Query 027217
Match_columns 226
No_of_seqs 224 out of 756
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 06:42:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027217.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027217hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1940 Zn-finger protein [Gen 100.0 1.4E-56 3E-61 400.6 4.6 205 5-220 22-226 (276)
2 PF05495 zf-CHY: CHY zinc fing 99.9 1.5E-24 3.1E-29 159.1 4.0 70 18-100 1-71 (71)
3 COG4357 Zinc finger domain con 99.7 2.5E-18 5.5E-23 132.3 2.3 73 15-90 12-92 (105)
4 PF13639 zf-RING_2: Ring finge 99.4 2.6E-14 5.7E-19 94.6 1.8 44 151-196 1-44 (44)
5 PF12678 zf-rbx1: RING-H2 zinc 99.1 5.9E-11 1.3E-15 87.2 3.9 48 148-196 17-73 (73)
6 COG5243 HRD1 HRD ubiquitin lig 99.1 4.9E-11 1.1E-15 111.1 2.1 57 147-204 284-350 (491)
7 cd00162 RING RING-finger (Real 99.1 1.7E-10 3.7E-15 73.8 3.8 45 152-199 1-45 (45)
8 KOG4628 Predicted E3 ubiquitin 99.0 2.4E-10 5.1E-15 106.1 2.8 50 151-201 230-279 (348)
9 PF13923 zf-C3HC4_2: Zinc fing 98.9 6E-10 1.3E-14 72.1 2.6 39 153-195 1-39 (39)
10 PHA02929 N1R/p28-like protein; 98.9 1.3E-09 2.8E-14 96.8 4.5 54 147-201 171-228 (238)
11 PF13920 zf-C3HC4_3: Zinc fing 98.8 2.9E-09 6.3E-14 72.2 2.9 47 150-201 2-49 (50)
12 PF00097 zf-C3HC4: Zinc finger 98.8 3.8E-09 8.3E-14 68.3 2.7 40 153-195 1-41 (41)
13 smart00184 RING Ring finger. E 98.8 5.9E-09 1.3E-13 64.3 3.1 39 153-195 1-39 (39)
14 COG5540 RING-finger-containing 98.7 9.3E-09 2E-13 93.9 3.3 53 146-199 319-371 (374)
15 PF14634 zf-RING_5: zinc-RING 98.7 1.5E-08 3.3E-13 67.2 3.1 44 152-197 1-44 (44)
16 PF15227 zf-C3HC4_4: zinc fing 98.5 5.7E-08 1.2E-12 64.3 2.8 39 153-195 1-42 (42)
17 PF13445 zf-RING_UBOX: RING-ty 98.5 7.1E-08 1.5E-12 64.5 2.5 40 153-193 1-43 (43)
18 PF12861 zf-Apc11: Anaphase-pr 98.5 1E-07 2.2E-12 72.4 3.6 47 151-199 33-81 (85)
19 KOG0802 E3 ubiquitin ligase [P 98.5 4.7E-08 1E-12 95.4 1.1 52 147-199 288-340 (543)
20 PLN03208 E3 ubiquitin-protein 98.4 2.7E-07 5.8E-12 79.7 4.1 54 144-201 12-80 (193)
21 PHA02926 zinc finger-like prot 98.4 2.7E-07 5.8E-12 81.3 3.6 69 133-201 153-231 (242)
22 KOG0320 Predicted E3 ubiquitin 98.2 7.3E-07 1.6E-11 76.1 2.2 46 151-200 132-178 (187)
23 smart00504 Ubox Modified RING 98.1 3.2E-06 6.8E-11 58.9 3.8 45 151-200 2-46 (63)
24 smart00744 RINGv The RING-vari 98.1 2.9E-06 6.4E-11 58.0 2.9 43 152-196 1-49 (49)
25 KOG0804 Cytoplasmic Zn-finger 98.0 2E-06 4.3E-11 82.1 2.2 47 151-200 176-222 (493)
26 PF11793 FANCL_C: FANCL C-term 98.0 2E-06 4.3E-11 62.8 0.5 51 150-200 2-66 (70)
27 TIGR00599 rad18 DNA repair pro 97.9 9.1E-06 2E-10 77.1 4.1 47 150-201 26-72 (397)
28 COG5194 APC11 Component of SCF 97.8 1.3E-05 2.9E-10 60.4 3.2 48 152-200 33-81 (88)
29 PF14599 zinc_ribbon_6: Zinc-r 97.8 3.4E-06 7.3E-11 60.5 0.0 22 199-220 1-22 (61)
30 KOG0317 Predicted E3 ubiquitin 97.7 1.5E-05 3.2E-10 72.5 1.8 46 151-201 240-285 (293)
31 KOG0827 Predicted E3 ubiquitin 97.7 1.8E-05 3.8E-10 74.7 1.9 46 150-196 4-52 (465)
32 TIGR00570 cdk7 CDK-activating 97.7 3.8E-05 8.2E-10 70.7 4.0 51 150-200 3-54 (309)
33 KOG2177 Predicted E3 ubiquitin 97.7 2.2E-05 4.7E-10 66.2 2.2 44 149-197 12-55 (386)
34 KOG0828 Predicted E3 ubiquitin 97.6 3E-05 6.6E-10 75.0 1.7 51 150-200 571-634 (636)
35 KOG2164 Predicted E3 ubiquitin 97.4 8E-05 1.7E-09 72.2 2.5 50 148-201 184-237 (513)
36 KOG0823 Predicted E3 ubiquitin 97.4 9.8E-05 2.1E-09 65.3 2.8 50 148-201 45-96 (230)
37 KOG1734 Predicted RING-contain 97.3 6.5E-05 1.4E-09 68.1 0.2 52 149-200 223-281 (328)
38 PF14835 zf-RING_6: zf-RING of 97.3 0.0001 2.2E-09 53.5 1.0 56 151-213 8-65 (65)
39 KOG0287 Postreplication repair 97.2 0.00029 6.2E-09 65.9 3.5 58 152-214 25-83 (442)
40 PF04564 U-box: U-box domain; 97.2 0.00041 9E-09 50.6 3.5 47 151-201 5-51 (73)
41 KOG1493 Anaphase-promoting com 97.0 0.00023 5E-09 53.3 1.1 29 171-199 50-80 (84)
42 KOG1941 Acetylcholine receptor 97.0 0.00016 3.5E-09 68.5 -0.1 62 141-203 357-419 (518)
43 KOG4265 Predicted E3 ubiquitin 96.8 0.00085 1.8E-08 62.7 2.9 50 147-201 287-337 (349)
44 COG5574 PEX10 RING-finger-cont 96.7 0.00077 1.7E-08 60.9 2.0 47 150-200 215-262 (271)
45 PF14570 zf-RING_4: RING/Ubox 96.5 0.0021 4.6E-08 44.0 2.5 44 153-198 1-46 (48)
46 KOG2930 SCF ubiquitin ligase, 96.4 0.0019 4.1E-08 51.1 2.2 27 171-198 80-106 (114)
47 KOG0825 PHD Zn-finger protein 96.4 0.001 2.2E-08 67.8 0.8 76 124-201 96-172 (1134)
48 COG5219 Uncharacterized conser 96.4 0.0014 3.1E-08 67.9 1.7 53 147-199 1466-1522(1525)
49 KOG0311 Predicted E3 ubiquitin 96.3 0.0011 2.4E-08 62.1 0.1 49 150-201 43-91 (381)
50 KOG4172 Predicted E3 ubiquitin 96.3 0.0011 2.3E-08 46.9 -0.0 53 148-204 5-58 (62)
51 PF11789 zf-Nse: Zinc-finger o 96.3 0.0027 5.9E-08 44.7 2.0 44 148-194 9-53 (57)
52 KOG3002 Zn finger protein [Gen 96.2 0.0048 1E-07 56.8 3.7 59 150-219 48-108 (299)
53 KOG0978 E3 ubiquitin ligase in 96.2 0.0016 3.4E-08 65.8 0.5 47 151-201 644-690 (698)
54 KOG1785 Tyrosine kinase negati 96.0 0.0021 4.7E-08 61.3 0.5 54 144-201 363-417 (563)
55 KOG1428 Inhibitor of type V ad 96.0 0.0047 1E-07 66.6 2.9 74 119-200 3462-3544(3738)
56 KOG1645 RING-finger-containing 95.9 0.0059 1.3E-07 58.3 3.1 49 150-198 4-54 (463)
57 PF10367 Vps39_2: Vacuolar sor 95.9 0.0038 8.2E-08 47.2 1.3 38 143-182 71-108 (109)
58 PRK14890 putative Zn-ribbon RN 95.6 0.01 2.2E-07 42.4 2.5 46 63-115 5-56 (59)
59 PF12906 RINGv: RING-variant d 95.5 0.0076 1.6E-07 40.7 1.5 41 153-195 1-47 (47)
60 KOG1039 Predicted E3 ubiquitin 95.3 0.0082 1.8E-07 56.3 1.6 60 148-207 159-230 (344)
61 KOG3970 Predicted E3 ubiquitin 95.1 0.033 7.2E-07 49.8 4.9 52 148-201 48-106 (299)
62 KOG1571 Predicted E3 ubiquitin 94.8 0.0099 2.1E-07 55.8 0.8 48 146-201 301-348 (355)
63 COG5432 RAD18 RING-finger-cont 94.6 0.021 4.4E-07 52.8 2.1 44 151-199 26-69 (391)
64 KOG2879 Predicted E3 ubiquitin 94.5 0.03 6.5E-07 51.2 3.1 53 148-203 237-290 (298)
65 PF14447 Prok-RING_4: Prokaryo 94.4 0.014 3.1E-07 41.1 0.6 33 166-201 19-51 (55)
66 PF05883 Baculo_RING: Baculovi 94.4 0.019 4E-07 47.3 1.2 36 150-186 26-67 (134)
67 KOG4275 Predicted E3 ubiquitin 94.1 0.0061 1.3E-07 56.1 -2.4 62 138-207 285-349 (350)
68 KOG3800 Predicted E3 ubiquitin 93.7 0.051 1.1E-06 49.9 2.8 49 152-200 2-51 (300)
69 KOG3268 Predicted E3 ubiquitin 93.4 0.051 1.1E-06 47.1 2.2 52 152-203 167-232 (234)
70 KOG0824 Predicted E3 ubiquitin 93.3 0.044 9.5E-07 50.6 1.7 49 148-200 5-53 (324)
71 KOG4185 Predicted E3 ubiquitin 93.0 0.071 1.5E-06 47.9 2.6 48 151-199 4-54 (296)
72 KOG4739 Uncharacterized protei 93.0 0.043 9.4E-07 48.9 1.2 37 161-200 12-48 (233)
73 KOG4159 Predicted E3 ubiquitin 92.8 0.073 1.6E-06 50.9 2.5 52 148-204 82-133 (398)
74 PF12773 DZR: Double zinc ribb 92.6 0.12 2.7E-06 34.4 2.8 22 68-89 1-23 (50)
75 KOG2660 Locus-specific chromos 92.6 0.018 3.9E-07 53.6 -1.9 71 149-223 14-85 (331)
76 COG2888 Predicted Zn-ribbon RN 92.4 0.097 2.1E-06 37.5 2.1 45 65-115 9-58 (61)
77 KOG0297 TNF receptor-associate 91.7 0.1 2.3E-06 49.5 2.1 52 149-204 20-71 (391)
78 PF04641 Rtf2: Rtf2 RING-finge 91.1 0.18 3.9E-06 45.1 2.9 50 148-200 111-161 (260)
79 KOG0309 Conserved WD40 repeat- 90.6 0.16 3.5E-06 52.1 2.4 42 150-194 1028-1069(1081)
80 KOG1814 Predicted E3 ubiquitin 90.6 0.15 3.3E-06 48.9 2.1 46 150-196 184-236 (445)
81 PF07800 DUF1644: Protein of u 90.4 0.3 6.5E-06 41.4 3.4 48 150-201 2-92 (162)
82 PHA02862 5L protein; Provision 90.2 0.16 3.4E-06 42.6 1.5 56 150-211 2-63 (156)
83 PF07191 zinc-ribbons_6: zinc- 90.2 0.18 4E-06 37.2 1.7 36 64-99 16-59 (70)
84 KOG2114 Vacuolar assembly/sort 90.1 0.2 4.4E-06 51.8 2.6 42 151-199 841-882 (933)
85 COG5175 MOT2 Transcriptional r 89.7 0.082 1.8E-06 49.9 -0.5 57 150-206 14-70 (480)
86 KOG1002 Nucleotide excision re 89.5 0.14 3E-06 50.8 0.8 52 145-200 531-586 (791)
87 KOG4445 Uncharacterized conser 89.3 0.19 4E-06 46.8 1.4 53 148-201 113-187 (368)
88 KOG3161 Predicted E3 ubiquitin 88.8 0.21 4.5E-06 50.5 1.5 53 151-207 12-68 (861)
89 KOG3039 Uncharacterized conser 88.5 0.45 9.7E-06 43.2 3.2 53 147-201 218-271 (303)
90 PF13248 zf-ribbon_3: zinc-rib 87.7 0.26 5.7E-06 29.2 0.9 24 65-88 2-26 (26)
91 KOG2817 Predicted E3 ubiquitin 87.6 0.53 1.1E-05 45.0 3.3 46 152-198 336-383 (394)
92 PHA02825 LAP/PHD finger-like p 87.4 0.56 1.2E-05 39.8 3.0 46 149-199 7-58 (162)
93 COG5236 Uncharacterized conser 86.8 0.57 1.2E-05 44.5 3.0 65 131-199 42-107 (493)
94 KOG2034 Vacuolar sorting prote 86.4 0.36 7.8E-06 50.2 1.6 43 142-186 809-851 (911)
95 KOG1952 Transcription factor N 86.4 0.4 8.7E-06 49.7 1.9 51 150-201 191-248 (950)
96 PF03854 zf-P11: P-11 zinc fin 86.2 0.41 8.8E-06 33.0 1.3 31 169-200 15-46 (50)
97 KOG1813 Predicted E3 ubiquitin 85.9 0.48 1E-05 43.8 2.0 64 151-219 242-305 (313)
98 KOG4692 Predicted E3 ubiquitin 85.5 0.43 9.4E-06 45.4 1.5 58 147-214 419-476 (489)
99 PRK04023 DNA polymerase II lar 85.4 0.75 1.6E-05 48.7 3.4 31 80-114 628-658 (1121)
100 COG5152 Uncharacterized conser 85.4 0.54 1.2E-05 41.5 2.0 60 151-215 197-256 (259)
101 smart00734 ZnF_Rad18 Rad18-lik 85.2 0.7 1.5E-05 27.5 1.8 21 190-211 2-22 (26)
102 PF10571 UPF0547: Uncharacteri 84.9 0.63 1.4E-05 27.9 1.6 22 68-89 3-25 (26)
103 PF09538 FYDLN_acid: Protein o 84.8 0.7 1.5E-05 36.6 2.2 28 76-115 7-34 (108)
104 PF13240 zinc_ribbon_2: zinc-r 84.7 0.52 1.1E-05 27.3 1.1 21 68-88 2-23 (23)
105 PF02891 zf-MIZ: MIZ/SP-RING z 83.4 1.1 2.5E-05 30.5 2.5 41 152-198 4-50 (50)
106 PRK14559 putative protein seri 82.9 0.89 1.9E-05 46.1 2.6 33 66-98 2-35 (645)
107 PF07191 zinc-ribbons_6: zinc- 82.2 1.2 2.5E-05 32.9 2.3 58 66-137 2-63 (70)
108 PHA00626 hypothetical protein 81.9 1.1 2.4E-05 31.9 2.0 7 80-86 2-8 (59)
109 PF13894 zf-C2H2_4: C2H2-type 80.9 1.4 3E-05 23.9 1.9 21 190-210 1-21 (24)
110 PF14446 Prok-RING_1: Prokaryo 80.8 1.6 3.5E-05 30.6 2.5 36 148-183 3-38 (54)
111 PF08746 zf-RING-like: RING-li 80.3 1.2 2.5E-05 29.5 1.6 25 171-195 18-43 (43)
112 smart00132 LIM Zinc-binding do 80.0 1 2.2E-05 27.4 1.2 37 153-200 2-38 (39)
113 PHA03096 p28-like protein; Pro 80.0 0.75 1.6E-05 42.2 0.8 48 151-198 179-232 (284)
114 TIGR00595 priA primosomal prot 79.9 1.4 3.1E-05 43.1 2.8 50 26-87 213-262 (505)
115 PRK14714 DNA polymerase II lar 79.4 2 4.3E-05 46.6 3.8 33 65-98 667-700 (1337)
116 KOG0801 Predicted E3 ubiquitin 78.1 0.9 2E-05 39.0 0.7 31 147-178 174-204 (205)
117 COG5222 Uncharacterized conser 76.6 1.6 3.5E-05 40.8 1.9 45 151-198 275-319 (427)
118 KOG0269 WD40 repeat-containing 76.2 2.4 5.2E-05 43.7 3.2 79 105-203 751-836 (839)
119 PF05605 zf-Di19: Drought indu 75.2 3 6.5E-05 28.4 2.6 9 191-199 33-41 (54)
120 KOG0827 Predicted E3 ubiquitin 75.0 0.28 6.1E-06 47.0 -3.5 50 150-200 196-245 (465)
121 COG1198 PriA Primosomal protei 74.5 3.1 6.7E-05 42.9 3.5 43 64-114 434-482 (730)
122 KOG2066 Vacuolar assembly/sort 74.0 1.5 3.2E-05 45.3 1.1 48 150-199 784-834 (846)
123 COG1198 PriA Primosomal protei 73.9 3 6.6E-05 42.9 3.3 54 26-91 435-488 (730)
124 COG5220 TFB3 Cdk activating ki 73.4 1.3 2.8E-05 40.2 0.5 51 150-200 10-64 (314)
125 PLN03086 PRLI-interacting fact 72.1 1.8 3.9E-05 43.4 1.1 84 62-160 404-514 (567)
126 PRK14714 DNA polymerase II lar 71.9 3.3 7.1E-05 45.0 3.1 33 79-115 668-700 (1337)
127 TIGR02300 FYDLN_acid conserved 70.2 3.2 6.9E-05 34.0 2.0 28 77-116 8-35 (129)
128 PRK04023 DNA polymerase II lar 68.5 4.2 9E-05 43.4 2.9 50 63-118 624-674 (1121)
129 PRK05580 primosome assembly pr 68.4 3.8 8.3E-05 41.6 2.6 51 26-88 381-431 (679)
130 PF07754 DUF1610: Domain of un 67.7 4.6 9.9E-05 23.9 1.8 9 106-114 15-23 (24)
131 PRK14873 primosome assembly pr 66.8 4.2 9.2E-05 41.4 2.5 49 26-87 383-431 (665)
132 KOG1940 Zn-finger protein [Gen 66.3 3.4 7.4E-05 37.9 1.6 29 14-43 176-204 (276)
133 KOG2068 MOT2 transcription fac 66.2 4.6 9.9E-05 37.9 2.4 51 149-200 248-298 (327)
134 PF05502 Dynactin_p62: Dynacti 64.9 3.7 7.9E-05 40.3 1.6 98 90-210 5-107 (483)
135 PF07282 OrfB_Zn_ribbon: Putat 64.8 5.2 0.00011 28.2 2.0 27 78-115 28-54 (69)
136 smart00249 PHD PHD zinc finger 64.6 2.1 4.6E-05 26.7 -0.1 42 153-195 2-47 (47)
137 KOG2272 Focal adhesion protein 64.1 4.4 9.5E-05 37.1 1.9 51 36-103 100-151 (332)
138 COG5109 Uncharacterized conser 63.7 6.4 0.00014 37.1 2.9 44 152-196 338-383 (396)
139 PF03107 C1_2: C1 domain; Int 63.4 5.5 0.00012 24.1 1.7 20 112-131 2-22 (30)
140 PF00096 zf-C2H2: Zinc finger, 62.9 5.9 0.00013 21.8 1.6 17 190-206 1-17 (23)
141 KOG1001 Helicase-like transcri 62.6 3.7 8E-05 42.0 1.2 45 151-200 455-500 (674)
142 KOG0298 DEAD box-containing he 61.1 3.2 7E-05 45.1 0.5 52 148-203 1151-1202(1394)
143 PRK14559 putative protein seri 60.9 4.2 9.1E-05 41.3 1.3 34 65-99 15-50 (645)
144 PF13453 zf-TFIIB: Transcripti 60.5 6.9 0.00015 25.2 1.9 26 80-114 1-26 (41)
145 KOG3053 Uncharacterized conser 60.2 4.3 9.2E-05 37.2 1.1 68 148-215 18-104 (293)
146 KOG2462 C2H2-type Zn-finger pr 59.7 9.6 0.00021 35.0 3.2 20 188-207 242-261 (279)
147 PF04216 FdhE: Protein involve 59.6 6.6 0.00014 35.5 2.2 47 64-114 196-245 (290)
148 PF05191 ADK_lid: Adenylate ki 59.1 2.5 5.4E-05 27.1 -0.5 27 80-115 3-29 (36)
149 PF04423 Rad50_zn_hook: Rad50 57.8 6.5 0.00014 26.8 1.4 26 190-215 21-48 (54)
150 COG3809 Uncharacterized protei 57.1 12 0.00027 28.4 2.9 50 152-225 3-52 (88)
151 PRK00415 rps27e 30S ribosomal 56.6 6.4 0.00014 28.2 1.2 35 64-98 10-50 (59)
152 PF06524 NOA36: NOA36 protein; 56.2 3.8 8.1E-05 37.6 0.0 51 33-98 140-190 (314)
153 PF08271 TF_Zn_Ribbon: TFIIB z 56.0 9.6 0.00021 24.7 2.0 7 81-87 3-9 (43)
154 PF05290 Baculo_IE-1: Baculovi 56.0 7.4 0.00016 32.3 1.7 49 151-203 81-135 (140)
155 PF15353 HECA: Headcase protei 55.5 6.1 0.00013 31.4 1.1 15 172-186 40-54 (107)
156 PRK14890 putative Zn-ribbon RN 55.4 8.3 0.00018 27.6 1.7 34 63-98 23-56 (59)
157 PRK00398 rpoP DNA-directed RNA 54.9 11 0.00024 24.8 2.1 8 107-114 21-28 (46)
158 smart00659 RPOLCX RNA polymera 54.6 7.1 0.00015 26.0 1.2 21 67-87 4-28 (44)
159 KOG1812 Predicted E3 ubiquitin 54.6 6.2 0.00013 37.6 1.2 37 150-186 146-182 (384)
160 KOG1609 Protein involved in mR 50.1 7.6 0.00017 34.4 1.0 51 150-200 78-134 (323)
161 KOG1311 DHHC-type Zn-finger pr 49.3 11 0.00023 34.0 1.8 49 81-135 104-152 (299)
162 PF14569 zf-UDP: Zinc-binding 48.2 26 0.00056 26.5 3.4 52 148-199 7-61 (80)
163 PF13717 zinc_ribbon_4: zinc-r 48.1 12 0.00026 23.7 1.4 10 64-73 24-33 (36)
164 PHA00626 hypothetical protein 47.4 12 0.00026 26.7 1.4 34 66-101 1-34 (59)
165 COG2051 RPS27A Ribosomal prote 47.3 8.9 0.00019 28.1 0.8 28 64-91 18-51 (67)
166 KOG1312 DHHC-type Zn-finger pr 47.1 6.3 0.00014 36.7 -0.0 32 111-145 149-180 (341)
167 KOG4185 Predicted E3 ubiquitin 46.7 3.1 6.6E-05 37.3 -2.1 49 151-199 208-266 (296)
168 KOG4399 C2HC-type Zn-finger pr 45.9 4.1 9E-05 37.4 -1.4 72 85-159 199-270 (325)
169 PF07649 C1_3: C1-like domain; 45.3 12 0.00026 22.4 1.0 20 113-132 3-23 (30)
170 PF01096 TFIIS_C: Transcriptio 45.2 18 0.00038 23.3 1.9 34 80-114 2-35 (39)
171 TIGR00373 conserved hypothetic 44.5 35 0.00076 28.4 4.1 28 188-215 127-156 (158)
172 PF13719 zinc_ribbon_5: zinc-r 44.0 15 0.00032 23.3 1.4 9 65-73 25-33 (37)
173 TIGR00595 priA primosomal prot 43.9 25 0.00054 34.5 3.5 46 63-116 211-262 (505)
174 PRK00432 30S ribosomal protein 43.7 16 0.00035 24.9 1.6 9 106-114 36-44 (50)
175 KOG3362 Predicted BBOX Zn-fing 43.6 8 0.00017 32.5 0.1 25 89-119 117-143 (156)
176 PRK06266 transcription initiat 43.4 35 0.00077 29.0 4.0 27 188-214 135-163 (178)
177 PF12874 zf-met: Zinc-finger o 43.3 16 0.00034 20.4 1.3 16 190-205 1-16 (25)
178 PF01529 zf-DHHC: DHHC palmito 43.1 13 0.00029 30.0 1.4 50 82-137 40-89 (174)
179 COG1996 RPC10 DNA-directed RNA 42.7 17 0.00037 25.0 1.6 27 89-115 5-32 (49)
180 KOG0006 E3 ubiquitin-protein l 41.8 23 0.00049 33.7 2.7 88 90-186 149-255 (446)
181 PF01529 zf-DHHC: DHHC palmito 41.7 21 0.00045 28.9 2.3 30 113-145 51-80 (174)
182 KOG2462 C2H2-type Zn-finger pr 41.5 21 0.00046 32.9 2.4 88 89-204 129-230 (279)
183 PF01667 Ribosomal_S27e: Ribos 41.2 14 0.00031 26.0 1.1 34 65-98 7-46 (55)
184 cd00350 rubredoxin_like Rubred 41.1 21 0.00046 22.0 1.7 24 91-115 2-25 (33)
185 PF14353 CpXC: CpXC protein 40.9 25 0.00055 27.7 2.6 11 80-90 3-13 (128)
186 PF03833 PolC_DP2: DNA polymer 40.6 9.2 0.0002 40.2 0.0 44 80-132 657-700 (900)
187 cd00729 rubredoxin_SM Rubredox 40.4 21 0.00046 22.3 1.6 22 66-87 3-27 (34)
188 PF04438 zf-HIT: HIT zinc fing 38.8 16 0.00034 22.4 0.8 16 81-97 5-20 (30)
189 KOG4367 Predicted Zn-finger pr 38.6 16 0.00035 36.0 1.3 33 150-186 4-36 (699)
190 PF00412 LIM: LIM domain; Int 38.5 12 0.00027 24.8 0.4 39 153-202 1-39 (58)
191 PF08274 PhnA_Zn_Ribbon: PhnA 38.3 18 0.0004 22.3 1.1 23 80-114 4-26 (30)
192 PF15616 TerY-C: TerY-C metal 38.0 29 0.00062 28.5 2.5 20 79-99 78-98 (131)
193 PF06827 zf-FPG_IleRS: Zinc fi 37.5 24 0.00052 21.0 1.5 10 79-88 2-11 (30)
194 PLN02189 cellulose synthase 37.1 29 0.00064 37.3 3.0 56 145-200 29-87 (1040)
195 PF13824 zf-Mss51: Zinc-finger 36.6 30 0.00066 24.4 2.1 21 188-208 13-33 (55)
196 PF03604 DNA_RNApol_7kD: DNA d 36.6 22 0.00048 22.2 1.3 9 106-114 16-24 (32)
197 smart00355 ZnF_C2H2 zinc finge 36.5 33 0.00072 18.2 1.9 17 190-206 1-17 (26)
198 COG2888 Predicted Zn-ribbon RN 36.1 22 0.00048 25.6 1.4 33 64-98 26-58 (61)
199 cd02337 ZZ_CBP Zinc finger, ZZ 36.1 27 0.00059 22.8 1.7 20 108-131 1-20 (41)
200 KOG4399 C2HC-type Zn-finger pr 36.0 8.4 0.00018 35.4 -1.0 53 79-135 250-302 (325)
201 TIGR00100 hypA hydrogenase nic 35.9 17 0.00038 28.6 0.9 11 78-88 70-80 (115)
202 PF12760 Zn_Tnp_IS1595: Transp 35.8 46 0.00099 21.8 2.8 9 79-87 19-27 (46)
203 PF00643 zf-B_box: B-box zinc 35.7 30 0.00065 21.8 1.9 21 79-99 4-24 (42)
204 PF01599 Ribosomal_S27: Riboso 35.2 25 0.00053 24.0 1.4 22 77-98 17-46 (47)
205 smart00778 Prim_Zn_Ribbon Zinc 35.2 39 0.00084 21.8 2.3 30 79-115 4-33 (37)
206 PRK03564 formate dehydrogenase 34.8 43 0.00092 31.2 3.4 25 63-87 210-235 (309)
207 PRK14873 primosome assembly pr 34.3 35 0.00076 34.9 3.0 23 64-90 382-404 (665)
208 smart00661 RPOL9 RNA polymeras 34.0 33 0.00071 22.5 1.9 8 107-114 20-27 (52)
209 PLN02436 cellulose synthase A 33.8 35 0.00077 36.9 3.0 56 145-200 31-89 (1094)
210 TIGR02098 MJ0042_CXXC MJ0042 f 33.7 30 0.00064 21.5 1.6 10 65-74 25-34 (38)
211 PF03833 PolC_DP2: DNA polymer 33.3 14 0.00031 38.8 0.0 47 63-115 653-700 (900)
212 PF12172 DUF35_N: Rubredoxin-l 33.2 21 0.00045 22.3 0.8 23 64-86 10-33 (37)
213 PRK00420 hypothetical protein; 32.9 30 0.00065 27.7 1.8 19 79-97 24-47 (112)
214 COG1645 Uncharacterized Zn-fin 32.8 24 0.00052 29.0 1.3 19 79-97 29-51 (131)
215 PF13913 zf-C2HC_2: zinc-finge 32.5 18 0.00039 21.0 0.4 12 79-90 3-14 (25)
216 PF09723 Zn-ribbon_8: Zinc rib 31.7 33 0.00071 22.3 1.6 6 109-114 28-33 (42)
217 cd02249 ZZ Zinc finger, ZZ typ 31.7 34 0.00074 22.4 1.7 9 123-131 13-21 (46)
218 cd02341 ZZ_ZZZ3 Zinc finger, Z 31.0 36 0.00078 23.0 1.7 7 124-130 15-21 (48)
219 PRK14892 putative transcriptio 31.0 45 0.00096 26.1 2.4 32 122-159 19-51 (99)
220 cd07973 Spt4 Transcription elo 30.3 28 0.0006 27.2 1.2 20 67-86 5-28 (98)
221 PTZ00083 40S ribosomal protein 29.9 28 0.00061 26.7 1.1 35 65-99 35-75 (85)
222 PLN00209 ribosomal protein S27 29.9 33 0.00073 26.3 1.5 35 65-99 36-76 (86)
223 PRK08351 DNA-directed RNA poly 29.9 32 0.00069 24.7 1.3 20 67-87 5-24 (61)
224 PRK00464 nrdR transcriptional 29.6 31 0.00068 28.9 1.5 12 80-91 30-41 (154)
225 TIGR03830 CxxCG_CxxCG_HTH puta 29.0 26 0.00057 26.9 0.9 64 153-223 1-68 (127)
226 COG3024 Uncharacterized protei 28.8 29 0.00063 25.3 1.0 26 76-101 5-38 (65)
227 PRK14810 formamidopyrimidine-D 28.6 32 0.00069 31.0 1.5 20 78-97 244-271 (272)
228 PF09297 zf-NADH-PPase: NADH p 28.6 25 0.00054 21.4 0.6 21 67-87 5-30 (32)
229 COG5273 Uncharacterized protei 28.2 35 0.00077 31.5 1.7 21 79-99 98-118 (309)
230 PF01363 FYVE: FYVE zinc finge 28.1 34 0.00073 23.9 1.2 25 78-115 9-33 (69)
231 PF11781 RRN7: RNA polymerase 28.0 39 0.00085 21.5 1.4 24 153-176 11-35 (36)
232 PF11023 DUF2614: Protein of u 28.0 38 0.00082 27.3 1.6 27 62-88 66-95 (114)
233 KOG1829 Uncharacterized conser 28.0 20 0.00044 36.2 0.1 27 166-196 531-557 (580)
234 PRK14811 formamidopyrimidine-D 27.6 35 0.00075 30.8 1.5 20 78-97 235-262 (269)
235 PF15389 DUF4612: Domain of un 27.5 45 0.00098 26.9 2.0 15 203-217 92-106 (115)
236 KOG1100 Predicted E3 ubiquitin 27.3 34 0.00073 30.0 1.3 39 153-200 161-200 (207)
237 KOG4317 Predicted Zn-finger pr 27.3 28 0.00061 32.9 0.9 20 80-99 9-28 (383)
238 PRK10445 endonuclease VIII; Pr 27.3 36 0.00077 30.5 1.5 20 78-97 235-262 (263)
239 KOG0802 E3 ubiquitin ligase [P 27.0 38 0.00082 33.5 1.8 44 148-200 477-520 (543)
240 PF08792 A2L_zn_ribbon: A2L zi 26.9 39 0.00085 21.2 1.2 12 66-77 4-15 (33)
241 PF12675 DUF3795: Protein of u 26.9 35 0.00075 25.0 1.1 37 78-114 34-70 (78)
242 PF12171 zf-C2H2_jaz: Zinc-fin 26.6 49 0.0011 19.0 1.5 14 190-203 2-15 (27)
243 TIGR00244 transcriptional regu 26.6 38 0.00083 28.4 1.5 13 80-92 30-42 (147)
244 PF06677 Auto_anti-p27: Sjogre 26.4 46 0.00099 21.9 1.5 12 79-90 18-29 (41)
245 PF13912 zf-C2H2_6: C2H2-type 26.3 43 0.00094 18.9 1.3 18 190-207 2-19 (27)
246 PRK04136 rpl40e 50S ribosomal 26.2 42 0.00092 23.1 1.4 23 64-86 13-36 (48)
247 COG1144 Pyruvate:ferredoxin ox 26.1 34 0.00074 26.5 1.0 15 122-136 63-77 (91)
248 PF00130 C1_1: Phorbol esters/ 26.1 54 0.0012 21.5 1.9 11 104-114 25-35 (53)
249 PF11331 DUF3133: Protein of u 26.1 58 0.0013 22.1 2.0 37 37-78 8-44 (46)
250 PF06220 zf-U1: U1 zinc finger 26.1 26 0.00057 22.5 0.3 13 88-100 1-13 (38)
251 COG1998 RPS31 Ribosomal protei 25.6 43 0.00094 23.3 1.3 19 79-97 20-44 (51)
252 COG5273 Uncharacterized protei 25.4 32 0.00069 31.8 0.9 31 112-145 111-141 (309)
253 KOG3005 GIY-YIG type nuclease 25.4 87 0.0019 28.9 3.6 50 151-200 183-243 (276)
254 PRK01103 formamidopyrimidine/5 25.2 41 0.00089 30.2 1.5 20 78-97 245-272 (274)
255 smart00451 ZnF_U1 U1-like zinc 25.0 52 0.0011 19.6 1.5 16 189-204 3-18 (35)
256 PF14445 Prok-RING_2: Prokaryo 24.1 4.7 0.0001 28.2 -3.6 46 86-136 3-53 (57)
257 PF05458 Siva: Cd27 binding pr 23.5 62 0.0013 27.6 2.2 35 66-100 112-157 (175)
258 PRK13945 formamidopyrimidine-D 23.4 47 0.001 30.0 1.6 19 78-96 254-280 (282)
259 PF10272 Tmpp129: Putative tra 23.3 39 0.00084 32.2 1.0 36 153-200 316-351 (358)
260 TIGR00577 fpg formamidopyrimid 23.2 47 0.001 29.9 1.5 19 78-96 245-271 (272)
261 PRK05580 primosome assembly pr 23.1 82 0.0018 32.1 3.3 45 63-115 379-429 (679)
262 KOG1815 Predicted E3 ubiquitin 22.8 47 0.001 32.0 1.5 38 147-187 67-104 (444)
263 smart00586 ZnF_DBF Zinc finger 22.8 51 0.0011 22.7 1.3 14 202-215 33-46 (49)
264 TIGR01384 TFS_arch transcripti 22.6 63 0.0014 24.5 1.9 9 80-88 2-10 (104)
265 KOG4362 Transcriptional regula 22.6 40 0.00086 34.8 1.0 66 149-218 20-91 (684)
266 TIGR01562 FdhE formate dehydro 22.6 94 0.002 28.9 3.4 25 63-87 208-233 (305)
267 PF06937 EURL: EURL protein; 22.3 83 0.0018 29.1 2.9 46 147-193 27-74 (285)
268 PLN02638 cellulose synthase A 22.0 80 0.0017 34.3 3.1 56 145-200 12-70 (1079)
269 PRK00564 hypA hydrogenase nick 22.0 58 0.0013 25.8 1.7 11 78-88 71-81 (117)
270 PF14803 Nudix_N_2: Nudix N-te 21.8 54 0.0012 20.7 1.1 11 104-114 19-29 (34)
271 smart00834 CxxC_CXXC_SSSS Puta 21.7 82 0.0018 19.4 2.0 8 80-87 28-35 (41)
272 cd00112 LDLa Low Density Lipop 21.1 70 0.0015 19.8 1.6 29 123-152 4-34 (35)
273 PF13901 DUF4206: Domain of un 21.0 67 0.0014 27.7 2.0 31 161-197 167-197 (202)
274 COG5183 SSM4 Protein involved 21.0 61 0.0013 34.4 1.9 50 148-199 10-65 (1175)
275 KOG0269 WD40 repeat-containing 20.9 51 0.0011 34.5 1.3 49 79-136 754-805 (839)
276 PF00301 Rubredoxin: Rubredoxi 20.7 76 0.0016 21.4 1.8 9 90-98 1-9 (47)
277 KOG1311 DHHC-type Zn-finger pr 20.4 53 0.0011 29.5 1.3 34 106-145 112-145 (299)
No 1
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=100.00 E-value=1.4e-56 Score=400.64 Aligned_cols=205 Identities=49% Similarity=1.043 Sum_probs=198.3
Q ss_pred ccccccCCCCccCcccccccceeecCCCCCcccChhhHHhhhcCCCCCCCCccccccccceeEeCCCCccccccccCCCC
Q 027217 5 ANERITFGKMGYGCKHYRRRCRIRAPCCNEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVAQVCTNC 84 (226)
Q Consensus 5 ~~~~~~~~~~~~gC~HY~r~c~l~~pCC~~~y~Cr~CHde~~~h~~~~~~~H~~~r~~~~~v~Cg~C~~~q~v~~~C~~C 84 (226)
.+++.|++.++.+|+||+|++++++|+|+++|.|++||+++. +|.++|+.+.+|+|+.|+++|++++.|.+|
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 456789999999999999999999999999999999999984 699999999999999999999999999999
Q ss_pred CCCcceeecCccccccCCCCCCeeccCCCCcceeCCccceeeccccCccccccccCcceeecCCCCCCCccchhhcccCC
Q 027217 85 GVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYSTSLRNNHLCIENSMHHHCPICYEYLFDSL 164 (226)
Q Consensus 85 g~~f~~Y~C~~C~l~dd~~~k~~yHC~~CgiCR~G~~~~~fHC~~C~~C~s~~l~~~H~C~e~~~~~~CpICle~lf~s~ 164 (226)
+..+++|||++|+||||+++ +||||+.|||||+|++++||||++|+.|++..+.+.|+|+|++++.|||||.|+||++.
