Query 021781
Match_columns 307
No_of_seqs 268 out of 1427
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 05:37:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021781.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021781hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1940 Zn-finger protein [Gen 100.0 2.7E-56 5.9E-61 417.8 4.9 235 57-303 19-266 (276)
2 PF05495 zf-CHY: CHY zinc fing 99.9 1.1E-23 2.3E-28 161.9 4.3 70 73-156 1-71 (71)
3 PF13639 zf-RING_2: Ring finge 99.3 7.9E-13 1.7E-17 91.7 1.9 44 207-252 1-44 (44)
4 COG4357 Zinc finger domain con 99.3 7.2E-13 1.6E-17 107.3 1.4 68 70-146 12-92 (105)
5 PF12861 zf-Apc11: Anaphase-pr 99.1 3.2E-11 6.9E-16 96.0 4.0 51 204-256 30-82 (85)
6 PF12678 zf-rbx1: RING-H2 zinc 99.0 3.4E-10 7.3E-15 87.3 4.0 47 205-252 18-73 (73)
7 KOG4628 Predicted E3 ubiquitin 98.9 4.6E-10 9.9E-15 109.3 3.2 50 207-257 230-279 (348)
8 cd00162 RING RING-finger (Real 98.9 1.2E-09 2.7E-14 73.0 3.8 45 208-255 1-45 (45)
9 PF13923 zf-C3HC4_2: Zinc fing 98.8 2.2E-09 4.7E-14 72.9 3.1 39 209-251 1-39 (39)
10 PHA02929 N1R/p28-like protein; 98.8 6.3E-09 1.4E-13 97.0 4.4 54 203-257 171-228 (238)
11 PF14599 zinc_ribbon_6: Zinc-r 98.7 3E-09 6.5E-14 80.0 1.4 46 255-300 1-59 (61)
12 PF15227 zf-C3HC4_4: zinc fing 98.7 9.4E-09 2E-13 71.5 3.4 39 209-251 1-42 (42)
13 COG5243 HRD1 HRD ubiquitin lig 98.7 5.5E-09 1.2E-13 102.2 2.2 56 203-259 284-349 (491)
14 PF13920 zf-C3HC4_3: Zinc fing 98.7 1.2E-08 2.5E-13 72.7 3.2 47 206-257 2-49 (50)
15 PF00097 zf-C3HC4: Zinc finger 98.7 1.8E-08 4E-13 68.3 3.3 40 209-251 1-41 (41)
16 smart00184 RING Ring finger. E 98.6 2.8E-08 6E-13 64.1 3.2 39 209-251 1-39 (39)
17 COG5540 RING-finger-containing 98.6 2.1E-08 4.6E-13 96.0 3.4 56 201-257 318-373 (374)
18 KOG1493 Anaphase-promoting com 98.6 7.7E-09 1.7E-13 81.0 0.1 51 204-256 29-81 (84)
19 PF13445 zf-RING_UBOX: RING-ty 98.6 3.9E-08 8.4E-13 69.1 2.5 40 209-249 1-43 (43)
20 PF14634 zf-RING_5: zinc-RING 98.5 6.8E-08 1.5E-12 67.3 3.6 44 208-253 1-44 (44)
21 COG5194 APC11 Component of SCF 98.5 5.8E-08 1.3E-12 76.7 3.4 50 206-256 31-81 (88)
22 PLN03208 E3 ubiquitin-protein 98.5 1.3E-07 2.8E-12 85.7 4.7 56 198-257 10-80 (193)
23 KOG0804 Cytoplasmic Zn-finger 98.4 1.7E-07 3.7E-12 93.5 3.1 82 206-301 175-257 (493)
24 PHA02926 zinc finger-like prot 98.3 4.7E-07 1E-11 83.7 3.5 56 202-257 166-231 (242)
25 smart00504 Ubox Modified RING 98.3 1E-06 2.3E-11 64.3 4.1 45 207-256 2-46 (63)
26 KOG0320 Predicted E3 ubiquitin 98.1 2.1E-06 4.5E-11 77.0 3.1 48 206-256 131-178 (187)
27 KOG0802 E3 ubiquitin ligase [P 98.0 1.8E-06 3.9E-11 88.6 1.7 53 202-255 287-340 (543)
28 KOG0317 Predicted E3 ubiquitin 97.9 8E-06 1.7E-10 77.9 2.6 47 206-257 239-285 (293)
29 KOG2177 Predicted E3 ubiquitin 97.8 7.3E-06 1.6E-10 72.3 2.1 44 205-253 12-55 (386)
30 TIGR00599 rad18 DNA repair pro 97.8 1.2E-05 2.5E-10 80.2 3.5 47 205-256 25-71 (397)
31 KOG2930 SCF ubiquitin ligase, 97.8 4.8E-06 1E-10 68.8 0.6 34 222-256 75-108 (114)
32 smart00744 RINGv The RING-vari 97.8 1.8E-05 3.9E-10 56.9 3.3 43 208-252 1-49 (49)
33 TIGR00570 cdk7 CDK-activating 97.8 2.2E-05 4.8E-10 75.8 4.4 52 206-257 3-55 (309)
34 KOG0823 Predicted E3 ubiquitin 97.6 3.7E-05 8.1E-10 71.4 3.0 50 204-257 45-96 (230)
35 PF11793 FANCL_C: FANCL C-term 97.6 1.4E-05 3.1E-10 61.2 -0.0 51 206-256 2-66 (70)
36 KOG0828 Predicted E3 ubiquitin 97.6 3.1E-05 6.7E-10 78.6 1.8 52 206-257 571-635 (636)
37 KOG2164 Predicted E3 ubiquitin 97.5 6.3E-05 1.4E-09 76.5 2.6 49 205-257 185-237 (513)
38 PF04564 U-box: U-box domain; 97.4 0.00012 2.6E-09 56.2 3.4 48 206-257 4-51 (73)
39 KOG0287 Postreplication repair 97.4 8.2E-05 1.8E-09 72.8 3.0 45 207-256 24-68 (442)
40 KOG0827 Predicted E3 ubiquitin 97.1 0.0002 4.2E-09 71.1 1.8 46 206-252 4-52 (465)
41 COG5574 PEX10 RING-finger-cont 97.0 0.00035 7.7E-09 66.2 2.2 49 205-257 214-263 (271)
42 PF14835 zf-RING_6: zf-RING of 96.9 0.00045 9.7E-09 52.7 1.7 55 207-268 8-64 (65)
43 KOG1734 Predicted RING-contain 96.8 0.00035 7.5E-09 66.6 0.4 52 205-256 223-281 (328)
44 KOG4172 Predicted E3 ubiquitin 96.8 0.00031 6.8E-09 52.2 -0.1 51 205-259 6-57 (62)
45 KOG4265 Predicted E3 ubiquitin 96.7 0.0012 2.7E-08 64.7 3.0 49 204-257 288-337 (349)
46 PF14570 zf-RING_4: RING/Ubox 96.5 0.0019 4E-08 46.7 2.4 47 209-255 1-47 (48)
47 KOG0311 Predicted E3 ubiquitin 96.5 0.00058 1.3E-08 67.1 -0.5 49 206-257 43-91 (381)
48 COG5432 RAD18 RING-finger-cont 96.5 0.0017 3.7E-08 62.7 2.5 46 206-256 25-70 (391)
49 KOG1941 Acetylcholine receptor 96.4 0.00065 1.4E-08 67.7 -0.8 59 197-256 357-416 (518)
50 KOG0978 E3 ubiquitin ligase in 96.4 0.0011 2.4E-08 70.2 0.6 47 207-257 644-690 (698)
51 PF11789 zf-Nse: Zinc-finger o 96.2 0.0041 8.8E-08 46.1 3.0 44 204-250 9-53 (57)
52 KOG2879 Predicted E3 ubiquitin 96.2 0.004 8.6E-08 59.6 3.3 53 204-259 237-290 (298)
53 KOG1039 Predicted E3 ubiquitin 96.1 0.0018 4E-08 63.6 0.6 53 204-256 159-221 (344)
54 KOG1785 Tyrosine kinase negati 96.1 0.0018 3.8E-08 64.8 0.5 54 199-256 362-416 (563)
55 KOG0824 Predicted E3 ubiquitin 96.0 0.0046 1E-07 59.8 2.9 50 203-256 4-53 (324)
56 KOG3002 Zn finger protein [Gen 95.6 0.012 2.5E-07 57.0 3.8 64 206-280 48-113 (299)
57 KOG0825 PHD Zn-finger protein 95.4 0.0052 1.1E-07 65.7 0.6 51 205-257 122-172 (1134)
58 PRK14890 putative Zn-ribbon RN 95.3 0.013 2.9E-07 44.0 2.3 46 119-171 5-56 (59)
59 KOG1645 RING-finger-containing 95.3 0.022 4.7E-07 57.2 4.5 51 206-256 4-56 (463)
60 COG5219 Uncharacterized conser 95.2 0.0093 2E-07 65.0 1.9 53 204-256 1467-1523(1525)
61 PF10367 Vps39_2: Vacuolar sor 94.9 0.011 2.3E-07 47.0 1.1 33 204-238 76-108 (109)
62 PF12906 RINGv: RING-variant d 94.8 0.02 4.2E-07 40.8 2.0 41 209-251 1-47 (47)
63 KOG1428 Inhibitor of type V ad 94.6 0.028 6.1E-07 63.7 3.7 74 175-256 3462-3544(3738)
64 KOG4185 Predicted E3 ubiquitin 94.6 0.045 9.7E-07 51.7 4.6 49 207-256 4-55 (296)
65 PF14447 Prok-RING_4: Prokaryo 94.5 0.015 3.2E-07 43.2 0.8 33 222-257 19-51 (55)
66 KOG3800 Predicted E3 ubiquitin 94.3 0.034 7.4E-07 53.6 3.1 49 208-256 2-51 (300)
67 KOG4445 Uncharacterized conser 94.2 0.015 3.3E-07 56.5 0.5 53 204-257 113-187 (368)
68 KOG4739 Uncharacterized protei 93.9 0.026 5.7E-07 52.9 1.3 36 218-256 13-48 (233)
69 COG5175 MOT2 Transcriptional r 93.5 0.027 5.9E-07 55.6 0.8 54 206-259 14-67 (480)
70 KOG3268 Predicted E3 ubiquitin 93.4 0.049 1.1E-06 49.6 2.2 31 226-256 188-228 (234)
71 KOG1571 Predicted E3 ubiquitin 93.3 0.046 1E-06 54.0 2.1 47 202-256 301-347 (355)
72 KOG0297 TNF receptor-associate 93.1 0.056 1.2E-06 53.9 2.3 50 204-257 19-68 (391)
73 PF05883 Baculo_RING: Baculovi 92.7 0.059 1.3E-06 46.7 1.6 35 206-241 26-66 (134)
74 KOG4159 Predicted E3 ubiquitin 92.6 0.12 2.5E-06 52.1 3.7 49 204-257 82-130 (398)
75 KOG3970 Predicted E3 ubiquitin 92.5 0.18 3.8E-06 47.6 4.5 52 204-257 48-106 (299)
76 KOG4275 Predicted E3 ubiquitin 92.5 0.02 4.4E-07 55.4 -1.7 55 195-258 286-344 (350)
77 PF07191 zinc-ribbons_6: zinc- 92.2 0.082 1.8E-06 41.1 1.7 36 120-155 16-59 (70)
78 PF04641 Rtf2: Rtf2 RING-finge 92.2 0.15 3.3E-06 47.9 3.8 51 203-256 110-161 (260)
79 COG2888 Predicted Zn-ribbon RN 92.0 0.11 2.4E-06 39.3 2.0 45 121-171 9-58 (61)
80 PF12773 DZR: Double zinc ribb 91.9 0.16 3.5E-06 35.7 2.8 22 124-145 1-23 (50)
81 COG5152 Uncharacterized conser 91.5 0.11 2.4E-06 48.1 1.9 60 206-270 196-255 (259)
82 KOG1813 Predicted E3 ubiquitin 91.5 0.13 2.9E-06 49.8 2.5 63 204-271 239-301 (313)
83 PF07800 DUF1644: Protein of u 91.2 0.21 4.6E-06 44.4 3.4 33 206-242 2-47 (162)
84 KOG1814 Predicted E3 ubiquitin 90.8 0.15 3.3E-06 51.3 2.3 49 205-254 183-238 (445)
85 KOG2817 Predicted E3 ubiquitin 90.5 0.2 4.4E-06 50.2 2.9 48 207-255 335-384 (394)
86 KOG1002 Nucleotide excision re 89.9 0.14 2.9E-06 53.4 1.1 54 199-256 529-586 (791)
87 KOG3039 Uncharacterized conser 89.4 0.37 8E-06 46.0 3.5 53 203-257 218-271 (303)
88 PHA02862 5L protein; Provision 89.3 0.26 5.6E-06 43.4 2.3 46 206-256 2-53 (156)
89 PHA02825 LAP/PHD finger-like p 88.0 0.46 1E-05 42.4 3.0 48 204-256 6-59 (162)
90 KOG2660 Locus-specific chromos 88.0 0.15 3.3E-06 49.9 -0.0 49 204-256 13-61 (331)
91 PF13248 zf-ribbon_3: zinc-rib 87.6 0.26 5.6E-06 30.8 0.9 24 121-144 2-26 (26)
92 COG5236 Uncharacterized conser 87.6 0.55 1.2E-05 46.8 3.5 66 187-256 42-108 (493)
93 KOG3161 Predicted E3 ubiquitin 87.4 0.22 4.8E-06 52.8 0.7 44 207-254 12-55 (861)
94 KOG2114 Vacuolar assembly/sort 86.7 0.49 1.1E-05 51.5 2.9 43 207-256 841-883 (933)
95 PRK04023 DNA polymerase II lar 86.5 0.59 1.3E-05 51.9 3.4 31 136-170 628-658 (1121)
96 PF08746 zf-RING-like: RING-li 85.4 0.59 1.3E-05 32.7 1.8 25 227-251 18-43 (43)
97 KOG0309 Conserved WD40 repeat- 84.8 0.59 1.3E-05 50.6 2.3 44 204-250 1026-1069(1081)
98 COG5222 Uncharacterized conser 84.5 0.62 1.3E-05 45.6 2.1 44 207-253 275-318 (427)
99 PF03854 zf-P11: P-11 zinc fin 84.1 0.45 9.8E-06 34.6 0.8 32 225-257 15-47 (50)
100 PF13240 zinc_ribbon_2: zinc-r 83.3 0.58 1.3E-05 28.7 0.9 21 124-144 2-23 (23)
101 COG5220 TFB3 Cdk activating ki 83.2 0.44 9.6E-06 45.3 0.6 51 206-256 10-64 (314)
102 PHA00626 hypothetical protein 83.2 0.84 1.8E-05 34.2 1.9 29 136-171 2-31 (59)
103 PRK14559 putative protein seri 82.6 0.87 1.9E-05 48.6 2.5 33 122-154 2-35 (645)
104 PF09538 FYDLN_acid: Protein o 81.7 0.96 2.1E-05 37.8 2.0 27 133-171 8-34 (108)
105 KOG2034 Vacuolar sorting prote 80.3 0.78 1.7E-05 50.2 1.2 36 205-242 816-851 (911)
106 PRK14714 DNA polymerase II lar 79.5 1.8 3.9E-05 49.3 3.6 47 122-170 668-716 (1337)
107 PF10571 UPF0547: Uncharacteri 79.2 1.3 2.8E-05 28.0 1.5 23 123-145 2-25 (26)
108 PHA03096 p28-like protein; Pro 78.5 1.2 2.6E-05 43.0 1.7 48 207-254 179-232 (284)
109 KOG1001 Helicase-like transcri 77.9 1.2 2.6E-05 47.8 1.7 45 207-256 455-500 (674)
110 TIGR00595 priA primosomal prot 76.4 1.9 4.2E-05 44.4 2.7 49 82-143 214-262 (505)
111 KOG1952 Transcription factor N 76.2 1.5 3.4E-05 47.9 2.0 48 205-255 190-246 (950)
112 PF12773 DZR: Double zinc ribb 74.7 2.2 4.7E-05 29.9 1.8 32 121-152 12-49 (50)
113 KOG2272 Focal adhesion protein 73.8 1.2 2.5E-05 42.9 0.3 53 120-192 119-175 (332)
114 KOG4692 Predicted E3 ubiquitin 73.4 2.3 5E-05 42.6 2.2 51 202-257 418-468 (489)
115 PF14446 Prok-RING_1: Prokaryo 73.4 3.7 7.9E-05 30.5 2.7 36 205-240 4-39 (54)
116 PF02891 zf-MIZ: MIZ/SP-RING z 72.2 2.9 6.2E-05 30.0 2.0 44 207-254 3-50 (50)
117 COG5109 Uncharacterized conser 72.1 2.7 5.8E-05 41.6 2.3 46 207-253 337-384 (396)
118 PRK04023 DNA polymerase II lar 71.1 3.3 7.2E-05 46.3 3.0 48 121-174 626-674 (1121)
119 COG1198 PriA Primosomal protei 71.1 3.5 7.6E-05 44.7 3.1 54 82-148 436-489 (730)
120 PRK14714 DNA polymerase II lar 68.7 4.3 9.2E-05 46.4 3.2 33 135-171 668-700 (1337)
121 KOG1812 Predicted E3 ubiquitin 67.9 2.5 5.4E-05 42.3 1.1 44 206-250 146-195 (384)
122 KOG4367 Predicted Zn-finger pr 67.6 3 6.6E-05 42.8 1.7 33 206-242 4-36 (699)
123 PRK14873 primosome assembly pr 67.4 4 8.7E-05 43.7 2.6 49 82-144 384-432 (665)
124 TIGR02300 FYDLN_acid conserved 67.1 3.5 7.6E-05 35.6 1.7 27 134-172 9-35 (129)
125 PF04216 FdhE: Protein involve 65.7 4.1 9E-05 38.7 2.2 48 119-170 195-245 (290)
126 PRK05580 primosome assembly pr 65.0 4.6 0.0001 43.1 2.5 50 82-144 382-431 (679)
127 KOG2462 C2H2-type Zn-finger pr 64.8 6.2 0.00013 38.2 3.1 95 141-259 125-229 (279)
128 PRK14559 putative protein seri 62.8 3.9 8.5E-05 43.7 1.5 34 121-155 15-50 (645)
129 PF07282 OrfB_Zn_ribbon: Putat 62.7 5.6 0.00012 29.5 2.0 27 134-171 28-54 (69)
130 PF03107 C1_2: C1 domain; Int 62.4 5.7 0.00012 25.4 1.7 20 168-187 2-22 (30)
131 smart00132 LIM Zinc-binding do 61.7 6.4 0.00014 25.0 1.9 37 209-256 2-38 (39)
132 PF07191 zinc-ribbons_6: zinc- 60.6 1.3 2.8E-05 34.5 -1.9 41 207-257 2-42 (70)
133 PF14569 zf-UDP: Zinc-binding 60.3 9.1 0.0002 30.5 2.8 53 204-256 7-62 (80)
134 KOG3053 Uncharacterized conser 58.2 6.2 0.00013 38.0 1.8 70 202-271 16-104 (293)
135 PRK14890 putative Zn-ribbon RN 57.2 7.7 0.00017 29.3 1.8 34 119-154 23-56 (59)
136 PF06524 NOA36: NOA36 protein; 56.6 4.4 9.6E-05 39.1 0.6 51 88-154 140-190 (314)
137 COG1198 PriA Primosomal protei 56.6 12 0.00025 40.8 3.8 43 120-170 434-482 (730)
138 KOG2068 MOT2 transcription fac 56.4 9.5 0.00021 37.7 2.8 53 204-257 247-299 (327)
139 COG3809 Uncharacterized protei 55.6 9.1 0.0002 30.7 2.1 31 246-280 22-54 (88)
140 KOG1701 Focal adhesion adaptor 54.3 2.2 4.7E-05 43.6 -2.0 93 161-288 295-419 (468)
141 KOG0827 Predicted E3 ubiquitin 54.2 0.99 2.1E-05 45.5 -4.3 53 204-257 194-246 (465)
142 KOG1100 Predicted E3 ubiquitin 53.8 8.5 0.00018 35.5 1.9 38 209-255 161-199 (207)
143 smart00249 PHD PHD zinc finger 53.7 5.8 0.00013 26.0 0.7 41 209-251 2-47 (47)
144 KOG2066 Vacuolar assembly/sort 53.3 5.2 0.00011 43.6 0.5 45 206-252 784-831 (846)
145 PF13894 zf-C2H2_4: C2H2-type 53.3 7.7 0.00017 22.0 1.1 20 246-265 1-20 (24)
146 PRK00398 rpoP DNA-directed RNA 53.1 12 0.00027 25.9 2.3 8 163-170 21-28 (46)
147 PF13453 zf-TFIIB: Transcripti 51.3 12 0.00025 25.5 1.8 26 136-170 1-26 (41)
148 COG5183 SSM4 Protein involved 51.2 6 0.00013 43.5 0.6 53 203-257 9-67 (1175)
149 PF01599 Ribosomal_S27: Riboso 50.9 10 0.00023 27.3 1.6 23 132-154 16-46 (47)
150 PF05191 ADK_lid: Adenylate ki 50.0 4.3 9.4E-05 27.4 -0.5 27 136-171 3-29 (36)
151 KOG1609 Protein involved in mR 49.1 11 0.00023 35.3 1.9 52 206-257 78-135 (323)
152 PF08271 TF_Zn_Ribbon: TFIIB z 48.4 14 0.00031 25.3 2.0 7 137-143 3-9 (43)
153 PF01529 zf-DHHC: DHHC palmito 48.3 14 0.00029 31.6 2.2 49 139-193 41-89 (174)
154 KOG0298 DEAD box-containing he 48.0 6.7 0.00014 44.9 0.3 52 204-259 1151-1202(1394)
155 KOG0269 WD40 repeat-containing 47.7 17 0.00037 39.7 3.3 70 161-250 751-820 (839)
156 PLN03086 PRLI-interacting fact 45.6 16 0.00035 38.6 2.7 17 117-133 403-419 (567)
157 smart00734 ZnF_Rad18 Rad18-lik 45.5 18 0.00039 22.7 1.9 20 246-266 2-21 (26)
158 PF15616 TerY-C: TerY-C metal 44.5 20 0.00043 31.1 2.6 33 135-170 78-112 (131)
159 KOG2462 C2H2-type Zn-finger pr 43.9 34 0.00074 33.2 4.4 114 136-264 132-262 (279)
160 PHA00626 hypothetical protein 43.5 16 0.00036 27.5 1.7 33 122-156 1-33 (59)
161 PRK00432 30S ribosomal protein 43.5 17 0.00037 26.3 1.8 9 162-170 36-44 (50)
162 PLN02189 cellulose synthase 43.4 20 0.00043 40.5 3.1 56 201-256 29-87 (1040)
163 COG1998 RPS31 Ribosomal protei 43.2 15 0.00033 26.9 1.5 20 134-153 19-44 (51)
164 PF05605 zf-Di19: Drought indu 43.1 26 0.00056 25.1 2.7 8 246-253 3-10 (54)
165 PF06677 Auto_anti-p27: Sjogre 42.0 16 0.00036 25.4 1.4 13 134-146 17-29 (41)
166 PRK00420 hypothetical protein; 42.0 17 0.00036 30.7 1.7 21 134-154 23-48 (112)
167 PF14353 CpXC: CpXC protein 41.5 22 0.00049 29.5 2.5 11 136-146 3-13 (128)
168 PF04710 Pellino: Pellino; In 41.4 9.1 0.0002 38.8 0.1 50 203-255 274-338 (416)
169 PF05290 Baculo_IE-1: Baculovi 40.9 20 0.00044 31.3 2.2 47 207-257 81-133 (140)
170 PLN02436 cellulose synthase A 40.7 23 0.0005 40.1 3.1 56 201-256 31-89 (1094)
171 KOG1940 Zn-finger protein [Gen 40.6 11 0.00024 36.4 0.5 29 69-98 176-204 (276)
172 PF13717 zinc_ribbon_4: zinc-r 40.3 18 0.00039 24.2 1.4 9 121-129 25-33 (36)
173 PF05502 Dynactin_p62: Dynacti 39.8 17 0.00036 37.6 1.7 15 180-194 52-66 (483)
174 KOG0006 E3 ubiquitin-protein l 39.7 27 0.0006 34.8 3.1 79 154-241 168-254 (446)
175 PF04438 zf-HIT: HIT zinc fing 39.6 15 0.00032 23.9 0.8 16 137-153 5-20 (30)
176 COG2888 Predicted Zn-ribbon RN 39.5 18 0.0004 27.5 1.4 34 119-154 25-58 (61)
177 COG1996 RPC10 DNA-directed RNA 39.3 19 0.00041 26.2 1.5 29 144-172 4-33 (49)
178 PF03833 PolC_DP2: DNA polymer 39.1 10 0.00022 41.9 0.0 46 135-189 656-701 (900)
179 PRK03564 formate dehydrogenase 38.5 30 0.00065 34.0 3.2 25 119-143 210-235 (309)
180 PF00096 zf-C2H2: Zinc finger, 38.5 14 0.00031 21.3 0.6 15 246-260 1-15 (23)
181 PF01096 TFIIS_C: Transcriptio 38.5 20 0.00043 24.4 1.4 33 136-170 2-35 (39)
182 cd00350 rubredoxin_like Rubred 38.4 25 0.00055 22.9 1.8 25 146-171 1-25 (33)
183 PF05502 Dynactin_p62: Dynacti 37.6 26 0.00057 36.2 2.7 21 196-218 44-64 (483)
184 PF07649 C1_3: C1-like domain; 36.8 19 0.0004 22.8 1.0 20 169-188 3-23 (30)
185 PRK00415 rps27e 30S ribosomal 36.8 26 0.00056 26.5 1.9 37 119-155 9-51 (59)
186 COG1645 Uncharacterized Zn-fin 36.7 19 0.00042 31.2 1.4 19 135-153 29-51 (131)
187 PF03833 PolC_DP2: DNA polymer 36.6 12 0.00025 41.4 0.0 45 121-171 655-700 (900)
188 PF03604 DNA_RNApol_7kD: DNA d 36.1 24 0.00052 23.3 1.5 24 147-170 1-24 (32)
189 KOG4399 C2HC-type Zn-finger pr 34.9 8.3 0.00018 37.3 -1.3 73 140-215 198-270 (325)
190 cd02337 ZZ_CBP Zinc finger, ZZ 34.5 28 0.00061 24.0 1.7 20 164-187 1-20 (41)
191 smart00661 RPOL9 RNA polymeras 34.3 31 0.00067 23.9 1.9 8 163-170 20-27 (52)
192 PF04423 Rad50_zn_hook: Rad50 33.9 14 0.0003 26.5 0.0 12 246-257 21-32 (54)
193 KOG2932 E3 ubiquitin ligase in 33.9 17 0.00038 36.0 0.7 30 224-256 105-134 (389)
194 TIGR00100 hypA hydrogenase nic 33.8 21 0.00046 29.7 1.2 13 132-144 68-80 (115)
195 PRK00366 ispG 4-hydroxy-3-meth 33.7 58 0.0013 32.7 4.3 44 246-296 269-312 (360)
196 PF06827 zf-FPG_IleRS: Zinc fi 32.9 30 0.00066 21.8 1.5 18 135-152 2-27 (30)
197 KOG4185 Predicted E3 ubiquitin 32.6 7.9 0.00017 36.5 -1.8 49 206-254 207-265 (296)
198 PF00643 zf-B_box: B-box zinc 32.6 35 0.00075 22.7 1.8 21 135-155 4-24 (42)
199 TIGR00595 priA primosomal prot 32.1 47 0.001 34.3 3.5 46 119-172 211-262 (505)
200 PF15353 HECA: Headcase protei 32.0 27 0.00058 29.4 1.4 16 227-242 39-54 (107)
201 cd02249 ZZ Zinc finger, ZZ typ 31.9 31 0.00068 23.9 1.6 21 164-187 1-21 (46)
202 PF13719 zinc_ribbon_5: zinc-r 31.4 29 0.00063 23.2 1.3 9 121-129 25-33 (37)
203 PRK00464 nrdR transcriptional 31.1 29 0.00062 30.7 1.6 11 137-147 31-41 (154)
204 KOG4317 Predicted Zn-finger pr 30.7 22 0.00049 35.3 0.9 21 135-155 8-28 (383)
205 PF01529 zf-DHHC: DHHC palmito 30.5 30 0.00064 29.5 1.5 38 158-201 43-80 (174)
206 KOG3362 Predicted BBOX Zn-fing 30.0 17 0.00037 32.2 -0.0 25 145-175 117-143 (156)
207 PLN02638 cellulose synthase A 29.6 44 0.00096 38.0 3.0 56 201-256 12-70 (1079)
208 PF06906 DUF1272: Protein of u 29.3 87 0.0019 23.6 3.6 48 205-257 4-53 (57)
209 KOG3113 Uncharacterized conser 29.1 50 0.0011 31.9 2.9 49 204-256 109-158 (293)
210 PF06220 zf-U1: U1 zinc finger 28.7 23 0.00049 24.1 0.4 13 144-156 1-13 (38)
211 TIGR00373 conserved hypothetic 28.6 26 0.00057 30.7 0.9 7 181-187 129-135 (158)
212 KOG1815 Predicted E3 ubiquitin 28.6 37 0.0008 34.4 2.1 37 204-243 68-104 (444)
213 PRK14810 formamidopyrimidine-D 28.4 32 0.0007 32.7 1.5 20 134-153 244-271 (272)
214 PRK06266 transcription initiat 28.4 30 0.00065 31.1 1.2 11 206-216 136-146 (178)
215 PF14803 Nudix_N_2: Nudix N-te 28.1 37 0.00081 22.7 1.3 28 136-170 2-29 (34)
216 smart00451 ZnF_U1 U1-like zinc 28.0 28 0.00061 22.0 0.7 11 145-155 2-12 (35)
217 PRK10445 endonuclease VIII; Pr 27.4 35 0.00076 32.2 1.6 20 134-153 235-262 (263)
218 PF06937 EURL: EURL protein; 27.2 50 0.0011 32.1 2.5 43 204-249 28-74 (285)
219 TIGR02098 MJ0042_CXXC MJ0042 f 27.2 43 0.00094 22.0 1.6 9 121-129 25-33 (38)
220 KOG0801 Predicted E3 ubiquitin 27.1 23 0.00049 32.2 0.2 29 205-234 176-204 (205)
221 PRK14811 formamidopyrimidine-D 27.1 36 0.00077 32.3 1.6 20 134-153 235-262 (269)
222 KOG3842 Adaptor protein Pellin 27.1 31 0.00067 34.4 1.2 47 203-254 287-350 (429)
223 PF12760 Zn_Tnp_IS1595: Transp 27.0 70 0.0015 22.2 2.7 9 135-143 19-27 (46)
224 PF08274 PhnA_Zn_Ribbon: PhnA 26.8 32 0.0007 22.5 0.8 23 136-170 4-26 (30)
225 KOG3507 DNA-directed RNA polym 26.6 72 0.0016 24.3 2.8 18 116-133 15-32 (62)
226 PF09723 Zn-ribbon_8: Zinc rib 26.3 43 0.00093 23.0 1.4 9 206-214 26-34 (42)
227 KOG4362 Transcriptional regula 26.2 32 0.00069 37.3 1.2 48 205-256 20-69 (684)
228 KOG1312 DHHC-type Zn-finger pr 26.2 19 0.00041 35.4 -0.4 32 167-201 149-180 (341)
229 PRK04136 rpl40e 50S ribosomal 26.0 37 0.00081 24.7 1.1 24 119-142 12-36 (48)
230 TIGR01562 FdhE formate dehydro 25.8 66 0.0014 31.5 3.2 25 119-143 208-233 (305)
231 COG2051 RPS27A Ribosomal prote 25.8 38 0.00082 26.3 1.2 29 119-147 17-51 (67)
232 PF01667 Ribosomal_S27e: Ribos 25.7 42 0.00092 24.9 1.4 35 120-154 6-46 (55)
233 KOG3842 Adaptor protein Pellin 25.7 67 0.0015 32.1 3.2 51 206-256 341-414 (429)
234 PRK14892 putative transcriptio 25.5 55 0.0012 27.0 2.2 32 178-215 19-51 (99)
235 KOG1311 DHHC-type Zn-finger pr 25.5 59 0.0013 30.8 2.7 46 141-192 108-153 (299)
236 KOG4399 C2HC-type Zn-finger pr 25.5 18 0.00038 35.1 -0.8 53 135-191 250-302 (325)
237 KOG0826 Predicted E3 ubiquitin 25.3 55 0.0012 32.7 2.5 49 204-256 298-346 (357)
238 PF12172 DUF35_N: Rubredoxin-l 25.3 34 0.00074 22.6 0.8 23 120-142 10-33 (37)
239 PF00412 LIM: LIM domain; Int 24.8 33 0.00071 23.9 0.7 38 209-257 1-38 (58)
240 PRK01103 formamidopyrimidine/5 24.7 42 0.00092 31.8 1.6 20 134-153 245-272 (274)
241 smart00778 Prim_Zn_Ribbon Zinc 24.5 67 0.0015 22.0 2.1 30 135-171 4-33 (37)
242 smart00647 IBR In Between Ring 23.8 33 0.00071 24.3 0.5 18 223-240 40-58 (64)
243 cd02341 ZZ_ZZZ3 Zinc finger, Z 23.8 53 0.0011 23.5 1.6 22 164-187 1-22 (48)
244 PRK00564 hypA hydrogenase nick 23.8 51 0.0011 27.6 1.7 13 132-144 69-81 (117)
245 COG5273 Uncharacterized protei 23.6 47 0.001 32.4 1.7 37 135-174 98-134 (309)
246 PF05458 Siva: Cd27 binding pr 23.5 58 0.0013 29.3 2.1 32 122-157 125-158 (175)
247 PF00130 C1_1: Phorbol esters/ 23.2 60 0.0013 22.5 1.8 11 160-170 25-35 (53)
248 cd07973 Spt4 Transcription elo 23.2 42 0.00091 27.6 1.1 20 123-142 5-28 (98)
249 TIGR00577 fpg formamidopyrimid 23.0 48 0.001 31.5 1.6 20 134-153 245-272 (272)
250 TIGR01384 TFS_arch transcripti 22.6 67 0.0014 25.7 2.2 9 136-144 2-10 (104)
251 PRK08351 DNA-directed RNA poly 22.5 47 0.001 25.2 1.2 20 123-143 5-24 (61)
252 PF13824 zf-Mss51: Zinc-finger 22.2 65 0.0014 24.0 1.8 12 160-171 11-22 (55)
253 PRK13945 formamidopyrimidine-D 22.1 52 0.0011 31.4 1.6 20 134-153 254-281 (282)
254 PLN02400 cellulose synthase 22.0 53 0.0012 37.4 1.9 56 201-256 31-89 (1085)
255 PF10058 DUF2296: Predicted in 21.6 66 0.0014 23.6 1.7 9 121-129 22-30 (54)
256 KOG0269 WD40 repeat-containing 21.1 46 0.00099 36.6 1.1 49 136-193 755-806 (839)
257 TIGR00244 transcriptional regu 20.9 62 0.0013 28.7 1.7 13 136-148 30-42 (147)
258 PF11023 DUF2614: Protein of u 20.9 61 0.0013 27.6 1.6 27 118-144 66-95 (114)
259 PF09889 DUF2116: Uncharacteri 20.7 36 0.00079 25.6 0.2 19 135-153 4-25 (59)
260 PRK03681 hypA hydrogenase nick 20.6 64 0.0014 26.8 1.7 14 131-144 67-80 (114)
261 smart00531 TFIIE Transcription 20.5 36 0.00077 29.3 0.2 10 136-145 101-110 (147)
262 PRK14873 primosome assembly pr 20.3 92 0.002 33.6 3.2 44 120-172 382-431 (665)
263 COG5273 Uncharacterized protei 20.3 49 0.0011 32.2 1.1 31 168-201 111-141 (309)
264 PLN02915 cellulose synthase A 20.2 83 0.0018 35.8 2.9 52 205-256 14-68 (1044)
265 PRK12496 hypothetical protein; 20.1 48 0.001 29.3 0.9 24 122-145 128-154 (164)
No 1
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=100.00 E-value=2.7e-56 Score=417.82 Aligned_cols=235 Identities=47% Similarity=0.955 Sum_probs=219.0
Q ss_pred cCCCchhcccCCCccCcccccccceeEcCCCCCeecCchhHhhhhcCCCccccCCCCCCcccCceeeeCCCCcccccccc
Q 021781 57 HNGSTELLRKGFMEYGCQHYRRRCRIRAPCCNEIFDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKVQQV 136 (307)
Q Consensus 57 ~~~~~~~~~~~~~~~GC~HY~R~c~i~~pCC~k~y~Cr~CHde~~~~~~~~~~~~H~ldR~~v~~v~C~~C~~eQ~v~~~ 136 (307)
+.-+.++.|++.+++||+||+|+|++++|||++||+||+||+++. +|.++|+.|.+++|+.|+++|++++.
