Query psy16834
Match_columns 488
No_of_seqs 525 out of 2450
Neff 10.4
Searched_HMMs 46136
Date Fri Aug 16 23:14:48 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16834.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16834hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1074|consensus 100.0 1.3E-33 2.9E-38 273.9 3.9 226 247-473 604-935 (958)
2 KOG2462|consensus 100.0 1.1E-30 2.5E-35 224.2 3.3 136 329-467 127-265 (279)
3 KOG2462|consensus 100.0 1.3E-29 2.8E-34 217.8 6.1 127 357-487 127-256 (279)
4 KOG1074|consensus 100.0 5.3E-30 1.2E-34 248.9 3.0 292 123-447 605-937 (958)
5 KOG3608|consensus 99.9 1.1E-27 2.5E-32 210.5 9.5 247 209-485 139-397 (467)
6 KOG3608|consensus 99.9 6.6E-26 1.4E-30 199.4 13.5 233 68-385 135-377 (467)
7 KOG3623|consensus 99.9 8.6E-24 1.9E-28 202.4 5.9 121 152-298 211-331 (1007)
8 KOG3623|consensus 99.9 2.6E-22 5.6E-27 192.4 8.4 119 40-173 211-331 (1007)
9 KOG3576|consensus 99.7 9.5E-18 2.1E-22 136.9 2.5 110 330-440 115-235 (267)
10 KOG3576|consensus 99.7 6.9E-18 1.5E-22 137.7 1.0 115 358-473 115-240 (267)
11 PLN03086 PRLI-interacting fact 99.4 4.3E-13 9.3E-18 131.1 6.5 135 332-486 407-553 (567)
12 PLN03086 PRLI-interacting fact 99.3 4.1E-12 8.9E-17 124.3 5.0 118 332-467 433-562 (567)
13 PHA00733 hypothetical protein 99.2 3.8E-12 8.3E-17 101.5 3.2 56 413-470 69-124 (128)
14 PHA00733 hypothetical protein 99.2 3.2E-11 6.9E-16 96.2 5.4 82 358-441 38-123 (128)
15 PHA02768 hypothetical protein; 99.2 1.6E-11 3.4E-16 79.5 2.2 45 417-463 5-49 (55)
16 PF13465 zf-H2C2_2: Zinc-finge 99.0 2.2E-10 4.7E-15 63.5 1.3 26 432-457 1-26 (26)
17 KOG3993|consensus 98.9 5.7E-10 1.2E-14 102.1 2.2 52 248-301 267-320 (500)
18 PHA02768 hypothetical protein; 98.9 6.4E-10 1.4E-14 72.1 1.5 42 361-405 6-47 (55)
19 KOG3993|consensus 98.9 9.2E-10 2E-14 100.7 2.1 195 39-234 267-486 (500)
20 PF13465 zf-H2C2_2: Zinc-finge 98.8 2.1E-09 4.5E-14 59.6 0.7 26 460-486 1-26 (26)
21 PHA00616 hypothetical protein 98.7 1.1E-08 2.4E-13 62.9 1.7 34 417-450 1-34 (44)
22 PHA00732 hypothetical protein 98.6 4.6E-08 9.9E-13 70.4 2.9 49 417-471 1-50 (79)
23 PHA00616 hypothetical protein 98.5 1.7E-08 3.8E-13 62.1 0.5 34 445-479 1-34 (44)
24 PHA00732 hypothetical protein 98.4 1.4E-07 3.1E-12 67.8 2.7 46 360-411 1-46 (79)
25 PF05605 zf-Di19: Drought indu 98.3 1.3E-06 2.7E-11 58.5 4.2 50 361-413 3-53 (54)
26 PF05605 zf-Di19: Drought indu 98.2 3E-06 6.6E-11 56.6 4.2 51 10-63 2-53 (54)
27 PF00096 zf-C2H2: Zinc finger, 98.0 2.9E-06 6.2E-11 45.6 1.9 23 418-440 1-23 (23)
28 PF12756 zf-C2H2_2: C2H2 type 97.8 8.6E-06 1.9E-10 62.9 2.3 71 363-439 2-72 (100)
29 PF00096 zf-C2H2: Zinc finger, 97.8 1.5E-05 3.2E-10 42.8 2.2 23 277-299 1-23 (23)
30 PF12756 zf-C2H2_2: C2H2 type 97.7 1.8E-05 3.9E-10 61.1 2.0 73 12-90 1-73 (100)
31 COG5189 SFP1 Putative transcri 97.6 1.9E-05 4.1E-10 70.2 0.9 52 415-466 347-419 (423)
32 PF13894 zf-C2H2_4: C2H2-type 97.6 5E-05 1.1E-09 41.1 2.1 23 418-440 1-23 (24)
33 PF13894 zf-C2H2_4: C2H2-type 97.6 5E-05 1.1E-09 41.2 1.9 22 361-382 1-22 (24)
34 PF13912 zf-C2H2_6: C2H2-type 97.5 6.2E-05 1.3E-09 42.2 1.7 23 418-440 2-24 (27)
35 PF13912 zf-C2H2_6: C2H2-type 97.4 7.6E-05 1.7E-09 41.8 1.7 25 151-175 1-25 (27)
36 COG5189 SFP1 Putative transcri 97.2 0.00012 2.5E-09 65.3 1.1 69 357-437 346-418 (423)
37 smart00355 ZnF_C2H2 zinc finge 97.1 0.00047 1E-08 38.0 2.5 24 418-441 1-24 (26)
38 PF09237 GAGA: GAGA factor; I 97.1 0.00024 5.2E-09 44.8 1.2 31 415-445 22-52 (54)
39 PRK04860 hypothetical protein; 97.0 0.00028 6.1E-09 58.6 1.2 39 417-459 119-157 (160)
40 smart00355 ZnF_C2H2 zinc finge 96.9 0.00038 8.3E-09 38.3 0.8 25 446-470 1-25 (26)
41 KOG2231|consensus 96.9 0.0025 5.3E-08 64.4 6.8 17 130-146 219-235 (669)
42 PF09237 GAGA: GAGA factor; I 96.8 0.00079 1.7E-08 42.5 2.1 41 27-67 12-52 (54)
43 PF12874 zf-met: Zinc-finger o 96.8 0.00078 1.7E-08 36.8 1.5 23 418-440 1-23 (25)
44 KOG2785|consensus 96.6 0.0039 8.4E-08 57.8 5.5 54 245-298 163-242 (390)
45 PF12874 zf-met: Zinc-finger o 96.4 0.0027 5.7E-08 34.6 1.9 23 277-299 1-23 (25)
46 KOG2231|consensus 96.3 0.0047 1E-07 62.4 4.6 103 69-184 117-240 (669)
47 PF13909 zf-H2C2_5: C2H2-type 96.2 0.003 6.5E-08 34.0 1.7 23 11-34 1-23 (24)
48 PF12171 zf-C2H2_jaz: Zinc-fin 96.1 0.0033 7.2E-08 35.0 1.4 22 446-467 2-23 (27)
49 PRK04860 hypothetical protein; 95.9 0.0054 1.2E-07 51.0 2.5 38 123-164 119-156 (160)
50 PF13909 zf-H2C2_5: C2H2-type 95.9 0.0058 1.3E-07 32.9 1.7 21 418-439 1-21 (24)
51 PF12171 zf-C2H2_jaz: Zinc-fin 95.8 0.0027 5.8E-08 35.4 0.3 22 418-439 2-23 (27)
52 KOG1146|consensus 95.7 0.0039 8.5E-08 66.7 1.1 105 359-467 464-611 (1406)
53 KOG2482|consensus 95.7 0.02 4.3E-07 52.1 5.3 108 360-467 195-356 (423)
54 COG5236 Uncharacterized conser 95.6 0.012 2.6E-07 53.5 3.5 135 10-176 151-306 (493)
55 COG5236 Uncharacterized conser 95.5 0.036 7.8E-07 50.5 6.2 122 152-298 152-303 (493)
56 KOG1146|consensus 95.3 0.007 1.5E-07 64.9 1.3 101 42-145 439-540 (1406)
57 KOG2482|consensus 95.2 0.021 4.6E-07 51.9 3.9 109 123-231 195-359 (423)
58 KOG2785|consensus 95.1 0.082 1.8E-06 49.3 7.3 66 205-270 165-242 (390)
59 COG5048 FOG: Zn-finger [Genera 95.0 0.0088 1.9E-07 59.9 1.0 150 332-483 289-455 (467)
60 PF13913 zf-C2HC_2: zinc-finge 94.5 0.03 6.5E-07 30.4 1.9 18 419-437 4-21 (25)
61 KOG4173|consensus 94.1 0.031 6.8E-07 47.0 2.0 86 8-97 77-176 (253)
62 KOG4173|consensus 93.9 0.03 6.6E-07 47.1 1.5 44 338-384 87-130 (253)
63 PF13913 zf-C2HC_2: zinc-finge 93.8 0.051 1.1E-06 29.5 1.8 19 125-144 4-22 (25)
64 smart00451 ZnF_U1 U1-like zinc 93.2 0.067 1.5E-06 31.8 1.9 22 417-438 3-24 (35)
65 smart00451 ZnF_U1 U1-like zinc 92.9 0.069 1.5E-06 31.7 1.7 22 360-381 3-24 (35)
66 COG5048 FOG: Zn-finger [Genera 92.7 0.037 7.9E-07 55.4 0.4 57 122-178 32-90 (467)
67 KOG2893|consensus 92.4 0.032 7E-07 48.0 -0.4 47 250-300 12-59 (341)
68 KOG2893|consensus 91.6 0.049 1.1E-06 46.9 -0.2 45 392-440 13-58 (341)
69 TIGR00622 ssl1 transcription f 91.6 0.44 9.6E-06 36.6 4.9 46 183-228 58-103 (112)
70 cd00350 rubredoxin_like Rubred 91.5 0.087 1.9E-06 30.8 0.9 10 444-453 16-25 (33)
71 cd00350 rubredoxin_like Rubred 89.7 0.23 5E-06 29.0 1.6 24 124-159 2-25 (33)
72 TIGR00622 ssl1 transcription f 88.2 0.45 9.8E-06 36.6 2.6 22 358-379 13-34 (112)
73 cd00729 rubredoxin_SM Rubredox 87.4 0.31 6.6E-06 28.7 1.0 10 446-455 3-12 (34)
74 TIGR02098 MJ0042_CXXC MJ0042 f 85.1 0.46 9.9E-06 28.8 1.0 34 446-485 3-36 (38)
75 KOG2186|consensus 84.9 0.41 8.8E-06 42.1 1.0 46 333-381 4-49 (276)
76 COG4049 Uncharacterized protei 84.9 0.55 1.2E-05 30.4 1.3 28 36-63 14-41 (65)
77 COG4049 Uncharacterized protei 83.5 0.58 1.3E-05 30.3 1.0 28 64-91 14-41 (65)
78 PF09986 DUF2225: Uncharacteri 82.4 0.35 7.6E-06 42.8 -0.4 19 360-378 5-23 (214)
79 PF09538 FYDLN_acid: Protein o 81.1 1.1 2.3E-05 34.7 1.8 30 40-80 10-39 (108)
80 PF09538 FYDLN_acid: Protein o 79.9 1 2.2E-05 34.7 1.4 29 68-108 10-38 (108)
81 smart00531 TFIIE Transcription 79.0 1.6 3.5E-05 36.0 2.5 14 417-430 99-112 (147)
82 PF12013 DUF3505: Protein of u 78.7 3.3 7.1E-05 32.2 4.0 24 360-384 11-34 (109)
83 KOG2186|consensus 78.4 1.1 2.3E-05 39.6 1.2 46 97-144 4-49 (276)
84 PF09986 DUF2225: Uncharacteri 78.1 0.57 1.2E-05 41.5 -0.5 44 387-430 3-61 (214)
85 COG1997 RPL43A Ribosomal prote 78.1 1.3 2.8E-05 32.1 1.3 30 445-485 35-64 (89)
86 smart00659 RPOLCX RNA polymera 77.5 1.4 3E-05 27.7 1.2 11 40-50 3-13 (44)
87 PF13717 zinc_ribbon_4: zinc-r 77.5 1.7 3.7E-05 25.9 1.6 10 390-399 26-35 (36)
88 PF10571 UPF0547: Uncharacteri 77.0 1.3 2.8E-05 24.2 0.9 10 362-371 16-25 (26)
89 PF02892 zf-BED: BED zinc fing 76.8 2 4.3E-05 27.1 1.9 26 359-384 15-44 (45)
90 PF02892 zf-BED: BED zinc fing 76.5 2 4.3E-05 27.0 1.8 28 7-34 13-44 (45)
91 PF14353 CpXC: CpXC protein 76.2 1.1 2.4E-05 36.0 0.7 12 474-485 38-49 (128)
92 smart00834 CxxC_CXXC_SSSS Puta 75.6 1 2.2E-05 27.7 0.2 13 446-458 6-18 (41)
93 PF12013 DUF3505: Protein of u 75.2 4.9 0.00011 31.2 4.1 26 205-231 10-35 (109)
94 PF09723 Zn-ribbon_8: Zinc rib 74.8 1.4 3E-05 27.4 0.7 29 361-397 6-34 (42)
95 TIGR00373 conserved hypothetic 73.8 2.7 5.9E-05 35.2 2.5 30 416-454 108-137 (158)
96 smart00734 ZnF_Rad18 Rad18-lik 73.7 3.4 7.4E-05 22.6 2.0 19 334-353 3-21 (26)
97 PF13719 zinc_ribbon_5: zinc-r 72.7 3.6 7.7E-05 24.7 2.1 11 151-161 25-35 (37)
98 PHA00626 hypothetical protein 72.6 0.84 1.8E-05 29.7 -0.6 15 359-373 22-36 (59)
99 smart00531 TFIIE Transcription 72.0 2.3 5E-05 35.1 1.6 37 387-427 97-133 (147)
100 COG1592 Rubrerythrin [Energy p 71.8 2.3 5E-05 35.5 1.6 10 332-341 134-143 (166)
101 smart00614 ZnF_BED BED zinc fi 71.8 3 6.5E-05 27.0 1.8 24 361-384 19-47 (50)
102 COG1592 Rubrerythrin [Energy p 71.8 2.1 4.6E-05 35.7 1.3 13 440-452 144-156 (166)
103 TIGR00373 conserved hypothetic 71.6 3 6.6E-05 34.9 2.3 32 386-426 106-137 (158)
104 KOG2272|consensus 69.7 4 8.7E-05 35.9 2.6 40 180-219 137-176 (332)
105 PF12907 zf-met2: Zinc-binding 68.1 3.3 7.1E-05 25.3 1.2 32 11-42 2-36 (40)
106 PRK09678 DNA-binding transcrip 67.4 2 4.3E-05 30.3 0.3 43 418-462 2-46 (72)
107 PRK06266 transcription initiat 67.4 3.9 8.4E-05 35.0 2.1 14 390-403 118-131 (178)
108 TIGR02605 CxxC_CxxC_SSSS putat 66.7 1.8 3.9E-05 28.3 -0.1 11 418-428 6-16 (52)
109 PF03604 DNA_RNApol_7kD: DNA d 66.2 4 8.6E-05 23.6 1.3 7 68-74 18-24 (32)
110 PRK00398 rpoP DNA-directed RNA 65.6 5.1 0.00011 25.4 1.9 11 124-134 4-14 (46)
111 TIGR02300 FYDLN_acid conserved 64.4 4.2 9.2E-05 31.9 1.5 13 66-78 25-37 (129)
112 PRK00464 nrdR transcriptional 64.2 1.3 2.9E-05 36.6 -1.3 13 361-373 29-41 (154)
113 TIGR02300 FYDLN_acid conserved 63.9 5.1 0.00011 31.5 1.9 14 360-373 26-39 (129)
114 PRK06266 transcription initiat 63.1 5.6 0.00012 34.0 2.2 16 123-138 117-132 (178)
115 PF02176 zf-TRAF: TRAF-type zi 62.5 7.6 0.00016 26.1 2.4 40 123-163 9-54 (60)
116 COG2888 Predicted Zn-ribbon RN 61.1 7.3 0.00016 26.0 1.9 32 39-75 27-58 (61)
117 COG1996 RPC10 DNA-directed RNA 58.8 5 0.00011 25.8 0.9 11 39-49 6-16 (49)
118 PF04959 ARS2: Arsenite-resist 58.7 6 0.00013 34.7 1.7 31 6-36 73-103 (214)
119 COG1198 PriA Primosomal protei 55.9 8.5 0.00019 40.6 2.5 40 361-426 445-484 (730)
120 PF15269 zf-C2H2_7: Zinc-finge 55.2 7.7 0.00017 24.0 1.2 22 10-31 20-41 (54)
121 PF06524 NOA36: NOA36 protein; 54.4 9.7 0.00021 33.9 2.2 25 444-468 208-232 (314)
122 PRK14890 putative Zn-ribbon RN 53.9 6.3 0.00014 26.3 0.8 11 387-397 46-56 (59)
123 TIGR01206 lysW lysine biosynth 52.5 6.6 0.00014 25.9 0.7 30 446-484 3-32 (54)
124 PF08274 PhnA_Zn_Ribbon: PhnA 51.9 6.4 0.00014 22.4 0.5 25 447-483 4-28 (30)
125 KOG2807|consensus 51.4 23 0.0005 32.8 4.2 99 246-396 274-374 (378)
126 KOG2593|consensus 51.4 12 0.00027 36.1 2.6 15 417-431 128-142 (436)
127 PRK04023 DNA polymerase II lar 50.7 14 0.0003 40.0 3.0 10 360-369 626-635 (1121)
128 COG4888 Uncharacterized Zn rib 50.6 4.5 9.7E-05 30.2 -0.3 37 444-485 21-57 (104)
129 PF06524 NOA36: NOA36 protein; 50.4 7.5 0.00016 34.6 0.9 39 93-131 139-179 (314)
130 cd00730 rubredoxin Rubredoxin; 49.6 4.6 0.0001 26.2 -0.3 7 390-396 35-41 (50)
131 PF13451 zf-trcl: Probable zin 49.3 12 0.00025 24.2 1.4 14 67-80 4-17 (49)
132 PRK09678 DNA-binding transcrip 48.8 6.3 0.00014 27.8 0.2 10 152-161 2-11 (72)
133 KOG4167|consensus 47.1 4.1 8.9E-05 41.8 -1.3 25 445-469 792-816 (907)
134 PF01780 Ribosomal_L37ae: Ribo 46.5 6.7 0.00015 28.9 0.0 31 444-485 34-64 (90)
135 PF02176 zf-TRAF: TRAF-type zi 44.6 14 0.00031 24.8 1.4 29 106-134 21-53 (60)
136 PF04959 ARS2: Arsenite-resist 44.5 13 0.00028 32.7 1.5 25 360-384 77-101 (214)
137 PF08790 zf-LYAR: LYAR-type C2 44.0 4.1 8.9E-05 22.6 -1.0 9 362-370 2-10 (28)
138 PF05443 ROS_MUCR: ROS/MUCR tr 43.8 12 0.00025 30.2 1.0 27 150-179 71-97 (132)
139 PF12760 Zn_Tnp_IS1595: Transp 42.9 33 0.00071 21.7 2.8 27 446-482 19-45 (46)
140 PF09845 DUF2072: Zn-ribbon co 42.5 16 0.00035 29.0 1.6 10 362-371 3-12 (131)
141 COG1198 PriA Primosomal protei 42.4 17 0.00038 38.4 2.3 8 69-76 446-453 (730)
142 PF13240 zinc_ribbon_2: zinc-r 42.1 14 0.0003 19.5 0.8 6 392-397 2-7 (23)
143 TIGR01384 TFS_arch transcripti 41.7 2.3 4.9E-05 32.8 -3.3 38 248-287 62-101 (104)
144 PRK04023 DNA polymerase II lar 41.6 25 0.00054 38.1 3.2 50 331-428 625-674 (1121)
145 KOG2593|consensus 40.9 24 0.00051 34.3 2.7 18 358-375 126-143 (436)
146 TIGR00280 L37a ribosomal prote 40.1 14 0.00029 27.4 0.8 10 475-484 54-63 (91)
147 PRK01343 zinc-binding protein; 39.9 18 0.00038 24.2 1.2 10 446-455 10-19 (57)
148 PF14446 Prok-RING_1: Prokaryo 39.4 20 0.00043 23.6 1.4 11 390-400 6-16 (54)
149 PF07754 DUF1610: Domain of un 39.0 11 0.00023 20.2 0.1 8 445-452 16-23 (24)
150 COG4530 Uncharacterized protei 39.0 22 0.00047 27.0 1.7 26 41-77 11-36 (129)
151 PF10013 DUF2256: Uncharacteri 38.2 19 0.00041 22.2 1.1 14 473-486 7-20 (42)
152 PRK00432 30S ribosomal protein 37.4 14 0.00031 23.9 0.5 12 359-370 36-47 (50)
153 PF05191 ADK_lid: Adenylate ki 36.6 10 0.00022 22.6 -0.2 6 393-398 5-10 (36)
154 PF01363 FYVE: FYVE zinc finge 35.3 19 0.0004 25.1 0.9 27 418-456 10-36 (69)
155 PRK03976 rpl37ae 50S ribosomal 34.0 19 0.00042 26.6 0.8 11 475-485 55-65 (90)
156 PF09963 DUF2197: Uncharacteri 34.0 18 0.00039 24.0 0.5 37 12-48 4-40 (56)
157 COG4957 Predicted transcriptio 33.4 26 0.00056 27.8 1.4 25 152-179 77-101 (148)
158 KOG4167|consensus 32.6 13 0.00029 38.3 -0.3 26 151-176 792-817 (907)
159 PF11789 zf-Nse: Zinc-finger o 32.4 44 0.00094 22.4 2.2 29 97-128 25-53 (57)
160 smart00154 ZnF_AN1 AN1-like Zi 32.3 17 0.00037 22.1 0.2 13 445-457 12-24 (39)
161 PF05290 Baculo_IE-1: Baculovi 32.1 23 0.0005 28.2 1.0 55 414-487 77-134 (140)
162 PF09416 UPF1_Zn_bind: RNA hel 31.5 49 0.0011 27.3 2.8 25 358-382 12-42 (152)
163 KOG1280|consensus 31.3 30 0.00064 32.4 1.7 28 414-441 76-104 (381)
164 PF05443 ROS_MUCR: ROS/MUCR tr 31.0 24 0.00052 28.4 0.9 23 418-443 73-95 (132)
165 KOG1280|consensus 30.6 47 0.001 31.2 2.8 40 357-396 76-116 (381)
166 smart00249 PHD PHD zinc finger 30.6 72 0.0016 19.4 3.1 11 180-190 14-24 (47)
167 COG0068 HypF Hydrogenase matur 30.4 11 0.00023 39.1 -1.4 78 11-104 102-181 (750)
168 COG4957 Predicted transcriptio 30.4 33 0.00072 27.3 1.6 24 418-444 77-100 (148)
169 PRK14714 DNA polymerase II lar 30.4 48 0.001 37.2 3.3 8 361-368 668-675 (1337)
170 KOG4124|consensus 30.2 16 0.00034 34.2 -0.3 25 443-467 396-420 (442)
171 PRK14892 putative transcriptio 30.0 20 0.00042 27.2 0.3 7 418-424 22-28 (99)
172 PF08271 TF_Zn_Ribbon: TFIIB z 29.5 22 0.00048 22.1 0.4 10 475-484 20-29 (43)
173 PF08209 Sgf11: Sgf11 (transcr 29.4 42 0.00091 19.6 1.5 20 97-116 5-24 (33)
174 TIGR00595 priA primosomal prot 29.4 36 0.00079 34.7 2.2 12 386-397 237-248 (505)
175 COG5151 SSL1 RNA polymerase II 29.3 61 0.0013 29.9 3.2 46 183-228 365-410 (421)
176 PF13453 zf-TFIIB: Transcripti 29.2 29 0.00064 21.2 0.9 16 124-139 20-35 (41)
177 PRK03824 hypA hydrogenase nick 29.2 18 0.0004 29.3 0.0 13 332-344 70-82 (135)
178 cd00065 FYVE FYVE domain; Zinc 29.1 33 0.00072 22.6 1.3 9 392-400 5-13 (57)
179 COG1773 Rubredoxin [Energy pro 29.0 42 0.00091 22.2 1.6 34 181-214 4-44 (55)
180 PF07295 DUF1451: Protein of u 28.9 28 0.00062 28.6 1.1 35 438-483 101-139 (146)
181 KOG1842|consensus 28.2 31 0.00067 33.5 1.3 31 8-38 13-43 (505)
182 COG5151 SSL1 RNA polymerase II 27.8 14 0.00031 33.7 -0.9 19 360-378 322-340 (421)
183 KOG0717|consensus 27.6 33 0.00072 33.6 1.4 20 418-437 293-312 (508)
184 PTZ00255 60S ribosomal protein 27.1 32 0.0007 25.4 1.0 12 389-400 54-65 (90)
185 PF00301 Rubredoxin: Rubredoxi 26.4 39 0.00084 21.6 1.1 35 181-215 2-43 (47)
186 PF06220 zf-U1: U1 zinc finger 25.7 53 0.0012 19.8 1.6 11 360-370 3-13 (38)
187 KOG0801|consensus 24.9 34 0.00073 28.1 0.8 32 432-467 128-159 (205)
188 PF01096 TFIIS_C: Transcriptio 24.9 26 0.00056 21.3 0.1 12 205-216 27-38 (39)
189 PF07282 OrfB_Zn_ribbon: Putat 24.6 46 0.00099 23.1 1.4 29 334-372 30-58 (69)
190 PF13878 zf-C2H2_3: zinc-finge 24.6 72 0.0016 19.6 2.1 23 419-441 15-39 (41)
191 PF13824 zf-Mss51: Zinc-finger 24.5 49 0.0011 22.0 1.3 11 417-427 14-24 (55)
192 KOG0782|consensus 24.4 23 0.0005 35.4 -0.3 50 404-459 240-290 (1004)
193 smart00064 FYVE Protein presen 24.0 64 0.0014 22.2 2.1 10 391-400 12-21 (68)
194 PF01428 zf-AN1: AN1-like Zinc 24.0 18 0.0004 22.5 -0.7 13 444-456 12-24 (43)
195 PF07649 C1_3: C1-like domain; 23.9 37 0.00081 19.0 0.7 10 360-369 15-24 (30)
196 PF04216 FdhE: Protein involve 23.3 8.9 0.00019 35.9 -3.2 38 181-218 212-250 (290)
197 COG1655 Uncharacterized protei 23.3 31 0.00067 30.3 0.3 28 444-471 18-45 (267)
198 PF05129 Elf1: Transcription e 23.2 19 0.0004 26.2 -0.9 12 475-486 47-58 (81)
199 COG2331 Uncharacterized protei 23.0 40 0.00087 23.8 0.8 10 124-133 13-22 (82)
200 PF04780 DUF629: Protein of un 23.0 52 0.0011 32.8 1.8 26 11-36 58-83 (466)
201 PF04780 DUF629: Protein of un 22.9 52 0.0011 32.8 1.8 28 68-95 58-85 (466)
202 PF05495 zf-CHY: CHY zinc fing 22.7 23 0.00049 25.0 -0.5 14 123-136 41-54 (71)
203 KOG3214|consensus 22.5 30 0.00066 25.8 0.1 8 417-424 23-30 (109)
204 smart00440 ZnF_C2C2 C2C2 Zinc 22.4 9 0.0002 23.5 -2.2 10 361-370 29-38 (40)
205 KOG0717|consensus 22.0 49 0.0011 32.5 1.4 22 124-145 293-314 (508)
206 PF10263 SprT-like: SprT-like 21.9 35 0.00075 28.4 0.4 10 418-427 124-133 (157)
207 PF13248 zf-ribbon_3: zinc-rib 21.8 66 0.0014 17.4 1.3 7 334-340 4-10 (26)
208 PRK14873 primosome assembly pr 21.4 57 0.0012 34.5 1.9 46 333-424 384-429 (665)
209 cd00924 Cyt_c_Oxidase_Vb Cytoc 21.3 24 0.00052 26.6 -0.6 18 438-456 73-90 (97)
210 COG3357 Predicted transcriptio 21.3 36 0.00078 25.0 0.3 12 67-78 58-69 (97)
211 KOG3408|consensus 21.1 40 0.00088 26.3 0.5 22 445-466 57-78 (129)
212 PHA02998 RNA polymerase subuni 20.9 47 0.001 27.9 0.9 10 475-484 172-181 (195)
213 PRK12380 hydrogenase nickel in 20.5 55 0.0012 25.6 1.2 25 123-159 70-94 (113)
214 TIGR00244 transcriptional regu 20.5 21 0.00045 29.2 -1.2 13 361-373 29-41 (147)
215 TIGR00100 hypA hydrogenase nic 20.4 53 0.0012 25.7 1.1 25 123-159 70-94 (115)
216 PRK05580 primosome assembly pr 20.3 67 0.0015 34.2 2.2 10 361-370 391-400 (679)
217 COG3091 SprT Zn-dependent meta 20.2 38 0.00082 27.7 0.2 8 445-452 140-147 (156)
218 KOG1842|consensus 20.1 65 0.0014 31.4 1.8 34 205-238 14-47 (505)
219 COG0068 HypF Hydrogenase matur 20.1 21 0.00045 37.1 -1.5 57 334-398 125-182 (750)
No 1
>KOG1074|consensus
Probab=99.98 E-value=1.3e-33 Score=273.85 Aligned_cols=226 Identities=24% Similarity=0.450 Sum_probs=171.2
Q ss_pred CCCCCcchHHhhcCHHHHHHHHhhhccCceeecccccccccCHHHHHhHHhhhccCCc----eeec----CCcccCChhH
Q psy16834 247 EKVQCPYCAKFLSRKEKLNRHIRTVHTDVNYKCEICGEEFLSKTRYNRHVVTHEEKQK----FECE----CGYVTCNKYR 318 (488)
Q Consensus 247 ~~~~C~~C~~~f~~~~~L~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~H~~~~~----~~C~----C~~~~~~~~~ 318 (488)
.+.+|-+|.+...-++.|+-|.++|+|++||+|.|||+.|.++.+|+.||.+|....+ +.|. |...|.+...
