Query psy15165
Match_columns 606
No_of_seqs 658 out of 3671
Neff 9.7
Searched_HMMs 46136
Date Fri Aug 16 22:14:09 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15165.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15165hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1074|consensus 99.9 1.1E-28 2.4E-33 254.2 6.0 242 336-588 604-936 (958)
2 KOG2462|consensus 99.9 1.5E-27 3.3E-32 218.0 6.5 136 396-581 129-265 (279)
3 KOG2462|consensus 99.9 1.4E-25 2.9E-30 205.2 5.3 139 249-424 131-270 (279)
4 KOG3608|consensus 99.9 3.4E-24 7.3E-29 200.1 13.3 230 279-586 135-379 (467)
5 KOG3623|consensus 99.9 1.3E-25 2.9E-30 227.2 3.9 121 249-391 211-331 (1007)
6 KOG3608|consensus 99.9 1.7E-23 3.7E-28 195.5 10.1 239 249-571 135-398 (467)
7 KOG1074|consensus 99.9 9.9E-24 2.1E-28 217.9 4.9 243 311-561 604-936 (958)
8 KOG3623|consensus 99.8 1.2E-20 2.6E-25 191.7 4.0 101 214-324 210-321 (1007)
9 KOG3576|consensus 99.6 1.1E-16 2.4E-21 138.7 3.0 114 442-587 115-240 (267)
10 KOG3576|consensus 99.6 2.1E-16 4.6E-21 137.0 3.0 126 335-472 115-240 (267)
11 PLN03086 PRLI-interacting fact 99.2 3.7E-11 8.1E-16 125.0 9.7 145 370-584 408-565 (567)
12 PHA00733 hypothetical protein 99.1 4.6E-11 9.9E-16 101.4 4.1 83 500-585 40-125 (128)
13 PLN03086 PRLI-interacting fact 99.1 5.1E-10 1.1E-14 116.6 9.3 101 370-524 454-564 (567)
14 PHA02768 hypothetical protein; 98.9 3.3E-10 7.1E-15 78.2 1.9 42 533-576 6-48 (55)
15 PHA00733 hypothetical protein 98.8 4.1E-09 8.8E-14 89.6 5.6 87 442-557 38-124 (128)
16 KOG3993|consensus 98.7 4.5E-09 9.8E-14 102.1 1.3 114 337-469 267-381 (500)
17 KOG3993|consensus 98.7 5.2E-09 1.1E-13 101.7 1.4 84 336-419 355-480 (500)
18 PHA02768 hypothetical protein; 98.7 7.5E-09 1.6E-13 71.6 1.6 45 369-415 5-49 (55)
19 PF13465 zf-H2C2_2: Zinc-finge 98.6 3.2E-08 6.9E-13 58.4 1.9 25 547-571 1-26 (26)
20 PHA00616 hypothetical protein 98.4 1.4E-07 3E-12 61.9 2.1 33 532-564 1-33 (44)
21 PF13465 zf-H2C2_2: Zinc-finge 98.4 1.3E-07 2.8E-12 55.8 1.7 26 384-409 1-26 (26)
22 PHA00616 hypothetical protein 98.3 2.8E-07 6.1E-12 60.5 0.8 32 560-591 1-33 (44)
23 PHA00732 hypothetical protein 98.1 1.5E-06 3.1E-11 66.7 2.7 48 501-557 2-49 (79)
24 PHA00732 hypothetical protein 98.1 2.5E-06 5.4E-11 65.4 3.1 47 532-584 1-49 (79)
25 PF05605 zf-Di19: Drought indu 98.0 6.8E-06 1.5E-10 58.5 4.3 51 501-556 3-53 (54)
26 PF01352 KRAB: KRAB box; Inte 98.0 9.3E-07 2E-11 58.1 -0.6 22 2-23 11-41 (41)
27 PF05605 zf-Di19: Drought indu 98.0 9.6E-06 2.1E-10 57.7 4.4 51 249-302 3-53 (54)
28 PF00096 zf-C2H2: Zinc finger, 97.7 1.5E-05 3.3E-10 45.6 1.6 23 533-555 1-23 (23)
29 PF12756 zf-C2H2_2: C2H2 type 97.4 7.6E-05 1.6E-09 61.2 1.8 72 502-582 1-73 (100)
30 PF00096 zf-C2H2: Zinc finger, 97.3 0.00011 2.4E-09 41.9 1.5 21 371-391 2-22 (23)
31 PF13894 zf-C2H2_4: C2H2-type 97.3 0.00014 3E-09 42.0 1.8 23 533-555 1-23 (24)
32 PF13912 zf-C2H2_6: C2H2-type 97.2 0.00018 3.8E-09 43.0 1.4 24 533-556 2-25 (27)
33 KOG2231|consensus 97.0 0.0012 2.6E-08 70.5 6.5 80 501-592 183-276 (669)
34 COG5189 SFP1 Putative transcri 97.0 0.0002 4.2E-09 67.7 0.5 55 498-552 347-418 (423)
35 PF13894 zf-C2H2_4: C2H2-type 97.0 0.00048 1E-08 39.6 2.0 22 280-301 2-23 (24)
36 PF12756 zf-C2H2_2: C2H2 type 97.0 0.00042 9E-09 56.7 2.3 74 216-302 1-74 (100)
37 COG5189 SFP1 Putative transcri 96.9 0.00028 6E-09 66.7 0.9 52 529-580 346-419 (423)
38 PF13912 zf-C2H2_6: C2H2-type 96.9 0.00049 1.1E-08 41.0 1.5 25 560-584 1-26 (27)
39 PF09237 GAGA: GAGA factor; I 96.9 0.00076 1.6E-08 45.4 2.3 33 528-560 20-52 (54)
40 KOG2231|consensus 96.7 0.0028 6.1E-08 67.8 6.4 81 215-303 100-207 (669)
41 smart00355 ZnF_C2H2 zinc finge 96.6 0.0015 3.4E-08 38.2 2.3 23 533-555 1-23 (26)
42 KOG1146|consensus 96.6 0.0005 1.1E-08 77.4 -0.3 84 335-418 516-639 (1406)
43 PF13909 zf-H2C2_5: C2H2-type 96.3 0.0025 5.5E-08 36.7 1.5 23 533-556 1-23 (24)
44 PRK04860 hypothetical protein; 96.2 0.0019 4.1E-08 57.1 1.4 38 532-573 119-157 (160)
45 COG5236 Uncharacterized conser 96.0 0.011 2.3E-07 56.9 5.3 83 214-304 151-246 (493)
46 PF12874 zf-met: Zinc-finger o 95.9 0.0043 9.3E-08 36.1 1.3 22 533-554 1-22 (25)
47 PF09237 GAGA: GAGA factor; I 95.8 0.0082 1.8E-07 40.5 2.4 33 365-397 20-52 (54)
48 smart00355 ZnF_C2H2 zinc finge 95.6 0.015 3.3E-07 33.8 2.9 24 445-468 1-24 (26)
49 PF13909 zf-H2C2_5: C2H2-type 95.5 0.011 2.3E-07 34.0 2.0 23 279-302 1-23 (24)
50 PF12874 zf-met: Zinc-finger o 95.3 0.01 2.2E-07 34.5 1.5 20 371-390 2-21 (25)
51 COG5236 Uncharacterized conser 95.2 0.036 7.8E-07 53.4 5.4 123 445-584 152-306 (493)
52 KOG2482|consensus 95.0 0.08 1.7E-06 51.2 7.2 147 262-418 129-355 (423)
53 PRK04860 hypothetical protein; 95.0 0.0099 2.2E-07 52.6 1.0 38 369-410 119-156 (160)
54 KOG2785|consensus 94.7 0.05 1.1E-06 53.7 5.1 50 532-581 166-242 (390)
55 PF12171 zf-C2H2_jaz: Zinc-fin 94.5 0.025 5.5E-07 33.5 1.6 21 215-235 2-22 (27)
56 PF12171 zf-C2H2_jaz: Zinc-fin 94.4 0.023 4.9E-07 33.7 1.4 21 370-390 2-22 (27)
57 KOG2785|consensus 94.2 0.08 1.7E-06 52.3 5.4 55 336-390 165-241 (390)
58 KOG1146|consensus 94.1 0.021 4.6E-07 64.9 1.3 79 501-582 437-541 (1406)
59 smart00349 KRAB krueppel assoc 93.8 0.019 4.2E-07 39.6 0.3 34 10-43 28-61 (61)
60 KOG2482|consensus 93.7 0.17 3.6E-06 49.1 6.3 145 429-582 129-357 (423)
61 COG5048 FOG: Zn-finger [Genera 93.5 0.029 6.3E-07 59.5 1.1 70 506-577 394-463 (467)
62 KOG2893|consensus 93.5 0.024 5.3E-07 51.6 0.4 47 502-556 12-59 (341)
63 PF13913 zf-C2HC_2: zinc-finge 92.0 0.11 2.4E-06 30.1 1.7 18 502-520 4-21 (25)
64 PF13913 zf-C2HC_2: zinc-finge 91.2 0.16 3.4E-06 29.5 1.7 20 534-554 4-23 (25)
65 smart00451 ZnF_U1 U1-like zinc 90.3 0.18 3.9E-06 31.9 1.6 22 532-553 3-24 (35)
66 COG5048 FOG: Zn-finger [Genera 89.3 0.13 2.7E-06 54.6 0.4 72 500-574 289-368 (467)
67 smart00451 ZnF_U1 U1-like zinc 88.4 0.4 8.7E-06 30.2 2.1 22 500-521 3-24 (35)
68 TIGR00622 ssl1 transcription f 88.3 0.65 1.4E-05 38.0 3.7 93 442-556 13-105 (112)
69 KOG4173|consensus 88.1 0.15 3.2E-06 45.7 -0.0 52 502-553 108-167 (253)
70 PF12013 DUF3505: Protein of u 87.6 0.52 1.1E-05 39.1 2.9 23 501-524 12-34 (109)
71 COG4049 Uncharacterized protei 86.8 0.24 5.2E-06 34.1 0.4 26 499-524 16-41 (65)
72 KOG4173|consensus 86.2 0.34 7.3E-06 43.5 1.1 76 501-583 80-170 (253)
73 KOG2893|consensus 86.1 0.25 5.4E-06 45.2 0.3 62 530-596 9-71 (341)
74 cd00350 rubredoxin_like Rubred 84.7 0.45 9.7E-06 29.7 0.9 10 396-405 16-25 (33)
75 COG4049 Uncharacterized protei 83.7 0.39 8.4E-06 33.1 0.3 29 528-556 13-41 (65)
76 PF09538 FYDLN_acid: Protein o 82.7 0.81 1.7E-05 37.5 1.8 14 531-544 25-38 (108)
77 KOG2186|consensus 81.0 1 2.2E-05 42.1 2.0 48 533-583 4-52 (276)
78 PF09986 DUF2225: Uncharacteri 79.2 0.62 1.3E-05 43.8 0.0 45 501-545 6-61 (214)
79 PF12013 DUF3505: Protein of u 76.3 2.8 6.2E-05 34.6 3.2 21 373-393 88-108 (109)
80 TIGR02300 FYDLN_acid conserved 73.1 2.5 5.3E-05 35.3 2.0 15 531-545 25-39 (129)
81 PF09986 DUF2225: Uncharacteri 71.0 1.1 2.3E-05 42.2 -0.7 43 368-410 4-61 (214)
82 TIGR02098 MJ0042_CXXC MJ0042 f 70.6 2.1 4.5E-05 27.6 0.8 34 501-543 3-36 (38)
83 PHA00626 hypothetical protein 69.4 2.5 5.4E-05 29.4 1.0 12 501-512 24-35 (59)
84 cd00729 rubredoxin_SM Rubredox 69.3 2.2 4.8E-05 26.8 0.7 9 397-405 18-26 (34)
85 TIGR00622 ssl1 transcription f 69.1 6.6 0.00014 32.2 3.6 80 500-583 15-105 (112)
86 PRK00464 nrdR transcriptional 68.8 1.4 3.1E-05 38.7 -0.3 12 533-544 29-40 (154)
87 KOG2186|consensus 66.5 2.5 5.5E-05 39.5 0.8 44 370-416 4-47 (276)
88 COG1198 PriA Primosomal protei 66.5 5 0.00011 44.7 3.2 39 501-568 445-484 (730)
89 PF13717 zinc_ribbon_4: zinc-r 66.2 5.1 0.00011 25.5 1.9 11 339-349 4-14 (36)
90 PF13719 zinc_ribbon_5: zinc-r 66.1 3.4 7.4E-05 26.5 1.1 34 501-543 3-36 (37)
91 PF15269 zf-C2H2_7: Zinc-finge 65.0 5.2 0.00011 26.3 1.8 25 245-269 17-41 (54)
92 COG2888 Predicted Zn-ribbon RN 64.7 4.6 0.0001 28.6 1.6 31 501-540 28-58 (61)
93 PF02892 zf-BED: BED zinc fing 63.0 4.9 0.00011 26.9 1.6 11 533-543 17-27 (45)
94 smart00659 RPOLCX RNA polymera 61.1 4.5 9.7E-05 27.1 1.0 11 370-380 3-13 (44)
95 COG1592 Rubrerythrin [Energy p 60.4 5.5 0.00012 35.4 1.7 25 336-377 133-157 (166)
96 smart00614 ZnF_BED BED zinc fi 60.1 6.1 0.00013 27.3 1.6 21 501-521 19-44 (50)
97 PRK09678 DNA-binding transcrip 58.6 2.8 6E-05 31.5 -0.3 16 557-572 24-42 (72)
98 smart00531 TFIIE Transcription 58.2 7 0.00015 34.3 2.0 35 500-542 99-133 (147)
99 PRK14890 putative Zn-ribbon RN 57.8 7.1 0.00015 27.8 1.6 12 442-453 46-57 (59)
100 PRK00398 rpoP DNA-directed RNA 57.3 7.2 0.00016 26.4 1.6 10 338-347 4-13 (46)
101 smart00734 ZnF_Rad18 Rad18-lik 56.8 9.6 0.00021 22.2 1.8 19 502-521 3-21 (26)
102 PF09538 FYDLN_acid: Protein o 56.4 7 0.00015 32.1 1.6 30 476-513 10-39 (108)
103 smart00531 TFIIE Transcription 56.3 13 0.00028 32.7 3.4 36 336-379 98-133 (147)
104 COG1592 Rubrerythrin [Energy p 56.3 6.8 0.00015 34.8 1.6 23 500-539 134-156 (166)
105 TIGR00373 conserved hypothetic 55.4 11 0.00024 33.5 2.9 18 336-353 108-125 (158)
106 COG5151 SSL1 RNA polymerase II 53.6 14 0.0003 35.7 3.3 21 442-462 320-340 (421)
107 PRK06266 transcription initiat 53.5 6.1 0.00013 35.9 1.0 16 336-351 116-131 (178)
108 KOG2807|consensus 52.1 22 0.00048 34.8 4.4 24 442-465 288-311 (378)
109 PF15269 zf-C2H2_7: Zinc-finge 51.7 14 0.0003 24.4 2.0 21 501-521 21-41 (54)
110 TIGR00373 conserved hypothetic 51.5 15 0.00032 32.7 3.0 33 366-407 106-138 (158)
111 PF05443 ROS_MUCR: ROS/MUCR tr 50.8 7.1 0.00015 33.3 0.9 24 561-587 73-97 (132)
112 PF04959 ARS2: Arsenite-resist 50.5 8.6 0.00019 35.9 1.4 29 496-524 73-101 (214)
113 TIGR02605 CxxC_CxxC_SSSS putat 49.5 4.7 0.0001 28.1 -0.4 11 370-380 6-16 (52)
114 smart00834 CxxC_CXXC_SSSS Puta 49.4 4.6 0.0001 26.3 -0.4 11 370-380 6-16 (41)
115 PF08788 NHR2: NHR2 domain lik 48.7 3.4 7.3E-05 29.5 -1.2 11 3-13 15-25 (67)
116 PF09723 Zn-ribbon_8: Zinc rib 48.6 7.2 0.00016 25.8 0.4 11 370-380 6-16 (42)
117 PRK06266 transcription initiat 48.2 8.8 0.00019 34.9 1.1 16 214-229 117-132 (178)
118 TIGR01384 TFS_arch transcripti 48.1 9.4 0.0002 31.2 1.2 14 443-456 15-28 (104)
119 PRK00464 nrdR transcriptional 46.9 9.5 0.00021 33.6 1.1 18 501-518 29-46 (154)
120 COG1198 PriA Primosomal protei 45.0 14 0.00031 41.3 2.2 28 364-406 457-484 (730)
121 COG1996 RPC10 DNA-directed RNA 44.6 10 0.00022 26.0 0.7 10 370-379 7-16 (49)
122 PF05443 ROS_MUCR: ROS/MUCR tr 44.5 10 0.00022 32.4 0.8 25 533-560 73-97 (132)
123 PRK04023 DNA polymerase II lar 44.1 21 0.00045 40.8 3.3 10 444-453 626-635 (1121)
124 KOG1280|consensus 43.2 26 0.00056 34.7 3.4 26 278-303 79-104 (381)
125 cd00730 rubredoxin Rubredoxin; 42.6 7.6 0.00017 26.8 -0.2 12 215-226 2-13 (50)
126 PF00301 Rubredoxin: Rubredoxi 42.5 6.7 0.00015 26.7 -0.4 13 215-227 2-14 (47)
127 PF03604 DNA_RNApol_7kD: DNA d 41.4 16 0.00034 22.6 1.1 12 442-453 15-26 (32)
128 COG1997 RPL43A Ribosomal prote 41.4 15 0.00032 28.5 1.2 13 531-543 52-64 (89)
129 TIGR02300 FYDLN_acid conserved 41.0 17 0.00037 30.5 1.6 17 501-517 27-43 (129)
130 PF10571 UPF0547: Uncharacteri 40.8 16 0.00034 21.4 1.0 11 501-511 15-25 (26)
131 PRK09678 DNA-binding transcrip 40.4 9 0.00019 28.8 -0.1 18 394-411 24-43 (72)
132 KOG4377|consensus 40.1 23 0.0005 35.8 2.6 24 561-584 402-428 (480)
133 PHA02644 hypothetical protein; 39.3 27 0.00058 26.4 2.3 35 12-46 1-35 (112)
134 smart00440 ZnF_C2C2 C2C2 Zinc 39.3 17 0.00037 23.8 1.1 11 501-511 29-39 (40)
135 COG4530 Uncharacterized protei 39.0 18 0.00038 29.2 1.3 13 530-542 24-36 (129)
136 PF12907 zf-met2: Zinc-binding 38.1 20 0.00043 23.5 1.2 26 249-274 2-30 (40)
137 COG2331 Uncharacterized protei 36.9 15 0.00033 27.4 0.7 11 214-224 12-22 (82)
138 KOG4167|consensus 36.8 11 0.00024 41.0 -0.1 25 532-556 792-816 (907)
139 PRK04023 DNA polymerase II lar 36.8 28 0.00061 39.8 2.9 10 337-346 626-635 (1121)
140 PF14353 CpXC: CpXC protein 35.9 3.5 7.5E-05 35.3 -3.4 21 397-417 38-58 (128)
141 PF06524 NOA36: NOA36 protein; 35.8 20 0.00043 33.9 1.4 97 271-393 137-233 (314)
142 KOG2807|consensus 33.9 39 0.00085 33.2 3.0 20 501-520 291-310 (378)
143 PRK14714 DNA polymerase II lar 33.3 42 0.0009 39.6 3.6 53 445-543 668-720 (1337)
144 PRK00432 30S ribosomal protein 33.3 23 0.0005 24.5 1.0 11 532-542 37-47 (50)
145 PF01096 TFIIS_C: Transcriptio 33.1 14 0.00029 24.1 -0.1 10 501-510 29-38 (39)
146 KOG1280|consensus 33.1 41 0.00089 33.4 3.0 41 442-483 77-117 (381)
147 COG3357 Predicted transcriptio 32.5 23 0.00049 27.6 1.0 14 396-409 57-70 (97)
148 PF09416 UPF1_Zn_bind: RNA hel 32.3 34 0.00075 29.9 2.2 43 364-406 9-69 (152)
149 KOG2593|consensus 32.1 29 0.00062 35.6 1.9 34 501-541 129-162 (436)
150 COG5188 PRP9 Splicing factor 3 32.0 43 0.00093 33.2 3.0 26 368-393 237-264 (470)
151 COG3779 Uncharacterized protei 31.8 27 0.00058 29.3 1.3 42 15-57 78-119 (151)
152 PF04959 ARS2: Arsenite-resist 31.3 20 0.00044 33.5 0.7 22 214-235 77-98 (214)
153 COG4957 Predicted transcriptio 31.2 28 0.00061 29.3 1.4 24 534-560 78-101 (148)
154 PRK14873 primosome assembly pr 31.0 35 0.00075 38.2 2.5 8 446-453 385-392 (665)
155 PF08274 PhnA_Zn_Ribbon: PhnA 30.9 21 0.00046 21.7 0.5 10 396-405 18-27 (30)
156 PRK14714 DNA polymerase II lar 30.9 41 0.00088 39.7 3.0 23 371-408 681-703 (1337)
157 KOG2907|consensus 30.2 33 0.00071 28.0 1.6 12 501-512 103-114 (116)
158 COG5188 PRP9 Splicing factor 3 29.9 31 0.00067 34.1 1.6 24 395-418 372-396 (470)
159 TIGR00595 priA primosomal prot 29.8 42 0.00092 36.2 2.9 9 445-453 214-222 (505)
160 KOG2272|consensus 29.8 57 0.0012 30.7 3.2 26 486-515 211-236 (332)
161 PF02176 zf-TRAF: TRAF-type zi 29.4 31 0.00068 24.6 1.3 27 382-408 23-53 (60)
162 PF06524 NOA36: NOA36 protein; 28.4 41 0.00089 31.9 2.1 83 332-418 137-230 (314)
163 COG4957 Predicted transcriptio 28.3 28 0.00061 29.3 0.9 25 370-397 77-101 (148)
164 cd07765 KRAB_A-box KRAB (Krupp 28.2 14 0.00031 21.6 -0.7 19 3-21 12-39 (40)
165 PF05290 Baculo_IE-1: Baculovi 28.2 30 0.00065 29.3 1.1 59 442-515 78-136 (140)
166 PHA02998 RNA polymerase subuni 27.6 34 0.00073 30.5 1.4 12 501-512 172-183 (195)
167 TIGR00595 priA primosomal prot 26.9 38 0.00082 36.6 1.9 24 367-405 238-261 (505)
168 PF03833 PolC_DP2: DNA polymer 26.6 22 0.00047 39.9 0.0 10 444-453 655-664 (900)
169 PLN00010 cyclin-dependent kina 26.4 30 0.00065 26.7 0.7 24 2-32 37-63 (86)
170 PRK14873 primosome assembly pr 26.3 41 0.00088 37.7 2.0 24 367-406 408-431 (665)
171 PRK03564 formate dehydrogenase 25.1 28 0.00062 34.5 0.5 14 396-409 251-264 (309)
172 COG3677 Transposase and inacti 24.8 83 0.0018 26.9 3.2 12 501-512 54-65 (129)
173 KOG3408|consensus 24.6 38 0.00081 28.1 1.0 20 532-551 57-76 (129)
174 COG1571 Predicted DNA-binding 24.6 41 0.00089 34.8 1.5 14 532-545 367-380 (421)
175 TIGR01206 lysW lysine biosynth 24.4 22 0.00048 25.1 -0.3 10 501-510 3-12 (54)
176 KOG2272|consensus 24.2 29 0.00063 32.6 0.4 13 533-545 222-234 (332)
177 PTZ00255 60S ribosomal protein 22.5 37 0.0008 26.8 0.6 13 531-543 53-65 (90)
178 PF09845 DUF2072: Zn-ribbon co 22.4 36 0.00079 28.8 0.6 15 397-411 1-15 (131)
179 PF07754 DUF1610: Domain of un 22.3 44 0.00095 19.2 0.7 9 500-508 16-24 (24)
180 KOG3408|consensus 22.2 53 0.0011 27.3 1.4 24 498-521 55-78 (129)
181 PRK03824 hypA hydrogenase nick 22.2 33 0.00072 29.6 0.3 11 338-348 71-81 (135)
182 TIGR00280 L37a ribosomal prote 21.9 33 0.00072 27.0 0.2 12 532-543 53-64 (91)
183 KOG2593|consensus 21.8 1.1E+02 0.0023 31.7 3.8 20 276-295 126-145 (436)
184 KOG4167|consensus 21.6 25 0.00055 38.4 -0.6 24 248-271 792-815 (907)
185 COG1594 RPB9 DNA-directed RNA 21.5 40 0.00087 28.0 0.7 11 501-511 101-111 (113)
186 PF08271 TF_Zn_Ribbon: TFIIB z 21.3 32 0.0007 22.8 0.1 8 501-508 20-27 (43)
187 PTZ00453 cyclin-dependent kina 21.3 39 0.00084 26.6 0.5 23 2-31 61-86 (96)
188 KOG3002|consensus 21.2 53 0.0011 32.6 1.5 55 501-563 81-139 (299)
189 PF01780 Ribosomal_L37ae: Ribo 21.0 32 0.0007 27.0 0.0 30 214-259 35-64 (90)
190 COG0068 HypF Hydrogenase matur 20.9 34 0.00073 37.6 0.1 15 339-353 125-139 (750)
191 COG1655 Uncharacterized protei 20.7 30 0.00065 32.2 -0.3 8 399-406 64-71 (267)
192 TIGR00244 transcriptional regu 20.4 57 0.0012 28.3 1.4 17 501-517 29-45 (147)
193 smart00504 Ubox Modified RING 20.3 1.4E+02 0.0031 21.1 3.4 46 398-456 2-47 (63)
194 PF07975 C1_4: TFIIH C1-like d 20.2 20 0.00044 24.9 -1.1 21 501-521 22-42 (51)
195 KOG4377|consensus 20.0 60 0.0013 33.0 1.6 19 450-468 409-427 (480)
No 1
>KOG1074|consensus
Probab=99.95 E-value=1.1e-28 Score=254.17 Aligned_cols=242 Identities=22% Similarity=0.357 Sum_probs=164.0
Q ss_pred cceecccCccccCCHHHHHHHHhccccccCCCCcccccccccccCchHHHHhhhhhcCCC----CccccC---cchhccC
Q psy15165 336 QYHVCPHCGKKFTRKAELQLHIKGIHLKHQLEKTYICEYCHKEFTFYNYLRRHMRVHTNE----KPYKCK---DCGAAFN 408 (606)
Q Consensus 336 ~~~~C~~C~~~f~~~~~l~~H~~~~h~~h~~~~~~~C~~C~k~f~~~~~L~~H~~~H~~~----~~~~C~---~C~~~f~ 408 (606)
.|.+|-+|-+.....++|+.|.+ +|+|++||+|.+||+.|+++.+|+.||.+|... .+|.|+ +|-+.|.
T Consensus 604 dPNqCiiC~rVlSC~saLqmHyr----tHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kft 679 (958)
T KOG1074|consen 604 DPNQCIICLRVLSCPSALQMHYR----THTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKKFT 679 (958)
T ss_pred Cccceeeeeecccchhhhhhhhh----cccCcCccccccccchhccccchhhcccccccCccccccccCCchhhhccccc
Confidence 35789999999999999999999 899999999999999999999999999999754 347899 9999999
Q ss_pred ChhHHhcccccCCCCCCChHHHHHHHHHhcCCCCCcccCCCCCCccCCHHHHHHHHHHhcCCCC----------------
Q psy15165 409 HNVSLKNHKNSSCPKLYSYETYLKHLKTNHHGYEVSNLCYICGFFSAKRSTLAHHIQDHIQPRM---------------- 472 (606)
Q Consensus 409 ~~~~L~~H~~~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~~~L~~H~~~h~~~~~---------------- 472 (606)
....|..|++.+-+-....-.... .+....-.|..|.+.|.....+..++..|.+...
T Consensus 680 n~V~lpQhIriH~~~~~s~g~~a~------e~~~~adq~~~~qk~~~~a~~f~~~~se~~~~~s~~~~~~~~~t~t~~~~ 753 (958)
T KOG1074|consen 680 NAVTLPQHIRIHLGGQISNGGTAA------EGILAADQCSSCQKTFSDARSFSQQISEQPSPESEPDEQMDERTETEELD 753 (958)
T ss_pred ccccccceEEeecCCCCCCCcccc------cccchhcccchhhhcccccccchhhhhccCCcccCCcccccccccccccc
Confidence 999999998753311111000000 0001224599999999999999999887732211
Q ss_pred -CcCccccccccch---hhhhc-----------------------ccccccCCccc-cCCCCCCcCCChHHHHHhhhccc
Q psy15165 473 -KQKQICEICCAEV---YHING-----------------------HIKDKHSGFFL-QCPHCPKTFPRKTELSNHIKGIH 524 (606)
Q Consensus 473 -~~~~~C~~c~~~~---~~l~~-----------------------H~~~~h~~~~~-~C~~C~~~f~~~~~L~~H~~~~H 524 (606)
..-..+..|+... ..+.. +.....++.+. .+..++-.........- +.+.-
T Consensus 754 ~tp~~~e~~~~~~~~~e~~i~~~g~te~asa~~~~vg~~s~~~~~~~~~~T~~k~~~~~~~~~~~~~~~v~~~p-vl~~~ 832 (958)
T KOG1074|consen 754 VTPPPPENSCGRELEGEMAISVRGSTEEASANLDEVGTVSAAGEAGEEDDTSEKPTQASSFPGEILAPSVNMDP-VLWNQ 832 (958)
T ss_pred cCCCccccccccccCcccccccccchhhhhcChhhhcCccccchhhhhcccCCCCcccccCCCcCCccccccCc-hhhcc
Confidence 1113344454111 00000 01111222333 56666644333221110 00000
Q ss_pred ---------------ccCCC------------------------CccccccccchhccChhhHHHHHhhhcCCCCcccc-
Q psy15165 525 ---------------MKHEL------------------------RQTFVCEYCNKEFTFLQYLKRHMRTHTNEKPYKCV- 564 (606)
Q Consensus 525 ---------------~~~~~------------------------~k~y~C~~C~k~f~~~~~L~~H~~~H~~~kp~~C~- 564 (606)
..+.+ .....|.+||+.|.+.++|..|||+|+|+|||.|.
