Query 010003
Match_columns 520
No_of_seqs 447 out of 1659
Neff 7.8
Searched_HMMs 46136
Date Thu Mar 28 19:53:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/010003.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/010003hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1812 Predicted E3 ubiquitin 100.0 1.3E-51 2.7E-56 426.1 16.4 341 60-415 1-348 (384)
2 KOG1814 Predicted E3 ubiquitin 100.0 4.7E-33 1E-37 276.5 7.5 196 202-411 182-407 (445)
3 KOG1815 Predicted E3 ubiquitin 99.9 2.3E-27 5E-32 252.0 11.9 210 200-425 66-283 (444)
4 KOG0006 E3 ubiquitin-protein l 99.9 4.3E-24 9.4E-29 205.1 9.5 201 201-420 218-444 (446)
5 PRK07708 hypothetical protein; 99.8 2E-19 4.4E-24 172.7 12.6 133 58-195 73-210 (219)
6 PRK13907 rnhA ribonuclease H; 99.8 4.9E-19 1.1E-23 157.1 11.9 126 58-192 1-126 (128)
7 COG0328 RnhA Ribonuclease HI [ 99.8 1.6E-18 3.4E-23 155.6 8.8 128 58-194 3-146 (154)
8 PRK07238 bifunctional RNase H/ 99.7 7.1E-18 1.5E-22 176.3 12.0 131 58-194 2-133 (372)
9 PRK08719 ribonuclease H; Revie 99.6 1.4E-14 2.9E-19 131.2 10.0 126 57-192 3-146 (147)
10 PRK06548 ribonuclease H; Provi 99.4 5.8E-13 1.3E-17 121.8 10.2 124 57-193 4-142 (161)
11 cd06222 RnaseH RNase H (RNase 99.4 8.2E-13 1.8E-17 114.5 10.1 125 60-190 1-129 (130)
12 PRK00203 rnhA ribonuclease H; 99.4 1.5E-12 3.3E-17 118.7 9.2 128 58-196 3-145 (150)
13 PF00075 RNase_H: RNase H; In 99.1 1.3E-10 2.9E-15 102.9 6.9 119 58-191 3-131 (132)
14 PF13456 RVT_3: Reverse transc 99.0 4.2E-10 9E-15 92.0 5.1 85 106-191 1-85 (87)
15 smart00647 IBR In Between Ring 98.9 1.6E-09 3.5E-14 83.6 5.2 62 275-346 2-64 (64)
16 PF01485 IBR: IBR domain; Int 98.8 1.2E-09 2.7E-14 84.3 1.4 62 275-346 2-64 (64)
17 KOG3752 Ribonuclease H [Replic 98.7 4.1E-08 8.8E-13 99.0 7.7 81 58-144 212-294 (371)
18 PF15227 zf-C3HC4_4: zinc fing 98.3 1.9E-07 4.2E-12 65.7 1.7 41 207-252 1-41 (42)
19 smart00647 IBR In Between Ring 98.2 1.4E-06 3E-11 67.1 4.8 44 368-411 13-61 (64)
20 PF13639 zf-RING_2: Ring finge 98.2 1.1E-06 2.4E-11 62.6 2.4 40 206-252 2-42 (44)
21 PF01485 IBR: IBR domain; Int 98.1 6.8E-07 1.5E-11 68.8 0.9 43 369-411 14-61 (64)
22 KOG0320 Predicted E3 ubiquitin 98.1 1.4E-06 3E-11 79.0 2.8 56 202-266 129-184 (187)
23 PF13923 zf-C3HC4_2: Zinc fing 98.1 2.3E-06 5.1E-11 59.2 2.6 38 207-252 1-38 (39)
24 PF00097 zf-C3HC4: Zinc finger 98.0 3.6E-06 7.8E-11 58.9 3.1 40 207-252 1-40 (41)
25 PLN03208 E3 ubiquitin-protein 98.0 4.4E-06 9.6E-11 77.8 4.1 62 203-268 17-87 (193)
26 PF14634 zf-RING_5: zinc-RING 97.8 1.8E-05 3.9E-10 56.3 3.2 42 206-256 1-43 (44)
27 cd00162 RING RING-finger (Real 97.8 2.9E-05 6.2E-10 54.6 4.0 44 206-258 1-44 (45)
28 PF13920 zf-C3HC4_3: Zinc fing 97.7 4.1E-05 8.8E-10 56.0 3.4 46 204-260 2-48 (50)
29 PF13445 zf-RING_UBOX: RING-ty 97.6 5.3E-05 1.1E-09 53.4 3.2 41 207-251 1-43 (43)
30 KOG2164 Predicted E3 ubiquitin 97.5 5.6E-05 1.2E-09 79.2 2.5 59 204-268 186-244 (513)
31 smart00184 RING Ring finger. E 97.5 0.00011 2.4E-09 49.6 3.2 38 207-252 1-38 (39)
32 PHA02926 zinc finger-like prot 97.4 0.00011 2.4E-09 69.3 3.8 56 202-260 168-230 (242)
33 KOG2177 Predicted E3 ubiquitin 97.4 0.00017 3.6E-09 72.5 5.3 108 202-346 11-122 (386)
34 KOG0823 Predicted E3 ubiquitin 97.4 7.2E-05 1.6E-09 71.0 2.4 60 201-268 44-103 (230)
35 smart00504 Ubox Modified RING 97.3 0.00027 5.8E-09 54.1 4.2 49 205-264 2-50 (63)
36 PHA02929 N1R/p28-like protein; 97.3 0.00019 4.1E-09 69.7 3.8 49 203-260 173-227 (238)
37 KOG0317 Predicted E3 ubiquitin 96.9 0.00058 1.3E-08 66.9 3.0 51 202-263 237-287 (293)
38 TIGR00599 rad18 DNA repair pro 96.9 0.0013 2.9E-08 68.5 5.5 50 202-262 24-73 (397)
39 TIGR00570 cdk7 CDK-activating 96.8 0.0011 2.4E-08 66.5 4.2 54 205-266 4-60 (309)
40 KOG0287 Postreplication repair 96.7 0.0006 1.3E-08 67.7 1.5 62 204-276 23-85 (442)
41 KOG0978 E3 ubiquitin ligase in 96.7 0.00049 1.1E-08 75.7 0.8 56 202-267 641-696 (698)
42 COG5540 RING-finger-containing 96.6 0.0013 2.8E-08 64.6 2.6 53 201-261 320-373 (374)
43 KOG1002 Nucleotide excision re 96.5 0.0025 5.4E-08 66.8 4.5 59 201-265 533-591 (791)
44 KOG4628 Predicted E3 ubiquitin 96.4 0.0029 6.4E-08 64.5 3.7 47 205-259 230-277 (348)
45 PF11789 zf-Nse: Zinc-finger o 96.1 0.0049 1.1E-07 46.3 3.0 49 202-256 9-57 (57)
46 PF12678 zf-rbx1: RING-H2 zinc 96.1 0.0048 1.1E-07 48.9 3.1 42 204-252 19-71 (73)
47 PF14835 zf-RING_6: zf-RING of 95.6 0.0019 4E-08 49.1 -1.4 45 204-261 7-52 (65)
48 COG5574 PEX10 RING-finger-cont 95.5 0.0083 1.8E-07 58.2 2.5 53 203-264 214-266 (271)
49 COG5243 HRD1 HRD ubiquitin lig 94.9 0.059 1.3E-06 54.6 6.5 53 202-263 285-348 (491)
50 PF11793 FANCL_C: FANCL C-term 94.6 0.025 5.5E-07 44.4 2.4 56 204-261 2-67 (70)
51 KOG0824 Predicted E3 ubiquitin 94.4 0.021 4.6E-07 56.4 2.0 52 203-264 6-57 (324)
52 PF04564 U-box: U-box domain; 94.3 0.033 7.1E-07 44.1 2.5 50 203-262 3-52 (73)
53 KOG1039 Predicted E3 ubiquitin 94.2 0.036 7.7E-07 56.9 3.0 55 202-258 159-219 (344)
54 COG5432 RAD18 RING-finger-cont 93.9 0.025 5.5E-07 55.3 1.4 48 201-259 22-69 (391)
55 KOG4367 Predicted Zn-finger pr 93.8 0.038 8.2E-07 56.9 2.4 33 203-237 3-35 (699)
56 KOG2879 Predicted E3 ubiquitin 93.1 0.11 2.3E-06 50.9 4.0 52 201-260 236-287 (298)
57 PF10571 UPF0547: Uncharacteri 92.9 0.041 8.8E-07 34.4 0.6 23 374-400 1-24 (26)
58 KOG1814 Predicted E3 ubiquitin 92.5 0.074 1.6E-06 54.8 2.3 44 371-415 271-317 (445)
59 KOG1428 Inhibitor of type V ad 91.5 0.18 4E-06 58.9 4.0 67 202-270 3484-3554(3738)
60 KOG2660 Locus-specific chromos 91.4 0.094 2E-06 52.7 1.6 48 202-259 13-60 (331)
61 KOG1645 RING-finger-containing 91.2 0.14 3.1E-06 52.6 2.6 49 204-259 4-55 (463)
62 PF14570 zf-RING_4: RING/Ubox 90.9 0.14 2.9E-06 36.9 1.5 44 207-258 1-46 (48)
63 COG5220 TFB3 Cdk activating ki 90.5 0.093 2E-06 50.2 0.5 51 204-260 10-64 (314)
64 KOG0311 Predicted E3 ubiquitin 90.3 0.046 9.9E-07 55.2 -1.8 48 203-259 42-89 (381)
65 KOG4265 Predicted E3 ubiquitin 90.2 0.27 5.9E-06 50.0 3.6 65 185-260 266-336 (349)
66 PF05883 Baculo_RING: Baculovi 90.0 0.15 3.1E-06 45.0 1.3 36 203-238 25-67 (134)
67 smart00744 RINGv The RING-vari 89.7 0.42 9.1E-06 34.7 3.3 42 206-252 1-47 (49)
68 PF12861 zf-Apc11: Anaphase-pr 89.5 0.32 6.9E-06 39.5 2.8 51 204-260 21-82 (85)
69 KOG0802 E3 ubiquitin ligase [P 89.5 0.22 4.7E-06 55.0 2.5 46 203-257 290-338 (543)
70 KOG4739 Uncharacterized protei 89.2 0.11 2.4E-06 50.1 -0.1 56 204-270 3-58 (233)
71 KOG1812 Predicted E3 ubiquitin 89.2 0.15 3.3E-06 53.6 0.9 103 204-345 238-346 (384)
72 KOG4172 Predicted E3 ubiquitin 89.1 0.11 2.4E-06 38.0 -0.0 45 205-259 8-53 (62)
73 KOG4159 Predicted E3 ubiquitin 89.1 0.34 7.4E-06 50.8 3.4 48 202-260 82-129 (398)
74 COG5152 Uncharacterized conser 88.5 0.2 4.4E-06 46.5 1.1 36 201-238 193-228 (259)
75 KOG1815 Predicted E3 ubiquitin 88.3 0.29 6.3E-06 52.6 2.4 42 370-411 155-199 (444)
76 smart00661 RPOL9 RNA polymeras 88.0 0.34 7.5E-06 35.3 1.9 27 374-400 1-30 (52)
77 KOG0828 Predicted E3 ubiquitin 87.6 0.28 6E-06 51.7 1.6 51 202-260 569-634 (636)
78 PHA00626 hypothetical protein 87.4 0.41 8.9E-06 35.3 1.9 26 375-400 2-33 (59)
79 KOG4445 Uncharacterized conser 87.3 0.8 1.7E-05 45.4 4.5 40 202-241 113-153 (368)
80 KOG0006 E3 ubiquitin-protein l 87.3 0.99 2.1E-05 45.1 5.1 96 220-343 336-438 (446)
81 KOG3002 Zn finger protein [Gen 85.2 1.1 2.4E-05 45.4 4.4 48 200-260 44-91 (299)
82 PF08274 PhnA_Zn_Ribbon: PhnA 85.1 0.59 1.3E-05 30.2 1.6 26 374-400 3-29 (30)
83 PF13719 zinc_ribbon_5: zinc-r 84.5 0.97 2.1E-05 30.7 2.5 34 290-332 2-35 (37)
84 KOG4692 Predicted E3 ubiquitin 84.0 0.95 2.1E-05 45.8 3.2 48 202-260 420-467 (489)
85 PF14952 zf-tcix: Putative tre 83.9 0.52 1.1E-05 33.0 1.0 26 371-400 9-37 (44)
86 PF13248 zf-ribbon_3: zinc-rib 83.6 0.62 1.3E-05 29.0 1.1 23 374-407 3-25 (26)
87 PF13240 zinc_ribbon_2: zinc-r 82.6 0.62 1.3E-05 28.2 0.8 11 375-385 1-11 (23)
88 PRK00398 rpoP DNA-directed RNA 82.1 1.1 2.4E-05 31.9 2.2 29 374-402 4-33 (46)
89 KOG1734 Predicted RING-contain 81.7 0.49 1.1E-05 46.2 0.3 56 202-264 222-285 (328)
90 PF13717 zinc_ribbon_4: zinc-r 81.6 1.6 3.4E-05 29.5 2.6 34 290-332 2-35 (36)
91 KOG0804 Cytoplasmic Zn-finger 81.4 1 2.2E-05 47.2 2.4 53 197-260 168-222 (493)
92 PRK05654 acetyl-CoA carboxylas 80.2 0.4 8.6E-06 48.5 -1.0 30 371-400 25-56 (292)
93 KOG1001 Helicase-like transcri 80.2 0.76 1.7E-05 51.7 1.1 52 205-266 455-506 (674)
94 PLN03086 PRLI-interacting fact 79.7 2.2 4.7E-05 46.9 4.3 127 247-409 407-552 (567)
95 PRK14559 putative protein seri 79.4 1.1 2.4E-05 50.2 2.1 13 397-409 40-52 (645)
96 KOG1952 Transcription factor N 78.8 1.7 3.6E-05 49.0 3.2 53 202-256 189-243 (950)
97 COG5175 MOT2 Transcriptional r 78.5 1.8 3.8E-05 43.7 2.9 54 205-266 15-70 (480)
98 PRK00432 30S ribosomal protein 77.9 1.4 3E-05 32.2 1.5 25 374-400 21-47 (50)
99 PF04641 Rtf2: Rtf2 RING-finge 77.8 2.8 6.1E-05 41.7 4.2 70 201-280 110-182 (260)
100 KOG0317 Predicted E3 ubiquitin 77.7 0.5 1.1E-05 46.7 -1.1 30 391-422 251-281 (293)
101 KOG0827 Predicted E3 ubiquitin 77.4 1.5 3.3E-05 45.1 2.2 47 204-256 4-52 (465)
102 PF09538 FYDLN_acid: Protein o 77.4 1.2 2.5E-05 38.2 1.2 26 374-400 10-36 (108)
103 KOG2906 RNA polymerase III sub 77.2 1.6 3.5E-05 36.1 1.9 29 375-403 3-34 (105)
104 PF15227 zf-C3HC4_4: zinc fing 77.0 1.1 2.3E-05 31.4 0.7 30 376-410 1-30 (42)
105 KOG3800 Predicted E3 ubiquitin 76.9 3.4 7.4E-05 41.0 4.4 52 206-265 2-56 (300)
106 PHA03096 p28-like protein; Pro 76.6 1.4 3E-05 44.3 1.7 38 205-242 179-222 (284)
107 CHL00174 accD acetyl-CoA carbo 76.2 0.59 1.3E-05 47.1 -1.1 33 371-403 36-70 (296)
108 PF14447 Prok-RING_4: Prokaryo 75.6 0.92 2E-05 33.6 0.1 46 204-262 7-52 (55)
109 KOG4684 Uncharacterized conser 75.3 3.3 7.2E-05 39.2 3.7 46 287-332 135-180 (275)
110 PF07975 C1_4: TFIIH C1-like d 75.1 0.93 2E-05 33.2 -0.0 23 321-343 20-42 (51)
111 PF09788 Tmemb_55A: Transmembr 74.9 3.6 7.9E-05 40.2 3.9 102 200-333 61-168 (256)
112 TIGR00515 accD acetyl-CoA carb 74.8 0.7 1.5E-05 46.5 -0.9 31 371-401 24-56 (285)
113 KOG0297 TNF receptor-associate 74.5 2.6 5.6E-05 44.6 3.1 47 202-259 19-66 (391)
114 PF09297 zf-NADH-PPase: NADH p 74.3 3.3 7.1E-05 27.0 2.5 26 374-399 4-30 (32)
115 COG0777 AccD Acetyl-CoA carbox 72.7 1.3 2.8E-05 43.8 0.3 37 370-406 25-63 (294)
116 PF10367 Vps39_2: Vacuolar sor 72.6 1.6 3.4E-05 36.7 0.8 31 204-234 78-108 (109)
117 PRK14714 DNA polymerase II lar 72.1 3.1 6.7E-05 49.3 3.2 16 483-498 798-813 (1337)
118 PF12773 DZR: Double zinc ribb 71.8 3.2 7E-05 29.9 2.2 12 374-385 30-41 (50)
119 KOG2817 Predicted E3 ubiquitin 71.8 3.7 8.1E-05 42.5 3.4 59 202-266 332-391 (394)
120 COG1198 PriA Primosomal protei 71.3 3 6.4E-05 47.4 2.8 34 374-407 445-484 (730)
121 PF02150 RNA_POL_M_15KD: RNA p 71.2 3.5 7.6E-05 27.6 2.0 26 374-400 2-30 (35)
122 KOG3039 Uncharacterized conser 70.5 3 6.5E-05 40.4 2.2 52 203-263 220-273 (303)
123 KOG4185 Predicted E3 ubiquitin 70.1 6.2 0.00013 39.9 4.6 47 204-258 3-53 (296)
124 PF05290 Baculo_IE-1: Baculovi 70.1 5.4 0.00012 35.1 3.5 51 203-259 79-131 (140)
125 KOG1785 Tyrosine kinase negati 70.1 1.9 4E-05 44.5 0.8 44 204-255 369-413 (563)
126 PRK08665 ribonucleotide-diphos 69.8 2.4 5.2E-05 48.6 1.7 26 374-401 725-751 (752)
127 COG1998 RPS31 Ribosomal protei 69.4 2.9 6.3E-05 30.1 1.4 25 374-398 20-45 (51)
128 TIGR02098 MJ0042_CXXC MJ0042 f 68.5 4.9 0.00011 27.1 2.4 33 291-332 3-35 (38)
129 COG5219 Uncharacterized conser 67.7 2.7 5.9E-05 47.9 1.5 50 203-260 1468-1523(1525)
130 KOG3579 Predicted E3 ubiquitin 65.3 4.7 0.0001 39.9 2.4 53 202-256 266-321 (352)
131 PRK04023 DNA polymerase II lar 64.9 5.1 0.00011 46.4 2.9 26 108-134 386-411 (1121)
132 KOG2807 RNA polymerase II tran 64.8 1.7 3.8E-05 43.7 -0.6 22 322-343 345-366 (378)
133 PRK14559 putative protein seri 64.2 5 0.00011 45.1 2.8 12 374-385 42-53 (645)
134 COG1645 Uncharacterized Zn-fin 64.0 4.3 9.2E-05 35.8 1.7 24 374-406 29-52 (131)
135 KOG0823 Predicted E3 ubiquitin 64.0 1.9 4.2E-05 41.4 -0.4 16 396-411 65-80 (230)
136 KOG2034 Vacuolar sorting prote 63.9 11 0.00025 43.0 5.4 38 203-240 816-853 (911)
137 TIGR00622 ssl1 transcription f 63.4 4.9 0.00011 34.5 1.9 23 321-343 80-102 (112)
138 KOG3053 Uncharacterized conser 63.0 5.5 0.00012 38.9 2.4 55 202-258 18-80 (293)
139 PLN03208 E3 ubiquitin-protein 62.9 1.3 2.9E-05 41.6 -1.7 32 373-409 18-49 (193)
140 KOG4275 Predicted E3 ubiquitin 62.0 1.7 3.6E-05 43.2 -1.3 40 204-258 300-340 (350)
141 PF04216 FdhE: Protein involve 61.7 5.1 0.00011 40.5 2.1 48 324-400 174-248 (290)
142 KOG1813 Predicted E3 ubiquitin 61.3 2.9 6.2E-05 41.7 0.2 45 204-259 241-285 (313)
143 PRK00420 hypothetical protein; 60.7 5.7 0.00012 34.2 1.8 27 374-409 24-51 (112)
144 PF14149 YhfH: YhfH-like prote 60.7 1.2 2.6E-05 30.2 -1.8 30 367-396 7-37 (37)
145 KOG2114 Vacuolar assembly/sort 60.5 18 0.00038 41.3 6.0 41 204-257 840-880 (933)
146 KOG0826 Predicted E3 ubiquitin 60.5 8.3 0.00018 39.0 3.2 48 203-258 299-346 (357)
147 PF14803 Nudix_N_2: Nudix N-te 60.2 7.7 0.00017 25.9 2.0 25 374-398 1-30 (34)
148 PF06677 Auto_anti-p27: Sjogre 59.8 7.8 0.00017 27.0 2.1 22 374-397 18-41 (41)
149 TIGR01384 TFS_arch transcripti 59.4 5.6 0.00012 33.5 1.6 23 375-399 2-25 (104)
150 COG5432 RAD18 RING-finger-cont 58.8 3.2 6.8E-05 41.1 -0.0 40 374-422 26-67 (391)
151 KOG0825 PHD Zn-finger protein 58.7 2.5 5.4E-05 47.2 -0.8 19 223-241 120-138 (1134)
152 TIGR00686 phnA alkylphosphonat 58.5 6.7 0.00014 33.2 1.8 26 374-400 3-29 (109)
153 COG5175 MOT2 Transcriptional r 58.5 3.3 7.2E-05 41.8 0.1 34 375-409 16-49 (480)
154 PF14835 zf-RING_6: zf-RING of 58.0 5 0.00011 30.8 0.9 27 374-407 8-37 (65)
155 COG1997 RPL43A Ribosomal prote 57.8 7.5 0.00016 31.6 1.9 27 374-400 36-63 (89)
156 KOG1493 Anaphase-promoting com 57.2 3.7 8.1E-05 32.4 0.1 51 204-260 20-81 (84)
157 KOG0978 E3 ubiquitin ligase in 56.8 2.8 6.2E-05 46.9 -0.8 14 326-339 659-672 (698)
158 KOG3161 Predicted E3 ubiquitin 56.7 3.3 7.1E-05 45.3 -0.3 36 204-239 11-48 (861)
159 TIGR02300 FYDLN_acid conserved 55.4 6.1 0.00013 34.5 1.2 26 374-400 10-36 (129)
160 PRK14892 putative transcriptio 55.1 8.7 0.00019 32.3 2.0 28 373-400 21-52 (99)
161 PF01428 zf-AN1: AN1-like Zinc 54.8 7.7 0.00017 27.1 1.4 24 323-348 14-37 (43)
162 PF01599 Ribosomal_S27: Riboso 54.2 8.6 0.00019 27.6 1.6 25 374-398 19-46 (47)
163 PF07282 OrfB_Zn_ribbon: Putat 54.1 8.4 0.00018 29.7 1.7 27 373-399 28-55 (69)
164 KOG1571 Predicted E3 ubiquitin 54.1 13 0.00029 38.2 3.5 45 201-259 302-346 (355)
165 TIGR01206 lysW lysine biosynth 53.8 11 0.00025 27.9 2.2 27 374-400 3-32 (54)
166 PF02891 zf-MIZ: MIZ/SP-RING z 52.9 11 0.00025 27.3 2.1 47 205-257 3-49 (50)
167 TIGR02443 conserved hypothetic 52.6 13 0.00029 28.0 2.4 27 374-400 10-41 (59)
168 PRK10220 hypothetical protein; 51.2 11 0.00024 32.0 2.0 25 374-399 4-29 (111)
169 COG5574 PEX10 RING-finger-cont 49.9 4.6 9.9E-05 39.7 -0.5 39 374-419 216-256 (271)
170 KOG2930 SCF ubiquitin ligase, 49.9 14 0.00031 30.9 2.4 23 223-252 80-102 (114)
171 PF12906 RINGv: RING-variant d 49.8 15 0.00032 26.3 2.2 33 207-239 1-38 (47)
172 PF07191 zinc-ribbons_6: zinc- 49.5 14 0.0003 28.9 2.2 43 375-419 3-55 (70)
173 PHA02929 N1R/p28-like protein; 48.8 9.7 0.00021 37.3 1.5 42 373-414 174-218 (238)
174 KOG3970 Predicted E3 ubiquitin 48.4 17 0.00036 34.9 2.9 53 204-259 50-104 (299)
175 PF08271 TF_Zn_Ribbon: TFIIB z 48.4 18 0.00039 25.2 2.5 24 375-398 2-27 (43)
176 TIGR00595 priA primosomal prot 48.0 13 0.00028 40.7 2.6 34 374-407 223-262 (505)
177 PF14353 CpXC: CpXC protein 47.9 9.5 0.00021 33.4 1.2 14 248-263 2-15 (128)
178 KOG0824 Predicted E3 ubiquitin 47.7 6.8 0.00015 39.2 0.3 20 396-415 25-45 (324)
179 PF03119 DNA_ligase_ZBD: NAD-d 47.3 18 0.00038 23.0 2.0 21 375-395 1-21 (28)
180 PF09526 DUF2387: Probable met 46.8 17 0.00037 28.6 2.4 26 374-399 9-39 (71)
181 PHA02926 zinc finger-like prot 46.5 4.3 9.3E-05 39.0 -1.2 36 326-384 195-230 (242)
182 PRK14714 DNA polymerase II lar 45.3 11 0.00024 44.9 1.5 30 374-409 668-703 (1337)
183 KOG1940 Zn-finger protein [Gen 45.2 31 0.00068 34.5 4.5 47 202-257 156-204 (276)
184 PRK14873 primosome assembly pr 44.8 15 0.00032 41.7 2.4 34 374-407 393-431 (665)
185 KOG1941 Acetylcholine receptor 44.2 8.7 0.00019 39.7 0.5 49 203-258 364-414 (518)
186 COG1594 RPB9 DNA-directed RNA 44.2 18 0.0004 31.1 2.4 27 374-400 3-32 (113)
187 COG5236 Uncharacterized conser 42.7 15 0.00033 37.4 1.8 50 201-259 58-107 (493)
188 PF01363 FYVE: FYVE zinc finge 42.3 19 0.00041 27.6 2.0 34 373-408 9-43 (69)
189 smart00659 RPOLCX RNA polymera 42.0 19 0.00042 25.4 1.8 23 375-398 4-27 (44)
190 TIGR03655 anti_R_Lar restricti 41.6 22 0.00047 26.1 2.1 11 374-384 2-12 (53)
191 TIGR00570 cdk7 CDK-activating 41.3 11 0.00024 38.2 0.7 34 374-407 4-37 (309)
192 PRK11827 hypothetical protein; 40.6 22 0.00047 27.0 2.0 25 374-398 9-34 (60)
193 COG5222 Uncharacterized conser 40.6 19 0.0004 36.0 2.1 45 204-257 274-318 (427)
194 PF09723 Zn-ribbon_8: Zinc rib 40.2 28 0.0006 24.2 2.4 12 374-385 27-39 (42)
195 PF09538 FYDLN_acid: Protein o 40.1 17 0.00036 31.1 1.5 10 323-332 27-36 (108)
196 PF06906 DUF1272: Protein of u 39.9 15 0.00033 27.3 1.1 45 205-260 6-52 (57)
197 PF12861 zf-Apc11: Anaphase-pr 39.4 16 0.00035 29.7 1.2 45 374-421 33-78 (85)
198 PF14569 zf-UDP: Zinc-binding 39.4 8.9 0.00019 30.5 -0.2 20 372-391 50-69 (80)
199 PF06844 DUF1244: Protein of u 39.3 20 0.00044 27.5 1.6 18 227-244 11-28 (68)
200 COG3813 Uncharacterized protei 39.2 15 0.00032 28.7 0.9 46 205-261 6-53 (84)
201 PLN03086 PRLI-interacting fact 39.2 39 0.00085 37.4 4.5 27 374-400 434-463 (567)
202 COG5194 APC11 Component of SCF 39.1 30 0.00064 27.7 2.6 28 223-259 53-80 (88)
203 PRK05580 primosome assembly pr 39.0 21 0.00046 40.6 2.6 34 374-407 391-430 (679)
204 KOG0309 Conserved WD40 repeat- 38.8 22 0.00048 40.0 2.5 49 202-257 1026-1075(1081)
205 PF05129 Elf1: Transcription e 38.4 20 0.00043 29.0 1.6 27 374-400 23-56 (81)
206 TIGR01562 FdhE formate dehydro 37.9 22 0.00048 36.2 2.3 18 106-123 44-61 (305)
207 PF14445 Prok-RING_2: Prokaryo 37.9 6.6 0.00014 28.4 -1.1 34 203-236 6-40 (57)
208 PF13834 DUF4193: Domain of un 37.6 13 0.00028 31.0 0.4 32 201-232 67-98 (99)
209 PRK04023 DNA polymerase II lar 37.5 20 0.00044 41.8 2.1 31 373-409 626-662 (1121)
210 PHA02825 LAP/PHD finger-like p 37.4 32 0.0007 31.4 2.9 51 203-261 7-60 (162)
211 PRK03564 formate dehydrogenase 37.0 23 0.00051 36.1 2.2 18 106-123 48-65 (309)
212 PF03854 zf-P11: P-11 zinc fin 36.8 9.4 0.0002 27.4 -0.4 44 205-261 3-47 (50)
213 PF14471 DUF4428: Domain of un 36.6 29 0.00063 25.3 2.1 30 206-236 1-30 (51)
214 PF12760 Zn_Tnp_IS1595: Transp 36.2 68 0.0015 22.6 4.0 25 374-398 19-45 (46)
215 KOG3268 Predicted E3 ubiquitin 35.7 39 0.00085 31.2 3.2 59 200-260 161-228 (234)
216 COG2824 PhnA Uncharacterized Z 35.5 27 0.00059 29.5 2.0 25 374-399 4-29 (112)
217 PF06827 zf-FPG_IleRS: Zinc fi 34.9 31 0.00068 21.9 1.8 21 374-394 2-24 (30)
218 PF13453 zf-TFIIB: Transcripti 34.8 26 0.00057 24.1 1.6 13 375-387 1-13 (41)
219 PF10083 DUF2321: Uncharacteri 34.6 11 0.00025 34.0 -0.4 32 374-408 40-78 (158)
220 smart00834 CxxC_CXXC_SSSS Puta 33.4 22 0.00047 24.1 1.0 11 374-384 27-37 (41)
221 KOG2164 Predicted E3 ubiquitin 33.1 30 0.00066 37.3 2.4 35 327-385 203-237 (513)
222 smart00249 PHD PHD zinc finger 32.2 23 0.0005 24.1 1.0 33 206-238 1-34 (47)
223 PF08792 A2L_zn_ribbon: A2L zi 32.0 42 0.00092 22.1 2.1 25 374-398 4-29 (33)
224 PRK09521 exosome complex RNA-b 31.5 31 0.00068 32.4 2.0 25 374-399 150-175 (189)
225 PF08882 Acetone_carb_G: Aceto 31.3 32 0.0007 29.3 1.8 13 390-402 23-35 (112)
226 COG3492 Uncharacterized protei 31.2 36 0.00079 27.8 2.0 21 227-247 42-62 (104)
227 PRK09710 lar restriction allev 30.8 48 0.001 25.5 2.5 14 373-386 6-19 (64)
228 PF03833 PolC_DP2: DNA polymer 30.6 17 0.00036 41.7 0.0 32 373-410 655-692 (900)
229 COG0266 Nei Formamidopyrimidin 30.4 35 0.00076 34.1 2.2 24 374-397 246-272 (273)
230 PF07800 DUF1644: Protein of u 30.3 78 0.0017 28.9 4.2 36 204-241 2-50 (162)
231 PF03604 DNA_RNApol_7kD: DNA d 30.2 20 0.00043 23.5 0.3 10 374-383 18-27 (32)
232 PF12677 DUF3797: Domain of un 30.1 43 0.00094 24.2 2.0 27 373-399 13-47 (49)
233 COG5151 SSL1 RNA polymerase II 29.7 14 0.00031 37.1 -0.7 21 323-343 389-409 (421)
234 smart00531 TFIIE Transcription 29.6 47 0.001 29.9 2.8 38 287-332 96-133 (147)
235 PRK08115 ribonucleotide-diphos 29.5 25 0.00053 40.8 1.1 24 374-399 828-853 (858)
236 COG1096 Predicted RNA-binding 29.4 34 0.00074 32.1 1.8 24 374-399 150-174 (188)
237 COG0450 AhpC Peroxiredoxin [Po 28.9 1.2E+02 0.0027 28.6 5.4 48 75-124 119-166 (194)
238 PRK14890 putative Zn-ribbon RN 28.6 38 0.00082 25.6 1.6 34 374-407 8-45 (59)
239 KOG4362 Transcriptional regula 28.4 14 0.0003 41.4 -1.1 56 203-266 20-75 (684)
240 COG2816 NPY1 NTP pyrophosphohy 28.3 52 0.0011 32.9 3.0 27 374-400 112-139 (279)
241 PF01873 eIF-5_eIF-2B: Domain 28.1 52 0.0011 28.9 2.6 27 373-399 93-123 (125)
242 PF11023 DUF2614: Protein of u 27.8 32 0.0007 29.4 1.2 20 323-342 70-97 (114)
243 COG3357 Predicted transcriptio 27.8 87 0.0019 25.8 3.6 14 258-271 18-31 (97)
244 PF05715 zf-piccolo: Piccolo Z 27.5 19 0.0004 27.1 -0.2 35 374-408 3-40 (61)
245 PF01396 zf-C4_Topoisom: Topoi 27.5 58 0.0012 22.3 2.2 20 374-394 2-24 (39)
246 TIGR00373 conserved hypothetic 27.3 50 0.0011 30.2 2.5 32 287-331 106-137 (158)
247 smart00064 FYVE Protein presen 27.0 28 0.0006 26.6 0.7 36 204-239 10-47 (68)
248 PF03833 PolC_DP2: DNA polymer 26.6 22 0.00047 40.8 0.0 16 483-498 780-795 (900)
249 PRK06266 transcription initiat 26.4 51 0.0011 30.8 2.5 32 287-331 114-145 (178)
250 PF08746 zf-RING-like: RING-li 26.3 52 0.0011 23.1 1.9 41 207-252 1-42 (43)
251 PRK12286 rpmF 50S ribosomal pr 26.2 38 0.00081 25.4 1.2 13 372-384 26-38 (57)
252 PF02318 FYVE_2: FYVE-type zin 26.2 79 0.0017 27.3 3.5 35 372-407 53-88 (118)
253 PF14446 Prok-RING_1: Prokaryo 26.1 66 0.0014 23.9 2.5 33 204-236 5-39 (54)
254 PLN02189 cellulose synthase 25.9 47 0.001 39.2 2.5 49 203-259 33-86 (1040)
255 KOG3039 Uncharacterized conser 25.9 50 0.0011 32.3 2.3 38 203-242 42-79 (303)
256 PF14569 zf-UDP: Zinc-binding 25.9 82 0.0018 25.2 3.1 48 203-258 8-60 (80)
257 KOG2932 E3 ubiquitin ligase in 25.7 17 0.00037 36.5 -0.9 16 374-389 124-139 (389)
258 PF10122 Mu-like_Com: Mu-like 25.6 28 0.0006 25.4 0.4 11 375-385 6-16 (51)
259 PHA02862 5L protein; Provision 25.6 54 0.0012 29.4 2.3 48 205-260 3-53 (156)
260 cd00021 BBOX B-Box-type zinc f 24.8 39 0.00084 22.4 1.0 24 322-345 12-35 (39)
261 PF07754 DUF1610: Domain of un 24.7 51 0.0011 20.2 1.4 7 374-380 17-23 (24)
262 PF14354 Lar_restr_allev: Rest 24.5 63 0.0014 24.0 2.2 12 373-384 3-14 (61)
263 COG1996 RPC10 DNA-directed RNA 24.4 40 0.00086 24.5 1.0 10 374-383 25-34 (49)
264 PF01927 Mut7-C: Mut7-C RNAse 23.9 1.5E+02 0.0034 26.5 5.1 59 272-332 70-134 (147)
265 PRK14811 formamidopyrimidine-D 23.8 55 0.0012 32.7 2.3 25 374-405 236-262 (269)
266 smart00440 ZnF_C2C2 C2C2 Zinc 23.3 52 0.0011 22.6 1.4 10 322-331 28-37 (40)
267 PLN02189 cellulose synthase 23.1 54 0.0012 38.7 2.3 44 321-392 52-95 (1040)
268 KOG4218 Nuclear hormone recept 23.1 36 0.00079 34.8 0.8 8 374-381 68-75 (475)
269 PF15135 UPF0515: Uncharacteri 23.0 44 0.00096 32.7 1.4 36 374-409 133-185 (278)
270 PRK08332 ribonucleotide-diphos 22.9 47 0.001 41.6 1.9 27 374-402 1705-1738(1740)
271 PRK01103 formamidopyrimidine/5 22.8 60 0.0013 32.5 2.4 13 374-386 246-258 (274)
272 TIGR00100 hypA hydrogenase nic 22.5 60 0.0013 28.0 2.0 27 288-330 68-94 (115)
273 TIGR00577 fpg formamidopyrimid 22.3 58 0.0013 32.6 2.2 13 374-386 246-258 (272)
274 KOG2462 C2H2-type Zn-finger pr 22.2 26 0.00056 34.8 -0.4 109 202-332 128-253 (279)
275 PF01783 Ribosomal_L32p: Ribos 21.9 36 0.00078 25.3 0.4 13 372-384 25-37 (56)
276 KOG2807 RNA polymerase II tran 21.8 67 0.0015 32.7 2.4 40 206-252 332-372 (378)
277 PLN02436 cellulose synthase A 21.8 71 0.0015 37.9 2.9 49 203-259 35-88 (1094)
278 PRK14810 formamidopyrimidine-D 21.6 61 0.0013 32.4 2.1 13 374-386 245-257 (272)
279 PF00643 zf-B_box: B-box zinc 21.6 25 0.00054 24.0 -0.5 22 323-344 16-37 (42)
280 KOG2932 E3 ubiquitin ligase in 21.5 41 0.0009 33.9 0.9 28 373-407 90-120 (389)
281 PRK13945 formamidopyrimidine-D 21.4 61 0.0013 32.6 2.1 21 374-394 255-277 (282)
282 PRK10445 endonuclease VIII; Pr 21.2 64 0.0014 32.1 2.2 16 374-389 236-253 (263)
283 PF02748 PyrI_C: Aspartate car 21.2 40 0.00087 24.8 0.5 13 289-301 5-17 (52)
284 PF02318 FYVE_2: FYVE-type zin 21.2 1.2E+02 0.0026 26.1 3.7 33 203-235 53-88 (118)
285 PF13913 zf-C2HC_2: zinc-finge 21.1 48 0.001 20.2 0.8 10 323-332 3-12 (25)
286 smart00154 ZnF_AN1 AN1-like Zi 21.0 60 0.0013 22.2 1.3 18 322-339 12-29 (39)
287 smart00336 BBOX B-Box-type zin 20.8 67 0.0015 21.5 1.6 23 322-344 15-37 (42)
288 PF01096 TFIIS_C: Transcriptio 20.7 43 0.00093 22.9 0.6 11 322-332 28-38 (39)
289 cd00350 rubredoxin_like Rubred 20.5 85 0.0018 20.5 2.0 23 292-330 3-25 (33)
290 KOG0825 PHD Zn-finger protein 20.4 83 0.0018 35.8 2.9 49 204-261 123-172 (1134)
291 PF11682 DUF3279: Protein of u 20.2 60 0.0013 28.6 1.5 14 374-387 111-124 (128)
292 PRK12380 hydrogenase nickel in 20.1 72 0.0016 27.4 2.0 15 288-304 68-82 (113)
No 1
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.3e-51 Score=426.08 Aligned_cols=341 Identities=34% Similarity=0.670 Sum_probs=281.5
Q ss_pred EEEeecccccccCCCCCcccceEEEEeec-CCCceEEEeecccc--cchhhHHHHHHHHHHHHHHHHcCcceeeeecccH
Q 010003 60 KMFFKGMSITEVGESSSGFSGIGVVMERS-FNIPIMQVQKKLDF--FVEESVADYLALMDGLITAVQNKIRCVYAFTDSE 136 (520)
Q Consensus 60 ~~~fdG~~~~~~~~~n~~~ag~g~~i~~~-~~~~~~~~~~~~~~--~~tnn~AE~~ALi~~l~~a~~~~i~~v~i~~Dse 136 (520)
++||+|++++|.++. .+.+|+||+|+|. ++++.+....+... .+|...||++||+.+|.+|+++++..+.++.|+.
T Consensus 1 ~l~~k~lv~~e~~~~-~~~~g~~vai~d~~d~~~~f~~k~~~~~~~~~~~~~ae~~al~~~l~ea~~~~~~~~~~~~d~~ 79 (384)
T KOG1812|consen 1 RLYFKGLVSEESIND-ILLAGFGVAICDEHDDDLLFQMKASDHDSDSITPLEAELMALKRGLTEALELGLNHIVIYCDDE 79 (384)
T ss_pred CCccccchhhhhhhh-hhcccCceeeeccccHHHHHHhhcCcccccccchhhHHHHHHhhccHHHHhhccccceEecccH
Confidence 479999999776422 5789999999997 45554444444433 2688999999999999999999999999999999
Q ss_pred HHHHHhhhhhhcchh-HHHHHHHHHHHHhhhhhhHHhhccccc-ccccHHHHHHHhhccCCCCCCCCCcccccccccccc
Q 010003 137 LLYDQITREEKLDIP-LLVALRQRILEYTSNLEAFVLKLVPSI-ELERPLRLAQIAVGIVSSPSQGDKSPENCSICCEDK 214 (520)
Q Consensus 137 lv~~ql~g~~~~~~~-~L~~l~~ril~l~~~f~~~~l~lvpr~-~~~~a~klA~~Ai~~~~~~~~~~~~~~~C~IC~e~~ 214 (520)
++++.+.+....... .+..+..++....+.|......++++. +.+.+.++|.+++.. .........+|.||+.+.
