Query psy6546
Match_columns 294
No_of_seqs 171 out of 1539
Neff 10.8
Searched_HMMs 46136
Date Fri Aug 16 20:46:24 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6546.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6546hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.9 4.2E-28 9.1E-33 186.2 4.9 127 151-278 131-263 (279)
2 KOG2462|consensus 99.9 2.5E-27 5.5E-32 181.9 7.0 137 29-199 127-265 (279)
3 KOG1074|consensus 99.9 3.9E-28 8.5E-33 210.4 2.0 142 151-292 606-941 (958)
4 KOG3608|consensus 99.9 5.5E-26 1.2E-30 179.2 10.4 232 27-283 129-377 (467)
5 KOG3608|consensus 99.9 1.2E-23 2.6E-28 166.0 13.5 183 99-282 139-345 (467)
6 KOG1074|consensus 99.9 1.8E-22 3.9E-27 175.6 7.9 161 95-255 604-931 (958)
7 KOG3623|consensus 99.8 1.2E-21 2.6E-26 168.0 6.9 116 30-145 208-331 (1007)
8 KOG3623|consensus 99.8 3.2E-19 7E-24 153.2 8.1 102 97-198 211-330 (1007)
9 KOG3576|consensus 99.6 3.5E-17 7.6E-22 120.0 1.2 77 151-227 118-196 (267)
10 KOG3576|consensus 99.6 9E-16 1.9E-20 112.7 3.1 106 124-229 118-237 (267)
11 PLN03086 PRLI-interacting fact 99.3 2E-12 4.4E-17 112.2 7.4 145 124-283 408-565 (567)
12 PLN03086 PRLI-interacting fact 99.2 1.2E-10 2.5E-15 101.5 12.0 154 30-225 405-561 (567)
13 PHA00733 hypothetical protein 99.1 3.7E-11 8.1E-16 85.4 3.3 79 204-283 40-124 (128)
14 PHA02768 hypothetical protein; 99.0 1.5E-10 3.2E-15 67.5 2.2 43 232-275 6-48 (55)
15 KOG3993|consensus 98.9 1.1E-10 2.5E-15 95.4 -0.3 160 124-283 268-483 (500)
16 PHA00733 hypothetical protein 98.9 1.2E-09 2.6E-14 77.7 4.4 60 168-228 64-123 (128)
17 PHA02768 hypothetical protein; 98.9 8.2E-10 1.8E-14 64.4 2.1 43 204-247 5-47 (55)
18 KOG3993|consensus 98.8 3.3E-10 7.1E-15 92.8 -1.7 163 91-253 262-480 (500)
19 PHA00616 hypothetical protein 98.5 2.8E-08 6E-13 55.1 0.8 32 258-289 1-32 (44)
20 PF13465 zf-H2C2_2: Zinc-finge 98.4 1.9E-07 4.2E-12 46.5 1.9 24 246-269 1-25 (26)
21 PHA00732 hypothetical protein 98.3 7.1E-07 1.5E-11 57.5 2.7 47 204-255 1-48 (79)
22 PHA00732 hypothetical protein 98.3 8E-07 1.7E-11 57.2 2.9 43 178-225 2-45 (79)
23 PF13465 zf-H2C2_2: Zinc-finge 98.2 1.2E-06 2.6E-11 43.6 2.3 24 219-242 1-25 (26)
24 PHA00616 hypothetical protein 98.1 1.2E-06 2.7E-11 48.6 1.7 27 204-230 1-27 (44)
25 PF05605 zf-Di19: Drought indu 98.1 3.1E-06 6.8E-11 50.6 3.3 49 232-283 3-54 (54)
26 PF00096 zf-C2H2: Zinc finger, 97.9 1.1E-05 2.3E-10 38.9 2.4 22 205-226 1-22 (23)
27 PF12756 zf-C2H2_2: C2H2 type 97.9 5.5E-06 1.2E-10 56.8 1.3 71 207-280 2-72 (100)
28 PF00096 zf-C2H2: Zinc finger, 97.8 1.1E-05 2.5E-10 38.8 1.9 22 259-280 1-22 (23)
29 PF05605 zf-Di19: Drought indu 97.8 4.7E-05 1E-09 45.5 4.3 46 205-253 3-51 (54)
30 PF12756 zf-C2H2_2: C2H2 type 97.8 2.4E-05 5.1E-10 53.6 3.1 72 153-227 2-73 (100)
31 PF13894 zf-C2H2_4: C2H2-type 97.8 9.9E-06 2.2E-10 39.4 0.9 24 259-282 1-24 (24)
32 PF13912 zf-C2H2_6: C2H2-type 97.7 1.8E-05 4E-10 39.8 1.2 26 258-283 1-26 (27)
33 PF13894 zf-C2H2_4: C2H2-type 97.7 5.6E-05 1.2E-09 36.7 2.8 23 205-227 1-23 (24)
34 PF13912 zf-C2H2_6: C2H2-type 97.5 7.5E-05 1.6E-09 37.5 1.7 24 204-227 1-24 (27)
35 COG5189 SFP1 Putative transcri 97.5 6.1E-05 1.3E-09 60.2 1.9 72 28-116 345-418 (423)
36 PF13909 zf-H2C2_5: C2H2-type 97.2 0.00011 2.4E-09 35.7 0.5 24 259-283 1-24 (24)
37 PF09237 GAGA: GAGA factor; I 97.0 0.00022 4.9E-09 40.5 0.2 39 248-286 12-52 (54)
38 KOG2231|consensus 96.9 0.0051 1.1E-07 55.4 8.6 50 206-255 184-236 (669)
39 smart00355 ZnF_C2H2 zinc finge 96.8 0.001 2.3E-08 32.6 2.2 19 234-252 3-21 (26)
40 smart00355 ZnF_C2H2 zinc finge 96.8 0.0014 3.1E-08 32.1 2.5 24 205-228 1-24 (26)
41 COG5189 SFP1 Putative transcri 96.8 0.00036 7.9E-09 55.9 0.4 68 202-279 347-419 (423)
42 PF12874 zf-met: Zinc-finger o 96.7 0.0012 2.6E-08 32.3 1.6 22 205-226 1-22 (25)
43 KOG2231|consensus 96.6 0.0092 2E-07 53.8 7.8 102 98-201 117-236 (669)
44 PF13909 zf-H2C2_5: C2H2-type 96.6 0.002 4.4E-08 31.1 2.2 22 205-227 1-22 (24)
45 PF09237 GAGA: GAGA factor; I 96.5 0.0035 7.7E-08 35.7 2.9 28 203-230 23-50 (54)
46 PF12874 zf-met: Zinc-finger o 96.4 0.0014 3.1E-08 32.0 0.8 22 259-280 1-22 (25)
47 PF12171 zf-C2H2_jaz: Zinc-fin 96.3 0.0021 4.5E-08 32.1 1.2 22 259-280 2-23 (27)
48 KOG1146|consensus 96.2 0.0026 5.6E-08 60.8 2.3 104 31-145 464-611 (1406)
49 KOG1146|consensus 96.2 0.0011 2.4E-08 63.1 -0.3 99 126-226 439-540 (1406)
50 PRK04860 hypothetical protein; 95.3 0.0081 1.8E-07 44.5 1.4 36 204-243 119-155 (160)
51 PRK04860 hypothetical protein; 95.3 0.013 2.7E-07 43.5 2.2 35 232-270 120-155 (160)
52 KOG2785|consensus 95.1 0.016 3.4E-07 48.2 2.5 82 32-119 3-91 (390)
53 PF12171 zf-C2H2_jaz: Zinc-fin 95.0 0.01 2.3E-07 29.5 0.8 21 232-252 2-22 (27)
54 PF13913 zf-C2HC_2: zinc-finge 94.7 0.038 8.2E-07 26.9 2.4 22 32-54 2-23 (25)
55 COG5236 Uncharacterized conser 94.5 0.048 1E-06 44.7 3.7 79 206-284 222-307 (493)
56 KOG2482|consensus 94.5 0.33 7.2E-06 39.9 8.4 63 111-173 130-218 (423)
57 COG5236 Uncharacterized conser 94.3 0.15 3.3E-06 41.9 6.2 137 32-175 151-306 (493)
58 PF13913 zf-C2HC_2: zinc-finge 94.2 0.053 1.2E-06 26.4 2.2 19 206-225 4-22 (25)
59 KOG2785|consensus 94.2 0.18 4E-06 42.1 6.5 49 204-252 166-241 (390)
60 smart00451 ZnF_U1 U1-like zinc 94.1 0.049 1.1E-06 28.9 2.1 23 204-226 3-25 (35)
61 smart00451 ZnF_U1 U1-like zinc 92.1 0.14 3.1E-06 27.0 2.1 23 96-118 3-25 (35)
62 KOG2482|consensus 91.0 0.39 8.4E-06 39.6 4.3 53 94-146 142-218 (423)
63 COG4049 Uncharacterized protei 90.9 0.14 3.1E-06 29.8 1.3 30 28-57 13-42 (65)
64 KOG4173|consensus 90.9 0.17 3.7E-06 38.4 2.1 46 151-198 80-127 (253)
65 cd00350 rubredoxin_like Rubred 90.8 0.12 2.6E-06 27.1 0.8 11 205-215 2-12 (33)
66 KOG2893|consensus 90.1 0.092 2E-06 40.7 0.1 42 98-142 12-53 (341)
67 PF12013 DUF3505: Protein of u 88.9 0.46 1E-05 32.9 2.9 80 203-283 10-109 (109)
68 COG5048 FOG: Zn-finger [Genera 87.0 0.099 2.1E-06 45.9 -1.8 53 124-176 290-349 (467)
69 TIGR00622 ssl1 transcription f 86.9 0.67 1.5E-05 31.9 2.6 20 31-50 14-33 (112)
70 KOG2893|consensus 86.3 0.21 4.5E-06 38.9 -0.1 47 204-254 11-58 (341)
71 KOG2186|consensus 84.3 0.57 1.2E-05 37.0 1.4 45 124-170 4-48 (276)
72 COG5048 FOG: Zn-finger [Genera 83.8 0.34 7.3E-06 42.5 0.0 58 231-288 289-353 (467)
73 TIGR00622 ssl1 transcription f 83.5 2.3 5E-05 29.3 3.9 49 98-147 57-105 (112)
74 PF06524 NOA36: NOA36 protein; 83.5 0.5 1.1E-05 37.4 0.8 26 256-281 207-232 (314)
75 PF10571 UPF0547: Uncharacteri 83.1 0.74 1.6E-05 22.6 1.1 6 207-212 17-22 (26)
76 COG2888 Predicted Zn-ribbon RN 82.8 0.94 2E-05 27.0 1.6 31 232-266 28-58 (61)
77 KOG2186|consensus 82.1 0.93 2E-05 35.8 1.8 47 178-226 4-50 (276)
78 PF12013 DUF3505: Protein of u 82.0 3.4 7.4E-05 28.5 4.5 27 31-57 79-109 (109)
79 cd00729 rubredoxin_SM Rubredox 81.6 0.7 1.5E-05 24.4 0.7 9 258-266 18-26 (34)
80 KOG4173|consensus 81.6 0.72 1.6E-05 35.1 1.0 81 177-259 79-176 (253)
81 smart00659 RPOLCX RNA polymera 79.9 0.9 2E-05 25.6 0.8 11 205-215 3-13 (44)
82 COG4049 Uncharacterized protei 79.8 1 2.2E-05 26.3 1.0 25 204-228 17-41 (65)
83 PF09538 FYDLN_acid: Protein o 79.5 1.8 3.9E-05 29.8 2.4 11 59-69 9-19 (108)
84 PF06524 NOA36: NOA36 protein; 78.2 0.76 1.7E-05 36.4 0.3 20 121-140 207-226 (314)
85 PF14353 CpXC: CpXC protein 77.7 1.1 2.3E-05 32.1 0.9 20 94-113 36-55 (128)
86 PRK00464 nrdR transcriptional 77.2 1.3 2.8E-05 32.7 1.2 18 96-113 28-45 (154)
87 PF05443 ROS_MUCR: ROS/MUCR tr 76.3 2.2 4.8E-05 30.5 2.1 33 23-58 63-95 (132)
88 TIGR00373 conserved hypothetic 75.7 3.2 6.8E-05 31.0 2.9 17 204-220 109-125 (158)
89 PF13719 zinc_ribbon_5: zinc-r 75.0 1.5 3.3E-05 23.5 0.8 11 96-106 25-35 (37)
90 PF13717 zinc_ribbon_4: zinc-r 74.0 1.9 4.2E-05 23.0 1.1 10 97-106 26-35 (36)
91 PF12907 zf-met2: Zinc-binding 73.8 2 4.3E-05 23.6 1.1 29 259-287 2-33 (40)
92 TIGR02098 MJ0042_CXXC MJ0042 f 73.4 2.1 4.6E-05 23.0 1.2 10 97-106 26-35 (38)
93 smart00834 CxxC_CXXC_SSSS Puta 73.1 0.58 1.3E-05 25.7 -1.2 11 33-43 6-16 (41)
94 PF13878 zf-C2H2_3: zinc-finge 72.6 6.6 0.00014 21.7 3.0 25 32-56 13-39 (41)
95 COG1996 RPC10 DNA-directed RNA 72.3 1.6 3.5E-05 25.1 0.5 10 232-241 7-16 (49)
96 cd00730 rubredoxin Rubredoxin; 70.2 4.7 0.0001 23.4 2.1 12 60-71 2-13 (50)
97 TIGR02605 CxxC_CxxC_SSSS putat 69.1 0.85 1.8E-05 26.6 -1.1 29 33-67 6-34 (52)
98 PRK06266 transcription initiat 69.1 2.3 5E-05 32.4 0.9 31 204-242 117-147 (178)
99 TIGR00373 conserved hypothetic 68.6 3.7 8.1E-05 30.6 1.9 30 177-214 109-138 (158)
100 smart00531 TFIIE Transcription 68.5 5.8 0.00013 29.1 2.9 12 232-243 100-111 (147)
101 smart00734 ZnF_Rad18 Rad18-lik 68.2 5.5 0.00012 19.4 1.9 19 206-225 3-21 (26)
102 COG4957 Predicted transcriptio 67.5 10 0.00022 27.0 3.6 34 22-58 66-99 (148)
103 COG1592 Rubrerythrin [Energy p 67.3 2.7 5.9E-05 31.4 1.0 9 205-213 135-143 (166)
104 PF03604 DNA_RNApol_7kD: DNA d 66.9 1.9 4.2E-05 22.3 0.1 7 232-238 18-24 (32)
105 PF02892 zf-BED: BED zinc fing 65.8 2.3 5E-05 23.8 0.3 20 259-278 17-40 (45)
106 PRK14890 putative Zn-ribbon RN 65.3 4.1 9E-05 24.4 1.3 8 204-211 48-55 (59)
107 PF09986 DUF2225: Uncharacteri 65.0 1 2.3E-05 35.4 -1.7 11 124-134 49-59 (214)
108 PF08274 PhnA_Zn_Ribbon: PhnA 64.9 2.3 5E-05 21.7 0.1 11 256-266 17-27 (30)
109 smart00614 ZnF_BED BED zinc fi 64.7 6.3 0.00014 22.7 2.0 21 205-225 19-44 (50)
110 PRK00398 rpoP DNA-directed RNA 63.8 4.4 9.6E-05 22.9 1.2 11 59-69 3-13 (46)
111 PRK06266 transcription initiat 63.6 5.1 0.00011 30.5 1.8 30 177-214 117-146 (178)
112 PF09788 Tmemb_55A: Transmembr 63.4 6.7 0.00015 31.3 2.5 32 31-69 64-95 (256)
113 PF00301 Rubredoxin: Rubredoxi 62.1 3.4 7.4E-05 23.6 0.5 11 95-105 33-43 (47)
114 TIGR02300 FYDLN_acid conserved 60.2 8.2 0.00018 27.2 2.2 10 60-69 10-19 (129)
115 PHA00626 hypothetical protein 59.3 4.2 9.1E-05 24.0 0.5 16 30-45 21-36 (59)
116 PF09723 Zn-ribbon_8: Zinc rib 59.0 6.3 0.00014 21.8 1.2 10 60-69 6-15 (42)
117 COG1998 RPS31 Ribosomal protei 58.4 6.4 0.00014 22.5 1.2 14 227-240 33-46 (51)
118 KOG4167|consensus 57.3 8.5 0.00018 35.6 2.4 27 94-120 790-816 (907)
119 PF15269 zf-C2H2_7: Zinc-finge 57.2 15 0.00033 20.5 2.5 26 30-55 18-43 (54)
120 PF05290 Baculo_IE-1: Baculovi 57.2 3.3 7.1E-05 29.4 -0.1 10 178-187 81-90 (140)
121 PF05443 ROS_MUCR: ROS/MUCR tr 56.3 5.4 0.00012 28.6 0.8 24 259-285 73-96 (132)
122 KOG4377|consensus 56.3 5.1 0.00011 34.2 0.8 102 151-255 272-427 (480)
123 COG1997 RPL43A Ribosomal prote 55.2 8.4 0.00018 25.1 1.5 14 95-108 52-65 (89)
124 COG1198 PriA Primosomal protei 53.4 11 0.00024 35.5 2.5 10 123-132 475-484 (730)
125 PF07754 DUF1610: Domain of un 52.7 5.6 0.00012 19.1 0.3 7 232-238 17-23 (24)
126 PF04959 ARS2: Arsenite-resist 52.4 4.3 9.4E-05 31.8 -0.2 21 232-252 78-98 (214)
127 PRK04023 DNA polymerase II lar 49.6 21 0.00045 34.8 3.6 9 124-132 627-635 (1121)
128 PF02176 zf-TRAF: TRAF-type zi 49.5 9.7 0.00021 22.7 1.1 7 111-117 25-31 (60)
129 KOG4167|consensus 48.5 14 0.00031 34.2 2.4 27 30-56 790-816 (907)
130 PRK04023 DNA polymerase II lar 48.3 19 0.00042 34.9 3.3 11 232-242 664-674 (1121)
131 KOG2593|consensus 47.9 11 0.00024 32.6 1.5 11 59-69 128-138 (436)
132 PF04959 ARS2: Arsenite-resist 47.7 17 0.00036 28.6 2.4 26 204-229 77-102 (214)
133 KOG2807|consensus 46.4 26 0.00056 29.2 3.3 17 204-220 290-306 (378)
134 PRK09678 DNA-binding transcrip 45.6 3 6.5E-05 26.3 -1.6 18 257-274 26-45 (72)
135 smart00440 ZnF_C2C2 C2C2 Zinc 45.0 14 0.00031 20.2 1.2 13 95-107 27-39 (40)
136 PF01096 TFIIS_C: Transcriptio 44.7 8.3 0.00018 21.0 0.2 12 95-106 27-38 (39)
137 KOG1701|consensus 44.7 5.2 0.00011 34.4 -0.8 11 259-269 428-438 (468)
138 KOG2272|consensus 43.7 18 0.00038 28.9 1.9 15 123-137 99-113 (332)
139 COG1773 Rubredoxin [Energy pro 43.5 21 0.00045 21.2 1.7 9 96-104 36-44 (55)
140 KOG2071|consensus 41.9 22 0.00048 32.2 2.5 31 27-57 413-443 (579)
141 PF09845 DUF2072: Zn-ribbon co 39.8 16 0.00034 26.1 1.0 12 205-216 2-13 (131)
142 COG3091 SprT Zn-dependent meta 39.8 13 0.00029 27.2 0.7 33 204-240 117-149 (156)
143 PRK03824 hypA hydrogenase nick 39.2 21 0.00045 25.8 1.6 13 96-108 70-82 (135)
144 PF12760 Zn_Tnp_IS1595: Transp 38.8 23 0.00051 19.9 1.5 9 257-265 36-44 (46)
145 KOG4377|consensus 38.5 18 0.00039 31.1 1.3 79 205-288 272-375 (480)
146 PF13451 zf-trcl: Probable zin 37.5 18 0.00039 20.9 0.9 12 232-243 5-16 (49)
147 COG3364 Zn-ribbon containing p 36.2 24 0.00052 23.8 1.4 12 205-216 3-14 (112)
148 KOG2593|consensus 34.4 24 0.00051 30.7 1.5 39 91-131 123-161 (436)
149 KOG3408|consensus 34.2 26 0.00056 24.5 1.3 29 91-119 52-80 (129)
150 PF14369 zf-RING_3: zinc-finge 34.0 19 0.00041 19.0 0.6 11 33-43 3-13 (35)
151 KOG2907|consensus 33.6 27 0.00058 24.1 1.3 11 259-269 103-113 (116)
152 COG1198 PriA Primosomal protei 31.4 13 0.00029 35.0 -0.4 12 256-267 473-484 (730)
153 PF13453 zf-TFIIB: Transcripti 31.2 37 0.00081 18.5 1.5 19 204-222 19-37 (41)
154 PF03811 Zn_Tnp_IS1: InsA N-te 30.8 34 0.00073 18.3 1.2 15 88-102 21-35 (36)
155 PRK12496 hypothetical protein; 30.6 13 0.00029 27.8 -0.5 10 205-214 128-137 (164)
156 TIGR01206 lysW lysine biosynth 30.3 24 0.00052 20.9 0.6 9 98-106 4-12 (54)
157 PF03145 Sina: Seven in absent 30.1 34 0.00074 26.5 1.7 48 236-285 23-74 (198)
158 COG5151 SSL1 RNA polymerase II 30.1 54 0.0012 27.2 2.7 26 94-119 386-411 (421)
159 KOG3408|consensus 30.0 29 0.00063 24.3 1.1 21 232-252 58-78 (129)
160 PF04780 DUF629: Protein of un 29.3 48 0.001 29.5 2.5 25 203-227 56-80 (466)
161 PTZ00255 60S ribosomal protein 29.3 28 0.0006 23.1 0.8 14 95-108 53-66 (90)
162 KOG1280|consensus 28.9 64 0.0014 27.3 3.0 39 28-66 75-116 (381)
163 PF01780 Ribosomal_L37ae: Ribo 28.6 17 0.00037 24.1 -0.2 13 95-107 52-64 (90)
164 PF14446 Prok-RING_1: Prokaryo 28.6 34 0.00074 20.2 1.0 10 97-106 22-31 (54)
165 PF04216 FdhE: Protein involve 28.0 6 0.00013 32.8 -3.0 10 151-160 198-207 (290)
166 KOG4727|consensus 28.0 26 0.00056 26.2 0.6 22 257-278 74-95 (193)
167 TIGR00280 L37a ribosomal prote 27.4 29 0.00062 23.1 0.7 14 95-108 52-65 (91)
168 PRK00432 30S ribosomal protein 27.3 25 0.00055 20.4 0.4 10 231-240 37-46 (50)
169 PRK04351 hypothetical protein; 27.1 31 0.00068 25.4 0.9 31 204-241 112-142 (149)
170 PF04423 Rad50_zn_hook: Rad50 26.9 23 0.0005 20.7 0.2 14 34-47 22-35 (54)
171 smart00154 ZnF_AN1 AN1-like Zi 26.6 38 0.00083 18.4 1.0 14 204-217 12-25 (39)
172 PF10013 DUF2256: Uncharacteri 26.5 26 0.00057 19.4 0.3 13 260-272 10-22 (42)
173 COG0068 HypF Hydrogenase matur 26.5 30 0.00064 32.3 0.8 83 30-132 99-182 (750)
174 COG1656 Uncharacterized conser 25.9 82 0.0018 23.6 2.8 17 204-220 130-146 (165)
175 COG1675 TFA1 Transcription ini 25.8 91 0.002 23.7 3.2 13 204-216 113-125 (176)
176 KOG1280|consensus 25.6 61 0.0013 27.4 2.4 21 124-144 80-100 (381)
177 TIGR00100 hypA hydrogenase nic 25.5 26 0.00056 24.5 0.2 12 205-216 71-82 (115)
178 PRK12380 hydrogenase nickel in 25.4 25 0.00054 24.5 0.1 10 205-214 71-80 (113)
179 PF07975 C1_4: TFIIH C1-like d 25.0 16 0.00035 21.3 -0.7 23 232-254 22-44 (51)
180 PF01155 HypA: Hydrogenase exp 24.8 22 0.00047 24.8 -0.3 12 205-216 71-82 (113)
181 PRK03976 rpl37ae 50S ribosomal 24.4 34 0.00073 22.7 0.6 14 95-108 53-66 (90)
182 PF10263 SprT-like: SprT-like 24.1 20 0.00044 26.4 -0.5 31 204-241 123-153 (157)
183 PF12773 DZR: Double zinc ribb 24.0 45 0.00097 19.0 1.0 6 179-184 31-36 (50)
184 PF09963 DUF2197: Uncharacteri 23.8 19 0.00042 21.4 -0.5 8 123-130 31-38 (56)
185 COG2879 Uncharacterized small 23.7 45 0.00097 20.3 1.0 21 267-287 21-41 (65)
186 PF08790 zf-LYAR: LYAR-type C2 23.6 39 0.00084 16.9 0.6 9 260-268 2-10 (28)
187 PF01363 FYVE: FYVE zinc finge 23.5 43 0.00094 20.6 1.0 8 180-187 12-19 (69)
188 PF01927 Mut7-C: Mut7-C RNAse 23.5 50 0.0011 24.2 1.5 12 124-135 125-136 (147)
189 PF08271 TF_Zn_Ribbon: TFIIB z 23.1 37 0.0008 18.7 0.5 14 94-107 17-30 (43)
190 PF13824 zf-Mss51: Zinc-finger 22.8 70 0.0015 19.0 1.6 18 28-45 10-27 (55)
191 TIGR00244 transcriptional regu 22.6 55 0.0012 24.0 1.4 16 97-112 29-44 (147)
192 COG0068 HypF Hydrogenase matur 21.7 23 0.00049 33.0 -0.8 57 152-213 125-182 (750)
193 PF01428 zf-AN1: AN1-like Zinc 20.9 42 0.0009 18.6 0.4 13 204-216 13-25 (43)
194 smart00731 SprT SprT homologue 20.9 37 0.0008 24.8 0.3 32 204-241 112-143 (146)
195 PF06220 zf-U1: U1 zinc finger 20.6 97 0.0021 16.7 1.8 21 32-52 3-25 (38)
196 PF07282 OrfB_Zn_ribbon: Putat 20.6 95 0.0021 19.0 2.1 12 204-215 46-57 (69)
197 TIGR00686 phnA alkylphosphonat 20.4 62 0.0013 22.2 1.2 11 204-214 19-29 (109)
198 KOG4124|consensus 20.4 18 0.00039 30.3 -1.5 70 29-115 346-417 (442)
No 1
>KOG2462|consensus
Probab=99.94 E-value=4.2e-28 Score=186.19 Aligned_cols=127 Identities=28% Similarity=0.694 Sum_probs=79.6
Q ss_pred ccCCCCCcccCCHHHHHHHHHhhcC----CCcccCcchhccCCchHHHhHHhhcCCCceeCCCCccccCCHHHHHHHHHH
Q psy6546 151 YICHACPREFSSEATMKAHVASHNG----VQHACDQCDRTFSCMPYLRQHQKLHSGITYSCPSCSKSFNRKDRYRMHLKL 226 (294)
Q Consensus 151 ~~C~~C~~~f~~~~~l~~H~~~~~~----~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~C~~~f~~~~~l~~H~~~ 226 (294)
|.|+.||+.+.+.+.|.+|.+.|-. ..+.|++|++++.+...|..|+++|. -+++|.+||+.|.+..-|+.|+++
T Consensus 131 ~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~-l~c~C~iCGKaFSRPWLLQGHiRT 209 (279)
T KOG2462|consen 131 YKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT-LPCECGICGKAFSRPWLLQGHIRT 209 (279)
T ss_pred eeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccC-CCcccccccccccchHHhhccccc
Confidence 5555555555555555555555432 24566666666666666666666665 266666666666666666666666
Q ss_pred hCCCc-cccccccccccCHHHHHHHHhhhc-ccccccccccccccchhhhhhhh
Q psy6546 227 HQGVR-HTCKECSKEFSNEYNLKNHMVLHD-VRAYVCELCARQFTRVDHFNHHR 278 (294)
Q Consensus 227 h~~~~-~~C~~C~~~f~~~~~l~~H~~~h~-~~~~~C~~C~~~f~~~~~l~~H~ 278 (294)
|+|++ |.|+.|+++|.++++|+.|+++|. .+.|+|..|++.|..++.|.+|.