T Consensus 833 ~~~~l~eg~~t~~n~~t~~~~~~sv~qs~~~p~l~p~l~~~~pvnn~h~C~vCgk~FsSSsALqiH~rTHtg~KPF~C~f 912 (958)
T KOG1074|consen 833 ETSMLNEGLATKTNEITPEGPADSVIQSGGVPTLEPSLGRPGPVNNAHVCNVCGKQFSSSAALEIHMRTHTGPKPFFCHF 912 (958)
T ss_pred cccccccccccccccccCCCcchhhhhhccccccCCCCCCCCcccchhhhccchhcccchHHHHHhhhcCCCCCCccchh
Confidence 00000 11268999999999999999999999999999998
Q ss_pred cCccCCchhhHHHhhhccccccch
Q psy15165 565 CGLGFNFNVSLKNHKQKCSVFLLT 588 (606)
Q Consensus 565 C~~~F~~~~~L~~H~~~h~~~~~~ 588 (606)
|+++|..+.+|+.||.+|....|+
T Consensus 913 C~~aFttrgnLKvHMgtH~w~q~~ 936 (958)
T KOG1074|consen 913 CEEAFTTRGNLKVHMGTHMWVQPP 936 (958)
T ss_pred hhhhhhhhhhhhhhhccccccCCC
Confidence 999999999999999999976654
No 2
>KOG2462|consensus
Probab=99.94 E-value=1.5e-27 Score=217.99 Aligned_cols=136 Identities=30% Similarity=0.596 Sum_probs=118.1
Q ss_pred CccccCcchhccCChhHHhcccccCCCCCCChHHHHHHHHHhcCCCCCcccCCCCCCccCCHHHHHHHHHHhcCCCCCcC
Q psy15165 396 KPYKCKDCGAAFNHNVSLKNHKNSSCPKLYSYETYLKHLKTNHHGYEVSNLCYICGFFSAKRSTLAHHIQDHIQPRMKQK 475 (606)
Q Consensus 396 ~~~~C~~C~~~f~~~~~L~~H~~~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~~ 475 (606)
..|+|+.||+.+.+..+|.+|+..+|+. ...+.+.|++||+.+.+-..|..|+++|+- +
T Consensus 129 ~r~~c~eCgk~ysT~snLsrHkQ~H~~~----------------~s~ka~~C~~C~K~YvSmpALkMHirTH~l--~--- 187 (279)
T KOG2462|consen 129 PRYKCPECGKSYSTSSNLSRHKQTHRSL----------------DSKKAFSCKYCGKVYVSMPALKMHIRTHTL--P--- 187 (279)
T ss_pred Cceeccccccccccccccchhhcccccc----------------cccccccCCCCCceeeehHHHhhHhhccCC--C---
Confidence 3466666777777666777666655442 115678999999999999999999999862 2
Q ss_pred ccccccccchhhhhcccccccCCccccCCCCCCcCCChHHHHHhhhcccccCCCCccccccccchhccChhhHHHHHhhh
Q psy15165 476 QICEICCAEVYHINGHIKDKHSGFFLQCPHCPKTFPRKTELSNHIKGIHMKHELRQTFVCEYCNKEFTFLQYLKRHMRTH 555 (606)
Q Consensus 476 ~~C~~c~~~~~~l~~H~~~~h~~~~~~C~~C~~~f~~~~~L~~H~~~~H~~~~~~k~y~C~~C~k~f~~~~~L~~H~~~H 555 (606)
+.|.+|||.|.....|+-|+| .| ||||||.|..|+|+|..+++|+.||+||
T Consensus 188 -------------------------c~C~iCGKaFSRPWLLQGHiR-TH---TGEKPF~C~hC~kAFADRSNLRAHmQTH 238 (279)
T KOG2462|consen 188 -------------------------CECGICGKAFSRPWLLQGHIR-TH---TGEKPFSCPHCGKAFADRSNLRAHMQTH 238 (279)
T ss_pred -------------------------cccccccccccchHHhhcccc-cc---cCCCCccCCcccchhcchHHHHHHHHhh
Confidence 789999999999999999999 66 9999999999999999999999999999
Q ss_pred cCCCCcccc-cCccCCchhhHHHhhhc
Q psy15165 556 TNEKPYKCV-CGLGFNFNVSLKNHKQK 581 (606)
Q Consensus 556 ~~~kp~~C~-C~~~F~~~~~L~~H~~~ 581 (606)
.+.|+|.|. |+++|+..+.|.+|...
T Consensus 239 S~~K~~qC~~C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 239 SDVKKHQCPRCGKSFALKSYLNKHSES 265 (279)
T ss_pred cCCccccCcchhhHHHHHHHHHHhhhh
Confidence 999999998 99999999999999865
No 3
>KOG2462|consensus
Probab=99.91 E-value=1.4e-25 Score=205.24 Aligned_cols=139 Identities=32% Similarity=0.563 Sum_probs=111.3
Q ss_pred ccccccccccCCHHHHHHhHhhhcCC-CCCCcccCccccccCCHHHHHHHHHHhhCCccccccccccccccccchHhHHH
Q psy15165 249 FKCRVCDWKLNSYDKLLRHIKSDHGG-YETSSLCYHCGYYSKNRSTLKNHVRVEHGENQAKRKEKKICDICSAEVVHLAI 327 (606)
Q Consensus 249 ~~C~~C~~~f~~~~~L~~H~~~~H~~-~~~~~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~~~~~~~C~~C~~~~~~l~~ 327 (606)
|+|+.|++.+.+..+|.+|...|-.. ..+.+.|..||+.|.+...|+.|+++|.-
T Consensus 131 ~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~l------------------------ 186 (279)
T KOG2462|consen 131 YKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHTL------------------------ 186 (279)
T ss_pred eeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccCC------------------------
Confidence 55555555555555555555532221 13457788888888888888888877742
Q ss_pred HHHhccCCcceecccCccccCCHHHHHHHHhccccccCCCCcccccccccccCchHHHHhhhhhcCCCCccccCcchhcc
Q psy15165 328 HKKHSHSGQYHVCPHCGKKFTRKAELQLHIKGIHLKHQLEKTYICEYCHKEFTFYNYLRRHMRVHTNEKPYKCKDCGAAF 407 (606)
Q Consensus 328 h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~h~~~~~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~~C~~C~~~f 407 (606)
++.|.+||+.|.....|+-|++ +|+|||||.|..|++.|..+++|+.||++|.+.++|+|..|+|+|
T Consensus 187 ---------~c~C~iCGKaFSRPWLLQGHiR----THTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsF 253 (279)
T KOG2462|consen 187 ---------PCECGICGKAFSRPWLLQGHIR----THTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSF 253 (279)
T ss_pred ---------CcccccccccccchHHhhcccc----cccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHH
Confidence 4788888889998889999998 899999999999999999999999999999999999999999999
Q ss_pred CChhHHhcccccCCCCC
Q psy15165 408 NHNVSLKNHKNSSCPKL 424 (606)
Q Consensus 408 ~~~~~L~~H~~~~C~~~ 424 (606)
..++.|.+|..+.|-+.
T Consensus 254 sl~SyLnKH~ES~C~~~ 270 (279)
T KOG2462|consen 254 ALKSYLNKHSESACLKY 270 (279)
T ss_pred HHHHHHHHhhhhccccc
Confidence 99999999988777653
No 4
>KOG3608|consensus
Probab=99.91 E-value=3.4e-24 Score=200.13 Aligned_cols=230 Identities=25% Similarity=0.465 Sum_probs=171.3
Q ss_pred cccC--ccccccCCHHHHHHHHHHhhCCccccccccccccccccchHhHHHHHHhccC-C-cceeccc--CccccCCHHH
Q psy15165 279 SLCY--HCGYYSKNRSTLKNHVRVEHGENQAKRKEKKICDICSAEVVHLAIHKKHSHS-G-QYHVCPH--CGKKFTRKAE 352 (606)
Q Consensus 279 ~~C~--~C~~~f~~~~~L~~H~~~h~~~~~~~~~~~~~C~~C~~~~~~l~~h~~~~~~-~-~~~~C~~--C~~~f~~~~~ 352 (606)
|.|. .|+..|.+...|..|+..|.-. |++ . +..... + ..+.|.. |-+.|.+++.
T Consensus 135 f~C~WedCe~~F~s~~ef~dHV~~H~l~----------cey---d-------~~~~~~D~~pv~~C~W~~Ct~~~~~k~~ 194 (467)
T KOG3608|consen 135 FRCGWEDCEREFVSIVEFQDHVVKHALF----------CEY---D-------IQKTPEDERPVTMCNWAMCTKHMGNKYR 194 (467)
T ss_pred hccChhhcCCcccCHHHHHHHHHHhhhh----------hhh---h-------hhhCCCCCCceeeccchhhhhhhccHHH
Confidence 5564 6999999999999999877532 110 0 010111 1 3366754 8888999999
Q ss_pred HHHHHhccccccCCCCcccccccccccCchHHHHhhhhhcC--CCCccccCcchhccCChhHHhcccccCCCCCCChHHH
Q psy15165 353 LQLHIKGIHLKHQLEKTYICEYCHKEFTFYNYLRRHMRVHT--NEKPYKCKDCGAAFNHNVSLKNHKNSSCPKLYSYETY 430 (606)
Q Consensus 353 l~~H~~~~h~~h~~~~~~~C~~C~k~f~~~~~L~~H~~~H~--~~~~~~C~~C~~~f~~~~~L~~H~~~~C~~~f~~~~~ 430 (606)
|+.|++ .|++++...|+.||..|+++..|..|++.-+ ...+|+|..|.+.|.+...|..|+.
T Consensus 195 LreH~r----~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~------------ 258 (467)
T KOG3608|consen 195 LREHIR----THSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVV------------ 258 (467)
T ss_pred HHHHHH----hcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHH------------
Confidence 999998 7889999999999999999999999977544 4568999999999998888877754
Q ss_pred HHHHHHhcCCCCCcccCCCCCCccCCHHHHHHHHHH-hcCCCCCcCccccccccchhhhhcccccccCCccccCCCCCCc
Q psy15165 431 LKHLKTNHHGYEVSNLCYICGFFSAKRSTLAHHIQD-HIQPRMKQKQICEICCAEVYHINGHIKDKHSGFFLQCPHCPKT 509 (606)
Q Consensus 431 l~~h~~~~~~~~~~~~C~~C~~~f~~~~~L~~H~~~-h~~~~~~~~~~C~~c~~~~~~l~~H~~~~h~~~~~~C~~C~~~ 509 (606)
.| -..|+|+.|+.+...++.|..|++. |..++| |+|+.|++.
T Consensus 259 ------rH---vn~ykCplCdmtc~~~ssL~~H~r~rHs~dkp----------------------------fKCd~Cd~~ 301 (467)
T KOG3608|consen 259 ------RH---VNCYKCPLCDMTCSSASSLTTHIRYRHSKDKP----------------------------FKCDECDTR 301 (467)
T ss_pred ------Hh---hhcccccccccCCCChHHHHHHHHhhhccCCC----------------------------ccccchhhh
Confidence 22 3468899999998888888888876 444444 788888888
Q ss_pred CCChHHHHHhhhcccccCCCCccccccc--cchhccChhhHHHHHhhhc-CC--CCcccc-cCccCCchhhHHHhhhccc
Q psy15165 510 FPRKTELSNHIKGIHMKHELRQTFVCEY--CNKEFTFLQYLKRHMRTHT-NE--KPYKCV-CGLGFNFNVSLKNHKQKCS 583 (606)
Q Consensus 510 f~~~~~L~~H~~~~H~~~~~~k~y~C~~--C~k~f~~~~~L~~H~~~H~-~~--kp~~C~-C~~~F~~~~~L~~H~~~h~ 583 (606)
|.+.+.|.+|+. +| . +-.|.|.. |.++|.+...|++|++-|+ |. -+|.|. |++.|++..+|..|+++-|
T Consensus 302 c~~esdL~kH~~-~H---S-~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~Y~CH~Cdr~ft~G~~L~~HL~kkH 376 (467)
T KOG3608|consen 302 CVRESDLAKHVQ-VH---S-KTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPILYACHCCDRFFTSGKSLSAHLMKKH 376 (467)
T ss_pred hccHHHHHHHHH-hc---c-ccceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCceeeecchhhhccchhHHHHHHHhh
Confidence 888888888877 56 3 55688877 8888888888888877544 43 458887 8888888888888877666
Q ss_pred ccc
Q psy15165 584 VFL 586 (606)
Q Consensus 584 ~~~ 586 (606)
+.+
T Consensus 377 ~f~ 379 (467)
T KOG3608|consen 377 GFR 379 (467)
T ss_pred ccc
Confidence 554
No 5
>KOG3623|consensus
Probab=99.91 E-value=1.3e-25 Score=227.21 Aligned_cols=121 Identities=28% Similarity=0.506 Sum_probs=96.6
Q ss_pred ccccccccccCCHHHHHHhHhhhcCCCCCCcccCccccccCCHHHHHHHHHHhhCCccccccccccccccccchHhHHHH
Q psy15165 249 FKCRVCDWKLNSYDKLLRHIKSDHGGYETSSLCYHCGYYSKNRSTLKNHVRVEHGENQAKRKEKKICDICSAEVVHLAIH 328 (606)
Q Consensus 249 ~~C~~C~~~f~~~~~L~~H~~~~H~~~~~~~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~~~~~~~C~~C~~~~~~l~~h 328 (606)
..|++|...+.....|..|++..|...+..|.|..|.++|..+..|.+||.+|....... .+
T Consensus 211 ltcpycdrgykrltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa------------------~s 272 (1007)
T KOG3623|consen 211 LTCPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQA------------------IS 272 (1007)
T ss_pred hcchhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCccc------------------cc
Confidence 578888888888888888887777665777889999999999999999988886542210 00
Q ss_pred HHhccCCcceecccCccccCCHHHHHHHHhccccccCCCCcccccccccccCchHHHHhhhhh
Q psy15165 329 KKHSHSGQYHVCPHCGKKFTRKAELQLHIKGIHLKHQLEKTYICEYCHKEFTFYNYLRRHMRV 391 (606)
Q Consensus 329 ~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~h~~~~~~~C~~C~k~f~~~~~L~~H~~~ 391 (606)
....-..+.|+|..||+.|..+..|+.|++ +|.|++||.|+-|+|+|.....+..||..
T Consensus 273 ltqsa~lRKFKCtECgKAFKfKHHLKEHlR----IHSGEKPfeCpnCkKRFSHSGSySSHmSS 331 (1007)
T KOG3623|consen 273 LTQSALLRKFKCTECGKAFKFKHHLKEHLR----IHSGEKPFECPNCKKRFSHSGSYSSHMSS 331 (1007)
T ss_pred ccchhhhccccccccchhhhhHHHHHhhhe----eecCCCCcCCcccccccccCCcccccccc
Confidence 000111267999999999999999999999 99999999999999999999999999753
No 6
>KOG3608|consensus
Probab=99.89 E-value=1.7e-23 Score=195.45 Aligned_cols=239 Identities=26% Similarity=0.493 Sum_probs=180.9
Q ss_pred cccc--ccccccCCHHHHHHhHhhhcCC-----------CC-CCcccC--ccccccCCHHHHHHHHHHhhCCcccccccc
Q psy15165 249 FKCR--VCDWKLNSYDKLLRHIKSDHGG-----------YE-TSSLCY--HCGYYSKNRSTLKNHVRVEHGENQAKRKEK 312 (606)
Q Consensus 249 ~~C~--~C~~~f~~~~~L~~H~~~~H~~-----------~~-~~~~C~--~C~~~f~~~~~L~~H~~~h~~~~~~~~~~~ 312 (606)
|.|. .|+..|.+...|..|+. +|.. .+ ..+.|. -|.+.|.++..|++|++.|.++
T Consensus 135 f~C~WedCe~~F~s~~ef~dHV~-~H~l~ceyd~~~~~~D~~pv~~C~W~~Ct~~~~~k~~LreH~r~Hs~e-------- 205 (467)
T KOG3608|consen 135 FRCGWEDCEREFVSIVEFQDHVV-KHALFCEYDIQKTPEDERPVTMCNWAMCTKHMGNKYRLREHIRTHSNE-------- 205 (467)
T ss_pred hccChhhcCCcccCHHHHHHHHH-HhhhhhhhhhhhCCCCCCceeeccchhhhhhhccHHHHHHHHHhcCCC--------
Confidence 5564 47888888888888876 4431 01 123454 4777777777777777777665
Q ss_pred ccccccccchHhHHHHHHhccCCcceecccCccccCCHHHHHHHHhccccccCCCCcccccccccccCchHHHHhhhhhc
Q psy15165 313 KICDICSAEVVHLAIHKKHSHSGQYHVCPHCGKKFTRKAELQLHIKGIHLKHQLEKTYICEYCHKEFTFYNYLRRHMRVH 392 (606)
Q Consensus 313 ~~C~~C~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~h~~~~~~~C~~C~k~f~~~~~L~~H~~~H 392 (606)
+...|+.||..|.++..|-.|++.- +-....+|.|..|.|.|.+...|..|+..|
T Consensus 206 -----------------------KvvACp~Cg~~F~~~tkl~DH~rRq--t~l~~n~fqC~~C~KrFaTeklL~~Hv~rH 260 (467)
T KOG3608|consen 206 -----------------------KVVACPHCGELFRTKTKLFDHLRRQ--TELNTNSFQCAQCFKRFATEKLLKSHVVRH 260 (467)
T ss_pred -----------------------eEEecchHHHHhccccHHHHHHHhh--hhhcCCchHHHHHHHHHhHHHHHHHHHHHh
Confidence 4467899999999999999998743 223346899999999999999999999988
Q ss_pred CCCCccccCcchhccCChhHHhcccccCCCCCCChHHHHHHHHHhcCCCCCcccCCCCCCccCCHHHHHHHHHHhcCCCC
Q psy15165 393 TNEKPYKCKDCGAAFNHNVSLKNHKNSSCPKLYSYETYLKHLKTNHHGYEVSNLCYICGFFSAKRSTLAHHIQDHIQPRM 472 (606)
Q Consensus 393 ~~~~~~~C~~C~~~f~~~~~L~~H~~~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~~~L~~H~~~h~~~~~ 472 (606)
- .-|+|+.|+.+....++|..|++. . +...+||+|+.|++.|.+.+.|..|...|. +.
T Consensus 261 v--n~ykCplCdmtc~~~ssL~~H~r~-----------------r-Hs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~- 318 (467)
T KOG3608|consen 261 V--NCYKCPLCDMTCSSASSLTTHIRY-----------------R-HSKDKPFKCDECDTRCVRESDLAKHVQVHS-KT- 318 (467)
T ss_pred h--hcccccccccCCCChHHHHHHHHh-----------------h-hccCCCccccchhhhhccHHHHHHHHHhcc-cc-
Confidence 6 468999999999999888888652 2 333889999999999999999999998775 21
Q ss_pred CcCccccccccchhhhhcccccccCCccccCCC--CCCcCCChHHHHHhhhcccccCCCCccccccccchhccChhhHHH
Q psy15165 473 KQKQICEICCAEVYHINGHIKDKHSGFFLQCPH--CPKTFPRKTELSNHIKGIHMKHELRQTFVCEYCNKEFTFLQYLKR 550 (606)
Q Consensus 473 ~~~~~C~~c~~~~~~l~~H~~~~h~~~~~~C~~--C~~~f~~~~~L~~H~~~~H~~~~~~k~y~C~~C~k~f~~~~~L~~ 550 (606)
.|.|.. |.++|.+...|++|++.+| .....-+|.|..|++.|++-.+|.+
T Consensus 319 ---------------------------~y~C~h~~C~~s~r~~~q~~~H~~evh-Eg~np~~Y~CH~Cdr~ft~G~~L~~ 370 (467)
T KOG3608|consen 319 ---------------------------VYQCEHPDCHYSVRTYTQMRRHFLEVH-EGNNPILYACHCCDRFFTSGKSLSA 370 (467)
T ss_pred ---------------------------ceecCCCCCcHHHHHHHHHHHHHHHhc-cCCCCCceeeecchhhhccchhHHH
Confidence 289988 9999999999999999777 2245667999999999999999999
Q ss_pred HHhhhcC------CCCcccc-cCccCCc
Q psy15165 551 HMRTHTN------EKPYKCV-CGLGFNF 571 (606)
Q Consensus 551 H~~~H~~------~kp~~C~-C~~~F~~ 571 (606)
|++.-++ -+.|.=. |.-+|.+
T Consensus 371 HL~kkH~f~~PsGh~RFtYk~~edG~mR 398 (467)
T KOG3608|consen 371 HLMKKHGFRLPSGHKRFTYKVDEDGFMR 398 (467)
T ss_pred HHHHhhcccCCCCCCceeeeeccCceee
Confidence 9765443 2344443 5555543
No 7
>KOG1074|consensus
Probab=99.88 E-value=9.9e-24 Score=217.88 Aligned_cols=243 Identities=21% Similarity=0.325 Sum_probs=172.7
Q ss_pred ccccccccccc---hHhHHHHHHhccCCcceecccCccccCCHHHHHHHHhccccccCCCCccccc---ccccccCchHH
Q psy15165 311 EKKICDICSAE---VVHLAIHKKHSHSGQYHVCPHCGKKFTRKAELQLHIKGIHLKHQLEKTYICE---YCHKEFTFYNY 384 (606)
Q Consensus 311 ~~~~C~~C~~~---~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~h~~~~~~~C~---~C~k~f~~~~~ 384 (606)
.+..|-+|-+. .+.|..|.+.|.+++||+|.+||+.|.++.+|+.||-.+...+...-.+.|+ +|-+.|...-.
T Consensus 604 dPNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kftn~V~ 683 (958)
T KOG1074|consen 604 DPNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKKFTNAVT 683 (958)
T ss_pred CccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccccccccCCchhhhccccccccc
Confidence 45679999984 4689999998888899999999999999999999998554555556779999 99999999999
Q ss_pred HHhhhhhcCCC-Cc------------cccCcchhccCChhHHhcccccCCCCCCChHHHHHHHHHhcCC---CCCcccCC
Q psy15165 385 LRRHMRVHTNE-KP------------YKCKDCGAAFNHNVSLKNHKNSSCPKLYSYETYLKHLKTNHHG---YEVSNLCY 448 (606)
Q Consensus 385 L~~H~~~H~~~-~~------------~~C~~C~~~f~~~~~L~~H~~~~C~~~f~~~~~l~~h~~~~~~---~~~~~~C~ 448 (606)
|..|+++|.+. .+ -+|..|.+.|.....+..++...++..-.- ......+.+.. ...+..+.
T Consensus 684 lpQhIriH~~~~~s~g~~a~e~~~~adq~~~~qk~~~~a~~f~~~~se~~~~~s~~--~~~~~~~t~t~~~~~tp~~~e~ 761 (958)
T KOG1074|consen 684 LPQHIRIHLGGQISNGGTAAEGILAADQCSSCQKTFSDARSFSQQISEQPSPESEP--DEQMDERTETEELDVTPPPPEN 761 (958)
T ss_pred ccceEEeecCCCCCCCcccccccchhcccchhhhcccccccchhhhhccCCcccCC--cccccccccccccccCCCcccc
Confidence 99999999832 11 369999999999888888876555432211 01111122221 12366788
Q ss_pred CCCCccCCHHHHHHHHHHh-----------------------cCCCCCcCccccccccch---------------hhhhc
Q psy15165 449 ICGFFSAKRSTLAHHIQDH-----------------------IQPRMKQKQICEICCAEV---------------YHING 490 (606)
Q Consensus 449 ~C~~~f~~~~~L~~H~~~h-----------------------~~~~~~~~~~C~~c~~~~---------------~~l~~ 490 (606)
.|+..+.....+..+-..+ +.+++. ..+.+++... +.|..
T Consensus 762 ~~~~~~~~e~~i~~~g~te~asa~~~~vg~~s~~~~~~~~~~T~~k~~--~~~~~~~~~~~~~v~~~pvl~~~~~~~l~e 839 (958)
T KOG1074|consen 762 SCGRELEGEMAISVRGSTEEASANLDEVGTVSAAGEAGEEDDTSEKPT--QASSFPGEILAPSVNMDPVLWNQETSMLNE 839 (958)
T ss_pred ccccccCcccccccccchhhhhcChhhhcCccccchhhhhcccCCCCc--ccccCCCcCCccccccCchhhccccccccc
Confidence 8888877666655443222 333332 1344443100 00000
Q ss_pred cccc----------------------------ccC--CccccCCCCCCcCCChHHHHHhhhcccccCCCCccccccccch
Q psy15165 491 HIKD----------------------------KHS--GFFLQCPHCPKTFPRKTELSNHIKGIHMKHELRQTFVCEYCNK 540 (606)
Q Consensus 491 H~~~----------------------------~h~--~~~~~C~~C~~~f~~~~~L~~H~~~~H~~~~~~k~y~C~~C~k 540 (606)
-... ... ..+..|..||+.|.+.++|..|++ .| +++|||.|.+|++
T Consensus 840 g~~t~~n~~t~~~~~~sv~qs~~~p~l~p~l~~~~pvnn~h~C~vCgk~FsSSsALqiH~r-TH---tg~KPF~C~fC~~ 915 (958)
T KOG1074|consen 840 GLATKTNEITPEGPADSVIQSGGVPTLEPSLGRPGPVNNAHVCNVCGKQFSSSAALEIHMR-TH---TGPKPFFCHFCEE 915 (958)
T ss_pred ccccccccccCCCcchhhhhhccccccCCCCCCCCcccchhhhccchhcccchHHHHHhhh-cC---CCCCCccchhhhh
Confidence 0000 000 012679999999999999999999 56 9999999999999
Q ss_pred hccChhhHHHHHhhhcCCCCc
Q psy15165 541 EFTFLQYLKRHMRTHTNEKPY 561 (606)
Q Consensus 541 ~f~~~~~L~~H~~~H~~~kp~ 561 (606)
.|..+.+|+.||.+|.+..|+
T Consensus 916 aFttrgnLKvHMgtH~w~q~~ 936 (958)
T KOG1074|consen 916 AFTTRGNLKVHMGTHMWVQPP 936 (958)
T ss_pred hhhhhhhhhhhhccccccCCC
Confidence 999999999999999987664
No 8
>KOG3623|consensus
Probab=99.80 E-value=1.2e-20 Score=191.65 Aligned_cols=101 Identities=25% Similarity=0.511 Sum_probs=86.1
Q ss_pred CcccccCccccCCHHHHHhhhhccccccCCCCCCcccccccccccCCHHHHHHhHhhhcCCC-----------CCCcccC
Q psy15165 214 EFKCRVCDWKLNSYDKLLRHMDWDEVHLGQFSPYEFKCRVCDWKLNSYDKLLRHIKSDHGGY-----------ETSSLCY 282 (606)
Q Consensus 214 ~~~C~~C~~~f~~~~~l~~H~~~~~~h~~~~~~~~~~C~~C~~~f~~~~~L~~H~~~~H~~~-----------~~~~~C~ 282 (606)
...|+.|++.+.....|..|+++.+.- .+..|.|.+|..+|..+..|.+||..|-.+. .+.|+|.
