Query 027385
Match_columns 224
No_of_seqs 241 out of 769
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 09:10:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027385.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027385hhsearch_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 6.6E-58 1.4E-62 408.3 4.6 209 4-223 21-229 (276)
2 PF05495 zf-CHY: CHY zinc fing 99.9 1.1E-24 2.3E-29 159.4 3.6 70 18-100 1-71 (71)
3 COG4357 Zinc finger domain con 99.7 5E-18 1.1E-22 130.3 2.4 74 14-90 11-92 (105)
4 PF13639 zf-RING_2: Ring finge 99.5 2E-14 4.3E-19 95.0 2.1 44 151-196 1-44 (44)
5 PF12678 zf-rbx1: RING-H2 zinc 99.1 4.6E-11 1E-15 87.6 3.9 48 148-196 17-73 (73)
6 cd00162 RING RING-finger (Real 99.1 1.4E-10 3.1E-15 74.0 3.8 45 152-199 1-45 (45)
7 COG5243 HRD1 HRD ubiquitin lig 99.1 4.8E-11 1E-15 110.8 2.1 57 147-204 284-350 (491)
8 KOG4628 Predicted E3 ubiquitin 99.0 1.6E-10 3.5E-15 106.9 2.8 50 151-201 230-279 (348)
9 PF13923 zf-C3HC4_2: Zinc fing 98.9 4.9E-10 1.1E-14 72.3 2.6 39 153-195 1-39 (39)
10 PHA02929 N1R/p28-like protein; 98.9 1E-09 2.2E-14 97.2 4.4 54 147-201 171-228 (238)
11 PF13920 zf-C3HC4_3: Zinc fing 98.8 1.9E-09 4.2E-14 72.9 3.0 47 150-201 2-49 (50)
12 PF00097 zf-C3HC4: Zinc finger 98.8 3.6E-09 7.8E-14 68.3 2.7 40 153-195 1-41 (41)
13 PF12861 zf-Apc11: Anaphase-pr 98.8 5E-09 1.1E-13 79.3 3.7 48 151-200 33-82 (85)
14 smart00184 RING Ring finger. E 98.8 5.3E-09 1.1E-13 64.4 3.1 39 153-195 1-39 (39)
15 PF14634 zf-RING_5: zinc-RING 98.7 9.6E-09 2.1E-13 68.0 3.1 44 152-197 1-44 (44)
16 COG5540 RING-finger-containing 98.7 1.2E-08 2.5E-13 93.1 3.3 53 146-199 319-371 (374)
17 PF15227 zf-C3HC4_4: zinc fing 98.6 3.1E-08 6.6E-13 65.4 3.0 39 153-195 1-42 (42)
18 PF13445 zf-RING_UBOX: RING-ty 98.5 5.7E-08 1.2E-12 64.8 2.6 40 153-193 1-43 (43)
19 PF14599 zinc_ribbon_6: Zinc-r 98.5 2.8E-08 6.1E-13 71.0 0.0 26 199-224 1-26 (61)
20 KOG0802 E3 ubiquitin ligase [P 98.5 4.5E-08 9.8E-13 95.4 1.2 53 147-200 288-341 (543)
21 PLN03208 E3 ubiquitin-protein 98.4 1.9E-07 4.1E-12 80.5 4.2 55 143-201 11-80 (193)
22 PHA02926 zinc finger-like prot 98.3 2.2E-07 4.7E-12 81.7 2.3 62 146-207 166-239 (242)
23 KOG0320 Predicted E3 ubiquitin 98.2 5.5E-07 1.2E-11 76.7 2.3 47 151-200 132-178 (187)
24 smart00504 Ubox Modified RING 98.1 2.5E-06 5.5E-11 59.2 3.7 45 151-200 2-46 (63)
25 smart00744 RINGv The RING-vari 98.1 2.1E-06 4.5E-11 58.5 2.9 43 152-196 1-49 (49)
26 KOG0804 Cytoplasmic Zn-finger 98.1 1.8E-06 3.9E-11 82.2 2.3 47 151-200 176-222 (493)
27 PF11793 FANCL_C: FANCL C-term 98.0 2.4E-06 5.2E-11 62.2 0.8 51 150-200 2-66 (70)
28 TIGR00599 rad18 DNA repair pro 97.9 7.7E-06 1.7E-10 77.4 4.2 46 150-200 26-71 (397)
29 COG5194 APC11 Component of SCF 97.9 9.9E-06 2.2E-10 60.9 3.3 48 152-200 33-81 (88)
30 KOG0317 Predicted E3 ubiquitin 97.8 1.1E-05 2.5E-10 73.0 1.8 45 151-200 240-284 (293)
31 KOG0827 Predicted E3 ubiquitin 97.7 1.4E-05 2.9E-10 75.3 1.9 46 150-196 4-52 (465)
32 KOG1493 Anaphase-promoting com 97.7 1.3E-05 2.9E-10 59.7 1.4 29 171-199 50-80 (84)
33 TIGR00570 cdk7 CDK-activating 97.7 3.2E-05 7E-10 71.0 4.0 52 150-201 3-55 (309)
34 KOG2177 Predicted E3 ubiquitin 97.7 2.2E-05 4.8E-10 66.1 2.2 44 149-197 12-55 (386)
35 KOG2164 Predicted E3 ubiquitin 97.6 3E-05 6.5E-10 74.9 2.7 50 148-201 184-237 (513)
36 KOG0823 Predicted E3 ubiquitin 97.6 4.7E-05 1E-09 67.2 2.8 50 148-201 45-96 (230)
37 PF14835 zf-RING_6: zf-RING of 97.4 5.5E-05 1.2E-09 54.7 1.1 56 151-213 8-65 (65)
38 KOG0828 Predicted E3 ubiquitin 97.4 5.4E-05 1.2E-09 73.2 1.1 51 150-200 571-634 (636)
39 KOG0287 Postreplication repair 97.4 0.00012 2.6E-09 68.1 3.3 59 152-215 25-84 (442)
40 PF04564 U-box: U-box domain; 97.4 0.0002 4.4E-09 52.1 3.7 48 150-201 4-51 (73)
41 KOG1734 Predicted RING-contain 97.2 8.3E-05 1.8E-09 67.3 0.4 52 149-200 223-281 (328)
42 KOG1941 Acetylcholine receptor 97.2 8.7E-05 1.9E-09 70.1 0.4 62 141-203 357-419 (518)
43 KOG4265 Predicted E3 ubiquitin 97.0 0.00043 9.4E-09 64.4 2.9 51 146-201 286-337 (349)
44 COG5574 PEX10 RING-finger-cont 96.9 0.00046 9.9E-09 62.1 2.0 47 150-200 215-262 (271)
45 KOG2930 SCF ubiquitin ligase, 96.7 0.00096 2.1E-08 52.5 2.3 28 171-199 80-107 (114)
46 PF14570 zf-RING_4: RING/Ubox 96.7 0.0015 3.2E-08 44.7 2.5 47 153-199 1-47 (48)
47 KOG4172 Predicted E3 ubiquitin 96.6 0.00054 1.2E-08 48.3 0.2 53 148-204 5-58 (62)
48 KOG0825 PHD Zn-finger protein 96.5 0.00085 1.8E-08 68.1 0.8 76 124-201 96-172 (1134)
49 KOG0978 E3 ubiquitin ligase in 96.4 0.00091 2E-08 67.3 0.4 46 151-200 644-689 (698)
50 KOG0311 Predicted E3 ubiquitin 96.4 0.00091 2E-08 62.5 0.1 49 150-201 43-91 (381)
51 PF11789 zf-Nse: Zinc-finger o 96.3 0.0025 5.3E-08 44.8 2.0 44 148-194 9-53 (57)
52 KOG1039 Predicted E3 ubiquitin 96.3 0.00074 1.6E-08 63.1 -1.2 74 147-222 158-243 (344)
53 KOG1785 Tyrosine kinase negati 96.2 0.0013 2.8E-08 62.6 0.3 55 144-202 363-418 (563)
54 COG5219 Uncharacterized conser 96.2 0.002 4.3E-08 66.7 1.7 52 148-199 1467-1522(1525)
55 KOG1645 RING-finger-containing 96.2 0.0039 8.4E-08 59.3 3.1 49 150-198 4-54 (463)
56 COG5432 RAD18 RING-finger-cont 96.0 0.004 8.7E-08 57.2 2.2 44 151-199 26-69 (391)
57 PF12906 RINGv: RING-variant d 96.0 0.0043 9.3E-08 41.8 1.7 41 153-195 1-47 (47)
58 PF10367 Vps39_2: Vacuolar sor 95.8 0.0043 9.3E-08 46.9 1.4 38 143-182 71-108 (109)
59 KOG1428 Inhibitor of type V ad 95.7 0.012 2.5E-07 63.6 4.5 74 119-200 3462-3544(3738)
60 PRK14890 putative Zn-ribbon RN 95.7 0.0088 1.9E-07 42.6 2.5 46 63-115 5-56 (59)
61 KOG3970 Predicted E3 ubiquitin 95.6 0.017 3.7E-07 51.5 4.7 66 148-215 48-124 (299)
62 KOG2879 Predicted E3 ubiquitin 94.8 0.025 5.3E-07 51.5 3.1 53 148-203 237-290 (298)
63 PF14447 Prok-RING_4: Prokaryo 94.4 0.015 3.2E-07 40.9 0.7 33 165-200 18-50 (55)
64 KOG1571 Predicted E3 ubiquitin 94.3 0.027 5.8E-07 52.8 2.2 48 146-201 301-348 (355)
65 PF05883 Baculo_RING: Baculovi 94.2 0.022 4.7E-07 46.8 1.2 36 150-186 26-67 (134)
66 KOG4739 Uncharacterized protei 94.0 0.023 5E-07 50.6 1.2 37 161-200 12-48 (233)
67 KOG0824 Predicted E3 ubiquitin 94.0 0.029 6.2E-07 51.7 1.8 49 148-200 5-53 (324)
68 KOG4275 Predicted E3 ubiquitin 93.9 0.0095 2.1E-07 54.7 -1.5 60 139-207 286-349 (350)
69 KOG3002 Zn finger protein [Gen 93.9 0.069 1.5E-06 49.1 4.1 63 150-223 48-112 (299)
70 KOG4185 Predicted E3 ubiquitin 93.7 0.044 9.6E-07 49.1 2.4 48 151-199 4-54 (296)
71 KOG3800 Predicted E3 ubiquitin 93.6 0.055 1.2E-06 49.5 2.9 49 152-200 2-51 (300)
72 KOG3268 Predicted E3 ubiquitin 93.2 0.06 1.3E-06 46.5 2.3 35 169-203 187-232 (234)
73 COG2888 Predicted Zn-ribbon RN 92.5 0.092 2E-06 37.5 2.1 45 65-115 9-58 (61)
74 KOG0297 TNF receptor-associate 92.3 0.085 1.8E-06 50.0 2.3 53 149-205 20-72 (391)
75 PF12773 DZR: Double zinc ribb 92.2 0.16 3.4E-06 33.9 2.8 22 68-89 1-23 (50)
76 COG5175 MOT2 Transcriptional r 92.0 0.043 9.4E-07 51.5 -0.1 57 150-206 14-70 (480)
77 PHA02862 5L protein; Provision 91.9 0.086 1.9E-06 44.0 1.6 60 149-212 1-64 (156)
78 KOG1813 Predicted E3 ubiquitin 91.5 0.11 2.4E-06 47.8 1.9 67 151-222 242-308 (313)
79 PF04641 Rtf2: Rtf2 RING-finge 91.4 0.16 3.5E-06 45.4 2.9 50 148-200 111-161 (260)
80 KOG1002 Nucleotide excision re 91.1 0.083 1.8E-06 52.2 0.8 52 145-200 531-586 (791)
81 PF07191 zinc-ribbons_6: zinc- 91.1 0.13 2.9E-06 37.8 1.6 36 64-99 16-59 (70)
82 PF07800 DUF1644: Protein of u 91.0 0.25 5.3E-06 41.8 3.4 48 150-201 2-92 (162)
83 KOG4445 Uncharacterized conser 90.9 0.12 2.5E-06 47.9 1.5 54 147-201 112-187 (368)
84 KOG1814 Predicted E3 ubiquitin 90.6 0.15 3.4E-06 48.7 2.1 46 150-196 184-236 (445)
85 KOG2660 Locus-specific chromos 90.4 0.06 1.3E-06 50.0 -0.9 64 148-215 13-77 (331)
86 KOG3161 Predicted E3 ubiquitin 90.0 0.15 3.4E-06 51.3 1.6 67 151-221 12-89 (861)
87 KOG3039 Uncharacterized conser 89.7 0.32 7E-06 44.0 3.2 53 147-201 218-271 (303)
88 KOG4159 Predicted E3 ubiquitin 89.7 0.39 8.6E-06 45.9 4.0 49 148-201 82-130 (398)
89 COG5152 Uncharacterized conser 89.4 0.22 4.7E-06 43.8 1.9 58 152-214 198-255 (259)
90 KOG2114 Vacuolar assembly/sort 89.1 0.28 6E-06 50.7 2.7 41 151-198 841-881 (933)
91 KOG0309 Conserved WD40 repeat- 89.1 0.25 5.5E-06 50.7 2.3 41 151-194 1029-1069(1081)
92 PHA02825 LAP/PHD finger-like p 89.0 0.36 7.8E-06 40.8 2.8 48 148-200 6-59 (162)
93 PF03854 zf-P11: P-11 zinc fin 88.5 0.22 4.8E-06 34.1 1.0 32 168-200 14-46 (50)
94 KOG2817 Predicted E3 ubiquitin 87.4 0.56 1.2E-05 44.7 3.3 46 152-198 336-383 (394)
95 PF13248 zf-ribbon_3: zinc-rib 86.8 0.32 7E-06 28.7 0.9 24 65-88 2-26 (26)
96 KOG1952 Transcription factor N 86.7 0.38 8.1E-06 49.8 1.9 51 149-200 190-247 (950)
97 KOG2034 Vacuolar sorting prote 86.5 0.36 7.7E-06 50.1 1.6 43 142-186 809-851 (911)
98 PRK04023 DNA polymerase II lar 86.4 0.64 1.4E-05 49.1 3.4 29 67-96 628-657 (1121)
99 COG5236 Uncharacterized conser 85.1 0.85 1.8E-05 43.2 3.3 64 131-198 42-106 (493)
100 PF10571 UPF0547: Uncharacteri 84.7 0.67 1.5E-05 27.6 1.6 23 67-89 2-25 (26)
101 KOG4692 Predicted E3 ubiquitin 84.6 0.6 1.3E-05 44.3 2.0 51 146-201 418-468 (489)
102 PF02891 zf-MIZ: MIZ/SP-RING z 84.2 1.1 2.3E-05 30.5 2.7 42 151-198 3-50 (50)
103 smart00734 ZnF_Rad18 Rad18-lik 84.0 0.9 1.9E-05 27.0 1.9 21 190-211 2-22 (26)
104 PF13240 zinc_ribbon_2: zinc-r 83.7 0.62 1.3E-05 26.9 1.1 21 68-88 2-23 (23)
105 PF08746 zf-RING-like: RING-li 82.8 0.85 1.8E-05 30.1 1.7 25 171-195 18-43 (43)
106 PF09538 FYDLN_acid: Protein o 82.5 1 2.2E-05 35.6 2.3 27 77-115 8-34 (108)
107 PF07191 zinc-ribbons_6: zinc- 81.9 1.2 2.6E-05 32.8 2.3 44 89-137 16-63 (70)
108 PRK14559 putative protein seri 81.6 1.1 2.4E-05 45.3 2.7 33 66-98 2-35 (645)
109 PHA00626 hypothetical protein 81.2 1.2 2.7E-05 31.5 2.0 6 81-86 3-8 (59)
110 PF14446 Prok-RING_1: Prokaryo 81.0 1.6 3.4E-05 30.6 2.5 37 148-184 3-39 (54)
111 PRK14714 DNA polymerase II lar 80.4 1.8 3.9E-05 46.8 3.9 48 65-114 667-716 (1337)
112 smart00132 LIM Zinc-binding do 79.4 1.1 2.3E-05 27.2 1.2 37 153-200 2-38 (39)
113 TIGR00595 priA primosomal prot 78.8 1.7 3.6E-05 42.5 2.9 49 27-87 214-262 (505)
114 KOG0827 Predicted E3 ubiquitin 78.8 0.21 4.6E-06 47.7 -3.2 50 150-200 196-245 (465)
115 PF13894 zf-C2H2_4: C2H2-type 78.7 1.6 3.5E-05 23.6 1.6 21 190-210 1-21 (24)
116 KOG0801 Predicted E3 ubiquitin 77.6 0.92 2E-05 38.8 0.6 30 148-178 175-204 (205)
117 COG5220 TFB3 Cdk activating ki 75.4 1.2 2.6E-05 40.3 0.8 51 150-200 10-64 (314)
118 COG1198 PriA Primosomal protei 74.2 3.2 7E-05 42.7 3.6 44 64-115 434-483 (730)
119 COG5222 Uncharacterized conser 73.5 2.2 4.8E-05 39.8 2.0 44 151-197 275-318 (427)
120 KOG0269 WD40 repeat-containing 72.8 3.5 7.5E-05 42.5 3.4 49 152-203 781-836 (839)
121 KOG2068 MOT2 transcription fac 72.4 2.9 6.3E-05 39.1 2.5 52 149-201 248-299 (327)
122 smart00249 PHD PHD zinc finger 72.3 1.2 2.5E-05 27.9 -0.0 42 153-195 2-47 (47)
123 PLN03086 PRLI-interacting fact 71.0 2 4.4E-05 42.9 1.2 85 61-160 403-514 (567)
124 COG1198 PriA Primosomal protei 70.9 4.1 8.9E-05 41.9 3.4 53 27-91 436-488 (730)
125 PRK14714 DNA polymerase II lar 70.3 3.8 8.2E-05 44.5 3.1 33 79-115 668-700 (1337)
126 PF05605 zf-Di19: Drought indu 69.5 4.7 0.0001 27.3 2.5 11 190-200 32-42 (54)
127 PF07282 OrfB_Zn_ribbon: Putat 68.4 4 8.7E-05 28.7 2.0 27 78-115 28-54 (69)
128 PRK04023 DNA polymerase II lar 67.8 4.4 9.6E-05 43.1 2.9 48 79-135 627-674 (1121)
129 PF07754 DUF1610: Domain of un 67.6 4.7 0.0001 23.8 1.8 9 106-114 15-23 (24)
130 PRK05580 primosome assembly pr 67.6 4.3 9.2E-05 41.1 2.7 50 27-88 382-431 (679)
131 KOG2066 Vacuolar assembly/sort 67.5 2.1 4.6E-05 44.2 0.6 44 151-196 785-831 (846)
132 KOG1001 Helicase-like transcri 67.4 2.6 5.5E-05 43.0 1.1 45 151-200 455-500 (674)
133 TIGR02300 FYDLN_acid conserved 66.8 4.2 9E-05 33.3 2.0 27 78-116 9-35 (129)
134 PHA03096 p28-like protein; Pro 66.6 2.9 6.2E-05 38.3 1.2 47 151-197 179-231 (284)
135 PF03107 C1_2: C1 domain; Int 65.3 4.8 0.0001 24.3 1.7 20 112-131 2-22 (30)
136 PF05502 Dynactin_p62: Dynacti 65.0 3.6 7.8E-05 40.2 1.6 98 91-211 6-108 (483)
137 KOG1940 Zn-finger protein [Gen 64.4 3 6.6E-05 38.1 0.9 29 14-43 176-204 (276)
138 KOG3053 Uncharacterized conser 63.3 4.5 9.8E-05 36.9 1.8 68 148-215 18-104 (293)
139 PRK14873 primosome assembly pr 63.0 5.8 0.00012 40.3 2.7 48 27-87 384-431 (665)
140 COG5109 Uncharacterized conser 62.4 7.1 0.00015 36.7 2.9 44 152-196 338-383 (396)
141 PRK14890 putative Zn-ribbon RN 61.6 5.5 0.00012 28.4 1.6 35 63-99 23-57 (59)
142 KOG2462 C2H2-type Zn-finger pr 61.3 7.8 0.00017 35.5 2.9 20 189-208 243-262 (279)
143 PF14569 zf-UDP: Zinc-binding 60.1 12 0.00027 28.1 3.3 53 148-200 7-62 (80)
144 PF00096 zf-C2H2: Zinc finger, 60.0 5.8 0.00013 21.7 1.3 16 190-205 1-16 (23)
145 KOG0298 DEAD box-containing he 59.8 4.4 9.5E-05 44.0 1.2 52 148-203 1151-1202(1394)
146 KOG1812 Predicted E3 ubiquitin 59.5 4.3 9.3E-05 38.5 1.0 37 150-186 146-182 (384)
147 PF05290 Baculo_IE-1: Baculovi 58.9 6.2 0.00013 32.6 1.7 49 151-203 81-135 (140)
148 PF06524 NOA36: NOA36 protein; 58.4 3.2 7E-05 38.0 -0.0 51 33-98 140-190 (314)
149 PF05191 ADK_lid: Adenylate ki 58.3 2.6 5.6E-05 26.9 -0.5 27 80-115 3-29 (36)
150 PRK00415 rps27e 30S ribosomal 57.9 5.8 0.00013 28.3 1.2 35 64-98 10-50 (59)
151 PF13453 zf-TFIIB: Transcripti 57.7 8.5 0.00018 24.7 1.9 26 80-114 1-26 (41)
152 PRK14559 putative protein seri 57.4 5.3 0.00012 40.5 1.3 34 65-99 15-50 (645)
153 smart00659 RPOLCX RNA polymera 57.3 6.1 0.00013 26.3 1.2 21 67-87 4-28 (44)
154 PRK00398 rpoP DNA-directed RNA 56.1 10 0.00022 24.8 2.1 8 107-114 21-28 (46)
155 KOG1609 Protein involved in mR 54.6 5.6 0.00012 35.3 0.9 51 150-200 78-134 (323)
156 PF04423 Rad50_zn_hook: Rad50 54.6 7.5 0.00016 26.4 1.3 26 189-214 20-47 (54)
157 PF08271 TF_Zn_Ribbon: TFIIB z 53.7 11 0.00025 24.3 2.0 8 80-87 2-9 (43)
158 PF04216 FdhE: Protein involve 53.7 9.3 0.0002 34.4 2.2 48 63-114 195-245 (290)
159 PHA00626 hypothetical protein 53.1 8.8 0.00019 27.2 1.5 34 66-101 1-34 (59)
160 COG3809 Uncharacterized protei 52.8 14 0.0003 28.1 2.6 49 152-223 3-53 (88)
161 KOG4185 Predicted E3 ubiquitin 52.8 2 4.3E-05 38.5 -2.3 49 151-199 208-266 (296)
162 PF15353 HECA: Headcase protei 52.6 7.5 0.00016 30.8 1.2 16 171-186 39-54 (107)
163 COG5273 Uncharacterized protei 52.5 8.5 0.00018 35.5 1.7 21 79-99 98-118 (309)
164 KOG4367 Predicted Zn-finger pr 50.1 8.7 0.00019 37.7 1.4 33 150-186 4-36 (699)
165 COG2051 RPS27A Ribosomal prote 49.4 7.7 0.00017 28.3 0.7 28 64-91 18-51 (67)
166 PF01096 TFIIS_C: Transcriptio 49.0 15 0.00033 23.5 2.0 34 80-114 2-35 (39)
167 PF13717 zinc_ribbon_4: zinc-r 48.2 11 0.00025 23.7 1.3 10 64-73 24-33 (36)
168 KOG1100 Predicted E3 ubiquitin 46.7 11 0.00024 32.9 1.4 39 153-200 161-200 (207)
169 PF01529 zf-DHHC: DHHC palmito 45.6 16 0.00036 29.5 2.2 49 83-137 41-89 (174)
170 PF13719 zinc_ribbon_5: zinc-r 45.4 14 0.0003 23.4 1.4 9 65-73 25-33 (37)
171 PF14353 CpXC: CpXC protein 44.3 21 0.00046 28.0 2.6 11 80-90 3-13 (128)
172 PF15616 TerY-C: TerY-C metal 43.8 23 0.00051 29.0 2.8 33 79-114 78-112 (131)
173 TIGR00595 priA primosomal prot 43.5 26 0.00056 34.3 3.6 46 63-116 211-262 (505)
174 KOG2462 C2H2-type Zn-finger pr 43.0 38 0.00082 31.2 4.3 88 89-204 129-230 (279)
175 PRK00432 30S ribosomal protein 42.9 17 0.00037 24.7 1.6 9 106-114 36-44 (50)
176 COG1996 RPC10 DNA-directed RNA 42.8 17 0.00037 25.0 1.6 26 90-115 6-32 (49)
177 PF07649 C1_3: C1-like domain; 42.5 14 0.00031 22.0 1.0 20 113-132 3-23 (30)
178 PF00412 LIM: LIM domain; Int 42.3 10 0.00023 25.1 0.5 40 153-203 1-40 (58)
179 PF12874 zf-met: Zinc-finger o 42.2 14 0.0003 20.6 0.9 16 190-205 1-16 (25)
180 PF01667 Ribosomal_S27e: Ribos 41.8 14 0.0003 26.0 1.0 34 65-98 7-46 (55)
181 PF03833 PolC_DP2: DNA polymer 41.7 8.6 0.00019 40.3 0.0 44 80-132 657-700 (900)
182 PF04438 zf-HIT: HIT zinc fing 41.5 13 0.00029 22.7 0.8 16 81-97 5-20 (30)
183 cd00350 rubredoxin_like Rubred 41.4 21 0.00045 22.0 1.7 24 91-115 2-25 (33)
184 PF06827 zf-FPG_IleRS: Zinc fi 41.4 20 0.00043 21.3 1.6 10 79-88 2-11 (30)
185 PLN02189 cellulose synthase 41.3 24 0.00051 37.9 3.1 56 145-200 29-87 (1040)
186 COG2888 Predicted Zn-ribbon RN 40.9 16 0.00036 26.1 1.3 34 63-98 25-58 (61)
187 KOG4399 C2HC-type Zn-finger pr 39.4 5.8 0.00013 36.3 -1.4 73 85-160 199-271 (325)
188 KOG1312 DHHC-type Zn-finger pr 39.4 10 0.00022 35.3 0.1 32 111-145 149-180 (341)
189 KOG3362 Predicted BBOX Zn-fing 39.3 10 0.00022 31.8 0.1 25 89-119 117-143 (156)
190 PLN02436 cellulose synthase A 38.9 27 0.00059 37.6 3.1 56 145-200 31-89 (1094)
191 KOG0006 E3 ubiquitin-protein l 38.5 27 0.00058 33.1 2.7 80 98-186 168-255 (446)
192 PF03604 DNA_RNApol_7kD: DNA d 38.4 20 0.00043 22.4 1.3 10 105-114 15-24 (32)
193 PRK06266 transcription initiat 38.2 46 0.001 28.2 3.9 33 188-220 135-176 (178)
194 PF08274 PhnA_Zn_Ribbon: PhnA 38.0 18 0.00039 22.3 1.0 23 80-114 4-26 (30)
195 PF13824 zf-Mss51: Zinc-finger 37.7 29 0.00062 24.4 2.1 21 188-208 13-33 (55)
196 PF00643 zf-B_box: B-box zinc 37.5 27 0.0006 21.9 1.9 21 79-99 4-24 (42)
197 PF12760 Zn_Tnp_IS1595: Transp 37.3 43 0.00093 21.9 2.9 9 79-87 19-27 (46)
198 PF01529 zf-DHHC: DHHC palmito 37.2 19 0.00041 29.1 1.3 36 104-145 45-80 (174)
199 smart00661 RPOL9 RNA polymeras 36.2 29 0.00062 22.8 1.9 8 107-114 20-27 (52)
200 PF11781 RRN7: RNA polymerase 36.2 24 0.00053 22.4 1.5 24 153-176 11-35 (36)
201 TIGR00100 hypA hydrogenase nic 36.2 17 0.00037 28.6 0.9 11 78-88 70-80 (115)
202 PRK00420 hypothetical protein; 36.1 25 0.00054 28.0 1.8 22 78-99 23-49 (112)
203 PRK03564 formate dehydrogenase 36.1 40 0.00087 31.3 3.5 26 62-87 209-235 (309)
204 cd00729 rubredoxin_SM Rubredox 35.9 27 0.00059 21.8 1.6 22 66-87 3-27 (34)
205 COG1998 RPS31 Ribosomal protei 35.4 23 0.00051 24.5 1.3 19 79-97 20-44 (51)
206 KOG2272 Focal adhesion protein 35.4 25 0.00053 32.3 1.9 94 36-158 100-200 (332)
207 cd02337 ZZ_CBP Zinc finger, ZZ 34.8 29 0.00064 22.6 1.7 20 108-131 1-20 (41)
208 smart00355 ZnF_C2H2 zinc finge 34.0 37 0.00081 17.9 1.9 16 190-205 1-16 (26)
209 KOG0802 E3 ubiquitin ligase [P 33.1 27 0.00059 34.4 1.9 44 148-200 477-520 (543)
210 PF13913 zf-C2HC_2: zinc-finge 32.8 19 0.00042 20.9 0.5 12 79-90 3-14 (25)
211 cd02341 ZZ_ZZZ3 Zinc finger, Z 32.7 33 0.00071 23.2 1.7 7 109-115 2-8 (48)
212 KOG4317 Predicted Zn-finger pr 32.5 20 0.00044 33.7 0.9 21 79-99 8-28 (383)
213 TIGR02098 MJ0042_CXXC MJ0042 f 31.9 35 0.00075 21.1 1.7 10 65-74 25-34 (38)
214 PRK14873 primosome assembly pr 31.2 43 0.00093 34.2 3.0 23 64-90 382-404 (665)
215 PLN00209 ribosomal protein S27 30.9 32 0.00068 26.3 1.5 37 64-100 35-77 (86)
216 KOG3005 GIY-YIG type nuclease 30.8 58 0.0013 29.9 3.5 64 151-219 183-257 (276)
217 PF03833 PolC_DP2: DNA polymer 30.8 16 0.00036 38.3 0.0 46 64-115 654-700 (900)
218 PTZ00083 40S ribosomal protein 30.6 27 0.00058 26.7 1.1 36 64-99 34-75 (85)
219 cd02249 ZZ Zinc finger, ZZ typ 30.6 37 0.0008 22.2 1.7 9 123-131 13-21 (46)
220 PF12171 zf-C2H2_jaz: Zinc-fin 30.5 36 0.00079 19.5 1.5 15 189-203 1-15 (27)
221 PF01599 Ribosomal_S27: Riboso 29.9 32 0.0007 23.4 1.3 21 78-98 18-46 (47)
222 cd07973 Spt4 Transcription elo 29.6 29 0.00064 27.0 1.2 19 67-85 5-27 (98)
223 PRK00464 nrdR transcriptional 29.4 33 0.00071 28.7 1.6 12 80-91 30-41 (154)
224 PRK14810 formamidopyrimidine-D 29.1 31 0.00068 31.0 1.5 20 78-97 244-271 (272)
225 PF06677 Auto_anti-p27: Sjogre 28.3 41 0.0009 22.1 1.6 13 78-90 17-29 (41)
226 PRK14892 putative transcriptio 28.1 54 0.0012 25.5 2.5 32 122-159 19-51 (99)
227 PRK08351 DNA-directed RNA poly 27.7 37 0.00081 24.3 1.4 20 67-87 5-24 (61)
228 smart00451 ZnF_U1 U1-like zinc 27.5 42 0.00091 19.9 1.5 16 189-204 3-18 (35)
229 PF11023 DUF2614: Protein of u 27.5 39 0.00084 27.1 1.6 27 62-88 66-95 (114)