T Consensus 210 HTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~ 263 (279)
T KOG2462|consen 210 HTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHS 263 (279)
T ss_pred ccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhh
Confidence 66665 666666666666666666666664 56666666666666666666664
No 2
>KOG2462|consensus
Probab=99.94 E-value=2.5e-27 Score=181.90 Aligned_cols=137 Identities=28% Similarity=0.677 Sum_probs=119.9
Q ss_pred CCCCccCccchhccCCHHHHHHHHHHhCCcccCCccCccchhccccCCCCCCCccchhhcccCCCCCcccCCccCccccC
Q psy6546 29 TPTRHPCPQCSRDFATVKILKTHLKTHEGIIYPCPECDKTFLSTLTGTPQGARGRAVYLSRMSTTLTRHPCPQCSRDFAT 108 (294)
Q Consensus 29 ~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~f~~ 108 (294)
....|+|+.||+.|++...|.+|.+.|-. . ...+.+.|+.|++.|.+
T Consensus 127 ~~~r~~c~eCgk~ysT~snLsrHkQ~H~~------~---------------------------~s~ka~~C~~C~K~YvS 173 (279)
T KOG2462|consen 127 KHPRYKCPECGKSYSTSSNLSRHKQTHRS------L---------------------------DSKKAFSCKYCGKVYVS 173 (279)
T ss_pred cCCceeccccccccccccccchhhccccc------c---------------------------cccccccCCCCCceeee
Confidence 34569999999999999999999988731 0 11456889999999999
Q ss_pred hHHHHHHHhhccCcccCCcccccccCChHhHHHHHhhhCCCC-ccCCCCCcccCCHHHHHHHHHhhcCC-CcccCcchhc
Q psy6546 109 VKILKTHLKTHEGIIYPCPECDKTFLSTSGLREHRKVHAGVR-YICHACPREFSSEATMKAHVASHNGV-QHACDQCDRT 186 (294)
Q Consensus 109 ~~~l~~H~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~-~~C~~C~~~f~~~~~l~~H~~~~~~~-~~~C~~C~~~ 186 (294)
...|..|+++|. .+.+|.+||+.|...+.|+.|++.|+|++ |.|+.|++.|.++++|+.||++|.+. +|.|..|+|.
T Consensus 174 mpALkMHirTH~-l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~Ks 252 (279)
T KOG2462|consen 174 MPALKMHIRTHT-LPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKS 252 (279)
T ss_pred hHHHhhHhhccC-CCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhH
Confidence 999999999988 67999999999999999999999999988 99999999999999999999999885 8888888888
Q ss_pred cCCchHHHhHHhh
Q psy6546 187 FSCMPYLRQHQKL 199 (294)
Q Consensus 187 f~~~~~l~~H~~~ 199 (294)
|...+.|..|...
T Consensus 253 Fsl~SyLnKH~ES 265 (279)
T KOG2462|consen 253 FALKSYLNKHSES 265 (279)
T ss_pred HHHHHHHHHhhhh
Confidence 8888888888654
No 3
>KOG1074|consensus
Probab=99.94 E-value=3.9e-28 Score=210.37 Aligned_cols=142 Identities=27% Similarity=0.596 Sum_probs=128.6
Q ss_pred ccCCCCCcccCCHHHHHHHHHhhcCC-CcccCcchhccCCchHHHhHHhhcCCC-----ceeCC---CCccccCCHHHHH
Q psy6546 151 YICHACPREFSSEATMKAHVASHNGV-QHACDQCDRTFSCMPYLRQHQKLHSGI-----TYSCP---SCSKSFNRKDRYR 221 (294)
Q Consensus 151 ~~C~~C~~~f~~~~~l~~H~~~~~~~-~~~C~~C~~~f~~~~~l~~H~~~h~~~-----~~~C~---~C~~~f~~~~~l~ 221 (294)
..|-.|.+++.-.+.|+.|.++|+|+ ||+|.+|++.|..+.+|+.|+-.|..+ .+.|+ +|.+.|...-.|.
T Consensus 606 NqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kftn~V~lp 685 (958)
T KOG1074|consen 606 NQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKKFTNAVTLP 685 (958)
T ss_pred cceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccccccccCCchhhhccccccccccc
Confidence 67999999999999999999999998 999999999999999999999999775 58899 9999999999999
Q ss_pred HHHHHhCC------------------------------------------------------------------------
Q psy6546 222 MHLKLHQG------------------------------------------------------------------------ 229 (294)
Q Consensus 222 ~H~~~h~~------------------------------------------------------------------------ 229 (294)
+|+++|.+
T Consensus 686 QhIriH~~~~~s~g~~a~e~~~~adq~~~~qk~~~~a~~f~~~~se~~~~~s~~~~~~~~~t~t~~~~~tp~~~e~~~~~ 765 (958)
T KOG1074|consen 686 QHIRIHLGGQISNGGTAAEGILAADQCSSCQKTFSDARSFSQQISEQPSPESEPDEQMDERTETEELDVTPPPPENSCGR 765 (958)
T ss_pred ceEEeecCCCCCCCcccccccchhcccchhhhcccccccchhhhhccCCcccCCcccccccccccccccCCCcccccccc
Confidence 99888740
Q ss_pred --------------------------------------------------------------------------------
Q psy6546 230 -------------------------------------------------------------------------------- 229 (294)
Q Consensus 230 -------------------------------------------------------------------------------- 229 (294)
T Consensus 766 ~~~~e~~i~~~g~te~asa~~~~vg~~s~~~~~~~~~~T~~k~~~~~~~~~~~~~~~v~~~pvl~~~~~~~l~eg~~t~~ 845 (958)
T KOG1074|consen 766 ELEGEMAISVRGSTEEASANLDEVGTVSAAGEAGEEDDTSEKPTQASSFPGEILAPSVNMDPVLWNQETSMLNEGLATKT 845 (958)
T ss_pred ccCcccccccccchhhhhcChhhhcCccccchhhhhcccCCCCcccccCCCcCCccccccCchhhccccccccccccccc
Confidence
Q ss_pred --------------------------C------ccccccccccccCHHHHHHHHhhhc-ccccccccccccccchhhhhh
Q psy6546 230 --------------------------V------RHTCKECSKEFSNEYNLKNHMVLHD-VRAYVCELCARQFTRVDHFNH 276 (294)
Q Consensus 230 --------------------------~------~~~C~~C~~~f~~~~~l~~H~~~h~-~~~~~C~~C~~~f~~~~~l~~ 276 (294)
+ +..|..||+.|...++|..|+++|. ++||.|..|+++|+.+.+|+.
T Consensus 846 n~~t~~~~~~sv~qs~~~p~l~p~l~~~~pvnn~h~C~vCgk~FsSSsALqiH~rTHtg~KPF~C~fC~~aFttrgnLKv 925 (958)
T KOG1074|consen 846 NEITPEGPADSVIQSGGVPTLEPSLGRPGPVNNAHVCNVCGKQFSSSAALEIHMRTHTGPKPFFCHFCEEAFTTRGNLKV 925 (958)
T ss_pred ccccCCCcchhhhhhccccccCCCCCCCCcccchhhhccchhcccchHHHHHhhhcCCCCCCccchhhhhhhhhhhhhhh
Confidence 0 1679999999999999999999997 999999999999999999999
Q ss_pred hhhhccCccccccccc
Q psy6546 277 HRRLQHDPEEFEKVGA 292 (294)
Q Consensus 277 H~~~~h~~~~~~~~~~ 292 (294)
||.+|+-..+.--+++
T Consensus 926 HMgtH~w~q~~srrG~ 941 (958)
T KOG1074|consen 926 HMGTHMWVQPPSRRGP 941 (958)
T ss_pred hhccccccCCCccCCC
Confidence 9999998887755544
No 4
>KOG3608|consensus
Probab=99.93 E-value=5.5e-26 Score=179.17 Aligned_cols=232 Identities=22% Similarity=0.495 Sum_probs=192.8
Q ss_pred CCCCCCccCc--cchhccCCHHHHHHHHHHhCCcccCCccCccchhccccCCCCCCCccchhhcccCCCC---CcccCCc
Q psy6546 27 STTPTRHPCP--QCSRDFATVKILKTHLKTHEGIIYPCPECDKTFLSTLTGTPQGARGRAVYLSRMSTTL---TRHPCPQ 101 (294)
Q Consensus 27 ~~~~~~~~C~--~C~~~f~~~~~l~~H~~~~~~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~C~~ 101 (294)
+.-+..|.|. .|++.|.+...|..|+..|... | ...+ ......+ .+-.+..
T Consensus 129 p~~g~~f~C~WedCe~~F~s~~ef~dHV~~H~l~---c---eyd~------------------~~~~~D~~pv~~C~W~~ 184 (467)
T KOG3608|consen 129 PALGQNFRCGWEDCEREFVSIVEFQDHVVKHALF---C---EYDI------------------QKTPEDERPVTMCNWAM 184 (467)
T ss_pred ccchhhhccChhhcCCcccCHHHHHHHHHHhhhh---h---hhhh------------------hhCCCCCCceeeccchh
Confidence 3345568886 4999999999999999887531 1 1110 0011111 2234568
Q ss_pred cCccccChHHHHHHHhhccCc-ccCCcccccccCChHhHHHHHhhhCCC---CccCCCCCcccCCHHHHHHHHHhhcCCC
Q psy6546 102 CSRDFATVKILKTHLKTHEGI-IYPCPECDKTFLSTSGLREHRKVHAGV---RYICHACPREFSSEATMKAHVASHNGVQ 177 (294)
Q Consensus 102 C~~~f~~~~~l~~H~~~~~~~-~~~C~~C~~~f~~~~~l~~H~~~h~~~---~~~C~~C~~~f~~~~~l~~H~~~~~~~~ 177 (294)
|-+.+.++..|..|++.|.++ ...|+.|+..|.+...|-.|++..+.. .|.|..|.+.|.++..|..|+..|-. -
T Consensus 185 Ct~~~~~k~~LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn-~ 263 (467)
T KOG3608|consen 185 CTKHMGNKYRLREHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVN-C 263 (467)
T ss_pred hhhhhccHHHHHHHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhh-c
Confidence 999999999999999999986 789999999999999999999876653 39999999999999999999999877 7
Q ss_pred cccCcchhccCCchHHHhHHhhcCC--CceeCCCCccccCCHHHHHHHHHHhCCCcccccc--ccccccCHHHHHHHHhh
Q psy6546 178 HACDQCDRTFSCMPYLRQHQKLHSG--ITYSCPSCSKSFNRKDRYRMHLKLHQGVRHTCKE--CSKEFSNEYNLKNHMVL 253 (294)
Q Consensus 178 ~~C~~C~~~f~~~~~l~~H~~~h~~--~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~--C~~~f~~~~~l~~H~~~ 253 (294)
|.|+.|+......+.|..|++.-+. +||+|+.|.+.|.+.+.|.+|+..|....|.|.. |.+.|.+..+|++|.+.
T Consensus 264 ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS~~~y~C~h~~C~~s~r~~~q~~~H~~e 343 (467)
T KOG3608|consen 264 YKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHSKTVYQCEHPDCHYSVRTYTQMRRHFLE 343 (467)
T ss_pred ccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhccccceecCCCCCcHHHHHHHHHHHHHHH
Confidence 9999999999999999999986655 5999999999999999999999999855599988 99999999999999766
Q ss_pred hc----ccccccccccccccchhhhhhhhhhccC
Q psy6546 254 HD----VRAYVCELCARQFTRVDHFNHHRRLQHD 283 (294)
Q Consensus 254 h~----~~~~~C~~C~~~f~~~~~l~~H~~~~h~ 283 (294)
++ +-+|.|-.|++-|+.=-+|..|++..|+
T Consensus 344 vhEg~np~~Y~CH~Cdr~ft~G~~L~~HL~kkH~ 377 (467)
T KOG3608|consen 344 VHEGNNPILYACHCCDRFFTSGKSLSAHLMKKHG 377 (467)
T ss_pred hccCCCCCceeeecchhhhccchhHHHHHHHhhc
Confidence 63 5689999999999999999999866554
No 5
>KOG3608|consensus
Probab=99.91 E-value=1.2e-23 Score=166.03 Aligned_cols=183 Identities=23% Similarity=0.506 Sum_probs=165.5
Q ss_pred CCccCccccChHHHHHHHhhccC-------------c-ccCCc--ccccccCChHhHHHHHhhhCCCC-ccCCCCCcccC
Q psy6546 99 CPQCSRDFATVKILKTHLKTHEG-------------I-IYPCP--ECDKTFLSTSGLREHRKVHAGVR-YICHACPREFS 161 (294)
Q Consensus 99 C~~C~~~f~~~~~l~~H~~~~~~-------------~-~~~C~--~C~~~f~~~~~l~~H~~~h~~~~-~~C~~C~~~f~ 161 (294)
+..|++.|.+...+..|+..|.- + .+.|. .|.+.|.++..|+.|++.|.+++ ..|+.||..|.
T Consensus 139 WedCe~~F~s~~ef~dHV~~H~l~ceyd~~~~~~D~~pv~~C~W~~Ct~~~~~k~~LreH~r~Hs~eKvvACp~Cg~~F~ 218 (467)
T KOG3608|consen 139 WEDCEREFVSIVEFQDHVVKHALFCEYDIQKTPEDERPVTMCNWAMCTKHMGNKYRLREHIRTHSNEKVVACPHCGELFR 218 (467)
T ss_pred hhhcCCcccCHHHHHHHHHHhhhhhhhhhhhCCCCCCceeeccchhhhhhhccHHHHHHHHHhcCCCeEEecchHHHHhc
Confidence 36899999999999999887731 1 24555 48999999999999999999999 89999999999
Q ss_pred CHHHHHHHHHhhcC---CCcccCcchhccCCchHHHhHHhhcCCCceeCCCCccccCCHHHHHHHHHHh-CCCc-ccccc
Q psy6546 162 SEATMKAHVASHNG---VQHACDQCDRTFSCMPYLRQHQKLHSGITYSCPSCSKSFNRKDRYRMHLKLH-QGVR-HTCKE 236 (294)
Q Consensus 162 ~~~~l~~H~~~~~~---~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~C~~~f~~~~~l~~H~~~h-~~~~-~~C~~ 236 (294)
++..|..|.+..+. .+|.|..|.+.|..+..|..|+..|-. -|+|+.|.......++|..|++.- ...+ |+|..
T Consensus 219 ~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn-~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~ 297 (467)
T KOG3608|consen 219 TKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVN-CYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDE 297 (467)
T ss_pred cccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhh-cccccccccCCCChHHHHHHHHhhhccCCCccccc
Confidence 99999999987765 389999999999999999999999876 899999999999999999999874 4433 99999
Q ss_pred ccccccCHHHHHHHHhhhccccccccc--ccccccchhhhhhhhhhcc
Q psy6546 237 CSKEFSNEYNLKNHMVLHDVRAYVCEL--CARQFTRVDHFNHHRRLQH 282 (294)
Q Consensus 237 C~~~f~~~~~l~~H~~~h~~~~~~C~~--C~~~f~~~~~l~~H~~~~h 282 (294)
|.+.|...+.|.+|+.+|.+-.|+|.. |.++|.+..+|.+|++.+|
T Consensus 298 Cd~~c~~esdL~kH~~~HS~~~y~C~h~~C~~s~r~~~q~~~H~~evh 345 (467)
T KOG3608|consen 298 CDTRCVRESDLAKHVQVHSKTVYQCEHPDCHYSVRTYTQMRRHFLEVH 345 (467)
T ss_pred hhhhhccHHHHHHHHHhccccceecCCCCCcHHHHHHHHHHHHHHHhc
Confidence 999999999999999999999999976 9999999999999999988
No 6
>KOG1074|consensus
Probab=99.87 E-value=1.8e-22 Score=175.60 Aligned_cols=161 Identities=28% Similarity=0.590 Sum_probs=136.0
Q ss_pred CcccCCccCccccChHHHHHHHhhccCc-ccCCcccccccCChHhHHHHHhhhCCCC-----ccCC---CCCcccCCHHH
Q psy6546 95 TRHPCPQCSRDFATVKILKTHLKTHEGI-IYPCPECDKTFLSTSGLREHRKVHAGVR-----YICH---ACPREFSSEAT 165 (294)
Q Consensus 95 ~~~~C~~C~~~f~~~~~l~~H~~~~~~~-~~~C~~C~~~f~~~~~l~~H~~~h~~~~-----~~C~---~C~~~f~~~~~ 165 (294)
.+-+|-.|.++..-+..|+.|.++|.+. ||+|.+|++.|.++.+|+.||..|.... +.|+ +|-+.|...-.
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 4457999999999999999999999996 9999999999999999999999887643 8899 99999999999
Q ss_pred HHHHHHhhcCC--------------CcccCcchhccCCchHHHhHHhhc-------------------------------
Q psy6546 166 MKAHVASHNGV--------------QHACDQCDRTFSCMPYLRQHQKLH------------------------------- 200 (294)
Q Consensus 166 l~~H~~~~~~~--------------~~~C~~C~~~f~~~~~l~~H~~~h------------------------------- 200 (294)
|..|+++|.+. .-.|..|.+.|.....+..++-.+
T Consensus 684 lpQhIriH~~~~~s~g~~a~e~~~~adq~~~~qk~~~~a~~f~~~~se~~~~~s~~~~~~~~~t~t~~~~~tp~~~e~~~ 763 (958)
T KOG1074|consen 684 LPQHIRIHLGGQISNGGTAAEGILAADQCSSCQKTFSDARSFSQQISEQPSPESEPDEQMDERTETEELDVTPPPPENSC 763 (958)
T ss_pred ccceEEeecCCCCCCCcccccccchhcccchhhhcccccccchhhhhccCCcccCCcccccccccccccccCCCcccccc
Confidence 99999998732 135777777776555555443322
Q ss_pred --------------------------------------------------------------------------------
Q psy6546 201 -------------------------------------------------------------------------------- 200 (294)
Q Consensus 201 -------------------------------------------------------------------------------- 200 (294)
T Consensus 764 ~~~~~~e~~i~~~g~te~asa~~~~vg~~s~~~~~~~~~~T~~k~~~~~~~~~~~~~~~v~~~pvl~~~~~~~l~eg~~t 843 (958)
T KOG1074|consen 764 GRELEGEMAISVRGSTEEASANLDEVGTVSAAGEAGEEDDTSEKPTQASSFPGEILAPSVNMDPVLWNQETSMLNEGLAT 843 (958)
T ss_pred ccccCcccccccccchhhhhcChhhhcCccccchhhhhcccCCCCcccccCCCcCCccccccCchhhccccccccccccc
Confidence
Q ss_pred --------------------------CCC------ceeCCCCccccCCHHHHHHHHHHhCCCc-cccccccccccCHHHH
Q psy6546 201 --------------------------SGI------TYSCPSCSKSFNRKDRYRMHLKLHQGVR-HTCKECSKEFSNEYNL 247 (294)
Q Consensus 201 --------------------------~~~------~~~C~~C~~~f~~~~~l~~H~~~h~~~~-~~C~~C~~~f~~~~~l 247 (294)
.++ ...|.+|++.|.++++|+.|+++|++++ |.|..|++.|...++|
T Consensus 844 ~~n~~t~~~~~~sv~qs~~~p~l~p~l~~~~pvnn~h~C~vCgk~FsSSsALqiH~rTHtg~KPF~C~fC~~aFttrgnL 923 (958)
T KOG1074|consen 844 KTNEITPEGPADSVIQSGGVPTLEPSLGRPGPVNNAHVCNVCGKQFSSSAALEIHMRTHTGPKPFFCHFCEEAFTTRGNL 923 (958)
T ss_pred ccccccCCCcchhhhhhccccccCCCCCCCCcccchhhhccchhcccchHHHHHhhhcCCCCCCccchhhhhhhhhhhhh
Confidence 000 1669999999999999999999999988 9999999999999999
Q ss_pred HHHHhhhc
Q psy6546 248 KNHMVLHD 255 (294)
Q Consensus 248 ~~H~~~h~ 255 (294)
+.|+.+|.
T Consensus 924 KvHMgtH~ 931 (958)
T KOG1074|consen 924 KVHMGTHM 931 (958)
T ss_pred hhhhcccc
Confidence 99999995
No 7
>KOG3623|consensus
Probab=99.85 E-value=1.2e-21 Score=167.99 Aligned_cols=116 Identities=26% Similarity=0.517 Sum_probs=89.2
Q ss_pred CCCccCccchhccCCHHHHHHHHHHhCCc---ccCCccCccchhccccCC----CCCCCccchhhcccCCCCCcccCCcc
Q psy6546 30 PTRHPCPQCSRDFATVKILKTHLKTHEGI---IYPCPECDKTFLSTLTGT----PQGARGRAVYLSRMSTTLTRHPCPQC 102 (294)
Q Consensus 30 ~~~~~C~~C~~~f~~~~~l~~H~~~~~~~---~~~c~~c~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~C~~C 102 (294)
.....|+.|.+.+.....|+.|++.-+.. -+.|..|...|..+.... .+..................|+|..|
T Consensus 208 sqlltcpycdrgykrltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtEC 287 (1007)
T KOG3623|consen 208 SQLLTCPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTEC 287 (1007)
T ss_pred hhhhcchhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhcccccccc
Confidence 44689999999999999999999865443 688999999997665211 11111111111222234678999999
Q ss_pred CccccChHHHHHHHhhccCc-ccCCcccccccCChHhHHHHHhh
Q psy6546 103 SRDFATVKILKTHLKTHEGI-IYPCPECDKTFLSTSGLREHRKV 145 (294)
Q Consensus 103 ~~~f~~~~~l~~H~~~~~~~-~~~C~~C~~~f~~~~~l~~H~~~ 145 (294)
+|.|+-+-.|+.|+++|.|. ||.|+.|++.|.....+..||..
T Consensus 288 gKAFKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmSS 331 (1007)
T KOG3623|consen 288 GKAFKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMSS 331 (1007)
T ss_pred chhhhhHHHHHhhheeecCCCCcCCcccccccccCCcccccccc
Confidence 99999999999999999995 99999999999999998888853
No 8
>KOG3623|consensus
Probab=99.78 E-value=3.2e-19 Score=153.22 Aligned_cols=102 Identities=26% Similarity=0.594 Sum_probs=87.6
Q ss_pred ccCCccCccccChHHHHHHHhhccCc---ccCCcccccccCChHhHHHHHhhhCCC--------------CccCCCCCcc
Q psy6546 97 HPCPQCSRDFATVKILKTHLKTHEGI---IYPCPECDKTFLSTSGLREHRKVHAGV--------------RYICHACPRE 159 (294)
Q Consensus 97 ~~C~~C~~~f~~~~~l~~H~~~~~~~---~~~C~~C~~~f~~~~~l~~H~~~h~~~--------------~~~C~~C~~~ 159 (294)
..|++|.+.+....+|..|++.-+.+ .|.|..|.+.|-.+..|.+||..|... +|+|..||+.
T Consensus 211 ltcpycdrgykrltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgKA 290 (1007)
T KOG3623|consen 211 LTCPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGKA 290 (1007)
T ss_pred hcchhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccchh
Confidence 46999999999999999998877654 688999999999999999999887421 3999999999
Q ss_pred cCCHHHHHHHHHhhcCC-CcccCcchhccCCchHHHhHHh
Q psy6546 160 FSSEATMKAHVASHNGV-QHACDQCDRTFSCMPYLRQHQK 198 (294)
Q Consensus 160 f~~~~~l~~H~~~~~~~-~~~C~~C~~~f~~~~~l~~H~~ 198 (294)
|+.+..|+.|+++|.|+ ||.|+.|.+.|..+..+..|+.
T Consensus 291 FKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmS 330 (1007)
T KOG3623|consen 291 FKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMS 330 (1007)
T ss_pred hhhHHHHHhhheeecCCCCcCCcccccccccCCccccccc
Confidence 99999999999999997 8999999999988888888854
No 9
>KOG3576|consensus
Probab=99.64 E-value=3.5e-17 Score=120.02 Aligned_cols=77 Identities=29% Similarity=0.719 Sum_probs=45.4
Q ss_pred ccCCCCCcccCCHHHHHHHHHhhcCC-CcccCcchhccCCchHHHhHHhhcCCC-ceeCCCCccccCCHHHHHHHHHHh
Q psy6546 151 YICHACPREFSSEATMKAHVASHNGV-QHACDQCDRTFSCMPYLRQHQKLHSGI-TYSCPSCSKSFNRKDRYRMHLKLH 227 (294)
Q Consensus 151 ~~C~~C~~~f~~~~~l~~H~~~~~~~-~~~C~~C~~~f~~~~~l~~H~~~h~~~-~~~C~~C~~~f~~~~~l~~H~~~h 227 (294)
|.|.+|++.|.-...|.+|++-|... .|-|..||+.|...-+|++|.++|++. ||+|..|++.|+..-.|..|++.-
T Consensus 118 ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~kv 196 (267)
T KOG3576|consen 118 FTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLKKV 196 (267)
T ss_pred eeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHHHH
Confidence 66666666666555566666655553 555666666666666666666666553 566666666666655566665433
No 10
>KOG3576|consensus
Probab=99.58 E-value=9e-16 Score=112.71 Aligned_cols=106 Identities=32% Similarity=0.649 Sum_probs=57.9
Q ss_pred cCCcccccccCChHhHHHHHhhhCCCC-ccCCCCCcccCCHHHHHHHHHhhcCC-CcccCcchhccCCchHHHhHHhhcC
Q psy6546 124 YPCPECDKTFLSTSGLREHRKVHAGVR-YICHACPREFSSEATMKAHVASHNGV-QHACDQCDRTFSCMPYLRQHQKLHS 201 (294)
Q Consensus 124 ~~C~~C~~~f~~~~~l~~H~~~h~~~~-~~C~~C~~~f~~~~~l~~H~~~~~~~-~~~C~~C~~~f~~~~~l~~H~~~h~ 201 (294)
|.|.+|++.|.-..-|.+|++-|...+ +.|..||+.|.+.-+|.+|+++|+|. ||.|..|++.|...-.|..|.+.-+
T Consensus 118 ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~kvh 197 (267)
T KOG3576|consen 118 FTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLKKVH 197 (267)
T ss_pred eeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHHHHc
Confidence 445555555555555555555554433 55555555555555555555555554 5555555555555555555543222
Q ss_pred C------------CceeCCCCccccCCHHHHHHHHHHhCC
Q psy6546 202 G------------ITYSCPSCSKSFNRKDRYRMHLKLHQG 229 (294)
Q Consensus 202 ~------------~~~~C~~C~~~f~~~~~l~~H~~~h~~ 229 (294)
+ +.|.|..||+.-.....+..|++.|+.