T Consensus 80 ~~~~~v~~~~~~~~~~~~~~l~~~v~~~r~~l~~~~~i~~~~~~d~~~~~~lA~e~i~s---~~~~~~~~~~C~iC~~e~ 156 (384)
T KOG1812|consen 80 LIYESVAGREKPEQHRKIVLLVELVQRIREQLTSSEPILVPKNADIKFAYKLAREAIVS---QLPSKLPKEECGICFVED 156 (384)
T ss_pred HHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHhhcccceecccchhhHHHHHHHHHhhcc---ccccccccccCccCcccc
Confidence 999988888777665 677777888777777777777777664 778899999999876 223345678999999555
Q ss_pred CCC-Ceeec-cCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCcccchHHHhhcCCcccHHHHHHHHHHHhhcCCCcee
Q 010003 215 PYP-MMITM-KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTVECKSFLPLSSYESLETALAEANILHSDRIY 292 (520)
Q Consensus 215 ~~~-~~~~l-~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~L~~~~~e~~~~~~~e~~~~~~~~~~ 292 (520)
+.. .++.. .|+|.||.+|+++|++++ ..+...|+||..+|+..++.+.+..+|++++.++|++++.+..++..+.+|
T Consensus 157 ~~~~~~f~~~~C~H~fC~~C~k~~iev~-~~~~~~~~C~~~~C~~~l~~~~c~~llt~kl~e~~e~~~~e~~i~~~~~~y 235 (384)
T KOG1812|consen 157 PEAEDMFSVLKCGHRFCKDCVKQHIEVK-LLSGTVIRCPHDGCESRLTLESCRKLLTPKLREMWEQRLKEEVIPSLDRVY 235 (384)
T ss_pred ccHhhhHHHhcccchhhhHHhHHHhhhh-hccCCCccCCCCCCCccCCHHHHhhhcCHHHHHHHHHHHHHHhhhhhhccc
Confidence 544 55554 899999999999999999 445567899999999999999999999999999999999999998777779
Q ss_pred ccCCCCCeeecCcccccccccCCCCCCCCceeCCCCCcceeccCCCccCCCCCchhhhcCchhhcCchHHHHHHHHhccC
Q 010003 293 CPFPNCSVLLDPRECLSARASSSSQSDNSCVECPVCERFICVECGVPWHSSLSCEEYQNLPLEERDAGDITLHRLAQNKR 372 (520)
Q Consensus 293 CP~p~C~~~~~~~~~~~~~~~~~~~~~~~~~~Cp~C~~~fC~~C~~~wH~~~tC~e~~~~~~~~~~~~~~~l~~l~~~~~ 372 (520)
||+|+|+.++...+..+ ........|+.|+..||..|+.+||.+.+|++|+++.. +...++..++.++ +.
T Consensus 236 cp~~~C~~l~~~~el~~-------~~~~~~~~C~~C~~~fCv~C~~~wh~~~sC~eykk~~~-~~~~d~~~~~~la--~~ 305 (384)
T KOG1812|consen 236 CPYPRCSSLMSKTELSS-------EVKSKRRPCVKCHELFCVKCKVPWHANLSCEEYKKLNP-EEYVDDITLKYLA--KR 305 (384)
T ss_pred CCCCCchHhhhhhhhcc-------chhhcccccccCCCceeecCCCcCCCCCCHHHHHHhCC-cccccHHHHHHHH--Hh
Confidence 99999999987766431 11123367999999999999999999999999999875 3344567777888 78
Q ss_pred CccCccccceeeecCCcceEEecccccccccccccccCCCCcc
Q 010003 373 WRRCQQCRRMIELTHGCYHMTCWCGHEFCYSCGAEYRDGQQTC 415 (520)
Q Consensus 373 ~k~CP~C~~~IeK~~GCnhMtC~Cg~~FCy~C~~~~~~~~~~c 415 (520)
||+||+|+.+|+|++|||||||+|||+|||.|+.+|..+...|
T Consensus 306 wr~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~~~~~~~~~~~ 348 (384)
T KOG1812|consen 306 WRQCPKCKFMIELSEGCNHMTCRCGHQFCYMCGGDWKTHNGEC 348 (384)
T ss_pred cCcCcccceeeeecCCcceEEeeccccchhhcCcchhhCCccc
Confidence 9999999999999999999999999999999999998766544
No 2
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.98 E-value=4.7e-33 Score=276.49 Aligned_cols=196 Identities=26% Similarity=0.623 Sum_probs=156.5
Q ss_pred CccccccccccccCCC-CeeeccCCCcccHHHHHHHHHHhhhCCCC-ccccCCCCcCcccchHHHhhcCCcccHHHHHHH
Q 010003 202 KSPENCSICCEDKPYP-MMITMKCSHKFCSHCMRTYIDGKVQSSQV-PIRCPQLRCKYFISTVECKSFLPLSSYESLETA 279 (520)
Q Consensus 202 ~~~~~C~IC~e~~~~~-~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~-~i~CP~~~C~~~l~~~~i~~~L~~~~~e~~~~~ 279 (520)
...+.|.|||++..+. .|..++|+|+||+.|++.|+...|++|.+ .++||+.+|+...++..++++++.+++++|++.
T Consensus 182 ~slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C~~~a~~g~vKelvg~EL~arYe~l 261 (445)
T KOG1814|consen 182 NSLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCGSVAPPGQVKELVGDELFARYEKL 261 (445)
T ss_pred hhcccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCCcccCCchHHHHHHHHHHHHHHHHH
Confidence 3579999999999884 45566999999999999999999999875 799999999999999999999999999999998
Q ss_pred HHHHhhc-CCCceeccCCCCCeeecCcccccccccCCCCCCCCceeCCCCCcceeccCCCccCCCCCchhh--------h
Q 010003 280 LAEANIL-HSDRIYCPFPNCSVLLDPRECLSARASSSSQSDNSCVECPVCERFICVECGVPWHSSLSCEEY--------Q 350 (520)
Q Consensus 280 ~~e~~~~-~~~~~~CP~p~C~~~~~~~~~~~~~~~~~~~~~~~~~~Cp~C~~~fC~~C~~~wH~~~tC~e~--------~ 350 (520)
+.+..+. .++.+|||++.|....- .+ ++.....|.+|+.+||..|+..||+...|.-- .
T Consensus 262 ~lqk~l~~msdv~yCPr~~Cq~p~~-~d-----------~~~~l~~CskCnFaFCtlCk~t~HG~s~Ck~~~~~~~~l~~ 329 (445)
T KOG1814|consen 262 MLQKTLELMSDVVYCPRACCQLPVK-QD-----------PGRALAICSKCNFAFCTLCKLTWHGVSPCKVKAEKLIELYL 329 (445)
T ss_pred HHHHHHHhhcccccCChhhccCccc-cC-----------chhhhhhhccCccHHHHHHHHhhcCCCcccCchHHHHHHHH
Confidence 8877765 67899999999997652 11 12234789999999999999999999999521 1
Q ss_pred cCc---hhh-----cCchH----------HHHHHHHhccCCccCccccceeeecCCcceEEec-ccccccccccccccCC
Q 010003 351 NLP---LEE-----RDAGD----------ITLHRLAQNKRWRRCQQCRRMIELTHGCYHMTCW-CGHEFCYSCGAEYRDG 411 (520)
Q Consensus 351 ~~~---~~~-----~~~~~----------~~l~~l~~~~~~k~CP~C~~~IeK~~GCnhMtC~-Cg~~FCy~C~~~~~~~ 411 (520)
.+. ... ++.+. ...+|+..| .|+||+|+++|+|++|||||+|. |++.|||+|+..+..+
T Consensus 330 ~~~~~d~a~k~ele~Ryg~rvve~~vn~~lsekwl~~N--~krCP~C~v~IEr~eGCnKM~C~~c~~~fc~~c~~~l~~~ 407 (445)
T KOG1814|consen 330 EYLEADEARKRELEKRYGKRVVEELVNDFLSEKWLESN--SKRCPKCKVVIERSEGCNKMHCTKCGTYFCWICAELLYPE 407 (445)
T ss_pred HHhhcCHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhc--CCCCCcccceeecCCCccceeeccccccceeehhhhcCCC
Confidence 111 000 00010 011233333 39999999999999999999996 9999999999887643
No 3
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.94 E-value=2.3e-27 Score=252.04 Aligned_cols=210 Identities=27% Similarity=0.598 Sum_probs=172.3
Q ss_pred CCCccccccccccccCCCCeeeccCCCcccHHHHHHHHHHhhhCCCC-ccccCCCCcCcccchHHHhhcCCc-ccHHHHH
Q 010003 200 GDKSPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQV-PIRCPQLRCKYFISTVECKSFLPL-SSYESLE 277 (520)
Q Consensus 200 ~~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~-~i~CP~~~C~~~l~~~~i~~~L~~-~~~e~~~ 277 (520)
......+|.||++.++. .++.+.|+|.||..||..|+..+|..+.. .|+||..+|...+..+.+..+++. ...++|.
T Consensus 66 ~~~~~~~c~ic~~~~~~-~~~~~~c~H~~c~~cw~~yl~~kI~~~~~~~i~cp~~~C~a~v~~~~i~~~~s~~~~~~ky~ 144 (444)
T KOG1815|consen 66 KKKGDVQCGICVESYDG-EIIGLGCGHPFCPPCWTGYLGTKIHEGEEAKIKCPAHGCPALVGEDTVEKLVSDKEDKEKYQ 144 (444)
T ss_pred CCCccccCCcccCCCcc-hhhhcCCCcHHHHHHHHHHhhheeeccccccccCCCCCccccCCCceeeeecCCHHHHHHHH
Confidence 34567999999999876 66778999999999999999999987543 389999999999999999999888 4888999
Q ss_pred HHHHHHhhc-CCCceeccCCCCCeeecCcccccccccCCCCCCCCceeCCCCCcceeccCCCccCCCCCchhhhcCchhh
Q 010003 278 TALAEANIL-HSDRIYCPFPNCSVLLDPRECLSARASSSSQSDNSCVECPVCERFICVECGVPWHSSLSCEEYQNLPLEE 356 (520)
Q Consensus 278 ~~~~e~~~~-~~~~~~CP~p~C~~~~~~~~~~~~~~~~~~~~~~~~~~Cp~C~~~fC~~C~~~wH~~~tC~e~~~~~~~~ 356 (520)
+.+...++. .....|||.|+|+.++..... ....+.|. |++.||+.|+.+||.+.+|.....|....
T Consensus 145 ~~i~~syve~~~~lkwCP~~~C~~av~~~~~-----------~~~~v~C~-~g~~FC~~C~~~~H~p~~C~~~~~wl~k~ 212 (444)
T KOG1815|consen 145 RYILRSYVEDNVPLKWCPAPGCGLAVKFGSL-----------ESVEVDCG-CGHEFCFACGEESHSPVSCPGAKKWLKKC 212 (444)
T ss_pred HHHHHHHHhcCCccccCCCCCCCceeeccCC-----------CccceeCC-CCchhHhhccccccCCCcccchHHHHHhh
Confidence 998888886 345789999999998765311 12237885 77799999999999999999988886543
Q ss_pred cCchHHHHHHHHhccCCccCccccceeeecCCcceEEec---ccccccccccccccCCCC--cccCCCCCCCch
Q 010003 357 RDAGDITLHRLAQNKRWRRCQQCRRMIELTHGCYHMTCW---CGHEFCYSCGAEYRDGQQ--TCQCAFWDEDNS 425 (520)
Q Consensus 357 ~~~~~~~l~~l~~~~~~k~CP~C~~~IeK~~GCnhMtC~---Cg~~FCy~C~~~~~~~~~--~c~C~~~~~~~~ 425 (520)
.. ....+.++..+ +++||+|.++|+|++|||||+|. |+++|||+|++.|.+++. ...|++|..+..
T Consensus 213 ~~-~se~~~wi~~n--tk~CP~c~~~iek~~gc~~~~~~~~~c~~~FCw~Cl~~~~~h~~~~~~~c~~~~~~~~ 283 (444)
T KOG1815|consen 213 RD-DSETINWILAN--TKECPKCKVPIEKDGGCNHMTCKSASCKHEFCWVCLASLSDHGSSTGYSCNRYVDGKS 283 (444)
T ss_pred hh-hhhhhhhhhcc--CccCCCcccchhccCCccccccccCCcCCeeceeeecccccccccceeeeeeeechhh
Confidence 32 23344444444 48899999999999999999995 999999999999998764 588999988875
No 4
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=99.90 E-value=4.3e-24 Score=205.14 Aligned_cols=201 Identities=25% Similarity=0.605 Sum_probs=148.3
Q ss_pred CCccccccccccccCCCCeeeccCC--CcccHHHHHHHHHHhhhCCC--------CccccCCCCcCcccchH-HHhhcCC
Q 010003 201 DKSPENCSICCEDKPYPMMITMKCS--HKFCSHCMRTYIDGKVQSSQ--------VPIRCPQLRCKYFISTV-ECKSFLP 269 (520)
Q Consensus 201 ~~~~~~C~IC~e~~~~~~~~~l~Cg--H~fC~~Cl~~~i~~~i~~~~--------~~i~CP~~~C~~~l~~~-~i~~~L~ 269 (520)
+....+|..|-+.. ..++.++|. |..|.+|++.|..+.+.+.+ +.+.||. +|...+-.+ +-.++|+
T Consensus 218 N~~ni~C~~Ctdv~--~~vlvf~Cns~HvtC~dCFr~yc~~Rl~~rqf~~~p~~gyslpc~a-gc~~s~i~e~HHF~ilg 294 (446)
T KOG0006|consen 218 NSRNITCITCTDVR--SPVLVFQCNSRHVTCLDCFRLYCVTRLNDRQFVHDPQLGYSLPCVA-GCPNSLIKELHHFRILG 294 (446)
T ss_pred ccccceeEEecCCc--cceEEEecCCceeehHHhhhhHhhhcccccccccCccccccccccC-CCchHHHHhhhhheecc
Confidence 34578999997654 234556887 99999999999999987654 3477886 587665433 3446899
Q ss_pred cccHHHHHHHHHHHhhcCCCceeccCCCCCeeecCcccccccccCCCCCCCCceeCCC-CCcceeccCCCccCCCCCchh
Q 010003 270 LSSYESLETALAEANILHSDRIYCPFPNCSVLLDPRECLSARASSSSQSDNSCVECPV-CERFICVECGVPWHSSLSCEE 348 (520)
Q Consensus 270 ~~~~e~~~~~~~e~~~~~~~~~~CP~p~C~~~~~~~~~~~~~~~~~~~~~~~~~~Cp~-C~~~fC~~C~~~wH~~~tC~e 348 (520)
.+.|.+|+++..+..+...+.+.||+|+|+..+.+. ++.+.++|+. |++.||..|+..+|.+. |.+
T Consensus 295 ~e~Y~rYQr~atEe~vlq~gGVlCP~pgCG~gll~E------------PD~rkvtC~~gCgf~FCR~C~e~yh~ge-C~~ 361 (446)
T KOG0006|consen 295 EEQYNRYQRYATEECVLQMGGVLCPRPGCGAGLLPE------------PDQRKVTCEGGCGFAFCRECKEAYHEGE-CSA 361 (446)
T ss_pred hhHHHHHHHhhhhhheeecCCEecCCCCCCcccccC------------CCCCcccCCCCchhHhHHHHHhhhcccc-cee
Confidence 999999999999999888889999999999766543 2445689997 99999999999999884 531
Q ss_pred h--------hcCchhhcCchHH---HHHHHHhccCCccCccccceeeecCCcceEEec---ccccccccccccccCCCCc
Q 010003 349 Y--------QNLPLEERDAGDI---TLHRLAQNKRWRRCQQCRRMIELTHGCYHMTCW---CGHEFCYSCGAEYRDGQQT 414 (520)
Q Consensus 349 ~--------~~~~~~~~~~~~~---~l~~l~~~~~~k~CP~C~~~IeK~~GCnhMtC~---Cg~~FCy~C~~~~~~~~~~ 414 (520)
. ..+..+++.+... .+.....++.+|+||+|+++.|+++||.||.|+ ||.+|||.|+-+|+. .
T Consensus 362 ~~~as~t~tc~y~vde~~a~~arwd~as~~TIk~tTkpCPkChvptErnGGCmHm~Ct~~~Cg~eWCw~C~tEW~r---~ 438 (446)
T KOG0006|consen 362 VFEASGTTTCAYRVDERAAEQARWDAASKETIKKTTKPCPKCHVPTERNGGCMHMKCTQPQCGLEWCWNCGTEWNR---V 438 (446)
T ss_pred eeccccccceeeecChhhhhhhhhhhhhhhhhhhccCCCCCccCccccCCceEEeecCCCCCCceeEeccCChhhh---h
Confidence 1 0111112111110 111222345569999999999999999999994 999999999999985 3
Q ss_pred ccCCCC
Q 010003 415 CQCAFW 420 (520)
Q Consensus 415 c~C~~~ 420 (520)
|--.||
T Consensus 439 CmgdHW 444 (446)
T KOG0006|consen 439 CMGDHW 444 (446)
T ss_pred hccccc
Confidence 443444
No 5
>PRK07708 hypothetical protein; Validated
Probab=99.81 E-value=2e-19 Score=172.68 Aligned_cols=133 Identities=17% Similarity=0.149 Sum_probs=116.5
Q ss_pred eEEEEeecccccccCCCCCcccceEEEEeecCCCceEEE--eecccccchhhHHHHHHHHHHHHHHHHcCcce--eeeec
Q 010003 58 SVKMFFKGMSITEVGESSSGFSGIGVVMERSFNIPIMQV--QKKLDFFVEESVADYLALMDGLITAVQNKIRC--VYAFT 133 (520)
Q Consensus 58 ~~~~~fdG~~~~~~~~~n~~~ag~g~~i~~~~~~~~~~~--~~~~~~~~tnn~AE~~ALi~~l~~a~~~~i~~--v~i~~ 133 (520)
.|.|||||+++ + |+|.+|+|++|.++.|...+.. +..+++..|||+|||.||+.||..|..+|++. |.+++
T Consensus 73 ~~~vY~DGs~~---~--n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~ 147 (219)
T PRK07708 73 EILVYFDGGFD---K--ETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFRG 147 (219)
T ss_pred cEEEEEeeccC---C--CCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHcCCCcceEEEEe
Confidence 59999999998 6 8999999999998777654433 35666656999999999999999999999986 88999
Q ss_pred ccHHHHHHhhhhhhcchhHHHHHHHHHHHHhhhhhh-HHhhcccccccccHHHHHHHhhccCC
Q 010003 134 DSELLYDQITREEKLDIPLLVALRQRILEYTSNLEA-FVLKLVPSIELERPLRLAQIAVGIVS 195 (520)
Q Consensus 134 Dselv~~ql~g~~~~~~~~L~~l~~ril~l~~~f~~-~~l~lvpr~~~~~a~klA~~Ai~~~~ 195 (520)
||++|++|++|+|+.+.+.+..+.+++..+.+.|.- +.+.+|+|..|..|++||+.|+....
T Consensus 148 DSqlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~VpR~~N~~AD~LAk~Al~~~~ 210 (219)
T PRK07708 148 DSQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPISRKQNKEADQLATQALEGTV 210 (219)
T ss_pred ccHHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECCchhhhHHHHHHHHHHhcCC
Confidence 999999999999999999999999999988888764 66789999999999999999976544
No 6
>PRK13907 rnhA ribonuclease H; Provisional
Probab=99.79 E-value=4.9e-19 Score=157.06 Aligned_cols=126 Identities=25% Similarity=0.353 Sum_probs=110.4
Q ss_pred eEEEEeecccccccCCCCCcccceEEEEeecCCCceEEEeecccccchhhHHHHHHHHHHHHHHHHcCcceeeeecccHH
Q 010003 58 SVKMFFKGMSITEVGESSSGFSGIGVVMERSFNIPIMQVQKKLDFFVEESVADYLALMDGLITAVQNKIRCVYAFTDSEL 137 (520)
Q Consensus 58 ~~~~~fdG~~~~~~~~~n~~~ag~g~~i~~~~~~~~~~~~~~~~~~~tnn~AE~~ALi~~l~~a~~~~i~~v~i~~Dsel 137 (520)
++.|||||+++ + |||++|+|++|.+.++.. ..+..++. .|||.|||.|++.||..|...++..|.+++||++
T Consensus 1 ~~~iy~DGa~~---~--~~g~~G~G~vi~~~~~~~--~~~~~~~~-~tn~~AE~~All~aL~~a~~~g~~~v~i~sDS~~ 72 (128)
T PRK13907 1 MIEVYIDGASK---G--NPGPSGAGVFIKGVQPAV--QLSLPLGT-MSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQL 72 (128)
T ss_pred CEEEEEeeCCC---C--CCCccEEEEEEEECCeeE--EEEecccc-cCCcHHHHHHHHHHHHHHHhCCCCEEEEEechHH
Confidence 37899999999 7 899999999998866543 33444443 4999999999999999999999999999999999
Q ss_pred HHHHhhhhhhcchhHHHHHHHHHHHHhhhhhhHHhhcccccccccHHHHHHHhhc
Q 010003 138 LYDQITREEKLDIPLLVALRQRILEYTSNLEAFVLKLVPSIELERPLRLAQIAVG 192 (520)
Q Consensus 138 v~~ql~g~~~~~~~~L~~l~~ril~l~~~f~~~~l~lvpr~~~~~a~klA~~Ai~ 192 (520)
|+++++++|. +.+.+..+.+.+..+...|..+.+.|+||..|..|+.||+.++.
T Consensus 73 vi~~~~~~~~-~~~~~~~l~~~~~~l~~~f~~~~~~~v~r~~N~~Ad~LA~~a~~ 126 (128)
T PRK13907 73 VERAVEKEYA-KNKMFAPLLEEALQYIKSFDLFFIKWIPSSQNKVADELARKAIL 126 (128)
T ss_pred HHHHHhHHHh-cChhHHHHHHHHHHHHhcCCceEEEEcCchhchhHHHHHHHHHh
Confidence 9999999886 45678899999999999999988999999999999999998864
No 7
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=99.76 E-value=1.6e-18 Score=155.57 Aligned_cols=128 Identities=22% Similarity=0.193 Sum_probs=107.9
Q ss_pred eEEEEeecccccccCCCCCcccceEEEEeecCCCceEEEeecccccchhhHHHHHHHHHHHHHHHHcCcceeeeecccHH
Q 010003 58 SVKMFFKGMSITEVGESSSGFSGIGVVMERSFNIPIMQVQKKLDFFVEESVADYLALMDGLITAVQNKIRCVYAFTDSEL 137 (520)
Q Consensus 58 ~~~~~fdG~~~~~~~~~n~~~ag~g~~i~~~~~~~~~~~~~~~~~~~tnn~AE~~ALi~~l~~a~~~~i~~v~i~~Dsel 137 (520)
.+.|||||+|+ | |||++|+|+++...++.. ..+..... .|||.|||+|||.||..+.+.+...|.+++||++
T Consensus 3 ~v~if~DGa~~---g--NpG~gG~g~vl~~~~~~~--~~s~~~~~-tTNNraEl~A~i~AL~~l~~~~~~~v~l~tDS~y 74 (154)
T COG0328 3 KVEIFTDGACL---G--NPGPGGWGAVLRYGDGEK--ELSGGEGR-TTNNRAELRALIEALEALKELGACEVTLYTDSKY 74 (154)
T ss_pred ceEEEecCccC---C--CCCCceEEEEEEcCCceE--EEeeeeec-ccChHHHHHHHHHHHHHHHhcCCceEEEEecHHH
Confidence 47899999999 8 999999999999654443 56666664 4999999999999999999999999999999999
Q ss_pred HHHHhhhhhhcchhH------------HHHHHHHHHHHhhhhhhHHhhccc----ccccccHHHHHHHhhccC
Q 010003 138 LYDQITREEKLDIPL------------LVALRQRILEYTSNLEAFVLKLVP----SIELERPLRLAQIAVGIV 194 (520)
Q Consensus 138 v~~ql~g~~~~~~~~------------L~~l~~ril~l~~~f~~~~l~lvp----r~~~~~a~klA~~Ai~~~ 194 (520)
|+++|+ .|..+.+. -..+++++.++...+..+...||+ ...|+++|+||+.++...
T Consensus 75 v~~~i~-~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~~~~~~ 146 (154)
T COG0328 75 VVEGIT-RWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAREAARAA 146 (154)
T ss_pred HHHHHH-HHHhhccccCccccccCccccHHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHHHHHHhh
Confidence 999999 55332221 136789999999999888999999 789999999999987655
No 8
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=99.74 E-value=7.1e-18 Score=176.35 Aligned_cols=131 Identities=23% Similarity=0.239 Sum_probs=119.6
Q ss_pred eEEEEeecccccccCCCCCcccceEEEEeecCCC-ceEEEeecccccchhhHHHHHHHHHHHHHHHHcCcceeeeecccH
Q 010003 58 SVKMFFKGMSITEVGESSSGFSGIGVVMERSFNI-PIMQVQKKLDFFVEESVADYLALMDGLITAVQNKIRCVYAFTDSE 136 (520)
Q Consensus 58 ~~~~~fdG~~~~~~~~~n~~~ag~g~~i~~~~~~-~~~~~~~~~~~~~tnn~AE~~ALi~~l~~a~~~~i~~v~i~~Dse 136 (520)
.+.|||||+++ + |||+||+|++|.++++. ++.+.+..++ ..|||.|||.||+.||..+..+++++|.+++||+
T Consensus 2 ~~~i~~DGa~~---~--n~g~aG~G~vi~~~~~~~~~~~~~~~~~-~~tnn~AE~~All~gL~~a~~~g~~~v~i~~DS~ 75 (372)
T PRK07238 2 KVVVEADGGSR---G--NPGPAGYGAVVWDADRGEVLAERAEAIG-RATNNVAEYRGLIAGLEAAAELGATEVEVRMDSK 75 (372)
T ss_pred eEEEEecCCCC---C--CCCceEEEEEEEeCCCCcEEEEeecccC-CCCchHHHHHHHHHHHHHHHhCCCCeEEEEeCcH
Confidence 47899999999 7 89999999999998755 4467777777 4499999999999999999999999999999999
Q ss_pred HHHHHhhhhhhcchhHHHHHHHHHHHHhhhhhhHHhhcccccccccHHHHHHHhhccC
Q 010003 137 LLYDQITREEKLDIPLLVALRQRILEYTSNLEAFVLKLVPSIELERPLRLAQIAVGIV 194 (520)
Q Consensus 137 lv~~ql~g~~~~~~~~L~~l~~ril~l~~~f~~~~l~lvpr~~~~~a~klA~~Ai~~~ 194 (520)
+|+++++++|+.+++.|..+.+++..+.+.|..+.+.|++|.+|..|+.||+.++...
T Consensus 76 lvi~~i~~~~~~~~~~l~~~~~~i~~l~~~f~~~~i~~v~r~~N~~AD~LA~~a~~~~ 133 (372)
T PRK07238 76 LVVEQMSGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPRARNAHADRLANEAMDAA 133 (372)
T ss_pred HHHHHhCCCCccCChHHHHHHHHHHHHHhcCCceEEEECCchhhhHHHHHHHHHHHhh
Confidence 9999999999999999999999999999999999999999999999999999986443
No 9
>PRK08719 ribonuclease H; Reviewed
Probab=99.56 E-value=1.4e-14 Score=131.24 Aligned_cols=126 Identities=17% Similarity=0.154 Sum_probs=97.0
Q ss_pred ceEEEEeecccccccCCCCCc---ccceEEEEeecCCCceEEEeecccccchhhHHHHHHHHHHHHHHHHcCcceeeeec
Q 010003 57 FSVKMFFKGMSITEVGESSSG---FSGIGVVMERSFNIPIMQVQKKLDFFVEESVADYLALMDGLITAVQNKIRCVYAFT 133 (520)
Q Consensus 57 ~~~~~~fdG~~~~~~~~~n~~---~ag~g~~i~~~~~~~~~~~~~~~~~~~tnn~AE~~ALi~~l~~a~~~~i~~v~i~~ 133 (520)
..+.|||||+++ + ||+ +||+|+++.++++..+...+..+.+..|||.||+.|++.+|..+... ..|++
T Consensus 3 ~~~~iYtDGs~~---~--n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~----~~i~t 73 (147)
T PRK08719 3 ASYSIYIDGAAP---N--NQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARDG----DVIYS 73 (147)
T ss_pred ceEEEEEecccC---C--CCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCC----CEEEe
Confidence 358999999999 6 454 78999999998777655667777766699999999999999987654 36999
Q ss_pred ccHHHHHHhh--------hhhhcchhH---HHHHHHHHHHHhhhhhhHHhhcccc----cccccHHHHHHHhhc
Q 010003 134 DSELLYDQIT--------REEKLDIPL---LVALRQRILEYTSNLEAFVLKLVPS----IELERPLRLAQIAVG 192 (520)
Q Consensus 134 Dselv~~ql~--------g~~~~~~~~---L~~l~~ril~l~~~f~~~~l~lvpr----~~~~~a~klA~~Ai~ 192 (520)
||++++++|+ ++|+..... -.++.+.+..+.+ ...+.+.||+. ..|+.+|+||+.|..
T Consensus 74 DS~yvi~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~-~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~ 146 (147)
T PRK08719 74 DSDYCVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRA-RKYVEVEKVTAHSGIEGNEAADMLAQAAAE 146 (147)
T ss_pred chHHHHHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhC-CCcEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence 9999999994 445432221 1456677666655 45677899998 668999999998754
No 10
>PRK06548 ribonuclease H; Provisional
Probab=99.43 E-value=5.8e-13 Score=121.77 Aligned_cols=124 Identities=19% Similarity=0.199 Sum_probs=89.8
Q ss_pred ceEEEEeecccccccCCCCCcccceEEEEeecCCCceEEEeecccccchhhHHHHHHHHHHHHHHHHcCcceeeeecccH
Q 010003 57 FSVKMFFKGMSITEVGESSSGFSGIGVVMERSFNIPIMQVQKKLDFFVEESVADYLALMDGLITAVQNKIRCVYAFTDSE 136 (520)
Q Consensus 57 ~~~~~~fdG~~~~~~~~~n~~~ag~g~~i~~~~~~~~~~~~~~~~~~~tnn~AE~~ALi~~l~~a~~~~i~~v~i~~Dse 136 (520)
..+.|||||+++ + |||++|+|+++.+. + ..+.... ..|||.||++|++.+|.. +......|.|++||+
T Consensus 4 ~~~~IytDGa~~---g--npg~~G~g~~~~~~-~----~~~g~~~-~~TNnraEl~Aii~aL~~-~~~~~~~v~I~TDS~ 71 (161)
T PRK06548 4 NEIIAATDGSSL---A--NPGPSGWAWYVDEN-T----WDSGGWD-IATNNIAELTAVRELLIA-TRHTDRPILILSDSK 71 (161)
T ss_pred CEEEEEEeeccC---C--CCCceEEEEEEeCC-c----EEccCCC-CCCHHHHHHHHHHHHHHh-hhcCCceEEEEeChH
Confidence 358999999999 7 89999999998742 1 2233333 349999999999999964 445556799999999
Q ss_pred HHHHHhhh--------hhhc--chhHH-HHHHHHHHHHhhhhhhHHhhcccc----cccccHHHHHHHhhcc
Q 010003 137 LLYDQITR--------EEKL--DIPLL-VALRQRILEYTSNLEAFVLKLVPS----IELERPLRLAQIAVGI 193 (520)
Q Consensus 137 lv~~ql~g--------~~~~--~~~~L-~~l~~ril~l~~~f~~~~l~lvpr----~~~~~a~klA~~Ai~~ 193 (520)
++++.|+. +|+. ..|.. +++.+++..+.+.. .+.+.||+- ..|+.+|+||+++...
T Consensus 72 yvi~~i~~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~~-~v~~~wVkgHsg~~gNe~aD~LA~~aa~~ 142 (161)
T PRK06548 72 YVINSLTKWVYSWKMRKWRKADGKPVLNQEIIQEIDSLMENR-NIRMSWVNAHTGHPLNEAADSLARQAANN 142 (161)
T ss_pred HHHHHHHHHHHHHHHCCCcccCCCccccHHHHHHHHHHHhcC-ceEEEEEecCCCCHHHHHHHHHHHHHHHH
Confidence 99999985 3332 12322 56677777666553 466777764 5588899999988543
No 11
>cd06222 RnaseH RNase H (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a not sequence-specific manner. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H knockout mice lack mitochondrial DNA replication and die as embryos. The retroviral reverse transcriptase contains an RNase H domain that plays an important role in converting a single stranded retroviral genomic RNA into a dsDNA for integration into host chromosomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.
Probab=99.42 E-value=8.2e-13 Score=114.54 Aligned_cols=125 Identities=24% Similarity=0.211 Sum_probs=107.0
Q ss_pred EEEeecccccccCCCCCcccceEEEEeecCCCceEEEeecccccchhhHHHHHHHHHHHHHHHHcCcceeeeecccHHHH
Q 010003 60 KMFFKGMSITEVGESSSGFSGIGVVMERSFNIPIMQVQKKLDFFVEESVADYLALMDGLITAVQNKIRCVYAFTDSELLY 139 (520)
Q Consensus 60 ~~~fdG~~~~~~~~~n~~~ag~g~~i~~~~~~~~~~~~~~~~~~~tnn~AE~~ALi~~l~~a~~~~i~~v~i~~Dselv~ 139 (520)
.+||||++. . +.+.+|+|+++.++.+...+...... ...|++.||+.||+.||..+...+.+.+.+++||+.++
T Consensus 1 ~~~~Dgs~~---~--~~~~~g~g~v~~~~~~~~~~~~~~~~-~~~s~~~aEl~al~~al~~~~~~~~~~i~i~~Ds~~~~ 74 (130)
T cd06222 1 VIYTDGSCR---G--NPGPAGAGVVLRDPGGEVLLSGGLLG-GNTTNNRAELLALIEALELALELGGKKVNIYTDSQYVI 74 (130)
T ss_pred CEEecccCC---C--CCCceEEEEEEEeCCCeEEEeccccC-CCCcHHHHHHHHHHHHHHHHHhCCCceEEEEECHHHHH
Confidence 389999997 4 45789999999998777655555544 34499999999999999999999999999999999999
Q ss_pred HHhhhhhhcchhHHHHHHHHHHHHhhhhhhHHhhcccc----cccccHHHHHHHh
Q 010003 140 DQITREEKLDIPLLVALRQRILEYTSNLEAFVLKLVPS----IELERPLRLAQIA 190 (520)
Q Consensus 140 ~ql~g~~~~~~~~L~~l~~ril~l~~~f~~~~l~lvpr----~~~~~a~klA~~A 190 (520)
+++++.+....+.+..+...+..+...+..+.+.++++ ..+..|+.+|+.+
T Consensus 75 ~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~~ 129 (130)
T cd06222 75 NALTGWYEGKPVKNVDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKEA 129 (130)
T ss_pred HHhhccccCCChhhHHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHhh
Confidence 99999877666677888888888877788889999999 8999999998875
No 12
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=99.38 E-value=1.5e-12 Score=118.66 Aligned_cols=128 Identities=20% Similarity=0.217 Sum_probs=93.8
Q ss_pred eEEEEeecccccccCCCCCcccceEEEEeecCCCceEEEeecccccchhhHHHHHHHHHHHHHHHHcCcceeeeecccHH
Q 010003 58 SVKMFFKGMSITEVGESSSGFSGIGVVMERSFNIPIMQVQKKLDFFVEESVADYLALMDGLITAVQNKIRCVYAFTDSEL 137 (520)
Q Consensus 58 ~~~~~fdG~~~~~~~~~n~~~ag~g~~i~~~~~~~~~~~~~~~~~~~tnn~AE~~ALi~~l~~a~~~~i~~v~i~~Dsel 137 (520)
.++||+||+++ + ||+.+|+|+++...++ . ...+..... .|||.||++|++.+|..+.. ...|.|++||++
T Consensus 3 ~v~iytDGs~~---~--n~~~~g~g~v~~~~~~-~-~~~~~~~~~-~TN~~aEL~Ai~~AL~~~~~--~~~v~I~tDS~y 72 (150)
T PRK00203 3 QVEIYTDGACL---G--NPGPGGWGAILRYKGH-E-KELSGGEAL-TTNNRMELMAAIEALEALKE--PCEVTLYTDSQY 72 (150)
T ss_pred eEEEEEEeccc---C--CCCceEEEEEEEECCe-e-EEEecCCCC-CcHHHHHHHHHHHHHHHcCC--CCeEEEEECHHH
Confidence 48899999999 6 8889999999987433 2 345554443 49999999999999997643 357999999999
Q ss_pred HHHHhhh--------hhhcc--hhH-HHHHHHHHHHHhhhhhhHHhhccc----ccccccHHHHHHHhhccCCC
Q 010003 138 LYDQITR--------EEKLD--IPL-LVALRQRILEYTSNLEAFVLKLVP----SIELERPLRLAQIAVGIVSS 196 (520)
Q Consensus 138 v~~ql~g--------~~~~~--~~~-L~~l~~ril~l~~~f~~~~l~lvp----r~~~~~a~klA~~Ai~~~~~ 196 (520)
+++.|++ +|+.. .|. -.++.+++..++.. ..+.+.||| ...|+.||+||+.++.....
T Consensus 73 vi~~i~~w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~~-~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~~~~ 145 (150)
T PRK00203 73 VRQGITEWIHGWKKNGWKTADKKPVKNVDLWQRLDAALKR-HQIKWHWVKGHAGHPENERCDELARAGAEEATL 145 (150)
T ss_pred HHHHHHHHHHHHHHcCCcccCCCccccHHHHHHHHHHhcc-CceEEEEecCCCCCHHHHHHHHHHHHHHHHhhh
Confidence 9999986 23221 111 23556666665554 456788888 56689999999998765543
No 13
>PF00075 RNase_H: RNase H; InterPro: IPR002156 The RNase H domain is responsible for hydrolysis of the RNA portion of RNA x DNA hybrids, and this activity requires the presence of divalent cations (Mg2+ or Mn2+) that bind its active site. This domain is a part of a large family of homologous RNase H enzymes of which the RNase HI protein from Escherichia coli is the best characterised []. Secondary structure predictions for the enzymes from E. coli, yeast, human liver and diverse retroviruses (such as Rous sarcoma virus and the Foamy viruses) supported, in every case, the five beta-strands (1 to 5) and four or five alpha-helices (A, B/C, D, E) that have been identified by crystallography in the RNase H domain of Human immunodeficiency virus 1 (HIV-1) reverse transcriptase and in E. coli RNase H []. Reverse transcriptase (RT) is a modular enzyme carrying polymerase and ribonuclease H (RNase H) activities in separable domains. Reverse transcriptase (RT) converts the single-stranded RNA genome of a retrovirus into a double-stranded DNA copy for integration into the host genome. This process requires ribonuclease H as well as RNA- and DNA-directed DNA polymerase activities. Retroviral RNase H is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. Bacterial RNase H 3.1.26.4 from EC catalyses endonucleolytic cleavage to 5'-phosphomonoester acting on RNA-DNA hybrids. The 3D structure of the RNase H domain from diverse bacteria and retroviruses has been solved [, , ]. All have four beta strands and four to five alpha helices. The E. coli RNase H1 protein binds a single Mg2+ ion cofactor in the active site of the enzyme. The divalent cation is bound by the carboxyl groups of four acidic residues, Asp-10, Glu-48, Asp-70, and Asp-134 []. The first three acidic residues are highly conserved in all bacterial and retroviral RNase H sequences. ; GO: 0003676 nucleic acid binding, 0004523 ribonuclease H activity; PDB: 3LP3_B 2KW4_A 3P1G_A 1RIL_A 2RPI_A 4EQJ_G 4EP2_B 3OTY_P 3U3G_D 2ZQB_D ....
Probab=99.11 E-value=1.3e-10 Score=102.91 Aligned_cols=119 Identities=23% Similarity=0.257 Sum_probs=86.1
Q ss_pred eEEEEeecccccccCCCCCcccceEEEEeecCCCceEEEeecccccchhhHHHHHHHHHHHHHHHHcCcceeeeecccHH
Q 010003 58 SVKMFFKGMSITEVGESSSGFSGIGVVMERSFNIPIMQVQKKLDFFVEESVADYLALMDGLITAVQNKIRCVYAFTDSEL 137 (520)
Q Consensus 58 ~~~~~fdG~~~~~~~~~n~~~ag~g~~i~~~~~~~~~~~~~~~~~~~tnn~AE~~ALi~~l~~a~~~~i~~v~i~~Dsel 137 (520)
.+.+|+||+++ . +++.+|+|+++.. + ...+..++ ..||+.||+.|++.+|. ++ .. +.+.|++||..
T Consensus 3 ~~~iytDgS~~---~--~~~~~~~g~v~~~--~---~~~~~~~~-~~s~~~aEl~Ai~~AL~-~~-~~-~~v~I~tDS~~ 68 (132)
T PF00075_consen 3 AIIIYTDGSCR---P--NPGKGGAGYVVWG--G---RNFSFRLG-GQSNNRAELQAIIEALK-AL-EH-RKVTIYTDSQY 68 (132)
T ss_dssp SEEEEEEEEEC---T--TTTEEEEEEEEET--T---EEEEEEEE-SECHHHHHHHHHHHHHH-TH-ST-SEEEEEES-HH
T ss_pred cEEEEEeCCcc---C--CCCceEEEEEEEC--C---eEEEeccc-ccchhhhheehHHHHHH-Hh-hc-ccccccccHHH
Confidence 47899999998 5 6777899996633 3 25556666 56999999999999999 66 33 89999999999
Q ss_pred HHHHhhh-----hhhcchhHHHHHHHHHHHHhhhhhhHHhhccccc-----ccccHHHHHHHhh
Q 010003 138 LYDQITR-----EEKLDIPLLVALRQRILEYTSNLEAFVLKLVPSI-----ELERPLRLAQIAV 191 (520)
Q Consensus 138 v~~ql~g-----~~~~~~~~L~~l~~ril~l~~~f~~~~l~lvpr~-----~~~~a~klA~~Ai 191 (520)
+++.++. .++.... ..++..++.++......+.+.|||.. .|+.||+||+.+.