T Consensus 210 lltcpycdrgykrltslkeHikyrhek----ne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCt 285 (1007)
T KOG3623|consen 210 LLTCPYCDRGYKRLTSLKEHIKYRHEK----NEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCT 285 (1007)
T ss_pred hhcchhHHHHHHHHHHHHHHHHHHHhh----CCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhcccccc
Confidence 578999999999999999999864322 3345999999999999999999998553321 2569999
Q ss_pred ccccccCCHHHHHHHHHHhhCCccccccccccccccccchHh
Q psy15165 283 HCGYYSKNRSTLKNHVRVEHGENQAKRKEKKICDICSAEVVH 324 (606)
Q Consensus 283 ~C~~~f~~~~~L~~H~~~h~~~~~~~~~~~~~C~~C~~~~~~ 324 (606)
+||+.|..+..|+.|+|+|.|+ ++|.|+-|.+.|++
T Consensus 286 ECgKAFKfKHHLKEHlRIHSGE------KPfeCpnCkKRFSH 321 (1007)
T KOG3623|consen 286 ECGKAFKFKHHLKEHLRIHSGE------KPFECPNCKKRFSH 321 (1007)
T ss_pred ccchhhhhHHHHHhhheeecCC------CCcCCccccccccc
Confidence 9999999999999999999999 88999999997754
No 9
>KOG3576|consensus
Probab=99.63 E-value=1.1e-16 Score=138.68 Aligned_cols=114 Identities=25% Similarity=0.411 Sum_probs=101.4
Q ss_pred CCcccCCCCCCccCCHHHHHHHHHHhcCCCCCcCccccccccchhhhhcccccccCCccccCCCCCCcCCChHHHHHhhh
Q psy15165 442 EVSNLCYICGFFSAKRSTLAHHIQDHIQPRMKQKQICEICCAEVYHINGHIKDKHSGFFLQCPHCPKTFPRKTELSNHIK 521 (606)
Q Consensus 442 ~~~~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~~~~C~~c~~~~~~l~~H~~~~h~~~~~~C~~C~~~f~~~~~L~~H~~ 521 (606)
...|.|.+||+.|.....|.+|++-|...+. |.|..||+.|.....|++|++
T Consensus 115 ~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr----------------------------~lct~cgkgfndtfdlkrh~r 166 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQRMLNRHLKCHSDVKR----------------------------HLCTFCGKGFNDTFDLKRHTR 166 (267)
T ss_pred CCeeeeehhhhhhhHHHHHHHHhhhccHHHH----------------------------HHHhhccCcccchhhhhhhhc
Confidence 4568999999999999999999998865444 899999999999999999999
Q ss_pred cccccCCCCccccccccchhccChhhHHHHHhhhcC-----------CCCcccc-cCccCCchhhHHHhhhccccccc
Q psy15165 522 GIHMKHELRQTFVCEYCNKEFTFLQYLKRHMRTHTN-----------EKPYKCV-CGLGFNFNVSLKNHKQKCSVFLL 587 (606)
Q Consensus 522 ~~H~~~~~~k~y~C~~C~k~f~~~~~L~~H~~~H~~-----------~kp~~C~-C~~~F~~~~~L~~H~~~h~~~~~ 587 (606)
.| +|.+||+|..|+++|++.-.|..|++.-+| .+-|.|. ||++-.....+..|++.|+..-|
T Consensus 167 -th---tgvrpykc~~c~kaftqrcsleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~Sp 240 (267)
T KOG3576|consen 167 -TH---TGVRPYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPFSP 240 (267)
T ss_pred -cc---cCccccchhhhhHHHHhhccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCCCCH
Confidence 56 999999999999999999999999875443 4679998 99999999999999999997644
No 10
>KOG3576|consensus
Probab=99.61 E-value=2.1e-16 Score=137.00 Aligned_cols=126 Identities=30% Similarity=0.486 Sum_probs=108.0
Q ss_pred CcceecccCccccCCHHHHHHHHhccccccCCCCcccccccccccCchHHHHhhhhhcCCCCccccCcchhccCChhHHh
Q psy15165 335 GQYHVCPHCGKKFTRKAELQLHIKGIHLKHQLEKTYICEYCHKEFTFYNYLRRHMRVHTNEKPYKCKDCGAAFNHNVSLK 414 (606)
Q Consensus 335 ~~~~~C~~C~~~f~~~~~l~~H~~~~h~~h~~~~~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~~C~~C~~~f~~~~~L~ 414 (606)
+..|.|.+|++.|.-...|.+|++ -|...+.+-|..||+.|.....|++|+++|+|.+||+|..|+++|...-.|.
T Consensus 115 ~d~ftCrvCgK~F~lQRmlnrh~k----ch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsle 190 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQRMLNRHLK----CHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLE 190 (267)
T ss_pred CCeeeeehhhhhhhHHHHHHHHhh----hccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHH
Confidence 467999999999999999999999 8988999999999999999999999999999999999999999999999999
Q ss_pred cccccCCCCCCChHHHHHHHHHhcCCCCCcccCCCCCCccCCHHHHHHHHHHhcCCCC
Q psy15165 415 NHKNSSCPKLYSYETYLKHLKTNHHGYEVSNLCYICGFFSAKRSTLAHHIQDHIQPRM 472 (606)
Q Consensus 415 ~H~~~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~~~~L~~H~~~h~~~~~ 472 (606)
.|++.+.+-.-.+ ..- ....+.|.|..||++-.....+..|++.|+...|
T Consensus 191 shl~kvhgv~~~y----ayk----err~kl~vcedcg~t~~~~e~~~~h~~~~hp~Sp 240 (267)
T KOG3576|consen 191 SHLKKVHGVQHQY----AYK----ERRAKLYVCEDCGYTSERPEVYYLHLKLHHPFSP 240 (267)
T ss_pred HHHHHHcCchHHH----HHH----HhhhheeeecccCCCCCChhHHHHHHHhcCCCCH
Confidence 9987554432111 000 1126789999999999999999999999876554
No 11
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.21 E-value=3.7e-11 Score=125.00 Aligned_cols=145 Identities=19% Similarity=0.380 Sum_probs=104.9
Q ss_pred ccccccccccCchHHHHhhhhhcCCCCccccCc--chhccCChhHHhcccccCCCCCCChHHHHHHHHHhcCCCCCcccC
Q psy15165 370 YICEYCHKEFTFYNYLRRHMRVHTNEKPYKCKD--CGAAFNHNVSLKNHKNSSCPKLYSYETYLKHLKTNHHGYEVSNLC 447 (606)
Q Consensus 370 ~~C~~C~k~f~~~~~L~~H~~~H~~~~~~~C~~--C~~~f~~~~~L~~H~~~~C~~~f~~~~~l~~h~~~~~~~~~~~~C 447 (606)
..|..|...... ..|..|...-. -..-.|+. ||..|.. ..|.. .+.|
T Consensus 408 V~C~NC~~~i~l-~~l~lHe~~C~-r~~V~Cp~~~Cg~v~~r-~el~~----------------------------H~~C 456 (567)
T PLN03086 408 VECRNCKHYIPS-RSIALHEAYCS-RHNVVCPHDGCGIVLRV-EEAKN----------------------------HVHC 456 (567)
T ss_pred EECCCCCCccch-hHHHHHHhhCC-CcceeCCcccccceeec-ccccc----------------------------CccC
Confidence 457777766553 34556653322 23446774 8887743 23333 3469
Q ss_pred CCCCCccCCHHHHHHHHHHhcCCCCCcCccccccccchhhhhcccccccCCccccCCCCCCcCCChHHHHHhhhcccccC
Q psy15165 448 YICGFFSAKRSTLAHHIQDHIQPRMKQKQICEICCAEVYHINGHIKDKHSGFFLQCPHCPKTFPRKTELSNHIKGIHMKH 527 (606)
Q Consensus 448 ~~C~~~f~~~~~L~~H~~~h~~~~~~~~~~C~~c~~~~~~l~~H~~~~h~~~~~~C~~C~~~f~~~~~L~~H~~~~H~~~ 527 (606)
+.|++.|. ...|..|++.|+ .+ |.|+ ||+.+ .+..|..|+. .|
T Consensus 457 ~~Cgk~f~-~s~LekH~~~~H--kp----------------------------v~Cp-Cg~~~-~R~~L~~H~~-th--- 499 (567)
T PLN03086 457 EKCGQAFQ-QGEMEKHMKVFH--EP----------------------------LQCP-CGVVL-EKEQMVQHQA-ST--- 499 (567)
T ss_pred CCCCCccc-hHHHHHHHHhcC--CC----------------------------ccCC-CCCCc-chhHHHhhhh-cc---
Confidence 99999885 677889988874 33 8899 99765 6689999987 45
Q ss_pred CCCccccccccchhcc----------ChhhHHHHHhhhcCCCCcccc-cCccCCchhhHHHhhhcccc
Q psy15165 528 ELRQTFVCEYCNKEFT----------FLQYLKRHMRTHTNEKPYKCV-CGLGFNFNVSLKNHKQKCSV 584 (606)
Q Consensus 528 ~~~k~y~C~~C~k~f~----------~~~~L~~H~~~H~~~kp~~C~-C~~~F~~~~~L~~H~~~h~~ 584 (606)
.+.+++.|.+|++.|. ..+.|..|..++ |.+++.|. ||+.|.. ..|..|+...|.
T Consensus 500 Cp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt~~C~~Cgk~Vrl-rdm~~H~~~~h~ 565 (567)
T PLN03086 500 CPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-GSRTAPCDSCGRSVML-KEMDIHQIAVHQ 565 (567)
T ss_pred CCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-CCcceEccccCCeeee-hhHHHHHHHhhc
Confidence 8889999999999995 245899999886 89999998 9999855 568889877664
No 12
>PHA00733 hypothetical protein
Probab=99.12 E-value=4.6e-11 Score=101.43 Aligned_cols=83 Identities=22% Similarity=0.268 Sum_probs=72.2
Q ss_pred cccCCCCCCcCCChHHHHHh--hhcccccCCCCccccccccchhccChhhHHHHHhhhcCCCCcccc-cCccCCchhhHH
Q psy15165 500 FLQCPHCPKTFPRKTELSNH--IKGIHMKHELRQTFVCEYCNKEFTFLQYLKRHMRTHTNEKPYKCV-CGLGFNFNVSLK 576 (606)
Q Consensus 500 ~~~C~~C~~~f~~~~~L~~H--~~~~H~~~~~~k~y~C~~C~k~f~~~~~L~~H~~~H~~~kp~~C~-C~~~F~~~~~L~ 576 (606)
++.|.+|...|.....|..| ++ .|+.+.+.+||.|+.||+.|.+...|..|++.| +.+|.|. |+++|.....|.
T Consensus 40 ~~~~~~~~~~~~~~~~l~~~~~l~-~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~sL~ 116 (128)
T PHA00733 40 RLIRAVVKTLIYNPQLLDESSYLY-KLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDSTL 116 (128)
T ss_pred hHHHHHHhhhccChhhhcchHHHH-hhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHHHH
Confidence 38999999999998888887 44 334446689999999999999999999999987 4689998 999999999999
Q ss_pred Hhhhccccc
Q psy15165 577 NHKQKCSVF 585 (606)
Q Consensus 577 ~H~~~h~~~ 585 (606)
.|+++.|++
T Consensus 117 ~H~~~~h~~ 125 (128)
T PHA00733 117 DHVCKKHNI 125 (128)
T ss_pred HHHHHhcCc
Confidence 999988864
No 13
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.05 E-value=5.1e-10 Score=116.64 Aligned_cols=101 Identities=25% Similarity=0.560 Sum_probs=57.7
Q ss_pred ccccccccccCchHHHHhhhhhcCCCCccccCcchhccCChhHHhcccccCCCCCCChHHHHHHHHHhcCCCCCcccCCC
Q psy15165 370 YICEYCHKEFTFYNYLRRHMRVHTNEKPYKCKDCGAAFNHNVSLKNHKNSSCPKLYSYETYLKHLKTNHHGYEVSNLCYI 449 (606)
Q Consensus 370 ~~C~~C~k~f~~~~~L~~H~~~H~~~~~~~C~~C~~~f~~~~~L~~H~~~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~ 449 (606)
+.|+.|++.|. ...|..|+.+|+ +++.|+ ||+.+ ....|..|+..+|+ .+++.|..
T Consensus 454 ~~C~~Cgk~f~-~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp-------------------~Kpi~C~f 509 (567)
T PLN03086 454 VHCEKCGQAFQ-QGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCP-------------------LRLITCRF 509 (567)
T ss_pred ccCCCCCCccc-hHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCC-------------------CCceeCCC
Confidence 45666766664 455666666654 566666 66543 34555555443333 55666777
Q ss_pred CCCccCC----------HHHHHHHHHHhcCCCCCcCccccccccchhhhhcccccccCCccccCCCCCCcCCChHHHHHh
Q psy15165 450 CGFFSAK----------RSTLAHHIQDHIQPRMKQKQICEICCAEVYHINGHIKDKHSGFFLQCPHCPKTFPRKTELSNH 519 (606)
Q Consensus 450 C~~~f~~----------~~~L~~H~~~h~~~~~~~~~~C~~c~~~~~~l~~H~~~~h~~~~~~C~~C~~~f~~~~~L~~H 519 (606)
|++.|.. .+.|..|.... +.++ +.|..||+.|.. ..|..|
T Consensus 510 C~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt----------------------------~~C~~Cgk~Vrl-rdm~~H 559 (567)
T PLN03086 510 CGDMVQAGGSAMDVRDRLRGMSEHESIC-GSRT----------------------------APCDSCGRSVML-KEMDIH 559 (567)
T ss_pred CCCccccCccccchhhhhhhHHHHHHhc-CCcc----------------------------eEccccCCeeee-hhHHHH
Confidence 7666631 23555555543 3333 667777766654 346666
Q ss_pred hhccc
Q psy15165 520 IKGIH 524 (606)
Q Consensus 520 ~~~~H 524 (606)
+..+|
T Consensus 560 ~~~~h 564 (567)
T PLN03086 560 QIAVH 564 (567)
T ss_pred HHHhh
Confidence 66555
No 14
>PHA02768 hypothetical protein; Provisional
Probab=98.94 E-value=3.3e-10 Score=78.23 Aligned_cols=42 Identities=17% Similarity=0.263 Sum_probs=33.0
Q ss_pred ccccccchhccChhhHHHHHhhhcCCCCcccc-cCccCCchhhHH
Q psy15165 533 FVCEYCNKEFTFLQYLKRHMRTHTNEKPYKCV-CGLGFNFNVSLK 576 (606)
Q Consensus 533 y~C~~C~k~f~~~~~L~~H~~~H~~~kp~~C~-C~~~F~~~~~L~ 576 (606)
|.|+.||+.|+..++|..|+++|+ +||+|. |++.|.+.+.|.
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceecccceeE
Confidence 778888888888888888888887 678887 888887776654
No 15
>PHA00733 hypothetical protein
Probab=98.84 E-value=4.1e-09 Score=89.56 Aligned_cols=87 Identities=18% Similarity=0.253 Sum_probs=70.2
Q ss_pred CCcccCCCCCCccCCHHHHHHHHHHhcCCCCCcCccccccccchhhhhcccccccCCccccCCCCCCcCCChHHHHHhhh
Q psy15165 442 EVSNLCYICGFFSAKRSTLAHHIQDHIQPRMKQKQICEICCAEVYHINGHIKDKHSGFFLQCPHCPKTFPRKTELSNHIK 521 (606)
Q Consensus 442 ~~~~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~~~~C~~c~~~~~~l~~H~~~~h~~~~~~C~~C~~~f~~~~~L~~H~~ 521 (606)
.+++.|.+|...|.....|..|... ..|+.. ++..+|.|+.||+.|.+...|..|++
T Consensus 38 ~~~~~~~~~~~~~~~~~~l~~~~~l----------------------~~~~~~-~~~kPy~C~~Cgk~Fss~s~L~~H~r 94 (128)
T PHA00733 38 QKRLIRAVVKTLIYNPQLLDESSYL----------------------YKLLTS-KAVSPYVCPLCLMPFSSSVSLKQHIR 94 (128)
T ss_pred hhhHHHHHHhhhccChhhhcchHHH----------------------Hhhccc-CCCCCccCCCCCCcCCCHHHHHHHHh
Confidence 5789999999999998888877321 122222 44556999999999999999999998
Q ss_pred cccccCCCCccccccccchhccChhhHHHHHhhhcC
Q psy15165 522 GIHMKHELRQTFVCEYCNKEFTFLQYLKRHMRTHTN 557 (606)
Q Consensus 522 ~~H~~~~~~k~y~C~~C~k~f~~~~~L~~H~~~H~~ 557 (606)
.| ..+|.|..|++.|.....|.+|+...++
T Consensus 95 -~h-----~~~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 95 -YT-----EHSKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred -cC-----CcCccCCCCCCccCCHHHHHHHHHHhcC
Confidence 33 3579999999999999999999987665
No 16
>KOG3993|consensus
Probab=98.69 E-value=4.5e-09 Score=102.08 Aligned_cols=114 Identities=18% Similarity=0.242 Sum_probs=63.9
Q ss_pred ceecccCccccCCHHHHHHHHhccccccCCCCcccccccccccCchHHHHhhhhhcCCCCccccCcchhccCChhHHhcc
Q psy15165 337 YHVCPHCGKKFTRKAELQLHIKGIHLKHQLEKTYICEYCHKEFTFYNYLRRHMRVHTNEKPYKCKDCGAAFNHNVSLKNH 416 (606)
Q Consensus 337 ~~~C~~C~~~f~~~~~l~~H~~~~h~~h~~~~~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~~C~~C~~~f~~~~~L~~H 416 (606)
.|.|.+|...|.....|.+|.- .....--|+|+.|+|.|+-..+|-.|.|.|....--. ++-.....
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC----~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa-----~a~~~P~k---- 333 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRC----PRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAA-----KAGSPPPK---- 333 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccC----CeeEEeeecCCcccccccCchhhhhhhcccCCchhhh-----hcCCCChh----
Confidence 4777777777777777777754 1111224777777777777777777777775321100 00000000
Q ss_pred cccCCCCCCChHHHHHHHHH-hcCCCCCcccCCCCCCccCCHHHHHHHHHHhcC
Q psy15165 417 KNSSCPKLYSYETYLKHLKT-NHHGYEVSNLCYICGFFSAKRSTLAHHIQDHIQ 469 (606)
Q Consensus 417 ~~~~C~~~f~~~~~l~~h~~-~~~~~~~~~~C~~C~~~f~~~~~L~~H~~~h~~ 469 (606)
+........+.-.+ -....+..|.|.+|++.|+....|+.|+.+|+.
T Consensus 334 ------~~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~ 381 (500)
T KOG3993|consen 334 ------QAVETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQR 381 (500)
T ss_pred ------hhhhhhhhhhhccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhc
Confidence 00000000000000 001224579999999999999999999988864
No 17
>KOG3993|consensus
Probab=98.68 E-value=5.2e-09 Score=101.67 Aligned_cols=84 Identities=25% Similarity=0.312 Sum_probs=57.6
Q ss_pred cceecccCccccCCHHHHHHHHhccccccCCC------------------------------------------Cccccc
Q psy15165 336 QYHVCPHCGKKFTRKAELQLHIKGIHLKHQLE------------------------------------------KTYICE 373 (606)
Q Consensus 336 ~~~~C~~C~~~f~~~~~l~~H~~~~h~~h~~~------------------------------------------~~~~C~ 373 (606)
..|.|.+|++.|.....|+.|+.++|..-... ....|+
T Consensus 355 gi~~C~~C~KkFrRqAYLrKHqlthq~~~~~k~~a~~f~~s~~~~l~~~~~~~a~h~~a~~~~g~~vl~~a~sael~~pp 434 (500)
T KOG3993|consen 355 GIFSCHTCGKKFRRQAYLRKHQLTHQRAPLAKEKAPKFLLSRVIPLMHFNQAVATHSSASDSHGDEVLYVAGSAELELPP 434 (500)
T ss_pred ceeecHHhhhhhHHHHHHHHhHHhhhccccchhcccCcchhhcccccccccccccccccccccccceeeeeccccccCCC
Confidence 46999999999999999999976544211100 013466
Q ss_pred ccccccCchHHHHhhhhhcCCCCccccCcchhccCChhHHhccccc
Q psy15165 374 YCHKEFTFYNYLRRHMRVHTNEKPYKCKDCGAAFNHNVSLKNHKNS 419 (606)
Q Consensus 374 ~C~k~f~~~~~L~~H~~~H~~~~~~~C~~C~~~f~~~~~L~~H~~~ 419 (606)
+||..+.++..--.+.+.-..+.-|.|.+|..+|.+..+|.+|+..
T Consensus 435 ~~~~ppsss~~sgg~~rlg~~~q~f~~ky~~atfyss~~ltrhin~ 480 (500)
T KOG3993|consen 435 YDGSPPSSSGSSGGYGRLGIAEQGFTCKYCPATFYSSPGLTRHINK 480 (500)
T ss_pred CCCCCcccCCCCCccccccchhhccccccchHhhhcCcchHhHhhh
Confidence 6666666555544454444456678899999999999999988753
No 18
>PHA02768 hypothetical protein; Provisional
Probab=98.67 E-value=7.5e-09 Score=71.58 Aligned_cols=45 Identities=18% Similarity=0.319 Sum_probs=36.2
Q ss_pred cccccccccccCchHHHHhhhhhcCCCCccccCcchhccCChhHHhc
Q psy15165 369 TYICEYCHKEFTFYNYLRRHMRVHTNEKPYKCKDCGAAFNHNVSLKN 415 (606)
Q Consensus 369 ~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~~C~~C~~~f~~~~~L~~ 415 (606)
.|.|+.||+.|...+.|..|+++|+ ++|+|..|++.|...+.|..
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l~~ 49 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEYIE 49 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceecccceeEE
Confidence 4788888888888888888888887 68888888888887766643
No 19
>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=98.56 E-value=3.2e-08 Score=58.41 Aligned_cols=25 Identities=68% Similarity=1.234 Sum_probs=19.8
Q ss_pred hHHHHHhhhcCCCCcccc-cCccCCc
Q psy15165 547 YLKRHMRTHTNEKPYKCV-CGLGFNF 571 (606)
Q Consensus 547 ~L~~H~~~H~~~kp~~C~-C~~~F~~ 571 (606)
+|.+||++|+|++||.|. |+++|.+
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 477888888888888887 8888863
No 20
>PHA00616 hypothetical protein
Probab=98.41 E-value=1.4e-07 Score=61.94 Aligned_cols=33 Identities=12% Similarity=0.239 Sum_probs=27.2
Q ss_pred cccccccchhccChhhHHHHHhhhcCCCCcccc
Q psy15165 532 TFVCEYCNKEFTFLQYLKRHMRTHTNEKPYKCV 564 (606)
Q Consensus 532 ~y~C~~C~k~f~~~~~L~~H~~~H~~~kp~~C~ 564 (606)
||+|+.||+.|..++.|..|++.|+|++|+.|.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~ 33 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLE 33 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCcccee
Confidence 578888888888888888888888888888774
No 21
>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=98.40 E-value=1.3e-07 Score=55.79 Aligned_cols=26 Identities=65% Similarity=1.246 Sum_probs=21.3
Q ss_pred HHHhhhhhcCCCCccccCcchhccCC
Q psy15165 384 YLRRHMRVHTNEKPYKCKDCGAAFNH 409 (606)
Q Consensus 384 ~L~~H~~~H~~~~~~~C~~C~~~f~~ 409 (606)
+|.+|+++|+|++||.|+.|+++|.+
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 47888888888888888888888863
No 22
>PHA00616 hypothetical protein
Probab=98.25 E-value=2.8e-07 Score=60.52 Aligned_cols=32 Identities=19% Similarity=0.216 Sum_probs=30.5
Q ss_pred Ccccc-cCccCCchhhHHHhhhccccccchhhc
Q psy15165 560 PYKCV-CGLGFNFNVSLKNHKQKCSVFLLTESM 591 (606)
Q Consensus 560 p~~C~-C~~~F~~~~~L~~H~~~h~~~~~~~c~ 591 (606)
||.|. ||+.|...+.|.+|+++||+++|+.|.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~ 33 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLE 33 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCcccee
Confidence 79998 999999999999999999999999875
No 23
>PHA00732 hypothetical protein
Probab=98.13 E-value=1.5e-06 Score=66.70 Aligned_cols=48 Identities=27% Similarity=0.538 Sum_probs=34.4
Q ss_pred ccCCCCCCcCCChHHHHHhhhcccccCCCCccccccccchhccChhhHHHHHhhhcC
Q psy15165 501 LQCPHCPKTFPRKTELSNHIKGIHMKHELRQTFVCEYCNKEFTFLQYLKRHMRTHTN 557 (606)
Q Consensus 501 ~~C~~C~~~f~~~~~L~~H~~~~H~~~~~~k~y~C~~C~k~f~~~~~L~~H~~~H~~ 557 (606)
|.|+.||+.|.+...|..|++..| . ++.|+.||++|. .|..|++++..
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r~~H---~---~~~C~~CgKsF~---~l~~H~~~~~~ 49 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHARRNH---T---LTKCPVCNKSYR---RLNQHFYSQYD 49 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhhccc---C---CCccCCCCCEeC---ChhhhhcccCC
Confidence 678888888888888888876334 2 357888888887 47777765543
No 24
>PHA00732 hypothetical protein
Probab=98.09 E-value=2.5e-06 Score=65.43 Aligned_cols=47 Identities=32% Similarity=0.489 Sum_probs=40.7
Q ss_pred cccccccchhccChhhHHHHHhh-hcCCCCcccc-cCccCCchhhHHHhhhcccc
Q psy15165 532 TFVCEYCNKEFTFLQYLKRHMRT-HTNEKPYKCV-CGLGFNFNVSLKNHKQKCSV 584 (606)
Q Consensus 532 ~y~C~~C~k~f~~~~~L~~H~~~-H~~~kp~~C~-C~~~F~~~~~L~~H~~~h~~ 584 (606)
||.|+.||+.|.+...|..|++. |+ ++.|. |+++|. .|..|+++...
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~---~l~~H~~~~~~ 49 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYR---RLNQHFYSQYD 49 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeC---ChhhhhcccCC
Confidence 68999999999999999999985 65 46898 999997 58899987653
No 25
>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=98.03 E-value=6.8e-06 Score=58.49 Aligned_cols=51 Identities=27% Similarity=0.546 Sum_probs=38.2
Q ss_pred ccCCCCCCcCCChHHHHHhhhcccccCCCCccccccccchhccChhhHHHHHhhhc
Q psy15165 501 LQCPHCPKTFPRKTELSNHIKGIHMKHELRQTFVCEYCNKEFTFLQYLKRHMRTHT 556 (606)
Q Consensus 501 ~~C~~C~~~f~~~~~L~~H~~~~H~~~~~~k~y~C~~C~k~f~~~~~L~~H~~~H~ 556 (606)
|.||+|++ ..+...|..|+...|. ...+.+.|++|...+. .+|..|+..++
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~~~H~--~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCEDEHR--SESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHHhHCc--CCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 78999999 4556789999887773 2345688999988655 48888887765
No 26
>PF01352 KRAB: KRAB box; InterPro: IPR001909 The Krueppel-associated box (KRAB) is a domain of around 75 amino acids that is found in the N-terminal part of about one third of eukaryotic Krueppel-type C2H2 zinc finger proteins (ZFPs) []. It is enriched in charged amino acids and can be divided into subregions A and B, which are predicted to fold into two amphipathic alpha-helices. The KRAB A and B boxes can be separated by variable spacer segments and many KRAB proteins contain only the A box []. The functions currently known for members of the KRAB-containing protein family include transcriptional repression of RNA polymerase I, II, and III promoters, binding and splicing of RNA, and control of nucleolus function. The KRAB domain functions as a transcriptional repressor when tethered to the template DNA by a DNA-binding domain. A sequence of 45 amino acids in the KRAB A subdomain has been shown to be necessary and sufficient for transcriptional repression. The B box does not repress by itself but does potentiate the repression exerted by the KRAB A subdomain [, ]. Gene silencing requires the binding of the KRAB domain to the RING-B box-coiled coil (RBCC) domain of the KAP-1/TIF1-beta corepressor. As KAP-1 binds to the heterochromatin proteins HP1, it has been proposed that the KRAB-ZFP-bound target gene could be silenced following recruitment to heterochromatin [, ]. KRAB-ZFPs probably constitute the single largest class of transcription factors within the human genome []. Although the function of KRAB-ZFPs is largely unknown, they appear to play important roles during cell differentiation and development. The KRAB domain is generally encoded by two exons. The regions coded by the two exons are known as KRAB-A and KRAB-B.; GO: 0003676 nucleic acid binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1V65_A.
Probab=98.00 E-value=9.3e-07 Score=58.07 Aligned_cols=22 Identities=27% Similarity=0.431 Sum_probs=14.5
Q ss_pred ccccccccc---------ccccCCCceeeec
Q psy15165 2 YDDDWNNLD---------DHVGKPSRRRSLG 23 (606)
Q Consensus 2 ~~~~~~~~~---------~~~~~~~~~~~~g 23 (606)
+.|||..|| ||+|||+||+|||
T Consensus 11 s~eEW~~L~~~Qk~ly~dvm~Eny~~l~slG 41 (41)
T PF01352_consen 11 SQEEWELLDPAQKNLYRDVMLENYRNLVSLG 41 (41)
T ss_dssp -HHHHHTS-HHHHHHHHHHHHHTTTS---S-
T ss_pred ChhhcccccceecccchhHHHHhhcccEecC
Confidence 368999885 8899999999998
No 27
>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=97.99 E-value=9.6e-06 Score=57.70 Aligned_cols=51 Identities=24% Similarity=0.452 Sum_probs=33.7
Q ss_pred ccccccccccCCHHHHHHhHhhhcCCCCCCcccCccccccCCHHHHHHHHHHhh
Q psy15165 249 FKCRVCDWKLNSYDKLLRHIKSDHGGYETSSLCYHCGYYSKNRSTLKNHVRVEH 302 (606)
Q Consensus 249 ~~C~~C~~~f~~~~~L~~H~~~~H~~~~~~~~C~~C~~~f~~~~~L~~H~~~h~ 302 (606)
|.|++|++ ..+...|..|....|....+.+.|++|...+. ..|..|+..+|
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 67777777 44566777777766765445677777776544 36777776665
No 28
>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=97.74 E-value=1.5e-05 Score=45.58 Aligned_cols=23 Identities=48% Similarity=0.928 Sum_probs=14.3
Q ss_pred ccccccchhccChhhHHHHHhhh
Q psy15165 533 FVCEYCNKEFTFLQYLKRHMRTH 555 (606)
Q Consensus 533 y~C~~C~k~f~~~~~L~~H~~~H 555 (606)
|.|+.|++.|.+...|..|+++|
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 45666666666666666666554
No 29
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.38 E-value=7.6e-05 Score=61.19 Aligned_cols=72 Identities=22% Similarity=0.382 Sum_probs=18.9
Q ss_pred cCCCCCCcCCChHHHHHhhhcccccCCCCccccccccchhccChhhHHHHHhhhcCCCCcccc-cCccCCchhhHHHhhh
Q psy15165 502 QCPHCPKTFPRKTELSNHIKGIHMKHELRQTFVCEYCNKEFTFLQYLKRHMRTHTNEKPYKCV-CGLGFNFNVSLKNHKQ 580 (606)
Q Consensus 502 ~C~~C~~~f~~~~~L~~H~~~~H~~~~~~k~y~C~~C~k~f~~~~~L~~H~~~H~~~kp~~C~-C~~~F~~~~~L~~H~~ 580 (606)
+|..|+..|.+...|..|+...|..... ....+.....|..+++.-. ..++.|. |++.|.+...|..||+
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~--------~~~~l~~~~~~~~~~~~~~-~~~~~C~~C~~~f~s~~~l~~Hm~ 71 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIP--------DQKYLVDPNRLLNYLRKKV-KESFRCPYCNKTFRSREALQEHMR 71 (100)
T ss_dssp ---------------------------------------------------------SSEEBSSSS-EESSHHHHHHHHH
T ss_pred Cccccccccccccccccccccccccccc--------ccccccccccccccccccc-CCCCCCCccCCCCcCHHHHHHHHc
Confidence 5899999999999999999877732211 1222234445555544322 2268887 9988888888999988
Q ss_pred cc
Q psy15165 581 KC 582 (606)
Q Consensus 581 ~h 582 (606)
.+
T Consensus 72 ~~ 73 (100)
T PF12756_consen 72 SK 73 (100)
T ss_dssp HT
T ss_pred Cc
Confidence 64
No 30
>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=97.33 E-value=0.00011 Score=41.94 Aligned_cols=21 Identities=43% Similarity=0.781 Sum_probs=9.9
Q ss_pred cccccccccCchHHHHhhhhh
Q psy15165 371 ICEYCHKEFTFYNYLRRHMRV 391 (606)
Q Consensus 371 ~C~~C~k~f~~~~~L~~H~~~ 391 (606)
.|+.|++.|.+...|..|++.