230 PRK10445 endonuclease VIII; Pr 27.5 36 0.00077 30.5 1.6 20 78-97 235-262 (263)
231 KOG1829 Uncharacterized conser 27.5 21 0.00046 35.9 0.1 26 167-196 532-557 (580)
232 PRK14811 formamidopyrimidine-D 27.3 36 0.00078 30.6 1.6 20 78-97 235-262 (269)
233 PF08792 A2L_zn_ribbon: A2L zi 27.2 39 0.00084 21.1 1.2 11 66-76 4-14 (33)
234 PF00628 PHD: PHD-finger; Int 27.0 24 0.00051 23.0 0.3 43 153-196 2-49 (51)
235 COG3024 Uncharacterized protei 26.4 35 0.00075 24.8 1.0 26 76-101 5-38 (65)
236 PF12172 DUF35_N: Rubredoxin-l 26.1 31 0.00068 21.4 0.7 23 64-86 10-33 (37)
237 PF05458 Siva: Cd27 binding pr 26.1 53 0.0012 28.0 2.3 36 65-100 111-157 (175)
238 smart00586 ZnF_DBF Zinc finger 26.1 39 0.00085 23.1 1.2 14 203-216 34-47 (49)
239 PF11331 DUF3133: Protein of u 25.6 59 0.0013 22.0 2.0 38 36-78 7-44 (46)
240 PF09297 zf-NADH-PPase: NADH p 25.6 26 0.00055 21.3 0.2 20 67-86 5-29 (32)
241 PLN02638 cellulose synthase A 25.4 63 0.0014 34.9 3.1 56 145-200 12-70 (1079)
242 PRK01103 formamidopyrimidine/5 25.3 41 0.0009 30.1 1.6 20 78-97 245-272 (274)
243 PF00130 C1_1: Phorbol esters/ 25.1 58 0.0013 21.3 1.9 11 104-114 25-35 (53)
244 TIGR00373 conserved hypothetic 25.0 98 0.0021 25.6 3.6 28 188-215 127-156 (158)
245 KOG4275 Predicted E3 ubiquitin 24.9 22 0.00049 33.1 -0.2 20 79-100 322-341 (350)
246 KOG2593 Transcription initiati 24.8 35 0.00077 33.2 1.1 10 123-132 152-161 (436)
247 PF13912 zf-C2H2_6: C2H2-type 24.6 40 0.00087 19.0 0.9 17 190-206 2-18 (27)
248 PF12675 DUF3795: Protein of u 24.0 42 0.00091 24.5 1.2 37 78-114 34-70 (78)
249 TIGR01562 FdhE formate dehydro 24.0 87 0.0019 29.1 3.4 25 63-87 208-233 (305)
250 KOG0826 Predicted E3 ubiquitin 23.6 73 0.0016 30.2 2.9 48 149-200 299-346 (357)
251 KOG1815 Predicted E3 ubiquitin 23.6 46 0.00099 32.0 1.6 38 147-187 67-104 (444)
252 PRK00564 hypA hydrogenase nick 23.4 52 0.0011 26.0 1.7 11 78-88 71-81 (117)
253 TIGR00577 fpg formamidopyrimid 23.4 47 0.001 29.8 1.6 19 78-96 245-271 (272)
254 PRK13945 formamidopyrimidine-D 23.1 49 0.0011 29.9 1.6 19 78-96 254-280 (282)
255 PRK12380 hydrogenase nickel in 23.1 39 0.00084 26.5 0.9 10 79-88 71-80 (113)
256 PF06220 zf-U1: U1 zinc finger 22.8 33 0.00072 22.0 0.3 13 88-100 1-13 (38)
257 PRK05580 primosome assembly pr 22.7 85 0.0018 31.9 3.4 45 63-115 379-429 (679)
258 PF02318 FYVE_2: FYVE-type zin 22.7 30 0.00066 27.1 0.2 40 65-110 54-97 (118)
259 PRK04136 rpl40e 50S ribosomal 22.7 54 0.0012 22.5 1.3 24 63-86 12-36 (48)
260 KOG1812 Predicted E3 ubiquitin 22.4 43 0.00092 31.9 1.1 65 150-215 306-373 (384)
261 COG5183 SSM4 Protein involved 22.3 56 0.0012 34.6 2.0 49 150-200 12-66 (1175)
262 TIGR00244 transcriptional regu 22.3 58 0.0012 27.3 1.7 12 80-91 30-41 (147)
263 smart00440 ZnF_C2C2 C2C2 Zinc 22.2 94 0.002 19.9 2.4 33 80-114 2-35 (40)
264 smart00531 TFIIE Transcription 22.1 32 0.0007 28.0 0.2 9 80-88 101-109 (147)
265 COG1144 Pyruvate:ferredoxin ox 21.7 47 0.001 25.7 1.0 15 122-136 63-77 (91)
266 smart00834 CxxC_CXXC_SSSS Puta 21.5 80 0.0017 19.4 2.0 7 80-86 28-34 (41)
267 TIGR01384 TFS_arch transcripti 21.3 70 0.0015 24.2 1.9 8 81-88 3-10 (104)
268 PHA00616 hypothetical protein 21.0 62 0.0013 21.7 1.4 29 190-218 2-30 (44)
269 PF00301 Rubredoxin: Rubredoxi 20.7 77 0.0017 21.3 1.8 10 90-99 1-10 (47)
270 KOG1311 DHHC-type Zn-finger pr 20.5 79 0.0017 28.4 2.4 48 83-136 106-153 (299)
271 PRK12496 hypothetical protein; 20.5 48 0.001 27.8 0.9 22 67-88 129-153 (164)
272 PRK00366 ispG 4-hydroxy-3-meth 20.4 85 0.0018 29.9 2.6 31 189-219 268-298 (360)
273 PRK03681 hypA hydrogenase nick 20.3 66 0.0014 25.3 1.6 13 76-88 68-80 (114)
274 KOG3990 Uncharacterized conser 20.2 9.3 0.0002 34.8 -3.6 63 35-121 6-85 (305)
275 PRK00418 DNA gyrase inhibitor; 20.1 51 0.0011 23.7 0.9 12 189-200 6-17 (62)
No 1
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=100.00 E-value=6.6e-58 Score=408.28 Aligned_cols=209 Identities=48% Similarity=1.034 Sum_probs=201.9
Q ss_pred CccccccCCCCccCccccccccceecCCCCCcccChhhHHhhhcCCCCCCCcccccccccCeeEeCCCCccccccccCCC
Q 027385 4 SANERITFGKMGYGCKHYRRRCRIRAPCCNEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVAQVCTN 83 (224)
Q Consensus 4 ~~~~~~~~~~~~~gC~HY~r~c~l~~pCC~~~y~Cr~CHde~~~~~~~~~~~H~~~r~~~~~vlC~~C~~~q~~~~~C~~ 83 (224)
..+++.|++.++.+|+||+|++.+++|+|+++|+|++||+++. +|.++|+.|.+|+|+.|.++|+++++|.+
T Consensus 21 ~~~~~~d~~~~~~~c~hy~r~~~~~a~ccd~~~~C~hCH~~s~--------~h~~~r~~v~~~~C~~C~~~q~~~~~c~~ 92 (276)
T KOG1940|consen 21 IHSDAEDEIAFPYGCPHYRRNCKSRAPCCDREITCRHCHNESE--------DHDLDRKTVYELLCMKCRKIQPVGQICSN 92 (276)
T ss_pred cccccccccccccCCchhhhccccccccccceeeeEEecChhh--------hcccchhhhhhhhhhhHHhhhhhhhcccc
Confidence 3556789999999999999999999999999999999999974 69999999999999999999999999999
Q ss_pred CCCCcceeecCccccccCCCCcCeeccCCCCcceeCCccceeecCccCccccccccCcceeecCCCCCCCccchhhcccC
Q 027385 84 CGVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYSTSLRNNHLCIENSMHHHCPICYEYLFDS 163 (224)
Q Consensus 84 Cg~~f~~Y~C~~C~l~dd~~~k~~yHC~~CgiCR~G~~~~~fHC~~C~~C~s~~l~~~H~C~e~~~~~~CpICle~lf~s 163 (224)
|+..+++|||.+|+||||+++ .||||+.|||||+|++++||||++|+.|++..+.++|+|+|++++.|||||.|+||++
T Consensus 93 c~~~~g~~~c~~C~l~dd~~~-~~~hC~~C~icr~g~~~~~fhc~~c~~c~~~~~~~~H~c~e~~~~~ncPic~e~l~~s 171 (276)
T KOG1940|consen 93 CHVELGEYYCLICKLFDDDPS-KQYHCDLCGICREGLGLDFFHCKKCKACLSAYLSNWHKCVERSSEFNCPICKEYLFLS 171 (276)
T ss_pred chhhhhhhcCccccccccccc-ceeccccccccccccccchhHHhhhHhHHhhhcccccchhhhcccCCCchhHHHhccc
Confidence 999999999999999999999 9999999999999999999999999999999999999999999999999999999999
Q ss_pred CCceeEeccCCccCHHHHHHHHhcCcCCCCCCccccccchHHHHHHHHHHhcCCCCcCcc
Q 027385 164 LRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRTWKRIDEEMNSSIFFPSFF 223 (224)
Q Consensus 164 ~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~dm~~~~~~lD~~i~~~pmp~~y~ 223 (224)
...+.+|+|||.+|..||++++..+ |+||+|.+ +.||+.+|+++|.+|+++|||++|.
T Consensus 172 ~~~~~~~~CgH~~h~~cf~e~~~~~-y~CP~C~~-~~d~~~~~~~~d~~l~~~~~p~~y~ 229 (276)
T KOG1940|consen 172 FEDAGVLKCGHYMHSRCFEEMICEG-YTCPICSK-PGDMSHYFRKLDKELAGSPMPEEYK 229 (276)
T ss_pred cccCCccCcccchHHHHHHHHhccC-CCCCcccc-hHHHHHHHHHHHHHHhcCCCCchhh
Confidence 9999999999999999999999865 99999999 9999999999999999999999985
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=1.1e-24 Score=159.40 Aligned_cols=70 Identities=51% Similarity=1.212 Sum_probs=53.0
Q ss_pred ccccccc-cceecCCCCCcccChhhHHhhhcCCCCCCCcccccccccCeeEeCCCCccccccccCCCCCCCcceeecCcc
Q 027385 18 CKHYRRR-CRIRAPCCNEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVAQVCTNCGVNMGEYFCDIC 96 (224)
Q Consensus 18 C~HY~r~-c~l~~pCC~~~y~Cr~CHde~~~~~~~~~~~H~~~r~~~~~vlC~~C~~~q~~~~~C~~Cg~~f~~Y~C~~C 96 (224)
|+||+|+ ++|+||||++|||||+||||++ +|+++|+++++|+||.|+++|++++. +|+ ++|+|++|
T Consensus 1 C~HY~~~~~~~~~~cC~~~y~C~~CHde~~--------~H~~~~~~~~~v~Cg~C~~~~~~~~~--~c~---~~~~C~~C 67 (71)
T PF05495_consen 1 CKHYHRSLCAIRFPCCGKYYPCRFCHDELE--------DHPFDRWPVKRVICGKCRTEQPIDEY--SCG---ADYFCPIC 67 (71)
T ss_dssp -SS---S-EEEEETTTTEEESSHHHHHHCS--------SS---TTT--EEEETTT--EEES-SB--TT-----SEEETTT
T ss_pred CCCCCCCcEEEECCcccCeecHHHHHHHhc--------cCccccccccCeECCCCCCccChhhh--hcC---CCccCcCc
Confidence 8999999 9999999999999999999975 59999999999999999999999988 777 99999999
Q ss_pred cccc
Q 027385 97 KFYD 100 (224)
Q Consensus 97 ~l~d 100 (224)
++||
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=99.70 E-value=5e-18 Score=130.27 Aligned_cols=74 Identities=26% Similarity=0.598 Sum_probs=67.3
Q ss_pred CccCcccccc---ccceecCCCCCcccChhhHHhhhcCCCCCCCcccccccccCeeEeCCCCcccccc-----ccCCCCC
Q 027385 14 MGYGCKHYRR---RCRIRAPCCNEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVA-----QVCTNCG 85 (224)
Q Consensus 14 ~~~gC~HY~r---~c~l~~pCC~~~y~Cr~CHde~~~~~~~~~~~H~~~r~~~~~vlC~~C~~~q~~~-----~~C~~Cg 85 (224)
.++||.||++ .++|||.+|+|||+|++||||+++|++ +.++++.+..+.||||+|.++++++ +.||+|.
T Consensus 11 ~etRC~Hyht~~Diialkc~~C~kyYaCy~CHdel~~Hpf---~p~~~~~~~~~~iiCGvC~~~LT~~EY~~~~~Cp~C~ 87 (105)
T COG4357 11 QETRCLHYHTPLDIIALKCKCCQKYYACYHCHDELEDHPF---EPWGLQEFNPKAIICGVCRKLLTRAEYGMCGSCPYCQ 87 (105)
T ss_pred ccceeeEecCccceEeeeechhhhhhhHHHHHhHHhcCCC---ccCChhhcCCccEEhhhhhhhhhHHHHhhcCCCCCcC
Confidence 3689999999 688999999999999999999999886 7788888888999999999999984 5899999
Q ss_pred CCcce
Q 027385 86 VNMGE 90 (224)
Q Consensus 86 ~~f~~ 90 (224)
.+||.
T Consensus 88 spFNp 92 (105)
T COG4357 88 SPFNP 92 (105)
T ss_pred CCCCc
Confidence 99985
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=99.46 E-value=2e-14 Score=95.00 Aligned_cols=44 Identities=39% Similarity=0.937 Sum_probs=37.7
Q ss_pred CCCccchhhcccCCCceeEeccCCccCHHHHHHHHhcCcCCCCCCc
Q 027385 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICS 196 (224)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCr 196 (224)
++||||++++.+ .+.+..|+|||.||.+|+.+|+++ +.+||+||
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 479999999655 678889999999999999999985 68999997
No 5
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=99.13 E-value=4.6e-11 Score=87.57 Aligned_cols=48 Identities=31% Similarity=0.688 Sum_probs=36.8
Q ss_pred CCCCCCccchhhcccC---------CCceeEeccCCccCHHHHHHHHhcCcCCCCCCc
Q 027385 148 SMHHHCPICYEYLFDS---------LRNTTVMKCGHTMHCECYHEMIKRDKYCCPICS 196 (224)
Q Consensus 148 ~~~~~CpICle~lf~s---------~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCr 196 (224)
..+.+|+||++.|.+. ..++...+|||.||..||.+||+. +.+||+||
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 234556799999999999999984 67999997
No 6
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=99.07 E-value=1.4e-10 Score=74.04 Aligned_cols=45 Identities=31% Similarity=0.866 Sum_probs=37.8
Q ss_pred CCccchhhcccCCCceeEeccCCccCHHHHHHHHhcCcCCCCCCcccc
Q 027385 152 HCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSV 199 (224)
Q Consensus 152 ~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi 199 (224)
.|+||++.+ ..++..++|||.||..|++.|++..+.+||+|++.+
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 345666779999999999999985578899999764
No 7
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=99.06 E-value=4.8e-11 Score=110.85 Aligned_cols=57 Identities=26% Similarity=0.742 Sum_probs=49.0
Q ss_pred CCCCCCCccchhhcccCC---------CceeEeccCCccCHHHHHHHHhcCcCCCCCCccc-cccchH
Q 027385 147 NSMHHHCPICYEYLFDSL---------RNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKS-VIDMSR 204 (224)
Q Consensus 147 ~~~~~~CpICle~lf~s~---------~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrks-i~dm~~ 204 (224)
.+.+..|.||+|+|+.+. ...+.|||||.+|.+|++.|++ ++.+|||||.+ +.||++
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 566788999999998865 2348899999999999999998 57899999999 678764
No 8
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.00 E-value=1.6e-10 Score=106.95 Aligned_cols=50 Identities=22% Similarity=0.762 Sum_probs=44.2
Q ss_pred CCCccchhhcccCCCceeEeccCCccCHHHHHHHHhcCcCCCCCCcccccc
Q 027385 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID 201 (224)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~d 201 (224)
..|.||||+ |..++.++.|||+|.||..|++.||......||+|+..+..
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 67789999999999999999999998544459999998874
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=98.94 E-value=4.9e-10 Score=72.31 Aligned_cols=39 Identities=38% Similarity=0.987 Sum_probs=33.4
Q ss_pred CccchhhcccCCCceeEeccCCccCHHHHHHHHhcCcCCCCCC
Q 027385 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPIC 195 (224)
Q Consensus 153 CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiC 195 (224)
||||++.+.+ ++++++|||+|...|+.+|++. +.+||+|
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 8999998644 6789999999999999999996 7899998
No 10
>PHA02929 N1R/p28-like protein; Provisional
Probab=98.91 E-value=1e-09 Score=97.22 Aligned_cols=54 Identities=30% Similarity=0.654 Sum_probs=42.8
Q ss_pred CCCCCCCccchhhcccCCC----ceeEeccCCccCHHHHHHHHhcCcCCCCCCcccccc
Q 027385 147 NSMHHHCPICYEYLFDSLR----NTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID 201 (224)
Q Consensus 147 ~~~~~~CpICle~lf~s~~----~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~d 201 (224)
.+.+..||||+|.+.+... -.+.++|||.||..|+.+|++ .+.+||+||+.+..
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 3556789999999765321 124458999999999999998 57899999999874
No 11
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=98.85 E-value=1.9e-09 Score=72.95 Aligned_cols=47 Identities=36% Similarity=0.918 Sum_probs=39.0
Q ss_pred CCCCccchhhcccCCCceeEeccCCc-cCHHHHHHHHhcCcCCCCCCcccccc
Q 027385 150 HHHCPICYEYLFDSLRNTTVMKCGHT-MHCECYHEMIKRDKYCCPICSKSVID 201 (224)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCGH~-~H~~C~~~~l~~~~~~CPiCrksi~d 201 (224)
+..|+||++.. ..+..+||||. |...|+.+|++ +..+||+||++|.+
T Consensus 2 ~~~C~iC~~~~----~~~~~~pCgH~~~C~~C~~~~~~-~~~~CP~Cr~~i~~ 49 (50)
T PF13920_consen 2 DEECPICFENP----RDVVLLPCGHLCFCEECAERLLK-RKKKCPICRQPIES 49 (50)
T ss_dssp HSB-TTTSSSB----SSEEEETTCEEEEEHHHHHHHHH-TTSBBTTTTBB-SE
T ss_pred cCCCccCCccC----CceEEeCCCChHHHHHHhHHhcc-cCCCCCcCChhhcC
Confidence 45799999972 35788999999 99999999998 67899999999864
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=98.79 E-value=3.6e-09 Score=68.32 Aligned_cols=40 Identities=33% Similarity=0.938 Sum_probs=34.6
Q ss_pred CccchhhcccCCCceeEeccCCccCHHHHHHHHh-cCcCCCCCC
Q 027385 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIK-RDKYCCPIC 195 (224)
Q Consensus 153 CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~-~~~~~CPiC 195 (224)
||||++.+.+ ++..++|||.|+..|+.+|++ ....+||+|
T Consensus 1 C~iC~~~~~~---~~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEPFED---PVILLPCGHSFCRDCLRKWLENSGSVKCPLC 41 (41)
T ss_dssp ETTTSSBCSS---EEEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred CCcCCccccC---CCEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence 8999998543 457899999999999999998 568889998
No 13
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=98.78 E-value=5e-09 Score=79.34 Aligned_cols=48 Identities=25% Similarity=0.414 Sum_probs=33.8
Q ss_pred CCCccchhhcccCCCceeEeccCCccCHHHHHHHHhc--CcCCCCCCccccc
Q 027385 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR--DKYCCPICSKSVI 200 (224)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~--~~~~CPiCrksi~ 200 (224)
..||.|..+-- .-++..-.|||.||..||.+||.. ++.+||+||+...
T Consensus 33 g~Cp~Ck~Pgd--~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~ 82 (85)
T PF12861_consen 33 GCCPDCKFPGD--DCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWK 82 (85)
T ss_pred cCCCCccCCCC--CCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeee
Confidence 44566655421 123444479999999999999985 3678999998653
No 14
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=98.78 E-value=5.3e-09 Score=64.40 Aligned_cols=39 Identities=44% Similarity=1.076 Sum_probs=33.8
Q ss_pred CccchhhcccCCCceeEeccCCccCHHHHHHHHhcCcCCCCCC
Q 027385 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPIC 195 (224)
Q Consensus 153 CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiC 195 (224)
|+||++. .+....++|||.||..|++.|++....+||+|
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 34678899999999999999998557789987
No 15
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.72 E-value=9.6e-09 Score=68.03 Aligned_cols=44 Identities=34% Similarity=0.848 Sum_probs=38.0
Q ss_pred CCccchhhcccCCCceeEeccCCccCHHHHHHHHhcCcCCCCCCcc
Q 027385 152 HCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSK 197 (224)
Q Consensus 152 ~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrk 197 (224)
.|+||++.+ +......+|+|||+|...|+..+.. ....||+|++
T Consensus 1 ~C~~C~~~~-~~~~~~~l~~CgH~~C~~C~~~~~~-~~~~CP~C~k 44 (44)
T PF14634_consen 1 HCNICFEKY-SEERRPRLTSCGHIFCEKCLKKLKG-KSVKCPICRK 44 (44)
T ss_pred CCcCcCccc-cCCCCeEEcccCCHHHHHHHHhhcC-CCCCCcCCCC
Confidence 489999996 5556788999999999999999983 5789999986
No 16
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.67 E-value=1.2e-08 Score=93.06 Aligned_cols=53 Identities=25% Similarity=0.601 Sum_probs=45.2
Q ss_pred cCCCCCCCccchhhcccCCCceeEeccCCccCHHHHHHHHhcCcCCCCCCcccc
Q 027385 146 ENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSV 199 (224)
Q Consensus 146 e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi 199 (224)
|.....+|.|||++ |...+.+++|||.|.||..|+++|+.....+||+||..+
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 33445789999999 567888999999999999999999985578999999665
No 17
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.61 E-value=3.1e-08 Score=65.45 Aligned_cols=39 Identities=33% Similarity=0.974 Sum_probs=28.7
Q ss_pred CccchhhcccCCCceeEeccCCccCHHHHHHHHhcC---cCCCCCC
Q 027385 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRD---KYCCPIC 195 (224)
Q Consensus 153 CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~---~~~CPiC 195 (224)
||||++.|.+ .+.|+|||.|-..|+.+|.+.. .+.||+|
T Consensus 1 CpiC~~~~~~----Pv~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDLFKD----PVSLPCGHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB-SS----EEE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCccchhhCC----ccccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 8999998543 5679999999999999998753 2579987
No 18
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.53 E-value=5.7e-08 Score=64.77 Aligned_cols=40 Identities=33% Similarity=0.890 Sum_probs=24.0
Q ss_pred CccchhhcccCCCceeEeccCCccCHHHHHHHHhcC---cCCCC
Q 027385 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRD---KYCCP 193 (224)
Q Consensus 153 CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~---~~~CP 193 (224)
||||.| +.+...+.++|+|||+|-++|+++|++++ ..+||
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 55545667889999999999999999843 56677
No 19
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=98.47 E-value=2.8e-08 Score=70.99 Aligned_cols=26 Identities=27% Similarity=0.557 Sum_probs=0.0
Q ss_pred cccchHHHHHHHHHHhcCCCCcCccC
Q 027385 199 VIDMSRTWKRIDEEMNSSIFFPSFFR 224 (224)
Q Consensus 199 i~dm~~~~~~lD~~i~~~pmp~~y~~ 224 (224)
|+||+++|++||++||++|||++|+.
T Consensus 1 v~dM~~~w~~LD~~i~~~pmP~~Y~~ 26 (61)
T PF14599_consen 1 VVDMSAYWRMLDAEIAATPMPEEYRN 26 (61)
T ss_dssp --------------------------
T ss_pred CCCHHHHHHHHHHHHHhCCCCHHHhC
Confidence 57999999999999999999999973
No 20
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.46 E-value=4.5e-08 Score=95.35 Aligned_cols=53 Identities=25% Similarity=0.582 Sum_probs=43.8
Q ss_pred CCCCCCCccchhhcccCC-CceeEeccCCccCHHHHHHHHhcCcCCCCCCccccc
Q 027385 147 NSMHHHCPICYEYLFDSL-RNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (224)
Q Consensus 147 ~~~~~~CpICle~lf~s~-~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (224)
......|+||+|.|+.+. ..+..|+|||.||..|+..|++ ...+||+||..+.
T Consensus 288 ~~~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~e-r~qtCP~CR~~~~ 341 (543)
T KOG0802|consen 288 ALSDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFE-RQQTCPTCRTVLY 341 (543)
T ss_pred hhcCCeeeeechhhccccccccceeecccchHHHHHHHHHH-HhCcCCcchhhhh
Confidence 355778999999998742 2367899999999999999999 5899999998443
No 21
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.44 E-value=1.9e-07 Score=80.47 Aligned_cols=55 Identities=24% Similarity=0.609 Sum_probs=42.2
Q ss_pred eeecCCCCCCCccchhhcccCCCceeEeccCCccCHHHHHHHHhc---------------CcCCCCCCcccccc
Q 027385 143 LCIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR---------------DKYCCPICSKSVID 201 (224)
Q Consensus 143 ~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~---------------~~~~CPiCrksi~d 201 (224)
+=++...+..||||++.+. ..++++|||.|+..|+.+|+.. +..+||+||..|..