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 4679999999999999999999999999999999999999999999999999977654 4563 8888999999
Q ss_pred HHHHHHhhcc-CC------------CcccCCCCCCccCChHHHHHHHHhhcC----------------C----Ccccccc
Q psy16834 319 LTEHVRRTHL-KD------------YKVLCPICGYGCFRNAELEEHFISAHS----------------A----DRFKCVF 365 (488)
Q Consensus 319 l~~H~~~~h~-~~------------~~~~C~~C~~~f~~~~~l~~H~~~~~~----------------~----~~~~C~~ 365 (488)
|..|++ .|+ +. ..-+|..|.++|.....+..++..+-+ + .+..+..
T Consensus 684 lpQhIr-iH~~~~~s~g~~a~e~~~~adq~~~~qk~~~~a~~f~~~~se~~~~~s~~~~~~~~~t~t~~~~~tp~~~e~~ 762 (958)
T KOG1074|consen 684 LPQHIR-IHLGGQISNGGTAAEGILAADQCSSCQKTFSDARSFSQQISEQPSPESEPDEQMDERTETEELDVTPPPPENS 762 (958)
T ss_pred ccceEE-eecCCCCCCCcccccccchhcccchhhhcccccccchhhhhccCCcccCCcccccccccccccccCCCccccc
Confidence 999865 443 21 124688999999888877777654411 1 1567888
Q ss_pred ccccccChhHHHHHHh----------------------hhcCCCCCc-cCCccCCcCCCchHHH----hh--------hh
Q psy16834 366 CEKSFARNCNLKLHIR----------------------RYHDKSDNT-ECPLCGKSFPSRGRLN----EH--------LI 410 (488)
Q Consensus 366 C~k~F~~~~~l~~H~~----------------------~~H~~~~~~-~C~~C~k~F~~~~~L~----~H--------~~ 410 (488)
|+..+.....+..+-- ..++.+++. .+..++..-...-... .- ..
T Consensus 763 ~~~~~~~e~~i~~~g~te~asa~~~~vg~~s~~~~~~~~~~T~~k~~~~~~~~~~~~~~~v~~~pvl~~~~~~~l~eg~~ 842 (958)
T KOG1074|consen 763 CGRELEGEMAISVRGSTEEASANLDEVGTVSAAGEAGEEDDTSEKPTQASSFPGEILAPSVNMDPVLWNQETSMLNEGLA 842 (958)
T ss_pred cccccCcccccccccchhhhhcChhhhcCccccchhhhhcccCCCCcccccCCCcCCccccccCchhhcccccccccccc
Confidence 8888888776665421 113345555 5666665443322111 00 00
Q ss_pred h----hc-----------c---------------CCcccccccccccCChHHHHHHHHhhcCCCCcCCcchhhccCChhh
Q psy16834 411 Q----VH-----------P---------------AQKHQCHICNKIVVSEKTLKKHLLLHTNSEPFHCPECGKAFKFKRY 460 (488)
Q Consensus 411 ~----~h-----------~---------------~~~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~~C~~C~~~F~~~~~ 460 (488)
. .. + .....|.+||+.|.+.++|..||++|+|+|||.|.+|+++|.++.+
T Consensus 843 t~~n~~t~~~~~~sv~qs~~~p~l~p~l~~~~pvnn~h~C~vCgk~FsSSsALqiH~rTHtg~KPF~C~fC~~aFttrgn 922 (958)
T KOG1074|consen 843 TKTNEITPEGPADSVIQSGGVPTLEPSLGRPGPVNNAHVCNVCGKQFSSSAALEIHMRTHTGPKPFFCHFCEEAFTTRGN 922 (958)
T ss_pred cccccccCCCcchhhhhhccccccCCCCCCCCcccchhhhccchhcccchHHHHHhhhcCCCCCCccchhhhhhhhhhhh
Confidence 0 00 0 0127899999999999999999999999999999999999999999
Q ss_pred HhccccccccCcC
Q psy16834 461 VTLHMRTHTGNWP 473 (488)
Q Consensus 461 L~~H~~~H~~~~~ 473 (488)
|+.||.+|.+..|
T Consensus 923 LKvHMgtH~w~q~ 935 (958)
T KOG1074|consen 923 LKVHMGTHMWVQP 935 (958)
T ss_pred hhhhhccccccCC
Confidence 9999999988755
No 2
>KOG2462|consensus
Probab=99.96 E-value=1.1e-30 Score=224.24 Aligned_cols=136 Identities=30% Similarity=0.640 Sum_probs=109.5
Q ss_pred CCCcccCCCCCCccCChHHHHHHHHhhcC---CCccccccccccccChhHHHHHHhhhcCCCCCccCCccCCcCCCchHH
Q psy16834 329 KDYKVLCPICGYGCFRNAELEEHFISAHS---ADRFKCVFCEKSFARNCNLKLHIRRYHDKSDNTECPLCGKSFPSRGRL 405 (488)
Q Consensus 329 ~~~~~~C~~C~~~f~~~~~l~~H~~~~~~---~~~~~C~~C~k~F~~~~~l~~H~~~~H~~~~~~~C~~C~k~F~~~~~L 405 (488)
....|.|+.||+.+.+...|.+|...|-. .+.+.|++|||.|.+-..|+.|+|. |+ -+.+|.+|||.|....-|
T Consensus 127 ~~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirT-H~--l~c~C~iCGKaFSRPWLL 203 (279)
T KOG2462|consen 127 KHPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRT-HT--LPCECGICGKAFSRPWLL 203 (279)
T ss_pred cCCceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhc-cC--CCcccccccccccchHHh
Confidence 44567888888888888888888776654 4568888888888888888888863 54 678888888888888888
Q ss_pred HhhhhhhccCCcccccccccccCChHHHHHHHHhhcCCCCcCCcchhhccCChhhHhccccc
Q psy16834 406 NEHLIQVHPAQKHQCHICNKIVVSEKTLKKHLLLHTNSEPFHCPECGKAFKFKRYVTLHMRT 467 (488)
Q Consensus 406 ~~H~~~~h~~~~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~~C~~C~~~F~~~~~L~~H~~~ 467 (488)
+.|+|+|+||+||.|+.|+|+|+.+++|+.||++|.+.|+|+|+.|+|+|..++.|.+|...
T Consensus 204 QGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 204 QGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSES 265 (279)
T ss_pred hcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhhh
Confidence 88888888888888888888888888888888888888888888888888888888888653
No 3
>KOG2462|consensus
Probab=99.96 E-value=1.3e-29 Score=217.77 Aligned_cols=127 Identities=31% Similarity=0.613 Sum_probs=117.8
Q ss_pred CCCccccccccccccChhHHHHHHhhhcC---CCCCccCCccCCcCCCchHHHhhhhhhccCCcccccccccccCChHHH
Q psy16834 357 SADRFKCVFCEKSFARNCNLKLHIRRYHD---KSDNTECPLCGKSFPSRGRLNEHLIQVHPAQKHQCHICNKIVVSEKTL 433 (488)
Q Consensus 357 ~~~~~~C~~C~k~F~~~~~l~~H~~~~H~---~~~~~~C~~C~k~F~~~~~L~~H~~~~h~~~~~~C~~C~k~f~~~~~L 433 (488)
....|+|+.|||.+.+.++|.+|.+. |. ..+.+.|++|||.|.+-..|..|+++|. -+++|.+|||.|...+-|
T Consensus 127 ~~~r~~c~eCgk~ysT~snLsrHkQ~-H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLL 203 (279)
T KOG2462|consen 127 KHPRYKCPECGKSYSTSSNLSRHKQT-HRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLL 203 (279)
T ss_pred cCCceeccccccccccccccchhhcc-cccccccccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHh
Confidence 35679999999999999999999874 53 3467899999999999999999999865 689999999999999999
Q ss_pred HHHHHhhcCCCCcCCcchhhccCChhhHhccccccccCcCccccccCccccccC
Q psy16834 434 KKHLLLHTNSEPFHCPECGKAFKFKRYVTLHMRTHTGNWPTFVCKICNATISSE 487 (488)
Q Consensus 434 ~~H~~~H~~~~~~~C~~C~~~F~~~~~L~~H~~~H~~~~~~~~C~~C~k~f~~~ 487 (488)
+-|+|+|||||||.|++|+|+|..+++|+.||+||.+.++ |+|+.|+|+|+.+
T Consensus 204 QGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~-~qC~~C~KsFsl~ 256 (279)
T KOG2462|consen 204 QGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKK-HQCPRCGKSFALK 256 (279)
T ss_pred hcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCcc-ccCcchhhHHHHH
Confidence 9999999999999999999999999999999999999987 9999999999864
No 4
>KOG1074|consensus
Probab=99.96 E-value=5.3e-30 Score=248.94 Aligned_cols=292 Identities=18% Similarity=0.284 Sum_probs=178.1
Q ss_pred ceecCccCccccChhhHHHHHHhccCCCceeCccccccccchhhHHhHhhhccCCCCceecccchhhhhcccCCCCCCcC
Q psy16834 123 LFDCHICGKTVVTEKNYKKHMQLHSDDKPFECQFCRKAFKLKYYLTLHLRTHTGVRPMFECDICHKVLKTKSKKSSGISK 202 (488)
Q Consensus 123 ~~~C~~C~~~f~~~~~l~~H~~~H~~~~~~~C~~C~~~F~~~~~L~~H~~~h~~~~~~~~C~~C~~~f~~~~~~~~~~~~ 202 (488)
+.+|-+|-+...-.++|+.|.++|+|++||+|.+||+.|.++.+|+.||-+|....+.
T Consensus 605 PNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~---------------------- 662 (958)
T KOG1074|consen 605 PNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPA---------------------- 662 (958)
T ss_pred ccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccc----------------------
Confidence 5789999999999999999999999999999999999999999999999998765542
Q ss_pred CCCccccc---cccccccChhHHHHHHhhcCCCCchhhhHhhhhcccCCCCCcchHHhhcCHHHHHHHHhhhccC-----
Q psy16834 203 NENLRPCT---LCDKKLASERKLKEHIRKQHPTSVEADLIRREKYEREKVQCPYCAKFLSRKEKLNRHIRTVHTD----- 274 (488)
Q Consensus 203 ~~~~~~C~---~C~~~f~~~~~L~~H~~~~h~~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~L~~H~~~~~~~----- 274 (488)
...+.|+ +|.+.|.....|..|++.|-........... ......-+|..|.+.|.....+..++..+-+.
T Consensus 663 -R~q~ScP~~~ic~~kftn~V~lpQhIriH~~~~~s~g~~a~-e~~~~adq~~~~qk~~~~a~~f~~~~se~~~~~s~~~ 740 (958)
T KOG1074|consen 663 -RVQFSCPSTFICQKKFTNAVTLPQHIRIHLGGQISNGGTAA-EGILAADQCSSCQKTFSDARSFSQQISEQPSPESEPD 740 (958)
T ss_pred -cccccCCchhhhcccccccccccceEEeecCCCCCCCcccc-cccchhcccchhhhcccccccchhhhhccCCcccCCc
Confidence 1357788 9999999999999999986643322211111 11122357999999998888888887766321
Q ss_pred -----------c----eeecccccccccCHHHHHhHHhhhccCCceeecCCcccCChhHHHHHHHhhccCCCcc-cCCCC
Q psy16834 275 -----------V----NYKCEICGEEFLSKTRYNRHVVTHEEKQKFECECGYVTCNKYRLTEHVRRTHLKDYKV-LCPIC 338 (488)
Q Consensus 275 -----------~----~~~C~~C~~~f~~~~~l~~H~~~H~~~~~~~C~C~~~~~~~~~l~~H~~~~h~~~~~~-~C~~C 338 (488)
. +..+..|+..+.....+..+-.++.... + .....+...-..-.....+.+.+. .+.++
T Consensus 741 ~~~~~~t~t~~~~~tp~~~e~~~~~~~~~e~~i~~~g~te~asa---~--~~~vg~~s~~~~~~~~~~T~~k~~~~~~~~ 815 (958)
T KOG1074|consen 741 EQMDERTETEELDVTPPPPENSCGRELEGEMAISVRGSTEEASA---N--LDEVGTVSAAGEAGEEDDTSEKPTQASSFP 815 (958)
T ss_pred ccccccccccccccCCCccccccccccCcccccccccchhhhhc---C--hhhhcCccccchhhhhcccCCCCcccccCC
Confidence 1 3456666666665555544432221000 0 000000000001112233444444 45555
Q ss_pred CCccCChHHHH----HHHHhhcCCCcccccccccccc--Chh-HHHHHHhhhc--------CCC--CCccCCccCCcCCC
Q psy16834 339 GYGCFRNAELE----EHFISAHSADRFKCVFCEKSFA--RNC-NLKLHIRRYH--------DKS--DNTECPLCGKSFPS 401 (488)
Q Consensus 339 ~~~f~~~~~l~----~H~~~~~~~~~~~C~~C~k~F~--~~~-~l~~H~~~~H--------~~~--~~~~C~~C~k~F~~ 401 (488)
+..-...-... .-...--++.. .=.. ..+. ... .+.. ...+- ... ....|.+||+.|..
T Consensus 816 ~~~~~~~v~~~pvl~~~~~~~l~eg~-~t~~--n~~t~~~~~~sv~q-s~~~p~l~p~l~~~~pvnn~h~C~vCgk~FsS 891 (958)
T KOG1074|consen 816 GEILAPSVNMDPVLWNQETSMLNEGL-ATKT--NEITPEGPADSVIQ-SGGVPTLEPSLGRPGPVNNAHVCNVCGKQFSS 891 (958)
T ss_pred CcCCccccccCchhhccccccccccc-cccc--ccccCCCcchhhhh-hccccccCCCCCCCCcccchhhhccchhcccc
Confidence 54333222111 00000000000 0000 0000 000 0000 00000 011 12569999999999
Q ss_pred chHHHhhhhhhccCCcccccccccccCChHHHHHHHHhhcCCCCcC
Q psy16834 402 RGRLNEHLIQVHPAQKHQCHICNKIVVSEKTLKKHLLLHTNSEPFH 447 (488)
Q Consensus 402 ~~~L~~H~~~~h~~~~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~~ 447 (488)
.+.|..|+++|.+++||.|.+|++.|..+.+|+.||.+|....|+.
T Consensus 892 SsALqiH~rTHtg~KPF~C~fC~~aFttrgnLKvHMgtH~w~q~~s 937 (958)
T KOG1074|consen 892 SAALEIHMRTHTGPKPFFCHFCEEAFTTRGNLKVHMGTHMWVQPPS 937 (958)
T ss_pred hHHHHHhhhcCCCCCCccchhhhhhhhhhhhhhhhhccccccCCCc
Confidence 9999999999999999999999999999999999999998776553
No 5
>KOG3608|consensus
Probab=99.95 E-value=1.1e-27 Score=210.47 Aligned_cols=247 Identities=23% Similarity=0.454 Sum_probs=190.0
Q ss_pred cccccccccChhHHHHHHhhcCCCCchhhhHhhhhcccCCCCCc--chHHhhcCHHHHHHHHhhhccCceeecccccccc
Q psy16834 209 CTLCDKKLASERKLKEHIRKQHPTSVEADLIRREKYEREKVQCP--YCAKFLSRKEKLNRHIRTVHTDVNYKCEICGEEF 286 (488)
Q Consensus 209 C~~C~~~f~~~~~L~~H~~~~h~~~~~~~~~~~~~~~~~~~~C~--~C~~~f~~~~~L~~H~~~~~~~~~~~C~~C~~~f 286 (488)
.+.|+..|.+...|..|+..+ ..-.+.+.......++..+.|. .|.+.|.++..|++|++.|.+++...|+.||..|
T Consensus 139 WedCe~~F~s~~ef~dHV~~H-~l~ceyd~~~~~~D~~pv~~C~W~~Ct~~~~~k~~LreH~r~Hs~eKvvACp~Cg~~F 217 (467)
T KOG3608|consen 139 WEDCEREFVSIVEFQDHVVKH-ALFCEYDIQKTPEDERPVTMCNWAMCTKHMGNKYRLREHIRTHSNEKVVACPHCGELF 217 (467)
T ss_pred hhhcCCcccCHHHHHHHHHHh-hhhhhhhhhhCCCCCCceeeccchhhhhhhccHHHHHHHHHhcCCCeEEecchHHHHh
Confidence 378999999999999999874 3333333222222222334454 5888888888888888888888888888888888
Q ss_pred cCHHHHHhHHhhhccCCceeecCCcccCChhHHHHHHHhhccCCCcccCCCCCCccCChHHHHHHHHhhcCCCccccccc
Q psy16834 287 LSKTRYNRHVVTHEEKQKFECECGYVTCNKYRLTEHVRRTHLKDYKVLCPICGYGCFRNAELEEHFISAHSADRFKCVFC 366 (488)
Q Consensus 287 ~~~~~l~~H~~~H~~~~~~~C~C~~~~~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C 366 (488)
.++..|..|++.-+ -....+|.|..|.|.|++...|..|+..|- .-|+|+.|
T Consensus 218 ~~~tkl~DH~rRqt--------------------------~l~~n~fqC~~C~KrFaTeklL~~Hv~rHv--n~ykCplC 269 (467)
T KOG3608|consen 218 RTKTKLFDHLRRQT--------------------------ELNTNSFQCAQCFKRFATEKLLKSHVVRHV--NCYKCPLC 269 (467)
T ss_pred ccccHHHHHHHhhh--------------------------hhcCCchHHHHHHHHHhHHHHHHHHHHHhh--hccccccc
Confidence 88888888876432 233447888888888888888888887553 35899999
Q ss_pred cccccChhHHHHHHhhhcCCCCCccCCccCCcCCCchHHHhhhhhhccCCcccccc--cccccCChHHHHHHHHh-hcC-
Q psy16834 367 EKSFARNCNLKLHIRRYHDKSDNTECPLCGKSFPSRGRLNEHLIQVHPAQKHQCHI--CNKIVVSEKTLKKHLLL-HTN- 442 (488)
Q Consensus 367 ~k~F~~~~~l~~H~~~~H~~~~~~~C~~C~k~F~~~~~L~~H~~~~h~~~~~~C~~--C~k~f~~~~~L~~H~~~-H~~- 442 (488)
+.+....+.|.+||+..|..++||+|+.|++.|.+.+.|.+|... |.+..|+|+. |..+|.+...|++|++. |.|
T Consensus 270 dmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~-HS~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~ 348 (467)
T KOG3608|consen 270 DMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQV-HSKTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGN 348 (467)
T ss_pred ccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHh-ccccceecCCCCCcHHHHHHHHHHHHHHHhccCC
Confidence 999999999999999889999999999999999999999999885 5577899988 99999999999999875 434
Q ss_pred -CCCcCCcchhhccCChhhHhcccccccc-Cc----CccccccCccccc
Q psy16834 443 -SEPFHCPECGKAFKFKRYVTLHMRTHTG-NW----PTFVCKICNATIS 485 (488)
Q Consensus 443 -~~~~~C~~C~~~F~~~~~L~~H~~~H~~-~~----~~~~C~~C~k~f~ 485 (488)
+-+|.|-.|++.|++..+|.+|++.-++ .. ++|.=.+|.-+|.
T Consensus 349 np~~Y~CH~Cdr~ft~G~~L~~HL~kkH~f~~PsGh~RFtYk~~edG~m 397 (467)
T KOG3608|consen 349 NPILYACHCCDRFFTSGKSLSAHLMKKHGFRLPSGHKRFTYKVDEDGFM 397 (467)
T ss_pred CCCceeeecchhhhccchhHHHHHHHhhcccCCCCCCceeeeeccCcee
Confidence 4579999999999999999999866443 22 2455555555553
No 6
>KOG3608|consensus
Probab=99.93 E-value=6.6e-26 Score=199.43 Aligned_cols=233 Identities=27% Similarity=0.552 Sum_probs=172.7
Q ss_pred ccC--CCCCCccCChhhHHHHHhhhccCCCccccccchhhccchhHHHHHHHHhc-C-CceecC--ccCccccChhhHHH
Q psy16834 68 FLC--IPCNKPFSKIENYRLHQRRYHLNSVNKECKICHKVLRTARLSEHMKQVHY-A-KLFDCH--ICGKTVVTEKNYKK 141 (488)
Q Consensus 68 ~~C--~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~l~~h~~~~~~-~-~~~~C~--~C~~~f~~~~~l~~ 141 (488)
|.| +.|+..|.+...|..|+.. |..-..|. +....+ + ..+.|. .|.+.|.+++.|.+
T Consensus 135 f~C~WedCe~~F~s~~ef~dHV~~-H~l~ceyd----------------~~~~~~D~~pv~~C~W~~Ct~~~~~k~~Lre 197 (467)
T KOG3608|consen 135 FRCGWEDCEREFVSIVEFQDHVVK-HALFCEYD----------------IQKTPEDERPVTMCNWAMCTKHMGNKYRLRE 197 (467)
T ss_pred hccChhhcCCcccCHHHHHHHHHH-hhhhhhhh----------------hhhCCCCCCceeeccchhhhhhhccHHHHHH
Confidence 566 4688888888888888863 32110110 011111 1 235564 59999999999999
Q ss_pred HHHhccCCCceeCccccccccchhhHHhHhhhccCCCCceecccchhhhhcccCCCCCCcCCCCccccccccccccChhH
Q psy16834 142 HMQLHSDDKPFECQFCRKAFKLKYYLTLHLRTHTGVRPMFECDICHKVLKTKSKKSSGISKNENLRPCTLCDKKLASERK 221 (488)
Q Consensus 142 H~~~H~~~~~~~C~~C~~~F~~~~~L~~H~~~h~~~~~~~~C~~C~~~f~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~ 221 (488)
|++.|++++...|+.||..|.++..|-.|++.-+.. +.++|.|..|.|.|+++..
T Consensus 198 H~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l-------------------------~~n~fqC~~C~KrFaTekl 252 (467)
T KOG3608|consen 198 HIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTEL-------------------------NTNSFQCAQCFKRFATEKL 252 (467)
T ss_pred HHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhh-------------------------cCCchHHHHHHHHHhHHHH
Confidence 999999999999999999999999999999876543 2357899999999999999
Q ss_pred HHHHHhhcCCCCchhhhHhhhhcccCCCCCcchHHhhcCHHHHHHHHhhhc-cCceeecccccccccCHHHHHhHHhhhc
Q psy16834 222 LKEHIRKQHPTSVEADLIRREKYEREKVQCPYCAKFLSRKEKLNRHIRTVH-TDVNYKCEICGEEFLSKTRYNRHVVTHE 300 (488)
Q Consensus 222 L~~H~~~~h~~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~L~~H~~~~~-~~~~~~C~~C~~~f~~~~~l~~H~~~H~ 300 (488)
|..|+..+- .-|+||.|+......++|.+||+.-| .++||+|+.|++.|.+.+.|.+|+.+|+
T Consensus 253 L~~Hv~rHv----------------n~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS 316 (467)
T KOG3608|consen 253 LKSHVVRHV----------------NCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS 316 (467)
T ss_pred HHHHHHHhh----------------hcccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc
Confidence 999998753 34899999999999999999998755 5799999999999999999999999988
Q ss_pred cCCceeec---CCcccCChhHHHHHHHhhccCCCcccCCCCCCccCChHHHHHHHHhhcCCCccccccccccccChhHHH
Q psy16834 301 EKQKFECE---CGYVTCNKYRLTEHVRRTHLKDYKVLCPICGYGCFRNAELEEHFISAHSADRFKCVFCEKSFARNCNLK 377 (488)
Q Consensus 301 ~~~~~~C~---C~~~~~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~k~F~~~~~l~ 377 (488)
+..|.|+ |.+++.+...|..|.+..|.++. +-+|.|..|++.|++-.+|.
T Consensus 317 -~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~n--------------------------p~~Y~CH~Cdr~ft~G~~L~ 369 (467)
T KOG3608|consen 317 -KTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNN--------------------------PILYACHCCDRFFTSGKSLS 369 (467)
T ss_pred -ccceecCCCCCcHHHHHHHHHHHHHHHhccCCC--------------------------CCceeeecchhhhccchhHH
Confidence 5566662 55555555555555444443321 33566666777776666666
Q ss_pred HHHhhhcC
Q psy16834 378 LHIRRYHD 385 (488)
Q Consensus 378 ~H~~~~H~ 385 (488)
+|+++.|.
T Consensus 370 ~HL~kkH~ 377 (467)
T KOG3608|consen 370 AHLMKKHG 377 (467)
T ss_pred HHHHHhhc
Confidence 66665553
No 7
>KOG3623|consensus
Probab=99.89 E-value=8.6e-24 Score=202.39 Aligned_cols=121 Identities=22% Similarity=0.468 Sum_probs=101.8
Q ss_pred eeCccccccccchhhHHhHhhhccCCCCceecccchhhhhcccCCCCCCcCCCCccccccccccccChhHHHHHHhhcCC
Q psy16834 152 FECQFCRKAFKLKYYLTLHLRTHTGVRPMFECDICHKVLKTKSKKSSGISKNENLRPCTLCDKKLASERKLKEHIRKQHP 231 (488)
Q Consensus 152 ~~C~~C~~~F~~~~~L~~H~~~h~~~~~~~~C~~C~~~f~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~L~~H~~~~h~ 231 (488)
..|+.|++.+....+|+.|++.-+... +..|.|.+|..+|++...|.+|+..+-+
T Consensus 211 ltcpycdrgykrltslkeHikyrhekn-------------------------e~nfsC~lCsytFAyRtQLErhm~~hkp 265 (1007)
T KOG3623|consen 211 LTCPYCDRGYKRLTSLKEHIKYRHEKN-------------------------EPNFSCMLCSYTFAYRTQLERHMQLHKP 265 (1007)
T ss_pred hcchhHHHHHHHHHHHHHHHHHHHhhC-------------------------CCCCcchhhhhhhhhHHHHHHHHHhhcC
Confidence 689999999999999999998655432 3457899999999999999999998766
Q ss_pred CCchhhhHhhhhcccCCCCCcchHHhhcCHHHHHHHHhhhccCceeecccccccccCHHHHHhHHhh
Q psy16834 232 TSVEADLIRREKYEREKVQCPYCAKFLSRKEKLNRHIRTVHTDVNYKCEICGEEFLSKTRYNRHVVT 298 (488)
Q Consensus 232 ~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~L~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~ 298 (488)
....+. ...+....++|+|+.|+|.|..+..|+.|+|+|.|++||.|+-|+|+|.....+..||..
T Consensus 266 g~dqa~-sltqsa~lRKFKCtECgKAFKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmSS 331 (1007)
T KOG3623|consen 266 GGDQAI-SLTQSALLRKFKCTECGKAFKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMSS 331 (1007)
T ss_pred CCcccc-cccchhhhccccccccchhhhhHHHHHhhheeecCCCCcCCcccccccccCCcccccccc
Confidence 544321 112233457899999999999999999999999999999999999999999999999853
No 8
>KOG3623|consensus
Probab=99.87 E-value=2.6e-22 Score=192.36 Aligned_cols=119 Identities=27% Similarity=0.550 Sum_probs=96.6
Q ss_pred ccCccccCcCCChHHHHHHHHhhh--CCCCccCCCCCCccCChhhHHHHHhhhccCCCccccccchhhccchhHHHHHHH
Q psy16834 40 ILCPECGRGFFNEKELAAHKIEIH--GADPFLCIPCNKPFSKIENYRLHQRRYHLNSVNKECKICHKVLRTARLSEHMKQ 117 (488)
Q Consensus 40 ~~C~~C~~~f~~~~~l~~H~~~~h--~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~l~~h~~~ 117 (488)
..|++|++.+.....|+.|+...| .+..|.|..|..+|..+..|.+||..+-.+... ..++..
T Consensus 211 ltcpycdrgykrltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~~hkpg~dq---------------a~sltq 275 (1007)
T KOG3623|consen 211 LTCPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQ---------------AISLTQ 275 (1007)
T ss_pred hcchhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcc---------------cccccc
Confidence 579999999999999999987777 345689999999999999999999754322210 011222
Q ss_pred HhcCCceecCccCccccChhhHHHHHHhccCCCceeCccccccccchhhHHhHhhh
Q psy16834 118 VHYAKLFDCHICGKTVVTEKNYKKHMQLHSDDKPFECQFCRKAFKLKYYLTLHLRT 173 (488)
Q Consensus 118 ~~~~~~~~C~~C~~~f~~~~~l~~H~~~H~~~~~~~C~~C~~~F~~~~~L~~H~~~ 173 (488)
....+.|+|..|||.|..+-.|+.|+|+|+|+|||.|+.|+|+|....++..||-.