T Consensus 198 gv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp 237 (267)
T KOG3576|consen 198 GVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHP 237 (267)
T ss_pred CchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCC
Confidence 2 357777777777666667777766554
No 11
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.35 E-value=2e-12 Score=112.23 Aligned_cols=145 Identities=19% Similarity=0.448 Sum_probs=107.3
Q ss_pred cCCcccccccCChHhHHHHHhhhCCCCccCCC--CCcccCCHHHHHHHHHhhcCCCcccCcchhccCCchHHHhHHhhcC
Q psy6546 124 YPCPECDKTFLSTSGLREHRKVHAGVRYICHA--CPREFSSEATMKAHVASHNGVQHACDQCDRTFSCMPYLRQHQKLHS 201 (294)
Q Consensus 124 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~--C~~~f~~~~~l~~H~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 201 (294)
-.|+.|... ....+|..|..........|+. |+..|.. ..+..| +.|+.|++.|. ...|..|+..++
T Consensus 408 V~C~NC~~~-i~l~~l~lHe~~C~r~~V~Cp~~~Cg~v~~r-~el~~H--------~~C~~Cgk~f~-~s~LekH~~~~H 476 (567)
T PLN03086 408 VECRNCKHY-IPSRSIALHEAYCSRHNVVCPHDGCGIVLRV-EEAKNH--------VHCEKCGQAFQ-QGEMEKHMKVFH 476 (567)
T ss_pred EECCCCCCc-cchhHHHHHHhhCCCcceeCCcccccceeec-cccccC--------ccCCCCCCccc-hHHHHHHHHhcC
Confidence 457777665 3345666777776666677874 8888842 233333 48999988885 577889988875
Q ss_pred CCceeCCCCccccCCHHHHHHHHHHhCCCc-ccccccccccc----------CHHHHHHHHhhhcccccccccccccccc
Q psy6546 202 GITYSCPSCSKSFNRKDRYRMHLKLHQGVR-HTCKECSKEFS----------NEYNLKNHMVLHDVRAYVCELCARQFTR 270 (294)
Q Consensus 202 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~-~~C~~C~~~f~----------~~~~l~~H~~~h~~~~~~C~~C~~~f~~ 270 (294)
+++.|+ |++.+ .+..|..|+.+|-+.+ +.|..|+..|. ....|..|......+++.|..|++.+..
T Consensus 477 -kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~CG~rt~~C~~Cgk~Vrl 553 (567)
T PLN03086 477 -EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESICGSRTAPCDSCGRSVML 553 (567)
T ss_pred -CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhcCCcceEccccCCeeee
Confidence 688998 98654 6688999988887766 89999998884 2457889988888999999999998876
Q ss_pred hhhhhhhhhhccC
Q psy6546 271 VDHFNHHRRLQHD 283 (294)
Q Consensus 271 ~~~l~~H~~~~h~ 283 (294)
+ .|..|+..-|.
T Consensus 554 r-dm~~H~~~~h~ 565 (567)
T PLN03086 554 K-EMDIHQIAVHQ 565 (567)
T ss_pred h-hHHHHHHHhhc
Confidence 5 47778765543
No 12
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.23 E-value=1.2e-10 Score=101.47 Aligned_cols=154 Identities=17% Similarity=0.376 Sum_probs=78.2
Q ss_pred CCCccCccchhccCCHHHHHHHHHHhCCcccCCcc--CccchhccccCCCCCCCccchhhcccCCCCCcccCCccCcccc
Q psy6546 30 PTRHPCPQCSRDFATVKILKTHLKTHEGIIYPCPE--CDKTFLSTLTGTPQGARGRAVYLSRMSTTLTRHPCPQCSRDFA 107 (294)
Q Consensus 30 ~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~c~~--c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~f~ 107 (294)
...-.|+.|.+... ...|..|.....-....|+. |+..|.... ....+.|+.|++.|.
T Consensus 405 ~~~V~C~NC~~~i~-l~~l~lHe~~C~r~~V~Cp~~~Cg~v~~r~e-------------------l~~H~~C~~Cgk~f~ 464 (567)
T PLN03086 405 VDTVECRNCKHYIP-SRSIALHEAYCSRHNVVCPHDGCGIVLRVEE-------------------AKNHVHCEKCGQAFQ 464 (567)
T ss_pred CCeEECCCCCCccc-hhHHHHHHhhCCCcceeCCcccccceeeccc-------------------cccCccCCCCCCccc
Confidence 34457999999887 44555777554444555653 655552211 112235666666664
Q ss_pred ChHHHHHHHhhccCcccCCcccccccCChHhHHHHHhhhCCCC-ccCCCCCcccCCHHHHHHHHHhhcCCCcccCcchhc
Q psy6546 108 TVKILKTHLKTHEGIIYPCPECDKTFLSTSGLREHRKVHAGVR-YICHACPREFSSEATMKAHVASHNGVQHACDQCDRT 186 (294)
Q Consensus 108 ~~~~l~~H~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~-~~C~~C~~~f~~~~~l~~H~~~~~~~~~~C~~C~~~ 186 (294)
...|..|++.++ .++.|+ |++.+ ....|..|+..|.+.+ +.|..|++.+...... ..+.
T Consensus 465 -~s~LekH~~~~H-kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~---------~d~~------- 524 (567)
T PLN03086 465 -QGEMEKHMKVFH-EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSA---------MDVR------- 524 (567)
T ss_pred -hHHHHHHHHhcC-CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccc---------cchh-------
Confidence 455666666553 455665 65433 3455555555554444 5555555555310000 0000
Q ss_pred cCCchHHHhHHhhcCCCceeCCCCccccCCHHHHHHHHH
Q psy6546 187 FSCMPYLRQHQKLHSGITYSCPSCSKSFNRKDRYRMHLK 225 (294)
Q Consensus 187 f~~~~~l~~H~~~h~~~~~~C~~C~~~f~~~~~l~~H~~ 225 (294)
...+.|..|...+..+++.|..||+.+..+ .+..|+.
T Consensus 525 -d~~s~Lt~HE~~CG~rt~~C~~Cgk~Vrlr-dm~~H~~ 561 (567)
T PLN03086 525 -DRLRGMSEHESICGSRTAPCDSCGRSVMLK-EMDIHQI 561 (567)
T ss_pred -hhhhhHHHHHHhcCCcceEccccCCeeeeh-hHHHHHH
Confidence 012355566655555566666666655443 2445543
No 13
>PHA00733 hypothetical protein
Probab=99.12 E-value=3.7e-11 Score=85.38 Aligned_cols=79 Identities=19% Similarity=0.286 Sum_probs=47.5
Q ss_pred ceeCCCCccccCCHHHH------HHHHHHhCCCccccccccccccCHHHHHHHHhhhcccccccccccccccchhhhhhh
Q psy6546 204 TYSCPSCSKSFNRKDRY------RMHLKLHQGVRHTCKECSKEFSNEYNLKNHMVLHDVRAYVCELCARQFTRVDHFNHH 277 (294)
Q Consensus 204 ~~~C~~C~~~f~~~~~l------~~H~~~h~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~C~~~f~~~~~l~~H 277 (294)
++.|.+|...|.....| .+|+..+...+|.|..|++.|.....|..|++.| ..+|.|+.|++.|.....|..|
T Consensus 40 ~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h-~~~~~C~~CgK~F~~~~sL~~H 118 (128)
T PHA00733 40 RLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT-EHSKVCPVCGKEFRNTDSTLDH 118 (128)
T ss_pred hHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC-CcCccCCCCCCccCCHHHHHHH
Confidence 44444444444443333 3333333444477777777777777777776655 3457777777777777777777
Q ss_pred hhhccC
Q psy6546 278 RRLQHD 283 (294)
Q Consensus 278 ~~~~h~ 283 (294)
+...|+
T Consensus 119 ~~~~h~ 124 (128)
T PHA00733 119 VCKKHN 124 (128)
T ss_pred HHHhcC
Confidence 766665
No 14
>PHA02768 hypothetical protein; Provisional
Probab=99.02 E-value=1.5e-10 Score=67.53 Aligned_cols=43 Identities=16% Similarity=0.346 Sum_probs=30.7
Q ss_pred cccccccccccCHHHHHHHHhhhcccccccccccccccchhhhh
Q psy6546 232 HTCKECSKEFSNEYNLKNHMVLHDVRAYVCELCARQFTRVDHFN 275 (294)
Q Consensus 232 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~C~~~f~~~~~l~ 275 (294)
|.|+.||+.|+....|..|+++|. ++|+|..|++.|.+.++|.
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~-k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN-TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC-CcccCCcccceecccceeE
Confidence 667777777777777777777776 5777777777777666554
No 15
>KOG3993|consensus
Probab=98.95 E-value=1.1e-10 Score=95.38 Aligned_cols=160 Identities=21% Similarity=0.281 Sum_probs=103.9
Q ss_pred cCCcccccccCChHhHHHHHhhhCCCC-ccCCCCCcccCCHHHHHHHHHhhcCCCccc--C-cchhccCCchHHHhHHh-
Q psy6546 124 YPCPECDKTFLSTSGLREHRKVHAGVR-YICHACPREFSSEATMKAHVASHNGVQHAC--D-QCDRTFSCMPYLRQHQK- 198 (294)
Q Consensus 124 ~~C~~C~~~f~~~~~l~~H~~~h~~~~-~~C~~C~~~f~~~~~l~~H~~~~~~~~~~C--~-~C~~~f~~~~~l~~H~~- 198 (294)
|.|+.|...|.+...|.+|.-...-.. |+|+.|+++|.-..+|..|.+.|..++-.- . .=.+.-.....+.....
T Consensus 268 yiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~r 347 (500)
T KOG3993|consen 268 YICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAER 347 (500)
T ss_pred HHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccc
Confidence 789999988988888888887666533 899999999999999999988887642111 0 00000000011111110
Q ss_pred h---cCCCceeCCCCccccCCHHHHHHHHHHhCCCc--------------------------------------------
Q psy6546 199 L---HSGITYSCPSCSKSFNRKDRYRMHLKLHQGVR-------------------------------------------- 231 (294)
Q Consensus 199 ~---h~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~-------------------------------------------- 231 (294)
. .....|.|.+|++.|.+...|++|+.+|+...
T Consensus 348 sg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~~~~k~~a~~f~~s~~~~l~~~~~~~a~h~~a~~~~g~~vl~~a~s 427 (500)
T KOG3993|consen 348 SGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRAPLAKEKAPKFLLSRVIPLMHFNQAVATHSSASDSHGDEVLYVAGS 427 (500)
T ss_pred cCCcccCceeecHHhhhhhHHHHHHHHhHHhhhccccchhcccCcchhhcccccccccccccccccccccccceeeeecc
Confidence 0 11126999999999999999999988875210
Q ss_pred ---cccccccccccCHHHHHHHHhhhc-ccccccccccccccchhhhhhhhhhccC
Q psy6546 232 ---HTCKECSKEFSNEYNLKNHMVLHD-VRAYVCELCARQFTRVDHFNHHRRLQHD 283 (294)
Q Consensus 232 ---~~C~~C~~~f~~~~~l~~H~~~h~-~~~~~C~~C~~~f~~~~~l~~H~~~~h~ 283 (294)
..|+.|+..+.++..---+.+.-. ...|-|.+|.-.|.....|.+|+..-|.
T Consensus 428 ael~~pp~~~~ppsss~~sgg~~rlg~~~q~f~~ky~~atfyss~~ltrhin~~Hp 483 (500)
T KOG3993|consen 428 AELELPPYDGSPPSSSGSSGGYGRLGIAEQGFTCKYCPATFYSSPGLTRHINKCHP 483 (500)
T ss_pred ccccCCCCCCCCcccCCCCCccccccchhhccccccchHhhhcCcchHhHhhhcCh
Confidence 235555555544433333332222 4458899999999999999999876665
No 16
>PHA00733 hypothetical protein
Probab=98.93 E-value=1.2e-09 Score=77.71 Aligned_cols=60 Identities=25% Similarity=0.389 Sum_probs=32.1
Q ss_pred HHHHhhcCCCcccCcchhccCCchHHHhHHhhcCCCceeCCCCccccCCHHHHHHHHHHhC
Q psy6546 168 AHVASHNGVQHACDQCDRTFSCMPYLRQHQKLHSGITYSCPSCSKSFNRKDRYRMHLKLHQ 228 (294)
Q Consensus 168 ~H~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 228 (294)
.|+..+...+|.|+.|++.|.....|..|++.+ ..++.|..|++.|.....|..|+...+
T Consensus 64 ~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h-~~~~~C~~CgK~F~~~~sL~~H~~~~h 123 (128)
T PHA00733 64 KLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT-EHSKVCPVCGKEFRNTDSTLDHVCKKH 123 (128)
T ss_pred hhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC-CcCccCCCCCCccCCHHHHHHHHHHhc
Confidence 333333334555666666666555555555544 234556666666666666666555433
No 17
>PHA02768 hypothetical protein; Provisional
Probab=98.89 E-value=8.2e-10 Score=64.44 Aligned_cols=43 Identities=19% Similarity=0.461 Sum_probs=30.8
Q ss_pred ceeCCCCccccCCHHHHHHHHHHhCCCccccccccccccCHHHH
Q psy6546 204 TYSCPSCSKSFNRKDRYRMHLKLHQGVRHTCKECSKEFSNEYNL 247 (294)
Q Consensus 204 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~C~~~f~~~~~l 247 (294)
.|.|+.||+.|...++|..|+++|+ .+|+|..|++.|...+.|
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~-k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN-TNLKLSNCKRISLRTGEY 47 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC-CcccCCcccceeccccee
Confidence 4677777777777777777777777 457777777777766554
No 18
>KOG3993|consensus
Probab=98.82 E-value=3.3e-10 Score=92.77 Aligned_cols=163 Identities=21% Similarity=0.338 Sum_probs=103.7
Q ss_pred CCCCCcccCCccCccccChHHHHHHHhhccC-cccCCcccccccCChHhHHHHHhhhCCC--------------------
Q psy6546 91 STTLTRHPCPQCSRDFATVKILKTHLKTHEG-IIYPCPECDKTFLSTSGLREHRKVHAGV-------------------- 149 (294)
Q Consensus 91 ~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~-~~~~C~~C~~~f~~~~~l~~H~~~h~~~-------------------- 149 (294)
.....-|.|.+|...|.+.-.|.+|.-...- .-|+|++|+++|+...+|..|.++|...
T Consensus 262 ~n~iGdyiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae 341 (500)
T KOG3993|consen 262 PNVIGDYICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAE 341 (500)
T ss_pred cccHHHHHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhh
Confidence 3344668999999999999999999654433 2699999999999999999999998432
Q ss_pred --------------CccCCCCCcccCCHHHHHHHHHhhcCCC------------------cccCcchhccCCchHHHhHH
Q psy6546 150 --------------RYICHACPREFSSEATMKAHVASHNGVQ------------------HACDQCDRTFSCMPYLRQHQ 197 (294)
Q Consensus 150 --------------~~~C~~C~~~f~~~~~l~~H~~~~~~~~------------------~~C~~C~~~f~~~~~l~~H~ 197 (294)
.|.|..|++.|.+..-|+.|+.+|.... +.+..+.-.+.....--.+.
T Consensus 342 ~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~~~~k~~a~~f~~s~~~~l~~~~~~~a~h~~a~~~~g~~v 421 (500)
T KOG3993|consen 342 VQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRAPLAKEKAPKFLLSRVIPLMHFNQAVATHSSASDSHGDEV 421 (500)
T ss_pred hhhccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhccccchhcccCcchhhcccccccccccccccccccccccce
Confidence 1677777777777777777777665421 12233322221111111111
Q ss_pred hhcCC--CceeCCCCccccCCHHHHHHHHHHhCCCc-cccccccccccCHHHHHHHHhh
Q psy6546 198 KLHSG--ITYSCPSCSKSFNRKDRYRMHLKLHQGVR-HTCKECSKEFSNEYNLKNHMVL 253 (294)
Q Consensus 198 ~~h~~--~~~~C~~C~~~f~~~~~l~~H~~~h~~~~-~~C~~C~~~f~~~~~l~~H~~~ 253 (294)
..+.+ .-..|+.||-.+.++..--.+.+.-.... |.|.+|...|.+...|.+|+..
T Consensus 422 l~~a~sael~~pp~~~~ppsss~~sgg~~rlg~~~q~f~~ky~~atfyss~~ltrhin~ 480 (500)
T KOG3993|consen 422 LYVAGSAELELPPYDGSPPSSSGSSGGYGRLGIAEQGFTCKYCPATFYSSPGLTRHINK 480 (500)
T ss_pred eeeeccccccCCCCCCCCcccCCCCCccccccchhhccccccchHhhhcCcchHhHhhh
Confidence 11111 12446777766655543333322222222 8899999999999999998643
No 19
>PHA00616 hypothetical protein
Probab=98.52 E-value=2.8e-08 Score=55.13 Aligned_cols=32 Identities=19% Similarity=0.353 Sum_probs=24.1
Q ss_pred ccccccccccccchhhhhhhhhhccCcccccc
Q psy6546 258 AYVCELCARQFTRVDHFNHHRRLQHDPEEFEK 289 (294)
Q Consensus 258 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~ 289 (294)
||+|+.||+.|.++++|..|++.||+++++.+
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~ 32 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTL 32 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccce
Confidence 57777777777777777777777777777654
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=98.39 E-value=1.9e-07 Score=46.46 Aligned_cols=24 Identities=38% Similarity=0.908 Sum_probs=16.1
Q ss_pred HHHHHHhhhc-cccccccccccccc
Q psy6546 246 NLKNHMVLHD-VRAYVCELCARQFT 269 (294)
Q Consensus 246 ~l~~H~~~h~-~~~~~C~~C~~~f~ 269 (294)
+|..|+++|. ++||.|+.|++.|.
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEES
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeC
Confidence 3666777775 66777777777665
No 21
>PHA00732 hypothetical protein
Probab=98.26 E-value=7.1e-07 Score=57.47 Aligned_cols=47 Identities=21% Similarity=0.475 Sum_probs=34.1
Q ss_pred ceeCCCCccccCCHHHHHHHHHH-hCCCccccccccccccCHHHHHHHHhhhc
Q psy6546 204 TYSCPSCSKSFNRKDRYRMHLKL-HQGVRHTCKECSKEFSNEYNLKNHMVLHD 255 (294)
Q Consensus 204 ~~~C~~C~~~f~~~~~l~~H~~~-h~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 255 (294)
||.|..|++.|.+.+.|..|++. |.+ +.|..|++.|. .|..|.+.+.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~--~~C~~CgKsF~---~l~~H~~~~~ 48 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTL--TKCPVCNKSYR---RLNQHFYSQY 48 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCC--CccCCCCCEeC---ChhhhhcccC
Confidence 56788888888888888888874 543 57888888887 4677765553
No 22
>PHA00732 hypothetical protein
Probab=98.25 E-value=8e-07 Score=57.24 Aligned_cols=43 Identities=33% Similarity=0.649 Sum_probs=21.8
Q ss_pred cccCcchhccCCchHHHhHHhh-cCCCceeCCCCccccCCHHHHHHHHH
Q psy6546 178 HACDQCDRTFSCMPYLRQHQKL-HSGITYSCPSCSKSFNRKDRYRMHLK 225 (294)
Q Consensus 178 ~~C~~C~~~f~~~~~l~~H~~~-h~~~~~~C~~C~~~f~~~~~l~~H~~ 225 (294)
|.|++|++.|.....|..|++. |. ++.|+.|++.|. .|..|.+
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r~~H~--~~~C~~CgKsF~---~l~~H~~ 45 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHARRNHT--LTKCPVCNKSYR---RLNQHFY 45 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhhcccC--CCccCCCCCEeC---Chhhhhc
Confidence 4555555555555555555543 32 235555555554 2444543
No 23
>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=98.21 E-value=1.2e-06 Score=43.60 Aligned_cols=24 Identities=38% Similarity=0.798 Sum_probs=15.0
Q ss_pred HHHHHHHHhCCCc-ccccccccccc
Q psy6546 219 RYRMHLKLHQGVR-HTCKECSKEFS 242 (294)
Q Consensus 219 ~l~~H~~~h~~~~-~~C~~C~~~f~ 242 (294)
+|.+|+++|++++ |.|+.|++.|.
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEES
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeC
Confidence 3566666666655 66666666664
No 24
>PHA00616 hypothetical protein
Probab=98.14 E-value=1.2e-06 Score=48.62 Aligned_cols=27 Identities=26% Similarity=0.450 Sum_probs=13.9
Q ss_pred ceeCCCCccccCCHHHHHHHHHHhCCC
Q psy6546 204 TYSCPSCSKSFNRKDRYRMHLKLHQGV 230 (294)
Q Consensus 204 ~~~C~~C~~~f~~~~~l~~H~~~h~~~ 230 (294)
||+|+.||+.|..++.|..|++.|++.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~ 27 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQ 27 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCC
Confidence 345555555555555555555554444
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=98.12 E-value=3.1e-06 Score=50.57 Aligned_cols=49 Identities=33% Similarity=0.541 Sum_probs=28.8
Q ss_pred cccccccccccCHHHHHHHHhh-hc--ccccccccccccccchhhhhhhhhhccC
Q psy6546 232 HTCKECSKEFSNEYNLKNHMVL-HD--VRAYVCELCARQFTRVDHFNHHRRLQHD 283 (294)
Q Consensus 232 ~~C~~C~~~f~~~~~l~~H~~~-h~--~~~~~C~~C~~~f~~~~~l~~H~~~~h~ 283 (294)
|.|+.|++ -.+...|..|... |. .+.+.|++|...++ .+|..|++.+|+
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQHR 54 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhcC
Confidence 56666666 3445566666433 32 34567777766544 367777766653
No 26
>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=97.91 E-value=1.1e-05 Score=38.94 Aligned_cols=22 Identities=41% Similarity=0.976 Sum_probs=11.6
Q ss_pred eeCCCCccccCCHHHHHHHHHH
Q psy6546 205 YSCPSCSKSFNRKDRYRMHLKL 226 (294)
Q Consensus 205 ~~C~~C~~~f~~~~~l~~H~~~ 226 (294)
|.|+.|++.|.+...|..|++.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 3455555555555555555544
No 27
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.87 E-value=5.5e-06 Score=56.80 Aligned_cols=71 Identities=23% Similarity=0.416 Sum_probs=14.0
Q ss_pred CCCCccccCCHHHHHHHHHHhCCCccccccccccccCHHHHHHHHhhhcccccccccccccccchhhhhhhhhh
Q psy6546 207 CPSCSKSFNRKDRYRMHLKLHQGVRHTCKECSKEFSNEYNLKNHMVLHDVRAYVCELCARQFTRVDHFNHHRRL 280 (294)
Q Consensus 207 C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~C~~~f~~~~~l~~H~~~ 280 (294)
|..|+..|.+...|..|+...++.... ....+.....+..+.+.--...+.|.+|++.|.+...|..|++.
T Consensus 2 C~~C~~~f~~~~~l~~H~~~~H~~~~~---~~~~l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~~l~~Hm~~ 72 (100)
T PF12756_consen 2 CLFCDESFSSVDDLLQHMKKKHGFDIP---DQKYLVDPNRLLNYLRKKVKESFRCPYCNKTFRSREALQEHMRS 72 (100)
T ss_dssp --------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHH
T ss_pred ccccccccccccccccccccccccccc---cccccccccccccccccccCCCCCCCccCCCCcCHHHHHHHHcC
Confidence 556666666666666666554443211 11112223333333222222346666666666666666666654
No 28
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.85 E-value=1.1e-05 Score=38.82 Aligned_cols=22 Identities=27% Similarity=0.807 Sum_probs=11.7
Q ss_pred cccccccccccchhhhhhhhhh
Q psy6546 259 YVCELCARQFTRVDHFNHHRRL 280 (294)
Q Consensus 259 ~~C~~C~~~f~~~~~l~~H~~~ 280 (294)
|+|++|++.|.++.+|..|++.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 4455555555555555555544
No 29
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=97.79 E-value=4.7e-05 Score=45.46 Aligned_cols=46 Identities=26% Similarity=0.473 Sum_probs=23.8
Q ss_pred eeCCCCccccCCHHHHHHHHHH-hCCCc--cccccccccccCHHHHHHHHhh
Q psy6546 205 YSCPSCSKSFNRKDRYRMHLKL-HQGVR--HTCKECSKEFSNEYNLKNHMVL 253 (294)
Q Consensus 205 ~~C~~C~~~f~~~~~l~~H~~~-h~~~~--~~C~~C~~~f~~~~~l~~H~~~ 253 (294)
|.|++|++ -.+...|..|... |...+ +.|++|...+. ..|..|+..