T Consensus 19 ~~~~~~~~d~~~~~~~c~hy~r~~~~~a~ccd~~~~C~hCH~~s~---------~h~~~r~~v~~~~C~~C~~~q~~~~~ 89 (276)
T KOG1940|consen 19 SSIHSDAEDEIAFPYGCPHYRRNCKSRAPCCDREITCRHCHNESE---------DHDLDRKTVYELLCMKCRKIQPVGQI 89 (276)
T ss_pred hhcccccccccccccCCchhhhccccccccccceeeeEEecChhh---------hcccchhhhhhhhhhhHHhhhhhhhc
Confidence 333457889999999999999999999999999999999999864 89999999999999999999999999
Q ss_pred CcCCCCccceEecCccccccCCCCCCeecCCCCCcccccCCccceecCCccceeeccccccccccCCCCCCCCccccccc
Q 021781 137 CVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGICRIGGCDNFFHCNKCRCCYSMLLKNSHPCVEGAMHHDCPVCCEYL 216 (307)
Q Consensus 137 C~~Cg~~fa~YfC~~Ckl~ddd~~k~~yHC~~CgiCR~G~~e~ffHC~~C~~C~s~~l~~~H~CiE~~~~~~CPIClE~l 216 (307)
|.+|+..+|+|||.+|+||||+++ +||||+.|||||+|++++||||++|+.|++..+.+.|+|+|++++.+||||.|++
T Consensus 90 c~~c~~~~g~~~c~~C~l~dd~~~-~~~hC~~C~icr~g~~~~~fhc~~c~~c~~~~~~~~H~c~e~~~~~ncPic~e~l 168 (276)
T KOG1940|consen 90 CSNCHVELGEYYCLICKLFDDDPS-KQYHCDLCGICREGLGLDFFHCKKCKACLSAYLSNWHKCVERSSEFNCPICKEYL 168 (276)
T ss_pred cccchhhhhhhcCccccccccccc-ceeccccccccccccccchhHHhhhHhHHhhhcccccchhhhcccCCCchhHHHh
Confidence 999999999999999999999998 9999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCceeEEcCCCCccchHHHHHHhhcCCCCCCCCCcCccchhHHHHhhHHHHHcCCCChhhcCceEEEEEe--------
Q 021781 217 FETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCDMSKVWEKYDREIAATPMPEAYLNKKVSFSYV-------- 288 (307)
Q Consensus 217 f~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlCrks~~dm~~~~~~lD~eia~~pmP~ey~n~~v~Is~~-------- 288 (307)
|++...+..|+|||.+|..|++++.... |+||+|.+ +.||+.+|+.+|.+|+.+|||.+|++++++|++=
T Consensus 169 ~~s~~~~~~~~CgH~~h~~cf~e~~~~~-y~CP~C~~-~~d~~~~~~~~d~~l~~~~~p~~y~~~~~~i~cndC~~~~~~ 246 (276)
T KOG1940|consen 169 FLSFEDAGVLKCGHYMHSRCFEEMICEG-YTCPICSK-PGDMSHYFRKLDKELAGSPMPEEYKNKTQDILCNDCGSGTNV 246 (276)
T ss_pred ccccccCCccCcccchHHHHHHHHhccC-CCCCcccc-hHHHHHHHHHHHHHHhcCCCCchhhchhheeeccCCCCCCcc
Confidence 9999999999999999999999999876 99999999 9999999999999999999999999999999982
Q ss_pred eec-----CCcccccccccc
Q 021781 289 SLW-----SDGCLSVDKILT 303 (307)
Q Consensus 289 r~~-----~~~C~s~~~~~~ 303 (307)
+.| ...|.+|-+-+.
T Consensus 247 k~~~l~~kc~~c~~~~~r~~ 266 (276)
T KOG1940|consen 247 KYHILYHKCGKCGSYNTRMI 266 (276)
T ss_pred ceehhhhhCCCcccceeeec
Confidence 333 445777665443
No 2
>PF05495 zf-CHY: CHY zinc finger; InterPro: IPR008913 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Pirh2 is an eukaryotic ubiquitin protein ligase, which has been shown to promote p53 degradation in mammals. Pirh2 physically interacts with p53 and promotes ubiquitination of p53 independently of MDM2. Like MDM2, Pirh2 is thought to participate in an autoregulatory feedback loop that controls p53 function. Pirh2 proteins contain three distinct zinc fingers, the CHY-type, the CTCHY-type which is C-terminal to the CHY-type zinc finger and a RING finger. The CHY-type zinc finger has no currently known function []. As well as Pirh2, the CHY-type zinc finger is also found in the following proteins: Yeast helper of Tim protein 13. Hot13 may have a role in the assembly and recycling of the small Tims, a complex of the mitochondrial intermembrane space that participates in the TIM22 import pathway for assembly of the inner membrane [] Several plant hypothetical proteins that also contain haemerythrin cation binding domains Several protozoan hypothetical proteins that also contain a Myb domain The solution structure of this zinc finger has been solved and binds 3 zinc atoms as shown in the following schematic representation: ++---------+-----+ || | | CXHYxxxxxxxxxCCxxxxxCxxCHxxxxxHxxxxxxxxxxxCxxCxxxxxxxxxCxxC | | | | | | | | +-+-----------------+--+ +--+---------+--+ 'C': conserved cysteine involved in the binding of one zinc atom. 'H': conserved histidine involved in the binding of one zinc atom. More information about these proteins can be found at Protein of the Month: Zinc Fingers []; GO: 0008270 zinc ion binding; PDB: 2DKT_A 2K2C_A.
Probab=99.88 E-value=1.1e-23 Score=161.88 Aligned_cols=70 Identities=46% Similarity=1.129 Sum_probs=53.5
Q ss_pred ccccccc-ceeEcCCCCCeecCchhHhhhhcCCCccccCCCCCCcccCceeeeCCCCccccccccCcCCCCccceEecCc
Q 021781 73 CQHYRRR-CRIRAPCCNEIFDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKVQQVCVNCGVCMGEYFCES 151 (307)
Q Consensus 73 C~HY~R~-c~i~~pCC~k~y~Cr~CHde~~~~~~~~~~~~H~ldR~~v~~v~C~~C~~eQ~v~~~C~~Cg~~fa~YfC~~ 151 (307)
|+||+|+ |+|+||||++|||||+||||+. +|+++|+.+++|+||.|+++|+++++ +|| |+|+|++
T Consensus 1 C~HY~~~~~~~~~~cC~~~y~C~~CHde~~---------~H~~~~~~~~~v~Cg~C~~~~~~~~~--~c~---~~~~C~~ 66 (71)
T PF05495_consen 1 CKHYHRSLCAIRFPCCGKYYPCRFCHDELE---------DHPFDRWPVKRVICGKCRTEQPIDEY--SCG---ADYFCPI 66 (71)
T ss_dssp -SS---S-EEEEETTTTEEESSHHHHHHCS---------SS---TTT--EEEETTT--EEES-SB--TT-----SEEETT
T ss_pred CCCCCCCcEEEECCcccCeecHHHHHHHhc---------cCccccccccCeECCCCCCccChhhh--hcC---CCccCcC
Confidence 8999999 9999999999999999999975 79999999999999999999999998 888 9999999
Q ss_pred ccccc
Q 021781 152 CKLFD 156 (307)
Q Consensus 152 Ckl~d 156 (307)
|++||
T Consensus 67 C~~~~ 71 (71)
T PF05495_consen 67 CGLYF 71 (71)
T ss_dssp TTEEE
T ss_pred cCCCC
Confidence 99986
No 3
>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=99.30 E-value=7.9e-13 Score=91.70 Aligned_cols=44 Identities=39% Similarity=1.081 Sum_probs=37.0
Q ss_pred CCCcccccccccCCceeEEcCCCCccchHHHHHHhhcCCCCCCCCC
Q 021781 207 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICS 252 (307)
Q Consensus 207 ~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlCr 252 (307)
++||||++.+.. .+.++.|+|||.||.+|+.+|++. +.+||+||
T Consensus 1 d~C~IC~~~~~~-~~~~~~l~C~H~fh~~Ci~~~~~~-~~~CP~CR 44 (44)
T PF13639_consen 1 DECPICLEEFED-GEKVVKLPCGHVFHRSCIKEWLKR-NNSCPVCR 44 (44)
T ss_dssp -CETTTTCBHHT-TSCEEEETTSEEEEHHHHHHHHHH-SSB-TTTH
T ss_pred CCCcCCChhhcC-CCeEEEccCCCeeCHHHHHHHHHh-CCcCCccC
Confidence 379999997544 667889999999999999999986 68999997
No 4
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=99.29 E-value=7.2e-13 Score=107.26 Aligned_cols=68 Identities=25% Similarity=0.655 Sum_probs=57.0
Q ss_pred ccCcccccc---cceeEcCCCCCeecCchhHhhhhcCCCccccCCCCCCcc-----cCceeeeCCCCcccccc-----cc
Q 021781 70 EYGCQHYRR---RCRIRAPCCNEIFDCRHCHNEAMNNINVDQKLRHDIPRH-----EVNQVICSLCGTEQKVQ-----QV 136 (307)
Q Consensus 70 ~~GC~HY~R---~c~i~~pCC~k~y~Cr~CHde~~~~~~~~~~~~H~ldR~-----~v~~v~C~~C~~eQ~v~-----~~ 136 (307)
+.+|.||+. .++|||.+|+|+|+|.+||||++ +||+.++ ..+.|+||.|..+..++ ..
T Consensus 12 etRC~Hyht~~Diialkc~~C~kyYaCy~CHdel~---------~Hpf~p~~~~~~~~~~iiCGvC~~~LT~~EY~~~~~ 82 (105)
T COG4357 12 ETRCLHYHTPLDIIALKCKCCQKYYACYHCHDELE---------DHPFEPWGLQEFNPKAIICGVCRKLLTRAEYGMCGS 82 (105)
T ss_pred cceeeEecCccceEeeeechhhhhhhHHHHHhHHh---------cCCCccCChhhcCCccEEhhhhhhhhhHHHHhhcCC
Confidence 348999999 58899999999999999999986 5776554 45569999999887764 45
Q ss_pred CcCCCCccce
Q 021781 137 CVNCGVCMGE 146 (307)
Q Consensus 137 C~~Cg~~fa~ 146 (307)
||+|..+||.
T Consensus 83 Cp~C~spFNp 92 (105)
T COG4357 83 CPYCQSPFNP 92 (105)
T ss_pred CCCcCCCCCc
Confidence 9999999974
No 5
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=99.14 E-value=3.2e-11 Score=96.05 Aligned_cols=51 Identities=20% Similarity=0.471 Sum_probs=41.0
Q ss_pred CCCCCCcccccccccCCceeEEcCCCCccchHHHHHHhhcC--CCCCCCCCcCcc
Q 021781 204 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHH--QYACPICSKSVC 256 (307)
Q Consensus 204 ~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~--~~~CPlCrks~~ 256 (307)
++++.||.|..+ ...-+++...|+|.||..||.+||+.. +.+||+||+++.
T Consensus 30 ~fdg~Cp~Ck~P--gd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~ 82 (85)
T PF12861_consen 30 PFDGCCPDCKFP--GDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWK 82 (85)
T ss_pred ccccCCCCccCC--CCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeee
Confidence 456789999854 334567888999999999999999853 578999998875
No 6
>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=98.99 E-value=3.4e-10 Score=87.26 Aligned_cols=47 Identities=28% Similarity=0.786 Sum_probs=36.3
Q ss_pred CCCCCcccccccccC---------CceeEEcCCCCccchHHHHHHhhcCCCCCCCCC
Q 021781 205 MHHDCPVCCEYLFET---------RQDVIVLPCGHTIHKNCLKEMREHHQYACPICS 252 (307)
Q Consensus 205 ~~~~CPIClE~lf~s---------~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlCr 252 (307)
.+++|+||++.|.+. ..+++.++|||.||..||.+||+. +.+||+||
T Consensus 18 ~~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~-~~~CP~CR 73 (73)
T PF12678_consen 18 ADDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQ-NNTCPLCR 73 (73)
T ss_dssp CCSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTT-SSB-TTSS
T ss_pred cCCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhc-CCcCCCCC
Confidence 356799999987332 245567799999999999999985 56999998
No 7
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.93 E-value=4.6e-10 Score=109.32 Aligned_cols=50 Identities=28% Similarity=0.824 Sum_probs=45.2
Q ss_pred CCCcccccccccCCceeEEcCCCCccchHHHHHHhhcCCCCCCCCCcCccc
Q 021781 207 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 257 (307)
Q Consensus 207 ~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlCrks~~d 257 (307)
..|+||||+ |..++.++.|||+|.||..|++.||...+..||+|+.++..
T Consensus 230 ~~CaIClEd-Y~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~di~~ 279 (348)
T KOG4628|consen 230 DTCAICLED-YEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRDIRT 279 (348)
T ss_pred ceEEEeecc-cccCCeeeEecCCCchhhccchhhHhhcCccCCCCCCcCCC
Confidence 699999997 77889999999999999999999998765669999998874
No 8
>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=98.91 E-value=1.2e-09 Score=72.98 Aligned_cols=45 Identities=33% Similarity=1.041 Sum_probs=37.1
Q ss_pred CCcccccccccCCceeEEcCCCCccchHHHHHHhhcCCCCCCCCCcCc
Q 021781 208 DCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSV 255 (307)
Q Consensus 208 ~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlCrks~ 255 (307)
.|+||++.+ ..++.+++|||.||..|+..|++..+.+||+|++.+
T Consensus 1 ~C~iC~~~~---~~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~~ 45 (45)
T cd00162 1 ECPICLEEF---REPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45 (45)
T ss_pred CCCcCchhh---hCceEecCCCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence 499999975 335666779999999999999986568899999764
No 9
>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=98.84 E-value=2.2e-09 Score=72.86 Aligned_cols=39 Identities=41% Similarity=1.110 Sum_probs=32.8
Q ss_pred CcccccccccCCceeEEcCCCCccchHHHHHHhhcCCCCCCCC
Q 021781 209 CPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPIC 251 (307)
Q Consensus 209 CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlC 251 (307)
||||++.+.+ ++++++|||+|+.+|+.+|++. +.+||+|
T Consensus 1 C~iC~~~~~~---~~~~~~CGH~fC~~C~~~~~~~-~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDELRD---PVVVTPCGHSFCKECIEKYLEK-NPKCPVC 39 (39)
T ss_dssp ETTTTSB-SS---EEEECTTSEEEEHHHHHHHHHC-TSB-TTT
T ss_pred CCCCCCcccC---cCEECCCCCchhHHHHHHHHHC-cCCCcCC
Confidence 7999996443 5688999999999999999997 7899998
No 10
>PHA02929 N1R/p28-like protein; Provisional
Probab=98.76 E-value=6.3e-09 Score=96.97 Aligned_cols=54 Identities=19% Similarity=0.609 Sum_probs=42.1
Q ss_pred CCCCCCCcccccccccCCc----eeEEcCCCCccchHHHHHHhhcCCCCCCCCCcCccc
Q 021781 203 GAMHHDCPVCCEYLFETRQ----DVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 257 (307)
Q Consensus 203 ~~~~~~CPIClE~lf~s~~----~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlCrks~~d 257 (307)
.+.+..||||+|.+.+... -.++++|||.||.+||.+|++. +.+||+||..+..
T Consensus 171 ~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~-~~tCPlCR~~~~~ 228 (238)
T PHA02929 171 RSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKE-KNTCPVCRTPFIS 228 (238)
T ss_pred CCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhc-CCCCCCCCCEeeE
Confidence 3456899999998654321 1245689999999999999985 6899999998763
No 11
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=98.74 E-value=3e-09 Score=80.02 Aligned_cols=46 Identities=48% Similarity=0.647 Sum_probs=10.1
Q ss_pred ccchhHHHHhhHHHHHcCCCChhhcCceEEEEE-------------eeecCCccccccc
Q 021781 255 VCDMSKVWEKYDREIAATPMPEAYLNKKVSFSY-------------VSLWSDGCLSVDK 300 (307)
Q Consensus 255 ~~dm~~~~~~lD~eia~~pmP~ey~n~~v~Is~-------------~r~~~~~C~s~~~ 300 (307)
+.||+++|+.||++|+++|||++|++++|+|.| +.+.+..|.||-|
T Consensus 1 v~dM~~~w~~LD~~i~~~pmP~~Y~~~~v~IlCNDC~~~s~v~fH~lg~KC~~C~SYNT 59 (61)
T PF14599_consen 1 VVDMSAYWRMLDAEIAATPMPEEYRNKKVWILCNDCNAKSEVPFHFLGHKCSHCGSYNT 59 (61)
T ss_dssp ---------------------------EEEEEESSS--EEEEE--TT----TTTS---E
T ss_pred CCCHHHHHHHHHHHHHhCCCCHHHhCCEEEEECCCCCCccceeeeHhhhcCCCCCCccc
Confidence 468999999999999999999999999999988 4555777999976
No 12
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.73 E-value=9.4e-09 Score=71.50 Aligned_cols=39 Identities=33% Similarity=1.101 Sum_probs=28.4
Q ss_pred CcccccccccCCceeEEcCCCCccchHHHHHHhhcC---CCCCCCC
Q 021781 209 CPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHH---QYACPIC 251 (307)
Q Consensus 209 CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~---~~~CPlC 251 (307)
||||+++|.+ .+.|+|||+|++.||..|.+.. .+.||+|
T Consensus 1 CpiC~~~~~~----Pv~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDLFKD----PVSLPCGHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB-SS----EEE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCccchhhCC----ccccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 8999996433 6889999999999999988653 2579987
No 13
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=98.70 E-value=5.5e-09 Score=102.25 Aligned_cols=56 Identities=38% Similarity=0.818 Sum_probs=47.0
Q ss_pred CCCCCCCcccccccccCC---------ceeEEcCCCCccchHHHHHHhhcCCCCCCCCCcCcc-chh
Q 021781 203 GAMHHDCPVCCEYLFETR---------QDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC-DMS 259 (307)
Q Consensus 203 ~~~~~~CPIClE~lf~s~---------~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlCrks~~-dm~ 259 (307)
...+..|.||+|.|+.++ ..+..|||||.+|.+|++.|+.+ +.+||+||.++. |++
T Consensus 284 ~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ER-qQTCPICr~p~ifd~~ 349 (491)
T COG5243 284 TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLER-QQTCPICRRPVIFDQS 349 (491)
T ss_pred cCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHh-ccCCCcccCccccccC
Confidence 456889999999988765 33477999999999999999986 689999999954 553
No 14
>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=98.70 E-value=1.2e-08 Score=72.67 Aligned_cols=47 Identities=34% Similarity=0.982 Sum_probs=38.0
Q ss_pred CCCCcccccccccCCceeEEcCCCCc-cchHHHHHHhhcCCCCCCCCCcCccc
Q 021781 206 HHDCPVCCEYLFETRQDVIVLPCGHT-IHKNCLKEMREHHQYACPICSKSVCD 257 (307)
Q Consensus 206 ~~~CPIClE~lf~s~~~v~~LpCGH~-fH~~Ci~~wl~~~~~~CPlCrks~~d 257 (307)
+..|+||++. ...++++||||. |+..|+.+|++ ...+||+||+++..
T Consensus 2 ~~~C~iC~~~----~~~~~~~pCgH~~~C~~C~~~~~~-~~~~CP~Cr~~i~~ 49 (50)
T PF13920_consen 2 DEECPICFEN----PRDVVLLPCGHLCFCEECAERLLK-RKKKCPICRQPIES 49 (50)
T ss_dssp HSB-TTTSSS----BSSEEEETTCEEEEEHHHHHHHHH-TTSBBTTTTBB-SE
T ss_pred cCCCccCCcc----CCceEEeCCCChHHHHHHhHHhcc-cCCCCCcCChhhcC
Confidence 3579999985 234788999999 99999999998 47899999998753
No 15
>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=98.66 E-value=1.8e-08 Score=68.32 Aligned_cols=40 Identities=43% Similarity=1.116 Sum_probs=33.5
Q ss_pred CcccccccccCCceeEEcCCCCccchHHHHHHhh-cCCCCCCCC
Q 021781 209 CPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMRE-HHQYACPIC 251 (307)
Q Consensus 209 CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~-~~~~~CPlC 251 (307)
||||++.+.. ++.+++|||.|+..|+.+|++ .....||+|
T Consensus 1 C~iC~~~~~~---~~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEPFED---PVILLPCGHSFCRDCLRKWLENSGSVKCPLC 41 (41)
T ss_dssp ETTTSSBCSS---EEEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred CCcCCccccC---CCEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence 7999996433 346899999999999999998 567889998
No 16
>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=98.63 E-value=2.8e-08 Score=64.08 Aligned_cols=39 Identities=44% Similarity=1.130 Sum_probs=33.0
Q ss_pred CcccccccccCCceeEEcCCCCccchHHHHHHhhcCCCCCCCC
Q 021781 209 CPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPIC 251 (307)
Q Consensus 209 CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlC 251 (307)
|+||++. ....+.++|||.||..|++.|++....+||+|
T Consensus 1 C~iC~~~----~~~~~~~~C~H~~c~~C~~~~~~~~~~~CP~C 39 (39)
T smart00184 1 CPICLEE----LKDPVVLPCGHTFCRSCIRKWLKSGNNTCPIC 39 (39)
T ss_pred CCcCccC----CCCcEEecCCChHHHHHHHHHHHhCcCCCCCC
Confidence 7999985 34578889999999999999998556789987
No 17
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.62 E-value=2.1e-08 Score=96.03 Aligned_cols=56 Identities=25% Similarity=0.625 Sum_probs=46.8
Q ss_pred cCCCCCCCCcccccccccCCceeEEcCCCCccchHHHHHHhhcCCCCCCCCCcCccc
Q 021781 201 VEGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 257 (307)
Q Consensus 201 iE~~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlCrks~~d 257 (307)
+|....-+|+|||+++ ...+.+++|||.|.||..|+++|+...+..||+||..+.+
T Consensus 318 ~ea~~GveCaICms~f-iK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iPP 373 (374)
T COG5540 318 VEADKGVECAICMSNF-IKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIPP 373 (374)
T ss_pred HhcCCCceEEEEhhhh-cccceEEEeccCceechhHHHHHHhhhcccCCccCCCCCC
Confidence 3444567899999985 5567799999999999999999998667889999987653
No 18
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=98.61 E-value=7.7e-09 Score=80.98 Aligned_cols=51 Identities=22% Similarity=0.440 Sum_probs=39.5
Q ss_pred CCCCCCcccccccccCCceeEEcCCCCccchHHHHHHhhcC--CCCCCCCCcCcc
Q 021781 204 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHH--QYACPICSKSVC 256 (307)
Q Consensus 204 ~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~--~~~CPlCrks~~ 256 (307)
++++.||-|.- ....-+.++..|.|.||..||.+|+... +-.||+||+++.
T Consensus 29 ~Fdg~Cp~Ck~--PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~ 81 (84)
T KOG1493|consen 29 PFDGCCPDCKL--PGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQ 81 (84)
T ss_pred ccCCcCCCCcC--CCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeE
Confidence 56778999984 4444566666899999999999999653 355999998764
No 19
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.56 E-value=3.9e-08 Score=69.08 Aligned_cols=40 Identities=38% Similarity=1.053 Sum_probs=24.2
Q ss_pred CcccccccccCCceeEEcCCCCccchHHHHHHhhcC---CCCCC
Q 021781 209 CPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHH---QYACP 249 (307)
Q Consensus 209 CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~---~~~CP 249 (307)
||||.| +.+...+.++|+|||+|.++|+++|++.+ .++||
T Consensus 1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~~~~~~kCP 43 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKSDRNRFKCP 43 (43)
T ss_dssp -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcCCCCeeeCc
Confidence 899999 55555677889999999999999998843 46687
No 20
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.55 E-value=6.8e-08 Score=67.27 Aligned_cols=44 Identities=32% Similarity=0.839 Sum_probs=36.8
Q ss_pred CCcccccccccCCceeEEcCCCCccchHHHHHHhhcCCCCCCCCCc
Q 021781 208 DCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSK 253 (307)
Q Consensus 208 ~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlCrk 253 (307)
.|+||.+.+ +......+++|||+|+..|+..+. .....||+||+
T Consensus 1 ~C~~C~~~~-~~~~~~~l~~CgH~~C~~C~~~~~-~~~~~CP~C~k 44 (44)
T PF14634_consen 1 HCNICFEKY-SEERRPRLTSCGHIFCEKCLKKLK-GKSVKCPICRK 44 (44)
T ss_pred CCcCcCccc-cCCCCeEEcccCCHHHHHHHHhhc-CCCCCCcCCCC
Confidence 489999964 555678889999999999999998 34678999986
No 21
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=98.54 E-value=5.8e-08 Score=76.70 Aligned_cols=50 Identities=20% Similarity=0.436 Sum_probs=38.3
Q ss_pred CCCCcccccccccC-CceeEEcCCCCccchHHHHHHhhcCCCCCCCCCcCcc
Q 021781 206 HHDCPVCCEYLFET-RQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 256 (307)
Q Consensus 206 ~~~CPIClE~lf~s-~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlCrks~~ 256 (307)
.+.||-|.-.+... .-+++...|.|.||..||.+||.. +..||++|+++.
T Consensus 31 m~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~T-k~~CPld~q~w~ 81 (88)
T COG5194 31 MGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDT-KGVCPLDRQTWV 81 (88)
T ss_pred cCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhh-CCCCCCCCceeE
Confidence 35677777544222 235667799999999999999985 689999999875
No 22
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.49 E-value=1.3e-07 Score=85.74 Aligned_cols=56 Identities=25% Similarity=0.633 Sum_probs=42.3
Q ss_pred ccccCCCCCCCCcccccccccCCceeEEcCCCCccchHHHHHHhhc---------------CCCCCCCCCcCccc
Q 021781 198 HPCVEGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH---------------HQYACPICSKSVCD 257 (307)
Q Consensus 198 H~CiE~~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~---------------~~~~CPlCrks~~d 257 (307)
.+-++...+..||||++.+ . +.++++|||.||..||.+|+.. ...+||+||..+..
T Consensus 10 ~~~~~~~~~~~CpICld~~-~---dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~ 80 (193)
T PLN03208 10 TTLVDSGGDFDCNICLDQV-R---DPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE 80 (193)
T ss_pred ceeccCCCccCCccCCCcC-C---CcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence 3344445578999999963 2 3466799999999999999852 23579999999864
No 23
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=98.38 E-value=1.7e-07 Score=93.54 Aligned_cols=82 Identities=22% Similarity=0.429 Sum_probs=60.3
Q ss_pred CCCCcccccccccCCceeEEcCCCCccchHHHHHHhhcCCCCCCCCCcCccchhHHHHhhHHHHHcCCCChhh-cCceEE
Q 021781 206 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCDMSKVWEKYDREIAATPMPEAY-LNKKVS 284 (307)
Q Consensus 206 ~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlCrks~~dm~~~~~~lD~eia~~pmP~ey-~n~~v~ 284 (307)
-..||||||.|..+...++...|.|+||-.|+..|- ..+||+||....+ +..... .--.. .....|
T Consensus 175 LPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~---~~scpvcR~~q~p-~~ve~~---------~c~~c~~~~~Lw 241 (493)
T KOG0804|consen 175 LPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWW---DSSCPVCRYCQSP-SVVESS---------LCLACGCTEDLW 241 (493)
T ss_pred CCCcchhHhhcCccccceeeeecccccchHHHhhcc---cCcChhhhhhcCc-chhhhh---------hhhhhcccccEE
Confidence 357999999999998888999999999999999994 5789999976542 111111 00111 123456
Q ss_pred EEEeeecCCcccccccc
Q 021781 285 FSYVSLWSDGCLSVDKI 301 (307)
Q Consensus 285 Is~~r~~~~~C~s~~~~ 301 (307)
|. +.+++.||..|.+-
T Consensus 242 ic-liCg~vgcgrY~eg 257 (493)
T KOG0804|consen 242 IC-LICGNVGCGRYKEG 257 (493)
T ss_pred EE-EEccceecccccch
Confidence 65 99999999999763
No 24
>PHA02926 zinc finger-like protein; Provisional
Probab=98.29 E-value=4.7e-07 Score=83.73 Aligned_cols=56 Identities=20% Similarity=0.536 Sum_probs=42.4
Q ss_pred CCCCCCCCcccccccccCC-----ceeEEcCCCCccchHHHHHHhhcC-----CCCCCCCCcCccc
Q 021781 202 EGAMHHDCPVCCEYLFETR-----QDVIVLPCGHTIHKNCLKEMREHH-----QYACPICSKSVCD 257 (307)
Q Consensus 202 E~~~~~~CPIClE~lf~s~-----~~v~~LpCGH~fH~~Ci~~wl~~~-----~~~CPlCrks~~d 257 (307)
..+.+..|+||||.+++.+ ...++.+|+|.||..|+..|.+.. ..+||+||..+..
T Consensus 166 ~~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~ 231 (242)
T PHA02926 166 RVSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFRN 231 (242)
T ss_pred hccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceeee
Confidence 4566789999999765431 223556999999999999999742 2459999988764
No 25
>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=98.26 E-value=1e-06 Score=64.30 Aligned_cols=45 Identities=18% Similarity=0.434 Sum_probs=38.1
Q ss_pred CCCcccccccccCCceeEEcCCCCccchHHHHHHhhcCCCCCCCCCcCcc
Q 021781 207 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 256 (307)
Q Consensus 207 ~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlCrks~~ 256 (307)
..||||++.|.+ .++++|||+|.++|+.+|++. +.+||+|++.+.
T Consensus 2 ~~Cpi~~~~~~~----Pv~~~~G~v~~~~~i~~~~~~-~~~cP~~~~~~~ 46 (63)
T smart00504 2 FLCPISLEVMKD----PVILPSGQTYERRAIEKWLLS-HGTDPVTGQPLT 46 (63)
T ss_pred cCCcCCCCcCCC----CEECCCCCEEeHHHHHHHHHH-CCCCCCCcCCCC
Confidence 469999996433 367899999999999999986 688999999884
No 26
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.09 E-value=2.1e-06 Score=76.99 Aligned_cols=48 Identities=25% Similarity=0.754 Sum_probs=38.3
Q ss_pred CCCCcccccccccCCceeEEcCCCCccchHHHHHHhhcCCCCCCCCCcCcc
Q 021781 206 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 256 (307)
Q Consensus 206 ~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlCrks~~ 256 (307)
-..|||||+.+ . .+-.+.-.|||.|+++||+..++. ...||+|+|.+.
T Consensus 131 ~~~CPiCl~~~-s-ek~~vsTkCGHvFC~~Cik~alk~-~~~CP~C~kkIt 178 (187)
T KOG0320|consen 131 TYKCPICLDSV-S-EKVPVSTKCGHVFCSQCIKDALKN-TNKCPTCRKKIT 178 (187)
T ss_pred ccCCCceecch-h-hccccccccchhHHHHHHHHHHHh-CCCCCCcccccc
Confidence 37999999963 2 222355799999999999999985 589999998664
No 27
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.03 E-value=1.8e-06 Score=88.59 Aligned_cols=53 Identities=32% Similarity=0.676 Sum_probs=43.5
Q ss_pred CCCCCCCCcccccccccCCc-eeEEcCCCCccchHHHHHHhhcCCCCCCCCCcCc
Q 021781 202 EGAMHHDCPVCCEYLFETRQ-DVIVLPCGHTIHKNCLKEMREHHQYACPICSKSV 255 (307)
Q Consensus 202 E~~~~~~CPIClE~lf~s~~-~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlCrks~ 255 (307)
.......|+||+|.|..+.. .+..|+|||.||..|+..|++. ..+||+||..+
T Consensus 287 ~~~~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er-~qtCP~CR~~~ 340 (543)
T KOG0802|consen 287 LALSDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFER-QQTCPTCRTVL 340 (543)
T ss_pred hhhcCCeeeeechhhccccccccceeecccchHHHHHHHHHHH-hCcCCcchhhh
Confidence 34557899999998876432 2467899999999999999996 68999999844
No 28
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=97.85 E-value=8e-06 Score=77.89 Aligned_cols=47 Identities=26% Similarity=0.669 Sum_probs=38.9
Q ss_pred CCCCcccccccccCCceeEEcCCCCccchHHHHHHhhcCCCCCCCCCcCccc
Q 021781 206 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 257 (307)
Q Consensus 206 ~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlCrks~~d 257 (307)
...|.+|||.. ......||||.|+-.||.+|... ..-||+||..+.+
T Consensus 239 ~~kC~LCLe~~----~~pSaTpCGHiFCWsCI~~w~~e-k~eCPlCR~~~~p 285 (293)
T KOG0317|consen 239 TRKCSLCLENR----SNPSATPCGHIFCWSCILEWCSE-KAECPLCREKFQP 285 (293)
T ss_pred CCceEEEecCC----CCCCcCcCcchHHHHHHHHHHcc-ccCCCcccccCCC
Confidence 46899999953 34567899999999999999985 5679999987764
No 29
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.85 E-value=7.3e-06 Score=72.27 Aligned_cols=44 Identities=39% Similarity=1.013 Sum_probs=37.3
Q ss_pred CCCCCcccccccccCCceeEEcCCCCccchHHHHHHhhcCCCCCCCCCc
Q 021781 205 MHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSK 253 (307)
Q Consensus 205 ~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlCrk 253 (307)
.+..||||++++.. + ++|||||+|+..|+..+.. ....||.||.
T Consensus 12 ~~~~C~iC~~~~~~-p---~~l~C~H~~c~~C~~~~~~-~~~~Cp~cr~ 55 (386)
T KOG2177|consen 12 EELTCPICLEYFRE-P---VLLPCGHNFCRACLTRSWE-GPLSCPVCRP 55 (386)
T ss_pred ccccChhhHHHhhc-C---ccccccchHhHHHHHHhcC-CCcCCcccCC
Confidence 46789999997443 2 8899999999999999877 5688999994
No 30
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.83 E-value=1.2e-05 Score=80.19 Aligned_cols=47 Identities=21% Similarity=0.665 Sum_probs=38.9
Q ss_pred CCCCCcccccccccCCceeEEcCCCCccchHHHHHHhhcCCCCCCCCCcCcc
Q 021781 205 MHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 256 (307)
Q Consensus 205 ~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlCrks~~ 256 (307)
....|+||++.+ .. .++++|||.||..|+..|+.. ...||+|+..+.
T Consensus 25 ~~l~C~IC~d~~-~~---PvitpCgH~FCs~CI~~~l~~-~~~CP~Cr~~~~ 71 (397)
T TIGR00599 25 TSLRCHICKDFF-DV---PVLTSCSHTFCSLCIRRCLSN-QPKCPLCRAEDQ 71 (397)
T ss_pred cccCCCcCchhh-hC---ccCCCCCCchhHHHHHHHHhC-CCCCCCCCCccc
Confidence 357999999964 32 357899999999999999985 468999999875
No 31
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=97.83 E-value=4.8e-06 Score=68.82 Aligned_cols=34 Identities=24% Similarity=0.494 Sum_probs=29.8
Q ss_pred eeEEcCCCCccchHHHHHHhhcCCCCCCCCCcCcc
Q 021781 222 DVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 256 (307)
Q Consensus 222 ~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlCrks~~ 256 (307)
.+...-|.|+||..||.+||+. +..||++.+.+.