T Consensus 276 sa~lRKFKCtECgKAFKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmSS 331 (1007)
T KOG3623|consen 276 SALLRKFKCTECGKAFKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMSS 331 (1007)
T ss_pred hhhhccccccccchhhhhHHHHHhhheeecCCCCcCCcccccccccCCcccccccc
Confidence 23346799999999999999999999999999999999999999999999999753
No 9
>KOG3576|consensus
Probab=99.68 E-value=9.5e-18 Score=136.88 Aligned_cols=110 Identities=31% Similarity=0.529 Sum_probs=77.7
Q ss_pred CCcccCCCCCCccCChHHHHHHHHhhcCCCccccccccccccChhHHHHHHhhhcCCCCCccCCccCCcCCCchHHHhhh
Q psy16834 330 DYKVLCPICGYGCFRNAELEEHFISAHSADRFKCVFCEKSFARNCNLKLHIRRYHDKSDNTECPLCGKSFPSRGRLNEHL 409 (488)
Q Consensus 330 ~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~k~F~~~~~l~~H~~~~H~~~~~~~C~~C~k~F~~~~~L~~H~ 409 (488)
...+.|.+|||+|.-...|.+|++-|...+++-|..|||.|...-+|++|+| .|+|.+||+|..|+|.|.++-+|..|+
T Consensus 115 ~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~r-thtgvrpykc~~c~kaftqrcsleshl 193 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTR-THTGVRPYKCSLCEKAFTQRCSLESHL 193 (267)
T ss_pred CCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhc-cccCccccchhhhhHHHHhhccHHHHH
Confidence 3456788888888877788888777777777888888888888888888876 477888888888888888888888887
Q ss_pred hhhccCC-----------cccccccccccCChHHHHHHHHhh
Q psy16834 410 IQVHPAQ-----------KHQCHICNKIVVSEKTLKKHLLLH 440 (488)
Q Consensus 410 ~~~h~~~-----------~~~C~~C~k~f~~~~~L~~H~~~H 440 (488)
+.+|+.. .|.|+.||.+-.....+..|++.|
T Consensus 194 ~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~ 235 (267)
T KOG3576|consen 194 KKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLH 235 (267)
T ss_pred HHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhc
Confidence 7777642 355555555555555555555444
No 10
>KOG3576|consensus
Probab=99.68 E-value=6.9e-18 Score=137.70 Aligned_cols=115 Identities=26% Similarity=0.541 Sum_probs=104.5
Q ss_pred CCccccccccccccChhHHHHHHhhhcCCCCCccCCccCCcCCCchHHHhhhhhhccCCcccccccccccCChHHHHHHH
Q psy16834 358 ADRFKCVFCEKSFARNCNLKLHIRRYHDKSDNTECPLCGKSFPSRGRLNEHLIQVHPAQKHQCHICNKIVVSEKTLKKHL 437 (488)
Q Consensus 358 ~~~~~C~~C~k~F~~~~~l~~H~~~~H~~~~~~~C~~C~k~F~~~~~L~~H~~~~h~~~~~~C~~C~k~f~~~~~L~~H~ 437 (488)
...|.|.+|+|.|.....|.+|++ .|...+.+.|..|||.|...-+|.+|+++|++.+||+|..|+|+|+++-+|..|+
T Consensus 115 ~d~ftCrvCgK~F~lQRmlnrh~k-ch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl 193 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQRMLNRHLK-CHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHL 193 (267)
T ss_pred CCeeeeehhhhhhhHHHHHHHHhh-hccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHH
Confidence 567999999999999999999997 7999999999999999999999999999999999999999999999999999998
Q ss_pred H-hhc----------CCCCcCCcchhhccCChhhHhccccccccCcC
Q psy16834 438 L-LHT----------NSEPFHCPECGKAFKFKRYVTLHMRTHTGNWP 473 (488)
Q Consensus 438 ~-~H~----------~~~~~~C~~C~~~F~~~~~L~~H~~~H~~~~~ 473 (488)
+ +|. .++-|.|+.||.+-.....+..|++.|+...|
T Consensus 194 ~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~Sp 240 (267)
T KOG3576|consen 194 KKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPFSP 240 (267)
T ss_pred HHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCCCCH
Confidence 5 453 24679999999999999999999999876544
No 11
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.39 E-value=4.3e-13 Score=131.12 Aligned_cols=135 Identities=21% Similarity=0.408 Sum_probs=96.8
Q ss_pred cccCCCCCCccCChHHHHHHHHhhcCCCcccccc--ccccccChhHHHHHHhhhcCCCCCccCCccCCcCCCchHHHhhh
Q psy16834 332 KVLCPICGYGCFRNAELEEHFISAHSADRFKCVF--CEKSFARNCNLKLHIRRYHDKSDNTECPLCGKSFPSRGRLNEHL 409 (488)
Q Consensus 332 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~--C~k~F~~~~~l~~H~~~~H~~~~~~~C~~C~k~F~~~~~L~~H~ 409 (488)
...|+.|..... ...|..|.. .-.-..-.|+. ||..|. +..|..| +.|+.||+.|. .+.|..|+
T Consensus 407 ~V~C~NC~~~i~-l~~l~lHe~-~C~r~~V~Cp~~~Cg~v~~-r~el~~H----------~~C~~Cgk~f~-~s~LekH~ 472 (567)
T PLN03086 407 TVECRNCKHYIP-SRSIALHEA-YCSRHNVVCPHDGCGIVLR-VEEAKNH----------VHCEKCGQAFQ-QGEMEKHM 472 (567)
T ss_pred eEECCCCCCccc-hhHHHHHHh-hCCCcceeCCcccccceee-ccccccC----------ccCCCCCCccc-hHHHHHHH
Confidence 356888876644 344556654 22233446774 888883 3344444 36888888885 67788888
Q ss_pred hhhccCCcccccccccccCChHHHHHHHHhhcCCCCcCCcchhhccC----------ChhhHhccccccccCcCcccccc
Q psy16834 410 IQVHPAQKHQCHICNKIVVSEKTLKKHLLLHTNSEPFHCPECGKAFK----------FKRYVTLHMRTHTGNWPTFVCKI 479 (488)
Q Consensus 410 ~~~h~~~~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~~C~~C~~~F~----------~~~~L~~H~~~H~~~~~~~~C~~ 479 (488)
..+| .|+.|+ ||+.+ .+..|..|+.+|.+++|+.|++|++.|. ..+.|..|+.+. |.++ +.|..
T Consensus 473 ~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt-~~C~~ 546 (567)
T PLN03086 473 KVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-GSRT-APCDS 546 (567)
T ss_pred HhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-CCcc-eEccc
Confidence 8865 788888 88654 6688888888888888888988888885 235788888885 7766 88888
Q ss_pred Ccccccc
Q psy16834 480 CNATISS 486 (488)
Q Consensus 480 C~k~f~~ 486 (488)
||+.|..
T Consensus 547 Cgk~Vrl 553 (567)
T PLN03086 547 CGRSVML 553 (567)
T ss_pred cCCeeee
Confidence 8888764
No 12
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.26 E-value=4.1e-12 Score=124.35 Aligned_cols=118 Identities=25% Similarity=0.639 Sum_probs=93.5
Q ss_pred cccCCC--CCCccCChHHHHHHHHhhcCCCccccccccccccChhHHHHHHhhhcCCCCCccCCccCCcCCCchHHHhhh
Q psy16834 332 KVLCPI--CGYGCFRNAELEEHFISAHSADRFKCVFCEKSFARNCNLKLHIRRYHDKSDNTECPLCGKSFPSRGRLNEHL 409 (488)
Q Consensus 332 ~~~C~~--C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~k~F~~~~~l~~H~~~~H~~~~~~~C~~C~k~F~~~~~L~~H~ 409 (488)
...|+. ||..| ....+..| +.|+.|++.|. ...|..|++.+| .++.|+ ||+.+ .+..|..|+
T Consensus 433 ~V~Cp~~~Cg~v~-~r~el~~H---------~~C~~Cgk~f~-~s~LekH~~~~H---kpv~Cp-Cg~~~-~R~~L~~H~ 496 (567)
T PLN03086 433 NVVCPHDGCGIVL-RVEEAKNH---------VHCEKCGQAFQ-QGEMEKHMKVFH---EPLQCP-CGVVL-EKEQMVQHQ 496 (567)
T ss_pred ceeCCccccccee-eccccccC---------ccCCCCCCccc-hHHHHHHHHhcC---CCccCC-CCCCc-chhHHHhhh
Confidence 346874 88887 34444444 58999999996 678999988654 789999 99755 678999999
Q ss_pred hhhccCCcccccccccccCC----------hHHHHHHHHhhcCCCCcCCcchhhccCChhhHhccccc
Q psy16834 410 IQVHPAQKHQCHICNKIVVS----------EKTLKKHLLLHTNSEPFHCPECGKAFKFKRYVTLHMRT 467 (488)
Q Consensus 410 ~~~h~~~~~~C~~C~k~f~~----------~~~L~~H~~~H~~~~~~~C~~C~~~F~~~~~L~~H~~~ 467 (488)
..+.+.+++.|++|++.|.. .+.|..|+.+. |.+++.|..||+.|..+ .|..|+..
T Consensus 497 ~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt~~C~~Cgk~Vrlr-dm~~H~~~ 562 (567)
T PLN03086 497 ASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-GSRTAPCDSCGRSVMLK-EMDIHQIA 562 (567)
T ss_pred hccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-CCcceEccccCCeeeeh-hHHHHHHH
Confidence 88889999999999999952 35899999885 89999999999887754 47777654
No 13
>PHA00733 hypothetical protein
Probab=99.24 E-value=3.8e-12 Score=101.46 Aligned_cols=56 Identities=23% Similarity=0.421 Sum_probs=41.3
Q ss_pred ccCCcccccccccccCChHHHHHHHHhhcCCCCcCCcchhhccCChhhHhcccccccc
Q psy16834 413 HPAQKHQCHICNKIVVSEKTLKKHLLLHTNSEPFHCPECGKAFKFKRYVTLHMRTHTG 470 (488)
Q Consensus 413 h~~~~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~~C~~C~~~F~~~~~L~~H~~~H~~ 470 (488)
++.+||.|+.|++.|.+...|..|+++| +.+|.|++|+++|.....|..|+...++
T Consensus 69 ~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 69 KAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHHHHHHHHHhcC
Confidence 4566777777777777777777777766 3567888888888888888877776554
No 14
>PHA00733 hypothetical protein
Probab=99.17 E-value=3.2e-11 Score=96.20 Aligned_cols=82 Identities=17% Similarity=0.278 Sum_probs=61.5
Q ss_pred CCccccccccccccChhHHHHH--Hhh--hcCCCCCccCCccCCcCCCchHHHhhhhhhccCCcccccccccccCChHHH
Q psy16834 358 ADRFKCVFCEKSFARNCNLKLH--IRR--YHDKSDNTECPLCGKSFPSRGRLNEHLIQVHPAQKHQCHICNKIVVSEKTL 433 (488)
Q Consensus 358 ~~~~~C~~C~k~F~~~~~l~~H--~~~--~H~~~~~~~C~~C~k~F~~~~~L~~H~~~~h~~~~~~C~~C~k~f~~~~~L 433 (488)
.+++.|.+|++.|.....|..+ +++ .+.+++||.|+.||+.|.+.+.|..|++.+ +.+|.|++|++.|.....|
T Consensus 38 ~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~sL 115 (128)
T PHA00733 38 QKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDST 115 (128)
T ss_pred hhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHHH
Confidence 4567788888777776666655 221 234578888999999999888888888763 4578999999999999999
Q ss_pred HHHHHhhc
Q psy16834 434 KKHLLLHT 441 (488)
Q Consensus 434 ~~H~~~H~ 441 (488)
.+|+....
T Consensus 116 ~~H~~~~h 123 (128)
T PHA00733 116 LDHVCKKH 123 (128)
T ss_pred HHHHHHhc
Confidence 88886544
No 15
>PHA02768 hypothetical protein; Provisional
Probab=99.15 E-value=1.6e-11 Score=79.50 Aligned_cols=45 Identities=20% Similarity=0.354 Sum_probs=39.1
Q ss_pred cccccccccccCChHHHHHHHHhhcCCCCcCCcchhhccCChhhHhc
Q psy16834 417 KHQCHICNKIVVSEKTLKKHLLLHTNSEPFHCPECGKAFKFKRYVTL 463 (488)
Q Consensus 417 ~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~~C~~C~~~F~~~~~L~~ 463 (488)
.|+|+.||+.|+..++|..||++|+ +||+|..|++.|.+.+.|..
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 4789999999999999999999998 78999999999998887753
No 16
>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=98.96 E-value=2.2e-10 Score=63.51 Aligned_cols=26 Identities=42% Similarity=1.045 Sum_probs=19.3
Q ss_pred HHHHHHHhhcCCCCcCCcchhhccCC
Q psy16834 432 TLKKHLLLHTNSEPFHCPECGKAFKF 457 (488)
Q Consensus 432 ~L~~H~~~H~~~~~~~C~~C~~~F~~ 457 (488)
+|++||++|+|++||.|++|+++|.+
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 46777777777777777777777753
No 17
>KOG3993|consensus
Probab=98.89 E-value=5.7e-10 Score=102.07 Aligned_cols=52 Identities=27% Similarity=0.509 Sum_probs=46.2
Q ss_pred CCCCcchHHhhcCHHHHHHHH--hhhccCceeecccccccccCHHHHHhHHhhhcc
Q psy16834 248 KVQCPYCAKFLSRKEKLNRHI--RTVHTDVNYKCEICGEEFLSKTRYNRHVVTHEE 301 (488)
Q Consensus 248 ~~~C~~C~~~f~~~~~L~~H~--~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~H~~ 301 (488)
.|.|.+|...|.+.-.|.+|. ++++ ..|+|+.|+|.|.-..+|..|.|.|..
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC~RIV~--vEYrCPEC~KVFsCPANLASHRRWHKP 320 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRCPRIVH--VEYRCPECDKVFSCPANLASHRRWHKP 320 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccCCeeEE--eeecCCcccccccCchhhhhhhcccCC
Confidence 488999999999999999997 4444 459999999999999999999999964
No 18
>PHA02768 hypothetical protein; Provisional
Probab=98.88 E-value=6.4e-10 Score=72.11 Aligned_cols=42 Identities=19% Similarity=0.546 Sum_probs=24.0
Q ss_pred cccccccccccChhHHHHHHhhhcCCCCCccCCccCCcCCCchHH
Q psy16834 361 FKCVFCEKSFARNCNLKLHIRRYHDKSDNTECPLCGKSFPSRGRL 405 (488)
Q Consensus 361 ~~C~~C~k~F~~~~~l~~H~~~~H~~~~~~~C~~C~k~F~~~~~L 405 (488)
|.|+.||+.|.+.++|..|++. |+ ++++|..|++.|...+.|
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~-H~--k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRK-HN--TNLKLSNCKRISLRTGEY 47 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHh-cC--CcccCCcccceeccccee
Confidence 5566666666666666666553 43 455566666665555544
No 19
>KOG3993|consensus
Probab=98.85 E-value=9.2e-10 Score=100.75 Aligned_cols=195 Identities=18% Similarity=0.239 Sum_probs=116.4
Q ss_pred cccCccccCcCCChHHHHHHHHhhhCCCCccCCCCCCccCChhhHHHHHhhhccCCCccc---cccchhhccchhHHHHH
Q psy16834 39 SILCPECGRGFFNEKELAAHKIEIHGADPFLCIPCNKPFSKIENYRLHQRRYHLNSVNKE---CKICHKVLRTARLSEHM 115 (488)
Q Consensus 39 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~---C~~C~~~f~~~~l~~h~ 115 (488)
.|.|..|...|.+.-.|.+|.-...-...|+|++|+|.|+-..+|..|.| +|.....-. -+-=.+...+..+.+-.
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRR-WHKPR~eaa~a~~~P~k~~~~~rae~~ea 345 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRR-WHKPRPEAAKAGSPPPKQAVETRAEVQEA 345 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhc-ccCCchhhhhcCCCChhhhhhhhhhhhhc
Confidence 38899999999999999998532222345899999999999999999987 554321100 00000000000010000
Q ss_pred H---HHhcCCceecCccCccccChhhHHHHHHhccCCC-----------------ceeCccccccccchhhHHhHhhhcc
Q psy16834 116 K---QVHYAKLFDCHICGKTVVTEKNYKKHMQLHSDDK-----------------PFECQFCRKAFKLKYYLTLHLRTHT 175 (488)
Q Consensus 116 ~---~~~~~~~~~C~~C~~~f~~~~~l~~H~~~H~~~~-----------------~~~C~~C~~~F~~~~~L~~H~~~h~ 175 (488)
. ....+..|.|.+|+++|.....|+.|+.+|.... .+-|+.+.-.+.....-..+...+.
T Consensus 346 ~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~~~~k~~a~~f~~s~~~~l~~~~~~~a~h~~a~~~~g~~vl~~a 425 (500)
T KOG3993|consen 346 ERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRAPLAKEKAPKFLLSRVIPLMHFNQAVATHSSASDSHGDEVLYVA 425 (500)
T ss_pred cccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhccccchhcccCcchhhcccccccccccccccccccccccceeeee
Confidence 0 0022347889999999999999999877764311 1234444444443333333333333
Q ss_pred CCCCceecccchhhhhcccCCCC--CCcCCCCccccccccccccChhHHHHHHhhcCCCCc
Q psy16834 176 GVRPMFECDICHKVLKTKSKKSS--GISKNENLRPCTLCDKKLASERKLKEHIRKQHPTSV 234 (488)
Q Consensus 176 ~~~~~~~C~~C~~~f~~~~~~~~--~~~~~~~~~~C~~C~~~f~~~~~L~~H~~~~h~~~~ 234 (488)
+......++.++..+.++..... .+...+..|.|.+|.-+|.+...|.+|+...|+...
T Consensus 426 ~sael~~pp~~~~ppsss~~sgg~~rlg~~~q~f~~ky~~atfyss~~ltrhin~~Hpse~ 486 (500)
T KOG3993|consen 426 GSAELELPPYDGSPPSSSGSSGGYGRLGIAEQGFTCKYCPATFYSSPGLTRHINKCHPSEL 486 (500)
T ss_pred ccccccCCCCCCCCcccCCCCCccccccchhhccccccchHhhhcCcchHhHhhhcChHHh
Confidence 33333446666644444332222 123345678999999999999999999999998543
No 20
>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=98.76 E-value=2.1e-09 Score=59.58 Aligned_cols=26 Identities=42% Similarity=0.850 Sum_probs=24.1
Q ss_pred hHhccccccccCcCccccccCcccccc
Q psy16834 460 YVTLHMRTHTGNWPTFVCKICNATISS 486 (488)
Q Consensus 460 ~L~~H~~~H~~~~~~~~C~~C~k~f~~ 486 (488)
+|+.||++|+|++| |.|++|+++|.+
T Consensus 1 ~l~~H~~~H~~~k~-~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGEKP-YKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSSSS-EEESSSSEEESS
T ss_pred CHHHHhhhcCCCCC-CCCCCCcCeeCc
Confidence 58999999999998 999999999974
No 21
>PHA00616 hypothetical protein
Probab=98.65 E-value=1.1e-08 Score=62.92 Aligned_cols=34 Identities=24% Similarity=0.319 Sum_probs=25.2
Q ss_pred cccccccccccCChHHHHHHHHhhcCCCCcCCcc
Q psy16834 417 KHQCHICNKIVVSEKTLKKHLLLHTNSEPFHCPE 450 (488)
Q Consensus 417 ~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~~C~~ 450 (488)
||+|+.||+.|.+++.|..|++.|+|++||.|+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 5677777777777777777777777777777764
No 22
>PHA00732 hypothetical protein
Probab=98.56 E-value=4.6e-08 Score=70.36 Aligned_cols=49 Identities=29% Similarity=0.541 Sum_probs=36.0
Q ss_pred cccccccccccCChHHHHHHHHh-hcCCCCcCCcchhhccCChhhHhccccccccC
Q psy16834 417 KHQCHICNKIVVSEKTLKKHLLL-HTNSEPFHCPECGKAFKFKRYVTLHMRTHTGN 471 (488)
Q Consensus 417 ~~~C~~C~k~f~~~~~L~~H~~~-H~~~~~~~C~~C~~~F~~~~~L~~H~~~H~~~ 471 (488)
||.|++||+.|.+..+|+.|++. |+ ++.|+.||++|. .|..|+++..+-
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~---~l~~H~~~~~~~ 50 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYR---RLNQHFYSQYDI 50 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeC---ChhhhhcccCCc
Confidence 57788888888888888888774 55 357888888887 577888766543
No 23
>PHA00616 hypothetical protein
Probab=98.55 E-value=1.7e-08 Score=62.09 Aligned_cols=34 Identities=21% Similarity=0.408 Sum_probs=31.9
Q ss_pred CcCCcchhhccCChhhHhccccccccCcCcccccc
Q psy16834 445 PFHCPECGKAFKFKRYVTLHMRTHTGNWPTFVCKI 479 (488)
Q Consensus 445 ~~~C~~C~~~F~~~~~L~~H~~~H~~~~~~~~C~~ 479 (488)
||+|+.||+.|.++++|..|++.|+|+.| |.|+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~-~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNK-LTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCc-cceeE
Confidence 79999999999999999999999999987 88864
No 24
>PHA00732 hypothetical protein
Probab=98.42 E-value=1.4e-07 Score=67.80 Aligned_cols=46 Identities=43% Similarity=0.806 Sum_probs=31.3
Q ss_pred ccccccccccccChhHHHHHHhhhcCCCCCccCCccCCcCCCchHHHhhhhh
Q psy16834 360 RFKCVFCEKSFARNCNLKLHIRRYHDKSDNTECPLCGKSFPSRGRLNEHLIQ 411 (488)
Q Consensus 360 ~~~C~~C~k~F~~~~~l~~H~~~~H~~~~~~~C~~C~k~F~~~~~L~~H~~~ 411 (488)
||.|+.||+.|.+.++|+.|++..|. ++.|++||++|. .|..|+..
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~---~l~~H~~~ 46 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYR---RLNQHFYS 46 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeC---Chhhhhcc
Confidence 46777777777777777777764454 346777777776 46666643
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=98.26 E-value=1.3e-06 Score=58.46 Aligned_cols=50 Identities=30% Similarity=0.624 Sum_probs=25.5
Q ss_pred cccccccccccChhHHHHHHhhhcCCC-CCccCCccCCcCCCchHHHhhhhhhc
Q psy16834 361 FKCVFCEKSFARNCNLKLHIRRYHDKS-DNTECPLCGKSFPSRGRLNEHLIQVH 413 (488)
Q Consensus 361 ~~C~~C~k~F~~~~~l~~H~~~~H~~~-~~~~C~~C~k~F~~~~~L~~H~~~~h 413 (488)
|.|++|++. -+...|..|+...|..+ +.+.||+|...+. .+|..|+...|
T Consensus 3 f~CP~C~~~-~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 3 FTCPYCGKG-FSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred cCCCCCCCc-cCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 555556653 33455666655555443 3455666655433 25555554443
No 26
>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=98.16 E-value=3e-06 Score=56.60 Aligned_cols=51 Identities=25% Similarity=0.548 Sum_probs=33.2
Q ss_pred cccCCcccccccchhhHHHHHHhhcCCC-ccccCccccCcCCChHHHHHHHHhhh
Q psy16834 10 KFSCSLCSYSVTIKRNLIMHIKRKHTDE-FSILCPECGRGFFNEKELAAHKIEIH 63 (488)
Q Consensus 10 ~~~C~~C~~~f~~~~~L~~H~~~~h~~~-~~~~C~~C~~~f~~~~~l~~H~~~~h 63 (488)
.|.|++|++ ..+...|..|+...|..+ +.+.|++|...+. .+|..|+...|
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 477777777 445667777777777654 3567777776544 36777765554
No 27
>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=98.03 E-value=2.9e-06 Score=45.64 Aligned_cols=23 Identities=39% Similarity=0.730 Sum_probs=14.2
Q ss_pred ccccccccccCChHHHHHHHHhh
Q psy16834 418 HQCHICNKIVVSEKTLKKHLLLH 440 (488)
Q Consensus 418 ~~C~~C~k~f~~~~~L~~H~~~H 440 (488)
|+|++|++.|.++..|+.|++.|
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 28
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.85 E-value=8.6e-06 Score=62.95 Aligned_cols=71 Identities=27% Similarity=0.475 Sum_probs=14.9
Q ss_pred cccccccccChhHHHHHHhhhcCCCCCccCCccCCcCCCchHHHhhhhhhccCCcccccccccccCChHHHHHHHHh
Q psy16834 363 CVFCEKSFARNCNLKLHIRRYHDKSDNTECPLCGKSFPSRGRLNEHLIQVHPAQKHQCHICNKIVVSEKTLKKHLLL 439 (488)
Q Consensus 363 C~~C~k~F~~~~~l~~H~~~~H~~~~~~~C~~C~k~F~~~~~L~~H~~~~h~~~~~~C~~C~k~f~~~~~L~~H~~~ 439 (488)
|.+|+..|.+...|..||...|.-..+ ....+.....|..++.. ....++.|.+|++.|.+...|+.||+.
T Consensus 2 C~~C~~~f~~~~~l~~H~~~~H~~~~~-----~~~~l~~~~~~~~~~~~-~~~~~~~C~~C~~~f~s~~~l~~Hm~~ 72 (100)
T PF12756_consen 2 CLFCDESFSSVDDLLQHMKKKHGFDIP-----DQKYLVDPNRLLNYLRK-KVKESFRCPYCNKTFRSREALQEHMRS 72 (100)
T ss_dssp -----------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHH
T ss_pred ccccccccccccccccccccccccccc-----ccccccccccccccccc-ccCCCCCCCccCCCCcCHHHHHHHHcC
Confidence 566666666666666666555543222 11122233333333322 112246666666666666666666664
No 29
>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=97.81 E-value=1.5e-05 Score=42.79 Aligned_cols=23 Identities=52% Similarity=1.078 Sum_probs=17.0
Q ss_pred eecccccccccCHHHHHhHHhhh
Q psy16834 277 YKCEICGEEFLSKTRYNRHVVTH 299 (488)
Q Consensus 277 ~~C~~C~~~f~~~~~l~~H~~~H 299 (488)
|+|++|++.|.++..|..|++.|
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 56777777777777777777654
No 30
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.70 E-value=1.8e-05 Score=61.14 Aligned_cols=73 Identities=25% Similarity=0.415 Sum_probs=21.8
Q ss_pred cCCcccccccchhhHHHHHHhhcCCCccccCccccCcCCChHHHHHHHHhhhCCCCccCCCCCCccCChhhHHHHHhhh
Q psy16834 12 SCSLCSYSVTIKRNLIMHIKRKHTDEFSILCPECGRGFFNEKELAAHKIEIHGADPFLCIPCNKPFSKIENYRLHQRRY 90 (488)
Q Consensus 12 ~C~~C~~~f~~~~~L~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~C~~C~~~f~~~~~l~~H~~~~ 90 (488)
+|.+|+..|.+...|..||...|.-..+ ....+.....+..+... .....+.|..|++.|.+...|..|++..
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~-----~~~~l~~~~~~~~~~~~-~~~~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIP-----DQKYLVDPNRLLNYLRK-KVKESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp ------------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred Cccccccccccccccccccccccccccc-----ccccccccccccccccc-ccCCCCCCCccCCCCcCHHHHHHHHcCc
Confidence 5999999999999999999888864433 22223344455554422 2233699999999999999999999864
No 31
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.60 E-value=1.9e-05 Score=70.19 Aligned_cols=52 Identities=29% Similarity=0.626 Sum_probs=36.4
Q ss_pred CCcccccc--cccccCChHHHHHHHH-hh------------------cCCCCcCCcchhhccCChhhHhcccc
Q psy16834 415 AQKHQCHI--CNKIVVSEKTLKKHLL-LH------------------TNSEPFHCPECGKAFKFKRYVTLHMR 466 (488)
Q Consensus 415 ~~~~~C~~--C~k~f~~~~~L~~H~~-~H------------------~~~~~~~C~~C~~~F~~~~~L~~H~~ 466 (488)
++||+|++ |.|+|.+...|+-||. .| ...|||+|++|+|+|+....|+-|..
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceeccc
Confidence 35566655 5566666666666553 23 13489999999999999999998865
No 32
>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=97.57 E-value=5e-05 Score=41.15 Aligned_cols=23 Identities=39% Similarity=0.743 Sum_probs=11.3
Q ss_pred ccccccccccCChHHHHHHHHhh
Q psy16834 418 HQCHICNKIVVSEKTLKKHLLLH 440 (488)
Q Consensus 418 ~~C~~C~k~f~~~~~L~~H~~~H 440 (488)
|.|++|++.|.+...|+.|+++|
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 44555555555555555555543
No 33
>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=97.56 E-value=5e-05 Score=41.17 Aligned_cols=22 Identities=41% Similarity=0.930 Sum_probs=10.4
Q ss_pred cccccccccccChhHHHHHHhh
Q psy16834 361 FKCVFCEKSFARNCNLKLHIRR 382 (488)
Q Consensus 361 ~~C~~C~k~F~~~~~l~~H~~~ 382 (488)
|.|++|+++|.+...|+.|++.
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~ 22 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRT 22 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHh
Confidence 3455555555555555555544
No 34
>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=97.48 E-value=6.2e-05 Score=42.18 Aligned_cols=23 Identities=30% Similarity=0.551 Sum_probs=11.5
Q ss_pred ccccccccccCChHHHHHHHHhh
Q psy16834 418 HQCHICNKIVVSEKTLKKHLLLH 440 (488)
Q Consensus 418 ~~C~~C~k~f~~~~~L~~H~~~H 440 (488)
|+|++|++.|.+..+|..|++.|
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~~h 24 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKRSH 24 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHCTT
T ss_pred CCCCccCCccCChhHHHHHhHHh
Confidence 44555555555555555554444
No 35
>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=97.44 E-value=7.6e-05 Score=41.79 Aligned_cols=25 Identities=44% Similarity=0.752 Sum_probs=15.0
Q ss_pred ceeCccccccccchhhHHhHhhhcc
Q psy16834 151 PFECQFCRKAFKLKYYLTLHLRTHT 175 (488)
Q Consensus 151 ~~~C~~C~~~F~~~~~L~~H~~~h~ 175 (488)
||.|..|++.|.+...|..|++.|.
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhc
Confidence 4566666666666666666665553
No 36
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.21 E-value=0.00012 Score=65.28 Aligned_cols=69 Identities=25% Similarity=0.441 Sum_probs=43.2
Q ss_pred CCCcccccc--ccccccChhHHHHHHhhhcCCCCCccC--CccCCcCCCchHHHhhhhhhccCCcccccccccccCChHH
Q psy16834 357 SADRFKCVF--CEKSFARNCNLKLHIRRYHDKSDNTEC--PLCGKSFPSRGRLNEHLIQVHPAQKHQCHICNKIVVSEKT 432 (488)
Q Consensus 357 ~~~~~~C~~--C~k~F~~~~~l~~H~~~~H~~~~~~~C--~~C~k~F~~~~~L~~H~~~~h~~~~~~C~~C~k~f~~~~~ 432 (488)
+++||+|++ |+|+|+....|+.|+.--|...+..+= ++=-..| .-..+||.|++|+|.|.+-..
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F------------~~~~KPYrCevC~KRYKNlNG 413 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIF------------SAKDKPYRCEVCDKRYKNLNG 413 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccc------------cccCCceeccccchhhccCcc
Confidence 358899988 999999999999997643422211111 1111111 234467777777777777777
Q ss_pred HHHHH
Q psy16834 433 LKKHL 437 (488)
Q Consensus 433 L~~H~ 437 (488)
|+-|.
