHHHh
Q psy4272 147 FPCLYCSYRARHKHDLKKHVTF 168 (575)
Q Consensus 147 ~~C~~Cgk~F~~~~~L~~H~r~ 168 (575)
|.|..|++.|.....|..|++.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~ 22 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRT 22 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHH
Confidence 6899999999999999999986
No 78
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=94.90 E-value=0.0084 Score=64.08 Aligned_cols=72 Identities=21% Similarity=0.299 Sum_probs=55.1
Q ss_pred CCCCCCCCcchhhcchhHHHHHhh--hcCCC--Cccccc--ccCccccChhhHHHHhhhhhCCCCCccccc--ccccccC
Q psy4272 87 LPSPLKAKLSDYENKMKNVRESIR--QKRLA--QGLTCL--QCGRSYCRPYNLKRHIQYECGKAPQFPCLY--CSYRARH 158 (575)
Q Consensus 87 ~p~~C~~C~~~f~~~~~~L~~H~r--~H~~~--kp~~C~--~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~--Cgk~F~~ 158 (575)
.++.|..|...|... ..+..|.+ .|+++ +++.|. .|++.|.+...+.+|..+|++.++ +.|.. |.+.+..
T Consensus 288 ~~~~~~~~~~~~s~~-~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~ 365 (467)
T COG5048 288 LPIKSKQCNISFSRS-SPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISP-AKEKLLNSSSKFSP 365 (467)
T ss_pred cCCCCccccCCcccc-ccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCc-cccccccCcccccc
Confidence 567888888888777 67888888 78888 888888 688888888888888888888877 77754 4444444
Q ss_pred hh
Q psy4272 159 KH 160 (575)
Q Consensus 159 ~~ 160 (575)
..
T Consensus 366 ~~ 367 (467)
T COG5048 366 LL 367 (467)
T ss_pred cc
Confidence 43
No 79
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 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. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=94.83 E-value=0.015 Score=42.50 Aligned_cols=38 Identities=18% Similarity=0.499 Sum_probs=23.8
Q ss_pred HHHhhhhh-CCCCCcccccccccccChhhHHHHHHhhccC
Q psy4272 134 KRHIQYEC-GKAPQFPCLYCSYRARHKHDLKKHVTFKHAA 172 (575)
Q Consensus 134 ~~H~r~H~-gekp~~~C~~Cgk~F~~~~~L~~H~r~~H~~ 172 (575)
..+.+.|. .+.| ..|++|+..+.+..+|++|+.++|..
T Consensus 12 ~~~~k~~~~S~~P-atCP~C~a~~~~srnLrRHle~~H~~ 50 (54)
T PF09237_consen 12 TKKPKSKSQSEQP-ATCPICGAVIRQSRNLRRHLEIRHFK 50 (54)
T ss_dssp ----CCCCTTS---EE-TTT--EESSHHHHHHHHHHHTTT
T ss_pred hhHHHHhhccCCC-CCCCcchhhccchhhHHHHHHHHhcc
Confidence 45555443 4667 99999999999999999999986653
No 80
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=93.85 E-value=0.036 Score=34.47 Aligned_cols=22 Identities=23% Similarity=0.653 Sum_probs=11.9
Q ss_pred ccccccCccccChhhHHHHhhh
Q psy4272 118 LTCLQCGRSYCRPYNLKRHIQY 139 (575)
Q Consensus 118 ~~C~~Cgk~F~~~~~L~~H~r~ 139 (575)
|.|.+|++.|.....|..|++.
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTT
T ss_pred CCCCCCCCCcCCHHHHHHHHCc
Confidence 3455555555555555555543
No 81
>KOG0773|consensus
Probab=93.41 E-value=0.11 Score=54.67 Aligned_cols=60 Identities=25% Similarity=0.415 Sum_probs=49.3
Q ss_pred CCCCCcccCCHHHHHHHHHHh-h--hCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhc
Q psy4272 322 NTGRFRQVYSSHQIVELEKEF-R--LTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRT 381 (575)
Q Consensus 322 ~~rr~Rt~~t~~ql~~L~~~F-~--~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~ 381 (575)
..+|.+..+......+|+.+. + ..+||+..++..||.++||+..||..||-|.|-+..+-
T Consensus 238 ~~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p 300 (342)
T KOG0773|consen 238 SKWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKP 300 (342)
T ss_pred CCCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCc
Confidence 355666688888888888773 3 25799999999999999999999999999998775543
No 82
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=93.11 E-value=0.052 Score=33.45 Aligned_cols=23 Identities=39% Similarity=0.863 Sum_probs=10.2
Q ss_pred cccccccccccChhhHHHHHHhhc
Q psy4272 147 FPCLYCSYRARHKHDLKKHVTFKH 170 (575)
Q Consensus 147 ~~C~~Cgk~F~~~~~L~~H~r~~H 170 (575)
|+|..|+.... ...|.+|++.+|
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhC
Confidence 34555554444 445555555433
No 83
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=92.61 E-value=0.054 Score=33.62 Aligned_cols=22 Identities=23% Similarity=0.516 Sum_probs=20.6
Q ss_pred cccccccccccChhhHHHHHHh
Q psy4272 147 FPCLYCSYRARHKHDLKKHVTF 168 (575)
Q Consensus 147 ~~C~~Cgk~F~~~~~L~~H~r~ 168 (575)
|.|.+|++.|.....|..|++.
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTT
T ss_pred CCCCCCCCCcCCHHHHHHHHCc
Confidence 6799999999999999999976
No 84
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=92.59 E-value=0.17 Score=37.95 Aligned_cols=46 Identities=15% Similarity=0.355 Sum_probs=35.8
Q ss_pred CCCcccCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccch
Q psy4272 324 GRFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNR 374 (575)
Q Consensus 324 rr~Rt~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNr 374 (575)
||+|..+|-++-..+-..++... ...+||..+|++..+|..|..|+
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k 46 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNK 46 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhH
Confidence 57889999998888888888776 57789999999999999999885
No 85
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=92.29 E-value=0.1 Score=32.09 Aligned_cols=23 Identities=35% Similarity=0.606 Sum_probs=17.0
Q ss_pred ccccccCccccChhhHHHHhhhhh
Q psy4272 118 LTCLQCGRSYCRPYNLKRHIQYEC 141 (575)
Q Consensus 118 ~~C~~Cgk~F~~~~~L~~H~r~H~ 141 (575)
|+|..|+.... ...|.+|++.|.
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhC
Confidence 67888988777 788899988765
No 86
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=91.84 E-value=0.069 Score=34.01 Aligned_cols=22 Identities=23% Similarity=0.612 Sum_probs=14.7
Q ss_pred ccccccCccccChhhHHHHhhh
Q psy4272 118 LTCLQCGRSYCRPYNLKRHIQY 139 (575)
Q Consensus 118 ~~C~~Cgk~F~~~~~L~~H~r~ 139 (575)
|.|..|++.|.....|..|++.
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCcccCCCCcCCHHHHHHHHcc
Confidence 5677777777777777666653
No 87
>KOG2482|consensus
Probab=90.39 E-value=0.19 Score=51.26 Aligned_cols=127 Identities=19% Similarity=0.207 Sum_probs=84.9
Q ss_pred CCCCCCCcchhhcchhHHHHHhh-hcC---C----------------C--CcccccccCccccChhhHHHHhhh--hhCC
Q psy4272 88 PSPLKAKLSDYENKMKNVRESIR-QKR---L----------------A--QGLTCLQCGRSYCRPYNLKRHIQY--ECGK 143 (575)
Q Consensus 88 p~~C~~C~~~f~~~~~~L~~H~r-~H~---~----------------~--kp~~C~~Cgk~F~~~~~L~~H~r~--H~ge 143 (575)
.-.|-+|...+...++..-.|+- +|. | + ..+.|-.|.|.|..+..|+.|||. |...
T Consensus 144 slqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrdkntLkeHMrkK~Hrri 223 (423)
T KOG2482|consen 144 SLQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRDKNTLKEHMRKKRHRRI 223 (423)
T ss_pred eeEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCCcHHHHHHHHhccCccc
Confidence 34799998877666666656653 232 1 1 237999999999999999999974 4311
Q ss_pred CCC-----------------------------------------------------cccccccccccChhhHHHHHHhhc
Q psy4272 144 APQ-----------------------------------------------------FPCLYCSYRARHKHDLKKHVTFKH 170 (575)
Q Consensus 144 kp~-----------------------------------------------------~~C~~Cgk~F~~~~~L~~H~r~~H 170 (575)
.|. .+|-+|....-....|..||++.|
T Consensus 224 nPknreYDkfyiINY~ev~ks~t~~~~e~dret~~d~~E~D~~wsDw~ed~a~a~~v~CLfC~~~~en~~~l~eHmk~vH 303 (423)
T KOG2482|consen 224 NPKNREYDKFYIINYLEVGKSWTIVHSEDDRETNEDINETDDTWSDWNEDDAEALSVVCLFCTNFYENPVFLFEHMKIVH 303 (423)
T ss_pred CCCccccceEEEEeHhhcCCccchhhhhhhhhhhccccccccchhhhhcCCCCccceEEEeeccchhhHHHHHHHHHHHH
Confidence 100 378999998888999999999877
Q ss_pred cCc---------ccchhhhhhhhhc-ccccCCCCCCCcchhhhhhccChhhhHhhhhhh
Q psy4272 171 AAY---------LDHFQAVQEELEV-TTKELSPGPKAENRHRFREFLNEHRNLERNVSH 219 (575)
Q Consensus 171 ~~~---------~~~~~~~~~~~~~-~t~e~sp~p~~~C~~C~k~F~~~~~l~~H~~th 219 (575)
.-. +.+.++....... .++ -...|-.|.-.|-.+..|+.|+..+
T Consensus 304 e~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~-----~~~~c~~cd~~F~~e~~l~~hm~e~ 357 (423)
T KOG2482|consen 304 EFDLLKIQSDYSLNFYQRVRVINYIRKQK-----KKSRCAECDLSFWKEPGLLIHMVED 357 (423)
T ss_pred HhhHHhhccccccchhhhhhHHHHHHHHh-----hccccccccccccCcchhhhhcccc
Confidence 521 2222222221111 111 2337999999999999999998654
No 88
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=89.87 E-value=0.084 Score=33.60 Aligned_cols=22 Identities=27% Similarity=0.478 Sum_probs=20.5
Q ss_pred cccccccccccChhhHHHHHHh
Q psy4272 147 FPCLYCSYRARHKHDLKKHVTF 168 (575)
Q Consensus 147 ~~C~~Cgk~F~~~~~L~~H~r~ 168 (575)
|.|..|++.|.....|..|++.
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCcccCCCCcCCHHHHHHHHcc
Confidence 8899999999999999999875
No 89
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=89.84 E-value=0.096 Score=55.88 Aligned_cols=59 Identities=27% Similarity=0.560 Sum_probs=53.3
Q ss_pred CcccccccCccccChhhHHHHhh--hhhCC--CCCcccc--cccccccChhhHHHHHHhhccCcccc
Q psy4272 116 QGLTCLQCGRSYCRPYNLKRHIQ--YECGK--APQFPCL--YCSYRARHKHDLKKHVTFKHAAYLDH 176 (575)
Q Consensus 116 kp~~C~~Cgk~F~~~~~L~~H~r--~H~ge--kp~~~C~--~Cgk~F~~~~~L~~H~r~~H~~~~~~ 176 (575)
.++.|..|...|.+...|.+|.+ .|+++ ++ +.|. .|++.|.+...+..|..+ |.+...+
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~-~~~p~~~~~~~~~~~~~~~~~~~~-~~~~~~~ 352 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKP-FSCPYSLCGKLFSRNDALKRHILL-HTSISPA 352 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCc-eeeeccCCCccccccccccCCccc-ccCCCcc
Confidence 57999999999999999999999 89999 99 9999 799999999999999998 5554444
No 90
>KOG2231|consensus
Probab=89.16 E-value=0.46 Score=53.46 Aligned_cols=22 Identities=27% Similarity=0.677 Sum_probs=13.0
Q ss_pred ccccccccccChhhHHHHHHhh
Q psy4272 148 PCLYCSYRARHKHDLKKHVTFK 169 (575)
Q Consensus 148 ~C~~Cgk~F~~~~~L~~H~r~~ 169 (575)
.|.+|...|.....|.+|++.+
T Consensus 184 ~C~~C~~~fld~~el~rH~~~~ 205 (669)
T KOG2231|consen 184 LCKFCHERFLDDDELYRHLRFD 205 (669)
T ss_pred cchhhhhhhccHHHHHHhhccc
Confidence 4556666666666666666553
No 91
>KOG2893|consensus
Probab=88.90 E-value=0.13 Score=49.84 Aligned_cols=47 Identities=23% Similarity=0.403 Sum_probs=32.2
Q ss_pred ccccCccccChhhHHHHhhhhhCCCCCcccccccccccChhhHHHHHHhhcc
Q psy4272 120 CLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSYRARHKHDLKKHVTFKHA 171 (575)
Q Consensus 120 C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk~F~~~~~L~~H~r~~H~ 171 (575)
|=+|.+-|.....|..|++. |- |+|.+|.|.....-.|..|-...|.
T Consensus 13 cwycnrefddekiliqhqka----kh-fkchichkkl~sgpglsihcmqvhk 59 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQKA----KH-FKCHICHKKLFSGPGLSIHCMQVHK 59 (341)
T ss_pred eeecccccchhhhhhhhhhh----cc-ceeeeehhhhccCCCceeehhhhhh
Confidence 66788888888888777764 34 8888888776666666666333343
No 92
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=87.48 E-value=0.42 Score=29.96 Aligned_cols=19 Identities=32% Similarity=0.700 Sum_probs=10.6
Q ss_pred ccccccccccChhhHHHHHH
Q psy4272 148 PCLYCSYRARHKHDLKKHVT 167 (575)
Q Consensus 148 ~C~~Cgk~F~~~~~L~~H~r 167 (575)
.|..||+.| ....|.+|++
T Consensus 4 ~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred cCCCCCCEE-CHHHHHHHHH
Confidence 466666666 4445555554
No 93
>KOG2231|consensus
Probab=87.12 E-value=0.7 Score=52.05 Aligned_cols=86 Identities=16% Similarity=0.213 Sum_probs=54.3
Q ss_pred cccccCccccChhhHHHHhhhhhCCCCCccccccc------ccccChhhHHHHHHhhccCcccchhhhhhhhhcccccCC
Q psy4272 119 TCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCS------YRARHKHDLKKHVTFKHAAYLDHFQAVQEELEVTTKELS 192 (575)
Q Consensus 119 ~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cg------k~F~~~~~L~~H~r~~H~~~~~~~~~~~~~~~~~t~e~s 192 (575)
.|..|...|.....|.+|++.++ |.|.+|. .-|..-..|..|.|.+|---- .
T Consensus 184 ~C~~C~~~fld~~el~rH~~~~h-----~~chfC~~~~~~neyy~~~~dLe~HfR~~HflCE-~---------------- 241 (669)
T KOG2231|consen 184 LCKFCHERFLDDDELYRHLRFDH-----EFCHFCDYKTGQNEYYNDYDDLEEHFRKGHFLCE-E---------------- 241 (669)
T ss_pred cchhhhhhhccHHHHHHhhccce-----eheeecCcccccchhcccchHHHHHhhhcCcccc-c----------------
Confidence 58888888888888888888654 6777774 357778899999988663100 0
Q ss_pred CCCCCcchhhhhhccChhhhHhhhhhhhhhhccccC
Q psy4272 193 PGPKAENRHRFREFLNEHRNLERNVSHEEIRTHKKH 228 (575)
Q Consensus 193 p~p~~~C~~C~k~F~~~~~l~~H~~th~~~~~~~~~ 228 (575)
....|..+...|..+.+|..|...+..++.|...
T Consensus 242 --~~C~~~~f~~~~~~ei~lk~~~~~~~~e~~~~~~ 275 (669)
T KOG2231|consen 242 --EFCRTKKFYVAFELEIELKAHNRFIQHEKCYICR 275 (669)
T ss_pred --cccccceeeehhHHHHHHHhhccccchheeccCC
Confidence 0013344444455666677666544444444443
No 94
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=86.59 E-value=0.51 Score=29.56 Aligned_cols=20 Identities=35% Similarity=0.921 Sum_probs=14.1
Q ss_pred ccccccCccccChhhHHHHhh
Q psy4272 118 LTCLQCGRSYCRPYNLKRHIQ 138 (575)
Q Consensus 118 ~~C~~Cgk~F~~~~~L~~H~r 138 (575)
..|..||+.| ....|.+|+.
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHH
Confidence 3578888888 5566777765
No 95
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=82.27 E-value=0.87 Score=30.52 Aligned_cols=21 Identities=14% Similarity=0.572 Sum_probs=12.0
Q ss_pred ccccccCccccChhhHHHHhh
Q psy4272 118 LTCLQCGRSYCRPYNLKRHIQ 138 (575)
Q Consensus 118 ~~C~~Cgk~F~~~~~L~~H~r 138 (575)
|.|.+|++.|.....+..|+.
T Consensus 4 ~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 4 FYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred eEccccCCccCCHHHHHHHHC
Confidence 556666666665555555553
No 96
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=81.64 E-value=1 Score=39.06 Aligned_cols=30 Identities=27% Similarity=0.598 Sum_probs=19.2
Q ss_pred ccccccCccccChhhHHHHhhhhhCCCCCcccccccccccCh
Q psy4272 118 LTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSYRARHK 159 (575)
Q Consensus 118 ~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk~F~~~ 159 (575)
..|..||++|.-. +..| -.|+.||..|.-.
T Consensus 10 R~Cp~CG~kFYDL-----------nk~P-ivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFYDL-----------NKDP-IVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchhccC-----------CCCC-ccCCCCCCccCcc
Confidence 4677777777542 1245 6777777777665
No 97
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=80.25 E-value=1.8 Score=37.67 Aligned_cols=91 Identities=12% Similarity=0.022 Sum_probs=52.3
Q ss_pred CCCCCCcchhhcchhHHHHHhhhcCCCCcccccccCccccChhhHHHHhhhhh-CCCC-----------Ccccccccccc
Q psy4272 89 SPLKAKLSDYENKMKNVRESIRQKRLAQGLTCLQCGRSYCRPYNLKRHIQYEC-GKAP-----------QFPCLYCSYRA 156 (575)
Q Consensus 89 ~~C~~C~~~f~~~~~~L~~H~r~H~~~kp~~C~~Cgk~F~~~~~L~~H~r~H~-gekp-----------~~~C~~Cgk~F 156 (575)
|.|+.|+...... |-.|++||-......+|.|.-. |. -.++ ...|--|.+.|
T Consensus 2 Y~CPrC~skvC~L---------------P~~CpiCgLtLVss~HLARSyH-HLfPl~~f~ev~~~~~~~~~~C~~C~~~f 65 (112)
T TIGR00622 2 YFCPQCRAKVCEL---------------PVECPICGLTLILSTHLARSYH-HLFPLKAFQEIPLEEYNGSRFCFGCQGPF 65 (112)
T ss_pred ccCCCCCCCccCC---------------CCcCCcCCCEEeccchHHHhhh-ccCCCcccccccccccCCCCcccCcCCCC
Confidence 6677776655443 5678888888877777765421 10 1111 01377777777
Q ss_pred cChhhHHHHHHhhccCcccchhhhhhhhhcccccCCCCCCCcchhhhhhccChhhhHhhhhhh
Q psy4272 157 RHKHDLKKHVTFKHAAYLDHFQAVQEELEVTTKELSPGPKAENRHRFREFLNEHRNLERNVSH 219 (575)
Q Consensus 157 ~~~~~L~~H~r~~H~~~~~~~~~~~~~~~~~t~e~sp~p~~~C~~C~k~F~~~~~l~~H~~th 219 (575)
....... .+ +.+....+.|..|...|-..-+...|...|
T Consensus 66 ~~~~~~~-------~~-----------------~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh 104 (112)
T TIGR00622 66 PKPPVSP-------FD-----------------ELKDSHRYVCAVCKNVFCVDCDVFVHESLH 104 (112)
T ss_pred CCccccc-------cc-----------------ccccccceeCCCCCCccccccchhhhhhcc
Confidence 6543111 00 011122347888888888777777776655
No 98
>KOG2893|consensus
Probab=79.97 E-value=0.58 Score=45.42 Aligned_cols=47 Identities=13% Similarity=0.176 Sum_probs=35.5
Q ss_pred CCCCCcchhhcchhHHHHHhhhcCCCCcccccccCccccChhhHHHH-hhhhh
Q psy4272 90 PLKAKLSDYENKMKNVRESIRQKRLAQGLTCLQCGRSYCRPYNLKRH-IQYEC 141 (575)
Q Consensus 90 ~C~~C~~~f~~~~~~L~~H~r~H~~~kp~~C~~Cgk~F~~~~~L~~H-~r~H~ 141 (575)
=|.+|.+.|... .-|..|++. |-|+|.+|.|.+..-..|..| |.+|.
T Consensus 12 wcwycnrefdde-kiliqhqka----khfkchichkkl~sgpglsihcmqvhk 59 (341)
T KOG2893|consen 12 WCWYCNREFDDE-KILIQHQKA----KHFKCHICHKKLFSGPGLSIHCMQVHK 59 (341)
T ss_pred eeeecccccchh-hhhhhhhhh----ccceeeeehhhhccCCCceeehhhhhh
Confidence 499999999887 466666654 559999999887777677666 45554
No 99
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=79.75 E-value=1.1 Score=30.08 Aligned_cols=22 Identities=18% Similarity=0.412 Sum_probs=20.3
Q ss_pred cccccccccccChhhHHHHHHh
Q psy4272 147 FPCLYCSYRARHKHDLKKHVTF 168 (575)
Q Consensus 147 ~~C~~Cgk~F~~~~~L~~H~r~ 168 (575)
|.|.+|++.|.....+..|++.
T Consensus 4 ~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 4 FYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred eEccccCCccCCHHHHHHHHCh
Confidence 8899999999999999999865
No 100
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=78.26 E-value=0.9 Score=33.96 Aligned_cols=31 Identities=26% Similarity=0.471 Sum_probs=19.4
Q ss_pred hhCCCCCcccccccccccChhhHHHHHHhhcc
Q psy4272 140 ECGKAPQFPCLYCSYRARHKHDLKKHVTFKHA 171 (575)
Q Consensus 140 H~gekp~~~C~~Cgk~F~~~~~L~~H~r~~H~ 171 (575)
..||.- ++|+-||+.|.....+.+|....|.