T Consensus 75 ~VaWG~CNHaFH~hCisrWlkt-r~vCPLdn~eW~ 108 (114)
T KOG2930|consen 75 TVAWGVCNHAFHFHCISRWLKT-RNVCPLDNKEWV 108 (114)
T ss_pred EEEeeecchHHHHHHHHHHHhh-cCcCCCcCccee
Confidence 3566799999999999999995 789999999875
No 32
>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=97.82 E-value=1.8e-05 Score=56.85 Aligned_cols=43 Identities=28% Similarity=0.724 Sum_probs=33.3
Q ss_pred CCcccccccccCCceeEEcCCC-----CccchHHHHHHhhcC-CCCCCCCC
Q 021781 208 DCPVCCEYLFETRQDVIVLPCG-----HTIHKNCLKEMREHH-QYACPICS 252 (307)
Q Consensus 208 ~CPIClE~lf~s~~~v~~LpCG-----H~fH~~Ci~~wl~~~-~~~CPlCr 252 (307)
.|-||++ +.+.....++||. |.+|..|+++|+... +.+||+|+
T Consensus 1 ~CrIC~~--~~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~ 49 (49)
T smart00744 1 ICRICHD--EGDEGDPLVSPCRCKGSLKYVHQECLERWINESGNKTCEICK 49 (49)
T ss_pred CccCCCC--CCCCCCeeEeccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence 3889997 3344556678994 999999999999753 45799995
No 33
>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=97.78 E-value=2.2e-05 Score=75.85 Aligned_cols=52 Identities=23% Similarity=0.568 Sum_probs=39.4
Q ss_pred CCCCcccccccccCCcee-EEcCCCCccchHHHHHHhhcCCCCCCCCCcCccc
Q 021781 206 HHDCPVCCEYLFETRQDV-IVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 257 (307)
Q Consensus 206 ~~~CPIClE~lf~s~~~v-~~LpCGH~fH~~Ci~~wl~~~~~~CPlCrks~~d 257 (307)
+..||||+...+.++.-. .+.+|||.|+..|++.++..+...||+|++++..
T Consensus 3 ~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk 55 (309)
T TIGR00570 3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLRK 55 (309)
T ss_pred CCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCccch
Confidence 467999998655554322 2238999999999999766566789999998763
No 34
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.61 E-value=3.7e-05 Score=71.36 Aligned_cols=50 Identities=28% Similarity=0.670 Sum_probs=38.5
Q ss_pred CCCCCCcccccccccCCceeEEcCCCCccchHHHHHHhhcC--CCCCCCCCcCccc
Q 021781 204 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHH--QYACPICSKSVCD 257 (307)
Q Consensus 204 ~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~--~~~CPlCrks~~d 257 (307)
....+|-||||- .. +.++-.|||.|+--||-+||... +..||+|+..+..
T Consensus 45 ~~~FdCNICLd~---ak-dPVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~ 96 (230)
T KOG0823|consen 45 GGFFDCNICLDL---AK-DPVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSI 96 (230)
T ss_pred CCceeeeeeccc---cC-CCEEeecccceehHHHHHHHhhcCCCeeCCcccccccc
Confidence 446899999983 23 34555699999999999999763 3448999988864
No 35
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=97.59 E-value=1.4e-05 Score=61.24 Aligned_cols=51 Identities=27% Similarity=0.671 Sum_probs=23.4
Q ss_pred CCCCcccccccccC-CceeEEc---CCCCccchHHHHHHhhc--C-C-------CCCCCCCcCcc
Q 021781 206 HHDCPVCCEYLFET-RQDVIVL---PCGHTIHKNCLKEMREH--H-Q-------YACPICSKSVC 256 (307)
Q Consensus 206 ~~~CPIClE~lf~s-~~~v~~L---pCGH~fH~~Ci~~wl~~--~-~-------~~CPlCrks~~ 256 (307)
+..|+||.+++.+. ..+.++- .|+..||..||.+|+.. . + -.||.|++++.
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~ 66 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPIS 66 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEE
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeee
Confidence 45899999876523 2333332 69999999999999863 1 1 13999998874
No 36
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.56 E-value=3.1e-05 Score=78.59 Aligned_cols=52 Identities=25% Similarity=0.699 Sum_probs=39.6
Q ss_pred CCCCccccccccc----C---------CceeEEcCCCCccchHHHHHHhhcCCCCCCCCCcCccc
Q 021781 206 HHDCPVCCEYLFE----T---------RQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 257 (307)
Q Consensus 206 ~~~CPIClE~lf~----s---------~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlCrks~~d 257 (307)
..+|+|||.++.- + ++..++-||.|.||+.|+++|+...+..||+||.++..
T Consensus 571 t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLPp 635 (636)
T KOG0828|consen 571 TNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLPP 635 (636)
T ss_pred cccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCCCC
Confidence 4689999976521 1 12355669999999999999998556679999988753
No 37
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.46 E-value=6.3e-05 Score=76.54 Aligned_cols=49 Identities=27% Similarity=0.649 Sum_probs=36.6
Q ss_pred CCCCCcccccccccCCceeEEcCCCCccchHHHHHHhhcC----CCCCCCCCcCccc
Q 021781 205 MHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHH----QYACPICSKSVCD 257 (307)
Q Consensus 205 ~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~----~~~CPlCrks~~d 257 (307)
++..|||||++ ..-+++ ..|||.|+..||-+|+... --.||+|+..+..
T Consensus 185 t~~~CPICL~~---~~~p~~-t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~ 237 (513)
T KOG2164|consen 185 TDMQCPICLEP---PSVPVR-TNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITL 237 (513)
T ss_pred cCCcCCcccCC---CCcccc-cccCceeeHHHHHHHHhhhcccCCccCCchhhhccc
Confidence 37899999996 223344 4599999999999966542 2459999988764
No 38
>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=97.45 E-value=0.00012 Score=56.18 Aligned_cols=48 Identities=21% Similarity=0.493 Sum_probs=36.6
Q ss_pred CCCCcccccccccCCceeEEcCCCCccchHHHHHHhhcCCCCCCCCCcCccc
Q 021781 206 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 257 (307)
Q Consensus 206 ~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlCrks~~d 257 (307)
+..|||+++-|.+ .+++|+||+|-+.+|++|+.....+||+++..+..
T Consensus 4 ~f~CpIt~~lM~d----PVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~ 51 (73)
T PF04564_consen 4 EFLCPITGELMRD----PVILPSGHTYERSAIERWLEQNGGTDPFTRQPLSE 51 (73)
T ss_dssp GGB-TTTSSB-SS----EEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SG
T ss_pred ccCCcCcCcHhhC----ceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCc
Confidence 4679999995433 57889999999999999998767899999988874
No 39
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=97.44 E-value=8.2e-05 Score=72.76 Aligned_cols=45 Identities=31% Similarity=0.845 Sum_probs=38.4
Q ss_pred CCCcccccccccCCceeEEcCCCCccchHHHHHHhhcCCCCCCCCCcCcc
Q 021781 207 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 256 (307)
Q Consensus 207 ~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlCrks~~ 256 (307)
..|-||.|| |.- .++.||||+|+.-||+.+|.. +..||.|+-++.
T Consensus 24 LRC~IC~ey-f~i---p~itpCsHtfCSlCIR~~L~~-~p~CP~C~~~~~ 68 (442)
T KOG0287|consen 24 LRCGICFEY-FNI---PMITPCSHTFCSLCIRKFLSY-KPQCPTCCVTVT 68 (442)
T ss_pred HHHhHHHHH-hcC---ceeccccchHHHHHHHHHhcc-CCCCCceecccc
Confidence 479999997 442 467799999999999999984 799999999886
No 40
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.13 E-value=0.0002 Score=71.12 Aligned_cols=46 Identities=28% Similarity=0.692 Sum_probs=36.6
Q ss_pred CCCCcccccccccCCceeEEc-CCCCccchHHHHHHhhcC--CCCCCCCC
Q 021781 206 HHDCPVCCEYLFETRQDVIVL-PCGHTIHKNCLKEMREHH--QYACPICS 252 (307)
Q Consensus 206 ~~~CPIClE~lf~s~~~v~~L-pCGH~fH~~Ci~~wl~~~--~~~CPlCr 252 (307)
...|.|| ++++.....+... .|||+||..|+.+|+... +..||+|+
T Consensus 4 ~A~C~Ic-~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ 52 (465)
T KOG0827|consen 4 MAECHIC-IDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQ 52 (465)
T ss_pred cceeeEe-ccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCcee
Confidence 3579999 5577766666655 599999999999999863 24699999
No 41
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.01 E-value=0.00035 Score=66.16 Aligned_cols=49 Identities=27% Similarity=0.501 Sum_probs=38.4
Q ss_pred CCCCCcccccccccCCceeEEcCCCCccchHHHHH-HhhcCCCCCCCCCcCccc
Q 021781 205 MHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKE-MREHHQYACPICSKSVCD 257 (307)
Q Consensus 205 ~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~-wl~~~~~~CPlCrks~~d 257 (307)
.+..|+||+|... .....+|||.|+-.||.. |.+...-.||+||.-+..
T Consensus 214 ~d~kC~lC~e~~~----~ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~p 263 (271)
T COG5574 214 ADYKCFLCLEEPE----VPSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVYP 263 (271)
T ss_pred cccceeeeecccC----CcccccccchhhHHHHHHHHHhhccccCchhhhhccc
Confidence 3678999999533 356789999999999999 987543449999976543
No 42
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=96.92 E-value=0.00045 Score=52.73 Aligned_cols=55 Identities=24% Similarity=0.627 Sum_probs=26.9
Q ss_pred CCCcccccccccCCceeEEcCCCCccchHHHHHHhhcCCCCCCCCCcCcc--chhHHHHhhHHH
Q 021781 207 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC--DMSKVWEKYDRE 268 (307)
Q Consensus 207 ~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlCrks~~--dm~~~~~~lD~e 268 (307)
..|++|.+.|.. ++.+..|.|.|+..|+.+.+. ..||+|+.+.. |+ ..-++||..
T Consensus 8 LrCs~C~~~l~~---pv~l~~CeH~fCs~Ci~~~~~---~~CPvC~~Paw~qD~-~~NrqLd~~ 64 (65)
T PF14835_consen 8 LRCSICFDILKE---PVCLGGCEHIFCSSCIRDCIG---SECPVCHTPAWIQDI-QINRQLDSM 64 (65)
T ss_dssp TS-SSS-S--SS----B---SSS--B-TTTGGGGTT---TB-SSS--B-S-SS-----HHHHHH
T ss_pred cCCcHHHHHhcC---CceeccCccHHHHHHhHHhcC---CCCCCcCChHHHHHH-Hhhhhhhcc
Confidence 479999996433 567779999999999988765 45999999874 43 233455554
No 43
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.80 E-value=0.00035 Score=66.64 Aligned_cols=52 Identities=23% Similarity=0.553 Sum_probs=41.4
Q ss_pred CCCCCcccccccccCC------ceeEEcCCCCccchHHHHHHhhc-CCCCCCCCCcCcc
Q 021781 205 MHHDCPVCCEYLFETR------QDVIVLPCGHTIHKNCLKEMREH-HQYACPICSKSVC 256 (307)
Q Consensus 205 ~~~~CPIClE~lf~s~------~~v~~LpCGH~fH~~Ci~~wl~~-~~~~CPlCrks~~ 256 (307)
.+..|+||...++.+. +..-.|.|+|.||.-||+-|--. ...+||.|++.+.
T Consensus 223 ~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVd 281 (328)
T KOG1734|consen 223 SDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVD 281 (328)
T ss_pred CcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhh
Confidence 3578999988776554 24567999999999999999644 4688999998765
No 44
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.78 E-value=0.00031 Score=52.21 Aligned_cols=51 Identities=25% Similarity=0.670 Sum_probs=38.9
Q ss_pred CCCCCcccccccccCCceeEEcCCCCc-cchHHHHHHhhcCCCCCCCCCcCccchh
Q 021781 205 MHHDCPVCCEYLFETRQDVIVLPCGHT-IHKNCLKEMREHHQYACPICSKSVCDMS 259 (307)
Q Consensus 205 ~~~~CPIClE~lf~s~~~v~~LpCGH~-fH~~Ci~~wl~~~~~~CPlCrks~~dm~ 259 (307)
....|.||+|.- -+.++.-|||. ++-+|-.+.++..+-.||+||.++.+.-
T Consensus 6 ~~dECTICye~p----vdsVlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~dvI 57 (62)
T KOG4172|consen 6 WSDECTICYEHP----VDSVLYTCGHMCMCYACGLRLKKALHGCCPICRAPIKDVI 57 (62)
T ss_pred cccceeeeccCc----chHHHHHcchHHhHHHHHHHHHHccCCcCcchhhHHHHHH
Confidence 357899999952 23456689998 8889987765556788999999887643
No 45
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.65 E-value=0.0012 Score=64.69 Aligned_cols=49 Identities=31% Similarity=0.811 Sum_probs=39.7
Q ss_pred CCCCCCcccccccccCCceeEEcCCCCc-cchHHHHHHhhcCCCCCCCCCcCccc
Q 021781 204 AMHHDCPVCCEYLFETRQDVIVLPCGHT-IHKNCLKEMREHHQYACPICSKSVCD 257 (307)
Q Consensus 204 ~~~~~CPIClE~lf~s~~~v~~LpCGH~-fH~~Ci~~wl~~~~~~CPlCrks~~d 257 (307)
.....|.|||.. .++.++|||.|. ++..|.+...- ....|||||..+..
T Consensus 288 ~~gkeCVIClse----~rdt~vLPCRHLCLCs~Ca~~Lr~-q~n~CPICRqpi~~ 337 (349)
T KOG4265|consen 288 ESGKECVICLSE----SRDTVVLPCRHLCLCSGCAKSLRY-QTNNCPICRQPIEE 337 (349)
T ss_pred cCCCeeEEEecC----CcceEEecchhhehhHhHHHHHHH-hhcCCCccccchHh
Confidence 345789999974 456899999998 99999988753 35789999998864
No 46
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=96.52 E-value=0.0019 Score=46.68 Aligned_cols=47 Identities=34% Similarity=0.699 Sum_probs=25.5
Q ss_pred CcccccccccCCceeEEcCCCCccchHHHHHHhhcCCCCCCCCCcCc
Q 021781 209 CPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSV 255 (307)
Q Consensus 209 CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlCrks~ 255 (307)
||+|.|.+..+......=+||+.+++.|+..-+...+-+||-||++.
T Consensus 1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y 47 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILENEGGRCPGCREPY 47 (48)
T ss_dssp -TTTS-B--CCCTT--SSTTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred CCCcccccccCCCccccCcCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence 79999988555444444477999999999999875578999999864
No 47
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.49 E-value=0.00058 Score=67.08 Aligned_cols=49 Identities=22% Similarity=0.560 Sum_probs=40.8
Q ss_pred CCCCcccccccccCCceeEEcCCCCccchHHHHHHhhcCCCCCCCCCcCccc
Q 021781 206 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 257 (307)
Q Consensus 206 ~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlCrks~~d 257 (307)
+..|||||+-|.. ...+.-|+|.|+.+||..-+..++..||.||+.+..
T Consensus 43 ~v~c~icl~llk~---tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~S 91 (381)
T KOG0311|consen 43 QVICPICLSLLKK---TMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVS 91 (381)
T ss_pred hhccHHHHHHHHh---hcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhccc
Confidence 4579999995443 356678999999999999888888999999999873
No 48
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=96.47 E-value=0.0017 Score=62.69 Aligned_cols=46 Identities=26% Similarity=0.605 Sum_probs=37.7
Q ss_pred CCCCcccccccccCCceeEEcCCCCccchHHHHHHhhcCCCCCCCCCcCcc
Q 021781 206 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 256 (307)
Q Consensus 206 ~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlCrks~~ 256 (307)
-..|-||.+++.- ...-+|||+|+.-||..+|.. +..||+||.+..
T Consensus 25 ~lrC~IC~~~i~i----p~~TtCgHtFCslCIR~hL~~-qp~CP~Cr~~~~ 70 (391)
T COG5432 25 MLRCRICDCRISI----PCETTCGHTFCSLCIRRHLGT-QPFCPVCREDPC 70 (391)
T ss_pred HHHhhhhhheeec----ceecccccchhHHHHHHHhcC-CCCCccccccHH
Confidence 4579999996432 356699999999999999984 799999998764
No 49
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=96.38 E-value=0.00065 Score=67.67 Aligned_cols=59 Identities=34% Similarity=0.702 Sum_probs=48.5
Q ss_pred cccccCCCCCCCCcccccccccCCceeEEcCCCCccchHHHHHHhhc-CCCCCCCCCcCcc
Q 021781 197 SHPCVEGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH-HQYACPICSKSVC 256 (307)
Q Consensus 197 ~H~CiE~~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~-~~~~CPlCrks~~ 256 (307)
.|.|++ .++-.|-.|.|.+-...+....|||.|.||..|+.++|.. ...+||-||+-..
T Consensus 357 a~~~~~-e~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~CrklrS 416 (518)
T KOG1941|consen 357 AHECVE-ETELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRKLRS 416 (518)
T ss_pred HHHHHH-HHhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHHHHh
Confidence 577876 5789999999987777777889999999999999998854 4467999995443
No 50
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=96.36 E-value=0.0011 Score=70.18 Aligned_cols=47 Identities=28% Similarity=0.710 Sum_probs=40.1
Q ss_pred CCCcccccccccCCceeEEcCCCCccchHHHHHHhhcCCCCCCCCCcCccc
Q 021781 207 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 257 (307)
Q Consensus 207 ~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlCrks~~d 257 (307)
..||+|-.. ..+.++..|||.||..|++..+.....+||.|+.+|+.
T Consensus 644 LkCs~Cn~R----~Kd~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFga 690 (698)
T KOG0978|consen 644 LKCSVCNTR----WKDAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGA 690 (698)
T ss_pred eeCCCccCc----hhhHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCc
Confidence 579999863 45577889999999999999887767889999999984
No 51
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=96.25 E-value=0.0041 Score=46.13 Aligned_cols=44 Identities=25% Similarity=0.582 Sum_probs=29.6
Q ss_pred CCCCCCcccccccccCCceeEEcCCCCccchHHHHHHhhc-CCCCCCC
Q 021781 204 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH-HQYACPI 250 (307)
Q Consensus 204 ~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~-~~~~CPl 250 (307)
.....|||-+..| . +|++...|||+|-++.|.+||+. ....||+
T Consensus 9 ~~~~~CPiT~~~~-~--~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv 53 (57)
T PF11789_consen 9 TISLKCPITLQPF-E--DPVKSKKCGHTFEKEAILQYIQRNGSKRCPV 53 (57)
T ss_dssp B--SB-TTTSSB--S--SEEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred EeccCCCCcCChh-h--CCcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence 4467899999864 3 46888899999999999999943 3566998
No 52
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.18 E-value=0.004 Score=59.57 Aligned_cols=53 Identities=26% Similarity=0.676 Sum_probs=42.5
Q ss_pred CCCCCCcccccccccCCceeEEcCCCCccchHHHHHHhh-cCCCCCCCCCcCccchh
Q 021781 204 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMRE-HHQYACPICSKSVCDMS 259 (307)
Q Consensus 204 ~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~-~~~~~CPlCrks~~dm~ 259 (307)
+....||+|.++ +.-|.+..+|||.++--|+..-+. ..+++||.|+.+...|.
T Consensus 237 t~~~~C~~Cg~~---PtiP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~~lq 290 (298)
T KOG2879|consen 237 TSDTECPVCGEP---PTIPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVEPLQ 290 (298)
T ss_pred cCCceeeccCCC---CCCCeeeccccceeehhhhhhhhcchhhcccCccCCCCcchh
Confidence 456789999996 556778889999999999998443 23589999999887664
No 53
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.09 E-value=0.0018 Score=63.63 Aligned_cols=53 Identities=23% Similarity=0.629 Sum_probs=39.4
Q ss_pred CCCCCCcccccccccCC---ceeEE-cCCCCccchHHHHHHhhcC------CCCCCCCCcCcc
Q 021781 204 AMHHDCPVCCEYLFETR---QDVIV-LPCGHTIHKNCLKEMREHH------QYACPICSKSVC 256 (307)
Q Consensus 204 ~~~~~CPIClE~lf~s~---~~v~~-LpCGH~fH~~Ci~~wl~~~------~~~CPlCrks~~ 256 (307)
+.+..|-||||.+.+.. ....+ ++|.|.|+..|+..|.+.. ...||+||....
T Consensus 159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~ 221 (344)
T KOG1039|consen 159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSS 221 (344)
T ss_pred cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccc
Confidence 55779999999765533 11222 4699999999999998543 367999998865
No 54
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=96.09 E-value=0.0018 Score=64.84 Aligned_cols=54 Identities=30% Similarity=0.765 Sum_probs=44.4
Q ss_pred cccCCCCCCCCcccccccccCCceeEEcCCCCccchHHHHHHhhcC-CCCCCCCCcCcc
Q 021781 199 PCVEGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHH-QYACPICSKSVC 256 (307)
Q Consensus 199 ~CiE~~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~-~~~CPlCrks~~ 256 (307)
-|.-+++-..|-||-| +.+++.+=||||.++..|+..|-.+. ..+||.||..+.
T Consensus 362 YceMgsTFeLCKICae----ndKdvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIK 416 (563)
T KOG1785|consen 362 YCEMGSTFELCKICAE----NDKDVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIK 416 (563)
T ss_pred HHHccchHHHHHHhhc----cCCCcccccccchHHHHHHHhhcccCCCCCCCceeeEec
Confidence 3556677789999998 35668888999999999999997443 688999998764
No 55
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.02 E-value=0.0046 Score=59.80 Aligned_cols=50 Identities=18% Similarity=0.404 Sum_probs=40.1
Q ss_pred CCCCCCCcccccccccCCceeEEcCCCCccchHHHHHHhhcCCCCCCCCCcCcc
Q 021781 203 GAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 256 (307)
Q Consensus 203 ~~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlCrks~~ 256 (307)
+.+...|+||+...- -.+.|+|+|.|+..||+--.+....+||+||.++.
T Consensus 4 ~~~~~eC~IC~nt~n----~Pv~l~C~HkFCyiCiKGsy~ndk~~CavCR~pid 53 (324)
T KOG0824|consen 4 RTKKKECLICYNTGN----CPVNLYCFHKFCYICIKGSYKNDKKTCAVCRFPID 53 (324)
T ss_pred cccCCcceeeeccCC----cCccccccchhhhhhhcchhhcCCCCCceecCCCC
Confidence 356789999997532 23789999999999999865555677999999987
No 56
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=95.60 E-value=0.012 Score=57.04 Aligned_cols=64 Identities=23% Similarity=0.546 Sum_probs=50.2
Q ss_pred CCCCcccccccccCCceeEEcCC--CCccchHHHHHHhhcCCCCCCCCCcCccchhHHHHhhHHHHHcCCCChhhcC
Q 021781 206 HHDCPVCCEYLFETRQDVIVLPC--GHTIHKNCLKEMREHHQYACPICSKSVCDMSKVWEKYDREIAATPMPEAYLN 280 (307)
Q Consensus 206 ~~~CPIClE~lf~s~~~v~~LpC--GH~fH~~Ci~~wl~~~~~~CPlCrks~~dm~~~~~~lD~eia~~pmP~ey~n 280 (307)
-.+||||.++|.- -++.| ||..+..|-.+. ...||.||.++++. .-+.+++.+++...|..+.+
T Consensus 48 lleCPvC~~~l~~-----Pi~QC~nGHlaCssC~~~~----~~~CP~Cr~~~g~~--R~~amEkV~e~~~vpC~~~~ 113 (299)
T KOG3002|consen 48 LLDCPVCFNPLSP-----PIFQCDNGHLACSSCRTKV----SNKCPTCRLPIGNI--RCRAMEKVAEAVLVPCKNAK 113 (299)
T ss_pred hccCchhhccCcc-----cceecCCCcEehhhhhhhh----cccCCccccccccH--HHHHHHHHHHhceecccccc
Confidence 4689999997643 23567 899999998754 46899999999975 34578888999999987755
No 57
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=95.35 E-value=0.0052 Score=65.73 Aligned_cols=51 Identities=14% Similarity=0.379 Sum_probs=39.6
Q ss_pred CCCCCcccccccccCCceeEEcCCCCccchHHHHHHhhcCCCCCCCCCcCccc
Q 021781 205 MHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 257 (307)
Q Consensus 205 ~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlCrks~~d 257 (307)
.+..||+|+.. +.........+|+|.||.+||..|-+. ..+||+||+.+..
T Consensus 122 ~~~~CP~Ci~s-~~DqL~~~~k~c~H~FC~~Ci~sWsR~-aqTCPiDR~EF~~ 172 (1134)
T KOG0825|consen 122 VENQCPNCLKS-CNDQLEESEKHTAHYFCEECVGSWSRC-AQTCPVDRGEFGE 172 (1134)
T ss_pred hhhhhhHHHHH-HHHHhhccccccccccHHHHhhhhhhh-cccCchhhhhhhe
Confidence 35689999975 333333345699999999999999874 5899999999863
No 58
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=95.27 E-value=0.013 Score=44.01 Aligned_cols=46 Identities=33% Similarity=0.853 Sum_probs=33.4
Q ss_pred CceeeeCCCCccccc-----cccCcCCCCc-cceEecCccccccCCCCCCeecCCCCCc
Q 021781 119 VNQVICSLCGTEQKV-----QQVCVNCGVC-MGEYFCESCKLFDDDTSKKQYHCDGCGI 171 (307)
Q Consensus 119 v~~v~C~~C~~eQ~v-----~~~C~~Cg~~-fa~YfC~~Ckl~ddd~~k~~yHC~~Cgi 171 (307)
.+...|..|+.+... .-.|||||.. ..| |.+|+-+. ..|.|++||+
T Consensus 5 ~~~~~CtSCg~~i~~~~~~~~F~CPnCG~~~I~R--C~~CRk~~-----~~Y~CP~CGF 56 (59)
T PRK14890 5 MEPPKCTSCGIEIAPREKAVKFLCPNCGEVIIYR--CEKCRKQS-----NPYTCPKCGF 56 (59)
T ss_pred ccCccccCCCCcccCCCccCEeeCCCCCCeeEee--chhHHhcC-----CceECCCCCC
Confidence 345678889876443 3469999986 544 99998774 3799999985
No 59
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.27 E-value=0.022 Score=57.23 Aligned_cols=51 Identities=24% Similarity=0.719 Sum_probs=39.0
Q ss_pred CCCCcccccccccCC-ceeEEcCCCCccchHHHHHHhhc-CCCCCCCCCcCcc
Q 021781 206 HHDCPVCCEYLFETR-QDVIVLPCGHTIHKNCLKEMREH-HQYACPICSKSVC 256 (307)
Q Consensus 206 ~~~CPIClE~lf~s~-~~v~~LpCGH~fH~~Ci~~wl~~-~~~~CPlCrks~~ 256 (307)
...||||++.+..++ ..++.|.|||.|-..|++.||.. ....||.|.....
T Consensus 4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~kat 56 (463)
T KOG1645|consen 4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKAT 56 (463)
T ss_pred cccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChhH
Confidence 357999998765544 35577899999999999999952 2355999986543
No 60
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=95.20 E-value=0.0093 Score=65.04 Aligned_cols=53 Identities=21% Similarity=0.570 Sum_probs=37.3
Q ss_pred CCCCCCcccccccc--cCCcee-EEcCCCCccchHHHHHHhhc-CCCCCCCCCcCcc
Q 021781 204 AMHHDCPVCCEYLF--ETRQDV-IVLPCGHTIHKNCLKEMREH-HQYACPICSKSVC 256 (307)
Q Consensus 204 ~~~~~CPIClE~lf--~s~~~v-~~LpCGH~fH~~Ci~~wl~~-~~~~CPlCrks~~ 256 (307)
+....||||..-+. +..-|. +-..|.|-||..|+-+|+++ .+.+||+||.++.
T Consensus 1467 sG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219 1467 SGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred CCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence 34678999976432 222122 23358899999999999976 4678999997664
No 61
>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=94.95 E-value=0.011 Score=47.02 Aligned_cols=33 Identities=36% Similarity=0.850 Sum_probs=27.5
Q ss_pred CCCCCCcccccccccCCceeEEcCCCCccchHHHH
Q 021781 204 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLK 238 (307)
Q Consensus 204 ~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~ 238 (307)
.....|++|...|.. ....+.||||.+|..|++
T Consensus 76 ~~~~~C~vC~k~l~~--~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 76 TESTKCSVCGKPLGN--SVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCCCccCcCCcCCC--ceEEEeCCCeEEeccccc
Confidence 446789999998876 357888999999999985
No 62
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=94.79 E-value=0.02 Score=40.76 Aligned_cols=41 Identities=29% Similarity=0.752 Sum_probs=26.3
Q ss_pred CcccccccccCCceeEEcCCC-----CccchHHHHHHhhc-CCCCCCCC
Q 021781 209 CPVCCEYLFETRQDVIVLPCG-----HTIHKNCLKEMREH-HQYACPIC 251 (307)
Q Consensus 209 CPIClE~lf~s~~~v~~LpCG-----H~fH~~Ci~~wl~~-~~~~CPlC 251 (307)
|-||++...++ +..+.||+ -..|.+|+++|+.. .+.+|++|
T Consensus 1 CrIC~~~~~~~--~~li~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C 47 (47)
T PF12906_consen 1 CRICLEGEEED--EPLISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC 47 (47)
T ss_dssp ETTTTEE-SSS--S-EE-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred CeEeCCcCCCC--CceecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence 56888753332 24567884 57899999999975 45679987
No 63
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=94.65 E-value=0.028 Score=63.75 Aligned_cols=74 Identities=27% Similarity=0.578 Sum_probs=54.0
Q ss_pred cCCccceecCCccceeeccccccccccCCCCCCCCcccccccccCCceeEEcCCCCccchHHHHHHhhc----C-----C
Q 021781 175 GGCDNFFHCNKCRCCYSMLLKNSHPCVEGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH----H-----Q 245 (307)
Q Consensus 175 G~~e~ffHC~~C~~C~s~~l~~~H~CiE~~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~----~-----~ 245 (307)
||.+|--||.-|-.|-.-.. ....++.|.||.-. ..+.-+.+.|.|||.||.+|.+.-|.. . -
T Consensus 3462 GGvkNEE~CLPCl~Cdks~t-------kQD~DDmCmICFTE-~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~F 3533 (3738)
T KOG1428|consen 3462 GGVKNEEHCLPCLHCDKSAT-------KQDADDMCMICFTE-ALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGF 3533 (3738)
T ss_pred cCccchhhcccccccChhhh-------hcccCceEEEEehh-hhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEee
Confidence 56678888888887753321 22457889999864 445667899999999999999875543 1 1
Q ss_pred CCCCCCCcCcc
Q 021781 246 YACPICSKSVC 256 (307)
Q Consensus 246 ~~CPlCrks~~ 256 (307)
..||+|...+.
T Consensus 3534 isCPiC~n~In 3544 (3738)
T KOG1428|consen 3534 ISCPICKNKIN 3544 (3738)
T ss_pred eecccccchhh
Confidence 45999998875
No 64
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.61 E-value=0.045 Score=51.67 Aligned_cols=49 Identities=31% Similarity=0.756 Sum_probs=38.3
Q ss_pred CCCcccccccccCC---ceeEEcCCCCccchHHHHHHhhcCCCCCCCCCcCcc
Q 021781 207 HDCPVCCEYLFETR---QDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 256 (307)
Q Consensus 207 ~~CPIClE~lf~s~---~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlCrks~~ 256 (307)
..|-||-++ |.+. ..++.|.|||+|+..|+...+......||.||.+..
T Consensus 4 ~~c~~c~~~-~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~~~i~cpfcR~~~~ 55 (296)
T KOG4185|consen 4 PECEICNED-YSSEDGDHIPRVLKCGHTICQNCASKLLGNSRILCPFCRETTE 55 (296)
T ss_pred CceeecCcc-ccccCcccCCcccccCceehHhHHHHHhcCceeeccCCCCccc
Confidence 457788776 3333 345778999999999999999877777999999953
No 65
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=94.49 E-value=0.015 Score=43.22 Aligned_cols=33 Identities=39% Similarity=0.785 Sum_probs=26.3
Q ss_pred eeEEcCCCCccchHHHHHHhhcCCCCCCCCCcCccc
Q 021781 222 DVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 257 (307)
Q Consensus 222 ~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlCrks~~d 257 (307)
.-++|||||.+...|+.-+-. ..||+|.+++..
T Consensus 19 ~~~~~pCgH~I~~~~f~~~rY---ngCPfC~~~~~~ 51 (55)
T PF14447_consen 19 KGTVLPCGHLICDNCFPGERY---NGCPFCGTPFEF 51 (55)
T ss_pred ccccccccceeeccccChhhc---cCCCCCCCcccC
Confidence 356789999999999977632 359999998863
No 66
>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=94.34 E-value=0.034 Score=53.58 Aligned_cols=49 Identities=20% Similarity=0.532 Sum_probs=39.3
Q ss_pred CCcccccccccCCceeE-EcCCCCccchHHHHHHhhcCCCCCCCCCcCcc
Q 021781 208 DCPVCCEYLFETRQDVI-VLPCGHTIHKNCLKEMREHHQYACPICSKSVC 256 (307)
Q Consensus 208 ~CPIClE~lf~s~~~v~-~LpCGH~fH~~Ci~~wl~~~~~~CPlCrks~~ 256 (307)
.||+|.-+.+.++.-.. +=+|||.++.+|+...+..+.+.||.|.+.+.
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iLR 51 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGPAQCPECMVILR 51 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHhcCCCCCCcccchhh
Confidence 59999877666553222 22999999999999998888899999998875
No 67
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=94.22 E-value=0.015 Score=56.46 Aligned_cols=53 Identities=23% Similarity=0.538 Sum_probs=41.2
Q ss_pred CCCCCCcccccccccCCceeEEcCCCCccchHHHHHHhhc----------------------CCCCCCCCCcCccc
Q 021781 204 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH----------------------HQYACPICSKSVCD 257 (307)
Q Consensus 204 ~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~----------------------~~~~CPlCrks~~d 257 (307)
--.+.|.|||= -|-+.....+.+|-|+||..||..+|.. ..-.||+||-.+.+
T Consensus 113 ~p~gqCvICLy-gfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~ 187 (368)
T KOG4445|consen 113 HPNGQCVICLY-GFASSPAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKI 187 (368)
T ss_pred CCCCceEEEEE-eecCCCceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccc
Confidence 34679999995 4666667888899999999999888751 12349999988864
No 68
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=93.88 E-value=0.026 Score=52.90 Aligned_cols=36 Identities=28% Similarity=0.693 Sum_probs=26.7
Q ss_pred cCCceeEEcCCCCccchHHHHHHhhcCCCCCCCCCcCcc
Q 021781 218 ETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 256 (307)
Q Consensus 218 ~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlCrks~~ 256 (307)
.+..+..+..|+|+|+..|...-.. ..||+|++++.
T Consensus 13 ~~~~~f~LTaC~HvfC~~C~k~~~~---~~C~lCkk~ir 48 (233)
T KOG4739|consen 13 PSQDPFFLTACRHVFCEPCLKASSP---DVCPLCKKSIR 48 (233)
T ss_pred CCCCceeeeechhhhhhhhcccCCc---cccccccceee
Confidence 3444556679999999999965422 38999999964
No 69
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=93.54 E-value=0.027 Score=55.61 Aligned_cols=54 Identities=28% Similarity=0.635 Sum_probs=43.8
Q ss_pred CCCCcccccccccCCceeEEcCCCCccchHHHHHHhhcCCCCCCCCCcCccchh
Q 021781 206 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCDMS 259 (307)
Q Consensus 206 ~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlCrks~~dm~ 259 (307)
++-||.|+|+|.-+.+....-|||-.+++-|+....+.-+-+||-||+...+..
T Consensus 14 ed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~den 67 (480)
T COG5175 14 EDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDEN 67 (480)
T ss_pred cccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhccccc
Confidence 455999999987776666667899999999998876655678999999887643
No 70
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.37 E-value=0.049 Score=49.57 Aligned_cols=31 Identities=29% Similarity=0.808 Sum_probs=25.3
Q ss_pred cCCCCccchHHHHHHhhc-----CC-----CCCCCCCcCcc
Q 021781 226 LPCGHTIHKNCLKEMREH-----HQ-----YACPICSKSVC 256 (307)
Q Consensus 226 LpCGH~fH~~Ci~~wl~~-----~~-----~~CPlCrks~~ 256 (307)
..||..||+-|+..||+. .+ -.||.|++++.