T Consensus 11 ~~~~~~~~~~CpICld~~~----dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~ 80 (193)
T PLN03208 11 TLVDSGGDFDCNICLDQVR----DPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE 80 (193)
T ss_pred eeccCCCccCCccCCCcCC----CcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence 3344456778999999742 3456799999999999999852 23589999999864
No 22
>PHA02926 zinc finger-like protein; Provisional
Probab=98.34 E-value=2.2e-07 Score=81.71 Aligned_cols=62 Identities=26% Similarity=0.547 Sum_probs=45.6
Q ss_pred cCCCCCCCccchhhcccCC-----CceeEeccCCccCHHHHHHHHhcC-----cCCCCCCcccccc--chHHHH
Q 027385 146 ENSMHHHCPICYEYLFDSL-----RNTTVMKCGHTMHCECYHEMIKRD-----KYCCPICSKSVID--MSRTWK 207 (224)
Q Consensus 146 e~~~~~~CpICle~lf~s~-----~~v~~LpCGH~~H~~C~~~~l~~~-----~~~CPiCrksi~d--m~~~~~ 207 (224)
..+.+..|+||+|.+++.. ......+|+|.|+..|+.+|.+.. ..+||+||..+.. +|.+|.
T Consensus 166 ~~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~I~pSrf~~ 239 (242)
T PHA02926 166 RVSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFRNITMSKFYK 239 (242)
T ss_pred hccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceeeeecccccee
Confidence 4577889999999876531 123445999999999999998742 3459999998763 455543
No 23
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.23 E-value=5.5e-07 Score=76.66 Aligned_cols=47 Identities=30% Similarity=0.829 Sum_probs=38.2
Q ss_pred CCCccchhhcccCCCceeEeccCCccCHHHHHHHHhcCcCCCCCCccccc
Q 027385 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (224)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (224)
..|||||+.... .......|||+|.++|++.-++ ...+||+|+|.|.
T Consensus 132 ~~CPiCl~~~se--k~~vsTkCGHvFC~~Cik~alk-~~~~CP~C~kkIt 178 (187)
T KOG0320|consen 132 YKCPICLDSVSE--KVPVSTKCGHVFCSQCIKDALK-NTNKCPTCRKKIT 178 (187)
T ss_pred cCCCceecchhh--ccccccccchhHHHHHHHHHHH-hCCCCCCcccccc
Confidence 689999998422 2224479999999999999998 4689999999665
No 24
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=98.14 E-value=2.5e-06 Score=59.24 Aligned_cols=45 Identities=18% Similarity=0.361 Sum_probs=38.2
Q ss_pred CCCccchhhcccCCCceeEeccCCccCHHHHHHHHhcCcCCCCCCccccc
Q 027385 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (224)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (224)
-.||||++.|.+ + +.++|||+|-+.|+.+|++. +.+||+|++.+.
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 469999998543 3 56799999999999999985 789999999884
No 25
>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class
Probab=98.12 E-value=2.1e-06 Score=58.54 Aligned_cols=43 Identities=28% Similarity=0.617 Sum_probs=33.6
Q ss_pred CCccchhhcccCCCceeEeccC-----CccCHHHHHHHHhcC-cCCCCCCc
Q 027385 152 HCPICYEYLFDSLRNTTVMKCG-----HTMHCECYHEMIKRD-KYCCPICS 196 (224)
Q Consensus 152 ~CpICle~lf~s~~~v~~LpCG-----H~~H~~C~~~~l~~~-~~~CPiCr 196 (224)
.|-||++ +++.+...++||. |++|..|+.+|+..+ +.+||||+
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 3334556678984 999999999999753 55899995
No 26
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=98.06 E-value=1.8e-06 Score=82.21 Aligned_cols=47 Identities=28% Similarity=0.757 Sum_probs=42.7
Q ss_pred CCCccchhhcccCCCceeEeccCCccCHHHHHHHHhcCcCCCCCCccccc
Q 027385 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (224)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (224)
..||||||.|-+|++.+....|.|+||..|+..|. ..+||+||....
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 47999999999999999999999999999999994 579999997665
No 27
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=97.96 E-value=2.4e-06 Score=62.24 Aligned_cols=51 Identities=31% Similarity=0.626 Sum_probs=24.2
Q ss_pred CCCCccchhhcc-cCCCceeEe---ccCCccCHHHHHHHHhcC----------cCCCCCCccccc
Q 027385 150 HHHCPICYEYLF-DSLRNTTVM---KCGHTMHCECYHEMIKRD----------KYCCPICSKSVI 200 (224)
Q Consensus 150 ~~~CpICle~lf-~s~~~v~~L---pCGH~~H~~C~~~~l~~~----------~~~CPiCrksi~ 200 (224)
+.+|+||.+++. +...+..+- .|+..||..||.+|++.. ..+||.|++.|.
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~ 66 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPIS 66 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEE
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeee
Confidence 457999999876 333333433 699999999999998741 236999999885
No 28
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.94 E-value=7.7e-06 Score=77.44 Aligned_cols=46 Identities=22% Similarity=0.587 Sum_probs=38.5
Q ss_pred CCCCccchhhcccCCCceeEeccCCccCHHHHHHHHhcCcCCCCCCccccc
Q 027385 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (224)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (224)
...|+||++.+.. + ++++|||.|+..|+..|+.. ...||+|+..+.
T Consensus 26 ~l~C~IC~d~~~~---P-vitpCgH~FCs~CI~~~l~~-~~~CP~Cr~~~~ 71 (397)
T TIGR00599 26 SLRCHICKDFFDV---P-VLTSCSHTFCSLCIRRCLSN-QPKCPLCRAEDQ 71 (397)
T ss_pred ccCCCcCchhhhC---c-cCCCCCCchhHHHHHHHHhC-CCCCCCCCCccc
Confidence 4589999998533 3 36899999999999999984 568999999876
No 29
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=97.90 E-value=9.9e-06 Score=60.89 Aligned_cols=48 Identities=23% Similarity=0.465 Sum_probs=33.9
Q ss_pred CCccchhhcccCCCceeE-eccCCccCHHHHHHHHhcCcCCCCCCccccc
Q 027385 152 HCPICYEYLFDSLRNTTV-MKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (224)
Q Consensus 152 ~CpICle~lf~s~~~v~~-LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (224)
.||-|+-.+....+-..+ =-|.|.||..|+..||.+ ...||+++++..
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 455555544332222223 269999999999999985 789999998864
No 30
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=97.75 E-value=1.1e-05 Score=73.03 Aligned_cols=45 Identities=29% Similarity=0.712 Sum_probs=38.1
Q ss_pred CCCccchhhcccCCCceeEeccCCccCHHHHHHHHhcCcCCCCCCccccc
Q 027385 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (224)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (224)
..|.+|||.. +.....||||.|.-.|+.+|+.. ...||+||..+-
T Consensus 240 ~kC~LCLe~~----~~pSaTpCGHiFCWsCI~~w~~e-k~eCPlCR~~~~ 284 (293)
T KOG0317|consen 240 RKCSLCLENR----SNPSATPCGHIFCWSCILEWCSE-KAECPLCREKFQ 284 (293)
T ss_pred CceEEEecCC----CCCCcCcCcchHHHHHHHHHHcc-ccCCCcccccCC
Confidence 4799999984 34568899999999999999985 567999998765
No 31
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.73 E-value=1.4e-05 Score=75.28 Aligned_cols=46 Identities=26% Similarity=0.594 Sum_probs=39.4
Q ss_pred CCCCccchhhcccCCCceeEec-cCCccCHHHHHHHHhc--CcCCCCCCc
Q 027385 150 HHHCPICYEYLFDSLRNTTVMK-CGHTMHCECYHEMIKR--DKYCCPICS 196 (224)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~Lp-CGH~~H~~C~~~~l~~--~~~~CPiCr 196 (224)
...|.|| ++++.....+..+. |||+||..|+.+|.+. ++.+||||+
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 77888888888876 9999999999999985 246899999
No 32
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=97.72 E-value=1.3e-05 Score=59.75 Aligned_cols=29 Identities=24% Similarity=0.707 Sum_probs=24.9
Q ss_pred ccCCccCHHHHHHHHhc--CcCCCCCCcccc
Q 027385 171 KCGHTMHCECYHEMIKR--DKYCCPICSKSV 199 (224)
Q Consensus 171 pCGH~~H~~C~~~~l~~--~~~~CPiCrksi 199 (224)
-|.|.||..|+.+|+.. ++..||+||++.
T Consensus 50 ~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~ 80 (84)
T KOG1493|consen 50 YCLHAFHAHCILKWLNTPTSQGQCPMCRQTW 80 (84)
T ss_pred HHHHHHHHHHHHHHhcCccccccCCcchhee
Confidence 49999999999999964 466799999865
No 33
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.71 E-value=3.2e-05 Score=71.02 Aligned_cols=52 Identities=25% Similarity=0.556 Sum_probs=39.2
Q ss_pred CCCCccchhhcccCCCce-eEeccCCccCHHHHHHHHhcCcCCCCCCcccccc
Q 027385 150 HHHCPICYEYLFDSLRNT-TVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID 201 (224)
Q Consensus 150 ~~~CpICle~lf~s~~~v-~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~d 201 (224)
+..||||+.....+.+.. .+.+|||.|..+|++.++......||+|++++-.
T Consensus 3 ~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk 55 (309)
T TIGR00570 3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLRK 55 (309)
T ss_pred CCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCccch
Confidence 357999999655543322 2228999999999999776567799999988763
No 34
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.66 E-value=2.2e-05 Score=66.08 Aligned_cols=44 Identities=30% Similarity=0.845 Sum_probs=38.0
Q ss_pred CCCCCccchhhcccCCCceeEeccCCccCHHHHHHHHhcCcCCCCCCcc
Q 027385 149 MHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSK 197 (224)
Q Consensus 149 ~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrk 197 (224)
.+..||||++++.. + .+|||||.|-..|+..++. ....||.||.
T Consensus 12 ~~~~C~iC~~~~~~---p-~~l~C~H~~c~~C~~~~~~-~~~~Cp~cr~ 55 (386)
T KOG2177|consen 12 EELTCPICLEYFRE---P-VLLPCGHNFCRACLTRSWE-GPLSCPVCRP 55 (386)
T ss_pred ccccChhhHHHhhc---C-ccccccchHhHHHHHHhcC-CCcCCcccCC
Confidence 45689999999544 2 8899999999999999987 6789999994
No 35
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.63 E-value=3e-05 Score=74.93 Aligned_cols=50 Identities=28% Similarity=0.614 Sum_probs=39.1
Q ss_pred CCCCCCccchhhcccCCCceeEeccCCccCHHHHHHHHhcC----cCCCCCCcccccc
Q 027385 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRD----KYCCPICSKSVID 201 (224)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~----~~~CPiCrksi~d 201 (224)
+++..|||||++ . .....+.|||+|.-.||-+|+..+ -..||||+.+|.-
T Consensus 184 ~t~~~CPICL~~-~---~~p~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~ 237 (513)
T KOG2164|consen 184 STDMQCPICLEP-P---SVPVRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITL 237 (513)
T ss_pred CcCCcCCcccCC-C---CcccccccCceeeHHHHHHHHhhhcccCCccCCchhhhccc
Confidence 448899999998 2 233445699999999999988642 4579999999863
No 36
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.56 E-value=4.7e-05 Score=67.16 Aligned_cols=50 Identities=24% Similarity=0.615 Sum_probs=39.1
Q ss_pred CCCCCCccchhhcccCCCceeEeccCCccCHHHHHHHHhcC--cCCCCCCcccccc
Q 027385 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRD--KYCCPICSKSVID 201 (224)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~--~~~CPiCrksi~d 201 (224)
...-+|-||||- .+..++..|||+|.-.||.+||..+ ...||+|+..|.+
T Consensus 45 ~~~FdCNICLd~----akdPVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~ 96 (230)
T KOG0823|consen 45 GGFFDCNICLDL----AKDPVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSI 96 (230)
T ss_pred CCceeeeeeccc----cCCCEEeecccceehHHHHHHHhhcCCCeeCCcccccccc
Confidence 445689999986 2345677799999999999999753 4458999988764
No 37
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=97.41 E-value=5.5e-05 Score=54.65 Aligned_cols=56 Identities=23% Similarity=0.644 Sum_probs=29.8
Q ss_pred CCCccchhhcccCCCceeEeccCCccCHHHHHHHHhcCcCCCCCCccccc--cchHHHHHHHHHH
Q 027385 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI--DMSRTWKRIDEEM 213 (224)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~--dm~~~~~~lD~~i 213 (224)
..|++|.+.|.. +|..-.|.|.|.+.|+.+-+. +.||+|+.+.. |+. ..++||.+|
T Consensus 8 LrCs~C~~~l~~---pv~l~~CeH~fCs~Ci~~~~~---~~CPvC~~Paw~qD~~-~NrqLd~~i 65 (65)
T PF14835_consen 8 LRCSICFDILKE---PVCLGGCEHIFCSSCIRDCIG---SECPVCHTPAWIQDIQ-INRQLDSMI 65 (65)
T ss_dssp TS-SSS-S--SS----B---SSS--B-TTTGGGGTT---TB-SSS--B-S-SS-----HHHHHHH
T ss_pred cCCcHHHHHhcC---CceeccCccHHHHHHhHHhcC---CCCCCcCChHHHHHHH-hhhhhhccC
Confidence 369999998644 677789999999999988664 46999999995 443 578999876
No 38
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.39 E-value=5.4e-05 Score=73.16 Aligned_cols=51 Identities=24% Similarity=0.533 Sum_probs=37.8
Q ss_pred CCCCccchhhccc--CCC-----------ceeEeccCCccCHHHHHHHHhcCcCCCCCCccccc
Q 027385 150 HHHCPICYEYLFD--SLR-----------NTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (224)
Q Consensus 150 ~~~CpICle~lf~--s~~-----------~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (224)
..+|+||+.++-- .+. ...+.||.|.||+.|+.+|+...+..||+||..+-
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 3579999976422 111 13345999999999999999866778999998763
No 39
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=97.39 E-value=0.00012 Score=68.12 Aligned_cols=59 Identities=31% Similarity=0.651 Sum_probs=45.3
Q ss_pred CCccchhhcccCCCceeEeccCCccCHHHHHHHHhcCcCCCCCCcccccc-chHHHHHHHHHHhc
Q 027385 152 HCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID-MSRTWKRIDEEMNS 215 (224)
Q Consensus 152 ~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~d-m~~~~~~lD~~i~~ 215 (224)
.|-||.|++. ...+.||||+|.+-||+.+|. .+-.||.|+.++.. ..+--+.||++|++
T Consensus 25 RC~IC~eyf~----ip~itpCsHtfCSlCIR~~L~-~~p~CP~C~~~~~Es~Lr~n~il~Eiv~S 84 (442)
T KOG0287|consen 25 RCGICFEYFN----IPMITPCSHTFCSLCIRKFLS-YKPQCPTCCVTVTESDLRNNRILDEIVKS 84 (442)
T ss_pred HHhHHHHHhc----CceeccccchHHHHHHHHHhc-cCCCCCceecccchhhhhhhhHHHHHHHH
Confidence 5999999943 345678999999999999998 58899999998863 22234566666554
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=97.37 E-value=0.0002 Score=52.14 Aligned_cols=48 Identities=19% Similarity=0.381 Sum_probs=36.2
Q ss_pred CCCCccchhhcccCCCceeEeccCCccCHHHHHHHHhcCcCCCCCCcccccc
Q 027385 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID 201 (224)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~d 201 (224)
+-.|||+++-|.+ .+++|+||+|=+.++.+|++..+.+||+++..+..
T Consensus 4 ~f~CpIt~~lM~d----PVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~ 51 (73)
T PF04564_consen 4 EFLCPITGELMRD----PVILPSGHTYERSAIERWLEQNGGTDPFTRQPLSE 51 (73)
T ss_dssp GGB-TTTSSB-SS----EEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SG
T ss_pred ccCCcCcCcHhhC----ceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCc
Confidence 3469999997644 45789999999999999998668999999988864
No 41
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.24 E-value=8.3e-05 Score=67.29 Aligned_cols=52 Identities=27% Similarity=0.515 Sum_probs=41.9
Q ss_pred CCCCCccchhhcccCCC------ceeEeccCCccCHHHHHHHHh-cCcCCCCCCccccc
Q 027385 149 MHHHCPICYEYLFDSLR------NTTVMKCGHTMHCECYHEMIK-RDKYCCPICSKSVI 200 (224)
Q Consensus 149 ~~~~CpICle~lf~s~~------~v~~LpCGH~~H~~C~~~~l~-~~~~~CPiCrksi~ 200 (224)
+++.|.||...+..|.+ ..-.|.|+|.||..|++-|-. ....+||.|++.+.
T Consensus 223 ~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVd 281 (328)
T KOG1734|consen 223 SDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVD 281 (328)
T ss_pred CcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhh
Confidence 35679999999877652 456799999999999999953 35789999998775
No 42
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=97.22 E-value=8.7e-05 Score=70.13 Aligned_cols=62 Identities=26% Similarity=0.573 Sum_probs=51.7
Q ss_pred cceeecCCCCCCCccchhhcccCCCceeEeccCCccCHHHHHHHHhc-CcCCCCCCccccccch
Q 027385 141 NHLCIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR-DKYCCPICSKSVIDMS 203 (224)
Q Consensus 141 ~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~-~~~~CPiCrksi~dm~ 203 (224)
-|.|++ .++.+|-.|.|.+-...+....|||.|+||..|+.++|.+ ...+||-|||.+..|+
T Consensus 357 a~~~~~-e~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~CrklrSs~~ 419 (518)
T KOG1941|consen 357 AHECVE-ETELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRKLRSSMK 419 (518)
T ss_pred HHHHHH-HHhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHHHHhhcc
Confidence 355554 4678999999998888888899999999999999999864 4678999998777766
No 43
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.02 E-value=0.00043 Score=64.44 Aligned_cols=51 Identities=27% Similarity=0.655 Sum_probs=41.4
Q ss_pred cCCCCCCCccchhhcccCCCceeEeccCCc-cCHHHHHHHHhcCcCCCCCCcccccc
Q 027385 146 ENSMHHHCPICYEYLFDSLRNTTVMKCGHT-MHCECYHEMIKRDKYCCPICSKSVID 201 (224)
Q Consensus 146 e~~~~~~CpICle~lf~s~~~v~~LpCGH~-~H~~C~~~~l~~~~~~CPiCrksi~d 201 (224)
++....+|.|||.+ .+.+.+|||.|+ +.+.|.+.+.- ...+|||||..|..
T Consensus 286 ~~~~gkeCVIClse----~rdt~vLPCRHLCLCs~Ca~~Lr~-q~n~CPICRqpi~~ 337 (349)
T KOG4265|consen 286 ESESGKECVICLSE----SRDTVVLPCRHLCLCSGCAKSLRY-QTNNCPICRQPIEE 337 (349)
T ss_pred cccCCCeeEEEecC----CcceEEecchhhehhHhHHHHHHH-hhcCCCccccchHh
Confidence 34446789999987 456899999997 89999998763 46789999998874
No 44
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.92 E-value=0.00046 Score=62.14 Aligned_cols=47 Identities=26% Similarity=0.578 Sum_probs=37.6
Q ss_pred CCCCccchhhcccCCCceeEeccCCccCHHHHHH-HHhcCcCCCCCCccccc
Q 027385 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHE-MIKRDKYCCPICSKSVI 200 (224)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~-~l~~~~~~CPiCrksi~ 200 (224)
+..|+||+|.. .....++|||+|...|+.. |...+...||+||.-+.
T Consensus 215 d~kC~lC~e~~----~~ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~ 262 (271)
T COG5574 215 DYKCFLCLEEP----EVPSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVY 262 (271)
T ss_pred ccceeeeeccc----CCcccccccchhhHHHHHHHHHhhccccCchhhhhcc
Confidence 44699999984 3467789999999999999 88754444999997665
No 45
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=96.73 E-value=0.00096 Score=52.55 Aligned_cols=28 Identities=29% Similarity=0.734 Sum_probs=25.0
Q ss_pred ccCCccCHHHHHHHHhcCcCCCCCCcccc
Q 027385 171 KCGHTMHCECYHEMIKRDKYCCPICSKSV 199 (224)
Q Consensus 171 pCGH~~H~~C~~~~l~~~~~~CPiCrksi 199 (224)
-|.|.||..|+..||+ ++..|||+.+.-
T Consensus 80 ~CNHaFH~hCisrWlk-tr~vCPLdn~eW 107 (114)
T KOG2930|consen 80 VCNHAFHFHCISRWLK-TRNVCPLDNKEW 107 (114)
T ss_pred ecchHHHHHHHHHHHh-hcCcCCCcCcce
Confidence 6999999999999998 478999998753
No 46
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=96.66 E-value=0.0015 Score=44.68 Aligned_cols=47 Identities=28% Similarity=0.711 Sum_probs=25.2
Q ss_pred CccchhhcccCCCceeEeccCCccCHHHHHHHHhcCcCCCCCCcccc
Q 027385 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSV 199 (224)
Q Consensus 153 CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi 199 (224)
||+|.|+|..+......-+||..+-+.|+..-+++.+.+||-||+..
T Consensus 1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y 47 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILENEGGRCPGCREPY 47 (48)
T ss_dssp -TTTS-B--CCCTT--SSTTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred CCCcccccccCCCccccCcCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence 79999998554333333467999999999999875688999999763
No 47
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.62 E-value=0.00054 Score=48.28 Aligned_cols=53 Identities=34% Similarity=0.778 Sum_probs=38.7
Q ss_pred CCCCCCccchhhcccCCCceeEeccCCc-cCHHHHHHHHhcCcCCCCCCccccccchH
Q 027385 148 SMHHHCPICYEYLFDSLRNTTVMKCGHT-MHCECYHEMIKRDKYCCPICSKSVIDMSR 204 (224)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~-~H~~C~~~~l~~~~~~CPiCrksi~dm~~ 204 (224)
+...+|.||+|.-.+ .+.--|||+ |.-.|-.+.++..+..|||||.+|-|.-+
T Consensus 5 ~~~dECTICye~pvd----sVlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~dvIk 58 (62)
T KOG4172|consen 5 QWSDECTICYEHPVD----SVLYTCGHMCMCYACGLRLKKALHGCCPICRAPIKDVIK 58 (62)
T ss_pred ccccceeeeccCcch----HHHHHcchHHhHHHHHHHHHHccCCcCcchhhHHHHHHH
Confidence 445789999997333 234589997 66678766665468899999999887543
No 48
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=96.51 E-value=0.00085 Score=68.10 Aligned_cols=76 Identities=16% Similarity=0.305 Sum_probs=55.0
Q ss_pred eeecCccCccccccccCcceee-cCCCCCCCccchhhcccCCCceeEeccCCccCHHHHHHHHhcCcCCCCCCcccccc
Q 027385 124 YFHCKRCGSCYSTSLRNNHLCI-ENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID 201 (224)
Q Consensus 124 ~fHC~~C~~C~s~~l~~~H~C~-e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~d 201 (224)
-..+..|-.++|...-..-.|+ .+-....||+|+-...+ .......+|+|.||..||..|-+ ...+|||+|+.++.
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-QLEESEKHTAHYFCEECVGSWSR-CAQTCPVDRGEFGE 172 (1134)
T ss_pred ccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHH-HhhccccccccccHHHHhhhhhh-hcccCchhhhhhhe
Confidence 4556667777766433344554 23445679999987443 44555679999999999999998 47899999998764
No 49
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=96.42 E-value=0.00091 Score=67.29 Aligned_cols=46 Identities=24% Similarity=0.651 Sum_probs=40.8
Q ss_pred CCCccchhhcccCCCceeEeccCCccCHHHHHHHHhcCcCCCCCCccccc
Q 027385 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (224)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (224)
..||+|-.. ...++...|||.|...|+...+..+..+||.|+.+++
T Consensus 644 LkCs~Cn~R----~Kd~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFg 689 (698)
T KOG0978|consen 644 LKCSVCNTR----WKDAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFG 689 (698)
T ss_pred eeCCCccCc----hhhHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCC
Confidence 469999855 4567788999999999999999989999999999998
No 50
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.38 E-value=0.00091 Score=62.46 Aligned_cols=49 Identities=27% Similarity=0.688 Sum_probs=41.9
Q ss_pred CCCCccchhhcccCCCceeEeccCCccCHHHHHHHHhcCcCCCCCCcccccc
Q 027385 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID 201 (224)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~d 201 (224)
+..|||||+-|.. .+....|+|-|...||..-++.++..||.|||.+..
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 4579999997644 466789999999999998888889999999999973
No 51
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=96.32 E-value=0.0025 Score=44.81 Aligned_cols=44 Identities=27% Similarity=0.563 Sum_probs=30.4
Q ss_pred CCCCCCccchhhcccCCCceeEeccCCccCHHHHHHHHh-cCcCCCCC
Q 027385 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIK-RDKYCCPI 194 (224)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~-~~~~~CPi 194 (224)
.....|||-+..|. ++|+...|||+|=+.-+.+||. +...+||+
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 34567999999853 5899999999999999999993 35778998
No 52
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.26 E-value=0.00074 Score=63.05 Aligned_cols=74 Identities=19% Similarity=0.481 Sum_probs=50.0
Q ss_pred CCCCCCCccchhhcccCCC---ceeE-eccCCccCHHHHHHHHhcC------cCCCCCCccccc--cchHHHHHHHHHHh
Q 027385 147 NSMHHHCPICYEYLFDSLR---NTTV-MKCGHTMHCECYHEMIKRD------KYCCPICSKSVI--DMSRTWKRIDEEMN 214 (224)
Q Consensus 147 ~~~~~~CpICle~lf~s~~---~v~~-LpCGH~~H~~C~~~~l~~~------~~~CPiCrksi~--dm~~~~~~lD~~i~ 214 (224)
++.+..|-||+|.+.+... .-.. ++|.|+|-..|++.|-... ...||+||.+.. .-+.+|-.-.+ +
T Consensus 158 ~s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~~v~pS~~Wv~t~~--~ 235 (344)
T KOG1039|consen 158 KSSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSSFVNPSSFWVETKE--E 235 (344)
T ss_pred ccccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccccccccceeeeecc--c
Confidence 3667889999999877431 1222 4699999999999998432 478999998875 45556744333 3
Q ss_pred cCCCCcCc
Q 027385 215 SSIFFPSF 222 (224)
Q Consensus 215 ~~pmp~~y 222 (224)
.++.+++|
T Consensus 236 k~~li~e~ 243 (344)
T KOG1039|consen 236 KQKLIEEY 243 (344)
T ss_pred ccccHHHH
Confidence 44444443
No 53
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=96.24 E-value=0.0013 Score=62.63 Aligned_cols=55 Identities=25% Similarity=0.594 Sum_probs=45.4
Q ss_pred eecCCCCCCCccchhhcccCCCceeEeccCCccCHHHHHHHHhcC-cCCCCCCccccccc
Q 027385 144 CIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRD-KYCCPICSKSVIDM 202 (224)
Q Consensus 144 C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~-~~~CPiCrksi~dm 202 (224)
|.=+++-..|-||.|. ...|++=||||.+...|+..|-.+. ..+||.||-.|-..
T Consensus 363 ceMgsTFeLCKICaen----dKdvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKGt 418 (563)
T KOG1785|consen 363 CEMGSTFELCKICAEN----DKDVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIKGT 418 (563)
T ss_pred HHccchHHHHHHhhcc----CCCcccccccchHHHHHHHhhcccCCCCCCCceeeEeccc
Confidence 3346777899999986 5678889999999999999998654 67999999887643
No 54
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=96.24 E-value=0.002 Score=66.74 Aligned_cols=52 Identities=27% Similarity=0.653 Sum_probs=38.4
Q ss_pred CCCCCCccchhhcc--cCCCceeE-eccCCccCHHHHHHHHhc-CcCCCCCCcccc
Q 027385 148 SMHHHCPICYEYLF--DSLRNTTV-MKCGHTMHCECYHEMIKR-DKYCCPICSKSV 199 (224)
Q Consensus 148 ~~~~~CpICle~lf--~s~~~v~~-LpCGH~~H~~C~~~~l~~-~~~~CPiCrksi 199 (224)
+...+|+||.--|. ++.-|.+. -.|.|-||..|+..|.++ ++.+||+||.+|
T Consensus 1467 sG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRsei 1522 (1525)
T COG5219 1467 SGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEI 1522 (1525)
T ss_pred CCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCcccccc
Confidence 44678999987765 22222222 347899999999999986 477899999765
No 55
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.15 E-value=0.0039 Score=59.35 Aligned_cols=49 Identities=27% Similarity=0.737 Sum_probs=38.6
Q ss_pred CCCCccchhhcccCCCce-eEeccCCccCHHHHHHHHhc-CcCCCCCCccc
Q 027385 150 HHHCPICYEYLFDSLRNT-TVMKCGHTMHCECYHEMIKR-DKYCCPICSKS 198 (224)
Q Consensus 150 ~~~CpICle~lf~s~~~v-~~LpCGH~~H~~C~~~~l~~-~~~~CPiCrks 198 (224)
...|||||+.+..+.+.- ..|.|||.|=+.|++.||-. ....||.|.-.