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 cceeeeccCCccCHHHHHHHHhcCcCCCCCCCeecccchHHHHHHHHHHHhCCCCC
Q 027217 165 RNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRTWKRIDEELQMNSSIF 220 (226)
Q Consensus 165 ~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~dm~~~~~~lD~~i~~~pm~~ 220 (226)
..+.+|+|||.+|..||++++..+ |+||+|.| +.||+.+|+++|.+|+++|||.
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 999999999999999999999875 99999999 9999999999999999999973
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=1.5e-24 Score=159.05 Aligned_cols=70 Identities=51% Similarity=1.212 Sum_probs=53.0
Q ss_pred ccccccc-ceeecCCCCCcccChhhHHhhhcCCCCCCCCccccccccceeEeCCCCccccccccCCCCCCCcceeecCcc
Q 027217 18 CKHYRRR-CRIRAPCCNEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVAQVCTNCGVNMGEYFCDIC 96 (226)
Q Consensus 18 C~HY~r~-c~l~~pCC~~~y~Cr~CHde~~~h~~~~~~~H~~~r~~~~~v~Cg~C~~~q~v~~~C~~Cg~~f~~Y~C~~C 96 (226)
|+||+|+ |+|+||||++|||||+||||++ +|+++|+.+++|+||.|+++|++++. +|+ ++|+|++|
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 9999999999999999999985 59999999999999999999999988 777 99999999
Q ss_pred cccc
Q 027217 97 KFYD 100 (226)
Q Consensus 97 ~l~d 100 (226)
++||
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=99.71 E-value=2.5e-18 Score=132.25 Aligned_cols=73 Identities=26% Similarity=0.611 Sum_probs=67.0
Q ss_pred ccCcccccc---cceeecCCCCCcccChhhHHhhhcCCCCCCCCccccccccceeEeCCCCcccccc-----ccCCCCCC
Q 027217 15 GYGCKHYRR---RCRIRAPCCNEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVA-----QVCTNCGV 86 (226)
Q Consensus 15 ~~gC~HY~r---~c~l~~pCC~~~y~Cr~CHde~~~h~~~~~~~H~~~r~~~~~v~Cg~C~~~q~v~-----~~C~~Cg~ 86 (226)
++||.||++ +++|||.+|+|||+|++||||+++|++ +.++++.+..+.||||+|.++++++ +.||+|.+
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 689999998 789999999999999999999999886 7788888888999999999999885 57999999
Q ss_pred Ccce
Q 027217 87 NMGE 90 (226)
Q Consensus 87 ~f~~ 90 (226)
+||.
T Consensus 89 pFNp 92 (105)
T COG4357 89 PFNP 92 (105)
T ss_pred CCCc
Confidence 9986
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=99.45 E-value=2.6e-14 Score=94.59 Aligned_cols=44 Identities=39% Similarity=0.937 Sum_probs=37.6
Q ss_pred CCCccchhhcccCCcceeeeccCCccCHHHHHHHHhcCcCCCCCCC
Q 027217 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICS 196 (226)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCr 196 (226)
.+||||++++.+ .+.+..|+|||+||.+|+.+|++. +.+||+||
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 379999999655 678889999999999999999986 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=99.11 E-value=5.9e-11 Score=87.19 Aligned_cols=48 Identities=31% Similarity=0.688 Sum_probs=36.8
Q ss_pred CCCCCCccchhhcccC---------CcceeeeccCCccCHHHHHHHHhcCcCCCCCCC
Q 027217 148 SMHHHCPICYEYLFDS---------LRNTTVMKCGHTMHCECYHEMIKRDKYCCPICS 196 (226)
Q Consensus 148 ~~~~~CpICle~lf~s---------~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCr 196 (226)
..+.+|+||++.|.+. ..++...+|||.||..||.+||+. +.+||+||
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 3456799999998443 234556689999999999999985 66999997
No 6
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=99.06 E-value=4.9e-11 Score=111.08 Aligned_cols=57 Identities=26% Similarity=0.742 Sum_probs=48.8
Q ss_pred CCCCCCCccchhhcccCC---------cceeeeccCCccCHHHHHHHHhcCcCCCCCCCee-cccchH
Q 027217 147 NSMHHHCPICYEYLFDSL---------RNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKS-VIDMSR 204 (226)
Q Consensus 147 ~~~~~~CpICle~lf~s~---------~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrks-i~dm~~ 204 (226)
.+.+..|.||+|+|+.+. ...+.|||||.+|.+|++.|++ ++.+|||||.+ +.||+.
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 566788999999998876 2347899999999999999998 57899999999 678764
No 7
>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=99.05 E-value=1.7e-10 Score=73.78 Aligned_cols=45 Identities=31% Similarity=0.866 Sum_probs=37.7
Q ss_pred CCccchhhcccCCcceeeeccCCccCHHHHHHHHhcCcCCCCCCCeec
Q 027217 152 HCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSV 199 (226)
Q Consensus 152 ~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi 199 (226)
.|+||++.+ ..++..++|||.||..|+++|++..+.+||+|++.+
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 599999986 345666779999999999999986578899999764
No 8
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.97 E-value=2.4e-10 Score=106.07 Aligned_cols=50 Identities=22% Similarity=0.762 Sum_probs=44.7
Q ss_pred CCCccchhhcccCCcceeeeccCCccCHHHHHHHHhcCcCCCCCCCeeccc
Q 027217 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID 201 (226)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~d 201 (226)
..|.||||+ |..++.++.|||+|.||..|++.||......||+|+..+..
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 77789999999999999999999998654559999998874
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=98.93 E-value=6e-10 Score=72.06 Aligned_cols=39 Identities=38% Similarity=0.987 Sum_probs=33.4
Q ss_pred CccchhhcccCCcceeeeccCCccCHHHHHHHHhcCcCCCCCC
Q 027217 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPIC 195 (226)
Q Consensus 153 CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiC 195 (226)
||||++.+.+ ++++++|||+|...|+.+|++. +.+||+|
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 8999998554 7788999999999999999996 7899998
No 10
>PHA02929 N1R/p28-like protein; Provisional
Probab=98.89 E-value=1.3e-09 Score=96.76 Aligned_cols=54 Identities=30% Similarity=0.664 Sum_probs=42.6
Q ss_pred CCCCCCCccchhhcccCCc---c-eeeeccCCccCHHHHHHHHhcCcCCCCCCCeeccc
Q 027217 147 NSMHHHCPICYEYLFDSLR---N-TTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID 201 (226)
Q Consensus 147 ~~~~~~CpICle~lf~s~~---~-v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~d 201 (226)
.+.+..||||+|.+.+... . ...++|||.||..|+.+|++ .+.+||+||+.+..
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 3456789999999765321 1 23457999999999999998 47899999999874
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=72.21 Aligned_cols=47 Identities=36% Similarity=0.918 Sum_probs=38.7
Q ss_pred CCCCccchhhcccCCcceeeeccCCc-cCHHHHHHHHhcCcCCCCCCCeeccc
Q 027217 150 HHHCPICYEYLFDSLRNTTVMKCGHT-MHCECYHEMIKRDKYCCPICSKSVID 201 (226)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCGH~-~H~~C~~~~l~~~~~~CPiCrksi~d 201 (226)
+..|+||++. ...+..+||||. |...|+.+|+. ...+||+||+.|.+
T Consensus 2 ~~~C~iC~~~----~~~~~~~pCgH~~~C~~C~~~~~~-~~~~CP~Cr~~i~~ 49 (50)
T PF13920_consen 2 DEECPICFEN----PRDVVLLPCGHLCFCEECAERLLK-RKKKCPICRQPIES 49 (50)
T ss_dssp HSB-TTTSSS----BSSEEEETTCEEEEEHHHHHHHHH-TTSBBTTTTBB-SE
T ss_pred cCCCccCCcc----CCceEEeCCCChHHHHHHhHHhcc-cCCCCCcCChhhcC
Confidence 3579999997 235788999999 99999999998 57899999999864
No 12
>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=98.78 E-value=3.8e-09 Score=68.35 Aligned_cols=40 Identities=33% Similarity=0.938 Sum_probs=34.5
Q ss_pred CccchhhcccCCcceeeeccCCccCHHHHHHHHh-cCcCCCCCC
Q 027217 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIK-RDKYCCPIC 195 (226)
Q Consensus 153 CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~-~~~~~CPiC 195 (226)
||||++.+.+ ++..++|||.|+..|+.+|++ ....+||+|
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 8999998443 456899999999999999998 568889998
No 13
>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=98.77 E-value=5.9e-09 Score=64.27 Aligned_cols=39 Identities=44% Similarity=1.076 Sum_probs=33.6
Q ss_pred CccchhhcccCCcceeeeccCCccCHHHHHHHHhcCcCCCCCC
Q 027217 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPIC 195 (226)
Q Consensus 153 CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiC 195 (226)
|+||++. .+....++|||.||..|+++|++....+||+|
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 34677899999999999999998556789987
No 14
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.69 E-value=9.3e-09 Score=93.93 Aligned_cols=53 Identities=25% Similarity=0.601 Sum_probs=45.6
Q ss_pred cCCCCCCCccchhhcccCCcceeeeccCCccCHHHHHHHHhcCcCCCCCCCeec
Q 027217 146 ENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSV 199 (226)
Q Consensus 146 e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi 199 (226)
|....-+|.|||++ |...+.+++|||.|.||..|+++|+...+.+||+||..+
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 667888999999999999999999986678999999765
No 15
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.67 E-value=1.5e-08 Score=67.25 Aligned_cols=44 Identities=34% Similarity=0.849 Sum_probs=37.8
Q ss_pred CCccchhhcccCCcceeeeccCCccCHHHHHHHHhcCcCCCCCCCe
Q 027217 152 HCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSK 197 (226)
Q Consensus 152 ~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrk 197 (226)
.|+||++.+ +...+..+|+|||+|...|+..+. .....||+|+|
T Consensus 1 ~C~~C~~~~-~~~~~~~l~~CgH~~C~~C~~~~~-~~~~~CP~C~k 44 (44)
T PF14634_consen 1 HCNICFEKY-SEERRPRLTSCGHIFCEKCLKKLK-GKSVKCPICRK 44 (44)
T ss_pred CCcCcCccc-cCCCCeEEcccCCHHHHHHHHhhc-CCCCCCcCCCC
Confidence 489999996 556678889999999999999998 35789999986
No 16
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.54 E-value=5.7e-08 Score=64.31 Aligned_cols=39 Identities=33% Similarity=0.985 Sum_probs=28.3
Q ss_pred CccchhhcccCCcceeeeccCCccCHHHHHHHHhcCc---CCCCCC
Q 027217 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDK---YCCPIC 195 (226)
Q Consensus 153 CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~---~~CPiC 195 (226)
||||++.|.+ .+.|+|||+|-..|+.+|.+... +.||+|
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 8999998544 34699999999999999987532 579987
No 17
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.50 E-value=7.1e-08 Score=64.48 Aligned_cols=40 Identities=33% Similarity=0.890 Sum_probs=23.9
Q ss_pred CccchhhcccCCcceeeeccCCccCHHHHHHHHhcC---cCCCC
Q 027217 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRD---KYCCP 193 (226)
Q Consensus 153 CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~---~~~CP 193 (226)
||||.| +.+...+.++|+|||+|-++|+++|++.+ ..+||
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 55545566789999999999999999843 56677
No 18
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=98.50 E-value=1e-07 Score=72.44 Aligned_cols=47 Identities=28% Similarity=0.499 Sum_probs=33.1
Q ss_pred CCCccchhhcccCCcceeeeccCCccCHHHHHHHHhc--CcCCCCCCCeec
Q 027217 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR--DKYCCPICSKSV 199 (226)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~--~~~~CPiCrksi 199 (226)
+.||.|..+-.+ -++..-.|||.||..||.+||.. .+.+||+||+..
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 445555544211 23344469999999999999985 357899999865
No 19
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.46 E-value=4.7e-08 Score=95.43 Aligned_cols=52 Identities=27% Similarity=0.629 Sum_probs=43.2
Q ss_pred CCCCCCCccchhhcccCC-cceeeeccCCccCHHHHHHHHhcCcCCCCCCCeec
Q 027217 147 NSMHHHCPICYEYLFDSL-RNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSV 199 (226)
Q Consensus 147 ~~~~~~CpICle~lf~s~-~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi 199 (226)
......|+||+|.|+.+. ...+.|+|||.||..|+.+|++. ..+||+||..+
T Consensus 288 ~~~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er-~qtCP~CR~~~ 340 (543)
T KOG0802|consen 288 ALSDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFER-QQTCPTCRTVL 340 (543)
T ss_pred hhcCCeeeeechhhccccccccceeecccchHHHHHHHHHHH-hCcCCcchhhh
Confidence 455778999999998742 22578999999999999999994 78999999933
No 20
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.39 E-value=2.7e-07 Score=79.73 Aligned_cols=54 Identities=24% Similarity=0.628 Sum_probs=41.2
Q ss_pred eecCCCCCCCccchhhcccCCcceeeeccCCccCHHHHHHHHhc---------------CcCCCCCCCeeccc
Q 027217 144 CIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR---------------DKYCCPICSKSVID 201 (226)
Q Consensus 144 C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~---------------~~~~CPiCrksi~d 201 (226)
=++...+..||||++.+. ..++++|||.|+..|+.+|+.. +..+||+|+..|..
T Consensus 12 ~~~~~~~~~CpICld~~~----dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~ 80 (193)
T PLN03208 12 LVDSGGDFDCNICLDQVR----DPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE 80 (193)
T ss_pred eccCCCccCCccCCCcCC----CcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence 344455678999999743 2345789999999999999852 23589999999864
No 21
>PHA02926 zinc finger-like protein; Provisional
Probab=98.37 E-value=2.7e-07 Score=81.32 Aligned_cols=69 Identities=20% Similarity=0.382 Sum_probs=47.8
Q ss_pred cccccccCcceeecCCCCCCCccchhhcccCC-----cceeeeccCCccCHHHHHHHHhcC-----cCCCCCCCeeccc
Q 027217 133 CYSTSLRNNHLCIENSMHHHCPICYEYLFDSL-----RNTTVMKCGHTMHCECYHEMIKRD-----KYCCPICSKSVID 201 (226)
Q Consensus 133 C~s~~l~~~H~C~e~~~~~~CpICle~lf~s~-----~~v~~LpCGH~~H~~C~~~~l~~~-----~~~CPiCrksi~d 201 (226)
++..-|.+-..=.+.+.+..|+||||.+++.+ ......+|+|.|+..|+.+|.+.. ..+||+||..+..
T Consensus 153 ~i~~il~~ye~~~~~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~ 231 (242)
T PHA02926 153 DIIKILDKYEDVYRVSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFRN 231 (242)
T ss_pred chhHHHHHHHHHHhccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceeee
Confidence 44444433333344577889999999876531 123445899999999999999742 3459999998763
No 22
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.19 E-value=7.3e-07 Score=76.09 Aligned_cols=46 Identities=30% Similarity=0.829 Sum_probs=37.8
Q ss_pred CCCccchhhcccCCcce-eeeccCCccCHHHHHHHHhcCcCCCCCCCeecc
Q 027217 151 HHCPICYEYLFDSLRNT-TVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (226)
Q Consensus 151 ~~CpICle~lf~s~~~v-~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (226)
..|||||+. ++. .+ ..-.|||+|.+.|++..++. ..+||+|+|.|.
T Consensus 132 ~~CPiCl~~-~se--k~~vsTkCGHvFC~~Cik~alk~-~~~CP~C~kkIt 178 (187)
T KOG0320|consen 132 YKCPICLDS-VSE--KVPVSTKCGHVFCSQCIKDALKN-TNKCPTCRKKIT 178 (187)
T ss_pred cCCCceecc-hhh--ccccccccchhHHHHHHHHHHHh-CCCCCCcccccc
Confidence 689999998 432 33 34689999999999999985 679999999665
No 23
>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=98.11 E-value=3.2e-06 Score=58.85 Aligned_cols=45 Identities=18% Similarity=0.361 Sum_probs=38.0
Q ss_pred CCCccchhhcccCCcceeeeccCCccCHHHHHHHHhcCcCCCCCCCeecc
Q 027217 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (226)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (226)
-.||||++.|.+ + .+++|||+|-+.|+.+|++. +.+||+|++.+.
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 369999997544 4 45799999999999999985 789999999874
No 24
>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=98.07 E-value=2.9e-06 Score=57.97 Aligned_cols=43 Identities=28% Similarity=0.617 Sum_probs=33.3
Q ss_pred CCccchhhcccCCcceeeeccC-----CccCHHHHHHHHhcC-cCCCCCCC
Q 027217 152 HCPICYEYLFDSLRNTTVMKCG-----HTMHCECYHEMIKRD-KYCCPICS 196 (226)
Q Consensus 152 ~CpICle~lf~s~~~v~~LpCG-----H~~H~~C~~~~l~~~-~~~CPiCr 196 (226)
.|-||++ +++.+...++||. |++|..|+.+|+..+ +.+||||+
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 3334555678984 999999999999753 55899995
No 25
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=98.04 E-value=2e-06 Score=82.11 Aligned_cols=47 Identities=28% Similarity=0.757 Sum_probs=42.8
Q ss_pred CCCccchhhcccCCcceeeeccCCccCHHHHHHHHhcCcCCCCCCCeecc
Q 027217 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (226)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (226)
..||||||.|.+|++.+....|.|+||..|+..|. ..+||+||-...
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 47999999999999999999999999999999995 579999997766
No 26
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=97.96 E-value=2e-06 Score=62.80 Aligned_cols=51 Identities=31% Similarity=0.656 Sum_probs=24.0
Q ss_pred CCCCccchhhcc-cCCcceeee---ccCCccCHHHHHHHHhc--C--------cCCCCCCCeecc
Q 027217 150 HHHCPICYEYLF-DSLRNTTVM---KCGHTMHCECYHEMIKR--D--------KYCCPICSKSVI 200 (226)
Q Consensus 150 ~~~CpICle~lf-~s~~~v~~L---pCGH~~H~~C~~~~l~~--~--------~~~CPiCrksi~ 200 (226)
+.+|+||.+++. +...+..+- .|+..||..|+.+|+.. . ..+||.|++.|.
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 457999999866 333333333 59999999999999873 1 236999999885
No 27
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.91 E-value=9.1e-06 Score=77.12 Aligned_cols=47 Identities=21% Similarity=0.594 Sum_probs=38.8
Q ss_pred CCCCccchhhcccCCcceeeeccCCccCHHHHHHHHhcCcCCCCCCCeeccc
Q 027217 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID 201 (226)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~d 201 (226)
...|+||++.+.. ++ +++|||.|+..|+..|+.. ...||+|+..+..
T Consensus 26 ~l~C~IC~d~~~~---Pv-itpCgH~FCs~CI~~~l~~-~~~CP~Cr~~~~~ 72 (397)
T TIGR00599 26 SLRCHICKDFFDV---PV-LTSCSHTFCSLCIRRCLSN-QPKCPLCRAEDQE 72 (397)
T ss_pred ccCCCcCchhhhC---cc-CCCCCCchhHHHHHHHHhC-CCCCCCCCCcccc
Confidence 4589999997543 33 6899999999999999985 5689999998763
No 28
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=97.85 E-value=1.3e-05 Score=60.39 Aligned_cols=48 Identities=23% Similarity=0.482 Sum_probs=33.2
Q ss_pred CCccchhhcccCCcceeee-ccCCccCHHHHHHHHhcCcCCCCCCCeecc
Q 027217 152 HCPICYEYLFDSLRNTTVM-KCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (226)
Q Consensus 152 ~CpICle~lf~s~~~v~~L-pCGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (226)
.||-|.-.+-...+-..+. -|.|.||..|+..||.+ ...||+++++..
T Consensus 33 ~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~T-k~~CPld~q~w~ 81 (88)
T COG5194 33 TCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDT-KGVCPLDRQTWV 81 (88)
T ss_pred cCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhh-CCCCCCCCceeE
Confidence 4555554442222222233 59999999999999985 689999998764
No 29
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=97.85 E-value=3.4e-06 Score=60.49 Aligned_cols=22 Identities=32% Similarity=0.552 Sum_probs=0.0
Q ss_pred cccchHHHHHHHHHHHhCCCCC
Q 027217 199 VIDMSRTWKRIDEELQMNSSIF 220 (226)
Q Consensus 199 i~dm~~~~~~lD~~i~~~pm~~ 220 (226)
|+||+++|++||++|+++|||.
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 5799999999999999999964
No 30
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=97.71 E-value=1.5e-05 Score=72.54 Aligned_cols=46 Identities=26% Similarity=0.661 Sum_probs=38.1
Q ss_pred CCCccchhhcccCCcceeeeccCCccCHHHHHHHHhcCcCCCCCCCeeccc
Q 027217 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID 201 (226)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~d 201 (226)
..|.+|||...+ ....||||.|.-.|+.+|... ...||+||..+-.
T Consensus 240 ~kC~LCLe~~~~----pSaTpCGHiFCWsCI~~w~~e-k~eCPlCR~~~~p 285 (293)
T KOG0317|consen 240 RKCSLCLENRSN----PSATPCGHIFCWSCILEWCSE-KAECPLCREKFQP 285 (293)
T ss_pred CceEEEecCCCC----CCcCcCcchHHHHHHHHHHcc-ccCCCcccccCCC
Confidence 469999998433 347899999999999999985 5679999987653
No 31
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.68 E-value=1.8e-05 Score=74.69 Aligned_cols=46 Identities=28% Similarity=0.624 Sum_probs=39.4
Q ss_pred CCCCccchhhcccCCcceeeec-cCCccCHHHHHHHHhcC--cCCCCCCC
Q 027217 150 HHHCPICYEYLFDSLRNTTVMK-CGHTMHCECYHEMIKRD--KYCCPICS 196 (226)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~Lp-CGH~~H~~C~~~~l~~~--~~~CPiCr 196 (226)
...|.|| ++++.....+..+. |||+||..|+.+|++.. +.+||||+
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 77888888888886 99999999999999853 35899999
No 32
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.67 E-value=3.8e-05 Score=70.74 Aligned_cols=51 Identities=25% Similarity=0.554 Sum_probs=38.8
Q ss_pred CCCCccchhhcccCCcc-eeeeccCCccCHHHHHHHHhcCcCCCCCCCeecc
Q 027217 150 HHHCPICYEYLFDSLRN-TTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (226)
Q Consensus 150 ~~~CpICle~lf~s~~~-v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (226)
+..||||+.+.+.+.+- +.+.+|||.|..+|++.++..+...||+|++++-
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 35799999975544332 2222799999999999977666779999998875
No 33
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.67 E-value=2.2e-05 Score=66.18 Aligned_cols=44 Identities=30% Similarity=0.855 Sum_probs=37.9
Q ss_pred CCCCCccchhhcccCCcceeeeccCCccCHHHHHHHHhcCcCCCCCCCe
Q 027217 149 MHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSK 197 (226)
Q Consensus 149 ~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrk 197 (226)
.+..||||++++... .+|||||+|-..|+..++. ....||.||.