T Consensus 188 ~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~Pia 228 (234)
T KOG3268|consen 188 IQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIA 228 (234)
T ss_pred cccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcce
Confidence 579999999999999974 11 23999999885
No 71
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.33 E-value=0.046 Score=53.98 Aligned_cols=47 Identities=26% Similarity=0.639 Sum_probs=35.4
Q ss_pred CCCCCCCCcccccccccCCceeEEcCCCCccchHHHHHHhhcCCCCCCCCCcCcc
Q 021781 202 EGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 256 (307)
Q Consensus 202 E~~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlCrks~~ 256 (307)
|.+...+|.||++. .+..+.+||||.-+ |..-... ...||+||..+.
T Consensus 301 ~~~~p~lcVVcl~e----~~~~~fvpcGh~cc--ct~cs~~--l~~CPvCR~rI~ 347 (355)
T KOG1571|consen 301 ELPQPDLCVVCLDE----PKSAVFVPCGHVCC--CTLCSKH--LPQCPVCRQRIR 347 (355)
T ss_pred ccCCCCceEEecCC----ccceeeecCCcEEE--chHHHhh--CCCCchhHHHHH
Confidence 45678999999984 44578999999966 6555433 356999998775
No 72
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=93.06 E-value=0.056 Score=53.91 Aligned_cols=50 Identities=28% Similarity=0.686 Sum_probs=40.0
Q ss_pred CCCCCCcccccccccCCceeEEcCCCCccchHHHHHHhhcCCCCCCCCCcCccc
Q 021781 204 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 257 (307)
Q Consensus 204 ~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlCrks~~d 257 (307)
..+..||+|..-+-+ ++....|||.|+..|+..|+.. +..||.|+..+..
T Consensus 19 ~~~l~C~~C~~vl~~---p~~~~~cgh~fC~~C~~~~~~~-~~~cp~~~~~~~~ 68 (391)
T KOG0297|consen 19 DENLLCPICMSVLRD---PVQTTTCGHRFCAGCLLESLSN-HQKCPVCRQELTQ 68 (391)
T ss_pred cccccCccccccccC---CCCCCCCCCcccccccchhhcc-CcCCcccccccch
Confidence 345789999975433 3444789999999999999986 7899999988764
No 73
>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=92.71 E-value=0.059 Score=46.67 Aligned_cols=35 Identities=20% Similarity=0.514 Sum_probs=30.1
Q ss_pred CCCCcccccccccCCceeEEcCCC------CccchHHHHHHh
Q 021781 206 HHDCPVCCEYLFETRQDVIVLPCG------HTIHKNCLKEMR 241 (307)
Q Consensus 206 ~~~CPIClE~lf~s~~~v~~LpCG------H~fH~~Ci~~wl 241 (307)
...|.||++.+-+ ...++.++|| |.||.+|+++|-
T Consensus 26 ~~EC~IC~~~I~~-~~GvV~vt~~g~lnLEkmfc~~C~~rw~ 66 (134)
T PF05883_consen 26 TVECQICFDRIDN-NDGVVYVTDGGTLNLEKMFCADCDKRWR 66 (134)
T ss_pred Ceeehhhhhhhhc-CCCEEEEecCCeehHHHHHHHHHHHHHH
Confidence 4689999998766 5678999997 789999999994
No 74
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.56 E-value=0.12 Score=52.07 Aligned_cols=49 Identities=29% Similarity=0.824 Sum_probs=39.0
Q ss_pred CCCCCCcccccccccCCceeEEcCCCCccchHHHHHHhhcCCCCCCCCCcCccc
Q 021781 204 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 257 (307)
Q Consensus 204 ~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlCrks~~d 257 (307)
..+..|-||+.-++. .+++||||+|+..|+.+-+. ...-||+||-.+..
T Consensus 82 ~sef~c~vc~~~l~~----pv~tpcghs~c~~Cl~r~ld-~~~~cp~Cr~~l~e 130 (398)
T KOG4159|consen 82 RSEFECCVCSRALYP----PVVTPCGHSFCLECLDRSLD-QETECPLCRDELVE 130 (398)
T ss_pred cchhhhhhhHhhcCC----CccccccccccHHHHHHHhc-cCCCCccccccccc
Confidence 457889999875443 45669999999999999766 45779999998874
No 75
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.50 E-value=0.18 Score=47.58 Aligned_cols=52 Identities=31% Similarity=0.654 Sum_probs=41.2
Q ss_pred CCCCCCcccccccccCCceeEEcCCCCccchHHHHHHhhc-------CCCCCCCCCcCccc
Q 021781 204 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH-------HQYACPICSKSVCD 257 (307)
Q Consensus 204 ~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~-------~~~~CPlCrks~~d 257 (307)
....+|..|.-.|.. + +.+.|.|=|.||-.|+++|... ..|.||-|..++.+
T Consensus 48 DY~pNC~LC~t~La~-g-dt~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFP 106 (299)
T KOG3970|consen 48 DYNPNCRLCNTPLAS-G-DTTRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFP 106 (299)
T ss_pred CCCCCCceeCCcccc-C-cceeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCC
Confidence 456799999876543 3 4566889999999999999753 25899999999863
No 76
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.48 E-value=0.02 Score=55.40 Aligned_cols=55 Identities=27% Similarity=0.690 Sum_probs=37.4
Q ss_pred cccccccCCCC---CCCCcccccccccCCceeEEcCCCCcc-chHHHHHHhhcCCCCCCCCCcCccch
Q 021781 195 KNSHPCVEGAM---HHDCPVCCEYLFETRQDVIVLPCGHTI-HKNCLKEMREHHQYACPICSKSVCDM 258 (307)
Q Consensus 195 ~~~H~CiE~~~---~~~CPIClE~lf~s~~~v~~LpCGH~f-H~~Ci~~wl~~~~~~CPlCrks~~dm 258 (307)
++.|.+-.... +..|.||++ .+.+-++|+|||.. +.+|-..+ ..|||||+-+...
T Consensus 286 k~~~g~~~~~s~~~~~LC~ICmD----aP~DCvfLeCGHmVtCt~CGkrm-----~eCPICRqyi~rv 344 (350)
T KOG4275|consen 286 KGNDGEQHSRSLATRRLCAICMD----APRDCVFLECGHMVTCTKCGKRM-----NECPICRQYIVRV 344 (350)
T ss_pred hcccccccccchhHHHHHHHHhc----CCcceEEeecCcEEeehhhcccc-----ccCchHHHHHHHH
Confidence 34444443333 789999998 46678999999973 55555433 2699999876543
No 77
>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=92.25 E-value=0.082 Score=41.07 Aligned_cols=36 Identities=28% Similarity=0.813 Sum_probs=24.8
Q ss_pred ceeeeCCCCccccccccCcCCCCcc--------ceEecCccccc
Q 021781 120 NQVICSLCGTEQKVQQVCVNCGVCM--------GEYFCESCKLF 155 (307)
Q Consensus 120 ~~v~C~~C~~eQ~v~~~C~~Cg~~f--------a~YfC~~Ckl~ 155 (307)
....|..|+..-.....||.||..+ +.|||..|+=.
T Consensus 16 ~~~~C~~C~~~~~~~a~CPdC~~~Le~LkACGAvdYFC~~c~gL 59 (70)
T PF07191_consen 16 GHYHCEACQKDYKKEAFCPDCGQPLEVLKACGAVDYFCNHCHGL 59 (70)
T ss_dssp TEEEETTT--EEEEEEE-TTT-SB-EEEEETTEEEEE-TTTT-E
T ss_pred CEEECccccccceecccCCCcccHHHHHHHhcccceeeccCCce
Confidence 5788999999888888999999887 68999999744
No 78
>PF04641 Rtf2: Rtf2 RING-finger
Probab=92.21 E-value=0.15 Score=47.94 Aligned_cols=51 Identities=27% Similarity=0.680 Sum_probs=40.1
Q ss_pred CCCCCCCcccccccccCCceeEEc-CCCCccchHHHHHHhhcCCCCCCCCCcCcc
Q 021781 203 GAMHHDCPVCCEYLFETRQDVIVL-PCGHTIHKNCLKEMREHHQYACPICSKSVC 256 (307)
Q Consensus 203 ~~~~~~CPIClE~lf~s~~~v~~L-pCGH~fH~~Ci~~wl~~~~~~CPlCrks~~ 256 (307)
......|||....| ++....+.| ||||+|-..++++.- ....||+|.+++.
T Consensus 110 ~~~~~~CPvt~~~~-~~~~~fv~l~~cG~V~s~~alke~k--~~~~Cp~c~~~f~ 161 (260)
T PF04641_consen 110 SEGRFICPVTGKEF-NGKHKFVYLRPCGCVFSEKALKELK--KSKKCPVCGKPFT 161 (260)
T ss_pred CCceeECCCCCccc-CCceeEEEEcCCCCEeeHHHHHhhc--ccccccccCCccc
Confidence 45678999999865 444455555 999999999999984 3467999999976
No 79
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=91.97 E-value=0.11 Score=39.27 Aligned_cols=45 Identities=33% Similarity=0.878 Sum_probs=33.3
Q ss_pred eeeeCCCCcccccc-----ccCcCCCCccceEecCccccccCCCCCCeecCCCCCc
Q 021781 121 QVICSLCGTEQKVQ-----QVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGI 171 (307)
Q Consensus 121 ~v~C~~C~~eQ~v~-----~~C~~Cg~~fa~YfC~~Ckl~ddd~~k~~yHC~~Cgi 171 (307)
...|..|+.+-.+. -.|||||... =|-|.+|+.+.+ +|.|++||+
T Consensus 9 ~~~CtSCg~~i~p~e~~v~F~CPnCGe~~-I~Rc~~CRk~g~-----~Y~Cp~CGF 58 (61)
T COG2888 9 PPVCTSCGREIAPGETAVKFPCPNCGEVE-IYRCAKCRKLGN-----PYRCPKCGF 58 (61)
T ss_pred CceeccCCCEeccCCceeEeeCCCCCcee-eehhhhHHHcCC-----ceECCCcCc
Confidence 46799999876442 3599999443 366889988754 799999985
No 80
>PF12773 DZR: Double zinc ribbon
Probab=91.90 E-value=0.16 Score=35.69 Aligned_cols=22 Identities=32% Similarity=0.845 Sum_probs=15.5
Q ss_pred eCCCCccccc-cccCcCCCCccc
Q 021781 124 CSLCGTEQKV-QQVCVNCGVCMG 145 (307)
Q Consensus 124 C~~C~~eQ~v-~~~C~~Cg~~fa 145 (307)
|..|+++.+. +..|++||..+.
T Consensus 1 Cp~Cg~~~~~~~~fC~~CG~~l~ 23 (50)
T PF12773_consen 1 CPHCGTPNPDDAKFCPHCGTPLP 23 (50)
T ss_pred CCCcCCcCCccccCChhhcCChh
Confidence 5667777554 567888888776
No 81
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=91.46 E-value=0.11 Score=48.08 Aligned_cols=60 Identities=20% Similarity=0.449 Sum_probs=43.1
Q ss_pred CCCCcccccccccCCceeEEcCCCCccchHHHHHHhhcCCCCCCCCCcCccchhHHHHhhHHHHH
Q 021781 206 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCDMSKVWEKYDREIA 270 (307)
Q Consensus 206 ~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlCrks~~dm~~~~~~lD~eia 270 (307)
...|.||.++ |.+ .++..|||.|+..|+-.-.+ ....|-+|.+..--.......+++.+.
T Consensus 196 PF~C~iCKkd-y~s---pvvt~CGH~FC~~Cai~~y~-kg~~C~~Cgk~t~G~f~V~~d~~kmL~ 255 (259)
T COG5152 196 PFLCGICKKD-YES---PVVTECGHSFCSLCAIRKYQ-KGDECGVCGKATYGRFWVVSDLQKMLN 255 (259)
T ss_pred ceeehhchhh-ccc---hhhhhcchhHHHHHHHHHhc-cCCcceecchhhccceeHHhhHHHHHh
Confidence 4689999986 554 46678999999999877555 358899999987543333445555543
No 82
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.46 E-value=0.13 Score=49.83 Aligned_cols=63 Identities=19% Similarity=0.448 Sum_probs=45.2
Q ss_pred CCCCCCcccccccccCCceeEEcCCCCccchHHHHHHhhcCCCCCCCCCcCccchhHHHHhhHHHHHc
Q 021781 204 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCDMSKVWEKYDREIAA 271 (307)
Q Consensus 204 ~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlCrks~~dm~~~~~~lD~eia~ 271 (307)
.....|-||.+++.. .++-.|||.|+..|...-++. ...|++|.+.+-........|...|..
T Consensus 239 ~~Pf~c~icr~~f~~----pVvt~c~h~fc~~ca~~~~qk-~~~c~vC~~~t~g~~~~akeL~~~L~~ 301 (313)
T KOG1813|consen 239 LLPFKCFICRKYFYR----PVVTKCGHYFCEVCALKPYQK-GEKCYVCSQQTHGSFNVAKELLVSLKL 301 (313)
T ss_pred cCCcccccccccccc----chhhcCCceeehhhhcccccc-CCcceecccccccccchHHHHHHHHHh
Confidence 456779999997543 467799999999999887663 588999999886433333344444443
No 83
>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=91.18 E-value=0.21 Score=44.45 Aligned_cols=33 Identities=33% Similarity=0.893 Sum_probs=23.6
Q ss_pred CCCCcccccccccCCceeEEcCCC-C------------ccchHHHHHHhh
Q 021781 206 HHDCPVCCEYLFETRQDVIVLPCG-H------------TIHKNCLKEMRE 242 (307)
Q Consensus 206 ~~~CPIClE~lf~s~~~v~~LpCG-H------------~fH~~Ci~~wl~ 242 (307)
+..||||||. +-..++|-|. | .-|..||+++-+
T Consensus 2 d~~CpICme~----PHNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkk 47 (162)
T PF07800_consen 2 DVTCPICMEH----PHNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKK 47 (162)
T ss_pred CccCceeccC----CCceEEEEeccccCCccccccCCccchhHHHHHHHH
Confidence 4589999995 3345677773 2 268899999865
No 84
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.75 E-value=0.15 Score=51.33 Aligned_cols=49 Identities=29% Similarity=0.492 Sum_probs=38.0
Q ss_pred CCCCCcccccccccCCceeEEcCCCCccchHHHHHHhhc-------CCCCCCCCCcC
Q 021781 205 MHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH-------HQYACPICSKS 254 (307)
Q Consensus 205 ~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~-------~~~~CPlCrks 254 (307)
+-..|-||++. +........|||+|+|++.|+..|... ...+||-+.-.
T Consensus 183 slf~C~ICf~e-~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C~ 238 (445)
T KOG1814|consen 183 SLFDCCICFEE-QMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCG 238 (445)
T ss_pred hcccceeeehh-hcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCCc
Confidence 35789999984 655567889999999999999998742 34669876643
No 85
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.55 E-value=0.2 Score=50.16 Aligned_cols=48 Identities=29% Similarity=0.647 Sum_probs=40.0
Q ss_pred CCCcccccccccCCceeEEcCCCCccchHHHHHHhhcCC--CCCCCCCcCc
Q 021781 207 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQ--YACPICSKSV 255 (307)
Q Consensus 207 ~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~--~~CPlCrks~ 255 (307)
..|||=.|- .+...|++.|.|||++-++-+.++.+.+. ++||.|-...
T Consensus 335 F~CPVlKeq-tsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~e~ 384 (394)
T KOG2817|consen 335 FICPVLKEQ-TSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPVEQ 384 (394)
T ss_pred eecccchhh-ccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCccc
Confidence 579998884 55567889999999999999999988776 8899997543
No 86
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=89.91 E-value=0.14 Score=53.37 Aligned_cols=54 Identities=26% Similarity=0.571 Sum_probs=43.2
Q ss_pred cccCCCCCCCCcccccccccCCceeEEcCCCCccchHHHHHHhhc----CCCCCCCCCcCcc
Q 021781 199 PCVEGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH----HQYACPICSKSVC 256 (307)
Q Consensus 199 ~CiE~~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~----~~~~CPlCrks~~ 256 (307)
.=.|+..+..|-+|-++ .++++.-.|.|.|++-|+.+|+.. .+.+||+|.+.+.
T Consensus 529 ~~~enk~~~~C~lc~d~----aed~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~Ls 586 (791)
T KOG1002|consen 529 LPDENKGEVECGLCHDP----AEDYIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLS 586 (791)
T ss_pred CCccccCceeecccCCh----hhhhHhhhhhHHHHHHHHHHHHHhhhcccCCCCcccccccc
Confidence 34577788899999985 344677799999999999998753 4588999998875
No 87
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=89.41 E-value=0.37 Score=45.97 Aligned_cols=53 Identities=26% Similarity=0.527 Sum_probs=43.5
Q ss_pred CCCCCCCcccccccccCCceeEEc-CCCCccchHHHHHHhhcCCCCCCCCCcCccc
Q 021781 203 GAMHHDCPVCCEYLFETRQDVIVL-PCGHTIHKNCLKEMREHHQYACPICSKSVCD 257 (307)
Q Consensus 203 ~~~~~~CPIClE~lf~s~~~v~~L-pCGH~fH~~Ci~~wl~~~~~~CPlCrks~~d 257 (307)
.+....||||.+.|.+ ..+..+| ||||++..+|.++++.. ...||+|.+++.+
T Consensus 218 ~s~ryiCpvtrd~LtN-t~~ca~Lr~sg~Vv~~ecvEklir~-D~v~pv~d~plkd 271 (303)
T KOG3039|consen 218 ASKRYICPVTRDTLTN-TTPCAVLRPSGHVVTKECVEKLIRK-DMVDPVTDKPLKD 271 (303)
T ss_pred hccceecccchhhhcC-ccceEEeccCCcEeeHHHHHHhccc-cccccCCCCcCcc
Confidence 3457899999997655 4455555 99999999999999984 6899999999875
No 88
>PHA02862 5L protein; Provisional
Probab=89.35 E-value=0.26 Score=43.45 Aligned_cols=46 Identities=17% Similarity=0.466 Sum_probs=33.4
Q ss_pred CCCCcccccccccCCceeEEcCCC-----CccchHHHHHHhhcC-CCCCCCCCcCcc
Q 021781 206 HHDCPVCCEYLFETRQDVIVLPCG-----HTIHKNCLKEMREHH-QYACPICSKSVC 256 (307)
Q Consensus 206 ~~~CPIClE~lf~s~~~v~~LpCG-----H~fH~~Ci~~wl~~~-~~~CPlCrks~~ 256 (307)
...|=||.+.- .+. .-||. -..|++|+++|+... +..||+|+.++.
T Consensus 2 ~diCWIC~~~~---~e~--~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~ 53 (156)
T PHA02862 2 SDICWICNDVC---DER--NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYN 53 (156)
T ss_pred CCEEEEecCcC---CCC--cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEE
Confidence 46788998741 122 34664 569999999999763 456999998875
No 89
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=88.00 E-value=0.46 Score=42.37 Aligned_cols=48 Identities=25% Similarity=0.562 Sum_probs=34.1
Q ss_pred CCCCCCcccccccccCCceeEEcCCC--C---ccchHHHHHHhhcC-CCCCCCCCcCcc
Q 021781 204 AMHHDCPVCCEYLFETRQDVIVLPCG--H---TIHKNCLKEMREHH-QYACPICSKSVC 256 (307)
Q Consensus 204 ~~~~~CPIClE~lf~s~~~v~~LpCG--H---~fH~~Ci~~wl~~~-~~~CPlCrks~~ 256 (307)
.++..|-||.+.- +. ..-||. . ..|++|++.|+..+ ..+||+|+..+.
T Consensus 6 ~~~~~CRIC~~~~---~~--~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~ 59 (162)
T PHA02825 6 LMDKCCWICKDEY---DV--VTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYN 59 (162)
T ss_pred CCCCeeEecCCCC---CC--ccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEE
Confidence 3467899998752 11 224664 3 56999999999764 466999998764
No 90
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=87.95 E-value=0.15 Score=49.93 Aligned_cols=49 Identities=29% Similarity=0.673 Sum_probs=40.4
Q ss_pred CCCCCCcccccccccCCceeEEcCCCCccchHHHHHHhhcCCCCCCCCCcCcc
Q 021781 204 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 256 (307)
Q Consensus 204 ~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlCrks~~ 256 (307)
.....|++|..||.+. ..+.-|=|+|++.||-++|.. +..||.|.-.+.
T Consensus 13 n~~itC~LC~GYliDA---TTI~eCLHTFCkSCivk~l~~-~~~CP~C~i~ih 61 (331)
T KOG2660|consen 13 NPHITCRLCGGYLIDA---TTITECLHTFCKSCIVKYLEE-SKYCPTCDIVIH 61 (331)
T ss_pred ccceehhhccceeecc---hhHHHHHHHHHHHHHHHHHHH-hccCCccceecc
Confidence 3456899999998764 345579999999999999986 789999997764
No 91
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=87.64 E-value=0.26 Score=30.81 Aligned_cols=24 Identities=33% Similarity=0.908 Sum_probs=18.3
Q ss_pred eeeeCCCCccccc-cccCcCCCCcc
Q 021781 121 QVICSLCGTEQKV-QQVCVNCGVCM 144 (307)
Q Consensus 121 ~v~C~~C~~eQ~v-~~~C~~Cg~~f 144 (307)
++.|..|+++-+. +..|++||+.+
T Consensus 2 ~~~Cp~Cg~~~~~~~~fC~~CG~~L 26 (26)
T PF13248_consen 2 EMFCPNCGAEIDPDAKFCPNCGAKL 26 (26)
T ss_pred cCCCcccCCcCCcccccChhhCCCC
Confidence 4678999987443 67899999864
No 92
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=87.60 E-value=0.55 Score=46.82 Aligned_cols=66 Identities=23% Similarity=0.450 Sum_probs=44.3
Q ss_pred cceeeccccccccccCCCCCCCCcccccccccCCceeEEcCCCCccchHHHHHHhhc-CCCCCCCCCcCcc
Q 021781 187 RCCYSMLLKNSHPCVEGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH-HQYACPICSKSVC 256 (307)
Q Consensus 187 ~~C~s~~l~~~H~CiE~~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~-~~~~CPlCrks~~ 256 (307)
+.|....|-++-.=........|-||.+. ...+.++||||.++-.|.-....- ..-.||+||..+.
T Consensus 42 nlsaEPnlttsSaddtDEen~~C~ICA~~----~TYs~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~e 108 (493)
T COG5236 42 NLSAEPNLTTSSADDTDEENMNCQICAGS----TTYSARYPCGHQICHACAVRLRALYMQKGCPLCRTETE 108 (493)
T ss_pred ccccCCccccccccccccccceeEEecCC----ceEEEeccCCchHHHHHHHHHHHHHhccCCCccccccc
Confidence 44554444433333334457899999984 334678899999999998764322 2456999998875
No 93
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.37 E-value=0.22 Score=52.79 Aligned_cols=44 Identities=27% Similarity=0.704 Sum_probs=36.3
Q ss_pred CCCcccccccccCCceeEEcCCCCccchHHHHHHhhcCCCCCCCCCcC
Q 021781 207 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKS 254 (307)
Q Consensus 207 ~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlCrks 254 (307)
..|+||+..++.++...+.|-|||++++.|++... +.+|| |..+
T Consensus 12 l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~ly---n~scp-~~~D 55 (861)
T KOG3161|consen 12 LLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLY---NASCP-TKRD 55 (861)
T ss_pred hhchHHHHHHHHHhcCcccccccchHHHHHHHhHh---hccCC-CCcc
Confidence 47999988788888888999999999999998864 46788 5543
No 94
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=86.74 E-value=0.49 Score=51.52 Aligned_cols=43 Identities=28% Similarity=0.710 Sum_probs=32.1
Q ss_pred CCCcccccccccCCceeEEcCCCCccchHHHHHHhhcCCCCCCCCCcCcc
Q 021781 207 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 256 (307)
Q Consensus 207 ~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlCrks~~ 256 (307)
..|..|--.|. -|.+...|||.||++|+. .....||-|+-...
T Consensus 841 skCs~C~~~Ld---lP~VhF~CgHsyHqhC~e----~~~~~CP~C~~e~~ 883 (933)
T KOG2114|consen 841 SKCSACEGTLD---LPFVHFLCGHSYHQHCLE----DKEDKCPKCLPELR 883 (933)
T ss_pred eeecccCCccc---cceeeeecccHHHHHhhc----cCcccCCccchhhh
Confidence 36777765432 357778899999999998 34577999998554
No 95
>PRK04023 DNA polymerase II large subunit; Validated
Probab=86.46 E-value=0.59 Score=51.89 Aligned_cols=31 Identities=29% Similarity=0.676 Sum_probs=13.9
Q ss_pred cCcCCCCccceEecCccccccCCCCCCeecCCCCC
Q 021781 136 VCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCG 170 (307)
Q Consensus 136 ~C~~Cg~~fa~YfC~~Ckl~ddd~~k~~yHC~~Cg 170 (307)
.|+.||......+|+.|.-. ...+|.|+.||
T Consensus 628 fCpsCG~~t~~frCP~CG~~----Te~i~fCP~CG 658 (1121)
T PRK04023 628 KCPSCGKETFYRRCPFCGTH----TEPVYRCPRCG 658 (1121)
T ss_pred cCCCCCCcCCcccCCCCCCC----CCcceeCcccc
Confidence 34444444444444444322 23445555553
No 96
>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=85.37 E-value=0.59 Score=32.68 Aligned_cols=25 Identities=32% Similarity=0.886 Sum_probs=15.3
Q ss_pred CCCCccchHHHHHHhhcCC-CCCCCC
Q 021781 227 PCGHTIHKNCLKEMREHHQ-YACPIC 251 (307)
Q Consensus 227 pCGH~fH~~Ci~~wl~~~~-~~CPlC 251 (307)
.|+=.+|..|++.|++..+ .+||.|
T Consensus 18 ~C~~r~H~~C~~~y~r~~~~~~CP~C 43 (43)
T PF08746_consen 18 DCNVRLHDDCFKKYFRHRSNPKCPNC 43 (43)
T ss_dssp -S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred ccCchHHHHHHHHHHhcCCCCCCcCC
Confidence 4777899999999987633 369987
No 97
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=84.77 E-value=0.59 Score=50.57 Aligned_cols=44 Identities=23% Similarity=0.518 Sum_probs=31.6
Q ss_pred CCCCCCcccccccccCCceeEEcCCCCccchHHHHHHhhcCCCCCCC
Q 021781 204 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPI 250 (307)
Q Consensus 204 ~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPl 250 (307)
.....|.||--.+.. ...+-+.|||.+|..|+.+|++. .-.||-
T Consensus 1026 ~~~~~C~~C~l~V~g--ss~~Cg~C~Hv~H~sc~~eWf~~-gd~Cps 1069 (1081)
T KOG0309|consen 1026 GFTFQCAICHLAVRG--SSNFCGTCGHVGHTSCMMEWFRT-GDVCPS 1069 (1081)
T ss_pred cceeeeeeEeeEeec--cchhhccccccccHHHHHHHHhc-CCcCCC
Confidence 344558888744333 33556789999999999999985 457774
No 98
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=84.47 E-value=0.62 Score=45.63 Aligned_cols=44 Identities=30% Similarity=0.721 Sum_probs=35.1
Q ss_pred CCCcccccccccCCceeEEcCCCCccchHHHHHHhhcCCCCCCCCCc
Q 021781 207 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSK 253 (307)
Q Consensus 207 ~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlCrk 253 (307)
..||.|.--+. .++..--|||.|+.+||..-|....+.||.|.+
T Consensus 275 LkCplc~~Llr---np~kT~cC~~~fc~eci~~al~dsDf~CpnC~r 318 (427)
T COG5222 275 LKCPLCHCLLR---NPMKTPCCGHTFCDECIGTALLDSDFKCPNCSR 318 (427)
T ss_pred ccCcchhhhhh---CcccCccccchHHHHHHhhhhhhccccCCCccc
Confidence 68999987432 345665789999999999876666799999987
No 99
>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=84.07 E-value=0.45 Score=34.55 Aligned_cols=32 Identities=34% Similarity=0.760 Sum_probs=22.6
Q ss_pred EcCCC-CccchHHHHHHhhcCCCCCCCCCcCccc
Q 021781 225 VLPCG-HTIHKNCLKEMREHHQYACPICSKSVCD 257 (307)
Q Consensus 225 ~LpCG-H~fH~~Ci~~wl~~~~~~CPlCrks~~d 257 (307)
.+.|. |.++..|+..+++. +..||+|.+++..
T Consensus 15 Li~C~dHYLCl~CLt~ml~~-s~~C~iC~~~LPt 47 (50)
T PF03854_consen 15 LIKCSDHYLCLNCLTLMLSR-SDRCPICGKPLPT 47 (50)
T ss_dssp EEE-SS-EEEHHHHHHT-SS-SSEETTTTEE---
T ss_pred eeeecchhHHHHHHHHHhcc-ccCCCcccCcCcc
Confidence 45785 99999999999985 6899999998753
No 100
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=83.28 E-value=0.58 Score=28.68 Aligned_cols=21 Identities=38% Similarity=0.956 Sum_probs=15.1
Q ss_pred eCCCCcccc-ccccCcCCCCcc
Q 021781 124 CSLCGTEQK-VQQVCVNCGVCM 144 (307)
Q Consensus 124 C~~C~~eQ~-v~~~C~~Cg~~f 144 (307)
|..|+.+.+ .+..|++||..+
T Consensus 2 Cp~CG~~~~~~~~fC~~CG~~l 23 (23)
T PF13240_consen 2 CPNCGAEIEDDAKFCPNCGTPL 23 (23)
T ss_pred CcccCCCCCCcCcchhhhCCcC
Confidence 677887744 467788888764
No 101
>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=83.21 E-value=0.44 Score=45.32 Aligned_cols=51 Identities=25% Similarity=0.621 Sum_probs=40.5
Q ss_pred CCCCcccccccccCCceeEEc-C-CCCccchHHHHHHhhcCCCCCC--CCCcCcc
Q 021781 206 HHDCPVCCEYLFETRQDVIVL-P-CGHTIHKNCLKEMREHHQYACP--ICSKSVC 256 (307)
Q Consensus 206 ~~~CPIClE~lf~s~~~v~~L-p-CGH~fH~~Ci~~wl~~~~~~CP--lCrks~~ 256 (307)
+..||||..+.+.+++-..++ | |=|.++.+|.+..++.+.-.|| -|.+.+.
T Consensus 10 d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kILR 64 (314)
T COG5220 10 DRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKILR 64 (314)
T ss_pred cccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHHH
Confidence 458999998888776533333 6 9999999999999988777899 8887653
No 102
>PHA00626 hypothetical protein
Probab=83.19 E-value=0.84 Score=34.23 Aligned_cols=29 Identities=24% Similarity=0.668 Sum_probs=15.2
Q ss_pred cCcCCCCc-cceEecCccccccCCCCCCeecCCCCCc
Q 021781 136 VCVNCGVC-MGEYFCESCKLFDDDTSKKQYHCDGCGI 171 (307)
Q Consensus 136 ~C~~Cg~~-fa~YfC~~Ckl~ddd~~k~~yHC~~Cgi 171 (307)
.||+||.. .. -|.+|+.+ .+.|-|++||.
T Consensus 2 ~CP~CGS~~Iv--rcg~cr~~-----snrYkCkdCGY 31 (59)
T PHA00626 2 SCPKCGSGNIA--KEKTMRGW-----SDDYVCCDCGY 31 (59)
T ss_pred CCCCCCCceee--eeceeccc-----CcceEcCCCCC
Confidence 46777663 32 45555554 23455555553
No 103
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=82.63 E-value=0.87 Score=48.55 Aligned_cols=33 Identities=27% Similarity=0.744 Sum_probs=21.4
Q ss_pred eeeCCCCccccc-cccCcCCCCccceEecCcccc
Q 021781 122 VICSLCGTEQKV-QQVCVNCGVCMGEYFCESCKL 154 (307)
Q Consensus 122 v~C~~C~~eQ~v-~~~C~~Cg~~fa~YfC~~Ckl 154 (307)
++|..|+.+.+. +..|++||..+..-.|+.|.-
T Consensus 2 ~~Cp~Cg~~n~~~akFC~~CG~~l~~~~Cp~CG~ 35 (645)
T PRK14559 2 LICPQCQFENPNNNRFCQKCGTSLTHKPCPQCGT 35 (645)
T ss_pred CcCCCCCCcCCCCCccccccCCCCCCCcCCCCCC
Confidence 467777777544 566777777776555666643
No 104
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=81.72 E-value=0.96 Score=37.77 Aligned_cols=27 Identities=33% Similarity=0.918 Sum_probs=20.4
Q ss_pred ccccCcCCCCccceEecCccccccCCCCCCeecCCCCCc
Q 021781 133 VQQVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGI 171 (307)
Q Consensus 133 v~~~C~~Cg~~fa~YfC~~Ckl~ddd~~k~~yHC~~Cgi 171 (307)
....|++||+ ||| |.+|.+-.|++||-
T Consensus 8 tKR~Cp~CG~----------kFY--DLnk~PivCP~CG~ 34 (108)
T PF09538_consen 8 TKRTCPSCGA----------KFY--DLNKDPIVCPKCGT 34 (108)
T ss_pred CcccCCCCcc----------hhc--cCCCCCccCCCCCC
Confidence 3467999998 456 46788999999974
No 105
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=80.33 E-value=0.78 Score=50.18 Aligned_cols=36 Identities=31% Similarity=0.694 Sum_probs=28.8
Q ss_pred CCCCCcccccccccCCceeEEcCCCCccchHHHHHHhh
Q 021781 205 MHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMRE 242 (307)
Q Consensus 205 ~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~ 242 (307)
-...|-+|.-+++. ++-.+.||||.||+.|+.+-..
T Consensus 816 p~d~C~~C~~~ll~--~pF~vf~CgH~FH~~Cl~~~v~ 851 (911)
T KOG2034|consen 816 PQDSCDHCGRPLLI--KPFYVFPCGHCFHRDCLIRHVL 851 (911)
T ss_pred CccchHHhcchhhc--CcceeeeccchHHHHHHHHHHH
Confidence 35789999976654 4678889999999999988553
No 106
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=79.50 E-value=1.8 Score=49.30 Aligned_cols=47 Identities=32% Similarity=0.694 Sum_probs=24.8
Q ss_pred eeeCCCCccccccccCcCCCCcc-ceEecCcccccc-CCCCCCeecCCCCC
Q 021781 122 VICSLCGTEQKVQQVCVNCGVCM-GEYFCESCKLFD-DDTSKKQYHCDGCG 170 (307)
Q Consensus 122 v~C~~C~~eQ~v~~~C~~Cg~~f-a~YfC~~Ckl~d-dd~~k~~yHC~~Cg 170 (307)
..|..|+++-+. ..|+.||... ..|+|+.|..-- .+++. ...|+.||
T Consensus 668 rkCPkCG~~t~~-~fCP~CGs~te~vy~CPsCGaev~~des~-a~~CP~CG 716 (1337)
T PRK14714 668 RRCPSCGTETYE-NRCPDCGTHTEPVYVCPDCGAEVPPDESG-RVECPRCD 716 (1337)
T ss_pred EECCCCCCcccc-ccCcccCCcCCCceeCccCCCccCCCccc-cccCCCCC
Confidence 567777665332 3677776665 345566665421 11122 44566665
No 107
>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=79.22 E-value=1.3 Score=28.01 Aligned_cols=23 Identities=30% Similarity=0.778 Sum_probs=18.0
Q ss_pred eeCCCCccccc-cccCcCCCCccc
Q 021781 123 ICSLCGTEQKV-QQVCVNCGVCMG 145 (307)
Q Consensus 123 ~C~~C~~eQ~v-~~~C~~Cg~~fa 145 (307)
.|..|+.+-+. +..|++||..|.