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~ 51 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNS 51 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHH
Confidence 55666666 3444556666544 33222 56666655433 255566543
No 30
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.76 E-value=2.4e-05 Score=53.60 Aligned_cols=72 Identities=19% Similarity=0.425 Sum_probs=16.3
Q ss_pred CCCCCcccCCHHHHHHHHHhhcCCCcccCcchhccCCchHHHhHHhhcCCCceeCCCCccccCCHHHHHHHHHHh
Q psy6546 153 CHACPREFSSEATMKAHVASHNGVQHACDQCDRTFSCMPYLRQHQKLHSGITYSCPSCSKSFNRKDRYRMHLKLH 227 (294)
Q Consensus 153 C~~C~~~f~~~~~l~~H~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~C~~~f~~~~~l~~H~~~h 227 (294)
|..|+..|.....|..|+...++.... ....+.....+..+.+.-....+.|..|++.|.+...|..|++.+
T Consensus 2 C~~C~~~f~~~~~l~~H~~~~H~~~~~---~~~~l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 2 CLFCDESFSSVDDLLQHMKKKHGFDIP---DQKYLVDPNRLLNYLRKKVKESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp --------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred ccccccccccccccccccccccccccc---cccccccccccccccccccCCCCCCCccCCCCcCHHHHHHHHcCc
Confidence 556666666666666666554443211 001111222222232222222567777777777777777777653
No 31
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.76 E-value=9.9e-06 Score=39.43 Aligned_cols=24 Identities=25% Similarity=0.784 Sum_probs=12.5
Q ss_pred cccccccccccchhhhhhhhhhcc
Q psy6546 259 YVCELCARQFTRVDHFNHHRRLQH 282 (294)
Q Consensus 259 ~~C~~C~~~f~~~~~l~~H~~~~h 282 (294)
|+|++|++.|.+...|..|++++|
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHHS
T ss_pred CCCcCCCCcCCcHHHHHHHHHhhC
Confidence 455556666665566665555544
No 32
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.68 E-value=1.8e-05 Score=39.79 Aligned_cols=26 Identities=19% Similarity=0.690 Sum_probs=19.8
Q ss_pred ccccccccccccchhhhhhhhhhccC
Q psy6546 258 AYVCELCARQFTRVDHFNHHRRLQHD 283 (294)
Q Consensus 258 ~~~C~~C~~~f~~~~~l~~H~~~~h~ 283 (294)
+|.|..|++.|.....|..|++.|+.
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHCS 26 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhcC
Confidence 57788888888888888888777654
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=97.67 E-value=5.6e-05 Score=36.66 Aligned_cols=23 Identities=43% Similarity=1.028 Sum_probs=12.7
Q ss_pred eeCCCCccccCCHHHHHHHHHHh
Q psy6546 205 YSCPSCSKSFNRKDRYRMHLKLH 227 (294)
Q Consensus 205 ~~C~~C~~~f~~~~~l~~H~~~h 227 (294)
|.|++|++.|.+...|..|+..|
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHhh
Confidence 45666666666666666666554
No 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=97.46 E-value=7.5e-05 Score=37.49 Aligned_cols=24 Identities=29% Similarity=0.718 Sum_probs=13.5
Q ss_pred ceeCCCCccccCCHHHHHHHHHHh
Q psy6546 204 TYSCPSCSKSFNRKDRYRMHLKLH 227 (294)
Q Consensus 204 ~~~C~~C~~~f~~~~~l~~H~~~h 227 (294)
+|.|..|++.|.+...|..|++.|
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h 24 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSH 24 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTT
T ss_pred CCCCCccCCccCChhHHHHHhHHh
Confidence 355555555555555555555544
No 35
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.46 E-value=6.1e-05 Score=60.18 Aligned_cols=72 Identities=17% Similarity=0.304 Sum_probs=48.4
Q ss_pred CCCCCccCcc--chhccCCHHHHHHHHHHhCCcccCCccCccchhccccCCCCCCCccchhhcccCCCCCcccCCccCcc
Q psy6546 28 TTPTRHPCPQ--CSRDFATVKILKTHLKTHEGIIYPCPECDKTFLSTLTGTPQGARGRAVYLSRMSTTLTRHPCPQCSRD 105 (294)
Q Consensus 28 ~~~~~~~C~~--C~~~f~~~~~l~~H~~~~~~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~ 105 (294)
.+.+||+|++ |.+.|..+..|+-|+.--+.. .+..... .......+....+||+|++|+|.
T Consensus 345 ~d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~--------~~~~~~p---------~p~~~~~F~~~~KPYrCevC~KR 407 (423)
T COG5189 345 KDGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQN--------QKLHENP---------SPEKMNIFSAKDKPYRCEVCDKR 407 (423)
T ss_pred ecCceecCCCCCchhhhccccchhhhhhccccC--------cccCCCC---------CccccccccccCCceeccccchh
Confidence 3469999997 999999999999999743321 1110000 11111222345689999999999
Q ss_pred ccChHHHHHHH
Q psy6546 106 FATVKILKTHL 116 (294)
Q Consensus 106 f~~~~~l~~H~ 116 (294)
|+....|+.|.
T Consensus 408 YKNlNGLKYHr 418 (423)
T COG5189 408 YKNLNGLKYHR 418 (423)
T ss_pred hccCccceecc
Confidence 99888887774
No 36
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.21 E-value=0.00011 Score=35.69 Aligned_cols=24 Identities=21% Similarity=0.552 Sum_probs=15.6
Q ss_pred cccccccccccchhhhhhhhhhccC
Q psy6546 259 YVCELCARQFTRVDHFNHHRRLQHD 283 (294)
Q Consensus 259 ~~C~~C~~~f~~~~~l~~H~~~~h~ 283 (294)
|+|+.|++..+ ...|..|++.+|+
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H~ 24 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHHP 24 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHHS
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhCc
Confidence 56777777776 6677777777664
No 37
>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=96.95 E-value=0.00022 Score=40.52 Aligned_cols=39 Identities=10% Similarity=0.284 Sum_probs=22.3
Q ss_pred HHHHhhhc--ccccccccccccccchhhhhhhhhhccCccc
Q psy6546 248 KNHMVLHD--VRAYVCELCARQFTRVDHFNHHRRLQHDPEE 286 (294)
Q Consensus 248 ~~H~~~h~--~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~ 286 (294)
..+.+.+. +.|-.|++|+..+.+..+|.+|+.+.|..++
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 34444443 6778888888888888888888888887664
No 38
>KOG2231|consensus
Probab=96.93 E-value=0.0051 Score=55.41 Aligned_cols=50 Identities=20% Similarity=0.418 Sum_probs=30.2
Q ss_pred eCCCCccccCCHHHHHHHHHHhCCCcccc---ccccccccCHHHHHHHHhhhc
Q psy6546 206 SCPSCSKSFNRKDRYRMHLKLHQGVRHTC---KECSKEFSNEYNLKNHMVLHD 255 (294)
Q Consensus 206 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~C---~~C~~~f~~~~~l~~H~~~h~ 255 (294)
.|..|...|.....|.+|++.++..-.-| ..++.-|.....|..|.+.++
T Consensus 184 ~C~~C~~~fld~~el~rH~~~~h~~chfC~~~~~~neyy~~~~dLe~HfR~~H 236 (669)
T KOG2231|consen 184 LCKFCHERFLDDDELYRHLRFDHEFCHFCDYKTGQNEYYNDYDDLEEHFRKGH 236 (669)
T ss_pred cchhhhhhhccHHHHHHhhccceeheeecCcccccchhcccchHHHHHhhhcC
Confidence 56777777777777777776554433223 233456666677777765553
No 39
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.84 E-value=0.001 Score=32.59 Aligned_cols=19 Identities=47% Similarity=0.896 Sum_probs=7.6
Q ss_pred cccccccccCHHHHHHHHh
Q psy6546 234 CKECSKEFSNEYNLKNHMV 252 (294)
Q Consensus 234 C~~C~~~f~~~~~l~~H~~ 252 (294)
|..|++.|.....|..|++
T Consensus 3 C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 3 CPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCcchhCCHHHHHHHHH
Confidence 3344444444444444433
No 40
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.80 E-value=0.0014 Score=32.08 Aligned_cols=24 Identities=38% Similarity=0.952 Sum_probs=18.1
Q ss_pred eeCCCCccccCCHHHHHHHHHHhC
Q psy6546 205 YSCPSCSKSFNRKDRYRMHLKLHQ 228 (294)
Q Consensus 205 ~~C~~C~~~f~~~~~l~~H~~~h~ 228 (294)
|.|..|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 467788888888888888877554
No 41
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=96.79 E-value=0.00036 Score=55.90 Aligned_cols=68 Identities=24% Similarity=0.644 Sum_probs=40.6
Q ss_pred CCceeCCC--CccccCCHHHHHHHHHH-hCCCc-cccccccccccCHHHHHHHH-hhhcccccccccccccccchhhhhh
Q psy6546 202 GITYSCPS--CSKSFNRKDRYRMHLKL-HQGVR-HTCKECSKEFSNEYNLKNHM-VLHDVRAYVCELCARQFTRVDHFNH 276 (294)
Q Consensus 202 ~~~~~C~~--C~~~f~~~~~l~~H~~~-h~~~~-~~C~~C~~~f~~~~~l~~H~-~~h~~~~~~C~~C~~~f~~~~~l~~ 276 (294)
++||+|++ |++.+.....|+-|+.. |.... ..=+ .-..|. ..-..+||+|++|++.+...-.|+.
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p----------~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKY 416 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENP----------SPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKY 416 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCC----------CccccccccccCCceeccccchhhccCcccee
Confidence 35777744 77777777777777653 21111 0000 000000 0112589999999999999999999
Q ss_pred hhh
Q psy6546 277 HRR 279 (294)
Q Consensus 277 H~~ 279 (294)
|+.
T Consensus 417 Hr~ 419 (423)
T COG5189 417 HRK 419 (423)
T ss_pred ccc
Confidence 963
No 42
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.66 E-value=0.0012 Score=32.29 Aligned_cols=22 Identities=36% Similarity=0.836 Sum_probs=12.4
Q ss_pred eeCCCCccccCCHHHHHHHHHH
Q psy6546 205 YSCPSCSKSFNRKDRYRMHLKL 226 (294)
Q Consensus 205 ~~C~~C~~~f~~~~~l~~H~~~ 226 (294)
|.|.+|+..|.+...|..|+++
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTT
T ss_pred CCCCCCCCCcCCHHHHHHHHCc
Confidence 4455566666665555555543
No 43
>KOG2231|consensus
Probab=96.62 E-value=0.0092 Score=53.82 Aligned_cols=102 Identities=20% Similarity=0.419 Sum_probs=61.7
Q ss_pred cCCccCccccChHHHHHHHhhccCcccCCccccc---------ccCChHhHHHHHhhhCC-CC-----ccCCCCCcccCC
Q psy6546 98 PCPQCSRDFATVKILKTHLKTHEGIIYPCPECDK---------TFLSTSGLREHRKVHAG-VR-----YICHACPREFSS 162 (294)
Q Consensus 98 ~C~~C~~~f~~~~~l~~H~~~~~~~~~~C~~C~~---------~f~~~~~l~~H~~~h~~-~~-----~~C~~C~~~f~~ 162 (294)
.|..| -.|.....|+.|+...+.. +.|.+|-. ...+...|+.|++.--. .+ -.|..|...|..
T Consensus 117 ~~~~c-~~~~s~~~Lk~H~~~~H~~-~~c~lC~~~~kif~~e~k~Yt~~el~~h~~~gd~d~~s~rGhp~C~~C~~~fld 194 (669)
T KOG2231|consen 117 ECLHC-TEFKSVENLKNHMRDQHKL-HLCSLCLQNLKIFINERKLYTRAELNLHLMFGDPDDESCRGHPLCKFCHERFLD 194 (669)
T ss_pred CCccc-cchhHHHHHHHHHHHhhhh-hccccccccceeeeeeeehehHHHHHHHHhcCCCccccccCCccchhhhhhhcc
Confidence 46666 6667778888888655543 45555432 22345566677653322 22 457777777777
Q ss_pred HHHHHHHHHhhcCCCcccC---cchhccCCchHHHhHHhhcC
Q psy6546 163 EATMKAHVASHNGVQHACD---QCDRTFSCMPYLRQHQKLHS 201 (294)
Q Consensus 163 ~~~l~~H~~~~~~~~~~C~---~C~~~f~~~~~l~~H~~~h~ 201 (294)
...|..|++.++.....|+ .++..|..-..|..|.+..+
T Consensus 195 ~~el~rH~~~~h~~chfC~~~~~~neyy~~~~dLe~HfR~~H 236 (669)
T KOG2231|consen 195 DDELYRHLRFDHEFCHFCDYKTGQNEYYNDYDDLEEHFRKGH 236 (669)
T ss_pred HHHHHHhhccceeheeecCcccccchhcccchHHHHHhhhcC
Confidence 7777777777666544442 34455566667777766654
No 44
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.62 E-value=0.002 Score=31.10 Aligned_cols=22 Identities=50% Similarity=0.928 Sum_probs=11.6
Q ss_pred eeCCCCccccCCHHHHHHHHHHh
Q psy6546 205 YSCPSCSKSFNRKDRYRMHLKLH 227 (294)
Q Consensus 205 ~~C~~C~~~f~~~~~l~~H~~~h 227 (294)
|+|+.|++... ...|.+|++.+
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~ 22 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRH 22 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhh
Confidence 45666666665 55666666554
No 45
>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=96.51 E-value=0.0035 Score=35.75 Aligned_cols=28 Identities=21% Similarity=0.478 Sum_probs=18.2
Q ss_pred CceeCCCCccccCCHHHHHHHHHHhCCC
Q psy6546 203 ITYSCPSCSKSFNRKDRYRMHLKLHQGV 230 (294)
Q Consensus 203 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~ 230 (294)
.|..|++|+..+.+..+|++|+...++.
T Consensus 23 ~PatCP~C~a~~~~srnLrRHle~~H~~ 50 (54)
T PF09237_consen 23 QPATCPICGAVIRQSRNLRRHLEIRHFK 50 (54)
T ss_dssp --EE-TTT--EESSHHHHHHHHHHHTTT
T ss_pred CCCCCCcchhhccchhhHHHHHHHHhcc
Confidence 4788888888888888888888766553
No 46
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.37 E-value=0.0014 Score=32.00 Aligned_cols=22 Identities=23% Similarity=0.809 Sum_probs=12.3
Q ss_pred cccccccccccchhhhhhhhhh
Q psy6546 259 YVCELCARQFTRVDHFNHHRRL 280 (294)
Q Consensus 259 ~~C~~C~~~f~~~~~l~~H~~~ 280 (294)
|.|.+|++.|.+...|..|++.
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTT
T ss_pred CCCCCCCCCcCCHHHHHHHHCc
Confidence 4455555555555555555543
No 47
>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=96.31 E-value=0.0021 Score=32.11 Aligned_cols=22 Identities=18% Similarity=0.726 Sum_probs=17.4
Q ss_pred cccccccccccchhhhhhhhhh
Q psy6546 259 YVCELCARQFTRVDHFNHHRRL 280 (294)
Q Consensus 259 ~~C~~C~~~f~~~~~l~~H~~~ 280 (294)
|.|..|++.|.+...|..|+++
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 6788888888888888888765
No 48
>KOG1146|consensus
Probab=96.25 E-value=0.0026 Score=60.80 Aligned_cols=104 Identities=18% Similarity=0.290 Sum_probs=71.5
Q ss_pred CCccCccchhccCCHHHHHHHHHHhCCcccCCccCccchhccccCCCCCCCccchhhcccCCCCCcccCCccCccccChH
Q psy6546 31 TRHPCPQCSRDFATVKILKTHLKTHEGIIYPCPECDKTFLSTLTGTPQGARGRAVYLSRMSTTLTRHPCPQCSRDFATVK 110 (294)
Q Consensus 31 ~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~ 110 (294)
+.++|+.|++.|.....|..||+..+...-. .+|.-.-.. .+...-......-++|.|..|...+....
T Consensus 464 kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~-~~c~~gq~~----------~~~arg~~~~~~~~p~~C~~C~~stttng 532 (1406)
T KOG1146|consen 464 KTLKCPKCNWHYKLAQTLGVHMRSKHPESQS-AYCKAGQNH----------PRLARGEVYRCPGKPYPCRACNYSTTTNG 532 (1406)
T ss_pred ccccCCccchhhhhHHHhhhcccccccccch-hHhHhcccc----------ccccccccccCCCCcccceeeeeeeecch
Confidence 5589999999999999999999864332111 222111100 01222222344568899999999999999
Q ss_pred HHHHHHhhcc--------------------------------------------CcccCCcccccccCChHhHHHHHhh
Q psy6546 111 ILKTHLKTHE--------------------------------------------GIIYPCPECDKTFLSTSGLREHRKV 145 (294)
Q Consensus 111 ~l~~H~~~~~--------------------------------------------~~~~~C~~C~~~f~~~~~l~~H~~~ 145 (294)
.|.+|++... ..+|.|.+|++..+-..+|+.||..
T Consensus 533 ~LsihlqS~~h~~~lee~~~~~g~~v~~~~~~v~s~~P~~ag~~~~ags~~pktkP~~~C~vc~yetniarnlrihmts 611 (1406)
T KOG1146|consen 533 NLSIHLQSDLHRNELEEAEENAGEQVRLLPASVTSAVPEEAGLGPSAGSSGPKTKPSWRCEVCSYETNIARNLRIHMTA 611 (1406)
T ss_pred HHHHHHHHHhhHHHHHHHHhccccchhhhhhhhcccCcccccCCCCCCCCCCCCCCCcchhhhcchhhhhhcccccccc
Confidence 9999986641 0147899998888888888888853
No 49
>KOG1146|consensus
Probab=96.21 E-value=0.0011 Score=63.14 Aligned_cols=99 Identities=18% Similarity=0.332 Sum_probs=60.3
Q ss_pred CcccccccCChHhHHHHHhhh-CCCC-ccCCCCCcccCCHHHHHHHHHhhcCCCcccCcchhccCCchHHHh-HHhhcCC
Q psy6546 126 CPECDKTFLSTSGLREHRKVH-AGVR-YICHACPREFSSEATMKAHVASHNGVQHACDQCDRTFSCMPYLRQ-HQKLHSG 202 (294)
Q Consensus 126 C~~C~~~f~~~~~l~~H~~~h-~~~~-~~C~~C~~~f~~~~~l~~H~~~~~~~~~~C~~C~~~f~~~~~l~~-H~~~h~~ 202 (294)
|.-++..+.....+..|+..- ...+ +.|+.|+..|+....|..||+..+.+.-. .+|... ..-..+.+ -.....+
T Consensus 439 ~~~~e~~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~-~~c~~g-q~~~~~arg~~~~~~~ 516 (1406)
T KOG1146|consen 439 LTKAEPLLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQS-AYCKAG-QNHPRLARGEVYRCPG 516 (1406)
T ss_pred ccchhhhhhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccch-hHhHhc-cccccccccccccCCC
Confidence 333444444444444444322 2223 89999999999999999999986664222 333221 11111111 1123334
Q ss_pred CceeCCCCccccCCHHHHHHHHHH
Q psy6546 203 ITYSCPSCSKSFNRKDRYRMHLKL 226 (294)
Q Consensus 203 ~~~~C~~C~~~f~~~~~l~~H~~~ 226 (294)
++|.|..|+..++...+|..|++.
T Consensus 517 ~p~~C~~C~~stttng~LsihlqS 540 (1406)
T KOG1146|consen 517 KPYPCRACNYSTTTNGNLSIHLQS 540 (1406)
T ss_pred CcccceeeeeeeecchHHHHHHHH
Confidence 689999999999999999999864
No 50
>PRK04860 hypothetical protein; Provisional
Probab=95.34 E-value=0.0081 Score=44.53 Aligned_cols=36 Identities=22% Similarity=0.607 Sum_probs=24.1
Q ss_pred ceeCCCCccccCCHHHHHHHHHHhCCCc-cccccccccccC
Q psy6546 204 TYSCPSCSKSFNRKDRYRMHLKLHQGVR-HTCKECSKEFSN 243 (294)
Q Consensus 204 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~-~~C~~C~~~f~~ 243 (294)
+|.|. |+. ....+.+|.++|.++. |.|..|+..|..
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~ 155 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVF 155 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEE
Confidence 67776 776 4555677777777755 777777766654
No 51
>PRK04860 hypothetical protein; Provisional
Probab=95.28 E-value=0.013 Score=43.53 Aligned_cols=35 Identities=20% Similarity=0.562 Sum_probs=20.3
Q ss_pred cccccccccccCHHHHHHHHhhhc-ccccccccccccccc
Q psy6546 232 HTCKECSKEFSNEYNLKNHMVLHD-VRAYVCELCARQFTR 270 (294)
Q Consensus 232 ~~C~~C~~~f~~~~~l~~H~~~h~-~~~~~C~~C~~~f~~ 270 (294)
|.|. |+. ....+..|.++|. +++|.|..|+..|..
T Consensus 120 Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~ 155 (160)
T PRK04860 120 YRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVF 155 (160)
T ss_pred EEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEE
Confidence 6665 654 4455566666664 455666666665543
No 52
>KOG2785|consensus
Probab=95.11 E-value=0.016 Score=48.23 Aligned_cols=82 Identities=18% Similarity=0.340 Sum_probs=49.7
Q ss_pred CccCccchhccCCHHHHHHHHHHhCCc------ccC-CccCccchhccccCCCCCCCccchhhcccCCCCCcccCCccCc
Q psy6546 32 RHPCPQCSRDFATVKILKTHLKTHEGI------IYP-CPECDKTFLSTLTGTPQGARGRAVYLSRMSTTLTRHPCPQCSR 104 (294)
Q Consensus 32 ~~~C~~C~~~f~~~~~l~~H~~~~~~~------~~~-c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~ 104 (294)
.|.|.-|...|.+...-+.|++.-+.. ... -++-...|....... ..........+..++.|..|.+
T Consensus 3 ~ftC~tC~v~F~~ad~Qr~HyKSdWHRYNLKRkVA~lPPItaE~F~~k~~s~------~~~~~~~~e~~~~~~~c~~c~k 76 (390)
T KOG2785|consen 3 GFTCNTCNVEFDDADEQRAHYKSDWHRYNLKRKVASLPPITAEEFNEKVLSD------DSEKEENLEEAESVVYCEACNK 76 (390)
T ss_pred cceeeceeeeeccHHHHHHHhhhhHHHhhHHhHhhcCCCcCHHHHhHHHhhh------hhhhhhhhhhcccceehHHhhc
Confidence 589999999999999999999754331 111 111222232221000 0000011234566788999999
Q ss_pred cccChHHHHHHHhhc
Q psy6546 105 DFATVKILKTHLKTH 119 (294)
Q Consensus 105 ~f~~~~~l~~H~~~~ 119 (294)
.|........|+..-
T Consensus 77 ~~~s~~a~~~hl~Sk 91 (390)
T KOG2785|consen 77 SFASPKAHENHLKSK 91 (390)
T ss_pred cccChhhHHHHHHHh
Confidence 999998888887654
No 53
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=94.99 E-value=0.01 Score=29.51 Aligned_cols=21 Identities=48% Similarity=0.825 Sum_probs=13.1
Q ss_pred cccccccccccCHHHHHHHHh
Q psy6546 232 HTCKECSKEFSNEYNLKNHMV 252 (294)
Q Consensus 232 ~~C~~C~~~f~~~~~l~~H~~ 252 (294)
|.|..|++.|.+...|..|++
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~ 22 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMK 22 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTT
T ss_pred CCcccCCCCcCCHHHHHHHHc
Confidence 456666666666666666654
No 54
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=94.75 E-value=0.038 Score=26.91 Aligned_cols=22 Identities=41% Similarity=0.797 Sum_probs=18.3
Q ss_pred CccCccchhccCCHHHHHHHHHH
Q psy6546 32 RHPCPQCSRDFATVKILKTHLKT 54 (294)
Q Consensus 32 ~~~C~~C~~~f~~~~~l~~H~~~ 54 (294)
...|+.||+.| ....|..|+..
T Consensus 2 l~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 2 LVPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CCcCCCCCCEE-CHHHHHHHHHh
Confidence 46899999999 68889999764
No 55
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=94.49 E-value=0.048 Score=44.71 Aligned_cols=79 Identities=20% Similarity=0.340 Sum_probs=45.9
Q ss_pred eCCCCccccCCHHHHHHHHHHhCCCcccccccc----ccccCHHHHHHHHhhhc-cccc-cccccc-ccccchhhhhhhh
Q psy6546 206 SCPSCSKSFNRKDRYRMHLKLHQGVRHTCKECS----KEFSNEYNLKNHMVLHD-VRAY-VCELCA-RQFTRVDHFNHHR 278 (294)
Q Consensus 206 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~C~----~~f~~~~~l~~H~~~h~-~~~~-~C~~C~-~~f~~~~~l~~H~ 278 (294)
.|..|+..|.+...|..|++..+..-|.|..-+ .-|.+..+|..|-+.-+ .-.| .|.+-. +.|....+|..|+
T Consensus 222 ~C~FC~~~FYdDDEL~~HcR~~HE~ChICD~v~p~~~QYFK~Y~~Le~HF~~~hy~ct~qtc~~~k~~vf~~~~el~~h~ 301 (493)
T COG5236 222 LCIFCKIYFYDDDELRRHCRLRHEACHICDMVGPIRYQYFKSYEDLEAHFRNAHYCCTFQTCRVGKCYVFPYHTELLEHL 301 (493)
T ss_pred hhhhccceecChHHHHHHHHhhhhhhhhhhccCccchhhhhCHHHHHHHhhcCceEEEEEEEecCcEEEeccHHHHHHHH
Confidence 577788888888888888777666556665544 24556666666633221 1111 121111 2567777777777
Q ss_pred hhccCc
Q psy6546 279 RLQHDP 284 (294)
Q Consensus 279 ~~~h~~ 284 (294)
..-|+.
T Consensus 302 ~~~h~~ 307 (493)
T COG5236 302 TRFHKV 307 (493)
T ss_pred HHHhhc
Confidence 666554
No 56
>KOG2482|consensus
Probab=94.48 E-value=0.33 Score=39.95 Aligned_cols=63 Identities=25% Similarity=0.395 Sum_probs=39.9
Q ss_pred HHHHHHhhccCc--ccCCccccccc-CChHhHHHHHhhhCCC-----------------------CccCCCCCcccCCHH
Q psy6546 111 ILKTHLKTHEGI--IYPCPECDKTF-LSTSGLREHRKVHAGV-----------------------RYICHACPREFSSEA 164 (294)
Q Consensus 111 ~l~~H~~~~~~~--~~~C~~C~~~f-~~~~~l~~H~~~h~~~-----------------------~~~C~~C~~~f~~~~ 164 (294)
.|..+++...+. ..+|-.|...+ .+++.+..|+-.-++- ++.|-.|.+.|+.+.
T Consensus 130 aLeqqQ~Eredt~fslqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrdkn 209 (423)
T KOG2482|consen 130 ALEQQQKEREDTIFSLQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRDKN 209 (423)
T ss_pred HHHHHHHHhcCCeeeeEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCCcH
Confidence 344555554443 56788887654 4567777776432211 267888888888888
Q ss_pred HHHHHHHhh
Q psy6546 165 TMKAHVASH 173 (294)
Q Consensus 165 ~l~~H~~~~ 173 (294)
.|+.||+..
