Query 027589
Match_columns 221
No_of_seqs 234 out of 778
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 12:11:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027589.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027589hhsearch_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 5.9E-57 1.3E-61 401.4 5.2 205 5-220 22-226 (276)
2 PF05495 zf-CHY: CHY zinc fing 99.9 6.9E-25 1.5E-29 160.1 3.5 70 18-100 1-71 (71)
3 COG4357 Zinc finger domain con 99.7 5E-18 1.1E-22 130.0 2.2 73 15-90 12-92 (105)
4 PF13639 zf-RING_2: Ring finge 99.5 1.7E-14 3.7E-19 95.1 2.0 44 151-196 1-44 (44)
5 PF12678 zf-rbx1: RING-H2 zinc 99.1 4E-11 8.6E-16 87.7 3.9 48 148-196 17-73 (73)
6 cd00162 RING RING-finger (Real 99.1 1.4E-10 3E-15 73.9 3.8 45 152-199 1-45 (45)
7 COG5243 HRD1 HRD ubiquitin lig 99.0 6.4E-11 1.4E-15 109.9 2.1 57 147-204 284-350 (491)
8 KOG4628 Predicted E3 ubiquitin 99.0 8.4E-11 1.8E-15 108.6 2.8 50 151-201 230-279 (348)
9 PF13923 zf-C3HC4_2: Zinc fing 98.9 6.5E-10 1.4E-14 71.6 2.6 39 153-195 1-39 (39)
10 PHA02929 N1R/p28-like protein; 98.9 1E-09 2.2E-14 97.0 4.4 54 147-201 171-228 (238)
11 PF13920 zf-C3HC4_3: Zinc fing 98.8 2.9E-09 6.3E-14 71.9 2.9 47 150-201 2-49 (50)
12 PF12861 zf-Apc11: Anaphase-pr 98.8 5.3E-09 1.1E-13 79.1 3.6 47 151-199 33-81 (85)
13 PF00097 zf-C3HC4: Zinc finger 98.8 4.6E-09 9.9E-14 67.7 2.7 40 153-195 1-41 (41)
14 smart00184 RING Ring finger. E 98.8 6.1E-09 1.3E-13 64.0 3.1 39 153-195 1-39 (39)
15 COG5540 RING-finger-containing 98.7 6.8E-09 1.5E-13 94.4 3.3 53 146-199 319-371 (374)
16 PF14634 zf-RING_5: zinc-RING 98.7 1.7E-08 3.8E-13 66.7 3.1 44 152-197 1-44 (44)
17 PF15227 zf-C3HC4_4: zinc fing 98.5 9.4E-08 2E-12 63.0 2.9 39 153-195 1-42 (42)
18 PF13445 zf-RING_UBOX: RING-ty 98.5 8.8E-08 1.9E-12 63.7 2.6 40 153-193 1-43 (43)
19 KOG0802 E3 ubiquitin ligase [P 98.5 4E-08 8.6E-13 95.5 1.3 53 146-199 287-340 (543)
20 PLN03208 E3 ubiquitin-protein 98.4 2.3E-07 5E-12 79.7 4.1 54 144-201 12-80 (193)
21 PHA02926 zinc finger-like prot 98.3 2.2E-07 4.8E-12 81.5 2.2 75 133-207 153-239 (242)
22 KOG0320 Predicted E3 ubiquitin 98.1 1.1E-06 2.3E-11 74.8 2.2 46 151-200 132-178 (187)
23 smart00744 RINGv The RING-vari 98.1 2E-06 4.3E-11 58.6 2.9 43 152-196 1-49 (49)
24 smart00504 Ubox Modified RING 98.1 3.5E-06 7.5E-11 58.4 3.9 45 151-200 2-46 (63)
25 PF11793 FANCL_C: FANCL C-term 98.0 1.6E-06 3.5E-11 63.0 0.6 51 150-200 2-66 (70)
26 PF14599 zinc_ribbon_6: Zinc-r 97.9 1.8E-06 3.9E-11 61.6 0.0 22 199-220 1-22 (61)
27 KOG0804 Cytoplasmic Zn-finger 97.9 4.3E-06 9.3E-11 79.5 2.2 47 151-200 176-222 (493)
28 TIGR00599 rad18 DNA repair pro 97.9 9.4E-06 2E-10 76.7 4.0 46 150-200 26-71 (397)
29 COG5194 APC11 Component of SCF 97.7 2.6E-05 5.7E-10 58.6 3.2 29 171-200 53-81 (88)
30 KOG0827 Predicted E3 ubiquitin 97.7 1.5E-05 3.2E-10 74.9 1.9 46 150-196 4-52 (465)
31 TIGR00570 cdk7 CDK-activating 97.7 4.2E-05 9E-10 70.2 4.0 51 150-200 3-54 (309)
32 KOG2177 Predicted E3 ubiquitin 97.6 2.7E-05 5.8E-10 65.4 2.2 44 149-197 12-55 (386)
33 KOG0317 Predicted E3 ubiquitin 97.6 2.2E-05 4.8E-10 71.1 1.7 45 151-200 240-284 (293)
34 KOG2164 Predicted E3 ubiquitin 97.5 6.8E-05 1.5E-09 72.4 2.8 50 148-201 184-237 (513)
35 KOG0828 Predicted E3 ubiquitin 97.4 5E-05 1.1E-09 73.3 1.1 51 150-200 571-634 (636)
36 KOG1734 Predicted RING-contain 97.4 4.8E-05 1E-09 68.7 0.4 52 149-200 223-281 (328)
37 KOG0287 Postreplication repair 97.3 0.00016 3.5E-09 67.1 3.6 59 152-215 25-84 (442)
38 KOG1493 Anaphase-promoting com 97.3 9.6E-05 2.1E-09 55.1 1.1 29 171-199 50-80 (84)
39 KOG0823 Predicted E3 ubiquitin 97.3 0.00021 4.6E-09 63.0 3.1 50 148-201 45-96 (230)
40 PF14835 zf-RING_6: zf-RING of 97.2 0.0001 2.2E-09 53.2 0.9 56 151-213 8-65 (65)
41 PF04564 U-box: U-box domain; 97.1 0.0006 1.3E-08 49.5 3.5 48 150-201 4-51 (73)
42 KOG1941 Acetylcholine receptor 97.0 0.0002 4.4E-09 67.6 0.3 62 141-203 357-419 (518)
43 KOG4172 Predicted E3 ubiquitin 96.8 0.00038 8.3E-09 48.9 0.7 54 148-205 5-59 (62)
44 KOG4265 Predicted E3 ubiquitin 96.8 0.00095 2.1E-08 62.1 3.0 50 148-202 288-338 (349)
45 COG5574 PEX10 RING-finger-cont 96.6 0.0011 2.4E-08 59.6 2.1 47 150-200 215-262 (271)
46 KOG2930 SCF ubiquitin ligase, 96.6 0.0014 3E-08 51.5 2.3 28 171-199 80-107 (114)
47 PF14570 zf-RING_4: RING/Ubox 96.5 0.0021 4.6E-08 43.8 2.5 45 153-199 1-47 (48)
48 COG5219 Uncharacterized conser 96.5 0.0013 2.9E-08 67.8 2.2 53 147-199 1466-1522(1525)
49 KOG0825 PHD Zn-finger protein 96.5 0.00096 2.1E-08 67.6 0.8 77 123-201 95-172 (1134)
50 KOG0311 Predicted E3 ubiquitin 96.3 0.0011 2.3E-08 61.9 0.2 49 150-201 43-91 (381)
51 PF11789 zf-Nse: Zinc-finger o 96.2 0.0032 6.9E-08 44.1 2.0 43 149-194 10-53 (57)
52 KOG3002 Zn finger protein [Gen 96.2 0.0048 1E-07 56.5 3.6 59 150-219 48-108 (299)
53 KOG1428 Inhibitor of type V ad 95.9 0.0088 1.9E-07 64.3 4.7 74 119-200 3462-3544(3738)
54 PF10367 Vps39_2: Vacuolar sor 95.9 0.0035 7.6E-08 47.2 1.4 37 144-182 72-108 (109)
55 PRK14890 putative Zn-ribbon RN 95.8 0.008 1.7E-07 42.7 2.6 46 63-115 5-56 (59)
56 KOG0978 E3 ubiquitin ligase in 95.8 0.0029 6.3E-08 63.6 0.5 46 151-200 644-689 (698)
57 KOG1645 RING-finger-containing 95.7 0.0074 1.6E-07 57.4 3.0 48 151-198 5-54 (463)
58 KOG1785 Tyrosine kinase negati 95.7 0.003 6.6E-08 60.0 0.3 54 146-203 365-419 (563)
59 PF12906 RINGv: RING-variant d 95.7 0.0059 1.3E-07 41.1 1.5 41 153-195 1-47 (47)
60 KOG3970 Predicted E3 ubiquitin 95.4 0.024 5.1E-07 50.5 4.7 65 148-214 48-123 (299)
61 COG5432 RAD18 RING-finger-cont 95.3 0.01 2.3E-07 54.4 2.1 44 151-199 26-69 (391)
62 KOG1039 Predicted E3 ubiquitin 95.0 0.013 2.9E-07 54.7 2.2 61 148-208 159-231 (344)
63 KOG2879 Predicted E3 ubiquitin 94.4 0.036 7.9E-07 50.4 3.1 53 148-203 237-290 (298)
64 PF05883 Baculo_RING: Baculovi 94.2 0.021 4.5E-07 46.8 1.2 36 150-186 26-67 (134)
65 KOG4275 Predicted E3 ubiquitin 93.7 0.011 2.4E-07 54.2 -1.3 60 139-207 286-349 (350)
66 PF14447 Prok-RING_4: Prokaryo 93.7 0.023 5E-07 39.8 0.4 32 166-200 19-50 (55)
67 KOG3268 Predicted E3 ubiquitin 93.7 0.045 9.7E-07 47.2 2.2 35 169-203 187-232 (234)
68 KOG3800 Predicted E3 ubiquitin 93.4 0.061 1.3E-06 49.2 2.8 49 152-200 2-51 (300)
69 KOG4185 Predicted E3 ubiquitin 93.3 0.058 1.2E-06 48.3 2.6 48 151-199 4-54 (296)
70 KOG0824 Predicted E3 ubiquitin 93.2 0.047 1E-06 50.2 1.8 49 148-200 5-53 (324)
71 PHA02862 5L protein; Provision 93.1 0.041 8.8E-07 45.8 1.1 56 150-211 2-63 (156)
72 KOG1571 Predicted E3 ubiquitin 93.0 0.062 1.3E-06 50.3 2.3 48 146-201 301-348 (355)
73 KOG4739 Uncharacterized protei 92.5 0.057 1.2E-06 48.0 1.2 37 161-200 12-48 (233)
74 PF07800 DUF1644: Protein of u 92.3 0.15 3.3E-06 43.0 3.4 48 150-201 2-92 (162)
75 PF12773 DZR: Double zinc ribb 92.2 0.15 3.3E-06 33.9 2.8 22 68-89 1-23 (50)
76 COG2888 Predicted Zn-ribbon RN 92.2 0.11 2.4E-06 37.1 2.1 45 65-115 9-58 (61)
77 KOG4445 Uncharacterized conser 92.1 0.065 1.4E-06 49.5 1.1 53 148-201 113-187 (368)
78 KOG0297 TNF receptor-associate 92.1 0.091 2E-06 49.7 2.2 54 148-205 19-72 (391)
79 PF04641 Rtf2: Rtf2 RING-finge 90.9 0.19 4.2E-06 44.7 2.9 50 148-200 111-161 (260)
80 KOG2660 Locus-specific chromos 90.9 0.057 1.2E-06 50.1 -0.5 64 148-215 13-77 (331)
81 KOG0309 Conserved WD40 repeat- 90.9 0.15 3.3E-06 52.1 2.4 42 150-194 1028-1069(1081)
82 COG5175 MOT2 Transcriptional r 90.8 0.063 1.4E-06 50.4 -0.4 57 150-206 14-70 (480)
83 PF07191 zinc-ribbons_6: zinc- 90.6 0.16 3.4E-06 37.3 1.7 36 64-99 16-59 (70)
84 KOG1814 Predicted E3 ubiquitin 90.3 0.17 3.7E-06 48.3 2.1 46 150-196 184-236 (445)
85 KOG2114 Vacuolar assembly/sort 90.2 0.21 4.6E-06 51.5 2.8 43 151-200 841-883 (933)
86 KOG1002 Nucleotide excision re 89.3 0.14 3.1E-06 50.5 0.8 52 145-200 531-586 (791)
87 KOG4159 Predicted E3 ubiquitin 88.2 0.6 1.3E-05 44.5 4.1 50 148-202 82-131 (398)
88 KOG3039 Uncharacterized conser 88.1 0.5 1.1E-05 42.7 3.3 53 147-201 218-271 (303)
89 COG5236 Uncharacterized conser 88.0 0.45 9.7E-06 45.0 3.1 64 131-198 42-106 (493)
90 PF03854 zf-P11: P-11 zinc fin 87.3 0.28 6.1E-06 33.6 1.0 31 169-200 15-46 (50)
91 KOG3161 Predicted E3 ubiquitin 87.2 0.31 6.8E-06 49.1 1.6 43 151-197 12-54 (861)
92 PF13248 zf-ribbon_3: zinc-rib 86.9 0.32 6.9E-06 28.6 0.9 24 65-88 2-26 (26)
93 COG5152 Uncharacterized conser 86.5 0.42 9.1E-06 42.0 1.8 58 152-214 198-255 (259)
94 KOG2817 Predicted E3 ubiquitin 86.4 0.68 1.5E-05 44.0 3.3 47 152-199 336-384 (394)
95 PRK04023 DNA polymerase II lar 86.4 0.64 1.4E-05 49.0 3.4 45 80-133 628-672 (1121)
96 PHA02825 LAP/PHD finger-like p 86.3 0.63 1.4E-05 39.3 2.7 47 149-200 7-59 (162)
97 PF09538 FYDLN_acid: Protein o 86.2 0.54 1.2E-05 37.1 2.2 28 76-115 7-34 (108)
98 KOG1952 Transcription factor N 86.2 0.41 8.9E-06 49.4 1.9 52 150-202 191-249 (950)
99 KOG2034 Vacuolar sorting prote 85.4 0.43 9.3E-06 49.4 1.6 37 148-186 815-851 (911)
100 smart00734 ZnF_Rad18 Rad18-lik 85.2 0.79 1.7E-05 27.1 2.1 21 190-211 2-22 (26)
101 PF10571 UPF0547: Uncharacteri 84.6 0.68 1.5E-05 27.6 1.6 22 68-89 3-25 (26)
102 KOG0827 Predicted E3 ubiquitin 84.2 0.098 2.1E-06 49.7 -3.3 52 148-200 194-245 (465)
103 PF14446 Prok-RING_1: Prokaryo 83.4 1.1 2.5E-05 31.2 2.6 35 149-183 4-38 (54)
104 PF07191 zinc-ribbons_6: zinc- 83.4 1.1 2.3E-05 33.0 2.5 44 89-137 16-63 (70)
105 PF08746 zf-RING-like: RING-li 83.4 0.83 1.8E-05 30.1 1.8 25 171-195 18-43 (43)
106 PF13240 zinc_ribbon_2: zinc-r 82.8 0.71 1.5E-05 26.6 1.1 21 68-88 2-23 (23)
107 KOG1813 Predicted E3 ubiquitin 82.6 0.78 1.7E-05 42.3 1.9 60 151-215 242-301 (313)
108 PHA00626 hypothetical protein 82.6 1.1 2.3E-05 31.8 2.1 6 81-86 3-8 (59)
109 PRK14559 putative protein seri 82.6 0.95 2.1E-05 45.7 2.7 33 66-98 2-35 (645)
110 PF02891 zf-MIZ: MIZ/SP-RING z 81.7 1.5 3.2E-05 29.7 2.6 41 152-198 4-50 (50)
111 PF13894 zf-C2H2_4: C2H2-type 81.0 1.4 3.1E-05 23.8 1.9 21 190-210 1-21 (24)
112 PRK14714 DNA polymerase II lar 81.0 1.7 3.6E-05 47.0 3.8 33 65-98 667-700 (1337)
113 KOG4692 Predicted E3 ubiquitin 80.3 1.1 2.3E-05 42.6 2.0 50 147-201 419-468 (489)
114 COG5220 TFB3 Cdk activating ki 80.2 0.73 1.6E-05 41.6 0.8 52 149-200 9-64 (314)
115 KOG0801 Predicted E3 ubiquitin 79.6 0.75 1.6E-05 39.2 0.7 30 148-178 175-204 (205)
116 smart00132 LIM Zinc-binding do 78.7 1.2 2.5E-05 27.0 1.2 37 153-200 2-38 (39)
117 KOG0269 WD40 repeat-containing 77.9 2 4.4E-05 44.1 3.2 80 105-204 751-837 (839)
118 PF05605 zf-Di19: Drought indu 77.4 2.5 5.5E-05 28.6 2.7 11 190-200 32-42 (54)
119 TIGR00595 priA primosomal prot 77.0 2.1 4.5E-05 41.8 3.0 50 26-87 213-262 (505)
120 KOG3053 Uncharacterized conser 75.6 1.1 2.3E-05 40.8 0.5 68 148-215 18-104 (293)
121 PRK14714 DNA polymerase II lar 73.8 2.9 6.2E-05 45.3 3.1 33 79-115 668-700 (1337)
122 TIGR02300 FYDLN_acid conserved 72.7 2.6 5.6E-05 34.4 2.0 28 77-116 8-35 (129)
123 COG1198 PriA Primosomal protei 72.4 3.6 7.9E-05 42.2 3.4 54 26-91 435-488 (730)
124 PHA03096 p28-like protein; Pro 71.9 1.7 3.7E-05 39.7 0.9 47 151-197 179-231 (284)
125 PRK04023 DNA polymerase II lar 71.6 3.3 7.2E-05 43.9 3.0 49 64-118 625-674 (1121)
126 PF07754 DUF1610: Domain of un 71.0 3.8 8.2E-05 24.1 1.9 9 106-114 15-23 (24)
127 COG1198 PriA Primosomal protei 70.3 4.4 9.6E-05 41.6 3.5 43 64-114 434-482 (730)
128 KOG2066 Vacuolar assembly/sort 70.1 1.7 3.6E-05 44.8 0.5 47 151-199 785-834 (846)
129 PLN03086 PRLI-interacting fact 69.5 2.7 5.8E-05 41.9 1.7 84 62-160 404-514 (567)
130 PF07282 OrfB_Zn_ribbon: Putat 69.4 4 8.6E-05 28.6 2.2 27 78-115 28-54 (69)
131 smart00249 PHD PHD zinc finger 68.9 1.6 3.4E-05 27.2 -0.0 42 153-195 2-47 (47)
132 PF05502 Dynactin_p62: Dynacti 66.3 3.3 7.3E-05 40.4 1.7 98 91-211 6-108 (483)
133 PRK14890 putative Zn-ribbon RN 65.9 4.1 8.9E-05 29.0 1.6 34 63-98 23-56 (59)
134 KOG2068 MOT2 transcription fac 65.6 4.8 0.0001 37.6 2.5 50 150-200 249-298 (327)
135 PF03107 C1_2: C1 domain; Int 65.4 4.8 0.0001 24.2 1.7 20 112-131 2-22 (30)
136 COG5222 Uncharacterized conser 64.9 4.2 9.1E-05 37.9 1.9 44 151-197 275-318 (427)
137 KOG1940 Zn-finger protein [Gen 64.7 4 8.6E-05 37.3 1.7 29 14-43 176-204 (276)
138 PRK05580 primosome assembly pr 64.4 5.5 0.00012 40.3 2.8 51 26-88 381-431 (679)
139 PF13453 zf-TFIIB: Transcripti 64.2 6 0.00013 25.4 2.1 26 80-114 1-26 (41)
140 PRK14559 putative protein seri 63.6 3.8 8.3E-05 41.5 1.5 34 65-99 15-50 (645)
141 KOG1001 Helicase-like transcri 63.2 3.3 7.2E-05 42.1 1.0 45 151-200 455-500 (674)
142 PF00096 zf-C2H2: Zinc finger, 63.0 5.6 0.00012 21.7 1.6 17 190-206 1-17 (23)
143 PRK14873 primosome assembly pr 61.9 6.3 0.00014 40.0 2.7 49 26-87 383-431 (665)
144 PRK00398 rpoP DNA-directed RNA 60.5 8.3 0.00018 25.3 2.3 8 107-114 21-28 (46)
145 PF04216 FdhE: Protein involve 59.5 6.6 0.00014 35.3 2.2 48 63-114 195-245 (290)
146 PF04423 Rad50_zn_hook: Rad50 59.2 7.4 0.00016 26.3 1.9 27 189-215 20-48 (54)
147 COG5109 Uncharacterized conser 58.8 9 0.0002 36.0 2.9 44 152-196 338-383 (396)
148 PF05191 ADK_lid: Adenylate ki 58.7 2.4 5.2E-05 27.0 -0.6 27 80-115 3-29 (36)
149 PRK00415 rps27e 30S ribosomal 58.4 5.7 0.00012 28.3 1.2 35 64-98 10-50 (59)
150 PF06524 NOA36: NOA36 protein; 58.3 3.5 7.6E-05 37.7 0.2 51 33-98 140-190 (314)
151 KOG1812 Predicted E3 ubiquitin 58.0 4.7 0.0001 38.2 1.0 37 150-186 146-182 (384)
152 KOG2462 C2H2-type Zn-finger pr 57.8 12 0.00025 34.3 3.4 21 189-209 243-263 (279)
153 PF08271 TF_Zn_Ribbon: TFIIB z 57.4 9.5 0.00021 24.6 2.1 7 81-87 3-9 (43)
154 PF15353 HECA: Headcase protei 57.2 5.5 0.00012 31.5 1.1 15 172-186 40-54 (107)
155 KOG0298 DEAD box-containing he 56.6 4.5 9.7E-05 43.9 0.7 52 148-203 1151-1202(1394)
156 COG3809 Uncharacterized protei 56.1 9.6 0.00021 28.8 2.2 46 152-220 3-48 (88)
157 PHA00626 hypothetical protein 55.6 7.7 0.00017 27.5 1.5 34 66-101 1-34 (59)
158 KOG1609 Protein involved in mR 55.1 6.5 0.00014 34.8 1.3 51 150-200 78-134 (323)
159 PF14569 zf-UDP: Zinc-binding 50.2 21 0.00046 26.8 3.2 51 149-199 8-61 (80)
160 PF01096 TFIIS_C: Transcriptio 49.9 15 0.00033 23.4 2.2 34 80-114 2-35 (39)
161 PF13717 zinc_ribbon_4: zinc-r 48.9 11 0.00024 23.8 1.3 9 80-88 27-35 (36)
162 COG2051 RPS27A Ribosomal prote 48.4 8.4 0.00018 28.1 0.8 28 64-91 18-51 (67)
163 PF05290 Baculo_IE-1: Baculovi 47.7 12 0.00026 30.9 1.7 48 151-202 81-134 (140)
164 PF14353 CpXC: CpXC protein 46.8 20 0.00043 28.1 2.8 11 80-90 3-13 (128)
165 PF13719 zinc_ribbon_5: zinc-r 46.6 13 0.00028 23.5 1.4 9 80-88 27-35 (37)
166 cd00350 rubredoxin_like Rubred 46.5 15 0.00033 22.5 1.7 25 90-115 1-25 (33)
167 PF07649 C1_3: C1-like domain; 46.3 11 0.00025 22.4 1.1 20 113-132 3-23 (30)
168 KOG1311 DHHC-type Zn-finger pr 46.2 13 0.00028 33.4 1.8 49 81-135 104-152 (299)
169 PF04438 zf-HIT: HIT zinc fing 45.6 10 0.00023 23.1 0.8 16 81-97 5-20 (30)
170 KOG1312 DHHC-type Zn-finger pr 45.2 6.9 0.00015 36.3 -0.1 32 111-145 149-180 (341)
171 COG2888 Predicted Zn-ribbon RN 45.1 13 0.00028 26.6 1.3 34 63-98 25-58 (61)
172 PRK00432 30S ribosomal protein 44.7 16 0.00034 24.9 1.7 9 106-114 36-44 (50)
173 PF03833 PolC_DP2: DNA polymer 43.4 7.8 0.00017 40.5 0.0 44 80-132 657-700 (900)
174 PF12874 zf-met: Zinc-finger o 43.1 15 0.00033 20.3 1.2 16 190-205 1-16 (25)
175 PF00412 LIM: LIM domain; Int 42.8 9.8 0.00021 25.2 0.4 39 153-202 1-39 (58)
176 KOG2462 C2H2-type Zn-finger pr 42.3 43 0.00093 30.7 4.5 89 88-204 128-230 (279)
177 PF01667 Ribosomal_S27e: Ribos 42.2 14 0.00029 25.9 1.0 34 65-98 7-46 (55)
178 KOG3362 Predicted BBOX Zn-fing 41.8 8.4 0.00018 32.2 -0.1 25 89-119 117-143 (156)
179 COG1996 RPC10 DNA-directed RNA 41.4 19 0.00042 24.6 1.7 26 90-115 6-32 (49)
180 PF06827 zf-FPG_IleRS: Zinc fi 41.2 20 0.00043 21.3 1.5 10 79-88 2-11 (30)
181 PF12760 Zn_Tnp_IS1595: Transp 41.0 37 0.00081 22.2 3.0 9 79-87 19-27 (46)
182 PF01529 zf-DHHC: DHHC palmito 40.7 23 0.0005 28.6 2.4 49 83-137 41-89 (174)
183 KOG4399 C2HC-type Zn-finger pr 40.3 5.5 0.00012 36.4 -1.5 72 85-159 199-270 (325)
184 TIGR00100 hypA hydrogenase nic 39.8 14 0.0003 29.1 0.9 11 78-88 70-80 (115)
185 PF01529 zf-DHHC: DHHC palmito 39.5 17 0.00036 29.4 1.4 36 104-145 45-80 (174)
186 PF08274 PhnA_Zn_Ribbon: PhnA 39.4 17 0.00037 22.3 1.1 23 80-114 4-26 (30)
187 smart00661 RPOL9 RNA polymeras 39.1 26 0.00056 22.9 2.0 8 107-114 20-27 (52)
188 KOG4367 Predicted Zn-finger pr 38.9 16 0.00036 35.8 1.4 33 150-186 4-36 (699)
189 PRK00420 hypothetical protein; 38.5 22 0.00047 28.3 1.8 19 79-97 24-47 (112)
190 TIGR00595 priA primosomal prot 38.1 35 0.00075 33.4 3.5 46 63-116 211-262 (505)
191 smart00355 ZnF_C2H2 zinc finge 37.7 33 0.00071 18.1 2.0 18 190-207 1-18 (26)
192 PF03604 DNA_RNApol_7kD: DNA d 37.0 20 0.00044 22.3 1.1 10 105-114 15-24 (32)
193 cd02337 ZZ_CBP Zinc finger, ZZ 36.9 26 0.00056 22.8 1.7 20 108-131 1-20 (41)
194 KOG4185 Predicted E3 ubiquitin 36.6 5.4 0.00012 35.6 -2.1 48 151-198 208-265 (296)
195 PF15616 TerY-C: TerY-C metal 36.5 37 0.0008 27.7 2.9 20 79-99 78-98 (131)
196 COG1645 Uncharacterized Zn-fin 36.5 21 0.00045 29.3 1.4 19 79-97 29-51 (131)
197 PLN02189 cellulose synthase 36.4 31 0.00068 36.9 3.1 56 145-200 29-87 (1040)
198 PRK14892 putative transcriptio 36.0 35 0.00077 26.5 2.6 32 122-159 19-51 (99)
199 PF00643 zf-B_box: B-box zinc 35.6 30 0.00066 21.6 1.9 21 79-99 4-24 (42)
200 PF13824 zf-Mss51: Zinc-finger 35.5 33 0.00071 24.1 2.1 21 188-208 13-33 (55)
201 KOG0802 E3 ubiquitin ligase [P 34.4 25 0.00055 34.5 2.0 44 148-200 477-520 (543)
202 KOG4317 Predicted Zn-finger pr 34.4 18 0.00039 34.0 0.9 20 80-99 9-28 (383)
203 COG5183 SSM4 Protein involved 34.4 25 0.00053 37.0 1.9 49 150-200 12-66 (1175)
204 PF03833 PolC_DP2: DNA polymer 33.6 14 0.0003 38.7 0.0 47 63-115 653-700 (900)
205 KOG2272 Focal adhesion protein 33.3 28 0.0006 31.9 1.8 94 36-158 100-200 (332)
206 TIGR02098 MJ0042_CXXC MJ0042 f 33.2 32 0.00068 21.3 1.6 10 65-74 25-34 (38)
207 PF01599 Ribosomal_S27: Riboso 32.8 28 0.0006 23.7 1.3 21 78-98 18-46 (47)
208 cd02249 ZZ Zinc finger, ZZ typ 32.2 33 0.00072 22.4 1.7 9 123-131 13-21 (46)
209 PRK03564 formate dehydrogenase 31.6 56 0.0012 30.3 3.6 25 63-87 210-235 (309)
210 PF12171 zf-C2H2_jaz: Zinc-fin 31.4 38 0.00082 19.4 1.7 14 190-203 2-15 (27)
211 PF06677 Auto_anti-p27: Sjogre 31.3 34 0.00073 22.4 1.6 12 79-90 18-29 (41)
212 PLN00209 ribosomal protein S27 30.8 32 0.00069 26.3 1.5 37 64-100 35-77 (86)
213 PF13913 zf-C2HC_2: zinc-finge 30.8 21 0.00045 20.7 0.4 12 79-90 3-14 (25)
214 PTZ00083 40S ribosomal protein 30.5 27 0.00059 26.6 1.1 36 64-99 34-75 (85)
215 PRK14810 formamidopyrimidine-D 30.3 29 0.00063 31.1 1.5 20 78-97 244-271 (272)
216 COG1998 RPS31 Ribosomal protei 30.0 33 0.00071 23.7 1.3 19 79-97 20-44 (51)
217 KOG0006 E3 ubiquitin-protein l 29.4 48 0.001 31.4 2.8 80 98-186 168-255 (446)
218 PF12172 DUF35_N: Rubredoxin-l 29.3 25 0.00054 21.8 0.7 23 64-86 10-33 (37)
219 TIGR00373 conserved hypothetic 29.1 80 0.0017 26.1 3.8 28 188-215 127-156 (158)
220 smart00586 ZnF_DBF Zinc finger 28.8 39 0.00085 23.1 1.6 14 203-216 34-47 (49)
221 PRK10445 endonuclease VIII; Pr 28.8 33 0.00071 30.7 1.5 20 78-97 235-262 (263)
222 PRK06266 transcription initiat 28.7 82 0.0018 26.6 3.9 27 188-214 135-163 (178)
223 PRK14811 formamidopyrimidine-D 28.5 33 0.00072 30.8 1.5 20 78-97 235-262 (269)
224 cd07973 Spt4 Transcription elo 28.4 32 0.00069 26.7 1.2 19 67-85 5-27 (98)
225 PF00130 C1_1: Phorbol esters/ 28.3 49 0.0011 21.7 2.0 11 104-114 25-35 (53)
226 PF11781 RRN7: RNA polymerase 28.1 40 0.00086 21.4 1.4 25 152-176 10-35 (36)
227 PLN02436 cellulose synthase A 28.0 52 0.0011 35.5 3.0 56 145-200 31-89 (1094)
228 PRK14873 primosome assembly pr 27.9 53 0.0011 33.5 3.0 23 64-90 382-404 (665)
229 COG5273 Uncharacterized protei 27.7 28 0.00061 32.0 1.0 44 79-145 98-141 (309)
230 KOG3005 GIY-YIG type nuclease 27.7 74 0.0016 29.2 3.6 49 151-200 183-243 (276)
231 PF06220 zf-U1: U1 zinc finger 27.4 24 0.00052 22.6 0.3 13 88-100 1-13 (38)
232 PRK08351 DNA-directed RNA poly 27.4 39 0.00084 24.1 1.4 20 67-87 5-24 (61)
233 PF13912 zf-C2H2_6: C2H2-type 27.2 39 0.00085 19.0 1.2 18 190-207 2-19 (27)
234 KOG1829 Uncharacterized conser 27.1 22 0.00048 35.7 0.2 26 167-196 532-557 (580)
235 KOG4399 C2HC-type Zn-finger pr 27.1 15 0.00032 33.7 -1.0 53 79-135 250-302 (325)
236 PF01363 FYVE: FYVE zinc finge 27.0 39 0.00085 23.4 1.4 25 78-115 9-33 (69)
237 PRK12380 hydrogenase nickel in 26.8 30 0.00065 27.1 0.8 10 79-88 71-80 (113)
238 PRK01103 formamidopyrimidine/5 26.5 38 0.00082 30.3 1.6 20 78-97 245-272 (274)
239 PRK04136 rpl40e 50S ribosomal 26.3 44 0.00095 22.9 1.4 24 63-86 12-36 (48)
240 smart00451 ZnF_U1 U1-like zinc 26.0 52 0.0011 19.5 1.7 16 189-204 3-18 (35)
241 KOG4275 Predicted E3 ubiquitin 26.0 21 0.00045 33.3 -0.2 19 79-99 322-340 (350)
242 COG5273 Uncharacterized protei 25.9 41 0.0009 30.9 1.7 32 60-91 104-136 (309)
243 cd02341 ZZ_ZZZ3 Zinc finger, Z 25.8 48 0.001 22.3 1.6 22 108-131 1-22 (48)
244 PRK00564 hypA hydrogenase nick 25.4 45 0.00097 26.3 1.6 11 78-88 71-81 (117)
245 PF11331 DUF3133: Protein of u 25.4 60 0.0013 21.9 2.0 36 37-77 8-43 (46)
246 COG3024 Uncharacterized protei 25.1 38 0.00082 24.6 1.0 26 76-101 5-38 (65)
247 KOG2593 Transcription initiati 25.0 40 0.00087 32.7 1.5 10 123-132 152-161 (436)
248 PRK00464 nrdR transcriptional 25.0 44 0.00094 27.9 1.5 12 80-91 30-41 (154)
249 KOG1100 Predicted E3 ubiquitin 24.7 29 0.00063 30.2 0.4 39 153-200 161-200 (207)
250 TIGR01384 TFS_arch transcripti 24.6 59 0.0013 24.5 2.1 8 81-88 3-10 (104)
251 PRK13945 formamidopyrimidine-D 24.5 44 0.00095 30.1 1.6 19 78-96 254-280 (282)
252 TIGR00577 fpg formamidopyrimid 24.3 44 0.00095 29.9 1.5 19 78-96 245-271 (272)
253 smart00531 TFIIE Transcription 23.8 28 0.0006 28.3 0.1 9 80-88 101-109 (147)
254 COG1144 Pyruvate:ferredoxin ox 23.7 41 0.00088 26.0 1.0 15 122-136 63-77 (91)
255 PF11023 DUF2614: Protein of u 23.6 50 0.0011 26.4 1.6 27 62-88 66-95 (114)
256 PF12756 zf-C2H2_2: C2H2 type 23.5 64 0.0014 23.0 2.1 23 189-211 50-72 (100)
257 PF08792 A2L_zn_ribbon: A2L zi 23.5 51 0.0011 20.5 1.3 10 66-75 4-13 (33)
258 PF05458 Siva: Cd27 binding pr 23.5 63 0.0014 27.5 2.3 23 66-88 112-134 (175)
259 KOG1815 Predicted E3 ubiquitin 23.3 46 0.001 31.9 1.6 39 146-187 66-104 (444)
260 PF09297 zf-NADH-PPase: NADH p 23.2 27 0.00058 21.1 -0.0 21 67-87 5-30 (32)
261 PF14803 Nudix_N_2: Nudix N-te 23.2 49 0.0011 20.8 1.2 11 104-114 19-29 (34)
262 KOG0269 WD40 repeat-containing 23.1 43 0.00093 34.8 1.4 50 79-137 754-806 (839)
263 smart00440 ZnF_C2C2 C2C2 Zinc 23.0 97 0.0021 19.8 2.6 33 80-114 2-35 (40)
264 PF00301 Rubredoxin: Rubredoxi 22.7 62 0.0013 21.8 1.7 10 90-99 1-10 (47)
265 smart00659 RPOLCX RNA polymera 22.5 80 0.0017 20.8 2.2 12 104-115 16-27 (44)
266 COG4888 Uncharacterized Zn rib 22.5 64 0.0014 25.4 1.9 27 106-132 21-54 (104)
267 PF12675 DUF3795: Protein of u 22.4 49 0.0011 24.1 1.2 37 78-114 34-70 (78)
268 PRK03681 hypA hydrogenase nick 21.8 58 0.0013 25.5 1.6 13 76-88 68-80 (114)
269 KOG2932 E3 ubiquitin ligase in 21.7 40 0.00086 31.7 0.8 33 167-202 104-136 (389)
270 PF00628 PHD: PHD-finger; Int 21.7 32 0.0007 22.3 0.1 44 153-197 2-50 (51)
271 TIGR01562 FdhE formate dehydro 21.5 1.1E+02 0.0024 28.4 3.6 25 63-87 208-233 (305)
272 PRK00418 DNA gyrase inhibitor; 21.3 48 0.001 23.8 0.9 12 189-200 6-17 (62)
273 PF10272 Tmpp129: Putative tra 21.3 49 0.0011 31.4 1.3 35 153-199 316-350 (358)
274 TIGR00244 transcriptional regu 21.2 62 0.0013 27.0 1.7 13 80-92 30-42 (147)
275 PRK12496 hypothetical protein; 21.1 45 0.00098 27.8 0.9 22 67-88 129-153 (164)
276 PF06937 EURL: EURL protein; 20.9 92 0.002 28.6 2.9 46 147-193 27-74 (285)
277 KOG1311 DHHC-type Zn-finger pr 20.6 53 0.0011 29.4 1.3 34 106-145 112-145 (299)
278 PF12088 DUF3565: Protein of u 20.4 64 0.0014 23.1 1.4 17 163-179 8-24 (61)
279 TIGR01206 lysW lysine biosynth 20.2 98 0.0021 21.4 2.3 9 80-88 4-12 (54)
280 PRK00366 ispG 4-hydroxy-3-meth 20.1 92 0.002 29.6 2.8 32 189-220 268-299 (360)
281 smart00834 CxxC_CXXC_SSSS Puta 20.0 91 0.002 19.1 2.0 7 80-86 28-34 (41)
No 1
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=100.00 E-value=5.9e-57 Score=401.37 Aligned_cols=205 Identities=48% Similarity=1.044 Sum_probs=198.5
Q ss_pred ccccccCCCCccCcccccccceeecCCCCCcccCchhHHhhhcCCCCCCCCccccccccceeecCCCCccccccccCCCC
Q 027589 5 ANERITFGKMGYGCKHYRRRCRIRAPCCNEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVAQVCTNC 84 (221)
Q Consensus 5 ~~~~~~~~~~~~gC~HY~r~c~l~~pCC~~~ypCr~CHde~~~~~~~~~~~H~~~r~~~~~v~C~~C~~~q~~~~~C~~C 84 (221)
.+++.|++.++.+|+||+|++++++|+|+++|+|++||+++. +|.++|+.|.+|+|+.|+++|++++.|.+|
T Consensus 22 ~~~~~d~~~~~~~c~hy~r~~~~~a~ccd~~~~C~hCH~~s~--------~h~~~r~~v~~~~C~~C~~~q~~~~~c~~c 93 (276)
T KOG1940|consen 22 HSDAEDEIAFPYGCPHYRRNCKSRAPCCDREITCRHCHNESE--------DHDLDRKTVYELLCMKCRKIQPVGQICSNC 93 (276)
T ss_pred ccccccccccccCCchhhhccccccccccceeeeEEecChhh--------hcccchhhhhhhhhhhHHhhhhhhhccccc
Confidence 455789999999999999999999999999999999999974 699999999999999999999999999999
Q ss_pred CCCcceeeccccccccCCCCcCeeeCCCCCcceeCCccceeecCccCccccccccCcceeecCCCCCCCccchhhcccCC
Q 027589 85 GVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYSTSLRNNHLCIENSMHHHCPICYEYLFDSL 164 (221)
Q Consensus 85 g~~f~~y~C~~C~l~dd~~~k~~yHC~~CgiCR~G~~~~~fHC~~C~~C~s~~~~~~H~C~e~~~~~~CpICle~lf~s~ 164 (221)
+..+++|||.+|+||||+++ .||||+.|||||+|++++||||++|+.|++..+.+.|+|+|++++.+||||.|+||++.