T Consensus 2 ~CP~C~~~V~~~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCPHCGYDFE 25 (26)
T ss_pred cCCCCcCCchhhcCcCCCCCCCCc
Confidence 37778877665 678999999885
No 108
>PHA03096 p28-like protein; Provisional
Probab=78.51 E-value=1.2 Score=43.02 Aligned_cols=48 Identities=17% Similarity=0.226 Sum_probs=32.2
Q ss_pred CCCcccccccccCC---ceeEEc-CCCCccchHHHHHHhhcC--CCCCCCCCcC
Q 021781 207 HDCPVCCEYLFETR---QDVIVL-PCGHTIHKNCLKEMREHH--QYACPICSKS 254 (307)
Q Consensus 207 ~~CPIClE~lf~s~---~~v~~L-pCGH~fH~~Ci~~wl~~~--~~~CPlCrks 254 (307)
-.|.||+|...... .....| .|.|.|+..|+..|.... .-+||.||.-
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~~ 232 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRRL 232 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCccccch
Confidence 46889988765421 122334 799999999999998753 2346666543
No 109
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=77.94 E-value=1.2 Score=47.80 Aligned_cols=45 Identities=29% Similarity=0.856 Sum_probs=35.8
Q ss_pred CCCcccccccccCCceeEEcCCCCccchHHHHHHhhcCCC-CCCCCCcCcc
Q 021781 207 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQY-ACPICSKSVC 256 (307)
Q Consensus 207 ~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~-~CPlCrks~~ 256 (307)
..|+||++ .+..+..+|||.|+.+|+.+.+..... .||+||..+.
T Consensus 455 ~~c~ic~~-----~~~~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~ 500 (674)
T KOG1001|consen 455 HWCHICCD-----LDSFFITRCGHDFCVECLKKSIQQSENAPCPLCRNVLK 500 (674)
T ss_pred cccccccc-----cccceeecccchHHHHHHHhccccccCCCCcHHHHHHH
Confidence 78999998 234677899999999999997765444 4999996654
No 110
>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=76.43 E-value=1.9 Score=44.38 Aligned_cols=49 Identities=22% Similarity=0.658 Sum_probs=41.1
Q ss_pred eEcCCCCCeecCchhHhhhhcCCCccccCCCCCCcccCceeeeCCCCccccccccCcCCCCc
Q 021781 82 IRAPCCNEIFDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKVQQVCVNCGVC 143 (307)
Q Consensus 82 i~~pCC~k~y~Cr~CHde~~~~~~~~~~~~H~ldR~~v~~v~C~~C~~eQ~v~~~C~~Cg~~ 143 (307)
+.|.-||....|.+|.--.. -|. ....+.|-.|+..+++...||+||..
T Consensus 214 ~~C~~Cg~~~~C~~C~~~l~---------~h~----~~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 214 LLCRSCGYILCCPNCDVSLT---------YHK----KEGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred eEhhhCcCccCCCCCCCceE---------Eec----CCCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 78999999999999976554 242 24589999999999999999999885
No 111
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=76.18 E-value=1.5 Score=47.86 Aligned_cols=48 Identities=29% Similarity=0.678 Sum_probs=35.0
Q ss_pred CCCCCcccccccccCCceeEEcC---CCCccchHHHHHHhhc------CCCCCCCCCcCc
Q 021781 205 MHHDCPVCCEYLFETRQDVIVLP---CGHTIHKNCLKEMREH------HQYACPICSKSV 255 (307)
Q Consensus 205 ~~~~CPIClE~lf~s~~~v~~Lp---CGH~fH~~Ci~~wl~~------~~~~CPlCrks~ 255 (307)
....|.||.|.+..+ . -++. |=|+||..||++|.+. ...+||-|+...
T Consensus 190 ~~yeCmIC~e~I~~t-~--~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv~ 246 (950)
T KOG1952|consen 190 RKYECMICTERIKRT-A--PVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSVS 246 (950)
T ss_pred CceEEEEeeeecccc-C--CceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccchh
Confidence 357899999976443 2 2344 4599999999999864 247799999433
No 112
>PF12773 DZR: Double zinc ribbon
Probab=74.75 E-value=2.2 Score=29.87 Aligned_cols=32 Identities=34% Similarity=0.889 Sum_probs=17.1
Q ss_pred eeeeCCCCcccc--c--cccCcCCCCcc--ceEecCcc
Q 021781 121 QVICSLCGTEQK--V--QQVCVNCGVCM--GEYFCESC 152 (307)
Q Consensus 121 ~v~C~~C~~eQ~--v--~~~C~~Cg~~f--a~YfC~~C 152 (307)
.-.|..|++..+ . ...|++||... +..||..|
T Consensus 12 ~~fC~~CG~~l~~~~~~~~~C~~Cg~~~~~~~~fC~~C 49 (50)
T PF12773_consen 12 AKFCPHCGTPLPPPDQSKKICPNCGAENPPNAKFCPNC 49 (50)
T ss_pred ccCChhhcCChhhccCCCCCCcCCcCCCcCCcCccCcc
Confidence 456677766655 1 24577776653 33344443
No 113
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=73.81 E-value=1.2 Score=42.86 Aligned_cols=53 Identities=25% Similarity=0.683 Sum_probs=32.5
Q ss_pred ceeeeCCCCccccccccCcCCCCccceEecCccccc-cCCC---CCCeecCCCCCcccccCCccceecCCccceeec
Q 021781 120 NQVICSLCGTEQKVQQVCVNCGVCMGEYFCESCKLF-DDDT---SKKQYHCDGCGICRIGGCDNFFHCNKCRCCYSM 192 (307)
Q Consensus 120 ~~v~C~~C~~eQ~v~~~C~~Cg~~fa~YfC~~Ckl~-ddd~---~k~~yHC~~CgiCR~G~~e~ffHC~~C~~C~s~ 192 (307)
.+.+|-.|+....+ .--|+|-|.+|+-. |+++ .-++|| -.-|.|.+||-=+..
T Consensus 119 gr~LC~~Cn~k~Ka--------~~~g~YvC~KCh~~iD~~~l~fr~d~yH------------~yHFkCt~C~keL~s 175 (332)
T KOG2272|consen 119 GRALCRECNQKEKA--------KGRGRYVCQKCHAHIDEQPLTFRGDPYH------------PYHFKCTTCGKELTS 175 (332)
T ss_pred chHHhhhhhhhhcc--------cccceeehhhhhhhcccccccccCCCCC------------ccceecccccccccc
Confidence 35666666654433 23589999999744 5543 224554 256778888866543
No 114
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=73.39 E-value=2.3 Score=42.61 Aligned_cols=51 Identities=22% Similarity=0.544 Sum_probs=40.9
Q ss_pred CCCCCCCCcccccccccCCceeEEcCCCCccchHHHHHHhhcCCCCCCCCCcCccc
Q 021781 202 EGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 257 (307)
Q Consensus 202 E~~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlCrks~~d 257 (307)
..+.+..||||.-. +-..+.-||||.-+..||.+.+.. ...|=.|+.++.+
T Consensus 418 p~sEd~lCpICyA~----pi~Avf~PC~H~SC~~CI~qHlmN-~k~CFfCktTv~~ 468 (489)
T KOG4692|consen 418 PDSEDNLCPICYAG----PINAVFAPCSHRSCYGCITQHLMN-CKRCFFCKTTVID 468 (489)
T ss_pred CCcccccCcceecc----cchhhccCCCCchHHHHHHHHHhc-CCeeeEecceeee
Confidence 34567899999852 334577799999999999998874 5789999988876
No 115
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=73.37 E-value=3.7 Score=30.49 Aligned_cols=36 Identities=25% Similarity=0.628 Sum_probs=27.0
Q ss_pred CCCCCcccccccccCCceeEEcCCCCccchHHHHHH
Q 021781 205 MHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEM 240 (307)
Q Consensus 205 ~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~w 240 (307)
+...|++|.+.|.+..+-++=--||=.+|+.|..+.
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~ 39 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKA 39 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCCCcccHHHHhhC
Confidence 457899999986655544444579999999998553
No 116
>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=72.17 E-value=2.9 Score=30.04 Aligned_cols=44 Identities=27% Similarity=0.544 Sum_probs=19.8
Q ss_pred CCCcccccccccCCceeEEcCCCCccchHHHHHHhh----cCCCCCCCCCcC
Q 021781 207 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMRE----HHQYACPICSKS 254 (307)
Q Consensus 207 ~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~----~~~~~CPlCrks 254 (307)
..|||-...+. .+++...|.|.-+.+ ++.||. .....||+|+++
T Consensus 3 L~CPls~~~i~---~P~Rg~~C~H~~CFD-l~~fl~~~~~~~~W~CPiC~~~ 50 (50)
T PF02891_consen 3 LRCPLSFQRIR---IPVRGKNCKHLQCFD-LESFLESNQRTPKWKCPICNKP 50 (50)
T ss_dssp SB-TTTSSB-S---SEEEETT--SS--EE-HHHHHHHHHHS---B-TTT---
T ss_pred eeCCCCCCEEE---eCccCCcCcccceEC-HHHHHHHhhccCCeECcCCcCc
Confidence 36899887653 367888999873221 223443 245789999874
No 117
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=72.13 E-value=2.7 Score=41.56 Aligned_cols=46 Identities=33% Similarity=0.746 Sum_probs=37.4
Q ss_pred CCCcccccccccCCceeEEcCCCCccchHHHHHHhhcC--CCCCCCCCc
Q 021781 207 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHH--QYACPICSK 253 (307)
Q Consensus 207 ~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~--~~~CPlCrk 253 (307)
..|||=.| +-+...+++.|.|||.+=.+-+...-+.+ ++.||.|--
T Consensus 337 FiCPVlKe-~~t~ENpP~ml~CgHVIskeal~~LS~nG~~~FKCPYCP~ 384 (396)
T COG5109 337 FICPVLKE-LCTDENPPVMLECGHVISKEALSVLSQNGVLSFKCPYCPE 384 (396)
T ss_pred eeccccHh-hhcccCCCeeeeccceeeHHHHHHHhhcCcEEeeCCCCCc
Confidence 57999887 46666788999999999999999987654 477999963
No 118
>PRK04023 DNA polymerase II large subunit; Validated
Probab=71.08 E-value=3.3 Score=46.28 Aligned_cols=48 Identities=27% Similarity=0.643 Sum_probs=36.5
Q ss_pred eeeeCCCCccccccccCcCCCCc-cceEecCccccccCCCCCCeecCCCCCcccc
Q 021781 121 QVICSLCGTEQKVQQVCVNCGVC-MGEYFCESCKLFDDDTSKKQYHCDGCGICRI 174 (307)
Q Consensus 121 ~v~C~~C~~eQ~v~~~C~~Cg~~-fa~YfC~~Ckl~ddd~~k~~yHC~~CgiCR~ 174 (307)
.-.|..|+++. +...|++||.. -.-|||+.|.-- -..|.|+.||.=..
T Consensus 626 ~RfCpsCG~~t-~~frCP~CG~~Te~i~fCP~CG~~-----~~~y~CPKCG~El~ 674 (1121)
T PRK04023 626 RRKCPSCGKET-FYRRCPFCGTHTEPVYRCPRCGIE-----VEEDECEKCGREPT 674 (1121)
T ss_pred CccCCCCCCcC-CcccCCCCCCCCCcceeCccccCc-----CCCCcCCCCCCCCC
Confidence 45899999986 56799999975 677899999332 33588999996443
No 119
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=71.07 E-value=3.5 Score=44.68 Aligned_cols=54 Identities=24% Similarity=0.568 Sum_probs=43.1
Q ss_pred eEcCCCCCeecCchhHhhhhcCCCccccCCCCCCcccCceeeeCCCCccccccccCcCCCCccceEe
Q 021781 82 IRAPCCNEIFDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKVQQVCVNCGVCMGEYF 148 (307)
Q Consensus 82 i~~pCC~k~y~Cr~CHde~~~~~~~~~~~~H~ldR~~v~~v~C~~C~~eQ~v~~~C~~Cg~~fa~Yf 148 (307)
+.|.-||-.+.|++|=.-.. -|. ....+.|-+|+..+++-..|++||...=+|+
T Consensus 436 l~C~~Cg~v~~Cp~Cd~~lt---------~H~----~~~~L~CH~Cg~~~~~p~~Cp~Cgs~~L~~~ 489 (730)
T COG1198 436 LLCRDCGYIAECPNCDSPLT---------LHK----ATGQLRCHYCGYQEPIPQSCPECGSEHLRAV 489 (730)
T ss_pred eecccCCCcccCCCCCcceE---------Eec----CCCeeEeCCCCCCCCCCCCCCCCCCCeeEEe
Confidence 88999999999999954332 121 2478999999999999999999999854443
No 120
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=68.71 E-value=4.3 Score=46.40 Aligned_cols=33 Identities=30% Similarity=0.754 Sum_probs=25.6
Q ss_pred ccCcCCCCccceEecCccccccCCCCCCeecCCCCCc
Q 021781 135 QVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGI 171 (307)
Q Consensus 135 ~~C~~Cg~~fa~YfC~~Ckl~ddd~~k~~yHC~~Cgi 171 (307)
-.||+||......||+.|.-. .+.+|+|+.||.
T Consensus 668 rkCPkCG~~t~~~fCP~CGs~----te~vy~CPsCGa 700 (1337)
T PRK14714 668 RRCPSCGTETYENRCPDCGTH----TEPVYVCPDCGA 700 (1337)
T ss_pred EECCCCCCccccccCcccCCc----CCCceeCccCCC
Confidence 469999998767799999654 245788888876
No 121
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=67.95 E-value=2.5 Score=42.33 Aligned_cols=44 Identities=34% Similarity=0.689 Sum_probs=31.0
Q ss_pred CCCCcccc-cccccCCceeEEcCCCCccchHHHHHHhhc-----CCCCCCC
Q 021781 206 HHDCPVCC-EYLFETRQDVIVLPCGHTIHKNCLKEMREH-----HQYACPI 250 (307)
Q Consensus 206 ~~~CPICl-E~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~-----~~~~CPl 250 (307)
...|.||. ++ ........++.|||.|+.+|+.+++.. ...+||-
T Consensus 146 ~~~C~iC~~e~-~~~~~~f~~~~C~H~fC~~C~k~~iev~~~~~~~~~C~~ 195 (384)
T KOG1812|consen 146 KEECGICFVED-PEAEDMFSVLKCGHRFCKDCVKQHIEVKLLSGTVIRCPH 195 (384)
T ss_pred cccCccCcccc-ccHhhhHHHhcccchhhhHHhHHHhhhhhccCCCccCCC
Confidence 56899999 54 333233336789999999999998873 2455753
No 122
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=67.65 E-value=3 Score=42.85 Aligned_cols=33 Identities=30% Similarity=0.926 Sum_probs=27.1
Q ss_pred CCCCcccccccccCCceeEEcCCCCccchHHHHHHhh
Q 021781 206 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMRE 242 (307)
Q Consensus 206 ~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~ 242 (307)
+..||||.. +|. +.++|||||.+++.|...-+.
T Consensus 4 elkc~vc~~-f~~---epiil~c~h~lc~~ca~~~~~ 36 (699)
T KOG4367|consen 4 ELKCPVCGS-FYR---EPIILPCSHNLCQACARNILV 36 (699)
T ss_pred cccCceehh-hcc---CceEeecccHHHHHHHHhhcc
Confidence 578999998 455 357899999999999987654
No 123
>PRK14873 primosome assembly protein PriA; Provisional
Probab=67.36 E-value=4 Score=43.71 Aligned_cols=49 Identities=22% Similarity=0.483 Sum_probs=39.5
Q ss_pred eEcCCCCCeecCchhHhhhhcCCCccccCCCCCCcccCceeeeCCCCccccccccCcCCCCcc
Q 021781 82 IRAPCCNEIFDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKVQQVCVNCGVCM 144 (307)
Q Consensus 82 i~~pCC~k~y~Cr~CHde~~~~~~~~~~~~H~ldR~~v~~v~C~~C~~eQ~v~~~C~~Cg~~f 144 (307)
+.|.-|+....|.+|.--.. -|. ....+.|-.|+..+ ....|++||...
T Consensus 384 l~C~~Cg~~~~C~~C~~~L~---------~h~----~~~~l~Ch~CG~~~-~p~~Cp~Cgs~~ 432 (665)
T PRK14873 384 LACARCRTPARCRHCTGPLG---------LPS----AGGTPRCRWCGRAA-PDWRCPRCGSDR 432 (665)
T ss_pred eEhhhCcCeeECCCCCCcee---------Eec----CCCeeECCCCcCCC-cCccCCCCcCCc
Confidence 89999999999999987654 132 23579999999976 578999999873
No 124
>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=67.14 E-value=3.5 Score=35.62 Aligned_cols=27 Identities=19% Similarity=0.380 Sum_probs=20.3
Q ss_pred cccCcCCCCccceEecCccccccCCCCCCeecCCCCCcc
Q 021781 134 QQVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGIC 172 (307)
Q Consensus 134 ~~~C~~Cg~~fa~YfC~~Ckl~ddd~~k~~yHC~~CgiC 172 (307)
...|++||+. || |.+|.+-.|++||.=
T Consensus 9 Kr~Cp~cg~k----------FY--DLnk~p~vcP~cg~~ 35 (129)
T TIGR02300 9 KRICPNTGSK----------FY--DLNRRPAVSPYTGEQ 35 (129)
T ss_pred cccCCCcCcc----------cc--ccCCCCccCCCcCCc
Confidence 4579999984 46 457889999998853
No 125
>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=65.74 E-value=4.1 Score=38.74 Aligned_cols=48 Identities=31% Similarity=0.703 Sum_probs=22.8
Q ss_pred CceeeeCCCCccccc-cccCcCCCCccceEecCccccc--cCCCCCCeecCCCCC
Q 021781 119 VNQVICSLCGTEQKV-QQVCVNCGVCMGEYFCESCKLF--DDDTSKKQYHCDGCG 170 (307)
Q Consensus 119 v~~v~C~~C~~eQ~v-~~~C~~Cg~~fa~YfC~~Ckl~--ddd~~k~~yHC~~Cg 170 (307)
.+-..|+.|+++..+ -..|++||..-..-+ .+| ++++.-.++.|+.||
T Consensus 195 ~R~L~Cs~C~t~W~~~R~~Cp~Cg~~~~~~l----~~~~~e~~~~~rve~C~~C~ 245 (290)
T PF04216_consen 195 KRYLHCSLCGTEWRFVRIKCPYCGNTDHEKL----EYFTVEGEPAYRVEVCESCG 245 (290)
T ss_dssp EEEEEETTT--EEE--TTS-TTT---SS-EE----E--------SEEEEEETTTT
T ss_pred cEEEEcCCCCCeeeecCCCCcCCCCCCCcce----eeEecCCCCcEEEEECCccc
Confidence 367999999999887 467999998865544 344 333344455555443
No 126
>PRK05580 primosome assembly protein PriA; Validated
Probab=65.02 E-value=4.6 Score=43.13 Aligned_cols=50 Identities=22% Similarity=0.608 Sum_probs=41.5
Q ss_pred eEcCCCCCeecCchhHhhhhcCCCccccCCCCCCcccCceeeeCCCCccccccccCcCCCCcc
Q 021781 82 IRAPCCNEIFDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKVQQVCVNCGVCM 144 (307)
Q Consensus 82 i~~pCC~k~y~Cr~CHde~~~~~~~~~~~~H~ldR~~v~~v~C~~C~~eQ~v~~~C~~Cg~~f 144 (307)
+.|.-|+....|.+|.--.. -|. ....+.|-.|+..++....|++||...
T Consensus 382 ~~C~~Cg~~~~C~~C~~~l~---------~h~----~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~ 431 (679)
T PRK05580 382 LLCRDCGWVAECPHCDASLT---------LHR----FQRRLRCHHCGYQEPIPKACPECGSTD 431 (679)
T ss_pred eEhhhCcCccCCCCCCCcee---------EEC----CCCeEECCCCcCCCCCCCCCCCCcCCe
Confidence 88999999999999986543 232 246899999999999999999998874
No 127
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=64.84 E-value=6.2 Score=38.16 Aligned_cols=95 Identities=27% Similarity=0.562 Sum_probs=55.8
Q ss_pred CCccceEecCcc-ccccCCC---CCCeecCCCCCcccccCCccceecCCccceeec--cc---cccccccCCCCCCCCcc
Q 021781 141 GVCMGEYFCESC-KLFDDDT---SKKQYHCDGCGICRIGGCDNFFHCNKCRCCYSM--LL---KNSHPCVEGAMHHDCPV 211 (307)
Q Consensus 141 g~~fa~YfC~~C-kl~ddd~---~k~~yHC~~CgiCR~G~~e~ffHC~~C~~C~s~--~l---~~~H~CiE~~~~~~CPI 211 (307)
...-++|-|+.| |-|.... .-+|+||+-= -..-|+|..||-=|.. .| .-+|. ....|+|
T Consensus 125 ~~~~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~-------s~ka~~C~~C~K~YvSmpALkMHirTH~-----l~c~C~i 192 (279)
T KOG2462|consen 125 AAKHPRYKCPECGKSYSTSSNLSRHKQTHRSLD-------SKKAFSCKYCGKVYVSMPALKMHIRTHT-----LPCECGI 192 (279)
T ss_pred cccCCceeccccccccccccccchhhccccccc-------ccccccCCCCCceeeehHHHhhHhhccC-----CCccccc
Confidence 344578888888 6665433 2378888421 2467899999987743 11 12343 4567888
Q ss_pred cccccccCCceeEEcCCCCc-cchHHHHHHhhcCCCCCCCCCcCccchh
Q 021781 212 CCEYLFETRQDVIVLPCGHT-IHKNCLKEMREHHQYACPICSKSVCDMS 259 (307)
Q Consensus 212 ClE~lf~s~~~v~~LpCGH~-fH~~Ci~~wl~~~~~~CPlCrks~~dm~ 259 (307)
|.-. |..+ +|-=||+ .|. .+.-+.||.|+|.|.|.+
T Consensus 193 CGKa-FSRP----WLLQGHiRTHT-------GEKPF~C~hC~kAFADRS 229 (279)
T KOG2462|consen 193 CGKA-FSRP----WLLQGHIRTHT-------GEKPFSCPHCGKAFADRS 229 (279)
T ss_pred cccc-ccch----HHhhccccccc-------CCCCccCCcccchhcchH
Confidence 8863 5421 1111221 111 123477999999999865
No 128
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=62.84 E-value=3.9 Score=43.71 Aligned_cols=34 Identities=29% Similarity=0.706 Sum_probs=18.7
Q ss_pred eeeeCCCCccccccccCcCCCCc--cceEecCccccc
Q 021781 121 QVICSLCGTEQKVQQVCVNCGVC--MGEYFCESCKLF 155 (307)
Q Consensus 121 ~v~C~~C~~eQ~v~~~C~~Cg~~--fa~YfC~~Ckl~ 155 (307)
.-.|..|++.... ..|++||+. .+.-||+.|-..
T Consensus 15 akFC~~CG~~l~~-~~Cp~CG~~~~~~~~fC~~CG~~ 50 (645)
T PRK14559 15 NRFCQKCGTSLTH-KPCPQCGTEVPVDEAHCPNCGAE 50 (645)
T ss_pred CccccccCCCCCC-CcCCCCCCCCCcccccccccCCc
Confidence 3456666665432 356666655 355566666433
No 129
>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=62.66 E-value=5.6 Score=29.52 Aligned_cols=27 Identities=30% Similarity=0.760 Sum_probs=16.5
Q ss_pred cccCcCCCCccceEecCccccccCCCCCCeecCCCCCc
Q 021781 134 QQVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGI 171 (307)
Q Consensus 134 ~~~C~~Cg~~fa~YfC~~Ckl~ddd~~k~~yHC~~Cgi 171 (307)
++.|+.||..... ......|.|+.||.
T Consensus 28 Sq~C~~CG~~~~~-----------~~~~r~~~C~~Cg~ 54 (69)
T PF07282_consen 28 SQTCPRCGHRNKK-----------RRSGRVFTCPNCGF 54 (69)
T ss_pred ccCccCccccccc-----------ccccceEEcCCCCC
Confidence 5678888877655 23344566666654
No 130
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=62.36 E-value=5.7 Score=25.43 Aligned_cols=20 Identities=35% Similarity=0.894 Sum_probs=14.0
Q ss_pred CCCcccccCCcc-ceecCCcc
Q 021781 168 GCGICRIGGCDN-FFHCNKCR 187 (307)
Q Consensus 168 ~CgiCR~G~~e~-ffHC~~C~ 187 (307)
.|++||.-.... +|+|..|+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~ 22 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECC 22 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCC
Confidence 467776654444 88998888
No 131
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=61.67 E-value=6.4 Score=24.97 Aligned_cols=37 Identities=22% Similarity=0.577 Sum_probs=23.1
Q ss_pred CcccccccccCCceeEEcCCCCccchHHHHHHhhcCCCCCCCCCcCcc
Q 021781 209 CPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 256 (307)
Q Consensus 209 CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlCrks~~ 256 (307)
|+.|.+.+..... .+..=|..||.+|+ +|..|++++.
T Consensus 2 C~~C~~~i~~~~~--~~~~~~~~~H~~Cf---------~C~~C~~~L~ 38 (39)
T smart00132 2 CAGCGKPIRGGEL--VLRALGKVWHPECF---------KCSKCGKPLG 38 (39)
T ss_pred ccccCCcccCCcE--EEEeCCccccccCC---------CCcccCCcCc
Confidence 7778776654312 22223788888765 5778887764
No 132
>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=60.56 E-value=1.3 Score=34.53 Aligned_cols=41 Identities=27% Similarity=0.570 Sum_probs=24.6
Q ss_pred CCCcccccccccCCceeEEcCCCCccchHHHHHHhhcCCCCCCCCCcCccc
Q 021781 207 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 257 (307)
Q Consensus 207 ~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlCrks~~d 257 (307)
..||.|...|.... ||..+..|-..+... ..||-|..++..
T Consensus 2 ~~CP~C~~~L~~~~--------~~~~C~~C~~~~~~~--a~CPdC~~~Le~ 42 (70)
T PF07191_consen 2 NTCPKCQQELEWQG--------GHYHCEACQKDYKKE--AFCPDCGQPLEV 42 (70)
T ss_dssp -B-SSS-SBEEEET--------TEEEETTT--EEEEE--EE-TTT-SB-EE
T ss_pred CcCCCCCCccEEeC--------CEEECccccccceec--ccCCCcccHHHH
Confidence 57999998653321 888899999887653 679999998864
No 133
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=60.28 E-value=9.1 Score=30.55 Aligned_cols=53 Identities=17% Similarity=0.434 Sum_probs=24.4
Q ss_pred CCCCCCcccccccccCCceeEEc---CCCCccchHHHHHHhhcCCCCCCCCCcCcc
Q 021781 204 AMHHDCPVCCEYLFETRQDVIVL---PCGHTIHKNCLKEMREHHQYACPICSKSVC 256 (307)
Q Consensus 204 ~~~~~CPIClE~lf~s~~~v~~L---pCGH~fH~~Ci~~wl~~~~~~CPlCrks~~ 256 (307)
.....|-||.|.+-.....-.+. -|+--.++.|++-=.+.++..||.|+....
T Consensus 7 ~~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg~q~CpqCkt~yk 62 (80)
T PF14569_consen 7 LNGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEGNQVCPQCKTRYK 62 (80)
T ss_dssp -SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS-SB-TTT--B--
T ss_pred cCCcccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcCcccccccCCCcc
Confidence 34578999999875443333333 567889999999888888889999996554
No 134
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=58.17 E-value=6.2 Score=38.01 Aligned_cols=70 Identities=24% Similarity=0.529 Sum_probs=44.5
Q ss_pred CCCCCCCCcccccccccCCceeEEcCC---C--CccchHHHHHHhhcC-------CCCCCCCCcCcc----ch---hHHH
Q 021781 202 EGAMHHDCPVCCEYLFETRQDVIVLPC---G--HTIHKNCLKEMREHH-------QYACPICSKSVC----DM---SKVW 262 (307)
Q Consensus 202 E~~~~~~CPIClE~lf~s~~~v~~LpC---G--H~fH~~Ci~~wl~~~-------~~~CPlCrks~~----dm---~~~~ 262 (307)
+...+-.|=||+.--.+.+...-+=|| | |..|..|+..|+.+. .-+||.|+.... .| +...
T Consensus 16 ~~e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYiiv~P~l~~~~~~L 95 (293)
T KOG3053|consen 16 NQELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYIIVFPQLGPFDRVL 95 (293)
T ss_pred ccccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchheeeccccChHHHHH
Confidence 345678899999743333322233477 3 889999999999652 245999998754 23 3344
Q ss_pred HhhHHHHHc
Q 021781 263 EKYDREIAA 271 (307)
Q Consensus 263 ~~lD~eia~ 271 (307)
+.+|..+..
T Consensus 96 e~~d~~i~r 104 (293)
T KOG3053|consen 96 ERLDILIFR 104 (293)
T ss_pred HHhhhHHhh
Confidence 455555544
No 135
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=57.18 E-value=7.7 Score=29.33 Aligned_cols=34 Identities=24% Similarity=0.634 Sum_probs=24.5
Q ss_pred CceeeeCCCCccccccccCcCCCCccceEecCcccc
Q 021781 119 VNQVICSLCGTEQKVQQVCVNCGVCMGEYFCESCKL 154 (307)
Q Consensus 119 v~~v~C~~C~~eQ~v~~~C~~Cg~~fa~YfC~~Ckl 154 (307)
.....|..|+.+--+ .|..|....+.|-|++|-|
T Consensus 23 ~~~F~CPnCG~~~I~--RC~~CRk~~~~Y~CP~CGF 56 (59)
T PRK14890 23 AVKFLCPNCGEVIIY--RCEKCRKQSNPYTCPKCGF 56 (59)
T ss_pred cCEeeCCCCCCeeEe--echhHHhcCCceECCCCCC
Confidence 357778888764322 5888888888888888876
No 136
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=56.62 E-value=4.4 Score=39.09 Aligned_cols=51 Identities=25% Similarity=0.640 Sum_probs=28.6
Q ss_pred CCeecCchhHhhhhcCCCccccCCCCCCcccCceeeeCCCCccccccccCcCCCCccceEecCcccc
Q 021781 88 NEIFDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKVQQVCVNCGVCMGEYFCESCKL 154 (307)
Q Consensus 88 ~k~y~Cr~CHde~~~~~~~~~~~~H~ldR~~v~~v~C~~C~~eQ~v~~~C~~Cg~~fa~YfC~~Ckl 154 (307)
|++|.|-+|++-+- ++-++...+ .|+....-.-.|.+|+. +|.|.|-.||.
T Consensus 140 Grif~CsfC~~flC--------EDDQFEHQA-------sCQvLe~E~~KC~SCNr-lGq~sCLRCK~ 190 (314)
T PF06524_consen 140 GRIFKCSFCDNFLC--------EDDQFEHQA-------SCQVLESETFKCQSCNR-LGQYSCLRCKI 190 (314)
T ss_pred CeEEEeecCCCeee--------ccchhhhhh-------hhhhhhccccccccccc-ccchhhhheee
Confidence 56788888887654 222222221 13333333445666653 67788888874
No 137
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=56.59 E-value=12 Score=40.79 Aligned_cols=43 Identities=28% Similarity=0.705 Sum_probs=30.9
Q ss_pred ceeeeCCCCccccccccCcCCCCcc------ceEecCccccccCCCCCCeecCCCCC
Q 021781 120 NQVICSLCGTEQKVQQVCVNCGVCM------GEYFCESCKLFDDDTSKKQYHCDGCG 170 (307)
Q Consensus 120 ~~v~C~~C~~eQ~v~~~C~~Cg~~f------a~YfC~~Ckl~ddd~~k~~yHC~~Cg 170 (307)
..++|..|+.. -.|+||+..| +...|--|..= ++.+.+|+.||
T Consensus 434 ~~l~C~~Cg~v----~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~----~~~p~~Cp~Cg 482 (730)
T COG1198 434 PLLLCRDCGYI----AECPNCDSPLTLHKATGQLRCHYCGYQ----EPIPQSCPECG 482 (730)
T ss_pred ceeecccCCCc----ccCCCCCcceEEecCCCeeEeCCCCCC----CCCCCCCCCCC
Confidence 36899999875 3699998887 55666666543 45677788887
No 138
>KOG2068 consensus MOT2 transcription factor [Transcription]
Probab=56.44 E-value=9.5 Score=37.70 Aligned_cols=53 Identities=28% Similarity=0.600 Sum_probs=40.1
Q ss_pred CCCCCCcccccccccCCceeEEcCCCCccchHHHHHHhhcCCCCCCCCCcCccc
Q 021781 204 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 257 (307)
Q Consensus 204 ~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlCrks~~d 257 (307)
+-...||||-+++.........-|||+.++..|+..-.. ...+||.||++...
T Consensus 247 ~v~~s~p~~~~~~~~~d~~~lP~~~~~~~~l~~~~t~~~-~~~~~~~~rk~~~~ 299 (327)
T KOG2068|consen 247 SVPPSCPICYEDLDLTDSNFLPCPCGFRLCLFCHKTISD-GDGRCPGCRKPYER 299 (327)
T ss_pred ccCCCCCCCCCcccccccccccccccccchhhhhhcccc-cCCCCCccCCcccc
Confidence 335789999997655444455557899999999988766 46899999987763
No 139
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=55.59 E-value=9.1 Score=30.73 Aligned_cols=31 Identities=29% Similarity=0.518 Sum_probs=21.2
Q ss_pred CCCCCCCcCccchhHHHHhhHHHHHc--CCCChhhcC
Q 021781 246 YACPICSKSVCDMSKVWEKYDREIAA--TPMPEAYLN 280 (307)
Q Consensus 246 ~~CPlCrks~~dm~~~~~~lD~eia~--~pmP~ey~n 280 (307)
-.||-||..+.|.. .||++|+. .|.|.+|..
T Consensus 22 D~CPrCrGVWLDrG----ELdKli~r~r~pqpa~ys~ 54 (88)
T COG3809 22 DYCPRCRGVWLDRG----ELDKLIERSRYPQPAEYSQ 54 (88)
T ss_pred eeCCccccEeecch----hHHHHHHHhcCCCCcccCC
Confidence 45999999998863 56666665 456666643
No 140
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=54.27 E-value=2.2 Score=43.56 Aligned_cols=93 Identities=23% Similarity=0.643 Sum_probs=0.0
Q ss_pred CCeec--CCCCCcccccC-CccceecCC---ccceeeccccccccccCCCCCCCCcccccccccCCceeEEc-CCCCccc
Q 021781 161 KKQYH--CDGCGICRIGG-CDNFFHCNK---CRCCYSMLLKNSHPCVEGAMHHDCPVCCEYLFETRQDVIVL-PCGHTIH 233 (307)
Q Consensus 161 k~~yH--C~~CgiCR~G~-~e~ffHC~~---C~~C~s~~l~~~H~CiE~~~~~~CPIClE~lf~s~~~v~~L-pCGH~fH 233 (307)
+++|| |=.|+.||.-. +..||.=+. |--||-.+|+ .|..|.+.+.+ ++| .+|-+||
T Consensus 295 ~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~tle------------kC~~Cg~~I~d-----~iLrA~GkayH 357 (468)
T KOG1701|consen 295 DQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDTLE------------KCNKCGEPIMD-----RILRALGKAYH 357 (468)
T ss_pred hhhhcccceehHhhhhhhccccccccCCcccchHHHHHHHH------------HHhhhhhHHHH-----HHHHhcccccC
Q ss_pred hH-------------------------HHHHHhhcCCCCCCCCCcCccchhHHHHhhHHHHHcCCCChhhcCceEEEEEe
Q 021781 234 KN-------------------------CLKEMREHHQYACPICSKSVCDMSKVWEKYDREIAATPMPEAYLNKKVSFSYV 288 (307)
Q Consensus 234 ~~-------------------------Ci~~wl~~~~~~CPlCrks~~dm~~~~~~lD~eia~~pmP~ey~n~~v~Is~~ 288 (307)
-. |+..+-+....+|-+|.++| ||.+.++..|.|..|
T Consensus 358 p~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAPrCs~C~~PI------------------~P~~G~~etvRvvam 419 (468)
T KOG1701|consen 358 PGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAPRCSVCGNPI------------------LPRDGKDETVRVVAM 419 (468)
T ss_pred CCceEEEEeccccCCccccccCCCceeeehhhhhhcCcchhhccCCc------------------cCCCCCcceEEEEEc
No 141
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=54.20 E-value=0.99 Score=45.53 Aligned_cols=53 Identities=19% Similarity=0.417 Sum_probs=43.7
Q ss_pred CCCCCCcccccccccCCceeEEcCCCCccchHHHHHHhhcCCCCCCCCCcCccc
Q 021781 204 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 257 (307)
Q Consensus 204 ~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlCrks~~d 257 (307)
+.-..+.||.+.+...-.....+.|||..|.+++.+||.. ...+|-|++.+..