T Consensus 414 LKYHr 418 (423)
T COG5189 414 LKYHR 418 (423)
T ss_pred ceecc
Confidence 77773
No 37
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.09 E-value=0.00047 Score=37.96 Aligned_cols=24 Identities=33% Similarity=0.609 Sum_probs=12.7
Q ss_pred ccccccccccCChHHHHHHHHhhc
Q psy16834 418 HQCHICNKIVVSEKTLKKHLLLHT 441 (488)
Q Consensus 418 ~~C~~C~k~f~~~~~L~~H~~~H~ 441 (488)
|+|+.|++.|.+...|..|+++|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 345555555555555555555443
No 38
>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=97.07 E-value=0.00024 Score=44.80 Aligned_cols=31 Identities=26% Similarity=0.651 Sum_probs=15.8
Q ss_pred CCcccccccccccCChHHHHHHHHhhcCCCC
Q psy16834 415 AQKHQCHICNKIVVSEKTLKKHLLLHTNSEP 445 (488)
Q Consensus 415 ~~~~~C~~C~k~f~~~~~L~~H~~~H~~~~~ 445 (488)
+.|..|++|+..+.+..+|++||.++.+.+|
T Consensus 22 ~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 22 EQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp S--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred CCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 3466666666666666666666666555554
No 39
>PRK04860 hypothetical protein; Provisional
Probab=96.99 E-value=0.00028 Score=58.58 Aligned_cols=39 Identities=23% Similarity=0.672 Sum_probs=32.9
Q ss_pred cccccccccccCChHHHHHHHHhhcCCCCcCCcchhhccCChh
Q psy16834 417 KHQCHICNKIVVSEKTLKKHLLLHTNSEPFHCPECGKAFKFKR 459 (488)
Q Consensus 417 ~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~~C~~C~~~F~~~~ 459 (488)
+|.|. |++ ....+++|.++|+|+++|.|..|+..|....
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 68888 887 6777889999999999999999999887554
No 40
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.88 E-value=0.00038 Score=38.32 Aligned_cols=25 Identities=56% Similarity=1.015 Sum_probs=22.7
Q ss_pred cCCcchhhccCChhhHhcccccccc
Q psy16834 446 FHCPECGKAFKFKRYVTLHMRTHTG 470 (488)
Q Consensus 446 ~~C~~C~~~F~~~~~L~~H~~~H~~ 470 (488)
|.|+.|+++|...+.|..|++.|..
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~~ 25 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHXX 25 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhcc
Confidence 6899999999999999999997753
No 41
>KOG2231|consensus
Probab=96.86 E-value=0.0025 Score=64.36 Aligned_cols=17 Identities=6% Similarity=0.089 Sum_probs=9.5
Q ss_pred CccccChhhHHHHHHhc
Q psy16834 130 GKTVVTEKNYKKHMQLH 146 (488)
Q Consensus 130 ~~~f~~~~~l~~H~~~H 146 (488)
+.-|.....|..|.+.+
T Consensus 219 neyy~~~~dLe~HfR~~ 235 (669)
T KOG2231|consen 219 NEYYNDYDDLEEHFRKG 235 (669)
T ss_pred chhcccchHHHHHhhhc
Confidence 34455566666666543
No 42
>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=96.85 E-value=0.00079 Score=42.51 Aligned_cols=41 Identities=27% Similarity=0.344 Sum_probs=22.1
Q ss_pred HHHHHhhcCCCccccCccccCcCCChHHHHHHHHhhhCCCC
Q psy16834 27 IMHIKRKHTDEFSILCPECGRGFFNEKELAAHKIEIHGADP 67 (488)
Q Consensus 27 ~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~ 67 (488)
..+.+.++..+.|-.|++|+..+.+..+|.+|+...|+.+|
T Consensus 12 ~~~~k~~~~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 12 TKKPKSKSQSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp ----CCCCTTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred hhHHHHhhccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 44544455566677788888887777778887777776654
No 43
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.77 E-value=0.00078 Score=36.80 Aligned_cols=23 Identities=43% Similarity=0.761 Sum_probs=15.3
Q ss_pred ccccccccccCChHHHHHHHHhh
Q psy16834 418 HQCHICNKIVVSEKTLKKHLLLH 440 (488)
Q Consensus 418 ~~C~~C~k~f~~~~~L~~H~~~H 440 (488)
|.|++|++.|.+...|+.|++.+
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSK 23 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcC
Confidence 45677777777777777776543
No 44
>KOG2785|consensus
Probab=96.59 E-value=0.0039 Score=57.76 Aligned_cols=54 Identities=22% Similarity=0.384 Sum_probs=45.3
Q ss_pred ccCCCCCcchHHhhcCHHHHHHHHhhhccC-----------------------ceeeccccc---ccccCHHHHHhHHhh
Q psy16834 245 EREKVQCPYCAKFLSRKEKLNRHIRTVHTD-----------------------VNYKCEICG---EEFLSKTRYNRHVVT 298 (488)
Q Consensus 245 ~~~~~~C~~C~~~f~~~~~L~~H~~~~~~~-----------------------~~~~C~~C~---~~f~~~~~l~~H~~~ 298 (488)
+..|-.|-.|++.+.+...-..||..+|+- ..+.|-.|+ +.|.+....+.||..
T Consensus 163 e~~Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 163 ELIPTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred ccCCcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhh
Confidence 344578999999999999999999999862 237888888 999999999999964
No 45
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.37 E-value=0.0027 Score=34.64 Aligned_cols=23 Identities=26% Similarity=0.765 Sum_probs=18.1
Q ss_pred eecccccccccCHHHHHhHHhhh
Q psy16834 277 YKCEICGEEFLSKTRYNRHVVTH 299 (488)
Q Consensus 277 ~~C~~C~~~f~~~~~l~~H~~~H 299 (488)
|.|++|++.|.+...|..|++.+
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSK 23 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcC
Confidence 56888888888888888887654
No 46
>KOG2231|consensus
Probab=96.29 E-value=0.0047 Score=62.40 Aligned_cols=103 Identities=24% Similarity=0.525 Sum_probs=73.5
Q ss_pred cCCCCCCccCChhhHHHHHhhhccCCCccccccc----------hhhccchhHHHHHHHHhc-CCc----eecCccCccc
Q psy16834 69 LCIPCNKPFSKIENYRLHQRRYHLNSVNKECKIC----------HKVLRTARLSEHMKQVHY-AKL----FDCHICGKTV 133 (488)
Q Consensus 69 ~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C----------~~~f~~~~l~~h~~~~~~-~~~----~~C~~C~~~f 133 (488)
.|..| -.|.+...|+.|++..|.. +.|.+| .+.+..+.|..|+..-.. ++. -.|..|...|
T Consensus 117 ~~~~c-~~~~s~~~Lk~H~~~~H~~---~~c~lC~~~~kif~~e~k~Yt~~el~~h~~~gd~d~~s~rGhp~C~~C~~~f 192 (669)
T KOG2231|consen 117 ECLHC-TEFKSVENLKNHMRDQHKL---HLCSLCLQNLKIFINERKLYTRAELNLHLMFGDPDDESCRGHPLCKFCHERF 192 (669)
T ss_pred CCccc-cchhHHHHHHHHHHHhhhh---hccccccccceeeeeeeehehHHHHHHHHhcCCCccccccCCccchhhhhhh
Confidence 35555 5556888999999877754 345555 344556678888775332 221 3699999999
Q ss_pred cChhhHHHHHHhccCCCceeCccc------cccccchhhHHhHhhhccCCCCceecc
Q psy16834 134 VTEKNYKKHMQLHSDDKPFECQFC------RKAFKLKYYLTLHLRTHTGVRPMFECD 184 (488)
Q Consensus 134 ~~~~~l~~H~~~H~~~~~~~C~~C------~~~F~~~~~L~~H~~~h~~~~~~~~C~ 184 (488)
.....|.+|++.++ |.|.+| +.-|.....|..|.+.+| |.|.
T Consensus 193 ld~~el~rH~~~~h----~~chfC~~~~~~neyy~~~~dLe~HfR~~H-----flCE 240 (669)
T KOG2231|consen 193 LDDDELYRHLRFDH----EFCHFCDYKTGQNEYYNDYDDLEEHFRKGH-----FLCE 240 (669)
T ss_pred ccHHHHHHhhccce----eheeecCcccccchhcccchHHHHHhhhcC-----cccc
Confidence 99999999998764 567666 356788889999998876 6666
No 47
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.24 E-value=0.003 Score=34.04 Aligned_cols=23 Identities=52% Similarity=1.024 Sum_probs=14.8
Q ss_pred ccCCcccccccchhhHHHHHHhhc
Q psy16834 11 FSCSLCSYSVTIKRNLIMHIKRKH 34 (488)
Q Consensus 11 ~~C~~C~~~f~~~~~L~~H~~~~h 34 (488)
|+|+.|++... ...|.+|++.+|
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 56777777776 777777776555
No 48
>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=96.07 E-value=0.0033 Score=35.00 Aligned_cols=22 Identities=32% Similarity=0.714 Sum_probs=17.0
Q ss_pred cCCcchhhccCChhhHhccccc
Q psy16834 446 FHCPECGKAFKFKRYVTLHMRT 467 (488)
Q Consensus 446 ~~C~~C~~~F~~~~~L~~H~~~ 467 (488)
|-|++|++.|.....|..|+++
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCcccCCCCcCCHHHHHHHHcc
Confidence 6677888888888888887765
No 49
>PRK04860 hypothetical protein; Provisional
Probab=95.91 E-value=0.0054 Score=51.00 Aligned_cols=38 Identities=16% Similarity=0.606 Sum_probs=29.5
Q ss_pred ceecCccCccccChhhHHHHHHhccCCCceeCccccccccch
Q psy16834 123 LFDCHICGKTVVTEKNYKKHMQLHSDDKPFECQFCRKAFKLK 164 (488)
Q Consensus 123 ~~~C~~C~~~f~~~~~l~~H~~~H~~~~~~~C~~C~~~F~~~ 164 (488)
+|.|. |+. ...++.+|.++|.++++|.|..|+..|...
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 667778888888888888888888877654
No 50
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=95.87 E-value=0.0058 Score=32.89 Aligned_cols=21 Identities=29% Similarity=0.515 Sum_probs=9.2
Q ss_pred ccccccccccCChHHHHHHHHh
Q psy16834 418 HQCHICNKIVVSEKTLKKHLLL 439 (488)
Q Consensus 418 ~~C~~C~k~f~~~~~L~~H~~~ 439 (488)
|+|+.|+.... +..|.+|+++
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~ 21 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKR 21 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHh
Confidence 34555554444 4455555444
No 51
>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=95.85 E-value=0.0027 Score=35.37 Aligned_cols=22 Identities=36% Similarity=0.674 Sum_probs=13.8
Q ss_pred ccccccccccCChHHHHHHHHh
Q psy16834 418 HQCHICNKIVVSEKTLKKHLLL 439 (488)
Q Consensus 418 ~~C~~C~k~f~~~~~L~~H~~~ 439 (488)
|.|.+|++.|.+...|+.|++.
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCcccCCCCcCCHHHHHHHHcc
Confidence 4566666666666666666543
No 52
>KOG1146|consensus
Probab=95.71 E-value=0.0039 Score=66.74 Aligned_cols=105 Identities=25% Similarity=0.483 Sum_probs=57.5
Q ss_pred CccccccccccccChhHHHHHHhhhcCCCCCccCCccCCcCCCchHHHhhhhhhccCCcccccccccccCChHHHHHHHH
Q psy16834 359 DRFKCVFCEKSFARNCNLKLHIRRYHDKSDNTECPLCGKSFPSRGRLNEHLIQVHPAQKHQCHICNKIVVSEKTLKKHLL 438 (488)
Q Consensus 359 ~~~~C~~C~k~F~~~~~l~~H~~~~H~~~~~~~C~~C~k~F~~~~~L~~H~~~~h~~~~~~C~~C~k~f~~~~~L~~H~~ 438 (488)
+.|+|+.|+..|+....|..|||..|..... .+|- .+.+.-.+.+=..-.-+.+||.|..|.-+++.+.+|.+||.
T Consensus 464 kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~---~~c~-~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~Lsihlq 539 (1406)
T KOG1146|consen 464 KTLKCPKCNWHYKLAQTLGVHMRSKHPESQS---AYCK-AGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHLQ 539 (1406)
T ss_pred ccccCCccchhhhhHHHhhhcccccccccch---hHhH-hccccccccccccccCCCCcccceeeeeeeecchHHHHHHH
Confidence 5567777777777777777777664432221 1110 00000000000000012346777777777777777777764
Q ss_pred --hhcC-----------------------------------------CCCcCCcchhhccCChhhHhccccc
Q psy16834 439 --LHTN-----------------------------------------SEPFHCPECGKAFKFKRYVTLHMRT 467 (488)
Q Consensus 439 --~H~~-----------------------------------------~~~~~C~~C~~~F~~~~~L~~H~~~ 467 (488)
+|.. +-++.|.+|+..-+-..+|+.||..
T Consensus 540 S~~h~~~lee~~~~~g~~v~~~~~~v~s~~P~~ag~~~~ags~~pktkP~~~C~vc~yetniarnlrihmts 611 (1406)
T KOG1146|consen 540 SDLHRNELEEAEENAGEQVRLLPASVTSAVPEEAGLGPSAGSSGPKTKPSWRCEVCSYETNIARNLRIHMTA 611 (1406)
T ss_pred HHhhHHHHHHHHhccccchhhhhhhhcccCcccccCCCCCCCCCCCCCCCcchhhhcchhhhhhcccccccc
Confidence 2311 0147888888888888888888865
No 53
>KOG2482|consensus
Probab=95.70 E-value=0.02 Score=52.09 Aligned_cols=108 Identities=24% Similarity=0.434 Sum_probs=64.5
Q ss_pred ccccccccccccChhHHHHHHhhh-cCCCCC----cc------CCccCCcCCCc-hHHH-----hhhh--------hhcc
Q psy16834 360 RFKCVFCEKSFARNCNLKLHIRRY-HDKSDN----TE------CPLCGKSFPSR-GRLN-----EHLI--------QVHP 414 (488)
Q Consensus 360 ~~~C~~C~k~F~~~~~l~~H~~~~-H~~~~~----~~------C~~C~k~F~~~-~~L~-----~H~~--------~~h~ 414 (488)
++.|-+|.|.|+.+..|+.|||.. |....| |- =..=||+.... +.+. .+.- .-++
T Consensus 195 r~~CLyCekifrdkntLkeHMrkK~HrrinPknreYDkfyiINY~ev~ks~t~~~~e~dret~~d~~E~D~~wsDw~ed~ 274 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRKKRHRRINPKNREYDKFYIINYLEVGKSWTIVHSEDDRETNEDINETDDTWSDWNEDD 274 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHhccCcccCCCccccceEEEEeHhhcCCccchhhhhhhhhhhccccccccchhhhhcCC
Confidence 578999999999999999999743 322111 10 00012221111 1110 0000 0011
Q ss_pred CCc--ccccccccccCChHHHHHHHHh-hcC--------------------------CCCcCCcchhhccCChhhHhccc
Q psy16834 415 AQK--HQCHICNKIVVSEKTLKKHLLL-HTN--------------------------SEPFHCPECGKAFKFKRYVTLHM 465 (488)
Q Consensus 415 ~~~--~~C~~C~k~f~~~~~L~~H~~~-H~~--------------------------~~~~~C~~C~~~F~~~~~L~~H~ 465 (488)
+.+ .+|-.|....-+...|..||.+ |.= ...-.|-.|.-.|.....|..||
T Consensus 275 a~a~~v~CLfC~~~~en~~~l~eHmk~vHe~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c~~cd~~F~~e~~l~~hm 354 (423)
T KOG2482|consen 275 AEALSVVCLFCTNFYENPVFLFEHMKIVHEFDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCAECDLSFWKEPGLLIHM 354 (423)
T ss_pred CCccceEEEeeccchhhHHHHHHHHHHHHHhhHHhhccccccchhhhhhHHHHHHHHhhccccccccccccCcchhhhhc
Confidence 223 5899999888888899999875 520 01345778889999999999999
Q ss_pred cc
Q psy16834 466 RT 467 (488)
Q Consensus 466 ~~ 467 (488)
.-
T Consensus 355 ~e 356 (423)
T KOG2482|consen 355 VE 356 (423)
T ss_pred cc
Confidence 75
No 54
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=95.58 E-value=0.012 Score=53.48 Aligned_cols=135 Identities=28% Similarity=0.468 Sum_probs=79.9
Q ss_pred cccCCc--ccccccchhhHHHHHHhhcCCCccccCcccc---CcC------CChHHHHHHHHhhhCCCC----ccCCCCC
Q psy16834 10 KFSCSL--CSYSVTIKRNLIMHIKRKHTDEFSILCPECG---RGF------FNEKELAAHKIEIHGADP----FLCIPCN 74 (488)
Q Consensus 10 ~~~C~~--C~~~f~~~~~L~~H~~~~h~~~~~~~C~~C~---~~f------~~~~~l~~H~~~~h~~~~----~~C~~C~ 74 (488)
.|.|+. |.........|..|.+..|.. +.|.+|- +.| .++..|..|...-..+.- -.|..|+
T Consensus 151 ~F~CP~skc~~~C~~~k~lk~H~K~~H~~---~~C~~C~~nKk~F~~E~~lF~~~~Lr~H~~~G~~e~GFKGHP~C~FC~ 227 (493)
T COG5236 151 SFKCPKSKCHRRCGSLKELKKHYKAQHGF---VLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGHPLCIFCK 227 (493)
T ss_pred HhcCCchhhhhhhhhHHHHHHHHHhhcCc---EEhHhhhcCcccCccceeeeecccccccccCCccccCcCCCchhhhcc
Confidence 366754 666666677888888766643 5566663 233 345566666422111111 2588888
Q ss_pred CccCChhhHHHHHhhhccCCCccccccchhhccchhHHHHHHHHhcCCceecCccCccccChhhHHHHHHhccCCCceeC
Q psy16834 75 KPFSKIENYRLHQRRYHLNSVNKECKICHKVLRTARLSEHMKQVHYAKLFDCHICGKTVVTEKNYKKHMQLHSDDKPFEC 154 (488)
Q Consensus 75 ~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~H~~~~~~~C 154 (488)
+.|-+-..|.+|+|..|. .|-+|+++-... ..-|.+..+|..|.+.- -|.|
T Consensus 228 ~~FYdDDEL~~HcR~~HE-----~ChICD~v~p~~--------------------~QYFK~Y~~Le~HF~~~----hy~c 278 (493)
T COG5236 228 IYFYDDDELRRHCRLRHE-----ACHICDMVGPIR--------------------YQYFKSYEDLEAHFRNA----HYCC 278 (493)
T ss_pred ceecChHHHHHHHHhhhh-----hhhhhhccCccc--------------------hhhhhCHHHHHHHhhcC----ceEE
Confidence 888888888888876552 355555543111 12477777787776532 2555
Q ss_pred cc--cc----ccccchhhHHhHhhhccC
Q psy16834 155 QF--CR----KAFKLKYYLTLHLRTHTG 176 (488)
Q Consensus 155 ~~--C~----~~F~~~~~L~~H~~~h~~ 176 (488)
.+ |- ..|.....|..|+..-++
T Consensus 279 t~qtc~~~k~~vf~~~~el~~h~~~~h~ 306 (493)
T COG5236 279 TFQTCRVGKCYVFPYHTELLEHLTRFHK 306 (493)
T ss_pred EEEEEecCcEEEeccHHHHHHHHHHHhh
Confidence 43 32 368888888888765443
No 55
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=95.51 E-value=0.036 Score=50.50 Aligned_cols=122 Identities=23% Similarity=0.466 Sum_probs=73.8
Q ss_pred eeCcc--ccccccchhhHHhHhhhccCCCCceecccchh---hhh------cccCCCCCCcCCC------Cccccccccc
Q psy16834 152 FECQF--CRKAFKLKYYLTLHLRTHTGVRPMFECDICHK---VLK------TKSKKSSGISKNE------NLRPCTLCDK 214 (488)
Q Consensus 152 ~~C~~--C~~~F~~~~~L~~H~~~h~~~~~~~~C~~C~~---~f~------~~~~~~~~~~~~~------~~~~C~~C~~ 214 (488)
|.|+. |..+-.....|+.|.+..++. +-|++|-. .|. +++.+..|...+. .--.|..|..
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~~ 228 (493)
T COG5236 152 FKCPKSKCHRRCGSLKELKKHYKAQHGF---VLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGHPLCIFCKI 228 (493)
T ss_pred hcCCchhhhhhhhhHHHHHHHHHhhcCc---EEhHhhhcCcccCccceeeeecccccccccCCccccCcCCCchhhhccc
Confidence 55553 444444455666666655543 55666632 222 2222333322221 1125889999
Q ss_pred cccChhHHHHHHhhcCCCCchhhhHhhhhcccCCCCCcchHH-------hhcCHHHHHHHHhhhccCceeeccc--cc--
Q psy16834 215 KLASERKLKEHIRKQHPTSVEADLIRREKYEREKVQCPYCAK-------FLSRKEKLNRHIRTVHTDVNYKCEI--CG-- 283 (488)
Q Consensus 215 ~f~~~~~L~~H~~~~h~~~~~~~~~~~~~~~~~~~~C~~C~~-------~f~~~~~L~~H~~~~~~~~~~~C~~--C~-- 283 (488)
.|-+.++|..|++..|. .|-+|++ -|.+-.+|.+|.+.-| |.|.+ |-
T Consensus 229 ~FYdDDEL~~HcR~~HE------------------~ChICD~v~p~~~QYFK~Y~~Le~HF~~~h----y~ct~qtc~~~ 286 (493)
T COG5236 229 YFYDDDELRRHCRLRHE------------------ACHICDMVGPIRYQYFKSYEDLEAHFRNAH----YCCTFQTCRVG 286 (493)
T ss_pred eecChHHHHHHHHhhhh------------------hhhhhhccCccchhhhhCHHHHHHHhhcCc----eEEEEEEEecC
Confidence 99999999999988774 3666654 5777888888876544 66643 32
Q ss_pred --ccccCHHHHHhHHhh
Q psy16834 284 --EEFLSKTRYNRHVVT 298 (488)
Q Consensus 284 --~~f~~~~~l~~H~~~ 298 (488)
..|.....|..|+..
T Consensus 287 k~~vf~~~~el~~h~~~ 303 (493)
T COG5236 287 KCYVFPYHTELLEHLTR 303 (493)
T ss_pred cEEEeccHHHHHHHHHH
Confidence 357788888888754
No 56
>KOG1146|consensus
Probab=95.32 E-value=0.007 Score=64.95 Aligned_cols=101 Identities=19% Similarity=0.295 Sum_probs=58.8
Q ss_pred CccccCcCCChHHHHHHHHhhh-CCCCccCCCCCCccCChhhHHHHHhhhccCCCccccccchhhccchhHHHHHHHHhc
Q psy16834 42 CPECGRGFFNEKELAAHKIEIH-GADPFLCIPCNKPFSKIENYRLHQRRYHLNSVNKECKICHKVLRTARLSEHMKQVHY 120 (488)
Q Consensus 42 C~~C~~~f~~~~~l~~H~~~~h-~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~l~~h~~~~~~ 120 (488)
|.-|+..+.+...+..|+...+ -.+.++|+.|+..|.....|..|||..|..... ..|...-....+.+-....-.
T Consensus 439 ~~~~e~~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~---~~c~~gq~~~~~arg~~~~~~ 515 (1406)
T KOG1146|consen 439 LTKAEPLLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQS---AYCKAGQNHPRLARGEVYRCP 515 (1406)
T ss_pred ccchhhhhhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccch---hHhHhccccccccccccccCC
Confidence 3344445555555555543333 235688999999999999999999987765543 222111100011110011112
Q ss_pred CCceecCccCccccChhhHHHHHHh
Q psy16834 121 AKLFDCHICGKTVVTEKNYKKHMQL 145 (488)
Q Consensus 121 ~~~~~C~~C~~~f~~~~~l~~H~~~ 145 (488)
.++|.|..|+..+..+.+|.+||+.
T Consensus 516 ~~p~~C~~C~~stttng~LsihlqS 540 (1406)
T KOG1146|consen 516 GKPYPCRACNYSTTTNGNLSIHLQS 540 (1406)
T ss_pred CCcccceeeeeeeecchHHHHHHHH
Confidence 3567888888888888888888764
No 57
>KOG2482|consensus
Probab=95.23 E-value=0.021 Score=51.92 Aligned_cols=109 Identities=18% Similarity=0.308 Sum_probs=66.1
Q ss_pred ceecCccCccccChhhHHHHHHh--ccC----------------------------------------------------
Q psy16834 123 LFDCHICGKTVVTEKNYKKHMQL--HSD---------------------------------------------------- 148 (488)
Q Consensus 123 ~~~C~~C~~~f~~~~~l~~H~~~--H~~---------------------------------------------------- 148 (488)
.+.|-.|.+.|.++..|+.||+. |..
T Consensus 195 r~~CLyCekifrdkntLkeHMrkK~HrrinPknreYDkfyiINY~ev~ks~t~~~~e~dret~~d~~E~D~~wsDw~ed~ 274 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRKKRHRRINPKNREYDKFYIINYLEVGKSWTIVHSEDDRETNEDINETDDTWSDWNEDD 274 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHhccCcccCCCccccceEEEEeHhhcCCccchhhhhhhhhhhccccccccchhhhhcCC
Confidence 48899999999999999999973 210
Q ss_pred CCc--eeCccccccccchhhHHhHhhhccCCCCceecccchhhhhcccCCCCCCcCCCCccccccccccccChhHHHHHH
Q psy16834 149 DKP--FECQFCRKAFKLKYYLTLHLRTHTGVRPMFECDICHKVLKTKSKKSSGISKNENLRPCTLCDKKLASERKLKEHI 226 (488)
Q Consensus 149 ~~~--~~C~~C~~~F~~~~~L~~H~~~h~~~~~~~~C~~C~~~f~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~L~~H~ 226 (488)
..+ ..|-.|.....+...|..||++-+.-.-.-.-+.-+-.|..+-.+..-+......-.|-.|+-.|..+..|..||
T Consensus 275 a~a~~v~CLfC~~~~en~~~l~eHmk~vHe~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c~~cd~~F~~e~~l~~hm 354 (423)
T KOG2482|consen 275 AEALSVVCLFCTNFYENPVFLFEHMKIVHEFDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCAECDLSFWKEPGLLIHM 354 (423)
T ss_pred CCccceEEEeeccchhhHHHHHHHHHHHHHhhHHhhccccccchhhhhhHHHHHHHHhhccccccccccccCcchhhhhc
Confidence 011 578888888888888888887654321100000000000000000000111122346899999999999999999
Q ss_pred hhcCC
Q psy16834 227 RKQHP 231 (488)
Q Consensus 227 ~~~h~ 231 (488)
...-+
T Consensus 355 ~e~k~ 359 (423)
T KOG2482|consen 355 VEDKH 359 (423)
T ss_pred ccccc
Confidence 76543
No 58
>KOG2785|consensus
Probab=95.08 E-value=0.082 Score=49.32 Aligned_cols=66 Identities=24% Similarity=0.378 Sum_probs=49.2
Q ss_pred CccccccccccccChhHHHHHHhhcCCCCchhh--------hHhhh-hcccCCCCCcchH---HhhcCHHHHHHHHhh
Q psy16834 205 NLRPCTLCDKKLASERKLKEHIRKQHPTSVEAD--------LIRRE-KYEREKVQCPYCA---KFLSRKEKLNRHIRT 270 (488)
Q Consensus 205 ~~~~C~~C~~~f~~~~~L~~H~~~~h~~~~~~~--------~~~~~-~~~~~~~~C~~C~---~~f~~~~~L~~H~~~ 270 (488)
.|-.|-.|++.+.+...-..||...|.+-.+.. ++... ..-...+.|-.|+ +.|.+....+.||..
T Consensus 165 ~Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 165 IPTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred CCcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhh
Confidence 356799999999999999999999998654321 11111 0123457788898 999999999999975
No 59
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=95.00 E-value=0.0088 Score=59.94 Aligned_cols=150 Identities=22% Similarity=0.383 Sum_probs=92.7
Q ss_pred cccCCCCCCccCChHHHHHHHH--hhcCC--Cccccc--cccccccChhHHHHHHhhhcCCCCCccCCc--cCCcCCCch
Q psy16834 332 KVLCPICGYGCFRNAELEEHFI--SAHSA--DRFKCV--FCEKSFARNCNLKLHIRRYHDKSDNTECPL--CGKSFPSRG 403 (488)
Q Consensus 332 ~~~C~~C~~~f~~~~~l~~H~~--~~~~~--~~~~C~--~C~k~F~~~~~l~~H~~~~H~~~~~~~C~~--C~k~F~~~~ 403 (488)
++.|..|...|.....|..|.. .+.++ .++.|+ .|++.|.+...+..|.. .|.+..++.+.. +...+....
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~ 367 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHIL-LHTSISPAKEKLLNSSSKFSPLL 367 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcc-cccCCCccccccccCcccccccc
Confidence 4566667777777777766666 45556 667776 57777777777777764 455555554433 222222222
Q ss_pred H-----HHhhhhhhccCCcccccc--cccccCChHHHHHHHHhhcCCC--CcCCcchhhccCChhhHhccccccccCcCc
Q psy16834 404 R-----LNEHLIQVHPAQKHQCHI--CNKIVVSEKTLKKHLLLHTNSE--PFHCPECGKAFKFKRYVTLHMRTHTGNWPT 474 (488)
Q Consensus 404 ~-----L~~H~~~~h~~~~~~C~~--C~k~f~~~~~L~~H~~~H~~~~--~~~C~~C~~~F~~~~~L~~H~~~H~~~~~~ 474 (488)
. .............+.+.. |...+.....+..|...|...+ .+.+..|++.|.....|..|++.|....+
T Consensus 368 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~- 446 (467)
T COG5048 368 NNEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITHLSFRPYNCKNPPCSKSFNRHYNLIPHKKIHTNHAP- 446 (467)
T ss_pred CCCCccchhhccCccCCccccccccchhhhhccccccccccccccccCCcCCCCCcchhhccCcccccccccccccCCc-
Confidence 2 011111112223444433 6677777777778877777665 57778899999999999999999887765
Q ss_pred cccccCccc
Q psy16834 475 FVCKICNAT 483 (488)
Q Consensus 475 ~~C~~C~k~ 483 (488)
+.|..++..