T Consensus 94 ~~~~g~~~c~~C~l~dd~~~-~~~hC~~C~icr~g~~~~~fhc~~c~~c~~~~~~~~H~c~e~~~~~ncPic~e~l~~s~ 172 (276)
T KOG1940|consen 94 HVELGEYYCLICKLFDDDPS-KQYHCDLCGICREGLGLDFFHCKKCKACLSAYLSNWHKCVERSSEFNCPICKEYLFLSF 172 (276)
T ss_pred hhhhhhhcCccccccccccc-ceeccccccccccccccchhHHhhhHhHHhhhcccccchhhhcccCCCchhHHHhcccc
Confidence 99999999999999999999 99999999999999999999999999999999999999999999999999999999999
Q ss_pred CceeeeccCCccCHHHHHHHHhcCcCCCCCCcccccchhHHHHHHHHHHHhCCCCC
Q 027589 165 RNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRTWKRIDEEVSLFNLSF 220 (221)
Q Consensus 165 ~~v~~L~CGH~~H~~C~~~~l~~~~~~CPiCrksi~dm~~~~~~lD~~i~~~pmP~ 220 (221)
..+.+|+|||.+|..||++++.++ |+||+|.| ++||+.+|+++|.+|+++|||.
T Consensus 173 ~~~~~~~CgH~~h~~cf~e~~~~~-y~CP~C~~-~~d~~~~~~~~d~~l~~~~~p~ 226 (276)
T KOG1940|consen 173 EDAGVLKCGHYMHSRCFEEMICEG-YTCPICSK-PGDMSHYFRKLDKELAGSPMPE 226 (276)
T ss_pred ccCCccCcccchHHHHHHHHhccC-CCCCcccc-hHHHHHHHHHHHHHHhcCCCCc
Confidence 999999999999999999999865 99999999 9999999999999999999995
No 2
>PF05495 zf-CHY: CHY zinc finger; InterPro: IPR008913 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Pirh2 is an eukaryotic ubiquitin protein ligase, which has been shown to promote p53 degradation in mammals. Pirh2 physically interacts with p53 and promotes ubiquitination of p53 independently of MDM2. Like MDM2, Pirh2 is thought to participate in an autoregulatory feedback loop that controls p53 function. Pirh2 proteins contain three distinct zinc fingers, the CHY-type, the CTCHY-type which is C-terminal to the CHY-type zinc finger and a RING finger. The CHY-type zinc finger has no currently known function []. As well as Pirh2, the CHY-type zinc finger is also found in the following proteins: Yeast helper of Tim protein 13. Hot13 may have a role in the assembly and recycling of the small Tims, a complex of the mitochondrial intermembrane space that participates in the TIM22 import pathway for assembly of the inner membrane [] Several plant hypothetical proteins that also contain haemerythrin cation binding domains Several protozoan hypothetical proteins that also contain a Myb domain The solution structure of this zinc finger has been solved and binds 3 zinc atoms as shown in the following schematic representation: ++---------+-----+ || | | CXHYxxxxxxxxxCCxxxxxCxxCHxxxxxHxxxxxxxxxxxCxxCxxxxxxxxxCxxC | | | | | | | | +-+-----------------+--+ +--+---------+--+ 'C': conserved cysteine involved in the binding of one zinc atom. 'H': conserved histidine involved in the binding of one zinc atom. More information about these proteins can be found at Protein of the Month: Zinc Fingers []; GO: 0008270 zinc ion binding; PDB: 2DKT_A 2K2C_A.
Probab=99.90 E-value=6.9e-25 Score=160.08 Aligned_cols=70 Identities=51% Similarity=1.212 Sum_probs=53.1
Q ss_pred ccccccc-ceeecCCCCCcccCchhHHhhhcCCCCCCCCccccccccceeecCCCCccccccccCCCCCCCcceeecccc
Q 027589 18 CKHYRRR-CRIRAPCCNEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVAQVCTNCGVNMGEYFCDIC 96 (221)
Q Consensus 18 C~HY~r~-c~l~~pCC~~~ypCr~CHde~~~~~~~~~~~H~~~r~~~~~v~C~~C~~~q~~~~~C~~Cg~~f~~y~C~~C 96 (221)
|+||+|+ ++|+||||++|||||+||||++ +|+++|+.+++|+||.|+++|++++. +|+ ++|+|++|
T Consensus 1 C~HY~~~~~~~~~~cC~~~y~C~~CHde~~--------~H~~~~~~~~~v~Cg~C~~~~~~~~~--~c~---~~~~C~~C 67 (71)
T PF05495_consen 1 CKHYHRSLCAIRFPCCGKYYPCRFCHDELE--------DHPFDRWPVKRVICGKCRTEQPIDEY--SCG---ADYFCPIC 67 (71)
T ss_dssp -SS---S-EEEEETTTTEEESSHHHHHHCS--------SS---TTT--EEEETTT--EEES-SB--TT-----SEEETTT
T ss_pred CCCCCCCcEEEECCcccCeecHHHHHHHhc--------cCccccccccCeECCCCCCccChhhh--hcC---CCccCcCc
Confidence 8999999 9999999999999999999975 59999999999999999999999988 777 99999999
Q ss_pred cccc
Q 027589 97 KFYD 100 (221)
Q Consensus 97 ~l~d 100 (221)
++||
T Consensus 68 ~~~~ 71 (71)
T PF05495_consen 68 GLYF 71 (71)
T ss_dssp TEEE
T ss_pred CCCC
Confidence 9986
No 3
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=99.69 E-value=5e-18 Score=130.02 Aligned_cols=73 Identities=26% Similarity=0.611 Sum_probs=66.4
Q ss_pred ccCcccccc---cceeecCCCCCcccCchhHHhhhcCCCCCCCCccccccccceeecCCCCcccccc-----ccCCCCCC
Q 027589 15 GYGCKHYRR---RCRIRAPCCNEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVA-----QVCTNCGV 86 (221)
Q Consensus 15 ~~gC~HY~r---~c~l~~pCC~~~ypCr~CHde~~~~~~~~~~~H~~~r~~~~~v~C~~C~~~q~~~-----~~C~~Cg~ 86 (221)
++||.||++ +++|||.+|+|||+|++||||+++|++ +.++++.+..+.|+||+|..+++++ +.||+|.+
T Consensus 12 etRC~Hyht~~Diialkc~~C~kyYaCy~CHdel~~Hpf---~p~~~~~~~~~~iiCGvC~~~LT~~EY~~~~~Cp~C~s 88 (105)
T COG4357 12 ETRCLHYHTPLDIIALKCKCCQKYYACYHCHDELEDHPF---EPWGLQEFNPKAIICGVCRKLLTRAEYGMCGSCPYCQS 88 (105)
T ss_pred cceeeEecCccceEeeeechhhhhhhHHHHHhHHhcCCC---ccCChhhcCCccEEhhhhhhhhhHHHHhhcCCCCCcCC
Confidence 689999999 789999999999999999999998875 7778888888999999999999885 57999999
Q ss_pred Ccce
Q 027589 87 NMGE 90 (221)
Q Consensus 87 ~f~~ 90 (221)
+||.
T Consensus 89 pFNp 92 (105)
T COG4357 89 PFNP 92 (105)
T ss_pred CCCc
Confidence 9985
No 4
>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=99.47 E-value=1.7e-14 Score=95.10 Aligned_cols=44 Identities=39% Similarity=0.937 Sum_probs=37.5
Q ss_pred CCCccchhhcccCCCceeeeccCCccCHHHHHHHHhcCcCCCCCCc
Q 027589 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICS 196 (221)
Q Consensus 151 ~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~~~~~CPiCr 196 (221)
++||||++++.+ .+.+..|+|||+||.+|+.+|+++ +.+||+||
T Consensus 1 d~C~IC~~~~~~-~~~~~~l~C~H~fh~~Ci~~~~~~-~~~CP~CR 44 (44)
T PF13639_consen 1 DECPICLEEFED-GEKVVKLPCGHVFHRSCIKEWLKR-NNSCPVCR 44 (44)
T ss_dssp -CETTTTCBHHT-TSCEEEETTSEEEEHHHHHHHHHH-SSB-TTTH
T ss_pred CCCcCCChhhcC-CCeEEEccCCCeeCHHHHHHHHHh-CCcCCccC
Confidence 379999999654 578889999999999999999985 68999997
No 5
>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=99.13 E-value=4e-11 Score=87.74 Aligned_cols=48 Identities=31% Similarity=0.688 Sum_probs=36.8
Q ss_pred CCCCCCccchhhcccC---------CCceeeeccCCccCHHHHHHHHhcCcCCCCCCc
Q 027589 148 SMHHHCPICYEYLFDS---------LRNTTVMKCGHTMHCECYHEMIKRDKYCCPICS 196 (221)
Q Consensus 148 ~~~~~CpICle~lf~s---------~~~v~~L~CGH~~H~~C~~~~l~~~~~~CPiCr 196 (221)
..+++|+||++.|.+. .-++...+|||.||..||.+||+. +.+||+||
T Consensus 17 ~~~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~-~~~CP~CR 73 (73)
T PF12678_consen 17 IADDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQ-NNTCPLCR 73 (73)
T ss_dssp SCCSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTT-SSB-TTSS
T ss_pred CcCCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhc-CCcCCCCC
Confidence 3466799999998443 234556689999999999999984 66999997
No 6
>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=99.07 E-value=1.4e-10 Score=73.91 Aligned_cols=45 Identities=31% Similarity=0.866 Sum_probs=37.8
Q ss_pred CCccchhhcccCCCceeeeccCCccCHHHHHHHHhcCcCCCCCCcccc
Q 027589 152 HCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSV 199 (221)
Q Consensus 152 ~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~~~~~CPiCrksi 199 (221)
.|+||++.+ ..++..++|||.||..|++.|++..+.+||+|++.+
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 499999986 245666779999999999999985578899999764
No 7
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=99.05 E-value=6.4e-11 Score=109.86 Aligned_cols=57 Identities=26% Similarity=0.742 Sum_probs=48.6
Q ss_pred CCCCCCCccchhhcccCC---------CceeeeccCCccCHHHHHHHHhcCcCCCCCCccc-ccchhH
Q 027589 147 NSMHHHCPICYEYLFDSL---------RNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKS-VIDMSR 204 (221)
Q Consensus 147 ~~~~~~CpICle~lf~s~---------~~v~~L~CGH~~H~~C~~~~l~~~~~~CPiCrks-i~dm~~ 204 (221)
.+.+..|.||+|+||.+. ...+.|||||.+|-+|++.|++ ++.+|||||.+ +.||++
T Consensus 284 ~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~E-RqQTCPICr~p~ifd~~~ 350 (491)
T COG5243 284 TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLE-RQQTCPICRRPVIFDQSS 350 (491)
T ss_pred cCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHH-hccCCCcccCccccccCC
Confidence 566788999999998875 2247899999999999999998 57899999999 568765
No 8
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.04 E-value=8.4e-11 Score=108.58 Aligned_cols=50 Identities=22% Similarity=0.762 Sum_probs=44.2
Q ss_pred CCCccchhhcccCCCceeeeccCCccCHHHHHHHHhcCcCCCCCCcccccc
Q 027589 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID 201 (221)
Q Consensus 151 ~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~~~~~CPiCrksi~d 201 (221)
..|+||||+ |..++.+++|||+|.||..|++.||......||+|+..+..
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 489999999 77789999999999999999999998543459999998874
No 9
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=98.92 E-value=6.5e-10 Score=71.58 Aligned_cols=39 Identities=38% Similarity=0.987 Sum_probs=33.3
Q ss_pred CccchhhcccCCCceeeeccCCccCHHHHHHHHhcCcCCCCCC
Q 027589 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPIC 195 (221)
Q Consensus 153 CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~~~~~CPiC 195 (221)
||||++.+.+ ++.+++|||+|...|+.+|++. +.+||+|
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 8999998543 6789999999999999999996 7899998
No 10
>PHA02929 N1R/p28-like protein; Provisional
Probab=98.91 E-value=1e-09 Score=97.01 Aligned_cols=54 Identities=30% Similarity=0.664 Sum_probs=42.7
Q ss_pred CCCCCCCccchhhcccCCC---c-eeeeccCCccCHHHHHHHHhcCcCCCCCCcccccc
Q 027589 147 NSMHHHCPICYEYLFDSLR---N-TTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID 201 (221)
Q Consensus 147 ~~~~~~CpICle~lf~s~~---~-v~~L~CGH~~H~~C~~~~l~~~~~~CPiCrksi~d 201 (221)
.+.+..||||+|.+.+... . ...++|||.||..|+.+|++ .+.+||+||..+..
T Consensus 171 ~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~-~~~tCPlCR~~~~~ 228 (238)
T PHA02929 171 RSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKK-EKNTCPVCRTPFIS 228 (238)
T ss_pred CCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHh-cCCCCCCCCCEeeE
Confidence 4556789999999765321 1 23458999999999999998 57899999999874
No 11
>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=98.81 E-value=2.9e-09 Score=71.90 Aligned_cols=47 Identities=36% Similarity=0.918 Sum_probs=38.9
Q ss_pred CCCCccchhhcccCCCceeeeccCCc-cCHHHHHHHHhcCcCCCCCCcccccc
Q 027589 150 HHHCPICYEYLFDSLRNTTVMKCGHT-MHCECYHEMIKRDKYCCPICSKSVID 201 (221)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~L~CGH~-~H~~C~~~~l~~~~~~CPiCrksi~d 201 (221)
+..|+||++.. ..+..+||||. |...|+.+|++ ...+||+||+.|.+
T Consensus 2 ~~~C~iC~~~~----~~~~~~pCgH~~~C~~C~~~~~~-~~~~CP~Cr~~i~~ 49 (50)
T PF13920_consen 2 DEECPICFENP----RDVVLLPCGHLCFCEECAERLLK-RKKKCPICRQPIES 49 (50)
T ss_dssp HSB-TTTSSSB----SSEEEETTCEEEEEHHHHHHHHH-TTSBBTTTTBB-SE
T ss_pred cCCCccCCccC----CceEEeCCCChHHHHHHhHHhcc-cCCCCCcCChhhcC
Confidence 46799999973 35788999999 99999999998 67899999999864
No 12
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=98.77 E-value=5.3e-09 Score=79.06 Aligned_cols=47 Identities=28% Similarity=0.499 Sum_probs=32.8
Q ss_pred CCCccchhhcccCCCceeeeccCCccCHHHHHHHHhc--CcCCCCCCcccc
Q 027589 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR--DKYCCPICSKSV 199 (221)
Q Consensus 151 ~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~--~~~~CPiCrksi 199 (221)
+.||.|..+--+ -++..-.|||.||..||.+||++ ++.+||+||+..
T Consensus 33 g~Cp~Ck~Pgd~--Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w 81 (85)
T PF12861_consen 33 GCCPDCKFPGDD--CPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPW 81 (85)
T ss_pred cCCCCccCCCCC--CceeeccCccHHHHHHHHHHHccccCCCCCCCcCCee
Confidence 345555544211 23344469999999999999985 367899999875
No 13
>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=98.77 E-value=4.6e-09 Score=67.71 Aligned_cols=40 Identities=33% Similarity=0.938 Sum_probs=34.5
Q ss_pred CccchhhcccCCCceeeeccCCccCHHHHHHHHh-cCcCCCCCC
Q 027589 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIK-RDKYCCPIC 195 (221)
Q Consensus 153 CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~-~~~~~CPiC 195 (221)
||||++.+.+ ++.+++|||.|+..|+.+|++ ....+||+|
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 8999998543 457899999999999999998 568899998
No 14
>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=98.76 E-value=6.1e-09 Score=63.98 Aligned_cols=39 Identities=44% Similarity=1.076 Sum_probs=33.5
Q ss_pred CccchhhcccCCCceeeeccCCccCHHHHHHHHhcCcCCCCCC
Q 027589 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPIC 195 (221)
Q Consensus 153 CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~~~~~CPiC 195 (221)
|+||++. .+....++|||.||..|++.|++....+||+|
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 7899987 24677899999999999999998556789987
No 15
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.72 E-value=6.8e-09 Score=94.38 Aligned_cols=53 Identities=25% Similarity=0.601 Sum_probs=45.1
Q ss_pred cCCCCCCCccchhhcccCCCceeeeccCCccCHHHHHHHHhcCcCCCCCCcccc
Q 027589 146 ENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSV 199 (221)
Q Consensus 146 e~~~~~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~~~~~CPiCrksi 199 (221)
|....-+|+|||++ |...+.+++|||.|.||..|+++|+...+.+||+||..+
T Consensus 319 ea~~GveCaICms~-fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~i 371 (374)
T COG5540 319 EADKGVECAICMSN-FIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAI 371 (374)
T ss_pred hcCCCceEEEEhhh-hcccceEEEeccCceechhHHHHHHhhhcccCCccCCCC
Confidence 33445689999999 567788999999999999999999985678999999765
No 16
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.66 E-value=1.7e-08 Score=66.66 Aligned_cols=44 Identities=34% Similarity=0.848 Sum_probs=37.7
Q ss_pred CCccchhhcccCCCceeeeccCCccCHHHHHHHHhcCcCCCCCCcc
Q 027589 152 HCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSK 197 (221)
Q Consensus 152 ~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~~~~~CPiCrk 197 (221)
.|+||++.+ +......+|+|||+|...|+..+.. ....||+|++
T Consensus 1 ~C~~C~~~~-~~~~~~~l~~CgH~~C~~C~~~~~~-~~~~CP~C~k 44 (44)
T PF14634_consen 1 HCNICFEKY-SEERRPRLTSCGHIFCEKCLKKLKG-KSVKCPICRK 44 (44)
T ss_pred CCcCcCccc-cCCCCeEEcccCCHHHHHHHHhhcC-CCCCCcCCCC
Confidence 489999996 5556788899999999999999983 5789999986
No 17
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.49 E-value=9.4e-08 Score=62.99 Aligned_cols=39 Identities=33% Similarity=0.974 Sum_probs=28.2
Q ss_pred CccchhhcccCCCceeeeccCCccCHHHHHHHHhcC---cCCCCCC
Q 027589 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRD---KYCCPIC 195 (221)
Q Consensus 153 CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~~---~~~CPiC 195 (221)
||||++.|.+ .+.|+|||.|-..||..|.+.. .+.||+|
T Consensus 1 CpiC~~~~~~----Pv~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDLFKD----PVSLPCGHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB-SS----EEE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCccchhhCC----ccccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 8999998543 4569999999999999998753 2579987
No 18
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.48 E-value=8.8e-08 Score=63.73 Aligned_cols=40 Identities=33% Similarity=0.890 Sum_probs=23.7
Q ss_pred CccchhhcccCCCceeeeccCCccCHHHHHHHHhcC---cCCCC
Q 027589 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRD---KYCCP 193 (221)
Q Consensus 153 CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~~---~~~CP 193 (221)
||||.| +.+...+.++|+|||+|-++|+++|++.+ ..+||
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 54544556789999999999999999843 56777
No 19
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.48 E-value=4e-08 Score=95.53 Aligned_cols=53 Identities=25% Similarity=0.568 Sum_probs=43.8
Q ss_pred cCCCCCCCccchhhcccCC-CceeeeccCCccCHHHHHHHHhcCcCCCCCCcccc
Q 027589 146 ENSMHHHCPICYEYLFDSL-RNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSV 199 (221)
Q Consensus 146 e~~~~~~CpICle~lf~s~-~~v~~L~CGH~~H~~C~~~~l~~~~~~CPiCrksi 199 (221)
+...+..|+||+|.|+.+. ...++|+|||.||..|+..|++ ...+||+||..+
T Consensus 287 ~~~~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~e-r~qtCP~CR~~~ 340 (543)
T KOG0802|consen 287 LALSDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFE-RQQTCPTCRTVL 340 (543)
T ss_pred hhhcCCeeeeechhhccccccccceeecccchHHHHHHHHHH-HhCcCCcchhhh
Confidence 3455788999999998742 2267899999999999999999 488999999943
No 20
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.41 E-value=2.3e-07 Score=79.74 Aligned_cols=54 Identities=24% Similarity=0.646 Sum_probs=41.3
Q ss_pred eecCCCCCCCccchhhcccCCCceeeeccCCccCHHHHHHHHhc---------------CcCCCCCCcccccc
Q 027589 144 CIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR---------------DKYCCPICSKSVID 201 (221)
Q Consensus 144 C~e~~~~~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~---------------~~~~CPiCrksi~d 201 (221)
=++...+..||||++.+ . ..++++|||.|+..||.+|+.. +..+||+||..|..
T Consensus 12 ~~~~~~~~~CpICld~~-~---dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~ 80 (193)
T PLN03208 12 LVDSGGDFDCNICLDQV-R---DPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE 80 (193)
T ss_pred eccCCCccCCccCCCcC-C---CcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence 34445567899999974 2 2355799999999999999852 23589999999863
No 21
>PHA02926 zinc finger-like protein; Provisional
Probab=98.33 E-value=2.2e-07 Score=81.46 Aligned_cols=75 Identities=23% Similarity=0.405 Sum_probs=51.2
Q ss_pred cccccccCcceeecCCCCCCCccchhhcccCC-----CceeeeccCCccCHHHHHHHHhcC-----cCCCCCCccccc--
Q 027589 133 CYSTSLRNNHLCIENSMHHHCPICYEYLFDSL-----RNTTVMKCGHTMHCECYHEMIKRD-----KYCCPICSKSVI-- 200 (221)
Q Consensus 133 C~s~~~~~~H~C~e~~~~~~CpICle~lf~s~-----~~v~~L~CGH~~H~~C~~~~l~~~-----~~~CPiCrksi~-- 200 (221)
+++.-|.+-..=...+.+..|+||||.+++.+ ......+|+|.|+..|+.+|.+.. ..+||+||..+.
T Consensus 153 ~i~~il~~ye~~~~~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~I 232 (242)
T PHA02926 153 DIIKILDKYEDVYRVSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFRNI 232 (242)
T ss_pred chhHHHHHHHHHHhccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceeeee
Confidence 44444433333345677889999999876531 113345899999999999999742 245999999875
Q ss_pred chhHHHH
Q 027589 201 DMSRTWK 207 (221)
Q Consensus 201 dm~~~~~ 207 (221)
.++++|.
T Consensus 233 ~pSrf~~ 239 (242)
T PHA02926 233 TMSKFYK 239 (242)
T ss_pred cccccee
Confidence 4555554
No 22
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.14 E-value=1.1e-06 Score=74.80 Aligned_cols=46 Identities=30% Similarity=0.855 Sum_probs=37.9
Q ss_pred CCCccchhhcccCCCce-eeeccCCccCHHHHHHHHhcCcCCCCCCccccc
Q 027589 151 HHCPICYEYLFDSLRNT-TVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (221)
Q Consensus 151 ~~CpICle~lf~s~~~v-~~L~CGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (221)
..|||||+.. +. .+ ..-.|||+|.+.||+.-++ ...+||+|+|.|.
T Consensus 132 ~~CPiCl~~~-se--k~~vsTkCGHvFC~~Cik~alk-~~~~CP~C~kkIt 178 (187)
T KOG0320|consen 132 YKCPICLDSV-SE--KVPVSTKCGHVFCSQCIKDALK-NTNKCPTCRKKIT 178 (187)
T ss_pred cCCCceecch-hh--ccccccccchhHHHHHHHHHHH-hCCCCCCcccccc
Confidence 6899999984 32 34 3478999999999999998 4689999999664
No 23
>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=98.12 E-value=2e-06 Score=58.55 Aligned_cols=43 Identities=28% Similarity=0.617 Sum_probs=33.5
Q ss_pred CCccchhhcccCCCceeeeccC-----CccCHHHHHHHHhcC-cCCCCCCc
Q 027589 152 HCPICYEYLFDSLRNTTVMKCG-----HTMHCECYHEMIKRD-KYCCPICS 196 (221)
Q Consensus 152 ~CpICle~lf~s~~~v~~L~CG-----H~~H~~C~~~~l~~~-~~~CPiCr 196 (221)
.|-||++ +++.+...++||. |++|..|+.+|+..+ +.+||||+
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 3889998 3334556688984 999999999999743 55899995
No 24
>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=98.10 E-value=3.5e-06 Score=58.42 Aligned_cols=45 Identities=18% Similarity=0.361 Sum_probs=37.8
Q ss_pred CCCccchhhcccCCCceeeeccCCccCHHHHHHHHhcCcCCCCCCccccc
Q 027589 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (221)
Q Consensus 151 ~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (221)
-.||||++.|.+ + .+++|||+|-+.|+.+|++. +.+||+|++.+.
T Consensus 2 ~~Cpi~~~~~~~---P-v~~~~G~v~~~~~i~~~~~~-~~~cP~~~~~~~ 46 (63)
T smart00504 2 FLCPISLEVMKD---P-VILPSGQTYERRAIEKWLLS-HGTDPVTGQPLT 46 (63)
T ss_pred cCCcCCCCcCCC---C-EECCCCCEEeHHHHHHHHHH-CCCCCCCcCCCC
Confidence 369999997543 4 45799999999999999985 789999999873
No 25
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=98.00 E-value=1.6e-06 Score=62.99 Aligned_cols=51 Identities=31% Similarity=0.626 Sum_probs=24.2
Q ss_pred CCCCccchhhcc-cCCCceeee---ccCCccCHHHHHHHHhcC----------cCCCCCCccccc
Q 027589 150 HHHCPICYEYLF-DSLRNTTVM---KCGHTMHCECYHEMIKRD----------KYCCPICSKSVI 200 (221)
Q Consensus 150 ~~~CpICle~lf-~s~~~v~~L---~CGH~~H~~C~~~~l~~~----------~~~CPiCrksi~ 200 (221)
+.+|+||.+++. +...+..+- .|+..||..|+.+|+... ..+||.|++.|.
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 457999999876 333333333 699999999999998731 236999999884
No 26
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=97.94 E-value=1.8e-06 Score=61.60 Aligned_cols=22 Identities=32% Similarity=0.617 Sum_probs=0.0
Q ss_pred ccchhHHHHHHHHHHHhCCCCC
Q 027589 199 VIDMSRTWKRIDEEVSLFNLSF 220 (221)
Q Consensus 199 i~dm~~~~~~lD~~i~~~pmP~ 220 (221)
|+||+++|++||++||++|||+
T Consensus 1 v~dM~~~w~~LD~~i~~~pmP~ 22 (61)
T PF14599_consen 1 VVDMSAYWRMLDAEIAATPMPE 22 (61)
T ss_dssp ----------------------
T ss_pred CCCHHHHHHHHHHHHHhCCCCH
Confidence 5799999999999999999997
No 27
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=97.93 E-value=4.3e-06 Score=79.49 Aligned_cols=47 Identities=28% Similarity=0.757 Sum_probs=42.2
Q ss_pred CCCccchhhcccCCCceeeeccCCccCHHHHHHHHhcCcCCCCCCccccc
Q 027589 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (221)
Q Consensus 151 ~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (221)
..||||||.|-++...+....|.|+||..|+..|. ..+||+||....
T Consensus 176 PTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~---~~scpvcR~~q~ 222 (493)
T KOG0804|consen 176 PTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWW---DSSCPVCRYCQS 222 (493)
T ss_pred CCcchhHhhcCccccceeeeecccccchHHHhhcc---cCcChhhhhhcC
Confidence 36999999999998888999999999999999995 469999997665
No 28
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.90 E-value=9.4e-06 Score=76.69 Aligned_cols=46 Identities=22% Similarity=0.587 Sum_probs=38.4
Q ss_pred CCCCccchhhcccCCCceeeeccCCccCHHHHHHHHhcCcCCCCCCccccc
Q 027589 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (221)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (221)
...|+||++.+.. ++ +++|||.|...|+..|+.. ...||+|+..+.
T Consensus 26 ~l~C~IC~d~~~~---Pv-itpCgH~FCs~CI~~~l~~-~~~CP~Cr~~~~ 71 (397)
T TIGR00599 26 SLRCHICKDFFDV---PV-LTSCSHTFCSLCIRRCLSN-QPKCPLCRAEDQ 71 (397)
T ss_pred ccCCCcCchhhhC---cc-CCCCCCchhHHHHHHHHhC-CCCCCCCCCccc
Confidence 4589999997532 33 6899999999999999984 568999999876
No 29
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=97.74 E-value=2.6e-05 Score=58.55 Aligned_cols=29 Identities=24% Similarity=0.620 Sum_probs=26.1
Q ss_pred ccCCccCHHHHHHHHhcCcCCCCCCccccc
Q 027589 171 KCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (221)
Q Consensus 171 ~CGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (221)
-|.|.||..||..||.+ ...||+++++..
T Consensus 53 ~CnHaFH~HCI~rWL~T-k~~CPld~q~w~ 81 (88)
T COG5194 53 VCNHAFHDHCIYRWLDT-KGVCPLDRQTWV 81 (88)
T ss_pred ecchHHHHHHHHHHHhh-CCCCCCCCceeE
Confidence 59999999999999985 789999998764
No 30
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.71 E-value=1.5e-05 Score=74.85 Aligned_cols=46 Identities=28% Similarity=0.624 Sum_probs=39.5
Q ss_pred CCCCccchhhcccCCCceeeec-cCCccCHHHHHHHHhcC--cCCCCCCc
Q 027589 150 HHHCPICYEYLFDSLRNTTVMK-CGHTMHCECYHEMIKRD--KYCCPICS 196 (221)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~L~-CGH~~H~~C~~~~l~~~--~~~CPiCr 196 (221)
...|.|| ++++.....+..+. |||+||..|+.+|+... +.+||||+
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 4579999 77888888888776 99999999999999852 46899999
No 31
>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=97.66 E-value=4.2e-05 Score=70.15 Aligned_cols=51 Identities=25% Similarity=0.563 Sum_probs=39.1
Q ss_pred CCCCccchhhcccCCCce-eeeccCCccCHHHHHHHHhcCcCCCCCCccccc
Q 027589 150 HHHCPICYEYLFDSLRNT-TVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (221)
Q Consensus 150 ~~~CpICle~lf~s~~~v-~~L~CGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (221)
+..||||+.+...+++.. .+.+|||.|..+|++.++......||+|++++-
T Consensus 3 ~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lr 54 (309)
T TIGR00570 3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLR 54 (309)
T ss_pred CCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCccc
Confidence 357999999755554322 222799999999999977656789999998775
No 32
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.63 E-value=2.7e-05 Score=65.42 Aligned_cols=44 Identities=30% Similarity=0.845 Sum_probs=37.8
Q ss_pred CCCCCccchhhcccCCCceeeeccCCccCHHHHHHHHhcCcCCCCCCcc
Q 027589 149 MHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSK 197 (221)
Q Consensus 149 ~~~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~~~~~CPiCrk 197 (221)
.+..||||++.+.. + ++|||||.|-..|+..++. ....||.||.
