Query 021215
Match_columns 316
No_of_seqs 282 out of 1407
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 08:30:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021215.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021215hhsearch_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 1.6E-65 3.5E-70 481.9 6.1 241 63-315 27-267 (276)
2 PF14599 zinc_ribbon_6: Zinc-r 99.9 2.2E-27 4.8E-32 178.4 0.1 61 253-313 1-61 (61)
3 PF05495 zf-CHY: CHY zinc fing 99.9 2E-23 4.4E-28 161.0 4.0 70 71-154 1-71 (71)
4 COG4357 Zinc finger domain con 99.4 1.5E-13 3.3E-18 111.6 1.2 65 71-144 15-92 (105)
5 PF13639 zf-RING_2: Ring finge 99.3 1.3E-12 2.9E-17 90.9 1.7 44 205-250 1-44 (44)
6 PF12861 zf-Apc11: Anaphase-pr 99.1 2.7E-11 5.8E-16 96.9 3.8 52 202-255 30-83 (85)
7 PF12678 zf-rbx1: RING-H2 zinc 98.9 6.8E-10 1.5E-14 85.9 3.7 47 203-250 18-73 (73)
8 KOG4628 Predicted E3 ubiquitin 98.9 8.3E-10 1.8E-14 108.0 3.2 50 205-255 230-279 (348)
9 cd00162 RING RING-finger (Real 98.9 2.1E-09 4.5E-14 72.2 3.7 45 206-253 1-45 (45)
10 PF13923 zf-C3HC4_2: Zinc fing 98.8 2.6E-09 5.6E-14 72.8 3.0 39 207-249 1-39 (39)
11 PF15227 zf-C3HC4_4: zinc fing 98.8 4.9E-09 1.1E-13 73.2 3.3 39 207-249 1-42 (42)
12 PHA02929 N1R/p28-like protein; 98.7 9.6E-09 2.1E-13 96.2 4.4 54 201-255 171-228 (238)
13 PF13920 zf-C3HC4_3: Zinc fing 98.7 1.1E-08 2.5E-13 73.0 2.8 47 204-255 2-49 (50)
14 COG5243 HRD1 HRD ubiquitin lig 98.7 7.1E-09 1.5E-13 101.8 2.1 56 201-257 284-349 (491)
15 PF00097 zf-C3HC4: Zinc finger 98.7 1.6E-08 3.4E-13 68.9 3.2 40 207-249 1-41 (41)
16 KOG1493 Anaphase-promoting com 98.6 8.7E-09 1.9E-13 81.0 -0.1 51 202-254 29-81 (84)
17 smart00184 RING Ring finger. E 98.6 4E-08 8.6E-13 63.6 2.9 39 207-249 1-39 (39)
18 PF13445 zf-RING_UBOX: RING-ty 98.6 3.6E-08 7.8E-13 69.5 2.3 40 207-247 1-43 (43)
19 COG5540 RING-finger-containing 98.5 4.4E-08 9.6E-13 94.2 3.4 54 200-254 319-372 (374)
20 PF14634 zf-RING_5: zinc-RING 98.5 8.8E-08 1.9E-12 67.0 3.4 44 206-251 1-44 (44)
21 PLN03208 E3 ubiquitin-protein 98.5 1.4E-07 3.1E-12 85.8 4.5 55 197-255 11-80 (193)
22 COG5194 APC11 Component of SCF 98.4 1.4E-07 3.1E-12 74.8 3.0 51 204-255 31-82 (88)
23 PHA02926 zinc finger-like prot 98.3 4.9E-07 1.1E-11 84.0 3.4 56 200-255 166-231 (242)
24 KOG0804 Cytoplasmic Zn-finger 98.3 4.9E-07 1.1E-11 90.7 2.9 81 205-313 176-258 (493)
25 smart00504 Ubox Modified RING 98.2 1.4E-06 3E-11 64.0 3.9 45 205-254 2-46 (63)
26 KOG0802 E3 ubiquitin ligase [P 98.0 1.8E-06 4E-11 88.9 1.2 53 200-253 287-340 (543)
27 KOG2177 Predicted E3 ubiquitin 98.0 1.2E-05 2.6E-10 71.2 5.8 44 203-251 12-55 (386)
28 KOG0320 Predicted E3 ubiquitin 98.0 4.5E-06 9.7E-11 75.2 2.8 48 204-254 131-178 (187)
29 KOG0317 Predicted E3 ubiquitin 97.9 5.5E-06 1.2E-10 79.3 2.1 47 204-255 239-285 (293)
30 KOG0823 Predicted E3 ubiquitin 97.8 1E-05 2.3E-10 75.3 2.8 50 202-255 45-96 (230)
31 TIGR00599 rad18 DNA repair pro 97.8 1.3E-05 2.8E-10 80.3 3.3 46 204-254 26-71 (397)
32 TIGR00570 cdk7 CDK-activating 97.8 2.4E-05 5.2E-10 75.9 4.2 52 204-255 3-55 (309)
33 smart00744 RINGv The RING-vari 97.7 2.9E-05 6.2E-10 56.0 2.8 43 206-250 1-49 (49)
34 PF11793 FANCL_C: FANCL C-term 97.6 1.3E-05 2.9E-10 61.7 -0.1 51 204-254 2-66 (70)
35 PF04564 U-box: U-box domain; 97.6 0.00012 2.6E-09 56.4 5.2 48 204-255 4-51 (73)
36 KOG0287 Postreplication repair 97.5 6E-05 1.3E-09 74.0 3.1 46 205-255 24-69 (442)
37 KOG2930 SCF ubiquitin ligase, 97.5 2.4E-05 5.2E-10 65.0 0.1 35 220-255 75-109 (114)
38 KOG2164 Predicted E3 ubiquitin 97.4 6.8E-05 1.5E-09 76.6 2.6 50 202-255 184-237 (513)
39 KOG0828 Predicted E3 ubiquitin 97.4 6.9E-05 1.5E-09 76.4 1.5 51 204-254 571-634 (636)
40 COG5574 PEX10 RING-finger-cont 97.1 0.00026 5.6E-09 67.3 2.0 46 204-254 215-262 (271)
41 KOG0827 Predicted E3 ubiquitin 97.0 0.0003 6.5E-09 70.1 1.8 46 204-250 4-52 (465)
42 PF14835 zf-RING_6: zf-RING of 97.0 0.00034 7.3E-09 53.6 1.6 55 205-266 8-64 (65)
43 KOG4172 Predicted E3 ubiquitin 96.9 0.00024 5.1E-09 53.1 0.0 51 203-257 6-57 (62)
44 KOG1734 Predicted RING-contain 96.7 0.00055 1.2E-08 65.6 0.5 52 203-254 223-281 (328)
45 COG5432 RAD18 RING-finger-cont 96.6 0.0011 2.4E-08 64.1 2.6 46 204-254 25-70 (391)
46 PF14570 zf-RING_4: RING/Ubox 96.5 0.0021 4.5E-08 46.6 2.4 47 207-253 1-47 (48)
47 KOG4265 Predicted E3 ubiquitin 96.4 0.002 4.3E-08 63.6 2.9 49 202-255 288-337 (349)
48 KOG0978 E3 ubiquitin ligase in 96.3 0.0011 2.4E-08 70.5 0.4 48 204-255 643-690 (698)
49 KOG1039 Predicted E3 ubiquitin 96.3 0.001 2.2E-08 65.7 0.1 80 202-283 159-250 (344)
50 KOG0311 Predicted E3 ubiquitin 96.2 0.001 2.2E-08 65.6 -0.5 48 204-254 43-90 (381)
51 KOG1941 Acetylcholine receptor 96.2 0.00092 2E-08 66.9 -1.1 58 195-253 357-415 (518)
52 PF11789 zf-Nse: Zinc-finger o 96.0 0.006 1.3E-07 45.4 2.7 44 202-248 9-53 (57)
53 KOG0824 Predicted E3 ubiquitin 95.7 0.0058 1.3E-07 59.4 2.1 49 202-254 5-53 (324)
54 KOG1785 Tyrosine kinase negati 95.5 0.0043 9.2E-08 62.4 0.5 53 197-253 362-415 (563)
55 COG5219 Uncharacterized conser 95.4 0.0072 1.6E-07 66.1 1.8 53 202-254 1467-1523(1525)
56 KOG2879 Predicted E3 ubiquitin 95.3 0.013 2.9E-07 56.3 3.2 53 202-257 237-290 (298)
57 PRK14890 putative Zn-ribbon RN 95.1 0.017 3.7E-07 43.6 2.6 46 117-169 5-56 (59)
58 KOG0825 PHD Zn-finger protein 94.5 0.012 2.6E-07 63.3 0.7 50 204-255 123-172 (1134)
59 PF10367 Vps39_2: Vacuolar sor 94.4 0.021 4.5E-07 45.5 1.5 33 202-236 76-108 (109)
60 KOG3800 Predicted E3 ubiquitin 94.3 0.037 8E-07 53.6 3.2 49 206-254 2-51 (300)
61 PF12906 RINGv: RING-variant d 94.2 0.028 6.1E-07 40.1 1.8 41 207-249 1-47 (47)
62 KOG3268 Predicted E3 ubiquitin 94.2 0.026 5.6E-07 51.6 2.0 50 205-254 166-228 (234)
63 KOG1645 RING-finger-containing 94.2 0.054 1.2E-06 54.7 4.2 50 204-253 4-55 (463)
64 KOG1428 Inhibitor of type V ad 94.0 0.048 1E-06 62.2 3.7 74 173-254 3462-3544(3738)
65 KOG4185 Predicted E3 ubiquitin 93.9 0.054 1.2E-06 51.3 3.6 49 205-254 4-55 (296)
66 PF14447 Prok-RING_4: Prokaryo 93.7 0.028 6E-07 41.9 1.0 33 220-255 19-51 (55)
67 KOG4159 Predicted E3 ubiquitin 93.6 0.067 1.4E-06 54.0 3.8 49 202-255 82-130 (398)
68 COG5175 MOT2 Transcriptional r 93.3 0.027 5.8E-07 55.9 0.4 57 204-260 14-70 (480)
69 KOG0297 TNF receptor-associate 93.2 0.054 1.2E-06 54.3 2.3 50 202-255 19-68 (391)
70 KOG1571 Predicted E3 ubiquitin 93.0 0.059 1.3E-06 53.5 2.3 47 200-254 301-347 (355)
71 KOG4739 Uncharacterized protei 93.0 0.043 9.4E-07 51.7 1.3 37 215-254 12-48 (233)
72 KOG1814 Predicted E3 ubiquitin 93.0 0.11 2.3E-06 52.6 4.1 53 196-250 177-236 (445)
73 KOG4445 Uncharacterized conser 92.3 0.043 9.4E-07 53.6 0.3 52 203-255 114-187 (368)
74 KOG2817 Predicted E3 ubiquitin 92.1 0.11 2.3E-06 52.3 2.8 47 205-252 335-383 (394)
75 PF12773 DZR: Double zinc ribb 92.0 0.15 3.3E-06 36.0 2.8 22 122-143 1-23 (50)
76 KOG3970 Predicted E3 ubiquitin 91.9 0.22 4.8E-06 47.1 4.4 51 203-255 49-106 (299)
77 KOG4275 Predicted E3 ubiquitin 91.7 0.032 6.8E-07 54.3 -1.4 55 193-256 286-344 (350)
78 COG5152 Uncharacterized conser 91.5 0.11 2.3E-06 48.3 1.8 59 204-267 196-254 (259)
79 PF05883 Baculo_RING: Baculovi 91.3 0.096 2.1E-06 45.6 1.3 35 204-239 26-66 (134)
80 KOG3002 Zn finger protein [Gen 90.7 0.28 6.2E-06 47.8 4.1 60 204-274 48-109 (299)
81 KOG1813 Predicted E3 ubiquitin 90.7 0.17 3.6E-06 49.3 2.5 64 202-270 239-302 (313)
82 PF04641 Rtf2: Rtf2 RING-finge 90.5 0.26 5.7E-06 46.5 3.6 50 202-254 111-161 (260)
83 TIGR00100 hypA hydrogenase nic 90.3 0.2 4.2E-06 42.1 2.3 35 280-316 68-102 (115)
84 COG2888 Predicted Zn-ribbon RN 90.1 0.19 4.1E-06 38.2 1.7 45 119-169 9-58 (61)
85 KOG1002 Nucleotide excision re 89.5 0.14 3.1E-06 53.5 0.9 53 198-254 530-586 (791)
86 PRK00564 hypA hydrogenase nick 89.2 0.27 5.9E-06 41.4 2.3 35 280-316 69-104 (117)
87 PF07191 zinc-ribbons_6: zinc- 89.2 0.19 4.1E-06 39.3 1.2 36 118-153 16-59 (70)
88 PF07191 zinc-ribbons_6: zinc- 88.9 0.092 2E-06 41.0 -0.7 65 205-298 2-69 (70)
89 PRK03824 hypA hydrogenase nick 88.5 0.33 7.2E-06 41.9 2.4 37 280-316 68-123 (135)
90 PF07800 DUF1644: Protein of u 88.3 0.47 1E-05 42.5 3.2 33 204-240 2-47 (162)
91 KOG2660 Locus-specific chromos 88.0 0.13 2.9E-06 50.6 -0.5 49 202-254 13-61 (331)
92 PRK12380 hydrogenase nickel in 87.8 0.37 7.9E-06 40.4 2.2 35 280-316 68-102 (113)
93 KOG2114 Vacuolar assembly/sort 87.6 0.4 8.6E-06 52.4 2.8 42 206-254 842-883 (933)
94 PF13248 zf-ribbon_3: zinc-rib 87.3 0.28 6.1E-06 30.8 0.9 24 119-142 2-26 (26)
95 PRK03681 hypA hydrogenase nick 87.2 0.43 9.4E-06 40.0 2.2 36 280-316 68-103 (114)
96 KOG3039 Uncharacterized conser 86.7 0.68 1.5E-05 44.4 3.5 54 202-257 219-273 (303)
97 PHA02862 5L protein; Provision 86.0 0.55 1.2E-05 41.6 2.3 46 204-254 2-53 (156)
98 PF08746 zf-RING-like: RING-li 85.8 0.56 1.2E-05 32.9 1.9 42 207-249 1-43 (43)
99 PHA02825 LAP/PHD finger-like p 85.3 0.8 1.7E-05 41.1 3.0 47 203-254 7-59 (162)
100 PF03854 zf-P11: P-11 zinc fin 84.9 0.43 9.3E-06 34.8 1.0 32 223-255 15-47 (50)
101 COG5236 Uncharacterized conser 84.7 0.9 1.9E-05 45.5 3.4 66 185-254 42-108 (493)
102 PF01155 HypA: Hydrogenase exp 84.6 0.31 6.7E-06 40.7 0.1 35 280-316 68-102 (113)
103 PF13240 zinc_ribbon_2: zinc-r 83.7 0.58 1.3E-05 28.8 1.1 21 122-142 2-23 (23)
104 PF10571 UPF0547: Uncharacteri 83.6 0.77 1.7E-05 29.2 1.6 23 121-143 2-25 (26)
105 COG5220 TFB3 Cdk activating ki 83.5 0.39 8.4E-06 45.9 0.3 51 203-253 9-63 (314)
106 KOG0309 Conserved WD40 repeat- 83.4 0.73 1.6E-05 50.1 2.3 44 202-248 1026-1069(1081)
107 PRK04023 DNA polymerase II lar 83.4 1 2.2E-05 50.4 3.4 46 133-187 627-672 (1121)
108 KOG4692 Predicted E3 ubiquitin 82.9 0.79 1.7E-05 46.0 2.2 52 199-255 417-468 (489)
109 PF09538 FYDLN_acid: Protein o 82.8 0.92 2E-05 38.0 2.2 27 131-169 8-34 (108)
110 COG5222 Uncharacterized conser 82.7 0.76 1.7E-05 45.2 2.0 44 205-251 275-318 (427)
111 KOG3161 Predicted E3 ubiquitin 82.6 0.51 1.1E-05 50.4 0.7 42 205-250 12-53 (861)
112 PRK00762 hypA hydrogenase nick 82.3 0.91 2E-05 38.6 2.1 36 280-316 68-108 (124)
113 PRK14559 putative protein seri 80.6 1.2 2.5E-05 47.8 2.6 33 120-152 2-35 (645)
114 PHA00626 hypothetical protein 78.9 1.5 3.4E-05 33.0 2.0 29 134-169 2-31 (59)
115 COG0375 HybF Zn finger protein 78.3 1.7 3.7E-05 37.0 2.4 36 279-316 67-102 (115)
116 PHA03096 p28-like protein; Pro 78.2 1.2 2.5E-05 43.3 1.6 47 205-251 179-231 (284)
117 COG5109 Uncharacterized conser 77.1 1.6 3.5E-05 43.2 2.2 45 205-250 337-383 (396)
118 KOG4367 Predicted Zn-finger pr 76.9 1.3 2.8E-05 45.7 1.5 34 203-240 3-36 (699)
119 KOG2034 Vacuolar sorting prote 76.7 1.2 2.5E-05 49.1 1.2 43 196-240 809-851 (911)
120 TIGR00595 priA primosomal prot 74.6 2.7 5.9E-05 43.5 3.2 50 79-141 213-262 (505)
121 KOG1952 Transcription factor N 74.3 1.7 3.8E-05 47.7 1.7 48 204-254 191-247 (950)
122 PF12773 DZR: Double zinc ribb 73.6 2.6 5.7E-05 29.6 2.0 32 119-150 12-49 (50)
123 PF02891 zf-MIZ: MIZ/SP-RING z 73.4 2.3 5.1E-05 30.7 1.7 42 205-252 3-50 (50)
124 KOG1001 Helicase-like transcri 72.9 1.8 3.8E-05 46.7 1.4 45 205-254 455-500 (674)
125 PRK14714 DNA polymerase II lar 72.8 3.5 7.7E-05 47.2 3.7 32 120-152 668-700 (1337)
126 KOG2272 Focal adhesion protein 72.4 3 6.4E-05 40.3 2.6 128 89-257 100-235 (332)
127 PF14446 Prok-RING_1: Prokaryo 69.6 5.1 0.00011 29.9 2.8 36 203-238 4-39 (54)
128 COG1198 PriA Primosomal protei 69.5 4.5 9.8E-05 44.1 3.6 55 79-146 435-489 (730)
129 COG1198 PriA Primosomal protei 68.9 4.7 0.0001 44.0 3.5 44 118-169 434-483 (730)
130 TIGR02300 FYDLN_acid conserved 67.3 3.8 8.2E-05 35.6 2.0 28 131-170 8-35 (129)
131 PRK04023 DNA polymerase II lar 65.9 4.9 0.00011 45.2 3.0 48 119-172 626-674 (1121)
132 PF07282 OrfB_Zn_ribbon: Putat 64.6 5.3 0.00012 29.8 2.1 27 132-169 28-54 (69)
133 KOG2068 MOT2 transcription fac 63.6 5.8 0.00013 39.3 2.7 53 202-255 247-299 (327)
134 PRK14873 primosome assembly pr 62.4 6.2 0.00014 42.5 3.0 50 79-142 383-432 (665)
135 PRK14714 DNA polymerase II lar 62.2 6.2 0.00013 45.3 3.0 33 133-169 668-700 (1337)
136 PRK05580 primosome assembly pr 61.9 6.7 0.00015 42.1 3.1 51 79-142 381-431 (679)
137 KOG1812 Predicted E3 ubiquitin 61.6 3.9 8.5E-05 41.1 1.2 44 204-247 146-194 (384)
138 PF05290 Baculo_IE-1: Baculovi 59.7 6 0.00013 34.7 1.8 47 205-255 81-133 (140)
139 PRK14559 putative protein seri 59.4 5.3 0.00012 42.9 1.8 34 119-153 15-50 (645)
140 COG3809 Uncharacterized protei 58.5 7.6 0.00016 31.3 2.1 31 244-278 22-54 (88)
141 KOG3053 Uncharacterized conser 58.1 4.2 9.2E-05 39.3 0.7 70 200-269 16-104 (293)
142 PF14569 zf-UDP: Zinc-binding 57.5 9.8 0.00021 30.5 2.5 53 202-254 7-62 (80)
143 COG5183 SSM4 Protein involved 56.3 4.1 8.8E-05 44.9 0.3 52 201-254 9-66 (1175)
144 PF03107 C1_2: C1 domain; Int 56.0 8.3 0.00018 24.8 1.6 20 166-185 2-22 (30)
145 KOG1940 Zn-finger protein [Gen 55.0 2.5 5.4E-05 41.0 -1.4 34 62-96 171-204 (276)
146 KOG1100 Predicted E3 ubiquitin 53.5 6.5 0.00014 36.4 1.1 39 207-254 161-200 (207)
147 smart00249 PHD PHD zinc finger 52.9 6 0.00013 26.0 0.6 41 207-249 2-47 (47)
148 PF06524 NOA36: NOA36 protein; 51.4 5.9 0.00013 38.5 0.5 51 86-152 140-190 (314)
149 PF08271 TF_Zn_Ribbon: TFIIB z 51.3 13 0.00029 25.5 2.2 8 134-141 2-9 (43)
150 PRK14890 putative Zn-ribbon RN 51.3 11 0.00023 28.7 1.8 34 117-152 23-56 (59)
151 PF14353 CpXC: CpXC protein 51.3 3.2 6.9E-05 34.8 -1.2 56 244-301 2-57 (128)
152 PF05605 zf-Di19: Drought indu 51.2 16 0.00036 26.2 2.7 8 244-251 3-10 (54)
153 KOG2462 C2H2-type Zn-finger pr 50.7 15 0.00033 35.7 3.1 111 139-292 125-253 (279)
154 smart00132 LIM Zinc-binding do 50.5 13 0.00028 23.6 1.9 37 207-254 2-38 (39)
155 PF05191 ADK_lid: Adenylate ki 50.1 4.2 9.1E-05 27.6 -0.5 27 134-169 3-29 (36)
156 PF04216 FdhE: Protein involve 49.7 12 0.00025 35.9 2.2 47 117-167 195-244 (290)
157 PRK00398 rpoP DNA-directed RNA 49.7 14 0.0003 25.8 2.1 30 282-311 3-32 (46)
158 KOG2907 RNA polymerase I trans 49.3 6.2 0.00014 33.6 0.3 19 298-316 72-94 (116)
159 KOG2066 Vacuolar assembly/sort 49.2 6.4 0.00014 43.2 0.4 45 204-250 784-831 (846)
160 PRK00398 rpoP DNA-directed RNA 47.9 18 0.00038 25.3 2.4 8 161-168 21-28 (46)
161 KOG0827 Predicted E3 ubiquitin 46.5 1.8 3.9E-05 43.9 -3.9 52 203-255 195-246 (465)
162 PF13894 zf-C2H2_4: C2H2-type 46.5 14 0.0003 20.9 1.5 18 244-261 1-18 (24)
163 TIGR02605 CxxC_CxxC_SSSS putat 46.2 15 0.00032 26.0 1.8 30 282-311 5-37 (52)
164 KOG0269 WD40 repeat-containing 46.1 18 0.00039 39.7 3.1 79 159-257 751-836 (839)
165 PRK12286 rpmF 50S ribosomal pr 46.0 21 0.00046 26.6 2.7 29 281-314 26-54 (57)
166 PF13453 zf-TFIIB: Transcripti 45.9 16 0.00035 24.9 1.9 26 134-168 1-26 (41)
167 COG1656 Uncharacterized conser 43.5 17 0.00038 32.8 2.2 51 243-299 97-147 (165)
168 KOG2462 C2H2-type Zn-finger pr 42.8 23 0.0005 34.5 3.0 29 116-144 158-199 (279)
169 PF05502 Dynactin_p62: Dynacti 42.4 14 0.00031 38.3 1.7 57 145-216 6-64 (483)
170 KOG0298 DEAD box-containing he 41.7 9 0.0002 44.1 0.1 52 202-257 1151-1202(1394)
171 PF02701 zf-Dof: Dof domain, z 40.9 14 0.0003 28.4 1.0 14 300-313 5-18 (63)
172 smart00734 ZnF_Rad18 Rad18-lik 40.6 26 0.00056 22.0 2.0 20 244-264 2-21 (26)
173 COG1996 RPC10 DNA-directed RNA 40.4 20 0.00043 26.3 1.7 28 142-169 4-32 (49)
174 PLN02189 cellulose synthase 40.1 23 0.00049 40.2 2.9 56 199-254 29-87 (1040)
175 TIGR00595 priA primosomal prot 39.4 32 0.00069 35.7 3.7 46 117-170 211-262 (505)
176 KOG1701 Focal adhesion adaptor 39.0 7.6 0.00016 39.9 -0.9 129 121-307 276-434 (468)
177 KOG1609 Protein involved in mR 38.1 20 0.00043 33.6 1.8 51 204-254 78-134 (323)
178 PRK00420 hypothetical protein; 38.0 21 0.00046 30.2 1.8 22 132-153 23-49 (112)
179 TIGR02159 PA_CoA_Oxy4 phenylac 37.0 17 0.00037 31.9 1.1 16 300-315 105-120 (146)
180 PLN02436 cellulose synthase A 36.6 28 0.0006 39.7 2.9 56 199-254 31-89 (1094)
181 PRK00366 ispG 4-hydroxy-3-meth 36.5 46 0.00099 33.6 4.1 53 244-300 269-323 (360)
182 KOG0801 Predicted E3 ubiquitin 36.5 13 0.00027 34.0 0.2 29 203-232 176-204 (205)
183 KOG2932 E3 ubiquitin ligase in 36.4 15 0.00033 36.5 0.8 30 222-254 105-134 (389)
184 smart00778 Prim_Zn_Ribbon Zinc 36.1 38 0.00083 23.3 2.5 31 132-169 3-33 (37)
185 PF01529 zf-DHHC: DHHC palmito 36.0 28 0.0006 29.9 2.3 47 138-190 42-88 (174)
186 PF00096 zf-C2H2: Zinc finger, 35.7 21 0.00046 20.7 1.1 15 244-258 1-15 (23)
187 PRK00432 30S ribosomal protein 35.3 25 0.00055 25.5 1.6 9 160-168 36-44 (50)
188 TIGR01031 rpmF_bact ribosomal 34.8 34 0.00074 25.3 2.2 29 281-314 25-53 (55)
189 cd00350 rubredoxin_like Rubred 34.3 31 0.00068 22.6 1.8 25 144-169 1-25 (33)
190 PF07649 C1_3: C1-like domain; 34.2 23 0.00049 22.6 1.1 20 167-186 3-23 (30)
191 PF06677 Auto_anti-p27: Sjogre 33.8 28 0.0006 24.4 1.5 13 132-144 17-29 (41)
192 PF01599 Ribosomal_S27: Riboso 33.7 26 0.00057 25.4 1.5 22 131-152 17-46 (47)
193 PF04438 zf-HIT: HIT zinc fing 33.7 21 0.00045 23.3 0.8 16 135-151 5-20 (30)
194 PF01529 zf-DHHC: DHHC palmito 33.5 23 0.00051 30.3 1.4 39 155-199 42-80 (174)
195 smart00659 RPOLCX RNA polymera 33.3 31 0.00068 24.4 1.8 25 283-308 3-27 (44)
196 KOG3362 Predicted BBOX Zn-fing 33.2 14 0.0003 33.0 -0.1 25 143-173 117-143 (156)
197 PF15616 TerY-C: TerY-C metal 33.1 40 0.00086 29.4 2.7 34 132-168 77-112 (131)
198 PRK14873 primosome assembly pr 33.0 36 0.00078 36.8 3.0 49 113-170 376-431 (665)
199 PF03833 PolC_DP2: DNA polymer 32.9 14 0.00031 40.9 0.0 46 133-187 656-701 (900)
200 PF01096 TFIIS_C: Transcriptio 32.2 30 0.00066 23.6 1.5 31 134-168 2-35 (39)
201 PF03833 PolC_DP2: DNA polymer 32.2 15 0.00033 40.8 0.0 32 120-152 656-688 (900)
202 KOG0006 E3 ubiquitin-protein l 32.1 42 0.00091 33.7 3.0 77 153-238 169-253 (446)
203 PF06827 zf-FPG_IleRS: Zinc fi 31.3 35 0.00076 21.6 1.6 18 133-150 2-27 (30)
204 cd01675 RNR_III Class III ribo 31.3 41 0.00088 35.5 3.0 30 280-314 517-546 (555)
205 smart00661 RPOL9 RNA polymeras 30.9 40 0.00087 23.5 2.0 9 160-168 19-27 (52)
206 KOG1312 DHHC-type Zn-finger pr 30.6 14 0.0003 36.5 -0.6 32 165-199 149-180 (341)
207 cd02337 ZZ_CBP Zinc finger, ZZ 30.6 34 0.00074 23.7 1.6 20 162-185 1-20 (41)
208 PF00643 zf-B_box: B-box zinc 30.5 40 0.00088 22.5 1.9 21 133-153 4-24 (42)
209 PF03604 DNA_RNApol_7kD: DNA d 30.3 33 0.00072 22.8 1.4 11 158-168 14-24 (32)
210 KOG0826 Predicted E3 ubiquitin 30.0 41 0.00088 33.7 2.5 49 202-254 298-346 (357)
211 KOG4185 Predicted E3 ubiquitin 29.9 9.6 0.00021 36.1 -1.8 49 205-253 208-266 (296)
212 PRK14810 formamidopyrimidine-D 29.8 30 0.00066 33.0 1.6 20 132-151 244-271 (272)
213 PHA00626 hypothetical protein 29.7 35 0.00075 25.9 1.5 34 120-155 1-34 (59)
214 PF06906 DUF1272: Protein of u 29.6 76 0.0017 24.0 3.3 51 203-256 4-54 (57)
215 COG1645 Uncharacterized Zn-fin 29.6 29 0.00063 30.3 1.3 20 132-151 28-51 (131)
216 PRK10445 endonuclease VIII; Pr 29.4 32 0.00069 32.7 1.7 20 132-151 235-262 (263)
217 cd02249 ZZ Zinc finger, ZZ typ 29.4 36 0.00079 23.7 1.6 21 162-185 1-21 (46)
218 PRK14811 formamidopyrimidine-D 29.4 32 0.00068 32.9 1.6 21 132-152 235-263 (269)
219 PF13717 zinc_ribbon_4: zinc-r 29.3 38 0.00082 22.8 1.6 10 80-89 3-12 (36)
220 KOG4362 Transcriptional regula 29.0 26 0.00057 38.0 1.1 48 204-255 21-70 (684)
221 KOG1815 Predicted E3 ubiquitin 28.9 34 0.00074 34.8 1.9 38 201-241 67-104 (444)
222 COG1998 RPS31 Ribosomal protei 28.9 36 0.00079 25.1 1.5 20 132-151 19-44 (51)
223 TIGR01562 FdhE formate dehydro 28.8 57 0.0012 32.1 3.3 23 282-308 210-232 (305)
224 PF06220 zf-U1: U1 zinc finger 28.8 22 0.00049 24.3 0.4 13 142-154 1-13 (38)
225 KOG4399 C2HC-type Zn-finger pr 28.7 11 0.00025 36.5 -1.4 73 138-213 198-270 (325)
226 PRK00415 rps27e 30S ribosomal 28.7 35 0.00075 25.9 1.4 36 118-153 10-51 (59)
227 PF12760 Zn_Tnp_IS1595: Transp 28.4 73 0.0016 22.2 3.0 9 133-141 19-27 (46)
228 PF12172 DUF35_N: Rubredoxin-l 28.4 26 0.00057 23.2 0.7 23 118-140 10-33 (37)
229 PF14952 zf-tcix: Putative tre 27.5 29 0.00063 24.9 0.8 12 302-313 13-24 (44)
230 PF13719 zinc_ribbon_5: zinc-r 27.2 42 0.00091 22.6 1.5 9 119-127 25-33 (37)
231 cd00729 rubredoxin_SM Rubredox 27.1 47 0.001 22.1 1.7 22 120-141 3-27 (34)
232 PF08273 Prim_Zn_Ribbon: Zinc- 26.7 32 0.0007 24.0 0.9 29 133-167 4-32 (40)
233 PRK01103 formamidopyrimidine/5 26.7 38 0.00083 32.2 1.7 20 132-151 245-272 (274)
234 PF08274 PhnA_Zn_Ribbon: PhnA 26.7 36 0.00078 22.4 1.0 23 134-168 4-26 (30)
235 KOG1044 Actin-binding LIM Zn-f 26.7 80 0.0017 34.0 4.1 136 156-308 11-168 (670)
236 PF09788 Tmemb_55A: Transmembr 26.4 77 0.0017 30.6 3.6 112 176-308 63-185 (256)
237 PF13695 zf-3CxxC: Zinc-bindin 26.2 55 0.0012 26.5 2.3 46 243-312 5-50 (98)
238 smart00451 ZnF_U1 U1-like zinc 25.9 32 0.00069 21.8 0.7 11 143-153 2-12 (35)
239 PRK04136 rpl40e 50S ribosomal 25.8 40 0.00087 24.6 1.3 23 118-140 13-36 (48)
240 KOG4317 Predicted Zn-finger pr 25.4 31 0.00067 34.4 0.8 21 133-153 8-28 (383)
241 PLN02638 cellulose synthase A 25.4 55 0.0012 37.4 2.8 56 199-254 12-70 (1079)
242 TIGR02098 MJ0042_CXXC MJ0042 f 25.2 50 0.0011 21.8 1.6 10 119-128 25-34 (38)
243 TIGR00577 fpg formamidopyrimid 24.9 43 0.00093 31.9 1.7 20 132-151 245-272 (272)
244 KOG4399 C2HC-type Zn-finger pr 24.6 18 0.00038 35.3 -1.0 53 133-189 250-302 (325)
245 COG2888 Predicted Zn-ribbon RN 24.5 47 0.001 25.4 1.5 33 118-152 26-58 (61)
246 PF04710 Pellino: Pellino; In 24.2 26 0.00057 35.8 0.1 49 201-252 274-337 (416)
247 PRK13945 formamidopyrimidine-D 24.1 46 0.00099 31.9 1.7 20 132-151 254-281 (282)
248 cd07973 Spt4 Transcription elo 24.0 42 0.00091 27.8 1.2 20 121-140 5-28 (98)
249 PLN03086 PRLI-interacting fact 23.8 50 0.0011 35.2 2.1 16 115-130 403-418 (567)
250 PRK06266 transcription initiat 23.8 48 0.001 29.9 1.7 11 204-214 136-146 (178)
251 PRK03564 formate dehydrogenase 23.6 84 0.0018 31.0 3.4 24 281-308 211-234 (309)
252 TIGR00373 conserved hypothetic 23.4 44 0.00095 29.5 1.3 9 160-168 108-116 (158)
253 PF09723 Zn-ribbon_8: Zinc rib 23.4 60 0.0013 22.4 1.7 31 282-312 5-38 (42)
254 PRK14892 putative transcriptio 23.1 72 0.0016 26.4 2.5 32 176-213 19-51 (99)
255 PRK00464 nrdR transcriptional 23.1 49 0.0011 29.4 1.6 12 134-145 30-41 (154)
256 KOG3842 Adaptor protein Pellin 23.0 40 0.00087 33.8 1.1 46 201-251 287-349 (429)
257 COG5273 Uncharacterized protei 22.7 39 0.00085 33.0 1.0 23 133-155 98-120 (309)
258 cd02345 ZZ_dah Zinc finger, ZZ 22.6 62 0.0013 23.1 1.8 27 283-312 1-27 (49)
259 PF10083 DUF2321: Uncharacteri 22.1 30 0.00066 31.0 0.1 29 118-148 27-56 (158)
260 PRK03564 formate dehydrogenase 21.8 95 0.0021 30.7 3.4 26 116-141 209-235 (309)
261 PF00412 LIM: LIM domain; Int 21.7 56 0.0012 22.9 1.4 39 207-256 1-39 (58)
262 PF05458 Siva: Cd27 binding pr 21.5 70 0.0015 28.9 2.3 13 143-155 146-158 (175)
263 PRK08351 DNA-directed RNA poly 21.4 55 0.0012 25.0 1.3 20 121-141 5-24 (61)
264 PF04423 Rad50_zn_hook: Rad50 21.3 58 0.0013 23.4 1.4 13 244-256 21-33 (54)
265 TIGR01384 TFS_arch transcripti 21.3 75 0.0016 25.5 2.2 10 243-252 62-71 (104)
266 PF00130 C1_1: Phorbol esters/ 21.2 76 0.0016 22.1 2.0 12 157-168 24-35 (53)
267 PF15353 HECA: Headcase protei 20.9 56 0.0012 27.6 1.4 16 225-240 39-54 (107)
268 PF06937 EURL: EURL protein; 20.6 74 0.0016 31.1 2.3 43 202-247 28-74 (285)
269 PRK05580 primosome assembly pr 20.5 95 0.0021 33.5 3.4 45 117-169 379-429 (679)
270 KOG0269 WD40 repeat-containing 20.4 51 0.0011 36.4 1.3 50 133-191 754-806 (839)
271 COG2051 RPS27A Ribosomal prote 20.3 51 0.0011 25.7 1.0 28 118-145 18-51 (67)
272 smart00647 IBR In Between Ring 20.2 44 0.00095 23.8 0.6 18 221-238 40-58 (64)
273 PF00628 PHD: PHD-finger; Int 20.2 1.3E+02 0.0027 20.8 2.9 20 146-167 1-20 (51)
274 PF14803 Nudix_N_2: Nudix N-te 20.0 66 0.0014 21.6 1.3 28 134-168 2-29 (34)
No 1
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=100.00 E-value=1.6e-65 Score=481.87 Aligned_cols=241 Identities=52% Similarity=1.046 Sum_probs=233.2
Q ss_pred cccCcccccccccccceeecCCCCCcccCchhhhhhccCcccCccCCCCCCCccCceeecCCCCcccccccCCCCCCCcc
Q 021215 63 LLRKGFMECQHYRRRCRIRAPCCNEIFDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKVQQVCVNCGVCM 142 (316)
Q Consensus 63 ~~~~~~~~C~HY~r~c~l~~pcC~~~y~Cr~CHde~~~~~~~~~~~~H~~dR~~v~~V~C~~C~~eq~v~~~C~~Cg~~f 142 (316)
++....+||+||+|++++++|+|++||+||+||+++. +|.++|+.|.+++|+.|+++|++++.|.+|+..|
T Consensus 27 d~~~~~~~c~hy~r~~~~~a~ccd~~~~C~hCH~~s~---------~h~~~r~~v~~~~C~~C~~~q~~~~~c~~c~~~~ 97 (276)
T KOG1940|consen 27 DEIAFPYGCPHYRRNCKSRAPCCDREITCRHCHNESE---------DHDLDRKTVYELLCMKCRKIQPVGQICSNCHVEL 97 (276)
T ss_pred cccccccCCchhhhccccccccccceeeeEEecChhh---------hcccchhhhhhhhhhhHHhhhhhhhccccchhhh
Confidence 4455666799999999999999999999999999975 8999999999999999999999999999999999
Q ss_pred ceEecCccccccCCCCCCeeecCCCCcceecCCcceeeccCCcceeeccccccccccCCCCCCCCcccccccccCcceeE
Q 021215 143 GEYFCESCKLFDDDTSKKQYHCDGCGICRIGGCDNFFHCNKCRCCYSMLLKNSHPCVEGAMHHDCPVCCEYLFETRQDVI 222 (316)
Q Consensus 143 ~~YfC~~Ckl~ddd~~k~~yHC~~CgiCR~G~~~~ffHC~~C~~C~s~~l~~~H~CiE~~~~~~CPIClE~lf~s~~~v~ 222 (316)
|+|||.+|+||||+++ +||||+.|||||+|++++||||++|+.|+++.+.+.|+|+|++++.+||||.|+||++...+.