T Consensus 447 ~~~~~~~~~ 455 (467)
T COG5048 447 LLCSILKSF 455 (467)
T ss_pred eeecccccc
Confidence 555555443
No 60
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=94.54 E-value=0.03 Score=30.37 Aligned_cols=18 Identities=33% Similarity=0.724 Sum_probs=9.0
Q ss_pred cccccccccCChHHHHHHH
Q psy16834 419 QCHICNKIVVSEKTLKKHL 437 (488)
Q Consensus 419 ~C~~C~k~f~~~~~L~~H~ 437 (488)
+|++||+.| ....|.+|+
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 444455554
No 61
>KOG4173|consensus
Probab=94.11 E-value=0.031 Score=46.98 Aligned_cols=86 Identities=26% Similarity=0.482 Sum_probs=64.2
Q ss_pred CCcccCCc--ccccccchhhHHHHHHhhcCCCccccCccccCcCCChHHHHHHHHhhh----------CCCCccC--CCC
Q psy16834 8 TEKFSCSL--CSYSVTIKRNLIMHIKRKHTDEFSILCPECGRGFFNEKELAAHKIEIH----------GADPFLC--IPC 73 (488)
Q Consensus 8 ~~~~~C~~--C~~~f~~~~~L~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~h----------~~~~~~C--~~C 73 (488)
...|.|.+ |...|........|....|+. .|.+|.+.|.+...|..|+..-| |.+.|.| +.|
T Consensus 77 ~~~~~cqvagc~~~~d~lD~~E~hY~~~h~~----sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgC 152 (253)
T KOG4173|consen 77 VPAFACQVAGCCQVFDALDDYEHHYHTLHGN----SCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGC 152 (253)
T ss_pred cccccccccchHHHHhhhhhHHHhhhhcccc----hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhh
Confidence 34577876 777888888888887666654 59999999999999999887655 4556788 568
Q ss_pred CCccCChhhHHHHHhhhccCCCcc
Q psy16834 74 NKPFSKIENYRLHQRRYHLNSVNK 97 (488)
Q Consensus 74 ~~~f~~~~~l~~H~~~~h~~~~~~ 97 (488)
+..|.+...-..|+-..|.-...|
T Consensus 153 t~KFkT~r~RkdH~I~~Hk~Pa~f 176 (253)
T KOG4173|consen 153 TEKFKTSRDRKDHMIRMHKYPADF 176 (253)
T ss_pred hhhhhhhhhhhhHHHHhccCCcce
Confidence 888888888888887666544333
No 62
>KOG4173|consensus
Probab=93.86 E-value=0.03 Score=47.05 Aligned_cols=44 Identities=27% Similarity=0.578 Sum_probs=21.1
Q ss_pred CCCccCChHHHHHHHHhhcCCCccccccccccccChhHHHHHHhhhc
Q psy16834 338 CGYGCFRNAELEEHFISAHSADRFKCVFCEKSFARNCNLKLHIRRYH 384 (488)
Q Consensus 338 C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~k~F~~~~~l~~H~~~~H 384 (488)
|...|......+.|...-|+. .|.+|.+.|.+...|..||..+|
T Consensus 87 c~~~~d~lD~~E~hY~~~h~~---sCs~C~r~~Pt~hLLd~HI~E~H 130 (253)
T KOG4173|consen 87 CCQVFDALDDYEHHYHTLHGN---SCSFCKRAFPTGHLLDAHILEWH 130 (253)
T ss_pred hHHHHhhhhhHHHhhhhcccc---hhHHHHHhCCchhhhhHHHHHHH
Confidence 334444444444443333332 45555555555555555554444
No 63
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=93.79 E-value=0.051 Score=29.48 Aligned_cols=19 Identities=32% Similarity=0.796 Sum_probs=10.4
Q ss_pred ecCccCccccChhhHHHHHH
Q psy16834 125 DCHICGKTVVTEKNYKKHMQ 144 (488)
Q Consensus 125 ~C~~C~~~f~~~~~l~~H~~ 144 (488)
.|++||++| ..+.|.+|+.
T Consensus 4 ~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred cCCCCCCEE-CHHHHHHHHH
Confidence 455566555 4555555543
No 64
>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=93.18 E-value=0.067 Score=31.76 Aligned_cols=22 Identities=27% Similarity=0.593 Sum_probs=13.7
Q ss_pred cccccccccccCChHHHHHHHH
Q psy16834 417 KHQCHICNKIVVSEKTLKKHLL 438 (488)
Q Consensus 417 ~~~C~~C~k~f~~~~~L~~H~~ 438 (488)
+|.|++|++.|.+..++..|+.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 4556666666666666666653
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=92.92 E-value=0.069 Score=31.71 Aligned_cols=22 Identities=23% Similarity=0.745 Sum_probs=13.2
Q ss_pred ccccccccccccChhHHHHHHh
Q psy16834 360 RFKCVFCEKSFARNCNLKLHIR 381 (488)
Q Consensus 360 ~~~C~~C~k~F~~~~~l~~H~~ 381 (488)
+|.|++|++.|.+...+..|++
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 4556666666666666666653
No 66
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=92.70 E-value=0.037 Score=55.44 Aligned_cols=57 Identities=28% Similarity=0.603 Sum_probs=47.5
Q ss_pred CceecCccCccccChhhHHHHHHhccCCCceeCcc--ccccccchhhHHhHhhhccCCC
Q psy16834 122 KLFDCHICGKTVVTEKNYKKHMQLHSDDKPFECQF--CRKAFKLKYYLTLHLRTHTGVR 178 (488)
Q Consensus 122 ~~~~C~~C~~~f~~~~~l~~H~~~H~~~~~~~C~~--C~~~F~~~~~L~~H~~~h~~~~ 178 (488)
..+.|+.|...|........|.+.+.+++++.|.. |...|.....+.+|.+.+....
T Consensus 32 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 90 (467)
T COG5048 32 RPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSRPLELSRHLRTHHNNP 90 (467)
T ss_pred chhhcccccccccccchhhhhcccccccCCccccccccccccCCcchhhhhcccccccc
Confidence 46789999999999999999999999999999975 6777888888888888776543
No 67
>KOG2893|consensus
Probab=92.37 E-value=0.032 Score=47.98 Aligned_cols=47 Identities=28% Similarity=0.647 Sum_probs=40.4
Q ss_pred CCcchHHhhcCHHHHHHHHhhhccCceeecccccccccCHHHHHhH-Hhhhc
Q psy16834 250 QCPYCAKFLSRKEKLNRHIRTVHTDVNYKCEICGEEFLSKTRYNRH-VVTHE 300 (488)
Q Consensus 250 ~C~~C~~~f~~~~~L~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H-~~~H~ 300 (488)
-|.+|++.|.....|.+|.+..| |+|.+|-+...+--.|..| |++|.
T Consensus 12 wcwycnrefddekiliqhqkakh----fkchichkkl~sgpglsihcmqvhk 59 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQKAKH----FKCHICHKKLFSGPGLSIHCMQVHK 59 (341)
T ss_pred eeeecccccchhhhhhhhhhhcc----ceeeeehhhhccCCCceeehhhhhh
Confidence 49999999999999999988655 9999999998888888888 45553
No 68
>KOG2893|consensus
Probab=91.59 E-value=0.049 Score=46.93 Aligned_cols=45 Identities=31% Similarity=0.648 Sum_probs=26.3
Q ss_pred CCccCCcCCCchHHHhhhhhhccCCcccccccccccCChHHHHHH-HHhh
Q psy16834 392 CPLCGKSFPSRGRLNEHLIQVHPAQKHQCHICNKIVVSEKTLKKH-LLLH 440 (488)
Q Consensus 392 C~~C~k~F~~~~~L~~H~~~~h~~~~~~C~~C~k~f~~~~~L~~H-~~~H 440 (488)
|-+|++.|.....|.+|++. +-|+|.+|.|...+--.|..| |.+|
T Consensus 13 cwycnrefddekiliqhqka----khfkchichkkl~sgpglsihcmqvh 58 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQKA----KHFKCHICHKKLFSGPGLSIHCMQVH 58 (341)
T ss_pred eeecccccchhhhhhhhhhh----ccceeeeehhhhccCCCceeehhhhh
Confidence 56666666666666665443 346666666666565555555 4444
No 69
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=91.57 E-value=0.44 Score=36.62 Aligned_cols=46 Identities=13% Similarity=0.226 Sum_probs=28.5
Q ss_pred cccchhhhhcccCCCCCCcCCCCccccccccccccChhHHHHHHhh
Q psy16834 183 CDICHKVLKTKSKKSSGISKNENLRPCTLCDKKLASERKLKEHIRK 228 (488)
Q Consensus 183 C~~C~~~f~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~L~~H~~~ 228 (488)
|--|...|........+.......|.|+.|...|-..-++..|...
T Consensus 58 C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~L 103 (112)
T TIGR00622 58 CFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHESL 103 (112)
T ss_pred ccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhhc
Confidence 6666666655432222223334568888888888877777777544
No 70
>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=91.53 E-value=0.087 Score=30.83 Aligned_cols=10 Identities=50% Similarity=1.467 Sum_probs=4.6
Q ss_pred CCcCCcchhh
Q psy16834 444 EPFHCPECGK 453 (488)
Q Consensus 444 ~~~~C~~C~~ 453 (488)
.|+.||+||.
T Consensus 16 ~~~~CP~Cg~ 25 (33)
T cd00350 16 APWVCPVCGA 25 (33)
T ss_pred CCCcCcCCCC
Confidence 3444555543
No 71
>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=89.68 E-value=0.23 Score=29.02 Aligned_cols=24 Identities=29% Similarity=0.850 Sum_probs=14.3
Q ss_pred eecCccCccccChhhHHHHHHhccCCCceeCccccc
Q psy16834 124 FDCHICGKTVVTEKNYKKHMQLHSDDKPFECQFCRK 159 (488)
Q Consensus 124 ~~C~~C~~~f~~~~~l~~H~~~H~~~~~~~C~~C~~ 159 (488)
|.|.+||..+.... .++.|++|+.
T Consensus 2 ~~C~~CGy~y~~~~------------~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGEE------------APWVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCCc------------CCCcCcCCCC
Confidence 56667766654332 5566777764
No 72
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=88.21 E-value=0.45 Score=36.57 Aligned_cols=22 Identities=14% Similarity=0.289 Sum_probs=15.7
Q ss_pred CCccccccccccccChhHHHHH
Q psy16834 358 ADRFKCVFCEKSFARNCNLKLH 379 (488)
Q Consensus 358 ~~~~~C~~C~k~F~~~~~l~~H 379 (488)
+-|-.|++||-+......|.+-
T Consensus 13 ~LP~~CpiCgLtLVss~HLARS 34 (112)
T TIGR00622 13 ELPVECPICGLTLILSTHLARS 34 (112)
T ss_pred CCCCcCCcCCCEEeccchHHHh
Confidence 3467788888777777777764
No 73
>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=87.40 E-value=0.31 Score=28.73 Aligned_cols=10 Identities=40% Similarity=1.128 Sum_probs=5.9
Q ss_pred cCCcchhhcc
Q psy16834 446 FHCPECGKAF 455 (488)
Q Consensus 446 ~~C~~C~~~F 455 (488)
|.|.+||..+
T Consensus 3 ~~C~~CG~i~ 12 (34)
T cd00729 3 WVCPVCGYIH 12 (34)
T ss_pred EECCCCCCEe
Confidence 5666666543
No 74
>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=85.12 E-value=0.46 Score=28.78 Aligned_cols=34 Identities=21% Similarity=0.443 Sum_probs=19.4
Q ss_pred cCCcchhhccCChhhHhccccccccCcCccccccCccccc
Q psy16834 446 FHCPECGKAFKFKRYVTLHMRTHTGNWPTFVCKICNATIS 485 (488)
Q Consensus 446 ~~C~~C~~~F~~~~~L~~H~~~H~~~~~~~~C~~C~k~f~ 485 (488)
+.|+.|+..|.-..+... ++.....|+.||..|.
T Consensus 3 ~~CP~C~~~~~v~~~~~~------~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLG------ANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHcC------CCCCEEECCCCCCEEE
Confidence 467777777765554432 1111367777777664
No 75
>KOG2186|consensus
Probab=84.92 E-value=0.41 Score=42.06 Aligned_cols=46 Identities=28% Similarity=0.691 Sum_probs=25.8
Q ss_pred ccCCCCCCccCChHHHHHHHHhhcCCCccccccccccccChhHHHHHHh
Q psy16834 333 VLCPICGYGCFRNAELEEHFISAHSADRFKCVFCEKSFARNCNLKLHIR 381 (488)
Q Consensus 333 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~k~F~~~~~l~~H~~ 381 (488)
|.|.+||....- ..+..|+..-++ .-|.|-.|+++|.. .++..|..
T Consensus 4 FtCnvCgEsvKK-p~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 4 FTCNVCGESVKK-PQVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred Eehhhhhhhccc-cchHHHHHhccC-CeeEEeeccccccc-chhhhhhh
Confidence 456666665433 334446655555 45666666666665 55556654
No 76
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=84.92 E-value=0.55 Score=30.40 Aligned_cols=28 Identities=32% Similarity=0.561 Sum_probs=14.8
Q ss_pred CCccccCccccCcCCChHHHHHHHHhhh
Q psy16834 36 DEFSILCPECGRGFFNEKELAAHKIEIH 63 (488)
Q Consensus 36 ~~~~~~C~~C~~~f~~~~~l~~H~~~~h 63 (488)
+|.-+.|+-||..|....++.+|....|
T Consensus 14 GE~~lrCPRC~~~FR~~K~Y~RHVNKaH 41 (65)
T COG4049 14 GEEFLRCPRCGMVFRRRKDYIRHVNKAH 41 (65)
T ss_pred CceeeeCCchhHHHHHhHHHHHHhhHHh
Confidence 4444555555555555555555554444
No 77
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=83.52 E-value=0.58 Score=30.30 Aligned_cols=28 Identities=25% Similarity=0.560 Sum_probs=13.8
Q ss_pred CCCCccCCCCCCccCChhhHHHHHhhhc
Q psy16834 64 GADPFLCIPCNKPFSKIENYRLHQRRYH 91 (488)
Q Consensus 64 ~~~~~~C~~C~~~f~~~~~l~~H~~~~h 91 (488)
|+.-+.|+-|++.|....++.+|+...|
T Consensus 14 GE~~lrCPRC~~~FR~~K~Y~RHVNKaH 41 (65)
T COG4049 14 GEEFLRCPRCGMVFRRRKDYIRHVNKAH 41 (65)
T ss_pred CceeeeCCchhHHHHHhHHHHHHhhHHh
Confidence 4444455555555555555555544333
No 78
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=82.36 E-value=0.35 Score=42.80 Aligned_cols=19 Identities=21% Similarity=0.412 Sum_probs=10.1
Q ss_pred ccccccccccccChhHHHH
Q psy16834 360 RFKCVFCEKSFARNCNLKL 378 (488)
Q Consensus 360 ~~~C~~C~k~F~~~~~l~~ 378 (488)
.+.|++|++.|.++.-+..
T Consensus 5 ~~~CPvC~~~F~~~~vrs~ 23 (214)
T PF09986_consen 5 KITCPVCGKEFKTKKVRSG 23 (214)
T ss_pred ceECCCCCCeeeeeEEEcC
Confidence 4556666666665543333
No 79
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=81.11 E-value=1.1 Score=34.66 Aligned_cols=30 Identities=33% Similarity=0.916 Sum_probs=17.7
Q ss_pred ccCccccCcCCChHHHHHHHHhhhCCCCccCCCCCCccCCh
Q psy16834 40 ILCPECGRGFFNEKELAAHKIEIHGADPFLCIPCNKPFSKI 80 (488)
Q Consensus 40 ~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~C~~C~~~f~~~ 80 (488)
..|+.||.+|... +..|..|+.||..|.-.
T Consensus 10 R~Cp~CG~kFYDL-----------nk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFYDL-----------NKDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchhccC-----------CCCCccCCCCCCccCcc
Confidence 3567777766531 23566677777666543
No 80
>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=79.92 E-value=1 Score=34.70 Aligned_cols=29 Identities=24% Similarity=0.456 Sum_probs=17.8
Q ss_pred ccCCCCCCccCChhhHHHHHhhhccCCCccccccchhhccc
Q psy16834 68 FLCIPCNKPFSKIENYRLHQRRYHLNSVNKECKICHKVLRT 108 (488)
Q Consensus 68 ~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~ 108 (488)
..|+.||+.|- -++..|..|+.||..|..
T Consensus 10 R~Cp~CG~kFY------------DLnk~PivCP~CG~~~~~ 38 (108)
T PF09538_consen 10 RTCPSCGAKFY------------DLNKDPIVCPKCGTEFPP 38 (108)
T ss_pred ccCCCCcchhc------------cCCCCCccCCCCCCccCc
Confidence 46888887773 444455566666665543
No 81
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=78.99 E-value=1.6 Score=36.02 Aligned_cols=14 Identities=14% Similarity=0.199 Sum_probs=7.4
Q ss_pred cccccccccccCCh
Q psy16834 417 KHQCHICNKIVVSE 430 (488)
Q Consensus 417 ~~~C~~C~k~f~~~ 430 (488)
-|.|+.|+..|...
T Consensus 99 ~Y~Cp~C~~~y~~~ 112 (147)
T smart00531 99 YYKCPNCQSKYTFL 112 (147)
T ss_pred EEECcCCCCEeeHH
Confidence 45555555555543
No 82
>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=78.67 E-value=3.3 Score=32.21 Aligned_cols=24 Identities=21% Similarity=0.533 Sum_probs=17.1
Q ss_pred ccccccccccccChhHHHHHHhhhc
Q psy16834 360 RFKCVFCEKSFARNCNLKLHIRRYH 384 (488)
Q Consensus 360 ~~~C~~C~k~F~~~~~l~~H~~~~H 384 (488)
...|..|+....- +.+..|++..|
T Consensus 11 vlIC~~C~~av~~-~~v~~HL~~~H 34 (109)
T PF12013_consen 11 VLICRQCQYAVQP-SEVESHLRKRH 34 (109)
T ss_pred EEEeCCCCcccCc-hHHHHHHHHhc
Confidence 3568888877665 77888887544
No 83
>KOG2186|consensus
Probab=78.42 E-value=1.1 Score=39.59 Aligned_cols=46 Identities=28% Similarity=0.691 Sum_probs=22.5
Q ss_pred cccccchhhccchhHHHHHHHHhcCCceecCccCccccChhhHHHHHH
Q psy16834 97 KECKICHKVLRTARLSEHMKQVHYAKLFDCHICGKTVVTEKNYKKHMQ 144 (488)
Q Consensus 97 ~~C~~C~~~f~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~ 144 (488)
|.|..||.......+..|+-.-++ .-|.|-.|+++|.. .++..|..
T Consensus 4 FtCnvCgEsvKKp~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 4 FTCNVCGESVKKPQVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred EehhhhhhhccccchHHHHHhccC-CeeEEeeccccccc-chhhhhhh
Confidence 345555555444444444444433 33555555555554 44455543
No 84
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=78.10 E-value=0.57 Score=41.45 Aligned_cols=44 Identities=20% Similarity=0.533 Sum_probs=27.8
Q ss_pred CCCccCCccCCcCCCchHHHhhhhhhcc----------CCc-----ccccccccccCCh
Q psy16834 387 SDNTECPLCGKSFPSRGRLNEHLIQVHP----------AQK-----HQCHICNKIVVSE 430 (488)
Q Consensus 387 ~~~~~C~~C~k~F~~~~~L~~H~~~~h~----------~~~-----~~C~~C~k~f~~~ 430 (488)
++...||+|++.|.+..-+....+.... ..| ..|+.||.+|...
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 3567899999999887665555443211 112 4688887776544
No 85
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=78.07 E-value=1.3 Score=32.05 Aligned_cols=30 Identities=33% Similarity=0.770 Sum_probs=14.8
Q ss_pred CcCCcchhhccCChhhHhccccccccCcCccccccCccccc
Q psy16834 445 PFHCPECGKAFKFKRYVTLHMRTHTGNWPTFVCKICNATIS 485 (488)
Q Consensus 445 ~~~C~~C~~~F~~~~~L~~H~~~H~~~~~~~~C~~C~k~f~ 485 (488)
+|.||.|++. .+.|+-+|- +.|..||..|.
T Consensus 35 ~~~Cp~C~~~--------~VkR~a~GI---W~C~kCg~~fA 64 (89)
T COG1997 35 KHVCPFCGRT--------TVKRIATGI---WKCRKCGAKFA 64 (89)
T ss_pred CCcCCCCCCc--------ceeeeccCe---EEcCCCCCeec
Confidence 4555555553 233444443 45666655553
No 86
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=77.53 E-value=1.4 Score=27.74 Aligned_cols=11 Identities=45% Similarity=0.927 Sum_probs=5.2
Q ss_pred ccCccccCcCC
Q psy16834 40 ILCPECGRGFF 50 (488)
Q Consensus 40 ~~C~~C~~~f~ 50 (488)
|.|..||..|.
T Consensus 3 Y~C~~Cg~~~~ 13 (44)
T smart00659 3 YICGECGRENE 13 (44)
T ss_pred EECCCCCCEee
Confidence 44555554443
No 87
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=77.45 E-value=1.7 Score=25.95 Aligned_cols=10 Identities=40% Similarity=1.162 Sum_probs=4.1
Q ss_pred ccCCccCCcC
Q psy16834 390 TECPLCGKSF 399 (488)
Q Consensus 390 ~~C~~C~k~F 399 (488)
.+|+.||..|
T Consensus 26 v~C~~C~~~f 35 (36)
T PF13717_consen 26 VRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEe
Confidence 3444444433
No 88
>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=76.96 E-value=1.3 Score=24.21 Aligned_cols=10 Identities=30% Similarity=0.746 Sum_probs=5.8
Q ss_pred cccccccccc
Q psy16834 362 KCVFCEKSFA 371 (488)
Q Consensus 362 ~C~~C~k~F~ 371 (488)
.|+.||..|.
T Consensus 16 ~Cp~CG~~F~ 25 (26)
T PF10571_consen 16 FCPHCGYDFE 25 (26)
T ss_pred cCCCCCCCCc
Confidence 4666666553
No 89
>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=76.77 E-value=2 Score=27.08 Aligned_cols=26 Identities=35% Similarity=0.746 Sum_probs=14.2
Q ss_pred CccccccccccccC----hhHHHHHHhhhc
Q psy16834 359 DRFKCVFCEKSFAR----NCNLKLHIRRYH 384 (488)
Q Consensus 359 ~~~~C~~C~k~F~~----~~~l~~H~~~~H 384 (488)
....|.+|++.+.. .++|.+|+++.|
T Consensus 15 ~~a~C~~C~~~~~~~~~~ts~l~~HL~~~h 44 (45)
T PF02892_consen 15 KKAKCKYCGKVIKYSSGGTSNLKRHLKKKH 44 (45)
T ss_dssp S-EEETTTTEE-----SSTHHHHHHHHHTT
T ss_pred CeEEeCCCCeEEeeCCCcHHHHHHhhhhhC
Confidence 44567777777665 367777775443
No 90
>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=76.49 E-value=2 Score=27.05 Aligned_cols=28 Identities=36% Similarity=0.687 Sum_probs=16.5
Q ss_pred CCCcccCCcccccccch----hhHHHHHHhhc
Q psy16834 7 DTEKFSCSLCSYSVTIK----RNLIMHIKRKH 34 (488)
Q Consensus 7 ~~~~~~C~~C~~~f~~~----~~L~~H~~~~h 34 (488)
+.....|.+|++.+... .+|.+|++..|
T Consensus 13 ~~~~a~C~~C~~~~~~~~~~ts~l~~HL~~~h 44 (45)
T PF02892_consen 13 DKKKAKCKYCGKVIKYSSGGTSNLKRHLKKKH 44 (45)
T ss_dssp CSS-EEETTTTEE-----SSTHHHHHHHHHTT
T ss_pred CcCeEEeCCCCeEEeeCCCcHHHHHHhhhhhC
Confidence 44567888888877653 67888875544
No 91
>PF14353 CpXC: CpXC protein
Probab=76.20 E-value=1.1 Score=36.01 Aligned_cols=12 Identities=25% Similarity=0.822 Sum_probs=5.7
Q ss_pred ccccccCccccc
Q psy16834 474 TFVCKICNATIS 485 (488)
Q Consensus 474 ~~~C~~C~k~f~ 485 (488)
.|.|+.||+.|.
T Consensus 38 ~~~CP~Cg~~~~ 49 (128)
T PF14353_consen 38 SFTCPSCGHKFR 49 (128)
T ss_pred EEECCCCCCcee
Confidence 344555554443
No 92
>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=75.61 E-value=1 Score=27.73 Aligned_cols=13 Identities=31% Similarity=1.150 Sum_probs=7.7
Q ss_pred cCCcchhhccCCh
Q psy16834 446 FHCPECGKAFKFK 458 (488)
Q Consensus 446 ~~C~~C~~~F~~~ 458 (488)
|+|+.||..|...
T Consensus 6 y~C~~Cg~~fe~~ 18 (41)
T smart00834 6 YRCEDCGHTFEVL 18 (41)
T ss_pred EEcCCCCCEEEEE
Confidence 5666666666533
No 93
>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=75.24 E-value=4.9 Score=31.22 Aligned_cols=26 Identities=23% Similarity=0.593 Sum_probs=19.2
Q ss_pred CccccccccccccChhHHHHHHhhcCC
Q psy16834 205 NLRPCTLCDKKLASERKLKEHIRKQHP 231 (488)
Q Consensus 205 ~~~~C~~C~~~f~~~~~L~~H~~~~h~ 231 (488)
....|..|+..... +++..|++..|.
T Consensus 10 ~vlIC~~C~~av~~-~~v~~HL~~~H~ 35 (109)
T PF12013_consen 10 RVLICRQCQYAVQP-SEVESHLRKRHH 35 (109)
T ss_pred CEEEeCCCCcccCc-hHHHHHHHHhcc
Confidence 34568888877665 889999996654
No 94
>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=74.76 E-value=1.4 Score=27.45 Aligned_cols=29 Identities=28% Similarity=0.754 Sum_probs=14.9
Q ss_pred cccccccccccChhHHHHHHhhhcCCCCCccCCccCC
Q psy16834 361 FKCVFCEKSFARNCNLKLHIRRYHDKSDNTECPLCGK 397 (488)
Q Consensus 361 ~~C~~C~k~F~~~~~l~~H~~~~H~~~~~~~C~~C~k 397 (488)
|.|..||..|..... ... ..+..|+.||.
T Consensus 6 y~C~~Cg~~fe~~~~-------~~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEECGHEFEVLQS-------ISE-DDPVPCPECGS 34 (42)
T ss_pred EEeCCCCCEEEEEEE-------cCC-CCCCcCCCCCC
Confidence 556666666654321 122 34556666665
No 95
>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=73.84 E-value=2.7 Score=35.16 Aligned_cols=30 Identities=20% Similarity=0.423 Sum_probs=16.7
Q ss_pred CcccccccccccCChHHHHHHHHhhcCCCCcCCcchhhc
Q psy16834 416 QKHQCHICNKIVVSEKTLKKHLLLHTNSEPFHCPECGKA 454 (488)
Q Consensus 416 ~~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~~C~~C~~~ 454 (488)
.-|.|+.|+..|+.-.++. --|.||.||..
T Consensus 108 ~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~ 137 (158)
T TIGR00373 108 MFFICPNMCVRFTFNEAME---------LNFTCPRCGAM 137 (158)
T ss_pred CeEECCCCCcEeeHHHHHH---------cCCcCCCCCCE
Confidence 3466666666666555553 14666666554
No 96
>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=73.69 E-value=3.4 Score=22.58 Aligned_cols=19 Identities=21% Similarity=0.515 Sum_probs=11.6
Q ss_pred cCCCCCCccCChHHHHHHHH
Q psy16834 334 LCPICGYGCFRNAELEEHFI 353 (488)
Q Consensus 334 ~C~~C~~~f~~~~~l~~H~~ 353 (488)
.||+|++.+ ....+..|+.
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 577777766 4455666653
No 97
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=72.69 E-value=3.6 Score=24.74 Aligned_cols=11 Identities=27% Similarity=0.791 Sum_probs=5.1
Q ss_pred ceeCccccccc
Q psy16834 151 PFECQFCRKAF 161 (488)
Q Consensus 151 ~~~C~~C~~~F 161 (488)
..+|+.|+..|
T Consensus 25 ~vrC~~C~~~f 35 (37)
T PF13719_consen 25 KVRCPKCGHVF 35 (37)
T ss_pred EEECCCCCcEe
Confidence 34444444444
No 98
>PHA00626 hypothetical protein
Probab=72.61 E-value=0.84 Score=29.73 Aligned_cols=15 Identities=20% Similarity=0.574 Sum_probs=8.8
Q ss_pred CccccccccccccCh
Q psy16834 359 DRFKCVFCEKSFARN 373 (488)
Q Consensus 359 ~~~~C~~C~k~F~~~ 373 (488)
.+|.|+.||..|+..
T Consensus 22 nrYkCkdCGY~ft~~ 36 (59)
T PHA00626 22 DDYVCCDCGYNDSKD 36 (59)
T ss_pred cceEcCCCCCeechh
Confidence 356666666666543
No 99
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=72.01 E-value=2.3 Score=35.12 Aligned_cols=37 Identities=14% Similarity=0.341 Sum_probs=19.2
Q ss_pred CCCccCCccCCcCCCchHHHhhhhhhccCCccccccccccc
Q psy16834 387 SDNTECPLCGKSFPSRGRLNEHLIQVHPAQKHQCHICNKIV 427 (488)
Q Consensus 387 ~~~~~C~~C~k~F~~~~~L~~H~~~~h~~~~~~C~~C~k~f 427 (488)
..-|.||.||..|.....+.. ......|.|+.||...
T Consensus 97 ~~~Y~Cp~C~~~y~~~ea~~~----~d~~~~f~Cp~Cg~~l 133 (147)
T smart00531 97 NAYYKCPNCQSKYTFLEANQL----LDMDGTFTCPRCGEEL 133 (147)
T ss_pred CcEEECcCCCCEeeHHHHHHh----cCCCCcEECCCCCCEE
Confidence 345667777777764443321 0112336666666543
No 100
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=71.82 E-value=2.3 Score=35.50 Aligned_cols=10 Identities=50% Similarity=1.481 Sum_probs=6.0
Q ss_pred cccCCCCCCc
Q psy16834 332 KVLCPICGYG 341 (488)
Q Consensus 332 ~~~C~~C~~~ 341 (488)
.|.|++||..