T Consensus 12 ~~~~C~iC~~~~~~---p-~~l~C~H~~c~~C~~~~~~-~~~~Cp~cr~ 55 (386)
T KOG2177|consen 12 EELTCPICLEYFRE---P-VLLPCGHNFCRACLTRSWE-GPLSCPVCRP 55 (386)
T ss_pred ccccChhhHHHhhc---C-ccccccchHhHHHHHHhcC-CCcCCcccCC
Confidence 45689999999543 3 8899999999999999987 6789999994
No 33
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=97.63 E-value=2.2e-05 Score=71.08 Aligned_cols=45 Identities=29% Similarity=0.693 Sum_probs=37.6
Q ss_pred CCCccchhhcccCCCceeeeccCCccCHHHHHHHHhcCcCCCCCCccccc
Q 027589 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (221)
Q Consensus 151 ~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (221)
..|.+|||... .....||||.|.-.||.+|..+ ...||+||..+-
T Consensus 240 ~kC~LCLe~~~----~pSaTpCGHiFCWsCI~~w~~e-k~eCPlCR~~~~ 284 (293)
T KOG0317|consen 240 RKCSLCLENRS----NPSATPCGHIFCWSCILEWCSE-KAECPLCREKFQ 284 (293)
T ss_pred CceEEEecCCC----CCCcCcCcchHHHHHHHHHHcc-ccCCCcccccCC
Confidence 46999999853 3457899999999999999985 578999998764
No 34
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.47 E-value=6.8e-05 Score=72.37 Aligned_cols=50 Identities=28% Similarity=0.613 Sum_probs=38.4
Q ss_pred CCCCCCccchhhcccCCCceeeeccCCccCHHHHHHHHhcC----cCCCCCCcccccc
Q 027589 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRD----KYCCPICSKSVID 201 (221)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~~----~~~CPiCrksi~d 201 (221)
+++..|||||++ .. .++ .+.|||+|.-.||-+|+... ...||||+..|.-
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 447899999998 22 233 34599999999999988642 4579999999863
No 35
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.41 E-value=5e-05 Score=73.27 Aligned_cols=51 Identities=24% Similarity=0.533 Sum_probs=37.6
Q ss_pred CCCCccchhhccc--CCC-----------ceeeeccCCccCHHHHHHHHhcCcCCCCCCccccc
Q 027589 150 HHHCPICYEYLFD--SLR-----------NTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (221)
Q Consensus 150 ~~~CpICle~lf~--s~~-----------~v~~L~CGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (221)
..+|+|||.++-- ... ...+-||-|.||+.|+.+|+...+..||+||..+-
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 3579999976421 111 13344999999999999999866778999998763
No 36
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.36 E-value=4.8e-05 Score=68.67 Aligned_cols=52 Identities=27% Similarity=0.520 Sum_probs=42.0
Q ss_pred CCCCCccchhhcccCC------CceeeeccCCccCHHHHHHHHh-cCcCCCCCCccccc
Q 027589 149 MHHHCPICYEYLFDSL------RNTTVMKCGHTMHCECYHEMIK-RDKYCCPICSKSVI 200 (221)
Q Consensus 149 ~~~~CpICle~lf~s~------~~v~~L~CGH~~H~~C~~~~l~-~~~~~CPiCrksi~ 200 (221)
+++.|+||...++.+. +....|.|+|+||..||+-|-. ....+||.|++.+.
T Consensus 223 ~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVd 281 (328)
T KOG1734|consen 223 SDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVD 281 (328)
T ss_pred CcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhh
Confidence 4567999999887764 2456899999999999999953 35789999998774
No 37
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=97.34 E-value=0.00016 Score=67.14 Aligned_cols=59 Identities=31% Similarity=0.663 Sum_probs=45.9
Q ss_pred CCccchhhcccCCCceeeeccCCccCHHHHHHHHhcCcCCCCCCcccccc-hhHHHHHHHHHHHh
Q 027589 152 HCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID-MSRTWKRIDEEVSL 215 (221)
Q Consensus 152 ~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~~~~~CPiCrksi~d-m~~~~~~lD~~i~~ 215 (221)
.|-||.|+| . ...+.||||+|.+.||..+|. .+-.||.|+..+.. ..+--+.||++|+.
T Consensus 25 RC~IC~eyf-~---ip~itpCsHtfCSlCIR~~L~-~~p~CP~C~~~~~Es~Lr~n~il~Eiv~S 84 (442)
T KOG0287|consen 25 RCGICFEYF-N---IPMITPCSHTFCSLCIRKFLS-YKPQCPTCCVTVTESDLRNNRILDEIVKS 84 (442)
T ss_pred HHhHHHHHh-c---CceeccccchHHHHHHHHHhc-cCCCCCceecccchhhhhhhhHHHHHHHH
Confidence 599999984 3 234568999999999999998 58899999998863 33355677777654
No 38
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=97.29 E-value=9.6e-05 Score=55.12 Aligned_cols=29 Identities=24% Similarity=0.707 Sum_probs=25.0
Q ss_pred ccCCccCHHHHHHHHhc--CcCCCCCCcccc
Q 027589 171 KCGHTMHCECYHEMIKR--DKYCCPICSKSV 199 (221)
Q Consensus 171 ~CGH~~H~~C~~~~l~~--~~~~CPiCrksi 199 (221)
-|.|.||..||.+|+.. ++..||+||+..
T Consensus 50 ~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~ 80 (84)
T KOG1493|consen 50 YCLHAFHAHCILKWLNTPTSQGQCPMCRQTW 80 (84)
T ss_pred HHHHHHHHHHHHHHhcCccccccCCcchhee
Confidence 59999999999999964 467799999865
No 39
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.26 E-value=0.00021 Score=62.98 Aligned_cols=50 Identities=24% Similarity=0.647 Sum_probs=38.6
Q ss_pred CCCCCCccchhhcccCCCceeeeccCCccCHHHHHHHHhc--CcCCCCCCcccccc
Q 027589 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR--DKYCCPICSKSVID 201 (221)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~--~~~~CPiCrksi~d 201 (221)
+..-+|-||||- + ++.++-.|||.|.-.||.+||.. ++..||+|+..|.+
T Consensus 45 ~~~FdCNICLd~---a-kdPVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~ 96 (230)
T KOG0823|consen 45 GGFFDCNICLDL---A-KDPVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSI 96 (230)
T ss_pred CCceeeeeeccc---c-CCCEEeecccceehHHHHHHHhhcCCCeeCCcccccccc
Confidence 445689999985 2 23445679999999999999974 34558999988764
No 40
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=97.25 E-value=0.0001 Score=53.20 Aligned_cols=56 Identities=23% Similarity=0.642 Sum_probs=29.7
Q ss_pred CCCccchhhcccCCCceeeeccCCccCHHHHHHHHhcCcCCCCCCccccc--chhHHHHHHHHHH
Q 027589 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI--DMSRTWKRIDEEV 213 (221)
Q Consensus 151 ~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~~~~~CPiCrksi~--dm~~~~~~lD~~i 213 (221)
-.|++|.+.|. ++|..-.|.|.|-+.|+.+-+. ..||+|+.+.. |+ .+.++||..|
T Consensus 8 LrCs~C~~~l~---~pv~l~~CeH~fCs~Ci~~~~~---~~CPvC~~Paw~qD~-~~NrqLd~~i 65 (65)
T PF14835_consen 8 LRCSICFDILK---EPVCLGGCEHIFCSSCIRDCIG---SECPVCHTPAWIQDI-QINRQLDSMI 65 (65)
T ss_dssp TS-SSS-S--S---S-B---SSS--B-TTTGGGGTT---TB-SSS--B-S-SS-----HHHHHHH
T ss_pred cCCcHHHHHhc---CCceeccCccHHHHHHhHHhcC---CCCCCcCChHHHHHH-HhhhhhhccC
Confidence 36999999864 3677779999999999988664 46999999985 44 3788999876
No 41
>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=97.08 E-value=0.0006 Score=49.51 Aligned_cols=48 Identities=19% Similarity=0.374 Sum_probs=35.6
Q ss_pred CCCCccchhhcccCCCceeeeccCCccCHHHHHHHHhcCcCCCCCCcccccc
Q 027589 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID 201 (221)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~~~~~CPiCrksi~d 201 (221)
+-.|||.++-|.+ +| ++++||+|=+.++.+|+..++.+||++++.+..
T Consensus 4 ~f~CpIt~~lM~d---PV-i~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~ 51 (73)
T PF04564_consen 4 EFLCPITGELMRD---PV-ILPSGHTYERSAIERWLEQNGGTDPFTRQPLSE 51 (73)
T ss_dssp GGB-TTTSSB-SS---EE-EETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SG
T ss_pred ccCCcCcCcHhhC---ce-eCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCc
Confidence 3469999987543 44 689999999999999998668999999988863
No 42
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=96.98 E-value=0.0002 Score=67.59 Aligned_cols=62 Identities=26% Similarity=0.573 Sum_probs=50.8
Q ss_pred cceeecCCCCCCCccchhhcccCCCceeeeccCCccCHHHHHHHHhc-CcCCCCCCcccccchh
Q 027589 141 NHLCIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR-DKYCCPICSKSVIDMS 203 (221)
Q Consensus 141 ~H~C~e~~~~~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~-~~~~CPiCrksi~dm~ 203 (221)
.|.|++ .++-+|-.|.|.+-...+....|||.|+||..|+.++|.. ...+||-|||.+..|+
T Consensus 357 a~~~~~-e~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~CrklrSs~~ 419 (518)
T KOG1941|consen 357 AHECVE-ETELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRKLRSSMK 419 (518)
T ss_pred HHHHHH-HHhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHHHHhhcc
Confidence 355554 3568899999998777788899999999999999999864 3567999998777665
No 43
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.83 E-value=0.00038 Score=48.95 Aligned_cols=54 Identities=37% Similarity=0.784 Sum_probs=38.8
Q ss_pred CCCCCCccchhhcccCCCceeeeccCCc-cCHHHHHHHHhcCcCCCCCCcccccchhHH
Q 027589 148 SMHHHCPICYEYLFDSLRNTTVMKCGHT-MHCECYHEMIKRDKYCCPICSKSVIDMSRT 205 (221)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~L~CGH~-~H~~C~~~~l~~~~~~CPiCrksi~dm~~~ 205 (221)
+.+.+|.||+|.-.+| ...-|||+ |.-.|-.+.++..+..|||||.+|-|.-+.
T Consensus 5 ~~~dECTICye~pvds----VlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~dvIkT 59 (62)
T KOG4172|consen 5 QWSDECTICYEHPVDS----VLYTCGHMCMCYACGLRLKKALHGCCPICRAPIKDVIKT 59 (62)
T ss_pred ccccceeeeccCcchH----HHHHcchHHhHHHHHHHHHHccCCcCcchhhHHHHHHHh
Confidence 3457899999974333 23479997 667776665554688999999999876443
No 44
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.77 E-value=0.00095 Score=62.09 Aligned_cols=50 Identities=28% Similarity=0.685 Sum_probs=40.3
Q ss_pred CCCCCCccchhhcccCCCceeeeccCCc-cCHHHHHHHHhcCcCCCCCCcccccch
Q 027589 148 SMHHHCPICYEYLFDSLRNTTVMKCGHT-MHCECYHEMIKRDKYCCPICSKSVIDM 202 (221)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~L~CGH~-~H~~C~~~~l~~~~~~CPiCrksi~dm 202 (221)
....+|.|||.+ + ..+.+|||.|. +.+.|-+.+.- .+.+|||||..|...
T Consensus 288 ~~gkeCVIClse---~-rdt~vLPCRHLCLCs~Ca~~Lr~-q~n~CPICRqpi~~l 338 (349)
T KOG4265|consen 288 ESGKECVICLSE---S-RDTVVLPCRHLCLCSGCAKSLRY-QTNNCPICRQPIEEL 338 (349)
T ss_pred cCCCeeEEEecC---C-cceEEecchhhehhHhHHHHHHH-hhcCCCccccchHhh
Confidence 345679999987 2 46789999996 89999998864 467899999998744
No 45
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.60 E-value=0.0011 Score=59.57 Aligned_cols=47 Identities=26% Similarity=0.548 Sum_probs=37.2
Q ss_pred CCCCccchhhcccCCCceeeeccCCccCHHHHHH-HHhcCcCCCCCCccccc
Q 027589 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHE-MIKRDKYCCPICSKSVI 200 (221)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~-~l~~~~~~CPiCrksi~ 200 (221)
+..|+||+|... .....+|||.|.-.|+.. |.......||+||.-+.
T Consensus 215 d~kC~lC~e~~~----~ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~ 262 (271)
T COG5574 215 DYKCFLCLEEPE----VPSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVY 262 (271)
T ss_pred ccceeeeecccC----CcccccccchhhHHHHHHHHHhhccccCchhhhhcc
Confidence 456999999753 345789999999999999 88754444999997665
No 46
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=96.58 E-value=0.0014 Score=51.53 Aligned_cols=28 Identities=29% Similarity=0.732 Sum_probs=24.8
Q ss_pred ccCCccCHHHHHHHHhcCcCCCCCCcccc
Q 027589 171 KCGHTMHCECYHEMIKRDKYCCPICSKSV 199 (221)
Q Consensus 171 ~CGH~~H~~C~~~~l~~~~~~CPiCrksi 199 (221)
-|.|+||..||..||+. ...|||+.+.-
T Consensus 80 ~CNHaFH~hCisrWlkt-r~vCPLdn~eW 107 (114)
T KOG2930|consen 80 VCNHAFHFHCISRWLKT-RNVCPLDNKEW 107 (114)
T ss_pred ecchHHHHHHHHHHHhh-cCcCCCcCcce
Confidence 59999999999999994 67999998753
No 47
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=96.52 E-value=0.0021 Score=43.84 Aligned_cols=45 Identities=29% Similarity=0.789 Sum_probs=24.3
Q ss_pred CccchhhcccCCCceeeec--cCCccCHHHHHHHHhcCcCCCCCCcccc
Q 027589 153 CPICYEYLFDSLRNTTVMK--CGHTMHCECYHEMIKRDKYCCPICSKSV 199 (221)
Q Consensus 153 CpICle~lf~s~~~v~~L~--CGH~~H~~C~~~~l~~~~~~CPiCrksi 199 (221)
||+|.|+|..+ ...++| ||..+-+.|+..-++..+.+||-||+..
T Consensus 1 cp~C~e~~d~~--d~~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y 47 (48)
T PF14570_consen 1 CPLCDEELDET--DKDFYPCECGFQICRFCYHDILENEGGRCPGCREPY 47 (48)
T ss_dssp -TTTS-B--CC--CTT--SSTTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred CCCcccccccC--CCccccCcCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence 79999998443 445555 7999999999999875688999999863
No 48
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=96.51 E-value=0.0013 Score=67.83 Aligned_cols=53 Identities=26% Similarity=0.622 Sum_probs=38.5
Q ss_pred CCCCCCCccchhhcc--cCCCceee-eccCCccCHHHHHHHHhc-CcCCCCCCcccc
Q 027589 147 NSMHHHCPICYEYLF--DSLRNTTV-MKCGHTMHCECYHEMIKR-DKYCCPICSKSV 199 (221)
Q Consensus 147 ~~~~~~CpICle~lf--~s~~~v~~-L~CGH~~H~~C~~~~l~~-~~~~CPiCrksi 199 (221)
-+....|+||..-|. +..-|.+. -.|.|.||..|+.+|.++ ++.+||+||.+|
T Consensus 1466 fsG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRsei 1522 (1525)
T COG5219 1466 FSGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEI 1522 (1525)
T ss_pred cCCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCcccccc
Confidence 356779999998764 22122222 237799999999999975 477899999766
No 49
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=96.46 E-value=0.00096 Score=67.61 Aligned_cols=77 Identities=16% Similarity=0.290 Sum_probs=54.9
Q ss_pred ceeecCccCccccccccCcceeec-CCCCCCCccchhhcccCCCceeeeccCCccCHHHHHHHHhcCcCCCCCCcccccc
Q 027589 123 NYFHCKRCGSCYSTSLRNNHLCIE-NSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID 201 (221)
Q Consensus 123 ~~fHC~~C~~C~s~~~~~~H~C~e-~~~~~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~~~~~CPiCrksi~d 201 (221)
.-..|..|-.+.|...-..-.|+- .-....||+|+-...+ .......+|+|.||..||..|.+ ...+||++|+.++.
T Consensus 95 ~s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~D-qL~~~~k~c~H~FC~~Ci~sWsR-~aqTCPiDR~EF~~ 172 (1134)
T KOG0825|consen 95 ESDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCND-QLEESEKHTAHYFCEECVGSWSR-CAQTCPVDRGEFGE 172 (1134)
T ss_pred cccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHH-HhhccccccccccHHHHhhhhhh-hcccCchhhhhhhe
Confidence 345566777777764334445542 2335679999987444 33445678999999999999998 46899999998764
No 50
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.30 E-value=0.0011 Score=61.88 Aligned_cols=49 Identities=27% Similarity=0.688 Sum_probs=41.4
Q ss_pred CCCCccchhhcccCCCceeeeccCCccCHHHHHHHHhcCcCCCCCCcccccc
Q 027589 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID 201 (221)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~~~~~CPiCrksi~d 201 (221)
+-.|||||+-|.. ...+..|+|-|...||..-++..+..||.|||.++.
T Consensus 43 ~v~c~icl~llk~---tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~S 91 (381)
T KOG0311|consen 43 QVICPICLSLLKK---TMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVS 91 (381)
T ss_pred hhccHHHHHHHHh---hcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhccc
Confidence 4579999997654 355778999999999998888889999999999973
No 51
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=96.19 E-value=0.0032 Score=44.14 Aligned_cols=43 Identities=28% Similarity=0.615 Sum_probs=30.0
Q ss_pred CCCCCccchhhcccCCCceeeeccCCccCHHHHHHHHh-cCcCCCCC
Q 027589 149 MHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIK-RDKYCCPI 194 (221)
Q Consensus 149 ~~~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~-~~~~~CPi 194 (221)
....|||-+..| . ++|+...|||+|=+.-|.+||. ....+||+
T Consensus 10 ~~~~CPiT~~~~-~--~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv 53 (57)
T PF11789_consen 10 ISLKCPITLQPF-E--DPVKSKKCGHTFEKEAILQYIQRNGSKRCPV 53 (57)
T ss_dssp --SB-TTTSSB--S--SEEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred eccCCCCcCChh-h--CCcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence 356799999974 3 4899999999999999999993 35778998
No 52
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=96.15 E-value=0.0048 Score=56.53 Aligned_cols=59 Identities=19% Similarity=0.584 Sum_probs=46.3
Q ss_pred CCCCccchhhcccCCCceeeecc--CCccCHHHHHHHHhcCcCCCCCCcccccchhHHHHHHHHHHHhCCCC
Q 027589 150 HHHCPICYEYLFDSLRNTTVMKC--GHTMHCECYHEMIKRDKYCCPICSKSVIDMSRTWKRIDEEVSLFNLS 219 (221)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~L~C--GH~~H~~C~~~~l~~~~~~CPiCrksi~dm~~~~~~lD~~i~~~pmP 219 (221)
-.+||||.++|.. -++.| ||..-+.|-.+. ..+||.||..|++... +.++..|++...|
T Consensus 48 lleCPvC~~~l~~-----Pi~QC~nGHlaCssC~~~~----~~~CP~Cr~~~g~~R~--~amEkV~e~~~vp 108 (299)
T KOG3002|consen 48 LLDCPVCFNPLSP-----PIFQCDNGHLACSSCRTKV----SNKCPTCRLPIGNIRC--RAMEKVAEAVLVP 108 (299)
T ss_pred hccCchhhccCcc-----cceecCCCcEehhhhhhhh----cccCCccccccccHHH--HHHHHHHHhceec
Confidence 3579999999753 35788 899999998744 4699999999997643 6777777877665
No 53
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=95.95 E-value=0.0088 Score=64.34 Aligned_cols=74 Identities=26% Similarity=0.631 Sum_probs=56.1
Q ss_pred CCccceeecCccCccccccccCcceeecCCCCCCCccchhhcccCCCceeeeccCCccCHHHHHHHHhcC---------c
Q 027589 119 GGRENYFHCKRCGSCYSTSLRNNHLCIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRD---------K 189 (221)
Q Consensus 119 G~~~~~fHC~~C~~C~s~~~~~~H~C~e~~~~~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~~---------~ 189 (221)
||.+|-.||--|--|-.-.. ....++.|.||..+- -+.-+.+.|.|||+||..|....|+++ -
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-------KQDADDMCMICFTEA-LSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGF 3533 (3738)
T ss_pred cCccchhhcccccccChhhh-------hcccCceEEEEehhh-hCCCcceecCCccchhHHHHHHHHHhcccCCeeEEee
Confidence 56778889888877643221 234467799999874 345789999999999999999877642 4
Q ss_pred CCCCCCccccc
Q 027589 190 YCCPICSKSVI 200 (221)
Q Consensus 190 ~~CPiCrksi~ 200 (221)
..||||...|.
T Consensus 3534 isCPiC~n~In 3544 (3738)
T KOG1428|consen 3534 ISCPICKNKIN 3544 (3738)
T ss_pred eecccccchhh
Confidence 57999998875
No 54
>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=95.93 E-value=0.0035 Score=47.24 Aligned_cols=37 Identities=27% Similarity=0.583 Sum_probs=29.7
Q ss_pred eecCCCCCCCccchhhcccCCCceeeeccCCccCHHHHH
Q 027589 144 CIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYH 182 (221)
Q Consensus 144 C~e~~~~~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~ 182 (221)
.+.-..+..|+||...|..+ ...+.||||.+|..|++
T Consensus 72 ~v~i~~~~~C~vC~k~l~~~--~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 72 SVVITESTKCSVCGKPLGNS--VFVVFPCGHVVHYSCIK 108 (109)
T ss_pred eEEECCCCCccCcCCcCCCc--eEEEeCCCeEEeccccc
Confidence 33334567799999998774 67889999999999974
No 55
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=95.80 E-value=0.008 Score=42.68 Aligned_cols=46 Identities=26% Similarity=0.768 Sum_probs=33.6
Q ss_pred cceeecCCCCcccccc-----ccCCCCCCC-cceeeccccccccCCCCcCeeeCCCCCc
Q 027589 63 VKQVICSVCDTEQPVA-----QVCTNCGVN-MGEYFCDICKFYDDDIEKGQFHCDDCGI 115 (221)
Q Consensus 63 ~~~v~C~~C~~~q~~~-----~~C~~Cg~~-f~~y~C~~C~l~dd~~~k~~yHC~~Cgi 115 (221)
++...|..|+.+.... -.||+||.. ..| |.+|+-+. ..|.|++||+
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 3456788898776543 379999986 544 89998774 4799999985
No 56
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=95.79 E-value=0.0029 Score=63.63 Aligned_cols=46 Identities=24% Similarity=0.651 Sum_probs=40.1
Q ss_pred CCCccchhhcccCCCceeeeccCCccCHHHHHHHHhcCcCCCCCCccccc
Q 027589 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (221)
Q Consensus 151 ~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (221)
-.||+|-+. ...+++..|||.|...|+...+...+.+||.|+.+++
T Consensus 644 LkCs~Cn~R----~Kd~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFg 689 (698)
T KOG0978|consen 644 LKCSVCNTR----WKDAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFG 689 (698)
T ss_pred eeCCCccCc----hhhHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCC
Confidence 469999855 2456778999999999999999988999999999997
No 57
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.74 E-value=0.0074 Score=57.38 Aligned_cols=48 Identities=27% Similarity=0.762 Sum_probs=37.7
Q ss_pred CCCccchhhcccCCCce-eeeccCCccCHHHHHHHHhc-CcCCCCCCccc
Q 027589 151 HHCPICYEYLFDSLRNT-TVMKCGHTMHCECYHEMIKR-DKYCCPICSKS 198 (221)
Q Consensus 151 ~~CpICle~lf~s~~~v-~~L~CGH~~H~~C~~~~l~~-~~~~CPiCrks 198 (221)
..|||||+..-.+.+.. ..|.|||.|=+.|++.||-. ...+||.|.-.
T Consensus 5 ~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~k 54 (463)
T KOG1645|consen 5 TTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGK 54 (463)
T ss_pred ccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCCh
Confidence 57999999976655444 45789999999999999952 35579999743
No 58
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=95.72 E-value=0.003 Score=60.02 Aligned_cols=54 Identities=24% Similarity=0.552 Sum_probs=44.2
Q ss_pred cCCCCCCCccchhhcccCCCceeeeccCCccCHHHHHHHHhcC-cCCCCCCcccccchh
Q 027589 146 ENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRD-KYCCPICSKSVIDMS 203 (221)
Q Consensus 146 e~~~~~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~~-~~~CPiCrksi~dm~ 203 (221)
-+++-..|-||.|. ...|++=||||.+...|+..|-.+. ..+||.||-.|-..+
T Consensus 365 MgsTFeLCKICaen----dKdvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKGte 419 (563)
T KOG1785|consen 365 MGSTFELCKICAEN----DKDVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIKGTE 419 (563)
T ss_pred ccchHHHHHHhhcc----CCCcccccccchHHHHHHHhhcccCCCCCCCceeeEecccc
Confidence 35777789999986 3568889999999999999998544 679999998875433
No 59
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=95.68 E-value=0.0059 Score=41.05 Aligned_cols=41 Identities=29% Similarity=0.704 Sum_probs=27.2
Q ss_pred CccchhhcccCCCceeeecc---C--CccCHHHHHHHHhc-CcCCCCCC
Q 027589 153 CPICYEYLFDSLRNTTVMKC---G--HTMHCECYHEMIKR-DKYCCPIC 195 (221)
Q Consensus 153 CpICle~lf~s~~~v~~L~C---G--H~~H~~C~~~~l~~-~~~~CPiC 195 (221)
|-||++.-.++ +..+.|| | -..|..|+.+|+.. ++.+|++|
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 56899874433 3456687 3 68999999999974 46779987
No 60
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.41 E-value=0.024 Score=50.52 Aligned_cols=65 Identities=26% Similarity=0.590 Sum_probs=50.0
Q ss_pred CCCCCCccchhhcccCCCceeeeccCCccCHHHHHHHHhc-------CcCCCCCCcccccc----hhHHHHHHHHHHH
Q 027589 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR-------DKYCCPICSKSVID----MSRTWKRIDEEVS 214 (221)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~-------~~~~CPiCrksi~d----m~~~~~~lD~~i~ 214 (221)
....||..|...|.+. +.+.|-|=|.||-.|+++|... ..|+||-|+..|.- .+.+-+.|-+.++
T Consensus 48 DY~pNC~LC~t~La~g--dt~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp~NlvsPva~aLre~L~ 123 (299)
T KOG3970|consen 48 DYNPNCRLCNTPLASG--DTTRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPPINLVSPVAEALREQLK 123 (299)
T ss_pred CCCCCCceeCCccccC--cceeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCCccccchhHHHHHHHHH
Confidence 4577999999997654 5678999999999999999863 37999999999872 3335555555444
No 61
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=95.26 E-value=0.01 Score=54.44 Aligned_cols=44 Identities=25% Similarity=0.599 Sum_probs=35.7
Q ss_pred CCCccchhhcccCCCceeeeccCCccCHHHHHHHHhcCcCCCCCCcccc
Q 027589 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSV 199 (221)
Q Consensus 151 ~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~~~~~CPiCrksi 199 (221)
..|-||-++|. ....-+|||.|...||..+|. .+..||+||-..
T Consensus 26 lrC~IC~~~i~----ip~~TtCgHtFCslCIR~hL~-~qp~CP~Cr~~~ 69 (391)
T COG5432 26 LRCRICDCRIS----IPCETTCGHTFCSLCIRRHLG-TQPFCPVCREDP 69 (391)
T ss_pred HHhhhhhheee----cceecccccchhHHHHHHHhc-CCCCCccccccH
Confidence 46999999852 123458999999999999998 589999999654
No 62
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.05 E-value=0.013 Score=54.67 Aligned_cols=61 Identities=21% Similarity=0.525 Sum_probs=44.3
Q ss_pred CCCCCCccchhhcccCCCc---eee-eccCCccCHHHHHHHHhcC------cCCCCCCccccc--chhHHHHH
Q 027589 148 SMHHHCPICYEYLFDSLRN---TTV-MKCGHTMHCECYHEMIKRD------KYCCPICSKSVI--DMSRTWKR 208 (221)
Q Consensus 148 ~~~~~CpICle~lf~s~~~---v~~-L~CGH~~H~~C~~~~l~~~------~~~CPiCrksi~--dm~~~~~~ 208 (221)
+.+..|-||+|.+.+.... -.+ ++|-|+|-..|+..|.... +..||+||.... .-+.+|-.
T Consensus 159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~~v~pS~~Wv~ 231 (344)
T KOG1039|consen 159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSSFVNPSSFWVE 231 (344)
T ss_pred cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccccccccceeee
Confidence 5677899999998765311 222 4699999999999998432 368999998774 44445643
No 63
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.35 E-value=0.036 Score=50.37 Aligned_cols=53 Identities=25% Similarity=0.589 Sum_probs=42.1
Q ss_pred CCCCCCccchhhcccCCCceeeeccCCccCHHHHHHHHhc-CcCCCCCCcccccchh
Q 027589 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR-DKYCCPICSKSVIDMS 203 (221)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~-~~~~CPiCrksi~dm~ 203 (221)
.....||+|.|+ ++.|-...+|||.+.--|+..=+.. .+.+||.|+.++..|+
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 446689999997 4457778899999999999875432 3589999999888664
No 64
>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=94.23 E-value=0.021 Score=46.76 Aligned_cols=36 Identities=14% Similarity=0.418 Sum_probs=31.6
Q ss_pred CCCCccchhhcccCCCceeeeccC------CccCHHHHHHHHh
Q 027589 150 HHHCPICYEYLFDSLRNTTVMKCG------HTMHCECYHEMIK 186 (221)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~L~CG------H~~H~~C~~~~l~ 186 (221)
...|.||++.+.+ ...|+.+++| |+||..|++.|.+
T Consensus 26 ~~EC~IC~~~I~~-~~GvV~vt~~g~lnLEkmfc~~C~~rw~~ 67 (134)
T PF05883_consen 26 TVECQICFDRIDN-NDGVVYVTDGGTLNLEKMFCADCDKRWRR 67 (134)
T ss_pred Ceeehhhhhhhhc-CCCEEEEecCCeehHHHHHHHHHHHHHHh
Confidence 4689999999877 6789999997 9999999999954
No 65
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.74 E-value=0.011 Score=54.17 Aligned_cols=60 Identities=23% Similarity=0.617 Sum_probs=42.0
Q ss_pred cCcceeecCCC---CCCCccchhhcccCCCceeeeccCCcc-CHHHHHHHHhcCcCCCCCCcccccchhHHHH
Q 027589 139 RNNHLCIENSM---HHHCPICYEYLFDSLRNTTVMKCGHTM-HCECYHEMIKRDKYCCPICSKSVIDMSRTWK 207 (221)
Q Consensus 139 ~~~H~C~e~~~---~~~CpICle~lf~s~~~v~~L~CGH~~-H~~C~~~~l~~~~~~CPiCrksi~dm~~~~~ 207 (221)
++.+.+.-..+ +..|.||++- +....+|+|||.. ..+|-.. -..|||||+-|...-.+|+
T Consensus 286 k~~~g~~~~~s~~~~~LC~ICmDa----P~DCvfLeCGHmVtCt~CGkr-----m~eCPICRqyi~rvvrif~ 349 (350)
T KOG4275|consen 286 KGNDGEQHSRSLATRRLCAICMDA----PRDCVFLECGHMVTCTKCGKR-----MNECPICRQYIVRVVRIFR 349 (350)
T ss_pred hcccccccccchhHHHHHHHHhcC----CcceEEeecCcEEeehhhccc-----cccCchHHHHHHHHHhhhc
Confidence 45555544433 7789999974 4678899999975 2333332 2389999999988777765
No 66
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=93.69 E-value=0.023 Score=39.85 Aligned_cols=32 Identities=28% Similarity=0.669 Sum_probs=26.2
Q ss_pred ceeeeccCCccCHHHHHHHHhcCcCCCCCCccccc
Q 027589 166 NTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (221)
Q Consensus 166 ~v~~L~CGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (221)
.-.+|||||++-..|++-+- -.-||+|.+.+.
T Consensus 19 ~~~~~pCgH~I~~~~f~~~r---YngCPfC~~~~~ 50 (55)
T PF14447_consen 19 KGTVLPCGHLICDNCFPGER---YNGCPFCGTPFE 50 (55)
T ss_pred ccccccccceeeccccChhh---ccCCCCCCCccc
Confidence 35679999999999998763 247999999875
No 67
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.65 E-value=0.045 Score=47.22 Aligned_cols=35 Identities=29% Similarity=0.655 Sum_probs=28.3
Q ss_pred eeccCCccCHHHHHHHHhcC----------cCCCCCCccccc-chh
Q 027589 169 VMKCGHTMHCECYHEMIKRD----------KYCCPICSKSVI-DMS 203 (221)
Q Consensus 169 ~L~CGH~~H~~C~~~~l~~~----------~~~CPiCrksi~-dm~ 203 (221)
-..||-.||+-|+.+||+.- -..||.|+++|. .|+
T Consensus 187 N~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialKmS 232 (234)
T KOG3268|consen 187 NIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALKMS 232 (234)
T ss_pred ccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceeecc
Confidence 46899999999999999841 246999999984 554
No 68
>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=93.43 E-value=0.061 Score=49.18 Aligned_cols=49 Identities=20% Similarity=0.501 Sum_probs=40.0
Q ss_pred CCccchhhcccCCCceeee-ccCCccCHHHHHHHHhcCcCCCCCCccccc
Q 027589 152 HCPICYEYLFDSLRNTTVM-KCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (221)
Q Consensus 152 ~CpICle~lf~s~~~v~~L-~CGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (221)
.||+|..+.+.+.+-+... +|||.+..+|++..+..+.+.||.|.+.+.
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 5899988877665433222 899999999999999888999999998876
No 69
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.35 E-value=0.058 Score=48.25 Aligned_cols=48 Identities=31% Similarity=0.749 Sum_probs=39.3
Q ss_pred CCCccchhhcccCCC---ceeeeccCCccCHHHHHHHHhcCcCCCCCCcccc
Q 027589 151 HHCPICYEYLFDSLR---NTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSV 199 (221)
Q Consensus 151 ~~CpICle~lf~s~~---~v~~L~CGH~~H~~C~~~~l~~~~~~CPiCrksi 199 (221)
..|-||-+++ ++.+ ..++|.|||++-..|+...+.+....||.||...