T Consensus 12 ~~~~C~iC~~~~~~p----~~l~C~H~~c~~C~~~~~~-~~~~Cp~cr~ 55 (386)
T KOG2177|consen 12 EELTCPICLEYFREP----VLLPCGHNFCRACLTRSWE-GPLSCPVCRP 55 (386)
T ss_pred ccccChhhHHHhhcC----ccccccchHhHHHHHHhcC-CCcCCcccCC
Confidence 456899999995542 7899999999999999987 6789999994
No 34
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.55 E-value=3e-05 Score=75.03 Aligned_cols=51 Identities=22% Similarity=0.523 Sum_probs=37.8
Q ss_pred CCCCccchhhccc--CCcc-----------eeeeccCCccCHHHHHHHHhcCcCCCCCCCeecc
Q 027217 150 HHHCPICYEYLFD--SLRN-----------TTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (226)
Q Consensus 150 ~~~CpICle~lf~--s~~~-----------v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (226)
..+|+|||.++-- ...+ ..+-||.|.||+.|+++|+...+..||+||..+-
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 4579999987421 1111 2334999999999999999866778999997653
No 35
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.41 E-value=8e-05 Score=72.22 Aligned_cols=50 Identities=28% Similarity=0.618 Sum_probs=38.4
Q ss_pred CCCCCCccchhhcccCCcceeeeccCCccCHHHHHHHHhcC----cCCCCCCCeeccc
Q 027217 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRD----KYCCPICSKSVID 201 (226)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~----~~~CPiCrksi~d 201 (226)
+++..|||||++ .. -...+.|||+|.-.||-+|+... --.||||+..|.-
T Consensus 184 ~t~~~CPICL~~-~~---~p~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~ 237 (513)
T KOG2164|consen 184 STDMQCPICLEP-PS---VPVRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITL 237 (513)
T ss_pred CcCCcCCcccCC-CC---cccccccCceeeHHHHHHHHhhhcccCCccCCchhhhccc
Confidence 458899999998 22 22344599999999999987642 4579999999864
No 36
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.41 E-value=9.8e-05 Score=65.33 Aligned_cols=50 Identities=24% Similarity=0.575 Sum_probs=38.1
Q ss_pred CCCCCCccchhhcccCCcceeeeccCCccCHHHHHHHHhcC--cCCCCCCCeeccc
Q 027217 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRD--KYCCPICSKSVID 201 (226)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~--~~~CPiCrksi~d 201 (226)
+..-+|-||||- +.++ ++-.|||.|.-.||.+||... +..||+|+..|.+
T Consensus 45 ~~~FdCNICLd~---akdP-VvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~ 96 (230)
T KOG0823|consen 45 GGFFDCNICLDL---AKDP-VVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSI 96 (230)
T ss_pred CCceeeeeeccc---cCCC-EEeecccceehHHHHHHHhhcCCCeeCCcccccccc
Confidence 445689999986 2334 456699999999999999753 4458999987764
No 37
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.27 E-value=6.5e-05 Score=68.13 Aligned_cols=52 Identities=27% Similarity=0.515 Sum_probs=41.6
Q ss_pred CCCCCccchhhcccCCc------ceeeeccCCccCHHHHHHHHh-cCcCCCCCCCeecc
Q 027217 149 MHHHCPICYEYLFDSLR------NTTVMKCGHTMHCECYHEMIK-RDKYCCPICSKSVI 200 (226)
Q Consensus 149 ~~~~CpICle~lf~s~~------~v~~LpCGH~~H~~C~~~~l~-~~~~~CPiCrksi~ 200 (226)
+++.|.||...++.|.+ ..-.|.|+|+||..|++-|-. .+..+||.|++.+.
T Consensus 223 ~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVd 281 (328)
T KOG1734|consen 223 SDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVD 281 (328)
T ss_pred CcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhh
Confidence 45679999998777652 456799999999999999953 35789999998764
No 38
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=97.26 E-value=0.0001 Score=53.49 Aligned_cols=56 Identities=23% Similarity=0.654 Sum_probs=29.3
Q ss_pred CCCccchhhcccCCcceeeeccCCccCHHHHHHHHhcCcCCCCCCCeecc--cchHHHHHHHHHH
Q 027217 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI--DMSRTWKRIDEEL 213 (226)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~--dm~~~~~~lD~~i 213 (226)
..|++|.+.|.. +|..-.|.|+|-+.|+.+-+. +.||+|+.+.. |+ ...|.||..|
T Consensus 8 LrCs~C~~~l~~---pv~l~~CeH~fCs~Ci~~~~~---~~CPvC~~Paw~qD~-~~NrqLd~~i 65 (65)
T PF14835_consen 8 LRCSICFDILKE---PVCLGGCEHIFCSSCIRDCIG---SECPVCHTPAWIQDI-QINRQLDSMI 65 (65)
T ss_dssp TS-SSS-S--SS----B---SSS--B-TTTGGGGTT---TB-SSS--B-S-SS-----HHHHHHH
T ss_pred cCCcHHHHHhcC---CceeccCccHHHHHHhHHhcC---CCCCCcCChHHHHHH-HhhhhhhccC
Confidence 369999998654 666678999999999988653 56999999985 44 2678888765
No 39
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=97.20 E-value=0.00029 Score=65.86 Aligned_cols=58 Identities=29% Similarity=0.673 Sum_probs=44.1
Q ss_pred CCccchhhcccCCcceeeeccCCccCHHHHHHHHhcCcCCCCCCCeecccch-HHHHHHHHHHH
Q 027217 152 HCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMS-RTWKRIDEELQ 214 (226)
Q Consensus 152 ~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~dm~-~~~~~lD~~i~ 214 (226)
-|-||.|+|.- ..+.||||+|.+-||+.+|. .+-.||.|...+.+.. ..-+.||++|+
T Consensus 25 RC~IC~eyf~i----p~itpCsHtfCSlCIR~~L~-~~p~CP~C~~~~~Es~Lr~n~il~Eiv~ 83 (442)
T KOG0287|consen 25 RCGICFEYFNI----PMITPCSHTFCSLCIRKFLS-YKPQCPTCCVTVTESDLRNNRILDEIVK 83 (442)
T ss_pred HHhHHHHHhcC----ceeccccchHHHHHHHHHhc-cCCCCCceecccchhhhhhhhHHHHHHH
Confidence 59999998443 34568999999999999998 4789999999887422 24455666554
No 40
>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=97.18 E-value=0.00041 Score=50.59 Aligned_cols=47 Identities=19% Similarity=0.379 Sum_probs=35.6
Q ss_pred CCCccchhhcccCCcceeeeccCCccCHHHHHHHHhcCcCCCCCCCeeccc
Q 027217 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID 201 (226)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~d 201 (226)
-.|||+++-|.+ +| ++|+||+|=+.++++|+.....+||+++..+..
T Consensus 5 f~CpIt~~lM~d---PV-i~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~ 51 (73)
T PF04564_consen 5 FLCPITGELMRD---PV-ILPSGHTYERSAIERWLEQNGGTDPFTRQPLSE 51 (73)
T ss_dssp GB-TTTSSB-SS---EE-EETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SG
T ss_pred cCCcCcCcHhhC---ce-eCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCc
Confidence 469999997554 44 689999999999999998668999999988764
No 41
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=97.04 E-value=0.00023 Score=53.35 Aligned_cols=29 Identities=24% Similarity=0.707 Sum_probs=24.7
Q ss_pred ccCCccCHHHHHHHHhc--CcCCCCCCCeec
Q 027217 171 KCGHTMHCECYHEMIKR--DKYCCPICSKSV 199 (226)
Q Consensus 171 pCGH~~H~~C~~~~l~~--~~~~CPiCrksi 199 (226)
-|-|.||..|+.+|+.. ++..||+||+..
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 456799999864
No 42
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=97.00 E-value=0.00016 Score=68.49 Aligned_cols=62 Identities=26% Similarity=0.573 Sum_probs=50.6
Q ss_pred cceeecCCCCCCCccchhhcccCCcceeeeccCCccCHHHHHHHHhc-CcCCCCCCCeecccch
Q 027217 141 NHLCIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR-DKYCCPICSKSVIDMS 203 (226)
Q Consensus 141 ~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~-~~~~CPiCrksi~dm~ 203 (226)
.|.|++ .++-+|-.|.|.+-...+....|||.|+||..|+.++|.+ ...+||-|||.+..|+
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 345553 4678999999998777788899999999999999999864 3567999998777665
No 43
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.81 E-value=0.00085 Score=62.70 Aligned_cols=50 Identities=26% Similarity=0.644 Sum_probs=40.6
Q ss_pred CCCCCCCccchhhcccCCcceeeeccCCc-cCHHHHHHHHhcCcCCCCCCCeeccc
Q 027217 147 NSMHHHCPICYEYLFDSLRNTTVMKCGHT-MHCECYHEMIKRDKYCCPICSKSVID 201 (226)
Q Consensus 147 ~~~~~~CpICle~lf~s~~~v~~LpCGH~-~H~~C~~~~l~~~~~~CPiCrksi~d 201 (226)
+....+|.|||.+ ...+.+|||-|+ +.+.|-+.+.- ...+|||||..|..
T Consensus 287 ~~~gkeCVIClse----~rdt~vLPCRHLCLCs~Ca~~Lr~-q~n~CPICRqpi~~ 337 (349)
T KOG4265|consen 287 SESGKECVICLSE----SRDTVVLPCRHLCLCSGCAKSLRY-QTNNCPICRQPIEE 337 (349)
T ss_pred ccCCCeeEEEecC----CcceEEecchhhehhHhHHHHHHH-hhcCCCccccchHh
Confidence 3445689999987 456789999996 89999998863 56789999998874
No 44
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.73 E-value=0.00077 Score=60.87 Aligned_cols=47 Identities=26% Similarity=0.548 Sum_probs=37.3
Q ss_pred CCCCccchhhcccCCcceeeeccCCccCHHHHHH-HHhcCcCCCCCCCeecc
Q 027217 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHE-MIKRDKYCCPICSKSVI 200 (226)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~-~l~~~~~~CPiCrksi~ 200 (226)
+-.|+||+|... .....+|||+|.-.|+.. |...+...||+||.-+.
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 446999999744 345789999999999999 88754344999997765
No 45
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=96.51 E-value=0.0021 Score=44.05 Aligned_cols=44 Identities=30% Similarity=0.828 Sum_probs=24.2
Q ss_pred CccchhhcccCCcceeee--ccCCccCHHHHHHHHhcCcCCCCCCCee
Q 027217 153 CPICYEYLFDSLRNTTVM--KCGHTMHCECYHEMIKRDKYCCPICSKS 198 (226)
Q Consensus 153 CpICle~lf~s~~~v~~L--pCGH~~H~~C~~~~l~~~~~~CPiCrks 198 (226)
||+|.|+|..+ ...++ +||.-|-+.|+..-+++.+.+||-||+.
T Consensus 1 cp~C~e~~d~~--d~~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~ 46 (48)
T PF14570_consen 1 CPLCDEELDET--DKDFYPCECGFQICRFCYHDILENEGGRCPGCREP 46 (48)
T ss_dssp -TTTS-B--CC--CTT--SSTTS----HHHHHHHTTSS-SB-TTT--B
T ss_pred CCCcccccccC--CCccccCcCCCcHHHHHHHHHHhccCCCCCCCCCC
Confidence 79999998443 44455 4799999999999987668899999975
No 46
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=96.44 E-value=0.0019 Score=51.07 Aligned_cols=27 Identities=30% Similarity=0.791 Sum_probs=24.4
Q ss_pred ccCCccCHHHHHHHHhcCcCCCCCCCee
Q 027217 171 KCGHTMHCECYHEMIKRDKYCCPICSKS 198 (226)
Q Consensus 171 pCGH~~H~~C~~~~l~~~~~~CPiCrks 198 (226)
-|.|.||..|+..||+. ...|||+.|.
T Consensus 80 ~CNHaFH~hCisrWlkt-r~vCPLdn~e 106 (114)
T KOG2930|consen 80 VCNHAFHFHCISRWLKT-RNVCPLDNKE 106 (114)
T ss_pred ecchHHHHHHHHHHHhh-cCcCCCcCcc
Confidence 59999999999999995 6799999875
No 47
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=96.43 E-value=0.001 Score=67.77 Aligned_cols=76 Identities=16% Similarity=0.294 Sum_probs=55.3
Q ss_pred eeeccccCccccccccCcceeec-CCCCCCCccchhhcccCCcceeeeccCCccCHHHHHHHHhcCcCCCCCCCeeccc
Q 027217 124 YFHCKRCGSCYSTSLRNNHLCIE-NSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID 201 (226)
Q Consensus 124 ~fHC~~C~~C~s~~l~~~H~C~e-~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~d 201 (226)
-..|..|-.+.|...-..-.|+- +-.+..||+|+....+ .......+|+|.||..||..|.+. ..+|||||+.++.
T Consensus 96 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 96 SDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCND-QLEESEKHTAHYFCEECVGSWSRC-AQTCPVDRGEFGE 172 (1134)
T ss_pred ccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHH-HhhccccccccccHHHHhhhhhhh-cccCchhhhhhhe
Confidence 45566777777764434455552 3446679999987444 444556789999999999999984 6899999998764
No 48
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=96.41 E-value=0.0014 Score=67.87 Aligned_cols=53 Identities=26% Similarity=0.622 Sum_probs=38.7
Q ss_pred CCCCCCCccchhhcc--cCCcceee-eccCCccCHHHHHHHHhc-CcCCCCCCCeec
Q 027217 147 NSMHHHCPICYEYLF--DSLRNTTV-MKCGHTMHCECYHEMIKR-DKYCCPICSKSV 199 (226)
Q Consensus 147 ~~~~~~CpICle~lf--~s~~~v~~-LpCGH~~H~~C~~~~l~~-~~~~CPiCrksi 199 (226)
-+...+|+||..-|. +..-|.+. -.|.|.||..|+.+|.++ ++.+||+||.+|
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 355789999998765 22222222 237799999999999985 477899999765
No 49
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.27 E-value=0.0011 Score=62.06 Aligned_cols=49 Identities=27% Similarity=0.688 Sum_probs=41.4
Q ss_pred CCCCccchhhcccCCcceeeeccCCccCHHHHHHHHhcCcCCCCCCCeeccc
Q 027217 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID 201 (226)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~d 201 (226)
+-.|||||+-|.. ......|+|-|...||..-++..+..||-|||.++.
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 455678999999999998888888999999999963
No 50
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.26 E-value=0.0011 Score=46.94 Aligned_cols=53 Identities=36% Similarity=0.783 Sum_probs=37.9
Q ss_pred CCCCCCccchhhcccCCcceeeeccCCc-cCHHHHHHHHhcCcCCCCCCCeecccchH
Q 027217 148 SMHHHCPICYEYLFDSLRNTTVMKCGHT-MHCECYHEMIKRDKYCCPICSKSVIDMSR 204 (226)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~-~H~~C~~~~l~~~~~~CPiCrksi~dm~~ 204 (226)
+...+|.||+|.-.+| +..-|||+ |.-.|-.+.++.....|||||..|-|.-+
T Consensus 5 ~~~dECTICye~pvds----VlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~dvIk 58 (62)
T KOG4172|consen 5 QWSDECTICYEHPVDS----VLYTCGHMCMCYACGLRLKKALHGCCPICRAPIKDVIK 58 (62)
T ss_pred ccccceeeeccCcchH----HHHHcchHHhHHHHHHHHHHccCCcCcchhhHHHHHHH
Confidence 3457899999973332 23479996 66677666555467899999999877543
No 51
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=96.26 E-value=0.0027 Score=44.72 Aligned_cols=44 Identities=27% Similarity=0.563 Sum_probs=30.2
Q ss_pred CCCCCCccchhhcccCCcceeeeccCCccCHHHHHHHHh-cCcCCCCC
Q 027217 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIK-RDKYCCPI 194 (226)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~-~~~~~CPi 194 (226)
.....|||-+..|- +||+...|||+|=+.-+.+|+. .+..+||+
T Consensus 9 ~~~~~CPiT~~~~~---~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv 53 (57)
T PF11789_consen 9 TISLKCPITLQPFE---DPVKSKKCGHTFEKEAILQYIQRNGSKRCPV 53 (57)
T ss_dssp B--SB-TTTSSB-S---SEEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred EeccCCCCcCChhh---CCcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence 33467999999744 4899999999999999999993 35678998
No 52
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=96.18 E-value=0.0048 Score=56.76 Aligned_cols=59 Identities=19% Similarity=0.555 Sum_probs=46.5
Q ss_pred CCCCccchhhcccCCcceeeecc--CCccCHHHHHHHHhcCcCCCCCCCeecccchHHHHHHHHHHHhCCCC
Q 027217 150 HHHCPICYEYLFDSLRNTTVMKC--GHTMHCECYHEMIKRDKYCCPICSKSVIDMSRTWKRIDEELQMNSSI 219 (226)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpC--GH~~H~~C~~~~l~~~~~~CPiCrksi~dm~~~~~~lD~~i~~~pm~ 219 (226)
-.+||||.++|..+ .+.| ||+.-+.|-.+. ..+||.|+..|.+.. =+.++..|++.+.|
T Consensus 48 lleCPvC~~~l~~P-----i~QC~nGHlaCssC~~~~----~~~CP~Cr~~~g~~R--~~amEkV~e~~~vp 108 (299)
T KOG3002|consen 48 LLDCPVCFNPLSPP-----IFQCDNGHLACSSCRTKV----SNKCPTCRLPIGNIR--CRAMEKVAEAVLVP 108 (299)
T ss_pred hccCchhhccCccc-----ceecCCCcEehhhhhhhh----cccCCccccccccHH--HHHHHHHHHhceec
Confidence 35899999997653 5788 899999999753 469999999999764 36777778877654
No 53
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=96.15 E-value=0.0016 Score=65.76 Aligned_cols=47 Identities=23% Similarity=0.635 Sum_probs=40.6
Q ss_pred CCCccchhhcccCCcceeeeccCCccCHHHHHHHHhcCcCCCCCCCeeccc
Q 027217 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID 201 (226)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~d 201 (226)
-.||+|-+. ...++...|||.|...|++..+..+..+||.|+.+++.
T Consensus 644 LkCs~Cn~R----~Kd~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFga 690 (698)
T KOG0978|consen 644 LKCSVCNTR----WKDAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGA 690 (698)
T ss_pred eeCCCccCc----hhhHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCc
Confidence 469999865 34566778999999999999999889999999999983
No 54
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=95.99 E-value=0.0021 Score=61.29 Aligned_cols=54 Identities=26% Similarity=0.608 Sum_probs=44.5
Q ss_pred eecCCCCCCCccchhhcccCCcceeeeccCCccCHHHHHHHHhcC-cCCCCCCCeeccc
Q 027217 144 CIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRD-KYCCPICSKSVID 201 (226)
Q Consensus 144 C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~-~~~CPiCrksi~d 201 (226)
|.-+++-+.|-||.|. ...|++=||||.+...|+..|-.+. ..+||.||-.|--
T Consensus 363 ceMgsTFeLCKICaen----dKdvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKG 417 (563)
T KOG1785|consen 363 CEMGSTFELCKICAEN----DKDVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIKG 417 (563)
T ss_pred HHccchHHHHHHhhcc----CCCcccccccchHHHHHHHhhcccCCCCCCCceeeEecc
Confidence 3336777889999986 5678888999999999999998543 6799999988743
No 55
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=95.96 E-value=0.0047 Score=66.58 Aligned_cols=74 Identities=26% Similarity=0.628 Sum_probs=56.0
Q ss_pred CCccceeeccccCccccccccCcceeecCCCCCCCccchhhcccCCcceeeeccCCccCHHHHHHHHhc---------Cc
Q 027217 119 GGRENYFHCKRCGSCYSTSLRNNHLCIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR---------DK 189 (226)
Q Consensus 119 G~~~~~fHC~~C~~C~s~~l~~~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~---------~~ 189 (226)
||.+|-.||--|-.|-.-.. ....+..|.||..+ .-+..+.+.|.|||+||..|.+..|++ +-
T Consensus 3462 GGvkNEE~CLPCl~Cdks~t-------kQD~DDmCmICFTE-~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~F 3533 (3738)
T KOG1428|consen 3462 GGVKNEEHCLPCLHCDKSAT-------KQDADDMCMICFTE-ALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGF 3533 (3738)
T ss_pred cCccchhhcccccccChhhh-------hcccCceEEEEehh-hhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEee
Confidence 56778888888877643321 23446679999987 444678999999999999999987764 24
Q ss_pred CCCCCCCeecc
Q 027217 190 YCCPICSKSVI 200 (226)
Q Consensus 190 ~~CPiCrksi~ 200 (226)
.+||||...|.
T Consensus 3534 isCPiC~n~In 3544 (3738)
T KOG1428|consen 3534 ISCPICKNKIN 3544 (3738)
T ss_pred eecccccchhh
Confidence 57999998875
No 56
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.93 E-value=0.0059 Score=58.28 Aligned_cols=49 Identities=27% Similarity=0.728 Sum_probs=37.9
Q ss_pred CCCCccchhhcccCCc-ceeeeccCCccCHHHHHHHHhc-CcCCCCCCCee
Q 027217 150 HHHCPICYEYLFDSLR-NTTVMKCGHTMHCECYHEMIKR-DKYCCPICSKS 198 (226)
Q Consensus 150 ~~~CpICle~lf~s~~-~v~~LpCGH~~H~~C~~~~l~~-~~~~CPiCrks 198 (226)
...|||||+..-.+.+ .+..|.|||.|=++|++.||.. ....||+|.-.
T Consensus 4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~k 54 (463)
T KOG1645|consen 4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGK 54 (463)
T ss_pred cccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCCh
Confidence 4579999998755444 4556789999999999999952 24569999744
No 57
>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=95.87 E-value=0.0038 Score=47.24 Aligned_cols=38 Identities=24% Similarity=0.528 Sum_probs=30.4
Q ss_pred eeecCCCCCCCccchhhcccCCcceeeeccCCccCHHHHH
Q 027217 143 LCIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYH 182 (226)
Q Consensus 143 ~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~ 182 (226)
..+.-..+..|+||...|.. ....+.||||.+|..|++
T Consensus 71 ~~v~i~~~~~C~vC~k~l~~--~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 71 RSVVITESTKCSVCGKPLGN--SVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred ceEEECCCCCccCcCCcCCC--ceEEEeCCCeEEeccccc
Confidence 33444556789999999877 477889999999999975
No 58
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=95.58 E-value=0.01 Score=42.39 Aligned_cols=46 Identities=26% Similarity=0.768 Sum_probs=33.8
Q ss_pred cceeEeCCCCcccccc-----ccCCCCCCC-cceeecCccccccCCCCCCeeccCCCCc
Q 027217 63 VKQVICSVCDTEQPVA-----QVCTNCGVN-MGEYFCDICKFYDDDIEKGQFHCDDCGI 115 (226)
Q Consensus 63 ~~~v~Cg~C~~~q~v~-----~~C~~Cg~~-f~~Y~C~~C~l~dd~~~k~~yHC~~Cgi 115 (226)
++...|..|+.+.... -.||+||.. ..| |.+|+-+. ..|.|++||+
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 99998774 4799999985
No 59
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=95.50 E-value=0.0076 Score=40.73 Aligned_cols=41 Identities=29% Similarity=0.704 Sum_probs=26.9
Q ss_pred CccchhhcccCCcceeeecc---C--CccCHHHHHHHHhc-CcCCCCCC
Q 027217 153 CPICYEYLFDSLRNTTVMKC---G--HTMHCECYHEMIKR-DKYCCPIC 195 (226)
Q Consensus 153 CpICle~lf~s~~~v~~LpC---G--H~~H~~C~~~~l~~-~~~~CPiC 195 (226)
|=||++.-.++ +..+.|| | -..|..|+++|+.. ++.+|++|
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 56898874433 2445677 3 68999999999974 46779987
No 60
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.31 E-value=0.0082 Score=56.29 Aligned_cols=60 Identities=23% Similarity=0.558 Sum_probs=43.6
Q ss_pred CCCCCCccchhhcccCC---cceee-eccCCccCHHHHHHHHhcC------cCCCCCCCeecc--cchHHHH
Q 027217 148 SMHHHCPICYEYLFDSL---RNTTV-MKCGHTMHCECYHEMIKRD------KYCCPICSKSVI--DMSRTWK 207 (226)
Q Consensus 148 ~~~~~CpICle~lf~s~---~~v~~-LpCGH~~H~~C~~~~l~~~------~~~CPiCrksi~--dm~~~~~ 207 (226)
+.+..|-||||.+.+.. ..-.. ++|-|+|-..|+..|.... +..||+||.... .-+++|-
T Consensus 159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~~v~pS~~Wv 230 (344)
T KOG1039|consen 159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSSFVNPSSFWV 230 (344)
T ss_pred cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccccccccceee
Confidence 56778999999977643 11222 4599999999999998432 368999998764 4455563
No 61
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.15 E-value=0.033 Score=49.82 Aligned_cols=52 Identities=29% Similarity=0.675 Sum_probs=43.6
Q ss_pred CCCCCCccchhhcccCCcceeeeccCCccCHHHHHHHHhc-------CcCCCCCCCeeccc
Q 027217 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR-------DKYCCPICSKSVID 201 (226)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~-------~~~~CPiCrksi~d 201 (226)
....||..|.-.|.+. +.+.|-|=|.||-.|+++|... ..|+||-|+..|..
T Consensus 48 DY~pNC~LC~t~La~g--dt~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFP 106 (299)
T KOG3970|consen 48 DYNPNCRLCNTPLASG--DTTRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFP 106 (299)
T ss_pred CCCCCCceeCCccccC--cceeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCC
Confidence 4578999999997653 4567999999999999999863 47999999999973
No 62
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.85 E-value=0.0099 Score=55.78 Aligned_cols=48 Identities=21% Similarity=0.501 Sum_probs=35.7
Q ss_pred cCCCCCCCccchhhcccCCcceeeeccCCccCHHHHHHHHhcCcCCCCCCCeeccc
Q 027217 146 ENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID 201 (226)
Q Consensus 146 e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~d 201 (226)
|.+...+|.||++. ......+||||+-- |..... ...+||+||.+|.-
T Consensus 301 ~~~~p~lcVVcl~e----~~~~~fvpcGh~cc--ct~cs~--~l~~CPvCR~rI~~ 348 (355)
T KOG1571|consen 301 ELPQPDLCVVCLDE----PKSAVFVPCGHVCC--CTLCSK--HLPQCPVCRQRIRL 348 (355)
T ss_pred ccCCCCceEEecCC----ccceeeecCCcEEE--chHHHh--hCCCCchhHHHHHH
Confidence 45667899999997 33578999999954 555443 34679999998863
No 63
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=94.57 E-value=0.021 Score=52.81 Aligned_cols=44 Identities=25% Similarity=0.591 Sum_probs=35.6
Q ss_pred CCCccchhhcccCCcceeeeccCCccCHHHHHHHHhcCcCCCCCCCeec
Q 027217 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSV 199 (226)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi 199 (226)
.-|-||-+++.- ...-+|||+|..-||..+|. .+.-||+|+-..
T Consensus 26 lrC~IC~~~i~i----p~~TtCgHtFCslCIR~hL~-~qp~CP~Cr~~~ 69 (391)
T COG5432 26 LRCRICDCRISI----PCETTCGHTFCSLCIRRHLG-TQPFCPVCREDP 69 (391)
T ss_pred HHhhhhhheeec----ceecccccchhHHHHHHHhc-CCCCCccccccH
Confidence 469999998432 23458999999999999998 478999999755
No 64
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.55 E-value=0.03 Score=51.15 Aligned_cols=53 Identities=25% Similarity=0.589 Sum_probs=42.4
Q ss_pred CCCCCCccchhhcccCCcceeeeccCCccCHHHHHHHHhc-CcCCCCCCCeecccch
Q 027217 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR-DKYCCPICSKSVIDMS 203 (226)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~-~~~~CPiCrksi~dm~ 203 (226)
.....||+|.|+ ++-|.+..+|||.+.--|+..=... .+.+||.|+.++..|.
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 5567778899999999999875432 3589999999988764
No 65
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=94.45 E-value=0.014 Score=41.08 Aligned_cols=33 Identities=27% Similarity=0.603 Sum_probs=26.5
Q ss_pred ceeeeccCCccCHHHHHHHHhcCcCCCCCCCeeccc
Q 027217 166 NTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID 201 (226)
Q Consensus 166 ~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~d 201 (226)
.-.+|||||++-..|++-+- -..||+|.+.+..
T Consensus 19 ~~~~~pCgH~I~~~~f~~~r---YngCPfC~~~~~~ 51 (55)
T PF14447_consen 19 KGTVLPCGHLICDNCFPGER---YNGCPFCGTPFEF 51 (55)
T ss_pred ccccccccceeeccccChhh---ccCCCCCCCcccC
Confidence 45679999999999998762 3579999998863
No 66
>PF05883 Baculo_RING: Baculovirus U-box/Ring-like domain; InterPro: IPR008573 This family consists of several Baculovirus proteins of around 130 residues in length. The function of this family is unknown, but it appears to be related to the U-box and ring finger domain by profile-profile comparison.
Probab=94.37 E-value=0.019 Score=47.29 Aligned_cols=36 Identities=14% Similarity=0.418 Sum_probs=32.0
Q ss_pred CCCCccchhhcccCCcceeeeccC------CccCHHHHHHHHh
Q 027217 150 HHHCPICYEYLFDSLRNTTVMKCG------HTMHCECYHEMIK 186 (226)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCG------H~~H~~C~~~~l~ 186 (226)
..+|.||++.+.+ ...|+.+++| |+||.+|++.|.+
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 4689999999887 7799999997 9999999999954
No 67
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.07 E-value=0.0061 Score=56.11 Aligned_cols=62 Identities=23% Similarity=0.561 Sum_probs=42.5
Q ss_pred ccCcceeecCCC---CCCCccchhhcccCCcceeeeccCCccCHHHHHHHHhcCcCCCCCCCeecccchHHHH
Q 027217 138 LRNNHLCIENSM---HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRTWK 207 (226)
Q Consensus 138 l~~~H~C~e~~~---~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~dm~~~~~ 207 (226)
+++++.+.-..+ +..|.||++- ...-..|+|||.. .|++-=. .-..|||||+-|...-.+|+
T Consensus 285 ~k~~~g~~~~~s~~~~~LC~ICmDa----P~DCvfLeCGHmV--tCt~CGk--rm~eCPICRqyi~rvvrif~ 349 (350)
T KOG4275|consen 285 YKGNDGEQHSRSLATRRLCAICMDA----PRDCVFLECGHMV--TCTKCGK--RMNECPICRQYIVRVVRIFR 349 (350)
T ss_pred HhcccccccccchhHHHHHHHHhcC----CcceEEeecCcEE--eehhhcc--ccccCchHHHHHHHHHhhhc
Confidence 345555554444 7789999985 5678899999985 3443221 12389999998887666654
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=93.67 E-value=0.051 Score=49.88 Aligned_cols=49 Identities=20% Similarity=0.469 Sum_probs=39.2
Q ss_pred CCccchhhcccCCcceee-eccCCccCHHHHHHHHhcCcCCCCCCCeecc
Q 027217 152 HCPICYEYLFDSLRNTTV-MKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (226)
Q Consensus 152 ~CpICle~lf~s~~~v~~-LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (226)
-||+|.-+.+.+..-+.. =+|||.+..+|++..+..+.+.||.|.+.+.
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 489998876654433222 2899999999999999889999999998775
No 69
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.41 E-value=0.051 Score=47.11 Aligned_cols=52 Identities=31% Similarity=0.734 Sum_probs=35.5
Q ss_pred CCccchhhcccCCcce---eeeccCCccCHHHHHHHHhc-----C-----cCCCCCCCeecc-cch
Q 027217 152 HCPICYEYLFDSLRNT---TVMKCGHTMHCECYHEMIKR-----D-----KYCCPICSKSVI-DMS 203 (226)
Q Consensus 152 ~CpICle~lf~s~~~v---~~LpCGH~~H~~C~~~~l~~-----~-----~~~CPiCrksi~-dm~ 203 (226)
.|-||..+-.+.+.+- --..||-.||+-|+.+||+. + -..||.|+++|. .||
T Consensus 167 ~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialKmS 232 (234)
T KOG3268|consen 167 ACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALKMS 232 (234)
T ss_pred cccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceeecc
Confidence 4555555544433322 24689999999999999973 1 236999999985 454
No 70
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.29 E-value=0.044 Score=50.64 Aligned_cols=49 Identities=24% Similarity=0.474 Sum_probs=39.5
Q ss_pred CCCCCCccchhhcccCCcceeeeccCCccCHHHHHHHHhcCcCCCCCCCeecc
Q 027217 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (226)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (226)
.+..+|+||+-...- + +.|+|+|.|.-.|++--..+...+||+||..|-
T Consensus 5 ~~~~eC~IC~nt~n~---P-v~l~C~HkFCyiCiKGsy~ndk~~CavCR~pid 53 (324)
T KOG0824|consen 5 TKKKECLICYNTGNC---P-VNLYCFHKFCYICIKGSYKNDKKTCAVCRFPID 53 (324)
T ss_pred ccCCcceeeeccCCc---C-ccccccchhhhhhhcchhhcCCCCCceecCCCC
Confidence 456789999987443 4 579999999999998765556778999999886
No 71
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.00 E-value=0.071 Score=47.87 Aligned_cols=48 Identities=31% Similarity=0.784 Sum_probs=39.5
Q ss_pred CCCccchhhcccCCc---ceeeeccCCccCHHHHHHHHhcCcCCCCCCCeec
Q 027217 151 HHCPICYEYLFDSLR---NTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSV 199 (226)
Q Consensus 151 ~~CpICle~lf~s~~---~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi 199 (226)
..|-||-++ |++.+ ..++|.|||++-..|+...+.+....||.||...