T Consensus 69 v~~~l~~~~~~~~~~~~~~-~~~i~~~i~~~~~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~ 131 (132)
T PF00075_consen 69 VLNALNKWLHGNGWKKTSN-GRPIKNEIWELLSRGIKVRFRWVPGHSGVPQGNERADRLAKEAA 131 (132)
T ss_dssp HHHHHHTHHHHTTSBSCTS-SSBHTHHHHHHHHHSSEEEEEESSSSSSSHHHHHHHHHHHHHHH
T ss_pred HHHHHHHhccccccccccc-cccchhheeeccccceEEeeeeccCcCCCchhHHHHHHHHHHhc
Confidence 9998887 4443221 11233455555555556778899986 5667899998874
No 14
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=99.00 E-value=4.2e-10 Score=92.03 Aligned_cols=85 Identities=25% Similarity=0.209 Sum_probs=73.7
Q ss_pred hhHHHHHHHHHHHHHHHHcCcceeeeecccHHHHHHhhhhhhcchhHHHHHHHHHHHHhhhhhhHHhhcccccccccHHH
Q 010003 106 ESVADYLALMDGLITAVQNKIRCVYAFTDSELLYDQITREEKLDIPLLVALRQRILEYTSNLEAFVLKLVPSIELERPLR 185 (520)
Q Consensus 106 nn~AE~~ALi~~l~~a~~~~i~~v~i~~Dselv~~ql~g~~~~~~~~L~~l~~ril~l~~~f~~~~l~lvpr~~~~~a~k 185 (520)
+++||+.||+.||..|.++|+++|.+.+||..+++++++...... .+..+.+.+..+.+.|..+.+.+++|..|..|+.
T Consensus 1 ~~~aE~~al~~al~~a~~~g~~~i~v~sDs~~vv~~i~~~~~~~~-~~~~~~~~i~~~~~~~~~~~~~~i~r~~N~~A~~ 79 (87)
T PF13456_consen 1 PLEAEALALLEALQLAWELGIRKIIVESDSQLVVDAINGRSSSRS-ELRPLIQDIRSLLDRFWNVSVSHIPREQNKVADA 79 (87)
T ss_dssp HHHHHHHHHHHHHHHHHCCT-SCEEEEES-HHHHHHHTTSS---S-CCHHHHHHHHHHHCCCSCEEEEE--GGGSHHHHH
T ss_pred CcHHHHHHHHHHHHHHHHCCCCEEEEEecCccccccccccccccc-cccccchhhhhhhccccceEEEEEChHHhHHHHH
Confidence 468999999999999999999999999999999999999987776 7889999999999999999999999999999999
Q ss_pred HHHHhh
Q 010003 186 LAQIAV 191 (520)
Q Consensus 186 lA~~Ai 191 (520)
||+.+.
T Consensus 80 LA~~a~ 85 (87)
T PF13456_consen 80 LAKFAL 85 (87)
T ss_dssp HHHHHH
T ss_pred HHHHHh
Confidence 999874
No 15
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=98.91 E-value=1.6e-09 Score=83.64 Aligned_cols=62 Identities=37% Similarity=0.782 Sum_probs=49.6
Q ss_pred HHHHHHHHHhhcC-CCceeccCCCCCeeecCcccccccccCCCCCCCCceeCCCCCcceeccCCCccCCCCCc
Q 010003 275 SLETALAEANILH-SDRIYCPFPNCSVLLDPRECLSARASSSSQSDNSCVECPVCERFICVECGVPWHSSLSC 346 (520)
Q Consensus 275 ~~~~~~~e~~~~~-~~~~~CP~p~C~~~~~~~~~~~~~~~~~~~~~~~~~~Cp~C~~~fC~~C~~~wH~~~tC 346 (520)
+|++++.+..+.. ++++|||+|+|+.++..... .....+.|+.|+..||+.|+.+||.+.+|
T Consensus 2 ~y~~~~~~~~i~~~~~~~~CP~~~C~~~~~~~~~----------~~~~~v~C~~C~~~fC~~C~~~~H~~~~C 64 (64)
T smart00647 2 KYERLLLESYVESNPDLKWCPAPDCSAAIIVTEE----------EGCNRVTCPKCGFSFCFRCKVPWHSPVSC 64 (64)
T ss_pred hHHHHHHHHHHhcCCCccCCCCCCCcceEEecCC----------CCCCeeECCCCCCeECCCCCCcCCCCCCC
Confidence 6777777777764 68899999999988865420 12234899999999999999999999987
No 16
>PF01485 IBR: IBR domain; InterPro: IPR002867 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 cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=98.82 E-value=1.2e-09 Score=84.29 Aligned_cols=62 Identities=26% Similarity=0.809 Sum_probs=36.6
Q ss_pred HHHHHHHHHhhc-CCCceeccCCCCCeeecCcccccccccCCCCCCCCceeCCCCCcceeccCCCccCCCCCc
Q 010003 275 SLETALAEANIL-HSDRIYCPFPNCSVLLDPRECLSARASSSSQSDNSCVECPVCERFICVECGVPWHSSLSC 346 (520)
Q Consensus 275 ~~~~~~~e~~~~-~~~~~~CP~p~C~~~~~~~~~~~~~~~~~~~~~~~~~~Cp~C~~~fC~~C~~~wH~~~tC 346 (520)
+|.+++.+..+. .++++|||+|+|+.++...... ....+.|+.|++.||+.|+.+||.+.+|
T Consensus 2 ky~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~----------~~~~~~C~~C~~~fC~~C~~~~H~~~~C 64 (64)
T PF01485_consen 2 KYQKFLLKRYLESDPNIRWCPNPDCEYIIEKDDGC----------NSPIVTCPSCGTEFCFKCGEPWHEGVTC 64 (64)
T ss_dssp CHHHCCCHS---S---CC--TTSST---ECS-SST----------TS--CCTTSCCSEECSSSTSESCTTS-H
T ss_pred hHHHHHHHHHHHCCCCccCCCCCCCcccEEecCCC----------CCCeeECCCCCCcCccccCcccCCCCCC
Confidence 445544444443 4566899999999998775432 1113889999999999999999999887
No 17
>KOG3752 consensus Ribonuclease H [Replication, recombination and repair]
Probab=98.68 E-value=4.1e-08 Score=99.00 Aligned_cols=81 Identities=23% Similarity=0.245 Sum_probs=69.8
Q ss_pred eEEEEeecccccccCCCCCc-ccceEEEEeecCCCceEEEeeccc-ccchhhHHHHHHHHHHHHHHHHcCcceeeeeccc
Q 010003 58 SVKMFFKGMSITEVGESSSG-FSGIGVVMERSFNIPIMQVQKKLD-FFVEESVADYLALMDGLITAVQNKIRCVYAFTDS 135 (520)
Q Consensus 58 ~~~~~fdG~~~~~~~~~n~~-~ag~g~~i~~~~~~~~~~~~~~~~-~~~tnn~AE~~ALi~~l~~a~~~~i~~v~i~~Ds 135 (520)
...||+||.+. +++.++ .||+||-+-+ |.. ...+.++. +.+|||.||+.|.+.+|..|++..+..|.|.|||
T Consensus 212 ~~vvytDGS~~---~ng~~~~~AGyGvywg~--~~e-~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~~~~kv~I~TDS 285 (371)
T KOG3752|consen 212 IQVVYTDGSSS---GNGRKSSRAGYGVYWGP--GHE-LNVSGPLAGGRQTNNRAELIAAIEALKKARSKNINKVVIRTDS 285 (371)
T ss_pred ceEEEecCccc---cCCCCCCcceeEEeeCC--CCc-ccccccCCCCcccccHHHHHHHHHHHHHHHhcCCCcEEEEech
Confidence 37799999999 766674 4999988766 343 57788876 7889999999999999999999999999999999
Q ss_pred HHHHHHhhh
Q 010003 136 ELLYDQITR 144 (520)
Q Consensus 136 elv~~ql~g 144 (520)
+++++.|+.
T Consensus 286 ~~~i~~l~~ 294 (371)
T KOG3752|consen 286 EYFINSLTL 294 (371)
T ss_pred HHHHHHHHH
Confidence 999998874
No 18
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.34 E-value=1.9e-07 Score=65.72 Aligned_cols=41 Identities=27% Similarity=0.790 Sum_probs=28.7
Q ss_pred ccccccccCCCCeeeccCCCcccHHHHHHHHHHhhhCCCCccccCC
Q 010003 207 CSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQ 252 (520)
Q Consensus 207 C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~ 252 (520)
|+||++.+..+ ++++|||.||..|+.++++..-. ..+.||.
T Consensus 1 CpiC~~~~~~P--v~l~CGH~FC~~Cl~~~~~~~~~---~~~~CP~ 41 (42)
T PF15227_consen 1 CPICLDLFKDP--VSLPCGHSFCRSCLERLWKEPSG---SGFSCPE 41 (42)
T ss_dssp ETTTTSB-SSE--EE-SSSSEEEHHHHHHHHCCSSS---ST---SS
T ss_pred CCccchhhCCc--cccCCcCHHHHHHHHHHHHccCC---cCCCCcC
Confidence 89999988655 88999999999999999864322 1277987
No 19
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=98.25 E-value=1.4e-06 Score=67.11 Aligned_cols=44 Identities=32% Similarity=0.881 Sum_probs=38.4
Q ss_pred HhccCCccCc--cccceeeecC--CcceEEe-cccccccccccccccCC
Q 010003 368 AQNKRWRRCQ--QCRRMIELTH--GCYHMTC-WCGHEFCYSCGAEYRDG 411 (520)
Q Consensus 368 ~~~~~~k~CP--~C~~~IeK~~--GCnhMtC-~Cg~~FCy~C~~~~~~~ 411 (520)
..+..++.|| +|+..|+..+ |.++|+| .|++.|||.|+.+|+.+
T Consensus 13 ~~~~~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H~~ 61 (64)
T smart00647 13 ESNPDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWHSP 61 (64)
T ss_pred hcCCCccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcCCCC
Confidence 3446789999 9999999975 9999999 69999999999999753
No 20
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=98.17 E-value=1.1e-06 Score=62.57 Aligned_cols=40 Identities=25% Similarity=0.752 Sum_probs=32.8
Q ss_pred cccccccccC-CCCeeeccCCCcccHHHHHHHHHHhhhCCCCccccCC
Q 010003 206 NCSICCEDKP-YPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQ 252 (520)
Q Consensus 206 ~C~IC~e~~~-~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~ 252 (520)
+|+||++++. ...++.++|+|.||.+|+..|++.. .+||.
T Consensus 2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~-------~~CP~ 42 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRN-------NSCPV 42 (44)
T ss_dssp CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHS-------SB-TT
T ss_pred CCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhC-------CcCCc
Confidence 6999999985 4566777999999999999999763 27987
No 21
>PF01485 IBR: IBR domain; InterPro: IPR002867 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 cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=98.14 E-value=6.8e-07 Score=68.80 Aligned_cols=43 Identities=40% Similarity=1.066 Sum_probs=30.6
Q ss_pred hccCCccCcc--ccceeeecCCcce--EEec-ccccccccccccccCC
Q 010003 369 QNKRWRRCQQ--CRRMIELTHGCYH--MTCW-CGHEFCYSCGAEYRDG 411 (520)
Q Consensus 369 ~~~~~k~CP~--C~~~IeK~~GCnh--MtC~-Cg~~FCy~C~~~~~~~ 411 (520)
.+..++.||+ |...|.+..|.++ |+|. |++.|||.|+.+|+.+
T Consensus 14 ~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~~ 61 (64)
T PF01485_consen 14 SDPNIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPWHEG 61 (64)
T ss_dssp S---CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSESCTT
T ss_pred CCCCccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCcccCCC
Confidence 3344589988 9999999999999 9998 9999999999999653
No 22
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.12 E-value=1.4e-06 Score=78.96 Aligned_cols=56 Identities=25% Similarity=0.713 Sum_probs=43.7
Q ss_pred CccccccccccccCCCCeeeccCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCcccchHHHhh
Q 010003 202 KSPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTVECKS 266 (520)
Q Consensus 202 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~~i~~ 266 (520)
...+.|+||++.+.....++..|||.||..|++..+... -+||. |...|...++..
T Consensus 129 ~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~-------~~CP~--C~kkIt~k~~~r 184 (187)
T KOG0320|consen 129 EGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNT-------NKCPT--CRKKITHKQFHR 184 (187)
T ss_pred ccccCCCceecchhhccccccccchhHHHHHHHHHHHhC-------CCCCC--cccccchhhhee
Confidence 456999999999876555778999999999999988754 36999 666776655443
No 23
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=98.08 E-value=2.3e-06 Score=59.20 Aligned_cols=38 Identities=29% Similarity=0.954 Sum_probs=29.0
Q ss_pred ccccccccCCCCeeeccCCCcccHHHHHHHHHHhhhCCCCccccCC
Q 010003 207 CSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQ 252 (520)
Q Consensus 207 C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~ 252 (520)
|+||++.... ..+.++|||.||.+|+.+|++.. .+||.
T Consensus 1 C~iC~~~~~~-~~~~~~CGH~fC~~C~~~~~~~~-------~~CP~ 38 (39)
T PF13923_consen 1 CPICLDELRD-PVVVTPCGHSFCKECIEKYLEKN-------PKCPV 38 (39)
T ss_dssp ETTTTSB-SS-EEEECTTSEEEEHHHHHHHHHCT-------SB-TT
T ss_pred CCCCCCcccC-cCEECCCCCchhHHHHHHHHHCc-------CCCcC
Confidence 8999987764 33567999999999999998852 47886
No 24
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 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 C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=98.05 E-value=3.6e-06 Score=58.85 Aligned_cols=40 Identities=35% Similarity=1.021 Sum_probs=32.0
Q ss_pred ccccccccCCCCeeeccCCCcccHHHHHHHHHHhhhCCCCccccCC
Q 010003 207 CSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQ 252 (520)
Q Consensus 207 C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~ 252 (520)
|+||++.+..+. +.++|+|.||..|+.++++. ...++||.
T Consensus 1 C~iC~~~~~~~~-~~~~C~H~fC~~C~~~~~~~-----~~~~~CP~ 40 (41)
T PF00097_consen 1 CPICLEPFEDPV-ILLPCGHSFCRDCLRKWLEN-----SGSVKCPL 40 (41)
T ss_dssp ETTTSSBCSSEE-EETTTSEEEEHHHHHHHHHH-----TSSSBTTT
T ss_pred CCcCCccccCCC-EEecCCCcchHHHHHHHHHh-----cCCccCCc
Confidence 899999876542 35799999999999999997 22457986
No 25
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.02 E-value=4.4e-06 Score=77.76 Aligned_cols=62 Identities=24% Similarity=0.600 Sum_probs=45.9
Q ss_pred ccccccccccccCCCCeeeccCCCcccHHHHHHHHHHhhh---------CCCCccccCCCCcCcccchHHHhhcC
Q 010003 203 SPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQ---------SSQVPIRCPQLRCKYFISTVECKSFL 268 (520)
Q Consensus 203 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~---------~~~~~i~CP~~~C~~~l~~~~i~~~L 268 (520)
..++|+||++....+ +.+.|||.||..|+..|+...-. ....+.+||. |+..++...+..+.
T Consensus 17 ~~~~CpICld~~~dP--VvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPv--CR~~Is~~~LvPiy 87 (193)
T PLN03208 17 GDFDCNICLDQVRDP--VVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPV--CKSDVSEATLVPIY 87 (193)
T ss_pred CccCCccCCCcCCCc--EEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCC--CCCcCChhcEEEee
Confidence 468999999987544 55799999999999999764211 1223568999 99999876665544
No 26
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=97.81 E-value=1.8e-05 Score=56.32 Aligned_cols=42 Identities=29% Similarity=0.827 Sum_probs=32.8
Q ss_pred cccccccccCCC-CeeeccCCCcccHHHHHHHHHHhhhCCCCccccCCCCcC
Q 010003 206 NCSICCEDKPYP-MMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCK 256 (520)
Q Consensus 206 ~C~IC~e~~~~~-~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~ 256 (520)
.|+||++.+... ..+.++|||.||..|+.... ...+.||. |+
T Consensus 1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~-------~~~~~CP~--C~ 43 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLK-------GKSVKCPI--CR 43 (44)
T ss_pred CCcCcCccccCCCCeEEcccCCHHHHHHHHhhc-------CCCCCCcC--CC
Confidence 499999999433 44556999999999999887 33568998 65
No 27
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=97.78 E-value=2.9e-05 Score=54.62 Aligned_cols=44 Identities=27% Similarity=0.807 Sum_probs=32.8
Q ss_pred cccccccccCCCCeeeccCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCcc
Q 010003 206 NCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYF 258 (520)
Q Consensus 206 ~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~ 258 (520)
+|+||++.+. ..+...+|+|.||..|+..|++. ...+||. |+..
T Consensus 1 ~C~iC~~~~~-~~~~~~~C~H~~c~~C~~~~~~~------~~~~Cp~--C~~~ 44 (45)
T cd00162 1 ECPICLEEFR-EPVVLLPCGHVFCRSCIDKWLKS------GKNTCPL--CRTP 44 (45)
T ss_pred CCCcCchhhh-CceEecCCCChhcHHHHHHHHHh------CcCCCCC--CCCc
Confidence 5999998872 23333469999999999999875 2357987 7654
No 28
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=97.67 E-value=4.1e-05 Score=56.04 Aligned_cols=46 Identities=30% Similarity=0.830 Sum_probs=35.2
Q ss_pred cccccccccccCCCCeeeccCCCc-ccHHHHHHHHHHhhhCCCCccccCCCCcCcccc
Q 010003 204 PENCSICCEDKPYPMMITMKCSHK-FCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFIS 260 (520)
Q Consensus 204 ~~~C~IC~e~~~~~~~~~l~CgH~-fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~ 260 (520)
...|.||++... +.+.++|||. ||..|+.+++. ...+||. |+..+.
T Consensus 2 ~~~C~iC~~~~~--~~~~~pCgH~~~C~~C~~~~~~-------~~~~CP~--Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFENPR--DVVLLPCGHLCFCEECAERLLK-------RKKKCPI--CRQPIE 48 (50)
T ss_dssp HSB-TTTSSSBS--SEEEETTCEEEEEHHHHHHHHH-------TTSBBTT--TTBB-S
T ss_pred cCCCccCCccCC--ceEEeCCCChHHHHHHhHHhcc-------cCCCCCc--CChhhc
Confidence 468999998754 4566699999 99999999988 2347998 888764
No 29
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=97.62 E-value=5.3e-05 Score=53.44 Aligned_cols=41 Identities=27% Similarity=0.732 Sum_probs=22.0
Q ss_pred ccccccccCCC-C-eeeccCCCcccHHHHHHHHHHhhhCCCCccccC
Q 010003 207 CSICCEDKPYP-M-MITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCP 251 (520)
Q Consensus 207 C~IC~e~~~~~-~-~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP 251 (520)
|+||.+ +..+ + -..|+|||.||++|+++...... ...++||
T Consensus 1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~~---~~~~kCP 43 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKSD---RNRFKCP 43 (43)
T ss_dssp -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH-S----S-B--T
T ss_pred CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcCC---CCeeeCc
Confidence 899999 6442 2 24469999999999999988543 2367887
No 30
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.48 E-value=5.6e-05 Score=79.19 Aligned_cols=59 Identities=27% Similarity=0.661 Sum_probs=46.0
Q ss_pred cccccccccccCCCCeeeccCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCcccchHHHhhcC
Q 010003 204 PENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTVECKSFL 268 (520)
Q Consensus 204 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~L 268 (520)
...|+||++..+.+.+ +.|||.||..|+-+|+..... ..+.+||. |...|...+++.+.
T Consensus 186 ~~~CPICL~~~~~p~~--t~CGHiFC~~CiLqy~~~s~~--~~~~~CPi--C~s~I~~kdl~pv~ 244 (513)
T KOG2164|consen 186 DMQCPICLEPPSVPVR--TNCGHIFCGPCILQYWNYSAI--KGPCSCPI--CRSTITLKDLLPVF 244 (513)
T ss_pred CCcCCcccCCCCcccc--cccCceeeHHHHHHHHhhhcc--cCCccCCc--hhhhccccceeeee
Confidence 6889999998876643 469999999999999997721 22568999 99888876665544
No 31
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=97.47 E-value=0.00011 Score=49.64 Aligned_cols=38 Identities=32% Similarity=0.893 Sum_probs=29.1
Q ss_pred ccccccccCCCCeeeccCCCcccHHHHHHHHHHhhhCCCCccccCC
Q 010003 207 CSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQ 252 (520)
Q Consensus 207 C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~ 252 (520)
|+||++.. ...+.++|+|.||..|+..|+. ....+||.
T Consensus 1 C~iC~~~~--~~~~~~~C~H~~c~~C~~~~~~------~~~~~CP~ 38 (39)
T smart00184 1 CPICLEEL--KDPVVLPCGHTFCRSCIRKWLK------SGNNTCPI 38 (39)
T ss_pred CCcCccCC--CCcEEecCCChHHHHHHHHHHH------hCcCCCCC
Confidence 78999873 3446679999999999999987 11346875
No 32
>PHA02926 zinc finger-like protein; Provisional
Probab=97.45 E-value=0.00011 Score=69.32 Aligned_cols=56 Identities=21% Similarity=0.571 Sum_probs=39.0
Q ss_pred CccccccccccccC-----CCCeee-c-cCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCcccc
Q 010003 202 KSPENCSICCEDKP-----YPMMIT-M-KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFIS 260 (520)
Q Consensus 202 ~~~~~C~IC~e~~~-----~~~~~~-l-~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~ 260 (520)
....+|+||++..- .+..+. + +|+|.||..|++.|....- +.+..-.||. |+..+.
T Consensus 168 SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~-~~~~~rsCPi--CR~~f~ 230 (242)
T PHA02926 168 SKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRR-ETGASDNCPI--CRTRFR 230 (242)
T ss_pred cCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhcc-ccCcCCcCCC--Ccceee
Confidence 34689999998752 222222 3 9999999999999998653 2222346999 887643
No 33
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.43 E-value=0.00017 Score=72.51 Aligned_cols=108 Identities=23% Similarity=0.506 Sum_probs=67.1
Q ss_pred CccccccccccccCCCCeeeccCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCcccchHHHhhcCCcccHHHHHHHHH
Q 010003 202 KSPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTVECKSFLPLSSYESLETALA 281 (520)
Q Consensus 202 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~L~~~~~e~~~~~~~ 281 (520)
....+|+||++.+..+ ..++|+|.||..|+...+. ..+.||. |.. ... .+.+......+...+.
T Consensus 11 ~~~~~C~iC~~~~~~p--~~l~C~H~~c~~C~~~~~~-------~~~~Cp~--cr~-~~~----~~~~n~~l~~~~~~~~ 74 (386)
T KOG2177|consen 11 QEELTCPICLEYFREP--VLLPCGHNFCRACLTRSWE-------GPLSCPV--CRP-PSR----NLRPNVLLANLVERLR 74 (386)
T ss_pred cccccChhhHHHhhcC--ccccccchHhHHHHHHhcC-------CCcCCcc--cCC-chh----ccCccHHHHHHHHHHH
Confidence 3578999999999877 5569999999999999988 3578999 773 221 2222223333333332
Q ss_pred HHhhcCC-C--ceeccCCCCCeeecCcccccccccCCCCCCCCceeCCCCCcceeccCC-CccCCCCCc
Q 010003 282 EANILHS-D--RIYCPFPNCSVLLDPRECLSARASSSSQSDNSCVECPVCERFICVECG-VPWHSSLSC 346 (520)
Q Consensus 282 e~~~~~~-~--~~~CP~p~C~~~~~~~~~~~~~~~~~~~~~~~~~~Cp~C~~~fC~~C~-~~wH~~~tC 346 (520)
....... . ...|+... ....+.|..|....|..|. ...|..+.-
T Consensus 75 ~~~~~~~~~~~~~~c~~~~---------------------~~~~~~c~~~~~~~c~~c~~~~~h~~h~~ 122 (386)
T KOG2177|consen 75 QLRLSRPLGSKEELCEKHG---------------------EELKLFCEEDEKLLCVLCRESGEHRGHPV 122 (386)
T ss_pred hcCCcccccccchhhhhcC---------------------CcceEEecccccccCCCCCCcccccCCcc
Confidence 2221110 0 01232200 0123789999999999998 667777653
No 34
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.43 E-value=7.2e-05 Score=71.01 Aligned_cols=60 Identities=27% Similarity=0.598 Sum_probs=46.5
Q ss_pred CCccccccccccccCCCCeeeccCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCcccchHHHhhcC
Q 010003 201 DKSPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTVECKSFL 268 (520)
Q Consensus 201 ~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~L 268 (520)
+...++|.||+|....+ +...|||.||-.||-+|+...... -.||. |+..++.+.+-.+.
T Consensus 44 ~~~~FdCNICLd~akdP--VvTlCGHLFCWpClyqWl~~~~~~----~~cPV--CK~~Vs~~~vvPlY 103 (230)
T KOG0823|consen 44 DGGFFDCNICLDLAKDP--VVTLCGHLFCWPCLYQWLQTRPNS----KECPV--CKAEVSIDTVVPLY 103 (230)
T ss_pred CCCceeeeeeccccCCC--EEeecccceehHHHHHHHhhcCCC----eeCCc--cccccccceEEeee
Confidence 46789999999987544 556999999999999999866532 24788 99888876655443
No 35
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=97.34 E-value=0.00027 Score=54.10 Aligned_cols=49 Identities=10% Similarity=0.139 Sum_probs=38.6
Q ss_pred ccccccccccCCCCeeeccCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCcccchHHH
Q 010003 205 ENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTVEC 264 (520)
Q Consensus 205 ~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~~i 264 (520)
+.|+||.+....+ +.++|||.||+.|+.+|+.. ...||. |+..++.+.+
T Consensus 2 ~~Cpi~~~~~~~P--v~~~~G~v~~~~~i~~~~~~-------~~~cP~--~~~~~~~~~l 50 (63)
T smart00504 2 FLCPISLEVMKDP--VILPSGQTYERRAIEKWLLS-------HGTDPV--TGQPLTHEDL 50 (63)
T ss_pred cCCcCCCCcCCCC--EECCCCCEEeHHHHHHHHHH-------CCCCCC--CcCCCChhhc
Confidence 5799999987654 56799999999999999975 236998 7777765443
No 36
>PHA02929 N1R/p28-like protein; Provisional
Probab=97.31 E-value=0.00019 Score=69.75 Aligned_cols=49 Identities=27% Similarity=0.657 Sum_probs=36.6
Q ss_pred ccccccccccccCCCC-----e-eeccCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCcccc
Q 010003 203 SPENCSICCEDKPYPM-----M-ITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFIS 260 (520)
Q Consensus 203 ~~~~C~IC~e~~~~~~-----~-~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~ 260 (520)
...+|+||++.+.... + +..+|+|.||.+|+..|... ...||. |+..+.
T Consensus 173 ~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~-------~~tCPl--CR~~~~ 227 (238)
T PHA02929 173 KDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKE-------KNTCPV--CRTPFI 227 (238)
T ss_pred CCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhc-------CCCCCC--CCCEee
Confidence 4689999999865432 1 23489999999999999763 237999 887654
No 37
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=96.93 E-value=0.00058 Score=66.89 Aligned_cols=51 Identities=27% Similarity=0.777 Sum_probs=40.4
Q ss_pred CccccccccccccCCCCeeeccCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCcccchHH
Q 010003 202 KSPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTVE 263 (520)
Q Consensus 202 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~~ 263 (520)
.....|.+|++....+ ...+|||.||-.|+..|...+- -||. |...+.+..
T Consensus 237 ~a~~kC~LCLe~~~~p--SaTpCGHiFCWsCI~~w~~ek~-------eCPl--CR~~~~psk 287 (293)
T KOG0317|consen 237 EATRKCSLCLENRSNP--SATPCGHIFCWSCILEWCSEKA-------ECPL--CREKFQPSK 287 (293)
T ss_pred CCCCceEEEecCCCCC--CcCcCcchHHHHHHHHHHcccc-------CCCc--ccccCCCcc
Confidence 4568899999987544 4469999999999999998654 2999 888776643
No 38
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=96.89 E-value=0.0013 Score=68.53 Aligned_cols=50 Identities=30% Similarity=0.725 Sum_probs=39.2
Q ss_pred CccccccccccccCCCCeeeccCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCcccchH
Q 010003 202 KSPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTV 262 (520)
Q Consensus 202 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~ 262 (520)
...+.|+||.+.+..+ +.++|+|.||..|+..|+... ..||. |+..+...
T Consensus 24 e~~l~C~IC~d~~~~P--vitpCgH~FCs~CI~~~l~~~-------~~CP~--Cr~~~~~~ 73 (397)
T TIGR00599 24 DTSLRCHICKDFFDVP--VLTSCSHTFCSLCIRRCLSNQ-------PKCPL--CRAEDQES 73 (397)
T ss_pred ccccCCCcCchhhhCc--cCCCCCCchhHHHHHHHHhCC-------CCCCC--CCCccccc
Confidence 3568999999987644 457999999999999998641 26998 88876543
No 39
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=96.84 E-value=0.0011 Score=66.47 Aligned_cols=54 Identities=22% Similarity=0.591 Sum_probs=38.7
Q ss_pred cccccccccc-CCCCeeec--cCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCcccchHHHhh
Q 010003 205 ENCSICCEDK-PYPMMITM--KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTVECKS 266 (520)
Q Consensus 205 ~~C~IC~e~~-~~~~~~~l--~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~~i~~ 266 (520)
..|++|..+. ..+.+..+ .|||.||.+|+...+. .+ +..||. |+..+....++.
T Consensus 4 ~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~----~~--~~~CP~--C~~~lrk~~fr~ 60 (309)
T TIGR00570 4 QGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFV----RG--SGSCPE--CDTPLRKNNFRV 60 (309)
T ss_pred CCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhc----CC--CCCCCC--CCCccchhhccc
Confidence 5799999873 33443212 7999999999999874 12 347997 998887766554
No 40
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=96.74 E-value=0.0006 Score=67.74 Aligned_cols=62 Identities=29% Similarity=0.629 Sum_probs=45.2
Q ss_pred cccccccccccCCCCeeeccCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCcccchHHHhh-cCCcccHHHH
Q 010003 204 PENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTVECKS-FLPLSSYESL 276 (520)
Q Consensus 204 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~~i~~-~L~~~~~e~~ 276 (520)
..-|.||++-+..+ ...+|+|.||.=|++.|+.. ...||. |-..+....+++ .+-.++++.|
T Consensus 23 lLRC~IC~eyf~ip--~itpCsHtfCSlCIR~~L~~-------~p~CP~--C~~~~~Es~Lr~n~il~Eiv~S~ 85 (442)
T KOG0287|consen 23 LLRCGICFEYFNIP--MITPCSHTFCSLCIRKFLSY-------KPQCPT--CCVTVTESDLRNNRILDEIVKSL 85 (442)
T ss_pred HHHHhHHHHHhcCc--eeccccchHHHHHHHHHhcc-------CCCCCc--eecccchhhhhhhhHHHHHHHHH
Confidence 56799999988766 33479999999999999874 347998 887777666654 3333444443
No 41
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=96.72 E-value=0.00049 Score=75.67 Aligned_cols=56 Identities=25% Similarity=0.665 Sum_probs=44.3
Q ss_pred CccccccccccccCCCCeeeccCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCcccchHHHhhc
Q 010003 202 KSPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTVECKSF 267 (520)
Q Consensus 202 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~ 267 (520)
....+|++|.+.. .+++...|+|.||..|++..+++.-. +||. |+..+...+++.+
T Consensus 641 K~~LkCs~Cn~R~--Kd~vI~kC~H~FC~~Cvq~r~etRqR------KCP~--Cn~aFganDv~~I 696 (698)
T KOG0978|consen 641 KELLKCSVCNTRW--KDAVITKCGHVFCEECVQTRYETRQR------KCPK--CNAAFGANDVHRI 696 (698)
T ss_pred HhceeCCCccCch--hhHHHHhcchHHHHHHHHHHHHHhcC------CCCC--CCCCCCccccccc
Confidence 4578999999432 34555699999999999999986643 7998 9999988877654
No 42
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.59 E-value=0.0013 Score=64.60 Aligned_cols=53 Identities=21% Similarity=0.555 Sum_probs=41.8
Q ss_pred CCccccccccccccCCCC-eeeccCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCcccch
Q 010003 201 DKSPENCSICCEDKPYPM-MITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFIST 261 (520)
Q Consensus 201 ~~~~~~C~IC~e~~~~~~-~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~ 261 (520)
+....+|.||++++...+ ...++|.|.|...|+.+|+. .+..+||. |...+++
T Consensus 320 a~~GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~------~y~~~CPv--Crt~iPP 373 (374)
T COG5540 320 ADKGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLL------GYSNKCPV--CRTAIPP 373 (374)
T ss_pred cCCCceEEEEhhhhcccceEEEeccCceechhHHHHHHh------hhcccCCc--cCCCCCC
Confidence 344589999999986544 44569999999999999987 23457999 9988764
No 43
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=96.55 E-value=0.0025 Score=66.85 Aligned_cols=59 Identities=25% Similarity=0.714 Sum_probs=45.5
Q ss_pred CCccccccccccccCCCCeeeccCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCcccchHHHh
Q 010003 201 DKSPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTVECK 265 (520)
Q Consensus 201 ~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~~i~ 265 (520)
+....+|.+|-+.. .+.+...|.|.||+-|++.|+.....+.. +.||. |...++.+.-.
T Consensus 533 nk~~~~C~lc~d~a--ed~i~s~ChH~FCrlCi~eyv~~f~~~~n--vtCP~--C~i~LsiDlse 591 (791)
T KOG1002|consen 533 NKGEVECGLCHDPA--EDYIESSCHHKFCRLCIKEYVESFMENNN--VTCPV--CHIGLSIDLSE 591 (791)
T ss_pred ccCceeecccCChh--hhhHhhhhhHHHHHHHHHHHHHhhhcccC--CCCcc--ccccccccccc
Confidence 45678999998754 34466699999999999999998765433 78999 88777665433
No 44
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.36 E-value=0.0029 Score=64.45 Aligned_cols=47 Identities=34% Similarity=0.742 Sum_probs=38.0
Q ss_pred ccccccccccCCCC-eeeccCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCccc
Q 010003 205 ENCSICCEDKPYPM-MITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFI 259 (520)
Q Consensus 205 ~~C~IC~e~~~~~~-~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l 259 (520)
.+|.||+|+|...+ ...|+|.|.|...|+..|+... .-.||. |+..+
T Consensus 230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~------r~~CPv--CK~di 277 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQT------RTFCPV--CKRDI 277 (348)
T ss_pred ceEEEeecccccCCeeeEecCCCchhhccchhhHhhc------CccCCC--CCCcC
Confidence 79999999998654 4556999999999999999854 124999 77754
No 45
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=96.14 E-value=0.0049 Score=46.33 Aligned_cols=49 Identities=27% Similarity=0.535 Sum_probs=31.0
Q ss_pred CccccccccccccCCCCeeeccCCCcccHHHHHHHHHHhhhCCCCccccCCCCcC
Q 010003 202 KSPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCK 256 (520)
Q Consensus 202 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~ 256 (520)
...+.|+|....+..+ +.+..|+|.|.++.+.+|+ .+...++||..||+
T Consensus 9 ~~~~~CPiT~~~~~~P-V~s~~C~H~fek~aI~~~i-----~~~~~~~CPv~GC~ 57 (57)
T PF11789_consen 9 TISLKCPITLQPFEDP-VKSKKCGHTFEKEAILQYI-----QRNGSKRCPVAGCN 57 (57)
T ss_dssp B--SB-TTTSSB-SSE-EEESSS--EEEHHHHHHHC-----TTTS-EE-SCCC-S
T ss_pred EeccCCCCcCChhhCC-cCcCCCCCeecHHHHHHHH-----HhcCCCCCCCCCCC
Confidence 4568999999876533 4556999999999999999 22346789999995
No 46
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=96.13 E-value=0.0048 Score=48.91 Aligned_cols=42 Identities=33% Similarity=0.747 Sum_probs=29.4
Q ss_pred cccccccccccCCC----------Ceee-ccCCCcccHHHHHHHHHHhhhCCCCccccCC
Q 010003 204 PENCSICCEDKPYP----------MMIT-MKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQ 252 (520)
Q Consensus 204 ~~~C~IC~e~~~~~----------~~~~-l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~ 252 (520)
...|.||++.+... -.+. ..|||.|...||.+|++..- .||.
T Consensus 19 ~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~~-------~CP~ 71 (73)
T PF12678_consen 19 DDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQNN-------TCPL 71 (73)
T ss_dssp CSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTSS-------B-TT
T ss_pred CCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcCC-------cCCC
Confidence 34599999988321 1223 38999999999999986432 6987
No 47
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=95.56 E-value=0.0019 Score=49.11 Aligned_cols=45 Identities=36% Similarity=0.780 Sum_probs=22.0
Q ss_pred cccccccccccCCCCeeec-cCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCcccch
Q 010003 204 PENCSICCEDKPYPMMITM-KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFIST 261 (520)
Q Consensus 204 ~~~C~IC~e~~~~~~~~~l-~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~ 261 (520)
..-|++|.+....+ +.+ .|.|.||..|++..+. -.||. |..+--.
T Consensus 7 lLrCs~C~~~l~~p--v~l~~CeH~fCs~Ci~~~~~---------~~CPv--C~~Paw~ 52 (65)
T PF14835_consen 7 LLRCSICFDILKEP--VCLGGCEHIFCSSCIRDCIG---------SECPV--CHTPAWI 52 (65)
T ss_dssp TTS-SSS-S--SS---B---SSS--B-TTTGGGGTT---------TB-SS--S--B-S-
T ss_pred hcCCcHHHHHhcCC--ceeccCccHHHHHHhHHhcC---------CCCCC--cCChHHH
Confidence 46799999887544 555 9999999999977433 24998 8766443
No 48
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.52 E-value=0.0083 Score=58.23 Aligned_cols=53 Identities=25% Similarity=0.544 Sum_probs=37.5
Q ss_pred ccccccccccccCCCCeeeccCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCcccchHHH
Q 010003 203 SPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTVEC 264 (520)
Q Consensus 203 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~~i 264 (520)
..+.|.||++....+ ...+|||.||..|+-..+..+- .-.||. |.....+..+
T Consensus 214 ~d~kC~lC~e~~~~p--s~t~CgHlFC~~Cl~~~~t~~k-----~~~Cpl--CRak~~pk~v 266 (271)
T COG5574 214 ADYKCFLCLEEPEVP--SCTPCGHLFCLSCLLISWTKKK-----YEFCPL--CRAKVYPKKV 266 (271)
T ss_pred cccceeeeecccCCc--ccccccchhhHHHHHHHHHhhc-----cccCch--hhhhccchhh
Confidence 468899999875433 4469999999999998533221 235998 8877665443
No 49
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=94.92 E-value=0.059 Score=54.62 Aligned_cols=53 Identities=23% Similarity=0.636 Sum_probs=39.0
Q ss_pred Ccccccccccccc-CCC--------Ce--eeccCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCcccchHH
Q 010003 202 KSPENCSICCEDK-PYP--------MM--ITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTVE 263 (520)
Q Consensus 202 ~~~~~C~IC~e~~-~~~--------~~--~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~~ 263 (520)
.....|.||+|+. ..+ ++ -.++|||.+..+|++.|.+.+- .||. |+.++-.++
T Consensus 285 n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERqQ-------TCPI--Cr~p~ifd~ 348 (491)
T COG5243 285 NSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQ-------TCPI--CRRPVIFDQ 348 (491)
T ss_pred CCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhcc-------CCCc--ccCcccccc
Confidence 4578999999993 222 11 3479999999999999998542 6998 888754443
No 50
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=94.59 E-value=0.025 Score=44.40 Aligned_cols=56 Identities=27% Similarity=0.545 Sum_probs=26.5
Q ss_pred cccccccccccC-CCCe--eec---cCCCcccHHHHHHHHHHhhhCC-CC-cc--ccCCCCcCcccch
Q 010003 204 PENCSICCEDKP-YPMM--ITM---KCSHKFCSHCMRTYIDGKVQSS-QV-PI--RCPQLRCKYFIST 261 (520)
Q Consensus 204 ~~~C~IC~e~~~-~~~~--~~l---~CgH~fC~~Cl~~~i~~~i~~~-~~-~i--~CP~~~C~~~l~~ 261 (520)
..+|.||+.... .... +.. .|++.|...||.+|+...-... .+ ++ .||. |+..|+.
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~--C~~~i~~ 67 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPY--CSSPISW 67 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TT--T-SEEEG
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcC--CCCeeeE
Confidence 468999998754 3222 222 6889999999999998765442 22 33 6998 9988764
No 51
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.42 E-value=0.021 Score=56.40 Aligned_cols=52 Identities=25% Similarity=0.673 Sum_probs=40.9
Q ss_pred ccccccccccccCCCCeeeccCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCcccchHHH
Q 010003 203 SPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTVEC 264 (520)
Q Consensus 203 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~~i 264 (520)
..-+|.||+.+-..+ +.+.|+|.||.-|++..+.... ..|+. |...|+.+.+
T Consensus 6 ~~~eC~IC~nt~n~P--v~l~C~HkFCyiCiKGsy~ndk------~~Cav--CR~pids~i~ 57 (324)
T KOG0824|consen 6 KKKECLICYNTGNCP--VNLYCFHKFCYICIKGSYKNDK------KTCAV--CRFPIDSTID 57 (324)
T ss_pred cCCcceeeeccCCcC--ccccccchhhhhhhcchhhcCC------CCCce--ecCCCCcchh
Confidence 467899999887655 7789999999999998766432 25988 9988876543
No 52
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=94.29 E-value=0.033 Score=44.13 Aligned_cols=50 Identities=14% Similarity=0.184 Sum_probs=35.3
Q ss_pred ccccccccccccCCCCeeeccCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCcccchH
Q 010003 203 SPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTV 262 (520)
Q Consensus 203 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~ 262 (520)
..+.|+|+.+-...+ +.+++||.|++.++.+|+.. ....||. |+..++..
T Consensus 3 ~~f~CpIt~~lM~dP--Vi~~~G~tyer~~I~~~l~~------~~~~~P~--t~~~l~~~ 52 (73)
T PF04564_consen 3 DEFLCPITGELMRDP--VILPSGHTYERSAIERWLEQ------NGGTDPF--TRQPLSES 52 (73)
T ss_dssp GGGB-TTTSSB-SSE--EEETTSEEEEHHHHHHHHCT------TSSB-TT--T-SB-SGG
T ss_pred cccCCcCcCcHhhCc--eeCCcCCEEcHHHHHHHHHc------CCCCCCC--CCCcCCcc
Confidence 368999999877655 66799999999999999985 2346988 67777654
No 53
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.16 E-value=0.036 Score=56.91 Aligned_cols=55 Identities=27% Similarity=0.660 Sum_probs=39.5
Q ss_pred CccccccccccccCCCC-----eeec-cCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCcc
Q 010003 202 KSPENCSICCEDKPYPM-----MITM-KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYF 258 (520)
Q Consensus 202 ~~~~~C~IC~e~~~~~~-----~~~l-~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~ 258 (520)
....+|.||++...... +-.+ +|.|.||..|++.|-...-.+....-.||. |...