T Consensus 4 ~~c~~c~~~~-s~~~~~~~p~~l~c~h~~c~~c~~~l~~~~~i~cpfcR~~~ 54 (296)
T KOG4185|consen 4 PECEICNEDY-SSEDGDHIPRVLKCGHTICQNCASKLLGNSRILCPFCRETT 54 (296)
T ss_pred CceeecCccc-cccCcccCCcccccCceehHhHHHHHhcCceeeccCCCCcc
Confidence 4688999984 4443 3467899999999999999987778899999994
No 70
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.25 E-value=0.047 Score=50.24 Aligned_cols=49 Identities=24% Similarity=0.480 Sum_probs=39.4
Q ss_pred CCCCCCccchhhcccCCCceeeeccCCccCHHHHHHHHhcCcCCCCCCccccc
Q 027589 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (221)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (221)
.+..+|+||+-... -+ ..|+|+|.|--.|++--......+||+||..|-
T Consensus 5 ~~~~eC~IC~nt~n---~P-v~l~C~HkFCyiCiKGsy~ndk~~CavCR~pid 53 (324)
T KOG0824|consen 5 TKKKECLICYNTGN---CP-VNLYCFHKFCYICIKGSYKNDKKTCAVCRFPID 53 (324)
T ss_pred ccCCcceeeeccCC---cC-ccccccchhhhhhhcchhhcCCCCCceecCCCC
Confidence 45678999997643 34 679999999999998755556778999999886
No 71
>PHA02862 5L protein; Provisional
Probab=93.09 E-value=0.041 Score=45.80 Aligned_cols=56 Identities=21% Similarity=0.491 Sum_probs=38.3
Q ss_pred CCCCccchhhcccCCCceeeecc---C--CccCHHHHHHHHhc-CcCCCCCCcccccchhHHHHHHHH
Q 027589 150 HHHCPICYEYLFDSLRNTTVMKC---G--HTMHCECYHEMIKR-DKYCCPICSKSVIDMSRTWKRIDE 211 (221)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~L~C---G--H~~H~~C~~~~l~~-~~~~CPiCrksi~dm~~~~~~lD~ 211 (221)
...|=||.+.- + +.+ -|| | -..|++|+.+|+.. .+.+||+|+.... +...|+.+.+
T Consensus 2 ~diCWIC~~~~-~--e~~--~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~-Ik~~yKpf~k 63 (156)
T PHA02862 2 SDICWICNDVC-D--ERN--NFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYN-IKKTYVSFKK 63 (156)
T ss_pred CCEEEEecCcC-C--CCc--ccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEE-EEEccccHHH
Confidence 45688999862 1 223 465 3 78999999999975 3667999998875 3444444433
No 72
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.01 E-value=0.062 Score=50.32 Aligned_cols=48 Identities=21% Similarity=0.491 Sum_probs=35.5
Q ss_pred cCCCCCCCccchhhcccCCCceeeeccCCccCHHHHHHHHhcCcCCCCCCcccccc
Q 027589 146 ENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID 201 (221)
Q Consensus 146 e~~~~~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~~~~~CPiCrksi~d 201 (221)
|.+...+|.||+++ + .....+||||+-- |..-.. ...+||+||.+|.-
T Consensus 301 ~~~~p~lcVVcl~e-~---~~~~fvpcGh~cc--ct~cs~--~l~~CPvCR~rI~~ 348 (355)
T KOG1571|consen 301 ELPQPDLCVVCLDE-P---KSAVFVPCGHVCC--CTLCSK--HLPQCPVCRQRIRL 348 (355)
T ss_pred ccCCCCceEEecCC-c---cceeeecCCcEEE--chHHHh--hCCCCchhHHHHHH
Confidence 45667899999997 3 3478999999954 555443 34679999988853
No 73
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=92.45 E-value=0.057 Score=48.00 Aligned_cols=37 Identities=27% Similarity=0.546 Sum_probs=27.7
Q ss_pred ccCCCceeeeccCCccCHHHHHHHHhcCcCCCCCCccccc
Q 027589 161 FDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (221)
Q Consensus 161 f~s~~~v~~L~CGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (221)
|.+.++-....|+|+|...|...=. ...||+|+|+|-
T Consensus 12 ~~~~~~f~LTaC~HvfC~~C~k~~~---~~~C~lCkk~ir 48 (233)
T KOG4739|consen 12 FPSQDPFFLTACRHVFCEPCLKASS---PDVCPLCKKSIR 48 (233)
T ss_pred cCCCCceeeeechhhhhhhhcccCC---ccccccccceee
Confidence 3444556677999999999997532 238999999974
No 74
>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=92.26 E-value=0.15 Score=42.95 Aligned_cols=48 Identities=29% Similarity=0.726 Sum_probs=34.8
Q ss_pred CCCCccchhhcccCCCceeeeccC-------------CccCHHHHHHHHhc-----------------------------
Q 027589 150 HHHCPICYEYLFDSLRNTTVMKCG-------------HTMHCECYHEMIKR----------------------------- 187 (221)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~L~CG-------------H~~H~~C~~~~l~~----------------------------- 187 (221)
+..||||||.= -..+.|-|. =.-|+.||+++.+.
T Consensus 2 d~~CpICme~P----HNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkka~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 77 (162)
T PF07800_consen 2 DVTCPICMEHP----HNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKKAYGKSSSSSSQSSSSAPSDSSSSESSESQE 77 (162)
T ss_pred CccCceeccCC----CceEEEEeccccCCccccccCCccchhHHHHHHHHHhcCCCCccccccccCcCCCcccccccccc
Confidence 45799999972 345666662 24599999999762
Q ss_pred -CcCCCCCCcccccc
Q 027589 188 -DKYCCPICSKSVID 201 (221)
Q Consensus 188 -~~~~CPiCrksi~d 201 (221)
....||+||-.|..
T Consensus 78 ~~~L~CPLCRG~V~G 92 (162)
T PF07800_consen 78 QPELACPLCRGEVKG 92 (162)
T ss_pred cccccCccccCceec
Confidence 14679999988863
No 75
>PF12773 DZR: Double zinc ribbon
Probab=92.24 E-value=0.15 Score=33.88 Aligned_cols=22 Identities=36% Similarity=0.970 Sum_probs=13.9
Q ss_pred cCCCCccccc-cccCCCCCCCcc
Q 027589 68 CSVCDTEQPV-AQVCTNCGVNMG 89 (221)
Q Consensus 68 C~~C~~~q~~-~~~C~~Cg~~f~ 89 (221)
|..|+++.+. +..|++||+.+.
T Consensus 1 Cp~Cg~~~~~~~~fC~~CG~~l~ 23 (50)
T PF12773_consen 1 CPHCGTPNPDDAKFCPHCGTPLP 23 (50)
T ss_pred CCCcCCcCCccccCChhhcCChh
Confidence 4556666544 456777777776
No 76
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=92.20 E-value=0.11 Score=37.06 Aligned_cols=45 Identities=29% Similarity=0.802 Sum_probs=33.3
Q ss_pred eeecCCCCcccccc-----ccCCCCCCCcceeeccccccccCCCCcCeeeCCCCCc
Q 027589 65 QVICSVCDTEQPVA-----QVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGI 115 (221)
Q Consensus 65 ~v~C~~C~~~q~~~-----~~C~~Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~Cgi 115 (221)
...|..|+.+..+. -.||+||... =|-|..|+...+ +|.|++||+
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 56889999887553 3699999443 356888887743 789999985
No 77
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=92.11 E-value=0.065 Score=49.48 Aligned_cols=53 Identities=26% Similarity=0.538 Sum_probs=41.0
Q ss_pred CCCCCCccchhhcccCCCceeeeccCCccCHHHHHHHHhc----------------------CcCCCCCCcccccc
Q 027589 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR----------------------DKYCCPICSKSVID 201 (221)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~----------------------~~~~CPiCrksi~d 201 (221)
-..++|.|||--|. +.....+.+|-|+||..||..+|.. ..--|||||-.|.+
T Consensus 113 ~p~gqCvICLygfa-~~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~ 187 (368)
T KOG4445|consen 113 HPNGQCVICLYGFA-SSPAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKI 187 (368)
T ss_pred CCCCceEEEEEeec-CCCceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccc
Confidence 44678999999854 4466888999999999999988762 12349999987764
No 78
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=92.10 E-value=0.091 Score=49.66 Aligned_cols=54 Identities=26% Similarity=0.645 Sum_probs=43.0
Q ss_pred CCCCCCccchhhcccCCCceeeeccCCccCHHHHHHHHhcCcCCCCCCcccccchhHH
Q 027589 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRT 205 (221)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~~~~~CPiCrksi~dm~~~ 205 (221)
..+..||||..-|-+ ++....|||.|-..|+.+|+.. +..||.|+..+..-..+
T Consensus 19 ~~~l~C~~C~~vl~~---p~~~~~cgh~fC~~C~~~~~~~-~~~cp~~~~~~~~~~~~ 72 (391)
T KOG0297|consen 19 DENLLCPICMSVLRD---PVQTTTCGHRFCAGCLLESLSN-HQKCPVCRQELTQAEEL 72 (391)
T ss_pred cccccCccccccccC---CCCCCCCCCcccccccchhhcc-CcCCcccccccchhhcc
Confidence 345679999988654 4555799999999999999985 88999999888754443
No 79
>PF04641 Rtf2: Rtf2 RING-finger
Probab=90.94 E-value=0.19 Score=44.72 Aligned_cols=50 Identities=18% Similarity=0.422 Sum_probs=38.6
Q ss_pred CCCCCCccchhhcccCCCceeee-ccCCccCHHHHHHHHhcCcCCCCCCccccc
Q 027589 148 SMHHHCPICYEYLFDSLRNTTVM-KCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (221)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~L-~CGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (221)
...--|||-...|.. ......| ||||+|=...+++.- ....||+|.+.+.
T Consensus 111 ~~~~~CPvt~~~~~~-~~~fv~l~~cG~V~s~~alke~k--~~~~Cp~c~~~f~ 161 (260)
T PF04641_consen 111 EGRFICPVTGKEFNG-KHKFVYLRPCGCVFSEKALKELK--KSKKCPVCGKPFT 161 (260)
T ss_pred CceeECCCCCcccCC-ceeEEEEcCCCCEeeHHHHHhhc--ccccccccCCccc
Confidence 445579999999744 3444444 999999999999984 3568999999865
No 80
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=90.92 E-value=0.057 Score=50.08 Aligned_cols=64 Identities=25% Similarity=0.497 Sum_probs=47.9
Q ss_pred CCCCCCccchhhcccCCCceeeeccCCccCHHHHHHHHhcCcCCCCCCcccccchh-HHHHHHHHHHHh
Q 027589 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMS-RTWKRIDEEVSL 215 (221)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~~~~~CPiCrksi~dm~-~~~~~lD~~i~~ 215 (221)
.....|.+|..+|.+++ .+.-|=|+|.++||-.+|.. +.+||.|+-.|...- ...-..|..+++
T Consensus 13 n~~itC~LC~GYliDAT---TI~eCLHTFCkSCivk~l~~-~~~CP~C~i~ih~t~pl~ni~~Drtlqd 77 (331)
T KOG2660|consen 13 NPHITCRLCGGYLIDAT---TITECLHTFCKSCIVKYLEE-SKYCPTCDIVIHKTHPLLNIRSDRTLQD 77 (331)
T ss_pred ccceehhhccceeecch---hHHHHHHHHHHHHHHHHHHH-hccCCccceeccCccccccCCcchHHHH
Confidence 34567999999987753 35679999999999999985 789999999887532 233345555544
No 81
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=90.87 E-value=0.15 Score=52.10 Aligned_cols=42 Identities=29% Similarity=0.583 Sum_probs=31.4
Q ss_pred CCCCccchhhcccCCCceeeeccCCccCHHHHHHHHhcCcCCCCC
Q 027589 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPI 194 (221)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~~~~~CPi 194 (221)
...|.||--.+..+ ...-+.|||.+|..|+.+|++. ...||.
T Consensus 1028 ~~~C~~C~l~V~gs--s~~Cg~C~Hv~H~sc~~eWf~~-gd~Cps 1069 (1081)
T KOG0309|consen 1028 TFQCAICHLAVRGS--SNFCGTCGHVGHTSCMMEWFRT-GDVCPS 1069 (1081)
T ss_pred eeeeeeEeeEeecc--chhhccccccccHHHHHHHHhc-CCcCCC
Confidence 34588887654433 4455789999999999999984 568884
No 82
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=90.75 E-value=0.063 Score=50.39 Aligned_cols=57 Identities=23% Similarity=0.470 Sum_probs=43.7
Q ss_pred CCCCccchhhcccCCCceeeeccCCccCHHHHHHHHhcCcCCCCCCcccccchhHHH
Q 027589 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRTW 206 (221)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~~~~~CPiCrksi~dm~~~~ 206 (221)
++-||.|+|+|.-+...-..-|||=-+.+-|+......-+.+||-||+...|-...|
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 445999999986654444445789999999998877666899999999887644444
No 83
>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=90.63 E-value=0.16 Score=37.34 Aligned_cols=36 Identities=25% Similarity=0.783 Sum_probs=22.3
Q ss_pred ceeecCCCCccccccccCCCCCCCc--------ceeeccccccc
Q 027589 64 KQVICSVCDTEQPVAQVCTNCGVNM--------GEYFCDICKFY 99 (221)
Q Consensus 64 ~~v~C~~C~~~q~~~~~C~~Cg~~f--------~~y~C~~C~l~ 99 (221)
....|..|+..-.....||.|+..+ +.|||..|+=.
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 5778888887766677888888877 58888888733
No 84
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.29 E-value=0.17 Score=48.34 Aligned_cols=46 Identities=20% Similarity=0.411 Sum_probs=37.0
Q ss_pred CCCCccchhhcccCCCceeeeccCCccCHHHHHHHHhc-------CcCCCCCCc
Q 027589 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR-------DKYCCPICS 196 (221)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~-------~~~~CPiCr 196 (221)
--+|.||++. +....-.+.|||+|+|.+.|+..|... +..+||-++
T Consensus 184 lf~C~ICf~e-~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~ 236 (445)
T KOG1814|consen 184 LFDCCICFEE-QMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPK 236 (445)
T ss_pred cccceeeehh-hcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCC
Confidence 4689999998 444466788999999999999998762 467898765
No 85
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=90.22 E-value=0.21 Score=51.45 Aligned_cols=43 Identities=26% Similarity=0.563 Sum_probs=33.5
Q ss_pred CCCccchhhcccCCCceeeeccCCccCHHHHHHHHhcCcCCCCCCccccc
Q 027589 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (221)
Q Consensus 151 ~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (221)
+.|..|--.|- -|++-..|||.||..|+. . +...||-|+-.+.
T Consensus 841 skCs~C~~~Ld---lP~VhF~CgHsyHqhC~e---~-~~~~CP~C~~e~~ 883 (933)
T KOG2114|consen 841 SKCSACEGTLD---LPFVHFLCGHSYHQHCLE---D-KEDKCPKCLPELR 883 (933)
T ss_pred eeecccCCccc---cceeeeecccHHHHHhhc---c-CcccCCccchhhh
Confidence 36888876653 377788999999999998 3 5679999998443
No 86
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=89.34 E-value=0.14 Score=50.50 Aligned_cols=52 Identities=21% Similarity=0.513 Sum_probs=42.9
Q ss_pred ecCCCCCCCccchhhcccCCCceeeeccCCccCHHHHHHHHhc----CcCCCCCCccccc
Q 027589 145 IENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR----DKYCCPICSKSVI 200 (221)
Q Consensus 145 ~e~~~~~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~----~~~~CPiCrksi~ 200 (221)
.|+..+..|-+|-+.- +...+-+|-|.|.+.|+.+|+.. .+.+||+|.+.+.
T Consensus 531 ~enk~~~~C~lc~d~a----ed~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~Ls 586 (791)
T KOG1002|consen 531 DENKGEVECGLCHDPA----EDYIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLS 586 (791)
T ss_pred ccccCceeecccCChh----hhhHhhhhhHHHHHHHHHHHHHhhhcccCCCCcccccccc
Confidence 4667788899999872 35677899999999999998863 5789999998774
No 87
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.17 E-value=0.6 Score=44.54 Aligned_cols=50 Identities=24% Similarity=0.752 Sum_probs=39.9
Q ss_pred CCCCCCccchhhcccCCCceeeeccCCccCHHHHHHHHhcCcCCCCCCcccccch
Q 027589 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDM 202 (221)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~~~~~CPiCrksi~dm 202 (221)
..+-.|-||+.-|.. .+++||||+|-..|++.-+. ....||+||-.+...
T Consensus 82 ~sef~c~vc~~~l~~----pv~tpcghs~c~~Cl~r~ld-~~~~cp~Cr~~l~e~ 131 (398)
T KOG4159|consen 82 RSEFECCVCSRALYP----PVVTPCGHSFCLECLDRSLD-QETECPLCRDELVEL 131 (398)
T ss_pred cchhhhhhhHhhcCC----CccccccccccHHHHHHHhc-cCCCCcccccccccc
Confidence 556789999887653 34559999999999999766 567899999998753
No 88
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=88.07 E-value=0.5 Score=42.74 Aligned_cols=53 Identities=25% Similarity=0.505 Sum_probs=44.2
Q ss_pred CCCCCCCccchhhcccCCCceeee-ccCCccCHHHHHHHHhcCcCCCCCCcccccc
Q 027589 147 NSMHHHCPICYEYLFDSLRNTTVM-KCGHTMHCECYHEMIKRDKYCCPICSKSVID 201 (221)
Q Consensus 147 ~~~~~~CpICle~lf~s~~~v~~L-~CGH~~H~~C~~~~l~~~~~~CPiCrksi~d 201 (221)
.+....|||+.+.|... .+..+| |+||++-..|.+.+++ ...-+||+.+.+-|
T Consensus 218 ~s~ryiCpvtrd~LtNt-~~ca~Lr~sg~Vv~~ecvEklir-~D~v~pv~d~plkd 271 (303)
T KOG3039|consen 218 ASKRYICPVTRDTLTNT-TPCAVLRPSGHVVTKECVEKLIR-KDMVDPVTDKPLKD 271 (303)
T ss_pred hccceecccchhhhcCc-cceEEeccCCcEeeHHHHHHhcc-ccccccCCCCcCcc
Confidence 34556899999997654 567777 8999999999999998 57899999999875
No 89
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=88.00 E-value=0.45 Score=44.96 Aligned_cols=64 Identities=17% Similarity=0.375 Sum_probs=45.8
Q ss_pred CccccccccCcceeecCCCCCCCccchhhcccCCCceeeeccCCccCHHHHHHHHh-cCcCCCCCCccc
Q 027589 131 GSCYSTSLRNNHLCIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIK-RDKYCCPICSKS 198 (221)
Q Consensus 131 ~~C~s~~~~~~H~C~e~~~~~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~-~~~~~CPiCrks 198 (221)
+.|....+-++.+=.....+.+|.||.+.+ +-+.++||||-|.--|--.... .....||+||..
T Consensus 42 nlsaEPnlttsSaddtDEen~~C~ICA~~~----TYs~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE 106 (493)
T COG5236 42 NLSAEPNLTTSSADDTDEENMNCQICAGST----TYSARYPCGHQICHACAVRLRALYMQKGCPLCRTE 106 (493)
T ss_pred ccccCCccccccccccccccceeEEecCCc----eEEEeccCCchHHHHHHHHHHHHHhccCCCccccc
Confidence 566666665555555556677899999874 4567899999999999755432 235689999964
No 90
>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=87.34 E-value=0.28 Score=33.58 Aligned_cols=31 Identities=32% Similarity=0.780 Sum_probs=23.1
Q ss_pred eeccC-CccCHHHHHHHHhcCcCCCCCCccccc
Q 027589 169 VMKCG-HTMHCECYHEMIKRDKYCCPICSKSVI 200 (221)
Q Consensus 169 ~L~CG-H~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (221)
.+.|. |.+-..|+..++. .+..||||.+++-
T Consensus 15 Li~C~dHYLCl~CLt~ml~-~s~~C~iC~~~LP 46 (50)
T PF03854_consen 15 LIKCSDHYLCLNCLTLMLS-RSDRCPICGKPLP 46 (50)
T ss_dssp EEE-SS-EEEHHHHHHT-S-SSSEETTTTEE--
T ss_pred eeeecchhHHHHHHHHHhc-cccCCCcccCcCc
Confidence 56896 9999999999998 5789999998874
No 91
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.18 E-value=0.31 Score=49.10 Aligned_cols=43 Identities=23% Similarity=0.620 Sum_probs=35.7
Q ss_pred CCCccchhhcccCCCceeeeccCCccCHHHHHHHHhcCcCCCCCCcc
Q 027589 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSK 197 (221)
Q Consensus 151 ~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~~~~~CPiCrk 197 (221)
..|+||+..+|.++..-+.|.|||++-+.|+...- +.+|| |..
T Consensus 12 l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~ly---n~scp-~~~ 54 (861)
T KOG3161|consen 12 LLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLY---NASCP-TKR 54 (861)
T ss_pred hhchHHHHHHHHHhcCcccccccchHHHHHHHhHh---hccCC-CCc
Confidence 36999988888887778889999999999998763 56899 653
No 92
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=86.89 E-value=0.32 Score=28.65 Aligned_cols=24 Identities=33% Similarity=0.924 Sum_probs=17.4
Q ss_pred eeecCCCCccccc-cccCCCCCCCc
Q 027589 65 QVICSVCDTEQPV-AQVCTNCGVNM 88 (221)
Q Consensus 65 ~v~C~~C~~~q~~-~~~C~~Cg~~f 88 (221)
.+.|..|+++.+. +..|++||+.+
T Consensus 2 ~~~Cp~Cg~~~~~~~~fC~~CG~~L 26 (26)
T PF13248_consen 2 EMFCPNCGAEIDPDAKFCPNCGAKL 26 (26)
T ss_pred cCCCcccCCcCCcccccChhhCCCC
Confidence 4678888886444 46799998864
No 93
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=86.47 E-value=0.42 Score=41.99 Aligned_cols=58 Identities=21% Similarity=0.477 Sum_probs=43.6
Q ss_pred CCccchhhcccCCCceeeeccCCccCHHHHHHHHhcCcCCCCCCcccccchhHHHHHHHHHHH
Q 027589 152 HCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRTWKRIDEEVS 214 (221)
Q Consensus 152 ~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~~~~~CPiCrksi~dm~~~~~~lD~~i~ 214 (221)
.|-||-++ +.| .++..|||.|...|+-.=.+ ...+|-+|.+..--.-.+-..||.++.
T Consensus 198 ~C~iCKkd-y~s---pvvt~CGH~FC~~Cai~~y~-kg~~C~~Cgk~t~G~f~V~~d~~kmL~ 255 (259)
T COG5152 198 LCGICKKD-YES---PVVTECGHSFCSLCAIRKYQ-KGDECGVCGKATYGRFWVVSDLQKMLN 255 (259)
T ss_pred eehhchhh-ccc---hhhhhcchhHHHHHHHHHhc-cCCcceecchhhccceeHHhhHHHHHh
Confidence 69999999 544 34678999999999876555 367999999988655444466666654
No 94
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=86.44 E-value=0.68 Score=44.04 Aligned_cols=47 Identities=21% Similarity=0.555 Sum_probs=37.9
Q ss_pred CCccchhhcccCCCceeeeccCCccCHHHHHHHHhcCc--CCCCCCcccc
Q 027589 152 HCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDK--YCCPICSKSV 199 (221)
Q Consensus 152 ~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~~~--~~CPiCrksi 199 (221)
.|||=-|. -+...|...|.|||++=+.=++.+.+++. ++||.|-...
T Consensus 336 ~CPVlKeq-tsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~e~ 384 (394)
T KOG2817|consen 336 ICPVLKEQ-TSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPVEQ 384 (394)
T ss_pred ecccchhh-ccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCccc
Confidence 58887776 34446778899999999999999998766 8999997543
No 95
>PRK04023 DNA polymerase II large subunit; Validated
Probab=86.36 E-value=0.64 Score=48.99 Aligned_cols=45 Identities=27% Similarity=0.640 Sum_probs=21.5
Q ss_pred cCCCCCCCcceeeccccccccCCCCcCeeeCCCCCcceeCCccceeecCccCcc
Q 027589 80 VCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSC 133 (221)
Q Consensus 80 ~C~~Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~CgiCR~G~~~~~fHC~~C~~C 133 (221)
.|++||......+|+.|.-. .+.+|.|++||.-..+ ..|.+||.=
T Consensus 628 fCpsCG~~t~~frCP~CG~~----Te~i~fCP~CG~~~~~-----y~CPKCG~E 672 (1121)
T PRK04023 628 KCPSCGKETFYRRCPFCGTH----TEPVYRCPRCGIEVEE-----DECEKCGRE 672 (1121)
T ss_pred cCCCCCCcCCcccCCCCCCC----CCcceeCccccCcCCC-----CcCCCCCCC
Confidence 45555555544455555322 3455566666433221 335555543
No 96
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=86.27 E-value=0.63 Score=39.29 Aligned_cols=47 Identities=30% Similarity=0.572 Sum_probs=33.8
Q ss_pred CCCCCccchhhcccCCCceeeecc--CC---ccCHHHHHHHHhc-CcCCCCCCccccc
Q 027589 149 MHHHCPICYEYLFDSLRNTTVMKC--GH---TMHCECYHEMIKR-DKYCCPICSKSVI 200 (221)
Q Consensus 149 ~~~~CpICle~lf~s~~~v~~L~C--GH---~~H~~C~~~~l~~-~~~~CPiCrksi~ 200 (221)
++..|=||.++- + .. .-|| .. ..|.+|++.|+.. +..+||+|+....
T Consensus 7 ~~~~CRIC~~~~-~--~~--~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~ 59 (162)
T PHA02825 7 MDKCCWICKDEY-D--VV--TNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYN 59 (162)
T ss_pred CCCeeEecCCCC-C--Cc--cCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEE
Confidence 456799998872 1 22 2466 34 6799999999975 3677999998764
No 97
>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=86.24 E-value=0.54 Score=37.08 Aligned_cols=28 Identities=32% Similarity=0.948 Sum_probs=20.9
Q ss_pred cccccCCCCCCCcceeeccccccccCCCCcCeeeCCCCCc
Q 027589 76 PVAQVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGI 115 (221)
Q Consensus 76 ~~~~~C~~Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~Cgi 115 (221)
-...+|++||+.| | +.+|.+-.|++||.
T Consensus 7 GtKR~Cp~CG~kF----------Y--DLnk~PivCP~CG~ 34 (108)
T PF09538_consen 7 GTKRTCPSCGAKF----------Y--DLNKDPIVCPKCGT 34 (108)
T ss_pred CCcccCCCCcchh----------c--cCCCCCccCCCCCC
Confidence 3456799999865 5 55688888998884
No 98
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=86.16 E-value=0.41 Score=49.43 Aligned_cols=52 Identities=23% Similarity=0.537 Sum_probs=37.6
Q ss_pred CCCCccchhhcccCCCceee-eccCCccCHHHHHHHHhc------CcCCCCCCcccccch
Q 027589 150 HHHCPICYEYLFDSLRNTTV-MKCGHTMHCECYHEMIKR------DKYCCPICSKSVIDM 202 (221)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~-L~CGH~~H~~C~~~~l~~------~~~~CPiCrksi~dm 202 (221)
...|.||.|.+..+ .++.. -.|=|+||..||..|.++ ...+||-|......+
T Consensus 191 ~yeCmIC~e~I~~t-~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv~~~~ 249 (950)
T KOG1952|consen 191 KYECMICTERIKRT-APVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSVSKTV 249 (950)
T ss_pred ceEEEEeeeecccc-CCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccchhccC
Confidence 45799999986543 34432 246699999999999874 367899999554433
No 99
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=85.45 E-value=0.43 Score=49.42 Aligned_cols=37 Identities=24% Similarity=0.523 Sum_probs=30.4
Q ss_pred CCCCCCccchhhcccCCCceeeeccCCccCHHHHHHHHh
Q 027589 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIK 186 (221)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~ 186 (221)
.....|.+|.-.|+. .+-.+.||||.||+.|+.+-..
T Consensus 815 ep~d~C~~C~~~ll~--~pF~vf~CgH~FH~~Cl~~~v~ 851 (911)
T KOG2034|consen 815 EPQDSCDHCGRPLLI--KPFYVFPCGHCFHRDCLIRHVL 851 (911)
T ss_pred cCccchHHhcchhhc--CcceeeeccchHHHHHHHHHHH
Confidence 345689999998775 4778899999999999987654
No 100
>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=85.22 E-value=0.79 Score=27.13 Aligned_cols=21 Identities=24% Similarity=0.539 Sum_probs=17.5
Q ss_pred CCCCCCcccccchhHHHHHHHH
Q 027589 190 YCCPICSKSVIDMSRTWKRIDE 211 (221)
Q Consensus 190 ~~CPiCrksi~dm~~~~~~lD~ 211 (221)
..||||.+.+ .+..+.+.||.
T Consensus 2 v~CPiC~~~v-~~~~in~HLD~ 22 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLDS 22 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHHH
Confidence 3699999998 66778899985
No 101
>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=84.64 E-value=0.68 Score=27.56 Aligned_cols=22 Identities=36% Similarity=1.011 Sum_probs=17.6
Q ss_pred cCCCCccccc-cccCCCCCCCcc
Q 027589 68 CSVCDTEQPV-AQVCTNCGVNMG 89 (221)
Q Consensus 68 C~~C~~~q~~-~~~C~~Cg~~f~ 89 (221)
|..|+.+-+. +..|++||..|.
T Consensus 3 CP~C~~~V~~~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 3 CPECGAEVPESAKFCPHCGYDFE 25 (26)
T ss_pred CCCCcCCchhhcCcCCCCCCCCc
Confidence 6778877666 468999999986
No 102
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=84.17 E-value=0.098 Score=49.75 Aligned_cols=52 Identities=23% Similarity=0.452 Sum_probs=45.0
Q ss_pred CCCCCCccchhhcccCCCceeeeccCCccCHHHHHHHHhcCcCCCCCCccccc
Q 027589 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (221)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (221)
+....++||.+.|...-+....+.|||..|..++.+||.. ..++|-|+..+-
T Consensus 194 slv~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~~-~~kl~~~~rel~ 245 (465)
T KOG0827|consen 194 SLVGSLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLAT-KRKLPSCRRELP 245 (465)
T ss_pred HHHhhhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHHH-HHHhHHHHhhhh
Confidence 3345799999999877677888999999999999999985 789999998875
No 103
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=83.44 E-value=1.1 Score=31.24 Aligned_cols=35 Identities=23% Similarity=0.582 Sum_probs=27.2
Q ss_pred CCCCCccchhhcccCCCceeeeccCCccCHHHHHH
Q 027589 149 MHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHE 183 (221)
Q Consensus 149 ~~~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~ 183 (221)
+...|++|.+.|.+..+.|+---||=.+|+.|++.
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~ 38 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK 38 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence 45689999999766645455556999999999864
No 104
>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=83.43 E-value=1.1 Score=32.96 Aligned_cols=44 Identities=34% Similarity=0.859 Sum_probs=20.9
Q ss_pred ceeeccccccccCCCCcCeeeCCCCC----cceeCCccceeecCccCcccccc
Q 027589 89 GEYFCDICKFYDDDIEKGQFHCDDCG----ICRIGGRENYFHCKRCGSCYSTS 137 (221)
Q Consensus 89 ~~y~C~~C~l~dd~~~k~~yHC~~Cg----iCR~G~~~~~fHC~~C~~C~s~~ 137 (221)
+.|+|+.|.-- -+..-.|++|| +-+.=|..||| |..|+.=+|++
T Consensus 16 ~~~~C~~C~~~----~~~~a~CPdC~~~Le~LkACGAvdYF-C~~c~gLiSKk 63 (70)
T PF07191_consen 16 GHYHCEACQKD----YKKEAFCPDCGQPLEVLKACGAVDYF-CNHCHGLISKK 63 (70)
T ss_dssp TEEEETTT--E----EEEEEE-TTT-SB-EEEEETTEEEEE--TTTT-EE-TT
T ss_pred CEEECcccccc----ceecccCCCcccHHHHHHHhccccee-eccCCceeecc
Confidence 46666666421 13456688887 44444555555 66666555543
No 105
>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=83.40 E-value=0.83 Score=30.11 Aligned_cols=25 Identities=24% Similarity=0.858 Sum_probs=15.6
Q ss_pred ccCCccCHHHHHHHHhcCcC-CCCCC
Q 027589 171 KCGHTMHCECYHEMIKRDKY-CCPIC 195 (221)
Q Consensus 171 ~CGH~~H~~C~~~~l~~~~~-~CPiC 195 (221)
.|+=.+|..|++.|+++... +||.|
T Consensus 18 ~C~~r~H~~C~~~y~r~~~~~~CP~C 43 (43)
T PF08746_consen 18 DCNVRLHDDCFKKYFRHRSNPKCPNC 43 (43)
T ss_dssp -S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred ccCchHHHHHHHHHHhcCCCCCCcCC
Confidence 47778999999999986433 69987
No 106
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=82.83 E-value=0.71 Score=26.62 Aligned_cols=21 Identities=38% Similarity=0.945 Sum_probs=14.6
Q ss_pred cCCCCccccc-cccCCCCCCCc
Q 027589 68 CSVCDTEQPV-AQVCTNCGVNM 88 (221)
Q Consensus 68 C~~C~~~q~~-~~~C~~Cg~~f 88 (221)
|..|+.+.+. +..|++||+.|
T Consensus 2 Cp~CG~~~~~~~~fC~~CG~~l 23 (23)
T PF13240_consen 2 CPNCGAEIEDDAKFCPNCGTPL 23 (23)
T ss_pred CcccCCCCCCcCcchhhhCCcC
Confidence 6677777654 46788888764
No 107
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=82.64 E-value=0.78 Score=42.27 Aligned_cols=60 Identities=25% Similarity=0.480 Sum_probs=44.0
Q ss_pred CCCccchhhcccCCCceeeeccCCccCHHHHHHHHhcCcCCCCCCcccccchhHHHHHHHHHHHh
Q 027589 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRTWKRIDEEVSL 215 (221)
Q Consensus 151 ~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~~~~~CPiCrksi~dm~~~~~~lD~~i~~ 215 (221)
..|-||.+++. + .++-.|||.|-..|...=+. ...+|+||.+.+-.....=..|+..|..
T Consensus 242 f~c~icr~~f~-~---pVvt~c~h~fc~~ca~~~~q-k~~~c~vC~~~t~g~~~~akeL~~~L~~ 301 (313)
T KOG1813|consen 242 FKCFICRKYFY-R---PVVTKCGHYFCEVCALKPYQ-KGEKCYVCSQQTHGSFNVAKELLVSLKL 301 (313)
T ss_pred ccccccccccc-c---chhhcCCceeehhhhccccc-cCCcceecccccccccchHHHHHHHHHh
Confidence 45999999943 2 34678999999999988776 4689999999987554444455555543
No 108
>PHA00626 hypothetical protein
Probab=82.61 E-value=1.1 Score=31.76 Aligned_cols=6 Identities=50% Similarity=1.636 Sum_probs=3.2
Q ss_pred CCCCCC
Q 027589 81 CTNCGV 86 (221)
Q Consensus 81 C~~Cg~ 86 (221)
||+||.