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 2 KCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCccCCHHHHHHHHhH
Confidence 444444444444444444443
No 31
>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=97.32 E-value=0.00014 Score=41.99 Aligned_cols=23 Identities=48% Similarity=0.901 Sum_probs=12.5
Q ss_pred ccccccchhccChhhHHHHHhhh
Q psy15165 533 FVCEYCNKEFTFLQYLKRHMRTH 555 (606)
Q Consensus 533 y~C~~C~k~f~~~~~L~~H~~~H 555 (606)
|.|++|++.|.+...|..|+++|
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 45666666666666666666554
No 32
>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=97.19 E-value=0.00018 Score=42.97 Aligned_cols=24 Identities=42% Similarity=0.870 Sum_probs=13.1
Q ss_pred ccccccchhccChhhHHHHHhhhc
Q psy15165 533 FVCEYCNKEFTFLQYLKRHMRTHT 556 (606)
Q Consensus 533 y~C~~C~k~f~~~~~L~~H~~~H~ 556 (606)
|.|..|++.|.+...|..|++.|.
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 455555555555555555555543
No 33
>KOG2231|consensus
Probab=97.02 E-value=0.0012 Score=70.49 Aligned_cols=80 Identities=23% Similarity=0.457 Sum_probs=56.1
Q ss_pred ccCCCCCCcCCChHHHHHhhhcccccCCCCccccccccc------hhccChhhHHHHHhhhcCCCCcccc---cCc----
Q psy15165 501 LQCPHCPKTFPRKTELSNHIKGIHMKHELRQTFVCEYCN------KEFTFLQYLKRHMRTHTNEKPYKCV---CGL---- 567 (606)
Q Consensus 501 ~~C~~C~~~f~~~~~L~~H~~~~H~~~~~~k~y~C~~C~------k~f~~~~~L~~H~~~H~~~kp~~C~---C~~---- 567 (606)
-.|..|...|-....|.+|++..| |.|.+|. -.|.....|..|.|.++ |.|. |.-
T Consensus 183 p~C~~C~~~fld~~el~rH~~~~h--------~~chfC~~~~~~neyy~~~~dLe~HfR~~H----flCE~~~C~~~~f~ 250 (669)
T KOG2231|consen 183 PLCKFCHERFLDDDELYRHLRFDH--------EFCHFCDYKTGQNEYYNDYDDLEEHFRKGH----FLCEEEFCRTKKFY 250 (669)
T ss_pred ccchhhhhhhccHHHHHHhhccce--------eheeecCcccccchhcccchHHHHHhhhcC----ccccccccccceee
Confidence 479999999999999999998666 7788874 56778888999888766 5562 432
Q ss_pred -cCCchhhHHHhhhccccccchhhcc
Q psy15165 568 -GFNFNVSLKNHKQKCSVFLLTESMN 592 (606)
Q Consensus 568 -~F~~~~~L~~H~~~h~~~~~~~c~~ 592 (606)
.|.....|+.|.+.+..++-|.|..
T Consensus 251 ~~~~~ei~lk~~~~~~~~e~~~~~~~ 276 (669)
T KOG2231|consen 251 VAFELEIELKAHNRFIQHEKCYICRP 276 (669)
T ss_pred ehhHHHHHHHhhccccchheeccCCc
Confidence 2233445555555555567777753
No 34
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.01 E-value=0.0002 Score=67.71 Aligned_cols=55 Identities=31% Similarity=0.601 Sum_probs=32.1
Q ss_pred CccccCCC--CCCcCCChHHHHHhhhccccc---C------------CCCccccccccchhccChhhHHHHH
Q psy15165 498 GFFLQCPH--CPKTFPRKTELSNHIKGIHMK---H------------ELRQTFVCEYCNKEFTFLQYLKRHM 552 (606)
Q Consensus 498 ~~~~~C~~--C~~~f~~~~~L~~H~~~~H~~---~------------~~~k~y~C~~C~k~f~~~~~L~~H~ 552 (606)
+++|+|++ |.|+|++...|+.|+..-|.. | ...|||+|++|+|++.....|+.|.
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr 418 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHR 418 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceecc
Confidence 45577765 777777777777777532300 0 0125566666666666666555553
No 35
>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=97.00 E-value=0.00048 Score=39.63 Aligned_cols=22 Identities=32% Similarity=0.673 Sum_probs=10.0
Q ss_pred ccCccccccCCHHHHHHHHHHh
Q psy15165 280 LCYHCGYYSKNRSTLKNHVRVE 301 (606)
Q Consensus 280 ~C~~C~~~f~~~~~L~~H~~~h 301 (606)
.|+.|++.|.+...|+.|+..+
T Consensus 2 ~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 2 QCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp E-SSTS-EESSHHHHHHHHHHH
T ss_pred CCcCCCCcCCcHHHHHHHHHhh
Confidence 4555555555555555555444
No 36
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.00 E-value=0.00042 Score=56.74 Aligned_cols=74 Identities=28% Similarity=0.418 Sum_probs=22.4
Q ss_pred ccccCccccCCHHHHHhhhhccccccCCCCCCcccccccccccCCHHHHHHhHhhhcCCCCCCcccCccccccCCHHHHH
Q psy15165 216 KCRVCDWKLNSYDKLLRHMDWDEVHLGQFSPYEFKCRVCDWKLNSYDKLLRHIKSDHGGYETSSLCYHCGYYSKNRSTLK 295 (606)
Q Consensus 216 ~C~~C~~~f~~~~~l~~H~~~~~~h~~~~~~~~~~C~~C~~~f~~~~~L~~H~~~~H~~~~~~~~C~~C~~~f~~~~~L~ 295 (606)
+|..|+..|.+...|..||.. .|.-. -. ....+.....+..+++..- ...+.|..|++.|.+...|.
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~--~H~~~-------~~-~~~~l~~~~~~~~~~~~~~---~~~~~C~~C~~~f~s~~~l~ 67 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKK--KHGFD-------IP-DQKYLVDPNRLLNYLRKKV---KESFRCPYCNKTFRSREALQ 67 (100)
T ss_dssp -------------------------------------------------------------SSEEBSSSS-EESSHHHHH
T ss_pred Ccccccccccccccccccccc--ccccc-------cc-ccccccccccccccccccc---CCCCCCCccCCCCcCHHHHH
Confidence 599999999999999999963 33211 11 1223335555555554221 34689999999999999999
Q ss_pred HHHHHhh
Q psy15165 296 NHVRVEH 302 (606)
Q Consensus 296 ~H~~~h~ 302 (606)
.|++.++
T Consensus 68 ~Hm~~~~ 74 (100)
T PF12756_consen 68 EHMRSKH 74 (100)
T ss_dssp HHHHHTT
T ss_pred HHHcCcc
Confidence 9999764
No 37
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=96.94 E-value=0.00028 Score=66.71 Aligned_cols=52 Identities=33% Similarity=0.660 Sum_probs=45.4
Q ss_pred CCccccccc--cchhccChhhHHHHHhh-hc------------------CCCCcccc-cCccCCchhhHHHhhh
Q psy15165 529 LRQTFVCEY--CNKEFTFLQYLKRHMRT-HT------------------NEKPYKCV-CGLGFNFNVSLKNHKQ 580 (606)
Q Consensus 529 ~~k~y~C~~--C~k~f~~~~~L~~H~~~-H~------------------~~kp~~C~-C~~~F~~~~~L~~H~~ 580 (606)
++|||+|++ |.|+++....|+.|+.- |. ..|||+|. |++.+.....|+.|+.
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceeccc
Confidence 459999998 99999999999999862 41 24899998 9999999999999975
No 38
>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=96.91 E-value=0.00049 Score=41.02 Aligned_cols=25 Identities=32% Similarity=0.744 Sum_probs=23.2
Q ss_pred Ccccc-cCccCCchhhHHHhhhcccc
Q psy15165 560 PYKCV-CGLGFNFNVSLKNHKQKCSV 584 (606)
Q Consensus 560 p~~C~-C~~~F~~~~~L~~H~~~h~~ 584 (606)
||.|. |++.|.+...|..|++.|..
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHCS 26 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhcC
Confidence 68998 99999999999999999864
No 39
>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=96.88 E-value=0.00076 Score=45.38 Aligned_cols=33 Identities=24% Similarity=0.464 Sum_probs=21.7
Q ss_pred CCCccccccccchhccChhhHHHHHhhhcCCCC
Q psy15165 528 ELRQTFVCEYCNKEFTFLQYLKRHMRTHTNEKP 560 (606)
Q Consensus 528 ~~~k~y~C~~C~k~f~~~~~L~~H~~~H~~~kp 560 (606)
..+.|-.|++|+..+.+..+|++|+.++++.+|
T Consensus 20 ~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 20 QSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred ccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 566778888888888888888888887777665
No 40
>KOG2231|consensus
Probab=96.71 E-value=0.0028 Score=67.76 Aligned_cols=81 Identities=26% Similarity=0.447 Sum_probs=44.0
Q ss_pred cccccCcccc---------------CCHHHHHhhhhccccccCCCCCCcccccccc---------cccCCHHHHHHhHhh
Q psy15165 215 FKCRVCDWKL---------------NSYDKLLRHMDWDEVHLGQFSPYEFKCRVCD---------WKLNSYDKLLRHIKS 270 (606)
Q Consensus 215 ~~C~~C~~~f---------------~~~~~l~~H~~~~~~h~~~~~~~~~~C~~C~---------~~f~~~~~L~~H~~~ 270 (606)
+.|.+|++.| .+...|..|+.. .|. - +.|.+|- ...-+...|..|+..
T Consensus 100 ~~C~~C~~~~~~~~~~~~~~~c~~~~s~~~Lk~H~~~--~H~----~--~~c~lC~~~~kif~~e~k~Yt~~el~~h~~~ 171 (669)
T KOG2231|consen 100 HSCHICDRRFRALYNKKECLHCTEFKSVENLKNHMRD--QHK----L--HLCSLCLQNLKIFINERKLYTRAELNLHLMF 171 (669)
T ss_pred hhcCccccchhhhcccCCCccccchhHHHHHHHHHHH--hhh----h--hccccccccceeeeeeeehehHHHHHHHHhc
Confidence 4566666655 367777777741 221 1 4455542 222355666666653
Q ss_pred hcCCC---CCCcccCccccccCCHHHHHHHHHHhhC
Q psy15165 271 DHGGY---ETSSLCYHCGYYSKNRSTLKNHVRVEHG 303 (606)
Q Consensus 271 ~H~~~---~~~~~C~~C~~~f~~~~~L~~H~~~h~~ 303 (606)
--... ..--.|..|...|-....|.+|++.+|-
T Consensus 172 gd~d~~s~rGhp~C~~C~~~fld~~el~rH~~~~h~ 207 (669)
T KOG2231|consen 172 GDPDDESCRGHPLCKFCHERFLDDDELYRHLRFDHE 207 (669)
T ss_pred CCCccccccCCccchhhhhhhccHHHHHHhhcccee
Confidence 21110 0113477777777777777777776553
No 41
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.64 E-value=0.0015 Score=38.17 Aligned_cols=23 Identities=48% Similarity=0.810 Sum_probs=12.4
Q ss_pred ccccccchhccChhhHHHHHhhh
Q psy15165 533 FVCEYCNKEFTFLQYLKRHMRTH 555 (606)
Q Consensus 533 y~C~~C~k~f~~~~~L~~H~~~H 555 (606)
|.|+.|+++|.....|..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 34555555555555555555544
No 42
>KOG1146|consensus
Probab=96.58 E-value=0.0005 Score=77.39 Aligned_cols=84 Identities=20% Similarity=0.320 Sum_probs=59.7
Q ss_pred CcceecccCccccCCHHHHHHHHhcc-cc-----------------cc---------------------CCCCccccccc
Q psy15165 335 GQYHVCPHCGKKFTRKAELQLHIKGI-HL-----------------KH---------------------QLEKTYICEYC 375 (606)
Q Consensus 335 ~~~~~C~~C~~~f~~~~~l~~H~~~~-h~-----------------~h---------------------~~~~~~~C~~C 375 (606)
+.+|.|..|...+.++.+|.+|+... |. .+ ...-.+.|.+|
T Consensus 516 ~~p~~C~~C~~stttng~LsihlqS~~h~~~lee~~~~~g~~v~~~~~~v~s~~P~~ag~~~~ags~~pktkP~~~C~vc 595 (1406)
T KOG1146|consen 516 GKPYPCRACNYSTTTNGNLSIHLQSDLHRNELEEAEENAGEQVRLLPASVTSAVPEEAGLGPSAGSSGPKTKPSWRCEVC 595 (1406)
T ss_pred CCcccceeeeeeeecchHHHHHHHHHhhHHHHHHHHhccccchhhhhhhhcccCcccccCCCCCCCCCCCCCCCcchhhh
Confidence 47899999999999999999998631 10 00 00123889999
Q ss_pred ccccCchHHHHhhhhh-cCCCCccccCcchhccCChhHHhcccc
Q psy15165 376 HKEFTFYNYLRRHMRV-HTNEKPYKCKDCGAAFNHNVSLKNHKN 418 (606)
Q Consensus 376 ~k~f~~~~~L~~H~~~-H~~~~~~~C~~C~~~f~~~~~L~~H~~ 418 (606)
++..+-..+|+.||.. ++..-|..|-.|.-.+.....+..+.+
T Consensus 596 ~yetniarnlrihmtss~~s~~p~~~Lq~~it~~l~~~~~~~~~ 639 (1406)
T KOG1146|consen 596 SYETNIARNLRIHMTASPSSSPPSLVLQQNITSSLASLLGGQGR 639 (1406)
T ss_pred cchhhhhhccccccccCCCCCChHHHhhhcchhhccccccCcCC
Confidence 9999989999999873 333444777777777777766666655
No 43
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.26 E-value=0.0025 Score=36.67 Aligned_cols=23 Identities=30% Similarity=0.690 Sum_probs=12.5
Q ss_pred ccccccchhccChhhHHHHHhhhc
Q psy15165 533 FVCEYCNKEFTFLQYLKRHMRTHT 556 (606)
Q Consensus 533 y~C~~C~k~f~~~~~L~~H~~~H~ 556 (606)
|+|+.|++... ...|.+|+++|+
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 45666666665 666666666543
No 44
>PRK04860 hypothetical protein; Provisional
Probab=96.25 E-value=0.0019 Score=57.08 Aligned_cols=38 Identities=29% Similarity=0.701 Sum_probs=28.9
Q ss_pred cccccccchhccChhhHHHHHhhhcCCCCcccc-cCccCCchh
Q psy15165 532 TFVCEYCNKEFTFLQYLKRHMRTHTNEKPYKCV-CGLGFNFNV 573 (606)
Q Consensus 532 ~y~C~~C~k~f~~~~~L~~H~~~H~~~kp~~C~-C~~~F~~~~ 573 (606)
+|.|. |+. ....+++|.++|+|+++|.|. |+..|....
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFKG 157 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEec
Confidence 57887 876 677778888888888888886 888776543
No 45
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=96.01 E-value=0.011 Score=56.90 Aligned_cols=83 Identities=25% Similarity=0.506 Sum_probs=57.1
Q ss_pred Cccccc--CccccCCHHHHHhhhhccccccCCCCCCcccccccc---ccc------CCHHHHHHhHhhhcC--CCCCCcc
Q psy15165 214 EFKCRV--CDWKLNSYDKLLRHMDWDEVHLGQFSPYEFKCRVCD---WKL------NSYDKLLRHIKSDHG--GYETSSL 280 (606)
Q Consensus 214 ~~~C~~--C~~~f~~~~~l~~H~~~~~~h~~~~~~~~~~C~~C~---~~f------~~~~~L~~H~~~~H~--~~~~~~~ 280 (606)
.|.|+. |.........|..|.+. ..+. +.|.+|- +.| -+...|+.|...--. ++..--.
T Consensus 151 ~F~CP~skc~~~C~~~k~lk~H~K~---~H~~-----~~C~~C~~nKk~F~~E~~lF~~~~Lr~H~~~G~~e~GFKGHP~ 222 (493)
T COG5236 151 SFKCPKSKCHRRCGSLKELKKHYKA---QHGF-----VLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGHPL 222 (493)
T ss_pred HhcCCchhhhhhhhhHHHHHHHHHh---hcCc-----EEhHhhhcCcccCccceeeeecccccccccCCccccCcCCCch
Confidence 478865 77777778899999873 2222 6788873 233 356677788652111 1122335
Q ss_pred cCccccccCCHHHHHHHHHHhhCC
Q psy15165 281 CYHCGYYSKNRSTLKNHVRVEHGE 304 (606)
Q Consensus 281 C~~C~~~f~~~~~L~~H~~~h~~~ 304 (606)
|..|...|-+-..|..|++..|..
T Consensus 223 C~FC~~~FYdDDEL~~HcR~~HE~ 246 (493)
T COG5236 223 CIFCKIYFYDDDELRRHCRLRHEA 246 (493)
T ss_pred hhhccceecChHHHHHHHHhhhhh
Confidence 999999999999999999988763
No 46
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=95.87 E-value=0.0043 Score=36.08 Aligned_cols=22 Identities=41% Similarity=0.954 Sum_probs=13.6
Q ss_pred ccccccchhccChhhHHHHHhh
Q psy15165 533 FVCEYCNKEFTFLQYLKRHMRT 554 (606)
Q Consensus 533 y~C~~C~k~f~~~~~L~~H~~~ 554 (606)
|.|.+|++.|.+...|..|++.
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 4566666666666666666654
No 47
>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=95.78 E-value=0.0082 Score=40.54 Aligned_cols=33 Identities=30% Similarity=0.518 Sum_probs=17.4
Q ss_pred CCCCcccccccccccCchHHHHhhhhhcCCCCc
Q psy15165 365 QLEKTYICEYCHKEFTFYNYLRRHMRVHTNEKP 397 (606)
Q Consensus 365 ~~~~~~~C~~C~k~f~~~~~L~~H~~~H~~~~~ 397 (606)
..+.|-.|++|+..+....+|++|+..+++.+|
T Consensus 20 ~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 20 QSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred ccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 345566677777777777777777766655544
No 48
>smart00355 ZnF_C2H2 zinc finger.
Probab=95.55 E-value=0.015 Score=33.75 Aligned_cols=24 Identities=29% Similarity=0.531 Sum_probs=21.8
Q ss_pred ccCCCCCCccCCHHHHHHHHHHhc
Q psy15165 445 NLCYICGFFSAKRSTLAHHIQDHI 468 (606)
Q Consensus 445 ~~C~~C~~~f~~~~~L~~H~~~h~ 468 (606)
|.|..|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 579999999999999999999774
No 49
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=95.54 E-value=0.011 Score=34.01 Aligned_cols=23 Identities=39% Similarity=0.834 Sum_probs=11.6
Q ss_pred cccCccccccCCHHHHHHHHHHhh
Q psy15165 279 SLCYHCGYYSKNRSTLKNHVRVEH 302 (606)
Q Consensus 279 ~~C~~C~~~f~~~~~L~~H~~~h~ 302 (606)
|+|+.|++... ...|..|++.+|
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 34555555555 555555555554
No 50
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=95.34 E-value=0.01 Score=34.49 Aligned_cols=20 Identities=45% Similarity=0.957 Sum_probs=10.5
Q ss_pred cccccccccCchHHHHhhhh
Q psy15165 371 ICEYCHKEFTFYNYLRRHMR 390 (606)
Q Consensus 371 ~C~~C~k~f~~~~~L~~H~~ 390 (606)
.|.+|++.|.+...|+.|++
T Consensus 2 ~C~~C~~~f~s~~~~~~H~~ 21 (25)
T PF12874_consen 2 YCDICNKSFSSENSLRQHLR 21 (25)
T ss_dssp EETTTTEEESSHHHHHHHHT
T ss_pred CCCCCCCCcCCHHHHHHHHC
Confidence 45555555555555555544
No 51
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=95.15 E-value=0.036 Score=53.43 Aligned_cols=123 Identities=22% Similarity=0.391 Sum_probs=82.7
Q ss_pred ccCCC--CCCccCCHHHHHHHHHHhcCCCCCcCccccccc------------cchhhhhcccccccCC--cc--ccCCCC
Q psy15165 445 NLCYI--CGFFSAKRSTLAHHIQDHIQPRMKQKQICEICC------------AEVYHINGHIKDKHSG--FF--LQCPHC 506 (606)
Q Consensus 445 ~~C~~--C~~~f~~~~~L~~H~~~h~~~~~~~~~~C~~c~------------~~~~~l~~H~~~~h~~--~~--~~C~~C 506 (606)
|.|+. |......-..|..|.+..++- ..|.+|- ...+.|..|...-..+ .+ -.|..|
T Consensus 152 F~CP~skc~~~C~~~k~lk~H~K~~H~~-----~~C~~C~~nKk~F~~E~~lF~~~~Lr~H~~~G~~e~GFKGHP~C~FC 226 (493)
T COG5236 152 FKCPKSKCHRRCGSLKELKKHYKAQHGF-----VLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGHPLCIFC 226 (493)
T ss_pred hcCCchhhhhhhhhHHHHHHHHHhhcCc-----EEhHhhhcCcccCccceeeeecccccccccCCccccCcCCCchhhhc
Confidence 44543 445555566777787765543 5677775 2334566665442222 22 469999
Q ss_pred CCcCCChHHHHHhhhcccccCCCCccccccccch-------hccChhhHHHHHhhhcCCCCccc--c-cC----ccCCch
Q psy15165 507 PKTFPRKTELSNHIKGIHMKHELRQTFVCEYCNK-------EFTFLQYLKRHMRTHTNEKPYKC--V-CG----LGFNFN 572 (606)
Q Consensus 507 ~~~f~~~~~L~~H~~~~H~~~~~~k~y~C~~C~k-------~f~~~~~L~~H~~~H~~~kp~~C--~-C~----~~F~~~ 572 (606)
...|.+-..|.+|+|..| + +|.+|++ .|.....|.+|.+.- -|.| . |. +.|...
T Consensus 227 ~~~FYdDDEL~~HcR~~H-----E---~ChICD~v~p~~~QYFK~Y~~Le~HF~~~----hy~ct~qtc~~~k~~vf~~~ 294 (493)
T COG5236 227 KIYFYDDDELRRHCRLRH-----E---ACHICDMVGPIRYQYFKSYEDLEAHFRNA----HYCCTFQTCRVGKCYVFPYH 294 (493)
T ss_pred cceecChHHHHHHHHhhh-----h---hhhhhhccCccchhhhhCHHHHHHHhhcC----ceEEEEEEEecCcEEEeccH
Confidence 999999999999999766 2 4666654 478888888887632 3777 2 64 469999
Q ss_pred hhHHHhhhcccc
Q psy15165 573 VSLKNHKQKCSV 584 (606)
Q Consensus 573 ~~L~~H~~~h~~ 584 (606)
..|..|+-.-|+
T Consensus 295 ~el~~h~~~~h~ 306 (493)
T COG5236 295 TELLEHLTRFHK 306 (493)
T ss_pred HHHHHHHHHHhh
Confidence 999999866553
No 52
>KOG2482|consensus
Probab=95.00 E-value=0.08 Score=51.15 Aligned_cols=147 Identities=23% Similarity=0.345 Sum_probs=86.4
Q ss_pred HHHHHhHhhhcCCCCCCcccCcccccc-CCHHHHHHHHHHhhCCccccccccccccccccchHhHHHHHHhccCCcceec
Q psy15165 262 DKLLRHIKSDHGGYETSSLCYHCGYYS-KNRSTLKNHVRVEHGENQAKRKEKKICDICSAEVVHLAIHKKHSHSGQYHVC 340 (606)
Q Consensus 262 ~~L~~H~~~~H~~~~~~~~C~~C~~~f-~~~~~L~~H~~~h~~~~~~~~~~~~~C~~C~~~~~~l~~h~~~~~~~~~~~C 340 (606)
..|.+|++.- .+.....+|-.|...+ .+++....|+-..|+-....+.+...| ..|..|.+.. -..+.|
T Consensus 129 eaLeqqQ~Er-edt~fslqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyv-------nelLehLkek--L~r~~C 198 (423)
T KOG2482|consen 129 EALEQQQKER-EDTIFSLQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYV-------NELLEHLKEK--LERLRC 198 (423)
T ss_pred HHHHHHHHHh-cCCeeeeEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeH-------HHHHHHHHHH--Hhhhee
Confidence 3555565533 2223445677776544 345556667666565433222121111 1233333210 024788
Q ss_pred ccCccccCCHHHHHHHHhccccccCC--------------------------------------------------CCc-
Q psy15165 341 PHCGKKFTRKAELQLHIKGIHLKHQL--------------------------------------------------EKT- 369 (606)
Q Consensus 341 ~~C~~~f~~~~~l~~H~~~~h~~h~~--------------------------------------------------~~~- 369 (606)
-+|.+.|..+..|+.||+........ ..+
T Consensus 199 LyCekifrdkntLkeHMrkK~HrrinPknreYDkfyiINY~ev~ks~t~~~~e~dret~~d~~E~D~~wsDw~ed~a~a~ 278 (423)
T KOG2482|consen 199 LYCEKIFRDKNTLKEHMRKKRHRRINPKNREYDKFYIINYLEVGKSWTIVHSEDDRETNEDINETDDTWSDWNEDDAEAL 278 (423)
T ss_pred eeeccccCCcHHHHHHHHhccCcccCCCccccceEEEEeHhhcCCccchhhhhhhhhhhccccccccchhhhhcCCCCcc
Confidence 89999999999999998743100000 011
Q ss_pred -ccccccccccCchHHHHhhhhh-cCC--------------------------CCccccCcchhccCChhHHhcccc
Q psy15165 370 -YICEYCHKEFTFYNYLRRHMRV-HTN--------------------------EKPYKCKDCGAAFNHNVSLKNHKN 418 (606)
Q Consensus 370 -~~C~~C~k~f~~~~~L~~H~~~-H~~--------------------------~~~~~C~~C~~~f~~~~~L~~H~~ 418 (606)
..|-.|....-+...|..||.. |.= ...-.|-.|.-.|.....|..||-
T Consensus 279 ~v~CLfC~~~~en~~~l~eHmk~vHe~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c~~cd~~F~~e~~l~~hm~ 355 (423)
T KOG2482|consen 279 SVVCLFCTNFYENPVFLFEHMKIVHEFDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCAECDLSFWKEPGLLIHMV 355 (423)
T ss_pred ceEEEeeccchhhHHHHHHHHHHHHHhhHHhhccccccchhhhhhHHHHHHHHhhccccccccccccCcchhhhhcc
Confidence 5899999988889999999874 420 011358888889999999999976
No 53
>PRK04860 hypothetical protein; Provisional
Probab=94.95 E-value=0.0099 Score=52.57 Aligned_cols=38 Identities=34% Similarity=0.804 Sum_probs=29.2
Q ss_pred cccccccccccCchHHHHhhhhhcCCCCccccCcchhccCCh
Q psy15165 369 TYICEYCHKEFTFYNYLRRHMRVHTNEKPYKCKDCGAAFNHN 410 (606)
Q Consensus 369 ~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~~C~~C~~~f~~~ 410 (606)
+|.|. |+. ....+++|.++|+++++|.|..|+..|...