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 457999999986665544 55899999999999999952 35579999743
No 56
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=95.98 E-value=0.004 Score=57.19 Aligned_cols=44 Identities=25% Similarity=0.599 Sum_probs=36.3
Q ss_pred CCCccchhhcccCCCceeEeccCCccCHHHHHHHHhcCcCCCCCCcccc
Q 027385 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSV 199 (224)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi 199 (224)
..|-||-+++. .....+|||+|..-||..+|. .+..||+||-..
T Consensus 26 lrC~IC~~~i~----ip~~TtCgHtFCslCIR~hL~-~qp~CP~Cr~~~ 69 (391)
T COG5432 26 LRCRICDCRIS----IPCETTCGHTFCSLCIRRHLG-TQPFCPVCREDP 69 (391)
T ss_pred HHhhhhhheee----cceecccccchhHHHHHHHhc-CCCCCccccccH
Confidence 46999999842 234569999999999999998 589999998654
No 57
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=95.96 E-value=0.0043 Score=41.82 Aligned_cols=41 Identities=29% Similarity=0.704 Sum_probs=27.1
Q ss_pred CccchhhcccCCCceeEecc---C--CccCHHHHHHHHhc-CcCCCCCC
Q 027385 153 CPICYEYLFDSLRNTTVMKC---G--HTMHCECYHEMIKR-DKYCCPIC 195 (224)
Q Consensus 153 CpICle~lf~s~~~v~~LpC---G--H~~H~~C~~~~l~~-~~~~CPiC 195 (224)
|-||++.-.++ ...+.|| | -..|..|+.+|+.. ++.+|++|
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 56898874443 2455677 3 68999999999974 46779987
No 58
>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=95.80 E-value=0.0043 Score=46.86 Aligned_cols=38 Identities=24% Similarity=0.528 Sum_probs=30.3
Q ss_pred eeecCCCCCCCccchhhcccCCCceeEeccCCccCHHHHH
Q 027385 143 LCIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYH 182 (224)
Q Consensus 143 ~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~ 182 (224)
..+.-..+..|+||...|.. ....+.||||.+|..|++
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 467888999999999974
No 59
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=95.71 E-value=0.012 Score=63.57 Aligned_cols=74 Identities=26% Similarity=0.626 Sum_probs=55.3
Q ss_pred CCccceeecCccCccccccccCcceeecCCCCCCCccchhhcccCCCceeEeccCCccCHHHHHHHHhcC---------c
Q 027385 119 GGRENYFHCKRCGSCYSTSLRNNHLCIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRD---------K 189 (224)
Q Consensus 119 G~~~~~fHC~~C~~C~s~~l~~~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~---------~ 189 (224)
||.+|-.||--|--|-.-.. .+..++.|.||..+ .-+--+.+.|.|||+||..|.+..|+++ -
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 56677788887766643221 23446779999977 3345789999999999999999888752 3
Q ss_pred CCCCCCccccc
Q 027385 190 YCCPICSKSVI 200 (224)
Q Consensus 190 ~~CPiCrksi~ 200 (224)
..||||...|.
T Consensus 3534 isCPiC~n~In 3544 (3738)
T KOG1428|consen 3534 ISCPICKNKIN 3544 (3738)
T ss_pred eecccccchhh
Confidence 57999998876
No 60
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=95.70 E-value=0.0088 Score=42.56 Aligned_cols=46 Identities=26% Similarity=0.742 Sum_probs=33.4
Q ss_pred cCeeEeCCCCcccccc-----ccCCCCCCC-cceeecCccccccCCCCcCeeccCCCCc
Q 027385 63 VKQVICSVCDTEQPVA-----QVCTNCGVN-MGEYFCDICKFYDDDIEKGQFHCDDCGI 115 (224)
Q Consensus 63 ~~~vlC~~C~~~q~~~-----~~C~~Cg~~-f~~Y~C~~C~l~dd~~~k~~yHC~~Cgi 115 (224)
++...|..|+.+.... -.||+||+. .. -|.+|+-+. ..|.|++||+
T Consensus 5 ~~~~~CtSCg~~i~~~~~~~~F~CPnCG~~~I~--RC~~CRk~~-----~~Y~CP~CGF 56 (59)
T PRK14890 5 MEPPKCTSCGIEIAPREKAVKFLCPNCGEVIIY--RCEKCRKQS-----NPYTCPKCGF 56 (59)
T ss_pred ccCccccCCCCcccCCCccCEeeCCCCCCeeEe--echhHHhcC-----CceECCCCCC
Confidence 3456788898776532 379999986 44 489998774 4799999985
No 61
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.65 E-value=0.017 Score=51.50 Aligned_cols=66 Identities=26% Similarity=0.583 Sum_probs=50.8
Q ss_pred CCCCCCccchhhcccCCCceeEeccCCccCHHHHHHHHhc-------CcCCCCCCcccccc----chHHHHHHHHHHhc
Q 027385 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR-------DKYCCPICSKSVID----MSRTWKRIDEEMNS 215 (224)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~-------~~~~CPiCrksi~d----m~~~~~~lD~~i~~ 215 (224)
....||..|.-.|.+ ...+.|-|=|.||-.|+++|... ..|+||-|+..|.. .+...+.|-+.+++
T Consensus 48 DY~pNC~LC~t~La~--gdt~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp~NlvsPva~aLre~L~q 124 (299)
T KOG3970|consen 48 DYNPNCRLCNTPLAS--GDTTRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPPINLVSPVAEALREQLKQ 124 (299)
T ss_pred CCCCCCceeCCcccc--CcceeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCCccccchhHHHHHHHHHh
Confidence 457799999999766 35678999999999999999864 37999999999873 33455555555443
No 62
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.80 E-value=0.025 Score=51.55 Aligned_cols=53 Identities=25% Similarity=0.589 Sum_probs=42.5
Q ss_pred CCCCCCccchhhcccCCCceeEeccCCccCHHHHHHHHhc-CcCCCCCCccccccch
Q 027385 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR-DKYCCPICSKSVIDMS 203 (224)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~-~~~~CPiCrksi~dm~ 203 (224)
.....||+|.|+ ++-|.+..+|||.+.--|+..=... ...+||.|+.++..|.
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 4567788899999999999875542 3589999999888664
No 63
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=94.45 E-value=0.015 Score=40.86 Aligned_cols=33 Identities=27% Similarity=0.668 Sum_probs=26.7
Q ss_pred CceeEeccCCccCHHHHHHHHhcCcCCCCCCccccc
Q 027385 165 RNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (224)
Q Consensus 165 ~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (224)
..-.+|||||++-..|++-+ +-.-||+|.+.+.
T Consensus 18 ~~~~~~pCgH~I~~~~f~~~---rYngCPfC~~~~~ 50 (55)
T PF14447_consen 18 TKGTVLPCGHLICDNCFPGE---RYNGCPFCGTPFE 50 (55)
T ss_pred cccccccccceeeccccChh---hccCCCCCCCccc
Confidence 34567999999999999865 2357999999886
No 64
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.28 E-value=0.027 Score=52.82 Aligned_cols=48 Identities=21% Similarity=0.503 Sum_probs=36.0
Q ss_pred cCCCCCCCccchhhcccCCCceeEeccCCccCHHHHHHHHhcCcCCCCCCcccccc
Q 027385 146 ENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID 201 (224)
Q Consensus 146 e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~d 201 (224)
|.+..++|.||++. ......+||||+-- |..-... ..+||+||.+|.-
T Consensus 301 ~~~~p~lcVVcl~e----~~~~~fvpcGh~cc--ct~cs~~--l~~CPvCR~rI~~ 348 (355)
T KOG1571|consen 301 ELPQPDLCVVCLDE----PKSAVFVPCGHVCC--CTLCSKH--LPQCPVCRQRIRL 348 (355)
T ss_pred ccCCCCceEEecCC----ccceeeecCCcEEE--chHHHhh--CCCCchhHHHHHH
Confidence 45667899999998 33488999999955 5554432 4679999998864
No 65
>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=94.15 E-value=0.022 Score=46.78 Aligned_cols=36 Identities=14% Similarity=0.418 Sum_probs=31.9
Q ss_pred CCCCccchhhcccCCCceeEeccC------CccCHHHHHHHHh
Q 027385 150 HHHCPICYEYLFDSLRNTTVMKCG------HTMHCECYHEMIK 186 (224)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCG------H~~H~~C~~~~l~ 186 (224)
..+|.||++.+.+ ...|+.+++| |+||..|+..|.+
T Consensus 26 ~~EC~IC~~~I~~-~~GvV~vt~~g~lnLEkmfc~~C~~rw~~ 67 (134)
T PF05883_consen 26 TVECQICFDRIDN-NDGVVYVTDGGTLNLEKMFCADCDKRWRR 67 (134)
T ss_pred Ceeehhhhhhhhc-CCCEEEEecCCeehHHHHHHHHHHHHHHh
Confidence 4689999999877 7889999997 9999999999954
No 66
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=94.04 E-value=0.023 Score=50.57 Aligned_cols=37 Identities=27% Similarity=0.546 Sum_probs=28.6
Q ss_pred ccCCCceeEeccCCccCHHHHHHHHhcCcCCCCCCccccc
Q 027385 161 FDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (224)
Q Consensus 161 f~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (224)
+.+.++-..+.|+|+|...|...-. ...||+|+|+|-
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 4555566778999999999997542 348999999974
No 67
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.00 E-value=0.029 Score=51.69 Aligned_cols=49 Identities=24% Similarity=0.474 Sum_probs=40.1
Q ss_pred CCCCCCccchhhcccCCCceeEeccCCccCHHHHHHHHhcCcCCCCCCccccc
Q 027385 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (224)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (224)
.+..+|+||+....- + +.|+|+|.|.--|++--..+...+||+||..|-
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 456789999987432 3 789999999999998866656778999999986
No 68
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.92 E-value=0.0095 Score=54.72 Aligned_cols=60 Identities=25% Similarity=0.648 Sum_probs=42.3
Q ss_pred cCcceeecCCC---CCCCccchhhcccCCCceeEeccCCcc-CHHHHHHHHhcCcCCCCCCccccccchHHHH
Q 027385 139 RNNHLCIENSM---HHHCPICYEYLFDSLRNTTVMKCGHTM-HCECYHEMIKRDKYCCPICSKSVIDMSRTWK 207 (224)
Q Consensus 139 ~~~H~C~e~~~---~~~CpICle~lf~s~~~v~~LpCGH~~-H~~C~~~~l~~~~~~CPiCrksi~dm~~~~~ 207 (224)
++.+.+--..+ +..|.||++- ...-.+|+|||.. ..+|-..+ ..|||||+-|...-.+|+
T Consensus 286 k~~~g~~~~~s~~~~~LC~ICmDa----P~DCvfLeCGHmVtCt~CGkrm-----~eCPICRqyi~rvvrif~ 349 (350)
T KOG4275|consen 286 KGNDGEQHSRSLATRRLCAICMDA----PRDCVFLECGHMVTCTKCGKRM-----NECPICRQYIVRVVRIFR 349 (350)
T ss_pred hcccccccccchhHHHHHHHHhcC----CcceEEeecCcEEeehhhcccc-----ccCchHHHHHHHHHhhhc
Confidence 45555544444 7789999985 5678999999975 23444333 389999999887666654
No 69
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=93.89 E-value=0.069 Score=49.13 Aligned_cols=63 Identities=17% Similarity=0.514 Sum_probs=48.8
Q ss_pred CCCCccchhhcccCCCceeEecc--CCccCHHHHHHHHhcCcCCCCCCccccccchHHHHHHHHHHhcCCCCcCcc
Q 027385 150 HHHCPICYEYLFDSLRNTTVMKC--GHTMHCECYHEMIKRDKYCCPICSKSVIDMSRTWKRIDEEMNSSIFFPSFF 223 (224)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpC--GH~~H~~C~~~~l~~~~~~CPiCrksi~dm~~~~~~lD~~i~~~pmp~~y~ 223 (224)
-.+||||.++|.. -.+.| ||+..+.|-.+. ..+||.||.+|++.. -+.++..+++...|=.|+
T Consensus 48 lleCPvC~~~l~~-----Pi~QC~nGHlaCssC~~~~----~~~CP~Cr~~~g~~R--~~amEkV~e~~~vpC~~~ 112 (299)
T KOG3002|consen 48 LLDCPVCFNPLSP-----PIFQCDNGHLACSSCRTKV----SNKCPTCRLPIGNIR--CRAMEKVAEAVLVPCKNA 112 (299)
T ss_pred hccCchhhccCcc-----cceecCCCcEehhhhhhhh----cccCCccccccccHH--HHHHHHHHHhceeccccc
Confidence 3589999999743 34566 999999998754 469999999999764 367888888888775543
No 70
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.67 E-value=0.044 Score=49.11 Aligned_cols=48 Identities=31% Similarity=0.784 Sum_probs=39.7
Q ss_pred CCCccchhhcccCCC---ceeEeccCCccCHHHHHHHHhcCcCCCCCCcccc
Q 027385 151 HHCPICYEYLFDSLR---NTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSV 199 (224)
Q Consensus 151 ~~CpICle~lf~s~~---~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi 199 (224)
..|-||-++ |+|.+ ..+.|.|||+|-..|+...+.++...||.||...
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 3467899999999999999988788899999994
No 71
>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=93.62 E-value=0.055 Score=49.53 Aligned_cols=49 Identities=20% Similarity=0.469 Sum_probs=39.6
Q ss_pred CCccchhhcccCCCceeE-eccCCccCHHHHHHHHhcCcCCCCCCccccc
Q 027385 152 HCPICYEYLFDSLRNTTV-MKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (224)
Q Consensus 152 ~CpICle~lf~s~~~v~~-LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (224)
.||+|.-+.+.+..-+.. =+|||.+..+|++.....+.+.||.|.+.+.
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 589998877665443322 2999999999999998888999999998876
No 72
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.21 E-value=0.06 Score=46.53 Aligned_cols=35 Identities=29% Similarity=0.655 Sum_probs=28.1
Q ss_pred EeccCCccCHHHHHHHHhcC----------cCCCCCCccccc-cch
Q 027385 169 VMKCGHTMHCECYHEMIKRD----------KYCCPICSKSVI-DMS 203 (224)
Q Consensus 169 ~LpCGH~~H~~C~~~~l~~~----------~~~CPiCrksi~-dm~ 203 (224)
-..||-.||+-|+.+||+.- -..||.|+++|. .||
T Consensus 187 N~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialKmS 232 (234)
T KOG3268|consen 187 NIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALKMS 232 (234)
T ss_pred ccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceeecc
Confidence 36899999999999999831 236999999985 554
No 73
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=92.53 E-value=0.092 Score=37.50 Aligned_cols=45 Identities=29% Similarity=0.802 Sum_probs=33.8
Q ss_pred eeEeCCCCcccccc-----ccCCCCCCCcceeecCccccccCCCCcCeeccCCCCc
Q 027385 65 QVICSVCDTEQPVA-----QVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGI 115 (224)
Q Consensus 65 ~vlC~~C~~~q~~~-----~~C~~Cg~~f~~Y~C~~C~l~dd~~~k~~yHC~~Cgi 115 (224)
...|..|+.+..+. -.|||||... =|-|.+|+.+.+ +|-|++||+
T Consensus 9 ~~~CtSCg~~i~p~e~~v~F~CPnCGe~~-I~Rc~~CRk~g~-----~Y~Cp~CGF 58 (61)
T COG2888 9 PPVCTSCGREIAPGETAVKFPCPNCGEVE-IYRCAKCRKLGN-----PYRCPKCGF 58 (61)
T ss_pred CceeccCCCEeccCCceeEeeCCCCCcee-eehhhhHHHcCC-----ceECCCcCc
Confidence 56899999887543 3799999543 366888887744 799999985
No 74
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=92.32 E-value=0.085 Score=49.98 Aligned_cols=53 Identities=26% Similarity=0.654 Sum_probs=42.5
Q ss_pred CCCCCccchhhcccCCCceeEeccCCccCHHHHHHHHhcCcCCCCCCccccccchHH
Q 027385 149 MHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRT 205 (224)
Q Consensus 149 ~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~dm~~~ 205 (224)
.+..||||..-|-+ ++....|||.|-..|+.+|+.. +..||.|+..+..-..+
T Consensus 20 ~~l~C~~C~~vl~~---p~~~~~cgh~fC~~C~~~~~~~-~~~cp~~~~~~~~~~~~ 72 (391)
T KOG0297|consen 20 ENLLCPICMSVLRD---PVQTTTCGHRFCAGCLLESLSN-HQKCPVCRQELTQAEEL 72 (391)
T ss_pred ccccCccccccccC---CCCCCCCCCcccccccchhhcc-CcCCcccccccchhhcc
Confidence 34679999987644 4555799999999999999985 88999999888754443
No 75
>PF12773 DZR: Double zinc ribbon
Probab=92.18 E-value=0.16 Score=33.87 Aligned_cols=22 Identities=36% Similarity=0.970 Sum_probs=14.2
Q ss_pred eCCCCccccc-cccCCCCCCCcc
Q 027385 68 CSVCDTEQPV-AQVCTNCGVNMG 89 (224)
Q Consensus 68 C~~C~~~q~~-~~~C~~Cg~~f~ 89 (224)
|..|+++.+. +..|++||+.+.
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 76
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=92.00 E-value=0.043 Score=51.54 Aligned_cols=57 Identities=23% Similarity=0.470 Sum_probs=45.4
Q ss_pred CCCCccchhhcccCCCceeEeccCCccCHHHHHHHHhcCcCCCCCCccccccchHHH
Q 027385 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRTW 206 (224)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~dm~~~~ 206 (224)
++-||.|+|+|--+...-..-|||=-+..-|+....+.-+.+||-||+...|-...|
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 455999999987765555556889999999998887766889999999887654444
No 77
>PHA02862 5L protein; Provisional
Probab=91.94 E-value=0.086 Score=43.98 Aligned_cols=60 Identities=20% Similarity=0.433 Sum_probs=39.8
Q ss_pred CCCCCccchhhcccCCCceeEecc-C--CccCHHHHHHHHhc-CcCCCCCCccccccchHHHHHHHHH
Q 027385 149 MHHHCPICYEYLFDSLRNTTVMKC-G--HTMHCECYHEMIKR-DKYCCPICSKSVIDMSRTWKRIDEE 212 (224)
Q Consensus 149 ~~~~CpICle~lf~s~~~v~~LpC-G--H~~H~~C~~~~l~~-~~~~CPiCrksi~dm~~~~~~lD~~ 212 (224)
|...|=||.+.- .+.+..-.| | -..|++|+.+|+.. ++.+||+|+.... +...|+.+.+-
T Consensus 1 ~~diCWIC~~~~---~e~~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~-Ik~~yKpf~kW 64 (156)
T PHA02862 1 MSDICWICNDVC---DERNNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYN-IKKTYVSFKKW 64 (156)
T ss_pred CCCEEEEecCcC---CCCcccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEE-EEEccccHHHh
Confidence 346688999872 223332234 2 78999999999975 3667999998875 44445544443
No 78
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.48 E-value=0.11 Score=47.80 Aligned_cols=67 Identities=21% Similarity=0.390 Sum_probs=50.0
Q ss_pred CCCccchhhcccCCCceeEeccCCccCHHHHHHHHhcCcCCCCCCccccccchHHHHHHHHHHhcCCCCcCc
Q 027385 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRTWKRIDEEMNSSIFFPSF 222 (224)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~dm~~~~~~lD~~i~~~pmp~~y 222 (224)
..|-||.+++.. .++..|||+|...|...=++ ...+|+||.+.+......-..|...|..-++-.||
T Consensus 242 f~c~icr~~f~~----pVvt~c~h~fc~~ca~~~~q-k~~~c~vC~~~t~g~~~~akeL~~~L~~kks~~E~ 308 (313)
T KOG1813|consen 242 FKCFICRKYFYR----PVVTKCGHYFCEVCALKPYQ-KGEKCYVCSQQTHGSFNVAKELLVSLKLKKSDSEY 308 (313)
T ss_pred cccccccccccc----chhhcCCceeehhhhccccc-cCCcceecccccccccchHHHHHHHHHhhhhhccc
Confidence 459999998433 56789999999999987776 46899999999976555555666666665554443
No 79
>PF04641 Rtf2: Rtf2 RING-finger
Probab=91.45 E-value=0.16 Score=45.36 Aligned_cols=50 Identities=18% Similarity=0.422 Sum_probs=39.1
Q ss_pred CCCCCCccchhhcccCCCceeEe-ccCCccCHHHHHHHHhcCcCCCCCCccccc
Q 027385 148 SMHHHCPICYEYLFDSLRNTTVM-KCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (224)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~L-pCGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (224)
...--|||-...|.. ....+.| ||||+|=...+.+.- ....||+|.+++.
T Consensus 111 ~~~~~CPvt~~~~~~-~~~fv~l~~cG~V~s~~alke~k--~~~~Cp~c~~~f~ 161 (260)
T PF04641_consen 111 EGRFICPVTGKEFNG-KHKFVYLRPCGCVFSEKALKELK--KSKKCPVCGKPFT 161 (260)
T ss_pred CceeECCCCCcccCC-ceeEEEEcCCCCEeeHHHHHhhc--ccccccccCCccc
Confidence 445579999999744 4445554 999999999999984 3568999999975
No 80
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=91.08 E-value=0.083 Score=52.21 Aligned_cols=52 Identities=21% Similarity=0.513 Sum_probs=43.6
Q ss_pred ecCCCCCCCccchhhcccCCCceeEeccCCccCHHHHHHHHhc----CcCCCCCCccccc
Q 027385 145 IENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR----DKYCCPICSKSVI 200 (224)
Q Consensus 145 ~e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~----~~~~CPiCrksi~ 200 (224)
.|+..+..|-+|-|. .+..++.+|-|.|.+.|+.+|+.. .+.+||+|.+.+.
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 345778899999999999998863 4789999998875
No 81
>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=91.07 E-value=0.13 Score=37.79 Aligned_cols=36 Identities=25% Similarity=0.783 Sum_probs=23.0
Q ss_pred CeeEeCCCCccccccccCCCCCCCc--------ceeecCccccc
Q 027385 64 KQVICSVCDTEQPVAQVCTNCGVNM--------GEYFCDICKFY 99 (224)
Q Consensus 64 ~~vlC~~C~~~q~~~~~C~~Cg~~f--------~~Y~C~~C~l~ 99 (224)
....|..|...-.....||.||..+ +.|||..|+=.
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 68999988744
No 82
>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.
Probab=91.05 E-value=0.25 Score=41.77 Aligned_cols=48 Identities=31% Similarity=0.769 Sum_probs=35.5
Q ss_pred CCCCccchhhcccCCCceeEeccC-C------------ccCHHHHHHHHhc-----------------------------
Q 027385 150 HHHCPICYEYLFDSLRNTTVMKCG-H------------TMHCECYHEMIKR----------------------------- 187 (224)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCG-H------------~~H~~C~~~~l~~----------------------------- 187 (224)
+..||||||. .-..+.|-|. | .-|+.||+++.+.
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 3456677773 3 4699999999762
Q ss_pred -CcCCCCCCcccccc
Q 027385 188 -DKYCCPICSKSVID 201 (224)
Q Consensus 188 -~~~~CPiCrksi~d 201 (224)
....|||||-.|..
T Consensus 78 ~~~L~CPLCRG~V~G 92 (162)
T PF07800_consen 78 QPELACPLCRGEVKG 92 (162)
T ss_pred cccccCccccCceec
Confidence 14679999988864
No 83
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=90.91 E-value=0.12 Score=47.94 Aligned_cols=54 Identities=30% Similarity=0.594 Sum_probs=42.3
Q ss_pred CCCCCCCccchhhcccCCCceeEeccCCccCHHHHHHHHhc----------------------CcCCCCCCcccccc
Q 027385 147 NSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR----------------------DKYCCPICSKSVID 201 (224)
Q Consensus 147 ~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~----------------------~~~~CPiCrksi~d 201 (224)
+-....|.|||-- |.+.....+.+|-|+||..||..+|.. ..--|||||-.|.+
T Consensus 112 n~p~gqCvICLyg-fa~~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~ 187 (368)
T KOG4445|consen 112 NHPNGQCVICLYG-FASSPAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKI 187 (368)
T ss_pred CCCCCceEEEEEe-ecCCCceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccc
Confidence 3456789999987 555677889999999999999988752 02349999988874
No 84
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.63 E-value=0.15 Score=48.75 Aligned_cols=46 Identities=20% Similarity=0.411 Sum_probs=37.4
Q ss_pred CCCCccchhhcccCCCceeEeccCCccCHHHHHHHHhc-------CcCCCCCCc
Q 027385 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR-------DKYCCPICS 196 (224)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~-------~~~~CPiCr 196 (224)
--.|.||.+. +..+.-.+.|||+|+|.+.|+..|... +..+||-++
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 4589999998 555577888999999999999998762 367898765
No 85
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=90.36 E-value=0.06 Score=50.03 Aligned_cols=64 Identities=27% Similarity=0.548 Sum_probs=47.3
Q ss_pred CCCCCCccchhhcccCCCceeEeccCCccCHHHHHHHHhcCcCCCCCCccccccch-HHHHHHHHHHhc
Q 027385 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMS-RTWKRIDEEMNS 215 (224)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~dm~-~~~~~lD~~i~~ 215 (224)
.....|++|.-+|.++ ..+.-|=|+|.++||-.+|.. +.+||.|...|...- ...-..|..++.
T Consensus 13 n~~itC~LC~GYliDA---TTI~eCLHTFCkSCivk~l~~-~~~CP~C~i~ih~t~pl~ni~~Drtlqd 77 (331)
T KOG2660|consen 13 NPHITCRLCGGYLIDA---TTITECLHTFCKSCIVKYLEE-SKYCPTCDIVIHKTHPLLNIRSDRTLQD 77 (331)
T ss_pred ccceehhhccceeecc---hhHHHHHHHHHHHHHHHHHHH-hccCCccceeccCccccccCCcchHHHH
Confidence 3456899999998775 345679999999999999985 789999998887532 223344444443
No 86
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.00 E-value=0.15 Score=51.29 Aligned_cols=67 Identities=18% Similarity=0.442 Sum_probs=47.6
Q ss_pred CCCccchhhcccCCCceeEeccCCccCHHHHHHHHhcCcCCCCCCcc----ccccchHHHH-------HHHHHHhcCCCC
Q 027385 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSK----SVIDMSRTWK-------RIDEEMNSSIFF 219 (224)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrk----si~dm~~~~~-------~lD~~i~~~pmp 219 (224)
.+|+||+..++.++...+.|-|||++...|+...- +.+|| |.. ++.+.+.+++ ..|++|-...|+
T Consensus 12 l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~ly---n~scp-~~~De~~~~~~~~e~p~n~alL~~~~d~~~~~~a~~ 87 (861)
T KOG3161|consen 12 LLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLY---NASCP-TKRDEDSSLMQLKEEPRNYALLRREHDAQIVHIAME 87 (861)
T ss_pred hhchHHHHHHHHHhcCcccccccchHHHHHHHhHh---hccCC-CCccccchhcChhhcchhHHHHHhhcchhhhhcccC
Confidence 47999998888888888899999999999998763 46899 653 3334444443 345666555555
Q ss_pred cC
Q 027385 220 PS 221 (224)
Q Consensus 220 ~~ 221 (224)
+.