T Consensus 98 g~~~c~~C~l~dd~~~-~~~hC~~C~icr~g~~~~~fhc~~c~~c~~~~~~~~H~c~e~~~~~ncPic~e~l~~s~~~~~ 176 (276)
T KOG1940|consen 98 GEYYCLICKLFDDDPS-KQYHCDLCGICREGLGLDFFHCKKCKACLSAYLSNWHKCVERSSEFNCPICKEYLFLSFEDAG 176 (276)
T ss_pred hhhcCccccccccccc-ceeccccccccccccccchhHHhhhHhHHhhhcccccchhhhcccCCCchhHHHhccccccCC
Confidence 9999999999999999 999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EcCCCCcccHHhHHHHhccCCCCCCCCCccccchhHHHHHhHHHHHcCCCChhhhcCcceEEcCCCCCCccccceeeeec
Q 021215 223 VLPCGHTIHKNCLKEMREHHQYACPICSKSVCDMSKVWEKYDREIAATPMPEAYLNKKVWILCNDCGKTSNVQFHVLAQK 302 (316)
Q Consensus 223 ~LpCGH~fH~~Ci~~wl~~~~~~CPiCrks~~d~~~~~~~lD~~i~~~pmP~ey~~~~~~IlCnDC~~~s~v~~H~lg~k 302 (316)
.|+|||++|..|++++.... |+||+|.+ +.||+.+|+++|.+|+++|||++|++++++|+||||+..++++|||||+|
T Consensus 177 ~~~CgH~~h~~cf~e~~~~~-y~CP~C~~-~~d~~~~~~~~d~~l~~~~~p~~y~~~~~~i~cndC~~~~~~k~~~l~~k 254 (276)
T KOG1940|consen 177 VLKCGHYMHSRCFEEMICEG-YTCPICSK-PGDMSHYFRKLDKELAGSPMPEEYKNKTQDILCNDCGSGTNVKYHILYHK 254 (276)
T ss_pred ccCcccchHHHHHHHHhccC-CCCCcccc-hHHHHHHHHHHHHHHhcCCCCchhhchhheeeccCCCCCCccceehhhhh
Confidence 99999999999999998865 99999999 99999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCccccccC
Q 021215 303 CPNCKSYNTRLTR 315 (316)
Q Consensus 303 C~~C~SyNT~~~~ 315 (316)
|+.|+|||||+++
T Consensus 255 c~~c~~~~~r~~~ 267 (276)
T KOG1940|consen 255 CGKCGSYNTRMIS 267 (276)
T ss_pred CCCcccceeeecc
Confidence 9999999999985
No 2
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=99.93 E-value=2.2e-27 Score=178.40 Aligned_cols=61 Identities=66% Similarity=1.160 Sum_probs=22.6
Q ss_pred ccchhHHHHHhHHHHHcCCCChhhhcCcceEEcCCCCCCccccceeeeecCCCCCCccccc
Q 021215 253 VCDMSKVWEKYDREIAATPMPEAYLNKKVWILCNDCGKTSNVQFHVLAQKCPNCKSYNTRL 313 (316)
Q Consensus 253 ~~d~~~~~~~lD~~i~~~pmP~ey~~~~~~IlCnDC~~~s~v~~H~lg~kC~~C~SyNT~~ 313 (316)
+.||+.+|+.||++|+++|||++|++++++|+||||+++|+|+||||||||.+|+||||||
T Consensus 1 v~dM~~~w~~LD~~i~~~pmP~~Y~~~~v~IlCNDC~~~s~v~fH~lg~KC~~C~SYNT~q 61 (61)
T PF14599_consen 1 VVDMSAYWRMLDAEIAATPMPEEYRNKKVWILCNDCNAKSEVPFHFLGHKCSHCGSYNTRQ 61 (61)
T ss_dssp ---------------------------EEEEEESSS--EEEEE--TT----TTTS---EEE
T ss_pred CCCHHHHHHHHHHHHHhCCCCHHHhCCEEEEECCCCCCccceeeeHhhhcCCCCCCcccCC
Confidence 4689999999999999999999999999999999999999999999999999999999997
No 3
>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=2e-23 Score=161.00 Aligned_cols=70 Identities=46% Similarity=1.129 Sum_probs=53.3
Q ss_pred ccccccc-ceeecCCCCCcccCchhhhhhccCcccCccCCCCCCCccCceeecCCCCcccccccCCCCCCCccceEecCc
Q 021215 71 CQHYRRR-CRIRAPCCNEIFDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKVQQVCVNCGVCMGEYFCES 149 (316)
Q Consensus 71 C~HY~r~-c~l~~pcC~~~y~Cr~CHde~~~~~~~~~~~~H~~dR~~v~~V~C~~C~~eq~v~~~C~~Cg~~f~~YfC~~ 149 (316)
|+||+|+ |+|+||||++|||||+||||++ +|+++|+.+++|+||.|+++|++++. +|+ ++|+|++
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 89999999999999999999999887 777 9999999
Q ss_pred ccccc
Q 021215 150 CKLFD 154 (316)
Q Consensus 150 Ckl~d 154 (316)
|++||
T Consensus 67 C~~~~ 71 (71)
T PF05495_consen 67 CGLYF 71 (71)
T ss_dssp TTEEE
T ss_pred cCCCC
Confidence 99986
No 4
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=99.36 E-value=1.5e-13 Score=111.57 Aligned_cols=65 Identities=25% Similarity=0.702 Sum_probs=57.1
Q ss_pred cccccc---cceeecCCCCCcccCchhhhhhccCcccCccCCCC-----CCCccCceeecCCCCcccccc-----cCCCC
Q 021215 71 CQHYRR---RCRIRAPCCNEIFDCRHCHNEAMNNINVDQKLRHD-----IPRHEVNQVICSLCGTEQKVQ-----QVCVN 137 (316)
Q Consensus 71 C~HY~r---~c~l~~pcC~~~y~Cr~CHde~~~~~~~~~~~~H~-----~dR~~v~~V~C~~C~~eq~v~-----~~C~~ 137 (316)
|.||++ +++|||.+|++||+|++||||++ +|| ++.+..+.||||+|+++++.+ ..||+
T Consensus 15 C~Hyht~~Diialkc~~C~kyYaCy~CHdel~---------~Hpf~p~~~~~~~~~~iiCGvC~~~LT~~EY~~~~~Cp~ 85 (105)
T COG4357 15 CLHYHTPLDIIALKCKCCQKYYACYHCHDELE---------DHPFEPWGLQEFNPKAIICGVCRKLLTRAEYGMCGSCPY 85 (105)
T ss_pred eeEecCccceEeeeechhhhhhhHHHHHhHHh---------cCCCccCChhhcCCccEEhhhhhhhhhHHHHhhcCCCCC
Confidence 999999 79999999999999999999987 565 455667789999999999853 68999
Q ss_pred CCCccce
Q 021215 138 CGVCMGE 144 (316)
Q Consensus 138 Cg~~f~~ 144 (316)
|..+||.
T Consensus 86 C~spFNp 92 (105)
T COG4357 86 CQSPFNP 92 (105)
T ss_pred cCCCCCc
Confidence 9999984
No 5
>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=99.27 E-value=1.3e-12 Score=90.92 Aligned_cols=44 Identities=39% Similarity=1.061 Sum_probs=36.8
Q ss_pred CCCcccccccccCcceeEEcCCCCcccHHhHHHHhccCCCCCCCCC
Q 021215 205 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICS 250 (316)
Q Consensus 205 ~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiCr 250 (316)
++||||++.+. ..+.++.|+|||.||.+||.+|++. +.+||+||
T Consensus 1 d~C~IC~~~~~-~~~~~~~l~C~H~fh~~Ci~~~~~~-~~~CP~CR 44 (44)
T PF13639_consen 1 DECPICLEEFE-DGEKVVKLPCGHVFHRSCIKEWLKR-NNSCPVCR 44 (44)
T ss_dssp -CETTTTCBHH-TTSCEEEETTSEEEEHHHHHHHHHH-SSB-TTTH
T ss_pred CCCcCCChhhc-CCCeEEEccCCCeeCHHHHHHHHHh-CCcCCccC
Confidence 47999999754 4667889999999999999999986 58999997
No 6
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=99.15 E-value=2.7e-11 Score=96.88 Aligned_cols=52 Identities=19% Similarity=0.429 Sum_probs=41.9
Q ss_pred CCCCCCcccccccccCcceeEEcCCCCcccHHhHHHHhccC--CCCCCCCCccccc
Q 021215 202 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHH--QYACPICSKSVCD 255 (316)
Q Consensus 202 ~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~--~~~CPiCrks~~d 255 (316)
+++..||.|.. ....-+++...|+|.||..||.+|++.. +.+||+||.++..
T Consensus 30 ~fdg~Cp~Ck~--Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~~ 83 (85)
T PF12861_consen 30 PFDGCCPDCKF--PGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWKF 83 (85)
T ss_pred ccccCCCCccC--CCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeeee
Confidence 55788999984 4445577788999999999999999853 5789999988753
No 7
>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=98.93 E-value=6.8e-10 Score=85.95 Aligned_cols=47 Identities=28% Similarity=0.786 Sum_probs=36.1
Q ss_pred CCCCCcccccccccC---------cceeEEcCCCCcccHHhHHHHhccCCCCCCCCC
Q 021215 203 MHHDCPVCCEYLFET---------RQDVIVLPCGHTIHKNCLKEMREHHQYACPICS 250 (316)
Q Consensus 203 ~~~~CPIClE~lf~s---------~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiCr 250 (316)
.+++|+||++.|.+. ..+++.++|||.||..||.+||+. +.+||+||
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 8
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.88 E-value=8.3e-10 Score=107.95 Aligned_cols=50 Identities=28% Similarity=0.824 Sum_probs=44.8
Q ss_pred CCCcccccccccCcceeEEcCCCCcccHHhHHHHhccCCCCCCCCCccccc
Q 021215 205 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 255 (316)
Q Consensus 205 ~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiCrks~~d 255 (316)
..|+||||+ |..++.++.|||+|.||..||++||...+-.||+|+..+..
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 589999996 88899999999999999999999998655669999988764
No 9
>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=98.87 E-value=2.1e-09 Score=72.19 Aligned_cols=45 Identities=33% Similarity=1.041 Sum_probs=36.9
Q ss_pred CCcccccccccCcceeEEcCCCCcccHHhHHHHhccCCCCCCCCCccc
Q 021215 206 DCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSV 253 (316)
Q Consensus 206 ~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiCrks~ 253 (316)
.|+||++.+ ..++.+++|||.||..|+..|++....+||+|++.+
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 499999964 235666779999999999999986568899999764
No 10
>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=98.82 E-value=2.6e-09 Score=72.78 Aligned_cols=39 Identities=41% Similarity=1.110 Sum_probs=32.6
Q ss_pred CcccccccccCcceeEEcCCCCcccHHhHHHHhccCCCCCCCC
Q 021215 207 CPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPIC 249 (316)
Q Consensus 207 CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiC 249 (316)
||||++.+.+ +++.++|||+|+.+|+.+|++. +.+||+|
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 8999996433 6689999999999999999986 7899997
No 11
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.78 E-value=4.9e-09 Score=73.23 Aligned_cols=39 Identities=38% Similarity=1.199 Sum_probs=28.8
Q ss_pred CcccccccccCcceeEEcCCCCcccHHhHHHHhccC---CCCCCCC
Q 021215 207 CPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHH---QYACPIC 249 (316)
Q Consensus 207 CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~---~~~CPiC 249 (316)
||||+++ |. +++.|+|||+|+..||..|++.. .+.||+|
T Consensus 1 CpiC~~~-~~---~Pv~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDL-FK---DPVSLPCGHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB--S---SEEE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCccchh-hC---CccccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 8999994 65 57899999999999999988653 2679987
No 12
>PHA02929 N1R/p28-like protein; Provisional
Probab=98.72 E-value=9.6e-09 Score=96.17 Aligned_cols=54 Identities=19% Similarity=0.609 Sum_probs=42.0
Q ss_pred CCCCCCCcccccccccCcc----eeEEcCCCCcccHHhHHHHhccCCCCCCCCCccccc
Q 021215 201 GAMHHDCPVCCEYLFETRQ----DVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 255 (316)
Q Consensus 201 ~~~~~~CPIClE~lf~s~~----~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiCrks~~d 255 (316)
.+.+..||||+|.+..... -.++++|||.||..||.+|++. +.+||+||..+..
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 3456899999997654321 1345689999999999999984 6899999988763
No 13
>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=98.68 E-value=1.1e-08 Score=72.97 Aligned_cols=47 Identities=34% Similarity=0.982 Sum_probs=38.1
Q ss_pred CCCCcccccccccCcceeEEcCCCCc-ccHHhHHHHhccCCCCCCCCCccccc
Q 021215 204 HHDCPVCCEYLFETRQDVIVLPCGHT-IHKNCLKEMREHHQYACPICSKSVCD 255 (316)
Q Consensus 204 ~~~CPIClE~lf~s~~~v~~LpCGH~-fH~~Ci~~wl~~~~~~CPiCrks~~d 255 (316)
+..|+||++. ...++++||||. |+..|+..|++ ...+||+||+++..
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 3579999984 235789999999 99999999998 56899999998753
No 14
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=98.67 E-value=7.1e-09 Score=101.83 Aligned_cols=56 Identities=38% Similarity=0.820 Sum_probs=47.1
Q ss_pred CCCCCCCcccccccccCc---------ceeEEcCCCCcccHHhHHHHhccCCCCCCCCCccc-cchh
Q 021215 201 GAMHHDCPVCCEYLFETR---------QDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSV-CDMS 257 (316)
Q Consensus 201 ~~~~~~CPIClE~lf~s~---------~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiCrks~-~d~~ 257 (316)
...+..|.||+|.|+.++ ..+..|||||.+|.+|++.|+.+ +.+||+||.++ .|+.
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 567889999999988765 34578999999999999999985 68999999994 4554
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=98.67 E-value=1.6e-08 Score=68.91 Aligned_cols=40 Identities=43% Similarity=1.116 Sum_probs=33.4
Q ss_pred CcccccccccCcceeEEcCCCCcccHHhHHHHhc-cCCCCCCCC
Q 021215 207 CPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMRE-HHQYACPIC 249 (316)
Q Consensus 207 CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~-~~~~~CPiC 249 (316)
||||++.+.. +..+++|||.|+..|+.+|++ .....||+|
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 7999996332 446999999999999999988 566889998
No 16
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=98.59 E-value=8.7e-09 Score=81.00 Aligned_cols=51 Identities=24% Similarity=0.490 Sum_probs=40.7
Q ss_pred CCCCCCcccccccccCcceeEEcCCCCcccHHhHHHHhcc--CCCCCCCCCcccc
Q 021215 202 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH--HQYACPICSKSVC 254 (316)
Q Consensus 202 ~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~--~~~~CPiCrks~~ 254 (316)
+++..||-|. +..+.-+.++..|.|.||..||.+|+.. ++..||+||.++.
T Consensus 29 ~Fdg~Cp~Ck--~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~ 81 (84)
T KOG1493|consen 29 PFDGCCPDCK--LPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQ 81 (84)
T ss_pred ccCCcCCCCc--CCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeE
Confidence 5678899998 4555556666689999999999999864 3467999998775
No 17
>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=98.58 E-value=4e-08 Score=63.61 Aligned_cols=39 Identities=44% Similarity=1.130 Sum_probs=33.1
Q ss_pred CcccccccccCcceeEEcCCCCcccHHhHHHHhccCCCCCCCC
Q 021215 207 CPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPIC 249 (316)
Q Consensus 207 CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiC 249 (316)
|+||++. ...++.++|||.||..|++.|++....+||+|
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 7899985 34678899999999999999997456789987
No 18
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.55 E-value=3.6e-08 Score=69.54 Aligned_cols=40 Identities=38% Similarity=1.053 Sum_probs=24.3
Q ss_pred CcccccccccCcceeEEcCCCCcccHHhHHHHhccC---CCCCC
Q 021215 207 CPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHH---QYACP 247 (316)
Q Consensus 207 CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~---~~~CP 247 (316)
||||+| +-+...++++|+|||+|+++|+++|++.+ .++||
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 55556678899999999999999998742 56787
No 19
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.54 E-value=4.4e-08 Score=94.22 Aligned_cols=54 Identities=26% Similarity=0.663 Sum_probs=45.9
Q ss_pred CCCCCCCCcccccccccCcceeEEcCCCCcccHHhHHHHhccCCCCCCCCCcccc
Q 021215 200 EGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 254 (316)
Q Consensus 200 E~~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiCrks~~ 254 (316)
|....-+|+|||++ |...+.+++|||.|.||..|+++|+...+.+||+||..+.
T Consensus 319 ea~~GveCaICms~-fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iP 372 (374)
T COG5540 319 EADKGVECAICMSN-FIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIP 372 (374)
T ss_pred hcCCCceEEEEhhh-hcccceEEEeccCceechhHHHHHHhhhcccCCccCCCCC
Confidence 44445789999997 6777889999999999999999999755678999998764
No 20
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.51 E-value=8.8e-08 Score=67.00 Aligned_cols=44 Identities=32% Similarity=0.882 Sum_probs=36.9
Q ss_pred CCcccccccccCcceeEEcCCCCcccHHhHHHHhccCCCCCCCCCc
Q 021215 206 DCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSK 251 (316)
Q Consensus 206 ~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiCrk 251 (316)
.|+||++. +.....+.+++|||+|+..|+..+.. ....||+||+
T Consensus 1 ~C~~C~~~-~~~~~~~~l~~CgH~~C~~C~~~~~~-~~~~CP~C~k 44 (44)
T PF14634_consen 1 HCNICFEK-YSEERRPRLTSCGHIFCEKCLKKLKG-KSVKCPICRK 44 (44)
T ss_pred CCcCcCcc-ccCCCCeEEcccCCHHHHHHHHhhcC-CCCCCcCCCC
Confidence 48999996 45556788999999999999999983 4678999985
No 21
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.47 E-value=1.4e-07 Score=85.81 Aligned_cols=55 Identities=25% Similarity=0.636 Sum_probs=42.3
Q ss_pred cccCCCCCCCCcccccccccCcceeEEcCCCCcccHHhHHHHhcc---------------CCCCCCCCCccccc
Q 021215 197 PCVEGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH---------------HQYACPICSKSVCD 255 (316)
Q Consensus 197 ~CiE~~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~---------------~~~~CPiCrks~~d 255 (316)
+=++...+..||||++. +. ++++++|||.||..||.+|+.. ...+||+||..+..
T Consensus 11 ~~~~~~~~~~CpICld~-~~---dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~ 80 (193)
T PLN03208 11 TLVDSGGDFDCNICLDQ-VR---DPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE 80 (193)
T ss_pred eeccCCCccCCccCCCc-CC---CcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence 33444557899999995 43 4577899999999999999742 23579999988864
No 22
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=98.43 E-value=1.4e-07 Score=74.79 Aligned_cols=51 Identities=20% Similarity=0.397 Sum_probs=38.8
Q ss_pred CCCCcccccccccCc-ceeEEcCCCCcccHHhHHHHhccCCCCCCCCCccccc
Q 021215 204 HHDCPVCCEYLFETR-QDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 255 (316)
Q Consensus 204 ~~~CPIClE~lf~s~-~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiCrks~~d 255 (316)
.+.||-|.-.+-... -+++...|.|.||.+||..||.. +..||++|+++..
T Consensus 31 m~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~T-k~~CPld~q~w~~ 82 (88)
T COG5194 31 MGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDT-KGVCPLDRQTWVL 82 (88)
T ss_pred cCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhh-CCCCCCCCceeEE
Confidence 456777775442222 34566789999999999999985 6899999998763
No 23
>PHA02926 zinc finger-like protein; Provisional
Probab=98.28 E-value=4.9e-07 Score=83.97 Aligned_cols=56 Identities=20% Similarity=0.536 Sum_probs=42.3
Q ss_pred CCCCCCCCcccccccccC-----cceeEEcCCCCcccHHhHHHHhccC-----CCCCCCCCccccc
Q 021215 200 EGAMHHDCPVCCEYLFET-----RQDVIVLPCGHTIHKNCLKEMREHH-----QYACPICSKSVCD 255 (316)
Q Consensus 200 E~~~~~~CPIClE~lf~s-----~~~v~~LpCGH~fH~~Ci~~wl~~~-----~~~CPiCrks~~d 255 (316)
+.+.+..|+||||.++.. +.-.++.+|+|.||..||..|.+.. ..+||+||..+..
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 456688999999976542 1224566999999999999998742 2459999987753
No 24
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=98.25 E-value=4.9e-07 Score=90.67 Aligned_cols=81 Identities=27% Similarity=0.680 Sum_probs=65.0
Q ss_pred CCCcccccccccCcceeEEcCCCCcccHHhHHHHhccCCCCCCCCCccccchhHHHHHhHHHHHcCCCChhhhcCcceEE
Q 021215 205 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCDMSKVWEKYDREIAATPMPEAYLNKKVWIL 284 (316)
Q Consensus 205 ~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiCrks~~d~~~~~~~lD~~i~~~pmP~ey~~~~~~Il 284 (316)
-.||||||.|..+...++...|.|+||-.|+..|.. .+||+||.... |+. -..-+
T Consensus 176 PTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~~---~scpvcR~~q~------------------p~~----ve~~~ 230 (493)
T KOG0804|consen 176 PTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWWD---SSCPVCRYCQS------------------PSV----VESSL 230 (493)
T ss_pred CCcchhHhhcCccccceeeeecccccchHHHhhccc---CcChhhhhhcC------------------cch----hhhhh
Confidence 479999999999888889999999999999999964 67999995332 111 11346
Q ss_pred cCCCCCCccccceeeeecCC--CCCCccccc
Q 021215 285 CNDCGKTSNVQFHVLAQKCP--NCKSYNTRL 313 (316)
Q Consensus 285 CnDC~~~s~v~~H~lg~kC~--~C~SyNT~~ 313 (316)
|..|+..-+. |+-+.|+ +||-|+-.-
T Consensus 231 c~~c~~~~~L---wicliCg~vgcgrY~egh 258 (493)
T KOG0804|consen 231 CLACGCTEDL---WICLICGNVGCGRYKEGH 258 (493)
T ss_pred hhhhcccccE---EEEEEccceecccccchh
Confidence 9999988887 8999998 599998643
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=98.21 E-value=1.4e-06 Score=63.95 Aligned_cols=45 Identities=20% Similarity=0.473 Sum_probs=38.1
Q ss_pred CCCcccccccccCcceeEEcCCCCcccHHhHHHHhccCCCCCCCCCcccc
Q 021215 205 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 254 (316)
Q Consensus 205 ~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiCrks~~ 254 (316)
..||||++. ++ ++++++|||+|.+.||.+|++. +.+||+|++.+.
T Consensus 2 ~~Cpi~~~~-~~---~Pv~~~~G~v~~~~~i~~~~~~-~~~cP~~~~~~~ 46 (63)
T smart00504 2 FLCPISLEV-MK---DPVILPSGQTYERRAIEKWLLS-HGTDPVTGQPLT 46 (63)
T ss_pred cCCcCCCCc-CC---CCEECCCCCEEeHHHHHHHHHH-CCCCCCCcCCCC
Confidence 469999995 44 3578899999999999999985 678999998874
No 26
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.00 E-value=1.8e-06 Score=88.93 Aligned_cols=53 Identities=32% Similarity=0.676 Sum_probs=43.3
Q ss_pred CCCCCCCCcccccccccCcc-eeEEcCCCCcccHHhHHHHhccCCCCCCCCCccc
Q 021215 200 EGAMHHDCPVCCEYLFETRQ-DVIVLPCGHTIHKNCLKEMREHHQYACPICSKSV 253 (316)
Q Consensus 200 E~~~~~~CPIClE~lf~s~~-~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiCrks~ 253 (316)
....+..|+||+|.|..+.. .+..|||||.||..|+.+|++. ..+||+||..+
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 34558899999998876422 2568999999999999999986 68999999843
No 27
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.97 E-value=1.2e-05 Score=71.18 Aligned_cols=44 Identities=39% Similarity=1.050 Sum_probs=37.4
Q ss_pred CCCCCcccccccccCcceeEEcCCCCcccHHhHHHHhccCCCCCCCCCc
Q 021215 203 MHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSK 251 (316)
Q Consensus 203 ~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiCrk 251 (316)
....||||+++ |..+ ++|||||+|+..|+..++. ....||.||.
T Consensus 12 ~~~~C~iC~~~-~~~p---~~l~C~H~~c~~C~~~~~~-~~~~Cp~cr~ 55 (386)
T KOG2177|consen 12 EELTCPICLEY-FREP---VLLPCGHNFCRACLTRSWE-GPLSCPVCRP 55 (386)
T ss_pred ccccChhhHHH-hhcC---ccccccchHhHHHHHHhcC-CCcCCcccCC
Confidence 46789999996 5532 8999999999999999887 5688999994
No 28
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.96 E-value=4.5e-06 Score=75.19 Aligned_cols=48 Identities=25% Similarity=0.742 Sum_probs=38.4
Q ss_pred CCCCcccccccccCcceeEEcCCCCcccHHhHHHHhccCCCCCCCCCcccc
Q 021215 204 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 254 (316)
Q Consensus 204 ~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiCrks~~ 254 (316)
-..|||||+. +. .+-++...|||.|+.+||+..++. ...||+|+|-+.
T Consensus 131 ~~~CPiCl~~-~s-ek~~vsTkCGHvFC~~Cik~alk~-~~~CP~C~kkIt 178 (187)
T KOG0320|consen 131 TYKCPICLDS-VS-EKVPVSTKCGHVFCSQCIKDALKN-TNKCPTCRKKIT 178 (187)
T ss_pred ccCCCceecc-hh-hccccccccchhHHHHHHHHHHHh-CCCCCCcccccc
Confidence 3789999996 33 223356899999999999999984 578999998654
No 29
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=97.88 E-value=5.5e-06 Score=79.30 Aligned_cols=47 Identities=28% Similarity=0.718 Sum_probs=38.8
Q ss_pred CCCCcccccccccCcceeEEcCCCCcccHHhHHHHhccCCCCCCCCCccccc
Q 021215 204 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 255 (316)
Q Consensus 204 ~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiCrks~~d 255 (316)
...|.+|||. +..+.-.||||.|+..||.+|... ..-||+||..+..
T Consensus 239 ~~kC~LCLe~----~~~pSaTpCGHiFCWsCI~~w~~e-k~eCPlCR~~~~p 285 (293)
T KOG0317|consen 239 TRKCSLCLEN----RSNPSATPCGHIFCWSCILEWCSE-KAECPLCREKFQP 285 (293)
T ss_pred CCceEEEecC----CCCCCcCcCcchHHHHHHHHHHcc-ccCCCcccccCCC
Confidence 3679999994 345678999999999999999984 5679999977653
No 30
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.82 E-value=1e-05 Score=75.29 Aligned_cols=50 Identities=28% Similarity=0.654 Sum_probs=38.9
Q ss_pred CCCCCCcccccccccCcceeEEcCCCCcccHHhHHHHhccC--CCCCCCCCccccc
Q 021215 202 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHH--QYACPICSKSVCD 255 (316)
Q Consensus 202 ~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~--~~~CPiCrks~~d 255 (316)
...-+|-||||- .+++++..|||.|+..||-+||... +..||+|+..+..
T Consensus 45 ~~~FdCNICLd~----akdPVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~ 96 (230)
T KOG0823|consen 45 GGFFDCNICLDL----AKDPVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSI 96 (230)
T ss_pred CCceeeeeeccc----cCCCEEeecccceehHHHHHHHhhcCCCeeCCcccccccc
Confidence 446799999983 3356677799999999999999753 3458999977653
No 31
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.81 E-value=1.3e-05 Score=80.28 Aligned_cols=46 Identities=24% Similarity=0.699 Sum_probs=38.7
Q ss_pred CCCCcccccccccCcceeEEcCCCCcccHHhHHHHhccCCCCCCCCCcccc
Q 021215 204 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 254 (316)
Q Consensus 204 ~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiCrks~~ 254 (316)
...|+||++. |. .+++++|||.||..||..|+.. ...||+|+..+.
T Consensus 26 ~l~C~IC~d~-~~---~PvitpCgH~FCs~CI~~~l~~-~~~CP~Cr~~~~ 71 (397)
T TIGR00599 26 SLRCHICKDF-FD---VPVLTSCSHTFCSLCIRRCLSN-QPKCPLCRAEDQ 71 (397)
T ss_pred ccCCCcCchh-hh---CccCCCCCCchhHHHHHHHHhC-CCCCCCCCCccc
Confidence 5799999995 54 3457899999999999999974 568999998876
No 32
>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=97.75 E-value=2.4e-05 Score=75.90 Aligned_cols=52 Identities=23% Similarity=0.568 Sum_probs=39.3
Q ss_pred CCCCcccccccccCccee-EEcCCCCcccHHhHHHHhccCCCCCCCCCccccc
Q 021215 204 HHDCPVCCEYLFETRQDV-IVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 255 (316)
Q Consensus 204 ~~~CPIClE~lf~s~~~v-~~LpCGH~fH~~Ci~~wl~~~~~~CPiCrks~~d 255 (316)
+..||||+...+.++.-. .+-+|||.||..|++.++..+...||+|++++..
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 2237999999999999766566789999987753
No 33
>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=97.70 E-value=2.9e-05 Score=56.04 Aligned_cols=43 Identities=28% Similarity=0.724 Sum_probs=33.3
Q ss_pred CCcccccccccCcceeEEcCCC-----CcccHHhHHHHhccC-CCCCCCCC
Q 021215 206 DCPVCCEYLFETRQDVIVLPCG-----HTIHKNCLKEMREHH-QYACPICS 250 (316)
Q Consensus 206 ~CPIClE~lf~s~~~v~~LpCG-----H~fH~~Ci~~wl~~~-~~~CPiCr 250 (316)
.|-||++ +.+...+.++||. |.+|..|+.+|+... +.+||+|+
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 3344566788994 999999999999643 45899995
No 34
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=97.60 E-value=1.3e-05 Score=61.65 Aligned_cols=51 Identities=27% Similarity=0.630 Sum_probs=23.5
Q ss_pred CCCCcccccccccCc-ceeEEc---CCCCcccHHhHHHHhcc---C-------CCCCCCCCcccc
Q 021215 204 HHDCPVCCEYLFETR-QDVIVL---PCGHTIHKNCLKEMREH---H-------QYACPICSKSVC 254 (316)
Q Consensus 204 ~~~CPIClE~lf~s~-~~v~~L---pCGH~fH~~Ci~~wl~~---~-------~~~CPiCrks~~ 254 (316)
+.+|+||++++.+.. .+.++- .|+..||..||.+|+.. . ...||.|++++.
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 457999998766332 233332 69999999999999863 1 125999998875
No 35
>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=97.60 E-value=0.00012 Score=56.42 Aligned_cols=48 Identities=25% Similarity=0.551 Sum_probs=36.6
Q ss_pred CCCCcccccccccCcceeEEcCCCCcccHHhHHHHhccCCCCCCCCCccccc
Q 021215 204 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 255 (316)
Q Consensus 204 ~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiCrks~~d 255 (316)
+..|||+++ ++. +++++|+||+|-+.+|..|+.....+||+++..+..