T Consensus 12 RDGE~~-lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 12 RDGEEF-LRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred cCCcee-eeCCchhHHHHHhHHHHHHhhHHhh
Confidence 345555 6677777777776666666655443
No 101
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=78.24 E-value=1.3 Score=29.68 Aligned_cols=24 Identities=33% Similarity=0.725 Sum_probs=13.4
Q ss_pred ccccccCccccChhhHHHHhhhhhCCCCCcccccccc
Q psy4272 118 LTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSY 154 (575)
Q Consensus 118 ~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk 154 (575)
|.|.+||..+.-.. .+ +.|++||.
T Consensus 2 ~~C~~CGy~y~~~~------------~~-~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGEE------------AP-WVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCCc------------CC-CcCcCCCC
Confidence 56666665443321 44 67777764
No 102
>KOG2186|consensus
Probab=74.00 E-value=1.8 Score=42.70 Aligned_cols=47 Identities=28% Similarity=0.578 Sum_probs=29.8
Q ss_pred ccccccCccccChhhHHHHhhhhhCCCCCcccccccccccChhhHHHHHHh
Q psy4272 118 LTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSYRARHKHDLKKHVTF 168 (575)
Q Consensus 118 ~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk~F~~~~~L~~H~r~ 168 (575)
|.|..||...... .+.+|+-.-++ .. |.|--||+.|.+ ..+..|..-
T Consensus 4 FtCnvCgEsvKKp-~vekH~srCrn-~~-fSCIDC~k~F~~-~sYknH~kC 50 (276)
T KOG2186|consen 4 FTCNVCGESVKKP-QVEKHMSRCRN-AY-FSCIDCGKTFER-VSYKNHTKC 50 (276)
T ss_pred Eehhhhhhhcccc-chHHHHHhccC-Ce-eEEeeccccccc-chhhhhhhh
Confidence 6677777665544 45667665555 44 777777777777 556666543
No 103
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=73.67 E-value=2.4 Score=37.53 Aligned_cols=33 Identities=15% Similarity=0.268 Sum_probs=22.2
Q ss_pred ccccccCccccChhhHHHHhhhhhCCCCCcccccccccccChhhH
Q psy4272 118 LTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSYRARHKHDL 162 (575)
Q Consensus 118 ~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk~F~~~~~L 162 (575)
..|+.||++|.-. +..| -.|+.||..|.....+
T Consensus 10 r~Cp~cg~kFYDL-----------nk~p-~vcP~cg~~~~~~~~~ 42 (129)
T TIGR02300 10 RICPNTGSKFYDL-----------NRRP-AVSPYTGEQFPPEEAL 42 (129)
T ss_pred ccCCCcCcccccc-----------CCCC-ccCCCcCCccCcchhh
Confidence 5688888887542 2346 7888888887665333
No 104
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=71.97 E-value=1 Score=44.17 Aligned_cols=44 Identities=25% Similarity=0.551 Sum_probs=26.6
Q ss_pred CcccccccCccccChhhHHHHhhh---h-------hCCCCC----cccccccccccCh
Q psy4272 116 QGLTCLQCGRSYCRPYNLKRHIQY---E-------CGKAPQ----FPCLYCSYRARHK 159 (575)
Q Consensus 116 kp~~C~~Cgk~F~~~~~L~~H~r~---H-------~gekp~----~~C~~Cgk~F~~~ 159 (575)
|.+.|++|++.|..+.-+....++ . .+..|- ..|+.||.+|...
T Consensus 4 k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred CceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 446777777777766554444432 1 222331 4699999887765
No 105
>KOG2186|consensus
Probab=71.14 E-value=1.6 Score=42.95 Aligned_cols=49 Identities=16% Similarity=0.333 Sum_probs=39.1
Q ss_pred CCCCCCcchhhcchhHHHHHhhhcCCCCcccccccCccccChhhHHHHhhhhh
Q psy4272 89 SPLKAKLSDYENKMKNVRESIRQKRLAQGLTCLQCGRSYCRPYNLKRHIQYEC 141 (575)
Q Consensus 89 ~~C~~C~~~f~~~~~~L~~H~r~H~~~kp~~C~~Cgk~F~~~~~L~~H~r~H~ 141 (575)
|.|.+||...... .+..|+..-++ .-|.|-.|++.|-+ ...+.|...-+
T Consensus 4 FtCnvCgEsvKKp--~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~kCIT 52 (276)
T KOG2186|consen 4 FTCNVCGESVKKP--QVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTKCIT 52 (276)
T ss_pred Eehhhhhhhcccc--chHHHHHhccC-CeeEEeeccccccc-chhhhhhhhcc
Confidence 6799999987665 67778877777 67999999999999 56777766444
No 106
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=70.77 E-value=7 Score=28.47 Aligned_cols=46 Identities=9% Similarity=0.143 Sum_probs=34.6
Q ss_pred cCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhh
Q psy4272 329 VYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLK 379 (575)
Q Consensus 329 ~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~k 379 (575)
.+++.+..+|...|... ..-.++|..+|++...|+.|...-..|-|
T Consensus 4 ~L~~~er~vi~~~y~~~-----~t~~eIa~~lg~s~~~V~~~~~~al~kLR 49 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG-----LTLEEIAERLGISRSTVRRILKRALKKLR 49 (50)
T ss_dssp TS-HHHHHHHHHHHTST------SHHHHHHHHTSCHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCC-----CCHHHHHHHHCCcHHHHHHHHHHHHHHhc
Confidence 46788899999988333 35678999999999999998865555544
No 107
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=70.72 E-value=1.9 Score=32.33 Aligned_cols=31 Identities=23% Similarity=0.443 Sum_probs=25.5
Q ss_pred hcCCCCcccccccCccccChhhHHHHhhhhh
Q psy4272 111 QKRLAQGLTCLQCGRSYCRPYNLKRHIQYEC 141 (575)
Q Consensus 111 ~H~~~kp~~C~~Cgk~F~~~~~L~~H~r~H~ 141 (575)
...|+.-+.|+.||+.|.......+|...-+
T Consensus 11 ~RDGE~~lrCPRC~~~FR~~K~Y~RHVNKaH 41 (65)
T COG4049 11 DRDGEEFLRCPRCGMVFRRRKDYIRHVNKAH 41 (65)
T ss_pred ccCCceeeeCCchhHHHHHhHHHHHHhhHHh
Confidence 4567788999999999999999999986433
No 108
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=69.58 E-value=2.4 Score=28.71 Aligned_cols=25 Identities=28% Similarity=0.486 Sum_probs=16.6
Q ss_pred cccccccCccccChhhHHHHhhhhhCCCCCcccccccc
Q psy4272 117 GLTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSY 154 (575)
Q Consensus 117 p~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk 154 (575)
.|+|.+||..+... +.| ..|++||.
T Consensus 2 ~~~C~~CG~i~~g~------------~~p-~~CP~Cg~ 26 (34)
T cd00729 2 VWVCPVCGYIHEGE------------EAP-EKCPICGA 26 (34)
T ss_pred eEECCCCCCEeECC------------cCC-CcCcCCCC
Confidence 37888998554321 145 78999985
No 109
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=69.45 E-value=2.9 Score=36.34 Aligned_cols=33 Identities=9% Similarity=0.213 Sum_probs=26.8
Q ss_pred CCCCCCCCCcchhhcchhHHHHHhhhcCCCCcccccccCccccCh
Q psy4272 86 TLPSPLKAKLSDYENKMKNVRESIRQKRLAQGLTCLQCGRSYCRP 130 (575)
Q Consensus 86 ~~p~~C~~C~~~f~~~~~~L~~H~r~H~~~kp~~C~~Cgk~F~~~ 130 (575)
++-..|..||+.|... ++.|-.|++||..|...
T Consensus 7 GtKR~Cp~CG~kFYDL------------nk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 7 GTKRTCPSCGAKFYDL------------NKDPIVCPKCGTEFPPE 39 (108)
T ss_pred CCcccCCCCcchhccC------------CCCCccCCCCCCccCcc
Confidence 4456899999999876 34788899999999776
No 110
>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=69.36 E-value=7.9 Score=29.04 Aligned_cols=42 Identities=17% Similarity=0.259 Sum_probs=34.2
Q ss_pred CCHHHHHHHHHHhhhCCC--CCHHHHHHHHHHhCCChhhhhhcc
Q psy4272 330 YSSHQIVELEKEFRLTNY--LPSDRRKVLSKELGLTERQIKIWF 371 (575)
Q Consensus 330 ~t~~ql~~L~~~F~~~~~--p~~~~r~~la~~l~l~~~~V~vWF 371 (575)
+|..|+++|...|...-| |-...-.+||..||++...|.--.
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~L 44 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHL 44 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHH
Confidence 578999999999987654 666778899999999998765433
No 111
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=68.84 E-value=4.2 Score=37.90 Aligned_cols=39 Identities=10% Similarity=0.098 Sum_probs=30.1
Q ss_pred hcCCCCcccccccCccccChhhHHHHhhhhhCCCCCcccccccccccCh
Q psy4272 111 QKRLAQGLTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSYRARHK 159 (575)
Q Consensus 111 ~H~~~kp~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk~F~~~ 159 (575)
...+..-|.|+.|+..|+.-..+. .- |.|+.||.....-
T Consensus 103 ~e~~~~~Y~Cp~c~~r~tf~eA~~---------~~-F~Cp~Cg~~L~~~ 141 (158)
T TIGR00373 103 FETNNMFFICPNMCVRFTFNEAME---------LN-FTCPRCGAMLDYL 141 (158)
T ss_pred hccCCCeEECCCCCcEeeHHHHHH---------cC-CcCCCCCCEeeec
Confidence 344556699999999999988874 25 9999999865443
No 112
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=66.09 E-value=4.4 Score=38.54 Aligned_cols=36 Identities=14% Similarity=0.226 Sum_probs=28.3
Q ss_pred CCCcccccccCccccChhhHHHHhhhhhCCCCCcccccccccccCh
Q psy4272 114 LAQGLTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSYRARHK 159 (575)
Q Consensus 114 ~~kp~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk~F~~~ 159 (575)
...-|.|+.|++.|+.-..+. .- |.|+.||.....-
T Consensus 114 ~~~~Y~Cp~C~~rytf~eA~~---------~~-F~Cp~Cg~~L~~~ 149 (178)
T PRK06266 114 NNMFFFCPNCHIRFTFDEAME---------YG-FRCPQCGEMLEEY 149 (178)
T ss_pred CCCEEECCCCCcEEeHHHHhh---------cC-CcCCCCCCCCeec
Confidence 445699999999999888763 25 9999999875554
No 113
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=65.85 E-value=2.4 Score=48.82 Aligned_cols=48 Identities=17% Similarity=0.186 Sum_probs=27.2
Q ss_pred CCCCCcchhhcchhHHHHHhhhcCCCCcccccccCccccChhhHHHHhhhhhCCCCCccccccccc
Q psy4272 90 PLKAKLSDYENKMKNVRESIRQKRLAQGLTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSYR 155 (575)
Q Consensus 90 ~C~~C~~~f~~~~~~L~~H~r~H~~~kp~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk~ 155 (575)
.|..||..+..... ..-+..|...+...|.+|| |....| +.|+.||-.
T Consensus 437 ~C~~Cg~v~~Cp~C--d~~lt~H~~~~~L~CH~Cg---------------~~~~~p-~~Cp~Cgs~ 484 (730)
T COG1198 437 LCRDCGYIAECPNC--DSPLTLHKATGQLRCHYCG---------------YQEPIP-QSCPECGSE 484 (730)
T ss_pred ecccCCCcccCCCC--CcceEEecCCCeeEeCCCC---------------CCCCCC-CCCCCCCCC
Confidence 58888766644311 1122334444456666666 334556 889999853
No 114
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=65.58 E-value=2.3 Score=34.97 Aligned_cols=33 Identities=21% Similarity=0.460 Sum_probs=23.0
Q ss_pred CcccccccCccccChhhHHHHhhhhhCCCCCcccccccccccCh
Q psy4272 116 QGLTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSYRARHK 159 (575)
Q Consensus 116 kp~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk~F~~~ 159 (575)
..|.|+.|++. .+.|+-+|. +.|..||..|.--
T Consensus 34 ~~~~Cp~C~~~--------~VkR~a~GI---W~C~kCg~~fAGg 66 (89)
T COG1997 34 AKHVCPFCGRT--------TVKRIATGI---WKCRKCGAKFAGG 66 (89)
T ss_pred cCCcCCCCCCc--------ceeeeccCe---EEcCCCCCeeccc
Confidence 45889999865 344555553 7899999888643
No 115
>KOG4173|consensus
Probab=65.53 E-value=3 Score=39.82 Aligned_cols=79 Identities=18% Similarity=0.308 Sum_probs=57.8
Q ss_pred CCCCCC--CcchhhcchhHHHHHhhhcCCCCcccccccCccccChhhHHHHhh-hh---------hCCCCCcccc--ccc
Q psy4272 88 PSPLKA--KLSDYENKMKNVRESIRQKRLAQGLTCLQCGRSYCRPYNLKRHIQ-YE---------CGKAPQFPCL--YCS 153 (575)
Q Consensus 88 p~~C~~--C~~~f~~~~~~L~~H~r~H~~~kp~~C~~Cgk~F~~~~~L~~H~r-~H---------~gekp~~~C~--~Cg 153 (575)
-+.|.+ |.+.|... +++.+|..+-.+ -.|.+|.+.|....-|..|+. .| .| ++.|.|- .|+
T Consensus 79 ~~~cqvagc~~~~d~l-D~~E~hY~~~h~---~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG-~dMy~ClvEgCt 153 (253)
T KOG4173|consen 79 AFACQVAGCCQVFDAL-DDYEHHYHTLHG---NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERG-QDMYQCLVEGCT 153 (253)
T ss_pred cccccccchHHHHhhh-hhHHHhhhhccc---chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcC-ccHHHHHHHhhh
Confidence 356776 55566555 556667654322 379999999999999999985 34 24 3449994 599
Q ss_pred ccccChhhHHHHHHhhcc
Q psy4272 154 YRARHKHDLKKHVTFKHA 171 (575)
Q Consensus 154 k~F~~~~~L~~H~r~~H~ 171 (575)
-.|.+....+.|+...|.
T Consensus 154 ~KFkT~r~RkdH~I~~Hk 171 (253)
T KOG4173|consen 154 EKFKTSRDRKDHMIRMHK 171 (253)
T ss_pred hhhhhhhhhhhHHHHhcc
Confidence 999999999999877664
No 116
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=65.00 E-value=1.8 Score=40.16 Aligned_cols=13 Identities=31% Similarity=0.462 Sum_probs=7.6
Q ss_pred cccccccccccCh
Q psy4272 147 FPCLYCSYRARHK 159 (575)
Q Consensus 147 ~~C~~Cgk~F~~~ 159 (575)
++|+.||++|..-
T Consensus 29 ~~c~~c~~~f~~~ 41 (154)
T PRK00464 29 RECLACGKRFTTF 41 (154)
T ss_pred eeccccCCcceEe
Confidence 5566666666544
No 117
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=64.74 E-value=5.3 Score=41.09 Aligned_cols=66 Identities=17% Similarity=0.436 Sum_probs=39.8
Q ss_pred hHHHHHhhhcCCCCcccccccC---ccc------cChhhHHHHhhhhhCC---CCCcccccccccccChhhHHHHHHhhc
Q psy4272 103 KNVRESIRQKRLAQGLTCLQCG---RSY------CRPYNLKRHIQYECGK---APQFPCLYCSYRARHKHDLKKHVTFKH 170 (575)
Q Consensus 103 ~~L~~H~r~H~~~kp~~C~~Cg---k~F------~~~~~L~~H~r~H~ge---kp~~~C~~Cgk~F~~~~~L~~H~r~~H 170 (575)
..|+.|..+..+ .+-|.+|- +.| -++..|+.|...-..+ |---.|.+|.+.|-..+.|.+|+|..|
T Consensus 167 k~lk~H~K~~H~--~~~C~~C~~nKk~F~~E~~lF~~~~Lr~H~~~G~~e~GFKGHP~C~FC~~~FYdDDEL~~HcR~~H 244 (493)
T COG5236 167 KELKKHYKAQHG--FVLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGHPLCIFCKIYFYDDDELRRHCRLRH 244 (493)
T ss_pred HHHHHHHHhhcC--cEEhHhhhcCcccCccceeeeecccccccccCCccccCcCCCchhhhccceecChHHHHHHHHhhh
Confidence 355666655332 25566653 233 3345566666543222 221259999999999999999998755
No 118
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=64.30 E-value=3.5 Score=38.60 Aligned_cols=24 Identities=33% Similarity=0.636 Sum_probs=19.7
Q ss_pred cccccccCccccChhhHHHHhhhhhCCCCCcccccccc
Q psy4272 117 GLTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSY 154 (575)
Q Consensus 117 p~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk 154 (575)
-|.|.+||. +|-|+-| -+|++||-
T Consensus 134 ~~vC~vCGy-------------~~~ge~P-~~CPiCga 157 (166)
T COG1592 134 VWVCPVCGY-------------THEGEAP-EVCPICGA 157 (166)
T ss_pred EEEcCCCCC-------------cccCCCC-CcCCCCCC
Confidence 599999984 4667777 99999983
No 119
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=63.38 E-value=3.4 Score=28.37 Aligned_cols=33 Identities=15% Similarity=0.262 Sum_probs=16.7
Q ss_pred ccccccCccccChhhHHHHhhhhhCCCCCcccccccccc
Q psy4272 118 LTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSYRA 156 (575)
Q Consensus 118 ~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk~F 156 (575)
+.|+.|+..|.-..... ...... ..|+.|+..|
T Consensus 3 ~~CP~C~~~~~v~~~~~-----~~~~~~-v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQL-----GANGGK-VRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEEEeCHHHc-----CCCCCE-EECCCCCCEE
Confidence 45666666665554321 111113 5666666655
No 120
>PF08456 Vmethyltransf_C: Viral methyltransferase C-terminal; InterPro: IPR013664 This domain is found in the central region of Virgaviridae (Tymoviruses) non-structural poly-protein, it spans the RNA helicase domain of the replicase large subunit, which is a RNA-dependent RNA polymerase active in viral RNA replication []. The poly-protein is processed into the replicase small subunit, which is the methyltransferase active in RNA capping and the RNA helicase. Methyltransferase displays a cytoplasmic capping enzyme activity. This function is necessary since all viral RNAs are synthesized in the cytoplasm, and host capping enzymes are restricted to the nucleus. The helicase region probably, which is immediately adjacent to the methyltransferase domain exhibits NTPase and RNA unwinding activities.
Probab=63.34 E-value=7.4 Score=37.55 Aligned_cols=50 Identities=26% Similarity=0.397 Sum_probs=39.1
Q ss_pred CCchhHHHhhhhhHHHHHHHHHHHHHHHhcccccccCCCCCCCCCcchhh
Q psy4272 502 LPPGQVEKLNDLYENERNMLIQELIRKKLGLLIQNNQNGGHAEDAPTDLS 551 (575)
Q Consensus 502 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 551 (575)
+++|.=+.||.-||.||+.|-+.++..|||.|.----+-|-+++.-.++-
T Consensus 86 ~Dldeki~lyee~ErEr~riS~~ivs~K~G~~~~~~~~~~~~~~~~~~~~ 135 (212)
T PF08456_consen 86 EDLDEKIRLYEEYERERKRISRKIVSDKLGDLWIEVSEDGSASESSSDLK 135 (212)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhccccceeEeecccccchhcccchh
Confidence 58999999999999999999999999999988543344444555555543
No 121
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=60.85 E-value=8.8 Score=39.58 Aligned_cols=90 Identities=20% Similarity=0.280 Sum_probs=56.8
Q ss_pred hhccCCCCCCCCCC---C-CCCCCCCcchhhcchhHHHHHhhhcCCCCcccccccCc-------cccChhhHHHHhhhhh
Q psy4272 73 LLSQRDGKPVGKAT---L-PSPLKAKLSDYENKMKNVRESIRQKRLAQGLTCLQCGR-------SYCRPYNLKRHIQYEC 141 (575)
Q Consensus 73 ~~~~~~~~~~~~~~---~-p~~C~~C~~~f~~~~~~L~~H~r~H~~~kp~~C~~Cgk-------~F~~~~~L~~H~r~H~ 141 (575)
...++.|...+..+ + -..|.+|...|..- +.|..|+|... =.|.+|++ -|+....|.+|-+.
T Consensus 201 ~~~Lr~H~~~G~~e~GFKGHP~C~FC~~~FYdD-DEL~~HcR~~H----E~ChICD~v~p~~~QYFK~Y~~Le~HF~~-- 273 (493)
T COG5236 201 SSTLRDHKNGGLEEEGFKGHPLCIFCKIYFYDD-DELRRHCRLRH----EACHICDMVGPIRYQYFKSYEDLEAHFRN-- 273 (493)
T ss_pred cccccccccCCccccCcCCCchhhhccceecCh-HHHHHHHHhhh----hhhhhhhccCccchhhhhCHHHHHHHhhc--
Confidence 44455555544333 2 23689999888776 67888887532 23555554 46777777777653
Q ss_pred CCCCCccccc--c--c--ccccChhhHHHHHHhhccC
Q psy4272 142 GKAPQFPCLY--C--S--YRARHKHDLKKHVTFKHAA 172 (575)
Q Consensus 142 gekp~~~C~~--C--g--k~F~~~~~L~~H~r~~H~~ 172 (575)
.- |.|.+ | | ..|.....|..|+-..|..
T Consensus 274 --~h-y~ct~qtc~~~k~~vf~~~~el~~h~~~~h~~ 307 (493)
T COG5236 274 --AH-YCCTFQTCRVGKCYVFPYHTELLEHLTRFHKV 307 (493)
T ss_pred --Cc-eEEEEEEEecCcEEEeccHHHHHHHHHHHhhc
Confidence 22 77754 5 2 3588888888998765654
No 122
>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=59.95 E-value=13 Score=26.43 Aligned_cols=44 Identities=9% Similarity=0.086 Sum_probs=32.8
Q ss_pred cCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhh
Q psy4272 329 VYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMK 377 (575)
Q Consensus 329 ~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak 377 (575)
.++..+..++...|... ....++|..+|++...|..|....+.+
T Consensus 10 ~l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 10 KLPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALKK 53 (55)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 46777778887776433 346788999999999999998755444
No 123
>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=59.68 E-value=13 Score=27.36 Aligned_cols=42 Identities=14% Similarity=0.127 Sum_probs=27.8
Q ss_pred CCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhh
Q psy4272 330 YSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRM 376 (575)
Q Consensus 330 ~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRa 376 (575)
+++.+..++.-.|-.. ....++|..+|++...|++|...-|.