T Consensus 134 ~~vC~vCGy~ 143 (166)
T COG1592 134 VWVCPVCGYT 143 (166)
T ss_pred EEEcCCCCCc
Confidence 4566666654
No 101
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=71.78 E-value=3 Score=27.03 Aligned_cols=24 Identities=46% Similarity=0.957 Sum_probs=14.5
Q ss_pred cccccccccccCh-----hHHHHHHhhhc
Q psy16834 361 FKCVFCEKSFARN-----CNLKLHIRRYH 384 (488)
Q Consensus 361 ~~C~~C~k~F~~~-----~~l~~H~~~~H 384 (488)
-.|..|++.+... ++|.+|++..|
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~~~h 47 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLRRKH 47 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHHhHC
Confidence 3566666666443 57777776444
No 102
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=71.78 E-value=2.1 Score=35.72 Aligned_cols=13 Identities=46% Similarity=1.094 Sum_probs=7.8
Q ss_pred hcCCCCcCCcchh
Q psy16834 440 HTNSEPFHCPECG 452 (488)
Q Consensus 440 H~~~~~~~C~~C~ 452 (488)
|.|+-|-+||+||
T Consensus 144 ~~ge~P~~CPiCg 156 (166)
T COG1592 144 HEGEAPEVCPICG 156 (166)
T ss_pred ccCCCCCcCCCCC
Confidence 3455666666666
No 103
>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=71.61 E-value=3 Score=34.87 Aligned_cols=32 Identities=16% Similarity=0.314 Sum_probs=19.1
Q ss_pred CCCCccCCccCCcCCCchHHHhhhhhhccCCcccccccccc
Q psy16834 386 KSDNTECPLCGKSFPSRGRLNEHLIQVHPAQKHQCHICNKI 426 (488)
Q Consensus 386 ~~~~~~C~~C~k~F~~~~~L~~H~~~~h~~~~~~C~~C~k~ 426 (488)
+..-|.|+.|+..|+....+. .-|.|+.||..
T Consensus 106 ~~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~ 137 (158)
T TIGR00373 106 NNMFFICPNMCVRFTFNEAME---------LNFTCPRCGAM 137 (158)
T ss_pred CCCeEECCCCCcEeeHHHHHH---------cCCcCCCCCCE
Confidence 344566666666666665553 14666666654
No 104
>KOG2272|consensus
Probab=69.73 E-value=4 Score=35.92 Aligned_cols=40 Identities=25% Similarity=0.500 Sum_probs=23.3
Q ss_pred ceecccchhhhhcccCCCCCCcCCCCccccccccccccCh
Q psy16834 180 MFECDICHKVLKTKSKKSSGISKNENLRPCTLCDKKLASE 219 (488)
Q Consensus 180 ~~~C~~C~~~f~~~~~~~~~~~~~~~~~~C~~C~~~f~~~ 219 (488)
.|.|..|..........-....-+..-|+|..|++...+.
T Consensus 137 ~YvC~KCh~~iD~~~l~fr~d~yH~yHFkCt~C~keL~sd 176 (332)
T KOG2272|consen 137 RYVCQKCHAHIDEQPLTFRGDPYHPYHFKCTTCGKELTSD 176 (332)
T ss_pred eeehhhhhhhcccccccccCCCCCccceecccccccccch
Confidence 4777777766655322222333344556788888876543
No 105
>PF12907 zf-met2: Zinc-binding
Probab=68.06 E-value=3.3 Score=25.35 Aligned_cols=32 Identities=22% Similarity=0.425 Sum_probs=21.2
Q ss_pred ccCCccccccc---chhhHHHHHHhhcCCCccccC
Q psy16834 11 FSCSLCSYSVT---IKRNLIMHIKRKHTDEFSILC 42 (488)
Q Consensus 11 ~~C~~C~~~f~---~~~~L~~H~~~~h~~~~~~~C 42 (488)
+.|.+|-.+|. +...|..|...+|....+-.|
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKHpK~~~~~C 36 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKHPKNTFEEC 36 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccCCCCCHHHc
Confidence 67888885553 446688888778876544333
No 106
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=67.38 E-value=2 Score=30.27 Aligned_cols=43 Identities=16% Similarity=0.344 Sum_probs=23.5
Q ss_pred ccccccccccCChHHHHHHHHhhcCCCCcCCc--chhhccCChhhHh
Q psy16834 418 HQCHICNKIVVSEKTLKKHLLLHTNSEPFHCP--ECGKAFKFKRYVT 462 (488)
Q Consensus 418 ~~C~~C~k~f~~~~~L~~H~~~H~~~~~~~C~--~C~~~F~~~~~L~ 462 (488)
+.|+.||..-....+-..... +.++-+.|. .||.+|.+...+.
T Consensus 2 m~CP~Cg~~a~irtSr~~s~~--~~~~Y~qC~N~eCg~tF~t~es~s 46 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYITDT--TKERYHQCQNVNCSATFITYESVQ 46 (72)
T ss_pred ccCCCCCCccEEEEChhcChh--hheeeeecCCCCCCCEEEEEEEEE
Confidence 457777765533333222211 445667776 7777777655443
No 107
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=67.38 E-value=3.9 Score=34.97 Aligned_cols=14 Identities=29% Similarity=0.501 Sum_probs=6.1
Q ss_pred ccCCccCCcCCCch
Q psy16834 390 TECPLCGKSFPSRG 403 (488)
Q Consensus 390 ~~C~~C~k~F~~~~ 403 (488)
|.|+.|+..|+...
T Consensus 118 Y~Cp~C~~rytf~e 131 (178)
T PRK06266 118 FFCPNCHIRFTFDE 131 (178)
T ss_pred EECCCCCcEEeHHH
Confidence 44444444444333
No 108
>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=66.68 E-value=1.8 Score=28.34 Aligned_cols=11 Identities=18% Similarity=0.546 Sum_probs=5.4
Q ss_pred ccccccccccC
Q psy16834 418 HQCHICNKIVV 428 (488)
Q Consensus 418 ~~C~~C~k~f~ 428 (488)
|.|..||..|.
T Consensus 6 y~C~~Cg~~fe 16 (52)
T TIGR02605 6 YRCTACGHRFE 16 (52)
T ss_pred EEeCCCCCEeE
Confidence 44555555443
No 109
>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=66.23 E-value=4 Score=23.62 Aligned_cols=7 Identities=29% Similarity=0.909 Sum_probs=3.0
Q ss_pred ccCCCCC
Q psy16834 68 FLCIPCN 74 (488)
Q Consensus 68 ~~C~~C~ 74 (488)
.+|+.||
T Consensus 18 irC~~CG 24 (32)
T PF03604_consen 18 IRCPECG 24 (32)
T ss_dssp SSBSSSS
T ss_pred EECCcCC
Confidence 3444444
No 110
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=65.60 E-value=5.1 Score=25.41 Aligned_cols=11 Identities=36% Similarity=1.093 Sum_probs=5.3
Q ss_pred eecCccCcccc
Q psy16834 124 FDCHICGKTVV 134 (488)
Q Consensus 124 ~~C~~C~~~f~ 134 (488)
|.|+.||..|.
T Consensus 4 y~C~~CG~~~~ 14 (46)
T PRK00398 4 YKCARCGREVE 14 (46)
T ss_pred EECCCCCCEEE
Confidence 44555554443
No 111
>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=64.37 E-value=4.2 Score=31.93 Aligned_cols=13 Identities=15% Similarity=0.245 Sum_probs=6.8
Q ss_pred CCccCCCCCCccC
Q psy16834 66 DPFLCIPCNKPFS 78 (488)
Q Consensus 66 ~~~~C~~C~~~f~ 78 (488)
.|..|+.||..|.
T Consensus 25 ~p~vcP~cg~~~~ 37 (129)
T TIGR02300 25 RPAVSPYTGEQFP 37 (129)
T ss_pred CCccCCCcCCccC
Confidence 4555555555543
No 112
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=64.16 E-value=1.3 Score=36.57 Aligned_cols=13 Identities=31% Similarity=0.692 Sum_probs=7.8
Q ss_pred cccccccccccCh
Q psy16834 361 FKCVFCEKSFARN 373 (488)
Q Consensus 361 ~~C~~C~k~F~~~ 373 (488)
++|+.||++|..-
T Consensus 29 ~~c~~c~~~f~~~ 41 (154)
T PRK00464 29 RECLACGKRFTTF 41 (154)
T ss_pred eeccccCCcceEe
Confidence 5666666666553
No 113
>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=63.94 E-value=5.1 Score=31.50 Aligned_cols=14 Identities=7% Similarity=0.142 Sum_probs=6.6
Q ss_pred ccccccccccccCh
Q psy16834 360 RFKCVFCEKSFARN 373 (488)
Q Consensus 360 ~~~C~~C~k~F~~~ 373 (488)
|-.|+.||..|...
T Consensus 26 p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 26 PAVSPYTGEQFPPE 39 (129)
T ss_pred CccCCCcCCccCcc
Confidence 44455555554433
No 114
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=63.08 E-value=5.6 Score=34.04 Aligned_cols=16 Identities=19% Similarity=0.447 Sum_probs=7.7
Q ss_pred ceecCccCccccChhh
Q psy16834 123 LFDCHICGKTVVTEKN 138 (488)
Q Consensus 123 ~~~C~~C~~~f~~~~~ 138 (488)
-|.|+.|+..|+...+
T Consensus 117 ~Y~Cp~C~~rytf~eA 132 (178)
T PRK06266 117 FFFCPNCHIRFTFDEA 132 (178)
T ss_pred EEECCCCCcEEeHHHH
Confidence 3445555555544444
No 115
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=62.51 E-value=7.6 Score=26.13 Aligned_cols=40 Identities=18% Similarity=0.585 Sum_probs=21.9
Q ss_pred ceecCc--cCccccChhhHHHHHHhccCCCceeCcc----ccccccc
Q psy16834 123 LFDCHI--CGKTVVTEKNYKKHMQLHSDDKPFECQF----CRKAFKL 163 (488)
Q Consensus 123 ~~~C~~--C~~~f~~~~~l~~H~~~H~~~~~~~C~~----C~~~F~~ 163 (488)
+..|+. |...+. +..|..|+...-..++..|+. |+..+..
T Consensus 9 ~v~C~~~cc~~~i~-r~~l~~H~~~~C~~~~v~C~~~~~GC~~~~~~ 54 (60)
T PF02176_consen 9 PVPCPNGCCNEMIP-RKELDDHLENECPKRPVPCPYSPYGCKERVPR 54 (60)
T ss_dssp EEE-TT--S-BEEE-CCCHHHHHHTTSTTSEEE-SS----S--EEEH
T ss_pred EeeCCCCCccccee-HHHHHHHHHccCCCCcEECCCCCCCCCCccch
Confidence 456766 434343 556777777666666777777 7776653
No 116
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=61.08 E-value=7.3 Score=25.96 Aligned_cols=32 Identities=22% Similarity=0.536 Sum_probs=17.2
Q ss_pred cccCccccCcCCChHHHHHHHHhhhCCCCccCCCCCC
Q psy16834 39 SILCPECGRGFFNEKELAAHKIEIHGADPFLCIPCNK 75 (488)
Q Consensus 39 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~C~~C~~ 75 (488)
.|.|+.||..--.+..-=+ .-..+|+|+.||.
T Consensus 27 ~F~CPnCGe~~I~Rc~~CR-----k~g~~Y~Cp~CGF 58 (61)
T COG2888 27 KFPCPNCGEVEIYRCAKCR-----KLGNPYRCPKCGF 58 (61)
T ss_pred EeeCCCCCceeeehhhhHH-----HcCCceECCCcCc
Confidence 4677777754333322111 1245778887774
No 117
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=58.82 E-value=5 Score=25.75 Aligned_cols=11 Identities=36% Similarity=0.960 Sum_probs=5.9
Q ss_pred cccCccccCcC
Q psy16834 39 SILCPECGRGF 49 (488)
Q Consensus 39 ~~~C~~C~~~f 49 (488)
.|.|..||+.|
T Consensus 6 ~Y~C~~Cg~~~ 16 (49)
T COG1996 6 EYKCARCGREV 16 (49)
T ss_pred EEEhhhcCCee
Confidence 35555555555
No 118
>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=58.75 E-value=6 Score=34.75 Aligned_cols=31 Identities=32% Similarity=0.544 Sum_probs=19.0
Q ss_pred CCCCcccCCcccccccchhhHHHHHHhhcCC
Q psy16834 6 EDTEKFSCSLCSYSVTIKRNLIMHIKRKHTD 36 (488)
Q Consensus 6 ~~~~~~~C~~C~~~f~~~~~L~~H~~~~h~~ 36 (488)
++..+|.|.+|+|.|.-..-...|+..+|.+
T Consensus 73 ~~~~K~~C~lc~KlFkg~eFV~KHI~nKH~e 103 (214)
T PF04959_consen 73 EDEDKWRCPLCGKLFKGPEFVRKHIFNKHPE 103 (214)
T ss_dssp SSSEEEEE-SSS-EESSHHHHHHHHHHH-HH
T ss_pred HcCCEECCCCCCcccCChHHHHHHHhhcCHH
Confidence 4555677777777777777777777666653
No 119
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=55.94 E-value=8.5 Score=40.65 Aligned_cols=40 Identities=20% Similarity=0.614 Sum_probs=23.3
Q ss_pred cccccccccccChhHHHHHHhhhcCCCCCccCCccCCcCCCchHHHhhhhhhccCCcccccccccc
Q psy16834 361 FKCVFCEKSFARNCNLKLHIRRYHDKSDNTECPLCGKSFPSRGRLNEHLIQVHPAQKHQCHICNKI 426 (488)
Q Consensus 361 ~~C~~C~k~F~~~~~l~~H~~~~H~~~~~~~C~~C~k~F~~~~~L~~H~~~~h~~~~~~C~~C~k~ 426 (488)
+.|+.|+-.++ .|.......|-+||. +...|..|+.||-.
T Consensus 445 ~~Cp~Cd~~lt-----------~H~~~~~L~CH~Cg~---------------~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 445 AECPNCDSPLT-----------LHKATGQLRCHYCGY---------------QEPIPQSCPECGSE 484 (730)
T ss_pred ccCCCCCcceE-----------EecCCCeeEeCCCCC---------------CCCCCCCCCCCCCC
Confidence 46777776543 244445566777765 23346667777654
No 120
>PF15269 zf-C2H2_7: Zinc-finger
Probab=55.18 E-value=7.7 Score=23.98 Aligned_cols=22 Identities=32% Similarity=0.765 Sum_probs=19.2
Q ss_pred cccCCcccccccchhhHHHHHH
Q psy16834 10 KFSCSLCSYSVTIKRNLIMHIK 31 (488)
Q Consensus 10 ~~~C~~C~~~f~~~~~L~~H~~ 31 (488)
.|+|-.|..+...++.|..||+
T Consensus 20 ~ykcfqcpftc~~kshl~nhmk 41 (54)
T PF15269_consen 20 KYKCFQCPFTCNEKSHLFNHMK 41 (54)
T ss_pred cceeecCCcccchHHHHHHHHH
Confidence 4789999999999999999985
No 121
>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=54.37 E-value=9.7 Score=33.89 Aligned_cols=25 Identities=28% Similarity=0.772 Sum_probs=18.1
Q ss_pred CCcCCcchhhccCChhhHhcccccc
Q psy16834 444 EPFHCPECGKAFKFKRYVTLHMRTH 468 (488)
Q Consensus 444 ~~~~C~~C~~~F~~~~~L~~H~~~H 468 (488)
+|+.||.||.--....+|..=.|+|
T Consensus 208 k~~PCPKCg~et~eTkdLSmStR~h 232 (314)
T PF06524_consen 208 KPIPCPKCGYETQETKDLSMSTRSH 232 (314)
T ss_pred CCCCCCCCCCcccccccceeeeecc
Confidence 6778888877777777776666665
No 122
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=53.87 E-value=6.3 Score=26.33 Aligned_cols=11 Identities=45% Similarity=1.008 Sum_probs=7.3
Q ss_pred CCCccCCccCC
Q psy16834 387 SDNTECPLCGK 397 (488)
Q Consensus 387 ~~~~~C~~C~k 397 (488)
..+|.|+.||.
T Consensus 46 ~~~Y~CP~CGF 56 (59)
T PRK14890 46 SNPYTCPKCGF 56 (59)
T ss_pred CCceECCCCCC
Confidence 35677777764
No 123
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=52.50 E-value=6.6 Score=25.92 Aligned_cols=30 Identities=30% Similarity=0.910 Sum_probs=17.2
Q ss_pred cCCcchhhccCChhhHhccccccccCcCccccccCcccc
Q psy16834 446 FHCPECGKAFKFKRYVTLHMRTHTGNWPTFVCKICNATI 484 (488)
Q Consensus 446 ~~C~~C~~~F~~~~~L~~H~~~H~~~~~~~~C~~C~k~f 484 (488)
|+|+.||..+.-.... -|+ ...|+.||..|
T Consensus 3 ~~CP~CG~~iev~~~~-------~Ge--iV~Cp~CGael 32 (54)
T TIGR01206 3 FECPDCGAEIELENPE-------LGE--LVICDECGAEL 32 (54)
T ss_pred cCCCCCCCEEecCCCc-------cCC--EEeCCCCCCEE
Confidence 6777777766433221 133 25777777655
No 124
>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=51.95 E-value=6.4 Score=22.39 Aligned_cols=25 Identities=32% Similarity=1.020 Sum_probs=10.6
Q ss_pred CCcchhhccCChhhHhccccccccCcCccccccCccc
Q psy16834 447 HCPECGKAFKFKRYVTLHMRTHTGNWPTFVCKICNAT 483 (488)
Q Consensus 447 ~C~~C~~~F~~~~~L~~H~~~H~~~~~~~~C~~C~k~ 483 (488)
+|+.|+..+.. +.|. .|.|+.|+-.
T Consensus 4 ~Cp~C~se~~y----------~D~~--~~vCp~C~~e 28 (30)
T PF08274_consen 4 KCPLCGSEYTY----------EDGE--LLVCPECGHE 28 (30)
T ss_dssp --TTT-----E----------E-SS--SEEETTTTEE
T ss_pred CCCCCCCccee----------ccCC--EEeCCccccc
Confidence 47777777665 2232 3788888753
No 125
>KOG2807|consensus
Probab=51.44 E-value=23 Score=32.81 Aligned_cols=99 Identities=21% Similarity=0.461 Sum_probs=54.8
Q ss_pred cCCCCCcchHHhhcCHHHHHHHHhhhccCceeecccccccccCHHHHHhHHhhhccCCceeecCCcccCChhHHHHHHHh
Q psy16834 246 REKVQCPYCAKFLSRKEKLNRHIRTVHTDVNYKCEICGEEFLSKTRYNRHVVTHEEKQKFECECGYVTCNKYRLTEHVRR 325 (488)
Q Consensus 246 ~~~~~C~~C~~~f~~~~~L~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~H~~~~~~~C~C~~~~~~~~~l~~H~~~ 325 (488)
...|.||.|....- +.|-.|++|+-+......|.+-..---.-++|.=
T Consensus 274 ~~Gy~CP~CkakvC--------------sLP~eCpiC~ltLVss~hLARSyhhL~PL~~F~E------------------ 321 (378)
T KOG2807|consen 274 GGGYFCPQCKAKVC--------------SLPIECPICSLTLVSSPHLARSYHHLFPLKPFVE------------------ 321 (378)
T ss_pred cCceeCCcccCeee--------------cCCccCCccceeEecchHHHHHHHhhcCCcchhh------------------
Confidence 34577888865433 4577888888888887777664322112222210
Q ss_pred hccCC--CcccCCCCCCccCChHHHHHHHHhhcCCCccccccccccccChhHHHHHHhhhcCCCCCccCCccC
Q psy16834 326 THLKD--YKVLCPICGYGCFRNAELEEHFISAHSADRFKCVFCEKSFARNCNLKLHIRRYHDKSDNTECPLCG 396 (488)
Q Consensus 326 ~h~~~--~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~k~F~~~~~l~~H~~~~H~~~~~~~C~~C~ 396 (488)
.-..+ ..-.|-.|+-. -.+...|.|+.|...|-.-.+.-.|... ..|+.|.
T Consensus 322 ip~~~~~~~~~Cf~C~~~-------------~~~~~~y~C~~Ck~~FCldCDv~iHesL-------h~CpgCe 374 (378)
T KOG2807|consen 322 IPETEYNGSRFCFACQGE-------------LLSSGRYRCESCKNVFCLDCDVFIHESL-------HNCPGCE 374 (378)
T ss_pred ccccccCCCcceeeeccc-------------cCCCCcEEchhccceeeccchHHHHhhh-------hcCCCcC
Confidence 00000 11114444211 1234468888888888888887777542 3466664
No 126
>KOG2593|consensus
Probab=51.39 E-value=12 Score=36.10 Aligned_cols=15 Identities=27% Similarity=0.348 Sum_probs=7.0
Q ss_pred cccccccccccCChH
Q psy16834 417 KHQCHICNKIVVSEK 431 (488)
Q Consensus 417 ~~~C~~C~k~f~~~~ 431 (488)
.|.|+.|++.|++-.
T Consensus 128 ~Y~Cp~C~kkyt~Le 142 (436)
T KOG2593|consen 128 GYVCPNCQKKYTSLE 142 (436)
T ss_pred cccCCccccchhhhH
Confidence 355555555544433
No 127
>PRK04023 DNA polymerase II large subunit; Validated
Probab=50.72 E-value=14 Score=39.98 Aligned_cols=10 Identities=50% Similarity=0.856 Sum_probs=6.1
Q ss_pred cccccccccc
Q psy16834 360 RFKCVFCEKS 369 (488)
Q Consensus 360 ~~~C~~C~k~ 369 (488)
...|+.||..
T Consensus 626 ~RfCpsCG~~ 635 (1121)
T PRK04023 626 RRKCPSCGKE 635 (1121)
T ss_pred CccCCCCCCc
Confidence 4566666655
No 128
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=50.58 E-value=4.5 Score=30.18 Aligned_cols=37 Identities=32% Similarity=0.541 Sum_probs=18.6
Q ss_pred CCcCCcchhhccCChhhHhccccccccCcCccccccCccccc
Q psy16834 444 EPFHCPECGKAFKFKRYVTLHMRTHTGNWPTFVCKICNATIS 485 (488)
Q Consensus 444 ~~~~C~~C~~~F~~~~~L~~H~~~H~~~~~~~~C~~C~k~f~ 485 (488)
+.|.|+.||.--...-.|+. +.....-.|.+||.+|.
T Consensus 21 k~FtCp~Cghe~vs~ctvkk-----~~~~g~~~Cg~CGls~e 57 (104)
T COG4888 21 KTFTCPRCGHEKVSSCTVKK-----TVNIGTAVCGNCGLSFE 57 (104)
T ss_pred ceEecCccCCeeeeEEEEEe-----cCceeEEEcccCcceEE
Confidence 45666666654333332221 12222356777777764
No 129
>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=50.36 E-value=7.5 Score=34.56 Aligned_cols=39 Identities=23% Similarity=0.490 Sum_probs=20.7
Q ss_pred CCCccccccchhhccchhHHHHHHH--HhcCCceecCccCc
Q psy16834 93 NSVNKECKICHKVLRTARLSEHMKQ--VHYAKLFDCHICGK 131 (488)
Q Consensus 93 ~~~~~~C~~C~~~f~~~~l~~h~~~--~~~~~~~~C~~C~~ 131 (488)
+.+.|+|..|...+=...-.+|... ......|+|..|++
T Consensus 139 GGrif~CsfC~~flCEDDQFEHQAsCQvLe~E~~KC~SCNr 179 (314)
T PF06524_consen 139 GGRIFKCSFCDNFLCEDDQFEHQASCQVLESETFKCQSCNR 179 (314)
T ss_pred CCeEEEeecCCCeeeccchhhhhhhhhhhhccccccccccc
Confidence 4456677777655443333344332 23345677777764
No 130
>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=49.63 E-value=4.6 Score=26.18 Aligned_cols=7 Identities=57% Similarity=1.597 Sum_probs=3.5
Q ss_pred ccCCccC
Q psy16834 390 TECPLCG 396 (488)
Q Consensus 390 ~~C~~C~ 396 (488)
+.|++||
T Consensus 35 w~CP~C~ 41 (50)
T cd00730 35 WVCPVCG 41 (50)
T ss_pred CCCCCCC
Confidence 4455554
No 131
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=49.29 E-value=12 Score=24.17 Aligned_cols=14 Identities=21% Similarity=0.539 Sum_probs=7.8
Q ss_pred CccCCCCCCccCCh
Q psy16834 67 PFLCIPCNKPFSKI 80 (488)
Q Consensus 67 ~~~C~~C~~~f~~~ 80 (488)
++.|..||..|.-.
T Consensus 4 ~l~C~dCg~~FvfT 17 (49)
T PF13451_consen 4 TLTCKDCGAEFVFT 17 (49)
T ss_pred eEEcccCCCeEEEe
Confidence 45566666655443
No 132
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=48.80 E-value=6.3 Score=27.81 Aligned_cols=10 Identities=40% Similarity=1.145 Sum_probs=5.6
Q ss_pred eeCccccccc
Q psy16834 152 FECQFCRKAF 161 (488)
Q Consensus 152 ~~C~~C~~~F 161 (488)
+.|+.||..-
T Consensus 2 m~CP~Cg~~a 11 (72)
T PRK09678 2 FHCPLCQHAA 11 (72)
T ss_pred ccCCCCCCcc
Confidence 3566666544
No 133
>KOG4167|consensus
Probab=47.09 E-value=4.1 Score=41.76 Aligned_cols=25 Identities=44% Similarity=0.755 Sum_probs=22.9
Q ss_pred CcCCcchhhccCChhhHhccccccc
Q psy16834 445 PFHCPECGKAFKFKRYVTLHMRTHT 469 (488)
Q Consensus 445 ~~~C~~C~~~F~~~~~L~~H~~~H~ 469 (488)
-|.|..|+|.|..-.+++.||++|.
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHH
Confidence 4999999999999999999999985
No 134
>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=46.46 E-value=6.7 Score=28.92 Aligned_cols=31 Identities=35% Similarity=0.793 Sum_probs=16.3
Q ss_pred CCcCCcchhhccCChhhHhccccccccCcCccccccCccccc
Q psy16834 444 EPFHCPECGKAFKFKRYVTLHMRTHTGNWPTFVCKICNATIS 485 (488)
Q Consensus 444 ~~~~C~~C~~~F~~~~~L~~H~~~H~~~~~~~~C~~C~k~f~ 485 (488)
..|.|+.||+.-. .|.-.|- +.|.-|++.|.
T Consensus 34 ~ky~Cp~Cgk~~v--------kR~a~GI---W~C~~C~~~~A 64 (90)
T PF01780_consen 34 AKYTCPFCGKTSV--------KRVATGI---WKCKKCGKKFA 64 (90)
T ss_dssp S-BEESSSSSSEE--------EEEETTE---EEETTTTEEEE
T ss_pred CCCcCCCCCCcee--------EEeeeEE---eecCCCCCEEe
Confidence 3566777766421 1233342 56777777664
No 135
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=44.63 E-value=14 Score=24.77 Aligned_cols=29 Identities=17% Similarity=0.408 Sum_probs=11.2
Q ss_pred ccchhHHHHHHHHhcCCceecCc----cCcccc
Q psy16834 106 LRTARLSEHMKQVHYAKLFDCHI----CGKTVV 134 (488)
Q Consensus 106 f~~~~l~~h~~~~~~~~~~~C~~----C~~~f~ 134 (488)
+....|..|....=..++..|+. |+..+.
T Consensus 21 i~r~~l~~H~~~~C~~~~v~C~~~~~GC~~~~~ 53 (60)
T PF02176_consen 21 IPRKELDDHLENECPKRPVPCPYSPYGCKERVP 53 (60)
T ss_dssp EECCCHHHHHHTTSTTSEEE-SS----S--EEE
T ss_pred eeHHHHHHHHHccCCCCcEECCCCCCCCCCccc
Confidence 33334444444332334455555 555544
No 136
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=44.54 E-value=13 Score=32.71 Aligned_cols=25 Identities=28% Similarity=0.594 Sum_probs=13.2
Q ss_pred ccccccccccccChhHHHHHHhhhc
Q psy16834 360 RFKCVFCEKSFARNCNLKLHIRRYH 384 (488)
Q Consensus 360 ~~~C~~C~k~F~~~~~l~~H~~~~H 384 (488)
.|.|..|+|.|.-..-...||...|
T Consensus 77 K~~C~lc~KlFkg~eFV~KHI~nKH 101 (214)
T PF04959_consen 77 KWRCPLCGKLFKGPEFVRKHIFNKH 101 (214)
T ss_dssp EEEE-SSS-EESSHHHHHHHHHHH-
T ss_pred EECCCCCCcccCChHHHHHHHhhcC
Confidence 4566666666666666666665544
No 137
>PF08790 zf-LYAR: LYAR-type C2HC zinc finger ; InterPro: IPR014898 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 C2HC zinc finger domain is found in LYAR proteins such as Q08288 from SWISSPROT, which are involved in cell growth regulation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1WJV_A.
Probab=44.01 E-value=4.1 Score=22.64 Aligned_cols=9 Identities=44% Similarity=1.206 Sum_probs=4.4
Q ss_pred ccccccccc
Q psy16834 362 KCVFCEKSF 370 (488)
Q Consensus 362 ~C~~C~k~F 370 (488)
.|-.|++.|
T Consensus 2 sCiDC~~~F 10 (28)
T PF08790_consen 2 SCIDCSKDF 10 (28)
T ss_dssp EETTTTEEE
T ss_pred eeecCCCCc
Confidence 344455555
No 138
>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=43.79 E-value=12 Score=30.15 Aligned_cols=27 Identities=48% Similarity=0.796 Sum_probs=14.8
Q ss_pred CceeCccccccccchhhHHhHhhhccCCCC
Q psy16834 150 KPFECQFCRKAFKLKYYLTLHLRTHTGVRP 179 (488)
Q Consensus 150 ~~~~C~~C~~~F~~~~~L~~H~~~h~~~~~ 179 (488)
.-..|-+||+.|+. |++|++.|+|..|
T Consensus 71 d~i~clecGk~~k~---LkrHL~~~~gltp 97 (132)
T PF05443_consen 71 DYIICLECGKKFKT---LKRHLRTHHGLTP 97 (132)
T ss_dssp S-EE-TBT--EESB---HHHHHHHTT-S-H
T ss_pred CeeEEccCCcccch---HHHHHHHccCCCH
Confidence 34678888887764 4788888877544
No 139
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=42.88 E-value=33 Score=21.68 Aligned_cols=27 Identities=30% Similarity=0.773 Sum_probs=15.9
Q ss_pred cCCcchhhccCChhhHhccccccccCcCccccccCcc
Q psy16834 446 FHCPECGKAFKFKRYVTLHMRTHTGNWPTFVCKICNA 482 (488)
Q Consensus 446 ~~C~~C~~~F~~~~~L~~H~~~H~~~~~~~~C~~C~k 482 (488)
|.||.||.. ....|.. ...|.|..|++
T Consensus 19 ~~CP~Cg~~--~~~~~~~--------~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGST--KHYRLKT--------RGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCe--eeEEeCC--------CCeEECCCCCC
Confidence 778888865 1111111 23588888875
No 140
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=42.48 E-value=16 Score=29.04 Aligned_cols=10 Identities=30% Similarity=0.969 Sum_probs=4.2
Q ss_pred cccccccccc
Q psy16834 362 KCVFCEKSFA 371 (488)
Q Consensus 362 ~C~~C~k~F~ 371 (488)
+|..||+.|.