T Consensus 210 tLkeHMrkK 218 (423)
T KOG2482|consen 210 TLKEHMRKK 218 (423)
T ss_pred HHHHHHHhc
Confidence 888887763
No 57
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=94.34 E-value=0.15 Score=41.90 Aligned_cols=137 Identities=22% Similarity=0.336 Sum_probs=83.0
Q ss_pred CccCcc--chhccCCHHHHHHHHHHhCCcccCCccCc---cchhccccCCCCCCCccchhhcccCC---C-CCcccCCcc
Q psy6546 32 RHPCPQ--CSRDFATVKILKTHLKTHEGIIYPCPECD---KTFLSTLTGTPQGARGRAVYLSRMST---T-LTRHPCPQC 102 (294)
Q Consensus 32 ~~~C~~--C~~~f~~~~~l~~H~~~~~~~~~~c~~c~---~~~~~~~~~~~~~~~~~~~~~~~~~~---~-~~~~~C~~C 102 (294)
.|.||. |.........|..|.+..++. +.|..|. +.|....+...+ ..+..+..... + .+--.|..|
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 226 (493)
T COG5236 151 SFKCPKSKCHRRCGSLKELKKHYKAQHGF-VLCSECIGNKKDFWNEIRLFRS---STLRDHKNGGLEEEGFKGHPLCIFC 226 (493)
T ss_pred HhcCCchhhhhhhhhHHHHHHHHHhhcCc-EEhHhhhcCcccCccceeeeec---ccccccccCCccccCcCCCchhhhc
Confidence 378985 888888899999999877664 3355553 233222111100 01111111111 1 222369999
Q ss_pred CccccChHHHHHHHhhccCcccCCccccc-------ccCChHhHHHHHhhhCCCC--ccCCC-CCcccCCHHHHHHHHHh
Q psy6546 103 SRDFATVKILKTHLKTHEGIIYPCPECDK-------TFLSTSGLREHRKVHAGVR--YICHA-CPREFSSEATMKAHVAS 172 (294)
Q Consensus 103 ~~~f~~~~~l~~H~~~~~~~~~~C~~C~~-------~f~~~~~l~~H~~~h~~~~--~~C~~-C~~~f~~~~~l~~H~~~ 172 (294)
..-|.+...|..|++..+.. |-+|++ -|.+...|..|.+.-+.-- -.|.. =-.+|+....|..|+..
T Consensus 227 ~~~FYdDDEL~~HcR~~HE~---ChICD~v~p~~~QYFK~Y~~Le~HF~~~hy~ct~qtc~~~k~~vf~~~~el~~h~~~ 303 (493)
T COG5236 227 KIYFYDDDELRRHCRLRHEA---CHICDMVGPIRYQYFKSYEDLEAHFRNAHYCCTFQTCRVGKCYVFPYHTELLEHLTR 303 (493)
T ss_pred cceecChHHHHHHHHhhhhh---hhhhhccCccchhhhhCHHHHHHHhhcCceEEEEEEEecCcEEEeccHHHHHHHHHH
Confidence 99999999999999998875 555543 4666677777776433211 11221 12578899999999877
Q ss_pred hcC
Q psy6546 173 HNG 175 (294)
Q Consensus 173 ~~~ 175 (294)
-++
T Consensus 304 ~h~ 306 (493)
T COG5236 304 FHK 306 (493)
T ss_pred Hhh
Confidence 654
No 58
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=94.21 E-value=0.053 Score=26.38 Aligned_cols=19 Identities=42% Similarity=0.945 Sum_probs=12.1
Q ss_pred eCCCCccccCCHHHHHHHHH
Q psy6546 206 SCPSCSKSFNRKDRYRMHLK 225 (294)
Q Consensus 206 ~C~~C~~~f~~~~~l~~H~~ 225 (294)
.|+.||+.| ..+.|.+|+.
T Consensus 4 ~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred cCCCCCCEE-CHHHHHHHHH
Confidence 567777777 4555666654
No 59
>KOG2785|consensus
Probab=94.18 E-value=0.18 Score=42.12 Aligned_cols=49 Identities=22% Similarity=0.417 Sum_probs=39.7
Q ss_pred ceeCCCCccccCCHHHHHHHHHHhCCC------------------------cccccccc---ccccCHHHHHHHHh
Q psy6546 204 TYSCPSCSKSFNRKDRYRMHLKLHQGV------------------------RHTCKECS---KEFSNEYNLKNHMV 252 (294)
Q Consensus 204 ~~~C~~C~~~f~~~~~l~~H~~~h~~~------------------------~~~C~~C~---~~f~~~~~l~~H~~ 252 (294)
|-.|..|+..+.+-..-..||..+||. .+.|-.|+ +.|.+..+.+.|+.
T Consensus 166 Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~ 241 (390)
T KOG2785|consen 166 PTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMR 241 (390)
T ss_pred CcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHh
Confidence 577999999999988889999887752 16788888 88888888888863
No 60
>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=94.06 E-value=0.049 Score=28.89 Aligned_cols=23 Identities=26% Similarity=0.506 Sum_probs=16.8
Q ss_pred ceeCCCCccccCCHHHHHHHHHH
Q psy6546 204 TYSCPSCSKSFNRKDRYRMHLKL 226 (294)
Q Consensus 204 ~~~C~~C~~~f~~~~~l~~H~~~ 226 (294)
+|.|..|+..|.+...+..|++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 56777888888777777777653
No 61
>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=92.08 E-value=0.14 Score=27.04 Aligned_cols=23 Identities=26% Similarity=0.479 Sum_probs=16.2
Q ss_pred cccCCccCccccChHHHHHHHhh
Q psy6546 96 RHPCPQCSRDFATVKILKTHLKT 118 (294)
Q Consensus 96 ~~~C~~C~~~f~~~~~l~~H~~~ 118 (294)
+|.|..|++.|.+...+..|+..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 46677777777777777777644
No 62
>KOG2482|consensus
Probab=90.97 E-value=0.39 Score=39.58 Aligned_cols=53 Identities=23% Similarity=0.416 Sum_probs=38.1
Q ss_pred CCcccCCccCcccc-ChHHHHHHHhhccC----c-------------------ccCCcccccccCChHhHHHHHhhh
Q psy6546 94 LTRHPCPQCSRDFA-TVKILKTHLKTHEG----I-------------------IYPCPECDKTFLSTSGLREHRKVH 146 (294)
Q Consensus 94 ~~~~~C~~C~~~f~-~~~~l~~H~~~~~~----~-------------------~~~C~~C~~~f~~~~~l~~H~~~h 146 (294)
....+|-.|...+. .++.+..|+-.-++ . .++|-.|++.|+++..|+.||+..
T Consensus 142 ~fslqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrdkntLkeHMrkK 218 (423)
T KOG2482|consen 142 IFSLQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRDKNTLKEHMRKK 218 (423)
T ss_pred eeeeEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCCcHHHHHHHHhc
Confidence 34567999976554 44556667644332 1 378999999999999999999753
No 63
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=90.91 E-value=0.14 Score=29.78 Aligned_cols=30 Identities=23% Similarity=0.406 Sum_probs=25.3
Q ss_pred CCCCCccCccchhccCCHHHHHHHHHHhCC
Q psy6546 28 TTPTRHPCPQCSRDFATVKILKTHLKTHEG 57 (294)
Q Consensus 28 ~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~ 57 (294)
.+...++||.|+..|+.+.+...|+...++
T Consensus 13 DGE~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 13 DGEEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred CCceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 456678999999999999999999975544
No 64
>KOG4173|consensus
Probab=90.88 E-value=0.17 Score=38.37 Aligned_cols=46 Identities=24% Similarity=0.574 Sum_probs=20.0
Q ss_pred ccCCC--CCcccCCHHHHHHHHHhhcCCCcccCcchhccCCchHHHhHHh
Q psy6546 151 YICHA--CPREFSSEATMKAHVASHNGVQHACDQCDRTFSCMPYLRQHQK 198 (294)
Q Consensus 151 ~~C~~--C~~~f~~~~~l~~H~~~~~~~~~~C~~C~~~f~~~~~l~~H~~ 198 (294)
+.|.. |-..|........|-.+.++ ..|..|.+.|.+...|-.|+.
T Consensus 80 ~~cqvagc~~~~d~lD~~E~hY~~~h~--~sCs~C~r~~Pt~hLLd~HI~ 127 (253)
T KOG4173|consen 80 FACQVAGCCQVFDALDDYEHHYHTLHG--NSCSFCKRAFPTGHLLDAHIL 127 (253)
T ss_pred ccccccchHHHHhhhhhHHHhhhhccc--chhHHHHHhCCchhhhhHHHH
Confidence 44444 33444433333333333222 245555555555555555443
No 65
>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=90.77 E-value=0.12 Score=27.10 Aligned_cols=11 Identities=36% Similarity=1.216 Sum_probs=5.2
Q ss_pred eeCCCCccccC
Q psy6546 205 YSCPSCSKSFN 215 (294)
Q Consensus 205 ~~C~~C~~~f~ 215 (294)
|+|..||..+.
T Consensus 2 ~~C~~CGy~y~ 12 (33)
T cd00350 2 YVCPVCGYIYD 12 (33)
T ss_pred EECCCCCCEEC
Confidence 44555554443
No 66
>KOG2893|consensus
Probab=90.12 E-value=0.092 Score=40.74 Aligned_cols=42 Identities=38% Similarity=0.709 Sum_probs=34.4
Q ss_pred cCCccCccccChHHHHHHHhhccCcccCCcccccccCChHhHHHH
Q psy6546 98 PCPQCSRDFATVKILKTHLKTHEGIIYPCPECDKTFLSTSGLREH 142 (294)
Q Consensus 98 ~C~~C~~~f~~~~~l~~H~~~~~~~~~~C~~C~~~f~~~~~l~~H 142 (294)
.|=.|++.|.+..-|.+|++.-+ |+|.+|.+.+.+--.|..|
T Consensus 12 wcwycnrefddekiliqhqkakh---fkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQKAKH---FKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred eeeecccccchhhhhhhhhhhcc---ceeeeehhhhccCCCceee
Confidence 68899999999999999987754 8999998887666666555
No 67
>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=88.85 E-value=0.46 Score=32.91 Aligned_cols=80 Identities=16% Similarity=0.291 Sum_probs=46.3
Q ss_pred CceeCCCCccccCCHHHHHHHHHH-hCCCc-cccccccccccCHHHH-HHHHhhh----------c---cccccc----c
Q psy6546 203 ITYSCPSCSKSFNRKDRYRMHLKL-HQGVR-HTCKECSKEFSNEYNL-KNHMVLH----------D---VRAYVC----E 262 (294)
Q Consensus 203 ~~~~C~~C~~~f~~~~~l~~H~~~-h~~~~-~~C~~C~~~f~~~~~l-~~H~~~h----------~---~~~~~C----~ 262 (294)
+-..|..|+....- +.+..|++. |+..+ ..-..=.+.+.....| .....+- + ..-|.| +
T Consensus 10 ~vlIC~~C~~av~~-~~v~~HL~~~H~~~~~~~~~~i~~~~~~~~~l~~~~~~~~~p~~~~~Pi~gLp~~~G~~C~~~~~ 88 (109)
T PF12013_consen 10 RVLICRQCQYAVQP-SEVESHLRKRHHILKSQERQRIVEAIRQWPDLLPDPDDLQIPPDPSPPIPGLPVYDGYRCQCDPP 88 (109)
T ss_pred CEEEeCCCCcccCc-hHHHHHHHHhcccccHHHHHHHHHHHHhhhhcccCccccCCCCCCCCcCCCCCCCCCeeeecCCC
Confidence 35789999988876 789999985 43321 1000000111111111 0000000 0 123889 9
Q ss_pred cccccccchhhhhhhhhhccC
Q psy6546 263 LCARQFTRVDHFNHHRRLQHD 283 (294)
Q Consensus 263 ~C~~~f~~~~~l~~H~~~~h~ 283 (294)
.|++.+.+...+..|.+.+|+
T Consensus 89 ~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 89 HCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CCCcEeccHHHHHHHHHHhcC
Confidence 999999999999999998885
No 68
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=86.95 E-value=0.099 Score=45.86 Aligned_cols=53 Identities=26% Similarity=0.607 Sum_probs=28.2
Q ss_pred cCCcccccccCChHhHHHHHh--hhCCC--C-ccCC--CCCcccCCHHHHHHHHHhhcCC
Q psy6546 124 YPCPECDKTFLSTSGLREHRK--VHAGV--R-YICH--ACPREFSSEATMKAHVASHNGV 176 (294)
Q Consensus 124 ~~C~~C~~~f~~~~~l~~H~~--~h~~~--~-~~C~--~C~~~f~~~~~l~~H~~~~~~~ 176 (294)
+.|..|...|.....|..|.. .|.++ + +.|+ .|++.|.....+..|...+++.
T Consensus 290 ~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~ 349 (467)
T COG5048 290 IKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSI 349 (467)
T ss_pred CCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCC
Confidence 445555555555555555555 45544 3 5555 4555555555555555555543
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=86.87 E-value=0.67 Score=31.91 Aligned_cols=20 Identities=20% Similarity=0.375 Sum_probs=12.2
Q ss_pred CCccCccchhccCCHHHHHH
Q psy6546 31 TRHPCPQCSRDFATVKILKT 50 (294)
Q Consensus 31 ~~~~C~~C~~~f~~~~~l~~ 50 (294)
-|..|+.||...-....|.+
T Consensus 14 LP~~CpiCgLtLVss~HLAR 33 (112)
T TIGR00622 14 LPVECPICGLTLILSTHLAR 33 (112)
T ss_pred CCCcCCcCCCEEeccchHHH
Confidence 35667777776665555553
No 70
>KOG2893|consensus
Probab=86.27 E-value=0.21 Score=38.87 Aligned_cols=47 Identities=26% Similarity=0.540 Sum_probs=31.7
Q ss_pred ceeCCCCccccCCHHHHHHHHHHhCCCccccccccccccCHHHHHHH-Hhhh
Q psy6546 204 TYSCPSCSKSFNRKDRYRMHLKLHQGVRHTCKECSKEFSNEYNLKNH-MVLH 254 (294)
Q Consensus 204 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~C~~~f~~~~~l~~H-~~~h 254 (294)
+| |=+|++-|....-|.+|++.. -|+|-+|.+.+-+.-.|..| +.+|
T Consensus 11 pw-cwycnrefddekiliqhqkak---hfkchichkkl~sgpglsihcmqvh 58 (341)
T KOG2893|consen 11 PW-CWYCNREFDDEKILIQHQKAK---HFKCHICHKKLFSGPGLSIHCMQVH 58 (341)
T ss_pred ce-eeecccccchhhhhhhhhhhc---cceeeeehhhhccCCCceeehhhhh
Confidence 44 667788888777777776541 17788887776666666666 4555
No 71
>KOG2186|consensus
Probab=84.27 E-value=0.57 Score=36.97 Aligned_cols=45 Identities=18% Similarity=0.522 Sum_probs=24.8
Q ss_pred cCCcccccccCChHhHHHHHhhhCCCCccCCCCCcccCCHHHHHHHH
Q psy6546 124 YPCPECDKTFLSTSGLREHRKVHAGVRYICHACPREFSSEATMKAHV 170 (294)
Q Consensus 124 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~C~~~f~~~~~l~~H~ 170 (294)
|.|..||.... +..+.+|+...++..|.|-.|++.|.. .....|.
T Consensus 4 FtCnvCgEsvK-Kp~vekH~srCrn~~fSCIDC~k~F~~-~sYknH~ 48 (276)
T KOG2186|consen 4 FTCNVCGESVK-KPQVEKHMSRCRNAYFSCIDCGKTFER-VSYKNHT 48 (276)
T ss_pred Eehhhhhhhcc-ccchHHHHHhccCCeeEEeeccccccc-chhhhhh
Confidence 45666665533 234445666666655666666666655 3444443
No 72
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=83.85 E-value=0.34 Score=42.49 Aligned_cols=58 Identities=26% Similarity=0.509 Sum_probs=43.1
Q ss_pred ccccccccccccCHHHHHHHHh--hhc-c--cccccc--cccccccchhhhhhhhhhccCccccc
Q psy6546 231 RHTCKECSKEFSNEYNLKNHMV--LHD-V--RAYVCE--LCARQFTRVDHFNHHRRLQHDPEEFE 288 (294)
Q Consensus 231 ~~~C~~C~~~f~~~~~l~~H~~--~h~-~--~~~~C~--~C~~~f~~~~~l~~H~~~~h~~~~~~ 288 (294)
++.|..|...|.....|..|.+ .|. + +++.|+ .|++.|.....+..|...|.+..+..
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAK 353 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCccc
Confidence 3677777777877777777777 665 5 677777 68888888877777777777766553
No 73
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=83.49 E-value=2.3 Score=29.34 Aligned_cols=49 Identities=18% Similarity=0.385 Sum_probs=32.7
Q ss_pred cCCccCccccChHHHHHHHhhccCcccCCcccccccCChHhHHHHHhhhC
Q psy6546 98 PCPQCSRDFATVKILKTHLKTHEGIIYPCPECDKTFLSTSGLREHRKVHA 147 (294)
Q Consensus 98 ~C~~C~~~f~~~~~l~~H~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 147 (294)
.|..|...|........-. ......|+|+.|...|-..-++-.|...|.
T Consensus 57 ~C~~C~~~f~~~~~~~~~~-~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 57 FCFGCQGPFPKPPVSPFDE-LKDSHRYVCAVCKNVFCVDCDVFVHESLHC 105 (112)
T ss_pred cccCcCCCCCCcccccccc-cccccceeCCCCCCccccccchhhhhhccC
Confidence 4999999887653211110 112236999999999988888877776654
No 74
>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=83.46 E-value=0.5 Score=37.36 Aligned_cols=26 Identities=12% Similarity=0.285 Sum_probs=17.5
Q ss_pred ccccccccccccccchhhhhhhhhhc
Q psy6546 256 VRAYVCELCARQFTRVDHFNHHRRLQ 281 (294)
Q Consensus 256 ~~~~~C~~C~~~f~~~~~l~~H~~~~ 281 (294)
.+++.|+.|++..+.-..|.--.|+|
T Consensus 207 ~k~~PCPKCg~et~eTkdLSmStR~h 232 (314)
T PF06524_consen 207 GKPIPCPKCGYETQETKDLSMSTRSH 232 (314)
T ss_pred CCCCCCCCCCCcccccccceeeeecc
Confidence 56777777777777766666555444
No 75
>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=83.08 E-value=0.74 Score=22.59 Aligned_cols=6 Identities=50% Similarity=1.591 Sum_probs=2.2
Q ss_pred CCCCcc
Q psy6546 207 CPSCSK 212 (294)
Q Consensus 207 C~~C~~ 212 (294)
|+.||+
T Consensus 17 Cp~CG~ 22 (26)
T PF10571_consen 17 CPHCGY 22 (26)
T ss_pred CCCCCC
Confidence 333333
No 76
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=82.80 E-value=0.94 Score=26.98 Aligned_cols=31 Identities=16% Similarity=0.309 Sum_probs=14.7
Q ss_pred cccccccccccCHHHHHHHHhhhcccccccccccc
Q psy6546 232 HTCKECSKEFSNEYNLKNHMVLHDVRAYVCELCAR 266 (294)
Q Consensus 232 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~C~~ 266 (294)
|.|+.||+.-.....- -.....+|+|+.||+
T Consensus 28 F~CPnCGe~~I~Rc~~----CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 28 FPCPNCGEVEIYRCAK----CRKLGNPYRCPKCGF 58 (61)
T ss_pred eeCCCCCceeeehhhh----HHHcCCceECCCcCc
Confidence 5566665443333221 111245666666664
No 77
>KOG2186|consensus
Probab=82.14 E-value=0.93 Score=35.80 Aligned_cols=47 Identities=28% Similarity=0.647 Sum_probs=30.7
Q ss_pred cccCcchhccCCchHHHhHHhhcCCCceeCCCCccccCCHHHHHHHHHH
Q psy6546 178 HACDQCDRTFSCMPYLRQHQKLHSGITYSCPSCSKSFNRKDRYRMHLKL 226 (294)
Q Consensus 178 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~C~~~f~~~~~l~~H~~~ 226 (294)
|.|..||.... +..+..|+...++.-|.|..|++.|.. .....|.+-
T Consensus 4 FtCnvCgEsvK-Kp~vekH~srCrn~~fSCIDC~k~F~~-~sYknH~kC 50 (276)
T KOG2186|consen 4 FTCNVCGESVK-KPQVEKHMSRCRNAYFSCIDCGKTFER-VSYKNHTKC 50 (276)
T ss_pred Eehhhhhhhcc-ccchHHHHHhccCCeeEEeeccccccc-chhhhhhhh
Confidence 56777775544 345556777777777777777777776 445566543
No 78
>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=81.98 E-value=3.4 Score=28.53 Aligned_cols=27 Identities=22% Similarity=0.534 Sum_probs=24.3
Q ss_pred CCccC----ccchhccCCHHHHHHHHHHhCC
Q psy6546 31 TRHPC----PQCSRDFATVKILKTHLKTHEG 57 (294)
Q Consensus 31 ~~~~C----~~C~~~f~~~~~l~~H~~~~~~ 57 (294)
..|.| ..|+....+...+..|++.+|+
T Consensus 79 ~G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 79 DGYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CCeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 56999 9999999999999999987764
No 79
>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=81.65 E-value=0.7 Score=24.36 Aligned_cols=9 Identities=22% Similarity=0.781 Sum_probs=4.4
Q ss_pred ccccccccc
Q psy6546 258 AYVCELCAR 266 (294)
Q Consensus 258 ~~~C~~C~~ 266 (294)
|..|++|+.
T Consensus 18 p~~CP~Cg~ 26 (34)
T cd00729 18 PEKCPICGA 26 (34)
T ss_pred CCcCcCCCC
Confidence 344555554
No 80
>KOG4173|consensus
Probab=81.57 E-value=0.72 Score=35.15 Aligned_cols=81 Identities=23% Similarity=0.541 Sum_probs=60.8
Q ss_pred CcccCc--chhccCCchHHHhHHhhcCCCceeCCCCccccCCHHHHHHHHHHhC----------CCc-ccc--ccccccc
Q psy6546 177 QHACDQ--CDRTFSCMPYLRQHQKLHSGITYSCPSCSKSFNRKDRYRMHLKLHQ----------GVR-HTC--KECSKEF 241 (294)
Q Consensus 177 ~~~C~~--C~~~f~~~~~l~~H~~~h~~~~~~C~~C~~~f~~~~~l~~H~~~h~----------~~~-~~C--~~C~~~f 241 (294)
.+.|+. |...|.+...+..|...-++. .|..|.+.|.+.--|..|+...+ |.. |.| ..|+..|
T Consensus 79 ~~~cqvagc~~~~d~lD~~E~hY~~~h~~--sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KF 156 (253)
T KOG4173|consen 79 AFACQVAGCCQVFDALDDYEHHYHTLHGN--SCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKF 156 (253)
T ss_pred cccccccchHHHHhhhhhHHHhhhhcccc--hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhh
Confidence 467865 778888888888887554443 69999999999999999976433 333 888 5699999
Q ss_pred cCHHHHHHHH-hhhc-cccc
Q psy6546 242 SNEYNLKNHM-VLHD-VRAY 259 (294)
Q Consensus 242 ~~~~~l~~H~-~~h~-~~~~ 259 (294)
.....-..|. ++|. ...|
T Consensus 157 kT~r~RkdH~I~~Hk~Pa~f 176 (253)
T KOG4173|consen 157 KTSRDRKDHMIRMHKYPADF 176 (253)
T ss_pred hhhhhhhhHHHHhccCCcce
Confidence 9999988894 6664 4433
No 81
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=79.94 E-value=0.9 Score=25.57 Aligned_cols=11 Identities=27% Similarity=0.869 Sum_probs=5.1
Q ss_pred eeCCCCccccC
Q psy6546 205 YSCPSCSKSFN 215 (294)
Q Consensus 205 ~~C~~C~~~f~ 215 (294)
|.|..||..|.
T Consensus 3 Y~C~~Cg~~~~ 13 (44)
T smart00659 3 YICGECGRENE 13 (44)
T ss_pred EECCCCCCEee
Confidence 44445554443
No 82
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=79.79 E-value=1 Score=26.32 Aligned_cols=25 Identities=28% Similarity=0.687 Sum_probs=18.9
Q ss_pred ceeCCCCccccCCHHHHHHHHHHhC
Q psy6546 204 TYSCPSCSKSFNRKDRYRMHLKLHQ 228 (294)
Q Consensus 204 ~~~C~~C~~~f~~~~~l~~H~~~h~ 228 (294)
-+.|+.|+..|..+....+|....+
T Consensus 17 ~lrCPRC~~~FR~~K~Y~RHVNKaH 41 (65)
T COG4049 17 FLRCPRCGMVFRRRKDYIRHVNKAH 41 (65)
T ss_pred eeeCCchhHHHHHhHHHHHHhhHHh
Confidence 5778888888888888888875433
No 83
>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=79.54 E-value=1.8 Score=29.81 Aligned_cols=11 Identities=36% Similarity=1.023 Sum_probs=5.5
Q ss_pred ccCCccCccch
Q psy6546 59 IYPCPECDKTF 69 (294)
Q Consensus 59 ~~~c~~c~~~~ 69 (294)
...|+.||.+|
T Consensus 9 KR~Cp~CG~kF 19 (108)
T PF09538_consen 9 KRTCPSCGAKF 19 (108)
T ss_pred cccCCCCcchh
Confidence 34455555555
No 84
>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=78.25 E-value=0.76 Score=36.39 Aligned_cols=20 Identities=35% Similarity=0.690 Sum_probs=10.9
Q ss_pred CcccCCcccccccCChHhHH
Q psy6546 121 GIIYPCPECDKTFLSTSGLR 140 (294)
Q Consensus 121 ~~~~~C~~C~~~f~~~~~l~ 140 (294)
+.++.|+.|+........|.
T Consensus 207 ~k~~PCPKCg~et~eTkdLS 226 (314)
T PF06524_consen 207 GKPIPCPKCGYETQETKDLS 226 (314)
T ss_pred CCCCCCCCCCCcccccccce
Confidence 34566666666555444443
No 85
>PF14353 CpXC: CpXC protein
Probab=77.67 E-value=1.1 Score=32.10 Aligned_cols=20 Identities=30% Similarity=0.572 Sum_probs=10.9
Q ss_pred CCcccCCccCccccChHHHH
Q psy6546 94 LTRHPCPQCSRDFATVKILK 113 (294)
Q Consensus 94 ~~~~~C~~C~~~f~~~~~l~ 113 (294)
...+.|+.||..|.-...+.