T Consensus 88 ~g 89 (861)
T KOG3161|consen 88 AG 89 (861)
T ss_pred Cc
Confidence 43
No 87
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=89.74 E-value=0.32 Score=44.01 Aligned_cols=53 Identities=25% Similarity=0.487 Sum_probs=44.3
Q ss_pred CCCCCCCccchhhcccCCCceeEe-ccCCccCHHHHHHHHhcCcCCCCCCcccccc
Q 027385 147 NSMHHHCPICYEYLFDSLRNTTVM-KCGHTMHCECYHEMIKRDKYCCPICSKSVID 201 (224)
Q Consensus 147 ~~~~~~CpICle~lf~s~~~v~~L-pCGH~~H~~C~~~~l~~~~~~CPiCrksi~d 201 (224)
.+....|||+.+.|.. ..+..+| |+||++-..|.+.+++ ..--+||+.+.+.|
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 3456689999999765 5566666 9999999999999998 57899999999876
No 88
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.72 E-value=0.39 Score=45.87 Aligned_cols=49 Identities=24% Similarity=0.748 Sum_probs=39.7
Q ss_pred CCCCCCccchhhcccCCCceeEeccCCccCHHHHHHHHhcCcCCCCCCcccccc
Q 027385 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID 201 (224)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~d 201 (224)
..+-.|-||..-|.. .+.+||||+|-..|++.-+. ...-||+||-.+..
T Consensus 82 ~sef~c~vc~~~l~~----pv~tpcghs~c~~Cl~r~ld-~~~~cp~Cr~~l~e 130 (398)
T KOG4159|consen 82 RSEFECCVCSRALYP----PVVTPCGHSFCLECLDRSLD-QETECPLCRDELVE 130 (398)
T ss_pred cchhhhhhhHhhcCC----CccccccccccHHHHHHHhc-cCCCCccccccccc
Confidence 556789999887654 34559999999999999776 56789999998875
No 89
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=89.41 E-value=0.22 Score=43.84 Aligned_cols=58 Identities=21% Similarity=0.463 Sum_probs=44.0
Q ss_pred CCccchhhcccCCCceeEeccCCccCHHHHHHHHhcCcCCCCCCccccccchHHHHHHHHHHh
Q 027385 152 HCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRTWKRIDEEMN 214 (224)
Q Consensus 152 ~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~dm~~~~~~lD~~i~ 214 (224)
.|-||.+++ . ..++..|||.|...|+-.=.+ ...+|=+|.+..-..-.+-..||.++.
T Consensus 198 ~C~iCKkdy-~---spvvt~CGH~FC~~Cai~~y~-kg~~C~~Cgk~t~G~f~V~~d~~kmL~ 255 (259)
T COG5152 198 LCGICKKDY-E---SPVVTECGHSFCSLCAIRKYQ-KGDECGVCGKATYGRFWVVSDLQKMLN 255 (259)
T ss_pred eehhchhhc-c---chhhhhcchhHHHHHHHHHhc-cCCcceecchhhccceeHHhhHHHHHh
Confidence 799999994 3 356789999999999876555 467999999988654444466666654
No 90
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=89.13 E-value=0.28 Score=50.72 Aligned_cols=41 Identities=27% Similarity=0.596 Sum_probs=32.6
Q ss_pred CCCccchhhcccCCCceeEeccCCccCHHHHHHHHhcCcCCCCCCccc
Q 027385 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKS 198 (224)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrks 198 (224)
+.|..|--.|- -|++-..|||.||..|+. . +...||-|+-.
T Consensus 841 skCs~C~~~Ld---lP~VhF~CgHsyHqhC~e---~-~~~~CP~C~~e 881 (933)
T KOG2114|consen 841 SKCSACEGTLD---LPFVHFLCGHSYHQHCLE---D-KEDKCPKCLPE 881 (933)
T ss_pred eeecccCCccc---cceeeeecccHHHHHhhc---c-CcccCCccchh
Confidence 36777876653 478888999999999998 3 56799999983
No 91
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=89.11 E-value=0.25 Score=50.66 Aligned_cols=41 Identities=27% Similarity=0.580 Sum_probs=31.0
Q ss_pred CCCccchhhcccCCCceeEeccCCccCHHHHHHHHhcCcCCCCC
Q 027385 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPI 194 (224)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPi 194 (224)
..|.||--.+.. ....-+.|||.+|..|+.+|.+. ...||.
T Consensus 1029 ~~C~~C~l~V~g--ss~~Cg~C~Hv~H~sc~~eWf~~-gd~Cps 1069 (1081)
T KOG0309|consen 1029 FQCAICHLAVRG--SSNFCGTCGHVGHTSCMMEWFRT-GDVCPS 1069 (1081)
T ss_pred eeeeeEeeEeec--cchhhccccccccHHHHHHHHhc-CCcCCC
Confidence 448888755433 34556789999999999999985 568884
No 92
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=88.97 E-value=0.36 Score=40.81 Aligned_cols=48 Identities=29% Similarity=0.546 Sum_probs=34.4
Q ss_pred CCCCCCccchhhcccCCCceeEecc--CC---ccCHHHHHHHHhc-CcCCCCCCccccc
Q 027385 148 SMHHHCPICYEYLFDSLRNTTVMKC--GH---TMHCECYHEMIKR-DKYCCPICSKSVI 200 (224)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpC--GH---~~H~~C~~~~l~~-~~~~CPiCrksi~ 200 (224)
.++..|=||.+.- + .. .-|| .. ..|.+|++.|+.. +..+||+|+....
T Consensus 6 ~~~~~CRIC~~~~-~--~~--~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~ 59 (162)
T PHA02825 6 LMDKCCWICKDEY-D--VV--TNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYN 59 (162)
T ss_pred CCCCeeEecCCCC-C--Cc--cCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEE
Confidence 3456799998872 1 22 2465 34 6799999999975 3677999998764
No 93
>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=88.51 E-value=0.22 Score=34.13 Aligned_cols=32 Identities=31% Similarity=0.745 Sum_probs=23.4
Q ss_pred eEeccC-CccCHHHHHHHHhcCcCCCCCCccccc
Q 027385 168 TVMKCG-HTMHCECYHEMIKRDKYCCPICSKSVI 200 (224)
Q Consensus 168 ~~LpCG-H~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (224)
..+.|. |.+...|+..++. .+..||||.+++-
T Consensus 14 ~Li~C~dHYLCl~CLt~ml~-~s~~C~iC~~~LP 46 (50)
T PF03854_consen 14 GLIKCSDHYLCLNCLTLMLS-RSDRCPICGKPLP 46 (50)
T ss_dssp SEEE-SS-EEEHHHHHHT-S-SSSEETTTTEE--
T ss_pred CeeeecchhHHHHHHHHHhc-cccCCCcccCcCc
Confidence 456895 9999999999997 5789999998864
No 94
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.36 E-value=0.56 Score=44.69 Aligned_cols=46 Identities=22% Similarity=0.578 Sum_probs=38.1
Q ss_pred CCccchhhcccCCCceeEeccCCccCHHHHHHHHhcCc--CCCCCCccc
Q 027385 152 HCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDK--YCCPICSKS 198 (224)
Q Consensus 152 ~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~--~~CPiCrks 198 (224)
.|||=-|. -+...|...|.|||++-+.=++.+.++.. .+||.|-..
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 58887776 45567888999999999999999998766 889999743
No 95
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=86.77 E-value=0.32 Score=28.68 Aligned_cols=24 Identities=33% Similarity=0.924 Sum_probs=17.4
Q ss_pred eeEeCCCCccccc-cccCCCCCCCc
Q 027385 65 QVICSVCDTEQPV-AQVCTNCGVNM 88 (224)
Q Consensus 65 ~vlC~~C~~~q~~-~~~C~~Cg~~f 88 (224)
.+.|..|+++.+. +..|++||+.+
T Consensus 2 ~~~Cp~Cg~~~~~~~~fC~~CG~~L 26 (26)
T PF13248_consen 2 EMFCPNCGAEIDPDAKFCPNCGAKL 26 (26)
T ss_pred cCCCcccCCcCCcccccChhhCCCC
Confidence 4678888886444 46799998864
No 96
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=86.73 E-value=0.38 Score=49.82 Aligned_cols=51 Identities=24% Similarity=0.507 Sum_probs=37.9
Q ss_pred CCCCCccchhhcccCCCceeE-eccCCccCHHHHHHHHhc------CcCCCCCCccccc
Q 027385 149 MHHHCPICYEYLFDSLRNTTV-MKCGHTMHCECYHEMIKR------DKYCCPICSKSVI 200 (224)
Q Consensus 149 ~~~~CpICle~lf~s~~~v~~-LpCGH~~H~~C~~~~l~~------~~~~CPiCrksi~ 200 (224)
....|.||.|.+.. +.++.. -.|=|+||..||..|.++ ...+||-|.....
T Consensus 190 ~~yeCmIC~e~I~~-t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv~~ 247 (950)
T KOG1952|consen 190 RKYECMICTERIKR-TAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSVSK 247 (950)
T ss_pred CceEEEEeeeeccc-cCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccchhc
Confidence 34589999999765 344443 357799999999999874 3678999984433
No 97
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=86.48 E-value=0.36 Score=50.10 Aligned_cols=43 Identities=21% Similarity=0.382 Sum_probs=32.9
Q ss_pred ceeecCCCCCCCccchhhcccCCCceeEeccCCccCHHHHHHHHh
Q 027385 142 HLCIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIK 186 (224)
Q Consensus 142 H~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~ 186 (224)
+.++--.....|-+|.-.|+. ++-.+.||||.||+.|+.+-+.
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 334333446789999998876 5778889999999999987654
No 98
>PRK04023 DNA polymerase II large subunit; Validated
Probab=86.38 E-value=0.64 Score=49.08 Aligned_cols=29 Identities=31% Similarity=0.785 Sum_probs=13.6
Q ss_pred EeCCCCccccccccCCCCCCC-cceeecCcc
Q 027385 67 ICSVCDTEQPVAQVCTNCGVN-MGEYFCDIC 96 (224)
Q Consensus 67 lC~~C~~~q~~~~~C~~Cg~~-f~~Y~C~~C 96 (224)
.|..|+++. +...|++||.. -..|||+.|
T Consensus 628 fCpsCG~~t-~~frCP~CG~~Te~i~fCP~C 657 (1121)
T PRK04023 628 KCPSCGKET-FYRRCPFCGTHTEPVYRCPRC 657 (1121)
T ss_pred cCCCCCCcC-CcccCCCCCCCCCcceeCccc
Confidence 455555542 33455555542 333444444
No 99
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=85.12 E-value=0.85 Score=43.23 Aligned_cols=64 Identities=17% Similarity=0.375 Sum_probs=44.8
Q ss_pred CccccccccCcceeecCCCCCCCccchhhcccCCCceeEeccCCccCHHHHHHHHh-cCcCCCCCCccc
Q 027385 131 GSCYSTSLRNNHLCIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIK-RDKYCCPICSKS 198 (224)
Q Consensus 131 ~~C~s~~l~~~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~-~~~~~CPiCrks 198 (224)
+.|....+-++..=.....+++|.||.+.+ +-+.++||||-+.-.|--.... ...-.||+||..
T Consensus 42 nlsaEPnlttsSaddtDEen~~C~ICA~~~----TYs~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE 106 (493)
T COG5236 42 NLSAEPNLTTSSADDTDEENMNCQICAGST----TYSARYPCGHQICHACAVRLRALYMQKGCPLCRTE 106 (493)
T ss_pred ccccCCccccccccccccccceeEEecCCc----eEEEeccCCchHHHHHHHHHHHHHhccCCCccccc
Confidence 455555555554444445567899999873 5678899999999999765432 235679999964
No 100
>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=84.72 E-value=0.67 Score=27.64 Aligned_cols=23 Identities=35% Similarity=0.959 Sum_probs=18.1
Q ss_pred EeCCCCccccc-cccCCCCCCCcc
Q 027385 67 ICSVCDTEQPV-AQVCTNCGVNMG 89 (224)
Q Consensus 67 lC~~C~~~q~~-~~~C~~Cg~~f~ 89 (224)
.|..|+.+-+. +..|++||..|.
T Consensus 2 ~CP~C~~~V~~~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCPHCGYDFE 25 (26)
T ss_pred cCCCCcCCchhhcCcCCCCCCCCc
Confidence 37778887776 468999999986
No 101
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=84.61 E-value=0.6 Score=44.31 Aligned_cols=51 Identities=29% Similarity=0.612 Sum_probs=42.3
Q ss_pred cCCCCCCCccchhhcccCCCceeEeccCCccCHHHHHHHHhcCcCCCCCCcccccc
Q 027385 146 ENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID 201 (224)
Q Consensus 146 e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~d 201 (224)
..+.+..||||... .-..+.-||||--...||.+-+. ++..|=.|+.++.+
T Consensus 418 p~sEd~lCpICyA~----pi~Avf~PC~H~SC~~CI~qHlm-N~k~CFfCktTv~~ 468 (489)
T KOG4692|consen 418 PDSEDNLCPICYAG----PINAVFAPCSHRSCYGCITQHLM-NCKRCFFCKTTVID 468 (489)
T ss_pred CCcccccCcceecc----cchhhccCCCCchHHHHHHHHHh-cCCeeeEecceeee
Confidence 34667889999875 33456779999999999999998 47799999999986
No 102
>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=84.22 E-value=1.1 Score=30.50 Aligned_cols=42 Identities=26% Similarity=0.771 Sum_probs=20.4
Q ss_pred CCCccchhhcccCCCceeEeccCCccCHHHHHH--HHh----cCcCCCCCCccc
Q 027385 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHE--MIK----RDKYCCPICSKS 198 (224)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~--~l~----~~~~~CPiCrks 198 (224)
..|||-...|. .+++...|.|. +||+. ||. ....+||+|+++
T Consensus 3 L~CPls~~~i~---~P~Rg~~C~H~---~CFDl~~fl~~~~~~~~W~CPiC~~~ 50 (50)
T PF02891_consen 3 LRCPLSFQRIR---IPVRGKNCKHL---QCFDLESFLESNQRTPKWKCPICNKP 50 (50)
T ss_dssp SB-TTTSSB-S---SEEEETT--SS-----EEHHHHHHHHHHS---B-TTT---
T ss_pred eeCCCCCCEEE---eCccCCcCccc---ceECHHHHHHHhhccCCeECcCCcCc
Confidence 36888887764 48888899976 46543 554 246789999874
No 103
>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=83.96 E-value=0.9 Score=26.95 Aligned_cols=21 Identities=24% Similarity=0.539 Sum_probs=17.1
Q ss_pred CCCCCCccccccchHHHHHHHH
Q 027385 190 YCCPICSKSVIDMSRTWKRIDE 211 (224)
Q Consensus 190 ~~CPiCrksi~dm~~~~~~lD~ 211 (224)
..||||.+.+ .++.+.+.||.
T Consensus 2 v~CPiC~~~v-~~~~in~HLD~ 22 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLDS 22 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHHH
Confidence 3699999998 66778888884
No 104
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=83.71 E-value=0.62 Score=26.92 Aligned_cols=21 Identities=38% Similarity=0.945 Sum_probs=14.8
Q ss_pred eCCCCccccc-cccCCCCCCCc
Q 027385 68 CSVCDTEQPV-AQVCTNCGVNM 88 (224)
Q Consensus 68 C~~C~~~q~~-~~~C~~Cg~~f 88 (224)
|..|+++.+. +..|++||+.|
T Consensus 2 Cp~CG~~~~~~~~fC~~CG~~l 23 (23)
T PF13240_consen 2 CPNCGAEIEDDAKFCPNCGTPL 23 (23)
T ss_pred CcccCCCCCCcCcchhhhCCcC
Confidence 6677777654 46788888764
No 105
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=82.85 E-value=0.85 Score=30.10 Aligned_cols=25 Identities=24% Similarity=0.858 Sum_probs=15.7
Q ss_pred ccCCccCHHHHHHHHhcCcC-CCCCC
Q 027385 171 KCGHTMHCECYHEMIKRDKY-CCPIC 195 (224)
Q Consensus 171 pCGH~~H~~C~~~~l~~~~~-~CPiC 195 (224)
.|+=.||..|++.|+++... +||.|
T Consensus 18 ~C~~r~H~~C~~~y~r~~~~~~CP~C 43 (43)
T PF08746_consen 18 DCNVRLHDDCFKKYFRHRSNPKCPNC 43 (43)
T ss_dssp -S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred ccCchHHHHHHHHHHhcCCCCCCcCC
Confidence 47778999999999986433 69987
No 106
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=82.54 E-value=1 Score=35.62 Aligned_cols=27 Identities=33% Similarity=1.003 Sum_probs=20.5
Q ss_pred ccccCCCCCCCcceeecCccccccCCCCcCeeccCCCCc
Q 027385 77 VAQVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGI 115 (224)
Q Consensus 77 ~~~~C~~Cg~~f~~Y~C~~C~l~dd~~~k~~yHC~~Cgi 115 (224)
...+|++||+.| | +.+|.|-.|++||.
T Consensus 8 tKR~Cp~CG~kF----------Y--DLnk~PivCP~CG~ 34 (108)
T PF09538_consen 8 TKRTCPSCGAKF----------Y--DLNKDPIVCPKCGT 34 (108)
T ss_pred CcccCCCCcchh----------c--cCCCCCccCCCCCC
Confidence 346799999855 6 45688999999984
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=81.87 E-value=1.2 Score=32.77 Aligned_cols=44 Identities=34% Similarity=0.859 Sum_probs=20.8
Q ss_pred ceeecCccccccCCCCcCeeccCCCC----cceeCCccceeecCccCcccccc
Q 027385 89 GEYFCDICKFYDDDIEKGQFHCDDCG----ICRIGGRENYFHCKRCGSCYSTS 137 (224)
Q Consensus 89 ~~Y~C~~C~l~dd~~~k~~yHC~~Cg----iCR~G~~~~~fHC~~C~~C~s~~ 137 (224)
+.|+|+.|.-- -+..-.|++|| +-+.=|..||| |..|+.=+|++
T Consensus 16 ~~~~C~~C~~~----~~~~a~CPdC~~~Le~LkACGAvdYF-C~~c~gLiSKk 63 (70)
T PF07191_consen 16 GHYHCEACQKD----YKKEAFCPDCGQPLEVLKACGAVDYF-CNHCHGLISKK 63 (70)
T ss_dssp TEEEETTT--E----EEEEEE-TTT-SB-EEEEETTEEEEE--TTTT-EE-TT
T ss_pred CEEECcccccc----ceecccCCCcccHHHHHHHhccccee-eccCCceeecc
Confidence 46666666421 13455677777 44444556665 66666655554
No 108
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=81.57 E-value=1.1 Score=45.34 Aligned_cols=33 Identities=30% Similarity=0.828 Sum_probs=19.7
Q ss_pred eEeCCCCccccc-cccCCCCCCCcceeecCcccc
Q 027385 66 VICSVCDTEQPV-AQVCTNCGVNMGEYFCDICKF 98 (224)
Q Consensus 66 vlC~~C~~~q~~-~~~C~~Cg~~f~~Y~C~~C~l 98 (224)
++|..|+++-+. +..|++||..+..-.|+.|.-
T Consensus 2 ~~Cp~Cg~~n~~~akFC~~CG~~l~~~~Cp~CG~ 35 (645)
T PRK14559 2 LICPQCQFENPNNNRFCQKCGTSLTHKPCPQCGT 35 (645)
T ss_pred CcCCCCCCcCCCCCccccccCCCCCCCcCCCCCC
Confidence 356667666544 345777777766555555543
No 109
>PHA00626 hypothetical protein
Probab=81.21 E-value=1.2 Score=31.52 Aligned_cols=6 Identities=50% Similarity=1.636 Sum_probs=3.3
Q ss_pred CCCCCC
Q 027385 81 CTNCGV 86 (224)
Q Consensus 81 C~~Cg~ 86 (224)
||+||.
T Consensus 3 CP~CGS 8 (59)
T PHA00626 3 CPKCGS 8 (59)
T ss_pred CCCCCC
Confidence 555555
No 110
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=81.01 E-value=1.6 Score=30.62 Aligned_cols=37 Identities=22% Similarity=0.528 Sum_probs=28.3
Q ss_pred CCCCCCccchhhcccCCCceeEeccCCccCHHHHHHH
Q 027385 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEM 184 (224)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~ 184 (224)
-+...|++|.+.|.+..+-|+---||=..|+.|.+..
T Consensus 3 ~~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~ 39 (54)
T PF14446_consen 3 YEGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKA 39 (54)
T ss_pred ccCccChhhCCcccCCCCEEECCCCCCcccHHHHhhC
Confidence 3467899999997665555555679999999998653
No 111
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=80.39 E-value=1.8 Score=46.79 Aligned_cols=48 Identities=27% Similarity=0.654 Sum_probs=26.2
Q ss_pred eeEeCCCCccccccccCCCCCCCc-ceeecCcccccc-CCCCcCeeccCCCC
Q 027385 65 QVICSVCDTEQPVAQVCTNCGVNM-GEYFCDICKFYD-DDIEKGQFHCDDCG 114 (224)
Q Consensus 65 ~vlC~~C~~~q~~~~~C~~Cg~~f-~~Y~C~~C~l~d-d~~~k~~yHC~~Cg 114 (224)
...|..|+++- +...|+.||... ..|+|+.|..-- .++.. ...|+.||
T Consensus 667 ~rkCPkCG~~t-~~~fCP~CGs~te~vy~CPsCGaev~~des~-a~~CP~CG 716 (1337)
T PRK14714 667 RRRCPSCGTET-YENRCPDCGTHTEPVYVCPDCGAEVPPDESG-RVECPRCD 716 (1337)
T ss_pred EEECCCCCCcc-ccccCcccCCcCCCceeCccCCCccCCCccc-cccCCCCC
Confidence 46777777753 334777777665 345566665431 11112 34566665
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=79.36 E-value=1.1 Score=27.19 Aligned_cols=37 Identities=24% Similarity=0.465 Sum_probs=23.5
Q ss_pred CccchhhcccCCCceeEeccCCccCHHHHHHHHhcCcCCCCCCccccc
Q 027385 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (224)
Q Consensus 153 CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (224)
|+.|.+.+..+...+. .=|..||..|| +|..|+++|.
T Consensus 2 C~~C~~~i~~~~~~~~--~~~~~~H~~Cf---------~C~~C~~~L~ 38 (39)
T smart00132 2 CAGCGKPIRGGELVLR--ALGKVWHPECF---------KCSKCGKPLG 38 (39)
T ss_pred ccccCCcccCCcEEEE--eCCccccccCC---------CCcccCCcCc
Confidence 6778887655312222 22788998876 6777877764
No 113
>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=78.80 E-value=1.7 Score=42.50 Aligned_cols=49 Identities=22% Similarity=0.702 Sum_probs=41.0
Q ss_pred eecCCCCCcccChhhHHhhhcCCCCCCCcccccccccCeeEeCCCCccccccccCCCCCCC
Q 027385 27 IRAPCCNEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVAQVCTNCGVN 87 (224)
Q Consensus 27 l~~pCC~~~y~Cr~CHde~~~~~~~~~~~H~~~r~~~~~vlC~~C~~~q~~~~~C~~Cg~~ 87 (224)
+.|.-||....|..|.-.+.- |. ....+.|-.|+..+++...||+||..
T Consensus 214 ~~C~~Cg~~~~C~~C~~~l~~--------h~----~~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 214 LLCRSCGYILCCPNCDVSLTY--------HK----KEGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred eEhhhCcCccCCCCCCCceEE--------ec----CCCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 789999999999999766543 22 24589999999999999999999875
No 114
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=78.75 E-value=0.21 Score=47.66 Aligned_cols=50 Identities=22% Similarity=0.436 Sum_probs=44.3
Q ss_pred CCCCccchhhcccCCCceeEeccCCccCHHHHHHHHhcCcCCCCCCccccc
Q 027385 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (224)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (224)
-..+.||.+.|...-+....+.|||..|..++.+||.. ..++|-|++.+-
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 34799999999886678889999999999999999985 789999998885
No 115
>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=78.67 E-value=1.6 Score=23.59 Aligned_cols=21 Identities=33% Similarity=0.697 Sum_probs=14.7
Q ss_pred CCCCCCccccccchHHHHHHH
Q 027385 190 YCCPICSKSVIDMSRTWKRID 210 (224)
Q Consensus 190 ~~CPiCrksi~dm~~~~~~lD 210 (224)
+.||+|.+++.+...+++-+.
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 479999999998877766553
No 116
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=77.61 E-value=0.92 Score=38.80 Aligned_cols=30 Identities=23% Similarity=0.303 Sum_probs=24.8
Q ss_pred CCCCCCccchhhcccCCCceeEeccCCccCH
Q 027385 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHC 178 (224)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~ 178 (224)
....+|.||||+|.. .+.+..|||==++|+
T Consensus 175 ddkGECvICLEdL~~-GdtIARLPCLCIYHK 204 (205)
T KOG0801|consen 175 DDKGECVICLEDLEA-GDTIARLPCLCIYHK 204 (205)
T ss_pred ccCCcEEEEhhhccC-CCceeccceEEEeec
Confidence 456789999999766 678999999877775
No 117
>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=75.40 E-value=1.2 Score=40.29 Aligned_cols=51 Identities=24% Similarity=0.546 Sum_probs=41.1
Q ss_pred CCCCccchhhcccCCCceeEe-c-cCCccCHHHHHHHHhcCcCCCC--CCccccc
Q 027385 150 HHHCPICYEYLFDSLRNTTVM-K-CGHTMHCECYHEMIKRDKYCCP--ICSKSVI 200 (224)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~L-p-CGH~~H~~C~~~~l~~~~~~CP--iCrksi~ 200 (224)
+..||||..+.+-+.+-...+ | |=|-|..+|.+..+..+.-.|| -|.|.+-
T Consensus 10 d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kILR 64 (314)
T COG5220 10 DRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKILR 64 (314)
T ss_pred cccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHHH
Confidence 457999999988765544433 5 9999999999999887788899 7887664
No 118
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=74.24 E-value=3.2 Score=42.67 Aligned_cols=44 Identities=27% Similarity=0.750 Sum_probs=32.1
Q ss_pred CeeEeCCCCccccccccCCCCCCCc------ceeecCccccccCCCCcCeeccCCCCc
Q 027385 64 KQVICSVCDTEQPVAQVCTNCGVNM------GEYFCDICKFYDDDIEKGQFHCDDCGI 115 (224)
Q Consensus 64 ~~vlC~~C~~~q~~~~~C~~Cg~~f------~~Y~C~~C~l~dd~~~k~~yHC~~Cgi 115 (224)
+.++|..|+.. ..|++|...+ +...|--|..= ++.+.+|+.||-
T Consensus 434 ~~l~C~~Cg~v----~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~----~~~p~~Cp~Cgs 483 (730)
T COG1198 434 PLLLCRDCGYI----AECPNCDSPLTLHKATGQLRCHYCGYQ----EPIPQSCPECGS 483 (730)
T ss_pred ceeecccCCCc----ccCCCCCcceEEecCCCeeEeCCCCCC----CCCCCCCCCCCC
Confidence 58999999976 5799998887 45566666543 456777777773
No 119
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=73.55 E-value=2.2 Score=39.79 Aligned_cols=44 Identities=32% Similarity=0.710 Sum_probs=36.0
Q ss_pred CCCccchhhcccCCCceeEeccCCccCHHHHHHHHhcCcCCCCCCcc
Q 027385 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSK 197 (224)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrk 197 (224)
..||.|.--|. .+++.--|||.|..+||..-|..+.+.||.|.+
T Consensus 275 LkCplc~~Llr---np~kT~cC~~~fc~eci~~al~dsDf~CpnC~r 318 (427)
T COG5222 275 LKCPLCHCLLR---NPMKTPCCGHTFCDECIGTALLDSDFKCPNCSR 318 (427)
T ss_pred ccCcchhhhhh---CcccCccccchHHHHHHhhhhhhccccCCCccc
Confidence 57999987653 366666689999999999866667899999987
No 120
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=72.83 E-value=3.5 Score=42.52 Aligned_cols=49 Identities=20% Similarity=0.301 Sum_probs=33.9
Q ss_pred CCccchhhcccCCCceeEeccCCccCHHHHHHHHhcCcCCCCC-------Cccccccch
Q 027385 152 HCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPI-------CSKSVIDMS 203 (224)
Q Consensus 152 ~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPi-------Crksi~dm~ 203 (224)
.|.||-..+.. ..+..--|||..|..++.+|+.. +..||. +++++.||.