T Consensus 4 ~~c~~c~~~-~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~~~i~cpfcR~~~ 54 (296)
T KOG4185|consen 4 PECEICNED-YSSEDGDHIPRVLKCGHTICQNCASKLLGNSRILCPFCRETT 54 (296)
T ss_pred CceeecCcc-ccccCcccCCcccccCceehHhHHHHHhcCceeeccCCCCcc
Confidence 468899998 44443 3467889999999999999988778899999994
No 72
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=92.98 E-value=0.043 Score=48.94 Aligned_cols=37 Identities=27% Similarity=0.546 Sum_probs=27.6
Q ss_pred ccCCcceeeeccCCccCHHHHHHHHhcCcCCCCCCCeecc
Q 027217 161 FDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (226)
Q Consensus 161 f~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (226)
|.+.++-....|+|+|...|...-. ...||+|+|+|-
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 4444455567899999999997532 338999999973
No 73
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.77 E-value=0.073 Score=50.89 Aligned_cols=52 Identities=23% Similarity=0.715 Sum_probs=41.2
Q ss_pred CCCCCCccchhhcccCCcceeeeccCCccCHHHHHHHHhcCcCCCCCCCeecccchH
Q 027217 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSR 204 (226)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~dm~~ 204 (226)
..+-.|-||+.-|.. ++ ++||||+|-..|++.-+. ....||+||-.+....+
T Consensus 82 ~sef~c~vc~~~l~~---pv-~tpcghs~c~~Cl~r~ld-~~~~cp~Cr~~l~e~~~ 133 (398)
T KOG4159|consen 82 RSEFECCVCSRALYP---PV-VTPCGHSFCLECLDRSLD-QETECPLCRDELVELPA 133 (398)
T ss_pred cchhhhhhhHhhcCC---Cc-cccccccccHHHHHHHhc-cCCCCcccccccccchH
Confidence 556789999887554 33 459999999999999776 56789999999986443
No 74
>PF12773 DZR: Double zinc ribbon
Probab=92.64 E-value=0.12 Score=34.43 Aligned_cols=22 Identities=36% Similarity=0.970 Sum_probs=14.1
Q ss_pred eCCCCccccc-cccCCCCCCCcc
Q 027217 68 CSVCDTEQPV-AQVCTNCGVNMG 89 (226)
Q Consensus 68 Cg~C~~~q~v-~~~C~~Cg~~f~ 89 (226)
|..|+++.+. +..|++||+.+.
T Consensus 1 Cp~Cg~~~~~~~~fC~~CG~~l~ 23 (50)
T PF12773_consen 1 CPHCGTPNPDDAKFCPHCGTPLP 23 (50)
T ss_pred CCCcCCcCCccccCChhhcCChh
Confidence 4566666554 456777777776
No 75
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=92.57 E-value=0.018 Score=53.58 Aligned_cols=71 Identities=25% Similarity=0.469 Sum_probs=54.4
Q ss_pred CCCCCccchhhcccCCcceeeeccCCccCHHHHHHHHhcCcCCCCCCCeecccch-HHHHHHHHHHHhCCCCCCCC
Q 027217 149 MHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMS-RTWKRIDEELQMNSSIFFPS 223 (226)
Q Consensus 149 ~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~dm~-~~~~~lD~~i~~~pm~~~~~ 223 (226)
....|++|.-+|.+.++ +.-|=|+|.++||.++|.. +.+||.|...|...- ...-..|+.+++.--+.+|+
T Consensus 14 ~~itC~LC~GYliDATT---I~eCLHTFCkSCivk~l~~-~~~CP~C~i~ih~t~pl~ni~~DrtlqdiVyKLVPg 85 (331)
T KOG2660|consen 14 PHITCRLCGGYLIDATT---ITECLHTFCKSCIVKYLEE-SKYCPTCDIVIHKTHPLLNIRSDRTLQDIVYKLVPG 85 (331)
T ss_pred cceehhhccceeecchh---HHHHHHHHHHHHHHHHHHH-hccCCccceeccCccccccCCcchHHHHHHHHHcch
Confidence 35579999999887543 5579999999999999986 789999999887532 23346677777766666665
No 76
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=92.40 E-value=0.097 Score=37.52 Aligned_cols=45 Identities=29% Similarity=0.789 Sum_probs=33.8
Q ss_pred eeEeCCCCcccccc-----ccCCCCCCCcceeecCccccccCCCCCCeeccCCCCc
Q 027217 65 QVICSVCDTEQPVA-----QVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGI 115 (226)
Q Consensus 65 ~v~Cg~C~~~q~v~-----~~C~~Cg~~f~~Y~C~~C~l~dd~~~k~~yHC~~Cgi 115 (226)
...|..|+.+..+. -.||+||... =|-|.+|+... .+|.|++||+
T Consensus 9 ~~~CtSCg~~i~p~e~~v~F~CPnCGe~~-I~Rc~~CRk~g-----~~Y~Cp~CGF 58 (61)
T COG2888 9 PPVCTSCGREIAPGETAVKFPCPNCGEVE-IYRCAKCRKLG-----NPYRCPKCGF 58 (61)
T ss_pred CceeccCCCEeccCCceeEeeCCCCCcee-eehhhhHHHcC-----CceECCCcCc
Confidence 56899999887553 3799999443 36688998774 4799999985
No 77
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=91.73 E-value=0.1 Score=49.47 Aligned_cols=52 Identities=27% Similarity=0.675 Sum_probs=41.9
Q ss_pred CCCCCccchhhcccCCcceeeeccCCccCHHHHHHHHhcCcCCCCCCCeecccchH
Q 027217 149 MHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSR 204 (226)
Q Consensus 149 ~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~dm~~ 204 (226)
.+..||||...|-+ ++....|||.|-..|+.+|+.. +..||.|+..+..-..
T Consensus 20 ~~l~C~~C~~vl~~---p~~~~~cgh~fC~~C~~~~~~~-~~~cp~~~~~~~~~~~ 71 (391)
T KOG0297|consen 20 ENLLCPICMSVLRD---PVQTTTCGHRFCAGCLLESLSN-HQKCPVCRQELTQAEE 71 (391)
T ss_pred ccccCccccccccC---CCCCCCCCCcccccccchhhcc-CcCCcccccccchhhc
Confidence 34679999988655 4545789999999999999985 7899999888875443
No 78
>PF04641 Rtf2: Rtf2 RING-finger
Probab=91.14 E-value=0.18 Score=45.15 Aligned_cols=50 Identities=18% Similarity=0.459 Sum_probs=39.1
Q ss_pred CCCCCCccchhhcccCCcceeee-ccCCccCHHHHHHHHhcCcCCCCCCCeecc
Q 027217 148 SMHHHCPICYEYLFDSLRNTTVM-KCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (226)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~L-pCGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (226)
...--|||-...| ++....+.| ||||+|=...+++.- ....||+|.+.+.
T Consensus 111 ~~~~~CPvt~~~~-~~~~~fv~l~~cG~V~s~~alke~k--~~~~Cp~c~~~f~ 161 (260)
T PF04641_consen 111 EGRFICPVTGKEF-NGKHKFVYLRPCGCVFSEKALKELK--KSKKCPVCGKPFT 161 (260)
T ss_pred CceeECCCCCccc-CCceeEEEEcCCCCEeeHHHHHhhc--ccccccccCCccc
Confidence 3445799999996 444555555 999999999999984 3568999999975
No 79
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=90.65 E-value=0.16 Score=52.12 Aligned_cols=42 Identities=29% Similarity=0.583 Sum_probs=31.2
Q ss_pred CCCCccchhhcccCCcceeeeccCCccCHHHHHHHHhcCcCCCCC
Q 027217 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPI 194 (226)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPi 194 (226)
...|.||--.+..| ...-+.|||.+|.+|+.+|++. ...||.
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 34588887654432 4455789999999999999985 568884
No 80
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.63 E-value=0.15 Score=48.91 Aligned_cols=46 Identities=20% Similarity=0.411 Sum_probs=37.4
Q ss_pred CCCCccchhhcccCCcceeeeccCCccCHHHHHHHHhc-------CcCCCCCCC
Q 027217 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR-------DKYCCPICS 196 (226)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~-------~~~~CPiCr 196 (226)
--+|.||++. +....-.+.|||+|+|.+.|+..|... +..+||-+.
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 4589999997 555677889999999999999998752 467898765
No 81
>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=90.42 E-value=0.3 Score=41.39 Aligned_cols=48 Identities=31% Similarity=0.769 Sum_probs=34.9
Q ss_pred CCCCccchhhcccCCcceeeeccC-C------------ccCHHHHHHHHhc-----------------------------
Q 027217 150 HHHCPICYEYLFDSLRNTTVMKCG-H------------TMHCECYHEMIKR----------------------------- 187 (226)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCG-H------------~~H~~C~~~~l~~----------------------------- 187 (226)
+..||||||. .-.++.|-|. | .-|+.||+++-+.
T Consensus 2 d~~CpICme~----PHNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkka~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 77 (162)
T PF07800_consen 2 DVTCPICMEH----PHNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKKAYGKSSSSSSQSSSSAPSDSSSSESSESQE 77 (162)
T ss_pred CccCceeccC----CCceEEEEeccccCCccccccCCccchhHHHHHHHHHhcCCCCccccccccCcCCCcccccccccc
Confidence 4579999997 3456667662 2 4699999998752
Q ss_pred -CcCCCCCCCeeccc
Q 027217 188 -DKYCCPICSKSVID 201 (226)
Q Consensus 188 -~~~~CPiCrksi~d 201 (226)
....|||||-.|..
T Consensus 78 ~~~L~CPLCRG~V~G 92 (162)
T PF07800_consen 78 QPELACPLCRGEVKG 92 (162)
T ss_pred cccccCccccCceec
Confidence 14679999988863
No 82
>PHA02862 5L protein; Provisional
Probab=90.18 E-value=0.16 Score=42.61 Aligned_cols=56 Identities=20% Similarity=0.444 Sum_probs=38.0
Q ss_pred CCCCccchhhcccCCcceeeecc---C--CccCHHHHHHHHhc-CcCCCCCCCeecccchHHHHHHHH
Q 027217 150 HHHCPICYEYLFDSLRNTTVMKC---G--HTMHCECYHEMIKR-DKYCCPICSKSVIDMSRTWKRIDE 211 (226)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpC---G--H~~H~~C~~~~l~~-~~~~CPiCrksi~dm~~~~~~lD~ 211 (226)
...|=||.+. - .+.+ -|| | -..|++|+.+|+.. +..+||+|+.... +...|+.+.+
T Consensus 2 ~diCWIC~~~-~--~e~~--~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~-Ik~~yKpf~k 63 (156)
T PHA02862 2 SDICWICNDV-C--DERN--NFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYN-IKKTYVSFKK 63 (156)
T ss_pred CCEEEEecCc-C--CCCc--ccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEE-EEEccccHHH
Confidence 4568899986 2 2222 465 2 78999999999975 3567999998774 4444444443
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=90.17 E-value=0.18 Score=37.17 Aligned_cols=36 Identities=25% Similarity=0.783 Sum_probs=22.9
Q ss_pred ceeEeCCCCccccccccCCCCCCCc--------ceeecCccccc
Q 027217 64 KQVICSVCDTEQPVAQVCTNCGVNM--------GEYFCDICKFY 99 (226)
Q Consensus 64 ~~v~Cg~C~~~q~v~~~C~~Cg~~f--------~~Y~C~~C~l~ 99 (226)
....|..|+..-.....||.|+.++ +.|||..|+=.
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 5788888888777777888888877 58999888733
No 84
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=90.14 E-value=0.2 Score=51.83 Aligned_cols=42 Identities=26% Similarity=0.596 Sum_probs=32.8
Q ss_pred CCCccchhhcccCCcceeeeccCCccCHHHHHHHHhcCcCCCCCCCeec
Q 027217 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSV 199 (226)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi 199 (226)
+.|..|--.|- -|++-..|||.||..|+. . +...||-|+-..
T Consensus 841 skCs~C~~~Ld---lP~VhF~CgHsyHqhC~e---~-~~~~CP~C~~e~ 882 (933)
T KOG2114|consen 841 SKCSACEGTLD---LPFVHFLCGHSYHQHCLE---D-KEDKCPKCLPEL 882 (933)
T ss_pred eeecccCCccc---cceeeeecccHHHHHhhc---c-CcccCCccchhh
Confidence 46778876644 377788999999999998 2 568999999833
No 85
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=89.73 E-value=0.082 Score=49.87 Aligned_cols=57 Identities=23% Similarity=0.470 Sum_probs=43.7
Q ss_pred CCCCccchhhcccCCcceeeeccCCccCHHHHHHHHhcCcCCCCCCCeecccchHHH
Q 027217 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRTW 206 (226)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~dm~~~~ 206 (226)
+.-||.|+|+|.-+...-..-|||=-+.+-|+......-+.+||-||+...|-...|
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 445999999987765555555789999999998876666789999999886533333
No 86
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=89.48 E-value=0.14 Score=50.84 Aligned_cols=52 Identities=21% Similarity=0.516 Sum_probs=42.7
Q ss_pred ecCCCCCCCccchhhcccCCcceeeeccCCccCHHHHHHHHh----cCcCCCCCCCeecc
Q 027217 145 IENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIK----RDKYCCPICSKSVI 200 (226)
Q Consensus 145 ~e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~----~~~~~CPiCrksi~ 200 (226)
.|+..+..|-+|-|+ .+..++-+|.|.|.+-|+.+|+. +.+.+||+|.+.+.
T Consensus 531 ~enk~~~~C~lc~d~----aed~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~Ls 586 (791)
T KOG1002|consen 531 DENKGEVECGLCHDP----AEDYIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLS 586 (791)
T ss_pred ccccCceeecccCCh----hhhhHhhhhhHHHHHHHHHHHHHhhhcccCCCCcccccccc
Confidence 467778899999987 34566789999999999999875 35789999998774
No 87
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=89.30 E-value=0.19 Score=46.76 Aligned_cols=53 Identities=28% Similarity=0.582 Sum_probs=41.3
Q ss_pred CCCCCCccchhhcccCCcceeeeccCCccCHHHHHHHHhc----------------------CcCCCCCCCeeccc
Q 027217 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR----------------------DKYCCPICSKSVID 201 (226)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~----------------------~~~~CPiCrksi~d 201 (226)
-....|.|||-- |.+.....+-+|-|+||..||..+|.. ..--|||||-.|.+
T Consensus 113 ~p~gqCvICLyg-fa~~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~ 187 (368)
T KOG4445|consen 113 HPNGQCVICLYG-FASSPAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKI 187 (368)
T ss_pred CCCCceEEEEEe-ecCCCceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccc
Confidence 346789999987 666667888999999999999988741 12249999988864
No 88
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.85 E-value=0.21 Score=50.53 Aligned_cols=53 Identities=21% Similarity=0.555 Sum_probs=39.9
Q ss_pred CCCccchhhcccCCcceeeeccCCccCHHHHHHHHhcCcCCCCCCCe----ecccchHHHH
Q 027217 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSK----SVIDMSRTWK 207 (226)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrk----si~dm~~~~~ 207 (226)
.+|+||+..++.++...+.|.|||++.+.|++..- +.+|| |.. ++.+.+.+++
T Consensus 12 l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~ly---n~scp-~~~De~~~~~~~~e~p~ 68 (861)
T KOG3161|consen 12 LLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLY---NASCP-TKRDEDSSLMQLKEEPR 68 (861)
T ss_pred hhchHHHHHHHHHhcCcccccccchHHHHHHHhHh---hccCC-CCccccchhcChhhcch
Confidence 37999988888888888889999999999998763 46898 553 3344554443
No 89
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=88.46 E-value=0.45 Score=43.23 Aligned_cols=53 Identities=25% Similarity=0.487 Sum_probs=44.1
Q ss_pred CCCCCCCccchhhcccCCcceeee-ccCCccCHHHHHHHHhcCcCCCCCCCeeccc
Q 027217 147 NSMHHHCPICYEYLFDSLRNTTVM-KCGHTMHCECYHEMIKRDKYCCPICSKSVID 201 (226)
Q Consensus 147 ~~~~~~CpICle~lf~s~~~v~~L-pCGH~~H~~C~~~~l~~~~~~CPiCrksi~d 201 (226)
.+..-.|||+.+.|-. ..+..+| |+||++-..|.+.++. ...-+||+.+.+-|
T Consensus 218 ~s~ryiCpvtrd~LtN-t~~ca~Lr~sg~Vv~~ecvEklir-~D~v~pv~d~plkd 271 (303)
T KOG3039|consen 218 ASKRYICPVTRDTLTN-TTPCAVLRPSGHVVTKECVEKLIR-KDMVDPVTDKPLKD 271 (303)
T ss_pred hccceecccchhhhcC-ccceEEeccCCcEeeHHHHHHhcc-ccccccCCCCcCcc
Confidence 3445679999999765 5667777 8999999999999998 57889999999875
No 90
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=87.67 E-value=0.26 Score=29.16 Aligned_cols=24 Identities=33% Similarity=0.924 Sum_probs=17.6
Q ss_pred eeEeCCCCccccc-cccCCCCCCCc
Q 027217 65 QVICSVCDTEQPV-AQVCTNCGVNM 88 (226)
Q Consensus 65 ~v~Cg~C~~~q~v-~~~C~~Cg~~f 88 (226)
.+.|..|+++.+. +..|++||+.+
T Consensus 2 ~~~Cp~Cg~~~~~~~~fC~~CG~~L 26 (26)
T PF13248_consen 2 EMFCPNCGAEIDPDAKFCPNCGAKL 26 (26)
T ss_pred cCCCcccCCcCCcccccChhhCCCC
Confidence 3678888886444 46899999864
No 91
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.60 E-value=0.53 Score=44.95 Aligned_cols=46 Identities=22% Similarity=0.578 Sum_probs=38.0
Q ss_pred CCccchhhcccCCcceeeeccCCccCHHHHHHHHhcCc--CCCCCCCee
Q 027217 152 HCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDK--YCCPICSKS 198 (226)
Q Consensus 152 ~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~--~~CPiCrks 198 (226)
-|||=.|. -+...|...|.|||++=++=+..+.+++. ++||.|-.-
T Consensus 336 ~CPVlKeq-tsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~e 383 (394)
T KOG2817|consen 336 ICPVLKEQ-TSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPVE 383 (394)
T ss_pred ecccchhh-ccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCcc
Confidence 58997776 44456778899999999999999998776 899999743
No 92
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=87.36 E-value=0.56 Score=39.77 Aligned_cols=46 Identities=30% Similarity=0.605 Sum_probs=33.3
Q ss_pred CCCCCccchhhcccCCcceeeecc--CC---ccCHHHHHHHHhc-CcCCCCCCCeec
Q 027217 149 MHHHCPICYEYLFDSLRNTTVMKC--GH---TMHCECYHEMIKR-DKYCCPICSKSV 199 (226)
Q Consensus 149 ~~~~CpICle~lf~s~~~v~~LpC--GH---~~H~~C~~~~l~~-~~~~CPiCrksi 199 (226)
++..|=||.+.- + .. .-|| .. ..|++|+++|+.. +..+||+|+...
T Consensus 7 ~~~~CRIC~~~~-~--~~--~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y 58 (162)
T PHA02825 7 MDKCCWICKDEY-D--VV--TNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPY 58 (162)
T ss_pred CCCeeEecCCCC-C--Cc--cCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeE
Confidence 456799998872 1 12 2465 34 6799999999975 366799999776
No 93
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=86.81 E-value=0.57 Score=44.48 Aligned_cols=65 Identities=17% Similarity=0.369 Sum_probs=46.3
Q ss_pred CccccccccCcceeecCCCCCCCccchhhcccCCcceeeeccCCccCHHHHHHHHh-cCcCCCCCCCeec
Q 027217 131 GSCYSTSLRNNHLCIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIK-RDKYCCPICSKSV 199 (226)
Q Consensus 131 ~~C~s~~l~~~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~-~~~~~CPiCrksi 199 (226)
+.|....+.++.+=.....+++|-||.+.+ +-+.++||||-+.--|--.... ...-.||+||..-
T Consensus 42 nlsaEPnlttsSaddtDEen~~C~ICA~~~----TYs~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~ 107 (493)
T COG5236 42 NLSAEPNLTTSSADDTDEENMNCQICAGST----TYSARYPCGHQICHACAVRLRALYMQKGCPLCRTET 107 (493)
T ss_pred ccccCCccccccccccccccceeEEecCCc----eEEEeccCCchHHHHHHHHHHHHHhccCCCcccccc
Confidence 556666665555555556677899999873 4567899999999999765432 2456899999643
No 94
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=86.38 E-value=0.36 Score=50.17 Aligned_cols=43 Identities=21% Similarity=0.382 Sum_probs=32.6
Q ss_pred ceeecCCCCCCCccchhhcccCCcceeeeccCCccCHHHHHHHHh
Q 027217 142 HLCIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIK 186 (226)
Q Consensus 142 H~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~ 186 (226)
+.++--.....|-+|.-.|+. ++-.+.||||.||++|+.+-+.
T Consensus 809 ~ry~v~ep~d~C~~C~~~ll~--~pF~vf~CgH~FH~~Cl~~~v~ 851 (911)
T KOG2034|consen 809 QRYRVLEPQDSCDHCGRPLLI--KPFYVFPCGHCFHRDCLIRHVL 851 (911)
T ss_pred cceEEecCccchHHhcchhhc--CcceeeeccchHHHHHHHHHHH
Confidence 333333445689999998775 4778889999999999987654
No 95
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=86.38 E-value=0.4 Score=49.72 Aligned_cols=51 Identities=24% Similarity=0.543 Sum_probs=36.6
Q ss_pred CCCCccchhhcccCCccee-eeccCCccCHHHHHHHHhc------CcCCCCCCCeeccc
Q 027217 150 HHHCPICYEYLFDSLRNTT-VMKCGHTMHCECYHEMIKR------DKYCCPICSKSVID 201 (226)
Q Consensus 150 ~~~CpICle~lf~s~~~v~-~LpCGH~~H~~C~~~~l~~------~~~~CPiCrksi~d 201 (226)
.-.|.||.|.+..+ .++- --.|=|+||..||.+|.+. ...+||-|......
T Consensus 191 ~yeCmIC~e~I~~t-~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv~~~ 248 (950)
T KOG1952|consen 191 KYECMICTERIKRT-APVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSVSKT 248 (950)
T ss_pred ceEEEEeeeecccc-CCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccchhcc
Confidence 45799999987653 2221 1235699999999999864 46789999944443
No 96
>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=86.17 E-value=0.41 Score=33.00 Aligned_cols=31 Identities=32% Similarity=0.780 Sum_probs=23.0
Q ss_pred eeccC-CccCHHHHHHHHhcCcCCCCCCCeecc
Q 027217 169 VMKCG-HTMHCECYHEMIKRDKYCCPICSKSVI 200 (226)
Q Consensus 169 ~LpCG-H~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (226)
.+.|. |.+-..|+..++. .+..||||.+.+-
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 56895 9999999999997 5789999998864
No 97
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.93 E-value=0.48 Score=43.83 Aligned_cols=64 Identities=25% Similarity=0.459 Sum_probs=48.5
Q ss_pred CCCccchhhcccCCcceeeeccCCccCHHHHHHHHhcCcCCCCCCCeecccchHHHHHHHHHHHhCCCC
Q 027217 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRTWKRIDEELQMNSSI 219 (226)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~dm~~~~~~lD~~i~~~pm~ 219 (226)
..|-||-+++.. .++-.|||.|...|...-++ ...+|+||.+.+-.....=..|+..|+..++.
T Consensus 242 f~c~icr~~f~~----pVvt~c~h~fc~~ca~~~~q-k~~~c~vC~~~t~g~~~~akeL~~~L~~kks~ 305 (313)
T KOG1813|consen 242 FKCFICRKYFYR----PVVTKCGHYFCEVCALKPYQ-KGEKCYVCSQQTHGSFNVAKELLVSLKLKKSD 305 (313)
T ss_pred cccccccccccc----chhhcCCceeehhhhccccc-cCCcceecccccccccchHHHHHHHHHhhhhh
Confidence 459999998443 34678999999999988776 46799999999986655556677777665553
No 98
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.53 E-value=0.43 Score=45.37 Aligned_cols=58 Identities=29% Similarity=0.590 Sum_probs=45.5
Q ss_pred CCCCCCCccchhhcccCCcceeeeccCCccCHHHHHHHHhcCcCCCCCCCeecccchHHHHHHHHHHH
Q 027217 147 NSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRTWKRIDEELQ 214 (226)
Q Consensus 147 ~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~dm~~~~~~lD~~i~ 214 (226)
.+.++.||||... .-..+.-||||--...||.+.+.+ +..|=.|+.++.+. .||.++.
T Consensus 419 ~sEd~lCpICyA~----pi~Avf~PC~H~SC~~CI~qHlmN-~k~CFfCktTv~~~-----~ld~~~~ 476 (489)
T KOG4692|consen 419 DSEDNLCPICYAG----PINAVFAPCSHRSCYGCITQHLMN-CKRCFFCKTTVIDV-----ILDKEEE 476 (489)
T ss_pred CcccccCcceecc----cchhhccCCCCchHHHHHHHHHhc-CCeeeEecceeeeh-----hcccccc
Confidence 3567789999875 334556799999999999999884 67999999999873 5665543
No 99
>PRK04023 DNA polymerase II large subunit; Validated
Probab=85.43 E-value=0.75 Score=48.71 Aligned_cols=31 Identities=26% Similarity=0.696 Sum_probs=13.7
Q ss_pred cCCCCCCCcceeecCccccccCCCCCCeeccCCCC
Q 027217 80 VCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCG 114 (226)
Q Consensus 80 ~C~~Cg~~f~~Y~C~~C~l~dd~~~k~~yHC~~Cg 114 (226)
.|++||.....-+|+.|.-- .+.+|.|++||
T Consensus 628 fCpsCG~~t~~frCP~CG~~----Te~i~fCP~CG 658 (1121)
T PRK04023 628 KCPSCGKETFYRRCPFCGTH----TEPVYRCPRCG 658 (1121)
T ss_pred cCCCCCCcCCcccCCCCCCC----CCcceeCcccc
Confidence 34444444444444444322 23455555553
No 100
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=85.36 E-value=0.54 Score=41.54 Aligned_cols=60 Identities=22% Similarity=0.464 Sum_probs=44.2
Q ss_pred CCCccchhhcccCCcceeeeccCCccCHHHHHHHHhcCcCCCCCCCeecccchHHHHHHHHHHHh
Q 027217 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRTWKRIDEELQM 215 (226)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~dm~~~~~~lD~~i~~ 215 (226)
-.|-||.++ |.| .++-.|||.|...|+-.=.+ ...+|=+|.+..--.-.+=..||..+..
T Consensus 197 F~C~iCKkd-y~s---pvvt~CGH~FC~~Cai~~y~-kg~~C~~Cgk~t~G~f~V~~d~~kmL~~ 256 (259)
T COG5152 197 FLCGICKKD-YES---PVVTECGHSFCSLCAIRKYQ-KGDECGVCGKATYGRFWVVSDLQKMLNK 256 (259)
T ss_pred eeehhchhh-ccc---hhhhhcchhHHHHHHHHHhc-cCCcceecchhhccceeHHhhHHHHHhh
Confidence 379999998 443 34678999999999877655 4679999999886544444566766653
No 101
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=85.17 E-value=0.7 Score=27.51 Aligned_cols=21 Identities=24% Similarity=0.539 Sum_probs=17.4
Q ss_pred CCCCCCCeecccchHHHHHHHH
Q 027217 190 YCCPICSKSVIDMSRTWKRIDE 211 (226)
Q Consensus 190 ~~CPiCrksi~dm~~~~~~lD~ 211 (226)
..||||.+.+ .++.+.+.||.
T Consensus 2 v~CPiC~~~v-~~~~in~HLD~ 22 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLDS 22 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHHH
Confidence 3799999998 66778888884
No 102
>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=84.94 E-value=0.63 Score=27.85 Aligned_cols=22 Identities=36% Similarity=1.011 Sum_probs=17.6
Q ss_pred eCCCCccccc-cccCCCCCCCcc
Q 027217 68 CSVCDTEQPV-AQVCTNCGVNMG 89 (226)
Q Consensus 68 Cg~C~~~q~v-~~~C~~Cg~~f~ 89 (226)
|..|+.+-+. +..|++||..|.
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 103
>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=84.78 E-value=0.7 Score=36.62 Aligned_cols=28 Identities=32% Similarity=0.948 Sum_probs=21.1
Q ss_pred cccccCCCCCCCcceeecCccccccCCCCCCeeccCCCCc
Q 027217 76 PVAQVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGI 115 (226)
Q Consensus 76 ~v~~~C~~Cg~~f~~Y~C~~C~l~dd~~~k~~yHC~~Cgi 115 (226)
.....|++||+.| | +.+|.+-.|++||.
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 3446799999865 5 55788899999884
No 104
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=84.73 E-value=0.52 Score=27.33 Aligned_cols=21 Identities=38% Similarity=0.945 Sum_probs=14.9
Q ss_pred eCCCCccccc-cccCCCCCCCc
Q 027217 68 CSVCDTEQPV-AQVCTNCGVNM 88 (226)
Q Consensus 68 Cg~C~~~q~v-~~~C~~Cg~~f 88 (226)
|..|+++.+. +..|++||+.+
T Consensus 2 Cp~CG~~~~~~~~fC~~CG~~l 23 (23)
T PF13240_consen 2 CPNCGAEIEDDAKFCPNCGTPL 23 (23)
T ss_pred CcccCCCCCCcCcchhhhCCcC
Confidence 6678777655 46788888764
No 105
>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=83.42 E-value=1.1 Score=30.46 Aligned_cols=41 Identities=27% Similarity=0.794 Sum_probs=20.0
Q ss_pred CCccchhhcccCCcceeeeccCCccCHHHHHH--HHh----cCcCCCCCCCee
Q 027217 152 HCPICYEYLFDSLRNTTVMKCGHTMHCECYHE--MIK----RDKYCCPICSKS 198 (226)
Q Consensus 152 ~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~--~l~----~~~~~CPiCrks 198 (226)
.|||-...|.. +++...|-|. +||+- ||. ....+||+|+++
T Consensus 4 ~CPls~~~i~~---P~Rg~~C~H~---~CFDl~~fl~~~~~~~~W~CPiC~~~ 50 (50)
T PF02891_consen 4 RCPLSFQRIRI---PVRGKNCKHL---QCFDLESFLESNQRTPKWKCPICNKP 50 (50)
T ss_dssp B-TTTSSB-SS---EEEETT--SS-----EEHHHHHHHHHHS---B-TTT---
T ss_pred eCCCCCCEEEe---CccCCcCccc---ceECHHHHHHHhhccCCeECcCCcCc
Confidence 58888877544 7888889887 46553 554 246789999874
No 106
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=82.94 E-value=0.89 Score=46.09 Aligned_cols=33 Identities=30% Similarity=0.828 Sum_probs=19.8
Q ss_pred eEeCCCCccccc-cccCCCCCCCcceeecCcccc
Q 027217 66 VICSVCDTEQPV-AQVCTNCGVNMGEYFCDICKF 98 (226)
Q Consensus 66 v~Cg~C~~~q~v-~~~C~~Cg~~f~~Y~C~~C~l 98 (226)
++|..|+.+-+. +..|++||.++..-.|..|.-
T Consensus 2 ~~Cp~Cg~~n~~~akFC~~CG~~l~~~~Cp~CG~ 35 (645)
T PRK14559 2 LICPQCQFENPNNNRFCQKCGTSLTHKPCPQCGT 35 (645)
T ss_pred CcCCCCCCcCCCCCccccccCCCCCCCcCCCCCC
Confidence 356677766544 345777777776555555543
No 107
>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=82.15 E-value=1.2 Score=32.93 Aligned_cols=58 Identities=31% Similarity=0.753 Sum_probs=26.0
Q ss_pred eEeCCCCccccccccCCCCCCCcceeecCccccccCCCCCCeeccCCCC----cceeCCccceeeccccCcccccc
Q 027217 66 VICSVCDTEQPVAQVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCG----ICRIGGRENYFHCKRCGSCYSTS 137 (226)
Q Consensus 66 v~Cg~C~~~q~v~~~C~~Cg~~f~~Y~C~~C~l~dd~~~k~~yHC~~Cg----iCR~G~~~~~fHC~~C~~C~s~~ 137 (226)
..|..|+.++...+ +.|+|+.|.-- -+.+-.|++|| +-+.=|..||| |..|+.=+|++
T Consensus 2 ~~CP~C~~~L~~~~---------~~~~C~~C~~~----~~~~a~CPdC~~~Le~LkACGAvdYF-C~~c~gLiSKk 63 (70)
T PF07191_consen 2 NTCPKCQQELEWQG---------GHYHCEACQKD----YKKEAFCPDCGQPLEVLKACGAVDYF-CNHCHGLISKK 63 (70)
T ss_dssp -B-SSS-SBEEEET---------TEEEETTT--E----EEEEEE-TTT-SB-EEEEETTEEEEE--TTTT-EE-TT
T ss_pred CcCCCCCCccEEeC---------CEEECcccccc----ceecccCCCcccHHHHHHHhccccee-eccCCceeecc
Confidence 34555555544432 46667766421 13456688887 44444555665 66666555543
No 108
>PHA00626 hypothetical protein
Probab=81.90 E-value=1.1 Score=31.86 Aligned_cols=7 Identities=43% Similarity=1.355 Sum_probs=3.7
Q ss_pred cCCCCCC
Q 027217 80 VCTNCGV 86 (226)
Q Consensus 80 ~C~~Cg~ 86 (226)
.||+||.