T Consensus 36 l~~~~CP~Cg~~~~~~~p~l 55 (128)
T PF14353_consen 36 LFSFTCPSCGHKFRLEYPLL 55 (128)
T ss_pred cCEEECCCCCCceecCCCEE
Confidence 34466666666665444333
No 86
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=77.23 E-value=1.3 Score=32.72 Aligned_cols=18 Identities=28% Similarity=0.743 Sum_probs=12.6
Q ss_pred cccCCccCccccChHHHH
Q psy6546 96 RHPCPQCSRDFATVKILK 113 (294)
Q Consensus 96 ~~~C~~C~~~f~~~~~l~ 113 (294)
.++|+.||+.|.+...+.
T Consensus 28 ~~~c~~c~~~f~~~e~~~ 45 (154)
T PRK00464 28 RRECLACGKRFTTFERVE 45 (154)
T ss_pred eeeccccCCcceEeEecc
Confidence 377888888887765543
No 87
>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=76.31 E-value=2.2 Score=30.53 Aligned_cols=33 Identities=39% Similarity=0.748 Sum_probs=20.5
Q ss_pred CCCCCCCCCCccCccchhccCCHHHHHHHHHHhCCc
Q psy6546 23 TQTSSTTPTRHPCPQCSRDFATVKILKTHLKTHEGI 58 (294)
Q Consensus 23 ~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~ 58 (294)
+...+..+....|-+||+.|... ++|++.|+|.
T Consensus 63 ~i~kSI~~d~i~clecGk~~k~L---krHL~~~~gl 95 (132)
T PF05443_consen 63 PIRKSITPDYIICLECGKKFKTL---KRHLRTHHGL 95 (132)
T ss_dssp -SSTTB-SS-EE-TBT--EESBH---HHHHHHTT-S
T ss_pred CHhhccccCeeEEccCCcccchH---HHHHHHccCC
Confidence 34444556668999999999976 8999999875
No 88
>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=75.68 E-value=3.2 Score=30.95 Aligned_cols=17 Identities=18% Similarity=0.499 Sum_probs=8.5
Q ss_pred ceeCCCCccccCCHHHH
Q psy6546 204 TYSCPSCSKSFNRKDRY 220 (294)
Q Consensus 204 ~~~C~~C~~~f~~~~~l 220 (294)
-|.|+.|+..|+...++
T Consensus 109 ~Y~Cp~c~~r~tf~eA~ 125 (158)
T TIGR00373 109 FFICPNMCVRFTFNEAM 125 (158)
T ss_pred eEECCCCCcEeeHHHHH
Confidence 45555555555444444
No 89
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=75.02 E-value=1.5 Score=23.54 Aligned_cols=11 Identities=36% Similarity=1.120 Sum_probs=5.4
Q ss_pred cccCCccCccc
Q psy6546 96 RHPCPQCSRDF 106 (294)
Q Consensus 96 ~~~C~~C~~~f 106 (294)
..+|..|+..|
T Consensus 25 ~vrC~~C~~~f 35 (37)
T PF13719_consen 25 KVRCPKCGHVF 35 (37)
T ss_pred EEECCCCCcEe
Confidence 34555555444
No 90
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=73.95 E-value=1.9 Score=23.00 Aligned_cols=10 Identities=30% Similarity=0.903 Sum_probs=4.6
Q ss_pred ccCCccCccc
Q psy6546 97 HPCPQCSRDF 106 (294)
Q Consensus 97 ~~C~~C~~~f 106 (294)
.+|..|+..|
T Consensus 26 v~C~~C~~~f 35 (36)
T PF13717_consen 26 VRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEe
Confidence 4455554443
No 91
>PF12907 zf-met2: Zinc-binding
Probab=73.84 E-value=2 Score=23.57 Aligned_cols=29 Identities=24% Similarity=0.675 Sum_probs=18.7
Q ss_pred cccccccccc---cchhhhhhhhhhccCcccc
Q psy6546 259 YVCELCARQF---TRVDHFNHHRRLQHDPEEF 287 (294)
Q Consensus 259 ~~C~~C~~~f---~~~~~l~~H~~~~h~~~~~ 287 (294)
++|.+|.-.| .....|..|....|++..+
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKHpK~~~ 33 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKHPKNTF 33 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccCCCCCH
Confidence 4677777444 4445677777777776644
No 92
>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=73.36 E-value=2.1 Score=23.01 Aligned_cols=10 Identities=20% Similarity=0.723 Sum_probs=5.2
Q ss_pred ccCCccCccc
Q psy6546 97 HPCPQCSRDF 106 (294)
Q Consensus 97 ~~C~~C~~~f 106 (294)
..|+.|+..|
T Consensus 26 v~C~~C~~~~ 35 (38)
T TIGR02098 26 VRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEE
Confidence 4555555544
No 93
>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=73.09 E-value=0.58 Score=25.67 Aligned_cols=11 Identities=27% Similarity=0.857 Sum_probs=5.3
Q ss_pred ccCccchhccC
Q psy6546 33 HPCPQCSRDFA 43 (294)
Q Consensus 33 ~~C~~C~~~f~ 43 (294)
|+|+.||..|.
T Consensus 6 y~C~~Cg~~fe 16 (41)
T smart00834 6 YRCEDCGHTFE 16 (41)
T ss_pred EEcCCCCCEEE
Confidence 44555555444
No 94
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=72.56 E-value=6.6 Score=21.67 Aligned_cols=25 Identities=28% Similarity=0.545 Sum_probs=19.0
Q ss_pred CccCccchhccC--CHHHHHHHHHHhC
Q psy6546 32 RHPCPQCSRDFA--TVKILKTHLKTHE 56 (294)
Q Consensus 32 ~~~C~~C~~~f~--~~~~l~~H~~~~~ 56 (294)
...|+.||+.|. ...+.+.|.+.|.
T Consensus 13 ~~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 13 ATTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred CcCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 468999999995 4567777877664
No 95
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=72.33 E-value=1.6 Score=25.08 Aligned_cols=10 Identities=30% Similarity=0.923 Sum_probs=5.4
Q ss_pred cccccccccc
Q psy6546 232 HTCKECSKEF 241 (294)
Q Consensus 232 ~~C~~C~~~f 241 (294)
|+|..||+.|
T Consensus 7 Y~C~~Cg~~~ 16 (49)
T COG1996 7 YKCARCGREV 16 (49)
T ss_pred EEhhhcCCee
Confidence 5555555554
No 96
>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=70.24 E-value=4.7 Score=23.42 Aligned_cols=12 Identities=25% Similarity=0.711 Sum_probs=7.2
Q ss_pred cCCccCccchhc
Q psy6546 60 YPCPECDKTFLS 71 (294)
Q Consensus 60 ~~c~~c~~~~~~ 71 (294)
|.|..|+..+..
T Consensus 2 y~C~~CgyiYd~ 13 (50)
T cd00730 2 YECRICGYIYDP 13 (50)
T ss_pred cCCCCCCeEECC
Confidence 556666666543
No 97
>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=69.11 E-value=0.85 Score=26.64 Aligned_cols=29 Identities=24% Similarity=0.755 Sum_probs=15.4
Q ss_pred ccCccchhccCCHHHHHHHHHHhCCcccCCccCcc
Q psy6546 33 HPCPQCSRDFATVKILKTHLKTHEGIIYPCPECDK 67 (294)
Q Consensus 33 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~c~~c~~ 67 (294)
|+|..||..|.....+. ......|+.|+.
T Consensus 6 y~C~~Cg~~fe~~~~~~------~~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCTACGHRFEVLQKMS------DDPLATCPECGG 34 (52)
T ss_pred EEeCCCCCEeEEEEecC------CCCCCCCCCCCC
Confidence 66777777776442221 123455666654
No 98
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=69.06 E-value=2.3 Score=32.35 Aligned_cols=31 Identities=19% Similarity=0.642 Sum_probs=18.0
Q ss_pred ceeCCCCccccCCHHHHHHHHHHhCCCcccccccccccc
Q psy6546 204 TYSCPSCSKSFNRKDRYRMHLKLHQGVRHTCKECSKEFS 242 (294)
Q Consensus 204 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~C~~~f~ 242 (294)
-|.|+.|+..|+...++. ..|.|+.||....
T Consensus 117 ~Y~Cp~C~~rytf~eA~~--------~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 117 FFFCPNCHIRFTFDEAME--------YGFRCPQCGEMLE 147 (178)
T ss_pred EEECCCCCcEEeHHHHhh--------cCCcCCCCCCCCe
Confidence 566766776666555442 1366666665443
No 99
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=68.56 E-value=3.7 Score=30.57 Aligned_cols=30 Identities=17% Similarity=0.541 Sum_probs=16.3
Q ss_pred CcccCcchhccCCchHHHhHHhhcCCCceeCCCCcccc
Q psy6546 177 QHACDQCDRTFSCMPYLRQHQKLHSGITYSCPSCSKSF 214 (294)
Q Consensus 177 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~C~~~f 214 (294)
-|.|+.|+..|+....+. -.|.|+.||...
T Consensus 109 ~Y~Cp~c~~r~tf~eA~~--------~~F~Cp~Cg~~L 138 (158)
T TIGR00373 109 FFICPNMCVRFTFNEAME--------LNFTCPRCGAML 138 (158)
T ss_pred eEECCCCCcEeeHHHHHH--------cCCcCCCCCCEe
Confidence 456666665555544432 156666666443
No 100
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=68.48 E-value=5.8 Score=29.13 Aligned_cols=12 Identities=17% Similarity=0.728 Sum_probs=6.0
Q ss_pred cccccccccccC
Q psy6546 232 HTCKECSKEFSN 243 (294)
Q Consensus 232 ~~C~~C~~~f~~ 243 (294)
|.|+.|+..|..
T Consensus 100 Y~Cp~C~~~y~~ 111 (147)
T smart00531 100 YKCPNCQSKYTF 111 (147)
T ss_pred EECcCCCCEeeH
Confidence 455555544443
No 101
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=68.24 E-value=5.5 Score=19.44 Aligned_cols=19 Identities=26% Similarity=0.684 Sum_probs=12.2
Q ss_pred eCCCCccccCCHHHHHHHHH
Q psy6546 206 SCPSCSKSFNRKDRYRMHLK 225 (294)
Q Consensus 206 ~C~~C~~~f~~~~~l~~H~~ 225 (294)
.|++|++.+ ....+..|+.
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 477777776 4456666654
No 102
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=67.47 E-value=10 Score=27.02 Aligned_cols=34 Identities=35% Similarity=0.515 Sum_probs=25.4
Q ss_pred CCCCCCCCCCCccCccchhccCCHHHHHHHHHHhCCc
Q psy6546 22 TTQTSSTTPTRHPCPQCSRDFATVKILKTHLKTHEGI 58 (294)
Q Consensus 22 ~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~ 58 (294)
.+...+..+....|-++|+.|. .|++|+..|.+.
T Consensus 66 V~~kKSVtpD~IicLEDGkkfK---SLKRHL~t~~gm 99 (148)
T COG4957 66 VPIKKSVTPDYIICLEDGKKFK---SLKRHLTTHYGL 99 (148)
T ss_pred CCcccccCCCeEEEeccCcchH---HHHHHHhcccCC
Confidence 3344455556688999999997 688999998764
No 103
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=67.33 E-value=2.7 Score=31.37 Aligned_cols=9 Identities=33% Similarity=1.202 Sum_probs=4.8
Q ss_pred eeCCCCccc
Q psy6546 205 YSCPSCSKS 213 (294)
Q Consensus 205 ~~C~~C~~~ 213 (294)
|.|++||+.
T Consensus 135 ~vC~vCGy~ 143 (166)
T COG1592 135 WVCPVCGYT 143 (166)
T ss_pred EEcCCCCCc
Confidence 555555543
No 104
>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=66.91 E-value=1.9 Score=22.32 Aligned_cols=7 Identities=43% Similarity=1.141 Sum_probs=3.1
Q ss_pred ccccccc
Q psy6546 232 HTCKECS 238 (294)
Q Consensus 232 ~~C~~C~ 238 (294)
.+|..||
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 105
>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=65.83 E-value=2.3 Score=23.83 Aligned_cols=20 Identities=15% Similarity=0.487 Sum_probs=7.6
Q ss_pred cccccccccccch----hhhhhhh
Q psy6546 259 YVCELCARQFTRV----DHFNHHR 278 (294)
Q Consensus 259 ~~C~~C~~~f~~~----~~l~~H~ 278 (294)
.+|..|++.+... ++|..|+
T Consensus 17 a~C~~C~~~~~~~~~~ts~l~~HL 40 (45)
T PF02892_consen 17 AKCKYCGKVIKYSSGGTSNLKRHL 40 (45)
T ss_dssp EEETTTTEE-----SSTHHHHHHH
T ss_pred EEeCCCCeEEeeCCCcHHHHHHhh
Confidence 3444444444332 4455554
No 106
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=65.31 E-value=4.1 Score=24.38 Aligned_cols=8 Identities=50% Similarity=1.684 Sum_probs=3.4
Q ss_pred ceeCCCCc
Q psy6546 204 TYSCPSCS 211 (294)
Q Consensus 204 ~~~C~~C~ 211 (294)
+|.|+.||
T Consensus 48 ~Y~CP~CG 55 (59)
T PRK14890 48 PYTCPKCG 55 (59)
T ss_pred ceECCCCC
Confidence 44444444
No 107
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=64.96 E-value=1 Score=35.38 Aligned_cols=11 Identities=27% Similarity=0.957 Sum_probs=6.7
Q ss_pred cCCcccccccC
Q psy6546 124 YPCPECDKTFL 134 (294)
Q Consensus 124 ~~C~~C~~~f~ 134 (294)
+.|+.||..+.
T Consensus 49 ~vCP~CgyA~~ 59 (214)
T PF09986_consen 49 WVCPHCGYAAF 59 (214)
T ss_pred EECCCCCCccc
Confidence 45666766554
No 108
>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=64.89 E-value=2.3 Score=21.66 Aligned_cols=11 Identities=27% Similarity=0.610 Sum_probs=5.7
Q ss_pred ccccccccccc
Q psy6546 256 VRAYVCELCAR 266 (294)
Q Consensus 256 ~~~~~C~~C~~ 266 (294)
...|.|+.|+.
T Consensus 17 ~~~~vCp~C~~ 27 (30)
T PF08274_consen 17 GELLVCPECGH 27 (30)
T ss_dssp SSSEEETTTTE
T ss_pred CCEEeCCcccc
Confidence 44555555554
No 109
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=64.71 E-value=6.3 Score=22.74 Aligned_cols=21 Identities=33% Similarity=0.735 Sum_probs=12.3
Q ss_pred eeCCCCccccCCH-----HHHHHHHH
Q psy6546 205 YSCPSCSKSFNRK-----DRYRMHLK 225 (294)
Q Consensus 205 ~~C~~C~~~f~~~-----~~l~~H~~ 225 (294)
-.|..|++.+... +.|.+|++
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHH
Confidence 3566666665443 46666665
No 110
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=63.78 E-value=4.4 Score=22.91 Aligned_cols=11 Identities=27% Similarity=0.939 Sum_probs=5.7
Q ss_pred ccCCccCccch
Q psy6546 59 IYPCPECDKTF 69 (294)
Q Consensus 59 ~~~c~~c~~~~ 69 (294)
.|.|+.|+..+
T Consensus 3 ~y~C~~CG~~~ 13 (46)
T PRK00398 3 EYKCARCGREV 13 (46)
T ss_pred EEECCCCCCEE
Confidence 35555555544
No 111
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=63.61 E-value=5.1 Score=30.51 Aligned_cols=30 Identities=20% Similarity=0.635 Sum_probs=16.0
Q ss_pred CcccCcchhccCCchHHHhHHhhcCCCceeCCCCcccc
Q psy6546 177 QHACDQCDRTFSCMPYLRQHQKLHSGITYSCPSCSKSF 214 (294)
Q Consensus 177 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~C~~~f 214 (294)
-|.|+.|+..|+....+. -.|.|+.||...
T Consensus 117 ~Y~Cp~C~~rytf~eA~~--------~~F~Cp~Cg~~L 146 (178)
T PRK06266 117 FFFCPNCHIRFTFDEAME--------YGFRCPQCGEML 146 (178)
T ss_pred EEECCCCCcEEeHHHHhh--------cCCcCCCCCCCC
Confidence 356666665555444321 156666666544
No 112
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=63.38 E-value=6.7 Score=31.31 Aligned_cols=32 Identities=16% Similarity=0.424 Sum_probs=24.6
Q ss_pred CCccCccchhccCCHHHHHHHHHHhCCcccCCccCccch
Q psy6546 31 TRHPCPQCSRDFATVKILKTHLKTHEGIIYPCPECDKTF 69 (294)
Q Consensus 31 ~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~c~~c~~~~ 69 (294)
....|..|+...+....+..|+ ++|..|++..
T Consensus 64 p~v~CrVCq~~I~i~gk~~QhV-------VkC~~CnEAT 95 (256)
T PF09788_consen 64 PVVTCRVCQSLIDIEGKMHQHV-------VKCSVCNEAT 95 (256)
T ss_pred ceEEeecCCceecccCccceee-------EECCCCCccc
Confidence 3468999999998877766664 7888887654
No 113
>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=62.10 E-value=3.4 Score=23.62 Aligned_cols=11 Identities=27% Similarity=0.767 Sum_probs=5.7
Q ss_pred CcccCCccCcc
Q psy6546 95 TRHPCPQCSRD 105 (294)
Q Consensus 95 ~~~~C~~C~~~ 105 (294)
.-+.|+.|+..
T Consensus 33 ~~w~CP~C~a~ 43 (47)
T PF00301_consen 33 DDWVCPVCGAP 43 (47)
T ss_dssp TT-B-TTTSSB
T ss_pred CCCcCcCCCCc
Confidence 44678888654
No 114
>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=60.24 E-value=8.2 Score=27.25 Aligned_cols=10 Identities=30% Similarity=0.747 Sum_probs=4.5
Q ss_pred cCCccCccch
Q psy6546 60 YPCPECDKTF 69 (294)
Q Consensus 60 ~~c~~c~~~~ 69 (294)
..|+.|+.+|
T Consensus 10 r~Cp~cg~kF 19 (129)
T TIGR02300 10 RICPNTGSKF 19 (129)
T ss_pred ccCCCcCccc
Confidence 3444444444
No 115
>PHA00626 hypothetical protein
Probab=59.27 E-value=4.2 Score=23.95 Aligned_cols=16 Identities=13% Similarity=0.241 Sum_probs=13.2
Q ss_pred CCCccCccchhccCCH
Q psy6546 30 PTRHPCPQCSRDFATV 45 (294)
Q Consensus 30 ~~~~~C~~C~~~f~~~ 45 (294)
...|.|+.||..|+..
T Consensus 21 snrYkCkdCGY~ft~~ 36 (59)
T PHA00626 21 SDDYVCCDCGYNDSKD 36 (59)
T ss_pred CcceEcCCCCCeechh
Confidence 5789999999999743
No 116
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=58.99 E-value=6.3 Score=21.83 Aligned_cols=10 Identities=50% Similarity=1.351 Sum_probs=5.9
Q ss_pred cCCccCccch
Q psy6546 60 YPCPECDKTF 69 (294)
Q Consensus 60 ~~c~~c~~~~ 69 (294)
|.|..|+..|
T Consensus 6 y~C~~Cg~~f 15 (42)
T PF09723_consen 6 YRCEECGHEF 15 (42)
T ss_pred EEeCCCCCEE
Confidence 5566666555
No 117
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=58.39 E-value=6.4 Score=22.54 Aligned_cols=14 Identities=21% Similarity=0.558 Sum_probs=8.5
Q ss_pred hCCCcccccccccc
Q psy6546 227 HQGVRHTCKECSKE 240 (294)
Q Consensus 227 h~~~~~~C~~C~~~ 240 (294)
+|..+|.|..||.+
T Consensus 33 ~H~dR~~CGkCgyT 46 (51)
T COG1998 33 DHKDRWACGKCGYT 46 (51)
T ss_pred hcCceeEeccccce
Confidence 34446777777754
No 118
>KOG4167|consensus
Probab=57.31 E-value=8.5 Score=35.60 Aligned_cols=27 Identities=33% Similarity=0.693 Sum_probs=20.4
Q ss_pred CCcccCCccCccccChHHHHHHHhhcc
Q psy6546 94 LTRHPCPQCSRDFATVKILKTHLKTHE 120 (294)
Q Consensus 94 ~~~~~C~~C~~~f~~~~~l~~H~~~~~ 120 (294)
...|.|..|++.|....++..||+.|.
T Consensus 790 ~giFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 790 TGIFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred CceeehHHHHHHHHHHhhhhHHHHHHH
Confidence 456778888888877777777877774
No 119
>PF15269 zf-C2H2_7: Zinc-finger
Probab=57.24 E-value=15 Score=20.46 Aligned_cols=26 Identities=27% Similarity=0.392 Sum_probs=22.0
Q ss_pred CCCccCccchhccCCHHHHHHHHHHh
Q psy6546 30 PTRHPCPQCSRDFATVKILKTHLKTH 55 (294)
Q Consensus 30 ~~~~~C~~C~~~f~~~~~l~~H~~~~ 55 (294)
+-.|+|-.|.......+.|-.||+..
T Consensus 18 p~~ykcfqcpftc~~kshl~nhmky~ 43 (54)
T PF15269_consen 18 PFKYKCFQCPFTCNEKSHLFNHMKYS 43 (54)
T ss_pred CccceeecCCcccchHHHHHHHHHHH
Confidence 33588999999999999999999753
No 120
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=57.19 E-value=3.3 Score=29.39 Aligned_cols=10 Identities=30% Similarity=0.723 Sum_probs=4.9
Q ss_pred cccCcchhcc
Q psy6546 178 HACDQCDRTF 187 (294)
Q Consensus 178 ~~C~~C~~~f 187 (294)
|+|.+|..+.
T Consensus 81 YeCnIC~etS 90 (140)
T PF05290_consen 81 YECNICKETS 90 (140)
T ss_pred eeccCccccc
Confidence 5555554433
No 121
>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=56.32 E-value=5.4 Score=28.60 Aligned_cols=24 Identities=25% Similarity=0.652 Sum_probs=12.7
Q ss_pred cccccccccccchhhhhhhhhhccCcc
Q psy6546 259 YVCELCARQFTRVDHFNHHRRLQHDPE 285 (294)
Q Consensus 259 ~~C~~C~~~f~~~~~l~~H~~~~h~~~ 285 (294)
-.|-.||+.|.. |++|++.|||=.
T Consensus 73 i~clecGk~~k~---LkrHL~~~~glt 96 (132)
T PF05443_consen 73 IICLECGKKFKT---LKRHLRTHHGLT 96 (132)
T ss_dssp EE-TBT--EESB---HHHHHHHTT-S-
T ss_pred eEEccCCcccch---HHHHHHHccCCC
Confidence 467777777764 367777776643
No 122
>KOG4377|consensus
Probab=56.30 E-value=5.1 Score=34.20 Aligned_cols=102 Identities=19% Similarity=0.429 Sum_probs=61.9
Q ss_pred ccC--CCCCcccCCHHHHHHHHHhhcCC-------------Cccc--CcchhccCCchHHHhHHhhcCCC--------ce
Q psy6546 151 YIC--HACPREFSSEATMKAHVASHNGV-------------QHAC--DQCDRTFSCMPYLRQHQKLHSGI--------TY 205 (294)
Q Consensus 151 ~~C--~~C~~~f~~~~~l~~H~~~~~~~-------------~~~C--~~C~~~f~~~~~l~~H~~~h~~~--------~~ 205 (294)
|.| +.|++.+..+..+.+|.+.|..+ .|.| ..|.+ +.++...|...|+.+ -|
T Consensus 272 yhcl~e~C~ykr~~k~DvirH~~~hkkrdnsL~dgf~rfs~syhC~~~~C~k---sTsdV~~h~nFht~~~n~Gfrrthf 348 (480)
T KOG4377|consen 272 YHCLNEYCFYKRGQKNDVIRHVEIHKKRDNSLIDGFHRFSNSYHCTGQICEK---STSDVLLHDNFHTDKRNNGFRRTHF 348 (480)
T ss_pred hcccCccccccccchhhhHHHHHHHhhcccccccchhhcCccchhhhcccCc---ccccccccCccccccccCceeccee
Confidence 555 45888888889999999888653 1455 45777 556677787777664 36
Q ss_pred eCCCCc--cccCCHHHHHHHHHHhCCC------------------c-------ccc--ccccccccCHHHHHHHHhhhc
Q psy6546 206 SCPSCS--KSFNRKDRYRMHLKLHQGV------------------R-------HTC--KECSKEFSNEYNLKNHMVLHD 255 (294)
Q Consensus 206 ~C~~C~--~~f~~~~~l~~H~~~h~~~------------------~-------~~C--~~C~~~f~~~~~l~~H~~~h~ 255 (294)
.|..|+ ..|.....-..|.+-+.++ . +.| ..|+..+.+.+++..|.+.|.
T Consensus 349 hC~r~gCTdtfK~~khk~yh~kdda~~~dGfkkf~k~e~cay~gCkys~~cnhfhc~r~Gc~~tl~s~sqm~shkrkhe 427 (480)
T KOG4377|consen 349 HCQRIGCTDTFKDSKHKPYHYKDDAGEIDGFKKFFKDENCAYTGCKYSGICNHFHCDRLGCEATLYSVSQMASHKRKHE 427 (480)
T ss_pred EEeccCCccccccccccccccCcchhhhhhhhhhhccccCCccCcccccceeeeeecccCCceEEEehhhhhhhhhhhh
Confidence 687766 4444322222222222211 0 122 347777777777777777773
No 123
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=55.21 E-value=8.4 Score=25.13 Aligned_cols=14 Identities=29% Similarity=0.650 Sum_probs=8.7
Q ss_pred CcccCCccCccccC
Q psy6546 95 TRHPCPQCSRDFAT 108 (294)
Q Consensus 95 ~~~~C~~C~~~f~~ 108 (294)
..+.|..|+..|..
T Consensus 52 GIW~C~kCg~~fAG 65 (89)
T COG1997 52 GIWKCRKCGAKFAG 65 (89)
T ss_pred CeEEcCCCCCeecc
Confidence 45667777666653
No 124
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=53.45 E-value=11 Score=35.55 Aligned_cols=10 Identities=40% Similarity=1.012 Sum_probs=6.4
Q ss_pred ccCCcccccc
Q psy6546 123 IYPCPECDKT 132 (294)
Q Consensus 123 ~~~C~~C~~~ 132 (294)
|..|+.||..
T Consensus 475 p~~Cp~Cgs~ 484 (730)
T COG1198 475 PQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCC
Confidence 5667777654
No 125
>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=52.65 E-value=5.6 Score=19.06 Aligned_cols=7 Identities=29% Similarity=1.127 Sum_probs=3.5
Q ss_pred ccccccc
Q psy6546 232 HTCKECS 238 (294)
Q Consensus 232 ~~C~~C~ 238 (294)
|.|+.||
T Consensus 17 f~CPnCG 23 (24)
T PF07754_consen 17 FPCPNCG 23 (24)
T ss_pred EeCCCCC
Confidence 4555554
No 126
>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=52.43 E-value=4.3 Score=31.79 Aligned_cols=21 Identities=24% Similarity=0.548 Sum_probs=10.3
Q ss_pred cccccccccccCHHHHHHHHh
Q psy6546 232 HTCKECSKEFSNEYNLKNHMV 252 (294)
Q Consensus 232 ~~C~~C~~~f~~~~~l~~H~~ 252 (294)
|.|..|++.|....-..+|+.