T Consensus 781 ~CtVC~~vi~G--~~~~c~~C~H~gH~sh~~sw~~~-~s~ca~~~C~~~c~~~~~~D~~ 836 (839)
T KOG0269|consen 781 KCTVCDLVIRG--VDVWCQVCGHGGHDSHLKSWFFK-ASPCAKSICPHLCHYSSFIDTF 836 (839)
T ss_pred Cceeecceeee--eEeecccccccccHHHHHHHHhc-CCCCccccCCccccccccchhh
Confidence 58888766433 23333469999999999999984 567776 445556653
No 121
>KOG2068 consensus MOT2 transcription factor [Transcription]
Probab=72.40 E-value=2.9 Score=39.08 Aligned_cols=52 Identities=29% Similarity=0.494 Sum_probs=40.7
Q ss_pred CCCCCccchhhcccCCCceeEeccCCccCHHHHHHHHhcCcCCCCCCcccccc
Q 027385 149 MHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID 201 (224)
Q Consensus 149 ~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~d 201 (224)
-...||||.+++.........-|||+.++..|+..-.. .+.+||.||+....
T Consensus 248 v~~s~p~~~~~~~~~d~~~lP~~~~~~~~l~~~~t~~~-~~~~~~~~rk~~~~ 299 (327)
T KOG2068|consen 248 VPPSCPICYEDLDLTDSNFLPCPCGFRLCLFCHKTISD-GDGRCPGCRKPYER 299 (327)
T ss_pred cCCCCCCCCCcccccccccccccccccchhhhhhcccc-cCCCCCccCCcccc
Confidence 34689999999755444445557899999999988877 58999999988763
No 122
>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 PLN03086 PRLI-interacting factor K; Provisional
Probab=71.01 E-value=2 Score=42.89 Aligned_cols=85 Identities=26% Similarity=0.592 Sum_probs=48.4
Q ss_pred cccCeeEeCCCCcccccc-------------ccCCC--CCCCcceeecCccccccCCCCcCeeccCCCCcceeCCc----
Q 027385 61 QDVKQVICSVCDTEQPVA-------------QVCTN--CGVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGR---- 121 (224)
Q Consensus 61 ~~~~~vlC~~C~~~q~~~-------------~~C~~--Cg~~f~~Y~C~~C~l~dd~~~k~~yHC~~CgiCR~G~~---- 121 (224)
.++..|.|..|....+.. ..|++ ||..|.+- .-+..+||+.||- ..+..
T Consensus 403 ~~~~~V~C~NC~~~i~l~~l~lHe~~C~r~~V~Cp~~~Cg~v~~r~-----------el~~H~~C~~Cgk-~f~~s~Lek 470 (567)
T PLN03086 403 MDVDTVECRNCKHYIPSRSIALHEAYCSRHNVVCPHDGCGIVLRVE-----------EAKNHVHCEKCGQ-AFQQGEMEK 470 (567)
T ss_pred CCCCeEECCCCCCccchhHHHHHHhhCCCcceeCCcccccceeecc-----------ccccCccCCCCCC-ccchHHHHH
Confidence 346688999998776642 25664 77766332 2345678888864 22210
Q ss_pred -----cceeecCccCccccccccCcce---eecCCCCCCCccchhhc
Q 027385 122 -----ENYFHCKRCGSCYSTSLRNNHL---CIENSMHHHCPICYEYL 160 (224)
Q Consensus 122 -----~~~fHC~~C~~C~s~~l~~~H~---C~e~~~~~~CpICle~l 160 (224)
..-+-|. ||.-+.......|. |.+ ....|+.|...+
T Consensus 471 H~~~~Hkpv~Cp-Cg~~~~R~~L~~H~~thCp~--Kpi~C~fC~~~v 514 (567)
T PLN03086 471 HMKVFHEPLQCP-CGVVLEKEQMVQHQASTCPL--RLITCRFCGDMV 514 (567)
T ss_pred HHHhcCCCccCC-CCCCcchhHHHhhhhccCCC--CceeCCCCCCcc
Confidence 1124566 76555444445664 333 235788888664
No 124
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=70.90 E-value=4.1 Score=41.91 Aligned_cols=53 Identities=23% Similarity=0.556 Sum_probs=43.1
Q ss_pred eecCCCCCcccChhhHHhhhcCCCCCCCcccccccccCeeEeCCCCccccccccCCCCCCCccee
Q 027385 27 IRAPCCNEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVAQVCTNCGVNMGEY 91 (224)
Q Consensus 27 l~~pCC~~~y~Cr~CHde~~~~~~~~~~~H~~~r~~~~~vlC~~C~~~q~~~~~C~~Cg~~f~~Y 91 (224)
+.|.-||-.+.|++|=.-..-|. .+..+.|-.|+.++++...|++||...=+|
T Consensus 436 l~C~~Cg~v~~Cp~Cd~~lt~H~------------~~~~L~CH~Cg~~~~~p~~Cp~Cgs~~L~~ 488 (730)
T COG1198 436 LLCRDCGYIAECPNCDSPLTLHK------------ATGQLRCHYCGYQEPIPQSCPECGSEHLRA 488 (730)
T ss_pred eecccCCCcccCCCCCcceEEec------------CCCeeEeCCCCCCCCCCCCCCCCCCCeeEE
Confidence 88999999999999965544321 247999999999999999999999884443
No 125
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=70.25 E-value=3.8 Score=44.48 Aligned_cols=33 Identities=30% Similarity=0.730 Sum_probs=25.5
Q ss_pred ccCCCCCCCcceeecCccccccCCCCcCeeccCCCCc
Q 027385 79 QVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGI 115 (224)
Q Consensus 79 ~~C~~Cg~~f~~Y~C~~C~l~dd~~~k~~yHC~~Cgi 115 (224)
-.||+||+.....||+.|.-. .+.+|+|+.||.
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 489999987777799999654 245788888876
No 126
>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=69.54 E-value=4.7 Score=27.35 Aligned_cols=11 Identities=55% Similarity=1.162 Sum_probs=6.8
Q ss_pred CCCCCCccccc
Q 027385 190 YCCPICSKSVI 200 (224)
Q Consensus 190 ~~CPiCrksi~ 200 (224)
+.||||...+.
T Consensus 32 v~CPiC~~~~~ 42 (54)
T PF05605_consen 32 VVCPICSSRVT 42 (54)
T ss_pred ccCCCchhhhh
Confidence 44777776544
No 127
>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=68.43 E-value=4 Score=28.68 Aligned_cols=27 Identities=30% Similarity=0.774 Sum_probs=16.2
Q ss_pred cccCCCCCCCcceeecCccccccCCCCcCeeccCCCCc
Q 027385 78 AQVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGI 115 (224)
Q Consensus 78 ~~~C~~Cg~~f~~Y~C~~C~l~dd~~~k~~yHC~~Cgi 115 (224)
++.|+.||..... ......|.|+.||.
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 5678888776655 22344566666554
No 128
>PRK04023 DNA polymerase II large subunit; Validated
Probab=67.76 E-value=4.4 Score=43.10 Aligned_cols=48 Identities=25% Similarity=0.600 Sum_probs=35.5
Q ss_pred ccCCCCCCCcceeecCccccccCCCCcCeeccCCCCcceeCCccceeecCccCcccc
Q 027385 79 QVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYS 135 (224)
Q Consensus 79 ~~C~~Cg~~f~~Y~C~~C~l~dd~~~k~~yHC~~CgiCR~G~~~~~fHC~~C~~C~s 135 (224)
..|++||+....-+|+.|.-. ...+|.|++||.-..+ ..|.+||.=.+
T Consensus 627 RfCpsCG~~t~~frCP~CG~~----Te~i~fCP~CG~~~~~-----y~CPKCG~El~ 674 (1121)
T PRK04023 627 RKCPSCGKETFYRRCPFCGTH----TEPVYRCPRCGIEVEE-----DECEKCGREPT 674 (1121)
T ss_pred ccCCCCCCcCCcccCCCCCCC----CCcceeCccccCcCCC-----CcCCCCCCCCC
Confidence 489999999988899999654 4678999999654332 34777775433
No 129
>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=67.59 E-value=4.7 Score=23.75 Aligned_cols=9 Identities=44% Similarity=1.239 Sum_probs=4.8
Q ss_pred CeeccCCCC
Q 027385 106 GQFHCDDCG 114 (224)
Q Consensus 106 ~~yHC~~Cg 114 (224)
..|.|++||
T Consensus 15 v~f~CPnCG 23 (24)
T PF07754_consen 15 VPFPCPNCG 23 (24)
T ss_pred ceEeCCCCC
Confidence 455555555
No 130
>PRK05580 primosome assembly protein PriA; Validated
Probab=67.57 E-value=4.3 Score=41.14 Aligned_cols=50 Identities=22% Similarity=0.666 Sum_probs=41.1
Q ss_pred eecCCCCCcccChhhHHhhhcCCCCCCCcccccccccCeeEeCCCCccccccccCCCCCCCc
Q 027385 27 IRAPCCNEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVAQVCTNCGVNM 88 (224)
Q Consensus 27 l~~pCC~~~y~Cr~CHde~~~~~~~~~~~H~~~r~~~~~vlC~~C~~~q~~~~~C~~Cg~~f 88 (224)
+.|.-||...-|..|...+.- |. ....+.|-.|+..+++...|++||...
T Consensus 382 ~~C~~Cg~~~~C~~C~~~l~~--------h~----~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~ 431 (679)
T PRK05580 382 LLCRDCGWVAECPHCDASLTL--------HR----FQRRLRCHHCGYQEPIPKACPECGSTD 431 (679)
T ss_pred eEhhhCcCccCCCCCCCceeE--------EC----CCCeEECCCCcCCCCCCCCCCCCcCCe
Confidence 789999999999999865542 22 246899999999999999999998763
No 131
>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]
Probab=67.45 E-value=2.1 Score=44.17 Aligned_cols=44 Identities=34% Similarity=0.631 Sum_probs=31.4
Q ss_pred CCCccchhhcccCC---CceeEeccCCccCHHHHHHHHhcCcCCCCCCc
Q 027385 151 HHCPICYEYLFDSL---RNTTVMKCGHTMHCECYHEMIKRDKYCCPICS 196 (224)
Q Consensus 151 ~~CpICle~lf~s~---~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCr 196 (224)
+.|.-|.+....+. ..+.++.|||.||+.|+.....+++ |-+|.
T Consensus 785 ~rc~~c~~~~l~~~~~~~~~~v~~c~h~yhk~c~~~~~~~~~--~~~~~ 831 (846)
T KOG2066|consen 785 ERCSSCFEPNLPSGAAFDSVVVFHCGHMYHKECLMMESLRNA--CNIES 831 (846)
T ss_pred hhhhhhcccccccCcccceeeEEEccchhhhcccccHHHhcc--cChhh
Confidence 35666666655444 5689999999999999987665333 65554
No 132
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=67.38 E-value=2.6 Score=42.98 Aligned_cols=45 Identities=31% Similarity=0.855 Sum_probs=36.3
Q ss_pred CCCccchhhcccCCCceeEeccCCccCHHHHHHHHhcCcC-CCCCCccccc
Q 027385 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKY-CCPICSKSVI 200 (224)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~-~CPiCrksi~ 200 (224)
..|+||++ .+.....+|||.|-..|+.+.+..... .||+|+..+.
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 356778899999999999998875444 5999996554
No 133
>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=66.78 E-value=4.2 Score=33.28 Aligned_cols=27 Identities=22% Similarity=0.471 Sum_probs=20.4
Q ss_pred cccCCCCCCCcceeecCccccccCCCCcCeeccCCCCcc
Q 027385 78 AQVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGIC 116 (224)
Q Consensus 78 ~~~C~~Cg~~f~~Y~C~~C~l~dd~~~k~~yHC~~CgiC 116 (224)
...|++||+.| | +.+|.+-.|++||.=
T Consensus 9 Kr~Cp~cg~kF----------Y--DLnk~p~vcP~cg~~ 35 (129)
T TIGR02300 9 KRICPNTGSKF----------Y--DLNRRPAVSPYTGEQ 35 (129)
T ss_pred cccCCCcCccc----------c--ccCCCCccCCCcCCc
Confidence 45789998855 5 456899999999854
No 134
>PHA03096 p28-like protein; Provisional
Probab=66.58 E-value=2.9 Score=38.33 Aligned_cols=47 Identities=17% Similarity=0.328 Sum_probs=32.3
Q ss_pred CCCccchhhcccCC---CceeEe-ccCCccCHHHHHHHHhcC--cCCCCCCcc
Q 027385 151 HHCPICYEYLFDSL---RNTTVM-KCGHTMHCECYHEMIKRD--KYCCPICSK 197 (224)
Q Consensus 151 ~~CpICle~lf~s~---~~v~~L-pCGH~~H~~C~~~~l~~~--~~~CPiCrk 197 (224)
-.|.||+|...... ..-..| .|-|.|-..|+..|...+ ..+||.|+.
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~ 231 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRR 231 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCccccc
Confidence 56999999876532 112234 699999999999998643 334555554
No 135
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=65.29 E-value=4.8 Score=24.30 Aligned_cols=20 Identities=30% Similarity=0.853 Sum_probs=13.7
Q ss_pred CCCcceeCCccc-eeecCccC
Q 027385 112 DCGICRIGGREN-YFHCKRCG 131 (224)
Q Consensus 112 ~CgiCR~G~~~~-~fHC~~C~ 131 (224)
.|++|+.-.... +++|..|+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~ 22 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECC 22 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCC
Confidence 467776654334 88888887
No 136
>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=65.01 E-value=3.6 Score=40.22 Aligned_cols=98 Identities=22% Similarity=0.448 Sum_probs=50.8
Q ss_pred eecCccccccCCCCcCeeccCCCCcceeCCccceeecCccCccccccc--cCcceeecCCCCCCCccchhhcccCCCcee
Q 027385 91 YFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYSTSL--RNNHLCIENSMHHHCPICYEYLFDSLRNTT 168 (224)
Q Consensus 91 Y~C~~C~l~dd~~~k~~yHC~~CgiCR~G~~~~~fHC~~C~~C~s~~l--~~~H~C~e~~~~~~CpICle~lf~s~~~v~ 168 (224)
|||..|.-. .|+-|-....+ .+=|..|-.=++.+- .+..+|..+- -+||+|.-.|........
T Consensus 6 ~fC~~C~~i------------rc~~c~~~Ei~-~~yCp~CL~~~p~~e~~~~~nrC~r~C--f~CP~C~~~L~~~~~~~~ 70 (483)
T PF05502_consen 6 YFCEHCHKI------------RCPRCVSEEID-SYYCPNCLFEVPSSEARSEKNRCSRNC--FDCPICFSPLSVRASDTP 70 (483)
T ss_pred eeccccccc------------CChhhcccccc-eeECccccccCChhhheeccceecccc--ccCCCCCCcceeEecccc
Confidence 788888765 13334444333 444555555554432 2456675443 479999988765433221
Q ss_pred E---eccCCccCHHHHHHHHhcCcCCCCCCccccccchHHHHHHHH
Q 027385 169 V---MKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRTWKRIDE 211 (224)
Q Consensus 169 ~---LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~dm~~~~~~lD~ 211 (224)
. -+-+=.-+ ......|+.|+=+-.++...|.+.+.
T Consensus 71 ~~~~~~~~~~~~--------~~~~l~C~~C~Wss~~igi~Fdkpt~ 108 (483)
T PF05502_consen 71 PSPPDPSSDSGG--------KPYYLSCSYCRWSSRDIGIKFDKPTG 108 (483)
T ss_pred cccccccccCCC--------CCEEEECCCceeeccccCccccCchh
Confidence 1 00000000 00134899999877665544555443
No 137
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=64.45 E-value=3 Score=38.11 Aligned_cols=29 Identities=21% Similarity=0.526 Sum_probs=25.6
Q ss_pred CccCccccccccceecCCCCCcccChhhHH
Q 027385 14 MGYGCKHYRRRCRIRAPCCNEIFDCRHCHN 43 (224)
Q Consensus 14 ~~~gC~HY~r~c~l~~pCC~~~y~Cr~CHd 43 (224)
..+.|.||...=.++..+|.. |+|..||+
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 346899999966699999999 99999999
No 138
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=63.34 E-value=4.5 Score=36.90 Aligned_cols=68 Identities=24% Similarity=0.466 Sum_probs=44.6
Q ss_pred CCCCCCccchhhcccCCCceeEecc-----CCccCHHHHHHHHhcC-------cCCCCCCccccc----cch---HHHHH
Q 027385 148 SMHHHCPICYEYLFDSLRNTTVMKC-----GHTMHCECYHEMIKRD-------KYCCPICSKSVI----DMS---RTWKR 208 (224)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpC-----GH~~H~~C~~~~l~~~-------~~~CPiCrksi~----dm~---~~~~~ 208 (224)
..+.-|=||++.=.+.....-+=|| .|+.|..|+..|+.+. .-+||.|+.... .|. ..-++
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 3455699999864444333345577 3999999999999753 346999997654 232 23455
Q ss_pred HHHHHhc
Q 027385 209 IDEEMNS 215 (224)
Q Consensus 209 lD~~i~~ 215 (224)
+|..|..
T Consensus 98 ~d~~i~r 104 (293)
T KOG3053|consen 98 LDILIFR 104 (293)
T ss_pred hhhHHhh
Confidence 5555543
No 139
>PRK14873 primosome assembly protein PriA; Provisional
Probab=62.95 E-value=5.8 Score=40.35 Aligned_cols=48 Identities=21% Similarity=0.503 Sum_probs=38.2
Q ss_pred eecCCCCCcccChhhHHhhhcCCCCCCCcccccccccCeeEeCCCCccccccccCCCCCCC
Q 027385 27 IRAPCCNEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVAQVCTNCGVN 87 (224)
Q Consensus 27 l~~pCC~~~y~Cr~CHde~~~~~~~~~~~H~~~r~~~~~vlC~~C~~~q~~~~~C~~Cg~~ 87 (224)
+.|.-||...-|..|...+.- |. ....+.|-.|+..+ ....|++||..
T Consensus 384 l~C~~Cg~~~~C~~C~~~L~~--------h~----~~~~l~Ch~CG~~~-~p~~Cp~Cgs~ 431 (665)
T PRK14873 384 LACARCRTPARCRHCTGPLGL--------PS----AGGTPRCRWCGRAA-PDWRCPRCGSD 431 (665)
T ss_pred eEhhhCcCeeECCCCCCceeE--------ec----CCCeeECCCCcCCC-cCccCCCCcCC
Confidence 799999999999999876542 21 23578899999876 57899999876
No 140
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=62.38 E-value=7.1 Score=36.73 Aligned_cols=44 Identities=23% Similarity=0.631 Sum_probs=35.5
Q ss_pred CCccchhhcccCCCceeEeccCCccCHHHHHHHHhcC--cCCCCCCc
Q 027385 152 HCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRD--KYCCPICS 196 (224)
Q Consensus 152 ~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~--~~~CPiCr 196 (224)
.|||=.|. -+...+...|.|||++=+.=++.+-+++ .++||.|-
T Consensus 338 iCPVlKe~-~t~ENpP~ml~CgHVIskeal~~LS~nG~~~FKCPYCP 383 (396)
T COG5109 338 ICPVLKEL-CTDENPPVMLECGHVISKEALSVLSQNGVLSFKCPYCP 383 (396)
T ss_pred eccccHhh-hcccCCCeeeeccceeeHHHHHHHhhcCcEEeeCCCCC
Confidence 58886665 5556778889999999999999987754 67899996
No 141
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=61.59 E-value=5.5 Score=28.39 Aligned_cols=35 Identities=23% Similarity=0.666 Sum_probs=27.1
Q ss_pred cCeeEeCCCCccccccccCCCCCCCcceeecCccccc
Q 027385 63 VKQVICSVCDTEQPVAQVCTNCGVNMGEYFCDICKFY 99 (224)
Q Consensus 63 ~~~vlC~~C~~~q~~~~~C~~Cg~~f~~Y~C~~C~l~ 99 (224)
...-.|..|+.+ +-..|..|....+.|-|++|.|-
T Consensus 23 ~~~F~CPnCG~~--~I~RC~~CRk~~~~Y~CP~CGF~ 57 (59)
T PRK14890 23 AVKFLCPNCGEV--IIYRCEKCRKQSNPYTCPKCGFE 57 (59)
T ss_pred cCEeeCCCCCCe--eEeechhHHhcCCceECCCCCCc
Confidence 357888889764 23469999999999999999773
No 142
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=61.32 E-value=7.8 Score=35.52 Aligned_cols=20 Identities=40% Similarity=0.431 Sum_probs=12.0
Q ss_pred cCCCCCCccccccchHHHHH
Q 027385 189 KYCCPICSKSVIDMSRTWKR 208 (224)
Q Consensus 189 ~~~CPiCrksi~dm~~~~~~ 208 (224)
+|.|+-|.|++.-|+-..+.
T Consensus 243 ~~qC~~C~KsFsl~SyLnKH 262 (279)
T KOG2462|consen 243 KHQCPRCGKSFALKSYLNKH 262 (279)
T ss_pred cccCcchhhHHHHHHHHHHh
Confidence 56666666666666544433
No 143
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=60.15 E-value=12 Score=28.14 Aligned_cols=53 Identities=19% Similarity=0.368 Sum_probs=25.0
Q ss_pred CCCCCCccchhhcccCCCceeE---eccCCccCHHHHHHHHhcCcCCCCCCccccc
Q 027385 148 SMHHHCPICYEYLFDSLRNTTV---MKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (224)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~---LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (224)
...+.|-||.|++-...+.-.+ .-|+=.+.+.|++--.+..+..||.|+...-
T Consensus 7 ~~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg~q~CpqCkt~yk 62 (80)
T PF14569_consen 7 LNGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEGNQVCPQCKTRYK 62 (80)
T ss_dssp -SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS-SB-TTT--B--
T ss_pred cCCcccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcCcccccccCCCcc
Confidence 4567899999997554333332 3689999999999888878889999995543
No 144
>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=60.03 E-value=5.8 Score=21.71 Aligned_cols=16 Identities=50% Similarity=0.916 Sum_probs=12.4
Q ss_pred CCCCCCccccccchHH
Q 027385 190 YCCPICSKSVIDMSRT 205 (224)
Q Consensus 190 ~~CPiCrksi~dm~~~ 205 (224)
|+||+|.+++.+.+.+
T Consensus 1 y~C~~C~~~f~~~~~l 16 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNL 16 (23)
T ss_dssp EEETTTTEEESSHHHH
T ss_pred CCCCCCCCccCCHHHH
Confidence 5799999999875443
No 145
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=59.80 E-value=4.4 Score=44.03 Aligned_cols=52 Identities=31% Similarity=0.650 Sum_probs=41.8
Q ss_pred CCCCCCccchhhcccCCCceeEeccCCccCHHHHHHHHhcCcCCCCCCccccccch
Q 027385 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMS 203 (224)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~dm~ 203 (224)
+....|+||++-|.. .-.+..|||.+-..|+..|+. .+..||+|+...+|-.
T Consensus 1151 ~~~~~c~ic~dil~~---~~~I~~cgh~~c~~c~~~~l~-~~s~~~~~ksi~~dfg 1202 (1394)
T KOG0298|consen 1151 SGHFVCEICLDILRN---QGGIAGCGHEPCCRCDELWLY-ASSRCPICKSIKGDFG 1202 (1394)
T ss_pred hcccchHHHHHHHHh---cCCeeeechhHhhhHHHHHHH-HhccCcchhhhhhhhc
Confidence 334589999998753 345668999999999999998 5789999997777643
No 146
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=59.54 E-value=4.3 Score=38.53 Aligned_cols=37 Identities=27% Similarity=0.608 Sum_probs=27.7
Q ss_pred CCCCccchhhcccCCCceeEeccCCccCHHHHHHHHh
Q 027385 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIK 186 (224)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~ 186 (224)
...|.||..+..+......++.|||.|...|+.++++
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 5679999943333333334789999999999999987
No 147
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=58.93 E-value=6.2 Score=32.62 Aligned_cols=49 Identities=31% Similarity=0.621 Sum_probs=35.4
Q ss_pred CCCccchhhcccCCCceeEe-c---cCCccCHHHHHHHHhc--CcCCCCCCccccccch
Q 027385 151 HHCPICYEYLFDSLRNTTVM-K---CGHTMHCECYHEMIKR--DKYCCPICSKSVIDMS 203 (224)
Q Consensus 151 ~~CpICle~lf~s~~~v~~L-p---CGH~~H~~C~~~~l~~--~~~~CPiCrksi~dm~ 203 (224)
-.|-||.|- |. +.+.| | ||=.+...|+.++.+. ..-.||+|+.|+-..+
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 468888875 22 34455 3 8999999999987664 3567999999986543
No 148
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=58.44 E-value=3.2 Score=37.96 Aligned_cols=51 Identities=27% Similarity=0.735 Sum_probs=30.5
Q ss_pred CCcccChhhHHhhhcCCCCCCCcccccccccCeeEeCCCCccccccccCCCCCCCcceeecCcccc
Q 027385 33 NEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVAQVCTNCGVNMGEYFCDICKF 98 (224)
Q Consensus 33 ~~~y~Cr~CHde~~~~~~~~~~~H~~~r~~~~~vlC~~C~~~q~~~~~C~~Cg~~f~~Y~C~~C~l 98 (224)
|++|.|-+|.+-+... ++++ |... |+...+-+-.|.+|+. ++.|.|..||.
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 5577888877655321 1112 3221 4444455567888875 78888888874
No 149
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=58.26 E-value=2.6 Score=26.92 Aligned_cols=27 Identities=33% Similarity=0.671 Sum_probs=14.7
Q ss_pred cCCCCCCCcceeecCccccccCCCCcCeeccCCCCc
Q 027385 80 VCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGI 115 (224)
Q Consensus 80 ~C~~Cg~~f~~Y~C~~C~l~dd~~~k~~yHC~~Cgi 115 (224)
.|++||+.++-+| ++.|..=-||.||-
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 3666776666554 34455555666664
No 150
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=57.90 E-value=5.8 Score=28.28 Aligned_cols=35 Identities=31% Similarity=0.510 Sum_probs=26.0
Q ss_pred CeeEeCCCCccccc------cccCCCCCCCcceeecCcccc
Q 027385 64 KQVICSVCDTEQPV------AQVCTNCGVNMGEYFCDICKF 98 (224)
Q Consensus 64 ~~vlC~~C~~~q~~------~~~C~~Cg~~f~~Y~C~~C~l 98 (224)
-.|.|..|.++|.+ ...|..||..+++-.=.+-+|
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 47899999999965 247999999887765444444
No 151
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=57.74 E-value=8.5 Score=24.70 Aligned_cols=26 Identities=23% Similarity=0.579 Sum_probs=14.8
Q ss_pred cCCCCCCCcceeecCccccccCCCCcCeeccCCCC
Q 027385 80 VCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCG 114 (224)
Q Consensus 80 ~C~~Cg~~f~~Y~C~~C~l~dd~~~k~~yHC~~Cg 114 (224)
+||.|+..|..+. + .+-.++.|+.||
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 3677777665542 1 224566666665
No 152
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=57.44 E-value=5.3 Score=40.52 Aligned_cols=34 Identities=26% Similarity=0.666 Sum_probs=21.1
Q ss_pred eeEeCCCCccccccccCCCCCCCc--ceeecCccccc
Q 027385 65 QVICSVCDTEQPVAQVCTNCGVNM--GEYFCDICKFY 99 (224)
Q Consensus 65 ~vlC~~C~~~q~~~~~C~~Cg~~f--~~Y~C~~C~l~ 99 (224)
.-.|..|++.++. ..|++||+.. +.-||+.|-..
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 4467777766543 4677777553 55677777544
No 153
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=57.25 E-value=6.1 Score=26.28 Aligned_cols=21 Identities=33% Similarity=0.918 Sum_probs=10.9
Q ss_pred EeCCCCcccccc----ccCCCCCCC
Q 027385 67 ICSVCDTEQPVA----QVCTNCGVN 87 (224)
Q Consensus 67 lC~~C~~~q~~~----~~C~~Cg~~ 87 (224)
+|+.|+.+.+.. ..|++||..
T Consensus 4 ~C~~Cg~~~~~~~~~~irC~~CG~r 28 (44)
T smart00659 4 ICGECGRENEIKSKDVVRCRECGYR 28 (44)
T ss_pred ECCCCCCEeecCCCCceECCCCCce
Confidence 456665554332 356666654
No 154
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=56.09 E-value=10 Score=24.85 Aligned_cols=8 Identities=38% Similarity=1.074 Sum_probs=4.3
Q ss_pred eeccCCCC
Q 027385 107 QFHCDDCG 114 (224)
Q Consensus 107 ~yHC~~Cg 114 (224)
..+|+.||
T Consensus 21 ~~~Cp~CG 28 (46)
T PRK00398 21 GVRCPYCG 28 (46)
T ss_pred ceECCCCC
Confidence 45555555
No 155
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=54.65 E-value=5.6 Score=35.26 Aligned_cols=51 Identities=25% Similarity=0.446 Sum_probs=38.5
Q ss_pred CCCCccchhhcccCCCceeEecc---C--CccCHHHHHHHHhc-CcCCCCCCccccc
Q 027385 150 HHHCPICYEYLFDSLRNTTVMKC---G--HTMHCECYHEMIKR-DKYCCPICSKSVI 200 (224)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpC---G--H~~H~~C~~~~l~~-~~~~CPiCrksi~ 200 (224)
+..|=||.+..+++.......|| | ...|+.|++.|+.. ++.+|.+|.....