T Consensus 3 ~Ct~Cg~~f~ 12 (131)
T PF09845_consen 3 QCTKCGRVFE 12 (131)
T ss_pred ccCcCCCCcC
Confidence 3444444444
No 141
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=42.38 E-value=17 Score=38.43 Aligned_cols=8 Identities=38% Similarity=1.107 Sum_probs=3.7
Q ss_pred cCCCCCCc
Q psy16834 69 LCIPCNKP 76 (488)
Q Consensus 69 ~C~~C~~~ 76 (488)
.|+.|+..
T Consensus 446 ~Cp~Cd~~ 453 (730)
T COG1198 446 ECPNCDSP 453 (730)
T ss_pred cCCCCCcc
Confidence 34555443
No 142
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=42.07 E-value=14 Score=19.47 Aligned_cols=6 Identities=67% Similarity=1.874 Sum_probs=2.4
Q ss_pred CCccCC
Q psy16834 392 CPLCGK 397 (488)
Q Consensus 392 C~~C~k 397 (488)
|+.||.
T Consensus 2 Cp~CG~ 7 (23)
T PF13240_consen 2 CPNCGA 7 (23)
T ss_pred CcccCC
Confidence 334443
No 143
>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=41.66 E-value=2.3 Score=32.76 Aligned_cols=38 Identities=29% Similarity=0.524 Sum_probs=19.3
Q ss_pred CCCCcchHHhhcCHHHHHHHHhhh--ccCceeeccccccccc
Q psy16834 248 KVQCPYCAKFLSRKEKLNRHIRTV--HTDVNYKCEICGEEFL 287 (488)
Q Consensus 248 ~~~C~~C~~~f~~~~~L~~H~~~~--~~~~~~~C~~C~~~f~ 287 (488)
...|+.||..-..-..++ ++.. ....-|.|..||..+.
T Consensus 62 ~~~Cp~Cg~~~a~f~~~Q--~RsadE~~T~fy~C~~C~~~w~ 101 (104)
T TIGR01384 62 RVECPKCGHKEAYYWLLQ--TRRADEPETRFYKCTKCGYVWR 101 (104)
T ss_pred cCCCCCCCCCeeEEEEec--cCCCCCCcEEEEEeCCCCCeeE
Confidence 467999875322111111 1110 1123488888887764
No 144
>PRK04023 DNA polymerase II large subunit; Validated
Probab=41.61 E-value=25 Score=38.14 Aligned_cols=50 Identities=26% Similarity=0.674 Sum_probs=34.1
Q ss_pred CcccCCCCCCccCChHHHHHHHHhhcCCCccccccccccccChhHHHHHHhhhcCCCCCccCCccCCcCCCchHHHhhhh
Q psy16834 331 YKVLCPICGYGCFRNAELEEHFISAHSADRFKCVFCEKSFARNCNLKLHIRRYHDKSDNTECPLCGKSFPSRGRLNEHLI 410 (488)
Q Consensus 331 ~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~k~F~~~~~l~~H~~~~H~~~~~~~C~~C~k~F~~~~~L~~H~~ 410 (488)
....|+.||... ..+.|+.||.. .+..+.|+.||...
T Consensus 625 g~RfCpsCG~~t----------------~~frCP~CG~~----------------Te~i~fCP~CG~~~----------- 661 (1121)
T PRK04023 625 GRRKCPSCGKET----------------FYRRCPFCGTH----------------TEPVYRCPRCGIEV----------- 661 (1121)
T ss_pred cCccCCCCCCcC----------------CcccCCCCCCC----------------CCcceeCccccCcC-----------
Confidence 356799999762 34799999976 23456788886532
Q ss_pred hhccCCcccccccccccC
Q psy16834 411 QVHPAQKHQCHICNKIVV 428 (488)
Q Consensus 411 ~~h~~~~~~C~~C~k~f~ 428 (488)
.++.|+.||..-.
T Consensus 662 -----~~y~CPKCG~El~ 674 (1121)
T PRK04023 662 -----EEDECEKCGREPT 674 (1121)
T ss_pred -----CCCcCCCCCCCCC
Confidence 2467888886543
No 145
>KOG2593|consensus
Probab=40.92 E-value=24 Score=34.27 Aligned_cols=18 Identities=17% Similarity=0.455 Sum_probs=8.5
Q ss_pred CCccccccccccccChhH
Q psy16834 358 ADRFKCVFCEKSFARNCN 375 (488)
Q Consensus 358 ~~~~~C~~C~k~F~~~~~ 375 (488)
..-|.|+.|+++|+.-..
T Consensus 126 ~~~Y~Cp~C~kkyt~Lea 143 (436)
T KOG2593|consen 126 VAGYVCPNCQKKYTSLEA 143 (436)
T ss_pred cccccCCccccchhhhHH
Confidence 334555555555544433
No 146
>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=40.09 E-value=14 Score=27.40 Aligned_cols=10 Identities=30% Similarity=1.036 Sum_probs=5.4
Q ss_pred cccccCcccc
Q psy16834 475 FVCKICNATI 484 (488)
Q Consensus 475 ~~C~~C~k~f 484 (488)
+.|..|++.|
T Consensus 54 W~C~~C~~~~ 63 (91)
T TIGR00280 54 WTCRKCGAKF 63 (91)
T ss_pred EEcCCCCCEE
Confidence 4555555555
No 147
>PRK01343 zinc-binding protein; Provisional
Probab=39.94 E-value=18 Score=24.16 Aligned_cols=10 Identities=60% Similarity=1.238 Sum_probs=5.8
Q ss_pred cCCcchhhcc
Q psy16834 446 FHCPECGKAF 455 (488)
Q Consensus 446 ~~C~~C~~~F 455 (488)
..|++|++.|
T Consensus 10 ~~CP~C~k~~ 19 (57)
T PRK01343 10 RPCPECGKPS 19 (57)
T ss_pred CcCCCCCCcC
Confidence 4466666654
No 148
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=39.44 E-value=20 Score=23.61 Aligned_cols=11 Identities=55% Similarity=1.494 Sum_probs=6.4
Q ss_pred ccCCccCCcCC
Q psy16834 390 TECPLCGKSFP 400 (488)
Q Consensus 390 ~~C~~C~k~F~ 400 (488)
..|+.||+.|.
T Consensus 6 ~~C~~Cg~~~~ 16 (54)
T PF14446_consen 6 CKCPVCGKKFK 16 (54)
T ss_pred ccChhhCCccc
Confidence 34666666664
No 149
>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=39.05 E-value=11 Score=20.22 Aligned_cols=8 Identities=75% Similarity=2.145 Sum_probs=3.7
Q ss_pred CcCCcchh
Q psy16834 445 PFHCPECG 452 (488)
Q Consensus 445 ~~~C~~C~ 452 (488)
+|.||.||
T Consensus 16 ~f~CPnCG 23 (24)
T PF07754_consen 16 PFPCPNCG 23 (24)
T ss_pred eEeCCCCC
Confidence 34444444
No 150
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.97 E-value=22 Score=27.02 Aligned_cols=26 Identities=27% Similarity=0.614 Sum_probs=14.8
Q ss_pred cCccccCcCCChHHHHHHHHhhhCCCCccCCCCCCcc
Q psy16834 41 LCPECGRGFFNEKELAAHKIEIHGADPFLCIPCNKPF 77 (488)
Q Consensus 41 ~C~~C~~~f~~~~~l~~H~~~~h~~~~~~C~~C~~~f 77 (488)
.|+.||+.|... +..|..|++||++|
T Consensus 11 idPetg~KFYDL-----------NrdPiVsPytG~s~ 36 (129)
T COG4530 11 IDPETGKKFYDL-----------NRDPIVSPYTGKSY 36 (129)
T ss_pred cCccccchhhcc-----------CCCccccCcccccc
Confidence 466666666431 34566666666666
No 151
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=38.20 E-value=19 Score=22.19 Aligned_cols=14 Identities=21% Similarity=0.797 Sum_probs=10.1
Q ss_pred CccccccCcccccc
Q psy16834 473 PTFVCKICNATISS 486 (488)
Q Consensus 473 ~~~~C~~C~k~f~~ 486 (488)
|.=.|++||+.|+-
T Consensus 7 p~K~C~~C~rpf~W 20 (42)
T PF10013_consen 7 PSKICPVCGRPFTW 20 (42)
T ss_pred CCCcCcccCCcchH
Confidence 44568899888863
No 152
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=37.43 E-value=14 Score=23.92 Aligned_cols=12 Identities=33% Similarity=0.686 Sum_probs=8.0
Q ss_pred Cccccccccccc
Q psy16834 359 DRFKCVFCEKSF 370 (488)
Q Consensus 359 ~~~~C~~C~k~F 370 (488)
..+.|..||.++
T Consensus 36 ~r~~C~~Cgyt~ 47 (50)
T PRK00432 36 DRWHCGKCGYTE 47 (50)
T ss_pred CcEECCCcCCEE
Confidence 467777777654
No 153
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=36.56 E-value=10 Score=22.63 Aligned_cols=6 Identities=50% Similarity=1.359 Sum_probs=2.2
Q ss_pred CccCCc
Q psy16834 393 PLCGKS 398 (488)
Q Consensus 393 ~~C~k~ 398 (488)
+.||+.
T Consensus 5 ~~Cg~~ 10 (36)
T PF05191_consen 5 PKCGRI 10 (36)
T ss_dssp TTTTEE
T ss_pred CCCCCc
Confidence 333333
No 154
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=35.30 E-value=19 Score=25.09 Aligned_cols=27 Identities=30% Similarity=0.698 Sum_probs=10.3
Q ss_pred ccccccccccCChHHHHHHHHhhcCCCCcCCcchhhccC
Q psy16834 418 HQCHICNKIVVSEKTLKKHLLLHTNSEPFHCPECGKAFK 456 (488)
Q Consensus 418 ~~C~~C~k~f~~~~~L~~H~~~H~~~~~~~C~~C~~~F~ 456 (488)
-.|.+|++.|.- -.+.+-|..||..|=
T Consensus 10 ~~C~~C~~~F~~------------~~rrhhCr~CG~~vC 36 (69)
T PF01363_consen 10 SNCMICGKKFSL------------FRRRHHCRNCGRVVC 36 (69)
T ss_dssp SB-TTT--B-BS------------SS-EEE-TTT--EEE
T ss_pred CcCcCcCCcCCC------------ceeeEccCCCCCEEC
Confidence 356677777742 134555666666654
No 155
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=33.99 E-value=19 Score=26.57 Aligned_cols=11 Identities=27% Similarity=0.917 Sum_probs=5.9
Q ss_pred cccccCccccc
Q psy16834 475 FVCKICNATIS 485 (488)
Q Consensus 475 ~~C~~C~k~f~ 485 (488)
+.|.-|++.|.
T Consensus 55 W~C~~C~~~~A 65 (90)
T PRK03976 55 WECRKCGAKFA 65 (90)
T ss_pred EEcCCCCCEEe
Confidence 45555555553
No 156
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=33.99 E-value=18 Score=24.03 Aligned_cols=37 Identities=19% Similarity=0.439 Sum_probs=16.5
Q ss_pred cCCcccccccchhhHHHHHHhhcCCCccccCccccCc
Q psy16834 12 SCSLCSYSVTIKRNLIMHIKRKHTDEFSILCPECGRG 48 (488)
Q Consensus 12 ~C~~C~~~f~~~~~L~~H~~~~h~~~~~~~C~~C~~~ 48 (488)
+|-+|++.+........=.+..-.....|.|+.|..+
T Consensus 4 kC~lCdk~~~Id~~~~~aKrLrnrPi~tYmC~eC~~R 40 (56)
T PF09963_consen 4 KCILCDKKEEIDEDTPEAKRLRNRPIHTYMCDECKER 40 (56)
T ss_pred EEEecCCEEEeccCCHHHHHhhcCCCcceeChhHHHH
Confidence 5667766655332211111111123344666666543
No 157
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=33.44 E-value=26 Score=27.85 Aligned_cols=25 Identities=44% Similarity=0.604 Sum_probs=18.8
Q ss_pred eeCccccccccchhhHHhHhhhccCCCC
Q psy16834 152 FECQFCRKAFKLKYYLTLHLRTHTGVRP 179 (488)
Q Consensus 152 ~~C~~C~~~F~~~~~L~~H~~~h~~~~~ 179 (488)
..|-.+|+.|+ +|++|+.+|.+-.|
T Consensus 77 IicLEDGkkfK---SLKRHL~t~~gmTP 101 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTHYGLTP 101 (148)
T ss_pred EEEeccCcchH---HHHHHHhcccCCCH
Confidence 56888888886 57888888877544
No 158
>KOG4167|consensus
Probab=32.55 E-value=13 Score=38.31 Aligned_cols=26 Identities=31% Similarity=0.490 Sum_probs=23.9
Q ss_pred ceeCccccccccchhhHHhHhhhccC
Q psy16834 151 PFECQFCRKAFKLKYYLTLHLRTHTG 176 (488)
Q Consensus 151 ~~~C~~C~~~F~~~~~L~~H~~~h~~ 176 (488)
-|.|..|++.|....+++.||++|.-
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 49999999999999999999999864
No 159
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=32.39 E-value=44 Score=22.39 Aligned_cols=29 Identities=10% Similarity=0.252 Sum_probs=11.4
Q ss_pred cccccchhhccchhHHHHHHHHhcCCceecCc
Q psy16834 97 KECKICHKVLRTARLSEHMKQVHYAKLFDCHI 128 (488)
Q Consensus 97 ~~C~~C~~~f~~~~l~~h~~~~~~~~~~~C~~ 128 (488)
.....|+-+|....+.+.+ ...+...|++
T Consensus 25 V~s~~C~H~fek~aI~~~i---~~~~~~~CPv 53 (57)
T PF11789_consen 25 VKSKKCGHTFEKEAILQYI---QRNGSKRCPV 53 (57)
T ss_dssp EEESSS--EEEHHHHHHHC---TTTS-EE-SC
T ss_pred cCcCCCCCeecHHHHHHHH---HhcCCCCCCC
Confidence 3344555555555544444 1233445554
No 160
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=32.28 E-value=17 Score=22.14 Aligned_cols=13 Identities=38% Similarity=0.864 Sum_probs=10.0
Q ss_pred CcCCcchhhccCC
Q psy16834 445 PFHCPECGKAFKF 457 (488)
Q Consensus 445 ~~~C~~C~~~F~~ 457 (488)
||.|+.|++.|=.
T Consensus 12 ~f~C~~C~~~FC~ 24 (39)
T smart00154 12 GFKCRHCGNLFCG 24 (39)
T ss_pred CeECCccCCcccc
Confidence 7888888888753
No 161
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=32.12 E-value=23 Score=28.18 Aligned_cols=55 Identities=24% Similarity=0.613 Sum_probs=35.9
Q ss_pred cCCcccccccccccCChHHHHHHHHhhcCCCCcCC---cchhhccCChhhHhccccccccCcCccccccCccccccC
Q psy16834 414 PAQKHQCHICNKIVVSEKTLKKHLLLHTNSEPFHC---PECGKAFKFKRYVTLHMRTHTGNWPTFVCKICNATISSE 487 (488)
Q Consensus 414 ~~~~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~~C---~~C~~~F~~~~~L~~H~~~H~~~~~~~~C~~C~k~f~~~ 487 (488)
..+-|+|++|..+...+.-| ||=.| .+|+.-+. .|..|-.+| | .||+|.-+|.+.
T Consensus 77 d~~lYeCnIC~etS~ee~FL----------KPneCCgY~iCn~Cya---~LWK~~~~y----p--vCPvCkTSFKss 134 (140)
T PF05290_consen 77 DPKLYECNICKETSAEERFL----------KPNECCGYSICNACYA---NLWKFCNLY----P--VCPVCKTSFKSS 134 (140)
T ss_pred CCCceeccCcccccchhhcC----------CcccccchHHHHHHHH---HHHHHcccC----C--CCCccccccccc
Confidence 34679999998876554322 56666 34555443 455554443 5 799999999875
No 162
>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=31.51 E-value=49 Score=27.25 Aligned_cols=25 Identities=28% Similarity=0.497 Sum_probs=15.2
Q ss_pred CCcccccccccccc------ChhHHHHHHhh
Q psy16834 358 ADRFKCVFCEKSFA------RNCNLKLHIRR 382 (488)
Q Consensus 358 ~~~~~C~~C~k~F~------~~~~l~~H~~~ 382 (488)
.-..+|..|+|.|- ..+.+..|+.+
T Consensus 12 ~~vv~C~~c~kWFCNg~~~~s~SHIv~HLv~ 42 (152)
T PF09416_consen 12 SCVVKCNTCNKWFCNGRGNTSGSHIVNHLVR 42 (152)
T ss_dssp CCEEEETTTTEEEES--TTSSS-HHHHHHHH
T ss_pred ccEeEcCCCCcEeecCCCCCcccHHHHHHHH
Confidence 33467888888884 34556666543
No 163
>KOG1280|consensus
Probab=31.29 E-value=30 Score=32.44 Aligned_cols=28 Identities=25% Similarity=0.551 Sum_probs=19.6
Q ss_pred cCCcccccccccccCChHHHHHHHH-hhc
Q psy16834 414 PAQKHQCHICNKIVVSEKTLKKHLL-LHT 441 (488)
Q Consensus 414 ~~~~~~C~~C~k~f~~~~~L~~H~~-~H~ 441 (488)
....|.|++|++.-.+...|..|.. .|.
T Consensus 76 ~~qSftCPyC~~~Gfte~~f~~Hv~s~Hp 104 (381)
T KOG1280|consen 76 DPQSFTCPYCGIMGFTERQFGTHVLSQHP 104 (381)
T ss_pred ccccccCCcccccccchhHHHHHhhhcCc
Confidence 3446888888888777788888864 343
No 164
>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=31.00 E-value=24 Score=28.39 Aligned_cols=23 Identities=35% Similarity=0.524 Sum_probs=11.8
Q ss_pred ccccccccccCChHHHHHHHHhhcCC
Q psy16834 418 HQCHICNKIVVSEKTLKKHLLLHTNS 443 (488)
Q Consensus 418 ~~C~~C~k~f~~~~~L~~H~~~H~~~ 443 (488)
-.|-+|||.|.. |++|++.|.|-
T Consensus 73 i~clecGk~~k~---LkrHL~~~~gl 95 (132)
T PF05443_consen 73 IICLECGKKFKT---LKRHLRTHHGL 95 (132)
T ss_dssp EE-TBT--EESB---HHHHHHHTT-S
T ss_pred eEEccCCcccch---HHHHHHHccCC
Confidence 566666666644 46777777554
No 165
>KOG1280|consensus
Probab=30.64 E-value=47 Score=31.20 Aligned_cols=40 Identities=23% Similarity=0.570 Sum_probs=27.2
Q ss_pred CCCccccccccccccChhHHHHHHhhhcCCCC-CccCCccC
Q psy16834 357 SADRFKCVFCEKSFARNCNLKLHIRRYHDKSD-NTECPLCG 396 (488)
Q Consensus 357 ~~~~~~C~~C~k~F~~~~~l~~H~~~~H~~~~-~~~C~~C~ 396 (488)
.+..|.|++|++.=.+...|..|+...|.... ...|++|+
T Consensus 76 ~~qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~ 116 (381)
T KOG1280|consen 76 DPQSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCA 116 (381)
T ss_pred ccccccCCcccccccchhHHHHHhhhcCcccCcceeeeccc
Confidence 34568888888887778888888877775543 23456654
No 166
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=30.44 E-value=11 Score=39.10 Aligned_cols=78 Identities=23% Similarity=0.454 Sum_probs=47.7
Q ss_pred ccCCcccccccchhhHHHHHHhhcCCCccc-cCccccCcCCChHHHHHHHHhhhCCCCc-cCCCCCCccCChhhHHHHHh
Q psy16834 11 FSCSLCSYSVTIKRNLIMHIKRKHTDEFSI-LCPECGRGFFNEKELAAHKIEIHGADPF-LCIPCNKPFSKIENYRLHQR 88 (488)
Q Consensus 11 ~~C~~C~~~f~~~~~L~~H~~~~h~~~~~~-~C~~C~~~f~~~~~l~~H~~~~h~~~~~-~C~~C~~~f~~~~~l~~H~~ 88 (488)
=.|+.|-+.+.+..+-+.+ .|| .|..||-+|+--..|---. .......| .|+.|.+.|.+..+-+-|.+
T Consensus 102 a~C~~Cl~Ei~dp~~rrY~--------YPF~~CT~CGPRfTIi~alPYDR-~nTsM~~F~lC~~C~~EY~dP~nRRfHAQ 172 (750)
T COG0068 102 ATCEDCLEEIFDPNSRRYL--------YPFINCTNCGPRFTIIEALPYDR-ENTSMADFPLCPFCDKEYKDPLNRRFHAQ 172 (750)
T ss_pred hhhHHHHHHhcCCCCccee--------ccccccCCCCcceeeeccCCCCc-ccCccccCcCCHHHHHHhcCccccccccc
Confidence 3677777666665553333 244 4888888887655543221 12222233 58888888888877555543
Q ss_pred hhccCCCccccccchh
Q psy16834 89 RYHLNSVNKECKICHK 104 (488)
Q Consensus 89 ~~h~~~~~~~C~~C~~ 104 (488)
+..|+.||-
T Consensus 173 -------p~aCp~CGP 181 (750)
T COG0068 173 -------PIACPKCGP 181 (750)
T ss_pred -------cccCcccCC
Confidence 567888884
No 168
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=30.38 E-value=33 Score=27.26 Aligned_cols=24 Identities=33% Similarity=0.355 Sum_probs=15.4
Q ss_pred ccccccccccCChHHHHHHHHhhcCCC
Q psy16834 418 HQCHICNKIVVSEKTLKKHLLLHTNSE 444 (488)
Q Consensus 418 ~~C~~C~k~f~~~~~L~~H~~~H~~~~ 444 (488)
..|-.+||.| .+|++|+.+|-|-.
T Consensus 77 IicLEDGkkf---KSLKRHL~t~~gmT 100 (148)
T COG4957 77 IICLEDGKKF---KSLKRHLTTHYGLT 100 (148)
T ss_pred EEEeccCcch---HHHHHHHhcccCCC
Confidence 3566667666 35777777776643
No 169
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=30.38 E-value=48 Score=37.16 Aligned_cols=8 Identities=25% Similarity=0.717 Sum_probs=3.9
Q ss_pred cccccccc
Q psy16834 361 FKCVFCEK 368 (488)
Q Consensus 361 ~~C~~C~k 368 (488)
++|+.||.
T Consensus 668 rkCPkCG~ 675 (1337)
T PRK14714 668 RRCPSCGT 675 (1337)
T ss_pred EECCCCCC
Confidence 44555543
No 170
>KOG4124|consensus
Probab=30.17 E-value=16 Score=34.15 Aligned_cols=25 Identities=24% Similarity=0.588 Sum_probs=20.3
Q ss_pred CCCcCCcchhhccCChhhHhccccc
Q psy16834 443 SEPFHCPECGKAFKFKRYVTLHMRT 467 (488)
Q Consensus 443 ~~~~~C~~C~~~F~~~~~L~~H~~~ 467 (488)
.|||+|++|.++++.-..|.-|...
T Consensus 396 nk~~r~~i~~~~~k~~~~l~~~~~~ 420 (442)
T KOG4124|consen 396 NKPYRCEVCSKRYKNLNGLKYHRTH 420 (442)
T ss_pred cCcccChhhhhhhccCCCCCceeeh
Confidence 4799999999999988887776543
No 171
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=30.04 E-value=20 Score=27.23 Aligned_cols=7 Identities=29% Similarity=1.023 Sum_probs=3.6
Q ss_pred ccccccc
Q psy16834 418 HQCHICN 424 (488)
Q Consensus 418 ~~C~~C~ 424 (488)
|.|+.|+
T Consensus 22 f~CP~Cg 28 (99)
T PRK14892 22 FECPRCG 28 (99)
T ss_pred eECCCCC
Confidence 4555555
No 172
>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=29.47 E-value=22 Score=22.06 Aligned_cols=10 Identities=30% Similarity=0.899 Sum_probs=6.2
Q ss_pred cccccCcccc
Q psy16834 475 FVCKICNATI 484 (488)
Q Consensus 475 ~~C~~C~k~f 484 (488)
+.|+.||...
T Consensus 20 ~vC~~CG~Vl 29 (43)
T PF08271_consen 20 LVCPNCGLVL 29 (43)
T ss_dssp EEETTT-BBE
T ss_pred EECCCCCCEe
Confidence 6788887643
No 173
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=29.37 E-value=42 Score=19.60 Aligned_cols=20 Identities=25% Similarity=0.687 Sum_probs=10.2
Q ss_pred cccccchhhccchhHHHHHH
Q psy16834 97 KECKICHKVLRTARLSEHMK 116 (488)
Q Consensus 97 ~~C~~C~~~f~~~~l~~h~~ 116 (488)
+.|+.|++.....++..|+.
T Consensus 5 ~~C~nC~R~v~a~RfA~HLe 24 (33)
T PF08209_consen 5 VECPNCGRPVAASRFAPHLE 24 (33)
T ss_dssp EE-TTTSSEEEGGGHHHHHH
T ss_pred EECCCCcCCcchhhhHHHHH
Confidence 34555555555555555544
No 174
>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=29.35 E-value=36 Score=34.70 Aligned_cols=12 Identities=33% Similarity=0.828 Sum_probs=6.4
Q ss_pred CCCCccCCccCC
Q psy16834 386 KSDNTECPLCGK 397 (488)
Q Consensus 386 ~~~~~~C~~C~k 397 (488)
......|..||.
T Consensus 237 ~~~~l~Ch~Cg~ 248 (505)
T TIGR00595 237 KEGKLRCHYCGY 248 (505)
T ss_pred CCCeEEcCCCcC
Confidence 334455666664
No 175
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=29.31 E-value=61 Score=29.86 Aligned_cols=46 Identities=17% Similarity=0.322 Sum_probs=32.3
Q ss_pred cccchhhhhcccCCCCCCcCCCCccccccccccccChhHHHHHHhh
Q psy16834 183 CDICHKVLKTKSKKSSGISKNENLRPCTLCDKKLASERKLKEHIRK 228 (488)
Q Consensus 183 C~~C~~~f~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~L~~H~~~ 228 (488)
|-.|.-.|................|.|+.|-..|-..-+...|...
T Consensus 365 Cf~CQ~~fp~~~~~~~~~~~ss~rY~Ce~CK~~FC~dCdvfiHe~L 410 (421)
T COG5151 365 CFVCQGPFPKPPVSPFDESTSSGRYQCELCKSTFCSDCDVFIHETL 410 (421)
T ss_pred ceeccCCCCCCCCCcccccccccceechhhhhhhhhhhHHHHHHHH
Confidence 6667666665554444555556678999999999888887777544
No 176
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=29.16 E-value=29 Score=21.25 Aligned_cols=16 Identities=19% Similarity=0.312 Sum_probs=7.6
Q ss_pred eecCccCccccChhhH
Q psy16834 124 FDCHICGKTVVTEKNY 139 (488)
Q Consensus 124 ~~C~~C~~~f~~~~~l 139 (488)
..|+.|+-.+-....|
T Consensus 20 d~C~~C~G~W~d~~el 35 (41)
T PF13453_consen 20 DVCPSCGGIWFDAGEL 35 (41)
T ss_pred EECCCCCeEEccHHHH
Confidence 4455555444444444
No 177
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=29.15 E-value=18 Score=29.29 Aligned_cols=13 Identities=23% Similarity=0.404 Sum_probs=6.8
Q ss_pred cccCCCCCCccCC
Q psy16834 332 KVLCPICGYGCFR 344 (488)
Q Consensus 332 ~~~C~~C~~~f~~ 344 (488)
.+.|+.||..|..
T Consensus 70 ~~~C~~CG~~~~~ 82 (135)
T PRK03824 70 VLKCRNCGNEWSL 82 (135)
T ss_pred EEECCCCCCEEec
Confidence 3455566555543
No 178
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=29.13 E-value=33 Score=22.62 Aligned_cols=9 Identities=56% Similarity=1.239 Sum_probs=4.9
Q ss_pred CCccCCcCC
Q psy16834 392 CPLCGKSFP 400 (488)
Q Consensus 392 C~~C~k~F~ 400 (488)
|..|++.|.
T Consensus 5 C~~C~~~F~ 13 (57)
T cd00065 5 CMGCGKPFT 13 (57)
T ss_pred CcccCcccc
Confidence 555555554
No 179
>COG1773 Rubredoxin [Energy production and conversion]
Probab=29.03 E-value=42 Score=22.23 Aligned_cols=34 Identities=21% Similarity=0.555 Sum_probs=16.7
Q ss_pred eecccchhhhhcccCCCC-CCcCC------CCccccccccc
Q psy16834 181 FECDICHKVLKTKSKKSS-GISKN------ENLRPCTLCDK 214 (488)
Q Consensus 181 ~~C~~C~~~f~~~~~~~~-~~~~~------~~~~~C~~C~~ 214 (488)
|+|..||.+|....-... .+..+ ..-+.|+.|+-
T Consensus 4 ~~C~~CG~vYd~e~Gdp~~gi~pgT~fedlPd~w~CP~Cg~ 44 (55)
T COG1773 4 WRCSVCGYVYDPEKGDPRCGIAPGTPFEDLPDDWVCPECGV 44 (55)
T ss_pred eEecCCceEeccccCCccCCCCCCCchhhCCCccCCCCCCC
Confidence 666666666654332211 22111 12356888874
No 180
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=28.91 E-value=28 Score=28.58 Aligned_cols=35 Identities=29% Similarity=0.757 Sum_probs=20.2
Q ss_pred HhhcCC----CCcCCcchhhccCChhhHhccccccccCcCccccccCccc
Q psy16834 438 LLHTNS----EPFHCPECGKAFKFKRYVTLHMRTHTGNWPTFVCKICNAT 483 (488)
Q Consensus 438 ~~H~~~----~~~~C~~C~~~F~~~~~L~~H~~~H~~~~~~~~C~~C~k~ 483 (488)
..++|| ..|.|..||..-. + .|.+.-| .|+.||..