T Consensus 78 ~~C~lc~KlFkg~eFV~KHI~ 98 (214)
T PF04959_consen 78 WRCPLCGKLFKGPEFVRKHIF 98 (214)
T ss_dssp EEE-SSS-EESSHHHHHHHHH
T ss_pred ECCCCCCcccCChHHHHHHHh
Confidence 555555555555555555543
No 127
>PRK04023 DNA polymerase II large subunit; Validated
Probab=49.61 E-value=21 Score=34.75 Aligned_cols=9 Identities=44% Similarity=1.169 Sum_probs=5.1
Q ss_pred cCCcccccc
Q psy6546 124 YPCPECDKT 132 (294)
Q Consensus 124 ~~C~~C~~~ 132 (294)
..|+.||..
T Consensus 627 RfCpsCG~~ 635 (1121)
T PRK04023 627 RKCPSCGKE 635 (1121)
T ss_pred ccCCCCCCc
Confidence 456666554
No 128
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=49.50 E-value=9.7 Score=22.74 Aligned_cols=7 Identities=43% Similarity=0.619 Sum_probs=2.8
Q ss_pred HHHHHHh
Q psy6546 111 ILKTHLK 117 (294)
Q Consensus 111 ~l~~H~~ 117 (294)
.|..|+.
T Consensus 25 ~l~~H~~ 31 (60)
T PF02176_consen 25 ELDDHLE 31 (60)
T ss_dssp CHHHHHH
T ss_pred HHHHHHH
Confidence 3334443
No 129
>KOG4167|consensus
Probab=48.46 E-value=14 Score=34.21 Aligned_cols=27 Identities=33% Similarity=0.710 Sum_probs=24.0
Q ss_pred CCCccCccchhccCCHHHHHHHHHHhC
Q psy6546 30 PTRHPCPQCSRDFATVKILKTHLKTHE 56 (294)
Q Consensus 30 ~~~~~C~~C~~~f~~~~~l~~H~~~~~ 56 (294)
.--|.|.+|++.|.-...+..||+.|.
T Consensus 790 ~giFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 790 TGIFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred CceeehHHHHHHHHHHhhhhHHHHHHH
Confidence 345999999999999999999999884
No 130
>PRK04023 DNA polymerase II large subunit; Validated
Probab=48.34 E-value=19 Score=34.92 Aligned_cols=11 Identities=27% Similarity=0.912 Sum_probs=6.1
Q ss_pred ccccccccccc
Q psy6546 232 HTCKECSKEFS 242 (294)
Q Consensus 232 ~~C~~C~~~f~ 242 (294)
+.|+.||....
T Consensus 664 y~CPKCG~El~ 674 (1121)
T PRK04023 664 DECEKCGREPT 674 (1121)
T ss_pred CcCCCCCCCCC
Confidence 55666665443
No 131
>KOG2593|consensus
Probab=47.94 E-value=11 Score=32.60 Aligned_cols=11 Identities=45% Similarity=1.280 Sum_probs=5.4
Q ss_pred ccCCccCccch
Q psy6546 59 IYPCPECDKTF 69 (294)
Q Consensus 59 ~~~c~~c~~~~ 69 (294)
.|.|+.|.++|
T Consensus 128 ~Y~Cp~C~kky 138 (436)
T KOG2593|consen 128 GYVCPNCQKKY 138 (436)
T ss_pred cccCCccccch
Confidence 34455555544
No 132
>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=47.74 E-value=17 Score=28.63 Aligned_cols=26 Identities=27% Similarity=0.572 Sum_probs=20.5
Q ss_pred ceeCCCCccccCCHHHHHHHHHHhCC
Q psy6546 204 TYSCPSCSKSFNRKDRYRMHLKLHQG 229 (294)
Q Consensus 204 ~~~C~~C~~~f~~~~~l~~H~~~h~~ 229 (294)
.|.|+.|+|.|.-...+.+|+..-|.
T Consensus 77 K~~C~lc~KlFkg~eFV~KHI~nKH~ 102 (214)
T PF04959_consen 77 KWRCPLCGKLFKGPEFVRKHIFNKHP 102 (214)
T ss_dssp EEEE-SSS-EESSHHHHHHHHHHH-H
T ss_pred EECCCCCCcccCChHHHHHHHhhcCH
Confidence 69999999999999999999987554
No 133
>KOG2807|consensus
Probab=46.41 E-value=26 Score=29.22 Aligned_cols=17 Identities=24% Similarity=0.581 Sum_probs=8.7
Q ss_pred ceeCCCCccccCCHHHH
Q psy6546 204 TYSCPSCSKSFNRKDRY 220 (294)
Q Consensus 204 ~~~C~~C~~~f~~~~~l 220 (294)
|-.|+.|+-...+.-+|
T Consensus 290 P~eCpiC~ltLVss~hL 306 (378)
T KOG2807|consen 290 PIECPICSLTLVSSPHL 306 (378)
T ss_pred CccCCccceeEecchHH
Confidence 44555555555544444
No 134
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=45.60 E-value=3 Score=26.32 Aligned_cols=18 Identities=22% Similarity=0.532 Sum_probs=9.3
Q ss_pred cccccc--cccccccchhhh
Q psy6546 257 RAYVCE--LCARQFTRVDHF 274 (294)
Q Consensus 257 ~~~~C~--~C~~~f~~~~~l 274 (294)
.-++|. .||..|.....+
T Consensus 26 ~Y~qC~N~eCg~tF~t~es~ 45 (72)
T PRK09678 26 RYHQCQNVNCSATFITYESV 45 (72)
T ss_pred eeeecCCCCCCCEEEEEEEE
Confidence 334554 566666554443
No 135
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=45.00 E-value=14 Score=20.16 Aligned_cols=13 Identities=15% Similarity=0.542 Sum_probs=8.6
Q ss_pred CcccCCccCcccc
Q psy6546 95 TRHPCPQCSRDFA 107 (294)
Q Consensus 95 ~~~~C~~C~~~f~ 107 (294)
.-|.|..|+..|.
T Consensus 27 ~fy~C~~C~~~w~ 39 (40)
T smart00440 27 VFYVCTKCGHRWR 39 (40)
T ss_pred EEEEeCCCCCEeC
Confidence 4477777776654
No 136
>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=44.75 E-value=8.3 Score=20.96 Aligned_cols=12 Identities=17% Similarity=0.456 Sum_probs=8.5
Q ss_pred CcccCCccCccc
Q psy6546 95 TRHPCPQCSRDF 106 (294)
Q Consensus 95 ~~~~C~~C~~~f 106 (294)
.-|.|..|+..|
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 447788888765
No 137
>KOG1701|consensus
Probab=44.71 E-value=5.2 Score=34.40 Aligned_cols=11 Identities=36% Similarity=0.875 Sum_probs=8.6
Q ss_pred ccccccccccc
Q psy6546 259 YVCELCARQFT 269 (294)
Q Consensus 259 ~~C~~C~~~f~ 269 (294)
|+|+.|+...+
T Consensus 428 Y~CEDCg~~LS 438 (468)
T KOG1701|consen 428 YKCEDCGLLLS 438 (468)
T ss_pred eehhhcCcccc
Confidence 78888887766
No 138
>KOG2272|consensus
Probab=43.65 E-value=18 Score=28.89 Aligned_cols=15 Identities=20% Similarity=0.654 Sum_probs=8.1
Q ss_pred ccCCcccccccCChH
Q psy6546 123 IYPCPECDKTFLSTS 137 (294)
Q Consensus 123 ~~~C~~C~~~f~~~~ 137 (294)
-|.|.+|.+...+..
T Consensus 99 CF~Cd~Cn~~Lad~g 113 (332)
T KOG2272|consen 99 CFRCDLCNKHLADQG 113 (332)
T ss_pred cchhHHHHHHHhhhh
Confidence 456666665544443
No 139
>COG1773 Rubredoxin [Energy production and conversion]
Probab=43.51 E-value=21 Score=21.19 Aligned_cols=9 Identities=33% Similarity=1.029 Sum_probs=5.3
Q ss_pred cccCCccCc
Q psy6546 96 RHPCPQCSR 104 (294)
Q Consensus 96 ~~~C~~C~~ 104 (294)
-..|+.|+.
T Consensus 36 ~w~CP~Cg~ 44 (55)
T COG1773 36 DWVCPECGV 44 (55)
T ss_pred ccCCCCCCC
Confidence 356677764
No 140
>KOG2071|consensus
Probab=41.86 E-value=22 Score=32.23 Aligned_cols=31 Identities=16% Similarity=0.401 Sum_probs=25.9
Q ss_pred CCCCCCccCccchhccCCHHHHHHHHHHhCC
Q psy6546 27 STTPTRHPCPQCSRDFATVKILKTHLKTHEG 57 (294)
Q Consensus 27 ~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~ 57 (294)
-....+-+|..||..|........||..|..
T Consensus 413 Ly~~~pnqC~~CG~R~~~~ee~sk~md~H~d 443 (579)
T KOG2071|consen 413 LYKDSPNQCKSCGLRFDDSEERSKHMDIHDD 443 (579)
T ss_pred hccCCcchhcccccccccchhhhhHhhhhhh
Confidence 3456678999999999999999999888754
No 141
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=39.84 E-value=16 Score=26.08 Aligned_cols=12 Identities=25% Similarity=0.858 Sum_probs=5.3
Q ss_pred eeCCCCccccCC
Q psy6546 205 YSCPSCSKSFNR 216 (294)
Q Consensus 205 ~~C~~C~~~f~~ 216 (294)
++|..||+.|..
T Consensus 2 H~Ct~Cg~~f~d 13 (131)
T PF09845_consen 2 HQCTKCGRVFED 13 (131)
T ss_pred cccCcCCCCcCC
Confidence 344444444443
No 142
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=39.76 E-value=13 Score=27.15 Aligned_cols=33 Identities=27% Similarity=0.713 Sum_probs=18.7
Q ss_pred ceeCCCCccccCCHHHHHHHHHHhCCCcccccccccc
Q psy6546 204 TYSCPSCSKSFNRKDRYRMHLKLHQGVRHTCKECSKE 240 (294)
Q Consensus 204 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~C~~~ 240 (294)
+|.|. |+..+.+. ++|-..-.|+.|.|..|+..
T Consensus 117 ~Y~C~-C~q~~l~~---RRhn~~~~g~~YrC~~C~gk 149 (156)
T COG3091 117 PYRCQ-CQQHYLRI---RRHNTVRRGEVYRCGKCGGK 149 (156)
T ss_pred eEEee-cCCccchh---hhcccccccceEEeccCCce
Confidence 67777 77665543 33433444445777777644
No 143
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=39.16 E-value=21 Score=25.83 Aligned_cols=13 Identities=15% Similarity=0.644 Sum_probs=6.4
Q ss_pred cccCCccCccccC
Q psy6546 96 RHPCPQCSRDFAT 108 (294)
Q Consensus 96 ~~~C~~C~~~f~~ 108 (294)
.+.|..||..|..
T Consensus 70 ~~~C~~CG~~~~~ 82 (135)
T PRK03824 70 VLKCRNCGNEWSL 82 (135)
T ss_pred EEECCCCCCEEec
Confidence 3455555555443
No 144
>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=38.80 E-value=23 Score=19.92 Aligned_cols=9 Identities=33% Similarity=0.984 Sum_probs=4.6
Q ss_pred ccccccccc
Q psy6546 257 RAYVCELCA 265 (294)
Q Consensus 257 ~~~~C~~C~ 265 (294)
..|+|..|+
T Consensus 36 ~~~~C~~C~ 44 (46)
T PF12760_consen 36 GRYRCKACR 44 (46)
T ss_pred CeEECCCCC
Confidence 445555554
No 145
>KOG4377|consensus
Probab=38.47 E-value=18 Score=31.11 Aligned_cols=79 Identities=19% Similarity=0.307 Sum_probs=47.2
Q ss_pred eeC--CCCccccCCHHHHHHHHHHhCCCc-------------ccc--ccccccccCHHHHHHHHhhhcc--------ccc
Q psy6546 205 YSC--PSCSKSFNRKDRYRMHLKLHQGVR-------------HTC--KECSKEFSNEYNLKNHMVLHDV--------RAY 259 (294)
Q Consensus 205 ~~C--~~C~~~f~~~~~l~~H~~~h~~~~-------------~~C--~~C~~~f~~~~~l~~H~~~h~~--------~~~ 259 (294)
|.| +.|++.+..+..+.+|..+|..+. |.| ..|.+ +-+....|...|.+ .-|
T Consensus 272 yhcl~e~C~ykr~~k~DvirH~~~hkkrdnsL~dgf~rfs~syhC~~~~C~k---sTsdV~~h~nFht~~~n~Gfrrthf 348 (480)
T KOG4377|consen 272 YHCLNEYCFYKRGQKNDVIRHVEIHKKRDNSLIDGFHRFSNSYHCTGQICEK---STSDVLLHDNFHTDKRNNGFRRTHF 348 (480)
T ss_pred hcccCccccccccchhhhHHHHHHHhhcccccccchhhcCccchhhhcccCc---ccccccccCccccccccCceeccee
Confidence 555 568888877888888888875421 455 34666 44555667666632 236
Q ss_pred ccccccccccchhhhhhhhhhccCccccc
Q psy6546 260 VCELCARQFTRVDHFNHHRRLQHDPEEFE 288 (294)
Q Consensus 260 ~C~~C~~~f~~~~~l~~H~~~~h~~~~~~ 288 (294)
-|--|+-.++.+ ...|...|-.+..++
T Consensus 349 hC~r~gCTdtfK--~~khk~yh~kdda~~ 375 (480)
T KOG4377|consen 349 HCQRIGCTDTFK--DSKHKPYHYKDDAGE 375 (480)
T ss_pred EEeccCCccccc--cccccccccCcchhh
Confidence 676666333333 556665555554444
No 146
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=37.51 E-value=18 Score=20.88 Aligned_cols=12 Identities=50% Similarity=0.999 Sum_probs=5.9
Q ss_pred cccccccccccC
Q psy6546 232 HTCKECSKEFSN 243 (294)
Q Consensus 232 ~~C~~C~~~f~~ 243 (294)
+.|..||..|.-
T Consensus 5 l~C~dCg~~Fvf 16 (49)
T PF13451_consen 5 LTCKDCGAEFVF 16 (49)
T ss_pred EEcccCCCeEEE
Confidence 445555554443
No 147
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=36.20 E-value=24 Score=23.78 Aligned_cols=12 Identities=25% Similarity=0.844 Sum_probs=6.2
Q ss_pred eeCCCCccccCC
Q psy6546 205 YSCPSCSKSFNR 216 (294)
Q Consensus 205 ~~C~~C~~~f~~ 216 (294)
++|..||..|.+
T Consensus 3 H~CtrCG~vf~~ 14 (112)
T COG3364 3 HQCTRCGEVFDD 14 (112)
T ss_pred ceeccccccccc
Confidence 445555555544
No 148
>KOG2593|consensus
Probab=34.35 E-value=24 Score=30.70 Aligned_cols=39 Identities=21% Similarity=0.600 Sum_probs=21.3
Q ss_pred CCCCCcccCCccCccccChHHHHHHHhhccCcccCCccccc
Q psy6546 91 STTLTRHPCPQCSRDFATVKILKTHLKTHEGIIYPCPECDK 131 (294)
Q Consensus 91 ~~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~C~~C~~ 131 (294)
......|.|+.|.+.|.....+..- .-....|.|..|+.
T Consensus 123 ~t~~~~Y~Cp~C~kkyt~Lea~~L~--~~~~~~F~C~~C~g 161 (436)
T KOG2593|consen 123 DTNVAGYVCPNCQKKYTSLEALQLL--DNETGEFHCENCGG 161 (436)
T ss_pred ccccccccCCccccchhhhHHHHhh--cccCceEEEecCCC
Confidence 3444557777777777665554321 11122467777764
No 149
>KOG3408|consensus
Probab=34.20 E-value=26 Score=24.52 Aligned_cols=29 Identities=38% Similarity=0.547 Sum_probs=23.6
Q ss_pred CCCCCcccCCccCccccChHHHHHHHhhc
Q psy6546 91 STTLTRHPCPQCSRDFATVKILKTHLKTH 119 (294)
Q Consensus 91 ~~~~~~~~C~~C~~~f~~~~~l~~H~~~~ 119 (294)
-++...|.|-.|.+-|.+...|..|.++-
T Consensus 52 lPG~GqfyCi~CaRyFi~~~~l~~H~ktK 80 (129)
T KOG3408|consen 52 LPGGGQFYCIECARYFIDAKALKTHFKTK 80 (129)
T ss_pred CCCCceeehhhhhhhhcchHHHHHHHhcc
Confidence 35667789999999999999999987653
No 150
>PF14369 zf-RING_3: zinc-finger
Probab=33.97 E-value=19 Score=19.05 Aligned_cols=11 Identities=36% Similarity=0.546 Sum_probs=4.9
Q ss_pred ccCccchhccC
Q psy6546 33 HPCPQCSRDFA 43 (294)
Q Consensus 33 ~~C~~C~~~f~ 43 (294)
|.|-.|.+..+
T Consensus 3 ywCh~C~~~V~ 13 (35)
T PF14369_consen 3 YWCHQCNRFVR 13 (35)
T ss_pred EeCccCCCEeE
Confidence 44444444433
No 151
>KOG2907|consensus
Probab=33.59 E-value=27 Score=24.08 Aligned_cols=11 Identities=45% Similarity=1.120 Sum_probs=5.6
Q ss_pred ccccccccccc
Q psy6546 259 YVCELCARQFT 269 (294)
Q Consensus 259 ~~C~~C~~~f~ 269 (294)
|-|+.|++.|+
T Consensus 103 YTC~kC~~k~~ 113 (116)
T KOG2907|consen 103 YTCPKCKYKFT 113 (116)
T ss_pred EEcCccceeee
Confidence 45555555544
No 152
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=31.40 E-value=13 Score=34.99 Aligned_cols=12 Identities=17% Similarity=0.420 Sum_probs=8.5
Q ss_pred cccccccccccc
Q psy6546 256 VRAYVCELCARQ 267 (294)
Q Consensus 256 ~~~~~C~~C~~~ 267 (294)
..|..|+.||-.
T Consensus 473 ~~p~~Cp~Cgs~ 484 (730)
T COG1198 473 PIPQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCCCC
Confidence 457778888764
No 153
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=31.24 E-value=37 Score=18.50 Aligned_cols=19 Identities=21% Similarity=0.443 Sum_probs=12.4
Q ss_pred ceeCCCCccccCCHHHHHH
Q psy6546 204 TYSCPSCSKSFNRKDRYRM 222 (294)
Q Consensus 204 ~~~C~~C~~~f~~~~~l~~ 222 (294)
-+.|+.|+-.+.....|.+
T Consensus 19 id~C~~C~G~W~d~~el~~ 37 (41)
T PF13453_consen 19 IDVCPSCGGIWFDAGELEK 37 (41)
T ss_pred EEECCCCCeEEccHHHHHH
Confidence 4567777777766666654
No 154
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=30.78 E-value=34 Score=18.27 Aligned_cols=15 Identities=20% Similarity=0.567 Sum_probs=9.6
Q ss_pred cccCCCCCcccCCcc
Q psy6546 88 SRMSTTLTRHPCPQC 102 (294)
Q Consensus 88 ~~~~~~~~~~~C~~C 102 (294)
.....+...|.|..|
T Consensus 21 G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 21 GKSPSGHQRYRCKDC 35 (36)
T ss_pred CCCCCCCEeEecCcC
Confidence 344556667777776
No 155
>PRK12496 hypothetical protein; Provisional
Probab=30.59 E-value=13 Score=27.85 Aligned_cols=10 Identities=30% Similarity=0.939 Sum_probs=5.2
Q ss_pred eeCCCCcccc
Q psy6546 205 YSCPSCSKSF 214 (294)
Q Consensus 205 ~~C~~C~~~f 214 (294)
|.|.-|++.|
T Consensus 128 ~~C~gC~~~~ 137 (164)
T PRK12496 128 KVCKGCKKKY 137 (164)
T ss_pred EECCCCCccc
Confidence 4455555554
No 156
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=30.29 E-value=24 Score=20.87 Aligned_cols=9 Identities=33% Similarity=1.276 Sum_probs=3.9
Q ss_pred cCCccCccc
Q psy6546 98 PCPQCSRDF 106 (294)
Q Consensus 98 ~C~~C~~~f 106 (294)
.|+.|+..+
T Consensus 4 ~CP~CG~~i 12 (54)
T TIGR01206 4 ECPDCGAEI 12 (54)
T ss_pred CCCCCCCEE
Confidence 444444433
No 157
>PF03145 Sina: Seven in absentia protein family; InterPro: IPR018121 The seven in absentia (sina) gene was first identified in Drosophila. The Drosophila Sina protein is essential for the determination of the R7 pathway in photoreceptor cell development: the loss of functional Sina results in the transformation of the R7 precursor cell to a non-neuronal cell type. The Sina protein contains an N-terminal RING finger domain C3HC4-type. Through this domain, Sina binds E2 ubiquitin-conjugating enzymes (UbcD1) Sina also interacts with Tramtrack (TTK88) via PHYL. Tramtrack is a transcriptional repressor that blocks photoreceptor determination, while PHYL down-regulates the activity of TTK88. In turn, the activity of PHYL requires the activation of the Sevenless receptor tyrosine kinase, a process essential for R7 determination. It is thought that Sina targets TTK88 for degradation, therefore promoting the R7 pathway. Murine and human homologues of Sina have also been identified. The human homologue Siah-1 [] also binds E2 enzymes (UbcH5) and through a series of physical interactions, targets beta-catenin for ubiquitin degradation. Siah-1 expression is enhanced by p53, itself promoted by DNA damage. Thus this pathway links DNA damage to beta-catenin degradation [, ]. Sina proteins, therefore, physically interact with a variety of proteins. The N-terminal RING finger domain that binds ubiquitin conjugating enzymes is a C3HC4-type, and does not form part of the alignment for this family. The remainder C-terminal part is involved in interactions with other proteins, and is included in this alignment. In addition to the Drosophila protein and mammalian homologues, whose similarity was noted previously, this family also includes putative homologues from Caenorhabditis elegans, Arabidopsis thaliana.; GO: 0006511 ubiquitin-dependent protein catabolic process, 0007275 multicellular organismal development, 0005634 nucleus; PDB: 2A25_A 1K2F_B 2AN6_C.
Probab=30.06 E-value=34 Score=26.47 Aligned_cols=48 Identities=21% Similarity=0.327 Sum_probs=24.4
Q ss_pred cccccccCHHHHHHHHhhhccccccccc----ccccccchhhhhhhhhhccCcc
Q psy6546 236 ECSKEFSNEYNLKNHMVLHDVRAYVCEL----CARQFTRVDHFNHHRRLQHDPE 285 (294)
Q Consensus 236 ~C~~~f~~~~~l~~H~~~h~~~~~~C~~----C~~~f~~~~~l~~H~~~~h~~~ 285 (294)
.|...+. ......|...-.-+||.|+. |+..= ....|..|....|...
T Consensus 23 GC~~~~~-~~~~~~HE~~C~~~p~~CP~~~~~C~~~G-~~~~l~~Hl~~~H~~~ 74 (198)
T PF03145_consen 23 GCTETFP-YSEKREHEEECPFRPCSCPFPGSGCDWQG-SYKELLDHLRDKHSWN 74 (198)
T ss_dssp T---EE--GGGHHHHHHT-TTSEEE-SSSSTT---EE-ECCCHHHHHHHHTTTS
T ss_pred CCccccc-ccChhhHhccCCCcCCcCCCCCCCccccC-CHHHHHHHHHHHCCCc
Confidence 4655533 34556677666677777766 65542 3456778877777664
No 158
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=30.05 E-value=54 Score=27.17 Aligned_cols=26 Identities=23% Similarity=0.326 Sum_probs=15.1
Q ss_pred CCcccCCccCccccChHHHHHHHhhc
Q psy6546 94 LTRHPCPQCSRDFATVKILKTHLKTH 119 (294)
Q Consensus 94 ~~~~~C~~C~~~f~~~~~l~~H~~~~ 119 (294)
...|+|+.|...|-.......|...|
T Consensus 386 s~rY~Ce~CK~~FC~dCdvfiHe~Lh 411 (421)
T COG5151 386 SGRYQCELCKSTFCSDCDVFIHETLH 411 (421)
T ss_pred ccceechhhhhhhhhhhHHHHHHHHh
Confidence 34566666666666666555555444
No 159
>KOG3408|consensus
Probab=30.00 E-value=29 Score=24.26 Aligned_cols=21 Identities=33% Similarity=0.670 Sum_probs=17.2
Q ss_pred cccccccccccCHHHHHHHHh
Q psy6546 232 HTCKECSKEFSNEYNLKNHMV 252 (294)
Q Consensus 232 ~~C~~C~~~f~~~~~l~~H~~ 252 (294)
|.|-.|.+-|.+...|..|.+
T Consensus 58 fyCi~CaRyFi~~~~l~~H~k 78 (129)
T KOG3408|consen 58 FYCIECARYFIDAKALKTHFK 78 (129)
T ss_pred eehhhhhhhhcchHHHHHHHh
Confidence 788888888888888888854
No 160
>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=29.27 E-value=48 Score=29.50 Aligned_cols=25 Identities=28% Similarity=0.640 Sum_probs=22.3
Q ss_pred CceeCCCCccccCCHHHHHHHHHHh
Q psy6546 203 ITYSCPSCSKSFNRKDRYRMHLKLH 227 (294)
Q Consensus 203 ~~~~C~~C~~~f~~~~~l~~H~~~h 227 (294)
+-|.|+.|.+.|.+...+..|+...
T Consensus 56 rFWiCp~CskkF~d~~~~~~H~~~e 80 (466)
T PF04780_consen 56 RFWICPRCSKKFSDAESCLSHMEQE 80 (466)
T ss_pred eEeeCCcccceeCCHHHHHHHHHHh
Confidence 4799999999999999999999753
No 161
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=29.25 E-value=28 Score=23.09 Aligned_cols=14 Identities=21% Similarity=0.487 Sum_probs=8.6
Q ss_pred CcccCCccCccccC
Q psy6546 95 TRHPCPQCSRDFAT 108 (294)
Q Consensus 95 ~~~~C~~C~~~f~~ 108 (294)
..+.|..|++.|..