T Consensus 4 ~f~CpIt~~-lM~---dPVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~ 51 (73)
T PF04564_consen 4 EFLCPITGE-LMR---DPVILPSGHTYERSAIERWLEQNGGTDPFTRQPLSE 51 (73)
T ss_dssp GGB-TTTSS-B-S---SEEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SG
T ss_pred ccCCcCcCc-Hhh---CceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCc
Confidence 457999998 455 577899999999999999998657899999988764
No 36
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=97.52 E-value=6e-05 Score=73.99 Aligned_cols=46 Identities=30% Similarity=0.823 Sum_probs=39.6
Q ss_pred CCCcccccccccCcceeEEcCCCCcccHHhHHHHhccCCCCCCCCCccccc
Q 021215 205 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 255 (316)
Q Consensus 205 ~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiCrks~~d 255 (316)
..|-||.|| |. .+++.||||+|+.-||..+|. .+..||.|+.++..
T Consensus 24 LRC~IC~ey-f~---ip~itpCsHtfCSlCIR~~L~-~~p~CP~C~~~~~E 69 (442)
T KOG0287|consen 24 LRCGICFEY-FN---IPMITPCSHTFCSLCIRKFLS-YKPQCPTCCVTVTE 69 (442)
T ss_pred HHHhHHHHH-hc---CceeccccchHHHHHHHHHhc-cCCCCCceecccch
Confidence 479999996 55 467889999999999999998 47999999988863
No 37
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=97.50 E-value=2.4e-05 Score=65.02 Aligned_cols=35 Identities=23% Similarity=0.437 Sum_probs=29.9
Q ss_pred eeEEcCCCCcccHHhHHHHhccCCCCCCCCCccccc
Q 021215 220 DVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 255 (316)
Q Consensus 220 ~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiCrks~~d 255 (316)
.++..-|.|.||..||..||+. +..||++.+.+..
T Consensus 75 ~VaWG~CNHaFH~hCisrWlkt-r~vCPLdn~eW~~ 109 (114)
T KOG2930|consen 75 TVAWGVCNHAFHFHCISRWLKT-RNVCPLDNKEWVF 109 (114)
T ss_pred EEEeeecchHHHHHHHHHHHhh-cCcCCCcCcceeE
Confidence 3556789999999999999985 6899999998763
No 38
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.45 E-value=6.8e-05 Score=76.61 Aligned_cols=50 Identities=26% Similarity=0.623 Sum_probs=37.2
Q ss_pred CCCCCCcccccccccCcceeEEcCCCCcccHHhHHHHhccC----CCCCCCCCccccc
Q 021215 202 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHH----QYACPICSKSVCD 255 (316)
Q Consensus 202 ~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~----~~~CPiCrks~~d 255 (316)
+++..|||||++ +. .++ .+.|||.||..||.+||..+ --.||+|+..+..
T Consensus 184 ~t~~~CPICL~~-~~--~p~-~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~ 237 (513)
T KOG2164|consen 184 STDMQCPICLEP-PS--VPV-RTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITL 237 (513)
T ss_pred CcCCcCCcccCC-CC--ccc-ccccCceeeHHHHHHHHhhhcccCCccCCchhhhccc
Confidence 337899999996 22 233 44599999999999977543 2459999987764
No 39
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.36 E-value=6.9e-05 Score=76.40 Aligned_cols=51 Identities=25% Similarity=0.706 Sum_probs=39.1
Q ss_pred CCCCcccccccccC-------------cceeEEcCCCCcccHHhHHHHhccCCCCCCCCCcccc
Q 021215 204 HHDCPVCCEYLFET-------------RQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 254 (316)
Q Consensus 204 ~~~CPIClE~lf~s-------------~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiCrks~~ 254 (316)
..+|+|||.++... ++..++.||.|.||..|+.+|....+..||+||.++.
T Consensus 571 t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLP 634 (636)
T KOG0828|consen 571 TNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLP 634 (636)
T ss_pred cccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCCC
Confidence 46899999765211 1235667999999999999999855567999998765
No 40
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.08 E-value=0.00026 Score=67.32 Aligned_cols=46 Identities=30% Similarity=0.696 Sum_probs=37.1
Q ss_pred CCCCcccccccccCcceeEEcCCCCcccHHhHHH-HhccCCCC-CCCCCcccc
Q 021215 204 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKE-MREHHQYA-CPICSKSVC 254 (316)
Q Consensus 204 ~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~-wl~~~~~~-CPiCrks~~ 254 (316)
+..|+||+|.. ..+..++|||.|+..||.. |-.. ++- ||+||.-..
T Consensus 215 d~kC~lC~e~~----~~ps~t~CgHlFC~~Cl~~~~t~~-k~~~CplCRak~~ 262 (271)
T COG5574 215 DYKCFLCLEEP----EVPSCTPCGHLFCLSCLLISWTKK-KYEFCPLCRAKVY 262 (271)
T ss_pred ccceeeeeccc----CCcccccccchhhHHHHHHHHHhh-ccccCchhhhhcc
Confidence 56799999853 3567889999999999999 8764 455 999997554
No 41
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.00 E-value=0.0003 Score=70.12 Aligned_cols=46 Identities=28% Similarity=0.680 Sum_probs=36.8
Q ss_pred CCCCcccccccccCcceeEEcC-CCCcccHHhHHHHhccC--CCCCCCCC
Q 021215 204 HHDCPVCCEYLFETRQDVIVLP-CGHTIHKNCLKEMREHH--QYACPICS 250 (316)
Q Consensus 204 ~~~CPIClE~lf~s~~~v~~Lp-CGH~fH~~Ci~~wl~~~--~~~CPiCr 250 (316)
...|.|| ++++....++..+. |||.||..|+.+|+... +..||+|+
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 55777766776664 99999999999999752 34799999
No 42
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=96.99 E-value=0.00034 Score=53.62 Aligned_cols=55 Identities=24% Similarity=0.619 Sum_probs=26.8
Q ss_pred CCCcccccccccCcceeEEcCCCCcccHHhHHHHhccCCCCCCCCCcccc--chhHHHHHhHHH
Q 021215 205 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC--DMSKVWEKYDRE 266 (316)
Q Consensus 205 ~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiCrks~~--d~~~~~~~lD~~ 266 (316)
..|++|.+.|.. ++.+..|.|.|+..|+.+-+. ..||+|+.+.- |+. ..+.||..
T Consensus 8 LrCs~C~~~l~~---pv~l~~CeH~fCs~Ci~~~~~---~~CPvC~~Paw~qD~~-~NrqLd~~ 64 (65)
T PF14835_consen 8 LRCSICFDILKE---PVCLGGCEHIFCSSCIRDCIG---SECPVCHTPAWIQDIQ-INRQLDSM 64 (65)
T ss_dssp TS-SSS-S--SS----B---SSS--B-TTTGGGGTT---TB-SSS--B-S-SS-----HHHHHH
T ss_pred cCCcHHHHHhcC---CceeccCccHHHHHHhHHhcC---CCCCCcCChHHHHHHH-hhhhhhcc
Confidence 579999986433 667789999999999988765 45999998874 332 23455554
No 43
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.89 E-value=0.00024 Score=53.07 Aligned_cols=51 Identities=25% Similarity=0.679 Sum_probs=39.1
Q ss_pred CCCCCcccccccccCcceeEEcCCCCc-ccHHhHHHHhccCCCCCCCCCccccchh
Q 021215 203 MHHDCPVCCEYLFETRQDVIVLPCGHT-IHKNCLKEMREHHQYACPICSKSVCDMS 257 (316)
Q Consensus 203 ~~~~CPIClE~lf~s~~~v~~LpCGH~-fH~~Ci~~wl~~~~~~CPiCrks~~d~~ 257 (316)
...+|.||+|. +.+.++.-|||. ++-+|-...++...-.||+||.++.+.-
T Consensus 6 ~~dECTICye~----pvdsVlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~dvI 57 (62)
T KOG4172|consen 6 WSDECTICYEH----PVDSVLYTCGHMCMCYACGLRLKKALHGCCPICRAPIKDVI 57 (62)
T ss_pred cccceeeeccC----cchHHHHHcchHHhHHHHHHHHHHccCCcCcchhhHHHHHH
Confidence 45789999995 234456689998 8889988865545688999999887643
No 44
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.65 E-value=0.00055 Score=65.57 Aligned_cols=52 Identities=23% Similarity=0.553 Sum_probs=40.5
Q ss_pred CCCCCcccccccccCc------ceeEEcCCCCcccHHhHHHHhcc-CCCCCCCCCcccc
Q 021215 203 MHHDCPVCCEYLFETR------QDVIVLPCGHTIHKNCLKEMREH-HQYACPICSKSVC 254 (316)
Q Consensus 203 ~~~~CPIClE~lf~s~------~~v~~LpCGH~fH~~Ci~~wl~~-~~~~CPiCrks~~ 254 (316)
.++.|+||...+..+. +..-.|.|+|.||.-||+-|--. ...+||.|++.+.
T Consensus 223 ~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVd 281 (328)
T KOG1734|consen 223 SDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVD 281 (328)
T ss_pred CcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhh
Confidence 3678999998766554 24568999999999999999433 4578999997654
No 45
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=96.65 E-value=0.0011 Score=64.13 Aligned_cols=46 Identities=26% Similarity=0.618 Sum_probs=38.0
Q ss_pred CCCCcccccccccCcceeEEcCCCCcccHHhHHHHhccCCCCCCCCCcccc
Q 021215 204 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 254 (316)
Q Consensus 204 ~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiCrks~~ 254 (316)
-..|-||.+++ . .+...+|||+|+.-||..+|. .+..||+||.+..
T Consensus 25 ~lrC~IC~~~i-~---ip~~TtCgHtFCslCIR~hL~-~qp~CP~Cr~~~~ 70 (391)
T COG5432 25 MLRCRICDCRI-S---IPCETTCGHTFCSLCIRRHLG-TQPFCPVCREDPC 70 (391)
T ss_pred HHHhhhhhhee-e---cceecccccchhHHHHHHHhc-CCCCCccccccHH
Confidence 35799999963 3 356779999999999999997 4799999997664
No 46
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=96.46 E-value=0.0021 Score=46.62 Aligned_cols=47 Identities=34% Similarity=0.699 Sum_probs=24.8
Q ss_pred CcccccccccCcceeEEcCCCCcccHHhHHHHhccCCCCCCCCCccc
Q 021215 207 CPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSV 253 (316)
Q Consensus 207 CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiCrks~ 253 (316)
||+|.|.|..++.....=+||+.+++.|+...+.....+||-||++.
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 79999988554443333467999999999998875578999999864
No 47
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.44 E-value=0.002 Score=63.58 Aligned_cols=49 Identities=31% Similarity=0.811 Sum_probs=39.4
Q ss_pred CCCCCCcccccccccCcceeEEcCCCCc-ccHHhHHHHhccCCCCCCCCCccccc
Q 021215 202 AMHHDCPVCCEYLFETRQDVIVLPCGHT-IHKNCLKEMREHHQYACPICSKSVCD 255 (316)
Q Consensus 202 ~~~~~CPIClE~lf~s~~~v~~LpCGH~-fH~~Ci~~wl~~~~~~CPiCrks~~d 255 (316)
....+|.|||.. .++.++|||-|. ++..|.+...- ...+||+||..+..
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 445789999974 457899999998 99999998752 35789999988764
No 48
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=96.32 E-value=0.0011 Score=70.48 Aligned_cols=48 Identities=27% Similarity=0.693 Sum_probs=41.1
Q ss_pred CCCCcccccccccCcceeEEcCCCCcccHHhHHHHhccCCCCCCCCCccccc
Q 021215 204 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 255 (316)
Q Consensus 204 ~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiCrks~~d 255 (316)
-..||+|-. ..++.++..|||.||..|++..+...+.+||.|..+|+.
T Consensus 643 ~LkCs~Cn~----R~Kd~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFga 690 (698)
T KOG0978|consen 643 LLKCSVCNT----RWKDAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGA 690 (698)
T ss_pred ceeCCCccC----chhhHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCc
Confidence 357999985 456788889999999999999887777899999999984
No 49
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.31 E-value=0.001 Score=65.68 Aligned_cols=80 Identities=21% Similarity=0.500 Sum_probs=51.5
Q ss_pred CCCCCCcccccccccCc---cee-EEcCCCCcccHHhHHHHhccC------CCCCCCCCccccch--hHHHHHhHHHHHc
Q 021215 202 AMHHDCPVCCEYLFETR---QDV-IVLPCGHTIHKNCLKEMREHH------QYACPICSKSVCDM--SKVWEKYDREIAA 269 (316)
Q Consensus 202 ~~~~~CPIClE~lf~s~---~~v-~~LpCGH~fH~~Ci~~wl~~~------~~~CPiCrks~~d~--~~~~~~lD~~i~~ 269 (316)
+.+..|.||+|.+.... ... ++++|.|.|+..||..|.+.. ...||+||...... +..|-.-.+ +.
T Consensus 159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~~v~pS~~Wv~t~~--~k 236 (344)
T KOG1039|consen 159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSSFVNPSSFWVETKE--EK 236 (344)
T ss_pred cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccccccccceeeeecc--cc
Confidence 55779999999765532 111 235699999999999998433 36799999776532 223422222 55
Q ss_pred CCCChhhhcCcceE
Q 021215 270 TPMPEAYLNKKVWI 283 (316)
Q Consensus 270 ~pmP~ey~~~~~~I 283 (316)
++++++|...+...
T Consensus 237 ~~li~e~~~~~s~~ 250 (344)
T KOG1039|consen 237 QKLIEEYEAEMSAK 250 (344)
T ss_pred cccHHHHHHHhhcc
Confidence 66667766654433
No 50
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.21 E-value=0.001 Score=65.64 Aligned_cols=48 Identities=23% Similarity=0.568 Sum_probs=39.5
Q ss_pred CCCCcccccccccCcceeEEcCCCCcccHHhHHHHhccCCCCCCCCCcccc
Q 021215 204 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 254 (316)
Q Consensus 204 ~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiCrks~~ 254 (316)
+..|||||+-|.. ...+.-|+|.|+.+||..-+..++..||.||+.+.
T Consensus 43 ~v~c~icl~llk~---tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~ 90 (381)
T KOG0311|consen 43 QVICPICLSLLKK---TMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLV 90 (381)
T ss_pred hhccHHHHHHHHh---hcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhcc
Confidence 4579999994433 34567899999999999988777889999998886
No 51
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=96.15 E-value=0.00092 Score=66.86 Aligned_cols=58 Identities=34% Similarity=0.713 Sum_probs=48.1
Q ss_pred cccccCCCCCCCCcccccccccCcceeEEcCCCCcccHHhHHHHhcc-CCCCCCCCCccc
Q 021215 195 SHPCVEGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH-HQYACPICSKSV 253 (316)
Q Consensus 195 ~H~CiE~~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~-~~~~CPiCrks~ 253 (316)
.|.|++ +++..|-.|.|.+-..++....|||.|.||..|+.++|.. ...+||-||+..
T Consensus 357 a~~~~~-e~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~Crklr 415 (518)
T KOG1941|consen 357 AHECVE-ETELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRKLR 415 (518)
T ss_pred HHHHHH-HHhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHHHH
Confidence 578887 6789999999987777777889999999999999998753 346799999433
No 52
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=95.96 E-value=0.006 Score=45.40 Aligned_cols=44 Identities=27% Similarity=0.619 Sum_probs=29.4
Q ss_pred CCCCCCcccccccccCcceeEEcCCCCcccHHhHHHHhcc-CCCCCCC
Q 021215 202 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH-HQYACPI 248 (316)
Q Consensus 202 ~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~-~~~~CPi 248 (316)
.....|||-+.. +. ++++...|||+|-++.|.+|++. ....||+
T Consensus 9 ~~~~~CPiT~~~-~~--~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv 53 (57)
T PF11789_consen 9 TISLKCPITLQP-FE--DPVKSKKCGHTFEKEAILQYIQRNGSKRCPV 53 (57)
T ss_dssp B--SB-TTTSSB--S--SEEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred EeccCCCCcCCh-hh--CCcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence 345789999985 44 37888899999999999999943 3567998
No 53
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.69 E-value=0.0058 Score=59.36 Aligned_cols=49 Identities=18% Similarity=0.444 Sum_probs=39.0
Q ss_pred CCCCCCcccccccccCcceeEEcCCCCcccHHhHHHHhccCCCCCCCCCcccc
Q 021215 202 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 254 (316)
Q Consensus 202 ~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiCrks~~ 254 (316)
.+..+|+||+... .-++.|+|+|.|+..||+--.+....+||+||.++.
T Consensus 5 ~~~~eC~IC~nt~----n~Pv~l~C~HkFCyiCiKGsy~ndk~~CavCR~pid 53 (324)
T KOG0824|consen 5 TKKKECLICYNTG----NCPVNLYCFHKFCYICIKGSYKNDKKTCAVCRFPID 53 (324)
T ss_pred ccCCcceeeeccC----CcCccccccchhhhhhhcchhhcCCCCCceecCCCC
Confidence 4577999999742 234789999999999999844445678999998886
No 54
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=95.51 E-value=0.0043 Score=62.42 Aligned_cols=53 Identities=30% Similarity=0.797 Sum_probs=43.7
Q ss_pred cccCCCCCCCCcccccccccCcceeEEcCCCCcccHHhHHHHhcc-CCCCCCCCCccc
Q 021215 197 PCVEGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH-HQYACPICSKSV 253 (316)
Q Consensus 197 ~CiE~~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~-~~~~CPiCrks~ 253 (316)
.|..+++-..|-||.| +.+++.+=||||.++..|+..|-.+ +...||.||-.+
T Consensus 362 YceMgsTFeLCKICae----ndKdvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEI 415 (563)
T KOG1785|consen 362 YCEMGSTFELCKICAE----NDKDVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEI 415 (563)
T ss_pred HHHccchHHHHHHhhc----cCCCcccccccchHHHHHHHhhcccCCCCCCCceeeEe
Confidence 4667788889999998 4567888899999999999999743 357899999554
No 55
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=95.42 E-value=0.0072 Score=66.14 Aligned_cols=53 Identities=21% Similarity=0.570 Sum_probs=37.6
Q ss_pred CCCCCCcccccccc--cCccee-EEcCCCCcccHHhHHHHhcc-CCCCCCCCCcccc
Q 021215 202 AMHHDCPVCCEYLF--ETRQDV-IVLPCGHTIHKNCLKEMREH-HQYACPICSKSVC 254 (316)
Q Consensus 202 ~~~~~CPIClE~lf--~s~~~v-~~LpCGH~fH~~Ci~~wl~~-~~~~CPiCrks~~ 254 (316)
+....||||..-|. ++.-|. +-..|.|-||..|+-+|+.+ .+.+||+||.++.
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 45789999986443 111111 22358899999999999875 4678999997764
No 56
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.33 E-value=0.013 Score=56.28 Aligned_cols=53 Identities=26% Similarity=0.676 Sum_probs=41.1
Q ss_pred CCCCCCcccccccccCcceeEEcCCCCcccHHhHHHHhc-cCCCCCCCCCccccchh
Q 021215 202 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMRE-HHQYACPICSKSVCDMS 257 (316)
Q Consensus 202 ~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~-~~~~~CPiCrks~~d~~ 257 (316)
+.+-.||+|.|+ +.-|.+..+|||.|+--|+..-+. ...++||.|+.+...+.
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 446789999995 345677788999999999998432 23589999998877553
No 57
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=95.12 E-value=0.017 Score=43.58 Aligned_cols=46 Identities=33% Similarity=0.853 Sum_probs=34.2
Q ss_pred CceeecCCCCccccc-----ccCCCCCCCc-cceEecCccccccCCCCCCeeecCCCCc
Q 021215 117 VNQVICSLCGTEQKV-----QQVCVNCGVC-MGEYFCESCKLFDDDTSKKQYHCDGCGI 169 (316)
Q Consensus 117 v~~V~C~~C~~eq~v-----~~~C~~Cg~~-f~~YfC~~Ckl~ddd~~k~~yHC~~Cgi 169 (316)
.....|..|+.+... .-.|||||.. ..| |.+|+-+. ..|.|++||+
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 345678899877652 3579999986 544 99998774 4799999985
No 58
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=94.55 E-value=0.012 Score=63.29 Aligned_cols=50 Identities=14% Similarity=0.376 Sum_probs=39.6
Q ss_pred CCCCcccccccccCcceeEEcCCCCcccHHhHHHHhccCCCCCCCCCccccc
Q 021215 204 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 255 (316)
Q Consensus 204 ~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiCrks~~d 255 (316)
+..||+|+.. +.........+|+|.||.+||..|-.. ..+||+||+.+..
T Consensus 123 ~~~CP~Ci~s-~~DqL~~~~k~c~H~FC~~Ci~sWsR~-aqTCPiDR~EF~~ 172 (1134)
T KOG0825|consen 123 ENQCPNCLKS-CNDQLEESEKHTAHYFCEECVGSWSRC-AQTCPVDRGEFGE 172 (1134)
T ss_pred hhhhhHHHHH-HHHHhhccccccccccHHHHhhhhhhh-cccCchhhhhhhe
Confidence 5689999974 444444456799999999999999874 5799999988763
No 59
>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=94.38 E-value=0.021 Score=45.53 Aligned_cols=33 Identities=36% Similarity=0.850 Sum_probs=27.6
Q ss_pred CCCCCCcccccccccCcceeEEcCCCCcccHHhHH
Q 021215 202 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLK 236 (316)
Q Consensus 202 ~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~ 236 (316)
.....|+||...|.. ...++.||||.+|..|++
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 446789999998766 367889999999999974
No 60
>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=94.26 E-value=0.037 Score=53.59 Aligned_cols=49 Identities=20% Similarity=0.522 Sum_probs=39.4
Q ss_pred CCcccccccccCcceeEE-cCCCCcccHHhHHHHhccCCCCCCCCCcccc
Q 021215 206 DCPVCCEYLFETRQDVIV-LPCGHTIHKNCLKEMREHHQYACPICSKSVC 254 (316)
Q Consensus 206 ~CPIClE~lf~s~~~v~~-LpCGH~fH~~Ci~~wl~~~~~~CPiCrks~~ 254 (316)
.||+|.-+.+.++.-... =+|||.++.+|++..+..+.+.||.|.+.+.
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 599998777766543322 2999999999999998888899999997765
No 61
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=94.25 E-value=0.028 Score=40.13 Aligned_cols=41 Identities=29% Similarity=0.752 Sum_probs=26.4
Q ss_pred CcccccccccCcceeEEcCCC-----CcccHHhHHHHhcc-CCCCCCCC
Q 021215 207 CPVCCEYLFETRQDVIVLPCG-----HTIHKNCLKEMREH-HQYACPIC 249 (316)
Q Consensus 207 CPIClE~lf~s~~~v~~LpCG-----H~fH~~Ci~~wl~~-~~~~CPiC 249 (316)
|-||++...++ +..+.||+ -..|.+||.+|+.. .+.+|++|
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 35677884 47899999999874 45779987
No 62
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.24 E-value=0.026 Score=51.59 Aligned_cols=50 Identities=24% Similarity=0.638 Sum_probs=32.8
Q ss_pred CCCcccccccccCccee---EEcCCCCcccHHhHHHHhcc-----CC-----CCCCCCCcccc
Q 021215 205 HDCPVCCEYLFETRQDV---IVLPCGHTIHKNCLKEMREH-----HQ-----YACPICSKSVC 254 (316)
Q Consensus 205 ~~CPIClE~lf~s~~~v---~~LpCGH~fH~~Ci~~wl~~-----~~-----~~CPiCrks~~ 254 (316)
..|-||..|..+.+.+- --..||-.||+-|+.+||.. .+ ..||.|++++.
T Consensus 166 ~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~Pia 228 (234)
T KOG3268|consen 166 GACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIA 228 (234)
T ss_pred hcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcce
Confidence 45555554433322111 24589999999999999863 11 24999999885
No 63
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.18 E-value=0.054 Score=54.75 Aligned_cols=50 Identities=24% Similarity=0.733 Sum_probs=37.9
Q ss_pred CCCCcccccccccCcc-eeEEcCCCCcccHHhHHHHhcc-CCCCCCCCCccc
Q 021215 204 HHDCPVCCEYLFETRQ-DVIVLPCGHTIHKNCLKEMREH-HQYACPICSKSV 253 (316)
Q Consensus 204 ~~~CPIClE~lf~s~~-~v~~LpCGH~fH~~Ci~~wl~~-~~~~CPiCrks~ 253 (316)
...||||++..-.+++ ..+.|.|||.|=..||+.||-. ...+||.|....
T Consensus 4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~ka 55 (463)
T KOG1645|consen 4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKA 55 (463)
T ss_pred cccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChh
Confidence 3579999987655543 4567899999999999999942 235699998443
No 64
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=93.96 E-value=0.048 Score=62.21 Aligned_cols=74 Identities=27% Similarity=0.577 Sum_probs=54.1
Q ss_pred cCCcceeeccCCcceeeccccccccccCCCCCCCCcccccccccCcceeEEcCCCCcccHHhHHHHhcc---------CC
Q 021215 173 GGCDNFFHCNKCRCCYSMLLKNSHPCVEGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH---------HQ 243 (316)
Q Consensus 173 G~~~~ffHC~~C~~C~s~~l~~~H~CiE~~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~---------~~ 243 (316)
||.+|-.||--|-.|-.-.. ..-.++.|.||+-+ -.+..+.+.|.|||.||.+|....|.. +-
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 56678888888877754322 22347889999864 445668899999999999999875542 11
Q ss_pred CCCCCCCcccc
Q 021215 244 YACPICSKSVC 254 (316)
Q Consensus 244 ~~CPiCrks~~ 254 (316)
.+||+|...+.
T Consensus 3534 isCPiC~n~In 3544 (3738)
T KOG1428|consen 3534 ISCPICKNKIN 3544 (3738)
T ss_pred eecccccchhh
Confidence 46999997775
No 65
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.92 E-value=0.054 Score=51.34 Aligned_cols=49 Identities=31% Similarity=0.756 Sum_probs=38.6
Q ss_pred CCCcccccccccCc---ceeEEcCCCCcccHHhHHHHhccCCCCCCCCCcccc
Q 021215 205 HDCPVCCEYLFETR---QDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 254 (316)
Q Consensus 205 ~~CPIClE~lf~s~---~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiCrks~~ 254 (316)
..|-||-++ |.+. .-+..|.|||+|+..|+...+......||.||.+..
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 467888876 4443 335788999999999999998876677999999854
No 66
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=93.73 E-value=0.028 Score=41.92 Aligned_cols=33 Identities=39% Similarity=0.785 Sum_probs=26.3
Q ss_pred eeEEcCCCCcccHHhHHHHhccCCCCCCCCCccccc
Q 021215 220 DVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 255 (316)
Q Consensus 220 ~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiCrks~~d 255 (316)
.-+++||||.+...|+.-+.- .-||+|.+++..
T Consensus 19 ~~~~~pCgH~I~~~~f~~~rY---ngCPfC~~~~~~ 51 (55)
T PF14447_consen 19 KGTVLPCGHLICDNCFPGERY---NGCPFCGTPFEF 51 (55)
T ss_pred ccccccccceeeccccChhhc---cCCCCCCCcccC
Confidence 456899999999999877632 349999998864
No 67
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.61 E-value=0.067 Score=54.02 Aligned_cols=49 Identities=29% Similarity=0.823 Sum_probs=39.0
Q ss_pred CCCCCCcccccccccCcceeEEcCCCCcccHHhHHHHhccCCCCCCCCCccccc
Q 021215 202 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 255 (316)
Q Consensus 202 ~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiCrks~~d 255 (316)
..+..|.||+.-++ +++++||||+|+..||..-+. ...-||+||-.+..
T Consensus 82 ~sef~c~vc~~~l~----~pv~tpcghs~c~~Cl~r~ld-~~~~cp~Cr~~l~e 130 (398)
T KOG4159|consen 82 RSEFECCVCSRALY----PPVVTPCGHSFCLECLDRSLD-QETECPLCRDELVE 130 (398)
T ss_pred cchhhhhhhHhhcC----CCccccccccccHHHHHHHhc-cCCCCccccccccc
Confidence 44778999998443 356779999999999999766 35779999988874
No 68
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=93.32 E-value=0.027 Score=55.85 Aligned_cols=57 Identities=26% Similarity=0.604 Sum_probs=44.6
Q ss_pred CCCCcccccccccCcceeEEcCCCCcccHHhHHHHhccCCCCCCCCCccccchhHHH
Q 021215 204 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCDMSKVW 260 (316)
Q Consensus 204 ~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiCrks~~d~~~~~ 260 (316)
++-||.|+|+|.-+.+....-|||-.+++-|+....+.-+.+||-||+...+.+..|
T Consensus 14 ed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~denv~~ 70 (480)
T COG5175 14 EDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDENVRY 70 (480)
T ss_pred cccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhccccceeE
Confidence 455999999987776666666899999999988876544678999999887654444
No 69
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=93.16 E-value=0.054 Score=54.26 Aligned_cols=50 Identities=28% Similarity=0.686 Sum_probs=39.6
Q ss_pred CCCCCCcccccccccCcceeEEcCCCCcccHHhHHHHhccCCCCCCCCCccccc
Q 021215 202 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 255 (316)
Q Consensus 202 ~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiCrks~~d 255 (316)
..+..||+|..-+-+ ++....|||.|+..|+.+|+.. +..||.|+..+..
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 335789999975333 4444799999999999999985 7899999877764
No 70
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.05 E-value=0.059 Score=53.46 Aligned_cols=47 Identities=26% Similarity=0.639 Sum_probs=35.4
Q ss_pred CCCCCCCCcccccccccCcceeEEcCCCCcccHHhHHHHhccCCCCCCCCCcccc
Q 021215 200 EGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 254 (316)
Q Consensus 200 E~~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiCrks~~ 254 (316)
|.+...+|.||++. ....+.+||||.-+ |...... ..+||+||..+.
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 44678999999984 34588999999976 6655543 356999998765
No 71
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=93.05 E-value=0.043 Score=51.68 Aligned_cols=37 Identities=30% Similarity=0.737 Sum_probs=27.6
Q ss_pred ccCcceeEEcCCCCcccHHhHHHHhccCCCCCCCCCcccc
Q 021215 215 FETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 254 (316)
Q Consensus 215 f~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiCrks~~ 254 (316)
+.+..+.-++.|+|.|+..|...-.. ..||+|++++-
T Consensus 12 ~~~~~~f~LTaC~HvfC~~C~k~~~~---~~C~lCkk~ir 48 (233)
T KOG4739|consen 12 FPSQDPFFLTACRHVFCEPCLKASSP---DVCPLCKKSIR 48 (233)
T ss_pred cCCCCceeeeechhhhhhhhcccCCc---cccccccceee
Confidence 44444556779999999999965432 38999999864
No 72
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.98 E-value=0.11 Score=52.64 Aligned_cols=53 Identities=26% Similarity=0.429 Sum_probs=39.5
Q ss_pred ccccCCCCCCCCcccccccccCcceeEEcCCCCcccHHhHHHHhcc-------CCCCCCCCC
Q 021215 196 HPCVEGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH-------HQYACPICS 250 (316)
Q Consensus 196 H~CiE~~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~-------~~~~CPiCr 250 (316)
+.+.-+ .-..|-||++. +........|||+|+|++.|+..|... ...+||-+.
T Consensus 177 ~~~F~~-slf~C~ICf~e-~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~ 236 (445)
T KOG1814|consen 177 LEKFVN-SLFDCCICFEE-QMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPK 236 (445)
T ss_pred HHHHHh-hcccceeeehh-hcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCC
Confidence 444433 35789999984 665567889999999999999998642 246798665
No 73
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=92.31 E-value=0.043 Score=53.58 Aligned_cols=52 Identities=23% Similarity=0.554 Sum_probs=40.3
Q ss_pred CCCCCcccccccccCcceeEEcCCCCcccHHhHHHHhcc----------------------CCCCCCCCCccccc
Q 021215 203 MHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH----------------------HQYACPICSKSVCD 255 (316)
Q Consensus 203 ~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~----------------------~~~~CPiCrks~~d 255 (316)
-...|.|||= =|.+.....+.+|-|+||..||..||.. ..-.||+||..+.+
T Consensus 114 p~gqCvICLy-gfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~ 187 (368)
T KOG4445|consen 114 PNGQCVICLY-GFASSPAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKI 187 (368)
T ss_pred CCCceEEEEE-eecCCCceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccc
Confidence 3678999994 4666667888999999999999887752 12349999977764
No 74
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.14 E-value=0.11 Score=52.33 Aligned_cols=47 Identities=30% Similarity=0.671 Sum_probs=39.8
Q ss_pred CCCcccccccccCcceeEEcCCCCcccHHhHHHHhccCC--CCCCCCCcc
Q 021215 205 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQ--YACPICSKS 252 (316)
Q Consensus 205 ~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~--~~CPiCrks 252 (316)
..|||=.|. -+...|++.|.|||.+-++-++.+.+.+. +.||.|-..
T Consensus 335 F~CPVlKeq-tsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~e 383 (394)
T KOG2817|consen 335 FICPVLKEQ-TSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPVE 383 (394)
T ss_pred eecccchhh-ccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCcc
Confidence 479999884 55567899999999999999999988766 889999753
No 75
>PF12773 DZR: Double zinc ribbon
Probab=92.02 E-value=0.15 Score=35.97 Aligned_cols=22 Identities=32% Similarity=0.845 Sum_probs=15.2
Q ss_pred cCCCCccccc-ccCCCCCCCccc
Q 021215 122 CSLCGTEQKV-QQVCVNCGVCMG 143 (316)
Q Consensus 122 C~~C~~eq~v-~~~C~~Cg~~f~ 143 (316)
|..|+++.+. +..|++||..+.
T Consensus 1 Cp~Cg~~~~~~~~fC~~CG~~l~ 23 (50)
T PF12773_consen 1 CPHCGTPNPDDAKFCPHCGTPLP 23 (50)
T ss_pred CCCcCCcCCccccCChhhcCChh
Confidence 5567777654 567888877776
No 76
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.88 E-value=0.22 Score=47.14 Aligned_cols=51 Identities=31% Similarity=0.669 Sum_probs=40.1
Q ss_pred CCCCCcccccccccCcceeEEcCCCCcccHHhHHHHhcc-------CCCCCCCCCccccc
Q 021215 203 MHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH-------HQYACPICSKSVCD 255 (316)
Q Consensus 203 ~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~-------~~~~CPiCrks~~d 255 (316)
...+|..|.-.|-. + +.+-|.|=|.||..|+++|... ..|+||-|...+..
T Consensus 49 Y~pNC~LC~t~La~-g-dt~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFP 106 (299)
T KOG3970|consen 49 YNPNCRLCNTPLAS-G-DTTRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFP 106 (299)
T ss_pred CCCCCceeCCcccc-C-cceeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCC
Confidence 46789999876543 3 4677889999999999999642 24899999988863
No 77
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.66 E-value=0.032 Score=54.31 Aligned_cols=55 Identities=27% Similarity=0.667 Sum_probs=37.9
Q ss_pred cccccccCCCC---CCCCcccccccccCcceeEEcCCCCc-ccHHhHHHHhccCCCCCCCCCccccch
Q 021215 193 KNSHPCVEGAM---HHDCPVCCEYLFETRQDVIVLPCGHT-IHKNCLKEMREHHQYACPICSKSVCDM 256 (316)
Q Consensus 193 ~~~H~CiE~~~---~~~CPIClE~lf~s~~~v~~LpCGH~-fH~~Ci~~wl~~~~~~CPiCrks~~d~ 256 (316)
++.|.+-.... +..|.||++ .+.+-++|+|||. -+.+|-+.+ ..|||||+-+...