T Consensus 11 L~~~~r~i~~l~~~~g-----~s~~eIa~~l~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 11 LPERQREIFLLRYFQG-----MSYAEIAEILGISESTVKRRLRRARK 52 (54)
T ss_dssp S-HHHHHHHHHHHTS--------HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHC-----cCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence 4566666666554443 46788999999999999999975443
No 124
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=59.66 E-value=10 Score=32.74 Aligned_cols=25 Identities=32% Similarity=0.716 Sum_probs=22.9
Q ss_pred ccc----ccccccccChhhHHHHHHhhcc
Q psy4272 147 FPC----LYCSYRARHKHDLKKHVTFKHA 171 (575)
Q Consensus 147 ~~C----~~Cgk~F~~~~~L~~H~r~~H~ 171 (575)
|.| ..|+..+.....+.+|++.+|+
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 899 9999999999999999998763
No 125
>KOG2785|consensus
Probab=59.11 E-value=10 Score=39.85 Aligned_cols=50 Identities=22% Similarity=0.392 Sum_probs=35.6
Q ss_pred ccccccCccccChhhHHHHhhhhhCC-----------------------CCCccccccc---ccccChhhHHHHHHh
Q psy4272 118 LTCLQCGRSYCRPYNLKRHIQYECGK-----------------------APQFPCLYCS---YRARHKHDLKKHVTF 168 (575)
Q Consensus 118 ~~C~~Cgk~F~~~~~L~~H~r~H~ge-----------------------kp~~~C~~Cg---k~F~~~~~L~~H~r~ 168 (575)
-.|-.|++.|..-..-..||..|+|- +- |.|-.|. +.|......+.||..
T Consensus 167 t~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~-~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 167 TDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIG-FICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred cceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccC-ceEEEeccccCcccccHHHHHHHhh
Confidence 44666666666666666666554432 23 7899998 999999999999986
No 126
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=58.51 E-value=5.3 Score=27.48 Aligned_cols=32 Identities=22% Similarity=0.462 Sum_probs=16.5
Q ss_pred cccccCccccChhhHHHHhhhhhCCCCCcccccccccc
Q psy4272 119 TCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSYRA 156 (575)
Q Consensus 119 ~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk~F 156 (575)
.|+.|+..|.-...- +-.+.+. .+|..|+..|
T Consensus 4 ~CP~C~~~f~v~~~~-----l~~~~~~-vrC~~C~~~f 35 (37)
T PF13719_consen 4 TCPNCQTRFRVPDDK-----LPAGGRK-VRCPKCGHVF 35 (37)
T ss_pred ECCCCCceEEcCHHH-----cccCCcE-EECCCCCcEe
Confidence 466666666555431 1122233 5666666655
No 127
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=58.34 E-value=7 Score=35.88 Aligned_cols=40 Identities=15% Similarity=0.290 Sum_probs=27.8
Q ss_pred CCCcccccccCccccChhhHHHHhhhhhCCCCCcccccccccccC
Q psy4272 114 LAQGLTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSYRARH 158 (575)
Q Consensus 114 ~~kp~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk~F~~ 158 (575)
+..-|.|+.|++.|.....+.. .+. ... |.|+.||.....
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea~~~---~d~-~~~-f~Cp~Cg~~l~~ 135 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEANQL---LDM-DGT-FTCPRCGEELEE 135 (147)
T ss_pred CCcEEECcCCCCEeeHHHHHHh---cCC-CCc-EECCCCCCEEEE
Confidence 4456999999999997655432 112 445 999999986543
No 128
>KOG2071|consensus
Probab=58.30 E-value=7.1 Score=43.32 Aligned_cols=14 Identities=14% Similarity=0.401 Sum_probs=7.2
Q ss_pred CCCCccccccccccc
Q psy4272 143 KAPQFPCLYCSYRAR 157 (575)
Q Consensus 143 ekp~~~C~~Cgk~F~ 157 (575)
++. +.|.+|+-.|.
T Consensus 511 e~~-~~C~IC~EkFe 524 (579)
T KOG2071|consen 511 ERQ-ASCPICQEKFE 524 (579)
T ss_pred ccc-cCCcccccccc
Confidence 344 55566655553
No 129
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=58.16 E-value=4.4 Score=36.47 Aligned_cols=26 Identities=38% Similarity=0.903 Sum_probs=16.3
Q ss_pred cccccccCccccChhhHHHHhhhhhCCCC
Q psy4272 117 GLTCLQCGRSYCRPYNLKRHIQYECGKAP 145 (575)
Q Consensus 117 p~~C~~Cgk~F~~~~~L~~H~r~H~gekp 145 (575)
--.|-+|||.|+. |++|++.|.|-.|
T Consensus 72 ~i~clecGk~~k~---LkrHL~~~~gltp 97 (132)
T PF05443_consen 72 YIICLECGKKFKT---LKRHLRTHHGLTP 97 (132)
T ss_dssp -EE-TBT--EESB---HHHHHHHTT-S-H
T ss_pred eeEEccCCcccch---HHHHHHHccCCCH
Confidence 3579999999876 5899999977654
No 130
>KOG2593|consensus
Probab=57.49 E-value=7.3 Score=41.57 Aligned_cols=39 Identities=21% Similarity=0.462 Sum_probs=26.9
Q ss_pred CCCCcccccccCccccChhhHHHHhhhhhCCCCCccccccccc
Q psy4272 113 RLAQGLTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSYR 155 (575)
Q Consensus 113 ~~~kp~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk~ 155 (575)
+...-|.|+.|.+.|.....+. .+-...-. |.|..|+-.
T Consensus 124 t~~~~Y~Cp~C~kkyt~Lea~~---L~~~~~~~-F~C~~C~ge 162 (436)
T KOG2593|consen 124 TNVAGYVCPNCQKKYTSLEALQ---LLDNETGE-FHCENCGGE 162 (436)
T ss_pred cccccccCCccccchhhhHHHH---hhcccCce-EEEecCCCc
Confidence 4455699999999998877663 22222334 999999753
No 131
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=56.96 E-value=6.9 Score=34.73 Aligned_cols=37 Identities=11% Similarity=-0.039 Sum_probs=27.6
Q ss_pred CCCCCCCCCcchhhcchhHHHHHhhhcCCCCcccccccCccccChhhHH
Q psy4272 86 TLPSPLKAKLSDYENKMKNVRESIRQKRLAQGLTCLQCGRSYCRPYNLK 134 (575)
Q Consensus 86 ~~p~~C~~C~~~f~~~~~~L~~H~r~H~~~kp~~C~~Cgk~F~~~~~L~ 134 (575)
++-..|..||+.|... ++.|-.|++||..|.....++
T Consensus 7 GtKr~Cp~cg~kFYDL------------nk~p~vcP~cg~~~~~~~~~~ 43 (129)
T TIGR02300 7 GTKRICPNTGSKFYDL------------NRRPAVSPYTGEQFPPEEALK 43 (129)
T ss_pred CccccCCCcCcccccc------------CCCCccCCCcCCccCcchhhc
Confidence 3456899999999766 347889999999887664443
No 132
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 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 predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=56.83 E-value=7.4 Score=27.66 Aligned_cols=23 Identities=35% Similarity=0.639 Sum_probs=12.2
Q ss_pred CCcccccccCccccCh----hhHHHHh
Q psy4272 115 AQGLTCLQCGRSYCRP----YNLKRHI 137 (575)
Q Consensus 115 ~kp~~C~~Cgk~F~~~----~~L~~H~ 137 (575)
..-.+|.+|++.+... ..|.+|+
T Consensus 14 ~~~a~C~~C~~~~~~~~~~ts~l~~HL 40 (45)
T PF02892_consen 14 KKKAKCKYCGKVIKYSSGGTSNLKRHL 40 (45)
T ss_dssp SS-EEETTTTEE-----SSTHHHHHHH
T ss_pred cCeEEeCCCCeEEeeCCCcHHHHHHhh
Confidence 3446777777777663 5677776
No 133
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=55.89 E-value=17 Score=33.24 Aligned_cols=50 Identities=12% Similarity=0.131 Sum_probs=40.0
Q ss_pred ccCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhcCC
Q psy4272 328 QVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTHP 383 (575)
Q Consensus 328 t~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~~~ 383 (575)
..+++.|..+|.. +... ....++|..+|++...|+.|-++.+.|.|+...
T Consensus 5 ~~Lt~rqreVL~l-r~~G-----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~ 54 (141)
T PRK03975 5 SFLTERQIEVLRL-RERG-----LTQQEIADILGTSRANVSSIEKRARENIEKARE 54 (141)
T ss_pred cCCCHHHHHHHHH-HHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 5788999999977 3322 357799999999999999999988888777543
No 134
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=55.17 E-value=3.7 Score=38.00 Aligned_cols=43 Identities=9% Similarity=0.119 Sum_probs=23.3
Q ss_pred CCCCCcchhhcchhHHHHHhhhcCCCCcccccccCccccChhhH
Q psy4272 90 PLKAKLSDYENKMKNVRESIRQKRLAQGLTCLQCGRSYCRPYNL 133 (575)
Q Consensus 90 ~C~~C~~~f~~~~~~L~~H~r~H~~~kp~~C~~Cgk~F~~~~~L 133 (575)
.|+.||..+..-.+.--.-..- ...+.|+|+.||+.|.....+
T Consensus 2 ~cp~c~~~~~~~~~s~~~~~~~-~~~~~~~c~~c~~~f~~~e~~ 44 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRPAEDGN-AIRRRRECLACGKRFTTFERV 44 (154)
T ss_pred cCCCCCCCCCEeEeccccCCCC-ceeeeeeccccCCcceEeEec
Confidence 6889987663322111000000 112338899999999876554
No 135
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=54.30 E-value=7.9 Score=34.60 Aligned_cols=31 Identities=23% Similarity=0.476 Sum_probs=19.9
Q ss_pred cccccccCccccChhhHHHHhhhhhCCCCCccccccc-ccccC
Q psy4272 117 GLTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCS-YRARH 158 (575)
Q Consensus 117 p~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cg-k~F~~ 158 (575)
||+|..||+.|..-+. .+. --|+.|| +.|.+
T Consensus 1 PH~Ct~Cg~~f~dgs~---eil--------~GCP~CGg~kF~y 32 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGSK---EIL--------SGCPECGGNKFQY 32 (131)
T ss_pred CcccCcCCCCcCCCcH---HHH--------ccCcccCCcceEE
Confidence 5788889988876542 122 3588887 34543
No 136
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=54.26 E-value=3.8 Score=29.59 Aligned_cols=29 Identities=31% Similarity=0.660 Sum_probs=15.6
Q ss_pred cccccccCccccChhhHHHHhhhhhCCCCCcccccccccc
Q psy4272 117 GLTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSYRA 156 (575)
Q Consensus 117 p~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk~F 156 (575)
.|.|..||..|...... .. +.|+.||..+
T Consensus 3 ~y~C~~CG~~~~~~~~~----------~~-~~Cp~CG~~~ 31 (46)
T PRK00398 3 EYKCARCGREVELDEYG----------TG-VRCPYCGYRI 31 (46)
T ss_pred EEECCCCCCEEEECCCC----------Cc-eECCCCCCeE
Confidence 36677777665443211 13 6677776544
No 137
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=53.66 E-value=8.6 Score=28.22 Aligned_cols=23 Identities=35% Similarity=0.791 Sum_probs=16.1
Q ss_pred ccccccCccccCh-----hhHHHHhh-hh
Q psy4272 118 LTCLQCGRSYCRP-----YNLKRHIQ-YE 140 (575)
Q Consensus 118 ~~C~~Cgk~F~~~-----~~L~~H~r-~H 140 (575)
-.|..|++.+... ++|.+|++ .|
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~~~h 47 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLRRKH 47 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHHhHC
Confidence 4688888877665 47777776 44
No 138
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=53.58 E-value=4.6 Score=29.84 Aligned_cols=13 Identities=23% Similarity=0.669 Sum_probs=8.5
Q ss_pred ccccccCccccCh
Q psy4272 118 LTCLQCGRSYCRP 130 (575)
Q Consensus 118 ~~C~~Cgk~F~~~ 130 (575)
|+|..||..|...
T Consensus 6 y~C~~Cg~~fe~~ 18 (52)
T TIGR02605 6 YRCTACGHRFEVL 18 (52)
T ss_pred EEeCCCCCEeEEE
Confidence 6677777766543
No 139
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=53.43 E-value=4.6 Score=28.03 Aligned_cols=13 Identities=23% Similarity=0.703 Sum_probs=8.2
Q ss_pred ccccccCccccCh
Q psy4272 118 LTCLQCGRSYCRP 130 (575)
Q Consensus 118 ~~C~~Cgk~F~~~ 130 (575)
|+|..||+.|...
T Consensus 6 y~C~~Cg~~fe~~ 18 (41)
T smart00834 6 YRCEDCGHTFEVL 18 (41)
T ss_pred EEcCCCCCEEEEE
Confidence 6677777666543
No 140
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 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 predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=53.37 E-value=8.3 Score=27.38 Aligned_cols=28 Identities=32% Similarity=0.594 Sum_probs=17.9
Q ss_pred CCCCCcccccccccccCh----hhHHHHHHhhc
Q psy4272 142 GKAPQFPCLYCSYRARHK----HDLKKHVTFKH 170 (575)
Q Consensus 142 gekp~~~C~~Cgk~F~~~----~~L~~H~r~~H 170 (575)
+... .+|.+|++.|... .+|.+|++..|
T Consensus 13 ~~~~-a~C~~C~~~~~~~~~~ts~l~~HL~~~h 44 (45)
T PF02892_consen 13 DKKK-AKCKYCGKVIKYSSGGTSNLKRHLKKKH 44 (45)
T ss_dssp CSS--EEETTTTEE-----SSTHHHHHHHHHTT
T ss_pred CcCe-EEeCCCCeEEeeCCCcHHHHHHhhhhhC
Confidence 3445 7899999988775 78999985534
No 141
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=53.36 E-value=6 Score=35.30 Aligned_cols=25 Identities=36% Similarity=0.788 Sum_probs=20.5
Q ss_pred ccccccCccccChhhHHHHhhhhhCCCC
Q psy4272 118 LTCLQCGRSYCRPYNLKRHIQYECGKAP 145 (575)
Q Consensus 118 ~~C~~Cgk~F~~~~~L~~H~r~H~gekp 145 (575)
..|-+|||.|+. |+||+.+|.|-.|
T Consensus 77 IicLEDGkkfKS---LKRHL~t~~gmTP 101 (148)
T COG4957 77 IICLEDGKKFKS---LKRHLTTHYGLTP 101 (148)
T ss_pred EEEeccCcchHH---HHHHHhcccCCCH
Confidence 479999999974 8999999987655
No 142
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=53.01 E-value=7.6 Score=33.35 Aligned_cols=27 Identities=11% Similarity=0.202 Sum_probs=19.0
Q ss_pred cccccCccccChhhHHHHhhhhhCCCCCccccccccccc
Q psy4272 119 TCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSYRAR 157 (575)
Q Consensus 119 ~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk~F~ 157 (575)
.|+.||+.|... ...| ..|++||+.|.
T Consensus 11 idPetg~KFYDL-----------NrdP-iVsPytG~s~P 37 (129)
T COG4530 11 IDPETGKKFYDL-----------NRDP-IVSPYTGKSYP 37 (129)
T ss_pred cCccccchhhcc-----------CCCc-cccCcccccch
Confidence 578888887542 2356 78888888883
No 143
>KOG4173|consensus
Probab=52.22 E-value=14 Score=35.38 Aligned_cols=86 Identities=16% Similarity=0.259 Sum_probs=57.2
Q ss_pred Ccccccc--cCccccChhhHHHHhhhhhCCCCCcccccccccccChhhHHHHHHhhccCcccchhhhhhhhhcccccCCC
Q psy4272 116 QGLTCLQ--CGRSYCRPYNLKRHIQYECGKAPQFPCLYCSYRARHKHDLKKHVTFKHAAYLDHFQAVQEELEVTTKELSP 193 (575)
Q Consensus 116 kp~~C~~--Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk~F~~~~~L~~H~r~~H~~~~~~~~~~~~~~~~~t~e~sp 193 (575)
..|.|.+ |-..|....+...|-.+-+| -.|.+|.+.|.+..-|..|+---|.... +.. ++ -.
T Consensus 78 ~~~~cqvagc~~~~d~lD~~E~hY~~~h~----~sCs~C~r~~Pt~hLLd~HI~E~HDs~F---qa~--------ve-RG 141 (253)
T KOG4173|consen 78 PAFACQVAGCCQVFDALDDYEHHYHTLHG----NSCSFCKRAFPTGHLLDAHILEWHDSLF---QAL--------VE-RG 141 (253)
T ss_pred ccccccccchHHHHhhhhhHHHhhhhccc----chhHHHHHhCCchhhhhHHHHHHHHHHH---HHH--------HH-cC
Confidence 3488987 88889888888777644222 4799999999999999999865443211 000 00 01
Q ss_pred CCCCcc--hhhhhhccChhhhHhhhh
Q psy4272 194 GPKAEN--RHRFREFLNEHRNLERNV 217 (575)
Q Consensus 194 ~p~~~C--~~C~k~F~~~~~l~~H~~ 217 (575)
...++| +.|...|.....-..|++
T Consensus 142 ~dMy~ClvEgCt~KFkT~r~RkdH~I 167 (253)
T KOG4173|consen 142 QDMYQCLVEGCTEKFKTSRDRKDHMI 167 (253)
T ss_pred ccHHHHHHHhhhhhhhhhhhhhhHHH
Confidence 233456 568888887777777764
No 144
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=51.94 E-value=6.7 Score=28.88 Aligned_cols=11 Identities=36% Similarity=0.999 Sum_probs=7.7
Q ss_pred cccccccCccc
Q psy4272 117 GLTCLQCGRSY 127 (575)
Q Consensus 117 p~~C~~Cgk~F 127 (575)
-|.|..||+.|
T Consensus 6 ~Y~C~~Cg~~~ 16 (49)
T COG1996 6 EYKCARCGREV 16 (49)
T ss_pred EEEhhhcCCee
Confidence 36777777776
No 145
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=51.55 E-value=8.3 Score=27.73 Aligned_cols=26 Identities=35% Similarity=0.712 Sum_probs=14.9
Q ss_pred ccccccCccccChhhHHHHhhhhhCCCCCccccccccc
Q psy4272 118 LTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSYR 155 (575)
Q Consensus 118 ~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk~ 155 (575)
|.|..||..|... ...+ .+|+.||..
T Consensus 3 Y~C~~Cg~~~~~~-----------~~~~-irC~~CG~r 28 (44)
T smart00659 3 YICGECGRENEIK-----------SKDV-VRCRECGYR 28 (44)
T ss_pred EECCCCCCEeecC-----------CCCc-eECCCCCce
Confidence 6677777666533 1223 567777643
No 146
>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=50.86 E-value=11 Score=29.81 Aligned_cols=44 Identities=18% Similarity=0.379 Sum_probs=28.9
Q ss_pred CCcccCCHHHHHHHHHHh-hhCCCCCHHHHHHHHHHhCCChhhhhhcccc
Q psy4272 325 RFRQVYSSHQIVELEKEF-RLTNYLPSDRRKVLSKELGLTERQIKIWFQN 373 (575)
Q Consensus 325 r~Rt~~t~~ql~~L~~~F-~~~~~p~~~~r~~la~~l~l~~~~V~vWFqN 373 (575)
+.|..||.++...+-..+ ... ....++|..+||+..+|..|-+-
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~g-----~sv~~va~~~gi~~~~l~~W~~~ 46 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLESG-----ESVSEVAREYGISPSTLYNWRKQ 46 (76)
T ss_dssp -SS----HHHHHHHHHHHHHHH-----CHHHHHHHHHTS-HHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHCC-----CceEeeecccccccccccHHHHH
Confidence 457889998877666665 332 46788999999999999999753
No 147
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=49.85 E-value=9.2 Score=26.17 Aligned_cols=33 Identities=18% Similarity=0.261 Sum_probs=17.9
Q ss_pred ccccccCccccChhhHHHHhhhhhCCCCCcccccccccc
Q psy4272 118 LTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSYRA 156 (575)
Q Consensus 118 ~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk~F 156 (575)
..|+.|+..|.-..... -...+. .+|..|+..|
T Consensus 3 i~Cp~C~~~y~i~d~~i-----p~~g~~-v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKI-----PPKGRK-VRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEeCCHHHC-----CCCCcE-EECCCCCCEe
Confidence 35677777766655431 111223 5677777665
No 148
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=49.66 E-value=21 Score=31.16 Aligned_cols=79 Identities=13% Similarity=0.102 Sum_probs=48.5
Q ss_pred CCCCCCCCCcchhhcchhHHHHHhhhcCCCCc------------ccccccCccccChhhHHHHhhhhhCCCCCccccccc
Q psy4272 86 TLPSPLKAKLSDYENKMKNVRESIRQKRLAQG------------LTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCS 153 (575)
Q Consensus 86 ~~p~~C~~C~~~f~~~~~~L~~H~r~H~~~kp------------~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cg 153 (575)
..|-.|++|+-..-.. .+|.+....--.-++ ..|--|.+.|........-. -..... |.|..|.
T Consensus 13 ~LP~~CpiCgLtLVss-~HLARSyHHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~~~--~~~~~~-y~C~~C~ 88 (112)
T TIGR00622 13 ELPVECPICGLTLILS-THLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPFDE--LKDSHR-YVCAVCK 88 (112)
T ss_pred CCCCcCCcCCCEEecc-chHHHhhhccCCCcccccccccccCCCCcccCcCCCCCCcccccccc--cccccc-eeCCCCC
Confidence 4677899998776544 344332111001111 24888999998654221100 112335 9999999
Q ss_pred ccccChhhHHHHHHh
Q psy4272 154 YRARHKHDLKKHVTF 168 (575)
Q Consensus 154 k~F~~~~~L~~H~r~ 168 (575)
..|-..-+.-.|...