T Consensus 53 GIW~C~~C~~~~AG 66 (90)
T PTZ00255 53 GIWRCKGCKKTVAG 66 (90)
T ss_pred EEEEcCCCCCEEeC
Confidence 45667777666653
No 162
>KOG1280|consensus
Probab=28.93 E-value=64 Score=27.28 Aligned_cols=39 Identities=26% Similarity=0.456 Sum_probs=29.1
Q ss_pred CCCCCccCccchhccCCHHHHHHHHHHhCCc---ccCCccCc
Q psy6546 28 TTPTRHPCPQCSRDFATVKILKTHLKTHEGI---IYPCPECD 66 (294)
Q Consensus 28 ~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~---~~~c~~c~ 66 (294)
..+.-|.|++|++.=-+...|..|+...|.. ...|+.|+
T Consensus 75 y~~qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~ 116 (381)
T KOG1280|consen 75 YDPQSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCA 116 (381)
T ss_pred cccccccCCcccccccchhHHHHHhhhcCcccCcceeeeccc
Confidence 3445799999999988999999999765544 44555554
No 163
>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=28.58 E-value=17 Score=24.07 Aligned_cols=13 Identities=31% Similarity=0.820 Sum_probs=8.6
Q ss_pred CcccCCccCcccc
Q psy6546 95 TRHPCPQCSRDFA 107 (294)
Q Consensus 95 ~~~~C~~C~~~f~ 107 (294)
..+.|..|++.|.
T Consensus 52 GIW~C~~C~~~~A 64 (90)
T PF01780_consen 52 GIWKCKKCGKKFA 64 (90)
T ss_dssp TEEEETTTTEEEE
T ss_pred EEeecCCCCCEEe
Confidence 3467777777664
No 164
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=28.57 E-value=34 Score=20.22 Aligned_cols=10 Identities=30% Similarity=1.089 Sum_probs=5.6
Q ss_pred ccCCccCccc
Q psy6546 97 HPCPQCSRDF 106 (294)
Q Consensus 97 ~~C~~C~~~f 106 (294)
..|+.|+..+
T Consensus 22 VvCp~Cgapy 31 (54)
T PF14446_consen 22 VVCPECGAPY 31 (54)
T ss_pred EECCCCCCcc
Confidence 4566666554
No 165
>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=28.03 E-value=6 Score=32.83 Aligned_cols=10 Identities=30% Similarity=0.826 Sum_probs=4.3
Q ss_pred ccCCCCCccc
Q psy6546 151 YICHACPREF 160 (294)
Q Consensus 151 ~~C~~C~~~f 160 (294)
..|..|+...
T Consensus 198 L~Cs~C~t~W 207 (290)
T PF04216_consen 198 LHCSLCGTEW 207 (290)
T ss_dssp EEETTT--EE
T ss_pred EEcCCCCCee
Confidence 4555665554
No 166
>KOG4727|consensus
Probab=28.01 E-value=26 Score=26.16 Aligned_cols=22 Identities=23% Similarity=0.516 Sum_probs=17.5
Q ss_pred cccccccccccccchhhhhhhh
Q psy6546 257 RAYVCELCARQFTRVDHFNHHR 278 (294)
Q Consensus 257 ~~~~C~~C~~~f~~~~~l~~H~ 278 (294)
.-|.|.+|+-.|.+.-++..|+
T Consensus 74 ~GyyCdVCdcvvKDSinflDHi 95 (193)
T KOG4727|consen 74 GGYYCDVCDCVVKDSINFLDHI 95 (193)
T ss_pred CceeeeecceeehhhHHHHHHh
Confidence 4588888888888888888876
No 167
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=27.40 E-value=29 Score=23.06 Aligned_cols=14 Identities=29% Similarity=0.667 Sum_probs=8.4
Q ss_pred CcccCCccCccccC
Q psy6546 95 TRHPCPQCSRDFAT 108 (294)
Q Consensus 95 ~~~~C~~C~~~f~~ 108 (294)
..+.|..|++.|..
T Consensus 52 GIW~C~~C~~~~AG 65 (91)
T TIGR00280 52 GIWTCRKCGAKFAG 65 (91)
T ss_pred EEEEcCCCCCEEeC
Confidence 34567777666543
No 168
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=27.28 E-value=25 Score=20.36 Aligned_cols=10 Identities=30% Similarity=0.830 Sum_probs=5.9
Q ss_pred cccccccccc
Q psy6546 231 RHTCKECSKE 240 (294)
Q Consensus 231 ~~~C~~C~~~ 240 (294)
++.|..||..
T Consensus 37 r~~C~~Cgyt 46 (50)
T PRK00432 37 RWHCGKCGYT 46 (50)
T ss_pred cEECCCcCCE
Confidence 4666666654
No 169
>PRK04351 hypothetical protein; Provisional
Probab=27.11 E-value=31 Score=25.39 Aligned_cols=31 Identities=29% Similarity=0.724 Sum_probs=14.6
Q ss_pred ceeCCCCccccCCHHHHHHHHHHhCCCccccccccccc
Q psy6546 204 TYSCPSCSKSFNRKDRYRMHLKLHQGVRHTCKECSKEF 241 (294)
Q Consensus 204 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~C~~~f 241 (294)
.|.|..|+..+.+. +.+...+|.|..|+-.+
T Consensus 112 ~Y~C~~Cg~~~~r~-------Rr~n~~~yrCg~C~g~L 142 (149)
T PRK04351 112 LYECQSCGQQYLRK-------RRINTKRYRCGKCRGKL 142 (149)
T ss_pred EEECCCCCCEeeee-------eecCCCcEEeCCCCcEe
Confidence 45665566444321 12223336666665444
No 170
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=26.94 E-value=23 Score=20.73 Aligned_cols=14 Identities=29% Similarity=0.672 Sum_probs=7.7
Q ss_pred cCccchhccCCHHH
Q psy6546 34 PCPQCSRDFATVKI 47 (294)
Q Consensus 34 ~C~~C~~~f~~~~~ 47 (294)
.||.|++.|.....
T Consensus 22 ~CPlC~r~l~~e~~ 35 (54)
T PF04423_consen 22 CCPLCGRPLDEEHR 35 (54)
T ss_dssp E-TTT--EE-HHHH
T ss_pred cCCCCCCCCCHHHH
Confidence 89999999975543
No 171
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=26.61 E-value=38 Score=18.36 Aligned_cols=14 Identities=21% Similarity=0.726 Sum_probs=11.5
Q ss_pred ceeCCCCccccCCH
Q psy6546 204 TYSCPSCSKSFNRK 217 (294)
Q Consensus 204 ~~~C~~C~~~f~~~ 217 (294)
|+.|..|+..|-.+
T Consensus 12 ~f~C~~C~~~FC~~ 25 (39)
T smart00154 12 GFKCRHCGNLFCGE 25 (39)
T ss_pred CeECCccCCccccc
Confidence 78899999988753
No 172
>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=26.51 E-value=26 Score=19.37 Aligned_cols=13 Identities=38% Similarity=0.994 Sum_probs=10.0
Q ss_pred ccccccccccchh
Q psy6546 260 VCELCARQFTRVD 272 (294)
Q Consensus 260 ~C~~C~~~f~~~~ 272 (294)
.|++|+..|+...
T Consensus 10 ~C~~C~rpf~WRK 22 (42)
T PF10013_consen 10 ICPVCGRPFTWRK 22 (42)
T ss_pred cCcccCCcchHHH
Confidence 5888888887654
No 173
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=26.47 E-value=30 Score=32.33 Aligned_cols=83 Identities=17% Similarity=0.397 Sum_probs=50.0
Q ss_pred CCCccCccchhccCCHHHHHHHHHHhCCcc-cCCccCccchhccccCCCCCCCccchhhcccCCCCCcccCCccCccccC
Q psy6546 30 PTRHPCPQCSRDFATVKILKTHLKTHEGII-YPCPECDKTFLSTLTGTPQGARGRAVYLSRMSTTLTRHPCPQCSRDFAT 108 (294)
Q Consensus 30 ~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~-~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~f~~ 108 (294)
+..-.|+.|-+.+.+..+-+-+ .| ..|..||-.|+.... +.+-+...+-..--.|+.|.+.|.+
T Consensus 99 pD~a~C~~Cl~Ei~dp~~rrY~------YPF~~CT~CGPRfTIi~a---------lPYDR~nTsM~~F~lC~~C~~EY~d 163 (750)
T COG0068 99 PDAATCEDCLEEIFDPNSRRYL------YPFINCTNCGPRFTIIEA---------LPYDRENTSMADFPLCPFCDKEYKD 163 (750)
T ss_pred CchhhhHHHHHHhcCCCCccee------ccccccCCCCcceeeecc---------CCCCcccCccccCcCCHHHHHHhcC
Confidence 3346799998777665443321 12 358999998876552 2222222222233369999999888
Q ss_pred hHHHHHHHhhccCcccCCcccccc
Q psy6546 109 VKILKTHLKTHEGIIYPCPECDKT 132 (294)
Q Consensus 109 ~~~l~~H~~~~~~~~~~C~~C~~~ 132 (294)
..+= +.|. .|..|+.||-.
T Consensus 164 P~nR----RfHA-Qp~aCp~CGP~ 182 (750)
T COG0068 164 PLNR----RFHA-QPIACPKCGPH 182 (750)
T ss_pred cccc----cccc-ccccCcccCCC
Confidence 7752 2222 36789999853
No 174
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=25.85 E-value=82 Score=23.58 Aligned_cols=17 Identities=29% Similarity=0.905 Sum_probs=9.3
Q ss_pred ceeCCCCccccCCHHHH
Q psy6546 204 TYSCPSCSKSFNRKDRY 220 (294)
Q Consensus 204 ~~~C~~C~~~f~~~~~l 220 (294)
-|.|+.|++.|-.-+++
T Consensus 130 f~~C~~CgkiYW~GsHw 146 (165)
T COG1656 130 FYRCPKCGKIYWKGSHW 146 (165)
T ss_pred eeECCCCcccccCchHH
Confidence 45566666666554443
No 175
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=25.82 E-value=91 Score=23.73 Aligned_cols=13 Identities=31% Similarity=0.958 Sum_probs=7.2
Q ss_pred ceeCCCCccccCC
Q psy6546 204 TYSCPSCSKSFNR 216 (294)
Q Consensus 204 ~~~C~~C~~~f~~ 216 (294)
.|.|+.|...++-
T Consensus 113 ~y~C~~~~~r~sf 125 (176)
T COG1675 113 YYVCPNCHVKYSF 125 (176)
T ss_pred ceeCCCCCCcccH
Confidence 4666666555443
No 176
>KOG1280|consensus
Probab=25.64 E-value=61 Score=27.36 Aligned_cols=21 Identities=19% Similarity=0.482 Sum_probs=10.4
Q ss_pred cCCcccccccCChHhHHHHHh
Q psy6546 124 YPCPECDKTFLSTSGLREHRK 144 (294)
Q Consensus 124 ~~C~~C~~~f~~~~~l~~H~~ 144 (294)
|.|++|+..-.+...|..|..
T Consensus 80 ftCPyC~~~Gfte~~f~~Hv~ 100 (381)
T KOG1280|consen 80 FTCPYCGIMGFTERQFGTHVL 100 (381)
T ss_pred ccCCcccccccchhHHHHHhh
Confidence 455555554444455555543
No 177
>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=25.47 E-value=26 Score=24.50 Aligned_cols=12 Identities=25% Similarity=0.733 Sum_probs=6.3
Q ss_pred eeCCCCccccCC
Q psy6546 205 YSCPSCSKSFNR 216 (294)
Q Consensus 205 ~~C~~C~~~f~~ 216 (294)
..|..|+..|..
T Consensus 71 ~~C~~Cg~~~~~ 82 (115)
T TIGR00100 71 CECEDCSEEVSP 82 (115)
T ss_pred EEcccCCCEEec
Confidence 455555555443
No 178
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=25.39 E-value=25 Score=24.48 Aligned_cols=10 Identities=30% Similarity=0.527 Sum_probs=4.6
Q ss_pred eeCCCCcccc
Q psy6546 205 YSCPSCSKSF 214 (294)
Q Consensus 205 ~~C~~C~~~f 214 (294)
..|..|+..|
T Consensus 71 ~~C~~Cg~~~ 80 (113)
T PRK12380 71 AWCWDCSQVV 80 (113)
T ss_pred EEcccCCCEE
Confidence 4444444444
No 179
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=25.03 E-value=16 Score=21.26 Aligned_cols=23 Identities=26% Similarity=0.593 Sum_probs=9.6
Q ss_pred cccccccccccCHHHHHHHHhhh
Q psy6546 232 HTCKECSKEFSNEYNLKNHMVLH 254 (294)
Q Consensus 232 ~~C~~C~~~f~~~~~l~~H~~~h 254 (294)
|+|+.|+..|=..-.+..|..+|
T Consensus 22 y~C~~C~~~FC~dCD~fiHE~LH 44 (51)
T PF07975_consen 22 YRCPKCKNHFCIDCDVFIHETLH 44 (51)
T ss_dssp E--TTTT--B-HHHHHTTTTTS-
T ss_pred EECCCCCCccccCcChhhhcccc
Confidence 66666666665555555554444
No 180
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=24.82 E-value=22 Score=24.79 Aligned_cols=12 Identities=25% Similarity=0.789 Sum_probs=5.5
Q ss_pred eeCCCCccccCC
Q psy6546 205 YSCPSCSKSFNR 216 (294)
Q Consensus 205 ~~C~~C~~~f~~ 216 (294)
..|..|+..|..
T Consensus 71 ~~C~~Cg~~~~~ 82 (113)
T PF01155_consen 71 ARCRDCGHEFEP 82 (113)
T ss_dssp EEETTTS-EEEC
T ss_pred EECCCCCCEEec
Confidence 445555555543
No 181
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=24.36 E-value=34 Score=22.69 Aligned_cols=14 Identities=29% Similarity=0.653 Sum_probs=8.8
Q ss_pred CcccCCccCccccC
Q psy6546 95 TRHPCPQCSRDFAT 108 (294)
Q Consensus 95 ~~~~C~~C~~~f~~ 108 (294)
..+.|..|++.|..
T Consensus 53 GIW~C~~C~~~~AG 66 (90)
T PRK03976 53 GIWECRKCGAKFAG 66 (90)
T ss_pred EEEEcCCCCCEEeC
Confidence 44667777776653
No 182
>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=24.11 E-value=20 Score=26.39 Aligned_cols=31 Identities=29% Similarity=0.853 Sum_probs=16.7
Q ss_pred ceeCCCCccccCCHHHHHHHHHHhCCCccccccccccc
Q psy6546 204 TYSCPSCSKSFNRKDRYRMHLKLHQGVRHTCKECSKEF 241 (294)
Q Consensus 204 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~C~~~f 241 (294)
.|.|..|+..+.... +. ....|.|..|+..+
T Consensus 123 ~~~C~~C~~~~~r~~------~~-~~~~~~C~~C~~~l 153 (157)
T PF10263_consen 123 VYRCPSCGREYKRHR------RS-KRKRYRCGRCGGPL 153 (157)
T ss_pred EEEcCCCCCEeeeec------cc-chhhEECCCCCCEE
Confidence 577777776653322 22 11226777776544
No 183
>PF12773 DZR: Double zinc ribbon
Probab=24.02 E-value=45 Score=18.96 Aligned_cols=6 Identities=33% Similarity=1.237 Sum_probs=2.4
Q ss_pred ccCcch
Q psy6546 179 ACDQCD 184 (294)
Q Consensus 179 ~C~~C~ 184 (294)
.|+.|+
T Consensus 31 ~C~~Cg 36 (50)
T PF12773_consen 31 ICPNCG 36 (50)
T ss_pred CCcCCc
Confidence 344443
No 184
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=23.84 E-value=19 Score=21.38 Aligned_cols=8 Identities=50% Similarity=1.298 Sum_probs=3.5
Q ss_pred ccCCcccc
Q psy6546 123 IYPCPECD 130 (294)
Q Consensus 123 ~~~C~~C~ 130 (294)
.|.|..|.
T Consensus 31 tYmC~eC~ 38 (56)
T PF09963_consen 31 TYMCDECK 38 (56)
T ss_pred ceeChhHH
Confidence 34444443
No 185
>COG2879 Uncharacterized small protein [Function unknown]
Probab=23.72 E-value=45 Score=20.29 Aligned_cols=21 Identities=19% Similarity=0.270 Sum_probs=16.1
Q ss_pred cccchhhhhhhhhhccCcccc
Q psy6546 267 QFTRVDHFNHHRRLQHDPEEF 287 (294)
Q Consensus 267 ~f~~~~~l~~H~~~~h~~~~~ 287 (294)
+..+..+...|++.+|+++|.
T Consensus 21 GvpdYdnYVehmr~~hPd~p~ 41 (65)
T COG2879 21 GVPDYDNYVEHMRKKHPDKPP 41 (65)
T ss_pred CCCcHHHHHHHHHHhCcCCCc
Confidence 345667888999999988864
No 186
>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=23.57 E-value=39 Score=16.91 Aligned_cols=9 Identities=33% Similarity=0.999 Sum_probs=4.8
Q ss_pred ccccccccc
Q psy6546 260 VCELCARQF 268 (294)
Q Consensus 260 ~C~~C~~~f 268 (294)
.|-.|++.|
T Consensus 2 sCiDC~~~F 10 (28)
T PF08790_consen 2 SCIDCSKDF 10 (28)
T ss_dssp EETTTTEEE
T ss_pred eeecCCCCc
Confidence 355555555
No 187
>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=23.53 E-value=43 Score=20.60 Aligned_cols=8 Identities=38% Similarity=1.165 Sum_probs=1.6
Q ss_pred cCcchhcc
Q psy6546 180 CDQCDRTF 187 (294)
Q Consensus 180 C~~C~~~f 187 (294)
|..|++.|
T Consensus 12 C~~C~~~F 19 (69)
T PF01363_consen 12 CMICGKKF 19 (69)
T ss_dssp -TTT--B-
T ss_pred CcCcCCcC
Confidence 33444444
No 188
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=23.51 E-value=50 Score=24.17 Aligned_cols=12 Identities=33% Similarity=1.118 Sum_probs=5.9
Q ss_pred cCCcccccccCC
Q psy6546 124 YPCPECDKTFLS 135 (294)
Q Consensus 124 ~~C~~C~~~f~~ 135 (294)
+.|+.|++.|..
T Consensus 125 ~~C~~C~kiyW~ 136 (147)
T PF01927_consen 125 WRCPGCGKIYWE 136 (147)
T ss_pred EECCCCCCEecc
Confidence 445555555443
No 189
>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=23.09 E-value=37 Score=18.74 Aligned_cols=14 Identities=21% Similarity=0.524 Sum_probs=7.5
Q ss_pred CCcccCCccCcccc
Q psy6546 94 LTRHPCPQCSRDFA 107 (294)
Q Consensus 94 ~~~~~C~~C~~~f~ 107 (294)
...+.|..||....
T Consensus 17 ~g~~vC~~CG~Vl~ 30 (43)
T PF08271_consen 17 RGELVCPNCGLVLE 30 (43)
T ss_dssp TTEEEETTT-BBEE
T ss_pred CCeEECCCCCCEee
Confidence 34456777766543
No 190
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=22.76 E-value=70 Score=19.00 Aligned_cols=18 Identities=17% Similarity=0.438 Sum_probs=13.1
Q ss_pred CCCCCccCccchhccCCH
Q psy6546 28 TTPTRHPCPQCSRDFATV 45 (294)
Q Consensus 28 ~~~~~~~C~~C~~~f~~~ 45 (294)
.....|.|+.||..+-..
T Consensus 10 ~~~v~~~Cp~cGipthcS 27 (55)
T PF13824_consen 10 PAHVNFECPDCGIPTHCS 27 (55)
T ss_pred ccccCCcCCCCCCcCccC
Confidence 345678999999887544
No 191
>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=22.56 E-value=55 Score=23.97 Aligned_cols=16 Identities=25% Similarity=0.629 Sum_probs=10.1
Q ss_pred ccCCccCccccChHHH
Q psy6546 97 HPCPQCSRDFATVKIL 112 (294)
Q Consensus 97 ~~C~~C~~~f~~~~~l 112 (294)
-.|..|++.|++...+
T Consensus 29 ReC~~C~~RFTTyErv 44 (147)
T TIGR00244 29 RECLECHERFTTFERA 44 (147)
T ss_pred ccCCccCCccceeeec
Confidence 3577777777765543
No 192
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=21.72 E-value=23 Score=33.03 Aligned_cols=57 Identities=16% Similarity=0.414 Sum_probs=29.8
Q ss_pred cCCCCCcccCCHHHHHHHHHhhcCCCc-ccCcchhccCCchHHHhHHhhcCCCceeCCCCccc
Q psy6546 152 ICHACPREFSSEATMKAHVASHNGVQH-ACDQCDRTFSCMPYLRQHQKLHSGITYSCPSCSKS 213 (294)
Q Consensus 152 ~C~~C~~~f~~~~~l~~H~~~~~~~~~-~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~C~~~ 213 (294)
.|..||-.|.....|-.-....+-..| .|+.|.+.+....+ |..+..|.-|+.||-.
T Consensus 125 ~CT~CGPRfTIi~alPYDR~nTsM~~F~lC~~C~~EY~dP~n-----RRfHAQp~aCp~CGP~ 182 (750)
T COG0068 125 NCTNCGPRFTIIEALPYDRENTSMADFPLCPFCDKEYKDPLN-----RRFHAQPIACPKCGPH 182 (750)
T ss_pred ccCCCCcceeeeccCCCCcccCccccCcCCHHHHHHhcCccc-----cccccccccCcccCCC
Confidence 466666666544333222111111123 57888777666544 2223347778888853
No 193
>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=20.93 E-value=42 Score=18.58 Aligned_cols=13 Identities=38% Similarity=0.930 Sum_probs=8.5
Q ss_pred ceeCCCCccccCC
Q psy6546 204 TYSCPSCSKSFNR 216 (294)
Q Consensus 204 ~~~C~~C~~~f~~ 216 (294)
|+.|+.|+..|-.
T Consensus 13 ~~~C~~C~~~FC~ 25 (43)
T PF01428_consen 13 PFKCKHCGKSFCL 25 (43)
T ss_dssp HEE-TTTS-EE-T
T ss_pred CeECCCCCcccCc
Confidence 7889999988865
No 194
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=20.91 E-value=37 Score=24.83 Aligned_cols=32 Identities=22% Similarity=0.642 Sum_probs=15.4
Q ss_pred ceeCCCCccccCCHHHHHHHHHHhCCCccccccccccc
Q psy6546 204 TYSCPSCSKSFNRKDRYRMHLKLHQGVRHTCKECSKEF 241 (294)
Q Consensus 204 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~C~~~f 241 (294)
.|.|..|+..+.+ +.+.....+|.|..|+..+
T Consensus 112 ~y~C~~C~~~~~~------~rr~~~~~~y~C~~C~g~l 143 (146)
T smart00731 112 PYRCTGCGQRYLR------VRRSNNVSRYRCGKCGGKL 143 (146)
T ss_pred EEECCCCCCCCce------EccccCcceEEcCCCCCEE
Confidence 5667666655431 1111111336666666544
No 195
>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=20.64 E-value=97 Score=16.69 Aligned_cols=21 Identities=29% Similarity=0.475 Sum_probs=9.3
Q ss_pred CccCccchhccC-CH-HHHHHHH
Q psy6546 32 RHPCPQCSRDFA-TV-KILKTHL 52 (294)
Q Consensus 32 ~~~C~~C~~~f~-~~-~~l~~H~ 52 (294)
.|-|+.|+.-|. .. ...+.|.
T Consensus 3 ryyCdyC~~~~~~d~~~~Rk~H~ 25 (38)
T PF06220_consen 3 RYYCDYCKKYLTHDSPSIRKQHE 25 (38)
T ss_dssp S-B-TTT--B-S--SHHHHHHHT
T ss_pred CeecccccceecCCChHHHHHhh
Confidence 588999999993 33 3445564
No 196
>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=20.60 E-value=95 Score=19.04 Aligned_cols=12 Identities=25% Similarity=1.088 Sum_probs=6.4
Q ss_pred ceeCCCCccccC
Q psy6546 204 TYSCPSCSKSFN 215 (294)
Q Consensus 204 ~~~C~~C~~~f~ 215 (294)
.|.|+.||....
T Consensus 46 ~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 46 VFTCPNCGFEMD 57 (69)
T ss_pred eEEcCCCCCEEC
Confidence 555555555543
No 197
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=20.41 E-value=62 Score=22.24 Aligned_cols=11 Identities=36% Similarity=0.927 Sum_probs=5.3
Q ss_pred ceeCCCCcccc
Q psy6546 204 TYSCPSCSKSF 214 (294)
Q Consensus 204 ~~~C~~C~~~f 214 (294)
.|.|++|+..+
T Consensus 19 ~~iCpeC~~EW 29 (109)
T TIGR00686 19 QLICPSCLYEW 29 (109)
T ss_pred eeECccccccc
Confidence 44555555444
No 198
>KOG4124|consensus
Probab=20.41 E-value=18 Score=30.33 Aligned_cols=70 Identities=19% Similarity=0.275 Sum_probs=39.6
Q ss_pred CCCCccCcc--chhccCCHHHHHHHHHHhCCcccCCccCccchhccccCCCCCCCccchhhcccCCCCCcccCCccCccc
Q psy6546 29 TPTRHPCPQ--CSRDFATVKILKTHLKTHEGIIYPCPECDKTFLSTLTGTPQGARGRAVYLSRMSTTLTRHPCPQCSRDF 106 (294)
Q Consensus 29 ~~~~~~C~~--C~~~f~~~~~l~~H~~~~~~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~f 106 (294)
..++|+|++ |.+.+.....|..|-..-+..++.- ... ....+.......++|+|++|.+.+
T Consensus 346 ~~~~~~~~vp~~~~~~~n~ng~~~~~~~~h~s~i~~--------~s~---------~~~ph~~~~~~nk~~r~~i~~~~~ 408 (442)
T KOG4124|consen 346 VDKPYKCPVPNCDKAYKNQNGLKYHKLHGHCSPITT--------PTP---------APIPHQGFVVENKPYRCEVCSKRY 408 (442)
T ss_pred ecCCCCCCCCcchhhcccCcceeeccccCcCCCCCC--------CCC---------CCCCcceeeeccCcccChhhhhhh
Confidence 356678864 8888888777776643222111110 000 122233344567889999998887
Q ss_pred cChHHHHHH
Q psy6546 107 ATVKILKTH 115 (294)
Q Consensus 107 ~~~~~l~~H 115 (294)
+....|..|
T Consensus 409 k~~~~l~~~ 417 (442)
T KOG4124|consen 409 KNLNGLKYH 417 (442)
T ss_pred ccCCCCCce
Confidence 776555433
Done!