T Consensus 3 CP~CGS 8 (59)
T PHA00626 3 CPKCGS 8 (59)
T ss_pred CCCCCC
Confidence 555554
No 109
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=82.55 E-value=0.95 Score=45.68 Aligned_cols=33 Identities=30% Similarity=0.828 Sum_probs=19.0
Q ss_pred eecCCCCccccc-cccCCCCCCCcceeecccccc
Q 027589 66 VICSVCDTEQPV-AQVCTNCGVNMGEYFCDICKF 98 (221)
Q Consensus 66 v~C~~C~~~q~~-~~~C~~Cg~~f~~y~C~~C~l 98 (221)
++|..|+.+-+. +..|++||..+..-.|+.|.-
T Consensus 2 ~~Cp~Cg~~n~~~akFC~~CG~~l~~~~Cp~CG~ 35 (645)
T PRK14559 2 LICPQCQFENPNNNRFCQKCGTSLTHKPCPQCGT 35 (645)
T ss_pred CcCCCCCCcCCCCCccccccCCCCCCCcCCCCCC
Confidence 356666666544 345666766665545555543
No 110
>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=81.67 E-value=1.5 Score=29.74 Aligned_cols=41 Identities=27% Similarity=0.805 Sum_probs=20.0
Q ss_pred CCccchhhcccCCCceeeeccCCccCHHHHHH--HHh----cCcCCCCCCccc
Q 027589 152 HCPICYEYLFDSLRNTTVMKCGHTMHCECYHE--MIK----RDKYCCPICSKS 198 (221)
Q Consensus 152 ~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~--~l~----~~~~~CPiCrks 198 (221)
.|||-...|. .+++...|.|. .|||. ||. ....+||+|+++
T Consensus 4 ~CPls~~~i~---~P~Rg~~C~H~---~CFDl~~fl~~~~~~~~W~CPiC~~~ 50 (50)
T PF02891_consen 4 RCPLSFQRIR---IPVRGKNCKHL---QCFDLESFLESNQRTPKWKCPICNKP 50 (50)
T ss_dssp B-TTTSSB-S---SEEEETT--SS-----EEHHHHHHHHHHS---B-TTT---
T ss_pred eCCCCCCEEE---eCccCCcCccc---ceECHHHHHHHhhccCCeECcCCcCc
Confidence 5888887753 47888889877 46654 554 245789999874
No 111
>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=81.03 E-value=1.4 Score=23.75 Aligned_cols=21 Identities=33% Similarity=0.697 Sum_probs=15.3
Q ss_pred CCCCCCcccccchhHHHHHHH
Q 027589 190 YCCPICSKSVIDMSRTWKRID 210 (221)
Q Consensus 190 ~~CPiCrksi~dm~~~~~~lD 210 (221)
+.||+|.+.+.+...+++-+.
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~ 21 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMR 21 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHH
Confidence 479999999999887776654
No 112
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=80.99 E-value=1.7 Score=46.98 Aligned_cols=33 Identities=30% Similarity=0.761 Sum_probs=19.4
Q ss_pred eeecCCCCccccccccCCCCCCCc-ceeecccccc
Q 027589 65 QVICSVCDTEQPVAQVCTNCGVNM-GEYFCDICKF 98 (221)
Q Consensus 65 ~v~C~~C~~~q~~~~~C~~Cg~~f-~~y~C~~C~l 98 (221)
...|..|+++- ....|+.||... ..|+|+.|..
T Consensus 667 ~rkCPkCG~~t-~~~fCP~CGs~te~vy~CPsCGa 700 (1337)
T PRK14714 667 RRRCPSCGTET-YENRCPDCGTHTEPVYVCPDCGA 700 (1337)
T ss_pred EEECCCCCCcc-ccccCcccCCcCCCceeCccCCC
Confidence 45677777653 334677777665 2445666654
No 113
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=80.33 E-value=1.1 Score=42.56 Aligned_cols=50 Identities=30% Similarity=0.628 Sum_probs=41.7
Q ss_pred CCCCCCCccchhhcccCCCceeeeccCCccCHHHHHHHHhcCcCCCCCCcccccc
Q 027589 147 NSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID 201 (221)
Q Consensus 147 ~~~~~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~~~~~CPiCrksi~d 201 (221)
.+.++.||||... ....++-||||--...||.+-+. ++..|=.|+.++.+
T Consensus 419 ~sEd~lCpICyA~----pi~Avf~PC~H~SC~~CI~qHlm-N~k~CFfCktTv~~ 468 (489)
T KOG4692|consen 419 DSEDNLCPICYAG----PINAVFAPCSHRSCYGCITQHLM-NCKRCFFCKTTVID 468 (489)
T ss_pred CcccccCcceecc----cchhhccCCCCchHHHHHHHHHh-cCCeeeEecceeee
Confidence 4667889999865 23456779999999999999998 57899999999986
No 114
>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=80.18 E-value=0.73 Score=41.61 Aligned_cols=52 Identities=23% Similarity=0.522 Sum_probs=42.0
Q ss_pred CCCCCccchhhcccCCCceeee-c-cCCccCHHHHHHHHhcCcCCCC--CCccccc
Q 027589 149 MHHHCPICYEYLFDSLRNTTVM-K-CGHTMHCECYHEMIKRDKYCCP--ICSKSVI 200 (221)
Q Consensus 149 ~~~~CpICle~lf~s~~~v~~L-~-CGH~~H~~C~~~~l~~~~~~CP--iCrksi~ 200 (221)
.+..||||..+.+-+++-...+ | |=|-|..+|.+..+..+...|| -|.|.+-
T Consensus 9 ~d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kILR 64 (314)
T COG5220 9 EDRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKILR 64 (314)
T ss_pred hcccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHHH
Confidence 3557999999988876544333 5 9999999999999988888999 8887664
No 115
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=79.64 E-value=0.75 Score=39.24 Aligned_cols=30 Identities=23% Similarity=0.303 Sum_probs=24.3
Q ss_pred CCCCCCccchhhcccCCCceeeeccCCccCH
Q 027589 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHC 178 (221)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~L~CGH~~H~ 178 (221)
....+|.||||+|.. .+.+..|||==+||+
T Consensus 175 ddkGECvICLEdL~~-GdtIARLPCLCIYHK 204 (205)
T KOG0801|consen 175 DDKGECVICLEDLEA-GDTIARLPCLCIYHK 204 (205)
T ss_pred ccCCcEEEEhhhccC-CCceeccceEEEeec
Confidence 446789999999765 478899999877775
No 116
>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=78.69 E-value=1.2 Score=26.98 Aligned_cols=37 Identities=24% Similarity=0.507 Sum_probs=23.6
Q ss_pred CccchhhcccCCCceeeeccCCccCHHHHHHHHhcCcCCCCCCccccc
Q 027589 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (221)
Q Consensus 153 CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (221)
|+.|.+.+.++. ..+..=|..||..|| +|..|+++|.
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 677887765531 222223788998876 6777887764
No 117
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=77.89 E-value=2 Score=44.07 Aligned_cols=80 Identities=21% Similarity=0.382 Sum_probs=50.1
Q ss_pred cCeeeCCCCCcceeCCccceeecCccCccccccccCcceeecCCCCCCCccchhhcccCCCceeeeccCCccCHHHHHHH
Q 027589 105 KGQFHCDDCGICRIGGRENYFHCKRCGSCYSTSLRNNHLCIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEM 184 (221)
Q Consensus 105 k~~yHC~~CgiCR~G~~~~~fHC~~C~~C~s~~~~~~H~C~e~~~~~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~ 184 (221)
.-+|-|+.|+-=-++++. --|++|-.+-+ ..|.||-..+-. ..+.---|||..|.+++.+|
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--WQCDRCESRAS---------------AKCTVCDLVIRG--VDVWCQVCGHGGHDSHLKSW 811 (839)
T ss_pred eeeccccccCCccccccc--eeechHHHHhh---------------cCceeecceeee--eEeecccccccccHHHHHHH
Confidence 356777777654444433 33444433322 358899876533 23334469999999999999
Q ss_pred HhcCcCCCCC-------CcccccchhH
Q 027589 185 IKRDKYCCPI-------CSKSVIDMSR 204 (221)
Q Consensus 185 l~~~~~~CPi-------Crksi~dm~~ 204 (221)
+.. +..||. +++++.||..
T Consensus 812 ~~~-~s~ca~~~C~~~c~~~~~~D~~~ 837 (839)
T KOG0269|consen 812 FFK-ASPCAKSICPHLCHYSSFIDTFM 837 (839)
T ss_pred Hhc-CCCCccccCCccccccccchhhh
Confidence 984 566776 5566777753
No 118
>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=77.42 E-value=2.5 Score=28.63 Aligned_cols=11 Identities=55% Similarity=1.162 Sum_probs=6.5
Q ss_pred CCCCCCccccc
Q 027589 190 YCCPICSKSVI 200 (221)
Q Consensus 190 ~~CPiCrksi~ 200 (221)
+.||||.+.+.
T Consensus 32 v~CPiC~~~~~ 42 (54)
T PF05605_consen 32 VVCPICSSRVT 42 (54)
T ss_pred ccCCCchhhhh
Confidence 44777776544
No 119
>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=77.03 E-value=2.1 Score=41.76 Aligned_cols=50 Identities=22% Similarity=0.690 Sum_probs=41.7
Q ss_pred eeecCCCCCcccCchhHHhhhcCCCCCCCCccccccccceeecCCCCccccccccCCCCCCC
Q 027589 26 RIRAPCCNEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVAQVCTNCGVN 87 (221)
Q Consensus 26 ~l~~pCC~~~ypCr~CHde~~~~~~~~~~~H~~~r~~~~~v~C~~C~~~q~~~~~C~~Cg~~ 87 (221)
.+.|.-||....|..|.-.+.- |. ....+.|-.|+..+++...||+||..
T Consensus 213 ~~~C~~Cg~~~~C~~C~~~l~~--------h~----~~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 213 NLLCRSCGYILCCPNCDVSLTY--------HK----KEGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred eeEhhhCcCccCCCCCCCceEE--------ec----CCCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 3789999999999999766653 32 24589999999999999999999885
No 120
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=75.62 E-value=1.1 Score=40.78 Aligned_cols=68 Identities=25% Similarity=0.470 Sum_probs=45.4
Q ss_pred CCCCCCccchhhcccCCCceeeecc---C--CccCHHHHHHHHhcC-------cCCCCCCcccccc-------hhHHHHH
Q 027589 148 SMHHHCPICYEYLFDSLRNTTVMKC---G--HTMHCECYHEMIKRD-------KYCCPICSKSVID-------MSRTWKR 208 (221)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~L~C---G--H~~H~~C~~~~l~~~-------~~~CPiCrksi~d-------m~~~~~~ 208 (221)
..+.-|=||++.=.+.+...-+=|| | |..|..|+..|+.+. .-+||.|+....- .....+.
T Consensus 18 e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYiiv~P~l~~~~~~Le~ 97 (293)
T KOG3053|consen 18 ELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYIIVFPQLGPFDRVLER 97 (293)
T ss_pred ccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchheeeccccChHHHHHHH
Confidence 3455699999864444433345576 3 999999999999753 3369999976542 2334466
Q ss_pred HHHHHHh
Q 027589 209 IDEEVSL 215 (221)
Q Consensus 209 lD~~i~~ 215 (221)
+|..|..
T Consensus 98 ~d~~i~r 104 (293)
T KOG3053|consen 98 LDILIFR 104 (293)
T ss_pred hhhHHhh
Confidence 6665544
No 121
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=73.79 E-value=2.9 Score=45.27 Aligned_cols=33 Identities=30% Similarity=0.730 Sum_probs=25.7
Q ss_pred ccCCCCCCCcceeeccccccccCCCCcCeeeCCCCCc
Q 027589 79 QVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGI 115 (221)
Q Consensus 79 ~~C~~Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~Cgi 115 (221)
-.|++||......||+.|.-. .+.+|+|+.||.
T Consensus 668 rkCPkCG~~t~~~fCP~CGs~----te~vy~CPsCGa 700 (1337)
T PRK14714 668 RRCPSCGTETYENRCPDCGTH----TEPVYVCPDCGA 700 (1337)
T ss_pred EECCCCCCccccccCcccCCc----CCCceeCccCCC
Confidence 479999998777799999654 245788888876
No 122
>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=72.69 E-value=2.6 Score=34.40 Aligned_cols=28 Identities=21% Similarity=0.455 Sum_probs=20.7
Q ss_pred ccccCCCCCCCcceeeccccccccCCCCcCeeeCCCCCcc
Q 027589 77 VAQVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGIC 116 (221)
Q Consensus 77 ~~~~C~~Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~CgiC 116 (221)
...+|++||+.| | +.+|.+-.|++||.=
T Consensus 8 tKr~Cp~cg~kF----------Y--DLnk~p~vcP~cg~~ 35 (129)
T TIGR02300 8 TKRICPNTGSKF----------Y--DLNRRPAVSPYTGEQ 35 (129)
T ss_pred ccccCCCcCccc----------c--ccCCCCccCCCcCCc
Confidence 345788888865 5 457889999998853
No 123
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=72.41 E-value=3.6 Score=42.22 Aligned_cols=54 Identities=22% Similarity=0.532 Sum_probs=42.6
Q ss_pred eeecCCCCCcccCchhHHhhhcCCCCCCCCccccccccceeecCCCCccccccccCCCCCCCccee
Q 027589 26 RIRAPCCNEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVAQVCTNCGVNMGEY 91 (221)
Q Consensus 26 ~l~~pCC~~~ypCr~CHde~~~~~~~~~~~H~~~r~~~~~v~C~~C~~~q~~~~~C~~Cg~~f~~y 91 (221)
.+.|.-||-.+.|++|=.-.+-|. .+..+.|-.|+.++++...|++||...=+|
T Consensus 435 ~l~C~~Cg~v~~Cp~Cd~~lt~H~------------~~~~L~CH~Cg~~~~~p~~Cp~Cgs~~L~~ 488 (730)
T COG1198 435 LLLCRDCGYIAECPNCDSPLTLHK------------ATGQLRCHYCGYQEPIPQSCPECGSEHLRA 488 (730)
T ss_pred eeecccCCCcccCCCCCcceEEec------------CCCeeEeCCCCCCCCCCCCCCCCCCCeeEE
Confidence 488999999999999965544322 247899999999999999999999885444
No 124
>PHA03096 p28-like protein; Provisional
Probab=71.91 E-value=1.7 Score=39.67 Aligned_cols=47 Identities=17% Similarity=0.328 Sum_probs=31.8
Q ss_pred CCCccchhhcccCC---Cceeee-ccCCccCHHHHHHHHhcC--cCCCCCCcc
Q 027589 151 HHCPICYEYLFDSL---RNTTVM-KCGHTMHCECYHEMIKRD--KYCCPICSK 197 (221)
Q Consensus 151 ~~CpICle~lf~s~---~~v~~L-~CGH~~H~~C~~~~l~~~--~~~CPiCrk 197 (221)
-.|.||+|...... ..-..| .|-|.|-..|+..|.... ..+||.|+.
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 46999998876532 112245 599999999999998743 334555554
No 125
>PRK04023 DNA polymerase II large subunit; Validated
Probab=71.63 E-value=3.3 Score=43.90 Aligned_cols=49 Identities=24% Similarity=0.578 Sum_probs=36.9
Q ss_pred ceeecCCCCccccccccCCCCCCC-cceeeccccccccCCCCcCeeeCCCCCccee
Q 027589 64 KQVICSVCDTEQPVAQVCTNCGVN-MGEYFCDICKFYDDDIEKGQFHCDDCGICRI 118 (221)
Q Consensus 64 ~~v~C~~C~~~q~~~~~C~~Cg~~-f~~y~C~~C~l~dd~~~k~~yHC~~CgiCR~ 118 (221)
..-.|..|+++. +...|++||.. -..|||+.|.-- -..|.|++||.=..
T Consensus 625 g~RfCpsCG~~t-~~frCP~CG~~Te~i~fCP~CG~~-----~~~y~CPKCG~El~ 674 (1121)
T PRK04023 625 GRRKCPSCGKET-FYRRCPFCGTHTEPVYRCPRCGIE-----VEEDECEKCGREPT 674 (1121)
T ss_pred cCccCCCCCCcC-CcccCCCCCCCCCcceeCccccCc-----CCCCcCCCCCCCCC
Confidence 355899999984 66899999974 677899999433 23488999996443
No 126
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=70.99 E-value=3.8 Score=24.10 Aligned_cols=9 Identities=44% Similarity=1.239 Sum_probs=5.2
Q ss_pred CeeeCCCCC
Q 027589 106 GQFHCDDCG 114 (221)
Q Consensus 106 ~~yHC~~Cg 114 (221)
..|.|++||
T Consensus 15 v~f~CPnCG 23 (24)
T PF07754_consen 15 VPFPCPNCG 23 (24)
T ss_pred ceEeCCCCC
Confidence 455666665
No 127
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=70.29 E-value=4.4 Score=41.62 Aligned_cols=43 Identities=28% Similarity=0.781 Sum_probs=29.2
Q ss_pred ceeecCCCCccccccccCCCCCCCc------ceeeccccccccCCCCcCeeeCCCCC
Q 027589 64 KQVICSVCDTEQPVAQVCTNCGVNM------GEYFCDICKFYDDDIEKGQFHCDDCG 114 (221)
Q Consensus 64 ~~v~C~~C~~~q~~~~~C~~Cg~~f------~~y~C~~C~l~dd~~~k~~yHC~~Cg 114 (221)
..++|..|+.. ..|++|+..+ +...|--|..= ++.+.+|+.||
T Consensus 434 ~~l~C~~Cg~v----~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~----~~~p~~Cp~Cg 482 (730)
T COG1198 434 PLLLCRDCGYI----AECPNCDSPLTLHKATGQLRCHYCGYQ----EPIPQSCPECG 482 (730)
T ss_pred ceeecccCCCc----ccCCCCCcceEEecCCCeeEeCCCCCC----CCCCCCCCCCC
Confidence 58999999966 4799998888 44455544432 34556666666
No 128
>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]
Probab=70.10 E-value=1.7 Score=44.79 Aligned_cols=47 Identities=32% Similarity=0.568 Sum_probs=32.4
Q ss_pred CCCccchhhcccCC---CceeeeccCCccCHHHHHHHHhcCcCCCCCCcccc
Q 027589 151 HHCPICYEYLFDSL---RNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSV 199 (221)
Q Consensus 151 ~~CpICle~lf~s~---~~v~~L~CGH~~H~~C~~~~l~~~~~~CPiCrksi 199 (221)
+.|.-|.+....+. ..+.++.|||.||..|+.....+++ |-+|.--.
T Consensus 785 ~rc~~c~~~~l~~~~~~~~~~v~~c~h~yhk~c~~~~~~~~~--~~~~~~~~ 834 (846)
T KOG2066|consen 785 ERCSSCFEPNLPSGAAFDSVVVFHCGHMYHKECLMMESLRNA--CNIESGKN 834 (846)
T ss_pred hhhhhhcccccccCcccceeeEEEccchhhhcccccHHHhcc--cChhhcee
Confidence 35666666655443 5688999999999999987665332 66665433
No 129
>PLN03086 PRLI-interacting factor K; Provisional
Probab=69.50 E-value=2.7 Score=41.95 Aligned_cols=84 Identities=26% Similarity=0.611 Sum_probs=48.6
Q ss_pred ccceeecCCCCcccccc-------------ccCCC--CCCCcceeeccccccccCCCCcCeeeCCCCCcceeCCc-----
Q 027589 62 DVKQVICSVCDTEQPVA-------------QVCTN--CGVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGR----- 121 (221)
Q Consensus 62 ~~~~v~C~~C~~~q~~~-------------~~C~~--Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~CgiCR~G~~----- 121 (221)
.+..|.|..|....+.. ..|++ ||..|.+- .-+..+||+.||- ..+..
T Consensus 404 ~~~~V~C~NC~~~i~l~~l~lHe~~C~r~~V~Cp~~~Cg~v~~r~-----------el~~H~~C~~Cgk-~f~~s~LekH 471 (567)
T PLN03086 404 DVDTVECRNCKHYIPSRSIALHEAYCSRHNVVCPHDGCGIVLRVE-----------EAKNHVHCEKCGQ-AFQQGEMEKH 471 (567)
T ss_pred CCCeEECCCCCCccchhHHHHHHhhCCCcceeCCcccccceeecc-----------ccccCccCCCCCC-ccchHHHHHH
Confidence 45688999998775542 24664 77766332 2345578888864 22211
Q ss_pred ----cceeecCccCccccccccCcce---eecCCCCCCCccchhhc
Q 027589 122 ----ENYFHCKRCGSCYSTSLRNNHL---CIENSMHHHCPICYEYL 160 (221)
Q Consensus 122 ----~~~fHC~~C~~C~s~~~~~~H~---C~e~~~~~~CpICle~l 160 (221)
..-+-|. ||.-+.......|. |.++ ...|+.|...+
T Consensus 472 ~~~~Hkpv~Cp-Cg~~~~R~~L~~H~~thCp~K--pi~C~fC~~~v 514 (567)
T PLN03086 472 MKVFHEPLQCP-CGVVLEKEQMVQHQASTCPLR--LITCRFCGDMV 514 (567)
T ss_pred HHhcCCCccCC-CCCCcchhHHHhhhhccCCCC--ceeCCCCCCcc
Confidence 1124576 77655444445664 4333 35799998764
No 130
>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=69.42 E-value=4 Score=28.65 Aligned_cols=27 Identities=30% Similarity=0.774 Sum_probs=16.9
Q ss_pred cccCCCCCCCcceeeccccccccCCCCcCeeeCCCCCc
Q 027589 78 AQVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGI 115 (221)
Q Consensus 78 ~~~C~~Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~Cgi 115 (221)
++.|+.||..... ......|.|+.||.
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 4678888877765 23445666666654
No 131
>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 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=66.34 E-value=3.3 Score=40.36 Aligned_cols=98 Identities=22% Similarity=0.446 Sum_probs=53.2
Q ss_pred eeccccccccCCCCcCeeeCCCCCcceeCCccceeecCccCccccccc--cCcceeecCCCCCCCccchhhcccCCCcee
Q 027589 91 YFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYSTSL--RNNHLCIENSMHHHCPICYEYLFDSLRNTT 168 (221)
Q Consensus 91 y~C~~C~l~dd~~~k~~yHC~~CgiCR~G~~~~~fHC~~C~~C~s~~~--~~~H~C~e~~~~~~CpICle~lf~s~~~v~ 168 (221)
|||..|+-. .|+-|-.... +.+=|..|-.=++.+. .+..+|..+- -+||+|.-.|........
T Consensus 6 ~fC~~C~~i------------rc~~c~~~Ei-~~~yCp~CL~~~p~~e~~~~~nrC~r~C--f~CP~C~~~L~~~~~~~~ 70 (483)
T PF05502_consen 6 YFCEHCHKI------------RCPRCVSEEI-DSYYCPNCLFEVPSSEARSEKNRCSRNC--FDCPICFSPLSVRASDTP 70 (483)
T ss_pred eeccccccc------------CChhhccccc-ceeECccccccCChhhheeccceecccc--ccCCCCCCcceeEecccc
Confidence 788888766 1333444433 3555666666565432 3567776554 479999988865433221
Q ss_pred e---eccCCccCHHHHHHHHhcCcCCCCCCcccccchhHHHHHHHH
Q 027589 169 V---MKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRTWKRIDE 211 (221)
Q Consensus 169 ~---L~CGH~~H~~C~~~~l~~~~~~CPiCrksi~dm~~~~~~lD~ 211 (221)
. -+-+=.-+ ......|+.|+=+-.++...|.+.+.
T Consensus 71 ~~~~~~~~~~~~--------~~~~l~C~~C~Wss~~igi~Fdkpt~ 108 (483)
T PF05502_consen 71 PSPPDPSSDSGG--------KPYYLSCSYCRWSSRDIGIKFDKPTG 108 (483)
T ss_pred cccccccccCCC--------CCEEEECCCceeeccccCccccCchh
Confidence 0 00000000 00135899999877665555555544
No 133
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=65.90 E-value=4.1 Score=28.99 Aligned_cols=34 Identities=24% Similarity=0.663 Sum_probs=25.4
Q ss_pred cceeecCCCCccccccccCCCCCCCcceeecccccc
Q 027589 63 VKQVICSVCDTEQPVAQVCTNCGVNMGEYFCDICKF 98 (221)
Q Consensus 63 ~~~v~C~~C~~~q~~~~~C~~Cg~~f~~y~C~~C~l 98 (221)
...-.|..|+.+. -..|..|....+.|-|++|.|
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 3577888887642 236888888888888888876
No 134
>KOG2068 consensus MOT2 transcription factor [Transcription]
Probab=65.63 E-value=4.8 Score=37.56 Aligned_cols=50 Identities=30% Similarity=0.505 Sum_probs=38.6
Q ss_pred CCCCccchhhcccCCCceeeeccCCccCHHHHHHHHhcCcCCCCCCccccc
Q 027589 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (221)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (221)
...||||-+++-........-|||+.++..|...-.. .+.+||.||+...
T Consensus 249 ~~s~p~~~~~~~~~d~~~lP~~~~~~~~l~~~~t~~~-~~~~~~~~rk~~~ 298 (327)
T KOG2068|consen 249 PPSCPICYEDLDLTDSNFLPCPCGFRLCLFCHKTISD-GDGRCPGCRKPYE 298 (327)
T ss_pred CCCCCCCCCcccccccccccccccccchhhhhhcccc-cCCCCCccCCccc
Confidence 4689999998744433444446799999999988876 5899999998765
No 135
>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=65.39 E-value=4.8 Score=24.25 Aligned_cols=20 Identities=30% Similarity=0.853 Sum_probs=13.5
Q ss_pred CCCcceeCCccc-eeecCccC
Q 027589 112 DCGICRIGGREN-YFHCKRCG 131 (221)
Q Consensus 112 ~CgiCR~G~~~~-~fHC~~C~ 131 (221)
.|++|+.-.... +++|..|+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~ 22 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECC 22 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCC
Confidence 467776654334 88888887
No 136
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=64.93 E-value=4.2 Score=37.93 Aligned_cols=44 Identities=32% Similarity=0.710 Sum_probs=35.5
Q ss_pred CCCccchhhcccCCCceeeeccCCccCHHHHHHHHhcCcCCCCCCcc
Q 027589 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSK 197 (221)
Q Consensus 151 ~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~~~~~CPiCrk 197 (221)
..||.|.--|- .+++.--|||.|..+||..-|..+.+.||.|..
T Consensus 275 LkCplc~~Llr---np~kT~cC~~~fc~eci~~al~dsDf~CpnC~r 318 (427)
T COG5222 275 LKCPLCHCLLR---NPMKTPCCGHTFCDECIGTALLDSDFKCPNCSR 318 (427)
T ss_pred ccCcchhhhhh---CcccCccccchHHHHHHhhhhhhccccCCCccc
Confidence 46999987553 466666689999999999766657899999987
No 137
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=64.72 E-value=4 Score=37.28 Aligned_cols=29 Identities=21% Similarity=0.526 Sum_probs=25.6
Q ss_pred CccCcccccccceeecCCCCCcccCchhHH
Q 027589 14 MGYGCKHYRRRCRIRAPCCNEIFDCRHCHN 43 (221)
Q Consensus 14 ~~~gC~HY~r~c~l~~pCC~~~ypCr~CHd 43 (221)
..+.|.||...=.+++.+|.. |+|..||+
T Consensus 176 ~~~~CgH~~h~~cf~e~~~~~-y~CP~C~~ 204 (276)
T KOG1940|consen 176 GVLKCGHYMHSRCFEEMICEG-YTCPICSK 204 (276)
T ss_pred CccCcccchHHHHHHHHhccC-CCCCcccc
Confidence 346899999866799999999 99999999
No 138
>PRK05580 primosome assembly protein PriA; Validated
Probab=64.37 E-value=5.5 Score=40.27 Aligned_cols=51 Identities=22% Similarity=0.632 Sum_probs=41.7
Q ss_pred eeecCCCCCcccCchhHHhhhcCCCCCCCCccccccccceeecCCCCccccccccCCCCCCCc
Q 027589 26 RIRAPCCNEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVAQVCTNCGVNM 88 (221)
Q Consensus 26 ~l~~pCC~~~ypCr~CHde~~~~~~~~~~~H~~~r~~~~~v~C~~C~~~q~~~~~C~~Cg~~f 88 (221)
.+.|.-||....|..|.-.+.- |. ....+.|-.|+..+++...|++||...
T Consensus 381 ~~~C~~Cg~~~~C~~C~~~l~~--------h~----~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~ 431 (679)
T PRK05580 381 FLLCRDCGWVAECPHCDASLTL--------HR----FQRRLRCHHCGYQEPIPKACPECGSTD 431 (679)
T ss_pred ceEhhhCcCccCCCCCCCceeE--------EC----CCCeEECCCCcCCCCCCCCCCCCcCCe
Confidence 4789999999999999876543 22 246899999999999999999998874
No 139
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=64.22 E-value=6 Score=25.36 Aligned_cols=26 Identities=23% Similarity=0.579 Sum_probs=15.8
Q ss_pred cCCCCCCCcceeeccccccccCCCCcCeeeCCCCC
Q 027589 80 VCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCG 114 (221)
Q Consensus 80 ~C~~Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~Cg 114 (221)
+||.|+..|..+. + .+-.++.|+.||
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 4777777776553 1 224667777765
No 140
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=63.59 E-value=3.8 Score=41.46 Aligned_cols=34 Identities=26% Similarity=0.666 Sum_probs=21.6
Q ss_pred eeecCCCCccccccccCCCCCCCc--ceeeccccccc
Q 027589 65 QVICSVCDTEQPVAQVCTNCGVNM--GEYFCDICKFY 99 (221)
Q Consensus 65 ~v~C~~C~~~q~~~~~C~~Cg~~f--~~y~C~~C~l~ 99 (221)
.-.|..|++.++. ..|++||+.. +.-||+.|-..
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 4467777776643 4677777654 55677777544
No 141
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=63.24 E-value=3.3 Score=42.09 Aligned_cols=45 Identities=31% Similarity=0.849 Sum_probs=35.8
Q ss_pred CCCccchhhcccCCCceeeeccCCccCHHHHHHHHhcCc-CCCCCCccccc
Q 027589 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDK-YCCPICSKSVI 200 (221)
Q Consensus 151 ~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~~~-~~CPiCrksi~ 200 (221)
..|+||++ .+...+-+|||.|-..|+.+.+.... ..||+||..+.
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 68999999 24567789999999999999886543 35999996654
No 142
>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=63.02 E-value=5.6 Score=21.73 Aligned_cols=17 Identities=47% Similarity=0.794 Sum_probs=13.0
Q ss_pred CCCCCCcccccchhHHH
Q 027589 190 YCCPICSKSVIDMSRTW 206 (221)
Q Consensus 190 ~~CPiCrksi~dm~~~~ 206 (221)
|+||+|.+++.+.+.+-
T Consensus 1 y~C~~C~~~f~~~~~l~ 17 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLK 17 (23)
T ss_dssp EEETTTTEEESSHHHHH
T ss_pred CCCCCCCCccCCHHHHH
Confidence 57999999998765433
No 143
>PRK14873 primosome assembly protein PriA; Provisional
Probab=61.93 E-value=6.3 Score=39.96 Aligned_cols=49 Identities=20% Similarity=0.491 Sum_probs=39.0
Q ss_pred eeecCCCCCcccCchhHHhhhcCCCCCCCCccccccccceeecCCCCccccccccCCCCCCC
Q 027589 26 RIRAPCCNEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVAQVCTNCGVN 87 (221)
Q Consensus 26 ~l~~pCC~~~ypCr~CHde~~~~~~~~~~~H~~~r~~~~~v~C~~C~~~q~~~~~C~~Cg~~ 87 (221)
.+.|.-||...-|..|.-.+.- |. ....+.|-.|+..+ +...|++||..
T Consensus 383 ~l~C~~Cg~~~~C~~C~~~L~~--------h~----~~~~l~Ch~CG~~~-~p~~Cp~Cgs~ 431 (665)
T PRK14873 383 SLACARCRTPARCRHCTGPLGL--------PS----AGGTPRCRWCGRAA-PDWRCPRCGSD 431 (665)
T ss_pred eeEhhhCcCeeECCCCCCceeE--------ec----CCCeeECCCCcCCC-cCccCCCCcCC
Confidence 4899999999999999876643 21 23578899999876 57899999886
No 144
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=60.51 E-value=8.3 Score=25.25 Aligned_cols=8 Identities=38% Similarity=1.074 Sum_probs=4.2
Q ss_pred eeeCCCCC
Q 027589 107 QFHCDDCG 114 (221)
Q Consensus 107 ~yHC~~Cg 114 (221)
..+|+.||
T Consensus 21 ~~~Cp~CG 28 (46)
T PRK00398 21 GVRCPYCG 28 (46)
T ss_pred ceECCCCC
Confidence 45555554
No 145
>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=59.48 E-value=6.6 Score=35.33 Aligned_cols=48 Identities=25% Similarity=0.607 Sum_probs=22.8
Q ss_pred cceeecCCCCcccccc-ccCCCCCCCcceeeccccccc--cCCCCcCeeeCCCCC
Q 027589 63 VKQVICSVCDTEQPVA-QVCTNCGVNMGEYFCDICKFY--DDDIEKGQFHCDDCG 114 (221)
Q Consensus 63 ~~~v~C~~C~~~q~~~-~~C~~Cg~~f~~y~C~~C~l~--dd~~~k~~yHC~~Cg 114 (221)
.+-..|+.|+++-.+. ..|++||..-..-+ .+| ++++.-.++-|+.||
T Consensus 195 ~R~L~Cs~C~t~W~~~R~~Cp~Cg~~~~~~l----~~~~~e~~~~~rve~C~~C~ 245 (290)
T PF04216_consen 195 KRYLHCSLCGTEWRFVRIKCPYCGNTDHEKL----EYFTVEGEPAYRVEVCESCG 245 (290)
T ss_dssp EEEEEETTT--EEE--TTS-TTT---SS-EE----E--------SEEEEEETTTT
T ss_pred cEEEEcCCCCCeeeecCCCCcCCCCCCCcce----eeEecCCCCcEEEEECCccc
Confidence 3688999999998774 68999998776544 333 333444555555554
No 146
>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=59.22 E-value=7.4 Score=26.34 Aligned_cols=27 Identities=26% Similarity=0.660 Sum_probs=13.4
Q ss_pred cCCCCCCcccccchh--HHHHHHHHHHHh
Q 027589 189 KYCCPICSKSVIDMS--RTWKRIDEEVSL 215 (221)
Q Consensus 189 ~~~CPiCrksi~dm~--~~~~~lD~~i~~ 215 (221)
...||+|.+++.+-. .+-+.+..+|..