T Consensus 89 ~~FC~dCD~fiHe~L 103 (112)
T TIGR00622 89 NVFCVDCDVFVHESL 103 (112)
T ss_pred Cccccccchhhhhhc
Confidence 999999998888877
No 149
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=49.64 E-value=10 Score=28.92 Aligned_cols=30 Identities=23% Similarity=0.492 Sum_probs=15.9
Q ss_pred ccccccCccccChhhHHHHhhhhhCCCCCccccccc
Q psy4272 118 LTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCS 153 (575)
Q Consensus 118 ~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cg 153 (575)
|.|+.||+.-..+..--| .-..+ |+|+.||
T Consensus 28 F~CPnCGe~~I~Rc~~CR-----k~g~~-Y~Cp~CG 57 (61)
T COG2888 28 FPCPNCGEVEIYRCAKCR-----KLGNP-YRCPKCG 57 (61)
T ss_pred eeCCCCCceeeehhhhHH-----HcCCc-eECCCcC
Confidence 677777755444332111 11245 7777776
No 150
>KOG3755|consensus
Probab=49.23 E-value=5.3 Score=44.07 Aligned_cols=60 Identities=17% Similarity=0.055 Sum_probs=37.5
Q ss_pred CCCcccCCHHHHH-HHHHHhhhCCCCCHHHHHHHHHHhCC-------ChhhhhhcccchhhhhhhcCC
Q psy4272 324 GRFRQVYSSHQIV-ELEKEFRLTNYLPSDRRKVLSKELGL-------TERQIKIWFQNRRMKLKRTHP 383 (575)
Q Consensus 324 rr~Rt~~t~~ql~-~L~~~F~~~~~p~~~~r~~la~~l~l-------~~~~V~vWFqNrRak~kk~~~ 383 (575)
||.|-.|-..|.. +-+.+|.+++.+......+--..+.| ....|+.||+|||+++++.+-
T Consensus 692 k~~~~k~f~~~~~ev~~~w~~k~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k~ 759 (769)
T KOG3755|consen 692 KKTIIKFFQNQRYEVKHHWKLKTRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLKM 759 (769)
T ss_pred HHHHHHhhhcceeecchhheecccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhhc
Confidence 3334333333333 33555777777776665555444433 445699999999999998654
No 151
>PF14353 CpXC: CpXC protein
Probab=49.07 E-value=12 Score=33.28 Aligned_cols=26 Identities=27% Similarity=0.350 Sum_probs=15.5
Q ss_pred hCCCCCcccccccccccChhhHHHHH
Q psy4272 141 CGKAPQFPCLYCSYRARHKHDLKKHV 166 (575)
Q Consensus 141 ~gekp~~~C~~Cgk~F~~~~~L~~H~ 166 (575)
.|.--.|.|+.||+.|.-...+.-|-
T Consensus 33 ~g~l~~~~CP~Cg~~~~~~~p~lY~D 58 (128)
T PF14353_consen 33 DGSLFSFTCPSCGHKFRLEYPLLYHD 58 (128)
T ss_pred cCCcCEEECCCCCCceecCCCEEEEc
Confidence 44332277888887776666554443
No 152
>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=48.75 E-value=26 Score=26.29 Aligned_cols=46 Identities=20% Similarity=0.204 Sum_probs=35.8
Q ss_pred cCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhh
Q psy4272 329 VYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKR 380 (575)
Q Consensus 329 ~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk 380 (575)
.||..++.+|.-...-. ...++|..+|+++..|..+..+=+.|..-
T Consensus 3 ~LT~~E~~vl~~l~~G~------~~~eIA~~l~is~~tV~~~~~~i~~Kl~~ 48 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM------SNKEIAEELGISEKTVKSHRRRIMKKLGV 48 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-------HHHHHHHHTSHHHHHHHHHHHHHHHHT-
T ss_pred ccCHHHHHHHHHHHhcC------CcchhHHhcCcchhhHHHHHHHHHHHhCC
Confidence 57888999987776654 47789999999999999999877766553
No 153
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=45.69 E-value=7 Score=31.33 Aligned_cols=40 Identities=13% Similarity=0.113 Sum_probs=19.6
Q ss_pred ccccccCccccChhhHHHHhhhhhCCCCCcccc--cccccccChh
Q psy4272 118 LTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCL--YCSYRARHKH 160 (575)
Q Consensus 118 ~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~--~Cgk~F~~~~ 160 (575)
+.|+.||........-..+. ...++- +.|. .||.+|....
T Consensus 2 m~CP~Cg~~a~irtSr~~s~--~~~~~Y-~qC~N~eCg~tF~t~e 43 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYITD--TTKERY-HQCQNVNCSATFITYE 43 (72)
T ss_pred ccCCCCCCccEEEEChhcCh--hhheee-eecCCCCCCCEEEEEE
Confidence 45666665543222211111 133455 6676 6777776543
No 154
>PF09110 HAND: HAND; InterPro: IPR015194 Nucleosome remodelling is an energy-dependent process that alters histone-DNA interactions within nucleosomes, thereby rendering nucleosomal DNA accessible to regulatory factors. The ATPases involved belong to the SWI2/SNF2 subfamily of DEAD/H-helicases, which contain a conserved ATPase domain characterised by seven motifs. Proteins within this family differ with regard to domain organisation, their associated proteins and the remodelling complex in which they reside. The ATPase ISWI is a member of this family. ISWI can be divided into two regions: an N-terminal region that contains the SWI2/SNF2 ATPase domain, and a C-terminal region that is responsible for substrate recognition. The C-terminal region contains 12 alpha-helices and can be divided into three domains and a spacer region: a HAND domain (named because its 4-helical structure resembles an open hand), a SANT domain (c-Myb DNA-binding like), a spacer helix, and a SLIDE domain (SANT-like but with several insertions). This entry represents the HAND domain, which adopts a secondary structure consisting of four alpha helices, three of which (H2, H3, H4) form an L-like configuration. Helix H2 runs antiparallel to helices H3 and H4, packing closely against helix H4, whilst helix H1 reposes in the concave surface formed by these three helices and runs perpendicular to them. This domain confers DNA and nucleosome binding properties to the protein []. ; GO: 0031491 nucleosome binding, 0043044 ATP-dependent chromatin remodeling, 0016585 chromatin remodeling complex; PDB: 1OFC_X 2Y9Y_A 2Y9Z_A 2NOG_A.
Probab=45.56 E-value=30 Score=30.35 Aligned_cols=46 Identities=24% Similarity=0.401 Sum_probs=27.2
Q ss_pred HhhhhhHHHHHHHHHHHHHHHhcccccccCCCCCCCCCcchhhHHhhhhhh
Q psy4272 509 KLNDLYENERNMLIQELIRKKLGLLIQNNQNGGHAEDAPTDLSRKLKSDME 559 (575)
Q Consensus 509 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 559 (575)
.|..|||.|++ ..||++|+-+.-..-+++.++..+...+..+..+|
T Consensus 43 rL~eL~EkE~~-----~y~K~i~yk~~~~d~~~~~~~~~~~~~~e~~~~~e 88 (113)
T PF09110_consen 43 RLKELQEKEQL-----YYKKKIGYKVPLDDGKDSYEEEEDEEEREAKRKLE 88 (113)
T ss_dssp HHHHHHHHHHH-----HHHHHCT----CCCHTTTS--SSSTTCHHHHHHHH
T ss_pred HHHHHHHHHHH-----HHHHHhCCCCCccccccccccccccccHHHHHHHH
Confidence 45667777754 57999999888887777766666666665555444
No 155
>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=45.54 E-value=53 Score=20.59 Aligned_cols=38 Identities=13% Similarity=0.225 Sum_probs=27.4
Q ss_pred cCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcc
Q psy4272 329 VYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWF 371 (575)
Q Consensus 329 ~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWF 371 (575)
.++..+...+...|... + ...++|..+|++...|..|.
T Consensus 5 ~~~~~~~~~i~~~~~~~-~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 5 KLTPEQIEEARRLLAAG-E----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred cCCHHHHHHHHHHHHcC-C----CHHHHHHHHCCCHHHHHHhC
Confidence 35666666666666533 2 45688999999999998884
No 156
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=45.31 E-value=11 Score=33.90 Aligned_cols=22 Identities=32% Similarity=0.700 Sum_probs=15.1
Q ss_pred cccccccccccChhhHHHHHHhhcc
Q psy4272 147 FPCLYCSYRARHKHDLKKHVTFKHA 171 (575)
Q Consensus 147 ~~C~~Cgk~F~~~~~L~~H~r~~H~ 171 (575)
..|-+|||.|.. |++|++.||+
T Consensus 73 i~clecGk~~k~---LkrHL~~~~g 94 (132)
T PF05443_consen 73 IICLECGKKFKT---LKRHLRTHHG 94 (132)
T ss_dssp EE-TBT--EESB---HHHHHHHTT-
T ss_pred eEEccCCcccch---HHHHHHHccC
Confidence 679999999876 5999999654
No 157
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=45.06 E-value=4 Score=40.00 Aligned_cols=25 Identities=12% Similarity=0.272 Sum_probs=18.7
Q ss_pred CCCCcccccccccccChhhHHHHHHh
Q psy4272 143 KAPQFPCLYCSYRARHKHDLKKHVTF 168 (575)
Q Consensus 143 ekp~~~C~~Cgk~F~~~~~L~~H~r~ 168 (575)
++. +.|++|++.|..+.-+....+.
T Consensus 3 ~k~-~~CPvC~~~F~~~~vrs~~~r~ 27 (214)
T PF09986_consen 3 DKK-ITCPVCGKEFKTKKVRSGKIRV 27 (214)
T ss_pred CCc-eECCCCCCeeeeeEEEcCCceE
Confidence 355 8999999999988666555543
No 158
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=44.40 E-value=7.3 Score=38.09 Aligned_cols=31 Identities=19% Similarity=0.357 Sum_probs=21.8
Q ss_pred CCCCCcccccccccccChhhHHHHHHhhccCc
Q psy4272 142 GKAPQFPCLYCSYRARHKHDLKKHVTFKHAAY 173 (575)
Q Consensus 142 gekp~~~C~~Cgk~F~~~~~L~~H~r~~H~~~ 173 (575)
.+.. |.|..|+|.|.-.....+|+...|...
T Consensus 74 ~~~K-~~C~lc~KlFkg~eFV~KHI~nKH~e~ 104 (214)
T PF04959_consen 74 DEDK-WRCPLCGKLFKGPEFVRKHIFNKHPEK 104 (214)
T ss_dssp SSEE-EEE-SSS-EESSHHHHHHHHHHH-HHH
T ss_pred cCCE-ECCCCCCcccCChHHHHHHHhhcCHHH
Confidence 3445 888889998888888888888877654
No 159
>PRK10072 putative transcriptional regulator; Provisional
Probab=43.94 E-value=30 Score=29.36 Aligned_cols=41 Identities=22% Similarity=0.288 Sum_probs=30.7
Q ss_pred cCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhh
Q psy4272 329 VYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRM 376 (575)
Q Consensus 329 ~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRa 376 (575)
..+...+..|...-.. ...+||..+|++...|..|.+.+|.
T Consensus 32 ~~~~~eik~LR~~~gl-------TQ~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 32 TTSFTEFEQLRKGTGL-------KIDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred cCChHHHHHHHHHcCC-------CHHHHHHHhCCCHHHHHHHHcCCCC
Confidence 4466667777544333 3778999999999999999987653
No 160
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=43.79 E-value=13 Score=35.43 Aligned_cols=57 Identities=23% Similarity=0.389 Sum_probs=34.4
Q ss_pred CCCCCCCCCCcchhhcchhHHHHHhhhcCCCCcccccccCccccChhhHHHHhhhhhCCCCCccccccccc----ccChh
Q psy4272 85 ATLPSPLKAKLSDYENKMKNVRESIRQKRLAQGLTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSYR----ARHKH 160 (575)
Q Consensus 85 ~~~p~~C~~C~~~f~~~~~~L~~H~r~H~~~kp~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk~----F~~~~ 160 (575)
...||.|.+|-+.|.... -..||..|......++-+ +. -.|.+||+. |.-..
T Consensus 193 e~IPF~C~iCKkdy~spv-----------------vt~CGH~FC~~Cai~~y~------kg-~~C~~Cgk~t~G~f~V~~ 248 (259)
T COG5152 193 EKIPFLCGICKKDYESPV-----------------VTECGHSFCSLCAIRKYQ------KG-DECGVCGKATYGRFWVVS 248 (259)
T ss_pred CCCceeehhchhhccchh-----------------hhhcchhHHHHHHHHHhc------cC-CcceecchhhccceeHHh
Confidence 357899999999887763 123555554444443322 23 579999873 55555
Q ss_pred hHHHH
Q psy4272 161 DLKKH 165 (575)
Q Consensus 161 ~L~~H 165 (575)
+|.+-
T Consensus 249 d~~km 253 (259)
T COG5152 249 DLQKM 253 (259)
T ss_pred hHHHH
Confidence 55543
No 161
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=43.48 E-value=12 Score=34.28 Aligned_cols=44 Identities=18% Similarity=0.301 Sum_probs=28.1
Q ss_pred HHHHHhhhcCCCCc----ccccccCccccChhhHHHHhhhhhCCCCCccccccccc-ccC
Q psy4272 104 NVRESIRQKRLAQG----LTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSYR-ARH 158 (575)
Q Consensus 104 ~L~~H~r~H~~~kp----~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk~-F~~ 158 (575)
.+.+|-.-|+|++. |.|..||..... .|.+.-| .|+.||.. |.+
T Consensus 95 d~~h~g~Y~sGE~~g~G~l~C~~Cg~~~~~---------~~~~~l~--~Cp~C~~~~F~R 143 (146)
T PF07295_consen 95 DLEHHGVYHSGEVVGPGTLVCENCGHEVEL---------THPERLP--PCPKCGHTEFTR 143 (146)
T ss_pred HHHhcCCeecCcEecCceEecccCCCEEEe---------cCCCcCC--CCCCCCCCeeee
Confidence 44455555777765 999999965321 2455555 79999864 544
No 162
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=43.28 E-value=9.9 Score=37.19 Aligned_cols=30 Identities=20% Similarity=0.412 Sum_probs=22.7
Q ss_pred CCCcccccccCccccChhhHHHHhhhhhCC
Q psy4272 114 LAQGLTCLQCGRSYCRPYNLKRHIQYECGK 143 (575)
Q Consensus 114 ~~kp~~C~~Cgk~F~~~~~L~~H~r~H~ge 143 (575)
.+..|.|..|+|.|+-...+++|+..-+.+
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~nKH~e 103 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFNKHPE 103 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHHH-HH
T ss_pred cCCEECCCCCCcccCChHHHHHHHhhcCHH
Confidence 455699999999999999999999864444
No 163
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=42.54 E-value=16 Score=37.12 Aligned_cols=27 Identities=7% Similarity=-0.064 Sum_probs=21.5
Q ss_pred CCCcchhhhhhccChhhhHhhhhhhhh
Q psy4272 195 PKAENRHRFREFLNEHRNLERNVSHEE 221 (575)
Q Consensus 195 p~~~C~~C~k~F~~~~~l~~H~~th~~ 221 (575)
..+.|+.|...|...-+...|...|..
T Consensus 387 ~rY~Ce~CK~~FC~dCdvfiHe~Lh~C 413 (421)
T COG5151 387 GRYQCELCKSTFCSDCDVFIHETLHFC 413 (421)
T ss_pred cceechhhhhhhhhhhHHHHHHHHhhC
Confidence 345899999999988888888777654
No 164
>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=42.31 E-value=18 Score=27.94 Aligned_cols=27 Identities=30% Similarity=0.559 Sum_probs=20.4
Q ss_pred HHHHHHHHhCCChhhhhhcccchhhhhhh
Q psy4272 352 RRKVLSKELGLTERQIKIWFQNRRMKLKR 380 (575)
Q Consensus 352 ~r~~la~~l~l~~~~V~vWFqNrRak~kk 380 (575)
.-.+||.+||+++.+|+.|=. +-||..
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK~--~dkW~~ 50 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWKS--RDKWDE 50 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHhh--hcchhh
Confidence 345789999999999999953 344543
No 165
>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=42.28 E-value=9 Score=42.66 Aligned_cols=10 Identities=30% Similarity=0.703 Sum_probs=6.6
Q ss_pred CCCcccccccc
Q psy4272 144 APQFPCLYCSY 154 (575)
Q Consensus 144 kp~~~C~~Cgk 154 (575)
.+ ..|+.||.
T Consensus 252 ~~-~~Cp~C~s 261 (505)
T TIGR00595 252 IP-KTCPQCGS 261 (505)
T ss_pred CC-CCCCCCCC
Confidence 35 67777765
No 166
>PRK14873 primosome assembly protein PriA; Provisional
Probab=41.98 E-value=8.2 Score=44.43 Aligned_cols=47 Identities=13% Similarity=0.226 Sum_probs=27.8
Q ss_pred CCCCCcchhhcchhHHHHHhhhcCCCCcccccccCccccChhhHHHHhhhhhCCCCCccccccccc
Q psy4272 90 PLKAKLSDYENKMKNVRESIRQKRLAQGLTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSYR 155 (575)
Q Consensus 90 ~C~~C~~~f~~~~~~L~~H~r~H~~~kp~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk~ 155 (575)
.|..||..+..... ...+..|...+...|.+||.. ..+ +.|+.||..
T Consensus 385 ~C~~Cg~~~~C~~C--~~~L~~h~~~~~l~Ch~CG~~----------------~~p-~~Cp~Cgs~ 431 (665)
T PRK14873 385 ACARCRTPARCRHC--TGPLGLPSAGGTPRCRWCGRA----------------APD-WRCPRCGSD 431 (665)
T ss_pred EhhhCcCeeECCCC--CCceeEecCCCeeECCCCcCC----------------CcC-ccCCCCcCC
Confidence 68888876654421 123334545556777777721 135 789999864
No 167
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=41.89 E-value=16 Score=30.19 Aligned_cols=34 Identities=12% Similarity=0.047 Sum_probs=23.8
Q ss_pred CCCCCCCCcchhhcchhHHHHHhhhcCCCCcccccccCccccChh
Q psy4272 87 LPSPLKAKLSDYENKMKNVRESIRQKRLAQGLTCLQCGRSYCRPY 131 (575)
Q Consensus 87 ~p~~C~~C~~~f~~~~~~L~~H~r~H~~~kp~~C~~Cgk~F~~~~ 131 (575)
..|.|+.|++..- .|+- ..-+.|..||..|.--.
T Consensus 34 ~~~~Cp~C~~~~V---------kR~a--~GIW~C~kCg~~fAGga 67 (89)
T COG1997 34 AKHVCPFCGRTTV---------KRIA--TGIWKCRKCGAKFAGGA 67 (89)
T ss_pred cCCcCCCCCCcce---------eeec--cCeEEcCCCCCeecccc
Confidence 4689999987632 2332 34589999999996543
No 168
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=40.55 E-value=18 Score=41.27 Aligned_cols=36 Identities=22% Similarity=0.386 Sum_probs=22.9
Q ss_pred ccccccCccccChhhHHHHhhhhhCCCCCcccccccccccChhh
Q psy4272 118 LTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSYRARHKHD 161 (575)
Q Consensus 118 ~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk~F~~~~~ 161 (575)
-.|..|++.|.....+ .+.+. +.|..||+.|.....
T Consensus 461 dtC~~C~kkFfSlsK~-------L~~RK-HHCRkCGrVFC~~CS 496 (1374)
T PTZ00303 461 DSCPSCGRAFISLSRP-------LGTRA-HHCRSCGIRLCVFCI 496 (1374)
T ss_pred CcccCcCCcccccccc-------ccccc-ccccCCccccCcccc
Confidence 4688999988654211 12345 678888887766543
No 169
>PRK00118 putative DNA-binding protein; Validated
Probab=40.23 E-value=45 Score=28.75 Aligned_cols=49 Identities=8% Similarity=0.032 Sum_probs=36.5
Q ss_pred cCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhcC
Q psy4272 329 VYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTH 382 (575)
Q Consensus 329 ~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~~ 382 (575)
.++..|..++...|... ....++|..+|++...|..|....|.+.|+..
T Consensus 17 ~L~ekqRevl~L~y~eg-----~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~ 65 (104)
T PRK00118 17 LLTEKQRNYMELYYLDD-----YSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYE 65 (104)
T ss_pred cCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 45677777776665554 25678999999999999999987776666543
No 170
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=40.22 E-value=18 Score=22.88 Aligned_cols=10 Identities=30% Similarity=0.903 Sum_probs=6.0
Q ss_pred cccccCcccc
Q psy4272 119 TCLQCGRSYC 128 (575)
Q Consensus 119 ~C~~Cgk~F~ 128 (575)
.|+.||..|.
T Consensus 16 ~Cp~CG~~F~ 25 (26)
T PF10571_consen 16 FCPHCGYDFE 25 (26)
T ss_pred cCCCCCCCCc
Confidence 4666666653
No 171
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=40.22 E-value=11 Score=26.59 Aligned_cols=13 Identities=23% Similarity=0.690 Sum_probs=7.3
Q ss_pred ccccccCccccCh
Q psy4272 118 LTCLQCGRSYCRP 130 (575)
Q Consensus 118 ~~C~~Cgk~F~~~ 130 (575)
|+|..||..|...
T Consensus 6 y~C~~Cg~~fe~~ 18 (42)
T PF09723_consen 6 YRCEECGHEFEVL 18 (42)
T ss_pred EEeCCCCCEEEEE
Confidence 5566666555443
No 172
>KOG4167|consensus
Probab=39.70 E-value=7.5 Score=43.94 Aligned_cols=26 Identities=15% Similarity=0.448 Sum_probs=21.7
Q ss_pred cccccccCccccChhhHHHHhhhhhC
Q psy4272 117 GLTCLQCGRSYCRPYNLKRHIQYECG 142 (575)
Q Consensus 117 p~~C~~Cgk~F~~~~~L~~H~r~H~g 142 (575)
-|.|..|+|.|-....+..||++|.-
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 38899999999888888888888853
No 173
>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=38.98 E-value=14 Score=29.64 Aligned_cols=35 Identities=20% Similarity=0.279 Sum_probs=26.6
Q ss_pred HHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccc
Q psy4272 339 EKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQN 373 (575)
Q Consensus 339 ~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqN 373 (575)
+..|...+|-......++|..+|+++..|+.|+.+
T Consensus 21 r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 21 EAAAALAREEAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 34455555545557889999999999999999863
No 174
>KOG1280|consensus
Probab=38.41 E-value=14 Score=38.27 Aligned_cols=29 Identities=24% Similarity=0.541 Sum_probs=22.0
Q ss_pred CCCCcccccccccccChhhHHHHHHhhccC
Q psy4272 143 KAPQFPCLYCSYRARHKHDLKKHVTFKHAA 172 (575)
Q Consensus 143 ekp~~~C~~Cgk~F~~~~~L~~H~r~~H~~ 172 (575)
..- |.|++|++.=.....|..|....|..