T Consensus 101 ~Y~sGE~~g~G~l~C~~Cg~~~~--------~-~~~~~l~--~Cp~C~~~ 139 (146)
T PF07295_consen 101 VYHSGEVVGPGTLVCENCGHEVE--------L-THPERLP--PCPKCGHT 139 (146)
T ss_pred CeecCcEecCceEecccCCCEEE--------e-cCCCcCC--CCCCCCCC
Confidence 345555 3577888876521 2 2445544 68888753
No 181
>KOG1842|consensus
Probab=28.19 E-value=31 Score=33.52 Aligned_cols=31 Identities=26% Similarity=0.426 Sum_probs=27.1
Q ss_pred CCcccCCcccccccchhhHHHHHHhhcCCCc
Q psy16834 8 TEKFSCSLCSYSVTIKRNLIMHIKRKHTDEF 38 (488)
Q Consensus 8 ~~~~~C~~C~~~f~~~~~L~~H~~~~h~~~~ 38 (488)
-+.|.|++|...|.+...|..|+...|.++.
T Consensus 13 ~egflCPiC~~dl~~~~~L~~H~d~eH~~ed 43 (505)
T KOG1842|consen 13 LEGFLCPICLLDLPNLSALNDHLDVEHFEED 43 (505)
T ss_pred hhcccCchHhhhhhhHHHHHHHHhhhccccc
Confidence 3569999999999999999999998887653
No 182
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=27.84 E-value=14 Score=33.71 Aligned_cols=19 Identities=16% Similarity=0.399 Sum_probs=9.7
Q ss_pred ccccccccccccChhHHHH
Q psy16834 360 RFKCVFCEKSFARNCNLKL 378 (488)
Q Consensus 360 ~~~C~~C~k~F~~~~~l~~ 378 (488)
|..|+.|+-......+|.+
T Consensus 322 Pi~CP~Csl~LilsthLar 340 (421)
T COG5151 322 PISCPICSLQLILSTHLAR 340 (421)
T ss_pred CccCcchhHHHHHHHHHHH
Confidence 4556666555444444433
No 183
>KOG0717|consensus
Probab=27.58 E-value=33 Score=33.60 Aligned_cols=20 Identities=50% Similarity=0.738 Sum_probs=12.3
Q ss_pred ccccccccccCChHHHHHHH
Q psy16834 418 HQCHICNKIVVSEKTLKKHL 437 (488)
Q Consensus 418 ~~C~~C~k~f~~~~~L~~H~ 437 (488)
+-|.+|+|+|.+..+|+.|.
T Consensus 293 lyC~vCnKsFKseKq~kNHE 312 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHE 312 (508)
T ss_pred eEEeeccccccchHHHHhhH
Confidence 55666666666666666664
No 184
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=27.13 E-value=32 Score=25.44 Aligned_cols=12 Identities=25% Similarity=0.448 Sum_probs=5.5
Q ss_pred CccCCccCCcCC
Q psy16834 389 NTECPLCGKSFP 400 (488)
Q Consensus 389 ~~~C~~C~k~F~ 400 (488)
...|..|++.|+
T Consensus 54 IW~C~~C~~~~A 65 (90)
T PTZ00255 54 IWRCKGCKKTVA 65 (90)
T ss_pred EEEcCCCCCEEe
Confidence 344444444443
No 185
>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=26.44 E-value=39 Score=21.61 Aligned_cols=35 Identities=20% Similarity=0.586 Sum_probs=15.0
Q ss_pred eecccchhhhhcccCCC-CCCc------CCCCcccccccccc
Q psy16834 181 FECDICHKVLKTKSKKS-SGIS------KNENLRPCTLCDKK 215 (488)
Q Consensus 181 ~~C~~C~~~f~~~~~~~-~~~~------~~~~~~~C~~C~~~ 215 (488)
|+|.+|+.++....-.. ..+. .-...+.|++|+..
T Consensus 2 y~C~~CgyvYd~~~Gd~~~~i~pGt~F~~Lp~~w~CP~C~a~ 43 (47)
T PF00301_consen 2 YQCPVCGYVYDPEKGDPENGIPPGTPFEDLPDDWVCPVCGAP 43 (47)
T ss_dssp EEETTTSBEEETTTBBGGGTB-TT--GGGS-TT-B-TTTSSB
T ss_pred cCCCCCCEEEcCCcCCcccCcCCCCCHHHCCCCCcCcCCCCc
Confidence 56666666554433211 1111 11234678888753
No 186
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 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. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=25.65 E-value=53 Score=19.83 Aligned_cols=11 Identities=36% Similarity=1.132 Sum_probs=4.1
Q ss_pred ccccccccccc
Q psy16834 360 RFKCVFCEKSF 370 (488)
Q Consensus 360 ~~~C~~C~k~F 370 (488)
.|-|++|+..|
T Consensus 3 ryyCdyC~~~~ 13 (38)
T PF06220_consen 3 RYYCDYCKKYL 13 (38)
T ss_dssp S-B-TTT--B-
T ss_pred Ceeccccccee
Confidence 46677777777
No 187
>KOG0801|consensus
Probab=24.89 E-value=34 Score=28.10 Aligned_cols=32 Identities=25% Similarity=0.542 Sum_probs=20.5
Q ss_pred HHHHHHHhhcCCCCcCCcchhhccCChhhHhccccc
Q psy16834 432 TLKKHLLLHTNSEPFHCPECGKAFKFKRYVTLHMRT 467 (488)
Q Consensus 432 ~L~~H~~~H~~~~~~~C~~C~~~F~~~~~L~~H~~~ 467 (488)
+|-.|+.-|.| ++|++|.| |.-..+...|+.+
T Consensus 128 slP~hi~~~~g---~KCPvC~K-~V~sDd~e~HlvM 159 (205)
T KOG0801|consen 128 SLPVHIMDHSG---MKCPVCHK-VVPSDDAEIHLVM 159 (205)
T ss_pred ccceeeeccCC---ccCCcccc-ccCCCcceEEEEE
Confidence 55566666654 66888876 4556677767643
No 188
>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=24.87 E-value=26 Score=21.30 Aligned_cols=12 Identities=17% Similarity=0.490 Sum_probs=7.6
Q ss_pred Cccccccccccc
Q psy16834 205 NLRPCTLCDKKL 216 (488)
Q Consensus 205 ~~~~C~~C~~~f 216 (488)
..|.|..|+..|
T Consensus 27 ~fy~C~~C~~~w 38 (39)
T PF01096_consen 27 LFYVCCNCGHRW 38 (39)
T ss_dssp EEEEESSSTEEE
T ss_pred EEEEeCCCCCee
Confidence 346677777654
No 189
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=24.63 E-value=46 Score=23.09 Aligned_cols=29 Identities=31% Similarity=0.639 Sum_probs=15.7
Q ss_pred cCCCCCCccCChHHHHHHHHhhcCCCccccccccccccC
Q psy16834 334 LCPICGYGCFRNAELEEHFISAHSADRFKCVFCEKSFAR 372 (488)
Q Consensus 334 ~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~k~F~~ 372 (488)
.|+.||..-.. .-..+.|.|+.||..+..
T Consensus 30 ~C~~CG~~~~~----------~~~~r~~~C~~Cg~~~~r 58 (69)
T PF07282_consen 30 TCPRCGHRNKK----------RRSGRVFTCPNCGFEMDR 58 (69)
T ss_pred CccCccccccc----------ccccceEEcCCCCCEECc
Confidence 47777755332 112345667777666544
No 190
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=24.63 E-value=72 Score=19.63 Aligned_cols=23 Identities=26% Similarity=0.436 Sum_probs=11.2
Q ss_pred cccccccccC--ChHHHHHHHHhhc
Q psy16834 419 QCHICNKIVV--SEKTLKKHLLLHT 441 (488)
Q Consensus 419 ~C~~C~k~f~--~~~~L~~H~~~H~ 441 (488)
.|+.||..|. ....-+.|.+.|.
T Consensus 15 ~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 15 TCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred CCCCCCCEECCCCHHHHHHHHHHHh
Confidence 4555555543 2334455555553
No 191
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=24.53 E-value=49 Score=21.95 Aligned_cols=11 Identities=18% Similarity=0.492 Sum_probs=5.7
Q ss_pred ccccccccccc
Q psy16834 417 KHQCHICNKIV 427 (488)
Q Consensus 417 ~~~C~~C~k~f 427 (488)
.|.|+.||-.+
T Consensus 14 ~~~Cp~cGipt 24 (55)
T PF13824_consen 14 NFECPDCGIPT 24 (55)
T ss_pred CCcCCCCCCcC
Confidence 45555555543
No 192
>KOG0782|consensus
Probab=24.36 E-value=23 Score=35.42 Aligned_cols=50 Identities=20% Similarity=0.393 Sum_probs=24.9
Q ss_pred HHHhhhhhhccCCcccccccccccCChHHHHHHHHhhcCC-CCcCCcchhhccCChh
Q psy16834 404 RLNEHLIQVHPAQKHQCHICNKIVVSEKTLKKHLLLHTNS-EPFHCPECGKAFKFKR 459 (488)
Q Consensus 404 ~L~~H~~~~h~~~~~~C~~C~k~f~~~~~L~~H~~~H~~~-~~~~C~~C~~~F~~~~ 459 (488)
.|.+|--.|-....-+|..|||.|-++-. .|..| -...|..|..+|..+.
T Consensus 240 ~fvrHHWVHrrRqeGkC~~CgKgFQQKf~------FhsKEivAisCSWCKqayH~Kv 290 (1004)
T KOG0782|consen 240 GFVRHHWVHRRRQEGKCNTCGKGFQQKFF------FHSKEIVAISCSWCKQAYHLKV 290 (1004)
T ss_pred cchHHhHhhHhhhccccchhhhhhhhhee------eccccEEEEEehHHHHHhhcch
Confidence 45555444333334456666666654432 23322 2355666666665544
No 193
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=23.97 E-value=18 Score=22.48 Aligned_cols=13 Identities=54% Similarity=1.288 Sum_probs=7.3
Q ss_pred CCcCCcchhhccC
Q psy16834 444 EPFHCPECGKAFK 456 (488)
Q Consensus 444 ~~~~C~~C~~~F~ 456 (488)
-||.|+.|++.|=
T Consensus 12 ~~~~C~~C~~~FC 24 (43)
T PF01428_consen 12 LPFKCKHCGKSFC 24 (43)
T ss_dssp SHEE-TTTS-EE-
T ss_pred CCeECCCCCcccC
Confidence 3677887777774
No 195
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=23.93 E-value=37 Score=19.04 Aligned_cols=10 Identities=20% Similarity=0.753 Sum_probs=3.6
Q ss_pred cccccccccc
Q psy16834 360 RFKCVFCEKS 369 (488)
Q Consensus 360 ~~~C~~C~k~ 369 (488)
.|.|..|+..
T Consensus 15 ~Y~C~~Cdf~ 24 (30)
T PF07649_consen 15 FYRCSECDFD 24 (30)
T ss_dssp EEE-TTT---
T ss_pred eEECccCCCc
Confidence 4666666543
No 196
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=23.28 E-value=8.9 Score=35.87 Aligned_cols=38 Identities=16% Similarity=0.283 Sum_probs=13.3
Q ss_pred eecccchhhhhcccCCC-CCCcCCCCccccccccccccC
Q psy16834 181 FECDICHKVLKTKSKKS-SGISKNENLRPCTLCDKKLAS 218 (488)
Q Consensus 181 ~~C~~C~~~f~~~~~~~-~~~~~~~~~~~C~~C~~~f~~ 218 (488)
..|+.||..-...-..- .......+...|..|+.-++.
T Consensus 212 ~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~YlK~ 250 (290)
T PF04216_consen 212 IKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYLKT 250 (290)
T ss_dssp TS-TTT---SS-EEE--------SEEEEEETTTTEEEEE
T ss_pred CCCcCCCCCCCcceeeEecCCCCcEEEEECCcccchHHH
Confidence 45666665432221111 122223445667777654443
No 197
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.27 E-value=31 Score=30.32 Aligned_cols=28 Identities=29% Similarity=0.583 Sum_probs=17.0
Q ss_pred CCcCCcchhhccCChhhHhccccccccC
Q psy16834 444 EPFHCPECGKAFKFKRYVTLHMRTHTGN 471 (488)
Q Consensus 444 ~~~~C~~C~~~F~~~~~L~~H~~~H~~~ 471 (488)
+.+.||+|+-.|.....+..=.|+=.|+
T Consensus 18 k~ieCPvC~tkFkkeev~tgsiRiiagD 45 (267)
T COG1655 18 KTIECPVCNTKFKKEEVKTGSIRIIAGD 45 (267)
T ss_pred ceeccCcccchhhhhheeccceeEeccc
Confidence 4566777777776666555555554443
No 198
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=23.22 E-value=19 Score=26.23 Aligned_cols=12 Identities=17% Similarity=0.955 Sum_probs=7.1
Q ss_pred cccccCcccccc
Q psy16834 475 FVCKICNATISS 486 (488)
Q Consensus 475 ~~C~~C~k~f~~ 486 (488)
..|.+||..|..
T Consensus 47 ~~C~~Cg~~~~~ 58 (81)
T PF05129_consen 47 LSCRVCGESFQT 58 (81)
T ss_dssp EEESSS--EEEE
T ss_pred EEecCCCCeEEE
Confidence 678888877754
No 199
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.02 E-value=40 Score=23.79 Aligned_cols=10 Identities=30% Similarity=1.168 Sum_probs=4.8
Q ss_pred eecCccCccc
Q psy16834 124 FDCHICGKTV 133 (488)
Q Consensus 124 ~~C~~C~~~f 133 (488)
|.|..|+..|
T Consensus 13 Y~c~~cg~~~ 22 (82)
T COG2331 13 YECTECGNRF 22 (82)
T ss_pred EeecccchHH
Confidence 4455554444
No 200
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=22.98 E-value=52 Score=32.76 Aligned_cols=26 Identities=19% Similarity=0.514 Sum_probs=14.8
Q ss_pred ccCCcccccccchhhHHHHHHhhcCC
Q psy16834 11 FSCSLCSYSVTIKRNLIMHIKRKHTD 36 (488)
Q Consensus 11 ~~C~~C~~~f~~~~~L~~H~~~~h~~ 36 (488)
+.|+.|++.|.+...+..|+...|.+
T Consensus 58 WiCp~CskkF~d~~~~~~H~~~eH~~ 83 (466)
T PF04780_consen 58 WICPRCSKKFSDAESCLSHMEQEHPA 83 (466)
T ss_pred eeCCcccceeCCHHHHHHHHHHhhhh
Confidence 34555666666666666665555544
No 201
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=22.88 E-value=52 Score=32.78 Aligned_cols=28 Identities=29% Similarity=0.570 Sum_probs=23.0
Q ss_pred ccCCCCCCccCChhhHHHHHhhhccCCC
Q psy16834 68 FLCIPCNKPFSKIENYRLHQRRYHLNSV 95 (488)
Q Consensus 68 ~~C~~C~~~f~~~~~l~~H~~~~h~~~~ 95 (488)
+.|+.|++.|.+...+..|+...|.+..
T Consensus 58 WiCp~CskkF~d~~~~~~H~~~eH~~~l 85 (466)
T PF04780_consen 58 WICPRCSKKFSDAESCLSHMEQEHPAGL 85 (466)
T ss_pred eeCCcccceeCCHHHHHHHHHHhhhhhc
Confidence 5788899999999999999888776643
No 202
>PF05495 zf-CHY: CHY zinc finger; InterPro: IPR008913 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. Pirh2 is an eukaryotic ubiquitin protein ligase, which has been shown to promote p53 degradation in mammals. Pirh2 physically interacts with p53 and promotes ubiquitination of p53 independently of MDM2. Like MDM2, Pirh2 is thought to participate in an autoregulatory feedback loop that controls p53 function. Pirh2 proteins contain three distinct zinc fingers, the CHY-type, the CTCHY-type which is C-terminal to the CHY-type zinc finger and a RING finger. The CHY-type zinc finger has no currently known function []. As well as Pirh2, the CHY-type zinc finger is also found in the following proteins: Yeast helper of Tim protein 13. Hot13 may have a role in the assembly and recycling of the small Tims, a complex of the mitochondrial intermembrane space that participates in the TIM22 import pathway for assembly of the inner membrane [] Several plant hypothetical proteins that also contain haemerythrin cation binding domains Several protozoan hypothetical proteins that also contain a Myb domain The solution structure of this zinc finger has been solved and binds 3 zinc atoms as shown in the following schematic representation: ++---------+-----+ || | | CXHYxxxxxxxxxCCxxxxxCxxCHxxxxxHxxxxxxxxxxxCxxCxxxxxxxxxCxxC | | | | | | | | +-+-----------------+--+ +--+---------+--+ 'C': conserved cysteine involved in the binding of one zinc atom. 'H': conserved histidine involved in the binding of one zinc atom. More information about these proteins can be found at Protein of the Month: Zinc Fingers []; GO: 0008270 zinc ion binding; PDB: 2DKT_A 2K2C_A.
Probab=22.70 E-value=23 Score=24.99 Aligned_cols=14 Identities=14% Similarity=0.273 Sum_probs=5.7
Q ss_pred ceecCccCccccCh
Q psy16834 123 LFDCHICGKTVVTE 136 (488)
Q Consensus 123 ~~~C~~C~~~f~~~ 136 (488)
...|..|+..++-.
T Consensus 41 ~v~Cg~C~~~~~~~ 54 (71)
T PF05495_consen 41 RVICGKCRTEQPID 54 (71)
T ss_dssp EEEETTT--EEES-
T ss_pred CeECCCCCCccChh
Confidence 44555555554443
No 203
>KOG3214|consensus
Probab=22.48 E-value=30 Score=25.81 Aligned_cols=8 Identities=38% Similarity=1.165 Sum_probs=4.2
Q ss_pred cccccccc
Q psy16834 417 KHQCHICN 424 (488)
Q Consensus 417 ~~~C~~C~ 424 (488)
.|.|++|+
T Consensus 23 ~FnClfcn 30 (109)
T KOG3214|consen 23 QFNCLFCN 30 (109)
T ss_pred eeccCccc
Confidence 35555554
No 204
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=22.39 E-value=9 Score=23.48 Aligned_cols=10 Identities=20% Similarity=0.876 Sum_probs=4.4
Q ss_pred cccccccccc
Q psy16834 361 FKCVFCEKSF 370 (488)
Q Consensus 361 ~~C~~C~k~F 370 (488)
|.|..|+..|
T Consensus 29 y~C~~C~~~w 38 (40)
T smart00440 29 YVCTKCGHRW 38 (40)
T ss_pred EEeCCCCCEe
Confidence 4444444433
No 205
>KOG0717|consensus
Probab=21.97 E-value=49 Score=32.48 Aligned_cols=22 Identities=32% Similarity=0.643 Sum_probs=20.1
Q ss_pred eecCccCccccChhhHHHHHHh
Q psy16834 124 FDCHICGKTVVTEKNYKKHMQL 145 (488)
Q Consensus 124 ~~C~~C~~~f~~~~~l~~H~~~ 145 (488)
+-|.+|+++|.+...|+.|...
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 7899999999999999999754
No 206
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=21.88 E-value=35 Score=28.36 Aligned_cols=10 Identities=20% Similarity=0.624 Sum_probs=5.2
Q ss_pred cccccccccc
Q psy16834 418 HQCHICNKIV 427 (488)
Q Consensus 418 ~~C~~C~k~f 427 (488)
|.|+.|+..+
T Consensus 124 ~~C~~C~~~~ 133 (157)
T PF10263_consen 124 YRCPSCGREY 133 (157)
T ss_pred EEcCCCCCEe
Confidence 5555555444
No 207
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=21.80 E-value=66 Score=17.40 Aligned_cols=7 Identities=57% Similarity=1.625 Sum_probs=4.1
Q ss_pred cCCCCCC
Q psy16834 334 LCPICGY 340 (488)
Q Consensus 334 ~C~~C~~ 340 (488)
.|+.||.
T Consensus 4 ~Cp~Cg~ 10 (26)
T PF13248_consen 4 FCPNCGA 10 (26)
T ss_pred CCcccCC
Confidence 4666665
No 208
>PRK14873 primosome assembly protein PriA; Provisional
Probab=21.36 E-value=57 Score=34.52 Aligned_cols=46 Identities=20% Similarity=0.664 Sum_probs=0.0
Q ss_pred ccCCCCCCccCChHHHHHHHHhhcCCCccccccccccccChhHHHHHHhhhcCCCCCccCCccCCcCCCchHHHhhhhhh
Q psy16834 333 VLCPICGYGCFRNAELEEHFISAHSADRFKCVFCEKSFARNCNLKLHIRRYHDKSDNTECPLCGKSFPSRGRLNEHLIQV 412 (488)
Q Consensus 333 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~k~F~~~~~l~~H~~~~H~~~~~~~C~~C~k~F~~~~~L~~H~~~~ 412 (488)
..|..||.. ..|+.|+-... .|.......|..||.
T Consensus 384 l~C~~Cg~~-------------------~~C~~C~~~L~-----------~h~~~~~l~Ch~CG~--------------- 418 (665)
T PRK14873 384 LACARCRTP-------------------ARCRHCTGPLG-----------LPSAGGTPRCRWCGR--------------- 418 (665)
T ss_pred eEhhhCcCe-------------------eECCCCCCcee-----------EecCCCeeECCCCcC---------------
Q ss_pred ccCCcccccccc
Q psy16834 413 HPAQKHQCHICN 424 (488)
Q Consensus 413 h~~~~~~C~~C~ 424 (488)
.. .|..|+.||
T Consensus 419 ~~-~p~~Cp~Cg 429 (665)
T PRK14873 419 AA-PDWRCPRCG 429 (665)
T ss_pred CC-cCccCCCCc
No 209
>cd00924 Cyt_c_Oxidase_Vb Cytochrome c oxidase subunit Vb. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Vb is one of three mammalian subunits that lacks a transmembrane region. Subunit Vb is located on the matrix side of the membrane and binds the regulatory subunit of protein kinase A. The abnormally extended conformation is stable only in the CcO assembly.
Probab=21.35 E-value=24 Score=26.64 Aligned_cols=18 Identities=50% Similarity=1.147 Sum_probs=12.6
Q ss_pred HhhcCCCCcCCcchhhccC
Q psy16834 438 LLHTNSEPFHCPECGKAFK 456 (488)
Q Consensus 438 ~~H~~~~~~~C~~C~~~F~ 456 (488)
.++.| +|++|+.||.-|.
T Consensus 73 ~l~~g-~~~rC~eCG~~fk 90 (97)
T cd00924 73 WLEKG-KPKRCPECGHVFK 90 (97)
T ss_pred EEeCC-CceeCCCCCcEEE
Confidence 45556 6788888887775
No 210
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=21.34 E-value=36 Score=24.99 Aligned_cols=12 Identities=33% Similarity=0.744 Sum_probs=6.0
Q ss_pred CccCCCCCCccC
Q psy16834 67 PFLCIPCNKPFS 78 (488)
Q Consensus 67 ~~~C~~C~~~f~ 78 (488)
|-.|..||..|.
T Consensus 58 Pa~CkkCGfef~ 69 (97)
T COG3357 58 PARCKKCGFEFR 69 (97)
T ss_pred ChhhcccCcccc
Confidence 444555555554
No 211
>KOG3408|consensus
Probab=21.08 E-value=40 Score=26.27 Aligned_cols=22 Identities=27% Similarity=0.621 Sum_probs=10.7
Q ss_pred CcCCcchhhccCChhhHhcccc
Q psy16834 445 PFHCPECGKAFKFKRYVTLHMR 466 (488)
Q Consensus 445 ~~~C~~C~~~F~~~~~L~~H~~ 466 (488)
.|-|-.|.+-|.....|..|.+
T Consensus 57 qfyCi~CaRyFi~~~~l~~H~k 78 (129)
T KOG3408|consen 57 QFYCIECARYFIDAKALKTHFK 78 (129)
T ss_pred eeehhhhhhhhcchHHHHHHHh
Confidence 3444455555555555555444
No 212
>PHA02998 RNA polymerase subunit; Provisional
Probab=20.94 E-value=47 Score=27.91 Aligned_cols=10 Identities=20% Similarity=0.766 Sum_probs=5.3
Q ss_pred cccccCcccc
Q psy16834 475 FVCKICNATI 484 (488)
Q Consensus 475 ~~C~~C~k~f 484 (488)
|.|..||+.|
T Consensus 172 YkC~~CG~~w 181 (195)
T PHA02998 172 HACRDCKKHF 181 (195)
T ss_pred EEcCCCCCcc
Confidence 4555555544
No 213
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=20.52 E-value=55 Score=25.55 Aligned_cols=25 Identities=20% Similarity=0.474 Sum_probs=15.0
Q ss_pred ceecCccCccccChhhHHHHHHhccCCCceeCccccc
Q psy16834 123 LFDCHICGKTVVTEKNYKKHMQLHSDDKPFECQFCRK 159 (488)
Q Consensus 123 ~~~C~~C~~~f~~~~~l~~H~~~H~~~~~~~C~~C~~ 159 (488)
...|..||..|.... ..+.||.||.
T Consensus 70 ~~~C~~Cg~~~~~~~------------~~~~CP~Cgs 94 (113)
T PRK12380 70 QAWCWDCSQVVEIHQ------------HDAQCPHCHG 94 (113)
T ss_pred EEEcccCCCEEecCC------------cCccCcCCCC
Confidence 466777776665322 3345777773
No 214
>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=20.48 E-value=21 Score=29.16 Aligned_cols=13 Identities=23% Similarity=0.631 Sum_probs=7.0
Q ss_pred cccccccccccCh
Q psy16834 361 FKCVFCEKSFARN 373 (488)
Q Consensus 361 ~~C~~C~k~F~~~ 373 (488)
=.|..||+.|++-
T Consensus 29 ReC~~C~~RFTTy 41 (147)
T TIGR00244 29 RECLECHERFTTF 41 (147)
T ss_pred ccCCccCCcccee
Confidence 3455555555553
No 215
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=20.40 E-value=53 Score=25.74 Aligned_cols=25 Identities=24% Similarity=0.648 Sum_probs=15.0
Q ss_pred ceecCccCccccChhhHHHHHHhccCCCceeCccccc
Q psy16834 123 LFDCHICGKTVVTEKNYKKHMQLHSDDKPFECQFCRK 159 (488)
Q Consensus 123 ~~~C~~C~~~f~~~~~l~~H~~~H~~~~~~~C~~C~~ 159 (488)
...|..|+..|..... .+.||.||.
T Consensus 70 ~~~C~~Cg~~~~~~~~------------~~~CP~Cgs 94 (115)
T TIGR00100 70 ECECEDCSEEVSPEID------------LYRCPKCHG 94 (115)
T ss_pred EEEcccCCCEEecCCc------------CccCcCCcC
Confidence 3667777766654321 356777774
No 216
>PRK05580 primosome assembly protein PriA; Validated
Probab=20.28 E-value=67 Score=34.24 Aligned_cols=10 Identities=30% Similarity=0.883 Sum_probs=5.3
Q ss_pred cccccccccc
Q psy16834 361 FKCVFCEKSF 370 (488)
Q Consensus 361 ~~C~~C~k~F 370 (488)
..|+.|+-..
T Consensus 391 ~~C~~C~~~l 400 (679)
T PRK05580 391 AECPHCDASL 400 (679)
T ss_pred cCCCCCCCce
Confidence 4566665443
No 217
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=20.23 E-value=38 Score=27.74 Aligned_cols=8 Identities=38% Similarity=1.377 Sum_probs=3.4
Q ss_pred CcCCcchh
Q psy16834 445 PFHCPECG 452 (488)
Q Consensus 445 ~~~C~~C~ 452 (488)
.|.|..|+
T Consensus 140 ~YrC~~C~ 147 (156)
T COG3091 140 VYRCGKCG 147 (156)
T ss_pred eEEeccCC
Confidence 34444443
No 218
>KOG1842|consensus
Probab=20.13 E-value=65 Score=31.43 Aligned_cols=34 Identities=24% Similarity=0.338 Sum_probs=29.3
Q ss_pred CccccccccccccChhHHHHHHhhcCCCCchhhh
Q psy16834 205 NLRPCTLCDKKLASERKLKEHIRKQHPTSVEADL 238 (488)
Q Consensus 205 ~~~~C~~C~~~f~~~~~L~~H~~~~h~~~~~~~~ 238 (488)
..|.|++|...|.+...|..|....|+...+.|+
T Consensus 14 egflCPiC~~dl~~~~~L~~H~d~eH~~ed~~D~ 47 (505)
T KOG1842|consen 14 EGFLCPICLLDLPNLSALNDHLDVEHFEEDEKDS 47 (505)
T ss_pred hcccCchHhhhhhhHHHHHHHHhhhccccchhhH
Confidence 3578999999999999999999999998776443
No 219
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=20.06 E-value=21 Score=37.11 Aligned_cols=57 Identities=28% Similarity=0.548 Sum_probs=35.4
Q ss_pred cCCCCCCccCChHHHHHHHHhhcCCCcc-ccccccccccChhHHHHHHhhhcCCCCCccCCccCCc
Q psy16834 334 LCPICGYGCFRNAELEEHFISAHSADRF-KCVFCEKSFARNCNLKLHIRRYHDKSDNTECPLCGKS 398 (488)
Q Consensus 334 ~C~~C~~~f~~~~~l~~H~~~~~~~~~~-~C~~C~k~F~~~~~l~~H~~~~H~~~~~~~C~~C~k~ 398 (488)
.|..||-+|+-..+|---.. .++...| .|+.|.+.|....+-+-|. .|..|+.||-.
T Consensus 125 ~CT~CGPRfTIi~alPYDR~-nTsM~~F~lC~~C~~EY~dP~nRRfHA-------Qp~aCp~CGP~ 182 (750)
T COG0068 125 NCTNCGPRFTIIEALPYDRE-NTSMADFPLCPFCDKEYKDPLNRRFHA-------QPIACPKCGPH 182 (750)
T ss_pred ccCCCCcceeeeccCCCCcc-cCccccCcCCHHHHHHhcCcccccccc-------ccccCcccCCC
Confidence 37777776665554432222 2233334 5888988888888755553 36789999864
Done!