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 44555544333 788999998 4567899999997 355565443 2599999866543
No 78
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=91.47 E-value=0.11 Score=48.34 Aligned_cols=59 Identities=20% Similarity=0.453 Sum_probs=43.0
Q ss_pred CCCCcccccccccCcceeEEcCCCCcccHHhHHHHhccCCCCCCCCCccccchhHHHHHhHHHH
Q 021215 204 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCDMSKVWEKYDREI 267 (316)
Q Consensus 204 ~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiCrks~~d~~~~~~~lD~~i 267 (316)
...|.||.++ |. .+++..|||.|+..|+-.-.+ ....|-+|.+...-.-.+.+.++..+
T Consensus 196 PF~C~iCKkd-y~---spvvt~CGH~FC~~Cai~~y~-kg~~C~~Cgk~t~G~f~V~~d~~kmL 254 (259)
T COG5152 196 PFLCGICKKD-YE---SPVVTECGHSFCSLCAIRKYQ-KGDECGVCGKATYGRFWVVSDLQKML 254 (259)
T ss_pred ceeehhchhh-cc---chhhhhcchhHHHHHHHHHhc-cCCcceecchhhccceeHHhhHHHHH
Confidence 4589999986 55 356788999999999877544 24789999988765433445555554
No 79
>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=91.31 E-value=0.096 Score=45.58 Aligned_cols=35 Identities=20% Similarity=0.514 Sum_probs=29.9
Q ss_pred CCCCcccccccccCcceeEEcCCC------CcccHHhHHHHh
Q 021215 204 HHDCPVCCEYLFETRQDVIVLPCG------HTIHKNCLKEMR 239 (316)
Q Consensus 204 ~~~CPIClE~lf~s~~~v~~LpCG------H~fH~~Ci~~wl 239 (316)
...|.||++.+-. .+.++.+++| |.||.+|+..|-
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 4689999998776 5678899997 789999999994
No 80
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=90.75 E-value=0.28 Score=47.78 Aligned_cols=60 Identities=25% Similarity=0.615 Sum_probs=44.2
Q ss_pred CCCCcccccccccCcceeEEcCC--CCcccHHhHHHHhccCCCCCCCCCccccchhHHHHHhHHHHHcCCCCh
Q 021215 204 HHDCPVCCEYLFETRQDVIVLPC--GHTIHKNCLKEMREHHQYACPICSKSVCDMSKVWEKYDREIAATPMPE 274 (316)
Q Consensus 204 ~~~CPIClE~lf~s~~~v~~LpC--GH~fH~~Ci~~wl~~~~~~CPiCrks~~d~~~~~~~lD~~i~~~pmP~ 274 (316)
-.+||||.++|.. + .+.| ||..+..|-.+. ...||.||.++++.. -+.++..+++...|=
T Consensus 48 lleCPvC~~~l~~---P--i~QC~nGHlaCssC~~~~----~~~CP~Cr~~~g~~R--~~amEkV~e~~~vpC 109 (299)
T KOG3002|consen 48 LLDCPVCFNPLSP---P--IFQCDNGHLACSSCRTKV----SNKCPTCRLPIGNIR--CRAMEKVAEAVLVPC 109 (299)
T ss_pred hccCchhhccCcc---c--ceecCCCcEehhhhhhhh----cccCCccccccccHH--HHHHHHHHHhceecc
Confidence 4689999997543 2 5567 899999998765 357999999999653 245666677666553
No 81
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.75 E-value=0.17 Score=49.34 Aligned_cols=64 Identities=20% Similarity=0.423 Sum_probs=45.2
Q ss_pred CCCCCCcccccccccCcceeEEcCCCCcccHHhHHHHhccCCCCCCCCCccccchhHHHHHhHHHHHcC
Q 021215 202 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCDMSKVWEKYDREIAAT 270 (316)
Q Consensus 202 ~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiCrks~~d~~~~~~~lD~~i~~~ 270 (316)
.....|-||.++ |. .+++..|||+|+..|...-++. ...|++|.+.+-.....-..|...+...
T Consensus 239 ~~Pf~c~icr~~-f~---~pVvt~c~h~fc~~ca~~~~qk-~~~c~vC~~~t~g~~~~akeL~~~L~~k 302 (313)
T KOG1813|consen 239 LLPFKCFICRKY-FY---RPVVTKCGHYFCEVCALKPYQK-GEKCYVCSQQTHGSFNVAKELLVSLKLK 302 (313)
T ss_pred cCCccccccccc-cc---cchhhcCCceeehhhhcccccc-CCcceecccccccccchHHHHHHHHHhh
Confidence 446679999997 44 3678899999999999886663 4789999998864322223444444433
No 82
>PF04641 Rtf2: Rtf2 RING-finger
Probab=90.50 E-value=0.26 Score=46.55 Aligned_cols=50 Identities=26% Similarity=0.650 Sum_probs=38.8
Q ss_pred CCCCCCcccccccccCcceeEE-cCCCCcccHHhHHHHhccCCCCCCCCCcccc
Q 021215 202 AMHHDCPVCCEYLFETRQDVIV-LPCGHTIHKNCLKEMREHHQYACPICSKSVC 254 (316)
Q Consensus 202 ~~~~~CPIClE~lf~s~~~v~~-LpCGH~fH~~Ci~~wl~~~~~~CPiCrks~~ 254 (316)
.....|||-...| ++....+. .||||+|-..+|.+.- ....||+|.+++.
T Consensus 111 ~~~~~CPvt~~~~-~~~~~fv~l~~cG~V~s~~alke~k--~~~~Cp~c~~~f~ 161 (260)
T PF04641_consen 111 EGRFICPVTGKEF-NGKHKFVYLRPCGCVFSEKALKELK--KSKKCPVCGKPFT 161 (260)
T ss_pred CceeECCCCCccc-CCceeEEEEcCCCCEeeHHHHHhhc--ccccccccCCccc
Confidence 4567899999865 44445554 5999999999999984 2467999998876
No 83
>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=90.34 E-value=0.2 Score=42.10 Aligned_cols=35 Identities=23% Similarity=0.601 Sum_probs=28.2
Q ss_pred cceEEcCCCCCCccccceeeeecCCCCCCccccccCC
Q 021215 280 KVWILCNDCGKTSNVQFHVLAQKCPNCKSYNTRLTRG 316 (316)
Q Consensus 280 ~~~IlCnDC~~~s~v~~H~lg~kC~~C~SyNT~~~~~ 316 (316)
.+...|++|+.......+ ...||.|+|+++++++|
T Consensus 68 p~~~~C~~Cg~~~~~~~~--~~~CP~Cgs~~~~i~~G 102 (115)
T TIGR00100 68 PVECECEDCSEEVSPEID--LYRCPKCHGIMLQVRAG 102 (115)
T ss_pred CcEEEcccCCCEEecCCc--CccCcCCcCCCcEEecC
Confidence 577899999987766532 35799999999998876
No 84
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=90.09 E-value=0.19 Score=38.17 Aligned_cols=45 Identities=33% Similarity=0.896 Sum_probs=34.2
Q ss_pred eeecCCCCccccc-----ccCCCCCCCccceEecCccccccCCCCCCeeecCCCCc
Q 021215 119 QVICSLCGTEQKV-----QQVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGI 169 (316)
Q Consensus 119 ~V~C~~C~~eq~v-----~~~C~~Cg~~f~~YfC~~Ckl~ddd~~k~~yHC~~Cgi 169 (316)
...|..|+.+..+ .-.|||||..+ =|-|.+|+.+.+ +|.|++||+
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 5689999988843 35799999443 366889987744 799999985
No 85
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=89.52 E-value=0.14 Score=53.46 Aligned_cols=53 Identities=26% Similarity=0.597 Sum_probs=42.9
Q ss_pred ccCCCCCCCCcccccccccCcceeEEcCCCCcccHHhHHHHhcc----CCCCCCCCCcccc
Q 021215 198 CVEGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH----HQYACPICSKSVC 254 (316)
Q Consensus 198 CiE~~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~----~~~~CPiCrks~~ 254 (316)
=.|+..+..|-+|-+. .++++.-.|.|.|++.|+.+|+.. .+.+||+|...+.
T Consensus 530 ~~enk~~~~C~lc~d~----aed~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~Ls 586 (791)
T KOG1002|consen 530 PDENKGEVECGLCHDP----AEDYIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLS 586 (791)
T ss_pred CccccCceeecccCCh----hhhhHhhhhhHHHHHHHHHHHHHhhhcccCCCCcccccccc
Confidence 3477788899999984 346778899999999999998753 3578999997764
No 86
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=89.18 E-value=0.27 Score=41.42 Aligned_cols=35 Identities=31% Similarity=0.630 Sum_probs=28.2
Q ss_pred cceEEcCCCCCCcccc-ceeeeecCCCCCCccccccCC
Q 021215 280 KVWILCNDCGKTSNVQ-FHVLAQKCPNCKSYNTRLTRG 316 (316)
Q Consensus 280 ~~~IlCnDC~~~s~v~-~H~lg~kC~~C~SyNT~~~~~ 316 (316)
.+...|++|+...... +++ .+||.|+|++...++|
T Consensus 69 p~~~~C~~Cg~~~~~~~~~~--~~CP~Cgs~~~~i~~G 104 (117)
T PRK00564 69 KVELECKDCSHVFKPNALDY--GVCEKCHSKNVIITQG 104 (117)
T ss_pred CCEEEhhhCCCccccCCccC--CcCcCCCCCceEEecC
Confidence 5788999999877665 333 3799999999998876
No 87
>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=89.16 E-value=0.19 Score=39.26 Aligned_cols=36 Identities=28% Similarity=0.813 Sum_probs=22.8
Q ss_pred ceeecCCCCcccccccCCCCCCCcc--------ceEecCccccc
Q 021215 118 NQVICSLCGTEQKVQQVCVNCGVCM--------GEYFCESCKLF 153 (316)
Q Consensus 118 ~~V~C~~C~~eq~v~~~C~~Cg~~f--------~~YfC~~Ckl~ 153 (316)
....|..|+..-.....||.||..+ +.|||..|+=.
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 4778888888777777888888877 58999888743
No 88
>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=88.86 E-value=0.092 Score=40.98 Aligned_cols=65 Identities=26% Similarity=0.546 Sum_probs=38.8
Q ss_pred CCCcccccccccCcceeEEcCCCCcccHHhHHHHhccCCCCCCCCCccccchhHHHHHhHHHHHcCCCChhhhcCcceEE
Q 021215 205 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCDMSKVWEKYDREIAATPMPEAYLNKKVWIL 284 (316)
Q Consensus 205 ~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiCrks~~d~~~~~~~lD~~i~~~pmP~ey~~~~~~Il 284 (316)
..||.|...|-... ||..+..|-..+... ..||-|..++..+.+ =..++.+
T Consensus 2 ~~CP~C~~~L~~~~--------~~~~C~~C~~~~~~~--a~CPdC~~~Le~LkA-------------------CGAvdYF 52 (70)
T PF07191_consen 2 NTCPKCQQELEWQG--------GHYHCEACQKDYKKE--AFCPDCGQPLEVLKA-------------------CGAVDYF 52 (70)
T ss_dssp -B-SSS-SBEEEET--------TEEEETTT--EEEEE--EE-TTT-SB-EEEEE-------------------TTEEEEE
T ss_pred CcCCCCCCccEEeC--------CEEECccccccceec--ccCCCcccHHHHHHH-------------------hccccee
Confidence 47999998653321 889999999887653 679999988875421 2347899
Q ss_pred cCCCCC---Ccccccee
Q 021215 285 CNDCGK---TSNVQFHV 298 (316)
Q Consensus 285 CnDC~~---~s~v~~H~ 298 (316)
||.|.+ ++.|.|.+
T Consensus 53 C~~c~gLiSKkrV~f~~ 69 (70)
T PF07191_consen 53 CNHCHGLISKKRVRFEF 69 (70)
T ss_dssp -TTTT-EE-TTTSEEEE
T ss_pred eccCCceeecceEEEEe
Confidence 999985 56666653
No 89
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=88.51 E-value=0.33 Score=41.85 Aligned_cols=37 Identities=27% Similarity=0.734 Sum_probs=27.5
Q ss_pred cceEEcCCCCCCcccc-------------cee------eeecCCCCCCccccccCC
Q 021215 280 KVWILCNDCGKTSNVQ-------------FHV------LAQKCPNCKSYNTRLTRG 316 (316)
Q Consensus 280 ~~~IlCnDC~~~s~v~-------------~H~------lg~kC~~C~SyNT~~~~~ 316 (316)
.....|.+|+...... +|+ ...+||.|||++.++++|
T Consensus 68 p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~G 123 (135)
T PRK03824 68 EAVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRDFEIVKG 123 (135)
T ss_pred ceEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCCcEEecC
Confidence 4678999999766443 222 336899999999988776
No 90
>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=88.28 E-value=0.47 Score=42.51 Aligned_cols=33 Identities=33% Similarity=0.893 Sum_probs=23.5
Q ss_pred CCCCcccccccccCcceeEEcCCC-C------------cccHHhHHHHhc
Q 021215 204 HHDCPVCCEYLFETRQDVIVLPCG-H------------TIHKNCLKEMRE 240 (316)
Q Consensus 204 ~~~CPIClE~lf~s~~~v~~LpCG-H------------~fH~~Ci~~wl~ 240 (316)
+..||||||. +-..++|-|. | .-|..||+++-+
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 4679999995 2346677773 3 268999999864
No 91
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=87.99 E-value=0.13 Score=50.58 Aligned_cols=49 Identities=29% Similarity=0.667 Sum_probs=39.2
Q ss_pred CCCCCCcccccccccCcceeEEcCCCCcccHHhHHHHhccCCCCCCCCCcccc
Q 021215 202 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 254 (316)
Q Consensus 202 ~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiCrks~~ 254 (316)
..+..|++|..||-+ +..+.-|=|+|++.||.++|.. ...||.|.-.+.
T Consensus 13 n~~itC~LC~GYliD---ATTI~eCLHTFCkSCivk~l~~-~~~CP~C~i~ih 61 (331)
T KOG2660|consen 13 NPHITCRLCGGYLID---ATTITECLHTFCKSCIVKYLEE-SKYCPTCDIVIH 61 (331)
T ss_pred ccceehhhccceeec---chhHHHHHHHHHHHHHHHHHHH-hccCCccceecc
Confidence 345689999998665 3345679999999999999985 688999996654
No 92
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=87.79 E-value=0.37 Score=40.39 Aligned_cols=35 Identities=26% Similarity=0.685 Sum_probs=27.3
Q ss_pred cceEEcCCCCCCccccceeeeecCCCCCCccccccCC
Q 021215 280 KVWILCNDCGKTSNVQFHVLAQKCPNCKSYNTRLTRG 316 (316)
Q Consensus 280 ~~~IlCnDC~~~s~v~~H~lg~kC~~C~SyNT~~~~~ 316 (316)
.....|++|+........ ...||.|+|++...++|
T Consensus 68 p~~~~C~~Cg~~~~~~~~--~~~CP~Cgs~~~~i~~G 102 (113)
T PRK12380 68 PAQAWCWDCSQVVEIHQH--DAQCPHCHGERLRVDTG 102 (113)
T ss_pred CcEEEcccCCCEEecCCc--CccCcCCCCCCcEEccC
Confidence 567899999987766422 23599999999998876
No 93
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=87.62 E-value=0.4 Score=52.44 Aligned_cols=42 Identities=29% Similarity=0.719 Sum_probs=31.3
Q ss_pred CCcccccccccCcceeEEcCCCCcccHHhHHHHhccCCCCCCCCCcccc
Q 021215 206 DCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 254 (316)
Q Consensus 206 ~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiCrks~~ 254 (316)
.|..|--.|-- |.+...|||.||++|+. .....||-|+-...
T Consensus 842 kCs~C~~~Ldl---P~VhF~CgHsyHqhC~e----~~~~~CP~C~~e~~ 883 (933)
T KOG2114|consen 842 KCSACEGTLDL---PFVHFLCGHSYHQHCLE----DKEDKCPKCLPELR 883 (933)
T ss_pred eecccCCcccc---ceeeeecccHHHHHhhc----cCcccCCccchhhh
Confidence 67777644333 67888999999999998 23477999997443
No 94
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=87.29 E-value=0.28 Score=30.79 Aligned_cols=24 Identities=33% Similarity=0.908 Sum_probs=18.4
Q ss_pred eeecCCCCccccc-ccCCCCCCCcc
Q 021215 119 QVICSLCGTEQKV-QQVCVNCGVCM 142 (316)
Q Consensus 119 ~V~C~~C~~eq~v-~~~C~~Cg~~f 142 (316)
++.|..|+++.+. +..|++||+.+
T Consensus 2 ~~~Cp~Cg~~~~~~~~fC~~CG~~L 26 (26)
T PF13248_consen 2 EMFCPNCGAEIDPDAKFCPNCGAKL 26 (26)
T ss_pred cCCCcccCCcCCcccccChhhCCCC
Confidence 4678899987554 67899999864
No 95
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=87.16 E-value=0.43 Score=40.01 Aligned_cols=36 Identities=17% Similarity=0.480 Sum_probs=27.7
Q ss_pred cceEEcCCCCCCccccceeeeecCCCCCCccccccCC
Q 021215 280 KVWILCNDCGKTSNVQFHVLAQKCPNCKSYNTRLTRG 316 (316)
Q Consensus 280 ~~~IlCnDC~~~s~v~~H~lg~kC~~C~SyNT~~~~~ 316 (316)
.+...|++|+.......+. ...||.|||+++..++|
T Consensus 68 p~~~~C~~Cg~~~~~~~~~-~~~CP~Cgs~~~~i~~G 103 (114)
T PRK03681 68 EAECWCETCQQYVTLLTQR-VRRCPQCHGDMLRIVAD 103 (114)
T ss_pred CcEEEcccCCCeeecCCcc-CCcCcCcCCCCcEEccC
Confidence 5678999999876654332 14699999999998876
No 96
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=86.75 E-value=0.68 Score=44.40 Aligned_cols=54 Identities=26% Similarity=0.504 Sum_probs=43.2
Q ss_pred CCCCCCcccccccccCcceeEEc-CCCCcccHHhHHHHhccCCCCCCCCCccccchh
Q 021215 202 AMHHDCPVCCEYLFETRQDVIVL-PCGHTIHKNCLKEMREHHQYACPICSKSVCDMS 257 (316)
Q Consensus 202 ~~~~~CPIClE~lf~s~~~v~~L-pCGH~fH~~Ci~~wl~~~~~~CPiCrks~~d~~ 257 (316)
+....|||+.+.|. ...+.++| ||||.+..+|...++.. ...+|++.+++.+.+
T Consensus 219 s~ryiCpvtrd~Lt-Nt~~ca~Lr~sg~Vv~~ecvEklir~-D~v~pv~d~plkdrd 273 (303)
T KOG3039|consen 219 SKRYICPVTRDTLT-NTTPCAVLRPSGHVVTKECVEKLIRK-DMVDPVTDKPLKDRD 273 (303)
T ss_pred ccceecccchhhhc-CccceEEeccCCcEeeHHHHHHhccc-cccccCCCCcCcccc
Confidence 34678999998654 44555665 99999999999999874 588999999988653
No 97
>PHA02862 5L protein; Provisional
Probab=86.04 E-value=0.55 Score=41.64 Aligned_cols=46 Identities=17% Similarity=0.471 Sum_probs=33.4
Q ss_pred CCCCcccccccccCcceeEEcCCC-----CcccHHhHHHHhccC-CCCCCCCCcccc
Q 021215 204 HHDCPVCCEYLFETRQDVIVLPCG-----HTIHKNCLKEMREHH-QYACPICSKSVC 254 (316)
Q Consensus 204 ~~~CPIClE~lf~s~~~v~~LpCG-----H~fH~~Ci~~wl~~~-~~~CPiCrks~~ 254 (316)
...|=||.+. . .++ .-||. -..|++|+.+|++.. ...||+|+.++.
T Consensus 2 ~diCWIC~~~-~--~e~--~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~ 53 (156)
T PHA02862 2 SDICWICNDV-C--DER--NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYN 53 (156)
T ss_pred CCEEEEecCc-C--CCC--cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEE
Confidence 4678899874 1 122 35774 469999999999753 456999998775
No 98
>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=85.82 E-value=0.56 Score=32.93 Aligned_cols=42 Identities=29% Similarity=0.698 Sum_probs=20.2
Q ss_pred CcccccccccCcceeEEcCCCCcccHHhHHHHhccCC-CCCCCC
Q 021215 207 CPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQ-YACPIC 249 (316)
Q Consensus 207 CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~-~~CPiC 249 (316)
|.+|.+ +.+-+..-....|+=.+|..|+..|+++.+ .+||.|
T Consensus 1 C~~C~~-iv~~G~~C~~~~C~~r~H~~C~~~y~r~~~~~~CP~C 43 (43)
T PF08746_consen 1 CEACKE-IVTQGQRCSNRDCNVRLHDDCFKKYFRHRSNPKCPNC 43 (43)
T ss_dssp -TTT-S-B-SSSEE-SS--S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred Ccccch-hHeeeccCCCCccCchHHHHHHHHHHhcCCCCCCcCC
Confidence 556776 344322111224888899999999987533 369987
No 99
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=85.30 E-value=0.8 Score=41.07 Aligned_cols=47 Identities=28% Similarity=0.617 Sum_probs=33.5
Q ss_pred CCCCCcccccccccCcceeEEcCCC--C---cccHHhHHHHhccC-CCCCCCCCcccc
Q 021215 203 MHHDCPVCCEYLFETRQDVIVLPCG--H---TIHKNCLKEMREHH-QYACPICSKSVC 254 (316)
Q Consensus 203 ~~~~CPIClE~lf~s~~~v~~LpCG--H---~fH~~Ci~~wl~~~-~~~CPiCrks~~ 254 (316)
++..|=||.+.- + ...-||. . ..|++|++.|+..+ ..+||+|+..+.
T Consensus 7 ~~~~CRIC~~~~---~--~~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~ 59 (162)
T PHA02825 7 MDKCCWICKDEY---D--VVTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYN 59 (162)
T ss_pred CCCeeEecCCCC---C--CccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEE
Confidence 466899998751 1 1234774 3 56999999999753 467999997664
No 100
>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=84.91 E-value=0.43 Score=34.83 Aligned_cols=32 Identities=34% Similarity=0.760 Sum_probs=22.8
Q ss_pred EcCCC-CcccHHhHHHHhccCCCCCCCCCccccc
Q 021215 223 VLPCG-HTIHKNCLKEMREHHQYACPICSKSVCD 255 (316)
Q Consensus 223 ~LpCG-H~fH~~Ci~~wl~~~~~~CPiCrks~~d 255 (316)
.+.|. |.++..|+..+++. +..||+|.+++..
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 66785 99999999999985 6899999998764
No 101
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=84.66 E-value=0.9 Score=45.53 Aligned_cols=66 Identities=23% Similarity=0.450 Sum_probs=44.3
Q ss_pred cceeeccccccccccCCCCCCCCcccccccccCcceeEEcCCCCcccHHhHHHHhcc-CCCCCCCCCcccc
Q 021215 185 RCCYSMLLKNSHPCVEGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH-HQYACPICSKSVC 254 (316)
Q Consensus 185 ~~C~s~~l~~~H~CiE~~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~-~~~~CPiCrks~~ 254 (316)
+.|....|-++.+=..+.....|.||.+. ..-+.++||||.++-.|....... .+-.||+||..+.
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 44554444444433345567899999984 335678999999999998764221 2356999996654
No 102
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=84.56 E-value=0.31 Score=40.68 Aligned_cols=35 Identities=26% Similarity=0.552 Sum_probs=24.8
Q ss_pred cceEEcCCCCCCccccceeeeecCCCCCCccccccCC
Q 021215 280 KVWILCNDCGKTSNVQFHVLAQKCPNCKSYNTRLTRG 316 (316)
Q Consensus 280 ~~~IlCnDC~~~s~v~~H~lg~kC~~C~SyNT~~~~~ 316 (316)
.+...|++|+....+..+. ..||.|+|++.+.++|
T Consensus 68 p~~~~C~~Cg~~~~~~~~~--~~CP~Cgs~~~~i~~G 102 (113)
T PF01155_consen 68 PARARCRDCGHEFEPDEFD--FSCPRCGSPDVEIISG 102 (113)
T ss_dssp --EEEETTTS-EEECHHCC--HH-SSSSSS-EEEEES
T ss_pred CCcEECCCCCCEEecCCCC--CCCcCCcCCCcEEccC
Confidence 5678999999998776554 5799999999888765
No 103
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=83.73 E-value=0.58 Score=28.80 Aligned_cols=21 Identities=38% Similarity=0.956 Sum_probs=15.9
Q ss_pred cCCCCccccc-ccCCCCCCCcc
Q 021215 122 CSLCGTEQKV-QQVCVNCGVCM 142 (316)
Q Consensus 122 C~~C~~eq~v-~~~C~~Cg~~f 142 (316)
|..|+++.+. ++.|++||+.+
T Consensus 2 Cp~CG~~~~~~~~fC~~CG~~l 23 (23)
T PF13240_consen 2 CPNCGAEIEDDAKFCPNCGTPL 23 (23)
T ss_pred CcccCCCCCCcCcchhhhCCcC
Confidence 6778877764 67899998764
No 104
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=83.59 E-value=0.77 Score=29.18 Aligned_cols=23 Identities=30% Similarity=0.778 Sum_probs=18.8
Q ss_pred ecCCCCccccc-ccCCCCCCCccc
Q 021215 121 ICSLCGTEQKV-QQVCVNCGVCMG 143 (316)
Q Consensus 121 ~C~~C~~eq~v-~~~C~~Cg~~f~ 143 (316)
.|..|+.+-+. +..|++||..|.
T Consensus 2 ~CP~C~~~V~~~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCPHCGYDFE 25 (26)
T ss_pred cCCCCcCCchhhcCcCCCCCCCCc
Confidence 37788888775 688999999986
No 105
>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=83.48 E-value=0.39 Score=45.90 Aligned_cols=51 Identities=25% Similarity=0.623 Sum_probs=40.2
Q ss_pred CCCCCcccccccccCcceeEEc-C-CCCcccHHhHHHHhccCCCCCC--CCCccc
Q 021215 203 MHHDCPVCCEYLFETRQDVIVL-P-CGHTIHKNCLKEMREHHQYACP--ICSKSV 253 (316)
Q Consensus 203 ~~~~CPIClE~lf~s~~~v~~L-p-CGH~fH~~Ci~~wl~~~~~~CP--iCrks~ 253 (316)
.+..||||..+.+.+++-..++ | |=|.++.+|.+..++.+.-.|| -|.+.+
T Consensus 9 ~d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kIL 63 (314)
T COG5220 9 EDRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKIL 63 (314)
T ss_pred hcccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHH
Confidence 3568999998888876433333 6 9999999999999888878899 787544
No 106
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=83.43 E-value=0.73 Score=50.08 Aligned_cols=44 Identities=23% Similarity=0.536 Sum_probs=31.5
Q ss_pred CCCCCCcccccccccCcceeEEcCCCCcccHHhHHHHhccCCCCCCC
Q 021215 202 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPI 248 (316)
Q Consensus 202 ~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPi 248 (316)
.....|.||--.+ .+...+-+.|||.+|..|+.+|++.+ ..||.
T Consensus 1026 ~~~~~C~~C~l~V--~gss~~Cg~C~Hv~H~sc~~eWf~~g-d~Cps 1069 (1081)
T KOG0309|consen 1026 GFTFQCAICHLAV--RGSSNFCGTCGHVGHTSCMMEWFRTG-DVCPS 1069 (1081)
T ss_pred cceeeeeeEeeEe--eccchhhccccccccHHHHHHHHhcC-CcCCC
Confidence 3344588887433 33345667899999999999999853 57873
No 107
>PRK04023 DNA polymerase II large subunit; Validated
Probab=83.42 E-value=1 Score=50.38 Aligned_cols=46 Identities=28% Similarity=0.556 Sum_probs=25.0
Q ss_pred cCCCCCCCccceEecCccccccCCCCCCeeecCCCCcceecCCcceeeccCCcce
Q 021215 133 QVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGICRIGGCDNFFHCNKCRCC 187 (316)
Q Consensus 133 ~~C~~Cg~~f~~YfC~~Ckl~ddd~~k~~yHC~~CgiCR~G~~~~ffHC~~C~~C 187 (316)
..|+.||......+|+.|.-. .+.+|.|+.||.--.+ ..|.+||.=
T Consensus 627 RfCpsCG~~t~~frCP~CG~~----Te~i~fCP~CG~~~~~-----y~CPKCG~E 672 (1121)
T PRK04023 627 RKCPSCGKETFYRRCPFCGTH----TEPVYRCPRCGIEVEE-----DECEKCGRE 672 (1121)
T ss_pred ccCCCCCCcCCcccCCCCCCC----CCcceeCccccCcCCC-----CcCCCCCCC
Confidence 356666666555556666433 3456666666443322 346666653
No 108
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=82.93 E-value=0.79 Score=45.99 Aligned_cols=52 Identities=21% Similarity=0.545 Sum_probs=41.7
Q ss_pred cCCCCCCCCcccccccccCcceeEEcCCCCcccHHhHHHHhccCCCCCCCCCccccc
Q 021215 199 VEGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 255 (316)
Q Consensus 199 iE~~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiCrks~~d 255 (316)
...+.+..||||.-. +-..+.-||||.-+..||.+.+. ....|=.|+.++.+
T Consensus 417 lp~sEd~lCpICyA~----pi~Avf~PC~H~SC~~CI~qHlm-N~k~CFfCktTv~~ 468 (489)
T KOG4692|consen 417 LPDSEDNLCPICYAG----PINAVFAPCSHRSCYGCITQHLM-NCKRCFFCKTTVID 468 (489)
T ss_pred CCCcccccCcceecc----cchhhccCCCCchHHHHHHHHHh-cCCeeeEecceeee
Confidence 344678899999862 33467889999999999999887 35789999988876
No 109
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=82.77 E-value=0.92 Score=38.04 Aligned_cols=27 Identities=33% Similarity=0.918 Sum_probs=20.6
Q ss_pred cccCCCCCCCccceEecCccccccCCCCCCeeecCCCCc
Q 021215 131 VQQVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGI 169 (316)
Q Consensus 131 v~~~C~~Cg~~f~~YfC~~Ckl~ddd~~k~~yHC~~Cgi 169 (316)
...+|++||+ |||| .+|.+-.|+.||.
T Consensus 8 tKR~Cp~CG~----------kFYD--Lnk~PivCP~CG~ 34 (108)
T PF09538_consen 8 TKRTCPSCGA----------KFYD--LNKDPIVCPKCGT 34 (108)
T ss_pred CcccCCCCcc----------hhcc--CCCCCccCCCCCC
Confidence 4568999998 5574 5688888988873
No 110
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=82.75 E-value=0.76 Score=45.21 Aligned_cols=44 Identities=30% Similarity=0.763 Sum_probs=34.3
Q ss_pred CCCcccccccccCcceeEEcCCCCcccHHhHHHHhccCCCCCCCCCc
Q 021215 205 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSK 251 (316)
Q Consensus 205 ~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiCrk 251 (316)
..||.|.- |.. .++.+--|||.|+.+||..-|....+.||.|.+
T Consensus 275 LkCplc~~-Llr--np~kT~cC~~~fc~eci~~al~dsDf~CpnC~r 318 (427)
T COG5222 275 LKCPLCHC-LLR--NPMKTPCCGHTFCDECIGTALLDSDFKCPNCSR 318 (427)
T ss_pred ccCcchhh-hhh--CcccCccccchHHHHHHhhhhhhccccCCCccc
Confidence 68999987 433 245555689999999999865545799999986
No 111
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=82.58 E-value=0.51 Score=50.42 Aligned_cols=42 Identities=29% Similarity=0.712 Sum_probs=34.9
Q ss_pred CCCcccccccccCcceeEEcCCCCcccHHhHHHHhccCCCCCCCCC
Q 021215 205 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICS 250 (316)
Q Consensus 205 ~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiCr 250 (316)
..|+||+..++.++..++.|.|||++++.|++... +-+|| |.
T Consensus 12 l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~ly---n~scp-~~ 53 (861)
T KOG3161|consen 12 LLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLY---NASCP-TK 53 (861)
T ss_pred hhchHHHHHHHHHhcCcccccccchHHHHHHHhHh---hccCC-CC
Confidence 47999987677778888999999999999998864 35688 55
No 112
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=82.28 E-value=0.91 Score=38.61 Aligned_cols=36 Identities=31% Similarity=0.608 Sum_probs=26.0
Q ss_pred cceEEcCCCCCCcccc-c---ee-eeecCCCCCCccccccCC
Q 021215 280 KVWILCNDCGKTSNVQ-F---HV-LAQKCPNCKSYNTRLTRG 316 (316)
Q Consensus 280 ~~~IlCnDC~~~s~v~-~---H~-lg~kC~~C~SyNT~~~~~ 316 (316)
.....| +|+...... + |+ ....||.|||++...++|
T Consensus 68 p~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~G 108 (124)
T PRK00762 68 PVEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKRAHILGG 108 (124)
T ss_pred CeeEEe-eCcCcccccccchhccccCCcCcCCCCCCCEEecC
Confidence 567899 999875432 1 11 235799999999998876
No 113
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=80.56 E-value=1.2 Score=47.85 Aligned_cols=33 Identities=27% Similarity=0.744 Sum_probs=20.0
Q ss_pred eecCCCCccccc-ccCCCCCCCccceEecCcccc
Q 021215 120 VICSLCGTEQKV-QQVCVNCGVCMGEYFCESCKL 152 (316)
Q Consensus 120 V~C~~C~~eq~v-~~~C~~Cg~~f~~YfC~~Ckl 152 (316)
++|..|+++-+. +..|++||..+..-+|+.|.-
T Consensus 2 ~~Cp~Cg~~n~~~akFC~~CG~~l~~~~Cp~CG~ 35 (645)
T PRK14559 2 LICPQCQFENPNNNRFCQKCGTSLTHKPCPQCGT 35 (645)
T ss_pred CcCCCCCCcCCCCCccccccCCCCCCCcCCCCCC
Confidence 356677766554 456777777765445555543
No 114
>PHA00626 hypothetical protein
Probab=78.89 E-value=1.5 Score=32.99 Aligned_cols=29 Identities=24% Similarity=0.637 Sum_probs=14.8
Q ss_pred CCCCCCCc-cceEecCccccccCCCCCCeeecCCCCc
Q 021215 134 VCVNCGVC-MGEYFCESCKLFDDDTSKKQYHCDGCGI 169 (316)
Q Consensus 134 ~C~~Cg~~-f~~YfC~~Ckl~ddd~~k~~yHC~~Cgi 169 (316)
.||+||.. . +-|.+|+.+ .+.|-|.+||.