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEe
Confidence 57887 876 556678888888888888888888877643
No 54
>KOG2785|consensus
Probab=94.69 E-value=0.05 Score=53.72 Aligned_cols=50 Identities=20% Similarity=0.392 Sum_probs=41.8
Q ss_pred cccccccchhccChhhHHHHHhhhcCC-----------------------CCcccc-cC---ccCCchhhHHHhhhc
Q psy15165 532 TFVCEYCNKEFTFLQYLKRHMRTHTNE-----------------------KPYKCV-CG---LGFNFNVSLKNHKQK 581 (606)
Q Consensus 532 ~y~C~~C~k~f~~~~~L~~H~~~H~~~-----------------------kp~~C~-C~---~~F~~~~~L~~H~~~ 581 (606)
|-.|-+|++.|.+-..-..||..++|- .-|.|. |+ +.|.+....+.||+.
T Consensus 166 Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 166 PTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred CcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhh
Confidence 467888999999988889999887762 237898 99 999999999999974
No 55
>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=94.46 E-value=0.025 Score=33.50 Aligned_cols=21 Identities=38% Similarity=0.748 Sum_probs=16.3
Q ss_pred cccccCccccCCHHHHHhhhh
Q psy15165 215 FKCRVCDWKLNSYDKLLRHMD 235 (606)
Q Consensus 215 ~~C~~C~~~f~~~~~l~~H~~ 235 (606)
|.|..|++.|.+...|..|++
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~ 22 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMK 22 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTT
T ss_pred CCcccCCCCcCCHHHHHHHHc
Confidence 567888888888888877775
No 56
>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=94.43 E-value=0.023 Score=33.70 Aligned_cols=21 Identities=38% Similarity=0.874 Sum_probs=11.8
Q ss_pred ccccccccccCchHHHHhhhh
Q psy15165 370 YICEYCHKEFTFYNYLRRHMR 390 (606)
Q Consensus 370 ~~C~~C~k~f~~~~~L~~H~~ 390 (606)
|.|..|++.|.+...|..|++
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~ 22 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMK 22 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTT
T ss_pred CCcccCCCCcCCHHHHHHHHc
Confidence 445555555555555555554
No 57
>KOG2785|consensus
Probab=94.21 E-value=0.08 Score=52.30 Aligned_cols=55 Identities=27% Similarity=0.447 Sum_probs=36.8
Q ss_pred cceecccCccccCCHHHHHHHHhccccccCCCC-------------------cccccccc---cccCchHHHHhhhh
Q psy15165 336 QYHVCPHCGKKFTRKAELQLHIKGIHLKHQLEK-------------------TYICEYCH---KEFTFYNYLRRHMR 390 (606)
Q Consensus 336 ~~~~C~~C~~~f~~~~~l~~H~~~~h~~h~~~~-------------------~~~C~~C~---k~f~~~~~L~~H~~ 390 (606)
.|-.|-.|++.|.+...-..||...|..-..++ .|.|-.|+ +.|.+..+.+.||.
T Consensus 165 ~Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~ 241 (390)
T KOG2785|consen 165 IPTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMR 241 (390)
T ss_pred CCcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHh
Confidence 346788888888888888888876654332221 25666666 66777777777765
No 58
>KOG1146|consensus
Probab=94.06 E-value=0.021 Score=64.87 Aligned_cols=79 Identities=28% Similarity=0.463 Sum_probs=59.0
Q ss_pred ccCCCCCCcCCChHHHHHhhhcccccCCCCccccccccchhccChhhHHHHHhh-hc-----------------------
Q psy15165 501 LQCPHCPKTFPRKTELSNHIKGIHMKHELRQTFVCEYCNKEFTFLQYLKRHMRT-HT----------------------- 556 (606)
Q Consensus 501 ~~C~~C~~~f~~~~~L~~H~~~~H~~~~~~k~y~C~~C~k~f~~~~~L~~H~~~-H~----------------------- 556 (606)
-.|.-|+..+.+...+.-|+...| .-.+.|+|+.|+..|+....|..|||. |.
T Consensus 437 ~e~~~~e~~~~s~r~~~~~t~~L~---S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~ 513 (1406)
T KOG1146|consen 437 VELTKAEPLLESKRSLEGQTVVLH---SFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYR 513 (1406)
T ss_pred ccccchhhhhhhhcccccceeeee---cccccccCCccchhhhhHHHhhhcccccccccchhHhHhcccccccccccccc
Confidence 346666677777777777766545 445777888888888888888888776 21
Q ss_pred -CCCCcccc-cCccCCchhhHHHhhhcc
Q psy15165 557 -NEKPYKCV-CGLGFNFNVSLKNHKQKC 582 (606)
Q Consensus 557 -~~kp~~C~-C~~~F~~~~~L~~H~~~h 582 (606)
+.+||.|. |.++|+.+.+|..|++..
T Consensus 514 ~~~~p~~C~~C~~stttng~LsihlqS~ 541 (1406)
T KOG1146|consen 514 CPGKPYPCRACNYSTTTNGNLSIHLQSD 541 (1406)
T ss_pred CCCCcccceeeeeeeecchHHHHHHHHH
Confidence 34689998 999999999999999865
No 59
>smart00349 KRAB krueppel associated box.
Probab=93.80 E-value=0.019 Score=39.63 Aligned_cols=34 Identities=26% Similarity=0.371 Sum_probs=31.2
Q ss_pred cccccCCCceeeecccCCCCceeeeeccccCCcc
Q psy15165 10 DDHVGKPSRRRSLGVESSVPKLKIKTETDDKSWE 43 (606)
Q Consensus 10 ~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~ 43 (606)
+.++++|.++..+|..+..|+++..+++++.||+
T Consensus 28 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 61 (61)
T smart00349 28 DVMLENYSNLVSLGFQVPKPDLISQLEQGEEPWI 61 (61)
T ss_pred HHHHHhhccccccCCCcCCcchhhhhhccCcCCC
Confidence 4678999999999999999999999999999995
No 60
>KOG2482|consensus
Probab=93.71 E-value=0.17 Score=49.07 Aligned_cols=145 Identities=23% Similarity=0.359 Sum_probs=94.4
Q ss_pred HHHHHHHHhcCCCCCcccCCCCCCcc-CCHHHHHHHHHHhcCC---CCCcCccccccccchhhhhcccccccCCccccCC
Q psy15165 429 TYLKHLKTNHHGYEVSNLCYICGFFS-AKRSTLAHHIQDHIQP---RMKQKQICEICCAEVYHINGHIKDKHSGFFLQCP 504 (606)
Q Consensus 429 ~~l~~h~~~~~~~~~~~~C~~C~~~f-~~~~~L~~H~~~h~~~---~~~~~~~C~~c~~~~~~l~~H~~~~h~~~~~~C~ 504 (606)
..|..++....+......|-.|...+ ..++....|+-.-++- .|..- .....|-.|+... -..+.|-
T Consensus 129 eaLeqqQ~Eredt~fslqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDni-------VyvnelLehLkek--L~r~~CL 199 (423)
T KOG2482|consen 129 EALEQQQKEREDTIFSLQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNI-------VYVNELLEHLKEK--LERLRCL 199 (423)
T ss_pred HHHHHHHHHhcCCeeeeEEEEecchhcccHHHHHHHHHHHhhhccCCCcce-------eeHHHHHHHHHHH--Hhhheee
Confidence 34555555555556677899998755 4677788887554332 11000 1223344444321 1128899
Q ss_pred CCCCcCCChHHHHHhhhcc-ccc----------------------------C---------------------CCCcc--
Q psy15165 505 HCPKTFPRKTELSNHIKGI-HMK----------------------------H---------------------ELRQT-- 532 (606)
Q Consensus 505 ~C~~~f~~~~~L~~H~~~~-H~~----------------------------~---------------------~~~k~-- 532 (606)
+|.+.|..+..|+.||+.. |.. + .+..+
T Consensus 200 yCekifrdkntLkeHMrkK~HrrinPknreYDkfyiINY~ev~ks~t~~~~e~dret~~d~~E~D~~wsDw~ed~a~a~~ 279 (423)
T KOG2482|consen 200 YCEKIFRDKNTLKEHMRKKRHRRINPKNREYDKFYIINYLEVGKSWTIVHSEDDRETNEDINETDDTWSDWNEDDAEALS 279 (423)
T ss_pred eeccccCCcHHHHHHHHhccCcccCCCccccceEEEEeHhhcCCccchhhhhhhhhhhccccccccchhhhhcCCCCccc
Confidence 9999999999999999842 200 0 00111
Q ss_pred ccccccchhccChhhHHHHHhhhcC---------------------------CCCcccc-cCccCCchhhHHHhhhcc
Q psy15165 533 FVCEYCNKEFTFLQYLKRHMRTHTN---------------------------EKPYKCV-CGLGFNFNVSLKNHKQKC 582 (606)
Q Consensus 533 y~C~~C~k~f~~~~~L~~H~~~H~~---------------------------~kp~~C~-C~~~F~~~~~L~~H~~~h 582 (606)
-.|-.|....-+...|..||.+-+. .+.-.|. |...|-....|..||.-+
T Consensus 280 v~CLfC~~~~en~~~l~eHmk~vHe~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c~~cd~~F~~e~~l~~hm~e~ 357 (423)
T KOG2482|consen 280 VVCLFCTNFYENPVFLFEHMKIVHEFDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCAECDLSFWKEPGLLIHMVED 357 (423)
T ss_pred eEEEeeccchhhHHHHHHHHHHHHHhhHHhhccccccchhhhhhHHHHHHHHhhccccccccccccCcchhhhhcccc
Confidence 4899999999999999999985331 0123566 999999999999999743
No 61
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=93.48 E-value=0.029 Score=59.52 Aligned_cols=70 Identities=30% Similarity=0.429 Sum_probs=47.1
Q ss_pred CCCcCCChHHHHHhhhcccccCCCCccccccccchhccChhhHHHHHhhhcCCCCcccccCccCCchhhHHH
Q psy15165 506 CPKTFPRKTELSNHIKGIHMKHELRQTFVCEYCNKEFTFLQYLKRHMRTHTNEKPYKCVCGLGFNFNVSLKN 577 (606)
Q Consensus 506 C~~~f~~~~~L~~H~~~~H~~~~~~k~y~C~~C~k~f~~~~~L~~H~~~H~~~kp~~C~C~~~F~~~~~L~~ 577 (606)
|-..+.....+..|.. .|.. .....+.+..|.+.|.....|..|++.|....++.|.+-+.|.....+..
T Consensus 394 ~~~~~~~~~~~~~~~~-~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 463 (467)
T COG5048 394 CIRNFKRDSNLSLHII-THLS-FRPYNCKNPPCSKSFNRHYNLIPHKKIHTNHAPLLCSILKSFRRDLDLSN 463 (467)
T ss_pred hhhhhccccccccccc-cccc-cCCcCCCCCcchhhccCcccccccccccccCCceeeccccccchhhhhhc
Confidence 6666666666666655 3411 22335778889999999999999999998888888874444544444433
No 62
>KOG2893|consensus
Probab=93.47 E-value=0.024 Score=51.59 Aligned_cols=47 Identities=32% Similarity=0.537 Sum_probs=38.9
Q ss_pred cCCCCCCcCCChHHHHHhhhcccccCCCCccccccccchhccChhhHHHH-Hhhhc
Q psy15165 502 QCPHCPKTFPRKTELSNHIKGIHMKHELRQTFVCEYCNKEFTFLQYLKRH-MRTHT 556 (606)
Q Consensus 502 ~C~~C~~~f~~~~~L~~H~~~~H~~~~~~k~y~C~~C~k~f~~~~~L~~H-~~~H~ 556 (606)
-|-+|++.|....-|..|++..| |+|.+|.|...+--.|..| |.+|.
T Consensus 12 wcwycnrefddekiliqhqkakh--------fkchichkkl~sgpglsihcmqvhk 59 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQKAKH--------FKCHICHKKLFSGPGLSIHCMQVHK 59 (341)
T ss_pred eeeecccccchhhhhhhhhhhcc--------ceeeeehhhhccCCCceeehhhhhh
Confidence 48899999999999999988555 8999999988888888888 55664
No 63
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=92.03 E-value=0.11 Score=30.07 Aligned_cols=18 Identities=33% Similarity=0.829 Sum_probs=8.6
Q ss_pred cCCCCCCcCCChHHHHHhh
Q psy15165 502 QCPHCPKTFPRKTELSNHI 520 (606)
Q Consensus 502 ~C~~C~~~f~~~~~L~~H~ 520 (606)
.|+.||+.| ....|.+|+
T Consensus 4 ~C~~CgR~F-~~~~l~~H~ 21 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHE 21 (25)
T ss_pred cCCCCCCEE-CHHHHHHHH
Confidence 455555555 344444444
No 64
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=91.24 E-value=0.16 Score=29.45 Aligned_cols=20 Identities=25% Similarity=0.650 Sum_probs=17.7
Q ss_pred cccccchhccChhhHHHHHhh
Q psy15165 534 VCEYCNKEFTFLQYLKRHMRT 554 (606)
Q Consensus 534 ~C~~C~k~f~~~~~L~~H~~~ 554 (606)
.|+.||+.| ....|.+|+.+
T Consensus 4 ~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred cCCCCCCEE-CHHHHHHHHHh
Confidence 699999999 78899999864
No 65
>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=90.29 E-value=0.18 Score=31.86 Aligned_cols=22 Identities=32% Similarity=0.656 Sum_probs=13.5
Q ss_pred cccccccchhccChhhHHHHHh
Q psy15165 532 TFVCEYCNKEFTFLQYLKRHMR 553 (606)
Q Consensus 532 ~y~C~~C~k~f~~~~~L~~H~~ 553 (606)
+|.|.+|++.|.....+..|++
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 3556666666666666666654
No 66
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=89.26 E-value=0.13 Score=54.59 Aligned_cols=72 Identities=28% Similarity=0.490 Sum_probs=50.8
Q ss_pred cccCCCCCCcCCChHHHHHhhhc-ccccCCCC--cccccc--ccchhccChhhHHHHHhhhcCCCCccc--c-cCccCCc
Q psy15165 500 FLQCPHCPKTFPRKTELSNHIKG-IHMKHELR--QTFVCE--YCNKEFTFLQYLKRHMRTHTNEKPYKC--V-CGLGFNF 571 (606)
Q Consensus 500 ~~~C~~C~~~f~~~~~L~~H~~~-~H~~~~~~--k~y~C~--~C~k~f~~~~~L~~H~~~H~~~kp~~C--~-C~~~F~~ 571 (606)
.+.|..|...|.....|..|.+. .| +++ +++.|+ .|++.|.+...+..|..+|++..++.| . |...+..
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h---~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 365 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNH---SGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSP 365 (467)
T ss_pred CCCCccccCCcccccccccccccccc---ccccCCceeeeccCCCccccccccccCCcccccCCCccccccccCcccccc
Confidence 36777777777777777777764 34 666 777777 677777777777777777777777777 2 6666555
Q ss_pred hhh
Q psy15165 572 NVS 574 (606)
Q Consensus 572 ~~~ 574 (606)
...
T Consensus 366 ~~~ 368 (467)
T COG5048 366 LLN 368 (467)
T ss_pred ccC
Confidence 443
No 67
>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=88.36 E-value=0.4 Score=30.23 Aligned_cols=22 Identities=27% Similarity=0.558 Sum_probs=20.2
Q ss_pred cccCCCCCCcCCChHHHHHhhh
Q psy15165 500 FLQCPHCPKTFPRKTELSNHIK 521 (606)
Q Consensus 500 ~~~C~~C~~~f~~~~~L~~H~~ 521 (606)
+|.|.+|++.|.+...+..|+.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 3789999999999999999986
No 68
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=88.29 E-value=0.65 Score=38.00 Aligned_cols=93 Identities=19% Similarity=0.278 Sum_probs=53.3
Q ss_pred CCcccCCCCCCccCCHHHHHHHHHHhcCCCCCcCccccccccchhhhhcccccccCCccccCCCCCCcCCChHHHHHhhh
Q psy15165 442 EVSNLCYICGFFSAKRSTLAHHIQDHIQPRMKQKQICEICCAEVYHINGHIKDKHSGFFLQCPHCPKTFPRKTELSNHIK 521 (606)
Q Consensus 442 ~~~~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~~~~C~~c~~~~~~l~~H~~~~h~~~~~~C~~C~~~f~~~~~L~~H~~ 521 (606)
+.|..|++||.+......|.+-..---...++... .+. .....-.|--|...|........=
T Consensus 13 ~LP~~CpiCgLtLVss~HLARSyHHLfPl~~f~ev----------~~~------~~~~~~~C~~C~~~f~~~~~~~~~-- 74 (112)
T TIGR00622 13 ELPVECPICGLTLILSTHLARSYHHLFPLKAFQEI----------PLE------EYNGSRFCFGCQGPFPKPPVSPFD-- 74 (112)
T ss_pred CCCCcCCcCCCEEeccchHHHhhhccCCCcccccc----------ccc------ccCCCCcccCcCCCCCCccccccc--
Confidence 56778999999888887777643211112221100 000 000013488888888765321100
Q ss_pred cccccCCCCccccccccchhccChhhHHHHHhhhc
Q psy15165 522 GIHMKHELRQTFVCEYCNKEFTFLQYLKRHMRTHT 556 (606)
Q Consensus 522 ~~H~~~~~~k~y~C~~C~k~f~~~~~L~~H~~~H~ 556 (606)
.-.....|.|+.|...|-..=..-.|...|.
T Consensus 75 ----~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 75 ----ELKDSHRYVCAVCKNVFCVDCDVFVHESLHC 105 (112)
T ss_pred ----ccccccceeCCCCCCccccccchhhhhhccC
Confidence 0123446888888888888888888877775
No 69
>KOG4173|consensus
Probab=88.11 E-value=0.15 Score=45.68 Aligned_cols=52 Identities=27% Similarity=0.521 Sum_probs=32.4
Q ss_pred cCCCCCCcCCChHHHHHhhhcccc------cCCCCccccccc--cchhccChhhHHHHHh
Q psy15165 502 QCPHCPKTFPRKTELSNHIKGIHM------KHELRQTFVCEY--CNKEFTFLQYLKRHMR 553 (606)
Q Consensus 502 ~C~~C~~~f~~~~~L~~H~~~~H~------~~~~~k~y~C~~--C~k~f~~~~~L~~H~~ 553 (606)
.|..|.+.|++...|..|+...|. ...|...|.|-+ |+-.|.+...-..|+-
T Consensus 108 sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFkT~r~RkdH~I 167 (253)
T KOG4173|consen 108 SCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKFKTSRDRKDHMI 167 (253)
T ss_pred hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhhhhhhhhhhHHH
Confidence 477777777777777777765551 112344566644 6666666666666643
No 70
>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=87.55 E-value=0.52 Score=39.05 Aligned_cols=23 Identities=26% Similarity=0.648 Sum_probs=16.9
Q ss_pred ccCCCCCCcCCChHHHHHhhhccc
Q psy15165 501 LQCPHCPKTFPRKTELSNHIKGIH 524 (606)
Q Consensus 501 ~~C~~C~~~f~~~~~L~~H~~~~H 524 (606)
..|..|+.+..- +.+..|++..|
T Consensus 12 lIC~~C~~av~~-~~v~~HL~~~H 34 (109)
T PF12013_consen 12 LICRQCQYAVQP-SEVESHLRKRH 34 (109)
T ss_pred EEeCCCCcccCc-hHHHHHHHHhc
Confidence 568888877766 77888887555
No 71
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=86.83 E-value=0.24 Score=34.08 Aligned_cols=26 Identities=35% Similarity=0.841 Sum_probs=18.2
Q ss_pred ccccCCCCCCcCCChHHHHHhhhccc
Q psy15165 499 FFLQCPHCPKTFPRKTELSNHIKGIH 524 (606)
Q Consensus 499 ~~~~C~~C~~~f~~~~~L~~H~~~~H 524 (606)
..+.||.||..|.....+.+|+...|
T Consensus 16 ~~lrCPRC~~~FR~~K~Y~RHVNKaH 41 (65)
T COG4049 16 EFLRCPRCGMVFRRRKDYIRHVNKAH 41 (65)
T ss_pred eeeeCCchhHHHHHhHHHHHHhhHHh
Confidence 33777777777777777777776555
No 72
>KOG4173|consensus
Probab=86.21 E-value=0.34 Score=43.46 Aligned_cols=76 Identities=22% Similarity=0.534 Sum_probs=62.0
Q ss_pred ccCCC--CCCcCCChHHHHHhhhcccccCCCCccccccccchhccChhhHHHHHh-hhc---------CCCCccc--c-c
Q psy15165 501 LQCPH--CPKTFPRKTELSNHIKGIHMKHELRQTFVCEYCNKEFTFLQYLKRHMR-THT---------NEKPYKC--V-C 565 (606)
Q Consensus 501 ~~C~~--C~~~f~~~~~L~~H~~~~H~~~~~~k~y~C~~C~k~f~~~~~L~~H~~-~H~---------~~kp~~C--~-C 565 (606)
|.|++ |...|.+...+..|....| + -.|.+|.+.|.+...|..|+. .|. |.--|.| . |
T Consensus 80 ~~cqvagc~~~~d~lD~~E~hY~~~h---~----~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgC 152 (253)
T KOG4173|consen 80 FACQVAGCCQVFDALDDYEHHYHTLH---G----NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGC 152 (253)
T ss_pred ccccccchHHHHhhhhhHHHhhhhcc---c----chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhh
Confidence 78876 8899999998998875445 4 369999999999999999985 343 5556999 3 9
Q ss_pred CccCCchhhHHHhhhccc
Q psy15165 566 GLGFNFNVSLKNHKQKCS 583 (606)
Q Consensus 566 ~~~F~~~~~L~~H~~~h~ 583 (606)
+..|.+......|+-.-|
T Consensus 153 t~KFkT~r~RkdH~I~~H 170 (253)
T KOG4173|consen 153 TEKFKTSRDRKDHMIRMH 170 (253)
T ss_pred hhhhhhhhhhhhHHHHhc
Confidence 999999999999975444
No 73
>KOG2893|consensus
Probab=86.07 E-value=0.25 Score=45.22 Aligned_cols=62 Identities=26% Similarity=0.449 Sum_probs=48.3
Q ss_pred CccccccccchhccChhhHHHHHhhhcCCCCcccc-cCccCCchhhHHHhhhccccccchhhccccCC
Q psy15165 530 RQTFVCEYCNKEFTFLQYLKRHMRTHTNEKPYKCV-CGLGFNFNVSLKNHKQKCSVFLLTESMNSVSG 596 (606)
Q Consensus 530 ~k~y~C~~C~k~f~~~~~L~~H~~~H~~~kp~~C~-C~~~F~~~~~L~~H~~~h~~~~~~~c~~~~~~ 596 (606)
.|++ |.+|++.|.....|..|++ .|-|+|. |.+...+--.|..|-...|.+.+-+-++.+.|
T Consensus 9 ~kpw-cwycnrefddekiliqhqk----akhfkchichkkl~sgpglsihcmqvhketid~ip~av~g 71 (341)
T KOG2893|consen 9 DKPW-CWYCNREFDDEKILIQHQK----AKHFKCHICHKKLFSGPGLSIHCMQVHKETIDKIPAAVHG 71 (341)
T ss_pred CCce-eeecccccchhhhhhhhhh----hccceeeeehhhhccCCCceeehhhhhhhhhhcccccccC
Confidence 3444 9999999999999999976 4569998 99998899999999666665555555555554
No 74
>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=84.66 E-value=0.45 Score=29.69 Aligned_cols=10 Identities=50% Similarity=1.268 Sum_probs=5.1
Q ss_pred CccccCcchh
Q psy15165 396 KPYKCKDCGA 405 (606)
Q Consensus 396 ~~~~C~~C~~ 405 (606)
.++.|+.||.
T Consensus 16 ~~~~CP~Cg~ 25 (33)
T cd00350 16 APWVCPVCGA 25 (33)
T ss_pred CCCcCcCCCC
Confidence 4455555543
No 75
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=83.71 E-value=0.39 Score=33.12 Aligned_cols=29 Identities=17% Similarity=0.296 Sum_probs=19.3
Q ss_pred CCCccccccccchhccChhhHHHHHhhhc
Q psy15165 528 ELRQTFVCEYCNKEFTFLQYLKRHMRTHT 556 (606)
Q Consensus 528 ~~~k~y~C~~C~k~f~~~~~L~~H~~~H~ 556 (606)
.|+.-+.|+.||..|.....+.+|...-+
T Consensus 13 DGE~~lrCPRC~~~FR~~K~Y~RHVNKaH 41 (65)
T COG4049 13 DGEEFLRCPRCGMVFRRRKDYIRHVNKAH 41 (65)
T ss_pred CCceeeeCCchhHHHHHhHHHHHHhhHHh
Confidence 45666677777777777777777765443
No 76
>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=82.68 E-value=0.81 Score=37.54 Aligned_cols=14 Identities=36% Similarity=0.790 Sum_probs=7.1
Q ss_pred ccccccccchhccC
Q psy15165 531 QTFVCEYCNKEFTF 544 (606)
Q Consensus 531 k~y~C~~C~k~f~~ 544 (606)
.|-.|++||..|.-
T Consensus 25 ~PivCP~CG~~~~~ 38 (108)
T PF09538_consen 25 DPIVCPKCGTEFPP 38 (108)
T ss_pred CCccCCCCCCccCc
Confidence 34455555555543
No 77
>KOG2186|consensus
Probab=80.97 E-value=1 Score=42.05 Aligned_cols=48 Identities=31% Similarity=0.682 Sum_probs=34.3
Q ss_pred ccccccchhccChhhHHHHHhhhcCCCCcccc-cCccCCchhhHHHhhhccc
Q psy15165 533 FVCEYCNKEFTFLQYLKRHMRTHTNEKPYKCV-CGLGFNFNVSLKNHKQKCS 583 (606)
Q Consensus 533 y~C~~C~k~f~~~~~L~~H~~~H~~~kp~~C~-C~~~F~~~~~L~~H~~~h~ 583 (606)
|.|..||-+..- ..+.+|+...+| .-|.|. |++.|.. ..+..|..==+
T Consensus 4 FtCnvCgEsvKK-p~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~kCIT 52 (276)
T KOG2186|consen 4 FTCNVCGESVKK-PQVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTKCIT 52 (276)
T ss_pred Eehhhhhhhccc-cchHHHHHhccC-CeeEEeeccccccc-chhhhhhhhcc
Confidence 678888876654 456668877777 668887 8888876 77777875433
No 78
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=79.17 E-value=0.62 Score=43.82 Aligned_cols=45 Identities=27% Similarity=0.417 Sum_probs=28.2
Q ss_pred ccCCCCCCcCCChHHHHHhhhccccc------CCCCcc-----ccccccchhccCh
Q psy15165 501 LQCPHCPKTFPRKTELSNHIKGIHMK------HELRQT-----FVCEYCNKEFTFL 545 (606)
Q Consensus 501 ~~C~~C~~~f~~~~~L~~H~~~~H~~------~~~~k~-----y~C~~C~k~f~~~ 545 (606)
+.||+|+..|.+..-+...++..... -.+..| ..|+.||++|...
T Consensus 6 ~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 6 ITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred eECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 78999999998887776666532210 012222 3788888877643
No 79
>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=76.34 E-value=2.8 Score=34.62 Aligned_cols=21 Identities=19% Similarity=0.200 Sum_probs=11.7
Q ss_pred cccccccCchHHHHhhhhhcC
Q psy15165 373 EYCHKEFTFYNYLRRHMRVHT 393 (606)
Q Consensus 373 ~~C~k~f~~~~~L~~H~~~H~ 393 (606)
..|++.+.+...++.|.+.++
T Consensus 88 ~~C~y~~~~~~~m~~H~~~~H 108 (109)
T PF12013_consen 88 PHCGYITRSKKTMRKHWRKEH 108 (109)
T ss_pred CCCCcEeccHHHHHHHHHHhc
Confidence 555555555555555555443
No 80
>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=73.15 E-value=2.5 Score=35.28 Aligned_cols=15 Identities=20% Similarity=0.299 Sum_probs=7.9
Q ss_pred ccccccccchhccCh
Q psy15165 531 QTFVCEYCNKEFTFL 545 (606)
Q Consensus 531 k~y~C~~C~k~f~~~ 545 (606)
.|-.|++||..|.-.
T Consensus 25 ~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 25 RPAVSPYTGEQFPPE 39 (129)
T ss_pred CCccCCCcCCccCcc
Confidence 345566666555443
No 81
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=70.96 E-value=1.1 Score=42.22 Aligned_cols=43 Identities=30% Similarity=0.577 Sum_probs=26.0
Q ss_pred CcccccccccccCchHHHHhhhhh---c-------CCCCc-----cccCcchhccCCh
Q psy15165 368 KTYICEYCHKEFTFYNYLRRHMRV---H-------TNEKP-----YKCKDCGAAFNHN 410 (606)
Q Consensus 368 ~~~~C~~C~k~f~~~~~L~~H~~~---H-------~~~~~-----~~C~~C~~~f~~~ 410 (606)
+.+.|++|+..|.+........++ . .+..| ..||.||.+|...
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 456777777777766544444432 1 12233 3699999988754
No 82
>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=70.62 E-value=2.1 Score=27.60 Aligned_cols=34 Identities=21% Similarity=0.508 Sum_probs=20.9
Q ss_pred ccCCCCCCcCCChHHHHHhhhcccccCCCCccccccccchhcc
Q psy15165 501 LQCPHCPKTFPRKTELSNHIKGIHMKHELRQTFVCEYCNKEFT 543 (606)
Q Consensus 501 ~~C~~C~~~f~~~~~L~~H~~~~H~~~~~~k~y~C~~C~k~f~ 543 (606)
+.|+.|+..|.-...... .......|+.|+..|.