T Consensus 194 slv~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~~-~~kl~~~~rel~~ 246 (465)
T KOG0827|consen 194 SLVGSLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLAT-KRKLPSCRRELPK 246 (465)
T ss_pred HHHhhhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHHH-HHHhHHHHhhhhh
Confidence 3456799999887665456677899999999999999985 6789999999873
No 142
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=53.82 E-value=8.5 Score=35.47 Aligned_cols=38 Identities=34% Similarity=0.795 Sum_probs=27.9
Q ss_pred CcccccccccCCceeEEcCCCCc-cchHHHHHHhhcCCCCCCCCCcCc
Q 021781 209 CPVCCEYLFETRQDVIVLPCGHT-IHKNCLKEMREHHQYACPICSKSV 255 (307)
Q Consensus 209 CPIClE~lf~s~~~v~~LpCGH~-fH~~Ci~~wl~~~~~~CPlCrks~ 255 (307)
|-.|.+. ...+.+|||.|. ++..|-.. -..||+|+-..
T Consensus 161 Cr~C~~~----~~~VlllPCrHl~lC~~C~~~-----~~~CPiC~~~~ 199 (207)
T KOG1100|consen 161 CRKCGER----EATVLLLPCRHLCLCGICDES-----LRICPICRSPK 199 (207)
T ss_pred ceecCcC----CceEEeecccceEeccccccc-----CccCCCCcChh
Confidence 8899874 334888999876 77788744 24599999654
No 143
>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 KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]
Probab=53.33 E-value=5.2 Score=43.62 Aligned_cols=45 Identities=36% Similarity=0.680 Sum_probs=31.1
Q ss_pred CCCCcccccccccCC---ceeEEcCCCCccchHHHHHHhhcCCCCCCCCC
Q 021781 206 HHDCPVCCEYLFETR---QDVIVLPCGHTIHKNCLKEMREHHQYACPICS 252 (307)
Q Consensus 206 ~~~CPIClE~lf~s~---~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlCr 252 (307)
+..|.-|.+....+. ..++++.|||.||..|+.....+. .|-+|.
T Consensus 784 e~rc~~c~~~~l~~~~~~~~~~v~~c~h~yhk~c~~~~~~~~--~~~~~~ 831 (846)
T KOG2066|consen 784 EERCSSCFEPNLPSGAAFDSVVVFHCGHMYHKECLMMESLRN--ACNIES 831 (846)
T ss_pred hhhhhhhcccccccCcccceeeEEEccchhhhcccccHHHhc--ccChhh
Confidence 346777777655444 457899999999999998865432 255544
No 145
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=53.25 E-value=7.7 Score=21.97 Aligned_cols=20 Identities=35% Similarity=0.800 Sum_probs=12.6
Q ss_pred CCCCCCCcCccchhHHHHhh
Q 021781 246 YACPICSKSVCDMSKVWEKY 265 (307)
Q Consensus 246 ~~CPlCrks~~dm~~~~~~l 265 (307)
+.||+|.+.+......++.+
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~ 20 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHM 20 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHH
Confidence 46999999998866555443
No 146
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=53.14 E-value=12 Score=25.92 Aligned_cols=8 Identities=38% Similarity=0.974 Sum_probs=4.4
Q ss_pred eecCCCCC
Q 021781 163 QYHCDGCG 170 (307)
Q Consensus 163 ~yHC~~Cg 170 (307)
..+|+.||
T Consensus 21 ~~~Cp~CG 28 (46)
T PRK00398 21 GVRCPYCG 28 (46)
T ss_pred ceECCCCC
Confidence 45555554
No 147
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=51.31 E-value=12 Score=25.53 Aligned_cols=26 Identities=27% Similarity=0.591 Sum_probs=15.9
Q ss_pred cCcCCCCccceEecCccccccCCCCCCeecCCCCC
Q 021781 136 VCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCG 170 (307)
Q Consensus 136 ~C~~Cg~~fa~YfC~~Ckl~ddd~~k~~yHC~~Cg 170 (307)
.||.|+..|..+. + .+-.+++|+.||
T Consensus 1 ~CP~C~~~l~~~~-----~----~~~~id~C~~C~ 26 (41)
T PF13453_consen 1 KCPRCGTELEPVR-----L----GDVEIDVCPSCG 26 (41)
T ss_pred CcCCCCcccceEE-----E----CCEEEEECCCCC
Confidence 4777777776543 1 225677777775
No 148
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=51.18 E-value=6 Score=43.52 Aligned_cols=53 Identities=28% Similarity=0.577 Sum_probs=36.4
Q ss_pred CCCCCCCcccccccccCCceeEEcCCC-----CccchHHHHHHhhcC-CCCCCCCCcCccc
Q 021781 203 GAMHHDCPVCCEYLFETRQDVIVLPCG-----HTIHKNCLKEMREHH-QYACPICSKSVCD 257 (307)
Q Consensus 203 ~~~~~~CPIClE~lf~s~~~v~~LpCG-----H~fH~~Ci~~wl~~~-~~~CPlCrks~~d 257 (307)
|+.+..|-||--. +.+++...-||. -.+|++|+.+|+..+ ...|-+|..++..
T Consensus 9 N~d~~~CRICr~e--~~~d~pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~F 67 (1175)
T COG5183 9 NEDKRSCRICRTE--DIRDDPLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKF 67 (1175)
T ss_pred CccchhceeecCC--CCCCCcCcccccccchhHHHHHHHHHHHHhcCCCcceeeecceeee
Confidence 3445789999642 123334445774 459999999999864 4569999988753
No 149
>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=50.90 E-value=10 Score=27.32 Aligned_cols=23 Identities=22% Similarity=0.797 Sum_probs=14.8
Q ss_pred cccccCc--CCCCc------cceEecCcccc
Q 021781 132 KVQQVCV--NCGVC------MGEYFCESCKL 154 (307)
Q Consensus 132 ~v~~~C~--~Cg~~------fa~YfC~~Ckl 154 (307)
.....|| .||.- +.|+||.+|.+
T Consensus 16 r~rk~CP~~~CG~GvFMA~H~dR~~CGKCg~ 46 (47)
T PF01599_consen 16 RLRKECPSPRCGAGVFMAEHKDRHYCGKCGY 46 (47)
T ss_dssp ESSEE-TSTTTTSSSEEEE-SSEEEETTTSS
T ss_pred EhhhcCCCcccCCceEeeecCCCccCCCccc
Confidence 3456788 78773 37778887754
No 150
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=49.98 E-value=4.3 Score=27.44 Aligned_cols=27 Identities=33% Similarity=0.725 Sum_probs=13.8
Q ss_pred cCcCCCCccceEecCccccccCCCCCCeecCCCCCc
Q 021781 136 VCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGI 171 (307)
Q Consensus 136 ~C~~Cg~~fa~YfC~~Ckl~ddd~~k~~yHC~~Cgi 171 (307)
.|++||+.++.+| ++.|..--||.||-
T Consensus 3 ~C~~Cg~~Yh~~~---------~pP~~~~~Cd~cg~ 29 (36)
T PF05191_consen 3 ICPKCGRIYHIEF---------NPPKVEGVCDNCGG 29 (36)
T ss_dssp EETTTTEEEETTT---------B--SSTTBCTTTTE
T ss_pred CcCCCCCcccccc---------CCCCCCCccCCCCC
Confidence 3556666555443 34455556666653
No 151
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=49.14 E-value=11 Score=35.28 Aligned_cols=52 Identities=23% Similarity=0.527 Sum_probs=37.1
Q ss_pred CCCCcccccccccCCceeEEcCCC-----CccchHHHHHHhhc-CCCCCCCCCcCccc
Q 021781 206 HHDCPVCCEYLFETRQDVIVLPCG-----HTIHKNCLKEMREH-HQYACPICSKSVCD 257 (307)
Q Consensus 206 ~~~CPIClE~lf~s~~~v~~LpCG-----H~fH~~Ci~~wl~~-~~~~CPlCrks~~d 257 (307)
+..|-||.+............||. ...|+.|++.|+.. .+..|.+|...+..
T Consensus 78 ~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~~ 135 (323)
T KOG1609|consen 78 GPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFIN 135 (323)
T ss_pred CCcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhccccCeeeeccccccee
Confidence 367999998654432224556773 67899999999974 35679999987653
No 152
>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=48.39 E-value=14 Score=25.25 Aligned_cols=7 Identities=57% Similarity=1.322 Sum_probs=3.7
Q ss_pred CcCCCCc
Q 021781 137 CVNCGVC 143 (307)
Q Consensus 137 C~~Cg~~ 143 (307)
||+||..
T Consensus 3 Cp~Cg~~ 9 (43)
T PF08271_consen 3 CPNCGSK 9 (43)
T ss_dssp BTTTSSS
T ss_pred CcCCcCC
Confidence 5555554
No 153
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 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 DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=48.30 E-value=14 Score=31.64 Aligned_cols=49 Identities=20% Similarity=0.447 Sum_probs=36.6
Q ss_pred CCCCccceEecCccccccCCCCCCeecCCCCCcccccCCccceecCCccceeecc
Q 021781 139 NCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGICRIGGCDNFFHCNKCRCCYSML 193 (307)
Q Consensus 139 ~Cg~~fa~YfC~~Ckl~ddd~~k~~yHC~~CgiCR~G~~e~ffHC~~C~~C~s~~ 193 (307)
..+......+|..|+.+- + ...+||..||.|-.+ --.||.-=|.|+...
T Consensus 41 ~~~~~~~~~~C~~C~~~k--p-~Rs~HC~~C~~CV~~---~DHHC~w~~~cIG~~ 89 (174)
T PF01529_consen 41 EDDENGELKYCSTCKIIK--P-PRSHHCRVCNRCVLR---FDHHCPWLGNCIGRR 89 (174)
T ss_pred ccccCCCCEECcccCCcC--C-Ccceecccccccccc---ccccchhhccccccc
Confidence 345677888999999883 2 347899999999885 346888888887653
No 154
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=47.99 E-value=6.7 Score=44.92 Aligned_cols=52 Identities=25% Similarity=0.459 Sum_probs=40.0
Q ss_pred CCCCCCcccccccccCCceeEEcCCCCccchHHHHHHhhcCCCCCCCCCcCccchh
Q 021781 204 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCDMS 259 (307)
Q Consensus 204 ~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlCrks~~dm~ 259 (307)
..+..|+||++-+..- -.+..|||.++..|+..|+.. +..||+|....++..
T Consensus 1151 ~~~~~c~ic~dil~~~---~~I~~cgh~~c~~c~~~~l~~-~s~~~~~ksi~~dfg 1202 (1394)
T KOG0298|consen 1151 SGHFVCEICLDILRNQ---GGIAGCGHEPCCRCDELWLYA-SSRCPICKSIKGDFG 1202 (1394)
T ss_pred hcccchHHHHHHHHhc---CCeeeechhHhhhHHHHHHHH-hccCcchhhhhhhhc
Confidence 3456899999965432 234579999999999999985 689999997666543
No 155
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=47.68 E-value=17 Score=39.66 Aligned_cols=70 Identities=26% Similarity=0.468 Sum_probs=43.2
Q ss_pred CCeecCCCCCcccccCCccceecCCccceeeccccccccccCCCCCCCCcccccccccCCceeEEcCCCCccchHHHHHH
Q 021781 161 KKQYHCDGCGICRIGGCDNFFHCNKCRCCYSMLLKNSHPCVEGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEM 240 (307)
Q Consensus 161 k~~yHC~~CgiCR~G~~e~ffHC~~C~~C~s~~l~~~H~CiE~~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~w 240 (307)
.-+|-|+.|+-=-+++++ --|++|- +.+ ...|.+|-..+.. ..+.---|||-.|.+++.+|
T Consensus 751 ~i~~~~~nc~a~~~~~~~--~~c~rc~---s~a------------~~~CtVC~~vi~G--~~~~c~~C~H~gH~sh~~sw 811 (839)
T KOG0269|consen 751 TIHYACPNCDAPMVLTKL--WQCDRCE---SRA------------SAKCTVCDLVIRG--VDVWCQVCGHGGHDSHLKSW 811 (839)
T ss_pred eeeccccccCCccccccc--eeechHH---HHh------------hcCceeecceeee--eEeecccccccccHHHHHHH
Confidence 357888888754444433 3344443 332 2479999864322 22222369999999999999
Q ss_pred hhcCCCCCCC
Q 021781 241 REHHQYACPI 250 (307)
Q Consensus 241 l~~~~~~CPl 250 (307)
+.. +.-||.
T Consensus 812 ~~~-~s~ca~ 820 (839)
T KOG0269|consen 812 FFK-ASPCAK 820 (839)
T ss_pred Hhc-CCCCcc
Confidence 974 455655
No 156
>PLN03086 PRLI-interacting factor K; Provisional
Probab=45.63 E-value=16 Score=38.65 Aligned_cols=17 Identities=24% Similarity=0.391 Sum_probs=11.7
Q ss_pred ccCceeeeCCCCccccc
Q 021781 117 HEVNQVICSLCGTEQKV 133 (307)
Q Consensus 117 ~~v~~v~C~~C~~eQ~v 133 (307)
..+..|.|..|...-+.
T Consensus 403 ~~~~~V~C~NC~~~i~l 419 (567)
T PLN03086 403 MDVDTVECRNCKHYIPS 419 (567)
T ss_pred CCCCeEECCCCCCccch
Confidence 34667889999876443
No 157
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=45.51 E-value=18 Score=22.67 Aligned_cols=20 Identities=25% Similarity=0.617 Sum_probs=13.2
Q ss_pred CCCCCCCcCccchhHHHHhhH
Q 021781 246 YACPICSKSVCDMSKVWEKYD 266 (307)
Q Consensus 246 ~~CPlCrks~~dm~~~~~~lD 266 (307)
..||+|.+.+ .+....+.+|
T Consensus 2 v~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLD 21 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHH
Confidence 3699999988 4344445555
No 158
>PF15616 TerY-C: TerY-C metal binding domain
Probab=44.51 E-value=20 Score=31.10 Aligned_cols=33 Identities=36% Similarity=0.792 Sum_probs=22.4
Q ss_pred ccCcCCCCccceEecCcc-cccc-CCCCCCeecCCCCC
Q 021781 135 QVCVNCGVCMGEYFCESC-KLFD-DDTSKKQYHCDGCG 170 (307)
Q Consensus 135 ~~C~~Cg~~fa~YfC~~C-kl~d-dd~~k~~yHC~~Cg 170 (307)
.-||.||..+|---| .| ||+- +++ ...+|+-||
T Consensus 78 PgCP~CGn~~~fa~C-~CGkl~Ci~g~--~~~~CPwCg 112 (131)
T PF15616_consen 78 PGCPHCGNQYAFAVC-GCGKLFCIDGE--GEVTCPWCG 112 (131)
T ss_pred CCCCCCcChhcEEEe-cCCCEEEeCCC--CCEECCCCC
Confidence 579999999999988 58 5653 221 245555554
No 159
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=43.90 E-value=34 Score=33.18 Aligned_cols=114 Identities=25% Similarity=0.421 Sum_probs=64.3
Q ss_pred cCcCCCCccceEec-Cccccc-cCCCCCCeecCCCCCcccccC-------C--ccceecCCccceeec--cccccccccC
Q 021781 136 VCVNCGVCMGEYFC-ESCKLF-DDDTSKKQYHCDGCGICRIGG-------C--DNFFHCNKCRCCYSM--LLKNSHPCVE 202 (307)
Q Consensus 136 ~C~~Cg~~fa~YfC-~~Ckl~-ddd~~k~~yHC~~CgiCR~G~-------~--e~ffHC~~C~~C~s~--~l~~~H~CiE 202 (307)
.|..||+..+.+-= ++=|-+ -+-.+++.+.|..||.=.|-- + .--+-|..||-=.|. -|++--+---
T Consensus 132 ~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSRPWLLQGHiRTHT 211 (279)
T KOG2462|consen 132 KCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSRPWLLQGHIRTHT 211 (279)
T ss_pred eccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccCCCcccccccccccchHHhhccccccc
Confidence 47777777766540 000111 111248899999999765542 1 235778888888874 2332111111
Q ss_pred CCCCCCCcccccccccCCceeEEcCCCCccchHHHHHHhh----cCCCCCCCCCcCccchhHHHHh
Q 021781 203 GAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMRE----HHQYACPICSKSVCDMSKVWEK 264 (307)
Q Consensus 203 ~~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~----~~~~~CPlCrks~~dm~~~~~~ 264 (307)
+.-...||.|--- |-.+.. |+.-++ ..+|.|+.|.|+|.-|+-..+.
T Consensus 212 GEKPF~C~hC~kA-FADRSN--------------LRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH 262 (279)
T KOG2462|consen 212 GEKPFSCPHCGKA-FADRSN--------------LRAHMQTHSDVKKHQCPRCGKSFALKSYLNKH 262 (279)
T ss_pred CCCCccCCcccch-hcchHH--------------HHHHHHhhcCCccccCcchhhHHHHHHHHHHh
Confidence 2335789999875 433322 222222 2469999999999877544443
No 160
>PHA00626 hypothetical protein
Probab=43.53 E-value=16 Score=27.46 Aligned_cols=33 Identities=21% Similarity=0.459 Sum_probs=22.5
Q ss_pred eeeCCCCccccccccCcCCCCccceEecCcccccc
Q 021781 122 VICSLCGTEQKVQQVCVNCGVCMGEYFCESCKLFD 156 (307)
Q Consensus 122 v~C~~C~~eQ~v~~~C~~Cg~~fa~YfC~~Ckl~d 156 (307)
|.|..|+..+-+ .|.-|...-++|-|..|.+++
T Consensus 1 m~CP~CGS~~Iv--rcg~cr~~snrYkCkdCGY~f 33 (59)
T PHA00626 1 MSCPKCGSGNIA--KEKTMRGWSDDYVCCDCGYND 33 (59)
T ss_pred CCCCCCCCceee--eeceecccCcceEcCCCCCee
Confidence 457777766555 556666667778888887764
No 161
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=43.48 E-value=17 Score=26.26 Aligned_cols=9 Identities=44% Similarity=1.505 Sum_probs=4.9
Q ss_pred CeecCCCCC
Q 021781 162 KQYHCDGCG 170 (307)
Q Consensus 162 ~~yHC~~Cg 170 (307)
+.|+|..||
T Consensus 36 ~r~~C~~Cg 44 (50)
T PRK00432 36 DRWHCGKCG 44 (50)
T ss_pred CcEECCCcC
Confidence 455555555
No 162
>PLN02189 cellulose synthase
Probab=43.43 E-value=20 Score=40.49 Aligned_cols=56 Identities=18% Similarity=0.418 Sum_probs=39.9
Q ss_pred cCCCCCCCCcccccccccC--CceeEEc-CCCCccchHHHHHHhhcCCCCCCCCCcCcc
Q 021781 201 VEGAMHHDCPVCCEYLFET--RQDVIVL-PCGHTIHKNCLKEMREHHQYACPICSKSVC 256 (307)
Q Consensus 201 iE~~~~~~CPIClE~lf~s--~~~v~~L-pCGH~fH~~Ci~~wl~~~~~~CPlCrks~~ 256 (307)
.++.....|.||.|++-.. ++..+.- -||--.++.|++.=.+.++..||.|+....
T Consensus 29 ~~~~~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cyeyer~eg~q~CpqCkt~Y~ 87 (1040)
T PLN02189 29 LRNLDGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCYEYERREGTQNCPQCKTRYK 87 (1040)
T ss_pred cccccCccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchh
Confidence 3444567999999986533 3333332 367779999997666667889999998765
No 163
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=43.23 E-value=15 Score=26.92 Aligned_cols=20 Identities=30% Similarity=0.926 Sum_probs=12.3
Q ss_pred cccCcCCCC--cc----ceEecCccc
Q 021781 134 QQVCVNCGV--CM----GEYFCESCK 153 (307)
Q Consensus 134 ~~~C~~Cg~--~f----a~YfC~~Ck 153 (307)
...||+||. -| .||+|.+|.
T Consensus 19 ~~~CPrCG~gvfmA~H~dR~~CGkCg 44 (51)
T COG1998 19 NRFCPRCGPGVFMADHKDRWACGKCG 44 (51)
T ss_pred cccCCCCCCcchhhhcCceeEecccc
Confidence 356899983 22 456666664
No 164
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=43.10 E-value=26 Score=25.05 Aligned_cols=8 Identities=50% Similarity=1.630 Sum_probs=4.1
Q ss_pred CCCCCCCc
Q 021781 246 YACPICSK 253 (307)
Q Consensus 246 ~~CPlCrk 253 (307)
|+||.|.+
T Consensus 3 f~CP~C~~ 10 (54)
T PF05605_consen 3 FTCPYCGK 10 (54)
T ss_pred cCCCCCCC
Confidence 44555555
No 165
>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=41.98 E-value=16 Score=25.44 Aligned_cols=13 Identities=23% Similarity=0.697 Sum_probs=8.6
Q ss_pred cccCcCCCCccce
Q 021781 134 QQVCVNCGVCMGE 146 (307)
Q Consensus 134 ~~~C~~Cg~~fa~ 146 (307)
++.|+.||.++-+
T Consensus 17 ~~~Cp~C~~PL~~ 29 (41)
T PF06677_consen 17 DEHCPDCGTPLMR 29 (41)
T ss_pred cCccCCCCCeeEE
Confidence 4568888777643
No 166
>PRK00420 hypothetical protein; Validated
Probab=41.96 E-value=17 Score=30.73 Aligned_cols=21 Identities=24% Similarity=0.472 Sum_probs=13.3
Q ss_pred cccCcCCCCccc-----eEecCcccc
Q 021781 134 QQVCVNCGVCMG-----EYFCESCKL 154 (307)
Q Consensus 134 ~~~C~~Cg~~fa-----~YfC~~Ckl 154 (307)
+..||.||.+|. ..||+.|.-
T Consensus 23 ~~~CP~Cg~pLf~lk~g~~~Cp~Cg~ 48 (112)
T PRK00420 23 SKHCPVCGLPLFELKDGEVVCPVHGK 48 (112)
T ss_pred cCCCCCCCCcceecCCCceECCCCCC
Confidence 357888888764 355555543
No 167
>PF14353 CpXC: CpXC protein
Probab=41.46 E-value=22 Score=29.49 Aligned_cols=11 Identities=27% Similarity=0.634 Sum_probs=7.5
Q ss_pred cCcCCCCccce
Q 021781 136 VCVNCGVCMGE 146 (307)
Q Consensus 136 ~C~~Cg~~fa~ 146 (307)
.||+||+.|..
T Consensus 3 tCP~C~~~~~~ 13 (128)
T PF14353_consen 3 TCPHCGHEFEF 13 (128)
T ss_pred CCCCCCCeeEE
Confidence 57777777743
No 168
>PF04710 Pellino: Pellino; InterPro: IPR006800 Pellino is involved in Toll-like signalling pathways, and associates with the kinase domain of the Pelle Ser/Thr kinase [, , ].; PDB: 3EGB_B 3EGA_A.
Probab=41.42 E-value=9.1 Score=38.84 Aligned_cols=50 Identities=28% Similarity=0.532 Sum_probs=0.6
Q ss_pred CCCCCCCccccccc----------ccCCceeEEcCCCCccchHHHHHHhhc-----CCCCCCCCCcCc
Q 021781 203 GAMHHDCPVCCEYL----------FETRQDVIVLPCGHTIHKNCLKEMREH-----HQYACPICSKSV 255 (307)
Q Consensus 203 ~~~~~~CPIClE~l----------f~s~~~v~~LpCGH~fH~~Ci~~wl~~-----~~~~CPlCrks~ 255 (307)
|++...|||=|.-| .+..++.+.|.|||.+=. -.|-.. ....||+||..-
T Consensus 274 Na~rpQCPVglnTL~fp~~~~~~~~~~~qP~VYl~CGHVhG~---h~Wg~~~~~~~~~r~CPlCr~~g 338 (416)
T PF04710_consen 274 NAGRPQCPVGLNTLVFPSKSRKDVPDERQPWVYLNCGHVHGY---HNWGQDSDRDPRSRTCPLCRQVG 338 (416)
T ss_dssp S-------------------------------------------------------------------
T ss_pred hhcCCCCCcCCCccccccccccccccccCceeeccccceeee---cccccccccccccccCCCccccC
Confidence 56788899987544 334577899999987532 246432 146799999653
No 169
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=40.94 E-value=20 Score=31.33 Aligned_cols=47 Identities=26% Similarity=0.618 Sum_probs=32.4
Q ss_pred CCCcccccccccCCceeEEc----CCCCccchHHHHHHhhc--CCCCCCCCCcCccc
Q 021781 207 HDCPVCCEYLFETRQDVIVL----PCGHTIHKNCLKEMREH--HQYACPICSKSVCD 257 (307)
Q Consensus 207 ~~CPIClE~lf~s~~~v~~L----pCGH~fH~~Ci~~wl~~--~~~~CPlCrks~~d 257 (307)
..|-||.|- |. +.+.| =||-.++..|.....+. ....||+|+.++..
T Consensus 81 YeCnIC~et---S~-ee~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKs 133 (140)
T PF05290_consen 81 YECNICKET---SA-EERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKS 133 (140)
T ss_pred eeccCcccc---cc-hhhcCCcccccchHHHHHHHHHHHHHcccCCCCCcccccccc
Confidence 467788773 21 23444 38999999999884343 24669999998864
No 170
>PLN02436 cellulose synthase A
Probab=40.65 E-value=23 Score=40.13 Aligned_cols=56 Identities=20% Similarity=0.445 Sum_probs=40.2
Q ss_pred cCCCCCCCCcccccccccCCceeEEcC---CCCccchHHHHHHhhcCCCCCCCCCcCcc
Q 021781 201 VEGAMHHDCPVCCEYLFETRQDVIVLP---CGHTIHKNCLKEMREHHQYACPICSKSVC 256 (307)
Q Consensus 201 iE~~~~~~CPIClE~lf~s~~~v~~Lp---CGH~fH~~Ci~~wl~~~~~~CPlCrks~~ 256 (307)
........|.||.|++-...+.-.... ||--.++.|++.=.+.++..||.|+....
T Consensus 31 ~~~~~~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cyeyer~eg~~~Cpqckt~Y~ 89 (1094)
T PLN02436 31 VQELSGQTCQICGDEIELTVDGEPFVACNECAFPVCRPCYEYERREGNQACPQCKTRYK 89 (1094)
T ss_pred ccccCCccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchh
Confidence 344456799999998744433334444 56779999996666667889999998765
No 171
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=40.65 E-value=11 Score=36.43 Aligned_cols=29 Identities=21% Similarity=0.543 Sum_probs=25.3
Q ss_pred CccCcccccccceeEcCCCCCeecCchhHh
Q 021781 69 MEYGCQHYRRRCRIRAPCCNEIFDCRHCHN 98 (307)
Q Consensus 69 ~~~GC~HY~R~c~i~~pCC~k~y~Cr~CHd 98 (307)
..+.|.||...=-++.++|.. |+|..||+
T Consensus 176 ~~~~CgH~~h~~cf~e~~~~~-y~CP~C~~ 204 (276)
T KOG1940|consen 176 GVLKCGHYMHSRCFEEMICEG-YTCPICSK 204 (276)
T ss_pred CccCcccchHHHHHHHHhccC-CCCCcccc
Confidence 446899999855689999999 99999999
No 172
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=40.29 E-value=18 Score=24.24 Aligned_cols=9 Identities=56% Similarity=1.180 Sum_probs=4.4
Q ss_pred eeeeCCCCc
Q 021781 121 QVICSLCGT 129 (307)
Q Consensus 121 ~v~C~~C~~ 129 (307)
.|.|+.|++
T Consensus 25 ~v~C~~C~~ 33 (36)
T PF13717_consen 25 KVRCSKCGH 33 (36)
T ss_pred EEECCCCCC
Confidence 455554443
No 173
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=39.84 E-value=17 Score=37.62 Aligned_cols=15 Identities=27% Similarity=0.463 Sum_probs=9.6
Q ss_pred ceecCCccceeeccc
Q 021781 180 FFHCNKCRCCYSMLL 194 (307)
Q Consensus 180 ffHC~~C~~C~s~~l 194 (307)
-|.|..|..-+++..
T Consensus 52 Cf~CP~C~~~L~~~~ 66 (483)
T PF05502_consen 52 CFDCPICFSPLSVRA 66 (483)
T ss_pred cccCCCCCCcceeEe
Confidence 366777776666653
No 174
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=39.67 E-value=27 Score=34.80 Aligned_cols=79 Identities=23% Similarity=0.514 Sum_probs=48.9
Q ss_pred cccCC--CCCCeecCCCCCcccccC-CccceecCCccceeecc---ccccccccCCCCCCCCcccccccccCCceeEEcC
Q 021781 154 LFDDD--TSKKQYHCDGCGICRIGG-CDNFFHCNKCRCCYSML---LKNSHPCVEGAMHHDCPVCCEYLFETRQDVIVLP 227 (307)
Q Consensus 154 l~ddd--~~k~~yHC~~CgiCR~G~-~e~ffHC~~C~~C~s~~---l~~~H~CiE~~~~~~CPIClE~lf~s~~~v~~Lp 227 (307)
-|||- +.+-+-||+.| |--|. .|=||.| +++.+-. --..|.=..|.-...|-.|-+ -+.++.+++
T Consensus 168 cWdDVLks~Ripg~Ces~--~~pg~fAEFfFKC---~ah~~~~k~~aa~lhli~~N~~ni~C~~Ctd----v~~~vlvf~ 238 (446)
T KOG0006|consen 168 CWDDVLKSKRIPGVCESC--CTPGLFAEFFFKC---GAHPTSDKETAAALHLIATNSRNITCITCTD----VRSPVLVFQ 238 (446)
T ss_pred chhhhhhcccCccccccc--cCCcchHhheehh---ccCCCccccchhHHHHhhcccccceeEEecC----CccceEEEe
Confidence 37762 45678888877 44444 3556655 4444331 011232333455667888886 245688899
Q ss_pred CC--CccchHHHHHHh
Q 021781 228 CG--HTIHKNCLKEMR 241 (307)
Q Consensus 228 CG--H~fH~~Ci~~wl 241 (307)
|. |..+..|+.-|-
T Consensus 239 Cns~HvtC~dCFr~yc 254 (446)
T KOG0006|consen 239 CNSRHVTCLDCFRLYC 254 (446)
T ss_pred cCCceeehHHhhhhHh
Confidence 98 999999998653
No 175
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 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 HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=39.60 E-value=15 Score=23.91 Aligned_cols=16 Identities=38% Similarity=1.026 Sum_probs=7.8
Q ss_pred CcCCCCccceEecCccc
Q 021781 137 CVNCGVCMGEYFCESCK 153 (307)
Q Consensus 137 C~~Cg~~fa~YfC~~Ck 153 (307)
|.-||. .++|-|+.|.
T Consensus 5 C~vC~~-~~kY~Cp~C~ 20 (30)
T PF04438_consen 5 CSVCGN-PAKYRCPRCG 20 (30)
T ss_dssp ETSSSS-EESEE-TTT-
T ss_pred CccCcC-CCEEECCCcC
Confidence 444555 5566655554
No 176
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=39.45 E-value=18 Score=27.45 Aligned_cols=34 Identities=24% Similarity=0.614 Sum_probs=20.5
Q ss_pred CceeeeCCCCccccccccCcCCCCccceEecCcccc
Q 021781 119 VNQVICSLCGTEQKVQQVCVNCGVCMGEYFCESCKL 154 (307)
Q Consensus 119 v~~v~C~~C~~eQ~v~~~C~~Cg~~fa~YfC~~Ckl 154 (307)
.....|..|+.++-. .|..|...=+.|-|++|-|
T Consensus 25 ~v~F~CPnCGe~~I~--Rc~~CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 25 AVKFPCPNCGEVEIY--RCAKCRKLGNPYRCPKCGF 58 (61)
T ss_pred eeEeeCCCCCceeee--hhhhHHHcCCceECCCcCc
Confidence 345666666655544 5666666666666666655
No 177
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=39.26 E-value=19 Score=26.23 Aligned_cols=29 Identities=31% Similarity=0.666 Sum_probs=19.8
Q ss_pred cceEecCcc-ccccCCCCCCeecCCCCCcc
Q 021781 144 MGEYFCESC-KLFDDDTSKKQYHCDGCGIC 172 (307)
Q Consensus 144 fa~YfC~~C-kl~ddd~~k~~yHC~~CgiC 172 (307)
+..|-|..| +.++.+..+.-.-|+.||.=
T Consensus 4 ~~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~r 33 (49)
T COG1996 4 MMEYKCARCGREVELDQETRGIRCPYCGSR 33 (49)
T ss_pred eEEEEhhhcCCeeehhhccCceeCCCCCcE
Confidence 445666677 35565667788889988853
No 178
>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=39.14 E-value=10 Score=41.93 Aligned_cols=46 Identities=28% Similarity=0.601 Sum_probs=0.0
Q ss_pred ccCcCCCCccceEecCccccccCCCCCCeecCCCCCcccccCCccceecCCccce
Q 021781 135 QVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGICRIGGCDNFFHCNKCRCC 189 (307)
Q Consensus 135 ~~C~~Cg~~fa~YfC~~Ckl~ddd~~k~~yHC~~CgiCR~G~~e~ffHC~~C~~C 189 (307)
-.|++||..--.-.|+.|.-. ....|.|+.||+ ++. -.+|.+|+.=
T Consensus 656 r~Cp~Cg~~t~~~~Cp~CG~~----T~~~~~Cp~C~~-~~~----~~~C~~C~~~ 701 (900)
T PF03833_consen 656 RRCPKCGKETFYNRCPECGSH----TEPVYVCPDCGI-EVE----EDECPKCGRE 701 (900)
T ss_dssp -------------------------------------------------------
T ss_pred ccCcccCCcchhhcCcccCCc----cccceecccccc-ccC----cccccccccc
Confidence 358888888777788888765 346888888877 222 1267777653
No 179
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=38.53 E-value=30 Score=33.96 Aligned_cols=25 Identities=32% Similarity=0.739 Sum_probs=21.0
Q ss_pred CceeeeCCCCccccc-cccCcCCCCc
Q 021781 119 VNQVICSLCGTEQKV-QQVCVNCGVC 143 (307)
Q Consensus 119 v~~v~C~~C~~eQ~v-~~~C~~Cg~~ 143 (307)
..-..|+.|+++..+ ...|++||..
T Consensus 210 ~RyL~CslC~teW~~~R~~C~~Cg~~ 235 (309)
T PRK03564 210 LRYLHCNLCESEWHVVRVKCSNCEQS 235 (309)
T ss_pred ceEEEcCCCCCcccccCccCCCCCCC
Confidence 467999999999887 5679999974
No 180
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=38.51 E-value=14 Score=21.31 Aligned_cols=15 Identities=53% Similarity=1.112 Sum_probs=11.6
Q ss_pred CCCCCCCcCccchhH
Q 021781 246 YACPICSKSVCDMSK 260 (307)
Q Consensus 246 ~~CPlCrks~~dm~~ 260 (307)
|.||.|.+.+.....
T Consensus 1 y~C~~C~~~f~~~~~ 15 (23)
T PF00096_consen 1 YKCPICGKSFSSKSN 15 (23)
T ss_dssp EEETTTTEEESSHHH
T ss_pred CCCCCCCCccCCHHH
Confidence 469999999987543
No 181
>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=38.46 E-value=20 Score=24.39 Aligned_cols=33 Identities=27% Similarity=0.632 Sum_probs=15.4
Q ss_pred cCcCCCCccceEecCccccc-cCCCCCCeecCCCCC
Q 021781 136 VCVNCGVCMGEYFCESCKLF-DDDTSKKQYHCDGCG 170 (307)
Q Consensus 136 ~C~~Cg~~fa~YfC~~Ckl~-ddd~~k~~yHC~~Cg 170 (307)
.|++||+.-+.|| .+ ..- -|++..-.|.|-+||
T Consensus 2 ~Cp~Cg~~~a~~~-~~-Q~rsaDE~~T~fy~C~~C~ 35 (39)
T PF01096_consen 2 KCPKCGHNEAVFF-QI-QTRSADEPMTLFYVCCNCG 35 (39)
T ss_dssp --SSS-SSEEEEE-EE-SSSSSSSSSEEEEEESSST
T ss_pred CCcCCCCCeEEEE-Ee-eccCCCCCCeEEEEeCCCC
Confidence 4788888776665 00 010 233445556666554
No 182
>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=38.39 E-value=25 Score=22.91 Aligned_cols=25 Identities=28% Similarity=0.787 Sum_probs=16.4
Q ss_pred eEecCccccccCCCCCCeecCCCCCc
Q 021781 146 EYFCESCKLFDDDTSKKQYHCDGCGI 171 (307)
Q Consensus 146 ~YfC~~Ckl~ddd~~k~~yHC~~Cgi 171 (307)
+|-|.+|-+.-+ +.+.++.|+.||.