T Consensus 77 ~qS-ftCPyC~~~Gfte~~f~~Hv~s~Hpd 105 (381)
T KOG1280|consen 77 PQS-FTCPYCGIMGFTERQFGTHVLSQHPE 105 (381)
T ss_pred ccc-ccCCcccccccchhHHHHHhhhcCcc
Confidence 345 99999998766677888888776654
No 175
>KOG0782|consensus
Probab=38.32 E-value=17 Score=40.01 Aligned_cols=34 Identities=18% Similarity=0.169 Sum_probs=26.6
Q ss_pred cChhhHHHHhhhhhCCCCCcccccccccccChhhH
Q psy4272 128 CRPYNLKRHIQYECGKAPQFPCLYCSYRARHKHDL 162 (575)
Q Consensus 128 ~~~~~L~~H~r~H~gekp~~~C~~Cgk~F~~~~~L 162 (575)
.+...|.+|-.+|....- -+|..|||.|-++..+
T Consensus 236 ~rE~~fvrHHWVHrrRqe-GkC~~CgKgFQQKf~F 269 (1004)
T KOG0782|consen 236 TRESGFVRHHWVHRRRQE-GKCNTCGKGFQQKFFF 269 (1004)
T ss_pred cccccchHHhHhhHhhhc-cccchhhhhhhhheee
Confidence 344578888888877666 7899999999887654
No 176
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=38.25 E-value=44 Score=30.11 Aligned_cols=47 Identities=13% Similarity=0.155 Sum_probs=35.2
Q ss_pred cCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhh
Q psy4272 329 VYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKR 380 (575)
Q Consensus 329 ~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk 380 (575)
.+++.+..++...|-.. ....++|..+|++...|+.|...-|.|-|+
T Consensus 106 ~L~~~~r~ii~l~~~~~-----~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 106 VLDEKEKYIIFERFFVG-----KTMGEIALETEMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 56677777776665443 347799999999999999998766666554
No 177
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=36.77 E-value=19 Score=33.82 Aligned_cols=24 Identities=13% Similarity=-0.014 Sum_probs=19.5
Q ss_pred CCCCCCCcchhhcchhHHHHHhhhcCCCCcccccccCc
Q psy4272 88 PSPLKAKLSDYENKMKNVRESIRQKRLAQGLTCLQCGR 125 (575)
Q Consensus 88 p~~C~~C~~~f~~~~~~L~~H~r~H~~~kp~~C~~Cgk 125 (575)
-|.|.+||- +|.|+-|-+|++||-
T Consensus 134 ~~vC~vCGy--------------~~~ge~P~~CPiCga 157 (166)
T COG1592 134 VWVCPVCGY--------------THEGEAPEVCPICGA 157 (166)
T ss_pred EEEcCCCCC--------------cccCCCCCcCCCCCC
Confidence 689999975 455678999999993
No 178
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=36.66 E-value=41 Score=32.75 Aligned_cols=47 Identities=23% Similarity=0.337 Sum_probs=37.4
Q ss_pred cCCHHHHHHHHHHhhhCC--CCCHHHHHHHHHHhCCChhhhhhcccchhhh
Q psy4272 329 VYSSHQIVELEKEFRLTN--YLPSDRRKVLSKELGLTERQIKIWFQNRRMK 377 (575)
Q Consensus 329 ~~t~~ql~~L~~~F~~~~--~p~~~~r~~la~~l~l~~~~V~vWFqNrRak 377 (575)
.+|..|+++|..+|...- ||-...-.+||..+|+++..+.- -=|||-
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~e--hLRrAe 203 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSE--HLRRAE 203 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHH--HHHHHH
Confidence 799999999999998765 47777788999999999987543 334444
No 179
>PF09607 BrkDBD: Brinker DNA-binding domain; InterPro: IPR018586 This DNA-binding domain is the first approx. 100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway []. ; PDB: 2GLO_A.
Probab=35.83 E-value=68 Score=24.55 Aligned_cols=44 Identities=18% Similarity=0.451 Sum_probs=23.1
Q ss_pred cccCCHH-HHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhccc
Q psy4272 327 RQVYSSH-QIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQ 372 (575)
Q Consensus 327 Rt~~t~~-ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFq 372 (575)
|..|+.. -|.+++.+...+. --...| ..|.++|+++++|+-|-+
T Consensus 3 rrsy~~~FKL~Vv~~a~~~~n-c~~~~R-Aaarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKDNN-CKGNQR-AAARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHHHHH-TT-TTT-HH-HHHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHHHHHccc-hhhhHH-HHHHHhCccHHHHHHHHH
Confidence 3445553 4556655554432 111223 359999999999999975
No 180
>KOG4167|consensus
Probab=35.62 E-value=9.6 Score=43.13 Aligned_cols=23 Identities=22% Similarity=0.398 Sum_probs=21.8
Q ss_pred cccccccccccChhhHHHHHHhh
Q psy4272 147 FPCLYCSYRARHKHDLKKHVTFK 169 (575)
Q Consensus 147 ~~C~~Cgk~F~~~~~L~~H~r~~ 169 (575)
|.|..|+|.|..-..++.||++|
T Consensus 793 FpCreC~kvF~KiKSrNAHMK~H 815 (907)
T KOG4167|consen 793 FPCRECGKVFFKIKSRNAHMKTH 815 (907)
T ss_pred eehHHHHHHHHHHhhhhHHHHHH
Confidence 89999999999999999999994
No 181
>PRK04217 hypothetical protein; Provisional
Probab=35.60 E-value=58 Score=28.41 Aligned_cols=48 Identities=10% Similarity=0.059 Sum_probs=37.0
Q ss_pred cCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhc
Q psy4272 329 VYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRT 381 (575)
Q Consensus 329 ~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~ 381 (575)
.++..|..++...|.... ...++|..+|++...|+..+..-|.+.+..
T Consensus 42 ~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~RArkkLre~ 89 (110)
T PRK04217 42 FMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTSARKKVAQM 89 (110)
T ss_pred cCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 567888888877765443 577899999999999999997766666553
No 182
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=35.47 E-value=19 Score=27.53 Aligned_cols=30 Identities=20% Similarity=0.681 Sum_probs=15.7
Q ss_pred ccccccCccccCh-hhHHHHhhhhhCCCCCcccccccc
Q psy4272 118 LTCLQCGRSYCRP-YNLKRHIQYECGKAPQFPCLYCSY 154 (575)
Q Consensus 118 ~~C~~Cgk~F~~~-~~L~~H~r~H~gekp~~~C~~Cgk 154 (575)
|.|+.||+....+ ..-++ ...+ |+|+.||.
T Consensus 26 F~CPnCG~~~I~RC~~CRk------~~~~-Y~CP~CGF 56 (59)
T PRK14890 26 FLCPNCGEVIIYRCEKCRK------QSNP-YTCPKCGF 56 (59)
T ss_pred eeCCCCCCeeEeechhHHh------cCCc-eECCCCCC
Confidence 6777777652222 11111 1245 88888873
No 183
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=35.24 E-value=29 Score=24.66 Aligned_cols=40 Identities=10% Similarity=0.138 Sum_probs=21.2
Q ss_pred ccCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhccc
Q psy4272 328 QVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQ 372 (575)
Q Consensus 328 t~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFq 372 (575)
..+|.++...++..+... ....+||..||.+...|.-|.+
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 467888888888887644 3566799999999999987763
No 184
>KOG4124|consensus
Probab=35.09 E-value=8.3 Score=39.83 Aligned_cols=50 Identities=28% Similarity=0.507 Sum_probs=32.2
Q ss_pred Ccccccc--cCccccChhhHHHHhhh---------------hh----CCCCCcccccccccccChhhHHHHH
Q psy4272 116 QGLTCLQ--CGRSYCRPYNLKRHIQY---------------EC----GKAPQFPCLYCSYRARHKHDLKKHV 166 (575)
Q Consensus 116 kp~~C~~--Cgk~F~~~~~L~~H~r~---------------H~----gekp~~~C~~Cgk~F~~~~~L~~H~ 166 (575)
++|+|.+ |.+.++....|+.|... |+ ..|+ |+|++|.++++....|+-|.
T Consensus 348 ~~~~~~vp~~~~~~~n~ng~~~~~~~~h~s~i~~~s~~~~ph~~~~~~nk~-~r~~i~~~~~k~~~~l~~~~ 418 (442)
T KOG4124|consen 348 KPYKCPVPNCDKAYKNQNGLKYHKLHGHCSPITTPTPAPIPHQGFVVENKP-YRCEVCSKRYKNLNGLKYHR 418 (442)
T ss_pred CCCCCCCCcchhhcccCcceeeccccCcCCCCCCCCCCCCCcceeeeccCc-ccChhhhhhhccCCCCCcee
Confidence 4555644 66666555555555321 22 2478 99999999988877777664
No 185
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=34.91 E-value=49 Score=31.38 Aligned_cols=48 Identities=8% Similarity=0.120 Sum_probs=36.4
Q ss_pred cCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhc
Q psy4272 329 VYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRT 381 (575)
Q Consensus 329 ~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~ 381 (575)
.++..+..+|.-.|-.. ..-.++|..||++...|++|...-|.+-|+.
T Consensus 142 ~L~~~~r~vl~l~~~~~-----~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~ 189 (194)
T PRK09646 142 ALTDTQRESVTLAYYGG-----LTYREVAERLAVPLGTVKTRMRDGLIRLRDC 189 (194)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHhCCChHhHHHHHHHHHHHHHHH
Confidence 46677777776655433 3567899999999999999998777776654
No 186
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=34.83 E-value=48 Score=30.54 Aligned_cols=47 Identities=6% Similarity=-0.028 Sum_probs=35.3
Q ss_pred cCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhh
Q psy4272 329 VYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKR 380 (575)
Q Consensus 329 ~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk 380 (575)
.+++.+..+|...|-.. ....++|..+|++...|+.|...-|.|.|+
T Consensus 128 ~L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 174 (182)
T PRK09652 128 SLPEELRTAITLREIEG-----LSYEEIAEIMGCPIGTVRSRIFRAREALRA 174 (182)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 56777778887665432 246689999999999999999866666665
No 187
>PHA00626 hypothetical protein
Probab=34.74 E-value=14 Score=27.93 Aligned_cols=12 Identities=25% Similarity=0.849 Sum_probs=6.8
Q ss_pred cccccccccccC
Q psy4272 147 FPCLYCSYRARH 158 (575)
Q Consensus 147 ~~C~~Cgk~F~~ 158 (575)
|+|..||..|+.
T Consensus 24 YkCkdCGY~ft~ 35 (59)
T PHA00626 24 YVCCDCGYNDSK 35 (59)
T ss_pred eEcCCCCCeech
Confidence 566666655543
No 188
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=34.36 E-value=15 Score=33.67 Aligned_cols=34 Identities=26% Similarity=0.590 Sum_probs=22.2
Q ss_pred CcccccccCccccChhhHHHHhhhhhCCCCCccccccccc
Q psy4272 116 QGLTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSYR 155 (575)
Q Consensus 116 kp~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk~ 155 (575)
-+|.|. |+..|.+. ++|-.+-.|+ . |.|..|+-.
T Consensus 116 ~~Y~C~-C~q~~l~~---RRhn~~~~g~-~-YrC~~C~gk 149 (156)
T COG3091 116 YPYRCQ-CQQHYLRI---RRHNTVRRGE-V-YRCGKCGGK 149 (156)
T ss_pred eeEEee-cCCccchh---hhcccccccc-e-EEeccCCce
Confidence 457888 88776553 4555555566 6 888888643
No 189
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=34.11 E-value=49 Score=31.85 Aligned_cols=49 Identities=14% Similarity=0.084 Sum_probs=36.0
Q ss_pred cCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhcC
Q psy4272 329 VYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTH 382 (575)
Q Consensus 329 ~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~~ 382 (575)
.++..+..+|...|-.. ....++|..+|++...|+++...-|.+.|+..
T Consensus 153 ~L~~~~r~vl~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 153 KLPEAQQTVVKGVYFQE-----LSQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 45667777776544333 35778999999999999999977777766643
No 190
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.05 E-value=14 Score=32.57 Aligned_cols=42 Identities=19% Similarity=0.295 Sum_probs=25.1
Q ss_pred ccccccCccccChhhHHHHhhh-hhCCCCCcccccccccccChh
Q psy4272 118 LTCLQCGRSYCRPYNLKRHIQY-ECGKAPQFPCLYCSYRARHKH 160 (575)
Q Consensus 118 ~~C~~Cgk~F~~~~~L~~H~r~-H~gekp~~~C~~Cgk~F~~~~ 160 (575)
..|++|.....-..+..--... |.-+.| --|..||+.|.+-.
T Consensus 40 ~qcp~csasirgd~~vegvlglg~dye~p-sfchncgs~fpwte 82 (160)
T COG4306 40 TQCPICSASIRGDYYVEGVLGLGGDYEPP-SFCHNCGSRFPWTE 82 (160)
T ss_pred hcCCccCCcccccceeeeeeccCCCCCCc-chhhcCCCCCCcHH
Confidence 4688887665544433222222 233445 67999999998754
No 191
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=34.03 E-value=16 Score=33.44 Aligned_cols=40 Identities=15% Similarity=0.130 Sum_probs=25.7
Q ss_pred CCCCCCCCCCcchhhcchhHHHHHhhhcCCCCcccccccCccccC
Q psy4272 85 ATLPSPLKAKLSDYENKMKNVRESIRQKRLAQGLTCLQCGRSYCR 129 (575)
Q Consensus 85 ~~~p~~C~~C~~~f~~~~~~L~~H~r~H~~~kp~~C~~Cgk~F~~ 129 (575)
...-|.|+.|+..|... ..+.. .+. ..-|.|+.||.....
T Consensus 96 ~~~~Y~Cp~C~~~y~~~-ea~~~---~d~-~~~f~Cp~Cg~~l~~ 135 (147)
T smart00531 96 NNAYYKCPNCQSKYTFL-EANQL---LDM-DGTFTCPRCGEELEE 135 (147)
T ss_pred CCcEEECcCCCCEeeHH-HHHHh---cCC-CCcEECCCCCCEEEE
Confidence 35578999999998754 22211 011 233999999987643
No 192
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.31 E-value=16 Score=29.32 Aligned_cols=31 Identities=23% Similarity=0.629 Sum_probs=16.4
Q ss_pred ccccccCccccChhhHHHHhhhhhCCCCCcccccccccc
Q psy4272 118 LTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSYRA 156 (575)
Q Consensus 118 ~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk~F 156 (575)
|+|..||..|. +..|++ +-|.-.|+.|+..|
T Consensus 13 Y~c~~cg~~~d----vvq~~~----ddplt~ce~c~a~~ 43 (82)
T COG2331 13 YECTECGNRFD----VVQAMT----DDPLTTCEECGARL 43 (82)
T ss_pred EeecccchHHH----HHHhcc----cCccccChhhChHH
Confidence 67777776552 333332 33314577776543
No 193
>PF08649 DASH_Dad1: DASH complex subunit Dad1; InterPro: IPR013958 The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis []. In Saccharomyces cerevisiae (Baker's yeast) DASH forms both rings and spiral structures on microtubules in vitro [, ]. Components of the DASH complex, including Dam1, Duo1, Spc34, Dad1 and Ask1, are essential and connect the centromere to the plus end of spindle microtubules []. Throughout the cell cycle Dad1 remains bound to kinetochores and its association is dependent on the Mis6 and Mal2 [].
Probab=33.23 E-value=29 Score=26.53 Aligned_cols=22 Identities=36% Similarity=0.672 Sum_probs=16.5
Q ss_pred hHHHHHHHHHHHHHHHhcccccc
Q psy4272 514 YENERNMLIQELIRKKLGLLIQN 536 (575)
Q Consensus 514 ~~~~~~~~~~~~~~~~~~~~~~~ 536 (575)
||.+|..||+| |.+-++-+++|
T Consensus 3 Fe~qR~~Li~e-I~~~~e~vl~n 24 (58)
T PF08649_consen 3 FERQRDRLIQE-ISESMESVLNN 24 (58)
T ss_pred HHHHHHHHHHH-HHHHHHHHHHH
Confidence 39999999998 55666665554
No 194
>KOG2785|consensus
Probab=32.65 E-value=39 Score=35.66 Aligned_cols=52 Identities=13% Similarity=0.256 Sum_probs=39.7
Q ss_pred CCCCCCCCCcchhhcchhHHHHHhhhcCC-----------------------CCcccccccC---ccccChhhHHHHhh
Q psy4272 86 TLPSPLKAKLSDYENKMKNVRESIRQKRL-----------------------AQGLTCLQCG---RSYCRPYNLKRHIQ 138 (575)
Q Consensus 86 ~~p~~C~~C~~~f~~~~~~L~~H~r~H~~-----------------------~kp~~C~~Cg---k~F~~~~~L~~H~r 138 (575)
..|--|-.|++.+.... .-..||..|+| ..-|.|-.|. +.|......+.||.
T Consensus 164 ~~Pt~CLfC~~~~k~~e-~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~ 241 (390)
T KOG2785|consen 164 LIPTDCLFCDKKSKSLE-ENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMR 241 (390)
T ss_pred cCCcceeecCCCcccHH-HHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHh
Confidence 34578999999988874 44467766554 1237899999 99999999999987
No 195
>PF05527 DUF758: Domain of unknown function (DUF758) ; InterPro: IPR008477 This is a family of eukaryotic proteins with unknown function, which are induced by tumour necrosis factor.; PDB: 3F4M_A.
Probab=32.13 E-value=43 Score=31.99 Aligned_cols=38 Identities=29% Similarity=0.494 Sum_probs=28.8
Q ss_pred chhHHHhhhhh---HHHHHHHHHHHHH--HHhcccccccCCCC
Q psy4272 504 PGQVEKLNDLY---ENERNMLIQELIR--KKLGLLIQNNQNGG 541 (575)
Q Consensus 504 i~~~~~~~~~~---~~~~~~~~~~~~~--~~~~~~~~~~~~~~ 541 (575)
+|.||.+--.| +.|-+.++..+|. -|+|+|++|||-++
T Consensus 39 LD~ly~l~K~~t~~kkeA~ki~KniIKi~vKigvl~rn~qf~~ 81 (186)
T PF05527_consen 39 LDELYRLLKEYTGNKKEAEKIIKNIIKIVVKIGVLYRNNQFSD 81 (186)
T ss_dssp HHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHHTT---H
T ss_pred HHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhheeeecCCCCH
Confidence 58888888888 6677788888875 58999999999764
No 196
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=31.11 E-value=24 Score=29.55 Aligned_cols=33 Identities=21% Similarity=0.452 Sum_probs=20.9
Q ss_pred CcccccccCccccChhhHHHHhhhhhCCCCCcccccccccccCh
Q psy4272 116 QGLTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSYRARHK 159 (575)
Q Consensus 116 kp~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk~F~~~ 159 (575)
..|.|+.||+.- ++ |.-+| . +.|..|++.|.--
T Consensus 35 a~y~CpfCgk~~-----vk---R~a~G--I-W~C~~C~~~~AGG 67 (90)
T PTZ00255 35 AKYFCPFCGKHA-----VK---RQAVG--I-WRCKGCKKTVAGG 67 (90)
T ss_pred CCccCCCCCCCc-----ee---eeeeE--E-EEcCCCCCEEeCC
Confidence 458899998542 11 22233 4 7899999887643
No 197
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=30.88 E-value=76 Score=22.70 Aligned_cols=43 Identities=19% Similarity=0.203 Sum_probs=30.7
Q ss_pred cCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhh
Q psy4272 329 VYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMK 377 (575)
Q Consensus 329 ~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak 377 (575)
.++..+..++...+. . ....++|..+|++...|..|.+.-+.|
T Consensus 3 ~l~~~e~~i~~~~~~-g-----~s~~eia~~l~is~~tv~~~~~~~~~k 45 (58)
T smart00421 3 SLTPREREVLRLLAE-G-----LTNKEIAERLGISEKTVKTHLSNIMRK 45 (58)
T ss_pred CCCHHHHHHHHHHHc-C-----CCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 467777777755332 2 256789999999999999998744433
No 198
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=30.88 E-value=63 Score=30.19 Aligned_cols=50 Identities=10% Similarity=0.041 Sum_probs=38.1
Q ss_pred cCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhcCC
Q psy4272 329 VYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTHP 383 (575)
Q Consensus 329 ~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~~~ 383 (575)
.++..+..+|.-.|-.. ..-.++|..+|++...|++++..-|.|.|+..+
T Consensus 131 ~L~~~~r~v~~l~~~~g-----~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l~ 180 (184)
T PRK12512 131 TLPPRQRDVVQSISVEG-----ASIKETAAKLSMSEGAVRVALHRGLAALAAKFR 180 (184)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Confidence 45667777777665443 356789999999999999999888888776543
No 199
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=30.78 E-value=9.1 Score=32.44 Aligned_cols=39 Identities=18% Similarity=0.449 Sum_probs=22.6
Q ss_pred CCcccccccCccccChhhHHHHhhhhhCCCCCcccccccccccC
Q psy4272 115 AQGLTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSYRARH 158 (575)
Q Consensus 115 ~kp~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk~F~~ 158 (575)
.+.|.|+.||..-.....++.-. +.-. ..|..||..|.-
T Consensus 20 ~k~FtCp~Cghe~vs~ctvkk~~----~~g~-~~Cg~CGls~e~ 58 (104)
T COG4888 20 PKTFTCPRCGHEKVSSCTVKKTV----NIGT-AVCGNCGLSFEC 58 (104)
T ss_pred CceEecCccCCeeeeEEEEEecC----ceeE-EEcccCcceEEE
Confidence 35588888886554443332211 1122 578899887754
No 200
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=30.72 E-value=18 Score=33.12 Aligned_cols=38 Identities=21% Similarity=0.291 Sum_probs=29.0
Q ss_pred CCCCCCCCCCcchhhcchhHHHHHhhhcCCCCcccccccCcccc
Q psy4272 85 ATLPSPLKAKLSDYENKMKNVRESIRQKRLAQGLTCLQCGRSYC 128 (575)
Q Consensus 85 ~~~p~~C~~C~~~f~~~~~~L~~H~r~H~~~kp~~C~~Cgk~F~ 128 (575)
..-+|.|. |+..|.+. ++|-.+-.|+ -|.|..|+-...