T Consensus 2 ~CP~CGS 8 (59)
T PHA00626 2 SCPKCGS 8 (59)
T ss_pred CCCCCCC
Confidence 3555555
No 109
>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=80.93 E-value=1.4 Score=23.90 Aligned_cols=21 Identities=33% Similarity=0.697 Sum_probs=15.3
Q ss_pred CCCCCCCeecccchHHHHHHH
Q 027217 190 YCCPICSKSVIDMSRTWKRID 210 (226)
Q Consensus 190 ~~CPiCrksi~dm~~~~~~lD 210 (226)
+.||+|.+++.+....++-+.
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 479999999999888776654
No 110
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=80.76 E-value=1.6 Score=30.63 Aligned_cols=36 Identities=22% Similarity=0.549 Sum_probs=27.5
Q ss_pred CCCCCCccchhhcccCCcceeeeccCCccCHHHHHH
Q 027217 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHE 183 (226)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~ 183 (226)
.+...|++|.+.|.+..+-|+---||=.+|+.|.+.
T Consensus 3 ~~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~ 38 (54)
T PF14446_consen 3 YEGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK 38 (54)
T ss_pred ccCccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence 345789999999766555454456999999999865
No 111
>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=80.26 E-value=1.2 Score=29.53 Aligned_cols=25 Identities=24% Similarity=0.858 Sum_probs=15.7
Q ss_pred ccCCccCHHHHHHHHhcCcC-CCCCC
Q 027217 171 KCGHTMHCECYHEMIKRDKY-CCPIC 195 (226)
Q Consensus 171 pCGH~~H~~C~~~~l~~~~~-~CPiC 195 (226)
.|+=.+|..|++.++++.+. +||.|
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 112
>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=80.01 E-value=1 Score=27.39 Aligned_cols=37 Identities=24% Similarity=0.469 Sum_probs=23.7
Q ss_pred CccchhhcccCCcceeeeccCCccCHHHHHHHHhcCcCCCCCCCeecc
Q 027217 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (226)
Q Consensus 153 CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (226)
|+.|.+.+..+...+.. =|..||..|| +|..|+++|.
T Consensus 2 C~~C~~~i~~~~~~~~~--~~~~~H~~Cf---------~C~~C~~~L~ 38 (39)
T smart00132 2 CAGCGKPIRGGELVLRA--LGKVWHPECF---------KCSKCGKPLG 38 (39)
T ss_pred ccccCCcccCCcEEEEe--CCccccccCC---------CCcccCCcCc
Confidence 67788876653122222 2788998876 6777877764
No 113
>PHA03096 p28-like protein; Provisional
Probab=79.96 E-value=0.75 Score=42.20 Aligned_cols=48 Identities=17% Similarity=0.306 Sum_probs=32.1
Q ss_pred CCCccchhhcccCC---cceeee-ccCCccCHHHHHHHHhcC--cCCCCCCCee
Q 027217 151 HHCPICYEYLFDSL---RNTTVM-KCGHTMHCECYHEMIKRD--KYCCPICSKS 198 (226)
Q Consensus 151 ~~CpICle~lf~s~---~~v~~L-pCGH~~H~~C~~~~l~~~--~~~CPiCrks 198 (226)
-.|.||+|...... ..-..| .|-|.|-..|+..|...+ .-+||.|+..
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~~ 232 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRRL 232 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCccccch
Confidence 46899998866532 112245 599999999999998643 3345555543
No 114
>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=79.93 E-value=1.4 Score=43.11 Aligned_cols=50 Identities=20% Similarity=0.642 Sum_probs=41.6
Q ss_pred eeecCCCCCcccChhhHHhhhcCCCCCCCCccccccccceeEeCCCCccccccccCCCCCCC
Q 027217 26 RIRAPCCNEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVAQVCTNCGVN 87 (226)
Q Consensus 26 ~l~~pCC~~~y~Cr~CHde~~~h~~~~~~~H~~~r~~~~~v~Cg~C~~~q~v~~~C~~Cg~~ 87 (226)
.+.|.-||....|..|.-.++-| . ....+.|-.|+..+++...||+||..
T Consensus 213 ~~~C~~Cg~~~~C~~C~~~l~~h--------~----~~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 213 NLLCRSCGYILCCPNCDVSLTYH--------K----KEGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred eeEhhhCcCccCCCCCCCceEEe--------c----CCCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 37899999999999997666532 2 23579999999999999999999875
No 115
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=79.44 E-value=2 Score=46.61 Aligned_cols=33 Identities=30% Similarity=0.761 Sum_probs=20.2
Q ss_pred eeEeCCCCccccccccCCCCCCCc-ceeecCcccc
Q 027217 65 QVICSVCDTEQPVAQVCTNCGVNM-GEYFCDICKF 98 (226)
Q Consensus 65 ~v~Cg~C~~~q~v~~~C~~Cg~~f-~~Y~C~~C~l 98 (226)
...|..|+++- ....|+.||+.. ..|.|..|..
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 46777777753 334777777665 2445666654
No 116
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=78.07 E-value=0.9 Score=38.97 Aligned_cols=31 Identities=23% Similarity=0.301 Sum_probs=25.3
Q ss_pred CCCCCCCccchhhcccCCcceeeeccCCccCH
Q 027217 147 NSMHHHCPICYEYLFDSLRNTTVMKCGHTMHC 178 (226)
Q Consensus 147 ~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~ 178 (226)
+....+|.||||+|.. .+.+..|||==++|+
T Consensus 174 ~ddkGECvICLEdL~~-GdtIARLPCLCIYHK 204 (205)
T KOG0801|consen 174 KDDKGECVICLEDLEA-GDTIARLPCLCIYHK 204 (205)
T ss_pred cccCCcEEEEhhhccC-CCceeccceEEEeec
Confidence 3556899999999776 678899999877775
No 117
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=76.55 E-value=1.6 Score=40.81 Aligned_cols=45 Identities=31% Similarity=0.695 Sum_probs=36.3
Q ss_pred CCCccchhhcccCCcceeeeccCCccCHHHHHHHHhcCcCCCCCCCee
Q 027217 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKS 198 (226)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrks 198 (226)
..||.|.--|- .+++.--|||.|..+||..-|....+.||.|.+.
T Consensus 275 LkCplc~~Llr---np~kT~cC~~~fc~eci~~al~dsDf~CpnC~rk 319 (427)
T COG5222 275 LKCPLCHCLLR---NPMKTPCCGHTFCDECIGTALLDSDFKCPNCSRK 319 (427)
T ss_pred ccCcchhhhhh---CcccCccccchHHHHHHhhhhhhccccCCCcccc
Confidence 46999987544 3666656899999999998776678999999873
No 118
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=76.16 E-value=2.4 Score=43.74 Aligned_cols=79 Identities=19% Similarity=0.377 Sum_probs=49.0
Q ss_pred CCeeccCCCCcceeCCccceeeccccCccccccccCcceeecCCCCCCCccchhhcccCCcceeeeccCCccCHHHHHHH
Q 027217 105 KGQFHCDDCGICRIGGRENYFHCKRCGSCYSTSLRNNHLCIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEM 184 (226)
Q Consensus 105 k~~yHC~~CgiCR~G~~~~~fHC~~C~~C~s~~l~~~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~ 184 (226)
.-+|-|+.|+-=-++++. - +|+.|-+.+ ...|.||-..+-. ..+----|||..|.+++.+|
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--W---QCDRCESRA------------SAKCTVCDLVIRG--VDVWCQVCGHGGHDSHLKSW 811 (839)
T ss_pred eeeccccccCCccccccc--e---eechHHHHh------------hcCceeecceeee--eEeecccccccccHHHHHHH
Confidence 346777777655454433 3 344444433 2368888876443 12233359999999999999
Q ss_pred HhcCcCCCCC-------CCeecccch
Q 027217 185 IKRDKYCCPI-------CSKSVIDMS 203 (226)
Q Consensus 185 l~~~~~~CPi-------Crksi~dm~ 203 (226)
+.. +..||. +++++.||.
T Consensus 812 ~~~-~s~ca~~~C~~~c~~~~~~D~~ 836 (839)
T KOG0269|consen 812 FFK-ASPCAKSICPHLCHYSSFIDTF 836 (839)
T ss_pred Hhc-CCCCccccCCccccccccchhh
Confidence 984 567776 445566664
No 119
>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=75.20 E-value=3 Score=28.39 Aligned_cols=9 Identities=67% Similarity=1.483 Sum_probs=4.9
Q ss_pred CCCCCCeec
Q 027217 191 CCPICSKSV 199 (226)
Q Consensus 191 ~CPiCrksi 199 (226)
.||||.+.+
T Consensus 33 ~CPiC~~~~ 41 (54)
T PF05605_consen 33 VCPICSSRV 41 (54)
T ss_pred cCCCchhhh
Confidence 366666543
No 120
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=74.97 E-value=0.28 Score=46.96 Aligned_cols=50 Identities=22% Similarity=0.436 Sum_probs=43.6
Q ss_pred CCCCccchhhcccCCcceeeeccCCccCHHHHHHHHhcCcCCCCCCCeecc
Q 027217 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (226)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (226)
-..+.||.+.|...-+....+.|||..|.+++.+||.. ..++|-|++.+-
T Consensus 196 v~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~~-~~kl~~~~rel~ 245 (465)
T KOG0827|consen 196 VGSLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLAT-KRKLPSCRRELP 245 (465)
T ss_pred HhhhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHHH-HHHhHHHHhhhh
Confidence 45799999998876677888999999999999999986 679999998875
No 121
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=74.50 E-value=3.1 Score=42.89 Aligned_cols=43 Identities=28% Similarity=0.781 Sum_probs=29.5
Q ss_pred ceeEeCCCCccccccccCCCCCCCc------ceeecCccccccCCCCCCeeccCCCC
Q 027217 64 KQVICSVCDTEQPVAQVCTNCGVNM------GEYFCDICKFYDDDIEKGQFHCDDCG 114 (226)
Q Consensus 64 ~~v~Cg~C~~~q~v~~~C~~Cg~~f------~~Y~C~~C~l~dd~~~k~~yHC~~Cg 114 (226)
+.++|..|+.. ..|++|+..+ +...|--|..= ++.+.+|+.||
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 58999999976 5799999888 44455555432 34566666666
No 122
>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]
Probab=73.96 E-value=1.5 Score=45.34 Aligned_cols=48 Identities=31% Similarity=0.565 Sum_probs=33.9
Q ss_pred CCCCccchhhcccCC---cceeeeccCCccCHHHHHHHHhcCcCCCCCCCeec
Q 027217 150 HHHCPICYEYLFDSL---RNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSV 199 (226)
Q Consensus 150 ~~~CpICle~lf~s~---~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi 199 (226)
++-|.-|.+....+. ..+.++.|||.||+.|+.....++ .|-+|.--.
T Consensus 784 e~rc~~c~~~~l~~~~~~~~~~v~~c~h~yhk~c~~~~~~~~--~~~~~~~~~ 834 (846)
T KOG2066|consen 784 EERCSSCFEPNLPSGAAFDSVVVFHCGHMYHKECLMMESLRN--ACNIESGKN 834 (846)
T ss_pred hhhhhhhcccccccCcccceeeEEEccchhhhcccccHHHhc--ccChhhcee
Confidence 346777777765444 578899999999999998776533 266665433
No 123
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=73.90 E-value=3 Score=42.94 Aligned_cols=54 Identities=22% Similarity=0.532 Sum_probs=43.9
Q ss_pred eeecCCCCCcccChhhHHhhhcCCCCCCCCccccccccceeEeCCCCccccccccCCCCCCCccee
Q 027217 26 RIRAPCCNEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVAQVCTNCGVNMGEY 91 (226)
Q Consensus 26 ~l~~pCC~~~y~Cr~CHde~~~h~~~~~~~H~~~r~~~~~v~Cg~C~~~q~v~~~C~~Cg~~f~~Y 91 (226)
.+.|.-||..+.|.+|=.-.+-|. .+..+.|-.|+..+++-..||+||...=+|
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 488999999999999965554332 247899999999999999999999985444
No 124
>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=73.43 E-value=1.3 Score=40.23 Aligned_cols=51 Identities=24% Similarity=0.546 Sum_probs=40.6
Q ss_pred CCCCccchhhcccCCcceeee-c-cCCccCHHHHHHHHhcCcCCCC--CCCeecc
Q 027217 150 HHHCPICYEYLFDSLRNTTVM-K-CGHTMHCECYHEMIKRDKYCCP--ICSKSVI 200 (226)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~L-p-CGH~~H~~C~~~~l~~~~~~CP--iCrksi~ 200 (226)
+..||||..+.+-+++-...+ | |=|-|..+|.+.-+..+.-.|| -|.|.+-
T Consensus 10 d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kILR 64 (314)
T COG5220 10 DRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKILR 64 (314)
T ss_pred cccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHHH
Confidence 457999999987765433333 5 9999999999999988888999 7877653
No 125
>PLN03086 PRLI-interacting factor K; Provisional
Probab=72.15 E-value=1.8 Score=43.38 Aligned_cols=84 Identities=26% Similarity=0.603 Sum_probs=49.0
Q ss_pred ccceeEeCCCCcccccc-------------ccCCC--CCCCcceeecCccccccCCCCCCeeccCCCCcceeCCc-----
Q 027217 62 DVKQVICSVCDTEQPVA-------------QVCTN--CGVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGR----- 121 (226)
Q Consensus 62 ~~~~v~Cg~C~~~q~v~-------------~~C~~--Cg~~f~~Y~C~~C~l~dd~~~k~~yHC~~CgiCR~G~~----- 121 (226)
++..|.|..|....+.. ..|++ ||..|.+- .-+..+||+.||- ..+..
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 45688999998776552 24664 77766332 2345678888864 22211
Q ss_pred ----cceeeccccCccccccccCcce---eecCCCCCCCccchhhc
Q 027217 122 ----ENYFHCKRCGSCYSTSLRNNHL---CIENSMHHHCPICYEYL 160 (226)
Q Consensus 122 ----~~~fHC~~C~~C~s~~l~~~H~---C~e~~~~~~CpICle~l 160 (226)
..-+-|. ||.-+.......|. |.+ ....|+.|...+
T Consensus 472 ~~~~Hkpv~Cp-Cg~~~~R~~L~~H~~thCp~--Kpi~C~fC~~~v 514 (567)
T PLN03086 472 MKVFHEPLQCP-CGVVLEKEQMVQHQASTCPL--RLITCRFCGDMV 514 (567)
T ss_pred HHhcCCCccCC-CCCCcchhHHHhhhhccCCC--CceeCCCCCCcc
Confidence 1124576 77655544445564 333 245799998764
No 126
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=71.89 E-value=3.3 Score=45.02 Aligned_cols=33 Identities=30% Similarity=0.730 Sum_probs=25.5
Q ss_pred ccCCCCCCCcceeecCccccccCCCCCCeeccCCCCc
Q 027217 79 QVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGI 115 (226)
Q Consensus 79 ~~C~~Cg~~f~~Y~C~~C~l~dd~~~k~~yHC~~Cgi 115 (226)
-.||+||+.....||+.|.-. .+.+|+|+.||.
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 479999988777799999654 245788888876
No 127
>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=70.19 E-value=3.2 Score=34.04 Aligned_cols=28 Identities=21% Similarity=0.455 Sum_probs=20.9
Q ss_pred ccccCCCCCCCcceeecCccccccCCCCCCeeccCCCCcc
Q 027217 77 VAQVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGIC 116 (226)
Q Consensus 77 v~~~C~~Cg~~f~~Y~C~~C~l~dd~~~k~~yHC~~CgiC 116 (226)
....|++||+.| | +.+|.+-.|++||.=
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 557889999998854
No 128
>PRK04023 DNA polymerase II large subunit; Validated
Probab=68.51 E-value=4.2 Score=43.39 Aligned_cols=50 Identities=24% Similarity=0.587 Sum_probs=37.0
Q ss_pred cceeEeCCCCccccccccCCCCCCC-cceeecCccccccCCCCCCeeccCCCCccee
Q 027217 63 VKQVICSVCDTEQPVAQVCTNCGVN-MGEYFCDICKFYDDDIEKGQFHCDDCGICRI 118 (226)
Q Consensus 63 ~~~v~Cg~C~~~q~v~~~C~~Cg~~-f~~Y~C~~C~l~dd~~~k~~yHC~~CgiCR~ 118 (226)
+..-.|..|+++. +...|++||.. -..|||+.|.-- -..|.|++||.=..
T Consensus 624 Vg~RfCpsCG~~t-~~frCP~CG~~Te~i~fCP~CG~~-----~~~y~CPKCG~El~ 674 (1121)
T PRK04023 624 IGRRKCPSCGKET-FYRRCPFCGTHTEPVYRCPRCGIE-----VEEDECEKCGREPT 674 (1121)
T ss_pred ccCccCCCCCCcC-CcccCCCCCCCCCcceeCccccCc-----CCCCcCCCCCCCCC
Confidence 3455899999984 66899999974 677899999433 23478999986433
No 129
>PRK05580 primosome assembly protein PriA; Validated
Probab=68.37 E-value=3.8 Score=41.55 Aligned_cols=51 Identities=22% Similarity=0.632 Sum_probs=41.6
Q ss_pred eeecCCCCCcccChhhHHhhhcCCCCCCCCccccccccceeEeCCCCccccccccCCCCCCCc
Q 027217 26 RIRAPCCNEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVAQVCTNCGVNM 88 (226)
Q Consensus 26 ~l~~pCC~~~y~Cr~CHde~~~h~~~~~~~H~~~r~~~~~v~Cg~C~~~q~v~~~C~~Cg~~f 88 (226)
.+.|.-||...-|..|.-...- |. ....+.|-.|+..+++...|++||...
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 3789999999999999876543 22 246799999999999999999998864
No 130
>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=67.74 E-value=4.6 Score=23.88 Aligned_cols=9 Identities=44% Similarity=1.239 Sum_probs=5.2
Q ss_pred CeeccCCCC
Q 027217 106 GQFHCDDCG 114 (226)
Q Consensus 106 ~~yHC~~Cg 114 (226)
..|.|++||
T Consensus 15 v~f~CPnCG 23 (24)
T PF07754_consen 15 VPFPCPNCG 23 (24)
T ss_pred ceEeCCCCC
Confidence 456666665
No 131
>PRK14873 primosome assembly protein PriA; Provisional
Probab=66.83 E-value=4.2 Score=41.39 Aligned_cols=49 Identities=20% Similarity=0.491 Sum_probs=39.0
Q ss_pred eeecCCCCCcccChhhHHhhhcCCCCCCCCccccccccceeEeCCCCccccccccCCCCCCC
Q 027217 26 RIRAPCCNEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVAQVCTNCGVN 87 (226)
Q Consensus 26 ~l~~pCC~~~y~Cr~CHde~~~h~~~~~~~H~~~r~~~~~v~Cg~C~~~q~v~~~C~~Cg~~ 87 (226)
.+.|.-||...-|..|.-.++- |. ....+.|-.|+..+ ....|++||..
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 4899999999999999876653 21 23578899999876 57899999886
No 132
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=66.26 E-value=3.4 Score=37.87 Aligned_cols=29 Identities=21% Similarity=0.526 Sum_probs=25.7
Q ss_pred CccCcccccccceeecCCCCCcccChhhHH
Q 027217 14 MGYGCKHYRRRCRIRAPCCNEIFDCRHCHN 43 (226)
Q Consensus 14 ~~~gC~HY~r~c~l~~pCC~~~y~Cr~CHd 43 (226)
..+.|.||...=.++..+|.. |+|..||+
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 346799999866799999999 99999999
No 133
>KOG2068 consensus MOT2 transcription factor [Transcription]
Probab=66.17 E-value=4.6 Score=37.89 Aligned_cols=51 Identities=29% Similarity=0.505 Sum_probs=39.5
Q ss_pred CCCCCccchhhcccCCcceeeeccCCccCHHHHHHHHhcCcCCCCCCCeecc
Q 027217 149 MHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (226)
Q Consensus 149 ~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (226)
....||||-+++.........-|||+-++..|...-.. .+.+||.|+|...
T Consensus 248 v~~s~p~~~~~~~~~d~~~lP~~~~~~~~l~~~~t~~~-~~~~~~~~rk~~~ 298 (327)
T KOG2068|consen 248 VPPSCPICYEDLDLTDSNFLPCPCGFRLCLFCHKTISD-GDGRCPGCRKPYE 298 (327)
T ss_pred cCCCCCCCCCcccccccccccccccccchhhhhhcccc-cCCCCCccCCccc
Confidence 34689999999755444444456899999999988776 5789999998775
No 134
>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=64.91 E-value=3.7 Score=40.27 Aligned_cols=98 Identities=22% Similarity=0.431 Sum_probs=53.9
Q ss_pred eeecCccccccCCCCCCeeccCCCCcceeCCccceeeccccCccccccc--cCcceeecCCCCCCCccchhhcccCCcce
Q 027217 90 EYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYSTSL--RNNHLCIENSMHHHCPICYEYLFDSLRNT 167 (226)
Q Consensus 90 ~Y~C~~C~l~dd~~~k~~yHC~~CgiCR~G~~~~~fHC~~C~~C~s~~l--~~~H~C~e~~~~~~CpICle~lf~s~~~v 167 (226)
-|||..|+-. .|+-|-....+ .+=|..|-.=++.+- .++.+|..+- -+||+|.-.|.......
T Consensus 5 L~fC~~C~~i------------rc~~c~~~Ei~-~~yCp~CL~~~p~~e~~~~~nrC~r~C--f~CP~C~~~L~~~~~~~ 69 (483)
T PF05502_consen 5 LYFCEHCHKI------------RCPRCVSEEID-SYYCPNCLFEVPSSEARSEKNRCSRNC--FDCPICFSPLSVRASDT 69 (483)
T ss_pred ceeccccccc------------CChhhcccccc-eeECccccccCChhhheeccceecccc--ccCCCCCCcceeEeccc
Confidence 4889988766 23445544444 445666665555432 3567777553 47999998876643332
Q ss_pred ee---eccCCccCHHHHHHHHhcCcCCCCCCCeecccchHHHHHHH
Q 027217 168 TV---MKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRTWKRID 210 (226)
Q Consensus 168 ~~---LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~dm~~~~~~lD 210 (226)
.. -+-+=.- -......|+.|+=+-.++...|.+.+
T Consensus 70 ~~~~~~~~~~~~--------~~~~~l~C~~C~Wss~~igi~Fdkpt 107 (483)
T PF05502_consen 70 PPSPPDPSSDSG--------GKPYYLSCSYCRWSSRDIGIKFDKPT 107 (483)
T ss_pred ccccccccccCC--------CCCEEEECCCceeeccccCccccCch
Confidence 11 0000000 00123589999988776554444444
No 135
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=64.84 E-value=5.2 Score=28.17 Aligned_cols=27 Identities=30% Similarity=0.774 Sum_probs=15.9
Q ss_pred cccCCCCCCCcceeecCccccccCCCCCCeeccCCCCc
Q 027217 78 AQVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGI 115 (226)
Q Consensus 78 ~~~C~~Cg~~f~~Y~C~~C~l~dd~~~k~~yHC~~Cgi 115 (226)
++.|+.||..... ......|.|+.||.
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 4667777776655 22344566666554
No 136
>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 KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=64.11 E-value=4.4 Score=37.13 Aligned_cols=51 Identities=24% Similarity=0.661 Sum_probs=29.6
Q ss_pred ccChhhHHhhhcCCCCCCCCccccccccceeEeCCCCccccccccCCCCCCCcceeecCccccc-cCCC
Q 027217 36 FDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVAQVCTNCGVNMGEYFCDICKFY-DDDI 103 (226)
Q Consensus 36 y~Cr~CHde~~~h~~~~~~~H~~~r~~~~~v~Cg~C~~~q~v~~~C~~Cg~~f~~Y~C~~C~l~-dd~~ 103 (226)
|.|.+|-..+++ --..|. ..+++|-.|...-.+ +.-|+|-|.+|+-. |+++
T Consensus 100 F~Cd~Cn~~Lad--------~gf~rn-qgr~LC~~Cn~k~Ka--------~~~g~YvC~KCh~~iD~~~ 151 (332)
T KOG2272|consen 100 FRCDLCNKHLAD--------QGFYRN-QGRALCRECNQKEKA--------KGRGRYVCQKCHAHIDEQP 151 (332)
T ss_pred chhHHHHHHHhh--------hhhHhh-cchHHhhhhhhhhcc--------cccceeehhhhhhhccccc
Confidence 456666665543 122333 346777777654332 23589999999744 5543
No 138
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=63.74 E-value=6.4 Score=37.11 Aligned_cols=44 Identities=23% Similarity=0.631 Sum_probs=35.4
Q ss_pred CCccchhhcccCCcceeeeccCCccCHHHHHHHHhcC--cCCCCCCC
Q 027217 152 HCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRD--KYCCPICS 196 (226)
Q Consensus 152 ~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~--~~~CPiCr 196 (226)
-|||=.|. -+...+...|.|||++=+.=++.+-+++ .++||.|-
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 58887765 5556677889999999999999987764 67799996
No 139
>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=63.43 E-value=5.5 Score=24.14 Aligned_cols=20 Identities=30% Similarity=0.853 Sum_probs=13.3
Q ss_pred CCCcceeCCccc-eeeccccC
Q 027217 112 DCGICRIGGREN-YFHCKRCG 131 (226)
Q Consensus 112 ~CgiCR~G~~~~-~fHC~~C~ 131 (226)
.|++|+.-.... +++|..|+
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 140
>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=62.93 E-value=5.9 Score=21.75 Aligned_cols=17 Identities=47% Similarity=0.794 Sum_probs=13.1
Q ss_pred CCCCCCCeecccchHHH
Q 027217 190 YCCPICSKSVIDMSRTW 206 (226)
Q Consensus 190 ~~CPiCrksi~dm~~~~ 206 (226)
|+||+|.+++.+.+.+-
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 141
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=62.63 E-value=3.7 Score=41.96 Aligned_cols=45 Identities=31% Similarity=0.855 Sum_probs=35.6
Q ss_pred CCCccchhhcccCCcceeeeccCCccCHHHHHHHHhcCcC-CCCCCCeecc
Q 027217 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKY-CCPICSKSVI 200 (226)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~-~CPiCrksi~ 200 (226)
..|+||++ .+....-+|||.|-..|+.+.+..... .||+|+..+.
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 78999999 245667799999999999998875433 5999996553
No 142
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=61.08 E-value=3.2 Score=45.11 Aligned_cols=52 Identities=31% Similarity=0.650 Sum_probs=41.3
Q ss_pred CCCCCCccchhhcccCCcceeeeccCCccCHHHHHHHHhcCcCCCCCCCeecccch
Q 027217 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMS 203 (226)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~dm~ 203 (226)
+....|+||++.|-. .-.+..|||.+-..|+..|+. .+..||+|+....|-.
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 334589999998763 234568999999999999998 4789999997776644
No 143
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=60.93 E-value=4.2 Score=41.33 Aligned_cols=34 Identities=26% Similarity=0.666 Sum_probs=20.9
Q ss_pred eeEeCCCCccccccccCCCCCCCc--ceeecCccccc
Q 027217 65 QVICSVCDTEQPVAQVCTNCGVNM--GEYFCDICKFY 99 (226)
Q Consensus 65 ~v~Cg~C~~~q~v~~~C~~Cg~~f--~~Y~C~~C~l~ 99 (226)
.-.|..|++.++. ..|++||+.. +.-||+.|-..
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 4567777766543 4677777553 55667766544
No 144
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=60.48 E-value=6.9 Score=25.20 Aligned_cols=26 Identities=23% Similarity=0.579 Sum_probs=15.0
Q ss_pred cCCCCCCCcceeecCccccccCCCCCCeeccCCCC
Q 027217 80 VCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCG 114 (226)
Q Consensus 80 ~C~~Cg~~f~~Y~C~~C~l~dd~~~k~~yHC~~Cg 114 (226)
+||.|+..|..+. + .+-.++.|+.||
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 124566666665
No 145
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=60.21 E-value=4.3 Score=37.15 Aligned_cols=68 Identities=25% Similarity=0.487 Sum_probs=45.3
Q ss_pred CCCCCCccchhhcccCCcceeeecc---C--CccCHHHHHHHHhcC-------cCCCCCCCeecc-------cchHHHHH
Q 027217 148 SMHHHCPICYEYLFDSLRNTTVMKC---G--HTMHCECYHEMIKRD-------KYCCPICSKSVI-------DMSRTWKR 208 (226)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpC---G--H~~H~~C~~~~l~~~-------~~~CPiCrksi~-------dm~~~~~~ 208 (226)
..+--|=||++.=.+.+...-+=|| | |..|..|+..|+.++ .-+||.|+.... ..+..-+.
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 3455699999863333333234576 3 999999999999753 346999997643 23345567
Q ss_pred HHHHHHh
Q 027217 209 IDEELQM 215 (226)
Q Consensus 209 lD~~i~~ 215 (226)
+|..|..