T Consensus 1 ~~~C~~CGy~y~-~~~~~~~CP~Cg~ 25 (33)
T cd00350 1 KYVCPVCGYIYD-GEEAPWVCPVCGA 25 (33)
T ss_pred CEECCCCCCEEC-CCcCCCcCcCCCC
Confidence 366777865533 2457888888875
No 183
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=37.57 E-value=26 Score=36.21 Aligned_cols=21 Identities=29% Similarity=0.746 Sum_probs=14.0
Q ss_pred ccccccCCCCCCCCccccccccc
Q 021781 196 NSHPCVEGAMHHDCPVCCEYLFE 218 (307)
Q Consensus 196 ~~H~CiE~~~~~~CPIClE~lf~ 218 (307)
.+.+|..+- .+||+|.-.|..
T Consensus 44 ~~nrC~r~C--f~CP~C~~~L~~ 64 (483)
T PF05502_consen 44 EKNRCSRNC--FDCPICFSPLSV 64 (483)
T ss_pred ccceecccc--ccCCCCCCccee
Confidence 456776443 589999876643
No 184
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=36.79 E-value=19 Score=22.84 Aligned_cols=20 Identities=25% Similarity=0.718 Sum_probs=6.1
Q ss_pred CCcccccCCc-cceecCCccc
Q 021781 169 CGICRIGGCD-NFFHCNKCRC 188 (307)
Q Consensus 169 CgiCR~G~~e-~ffHC~~C~~ 188 (307)
|++|+..+.. .+|+|..|+.
T Consensus 3 C~~C~~~~~~~~~Y~C~~Cdf 23 (30)
T PF07649_consen 3 CDACGKPIDGGWFYRCSECDF 23 (30)
T ss_dssp -TTTS----S--EEE-TTT--
T ss_pred CCcCCCcCCCCceEECccCCC
Confidence 4444444332 5666666654
No 185
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=36.77 E-value=26 Score=26.49 Aligned_cols=37 Identities=32% Similarity=0.528 Sum_probs=27.5
Q ss_pred CceeeeCCCCccccc------cccCcCCCCccceEecCccccc
Q 021781 119 VNQVICSLCGTEQKV------QQVCVNCGVCMGEYFCESCKLF 155 (307)
Q Consensus 119 v~~v~C~~C~~eQ~v------~~~C~~Cg~~fa~YfC~~Ckl~ 155 (307)
--.|.|..|+.+|.+ .-.|..||..+++-.=++-+|.
T Consensus 9 F~~VkCp~C~n~q~vFsha~t~V~C~~Cg~~L~~PtGGKa~i~ 51 (59)
T PRK00415 9 FLKVKCPDCGNEQVVFSHASTVVRCLVCGKTLAEPTGGKAKIK 51 (59)
T ss_pred EEEEECCCCCCeEEEEecCCcEEECcccCCCcccCCCcceeee
Confidence 347999999999865 2469999999887665555544
No 186
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=36.74 E-value=19 Score=31.21 Aligned_cols=19 Identities=42% Similarity=1.127 Sum_probs=13.8
Q ss_pred ccCcCCCCcc----ceEecCccc
Q 021781 135 QVCVNCGVCM----GEYFCESCK 153 (307)
Q Consensus 135 ~~C~~Cg~~f----a~YfC~~Ck 153 (307)
..|+.||.++ |+-||++|-
T Consensus 29 ~hCp~Cg~PLF~KdG~v~CPvC~ 51 (131)
T COG1645 29 KHCPKCGTPLFRKDGEVFCPVCG 51 (131)
T ss_pred hhCcccCCcceeeCCeEECCCCC
Confidence 5688888886 556677775
No 187
>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=36.58 E-value=12 Score=41.45 Aligned_cols=45 Identities=29% Similarity=0.769 Sum_probs=0.0
Q ss_pred eeeeCCCCccccccccCcCCCCc-cceEecCccccccCCCCCCeecCCCCCc
Q 021781 121 QVICSLCGTEQKVQQVCVNCGVC-MGEYFCESCKLFDDDTSKKQYHCDGCGI 171 (307)
Q Consensus 121 ~v~C~~C~~eQ~v~~~C~~Cg~~-fa~YfC~~Ckl~ddd~~k~~yHC~~Cgi 171 (307)
.-.|..|+++ .....|+.||.. .-.|+|+.|+.--++. +|+.||.
T Consensus 655 ~r~Cp~Cg~~-t~~~~Cp~CG~~T~~~~~Cp~C~~~~~~~-----~C~~C~~ 700 (900)
T PF03833_consen 655 RRRCPKCGKE-TFYNRCPECGSHTEPVYVCPDCGIEVEED-----ECPKCGR 700 (900)
T ss_dssp ----------------------------------------------------
T ss_pred cccCcccCCc-chhhcCcccCCccccceeccccccccCcc-----ccccccc
Confidence 4679999887 455789999887 5678899997643321 8998884
No 188
>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=36.06 E-value=24 Score=23.34 Aligned_cols=24 Identities=25% Similarity=0.674 Sum_probs=10.8
Q ss_pred EecCccccccCCCCCCeecCCCCC
Q 021781 147 YFCESCKLFDDDTSKKQYHCDGCG 170 (307)
Q Consensus 147 YfC~~Ckl~ddd~~k~~yHC~~Cg 170 (307)
|-|..|..--+....++-.|..||
T Consensus 1 Y~C~~Cg~~~~~~~~~~irC~~CG 24 (32)
T PF03604_consen 1 YICGECGAEVELKPGDPIRCPECG 24 (32)
T ss_dssp EBESSSSSSE-BSTSSTSSBSSSS
T ss_pred CCCCcCCCeeEcCCCCcEECCcCC
Confidence 334444322222344555666666
No 189
>KOG4399 consensus C2HC-type Zn-finger protein [General function prediction only]
Probab=34.85 E-value=8.3 Score=37.30 Aligned_cols=73 Identities=26% Similarity=0.610 Sum_probs=53.2
Q ss_pred CCCccceEecCccccccCCCCCCeecCCCCCcccccCCccceecCCccceeeccccccccccCCCCCCCCcccccc
Q 021781 140 CGVCMGEYFCESCKLFDDDTSKKQYHCDGCGICRIGGCDNFFHCNKCRCCYSMLLKNSHPCVEGAMHHDCPVCCEY 215 (307)
Q Consensus 140 Cg~~fa~YfC~~Ckl~ddd~~k~~yHC~~CgiCR~G~~e~ffHC~~C~~C~s~~l~~~H~CiE~~~~~~CPIClE~ 215 (307)
=|..=+-.||+.|..| .++-.-||+.|+.|..-.++.|-||.+|-.|+-.++..--.|.--+-..-|-||.++
T Consensus 198 ~~~EE~~~~~~~~~~Y---v~~~~~H~~~~~S~~~~~~~~~~H~~~~~~~~~~~~i~C~~~~~~A~~~~C~iC~~~ 270 (325)
T KOG4399|consen 198 LPTEEGYRFCSPCQRY---VSLENQHCEHCNSCTSKDGRKWNHCFLCKKCVKPSWIHCSICNHCAVKHGCFICGEL 270 (325)
T ss_pred cccccceEEEeehHHH---HHHHhhhchhhcccccchhHHHhHhHHhhhhcccceeeeecccchhhhcceeecccc
Confidence 3455567789999988 457788999999998877778999999999998877432223222334567777774
No 190
>cd02337 ZZ_CBP Zinc finger, ZZ type. Zinc finger present in CBP/p300 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. CREB-binding protein (CBP) is a large multidomain protein that provides binding sites for transcriptional coactivators, the role of the ZZ domain in CBP/p300 is unclear.
Probab=34.54 E-value=28 Score=24.03 Aligned_cols=20 Identities=30% Similarity=0.856 Sum_probs=11.3
Q ss_pred ecCCCCCcccccCCccceecCCcc
Q 021781 164 YHCDGCGICRIGGCDNFFHCNKCR 187 (307)
Q Consensus 164 yHC~~CgiCR~G~~e~ffHC~~C~ 187 (307)
|+|+.|+- +++ ..|||..|.
T Consensus 1 y~C~~C~~--~~~--~r~~C~~C~ 20 (41)
T cd02337 1 YTCNECKH--HVE--TRWHCTVCE 20 (41)
T ss_pred CcCCCCCC--cCC--CceECCCCc
Confidence 56666654 332 566776663
No 191
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=34.32 E-value=31 Score=23.93 Aligned_cols=8 Identities=38% Similarity=1.364 Sum_probs=4.8
Q ss_pred eecCCCCC
Q 021781 163 QYHCDGCG 170 (307)
Q Consensus 163 ~yHC~~Cg 170 (307)
.|-|+.||
T Consensus 20 ~~vC~~Cg 27 (52)
T smart00661 20 RFVCRKCG 27 (52)
T ss_pred EEECCcCC
Confidence 56666665
No 192
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=33.94 E-value=14 Score=26.53 Aligned_cols=12 Identities=25% Similarity=0.963 Sum_probs=6.7
Q ss_pred CCCCCCCcCccc
Q 021781 246 YACPICSKSVCD 257 (307)
Q Consensus 246 ~~CPlCrks~~d 257 (307)
..||+|++++..
T Consensus 21 ~~CPlC~r~l~~ 32 (54)
T PF04423_consen 21 GCCPLCGRPLDE 32 (54)
T ss_dssp EE-TTT--EE-H
T ss_pred CcCCCCCCCCCH
Confidence 389999999985
No 193
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=33.85 E-value=17 Score=36.00 Aligned_cols=30 Identities=27% Similarity=0.752 Sum_probs=23.1
Q ss_pred EEcCCCCccchHHHHHHhhcCCCCCCCCCcCcc
Q 021781 224 IVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 256 (307)
Q Consensus 224 ~~LpCGH~fH~~Ci~~wl~~~~~~CPlCrks~~ 256 (307)
+.+||.|+|+.+|...- ....||.|.-.+.
T Consensus 105 RmIPCkHvFCl~CAr~~---~dK~Cp~C~d~Vq 134 (389)
T KOG2932|consen 105 RMIPCKHVFCLECARSD---SDKICPLCDDRVQ 134 (389)
T ss_pred cccccchhhhhhhhhcC---ccccCcCcccHHH
Confidence 56799999999998542 2457999987764
No 194
>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=33.83 E-value=21 Score=29.71 Aligned_cols=13 Identities=23% Similarity=0.529 Sum_probs=6.5
Q ss_pred cccccCcCCCCcc
Q 021781 132 KVQQVCVNCGVCM 144 (307)
Q Consensus 132 ~v~~~C~~Cg~~f 144 (307)
|+...|.+||..|
T Consensus 68 p~~~~C~~Cg~~~ 80 (115)
T TIGR00100 68 PVECECEDCSEEV 80 (115)
T ss_pred CcEEEcccCCCEE
Confidence 3444555555444
No 195
>PRK00366 ispG 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed
Probab=33.68 E-value=58 Score=32.74 Aligned_cols=44 Identities=16% Similarity=0.405 Sum_probs=36.0
Q ss_pred CCCCCCCcCccchhHHHHhhHHHHHcCCCChhhcCceEEEEEeeecCCccc
Q 021781 246 YACPICSKSVCDMSKVWEKYDREIAATPMPEAYLNKKVSFSYVSLWSDGCL 296 (307)
Q Consensus 246 ~~CPlCrks~~dm~~~~~~lD~eia~~pmP~ey~n~~v~Is~~r~~~~~C~ 296 (307)
.+||-|++...|.-.....+++.+...++| ..|.-|.|-+.+|.
T Consensus 269 isCPgCgR~~~D~~~la~~vee~~~~~~~P-------lkIAVmGC~VNgpG 312 (360)
T PRK00366 269 ISCPTCGRTEFDVIQELAEVEQRLEHIKMP-------LKVAVMGCVVNGPG 312 (360)
T ss_pred EECCCCCCCcccHHHHHHHHHHHhcCCCCC-------cEEEEeCCCCCCCC
Confidence 459999999999888889999999988888 56676777666664
No 196
>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=32.91 E-value=30 Score=21.79 Aligned_cols=18 Identities=28% Similarity=0.920 Sum_probs=7.5
Q ss_pred ccCcCCCCcc--------ceEecCcc
Q 021781 135 QVCVNCGVCM--------GEYFCESC 152 (307)
Q Consensus 135 ~~C~~Cg~~f--------a~YfC~~C 152 (307)
+.|+.|+..+ +.|||+.|
T Consensus 2 ~~C~rC~~~~~~~~~~~r~~~~C~rC 27 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGINGRSTYLCPRC 27 (30)
T ss_dssp SB-TTT--BBEEEEETTEEEEE-TTT
T ss_pred CcCccCCCcceEeEecCCCCeECcCC
Confidence 4566665554 34566655
No 197
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=32.61 E-value=7.9 Score=36.48 Aligned_cols=49 Identities=27% Similarity=0.604 Sum_probs=36.2
Q ss_pred CCCCcccccccc--cCCceeEEcC--------CCCccchHHHHHHhhcCCCCCCCCCcC
Q 021781 206 HHDCPVCCEYLF--ETRQDVIVLP--------CGHTIHKNCLKEMREHHQYACPICSKS 254 (307)
Q Consensus 206 ~~~CPIClE~lf--~s~~~v~~Lp--------CGH~fH~~Ci~~wl~~~~~~CPlCrks 254 (307)
...|.||..... +......++. |||+.+.+|++..+......||.|++.
T Consensus 207 ~~~c~ic~~~~~~n~~~~~p~vl~~~~~~~~~c~htlc~~c~~~~l~~~~~~cp~~~~~ 265 (296)
T KOG4185|consen 207 EKLCEICERIYSENDEKLAPLVLSLSRLKEKIEGHTLCKECIDTILLQAGIKCPFCTWS 265 (296)
T ss_pred HHHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcchHHHHHHhhhcCCcccce
Confidence 356888876433 1233445666 999999999999877655789999975
No 198
>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=32.55 E-value=35 Score=22.69 Aligned_cols=21 Identities=24% Similarity=0.360 Sum_probs=14.7
Q ss_pred ccCcCCCCccceEecCccccc
Q 021781 135 QVCVNCGVCMGEYFCESCKLF 155 (307)
Q Consensus 135 ~~C~~Cg~~fa~YfC~~Ckl~ 155 (307)
..|..++...+.|||..|+.+
T Consensus 4 ~~C~~H~~~~~~~~C~~C~~~ 24 (42)
T PF00643_consen 4 PKCPEHPEEPLSLFCEDCNEP 24 (42)
T ss_dssp SB-SSTTTSBEEEEETTTTEE
T ss_pred ccCccCCccceEEEecCCCCc
Confidence 457777777788888887654
No 199
>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=32.09 E-value=47 Score=34.34 Aligned_cols=46 Identities=26% Similarity=0.655 Sum_probs=29.7
Q ss_pred CceeeeCCCCccccccccCcCCCCccc------eEecCccccccCCCCCCeecCCCCCcc
Q 021781 119 VNQVICSLCGTEQKVQQVCVNCGVCMG------EYFCESCKLFDDDTSKKQYHCDGCGIC 172 (307)
Q Consensus 119 v~~v~C~~C~~eQ~v~~~C~~Cg~~fa------~YfC~~Ckl~ddd~~k~~yHC~~CgiC 172 (307)
...++|..|+.. ..|++|+..+. .-.|.-|.+- ...+..|+.||-=
T Consensus 211 a~~~~C~~Cg~~----~~C~~C~~~l~~h~~~~~l~Ch~Cg~~----~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 211 SKNLLCRSCGYI----LCCPNCDVSLTYHKKEGKLRCHYCGYQ----EPIPKTCPQCGSE 262 (505)
T ss_pred CCeeEhhhCcCc----cCCCCCCCceEEecCCCeEEcCCCcCc----CCCCCCCCCCCCC
Confidence 345788888864 36899987774 3456666533 3445677777653
No 200
>PF15353 HECA: Headcase protein family homologue
Probab=31.98 E-value=27 Score=29.37 Aligned_cols=16 Identities=25% Similarity=0.891 Sum_probs=13.7
Q ss_pred CCCCccchHHHHHHhh
Q 021781 227 PCGHTIHKNCLKEMRE 242 (307)
Q Consensus 227 pCGH~fH~~Ci~~wl~ 242 (307)
|-|+.+|++||++|-.
T Consensus 39 p~~~~MH~~CF~~wE~ 54 (107)
T PF15353_consen 39 PFGQYMHRECFEKWED 54 (107)
T ss_pred CCCCchHHHHHHHHHH
Confidence 4489999999999965
No 201
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=31.95 E-value=31 Score=23.90 Aligned_cols=21 Identities=48% Similarity=1.050 Sum_probs=10.5
Q ss_pred ecCCCCCcccccCCccceecCCcc
Q 021781 164 YHCDGCGICRIGGCDNFFHCNKCR 187 (307)
Q Consensus 164 yHC~~CgiCR~G~~e~ffHC~~C~ 187 (307)
|.|+.|+. -+-| ..|||..|.
T Consensus 1 ~~C~~C~~-~i~g--~r~~C~~C~ 21 (46)
T cd02249 1 YSCDGCLK-PIVG--VRYHCLVCE 21 (46)
T ss_pred CCCcCCCC-CCcC--CEEECCCCC
Confidence 45555555 2222 466666654
No 202
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=31.44 E-value=29 Score=23.24 Aligned_cols=9 Identities=44% Similarity=1.113 Sum_probs=4.0
Q ss_pred eeeeCCCCc
Q 021781 121 QVICSLCGT 129 (307)
Q Consensus 121 ~v~C~~C~~ 129 (307)
.|.|+.|++
T Consensus 25 ~vrC~~C~~ 33 (37)
T PF13719_consen 25 KVRCPKCGH 33 (37)
T ss_pred EEECCCCCc
Confidence 444444443
No 203
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=31.14 E-value=29 Score=30.72 Aligned_cols=11 Identities=27% Similarity=0.990 Sum_probs=5.6
Q ss_pred CcCCCCccceE
Q 021781 137 CVNCGVCMGEY 147 (307)
Q Consensus 137 C~~Cg~~fa~Y 147 (307)
|++||..|+.|
T Consensus 31 c~~c~~~f~~~ 41 (154)
T PRK00464 31 CLACGKRFTTF 41 (154)
T ss_pred ccccCCcceEe
Confidence 45555555444
No 204
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=30.66 E-value=22 Score=35.25 Aligned_cols=21 Identities=43% Similarity=0.934 Sum_probs=17.1
Q ss_pred ccCcCCCCccceEecCccccc
Q 021781 135 QVCVNCGVCMGEYFCESCKLF 155 (307)
Q Consensus 135 ~~C~~Cg~~fa~YfC~~Ckl~ 155 (307)
..|.-||+.+++|.|+-|+|.
T Consensus 8 ~~C~ic~vq~~~YtCPRCn~~ 28 (383)
T KOG4317|consen 8 LACGICGVQKREYTCPRCNLL 28 (383)
T ss_pred eeccccccccccccCCCCCcc
Confidence 357788899999999998875
No 205
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 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 DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=30.46 E-value=30 Score=29.53 Aligned_cols=38 Identities=26% Similarity=0.581 Sum_probs=25.4
Q ss_pred CCCCCeecCCCCCcccccCCccceecCCccceeecccccccccc
Q 021781 158 DTSKKQYHCDGCGICRIGGCDNFFHCNKCRCCYSMLLKNSHPCV 201 (307)
Q Consensus 158 d~~k~~yHC~~CgiCR~G~~e~ffHC~~C~~C~s~~l~~~H~Ci 201 (307)
+.....-.|..| ++-....-.||..||.|+-.- .|-|.
T Consensus 43 ~~~~~~~~C~~C---~~~kp~Rs~HC~~C~~CV~~~---DHHC~ 80 (174)
T PF01529_consen 43 DENGELKYCSTC---KIIKPPRSHHCRVCNRCVLRF---DHHCP 80 (174)
T ss_pred ccCCCCEECccc---CCcCCCcceeccccccccccc---cccch
Confidence 334445555554 555567899999999998753 56664
No 206
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=30.00 E-value=17 Score=32.22 Aligned_cols=25 Identities=32% Similarity=0.883 Sum_probs=16.7
Q ss_pred ceEecCccccccCCCCCCeecCCCCC--ccccc
Q 021781 145 GEYFCESCKLFDDDTSKKQYHCDGCG--ICRIG 175 (307)
Q Consensus 145 a~YfC~~Ckl~ddd~~k~~yHC~~Cg--iCR~G 175 (307)
.+-||++|-+| ++|-|-.|| +|-++
T Consensus 117 ~r~fCaVCG~~------S~ysC~~CG~kyCsv~ 143 (156)
T KOG3362|consen 117 LRKFCAVCGYD------SKYSCVNCGTKYCSVR 143 (156)
T ss_pred cchhhhhcCCC------chhHHHhcCCceeech
Confidence 45677777744 367777777 66665
No 207
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=29.56 E-value=44 Score=37.98 Aligned_cols=56 Identities=16% Similarity=0.425 Sum_probs=39.6
Q ss_pred cCCCCCCCCcccccccccCCceeEEcC---CCCccchHHHHHHhhcCCCCCCCCCcCcc
Q 021781 201 VEGAMHHDCPVCCEYLFETRQDVIVLP---CGHTIHKNCLKEMREHHQYACPICSKSVC 256 (307)
Q Consensus 201 iE~~~~~~CPIClE~lf~s~~~v~~Lp---CGH~fH~~Ci~~wl~~~~~~CPlCrks~~ 256 (307)
.++.....|-||.|++-...+.-.... ||--.++.|++-=.+.++..||.|+....
T Consensus 12 ~~~~~~qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCYEYEr~eG~q~CPqCktrYk 70 (1079)
T PLN02638 12 MKHGGGQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCYEYERKDGNQSCPQCKTKYK 70 (1079)
T ss_pred ccccCCceeeecccccCcCCCCCEEEEeccCCCccccchhhhhhhcCCccCCccCCchh
Confidence 344456799999998654433334444 56669999996666667889999997654
No 208
>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=29.29 E-value=87 Score=23.59 Aligned_cols=48 Identities=21% Similarity=0.521 Sum_probs=32.7
Q ss_pred CCCCCcccccccccCCceeEEcCCC--CccchHHHHHHhhcCCCCCCCCCcCccc
Q 021781 205 MHHDCPVCCEYLFETRQDVIVLPCG--HTIHKNCLKEMREHHQYACPICSKSVCD 257 (307)
Q Consensus 205 ~~~~CPIClE~lf~s~~~v~~LpCG--H~fH~~Ci~~wl~~~~~~CPlCrks~~d 257 (307)
+..+|-.|-.+|.....+.. -|. -+|+..|.+..|. ..||-|+..+..
T Consensus 4 lrpnCE~C~~dLp~~s~~A~--ICSfECTFC~~C~e~~l~---~~CPNCgGelv~ 53 (57)
T PF06906_consen 4 LRPNCECCDKDLPPDSPEAY--ICSFECTFCADCAETMLN---GVCPNCGGELVR 53 (57)
T ss_pred cCCCccccCCCCCCCCCcce--EEeEeCcccHHHHHHHhc---CcCcCCCCcccc
Confidence 45577778776654332222 243 4799999999884 689999988764
No 209
>KOG3113 consensus Uncharacterized conserved protein [Function unknown]
Probab=29.05 E-value=50 Score=31.93 Aligned_cols=49 Identities=20% Similarity=0.419 Sum_probs=35.7
Q ss_pred CCCCCCcccccccccCCcee-EEcCCCCccchHHHHHHhhcCCCCCCCCCcCcc
Q 021781 204 AMHHDCPVCCEYLFETRQDV-IVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 256 (307)
Q Consensus 204 ~~~~~CPIClE~lf~s~~~v-~~LpCGH~fH~~Ci~~wl~~~~~~CPlCrks~~ 256 (307)
.....|||=.-.|-. .... ...+|||+|-..-+++.- ...|++|...+.
T Consensus 109 ~a~fiCPvtgleMng-~~~F~~l~~CGcV~SerAlKeik---as~C~~C~a~y~ 158 (293)
T KOG3113|consen 109 RARFICPVTGLEMNG-KYRFCALRCCGCVFSERALKEIK---ASVCHVCGAAYQ 158 (293)
T ss_pred cceeecccccceecc-eEEEEEEeccceeccHHHHHHhh---hccccccCCccc
Confidence 456789998654433 3333 445999999999888763 468999998875
No 210
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=28.66 E-value=23 Score=24.14 Aligned_cols=13 Identities=38% Similarity=1.076 Sum_probs=5.5
Q ss_pred cceEecCcccccc
Q 021781 144 MGEYFCESCKLFD 156 (307)
Q Consensus 144 fa~YfC~~Ckl~d 156 (307)
|-+|||+-|+.|=
T Consensus 1 m~ryyCdyC~~~~ 13 (38)
T PF06220_consen 1 MPRYYCDYCKKYL 13 (38)
T ss_dssp --S-B-TTT--B-
T ss_pred CcCeeccccccee
Confidence 4689999998775
No 211
>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=28.61 E-value=26 Score=30.71 Aligned_cols=7 Identities=43% Similarity=1.450 Sum_probs=3.0
Q ss_pred eecCCcc
Q 021781 181 FHCNKCR 187 (307)
Q Consensus 181 fHC~~C~ 187 (307)
|+|..||
T Consensus 129 F~Cp~Cg 135 (158)
T TIGR00373 129 FTCPRCG 135 (158)
T ss_pred CcCCCCC
Confidence 4444444
No 212
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=28.61 E-value=37 Score=34.42 Aligned_cols=37 Identities=24% Similarity=0.551 Sum_probs=29.5
Q ss_pred CCCCCCcccccccccCCceeEEcCCCCccchHHHHHHhhc
Q 021781 204 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH 243 (307)
Q Consensus 204 ~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~ 243 (307)
.....|.||.+.. .. ....+.|||.|+..|...++..
T Consensus 68 ~~~~~c~ic~~~~-~~--~~~~~~c~H~~c~~cw~~yl~~ 104 (444)
T KOG1815|consen 68 KGDVQCGICVESY-DG--EIIGLGCGHPFCPPCWTGYLGT 104 (444)
T ss_pred CccccCCcccCCC-cc--hhhhcCCCcHHHHHHHHHHhhh
Confidence 4568899999853 22 4677899999999999999864
No 213
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=28.44 E-value=32 Score=32.67 Aligned_cols=20 Identities=25% Similarity=0.884 Sum_probs=16.0
Q ss_pred cccCcCCCCcc--------ceEecCccc
Q 021781 134 QQVCVNCGVCM--------GEYFCESCK 153 (307)
Q Consensus 134 ~~~C~~Cg~~f--------a~YfC~~Ck 153 (307)
++.|+.||..+ +.|||+.|.
T Consensus 244 g~pCprCG~~I~~~~~~gR~t~~CP~CQ 271 (272)
T PRK14810 244 GEPCLNCKTPIRRVVVAGRSSHYCPHCQ 271 (272)
T ss_pred CCcCCCCCCeeEEEEECCCccEECcCCc
Confidence 46799999887 678888884
No 214
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=28.35 E-value=30 Score=31.08 Aligned_cols=11 Identities=45% Similarity=0.990 Sum_probs=6.6
Q ss_pred CCCCccccccc
Q 021781 206 HHDCPVCCEYL 216 (307)
Q Consensus 206 ~~~CPIClE~l 216 (307)
...||+|.+.|
T Consensus 136 ~F~Cp~Cg~~L 146 (178)
T PRK06266 136 GFRCPQCGEML 146 (178)
T ss_pred CCcCCCCCCCC
Confidence 45677776543
No 215
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=28.07 E-value=37 Score=22.72 Aligned_cols=28 Identities=25% Similarity=0.799 Sum_probs=10.4
Q ss_pred cCcCCCCccceEecCccccccCCCCCCeecCCCCC
Q 021781 136 VCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCG 170 (307)
Q Consensus 136 ~C~~Cg~~fa~YfC~~Ckl~ddd~~k~~yHC~~Cg 170 (307)
.|++||..+.. ++-++| ++.-+-|+.||
T Consensus 2 fC~~CG~~l~~------~ip~gd-~r~R~vC~~Cg 29 (34)
T PF14803_consen 2 FCPQCGGPLER------RIPEGD-DRERLVCPACG 29 (34)
T ss_dssp B-TTT--B-EE------E--TT--SS-EEEETTTT
T ss_pred ccccccChhhh------hcCCCC-CccceECCCCC
Confidence 46666666532 222222 45556666665
No 216
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=27.96 E-value=28 Score=22.02 Aligned_cols=11 Identities=27% Similarity=1.165 Sum_probs=8.0
Q ss_pred ceEecCccccc
Q 021781 145 GEYFCESCKLF 155 (307)
Q Consensus 145 a~YfC~~Ckl~ 155 (307)
+.|||++|+.+
T Consensus 2 ~~~~C~~C~~~ 12 (35)
T smart00451 2 GGFYCKLCNVT 12 (35)
T ss_pred cCeEccccCCc
Confidence 56888888655
No 217
>PRK10445 endonuclease VIII; Provisional
Probab=27.40 E-value=35 Score=32.24 Aligned_cols=20 Identities=30% Similarity=0.953 Sum_probs=15.7
Q ss_pred cccCcCCCCcc--------ceEecCccc
Q 021781 134 QQVCVNCGVCM--------GEYFCESCK 153 (307)
Q Consensus 134 ~~~C~~Cg~~f--------a~YfC~~Ck 153 (307)
++.|+.||... +.|||+.|.
T Consensus 235 g~~Cp~Cg~~I~~~~~~gR~t~~CP~CQ 262 (263)
T PRK10445 235 GEACERCGGIIEKTTLSSRPFYWCPGCQ 262 (263)
T ss_pred CCCCCCCCCEeEEEEECCCCcEECCCCc
Confidence 47799999887 567787774
No 218
>PF06937 EURL: EURL protein; InterPro: IPR009704 This family consists of several animal EURL proteins. EURL is preferentially expressed in chick retinal precursor cells as well as in the anterior epithelial cells of the lens at early stages of development. EURL transcripts are found primarily in the peripheral dorsal retina, i.e., the most undifferentiated part of the dorsal retina. EURL transcripts are also detected in the lens at stage 18 and remain abundant in the proliferating epithelial cells of the lens until at least day 11. The distribution pattern of EURL in the developing retina and lens suggest a role before the events leading to cell determination and differentiation [].
Probab=27.24 E-value=50 Score=32.07 Aligned_cols=43 Identities=23% Similarity=0.390 Sum_probs=25.9
Q ss_pred CCCCCCcccccccccCCceeEEcCCCC----ccchHHHHHHhhcCCCCCC
Q 021781 204 AMHHDCPVCCEYLFETRQDVIVLPCGH----TIHKNCLKEMREHHQYACP 249 (307)
Q Consensus 204 ~~~~~CPIClE~lf~s~~~v~~LpCGH----~fH~~Ci~~wl~~~~~~CP 249 (307)
.+-.-|+||+| +.-.+.+..-| =| .=|++||++|=.-.+..||
T Consensus 28 ~tLsfChiCfE-l~iegvpks~l--lHtkSlRGHrdCFEK~HlIanQ~~p 74 (285)
T PF06937_consen 28 ETLSFCHICFE-LSIEGVPKSNL--LHTKSLRGHRDCFEKYHLIANQDCP 74 (285)
T ss_pred cceeecceeec-cccccCccccc--cccccccchHHHHHHHHHHHcCCCC
Confidence 34567888888 44333222212 12 2489999998544567898
No 219
>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=27.19 E-value=43 Score=21.97 Aligned_cols=9 Identities=44% Similarity=1.113 Sum_probs=4.2
Q ss_pred eeeeCCCCc
Q 021781 121 QVICSLCGT 129 (307)
Q Consensus 121 ~v~C~~C~~ 129 (307)
.+.|+.|++
T Consensus 25 ~v~C~~C~~ 33 (38)
T TIGR02098 25 KVRCGKCGH 33 (38)
T ss_pred EEECCCCCC
Confidence 454554443
No 220
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=27.13 E-value=23 Score=32.19 Aligned_cols=29 Identities=31% Similarity=0.553 Sum_probs=23.3
Q ss_pred CCCCCcccccccccCCceeEEcCCCCccch
Q 021781 205 MHHDCPVCCEYLFETRQDVIVLPCGHTIHK 234 (307)
Q Consensus 205 ~~~~CPIClE~lf~s~~~v~~LpCGH~fH~ 234 (307)
....|.||||+|.. .+.+..|||=-.+|+
T Consensus 176 dkGECvICLEdL~~-GdtIARLPCLCIYHK 204 (205)
T KOG0801|consen 176 DKGECVICLEDLEA-GDTIARLPCLCIYHK 204 (205)
T ss_pred cCCcEEEEhhhccC-CCceeccceEEEeec
Confidence 46899999998654 667888999877775
No 221
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=27.12 E-value=36 Score=32.35 Aligned_cols=20 Identities=40% Similarity=1.047 Sum_probs=16.1
Q ss_pred cccCcCCCCcc--------ceEecCccc
Q 021781 134 QQVCVNCGVCM--------GEYFCESCK 153 (307)
Q Consensus 134 ~~~C~~Cg~~f--------a~YfC~~Ck 153 (307)
++.|+.||..+ +.|||+.|.
T Consensus 235 g~pC~~Cg~~I~~~~~~gR~ty~Cp~CQ 262 (269)
T PRK14811 235 GQPCPRCGTPIEKIVVGGRGTHFCPQCQ 262 (269)
T ss_pred cCCCCcCCCeeEEEEECCCCcEECCCCc
Confidence 45799999887 678888885
No 222
>KOG3842 consensus Adaptor protein Pellino [Signal transduction mechanisms]
Probab=27.09 E-value=31 Score=34.40 Aligned_cols=47 Identities=30% Similarity=0.653 Sum_probs=32.4
Q ss_pred CCCCCCCccccccc----------ccCCceeEEcCCCCc--cchHHHHHHhhc-----CCCCCCCCCcC
Q 021781 203 GAMHHDCPVCCEYL----------FETRQDVIVLPCGHT--IHKNCLKEMREH-----HQYACPICSKS 254 (307)
Q Consensus 203 ~~~~~~CPIClE~l----------f~s~~~v~~LpCGH~--fH~~Ci~~wl~~-----~~~~CPlCrks 254 (307)
|+....||+=|.-| .+..++.+.|.|||. +|. |=.. ....||+|+..
T Consensus 287 NA~RPQCPVglnTL~~P~~~~~~~~~~~QP~vYl~CGHV~G~H~-----WG~~e~~g~~~r~CPmC~~~ 350 (429)
T KOG3842|consen 287 NAARPQCPVGLNTLAFPSKRRKRVVDEKQPWVYLNCGHVHGYHN-----WGVRENTGQRERECPMCRVV 350 (429)
T ss_pred hccCCCCCcccceeecccccccccccccCCeEEEeccccccccc-----cccccccCcccCcCCeeeee
Confidence 56678899998655 233468899999976 443 6432 13569999954
No 223
>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=26.96 E-value=70 Score=22.17 Aligned_cols=9 Identities=44% Similarity=1.047 Sum_probs=5.2
Q ss_pred ccCcCCCCc
Q 021781 135 QVCVNCGVC 143 (307)
Q Consensus 135 ~~C~~Cg~~ 143 (307)
-+||.||..