T Consensus 2 ~CP~CGS~~I--vrcg~cr~~-----snrYkCkdCGY 31 (59)
T PHA00626 2 SCPKCGSGNI--AKEKTMRGW-----SDDYVCCDCGY 31 (59)
T ss_pred CCCCCCCcee--eeeceeccc-----CcceEcCCCCC
Confidence 46677663 2 245555544 23455555553
No 115
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=78.32 E-value=1.7 Score=36.99 Aligned_cols=36 Identities=31% Similarity=0.632 Sum_probs=29.2
Q ss_pred CcceEEcCCCCCCccccceeeeecCCCCCCccccccCC
Q 021215 279 KKVWILCNDCGKTSNVQFHVLAQKCPNCKSYNTRLTRG 316 (316)
Q Consensus 279 ~~~~IlCnDC~~~s~v~~H~lg~kC~~C~SyNT~~~~~ 316 (316)
..+.+.|-+|+......-|.+. ||.|+|-|.++++|
T Consensus 67 ~p~~~~C~~C~~~~~~e~~~~~--CP~C~s~~~~i~~G 102 (115)
T COG0375 67 EPAECWCLDCGQEVELEELDYR--CPKCGSINLRIIGG 102 (115)
T ss_pred eccEEEeccCCCeecchhheeE--CCCCCCCceEEecC
Confidence 3578999999887766666554 99999999999876
No 116
>PHA03096 p28-like protein; Provisional
Probab=78.15 E-value=1.2 Score=43.28 Aligned_cols=47 Identities=17% Similarity=0.246 Sum_probs=31.4
Q ss_pred CCCcccccccccCc---ceeEEc-CCCCcccHHhHHHHhccC--CCCCCCCCc
Q 021215 205 HDCPVCCEYLFETR---QDVIVL-PCGHTIHKNCLKEMREHH--QYACPICSK 251 (316)
Q Consensus 205 ~~CPIClE~lf~s~---~~v~~L-pCGH~fH~~Ci~~wl~~~--~~~CPiCrk 251 (316)
-.|.||+|...... ...-.| .|.|.|+..|+..|.... .-+||.||.
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~ 231 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRR 231 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCccccc
Confidence 46889988765421 122344 699999999999998642 234666553
No 117
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=77.05 E-value=1.6 Score=43.21 Aligned_cols=45 Identities=33% Similarity=0.754 Sum_probs=37.7
Q ss_pred CCCcccccccccCcceeEEcCCCCcccHHhHHHHhccC--CCCCCCCC
Q 021215 205 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHH--QYACPICS 250 (316)
Q Consensus 205 ~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~--~~~CPiCr 250 (316)
..|||=.| +-+...+++.|.|||.+=.+-+...-+.+ ++.||.|-
T Consensus 337 FiCPVlKe-~~t~ENpP~ml~CgHVIskeal~~LS~nG~~~FKCPYCP 383 (396)
T COG5109 337 FICPVLKE-LCTDENPPVMLECGHVISKEALSVLSQNGVLSFKCPYCP 383 (396)
T ss_pred eeccccHh-hhcccCCCeeeeccceeeHHHHHHHhhcCcEEeeCCCCC
Confidence 47999888 57777899999999999999999986643 47899996
No 118
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=76.87 E-value=1.3 Score=45.66 Aligned_cols=34 Identities=29% Similarity=0.879 Sum_probs=28.3
Q ss_pred CCCCCcccccccccCcceeEEcCCCCcccHHhHHHHhc
Q 021215 203 MHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMRE 240 (316)
Q Consensus 203 ~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~ 240 (316)
.+..||||.. +|. ++++|||||.+++.|....+.
T Consensus 3 eelkc~vc~~-f~~---epiil~c~h~lc~~ca~~~~~ 36 (699)
T KOG4367|consen 3 EELKCPVCGS-FYR---EPIILPCSHNLCQACARNILV 36 (699)
T ss_pred ccccCceehh-hcc---CceEeecccHHHHHHHHhhcc
Confidence 3678999997 465 678999999999999988653
No 119
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=76.71 E-value=1.2 Score=49.11 Aligned_cols=43 Identities=26% Similarity=0.516 Sum_probs=31.6
Q ss_pred ccccCCCCCCCCcccccccccCcceeEEcCCCCcccHHhHHHHhc
Q 021215 196 HPCVEGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMRE 240 (316)
Q Consensus 196 H~CiE~~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~ 240 (316)
+.+.--.-...|-+|.-.|+. ++-.+.||||.||..|+.+-..
T Consensus 809 ~ry~v~ep~d~C~~C~~~ll~--~pF~vf~CgH~FH~~Cl~~~v~ 851 (911)
T KOG2034|consen 809 QRYRVLEPQDSCDHCGRPLLI--KPFYVFPCGHCFHRDCLIRHVL 851 (911)
T ss_pred cceEEecCccchHHhcchhhc--CcceeeeccchHHHHHHHHHHH
Confidence 333333346789999976554 4778889999999999998643
No 120
>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=74.61 E-value=2.7 Score=43.50 Aligned_cols=50 Identities=22% Similarity=0.647 Sum_probs=41.5
Q ss_pred eeecCCCCCcccCchhhhhhccCcccCccCCCCCCCccCceeecCCCCcccccccCCCCCCCc
Q 021215 79 RIRAPCCNEIFDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKVQQVCVNCGVC 141 (316)
Q Consensus 79 ~l~~pcC~~~y~Cr~CHde~~~~~~~~~~~~H~~dR~~v~~V~C~~C~~eq~v~~~C~~Cg~~ 141 (316)
.+.|.-||....|.+|.-.+. -|. ....+.|-.|+..+++...||+||..
T Consensus 213 ~~~C~~Cg~~~~C~~C~~~l~---------~h~----~~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 213 NLLCRSCGYILCCPNCDVSLT---------YHK----KEGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred eeEhhhCcCccCCCCCCCceE---------Eec----CCCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 378999999999999976654 342 23589999999999999999999885
No 121
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=74.28 E-value=1.7 Score=47.69 Aligned_cols=48 Identities=29% Similarity=0.668 Sum_probs=34.5
Q ss_pred CCCCcccccccccCcceeEEcC---CCCcccHHhHHHHhcc------CCCCCCCCCcccc
Q 021215 204 HHDCPVCCEYLFETRQDVIVLP---CGHTIHKNCLKEMREH------HQYACPICSKSVC 254 (316)
Q Consensus 204 ~~~CPIClE~lf~s~~~v~~Lp---CGH~fH~~Ci~~wl~~------~~~~CPiCrks~~ 254 (316)
...|.||.|.|..+. -++. |=|.||..||.+|... ...+||.|+....
T Consensus 191 ~yeCmIC~e~I~~t~---~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv~~ 247 (950)
T KOG1952|consen 191 KYECMICTERIKRTA---PVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSVSK 247 (950)
T ss_pred ceEEEEeeeeccccC---CceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccchhc
Confidence 468999999765432 2444 5599999999999753 2357999994443
No 122
>PF12773 DZR: Double zinc ribbon
Probab=73.58 E-value=2.6 Score=29.57 Aligned_cols=32 Identities=34% Similarity=0.889 Sum_probs=17.7
Q ss_pred eeecCCCCcccc--c--ccCCCCCCCcc--ceEecCcc
Q 021215 119 QVICSLCGTEQK--V--QQVCVNCGVCM--GEYFCESC 150 (316)
Q Consensus 119 ~V~C~~C~~eq~--v--~~~C~~Cg~~f--~~YfC~~C 150 (316)
...|..|++.++ . ...|++||... +..||..|
T Consensus 12 ~~fC~~CG~~l~~~~~~~~~C~~Cg~~~~~~~~fC~~C 49 (50)
T PF12773_consen 12 AKFCPHCGTPLPPPDQSKKICPNCGAENPPNAKFCPNC 49 (50)
T ss_pred ccCChhhcCChhhccCCCCCCcCCcCCCcCCcCccCcc
Confidence 456777776665 2 24577776654 33444443
No 123
>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=73.37 E-value=2.3 Score=30.65 Aligned_cols=42 Identities=29% Similarity=0.652 Sum_probs=19.9
Q ss_pred CCCcccccccccCcceeEEcCCCCcccHHhHH--HHhc----cCCCCCCCCCcc
Q 021215 205 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLK--EMRE----HHQYACPICSKS 252 (316)
Q Consensus 205 ~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~--~wl~----~~~~~CPiCrks 252 (316)
..|||-...|.. +++...|.|.- |++ .||+ .....||+|+++
T Consensus 3 L~CPls~~~i~~---P~Rg~~C~H~~---CFDl~~fl~~~~~~~~W~CPiC~~~ 50 (50)
T PF02891_consen 3 LRCPLSFQRIRI---PVRGKNCKHLQ---CFDLESFLESNQRTPKWKCPICNKP 50 (50)
T ss_dssp SB-TTTSSB-SS---EEEETT--SS-----EEHHHHHHHHHHS---B-TTT---
T ss_pred eeCCCCCCEEEe---CccCCcCcccc---eECHHHHHHHhhccCCeECcCCcCc
Confidence 368998876544 78888999873 433 2443 245789999874
No 124
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=72.94 E-value=1.8 Score=46.68 Aligned_cols=45 Identities=29% Similarity=0.856 Sum_probs=35.4
Q ss_pred CCCcccccccccCcceeEEcCCCCcccHHhHHHHhccCCC-CCCCCCcccc
Q 021215 205 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQY-ACPICSKSVC 254 (316)
Q Consensus 205 ~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~-~CPiCrks~~ 254 (316)
..|+||++ .+..+..+|||.|+.+|+.+.+..... .||+||..+.
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 235778899999999999997764333 5999995443
No 125
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=72.79 E-value=3.5 Score=47.21 Aligned_cols=32 Identities=34% Similarity=0.844 Sum_probs=15.7
Q ss_pred eecCCCCcccccccCCCCCCCcc-ceEecCcccc
Q 021215 120 VICSLCGTEQKVQQVCVNCGVCM-GEYFCESCKL 152 (316)
Q Consensus 120 V~C~~C~~eq~v~~~C~~Cg~~f-~~YfC~~Ckl 152 (316)
..|..|+++-+ ...|+.||... ..|+|..|..
T Consensus 668 rkCPkCG~~t~-~~fCP~CGs~te~vy~CPsCGa 700 (1337)
T PRK14714 668 RRCPSCGTETY-ENRCPDCGTHTEPVYVCPDCGA 700 (1337)
T ss_pred EECCCCCCccc-cccCcccCCcCCCceeCccCCC
Confidence 45555555422 23555555554 2344555543
No 126
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=72.41 E-value=3 Score=40.32 Aligned_cols=128 Identities=20% Similarity=0.488 Sum_probs=69.3
Q ss_pred ccCchhhhhhccCcccCccCCCCCCCccCceeecCCCCcccccccCCCCCCCccceEecCccccc-cCCC---CCCeeec
Q 021215 89 FDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKVQQVCVNCGVCMGEYFCESCKLF-DDDT---SKKQYHC 164 (316)
Q Consensus 89 y~Cr~CHde~~~~~~~~~~~~H~~dR~~v~~V~C~~C~~eq~v~~~C~~Cg~~f~~YfC~~Ckl~-ddd~---~k~~yHC 164 (316)
|.|.+|-..+. +--.-|.+ ...+|-.|+..-.+ ..-|+|-|.+|+-. |+++ .-.+||
T Consensus 100 F~Cd~Cn~~La---------d~gf~rnq-gr~LC~~Cn~k~Ka--------~~~g~YvC~KCh~~iD~~~l~fr~d~yH- 160 (332)
T KOG2272|consen 100 FRCDLCNKHLA---------DQGFYRNQ-GRALCRECNQKEKA--------KGRGRYVCQKCHAHIDEQPLTFRGDPYH- 160 (332)
T ss_pred chhHHHHHHHh---------hhhhHhhc-chHHhhhhhhhhcc--------cccceeehhhhhhhcccccccccCCCCC-
Confidence 46666666654 22234443 46778888765433 23589999999754 5543 224554
Q ss_pred CCCCcceecCCcceeeccCCcceeeccccccccccCCCCCCCCcccccccccCcceeEEcCCCCcccHHhHHH----Hhc
Q 021215 165 DGCGICRIGGCDNFFHCNKCRCCYSMLLKNSHPCVEGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKE----MRE 240 (316)
Q Consensus 165 ~~CgiCR~G~~~~ffHC~~C~~C~s~~l~~~H~CiE~~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~----wl~ 240 (316)
-.-|.|.+||-=+....+ |-..+.-|+-|.+.|-- ++-..|.-.+-..=+.. |-.
T Consensus 161 -----------~yHFkCt~C~keL~sdaR------evk~eLyClrChD~mgi----piCgaC~rpIeervi~amgKhWHv 219 (332)
T KOG2272|consen 161 -----------PYHFKCTTCGKELTSDAR------EVKGELYCLRCHDKMGI----PICGACRRPIEERVIFAMGKHWHV 219 (332)
T ss_pred -----------ccceecccccccccchhh------hhccceeccccccccCC----cccccccCchHHHHHHHhccccch
Confidence 256889999876644221 11234555555543211 11222222222332322 322
Q ss_pred cCCCCCCCCCccccchh
Q 021215 241 HHQYACPICSKSVCDMS 257 (316)
Q Consensus 241 ~~~~~CPiCrks~~d~~ 257 (316)
+.+.|..|-|++.-..
T Consensus 220 -eHFvCa~CekPFlGHr 235 (332)
T KOG2272|consen 220 -EHFVCAKCEKPFLGHR 235 (332)
T ss_pred -hheeehhcCCcccchh
Confidence 4688999999987543
No 127
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=69.58 E-value=5.1 Score=29.88 Aligned_cols=36 Identities=25% Similarity=0.628 Sum_probs=26.2
Q ss_pred CCCCCcccccccccCcceeEEcCCCCcccHHhHHHH
Q 021215 203 MHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEM 238 (316)
Q Consensus 203 ~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~w 238 (316)
+...|++|.+.+....+-++-..||=.+|+.|....
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~ 39 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKA 39 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCCCcccHHHHhhC
Confidence 456899999975544443444569999999998653
No 128
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=69.47 E-value=4.5 Score=44.06 Aligned_cols=55 Identities=24% Similarity=0.544 Sum_probs=43.8
Q ss_pred eeecCCCCCcccCchhhhhhccCcccCccCCCCCCCccCceeecCCCCcccccccCCCCCCCccceEe
Q 021215 79 RIRAPCCNEIFDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKVQQVCVNCGVCMGEYF 146 (316)
Q Consensus 79 ~l~~pcC~~~y~Cr~CHde~~~~~~~~~~~~H~~dR~~v~~V~C~~C~~eq~v~~~C~~Cg~~f~~Yf 146 (316)
.+.|.-||..+.|.+|=.-.. -|. ....+.|-.|+..+++...||+||...=+|+
T Consensus 435 ~l~C~~Cg~v~~Cp~Cd~~lt---------~H~----~~~~L~CH~Cg~~~~~p~~Cp~Cgs~~L~~~ 489 (730)
T COG1198 435 LLLCRDCGYIAECPNCDSPLT---------LHK----ATGQLRCHYCGYQEPIPQSCPECGSEHLRAV 489 (730)
T ss_pred eeecccCCCcccCCCCCcceE---------Eec----CCCeeEeCCCCCCCCCCCCCCCCCCCeeEEe
Confidence 488999999999999954433 121 2369999999999999999999999855554
No 129
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=68.85 E-value=4.7 Score=43.95 Aligned_cols=44 Identities=27% Similarity=0.676 Sum_probs=34.4
Q ss_pred ceeecCCCCcccccccCCCCCCCcc------ceEecCccccccCCCCCCeeecCCCCc
Q 021215 118 NQVICSLCGTEQKVQQVCVNCGVCM------GEYFCESCKLFDDDTSKKQYHCDGCGI 169 (316)
Q Consensus 118 ~~V~C~~C~~eq~v~~~C~~Cg~~f------~~YfC~~Ckl~ddd~~k~~yHC~~Cgi 169 (316)
+.++|..|+.. -.|++|...| +...|--|..= ++.+.+|+.||-
T Consensus 434 ~~l~C~~Cg~v----~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~----~~~p~~Cp~Cgs 483 (730)
T COG1198 434 PLLLCRDCGYI----AECPNCDSPLTLHKATGQLRCHYCGYQ----EPIPQSCPECGS 483 (730)
T ss_pred ceeecccCCCc----ccCCCCCcceEEecCCCeeEeCCCCCC----CCCCCCCCCCCC
Confidence 48999999987 5799998888 56777777653 457888888883
No 130
>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=67.27 E-value=3.8 Score=35.57 Aligned_cols=28 Identities=21% Similarity=0.438 Sum_probs=20.6
Q ss_pred cccCCCCCCCccceEecCccccccCCCCCCeeecCCCCcc
Q 021215 131 VQQVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGIC 170 (316)
Q Consensus 131 v~~~C~~Cg~~f~~YfC~~Ckl~ddd~~k~~yHC~~CgiC 170 (316)
....|++||+ ||| |.+|.+-.|+.||.=
T Consensus 8 tKr~Cp~cg~----------kFY--DLnk~p~vcP~cg~~ 35 (129)
T TIGR02300 8 TKRICPNTGS----------KFY--DLNRRPAVSPYTGEQ 35 (129)
T ss_pred ccccCCCcCc----------ccc--ccCCCCccCCCcCCc
Confidence 3467999998 556 456888888888743
No 131
>PRK04023 DNA polymerase II large subunit; Validated
Probab=65.86 E-value=4.9 Score=45.20 Aligned_cols=48 Identities=27% Similarity=0.643 Sum_probs=35.5
Q ss_pred eeecCCCCcccccccCCCCCCCc-cceEecCccccccCCCCCCeeecCCCCccee
Q 021215 119 QVICSLCGTEQKVQQVCVNCGVC-MGEYFCESCKLFDDDTSKKQYHCDGCGICRI 172 (316)
Q Consensus 119 ~V~C~~C~~eq~v~~~C~~Cg~~-f~~YfC~~Ckl~ddd~~k~~yHC~~CgiCR~ 172 (316)
.-.|..|+++. ....|++||.. -..|||+.|.-- -..|.|+.||.=..
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 44899999984 66799999974 577899999332 23478999986443
No 132
>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=64.61 E-value=5.3 Score=29.79 Aligned_cols=27 Identities=30% Similarity=0.760 Sum_probs=17.4
Q ss_pred ccCCCCCCCccceEecCccccccCCCCCCeeecCCCCc
Q 021215 132 QQVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGI 169 (316)
Q Consensus 132 ~~~C~~Cg~~f~~YfC~~Ckl~ddd~~k~~yHC~~Cgi 169 (316)
++.|+.||....+ ......|.|+.||.
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 5778888887765 23445666666654
No 133
>KOG2068 consensus MOT2 transcription factor [Transcription]
Probab=63.63 E-value=5.8 Score=39.34 Aligned_cols=53 Identities=28% Similarity=0.600 Sum_probs=40.2
Q ss_pred CCCCCCcccccccccCcceeEEcCCCCcccHHhHHHHhccCCCCCCCCCccccc
Q 021215 202 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 255 (316)
Q Consensus 202 ~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiCrks~~d 255 (316)
+-...||||.+++..........|||+.++..|+..-.. ...+||.||++...
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 445789999997644444444557899999999988776 46899999987763
No 134
>PRK14873 primosome assembly protein PriA; Provisional
Probab=62.44 E-value=6.2 Score=42.47 Aligned_cols=50 Identities=22% Similarity=0.472 Sum_probs=39.9
Q ss_pred eeecCCCCCcccCchhhhhhccCcccCccCCCCCCCccCceeecCCCCcccccccCCCCCCCcc
Q 021215 79 RIRAPCCNEIFDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKVQQVCVNCGVCM 142 (316)
Q Consensus 79 ~l~~pcC~~~y~Cr~CHde~~~~~~~~~~~~H~~dR~~v~~V~C~~C~~eq~v~~~C~~Cg~~f 142 (316)
.+.|.-||....|.+|.--+. -|. ....+.|-.|+..+ ....|++||...
T Consensus 383 ~l~C~~Cg~~~~C~~C~~~L~---------~h~----~~~~l~Ch~CG~~~-~p~~Cp~Cgs~~ 432 (665)
T PRK14873 383 SLACARCRTPARCRHCTGPLG---------LPS----AGGTPRCRWCGRAA-PDWRCPRCGSDR 432 (665)
T ss_pred eeEhhhCcCeeECCCCCCcee---------Eec----CCCeeECCCCcCCC-cCccCCCCcCCc
Confidence 489999999999999987654 232 23588999999976 578999999863
No 135
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=62.21 E-value=6.2 Score=45.35 Aligned_cols=33 Identities=30% Similarity=0.739 Sum_probs=25.9
Q ss_pred cCCCCCCCccceEecCccccccCCCCCCeeecCCCCc
Q 021215 133 QVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGI 169 (316)
Q Consensus 133 ~~C~~Cg~~f~~YfC~~Ckl~ddd~~k~~yHC~~Cgi 169 (316)
..||+||......||+.|.-.- +.+|+|+.||.
T Consensus 668 rkCPkCG~~t~~~fCP~CGs~t----e~vy~CPsCGa 700 (1337)
T PRK14714 668 RRCPSCGTETYENRCPDCGTHT----EPVYVCPDCGA 700 (1337)
T ss_pred EECCCCCCccccccCcccCCcC----CCceeCccCCC
Confidence 5799999987777999997542 45788888876
No 136
>PRK05580 primosome assembly protein PriA; Validated
Probab=61.89 E-value=6.7 Score=42.09 Aligned_cols=51 Identities=22% Similarity=0.575 Sum_probs=42.0
Q ss_pred eeecCCCCCcccCchhhhhhccCcccCccCCCCCCCccCceeecCCCCcccccccCCCCCCCcc
Q 021215 79 RIRAPCCNEIFDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKVQQVCVNCGVCM 142 (316)
Q Consensus 79 ~l~~pcC~~~y~Cr~CHde~~~~~~~~~~~~H~~dR~~v~~V~C~~C~~eq~v~~~C~~Cg~~f 142 (316)
.+.|.-||....|.+|.-... -|. ....+.|-.|+..+++...||+||...
T Consensus 381 ~~~C~~Cg~~~~C~~C~~~l~---------~h~----~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~ 431 (679)
T PRK05580 381 FLLCRDCGWVAECPHCDASLT---------LHR----FQRRLRCHHCGYQEPIPKACPECGSTD 431 (679)
T ss_pred ceEhhhCcCccCCCCCCCcee---------EEC----CCCeEECCCCcCCCCCCCCCCCCcCCe
Confidence 478999999999999987654 232 235899999999999999999998874
No 137
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=61.63 E-value=3.9 Score=41.10 Aligned_cols=44 Identities=32% Similarity=0.634 Sum_probs=30.7
Q ss_pred CCCCcccccccccCcceeEEcCCCCcccHHhHHHHhcc-----CCCCCC
Q 021215 204 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH-----HQYACP 247 (316)
Q Consensus 204 ~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~-----~~~~CP 247 (316)
...|.||+...........++.|+|.|+.+|..+++.. ...+||
T Consensus 146 ~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~~~~~~~~~C~ 194 (384)
T KOG1812|consen 146 KEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVKLLSGTVIRCP 194 (384)
T ss_pred cccCccCccccccHhhhHHHhcccchhhhHHhHHHhhhhhccCCCccCC
Confidence 56899999333333233337789999999999998763 235675
No 138
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=59.71 E-value=6 Score=34.73 Aligned_cols=47 Identities=26% Similarity=0.596 Sum_probs=33.6
Q ss_pred CCCcccccccccCcceeEEc----CCCCcccHHhHHHHhccC--CCCCCCCCccccc
Q 021215 205 HDCPVCCEYLFETRQDVIVL----PCGHTIHKNCLKEMREHH--QYACPICSKSVCD 255 (316)
Q Consensus 205 ~~CPIClE~lf~s~~~v~~L----pCGH~fH~~Ci~~wl~~~--~~~CPiCrks~~d 255 (316)
-.|-||.|- .. +...| =||-.++..|....|+.. ...||+|+.++-.
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 468888873 22 23455 289999999999966542 3579999988864
No 139
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=59.42 E-value=5.3 Score=42.90 Aligned_cols=34 Identities=29% Similarity=0.706 Sum_probs=18.7
Q ss_pred eeecCCCCcccccccCCCCCCCcc--ceEecCccccc
Q 021215 119 QVICSLCGTEQKVQQVCVNCGVCM--GEYFCESCKLF 153 (316)
Q Consensus 119 ~V~C~~C~~eq~v~~~C~~Cg~~f--~~YfC~~Ckl~ 153 (316)
.-.|..|++.++. ..|++||+.. +.-||+.|-..
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 3456666665532 4566666553 45566666543
No 140
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=58.50 E-value=7.6 Score=31.31 Aligned_cols=31 Identities=29% Similarity=0.554 Sum_probs=20.2
Q ss_pred CCCCCCCccccchhHHHHHhHHHHHcC--CCChhhhc
Q 021215 244 YACPICSKSVCDMSKVWEKYDREIAAT--PMPEAYLN 278 (316)
Q Consensus 244 ~~CPiCrks~~d~~~~~~~lD~~i~~~--pmP~ey~~ 278 (316)
-.||-||..++|... ||.+|+.. |-|.+|..
T Consensus 22 D~CPrCrGVWLDrGE----LdKli~r~r~pqpa~ys~ 54 (88)
T COG3809 22 DYCPRCRGVWLDRGE----LDKLIERSRYPQPAEYSQ 54 (88)
T ss_pred eeCCccccEeecchh----HHHHHHHhcCCCCcccCC
Confidence 469999999999754 55555533 44445543
No 141
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=58.07 E-value=4.2 Score=39.25 Aligned_cols=70 Identities=24% Similarity=0.523 Sum_probs=44.1
Q ss_pred CCCCCCCCcccccccccCcceeEEcCC---C--CcccHHhHHHHhccC-------CCCCCCCCcccc----c---hhHHH
Q 021215 200 EGAMHHDCPVCCEYLFETRQDVIVLPC---G--HTIHKNCLKEMREHH-------QYACPICSKSVC----D---MSKVW 260 (316)
Q Consensus 200 E~~~~~~CPIClE~lf~s~~~v~~LpC---G--H~fH~~Ci~~wl~~~-------~~~CPiCrks~~----d---~~~~~ 260 (316)
+...+..|=||++--.+.+...-+-|| | |..|..|+..|+... .-.||.|+.... . .+...
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 345577899999742332222234477 3 889999999998642 246999996654 2 23344
Q ss_pred HHhHHHHHc
Q 021215 261 EKYDREIAA 269 (316)
Q Consensus 261 ~~lD~~i~~ 269 (316)
+.+|..+..
T Consensus 96 e~~d~~i~r 104 (293)
T KOG3053|consen 96 ERLDILIFR 104 (293)
T ss_pred HHhhhHHhh
Confidence 556655543
No 142
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=57.47 E-value=9.8 Score=30.49 Aligned_cols=53 Identities=17% Similarity=0.434 Sum_probs=24.0
Q ss_pred CCCCCCcccccccccCcceeEEc---CCCCcccHHhHHHHhccCCCCCCCCCcccc
Q 021215 202 AMHHDCPVCCEYLFETRQDVIVL---PCGHTIHKNCLKEMREHHQYACPICSKSVC 254 (316)
Q Consensus 202 ~~~~~CPIClE~lf~s~~~v~~L---pCGH~fH~~Ci~~wl~~~~~~CPiCrks~~ 254 (316)
.....|.||.+.+-.....-++. -|+--.++.|+.--.+.++..||.|+....
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 34578999998875544333343 567889999998877777888999995544
No 143
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=56.31 E-value=4.1 Score=44.94 Aligned_cols=52 Identities=29% Similarity=0.616 Sum_probs=37.5
Q ss_pred CCCCCCCcccccccccCcceeEEcCCC-----CcccHHhHHHHhccC-CCCCCCCCcccc
Q 021215 201 GAMHHDCPVCCEYLFETRQDVIVLPCG-----HTIHKNCLKEMREHH-QYACPICSKSVC 254 (316)
Q Consensus 201 ~~~~~~CPIClE~lf~s~~~v~~LpCG-----H~fH~~Ci~~wl~~~-~~~CPiCrks~~ 254 (316)
|+.+..|-||.-. +.++++..-||. -.+|++|+.+|+..+ ...|-+|..++.
T Consensus 9 N~d~~~CRICr~e--~~~d~pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~ 66 (1175)
T COG5183 9 NEDKRSCRICRTE--DIRDDPLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYK 66 (1175)
T ss_pred CccchhceeecCC--CCCCCcCcccccccchhHHHHHHHHHHHHhcCCCcceeeecceee
Confidence 3446789999742 234456666885 459999999999763 456999997765
No 144
>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=56.02 E-value=8.3 Score=24.78 Aligned_cols=20 Identities=35% Similarity=0.894 Sum_probs=13.7
Q ss_pred CCCcceecCCcc-eeeccCCc
Q 021215 166 GCGICRIGGCDN-FFHCNKCR 185 (316)
Q Consensus 166 ~CgiCR~G~~~~-ffHC~~C~ 185 (316)
.|++||.-.... +++|..|+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~ 22 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECC 22 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCC
Confidence 467776654444 88888887
No 145
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=54.99 E-value=2.5 Score=40.97 Aligned_cols=34 Identities=21% Similarity=0.619 Sum_probs=28.5
Q ss_pred ccccCcccccccccccceeecCCCCCcccCchhhh
Q 021215 62 ELLRKGFMECQHYRRRCRIRAPCCNEIFDCRHCHN 96 (316)
Q Consensus 62 ~~~~~~~~~C~HY~r~c~l~~pcC~~~y~Cr~CHd 96 (316)
.....+.+.|.||...=.++.++|.. |+|..||+
T Consensus 171 s~~~~~~~~CgH~~h~~cf~e~~~~~-y~CP~C~~ 204 (276)
T KOG1940|consen 171 SFEDAGVLKCGHYMHSRCFEEMICEG-YTCPICSK 204 (276)
T ss_pred ccccCCccCcccchHHHHHHHHhccC-CCCCcccc
Confidence 34555666799999866799999999 99999999
No 146
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=53.53 E-value=6.5 Score=36.42 Aligned_cols=39 Identities=33% Similarity=0.766 Sum_probs=28.8
Q ss_pred CcccccccccCcceeEEcCCCCc-ccHHhHHHHhccCCCCCCCCCcccc
Q 021215 207 CPVCCEYLFETRQDVIVLPCGHT-IHKNCLKEMREHHQYACPICSKSVC 254 (316)
Q Consensus 207 CPIClE~lf~s~~~v~~LpCGH~-fH~~Ci~~wl~~~~~~CPiCrks~~ 254 (316)
|-.|.+. ...+++|||-|. ++..|-.. + ..||+|+.+..
T Consensus 161 Cr~C~~~----~~~VlllPCrHl~lC~~C~~~-~----~~CPiC~~~~~ 200 (207)
T KOG1100|consen 161 CRKCGER----EATVLLLPCRHLCLCGICDES-L----RICPICRSPKT 200 (207)
T ss_pred ceecCcC----CceEEeecccceEeccccccc-C----ccCCCCcChhh
Confidence 8899873 335889999876 77888754 2 45999996553
No 147
>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 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=51.41 E-value=5.9 Score=38.45 Aligned_cols=51 Identities=25% Similarity=0.664 Sum_probs=31.0
Q ss_pred CCcccCchhhhhhccCcccCccCCCCCCCccCceeecCCCCcccccccCCCCCCCccceEecCcccc
Q 021215 86 NEIFDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKVQQVCVNCGVCMGEYFCESCKL 152 (316)
Q Consensus 86 ~~~y~Cr~CHde~~~~~~~~~~~~H~~dR~~v~~V~C~~C~~eq~v~~~C~~Cg~~f~~YfC~~Ckl 152 (316)
|++|.|-+|++-+.. +-.+.-++ .|+....-.-.|.+|.. +|.|.|..||.
T Consensus 140 Grif~CsfC~~flCE--------DDQFEHQA-------sCQvLe~E~~KC~SCNr-lGq~sCLRCK~ 190 (314)
T PF06524_consen 140 GRIFKCSFCDNFLCE--------DDQFEHQA-------SCQVLESETFKCQSCNR-LGQYSCLRCKI 190 (314)
T ss_pred CeEEEeecCCCeeec--------cchhhhhh-------hhhhhhccccccccccc-ccchhhhheee
Confidence 668999999887652 22222211 14433344556777764 78888888884
No 149
>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=51.31 E-value=13 Score=25.54 Aligned_cols=8 Identities=50% Similarity=1.086 Sum_probs=4.3
Q ss_pred CCCCCCCc
Q 021215 134 VCVNCGVC 141 (316)
Q Consensus 134 ~C~~Cg~~ 141 (316)
.||+||..
T Consensus 2 ~Cp~Cg~~ 9 (43)
T PF08271_consen 2 KCPNCGSK 9 (43)
T ss_dssp SBTTTSSS
T ss_pred CCcCCcCC
Confidence 35556554
No 150
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=51.30 E-value=11 Score=28.67 Aligned_cols=34 Identities=24% Similarity=0.630 Sum_probs=26.3
Q ss_pred CceeecCCCCcccccccCCCCCCCccceEecCcccc
Q 021215 117 VNQVICSLCGTEQKVQQVCVNCGVCMGEYFCESCKL 152 (316)
Q Consensus 117 v~~V~C~~C~~eq~v~~~C~~Cg~~f~~YfC~~Ckl 152 (316)
-....|..|+++. -.+|..|....+.|.|++|-|
T Consensus 23 ~~~F~CPnCG~~~--I~RC~~CRk~~~~Y~CP~CGF 56 (59)
T PRK14890 23 AVKFLCPNCGEVI--IYRCEKCRKQSNPYTCPKCGF 56 (59)
T ss_pred cCEeeCCCCCCee--EeechhHHhcCCceECCCCCC
Confidence 3578888887752 246888888899999998876
No 151
>PF14353 CpXC: CpXC protein
Probab=51.27 E-value=3.2 Score=34.78 Aligned_cols=56 Identities=16% Similarity=0.390 Sum_probs=29.8
Q ss_pred CCCCCCCccccchhHHHHHhHHHHHcCCCChhhhcCcceEEcCCCCCCccccceeeee
Q 021215 244 YACPICSKSVCDMSKVWEKYDREIAATPMPEAYLNKKVWILCNDCGKTSNVQFHVLAQ 301 (316)
Q Consensus 244 ~~CPiCrks~~d~~~~~~~lD~~i~~~pmP~ey~~~~~~IlCnDC~~~s~v~~H~lg~ 301 (316)
.+||.|+..+... .|..++......-...-..+..-.+.|..|+.+..+.|=+|++
T Consensus 2 itCP~C~~~~~~~--v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~~p~lY~ 57 (128)
T PF14353_consen 2 ITCPHCGHEFEFE--VWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLEYPLLYH 57 (128)
T ss_pred cCCCCCCCeeEEE--EEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecCCCEEEE
Confidence 5799999877531 1221111000000001123334578899999998777766654
No 152
>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=51.19 E-value=16 Score=26.19 Aligned_cols=8 Identities=50% Similarity=1.630 Sum_probs=4.2
Q ss_pred CCCCCCCc
Q 021215 244 YACPICSK 251 (316)
Q Consensus 244 ~~CPiCrk 251 (316)
|+||.|.+
T Consensus 3 f~CP~C~~ 10 (54)
T PF05605_consen 3 FTCPYCGK 10 (54)
T ss_pred cCCCCCCC
Confidence 45555555
No 153
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=50.68 E-value=15 Score=35.69 Aligned_cols=111 Identities=24% Similarity=0.519 Sum_probs=68.8
Q ss_pred CCccceEecCcc-ccccCCC---CCCeeecCCCCcceecCCcceeeccCCcceeec-c-c---cccccccCCCCCCCCcc
Q 021215 139 GVCMGEYFCESC-KLFDDDT---SKKQYHCDGCGICRIGGCDNFFHCNKCRCCYSM-L-L---KNSHPCVEGAMHHDCPV 209 (316)
Q Consensus 139 g~~f~~YfC~~C-kl~ddd~---~k~~yHC~~CgiCR~G~~~~ffHC~~C~~C~s~-~-l---~~~H~CiE~~~~~~CPI 209 (316)
...-++|-|+.| |-|.... .-+|+||+- .-..-|.|..||-=|.. - | .-+|. ....|+|
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 AAKHPRYKCPECGKSYSTSSNLSRHKQTHRSL-------DSKKAFSCKYCGKVYVSMPALKMHIRTHT-----LPCECGI 192 (279)
T ss_pred cccCCceeccccccccccccccchhhcccccc-------cccccccCCCCCceeeehHHHhhHhhccC-----CCccccc
Confidence 345578899999 6775543 237899842 12567999999988743 1 1 13443 4678999
Q ss_pred cccccccCcceeEEcCCCCcccHHhHHHHhcc---------CCCCCCCCCccccchhHHHHHhHHHHHcCCCChhhhcCc
Q 021215 210 CCEYLFETRQDVIVLPCGHTIHKNCLKEMREH---------HQYACPICSKSVCDMSKVWEKYDREIAATPMPEAYLNKK 280 (316)
Q Consensus 210 ClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~---------~~~~CPiCrks~~d~~~~~~~lD~~i~~~pmP~ey~~~~ 280 (316)
|.. .|.. +||-. .-|.||.|+|.+.|++ +|.+-++.- .+.+
T Consensus 193 CGK-aFSR-------------------PWLLQGHiRTHTGEKPF~C~hC~kAFADRS----NLRAHmQTH------S~~K 242 (279)
T KOG2462|consen 193 CGK-AFSR-------------------PWLLQGHIRTHTGEKPFSCPHCGKAFADRS----NLRAHMQTH------SDVK 242 (279)
T ss_pred ccc-cccc-------------------hHHhhcccccccCCCCccCCcccchhcchH----HHHHHHHhh------cCCc
Confidence 987 4652 25432 2388999999999975 344433311 1222
Q ss_pred ceEEcCCCCCCc
Q 021215 281 VWILCNDCGKTS 292 (316)
Q Consensus 281 ~~IlCnDC~~~s 292 (316)
..-|.-|+++.