T Consensus 98 ~d~~i~r 104 (293)
T KOG3053|consen 98 LDILIFR 104 (293)
T ss_pred hhhHHhh
Confidence 7777665
No 146
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=59.67 E-value=9.6 Score=35.02 Aligned_cols=20 Identities=40% Similarity=0.429 Sum_probs=11.6
Q ss_pred CcCCCCCCCeecccchHHHH
Q 027217 188 DKYCCPICSKSVIDMSRTWK 207 (226)
Q Consensus 188 ~~~~CPiCrksi~dm~~~~~ 207 (226)
..|+|+-|.|++.-||-..+
T Consensus 242 K~~qC~~C~KsFsl~SyLnK 261 (279)
T KOG2462|consen 242 KKHQCPRCGKSFALKSYLNK 261 (279)
T ss_pred ccccCcchhhHHHHHHHHHH
Confidence 35666666666666654333
No 147
>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=59.55 E-value=6.6 Score=35.48 Aligned_cols=47 Identities=26% Similarity=0.632 Sum_probs=21.8
Q ss_pred ceeEeCCCCcccccc-ccCCCCCCCcceeecCccccc--cCCCCCCeeccCCCC
Q 027217 64 KQVICSVCDTEQPVA-QVCTNCGVNMGEYFCDICKFY--DDDIEKGQFHCDDCG 114 (226)
Q Consensus 64 ~~v~Cg~C~~~q~v~-~~C~~Cg~~f~~Y~C~~C~l~--dd~~~k~~yHC~~Cg 114 (226)
+-..|+.|+++-.+. ..|++||..-..-+ .+| ++++.-.++-|+.||
T Consensus 196 R~L~Cs~C~t~W~~~R~~Cp~Cg~~~~~~l----~~~~~e~~~~~rve~C~~C~ 245 (290)
T PF04216_consen 196 RYLHCSLCGTEWRFVRIKCPYCGNTDHEKL----EYFTVEGEPAYRVEVCESCG 245 (290)
T ss_dssp EEEEETTT--EEE--TTS-TTT---SS-EE----E--------SEEEEEETTTT
T ss_pred EEEEcCCCCCeeeecCCCCcCCCCCCCcce----eeEecCCCCcEEEEECCccc
Confidence 678999999998774 68999997765543 333 333344455555544
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=59.10 E-value=2.5 Score=27.08 Aligned_cols=27 Identities=33% Similarity=0.671 Sum_probs=14.7
Q ss_pred cCCCCCCCcceeecCccccccCCCCCCeeccCCCCc
Q 027217 80 VCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGI 115 (226)
Q Consensus 80 ~C~~Cg~~f~~Y~C~~C~l~dd~~~k~~yHC~~Cgi 115 (226)
.|++||+.++.+| ++.|..=-||.||-
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 3666676666554 34455555666664
No 149
>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=57.85 E-value=6.5 Score=26.75 Aligned_cols=26 Identities=23% Similarity=0.670 Sum_probs=12.9
Q ss_pred CCCCCCCeecccch--HHHHHHHHHHHh
Q 027217 190 YCCPICSKSVIDMS--RTWKRIDEELQM 215 (226)
Q Consensus 190 ~~CPiCrksi~dm~--~~~~~lD~~i~~ 215 (226)
..||||.+++.+=. .+-+.+..+|..
T Consensus 21 ~~CPlC~r~l~~e~~~~li~~~~~~i~~ 48 (54)
T PF04423_consen 21 GCCPLCGRPLDEEHRQELIKKYKSEIEE 48 (54)
T ss_dssp EE-TTT--EE-HHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCCCCHHHHHHHHHHHHHHHHh
Confidence 38999999998532 244455555443
No 150
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=57.10 E-value=12 Score=28.41 Aligned_cols=50 Identities=26% Similarity=0.458 Sum_probs=33.7
Q ss_pred CCccchhhcccCCcceeeeccCCccCHHHHHHHHhcCcCCCCCCCeecccchHHHHHHHHHHHhCCCCCCCCCC
Q 027217 152 HCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRTWKRIDEELQMNSSIFFPSFF 225 (226)
Q Consensus 152 ~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~dm~~~~~~lD~~i~~~pm~~~~~~~ 225 (226)
.||||--.|-.|...-+. -..||-||---+|-- .||.+|+.+-.|+ |.+|
T Consensus 3 lCP~C~v~l~~~~rs~vE-------------------iD~CPrCrGVWLDrG----ELdKli~r~r~pq-pa~y 52 (88)
T COG3809 3 LCPICGVELVMSVRSGVE-------------------IDYCPRCRGVWLDRG----ELDKLIERSRYPQ-PAEY 52 (88)
T ss_pred ccCcCCceeeeeeecCce-------------------eeeCCccccEeecch----hHHHHHHHhcCCC-Cccc
Confidence 599999887765433221 357999998777653 5888888776543 4444
No 151
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=56.60 E-value=6.4 Score=28.16 Aligned_cols=35 Identities=31% Similarity=0.510 Sum_probs=25.5
Q ss_pred ceeEeCCCCccccc------cccCCCCCCCcceeecCcccc
Q 027217 64 KQVICSVCDTEQPV------AQVCTNCGVNMGEYFCDICKF 98 (226)
Q Consensus 64 ~~v~Cg~C~~~q~v------~~~C~~Cg~~f~~Y~C~~C~l 98 (226)
-.|.|..|.++|.+ ...|..||..+++-.=.+-+|
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 36899999999866 247999999887655444443
No 152
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=56.17 E-value=3.8 Score=37.64 Aligned_cols=51 Identities=27% Similarity=0.735 Sum_probs=30.2
Q ss_pred CCcccChhhHHhhhcCCCCCCCCccccccccceeEeCCCCccccccccCCCCCCCcceeecCcccc
Q 027217 33 NEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVAQVCTNCGVNMGEYFCDICKF 98 (226)
Q Consensus 33 ~~~y~Cr~CHde~~~h~~~~~~~H~~~r~~~~~v~Cg~C~~~q~v~~~C~~Cg~~f~~Y~C~~C~l 98 (226)
|++|.|-+|.+-+-.. ++++ |+.. |+...+-+-.|.+|+. ++.|.|..||.
T Consensus 140 Grif~CsfC~~flCED--DQFE-HQAs-----------CQvLe~E~~KC~SCNr-lGq~sCLRCK~ 190 (314)
T PF06524_consen 140 GRIFKCSFCDNFLCED--DQFE-HQAS-----------CQVLESETFKCQSCNR-LGQYSCLRCKI 190 (314)
T ss_pred CeEEEeecCCCeeecc--chhh-hhhh-----------hhhhhccccccccccc-ccchhhhheee
Confidence 5678888887655321 1112 2221 5444455567888864 78888888874
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=55.98 E-value=9.6 Score=24.74 Aligned_cols=7 Identities=57% Similarity=1.583 Sum_probs=3.7
Q ss_pred CCCCCCC
Q 027217 81 CTNCGVN 87 (226)
Q Consensus 81 C~~Cg~~ 87 (226)
||+||+.
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
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=55.96 E-value=7.4 Score=32.28 Aligned_cols=49 Identities=31% Similarity=0.621 Sum_probs=35.7
Q ss_pred CCCccchhhcccCCcceeee-c---cCCccCHHHHHHHHhc--CcCCCCCCCeecccch
Q 027217 151 HHCPICYEYLFDSLRNTTVM-K---CGHTMHCECYHEMIKR--DKYCCPICSKSVIDMS 203 (226)
Q Consensus 151 ~~CpICle~lf~s~~~v~~L-p---CGH~~H~~C~~~~l~~--~~~~CPiCrksi~dm~ 203 (226)
-.|-||.|. |. +.+.| | ||=.+..-|+.++++. -.-.||+|+.|+-..+
T Consensus 81 YeCnIC~et---S~-ee~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKss~ 135 (140)
T PF05290_consen 81 YECNICKET---SA-EERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKSSS 135 (140)
T ss_pred eeccCcccc---cc-hhhcCCcccccchHHHHHHHHHHHHHcccCCCCCcccccccccc
Confidence 368888875 22 34456 3 8999999999997664 2456999999986544
No 155
>PF15353 HECA: Headcase protein family homologue
Probab=55.47 E-value=6.1 Score=31.42 Aligned_cols=15 Identities=33% Similarity=0.707 Sum_probs=13.4
Q ss_pred cCCccCHHHHHHHHh
Q 027217 172 CGHTMHCECYHEMIK 186 (226)
Q Consensus 172 CGH~~H~~C~~~~l~ 186 (226)
-|+.||++||++|-.
T Consensus 40 ~~~~MH~~CF~~wE~ 54 (107)
T PF15353_consen 40 FGQYMHRECFEKWED 54 (107)
T ss_pred CCCchHHHHHHHHHH
Confidence 489999999999965
No 156
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=55.41 E-value=8.3 Score=27.60 Aligned_cols=34 Identities=24% Similarity=0.663 Sum_probs=25.4
Q ss_pred cceeEeCCCCccccccccCCCCCCCcceeecCcccc
Q 027217 63 VKQVICSVCDTEQPVAQVCTNCGVNMGEYFCDICKF 98 (226)
Q Consensus 63 ~~~v~Cg~C~~~q~v~~~C~~Cg~~f~~Y~C~~C~l 98 (226)
...-.|..|+.+. -..|..|....+.|-|++|.|
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 235888888888888888876
No 157
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=54.93 E-value=11 Score=24.77 Aligned_cols=8 Identities=38% Similarity=1.074 Sum_probs=4.2
Q ss_pred eeccCCCC
Q 027217 107 QFHCDDCG 114 (226)
Q Consensus 107 ~yHC~~Cg 114 (226)
..+|+.||
T Consensus 21 ~~~Cp~CG 28 (46)
T PRK00398 21 GVRCPYCG 28 (46)
T ss_pred ceECCCCC
Confidence 45555554
No 158
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=54.63 E-value=7.1 Score=26.05 Aligned_cols=21 Identities=33% Similarity=0.918 Sum_probs=10.4
Q ss_pred EeCCCCcccccc----ccCCCCCCC
Q 027217 67 ICSVCDTEQPVA----QVCTNCGVN 87 (226)
Q Consensus 67 ~Cg~C~~~q~v~----~~C~~Cg~~ 87 (226)
+|+.|+.+.+.. ..|++||..
T Consensus 4 ~C~~Cg~~~~~~~~~~irC~~CG~r 28 (44)
T smart00659 4 ICGECGRENEIKSKDVVRCRECGYR 28 (44)
T ss_pred ECCCCCCEeecCCCCceECCCCCce
Confidence 455555554332 245555544
No 159
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=54.59 E-value=6.2 Score=37.57 Aligned_cols=37 Identities=27% Similarity=0.608 Sum_probs=27.4
Q ss_pred CCCCccchhhcccCCcceeeeccCCccCHHHHHHHHh
Q 027217 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIK 186 (226)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~ 186 (226)
...|+||............++.|||.|-..|+.++++
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 5679999933333323333678999999999999987
No 160
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=50.10 E-value=7.6 Score=34.44 Aligned_cols=51 Identities=24% Similarity=0.374 Sum_probs=37.8
Q ss_pred CCCCccchhhcccCCcceeeecc-----CCccCHHHHHHHHhc-CcCCCCCCCeecc
Q 027217 150 HHHCPICYEYLFDSLRNTTVMKC-----GHTMHCECYHEMIKR-DKYCCPICSKSVI 200 (226)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpC-----GH~~H~~C~~~~l~~-~~~~CPiCrksi~ 200 (226)
+..|=||.+..+.+.......|| ....|+.|++.|+.. ++.+|.+|.....
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 35799999986654333445677 278899999999873 4678999998554
No 161
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=49.34 E-value=11 Score=34.04 Aligned_cols=49 Identities=24% Similarity=0.632 Sum_probs=30.3
Q ss_pred CCCCCCCcceeecCccccccCCCCCCeeccCCCCcceeCCccceeeccccCcccc
Q 027217 81 CTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYS 135 (226)
Q Consensus 81 C~~Cg~~f~~Y~C~~C~l~dd~~~k~~yHC~~CgiCR~G~~~~~fHC~~C~~C~s 135 (226)
-..=|......||+.|+++-- +...||.-||.|-.+- ==||.==|.|+.
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 3456777777775542 135555555554
No 162
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=48.24 E-value=26 Score=26.54 Aligned_cols=52 Identities=19% Similarity=0.389 Sum_probs=24.7
Q ss_pred CCCCCCccchhhcccCCcceee---eccCCccCHHHHHHHHhcCcCCCCCCCeec
Q 027217 148 SMHHHCPICYEYLFDSLRNTTV---MKCGHTMHCECYHEMIKRDKYCCPICSKSV 199 (226)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~---LpCGH~~H~~C~~~~l~~~~~~CPiCrksi 199 (226)
...+.|-||.|++-...+.-.+ .-||=.+-+.|++--.+..+..||.|+...
T Consensus 7 ~~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg~q~CpqCkt~y 61 (80)
T PF14569_consen 7 LNGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEGNQVCPQCKTRY 61 (80)
T ss_dssp -SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS-SB-TTT--B-
T ss_pred cCCcccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcCcccccccCCCc
Confidence 4457899999986443333222 358999999999988888888999999554
No 163
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=48.11 E-value=12 Score=23.71 Aligned_cols=10 Identities=40% Similarity=0.949 Sum_probs=4.9
Q ss_pred ceeEeCCCCc
Q 027217 64 KQVICSVCDT 73 (226)
Q Consensus 64 ~~v~Cg~C~~ 73 (226)
..|.|+.|++
T Consensus 24 ~~v~C~~C~~ 33 (36)
T PF13717_consen 24 RKVRCSKCGH 33 (36)
T ss_pred cEEECCCCCC
Confidence 3455555543
No 164
>PHA00626 hypothetical protein
Probab=47.45 E-value=12 Score=26.69 Aligned_cols=34 Identities=18% Similarity=0.400 Sum_probs=22.3
Q ss_pred eEeCCCCccccccccCCCCCCCcceeecCccccccC
Q 027217 66 VICSVCDTEQPVAQVCTNCGVNMGEYFCDICKFYDD 101 (226)
Q Consensus 66 v~Cg~C~~~q~v~~~C~~Cg~~f~~Y~C~~C~l~dd 101 (226)
|.|..|+..+-+ .|.-|...-++|-|..|.+++.
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 456777765444 5566666677788888877644
No 165
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=47.27 E-value=8.9 Score=28.10 Aligned_cols=28 Identities=36% Similarity=0.692 Sum_probs=21.9
Q ss_pred ceeEeCCCCccccc------cccCCCCCCCccee
Q 027217 64 KQVICSVCDTEQPV------AQVCTNCGVNMGEY 91 (226)
Q Consensus 64 ~~v~Cg~C~~~q~v------~~~C~~Cg~~f~~Y 91 (226)
-.|.|.-|+++|.+ ...|..||..+++-
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 37999999999977 24799999877653
No 166
>KOG1312 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=47.12 E-value=6.3 Score=36.71 Aligned_cols=32 Identities=31% Similarity=0.782 Sum_probs=27.9
Q ss_pred CCCCcceeCCccceeeccccCccccccccCcceee
Q 027217 111 DDCGICRIGGRENYFHCKRCGSCYSTSLRNNHLCI 145 (226)
Q Consensus 111 ~~CgiCR~G~~~~~fHC~~C~~C~s~~l~~~H~C~ 145 (226)
.+|..|++.+.--..||..||.|+.+- .|.|+
T Consensus 149 ~kCSTCki~KPARSKHCsiCNrCV~rf---DHHCi 180 (341)
T KOG1312|consen 149 VKCSTCKIRKPARSKHCSICNRCVHRF---DHHCI 180 (341)
T ss_pred CccccccCCCccccccchHHHHHHHHh---ccceE
Confidence 679999999888899999999999875 68886
No 167
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=46.68 E-value=3.1 Score=37.33 Aligned_cols=49 Identities=27% Similarity=0.531 Sum_probs=37.7
Q ss_pred CCCccchhhccc--CCcceeeec--------cCCccCHHHHHHHHhcCcCCCCCCCeec
Q 027217 151 HHCPICYEYLFD--SLRNTTVMK--------CGHTMHCECYHEMIKRDKYCCPICSKSV 199 (226)
Q Consensus 151 ~~CpICle~lf~--s~~~v~~Lp--------CGH~~H~~C~~~~l~~~~~~CPiCrksi 199 (226)
..|.||...+.. ......++. |||++-..|.+..+.....+||.|+++.
T Consensus 208 ~~c~ic~~~~~~n~~~~~p~vl~~~~~~~~~c~htlc~~c~~~~l~~~~~~cp~~~~~~ 266 (296)
T KOG4185|consen 208 KLCEICERIYSENDEKLAPLVLSLSRLKEKIEGHTLCKECIDTILLQAGIKCPFCTWSH 266 (296)
T ss_pred HHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcchHHHHHHhhhcCCccccee
Confidence 469999988552 333345667 9999999999999876567899999863
No 168
>KOG4399 consensus C2HC-type Zn-finger protein [General function prediction only]
Probab=45.86 E-value=4.1 Score=37.37 Aligned_cols=72 Identities=28% Similarity=0.669 Sum_probs=54.8
Q ss_pred CCCcceeecCccccccCCCCCCeeccCCCCcceeCCccceeeccccCccccccccCcceeecCCCCCCCccchhh
Q 027217 85 GVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYSTSLRNNHLCIENSMHHHCPICYEY 159 (226)
Q Consensus 85 g~~f~~Y~C~~C~l~dd~~~k~~yHC~~CgiCR~G~~~~~fHC~~C~~C~s~~l~~~H~C~e~~~~~~CpICle~ 159 (226)
|..=+-.||+.|..| ..+..-||+.|+.|..-.++.|-||.+|-.|+-.++-.--.|-.-+...-|-||-+.
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 444466779999988 456778999999998877778999999999999887433333334556678888886
No 169
>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=45.30 E-value=12 Score=22.44 Aligned_cols=20 Identities=20% Similarity=0.667 Sum_probs=6.0
Q ss_pred CCcceeCCc-cceeeccccCc
Q 027217 113 CGICRIGGR-ENYFHCKRCGS 132 (226)
Q Consensus 113 CgiCR~G~~-~~~fHC~~C~~ 132 (226)
|++|+..+. ..+++|..|+.
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 444544433 25666666654
No 170
>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=45.22 E-value=18 Score=23.29 Aligned_cols=34 Identities=29% Similarity=0.629 Sum_probs=15.6
Q ss_pred cCCCCCCCcceeecCccccccCCCCCCeeccCCCC
Q 027217 80 VCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCG 114 (226)
Q Consensus 80 ~C~~Cg~~f~~Y~C~~C~l~dd~~~k~~yHC~~Cg 114 (226)
.|++||+.-+-|+ .+=--=-|++..-.|.|-+||
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 4788888776665 100000233455556666555
No 171
>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=44.50 E-value=35 Score=28.37 Aligned_cols=28 Identities=21% Similarity=0.604 Sum_probs=22.6
Q ss_pred CcCCCCCCCeecc--cchHHHHHHHHHHHh
Q 027217 188 DKYCCPICSKSVI--DMSRTWKRIDEELQM 215 (226)
Q Consensus 188 ~~~~CPiCrksi~--dm~~~~~~lD~~i~~ 215 (226)
..++||.|+..+. |-+..-+.|.+.|+.
T Consensus 127 ~~F~Cp~Cg~~L~~~dn~~~i~~l~~~i~~ 156 (158)
T TIGR00373 127 LNFTCPRCGAMLDYLDNSEAIEKLEEQIKF 156 (158)
T ss_pred cCCcCCCCCCEeeeccCHHHHHHHHHHHHh
Confidence 4799999999997 455688888888864
No 172
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=44.03 E-value=15 Score=23.33 Aligned_cols=9 Identities=33% Similarity=0.888 Sum_probs=4.4
Q ss_pred eeEeCCCCc
Q 027217 65 QVICSVCDT 73 (226)
Q Consensus 65 ~v~Cg~C~~ 73 (226)
.|.|+.|++
T Consensus 25 ~vrC~~C~~ 33 (37)
T PF13719_consen 25 KVRCPKCGH 33 (37)
T ss_pred EEECCCCCc
Confidence 455554443
No 173
>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=43.85 E-value=25 Score=34.50 Aligned_cols=46 Identities=28% Similarity=0.717 Sum_probs=30.0
Q ss_pred cceeEeCCCCccccccccCCCCCCCcc------eeecCccccccCCCCCCeeccCCCCcc
Q 027217 63 VKQVICSVCDTEQPVAQVCTNCGVNMG------EYFCDICKFYDDDIEKGQFHCDDCGIC 116 (226)
Q Consensus 63 ~~~v~Cg~C~~~q~v~~~C~~Cg~~f~------~Y~C~~C~l~dd~~~k~~yHC~~CgiC 116 (226)
.+.++|..|+.. ..|++|+..+. .-.|.-|.+- .+.+..|+.||-=
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 357889999866 57999998874 3446555532 2345567777643
No 174
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=43.70 E-value=16 Score=24.92 Aligned_cols=9 Identities=44% Similarity=1.531 Sum_probs=5.0
Q ss_pred CeeccCCCC
Q 027217 106 GQFHCDDCG 114 (226)
Q Consensus 106 ~~yHC~~Cg 114 (226)
+.|+|..||
T Consensus 36 ~r~~C~~Cg 44 (50)
T PRK00432 36 DRWHCGKCG 44 (50)
T ss_pred CcEECCCcC
Confidence 455555555
No 175
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=43.60 E-value=8 Score=32.49 Aligned_cols=25 Identities=28% Similarity=1.016 Sum_probs=19.1
Q ss_pred ceeecCccccccCCCCCCeeccCCCC--cceeC
Q 027217 89 GEYFCDICKFYDDDIEKGQFHCDDCG--ICRIG 119 (226)
Q Consensus 89 ~~Y~C~~C~l~dd~~~k~~yHC~~Cg--iCR~G 119 (226)
.+-||++|-+| ++|-|..|| +|-|+
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 77776
No 176
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=43.42 E-value=35 Score=29.01 Aligned_cols=27 Identities=22% Similarity=0.538 Sum_probs=18.4
Q ss_pred CcCCCCCCCeeccc--chHHHHHHHHHHH
Q 027217 188 DKYCCPICSKSVID--MSRTWKRIDEELQ 214 (226)
Q Consensus 188 ~~~~CPiCrksi~d--m~~~~~~lD~~i~ 214 (226)
..++||.|+..+.. -+...+.|+..|+
T Consensus 135 ~~F~Cp~Cg~~L~~~dn~~~~~~l~~~I~ 163 (178)
T PRK06266 135 YGFRCPQCGEMLEEYDNSELIKELKEQIK 163 (178)
T ss_pred cCCcCCCCCCCCeecccHHHHHHHHHHHH
Confidence 47999999999974 3345555555544
No 177
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=43.35 E-value=16 Score=20.40 Aligned_cols=16 Identities=31% Similarity=0.696 Sum_probs=12.4
Q ss_pred CCCCCCCeecccchHH
Q 027217 190 YCCPICSKSVIDMSRT 205 (226)
Q Consensus 190 ~~CPiCrksi~dm~~~ 205 (226)
+.|.+|.+++.+...+
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 178
>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=43.08 E-value=13 Score=30.05 Aligned_cols=50 Identities=24% Similarity=0.531 Sum_probs=37.0
Q ss_pred CCCCCCcceeecCccccccCCCCCCeeccCCCCcceeCCccceeeccccCcccccc
Q 027217 82 TNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYSTS 137 (226)
Q Consensus 82 ~~Cg~~f~~Y~C~~C~l~dd~~~k~~yHC~~CgiCR~G~~~~~fHC~~C~~C~s~~ 137 (226)
..-+......+|.+|+.+-- . ...||..||.|..+- -.||.-=|.|+...
T Consensus 40 ~~~~~~~~~~~C~~C~~~kp--~-Rs~HC~~C~~CV~~~---DHHC~w~~~cIG~~ 89 (174)
T PF01529_consen 40 PEDDENGELKYCSTCKIIKP--P-RSHHCRVCNRCVLRF---DHHCPWLGNCIGRR 89 (174)
T ss_pred hccccCCCCEECcccCCcCC--C-cceeccccccccccc---cccchhhccccccc
Confidence 34557788889999999833 2 477899998888873 45888888887754
No 179
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=42.67 E-value=17 Score=25.04 Aligned_cols=27 Identities=33% Similarity=0.639 Sum_probs=14.5
Q ss_pred ceeecCcc-ccccCCCCCCeeccCCCCc
Q 027217 89 GEYFCDIC-KFYDDDIEKGQFHCDDCGI 115 (226)
Q Consensus 89 ~~Y~C~~C-~l~dd~~~k~~yHC~~Cgi 115 (226)
..|-|..| +.++.+..+.-.-|+.||.
T Consensus 5 ~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~ 32 (49)
T COG1996 5 MEYKCARCGREVELDQETRGIRCPYCGS 32 (49)
T ss_pred EEEEhhhcCCeeehhhccCceeCCCCCc
Confidence 34455555 2334444556666776664
No 180
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=41.77 E-value=23 Score=33.66 Aligned_cols=88 Identities=25% Similarity=0.590 Sum_probs=57.6
Q ss_pred eeecCccc-----------cccC--CCCCCeeccCCCCcceeCC-ccceeeccccCcccccc---ccCcceeecCCCCCC
Q 027217 90 EYFCDICK-----------FYDD--DIEKGQFHCDDCGICRIGG-RENYFHCKRCGSCYSTS---LRNNHLCIENSMHHH 152 (226)
Q Consensus 90 ~Y~C~~C~-----------l~dd--~~~k~~yHC~~CgiCR~G~-~~~~fHC~~C~~C~s~~---l~~~H~C~e~~~~~~ 152 (226)
+-||.+|+ -||| .+.+.+-||+.| |--|. .|=|| +|+++.+.. -...|.=..++-...
T Consensus 149 RV~C~~C~~~s~tv~~~P~cWdDVLks~Ripg~Ces~--~~pg~fAEFfF---KC~ah~~~~k~~aa~lhli~~N~~ni~ 223 (446)
T KOG0006|consen 149 RVYCQKCSSTSVTVKSEPQCWDDVLKSKRIPGVCESC--CTPGLFAEFFF---KCGAHPTSDKETAAALHLIATNSRNIT 223 (446)
T ss_pred EEEeecccCceEEEecCccchhhhhhcccCccccccc--cCCcchHhhee---hhccCCCccccchhHHHHhhcccccce
Confidence 45666665 3666 245677888875 33343 35556 566666651 112344445666678
Q ss_pred CccchhhcccCCcceeeeccC--CccCHHHHHHHHh
Q 027217 153 CPICYEYLFDSLRNTTVMKCG--HTMHCECYHEMIK 186 (226)
Q Consensus 153 CpICle~lf~s~~~v~~LpCG--H~~H~~C~~~~l~ 186 (226)
|-.|-+- +++|-+++|. |+....||.-|-.
T Consensus 224 C~~Ctdv----~~~vlvf~Cns~HvtC~dCFr~yc~ 255 (446)
T KOG0006|consen 224 CITCTDV----RSPVLVFQCNSRHVTCLDCFRLYCV 255 (446)
T ss_pred eEEecCC----ccceEEEecCCceeehHHhhhhHhh
Confidence 9999875 5688899998 9999999986654
No 181
>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=41.73 E-value=21 Score=28.92 Aligned_cols=30 Identities=30% Similarity=0.791 Sum_probs=19.8
Q ss_pred CCcceeCCccceeeccccCccccccccCcceee
Q 027217 113 CGICRIGGRENYFHCKRCGSCYSTSLRNNHLCI 145 (226)
Q Consensus 113 CgiCR~G~~~~~fHC~~C~~C~s~~l~~~H~C~ 145 (226)
|-.|++-....-.||..||.|+-.- .|-|.
T Consensus 51 C~~C~~~kp~Rs~HC~~C~~CV~~~---DHHC~ 80 (174)
T PF01529_consen 51 CSTCKIIKPPRSHHCRVCNRCVLRF---DHHCP 80 (174)
T ss_pred CcccCCcCCCcceeccccccccccc---cccch
Confidence 3445555556688888888888764 56554
No 182
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=41.54 E-value=21 Score=32.85 Aligned_cols=88 Identities=27% Similarity=0.574 Sum_probs=51.1
Q ss_pred ceeecCcc-ccccCCC---CCCeeccCCCCcceeCCccceeeccccCccccc-cccCcceeecCCCCCCCccchhhcccC
Q 027217 89 GEYFCDIC-KFYDDDI---EKGQFHCDDCGICRIGGRENYFHCKRCGSCYST-SLRNNHLCIENSMHHHCPICYEYLFDS 163 (226)
Q Consensus 89 ~~Y~C~~C-~l~dd~~---~k~~yHC~~CgiCR~G~~~~~fHC~~C~~C~s~-~l~~~H~C~e~~~~~~CpICle~lf~s 163 (226)
++|-|+.| |-|.... .-+|+||+- .-...|.|..||-=|.. -...-|+=.- ...-.|+||... |+-
T Consensus 129 ~r~~c~eCgk~ysT~snLsrHkQ~H~~~-------~s~ka~~C~~C~K~YvSmpALkMHirTH-~l~c~C~iCGKa-FSR 199 (279)
T KOG2462|consen 129 PRYKCPECGKSYSTSSNLSRHKQTHRSL-------DSKKAFSCKYCGKVYVSMPALKMHIRTH-TLPCECGICGKA-FSR 199 (279)
T ss_pred Cceeccccccccccccccchhhcccccc-------cccccccCCCCCceeeehHHHhhHhhcc-CCCccccccccc-ccc
Confidence 44555555 3443322 236777743 12457778888766543 1112222221 235689999986 652
Q ss_pred CcceeeeccCCccCHHHHHHHHh---------cCcCCCCCCCeecccchH
Q 027217 164 LRNTTVMKCGHTMHCECYHEMIK---------RDKYCCPICSKSVIDMSR 204 (226)
Q Consensus 164 ~~~v~~LpCGH~~H~~C~~~~l~---------~~~~~CPiCrksi~dm~~ 204 (226)
.||. +.-+.||.|+|.+.|-|.
T Consensus 200 -------------------PWLLQGHiRTHTGEKPF~C~hC~kAFADRSN 230 (279)
T KOG2462|consen 200 -------------------PWLLQGHIRTHTGEKPFSCPHCGKAFADRSN 230 (279)
T ss_pred -------------------hHHhhcccccccCCCCccCCcccchhcchHH
Confidence 3664 246889999999998654
No 183
>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=41.23 E-value=14 Score=25.95 Aligned_cols=34 Identities=24% Similarity=0.457 Sum_probs=19.3
Q ss_pred eeEeCCCCccccc------cccCCCCCCCcceeecCcccc
Q 027217 65 QVICSVCDTEQPV------AQVCTNCGVNMGEYFCDICKF 98 (226)
Q Consensus 65 ~v~Cg~C~~~q~v------~~~C~~Cg~~f~~Y~C~~C~l 98 (226)
.|.|..|.++|.+ ...|..||..+++-.=.+-+|
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 5778888888766 236888888776654444333
No 184
>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=41.07 E-value=21 Score=22.00 Aligned_cols=24 Identities=33% Similarity=0.915 Sum_probs=15.3
Q ss_pred eecCccccccCCCCCCeeccCCCCc
Q 027217 91 YFCDICKFYDDDIEKGQFHCDDCGI 115 (226)
Q Consensus 91 Y~C~~C~l~dd~~~k~~yHC~~Cgi 115 (226)
|-|.+|-+.-+ +.+.++.|+.||.
T Consensus 2 ~~C~~CGy~y~-~~~~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYD-GEEAPWVCPVCGA 25 (33)
T ss_pred EECCCCCCEEC-CCcCCCcCcCCCC
Confidence 66777754422 2457788888775
No 185
>PF14353 CpXC: CpXC protein
Probab=40.95 E-value=25 Score=27.66 Aligned_cols=11 Identities=27% Similarity=0.809 Sum_probs=6.4
Q ss_pred cCCCCCCCcce
Q 027217 80 VCTNCGVNMGE 90 (226)
Q Consensus 80 ~C~~Cg~~f~~ 90 (226)
.||+||+.|..
T Consensus 3 tCP~C~~~~~~ 13 (128)
T PF14353_consen 3 TCPHCGHEFEF 13 (128)
T ss_pred CCCCCCCeeEE
Confidence 46666666643
No 186
>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=40.59 E-value=9.2 Score=40.17 Aligned_cols=44 Identities=30% Similarity=0.728 Sum_probs=0.0
Q ss_pred cCCCCCCCcceeecCccccccCCCCCCeeccCCCCcceeCCccceeeccccCc
Q 027217 80 VCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGS 132 (226)
Q Consensus 80 ~C~~Cg~~f~~Y~C~~C~l~dd~~~k~~yHC~~CgiCR~G~~~~~fHC~~C~~ 132 (226)
.|++||..--.-.|+.|.-. ....|.|+.||+ .+.. .+|.+|+.