T Consensus 159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~--CRv~ 219 (344)
T KOG1039|consen 159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPF--CRVP 219 (344)
T ss_pred cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCc--ccCc
Confidence 56799999999865433 2233 799999999999997554334444457998 7754
No 54
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=93.93 E-value=0.025 Score=55.32 Aligned_cols=48 Identities=31% Similarity=0.627 Sum_probs=36.0
Q ss_pred CCccccccccccccCCCCeeeccCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCccc
Q 010003 201 DKSPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFI 259 (520)
Q Consensus 201 ~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l 259 (520)
-....-|-||-+-+..+ ....|||.||.-|++.|+..+ ..||. |....
T Consensus 22 LDs~lrC~IC~~~i~ip--~~TtCgHtFCslCIR~hL~~q-------p~CP~--Cr~~~ 69 (391)
T COG5432 22 LDSMLRCRICDCRISIP--CETTCGHTFCSLCIRRHLGTQ-------PFCPV--CREDP 69 (391)
T ss_pred chhHHHhhhhhheeecc--eecccccchhHHHHHHHhcCC-------CCCcc--ccccH
Confidence 34567899998876544 445999999999999998743 35887 65543
No 55
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=93.82 E-value=0.038 Score=56.91 Aligned_cols=33 Identities=30% Similarity=0.777 Sum_probs=26.7
Q ss_pred ccccccccccccCCCCeeeccCCCcccHHHHHHHH
Q 010003 203 SPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYI 237 (520)
Q Consensus 203 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i 237 (520)
+...|+||-.-+..+ +.++|+|..|+.|.+...
T Consensus 3 eelkc~vc~~f~~ep--iil~c~h~lc~~ca~~~~ 35 (699)
T KOG4367|consen 3 EELKCPVCGSFYREP--IILPCSHNLCQACARNIL 35 (699)
T ss_pred ccccCceehhhccCc--eEeecccHHHHHHHHhhc
Confidence 357899998766544 778999999999998654
No 56
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.06 E-value=0.11 Score=50.93 Aligned_cols=52 Identities=27% Similarity=0.618 Sum_probs=38.7
Q ss_pred CCccccccccccccCCCCeeeccCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCcccc
Q 010003 201 DKSPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFIS 260 (520)
Q Consensus 201 ~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~ 260 (520)
.....+|++|-+.-..+ ++...|+|.||--|+........ .++||. |+....
T Consensus 236 ~t~~~~C~~Cg~~PtiP-~~~~~C~HiyCY~Ci~ts~~~~a-----sf~Cp~--Cg~~~~ 287 (298)
T KOG2879|consen 236 GTSDTECPVCGEPPTIP-HVIGKCGHIYCYYCIATSRLWDA-----SFTCPL--CGENVE 287 (298)
T ss_pred ccCCceeeccCCCCCCC-eeeccccceeehhhhhhhhcchh-----hcccCc--cCCCCc
Confidence 34578999998765433 44557999999999998876543 468998 877654
No 57
>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=92.86 E-value=0.041 Score=34.35 Aligned_cols=23 Identities=26% Similarity=0.759 Sum_probs=15.2
Q ss_pred ccCccccceeeecCCcceEEec-ccccc
Q 010003 374 RRCQQCRRMIELTHGCYHMTCW-CGHEF 400 (520)
Q Consensus 374 k~CP~C~~~IeK~~GCnhMtC~-Cg~~F 400 (520)
|.||.|+..|-.+ -..|+ |||.|
T Consensus 1 K~CP~C~~~V~~~----~~~Cp~CG~~F 24 (26)
T PF10571_consen 1 KTCPECGAEVPES----AKFCPHCGYDF 24 (26)
T ss_pred CcCCCCcCCchhh----cCcCCCCCCCC
Confidence 5788888888543 24554 66665
No 58
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.53 E-value=0.074 Score=54.80 Aligned_cols=44 Identities=20% Similarity=0.560 Sum_probs=37.6
Q ss_pred cCCccCcc--ccceeeecCCcceEEec-ccccccccccccccCCCCcc
Q 010003 371 KRWRRCQQ--CRRMIELTHGCYHMTCW-CGHEFCYSCGAEYRDGQQTC 415 (520)
Q Consensus 371 ~~~k~CP~--C~~~IeK~~GCnhMtC~-Cg~~FCy~C~~~~~~~~~~c 415 (520)
....-||+ |..++-...|++-..|. |.+-||.+|...|+. ...|
T Consensus 271 sdv~yCPr~~Cq~p~~~d~~~~l~~CskCnFaFCtlCk~t~HG-~s~C 317 (445)
T KOG1814|consen 271 SDVVYCPRACCQLPVKQDPGRALAICSKCNFAFCTLCKLTWHG-VSPC 317 (445)
T ss_pred cccccCChhhccCccccCchhhhhhhccCccHHHHHHHHhhcC-CCcc
Confidence 34589998 99999667899999995 999999999999986 3454
No 59
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=91.49 E-value=0.18 Score=58.93 Aligned_cols=67 Identities=27% Similarity=0.547 Sum_probs=52.3
Q ss_pred CccccccccccccC-CCCeeeccCCCcccHHHHHHHHHHhhhCCC--C-ccccCCCCcCcccchHHHhhcCCc
Q 010003 202 KSPENCSICCEDKP-YPMMITMKCSHKFCSHCMRTYIDGKVQSSQ--V-PIRCPQLRCKYFISTVECKSFLPL 270 (520)
Q Consensus 202 ~~~~~C~IC~e~~~-~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~--~-~i~CP~~~C~~~l~~~~i~~~L~~ 270 (520)
...-.|.|||.+.- ....+.+.|+|.|...|.+..++..-.+-. + -|.||. |++.|..-.++.+|++
T Consensus 3484 D~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPi--C~n~InH~~LkDLldP 3554 (3738)
T KOG1428|consen 3484 DADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPI--CKNKINHIVLKDLLDP 3554 (3738)
T ss_pred ccCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeeccc--ccchhhhHHHHHHHHH
Confidence 34567999997743 346688999999999999999887654422 1 378999 9999998888888764
No 60
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=91.44 E-value=0.094 Score=52.66 Aligned_cols=48 Identities=25% Similarity=0.686 Sum_probs=35.0
Q ss_pred CccccccccccccCCCCeeeccCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCccc
Q 010003 202 KSPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFI 259 (520)
Q Consensus 202 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l 259 (520)
....+|.+|-.-+... .....|-|.||+.||-.|++.. ..||. |+..+
T Consensus 13 n~~itC~LC~GYliDA-TTI~eCLHTFCkSCivk~l~~~-------~~CP~--C~i~i 60 (331)
T KOG2660|consen 13 NPHITCRLCGGYLIDA-TTITECLHTFCKSCIVKYLEES-------KYCPT--CDIVI 60 (331)
T ss_pred ccceehhhccceeecc-hhHHHHHHHHHHHHHHHHHHHh-------ccCCc--cceec
Confidence 3578999998655433 2223899999999999999973 26998 65443
No 61
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.18 E-value=0.14 Score=52.64 Aligned_cols=49 Identities=24% Similarity=0.740 Sum_probs=37.9
Q ss_pred cccccccccccCCC---CeeeccCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCccc
Q 010003 204 PENCSICCEDKPYP---MMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFI 259 (520)
Q Consensus 204 ~~~C~IC~e~~~~~---~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l 259 (520)
..+|+||++.+... .++++.|||.|=.+|+++|+- + ....+||. |+..-
T Consensus 4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~-k----~~~~~cp~--c~~ka 55 (463)
T KOG1645|consen 4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLG-K----KTKMQCPL--CSGKA 55 (463)
T ss_pred cccCceeeeeeeecCceEEeeecccccccHHHHHHHHh-h----hhhhhCcc--cCChh
Confidence 36899999987543 567889999999999999993 2 23557998 76543
No 62
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=90.94 E-value=0.14 Score=36.95 Aligned_cols=44 Identities=23% Similarity=0.677 Sum_probs=21.2
Q ss_pred ccccccccCCC--CeeeccCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCcc
Q 010003 207 CSICCEDKPYP--MMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYF 258 (520)
Q Consensus 207 C~IC~e~~~~~--~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~ 258 (520)
|++|.++.... ++....|++.+|+.|+.+-.+. + .=+||. |+..
T Consensus 1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~~---~---~g~CPg--Cr~~ 46 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILEN---E---GGRCPG--CREP 46 (48)
T ss_dssp -TTTS-B--CCCTT--SSTTS----HHHHHHHTTS---S----SB-TT--T--B
T ss_pred CCCcccccccCCCccccCcCCCcHHHHHHHHHHhc---c---CCCCCC--CCCC
Confidence 78898887433 4556699999999999877651 1 126987 7754
No 63
>COG5220 TFB3 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB3 [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]
Probab=90.47 E-value=0.093 Score=50.16 Aligned_cols=51 Identities=24% Similarity=0.694 Sum_probs=38.0
Q ss_pred cccccccccc-cCCCCeeec---cCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCcccc
Q 010003 204 PENCSICCED-KPYPMMITM---KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFIS 260 (520)
Q Consensus 204 ~~~C~IC~e~-~~~~~~~~l---~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~ 260 (520)
...|+||-.+ +-.+++..+ .|-|.+|-+|+.+-+.. .|-.||..+|+..|-
T Consensus 10 d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~------GpAqCP~~gC~kILR 64 (314)
T COG5220 10 DRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSR------GPAQCPYKGCGKILR 64 (314)
T ss_pred cccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcC------CCCCCCCccHHHHHH
Confidence 4579999977 444555443 49999999999887752 256799999987654
No 64
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.33 E-value=0.046 Score=55.24 Aligned_cols=48 Identities=27% Similarity=0.643 Sum_probs=34.2
Q ss_pred ccccccccccccCCCCeeeccCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCccc
Q 010003 203 SPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFI 259 (520)
Q Consensus 203 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l 259 (520)
..+.|+||++-.... |.+..|.|.||++|+-..+... .. .||. |+..+
T Consensus 42 ~~v~c~icl~llk~t-mttkeClhrfc~~ci~~a~r~g----n~--ecpt--cRk~l 89 (381)
T KOG0311|consen 42 IQVICPICLSLLKKT-MTTKECLHRFCFDCIWKALRSG----NN--ECPT--CRKKL 89 (381)
T ss_pred hhhccHHHHHHHHhh-cccHHHHHHHHHHHHHHHHHhc----CC--CCch--HHhhc
Confidence 368899999877644 3345999999999997765532 21 4887 76543
No 65
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.25 E-value=0.27 Score=50.03 Aligned_cols=65 Identities=31% Similarity=0.652 Sum_probs=43.8
Q ss_pred HHHHHhhccCCCCCCCC-----CccccccccccccCCCCeeeccCCCc-ccHHHHHHHHHHhhhCCCCccccCCCCcCcc
Q 010003 185 RLAQIAVGIVSSPSQGD-----KSPENCSICCEDKPYPMMITMKCSHK-FCSHCMRTYIDGKVQSSQVPIRCPQLRCKYF 258 (520)
Q Consensus 185 klA~~Ai~~~~~~~~~~-----~~~~~C~IC~e~~~~~~~~~l~CgH~-fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~ 258 (520)
.+.++..++.....++. ....+|.||+.+.. +.+.++|.|. .|.+|.+..- .+.+ +||. |.+.
T Consensus 266 y~LqEiyGien~~v~~~~~~~~~~gkeCVIClse~r--dt~vLPCRHLCLCs~Ca~~Lr---~q~n----~CPI--CRqp 334 (349)
T KOG4265|consen 266 YLLQEIYGIENSTVEGTDADESESGKECVICLSESR--DTVVLPCRHLCLCSGCAKSLR---YQTN----NCPI--CRQP 334 (349)
T ss_pred eeeehhhccccCCCCCCccccccCCCeeEEEecCCc--ceEEecchhhehhHhHHHHHH---Hhhc----CCCc--cccc
Confidence 34455566654443332 44789999998865 3466899998 8999998765 2221 5998 9887
Q ss_pred cc
Q 010003 259 IS 260 (520)
Q Consensus 259 l~ 260 (520)
+.
T Consensus 335 i~ 336 (349)
T KOG4265|consen 335 IE 336 (349)
T ss_pred hH
Confidence 53
No 66
>PF05883 Baculo_RING: Baculovirus U-box/Ring-like domain; InterPro: IPR008573 This family consists of several Baculovirus proteins of around 130 residues in length. The function of this family is unknown, but it appears to be related to the U-box and ring finger domain by profile-profile comparison.
Probab=90.04 E-value=0.15 Score=44.98 Aligned_cols=36 Identities=17% Similarity=0.491 Sum_probs=28.6
Q ss_pred ccccccccccccCC-CCeeeccCC------CcccHHHHHHHHH
Q 010003 203 SPENCSICCEDKPY-PMMITMKCS------HKFCSHCMRTYID 238 (520)
Q Consensus 203 ~~~~C~IC~e~~~~-~~~~~l~Cg------H~fC~~Cl~~~i~ 238 (520)
...+|.||++.... .-.+.+.|+ |+||.+|+++|-.
T Consensus 25 ~~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~~ 67 (134)
T PF05883_consen 25 CTVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWRR 67 (134)
T ss_pred cCeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHHh
Confidence 37899999999876 334556776 8899999999953
No 67
>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class
Probab=89.69 E-value=0.42 Score=34.69 Aligned_cols=42 Identities=17% Similarity=0.437 Sum_probs=29.2
Q ss_pred cccccccccCCCCeeeccCC-----CcccHHHHHHHHHHhhhCCCCccccCC
Q 010003 206 NCSICCEDKPYPMMITMKCS-----HKFCSHCMRTYIDGKVQSSQVPIRCPQ 252 (520)
Q Consensus 206 ~C~IC~e~~~~~~~~~l~Cg-----H~fC~~Cl~~~i~~~i~~~~~~i~CP~ 252 (520)
.|-||++.....+....+|. |.+...||.+|+..+-. .+||.
T Consensus 1 ~CrIC~~~~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~-----~~C~i 47 (49)
T smart00744 1 ICRICHDEGDEGDPLVSPCRCKGSLKYVHQECLERWINESGN-----KTCEI 47 (49)
T ss_pred CccCCCCCCCCCCeeEeccccCCchhHHHHHHHHHHHHHcCC-----CcCCC
Confidence 48899983333333445664 88999999999986532 36876
No 68
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=89.53 E-value=0.32 Score=39.48 Aligned_cols=51 Identities=27% Similarity=0.566 Sum_probs=34.4
Q ss_pred cccccccccccCC---------C--CeeeccCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCcccc
Q 010003 204 PENCSICCEDKPY---------P--MMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFIS 260 (520)
Q Consensus 204 ~~~C~IC~e~~~~---------~--~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~ 260 (520)
...|+||...+.. . .++.-.|+|.|...|+.++++++- + .-.||. |.+.+.
T Consensus 21 dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~--~--~~~CPm--CR~~w~ 82 (85)
T PF12861_consen 21 DDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQS--S--KGQCPM--CRQPWK 82 (85)
T ss_pred CCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHcccc--C--CCCCCC--cCCeee
Confidence 4567777665542 1 223237999999999999998652 1 237998 887653
No 69
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.45 E-value=0.22 Score=54.99 Aligned_cols=46 Identities=30% Similarity=0.729 Sum_probs=35.7
Q ss_pred ccccccccccccCCC-C--eeeccCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCc
Q 010003 203 SPENCSICCEDKPYP-M--MITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKY 257 (520)
Q Consensus 203 ~~~~C~IC~e~~~~~-~--~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~ 257 (520)
....|.||.|..... + ...++|+|.||..|++.|++.+ -.||. |..
T Consensus 290 ~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~-------qtCP~--CR~ 338 (543)
T KOG0802|consen 290 SDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQ-------QTCPT--CRT 338 (543)
T ss_pred cCCeeeeechhhccccccccceeecccchHHHHHHHHHHHh-------CcCCc--chh
Confidence 468899999997653 1 2346999999999999999972 25988 554
No 70
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=89.17 E-value=0.11 Score=50.15 Aligned_cols=56 Identities=25% Similarity=0.537 Sum_probs=38.4
Q ss_pred cccccccccccCCCCeeeccCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCcccchHHHhhcCCc
Q 010003 204 PENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTVECKSFLPL 270 (520)
Q Consensus 204 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~L~~ 270 (520)
-..|..|+--.+...++-+.|+|+||..|.+.-.. -.||. |+..+....+-.-|+.
T Consensus 3 ~VhCn~C~~~~~~~~f~LTaC~HvfC~~C~k~~~~---------~~C~l--Ckk~ir~i~l~~slp~ 58 (233)
T KOG4739|consen 3 FVHCNKCFRFPSQDPFFLTACRHVFCEPCLKASSP---------DVCPL--CKKSIRIIQLNRSLPT 58 (233)
T ss_pred eEEeccccccCCCCceeeeechhhhhhhhcccCCc---------ccccc--ccceeeeeecccccch
Confidence 35799998766655666669999999999865432 16998 9887655444333433
No 71
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.15 E-value=0.15 Score=53.56 Aligned_cols=103 Identities=20% Similarity=0.453 Sum_probs=58.8
Q ss_pred cccccccccccCCC---Ce--eec-cCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCcccchHHHhhcCCcccHHHHH
Q 010003 204 PENCSICCEDKPYP---MM--ITM-KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTVECKSFLPLSSYESLE 277 (520)
Q Consensus 204 ~~~C~IC~e~~~~~---~~--~~l-~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~L~~~~~e~~~ 277 (520)
...|+.|+...... +. ... .|+-.||.+|-..|.. + ++-++.+++.+....+.-.
T Consensus 238 ~~~C~~l~~~~el~~~~~~~~~~C~~C~~~fCv~C~~~wh~--------~-----------~sC~eykk~~~~~~~d~~~ 298 (384)
T KOG1812|consen 238 YPRCSSLMSKTELSSEVKSKRRPCVKCHELFCVKCKVPWHA--------N-----------LSCEEYKKLNPEEYVDDIT 298 (384)
T ss_pred CCCchHhhhhhhhccchhhcccccccCCCceeecCCCcCCC--------C-----------CCHHHHHHhCCcccccHHH
Confidence 45577776543321 11 112 6666777777665533 2 2334455555433332211
Q ss_pred HHHHHHhhcCCCceeccCCCCCeeecCcccccccccCCCCCCCCceeCCCCCcceeccCCCccCCCCC
Q 010003 278 TALAEANILHSDRIYCPFPNCSVLLDPRECLSARASSSSQSDNSCVECPVCERFICVECGVPWHSSLS 345 (520)
Q Consensus 278 ~~~~e~~~~~~~~~~CP~p~C~~~~~~~~~~~~~~~~~~~~~~~~~~Cp~C~~~fC~~C~~~wH~~~t 345 (520)
. ..+. ...+.||. |...+..... -+.++|. |++.||+.|..+|+.+..
T Consensus 299 ~----~~la-~~wr~Cpk--C~~~ie~~~G------------Cnhm~Cr-C~~~fcy~C~~~~~~~~~ 346 (384)
T KOG1812|consen 299 L----KYLA-KRWRQCPK--CKFMIELSEG------------CNHMTCR-CGHQFCYMCGGDWKTHNG 346 (384)
T ss_pred H----HHHH-HhcCcCcc--cceeeeecCC------------cceEEee-ccccchhhcCcchhhCCc
Confidence 1 1111 45788996 9988754321 2348998 999999999999966543
No 72
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.15 E-value=0.11 Score=37.96 Aligned_cols=45 Identities=27% Similarity=0.647 Sum_probs=31.8
Q ss_pred ccccccccccCCCCeeeccCCCc-ccHHHHHHHHHHhhhCCCCccccCCCCcCccc
Q 010003 205 ENCSICCEDKPYPMMITMKCSHK-FCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFI 259 (520)
Q Consensus 205 ~~C~IC~e~~~~~~~~~l~CgH~-fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l 259 (520)
-+|.||++....+ +.-.|||+ .|.+|-.+.... . .-.||. |..++
T Consensus 8 dECTICye~pvds--VlYtCGHMCmCy~Cg~rl~~~-~-----~g~CPi--CRapi 53 (62)
T KOG4172|consen 8 DECTICYEHPVDS--VLYTCGHMCMCYACGLRLKKA-L-----HGCCPI--CRAPI 53 (62)
T ss_pred cceeeeccCcchH--HHHHcchHHhHHHHHHHHHHc-c-----CCcCcc--hhhHH
Confidence 6899999864322 33489998 899999887764 2 125887 77654
No 73
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.07 E-value=0.34 Score=50.85 Aligned_cols=48 Identities=27% Similarity=0.748 Sum_probs=36.1
Q ss_pred CccccccccccccCCCCeeeccCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCcccc
Q 010003 202 KSPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFIS 260 (520)
Q Consensus 202 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~ 260 (520)
...++|.||+..+..+ ++++|||.||..|+.+... ..-.||. |...+.
T Consensus 82 ~sef~c~vc~~~l~~p--v~tpcghs~c~~Cl~r~ld-------~~~~cp~--Cr~~l~ 129 (398)
T KOG4159|consen 82 RSEFECCVCSRALYPP--VVTPCGHSFCLECLDRSLD-------QETECPL--CRDELV 129 (398)
T ss_pred cchhhhhhhHhhcCCC--ccccccccccHHHHHHHhc-------cCCCCcc--cccccc
Confidence 4679999999887655 6679999999999777322 1235887 877665
No 74
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=88.49 E-value=0.2 Score=46.53 Aligned_cols=36 Identities=36% Similarity=0.789 Sum_probs=28.7
Q ss_pred CCccccccccccccCCCCeeeccCCCcccHHHHHHHHH
Q 010003 201 DKSPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYID 238 (520)
Q Consensus 201 ~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~ 238 (520)
..-.|.|.||-.++..+ +...|||.||..|...-++
T Consensus 193 e~IPF~C~iCKkdy~sp--vvt~CGH~FC~~Cai~~y~ 228 (259)
T COG5152 193 EKIPFLCGICKKDYESP--VVTECGHSFCSLCAIRKYQ 228 (259)
T ss_pred CCCceeehhchhhccch--hhhhcchhHHHHHHHHHhc
Confidence 34568999999998766 6679999999999865443
No 75
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.32 E-value=0.29 Score=52.64 Aligned_cols=42 Identities=31% Similarity=0.831 Sum_probs=35.4
Q ss_pred ccCCccCc--cccceeee-cCCcceEEecccccccccccccccCC
Q 010003 370 NKRWRRCQ--QCRRMIEL-THGCYHMTCWCGHEFCYSCGAEYRDG 411 (520)
Q Consensus 370 ~~~~k~CP--~C~~~IeK-~~GCnhMtC~Cg~~FCy~C~~~~~~~ 411 (520)
+...|-|| .|+..+.- .+.+.-+.|.||+.|||.|+.+|+.+
T Consensus 155 ~~~lkwCP~~~C~~av~~~~~~~~~v~C~~g~~FC~~C~~~~H~p 199 (444)
T KOG1815|consen 155 NVPLKWCPAPGCGLAVKFGSLESVEVDCGCGHEFCFACGEESHSP 199 (444)
T ss_pred CCccccCCCCCCCceeeccCCCccceeCCCCchhHhhccccccCC
Confidence 44457777 69999887 78999999999999999999999753
No 76
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=87.99 E-value=0.34 Score=35.28 Aligned_cols=27 Identities=26% Similarity=0.593 Sum_probs=20.8
Q ss_pred ccCccccceeeecC--CcceEEec-ccccc
Q 010003 374 RRCQQCRRMIELTH--GCYHMTCW-CGHEF 400 (520)
Q Consensus 374 k~CP~C~~~IeK~~--GCnhMtC~-Cg~~F 400 (520)
+-||.|+.++...+ +-+++.|+ ||+.+
T Consensus 1 ~FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~ 30 (52)
T smart00661 1 KFCPKCGNMLIPKEGKEKRRFVCRKCGYEE 30 (52)
T ss_pred CCCCCCCCccccccCCCCCEEECCcCCCeE
Confidence 36999999987654 35799996 99764
No 77
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.56 E-value=0.28 Score=51.67 Aligned_cols=51 Identities=24% Similarity=0.701 Sum_probs=36.7
Q ss_pred CccccccccccccCC-----CCee---------ec-cCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCcccc
Q 010003 202 KSPENCSICCEDKPY-----PMMI---------TM-KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFIS 260 (520)
Q Consensus 202 ~~~~~C~IC~e~~~~-----~~~~---------~l-~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~ 260 (520)
.....|+||+.+.+. +.++ .+ +|.|.|...|+.+|...- .+.||. |..+++
T Consensus 569 ~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~y------kl~CPv--CR~pLP 634 (636)
T KOG0828|consen 569 RRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTY------KLICPV--CRCPLP 634 (636)
T ss_pred hccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhh------cccCCc--cCCCCC
Confidence 346789999988643 1111 12 899999999999998832 356999 777665
No 78
>PHA00626 hypothetical protein
Probab=87.39 E-value=0.41 Score=35.29 Aligned_cols=26 Identities=23% Similarity=0.520 Sum_probs=19.4
Q ss_pred cCccccc-eeeecCCcce----EEec-ccccc
Q 010003 375 RCQQCRR-MIELTHGCYH----MTCW-CGHEF 400 (520)
Q Consensus 375 ~CP~C~~-~IeK~~GCnh----MtC~-Cg~~F 400 (520)
.||+|+. -|.|.+-|+. -.|+ |||.|
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~f 33 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYND 33 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCee
Confidence 6999999 4888876655 6675 77766
No 79
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=87.29 E-value=0.8 Score=45.43 Aligned_cols=40 Identities=18% Similarity=0.417 Sum_probs=32.8
Q ss_pred CccccccccccccCCCC-eeeccCCCcccHHHHHHHHHHhh
Q 010003 202 KSPENCSICCEDKPYPM-MITMKCSHKFCSHCMRTYIDGKV 241 (520)
Q Consensus 202 ~~~~~C~IC~e~~~~~~-~~~l~CgH~fC~~Cl~~~i~~~i 241 (520)
-+...|.||+--+...+ ++...|.|.|...||.+|+...+
T Consensus 113 ~p~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~ 153 (368)
T KOG4445|consen 113 HPNGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTECL 153 (368)
T ss_pred CCCCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHHH
Confidence 45688999998887766 56669999999999999987654
No 80
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=87.25 E-value=0.99 Score=45.08 Aligned_cols=96 Identities=22% Similarity=0.551 Sum_probs=53.6
Q ss_pred eec--cCCCcccHHHHHHHHHHhhh---CCCCccccCCCCcCcccchHHHhhcCCcccHHHHHHHHHHHhhcCCCceecc
Q 010003 220 ITM--KCSHKFCSHCMRTYIDGKVQ---SSQVPIRCPQLRCKYFISTVECKSFLPLSSYESLETALAEANILHSDRIYCP 294 (520)
Q Consensus 220 ~~l--~CgH~fC~~Cl~~~i~~~i~---~~~~~i~CP~~~C~~~l~~~~i~~~L~~~~~e~~~~~~~e~~~~~~~~~~CP 294 (520)
+++ +||-.||++|++.|.+..-. +....-. |...++.... .-.+|+.+..+. .......||
T Consensus 336 vtC~~gCgf~FCR~C~e~yh~geC~~~~~as~t~t-----c~y~vde~~a-------~~arwd~as~~T--Ik~tTkpCP 401 (446)
T KOG0006|consen 336 VTCEGGCGFAFCRECKEAYHEGECSAVFEASGTTT-----CAYRVDERAA-------EQARWDAASKET--IKKTTKPCP 401 (446)
T ss_pred ccCCCCchhHhHHHHHhhhccccceeeeccccccc-----eeeecChhhh-------hhhhhhhhhhhh--hhhccCCCC
Confidence 444 59999999999998763321 1111112 4444433221 123455443222 122345676
Q ss_pred CCCCCeeecCcccccccccCCCCCCCCceeCCC--CCcceeccCCCccCCC
Q 010003 295 FPNCSVLLDPRECLSARASSSSQSDNSCVECPV--CERFICVECGVPWHSS 343 (520)
Q Consensus 295 ~p~C~~~~~~~~~~~~~~~~~~~~~~~~~~Cp~--C~~~fC~~C~~~wH~~ 343 (520)
. |......... -..+.|+. |+..+||.|+.+|...
T Consensus 402 k--ChvptErnGG------------CmHm~Ct~~~Cg~eWCw~C~tEW~r~ 438 (446)
T KOG0006|consen 402 K--CHVPTERNGG------------CMHMKCTQPQCGLEWCWNCGTEWNRV 438 (446)
T ss_pred C--ccCccccCCc------------eEEeecCCCCCCceeEeccCChhhhh
Confidence 4 8765543221 12267865 9999999999999654
No 81
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=85.20 E-value=1.1 Score=45.37 Aligned_cols=48 Identities=25% Similarity=0.584 Sum_probs=36.1
Q ss_pred CCCccccccccccccCCCCeeeccCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCcccc
Q 010003 200 GDKSPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFIS 260 (520)
Q Consensus 200 ~~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~ 260 (520)
.....++|+||++....+ ++++.=||..|..|-..- .-+||. |...+.
T Consensus 44 ~~~~lleCPvC~~~l~~P-i~QC~nGHlaCssC~~~~----------~~~CP~--Cr~~~g 91 (299)
T KOG3002|consen 44 LDLDLLDCPVCFNPLSPP-IFQCDNGHLACSSCRTKV----------SNKCPT--CRLPIG 91 (299)
T ss_pred cchhhccCchhhccCccc-ceecCCCcEehhhhhhhh----------cccCCc--cccccc
Confidence 345679999999987644 455666899999998722 347999 888776
No 82
>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=85.12 E-value=0.59 Score=30.23 Aligned_cols=26 Identities=31% Similarity=0.814 Sum_probs=14.1
Q ss_pred ccCccccceeeecCCcceEEec-ccccc
Q 010003 374 RRCQQCRRMIELTHGCYHMTCW-CGHEF 400 (520)
Q Consensus 374 k~CP~C~~~IeK~~GCnhMtC~-Cg~~F 400 (520)
-+||.|+.-....+|.. |.|. |+++|
T Consensus 3 p~Cp~C~se~~y~D~~~-~vCp~C~~ew 29 (30)
T PF08274_consen 3 PKCPLCGSEYTYEDGEL-LVCPECGHEW 29 (30)
T ss_dssp ---TTT-----EE-SSS-EEETTTTEEE
T ss_pred CCCCCCCCcceeccCCE-EeCCcccccC
Confidence 47999999988888876 7896 99875
No 83
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=84.54 E-value=0.97 Score=30.70 Aligned_cols=34 Identities=24% Similarity=0.506 Sum_probs=21.0
Q ss_pred ceeccCCCCCeeecCcccccccccCCCCCCCCceeCCCCCcce
Q 010003 290 RIYCPFPNCSVLLDPRECLSARASSSSQSDNSCVECPVCERFI 332 (520)
Q Consensus 290 ~~~CP~p~C~~~~~~~~~~~~~~~~~~~~~~~~~~Cp~C~~~f 332 (520)
++.||+ |+..+...+.. -......++|+.|+..|
T Consensus 2 ~i~CP~--C~~~f~v~~~~-------l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 2 IITCPN--CQTRFRVPDDK-------LPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EEECCC--CCceEEcCHHH-------cccCCcEEECCCCCcEe
Confidence 367986 88766554321 00123458999999876
No 84
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=83.98 E-value=0.95 Score=45.84 Aligned_cols=48 Identities=25% Similarity=0.542 Sum_probs=33.2
Q ss_pred CccccccccccccCCCCeeeccCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCcccc
Q 010003 202 KSPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFIS 260 (520)
Q Consensus 202 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~ 260 (520)
.+...|+||+-.- .+. +-.+|+|.-|..|+.+|+-..- +|-. |+..+.
T Consensus 420 sEd~lCpICyA~p-i~A-vf~PC~H~SC~~CI~qHlmN~k-------~CFf--CktTv~ 467 (489)
T KOG4692|consen 420 SEDNLCPICYAGP-INA-VFAPCSHRSCYGCITQHLMNCK-------RCFF--CKTTVI 467 (489)
T ss_pred cccccCcceeccc-chh-hccCCCCchHHHHHHHHHhcCC-------eeeE--ecceee
Confidence 3567899999542 222 2249999999999999976431 4654 776654
No 85
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=83.91 E-value=0.52 Score=32.95 Aligned_cols=26 Identities=27% Similarity=0.754 Sum_probs=20.6
Q ss_pred cCCccCccccceeeecCCcceEEec---ccccc
Q 010003 371 KRWRRCQQCRRMIELTHGCYHMTCW---CGHEF 400 (520)
Q Consensus 371 ~~~k~CP~C~~~IeK~~GCnhMtC~---Cg~~F 400 (520)
.++|+||+|++.- |+--+.|+ |++.|
T Consensus 9 RGirkCp~CGt~N----G~R~~~CKN~~C~~~~ 37 (44)
T PF14952_consen 9 RGIRKCPKCGTYN----GTRGLSCKNKSCPQVF 37 (44)
T ss_pred hccccCCcCcCcc----CcccccccCCccchhh
Confidence 3569999999965 88888885 87765
No 86
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=83.55 E-value=0.62 Score=28.98 Aligned_cols=23 Identities=35% Similarity=0.839 Sum_probs=16.7
Q ss_pred ccCccccceeeecCCcceEEeccccccccccccc
Q 010003 374 RRCQQCRRMIELTHGCYHMTCWCGHEFCYSCGAE 407 (520)
Q Consensus 374 k~CP~C~~~IeK~~GCnhMtC~Cg~~FCy~C~~~ 407 (520)
+.||+|+..|.. +..||-.||.+
T Consensus 3 ~~Cp~Cg~~~~~-----------~~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGAEIDP-----------DAKFCPNCGAK 25 (26)
T ss_pred CCCcccCCcCCc-----------ccccChhhCCC
Confidence 689999997653 36677777764
No 87
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=82.56 E-value=0.62 Score=28.15 Aligned_cols=11 Identities=36% Similarity=0.658 Sum_probs=7.9
Q ss_pred cCccccceeee
Q 010003 375 RCQQCRRMIEL 385 (520)
Q Consensus 375 ~CP~C~~~IeK 385 (520)
.||+|+..|+.
T Consensus 1 ~Cp~CG~~~~~ 11 (23)
T PF13240_consen 1 YCPNCGAEIED 11 (23)
T ss_pred CCcccCCCCCC
Confidence 37888887763
No 88
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=82.13 E-value=1.1 Score=31.92 Aligned_cols=29 Identities=28% Similarity=0.661 Sum_probs=21.6
Q ss_pred ccCccccceeeecCCcceEEec-ccccccc
Q 010003 374 RRCQQCRRMIELTHGCYHMTCW-CGHEFCY 402 (520)
Q Consensus 374 k~CP~C~~~IeK~~GCnhMtC~-Cg~~FCy 402 (520)
-+||+|+..++...+=..++|+ ||+.+=|
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~ 33 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGYRILF 33 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCCeEEE
Confidence 4799999988776544478886 8876654
No 89
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=81.69 E-value=0.49 Score=46.21 Aligned_cols=56 Identities=21% Similarity=0.496 Sum_probs=41.6
Q ss_pred CccccccccccccCCC--------CeeeccCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCcccchHHH
Q 010003 202 KSPENCSICCEDKPYP--------MMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTVEC 264 (520)
Q Consensus 202 ~~~~~C~IC~e~~~~~--------~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~~i 264 (520)
....-|.||-.....+ +..+++|+|.|...|++.|.-. |+.+ .||- |+..++...+
T Consensus 222 l~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWciv----GKkq-tCPY--CKekVdl~rm 285 (328)
T KOG1734|consen 222 LSDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIV----GKKQ-TCPY--CKEKVDLKRM 285 (328)
T ss_pred CCcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheee----cCCC-CCch--HHHHhhHhhh
Confidence 3467899998765432 4677899999999999999753 2323 7999 9988776443
No 90
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=81.61 E-value=1.6 Score=29.50 Aligned_cols=34 Identities=21% Similarity=0.447 Sum_probs=20.9
Q ss_pred ceeccCCCCCeeecCcccccccccCCCCCCCCceeCCCCCcce
Q 010003 290 RIYCPFPNCSVLLDPRECLSARASSSSQSDNSCVECPVCERFI 332 (520)
Q Consensus 290 ~~~CP~p~C~~~~~~~~~~~~~~~~~~~~~~~~~~Cp~C~~~f 332 (520)
.+.||+ |+..+...+.. -.+....++|+.|+..|
T Consensus 2 ~i~Cp~--C~~~y~i~d~~-------ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 2 IITCPN--CQAKYEIDDEK-------IPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EEECCC--CCCEEeCCHHH-------CCCCCcEEECCCCCCEe
Confidence 367886 88766554321 01233458999998875
No 91
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=81.37 E-value=1 Score=47.23 Aligned_cols=53 Identities=30% Similarity=0.748 Sum_probs=39.0
Q ss_pred CCCCCCccccccccccccCCC--CeeeccCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCcccc
Q 010003 197 PSQGDKSPENCSICCEDKPYP--MMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFIS 260 (520)
Q Consensus 197 ~~~~~~~~~~C~IC~e~~~~~--~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~ 260 (520)
+..+-.+..+|+||++....+ -+++..|.|.|.-.|+..|.. ..||. |....+
T Consensus 168 ~~~~~tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~~---------~scpv--cR~~q~ 222 (493)
T KOG0804|consen 168 PPTGLTELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWWD---------SSCPV--CRYCQS 222 (493)
T ss_pred CCCCcccCCCcchhHhhcCccccceeeeecccccchHHHhhccc---------CcChh--hhhhcC
Confidence 445556788999999987643 345569999999999998854 36887 655443
No 92
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=80.21 E-value=0.4 Score=48.47 Aligned_cols=30 Identities=23% Similarity=0.708 Sum_probs=24.9
Q ss_pred cCCccCccccceeeecC-CcceEEec-ccccc
Q 010003 371 KRWRRCQQCRRMIELTH-GCYHMTCW-CGHEF 400 (520)
Q Consensus 371 ~~~k~CP~C~~~IeK~~-GCnhMtC~-Cg~~F 400 (520)
..|.+||+|+.+|-+.+ .=|.+.|+ |+|+|
T Consensus 25 ~~~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 56 (292)
T PRK05654 25 GLWTKCPSCGQVLYRKELEANLNVCPKCGHHM 56 (292)
T ss_pred CCeeECCCccchhhHHHHHhcCCCCCCCCCCe
Confidence 46999999999987653 56778996 99998
No 93
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=80.16 E-value=0.76 Score=51.75 Aligned_cols=52 Identities=27% Similarity=0.793 Sum_probs=38.5
Q ss_pred ccccccccccCCCCeeeccCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCcccchHHHhh
Q 010003 205 ENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTVECKS 266 (520)
Q Consensus 205 ~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~~i~~ 266 (520)
++|.||.+ ....+...|+|.||.+|+..+++..-. ..||. |...+....+..
T Consensus 455 ~~c~ic~~---~~~~~it~c~h~~c~~c~~~~i~~~~~-----~~~~~--cr~~l~~~~l~s 506 (674)
T KOG1001|consen 455 HWCHICCD---LDSFFITRCGHDFCVECLKKSIQQSEN-----APCPL--CRNVLKEKKLLS 506 (674)
T ss_pred cccccccc---cccceeecccchHHHHHHHhccccccC-----CCCcH--HHHHHHHHHHhh
Confidence 89999998 344566699999999999999874322 16877 887766554443
No 94
>PLN03086 PRLI-interacting factor K; Provisional
Probab=79.66 E-value=2.2 Score=46.91 Aligned_cols=127 Identities=21% Similarity=0.443 Sum_probs=64.7
Q ss_pred ccccCCCCcCcccchHHHhhcCCcccHHHHHHHHHHHhhc-CCCceeccCCCCCeeecCcccccccccCCCCCCCCceeC
Q 010003 247 PIRCPQLRCKYFISTVECKSFLPLSSYESLETALAEANIL-HSDRIYCPFPNCSVLLDPRECLSARASSSSQSDNSCVEC 325 (520)
Q Consensus 247 ~i~CP~~~C~~~l~~~~i~~~L~~~~~e~~~~~~~e~~~~-~~~~~~CP~p~C~~~~~~~~~~~~~~~~~~~~~~~~~~C 325 (520)
.+.||. |+..++...+...+ .. .-..+-||..+|+..+...+.. ..+.|
T Consensus 407 ~V~C~N--C~~~i~l~~l~lHe----------------~~C~r~~V~Cp~~~Cg~v~~r~el~------------~H~~C 456 (567)
T PLN03086 407 TVECRN--CKHYIPSRSIALHE----------------AYCSRHNVVCPHDGCGIVLRVEEAK------------NHVHC 456 (567)
T ss_pred eEECCC--CCCccchhHHHHHH----------------hhCCCcceeCCcccccceeeccccc------------cCccC
Confidence 468998 98887764432111 01 1245789987899887544321 22679
Q ss_pred CCCCcceeccCC-----CccCCCCCchhhhcCchhhcCchHHHHHH-HHhccCCccCccccceeeec-----------CC
Q 010003 326 PVCERFICVECG-----VPWHSSLSCEEYQNLPLEERDAGDITLHR-LAQNKRWRRCQQCRRMIELT-----------HG 388 (520)
Q Consensus 326 p~C~~~fC~~C~-----~~wH~~~tC~e~~~~~~~~~~~~~~~l~~-l~~~~~~k~CP~C~~~IeK~-----------~G 388 (520)
+.|+..| ..-. ...|.+..|. -.... . ......+. ..-......|+-|+..+.+. +=
T Consensus 457 ~~Cgk~f-~~s~LekH~~~~Hkpv~Cp-Cg~~~--~--R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~L 530 (567)
T PLN03086 457 EKCGQAF-QQGEMEKHMKVFHEPLQCP-CGVVL--E--KEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGM 530 (567)
T ss_pred CCCCCcc-chHHHHHHHHhcCCCccCC-CCCCc--c--hhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhH
Confidence 9998776 2211 1124445564 21111 0 01111111 01122346788898887421 11
Q ss_pred cce-EEeccccccccccccccc
Q 010003 389 CYH-MTCWCGHEFCYSCGAEYR 409 (520)
Q Consensus 389 Cnh-MtC~Cg~~FCy~C~~~~~ 409 (520)
=.| .+|.-.+.-|..|++.+.