T Consensus 114 ~~~~Y~C~-C~q~~l~~----RRhn~~~~g~-~YrC~~C~gkL~ 151 (156)
T COG3091 114 TTYPYRCQ-CQQHYLRI----RRHNTVRRGE-VYRCGKCGGKLV 151 (156)
T ss_pred cceeEEee-cCCccchh----hhcccccccc-eEEeccCCceEE
Confidence 45689999 99988655 4666666777 899999986543
No 201
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=30.58 E-value=37 Score=21.38 Aligned_cols=19 Identities=16% Similarity=0.424 Sum_probs=12.6
Q ss_pred ccccccccccChhhHHHHHH
Q psy4272 148 PCLYCSYRARHKHDLKKHVT 167 (575)
Q Consensus 148 ~C~~Cgk~F~~~~~L~~H~r 167 (575)
.|++|++.+ ....++.|..
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 577787777 4456666654
No 202
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=30.47 E-value=52 Score=31.05 Aligned_cols=46 Identities=20% Similarity=0.220 Sum_probs=33.3
Q ss_pred CCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhh
Q psy4272 330 YSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKR 380 (575)
Q Consensus 330 ~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk 380 (575)
++..+..+|...|-. .....++|..+|++...|++|+..-|.|.|+
T Consensus 142 L~~~~~~v~~l~~~~-----g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 187 (194)
T PRK12519 142 LPESQRQVLELAYYE-----GLSQSEIAKRLGIPLGTVKARARQGLLKLRE 187 (194)
T ss_pred CCHHHhhhhhhhhhc-----CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 455566666554322 2357789999999999999999876766665
No 203
>KOG3362|consensus
Probab=30.37 E-value=18 Score=32.78 Aligned_cols=20 Identities=40% Similarity=0.956 Sum_probs=11.4
Q ss_pred ccccccCccccChhhHHHHh
Q psy4272 118 LTCLQCGRSYCRPYNLKRHI 137 (575)
Q Consensus 118 ~~C~~Cgk~F~~~~~L~~H~ 137 (575)
|.|.-||..+....-|..|.
T Consensus 130 ysC~~CG~kyCsv~C~~~Hn 149 (156)
T KOG3362|consen 130 YSCVNCGTKYCSVRCLKTHN 149 (156)
T ss_pred hHHHhcCCceeechhhhhcc
Confidence 55666666665555555554
No 204
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=30.12 E-value=70 Score=27.57 Aligned_cols=39 Identities=23% Similarity=0.531 Sum_probs=34.2
Q ss_pred CCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchh
Q psy4272 330 YSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRR 375 (575)
Q Consensus 330 ~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrR 375 (575)
++...+..+.+.+... +...|..||++...|+-|=|+|+
T Consensus 44 ls~~eIk~iRe~~~lS-------Q~vFA~~L~vs~~Tv~~WEqGr~ 82 (104)
T COG2944 44 LSPTEIKAIREKLGLS-------QPVFARYLGVSVSTVRKWEQGRK 82 (104)
T ss_pred CCHHHHHHHHHHhCCC-------HHHHHHHHCCCHHHHHHHHcCCc
Confidence 8888999998888765 56789999999999999999875
No 205
>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=30.00 E-value=34 Score=24.25 Aligned_cols=22 Identities=14% Similarity=0.164 Sum_probs=18.8
Q ss_pred HHHHHHHhCCChhhhhhcccch
Q psy4272 353 RKVLSKELGLTERQIKIWFQNR 374 (575)
Q Consensus 353 r~~la~~l~l~~~~V~vWFqNr 374 (575)
..++|..+|++...|+.|.++.
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g 24 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIG 24 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 4578999999999999997654
No 206
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=29.97 E-value=11 Score=34.76 Aligned_cols=43 Identities=16% Similarity=0.325 Sum_probs=23.9
Q ss_pred cccccCccccChhhHHHHhhh-hhCCCCCcccccccccccChhhH
Q psy4272 119 TCLQCGRSYCRPYNLKRHIQY-ECGKAPQFPCLYCSYRARHKHDL 162 (575)
Q Consensus 119 ~C~~Cgk~F~~~~~L~~H~r~-H~gekp~~~C~~Cgk~F~~~~~L 162 (575)
.|+.|+....-..+..--.-. .+-+.| .-|..||+.|.+-..-
T Consensus 41 ~Cp~C~~~IrG~y~v~gv~~~g~~~~~P-sYC~~CGkpyPWt~~~ 84 (158)
T PF10083_consen 41 SCPNCSTPIRGDYHVEGVFGLGGHYEAP-SYCHNCGKPYPWTENA 84 (158)
T ss_pred HCcCCCCCCCCceecCCeeeeCCCCCCC-hhHHhCCCCCchHHHH
Confidence 377776543333221111111 333567 8899999999886543
No 207
>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=29.76 E-value=17 Score=27.38 Aligned_cols=30 Identities=20% Similarity=0.385 Sum_probs=16.6
Q ss_pred ccccccCccccChhhHHHHhhhhhCCCCCcccccccccc
Q psy4272 118 LTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSYRA 156 (575)
Q Consensus 118 ~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk~F 156 (575)
|+|+.||..+.-.... .|+. ..|+.||..|
T Consensus 3 ~~CP~CG~~iev~~~~-------~Gei--V~Cp~CGael 32 (54)
T TIGR01206 3 FECPDCGAEIELENPE-------LGEL--VICDECGAEL 32 (54)
T ss_pred cCCCCCCCEEecCCCc-------cCCE--EeCCCCCCEE
Confidence 5677777665443221 1332 5677777654
No 208
>smart00426 TEA TEA domain.
Probab=29.66 E-value=35 Score=26.92 Aligned_cols=26 Identities=31% Similarity=0.374 Sum_probs=20.8
Q ss_pred HHHHHHHHHHHHHhcccccccCCCCC
Q psy4272 517 ERNMLIQELIRKKLGLLIQNNQNGGH 542 (575)
Q Consensus 517 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 542 (575)
-||+||.+.|-.+-|..----|-|.|
T Consensus 39 gRNelIs~YI~~~tGk~Rt~KQVsSh 64 (68)
T smart00426 39 GRNELIARYIKLRTGKTRTRKQVSSH 64 (68)
T ss_pred chhHHHHHHHHHHhCCccchhhhcch
Confidence 49999999999998877666666655
No 209
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=29.37 E-value=67 Score=29.17 Aligned_cols=48 Identities=4% Similarity=0.031 Sum_probs=35.3
Q ss_pred CCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhcC
Q psy4272 330 YSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTH 382 (575)
Q Consensus 330 ~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~~ 382 (575)
+++.+..++.-.|-... .-.++|..+|++...|+++...-|.+-|+..
T Consensus 107 Lp~~~r~v~~l~~~~g~-----s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (160)
T PRK09642 107 LPENYRDVVLAHYLEEK-----SYQEIALQEKIEVKTVEMKLYRARKWIKKHW 154 (160)
T ss_pred CCHHHHHHHHHHHHhCC-----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 56666677765554332 4668999999999999999987777766643
No 210
>PRK05580 primosome assembly protein PriA; Validated
Probab=29.32 E-value=19 Score=41.74 Aligned_cols=18 Identities=11% Similarity=0.171 Sum_probs=11.4
Q ss_pred HHhCCCh--hhhhhcccchh
Q psy4272 358 KELGLTE--RQIKIWFQNRR 375 (575)
Q Consensus 358 ~~l~l~~--~~V~vWFqNrR 375 (575)
+.+|+++ +.|++||.++.
T Consensus 574 ~~~~~PPf~~l~~i~~~~~~ 593 (679)
T PRK05580 574 RAAGYPPFGRLALLRASAKD 593 (679)
T ss_pred HhcCCCCHHHhhEeEEecCC
Confidence 4456777 45788886553
No 211
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=29.06 E-value=68 Score=28.07 Aligned_cols=47 Identities=17% Similarity=0.177 Sum_probs=34.3
Q ss_pred cCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhh
Q psy4272 329 VYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKR 380 (575)
Q Consensus 329 ~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk 380 (575)
.++..+..++...|-. .....++|..+|++...|+.|...-+.|.|+
T Consensus 110 ~L~~~~~~ii~~~~~~-----g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 110 KLPEREREVLVLRYLE-----GLSYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred hCCHHHHHHHhhHHhc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 4567777777655432 2356689999999999999999876666654
No 212
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=29.03 E-value=36 Score=25.74 Aligned_cols=26 Identities=12% Similarity=0.302 Sum_probs=18.3
Q ss_pred HHHHHHHHhCCChhhhhhcccchhhh
Q psy4272 352 RRKVLSKELGLTERQIKIWFQNRRMK 377 (575)
Q Consensus 352 ~r~~la~~l~l~~~~V~vWFqNrRak 377 (575)
...+||..+|++..+|.-|+.++..+
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~~ 37 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPSN 37 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT---
T ss_pred CHHHHHHHHCcCHHHHHHHHhccccc
Confidence 46689999999999999999876433
No 213
>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=28.99 E-value=22 Score=27.19 Aligned_cols=31 Identities=26% Similarity=0.412 Sum_probs=24.6
Q ss_pred HHHHHHHHHhCCChhhhhhcccchhhhhhhcCC
Q psy4272 351 DRRKVLSKELGLTERQIKIWFQNRRMKLKRTHP 383 (575)
Q Consensus 351 ~~r~~la~~l~l~~~~V~vWFqNrRak~kk~~~ 383 (575)
....++|..||++.++|..|-+ |.+|.....
T Consensus 14 ~~~~eIA~~Lg~~~~TV~~W~~--r~~W~~~~~ 44 (58)
T PF06056_consen 14 WSIKEIAEELGVPRSTVYSWKD--RYKWDELLP 44 (58)
T ss_pred CCHHHHHHHHCCChHHHHHHHH--hhCccccCc
Confidence 3567899999999999999985 677766443
No 214
>KOG0320|consensus
Probab=28.89 E-value=22 Score=33.47 Aligned_cols=52 Identities=19% Similarity=0.399 Sum_probs=31.4
Q ss_pred CCCCCCCCCcchhhcchhHHHHHhhhcCCCCcccccccCccccChhhHHHHhhhhhCCCCCcccccccccccCh
Q psy4272 86 TLPSPLKAKLSDYENKMKNVRESIRQKRLAQGLTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSYRARHK 159 (575)
Q Consensus 86 ~~p~~C~~C~~~f~~~~~~L~~H~r~H~~~kp~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk~F~~~ 159 (575)
..-|.|++|...|..+. + .-..||..|.... ++.-++ +. .+|+.|+|....+
T Consensus 129 ~~~~~CPiCl~~~sek~--------------~-vsTkCGHvFC~~C-ik~alk-----~~-~~CP~C~kkIt~k 180 (187)
T KOG0320|consen 129 EGTYKCPICLDSVSEKV--------------P-VSTKCGHVFCSQC-IKDALK-----NT-NKCPTCRKKITHK 180 (187)
T ss_pred ccccCCCceecchhhcc--------------c-cccccchhHHHHH-HHHHHH-----hC-CCCCCcccccchh
Confidence 33489999988887652 1 2356777776543 222222 23 6799999854433
No 215
>KOG0696|consensus
Probab=28.89 E-value=22 Score=38.11 Aligned_cols=46 Identities=20% Similarity=0.185 Sum_probs=31.3
Q ss_pred CCCCcccccccCccccChhhHHHHhhhhhCCCCCcccccccccccChhhHHHHHHh
Q psy4272 113 RLAQGLTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSYRARHKHDLKKHVTF 168 (575)
Q Consensus 113 ~~~kp~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk~F~~~~~L~~H~r~ 168 (575)
.|+.-|+|.+|. +..|.|.|.-. . |.|+--++.+.....-..|.-.
T Consensus 69 fgKQGfQCqvC~--------fvvHkrChefV-t-F~CPGadkg~dtDdpr~kHkf~ 114 (683)
T KOG0696|consen 69 FGKQGFQCQVCC--------FVVHKRCHEFV-T-FSCPGADKGPDTDDPRSKHKFK 114 (683)
T ss_pred cccCceeeeEEe--------ehhhhhhcceE-E-EECCCCCCCCCCCCccccccee
Confidence 356668888884 55777777533 3 7888778888777766666433
No 216
>PRK06930 positive control sigma-like factor; Validated
Probab=28.55 E-value=75 Score=29.89 Aligned_cols=49 Identities=8% Similarity=0.043 Sum_probs=37.7
Q ss_pred cCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhcC
Q psy4272 329 VYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTH 382 (575)
Q Consensus 329 ~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~~ 382 (575)
.+++.+..+|.-.|... ..-.++|..+|++...|++|...-|.|.++..
T Consensus 114 ~L~~rer~V~~L~~~eg-----~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l 162 (170)
T PRK06930 114 VLTEREKEVYLMHRGYG-----LSYSEIADYLNIKKSTVQSMIERAEKKIARQI 162 (170)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 57788888777655433 24678999999999999999987777776643
No 217
>PF09416 UPF1_Zn_bind: RNA helicase (UPF2 interacting domain); InterPro: IPR018999 UPF1 (or regulator of nonsense transcripts 1 homologue) is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. This domain contains 3 zinc binding motifs and forms interactions with another protein (UPF2) that is also involved nonsense-mediated mRNA decay (NMD) []. ; GO: 0003677 DNA binding, 0004386 helicase activity, 0005524 ATP binding, 0008270 zinc ion binding, 0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, 0005737 cytoplasm; PDB: 2IYK_B 2WJY_A 2WJV_A 2XZL_A.
Probab=28.50 E-value=43 Score=30.87 Aligned_cols=37 Identities=22% Similarity=0.665 Sum_probs=16.6
Q ss_pred ccccccCcccc------ChhhHHHHhhh--h----------hCCCCCccccccccc
Q psy4272 118 LTCLQCGRSYC------RPYNLKRHIQY--E----------CGKAPQFPCLYCSYR 155 (575)
Q Consensus 118 ~~C~~Cgk~F~------~~~~L~~H~r~--H----------~gekp~~~C~~Cgk~ 155 (575)
.+|..|+|-|- ..+++..|+.. | .|+.. ++|-.||-+
T Consensus 15 v~C~~c~kWFCNg~~~~s~SHIv~HLv~srh~ev~LH~~s~lgdt~-leCy~Cg~~ 69 (152)
T PF09416_consen 15 VKCNTCNKWFCNGRGNTSGSHIVNHLVRSRHKEVSLHPDSPLGDTV-LECYNCGSR 69 (152)
T ss_dssp EEETTTTEEEES--TTSSS-HHHHHHHHHT---EEE-TTSTT-S-B----TTT---
T ss_pred eEcCCCCcEeecCCCCCcccHHHHHHHHccCCceeeCCCCCCCCcE-EEEEecCCC
Confidence 56777777773 34556666431 2 13455 789888853
No 218
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=28.46 E-value=75 Score=29.56 Aligned_cols=46 Identities=17% Similarity=0.130 Sum_probs=35.0
Q ss_pred CCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhh
Q psy4272 330 YSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKR 380 (575)
Q Consensus 330 ~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk 380 (575)
+.+.+..++.-.|-.. ..-.++|..+|+++..|++....-|.+.|+
T Consensus 135 Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 180 (183)
T TIGR02999 135 VDPRQAEVVELRFFAG-----LTVEEIAELLGVSVRTVERDWRFARAWLAD 180 (183)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 5666777776665443 256789999999999999999877776665
No 219
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=28.07 E-value=23 Score=27.59 Aligned_cols=10 Identities=30% Similarity=1.298 Sum_probs=3.1
Q ss_pred cccccCcccc
Q psy4272 119 TCLQCGRSYC 128 (575)
Q Consensus 119 ~C~~Cgk~F~ 128 (575)
.|..|++.|.
T Consensus 11 ~C~~C~~~F~ 20 (69)
T PF01363_consen 11 NCMICGKKFS 20 (69)
T ss_dssp B-TTT--B-B
T ss_pred cCcCcCCcCC
Confidence 4555555553
No 220
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=28.01 E-value=37 Score=30.43 Aligned_cols=27 Identities=22% Similarity=0.412 Sum_probs=19.8
Q ss_pred CCCCCCCcchhhcchhHHHHHhhhcCCCCcccccccCc
Q psy4272 88 PSPLKAKLSDYENKMKNVRESIRQKRLAQGLTCLQCGR 125 (575)
Q Consensus 88 p~~C~~C~~~f~~~~~~L~~H~r~H~~~kp~~C~~Cgk 125 (575)
||.|..||+.|..-...+ . -.|+.||-
T Consensus 1 PH~Ct~Cg~~f~dgs~ei----l-------~GCP~CGg 27 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGSKEI----L-------SGCPECGG 27 (131)
T ss_pred CcccCcCCCCcCCCcHHH----H-------ccCcccCC
Confidence 689999999998763221 1 35999983
No 221
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=27.99 E-value=72 Score=29.23 Aligned_cols=47 Identities=13% Similarity=0.104 Sum_probs=33.9
Q ss_pred CCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhc
Q psy4272 330 YSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRT 381 (575)
Q Consensus 330 ~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~ 381 (575)
++..+..+|...|-.. ..-.++|..+|++...|+.|..--|.|.|+.
T Consensus 126 L~~~~r~i~~l~~~~~-----~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~ 172 (179)
T PRK11924 126 LPVKQREVFLLRYVEG-----LSYREIAEILGVPVGTVKSRLRRARQLLREC 172 (179)
T ss_pred CCHHHHHHhhHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 5555666665554332 3467899999999999999998777766653
No 222
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=27.94 E-value=26 Score=29.36 Aligned_cols=33 Identities=18% Similarity=0.418 Sum_probs=21.3
Q ss_pred CcccccccCccccChhhHHHHhhhhhCCCCCcccccccccccCh
Q psy4272 116 QGLTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSYRARHK 159 (575)
Q Consensus 116 kp~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk~F~~~ 159 (575)
..|.|+.||+.-. .|.-+| . +.|..|++.|.--
T Consensus 34 a~y~CpfCgk~~v--------kR~a~G--I-W~C~~C~~~~AGG 66 (91)
T TIGR00280 34 AKYVCPFCGKKTV--------KRGSTG--I-WTCRKCGAKFAGG 66 (91)
T ss_pred cCccCCCCCCCce--------EEEeeE--E-EEcCCCCCEEeCC
Confidence 4589999985421 133334 3 7899999887643
No 223
>KOG2461|consensus
Probab=27.79 E-value=1.1e+02 Score=32.83 Aligned_cols=62 Identities=8% Similarity=-0.133 Sum_probs=34.9
Q ss_pred HHHhhhcCCCCcccccccCccccChhhHHHHhhhhhCCCCCcccccccccccChhhHHHHHHh
Q psy4272 106 RESIRQKRLAQGLTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSYRARHKHDLKKHVTF 168 (575)
Q Consensus 106 ~~H~r~H~~~kp~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk~F~~~~~L~~H~r~ 168 (575)
..|...|++...+.+.+|.+.+.....+..|...|.++.+ +.|..|...+.....+..+..+
T Consensus 320 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~ 381 (396)
T KOG2461|consen 320 DQSEVPATVSVWTGETIPVRTPAGQLIYTQSHSMEVAEPT-DMAPNQIWKIYHTGVLGFLIIT 381 (396)
T ss_pred ccccccccccccCcCcccccccccccchhhhhhcccCCCC-cccccccccceeccccceeeee
Confidence 4455556666666666666666666666666666666655 5555444444444444444333
No 224
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=27.76 E-value=34 Score=36.82 Aligned_cols=30 Identities=33% Similarity=0.732 Sum_probs=17.7
Q ss_pred cccccCccccChhhHHHHhhhhhCCCCCcccccccccccChh
Q psy4272 119 TCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSYRARHKH 160 (575)
Q Consensus 119 ~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk~F~~~~ 160 (575)
.|+.||.+...+ |.+- |+|..||..+....
T Consensus 352 ~Cp~Cg~~m~S~-----------G~~g-~rC~kCg~~~~~~~ 381 (421)
T COG1571 352 VCPRCGGRMKSA-----------GRNG-FRCKKCGTRARETL 381 (421)
T ss_pred CCCccCCchhhc-----------CCCC-cccccccccCCccc
Confidence 577777654433 3334 77777777665543
No 225
>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=27.72 E-value=83 Score=28.18 Aligned_cols=47 Identities=11% Similarity=0.097 Sum_probs=33.3
Q ss_pred cCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhh
Q psy4272 329 VYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKR 380 (575)
Q Consensus 329 ~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk 380 (575)
.++..+..+|.-.|-.. ....++|..+|+++..|+.+...-|.|.|+
T Consensus 113 ~L~~~~r~il~l~~~~~-----~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 113 KLPEQCRKIFILSRFEG-----KSYKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred HCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 34566667776644322 246789999999999999998766666554
No 226
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=27.25 E-value=25 Score=31.77 Aligned_cols=15 Identities=27% Similarity=0.680 Sum_probs=11.0
Q ss_pred CcccccccCccccCh
Q psy4272 116 QGLTCLQCGRSYCRP 130 (575)
Q Consensus 116 kp~~C~~Cgk~F~~~ 130 (575)
..|.|..||..|...
T Consensus 69 ~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 69 AVLKCRNCGNEWSLK 83 (135)
T ss_pred eEEECCCCCCEEecc
Confidence 347888888877654
No 227
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=27.25 E-value=80 Score=29.64 Aligned_cols=48 Identities=10% Similarity=0.060 Sum_probs=35.9
Q ss_pred ccCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhh
Q psy4272 328 QVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKR 380 (575)
Q Consensus 328 t~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk 380 (575)
..++..|..++...|-.. ...+++|..+|++...|+++...-|.|-|+
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 356677777777665443 357799999999999999998766666655
No 228
>PF15269 zf-C2H2_7: Zinc-finger
Probab=27.20 E-value=36 Score=24.41 Aligned_cols=22 Identities=23% Similarity=0.788 Sum_probs=16.2
Q ss_pred cccccccccccChhhHHHHHHh
Q psy4272 147 FPCLYCSYRARHKHDLKKHVTF 168 (575)
Q Consensus 147 ~~C~~Cgk~F~~~~~L~~H~r~ 168 (575)
|+|-+|.-....+++|-.||+.
T Consensus 21 ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred ceeecCCcccchHHHHHHHHHH
Confidence 6677777777777777777765
No 229
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=27.09 E-value=30 Score=32.17 Aligned_cols=35 Identities=11% Similarity=0.172 Sum_probs=25.0
Q ss_pred CCCCCCCCCCcchhhcchhHHHHHhhhcCCCCcccccccCccccC
Q psy4272 85 ATLPSPLKAKLSDYENKMKNVRESIRQKRLAQGLTCLQCGRSYCR 129 (575)
Q Consensus 85 ~~~p~~C~~C~~~f~~~~~~L~~H~r~H~~~kp~~C~~Cgk~F~~ 129 (575)
...-|.|+.|+..|... ..+. .-|.|+.||.....