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 56666666555566666544 335677777776 2221 16777765
No 187
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=40.44 E-value=21 Score=22.33 Aligned_cols=22 Identities=27% Similarity=0.706 Sum_probs=13.2
Q ss_pred eEeCCCCccccc---cccCCCCCCC
Q 027217 66 VICSVCDTEQPV---AQVCTNCGVN 87 (226)
Q Consensus 66 v~Cg~C~~~q~v---~~~C~~Cg~~ 87 (226)
-+|..|+.+... -+.||.||+.
T Consensus 3 ~~C~~CG~i~~g~~~p~~CP~Cg~~ 27 (34)
T cd00729 3 WVCPVCGYIHEGEEAPEKCPICGAP 27 (34)
T ss_pred EECCCCCCEeECCcCCCcCcCCCCc
Confidence 467777765322 2467777764
No 188
>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=38.75 E-value=16 Score=22.43 Aligned_cols=16 Identities=38% Similarity=1.028 Sum_probs=6.9
Q ss_pred CCCCCCCcceeecCccc
Q 027217 81 CTNCGVNMGEYFCDICK 97 (226)
Q Consensus 81 C~~Cg~~f~~Y~C~~C~ 97 (226)
|.-||. .++|-|+.|.
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 344444 5555555553
No 189
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=38.65 E-value=16 Score=36.01 Aligned_cols=33 Identities=18% Similarity=0.773 Sum_probs=26.5
Q ss_pred CCCCccchhhcccCCcceeeeccCCccCHHHHHHHHh
Q 027217 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIK 186 (226)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~ 186 (226)
+..||||... |. +.++|||||.+.+.|-..-+.
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 456899999999999987654
No 190
>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=38.54 E-value=12 Score=24.81 Aligned_cols=39 Identities=26% Similarity=0.641 Sum_probs=25.9
Q ss_pred CccchhhcccCCcceeeeccCCccCHHHHHHHHhcCcCCCCCCCeecccc
Q 027217 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDM 202 (226)
Q Consensus 153 CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~dm 202 (226)
|+.|.+.+... .+.+..=|..+|..|| +|-.|+++|.+.
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 56677776642 2332356788998765 677888888754
No 191
>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=38.34 E-value=18 Score=22.33 Aligned_cols=23 Identities=26% Similarity=0.710 Sum_probs=10.0
Q ss_pred cCCCCCCCcceeecCccccccCCCCCCeeccCCCC
Q 027217 80 VCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCG 114 (226)
Q Consensus 80 ~C~~Cg~~f~~Y~C~~C~l~dd~~~k~~yHC~~Cg 114 (226)
.|+.|+..++- .+..+|-|+.||
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 57777776653 234677777776
No 192
>PF15616 TerY-C: TerY-C metal binding domain
Probab=37.98 E-value=29 Score=28.53 Aligned_cols=20 Identities=30% Similarity=0.816 Sum_probs=16.6
Q ss_pred ccCCCCCCCcceeecCcc-ccc
Q 027217 79 QVCTNCGVNMGEYFCDIC-KFY 99 (226)
Q Consensus 79 ~~C~~Cg~~f~~Y~C~~C-~l~ 99 (226)
..||.||..+|---| .| ||+
T Consensus 78 PgCP~CGn~~~fa~C-~CGkl~ 98 (131)
T PF15616_consen 78 PGCPHCGNQYAFAVC-GCGKLF 98 (131)
T ss_pred CCCCCCcChhcEEEe-cCCCEE
Confidence 579999999999888 58 455
No 193
>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=37.46 E-value=24 Score=21.03 Aligned_cols=10 Identities=20% Similarity=0.610 Sum_probs=3.6
Q ss_pred ccCCCCCCCc
Q 027217 79 QVCTNCGVNM 88 (226)
Q Consensus 79 ~~C~~Cg~~f 88 (226)
+.|+.|+..+
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 3455665544
No 194
>PLN02189 cellulose synthase
Probab=37.07 E-value=29 Score=37.29 Aligned_cols=56 Identities=20% Similarity=0.434 Sum_probs=40.8
Q ss_pred ecCCCCCCCccchhhcccCCcceeeec---cCCccCHHHHHHHHhcCcCCCCCCCeecc
Q 027217 145 IENSMHHHCPICYEYLFDSLRNTTVMK---CGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (226)
Q Consensus 145 ~e~~~~~~CpICle~lf~s~~~v~~Lp---CGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (226)
.++...+.|.||.|++-...+.-.... ||=-+.+.|++--.++.+..||-|+...-
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 445566789999999754333333333 78889999997666677889999997764
No 195
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=36.60 E-value=30 Score=24.36 Aligned_cols=21 Identities=19% Similarity=0.542 Sum_probs=17.1
Q ss_pred CcCCCCCCCeecccchHHHHH
Q 027217 188 DKYCCPICSKSVIDMSRTWKR 208 (226)
Q Consensus 188 ~~~~CPiCrksi~dm~~~~~~ 208 (226)
.++.||.|+-++--....|+.
T Consensus 13 v~~~Cp~cGipthcS~ehw~~ 33 (55)
T PF13824_consen 13 VNFECPDCGIPTHCSEEHWED 33 (55)
T ss_pred cCCcCCCCCCcCccCHHHHHH
Confidence 579999999998877777764
No 196
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=36.59 E-value=22 Score=22.22 Aligned_cols=9 Identities=33% Similarity=1.224 Sum_probs=4.6
Q ss_pred CeeccCCCC
Q 027217 106 GQFHCDDCG 114 (226)
Q Consensus 106 ~~yHC~~Cg 114 (226)
++-.|..||
T Consensus 16 ~~irC~~CG 24 (32)
T PF03604_consen 16 DPIRCPECG 24 (32)
T ss_dssp STSSBSSSS
T ss_pred CcEECCcCC
Confidence 344555555
No 197
>smart00355 ZnF_C2H2 zinc finger.
Probab=36.45 E-value=33 Score=18.18 Aligned_cols=17 Identities=35% Similarity=0.589 Sum_probs=12.7
Q ss_pred CCCCCCCeecccchHHH
Q 027217 190 YCCPICSKSVIDMSRTW 206 (226)
Q Consensus 190 ~~CPiCrksi~dm~~~~ 206 (226)
+.|+.|.+++...+...
T Consensus 1 ~~C~~C~~~f~~~~~l~ 17 (26)
T smart00355 1 YRCPECGKVFKSKSALK 17 (26)
T ss_pred CCCCCCcchhCCHHHHH
Confidence 57999999988765443
No 198
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=36.13 E-value=22 Score=25.57 Aligned_cols=33 Identities=24% Similarity=0.590 Sum_probs=20.7
Q ss_pred ceeEeCCCCccccccccCCCCCCCcceeecCcccc
Q 027217 64 KQVICSVCDTEQPVAQVCTNCGVNMGEYFCDICKF 98 (226)
Q Consensus 64 ~~v~Cg~C~~~q~v~~~C~~Cg~~f~~Y~C~~C~l 98 (226)
..-.|..|+.++-. .|..|-..=|.|-|++|-|
T Consensus 26 v~F~CPnCGe~~I~--Rc~~CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 26 VKFPCPNCGEVEIY--RCAKCRKLGNPYRCPKCGF 58 (61)
T ss_pred eEeeCCCCCceeee--hhhhHHHcCCceECCCcCc
Confidence 45667777755333 5666666667777777755
No 199
>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=36.10 E-value=27 Score=22.80 Aligned_cols=20 Identities=25% Similarity=0.861 Sum_probs=10.9
Q ss_pred eccCCCCcceeCCccceeeccccC
Q 027217 108 FHCDDCGICRIGGRENYFHCKRCG 131 (226)
Q Consensus 108 yHC~~CgiCR~G~~~~~fHC~~C~ 131 (226)
|+|+.|+. +++ ..+||..|.
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 200
>KOG4399 consensus C2HC-type Zn-finger protein [General function prediction only]
Probab=36.03 E-value=8.4 Score=35.42 Aligned_cols=53 Identities=17% Similarity=0.165 Sum_probs=41.7
Q ss_pred ccCCCCCCCcceeecCccccccCCCCCCeeccCCCCcceeCCccceeeccccCcccc
Q 027217 79 QVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYS 135 (226)
Q Consensus 79 ~~C~~Cg~~f~~Y~C~~C~l~dd~~~k~~yHC~~CgiCR~G~~~~~fHC~~C~~C~s 135 (226)
..|+-|+..-+.-+|.||--+|.. .-|||.|..||--.+-.+-||++|..|..
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 356667777778899999888663 27999999999877667888888888865
No 201
>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=35.89 E-value=17 Score=28.65 Aligned_cols=11 Identities=18% Similarity=0.661 Sum_probs=5.4
Q ss_pred cccCCCCCCCc
Q 027217 78 AQVCTNCGVNM 88 (226)
Q Consensus 78 ~~~C~~Cg~~f 88 (226)
...|.+||..|
T Consensus 70 ~~~C~~Cg~~~ 80 (115)
T TIGR00100 70 ECECEDCSEEV 80 (115)
T ss_pred EEEcccCCCEE
Confidence 34555555444
No 202
>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=35.83 E-value=46 Score=21.84 Aligned_cols=9 Identities=44% Similarity=1.154 Sum_probs=5.0
Q ss_pred ccCCCCCCC
Q 027217 79 QVCTNCGVN 87 (226)
Q Consensus 79 ~~C~~Cg~~ 87 (226)
..||.||..
T Consensus 19 ~~CP~Cg~~ 27 (46)
T PF12760_consen 19 FVCPHCGST 27 (46)
T ss_pred CCCCCCCCe
Confidence 346666654
No 203
>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=35.70 E-value=30 Score=21.75 Aligned_cols=21 Identities=19% Similarity=0.363 Sum_probs=15.5
Q ss_pred ccCCCCCCCcceeecCccccc
Q 027217 79 QVCTNCGVNMGEYFCDICKFY 99 (226)
Q Consensus 79 ~~C~~Cg~~f~~Y~C~~C~l~ 99 (226)
..|..++.....|||..|+.+
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 467888887788888888765
No 204
>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=35.23 E-value=25 Score=24.04 Aligned_cols=22 Identities=23% Similarity=0.883 Sum_probs=13.4
Q ss_pred ccccCC--CCCCC------cceeecCcccc
Q 027217 77 VAQVCT--NCGVN------MGEYFCDICKF 98 (226)
Q Consensus 77 v~~~C~--~Cg~~------f~~Y~C~~C~l 98 (226)
....|| .||.. ++++||.+|.+
T Consensus 17 ~rk~CP~~~CG~GvFMA~H~dR~~CGKCg~ 46 (47)
T PF01599_consen 17 LRKECPSPRCGAGVFMAEHKDRHYCGKCGY 46 (47)
T ss_dssp SSEE-TSTTTTSSSEEEE-SSEEEETTTSS
T ss_pred hhhcCCCcccCCceEeeecCCCccCCCccc
Confidence 345788 78774 36777777754
No 205
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=35.21 E-value=39 Score=21.84 Aligned_cols=30 Identities=33% Similarity=0.808 Sum_probs=19.3
Q ss_pred ccCCCCCCCcceeecCccccccCCCCCCeeccCCCCc
Q 027217 79 QVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGI 115 (226)
Q Consensus 79 ~~C~~Cg~~f~~Y~C~~C~l~dd~~~k~~yHC~~Cgi 115 (226)
..||.||..=.- + |+|...+..|+|..||.
T Consensus 4 ~pCP~CGG~DrF------r-~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 4 GPCPNCGGSDRF------R-FDDKDGRGTWFCSVCGA 33 (37)
T ss_pred cCCCCCCCcccc------c-cccCCCCcCEEeCCCCC
Confidence 468888762211 2 46666678888887764
No 206
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=34.77 E-value=43 Score=31.24 Aligned_cols=25 Identities=28% Similarity=0.790 Sum_probs=20.6
Q ss_pred cceeEeCCCCcccccc-ccCCCCCCC
Q 027217 63 VKQVICSVCDTEQPVA-QVCTNCGVN 87 (226)
Q Consensus 63 ~~~v~Cg~C~~~q~v~-~~C~~Cg~~ 87 (226)
.+-..|+.|+++-.+. ..|++||..
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 207
>PRK14873 primosome assembly protein PriA; Provisional
Probab=34.33 E-value=35 Score=34.87 Aligned_cols=23 Identities=26% Similarity=0.689 Sum_probs=18.3
Q ss_pred ceeEeCCCCccccccccCCCCCCCcce
Q 027217 64 KQVICSVCDTEQPVAQVCTNCGVNMGE 90 (226)
Q Consensus 64 ~~v~Cg~C~~~q~v~~~C~~Cg~~f~~ 90 (226)
..++|..|+.. ..|++|+..+.-
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 57899999866 579999988863
No 208
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=33.95 E-value=33 Score=22.53 Aligned_cols=8 Identities=50% Similarity=1.510 Sum_probs=3.8
Q ss_pred eeccCCCC
Q 027217 107 QFHCDDCG 114 (226)
Q Consensus 107 ~yHC~~Cg 114 (226)
.|-|+.||
T Consensus 20 ~~vC~~Cg 27 (52)
T smart00661 20 RFVCRKCG 27 (52)
T ss_pred EEECCcCC
Confidence 44444444
No 209
>PLN02436 cellulose synthase A
Probab=33.81 E-value=35 Score=36.86 Aligned_cols=56 Identities=16% Similarity=0.445 Sum_probs=40.7
Q ss_pred ecCCCCCCCccchhhcccCCcceeeec---cCCccCHHHHHHHHhcCcCCCCCCCeecc
Q 027217 145 IENSMHHHCPICYEYLFDSLRNTTVMK---CGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (226)
Q Consensus 145 ~e~~~~~~CpICle~lf~s~~~v~~Lp---CGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (226)
++....+.|.||.|++-.+.+.-.... ||=-+.+.|++--.++.+..||-|+...-
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 344556789999999754444433343 67779999997666667889999997664
No 210
>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=33.69 E-value=30 Score=21.53 Aligned_cols=10 Identities=30% Similarity=0.737 Sum_probs=5.2
Q ss_pred eeEeCCCCcc
Q 027217 65 QVICSVCDTE 74 (226)
Q Consensus 65 ~v~Cg~C~~~ 74 (226)
.|.|+.|++.
T Consensus 25 ~v~C~~C~~~ 34 (38)
T TIGR02098 25 KVRCGKCGHV 34 (38)
T ss_pred EEECCCCCCE
Confidence 4555555543
No 211
>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=33.28 E-value=14 Score=38.85 Aligned_cols=47 Identities=26% Similarity=0.693 Sum_probs=0.0
Q ss_pred cceeEeCCCCccccccccCCCCCCCc-ceeecCccccccCCCCCCeeccCCCCc
Q 027217 63 VKQVICSVCDTEQPVAQVCTNCGVNM-GEYFCDICKFYDDDIEKGQFHCDDCGI 115 (226)
Q Consensus 63 ~~~v~Cg~C~~~q~v~~~C~~Cg~~f-~~Y~C~~C~l~dd~~~k~~yHC~~Cgi 115 (226)
+-.-.|..|+++ ++...|+.||..- -.|+|+.|+.--++. .|+.||.
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 345678888877 6777888888664 567788887643221 7888774
No 212
>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=33.17 E-value=21 Score=22.29 Aligned_cols=23 Identities=35% Similarity=0.752 Sum_probs=12.3
Q ss_pred ceeEeCCCCccc-cccccCCCCCC
Q 027217 64 KQVICSVCDTEQ-PVAQVCTNCGV 86 (226)
Q Consensus 64 ~~v~Cg~C~~~q-~v~~~C~~Cg~ 86 (226)
..-.|..|++.+ |+...|++||.
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 356788888775 55678888874
No 213
>PRK00420 hypothetical protein; Validated
Probab=32.86 E-value=30 Score=27.67 Aligned_cols=19 Identities=26% Similarity=0.695 Sum_probs=12.1
Q ss_pred ccCCCCCCCcce-----eecCccc
Q 027217 79 QVCTNCGVNMGE-----YFCDICK 97 (226)
Q Consensus 79 ~~C~~Cg~~f~~-----Y~C~~C~ 97 (226)
..||.||.+|.+ .||+.|.
T Consensus 24 ~~CP~Cg~pLf~lk~g~~~Cp~Cg 47 (112)
T PRK00420 24 KHCPVCGLPLFELKDGEVVCPVHG 47 (112)
T ss_pred CCCCCCCCcceecCCCceECCCCC
Confidence 578888877743 4555553
No 214
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=32.84 E-value=24 Score=29.05 Aligned_cols=19 Identities=42% Similarity=1.267 Sum_probs=13.4
Q ss_pred ccCCCCCCCc----ceeecCccc
Q 027217 79 QVCTNCGVNM----GEYFCDICK 97 (226)
Q Consensus 79 ~~C~~Cg~~f----~~Y~C~~C~ 97 (226)
..||.||.++ |+-||++|-
T Consensus 29 ~hCp~Cg~PLF~KdG~v~CPvC~ 51 (131)
T COG1645 29 KHCPKCGTPLFRKDGEVFCPVCG 51 (131)
T ss_pred hhCcccCCcceeeCCeEECCCCC
Confidence 4788888887 455666664
No 215
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=32.53 E-value=18 Score=21.05 Aligned_cols=12 Identities=25% Similarity=0.664 Sum_probs=9.5
Q ss_pred ccCCCCCCCcce
Q 027217 79 QVCTNCGVNMGE 90 (226)
Q Consensus 79 ~~C~~Cg~~f~~ 90 (226)
..|+.||..|+.
T Consensus 3 ~~C~~CgR~F~~ 14 (25)
T PF13913_consen 3 VPCPICGRKFNP 14 (25)
T ss_pred CcCCCCCCEECH
Confidence 368999999864
No 216
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=31.73 E-value=33 Score=22.27 Aligned_cols=6 Identities=50% Similarity=1.691 Sum_probs=2.3
Q ss_pred ccCCCC
Q 027217 109 HCDDCG 114 (226)
Q Consensus 109 HC~~Cg 114 (226)
.|+.||
T Consensus 28 ~CP~Cg 33 (42)
T PF09723_consen 28 PCPECG 33 (42)
T ss_pred cCCCCC
Confidence 333333
No 217
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=31.71 E-value=34 Score=22.42 Aligned_cols=9 Identities=33% Similarity=0.932 Sum_probs=4.7
Q ss_pred ceeeccccC
Q 027217 123 NYFHCKRCG 131 (226)
Q Consensus 123 ~~fHC~~C~ 131 (226)
..|||..|.
T Consensus 13 ~r~~C~~C~ 21 (46)
T cd02249 13 VRYHCLVCE 21 (46)
T ss_pred CEEECCCCC
Confidence 355555554
No 218
>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=31.00 E-value=36 Score=23.04 Aligned_cols=7 Identities=43% Similarity=1.559 Sum_probs=3.1
Q ss_pred eeecccc
Q 027217 124 YFHCKRC 130 (226)
Q Consensus 124 ~fHC~~C 130 (226)
-|||..|
T Consensus 15 R~~C~~C 21 (48)
T cd02341 15 RYHCSEC 21 (48)
T ss_pred eEECCCC
Confidence 3444444
No 219
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=30.99 E-value=45 Score=26.08 Aligned_cols=32 Identities=31% Similarity=0.664 Sum_probs=21.6
Q ss_pred cceeeccccC-ccccccccCcceeecCCCCCCCccchhh
Q 027217 122 ENYFHCKRCG-SCYSTSLRNNHLCIENSMHHHCPICYEY 159 (226)
Q Consensus 122 ~~~fHC~~C~-~C~s~~l~~~H~C~e~~~~~~CpICle~ 159 (226)
..+|+|..|| .-+++.+. + +..+..||+|..+
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 33333332 1 4667889999987
No 220
>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=30.27 E-value=28 Score=27.20 Aligned_cols=20 Identities=25% Similarity=0.637 Sum_probs=15.0
Q ss_pred EeCCCCcccccc----ccCCCCCC
Q 027217 67 ICSVCDTEQPVA----QVCTNCGV 86 (226)
Q Consensus 67 ~Cg~C~~~q~v~----~~C~~Cg~ 86 (226)
-|..|+..++.. +.|+||+.
T Consensus 5 AC~~C~~I~~~~qf~~~gCpnC~~ 28 (98)
T cd07973 5 ACLLCSLIKTEDQFERDGCPNCEG 28 (98)
T ss_pred hhccCCcccccccccCCCCCCCcc
Confidence 588898887765 47888863
No 221
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=29.94 E-value=28 Score=26.66 Aligned_cols=35 Identities=20% Similarity=0.414 Sum_probs=25.8
Q ss_pred eeEeCCCCccccc------cccCCCCCCCcceeecCccccc
Q 027217 65 QVICSVCDTEQPV------AQVCTNCGVNMGEYFCDICKFY 99 (226)
Q Consensus 65 ~v~Cg~C~~~q~v------~~~C~~Cg~~f~~Y~C~~C~l~ 99 (226)
.|.|..|..+|.| ...|..||..+++-.=.+.+|-
T Consensus 35 ~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~~PTGGKa~l~ 75 (85)
T PTZ00083 35 DVKCPGCSQITTVFSHAQTVVLCGGCSSQLCQPTGGKAKLT 75 (85)
T ss_pred EEECCCCCCeeEEEecCceEEEccccCCEeeccCCCCeEec
Confidence 7889999999877 2478889888877655555544
No 222
>PLN00209 ribosomal protein S27; Provisional
Probab=29.92 E-value=33 Score=26.29 Aligned_cols=35 Identities=20% Similarity=0.354 Sum_probs=26.8
Q ss_pred eeEeCCCCccccc------cccCCCCCCCcceeecCccccc
Q 027217 65 QVICSVCDTEQPV------AQVCTNCGVNMGEYFCDICKFY 99 (226)
Q Consensus 65 ~v~Cg~C~~~q~v------~~~C~~Cg~~f~~Y~C~~C~l~ 99 (226)
.|.|..|..+|.+ ...|..||..+++-.=.+.+|-
T Consensus 36 ~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~~PTGGKa~l~ 76 (86)
T PLN00209 36 DVKCQGCFNITTVFSHSQTVVVCGSCQTVLCQPTGGKARLT 76 (86)
T ss_pred EEECCCCCCeeEEEecCceEEEccccCCEeeccCCCCeEec
Confidence 7899999999877 2479999998877665555554
No 223
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=29.92 E-value=32 Score=24.72 Aligned_cols=20 Identities=25% Similarity=0.693 Sum_probs=13.5
Q ss_pred EeCCCCccccccccCCCCCCC
Q 027217 67 ICSVCDTEQPVAQVCTNCGVN 87 (226)
Q Consensus 67 ~Cg~C~~~q~v~~~C~~Cg~~ 87 (226)
.|..|+..++ .+.||+||..
T Consensus 5 AC~~C~~i~~-~~~CP~Cgs~ 24 (61)
T PRK08351 5 ACRHCHYITT-EDRCPVCGSR 24 (61)
T ss_pred hhhhCCcccC-CCcCCCCcCC
Confidence 5777776663 3468888864
No 224
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=29.58 E-value=31 Score=28.89 Aligned_cols=12 Identities=25% Similarity=0.839 Sum_probs=6.7
Q ss_pred cCCCCCCCccee
Q 027217 80 VCTNCGVNMGEY 91 (226)
Q Consensus 80 ~C~~Cg~~f~~Y 91 (226)
.|++||..|+.|
T Consensus 30 ~c~~c~~~f~~~ 41 (154)
T PRK00464 30 ECLACGKRFTTF 41 (154)
T ss_pred eccccCCcceEe
Confidence 455555555555
No 225
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=29.01 E-value=26 Score=26.95 Aligned_cols=64 Identities=19% Similarity=0.475 Sum_probs=39.4
Q ss_pred Cccchh-hcccCCcceeeeccCCccCHHHHHHHHhcCcCCCCCCCeecccc---hHHHHHHHHHHHhCCCCCCCC
Q 027217 153 CPICYE-YLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDM---SRTWKRIDEELQMNSSIFFPS 223 (226)
Q Consensus 153 CpICle-~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~dm---~~~~~~lD~~i~~~pm~~~~~ 223 (226)
||+|.+ .+........+-=.|+.+-- ....+.||.|...+.+. ....+.++.......-..+|.
T Consensus 1 C~~C~~~~~~~~~~~~~~~~~G~~~~v-------~~~~~~C~~CGe~~~~~e~~~~~~~~i~~~~~~~~~~~~~~ 68 (127)
T TIGR03830 1 CPICGSGELVRDVKDEPYTYKGESITI-------GVPGWYCPACGEELLDPEESKRNSAALADFYRKVDGLLTPP 68 (127)
T ss_pred CCCCCCccceeeeecceEEEcCEEEEE-------eeeeeECCCCCCEEEcHHHHHHHHHHHHHHHHHccCCcCHH
Confidence 888883 45544444444447766532 12467899999998863 346667766666655444443
No 226
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.79 E-value=29 Score=25.30 Aligned_cols=26 Identities=31% Similarity=0.658 Sum_probs=16.8
Q ss_pred cccccCCCCCCCcce-------eecC-ccccccC
Q 027217 76 PVAQVCTNCGVNMGE-------YFCD-ICKFYDD 101 (226)
Q Consensus 76 ~v~~~C~~Cg~~f~~-------Y~C~-~C~l~dd 101 (226)
..+..||.||++... -||+ -|++.|-
T Consensus 5 ~~~v~CP~Cgkpv~w~~~s~frPFCSkRCklIDL 38 (65)
T COG3024 5 RITVPCPTCGKPVVWGEESPFRPFCSKRCKLIDL 38 (65)
T ss_pred cccccCCCCCCcccccccCCcCcchhHhhhhcch
Confidence 344578888877643 4565 4888864
No 227
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=28.64 E-value=32 Score=31.00 Aligned_cols=20 Identities=25% Similarity=0.858 Sum_probs=15.3
Q ss_pred cccCCCCCCCc--------ceeecCccc
Q 027217 78 AQVCTNCGVNM--------GEYFCDICK 97 (226)
Q Consensus 78 ~~~C~~Cg~~f--------~~Y~C~~C~ 97 (226)
++.|+.||..+ +.|||+.|.
T Consensus 244 g~pCprCG~~I~~~~~~gR~t~~CP~CQ 271 (272)
T PRK14810 244 GEPCLNCKTPIRRVVVAGRSSHYCPHCQ 271 (272)
T ss_pred CCcCCCCCCeeEEEEECCCccEECcCCc
Confidence 46899999887 567887774
No 228
>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=28.64 E-value=25 Score=21.37 Aligned_cols=21 Identities=29% Similarity=0.819 Sum_probs=9.6
Q ss_pred EeCCCCccccc-----cccCCCCCCC
Q 027217 67 ICSVCDTEQPV-----AQVCTNCGVN 87 (226)
Q Consensus 67 ~Cg~C~~~q~v-----~~~C~~Cg~~ 87 (226)
.|+.|+.+... +..|++||..
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 47777766443 2367777653
No 229
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=28.20 E-value=35 Score=31.50 Aligned_cols=21 Identities=29% Similarity=0.529 Sum_probs=17.5
Q ss_pred ccCCCCCCCcceeecCccccc
Q 027217 79 QVCTNCGVNMGEYFCDICKFY 99 (226)
Q Consensus 79 ~~C~~Cg~~f~~Y~C~~C~l~ 99 (226)
..+...|....+-||.+|+.|
T Consensus 98 ~~~~~~~~~~~~~~C~~C~~~ 118 (309)
T COG5273 98 SRLLDDGKFGTENFCSTCNIY 118 (309)
T ss_pred hhhhhcCccccceeccccccc
Confidence 466677888888999999999
No 230
>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=28.10 E-value=34 Score=23.85 Aligned_cols=25 Identities=32% Similarity=0.909 Sum_probs=10.9
Q ss_pred cccCCCCCCCcceeecCccccccCCCCCCeeccCCCCc
Q 027217 78 AQVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGI 115 (226)
Q Consensus 78 ~~~C~~Cg~~f~~Y~C~~C~l~dd~~~k~~yHC~~Cgi 115 (226)
+..|..|++.|+- + +..+||..||.
T Consensus 9 ~~~C~~C~~~F~~--------~-----~rrhhCr~CG~ 33 (69)
T PF01363_consen 9 ASNCMICGKKFSL--------F-----RRRHHCRNCGR 33 (69)
T ss_dssp -SB-TTT--B-BS--------S-----S-EEE-TTT--
T ss_pred CCcCcCcCCcCCC--------c-----eeeEccCCCCC
Confidence 3567788888852 2 56788888874
No 231
>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=28.04 E-value=39 Score=21.50 Aligned_cols=24 Identities=33% Similarity=0.683 Sum_probs=18.4
Q ss_pred CccchhhcccCCcceeee-ccCCcc
Q 027217 153 CPICYEYLFDSLRNTTVM-KCGHTM 176 (226)
Q Consensus 153 CpICle~lf~s~~~v~~L-pCGH~~ 176 (226)
|++|...+|.+.+....= .|||.+
T Consensus 11 C~~C~~~~~~~~dG~~yC~~cG~~~ 35 (36)
T PF11781_consen 11 CPVCGSRWFYSDDGFYYCDRCGHQS 35 (36)
T ss_pred CCCCCCeEeEccCCEEEhhhCceEc
Confidence 999999988776666654 788864
No 232
>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=28.03 E-value=38 Score=27.29 Aligned_cols=27 Identities=22% Similarity=0.618 Sum_probs=18.6
Q ss_pred ccceeEeCCCCccccc---cccCCCCCCCc
Q 027217 62 DVKQVICSVCDTEQPV---AQVCTNCGVNM 88 (226)
Q Consensus 62 ~~~~v~Cg~C~~~q~v---~~~C~~Cg~~f 88 (226)
.+..|.|..|+++-.. .+.|.+|+.++
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 4567888888766433 46788887776
No 233
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=28.01 E-value=20 Score=36.18 Aligned_cols=27 Identities=26% Similarity=0.753 Sum_probs=20.1
Q ss_pred ceeeeccCCccCHHHHHHHHhcCcCCCCCCC
Q 027217 166 NTTVMKCGHTMHCECYHEMIKRDKYCCPICS 196 (226)
Q Consensus 166 ~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCr 196 (226)
..+-..||++||+.|+.. .+..||.|-
T Consensus 531 ~~rC~~C~avfH~~C~~r----~s~~CPrC~ 557 (580)
T KOG1829|consen 531 TRRCSTCLAVFHKKCLRR----KSPCCPRCE 557 (580)
T ss_pred ceeHHHHHHHHHHHHHhc----cCCCCCchH
Confidence 344567999999999864 344599884
No 234
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=27.62 E-value=35 Score=30.75 Aligned_cols=20 Identities=40% Similarity=1.102 Sum_probs=15.4
Q ss_pred cccCCCCCCCc--------ceeecCccc
Q 027217 78 AQVCTNCGVNM--------GEYFCDICK 97 (226)
Q Consensus 78 ~~~C~~Cg~~f--------~~Y~C~~C~ 97 (226)
++.|+.||..+ +.|||+.|.
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 235
>PF15389 DUF4612: Domain of unknown function (DUF4612)
Probab=27.46 E-value=45 Score=26.88 Aligned_cols=15 Identities=13% Similarity=0.399 Sum_probs=12.4
Q ss_pred hHHHHHHHHHHHhCC
Q 027217 203 SRTWKRIDEELQMNS 217 (226)
Q Consensus 203 ~~~~~~lD~~i~~~p 217 (226)
..+|||||+.|+.=|
T Consensus 92 qdFFRMLDeKIekG~ 106 (115)
T PF15389_consen 92 QDFFRMLDEKIEKGR 106 (115)
T ss_pred HHHHHHHHHHHHcCC
Confidence 359999999999754
No 236
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=27.34 E-value=34 Score=29.95 Aligned_cols=39 Identities=26% Similarity=0.537 Sum_probs=28.1
Q ss_pred CccchhhcccCCcceeeeccCCcc-CHHHHHHHHhcCcCCCCCCCeecc
Q 027217 153 CPICYEYLFDSLRNTTVMKCGHTM-HCECYHEMIKRDKYCCPICSKSVI 200 (226)
Q Consensus 153 CpICle~lf~s~~~v~~LpCGH~~-H~~C~~~~l~~~~~~CPiCrksi~ 200 (226)
|-+|.+. ...|..|||.|.. ...|-.. ..+||||+....