T Consensus 3 ~~CP~C~~~~~v~~~~~~---------~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLG---------ANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHcC---------CCCCEEECCCCCCEEE
Confidence 568888887776654321 1112467888887664
No 83
>PHA00626 hypothetical protein
Probab=69.42 E-value=2.5 Score=29.45 Aligned_cols=12 Identities=17% Similarity=0.395 Sum_probs=7.0
Q ss_pred ccCCCCCCcCCC
Q psy15165 501 LQCPHCPKTFPR 512 (606)
Q Consensus 501 ~~C~~C~~~f~~ 512 (606)
|.|+.||+.|+.
T Consensus 24 YkCkdCGY~ft~ 35 (59)
T PHA00626 24 YVCCDCGYNDSK 35 (59)
T ss_pred eEcCCCCCeech
Confidence 566666665544
No 84
>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=69.30 E-value=2.2 Score=26.79 Aligned_cols=9 Identities=67% Similarity=1.320 Sum_probs=4.1
Q ss_pred ccccCcchh
Q psy15165 397 PYKCKDCGA 405 (606)
Q Consensus 397 ~~~C~~C~~ 405 (606)
|..|+.||.
T Consensus 18 p~~CP~Cg~ 26 (34)
T cd00729 18 PEKCPICGA 26 (34)
T ss_pred CCcCcCCCC
Confidence 344555543
No 85
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=69.06 E-value=6.6 Score=32.25 Aligned_cols=80 Identities=19% Similarity=0.294 Sum_probs=54.1
Q ss_pred cccCCCCCCcCCChHHHHHhhhcccccCC----------CCccccccccchhccChhhHHHHHhhhcCCCCcccc-cCcc
Q psy15165 500 FLQCPHCPKTFPRKTELSNHIKGIHMKHE----------LRQTFVCEYCNKEFTFLQYLKRHMRTHTNEKPYKCV-CGLG 568 (606)
Q Consensus 500 ~~~C~~C~~~f~~~~~L~~H~~~~H~~~~----------~~k~y~C~~C~k~f~~~~~L~~H~~~H~~~kp~~C~-C~~~ 568 (606)
+..|+.||-...+...|.+-.. |+... ....-.|--|...|........ ..-.....|.|. |...
T Consensus 15 P~~CpiCgLtLVss~HLARSyH--HLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~--~~~~~~~~y~C~~C~~~ 90 (112)
T TIGR00622 15 PVECPICGLTLILSTHLARSYH--HLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPF--DELKDSHRYVCAVCKNV 90 (112)
T ss_pred CCcCCcCCCEEeccchHHHhhh--ccCCCcccccccccccCCCCcccCcCCCCCCcccccc--cccccccceeCCCCCCc
Confidence 3689999999999988887642 31110 0112249999999986531110 001224579998 9999
Q ss_pred CCchhhHHHhhhccc
Q psy15165 569 FNFNVSLKNHKQKCS 583 (606)
Q Consensus 569 F~~~~~L~~H~~~h~ 583 (606)
|-..-++..|...|.
T Consensus 91 FC~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 91 FCVDCDVFVHESLHC 105 (112)
T ss_pred cccccchhhhhhccC
Confidence 999999999988875
No 86
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=68.82 E-value=1.4 Score=38.72 Aligned_cols=12 Identities=42% Similarity=0.672 Sum_probs=6.7
Q ss_pred ccccccchhccC
Q psy15165 533 FVCEYCNKEFTF 544 (606)
Q Consensus 533 y~C~~C~k~f~~ 544 (606)
|+|+.||++|.+
T Consensus 29 ~~c~~c~~~f~~ 40 (154)
T PRK00464 29 RECLACGKRFTT 40 (154)
T ss_pred eeccccCCcceE
Confidence 555555555554
No 87
>KOG2186|consensus
Probab=66.55 E-value=2.5 Score=39.52 Aligned_cols=44 Identities=34% Similarity=0.743 Sum_probs=20.9
Q ss_pred ccccccccccCchHHHHhhhhhcCCCCccccCcchhccCChhHHhcc
Q psy15165 370 YICEYCHKEFTFYNYLRRHMRVHTNEKPYKCKDCGAAFNHNVSLKNH 416 (606)
Q Consensus 370 ~~C~~C~k~f~~~~~L~~H~~~H~~~~~~~C~~C~~~f~~~~~L~~H 416 (606)
|.|.+||....- ..+.+|+..-++ .-|.|-.|++.|.. ..+..|
T Consensus 4 FtCnvCgEsvKK-p~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH 47 (276)
T KOG2186|consen 4 FTCNVCGESVKK-PQVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNH 47 (276)
T ss_pred Eehhhhhhhccc-cchHHHHHhccC-CeeEEeeccccccc-chhhhh
Confidence 445555544432 234445544444 44555555555554 344444
No 88
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=66.46 E-value=5 Score=44.74 Aligned_cols=39 Identities=31% Similarity=0.807 Sum_probs=22.6
Q ss_pred ccCCCCCCcCCChHHHHHhhhcccccCCCCccccccccchhccChhhHHHHHhhhcCCCCcccc-cCcc
Q psy15165 501 LQCPHCPKTFPRKTELSNHIKGIHMKHELRQTFVCEYCNKEFTFLQYLKRHMRTHTNEKPYKCV-CGLG 568 (606)
Q Consensus 501 ~~C~~C~~~f~~~~~L~~H~~~~H~~~~~~k~y~C~~C~k~f~~~~~L~~H~~~H~~~kp~~C~-C~~~ 568 (606)
++|+.|+.. |.-|. ..+...|.+||+ ....|..|+ ||-.
T Consensus 445 ~~Cp~Cd~~------lt~H~--------~~~~L~CH~Cg~---------------~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 445 AECPNCDSP------LTLHK--------ATGQLRCHYCGY---------------QEPIPQSCPECGSE 484 (730)
T ss_pred ccCCCCCcc------eEEec--------CCCeeEeCCCCC---------------CCCCCCCCCCCCCC
Confidence 467777654 33343 234567777773 344677777 7754
No 89
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=66.19 E-value=5.1 Score=25.51 Aligned_cols=11 Identities=36% Similarity=1.096 Sum_probs=5.1
Q ss_pred ecccCccccCC
Q psy15165 339 VCPHCGKKFTR 349 (606)
Q Consensus 339 ~C~~C~~~f~~ 349 (606)
.|+.|+..|.-
T Consensus 4 ~Cp~C~~~y~i 14 (36)
T PF13717_consen 4 TCPNCQAKYEI 14 (36)
T ss_pred ECCCCCCEEeC
Confidence 44455444443
No 90
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=66.07 E-value=3.4 Score=26.51 Aligned_cols=34 Identities=21% Similarity=0.550 Sum_probs=21.7
Q ss_pred ccCCCCCCcCCChHHHHHhhhcccccCCCCccccccccchhcc
Q psy15165 501 LQCPHCPKTFPRKTELSNHIKGIHMKHELRQTFVCEYCNKEFT 543 (606)
Q Consensus 501 ~~C~~C~~~f~~~~~L~~H~~~~H~~~~~~k~y~C~~C~k~f~ 543 (606)
..|+.|+..|.-...-.. .+.+..+|+.|+-.|.
T Consensus 3 i~CP~C~~~f~v~~~~l~---------~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKLP---------AGGRKVRCPKCGHVFR 36 (37)
T ss_pred EECCCCCceEEcCHHHcc---------cCCcEEECCCCCcEee
Confidence 468888888876654211 2334577888887764
No 91
>PF15269 zf-C2H2_7: Zinc-finger
Probab=65.01 E-value=5.2 Score=26.30 Aligned_cols=25 Identities=32% Similarity=0.841 Sum_probs=19.3
Q ss_pred CCCcccccccccccCCHHHHHHhHh
Q psy15165 245 SPYEFKCRVCDWKLNSYDKLLRHIK 269 (606)
Q Consensus 245 ~~~~~~C~~C~~~f~~~~~L~~H~~ 269 (606)
+|..|+|-.|..+....+.|-.||+
T Consensus 17 kp~~ykcfqcpftc~~kshl~nhmk 41 (54)
T PF15269_consen 17 KPFKYKCFQCPFTCNEKSHLFNHMK 41 (54)
T ss_pred CCccceeecCCcccchHHHHHHHHH
Confidence 4556788888888888888888876
No 92
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=64.69 E-value=4.6 Score=28.60 Aligned_cols=31 Identities=19% Similarity=0.549 Sum_probs=18.4
Q ss_pred ccCCCCCCcCCChHHHHHhhhcccccCCCCccccccccch
Q psy15165 501 LQCPHCPKTFPRKTELSNHIKGIHMKHELRQTFVCEYCNK 540 (606)
Q Consensus 501 ~~C~~C~~~f~~~~~L~~H~~~~H~~~~~~k~y~C~~C~k 540 (606)
|.|+.||..-.....--+ ....+|.|+.||+
T Consensus 28 F~CPnCGe~~I~Rc~~CR---------k~g~~Y~Cp~CGF 58 (61)
T COG2888 28 FPCPNCGEVEIYRCAKCR---------KLGNPYRCPKCGF 58 (61)
T ss_pred eeCCCCCceeeehhhhHH---------HcCCceECCCcCc
Confidence 888888865444332221 2235688888875
No 93
>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=63.01 E-value=4.9 Score=26.90 Aligned_cols=11 Identities=36% Similarity=0.933 Sum_probs=4.1
Q ss_pred ccccccchhcc
Q psy15165 533 FVCEYCNKEFT 543 (606)
Q Consensus 533 y~C~~C~k~f~ 543 (606)
.+|.+|++.+.
T Consensus 17 a~C~~C~~~~~ 27 (45)
T PF02892_consen 17 AKCKYCGKVIK 27 (45)
T ss_dssp EEETTTTEE--
T ss_pred EEeCCCCeEEe
Confidence 34444444443
No 94
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=61.08 E-value=4.5 Score=27.14 Aligned_cols=11 Identities=45% Similarity=0.999 Sum_probs=5.7
Q ss_pred ccccccccccC
Q psy15165 370 YICEYCHKEFT 380 (606)
Q Consensus 370 ~~C~~C~k~f~ 380 (606)
|.|..||..|.
T Consensus 3 Y~C~~Cg~~~~ 13 (44)
T smart00659 3 YICGECGRENE 13 (44)
T ss_pred EECCCCCCEee
Confidence 45555555544
No 95
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=60.44 E-value=5.5 Score=35.41 Aligned_cols=25 Identities=36% Similarity=0.842 Sum_probs=17.9
Q ss_pred cceecccCccccCCHHHHHHHHhccccccCCCCccccccccc
Q psy15165 336 QYHVCPHCGKKFTRKAELQLHIKGIHLKHQLEKTYICEYCHK 377 (606)
Q Consensus 336 ~~~~C~~C~~~f~~~~~l~~H~~~~h~~h~~~~~~~C~~C~k 377 (606)
+.|.|++||. ++.++.|-.|++||.
T Consensus 133 ~~~vC~vCGy-----------------~~~ge~P~~CPiCga 157 (166)
T COG1592 133 KVWVCPVCGY-----------------THEGEAPEVCPICGA 157 (166)
T ss_pred CEEEcCCCCC-----------------cccCCCCCcCCCCCC
Confidence 4688888876 345577788888873
No 96
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=60.07 E-value=6.1 Score=27.28 Aligned_cols=21 Identities=29% Similarity=0.752 Sum_probs=10.5
Q ss_pred ccCCCCCCcCCCh-----HHHHHhhh
Q psy15165 501 LQCPHCPKTFPRK-----TELSNHIK 521 (606)
Q Consensus 501 ~~C~~C~~~f~~~-----~~L~~H~~ 521 (606)
-.|.+|++.+... +.|.+|++
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHH
Confidence 4555555555433 35555544
No 97
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=58.64 E-value=2.8 Score=31.48 Aligned_cols=16 Identities=31% Similarity=0.592 Sum_probs=8.6
Q ss_pred CCCCccc--c-cCccCCch
Q psy15165 557 NEKPYKC--V-CGLGFNFN 572 (606)
Q Consensus 557 ~~kp~~C--~-C~~~F~~~ 572 (606)
.+.-+.| . ||.+|...
T Consensus 24 ~~~Y~qC~N~eCg~tF~t~ 42 (72)
T PRK09678 24 KERYHQCQNVNCSATFITY 42 (72)
T ss_pred heeeeecCCCCCCCEEEEE
Confidence 3445566 2 66666554
No 98
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=58.16 E-value=7 Score=34.32 Aligned_cols=35 Identities=23% Similarity=0.619 Sum_probs=23.0
Q ss_pred cccCCCCCCcCCChHHHHHhhhcccccCCCCccccccccchhc
Q psy15165 500 FLQCPHCPKTFPRKTELSNHIKGIHMKHELRQTFVCEYCNKEF 542 (606)
Q Consensus 500 ~~~C~~C~~~f~~~~~L~~H~~~~H~~~~~~k~y~C~~C~k~f 542 (606)
.|.|+.|+..|....++..- . . ...|.|+.||...
T Consensus 99 ~Y~Cp~C~~~y~~~ea~~~~----d---~-~~~f~Cp~Cg~~l 133 (147)
T smart00531 99 YYKCPNCQSKYTFLEANQLL----D---M-DGTFTCPRCGEEL 133 (147)
T ss_pred EEECcCCCCEeeHHHHHHhc----C---C-CCcEECCCCCCEE
Confidence 38899999888865544320 1 1 2338899998765
No 99
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=57.82 E-value=7.1 Score=27.80 Aligned_cols=12 Identities=33% Similarity=0.645 Sum_probs=9.8
Q ss_pred CCcccCCCCCCc
Q psy15165 442 EVSNLCYICGFF 453 (606)
Q Consensus 442 ~~~~~C~~C~~~ 453 (606)
..+|.|+.||+.
T Consensus 46 ~~~Y~CP~CGF~ 57 (59)
T PRK14890 46 SNPYTCPKCGFE 57 (59)
T ss_pred CCceECCCCCCc
Confidence 568999999974
No 100
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=57.34 E-value=7.2 Score=26.38 Aligned_cols=10 Identities=30% Similarity=1.019 Sum_probs=4.4
Q ss_pred eecccCcccc
Q psy15165 338 HVCPHCGKKF 347 (606)
Q Consensus 338 ~~C~~C~~~f 347 (606)
|.|+.||..|
T Consensus 4 y~C~~CG~~~ 13 (46)
T PRK00398 4 YKCARCGREV 13 (46)
T ss_pred EECCCCCCEE
Confidence 4444444433
No 101
>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=56.76 E-value=9.6 Score=22.24 Aligned_cols=19 Identities=26% Similarity=0.739 Sum_probs=12.2
Q ss_pred cCCCCCCcCCChHHHHHhhh
Q psy15165 502 QCPHCPKTFPRKTELSNHIK 521 (606)
Q Consensus 502 ~C~~C~~~f~~~~~L~~H~~ 521 (606)
.||+|++.+ ....+..|+.
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 577777776 4556666654
No 102
>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=56.39 E-value=7 Score=32.12 Aligned_cols=30 Identities=33% Similarity=0.827 Sum_probs=19.6
Q ss_pred ccccccccchhhhhcccccccCCccccCCCCCCcCCCh
Q psy15165 476 QICEICCAEVYHINGHIKDKHSGFFLQCPHCPKTFPRK 513 (606)
Q Consensus 476 ~~C~~c~~~~~~l~~H~~~~h~~~~~~C~~C~~~f~~~ 513 (606)
..|+.||+....|+. .+..||.||..|.-.
T Consensus 10 R~Cp~CG~kFYDLnk--------~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFYDLNK--------DPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchhccCCC--------CCccCCCCCCccCcc
Confidence 455555555555554 125699999998876
No 103
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=56.31 E-value=13 Score=32.66 Aligned_cols=36 Identities=33% Similarity=0.704 Sum_probs=20.2
Q ss_pred cceecccCccccCCHHHHHHHHhccccccCCCCccccccccccc
Q psy15165 336 QYHVCPHCGKKFTRKAELQLHIKGIHLKHQLEKTYICEYCHKEF 379 (606)
Q Consensus 336 ~~~~C~~C~~~f~~~~~l~~H~~~~h~~h~~~~~~~C~~C~k~f 379 (606)
..|.|+.|+..|.....+..- .. ...|.|+.||...
T Consensus 98 ~~Y~Cp~C~~~y~~~ea~~~~-------d~-~~~f~Cp~Cg~~l 133 (147)
T smart00531 98 AYYKCPNCQSKYTFLEANQLL-------DM-DGTFTCPRCGEEL 133 (147)
T ss_pred cEEECcCCCCEeeHHHHHHhc-------CC-CCcEECCCCCCEE
Confidence 557777777777754433220 11 2337777777654
No 104
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=56.28 E-value=6.8 Score=34.84 Aligned_cols=23 Identities=39% Similarity=0.761 Sum_probs=16.8
Q ss_pred cccCCCCCCcCCChHHHHHhhhcccccCCCCccccccccc
Q psy15165 500 FLQCPHCPKTFPRKTELSNHIKGIHMKHELRQTFVCEYCN 539 (606)
Q Consensus 500 ~~~C~~C~~~f~~~~~L~~H~~~~H~~~~~~k~y~C~~C~ 539 (606)
.|.|++||+. | .|+.|-+|++||
T Consensus 134 ~~vC~vCGy~--------------~---~ge~P~~CPiCg 156 (166)
T COG1592 134 VWVCPVCGYT--------------H---EGEAPEVCPICG 156 (166)
T ss_pred EEEcCCCCCc--------------c---cCCCCCcCCCCC
Confidence 3888888763 2 557788888887
No 105
>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=55.37 E-value=11 Score=33.47 Aligned_cols=18 Identities=22% Similarity=0.656 Sum_probs=9.6
Q ss_pred cceecccCccccCCHHHH
Q psy15165 336 QYHVCPHCGKKFTRKAEL 353 (606)
Q Consensus 336 ~~~~C~~C~~~f~~~~~l 353 (606)
..|.|+.|+..|+...++
T Consensus 108 ~~Y~Cp~c~~r~tf~eA~ 125 (158)
T TIGR00373 108 MFFICPNMCVRFTFNEAM 125 (158)
T ss_pred CeEECCCCCcEeeHHHHH
Confidence 445555555555554444
No 106
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=53.57 E-value=14 Score=35.71 Aligned_cols=21 Identities=24% Similarity=0.385 Sum_probs=13.7
Q ss_pred CCcccCCCCCCccCCHHHHHH
Q psy15165 442 EVSNLCYICGFFSAKRSTLAH 462 (606)
Q Consensus 442 ~~~~~C~~C~~~f~~~~~L~~ 462 (606)
..|..|+.|.........|.+
T Consensus 320 sLPi~CP~Csl~LilsthLar 340 (421)
T COG5151 320 SLPISCPICSLQLILSTHLAR 340 (421)
T ss_pred cCCccCcchhHHHHHHHHHHH
Confidence 456778888876655555543
No 107
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=53.53 E-value=6.1 Score=35.87 Aligned_cols=16 Identities=31% Similarity=0.872 Sum_probs=8.2
Q ss_pred cceecccCccccCCHH
Q psy15165 336 QYHVCPHCGKKFTRKA 351 (606)
Q Consensus 336 ~~~~C~~C~~~f~~~~ 351 (606)
..|.|+.|+..|+...
T Consensus 116 ~~Y~Cp~C~~rytf~e 131 (178)
T PRK06266 116 MFFFCPNCHIRFTFDE 131 (178)
T ss_pred CEEECCCCCcEEeHHH
Confidence 3455555555555443
No 108
>KOG2807|consensus
Probab=52.15 E-value=22 Score=34.80 Aligned_cols=24 Identities=21% Similarity=0.365 Sum_probs=18.9
Q ss_pred CCcccCCCCCCccCCHHHHHHHHH
Q psy15165 442 EVSNLCYICGFFSAKRSTLAHHIQ 465 (606)
Q Consensus 442 ~~~~~C~~C~~~f~~~~~L~~H~~ 465 (606)
..|-.|++|+.+......|.+-.+
T Consensus 288 sLP~eCpiC~ltLVss~hLARSyh 311 (378)
T KOG2807|consen 288 SLPIECPICSLTLVSSPHLARSYH 311 (378)
T ss_pred cCCccCCccceeEecchHHHHHHH
Confidence 567789999999988888876443
No 109
>PF15269 zf-C2H2_7: Zinc-finger
Probab=51.67 E-value=14 Score=24.40 Aligned_cols=21 Identities=43% Similarity=0.781 Sum_probs=17.6
Q ss_pred ccCCCCCCcCCChHHHHHhhh
Q psy15165 501 LQCPHCPKTFPRKTELSNHIK 521 (606)
Q Consensus 501 ~~C~~C~~~f~~~~~L~~H~~ 521 (606)
|+|-.|..+...++.|-.||+
T Consensus 21 ykcfqcpftc~~kshl~nhmk 41 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMK 41 (54)
T ss_pred ceeecCCcccchHHHHHHHHH
Confidence 888888888888888888876
No 110
>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=51.52 E-value=15 Score=32.74 Aligned_cols=33 Identities=27% Similarity=0.616 Sum_probs=21.0
Q ss_pred CCCcccccccccccCchHHHHhhhhhcCCCCccccCcchhcc
Q psy15165 366 LEKTYICEYCHKEFTFYNYLRRHMRVHTNEKPYKCKDCGAAF 407 (606)
Q Consensus 366 ~~~~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~~C~~C~~~f 407 (606)
...-|.|+.|+..|+...++.. .|.|+.||...
T Consensus 106 ~~~~Y~Cp~c~~r~tf~eA~~~---------~F~Cp~Cg~~L 138 (158)
T TIGR00373 106 NNMFFICPNMCVRFTFNEAMEL---------NFTCPRCGAML 138 (158)
T ss_pred CCCeEECCCCCcEeeHHHHHHc---------CCcCCCCCCEe
Confidence 3455777777777776666642 37777777653
No 111
>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=50.85 E-value=7.1 Score=33.30 Aligned_cols=24 Identities=29% Similarity=0.523 Sum_probs=9.7
Q ss_pred cccc-cCccCCchhhHHHhhhccccccc
Q psy15165 561 YKCV-CGLGFNFNVSLKNHKQKCSVFLL 587 (606)
Q Consensus 561 ~~C~-C~~~F~~~~~L~~H~~~h~~~~~ 587 (606)
..|. ||+.|.. |++|++.|||..|
T Consensus 73 i~clecGk~~k~---LkrHL~~~~gltp 97 (132)
T PF05443_consen 73 IICLECGKKFKT---LKRHLRTHHGLTP 97 (132)
T ss_dssp EE-TBT--EESB---HHHHHHHTT-S-H
T ss_pred eEEccCCcccch---HHHHHHHccCCCH
Confidence 3454 5555533 3556666655443
No 112
>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=50.54 E-value=8.6 Score=35.89 Aligned_cols=29 Identities=28% Similarity=0.418 Sum_probs=22.2
Q ss_pred cCCccccCCCCCCcCCChHHHHHhhhccc
Q psy15165 496 HSGFFLQCPHCPKTFPRKTELSNHIKGIH 524 (606)
Q Consensus 496 h~~~~~~C~~C~~~f~~~~~L~~H~~~~H 524 (606)
..+.+|.|+.|+|.|.......+||...|
T Consensus 73 ~~~~K~~C~lc~KlFkg~eFV~KHI~nKH 101 (214)
T PF04959_consen 73 EDEDKWRCPLCGKLFKGPEFVRKHIFNKH 101 (214)
T ss_dssp SSSEEEEE-SSS-EESSHHHHHHHHHHH-
T ss_pred HcCCEECCCCCCcccCChHHHHHHHhhcC
Confidence 34456999999999999999999998777
No 113
>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=49.52 E-value=4.7 Score=28.06 Aligned_cols=11 Identities=36% Similarity=0.987 Sum_probs=5.9
Q ss_pred ccccccccccC
Q psy15165 370 YICEYCHKEFT 380 (606)
Q Consensus 370 ~~C~~C~k~f~ 380 (606)
|.|..||..|.
T Consensus 6 y~C~~Cg~~fe 16 (52)
T TIGR02605 6 YRCTACGHRFE 16 (52)
T ss_pred EEeCCCCCEeE
Confidence 45555555554
No 114
>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=49.39 E-value=4.6 Score=26.35 Aligned_cols=11 Identities=45% Similarity=1.065 Sum_probs=5.2
Q ss_pred ccccccccccC
Q psy15165 370 YICEYCHKEFT 380 (606)
Q Consensus 370 ~~C~~C~k~f~ 380 (606)
|.|..||..|.
T Consensus 6 y~C~~Cg~~fe 16 (41)
T smart00834 6 YRCEDCGHTFE 16 (41)
T ss_pred EEcCCCCCEEE
Confidence 44555554443
No 115
>PF08788 NHR2: NHR2 domain like; InterPro: IPR014896 Transcriptional activation and repression are required for control of cell proliferation and differentiation during embryonic development and homeostasis in the adult organism. Perturbations of these processes can lead to the development of cancer []. The Eight-Twenty-One (ETO) gene product is able to form complexes with corepressors and deacetylases, such as nuclear receptor corepressor (N-CoR), which repress transcription when recruited by transcription factors []. The ETO gene derives its name from its association with many cases of acute myelogenous leukaemia (AML), in which a reciprocal translocation, t(8;21), brings together a large portion of the ETO gene from chromosome eight and part of the AML1 gene from chromosome 21. The human ETO gene family currently comprises three major subfamilies: ETO/myeloid transforming gene on chromosome 8 (MTG8); myeloid transforming gene related protein-1 (MTGR1) and myeloid transforming gene on chromosome 16 (MTG16). ETO proteins are composed of four evolutionarily conserved domains termed nervy homology regions (NHR) 1-4. NHR1 is thought to stabilise the formation of high molecular weight complexes, but is not directly responsible for repressor activity. NHR2 and its flanking sequence comprise the core repressor domain, which mediates 50% of the wild type repressor activity. Furthermore, there is evidence that the amphipathic helical structure of NHR2 promotes the formation of ETO/AML1 homodimers []. NHR3 and NHR4 have been shown to act in concert to bind N-CoR. NHR4 contains two zinc finger motifs, which are thought to play a role in protein interactions rather than DNA binding []. This entry represents the NHR2 (Nervy homology 2) domain found in ETO proteins. It mediates oligomerisation and protein-protein interactions, forming an alpha-helical tetramer []. ; PDB: 1WQ6_A.
Probab=48.70 E-value=3.4 Score=29.45 Aligned_cols=11 Identities=36% Similarity=0.996 Sum_probs=8.1
Q ss_pred ccccccccccc
Q psy15165 3 DDDWNNLDDHV 13 (606)
Q Consensus 3 ~~~~~~~~~~~ 13 (606)
+|||.+||.||
T Consensus 15 ~deWkh~~~mL 25 (67)
T PF08788_consen 15 ADEWKHLDHML 25 (67)
T ss_dssp HHHHHHHHHHH
T ss_pred HHHhcCHHHHH
Confidence 57777777775
No 116
>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=48.65 E-value=7.2 Score=25.83 Aligned_cols=11 Identities=55% Similarity=1.180 Sum_probs=5.2
Q ss_pred ccccccccccC
Q psy15165 370 YICEYCHKEFT 380 (606)
Q Consensus 370 ~~C~~C~k~f~ 380 (606)
|.|..||..|.
T Consensus 6 y~C~~Cg~~fe 16 (42)
T PF09723_consen 6 YRCEECGHEFE 16 (42)
T ss_pred EEeCCCCCEEE
Confidence 44555554443
No 117
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=48.20 E-value=8.8 Score=34.86 Aligned_cols=16 Identities=19% Similarity=0.422 Sum_probs=8.7
Q ss_pred CcccccCccccCCHHH
Q psy15165 214 EFKCRVCDWKLNSYDK 229 (606)
Q Consensus 214 ~~~C~~C~~~f~~~~~ 229 (606)
-|.|+.|+..|....+
T Consensus 117 ~Y~Cp~C~~rytf~eA 132 (178)
T PRK06266 117 FFFCPNCHIRFTFDEA 132 (178)
T ss_pred EEECCCCCcEEeHHHH
Confidence 3556666655554443
No 118
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=48.06 E-value=9.4 Score=31.16 Aligned_cols=14 Identities=29% Similarity=0.603 Sum_probs=10.2
Q ss_pred CcccCCCCCCccCC
Q psy15165 443 VSNLCYICGFFSAK 456 (606)
Q Consensus 443 ~~~~C~~C~~~f~~ 456 (606)
..+.|+.|++.+..
T Consensus 15 ~~~~C~~C~~~~~~ 28 (104)
T TIGR01384 15 GVYVCPSCGYEKEK 28 (104)
T ss_pred CeEECcCCCCcccc
Confidence 35789999987654
No 119
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=46.93 E-value=9.5 Score=33.59 Aligned_cols=18 Identities=22% Similarity=0.440 Sum_probs=14.6
Q ss_pred ccCCCCCCcCCChHHHHH
Q psy15165 501 LQCPHCPKTFPRKTELSN 518 (606)
Q Consensus 501 ~~C~~C~~~f~~~~~L~~ 518 (606)
++|+.||+.|.+...+..