T Consensus 243 -~~qC~~C~KsF 253 (279)
T KOG2462|consen 243 -KHQCPRCGKSF 253 (279)
T ss_pred -cccCcchhhHH
Confidence 45677777653
No 154
>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=50.52 E-value=13 Score=23.61 Aligned_cols=37 Identities=22% Similarity=0.608 Sum_probs=22.5
Q ss_pred CcccccccccCcceeEEcCCCCcccHHhHHHHhccCCCCCCCCCcccc
Q 021215 207 CPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 254 (316)
Q Consensus 207 CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiCrks~~ 254 (316)
|+.|.+.+.... ..+..=|..||.+|+ +|..|++++.
T Consensus 2 C~~C~~~i~~~~--~~~~~~~~~~H~~Cf---------~C~~C~~~L~ 38 (39)
T smart00132 2 CAGCGKPIRGGE--LVLRALGKVWHPECF---------KCSKCGKPLG 38 (39)
T ss_pred ccccCCcccCCc--EEEEeCCccccccCC---------CCcccCCcCc
Confidence 777877655431 222223778887764 5777887664
No 155
>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=50.13 E-value=4.2 Score=27.64 Aligned_cols=27 Identities=33% Similarity=0.725 Sum_probs=15.6
Q ss_pred CCCCCCCccceEecCccccccCCCCCCeeecCCCCc
Q 021215 134 VCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGI 169 (316)
Q Consensus 134 ~C~~Cg~~f~~YfC~~Ckl~ddd~~k~~yHC~~Cgi 169 (316)
.|++||+.++.+| ++.|..=-||.||-
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 4666776666554 34555666777764
No 156
>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=49.70 E-value=12 Score=35.89 Aligned_cols=47 Identities=30% Similarity=0.671 Sum_probs=22.7
Q ss_pred CceeecCCCCccccc-ccCCCCCCCccceEecCccccc--cCCCCCCeeecCCC
Q 021215 117 VNQVICSLCGTEQKV-QQVCVNCGVCMGEYFCESCKLF--DDDTSKKQYHCDGC 167 (316)
Q Consensus 117 v~~V~C~~C~~eq~v-~~~C~~Cg~~f~~YfC~~Ckl~--ddd~~k~~yHC~~C 167 (316)
.+-..|+.|+++=.. -..|++||..-..-+ .+| ++++.-.++.|+.|
T Consensus 195 ~R~L~Cs~C~t~W~~~R~~Cp~Cg~~~~~~l----~~~~~e~~~~~rve~C~~C 244 (290)
T PF04216_consen 195 KRYLHCSLCGTEWRFVRIKCPYCGNTDHEKL----EYFTVEGEPAYRVEVCESC 244 (290)
T ss_dssp EEEEEETTT--EEE--TTS-TTT---SS-EE----E--------SEEEEEETTT
T ss_pred cEEEEcCCCCCeeeecCCCCcCCCCCCCcce----eeEecCCCCcEEEEECCcc
Confidence 368999999999875 578999998876655 344 33333444444444
No 157
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=49.67 E-value=14 Score=25.79 Aligned_cols=30 Identities=20% Similarity=0.428 Sum_probs=19.0
Q ss_pred eEEcCCCCCCccccceeeeecCCCCCCccc
Q 021215 282 WILCNDCGKTSNVQFHVLAQKCPNCKSYNT 311 (316)
Q Consensus 282 ~IlCnDC~~~s~v~~H~lg~kC~~C~SyNT 311 (316)
...|.+|++.....-.....+|+.||+.-.
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCGYRIL 32 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCCCeEE
Confidence 467888887653333333678888887543
No 158
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=49.34 E-value=6.2 Score=33.62 Aligned_cols=19 Identities=47% Similarity=0.950 Sum_probs=16.0
Q ss_pred eeeecCCCCC----CccccccCC
Q 021215 298 VLAQKCPNCK----SYNTRLTRG 316 (316)
Q Consensus 298 ~lg~kC~~C~----SyNT~~~~~ 316 (316)
.|-+||+.|| +|+|+|+|+
T Consensus 72 ~I~~kCpkCghe~m~Y~T~QlRS 94 (116)
T KOG2907|consen 72 VIKHKCPKCGHEEMSYHTLQLRS 94 (116)
T ss_pred chhccCcccCCchhhhhhhhccc
Confidence 4678999997 899999973
No 159
>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]
Probab=49.22 E-value=6.4 Score=43.16 Aligned_cols=45 Identities=36% Similarity=0.680 Sum_probs=31.4
Q ss_pred CCCCcccccccccCc---ceeEEcCCCCcccHHhHHHHhccCCCCCCCCC
Q 021215 204 HHDCPVCCEYLFETR---QDVIVLPCGHTIHKNCLKEMREHHQYACPICS 250 (316)
Q Consensus 204 ~~~CPIClE~lf~s~---~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiCr 250 (316)
++.|.-|.+....++ ..++++.|||.||..|+.....+. .|-+|.
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 567899999999999998865432 254444
No 160
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=47.88 E-value=18 Score=25.27 Aligned_cols=8 Identities=38% Similarity=0.974 Sum_probs=4.5
Q ss_pred eeecCCCC
Q 021215 161 QYHCDGCG 168 (316)
Q Consensus 161 ~yHC~~Cg 168 (316)
.++|+.||
T Consensus 21 ~~~Cp~CG 28 (46)
T PRK00398 21 GVRCPYCG 28 (46)
T ss_pred ceECCCCC
Confidence 45555555
No 161
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=46.48 E-value=1.8 Score=43.90 Aligned_cols=52 Identities=19% Similarity=0.418 Sum_probs=42.4
Q ss_pred CCCCCcccccccccCcceeEEcCCCCcccHHhHHHHhccCCCCCCCCCccccc
Q 021215 203 MHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 255 (316)
Q Consensus 203 ~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiCrks~~d 255 (316)
.-..+.||.+.|...-+....+-|||.+|..+|.+||.. ...+|.|++.+..
T Consensus 195 lv~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~~-~~kl~~~~rel~~ 246 (465)
T KOG0827|consen 195 LVGSLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLAT-KRKLPSCRRELPK 246 (465)
T ss_pred HHhhhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHHH-HHHhHHHHhhhhh
Confidence 345799999877654456678899999999999999975 6789999988863
No 162
>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=46.47 E-value=14 Score=20.94 Aligned_cols=18 Identities=39% Similarity=0.881 Sum_probs=11.6
Q ss_pred CCCCCCCccccchhHHHH
Q 021215 244 YACPICSKSVCDMSKVWE 261 (316)
Q Consensus 244 ~~CPiCrks~~d~~~~~~ 261 (316)
+.||+|.+.+......++
T Consensus 1 ~~C~~C~~~~~~~~~l~~ 18 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQ 18 (24)
T ss_dssp EE-SSTS-EESSHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHH
Confidence 469999999888765443
No 163
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=46.18 E-value=15 Score=25.96 Aligned_cols=30 Identities=23% Similarity=0.518 Sum_probs=19.0
Q ss_pred eEEcCCCCCCcccccee---eeecCCCCCCccc
Q 021215 282 WILCNDCGKTSNVQFHV---LAQKCPNCKSYNT 311 (316)
Q Consensus 282 ~IlCnDC~~~s~v~~H~---lg~kC~~C~SyNT 311 (316)
...|.+|+...++-..+ ....|+.|+|-+.
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~ 37 (52)
T TIGR02605 5 EYRCTACGHRFEVLQKMSDDPLATCPECGGEKL 37 (52)
T ss_pred EEEeCCCCCEeEEEEecCCCCCCCCCCCCCCce
Confidence 45688888766553221 1237999998776
No 164
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=46.12 E-value=18 Score=39.71 Aligned_cols=79 Identities=25% Similarity=0.378 Sum_probs=46.8
Q ss_pred CCeeecCCCCcceecCCcceeeccCCcceeeccccccccccCCCCCCCCcccccccccCcceeEEcCCCCcccHHhHHHH
Q 021215 159 KKQYHCDGCGICRIGGCDNFFHCNKCRCCYSMLLKNSHPCVEGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEM 238 (316)
Q Consensus 159 k~~yHC~~CgiCR~G~~~~ffHC~~C~~C~s~~l~~~H~CiE~~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~w 238 (316)
.-+|-|+.|+-=-+++++ --|+ .|-+++ ...|.+|-..+- +..+.--.|||-.|.+++.+|
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--WQCD---RCESRA------------SAKCTVCDLVIR--GVDVWCQVCGHGGHDSHLKSW 811 (839)
T ss_pred eeeccccccCCccccccc--eeec---hHHHHh------------hcCceeecceee--eeEeecccccccccHHHHHHH
Confidence 357888888754444433 3333 343333 236899975322 222333369999999999999
Q ss_pred hccCCCCCCC-------CCccccchh
Q 021215 239 REHHQYACPI-------CSKSVCDMS 257 (316)
Q Consensus 239 l~~~~~~CPi-------Crks~~d~~ 257 (316)
+.. ..-||. +++++.|+.
T Consensus 812 ~~~-~s~ca~~~C~~~c~~~~~~D~~ 836 (839)
T KOG0269|consen 812 FFK-ASPCAKSICPHLCHYSSFIDTF 836 (839)
T ss_pred Hhc-CCCCccccCCccccccccchhh
Confidence 874 344554 445555553
No 165
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=45.95 E-value=21 Score=26.62 Aligned_cols=29 Identities=31% Similarity=0.748 Sum_probs=22.5
Q ss_pred ceEEcCCCCCCccccceeeeecCCCCCCcccccc
Q 021215 281 VWILCNDCGKTSNVQFHVLAQKCPNCKSYNTRLT 314 (316)
Q Consensus 281 ~~IlCnDC~~~s~v~~H~lg~kC~~C~SyNT~~~ 314 (316)
..+.|..|+.. ...| +-|+.||.|+-+++
T Consensus 26 ~l~~C~~CG~~--~~~H---~vC~~CG~Y~gr~v 54 (57)
T PRK12286 26 GLVECPNCGEP--KLPH---RVCPSCGYYKGREV 54 (57)
T ss_pred cceECCCCCCc--cCCe---EECCCCCcCCCEEe
Confidence 46789999975 3446 45999999999885
No 166
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=45.92 E-value=16 Score=24.89 Aligned_cols=26 Identities=27% Similarity=0.591 Sum_probs=15.0
Q ss_pred CCCCCCCccceEecCccccccCCCCCCeeecCCCC
Q 021215 134 VCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCG 168 (316)
Q Consensus 134 ~C~~Cg~~f~~YfC~~Ckl~ddd~~k~~yHC~~Cg 168 (316)
.||.|+..|..+. + .+-.+++|+.||
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 3677777665543 1 124666677664
No 167
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=43.48 E-value=17 Score=32.80 Aligned_cols=51 Identities=24% Similarity=0.402 Sum_probs=34.8
Q ss_pred CCCCCCCCccccchhHHHHHhHHHHHcCCCChhhhcCcceEEcCCCCCCccccceee
Q 021215 243 QYACPICSKSVCDMSKVWEKYDREIAATPMPEAYLNKKVWILCNDCGKTSNVQFHVL 299 (316)
Q Consensus 243 ~~~CPiCrks~~d~~~~~~~lD~~i~~~pmP~ey~~~~~~IlCnDC~~~s~v~~H~l 299 (316)
-.+||.|+..+...+. +++.++-.|..|.+......|..|++.-+..-||=
T Consensus 97 ~~RCp~CN~~L~~vs~------eev~~~Vp~~~~~~~~~f~~C~~CgkiYW~GsHw~ 147 (165)
T COG1656 97 FSRCPECNGELEKVSR------EEVKEKVPEKVYRNYEEFYRCPKCGKIYWKGSHWR 147 (165)
T ss_pred cccCcccCCEeccCcH------HHHhhccchhhhhcccceeECCCCcccccCchHHH
Confidence 4579999998876532 22222222345666666778999999988888873
No 168
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=42.82 E-value=23 Score=34.48 Aligned_cols=29 Identities=21% Similarity=0.505 Sum_probs=21.2
Q ss_pred cCceeecCCCCcccc-------------cccCCCCCCCccce
Q 021215 116 EVNQVICSLCGTEQK-------------VQQVCVNCGVCMGE 144 (316)
Q Consensus 116 ~v~~V~C~~C~~eq~-------------v~~~C~~Cg~~f~~ 144 (316)
+.+.-.|-.|++++. ..=.|.-||+.|.|
T Consensus 158 s~ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSR 199 (279)
T KOG2462|consen 158 SKKAFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSR 199 (279)
T ss_pred ccccccCCCCCceeeehHHHhhHhhccCCCcccccccccccc
Confidence 457888999998864 12368889998864
No 169
>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=42.37 E-value=14 Score=38.31 Aligned_cols=57 Identities=26% Similarity=0.656 Sum_probs=32.3
Q ss_pred EecCccccccCCCCCCeeecCCCCcceecCCcceeeccCCcceeeccc--cccccccCCCCCCCCccccccccc
Q 021215 145 YFCESCKLFDDDTSKKQYHCDGCGICRIGGCDNFFHCNKCRCCYSMLL--KNSHPCVEGAMHHDCPVCCEYLFE 216 (316)
Q Consensus 145 YfC~~Ckl~ddd~~k~~yHC~~CgiCR~G~~~~ffHC~~C~~C~s~~l--~~~H~CiE~~~~~~CPIClE~lf~ 216 (316)
|||..|.-.- |+-|-.... +.+=|..|-.=++.+. ..+.+|..+- .+||+|.-.|..
T Consensus 6 ~fC~~C~~ir------------c~~c~~~Ei-~~~yCp~CL~~~p~~e~~~~~nrC~r~C--f~CP~C~~~L~~ 64 (483)
T PF05502_consen 6 YFCEHCHKIR------------CPRCVSEEI-DSYYCPNCLFEVPSSEARSEKNRCSRNC--FDCPICFSPLSV 64 (483)
T ss_pred eecccccccC------------Chhhccccc-ceeECccccccCChhhheeccceecccc--ccCCCCCCccee
Confidence 8888886551 233333222 3444555555554432 3567887553 479999876644
No 170
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=41.71 E-value=9 Score=44.12 Aligned_cols=52 Identities=25% Similarity=0.464 Sum_probs=39.9
Q ss_pred CCCCCCcccccccccCcceeEEcCCCCcccHHhHHHHhccCCCCCCCCCccccchh
Q 021215 202 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCDMS 257 (316)
Q Consensus 202 ~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiCrks~~d~~ 257 (316)
..+-.|+||++.+-. .-....|||.++..|+..|+.. +..||+|....++..
T Consensus 1151 ~~~~~c~ic~dil~~---~~~I~~cgh~~c~~c~~~~l~~-~s~~~~~ksi~~dfg 1202 (1394)
T KOG0298|consen 1151 SGHFVCEICLDILRN---QGGIAGCGHEPCCRCDELWLYA-SSRCPICKSIKGDFG 1202 (1394)
T ss_pred hcccchHHHHHHHHh---cCCeeeechhHhhhHHHHHHHH-hccCcchhhhhhhhc
Confidence 335589999996543 2235679999999999999985 688999997666543
No 171
>PF02701 zf-Dof: Dof domain, zinc finger; InterPro: IPR003851 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 consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved []. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent
Probab=40.95 E-value=14 Score=28.45 Aligned_cols=14 Identities=43% Similarity=0.971 Sum_probs=12.1
Q ss_pred eecCCCCCCccccc
Q 021215 300 AQKCPNCKSYNTRL 313 (316)
Q Consensus 300 g~kC~~C~SyNT~~ 313 (316)
.++|+.|.|.||+.
T Consensus 5 ~~~CPRC~S~nTKF 18 (63)
T PF02701_consen 5 PLPCPRCDSTNTKF 18 (63)
T ss_pred CCCCCCcCCCCCEE
Confidence 36999999999975
No 172
>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=40.55 E-value=26 Score=22.04 Aligned_cols=20 Identities=25% Similarity=0.617 Sum_probs=13.0
Q ss_pred CCCCCCCccccchhHHHHHhH
Q 021215 244 YACPICSKSVCDMSKVWEKYD 264 (316)
Q Consensus 244 ~~CPiCrks~~d~~~~~~~lD 264 (316)
..||+|.+.+ .+....+-+|
T Consensus 2 v~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLD 21 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHH
Confidence 3599999888 4344445555
No 173
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=40.35 E-value=20 Score=26.27 Aligned_cols=28 Identities=32% Similarity=0.716 Sum_probs=17.1
Q ss_pred cceEecCcc-ccccCCCCCCeeecCCCCc
Q 021215 142 MGEYFCESC-KLFDDDTSKKQYHCDGCGI 169 (316)
Q Consensus 142 f~~YfC~~C-kl~ddd~~k~~yHC~~Cgi 169 (316)
+..|-|..| +.|+.+..+.-..|+.||.
T Consensus 4 ~~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~ 32 (49)
T COG1996 4 MMEYKCARCGREVELDQETRGIRCPYCGS 32 (49)
T ss_pred eEEEEhhhcCCeeehhhccCceeCCCCCc
Confidence 345666666 3445555666777777775
No 174
>PLN02189 cellulose synthase
Probab=40.07 E-value=23 Score=40.21 Aligned_cols=56 Identities=18% Similarity=0.436 Sum_probs=38.8
Q ss_pred cCCCCCCCCcccccccccCcceeEEc---CCCCcccHHhHHHHhccCCCCCCCCCcccc
Q 021215 199 VEGAMHHDCPVCCEYLFETRQDVIVL---PCGHTIHKNCLKEMREHHQYACPICSKSVC 254 (316)
Q Consensus 199 iE~~~~~~CPIClE~lf~s~~~v~~L---pCGH~fH~~Ci~~wl~~~~~~CPiCrks~~ 254 (316)
.++...+.|.||.|++-.....-... -||--.|+.|++-=.+.++..||.|+....
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 34455679999999875333322333 367779999995545667788999996554
No 175
>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=39.39 E-value=32 Score=35.74 Aligned_cols=46 Identities=26% Similarity=0.655 Sum_probs=31.9
Q ss_pred CceeecCCCCcccccccCCCCCCCccc------eEecCccccccCCCCCCeeecCCCCcc
Q 021215 117 VNQVICSLCGTEQKVQQVCVNCGVCMG------EYFCESCKLFDDDTSKKQYHCDGCGIC 170 (316)
Q Consensus 117 v~~V~C~~C~~eq~v~~~C~~Cg~~f~------~YfC~~Ckl~ddd~~k~~yHC~~CgiC 170 (316)
.+.++|..|+.. ..|++|+..+. .-.|..|.+- .+.+..|+.||-=
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 357899999887 57999998874 4457766533 3345677777754
No 176
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=39.02 E-value=7.6 Score=39.92 Aligned_cols=129 Identities=29% Similarity=0.706 Sum_probs=0.0
Q ss_pred ecCCCCcccccc---------------cCCCCCCCcc---------ceEecCccccccCCCCCCeeecCCCC------cc
Q 021215 121 ICSLCGTEQKVQ---------------QVCVNCGVCM---------GEYFCESCKLFDDDTSKKQYHCDGCG------IC 170 (316)
Q Consensus 121 ~C~~C~~eq~v~---------------~~C~~Cg~~f---------~~YfC~~Ckl~ddd~~k~~yHC~~Cg------iC 170 (316)
+|..|+++-.-+ -+|..|+..+ ++-||..| |-|..+| |..|| |=
T Consensus 276 iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~c--yq~tlek----C~~Cg~~I~d~iL 349 (468)
T KOG1701|consen 276 ICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGC--YQDTLEK----CNKCGEPIMDRIL 349 (468)
T ss_pred hhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccccccccCCcccchHH--HHHHHHH----HhhhhhHHHHHHH
Q ss_pred eecCCcceeeccCCcceeeccccccccccCCCCCCCCcccccccccCcceeEEcCCCCcccHHhHHHHhccCCCCCCCCC
Q 021215 171 RIGGCDNFFHCNKCRCCYSMLLKNSHPCVEGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICS 250 (316)
Q Consensus 171 R~G~~~~ffHC~~C~~C~s~~l~~~H~CiE~~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiCr 250 (316)
|.-|+.-.-||-+|=+| |+|++... |+-+..-.+. |+..+-+.--.+|-+|.
T Consensus 350 rA~GkayHp~CF~Cv~C--------~r~ldgip-----------Ftvd~~n~v~---------Cv~dfh~kfAPrCs~C~ 401 (468)
T KOG1701|consen 350 RALGKAYHPGCFTCVVC--------ARCLDGIP-----------FTVDSQNNVY---------CVPDFHKKFAPRCSVCG 401 (468)
T ss_pred HhcccccCCCceEEEEe--------ccccCCcc-----------ccccCCCcee---------eehhhhhhcCcchhhcc
Q ss_pred ccccchhHHHHHhHHHHHcCCCChhhhcCcceEEcCCCCCCccccceeeeecCCCCC
Q 021215 251 KSVCDMSKVWEKYDREIAATPMPEAYLNKKVWILCNDCGKTSNVQFHVLAQKCPNCK 307 (316)
Q Consensus 251 ks~~d~~~~~~~lD~~i~~~pmP~ey~~~~~~IlCnDC~~~s~v~~H~lg~kC~~C~ 307 (316)
++|. |++=++..+-|.+.| -.||+=-.||..|+
T Consensus 402 ~PI~------------------P~~G~~etvRvvamd------r~fHv~CY~CEDCg 434 (468)
T KOG1701|consen 402 NPIL------------------PRDGKDETVRVVAMD------RDFHVNCYKCEDCG 434 (468)
T ss_pred CCcc------------------CCCCCcceEEEEEcc------ccccccceehhhcC
No 177
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=38.06 E-value=20 Score=33.65 Aligned_cols=51 Identities=24% Similarity=0.523 Sum_probs=36.7
Q ss_pred CCCCcccccccccCcceeEEcCCC-----CcccHHhHHHHhcc-CCCCCCCCCcccc
Q 021215 204 HHDCPVCCEYLFETRQDVIVLPCG-----HTIHKNCLKEMREH-HQYACPICSKSVC 254 (316)
Q Consensus 204 ~~~CPIClE~lf~s~~~v~~LpCG-----H~fH~~Ci~~wl~~-~~~~CPiCrks~~ 254 (316)
+..|=||.+..+.+.......||. ...|+.|+..|+.. ++..|.+|.....
T Consensus 78 ~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~ 134 (323)
T KOG1609|consen 78 GPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFI 134 (323)
T ss_pred CCcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhccccCeeeecccccce
Confidence 467999998655432224566873 66899999999864 4577999997554
No 178
>PRK00420 hypothetical protein; Validated
Probab=37.97 E-value=21 Score=30.22 Aligned_cols=22 Identities=23% Similarity=0.452 Sum_probs=14.0
Q ss_pred ccCCCCCCCccc-----eEecCccccc
Q 021215 132 QQVCVNCGVCMG-----EYFCESCKLF 153 (316)
Q Consensus 132 ~~~C~~Cg~~f~-----~YfC~~Ckl~ 153 (316)
+..||.||.+|. ..||+.|.-.
T Consensus 23 ~~~CP~Cg~pLf~lk~g~~~Cp~Cg~~ 49 (112)
T PRK00420 23 SKHCPVCGLPLFELKDGEVVCPVHGKV 49 (112)
T ss_pred cCCCCCCCCcceecCCCceECCCCCCe
Confidence 467888888764 3556665433
No 179
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=37.02 E-value=17 Score=31.93 Aligned_cols=16 Identities=38% Similarity=0.843 Sum_probs=14.1
Q ss_pred eecCCCCCCccccccC
Q 021215 300 AQKCPNCKSYNTRLTR 315 (316)
Q Consensus 300 g~kC~~C~SyNT~~~~ 315 (316)
...|+.|||-||++++
T Consensus 105 ~~~cp~c~s~~t~~~s 120 (146)
T TIGR02159 105 SVQCPRCGSADTTITS 120 (146)
T ss_pred CCcCCCCCCCCcEeec
Confidence 4699999999999875
No 180
>PLN02436 cellulose synthase A
Probab=36.64 E-value=28 Score=39.71 Aligned_cols=56 Identities=20% Similarity=0.445 Sum_probs=39.2
Q ss_pred cCCCCCCCCcccccccccCcceeEEcC---CCCcccHHhHHHHhccCCCCCCCCCcccc
Q 021215 199 VEGAMHHDCPVCCEYLFETRQDVIVLP---CGHTIHKNCLKEMREHHQYACPICSKSVC 254 (316)
Q Consensus 199 iE~~~~~~CPIClE~lf~s~~~v~~Lp---CGH~fH~~Ci~~wl~~~~~~CPiCrks~~ 254 (316)
.+....+.|.||.+++-.+.+.-.... ||--.|+.|++-=.+.++..||.|+....
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 444556799999998754433333443 67779999995545667788999996554
No 181
>PRK00366 ispG 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed
Probab=36.54 E-value=46 Score=33.61 Aligned_cols=53 Identities=19% Similarity=0.453 Sum_probs=42.7
Q ss_pred CCCCCCCccccchhHHHHHhHHHHHcCCCChhhhcCcceEEc--CCCCCCccccceeee
Q 021215 244 YACPICSKSVCDMSKVWEKYDREIAATPMPEAYLNKKVWILC--NDCGKTSNVQFHVLA 300 (316)
Q Consensus 244 ~~CPiCrks~~d~~~~~~~lD~~i~~~pmP~ey~~~~~~IlC--nDC~~~s~v~~H~lg 300 (316)
..||.|++...|.-..-..+++.+...++| -+.+..=| |-|+......+=+.|
T Consensus 269 isCPgCgR~~~D~~~la~~vee~~~~~~~P----lkIAVmGC~VNgpGEa~~aDIGIaG 323 (360)
T PRK00366 269 ISCPTCGRTEFDVIQELAEVEQRLEHIKMP----LKVAVMGCVVNGPGEAKEADIGIAG 323 (360)
T ss_pred EECCCCCCCcccHHHHHHHHHHHhcCCCCC----cEEEEeCCCCCCCCchhhCcEeEec
Confidence 459999999999888888999999988888 34456678 899988777765554
No 182
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=36.48 E-value=13 Score=33.96 Aligned_cols=29 Identities=31% Similarity=0.553 Sum_probs=23.3
Q ss_pred CCCCCcccccccccCcceeEEcCCCCcccH
Q 021215 203 MHHDCPVCCEYLFETRQDVIVLPCGHTIHK 232 (316)
Q Consensus 203 ~~~~CPIClE~lf~s~~~v~~LpCGH~fH~ 232 (316)
...+|.||||+|.. ++.+.-|||=-.||+
T Consensus 176 dkGECvICLEdL~~-GdtIARLPCLCIYHK 204 (205)
T KOG0801|consen 176 DKGECVICLEDLEA-GDTIARLPCLCIYHK 204 (205)
T ss_pred cCCcEEEEhhhccC-CCceeccceEEEeec
Confidence 36799999998664 567889999877775
No 183
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=36.44 E-value=15 Score=36.51 Aligned_cols=30 Identities=27% Similarity=0.752 Sum_probs=22.9
Q ss_pred EEcCCCCcccHHhHHHHhccCCCCCCCCCcccc
Q 021215 222 IVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 254 (316)
Q Consensus 222 ~~LpCGH~fH~~Ci~~wl~~~~~~CPiCrks~~ 254 (316)
+++||.|+|+.+|...- ..-.||.|.-.+.
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 58899999999998543 2357999985554
No 184
>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=36.07 E-value=38 Score=23.26 Aligned_cols=31 Identities=35% Similarity=0.875 Sum_probs=20.2
Q ss_pred ccCCCCCCCccceEecCccccccCCCCCCeeecCCCCc
Q 021215 132 QQVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGI 169 (316)
Q Consensus 132 ~~~C~~Cg~~f~~YfC~~Ckl~ddd~~k~~yHC~~Cgi 169 (316)
...||.||..=. | + |+|...+.-|+|..||.
T Consensus 3 ~~pCP~CGG~Dr--F----r-~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 3 HGPCPNCGGSDR--F----R-FDDKDGRGTWFCSVCGA 33 (37)
T ss_pred ccCCCCCCCccc--c----c-cccCCCCcCEEeCCCCC
Confidence 357889987311 1 2 46666678888888764
No 185
>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=36.02 E-value=28 Score=29.85 Aligned_cols=47 Identities=21% Similarity=0.469 Sum_probs=33.3
Q ss_pred CCCccceEecCccccccCCCCCCeeecCCCCcceecCCcceeeccCCcceeec
Q 021215 138 CGVCMGEYFCESCKLFDDDTSKKQYHCDGCGICRIGGCDNFFHCNKCRCCYSM 190 (316)
Q Consensus 138 Cg~~f~~YfC~~Ckl~ddd~~k~~yHC~~CgiCR~G~~~~ffHC~~C~~C~s~ 190 (316)
.+......+|.+|+.+-- ....||..||.|-.+ --.||.==|.|+..
T Consensus 42 ~~~~~~~~~C~~C~~~kp---~Rs~HC~~C~~CV~~---~DHHC~w~~~cIG~ 88 (174)
T PF01529_consen 42 DDENGELKYCSTCKIIKP---PRSHHCRVCNRCVLR---FDHHCPWLGNCIGR 88 (174)
T ss_pred cccCCCCEECcccCCcCC---Ccceecccccccccc---ccccchhhcccccc
Confidence 456777889999998833 257788888888774 23577777777654
No 186
>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=35.71 E-value=21 Score=20.65 Aligned_cols=15 Identities=53% Similarity=1.112 Sum_probs=11.6
Q ss_pred CCCCCCCccccchhH
Q 021215 244 YACPICSKSVCDMSK 258 (316)
Q Consensus 244 ~~CPiCrks~~d~~~ 258 (316)
|.||.|.+.+.....
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 469999998887654
No 187
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=35.34 E-value=25 Score=25.47 Aligned_cols=9 Identities=44% Similarity=1.505 Sum_probs=5.3
Q ss_pred CeeecCCCC
Q 021215 160 KQYHCDGCG 168 (316)
Q Consensus 160 ~~yHC~~Cg 168 (316)
..|+|..||
T Consensus 36 ~r~~C~~Cg 44 (50)
T PRK00432 36 DRWHCGKCG 44 (50)
T ss_pred CcEECCCcC
Confidence 456666665
No 188
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=34.79 E-value=34 Score=25.29 Aligned_cols=29 Identities=31% Similarity=0.826 Sum_probs=22.4
Q ss_pred ceEEcCCCCCCccccceeeeecCCCCCCcccccc
Q 021215 281 VWILCNDCGKTSNVQFHVLAQKCPNCKSYNTRLT 314 (316)
Q Consensus 281 ~~IlCnDC~~~s~v~~H~lg~kC~~C~SyNT~~~ 314 (316)
..+.|..|++- ...| +-|+.||.|+-+++
T Consensus 25 ~l~~C~~cG~~--~~~H---~vc~~cG~Y~gr~v 53 (55)
T TIGR01031 25 TLVVCPNCGEF--KLPH---RVCPSCGYYKGRQV 53 (55)
T ss_pred cceECCCCCCc--ccCe---eECCccCeECCEEc
Confidence 45779999973 4455 45999999999886
No 189
>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=34.29 E-value=31 Score=22.57 Aligned_cols=25 Identities=28% Similarity=0.787 Sum_probs=15.9
Q ss_pred eEecCccccccCCCCCCeeecCCCCc
Q 021215 144 EYFCESCKLFDDDTSKKQYHCDGCGI 169 (316)
Q Consensus 144 ~YfC~~Ckl~ddd~~k~~yHC~~Cgi 169 (316)
+|-|.+|-+.-+ +.+.++.|+.||.
T Consensus 1 ~~~C~~CGy~y~-~~~~~~~CP~Cg~ 25 (33)
T cd00350 1 KYVCPVCGYIYD-GEEAPWVCPVCGA 25 (33)
T ss_pred CEECCCCCCEEC-CCcCCCcCcCCCC
Confidence 366777765433 3457788888864
No 190
>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=34.19 E-value=23 Score=22.56 Aligned_cols=20 Identities=25% Similarity=0.718 Sum_probs=6.1
Q ss_pred CCcceecCCc-ceeeccCCcc
Q 021215 167 CGICRIGGCD-NFFHCNKCRC 186 (316)
Q Consensus 167 CgiCR~G~~~-~ffHC~~C~~ 186 (316)
|.+|+..+.. .+|+|..|+.