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 35799999987664333455677 2 78899999999863 4678999998654
No 156
>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=54.55 E-value=7.5 Score=26.36 Aligned_cols=26 Identities=27% Similarity=0.722 Sum_probs=12.2
Q ss_pred cCCCCCCccccccch--HHHHHHHHHHh
Q 027385 189 KYCCPICSKSVIDMS--RTWKRIDEEMN 214 (224)
Q Consensus 189 ~~~CPiCrksi~dm~--~~~~~lD~~i~ 214 (224)
...||||.+++..-. .+-+.+..+|.
T Consensus 20 ~~~CPlC~r~l~~e~~~~li~~~~~~i~ 47 (54)
T PF04423_consen 20 KGCCPLCGRPLDEEHRQELIKKYKSEIE 47 (54)
T ss_dssp SEE-TTT--EE-HHHHHHHHHHHHHHHH
T ss_pred CCcCCCCCCCCCHHHHHHHHHHHHHHHH
Confidence 338999999998522 23344444443
No 157
>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=53.75 E-value=11 Score=24.32 Aligned_cols=8 Identities=50% Similarity=1.315 Sum_probs=4.2
Q ss_pred cCCCCCCC
Q 027385 80 VCTNCGVN 87 (224)
Q Consensus 80 ~C~~Cg~~ 87 (224)
.||+||..
T Consensus 2 ~Cp~Cg~~ 9 (43)
T PF08271_consen 2 KCPNCGSK 9 (43)
T ss_dssp SBTTTSSS
T ss_pred CCcCCcCC
Confidence 35555554
No 158
>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=53.72 E-value=9.3 Score=34.44 Aligned_cols=48 Identities=25% Similarity=0.607 Sum_probs=22.2
Q ss_pred cCeeEeCCCCcccccc-ccCCCCCCCcceeecCccccc--cCCCCcCeeccCCCC
Q 027385 63 VKQVICSVCDTEQPVA-QVCTNCGVNMGEYFCDICKFY--DDDIEKGQFHCDDCG 114 (224)
Q Consensus 63 ~~~vlC~~C~~~q~~~-~~C~~Cg~~f~~Y~C~~C~l~--dd~~~k~~yHC~~Cg 114 (224)
.+-..|+.|+++-.+. ..|++||..-..-+ .+| ++++.-.++-|+.||
T Consensus 195 ~R~L~Cs~C~t~W~~~R~~Cp~Cg~~~~~~l----~~~~~e~~~~~rve~C~~C~ 245 (290)
T PF04216_consen 195 KRYLHCSLCGTEWRFVRIKCPYCGNTDHEKL----EYFTVEGEPAYRVEVCESCG 245 (290)
T ss_dssp EEEEEETTT--EEE--TTS-TTT---SS-EE----E--------SEEEEEETTTT
T ss_pred cEEEEcCCCCCeeeecCCCCcCCCCCCCcce----eeEecCCCCcEEEEECCccc
Confidence 3688999999998874 68999997765433 223 333344455555554
No 159
>PHA00626 hypothetical protein
Probab=53.13 E-value=8.8 Score=27.25 Aligned_cols=34 Identities=18% Similarity=0.400 Sum_probs=23.0
Q ss_pred eEeCCCCccccccccCCCCCCCcceeecCccccccC
Q 027385 66 VICSVCDTEQPVAQVCTNCGVNMGEYFCDICKFYDD 101 (224)
Q Consensus 66 vlC~~C~~~q~~~~~C~~Cg~~f~~Y~C~~C~l~dd 101 (224)
|.|..|+..+-+ .|..|...-++|-|..|.+++.
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 5666667778888888877754
No 160
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=52.85 E-value=14 Score=28.05 Aligned_cols=49 Identities=27% Similarity=0.409 Sum_probs=33.0
Q ss_pred CCccchhhcccCCCceeEeccCCccCHHHHHHHHhcCcCCCCCCccccccchHHHHHHHHHHhcC--CCCcCcc
Q 027385 152 HCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRTWKRIDEEMNSS--IFFPSFF 223 (224)
Q Consensus 152 ~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~dm~~~~~~lD~~i~~~--pmp~~y~ 223 (224)
.||||.-.|-.|...-+. -..||-||---+|- -.||.+|+.+ |-|.+|.
T Consensus 3 lCP~C~v~l~~~~rs~vE-------------------iD~CPrCrGVWLDr----GELdKli~r~r~pqpa~ys 53 (88)
T COG3809 3 LCPICGVELVMSVRSGVE-------------------IDYCPRCRGVWLDR----GELDKLIERSRYPQPAEYS 53 (88)
T ss_pred ccCcCCceeeeeeecCce-------------------eeeCCccccEeecc----hhHHHHHHHhcCCCCcccC
Confidence 699999888765432221 24799999776664 4577777765 5666664
No 161
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=52.79 E-value=2 Score=38.47 Aligned_cols=49 Identities=27% Similarity=0.531 Sum_probs=38.1
Q ss_pred CCCccchhhccc--CCCceeEec--------cCCccCHHHHHHHHhcCcCCCCCCcccc
Q 027385 151 HHCPICYEYLFD--SLRNTTVMK--------CGHTMHCECYHEMIKRDKYCCPICSKSV 199 (224)
Q Consensus 151 ~~CpICle~lf~--s~~~v~~Lp--------CGH~~H~~C~~~~l~~~~~~CPiCrksi 199 (224)
..|.||...+.. ......++. |||++-..|.+..+.....+||.|+++.
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 569999988652 333345567 9999999999999876668999999863
No 162
>PF15353 HECA: Headcase protein family homologue
Probab=52.62 E-value=7.5 Score=30.85 Aligned_cols=16 Identities=31% Similarity=0.650 Sum_probs=13.8
Q ss_pred ccCCccCHHHHHHHHh
Q 027385 171 KCGHTMHCECYHEMIK 186 (224)
Q Consensus 171 pCGH~~H~~C~~~~l~ 186 (224)
|-|++||+.||++|-.
T Consensus 39 p~~~~MH~~CF~~wE~ 54 (107)
T PF15353_consen 39 PFGQYMHRECFEKWED 54 (107)
T ss_pred CCCCchHHHHHHHHHH
Confidence 3499999999999965
No 163
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=52.54 E-value=8.5 Score=35.48 Aligned_cols=21 Identities=29% Similarity=0.529 Sum_probs=17.9
Q ss_pred ccCCCCCCCcceeecCccccc
Q 027385 79 QVCTNCGVNMGEYFCDICKFY 99 (224)
Q Consensus 79 ~~C~~Cg~~f~~Y~C~~C~l~ 99 (224)
..+...|....+-||.+|+.|
T Consensus 98 ~~~~~~~~~~~~~~C~~C~~~ 118 (309)
T COG5273 98 SRLLDDGKFGTENFCSTCNIY 118 (309)
T ss_pred hhhhhcCccccceeccccccc
Confidence 566778888889999999999
No 164
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=50.07 E-value=8.7 Score=37.70 Aligned_cols=33 Identities=18% Similarity=0.773 Sum_probs=27.3
Q ss_pred CCCCccchhhcccCCCceeEeccCCccCHHHHHHHHh
Q 027385 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIK 186 (224)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~ 186 (224)
+..||||... |. ..++|||||.+...|...-+.
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 5679999987 33 478999999999999987665
No 165
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=49.39 E-value=7.7 Score=28.31 Aligned_cols=28 Identities=36% Similarity=0.692 Sum_probs=22.3
Q ss_pred CeeEeCCCCccccc------cccCCCCCCCccee
Q 027385 64 KQVICSVCDTEQPV------AQVCTNCGVNMGEY 91 (224)
Q Consensus 64 ~~vlC~~C~~~q~~------~~~C~~Cg~~f~~Y 91 (224)
-.|.|.-|+++|.+ ...|..||..++.-
T Consensus 18 l~VkCpdC~N~q~vFshast~V~C~~CG~~l~~P 51 (67)
T COG2051 18 LRVKCPDCGNEQVVFSHASTVVTCLICGTTLAEP 51 (67)
T ss_pred EEEECCCCCCEEEEeccCceEEEecccccEEEec
Confidence 48999999999976 24799999887653
No 166
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=49.05 E-value=15 Score=23.55 Aligned_cols=34 Identities=29% Similarity=0.629 Sum_probs=16.2
Q ss_pred cCCCCCCCcceeecCccccccCCCCcCeeccCCCC
Q 027385 80 VCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCG 114 (224)
Q Consensus 80 ~C~~Cg~~f~~Y~C~~C~l~dd~~~k~~yHC~~Cg 114 (224)
.|++||+.-+-|| .+=--=-|++..-.|.|-+||
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 100001234455566666665
No 167
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=48.21 E-value=11 Score=23.75 Aligned_cols=10 Identities=40% Similarity=0.949 Sum_probs=4.9
Q ss_pred CeeEeCCCCc
Q 027385 64 KQVICSVCDT 73 (224)
Q Consensus 64 ~~vlC~~C~~ 73 (224)
..|.|+.|++
T Consensus 24 ~~v~C~~C~~ 33 (36)
T PF13717_consen 24 RKVRCSKCGH 33 (36)
T ss_pred cEEECCCCCC
Confidence 3555555543
No 168
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=46.68 E-value=11 Score=32.88 Aligned_cols=39 Identities=26% Similarity=0.532 Sum_probs=28.6
Q ss_pred CccchhhcccCCCceeEeccCCccC-HHHHHHHHhcCcCCCCCCccccc
Q 027385 153 CPICYEYLFDSLRNTTVMKCGHTMH-CECYHEMIKRDKYCCPICSKSVI 200 (224)
Q Consensus 153 CpICle~lf~s~~~v~~LpCGH~~H-~~C~~~~l~~~~~~CPiCrksi~ 200 (224)
|-+|.+. ...|..|||.|..+ ..|-.. ..+||||+....
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 8999886 34588899997654 466643 357999997654
No 169
>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=45.56 E-value=16 Score=29.47 Aligned_cols=49 Identities=24% Similarity=0.556 Sum_probs=36.9
Q ss_pred CCCCCcceeecCccccccCCCCcCeeccCCCCcceeCCccceeecCccCcccccc
Q 027385 83 NCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYSTS 137 (224)
Q Consensus 83 ~Cg~~f~~Y~C~~C~l~dd~~~k~~yHC~~CgiCR~G~~~~~fHC~~C~~C~s~~ 137 (224)
.-+......+|..|+.+-- . ...||..||.|..+ --.||.-=|.|+...
T Consensus 41 ~~~~~~~~~~C~~C~~~kp--~-Rs~HC~~C~~CV~~---~DHHC~w~~~cIG~~ 89 (174)
T PF01529_consen 41 EDDENGELKYCSTCKIIKP--P-RSHHCRVCNRCVLR---FDHHCPWLGNCIGRR 89 (174)
T ss_pred ccccCCCCEECcccCCcCC--C-cceecccccccccc---ccccchhhccccccc
Confidence 3557778889999998833 2 47899999999887 345888888887754
No 170
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=45.36 E-value=14 Score=23.40 Aligned_cols=9 Identities=33% Similarity=0.888 Sum_probs=4.2
Q ss_pred eeEeCCCCc
Q 027385 65 QVICSVCDT 73 (224)
Q Consensus 65 ~vlC~~C~~ 73 (224)
.|.|+.|++
T Consensus 25 ~vrC~~C~~ 33 (37)
T PF13719_consen 25 KVRCPKCGH 33 (37)
T ss_pred EEECCCCCc
Confidence 444444443
No 171
>PF14353 CpXC: CpXC protein
Probab=44.32 E-value=21 Score=28.03 Aligned_cols=11 Identities=27% Similarity=0.809 Sum_probs=6.6
Q ss_pred cCCCCCCCcce
Q 027385 80 VCTNCGVNMGE 90 (224)
Q Consensus 80 ~C~~Cg~~f~~ 90 (224)
+||+||+.|..
T Consensus 3 tCP~C~~~~~~ 13 (128)
T PF14353_consen 3 TCPHCGHEFEF 13 (128)
T ss_pred CCCCCCCeeEE
Confidence 56666666643
No 172
>PF15616 TerY-C: TerY-C metal binding domain
Probab=43.77 E-value=23 Score=28.98 Aligned_cols=33 Identities=33% Similarity=0.805 Sum_probs=22.2
Q ss_pred ccCCCCCCCcceeecCcc-cccc-CCCCcCeeccCCCC
Q 027385 79 QVCTNCGVNMGEYFCDIC-KFYD-DDIEKGQFHCDDCG 114 (224)
Q Consensus 79 ~~C~~Cg~~f~~Y~C~~C-~l~d-d~~~k~~yHC~~Cg 114 (224)
..||.||..+|---| .| ||+- +.+ ....|+-||
T Consensus 78 PgCP~CGn~~~fa~C-~CGkl~Ci~g~--~~~~CPwCg 112 (131)
T PF15616_consen 78 PGCPHCGNQYAFAVC-GCGKLFCIDGE--GEVTCPWCG 112 (131)
T ss_pred CCCCCCcChhcEEEe-cCCCEEEeCCC--CCEECCCCC
Confidence 689999999999999 58 5553 211 244555554
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=43.51 E-value=26 Score=34.31 Aligned_cols=46 Identities=28% Similarity=0.717 Sum_probs=30.5
Q ss_pred cCeeEeCCCCccccccccCCCCCCCcc------eeecCccccccCCCCcCeeccCCCCcc
Q 027385 63 VKQVICSVCDTEQPVAQVCTNCGVNMG------EYFCDICKFYDDDIEKGQFHCDDCGIC 116 (224)
Q Consensus 63 ~~~vlC~~C~~~q~~~~~C~~Cg~~f~------~Y~C~~C~l~dd~~~k~~yHC~~CgiC 116 (224)
...++|..|+.. ..|++|+..+. .-.|.-|.+- ...+..|+.||-=
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 57999997774 3456666532 3345567777653
No 174
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=43.00 E-value=38 Score=31.15 Aligned_cols=88 Identities=27% Similarity=0.571 Sum_probs=50.2
Q ss_pred ceeecCcc-ccccCCC---CcCeeccCCCCcceeCCccceeecCccCccccccc-cCcceeecCCCCCCCccchhhcccC
Q 027385 89 GEYFCDIC-KFYDDDI---EKGQFHCDDCGICRIGGRENYFHCKRCGSCYSTSL-RNNHLCIENSMHHHCPICYEYLFDS 163 (224)
Q Consensus 89 ~~Y~C~~C-~l~dd~~---~k~~yHC~~CgiCR~G~~~~~fHC~~C~~C~s~~l-~~~H~C~e~~~~~~CpICle~lf~s 163 (224)
++|-|+.| |-|.... .-+|+||+- .-...|.|..|+-=|..-. ..-|+=.- .....|+||.-. |+
T Consensus 129 ~r~~c~eCgk~ysT~snLsrHkQ~H~~~-------~s~ka~~C~~C~K~YvSmpALkMHirTH-~l~c~C~iCGKa-FS- 198 (279)
T KOG2462|consen 129 PRYKCPECGKSYSTSSNLSRHKQTHRSL-------DSKKAFSCKYCGKVYVSMPALKMHIRTH-TLPCECGICGKA-FS- 198 (279)
T ss_pred Cceeccccccccccccccchhhcccccc-------cccccccCCCCCceeeehHHHhhHhhcc-CCCccccccccc-cc-
Confidence 45555555 4443322 236777743 1245677777776654311 11121111 145689999986 65
Q ss_pred CCceeEeccCCccCHHHHHHHHhc---------CcCCCCCCccccccchH
Q 027385 164 LRNTTVMKCGHTMHCECYHEMIKR---------DKYCCPICSKSVIDMSR 204 (224)
Q Consensus 164 ~~~v~~LpCGH~~H~~C~~~~l~~---------~~~~CPiCrksi~dm~~ 204 (224)
..||.. .-+.||.|+|.+.|-+.
T Consensus 199 ------------------RPWLLQGHiRTHTGEKPF~C~hC~kAFADRSN 230 (279)
T KOG2462|consen 199 ------------------RPWLLQGHIRTHTGEKPFSCPHCGKAFADRSN 230 (279)
T ss_pred ------------------chHHhhcccccccCCCCccCCcccchhcchHH
Confidence 247653 35789999999998653
No 175
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=42.91 E-value=17 Score=24.73 Aligned_cols=9 Identities=44% Similarity=1.531 Sum_probs=5.2
Q ss_pred CeeccCCCC
Q 027385 106 GQFHCDDCG 114 (224)
Q Consensus 106 ~~yHC~~Cg 114 (224)
+.|+|..||
T Consensus 36 ~r~~C~~Cg 44 (50)
T PRK00432 36 DRWHCGKCG 44 (50)
T ss_pred CcEECCCcC
Confidence 455666655
No 176
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=42.78 E-value=17 Score=24.95 Aligned_cols=26 Identities=35% Similarity=0.708 Sum_probs=13.8
Q ss_pred eeecCcc-ccccCCCCcCeeccCCCCc
Q 027385 90 EYFCDIC-KFYDDDIEKGQFHCDDCGI 115 (224)
Q Consensus 90 ~Y~C~~C-~l~dd~~~k~~yHC~~Cgi 115 (224)
.|-|..| +.++.+..+.-.-|+.||.
T Consensus 6 ~Y~C~~Cg~~~~~~~~~~~irCp~Cg~ 32 (49)
T COG1996 6 EYKCARCGREVELDQETRGIRCPYCGS 32 (49)
T ss_pred EEEhhhcCCeeehhhccCceeCCCCCc
Confidence 4444444 2334444556666666664
No 177
>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=42.47 E-value=14 Score=22.04 Aligned_cols=20 Identities=20% Similarity=0.667 Sum_probs=5.6
Q ss_pred CCcceeCCc-cceeecCccCc
Q 027385 113 CGICRIGGR-ENYFHCKRCGS 132 (224)
Q Consensus 113 CgiCR~G~~-~~~fHC~~C~~ 132 (224)
|++|+..+. ..+++|..|+.
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 444444432 25666666654
No 178
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=42.26 E-value=10 Score=25.09 Aligned_cols=40 Identities=25% Similarity=0.615 Sum_probs=26.8
Q ss_pred CccchhhcccCCCceeEeccCCccCHHHHHHHHhcCcCCCCCCccccccch
Q 027385 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMS 203 (224)
Q Consensus 153 CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~dm~ 203 (224)
|+.|.+.+.. ..+.+..=|..+|..|| +|-.|+++|.+.+
T Consensus 1 C~~C~~~I~~--~~~~~~~~~~~~H~~Cf---------~C~~C~~~l~~~~ 40 (58)
T PF00412_consen 1 CARCGKPIYG--TEIVIKAMGKFWHPECF---------KCSKCGKPLNDGD 40 (58)
T ss_dssp BTTTSSBESS--SSEEEEETTEEEETTTS---------BETTTTCBTTTSS
T ss_pred CCCCCCCccC--cEEEEEeCCcEEEcccc---------ccCCCCCccCCCe
Confidence 5667777654 23333356788998765 7888998887643
No 179
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=42.24 E-value=14 Score=20.60 Aligned_cols=16 Identities=31% Similarity=0.696 Sum_probs=12.3
Q ss_pred CCCCCCccccccchHH
Q 027385 190 YCCPICSKSVIDMSRT 205 (224)
Q Consensus 190 ~~CPiCrksi~dm~~~ 205 (224)
+.|.+|.+++.+...+
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 4699999999885543
No 180
>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=41.85 E-value=14 Score=25.97 Aligned_cols=34 Identities=24% Similarity=0.457 Sum_probs=19.7
Q ss_pred eeEeCCCCccccc------cccCCCCCCCcceeecCcccc
Q 027385 65 QVICSVCDTEQPV------AQVCTNCGVNMGEYFCDICKF 98 (224)
Q Consensus 65 ~vlC~~C~~~q~~------~~~C~~Cg~~f~~Y~C~~C~l 98 (224)
.|.|..|.++|.+ ...|..||..+++-.=.+-+|
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 6788888888776 246888888776654444443
No 181
>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=41.71 E-value=8.6 Score=40.27 Aligned_cols=44 Identities=30% Similarity=0.714 Sum_probs=0.0
Q ss_pred cCCCCCCCcceeecCccccccCCCCcCeeccCCCCcceeCCccceeecCccCc
Q 027385 80 VCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGS 132 (224)
Q Consensus 80 ~C~~Cg~~f~~Y~C~~C~l~dd~~~k~~yHC~~CgiCR~G~~~~~fHC~~C~~ 132 (224)
.|++||..--.-.|+.|.-. ....|.|+.||+ .+. -.+|.+|+.
T Consensus 657 ~Cp~Cg~~t~~~~Cp~CG~~----T~~~~~Cp~C~~-~~~----~~~C~~C~~ 700 (900)
T PF03833_consen 657 RCPKCGKETFYNRCPECGSH----TEPVYVCPDCGI-EVE----EDECPKCGR 700 (900)
T ss_dssp -----------------------------------------------------
T ss_pred cCcccCCcchhhcCcccCCc----cccceecccccc-ccC----ccccccccc
Confidence 56666665555556666443 335667776665 222 116666664
No 182
>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=41.52 E-value=13 Score=22.67 Aligned_cols=16 Identities=38% Similarity=1.028 Sum_probs=7.0
Q ss_pred CCCCCCCcceeecCccc
Q 027385 81 CTNCGVNMGEYFCDICK 97 (224)
Q Consensus 81 C~~Cg~~f~~Y~C~~C~ 97 (224)
|.-||. .++|-|+.|.
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 5555555554
No 183
>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=41.44 E-value=21 Score=21.97 Aligned_cols=24 Identities=33% Similarity=0.915 Sum_probs=15.5
Q ss_pred eecCccccccCCCCcCeeccCCCCc
Q 027385 91 YFCDICKFYDDDIEKGQFHCDDCGI 115 (224)
Q Consensus 91 Y~C~~C~l~dd~~~k~~yHC~~Cgi 115 (224)
|-|.+|-+.-+ +.+.++.|+.||.
T Consensus 2 ~~C~~CGy~y~-~~~~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYD-GEEAPWVCPVCGA 25 (33)
T ss_pred EECCCCCCEEC-CCcCCCcCcCCCC
Confidence 66777755422 2457788888875
No 184
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=41.35 E-value=20 Score=21.34 Aligned_cols=10 Identities=20% Similarity=0.610 Sum_probs=3.8
Q ss_pred ccCCCCCCCc
Q 027385 79 QVCTNCGVNM 88 (224)
Q Consensus 79 ~~C~~Cg~~f 88 (224)
+.|+.|+..+
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 4566666554
No 185
>PLN02189 cellulose synthase
Probab=41.31 E-value=24 Score=37.88 Aligned_cols=56 Identities=20% Similarity=0.444 Sum_probs=40.6
Q ss_pred ecCCCCCCCccchhhcccCCCceeEe---ccCCccCHHHHHHHHhcCcCCCCCCccccc
Q 027385 145 IENSMHHHCPICYEYLFDSLRNTTVM---KCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (224)
Q Consensus 145 ~e~~~~~~CpICle~lf~s~~~v~~L---pCGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (224)
+++...+.|.||.|++-...+.-... -||=-+.+.|++--.++.+..||-|+...-
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 45556678999999976433332223 378889999996656667889999998765
No 186
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=40.85 E-value=16 Score=26.14 Aligned_cols=34 Identities=24% Similarity=0.574 Sum_probs=23.4
Q ss_pred cCeeEeCCCCccccccccCCCCCCCcceeecCcccc
Q 027385 63 VKQVICSVCDTEQPVAQVCTNCGVNMGEYFCDICKF 98 (224)
Q Consensus 63 ~~~vlC~~C~~~q~~~~~C~~Cg~~f~~Y~C~~C~l 98 (224)
...-.|..|+.++-. .|..|...=|.|-|++|-|
T Consensus 25 ~v~F~CPnCGe~~I~--Rc~~CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 25 AVKFPCPNCGEVEIY--RCAKCRKLGNPYRCPKCGF 58 (61)
T ss_pred eeEeeCCCCCceeee--hhhhHHHcCCceECCCcCc
Confidence 346677777755433 6777777777888887766
No 187
>KOG4399 consensus C2HC-type Zn-finger protein [General function prediction only]
Probab=39.40 E-value=5.8 Score=36.32 Aligned_cols=73 Identities=27% Similarity=0.642 Sum_probs=54.9
Q ss_pred CCCcceeecCccccccCCCCcCeeccCCCCcceeCCccceeecCccCccccccccCcceeecCCCCCCCccchhhc
Q 027385 85 GVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYSTSLRNNHLCIENSMHHHCPICYEYL 160 (224)
Q Consensus 85 g~~f~~Y~C~~C~l~dd~~~k~~yHC~~CgiCR~G~~~~~fHC~~C~~C~s~~l~~~H~C~e~~~~~~CpICle~l 160 (224)
|..=+-.||+.|-.| ..+-.-||+.|+.|..-.++.|-||..|-.|+-.++-.--.|-.-+...-|-||.+..
T Consensus 199 ~~EE~~~~~~~~~~Y---v~~~~~H~~~~~S~~~~~~~~~~H~~~~~~~~~~~~i~C~~~~~~A~~~~C~iC~~~~ 271 (325)
T KOG4399|consen 199 PTEEGYRFCSPCQRY---VSLENQHCEHCNSCTSKDGRKWNHCFLCKKCVKPSWIHCSICNHCAVKHGCFICGELD 271 (325)
T ss_pred ccccceEEEeehHHH---HHHHhhhchhhcccccchhHHHhHhHHhhhhcccceeeeecccchhhhcceeeccccc
Confidence 344466779999988 4467789999999988777789999999999998874333343345566788998863
No 188
>KOG1312 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=39.39 E-value=10 Score=35.25 Aligned_cols=32 Identities=31% Similarity=0.782 Sum_probs=27.6
Q ss_pred CCCCcceeCCccceeecCccCccccccccCcceee
Q 027385 111 DDCGICRIGGRENYFHCKRCGSCYSTSLRNNHLCI 145 (224)
Q Consensus 111 ~~CgiCR~G~~~~~fHC~~C~~C~s~~l~~~H~C~ 145 (224)
.+|..|++.+.--..||..||.|+..- +|.|+
T Consensus 149 ~kCSTCki~KPARSKHCsiCNrCV~rf---DHHCi 180 (341)
T KOG1312|consen 149 VKCSTCKIRKPARSKHCSICNRCVHRF---DHHCI 180 (341)
T ss_pred CccccccCCCccccccchHHHHHHHHh---ccceE
Confidence 678899999888899999999999864 78886
No 189
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=39.32 E-value=10 Score=31.77 Aligned_cols=25 Identities=28% Similarity=1.016 Sum_probs=18.8
Q ss_pred ceeecCccccccCCCCcCeeccCCCC--cceeC
Q 027385 89 GEYFCDICKFYDDDIEKGQFHCDDCG--ICRIG 119 (224)
Q Consensus 89 ~~Y~C~~C~l~dd~~~k~~yHC~~Cg--iCR~G 119 (224)
.+-||++|-+| ++|-|..|| +|-|+
T Consensus 117 ~r~fCaVCG~~------S~ysC~~CG~kyCsv~ 143 (156)
T KOG3362|consen 117 LRKFCAVCGYD------SKYSCVNCGTKYCSVR 143 (156)
T ss_pred cchhhhhcCCC------chhHHHhcCCceeech
Confidence 46688888855 578888888 67776
No 190
>PLN02436 cellulose synthase A
Probab=38.93 E-value=27 Score=37.63 Aligned_cols=56 Identities=16% Similarity=0.454 Sum_probs=40.8
Q ss_pred ecCCCCCCCccchhhcccCCCceeEe---ccCCccCHHHHHHHHhcCcCCCCCCccccc
Q 027385 145 IENSMHHHCPICYEYLFDSLRNTTVM---KCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (224)
Q Consensus 145 ~e~~~~~~CpICle~lf~s~~~v~~L---pCGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (224)
+.+...+.|.||.|++-.+.+.-... -||=-+.+.|++--.+..+..||-|+...-
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 34456678999999975544433333 477889999996656667889999997765
No 191
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=38.49 E-value=27 Score=33.09 Aligned_cols=80 Identities=25% Similarity=0.540 Sum_probs=53.8
Q ss_pred cccC--CCCcCeeccCCCCcceeCC-ccceeecCccCcccccc---ccCcceeecCCCCCCCccchhhcccCCCceeEec
Q 027385 98 FYDD--DIEKGQFHCDDCGICRIGG-RENYFHCKRCGSCYSTS---LRNNHLCIENSMHHHCPICYEYLFDSLRNTTVMK 171 (224)
Q Consensus 98 l~dd--~~~k~~yHC~~CgiCR~G~-~~~~fHC~~C~~C~s~~---l~~~H~C~e~~~~~~CpICle~lf~s~~~v~~Lp 171 (224)
-||| .+.+.+-||+.| |--|. .|=|| +|+++.+.. --..|.=..|+-...|-.|-+- .++|.+++
T Consensus 168 cWdDVLks~Ripg~Ces~--~~pg~fAEFfF---KC~ah~~~~k~~aa~lhli~~N~~ni~C~~Ctdv----~~~vlvf~ 238 (446)
T KOG0006|consen 168 CWDDVLKSKRIPGVCESC--CTPGLFAEFFF---KCGAHPTSDKETAAALHLIATNSRNITCITCTDV----RSPVLVFQ 238 (446)
T ss_pred chhhhhhcccCccccccc--cCCcchHhhee---hhccCCCccccchhHHHHhhcccccceeEEecCC----ccceEEEe
Confidence 3666 245678888875 33344 35566 566666551 1134545556667789999875 46888999
Q ss_pred cC--CccCHHHHHHHHh
Q 027385 172 CG--HTMHCECYHEMIK 186 (224)
Q Consensus 172 CG--H~~H~~C~~~~l~ 186 (224)
|. |+....||.-|-.