T Consensus 29 ~~c~~c~~~f~~~e~~~~ 46 (154)
T PRK00464 29 RECLACGKRFTTFERVEL 46 (154)
T ss_pred eeccccCCcceEeEeccC
Confidence 899999999988765543
No 120
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=45.01 E-value=14 Score=41.33 Aligned_cols=28 Identities=29% Similarity=0.823 Sum_probs=19.3
Q ss_pred cCCCCcccccccccccCchHHHHhhhhhcCCCCccccCcchhc
Q psy15165 364 HQLEKTYICEYCHKEFTFYNYLRRHMRVHTNEKPYKCKDCGAA 406 (606)
Q Consensus 364 h~~~~~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~~C~~C~~~ 406 (606)
|.......|..||.. ...|..|+.||-.
T Consensus 457 H~~~~~L~CH~Cg~~---------------~~~p~~Cp~Cgs~ 484 (730)
T COG1198 457 HKATGQLRCHYCGYQ---------------EPIPQSCPECGSE 484 (730)
T ss_pred ecCCCeeEeCCCCCC---------------CCCCCCCCCCCCC
Confidence 333466778888753 3568899999865
No 121
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=44.61 E-value=10 Score=25.96 Aligned_cols=10 Identities=40% Similarity=1.062 Sum_probs=5.3
Q ss_pred cccccccccc
Q psy15165 370 YICEYCHKEF 379 (606)
Q Consensus 370 ~~C~~C~k~f 379 (606)
|.|..||+.|
T Consensus 7 Y~C~~Cg~~~ 16 (49)
T COG1996 7 YKCARCGREV 16 (49)
T ss_pred EEhhhcCCee
Confidence 5555555554
No 122
>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=44.48 E-value=10 Score=32.39 Aligned_cols=25 Identities=48% Similarity=0.935 Sum_probs=15.0
Q ss_pred ccccccchhccChhhHHHHHhhhcCCCC
Q psy15165 533 FVCEYCNKEFTFLQYLKRHMRTHTNEKP 560 (606)
Q Consensus 533 y~C~~C~k~f~~~~~L~~H~~~H~~~kp 560 (606)
-.|-.||+.|.. |.+|+++|+|-.|
T Consensus 73 i~clecGk~~k~---LkrHL~~~~gltp 97 (132)
T PF05443_consen 73 IICLECGKKFKT---LKRHLRTHHGLTP 97 (132)
T ss_dssp EE-TBT--EESB---HHHHHHHTT-S-H
T ss_pred eEEccCCcccch---HHHHHHHccCCCH
Confidence 578888888865 4888888877543
No 123
>PRK04023 DNA polymerase II large subunit; Validated
Probab=44.14 E-value=21 Score=40.81 Aligned_cols=10 Identities=30% Similarity=0.517 Sum_probs=6.3
Q ss_pred cccCCCCCCc
Q psy15165 444 SNLCYICGFF 453 (606)
Q Consensus 444 ~~~C~~C~~~ 453 (606)
...|+.||..
T Consensus 626 ~RfCpsCG~~ 635 (1121)
T PRK04023 626 RRKCPSCGKE 635 (1121)
T ss_pred CccCCCCCCc
Confidence 4557777765
No 124
>KOG1280|consensus
Probab=43.21 E-value=26 Score=34.68 Aligned_cols=26 Identities=27% Similarity=0.424 Sum_probs=12.2
Q ss_pred CcccCccccccCCHHHHHHHHHHhhC
Q psy15165 278 SSLCYHCGYYSKNRSTLKNHVRVEHG 303 (606)
Q Consensus 278 ~~~C~~C~~~f~~~~~L~~H~~~h~~ 303 (606)
.|.|++|+..=-+...|..|+...|.
T Consensus 79 SftCPyC~~~Gfte~~f~~Hv~s~Hp 104 (381)
T KOG1280|consen 79 SFTCPYCGIMGFTERQFGTHVLSQHP 104 (381)
T ss_pred cccCCcccccccchhHHHHHhhhcCc
Confidence 34455555444444444444444443
No 125
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=42.55 E-value=7.6 Score=26.85 Aligned_cols=12 Identities=25% Similarity=1.160 Sum_probs=7.7
Q ss_pred cccccCccccCC
Q psy15165 215 FKCRVCDWKLNS 226 (606)
Q Consensus 215 ~~C~~C~~~f~~ 226 (606)
|.|.+||..|.-
T Consensus 2 y~C~~CgyiYd~ 13 (50)
T cd00730 2 YECRICGYIYDP 13 (50)
T ss_pred cCCCCCCeEECC
Confidence 567777766653
No 126
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=42.51 E-value=6.7 Score=26.72 Aligned_cols=13 Identities=23% Similarity=0.884 Sum_probs=8.5
Q ss_pred cccccCccccCCH
Q psy15165 215 FKCRVCDWKLNSY 227 (606)
Q Consensus 215 ~~C~~C~~~f~~~ 227 (606)
|.|.+|+..|.-.
T Consensus 2 y~C~~CgyvYd~~ 14 (47)
T PF00301_consen 2 YQCPVCGYVYDPE 14 (47)
T ss_dssp EEETTTSBEEETT
T ss_pred cCCCCCCEEEcCC
Confidence 5677777666543
No 127
>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=41.42 E-value=16 Score=22.61 Aligned_cols=12 Identities=25% Similarity=0.340 Sum_probs=7.6
Q ss_pred CCcccCCCCCCc
Q psy15165 442 EVSNLCYICGFF 453 (606)
Q Consensus 442 ~~~~~C~~C~~~ 453 (606)
..+..|..||..
T Consensus 15 ~~~irC~~CG~R 26 (32)
T PF03604_consen 15 GDPIRCPECGHR 26 (32)
T ss_dssp SSTSSBSSSS-S
T ss_pred CCcEECCcCCCe
Confidence 345678888864
No 128
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=41.39 E-value=15 Score=28.48 Aligned_cols=13 Identities=23% Similarity=0.779 Sum_probs=6.9
Q ss_pred ccccccccchhcc
Q psy15165 531 QTFVCEYCNKEFT 543 (606)
Q Consensus 531 k~y~C~~C~k~f~ 543 (606)
..+.|..||..|.
T Consensus 52 GIW~C~kCg~~fA 64 (89)
T COG1997 52 GIWKCRKCGAKFA 64 (89)
T ss_pred CeEEcCCCCCeec
Confidence 3455555555554
No 129
>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=40.97 E-value=17 Score=30.45 Aligned_cols=17 Identities=24% Similarity=0.409 Sum_probs=12.5
Q ss_pred ccCCCCCCcCCChHHHH
Q psy15165 501 LQCPHCPKTFPRKTELS 517 (606)
Q Consensus 501 ~~C~~C~~~f~~~~~L~ 517 (606)
..|+.||..|.-...++
T Consensus 27 ~vcP~cg~~~~~~~~~~ 43 (129)
T TIGR02300 27 AVSPYTGEQFPPEEALK 43 (129)
T ss_pred ccCCCcCCccCcchhhc
Confidence 56999999887664444
No 130
>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=40.83 E-value=16 Score=21.38 Aligned_cols=11 Identities=45% Similarity=1.050 Sum_probs=8.9
Q ss_pred ccCCCCCCcCC
Q psy15165 501 LQCPHCPKTFP 511 (606)
Q Consensus 501 ~~C~~C~~~f~ 511 (606)
-.|+.||+.|.
T Consensus 15 ~~Cp~CG~~F~ 25 (26)
T PF10571_consen 15 KFCPHCGYDFE 25 (26)
T ss_pred CcCCCCCCCCc
Confidence 36999999885
No 131
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=40.41 E-value=9 Score=28.80 Aligned_cols=18 Identities=28% Similarity=0.630 Sum_probs=10.3
Q ss_pred CCCccccC--cchhccCChh
Q psy15165 394 NEKPYKCK--DCGAAFNHNV 411 (606)
Q Consensus 394 ~~~~~~C~--~C~~~f~~~~ 411 (606)
.+.-++|. .||.+|....
T Consensus 24 ~~~Y~qC~N~eCg~tF~t~e 43 (72)
T PRK09678 24 KERYHQCQNVNCSATFITYE 43 (72)
T ss_pred heeeeecCCCCCCCEEEEEE
Confidence 34455665 6666666543
No 132
>KOG4377|consensus
Probab=40.07 E-value=23 Score=35.83 Aligned_cols=24 Identities=21% Similarity=0.505 Sum_probs=21.2
Q ss_pred ccc--c-cCccCCchhhHHHhhhcccc
Q psy15165 561 YKC--V-CGLGFNFNVSLKNHKQKCSV 584 (606)
Q Consensus 561 ~~C--~-C~~~F~~~~~L~~H~~~h~~ 584 (606)
|.| . |+..|...+.+..|.|+|-.
T Consensus 402 fhc~r~Gc~~tl~s~sqm~shkrkheR 428 (480)
T KOG4377|consen 402 FHCDRLGCEATLYSVSQMASHKRKHER 428 (480)
T ss_pred eeecccCCceEEEehhhhhhhhhhhhh
Confidence 678 3 99999999999999999963
No 133
>PHA02644 hypothetical protein; Provisional
Probab=39.34 E-value=27 Score=26.37 Aligned_cols=35 Identities=11% Similarity=0.089 Sum_probs=31.1
Q ss_pred cccCCCceeeecccCCCCceeeeeccccCCccccc
Q psy15165 12 HVGKPSRRRSLGVESSVPKLKIKTETDDKSWEDKS 46 (606)
Q Consensus 12 ~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~ 46 (606)
|||-|....-|...||.-|-+.++=-|..|+|-.+
T Consensus 1 mlesyntyakvninvstkdqvikimigsspymdvr 35 (112)
T PHA02644 1 MLESYNTYAKVNINVSTKDQVIKIMIGSSPYMDVR 35 (112)
T ss_pred CcccccceeEEEeeccccceeEEEEecCCCcceEE
Confidence 89999999999999999888888888999988665
No 134
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=39.34 E-value=17 Score=23.77 Aligned_cols=11 Identities=18% Similarity=0.718 Sum_probs=7.5
Q ss_pred ccCCCCCCcCC
Q psy15165 501 LQCPHCPKTFP 511 (606)
Q Consensus 501 ~~C~~C~~~f~ 511 (606)
|.|..|+..|.
T Consensus 29 y~C~~C~~~w~ 39 (40)
T smart00440 29 YVCTKCGHRWR 39 (40)
T ss_pred EEeCCCCCEeC
Confidence 77777776653
No 135
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=39.01 E-value=18 Score=29.18 Aligned_cols=13 Identities=31% Similarity=0.664 Sum_probs=8.0
Q ss_pred Cccccccccchhc
Q psy15165 530 RQTFVCEYCNKEF 542 (606)
Q Consensus 530 ~k~y~C~~C~k~f 542 (606)
+.|..|++||++|
T Consensus 24 rdPiVsPytG~s~ 36 (129)
T COG4530 24 RDPIVSPYTGKSY 36 (129)
T ss_pred CCccccCcccccc
Confidence 3456666666666
No 136
>PF12907 zf-met2: Zinc-binding
Probab=38.09 E-value=20 Score=23.47 Aligned_cols=26 Identities=19% Similarity=0.510 Sum_probs=16.9
Q ss_pred cccccccccc---CCHHHHHHhHhhhcCC
Q psy15165 249 FKCRVCDWKL---NSYDKLLRHIKSDHGG 274 (606)
Q Consensus 249 ~~C~~C~~~f---~~~~~L~~H~~~~H~~ 274 (606)
++|.+|..+| .+...|..|..+.|..
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKHpK 30 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKHPK 30 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccCCC
Confidence 5677777544 4556677777766654
No 137
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.89 E-value=15 Score=27.43 Aligned_cols=11 Identities=18% Similarity=0.866 Sum_probs=5.9
Q ss_pred CcccccCcccc
Q psy15165 214 EFKCRVCDWKL 224 (606)
Q Consensus 214 ~~~C~~C~~~f 224 (606)
.|+|..|+..|
T Consensus 12 ~Y~c~~cg~~~ 22 (82)
T COG2331 12 SYECTECGNRF 22 (82)
T ss_pred EEeecccchHH
Confidence 45555555544
No 138
>KOG4167|consensus
Probab=36.82 E-value=11 Score=40.99 Aligned_cols=25 Identities=36% Similarity=0.669 Sum_probs=23.6
Q ss_pred cccccccchhccChhhHHHHHhhhc
Q psy15165 532 TFVCEYCNKEFTFLQYLKRHMRTHT 556 (606)
Q Consensus 532 ~y~C~~C~k~f~~~~~L~~H~~~H~ 556 (606)
-|.|..|+|.|..-..+..||++|.
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHH
Confidence 4999999999999999999999996
No 139
>PRK04023 DNA polymerase II large subunit; Validated
Probab=36.78 E-value=28 Score=39.79 Aligned_cols=10 Identities=50% Similarity=1.281 Sum_probs=5.7
Q ss_pred ceecccCccc
Q psy15165 337 YHVCPHCGKK 346 (606)
Q Consensus 337 ~~~C~~C~~~ 346 (606)
...|+.||..
T Consensus 626 ~RfCpsCG~~ 635 (1121)
T PRK04023 626 RRKCPSCGKE 635 (1121)
T ss_pred CccCCCCCCc
Confidence 3456666654
No 140
>PF14353 CpXC: CpXC protein
Probab=35.86 E-value=3.5 Score=35.25 Aligned_cols=21 Identities=29% Similarity=0.738 Sum_probs=14.2
Q ss_pred ccccCcchhccCChhHHhccc
Q psy15165 397 PYKCKDCGAAFNHNVSLKNHK 417 (606)
Q Consensus 397 ~~~C~~C~~~f~~~~~L~~H~ 417 (606)
.|.|+.||..|.-...+.-|-
T Consensus 38 ~~~CP~Cg~~~~~~~p~lY~D 58 (128)
T PF14353_consen 38 SFTCPSCGHKFRLEYPLLYHD 58 (128)
T ss_pred EEECCCCCCceecCCCEEEEc
Confidence 367888887777666665553
No 141
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=35.83 E-value=20 Score=33.90 Aligned_cols=97 Identities=22% Similarity=0.260 Sum_probs=53.2
Q ss_pred hcCCCCCCcccCccccccCCHHHHHHHHHHhhCCccccccccccccccccchHhHHHHHHhccCCcceecccCccccCCH
Q psy15165 271 DHGGYETSSLCYHCGYYSKNRSTLKNHVRVEHGENQAKRKEKKICDICSAEVVHLAIHKKHSHSGQYHVCPHCGKKFTRK 350 (606)
Q Consensus 271 ~H~~~~~~~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~~~~~~~C~~C~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~ 350 (606)
.|+ .+.|.|..|.. |--...-..|+...... ....|.|..|++. ..|.|--|.-.|-.
T Consensus 137 ~hG--Grif~CsfC~~-flCEDDQFEHQAsCQvL----e~E~~KC~SCNrl--------------Gq~sCLRCK~cfCd- 194 (314)
T PF06524_consen 137 DHG--GRIFKCSFCDN-FLCEDDQFEHQASCQVL----ESETFKCQSCNRL--------------GQYSCLRCKICFCD- 194 (314)
T ss_pred cCC--CeEEEeecCCC-eeeccchhhhhhhhhhh----hcccccccccccc--------------cchhhhheeeeehh-
Confidence 566 47789999875 33344444555443221 1245666666541 12344444443432
Q ss_pred HHHHHHHhccccccCCCCcccccccccccCchHHHHhhhhhcC
Q psy15165 351 AELQLHIKGIHLKHQLEKTYICEYCHKEFTFYNYLRRHMRVHT 393 (606)
Q Consensus 351 ~~l~~H~~~~h~~h~~~~~~~C~~C~k~f~~~~~L~~H~~~H~ 393 (606)
.|++..-......+++.|+.||........|..-.+.|.
T Consensus 195 ----dHvrrKg~ky~k~k~~PCPKCg~et~eTkdLSmStR~hk 233 (314)
T PF06524_consen 195 ----DHVRRKGFKYEKGKPIPCPKCGYETQETKDLSMSTRSHK 233 (314)
T ss_pred ----hhhhhcccccccCCCCCCCCCCCcccccccceeeeecch
Confidence 455533223344578888888887776666666666553
No 142
>KOG2807|consensus
Probab=33.90 E-value=39 Score=33.20 Aligned_cols=20 Identities=25% Similarity=0.647 Sum_probs=13.8
Q ss_pred ccCCCCCCcCCChHHHHHhh
Q psy15165 501 LQCPHCPKTFPRKTELSNHI 520 (606)
Q Consensus 501 ~~C~~C~~~f~~~~~L~~H~ 520 (606)
-.|+.|+-...+...|.+=.
T Consensus 291 ~eCpiC~ltLVss~hLARSy 310 (378)
T KOG2807|consen 291 IECPICSLTLVSSPHLARSY 310 (378)
T ss_pred ccCCccceeEecchHHHHHH
Confidence 56777777777777776543
No 143
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=33.33 E-value=42 Score=39.59 Aligned_cols=53 Identities=25% Similarity=0.544 Sum_probs=32.0
Q ss_pred ccCCCCCCccCCHHHHHHHHHHhcCCCCCcCccccccccchhhhhcccccccCCccccCCCCCCcCCChHHHHHhhhccc
Q psy15165 445 NLCYICGFFSAKRSTLAHHIQDHIQPRMKQKQICEICCAEVYHINGHIKDKHSGFFLQCPHCPKTFPRKTELSNHIKGIH 524 (606)
Q Consensus 445 ~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~~~~C~~c~~~~~~l~~H~~~~h~~~~~~C~~C~~~f~~~~~L~~H~~~~H 524 (606)
+.|+.||..... ..|+.||... ...|.|+.||.......
T Consensus 668 rkCPkCG~~t~~-------------------~fCP~CGs~t------------e~vy~CPsCGaev~~de---------- 706 (1337)
T PRK14714 668 RRCPSCGTETYE-------------------NRCPDCGTHT------------EPVYVCPDCGAEVPPDE---------- 706 (1337)
T ss_pred EECCCCCCcccc-------------------ccCcccCCcC------------CCceeCccCCCccCCCc----------
Confidence 679999874210 3688888542 12378888887644311
Q ss_pred ccCCCCccccccccchhcc
Q psy15165 525 MKHELRQTFVCEYCNKEFT 543 (606)
Q Consensus 525 ~~~~~~k~y~C~~C~k~f~ 543 (606)
++ ...|+.||....
T Consensus 707 ---s~--a~~CP~CGtplv 720 (1337)
T PRK14714 707 ---SG--RVECPRCDVELT 720 (1337)
T ss_pred ---cc--cccCCCCCCccc
Confidence 12 346888885543
No 144
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=33.31 E-value=23 Score=24.51 Aligned_cols=11 Identities=18% Similarity=0.480 Sum_probs=6.9
Q ss_pred cccccccchhc
Q psy15165 532 TFVCEYCNKEF 542 (606)
Q Consensus 532 ~y~C~~C~k~f 542 (606)
.+.|..||..+
T Consensus 37 r~~C~~Cgyt~ 47 (50)
T PRK00432 37 RWHCGKCGYTE 47 (50)
T ss_pred cEECCCcCCEE
Confidence 46677776654
No 145
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=33.09 E-value=14 Score=24.06 Aligned_cols=10 Identities=20% Similarity=0.733 Sum_probs=6.6
Q ss_pred ccCCCCCCcC
Q psy15165 501 LQCPHCPKTF 510 (606)
Q Consensus 501 ~~C~~C~~~f 510 (606)
|.|..|+..|
T Consensus 29 y~C~~C~~~w 38 (39)
T PF01096_consen 29 YVCCNCGHRW 38 (39)
T ss_dssp EEESSSTEEE
T ss_pred EEeCCCCCee
Confidence 6777776654
No 146
>KOG1280|consensus
Probab=33.09 E-value=41 Score=33.38 Aligned_cols=41 Identities=22% Similarity=0.488 Sum_probs=32.1
Q ss_pred CCcccCCCCCCccCCHHHHHHHHHHhcCCCCCcCcccccccc
Q psy15165 442 EVSNLCYICGFFSAKRSTLAHHIQDHIQPRMKQKQICEICCA 483 (606)
Q Consensus 442 ~~~~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~~~~C~~c~~ 483 (606)
...|.|++|+..-.+...|..|+..-+.+-+ ...+|++|+.
T Consensus 77 ~qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~-~~~icp~c~~ 117 (381)
T KOG1280|consen 77 PQSFTCPYCGIMGFTERQFGTHVLSQHPEAS-TSVICPLCAA 117 (381)
T ss_pred cccccCCcccccccchhHHHHHhhhcCcccC-cceeeecccc
Confidence 4578999999999999999999887666555 4467777763
No 147
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=32.52 E-value=23 Score=27.61 Aligned_cols=14 Identities=43% Similarity=1.177 Sum_probs=8.7
Q ss_pred CccccCcchhccCC
Q psy15165 396 KPYKCKDCGAAFNH 409 (606)
Q Consensus 396 ~~~~C~~C~~~f~~ 409 (606)
.|-.|..||+.|..
T Consensus 57 ~Pa~CkkCGfef~~ 70 (97)
T COG3357 57 RPARCKKCGFEFRD 70 (97)
T ss_pred cChhhcccCccccc
Confidence 45566666666655
No 148
>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=32.26 E-value=34 Score=29.86 Aligned_cols=43 Identities=26% Similarity=0.521 Sum_probs=19.2
Q ss_pred cCCCCccccccccccc------CchHHHHhhhh--hc------C----CCCccccCcchhc
Q psy15165 364 HQLEKTYICEYCHKEF------TFYNYLRRHMR--VH------T----NEKPYKCKDCGAA 406 (606)
Q Consensus 364 h~~~~~~~C~~C~k~f------~~~~~L~~H~~--~H------~----~~~~~~C~~C~~~ 406 (606)
|...-..+|..|++-| ++.+.+..|+. .| . |+..++|..||-.
T Consensus 9 ~~p~~vv~C~~c~kWFCNg~~~~s~SHIv~HLv~srh~ev~LH~~s~lgdt~leCy~Cg~~ 69 (152)
T PF09416_consen 9 HDPSCVVKCNTCNKWFCNGRGNTSGSHIVNHLVRSRHKEVSLHPDSPLGDTVLECYNCGSR 69 (152)
T ss_dssp --CCCEEEETTTTEEEES--TTSSS-HHHHHHHHHT---EEE-TTSTT-S-B---TTT---
T ss_pred CCcccEeEcCCCCcEeecCCCCCcccHHHHHHHHccCCceeeCCCCCCCCcEEEEEecCCC
Confidence 4445556787777777 24455666643 12 1 3456789888764
No 149
>KOG2593|consensus
Probab=32.14 E-value=29 Score=35.65 Aligned_cols=34 Identities=29% Similarity=0.604 Sum_probs=25.7
Q ss_pred ccCCCCCCcCCChHHHHHhhhcccccCCCCccccccccchh
Q psy15165 501 LQCPHCPKTFPRKTELSNHIKGIHMKHELRQTFVCEYCNKE 541 (606)
Q Consensus 501 ~~C~~C~~~f~~~~~L~~H~~~~H~~~~~~k~y~C~~C~k~ 541 (606)
|.|+.|.+.|+...+++-=- ...-.|.|..|+-.
T Consensus 129 Y~Cp~C~kkyt~Lea~~L~~-------~~~~~F~C~~C~ge 162 (436)
T KOG2593|consen 129 YVCPNCQKKYTSLEALQLLD-------NETGEFHCENCGGE 162 (436)
T ss_pred ccCCccccchhhhHHHHhhc-------ccCceEEEecCCCc
Confidence 99999999999888776421 22346999999754
No 150
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=32.03 E-value=43 Score=33.17 Aligned_cols=26 Identities=23% Similarity=0.488 Sum_probs=21.8
Q ss_pred CcccccccccccCchHHHHhhhh--hcC
Q psy15165 368 KTYICEYCHKEFTFYNYLRRHMR--VHT 393 (606)
Q Consensus 368 ~~~~C~~C~k~f~~~~~L~~H~~--~H~ 393 (606)
..+-|..|++-|.....+..|+. .|.
T Consensus 237 ~~~YC~~C~r~f~~~~VFe~Hl~gK~H~ 264 (470)
T COG5188 237 PKVYCVKCGREFSRSKVFEYHLEGKRHC 264 (470)
T ss_pred cceeeHhhhhHhhhhHHHHHHHhhhhhh
Confidence 45789999999999999999975 454
No 151
>COG3779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.80 E-value=27 Score=29.33 Aligned_cols=42 Identities=10% Similarity=-0.182 Sum_probs=33.4
Q ss_pred CCCceeeecccCCCCceeeeeccccCCccccccCCCceeeecc
Q psy15165 15 KPSRRRSLGVESSVPKLKIKTETDDKSWEDKSLLEPEIKIKVE 57 (606)
Q Consensus 15 ~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e 57 (606)
-|++|-.+|..-..|..+.-.|||++ |-++..-.+||.+...
T Consensus 78 ~~~~~~f~GVl~NePgevtNVe~Gqs-v~v~~dDISDWmy~~g 119 (151)
T COG3779 78 YFDGLYFYGVLNNEPGEVTNVEQGQS-VCVPVDDISDWMYVCG 119 (151)
T ss_pred EecCcEEEEEEcCCCceeeeeecCcE-EEEehhhhhhhheeeC
Confidence 37899999999999999999999965 8877655555655443
No 152
>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=31.32 E-value=20 Score=33.48 Aligned_cols=22 Identities=14% Similarity=0.481 Sum_probs=15.8
Q ss_pred CcccccCccccCCHHHHHhhhh
Q psy15165 214 EFKCRVCDWKLNSYDKLLRHMD 235 (606)
Q Consensus 214 ~~~C~~C~~~f~~~~~l~~H~~ 235 (606)
.|.|..|+|.|.-..-...|+.
T Consensus 77 K~~C~lc~KlFkg~eFV~KHI~ 98 (214)
T PF04959_consen 77 KWRCPLCGKLFKGPEFVRKHIF 98 (214)
T ss_dssp EEEE-SSS-EESSHHHHHHHHH
T ss_pred EECCCCCCcccCChHHHHHHHh
Confidence 5788888888888888888875
No 153
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=31.20 E-value=28 Score=29.34 Aligned_cols=24 Identities=42% Similarity=0.671 Sum_probs=13.3
Q ss_pred cccccchhccChhhHHHHHhhhcCCCC
Q psy15165 534 VCEYCNKEFTFLQYLKRHMRTHTNEKP 560 (606)
Q Consensus 534 ~C~~C~k~f~~~~~L~~H~~~H~~~kp 560 (606)
.|-.+|+.|. .|++|+.+|.|-.|
T Consensus 78 icLEDGkkfK---SLKRHL~t~~gmTP 101 (148)
T COG4957 78 ICLEDGKKFK---SLKRHLTTHYGLTP 101 (148)
T ss_pred EEeccCcchH---HHHHHHhcccCCCH
Confidence 5666666653 35566666555433
No 154
>PRK14873 primosome assembly protein PriA; Provisional
Probab=31.03 E-value=35 Score=38.17 Aligned_cols=8 Identities=25% Similarity=0.426 Sum_probs=4.4
Q ss_pred cCCCCCCc
Q psy15165 446 LCYICGFF 453 (606)
Q Consensus 446 ~C~~C~~~ 453 (606)
.|..||..
T Consensus 385 ~C~~Cg~~ 392 (665)
T PRK14873 385 ACARCRTP 392 (665)
T ss_pred EhhhCcCe
Confidence 46666553
No 155
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=30.90 E-value=21 Score=21.70 Aligned_cols=10 Identities=30% Similarity=0.936 Sum_probs=5.1
Q ss_pred CccccCcchh
Q psy15165 396 KPYKCKDCGA 405 (606)
Q Consensus 396 ~~~~C~~C~~ 405 (606)
..|.|+.|+.
T Consensus 18 ~~~vCp~C~~ 27 (30)
T PF08274_consen 18 ELLVCPECGH 27 (30)
T ss_dssp SSEEETTTTE
T ss_pred CEEeCCcccc
Confidence 3455555543
No 156
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=30.88 E-value=41 Score=39.68 Aligned_cols=23 Identities=39% Similarity=0.823 Sum_probs=15.0
Q ss_pred cccccccccCchHHHHhhhhhcCCCCccccCcchhccC
Q psy15165 371 ICEYCHKEFTFYNYLRRHMRVHTNEKPYKCKDCGAAFN 408 (606)
Q Consensus 371 ~C~~C~k~f~~~~~L~~H~~~H~~~~~~~C~~C~~~f~ 408 (606)
.|+.||... +.+|.|+.||....
T Consensus 681 fCP~CGs~t---------------e~vy~CPsCGaev~ 703 (1337)
T PRK14714 681 RCPDCGTHT---------------EPVYVCPDCGAEVP 703 (1337)
T ss_pred cCcccCCcC---------------CCceeCccCCCccC
Confidence 677777653 23577888887543
No 157
>KOG2907|consensus
Probab=30.24 E-value=33 Score=28.01 Aligned_cols=12 Identities=33% Similarity=1.002 Sum_probs=7.3
Q ss_pred ccCCCCCCcCCC
Q psy15165 501 LQCPHCPKTFPR 512 (606)
Q Consensus 501 ~~C~~C~~~f~~ 512 (606)
|.|+.|++.|+.