T Consensus 531 t~HE~~CG~rt~~C~~Cgk~Vr 552 (567)
T PLN03086 531 SEHESICGSRTAPCDSCGRSVM 552 (567)
T ss_pred HHHHHhcCCcceEccccCCeee
Confidence 123 345556777777777654
No 95
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=79.35 E-value=1.1 Score=50.18 Aligned_cols=13 Identities=38% Similarity=0.792 Sum_probs=9.5
Q ss_pred ccccccccccccc
Q 010003 397 GHEFCYSCGAEYR 409 (520)
Q Consensus 397 g~~FCy~C~~~~~ 409 (520)
+..||-.||.+..
T Consensus 40 ~~~fC~~CG~~~~ 52 (645)
T PRK14559 40 DEAHCPNCGAETG 52 (645)
T ss_pred ccccccccCCccc
Confidence 3449999998754
No 96
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=78.81 E-value=1.7 Score=49.04 Aligned_cols=53 Identities=25% Similarity=0.590 Sum_probs=40.6
Q ss_pred CccccccccccccCCC-Ceeec-cCCCcccHHHHHHHHHHhhhCCCCccccCCCCcC
Q 010003 202 KSPENCSICCEDKPYP-MMITM-KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCK 256 (520)
Q Consensus 202 ~~~~~C~IC~e~~~~~-~~~~l-~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~ 256 (520)
...++|.||++..... .+.+. .|-|+|...|++.|....-.++...-+||. |.
T Consensus 189 ~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~--Cq 243 (950)
T KOG1952|consen 189 NRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPA--CQ 243 (950)
T ss_pred cCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCc--cc
Confidence 3579999999987644 56676 899999999999999884444444457887 65
No 97
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=78.46 E-value=1.8 Score=43.73 Aligned_cols=54 Identities=19% Similarity=0.555 Sum_probs=39.0
Q ss_pred ccccccccccCC--CCeeeccCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCcccchHHHhh
Q 010003 205 ENCSICCEDKPY--PMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTVECKS 266 (520)
Q Consensus 205 ~~C~IC~e~~~~--~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~~i~~ 266 (520)
-.|+.|++.... ..++.++||-.+|+=||... ...+. =+||. |......+.++-
T Consensus 15 d~cplcie~mditdknf~pc~cgy~ic~fc~~~i-rq~ln-----grcpa--crr~y~denv~~ 70 (480)
T COG5175 15 DYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNI-RQNLN-----GRCPA--CRRKYDDENVRY 70 (480)
T ss_pred ccCcccccccccccCCcccCCcccHHHHHHHHHH-Hhhcc-----CCChH--hhhhccccceeE
Confidence 349999998764 45777899999999999754 33343 37998 887666555543
No 98
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=77.90 E-value=1.4 Score=32.16 Aligned_cols=25 Identities=20% Similarity=0.502 Sum_probs=18.9
Q ss_pred ccCccccc-eeeecCCcceEEec-ccccc
Q 010003 374 RRCQQCRR-MIELTHGCYHMTCW-CGHEF 400 (520)
Q Consensus 374 k~CP~C~~-~IeK~~GCnhMtC~-Cg~~F 400 (520)
+-||+|+. .+.... +.++|. ||+.+
T Consensus 21 ~fCP~Cg~~~m~~~~--~r~~C~~Cgyt~ 47 (50)
T PRK00432 21 KFCPRCGSGFMAEHL--DRWHCGKCGYTE 47 (50)
T ss_pred CcCcCCCcchheccC--CcEECCCcCCEE
Confidence 79999998 443333 799995 99875
No 99
>PF04641 Rtf2: Rtf2 RING-finger
Probab=77.80 E-value=2.8 Score=41.69 Aligned_cols=70 Identities=14% Similarity=0.323 Sum_probs=49.0
Q ss_pred CCccccccccccccCC-CCeeec-cCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCcccchHHHhhcCCc-ccHHHHH
Q 010003 201 DKSPENCSICCEDKPY-PMMITM-KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTVECKSFLPL-SSYESLE 277 (520)
Q Consensus 201 ~~~~~~C~IC~e~~~~-~~~~~l-~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~L~~-~~~e~~~ 277 (520)
....+.|+|...++.. ..++.+ +|||+|+..+++..- .+ -.||. |+..+...+|-.+-+. +.++.+.
T Consensus 110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k----~~----~~Cp~--c~~~f~~~DiI~Lnp~~ee~~~l~ 179 (260)
T PF04641_consen 110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK----KS----KKCPV--CGKPFTEEDIIPLNPPEEELEKLR 179 (260)
T ss_pred CCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc----cc----ccccc--cCCccccCCEEEecCCccHHHHHH
Confidence 4567999999988854 356666 999999999999882 11 24998 9999887766665543 3344444
Q ss_pred HHH
Q 010003 278 TAL 280 (520)
Q Consensus 278 ~~~ 280 (520)
..+
T Consensus 180 ~~~ 182 (260)
T PF04641_consen 180 ERM 182 (260)
T ss_pred HHH
Confidence 333
No 100
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=77.71 E-value=0.5 Score=46.75 Aligned_cols=30 Identities=33% Similarity=0.797 Sum_probs=21.6
Q ss_pred eEEec-ccccccccccccccCCCCcccCCCCCC
Q 010003 391 HMTCW-CGHEFCYSCGAEYRDGQQTCQCAFWDE 422 (520)
Q Consensus 391 hMtC~-Cg~~FCy~C~~~~~~~~~~c~C~~~~~ 422 (520)
|-+|+ |||-|||.|...|-....- ||+=+.
T Consensus 251 ~pSaTpCGHiFCWsCI~~w~~ek~e--CPlCR~ 281 (293)
T KOG0317|consen 251 NPSATPCGHIFCWSCILEWCSEKAE--CPLCRE 281 (293)
T ss_pred CCCcCcCcchHHHHHHHHHHccccC--CCcccc
Confidence 45675 9999999999999765444 554333
No 101
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=77.44 E-value=1.5 Score=45.06 Aligned_cols=47 Identities=26% Similarity=0.794 Sum_probs=33.4
Q ss_pred cccccccccccCCC-Ceeec-cCCCcccHHHHHHHHHHhhhCCCCccccCCCCcC
Q 010003 204 PENCSICCEDKPYP-MMITM-KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCK 256 (520)
Q Consensus 204 ~~~C~IC~e~~~~~-~~~~l-~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~ 256 (520)
+-.|.||-+-++.. +.-.. .|||.|...|+.+|++..-.. =.||. |+
T Consensus 4 ~A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~----R~cpi--c~ 52 (465)
T KOG0827|consen 4 MAECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSN----RGCPI--CQ 52 (465)
T ss_pred cceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCcc----CCCCc--ee
Confidence 46799996666654 34445 599999999999999855332 25776 55
No 102
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=77.42 E-value=1.2 Score=38.17 Aligned_cols=26 Identities=31% Similarity=0.655 Sum_probs=18.9
Q ss_pred ccCccccceeeecCCcceEEec-ccccc
Q 010003 374 RRCQQCRRMIELTHGCYHMTCW-CGHEF 400 (520)
Q Consensus 374 k~CP~C~~~IeK~~GCnhMtC~-Cg~~F 400 (520)
|.||+|++.+---.- +-++|+ ||+.|
T Consensus 10 R~Cp~CG~kFYDLnk-~PivCP~CG~~~ 36 (108)
T PF09538_consen 10 RTCPSCGAKFYDLNK-DPIVCPKCGTEF 36 (108)
T ss_pred ccCCCCcchhccCCC-CCccCCCCCCcc
Confidence 889999998654333 778885 76665
No 103
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=77.18 E-value=1.6 Score=36.07 Aligned_cols=29 Identities=31% Similarity=0.717 Sum_probs=22.0
Q ss_pred cCccccce--eeecCCcceEEec-cccccccc
Q 010003 375 RCQQCRRM--IELTHGCYHMTCW-CGHEFCYS 403 (520)
Q Consensus 375 ~CP~C~~~--IeK~~GCnhMtC~-Cg~~FCy~ 403 (520)
-||.|+.+ |++.+-||.+.|+ |+|.|=-.
T Consensus 3 FCP~Cgn~Live~g~~~~rf~C~tCpY~~~I~ 34 (105)
T KOG2906|consen 3 FCPTCGNMLIVESGESCNRFSCRTCPYVFPIS 34 (105)
T ss_pred ccCCCCCEEEEecCCeEeeEEcCCCCceeeEe
Confidence 59999987 4445569999996 99877433
No 104
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=76.99 E-value=1.1 Score=31.42 Aligned_cols=30 Identities=30% Similarity=0.730 Sum_probs=20.3
Q ss_pred CccccceeeecCCcceEEecccccccccccccccC
Q 010003 376 CQQCRRMIELTHGCYHMTCWCGHEFCYSCGAEYRD 410 (520)
Q Consensus 376 CP~C~~~IeK~~GCnhMtC~Cg~~FCy~C~~~~~~ 410 (520)
||-|...+. +-++=.|||.||..|...|.+
T Consensus 1 CpiC~~~~~-----~Pv~l~CGH~FC~~Cl~~~~~ 30 (42)
T PF15227_consen 1 CPICLDLFK-----DPVSLPCGHSFCRSCLERLWK 30 (42)
T ss_dssp ETTTTSB-S-----SEEE-SSSSEEEHHHHHHHHC
T ss_pred CCccchhhC-----CccccCCcCHHHHHHHHHHHH
Confidence 555555554 236667999999999988754
No 105
>KOG3800 consensus Predicted E3 ubiquitin ligase containing RING finger, subunit of transcription/repair factor TFIIH and CDK-activating kinase assembly factor [Posttranslational modification, protein turnover, chaperones]
Probab=76.93 E-value=3.4 Score=41.04 Aligned_cols=52 Identities=25% Similarity=0.751 Sum_probs=35.7
Q ss_pred ccccccccc-CCCCeeec--cCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCcccchHHHh
Q 010003 206 NCSICCEDK-PYPMMITM--KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTVECK 265 (520)
Q Consensus 206 ~C~IC~e~~-~~~~~~~l--~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~~i~ 265 (520)
.|++|-.+. ..++++.+ .|+|..|.+|+-..+.. | +-.||. |...+-..-++
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~----g--~~~Cpe--C~~iLRk~nfr 56 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSL----G--PAQCPE--CMVILRKNNFR 56 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHhc----C--CCCCCc--ccchhhhcccc
Confidence 489998664 34444433 89999999999887752 2 345994 98877554433
No 106
>PHA03096 p28-like protein; Provisional
Probab=76.57 E-value=1.4 Score=44.29 Aligned_cols=38 Identities=18% Similarity=0.499 Sum_probs=29.3
Q ss_pred ccccccccccCC----CCeee-c-cCCCcccHHHHHHHHHHhhh
Q 010003 205 ENCSICCEDKPY----PMMIT-M-KCSHKFCSHCMRTYIDGKVQ 242 (520)
Q Consensus 205 ~~C~IC~e~~~~----~~~~~-l-~CgH~fC~~Cl~~~i~~~i~ 242 (520)
..|.||++.... +..+. + .|.|.||..|++.|..+...
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~ 222 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLY 222 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhh
Confidence 679999987543 22333 4 89999999999999987753
No 107
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=76.20 E-value=0.59 Score=47.06 Aligned_cols=33 Identities=21% Similarity=0.480 Sum_probs=25.5
Q ss_pred cCCccCccccceeeecC-CcceEEec-cccccccc
Q 010003 371 KRWRRCQQCRRMIELTH-GCYHMTCW-CGHEFCYS 403 (520)
Q Consensus 371 ~~~k~CP~C~~~IeK~~-GCnhMtC~-Cg~~FCy~ 403 (520)
..|.+||+|+..|.+.+ .=|.+.|+ |+|+|=-.
T Consensus 36 ~lw~kc~~C~~~~~~~~l~~~~~vcp~c~~h~rlt 70 (296)
T CHL00174 36 HLWVQCENCYGLNYKKFLKSKMNICEQCGYHLKMS 70 (296)
T ss_pred CCeeECCCccchhhHHHHHHcCCCCCCCCCCcCCC
Confidence 35899999999987654 56778996 99987433
No 108
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=75.55 E-value=0.92 Score=33.56 Aligned_cols=46 Identities=20% Similarity=0.439 Sum_probs=30.5
Q ss_pred cccccccccccCCCCeeeccCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCcccchH
Q 010003 204 PENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTV 262 (520)
Q Consensus 204 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~ 262 (520)
...|..|..... .-+.++|+|.+|..|+...= +. -||. |...+...
T Consensus 7 ~~~~~~~~~~~~--~~~~~pCgH~I~~~~f~~~r--------Yn-gCPf--C~~~~~~~ 52 (55)
T PF14447_consen 7 EQPCVFCGFVGT--KGTVLPCGHLICDNCFPGER--------YN-GCPF--CGTPFEFD 52 (55)
T ss_pred ceeEEEcccccc--ccccccccceeeccccChhh--------cc-CCCC--CCCcccCC
Confidence 456666665433 33567999999999986431 11 4998 88877643
No 109
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=75.31 E-value=3.3 Score=39.16 Aligned_cols=46 Identities=24% Similarity=0.551 Sum_probs=28.4
Q ss_pred CCCceeccCCCCCeeecCcccccccccCCCCCCCCceeCCCCCcce
Q 010003 287 HSDRIYCPFPNCSVLLDPRECLSARASSSSQSDNSCVECPVCERFI 332 (520)
Q Consensus 287 ~~~~~~CP~p~C~~~~~~~~~~~~~~~~~~~~~~~~~~Cp~C~~~f 332 (520)
.+.++-||.|+|..+|..........+-..++..-.+.|.+|+..|
T Consensus 135 sSqRIACPRpnCkRiInL~p~~~~p~~P~~~P~gcRV~CgHC~~tF 180 (275)
T KOG4684|consen 135 SSQRIACPRPNCKRIINLDPLIEKPRDPGTAPTGCRVKCGHCNETF 180 (275)
T ss_pred ccceeccCCCCcceeeecCCCCCCCCCCCCCCcceEEEecCcccee
Confidence 3578899999999998765433211111112333347888888766
No 110
>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=75.05 E-value=0.93 Score=33.17 Aligned_cols=23 Identities=35% Similarity=0.941 Sum_probs=14.6
Q ss_pred CceeCCCCCcceeccCCCccCCC
Q 010003 321 SCVECPVCERFICVECGVPWHSS 343 (520)
Q Consensus 321 ~~~~Cp~C~~~fC~~C~~~wH~~ 343 (520)
....||+|+..||+.|-.-.|..
T Consensus 20 ~~y~C~~C~~~FC~dCD~fiHE~ 42 (51)
T PF07975_consen 20 SRYRCPKCKNHFCIDCDVFIHET 42 (51)
T ss_dssp EEE--TTTT--B-HHHHHTTTTT
T ss_pred CeEECCCCCCccccCcChhhhcc
Confidence 34889999999999998877765
No 111
>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=74.90 E-value=3.6 Score=40.18 Aligned_cols=102 Identities=23% Similarity=0.467 Sum_probs=54.9
Q ss_pred CCCccccccccccccCCCCeeeccCCCc-ccHHHHHHHHHHhhhC---CCCccccCCCCcCcccchHHHhhcCCcccHHH
Q 010003 200 GDKSPENCSICCEDKPYPMMITMKCSHK-FCSHCMRTYIDGKVQS---SQVPIRCPQLRCKYFISTVECKSFLPLSSYES 275 (520)
Q Consensus 200 ~~~~~~~C~IC~e~~~~~~~~~l~CgH~-fC~~Cl~~~i~~~i~~---~~~~i~CP~~~C~~~l~~~~i~~~L~~~~~e~ 275 (520)
+..+..+|.+|......+.- .=+|+ -|..|-..- -|+. |+.-++|| |+..|--
T Consensus 61 ~~~p~v~CrVCq~~I~i~gk---~~QhVVkC~~CnEAT---PIr~aPpGKKYVRCP---CNCLLIC-------------- 117 (256)
T PF09788_consen 61 GGAPVVTCRVCQSLIDIEGK---MHQHVVKCSVCNEAT---PIRNAPPGKKYVRCP---CNCLLIC-------------- 117 (256)
T ss_pred CCCceEEeecCCceecccCc---cceeeEECCCCCccc---cccCCCCCCeeEecC---CceEEEe--------------
Confidence 34568999999866543311 11232 244443321 2322 45557888 5443210
Q ss_pred HHHHHHHHhhcCCCceeccCCCCCeeecCccccccccc--CCCCCCCCceeCCCCCccee
Q 010003 276 LETALAEANILHSDRIYCPFPNCSVLLDPRECLSARAS--SSSQSDNSCVECPVCERFIC 333 (520)
Q Consensus 276 ~~~~~~e~~~~~~~~~~CP~p~C~~~~~~~~~~~~~~~--~~~~~~~~~~~Cp~C~~~fC 333 (520)
-..+.++.||+|+|..++........... ....+....+.|.+|+..|=
T Consensus 118 ---------k~sS~rIaCPRp~CkRiI~L~~~~~~p~~~~~~~~p~~~rv~CghC~~~Fl 168 (256)
T PF09788_consen 118 ---------KSSSQRIACPRPNCKRIINLGPSHQGPVTPPVPTQPGSCRVICGHCSNTFL 168 (256)
T ss_pred ---------ecccccccCCCCCCcceEEeCCccCCCCCCCCCCCCCceeEECCCCCCcEe
Confidence 01357899999999998876543210111 11123334488999987773
No 112
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=74.83 E-value=0.7 Score=46.51 Aligned_cols=31 Identities=19% Similarity=0.566 Sum_probs=24.6
Q ss_pred cCCccCccccceeeec-CCcceEEec-cccccc
Q 010003 371 KRWRRCQQCRRMIELT-HGCYHMTCW-CGHEFC 401 (520)
Q Consensus 371 ~~~k~CP~C~~~IeK~-~GCnhMtC~-Cg~~FC 401 (520)
..|.+||+|+.+|-+. -.=|.+.|+ |+|+|=
T Consensus 24 ~~~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~r 56 (285)
T TIGR00515 24 GVWTKCPKCGQVLYTKELERNLEVCPKCDHHMR 56 (285)
T ss_pred CCeeECCCCcchhhHHHHHhhCCCCCCCCCcCc
Confidence 4599999999998775 345678996 999864
No 113
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=74.50 E-value=2.6 Score=44.57 Aligned_cols=47 Identities=26% Similarity=0.734 Sum_probs=35.0
Q ss_pred CccccccccccccCCCCeee-ccCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCccc
Q 010003 202 KSPENCSICCEDKPYPMMIT-MKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFI 259 (520)
Q Consensus 202 ~~~~~C~IC~e~~~~~~~~~-l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l 259 (520)
.....|++|......+ +. ..|||.||..|+..+... ...||. |...+
T Consensus 19 ~~~l~C~~C~~vl~~p--~~~~~cgh~fC~~C~~~~~~~-------~~~cp~--~~~~~ 66 (391)
T KOG0297|consen 19 DENLLCPICMSVLRDP--VQTTTCGHRFCAGCLLESLSN-------HQKCPV--CRQEL 66 (391)
T ss_pred cccccCccccccccCC--CCCCCCCCcccccccchhhcc-------CcCCcc--ccccc
Confidence 4568999999877655 44 599999999999998775 235776 54433
No 114
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=74.26 E-value=3.3 Score=27.00 Aligned_cols=26 Identities=35% Similarity=0.756 Sum_probs=17.6
Q ss_pred ccCccccceeeecCCcceEEec-cccc
Q 010003 374 RRCQQCRRMIELTHGCYHMTCW-CGHE 399 (520)
Q Consensus 374 k~CP~C~~~IeK~~GCnhMtC~-Cg~~ 399 (520)
+-||+|+.+.+...+=-.|.|. ||++
T Consensus 4 rfC~~CG~~t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 4 RFCGRCGAPTKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp SB-TTT--BEEE-SSSS-EEESSSS-E
T ss_pred cccCcCCccccCCCCcCEeECCCCcCE
Confidence 7899999999999887889996 8875
No 115
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=72.70 E-value=1.3 Score=43.78 Aligned_cols=37 Identities=24% Similarity=0.590 Sum_probs=29.0
Q ss_pred ccCCccCccccceeeecC-CcceEEec-ccccccccccc
Q 010003 370 NKRWRRCQQCRRMIELTH-GCYHMTCW-CGHEFCYSCGA 406 (520)
Q Consensus 370 ~~~~k~CP~C~~~IeK~~-GCnhMtC~-Cg~~FCy~C~~ 406 (520)
...|-+||.|+.++-+.+ +=|...|. |+|+|=-.=..
T Consensus 25 e~lw~KCp~c~~~~y~~eL~~n~~vcp~c~~h~ri~A~~ 63 (294)
T COG0777 25 EGLWTKCPSCGEMLYRKELESNLKVCPKCGHHMRISARE 63 (294)
T ss_pred CCceeECCCccceeeHHHHHhhhhcccccCcccccCHHH
Confidence 567999999999988764 88889996 99998544433
No 116
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=72.61 E-value=1.6 Score=36.74 Aligned_cols=31 Identities=19% Similarity=0.647 Sum_probs=26.0
Q ss_pred cccccccccccCCCCeeeccCCCcccHHHHH
Q 010003 204 PENCSICCEDKPYPMMITMKCSHKFCSHCMR 234 (520)
Q Consensus 204 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~ 234 (520)
...|.+|...+..+.++..+|||.|+..|++
T Consensus 78 ~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 78 STKCSVCGKPLGNSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence 4569999998877666667999999999975
No 117
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=72.08 E-value=3.1 Score=49.27 Aligned_cols=16 Identities=19% Similarity=0.310 Sum_probs=10.7
Q ss_pred CCCCCCccchhhhccC
Q 010003 483 PPRCTDSYGDAMKDLH 498 (520)
Q Consensus 483 ~~~~~~~~~~~~~~~~ 498 (520)
.|+--+.+|+.|+.||
T Consensus 798 rp~Eigvs~eklreLG 813 (1337)
T PRK14714 798 RPREIGVSVEKLRELG 813 (1337)
T ss_pred cHHHcCCCHHHHHHcC
Confidence 3554456788888777
No 118
>PF12773 DZR: Double zinc ribbon
Probab=71.77 E-value=3.2 Score=29.87 Aligned_cols=12 Identities=17% Similarity=0.407 Sum_probs=8.8
Q ss_pred ccCccccceeee
Q 010003 374 RRCQQCRRMIEL 385 (520)
Q Consensus 374 k~CP~C~~~IeK 385 (520)
+.||+|+..+..
T Consensus 30 ~~C~~Cg~~~~~ 41 (50)
T PF12773_consen 30 KICPNCGAENPP 41 (50)
T ss_pred CCCcCCcCCCcC
Confidence 678888887654
No 119
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=71.77 E-value=3.7 Score=42.55 Aligned_cols=59 Identities=15% Similarity=0.301 Sum_probs=43.0
Q ss_pred CccccccccccccCCC-CeeeccCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCcccchHHHhh
Q 010003 202 KSPENCSICCEDKPYP-MMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTVECKS 266 (520)
Q Consensus 202 ~~~~~C~IC~e~~~~~-~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~~i~~ 266 (520)
-+.|.|||=-+....+ .-..+.|||+++++=+.+... +|...++||- |.........++
T Consensus 332 HSvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~----ng~~sfKCPY--CP~e~~~~~~kq 391 (394)
T KOG2817|consen 332 HSVFICPVLKEQTSDENPPMMLICGHVISKDALNRLSK----NGSQSFKCPY--CPVEQLASDTKQ 391 (394)
T ss_pred cceeecccchhhccCCCCCeeeeccceecHHHHHHHhh----CCCeeeeCCC--CCcccCHHhccc
Confidence 3578999977665433 335679999999998888765 3444789999 988776666554
No 120
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=71.34 E-value=3 Score=47.42 Aligned_cols=34 Identities=29% Similarity=0.824 Sum_probs=30.7
Q ss_pred ccCccccceeeecCCcceEEec-cccc-----cccccccc
Q 010003 374 RRCQQCRRMIELTHGCYHMTCW-CGHE-----FCYSCGAE 407 (520)
Q Consensus 374 k~CP~C~~~IeK~~GCnhMtC~-Cg~~-----FCy~C~~~ 407 (520)
-.||+|..+..-...=|.|.|. ||++ .|.-||..
T Consensus 445 ~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 445 AECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred ccCCCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCC
Confidence 5899999999888888999996 9998 89999987
No 121
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=71.16 E-value=3.5 Score=27.64 Aligned_cols=26 Identities=27% Similarity=0.581 Sum_probs=16.0
Q ss_pred ccCccccceeeec--CCcceEEec-ccccc
Q 010003 374 RRCQQCRRMIELT--HGCYHMTCW-CGHEF 400 (520)
Q Consensus 374 k~CP~C~~~IeK~--~GCnhMtC~-Cg~~F 400 (520)
+-||.|+.+..-. ..-.. .|+ |+|++
T Consensus 2 ~FCp~C~nlL~p~~~~~~~~-~C~~C~Y~~ 30 (35)
T PF02150_consen 2 RFCPECGNLLYPKEDKEKRV-ACRTCGYEE 30 (35)
T ss_dssp -BETTTTSBEEEEEETTTTE-EESSSS-EE
T ss_pred eeCCCCCccceEcCCCccCc-CCCCCCCcc
Confidence 5699999875433 33333 896 98864
No 122
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=70.49 E-value=3 Score=40.39 Aligned_cols=52 Identities=10% Similarity=0.170 Sum_probs=38.2
Q ss_pred ccccccccccccCCC-Ceeec-cCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCcccchHH
Q 010003 203 SPENCSICCEDKPYP-MMITM-KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTVE 263 (520)
Q Consensus 203 ~~~~C~IC~e~~~~~-~~~~l-~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~~ 263 (520)
..+.|++|-++.... ....+ +|||+||.+|+.+++..- ..||. |...+....
T Consensus 220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D-------~v~pv--~d~plkdrd 273 (303)
T KOG3039|consen 220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKD-------MVDPV--TDKPLKDRD 273 (303)
T ss_pred cceecccchhhhcCccceEEeccCCcEeeHHHHHHhcccc-------ccccC--CCCcCcccc
Confidence 578999999988654 44556 999999999999987632 24766 666665543
No 123
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=70.14 E-value=6.2 Score=39.86 Aligned_cols=47 Identities=30% Similarity=0.681 Sum_probs=34.9
Q ss_pred cccccccccccCCCCe----eeccCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCcc
Q 010003 204 PENCSICCEDKPYPMM----ITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYF 258 (520)
Q Consensus 204 ~~~C~IC~e~~~~~~~----~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~ 258 (520)
...|.||-+++..... ..+.|||.+|..|+...+... .+.||. |...
T Consensus 3 ~~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~~------~i~cpf--cR~~ 53 (296)
T KOG4185|consen 3 FPECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGNS------RILCPF--CRET 53 (296)
T ss_pred CCceeecCccccccCcccCCcccccCceehHhHHHHHhcCc------eeeccC--CCCc
Confidence 4689999999876421 234899999999999887632 345777 7776
No 124
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=70.10 E-value=5.4 Score=35.07 Aligned_cols=51 Identities=22% Similarity=0.421 Sum_probs=40.3
Q ss_pred ccccccccccccCCCCeeec--cCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCccc
Q 010003 203 SPENCSICCEDKPYPMMITM--KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFI 259 (520)
Q Consensus 203 ~~~~C~IC~e~~~~~~~~~l--~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l 259 (520)
...+|.||-|....+.+..- -||-.+|..|-...++..- ....||. |+..+
T Consensus 79 ~lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~----~ypvCPv--CkTSF 131 (140)
T PF05290_consen 79 KLYECNICKETSAEERFLKPNECCGYSICNACYANLWKFCN----LYPVCPV--CKTSF 131 (140)
T ss_pred CceeccCcccccchhhcCCcccccchHHHHHHHHHHHHHcc----cCCCCCc--ccccc
Confidence 67999999998877766544 4899999999999988653 3457999 88754
No 125
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=70.08 E-value=1.9 Score=44.51 Aligned_cols=44 Identities=34% Similarity=0.902 Sum_probs=30.7
Q ss_pred cccccccccccCCCCeeec-cCCCcccHHHHHHHHHHhhhCCCCccccCCCCc
Q 010003 204 PENCSICCEDKPYPMMITM-KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRC 255 (520)
Q Consensus 204 ~~~C~IC~e~~~~~~~~~l-~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C 255 (520)
...|.||-+... -+.. +|||..|..|+..|-.+. +|+ .||.+.|
T Consensus 369 FeLCKICaendK---dvkIEPCGHLlCt~CLa~WQ~sd--~gq---~CPFCRc 413 (563)
T KOG1785|consen 369 FELCKICAENDK---DVKIEPCGHLLCTSCLAAWQDSD--EGQ---TCPFCRC 413 (563)
T ss_pred HHHHHHhhccCC---CcccccccchHHHHHHHhhcccC--CCC---CCCceee
Confidence 456999987643 2445 999999999999885422 122 5998444
No 126
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=69.80 E-value=2.4 Score=48.60 Aligned_cols=26 Identities=35% Similarity=1.037 Sum_probs=23.2
Q ss_pred ccCccccceeeecCCcceEEec-cccccc
Q 010003 374 RRCQQCRRMIELTHGCYHMTCW-CGHEFC 401 (520)
Q Consensus 374 k~CP~C~~~IeK~~GCnhMtC~-Cg~~FC 401 (520)
..||.|+..+...+||. +|+ |||.=|
T Consensus 725 ~~Cp~Cg~~l~~~~GC~--~C~~CG~skC 751 (752)
T PRK08665 725 GACPECGSILEHEEGCV--VCHSCGYSKC 751 (752)
T ss_pred CCCCCCCcccEECCCCC--cCCCCCCCCC
Confidence 35999999999999998 997 999776
No 127
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=69.39 E-value=2.9 Score=30.11 Aligned_cols=25 Identities=24% Similarity=0.541 Sum_probs=18.2
Q ss_pred ccCccccceeeecCCcceEEe-cccc
Q 010003 374 RRCQQCRRMIELTHGCYHMTC-WCGH 398 (520)
Q Consensus 374 k~CP~C~~~IeK~~GCnhMtC-~Cg~ 398 (520)
+.||+|+--+....-=+...| +||+
T Consensus 20 ~~CPrCG~gvfmA~H~dR~~CGkCgy 45 (51)
T COG1998 20 RFCPRCGPGVFMADHKDRWACGKCGY 45 (51)
T ss_pred ccCCCCCCcchhhhcCceeEeccccc
Confidence 899999976665544457778 5876
No 128
>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=68.51 E-value=4.9 Score=27.11 Aligned_cols=33 Identities=21% Similarity=0.473 Sum_probs=18.7
Q ss_pred eeccCCCCCeeecCcccccccccCCCCCCCCceeCCCCCcce
Q 010003 291 IYCPFPNCSVLLDPRECLSARASSSSQSDNSCVECPVCERFI 332 (520)
Q Consensus 291 ~~CP~p~C~~~~~~~~~~~~~~~~~~~~~~~~~~Cp~C~~~f 332 (520)
+.||+ |+..+...... .......+.||.|+..|
T Consensus 3 ~~CP~--C~~~~~v~~~~-------~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCPN--CKTSFRVVDSQ-------LGANGGKVRCGKCGHVW 35 (38)
T ss_pred EECCC--CCCEEEeCHHH-------cCCCCCEEECCCCCCEE
Confidence 56886 88655443211 00112248899998765
No 129
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=67.68 E-value=2.7 Score=47.92 Aligned_cols=50 Identities=26% Similarity=0.681 Sum_probs=36.3
Q ss_pred ccccccccccccC-----CCCeeec-cCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCcccc
Q 010003 203 SPENCSICCEDKP-----YPMMITM-KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFIS 260 (520)
Q Consensus 203 ~~~~C~IC~e~~~-----~~~~~~l-~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~ 260 (520)
...+|+|||.-.. .+. -++ .|.|.|...|+-+|+.+.-. -+||. |...++
T Consensus 1468 G~eECaICYsvL~~vdr~lPs-krC~TCknKFH~~CLyKWf~Ss~~-----s~CPl--CRseit 1523 (1525)
T COG5219 1468 GHEECAICYSVLDMVDRSLPS-KRCATCKNKFHTRCLYKWFASSAR-----SNCPL--CRSEIT 1523 (1525)
T ss_pred CcchhhHHHHHHHHHhccCCc-cccchhhhhhhHHHHHHHHHhcCC-----CCCCc--cccccc
Confidence 4678999996543 111 123 79999999999999986543 26998 887664
No 130
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=65.25 E-value=4.7 Score=39.85 Aligned_cols=53 Identities=30% Similarity=0.627 Sum_probs=39.5
Q ss_pred CccccccccccccCCCCeeecc--CCCcccHHHHHHHHHHhhhCCCCccccCC-CCcC
Q 010003 202 KSPENCSICCEDKPYPMMITMK--CSHKFCSHCMRTYIDGKVQSSQVPIRCPQ-LRCK 256 (520)
Q Consensus 202 ~~~~~C~IC~e~~~~~~~~~l~--CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~-~~C~ 256 (520)
....-|.+|-+......|+.++ =.|.||+-|-++.|+.+-..+ .+.||. ..|.
T Consensus 266 ~apLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSResIK~Qg~sg--evYCPSGdkCP 321 (352)
T KOG3579|consen 266 SAPLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSRESIKQQGASG--EVYCPSGDKCP 321 (352)
T ss_pred CCceeehhhhhhhccCceeecCCCcccceecccCHHHHHhhcCCC--ceeCCCCCcCc
Confidence 3458999999988777776652 369999999999998765544 456774 3564
No 131
>PRK04023 DNA polymerase II large subunit; Validated
Probab=64.91 E-value=5.1 Score=46.44 Aligned_cols=26 Identities=12% Similarity=0.133 Sum_probs=12.8
Q ss_pred HHHHHHHHHHHHHHHHcCcceeeeecc
Q 010003 108 VADYLALMDGLITAVQNKIRCVYAFTD 134 (520)
Q Consensus 108 ~AE~~ALi~~l~~a~~~~i~~v~i~~D 134 (520)
.++-..+..+....+.+|- -+..|+|
T Consensus 386 ~~~A~~~~~~VeeIldlGe-iLi~yGd 411 (1121)
T PRK04023 386 VEEAKEIRDDVEEILDLGE-ILINYGD 411 (1121)
T ss_pred HHHHHHHhhchhhhhhhhh-hhcccch
Confidence 4555555555555554433 2334454
No 132
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=64.84 E-value=1.7 Score=43.65 Aligned_cols=22 Identities=32% Similarity=0.833 Sum_probs=18.8
Q ss_pred ceeCCCCCcceeccCCCccCCC
Q 010003 322 CVECPVCERFICVECGVPWHSS 343 (520)
Q Consensus 322 ~~~Cp~C~~~fC~~C~~~wH~~ 343 (520)
.++|..|+..||..|..-.|..
T Consensus 345 ~y~C~~Ck~~FCldCDv~iHes 366 (378)
T KOG2807|consen 345 RYRCESCKNVFCLDCDVFIHES 366 (378)
T ss_pred cEEchhccceeeccchHHHHhh
Confidence 4899999999999999876654
No 133
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=64.22 E-value=5 Score=45.10 Aligned_cols=12 Identities=17% Similarity=0.479 Sum_probs=8.8
Q ss_pred ccCccccceeee
Q 010003 374 RRCQQCRRMIEL 385 (520)
Q Consensus 374 k~CP~C~~~IeK 385 (520)
+-||+|++..-+
T Consensus 42 ~fC~~CG~~~~~ 53 (645)
T PRK14559 42 AHCPNCGAETGT 53 (645)
T ss_pred ccccccCCcccc
Confidence 788888886543
No 134
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=64.02 E-value=4.3 Score=35.78 Aligned_cols=24 Identities=29% Similarity=0.786 Sum_probs=19.0
Q ss_pred ccCccccceeeecCCcceEEecccccccccccc
Q 010003 374 RRCQQCRRMIELTHGCYHMTCWCGHEFCYSCGA 406 (520)
Q Consensus 374 k~CP~C~~~IeK~~GCnhMtC~Cg~~FCy~C~~ 406 (520)
..||.|+++..+-+ |.-||-+|+.
T Consensus 29 ~hCp~Cg~PLF~Kd---------G~v~CPvC~~ 52 (131)
T COG1645 29 KHCPKCGTPLFRKD---------GEVFCPVCGY 52 (131)
T ss_pred hhCcccCCcceeeC---------CeEECCCCCc
Confidence 89999999987643 5678888874
No 135
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=63.97 E-value=1.9 Score=41.41 Aligned_cols=16 Identities=38% Similarity=1.095 Sum_probs=14.1
Q ss_pred ccccccccccccccCC
Q 010003 396 CGHEFCYSCGAEYRDG 411 (520)
Q Consensus 396 Cg~~FCy~C~~~~~~~ 411 (520)
|||-|||-|+-.|-..
T Consensus 65 CGHLFCWpClyqWl~~ 80 (230)
T KOG0823|consen 65 CGHLFCWPCLYQWLQT 80 (230)
T ss_pred cccceehHHHHHHHhh
Confidence 9999999999999643
No 136
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=63.94 E-value=11 Score=42.96 Aligned_cols=38 Identities=16% Similarity=0.391 Sum_probs=32.1
Q ss_pred ccccccccccccCCCCeeeccCCCcccHHHHHHHHHHh
Q 010003 203 SPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGK 240 (520)
Q Consensus 203 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~ 240 (520)
+...|.+|.-..-...++.++|||.|..+|+.+++...
T Consensus 816 p~d~C~~C~~~ll~~pF~vf~CgH~FH~~Cl~~~v~~~ 853 (911)
T KOG2034|consen 816 PQDSCDHCGRPLLIKPFYVFPCGHCFHRDCLIRHVLSL 853 (911)
T ss_pred CccchHHhcchhhcCcceeeeccchHHHHHHHHHHHcc
Confidence 46789999988777777778999999999999987643
No 137
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=63.36 E-value=4.9 Score=34.48 Aligned_cols=23 Identities=39% Similarity=0.847 Sum_probs=19.8
Q ss_pred CceeCCCCCcceeccCCCccCCC
Q 010003 321 SCVECPVCERFICVECGVPWHSS 343 (520)
Q Consensus 321 ~~~~Cp~C~~~fC~~C~~~wH~~ 343 (520)
....|++|+..||..|..-+|..
T Consensus 80 ~~y~C~~C~~~FC~dCD~fiHe~ 102 (112)
T TIGR00622 80 HRYVCAVCKNVFCVDCDVFVHES 102 (112)
T ss_pred cceeCCCCCCccccccchhhhhh
Confidence 34789999999999999888864
No 138
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=63.01 E-value=5.5 Score=38.87 Aligned_cols=55 Identities=22% Similarity=0.515 Sum_probs=39.3
Q ss_pred CccccccccccccCCCCeee-c-cCC-----CcccHHHHHHHHHHhhhCC-CCccccCCCCcCcc
Q 010003 202 KSPENCSICCEDKPYPMMIT-M-KCS-----HKFCSHCMRTYIDGKVQSS-QVPIRCPQLRCKYF 258 (520)
Q Consensus 202 ~~~~~C~IC~e~~~~~~~~~-l-~Cg-----H~fC~~Cl~~~i~~~i~~~-~~~i~CP~~~C~~~ 258 (520)
.....|-|||.+...+.... + +|. |.....|+..|+..+-.++ ..++.||+ |+..
T Consensus 18 e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~Q--CqTE 80 (293)
T KOG3053|consen 18 ELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQ--CQTE 80 (293)
T ss_pred ccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechh--hcch
Confidence 45678999998766543321 1 553 6799999999998876643 34789999 8753
No 139
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=62.92 E-value=1.3 Score=41.64 Aligned_cols=32 Identities=25% Similarity=0.679 Sum_probs=24.2
Q ss_pred CccCccccceeeecCCcceEEeccccccccccccccc
Q 010003 373 WRRCQQCRRMIELTHGCYHMTCWCGHEFCYSCGAEYR 409 (520)
Q Consensus 373 ~k~CP~C~~~IeK~~GCnhMtC~Cg~~FCy~C~~~~~ 409 (520)
.-.||-|.-.+..- +.=.|||-|||.|...|.
T Consensus 18 ~~~CpICld~~~dP-----VvT~CGH~FC~~CI~~wl 49 (193)
T PLN03208 18 DFDCNICLDQVRDP-----VVTLCGHLFCWPCIHKWT 49 (193)
T ss_pred ccCCccCCCcCCCc-----EEcCCCchhHHHHHHHHH
Confidence 36899998876421 333599999999999884
No 140
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=62.00 E-value=1.7 Score=43.15 Aligned_cols=40 Identities=25% Similarity=0.801 Sum_probs=30.1
Q ss_pred cccccccccccCCCCeeeccCCCc-ccHHHHHHHHHHhhhCCCCccccCCCCcCcc
Q 010003 204 PENCSICCEDKPYPMMITMKCSHK-FCSHCMRTYIDGKVQSSQVPIRCPQLRCKYF 258 (520)
Q Consensus 204 ~~~C~IC~e~~~~~~~~~l~CgH~-fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~ 258 (520)
...|.||||.. -+.+-|.|||. -|..|=+..- -||. |.+.
T Consensus 300 ~~LC~ICmDaP--~DCvfLeCGHmVtCt~CGkrm~-----------eCPI--CRqy 340 (350)
T KOG4275|consen 300 RRLCAICMDAP--RDCVFLECGHMVTCTKCGKRMN-----------ECPI--CRQY 340 (350)
T ss_pred HHHHHHHhcCC--cceEEeecCcEEeehhhccccc-----------cCch--HHHH
Confidence 67899999754 35677899996 7999976553 4887 7554
No 141
>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=61.71 E-value=5.1 Score=40.52 Aligned_cols=48 Identities=29% Similarity=0.711 Sum_probs=0.0
Q ss_pred eCCCCC-----------------cceeccCCCccCCCCCchhhhcCchhhcCchHHHHHHHHhccCCccCccccc-----
Q 010003 324 ECPVCE-----------------RFICVECGVPWHSSLSCEEYQNLPLEERDAGDITLHRLAQNKRWRRCQQCRR----- 381 (520)
Q Consensus 324 ~Cp~C~-----------------~~fC~~C~~~wH~~~tC~e~~~~~~~~~~~~~~~l~~l~~~~~~k~CP~C~~----- 381 (520)
.||.|| +.+|..|...||-.. -.||.|+.