T Consensus 20 ~~~CPlC~r~l~~e~~~~li~~~~~~i~~ 48 (54)
T PF04423_consen 20 KGCCPLCGRPLDEEHRQELIKKYKSEIEE 48 (54)
T ss_dssp SEE-TTT--EE-HHHHHHHHHHHHHHHHH
T ss_pred CCcCCCCCCCCCHHHHHHHHHHHHHHHHh
Confidence 348999999998532 244555555543
No 147
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=58.76 E-value=9 Score=35.97 Aligned_cols=44 Identities=23% Similarity=0.631 Sum_probs=34.7
Q ss_pred CCccchhhcccCCCceeeeccCCccCHHHHHHHHhcC--cCCCCCCc
Q 027589 152 HCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRD--KYCCPICS 196 (221)
Q Consensus 152 ~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~~--~~~CPiCr 196 (221)
.|||=-|. -+...+...|.|||++=..=++.+-+++ .++||.|-
T Consensus 338 iCPVlKe~-~t~ENpP~ml~CgHVIskeal~~LS~nG~~~FKCPYCP 383 (396)
T COG5109 338 ICPVLKEL-CTDENPPVMLECGHVISKEALSVLSQNGVLSFKCPYCP 383 (396)
T ss_pred eccccHhh-hcccCCCeeeeccceeeHHHHHHHhhcCcEEeeCCCCC
Confidence 58886665 4445677889999999999999987754 67899996
No 148
>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=58.73 E-value=2.4 Score=27.03 Aligned_cols=27 Identities=33% Similarity=0.671 Sum_probs=15.1
Q ss_pred cCCCCCCCcceeeccccccccCCCCcCeeeCCCCCc
Q 027589 80 VCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGI 115 (221)
Q Consensus 80 ~C~~Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~Cgi 115 (221)
.|++||+.++-+| ++.|..=-|+.||-
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 4666777766554 34455556666664
No 149
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=58.44 E-value=5.7 Score=28.26 Aligned_cols=35 Identities=31% Similarity=0.510 Sum_probs=25.9
Q ss_pred ceeecCCCCccccc------cccCCCCCCCcceeecccccc
Q 027589 64 KQVICSVCDTEQPV------AQVCTNCGVNMGEYFCDICKF 98 (221)
Q Consensus 64 ~~v~C~~C~~~q~~------~~~C~~Cg~~f~~y~C~~C~l 98 (221)
-.|.|..|..+|.+ ...|..||..+++-.=.+-+|
T Consensus 10 ~~VkCp~C~n~q~vFsha~t~V~C~~Cg~~L~~PtGGKa~i 50 (59)
T PRK00415 10 LKVKCPDCGNEQVVFSHASTVVRCLVCGKTLAEPTGGKAKI 50 (59)
T ss_pred EEEECCCCCCeEEEEecCCcEEECcccCCCcccCCCcceee
Confidence 47899999999966 247999999887765444443
No 150
>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=58.31 E-value=3.5 Score=37.67 Aligned_cols=51 Identities=27% Similarity=0.750 Sum_probs=29.8
Q ss_pred CCcccCchhHHhhhcCCCCCCCCccccccccceeecCCCCccccccccCCCCCCCcceeecccccc
Q 027589 33 NEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVAQVCTNCGVNMGEYFCDICKF 98 (221)
Q Consensus 33 ~~~ypCr~CHde~~~~~~~~~~~H~~~r~~~~~v~C~~C~~~q~~~~~C~~Cg~~f~~y~C~~C~l 98 (221)
|++|.|-+|.+-+-.. |+++ |... |+...+-+-.|.+|+ .++.|.|..||.
T Consensus 140 Grif~CsfC~~flCED--DQFE-HQAs-----------CQvLe~E~~KC~SCN-rlGq~sCLRCK~ 190 (314)
T PF06524_consen 140 GRIFKCSFCDNFLCED--DQFE-HQAS-----------CQVLESETFKCQSCN-RLGQYSCLRCKI 190 (314)
T ss_pred CeEEEeecCCCeeecc--chhh-hhhh-----------hhhhhcccccccccc-cccchhhhheee
Confidence 5678888887765421 1112 2221 444444455677776 468888888874
No 151
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=57.98 E-value=4.7 Score=38.16 Aligned_cols=37 Identities=27% Similarity=0.608 Sum_probs=28.0
Q ss_pred CCCCccchhhcccCCCceeeeccCCccCHHHHHHHHh
Q 027589 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIK 186 (221)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~ 186 (221)
...|.||..+..+......++.|||.|-..|..+++.
T Consensus 146 ~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~ie 182 (384)
T KOG1812|consen 146 KEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIE 182 (384)
T ss_pred cccCccCccccccHhhhHHHhcccchhhhHHhHHHhh
Confidence 5679999944344433344789999999999999987
No 152
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=57.80 E-value=12 Score=34.32 Aligned_cols=21 Identities=38% Similarity=0.382 Sum_probs=12.8
Q ss_pred cCCCCCCcccccchhHHHHHH
Q 027589 189 KYCCPICSKSVIDMSRTWKRI 209 (221)
Q Consensus 189 ~~~CPiCrksi~dm~~~~~~l 209 (221)
+|+|+-|.|++.-|+-..+.+
T Consensus 243 ~~qC~~C~KsFsl~SyLnKH~ 263 (279)
T KOG2462|consen 243 KHQCPRCGKSFALKSYLNKHS 263 (279)
T ss_pred cccCcchhhHHHHHHHHHHhh
Confidence 566777777776665544433
No 153
>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=57.44 E-value=9.5 Score=24.65 Aligned_cols=7 Identities=57% Similarity=1.583 Sum_probs=3.6
Q ss_pred CCCCCCC
Q 027589 81 CTNCGVN 87 (221)
Q Consensus 81 C~~Cg~~ 87 (221)
||+||..
T Consensus 3 Cp~Cg~~ 9 (43)
T PF08271_consen 3 CPNCGSK 9 (43)
T ss_dssp BTTTSSS
T ss_pred CcCCcCC
Confidence 5555554
No 154
>PF15353 HECA: Headcase protein family homologue
Probab=57.20 E-value=5.5 Score=31.51 Aligned_cols=15 Identities=33% Similarity=0.707 Sum_probs=13.4
Q ss_pred cCCccCHHHHHHHHh
Q 027589 172 CGHTMHCECYHEMIK 186 (221)
Q Consensus 172 CGH~~H~~C~~~~l~ 186 (221)
-|++||+.||++|-.
T Consensus 40 ~~~~MH~~CF~~wE~ 54 (107)
T PF15353_consen 40 FGQYMHRECFEKWED 54 (107)
T ss_pred CCCchHHHHHHHHHH
Confidence 489999999999965
No 155
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=56.64 E-value=4.5 Score=43.87 Aligned_cols=52 Identities=31% Similarity=0.650 Sum_probs=41.7
Q ss_pred CCCCCCccchhhcccCCCceeeeccCCccCHHHHHHHHhcCcCCCCCCcccccchh
Q 027589 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMS 203 (221)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~~~~~CPiCrksi~dm~ 203 (221)
+....|+||++.|-. .-.+..|||.+-..|+..|+. .+..||+|+...+|..
T Consensus 1151 ~~~~~c~ic~dil~~---~~~I~~cgh~~c~~c~~~~l~-~~s~~~~~ksi~~dfg 1202 (1394)
T KOG0298|consen 1151 SGHFVCEICLDILRN---QGGIAGCGHEPCCRCDELWLY-ASSRCPICKSIKGDFG 1202 (1394)
T ss_pred hcccchHHHHHHHHh---cCCeeeechhHhhhHHHHHHH-HhccCcchhhhhhhhc
Confidence 334589999998753 234678999999999999998 5789999997777644
No 156
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=56.14 E-value=9.6 Score=28.85 Aligned_cols=46 Identities=26% Similarity=0.448 Sum_probs=31.8
Q ss_pred CCccchhhcccCCCceeeeccCCccCHHHHHHHHhcCcCCCCCCcccccchhHHHHHHHHHHHhCCCCC
Q 027589 152 HCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRTWKRIDEEVSLFNLSF 220 (221)
Q Consensus 152 ~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~~~~~CPiCrksi~dm~~~~~~lD~~i~~~pmP~ 220 (221)
.||||--+|-.+...-+ .-..||-||-.-+|- ..||.+|+.+..|.
T Consensus 3 lCP~C~v~l~~~~rs~v-------------------EiD~CPrCrGVWLDr----GELdKli~r~r~pq 48 (88)
T COG3809 3 LCPICGVELVMSVRSGV-------------------EIDYCPRCRGVWLDR----GELDKLIERSRYPQ 48 (88)
T ss_pred ccCcCCceeeeeeecCc-------------------eeeeCCccccEeecc----hhHHHHHHHhcCCC
Confidence 59999988765532111 135799999888876 56888888775543
No 157
>PHA00626 hypothetical protein
Probab=55.60 E-value=7.7 Score=27.50 Aligned_cols=34 Identities=18% Similarity=0.400 Sum_probs=22.8
Q ss_pred eecCCCCccccccccCCCCCCCcceeeccccccccC
Q 027589 66 VICSVCDTEQPVAQVCTNCGVNMGEYFCDICKFYDD 101 (221)
Q Consensus 66 v~C~~C~~~q~~~~~C~~Cg~~f~~y~C~~C~l~dd 101 (221)
|.|..|+..+-+ .|..|...-++|-|..|.+++.
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 457777765444 5666666677888888877654
No 158
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=55.13 E-value=6.5 Score=34.76 Aligned_cols=51 Identities=25% Similarity=0.446 Sum_probs=38.0
Q ss_pred CCCCccchhhcccCCCceeeecc---C--CccCHHHHHHHHhc-CcCCCCCCccccc
Q 027589 150 HHHCPICYEYLFDSLRNTTVMKC---G--HTMHCECYHEMIKR-DKYCCPICSKSVI 200 (221)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~L~C---G--H~~H~~C~~~~l~~-~~~~CPiCrksi~ 200 (221)
+..|=||.++.+++.......|| | ...|+.|++.|+.. ++.+|.+|.....
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 35799999987655332345676 2 88899999999873 4678999998654
No 159
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=50.18 E-value=21 Score=26.83 Aligned_cols=51 Identities=20% Similarity=0.410 Sum_probs=24.6
Q ss_pred CCCCCccchhhcccCCCceee---eccCCccCHHHHHHHHhcCcCCCCCCcccc
Q 027589 149 MHHHCPICYEYLFDSLRNTTV---MKCGHTMHCECYHEMIKRDKYCCPICSKSV 199 (221)
Q Consensus 149 ~~~~CpICle~lf~s~~~v~~---L~CGH~~H~~C~~~~l~~~~~~CPiCrksi 199 (221)
..+.|-||.|++-.+.+.-.+ .-|+=.+-+.|++--++..+..||-|+...
T Consensus 8 ~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg~q~CpqCkt~y 61 (80)
T PF14569_consen 8 NGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEGNQVCPQCKTRY 61 (80)
T ss_dssp SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS-SB-TTT--B-
T ss_pred CCcccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcCcccccccCCCc
Confidence 456799999987444333332 358999999999988888889999999544
No 160
>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=49.89 E-value=15 Score=23.45 Aligned_cols=34 Identities=29% Similarity=0.629 Sum_probs=16.3
Q ss_pred cCCCCCCCcceeeccccccccCCCCcCeeeCCCCC
Q 027589 80 VCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCG 114 (221)
Q Consensus 80 ~C~~Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~Cg 114 (221)
.|++||+.-+-|+ .+=--=-|++..-.|.|-+||
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 5788888777665 100001234455566666665
No 161
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=48.95 E-value=11 Score=23.77 Aligned_cols=9 Identities=33% Similarity=1.010 Sum_probs=4.0
Q ss_pred cCCCCCCCc
Q 027589 80 VCTNCGVNM 88 (221)
Q Consensus 80 ~C~~Cg~~f 88 (221)
.|++||+.|
T Consensus 27 ~C~~C~~~f 35 (36)
T PF13717_consen 27 RCSKCGHVF 35 (36)
T ss_pred ECCCCCCEe
Confidence 344444443
No 162
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=48.39 E-value=8.4 Score=28.09 Aligned_cols=28 Identities=36% Similarity=0.692 Sum_probs=22.3
Q ss_pred ceeecCCCCccccc------cccCCCCCCCccee
Q 027589 64 KQVICSVCDTEQPV------AQVCTNCGVNMGEY 91 (221)
Q Consensus 64 ~~v~C~~C~~~q~~------~~~C~~Cg~~f~~y 91 (221)
-.|.|..|+.+|.+ ...|..||..+++-
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 48999999999976 24799999887654
No 163
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=47.69 E-value=12 Score=30.88 Aligned_cols=48 Identities=31% Similarity=0.649 Sum_probs=35.4
Q ss_pred CCCccchhhcccCCCceeeec----cCCccCHHHHHHHHhc--CcCCCCCCcccccch
Q 027589 151 HHCPICYEYLFDSLRNTTVMK----CGHTMHCECYHEMIKR--DKYCCPICSKSVIDM 202 (221)
Q Consensus 151 ~~CpICle~lf~s~~~v~~L~----CGH~~H~~C~~~~l~~--~~~~CPiCrksi~dm 202 (221)
-.|-||.|. | .+.+.|. ||=.+...|+.++.+. ....||+|+.|+-.-
T Consensus 81 YeCnIC~et---S-~ee~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKss 134 (140)
T PF05290_consen 81 YECNICKET---S-AEERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKSS 134 (140)
T ss_pred eeccCcccc---c-chhhcCCcccccchHHHHHHHHHHHHHcccCCCCCccccccccc
Confidence 468888875 2 2345663 8999999999987664 356799999988643
No 164
>PF14353 CpXC: CpXC protein
Probab=46.80 E-value=20 Score=28.14 Aligned_cols=11 Identities=27% Similarity=0.809 Sum_probs=6.6
Q ss_pred cCCCCCCCcce
Q 027589 80 VCTNCGVNMGE 90 (221)
Q Consensus 80 ~C~~Cg~~f~~ 90 (221)
+||+||+.|..
T Consensus 3 tCP~C~~~~~~ 13 (128)
T PF14353_consen 3 TCPHCGHEFEF 13 (128)
T ss_pred CCCCCCCeeEE
Confidence 56666666643
No 165
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=46.64 E-value=13 Score=23.47 Aligned_cols=9 Identities=33% Similarity=0.958 Sum_probs=4.2
Q ss_pred cCCCCCCCc
Q 027589 80 VCTNCGVNM 88 (221)
Q Consensus 80 ~C~~Cg~~f 88 (221)
.|++|++.|
T Consensus 27 rC~~C~~~f 35 (37)
T PF13719_consen 27 RCPKCGHVF 35 (37)
T ss_pred ECCCCCcEe
Confidence 344444444
No 166
>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=46.48 E-value=15 Score=22.53 Aligned_cols=25 Identities=32% Similarity=0.894 Sum_probs=15.9
Q ss_pred eeeccccccccCCCCcCeeeCCCCCc
Q 027589 90 EYFCDICKFYDDDIEKGQFHCDDCGI 115 (221)
Q Consensus 90 ~y~C~~C~l~dd~~~k~~yHC~~Cgi 115 (221)
.|-|.+|-+.-+ +.+.++.|+.||.
T Consensus 1 ~~~C~~CGy~y~-~~~~~~~CP~Cg~ 25 (33)
T cd00350 1 KYVCPVCGYIYD-GEEAPWVCPVCGA 25 (33)
T ss_pred CEECCCCCCEEC-CCcCCCcCcCCCC
Confidence 366777765432 2457788888775
No 167
>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=46.32 E-value=11 Score=22.41 Aligned_cols=20 Identities=20% Similarity=0.667 Sum_probs=6.2
Q ss_pred CCcceeCCcc-ceeecCccCc
Q 027589 113 CGICRIGGRE-NYFHCKRCGS 132 (221)
Q Consensus 113 CgiCR~G~~~-~~fHC~~C~~ 132 (221)
|++|+..+.. .+++|..|+.
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 4445444332 5666666654
No 168
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=46.20 E-value=13 Score=33.40 Aligned_cols=49 Identities=24% Similarity=0.632 Sum_probs=29.6
Q ss_pred CCCCCCCcceeeccccccccCCCCcCeeeCCCCCcceeCCccceeecCccCcccc
Q 027589 81 CTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYS 135 (221)
Q Consensus 81 C~~Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~CgiCR~G~~~~~fHC~~C~~C~s 135 (221)
-..=|......||+.|+++-- +...||.-||.|-.+- ==||.==|.|+.
T Consensus 104 ~~~~~~~~~~~~C~~C~~~rP---pRs~HCsvC~~CV~rf---DHHC~WvnnCVG 152 (299)
T KOG1311|consen 104 VDVNGIQVEWKYCDTCQLYRP---PRSSHCSVCNNCVLRF---DHHCPWLNNCIG 152 (299)
T ss_pred cccCCcccceEEcCcCcccCC---CCcccchhhccccccc---CCCCCCccceEC
Confidence 333456667899999999932 3455776666665541 135555555544
No 169
>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=45.64 E-value=10 Score=23.11 Aligned_cols=16 Identities=38% Similarity=1.028 Sum_probs=7.7
Q ss_pred CCCCCCCcceeeccccc
Q 027589 81 CTNCGVNMGEYFCDICK 97 (221)
Q Consensus 81 C~~Cg~~f~~y~C~~C~ 97 (221)
|..||. .++|-|+.|.
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 5556555554
No 170
>KOG1312 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=45.16 E-value=6.9 Score=36.30 Aligned_cols=32 Identities=31% Similarity=0.782 Sum_probs=28.0
Q ss_pred CCCCcceeCCccceeecCccCccccccccCcceee
Q 027589 111 DDCGICRIGGRENYFHCKRCGSCYSTSLRNNHLCI 145 (221)
Q Consensus 111 ~~CgiCR~G~~~~~fHC~~C~~C~s~~~~~~H~C~ 145 (221)
.+|..|++.+.--..||..||.|+..- +|.|+
T Consensus 149 ~kCSTCki~KPARSKHCsiCNrCV~rf---DHHCi 180 (341)
T KOG1312|consen 149 VKCSTCKIRKPARSKHCSICNRCVHRF---DHHCI 180 (341)
T ss_pred CccccccCCCccccccchHHHHHHHHh---ccceE
Confidence 679999999988899999999999864 78886
No 171
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=45.06 E-value=13 Score=26.62 Aligned_cols=34 Identities=24% Similarity=0.574 Sum_probs=22.1
Q ss_pred cceeecCCCCccccccccCCCCCCCcceeecccccc
Q 027589 63 VKQVICSVCDTEQPVAQVCTNCGVNMGEYFCDICKF 98 (221)
Q Consensus 63 ~~~v~C~~C~~~q~~~~~C~~Cg~~f~~y~C~~C~l 98 (221)
...-.|..|+.++-. .|..|-..=|.|-|++|-|
T Consensus 25 ~v~F~CPnCGe~~I~--Rc~~CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 25 AVKFPCPNCGEVEIY--RCAKCRKLGNPYRCPKCGF 58 (61)
T ss_pred eeEeeCCCCCceeee--hhhhHHHcCCceECCCcCc
Confidence 346667777755433 5667777777777777765
No 172
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=44.67 E-value=16 Score=24.87 Aligned_cols=9 Identities=44% Similarity=1.531 Sum_probs=5.2
Q ss_pred CeeeCCCCC
Q 027589 106 GQFHCDDCG 114 (221)
Q Consensus 106 ~~yHC~~Cg 114 (221)
+.|+|..||
T Consensus 36 ~r~~C~~Cg 44 (50)
T PRK00432 36 DRWHCGKCG 44 (50)
T ss_pred CcEECCCcC
Confidence 455666555
No 173
>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=43.44 E-value=7.8 Score=40.49 Aligned_cols=44 Identities=30% Similarity=0.728 Sum_probs=0.0
Q ss_pred cCCCCCCCcceeeccccccccCCCCcCeeeCCCCCcceeCCccceeecCccCc
Q 027589 80 VCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGS 132 (221)
Q Consensus 80 ~C~~Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~CgiCR~G~~~~~fHC~~C~~ 132 (221)
.|++||..--.-.|+.|.-. ..+.|.|+.||+ .+.. .+|.+|+.
T Consensus 657 ~Cp~Cg~~t~~~~Cp~CG~~----T~~~~~Cp~C~~-~~~~----~~C~~C~~ 700 (900)
T PF03833_consen 657 RCPKCGKETFYNRCPECGSH----TEPVYVCPDCGI-EVEE----DECPKCGR 700 (900)
T ss_dssp -----------------------------------------------------
T ss_pred cCcccCCcchhhcCcccCCc----cccceecccccc-ccCc----cccccccc
Confidence 56666666666666666544 335677777776 2221 16777765
No 174
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=43.07 E-value=15 Score=20.34 Aligned_cols=16 Identities=31% Similarity=0.696 Sum_probs=12.4
Q ss_pred CCCCCCcccccchhHH
Q 027589 190 YCCPICSKSVIDMSRT 205 (221)
Q Consensus 190 ~~CPiCrksi~dm~~~ 205 (221)
+.|.+|.+++.+...+
T Consensus 1 ~~C~~C~~~f~s~~~~ 16 (25)
T PF12874_consen 1 FYCDICNKSFSSENSL 16 (25)
T ss_dssp EEETTTTEEESSHHHH
T ss_pred CCCCCCCCCcCCHHHH
Confidence 4699999999876543
No 175
>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=42.83 E-value=9.8 Score=25.19 Aligned_cols=39 Identities=26% Similarity=0.641 Sum_probs=25.4
Q ss_pred CccchhhcccCCCceeeeccCCccCHHHHHHHHhcCcCCCCCCcccccch
Q 027589 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDM 202 (221)
Q Consensus 153 CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~~~~~CPiCrksi~dm 202 (221)
|+.|.+.+... .+.+..=|..+|..|| +|=.|+++|.+.
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 56677776532 3333356788887765 677888888654
No 176
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=42.29 E-value=43 Score=30.73 Aligned_cols=89 Identities=27% Similarity=0.560 Sum_probs=51.8
Q ss_pred cceeecccc-ccccCCC---CcCeeeCCCCCcceeCCccceeecCccCcccccc-ccCcceeecCCCCCCCccchhhccc
Q 027589 88 MGEYFCDIC-KFYDDDI---EKGQFHCDDCGICRIGGRENYFHCKRCGSCYSTS-LRNNHLCIENSMHHHCPICYEYLFD 162 (221)
Q Consensus 88 f~~y~C~~C-~l~dd~~---~k~~yHC~~CgiCR~G~~~~~fHC~~C~~C~s~~-~~~~H~C~e~~~~~~CpICle~lf~ 162 (221)
-++|-|+.| |-|.... .-+|+||+- .-...|.|+.|+-=|..- ...-|+=.- ...-.|+||.-. |+
T Consensus 128 ~~r~~c~eCgk~ysT~snLsrHkQ~H~~~-------~s~ka~~C~~C~K~YvSmpALkMHirTH-~l~c~C~iCGKa-FS 198 (279)
T KOG2462|consen 128 HPRYKCPECGKSYSTSSNLSRHKQTHRSL-------DSKKAFSCKYCGKVYVSMPALKMHIRTH-TLPCECGICGKA-FS 198 (279)
T ss_pred CCceeccccccccccccccchhhcccccc-------cccccccCCCCCceeeehHHHhhHhhcc-CCCccccccccc-cc
Confidence 345555555 4443322 236777743 124577888888766432 112222221 135679999986 54
Q ss_pred CCCceeeeccCCccCHHHHHHHHhc---------CcCCCCCCcccccchhH
Q 027589 163 SLRNTTVMKCGHTMHCECYHEMIKR---------DKYCCPICSKSVIDMSR 204 (221)
Q Consensus 163 s~~~v~~L~CGH~~H~~C~~~~l~~---------~~~~CPiCrksi~dm~~ 204 (221)
- .||.. .-+.||.|+|.+.|-+.
T Consensus 199 R-------------------PWLLQGHiRTHTGEKPF~C~hC~kAFADRSN 230 (279)
T KOG2462|consen 199 R-------------------PWLLQGHIRTHTGEKPFSCPHCGKAFADRSN 230 (279)
T ss_pred c-------------------hHHhhcccccccCCCCccCCcccchhcchHH
Confidence 2 36652 35789999999998754
No 177
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=42.19 E-value=14 Score=25.94 Aligned_cols=34 Identities=24% Similarity=0.457 Sum_probs=19.7
Q ss_pred eeecCCCCccccc------cccCCCCCCCcceeecccccc
Q 027589 65 QVICSVCDTEQPV------AQVCTNCGVNMGEYFCDICKF 98 (221)
Q Consensus 65 ~v~C~~C~~~q~~------~~~C~~Cg~~f~~y~C~~C~l 98 (221)
.|.|..|..+|.+ ...|..||..+++-.=.+-+|
T Consensus 7 ~VkCp~C~~~q~vFSha~t~V~C~~Cg~~L~~PtGGKa~l 46 (55)
T PF01667_consen 7 DVKCPGCYNIQTVFSHAQTVVKCVVCGTVLAQPTGGKARL 46 (55)
T ss_dssp EEE-TTT-SEEEEETT-SS-EE-SSSTSEEEEE-SSSEEE
T ss_pred EEECCCCCCeeEEEecCCeEEEcccCCCEecCCCCcCeEE
Confidence 6788888888866 236888888877655444333
No 178
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=41.77 E-value=8.4 Score=32.20 Aligned_cols=25 Identities=28% Similarity=1.016 Sum_probs=18.7
Q ss_pred ceeeccccccccCCCCcCeeeCCCCC--cceeC
Q 027589 89 GEYFCDICKFYDDDIEKGQFHCDDCG--ICRIG 119 (221)
Q Consensus 89 ~~y~C~~C~l~dd~~~k~~yHC~~Cg--iCR~G 119 (221)
.+-||++|-+| ++|-|..|| +|-|+
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 46688888855 578888888 67776
No 179
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=41.41 E-value=19 Score=24.62 Aligned_cols=26 Identities=35% Similarity=0.708 Sum_probs=14.2
Q ss_pred eeecccc-ccccCCCCcCeeeCCCCCc
Q 027589 90 EYFCDIC-KFYDDDIEKGQFHCDDCGI 115 (221)
Q Consensus 90 ~y~C~~C-~l~dd~~~k~~yHC~~Cgi 115 (221)
.|-|..| +.++.+..+.-.-|+.||.
T Consensus 6 ~Y~C~~Cg~~~~~~~~~~~irCp~Cg~ 32 (49)
T COG1996 6 EYKCARCGREVELDQETRGIRCPYCGS 32 (49)
T ss_pred EEEhhhcCCeeehhhccCceeCCCCCc
Confidence 4445555 2334445566667777764
No 180
>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=41.22 E-value=20 Score=21.31 Aligned_cols=10 Identities=20% Similarity=0.610 Sum_probs=3.8
Q ss_pred ccCCCCCCCc
Q 027589 79 QVCTNCGVNM 88 (221)
Q Consensus 79 ~~C~~Cg~~f 88 (221)
+.|+.|+..+
T Consensus 2 ~~C~rC~~~~ 11 (30)
T PF06827_consen 2 EKCPRCWNYI 11 (30)
T ss_dssp SB-TTT--BB
T ss_pred CcCccCCCcc
Confidence 3566665554
No 181
>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=40.95 E-value=37 Score=22.17 Aligned_cols=9 Identities=44% Similarity=1.154 Sum_probs=5.4
Q ss_pred ccCCCCCCC
Q 027589 79 QVCTNCGVN 87 (221)
Q Consensus 79 ~~C~~Cg~~ 87 (221)
..||.||..
T Consensus 19 ~~CP~Cg~~ 27 (46)
T PF12760_consen 19 FVCPHCGST 27 (46)
T ss_pred CCCCCCCCe
Confidence 456666665
No 182
>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=40.70 E-value=23 Score=28.55 Aligned_cols=49 Identities=24% Similarity=0.541 Sum_probs=36.8
Q ss_pred CCCCCcceeeccccccccCCCCcCeeeCCCCCcceeCCccceeecCccCcccccc
Q 027589 83 NCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYSTS 137 (221)
Q Consensus 83 ~Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~CgiCR~G~~~~~fHC~~C~~C~s~~ 137 (221)
.-+......+|..|+.+-- . ...||..||.|..+- -.||.-=|.|+...
T Consensus 41 ~~~~~~~~~~C~~C~~~kp--~-Rs~HC~~C~~CV~~~---DHHC~w~~~cIG~~ 89 (174)
T PF01529_consen 41 EDDENGELKYCSTCKIIKP--P-RSHHCRVCNRCVLRF---DHHCPWLGNCIGRR 89 (174)
T ss_pred ccccCCCCEECcccCCcCC--C-cceeccccccccccc---cccchhhccccccc
Confidence 3457778889999998833 2 478999999998873 45888888887754
No 183
>KOG4399 consensus C2HC-type Zn-finger protein [General function prediction only]
Probab=40.27 E-value=5.5 Score=36.41 Aligned_cols=72 Identities=28% Similarity=0.669 Sum_probs=53.4
Q ss_pred CCCcceeeccccccccCCCCcCeeeCCCCCcceeCCccceeecCccCccccccccCcceeecCCCCCCCccchhh
Q 027589 85 GVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYSTSLRNNHLCIENSMHHHCPICYEY 159 (221)
Q Consensus 85 g~~f~~y~C~~C~l~dd~~~k~~yHC~~CgiCR~G~~~~~fHC~~C~~C~s~~~~~~H~C~e~~~~~~CpICle~ 159 (221)
|..=+-.||+.|..| ..+-.-||+.|+.|..-.++.|-||..|-.|+-.++-.--.|-.-+..--|-||-+.
T Consensus 199 ~~EE~~~~~~~~~~Y---v~~~~~H~~~~~S~~~~~~~~~~H~~~~~~~~~~~~i~C~~~~~~A~~~~C~iC~~~ 270 (325)
T KOG4399|consen 199 PTEEGYRFCSPCQRY---VSLENQHCEHCNSCTSKDGRKWNHCFLCKKCVKPSWIHCSICNHCAVKHGCFICGEL 270 (325)
T ss_pred ccccceEEEeehHHH---HHHHhhhchhhcccccchhHHHhHhHHhhhhcccceeeeecccchhhhcceeecccc
Confidence 444466779999888 456778999999998777778999999999998887433333333445568888876
No 184
>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=39.83 E-value=14 Score=29.12 Aligned_cols=11 Identities=18% Similarity=0.661 Sum_probs=5.7
Q ss_pred cccCCCCCCCc
Q 027589 78 AQVCTNCGVNM 88 (221)
Q Consensus 78 ~~~C~~Cg~~f 88 (221)
...|.+||..|
T Consensus 70 ~~~C~~Cg~~~ 80 (115)
T TIGR00100 70 ECECEDCSEEV 80 (115)
T ss_pred EEEcccCCCEE
Confidence 34555555444
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=39.47 E-value=17 Score=29.36 Aligned_cols=36 Identities=25% Similarity=0.591 Sum_probs=24.9
Q ss_pred CcCeeeCCCCCcceeCCccceeecCccCccccccccCcceee
Q 027589 104 EKGQFHCDDCGICRIGGRENYFHCKRCGSCYSTSLRNNHLCI 145 (221)
Q Consensus 104 ~k~~yHC~~CgiCR~G~~~~~fHC~~C~~C~s~~~~~~H~C~ 145 (221)
....-.|.. |++-......||..||.|+..- +|-|.
T Consensus 45 ~~~~~~C~~---C~~~kp~Rs~HC~~C~~CV~~~---DHHC~ 80 (174)
T PF01529_consen 45 NGELKYCST---CKIIKPPRSHHCRVCNRCVLRF---DHHCP 80 (174)
T ss_pred CCCCEECcc---cCCcCCCcceeccccccccccc---cccch
Confidence 334445555 5555666799999999998865 56664
No 186
>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=39.37 E-value=17 Score=22.33 Aligned_cols=23 Identities=26% Similarity=0.710 Sum_probs=10.2
Q ss_pred cCCCCCCCcceeeccccccccCCCCcCeeeCCCCC
Q 027589 80 VCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCG 114 (221)
Q Consensus 80 ~C~~Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~Cg 114 (221)
.|+.|+..++- .+..+|-|+.||
T Consensus 4 ~Cp~C~se~~y------------~D~~~~vCp~C~ 26 (30)
T PF08274_consen 4 KCPLCGSEYTY------------EDGELLVCPECG 26 (30)
T ss_dssp --TTT-----E------------E-SSSEEETTTT
T ss_pred CCCCCCCccee------------ccCCEEeCCccc
Confidence 57777777653 234678888776
No 187
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=39.12 E-value=26 Score=22.92 Aligned_cols=8 Identities=50% Similarity=1.510 Sum_probs=4.0
Q ss_pred eeeCCCCC
Q 027589 107 QFHCDDCG 114 (221)
Q Consensus 107 ~yHC~~Cg 114 (221)
.|-|+.||
T Consensus 20 ~~vC~~Cg 27 (52)
T smart00661 20 RFVCRKCG 27 (52)
T ss_pred EEECCcCC
Confidence 45555554
No 188
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=38.92 E-value=16 Score=35.79 Aligned_cols=33 Identities=18% Similarity=0.773 Sum_probs=26.6
Q ss_pred CCCCccchhhcccCCCceeeeccCCccCHHHHHHHHh
Q 027589 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIK 186 (221)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~ 186 (221)
+-.||||... |. +.++|||||.+.+.|...-+.
T Consensus 4 elkc~vc~~f-~~---epiil~c~h~lc~~ca~~~~~ 36 (699)
T KOG4367|consen 4 ELKCPVCGSF-YR---EPIILPCSHNLCQACARNILV 36 (699)
T ss_pred cccCceehhh-cc---CceEeecccHHHHHHHHhhcc
Confidence 4579999986 43 457899999999999987654
No 189
>PRK00420 hypothetical protein; Validated
Probab=38.53 E-value=22 Score=28.35 Aligned_cols=19 Identities=26% Similarity=0.695 Sum_probs=12.3
Q ss_pred ccCCCCCCCcce-----eeccccc
Q 027589 79 QVCTNCGVNMGE-----YFCDICK 97 (221)
Q Consensus 79 ~~C~~Cg~~f~~-----y~C~~C~ 97 (221)
..||.||.+|.+ .||++|.
T Consensus 24 ~~CP~Cg~pLf~lk~g~~~Cp~Cg 47 (112)
T PRK00420 24 KHCPVCGLPLFELKDGEVVCPVHG 47 (112)
T ss_pred CCCCCCCCcceecCCCceECCCCC
Confidence 578888887743 5555554
No 190
>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=38.14 E-value=35 Score=33.36 Aligned_cols=46 Identities=28% Similarity=0.689 Sum_probs=28.6
Q ss_pred cceeecCCCCccccccccCCCCCCCcce------eeccccccccCCCCcCeeeCCCCCcc
Q 027589 63 VKQVICSVCDTEQPVAQVCTNCGVNMGE------YFCDICKFYDDDIEKGQFHCDDCGIC 116 (221)
Q Consensus 63 ~~~v~C~~C~~~q~~~~~C~~Cg~~f~~------y~C~~C~l~dd~~~k~~yHC~~CgiC 116 (221)
...++|..|+.. ..|++|+..+.- -.|.-|.+- .+.+..|+.||-=
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 357889999865 479999987743 345555432 2334566666643
No 191
>smart00355 ZnF_C2H2 zinc finger.
Probab=37.75 E-value=33 Score=18.10 Aligned_cols=18 Identities=33% Similarity=0.578 Sum_probs=13.1
Q ss_pred CCCCCCcccccchhHHHH
Q 027589 190 YCCPICSKSVIDMSRTWK 207 (221)
Q Consensus 190 ~~CPiCrksi~dm~~~~~ 207 (221)
+.|+.|.+++...+.+..