T Consensus 103 YTC~kC~~k~~e 114 (116)
T KOG2907|consen 103 YTCPKCKYKFTE 114 (116)
T ss_pred EEcCccceeeec
Confidence 666666666543
No 158
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=29.90 E-value=31 Score=34.13 Aligned_cols=24 Identities=17% Similarity=0.517 Sum_probs=17.8
Q ss_pred CCccccCcch-hccCChhHHhcccc
Q psy15165 395 EKPYKCKDCG-AAFNHNVSLKNHKN 418 (606)
Q Consensus 395 ~~~~~C~~C~-~~f~~~~~L~~H~~ 418 (606)
.+.|.|.+|| +.+.-...+.+|..
T Consensus 372 d~ef~CEICgNyvy~GR~~FdrHF~ 396 (470)
T COG5188 372 DIEFECEICGNYVYYGRDRFDRHFE 396 (470)
T ss_pred CcceeeeecccccccchHHHHhhhh
Confidence 3458899999 67777777777754
No 159
>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=29.81 E-value=42 Score=36.24 Aligned_cols=9 Identities=44% Similarity=1.224 Sum_probs=5.8
Q ss_pred ccCCCCCCc
Q psy15165 445 NLCYICGFF 453 (606)
Q Consensus 445 ~~C~~C~~~ 453 (606)
..|..||..
T Consensus 214 ~~C~~Cg~~ 222 (505)
T TIGR00595 214 LLCRSCGYI 222 (505)
T ss_pred eEhhhCcCc
Confidence 457777764
No 160
>KOG2272|consensus
Probab=29.80 E-value=57 Score=30.74 Aligned_cols=26 Identities=23% Similarity=0.602 Sum_probs=14.9
Q ss_pred hhhhcccccccCCccccCCCCCCcCCChHH
Q psy15165 486 YHINGHIKDKHSGFFLQCPHCPKTFPRKTE 515 (606)
Q Consensus 486 ~~l~~H~~~~h~~~~~~C~~C~~~f~~~~~ 515 (606)
..|..|.-..| |.|..|.+-|--...
T Consensus 211 ~amgKhWHveH----FvCa~CekPFlGHrH 236 (332)
T KOG2272|consen 211 FAMGKHWHVEH----FVCAKCEKPFLGHRH 236 (332)
T ss_pred HHhccccchhh----eeehhcCCcccchhh
Confidence 33444444433 778888777765433
No 161
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=29.36 E-value=31 Score=24.56 Aligned_cols=27 Identities=19% Similarity=0.404 Sum_probs=11.8
Q ss_pred hHHHHhhhhhcCCCCccccCc----chhccC
Q psy15165 382 YNYLRRHMRVHTNEKPYKCKD----CGAAFN 408 (606)
Q Consensus 382 ~~~L~~H~~~H~~~~~~~C~~----C~~~f~ 408 (606)
+..|..|+...-..++..|+. |+..+.
T Consensus 23 r~~l~~H~~~~C~~~~v~C~~~~~GC~~~~~ 53 (60)
T PF02176_consen 23 RKELDDHLENECPKRPVPCPYSPYGCKERVP 53 (60)
T ss_dssp CCCHHHHHHTTSTTSEEE-SS----S--EEE
T ss_pred HHHHHHHHHccCCCCcEECCCCCCCCCCccc
Confidence 334555555444444555555 555443
No 162
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=28.42 E-value=41 Score=31.87 Aligned_cols=83 Identities=23% Similarity=0.484 Sum_probs=45.4
Q ss_pred ccCCcceecccCccccCCHHHHHHHHhccccccCCCCcccccccccccCchHHH-------Hhhhhh----cCCCCcccc
Q psy15165 332 SHSGQYHVCPHCGKKFTRKAELQLHIKGIHLKHQLEKTYICEYCHKEFTFYNYL-------RRHMRV----HTNEKPYKC 400 (606)
Q Consensus 332 ~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~h~~~~~~~C~~C~k~f~~~~~L-------~~H~~~----H~~~~~~~C 400 (606)
.|+++.|.|..|.. |.-...--.|+..-... ....|+|.-|++.=. .+-| ..|++. -...+++.|
T Consensus 137 ~hGGrif~CsfC~~-flCEDDQFEHQAsCQvL--e~E~~KC~SCNrlGq-~sCLRCK~cfCddHvrrKg~ky~k~k~~PC 212 (314)
T PF06524_consen 137 DHGGRIFKCSFCDN-FLCEDDQFEHQASCQVL--ESETFKCQSCNRLGQ-YSCLRCKICFCDDHVRRKGFKYEKGKPIPC 212 (314)
T ss_pred cCCCeEEEeecCCC-eeeccchhhhhhhhhhh--hcccccccccccccc-hhhhheeeeehhhhhhhcccccccCCCCCC
Confidence 56778888888864 33333333444321111 123566666665321 1112 234432 123488999
Q ss_pred CcchhccCChhHHhcccc
Q psy15165 401 KDCGAAFNHNVSLKNHKN 418 (606)
Q Consensus 401 ~~C~~~f~~~~~L~~H~~ 418 (606)
|.||........|..-.+
T Consensus 213 PKCg~et~eTkdLSmStR 230 (314)
T PF06524_consen 213 PKCGYETQETKDLSMSTR 230 (314)
T ss_pred CCCCCcccccccceeeee
Confidence 999998887777765544
No 163
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=28.25 E-value=28 Score=29.35 Aligned_cols=25 Identities=36% Similarity=0.571 Sum_probs=20.3
Q ss_pred ccccccccccCchHHHHhhhhhcCCCCc
Q psy15165 370 YICEYCHKEFTFYNYLRRHMRVHTNEKP 397 (606)
Q Consensus 370 ~~C~~C~k~f~~~~~L~~H~~~H~~~~~ 397 (606)
..|-.+|+.|.+ |++|+.+|.|-.|
T Consensus 77 IicLEDGkkfKS---LKRHL~t~~gmTP 101 (148)
T COG4957 77 IICLEDGKKFKS---LKRHLTTHYGLTP 101 (148)
T ss_pred EEEeccCcchHH---HHHHHhcccCCCH
Confidence 679999999875 8999999887544
No 164
>cd07765 KRAB_A-box KRAB (Kruppel-associated box) domain -A box. The KRAB domain is a transcription repression module, found in a subgroup of the zinc finger proteins (ZFPs) of the C2H2 family, KRAB-ZFPs. KRAB-ZFPs comprise the largest group of transcriptional regulators in mammals, and are only found in tetrapods. These proteins have been shown to play important roles in cell differentiation and organ development, and in regulating viral replication and transcription. A KRAB domain may consist of an A-box, or of an A-box plus either a B-box, a divergent B-box (b), or a C-box. Only the A-box is included in this model. The A-box is needed for repression, the B- and C- boxes are not. KRAB-ZFPs have one or two KRAB domains at their amino-terminal end, and multiple C2H2 zinc finger motifs at their C-termini. Some KRAB-ZFPs also contain a SCAN domain which mediates homo- and hetero-oligomerization. The KRAB domain is a protein-protein interaction module which represses transcription through
Probab=28.23 E-value=14 Score=21.59 Aligned_cols=19 Identities=21% Similarity=0.354 Sum_probs=11.1
Q ss_pred cccccccc---------ccccCCCceee
Q psy15165 3 DDDWNNLD---------DHVGKPSRRRS 21 (606)
Q Consensus 3 ~~~~~~~~---------~~~~~~~~~~~ 21 (606)
.++|..++ +++++|.++++
T Consensus 12 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 (40)
T cd07765 12 QEEWELLDPAQRDLYRDVMLENYENLVS 39 (40)
T ss_pred HHHHhcCCHHHHHHHHHHHHHhhccccC
Confidence 46787766 34556655543
No 165
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=28.21 E-value=30 Score=29.25 Aligned_cols=59 Identities=22% Similarity=0.267 Sum_probs=37.7
Q ss_pred CCcccCCCCCCccCCHHHHHHHHHHhcCCCCCcCccccccccchhhhhcccccccCCccccCCCCCCcCCChHH
Q psy15165 442 EVSNLCYICGFFSAKRSTLAHHIQDHIQPRMKQKQICEICCAEVYHINGHIKDKHSGFFLQCPHCPKTFPRKTE 515 (606)
Q Consensus 442 ~~~~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~~~~C~~c~~~~~~l~~H~~~~h~~~~~~C~~C~~~f~~~~~ 515 (606)
.+.|.|.+|..+...+.-| +|..+-.-.+|+.--..|+.|-..+ -.||.|.-+|++.+.
T Consensus 78 ~~lYeCnIC~etS~ee~FL----------KPneCCgY~iCn~Cya~LWK~~~~y-----pvCPvCkTSFKss~~ 136 (140)
T PF05290_consen 78 PKLYECNICKETSAEERFL----------KPNECCGYSICNACYANLWKFCNLY-----PVCPVCKTSFKSSSS 136 (140)
T ss_pred CCceeccCcccccchhhcC----------CcccccchHHHHHHHHHHHHHcccC-----CCCCccccccccccc
Confidence 4789999999877655433 3433322234445556677776652 368888888887653
No 166
>PHA02998 RNA polymerase subunit; Provisional
Probab=27.65 E-value=34 Score=30.46 Aligned_cols=12 Identities=33% Similarity=0.783 Sum_probs=7.8
Q ss_pred ccCCCCCCcCCC
Q psy15165 501 LQCPHCPKTFPR 512 (606)
Q Consensus 501 ~~C~~C~~~f~~ 512 (606)
|.|..||+.|.-
T Consensus 172 YkC~~CG~~wkp 183 (195)
T PHA02998 172 HACRDCKKHFKP 183 (195)
T ss_pred EEcCCCCCccCC
Confidence 677777766653
No 167
>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=26.85 E-value=38 Score=36.62 Aligned_cols=24 Identities=33% Similarity=0.829 Sum_probs=14.2
Q ss_pred CCcccccccccccCchHHHHhhhhhcCCCCccccCcchh
Q psy15165 367 EKTYICEYCHKEFTFYNYLRRHMRVHTNEKPYKCKDCGA 405 (606)
Q Consensus 367 ~~~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~~C~~C~~ 405 (606)
.....|..||... ..|..|+.||.
T Consensus 238 ~~~l~Ch~Cg~~~---------------~~~~~Cp~C~s 261 (505)
T TIGR00595 238 EGKLRCHYCGYQE---------------PIPKTCPQCGS 261 (505)
T ss_pred CCeEEcCCCcCcC---------------CCCCCCCCCCC
Confidence 4456677776433 23556777765
No 168
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=26.62 E-value=22 Score=39.90 Aligned_cols=10 Identities=30% Similarity=0.504 Sum_probs=0.0
Q ss_pred cccCCCCCCc
Q psy15165 444 SNLCYICGFF 453 (606)
Q Consensus 444 ~~~C~~C~~~ 453 (606)
.+.|+.||..
T Consensus 655 ~r~Cp~Cg~~ 664 (900)
T PF03833_consen 655 RRRCPKCGKE 664 (900)
T ss_dssp ----------
T ss_pred cccCcccCCc
Confidence 4568888764
No 169
>PLN00010 cyclin-dependent kinases regulatory subunit; Provisional
Probab=26.43 E-value=30 Score=26.65 Aligned_cols=24 Identities=17% Similarity=0.372 Sum_probs=17.0
Q ss_pred cccccccccccccCCCceeeecc---cCCCCcee
Q psy15165 2 YDDDWNNLDDHVGKPSRRRSLGV---ESSVPKLK 32 (606)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~g~---~~~~~~~~ 32 (606)
.|+||..|.|-+ |.|| .+.+|+.-
T Consensus 37 ~E~EWR~LGIqq-------S~GW~Hy~~h~pEph 63 (86)
T PLN00010 37 SENEWRAIGVQQ-------SRGWVHYAIHRPEPH 63 (86)
T ss_pred CHHHHHHhcccc-------CCCcEEeeecCCCce
Confidence 478898888875 6676 46677653
No 170
>PRK14873 primosome assembly protein PriA; Provisional
Probab=26.25 E-value=41 Score=37.65 Aligned_cols=24 Identities=25% Similarity=0.818 Sum_probs=15.6
Q ss_pred CCcccccccccccCchHHHHhhhhhcCCCCccccCcchhc
Q psy15165 367 EKTYICEYCHKEFTFYNYLRRHMRVHTNEKPYKCKDCGAA 406 (606)
Q Consensus 367 ~~~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~~C~~C~~~ 406 (606)
.....|..||.. ..|..|+.||..
T Consensus 408 ~~~l~Ch~CG~~----------------~~p~~Cp~Cgs~ 431 (665)
T PRK14873 408 GGTPRCRWCGRA----------------APDWRCPRCGSD 431 (665)
T ss_pred CCeeECCCCcCC----------------CcCccCCCCcCC
Confidence 456778888742 136788888764
No 171
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=25.09 E-value=28 Score=34.53 Aligned_cols=14 Identities=36% Similarity=0.788 Sum_probs=9.2
Q ss_pred CccccCcchhccCC
Q psy15165 396 KPYKCKDCGAAFNH 409 (606)
Q Consensus 396 ~~~~C~~C~~~f~~ 409 (606)
+-..|..|+.-++.
T Consensus 251 r~e~C~~C~~YlK~ 264 (309)
T PRK03564 251 KAESCGDCGTYLKI 264 (309)
T ss_pred Eeeeccccccccee
Confidence 45678888765554
No 172
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=24.83 E-value=83 Score=26.86 Aligned_cols=12 Identities=33% Similarity=0.827 Sum_probs=6.8
Q ss_pred ccCCCCCCcCCC
Q psy15165 501 LQCPHCPKTFPR 512 (606)
Q Consensus 501 ~~C~~C~~~f~~ 512 (606)
|.|+.|++.|..
T Consensus 54 yrC~~C~~tf~~ 65 (129)
T COG3677 54 YKCKSCGSTFTV 65 (129)
T ss_pred cccCCcCcceee
Confidence 556666655554
No 173
>KOG3408|consensus
Probab=24.57 E-value=38 Score=28.07 Aligned_cols=20 Identities=35% Similarity=0.604 Sum_probs=11.1
Q ss_pred cccccccchhccChhhHHHH
Q psy15165 532 TFVCEYCNKEFTFLQYLKRH 551 (606)
Q Consensus 532 ~y~C~~C~k~f~~~~~L~~H 551 (606)
.|.|-.|.+.|.+...|..|
T Consensus 57 qfyCi~CaRyFi~~~~l~~H 76 (129)
T KOG3408|consen 57 QFYCIECARYFIDAKALKTH 76 (129)
T ss_pred eeehhhhhhhhcchHHHHHH
Confidence 35555555555555555555
No 174
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=24.57 E-value=41 Score=34.76 Aligned_cols=14 Identities=21% Similarity=0.458 Sum_probs=8.4
Q ss_pred cccccccchhccCh
Q psy15165 532 TFVCEYCNKEFTFL 545 (606)
Q Consensus 532 ~y~C~~C~k~f~~~ 545 (606)
-|+|+.||+++...
T Consensus 367 g~rC~kCg~~~~~~ 380 (421)
T COG1571 367 GFRCKKCGTRARET 380 (421)
T ss_pred CcccccccccCCcc
Confidence 56666666665543
No 175
>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=24.42 E-value=22 Score=25.05 Aligned_cols=10 Identities=30% Similarity=1.119 Sum_probs=5.0
Q ss_pred ccCCCCCCcC
Q psy15165 501 LQCPHCPKTF 510 (606)
Q Consensus 501 ~~C~~C~~~f 510 (606)
+.|+.||..+
T Consensus 3 ~~CP~CG~~i 12 (54)
T TIGR01206 3 FECPDCGAEI 12 (54)
T ss_pred cCCCCCCCEE
Confidence 4455555544
No 176
>KOG2272|consensus
Probab=24.18 E-value=29 Score=32.57 Aligned_cols=13 Identities=46% Similarity=0.858 Sum_probs=9.5
Q ss_pred ccccccchhccCh
Q psy15165 533 FVCEYCNKEFTFL 545 (606)
Q Consensus 533 y~C~~C~k~f~~~ 545 (606)
|.|..|.+.|--.
T Consensus 222 FvCa~CekPFlGH 234 (332)
T KOG2272|consen 222 FVCAKCEKPFLGH 234 (332)
T ss_pred eeehhcCCcccch
Confidence 7788888877653
No 177
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=22.46 E-value=37 Score=26.75 Aligned_cols=13 Identities=23% Similarity=0.636 Sum_probs=7.6
Q ss_pred ccccccccchhcc
Q psy15165 531 QTFVCEYCNKEFT 543 (606)
Q Consensus 531 k~y~C~~C~k~f~ 543 (606)
..+.|..|++.|+
T Consensus 53 GIW~C~~C~~~~A 65 (90)
T PTZ00255 53 GIWRCKGCKKTVA 65 (90)
T ss_pred EEEEcCCCCCEEe
Confidence 3456666666654
No 178
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=22.36 E-value=36 Score=28.80 Aligned_cols=15 Identities=33% Similarity=0.984 Sum_probs=10.4
Q ss_pred ccccCcchhccCChh
Q psy15165 397 PYKCKDCGAAFNHNV 411 (606)
Q Consensus 397 ~~~C~~C~~~f~~~~ 411 (606)
|++|..||+.|....
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 567777777777643
No 179
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=22.32 E-value=44 Score=19.16 Aligned_cols=9 Identities=33% Similarity=0.921 Sum_probs=7.2
Q ss_pred cccCCCCCC
Q psy15165 500 FLQCPHCPK 508 (606)
Q Consensus 500 ~~~C~~C~~ 508 (606)
.|.|+.||+
T Consensus 16 ~f~CPnCG~ 24 (24)
T PF07754_consen 16 PFPCPNCGF 24 (24)
T ss_pred eEeCCCCCC
Confidence 388999985
No 180
>KOG3408|consensus
Probab=22.21 E-value=53 Score=27.25 Aligned_cols=24 Identities=29% Similarity=0.551 Sum_probs=20.7
Q ss_pred CccccCCCCCCcCCChHHHHHhhh
Q psy15165 498 GFFLQCPHCPKTFPRKTELSNHIK 521 (606)
Q Consensus 498 ~~~~~C~~C~~~f~~~~~L~~H~~ 521 (606)
+..|.|-.|.+-|.+...|..|.+
T Consensus 55 ~GqfyCi~CaRyFi~~~~l~~H~k 78 (129)
T KOG3408|consen 55 GGQFYCIECARYFIDAKALKTHFK 78 (129)
T ss_pred CceeehhhhhhhhcchHHHHHHHh
Confidence 334889999999999999999976
No 181
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=22.16 E-value=33 Score=29.55 Aligned_cols=11 Identities=27% Similarity=1.011 Sum_probs=5.6
Q ss_pred eecccCccccC
Q psy15165 338 HVCPHCGKKFT 348 (606)
Q Consensus 338 ~~C~~C~~~f~ 348 (606)
+.|..||..|.
T Consensus 71 ~~C~~CG~~~~ 81 (135)
T PRK03824 71 LKCRNCGNEWS 81 (135)
T ss_pred EECCCCCCEEe
Confidence 45555554444
No 182
>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=21.86 E-value=33 Score=27.02 Aligned_cols=12 Identities=25% Similarity=0.919 Sum_probs=7.2
Q ss_pred cccccccchhcc
Q psy15165 532 TFVCEYCNKEFT 543 (606)
Q Consensus 532 ~y~C~~C~k~f~ 543 (606)
.+.|..|++.|+
T Consensus 53 IW~C~~C~~~~A 64 (91)
T TIGR00280 53 IWTCRKCGAKFA 64 (91)
T ss_pred EEEcCCCCCEEe
Confidence 456666666654
No 183
>KOG2593|consensus
Probab=21.82 E-value=1.1e+02 Score=31.67 Aligned_cols=20 Identities=15% Similarity=0.303 Sum_probs=12.3
Q ss_pred CCCcccCccccccCCHHHHH
Q psy15165 276 ETSSLCYHCGYYSKNRSTLK 295 (606)
Q Consensus 276 ~~~~~C~~C~~~f~~~~~L~ 295 (606)
...|.|+.|.+.|..-..++
T Consensus 126 ~~~Y~Cp~C~kkyt~Lea~~ 145 (436)
T KOG2593|consen 126 VAGYVCPNCQKKYTSLEALQ 145 (436)
T ss_pred cccccCCccccchhhhHHHH
Confidence 34577777777776555443
No 184
>KOG4167|consensus
Probab=21.65 E-value=25 Score=38.35 Aligned_cols=24 Identities=25% Similarity=0.433 Sum_probs=21.9
Q ss_pred cccccccccccCCHHHHHHhHhhh
Q psy15165 248 EFKCRVCDWKLNSYDKLLRHIKSD 271 (606)
Q Consensus 248 ~~~C~~C~~~f~~~~~L~~H~~~~ 271 (606)
.|.|.+|++.|.....+..||++|
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~H 815 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTH 815 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHH
Confidence 599999999999999999999954
No 185
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=21.54 E-value=40 Score=27.99 Aligned_cols=11 Identities=18% Similarity=0.727 Sum_probs=6.2
Q ss_pred ccCCCCCCcCC
Q psy15165 501 LQCPHCPKTFP 511 (606)
Q Consensus 501 ~~C~~C~~~f~ 511 (606)
|.|..||..|.
T Consensus 101 y~C~~Cg~~wr 111 (113)
T COG1594 101 YKCTRCGYRWR 111 (113)
T ss_pred EEecccCCEee
Confidence 55666665543
No 186
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=21.33 E-value=32 Score=22.76 Aligned_cols=8 Identities=50% Similarity=1.273 Sum_probs=3.6
Q ss_pred ccCCCCCC
Q psy15165 501 LQCPHCPK 508 (606)
Q Consensus 501 ~~C~~C~~ 508 (606)
+.|+.||.
T Consensus 20 ~vC~~CG~ 27 (43)
T PF08271_consen 20 LVCPNCGL 27 (43)
T ss_dssp EEETTT-B
T ss_pred EECCCCCC
Confidence 45555554
No 187
>PTZ00453 cyclin-dependent kinase; Provisional
Probab=21.27 E-value=39 Score=26.56 Aligned_cols=23 Identities=22% Similarity=0.420 Sum_probs=16.2
Q ss_pred cccccccccccccCCCceeeecc---cCCCCce
Q psy15165 2 YDDDWNNLDDHVGKPSRRRSLGV---ESSVPKL 31 (606)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~g~---~~~~~~~ 31 (606)
.|+||..|.|-+ |.|| -+.+|+.
T Consensus 61 ~E~EWR~LGIqq-------S~GW~HY~~h~pEp 86 (96)
T PTZ00453 61 SESEWRQLGVQQ-------SVGWRHYMIHKPEP 86 (96)
T ss_pred cHHHHHHhhhcc-------CCCcEEeeecCCCC
Confidence 478888888875 6676 4666665
No 188
>KOG3002|consensus
Probab=21.25 E-value=53 Score=32.57 Aligned_cols=55 Identities=18% Similarity=0.402 Sum_probs=25.1
Q ss_pred ccCCCCCCcCCChHHHHHhhhcccccCCCCccccccc----cchhccChhhHHHHHhhhcCCCCccc
Q psy15165 501 LQCPHCPKTFPRKTELSNHIKGIHMKHELRQTFVCEY----CNKEFTFLQYLKRHMRTHTNEKPYKC 563 (606)
Q Consensus 501 ~~C~~C~~~f~~~~~L~~H~~~~H~~~~~~k~y~C~~----C~k~f~~~~~L~~H~~~H~~~kp~~C 563 (606)
..||.|...+.....|..=.- .....+.|+. |.+.|..... ..|.+.-.. .||.|
T Consensus 81 ~~CP~Cr~~~g~~R~~amEkV------~e~~~vpC~~~~~GC~~~~~Y~~~-~~HE~~C~f-~~~~C 139 (299)
T KOG3002|consen 81 NKCPTCRLPIGNIRCRAMEKV------AEAVLVPCKNAKLGCTKSFPYGEK-SKHEKVCEF-RPCSC 139 (299)
T ss_pred ccCCccccccccHHHHHHHHH------HHhceecccccccCCceeeccccc-ccccccccc-CCcCC
Confidence 556666665554433222111 1123345543 5555555554 444444333 55555
No 189
>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=20.98 E-value=32 Score=27.04 Aligned_cols=30 Identities=27% Similarity=0.632 Sum_probs=18.5
Q ss_pred CcccccCccccCCHHHHHhhhhccccccCCCCCCcccccccccccC
Q psy15165 214 EFKCRVCDWKLNSYDKLLRHMDWDEVHLGQFSPYEFKCRVCDWKLN 259 (606)
Q Consensus 214 ~~~C~~C~~~f~~~~~l~~H~~~~~~h~~~~~~~~~~C~~C~~~f~ 259 (606)
.|.|+.|++.-... .-.| .+.|..|++.|.
T Consensus 35 ky~Cp~Cgk~~vkR-----------~a~G-----IW~C~~C~~~~A 64 (90)
T PF01780_consen 35 KYTCPFCGKTSVKR-----------VATG-----IWKCKKCGKKFA 64 (90)
T ss_dssp -BEESSSSSSEEEE-----------EETT-----EEEETTTTEEEE
T ss_pred CCcCCCCCCceeEE-----------eeeE-----EeecCCCCCEEe
Confidence 68899888654211 2222 288888888774
No 190
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=20.89 E-value=34 Score=37.64 Aligned_cols=15 Identities=40% Similarity=0.884 Sum_probs=7.9
Q ss_pred ecccCccccCCHHHH
Q psy15165 339 VCPHCGKKFTRKAEL 353 (606)
Q Consensus 339 ~C~~C~~~f~~~~~l 353 (606)
.|..||-+|+-...|
T Consensus 125 ~CT~CGPRfTIi~al 139 (750)
T COG0068 125 NCTNCGPRFTIIEAL 139 (750)
T ss_pred ccCCCCcceeeeccC
Confidence 356666655554443
No 191
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.72 E-value=30 Score=32.18 Aligned_cols=8 Identities=38% Similarity=0.546 Sum_probs=6.1
Q ss_pred ccCcchhc
Q psy15165 399 KCKDCGAA 406 (606)
Q Consensus 399 ~C~~C~~~ 406 (606)
.||.|+.+
T Consensus 64 vCP~C~yA 71 (267)
T COG1655 64 VCPICYYA 71 (267)
T ss_pred EcchhhHH
Confidence 58888864
No 192
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=20.41 E-value=57 Score=28.30 Aligned_cols=17 Identities=18% Similarity=0.460 Sum_probs=11.2
Q ss_pred ccCCCCCCcCCChHHHH
Q psy15165 501 LQCPHCPKTFPRKTELS 517 (606)
Q Consensus 501 ~~C~~C~~~f~~~~~L~ 517 (606)
=.|..||+.|++...+.
T Consensus 29 ReC~~C~~RFTTyErve 45 (147)
T TIGR00244 29 RECLECHERFTTFERAE 45 (147)
T ss_pred ccCCccCCccceeeecc
Confidence 45777777777765443
No 193
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=20.34 E-value=1.4e+02 Score=21.15 Aligned_cols=46 Identities=11% Similarity=0.034 Sum_probs=25.4
Q ss_pred cccCcchhccCChhHHhcccccCCCCCCChHHHHHHHHHhcCCCCCcccCCCCCCccCC
Q psy15165 398 YKCKDCGAAFNHNVSLKNHKNSSCPKLYSYETYLKHLKTNHHGYEVSNLCYICGFFSAK 456 (606)
Q Consensus 398 ~~C~~C~~~f~~~~~L~~H~~~~C~~~f~~~~~l~~h~~~~~~~~~~~~C~~C~~~f~~ 456 (606)
+.|++|+..+... +...||..|........... ...|+.|+..+..
T Consensus 2 ~~Cpi~~~~~~~P------v~~~~G~v~~~~~i~~~~~~-------~~~cP~~~~~~~~ 47 (63)
T smart00504 2 FLCPISLEVMKDP------VILPSGQTYERRAIEKWLLS-------HGTDPVTGQPLTH 47 (63)
T ss_pred cCCcCCCCcCCCC------EECCCCCEEeHHHHHHHHHH-------CCCCCCCcCCCCh
Confidence 4566776666553 23345666655544443332 1258888877643
No 194
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=20.24 E-value=20 Score=24.86 Aligned_cols=21 Identities=24% Similarity=0.578 Sum_probs=9.5
Q ss_pred ccCCCCCCcCCChHHHHHhhh
Q psy15165 501 LQCPHCPKTFPRKTELSNHIK 521 (606)
Q Consensus 501 ~~C~~C~~~f~~~~~L~~H~~ 521 (606)
|.|+.|...|-..-.+-.|..
T Consensus 22 y~C~~C~~~FC~dCD~fiHE~ 42 (51)
T PF07975_consen 22 YRCPKCKNHFCIDCDVFIHET 42 (51)
T ss_dssp E--TTTT--B-HHHHHTTTTT
T ss_pred EECCCCCCccccCcChhhhcc
Confidence 666666666666555555543
No 195
>KOG4377|consensus
Probab=20.05 E-value=60 Score=33.04 Aligned_cols=19 Identities=26% Similarity=0.289 Sum_probs=16.9
Q ss_pred CCCccCCHHHHHHHHHHhc
Q psy15165 450 CGFFSAKRSTLAHHIQDHI 468 (606)
Q Consensus 450 C~~~f~~~~~L~~H~~~h~ 468 (606)
|+..+.+.+.+..|.+.|.
T Consensus 409 c~~tl~s~sqm~shkrkhe 427 (480)
T KOG4377|consen 409 CEATLYSVSQMASHKRKHE 427 (480)
T ss_pred CceEEEehhhhhhhhhhhh
Confidence 8889999999999998884
Done!