T Consensus 174 ~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R-----------------------------~~Cp~Cg~~~~~~ 224 (290)
T PF04216_consen 174 YCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVR-----------------------------IKCPYCGNTDHEK 224 (290)
T ss_dssp S-TTT---EEEEEEE------EEEEEETTT--EEE--T-----------------------------TS-TTT---SS-E
T ss_pred cCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecC-----------------------------CCCcCCCCCCCcc
Q ss_pred ----eeeecCCcceEEec-ccccc
Q 010003 382 ----MIELTHGCYHMTCW-CGHEF 400 (520)
Q Consensus 382 ----~IeK~~GCnhMtC~-Cg~~F 400 (520)
..+-..+---.+|. |+.++
T Consensus 225 l~~~~~e~~~~~rve~C~~C~~Yl 248 (290)
T PF04216_consen 225 LEYFTVEGEPAYRVEVCESCGSYL 248 (290)
T ss_dssp EE--------SEEEEEETTTTEEE
T ss_pred eeeEecCCCCcEEEEECCcccchH
No 142
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=61.34 E-value=2.9 Score=41.65 Aligned_cols=45 Identities=29% Similarity=0.587 Sum_probs=33.8
Q ss_pred cccccccccccCCCCeeeccCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCccc
Q 010003 204 PENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFI 259 (520)
Q Consensus 204 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l 259 (520)
.+-|.||-..+..+ +...|+|.||..|....++. .-+|+. |.+.+
T Consensus 241 Pf~c~icr~~f~~p--Vvt~c~h~fc~~ca~~~~qk-------~~~c~v--C~~~t 285 (313)
T KOG1813|consen 241 PFKCFICRKYFYRP--VVTKCGHYFCEVCALKPYQK-------GEKCYV--CSQQT 285 (313)
T ss_pred Cccccccccccccc--hhhcCCceeehhhhcccccc-------CCccee--ccccc
Confidence 57899999988655 66799999999998776652 135776 76543
No 143
>PRK00420 hypothetical protein; Validated
Probab=60.70 E-value=5.7 Score=34.16 Aligned_cols=27 Identities=22% Similarity=0.453 Sum_probs=20.9
Q ss_pred ccCccccceeee-cCCcceEEeccccccccccccccc
Q 010003 374 RRCQQCRRMIEL-THGCYHMTCWCGHEFCYSCGAEYR 409 (520)
Q Consensus 374 k~CP~C~~~IeK-~~GCnhMtC~Cg~~FCy~C~~~~~ 409 (520)
..||.|+.++.+ .+ |..||-.|+..+.
T Consensus 24 ~~CP~Cg~pLf~lk~---------g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 24 KHCPVCGLPLFELKD---------GEVVCPVHGKVYI 51 (112)
T ss_pred CCCCCCCCcceecCC---------CceECCCCCCeee
Confidence 899999999886 33 5667888887654
No 144
>PF14149 YhfH: YhfH-like protein
Probab=60.69 E-value=1.2 Score=30.15 Aligned_cols=30 Identities=30% Similarity=0.744 Sum_probs=24.3
Q ss_pred HHhccCCccCccccceeeecCCcceEEe-cc
Q 010003 367 LAQNKRWRRCQQCRRMIELTHGCYHMTC-WC 396 (520)
Q Consensus 367 l~~~~~~k~CP~C~~~IeK~~GCnhMtC-~C 396 (520)
+.++...|.|+.|+..|+--.-|..++| +|
T Consensus 7 FfrnLp~K~C~~CG~~i~EQ~E~Y~n~C~~C 37 (37)
T PF14149_consen 7 FFRNLPPKKCTECGKEIEEQAECYGNECDRC 37 (37)
T ss_pred HHHhCCCcccHHHHHHHHHHHHHHhCcCCCC
Confidence 3455666999999999998888888888 35
No 145
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=60.48 E-value=18 Score=41.31 Aligned_cols=41 Identities=27% Similarity=0.789 Sum_probs=30.9
Q ss_pred cccccccccccCCCCeeeccCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCc
Q 010003 204 PENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKY 257 (520)
Q Consensus 204 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~ 257 (520)
.-.|..|--+...+ ++.+.|||.|.+.|+. ++ .-.||. |..
T Consensus 840 ~skCs~C~~~LdlP-~VhF~CgHsyHqhC~e--------~~--~~~CP~--C~~ 880 (933)
T KOG2114|consen 840 VSKCSACEGTLDLP-FVHFLCGHSYHQHCLE--------DK--EDKCPK--CLP 880 (933)
T ss_pred eeeecccCCccccc-eeeeecccHHHHHhhc--------cC--cccCCc--cch
Confidence 35799998776544 6778999999999998 22 236987 765
No 146
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=60.46 E-value=8.3 Score=39.03 Aligned_cols=48 Identities=21% Similarity=0.520 Sum_probs=34.7
Q ss_pred ccccccccccccCCCCeeeccCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCcc
Q 010003 203 SPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYF 258 (520)
Q Consensus 203 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~ 258 (520)
....|++|......+ .+-.-=|-+||-.|+.+|+... + +||..+|+..
T Consensus 299 ~~~~CpvClk~r~Np-tvl~vSGyVfCY~Ci~~Yv~~~---~----~CPVT~~p~~ 346 (357)
T KOG0826|consen 299 DREVCPVCLKKRQNP-TVLEVSGYVFCYPCIFSYVVNY---G----HCPVTGYPAS 346 (357)
T ss_pred ccccChhHHhccCCC-ceEEecceEEeHHHHHHHHHhc---C----CCCccCCcch
Confidence 467899999876544 2222458999999999999832 2 6998777553
No 147
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=60.15 E-value=7.7 Score=25.85 Aligned_cols=25 Identities=28% Similarity=0.642 Sum_probs=13.4
Q ss_pred ccCccccceeeec----CCcceEEec-ccc
Q 010003 374 RRCQQCRRMIELT----HGCYHMTCW-CGH 398 (520)
Q Consensus 374 k~CP~C~~~IeK~----~GCnhMtC~-Cg~ 398 (520)
|-||+|+.+++.. ++=..+.|. ||+
T Consensus 1 kfC~~CG~~l~~~ip~gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 1 KFCPQCGGPLERRIPEGDDRERLVCPACGF 30 (34)
T ss_dssp -B-TTT--B-EEE--TT-SS-EEEETTTTE
T ss_pred CccccccChhhhhcCCCCCccceECCCCCC
Confidence 4699999988875 456667885 775
No 148
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=59.78 E-value=7.8 Score=27.02 Aligned_cols=22 Identities=27% Similarity=0.833 Sum_probs=16.9
Q ss_pred ccCccccceeee-cCCcceEEec-cc
Q 010003 374 RRCQQCRRMIEL-THGCYHMTCW-CG 397 (520)
Q Consensus 374 k~CP~C~~~IeK-~~GCnhMtC~-Cg 397 (520)
..||.|++++.+ .+| .+.|. |+
T Consensus 18 ~~Cp~C~~PL~~~k~g--~~~Cv~C~ 41 (41)
T PF06677_consen 18 EHCPDCGTPLMRDKDG--KIYCVSCG 41 (41)
T ss_pred CccCCCCCeeEEecCC--CEECCCCC
Confidence 789999999988 455 57774 53
No 149
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=59.37 E-value=5.6 Score=33.50 Aligned_cols=23 Identities=26% Similarity=0.636 Sum_probs=17.7
Q ss_pred cCccccceeeecCCcceEEec-cccc
Q 010003 375 RCQQCRRMIELTHGCYHMTCW-CGHE 399 (520)
Q Consensus 375 ~CP~C~~~IeK~~GCnhMtC~-Cg~~ 399 (520)
-||+|+.++...+ +.+.|+ |++.
T Consensus 2 fC~~Cg~~l~~~~--~~~~C~~C~~~ 25 (104)
T TIGR01384 2 FCPKCGSLMTPKN--GVYVCPSCGYE 25 (104)
T ss_pred CCcccCcccccCC--CeEECcCCCCc
Confidence 6999999987655 378885 7765
No 150
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=58.78 E-value=3.2 Score=41.13 Aligned_cols=40 Identities=35% Similarity=0.751 Sum_probs=28.3
Q ss_pred ccCccccceeeecCCcceEEe--cccccccccccccccCCCCcccCCCCCC
Q 010003 374 RRCQQCRRMIELTHGCYHMTC--WCGHEFCYSCGAEYRDGQQTCQCAFWDE 422 (520)
Q Consensus 374 k~CP~C~~~IeK~~GCnhMtC--~Cg~~FCy~C~~~~~~~~~~c~C~~~~~ 422 (520)
-+|--|+-.|. +-| +|||.||++|-..+-+.+.. ||.-..
T Consensus 26 lrC~IC~~~i~-------ip~~TtCgHtFCslCIR~hL~~qp~--CP~Cr~ 67 (391)
T COG5432 26 LRCRICDCRIS-------IPCETTCGHTFCSLCIRRHLGTQPF--CPVCRE 67 (391)
T ss_pred HHhhhhhheee-------cceecccccchhHHHHHHHhcCCCC--Cccccc
Confidence 47887877775 778 39999999998887655544 454333
No 151
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=58.65 E-value=2.5 Score=47.23 Aligned_cols=19 Identities=16% Similarity=0.429 Sum_probs=11.7
Q ss_pred cCCCcccHHHHHHHHHHhh
Q 010003 223 KCSHKFCSHCMRTYIDGKV 241 (520)
Q Consensus 223 ~CgH~fC~~Cl~~~i~~~i 241 (520)
.|+|.+|..||+.+...-+
T Consensus 120 ~~~~~~CP~Ci~s~~DqL~ 138 (1134)
T KOG0825|consen 120 THVENQCPNCLKSCNDQLE 138 (1134)
T ss_pred hhhhhhhhHHHHHHHHHhh
Confidence 3666666666666655444
No 152
>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=58.47 E-value=6.7 Score=33.24 Aligned_cols=26 Identities=23% Similarity=0.579 Sum_probs=18.3
Q ss_pred ccCccccceeeecCCcceEEec-ccccc
Q 010003 374 RRCQQCRRMIELTHGCYHMTCW-CGHEF 400 (520)
Q Consensus 374 k~CP~C~~~IeK~~GCnhMtC~-Cg~~F 400 (520)
-.||+|+.-..-.+|=+ +.|+ |+|+|
T Consensus 3 p~CP~C~seytY~dg~~-~iCpeC~~EW 29 (109)
T TIGR00686 3 PPCPKCNSEYTYHDGTQ-LICPSCLYEW 29 (109)
T ss_pred CcCCcCCCcceEecCCe-eECccccccc
Confidence 47999999877777754 6664 55543
No 153
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=58.45 E-value=3.3 Score=41.83 Aligned_cols=34 Identities=26% Similarity=0.662 Sum_probs=26.9
Q ss_pred cCccccceeeecCCcceEEeccccccccccccccc
Q 010003 375 RCQQCRRMIELTHGCYHMTCWCGHEFCYSCGAEYR 409 (520)
Q Consensus 375 ~CP~C~~~IeK~~GCnhMtC~Cg~~FCy~C~~~~~ 409 (520)
-||-|--+|.-++ =|..-|.|||+.|-.|...++
T Consensus 16 ~cplcie~mditd-knf~pc~cgy~ic~fc~~~ir 49 (480)
T COG5175 16 YCPLCIEPMDITD-KNFFPCPCGYQICQFCYNNIR 49 (480)
T ss_pred cCccccccccccc-CCcccCCcccHHHHHHHHHHH
Confidence 4999988876544 377889999998888877765
No 154
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=57.98 E-value=5 Score=30.79 Aligned_cols=27 Identities=37% Similarity=0.919 Sum_probs=11.8
Q ss_pred ccCccccceeeec---CCcceEEeccccccccccccc
Q 010003 374 RRCQQCRRMIELT---HGCYHMTCWCGHEFCYSCGAE 407 (520)
Q Consensus 374 k~CP~C~~~IeK~---~GCnhMtC~Cg~~FCy~C~~~ 407 (520)
-+|++|....... +||.|+ ||+.|-.+
T Consensus 8 LrCs~C~~~l~~pv~l~~CeH~-------fCs~Ci~~ 37 (65)
T PF14835_consen 8 LRCSICFDILKEPVCLGGCEHI-------FCSSCIRD 37 (65)
T ss_dssp TS-SSS-S--SS-B---SSS---------B-TTTGGG
T ss_pred cCCcHHHHHhcCCceeccCccH-------HHHHHhHH
Confidence 6899999876543 555555 55666544
No 155
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=57.83 E-value=7.5 Score=31.62 Aligned_cols=27 Identities=26% Similarity=0.534 Sum_probs=22.3
Q ss_pred ccCccccceeeecCCcceEEec-ccccc
Q 010003 374 RRCQQCRRMIELTHGCYHMTCW-CGHEF 400 (520)
Q Consensus 374 k~CP~C~~~IeK~~GCnhMtC~-Cg~~F 400 (520)
-.||.|+....|..+=---.|+ ||+.|
T Consensus 36 ~~Cp~C~~~~VkR~a~GIW~C~kCg~~f 63 (89)
T COG1997 36 HVCPFCGRTTVKRIATGIWKCRKCGAKF 63 (89)
T ss_pred CcCCCCCCcceeeeccCeEEcCCCCCee
Confidence 7899999999998887777775 76665
No 156
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=57.17 E-value=3.7 Score=32.41 Aligned_cols=51 Identities=24% Similarity=0.525 Sum_probs=34.0
Q ss_pred cccccccccccCC---------CCeeec--cCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCcccc
Q 010003 204 PENCSICCEDKPY---------PMMITM--KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFIS 260 (520)
Q Consensus 204 ~~~C~IC~e~~~~---------~~~~~l--~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~ 260 (520)
..+|.||--.|.. .+...+ .|.|.|-..|+.+++.+.-.. -.||. |.+.+.
T Consensus 20 ~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq----~~CPm--cRq~~~ 81 (84)
T KOG1493|consen 20 DETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQ----GQCPM--CRQTWQ 81 (84)
T ss_pred CCccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCcccc----ccCCc--chheeE
Confidence 3488888766543 222112 588999999999998865432 35888 776543
No 157
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=56.79 E-value=2.8 Score=46.86 Aligned_cols=14 Identities=29% Similarity=0.733 Sum_probs=11.2
Q ss_pred CCCCcceeccCCCc
Q 010003 326 PVCERFICVECGVP 339 (520)
Q Consensus 326 p~C~~~fC~~C~~~ 339 (520)
++|++.||..|-.+
T Consensus 659 ~kC~H~FC~~Cvq~ 672 (698)
T KOG0978|consen 659 TKCGHVFCEECVQT 672 (698)
T ss_pred HhcchHHHHHHHHH
Confidence 37899999988764
No 158
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=56.69 E-value=3.3 Score=45.34 Aligned_cols=36 Identities=22% Similarity=0.654 Sum_probs=28.3
Q ss_pred cccccccccccCCCCe--eeccCCCcccHHHHHHHHHH
Q 010003 204 PENCSICCEDKPYPMM--ITMKCSHKFCSHCMRTYIDG 239 (520)
Q Consensus 204 ~~~C~IC~e~~~~~~~--~~l~CgH~fC~~Cl~~~i~~ 239 (520)
...|.||+..+....+ +++.|||.+|..|++.....
T Consensus 11 ~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~lyn~ 48 (861)
T KOG3161|consen 11 LLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLYNA 48 (861)
T ss_pred HhhchHHHHHHHHHhcCcccccccchHHHHHHHhHhhc
Confidence 4679999887765433 56799999999999987653
No 159
>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=55.40 E-value=6.1 Score=34.52 Aligned_cols=26 Identities=15% Similarity=0.144 Sum_probs=17.9
Q ss_pred ccCccccceeeecCCcceEEec-ccccc
Q 010003 374 RRCQQCRRMIELTHGCYHMTCW-CGHEF 400 (520)
Q Consensus 374 k~CP~C~~~IeK~~GCnhMtC~-Cg~~F 400 (520)
|.||+|++.+---.- +-++|+ ||+.|
T Consensus 10 r~Cp~cg~kFYDLnk-~p~vcP~cg~~~ 36 (129)
T TIGR02300 10 RICPNTGSKFYDLNR-RPAVSPYTGEQF 36 (129)
T ss_pred ccCCCcCccccccCC-CCccCCCcCCcc
Confidence 789999998654333 667775 66653
No 160
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=55.15 E-value=8.7 Score=32.27 Aligned_cols=28 Identities=21% Similarity=0.532 Sum_probs=18.5
Q ss_pred CccCcccccee---eecCCcceEEec-ccccc
Q 010003 373 WRRCQQCRRMI---ELTHGCYHMTCW-CGHEF 400 (520)
Q Consensus 373 ~k~CP~C~~~I---eK~~GCnhMtC~-Cg~~F 400 (520)
.-.||+|+... .+..|=-|.+|. ||+.+
T Consensus 21 ~f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y~ 52 (99)
T PRK14892 21 IFECPRCGKVSISVKIKKNIAIITCGNCGLYT 52 (99)
T ss_pred EeECCCCCCeEeeeecCCCcceEECCCCCCcc
Confidence 36899999432 233466688885 77763
No 161
>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=54.82 E-value=7.7 Score=27.15 Aligned_cols=24 Identities=21% Similarity=0.778 Sum_probs=15.3
Q ss_pred eeCCCCCcceeccCCCccCCCCCchh
Q 010003 323 VECPVCERFICVECGVPWHSSLSCEE 348 (520)
Q Consensus 323 ~~Cp~C~~~fC~~C~~~wH~~~tC~e 348 (520)
+.|+.|+..||...+.+ ..+.|..
T Consensus 14 ~~C~~C~~~FC~~Hr~~--e~H~C~~ 37 (43)
T PF01428_consen 14 FKCKHCGKSFCLKHRLP--EDHNCSK 37 (43)
T ss_dssp EE-TTTS-EE-TTTHST--TTCT-SS
T ss_pred eECCCCCcccCccccCc--cccCCcc
Confidence 88999999999998875 3456654
No 162
>PF01599 Ribosomal_S27: Ribosomal protein S27a; InterPro: IPR002906 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 family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP) (IPR000626 from INTERPRO). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis []. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2K4X_A 3U5C_f 3U5G_f 2XZN_9 2XZM_9.
Probab=54.20 E-value=8.6 Score=27.64 Aligned_cols=25 Identities=20% Similarity=0.529 Sum_probs=19.7
Q ss_pred ccCc--cccceeeecCCcceEEe-cccc
Q 010003 374 RRCQ--QCRRMIELTHGCYHMTC-WCGH 398 (520)
Q Consensus 374 k~CP--~C~~~IeK~~GCnhMtC-~Cg~ 398 (520)
+.|| +|+.-+.-..--+..+| +||+
T Consensus 19 k~CP~~~CG~GvFMA~H~dR~~CGKCg~ 46 (47)
T PF01599_consen 19 KECPSPRCGAGVFMAEHKDRHYCGKCGY 46 (47)
T ss_dssp EE-TSTTTTSSSEEEE-SSEEEETTTSS
T ss_pred hcCCCcccCCceEeeecCCCccCCCccc
Confidence 8899 99998887777789999 5886
No 163
>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=54.12 E-value=8.4 Score=29.71 Aligned_cols=27 Identities=26% Similarity=0.540 Sum_probs=20.0
Q ss_pred CccCccccceeeecCCcceEEec-cccc
Q 010003 373 WRRCQQCRRMIELTHGCYHMTCW-CGHE 399 (520)
Q Consensus 373 ~k~CP~C~~~IeK~~GCnhMtC~-Cg~~ 399 (520)
.+.||.|+....+...=..++|+ ||+.
T Consensus 28 Sq~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 28 SQTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred ccCccCcccccccccccceEEcCCCCCE
Confidence 38999999999884444567775 7665
No 164
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=54.07 E-value=13 Score=38.16 Aligned_cols=45 Identities=24% Similarity=0.659 Sum_probs=30.1
Q ss_pred CCccccccccccccCCCCeeeccCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCccc
Q 010003 201 DKSPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFI 259 (520)
Q Consensus 201 ~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l 259 (520)
......|.||.++... .+-++|||+-| |.--+-. .+.||. |.+.|
T Consensus 302 ~~~p~lcVVcl~e~~~--~~fvpcGh~cc--ct~cs~~--------l~~CPv--CR~rI 346 (355)
T KOG1571|consen 302 LPQPDLCVVCLDEPKS--AVFVPCGHVCC--CTLCSKH--------LPQCPV--CRQRI 346 (355)
T ss_pred cCCCCceEEecCCccc--eeeecCCcEEE--chHHHhh--------CCCCch--hHHHH
Confidence 3456789999988653 45579999976 5543321 235998 76654
No 165
>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=53.81 E-value=11 Score=27.88 Aligned_cols=27 Identities=33% Similarity=0.630 Sum_probs=19.3
Q ss_pred ccCccccceeeecCCc--ceEEec-ccccc
Q 010003 374 RRCQQCRRMIELTHGC--YHMTCW-CGHEF 400 (520)
Q Consensus 374 k~CP~C~~~IeK~~GC--nhMtC~-Cg~~F 400 (520)
-.||.|+..|+..+.= -.+.|. ||.++
T Consensus 3 ~~CP~CG~~iev~~~~~GeiV~Cp~CGael 32 (54)
T TIGR01206 3 FECPDCGAEIELENPELGELVICDECGAEL 32 (54)
T ss_pred cCCCCCCCEEecCCCccCCEEeCCCCCCEE
Confidence 4799999999886522 257775 77665
No 166
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 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 MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=52.95 E-value=11 Score=27.30 Aligned_cols=47 Identities=17% Similarity=0.594 Sum_probs=23.4
Q ss_pred ccccccccccCCCCeeeccCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCc
Q 010003 205 ENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKY 257 (520)
Q Consensus 205 ~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~ 257 (520)
..|+|-+.....+ .....|.|.-|++ +..|++.....+.| +||. |++
T Consensus 3 L~CPls~~~i~~P-~Rg~~C~H~~CFD-l~~fl~~~~~~~~W--~CPi--C~~ 49 (50)
T PF02891_consen 3 LRCPLSFQRIRIP-VRGKNCKHLQCFD-LESFLESNQRTPKW--KCPI--CNK 49 (50)
T ss_dssp SB-TTTSSB-SSE-EEETT--SS--EE-HHHHHHHHHHS-----B-TT--T--
T ss_pred eeCCCCCCEEEeC-ccCCcCcccceEC-HHHHHHHhhccCCe--ECcC--CcC
Confidence 4677777655433 2334899998876 77788877665554 6998 764
No 167
>TIGR02443 conserved hypothetical metal-binding protein. Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various Proteobacteria.
Probab=52.57 E-value=13 Score=27.96 Aligned_cols=27 Identities=19% Similarity=0.423 Sum_probs=20.6
Q ss_pred ccCccccce----eeecCCcceEEec-ccccc
Q 010003 374 RRCQQCRRM----IELTHGCYHMTCW-CGHEF 400 (520)
Q Consensus 374 k~CP~C~~~----IeK~~GCnhMtC~-Cg~~F 400 (520)
-.||+|+.+ .-+..|=.++.|. |||..
T Consensus 10 A~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~~ 41 (59)
T TIGR02443 10 AVCPACSAQDTLAMWKENNIELVECVECGYQE 41 (59)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEeccCCCcc
Confidence 479999975 4456777899995 99853
No 168
>PRK10220 hypothetical protein; Provisional
Probab=51.19 E-value=11 Score=32.00 Aligned_cols=25 Identities=24% Similarity=0.628 Sum_probs=17.1
Q ss_pred ccCccccceeeecCCcceEEec-cccc
Q 010003 374 RRCQQCRRMIELTHGCYHMTCW-CGHE 399 (520)
Q Consensus 374 k~CP~C~~~IeK~~GCnhMtC~-Cg~~ 399 (520)
-.||+|..-..-.+|=+ +.|+ |+|+
T Consensus 4 P~CP~C~seytY~d~~~-~vCpeC~hE 29 (111)
T PRK10220 4 PHCPKCNSEYTYEDNGM-YICPECAHE 29 (111)
T ss_pred CcCCCCCCcceEcCCCe-EECCcccCc
Confidence 57999998877666643 5554 5544
No 169
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=49.94 E-value=4.6 Score=39.66 Aligned_cols=39 Identities=31% Similarity=0.702 Sum_probs=27.8
Q ss_pred ccCccccceeeecCCcceEEec-cccccccccccc-ccCCCCcccCCC
Q 010003 374 RRCQQCRRMIELTHGCYHMTCW-CGHEFCYSCGAE-YRDGQQTCQCAF 419 (520)
Q Consensus 374 k~CP~C~~~IeK~~GCnhMtC~-Cg~~FCy~C~~~-~~~~~~~c~C~~ 419 (520)
++|+=|-...++ -.|+ |||-|||.|+-. |.... +-+||+
T Consensus 216 ~kC~lC~e~~~~------ps~t~CgHlFC~~Cl~~~~t~~k-~~~Cpl 256 (271)
T COG5574 216 YKCFLCLEEPEV------PSCTPCGHLFCLSCLLISWTKKK-YEFCPL 256 (271)
T ss_pred cceeeeecccCC------cccccccchhhHHHHHHHHHhhc-cccCch
Confidence 789999887763 4565 999999999877 76433 223554
No 170
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=49.86 E-value=14 Score=30.94 Aligned_cols=23 Identities=30% Similarity=0.885 Sum_probs=20.0
Q ss_pred cCCCcccHHHHHHHHHHhhhCCCCccccCC
Q 010003 223 KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQ 252 (520)
Q Consensus 223 ~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~ 252 (520)
.|.|.|.+.|+.+|+++.- .||.
T Consensus 80 ~CNHaFH~hCisrWlktr~-------vCPL 102 (114)
T KOG2930|consen 80 VCNHAFHFHCISRWLKTRN-------VCPL 102 (114)
T ss_pred ecchHHHHHHHHHHHhhcC-------cCCC
Confidence 7999999999999998642 5987
No 171
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=49.76 E-value=15 Score=26.34 Aligned_cols=33 Identities=21% Similarity=0.507 Sum_probs=22.5
Q ss_pred ccccccccCCCCeeeccC--CC---cccHHHHHHHHHH
Q 010003 207 CSICCEDKPYPMMITMKC--SH---KFCSHCMRTYIDG 239 (520)
Q Consensus 207 C~IC~e~~~~~~~~~l~C--gH---~fC~~Cl~~~i~~ 239 (520)
|-||+++...+.....+| .= ....+||.+|+..
T Consensus 1 CrIC~~~~~~~~~li~pC~C~Gs~~~vH~~CL~~W~~~ 38 (47)
T PF12906_consen 1 CRICLEGEEEDEPLISPCRCKGSMKYVHRSCLERWIRE 38 (47)
T ss_dssp ETTTTEE-SSSS-EE-SSS-SSCCGSEECCHHHHHHHH
T ss_pred CeEeCCcCCCCCceecccccCCCcchhHHHHHHHHHHh
Confidence 779998876554233354 33 6889999999987
No 172
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=49.49 E-value=14 Score=28.95 Aligned_cols=43 Identities=28% Similarity=0.741 Sum_probs=25.7
Q ss_pred cCccccceeeecCCcceEEec-cccc-----ccccccccccC----CCCcccCCC
Q 010003 375 RCQQCRRMIELTHGCYHMTCW-CGHE-----FCYSCGAEYRD----GQQTCQCAF 419 (520)
Q Consensus 375 ~CP~C~~~IeK~~GCnhMtC~-Cg~~-----FCy~C~~~~~~----~~~~c~C~~ 419 (520)
.||.|+..++..+ .+.+|. |... +|-.|+.++.. |...++|++
T Consensus 3 ~CP~C~~~L~~~~--~~~~C~~C~~~~~~~a~CPdC~~~Le~LkACGAvdYFC~~ 55 (70)
T PF07191_consen 3 TCPKCQQELEWQG--GHYHCEACQKDYKKEAFCPDCGQPLEVLKACGAVDYFCNH 55 (70)
T ss_dssp B-SSS-SBEEEET--TEEEETTT--EEEEEEE-TTT-SB-EEEEETTEEEEE-TT
T ss_pred cCCCCCCccEEeC--CEEECccccccceecccCCCcccHHHHHHHhcccceeecc
Confidence 6999999999888 788995 8765 69999988743 323445553
No 173
>PHA02929 N1R/p28-like protein; Provisional
Probab=48.78 E-value=9.7 Score=37.32 Aligned_cols=42 Identities=19% Similarity=0.396 Sum_probs=30.3
Q ss_pred CccCccccceeeecCCcc---eEEecccccccccccccccCCCCc
Q 010003 373 WRRCQQCRRMIELTHGCY---HMTCWCGHEFCYSCGAEYRDGQQT 414 (520)
Q Consensus 373 ~k~CP~C~~~IeK~~GCn---hMtC~Cg~~FCy~C~~~~~~~~~~ 414 (520)
-..||=|.-.+.....-+ -+.-.|+|.||..|...|...+.+
T Consensus 174 ~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~t 218 (238)
T PHA02929 174 DKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNT 218 (238)
T ss_pred CCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCC
Confidence 378999999876544322 244469999999999999765544
No 174
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=48.45 E-value=17 Score=34.90 Aligned_cols=53 Identities=21% Similarity=0.472 Sum_probs=41.0
Q ss_pred cccccccccccCCCCeeeccCCCcccHHHHHHHHHHhhhCCC--CccccCCCCcCccc
Q 010003 204 PENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQ--VPIRCPQLRCKYFI 259 (520)
Q Consensus 204 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~--~~i~CP~~~C~~~l 259 (520)
.-.|..|-.+....+.+.+.|-|.|.-.|+...... +-.+. .-.+||. |.+.|
T Consensus 50 ~pNC~LC~t~La~gdt~RLvCyhlfHW~ClneraA~-lPanTAPaGyqCP~--Cs~ei 104 (299)
T KOG3970|consen 50 NPNCRLCNTPLASGDTTRLVCYHLFHWKCLNERAAN-LPANTAPAGYQCPC--CSQEI 104 (299)
T ss_pred CCCCceeCCccccCcceeehhhhhHHHHHhhHHHhh-CCCcCCCCcccCCC--CCCcc
Confidence 457999999988888999999999999999987653 32222 2357988 88765
No 175
>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=48.38 E-value=18 Score=25.18 Aligned_cols=24 Identities=25% Similarity=0.632 Sum_probs=12.6
Q ss_pred cCccccce-eeecCCcceEEec-ccc
Q 010003 375 RCQQCRRM-IELTHGCYHMTCW-CGH 398 (520)
Q Consensus 375 ~CP~C~~~-IeK~~GCnhMtC~-Cg~ 398 (520)
.||.|+.. |.-+..=..+.|+ ||.
T Consensus 2 ~Cp~Cg~~~~~~D~~~g~~vC~~CG~ 27 (43)
T PF08271_consen 2 KCPNCGSKEIVFDPERGELVCPNCGL 27 (43)
T ss_dssp SBTTTSSSEEEEETTTTEEEETTT-B
T ss_pred CCcCCcCCceEEcCCCCeEECCCCCC
Confidence 58888775 3333344445664 543
No 176
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=48.00 E-value=13 Score=40.72 Aligned_cols=34 Identities=26% Similarity=0.696 Sum_probs=27.7
Q ss_pred ccCccccceeeecCCcceEEec-cccc-----cccccccc
Q 010003 374 RRCQQCRRMIELTHGCYHMTCW-CGHE-----FCYSCGAE 407 (520)
Q Consensus 374 k~CP~C~~~IeK~~GCnhMtC~-Cg~~-----FCy~C~~~ 407 (520)
-+||+|..+..-...=|.+.|. ||+. .|..|+..
T Consensus 223 ~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 223 LCCPNCDVSLTYHKKEGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred cCCCCCCCceEEecCCCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 4799999988766666799996 9987 68889864
No 177
>PF14353 CpXC: CpXC protein
Probab=47.89 E-value=9.5 Score=33.40 Aligned_cols=14 Identities=29% Similarity=0.562 Sum_probs=9.1
Q ss_pred cccCCCCcCcccchHH
Q 010003 248 IRCPQLRCKYFISTVE 263 (520)
Q Consensus 248 i~CP~~~C~~~l~~~~ 263 (520)
|+||. |+..+..+.
T Consensus 2 itCP~--C~~~~~~~v 15 (128)
T PF14353_consen 2 ITCPH--CGHEFEFEV 15 (128)
T ss_pred cCCCC--CCCeeEEEE
Confidence 67887 777655443
No 178
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=47.74 E-value=6.8 Score=39.20 Aligned_cols=20 Identities=45% Similarity=1.225 Sum_probs=14.2
Q ss_pred cccccccccccc-ccCCCCcc
Q 010003 396 CGHEFCYSCGAE-YRDGQQTC 415 (520)
Q Consensus 396 Cg~~FCy~C~~~-~~~~~~~c 415 (520)
|+|.|||+|.+- +..+..+|
T Consensus 25 C~HkFCyiCiKGsy~ndk~~C 45 (324)
T KOG0824|consen 25 CFHKFCYICIKGSYKNDKKTC 45 (324)
T ss_pred ccchhhhhhhcchhhcCCCCC
Confidence 999999999754 44444445
No 179
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 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 zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=47.31 E-value=18 Score=22.96 Aligned_cols=21 Identities=19% Similarity=0.464 Sum_probs=13.5
Q ss_pred cCccccceeeecCCcceEEec
Q 010003 375 RCQQCRRMIELTHGCYHMTCW 395 (520)
Q Consensus 375 ~CP~C~~~IeK~~GCnhMtC~ 395 (520)
.||.|+..+.+..|=-++.|.
T Consensus 1 ~CP~C~s~l~~~~~ev~~~C~ 21 (28)
T PF03119_consen 1 TCPVCGSKLVREEGEVDIRCP 21 (28)
T ss_dssp B-TTT--BEEE-CCTTCEEE-
T ss_pred CcCCCCCEeEcCCCCEeEECC
Confidence 499999999999887777773
No 180
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=46.85 E-value=17 Score=28.58 Aligned_cols=26 Identities=27% Similarity=0.666 Sum_probs=20.2
Q ss_pred ccCccccce----eeecCCcceEEec-cccc
Q 010003 374 RRCQQCRRM----IELTHGCYHMTCW-CGHE 399 (520)
Q Consensus 374 k~CP~C~~~----IeK~~GCnhMtC~-Cg~~ 399 (520)
-.||+|+.+ .-+..|=.++.|. |||.
T Consensus 9 a~CP~C~~~D~i~~~~e~~ve~vECV~CGy~ 39 (71)
T PF09526_consen 9 AVCPKCQAMDTIMMWRENGVEYVECVECGYT 39 (71)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEecCCCCe
Confidence 479999985 4455788899995 9875
No 181
>PHA02926 zinc finger-like protein; Provisional
Probab=46.46 E-value=4.3 Score=38.96 Aligned_cols=36 Identities=22% Similarity=0.661 Sum_probs=26.0
Q ss_pred CCCCcceeccCCCccCCCCCchhhhcCchhhcCchHHHHHHHHhccCCccCccccceee
Q 010003 326 PVCERFICVECGVPWHSSLSCEEYQNLPLEERDAGDITLHRLAQNKRWRRCQQCRRMIE 384 (520)
Q Consensus 326 p~C~~~fC~~C~~~wH~~~tC~e~~~~~~~~~~~~~~~l~~l~~~~~~k~CP~C~~~Ie 384 (520)
+.|++.||+.|-..|..... .++..+.||-|+..+.
T Consensus 195 ~~CnHsFCl~CIr~Wr~~r~-----------------------~~~~~rsCPiCR~~f~ 230 (242)
T PHA02926 195 DSCNHIFCITCINIWHRTRR-----------------------ETGASDNCPICRTRFR 230 (242)
T ss_pred CCCCchHHHHHHHHHHHhcc-----------------------ccCcCCcCCCCcceee
Confidence 47999999999999864311 0122378999999865
No 182
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=45.27 E-value=11 Score=44.90 Aligned_cols=30 Identities=40% Similarity=0.854 Sum_probs=23.4
Q ss_pred ccCccccceeeecCCcceEEec-ccccc-----ccccccccc
Q 010003 374 RRCQQCRRMIELTHGCYHMTCW-CGHEF-----CYSCGAEYR 409 (520)
Q Consensus 374 k~CP~C~~~IeK~~GCnhMtC~-Cg~~F-----Cy~C~~~~~ 409 (520)
++||+|+..+... .|+ ||... |-.||....
T Consensus 668 rkCPkCG~~t~~~------fCP~CGs~te~vy~CPsCGaev~ 703 (1337)
T PRK14714 668 RRCPSCGTETYEN------RCPDCGTHTEPVYVCPDCGAEVP 703 (1337)
T ss_pred EECCCCCCccccc------cCcccCCcCCCceeCccCCCccC
Confidence 8999999986532 886 88774 888888764
No 183
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=45.17 E-value=31 Score=34.48 Aligned_cols=47 Identities=32% Similarity=0.559 Sum_probs=34.1
Q ss_pred CccccccccccccCCC--CeeeccCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCc
Q 010003 202 KSPENCSICCEDKPYP--MMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKY 257 (520)
Q Consensus 202 ~~~~~C~IC~e~~~~~--~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~ 257 (520)
.....|+||.+..... ....++|||..-..|++.++. ++ .+||. |..
T Consensus 156 ~~~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~----~~---y~CP~--C~~ 204 (276)
T KOG1940|consen 156 SSEFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMIC----EG---YTCPI--CSK 204 (276)
T ss_pred cccCCCchhHHHhccccccCCccCcccchHHHHHHHHhc----cC---CCCCc--ccc
Confidence 3456699999885432 223459999999999998865 33 46998 877
No 184
>PRK14873 primosome assembly protein PriA; Provisional
Probab=44.81 E-value=15 Score=41.70 Aligned_cols=34 Identities=29% Similarity=0.776 Sum_probs=26.6
Q ss_pred ccCccccceeeecCCcceEEec-cccc----cccccccc
Q 010003 374 RRCQQCRRMIELTHGCYHMTCW-CGHE----FCYSCGAE 407 (520)
Q Consensus 374 k~CP~C~~~IeK~~GCnhMtC~-Cg~~----FCy~C~~~ 407 (520)
-+||+|..+.....+=+.|.|. ||+. .|-.|+..
T Consensus 393 ~~C~~C~~~L~~h~~~~~l~Ch~CG~~~~p~~Cp~Cgs~ 431 (665)
T PRK14873 393 ARCRHCTGPLGLPSAGGTPRCRWCGRAAPDWRCPRCGSD 431 (665)
T ss_pred eECCCCCCceeEecCCCeeECCCCcCCCcCccCCCCcCC
Confidence 5899999888876667789996 9985 47777764
No 185
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=44.22 E-value=8.7 Score=39.72 Aligned_cols=49 Identities=22% Similarity=0.634 Sum_probs=36.5
Q ss_pred ccccccccccccC--CCCeeeccCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCcc
Q 010003 203 SPENCSICCEDKP--YPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYF 258 (520)
Q Consensus 203 ~~~~C~IC~e~~~--~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~ 258 (520)
....|..|-+.+- .+..-.++|.|.|...|+..|++.. .+-.||. |...
T Consensus 364 ~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n-----~~rsCP~--Crkl 414 (518)
T KOG1941|consen 364 TELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENN-----GTRSCPN--CRKL 414 (518)
T ss_pred HhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhC-----CCCCCcc--HHHH
Confidence 4578999998753 3455567999999999999998532 2346988 7743
No 186
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=44.19 E-value=18 Score=31.13 Aligned_cols=27 Identities=26% Similarity=0.591 Sum_probs=19.4
Q ss_pred ccCccccceeeec--CCcceEEec-ccccc
Q 010003 374 RRCQQCRRMIELT--HGCYHMTCW-CGHEF 400 (520)
Q Consensus 374 k~CP~C~~~IeK~--~GCnhMtC~-Cg~~F 400 (520)
+-||+|+.++.-. ++=+.+.|+ |||++
T Consensus 3 ~FCp~Cgsll~p~~~~~~~~l~C~kCgye~ 32 (113)
T COG1594 3 RFCPKCGSLLYPKKDDEGGKLVCRKCGYEE 32 (113)
T ss_pred cccCCccCeeEEeEcCCCcEEECCCCCcch
Confidence 6799999987652 123388886 88865
No 187
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=42.69 E-value=15 Score=37.39 Aligned_cols=50 Identities=26% Similarity=0.633 Sum_probs=33.4
Q ss_pred CCccccccccccccCCCCeeeccCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCccc
Q 010003 201 DKSPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFI 259 (520)
Q Consensus 201 ~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l 259 (520)
+.....|.||.+...-. ..++|+|.+|.-|--+.-..-. .-.||. |+...
T Consensus 58 DEen~~C~ICA~~~TYs--~~~PC~H~~CH~Ca~RlRALY~-----~K~C~~--CrTE~ 107 (493)
T COG5236 58 DEENMNCQICAGSTTYS--ARYPCGHQICHACAVRLRALYM-----QKGCPL--CRTET 107 (493)
T ss_pred ccccceeEEecCCceEE--EeccCCchHHHHHHHHHHHHHh-----ccCCCc--ccccc
Confidence 45678899998765432 3359999999999876533221 124887 77543
No 188
>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=42.30 E-value=19 Score=27.64 Aligned_cols=34 Identities=24% Similarity=0.564 Sum_probs=19.0
Q ss_pred CccCccccceeeecCCcceEEec-ccccccccccccc
Q 010003 373 WRRCQQCRRMIELTHGCYHMTCW-CGHEFCYSCGAEY 408 (520)
Q Consensus 373 ~k~CP~C~~~IeK~~GCnhMtC~-Cg~~FCy~C~~~~ 408 (520)
...|+.|+..+- ---..-.|+ ||.-||-.|....