T Consensus 1 ~~C~~C~~~f~~~~~l~~ 18 (26)
T smart00355 1 YRCPECGKVFKSKSALKE 18 (26)
T ss_pred CCCCCCcchhCCHHHHHH
Confidence 579999999887654433
No 192
>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=37.02 E-value=20 Score=22.27 Aligned_cols=10 Identities=30% Similarity=1.066 Sum_probs=5.3
Q ss_pred cCeeeCCCCC
Q 027589 105 KGQFHCDDCG 114 (221)
Q Consensus 105 k~~yHC~~Cg 114 (221)
.++-.|..||
T Consensus 15 ~~~irC~~CG 24 (32)
T PF03604_consen 15 GDPIRCPECG 24 (32)
T ss_dssp SSTSSBSSSS
T ss_pred CCcEECCcCC
Confidence 3444566655
No 193
>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=36.92 E-value=26 Score=22.78 Aligned_cols=20 Identities=25% Similarity=0.861 Sum_probs=11.0
Q ss_pred eeCCCCCcceeCCccceeecCccC
Q 027589 108 FHCDDCGICRIGGRENYFHCKRCG 131 (221)
Q Consensus 108 yHC~~CgiCR~G~~~~~fHC~~C~ 131 (221)
|+|+.|+. +++ ..+||..|.
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 45666654 332 566666663
No 194
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=36.57 E-value=5.4 Score=35.57 Aligned_cols=48 Identities=27% Similarity=0.555 Sum_probs=37.4
Q ss_pred CCCccchhhccc--CCCceeeec--------cCCccCHHHHHHHHhcCcCCCCCCccc
Q 027589 151 HHCPICYEYLFD--SLRNTTVMK--------CGHTMHCECYHEMIKRDKYCCPICSKS 198 (221)
Q Consensus 151 ~~CpICle~lf~--s~~~v~~L~--------CGH~~H~~C~~~~l~~~~~~CPiCrks 198 (221)
..|.||...+.. .....++|. |||.+-..|++..+.....+||.|++.
T Consensus 208 ~~c~ic~~~~~~n~~~~~p~vl~~~~~~~~~c~htlc~~c~~~~l~~~~~~cp~~~~~ 265 (296)
T KOG4185|consen 208 KLCEICERIYSENDEKLAPLVLSLSRLKEKIEGHTLCKECIDTILLQAGIKCPFCTWS 265 (296)
T ss_pred HHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcchHHHHHHhhhcCCcccce
Confidence 459999988652 223335667 999999999999987656799999985
No 195
>PF15616 TerY-C: TerY-C metal binding domain
Probab=36.55 E-value=37 Score=27.75 Aligned_cols=20 Identities=30% Similarity=0.816 Sum_probs=16.7
Q ss_pred ccCCCCCCCcceeecccc-ccc
Q 027589 79 QVCTNCGVNMGEYFCDIC-KFY 99 (221)
Q Consensus 79 ~~C~~Cg~~f~~y~C~~C-~l~ 99 (221)
..||.||..+|---| .| ||+
T Consensus 78 PgCP~CGn~~~fa~C-~CGkl~ 98 (131)
T PF15616_consen 78 PGCPHCGNQYAFAVC-GCGKLF 98 (131)
T ss_pred CCCCCCcChhcEEEe-cCCCEE
Confidence 689999999998888 57 455
No 196
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=36.50 E-value=21 Score=29.28 Aligned_cols=19 Identities=42% Similarity=1.267 Sum_probs=13.9
Q ss_pred ccCCCCCCCc----ceeeccccc
Q 027589 79 QVCTNCGVNM----GEYFCDICK 97 (221)
Q Consensus 79 ~~C~~Cg~~f----~~y~C~~C~ 97 (221)
..|+.||.++ |+-||++|-
T Consensus 29 ~hCp~Cg~PLF~KdG~v~CPvC~ 51 (131)
T COG1645 29 KHCPKCGTPLFRKDGEVFCPVCG 51 (131)
T ss_pred hhCcccCCcceeeCCeEECCCCC
Confidence 4788888887 555777775
No 197
>PLN02189 cellulose synthase
Probab=36.39 E-value=31 Score=36.92 Aligned_cols=56 Identities=20% Similarity=0.434 Sum_probs=40.2
Q ss_pred ecCCCCCCCccchhhcccCCCceeeec---cCCccCHHHHHHHHhcCcCCCCCCccccc
Q 027589 145 IENSMHHHCPICYEYLFDSLRNTTVMK---CGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (221)
Q Consensus 145 ~e~~~~~~CpICle~lf~s~~~v~~L~---CGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (221)
.++...+.|.||.|++-...+.-.... ||=...+.|++--.++.+..||-|+...-
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 344456689999999754333333333 78889999996666667889999997654
No 198
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=36.05 E-value=35 Score=26.50 Aligned_cols=32 Identities=31% Similarity=0.664 Sum_probs=20.8
Q ss_pred cceeecCccC-ccccccccCcceeecCCCCCCCccchhh
Q 027589 122 ENYFHCKRCG-SCYSTSLRNNHLCIENSMHHHCPICYEY 159 (221)
Q Consensus 122 ~~~fHC~~C~-~C~s~~~~~~H~C~e~~~~~~CpICle~ 159 (221)
..+|+|..|| .-+++.+. + +..+..|++|..+
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 4688888888 33333322 1 4567789999887
No 199
>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=35.58 E-value=30 Score=21.60 Aligned_cols=21 Identities=19% Similarity=0.363 Sum_probs=15.2
Q ss_pred ccCCCCCCCcceeeccccccc
Q 027589 79 QVCTNCGVNMGEYFCDICKFY 99 (221)
Q Consensus 79 ~~C~~Cg~~f~~y~C~~C~l~ 99 (221)
..|..++.....|||..|+.+
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 467788887788888888754
No 200
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=35.48 E-value=33 Score=24.07 Aligned_cols=21 Identities=19% Similarity=0.542 Sum_probs=17.1
Q ss_pred CcCCCCCCcccccchhHHHHH
Q 027589 188 DKYCCPICSKSVIDMSRTWKR 208 (221)
Q Consensus 188 ~~~~CPiCrksi~dm~~~~~~ 208 (221)
.++.||.|+-++---+..|+.
T Consensus 13 v~~~Cp~cGipthcS~ehw~~ 33 (55)
T PF13824_consen 13 VNFECPDCGIPTHCSEEHWED 33 (55)
T ss_pred cCCcCCCCCCcCccCHHHHHH
Confidence 579999999998876677765
No 201
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=34.44 E-value=25 Score=34.55 Aligned_cols=44 Identities=23% Similarity=0.704 Sum_probs=34.7
Q ss_pred CCCCCCccchhhcccCCCceeeeccCCccCHHHHHHHHhcCcCCCCCCccccc
Q 027589 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (221)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (221)
..+++|.||++.+ ..++-+|- |..|+.+|+. .+..||+|++.+.
T Consensus 477 ~~~~~~~~~~~~~-----~~~~~~~~---~~~~l~~~~~-~~~~~pl~~~~~~ 520 (543)
T KOG0802|consen 477 EPNDVCAICYQEM-----SARITPCS---HALCLRKWLY-VQEVCPLCHTYMK 520 (543)
T ss_pred cccCcchHHHHHH-----Hhcccccc---chhHHHhhhh-hccccCCCchhhh
Confidence 4578999999997 23344555 9999999997 4689999998775
No 202
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=34.44 E-value=18 Score=33.97 Aligned_cols=20 Identities=40% Similarity=0.989 Sum_probs=15.8
Q ss_pred cCCCCCCCcceeeccccccc
Q 027589 80 VCTNCGVNMGEYFCDICKFY 99 (221)
Q Consensus 80 ~C~~Cg~~f~~y~C~~C~l~ 99 (221)
.|.-||+++.+|.|+-|+|.
T Consensus 9 ~C~ic~vq~~~YtCPRCn~~ 28 (383)
T KOG4317|consen 9 ACGICGVQKREYTCPRCNLL 28 (383)
T ss_pred eccccccccccccCCCCCcc
Confidence 57778888888888888764
No 203
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=34.37 E-value=25 Score=37.04 Aligned_cols=49 Identities=27% Similarity=0.543 Sum_probs=34.0
Q ss_pred CCCCccchhhcccCCCceeeecc---C--CccCHHHHHHHHhcC-cCCCCCCccccc
Q 027589 150 HHHCPICYEYLFDSLRNTTVMKC---G--HTMHCECYHEMIKRD-KYCCPICSKSVI 200 (221)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~L~C---G--H~~H~~C~~~~l~~~-~~~CPiCrksi~ 200 (221)
+..|-||.-+ +.++..-.=|| | -.+|++|+.+|+..+ ..+|-||...+-
T Consensus 12 ~~~CRICr~e--~~~d~pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~ 66 (1175)
T COG5183 12 KRSCRICRTE--DIRDDPLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYK 66 (1175)
T ss_pred chhceeecCC--CCCCCcCcccccccchhHHHHHHHHHHHHhcCCCcceeeecceee
Confidence 4568899865 22223333466 3 689999999999853 566999997653
No 204
>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=33.61 E-value=14 Score=38.74 Aligned_cols=47 Identities=26% Similarity=0.693 Sum_probs=0.0
Q ss_pred cceeecCCCCccccccccCCCCCCCc-ceeeccccccccCCCCcCeeeCCCCCc
Q 027589 63 VKQVICSVCDTEQPVAQVCTNCGVNM-GEYFCDICKFYDDDIEKGQFHCDDCGI 115 (221)
Q Consensus 63 ~~~v~C~~C~~~q~~~~~C~~Cg~~f-~~y~C~~C~l~dd~~~k~~yHC~~Cgi 115 (221)
+-.-.|..|+++ ++...|+.||..- -.|+|+.|+.--++. .|+.||.
T Consensus 653 i~~r~Cp~Cg~~-t~~~~Cp~CG~~T~~~~~Cp~C~~~~~~~-----~C~~C~~ 700 (900)
T PF03833_consen 653 IGRRRCPKCGKE-TFYNRCPECGSHTEPVYVCPDCGIEVEED-----ECPKCGR 700 (900)
T ss_dssp ------------------------------------------------------
T ss_pred eecccCcccCCc-chhhcCcccCCccccceeccccccccCcc-----ccccccc
Confidence 345578888877 6777888888764 467788887643321 7888874
No 205
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=33.30 E-value=28 Score=31.93 Aligned_cols=94 Identities=22% Similarity=0.630 Sum_probs=0.0
Q ss_pred ccCchhHHhhhcCCCCCCCCccccccccceeecCCCCccccccccCCCCCCCcceeeccccc-cccCCC---CcCeeeCC
Q 027589 36 FDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVAQVCTNCGVNMGEYFCDICK-FYDDDI---EKGQFHCD 111 (221)
Q Consensus 36 ypCr~CHde~~~~~~~~~~~H~~~r~~~~~v~C~~C~~~q~~~~~C~~Cg~~f~~y~C~~C~-l~dd~~---~k~~yHC~ 111 (221)
|.|.+|-..+++ --.-|.+ .+++|-.|+..-.+ +--|+|-|.+|+ +.|+++ .-.+||=
T Consensus 100 F~Cd~Cn~~Lad--------~gf~rnq-gr~LC~~Cn~k~Ka--------~~~g~YvC~KCh~~iD~~~l~fr~d~yH~- 161 (332)
T KOG2272|consen 100 FRCDLCNKHLAD--------QGFYRNQ-GRALCRECNQKEKA--------KGRGRYVCQKCHAHIDEQPLTFRGDPYHP- 161 (332)
T ss_pred chhHHHHHHHhh--------hhhHhhc-chHHhhhhhhhhcc--------cccceeehhhhhhhcccccccccCCCCCc-
Q ss_pred CCCcceeCCccceeecCccCccccc---cccCcceeecCCCCCCCccchh
Q 027589 112 DCGICRIGGRENYFHCKRCGSCYST---SLRNNHLCIENSMHHHCPICYE 158 (221)
Q Consensus 112 ~CgiCR~G~~~~~fHC~~C~~C~s~---~~~~~H~C~e~~~~~~CpICle 158 (221)
.-|.|.+||-=+.. ++++.--|..=-...-+|||..
T Consensus 162 -----------yHFkCt~C~keL~sdaRevk~eLyClrChD~mgipiCga 200 (332)
T KOG2272|consen 162 -----------YHFKCTTCGKELTSDAREVKGELYCLRCHDKMGIPICGA 200 (332)
T ss_pred -----------cceecccccccccchhhhhccceeccccccccCCccccc
No 206
>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=33.18 E-value=32 Score=21.29 Aligned_cols=10 Identities=30% Similarity=0.737 Sum_probs=5.0
Q ss_pred eeecCCCCcc
Q 027589 65 QVICSVCDTE 74 (221)
Q Consensus 65 ~v~C~~C~~~ 74 (221)
.|.|+.|++.
T Consensus 25 ~v~C~~C~~~ 34 (38)
T TIGR02098 25 KVRCGKCGHV 34 (38)
T ss_pred EEECCCCCCE
Confidence 4555555543
No 207
>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=32.82 E-value=28 Score=23.67 Aligned_cols=21 Identities=24% Similarity=0.896 Sum_probs=13.0
Q ss_pred cccCC--CCCCC------cceeecccccc
Q 027589 78 AQVCT--NCGVN------MGEYFCDICKF 98 (221)
Q Consensus 78 ~~~C~--~Cg~~------f~~y~C~~C~l 98 (221)
...|| .||.- ++|+||.+|.+
T Consensus 18 rk~CP~~~CG~GvFMA~H~dR~~CGKCg~ 46 (47)
T PF01599_consen 18 RKECPSPRCGAGVFMAEHKDRHYCGKCGY 46 (47)
T ss_dssp SEE-TSTTTTSSSEEEE-SSEEEETTTSS
T ss_pred hhcCCCcccCCceEeeecCCCccCCCccc
Confidence 45688 78774 36777777754
No 208
>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=32.20 E-value=33 Score=22.37 Aligned_cols=9 Identities=33% Similarity=0.932 Sum_probs=4.9
Q ss_pred ceeecCccC
Q 027589 123 NYFHCKRCG 131 (221)
Q Consensus 123 ~~fHC~~C~ 131 (221)
..|+|.+|.
T Consensus 13 ~r~~C~~C~ 21 (46)
T cd02249 13 VRYHCLVCE 21 (46)
T ss_pred CEEECCCCC
Confidence 456665554
No 209
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=31.55 E-value=56 Score=30.33 Aligned_cols=25 Identities=28% Similarity=0.790 Sum_probs=20.6
Q ss_pred cceeecCCCCcccccc-ccCCCCCCC
Q 027589 63 VKQVICSVCDTEQPVA-QVCTNCGVN 87 (221)
Q Consensus 63 ~~~v~C~~C~~~q~~~-~~C~~Cg~~ 87 (221)
.+-..|+.|+++..+. ..|++||..
T Consensus 210 ~RyL~CslC~teW~~~R~~C~~Cg~~ 235 (309)
T PRK03564 210 LRYLHCNLCESEWHVVRVKCSNCEQS 235 (309)
T ss_pred ceEEEcCCCCCcccccCccCCCCCCC
Confidence 4678999999998774 689999964
No 210
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=31.37 E-value=38 Score=19.38 Aligned_cols=14 Identities=21% Similarity=0.610 Sum_probs=11.9
Q ss_pred CCCCCCcccccchh
Q 027589 190 YCCPICSKSVIDMS 203 (221)
Q Consensus 190 ~~CPiCrksi~dm~ 203 (221)
+.|++|.+.+.+..
T Consensus 2 ~~C~~C~k~f~~~~ 15 (27)
T PF12171_consen 2 FYCDACDKYFSSEN 15 (27)
T ss_dssp CBBTTTTBBBSSHH
T ss_pred CCcccCCCCcCCHH
Confidence 68999999998764
No 211
>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=31.29 E-value=34 Score=22.43 Aligned_cols=12 Identities=25% Similarity=0.844 Sum_probs=7.7
Q ss_pred ccCCCCCCCcce
Q 027589 79 QVCTNCGVNMGE 90 (221)
Q Consensus 79 ~~C~~Cg~~f~~ 90 (221)
..|+.||.++-+
T Consensus 18 ~~Cp~C~~PL~~ 29 (41)
T PF06677_consen 18 EHCPDCGTPLMR 29 (41)
T ss_pred CccCCCCCeeEE
Confidence 467777776643
No 212
>PLN00209 ribosomal protein S27; Provisional
Probab=30.80 E-value=32 Score=26.27 Aligned_cols=37 Identities=19% Similarity=0.346 Sum_probs=28.1
Q ss_pred ceeecCCCCccccc------cccCCCCCCCcceeecccccccc
Q 027589 64 KQVICSVCDTEQPV------AQVCTNCGVNMGEYFCDICKFYD 100 (221)
Q Consensus 64 ~~v~C~~C~~~q~~------~~~C~~Cg~~f~~y~C~~C~l~d 100 (221)
-.|.|..|..+|.+ ...|..||..+++-.=.+.+|-+
T Consensus 35 m~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~~PTGGKa~l~~ 77 (86)
T PLN00209 35 MDVKCQGCFNITTVFSHSQTVVVCGSCQTVLCQPTGGKARLTE 77 (86)
T ss_pred EEEECCCCCCeeEEEecCceEEEccccCCEeeccCCCCeEecC
Confidence 37899999999977 24799999998877655555543
No 213
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=30.80 E-value=21 Score=20.69 Aligned_cols=12 Identities=25% Similarity=0.664 Sum_probs=9.5
Q ss_pred ccCCCCCCCcce
Q 027589 79 QVCTNCGVNMGE 90 (221)
Q Consensus 79 ~~C~~Cg~~f~~ 90 (221)
..|+.||..|+.
T Consensus 3 ~~C~~CgR~F~~ 14 (25)
T PF13913_consen 3 VPCPICGRKFNP 14 (25)
T ss_pred CcCCCCCCEECH
Confidence 368999999864
No 214
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=30.47 E-value=27 Score=26.57 Aligned_cols=36 Identities=19% Similarity=0.390 Sum_probs=26.9
Q ss_pred ceeecCCCCccccc------cccCCCCCCCcceeeccccccc
Q 027589 64 KQVICSVCDTEQPV------AQVCTNCGVNMGEYFCDICKFY 99 (221)
Q Consensus 64 ~~v~C~~C~~~q~~------~~~C~~Cg~~f~~y~C~~C~l~ 99 (221)
-.|.|..|..+|.+ ...|..||..+++-.=.+.+|-
T Consensus 34 m~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~~PTGGKa~l~ 75 (85)
T PTZ00083 34 MDVKCPGCSQITTVFSHAQTVVLCGGCSSQLCQPTGGKAKLT 75 (85)
T ss_pred EEEECCCCCCeeEEEecCceEEEccccCCEeeccCCCCeEec
Confidence 37899999999877 2479999998877665555544
No 215
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=30.33 E-value=29 Score=31.13 Aligned_cols=20 Identities=25% Similarity=0.858 Sum_probs=15.2
Q ss_pred cccCCCCCCCc--------ceeeccccc
Q 027589 78 AQVCTNCGVNM--------GEYFCDICK 97 (221)
Q Consensus 78 ~~~C~~Cg~~f--------~~y~C~~C~ 97 (221)
++.|+.||..+ +.|||+.|.
T Consensus 244 g~pCprCG~~I~~~~~~gR~t~~CP~CQ 271 (272)
T PRK14810 244 GEPCLNCKTPIRRVVVAGRSSHYCPHCQ 271 (272)
T ss_pred CCcCCCCCCeeEEEEECCCccEECcCCc
Confidence 46799999887 567888774
No 216
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=30.04 E-value=33 Score=23.74 Aligned_cols=19 Identities=32% Similarity=0.933 Sum_probs=11.1
Q ss_pred ccCCCCCC--Cc----ceeeccccc
Q 027589 79 QVCTNCGV--NM----GEYFCDICK 97 (221)
Q Consensus 79 ~~C~~Cg~--~f----~~y~C~~C~ 97 (221)
..||+||. -| .+|+|.+|.
T Consensus 20 ~~CPrCG~gvfmA~H~dR~~CGkCg 44 (51)
T COG1998 20 RFCPRCGPGVFMADHKDRWACGKCG 44 (51)
T ss_pred ccCCCCCCcchhhhcCceeEecccc
Confidence 46888883 33 455555554
No 217
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=29.43 E-value=48 Score=31.36 Aligned_cols=80 Identities=25% Similarity=0.540 Sum_probs=52.3
Q ss_pred cccC--CCCcCeeeCCCCCcceeCC-ccceeecCccCcccccc---ccCcceeecCCCCCCCccchhhcccCCCceeeec
Q 027589 98 FYDD--DIEKGQFHCDDCGICRIGG-RENYFHCKRCGSCYSTS---LRNNHLCIENSMHHHCPICYEYLFDSLRNTTVMK 171 (221)
Q Consensus 98 l~dd--~~~k~~yHC~~CgiCR~G~-~~~~fHC~~C~~C~s~~---~~~~H~C~e~~~~~~CpICle~lf~s~~~v~~L~ 171 (221)
-||| .+.+.+-||+.| |--|. .|=|| +|+++.+.. -...|.=..++-...|-.|-+- +++|.+++
T Consensus 168 cWdDVLks~Ripg~Ces~--~~pg~fAEFfF---KC~ah~~~~k~~aa~lhli~~N~~ni~C~~Ctdv----~~~vlvf~ 238 (446)
T KOG0006|consen 168 CWDDVLKSKRIPGVCESC--CTPGLFAEFFF---KCGAHPTSDKETAAALHLIATNSRNITCITCTDV----RSPVLVFQ 238 (446)
T ss_pred chhhhhhcccCccccccc--cCCcchHhhee---hhccCCCccccchhHHHHhhcccccceeEEecCC----ccceEEEe
Confidence 3766 245677888875 33343 35555 666766652 1123433445666789999874 35789999
Q ss_pred cC--CccCHHHHHHHHh
Q 027589 172 CG--HTMHCECYHEMIK 186 (221)
Q Consensus 172 CG--H~~H~~C~~~~l~ 186 (221)
|. |+....||.-|-.
T Consensus 239 Cns~HvtC~dCFr~yc~ 255 (446)
T KOG0006|consen 239 CNSRHVTCLDCFRLYCV 255 (446)
T ss_pred cCCceeehHHhhhhHhh
Confidence 98 9999999987654
No 218
>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=29.33 E-value=25 Score=21.81 Aligned_cols=23 Identities=35% Similarity=0.752 Sum_probs=11.8
Q ss_pred ceeecCCCCccc-cccccCCCCCC
Q 027589 64 KQVICSVCDTEQ-PVAQVCTNCGV 86 (221)
Q Consensus 64 ~~v~C~~C~~~q-~~~~~C~~Cg~ 86 (221)
..-.|..|++.+ |+...|++|+.
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 455677887775 55677888764
No 219
>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=29.13 E-value=80 Score=26.10 Aligned_cols=28 Identities=21% Similarity=0.596 Sum_probs=22.6
Q ss_pred CcCCCCCCccccc--chhHHHHHHHHHHHh
Q 027589 188 DKYCCPICSKSVI--DMSRTWKRIDEEVSL 215 (221)
Q Consensus 188 ~~~~CPiCrksi~--dm~~~~~~lD~~i~~ 215 (221)
..++||.|+..+. |-+..-+.|.+.|+.
T Consensus 127 ~~F~Cp~Cg~~L~~~dn~~~i~~l~~~i~~ 156 (158)
T TIGR00373 127 LNFTCPRCGAMLDYLDNSEAIEKLEEQIKF 156 (158)
T ss_pred cCCcCCCCCCEeeeccCHHHHHHHHHHHHh
Confidence 4799999999996 555578888888865
No 220
>smart00586 ZnF_DBF Zinc finger in DBF-like proteins.
Probab=28.81 E-value=39 Score=23.08 Aligned_cols=14 Identities=14% Similarity=0.446 Sum_probs=11.4
Q ss_pred hHHHHHHHHHHHhC
Q 027589 203 SRTWKRIDEEVSLF 216 (221)
Q Consensus 203 ~~~~~~lD~~i~~~ 216 (221)
...|..||.+|+..
T Consensus 34 ~~Nf~~lD~Li~~l 47 (49)
T smart00586 34 NDNFQALDDLISQL 47 (49)
T ss_pred chhHHHHHHHHHHh
Confidence 44899999999864
No 221
>PRK10445 endonuclease VIII; Provisional
Probab=28.80 E-value=33 Score=30.66 Aligned_cols=20 Identities=30% Similarity=0.894 Sum_probs=14.7
Q ss_pred cccCCCCCCCc--------ceeeccccc
Q 027589 78 AQVCTNCGVNM--------GEYFCDICK 97 (221)
Q Consensus 78 ~~~C~~Cg~~f--------~~y~C~~C~ 97 (221)
++.|+.||... +.|||+.|.
T Consensus 235 g~~Cp~Cg~~I~~~~~~gR~t~~CP~CQ 262 (263)
T PRK10445 235 GEACERCGGIIEKTTLSSRPFYWCPGCQ 262 (263)
T ss_pred CCCCCCCCCEeEEEEECCCCcEECCCCc
Confidence 46799999888 457777663
No 222
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=28.71 E-value=82 Score=26.65 Aligned_cols=27 Identities=26% Similarity=0.549 Sum_probs=17.9
Q ss_pred CcCCCCCCccccc--chhHHHHHHHHHHH
Q 027589 188 DKYCCPICSKSVI--DMSRTWKRIDEEVS 214 (221)
Q Consensus 188 ~~~~CPiCrksi~--dm~~~~~~lD~~i~ 214 (221)
..++||.|+..+. |-+...+.|++.|+
T Consensus 135 ~~F~Cp~Cg~~L~~~dn~~~~~~l~~~I~ 163 (178)
T PRK06266 135 YGFRCPQCGEMLEEYDNSELIKELKEQIK 163 (178)
T ss_pred cCCcCCCCCCCCeecccHHHHHHHHHHHH
Confidence 4799999999987 33335555555443
No 223
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=28.50 E-value=33 Score=30.76 Aligned_cols=20 Identities=40% Similarity=1.102 Sum_probs=15.3
Q ss_pred cccCCCCCCCc--------ceeeccccc
Q 027589 78 AQVCTNCGVNM--------GEYFCDICK 97 (221)
Q Consensus 78 ~~~C~~Cg~~f--------~~y~C~~C~ 97 (221)
++.|+.||..+ +.|||+.|.
T Consensus 235 g~pC~~Cg~~I~~~~~~gR~ty~Cp~CQ 262 (269)
T PRK14811 235 GQPCPRCGTPIEKIVVGGRGTHFCPQCQ 262 (269)
T ss_pred cCCCCcCCCeeEEEEECCCCcEECCCCc
Confidence 35799998887 568888874
No 224
>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=28.38 E-value=32 Score=26.71 Aligned_cols=19 Identities=26% Similarity=0.728 Sum_probs=14.4
Q ss_pred ecCCCCcccccc----ccCCCCC
Q 027589 67 ICSVCDTEQPVA----QVCTNCG 85 (221)
Q Consensus 67 ~C~~C~~~q~~~----~~C~~Cg 85 (221)
-|..|+..++.. +.|++|+
T Consensus 5 AC~~C~~I~~~~qf~~~gCpnC~ 27 (98)
T cd07973 5 ACLLCSLIKTEDQFERDGCPNCE 27 (98)
T ss_pred hhccCCcccccccccCCCCCCCc
Confidence 588888887764 4788886
No 225
>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=28.31 E-value=49 Score=21.65 Aligned_cols=11 Identities=36% Similarity=0.939 Sum_probs=5.4
Q ss_pred CcCeeeCCCCC
Q 027589 104 EKGQFHCDDCG 114 (221)
Q Consensus 104 ~k~~yHC~~Cg 114 (221)
.++-|.|..|+
T Consensus 25 ~~~g~~C~~C~ 35 (53)
T PF00130_consen 25 GKQGYRCSWCG 35 (53)
T ss_dssp SSCEEEETTTT
T ss_pred CCCeEEECCCC
Confidence 44455555544
No 226
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=28.10 E-value=40 Score=21.37 Aligned_cols=25 Identities=32% Similarity=0.642 Sum_probs=18.9
Q ss_pred CCccchhhcccCCCceeee-ccCCcc
Q 027589 152 HCPICYEYLFDSLRNTTVM-KCGHTM 176 (221)
Q Consensus 152 ~CpICle~lf~s~~~v~~L-~CGH~~ 176 (221)
.|++|...+|.+.+....= .|||..
T Consensus 10 ~C~~C~~~~~~~~dG~~yC~~cG~~~ 35 (36)
T PF11781_consen 10 PCPVCGSRWFYSDDGFYYCDRCGHQS 35 (36)
T ss_pred cCCCCCCeEeEccCCEEEhhhCceEc
Confidence 3999999988776666654 788864
No 227
>PLN02436 cellulose synthase A
Probab=28.05 E-value=52 Score=35.52 Aligned_cols=56 Identities=16% Similarity=0.445 Sum_probs=40.4
Q ss_pred ecCCCCCCCccchhhcccCCCceeeec---cCCccCHHHHHHHHhcCcCCCCCCccccc
Q 027589 145 IENSMHHHCPICYEYLFDSLRNTTVMK---CGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (221)
Q Consensus 145 ~e~~~~~~CpICle~lf~s~~~v~~L~---CGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (221)
+.....+.|.||.|++-.+.+.-.... ||=.+.+.|++--.++.+..||-|+...-
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 334455689999999754444333443 77889999996666667889999997654
No 228
>PRK14873 primosome assembly protein PriA; Provisional
Probab=27.86 E-value=53 Score=33.47 Aligned_cols=23 Identities=26% Similarity=0.689 Sum_probs=17.6
Q ss_pred ceeecCCCCccccccccCCCCCCCcce
Q 027589 64 KQVICSVCDTEQPVAQVCTNCGVNMGE 90 (221)
Q Consensus 64 ~~v~C~~C~~~q~~~~~C~~Cg~~f~~ 90 (221)
..++|..|+.. ..|++|+..+.-
T Consensus 382 p~l~C~~Cg~~----~~C~~C~~~L~~ 404 (665)
T PRK14873 382 PSLACARCRTP----ARCRHCTGPLGL 404 (665)
T ss_pred CeeEhhhCcCe----eECCCCCCceeE
Confidence 57788888865 478999888863
No 229
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=27.73 E-value=28 Score=31.99 Aligned_cols=44 Identities=27% Similarity=0.594 Sum_probs=29.9
Q ss_pred ccCCCCCCCcceeeccccccccCCCCcCeeeCCCCCcceeCCccceeecCccCccccccccCcceee
Q 027589 79 QVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYSTSLRNNHLCI 145 (221)
Q Consensus 79 ~~C~~Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~CgiCR~G~~~~~fHC~~C~~C~s~~~~~~H~C~ 145 (221)
..+...+....+-||.+|+.|--+ -.-||..||.|+-+- +|-|+
T Consensus 98 ~~~~~~~~~~~~~~C~~C~~~KP~--------------------RS~HC~~Cn~CV~k~---DHHC~ 141 (309)
T COG5273 98 SRLLDDGKFGTENFCSTCNIYKPP--------------------RSHHCSICNRCVLKF---DHHCP 141 (309)
T ss_pred hhhhhcCccccceeccccccccCC--------------------CCccchhhcchhhcc---CccCc
Confidence 466677888888999999999332 255666666666543 45553
No 230
>KOG3005 consensus GIY-YIG type nuclease [General function prediction only]
Probab=27.65 E-value=74 Score=29.18 Aligned_cols=49 Identities=20% Similarity=0.497 Sum_probs=33.9
Q ss_pred CCCccchhhcccCCCceeee----ccCCccCHHHHHHHHhc--------CcCCCCCCccccc
Q 027589 151 HHCPICYEYLFDSLRNTTVM----KCGHTMHCECYHEMIKR--------DKYCCPICSKSVI 200 (221)
Q Consensus 151 ~~CpICle~lf~s~~~v~~L----~CGH~~H~~C~~~~l~~--------~~~~CPiCrksi~ 200 (221)
..|-+|.+.+.+. +..+.. .|+=..|..|+.+.+.. ....||.|++.+.
T Consensus 183 ~~celc~~ei~e~-~~~~a~c~~~~c~~~~h~~CLa~~~~~~e~g~~~p~eg~cp~C~~~~~ 243 (276)
T KOG3005|consen 183 VECELCEKEILET-DWSRATCPNPDCDSLNHLTCLAEELLEVEPGQLIPLEGMCPKCEKFLS 243 (276)
T ss_pred hhhHHHHHHhccc-cceeccCCCCCCCchhhhhhhhHHHhccCCCceeccCCCCCchhceee
Confidence 5799999887443 222221 37888999999984432 2468999999665
No 231
>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=27.42 E-value=24 Score=22.59 Aligned_cols=13 Identities=54% Similarity=1.196 Sum_probs=5.5
Q ss_pred cceeecccccccc
Q 027589 88 MGEYFCDICKFYD 100 (221)
Q Consensus 88 f~~y~C~~C~l~d 100 (221)
|-+|||+-|+.|-
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 4589999998775
No 232
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=27.39 E-value=39 Score=24.15 Aligned_cols=20 Identities=25% Similarity=0.693 Sum_probs=13.0
Q ss_pred ecCCCCccccccccCCCCCCC
Q 027589 67 ICSVCDTEQPVAQVCTNCGVN 87 (221)
Q Consensus 67 ~C~~C~~~q~~~~~C~~Cg~~ 87 (221)
.|..|+..++ .++||+||..
T Consensus 5 AC~~C~~i~~-~~~CP~Cgs~ 24 (61)
T PRK08351 5 ACRHCHYITT-EDRCPVCGSR 24 (61)
T ss_pred hhhhCCcccC-CCcCCCCcCC
Confidence 5667776663 3468888764
No 233
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=27.20 E-value=39 Score=18.97 Aligned_cols=18 Identities=22% Similarity=0.525 Sum_probs=13.7
Q ss_pred CCCCCCcccccchhHHHH
Q 027589 190 YCCPICSKSVIDMSRTWK 207 (221)
Q Consensus 190 ~~CPiCrksi~dm~~~~~ 207 (221)
++|.+|++.+.+.+.+.+
T Consensus 2 ~~C~~C~~~F~~~~~l~~ 19 (27)
T PF13912_consen 2 FECDECGKTFSSLSALRE 19 (27)
T ss_dssp EEETTTTEEESSHHHHHH
T ss_pred CCCCccCCccCChhHHHH
Confidence 579999999988765443
No 234
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=27.14 E-value=22 Score=35.69 Aligned_cols=26 Identities=27% Similarity=0.775 Sum_probs=19.6
Q ss_pred eeeeccCCccCHHHHHHHHhcCcCCCCCCc
Q 027589 167 TTVMKCGHTMHCECYHEMIKRDKYCCPICS 196 (221)
Q Consensus 167 v~~L~CGH~~H~~C~~~~l~~~~~~CPiCr 196 (221)
.+-..||++||+.|+.. .+..||.|-
T Consensus 532 ~rC~~C~avfH~~C~~r----~s~~CPrC~ 557 (580)
T KOG1829|consen 532 RRCSTCLAVFHKKCLRR----KSPCCPRCE 557 (580)
T ss_pred eeHHHHHHHHHHHHHhc----cCCCCCchH
Confidence 44567999999999853 345599994
No 235
>KOG4399 consensus C2HC-type Zn-finger protein [General function prediction only]
Probab=27.07 E-value=15 Score=33.74 Aligned_cols=53 Identities=17% Similarity=0.165 Sum_probs=40.2
Q ss_pred ccCCCCCCCcceeeccccccccCCCCcCeeeCCCCCcceeCCccceeecCccCcccc
Q 027589 79 QVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYS 135 (221)
Q Consensus 79 ~~C~~Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~CgiCR~G~~~~~fHC~~C~~C~s 135 (221)
..|+-|+..-+.-||.||--+|.. .-|||.|.-||--....+-||+.|..|..