T Consensus 161 Cr~C~~~----~~~VlllPCrHl~lC~~C~~~-----~~~CPiC~~~~~ 200 (207)
T KOG1100|consen 161 CRKCGER----EATVLLLPCRHLCLCGICDES-----LRICPICRSPKT 200 (207)
T ss_pred ceecCcC----CceEEeecccceEeccccccc-----CccCCCCcChhh
Confidence 9999886 3468889999765 4556532 356999997654
No 237
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=27.30 E-value=28 Score=32.88 Aligned_cols=20 Identities=40% Similarity=0.989 Sum_probs=15.5
Q ss_pred cCCCCCCCcceeecCccccc
Q 027217 80 VCTNCGVNMGEYFCDICKFY 99 (226)
Q Consensus 80 ~C~~Cg~~f~~Y~C~~C~l~ 99 (226)
.|+-||.++.+|.|+-|+|.
T Consensus 9 ~C~ic~vq~~~YtCPRCn~~ 28 (383)
T KOG4317|consen 9 ACGICGVQKREYTCPRCNLL 28 (383)
T ss_pred eccccccccccccCCCCCcc
Confidence 56777888888888888765
No 238
>PRK10445 endonuclease VIII; Provisional
Probab=27.26 E-value=36 Score=30.54 Aligned_cols=20 Identities=30% Similarity=0.894 Sum_probs=14.8
Q ss_pred cccCCCCCCCc--------ceeecCccc
Q 027217 78 AQVCTNCGVNM--------GEYFCDICK 97 (226)
Q Consensus 78 ~~~C~~Cg~~f--------~~Y~C~~C~ 97 (226)
++.|+.||... +.|||+.|.
T Consensus 235 g~~Cp~Cg~~I~~~~~~gR~t~~CP~CQ 262 (263)
T PRK10445 235 GEACERCGGIIEKTTLSSRPFYWCPGCQ 262 (263)
T ss_pred CCCCCCCCCEeEEEEECCCCcEECCCCc
Confidence 46899999887 457777663
No 239
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=27.03 E-value=38 Score=33.48 Aligned_cols=44 Identities=23% Similarity=0.704 Sum_probs=34.1
Q ss_pred CCCCCCccchhhcccCCcceeeeccCCccCHHHHHHHHhcCcCCCCCCCeecc
Q 027217 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (226)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (226)
..+.+|.||++.+ ..+.-+|- |..|+.+|+. .+..||+|++.+.
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 4467999999997 22334555 9999999997 4679999998775
No 240
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=26.94 E-value=39 Score=21.16 Aligned_cols=12 Identities=33% Similarity=0.540 Sum_probs=5.8
Q ss_pred eEeCCCCccccc
Q 027217 66 VICSVCDTEQPV 77 (226)
Q Consensus 66 v~Cg~C~~~q~v 77 (226)
.+|..|+...-+
T Consensus 4 ~~C~~C~~~~i~ 15 (33)
T PF08792_consen 4 KKCSKCGGNGIV 15 (33)
T ss_pred eEcCCCCCCeEE
Confidence 445555554433
No 241
>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=26.91 E-value=35 Score=24.99 Aligned_cols=37 Identities=30% Similarity=0.644 Sum_probs=23.9
Q ss_pred cccCCCCCCCcceeecCccccccCCCCCCeeccCCCC
Q 027217 78 AQVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCG 114 (226)
Q Consensus 78 ~~~C~~Cg~~f~~Y~C~~C~l~dd~~~k~~yHC~~Cg 114 (226)
...|+.|...=....+..|.+.+=-.+|++-||-.|.
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 3467777655444677777777655567776666653
No 242
>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=26.57 E-value=49 Score=19.01 Aligned_cols=14 Identities=21% Similarity=0.610 Sum_probs=11.8
Q ss_pred CCCCCCCeecccch
Q 027217 190 YCCPICSKSVIDMS 203 (226)
Q Consensus 190 ~~CPiCrksi~dm~ 203 (226)
+.|++|.+.+.+..
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 68999999998754
No 243
>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=26.56 E-value=38 Score=28.39 Aligned_cols=13 Identities=15% Similarity=0.496 Sum_probs=11.5
Q ss_pred cCCCCCCCcceee
Q 027217 80 VCTNCGVNMGEYF 92 (226)
Q Consensus 80 ~C~~Cg~~f~~Y~ 92 (226)
.|++||..|..|=
T Consensus 30 eC~~C~~RFTTyE 42 (147)
T TIGR00244 30 ECLECHERFTTFE 42 (147)
T ss_pred cCCccCCccceee
Confidence 6999999999983
No 244
>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=26.36 E-value=46 Score=21.92 Aligned_cols=12 Identities=25% Similarity=0.844 Sum_probs=7.7
Q ss_pred ccCCCCCCCcce
Q 027217 79 QVCTNCGVNMGE 90 (226)
Q Consensus 79 ~~C~~Cg~~f~~ 90 (226)
..|+.||.++-+
T Consensus 18 ~~Cp~C~~PL~~ 29 (41)
T PF06677_consen 18 EHCPDCGTPLMR 29 (41)
T ss_pred CccCCCCCeeEE
Confidence 467777766643
No 245
>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=26.29 E-value=43 Score=18.87 Aligned_cols=18 Identities=22% Similarity=0.525 Sum_probs=13.7
Q ss_pred CCCCCCCeecccchHHHH
Q 027217 190 YCCPICSKSVIDMSRTWK 207 (226)
Q Consensus 190 ~~CPiCrksi~dm~~~~~ 207 (226)
++|.+|++.+.+.+++-+
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 246
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=26.21 E-value=42 Score=23.06 Aligned_cols=23 Identities=35% Similarity=0.911 Sum_probs=19.3
Q ss_pred ceeEeCCCCccccc-cccCCCCCC
Q 027217 64 KQVICSVCDTEQPV-AQVCTNCGV 86 (226)
Q Consensus 64 ~~v~Cg~C~~~q~v-~~~C~~Cg~ 86 (226)
..+||+.|+...++ +..|..||.
T Consensus 13 ~k~ICrkC~ARnp~~A~~CRKCg~ 36 (48)
T PRK04136 13 NKKICMRCNARNPWRATKCRKCGY 36 (48)
T ss_pred cccchhcccCCCCccccccccCCC
Confidence 57899999999887 568888886
No 247
>COG1144 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, delta subunit [Energy production and conversion]
Probab=26.15 E-value=34 Score=26.50 Aligned_cols=15 Identities=40% Similarity=0.906 Sum_probs=12.5
Q ss_pred cceeeccccCccccc
Q 027217 122 ENYFHCKRCGSCYST 136 (226)
Q Consensus 122 ~~~fHC~~C~~C~s~ 136 (226)
.||-+|+.||.|.+.
T Consensus 63 idYdyCKGCGICa~v 77 (91)
T COG1144 63 IDYDYCKGCGICANV 77 (91)
T ss_pred eEcccccCceechhh
Confidence 488999999999764
No 248
>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=26.11 E-value=54 Score=21.54 Aligned_cols=11 Identities=36% Similarity=0.939 Sum_probs=4.8
Q ss_pred CCCeeccCCCC
Q 027217 104 EKGQFHCDDCG 114 (226)
Q Consensus 104 ~k~~yHC~~Cg 114 (226)
.+.-|.|..|+
T Consensus 25 ~~~g~~C~~C~ 35 (53)
T PF00130_consen 25 GKQGYRCSWCG 35 (53)
T ss_dssp SSCEEEETTTT
T ss_pred CCCeEEECCCC
Confidence 34444444444
No 249
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=26.07 E-value=58 Score=22.09 Aligned_cols=37 Identities=14% Similarity=0.422 Sum_probs=24.8
Q ss_pred cChhhHHhhhcCCCCCCCCccccccccceeEeCCCCcccccc
Q 027217 37 DCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVA 78 (226)
Q Consensus 37 ~Cr~CHde~~~h~~~~~~~H~~~r~~~~~v~Cg~C~~~q~v~ 78 (226)
.|..|-+-+.- | .+..+.++.+..+.||.|.++..++
T Consensus 8 ~C~~C~~lLql-P----~~~~~~~k~~~klrCGaCs~vl~~s 44 (46)
T PF11331_consen 8 VCSSCFELLQL-P----AKFSLSKKNQQKLRCGACSEVLSFS 44 (46)
T ss_pred ECccHHHHHcC-C----CccCCCccceeEEeCCCCceeEEEe
Confidence 56666655431 2 3456666678899999999886653
No 250
>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=26.06 E-value=26 Score=22.52 Aligned_cols=13 Identities=54% Similarity=1.196 Sum_probs=5.5
Q ss_pred cceeecCcccccc
Q 027217 88 MGEYFCDICKFYD 100 (226)
Q Consensus 88 f~~Y~C~~C~l~d 100 (226)
|-+|||+-|+.|-
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 251
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=25.56 E-value=43 Score=23.25 Aligned_cols=19 Identities=32% Similarity=0.933 Sum_probs=11.1
Q ss_pred ccCCCCCC--Cc----ceeecCccc
Q 027217 79 QVCTNCGV--NM----GEYFCDICK 97 (226)
Q Consensus 79 ~~C~~Cg~--~f----~~Y~C~~C~ 97 (226)
..||+||. -| .+|+|.+|.
T Consensus 20 ~~CPrCG~gvfmA~H~dR~~CGkCg 44 (51)
T COG1998 20 RFCPRCGPGVFMADHKDRWACGKCG 44 (51)
T ss_pred ccCCCCCCcchhhhcCceeEecccc
Confidence 47888884 22 355555553
No 252
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=25.45 E-value=32 Score=31.80 Aligned_cols=31 Identities=29% Similarity=0.668 Sum_probs=26.2
Q ss_pred CCCcceeCCccceeeccccCccccccccCcceee
Q 027217 112 DCGICRIGGRENYFHCKRCGSCYSTSLRNNHLCI 145 (226)
Q Consensus 112 ~CgiCR~G~~~~~fHC~~C~~C~s~~l~~~H~C~ 145 (226)
.|.-|+.-+.+-.-||..||.|+-+- .|.|+
T Consensus 111 ~C~~C~~~KP~RS~HC~~Cn~CV~k~---DHHC~ 141 (309)
T COG5273 111 FCSTCNIYKPPRSHHCSICNRCVLKF---DHHCP 141 (309)
T ss_pred eccccccccCCCCccchhhcchhhcc---CccCc
Confidence 48888888888899999999999865 67775
No 253
>KOG3005 consensus GIY-YIG type nuclease [General function prediction only]
Probab=25.36 E-value=87 Score=28.85 Aligned_cols=50 Identities=20% Similarity=0.464 Sum_probs=33.8
Q ss_pred CCCccchhhcccCCcceee---eccCCccCHHHHHHHHhc--------CcCCCCCCCeecc
Q 027217 151 HHCPICYEYLFDSLRNTTV---MKCGHTMHCECYHEMIKR--------DKYCCPICSKSVI 200 (226)
Q Consensus 151 ~~CpICle~lf~s~~~v~~---LpCGH~~H~~C~~~~l~~--------~~~~CPiCrksi~ 200 (226)
..|-+|.+.+.+....+.. --|+=..|..|+.+.+.. ....||.|++.+.
T Consensus 183 ~~celc~~ei~e~~~~~a~c~~~~c~~~~h~~CLa~~~~~~e~g~~~p~eg~cp~C~~~~~ 243 (276)
T KOG3005|consen 183 VECELCEKEILETDWSRATCPNPDCDSLNHLTCLAEELLEVEPGQLIPLEGMCPKCEKFLS 243 (276)
T ss_pred hhhHHHHHHhccccceeccCCCCCCCchhhhhhhhHHHhccCCCceeccCCCCCchhceee
Confidence 5799999987543222211 128889999999984431 2468999999665
No 254
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=25.18 E-value=41 Score=30.21 Aligned_cols=20 Identities=30% Similarity=1.090 Sum_probs=14.7
Q ss_pred cccCCCCCCCc--------ceeecCccc
Q 027217 78 AQVCTNCGVNM--------GEYFCDICK 97 (226)
Q Consensus 78 ~~~C~~Cg~~f--------~~Y~C~~C~ 97 (226)
++.|+.||... +.|||+.|.
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 567777663
No 255
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=25.01 E-value=52 Score=19.57 Aligned_cols=16 Identities=19% Similarity=0.617 Sum_probs=12.8
Q ss_pred cCCCCCCCeecccchH
Q 027217 189 KYCCPICSKSVIDMSR 204 (226)
Q Consensus 189 ~~~CPiCrksi~dm~~ 204 (226)
.+.|.+|.+++.+...
T Consensus 3 ~~~C~~C~~~~~~~~~ 18 (35)
T smart00451 3 GFYCKLCNVTFTDEIS 18 (35)
T ss_pred CeEccccCCccCCHHH
Confidence 5789999999986543
No 256
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=24.11 E-value=4.7 Score=28.24 Aligned_cols=46 Identities=24% Similarity=0.600 Sum_probs=25.9
Q ss_pred CCcceeecCccccccCCCCCCeeccCCCCcceeCC-----ccceeeccccCccccc
Q 027217 86 VNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGG-----RENYFHCKRCGSCYST 136 (226)
Q Consensus 86 ~~f~~Y~C~~C~l~dd~~~k~~yHC~~CgiCR~G~-----~~~~fHC~~C~~C~s~ 136 (226)
++|++|.|+.|+-- -+.+..=.|.-|| ..+ .+.|+-|+.||.=+.+
T Consensus 3 ~SFsry~CDLCn~~--~p~~~LRQCvlCG---RWaC~sCW~deYY~CksC~Gii~l 53 (57)
T PF14445_consen 3 HSFSRYSCDLCNSS--HPISELRQCVLCG---RWACNSCWQDEYYTCKSCNGIINL 53 (57)
T ss_pred hHHhhHhHHhhccc--CcHHHHHHHhhhc---hhhhhhhhhhhHhHHHhhhchhhh
Confidence 46788888887633 2223333333333 322 4678888888765544
No 257
>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=23.47 E-value=62 Score=27.63 Aligned_cols=35 Identities=34% Similarity=0.909 Sum_probs=20.5
Q ss_pred eEeCCCCccccccccCCCCCCCc-----------ceeecCcccccc
Q 027217 66 VICSVCDTEQPVAQVCTNCGVNM-----------GEYFCDICKFYD 100 (226)
Q Consensus 66 v~Cg~C~~~q~v~~~C~~Cg~~f-----------~~Y~C~~C~l~d 100 (226)
..|..|...+.+...|.+|...+ +.+||+.|-+.|
T Consensus 112 ~aCs~C~r~~~~~~~C~~Cdr~lC~~C~~~C~~C~~~~Cs~Cs~~~ 157 (175)
T PF05458_consen 112 RACSVCQRTQRIKSVCSQCDRALCESCIRSCSSCSEVFCSLCSTVN 157 (175)
T ss_pred ccCcCCcCCCCCCccccccCcHHHHHHHhhhhchhhhhhcCccccc
Confidence 34777765656666666665544 445566665553
No 258
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=23.42 E-value=47 Score=30.04 Aligned_cols=19 Identities=26% Similarity=0.933 Sum_probs=13.8
Q ss_pred cccCCCCCCCc--------ceeecCcc
Q 027217 78 AQVCTNCGVNM--------GEYFCDIC 96 (226)
Q Consensus 78 ~~~C~~Cg~~f--------~~Y~C~~C 96 (226)
++.|+.||... +.|||+.|
T Consensus 254 g~pC~~Cg~~I~~~~~~gR~t~~CP~C 280 (282)
T PRK13945 254 GKPCRKCGTPIERIKLAGRSTHWCPNC 280 (282)
T ss_pred cCCCCcCCCeeEEEEECCCccEECCCC
Confidence 46899999887 45666666
No 259
>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=23.32 E-value=39 Score=32.16 Aligned_cols=36 Identities=25% Similarity=0.537 Sum_probs=27.3
Q ss_pred CccchhhcccCCcceeeeccCCccCHHHHHHHHhcCcCCCCCCCeecc
Q 027217 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (226)
Q Consensus 153 CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (226)
|--||-..|.|+++-. |. +.||. +.-+||.||+.+-
T Consensus 316 C~~Cm~kwFasrQd~~--------~~---~~Wl~-~~~~CPtCRa~FC 351 (358)
T PF10272_consen 316 CLECMGKWFASRQDQQ--------HP---ETWLS-GKCPCPTCRAKFC 351 (358)
T ss_pred HHHHHHHHhhhcCCCC--------Ch---hhhhc-CCCCCCCCcccce
Confidence 7778888888876443 33 68997 5789999999863
No 260
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=23.16 E-value=47 Score=29.86 Aligned_cols=19 Identities=37% Similarity=1.111 Sum_probs=13.7
Q ss_pred cccCCCCCCCc--------ceeecCcc
Q 027217 78 AQVCTNCGVNM--------GEYFCDIC 96 (226)
Q Consensus 78 ~~~C~~Cg~~f--------~~Y~C~~C 96 (226)
++.|+.||... +.|||+.|
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~CP~C 271 (272)
T TIGR00577 245 GEPCRRCGTPIEKIKVGGRGTHFCPQC 271 (272)
T ss_pred CCCCCCCCCeeEEEEECCCCCEECCCC
Confidence 45899999887 45666666
No 261
>PRK05580 primosome assembly protein PriA; Validated
Probab=23.07 E-value=82 Score=32.10 Aligned_cols=45 Identities=22% Similarity=0.596 Sum_probs=27.9
Q ss_pred cceeEeCCCCccccccccCCCCCCCccee------ecCccccccCCCCCCeeccCCCCc
Q 027217 63 VKQVICSVCDTEQPVAQVCTNCGVNMGEY------FCDICKFYDDDIEKGQFHCDDCGI 115 (226)
Q Consensus 63 ~~~v~Cg~C~~~q~v~~~C~~Cg~~f~~Y------~C~~C~l~dd~~~k~~yHC~~Cgi 115 (226)
...+.|..|+.. ..|++|+..+.-. .|.-|..- ...+..|+.||-
T Consensus 379 ~~~~~C~~Cg~~----~~C~~C~~~l~~h~~~~~l~Ch~Cg~~----~~~~~~Cp~Cg~ 429 (679)
T PRK05580 379 APFLLCRDCGWV----AECPHCDASLTLHRFQRRLRCHHCGYQ----EPIPKACPECGS 429 (679)
T ss_pred CCceEhhhCcCc----cCCCCCCCceeEECCCCeEECCCCcCC----CCCCCCCCCCcC
Confidence 357889999866 4799999887433 35555432 123345666653
No 262
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=22.81 E-value=47 Score=31.99 Aligned_cols=38 Identities=21% Similarity=0.469 Sum_probs=30.3
Q ss_pred CCCCCCCccchhhcccCCcceeeeccCCccCHHHHHHHHhc
Q 027217 147 NSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR 187 (226)
Q Consensus 147 ~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~ 187 (226)
......|.||.+.+-. ....+.|||.|-..|...++..
T Consensus 67 ~~~~~~c~ic~~~~~~---~~~~~~c~H~~c~~cw~~yl~~ 104 (444)
T KOG1815|consen 67 KKGDVQCGICVESYDG---EIIGLGCGHPFCPPCWTGYLGT 104 (444)
T ss_pred CCccccCCcccCCCcc---hhhhcCCCcHHHHHHHHHHhhh
Confidence 3556789999987332 5677899999999999999874
No 263
>smart00586 ZnF_DBF Zinc finger in DBF-like proteins.
Probab=22.78 E-value=51 Score=22.65 Aligned_cols=14 Identities=7% Similarity=0.306 Sum_probs=11.4
Q ss_pred chHHHHHHHHHHHh
Q 027217 202 MSRTWKRIDEELQM 215 (226)
Q Consensus 202 m~~~~~~lD~~i~~ 215 (226)
-+..|..||.+|+.
T Consensus 33 ~~~Nf~~lD~Li~~ 46 (49)
T smart00586 33 NNDNFQALDDLISQ 46 (49)
T ss_pred CchhHHHHHHHHHH
Confidence 34589999999985
No 264
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=22.65 E-value=63 Score=24.46 Aligned_cols=9 Identities=44% Similarity=1.143 Sum_probs=4.8
Q ss_pred cCCCCCCCc
Q 027217 80 VCTNCGVNM 88 (226)
Q Consensus 80 ~C~~Cg~~f 88 (226)
.|+.||..|
T Consensus 2 fC~~Cg~~l 10 (104)
T TIGR01384 2 FCPKCGSLM 10 (104)
T ss_pred CCcccCccc
Confidence 355555555
No 265
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=22.60 E-value=40 Score=34.77 Aligned_cols=66 Identities=21% Similarity=0.518 Sum_probs=45.5
Q ss_pred CCCCCccchhhcccCCcceeeeccCCccCHHHHHHHHhc--CcCCCCCCCeecc----cchHHHHHHHHHHHhCCC
Q 027217 149 MHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR--DKYCCPICSKSVI----DMSRTWKRIDEELQMNSS 218 (226)
Q Consensus 149 ~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~--~~~~CPiCrksi~----dm~~~~~~lD~~i~~~pm 218 (226)
....||||++..++. ..+.|-|.|-..|+...+.. ....||||+..+- .++..+.++=++...++.
T Consensus 20 k~lEc~ic~~~~~~p----~~~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~eK~s~~Es~r~sq~vqe~lk~k~ 91 (684)
T KOG4362|consen 20 KILECPICLEHVKEP----SLLKCDHIFLKFCLNKLFESKKGPKQCALCKSDIEKRSLRESPRFSQLSKESLKTKS 91 (684)
T ss_pred hhccCCceeEEeecc----chhhhhHHHHhhhhhceeeccCccccchhhhhhhhhhhccccchHHHHHHHhcCCcc
Confidence 356899999998874 56899999999998875543 2467999995553 235555555554444443
No 266
>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=22.56 E-value=94 Score=28.89 Aligned_cols=25 Identities=28% Similarity=0.687 Sum_probs=20.9
Q ss_pred cceeEeCCCCcccccc-ccCCCCCCC
Q 027217 63 VKQVICSVCDTEQPVA-QVCTNCGVN 87 (226)
Q Consensus 63 ~~~v~Cg~C~~~q~v~-~~C~~Cg~~ 87 (226)
.+-..|+.|.++-.+. ..|++||..
T Consensus 208 ~RyL~CslC~teW~~~R~~C~~Cg~~ 233 (305)
T TIGR01562 208 LRYLSCSLCATEWHYVRVKCSHCEES 233 (305)
T ss_pred ceEEEcCCCCCcccccCccCCCCCCC
Confidence 3578999999998775 689999975
No 267
>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=22.27 E-value=83 Score=29.06 Aligned_cols=46 Identities=17% Similarity=0.332 Sum_probs=26.4
Q ss_pred CCCCCCCccchhhcccCCcceeeec-c-CCccCHHHHHHHHhcCcCCCC
Q 027217 147 NSMHHHCPICYEYLFDSLRNTTVMK-C-GHTMHCECYHEMIKRDKYCCP 193 (226)
Q Consensus 147 ~~~~~~CpICle~lf~s~~~v~~Lp-C-GH~~H~~C~~~~l~~~~~~CP 193 (226)
..+-+-|+||+|- ...+.+...|. = .=-=|++||++|=.-.+..||
T Consensus 27 ~~tLsfChiCfEl-~iegvpks~llHtkSlRGHrdCFEK~HlIanQ~~p 74 (285)
T PF06937_consen 27 TETLSFCHICFEL-SIEGVPKSNLLHTKSLRGHRDCFEKYHLIANQDCP 74 (285)
T ss_pred ccceeecceeecc-ccccCccccccccccccchHHHHHHHHHHHcCCCC
Confidence 3445678888874 43333322221 1 012389999999443567899
No 268
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=22.04 E-value=80 Score=34.30 Aligned_cols=56 Identities=18% Similarity=0.444 Sum_probs=40.2
Q ss_pred ecCCCCCCCccchhhcccCCcceeee---ccCCccCHHHHHHHHhcCcCCCCCCCeecc
Q 027217 145 IENSMHHHCPICYEYLFDSLRNTTVM---KCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (226)
Q Consensus 145 ~e~~~~~~CpICle~lf~s~~~v~~L---pCGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (226)
+++...+.|-||.|++--+.+.-... -||=-..+.|++-=.++++..||.|+...-
T Consensus 12 ~~~~~~qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCYEYEr~eG~q~CPqCktrYk 70 (1079)
T PLN02638 12 MKHGGGQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCYEYERKDGNQSCPQCKTKYK 70 (1079)
T ss_pred ccccCCceeeecccccCcCCCCCEEEEeccCCCccccchhhhhhhcCCccCCccCCchh
Confidence 34556678999999964433333333 467779999997666678889999987653
No 269
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=21.96 E-value=58 Score=25.77 Aligned_cols=11 Identities=18% Similarity=0.594 Sum_probs=5.3
Q ss_pred cccCCCCCCCc
Q 027217 78 AQVCTNCGVNM 88 (226)
Q Consensus 78 ~~~C~~Cg~~f 88 (226)
...|..||..|
T Consensus 71 ~~~C~~Cg~~~ 81 (117)
T PRK00564 71 ELECKDCSHVF 81 (117)
T ss_pred EEEhhhCCCcc
Confidence 34555555443
No 270
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=21.84 E-value=54 Score=20.72 Aligned_cols=11 Identities=27% Similarity=1.050 Sum_probs=5.3
Q ss_pred CCCeeccCCCC
Q 027217 104 EKGQFHCDDCG 114 (226)
Q Consensus 104 ~k~~yHC~~Cg 114 (226)
++.-+-|+.||
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 44555555555
No 271
>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=21.71 E-value=82 Score=19.44 Aligned_cols=8 Identities=38% Similarity=1.228 Sum_probs=3.9
Q ss_pred cCCCCCCC
Q 027217 80 VCTNCGVN 87 (226)
Q Consensus 80 ~C~~Cg~~ 87 (226)
.||.||+.
T Consensus 28 ~CP~Cg~~ 35 (41)
T smart00834 28 TCPECGGD 35 (41)
T ss_pred CCCCCCCc
Confidence 45555543
No 272
>cd00112 LDLa Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure
Probab=21.13 E-value=70 Score=19.79 Aligned_cols=29 Identities=28% Similarity=0.549 Sum_probs=17.7
Q ss_pred ceeeccccCcccccccc--CcceeecCCCCCC
Q 027217 123 NYFHCKRCGSCYSTSLR--NNHLCIENSMHHH 152 (226)
Q Consensus 123 ~~fHC~~C~~C~s~~l~--~~H~C~e~~~~~~ 152 (226)
+.|.|.. +.|++..+. +.--|..++.+.+
T Consensus 4 ~~f~C~~-~~Ci~~~~~CDg~~DC~dgsDE~~ 34 (35)
T cd00112 4 NEFRCAN-GRCIPSSWVCDGEDDCGDGSDEEN 34 (35)
T ss_pred CeEEcCC-CCeeCHHHcCCCccCCCCCccccc
Confidence 4788888 888887654 3334444444443
No 273
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=21.02 E-value=67 Score=27.72 Aligned_cols=31 Identities=29% Similarity=0.741 Sum_probs=21.6
Q ss_pred ccCCcceeeeccCCccCHHHHHHHHhcCcCCCCCCCe
Q 027217 161 FDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSK 197 (226)
Q Consensus 161 f~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrk 197 (226)
|+....++--.|+-+||+.|+. ...||-|.+
T Consensus 167 F~~~~~~~C~~C~~v~H~~C~~------~~~CpkC~R 197 (202)
T PF13901_consen 167 FQIDTTVRCPKCKSVFHKSCFR------KKSCPKCAR 197 (202)
T ss_pred CCCCCeeeCCcCccccchhhcC------CCCCCCcHh
Confidence 4433344445799999999995 257998864
No 274
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=21.01 E-value=61 Score=34.45 Aligned_cols=50 Identities=24% Similarity=0.454 Sum_probs=33.0
Q ss_pred CCCCCCccchhhcccCCcceeeecc---C--CccCHHHHHHHHhcC-cCCCCCCCeec
Q 027217 148 SMHHHCPICYEYLFDSLRNTTVMKC---G--HTMHCECYHEMIKRD-KYCCPICSKSV 199 (226)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpC---G--H~~H~~C~~~~l~~~-~~~CPiCrksi 199 (226)
..+..|-||--+ -. ++..-.=|| | -.+|++|+.+|+..+ .-+|-||...+
T Consensus 10 ~d~~~CRICr~e-~~-~d~pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~ 65 (1175)
T COG5183 10 EDKRSCRICRTE-DI-RDDPLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEY 65 (1175)
T ss_pred ccchhceeecCC-CC-CCCcCcccccccchhHHHHHHHHHHHHhcCCCcceeeeccee
Confidence 334678888754 22 112222355 3 679999999999853 55699998765
No 275
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=20.85 E-value=51 Score=34.50 Aligned_cols=49 Identities=27% Similarity=0.553 Sum_probs=39.5
Q ss_pred ccCCCCCCCccee---ecCccccccCCCCCCeeccCCCCcceeCCccceeeccccCccccc
Q 027217 79 QVCTNCGVNMGEY---FCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYST 136 (226)
Q Consensus 79 ~~C~~Cg~~f~~Y---~C~~C~l~dd~~~k~~yHC~~CgiCR~G~~~~~fHC~~C~~C~s~ 136 (226)
-.|++|++.++.- +|++|.--.- .+|-+|+.+-+.-+++|..|+-+.-.
T Consensus 754 ~~~~nc~a~~~~~~~~~c~rc~s~a~---------~~CtVC~~vi~G~~~~c~~C~H~gH~ 805 (839)
T KOG0269|consen 754 YACPNCDAPMVLTKLWQCDRCESRAS---------AKCTVCDLVIRGVDVWCQVCGHGGHD 805 (839)
T ss_pred ccccccCCccccccceeechHHHHhh---------cCceeecceeeeeEeecccccccccH
Confidence 4799999999765 8888876532 26888999988889999999988654
No 276
>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=20.68 E-value=76 Score=21.44 Aligned_cols=9 Identities=33% Similarity=1.324 Sum_probs=5.9
Q ss_pred eeecCcccc
Q 027217 90 EYFCDICKF 98 (226)
Q Consensus 90 ~Y~C~~C~l 98 (226)
+|.|.+|..
T Consensus 1 ky~C~~Cgy 9 (47)
T PF00301_consen 1 KYQCPVCGY 9 (47)
T ss_dssp EEEETTTSB
T ss_pred CcCCCCCCE
Confidence 567777753
No 277
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=20.44 E-value=53 Score=29.54 Aligned_cols=34 Identities=29% Similarity=0.665 Sum_probs=24.5
Q ss_pred CeeccCCCCcceeCCccceeeccccCccccccccCcceee
Q 027217 106 GQFHCDDCGICRIGGRENYFHCKRCGSCYSTSLRNNHLCI 145 (226)
Q Consensus 106 ~~yHC~~CgiCR~G~~~~~fHC~~C~~C~s~~l~~~H~C~ 145 (226)
+...|+.|.+-| ..-.-||..||.|+..- .|-|.
T Consensus 112 ~~~~C~~C~~~r---PpRs~HCsvC~~CV~rf---DHHC~ 145 (299)
T KOG1311|consen 112 EWKYCDTCQLYR---PPRSSHCSVCNNCVLRF---DHHCP 145 (299)
T ss_pred ceEEcCcCcccC---CCCcccchhhccccccc---CCCCC
Confidence 356677766654 44689999999999864 56663
Done!