T Consensus 9 ~~~C~~C~~~F~--~~~rrhhCr~CG~~vC~~Cs~~~ 43 (69)
T PF01363_consen 9 ASNCMICGKKFS--LFRRRHHCRNCGRVVCSSCSSQR 43 (69)
T ss_dssp -SB-TTT--B-B--SSS-EEE-TTT--EEECCCS-EE
T ss_pred CCcCcCcCCcCC--CceeeEccCCCCCEECCchhCCE
Confidence 378999999984 346678897 9999999998654
No 189
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=42.00 E-value=19 Score=25.41 Aligned_cols=23 Identities=30% Similarity=0.693 Sum_probs=11.1
Q ss_pred cCccccceeeecCCcceEEec-ccc
Q 010003 375 RCQQCRRMIELTHGCYHMTCW-CGH 398 (520)
Q Consensus 375 ~CP~C~~~IeK~~GCnhMtC~-Cg~ 398 (520)
.|.+|+..++...+ .-+.|+ ||+
T Consensus 4 ~C~~Cg~~~~~~~~-~~irC~~CG~ 27 (44)
T smart00659 4 ICGECGRENEIKSK-DVVRCRECGY 27 (44)
T ss_pred ECCCCCCEeecCCC-CceECCCCCc
Confidence 35555555554433 445553 544
No 190
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=41.63 E-value=22 Score=26.06 Aligned_cols=11 Identities=18% Similarity=0.413 Sum_probs=8.9
Q ss_pred ccCccccceee
Q 010003 374 RRCQQCRRMIE 384 (520)
Q Consensus 374 k~CP~C~~~Ie 384 (520)
|+||-|+-.-+
T Consensus 2 kPCPfCGg~~~ 12 (53)
T TIGR03655 2 KPCPFCGGADV 12 (53)
T ss_pred CCCCCCCCcce
Confidence 79999987655
No 191
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=41.26 E-value=11 Score=38.18 Aligned_cols=34 Identities=26% Similarity=0.550 Sum_probs=18.5
Q ss_pred ccCccccceeeecCCcceEEeccccccccccccc
Q 010003 374 RRCQQCRRMIELTHGCYHMTCWCGHEFCYSCGAE 407 (520)
Q Consensus 374 k~CP~C~~~IeK~~GCnhMtC~Cg~~FCy~C~~~ 407 (520)
..||.|++..-.+..=.-|.=.|||.||-.|...
T Consensus 4 ~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~ 37 (309)
T TIGR00570 4 QGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDL 37 (309)
T ss_pred CCCCcCCCCCccCcccccccCCCCCcccHHHHHH
Confidence 5799999954444321111114566666666554
No 192
>PRK11827 hypothetical protein; Provisional
Probab=40.59 E-value=22 Score=27.03 Aligned_cols=25 Identities=12% Similarity=0.229 Sum_probs=18.8
Q ss_pred ccCccccceeeecCCcceEEec-ccc
Q 010003 374 RRCQQCRRMIELTHGCYHMTCW-CGH 398 (520)
Q Consensus 374 k~CP~C~~~IeK~~GCnhMtC~-Cg~ 398 (520)
-.||.|+...+-..+=+.++|+ |+-
T Consensus 9 LaCP~ckg~L~~~~~~~~Lic~~~~l 34 (60)
T PRK11827 9 IACPVCNGKLWYNQEKQELICKLDNL 34 (60)
T ss_pred eECCCCCCcCeEcCCCCeEECCccCe
Confidence 6899999998877665677774 543
No 193
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=40.57 E-value=19 Score=35.99 Aligned_cols=45 Identities=33% Similarity=0.769 Sum_probs=31.0
Q ss_pred cccccccccccCCCCeeeccCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCc
Q 010003 204 PENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKY 257 (520)
Q Consensus 204 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~ 257 (520)
...|+.|-.-...+ +-+-.|+|.||.+|+..-+- ++ .+.||. |..
T Consensus 274 ~LkCplc~~Llrnp-~kT~cC~~~fc~eci~~al~----ds--Df~Cpn--C~r 318 (427)
T COG5222 274 SLKCPLCHCLLRNP-MKTPCCGHTFCDECIGTALL----DS--DFKCPN--CSR 318 (427)
T ss_pred cccCcchhhhhhCc-ccCccccchHHHHHHhhhhh----hc--cccCCC--ccc
Confidence 37899997655433 33347999999999976543 22 357998 765
No 194
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=40.18 E-value=28 Score=24.21 Aligned_cols=12 Identities=17% Similarity=0.548 Sum_probs=8.1
Q ss_pred ccCccccc-eeee
Q 010003 374 RRCQQCRR-MIEL 385 (520)
Q Consensus 374 k~CP~C~~-~IeK 385 (520)
..||+|+. .++|
T Consensus 27 ~~CP~Cg~~~~~r 39 (42)
T PF09723_consen 27 VPCPECGSTEVRR 39 (42)
T ss_pred CcCCCCCCCceEE
Confidence 57888877 5544
No 195
>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=40.07 E-value=17 Score=31.13 Aligned_cols=10 Identities=30% Similarity=0.873 Sum_probs=6.7
Q ss_pred eeCCCCCcce
Q 010003 323 VECPVCERFI 332 (520)
Q Consensus 323 ~~Cp~C~~~f 332 (520)
+.||+||..|
T Consensus 27 ivCP~CG~~~ 36 (108)
T PF09538_consen 27 IVCPKCGTEF 36 (108)
T ss_pred ccCCCCCCcc
Confidence 5677777664
No 196
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=39.94 E-value=15 Score=27.26 Aligned_cols=45 Identities=31% Similarity=0.668 Sum_probs=31.6
Q ss_pred ccccccccccCCCCeeeccCC--CcccHHHHHHHHHHhhhCCCCccccCCCCcCcccc
Q 010003 205 ENCSICCEDKPYPMMITMKCS--HKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFIS 260 (520)
Q Consensus 205 ~~C~IC~e~~~~~~~~~l~Cg--H~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~ 260 (520)
-.|..|-.+.+.+..-...|. ..||.+|....+. =.||. |+..|.
T Consensus 6 pnCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~---------~~CPN--CgGelv 52 (57)
T PF06906_consen 6 PNCECCDKDLPPDSPEAYICSFECTFCADCAETMLN---------GVCPN--CGGELV 52 (57)
T ss_pred CCccccCCCCCCCCCcceEEeEeCcccHHHHHHHhc---------CcCcC--CCCccc
Confidence 468899888876543333554 4799999987764 15988 887664
No 197
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=39.41 E-value=16 Score=29.72 Aligned_cols=45 Identities=22% Similarity=0.477 Sum_probs=33.7
Q ss_pred ccCccccceeeecCCcceEEecccccccccccccccCCC-CcccCCCCC
Q 010003 374 RRCQQCRRMIELTHGCYHMTCWCGHEFCYSCGAEYRDGQ-QTCQCAFWD 421 (520)
Q Consensus 374 k~CP~C~~~IeK~~GCnhMtC~Cg~~FCy~C~~~~~~~~-~~c~C~~~~ 421 (520)
..||.|+.+ .+.|--+.+.|+|.|=..|...|-... ..-.||.-+
T Consensus 33 g~Cp~Ck~P---gd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR 78 (85)
T PF12861_consen 33 GCCPDCKFP---GDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCR 78 (85)
T ss_pred cCCCCccCC---CCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcC
Confidence 468888887 467888888899999999999996532 234566543
No 198
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=39.37 E-value=8.9 Score=30.47 Aligned_cols=20 Identities=20% Similarity=0.401 Sum_probs=7.7
Q ss_pred CCccCccccceeeecCCcce
Q 010003 372 RWRRCQQCRRMIELTHGCYH 391 (520)
Q Consensus 372 ~~k~CP~C~~~IeK~~GCnh 391 (520)
+.+.||+|++...+..|+-.
T Consensus 50 g~q~CpqCkt~ykr~kgsp~ 69 (80)
T PF14569_consen 50 GNQVCPQCKTRYKRHKGSPR 69 (80)
T ss_dssp S-SB-TTT--B----TT---
T ss_pred CcccccccCCCcccccCCCC
Confidence 34899999999988877643
No 199
>PF06844 DUF1244: Protein of unknown function (DUF1244); InterPro: IPR009654 This family consists of several short bacterial proteins of around 100 residues in length. The function of this family is unknown.; PDB: 2O35_A 3FYB_B.
Probab=39.26 E-value=20 Score=27.54 Aligned_cols=18 Identities=17% Similarity=0.672 Sum_probs=12.9
Q ss_pred cccHHHHHHHHHHhhhCC
Q 010003 227 KFCSHCMRTYIDGKVQSS 244 (520)
Q Consensus 227 ~fC~~Cl~~~i~~~i~~~ 244 (520)
-||+.||.+|+..+-.+.
T Consensus 11 gFCRNCLskWy~~aA~~~ 28 (68)
T PF06844_consen 11 GFCRNCLSKWYREAAEER 28 (68)
T ss_dssp S--HHHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHHHHhc
Confidence 399999999998876643
No 200
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=39.17 E-value=15 Score=28.69 Aligned_cols=46 Identities=26% Similarity=0.627 Sum_probs=31.7
Q ss_pred ccccccccccCCCCeeeccC--CCcccHHHHHHHHHHhhhCCCCccccCCCCcCcccch
Q 010003 205 ENCSICCEDKPYPMMITMKC--SHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFIST 261 (520)
Q Consensus 205 ~~C~IC~e~~~~~~~~~l~C--gH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~ 261 (520)
-.|..|-.+.+....-.+-| .|.||.+|...-+. | .||. |+..+..
T Consensus 6 PnCECCDrDLpp~s~dA~ICtfEcTFCadCae~~l~-----g----~CPn--CGGelv~ 53 (84)
T COG3813 6 PNCECCDRDLPPDSTDARICTFECTFCADCAENRLH-----G----LCPN--CGGELVA 53 (84)
T ss_pred CCCcccCCCCCCCCCceeEEEEeeehhHhHHHHhhc-----C----cCCC--CCchhhc
Confidence 46888988877654433445 48999999865443 1 4988 8887654
No 201
>PLN03086 PRLI-interacting factor K; Provisional
Probab=39.17 E-value=39 Score=37.36 Aligned_cols=27 Identities=26% Similarity=0.748 Sum_probs=24.0
Q ss_pred ccCcc--ccceeeecCCcceEEec-ccccc
Q 010003 374 RRCQQ--CRRMIELTHGCYHMTCW-CGHEF 400 (520)
Q Consensus 374 k~CP~--C~~~IeK~~GCnhMtC~-Cg~~F 400 (520)
..||+ |+..+.+...=+|.+|. |+..|
T Consensus 434 V~Cp~~~Cg~v~~r~el~~H~~C~~Cgk~f 463 (567)
T PLN03086 434 VVCPHDGCGIVLRVEEAKNHVHCEKCGQAF 463 (567)
T ss_pred eeCCcccccceeeccccccCccCCCCCCcc
Confidence 78995 99999999999999996 98776
No 202
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=39.14 E-value=30 Score=27.73 Aligned_cols=28 Identities=32% Similarity=0.717 Sum_probs=21.7
Q ss_pred cCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCccc
Q 010003 223 KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFI 259 (520)
Q Consensus 223 ~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l 259 (520)
.|.|.|...|+.+|+.++- .||. +++.+
T Consensus 53 ~CnHaFH~HCI~rWL~Tk~-------~CPl--d~q~w 80 (88)
T COG5194 53 VCNHAFHDHCIYRWLDTKG-------VCPL--DRQTW 80 (88)
T ss_pred ecchHHHHHHHHHHHhhCC-------CCCC--CCcee
Confidence 6999999999999998721 4887 55443
No 203
>PRK05580 primosome assembly protein PriA; Validated
Probab=38.98 E-value=21 Score=40.63 Aligned_cols=34 Identities=26% Similarity=0.745 Sum_probs=27.0
Q ss_pred ccCccccceeeecCCcceEEec-cccc-----cccccccc
Q 010003 374 RRCQQCRRMIELTHGCYHMTCW-CGHE-----FCYSCGAE 407 (520)
Q Consensus 374 k~CP~C~~~IeK~~GCnhMtC~-Cg~~-----FCy~C~~~ 407 (520)
-+||+|..+..-...=|.|+|. ||+. .|..|+..
T Consensus 391 ~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 391 AECPHCDASLTLHRFQRRLRCHHCGYQEPIPKACPECGST 430 (679)
T ss_pred cCCCCCCCceeEECCCCeEECCCCcCCCCCCCCCCCCcCC
Confidence 3799999987755556889996 9987 59999765
No 204
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=38.76 E-value=22 Score=39.98 Aligned_cols=49 Identities=20% Similarity=0.376 Sum_probs=36.3
Q ss_pred CccccccccccccCCCCeeeccCCCcccHHHHHHHHHHhhhCCCCccccCC-CCcCc
Q 010003 202 KSPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQ-LRCKY 257 (520)
Q Consensus 202 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~-~~C~~ 257 (520)
...+.|.||.-......++-..|+|....+|++.|++..- .||. +||+.
T Consensus 1026 ~~~~~C~~C~l~V~gss~~Cg~C~Hv~H~sc~~eWf~~gd-------~CpsGCGC~C 1075 (1081)
T KOG0309|consen 1026 GFTFQCAICHLAVRGSSNFCGTCGHVGHTSCMMEWFRTGD-------VCPSGCGCHC 1075 (1081)
T ss_pred cceeeeeeEeeEeeccchhhccccccccHHHHHHHHhcCC-------cCCCCCCcCc
Confidence 4567788888777666666668999999999999998432 5885 34544
No 205
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=38.38 E-value=20 Score=28.95 Aligned_cols=27 Identities=30% Similarity=0.747 Sum_probs=14.6
Q ss_pred ccCccccc------eeeecCCcceEEec-ccccc
Q 010003 374 RRCQQCRR------MIELTHGCYHMTCW-CGHEF 400 (520)
Q Consensus 374 k~CP~C~~------~IeK~~GCnhMtC~-Cg~~F 400 (520)
-.||.|++ -|.+..|=-+++|+ ||..|
T Consensus 23 F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~ 56 (81)
T PF05129_consen 23 FDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESF 56 (81)
T ss_dssp ---TTT--SS-EEEEEETTTTEEEEEESSS--EE
T ss_pred EcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeE
Confidence 68999993 35556788888885 76554
No 206
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=37.92 E-value=22 Score=36.17 Aligned_cols=18 Identities=28% Similarity=0.564 Sum_probs=12.0
Q ss_pred hhHHHHHHHHHHHHHHHH
Q 010003 106 ESVADYLALMDGLITAVQ 123 (520)
Q Consensus 106 nn~AE~~ALi~~l~~a~~ 123 (520)
|-.++|.-++..+..++.
T Consensus 44 ~pl~dyL~f~A~la~aQ~ 61 (305)
T TIGR01562 44 HPLGDYLRFVAGICRLQQ 61 (305)
T ss_pred CCHHHHHHHHHHHHHHHH
Confidence 335777777777776654
No 207
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=37.86 E-value=6.6 Score=28.40 Aligned_cols=34 Identities=21% Similarity=0.552 Sum_probs=29.1
Q ss_pred ccccccccccccCCCCeeec-cCCCcccHHHHHHH
Q 010003 203 SPENCSICCEDKPYPMMITM-KCSHKFCSHCMRTY 236 (520)
Q Consensus 203 ~~~~C~IC~e~~~~~~~~~l-~CgH~fC~~Cl~~~ 236 (520)
..++|..|-+.++..+...+ -||..-|..||+.-
T Consensus 6 sry~CDLCn~~~p~~~LRQCvlCGRWaC~sCW~de 40 (57)
T PF14445_consen 6 SRYSCDLCNSSHPISELRQCVLCGRWACNSCWQDE 40 (57)
T ss_pred hhHhHHhhcccCcHHHHHHHhhhchhhhhhhhhhh
Confidence 46899999999887777666 89999999999963
No 208
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=37.55 E-value=13 Score=31.04 Aligned_cols=32 Identities=19% Similarity=0.377 Sum_probs=25.2
Q ss_pred CCccccccccccccCCCCeeeccCCCcccHHH
Q 010003 201 DKSPENCSICCEDKPYPMMITMKCSHKFCSHC 232 (520)
Q Consensus 201 ~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C 232 (520)
....|+|.-||--...+++..-.=|+.+|.+|
T Consensus 67 q~DEFTCssCFLV~HRSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 67 QADEFTCSSCFLVHHRSQLAREKDGQPICRDC 98 (99)
T ss_pred CCCceeeeeeeeEechhhhccccCCCEecccc
Confidence 34579999999877766665556689999998
No 209
>PRK04023 DNA polymerase II large subunit; Validated
Probab=37.52 E-value=20 Score=41.76 Aligned_cols=31 Identities=32% Similarity=0.814 Sum_probs=25.3
Q ss_pred CccCccccceeeecCCcceEEec-ccc-----ccccccccccc
Q 010003 373 WRRCQQCRRMIELTHGCYHMTCW-CGH-----EFCYSCGAEYR 409 (520)
Q Consensus 373 ~k~CP~C~~~IeK~~GCnhMtC~-Cg~-----~FCy~C~~~~~ 409 (520)
.+.||.|+... ....|+ ||. .||-.|+..-.
T Consensus 626 ~RfCpsCG~~t------~~frCP~CG~~Te~i~fCP~CG~~~~ 662 (1121)
T PRK04023 626 RRKCPSCGKET------FYRRCPFCGTHTEPVYRCPRCGIEVE 662 (1121)
T ss_pred CccCCCCCCcC------CcccCCCCCCCCCcceeCccccCcCC
Confidence 48999999985 567897 996 49999987754
No 210
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=37.44 E-value=32 Score=31.36 Aligned_cols=51 Identities=16% Similarity=0.358 Sum_probs=35.0
Q ss_pred ccccccccccccCCCCeeeccCCC---cccHHHHHHHHHHhhhCCCCccccCCCCcCcccch
Q 010003 203 SPENCSICCEDKPYPMMITMKCSH---KFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFIST 261 (520)
Q Consensus 203 ~~~~C~IC~e~~~~~~~~~l~CgH---~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~ 261 (520)
....|-||+++.... ...+.|.. ....+|+++|+..+ ...+|+. |+.....
T Consensus 7 ~~~~CRIC~~~~~~~-~~PC~CkGs~k~VH~sCL~rWi~~s-----~~~~Cei--C~~~Y~i 60 (162)
T PHA02825 7 MDKCCWICKDEYDVV-TNYCNCKNENKIVHKECLEEWINTS-----KNKSCKI--CNGPYNI 60 (162)
T ss_pred CCCeeEecCCCCCCc-cCCcccCCCchHHHHHHHHHHHhcC-----CCCcccc--cCCeEEE
Confidence 457899999886422 22235554 56999999999853 2457988 8876543
No 211
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=36.95 E-value=23 Score=36.07 Aligned_cols=18 Identities=22% Similarity=0.383 Sum_probs=11.9
Q ss_pred hhHHHHHHHHHHHHHHHH
Q 010003 106 ESVADYLALMDGLITAVQ 123 (520)
Q Consensus 106 nn~AE~~ALi~~l~~a~~ 123 (520)
|-.++|.-++..+..|+.
T Consensus 48 ~pl~dYL~f~A~i~~aQ~ 65 (309)
T PRK03564 48 NPLGDYLRFAALIAEAQE 65 (309)
T ss_pred CChHHHHHHHHHHHHHHH
Confidence 345777777777776654
No 212
>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 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 RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.
Probab=36.82 E-value=9.4 Score=27.38 Aligned_cols=44 Identities=34% Similarity=0.738 Sum_probs=21.4
Q ss_pred ccccccccccCCCCeeeccCC-CcccHHHHHHHHHHhhhCCCCccccCCCCcCcccch
Q 010003 205 ENCSICCEDKPYPMMITMKCS-HKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFIST 261 (520)
Q Consensus 205 ~~C~IC~e~~~~~~~~~l~Cg-H~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~ 261 (520)
+.|..|.-.. ...+ .|. |..|..|+...+... -+||. |+.+++.
T Consensus 3 ~nCKsCWf~~--k~Li--~C~dHYLCl~CLt~ml~~s-------~~C~i--C~~~LPt 47 (50)
T PF03854_consen 3 YNCKSCWFAN--KGLI--KCSDHYLCLNCLTLMLSRS-------DRCPI--CGKPLPT 47 (50)
T ss_dssp ----SS-S----SSEE--E-SS-EEEHHHHHHT-SSS-------SEETT--TTEE---
T ss_pred ccChhhhhcC--CCee--eecchhHHHHHHHHHhccc-------cCCCc--ccCcCcc
Confidence 5688887432 2333 554 999999998776522 26988 8887764
No 213
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=36.57 E-value=29 Score=25.34 Aligned_cols=30 Identities=20% Similarity=0.556 Sum_probs=23.7
Q ss_pred cccccccccCCCCeeeccCCCcccHHHHHHH
Q 010003 206 NCSICCEDKPYPMMITMKCSHKFCSHCMRTY 236 (520)
Q Consensus 206 ~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~ 236 (520)
.|.||-.....-..+.+.-| ..|.+|+.+.
T Consensus 1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDG-YICKDCLKKL 30 (51)
T ss_pred CCCccccccccccceeccCc-cchHHHHHHh
Confidence 49999988765444667778 8999999886
No 214
>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=36.24 E-value=68 Score=22.61 Aligned_cols=25 Identities=16% Similarity=0.284 Sum_probs=14.3
Q ss_pred ccCccccce-eeecCCcceEEec-ccc
Q 010003 374 RRCQQCRRM-IELTHGCYHMTCW-CGH 398 (520)
Q Consensus 374 k~CP~C~~~-IeK~~GCnhMtC~-Cg~ 398 (520)
-.||+|+.. +-...+=....|+ |++
T Consensus 19 ~~CP~Cg~~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGSTKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCeeeEEeCCCCeEECCCCCC
Confidence 569999974 3333333445554 554
No 215
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=35.70 E-value=39 Score=31.24 Aligned_cols=59 Identities=25% Similarity=0.594 Sum_probs=39.0
Q ss_pred CCCccccccccccccCC---CCee--eccCCCcccHHHHHHHHHHhhhCC-CCcc---ccCCCCcCcccc
Q 010003 200 GDKSPENCSICCEDKPY---PMMI--TMKCSHKFCSHCMRTYIDGKVQSS-QVPI---RCPQLRCKYFIS 260 (520)
Q Consensus 200 ~~~~~~~C~IC~e~~~~---~~~~--~l~CgH~fC~~Cl~~~i~~~i~~~-~~~i---~CP~~~C~~~l~ 260 (520)
.+.....|.||+--.-. ++.+ ...||..|..-|+..|+..-+... .+.| .||- |..++.
T Consensus 161 kdd~~~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPY--CS~Pia 228 (234)
T KOG3268|consen 161 KDDELGACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPY--CSDPIA 228 (234)
T ss_pred cchhhhcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCC--CCCcce
Confidence 34557789999854221 1111 237999999999999998776543 2332 5988 877664
No 216
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=35.48 E-value=27 Score=29.51 Aligned_cols=25 Identities=28% Similarity=0.749 Sum_probs=16.7
Q ss_pred ccCccccceeeecCCcceEEec-cccc
Q 010003 374 RRCQQCRRMIELTHGCYHMTCW-CGHE 399 (520)
Q Consensus 374 k~CP~C~~~IeK~~GCnhMtC~-Cg~~ 399 (520)
..||+|+.-..-.+|= +|.|+ |.|+
T Consensus 4 p~cp~c~sEytYed~~-~~~cpec~~e 29 (112)
T COG2824 4 PPCPKCNSEYTYEDGG-QLICPECAHE 29 (112)
T ss_pred CCCCccCCceEEecCc-eEeCchhccc
Confidence 5899997765554443 78775 6554
No 217
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 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 domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=34.88 E-value=31 Score=21.88 Aligned_cols=21 Identities=29% Similarity=0.672 Sum_probs=11.2
Q ss_pred ccCccccceeeec--CCcceEEe
Q 010003 374 RRCQQCRRMIELT--HGCYHMTC 394 (520)
Q Consensus 374 k~CP~C~~~IeK~--~GCnhMtC 394 (520)
++||+|...|++. .|=+...|
T Consensus 2 ~~C~rC~~~~~~~~~~~r~~~~C 24 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGINGRSTYLC 24 (30)
T ss_dssp SB-TTT--BBEEEEETTEEEEE-
T ss_pred CcCccCCCcceEeEecCCCCeEC
Confidence 5899999998765 34444444
No 218
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=34.77 E-value=26 Score=24.10 Aligned_cols=13 Identities=23% Similarity=0.731 Sum_probs=9.9
Q ss_pred cCccccceeeecC
Q 010003 375 RCQQCRRMIELTH 387 (520)
Q Consensus 375 ~CP~C~~~IeK~~ 387 (520)
+||+|++.++...
T Consensus 1 ~CP~C~~~l~~~~ 13 (41)
T PF13453_consen 1 KCPRCGTELEPVR 13 (41)
T ss_pred CcCCCCcccceEE
Confidence 5999999776553
No 219
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=34.65 E-value=11 Score=34.05 Aligned_cols=32 Identities=28% Similarity=0.707 Sum_probs=20.8
Q ss_pred ccCccccceeeecCCcceEEec-------ccccccccccccc
Q 010003 374 RRCQQCRRMIELTHGCYHMTCW-------CGHEFCYSCGAEY 408 (520)
Q Consensus 374 k~CP~C~~~IeK~~GCnhMtC~-------Cg~~FCy~C~~~~ 408 (520)
..||+|+++|.-. .|.-=. =--.||+.||++|
T Consensus 40 ~~Cp~C~~~IrG~---y~v~gv~~~g~~~~~PsYC~~CGkpy 78 (158)
T PF10083_consen 40 TSCPNCSTPIRGD---YHVEGVFGLGGHYEAPSYCHNCGKPY 78 (158)
T ss_pred HHCcCCCCCCCCc---eecCCeeeeCCCCCCChhHHhCCCCC
Confidence 6899999999744 221000 1346888888876
No 220
>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=33.43 E-value=22 Score=24.10 Aligned_cols=11 Identities=18% Similarity=0.673 Sum_probs=5.5
Q ss_pred ccCccccceee
Q 010003 374 RRCQQCRRMIE 384 (520)
Q Consensus 374 k~CP~C~~~Ie 384 (520)
..||.|+..++
T Consensus 27 ~~CP~Cg~~~~ 37 (41)
T smart00834 27 ATCPECGGDVR 37 (41)
T ss_pred CCCCCCCCcce
Confidence 44555555443
No 221
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=33.07 E-value=30 Score=37.26 Aligned_cols=35 Identities=26% Similarity=0.540 Sum_probs=24.6
Q ss_pred CCCcceeccCCCccCCCCCchhhhcCchhhcCchHHHHHHHHhccCCccCccccceeee
Q 010003 327 VCERFICVECGVPWHSSLSCEEYQNLPLEERDAGDITLHRLAQNKRWRRCQQCRRMIEL 385 (520)
Q Consensus 327 ~C~~~fC~~C~~~wH~~~tC~e~~~~~~~~~~~~~~~l~~l~~~~~~k~CP~C~~~IeK 385 (520)
.||+.||+.|-..+ ........|+.||-|...|-+
T Consensus 203 ~CGHiFC~~CiLqy------------------------~~~s~~~~~~~CPiC~s~I~~ 237 (513)
T KOG2164|consen 203 NCGHIFCGPCILQY------------------------WNYSAIKGPCSCPICRSTITL 237 (513)
T ss_pred ccCceeeHHHHHHH------------------------HhhhcccCCccCCchhhhccc
Confidence 59999999987542 111134567999999988764
No 222
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=31.98 E-value=42 Score=22.14 Aligned_cols=25 Identities=20% Similarity=0.510 Sum_probs=13.5
Q ss_pred ccCccccceeeecCCcceEEec-ccc
Q 010003 374 RRCQQCRRMIELTHGCYHMTCW-CGH 398 (520)
Q Consensus 374 k~CP~C~~~IeK~~GCnhMtC~-Cg~ 398 (520)
+.|+.|+....-+.-=..+.|. ||.
T Consensus 4 ~~C~~C~~~~i~~~~~~~~~C~~Cg~ 29 (33)
T PF08792_consen 4 KKCSKCGGNGIVNKEDDYEVCIFCGS 29 (33)
T ss_pred eEcCCCCCCeEEEecCCeEEcccCCc
Confidence 6788888764432222344553 544
No 224
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=31.47 E-value=31 Score=32.42 Aligned_cols=25 Identities=24% Similarity=0.587 Sum_probs=20.3
Q ss_pred ccCccccceeeecCCcceEEec-cccc
Q 010003 374 RRCQQCRRMIELTHGCYHMTCW-CGHE 399 (520)
Q Consensus 374 k~CP~C~~~IeK~~GCnhMtC~-Cg~~ 399 (520)
-.|++|+.+..+.+ .|+|.|+ ||+.
T Consensus 150 a~~~~~g~~~~~~~-~~~~~c~~~~~~ 175 (189)
T PRK09521 150 AMCSRCRTPLVKKG-ENELKCPNCGNI 175 (189)
T ss_pred EEccccCCceEECC-CCEEECCCCCCE
Confidence 37999999998854 4999996 9864
No 225
>PF08882 Acetone_carb_G: Acetone carboxylase gamma subunit; InterPro: IPR014979 Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO2 to form acetoacetate [] according to the following reaction: CH3COCH3 + CO2 + ATP = CH3COCH2COO- + AMP + 2P(i) + H+ It has the subunit composition: (alpha(2)beta(2)gamma(2) multimers of 85kDa, 78kDa, and 20kDa subunits). It is expressed to high levels (17 to 25% of soluble protein) in cells grown with acetone as the carbon source but are not present at detectable levels in cells grown with other carbon sources []. Acetone carboxylase may enable Helicobacter pylori to survive off acetone in the stomach of humans and other mammals where it is the etiological agent of peptic ulcer disease []. This entry represents the family of gamma subunit-related acetone carboxylase proteins.
Probab=31.28 E-value=32 Score=29.33 Aligned_cols=13 Identities=54% Similarity=1.211 Sum_probs=11.0
Q ss_pred ceEEecccccccc
Q 010003 390 YHMTCWCGHEFCY 402 (520)
Q Consensus 390 nhMtC~Cg~~FCy 402 (520)
..+.|.|||+||=
T Consensus 23 k~vkc~CGh~f~d 35 (112)
T PF08882_consen 23 KVVKCDCGHEFCD 35 (112)
T ss_pred ceeeccCCCeecC
Confidence 3788999999984
No 226
>COG3492 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.15 E-value=36 Score=27.85 Aligned_cols=21 Identities=19% Similarity=0.630 Sum_probs=16.4
Q ss_pred cccHHHHHHHHHHhhhCCCCc
Q 010003 227 KFCSHCMRTYIDGKVQSSQVP 247 (520)
Q Consensus 227 ~fC~~Cl~~~i~~~i~~~~~~ 247 (520)
-||+.|+..|+..+-.....+
T Consensus 42 gFCRNCLs~Wy~eaae~~gv~ 62 (104)
T COG3492 42 GFCRNCLSNWYREAAEAQGVD 62 (104)
T ss_pred HHHHHHHHHHHHHHHhccCCC
Confidence 499999999999887654433
No 227
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=30.78 E-value=48 Score=25.45 Aligned_cols=14 Identities=14% Similarity=0.211 Sum_probs=10.8
Q ss_pred CccCccccceeeec
Q 010003 373 WRRCQQCRRMIELT 386 (520)
Q Consensus 373 ~k~CP~C~~~IeK~ 386 (520)
+|+||-|+..+.+.
T Consensus 6 lKPCPFCG~~~~~v 19 (64)
T PRK09710 6 VKPCPFCGCPSVTV 19 (64)
T ss_pred ccCCCCCCCceeEE
Confidence 59999998875543
No 228
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=30.62 E-value=17 Score=41.66 Aligned_cols=32 Identities=34% Similarity=0.827 Sum_probs=0.0
Q ss_pred CccCccccceeeecCCcceEEec-cccc-----ccccccccccC
Q 010003 373 WRRCQQCRRMIELTHGCYHMTCW-CGHE-----FCYSCGAEYRD 410 (520)
Q Consensus 373 ~k~CP~C~~~IeK~~GCnhMtC~-Cg~~-----FCy~C~~~~~~ 410 (520)
.++||+|+.... ..+|+ ||.+ +|..|+.....
T Consensus 655 ~r~Cp~Cg~~t~------~~~Cp~CG~~T~~~~~Cp~C~~~~~~ 692 (900)
T PF03833_consen 655 RRRCPKCGKETF------YNRCPECGSHTEPVYVCPDCGIEVEE 692 (900)
T ss_dssp --------------------------------------------
T ss_pred cccCcccCCcch------hhcCcccCCccccceeccccccccCc
Confidence 389999999754 35785 9887 89999988764
No 229
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=30.43 E-value=35 Score=34.13 Aligned_cols=24 Identities=29% Similarity=0.616 Sum_probs=18.8
Q ss_pred ccCccccceeeec--CCcceEEec-cc
Q 010003 374 RRCQQCRRMIELT--HGCYHMTCW-CG 397 (520)
Q Consensus 374 k~CP~C~~~IeK~--~GCnhMtC~-Cg 397 (520)
++|++|+.+|+|. +|=+-..|+ |.
T Consensus 246 epC~~CGt~I~k~~~~gR~t~~CP~CQ 272 (273)
T COG0266 246 EPCRRCGTPIEKIKLGGRSTFYCPVCQ 272 (273)
T ss_pred CCCCccCCEeEEEEEcCCcCEeCCCCC
Confidence 8999999999987 676666664 53
No 230
>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.
Probab=30.31 E-value=78 Score=28.90 Aligned_cols=36 Identities=25% Similarity=0.675 Sum_probs=22.2
Q ss_pred cccccccccccCCCCeeec-------cCCCccc------HHHHHHHHHHhh
Q 010003 204 PENCSICCEDKPYPMMITM-------KCSHKFC------SHCMRTYIDGKV 241 (520)
Q Consensus 204 ~~~C~IC~e~~~~~~~~~l-------~CgH~fC------~~Cl~~~i~~~i 241 (520)
..+|+||+|- |.+- +-| +|.-.+| ..||.+|-+...
T Consensus 2 d~~CpICme~-PHNA-VLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkka~~ 50 (162)
T PF07800_consen 2 DVTCPICMEH-PHNA-VLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKKAYG 50 (162)
T ss_pred CccCceeccC-CCce-EEEEeccccCCccccccCCccchhHHHHHHHHHhc
Confidence 4689999974 4332 222 3444444 579999877654
No 231
>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=30.16 E-value=20 Score=23.54 Aligned_cols=10 Identities=40% Similarity=0.956 Sum_probs=5.7
Q ss_pred ccCcccccee
Q 010003 374 RRCQQCRRMI 383 (520)
Q Consensus 374 k~CP~C~~~I 383 (520)
-+||.|+..|
T Consensus 18 irC~~CG~RI 27 (32)
T PF03604_consen 18 IRCPECGHRI 27 (32)
T ss_dssp SSBSSSS-SE
T ss_pred EECCcCCCeE
Confidence 5677766654
No 232
>PF12677 DUF3797: Domain of unknown function (DUF3797); InterPro: IPR024256 This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif.
Probab=30.08 E-value=43 Score=24.16 Aligned_cols=27 Identities=22% Similarity=0.626 Sum_probs=19.3
Q ss_pred CccCccccceeeec--------CCcceEEeccccc
Q 010003 373 WRRCQQCRRMIELT--------HGCYHMTCWCGHE 399 (520)
Q Consensus 373 ~k~CP~C~~~IeK~--------~GCnhMtC~Cg~~ 399 (520)
+-.||+|+.-..-+ +.=.+=||+||..
T Consensus 13 Y~~Cp~CGN~~vGngEG~liV~edtfkRtCkCGfn 47 (49)
T PF12677_consen 13 YCKCPKCGNDKVGNGEGTLIVEEDTFKRTCKCGFN 47 (49)
T ss_pred hccCcccCCcEeecCcceEEEeccceeeeeccccc
Confidence 47899999876655 3455667888764
No 233
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=29.65 E-value=14 Score=37.05 Aligned_cols=21 Identities=29% Similarity=0.873 Sum_probs=17.9
Q ss_pred eeCCCCCcceeccCCCccCCC
Q 010003 323 VECPVCERFICVECGVPWHSS 343 (520)
Q Consensus 323 ~~Cp~C~~~fC~~C~~~wH~~ 343 (520)
..|+.|+..||..|.+-.|..
T Consensus 389 Y~Ce~CK~~FC~dCdvfiHe~ 409 (421)
T COG5151 389 YQCELCKSTFCSDCDVFIHET 409 (421)
T ss_pred eechhhhhhhhhhhHHHHHHH
Confidence 789999999999998876643
No 234
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=29.61 E-value=47 Score=29.87 Aligned_cols=38 Identities=18% Similarity=0.374 Sum_probs=20.8
Q ss_pred CCCceeccCCCCCeeecCcccccccccCCCCCCCCceeCCCCCcce
Q 010003 287 HSDRIYCPFPNCSVLLDPRECLSARASSSSQSDNSCVECPVCERFI 332 (520)
Q Consensus 287 ~~~~~~CP~p~C~~~~~~~~~~~~~~~~~~~~~~~~~~Cp~C~~~f 332 (520)
......||+ |+.-+...+.... ... ...+.||.||...
T Consensus 96 ~~~~Y~Cp~--C~~~y~~~ea~~~-----~d~-~~~f~Cp~Cg~~l 133 (147)
T smart00531 96 NNAYYKCPN--CQSKYTFLEANQL-----LDM-DGTFTCPRCGEEL 133 (147)
T ss_pred CCcEEECcC--CCCEeeHHHHHHh-----cCC-CCcEECCCCCCEE
Confidence 345678986 8866554332100 001 1238899888653
No 235
>PRK08115 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=29.52 E-value=25 Score=40.83 Aligned_cols=24 Identities=42% Similarity=0.987 Sum_probs=19.8
Q ss_pred ccCccccce-eeecCCcceEEec-cccc
Q 010003 374 RRCQQCRRM-IELTHGCYHMTCW-CGHE 399 (520)
Q Consensus 374 k~CP~C~~~-IeK~~GCnhMtC~-Cg~~ 399 (520)
-.||-|+.- |+..+||| ||+ ||.+
T Consensus 828 ~~cp~c~~~~~~~~~~c~--~c~~c~~~ 853 (858)
T PRK08115 828 NTCPVCREGTVEEIGGCN--TCTNCGAQ 853 (858)
T ss_pred CCCCccCCCceeecCCCc--cccchhhh
Confidence 489999986 78889999 785 7765
No 236
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=29.45 E-value=34 Score=32.05 Aligned_cols=24 Identities=29% Similarity=0.724 Sum_probs=19.8
Q ss_pred ccCccccceeeecCCcceEEec-cccc
Q 010003 374 RRCQQCRRMIELTHGCYHMTCW-CGHE 399 (520)
Q Consensus 374 k~CP~C~~~IeK~~GCnhMtC~-Cg~~ 399 (520)
-.|++|+...++ .=+.|+|+ ||+.
T Consensus 150 A~CsrC~~~L~~--~~~~l~Cp~Cg~t 174 (188)
T COG1096 150 ARCSRCRAPLVK--KGNMLKCPNCGNT 174 (188)
T ss_pred EEccCCCcceEE--cCcEEECCCCCCE
Confidence 589999999999 55788996 8864
No 237
>COG0450 AhpC Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]
Probab=28.91 E-value=1.2e+02 Score=28.62 Aligned_cols=48 Identities=13% Similarity=0.145 Sum_probs=37.7
Q ss_pred CCcccceEEEEeecCCCceEEEeecccccchhhHHHHHHHHHHHHHHHHc
Q 010003 75 SSGFSGIGVVMERSFNIPIMQVQKKLDFFVEESVADYLALMDGLITAVQN 124 (520)
Q Consensus 75 n~~~ag~g~~i~~~~~~~~~~~~~~~~~~~tnn~AE~~ALi~~l~~a~~~ 124 (520)
+.|.|--|+.|.|++|.+ +....-+.++.+|.-|...++++|+....+
T Consensus 119 ~~g~a~R~~FIIDp~g~i--r~~~v~~~~iGRn~dEilR~idAlq~~~~h 166 (194)
T COG0450 119 EEGLALRGTFIIDPDGVI--RHILVNPLTIGRNVDEILRVIDALQFVAKH 166 (194)
T ss_pred CCCcceeEEEEECCCCeE--EEEEEecCCCCcCHHHHHHHHHHHHHHHHh
Confidence 456788899999998876 555555556789999999999999976554
No 238
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=28.61 E-value=38 Score=25.55 Aligned_cols=34 Identities=24% Similarity=0.601 Sum_probs=22.8
Q ss_pred ccCccccceeeecCCcceEEec-cccc---cccccccc
Q 010003 374 RRCQQCRRMIELTHGCYHMTCW-CGHE---FCYSCGAE 407 (520)
Q Consensus 374 k~CP~C~~~IeK~~GCnhMtC~-Cg~~---FCy~C~~~ 407 (520)
..|-.|+..|.-.+..-+..|+ ||.. =|..|++.
T Consensus 8 ~~CtSCg~~i~~~~~~~~F~CPnCG~~~I~RC~~CRk~ 45 (59)
T PRK14890 8 PKCTSCGIEIAPREKAVKFLCPNCGEVIIYRCEKCRKQ 45 (59)
T ss_pred ccccCCCCcccCCCccCEeeCCCCCCeeEeechhHHhc
Confidence 4677777777766666777775 7766 35555543
No 239
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=28.44 E-value=14 Score=41.39 Aligned_cols=56 Identities=29% Similarity=0.602 Sum_probs=40.8
Q ss_pred ccccccccccccCCCCeeeccCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCcccchHHHhh
Q 010003 203 SPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFISTVECKS 266 (520)
Q Consensus 203 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~~~i~~ 266 (520)
...+|+||+..+..+ +.+.|.|.||..|+..-+...-. ...||. |+..+....++.
T Consensus 20 k~lEc~ic~~~~~~p--~~~kc~~~~l~~~~n~~f~~~~~----~~~~~l--c~~~~eK~s~~E 75 (684)
T KOG4362|consen 20 KILECPICLEHVKEP--SLLKCDHIFLKFCLNKLFESKKG----PKQCAL--CKSDIEKRSLRE 75 (684)
T ss_pred hhccCCceeEEeecc--chhhhhHHHHhhhhhceeeccCc----cccchh--hhhhhhhhhccc
Confidence 368899999987655 56799999999999887764432 557887 776665544443
No 240
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=28.33 E-value=52 Score=32.95 Aligned_cols=27 Identities=33% Similarity=0.707 Sum_probs=23.7
Q ss_pred ccCccccceeeecCCcceEEec-ccccc
Q 010003 374 RRCQQCRRMIELTHGCYHMTCW-CGHEF 400 (520)
Q Consensus 374 k~CP~C~~~IeK~~GCnhMtC~-Cg~~F 400 (520)
|-||+|++..+-..|=-.|.|. ||+.+
T Consensus 112 RFCg~CG~~~~~~~~g~~~~C~~cg~~~ 139 (279)
T COG2816 112 RFCGRCGTKTYPREGGWARVCPKCGHEH 139 (279)
T ss_pred cCCCCCCCcCccccCceeeeCCCCCCcc
Confidence 8999999999999888889986 87764
No 241
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=28.06 E-value=52 Score=28.90 Aligned_cols=27 Identities=19% Similarity=0.524 Sum_probs=22.7
Q ss_pred CccCccccce---eeecCCcceEEec-cccc
Q 010003 373 WRRCQQCRRM---IELTHGCYHMTCW-CGHE 399 (520)
Q Consensus 373 ~k~CP~C~~~---IeK~~GCnhMtC~-Cg~~ 399 (520)
.-.||.|+.+ +.|.++=..|.|. ||+.