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 357777777778899999888663 27899998888776556778888777755
No 236
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=26.97 E-value=39 Score=23.41 Aligned_cols=25 Identities=32% Similarity=0.789 Sum_probs=11.1
Q ss_pred cccCCCCCCCcceeeccccccccCCCCcCeeeCCCCCc
Q 027589 78 AQVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGI 115 (221)
Q Consensus 78 ~~~C~~Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~Cgi 115 (221)
+..|..|++.|+- -+..+||..||.
T Consensus 9 ~~~C~~C~~~F~~-------------~~rrhhCr~CG~ 33 (69)
T PF01363_consen 9 ASNCMICGKKFSL-------------FRRRHHCRNCGR 33 (69)
T ss_dssp -SB-TTT--B-BS-------------SS-EEE-TTT--
T ss_pred CCcCcCcCCcCCC-------------ceeeEccCCCCC
Confidence 3568888888852 256788888884
No 237
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=26.76 E-value=30 Score=27.14 Aligned_cols=10 Identities=20% Similarity=0.574 Sum_probs=5.2
Q ss_pred ccCCCCCCCc
Q 027589 79 QVCTNCGVNM 88 (221)
Q Consensus 79 ~~C~~Cg~~f 88 (221)
..|..||..|
T Consensus 71 ~~C~~Cg~~~ 80 (113)
T PRK12380 71 AWCWDCSQVV 80 (113)
T ss_pred EEcccCCCEE
Confidence 4555555444
No 238
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=26.52 E-value=38 Score=30.30 Aligned_cols=20 Identities=30% Similarity=1.090 Sum_probs=14.6
Q ss_pred cccCCCCCCCc--------ceeeccccc
Q 027589 78 AQVCTNCGVNM--------GEYFCDICK 97 (221)
Q Consensus 78 ~~~C~~Cg~~f--------~~y~C~~C~ 97 (221)
++.|+.||... +.|||+.|.
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 272 (274)
T PRK01103 245 GEPCRRCGTPIEKIKQGGRSTFFCPRCQ 272 (274)
T ss_pred CCCCCCCCCeeEEEEECCCCcEECcCCC
Confidence 35799999887 457777763
No 239
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=26.30 E-value=44 Score=22.87 Aligned_cols=24 Identities=33% Similarity=0.875 Sum_probs=19.8
Q ss_pred cceeecCCCCccccc-cccCCCCCC
Q 027589 63 VKQVICSVCDTEQPV-AQVCTNCGV 86 (221)
Q Consensus 63 ~~~v~C~~C~~~q~~-~~~C~~Cg~ 86 (221)
...++|+.|....++ +..|..||.
T Consensus 12 ~~k~ICrkC~ARnp~~A~~CRKCg~ 36 (48)
T PRK04136 12 FNKKICMRCNARNPWRATKCRKCGY 36 (48)
T ss_pred hcccchhcccCCCCccccccccCCC
Confidence 357899999999888 568988886
No 240
>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=26.01 E-value=52 Score=19.45 Aligned_cols=16 Identities=19% Similarity=0.617 Sum_probs=12.8
Q ss_pred cCCCCCCcccccchhH
Q 027589 189 KYCCPICSKSVIDMSR 204 (221)
Q Consensus 189 ~~~CPiCrksi~dm~~ 204 (221)
.+.|.+|.+++.+...
T Consensus 3 ~~~C~~C~~~~~~~~~ 18 (35)
T smart00451 3 GFYCKLCNVTFTDEIS 18 (35)
T ss_pred CeEccccCCccCCHHH
Confidence 5789999999986544
No 241
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=25.95 E-value=21 Score=33.27 Aligned_cols=19 Identities=47% Similarity=1.139 Sum_probs=16.9
Q ss_pred ccCCCCCCCcceeeccccccc
Q 027589 79 QVCTNCGVNMGEYFCDICKFY 99 (221)
Q Consensus 79 ~~C~~Cg~~f~~y~C~~C~l~ 99 (221)
.+|..||..|+ +|+||+-|
T Consensus 322 VtCt~CGkrm~--eCPICRqy 340 (350)
T KOG4275|consen 322 VTCTKCGKRMN--ECPICRQY 340 (350)
T ss_pred Eeehhhccccc--cCchHHHH
Confidence 47999999999 99999866
No 242
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=25.95 E-value=41 Score=30.92 Aligned_cols=32 Identities=19% Similarity=0.488 Sum_probs=20.8
Q ss_pred ccccceeecCCCCccccc-cccCCCCCCCccee
Q 027589 60 RQDVKQVICSVCDTEQPV-AQVCTNCGVNMGEY 91 (221)
Q Consensus 60 r~~~~~v~C~~C~~~q~~-~~~C~~Cg~~f~~y 91 (221)
-....+..|..|+..-|. +--|..|++...++
T Consensus 104 ~~~~~~~~C~~C~~~KP~RS~HC~~Cn~CV~k~ 136 (309)
T COG5273 104 GKFGTENFCSTCNIYKPPRSHHCSICNRCVLKF 136 (309)
T ss_pred CccccceeccccccccCCCCccchhhcchhhcc
Confidence 345678899999887666 34566655555443
No 243
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=25.78 E-value=48 Score=22.30 Aligned_cols=22 Identities=50% Similarity=1.284 Sum_probs=9.4
Q ss_pred eeCCCCCcceeCCccceeecCccC
Q 027589 108 FHCDDCGICRIGGRENYFHCKRCG 131 (221)
Q Consensus 108 yHC~~CgiCR~G~~~~~fHC~~C~ 131 (221)
|.|+.||.--+-| --|||..|.
T Consensus 1 y~Cd~C~~~pI~G--~R~~C~~C~ 22 (48)
T cd02341 1 FKCDSCGIEPIPG--TRYHCSECD 22 (48)
T ss_pred CCCCCCCCCcccc--ceEECCCCC
Confidence 3455555433322 245555443
No 244
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=25.44 E-value=45 Score=26.29 Aligned_cols=11 Identities=18% Similarity=0.594 Sum_probs=5.3
Q ss_pred cccCCCCCCCc
Q 027589 78 AQVCTNCGVNM 88 (221)
Q Consensus 78 ~~~C~~Cg~~f 88 (221)
...|..||..|
T Consensus 71 ~~~C~~Cg~~~ 81 (117)
T PRK00564 71 ELECKDCSHVF 81 (117)
T ss_pred EEEhhhCCCcc
Confidence 34555555444
No 245
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=25.38 E-value=60 Score=21.90 Aligned_cols=36 Identities=14% Similarity=0.468 Sum_probs=24.4
Q ss_pred cCchhHHhhhcCCCCCCCCccccccccceeecCCCCccccc
Q 027589 37 DCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPV 77 (221)
Q Consensus 37 pCr~CHde~~~~~~~~~~~H~~~r~~~~~v~C~~C~~~q~~ 77 (221)
.|..|-+-+. -| .+..+.++....+.||.|+....+
T Consensus 8 ~C~~C~~lLq-lP----~~~~~~~k~~~klrCGaCs~vl~~ 43 (46)
T PF11331_consen 8 VCSSCFELLQ-LP----AKFSLSKKNQQKLRCGACSEVLSF 43 (46)
T ss_pred ECccHHHHHc-CC----CccCCCccceeEEeCCCCceeEEE
Confidence 5666765543 12 345666667889999999988655
No 246
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.11 E-value=38 Score=24.57 Aligned_cols=26 Identities=31% Similarity=0.658 Sum_probs=16.6
Q ss_pred cccccCCCCCCCcce-------eecc-ccccccC
Q 027589 76 PVAQVCTNCGVNMGE-------YFCD-ICKFYDD 101 (221)
Q Consensus 76 ~~~~~C~~Cg~~f~~-------y~C~-~C~l~dd 101 (221)
..+..|+.||+.... -||+ -|++.|-
T Consensus 5 ~~~v~CP~Cgkpv~w~~~s~frPFCSkRCklIDL 38 (65)
T COG3024 5 RITVPCPTCGKPVVWGEESPFRPFCSKRCKLIDL 38 (65)
T ss_pred cccccCCCCCCcccccccCCcCcchhHhhhhcch
Confidence 345578888777643 4554 4888764
No 247
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=25.04 E-value=40 Score=32.75 Aligned_cols=10 Identities=50% Similarity=1.404 Sum_probs=5.8
Q ss_pred ceeecCccCc
Q 027589 123 NYFHCKRCGS 132 (221)
Q Consensus 123 ~~fHC~~C~~ 132 (221)
..|||..||.
T Consensus 152 ~~F~C~~C~g 161 (436)
T KOG2593|consen 152 GEFHCENCGG 161 (436)
T ss_pred ceEEEecCCC
Confidence 3566666654
No 248
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=24.98 E-value=44 Score=27.91 Aligned_cols=12 Identities=25% Similarity=0.839 Sum_probs=6.1
Q ss_pred cCCCCCCCccee
Q 027589 80 VCTNCGVNMGEY 91 (221)
Q Consensus 80 ~C~~Cg~~f~~y 91 (221)
.|++||..|+.|
T Consensus 30 ~c~~c~~~f~~~ 41 (154)
T PRK00464 30 ECLACGKRFTTF 41 (154)
T ss_pred eccccCCcceEe
Confidence 355555555544
No 249
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=24.68 E-value=29 Score=30.21 Aligned_cols=39 Identities=26% Similarity=0.584 Sum_probs=27.8
Q ss_pred CccchhhcccCCCceeeeccCCcc-CHHHHHHHHhcCcCCCCCCccccc
Q 027589 153 CPICYEYLFDSLRNTTVMKCGHTM-HCECYHEMIKRDKYCCPICSKSVI 200 (221)
Q Consensus 153 CpICle~lf~s~~~v~~L~CGH~~-H~~C~~~~l~~~~~~CPiCrksi~ 200 (221)
|-+|.+. + ..|..|||-|.. -..|-.. ..+||||+....
T Consensus 161 Cr~C~~~--~--~~VlllPCrHl~lC~~C~~~-----~~~CPiC~~~~~ 200 (207)
T KOG1100|consen 161 CRKCGER--E--ATVLLLPCRHLCLCGICDES-----LRICPICRSPKT 200 (207)
T ss_pred ceecCcC--C--ceEEeecccceEeccccccc-----CccCCCCcChhh
Confidence 9999886 2 358889999764 4566532 357999997654
No 250
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=24.57 E-value=59 Score=24.52 Aligned_cols=8 Identities=50% Similarity=1.281 Sum_probs=4.3
Q ss_pred CCCCCCCc
Q 027589 81 CTNCGVNM 88 (221)
Q Consensus 81 C~~Cg~~f 88 (221)
|+.||..|
T Consensus 3 C~~Cg~~l 10 (104)
T TIGR01384 3 CPKCGSLM 10 (104)
T ss_pred CcccCccc
Confidence 55555555
No 251
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=24.49 E-value=44 Score=30.10 Aligned_cols=19 Identities=26% Similarity=0.933 Sum_probs=13.7
Q ss_pred cccCCCCCCCc--------ceeecccc
Q 027589 78 AQVCTNCGVNM--------GEYFCDIC 96 (221)
Q Consensus 78 ~~~C~~Cg~~f--------~~y~C~~C 96 (221)
++.|+.||... +.|||+.|
T Consensus 254 g~pC~~Cg~~I~~~~~~gR~t~~CP~C 280 (282)
T PRK13945 254 GKPCRKCGTPIERIKLAGRSTHWCPNC 280 (282)
T ss_pred cCCCCcCCCeeEEEEECCCccEECCCC
Confidence 46799998887 45666666
No 252
>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=24.29 E-value=44 Score=29.93 Aligned_cols=19 Identities=37% Similarity=1.111 Sum_probs=13.6
Q ss_pred cccCCCCCCCc--------ceeecccc
Q 027589 78 AQVCTNCGVNM--------GEYFCDIC 96 (221)
Q Consensus 78 ~~~C~~Cg~~f--------~~y~C~~C 96 (221)
++.|+.||... +.|||+.|
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~CP~C 271 (272)
T TIGR00577 245 GEPCRRCGTPIEKIKVGGRGTHFCPQC 271 (272)
T ss_pred CCCCCCCCCeeEEEEECCCCCEECCCC
Confidence 45799998887 45666666
No 253
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=23.84 E-value=28 Score=28.32 Aligned_cols=9 Identities=33% Similarity=0.881 Sum_probs=4.4
Q ss_pred cCCCCCCCc
Q 027589 80 VCTNCGVNM 88 (221)
Q Consensus 80 ~C~~Cg~~f 88 (221)
.||+||..|
T Consensus 101 ~Cp~C~~~y 109 (147)
T smart00531 101 KCPNCQSKY 109 (147)
T ss_pred ECcCCCCEe
Confidence 355555444
No 254
>COG1144 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, delta subunit [Energy production and conversion]
Probab=23.72 E-value=41 Score=25.96 Aligned_cols=15 Identities=40% Similarity=0.906 Sum_probs=12.6
Q ss_pred cceeecCccCccccc
Q 027589 122 ENYFHCKRCGSCYST 136 (221)
Q Consensus 122 ~~~fHC~~C~~C~s~ 136 (221)
.||-+|+.||.|.+.
T Consensus 63 idYdyCKGCGICa~v 77 (91)
T COG1144 63 IDYDYCKGCGICANV 77 (91)
T ss_pred eEcccccCceechhh
Confidence 488999999999764
No 255
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=23.61 E-value=50 Score=26.44 Aligned_cols=27 Identities=22% Similarity=0.618 Sum_probs=18.4
Q ss_pred ccceeecCCCCccccc---cccCCCCCCCc
Q 027589 62 DVKQVICSVCDTEQPV---AQVCTNCGVNM 88 (221)
Q Consensus 62 ~~~~v~C~~C~~~q~~---~~~C~~Cg~~f 88 (221)
.+..|.|..|+++-.. .+.|++|++++
T Consensus 66 kav~V~CP~C~K~TKmLGr~D~CM~C~~pL 95 (114)
T PF11023_consen 66 KAVQVECPNCGKQTKMLGRVDACMHCKEPL 95 (114)
T ss_pred cceeeECCCCCChHhhhchhhccCcCCCcC
Confidence 3467788888776433 35788887776
No 256
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=23.48 E-value=64 Score=22.96 Aligned_cols=23 Identities=17% Similarity=0.505 Sum_probs=16.7
Q ss_pred cCCCCCCcccccchhHHHHHHHH
Q 027589 189 KYCCPICSKSVIDMSRTWKRIDE 211 (221)
Q Consensus 189 ~~~CPiCrksi~dm~~~~~~lD~ 211 (221)
.++|++|.+.+.+.+.+.+.|..
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~ 72 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRS 72 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHH
T ss_pred CCCCCccCCCCcCHHHHHHHHcC
Confidence 48999999999887666655543
No 257
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=23.46 E-value=51 Score=20.52 Aligned_cols=10 Identities=30% Similarity=0.620 Sum_probs=4.5
Q ss_pred eecCCCCccc
Q 027589 66 VICSVCDTEQ 75 (221)
Q Consensus 66 v~C~~C~~~q 75 (221)
.+|..|+...
T Consensus 4 ~~C~~C~~~~ 13 (33)
T PF08792_consen 4 KKCSKCGGNG 13 (33)
T ss_pred eEcCCCCCCe
Confidence 3444454443
No 258
>PF05458 Siva: Cd27 binding protein (Siva); InterPro: IPR022773 Siva binds to the CD27 cytoplasmic tail. It has a DD homology region, a box-B-like ring finger, and a zinc finger-like domain. Overexpression of Siva in various cell lines induces apoptosis, suggesting an important role for Siva in the CD27-transduced apoptotic pathway []. Siva-1 binds to and inhibits BCL-X(L)-mediated protection against UV radiation-induced apoptosis. Indeed, the unique amphipathic helical region (SAH) present in Siva-1 is required for its binding to BCL-X(L) and sensitising cells to UV radiation. Natural complexes of Siva-1/BCL-X(L) are detected in HUT78 and murine thymocyte, suggesting a potential role for Siva-1 in regulating T cell homeostasis []. This family contains both Siva-1 and the shorter Siva-2 lacking the sequence coded by exon 2. It has been suggested that Siva-2 could regulate the function of Siva-1 [].
Probab=23.46 E-value=63 Score=27.45 Aligned_cols=23 Identities=35% Similarity=0.873 Sum_probs=14.6
Q ss_pred eecCCCCccccccccCCCCCCCc
Q 027589 66 VICSVCDTEQPVAQVCTNCGVNM 88 (221)
Q Consensus 66 v~C~~C~~~q~~~~~C~~Cg~~f 88 (221)
..|..|...+.+...|.+|...+
T Consensus 112 ~aCs~C~r~~~~~~~C~~Cdr~l 134 (175)
T PF05458_consen 112 RACSVCQRTQRIKSVCSQCDRAL 134 (175)
T ss_pred ccCcCCcCCCCCCccccccCcHH
Confidence 34777766666666676666554
No 259
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=23.31 E-value=46 Score=31.86 Aligned_cols=39 Identities=21% Similarity=0.468 Sum_probs=30.9
Q ss_pred cCCCCCCCccchhhcccCCCceeeeccCCccCHHHHHHHHhc
Q 027589 146 ENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR 187 (221)
Q Consensus 146 e~~~~~~CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~ 187 (221)
.......|.||.+.+-. ....+.|||.|-..|...+|..
T Consensus 66 ~~~~~~~c~ic~~~~~~---~~~~~~c~H~~c~~cw~~yl~~ 104 (444)
T KOG1815|consen 66 KKKGDVQCGICVESYDG---EIIGLGCGHPFCPPCWTGYLGT 104 (444)
T ss_pred CCCccccCCcccCCCcc---hhhhcCCCcHHHHHHHHHHhhh
Confidence 34556789999987422 4677899999999999999974
No 260
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=23.23 E-value=27 Score=21.11 Aligned_cols=21 Identities=29% Similarity=0.819 Sum_probs=9.1
Q ss_pred ecCCCCccccc-----cccCCCCCCC
Q 027589 67 ICSVCDTEQPV-----AQVCTNCGVN 87 (221)
Q Consensus 67 ~C~~C~~~q~~-----~~~C~~Cg~~ 87 (221)
.|+.|+.+..+ +..|++||..
T Consensus 5 fC~~CG~~t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 5 FCGRCGAPTKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp B-TTT--BEEE-SSSS-EEESSSS-E
T ss_pred ccCcCCccccCCCCcCEeECCCCcCE
Confidence 46677665433 2357777653
No 261
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=23.22 E-value=49 Score=20.79 Aligned_cols=11 Identities=27% Similarity=1.050 Sum_probs=5.6
Q ss_pred CcCeeeCCCCC
Q 027589 104 EKGQFHCDDCG 114 (221)
Q Consensus 104 ~k~~yHC~~Cg 114 (221)
++.-+-|+.||
T Consensus 19 ~r~R~vC~~Cg 29 (34)
T PF14803_consen 19 DRERLVCPACG 29 (34)
T ss_dssp SS-EEEETTTT
T ss_pred CccceECCCCC
Confidence 45555566655
No 262
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=23.09 E-value=43 Score=34.83 Aligned_cols=50 Identities=28% Similarity=0.557 Sum_probs=40.3
Q ss_pred ccCCCCCCCccee---eccccccccCCCCcCeeeCCCCCcceeCCccceeecCccCcccccc
Q 027589 79 QVCTNCGVNMGEY---FCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYSTS 137 (221)
Q Consensus 79 ~~C~~Cg~~f~~y---~C~~C~l~dd~~~k~~yHC~~CgiCR~G~~~~~fHC~~C~~C~s~~ 137 (221)
-.|++|++.++.- +|+.|.--.. .+|-+|+.+-+.-+++|..|+-+.-.+
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 4799999999765 8888876533 268899999888999999999886543
No 263
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=22.95 E-value=97 Score=19.82 Aligned_cols=33 Identities=24% Similarity=0.691 Sum_probs=17.2
Q ss_pred cCCCCCCCcceeeccccccc-cCCCCcCeeeCCCCC
Q 027589 80 VCTNCGVNMGEYFCDICKFY-DDDIEKGQFHCDDCG 114 (221)
Q Consensus 80 ~C~~Cg~~f~~y~C~~C~l~-dd~~~k~~yHC~~Cg 114 (221)
.|++||..-+.|| .+ ..- -|++..-.|-|.+||
T Consensus 2 ~Cp~C~~~~a~~~-q~-Q~RsaDE~mT~fy~C~~C~ 35 (40)
T smart00440 2 PCPKCGNREATFF-QL-QTRSADEPMTVFYVCTKCG 35 (40)
T ss_pred cCCCCCCCeEEEE-EE-cccCCCCCCeEEEEeCCCC
Confidence 4777877766665 10 111 223444556666655
No 264
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=22.74 E-value=62 Score=21.77 Aligned_cols=10 Identities=30% Similarity=1.155 Sum_probs=6.7
Q ss_pred eeeccccccc
Q 027589 90 EYFCDICKFY 99 (221)
Q Consensus 90 ~y~C~~C~l~ 99 (221)
+|.|.+|.+.
T Consensus 1 ky~C~~Cgyv 10 (47)
T PF00301_consen 1 KYQCPVCGYV 10 (47)
T ss_dssp EEEETTTSBE
T ss_pred CcCCCCCCEE
Confidence 5778888643
No 265
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=22.52 E-value=80 Score=20.82 Aligned_cols=12 Identities=33% Similarity=0.944 Sum_probs=7.7
Q ss_pred CcCeeeCCCCCc
Q 027589 104 EKGQFHCDDCGI 115 (221)
Q Consensus 104 ~k~~yHC~~Cgi 115 (221)
.++...|+.||-
T Consensus 16 ~~~~irC~~CG~ 27 (44)
T smart00659 16 SKDVVRCRECGY 27 (44)
T ss_pred CCCceECCCCCc
Confidence 346677777773
No 266
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=22.49 E-value=64 Score=25.45 Aligned_cols=27 Identities=30% Similarity=0.779 Sum_probs=17.0
Q ss_pred CeeeCCCCC-----cceeCC--ccceeecCccCc
Q 027589 106 GQFHCDDCG-----ICRIGG--RENYFHCKRCGS 132 (221)
Q Consensus 106 ~~yHC~~Cg-----iCR~G~--~~~~fHC~~C~~ 132 (221)
..|.|+.|| +|.|-. ...+-+|..||.
T Consensus 21 k~FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGl 54 (104)
T COG4888 21 KTFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGL 54 (104)
T ss_pred ceEecCccCCeeeeEEEEEecCceeEEEcccCcc
Confidence 456666666 566543 345777777775
No 267
>PF12675 DUF3795: Protein of unknown function (DUF3795); InterPro: IPR024227 This family of proteins is functionally uncharacterised and is found in bacteria and archaea. Proteins in this family are typically between 99 and 171 amino acids in length. These proteins are likely to be zinc binding given the conserved cysteines.
Probab=22.37 E-value=49 Score=24.07 Aligned_cols=37 Identities=30% Similarity=0.644 Sum_probs=23.2
Q ss_pred cccCCCCCCCcceeeccccccccCCCCcCeeeCCCCC
Q 027589 78 AQVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCG 114 (221)
Q Consensus 78 ~~~C~~Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~Cg 114 (221)
...|+.|...=....+..|.+.+=-.+|++-||-.|.
T Consensus 34 ~~~C~GCr~~~~~~~~~~C~i~~C~~ekgv~~C~eC~ 70 (78)
T PF12675_consen 34 KIRCPGCRSGGGKCCCKSCKIRQCAKEKGVDFCGECP 70 (78)
T ss_pred CCcCcCCcCCCCCcCCCCCCcCcHHhhCCCCeeecCC
Confidence 3457777555444667777776555566676666553
No 268
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=21.83 E-value=58 Score=25.53 Aligned_cols=13 Identities=15% Similarity=0.404 Sum_probs=7.8
Q ss_pred cccccCCCCCCCc
Q 027589 76 PVAQVCTNCGVNM 88 (221)
Q Consensus 76 ~~~~~C~~Cg~~f 88 (221)
|+...|..||..|
T Consensus 68 p~~~~C~~Cg~~~ 80 (114)
T PRK03681 68 EAECWCETCQQYV 80 (114)
T ss_pred CcEEEcccCCCee
Confidence 4445677777654
No 269
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=21.75 E-value=40 Score=31.74 Aligned_cols=33 Identities=24% Similarity=0.645 Sum_probs=24.2
Q ss_pred eeeeccCCccCHHHHHHHHhcCcCCCCCCcccccch
Q 027589 167 TTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDM 202 (221)
Q Consensus 167 v~~L~CGH~~H~~C~~~~l~~~~~~CPiCrksi~dm 202 (221)
-+.+||.|+|..+|-..- ....||.|.-.|..+
T Consensus 104 GRmIPCkHvFCl~CAr~~---~dK~Cp~C~d~VqrI 136 (389)
T KOG2932|consen 104 GRMIPCKHVFCLECARSD---SDKICPLCDDRVQRI 136 (389)
T ss_pred ecccccchhhhhhhhhcC---ccccCcCcccHHHHH
Confidence 357899999988887532 345899998777643
No 270
>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=21.70 E-value=32 Score=22.29 Aligned_cols=44 Identities=27% Similarity=0.557 Sum_probs=28.0
Q ss_pred CccchhhcccCCCceeeeccCCccCHHHHHHHHh-----cCcCCCCCCcc
Q 027589 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIK-----RDKYCCPICSK 197 (221)
Q Consensus 153 CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~-----~~~~~CPiCrk 197 (221)
|+||... .+..+.+.=-.|+-.||..|+..-+. ...+.||.|+.
T Consensus 2 C~vC~~~-~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~~ 50 (51)
T PF00628_consen 2 CPVCGQS-DDDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCRP 50 (51)
T ss_dssp BTTTTSS-CTTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHHH
T ss_pred CcCCCCc-CCCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCcC
Confidence 7888883 22222222336899999999976433 13688888753
No 271
>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=21.53 E-value=1.1e+02 Score=28.35 Aligned_cols=25 Identities=28% Similarity=0.687 Sum_probs=21.0
Q ss_pred cceeecCCCCcccccc-ccCCCCCCC
Q 027589 63 VKQVICSVCDTEQPVA-QVCTNCGVN 87 (221)
Q Consensus 63 ~~~v~C~~C~~~q~~~-~~C~~Cg~~ 87 (221)
.+-..|+.|.++..+. ..|++||..
T Consensus 208 ~RyL~CslC~teW~~~R~~C~~Cg~~ 233 (305)
T TIGR01562 208 LRYLSCSLCATEWHYVRVKCSHCEES 233 (305)
T ss_pred ceEEEcCCCCCcccccCccCCCCCCC
Confidence 4678999999998774 689999975
No 272
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=21.34 E-value=48 Score=23.80 Aligned_cols=12 Identities=42% Similarity=0.886 Sum_probs=10.0
Q ss_pred cCCCCCCccccc
Q 027589 189 KYCCPICSKSVI 200 (221)
Q Consensus 189 ~~~CPiCrksi~ 200 (221)
..+||+|+|.+.
T Consensus 6 ~v~CP~C~k~~~ 17 (62)
T PRK00418 6 TVNCPTCGKPVE 17 (62)
T ss_pred cccCCCCCCccc
Confidence 468999999874
No 273
>PF10272 Tmpp129: Putative transmembrane protein precursor; InterPro: IPR018801 This entry consists of proteins conserved from worms to humans. They are purported to be transmembrane protein-precursors but their function is unknown.
Probab=21.32 E-value=49 Score=31.36 Aligned_cols=35 Identities=26% Similarity=0.562 Sum_probs=26.5
Q ss_pred CccchhhcccCCCceeeeccCCccCHHHHHHHHhcCcCCCCCCcccc
Q 027589 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSV 199 (221)
Q Consensus 153 CpICle~lf~s~~~v~~L~CGH~~H~~C~~~~l~~~~~~CPiCrksi 199 (221)
|--||...|-|+++-. |. +.||. ++-+||.||+.+
T Consensus 316 C~~Cm~kwFasrQd~~--------~~---~~Wl~-~~~~CPtCRa~F 350 (358)
T PF10272_consen 316 CLECMGKWFASRQDQQ--------HP---ETWLS-GKCPCPTCRAKF 350 (358)
T ss_pred HHHHHHHHhhhcCCCC--------Ch---hhhhc-CCCCCCCCcccc
Confidence 6778888888876332 33 68997 578999999986
No 274
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=21.17 E-value=62 Score=27.01 Aligned_cols=13 Identities=15% Similarity=0.496 Sum_probs=11.4
Q ss_pred cCCCCCCCcceee
Q 027589 80 VCTNCGVNMGEYF 92 (221)
Q Consensus 80 ~C~~Cg~~f~~y~ 92 (221)
.|++||..|..|=
T Consensus 30 eC~~C~~RFTTyE 42 (147)
T TIGR00244 30 ECLECHERFTTFE 42 (147)
T ss_pred cCCccCCccceee
Confidence 6999999999983
No 275
>PRK12496 hypothetical protein; Provisional
Probab=21.09 E-value=45 Score=27.83 Aligned_cols=22 Identities=32% Similarity=0.896 Sum_probs=9.5
Q ss_pred ecCCCCcccc---ccccCCCCCCCc
Q 027589 67 ICSVCDTEQP---VAQVCTNCGVNM 88 (221)
Q Consensus 67 ~C~~C~~~q~---~~~~C~~Cg~~f 88 (221)
.|..|+++-+ ..+.|+.||.++
T Consensus 129 ~C~gC~~~~~~~~~~~~C~~CG~~~ 153 (164)
T PRK12496 129 VCKGCKKKYPEDYPDDVCEICGSPV 153 (164)
T ss_pred ECCCCCccccCCCCCCcCCCCCChh
Confidence 3555554432 123455555443
No 276
>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=20.91 E-value=92 Score=28.62 Aligned_cols=46 Identities=17% Similarity=0.332 Sum_probs=26.2
Q ss_pred CCCCCCCccchhhcccCCCceeeec-c-CCccCHHHHHHHHhcCcCCCC
Q 027589 147 NSMHHHCPICYEYLFDSLRNTTVMK-C-GHTMHCECYHEMIKRDKYCCP 193 (221)
Q Consensus 147 ~~~~~~CpICle~lf~s~~~v~~L~-C-GH~~H~~C~~~~l~~~~~~CP 193 (221)
..+-+.|+||+|- ...+.+...|. = .=-=|+.||+.|=.-.+..||
T Consensus 27 ~~tLsfChiCfEl-~iegvpks~llHtkSlRGHrdCFEK~HlIanQ~~p 74 (285)
T PF06937_consen 27 TETLSFCHICFEL-SIEGVPKSNLLHTKSLRGHRDCFEKYHLIANQDCP 74 (285)
T ss_pred ccceeecceeecc-ccccCccccccccccccchHHHHHHHHHHHcCCCC
Confidence 3445568888874 33322322221 1 012389999999433578899
No 277
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=20.64 E-value=53 Score=29.42 Aligned_cols=34 Identities=29% Similarity=0.648 Sum_probs=24.9
Q ss_pred CeeeCCCCCcceeCCccceeecCccCccccccccCcceee
Q 027589 106 GQFHCDDCGICRIGGRENYFHCKRCGSCYSTSLRNNHLCI 145 (221)
Q Consensus 106 ~~yHC~~CgiCR~G~~~~~fHC~~C~~C~s~~~~~~H~C~ 145 (221)
+...|+.|.+-|- .-.-||..||.|+..- +|-|.
T Consensus 112 ~~~~C~~C~~~rP---pRs~HCsvC~~CV~rf---DHHC~ 145 (299)
T KOG1311|consen 112 EWKYCDTCQLYRP---PRSSHCSVCNNCVLRF---DHHCP 145 (299)
T ss_pred ceEEcCcCcccCC---CCcccchhhccccccc---CCCCC
Confidence 4577777766543 4589999999999864 67664
No 278
>PF12088 DUF3565: Protein of unknown function (DUF3565); InterPro: IPR021948 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 30 to 78 amino acids in length. This protein has two conserved sequence motifs: WVA and CGH.
Probab=20.35 E-value=64 Score=23.11 Aligned_cols=17 Identities=29% Similarity=0.518 Sum_probs=13.4
Q ss_pred CCCceeeeccCCccCHH
Q 027589 163 SLRNTTVMKCGHTMHCE 179 (221)
Q Consensus 163 s~~~v~~L~CGH~~H~~ 179 (221)
...-|..|.|||.=|..
T Consensus 8 e~hWVA~L~CGH~QHvR 24 (61)
T PF12088_consen 8 EGHWVAELSCGHTQHVR 24 (61)
T ss_pred cCCEEEEeccccccccc
Confidence 34678999999988854
No 279
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=20.23 E-value=98 Score=21.44 Aligned_cols=9 Identities=33% Similarity=1.239 Sum_probs=5.6
Q ss_pred cCCCCCCCc
Q 027589 80 VCTNCGVNM 88 (221)
Q Consensus 80 ~C~~Cg~~f 88 (221)
.||.||..+
T Consensus 4 ~CP~CG~~i 12 (54)
T TIGR01206 4 ECPDCGAEI 12 (54)
T ss_pred CCCCCCCEE
Confidence 566666655
No 280
>PRK00366 ispG 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed
Probab=20.14 E-value=92 Score=29.63 Aligned_cols=32 Identities=13% Similarity=0.538 Sum_probs=29.1
Q ss_pred cCCCCCCcccccchhHHHHHHHHHHHhCCCCC
Q 027589 189 KYCCPICSKSVIDMSRTWKRIDEEVSLFNLSF 220 (221)
Q Consensus 189 ~~~CPiCrksi~dm~~~~~~lD~~i~~~pmP~ 220 (221)
-..||-|++...|+..+=..+|+.+...++|.
T Consensus 268 IisCPgCgR~~~D~~~la~~vee~~~~~~~Pl 299 (360)
T PRK00366 268 VISCPTCGRTEFDVIQELAEVEQRLEHIKMPL 299 (360)
T ss_pred EEECCCCCCCcccHHHHHHHHHHHhcCCCCCc
Confidence 35799999999999999999999999999984
No 281
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=20.02 E-value=91 Score=19.13 Aligned_cols=7 Identities=43% Similarity=1.298 Sum_probs=3.4
Q ss_pred cCCCCCC
Q 027589 80 VCTNCGV 86 (221)
Q Consensus 80 ~C~~Cg~ 86 (221)
.|+.||+
T Consensus 28 ~CP~Cg~ 34 (41)
T smart00834 28 TCPECGG 34 (41)
T ss_pred CCCCCCC
Confidence 3555544
Done!