T Consensus 19 ~~CP~Cg~~ 27 (46)
T PF12760_consen 19 FVCPHCGST 27 (46)
T ss_pred CCCCCCCCe
Confidence 346666654
No 224
>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=26.76 E-value=32 Score=22.50 Aligned_cols=23 Identities=26% Similarity=0.527 Sum_probs=9.2
Q ss_pred cCcCCCCccceEecCccccccCCCCCCeecCCCCC
Q 021781 136 VCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCG 170 (307)
Q Consensus 136 ~C~~Cg~~fa~YfC~~Ckl~ddd~~k~~yHC~~Cg 170 (307)
.|+.|+..++- . +..+|-|+.||
T Consensus 4 ~Cp~C~se~~y--------~----D~~~~vCp~C~ 26 (30)
T PF08274_consen 4 KCPLCGSEYTY--------E----DGELLVCPECG 26 (30)
T ss_dssp --TTT-----E--------E-----SSSEEETTTT
T ss_pred CCCCCCCccee--------c----cCCEEeCCccc
Confidence 46666665543 2 24577777775
No 225
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=26.56 E-value=72 Score=24.30 Aligned_cols=18 Identities=33% Similarity=0.656 Sum_probs=13.9
Q ss_pred cccCceeeeCCCCccccc
Q 021781 116 RHEVNQVICSLCGTEQKV 133 (307)
Q Consensus 116 R~~v~~v~C~~C~~eQ~v 133 (307)
|.++.--+|+-|+.+...
T Consensus 15 r~~~miYiCgdC~~en~l 32 (62)
T KOG3507|consen 15 RTATMIYICGDCGQENTL 32 (62)
T ss_pred CcccEEEEeccccccccc
Confidence 667777888888887665
No 226
>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=26.30 E-value=43 Score=22.98 Aligned_cols=9 Identities=33% Similarity=0.855 Sum_probs=4.2
Q ss_pred CCCCccccc
Q 021781 206 HHDCPVCCE 214 (307)
Q Consensus 206 ~~~CPIClE 214 (307)
...||.|..
T Consensus 26 ~~~CP~Cg~ 34 (42)
T PF09723_consen 26 PVPCPECGS 34 (42)
T ss_pred CCcCCCCCC
Confidence 344555543
No 227
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=26.23 E-value=32 Score=37.25 Aligned_cols=48 Identities=29% Similarity=0.668 Sum_probs=37.3
Q ss_pred CCCCCcccccccccCCceeEEcCCCCccchHHHHHHhhc--CCCCCCCCCcCcc
Q 021781 205 MHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH--HQYACPICSKSVC 256 (307)
Q Consensus 205 ~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~--~~~~CPlCrks~~ 256 (307)
....||||++..++. ..+.|-|.|...|+...+.. ....||+|+..+.
T Consensus 20 k~lEc~ic~~~~~~p----~~~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~e 69 (684)
T KOG4362|consen 20 KILECPICLEHVKEP----SLLKCDHIFLKFCLNKLFESKKGPKQCALCKSDIE 69 (684)
T ss_pred hhccCCceeEEeecc----chhhhhHHHHhhhhhceeeccCccccchhhhhhhh
Confidence 357899999987763 67899999999999885543 2356999996664
No 228
>KOG1312 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=26.17 E-value=19 Score=35.37 Aligned_cols=32 Identities=28% Similarity=0.682 Sum_probs=26.6
Q ss_pred CCCCcccccCCccceecCCccceeecccccccccc
Q 021781 167 DGCGICRIGGCDNFFHCNKCRCCYSMLLKNSHPCV 201 (307)
Q Consensus 167 ~~CgiCR~G~~e~ffHC~~C~~C~s~~l~~~H~Ci 201 (307)
.+|..|++.+.-...||..||-|+.. -.|.|+
T Consensus 149 ~kCSTCki~KPARSKHCsiCNrCV~r---fDHHCi 180 (341)
T KOG1312|consen 149 VKCSTCKIRKPARSKHCSICNRCVHR---FDHHCI 180 (341)
T ss_pred CccccccCCCccccccchHHHHHHHH---hccceE
Confidence 57888888888888999999999875 368887
No 229
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=26.03 E-value=37 Score=24.69 Aligned_cols=24 Identities=29% Similarity=0.714 Sum_probs=19.7
Q ss_pred CceeeeCCCCccccc-cccCcCCCC
Q 021781 119 VNQVICSLCGTEQKV-QQVCVNCGV 142 (307)
Q Consensus 119 v~~v~C~~C~~eQ~v-~~~C~~Cg~ 142 (307)
...++|+.|+...++ +..|..||.
T Consensus 12 ~~k~ICrkC~ARnp~~A~~CRKCg~ 36 (48)
T PRK04136 12 FNKKICMRCNARNPWRATKCRKCGY 36 (48)
T ss_pred hcccchhcccCCCCccccccccCCC
Confidence 356899999999887 678988886
No 230
>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=25.79 E-value=66 Score=31.52 Aligned_cols=25 Identities=32% Similarity=0.692 Sum_probs=21.2
Q ss_pred CceeeeCCCCccccc-cccCcCCCCc
Q 021781 119 VNQVICSLCGTEQKV-QQVCVNCGVC 143 (307)
Q Consensus 119 v~~v~C~~C~~eQ~v-~~~C~~Cg~~ 143 (307)
..-..|+.|+++..+ ...|++||..
T Consensus 208 ~RyL~CslC~teW~~~R~~C~~Cg~~ 233 (305)
T TIGR01562 208 LRYLSCSLCATEWHYVRVKCSHCEES 233 (305)
T ss_pred ceEEEcCCCCCcccccCccCCCCCCC
Confidence 457899999999887 5679999985
No 231
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=25.78 E-value=38 Score=26.27 Aligned_cols=29 Identities=38% Similarity=0.715 Sum_probs=21.8
Q ss_pred CceeeeCCCCcccccc------ccCcCCCCccceE
Q 021781 119 VNQVICSLCGTEQKVQ------QVCVNCGVCMGEY 147 (307)
Q Consensus 119 v~~v~C~~C~~eQ~v~------~~C~~Cg~~fa~Y 147 (307)
--.|.|.-|+.+|-+= -.|..||..+++-
T Consensus 17 Fl~VkCpdC~N~q~vFshast~V~C~~CG~~l~~P 51 (67)
T COG2051 17 FLRVKCPDCGNEQVVFSHASTVVTCLICGTTLAEP 51 (67)
T ss_pred EEEEECCCCCCEEEEeccCceEEEecccccEEEec
Confidence 3478999999998761 3588998877654
No 232
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 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 [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=25.71 E-value=42 Score=24.94 Aligned_cols=35 Identities=29% Similarity=0.483 Sum_probs=21.1
Q ss_pred ceeeeCCCCccccc---c---ccCcCCCCccceEecCcccc
Q 021781 120 NQVICSLCGTEQKV---Q---QVCVNCGVCMGEYFCESCKL 154 (307)
Q Consensus 120 ~~v~C~~C~~eQ~v---~---~~C~~Cg~~fa~YfC~~Ckl 154 (307)
..|.|..|..+|.+ + -.|..||..+++-.=++-+|
T Consensus 6 m~VkCp~C~~~q~vFSha~t~V~C~~Cg~~L~~PtGGKa~l 46 (55)
T PF01667_consen 6 MDVKCPGCYNIQTVFSHAQTVVKCVVCGTVLAQPTGGKARL 46 (55)
T ss_dssp EEEE-TTT-SEEEEETT-SS-EE-SSSTSEEEEE-SSSEEE
T ss_pred EEEECCCCCCeeEEEecCCeEEEcccCCCEecCCCCcCeEE
Confidence 46888888888876 1 35888888887765555444
No 233
>KOG3842 consensus Adaptor protein Pellino [Signal transduction mechanisms]
Probab=25.65 E-value=67 Score=32.12 Aligned_cols=51 Identities=24% Similarity=0.610 Sum_probs=33.5
Q ss_pred CCCCccccccc--------------ccCCcee-EEcCCCCccchHHHHHHhhc--------CCCCCCCCCcCcc
Q 021781 206 HHDCPVCCEYL--------------FETRQDV-IVLPCGHTIHKNCLKEMREH--------HQYACPICSKSVC 256 (307)
Q Consensus 206 ~~~CPIClE~l--------------f~s~~~v-~~LpCGH~fH~~Ci~~wl~~--------~~~~CPlCrks~~ 256 (307)
+..||+|+.-- .+++-+. .+-||||.--.+=..-|.+. .+..||.|-..+.
T Consensus 341 ~r~CPmC~~~gp~V~L~lG~E~~f~vD~G~pthaF~PCGHv~sekt~~YWs~iplPhGT~~f~a~CPFC~~~L~ 414 (429)
T KOG3842|consen 341 ERECPMCRVVGPYVPLWLGCEAGFYVDAGPPTHAFNPCGHVCSEKTVKYWSQIPLPHGTHAFHAACPFCATQLA 414 (429)
T ss_pred cCcCCeeeeecceeeeeccccceeEecCCCcccccCCcccccchhhhhHhhcCcCCCccccccccCcchhhhhc
Confidence 77899998520 1222222 34499999888888888753 2456999987654
No 234
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=25.53 E-value=55 Score=27.01 Aligned_cols=32 Identities=25% Similarity=0.591 Sum_probs=20.8
Q ss_pred ccceecCCcc-ceeeccccccccccCCCCCCCCcccccc
Q 021781 178 DNFFHCNKCR-CCYSMLLKNSHPCVEGAMHHDCPVCCEY 215 (307)
Q Consensus 178 e~ffHC~~C~-~C~s~~l~~~H~CiE~~~~~~CPIClE~ 215 (307)
..+|+|..|| ..+++.+. + +..+..||+|..+
T Consensus 19 pt~f~CP~Cge~~v~v~~~--k----~~~h~~C~~CG~y 51 (99)
T PRK14892 19 PKIFECPRCGKVSISVKIK--K----NIAIITCGNCGLY 51 (99)
T ss_pred CcEeECCCCCCeEeeeecC--C----CcceEECCCCCCc
Confidence 4678888888 33333332 2 4568899999975
No 235
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=25.52 E-value=59 Score=30.81 Aligned_cols=46 Identities=24% Similarity=0.666 Sum_probs=33.7
Q ss_pred CCccceEecCccccccCCCCCCeecCCCCCcccccCCccceecCCccceeec
Q 021781 141 GVCMGEYFCESCKLFDDDTSKKQYHCDGCGICRIGGCDNFFHCNKCRCCYSM 192 (307)
Q Consensus 141 g~~fa~YfC~~Ckl~ddd~~k~~yHC~~CgiCR~G~~e~ffHC~~C~~C~s~ 192 (307)
|....-.||+.|+++- .+.-.||.-||.|-.+ ---||.==|.|+..
T Consensus 108 ~~~~~~~~C~~C~~~r---PpRs~HCsvC~~CV~r---fDHHC~WvnnCVG~ 153 (299)
T KOG1311|consen 108 GIQVEWKYCDTCQLYR---PPRSSHCSVCNNCVLR---FDHHCPWLNNCIGE 153 (299)
T ss_pred CcccceEEcCcCcccC---CCCcccchhhcccccc---cCCCCCCccceECC
Confidence 4555678999999993 3457799999888764 23678777777764
No 236
>KOG4399 consensus C2HC-type Zn-finger protein [General function prediction only]
Probab=25.45 E-value=18 Score=35.11 Aligned_cols=53 Identities=15% Similarity=0.159 Sum_probs=40.6
Q ss_pred ccCcCCCCccceEecCccccccCCCCCCeecCCCCCcccccCCccceecCCccceee
Q 021781 135 QVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGICRIGGCDNFFHCNKCRCCYS 191 (307)
Q Consensus 135 ~~C~~Cg~~fa~YfC~~Ckl~ddd~~k~~yHC~~CgiCR~G~~e~ffHC~~C~~C~s 191 (307)
-.|+-|.+..+.-||.+|-=+|-. .-|||.|.-||--....+-||.+|..|..
T Consensus 250 i~C~~~~~~A~~~~C~iC~~~~~~----R~~C~~~kA~~~~~Q~K~N~~~~~~~~~q 302 (325)
T KOG4399|consen 250 IHCSICNHCAVKHGCFICGELDHK----RSTCPNIKAVRKQKQRKSNKMKMETTKGQ 302 (325)
T ss_pred eeeecccchhhhcceeeccccccc----cccCccHHHHHHHHhcccchhhhhhhhhh
Confidence 357777777888899999888642 27999999998877667778887777654
No 237
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=25.35 E-value=55 Score=32.66 Aligned_cols=49 Identities=16% Similarity=0.316 Sum_probs=35.5
Q ss_pred CCCCCCcccccccccCCceeEEcCCCCccchHHHHHHhhcCCCCCCCCCcCcc
Q 021781 204 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 256 (307)
Q Consensus 204 ~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlCrks~~ 256 (307)
.....||||+...-+ +.+.--=|-+|+-.|+-.++.. ..+||+=.+++.
T Consensus 298 ~~~~~CpvClk~r~N---ptvl~vSGyVfCY~Ci~~Yv~~-~~~CPVT~~p~~ 346 (357)
T KOG0826|consen 298 PDREVCPVCLKKRQN---PTVLEVSGYVFCYPCIFSYVVN-YGHCPVTGYPAS 346 (357)
T ss_pred CccccChhHHhccCC---CceEEecceEEeHHHHHHHHHh-cCCCCccCCcch
Confidence 456789999974222 2233334999999999999984 578999887764
No 238
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=25.31 E-value=34 Score=22.56 Aligned_cols=23 Identities=35% Similarity=0.702 Sum_probs=11.2
Q ss_pred ceeeeCCCCccc-cccccCcCCCC
Q 021781 120 NQVICSLCGTEQ-KVQQVCVNCGV 142 (307)
Q Consensus 120 ~~v~C~~C~~eQ-~v~~~C~~Cg~ 142 (307)
.--.|..|++.+ |....|++||.
T Consensus 10 ~~~rC~~Cg~~~~pPr~~Cp~C~s 33 (37)
T PF12172_consen 10 LGQRCRDCGRVQFPPRPVCPHCGS 33 (37)
T ss_dssp EEEE-TTT--EEES--SEETTTT-
T ss_pred EEEEcCCCCCEecCCCcCCCCcCc
Confidence 345677777764 45677777764
No 239
>PF00412 LIM: LIM domain; InterPro: IPR001781 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 LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=24.77 E-value=33 Score=23.95 Aligned_cols=38 Identities=26% Similarity=0.780 Sum_probs=25.3
Q ss_pred CcccccccccCCceeEEcCCCCccchHHHHHHhhcCCCCCCCCCcCccc
Q 021781 209 CPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 257 (307)
Q Consensus 209 CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPlCrks~~d 257 (307)
|+.|.+.+... ..++..=|..||.+|+ +|-.|++++.+
T Consensus 1 C~~C~~~I~~~--~~~~~~~~~~~H~~Cf---------~C~~C~~~l~~ 38 (58)
T PF00412_consen 1 CARCGKPIYGT--EIVIKAMGKFWHPECF---------KCSKCGKPLND 38 (58)
T ss_dssp BTTTSSBESSS--SEEEEETTEEEETTTS---------BETTTTCBTTT
T ss_pred CCCCCCCccCc--EEEEEeCCcEEEcccc---------ccCCCCCccCC
Confidence 56677765532 2333356889998765 68889988865
No 240
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=24.72 E-value=42 Score=31.76 Aligned_cols=20 Identities=30% Similarity=1.039 Sum_probs=15.3
Q ss_pred cccCcCCCCcc--------ceEecCccc
Q 021781 134 QQVCVNCGVCM--------GEYFCESCK 153 (307)
Q Consensus 134 ~~~C~~Cg~~f--------a~YfC~~Ck 153 (307)
++.|+.||... +.|||+.|.
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 272 (274)
T PRK01103 245 GEPCRRCGTPIEKIKQGGRSTFFCPRCQ 272 (274)
T ss_pred CCCCCCCCCeeEEEEECCCCcEECcCCC
Confidence 35699999887 567888774
No 241
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=24.49 E-value=67 Score=21.95 Aligned_cols=30 Identities=33% Similarity=0.770 Sum_probs=19.2
Q ss_pred ccCcCCCCccceEecCccccccCCCCCCeecCCCCCc
Q 021781 135 QVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGI 171 (307)
Q Consensus 135 ~~C~~Cg~~fa~YfC~~Ckl~ddd~~k~~yHC~~Cgi 171 (307)
.-||.||-.=.. . |+|...+.-|+|..||.
T Consensus 4 ~pCP~CGG~DrF------r-~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 4 GPCPNCGGSDRF------R-FDDKDGRGTWFCSVCGA 33 (37)
T ss_pred cCCCCCCCcccc------c-cccCCCCcCEEeCCCCC
Confidence 468888773211 2 46656678888888764
No 242
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=23.82 E-value=33 Score=24.33 Aligned_cols=18 Identities=17% Similarity=0.397 Sum_probs=14.0
Q ss_pred eEEc-CCCCccchHHHHHH
Q 021781 223 VIVL-PCGHTIHKNCLKEM 240 (307)
Q Consensus 223 v~~L-pCGH~fH~~Ci~~w 240 (307)
.+.- .|||.|+..|..+|
T Consensus 40 ~v~C~~C~~~fC~~C~~~~ 58 (64)
T smart00647 40 RVTCPKCGFSFCFRCKVPW 58 (64)
T ss_pred eeECCCCCCeECCCCCCcC
Confidence 3444 68999999998888
No 243
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=23.80 E-value=53 Score=23.51 Aligned_cols=22 Identities=45% Similarity=1.251 Sum_probs=11.6
Q ss_pred ecCCCCCcccccCCccceecCCcc
Q 021781 164 YHCDGCGICRIGGCDNFFHCNKCR 187 (307)
Q Consensus 164 yHC~~CgiCR~G~~e~ffHC~~C~ 187 (307)
|.|+.||.--+-| --|||..|.
T Consensus 1 y~Cd~C~~~pI~G--~R~~C~~C~ 22 (48)
T cd02341 1 FKCDSCGIEPIPG--TRYHCSECD 22 (48)
T ss_pred CCCCCCCCCcccc--ceEECCCCC
Confidence 5566666544432 246666654
No 244
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=23.76 E-value=51 Score=27.57 Aligned_cols=13 Identities=31% Similarity=0.726 Sum_probs=6.4
Q ss_pred cccccCcCCCCcc
Q 021781 132 KVQQVCVNCGVCM 144 (307)
Q Consensus 132 ~v~~~C~~Cg~~f 144 (307)
|+...|..||..|
T Consensus 69 p~~~~C~~Cg~~~ 81 (117)
T PRK00564 69 KVELECKDCSHVF 81 (117)
T ss_pred CCEEEhhhCCCcc
Confidence 4444555555443
No 245
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=23.56 E-value=47 Score=32.35 Aligned_cols=37 Identities=24% Similarity=0.673 Sum_probs=25.1
Q ss_pred ccCcCCCCccceEecCccccccCCCCCCeecCCCCCcccc
Q 021781 135 QVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGICRI 174 (307)
Q Consensus 135 ~~C~~Cg~~fa~YfC~~Ckl~ddd~~k~~yHC~~CgiCR~ 174 (307)
..+...|....+-||.+|+.|--+ .-.||.-||.|-.
T Consensus 98 ~~~~~~~~~~~~~~C~~C~~~KP~---RS~HC~~Cn~CV~ 134 (309)
T COG5273 98 SRLLDDGKFGTENFCSTCNIYKPP---RSHHCSICNRCVL 134 (309)
T ss_pred hhhhhcCccccceeccccccccCC---CCccchhhcchhh
Confidence 556778888889999999999432 1345555555544
No 246
>PF05458 Siva: Cd27 binding protein (Siva); InterPro: IPR022773 Siva binds to the CD27 cytoplasmic tail. It has a DD homology region, a box-B-like ring finger, and a zinc finger-like domain. Overexpression of Siva in various cell lines induces apoptosis, suggesting an important role for Siva in the CD27-transduced apoptotic pathway []. Siva-1 binds to and inhibits BCL-X(L)-mediated protection against UV radiation-induced apoptosis. Indeed, the unique amphipathic helical region (SAH) present in Siva-1 is required for its binding to BCL-X(L) and sensitising cells to UV radiation. Natural complexes of Siva-1/BCL-X(L) are detected in HUT78 and murine thymocyte, suggesting a potential role for Siva-1 in regulating T cell homeostasis []. This family contains both Siva-1 and the shorter Siva-2 lacking the sequence coded by exon 2. It has been suggested that Siva-2 could regulate the function of Siva-1 [].
Probab=23.45 E-value=58 Score=29.34 Aligned_cols=32 Identities=28% Similarity=0.814 Sum_probs=16.7
Q ss_pred eeeCCCCcc--ccccccCcCCCCccceEecCccccccC
Q 021781 122 VICSLCGTE--QKVQQVCVNCGVCMGEYFCESCKLFDD 157 (307)
Q Consensus 122 v~C~~C~~e--Q~v~~~C~~Cg~~fa~YfC~~Ckl~dd 157 (307)
..|..|... +.-...|.+|+ .+||+.|-+.|-
T Consensus 125 ~~C~~Cdr~lC~~C~~~C~~C~----~~~Cs~Cs~~~y 158 (175)
T PF05458_consen 125 SVCSQCDRALCESCIRSCSSCS----EVFCSLCSTVNY 158 (175)
T ss_pred ccccccCcHHHHHHHhhhhchh----hhhhcCcccccc
Confidence 355555543 22233355554 356777776654
No 247
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=23.21 E-value=60 Score=22.53 Aligned_cols=11 Identities=45% Similarity=1.168 Sum_probs=5.3
Q ss_pred CCCeecCCCCC
Q 021781 160 SKKQYHCDGCG 170 (307)
Q Consensus 160 ~k~~yHC~~Cg 170 (307)
.++-|+|..|+
T Consensus 25 ~~~g~~C~~C~ 35 (53)
T PF00130_consen 25 GKQGYRCSWCG 35 (53)
T ss_dssp SSCEEEETTTT
T ss_pred CCCeEEECCCC
Confidence 34455555444
No 248
>cd07973 Spt4 Transcription elongation factor Spt4. Spt4 is a transcription elongation factor. Three transcription-elongation factors Spt4, Spt5, and Spt6, are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles. Spt4 functions entirely in the context of the Spt4-Spt5 heterodimer and it has been found only as a complex to Spt5 in Yeast and Human. Spt4 is a small protein that has zinc finger at the N-terminus. Spt5 is a large protein that has several interesting structural features of an acidic N-terminus, a single NGN domain, five or six KOW domains, and a set of simple C-termianl repeats. Spt4 binds to Spt5 NGN domain. Unlike Spt5, Spt4 is not essential for viability in yeast, however Spt4 is critical for normal function of the Spt4-Spt5 compl
Probab=23.16 E-value=42 Score=27.63 Aligned_cols=20 Identities=30% Similarity=0.660 Sum_probs=14.6
Q ss_pred eeCCCCcccccc----ccCcCCCC
Q 021781 123 ICSLCGTEQKVQ----QVCVNCGV 142 (307)
Q Consensus 123 ~C~~C~~eQ~v~----~~C~~Cg~ 142 (307)
.|+.|+..++.. +.|+||+.
T Consensus 5 AC~~C~~I~~~~qf~~~gCpnC~~ 28 (98)
T cd07973 5 ACLLCSLIKTEDQFERDGCPNCEG 28 (98)
T ss_pred hhccCCcccccccccCCCCCCCcc
Confidence 688888877654 46888863
No 249
>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=23.04 E-value=48 Score=31.47 Aligned_cols=20 Identities=35% Similarity=1.027 Sum_probs=14.8
Q ss_pred cccCcCCCCcc--------ceEecCccc
Q 021781 134 QQVCVNCGVCM--------GEYFCESCK 153 (307)
Q Consensus 134 ~~~C~~Cg~~f--------a~YfC~~Ck 153 (307)
++.|+.||... +.|||+.|.
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 272 (272)
T TIGR00577 245 GEPCRRCGTPIEKIKVGGRGTHFCPQCQ 272 (272)
T ss_pred CCCCCCCCCeeEEEEECCCCCEECCCCC
Confidence 45799999887 567777763
No 250
>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=22.58 E-value=67 Score=25.69 Aligned_cols=9 Identities=44% Similarity=1.128 Sum_probs=5.6
Q ss_pred cCcCCCCcc
Q 021781 136 VCVNCGVCM 144 (307)
Q Consensus 136 ~C~~Cg~~f 144 (307)
.|++||..|
T Consensus 2 fC~~Cg~~l 10 (104)
T TIGR01384 2 FCPKCGSLM 10 (104)
T ss_pred CCcccCccc
Confidence 466666665
No 251
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=22.53 E-value=47 Score=25.20 Aligned_cols=20 Identities=25% Similarity=0.620 Sum_probs=13.4
Q ss_pred eeCCCCccccccccCcCCCCc
Q 021781 123 ICSLCGTEQKVQQVCVNCGVC 143 (307)
Q Consensus 123 ~C~~C~~eQ~v~~~C~~Cg~~ 143 (307)
.|..|...++ .+.||+||..
T Consensus 5 AC~~C~~i~~-~~~CP~Cgs~ 24 (61)
T PRK08351 5 ACRHCHYITT-EDRCPVCGSR 24 (61)
T ss_pred hhhhCCcccC-CCcCCCCcCC
Confidence 5777776664 3468888774
No 252
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=22.18 E-value=65 Score=24.03 Aligned_cols=12 Identities=33% Similarity=1.088 Sum_probs=6.8
Q ss_pred CCCeecCCCCCc
Q 021781 160 SKKQYHCDGCGI 171 (307)
Q Consensus 160 ~k~~yHC~~Cgi 171 (307)
....|-|++|||
T Consensus 11 ~~v~~~Cp~cGi 22 (55)
T PF13824_consen 11 AHVNFECPDCGI 22 (55)
T ss_pred cccCCcCCCCCC
Confidence 345566666664
No 253
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=22.06 E-value=52 Score=31.40 Aligned_cols=20 Identities=25% Similarity=0.884 Sum_probs=15.1
Q ss_pred cccCcCCCCcc--------ceEecCccc
Q 021781 134 QQVCVNCGVCM--------GEYFCESCK 153 (307)
Q Consensus 134 ~~~C~~Cg~~f--------a~YfC~~Ck 153 (307)
++.|+.||... +.|||+.|.
T Consensus 254 g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 281 (282)
T PRK13945 254 GKPCRKCGTPIERIKLAGRSTHWCPNCQ 281 (282)
T ss_pred cCCCCcCCCeeEEEEECCCccEECCCCc
Confidence 46799999887 567777774
No 254
>PLN02400 cellulose synthase
Probab=22.05 E-value=53 Score=37.40 Aligned_cols=56 Identities=16% Similarity=0.428 Sum_probs=39.7
Q ss_pred cCCCCCCCCcccccccccCCceeEEc---CCCCccchHHHHHHhhcCCCCCCCCCcCcc
Q 021781 201 VEGAMHHDCPVCCEYLFETRQDVIVL---PCGHTIHKNCLKEMREHHQYACPICSKSVC 256 (307)
Q Consensus 201 iE~~~~~~CPIClE~lf~s~~~v~~L---pCGH~fH~~Ci~~wl~~~~~~CPlCrks~~ 256 (307)
.++.....|.||.|++-...+.-... -||=-.++.|++-=.+.++..||.|+....
T Consensus 31 ~~~~~gqiCqICGD~VG~t~dGe~FVAC~eCaFPVCRpCYEYERkeGnq~CPQCkTrYk 89 (1085)
T PLN02400 31 LKNLNGQICQICGDDVGVTETGDVFVACNECAFPVCRPCYEYERKDGTQCCPQCKTRYR 89 (1085)
T ss_pred ccccCCceeeecccccCcCCCCCEEEEEccCCCccccchhheecccCCccCcccCCccc
Confidence 34445679999999865443333334 466669999996656667888999997764
No 255
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=21.64 E-value=66 Score=23.60 Aligned_cols=9 Identities=44% Similarity=0.925 Sum_probs=5.0
Q ss_pred eeeeCCCCc
Q 021781 121 QVICSLCGT 129 (307)
Q Consensus 121 ~v~C~~C~~ 129 (307)
.++|..|..
T Consensus 22 aLIC~~C~~ 30 (54)
T PF10058_consen 22 ALICSKCFS 30 (54)
T ss_pred eEECcccch
Confidence 456666654
No 256
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=21.08 E-value=46 Score=36.56 Aligned_cols=49 Identities=20% Similarity=0.373 Sum_probs=39.7
Q ss_pred cCcCCCCccceE---ecCccccccCCCCCCeecCCCCCcccccCCccceecCCccceeecc
Q 021781 136 VCVNCGVCMGEY---FCESCKLFDDDTSKKQYHCDGCGICRIGGCDNFFHCNKCRCCYSML 193 (307)
Q Consensus 136 ~C~~Cg~~fa~Y---fC~~Ckl~ddd~~k~~yHC~~CgiCR~G~~e~ffHC~~C~~C~s~~ 193 (307)
.|++|++.++.- +|..|.--.- .+|-+|+.+-+.-+++|..|+-+.-.+
T Consensus 755 ~~~nc~a~~~~~~~~~c~rc~s~a~---------~~CtVC~~vi~G~~~~c~~C~H~gH~s 806 (839)
T KOG0269|consen 755 ACPNCDAPMVLTKLWQCDRCESRAS---------AKCTVCDLVIRGVDVWCQVCGHGGHDS 806 (839)
T ss_pred cccccCCccccccceeechHHHHhh---------cCceeecceeeeeEeecccccccccHH
Confidence 499999998665 8998876532 268899999988999999999887653
No 257
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=20.93 E-value=62 Score=28.65 Aligned_cols=13 Identities=15% Similarity=0.511 Sum_probs=11.4
Q ss_pred cCcCCCCccceEe
Q 021781 136 VCVNCGVCMGEYF 148 (307)
Q Consensus 136 ~C~~Cg~~fa~Yf 148 (307)
.|++||..|..|=
T Consensus 30 eC~~C~~RFTTyE 42 (147)
T TIGR00244 30 ECLECHERFTTFE 42 (147)
T ss_pred cCCccCCccceee
Confidence 5999999999983
No 258
>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=20.92 E-value=61 Score=27.56 Aligned_cols=27 Identities=30% Similarity=0.717 Sum_probs=18.0
Q ss_pred cCceeeeCCCCccccc---cccCcCCCCcc
Q 021781 118 EVNQVICSLCGTEQKV---QQVCVNCGVCM 144 (307)
Q Consensus 118 ~v~~v~C~~C~~eQ~v---~~~C~~Cg~~f 144 (307)
+...|.|..|+++-.. .+.|.+|+.++
T Consensus 66 kav~V~CP~C~K~TKmLGr~D~CM~C~~pL 95 (114)
T PF11023_consen 66 KAVQVECPNCGKQTKMLGRVDACMHCKEPL 95 (114)
T ss_pred cceeeECCCCCChHhhhchhhccCcCCCcC
Confidence 3457778888776433 35788887765
No 259
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=20.68 E-value=36 Score=25.58 Aligned_cols=19 Identities=37% Similarity=1.009 Sum_probs=13.5
Q ss_pred ccCcCCCCcc--ceEecC-ccc
Q 021781 135 QVCVNCGVCM--GEYFCE-SCK 153 (307)
Q Consensus 135 ~~C~~Cg~~f--a~YfC~-~Ck 153 (307)
..|++||.+. ++-||| .|+
T Consensus 4 kHC~~CG~~Ip~~~~fCS~~C~ 25 (59)
T PF09889_consen 4 KHCPVCGKPIPPDESFCSPKCR 25 (59)
T ss_pred CcCCcCCCcCCcchhhhCHHHH
Confidence 4688888764 677885 674
No 260
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=20.60 E-value=64 Score=26.83 Aligned_cols=14 Identities=21% Similarity=0.499 Sum_probs=8.5
Q ss_pred ccccccCcCCCCcc
Q 021781 131 QKVQQVCVNCGVCM 144 (307)
Q Consensus 131 Q~v~~~C~~Cg~~f 144 (307)
.|+.-.|..||..|
T Consensus 67 ~p~~~~C~~Cg~~~ 80 (114)
T PRK03681 67 QEAECWCETCQQYV 80 (114)
T ss_pred eCcEEEcccCCCee
Confidence 45556677777544
No 261
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=20.49 E-value=36 Score=29.32 Aligned_cols=10 Identities=30% Similarity=0.574 Sum_probs=5.8
Q ss_pred cCcCCCCccc
Q 021781 136 VCVNCGVCMG 145 (307)
Q Consensus 136 ~C~~Cg~~fa 145 (307)
.||+||..|.
T Consensus 101 ~Cp~C~~~y~ 110 (147)
T smart00531 101 KCPNCQSKYT 110 (147)
T ss_pred ECcCCCCEee
Confidence 4666665553
No 262
>PRK14873 primosome assembly protein PriA; Provisional
Probab=20.34 E-value=92 Score=33.59 Aligned_cols=44 Identities=25% Similarity=0.603 Sum_probs=26.2
Q ss_pred ceeeeCCCCccccccccCcCCCCccce------EecCccccccCCCCCCeecCCCCCcc
Q 021781 120 NQVICSLCGTEQKVQQVCVNCGVCMGE------YFCESCKLFDDDTSKKQYHCDGCGIC 172 (307)
Q Consensus 120 ~~v~C~~C~~eQ~v~~~C~~Cg~~fa~------YfC~~Ckl~ddd~~k~~yHC~~CgiC 172 (307)
..+.|..|+.. -.|++|+..+.- -.|.-|.+- . .+..|+.||-=
T Consensus 382 p~l~C~~Cg~~----~~C~~C~~~L~~h~~~~~l~Ch~CG~~----~-~p~~Cp~Cgs~ 431 (665)
T PRK14873 382 PSLACARCRTP----ARCRHCTGPLGLPSAGGTPRCRWCGRA----A-PDWRCPRCGSD 431 (665)
T ss_pred CeeEhhhCcCe----eECCCCCCceeEecCCCeeECCCCcCC----C-cCccCCCCcCC
Confidence 45788888864 368888887753 335544431 1 25556666543
No 263
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=20.29 E-value=49 Score=32.25 Aligned_cols=31 Identities=29% Similarity=0.648 Sum_probs=26.1
Q ss_pred CCCcccccCCccceecCCccceeecccccccccc
Q 021781 168 GCGICRIGGCDNFFHCNKCRCCYSMLLKNSHPCV 201 (307)
Q Consensus 168 ~CgiCR~G~~e~ffHC~~C~~C~s~~l~~~H~Ci 201 (307)
.|.-|+.-+.+..-||..||.|+-+- .|-|+
T Consensus 111 ~C~~C~~~KP~RS~HC~~Cn~CV~k~---DHHC~ 141 (309)
T COG5273 111 FCSTCNIYKPPRSHHCSICNRCVLKF---DHHCP 141 (309)
T ss_pred eccccccccCCCCccchhhcchhhcc---CccCc
Confidence 48888898889999999999999753 67775
No 264
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=20.25 E-value=83 Score=35.80 Aligned_cols=52 Identities=21% Similarity=0.461 Sum_probs=37.9
Q ss_pred CCCCCcccccccccCCceeEEc---CCCCccchHHHHHHhhcCCCCCCCCCcCcc
Q 021781 205 MHHDCPVCCEYLFETRQDVIVL---PCGHTIHKNCLKEMREHHQYACPICSKSVC 256 (307)
Q Consensus 205 ~~~~CPIClE~lf~s~~~v~~L---pCGH~fH~~Ci~~wl~~~~~~CPlCrks~~ 256 (307)
....|.||.|++-.....-... -||--.++.|++-=.+.++..||.|+....
T Consensus 14 ~~~~c~iCGd~vg~~~~Ge~FVAC~eC~fpvCr~cyeye~~~g~~~cp~c~t~y~ 68 (1044)
T PLN02915 14 DAKTCRVCGDEVGVKEDGQPFVACHVCGFPVCKPCYEYERSEGNQCCPQCNTRYK 68 (1044)
T ss_pred CcchhhccccccCcCCCCCEEEEeccCCCccccchhhhhhhcCCccCCccCCchh
Confidence 4578999999865443333344 456669999996666667888999997765
No 265
>PRK12496 hypothetical protein; Provisional
Probab=20.09 E-value=48 Score=29.33 Aligned_cols=24 Identities=25% Similarity=0.593 Sum_probs=15.2
Q ss_pred eeeCCCCcccc---ccccCcCCCCccc
Q 021781 122 VICSLCGTEQK---VQQVCVNCGVCMG 145 (307)
Q Consensus 122 v~C~~C~~eQ~---v~~~C~~Cg~~fa 145 (307)
..|..|+++-+ ..+.|+.||.+..
T Consensus 128 ~~C~gC~~~~~~~~~~~~C~~CG~~~~ 154 (164)
T PRK12496 128 KVCKGCKKKYPEDYPDDVCEICGSPVK 154 (164)
T ss_pred EECCCCCccccCCCCCCcCCCCCChhh
Confidence 45777777654 2356777777653
Done!