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 191
>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=33.75 E-value=28 Score=24.44 Aligned_cols=13 Identities=23% Similarity=0.697 Sum_probs=8.5
Q ss_pred ccCCCCCCCccce
Q 021215 132 QQVCVNCGVCMGE 144 (316)
Q Consensus 132 ~~~C~~Cg~~f~~ 144 (316)
+..|+.||.++-+
T Consensus 17 ~~~Cp~C~~PL~~ 29 (41)
T PF06677_consen 17 DEHCPDCGTPLMR 29 (41)
T ss_pred cCccCCCCCeeEE
Confidence 4577777776633
No 192
>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=33.73 E-value=26 Score=25.38 Aligned_cols=22 Identities=23% Similarity=0.792 Sum_probs=14.0
Q ss_pred cccCCC--CCCCc------cceEecCcccc
Q 021215 131 VQQVCV--NCGVC------MGEYFCESCKL 152 (316)
Q Consensus 131 v~~~C~--~Cg~~------f~~YfC~~Ckl 152 (316)
....|| .||.- ++|++|++|.+
T Consensus 17 ~rk~CP~~~CG~GvFMA~H~dR~~CGKCg~ 46 (47)
T PF01599_consen 17 LRKECPSPRCGAGVFMAEHKDRHYCGKCGY 46 (47)
T ss_dssp SSEE-TSTTTTSSSEEEE-SSEEEETTTSS
T ss_pred hhhcCCCcccCCceEeeecCCCccCCCccc
Confidence 456788 78774 26777777754
No 193
>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=33.73 E-value=21 Score=23.31 Aligned_cols=16 Identities=38% Similarity=1.026 Sum_probs=7.4
Q ss_pred CCCCCCccceEecCccc
Q 021215 135 CVNCGVCMGEYFCESCK 151 (316)
Q Consensus 135 C~~Cg~~f~~YfC~~Ck 151 (316)
|.-||. .++|.|+.|.
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 5555555554
No 194
>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=33.52 E-value=23 Score=30.30 Aligned_cols=39 Identities=28% Similarity=0.606 Sum_probs=25.8
Q ss_pred CCCCCCeeecCCCCcceecCCcceeeccCCcceeecccccccccc
Q 021215 155 DDTSKKQYHCDGCGICRIGGCDNFFHCNKCRCCYSMLLKNSHPCV 199 (316)
Q Consensus 155 dd~~k~~yHC~~CgiCR~G~~~~ffHC~~C~~C~s~~l~~~H~Ci 199 (316)
++.....-.|.. |++-....-.||..||.|+-.- .|.|.
T Consensus 42 ~~~~~~~~~C~~---C~~~kp~Rs~HC~~C~~CV~~~---DHHC~ 80 (174)
T PF01529_consen 42 DDENGELKYCST---CKIIKPPRSHHCRVCNRCVLRF---DHHCP 80 (174)
T ss_pred cccCCCCEECcc---cCCcCCCcceeccccccccccc---cccch
Confidence 333444455555 5555667899999999998754 46655
No 195
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=33.31 E-value=31 Score=24.36 Aligned_cols=25 Identities=20% Similarity=0.789 Sum_probs=14.7
Q ss_pred EEcCCCCCCccccceeeeecCCCCCC
Q 021215 283 ILCNDCGKTSNVQFHVLAQKCPNCKS 308 (316)
Q Consensus 283 IlCnDC~~~s~v~~H~lg~kC~~C~S 308 (316)
..|-+|+...... ---+.+|+.||+
T Consensus 3 Y~C~~Cg~~~~~~-~~~~irC~~CG~ 27 (44)
T smart00659 3 YICGECGRENEIK-SKDVVRCRECGY 27 (44)
T ss_pred EECCCCCCEeecC-CCCceECCCCCc
Confidence 4577777654443 224567777765
No 196
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=33.24 E-value=14 Score=32.95 Aligned_cols=25 Identities=32% Similarity=0.883 Sum_probs=17.5
Q ss_pred ceEecCccccccCCCCCCeeecCCCC--cceec
Q 021215 143 GEYFCESCKLFDDDTSKKQYHCDGCG--ICRIG 173 (316)
Q Consensus 143 ~~YfC~~Ckl~ddd~~k~~yHC~~Cg--iCR~G 173 (316)
.+-||++|-+| ++|-|-.|| +|-|+
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 45677777754 568888887 67665
No 197
>PF15616 TerY-C: TerY-C metal binding domain
Probab=33.09 E-value=40 Score=29.37 Aligned_cols=34 Identities=35% Similarity=0.767 Sum_probs=23.3
Q ss_pred ccCCCCCCCccceEecCcc-cccc-CCCCCCeeecCCCC
Q 021215 132 QQVCVNCGVCMGEYFCESC-KLFD-DDTSKKQYHCDGCG 168 (316)
Q Consensus 132 ~~~C~~Cg~~f~~YfC~~C-kl~d-dd~~k~~yHC~~Cg 168 (316)
...||.||..+|---| .| ||+- +++ ...+|+-||
T Consensus 77 ~PgCP~CGn~~~fa~C-~CGkl~Ci~g~--~~~~CPwCg 112 (131)
T PF15616_consen 77 APGCPHCGNQYAFAVC-GCGKLFCIDGE--GEVTCPWCG 112 (131)
T ss_pred CCCCCCCcChhcEEEe-cCCCEEEeCCC--CCEECCCCC
Confidence 3689999999998888 58 5653 221 255666665
No 198
>PRK14873 primosome assembly protein PriA; Provisional
Probab=33.04 E-value=36 Score=36.79 Aligned_cols=49 Identities=27% Similarity=0.606 Sum_probs=30.7
Q ss_pred CCccC-ceeecCCCCcccccccCCCCCCCccce------EecCccccccCCCCCCeeecCCCCcc
Q 021215 113 PRHEV-NQVICSLCGTEQKVQQVCVNCGVCMGE------YFCESCKLFDDDTSKKQYHCDGCGIC 170 (316)
Q Consensus 113 dR~~v-~~V~C~~C~~eq~v~~~C~~Cg~~f~~------YfC~~Ckl~ddd~~k~~yHC~~CgiC 170 (316)
+|..- ..+.|..|++. ..|++|+..+.- -.|.-|.+- ..+..|+.||-=
T Consensus 376 nRrGyap~l~C~~Cg~~----~~C~~C~~~L~~h~~~~~l~Ch~CG~~-----~~p~~Cp~Cgs~ 431 (665)
T PRK14873 376 PRRGYVPSLACARCRTP----ARCRHCTGPLGLPSAGGTPRCRWCGRA-----APDWRCPRCGSD 431 (665)
T ss_pred cCCCCCCeeEhhhCcCe----eECCCCCCceeEecCCCeeECCCCcCC-----CcCccCCCCcCC
Confidence 44433 57799999886 579999988852 345555531 135566666643
No 199
>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=32.86 E-value=14 Score=40.90 Aligned_cols=46 Identities=28% Similarity=0.590 Sum_probs=0.0
Q ss_pred cCCCCCCCccceEecCccccccCCCCCCeeecCCCCcceecCCcceeeccCCcce
Q 021215 133 QVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGICRIGGCDNFFHCNKCRCC 187 (316)
Q Consensus 133 ~~C~~Cg~~f~~YfC~~Ckl~ddd~~k~~yHC~~CgiCR~G~~~~ffHC~~C~~C 187 (316)
-.|++||..--.-.|+.|.-.. ...|.|+.||+ ++. -.+|.+||.=
T Consensus 656 r~Cp~Cg~~t~~~~Cp~CG~~T----~~~~~Cp~C~~-~~~----~~~C~~C~~~ 701 (900)
T PF03833_consen 656 RRCPKCGKETFYNRCPECGSHT----EPVYVCPDCGI-EVE----EDECPKCGRE 701 (900)
T ss_dssp -------------------------------------------------------
T ss_pred ccCcccCCcchhhcCcccCCcc----ccceecccccc-ccC----cccccccccc
Confidence 4688888887777788886553 46888888877 322 1278888753
No 200
>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=32.22 E-value=30 Score=23.58 Aligned_cols=31 Identities=29% Similarity=0.724 Sum_probs=15.6
Q ss_pred CCCCCCCccceEecCccccc---cCCCCCCeeecCCCC
Q 021215 134 VCVNCGVCMGEYFCESCKLF---DDDTSKKQYHCDGCG 168 (316)
Q Consensus 134 ~C~~Cg~~f~~YfC~~Ckl~---ddd~~k~~yHC~~Cg 168 (316)
.||+||+.-+-|| ..= -|.+..-.|.|-+||
T Consensus 2 ~Cp~Cg~~~a~~~----~~Q~rsaDE~~T~fy~C~~C~ 35 (39)
T PF01096_consen 2 KCPKCGHNEAVFF----QIQTRSADEPMTLFYVCCNCG 35 (39)
T ss_dssp --SSS-SSEEEEE----EESSSSSSSSSEEEEEESSST
T ss_pred CCcCCCCCeEEEE----EeeccCCCCCCeEEEEeCCCC
Confidence 4788888776666 111 233445566666665
No 201
>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=32.17 E-value=15 Score=40.77 Aligned_cols=32 Identities=31% Similarity=0.811 Sum_probs=0.0
Q ss_pred eecCCCCcccccccCCCCCCCc-cceEecCcccc
Q 021215 120 VICSLCGTEQKVQQVCVNCGVC-MGEYFCESCKL 152 (316)
Q Consensus 120 V~C~~C~~eq~v~~~C~~Cg~~-f~~YfC~~Ckl 152 (316)
-.|..|+++ +....|+.||.. .-.|+|+.|+.
T Consensus 656 r~Cp~Cg~~-t~~~~Cp~CG~~T~~~~~Cp~C~~ 688 (900)
T PF03833_consen 656 RRCPKCGKE-TFYNRCPECGSHTEPVYVCPDCGI 688 (900)
T ss_dssp ----------------------------------
T ss_pred ccCcccCCc-chhhcCcccCCccccceecccccc
Confidence 345555555 444556666544 23455666654
No 202
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=32.08 E-value=42 Score=33.70 Aligned_cols=77 Identities=23% Similarity=0.558 Sum_probs=48.6
Q ss_pred ccC--CCCCCeeecCCCCcceecC-CcceeeccCCcceeecc---ccccccccCCCCCCCCcccccccccCcceeEEcCC
Q 021215 153 FDD--DTSKKQYHCDGCGICRIGG-CDNFFHCNKCRCCYSML---LKNSHPCVEGAMHHDCPVCCEYLFETRQDVIVLPC 226 (316)
Q Consensus 153 ~dd--d~~k~~yHC~~CgiCR~G~-~~~ffHC~~C~~C~s~~---l~~~H~CiE~~~~~~CPIClE~lf~s~~~v~~LpC 226 (316)
||| .+.+-+-||+.| |--|. .|=||.| +++.+.. .-..|-=..|.-...|-.|-+ -++++.+++|
T Consensus 169 WdDVLks~Ripg~Ces~--~~pg~fAEFfFKC---~ah~~~~k~~aa~lhli~~N~~ni~C~~Ctd----v~~~vlvf~C 239 (446)
T KOG0006|consen 169 WDDVLKSKRIPGVCESC--CTPGLFAEFFFKC---GAHPTSDKETAAALHLIATNSRNITCITCTD----VRSPVLVFQC 239 (446)
T ss_pred hhhhhhcccCccccccc--cCCcchHhheehh---ccCCCccccchhHHHHhhcccccceeEEecC----CccceEEEec
Confidence 776 245678888877 44444 4666654 5554431 011132233455678999986 2347888999
Q ss_pred C--CcccHHhHHHH
Q 021215 227 G--HTIHKNCLKEM 238 (316)
Q Consensus 227 G--H~fH~~Ci~~w 238 (316)
. |..+..|+.-|
T Consensus 240 ns~HvtC~dCFr~y 253 (446)
T KOG0006|consen 240 NSRHVTCLDCFRLY 253 (446)
T ss_pred CCceeehHHhhhhH
Confidence 8 99999999865
No 203
>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=31.33 E-value=35 Score=21.61 Aligned_cols=18 Identities=28% Similarity=0.920 Sum_probs=7.9
Q ss_pred cCCCCCCCcc--------ceEecCcc
Q 021215 133 QVCVNCGVCM--------GEYFCESC 150 (316)
Q Consensus 133 ~~C~~Cg~~f--------~~YfC~~C 150 (316)
+.|+.|+..+ +.|||+.|
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 4566666554 34666665
No 204
>cd01675 RNR_III Class III ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit w
Probab=31.29 E-value=41 Score=35.47 Aligned_cols=30 Identities=33% Similarity=0.727 Sum_probs=22.3
Q ss_pred cceEEcCCCCCCccccceeeeecCCCCCCcccccc
Q 021215 280 KVWILCNDCGKTSNVQFHVLAQKCPNCKSYNTRLT 314 (316)
Q Consensus 280 ~~~IlCnDC~~~s~v~~H~lg~kC~~C~SyNT~~~ 314 (316)
... .|++|+.... -.+.+||.|||-|+.++
T Consensus 517 p~~-~C~~CG~~~~----~~~~~CP~CGs~~~~~~ 546 (555)
T cd01675 517 PID-ICNDCGYIGE----GEGFKCPKCGSEDVEVI 546 (555)
T ss_pred CCc-cCCCCCCCCc----CCCCCCcCCCCcCceEE
Confidence 344 8999997554 35689999999886554
No 205
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=30.95 E-value=40 Score=23.47 Aligned_cols=9 Identities=33% Similarity=1.313 Sum_probs=5.3
Q ss_pred CeeecCCCC
Q 021215 160 KQYHCDGCG 168 (316)
Q Consensus 160 ~~yHC~~Cg 168 (316)
..|-|+.||
T Consensus 19 ~~~vC~~Cg 27 (52)
T smart00661 19 RRFVCRKCG 27 (52)
T ss_pred CEEECCcCC
Confidence 356666665
No 206
>KOG1312 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=30.63 E-value=14 Score=36.51 Aligned_cols=32 Identities=28% Similarity=0.735 Sum_probs=26.8
Q ss_pred CCCCcceecCCcceeeccCCcceeecccccccccc
Q 021215 165 DGCGICRIGGCDNFFHCNKCRCCYSMLLKNSHPCV 199 (316)
Q Consensus 165 ~~CgiCR~G~~~~ffHC~~C~~C~s~~l~~~H~Ci 199 (316)
-+|..|++.+.-...||..||.|+.+- .|.|+
T Consensus 149 ~kCSTCki~KPARSKHCsiCNrCV~rf---DHHCi 180 (341)
T KOG1312|consen 149 VKCSTCKIRKPARSKHCSICNRCVHRF---DHHCI 180 (341)
T ss_pred CccccccCCCccccccchHHHHHHHHh---ccceE
Confidence 568888888888899999999998754 58887
No 207
>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=30.56 E-value=34 Score=23.75 Aligned_cols=20 Identities=30% Similarity=0.856 Sum_probs=11.0
Q ss_pred eecCCCCcceecCCcceeeccCCc
Q 021215 162 YHCDGCGICRIGGCDNFFHCNKCR 185 (316)
Q Consensus 162 yHC~~CgiCR~G~~~~ffHC~~C~ 185 (316)
|+|+.|+- +++ ..|||..|.
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 55666654 322 556666663
No 208
>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=30.50 E-value=40 Score=22.47 Aligned_cols=21 Identities=24% Similarity=0.360 Sum_probs=15.1
Q ss_pred cCCCCCCCccceEecCccccc
Q 021215 133 QVCVNCGVCMGEYFCESCKLF 153 (316)
Q Consensus 133 ~~C~~Cg~~f~~YfC~~Ckl~ 153 (316)
..|..++....+|||..|+.+
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 467778877788888888754
No 209
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=30.26 E-value=33 Score=22.78 Aligned_cols=11 Identities=27% Similarity=0.836 Sum_probs=6.0
Q ss_pred CCCeeecCCCC
Q 021215 158 SKKQYHCDGCG 168 (316)
Q Consensus 158 ~k~~yHC~~Cg 168 (316)
..++-.|..||
T Consensus 14 ~~~~irC~~CG 24 (32)
T PF03604_consen 14 PGDPIRCPECG 24 (32)
T ss_dssp TSSTSSBSSSS
T ss_pred CCCcEECCcCC
Confidence 34455666665
No 210
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=30.00 E-value=41 Score=33.71 Aligned_cols=49 Identities=16% Similarity=0.315 Sum_probs=35.1
Q ss_pred CCCCCCcccccccccCcceeEEcCCCCcccHHhHHHHhccCCCCCCCCCcccc
Q 021215 202 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 254 (316)
Q Consensus 202 ~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiCrks~~ 254 (316)
.....||||+...- .+.+.--=|-.||-.|+..++. ....||+=..++.
T Consensus 298 ~~~~~CpvClk~r~---Nptvl~vSGyVfCY~Ci~~Yv~-~~~~CPVT~~p~~ 346 (357)
T KOG0826|consen 298 PDREVCPVCLKKRQ---NPTVLEVSGYVFCYPCIFSYVV-NYGHCPVTGYPAS 346 (357)
T ss_pred CccccChhHHhccC---CCceEEecceEEeHHHHHHHHH-hcCCCCccCCcch
Confidence 44678999996322 2333333499999999999997 4578998776654
No 211
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=29.89 E-value=9.6 Score=36.10 Aligned_cols=49 Identities=27% Similarity=0.588 Sum_probs=35.7
Q ss_pred CCCcccccccc--cCcceeEEcC--------CCCcccHHhHHHHhccCCCCCCCCCccc
Q 021215 205 HDCPVCCEYLF--ETRQDVIVLP--------CGHTIHKNCLKEMREHHQYACPICSKSV 253 (316)
Q Consensus 205 ~~CPIClE~lf--~s~~~v~~Lp--------CGH~fH~~Ci~~wl~~~~~~CPiCrks~ 253 (316)
..|.||..... +....+.++. |||+.+..|++..+......||.|++..
T Consensus 208 ~~c~ic~~~~~~n~~~~~p~vl~~~~~~~~~c~htlc~~c~~~~l~~~~~~cp~~~~~~ 266 (296)
T KOG4185|consen 208 KLCEICERIYSENDEKLAPLVLSLSRLKEKIEGHTLCKECIDTILLQAGIKCPFCTWSH 266 (296)
T ss_pred HHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcchHHHHHHhhhcCCccccee
Confidence 56888876433 1233445667 9999999999998765457899999753
No 212
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=29.78 E-value=30 Score=32.98 Aligned_cols=20 Identities=25% Similarity=0.884 Sum_probs=16.5
Q ss_pred ccCCCCCCCcc--------ceEecCccc
Q 021215 132 QQVCVNCGVCM--------GEYFCESCK 151 (316)
Q Consensus 132 ~~~C~~Cg~~f--------~~YfC~~Ck 151 (316)
++.|+.||..+ +.|||+.|.
T Consensus 244 g~pCprCG~~I~~~~~~gR~t~~CP~CQ 271 (272)
T PRK14810 244 GEPCLNCKTPIRRVVVAGRSSHYCPHCQ 271 (272)
T ss_pred CCcCCCCCCeeEEEEECCCccEECcCCc
Confidence 47899999888 678898885
No 213
>PHA00626 hypothetical protein
Probab=29.69 E-value=35 Score=25.88 Aligned_cols=34 Identities=21% Similarity=0.450 Sum_probs=22.0
Q ss_pred eecCCCCcccccccCCCCCCCccceEecCccccccC
Q 021215 120 VICSLCGTEQKVQQVCVNCGVCMGEYFCESCKLFDD 155 (316)
Q Consensus 120 V~C~~C~~eq~v~~~C~~Cg~~f~~YfC~~Ckl~dd 155 (316)
|.|..|+..+-+ .|.-|...-++|-|..|.+++.
T Consensus 1 m~CP~CGS~~Iv--rcg~cr~~snrYkCkdCGY~ft 34 (59)
T PHA00626 1 MSCPKCGSGNIA--KEKTMRGWSDDYVCCDCGYNDS 34 (59)
T ss_pred CCCCCCCCceee--eeceecccCcceEcCCCCCeec
Confidence 356667665443 4555666667888888877754
No 214
>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=29.63 E-value=76 Score=23.99 Aligned_cols=51 Identities=18% Similarity=0.421 Sum_probs=33.7
Q ss_pred CCCCCcccccccccCcceeEEcCCCCcccHHhHHHHhccCCCCCCCCCccccch
Q 021215 203 MHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCDM 256 (316)
Q Consensus 203 ~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiCrks~~d~ 256 (316)
+.-+|-.|-.+|..+..+..+-.=--+|+..|.+..|. ..||-|+..+..+
T Consensus 4 lrpnCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~---~~CPNCgGelv~R 54 (57)
T PF06906_consen 4 LRPNCECCDKDLPPDSPEAYICSFECTFCADCAETMLN---GVCPNCGGELVRR 54 (57)
T ss_pred cCCCccccCCCCCCCCCcceEEeEeCcccHHHHHHHhc---CcCcCCCCccccC
Confidence 34577778777655432222211135799999999985 5799999877653
No 215
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=29.60 E-value=29 Score=30.27 Aligned_cols=20 Identities=40% Similarity=1.067 Sum_probs=14.2
Q ss_pred ccCCCCCCCcc----ceEecCccc
Q 021215 132 QQVCVNCGVCM----GEYFCESCK 151 (316)
Q Consensus 132 ~~~C~~Cg~~f----~~YfC~~Ck 151 (316)
+..||.||.++ |+-||++|-
T Consensus 28 ~~hCp~Cg~PLF~KdG~v~CPvC~ 51 (131)
T COG1645 28 AKHCPKCGTPLFRKDGEVFCPVCG 51 (131)
T ss_pred HhhCcccCCcceeeCCeEECCCCC
Confidence 46788888887 555677664
No 216
>PRK10445 endonuclease VIII; Provisional
Probab=29.43 E-value=32 Score=32.68 Aligned_cols=20 Identities=30% Similarity=0.953 Sum_probs=16.3
Q ss_pred ccCCCCCCCcc--------ceEecCccc
Q 021215 132 QQVCVNCGVCM--------GEYFCESCK 151 (316)
Q Consensus 132 ~~~C~~Cg~~f--------~~YfC~~Ck 151 (316)
++.|+.||... +.|||+.|.
T Consensus 235 g~~Cp~Cg~~I~~~~~~gR~t~~CP~CQ 262 (263)
T PRK10445 235 GEACERCGGIIEKTTLSSRPFYWCPGCQ 262 (263)
T ss_pred CCCCCCCCCEeEEEEECCCCcEECCCCc
Confidence 57899999988 568888875
No 217
>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=29.36 E-value=36 Score=23.70 Aligned_cols=21 Identities=43% Similarity=0.947 Sum_probs=10.5
Q ss_pred eecCCCCcceecCCcceeeccCCc
Q 021215 162 YHCDGCGICRIGGCDNFFHCNKCR 185 (316)
Q Consensus 162 yHC~~CgiCR~G~~~~ffHC~~C~ 185 (316)
|.|+.|+. -+- ...|||..|.
T Consensus 1 ~~C~~C~~-~i~--g~r~~C~~C~ 21 (46)
T cd02249 1 YSCDGCLK-PIV--GVRYHCLVCE 21 (46)
T ss_pred CCCcCCCC-CCc--CCEEECCCCC
Confidence 44555555 222 2466666654
No 218
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=29.35 E-value=32 Score=32.85 Aligned_cols=21 Identities=38% Similarity=0.961 Sum_probs=17.0
Q ss_pred ccCCCCCCCcc--------ceEecCcccc
Q 021215 132 QQVCVNCGVCM--------GEYFCESCKL 152 (316)
Q Consensus 132 ~~~C~~Cg~~f--------~~YfC~~Ckl 152 (316)
++.|+.||..+ +.|||+.|.-
T Consensus 235 g~pC~~Cg~~I~~~~~~gR~ty~Cp~CQ~ 263 (269)
T PRK14811 235 GQPCPRCGTPIEKIVVGGRGTHFCPQCQP 263 (269)
T ss_pred cCCCCcCCCeeEEEEECCCCcEECCCCcC
Confidence 46899999888 6799999863
No 219
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=29.29 E-value=38 Score=22.77 Aligned_cols=10 Identities=30% Similarity=0.843 Sum_probs=5.2
Q ss_pred eecCCCCCcc
Q 021215 80 IRAPCCNEIF 89 (316)
Q Consensus 80 l~~pcC~~~y 89 (316)
|.||.|+.-|
T Consensus 3 i~Cp~C~~~y 12 (36)
T PF13717_consen 3 ITCPNCQAKY 12 (36)
T ss_pred EECCCCCCEE
Confidence 4555555544
No 220
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=28.95 E-value=26 Score=38.01 Aligned_cols=48 Identities=29% Similarity=0.681 Sum_probs=37.3
Q ss_pred CCCCcccccccccCcceeEEcCCCCcccHHhHHHHhcc--CCCCCCCCCccccc
Q 021215 204 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH--HQYACPICSKSVCD 255 (316)
Q Consensus 204 ~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~--~~~~CPiCrks~~d 255 (316)
...||||++..++. +.+.|-|.|...|+..-+.. ..-.||+|+..+..
T Consensus 21 ~lEc~ic~~~~~~p----~~~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~eK 70 (684)
T KOG4362|consen 21 ILECPICLEHVKEP----SLLKCDHIFLKFCLNKLFESKKGPKQCALCKSDIEK 70 (684)
T ss_pred hccCCceeEEeecc----chhhhhHHHHhhhhhceeeccCccccchhhhhhhhh
Confidence 57899999977762 68899999999999884432 23569999976653
No 221
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=28.90 E-value=34 Score=34.83 Aligned_cols=38 Identities=24% Similarity=0.572 Sum_probs=30.1
Q ss_pred CCCCCCCcccccccccCcceeEEcCCCCcccHHhHHHHhcc
Q 021215 201 GAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH 241 (316)
Q Consensus 201 ~~~~~~CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~ 241 (316)
......|.||.+. +.. ....+.|||.|+..|...++..
T Consensus 67 ~~~~~~c~ic~~~-~~~--~~~~~~c~H~~c~~cw~~yl~~ 104 (444)
T KOG1815|consen 67 KKGDVQCGICVES-YDG--EIIGLGCGHPFCPPCWTGYLGT 104 (444)
T ss_pred CCccccCCcccCC-Ccc--hhhhcCCCcHHHHHHHHHHhhh
Confidence 3557889999984 332 4678899999999999999864
No 222
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=28.88 E-value=36 Score=25.11 Aligned_cols=20 Identities=30% Similarity=0.926 Sum_probs=12.2
Q ss_pred ccCCCCCCC--cc----ceEecCccc
Q 021215 132 QQVCVNCGV--CM----GEYFCESCK 151 (316)
Q Consensus 132 ~~~C~~Cg~--~f----~~YfC~~Ck 151 (316)
...||+||. -| .+|.|++|.
T Consensus 19 ~~~CPrCG~gvfmA~H~dR~~CGkCg 44 (51)
T COG1998 19 NRFCPRCGPGVFMADHKDRWACGKCG 44 (51)
T ss_pred cccCCCCCCcchhhhcCceeEecccc
Confidence 457889983 33 456666654
No 223
>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=28.79 E-value=57 Score=32.09 Aligned_cols=23 Identities=26% Similarity=0.931 Sum_probs=12.9
Q ss_pred eEEcCCCCCCccccceeeeecCCCCCC
Q 021215 282 WILCNDCGKTSNVQFHVLAQKCPNCKS 308 (316)
Q Consensus 282 ~IlCnDC~~~s~v~~H~lg~kC~~C~S 308 (316)
.-.|.-|+ ..||+.-.||++|++
T Consensus 210 yL~CslC~----teW~~~R~~C~~Cg~ 232 (305)
T TIGR01562 210 YLSCSLCA----TEWHYVRVKCSHCEE 232 (305)
T ss_pred EEEcCCCC----CcccccCccCCCCCC
Confidence 44565555 455555566666654
No 224
>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=28.78 E-value=22 Score=24.29 Aligned_cols=13 Identities=38% Similarity=1.076 Sum_probs=5.6
Q ss_pred cceEecCcccccc
Q 021215 142 MGEYFCESCKLFD 154 (316)
Q Consensus 142 f~~YfC~~Ckl~d 154 (316)
|-+|||+-|+.|=
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 225
>KOG4399 consensus C2HC-type Zn-finger protein [General function prediction only]
Probab=28.73 E-value=11 Score=36.51 Aligned_cols=73 Identities=26% Similarity=0.610 Sum_probs=53.5
Q ss_pred CCCccceEecCccccccCCCCCCeeecCCCCcceecCCcceeeccCCcceeeccccccccccCCCCCCCCcccccc
Q 021215 138 CGVCMGEYFCESCKLFDDDTSKKQYHCDGCGICRIGGCDNFFHCNKCRCCYSMLLKNSHPCVEGAMHHDCPVCCEY 213 (316)
Q Consensus 138 Cg~~f~~YfC~~Ckl~ddd~~k~~yHC~~CgiCR~G~~~~ffHC~~C~~C~s~~l~~~H~CiE~~~~~~CPIClE~ 213 (316)
=|..=+-.||+.|..| .++-.-||+.|+.|..-.++.|-||.+|-.|+-.++..--.|..-+...-|-||.++
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 3555577789999998 557788999999998777778999999999998877432223333445567777764
No 226
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=28.68 E-value=35 Score=25.94 Aligned_cols=36 Identities=33% Similarity=0.541 Sum_probs=27.0
Q ss_pred ceeecCCCCccccc------ccCCCCCCCccceEecCccccc
Q 021215 118 NQVICSLCGTEQKV------QQVCVNCGVCMGEYFCESCKLF 153 (316)
Q Consensus 118 ~~V~C~~C~~eq~v------~~~C~~Cg~~f~~YfC~~Ckl~ 153 (316)
-.|.|..|+.+|.+ ...|..||..+++-.=++-+|.
T Consensus 10 ~~VkCp~C~n~q~vFsha~t~V~C~~Cg~~L~~PtGGKa~i~ 51 (59)
T PRK00415 10 LKVKCPDCGNEQVVFSHASTVVRCLVCGKTLAEPTGGKAKIK 51 (59)
T ss_pred EEEECCCCCCeEEEEecCCcEEECcccCCCcccCCCcceeee
Confidence 37899999999974 2479999998887665555554
No 227
>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=28.40 E-value=73 Score=22.20 Aligned_cols=9 Identities=44% Similarity=1.047 Sum_probs=5.6
Q ss_pred cCCCCCCCc
Q 021215 133 QVCVNCGVC 141 (316)
Q Consensus 133 ~~C~~Cg~~ 141 (316)
.+||.||..
T Consensus 19 ~~CP~Cg~~ 27 (46)
T PF12760_consen 19 FVCPHCGST 27 (46)
T ss_pred CCCCCCCCe
Confidence 456666665
No 228
>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=28.38 E-value=26 Score=23.20 Aligned_cols=23 Identities=35% Similarity=0.702 Sum_probs=11.6
Q ss_pred ceeecCCCCccc-ccccCCCCCCC
Q 021215 118 NQVICSLCGTEQ-KVQQVCVNCGV 140 (316)
Q Consensus 118 ~~V~C~~C~~eq-~v~~~C~~Cg~ 140 (316)
..-.|..|++.+ |+...|++||.
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 355677787775 45677777764
No 229
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=27.53 E-value=29 Score=24.91 Aligned_cols=12 Identities=50% Similarity=1.196 Sum_probs=10.1
Q ss_pred cCCCCCCccccc
Q 021215 302 KCPNCKSYNTRL 313 (316)
Q Consensus 302 kC~~C~SyNT~~ 313 (316)
||+.||-||-..
T Consensus 13 kCp~CGt~NG~R 24 (44)
T PF14952_consen 13 KCPKCGTYNGTR 24 (44)
T ss_pred cCCcCcCccCcc
Confidence 899999999543
No 230
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=27.22 E-value=42 Score=22.58 Aligned_cols=9 Identities=44% Similarity=1.113 Sum_probs=4.5
Q ss_pred eeecCCCCc
Q 021215 119 QVICSLCGT 127 (316)
Q Consensus 119 ~V~C~~C~~ 127 (316)
.|.|+.|++
T Consensus 25 ~vrC~~C~~ 33 (37)
T PF13719_consen 25 KVRCPKCGH 33 (37)
T ss_pred EEECCCCCc
Confidence 555555443
No 231
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=27.07 E-value=47 Score=22.07 Aligned_cols=22 Identities=27% Similarity=0.788 Sum_probs=13.2
Q ss_pred eecCCCCcccc---cccCCCCCCCc
Q 021215 120 VICSLCGTEQK---VQQVCVNCGVC 141 (316)
Q Consensus 120 V~C~~C~~eq~---v~~~C~~Cg~~ 141 (316)
-+|..|+.... .-..||.||+.
T Consensus 3 ~~C~~CG~i~~g~~~p~~CP~Cg~~ 27 (34)
T cd00729 3 WVCPVCGYIHEGEEAPEKCPICGAP 27 (34)
T ss_pred EECCCCCCEeECCcCCCcCcCCCCc
Confidence 46777775533 23577777764
No 232
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=26.72 E-value=32 Score=23.98 Aligned_cols=29 Identities=28% Similarity=0.691 Sum_probs=14.7
Q ss_pred cCCCCCCCccceEecCccccccCCCCCCeeecCCC
Q 021215 133 QVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGC 167 (316)
Q Consensus 133 ~~C~~Cg~~f~~YfC~~Ckl~ddd~~k~~yHC~~C 167 (316)
..||.||..= .=++|+|...+..|+|..|
T Consensus 4 ~pCP~CGG~D------rFri~~d~~~~G~~~C~~C 32 (40)
T PF08273_consen 4 GPCPICGGKD------RFRIFDDKDGRGTWICRQC 32 (40)
T ss_dssp E--TTTT-TT------TEEEETT----S-EEETTT
T ss_pred CCCCCCcCcc------ccccCcCcccCCCEECCCC
Confidence 4688887632 1257888778888988888
No 233
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=26.69 E-value=38 Score=32.22 Aligned_cols=20 Identities=30% Similarity=1.039 Sum_probs=16.0
Q ss_pred ccCCCCCCCcc--------ceEecCccc
Q 021215 132 QQVCVNCGVCM--------GEYFCESCK 151 (316)
Q Consensus 132 ~~~C~~Cg~~f--------~~YfC~~Ck 151 (316)
++.|+.||... +.|||+.|.
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 272 (274)
T PRK01103 245 GEPCRRCGTPIEKIKQGGRSTFFCPRCQ 272 (274)
T ss_pred CCCCCCCCCeeEEEEECCCCcEECcCCC
Confidence 46899999887 568888885
No 234
>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=26.65 E-value=36 Score=22.39 Aligned_cols=23 Identities=26% Similarity=0.527 Sum_probs=9.9
Q ss_pred CCCCCCCccceEecCccccccCCCCCCeeecCCCC
Q 021215 134 VCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCG 168 (316)
Q Consensus 134 ~C~~Cg~~f~~YfC~~Ckl~ddd~~k~~yHC~~Cg 168 (316)
.|+.|+..++- . +..+|-|+.||
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 56777766643 2 24677787776
No 235
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=26.65 E-value=80 Score=34.00 Aligned_cols=136 Identities=24% Similarity=0.430 Sum_probs=71.1
Q ss_pred CCCCCeeecCCCCc---ceecC-Ccceee-----ccCCcceeeccccccccccCCCCCCCC-cccccccccCcceeEEcC
Q 021215 156 DTSKKQYHCDGCGI---CRIGG-CDNFFH-----CNKCRCCYSMLLKNSHPCVEGAMHHDC-PVCCEYLFETRQDVIVLP 225 (316)
Q Consensus 156 d~~k~~yHC~~Cgi---CR~G~-~~~ffH-----C~~C~~C~s~~l~~~H~CiE~~~~~~C-PIClE~lf~s~~~v~~Lp 225 (316)
...++.-||+.|+- +-|+. .+++|| |.+||.=+....+ -+++-|+ ..+ .-|.+. . +..++..