T Consensus 106 ~~~~Y~Cp~c~~r~tf~-eA~~---------~~F~Cp~Cg~~L~~ 140 (158)
T TIGR00373 106 NNMFFICPNMCVRFTFN-EAME---------LNFTCPRCGAMLDY 140 (158)
T ss_pred CCCeEECCCCCcEeeHH-HHHH---------cCCcCCCCCCEeee
Confidence 35568999999888655 3332 25999999987543
No 230
>KOG0782|consensus
Probab=27.01 E-value=13 Score=40.84 Aligned_cols=52 Identities=15% Similarity=0.326 Sum_probs=34.2
Q ss_pred hHHHHHhhhcCCCCcccccccCccccChhhHHHHhhhhhCCCCCcccccccccccChh
Q psy4272 103 KNVRESIRQKRLAQGLTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSYRARHKH 160 (575)
Q Consensus 103 ~~L~~H~r~H~~~kp~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk~F~~~~ 160 (575)
+.+.+|.-+|.-..-=+|..|||.|.++..+ |..|.--..|..|...|-.+.
T Consensus 239 ~~fvrHHWVHrrRqeGkC~~CgKgFQQKf~F------hsKEivAisCSWCKqayH~Kv 290 (1004)
T KOG0782|consen 239 SGFVRHHWVHRRRQEGKCNTCGKGFQQKFFF------HSKEIVAISCSWCKQAYHLKV 290 (1004)
T ss_pred ccchHHhHhhHhhhccccchhhhhhhhheee------ccccEEEEEehHHHHHhhcch
Confidence 3566676677655556899999999888654 333321156777877765554
No 231
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=26.90 E-value=83 Score=29.19 Aligned_cols=47 Identities=11% Similarity=0.270 Sum_probs=33.5
Q ss_pred CCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhc
Q psy4272 330 YSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRT 381 (575)
Q Consensus 330 ~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~ 381 (575)
++..+..++.-.|-.. ...+++|..+|++...|+++...-|.+.|+.
T Consensus 130 L~~~~r~i~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 130 LEKDRAAAVRRAYLEG-----LSYKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 4455555555554322 3477899999999999999998777776653
No 232
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=26.70 E-value=86 Score=28.27 Aligned_cols=47 Identities=17% Similarity=0.196 Sum_probs=33.8
Q ss_pred ccCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhh
Q psy4272 328 QVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLK 379 (575)
Q Consensus 328 t~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~k 379 (575)
..++..+..++...|-.. ....++|..+|++...|+++...-|.|-|
T Consensus 110 ~~L~~~~r~v~~l~~~~g-----~~~~eIA~~l~is~~tv~~~l~Rar~~Lr 156 (159)
T TIGR02989 110 EKLPERQRELLQLRYQRG-----VSLTALAEQLGRTVNAVYKALSRLRVRLR 156 (159)
T ss_pred HHCCHHHHHHHHHHHhcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 356677777777654332 35778999999999999998765555544
No 233
>KOG2593|consensus
Probab=26.48 E-value=40 Score=36.18 Aligned_cols=52 Identities=12% Similarity=0.058 Sum_probs=32.1
Q ss_pred HhhhccCCCCCCCCCCCCCCCCCCcchhhcchhHHHHHhhhcCCCCcccccccCcc
Q psy4272 71 QELLSQRDGKPVGKATLPSPLKAKLSDYENKMKNVRESIRQKRLAQGLTCLQCGRS 126 (575)
Q Consensus 71 ~~~~~~~~~~~~~~~~~p~~C~~C~~~f~~~~~~L~~H~r~H~~~kp~~C~~Cgk~ 126 (575)
+....+..-.+..+....|.|+.|.+.|... ..+ ...-....-|.|..|+--
T Consensus 111 ~m~krled~~~d~t~~~~Y~Cp~C~kkyt~L-ea~---~L~~~~~~~F~C~~C~ge 162 (436)
T KOG2593|consen 111 QMRKRLEDRLRDDTNVAGYVCPNCQKKYTSL-EAL---QLLDNETGEFHCENCGGE 162 (436)
T ss_pred HHHHHHHHHhhhccccccccCCccccchhhh-HHH---HhhcccCceEEEecCCCc
Confidence 3333444444455667889999999999765 222 222222345999999854
No 234
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=26.17 E-value=76 Score=24.02 Aligned_cols=35 Identities=29% Similarity=0.387 Sum_probs=26.5
Q ss_pred HHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcc
Q psy4272 333 HQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWF 371 (575)
Q Consensus 333 ~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWF 371 (575)
.|+..|+-.|. +...+.. +||..+|++++.|+.-.
T Consensus 6 rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~~~i 40 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITLK---ELAKKLNISERTIKNDI 40 (59)
T ss_dssp HHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHHHHH
T ss_pred HHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHHHHH
Confidence 57888888888 6555554 89999999999987643
No 235
>KOG0978|consensus
Probab=26.16 E-value=25 Score=40.29 Aligned_cols=19 Identities=16% Similarity=0.209 Sum_probs=13.9
Q ss_pred cccccccccccChhhHHHH
Q psy4272 147 FPCLYCSYRARHKHDLKKH 165 (575)
Q Consensus 147 ~~C~~Cgk~F~~~~~L~~H 165 (575)
-+|+.|+..|...+-+..|
T Consensus 679 RKCP~Cn~aFganDv~~I~ 697 (698)
T KOG0978|consen 679 RKCPKCNAAFGANDVHRIH 697 (698)
T ss_pred CCCCCCCCCCCcccccccC
Confidence 4699999988877665444
No 236
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=26.05 E-value=32 Score=32.72 Aligned_cols=34 Identities=15% Similarity=0.215 Sum_probs=24.7
Q ss_pred CCCCCCCCCcchhhcchhHHHHHhhhcCCCCcccccccCccccC
Q psy4272 86 TLPSPLKAKLSDYENKMKNVRESIRQKRLAQGLTCLQCGRSYCR 129 (575)
Q Consensus 86 ~~p~~C~~C~~~f~~~~~~L~~H~r~H~~~kp~~C~~Cgk~F~~ 129 (575)
..-|.|+.|+..|... ..+ +.-|.|+.||.....
T Consensus 115 ~~~Y~Cp~C~~rytf~-eA~---------~~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 115 NMFFFCPNCHIRFTFD-EAM---------EYGFRCPQCGEMLEE 148 (178)
T ss_pred CCEEECCCCCcEEeHH-HHh---------hcCCcCCCCCCCCee
Confidence 4568999999988665 222 135999999987644
No 237
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=25.76 E-value=89 Score=29.38 Aligned_cols=49 Identities=14% Similarity=0.128 Sum_probs=37.1
Q ss_pred cCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhcC
Q psy4272 329 VYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTH 382 (575)
Q Consensus 329 ~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~~ 382 (575)
.++..+..+|.-.|-.. ..-.++|..+|++...|++....-|.+.|+..
T Consensus 131 ~L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 179 (189)
T PRK12515 131 KLSPAHREIIDLVYYHE-----KSVEEVGEIVGIPESTVKTRMFYARKKLAELL 179 (189)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 56777777776655433 25678999999999999999887777777643
No 238
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=25.63 E-value=23 Score=41.06 Aligned_cols=36 Identities=17% Similarity=0.182 Sum_probs=21.6
Q ss_pred ccCCCCchhHHHhhhhh---HHHHHHHHHHHHHHHhccc
Q psy4272 498 LAGALPPGQVEKLNDLY---ENERNMLIQELIRKKLGLL 533 (575)
Q Consensus 498 ~~~~~~i~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~ 533 (575)
..++.||.++-..|... .-+....++.+++..+.++
T Consensus 674 GP~~a~~~r~~~~yR~qiLl~~~~~~~L~~~l~~~~~~~ 712 (730)
T COG1198 674 GPAPAPLAKLAGRYRYQILLKSPSRADLQKLLRAWLAVL 712 (730)
T ss_pred CCCcchhHHhCCceEEEEEEecCcHHHHHHHHHHHHHHh
Confidence 44445666665555543 5555666677777766654
No 239
>KOG4141|consensus
Probab=25.61 E-value=57 Score=31.56 Aligned_cols=31 Identities=29% Similarity=0.394 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHHHHHhcccccccCCCCCCCC
Q psy4272 515 ENERNMLIQELIRKKLGLLIQNNQNGGHAED 545 (575)
Q Consensus 515 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 545 (575)
-+|++.+||.+|++|||=-.-++.-|||.-.
T Consensus 32 ~~e~~~~iqk~L~~~lgpeYiS~R~g~gg~~ 62 (222)
T KOG4141|consen 32 TAEEYQAIQKKLRQKLGPEYISSRMGGGGQS 62 (222)
T ss_pred hhhhhHHHHHHHHHHhccHhhhccccCCCce
Confidence 5777799999999999998888888888643
No 240
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=25.42 E-value=95 Score=28.70 Aligned_cols=48 Identities=19% Similarity=0.097 Sum_probs=36.1
Q ss_pred cCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhc
Q psy4272 329 VYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRT 381 (575)
Q Consensus 329 ~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~ 381 (575)
.++..+..+|.-.|-.. ...+++|..+|++...|+++-..-|.+.|+.
T Consensus 100 ~L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 147 (170)
T TIGR02959 100 ELPDEYREAIRLTELEG-----LSQQEIAEKLGLSLSGAKSRVQRGRKKLKEL 147 (170)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 56677777777665443 3577899999999999999987666666653
No 241
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=25.35 E-value=89 Score=28.59 Aligned_cols=49 Identities=12% Similarity=-0.078 Sum_probs=35.2
Q ss_pred cCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhcC
Q psy4272 329 VYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTH 382 (575)
Q Consensus 329 ~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~~ 382 (575)
.++..+..++.-.|-.. ...+++|..+|++...|++|...-|.|.|+.-
T Consensus 108 ~L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 156 (165)
T PRK09644 108 TLPVIEAQAILLCDVHE-----LTYEEAASVLDLKLNTYKSHLFRGRKRLKALL 156 (165)
T ss_pred hCCHHHHHHHHhHHHhc-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 45666666666443222 25779999999999999999987777766643
No 242
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=25.25 E-value=26 Score=31.44 Aligned_cols=13 Identities=15% Similarity=0.475 Sum_probs=8.9
Q ss_pred cccccccccccCh
Q psy4272 147 FPCLYCSYRARHK 159 (575)
Q Consensus 147 ~~C~~Cgk~F~~~ 159 (575)
|+|..|++.|...
T Consensus 54 yrC~~C~~tf~~~ 66 (129)
T COG3677 54 YKCKSCGSTFTVE 66 (129)
T ss_pred cccCCcCcceeee
Confidence 7777777776654
No 243
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=24.08 E-value=1e+02 Score=29.16 Aligned_cols=47 Identities=11% Similarity=0.159 Sum_probs=34.1
Q ss_pred cCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhh
Q psy4272 329 VYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKR 380 (575)
Q Consensus 329 ~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk 380 (575)
.++..+..++.-.|-.. ....++|..+|+++..|++|...-|.+.|+
T Consensus 134 ~Lp~~~R~v~~L~~~~g-----~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 180 (189)
T PRK12530 134 HLPAQQARVFMMREYLE-----LSSEQICQECDISTSNLHVLLYRARLQLQA 180 (189)
T ss_pred hCCHHHHHHHhHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45666667776655433 246789999999999999998766665554
No 244
>KOG2807|consensus
Probab=24.06 E-value=79 Score=32.70 Aligned_cols=28 Identities=7% Similarity=-0.028 Sum_probs=21.3
Q ss_pred CCCCCcchhhhhhccChhhhHhhhhhhh
Q psy4272 193 PGPKAENRHRFREFLNEHRNLERNVSHE 220 (575)
Q Consensus 193 p~p~~~C~~C~k~F~~~~~l~~H~~th~ 220 (575)
+...+.|+.|...|.-.-+...|..-|.
T Consensus 342 ~~~~y~C~~Ck~~FCldCDv~iHesLh~ 369 (378)
T KOG2807|consen 342 SSGRYRCESCKNVFCLDCDVFIHESLHN 369 (378)
T ss_pred CCCcEEchhccceeeccchHHHHhhhhc
Confidence 3455689999999988888888876653
No 245
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=24.05 E-value=49 Score=22.09 Aligned_cols=11 Identities=27% Similarity=0.661 Sum_probs=4.9
Q ss_pred ccccccCcccc
Q psy4272 118 LTCLQCGRSYC 128 (575)
Q Consensus 118 ~~C~~Cgk~F~ 128 (575)
|.|..||..+.
T Consensus 1 Y~C~~Cg~~~~ 11 (32)
T PF03604_consen 1 YICGECGAEVE 11 (32)
T ss_dssp EBESSSSSSE-
T ss_pred CCCCcCCCeeE
Confidence 34555554444
No 246
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=24.04 E-value=89 Score=29.24 Aligned_cols=48 Identities=6% Similarity=0.034 Sum_probs=34.1
Q ss_pred CCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhcC
Q psy4272 330 YSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTH 382 (575)
Q Consensus 330 ~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~~ 382 (575)
+++.+..+|...|-.. ..-.++|..+|++...|+++...-|.+.|+..
T Consensus 129 L~~~~r~i~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (186)
T PRK05602 129 LPERQREAIVLQYYQG-----LSNIEAAAVMDISVDALESLLARGRRALRAQL 176 (186)
T ss_pred CCHHHHHHhhHHHhcC-----CCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 4555666665544322 34678999999999999999977777766643
No 247
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=24.01 E-value=33 Score=28.71 Aligned_cols=32 Identities=22% Similarity=0.520 Sum_probs=20.7
Q ss_pred CcccccccCccccChhhHHHHhhhhhCCCCCcccccccccccC
Q psy4272 116 QGLTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSYRARH 158 (575)
Q Consensus 116 kp~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk~F~~ 158 (575)
..|.|+.|++.-.. |.-+| . +.|..|++.|.-
T Consensus 35 a~y~CpfCgk~~vk--------R~a~G--I-W~C~~C~~~~AG 66 (90)
T PRK03976 35 AKHVCPVCGRPKVK--------RVGTG--I-WECRKCGAKFAG 66 (90)
T ss_pred cCccCCCCCCCceE--------EEEEE--E-EEcCCCCCEEeC
Confidence 45889999754221 23333 3 789999988764
No 248
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=24.01 E-value=36 Score=29.87 Aligned_cols=24 Identities=17% Similarity=0.499 Sum_probs=16.3
Q ss_pred ccccccCccccChhhHHHHhhhhhCCCCCcccccccc
Q psy4272 118 LTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSY 154 (575)
Q Consensus 118 ~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk 154 (575)
+.|..||+.|..... . +.|+.||.
T Consensus 71 ~~C~~Cg~~~~~~~~------------~-~~CP~Cgs 94 (115)
T TIGR00100 71 CECEDCSEEVSPEID------------L-YRCPKCHG 94 (115)
T ss_pred EEcccCCCEEecCCc------------C-ccCcCCcC
Confidence 678888877765432 3 67888874
No 249
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=23.98 E-value=98 Score=29.05 Aligned_cols=47 Identities=23% Similarity=0.174 Sum_probs=34.2
Q ss_pred cCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhh
Q psy4272 329 VYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKR 380 (575)
Q Consensus 329 ~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk 380 (575)
.++..+..+|.-.|-.. ...+++|..+|++...|+.++..-|.+.|+
T Consensus 106 ~L~~~~r~i~~l~~~~g-----~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 152 (181)
T PRK09637 106 ALPEKYAEALRLTELEG-----LSQKEIAEKLGLSLSGAKSRVQRGRVKLKE 152 (181)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 45666667766554332 357789999999999999999766666665
No 250
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=23.91 E-value=1e+02 Score=28.07 Aligned_cols=47 Identities=15% Similarity=0.212 Sum_probs=35.2
Q ss_pred cCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhc
Q psy4272 329 VYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRT 381 (575)
Q Consensus 329 ~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~ 381 (575)
.++..+..+|.-.| .. ..-.++|..+|++...|+.+...-|.+.|+.
T Consensus 112 ~L~~~~r~il~l~~-~g-----~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~ 158 (166)
T PRK09639 112 KMTERDRTVLLLRF-SG-----YSYKEIAEALGIKESSVGTTLARAKKKFRKI 158 (166)
T ss_pred cCCHHHHHHHHHHH-cC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 45666777776666 33 3567899999999999999997666666653
No 251
>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=23.71 E-value=1.3e+02 Score=27.36 Aligned_cols=48 Identities=19% Similarity=0.189 Sum_probs=37.9
Q ss_pred cccCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhh
Q psy4272 327 RQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKR 380 (575)
Q Consensus 327 Rt~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk 380 (575)
.+.++..|..+|.-. ... ....++|..+|++...|..|-+.-|.|.++
T Consensus 4 ~~~Lte~qr~VL~Lr-~~G-----lTq~EIAe~LgiS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 4 KTFLTERQIKVLELR-EKG-----LSQKEIAKELKTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred cCCCCHHHHHHHHHH-HcC-----CCHHHHHHHHCcCHHHHHHHHHhHHHHHHH
Confidence 467889999999774 222 357899999999999999998777777665
No 252
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=23.68 E-value=38 Score=29.59 Aligned_cols=24 Identities=17% Similarity=0.285 Sum_probs=15.5
Q ss_pred ccccccCccccChhhHHHHhhhhhCCCCCcccccccc
Q psy4272 118 LTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSY 154 (575)
Q Consensus 118 ~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk 154 (575)
+.|..||..|.... .. |.|+.||.
T Consensus 71 ~~C~~Cg~~~~~~~------------~~-~~CP~Cgs 94 (113)
T PRK12380 71 AWCWDCSQVVEIHQ------------HD-AQCPHCHG 94 (113)
T ss_pred EEcccCCCEEecCC------------cC-ccCcCCCC
Confidence 67888886665432 23 66888873
No 253
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=23.61 E-value=86 Score=29.17 Aligned_cols=48 Identities=15% Similarity=0.135 Sum_probs=34.9
Q ss_pred cCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhc
Q psy4272 329 VYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRT 381 (575)
Q Consensus 329 ~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~ 381 (575)
.+++.+..+|...|-. ...-+++|..+|++...|++++..-|.|.|+.
T Consensus 136 ~L~~~~r~v~~l~~~~-----g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 136 ALPPKYRMVIVLKYME-----DLSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred hCCHHHhHHhhhHHhc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4566666676654332 34577899999999999999998777766653
No 254
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=23.51 E-value=36 Score=34.43 Aligned_cols=43 Identities=21% Similarity=0.455 Sum_probs=27.4
Q ss_pred CCCCCCcchhhcchhHHHHHhhhcCCCCccccc-ccCccccChhhHHHHhhhhhCCCCCcccccccccc
Q psy4272 89 SPLKAKLSDYENKMKNVRESIRQKRLAQGLTCL-QCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSYRA 156 (575)
Q Consensus 89 ~~C~~C~~~f~~~~~~L~~H~r~H~~~kp~~C~-~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk~F 156 (575)
-.|.||...|.-. |. -||..|.... +|.|.|+.| -|+.|..-|
T Consensus 26 lrC~IC~~~i~ip------------------~~TtCgHtFCslC-----IR~hL~~qp--~CP~Cr~~~ 69 (391)
T COG5432 26 LRCRICDCRISIP------------------CETTCGHTFCSLC-----IRRHLGTQP--FCPVCREDP 69 (391)
T ss_pred HHhhhhhheeecc------------------eecccccchhHHH-----HHHHhcCCC--CCccccccH
Confidence 3588887665433 33 3787776542 566777777 488886543
No 255
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=23.31 E-value=24 Score=29.54 Aligned_cols=32 Identities=22% Similarity=0.561 Sum_probs=20.9
Q ss_pred CcccccccCccccChhhHHHHhhhhhCCCCCcccccccccccC
Q psy4272 116 QGLTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSYRARH 158 (575)
Q Consensus 116 kp~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk~F~~ 158 (575)
..|.|+.||+.-.. |.-+|. +.|..|++.|.-
T Consensus 34 ~ky~Cp~Cgk~~vk--------R~a~GI---W~C~~C~~~~AG 65 (90)
T PF01780_consen 34 AKYTCPFCGKTSVK--------RVATGI---WKCKKCGKKFAG 65 (90)
T ss_dssp S-BEESSSSSSEEE--------EEETTE---EEETTTTEEEE-
T ss_pred CCCcCCCCCCceeE--------EeeeEE---eecCCCCCEEeC
Confidence 45899999975322 334443 889999988753
No 256
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=23.19 E-value=1e+02 Score=27.93 Aligned_cols=48 Identities=17% Similarity=0.042 Sum_probs=34.9
Q ss_pred cCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhc
Q psy4272 329 VYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRT 381 (575)
Q Consensus 329 ~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~ 381 (575)
.++..|..+|.-.|-.. ..-.++|..+|++...|+++...-|.|-|+.
T Consensus 112 ~L~~~~r~v~~l~~~~~-----~s~~eIA~~lgis~~tv~~~l~Rar~~L~~~ 159 (161)
T PRK12541 112 SLPLERRNVLLLRDYYG-----FSYKEIAEMTGLSLAKVKIELHRGRKETKSI 159 (161)
T ss_pred HCCHHHHHHhhhHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 46677777776654433 2467899999999999999987666666543
No 257
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=23.17 E-value=22 Score=32.63 Aligned_cols=32 Identities=28% Similarity=0.578 Sum_probs=20.5
Q ss_pred cccccccCccccChhhHHHHhhhhhCCCCCccccccccccc
Q psy4272 117 GLTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSYRAR 157 (575)
Q Consensus 117 p~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk~F~ 157 (575)
.|.|..|+..+.+ |.+. .... |.|..|+..|.
T Consensus 123 ~~~C~~C~~~~~r------~~~~--~~~~-~~C~~C~~~l~ 154 (157)
T PF10263_consen 123 VYRCPSCGREYKR------HRRS--KRKR-YRCGRCGGPLV 154 (157)
T ss_pred EEEcCCCCCEeee------eccc--chhh-EECCCCCCEEE
Confidence 4788888877633 3333 2234 88888886654
No 258
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=23.16 E-value=45 Score=27.80 Aligned_cols=27 Identities=26% Similarity=0.684 Sum_probs=16.6
Q ss_pred CcccccccCccccChhhHHHHhhhhhCCCCCccccccc
Q psy4272 116 QGLTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCS 153 (575)
Q Consensus 116 kp~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cg 153 (575)
+|-.|..||..|..- .+ .+| -+|+.|.