T Consensus 93 yVlC~~C~spdT~l~k~~r~~~l~C~aCGa~ 123 (125)
T PF01873_consen 93 YVLCPECGSPDTELIKEGRLIFLKCKACGAS 123 (125)
T ss_dssp HSSCTSTSSSSEEEEEETTCCEEEETTTSCE
T ss_pred EEEcCCCCCCccEEEEcCCEEEEEecccCCc
Confidence 3789999986 7777999999996 9974
No 242
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=27.75 E-value=32 Score=29.40 Aligned_cols=20 Identities=40% Similarity=1.009 Sum_probs=13.2
Q ss_pred eeCCCCCcce--------eccCCCccCC
Q 010003 323 VECPVCERFI--------CVECGVPWHS 342 (520)
Q Consensus 323 ~~Cp~C~~~f--------C~~C~~~wH~ 342 (520)
+.||.|++.+ |..|+.|-+-
T Consensus 70 V~CP~C~K~TKmLGr~D~CM~C~~pLTL 97 (114)
T PF11023_consen 70 VECPNCGKQTKMLGRVDACMHCKEPLTL 97 (114)
T ss_pred eECCCCCChHhhhchhhccCcCCCcCcc
Confidence 5666666554 8888877543
No 243
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=27.75 E-value=87 Score=25.78 Aligned_cols=14 Identities=14% Similarity=0.024 Sum_probs=8.4
Q ss_pred ccchHHHhhcCCcc
Q 010003 258 FISTVECKSFLPLS 271 (520)
Q Consensus 258 ~l~~~~i~~~L~~~ 271 (520)
++....+..+++.+
T Consensus 18 plt~~ei~~~~~~~ 31 (97)
T COG3357 18 PLTVAEIFELLNGE 31 (97)
T ss_pred cchHHHHHHHHcCC
Confidence 45566666666554
No 244
>PF05715 zf-piccolo: Piccolo Zn-finger; InterPro: IPR008899 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 (predicted) zinc finger is found in the bassoon and piccolo proteins, both of which are components of the presynaptic cytoskeletal matrix (PCM) assembled at the active zone of neurotransmitter release, where Piccolo plays a role in the trafficking of synaptic vesicles (SVs) [, , ]. The Piccolo zinc fingers were found to interact with the dual prenylated rab3A and VAMP2/Synaptobrevin II receptor PRA1. There are eight conserved cysteines in Piccolo-type zinc fingers, suggesting that they coordinates two zinc ligands. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding, 0045202 synapse
Probab=27.54 E-value=19 Score=27.13 Aligned_cols=35 Identities=23% Similarity=0.563 Sum_probs=26.6
Q ss_pred ccCccccceeeec--CCcceEEec-ccccccccccccc
Q 010003 374 RRCQQCRRMIELT--HGCYHMTCW-CGHEFCYSCGAEY 408 (520)
Q Consensus 374 k~CP~C~~~IeK~--~GCnhMtC~-Cg~~FCy~C~~~~ 408 (520)
..||-|++-.-.. +-=|+=||+ |+...|-+||-.-
T Consensus 3 ~~CPlCkt~~n~gsk~~pNyntCT~Ck~~VCnlCGFNP 40 (61)
T PF05715_consen 3 SLCPLCKTTLNVGSKDPPNYNTCTECKSQVCNLCGFNP 40 (61)
T ss_pred ccCCcccchhhcCCCCCCCccHHHHHhhhhhcccCCCC
Confidence 5799999876221 344888997 9999999999554
No 245
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=27.46 E-value=58 Score=22.27 Aligned_cols=20 Identities=25% Similarity=0.765 Sum_probs=13.5
Q ss_pred ccCccccceeeec---CCcceEEe
Q 010003 374 RRCQQCRRMIELT---HGCYHMTC 394 (520)
Q Consensus 374 k~CP~C~~~IeK~---~GCnhMtC 394 (520)
+.||.|+..+... .| ..+.|
T Consensus 2 ~~CP~Cg~~lv~r~~k~g-~F~~C 24 (39)
T PF01396_consen 2 EKCPKCGGPLVLRRGKKG-KFLGC 24 (39)
T ss_pred cCCCCCCceeEEEECCCC-CEEEC
Confidence 6899999765443 35 66666
No 246
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=27.27 E-value=50 Score=30.18 Aligned_cols=32 Identities=22% Similarity=0.450 Sum_probs=19.7
Q ss_pred CCCceeccCCCCCeeecCcccccccccCCCCCCCCceeCCCCCcc
Q 010003 287 HSDRIYCPFPNCSVLLDPRECLSARASSSSQSDNSCVECPVCERF 331 (520)
Q Consensus 287 ~~~~~~CP~p~C~~~~~~~~~~~~~~~~~~~~~~~~~~Cp~C~~~ 331 (520)
.+....||+ |..-+...+..+ ..|.||.||..
T Consensus 106 ~~~~Y~Cp~--c~~r~tf~eA~~-----------~~F~Cp~Cg~~ 137 (158)
T TIGR00373 106 NNMFFICPN--MCVRFTFNEAME-----------LNFTCPRCGAM 137 (158)
T ss_pred CCCeEECCC--CCcEeeHHHHHH-----------cCCcCCCCCCE
Confidence 345677986 875554443221 13899999875
No 247
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=26.62 E-value=22 Score=40.80 Aligned_cols=16 Identities=19% Similarity=0.310 Sum_probs=0.0
Q ss_pred CCCCCCccchhhhccC
Q 010003 483 PPRCTDSYGDAMKDLH 498 (520)
Q Consensus 483 ~~~~~~~~~~~~~~~~ 498 (520)
.|+--+.+|+.|+.||
T Consensus 780 rP~EIgvsvEkLrELG 795 (900)
T PF03833_consen 780 RPREIGVSVEKLRELG 795 (900)
T ss_dssp ----------------
T ss_pred cHHhcCCCHHHHHHhC
Confidence 3555556788888877
No 249
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=26.37 E-value=51 Score=30.78 Aligned_cols=32 Identities=22% Similarity=0.654 Sum_probs=19.4
Q ss_pred CCCceeccCCCCCeeecCcccccccccCCCCCCCCceeCCCCCcc
Q 010003 287 HSDRIYCPFPNCSVLLDPRECLSARASSSSQSDNSCVECPVCERF 331 (520)
Q Consensus 287 ~~~~~~CP~p~C~~~~~~~~~~~~~~~~~~~~~~~~~~Cp~C~~~ 331 (520)
......||+ |+.-+...+.. ...|.||.||..
T Consensus 114 ~~~~Y~Cp~--C~~rytf~eA~-----------~~~F~Cp~Cg~~ 145 (178)
T PRK06266 114 NNMFFFCPN--CHIRFTFDEAM-----------EYGFRCPQCGEM 145 (178)
T ss_pred CCCEEECCC--CCcEEeHHHHh-----------hcCCcCCCCCCC
Confidence 345678987 87555443322 123889988865
No 250
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=26.25 E-value=52 Score=23.05 Aligned_cols=41 Identities=22% Similarity=0.660 Sum_probs=19.3
Q ss_pred ccccccccCCCCeee-ccCCCcccHHHHHHHHHHhhhCCCCccccCC
Q 010003 207 CSICCEDKPYPMMIT-MKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQ 252 (520)
Q Consensus 207 C~IC~e~~~~~~~~~-l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~ 252 (520)
|.+|-+-......-. ..|+=.+...|++.|+...-. + +||.
T Consensus 1 C~~C~~iv~~G~~C~~~~C~~r~H~~C~~~y~r~~~~----~-~CP~ 42 (43)
T PF08746_consen 1 CEACKEIVTQGQRCSNRDCNVRLHDDCFKKYFRHRSN----P-KCPN 42 (43)
T ss_dssp -TTT-SB-SSSEE-SS--S--EE-HHHHHHHTTT-SS------B-TT
T ss_pred CcccchhHeeeccCCCCccCchHHHHHHHHHHhcCCC----C-CCcC
Confidence 567766554332111 148888999999999874321 2 6886
No 251
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=26.23 E-value=38 Score=25.42 Aligned_cols=13 Identities=15% Similarity=0.317 Sum_probs=10.6
Q ss_pred CCccCccccceee
Q 010003 372 RWRRCQQCRRMIE 384 (520)
Q Consensus 372 ~~k~CP~C~~~Ie 384 (520)
.+-.||+|+.+..
T Consensus 26 ~l~~C~~CG~~~~ 38 (57)
T PRK12286 26 GLVECPNCGEPKL 38 (57)
T ss_pred cceECCCCCCccC
Confidence 3478999999887
No 252
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=26.21 E-value=79 Score=27.28 Aligned_cols=35 Identities=26% Similarity=0.645 Sum_probs=26.6
Q ss_pred CCccCccccceeeecCCcceEEec-cccccccccccc
Q 010003 372 RWRRCQQCRRMIELTHGCYHMTCW-CGHEFCYSCGAE 407 (520)
Q Consensus 372 ~~k~CP~C~~~IeK~~GCnhMtC~-Cg~~FCy~C~~~ 407 (520)
..+.|..|+.++-...+.. ..|. |++.+|=.|+..
T Consensus 53 ~~~~C~~C~~~fg~l~~~~-~~C~~C~~~VC~~C~~~ 88 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRG-RVCVDCKHRVCKKCGVY 88 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTC-EEETTTTEEEETTSEEE
T ss_pred CCcchhhhCCcccccCCCC-CcCCcCCccccCccCCc
Confidence 4589999999876665555 7886 999999999976
No 253
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=26.13 E-value=66 Score=23.87 Aligned_cols=33 Identities=12% Similarity=0.405 Sum_probs=26.6
Q ss_pred cccccccccccC-CCCeeec-cCCCcccHHHHHHH
Q 010003 204 PENCSICCEDKP-YPMMITM-KCSHKFCSHCMRTY 236 (520)
Q Consensus 204 ~~~C~IC~e~~~-~~~~~~l-~CgH~fC~~Cl~~~ 236 (520)
..-|.+|-+.+. ..+++.. .|+-.+.++||...
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~ 39 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKA 39 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcccHHHHhhC
Confidence 456999999986 5567777 89999999999654
No 254
>PLN02189 cellulose synthase
Probab=25.93 E-value=47 Score=39.18 Aligned_cols=49 Identities=24% Similarity=0.665 Sum_probs=33.3
Q ss_pred ccccccccccccC----CCCeeec-cCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCccc
Q 010003 203 SPENCSICCEDKP----YPMMITM-KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFI 259 (520)
Q Consensus 203 ~~~~C~IC~e~~~----~~~~~~l-~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l 259 (520)
....|.||-|+.- .+.++.+ .|+--.|+.|. .|-. ++|. =.||+ |+...
T Consensus 33 ~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cy-eyer---~eg~--q~Cpq--Ckt~Y 86 (1040)
T PLN02189 33 DGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCY-EYER---REGT--QNCPQ--CKTRY 86 (1040)
T ss_pred cCccccccccccCcCCCCCEEEeeccCCCccccchh-hhhh---hcCC--ccCcc--cCCch
Confidence 3468999999843 3445666 69999999999 4433 2332 25998 87643
No 255
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=25.89 E-value=50 Score=32.27 Aligned_cols=38 Identities=16% Similarity=0.200 Sum_probs=29.4
Q ss_pred ccccccccccccCCCCeeeccCCCcccHHHHHHHHHHhhh
Q 010003 203 SPENCSICCEDKPYPMMITMKCSHKFCSHCMRTYIDGKVQ 242 (520)
Q Consensus 203 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~Cl~~~i~~~i~ 242 (520)
+..-|..|+.....+ +..+=||.||++|+-+||-.+-+
T Consensus 42 ~FdcCsLtLqPc~dP--vit~~GylfdrEaILe~ilaqKk 79 (303)
T KOG3039|consen 42 PFDCCSLTLQPCRDP--VITPDGYLFDREAILEYILAQKK 79 (303)
T ss_pred CcceeeeecccccCC--ccCCCCeeeeHHHHHHHHHHHHH
Confidence 345688888776655 44688999999999999977654
No 256
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=25.87 E-value=82 Score=25.19 Aligned_cols=48 Identities=25% Similarity=0.638 Sum_probs=18.8
Q ss_pred ccccccccccccCC----CCeeec-cCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCcc
Q 010003 203 SPENCSICCEDKPY----PMMITM-KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYF 258 (520)
Q Consensus 203 ~~~~C~IC~e~~~~----~~~~~l-~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~ 258 (520)
....|.||-++.-. +-|+.+ .|+-..|+.|+.-=. ++|.. .||+ |+..
T Consensus 8 ~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYEr----keg~q--~Cpq--Ckt~ 60 (80)
T PF14569_consen 8 NGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYER----KEGNQ--VCPQ--CKTR 60 (80)
T ss_dssp SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHH----HTS-S--B-TT--T--B
T ss_pred CCcccccccCccccCCCCCEEEEEcccCCccchhHHHHHh----hcCcc--cccc--cCCC
Confidence 35789999998632 234444 799999999986433 33322 4888 7754
No 257
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=25.70 E-value=17 Score=36.55 Aligned_cols=16 Identities=13% Similarity=0.407 Sum_probs=14.3
Q ss_pred ccCccccceeeecCCc
Q 010003 374 RRCQQCRRMIELTHGC 389 (520)
Q Consensus 374 k~CP~C~~~IeK~~GC 389 (520)
|.||.|.-.|+|.+-|
T Consensus 124 K~Cp~C~d~VqrIeq~ 139 (389)
T KOG2932|consen 124 KICPLCDDRVQRIEQI 139 (389)
T ss_pred ccCcCcccHHHHHHHh
Confidence 8899999999998766
No 258
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=25.64 E-value=28 Score=25.44 Aligned_cols=11 Identities=27% Similarity=1.041 Sum_probs=5.2
Q ss_pred cCccccceeee
Q 010003 375 RCQQCRRMIEL 385 (520)
Q Consensus 375 ~CP~C~~~IeK 385 (520)
+|++|+..+-+
T Consensus 6 RC~~CnklLa~ 16 (51)
T PF10122_consen 6 RCGHCNKLLAK 16 (51)
T ss_pred eccchhHHHhh
Confidence 44444444444
No 259
>PHA02862 5L protein; Provisional
Probab=25.59 E-value=54 Score=29.45 Aligned_cols=48 Identities=21% Similarity=0.357 Sum_probs=32.4
Q ss_pred ccccccccccCCCCeeeccCC---CcccHHHHHHHHHHhhhCCCCccccCCCCcCcccc
Q 010003 205 ENCSICCEDKPYPMMITMKCS---HKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFIS 260 (520)
Q Consensus 205 ~~C~IC~e~~~~~~~~~l~Cg---H~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~ 260 (520)
..|-||+++.... ...+.|. .....+||++|+... .+..||. |+....
T Consensus 3 diCWIC~~~~~e~-~~PC~C~GS~K~VHq~CL~~WIn~S-----~k~~CeL--CkteY~ 53 (156)
T PHA02862 3 DICWICNDVCDER-NNFCGCNEEYKVVHIKCMQLWINYS-----KKKECNL--CKTKYN 53 (156)
T ss_pred CEEEEecCcCCCC-cccccccCcchhHHHHHHHHHHhcC-----CCcCccC--CCCeEE
Confidence 4699999886432 2223452 468999999999532 2568998 877653
No 260
>cd00021 BBOX B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
Probab=24.77 E-value=39 Score=22.36 Aligned_cols=24 Identities=25% Similarity=0.635 Sum_probs=20.0
Q ss_pred ceeCCCCCcceeccCCCccCCCCC
Q 010003 322 CVECPVCERFICVECGVPWHSSLS 345 (520)
Q Consensus 322 ~~~Cp~C~~~fC~~C~~~wH~~~t 345 (520)
.+.|..|+...|..|....|.++.
T Consensus 12 ~~fC~~~~~~iC~~C~~~~H~~H~ 35 (39)
T cd00021 12 SLFCETDRALLCVDCDLSVHSGHR 35 (39)
T ss_pred EEEeCccChhhhhhcChhhcCCCC
Confidence 478999999999999977687654
No 261
>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=24.65 E-value=51 Score=20.18 Aligned_cols=7 Identities=29% Similarity=0.876 Sum_probs=4.6
Q ss_pred ccCcccc
Q 010003 374 RRCQQCR 380 (520)
Q Consensus 374 k~CP~C~ 380 (520)
-.||+|+
T Consensus 17 f~CPnCG 23 (24)
T PF07754_consen 17 FPCPNCG 23 (24)
T ss_pred EeCCCCC
Confidence 4677775
No 262
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=24.50 E-value=63 Score=24.04 Aligned_cols=12 Identities=17% Similarity=0.382 Sum_probs=9.0
Q ss_pred CccCccccceee
Q 010003 373 WRRCQQCRRMIE 384 (520)
Q Consensus 373 ~k~CP~C~~~Ie 384 (520)
.|+||-|+....
T Consensus 3 LkPCPFCG~~~~ 14 (61)
T PF14354_consen 3 LKPCPFCGSADV 14 (61)
T ss_pred CcCCCCCCCcce
Confidence 489999986533
No 263
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=24.43 E-value=40 Score=24.49 Aligned_cols=10 Identities=40% Similarity=0.816 Sum_probs=5.3
Q ss_pred ccCcccccee
Q 010003 374 RRCQQCRRMI 383 (520)
Q Consensus 374 k~CP~C~~~I 383 (520)
-+||.|+..|
T Consensus 25 irCp~Cg~rI 34 (49)
T COG1996 25 IRCPYCGSRI 34 (49)
T ss_pred eeCCCCCcEE
Confidence 4555555544
No 264
>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=23.91 E-value=1.5e+02 Score=26.48 Aligned_cols=59 Identities=19% Similarity=0.303 Sum_probs=27.6
Q ss_pred cHHHHHHHHHHHhhc---CCCceeccCCCCCeeecCcccccccc---cCCCCCCCCceeCCCCCcce
Q 010003 272 SYESLETALAEANIL---HSDRIYCPFPNCSVLLDPRECLSARA---SSSSQSDNSCVECPVCERFI 332 (520)
Q Consensus 272 ~~e~~~~~~~e~~~~---~~~~~~CP~p~C~~~~~~~~~~~~~~---~~~~~~~~~~~~Cp~C~~~f 332 (520)
..+.+.+.+....+. .+....||. |+..+.+........ ............||.|++.|
T Consensus 70 ~~~QL~ev~~~~~l~~~~~~~~sRC~~--CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiy 134 (147)
T PF01927_consen 70 PEEQLREVLERFGLKLRLDPIFSRCPK--CNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIY 134 (147)
T ss_pred HHHHHHHHHHHcCCccccCCCCCccCC--CCcEeeechhhccccccCccccccCCeEEECCCCCCEe
Confidence 344444444444433 233678997 765443322111000 00011112346899998887
No 265
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=23.82 E-value=55 Score=32.68 Aligned_cols=25 Identities=36% Similarity=0.826 Sum_probs=18.3
Q ss_pred ccCccccceeeec--CCcceEEeccccccccccc
Q 010003 374 RRCQQCRRMIELT--HGCYHMTCWCGHEFCYSCG 405 (520)
Q Consensus 374 k~CP~C~~~IeK~--~GCnhMtC~Cg~~FCy~C~ 405 (520)
++||+|+..|++. +| =++.||-.|-
T Consensus 236 ~pC~~Cg~~I~~~~~~g-------R~ty~Cp~CQ 262 (269)
T PRK14811 236 QPCPRCGTPIEKIVVGG-------RGTHFCPQCQ 262 (269)
T ss_pred CCCCcCCCeeEEEEECC-------CCcEECCCCc
Confidence 7999999999975 45 3555666554
No 266
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=23.29 E-value=52 Score=22.64 Aligned_cols=10 Identities=20% Similarity=0.474 Sum_probs=5.5
Q ss_pred ceeCCCCCcc
Q 010003 322 CVECPVCERF 331 (520)
Q Consensus 322 ~~~Cp~C~~~ 331 (520)
.+.|..|++.
T Consensus 28 fy~C~~C~~~ 37 (40)
T smart00440 28 FYVCTKCGHR 37 (40)
T ss_pred EEEeCCCCCE
Confidence 3566666543
No 267
>PLN02189 cellulose synthase
Probab=23.08 E-value=54 Score=38.73 Aligned_cols=44 Identities=25% Similarity=0.564 Sum_probs=30.7
Q ss_pred CceeCCCCCcceeccCCCccCCCCCchhhhcCchhhcCchHHHHHHHHhccCCccCccccceeeecCCcceE
Q 010003 321 SCVECPVCERFICVECGVPWHSSLSCEEYQNLPLEERDAGDITLHRLAQNKRWRRCQQCRRMIELTHGCYHM 392 (520)
Q Consensus 321 ~~~~Cp~C~~~fC~~C~~~wH~~~tC~e~~~~~~~~~~~~~~~l~~l~~~~~~k~CP~C~~~IeK~~GCnhM 392 (520)
..+.|..|++-.|..|- ||.. +.+.+.||+|++...+..|++.+
T Consensus 52 ~fvaC~~C~fpvCr~Cy----------eyer------------------~eg~q~CpqCkt~Y~r~kgs~~v 95 (1040)
T PLN02189 52 LFVACNECGFPVCRPCY----------EYER------------------REGTQNCPQCKTRYKRLKGSPRV 95 (1040)
T ss_pred EEEeeccCCCccccchh----------hhhh------------------hcCCccCcccCCchhhccCCCCc
Confidence 34789999999987654 3321 12238999999998877777643
No 268
>KOG4218 consensus Nuclear hormone receptor betaFTZ-F1 [Transcription]
Probab=23.05 E-value=36 Score=34.75 Aligned_cols=8 Identities=50% Similarity=1.327 Sum_probs=5.2
Q ss_pred ccCccccc
Q 010003 374 RRCQQCRR 381 (520)
Q Consensus 374 k~CP~C~~ 381 (520)
|+||.|+-
T Consensus 68 KRCP~CRF 75 (475)
T KOG4218|consen 68 KRCPSCRF 75 (475)
T ss_pred ccCCchhH
Confidence 67777543
No 269
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=22.96 E-value=44 Score=32.65 Aligned_cols=36 Identities=36% Similarity=0.969 Sum_probs=23.4
Q ss_pred ccCcccccee-----eecCCcceEEec-ccccc-----------ccccccccc
Q 010003 374 RRCQQCRRMI-----ELTHGCYHMTCW-CGHEF-----------CYSCGAEYR 409 (520)
Q Consensus 374 k~CP~C~~~I-----eK~~GCnhMtC~-Cg~~F-----------Cy~C~~~~~ 409 (520)
-+|-+|++.. .|..|=-...|. |++.| ||.|+.+..
T Consensus 133 SRCr~C~~rYDPVP~dkmwG~aef~C~~C~h~F~G~~qm~v~sPCy~C~~~v~ 185 (278)
T PF15135_consen 133 SRCRKCRKRYDPVPCDKMWGIAEFHCPKCRHNFRGFAQMGVPSPCYGCGNPVY 185 (278)
T ss_pred ccccccccccCCCccccccceeeeecccccccchhhhhcCCCCCccCCCCccC
Confidence 4666666653 344566666774 77766 888888764
No 270
>PRK08332 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=22.85 E-value=47 Score=41.57 Aligned_cols=27 Identities=33% Similarity=0.862 Sum_probs=23.0
Q ss_pred ccCccccce------eeecCCcceEEec-ccccccc
Q 010003 374 RRCQQCRRM------IELTHGCYHMTCW-CGHEFCY 402 (520)
Q Consensus 374 k~CP~C~~~------IeK~~GCnhMtC~-Cg~~FCy 402 (520)
..||.|+.. +...+||. +|+ ||+.-|-
T Consensus 1705 ~~cp~c~~~~~~~~~~~~~~gc~--~c~~cg~s~c~ 1738 (1740)
T PRK08332 1705 VYCPVCYEKEGKLVELRMESGCA--TCPVCGWSKCV 1738 (1740)
T ss_pred CCCCCCCCCCCcceeeEecCCce--eCCCCCCcccc
Confidence 459999999 78889997 997 9988773
No 271
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=22.85 E-value=60 Score=32.46 Aligned_cols=13 Identities=31% Similarity=0.687 Sum_probs=11.9
Q ss_pred ccCccccceeeec
Q 010003 374 RRCQQCRRMIELT 386 (520)
Q Consensus 374 k~CP~C~~~IeK~ 386 (520)
++||+|+..|+|.
T Consensus 246 ~pC~~Cg~~I~~~ 258 (274)
T PRK01103 246 EPCRRCGTPIEKI 258 (274)
T ss_pred CCCCCCCCeeEEE
Confidence 7999999999986
No 272
>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=22.54 E-value=60 Score=27.97 Aligned_cols=27 Identities=26% Similarity=0.496 Sum_probs=16.8
Q ss_pred CCceeccCCCCCeeecCcccccccccCCCCCCCCceeCCCCCc
Q 010003 288 SDRIYCPFPNCSVLLDPRECLSARASSSSQSDNSCVECPVCER 330 (520)
Q Consensus 288 ~~~~~CP~p~C~~~~~~~~~~~~~~~~~~~~~~~~~~Cp~C~~ 330 (520)
+...+|+. |+..+..... .+.||.|+.
T Consensus 68 p~~~~C~~--Cg~~~~~~~~--------------~~~CP~Cgs 94 (115)
T TIGR00100 68 PVECECED--CSEEVSPEID--------------LYRCPKCHG 94 (115)
T ss_pred CcEEEccc--CCCEEecCCc--------------CccCcCCcC
Confidence 45678986 8765544321 266888875
No 273
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=22.33 E-value=58 Score=32.56 Aligned_cols=13 Identities=31% Similarity=0.687 Sum_probs=12.0
Q ss_pred ccCccccceeeec
Q 010003 374 RRCQQCRRMIELT 386 (520)
Q Consensus 374 k~CP~C~~~IeK~ 386 (520)
++||+|+..|+|.
T Consensus 246 ~pC~~Cg~~I~~~ 258 (272)
T TIGR00577 246 EPCRRCGTPIEKI 258 (272)
T ss_pred CCCCCCCCeeEEE
Confidence 7999999999986
No 274
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=22.18 E-value=26 Score=34.83 Aligned_cols=109 Identities=20% Similarity=0.395 Sum_probs=59.0
Q ss_pred CccccccccccccCCCCe----eeccC----CC-cccHHHHHHHHHH-----hhhCCCCccccCCCCcCcccchHHHhhc
Q 010003 202 KSPENCSICCEDKPYPMM----ITMKC----SH-KFCSHCMRTYIDG-----KVQSSQVPIRCPQLRCKYFISTVECKSF 267 (520)
Q Consensus 202 ~~~~~C~IC~e~~~~~~~----~~l~C----gH-~fC~~Cl~~~i~~-----~i~~~~~~i~CP~~~C~~~l~~~~i~~~ 267 (520)
.....|.-|-..+....- -.+.| .+ .-|..|=+.|+.. -|.....+..|+. |+..++...+.+
T Consensus 128 ~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~i--CGKaFSRPWLLQ- 204 (279)
T KOG2462|consen 128 HPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHTLPCECGI--CGKAFSRPWLLQ- 204 (279)
T ss_pred CCceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccCCCccccc--ccccccchHHhh-
Confidence 346778888776653321 11122 22 3578888887643 2333445677877 888776533211
Q ss_pred CCcccHHHHHHHHHHHhhc---CCCceeccCCCCCeeecCcccccccccCCCCCCCCceeCCCCCcce
Q 010003 268 LPLSSYESLETALAEANIL---HSDRIYCPFPNCSVLLDPRECLSARASSSSQSDNSCVECPVCERFI 332 (520)
Q Consensus 268 L~~~~~e~~~~~~~e~~~~---~~~~~~CP~p~C~~~~~~~~~~~~~~~~~~~~~~~~~~Cp~C~~~f 332 (520)
.-+. ...-+.||. |+.++-....+ |+--...++...+.|+.|++.|
T Consensus 205 ---------------GHiRTHTGEKPF~C~h--C~kAFADRSNL--RAHmQTHS~~K~~qC~~C~KsF 253 (279)
T KOG2462|consen 205 ---------------GHIRTHTGEKPFSCPH--CGKAFADRSNL--RAHMQTHSDVKKHQCPRCGKSF 253 (279)
T ss_pred ---------------cccccccCCCCccCCc--ccchhcchHHH--HHHHHhhcCCccccCcchhhHH
Confidence 1111 234477884 88665443322 1111123445568898888877
No 275
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 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 [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=21.87 E-value=36 Score=25.33 Aligned_cols=13 Identities=15% Similarity=0.409 Sum_probs=10.3
Q ss_pred CCccCccccceee
Q 010003 372 RWRRCQQCRRMIE 384 (520)
Q Consensus 372 ~~k~CP~C~~~Ie 384 (520)
....||.|+.+..
T Consensus 25 ~l~~c~~cg~~~~ 37 (56)
T PF01783_consen 25 NLVKCPNCGEPKL 37 (56)
T ss_dssp SEEESSSSSSEES
T ss_pred ceeeeccCCCEec
Confidence 4478999998776
No 276
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=21.77 E-value=67 Score=32.71 Aligned_cols=40 Identities=23% Similarity=0.564 Sum_probs=27.9
Q ss_pred cccccccccCCCCeeec-cCCCcccHHHHHHHHHHhhhCCCCccccCC
Q 010003 206 NCSICCEDKPYPMMITM-KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQ 252 (520)
Q Consensus 206 ~C~IC~e~~~~~~~~~l-~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~ 252 (520)
.|-.|.++......+.+ .|.|.||.+|=. ++...+. .||.
T Consensus 332 ~Cf~C~~~~~~~~~y~C~~Ck~~FCldCDv-~iHesLh------~Cpg 372 (378)
T KOG2807|consen 332 FCFACQGELLSSGRYRCESCKNVFCLDCDV-FIHESLH------NCPG 372 (378)
T ss_pred ceeeeccccCCCCcEEchhccceeeccchH-HHHhhhh------cCCC
Confidence 38899777666666777 899999999954 3333332 4876
No 277
>PLN02436 cellulose synthase A
Probab=21.75 E-value=71 Score=37.90 Aligned_cols=49 Identities=27% Similarity=0.672 Sum_probs=33.1
Q ss_pred ccccccccccccC----CCCeeec-cCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCccc
Q 010003 203 SPENCSICCEDKP----YPMMITM-KCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFI 259 (520)
Q Consensus 203 ~~~~C~IC~e~~~----~~~~~~l-~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l 259 (520)
....|.||-|+.- .+.++.+ .|+-..|+.|. .|-. ++|. =.||+ |+...
T Consensus 35 ~~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cy-eyer---~eg~--~~Cpq--ckt~Y 88 (1094)
T PLN02436 35 SGQTCQICGDEIELTVDGEPFVACNECAFPVCRPCY-EYER---REGN--QACPQ--CKTRY 88 (1094)
T ss_pred CCccccccccccCcCCCCCEEEeeccCCCccccchh-hhhh---hcCC--ccCcc--cCCch
Confidence 3568999999852 2345566 69999999999 4433 2332 25998 87643
No 278
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=21.62 E-value=61 Score=32.42 Aligned_cols=13 Identities=23% Similarity=0.613 Sum_probs=11.9
Q ss_pred ccCccccceeeec
Q 010003 374 RRCQQCRRMIELT 386 (520)
Q Consensus 374 k~CP~C~~~IeK~ 386 (520)
++||+|+..|++.
T Consensus 245 ~pCprCG~~I~~~ 257 (272)
T PRK14810 245 EPCLNCKTPIRRV 257 (272)
T ss_pred CcCCCCCCeeEEE
Confidence 7999999999975
No 279
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 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 B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=21.58 E-value=25 Score=24.04 Aligned_cols=22 Identities=32% Similarity=0.708 Sum_probs=19.7
Q ss_pred eeCCCCCcceeccCCCccCCCC
Q 010003 323 VECPVCERFICVECGVPWHSSL 344 (520)
Q Consensus 323 ~~Cp~C~~~fC~~C~~~wH~~~ 344 (520)
+.|..|+..+|..|...-|.++
T Consensus 16 ~~C~~C~~~~C~~C~~~~H~~H 37 (42)
T PF00643_consen 16 LFCEDCNEPLCSECTVSGHKGH 37 (42)
T ss_dssp EEETTTTEEEEHHHHHTSTTTS
T ss_pred EEecCCCCccCccCCCCCCCCC
Confidence 7899999999999998878775
No 280
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=21.46 E-value=41 Score=33.89 Aligned_cols=28 Identities=29% Similarity=0.716 Sum_probs=19.5
Q ss_pred CccCccccceeeecCCcceEEec---cccccccccccc
Q 010003 373 WRRCQQCRRMIELTHGCYHMTCW---CGHEFCYSCGAE 407 (520)
Q Consensus 373 ~k~CP~C~~~IeK~~GCnhMtC~---Cg~~FCy~C~~~ 407 (520)
+.-|-+|..+|- +.=| |+|-|||-|-..
T Consensus 90 VHfCd~Cd~PI~-------IYGRmIPCkHvFCl~CAr~ 120 (389)
T KOG2932|consen 90 VHFCDRCDFPIA-------IYGRMIPCKHVFCLECARS 120 (389)
T ss_pred eEeecccCCcce-------eeecccccchhhhhhhhhc
Confidence 467999999986 3333 777777777543
No 281
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=21.44 E-value=61 Score=32.61 Aligned_cols=21 Identities=29% Similarity=0.589 Sum_probs=15.4
Q ss_pred ccCccccceeeec--CCcceEEe
Q 010003 374 RRCQQCRRMIELT--HGCYHMTC 394 (520)
Q Consensus 374 k~CP~C~~~IeK~--~GCnhMtC 394 (520)
++||+|+..|+|. +|=.-..|
T Consensus 255 ~pC~~Cg~~I~~~~~~gR~t~~C 277 (282)
T PRK13945 255 KPCRKCGTPIERIKLAGRSTHWC 277 (282)
T ss_pred CCCCcCCCeeEEEEECCCccEEC
Confidence 7999999999986 56333333
No 282
>PRK10445 endonuclease VIII; Provisional
Probab=21.21 E-value=64 Score=32.10 Aligned_cols=16 Identities=31% Similarity=0.677 Sum_probs=13.3
Q ss_pred ccCccccceeeec--CCc
Q 010003 374 RRCQQCRRMIELT--HGC 389 (520)
Q Consensus 374 k~CP~C~~~IeK~--~GC 389 (520)
++||+|+..|++. +|=
T Consensus 236 ~~Cp~Cg~~I~~~~~~gR 253 (263)
T PRK10445 236 EACERCGGIIEKTTLSSR 253 (263)
T ss_pred CCCCCCCCEeEEEEECCC
Confidence 7999999999976 453
No 283
>PF02748 PyrI_C: Aspartate carbamoyltransferase regulatory chain, metal binding domain; InterPro: IPR020542 Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) 2.1.3.2 from EC is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity []. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme []. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies. A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme []. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold. ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation []. This entry represents the C-terminal domain.; PDB: 2YWW_B 1SKU_D 1Q95_L 8ATC_B 3AT1_D 1RAI_D 4E2F_D 1NBE_B 6AT1_B 2FZC_D ....
Probab=21.18 E-value=40 Score=24.77 Aligned_cols=13 Identities=38% Similarity=0.843 Sum_probs=9.7
Q ss_pred CceeccCCCCCee
Q 010003 289 DRIYCPFPNCSVL 301 (520)
Q Consensus 289 ~~~~CP~p~C~~~ 301 (520)
+.+.||+|+|-.-
T Consensus 5 gvl~C~Np~CITn 17 (52)
T PF02748_consen 5 GVLKCPNPNCITN 17 (52)
T ss_dssp SSSE-SSTTBTTT
T ss_pred eEEEcCCCCcccC
Confidence 5689999999754
No 284
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=21.16 E-value=1.2e+02 Score=26.08 Aligned_cols=33 Identities=18% Similarity=0.503 Sum_probs=21.5
Q ss_pred ccccccccccccCC--CCeeec-cCCCcccHHHHHH
Q 010003 203 SPENCSICCEDKPY--PMMITM-KCSHKFCSHCMRT 235 (520)
Q Consensus 203 ~~~~C~IC~e~~~~--~~~~~l-~CgH~fC~~Cl~~ 235 (520)
....|.+|...+.. +.-..+ .|+|.+|..|-..
T Consensus 53 ~~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~ 88 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVY 88 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEE
T ss_pred CCcchhhhCCcccccCCCCCcCCcCCccccCccCCc
Confidence 35689999987532 222334 8999999999755
No 285
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=21.11 E-value=48 Score=20.24 Aligned_cols=10 Identities=50% Similarity=1.271 Sum_probs=8.1
Q ss_pred eeCCCCCcce
Q 010003 323 VECPVCERFI 332 (520)
Q Consensus 323 ~~Cp~C~~~f 332 (520)
+.|+.|++.|
T Consensus 3 ~~C~~CgR~F 12 (25)
T PF13913_consen 3 VPCPICGRKF 12 (25)
T ss_pred CcCCCCCCEE
Confidence 5688888887
No 286
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=20.98 E-value=60 Score=22.23 Aligned_cols=18 Identities=28% Similarity=0.756 Sum_probs=15.6
Q ss_pred ceeCCCCCcceeccCCCc
Q 010003 322 CVECPVCERFICVECGVP 339 (520)
Q Consensus 322 ~~~Cp~C~~~fC~~C~~~ 339 (520)
.+.|..|+..||...+.+
T Consensus 12 ~f~C~~C~~~FC~~HR~~ 29 (39)
T smart00154 12 GFKCRHCGNLFCGEHRLP 29 (39)
T ss_pred CeECCccCCccccccCCc
Confidence 388999999999998865
No 287
>smart00336 BBOX B-Box-type zinc finger.
Probab=20.82 E-value=67 Score=21.53 Aligned_cols=23 Identities=22% Similarity=0.531 Sum_probs=19.2
Q ss_pred ceeCCCCCcceeccCCCccCCCC
Q 010003 322 CVECPVCERFICVECGVPWHSSL 344 (520)
Q Consensus 322 ~~~Cp~C~~~fC~~C~~~wH~~~ 344 (520)
.+.|..|+...|..|...-|.++
T Consensus 15 ~~~C~~c~~~iC~~C~~~~H~~H 37 (42)
T smart00336 15 EFFCEECGALLCRTCDEAEHRGH 37 (42)
T ss_pred EEECCCCCcccccccChhhcCCC
Confidence 37899999999999997777665
No 288
>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=20.65 E-value=43 Score=22.90 Aligned_cols=11 Identities=18% Similarity=0.265 Sum_probs=6.6
Q ss_pred ceeCCCCCcce
Q 010003 322 CVECPVCERFI 332 (520)
Q Consensus 322 ~~~Cp~C~~~f 332 (520)
.+.|..|++.+
T Consensus 28 fy~C~~C~~~w 38 (39)
T PF01096_consen 28 FYVCCNCGHRW 38 (39)
T ss_dssp EEEESSSTEEE
T ss_pred EEEeCCCCCee
Confidence 36677776543
No 289
>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=20.54 E-value=85 Score=20.48 Aligned_cols=23 Identities=39% Similarity=0.931 Sum_probs=14.3
Q ss_pred eccCCCCCeeecCcccccccccCCCCCCCCceeCCCCCc
Q 010003 292 YCPFPNCSVLLDPRECLSARASSSSQSDNSCVECPVCER 330 (520)
Q Consensus 292 ~CP~p~C~~~~~~~~~~~~~~~~~~~~~~~~~~Cp~C~~ 330 (520)
.|+. |++++..... -..||.|+.
T Consensus 3 ~C~~--CGy~y~~~~~--------------~~~CP~Cg~ 25 (33)
T cd00350 3 VCPV--CGYIYDGEEA--------------PWVCPVCGA 25 (33)
T ss_pred ECCC--CCCEECCCcC--------------CCcCcCCCC
Confidence 4664 8888765321 157888875
No 290
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=20.37 E-value=83 Score=35.83 Aligned_cols=49 Identities=16% Similarity=0.396 Sum_probs=32.3
Q ss_pred cccccccccccCCCCee-eccCCCcccHHHHHHHHHHhhhCCCCccccCCCCcCcccch
Q 010003 204 PENCSICCEDKPYPMMI-TMKCSHKFCSHCMRTYIDGKVQSSQVPIRCPQLRCKYFIST 261 (520)
Q Consensus 204 ~~~C~IC~e~~~~~~~~-~l~CgH~fC~~Cl~~~i~~~i~~~~~~i~CP~~~C~~~l~~ 261 (520)
...|++|+..+...... ...|+|.||..|+..|-..+- .||. |...+..
T Consensus 123 ~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~aq-------TCPi--DR~EF~~ 172 (1134)
T KOG0825|consen 123 ENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCAQ-------TCPV--DRGEFGE 172 (1134)
T ss_pred hhhhhHHHHHHHHHhhccccccccccHHHHhhhhhhhcc-------cCch--hhhhhhe
Confidence 34577777665432222 238999999999999976432 5887 6655443
No 291
>PF11682 DUF3279: Protein of unknown function (DUF3279); InterPro: IPR021696 This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.
Probab=20.23 E-value=60 Score=28.61 Aligned_cols=14 Identities=21% Similarity=0.465 Sum_probs=10.4
Q ss_pred ccCccccceeeecC
Q 010003 374 RRCQQCRRMIELTH 387 (520)
Q Consensus 374 k~CP~C~~~IeK~~ 387 (520)
|.||+|++-|--.+
T Consensus 111 K~C~~C~tGiYS~e 124 (128)
T PF11682_consen 111 KYCPKCGTGIYSIE 124 (128)
T ss_pred EecCCCCCccccee
Confidence 78999998775433
No 292
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=20.11 E-value=72 Score=27.41 Aligned_cols=15 Identities=20% Similarity=0.507 Sum_probs=9.7
Q ss_pred CCceeccCCCCCeeecC
Q 010003 288 SDRIYCPFPNCSVLLDP 304 (520)
Q Consensus 288 ~~~~~CP~p~C~~~~~~ 304 (520)
+...+|+. |+.....
T Consensus 68 p~~~~C~~--Cg~~~~~ 82 (113)
T PRK12380 68 PAQAWCWD--CSQVVEI 82 (113)
T ss_pred CcEEEccc--CCCEEec
Confidence 45678986 7765543
Done!