T Consensus 11 ~~~~~~i~c~~c~~kc~gevlrv~d~~fhi~cf~c~~cg~~la~~gf-f~k~~~~---~ygt~~c~~~--~--~gevvsa 82 (670)
T KOG1044|consen 11 QTGKQGIKCDKCRKKCSGEVLRVNDNHFHINCFQCKKCGRNLAEGGF-FTKPENR---LYGTDDCRAF--V--EGEVVST 82 (670)
T ss_pred cccccceehhhhCCccccceeEeeccccceeeeeccccCCCcccccc-eecccce---eecccchhhh--c--cceeEec
Confidence 34567788888872 22222 345554 5555544433322 1344442 222 234432 1 1334555
Q ss_pred CCCcccHHhHHHHhccCCCCCCCCCccccchhH-HH--HHhHHHHHcCCCChhhhcCcceEEcCCCCCCc---------c
Q 021215 226 CGHTIHKNCLKEMREHHQYACPICSKSVCDMSK-VW--EKYDREIAATPMPEAYLNKKVWILCNDCGKTS---------N 293 (316)
Q Consensus 226 CGH~fH~~Ci~~wl~~~~~~CPiCrks~~d~~~-~~--~~lD~~i~~~pmP~ey~~~~~~IlCnDC~~~s---------~ 293 (316)
=|-+||..|+ .|-+|++++..-+. .+ +...-+.-.|+||-.-......-.|--|+..- .
T Consensus 83 ~gktyh~~cf---------~cs~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk~gq~llald 153 (670)
T KOG1044|consen 83 LGKTYHPKCF---------SCSTCKSPFKSGDKVTFSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELKNGQALLALD 153 (670)
T ss_pred ccceeccccc---------eecccCCCCCCCCeeeecchhhhhhhhcCcccCCcccccCCccccchhhhhhccceeeeec
Confidence 6888888765 57788887752111 11 11222233555553322223445577777522 6
Q ss_pred ccceeeeecCCCCCC
Q 021215 294 VQFHVLAQKCPNCKS 308 (316)
Q Consensus 294 v~~H~lg~kC~~C~S 308 (316)
-++|+..-||..|.-
T Consensus 154 ~qwhv~cfkc~~c~~ 168 (670)
T KOG1044|consen 154 KQWHVSCFKCKSCSA 168 (670)
T ss_pred cceeeeeeehhhhcc
Confidence 689999999998864
No 236
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=26.41 E-value=77 Score=30.61 Aligned_cols=112 Identities=21% Similarity=0.485 Sum_probs=65.0
Q ss_pred cceeeccCCcceeeccccccccccCCCCCCCCccccccccc----CcceeEEcCCCCcccHHhHHHH-hccCCCCCCC--
Q 021215 176 DNFFHCNKCRCCYSMLLKNSHPCVEGAMHHDCPVCCEYLFE----TRQDVIVLPCGHTIHKNCLKEM-REHHQYACPI-- 248 (316)
Q Consensus 176 ~~ffHC~~C~~C~s~~l~~~H~CiE~~~~~~CPIClE~lf~----s~~~v~~LpCGH~fH~~Ci~~w-l~~~~~~CPi-- 248 (316)
.....|..|+.=++++.+. |.-+ -.|+.|.|-..- .+++++-=||. ||.-- .++.+..||-
T Consensus 63 ~p~v~CrVCq~~I~i~gk~-~QhV-----VkC~~CnEATPIr~aPpGKKYVRCPCN------CLLICk~sS~rIaCPRp~ 130 (256)
T PF09788_consen 63 APVVTCRVCQSLIDIEGKM-HQHV-----VKCSVCNEATPIRNAPPGKKYVRCPCN------CLLICKSSSQRIACPRPN 130 (256)
T ss_pred CceEEeecCCceecccCcc-ceee-----EECCCCCccccccCCCCCCeeEecCCc------eEEEeecccccccCCCCC
Confidence 4577888888888887642 3222 358888885422 23455666777 44332 1234577986
Q ss_pred CCccccchhHHHHHhHHHHHcCCCChhh--hcCcceEEcCCCCCCcccc-ceeee-ecCCCCCC
Q 021215 249 CSKSVCDMSKVWEKYDREIAATPMPEAY--LNKKVWILCNDCGKTSNVQ-FHVLA-QKCPNCKS 308 (316)
Q Consensus 249 Crks~~d~~~~~~~lD~~i~~~pmP~ey--~~~~~~IlCnDC~~~s~v~-~H~lg-~kC~~C~S 308 (316)
|++.+.-... .+.|..++. +....-+.|..|....-.. +..-+ .||++|..
T Consensus 131 CkRiI~L~~~---------~~~p~~~~~~~~p~~~rv~CghC~~~Fl~~~~~~~tlARCPHCrK 185 (256)
T PF09788_consen 131 CKRIINLGPS---------HQGPVTPPVPTQPGSCRVICGHCSNTFLFNTLTSNTLARCPHCRK 185 (256)
T ss_pred CcceEEeCCc---------cCCCCCCCCCCCCCceeEECCCCCCcEeccCCCCCccccCCCCce
Confidence 9987753221 122222111 3345678999999876222 22112 49999974
No 237
>PF13695 zf-3CxxC: Zinc-binding domain
Probab=26.15 E-value=55 Score=26.50 Aligned_cols=46 Identities=28% Similarity=0.724 Sum_probs=31.2
Q ss_pred CCCCCCCCccccchhHHHHHhHHHHHcCCCChhhhcCcceEEcCCCCCCccccceeeeecCCCCCCcccc
Q 021215 243 QYACPICSKSVCDMSKVWEKYDREIAATPMPEAYLNKKVWILCNDCGKTSNVQFHVLAQKCPNCKSYNTR 312 (316)
Q Consensus 243 ~~~CPiCrks~~d~~~~~~~lD~~i~~~pmP~ey~~~~~~IlCnDC~~~s~v~~H~lg~kC~~C~SyNT~ 312 (316)
.+.|+.|++.+..+ +++|+-.-- ....+...++|++|..|+.+..-
T Consensus 5 rF~C~~C~~~W~S~-----------------------~v~i~f~~~-~~g~v~~rv~~Q~C~~C~~~~~P 50 (98)
T PF13695_consen 5 RFQCSKCSRGWTSA-----------------------KVWILFHMY-RGGQVNMRVFGQRCKKCNPLERP 50 (98)
T ss_pred EEECCCCCCCCccC-----------------------EEEEEEEEc-CCCeEEEEEECCCCCCCCCCCCc
Confidence 47788888766543 234443333 34678888999999999776653
No 238
>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=25.87 E-value=32 Score=21.85 Aligned_cols=11 Identities=27% Similarity=1.165 Sum_probs=8.0
Q ss_pred ceEecCccccc
Q 021215 143 GEYFCESCKLF 153 (316)
Q Consensus 143 ~~YfC~~Ckl~ 153 (316)
+.|||.+|+.+
T Consensus 2 ~~~~C~~C~~~ 12 (35)
T smart00451 2 GGFYCKLCNVT 12 (35)
T ss_pred cCeEccccCCc
Confidence 56888888655
No 239
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=25.85 E-value=40 Score=24.63 Aligned_cols=23 Identities=30% Similarity=0.743 Sum_probs=19.6
Q ss_pred ceeecCCCCccccc-ccCCCCCCC
Q 021215 118 NQVICSLCGTEQKV-QQVCVNCGV 140 (316)
Q Consensus 118 ~~V~C~~C~~eq~v-~~~C~~Cg~ 140 (316)
..+||+.|....|+ +..|..||.
T Consensus 13 ~k~ICrkC~ARnp~~A~~CRKCg~ 36 (48)
T PRK04136 13 NKKICMRCNARNPWRATKCRKCGY 36 (48)
T ss_pred cccchhcccCCCCccccccccCCC
Confidence 57899999999987 678988886
No 240
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=25.40 E-value=31 Score=34.44 Aligned_cols=21 Identities=43% Similarity=0.934 Sum_probs=16.8
Q ss_pred cCCCCCCCccceEecCccccc
Q 021215 133 QVCVNCGVCMGEYFCESCKLF 153 (316)
Q Consensus 133 ~~C~~Cg~~f~~YfC~~Ckl~ 153 (316)
..|+-||+.+.+|.|+-|+|-
T Consensus 8 ~~C~ic~vq~~~YtCPRCn~~ 28 (383)
T KOG4317|consen 8 LACGICGVQKREYTCPRCNLL 28 (383)
T ss_pred eeccccccccccccCCCCCcc
Confidence 467788888888888888864
No 241
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=25.37 E-value=55 Score=37.43 Aligned_cols=56 Identities=16% Similarity=0.412 Sum_probs=38.2
Q ss_pred cCCCCCCCCcccccccccCcceeEEc---CCCCcccHHhHHHHhccCCCCCCCCCcccc
Q 021215 199 VEGAMHHDCPVCCEYLFETRQDVIVL---PCGHTIHKNCLKEMREHHQYACPICSKSVC 254 (316)
Q Consensus 199 iE~~~~~~CPIClE~lf~s~~~v~~L---pCGH~fH~~Ci~~wl~~~~~~CPiCrks~~ 254 (316)
.+....+.|.||.+++-.+.+.-... -||--.|+.|++-=.+.++..||.|+....
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 34445679999999865443333344 466679999995545557788999995443
No 242
>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=25.24 E-value=50 Score=21.79 Aligned_cols=10 Identities=40% Similarity=0.939 Sum_probs=5.1
Q ss_pred eeecCCCCcc
Q 021215 119 QVICSLCGTE 128 (316)
Q Consensus 119 ~V~C~~C~~e 128 (316)
.|.|+.|++.
T Consensus 25 ~v~C~~C~~~ 34 (38)
T TIGR02098 25 KVRCGKCGHV 34 (38)
T ss_pred EEECCCCCCE
Confidence 4555555543
No 243
>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=24.87 E-value=43 Score=31.91 Aligned_cols=20 Identities=35% Similarity=1.027 Sum_probs=15.5
Q ss_pred ccCCCCCCCcc--------ceEecCccc
Q 021215 132 QQVCVNCGVCM--------GEYFCESCK 151 (316)
Q Consensus 132 ~~~C~~Cg~~f--------~~YfC~~Ck 151 (316)
++.|+.||... +.|||+.|.
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 272 (272)
T TIGR00577 245 GEPCRRCGTPIEKIKVGGRGTHFCPQCQ 272 (272)
T ss_pred CCCCCCCCCeeEEEEECCCCCEECCCCC
Confidence 46899999887 567887774
No 244
>KOG4399 consensus C2HC-type Zn-finger protein [General function prediction only]
Probab=24.63 E-value=18 Score=35.27 Aligned_cols=53 Identities=15% Similarity=0.159 Sum_probs=41.7
Q ss_pred cCCCCCCCccceEecCccccccCCCCCCeeecCCCCcceecCCcceeeccCCcceee
Q 021215 133 QVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGICRIGGCDNFFHCNKCRCCYS 189 (316)
Q Consensus 133 ~~C~~Cg~~f~~YfC~~Ckl~ddd~~k~~yHC~~CgiCR~G~~~~ffHC~~C~~C~s 189 (316)
..|+-|...-+.-||.+|-=+|.. .-|||.|.-||--....+-||++|..|..
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 356677777778899999888652 27999999999887777888888887764
No 245
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=24.53 E-value=47 Score=25.43 Aligned_cols=33 Identities=24% Similarity=0.632 Sum_probs=21.4
Q ss_pred ceeecCCCCcccccccCCCCCCCccceEecCcccc
Q 021215 118 NQVICSLCGTEQKVQQVCVNCGVCMGEYFCESCKL 152 (316)
Q Consensus 118 ~~V~C~~C~~eq~v~~~C~~Cg~~f~~YfC~~Ckl 152 (316)
....|..|+.++-. .|..|...=+.|-|++|-|
T Consensus 26 v~F~CPnCGe~~I~--Rc~~CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 26 VKFPCPNCGEVEIY--RCAKCRKLGNPYRCPKCGF 58 (61)
T ss_pred eEeeCCCCCceeee--hhhhHHHcCCceECCCcCc
Confidence 46667777755332 5666777777777777765
No 246
>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=24.19 E-value=26 Score=35.79 Aligned_cols=49 Identities=29% Similarity=0.579 Sum_probs=0.6
Q ss_pred CCCCCCCccccccc----------ccCcceeEEcCCCCcccHHhHHHHhcc-----CCCCCCCCCcc
Q 021215 201 GAMHHDCPVCCEYL----------FETRQDVIVLPCGHTIHKNCLKEMREH-----HQYACPICSKS 252 (316)
Q Consensus 201 ~~~~~~CPIClE~l----------f~s~~~v~~LpCGH~fH~~Ci~~wl~~-----~~~~CPiCrks 252 (316)
|++.-.|||=|..| .+...+.+.|.|||.+= +-.|-.. ....||+||..
T Consensus 274 Na~rpQCPVglnTL~fp~~~~~~~~~~~qP~VYl~CGHVhG---~h~Wg~~~~~~~~~r~CPlCr~~ 337 (416)
T PF04710_consen 274 NAGRPQCPVGLNTLVFPSKSRKDVPDERQPWVYLNCGHVHG---YHNWGQDSDRDPRSRTCPLCRQV 337 (416)
T ss_dssp S------------------------------------------------------------------
T ss_pred hhcCCCCCcCCCccccccccccccccccCceeeccccceee---ecccccccccccccccCCCcccc
Confidence 56778899987544 23456789999998642 2346421 14679999954
No 247
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=24.11 E-value=46 Score=31.91 Aligned_cols=20 Identities=25% Similarity=0.884 Sum_probs=15.7
Q ss_pred ccCCCCCCCcc--------ceEecCccc
Q 021215 132 QQVCVNCGVCM--------GEYFCESCK 151 (316)
Q Consensus 132 ~~~C~~Cg~~f--------~~YfC~~Ck 151 (316)
++.|+.||... +.|||+.|.
T Consensus 254 g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 281 (282)
T PRK13945 254 GKPCRKCGTPIERIKLAGRSTHWCPNCQ 281 (282)
T ss_pred cCCCCcCCCeeEEEEECCCccEECCCCc
Confidence 47899999888 567777774
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=23.96 E-value=42 Score=27.77 Aligned_cols=20 Identities=30% Similarity=0.660 Sum_probs=15.0
Q ss_pred ecCCCCcccccc----cCCCCCCC
Q 021215 121 ICSLCGTEQKVQ----QVCVNCGV 140 (316)
Q Consensus 121 ~C~~C~~eq~v~----~~C~~Cg~ 140 (316)
.|+.|+..++.. +.||||+.
T Consensus 5 AC~~C~~I~~~~qf~~~gCpnC~~ 28 (98)
T cd07973 5 ACLLCSLIKTEDQFERDGCPNCEG 28 (98)
T ss_pred hhccCCcccccccccCCCCCCCcc
Confidence 688898888754 47888864
No 249
>PLN03086 PRLI-interacting factor K; Provisional
Probab=23.82 E-value=50 Score=35.23 Aligned_cols=16 Identities=25% Similarity=0.436 Sum_probs=12.1
Q ss_pred ccCceeecCCCCcccc
Q 021215 115 HEVNQVICSLCGTEQK 130 (316)
Q Consensus 115 ~~v~~V~C~~C~~eq~ 130 (316)
..+..|.|..|....+
T Consensus 403 ~~~~~V~C~NC~~~i~ 418 (567)
T PLN03086 403 MDVDTVECRNCKHYIP 418 (567)
T ss_pred CCCCeEECCCCCCccc
Confidence 4566889999987766
No 250
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=23.82 E-value=48 Score=29.91 Aligned_cols=11 Identities=45% Similarity=0.990 Sum_probs=6.7
Q ss_pred CCCCccccccc
Q 021215 204 HHDCPVCCEYL 214 (316)
Q Consensus 204 ~~~CPIClE~l 214 (316)
...||+|.+.|
T Consensus 136 ~F~Cp~Cg~~L 146 (178)
T PRK06266 136 GFRCPQCGEML 146 (178)
T ss_pred CCcCCCCCCCC
Confidence 45677776643
No 251
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=23.63 E-value=84 Score=31.04 Aligned_cols=24 Identities=38% Similarity=0.974 Sum_probs=14.5
Q ss_pred ceEEcCCCCCCccccceeeeecCCCCCC
Q 021215 281 VWILCNDCGKTSNVQFHVLAQKCPNCKS 308 (316)
Q Consensus 281 ~~IlCnDC~~~s~v~~H~lg~kC~~C~S 308 (316)
..-.|.-|+ ..+|+.-.||++|++
T Consensus 211 RyL~CslC~----teW~~~R~~C~~Cg~ 234 (309)
T PRK03564 211 RYLHCNLCE----SEWHVVRVKCSNCEQ 234 (309)
T ss_pred eEEEcCCCC----CcccccCccCCCCCC
Confidence 345566666 556666666666663
No 252
>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=23.43 E-value=44 Score=29.47 Aligned_cols=9 Identities=11% Similarity=0.268 Sum_probs=3.9
Q ss_pred CeeecCCCC
Q 021215 160 KQYHCDGCG 168 (316)
Q Consensus 160 ~~yHC~~Cg 168 (316)
.-|+|+.||
T Consensus 108 ~~Y~Cp~c~ 116 (158)
T TIGR00373 108 MFFICPNMC 116 (158)
T ss_pred CeEECCCCC
Confidence 444444443
No 253
>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=23.36 E-value=60 Score=22.36 Aligned_cols=31 Identities=29% Similarity=0.616 Sum_probs=18.2
Q ss_pred eEEcCCCCCCcccccee---eeecCCCCCCcccc
Q 021215 282 WILCNDCGKTSNVQFHV---LAQKCPNCKSYNTR 312 (316)
Q Consensus 282 ~IlCnDC~~~s~v~~H~---lg~kC~~C~SyNT~ 312 (316)
...|.+|+...++-..+ ....|+.|++-+.+
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~ 38 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSISEDDPVPCPECGSTEVR 38 (42)
T ss_pred EEEeCCCCCEEEEEEEcCCCCCCcCCCCCCCceE
Confidence 35577787655433222 34678888884443
No 254
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=23.14 E-value=72 Score=26.45 Aligned_cols=32 Identities=25% Similarity=0.591 Sum_probs=20.7
Q ss_pred cceeeccCCc-ceeeccccccccccCCCCCCCCcccccc
Q 021215 176 DNFFHCNKCR-CCYSMLLKNSHPCVEGAMHHDCPVCCEY 213 (316)
Q Consensus 176 ~~ffHC~~C~-~C~s~~l~~~H~CiE~~~~~~CPIClE~ 213 (316)
..+|+|..|| ..+++.+. + +..+..|++|..+
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 33333331 2 4568899999975
No 255
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=23.10 E-value=49 Score=29.42 Aligned_cols=12 Identities=25% Similarity=0.855 Sum_probs=6.2
Q ss_pred CCCCCCCccceE
Q 021215 134 VCVNCGVCMGEY 145 (316)
Q Consensus 134 ~C~~Cg~~f~~Y 145 (316)
.|++||..|+.|
T Consensus 30 ~c~~c~~~f~~~ 41 (154)
T PRK00464 30 ECLACGKRFTTF 41 (154)
T ss_pred eccccCCcceEe
Confidence 355555555544
No 256
>KOG3842 consensus Adaptor protein Pellino [Signal transduction mechanisms]
Probab=23.00 E-value=40 Score=33.78 Aligned_cols=46 Identities=30% Similarity=0.658 Sum_probs=31.1
Q ss_pred CCCCCCCcccccccc----------cCcceeEEcCCCCc--ccHHhHHHHhcc-----CCCCCCCCCc
Q 021215 201 GAMHHDCPVCCEYLF----------ETRQDVIVLPCGHT--IHKNCLKEMREH-----HQYACPICSK 251 (316)
Q Consensus 201 ~~~~~~CPIClE~lf----------~s~~~v~~LpCGH~--fH~~Ci~~wl~~-----~~~~CPiCrk 251 (316)
|+..-.||+=|..|- +..++.+.|.|||. +| .|=.. ....||+|+.
T Consensus 287 NA~RPQCPVglnTL~~P~~~~~~~~~~~QP~vYl~CGHV~G~H-----~WG~~e~~g~~~r~CPmC~~ 349 (429)
T KOG3842|consen 287 NAARPQCPVGLNTLAFPSKRRKRVVDEKQPWVYLNCGHVHGYH-----NWGVRENTGQRERECPMCRV 349 (429)
T ss_pred hccCCCCCcccceeecccccccccccccCCeEEEecccccccc-----ccccccccCcccCcCCeeee
Confidence 466778999987552 23467899999976 44 46321 1356999994
No 257
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=22.72 E-value=39 Score=33.04 Aligned_cols=23 Identities=22% Similarity=0.571 Sum_probs=17.8
Q ss_pred cCCCCCCCccceEecCccccccC
Q 021215 133 QVCVNCGVCMGEYFCESCKLFDD 155 (316)
Q Consensus 133 ~~C~~Cg~~f~~YfC~~Ckl~dd 155 (316)
..+...|.-..+-||.+|+.|--
T Consensus 98 ~~~~~~~~~~~~~~C~~C~~~KP 120 (309)
T COG5273 98 SRLLDDGKFGTENFCSTCNIYKP 120 (309)
T ss_pred hhhhhcCccccceeccccccccC
Confidence 45666778888889999999933
No 258
>cd02345 ZZ_dah Zinc finger, ZZ type. Zinc finger present in Drosophila dah and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dah (discontinuous actin hexagon) is a membrane associated protein essential for cortical furrow formation in Drosophila.
Probab=22.57 E-value=62 Score=23.11 Aligned_cols=27 Identities=22% Similarity=0.613 Sum_probs=17.7
Q ss_pred EEcCCCCCCccccceeeeecCCCCCCcccc
Q 021215 283 ILCNDCGKTSNVQFHVLAQKCPNCKSYNTR 312 (316)
Q Consensus 283 IlCnDC~~~s~v~~H~lg~kC~~C~SyNT~ 312 (316)
|.|+.|.+..-+.++ .+|..|..|+--
T Consensus 1 ~~C~~C~~~~i~g~R---~~C~~C~dydLC 27 (49)
T cd02345 1 LSCSACRKQDISGIR---FPCQVCRDYSLC 27 (49)
T ss_pred CcCCCCCCCCceEee---EECCCCCCcCch
Confidence 468888876444444 478777777643
No 259
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=22.06 E-value=30 Score=31.05 Aligned_cols=29 Identities=34% Similarity=0.863 Sum_probs=20.7
Q ss_pred ceeecCCCCcccccccCCCCCCCcc-ceEecC
Q 021215 118 NQVICSLCGTEQKVQQVCVNCGVCM-GEYFCE 148 (316)
Q Consensus 118 ~~V~C~~C~~eq~v~~~C~~Cg~~f-~~YfC~ 148 (316)
.+-.|..|+.+-- ..||+|+... |.|+.+
T Consensus 27 ~~~fC~kCG~~tI--~~Cp~C~~~IrG~y~v~ 56 (158)
T PF10083_consen 27 REKFCSKCGAKTI--TSCPNCSTPIRGDYHVE 56 (158)
T ss_pred HHHHHHHhhHHHH--HHCcCCCCCCCCceecC
Confidence 3567888887632 4799999887 677763
No 260
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=21.81 E-value=95 Score=30.68 Aligned_cols=26 Identities=31% Similarity=0.700 Sum_probs=21.2
Q ss_pred cCceeecCCCCccccc-ccCCCCCCCc
Q 021215 116 EVNQVICSLCGTEQKV-QQVCVNCGVC 141 (316)
Q Consensus 116 ~v~~V~C~~C~~eq~v-~~~C~~Cg~~ 141 (316)
..+-..|+.|+++=.. -..|++||..
T Consensus 209 G~RyL~CslC~teW~~~R~~C~~Cg~~ 235 (309)
T PRK03564 209 GLRYLHCNLCESEWHVVRVKCSNCEQS 235 (309)
T ss_pred CceEEEcCCCCCcccccCccCCCCCCC
Confidence 3468899999999875 6789999974
No 261
>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=21.73 E-value=56 Score=22.85 Aligned_cols=39 Identities=26% Similarity=0.730 Sum_probs=25.6
Q ss_pred CcccccccccCcceeEEcCCCCcccHHhHHHHhccCCCCCCCCCccccch
Q 021215 207 CPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCDM 256 (316)
Q Consensus 207 CPIClE~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~~CPiCrks~~d~ 256 (316)
|+.|.+.+... ..++..=|..||..|+ +|-.|++++.+.
T Consensus 1 C~~C~~~I~~~--~~~~~~~~~~~H~~Cf---------~C~~C~~~l~~~ 39 (58)
T PF00412_consen 1 CARCGKPIYGT--EIVIKAMGKFWHPECF---------KCSKCGKPLNDG 39 (58)
T ss_dssp BTTTSSBESSS--SEEEEETTEEEETTTS---------BETTTTCBTTTS
T ss_pred CCCCCCCccCc--EEEEEeCCcEEEcccc---------ccCCCCCccCCC
Confidence 56777765532 2333356888997764 688899887653
No 262
>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=21.45 E-value=70 Score=28.94 Aligned_cols=13 Identities=31% Similarity=0.751 Sum_probs=8.1
Q ss_pred ceEecCccccccC
Q 021215 143 GEYFCESCKLFDD 155 (316)
Q Consensus 143 ~~YfC~~Ckl~dd 155 (316)
+.+||..|-+.|-
T Consensus 146 ~~~~Cs~Cs~~~y 158 (175)
T PF05458_consen 146 SEVFCSLCSTVNY 158 (175)
T ss_pred hhhhhcCcccccc
Confidence 3456777776654
No 263
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=21.45 E-value=55 Score=24.95 Aligned_cols=20 Identities=25% Similarity=0.620 Sum_probs=13.5
Q ss_pred ecCCCCcccccccCCCCCCCc
Q 021215 121 ICSLCGTEQKVQQVCVNCGVC 141 (316)
Q Consensus 121 ~C~~C~~eq~v~~~C~~Cg~~ 141 (316)
.|..|...++ .+.||+||..
T Consensus 5 AC~~C~~i~~-~~~CP~Cgs~ 24 (61)
T PRK08351 5 ACRHCHYITT-EDRCPVCGSR 24 (61)
T ss_pred hhhhCCcccC-CCcCCCCcCC
Confidence 5777776663 3468888874
No 264
>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=21.31 E-value=58 Score=23.35 Aligned_cols=13 Identities=23% Similarity=0.838 Sum_probs=7.1
Q ss_pred CCCCCCCccccch
Q 021215 244 YACPICSKSVCDM 256 (316)
Q Consensus 244 ~~CPiCrks~~d~ 256 (316)
..||+|++++..-
T Consensus 21 ~~CPlC~r~l~~e 33 (54)
T PF04423_consen 21 GCCPLCGRPLDEE 33 (54)
T ss_dssp EE-TTT--EE-HH
T ss_pred CcCCCCCCCCCHH
Confidence 3899999999853
No 265
>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=21.25 E-value=75 Score=25.52 Aligned_cols=10 Identities=30% Similarity=0.999 Sum_probs=6.7
Q ss_pred CCCCCCCCcc
Q 021215 243 QYACPICSKS 252 (316)
Q Consensus 243 ~~~CPiCrks 252 (316)
...||.|+..
T Consensus 62 ~~~Cp~Cg~~ 71 (104)
T TIGR01384 62 RVECPKCGHK 71 (104)
T ss_pred cCCCCCCCCC
Confidence 4678888753
No 266
>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=21.19 E-value=76 Score=22.12 Aligned_cols=12 Identities=42% Similarity=1.035 Sum_probs=6.2
Q ss_pred CCCCeeecCCCC
Q 021215 157 TSKKQYHCDGCG 168 (316)
Q Consensus 157 ~~k~~yHC~~Cg 168 (316)
..++-|+|..|+
T Consensus 24 ~~~~g~~C~~C~ 35 (53)
T PF00130_consen 24 LGKQGYRCSWCG 35 (53)
T ss_dssp SSSCEEEETTTT
T ss_pred CCCCeEEECCCC
Confidence 345555555554
No 267
>PF15353 HECA: Headcase protein family homologue
Probab=20.85 E-value=56 Score=27.64 Aligned_cols=16 Identities=25% Similarity=0.891 Sum_probs=13.6
Q ss_pred CCCCcccHHhHHHHhc
Q 021215 225 PCGHTIHKNCLKEMRE 240 (316)
Q Consensus 225 pCGH~fH~~Ci~~wl~ 240 (316)
|-|+.+|.+|+++|-.
T Consensus 39 p~~~~MH~~CF~~wE~ 54 (107)
T PF15353_consen 39 PFGQYMHRECFEKWED 54 (107)
T ss_pred CCCCchHHHHHHHHHH
Confidence 4489999999999954
No 268
>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=20.59 E-value=74 Score=31.07 Aligned_cols=43 Identities=26% Similarity=0.411 Sum_probs=27.0
Q ss_pred CCCCCCcccccccccCcceeEEcCCCCc----ccHHhHHHHhccCCCCCC
Q 021215 202 AMHHDCPVCCEYLFETRQDVIVLPCGHT----IHKNCLKEMREHHQYACP 247 (316)
Q Consensus 202 ~~~~~CPIClE~lf~s~~~v~~LpCGH~----fH~~Ci~~wl~~~~~~CP 247 (316)
.+-..|+||+| |...+.+-.-| =|+ =|++|+.+|-.-.+..||
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 44567999998 55444333322 132 589999998332456788
No 269
>PRK05580 primosome assembly protein PriA; Validated
Probab=20.52 E-value=95 Score=33.48 Aligned_cols=45 Identities=22% Similarity=0.576 Sum_probs=29.8
Q ss_pred CceeecCCCCcccccccCCCCCCCccce------EecCccccccCCCCCCeeecCCCCc
Q 021215 117 VNQVICSLCGTEQKVQQVCVNCGVCMGE------YFCESCKLFDDDTSKKQYHCDGCGI 169 (316)
Q Consensus 117 v~~V~C~~C~~eq~v~~~C~~Cg~~f~~------YfC~~Ckl~ddd~~k~~yHC~~Cgi 169 (316)
...+.|..|+.. ..|++|+..+.- -.|.-|.+- ...+..|+.||-
T Consensus 379 ~~~~~C~~Cg~~----~~C~~C~~~l~~h~~~~~l~Ch~Cg~~----~~~~~~Cp~Cg~ 429 (679)
T PRK05580 379 APFLLCRDCGWV----AECPHCDASLTLHRFQRRLRCHHCGYQ----EPIPKACPECGS 429 (679)
T ss_pred CCceEhhhCcCc----cCCCCCCCceeEECCCCeEECCCCcCC----CCCCCCCCCCcC
Confidence 457899999887 579999988743 346666533 223455777764
No 270
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=20.44 E-value=51 Score=36.38 Aligned_cols=50 Identities=20% Similarity=0.355 Sum_probs=40.8
Q ss_pred cCCCCCCCccceE---ecCccccccCCCCCCeeecCCCCcceecCCcceeeccCCcceeecc
Q 021215 133 QVCVNCGVCMGEY---FCESCKLFDDDTSKKQYHCDGCGICRIGGCDNFFHCNKCRCCYSML 191 (316)
Q Consensus 133 ~~C~~Cg~~f~~Y---fC~~Ckl~ddd~~k~~yHC~~CgiCR~G~~~~ffHC~~C~~C~s~~ 191 (316)
-.|++|++.++.- .|.+|.--.- .+|-+|+.+-++-+++|..|+-+.-.+
T Consensus 754 ~~~~nc~a~~~~~~~~~c~rc~s~a~---------~~CtVC~~vi~G~~~~c~~C~H~gH~s 806 (839)
T KOG0269|consen 754 YACPNCDAPMVLTKLWQCDRCESRAS---------AKCTVCDLVIRGVDVWCQVCGHGGHDS 806 (839)
T ss_pred ccccccCCccccccceeechHHHHhh---------cCceeecceeeeeEeecccccccccHH
Confidence 5899999999765 8988876533 268899999999999999999887543
No 271
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=20.30 E-value=51 Score=25.67 Aligned_cols=28 Identities=39% Similarity=0.768 Sum_probs=21.7
Q ss_pred ceeecCCCCccccc---c---cCCCCCCCccceE
Q 021215 118 NQVICSLCGTEQKV---Q---QVCVNCGVCMGEY 145 (316)
Q Consensus 118 ~~V~C~~C~~eq~v---~---~~C~~Cg~~f~~Y 145 (316)
-.|.|.-|+.+|.+ + ..|..||..+++-
T Consensus 18 l~VkCpdC~N~q~vFshast~V~C~~CG~~l~~P 51 (67)
T COG2051 18 LRVKCPDCGNEQVVFSHASTVVTCLICGTTLAEP 51 (67)
T ss_pred EEEECCCCCCEEEEeccCceEEEecccccEEEec
Confidence 48899999999985 1 4799998877654
No 272
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=20.21 E-value=44 Score=23.78 Aligned_cols=18 Identities=17% Similarity=0.397 Sum_probs=14.3
Q ss_pred eEEc-CCCCcccHHhHHHH
Q 021215 221 VIVL-PCGHTIHKNCLKEM 238 (316)
Q Consensus 221 v~~L-pCGH~fH~~Ci~~w 238 (316)
.+.- .||+.|+..|..+|
T Consensus 40 ~v~C~~C~~~fC~~C~~~~ 58 (64)
T smart00647 40 RVTCPKCGFSFCFRCKVPW 58 (64)
T ss_pred eeECCCCCCeECCCCCCcC
Confidence 3444 68999999999888
No 273
>PF00628 PHD: PHD-finger; InterPro: IPR019787 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 PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=20.18 E-value=1.3e+02 Score=20.75 Aligned_cols=20 Identities=30% Similarity=0.888 Sum_probs=8.7
Q ss_pred ecCccccccCCCCCCeeecCCC
Q 021215 146 FCESCKLFDDDTSKKQYHCDGC 167 (316)
Q Consensus 146 fC~~Ckl~ddd~~k~~yHC~~C 167 (316)
||.+|+-. +......-|+.|
T Consensus 1 ~C~vC~~~--~~~~~~i~C~~C 20 (51)
T PF00628_consen 1 YCPVCGQS--DDDGDMIQCDSC 20 (51)
T ss_dssp EBTTTTSS--CTTSSEEEBSTT
T ss_pred eCcCCCCc--CCCCCeEEcCCC
Confidence 45555552 223344444444
No 274
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=20.04 E-value=66 Score=21.64 Aligned_cols=28 Identities=21% Similarity=0.743 Sum_probs=10.2
Q ss_pred CCCCCCCccceEecCccccccCCCCCCeeecCCCC
Q 021215 134 VCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCG 168 (316)
Q Consensus 134 ~C~~Cg~~f~~YfC~~Ckl~ddd~~k~~yHC~~Cg 168 (316)
.|+.||..+.. ++-++ .++.-+-|+.||
T Consensus 2 fC~~CG~~l~~------~ip~g-d~r~R~vC~~Cg 29 (34)
T PF14803_consen 2 FCPQCGGPLER------RIPEG-DDRERLVCPACG 29 (34)
T ss_dssp B-TTT--B-EE------E--TT--SS-EEEETTTT
T ss_pred ccccccChhhh------hcCCC-CCccceECCCCC
Confidence 46666665532 12222 245556666665
Done!