T Consensus 57 ~Pa~CkkCGfef~~~-~i---------k~p-SRCP~CK 83 (97)
T COG3357 57 RPARCKKCGFEFRDD-KI---------KKP-SRCPKCK 83 (97)
T ss_pred cChhhcccCcccccc-cc---------CCc-ccCCcch
Confidence 466788888777651 11 235 6777774
No 259
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=22.93 E-value=43 Score=23.25 Aligned_cols=25 Identities=20% Similarity=0.535 Sum_probs=20.9
Q ss_pred HHHHHHHhCCChhhhhhcccchhhh
Q psy4272 353 RKVLSKELGLTERQIKIWFQNRRMK 377 (575)
Q Consensus 353 r~~la~~l~l~~~~V~vWFqNrRak 377 (575)
..++|..+|++.+.|.-|.++.+..
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~~~ 27 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGKLK 27 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCCCC
Confidence 4678999999999999999776543
No 260
>KOG1813|consensus
Probab=22.73 E-value=51 Score=33.62 Aligned_cols=59 Identities=17% Similarity=0.172 Sum_probs=33.0
Q ss_pred CCCCCCCCCcchhhcchhHHHHHhhhcCCCCcccccccCccccChhhHHHHhhhhhCCCCCcccccccc----cccChhh
Q psy4272 86 TLPSPLKAKLSDYENKMKNVRESIRQKRLAQGLTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSY----RARHKHD 161 (575)
Q Consensus 86 ~~p~~C~~C~~~f~~~~~~L~~H~r~H~~~kp~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk----~F~~~~~ 161 (575)
..|+.|.+|.+.|.+.. -+.-+.|-|..| .|+.+++ . -+|-+|++ .|.....
T Consensus 239 ~~Pf~c~icr~~f~~pV---------vt~c~h~fc~~c--------a~~~~qk------~-~~c~vC~~~t~g~~~~ake 294 (313)
T KOG1813|consen 239 LLPFKCFICRKYFYRPV---------VTKCGHYFCEVC--------ALKPYQK------G-EKCYVCSQQTHGSFNVAKE 294 (313)
T ss_pred cCCccccccccccccch---------hhcCCceeehhh--------hcccccc------C-CcceecccccccccchHHH
Confidence 56777888887776652 111122444444 3433332 2 35777876 4666667
Q ss_pred HHHHHHh
Q psy4272 162 LKKHVTF 168 (575)
Q Consensus 162 L~~H~r~ 168 (575)
|..-+..
T Consensus 295 L~~~L~~ 301 (313)
T KOG1813|consen 295 LLVSLKL 301 (313)
T ss_pred HHHHHHh
Confidence 7666554
No 261
>cd00924 Cyt_c_Oxidase_Vb Cytochrome c oxidase subunit Vb. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Vb is one of three mammalian subunits that lacks a transmembrane region. Subunit Vb is located on the matrix side of the membrane and binds the regulatory subunit of protein kinase A. The abnormally extended conformation is stable only in the CcO assembly.
Probab=22.42 E-value=33 Score=29.17 Aligned_cols=23 Identities=13% Similarity=0.252 Sum_probs=17.7
Q ss_pred HHhhhcCCCCcccccccCccccCh
Q psy4272 107 ESIRQKRLAQGLTCLQCGRSYCRP 130 (575)
Q Consensus 107 ~H~r~H~~~kp~~C~~Cgk~F~~~ 130 (575)
..+..|.| ++++|..||..|.-.
T Consensus 70 ~W~~l~~g-~~~rC~eCG~~fkL~ 92 (97)
T cd00924 70 IWMWLEKG-KPKRCPECGHVFKLV 92 (97)
T ss_pred EEEEEeCC-CceeCCCCCcEEEEE
Confidence 44566777 799999999998753
No 262
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=22.40 E-value=57 Score=28.06 Aligned_cols=25 Identities=24% Similarity=0.519 Sum_probs=22.0
Q ss_pred ccc----cccCccccChhhHHHHhhhhhC
Q psy4272 118 LTC----LQCGRSYCRPYNLKRHIQYECG 142 (575)
Q Consensus 118 ~~C----~~Cgk~F~~~~~L~~H~r~H~g 142 (575)
|.| ..|+..+.....+.+|.+.++|
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 889 8999999999999999987654
No 263
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=22.34 E-value=48 Score=24.56 Aligned_cols=11 Identities=45% Similarity=1.373 Sum_probs=4.8
Q ss_pred ccccccCcccc
Q psy4272 118 LTCLQCGRSYC 128 (575)
Q Consensus 118 ~~C~~Cgk~F~ 128 (575)
+.|..||+.|-
T Consensus 19 ~~Cr~Cg~~~C 29 (57)
T cd00065 19 HHCRNCGRIFC 29 (57)
T ss_pred cccCcCcCCcC
Confidence 33444444443
No 264
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=22.26 E-value=1.1e+02 Score=28.43 Aligned_cols=47 Identities=11% Similarity=0.162 Sum_probs=33.1
Q ss_pred cCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhh
Q psy4272 329 VYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKR 380 (575)
Q Consensus 329 ~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk 380 (575)
.+++.+..++...|-.. ....++|..+|++...|++|-..-|.+.|+
T Consensus 133 ~L~~~~r~i~~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 179 (182)
T PRK12537 133 QLEPARRNCILHAYVDG-----CSHAEIAQRLGAPLGTVKAWIKRSLKALRE 179 (182)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCChhhHHHHHHHHHHHHHH
Confidence 35556666665555333 246789999999999999998766665554
No 265
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=22.15 E-value=90 Score=29.14 Aligned_cols=47 Identities=4% Similarity=-0.030 Sum_probs=31.8
Q ss_pred CCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhc
Q psy4272 330 YSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRT 381 (575)
Q Consensus 330 ~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~ 381 (575)
+++.+..++.-.| .....-.++|..+|++...|++|...-|.+-|+.
T Consensus 139 L~~~~r~v~~l~~-----~~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~ 185 (190)
T TIGR02939 139 LPEDLRTAITLRE-----LEGLSYEDIARIMDCPVGTVRSRIFRAREAIAIR 185 (190)
T ss_pred CCHHHhhhhhhhh-----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3444545554333 2334577899999999999999997666666554
No 266
>KOG2461|consensus
Probab=22.05 E-value=1.3e+02 Score=32.41 Aligned_cols=50 Identities=6% Similarity=-0.268 Sum_probs=24.1
Q ss_pred HHHHHhhhcCCCCcccccccCccccChhhHHHHhhhhhCCCCCcccccccc
Q psy4272 104 NVRESIRQKRLAQGLTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSY 154 (575)
Q Consensus 104 ~L~~H~r~H~~~kp~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk 154 (575)
.+..|...|.++.++.|..|...+.....+..+..+|+.... +.|..|++
T Consensus 346 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~ 395 (396)
T KOG2461|consen 346 IYTQSHSMEVAEPTDMAPNQIWKIYHTGVLGFLIITTDESEC-NNMSFVCK 395 (396)
T ss_pred chhhhhhcccCCCCcccccccccceeccccceeeeecccccc-ccccccCC
Confidence 334444455555554444443334444444444555555555 55555543
No 267
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=21.90 E-value=61 Score=23.22 Aligned_cols=22 Identities=18% Similarity=0.454 Sum_probs=17.4
Q ss_pred HHHHHHHHHhCCChhhhhhccc
Q psy4272 351 DRRKVLSKELGLTERQIKIWFQ 372 (575)
Q Consensus 351 ~~r~~la~~l~l~~~~V~vWFq 372 (575)
....++|..+|++...|.-|.+
T Consensus 18 ~s~~~ia~~lgvs~~Tv~~w~k 39 (50)
T PF13384_consen 18 WSIREIAKRLGVSRSTVYRWIK 39 (50)
T ss_dssp --HHHHHHHHTS-HHHHHHHHT
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 4567899999999999999975
No 268
>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=21.85 E-value=1.1e+02 Score=21.85 Aligned_cols=36 Identities=17% Similarity=0.272 Sum_probs=25.8
Q ss_pred CHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhccc
Q psy4272 331 SSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQ 372 (575)
Q Consensus 331 t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFq 372 (575)
+..+..++...+. .....++|..+|++...|+.|..
T Consensus 2 ~~~e~~i~~~~~~------~~s~~eia~~l~~s~~tv~~~~~ 37 (57)
T cd06170 2 TPREREVLRLLAE------GKTNKEIADILGISEKTVKTHLR 37 (57)
T ss_pred CHHHHHHHHHHHc------CCCHHHHHHHHCCCHHHHHHHHH
Confidence 4556666654332 12567889999999999999986
No 269
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=21.41 E-value=1.3e+02 Score=27.36 Aligned_cols=48 Identities=10% Similarity=0.191 Sum_probs=33.8
Q ss_pred cCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhc
Q psy4272 329 VYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRT 381 (575)
Q Consensus 329 ~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~ 381 (575)
.+++.+..+|.-.|-.. ....++|..+|++...|+.+..-.|.+.|+.
T Consensus 109 ~L~~~~r~v~~l~~~~~-----~s~~EIA~~lgis~~tV~~~l~ra~~~lr~~ 156 (163)
T PRK07037 109 ELPARTRYAFEMYRLHG-----ETQKDIARELGVSPTLVNFMIRDALVHCRKC 156 (163)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 45666666776554333 2477899999999999999876666665553
No 270
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=21.33 E-value=14 Score=42.11 Aligned_cols=72 Identities=11% Similarity=0.108 Sum_probs=0.0
Q ss_pred CCCCcchhhcchhHHHHHhhhcCCCCcc-----cccccCccccChhhHHHHhhhhhCCCCCcccccccccccChhhHHHH
Q psy4272 91 LKAKLSDYENKMKNVRESIRQKRLAQGL-----TCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSYRARHKHDLKKH 165 (575)
Q Consensus 91 C~~C~~~f~~~~~~L~~H~r~H~~~kp~-----~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk~F~~~~~L~~H 165 (575)
|..|-+.+... +.+.| .|..||-+|+--..|---+..-+-..- --|+.|.+.|....+-+-|
T Consensus 104 C~~Cl~Ei~dp------------~~rrY~YPF~~CT~CGPRfTIi~alPYDR~nTsM~~F-~lC~~C~~EY~dP~nRRfH 170 (750)
T COG0068 104 CEDCLEEIFDP------------NSRRYLYPFINCTNCGPRFTIIEALPYDRENTSMADF-PLCPFCDKEYKDPLNRRFH 170 (750)
T ss_pred hHHHHHHhcCC------------CCcceeccccccCCCCcceeeeccCCCCcccCccccC-cCCHHHHHHhcCccccccc
Q ss_pred HHhhccCcccchhhhhhhhhcccccCCCCCCCcchhhh
Q psy4272 166 VTFKHAAYLDHFQAVQEELEVTTKELSPGPKAENRHRF 203 (575)
Q Consensus 166 ~r~~H~~~~~~~~~~~~~~~~~t~e~sp~p~~~C~~C~ 203 (575)
... . .|..|+
T Consensus 171 AQp-------~---------------------aCp~CG 180 (750)
T COG0068 171 AQP-------I---------------------ACPKCG 180 (750)
T ss_pred ccc-------c---------------------cCcccC
No 271
>PRK05978 hypothetical protein; Provisional
Probab=21.31 E-value=41 Score=30.95 Aligned_cols=32 Identities=25% Similarity=0.337 Sum_probs=19.2
Q ss_pred ccccccCccccChhhHHHHhhhhhCCCCCcccccccccccCh
Q psy4272 118 LTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSYRARHK 159 (575)
Q Consensus 118 ~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk~F~~~ 159 (575)
-+|+.||+.=-.+..|+. + -.|+.||..|...
T Consensus 34 grCP~CG~G~LF~g~Lkv--------~--~~C~~CG~~~~~~ 65 (148)
T PRK05978 34 GRCPACGEGKLFRAFLKP--------V--DHCAACGEDFTHH 65 (148)
T ss_pred CcCCCCCCCccccccccc--------C--CCccccCCccccC
Confidence 468888865333333331 1 4688888777554
No 272
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=21.23 E-value=1.3e+02 Score=27.15 Aligned_cols=47 Identities=11% Similarity=0.069 Sum_probs=33.8
Q ss_pred cCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhh
Q psy4272 329 VYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKR 380 (575)
Q Consensus 329 ~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk 380 (575)
.++..+..++.-.|-.. ..-.++|..+|++...|+++...-|.+.|+
T Consensus 106 ~Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 152 (161)
T PRK09047 106 KLPARQREAFLLRYWED-----MDVAETAAAMGCSEGSVKTHCSRATHALAK 152 (161)
T ss_pred hCCHHHHHHHHHHHHhc-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46677777776654333 246789999999999999988765655554
No 273
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=21.07 E-value=55 Score=29.40 Aligned_cols=24 Identities=0% Similarity=-0.045 Sum_probs=19.8
Q ss_pred CCCCCcchhhcchhHHHHHhhhcCCCCc
Q psy4272 90 PLKAKLSDYENKMKNVRESIRQKRLAQG 117 (575)
Q Consensus 90 ~C~~C~~~f~~~~~~L~~H~r~H~~~kp 117 (575)
-|-+||+.|. .|++|..+|.|--|
T Consensus 78 icLEDGkkfK----SLKRHL~t~~gmTP 101 (148)
T COG4957 78 ICLEDGKKFK----SLKRHLTTHYGLTP 101 (148)
T ss_pred EEeccCcchH----HHHHHHhcccCCCH
Confidence 6999999994 67899999887655
No 274
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the PRK12529 RNA polymerase sigma factor; Provisional
Probab=21.03 E-value=1.3e+02 Score=28.02 Aligned_cols=48 Identities=6% Similarity=0.003 Sum_probs=36.4
Q ss_pred cCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhc
Q psy4272 329 VYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRT 381 (575)
Q Consensus 329 ~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~ 381 (575)
.+++.|..++.-.|-.. ..-+++|..||+++..|+++....+.+.+..
T Consensus 127 ~Lp~~~R~v~~L~~~~g-----~s~~EIA~~lgis~~tVk~~l~rAl~~~~~~ 174 (178)
T PRK12529 127 TLRPRVKQAFLMATLDG-----MKQKDIAQALDIALPTVKKYIHQAYVTCLSL 174 (178)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 46677777776655433 2567899999999999999998777776653
No 276
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=21.02 E-value=1.7e+02 Score=25.67 Aligned_cols=40 Identities=13% Similarity=0.413 Sum_probs=27.1
Q ss_pred cccCCHHHHH-HHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcc
Q psy4272 327 RQVYSSHQIV-ELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWF 371 (575)
Q Consensus 327 Rt~~t~~ql~-~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWF 371 (575)
|..|+.+... ++...+. +.+ ...++|.++|++..+|..|.
T Consensus 10 rr~ys~EfK~~aV~~~~~-~g~----sv~evA~e~gIs~~tl~~W~ 50 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFE-PGM----TVSLVARQHGVAASQLFLWR 50 (121)
T ss_pred CCCCCHHHHHHHHHHHHc-CCC----CHHHHHHHHCcCHHHHHHHH
Confidence 4457777644 4443444 322 35578999999999999995
No 277
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=20.91 E-value=1.3e+02 Score=28.03 Aligned_cols=50 Identities=8% Similarity=0.031 Sum_probs=36.3
Q ss_pred cCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhcCC
Q psy4272 329 VYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTHP 383 (575)
Q Consensus 329 ~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~~~ 383 (575)
.+++.+..++.-.|-.. ....++|..+|++...|++....-|.+.|+.-.
T Consensus 117 ~Lp~~~r~i~~l~~~e~-----~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 166 (179)
T PRK12543 117 KLPYKLRQVIILRYLHD-----YSQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQ 166 (179)
T ss_pred hCCHHHHHHHHHHHHcc-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 35566666666544333 256789999999999999999888888777543
No 278
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=20.87 E-value=70 Score=29.90 Aligned_cols=47 Identities=13% Similarity=0.239 Sum_probs=28.5
Q ss_pred ccccccCccccChh--hHH-----HHhhhhhCCCCCcccccccccccChhhHHHHHH
Q psy4272 118 LTCLQCGRSYCRPY--NLK-----RHIQYECGKAPQFPCLYCSYRARHKHDLKKHVT 167 (575)
Q Consensus 118 ~~C~~Cgk~F~~~~--~L~-----~H~r~H~gekp~~~C~~Cgk~F~~~~~L~~H~r 167 (575)
-.|++|+-.....+ ..+ .|.+.+. .- |.|..||+.|-..+++..-.+
T Consensus 98 ~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~--~f-~~C~~CgkiYW~GsHw~~m~~ 151 (165)
T COG1656 98 SRCPECNGELEKVSREEVKEKVPEKVYRNYE--EF-YRCPKCGKIYWKGSHWRRMVE 151 (165)
T ss_pred ccCcccCCEeccCcHHHHhhccchhhhhccc--ce-eECCCCcccccCchHHHHHHH
Confidence 36999987654332 221 1222222 33 779999999988887765444
No 279
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=20.85 E-value=1.1e+02 Score=29.99 Aligned_cols=48 Identities=13% Similarity=0.159 Sum_probs=36.6
Q ss_pred cCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhc
Q psy4272 329 VYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRT 381 (575)
Q Consensus 329 ~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~ 381 (575)
.+...+..+|...|... ....++|..+|++...|+.|...-|.|.|+.
T Consensus 184 ~L~~~~r~vl~l~~~~g-----~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 231 (236)
T PRK06986 184 SLPEREQLVLSLYYQEE-----LNLKEIGAVLGVSESRVSQIHSQAIKRLRAR 231 (236)
T ss_pred hCCHHHHHHHHhHhccC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 35666777776666433 3567899999999999999998888777764
No 280
>PF13518 HTH_28: Helix-turn-helix domain
Probab=20.84 E-value=63 Score=23.15 Aligned_cols=22 Identities=14% Similarity=0.569 Sum_probs=18.8
Q ss_pred HHHHHHHHhCCChhhhhhcccc
Q psy4272 352 RRKVLSKELGLTERQIKIWFQN 373 (575)
Q Consensus 352 ~r~~la~~l~l~~~~V~vWFqN 373 (575)
...++|..+|++..+|..|.+.
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~ 35 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKR 35 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHH
Confidence 3557899999999999999864
No 281
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=20.84 E-value=1e+02 Score=30.43 Aligned_cols=48 Identities=8% Similarity=0.124 Sum_probs=34.4
Q ss_pred CCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhcC
Q psy4272 330 YSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTH 382 (575)
Q Consensus 330 ~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~~ 382 (575)
++..|..+|.-.|-.. ....++|..+|++...|+++...-|.|.|+..
T Consensus 172 Lp~~~R~v~~L~~~eg-----~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l 219 (233)
T PRK12538 172 LPEQQRIAVILSYHEN-----MSNGEIAEVMDTTVAAVESLLKRGRQQLRDLL 219 (233)
T ss_pred CCHHHHHHhhhHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4555666655444332 35678999999999999999987777777643
No 282
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=20.80 E-value=1.2e+02 Score=27.48 Aligned_cols=48 Identities=10% Similarity=0.128 Sum_probs=34.7
Q ss_pred cCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcccchhhhhhhc
Q psy4272 329 VYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRT 381 (575)
Q Consensus 329 ~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWFqNrRak~kk~ 381 (575)
.++..+..+|...|-.. ..-.++|..+|++...|++|-..-|.+-|+.
T Consensus 110 ~L~~~~r~i~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 157 (162)
T TIGR02983 110 RLPARQRAVVVLRYYED-----LSEAQVAEALGISVGTVKSRLSRALARLREL 157 (162)
T ss_pred hCCHHHHHHhhhHHHhc-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 34566666666555332 3467899999999999999998777776663
No 283
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=20.69 E-value=58 Score=29.76 Aligned_cols=48 Identities=8% Similarity=0.082 Sum_probs=27.9
Q ss_pred ccccccCccccChhhHHHHhhhh-----hCCCCCcccccccccccChhhHHHHH
Q psy4272 118 LTCLQCGRSYCRPYNLKRHIQYE-----CGKAPQFPCLYCSYRARHKHDLKKHV 166 (575)
Q Consensus 118 ~~C~~Cgk~F~~~~~L~~H~r~H-----~gekp~~~C~~Cgk~F~~~~~L~~H~ 166 (575)
-.|..|+..+..-..-..--.+. ..+.- +.|+.|||.|-..+++.+-.
T Consensus 92 sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f-~~C~~C~kiyW~GsH~~~~~ 144 (147)
T PF01927_consen 92 SRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEF-WRCPGCGKIYWEGSHWRRME 144 (147)
T ss_pred CccCCCCcEeeechhhccccccCccccccCCeE-EECCCCCCEecccccHHHHH
Confidence 47999987664432211000111 12234 78999999998887766543
No 284
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=20.42 E-value=73 Score=32.63 Aligned_cols=47 Identities=17% Similarity=0.338 Sum_probs=30.9
Q ss_pred cccccCccccChhhHHHHhhhhhCCCCCcccccccccccChhhHHHHHHh
Q psy4272 119 TCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSYRARHKHDLKKHVTF 168 (575)
Q Consensus 119 ~C~~Cgk~F~~~~~L~~H~r~H~gekp~~~C~~Cgk~F~~~~~L~~H~r~ 168 (575)
.|-.|.-.|.....-..-.. +..-. |.|+.|...|....+.-.|...
T Consensus 364 ~Cf~CQ~~fp~~~~~~~~~~--~ss~r-Y~Ce~CK~~FC~dCdvfiHe~L 410 (421)
T COG5151 364 HCFVCQGPFPKPPVSPFDES--TSSGR-YQCELCKSTFCSDCDVFIHETL 410 (421)
T ss_pred cceeccCCCCCCCCCccccc--ccccc-eechhhhhhhhhhhHHHHHHHH
Confidence 47777777766533211111 12234 9999999999998888888776
No 285
>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=20.00 E-value=1.2e+02 Score=21.60 Aligned_cols=38 Identities=16% Similarity=0.266 Sum_probs=27.6
Q ss_pred cCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChhhhhhcc
Q psy4272 329 VYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWF 371 (575)
Q Consensus 329 ~~t~~ql~~L~~~F~~~~~p~~~~r~~la~~l~l~~~~V~vWF 371 (575)
.++.++.+.+.+++... ....++|..+|++...|.-|+
T Consensus 5 ~~~~~~~~~i~~l~~~G-----~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 5 KLSKEQIEEIKELYAEG-----MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHHHHHH
T ss_pred CCCHHHHHHHHHHHHCC-----CCHHHHHHHHCcCHHHHHHHH
Confidence 46666777777777766 246789999999999987765
Done!