T Consensus 239 Cns~HvtC~dCFr~yc~ 255 (446)
T KOG0006|consen 239 CNSRHVTCLDCFRLYCV 255 (446)
T ss_pred cCCceeehHHhhhhHhh
Confidence 98 9999999987654
No 192
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=38.44 E-value=20 Score=22.36 Aligned_cols=10 Identities=30% Similarity=1.066 Sum_probs=5.1
Q ss_pred cCeeccCCCC
Q 027385 105 KGQFHCDDCG 114 (224)
Q Consensus 105 k~~yHC~~Cg 114 (224)
.++-.|..||
T Consensus 15 ~~~irC~~CG 24 (32)
T PF03604_consen 15 GDPIRCPECG 24 (32)
T ss_dssp SSTSSBSSSS
T ss_pred CCcEECCcCC
Confidence 3444555555
No 193
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=38.22 E-value=46 Score=28.22 Aligned_cols=33 Identities=27% Similarity=0.564 Sum_probs=20.4
Q ss_pred CcCCCCCCccccc--cch-------HHHHHHHHHHhcCCCCc
Q 027385 188 DKYCCPICSKSVI--DMS-------RTWKRIDEEMNSSIFFP 220 (224)
Q Consensus 188 ~~~~CPiCrksi~--dm~-------~~~~~lD~~i~~~pmp~ 220 (224)
..++||.|+..+. |-+ ...+.|+.++...+.+.
T Consensus 135 ~~F~Cp~Cg~~L~~~dn~~~~~~l~~~I~~l~~~~~~~~~~~ 176 (178)
T PRK06266 135 YGFRCPQCGEMLEEYDNSELIKELKEQIKELEEELKLNPLFS 176 (178)
T ss_pred cCCcCCCCCCCCeecccHHHHHHHHHHHHHHHHHhccccccc
Confidence 4799999999987 323 34444555555544443
No 194
>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=38.04 E-value=18 Score=22.27 Aligned_cols=23 Identities=26% Similarity=0.710 Sum_probs=10.2
Q ss_pred cCCCCCCCcceeecCccccccCCCCcCeeccCCCC
Q 027385 80 VCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCG 114 (224)
Q Consensus 80 ~C~~Cg~~f~~Y~C~~C~l~dd~~~k~~yHC~~Cg 114 (224)
.|+.|+..++- .+..+|-|+.||
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 234677788776
No 195
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=37.69 E-value=29 Score=24.40 Aligned_cols=21 Identities=19% Similarity=0.542 Sum_probs=16.8
Q ss_pred CcCCCCCCccccccchHHHHH
Q 027385 188 DKYCCPICSKSVIDMSRTWKR 208 (224)
Q Consensus 188 ~~~~CPiCrksi~dm~~~~~~ 208 (224)
.++.||.|+-++---...|+.
T Consensus 13 v~~~Cp~cGipthcS~ehw~~ 33 (55)
T PF13824_consen 13 VNFECPDCGIPTHCSEEHWED 33 (55)
T ss_pred cCCcCCCCCCcCccCHHHHHH
Confidence 579999999998766667754
No 196
>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=37.48 E-value=27 Score=21.87 Aligned_cols=21 Identities=19% Similarity=0.363 Sum_probs=15.5
Q ss_pred ccCCCCCCCcceeecCccccc
Q 027385 79 QVCTNCGVNMGEYFCDICKFY 99 (224)
Q Consensus 79 ~~C~~Cg~~f~~Y~C~~C~l~ 99 (224)
..|..++.....|||..|+.+
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 467888887788888888754
No 197
>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=37.28 E-value=43 Score=21.91 Aligned_cols=9 Identities=44% Similarity=1.154 Sum_probs=5.4
Q ss_pred ccCCCCCCC
Q 027385 79 QVCTNCGVN 87 (224)
Q Consensus 79 ~~C~~Cg~~ 87 (224)
.+||.||..
T Consensus 19 ~~CP~Cg~~ 27 (46)
T PF12760_consen 19 FVCPHCGST 27 (46)
T ss_pred CCCCCCCCe
Confidence 456666665
No 198
>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=37.20 E-value=19 Score=29.13 Aligned_cols=36 Identities=25% Similarity=0.591 Sum_probs=24.7
Q ss_pred CcCeeccCCCCcceeCCccceeecCccCccccccccCcceee
Q 027385 104 EKGQFHCDDCGICRIGGRENYFHCKRCGSCYSTSLRNNHLCI 145 (224)
Q Consensus 104 ~k~~yHC~~CgiCR~G~~~~~fHC~~C~~C~s~~l~~~H~C~ 145 (224)
....-.|.. |++-....-.||..||.|+-.- +|-|.
T Consensus 45 ~~~~~~C~~---C~~~kp~Rs~HC~~C~~CV~~~---DHHC~ 80 (174)
T PF01529_consen 45 NGELKYCST---CKIIKPPRSHHCRVCNRCVLRF---DHHCP 80 (174)
T ss_pred CCCCEECcc---cCCcCCCcceeccccccccccc---cccch
Confidence 334444554 5555566799999999998864 67664
No 199
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=36.22 E-value=29 Score=22.76 Aligned_cols=8 Identities=50% Similarity=1.510 Sum_probs=4.1
Q ss_pred eeccCCCC
Q 027385 107 QFHCDDCG 114 (224)
Q Consensus 107 ~yHC~~Cg 114 (224)
.|-|+.||
T Consensus 20 ~~vC~~Cg 27 (52)
T smart00661 20 RFVCRKCG 27 (52)
T ss_pred EEECCcCC
Confidence 45555554
No 200
>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=36.20 E-value=24 Score=22.39 Aligned_cols=24 Identities=33% Similarity=0.683 Sum_probs=19.3
Q ss_pred CccchhhcccCCCceeEe-ccCCcc
Q 027385 153 CPICYEYLFDSLRNTTVM-KCGHTM 176 (224)
Q Consensus 153 CpICle~lf~s~~~v~~L-pCGH~~ 176 (224)
|++|...+|.+.+....- .|||.+
T Consensus 11 C~~C~~~~~~~~dG~~yC~~cG~~~ 35 (36)
T PF11781_consen 11 CPVCGSRWFYSDDGFYYCDRCGHQS 35 (36)
T ss_pred CCCCCCeEeEccCCEEEhhhCceEc
Confidence 999999988877777665 889864
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=36.15 E-value=17 Score=28.62 Aligned_cols=11 Identities=18% Similarity=0.661 Sum_probs=5.7
Q ss_pred cccCCCCCCCc
Q 027385 78 AQVCTNCGVNM 88 (224)
Q Consensus 78 ~~~C~~Cg~~f 88 (224)
...|.+||..|
T Consensus 70 ~~~C~~Cg~~~ 80 (115)
T TIGR00100 70 ECECEDCSEEV 80 (115)
T ss_pred EEEcccCCCEE
Confidence 34555555444
No 202
>PRK00420 hypothetical protein; Validated
Probab=36.14 E-value=25 Score=28.05 Aligned_cols=22 Identities=23% Similarity=0.550 Sum_probs=14.1
Q ss_pred cccCCCCCCCcc-----eeecCccccc
Q 027385 78 AQVCTNCGVNMG-----EYFCDICKFY 99 (224)
Q Consensus 78 ~~~C~~Cg~~f~-----~Y~C~~C~l~ 99 (224)
+..||.||.+|- ..||++|.-.
T Consensus 23 ~~~CP~Cg~pLf~lk~g~~~Cp~Cg~~ 49 (112)
T PRK00420 23 SKHCPVCGLPLFELKDGEVVCPVHGKV 49 (112)
T ss_pred cCCCCCCCCcceecCCCceECCCCCCe
Confidence 357888888764 3566666433
No 203
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=36.12 E-value=40 Score=31.32 Aligned_cols=26 Identities=27% Similarity=0.761 Sum_probs=21.3
Q ss_pred ccCeeEeCCCCcccccc-ccCCCCCCC
Q 027385 62 DVKQVICSVCDTEQPVA-QVCTNCGVN 87 (224)
Q Consensus 62 ~~~~vlC~~C~~~q~~~-~~C~~Cg~~ 87 (224)
..+-..|+.|+++-.+. ..|++||..
T Consensus 209 G~RyL~CslC~teW~~~R~~C~~Cg~~ 235 (309)
T PRK03564 209 GLRYLHCNLCESEWHVVRVKCSNCEQS 235 (309)
T ss_pred CceEEEcCCCCCcccccCccCCCCCCC
Confidence 34688999999998874 689999964
No 204
>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=35.87 E-value=27 Score=21.75 Aligned_cols=22 Identities=27% Similarity=0.757 Sum_probs=12.8
Q ss_pred eEeCCCCcccc---ccccCCCCCCC
Q 027385 66 VICSVCDTEQP---VAQVCTNCGVN 87 (224)
Q Consensus 66 vlC~~C~~~q~---~~~~C~~Cg~~ 87 (224)
-+|..|+.... .-..||.||+.
T Consensus 3 ~~C~~CG~i~~g~~~p~~CP~Cg~~ 27 (34)
T cd00729 3 WVCPVCGYIHEGEEAPEKCPICGAP 27 (34)
T ss_pred EECCCCCCEeECCcCCCcCcCCCCc
Confidence 45677765532 22467777764
No 205
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=35.43 E-value=23 Score=24.49 Aligned_cols=19 Identities=32% Similarity=0.933 Sum_probs=10.8
Q ss_pred ccCCCCCC--Cc----ceeecCccc
Q 027385 79 QVCTNCGV--NM----GEYFCDICK 97 (224)
Q Consensus 79 ~~C~~Cg~--~f----~~Y~C~~C~ 97 (224)
..||+||. -| .+|.|.+|.
T Consensus 20 ~~CPrCG~gvfmA~H~dR~~CGkCg 44 (51)
T COG1998 20 RFCPRCGPGVFMADHKDRWACGKCG 44 (51)
T ss_pred ccCCCCCCcchhhhcCceeEecccc
Confidence 46888883 23 345555553
No 206
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=35.37 E-value=25 Score=32.31 Aligned_cols=94 Identities=21% Similarity=0.596 Sum_probs=0.0
Q ss_pred ccChhhHHhhhcCCCCCCCcccccccccCeeEeCCCCccccccccCCCCCCCcceeecCccc-cccCCC---CcCeeccC
Q 027385 36 FDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVAQVCTNCGVNMGEYFCDICK-FYDDDI---EKGQFHCD 111 (224)
Q Consensus 36 y~Cr~CHde~~~~~~~~~~~H~~~r~~~~~vlC~~C~~~q~~~~~C~~Cg~~f~~Y~C~~C~-l~dd~~---~k~~yHC~ 111 (224)
|.|.+|-..+++ ..--+...++||-.|+..-.. +.-++|-|.+|+ +.|+++ .-++||=
T Consensus 100 F~Cd~Cn~~Lad---------~gf~rnqgr~LC~~Cn~k~Ka--------~~~g~YvC~KCh~~iD~~~l~fr~d~yH~- 161 (332)
T KOG2272|consen 100 FRCDLCNKHLAD---------QGFYRNQGRALCRECNQKEKA--------KGRGRYVCQKCHAHIDEQPLTFRGDPYHP- 161 (332)
T ss_pred chhHHHHHHHhh---------hhhHhhcchHHhhhhhhhhcc--------cccceeehhhhhhhcccccccccCCCCCc-
Q ss_pred CCCcceeCCccceeecCccCccccc---cccCcceeecCCCCCCCccchh
Q 027385 112 DCGICRIGGRENYFHCKRCGSCYST---SLRNNHLCIENSMHHHCPICYE 158 (224)
Q Consensus 112 ~CgiCR~G~~~~~fHC~~C~~C~s~---~l~~~H~C~e~~~~~~CpICle 158 (224)
.-|.|.+||-=+.. ++++.--|..=-...-+|||..
T Consensus 162 -----------yHFkCt~C~keL~sdaRevk~eLyClrChD~mgipiCga 200 (332)
T KOG2272|consen 162 -----------YHFKCTTCGKELTSDAREVKGELYCLRCHDKMGIPICGA 200 (332)
T ss_pred -----------cceecccccccccchhhhhccceeccccccccCCccccc
No 207
>cd02337 ZZ_CBP Zinc finger, ZZ type. Zinc finger present in CBP/p300 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. CREB-binding protein (CBP) is a large multidomain protein that provides binding sites for transcriptional coactivators, the role of the ZZ domain in CBP/p300 is unclear.
Probab=34.83 E-value=29 Score=22.56 Aligned_cols=20 Identities=25% Similarity=0.861 Sum_probs=11.3
Q ss_pred eccCCCCcceeCCccceeecCccC
Q 027385 108 FHCDDCGICRIGGRENYFHCKRCG 131 (224)
Q Consensus 108 yHC~~CgiCR~G~~~~~fHC~~C~ 131 (224)
|+|+.|+. +++ ..+||..|.
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 55666655 332 566776663
No 208
>smart00355 ZnF_C2H2 zinc finger.
Probab=33.96 E-value=37 Score=17.90 Aligned_cols=16 Identities=38% Similarity=0.698 Sum_probs=12.2
Q ss_pred CCCCCCccccccchHH
Q 027385 190 YCCPICSKSVIDMSRT 205 (224)
Q Consensus 190 ~~CPiCrksi~dm~~~ 205 (224)
+.|+.|.+++...+..
T Consensus 1 ~~C~~C~~~f~~~~~l 16 (26)
T smart00355 1 YRCPECGKVFKSKSAL 16 (26)
T ss_pred CCCCCCcchhCCHHHH
Confidence 5799999998875443
No 209
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=33.10 E-value=27 Score=34.43 Aligned_cols=44 Identities=23% Similarity=0.704 Sum_probs=34.7
Q ss_pred CCCCCCccchhhcccCCCceeEeccCCccCHHHHHHHHhcCcCCCCCCccccc
Q 027385 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (224)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (224)
..+.+|.||++.+ ..+.-+|- |..|+.+|+. .+..||+|++.+.
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 4567999999997 23444555 9999999997 4689999998876
No 210
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=32.79 E-value=19 Score=20.87 Aligned_cols=12 Identities=25% Similarity=0.664 Sum_probs=9.4
Q ss_pred ccCCCCCCCcce
Q 027385 79 QVCTNCGVNMGE 90 (224)
Q Consensus 79 ~~C~~Cg~~f~~ 90 (224)
..|+.||..|+.
T Consensus 3 ~~C~~CgR~F~~ 14 (25)
T PF13913_consen 3 VPCPICGRKFNP 14 (25)
T ss_pred CcCCCCCCEECH
Confidence 368999998864
No 211
>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=32.72 E-value=33 Score=23.17 Aligned_cols=7 Identities=71% Similarity=1.872 Sum_probs=3.1
Q ss_pred ccCCCCc
Q 027385 109 HCDDCGI 115 (224)
Q Consensus 109 HC~~Cgi 115 (224)
.|+.|+.
T Consensus 2 ~Cd~C~~ 8 (48)
T cd02341 2 KCDSCGI 8 (48)
T ss_pred CCCCCCC
Confidence 3444443
No 212
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=32.53 E-value=20 Score=33.72 Aligned_cols=21 Identities=38% Similarity=0.917 Sum_probs=16.4
Q ss_pred ccCCCCCCCcceeecCccccc
Q 027385 79 QVCTNCGVNMGEYFCDICKFY 99 (224)
Q Consensus 79 ~~C~~Cg~~f~~Y~C~~C~l~ 99 (224)
..|+-||+++++|.|+-|+|.
T Consensus 8 ~~C~ic~vq~~~YtCPRCn~~ 28 (383)
T KOG4317|consen 8 LACGICGVQKREYTCPRCNLL 28 (383)
T ss_pred eeccccccccccccCCCCCcc
Confidence 357778888888888888865
No 213
>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=31.93 E-value=35 Score=21.14 Aligned_cols=10 Identities=30% Similarity=0.737 Sum_probs=5.0
Q ss_pred eeEeCCCCcc
Q 027385 65 QVICSVCDTE 74 (224)
Q Consensus 65 ~vlC~~C~~~ 74 (224)
.|.|+.|++.
T Consensus 25 ~v~C~~C~~~ 34 (38)
T TIGR02098 25 KVRCGKCGHV 34 (38)
T ss_pred EEECCCCCCE
Confidence 4555555543
No 214
>PRK14873 primosome assembly protein PriA; Provisional
Probab=31.24 E-value=43 Score=34.18 Aligned_cols=23 Identities=26% Similarity=0.689 Sum_probs=18.1
Q ss_pred CeeEeCCCCccccccccCCCCCCCcce
Q 027385 64 KQVICSVCDTEQPVAQVCTNCGVNMGE 90 (224)
Q Consensus 64 ~~vlC~~C~~~q~~~~~C~~Cg~~f~~ 90 (224)
..++|..|+.. ..|++|+..+.-
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 57889999866 579999888753
No 215
>PLN00209 ribosomal protein S27; Provisional
Probab=30.87 E-value=32 Score=26.34 Aligned_cols=37 Identities=19% Similarity=0.346 Sum_probs=28.2
Q ss_pred CeeEeCCCCccccc------cccCCCCCCCcceeecCcccccc
Q 027385 64 KQVICSVCDTEQPV------AQVCTNCGVNMGEYFCDICKFYD 100 (224)
Q Consensus 64 ~~vlC~~C~~~q~~------~~~C~~Cg~~f~~Y~C~~C~l~d 100 (224)
-.|.|..|..+|.+ ...|..||..+++-.=++.+|-+
T Consensus 35 m~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~~PTGGKa~l~~ 77 (86)
T PLN00209 35 MDVKCQGCFNITTVFSHSQTVVVCGSCQTVLCQPTGGKARLTE 77 (86)
T ss_pred EEEECCCCCCeeEEEecCceEEEccccCCEeeccCCCCeEecC
Confidence 37899999999987 24799999988876666655543
No 216
>KOG3005 consensus GIY-YIG type nuclease [General function prediction only]
Probab=30.83 E-value=58 Score=29.89 Aligned_cols=64 Identities=17% Similarity=0.359 Sum_probs=40.8
Q ss_pred CCCccchhhcccCCCceeE---eccCCccCHHHHHHHHhc--------CcCCCCCCccccccchHHHHHHHHHHhcCCCC
Q 027385 151 HHCPICYEYLFDSLRNTTV---MKCGHTMHCECYHEMIKR--------DKYCCPICSKSVIDMSRTWKRIDEEMNSSIFF 219 (224)
Q Consensus 151 ~~CpICle~lf~s~~~v~~---LpCGH~~H~~C~~~~l~~--------~~~~CPiCrksi~dm~~~~~~lD~~i~~~pmp 219 (224)
..|-+|.+.+.+....+.. -.|+=..|..|+.+.+.. ....||.|++.+. |..|=.++-++|++
T Consensus 183 ~~celc~~ei~e~~~~~a~c~~~~c~~~~h~~CLa~~~~~~e~g~~~p~eg~cp~C~~~~~-----w~~lv~~~~~t~~e 257 (276)
T KOG3005|consen 183 VECELCEKEILETDWSRATCPNPDCDSLNHLTCLAEELLEVEPGQLIPLEGMCPKCEKFLS-----WTTLVDLDFMTPTE 257 (276)
T ss_pred hhhHHHHHHhccccceeccCCCCCCCchhhhhhhhHHHhccCCCceeccCCCCCchhceee-----HHHHHHHHhcCchh
Confidence 5799999987442222111 248889999999984432 2467999999665 54443344455554
No 217
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=30.81 E-value=16 Score=38.29 Aligned_cols=46 Identities=26% Similarity=0.676 Sum_probs=0.0
Q ss_pred CeeEeCCCCccccccccCCCCCCC-cceeecCccccccCCCCcCeeccCCCCc
Q 027385 64 KQVICSVCDTEQPVAQVCTNCGVN-MGEYFCDICKFYDDDIEKGQFHCDDCGI 115 (224)
Q Consensus 64 ~~vlC~~C~~~q~~~~~C~~Cg~~-f~~Y~C~~C~l~dd~~~k~~yHC~~Cgi 115 (224)
-.-.|..|+++ ++...|+.||.. .-.|+|+.|+.--++. .|+.||.
T Consensus 654 ~~r~Cp~Cg~~-t~~~~Cp~CG~~T~~~~~Cp~C~~~~~~~-----~C~~C~~ 700 (900)
T PF03833_consen 654 GRRRCPKCGKE-TFYNRCPECGSHTEPVYVCPDCGIEVEED-----ECPKCGR 700 (900)
T ss_dssp -----------------------------------------------------
T ss_pred ecccCcccCCc-chhhcCcccCCccccceeccccccccCcc-----ccccccc
Confidence 45578888877 667788888865 4567788887643221 7888774
No 218
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=30.63 E-value=27 Score=26.67 Aligned_cols=36 Identities=19% Similarity=0.390 Sum_probs=26.9
Q ss_pred CeeEeCCCCccccc------cccCCCCCCCcceeecCccccc
Q 027385 64 KQVICSVCDTEQPV------AQVCTNCGVNMGEYFCDICKFY 99 (224)
Q Consensus 64 ~~vlC~~C~~~q~~------~~~C~~Cg~~f~~Y~C~~C~l~ 99 (224)
-.|.|..|..+|.+ ...|..||..+++-.=.+.+|-
T Consensus 34 m~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~~PTGGKa~l~ 75 (85)
T PTZ00083 34 MDVKCPGCSQITTVFSHAQTVVLCGGCSSQLCQPTGGKAKLT 75 (85)
T ss_pred EEEECCCCCCeeEEEecCceEEEccccCCEeeccCCCCeEec
Confidence 37899999999887 2479999988877655555554
No 219
>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=30.62 E-value=37 Score=22.19 Aligned_cols=9 Identities=33% Similarity=0.932 Sum_probs=4.8
Q ss_pred ceeecCccC
Q 027385 123 NYFHCKRCG 131 (224)
Q Consensus 123 ~~fHC~~C~ 131 (224)
..|+|..|.
T Consensus 13 ~r~~C~~C~ 21 (46)
T cd02249 13 VRYHCLVCE 21 (46)
T ss_pred CEEECCCCC
Confidence 456665553
No 220
>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=30.54 E-value=36 Score=19.50 Aligned_cols=15 Identities=20% Similarity=0.603 Sum_probs=11.9
Q ss_pred cCCCCCCccccccch
Q 027385 189 KYCCPICSKSVIDMS 203 (224)
Q Consensus 189 ~~~CPiCrksi~dm~ 203 (224)
++.|++|.+.+.+..
T Consensus 1 q~~C~~C~k~f~~~~ 15 (27)
T PF12171_consen 1 QFYCDACDKYFSSEN 15 (27)
T ss_dssp -CBBTTTTBBBSSHH
T ss_pred CCCcccCCCCcCCHH
Confidence 368999999998854
No 221
>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=29.86 E-value=32 Score=23.37 Aligned_cols=21 Identities=24% Similarity=0.896 Sum_probs=12.8
Q ss_pred cccCC--CCCCC------cceeecCcccc
Q 027385 78 AQVCT--NCGVN------MGEYFCDICKF 98 (224)
Q Consensus 78 ~~~C~--~Cg~~------f~~Y~C~~C~l 98 (224)
...|| .||.. ++++||.+|.+
T Consensus 18 rk~CP~~~CG~GvFMA~H~dR~~CGKCg~ 46 (47)
T PF01599_consen 18 RKECPSPRCGAGVFMAEHKDRHYCGKCGY 46 (47)
T ss_dssp SEE-TSTTTTSSSEEEE-SSEEEETTTSS
T ss_pred hhcCCCcccCCceEeeecCCCccCCCccc
Confidence 35688 78774 26677777754
No 222
>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=29.57 E-value=29 Score=26.97 Aligned_cols=19 Identities=26% Similarity=0.728 Sum_probs=14.2
Q ss_pred EeCCCCcccccc----ccCCCCC
Q 027385 67 ICSVCDTEQPVA----QVCTNCG 85 (224)
Q Consensus 67 lC~~C~~~q~~~----~~C~~Cg 85 (224)
-|..|+..++.. +.|+||+
T Consensus 5 AC~~C~~I~~~~qf~~~gCpnC~ 27 (98)
T cd07973 5 ACLLCSLIKTEDQFERDGCPNCE 27 (98)
T ss_pred hhccCCcccccccccCCCCCCCc
Confidence 588888887754 4788886
No 223
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=29.42 E-value=33 Score=28.71 Aligned_cols=12 Identities=25% Similarity=0.839 Sum_probs=6.8
Q ss_pred cCCCCCCCccee
Q 027385 80 VCTNCGVNMGEY 91 (224)
Q Consensus 80 ~C~~Cg~~f~~Y 91 (224)
.|++||..|+.|
T Consensus 30 ~c~~c~~~f~~~ 41 (154)
T PRK00464 30 ECLACGKRFTTF 41 (154)
T ss_pred eccccCCcceEe
Confidence 455555555555
No 224
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=29.12 E-value=31 Score=30.98 Aligned_cols=20 Identities=25% Similarity=0.858 Sum_probs=15.5
Q ss_pred cccCCCCCCCc--------ceeecCccc
Q 027385 78 AQVCTNCGVNM--------GEYFCDICK 97 (224)
Q Consensus 78 ~~~C~~Cg~~f--------~~Y~C~~C~ 97 (224)
++.|+.||..+ +.|||+.|.
T Consensus 244 g~pCprCG~~I~~~~~~gR~t~~CP~CQ 271 (272)
T PRK14810 244 GEPCLNCKTPIRRVVVAGRSSHYCPHCQ 271 (272)
T ss_pred CCcCCCCCCeeEEEEECCCccEECcCCc
Confidence 46899999877 568888874
No 225
>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=28.26 E-value=41 Score=22.06 Aligned_cols=13 Identities=23% Similarity=0.772 Sum_probs=8.0
Q ss_pred cccCCCCCCCcce
Q 027385 78 AQVCTNCGVNMGE 90 (224)
Q Consensus 78 ~~~C~~Cg~~f~~ 90 (224)
+..|+.||.++-+
T Consensus 17 ~~~Cp~C~~PL~~ 29 (41)
T PF06677_consen 17 DEHCPDCGTPLMR 29 (41)
T ss_pred cCccCCCCCeeEE
Confidence 3567777766633
No 226
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=28.06 E-value=54 Score=25.53 Aligned_cols=32 Identities=31% Similarity=0.644 Sum_probs=21.8
Q ss_pred cceeecCccC-ccccccccCcceeecCCCCCCCccchhh
Q 027385 122 ENYFHCKRCG-SCYSTSLRNNHLCIENSMHHHCPICYEY 159 (224)
Q Consensus 122 ~~~fHC~~C~-~C~s~~l~~~H~C~e~~~~~~CpICle~ 159 (224)
..+|+|..|| .-+++.+ .+ +..+..||+|..+
T Consensus 19 pt~f~CP~Cge~~v~v~~--~k----~~~h~~C~~CG~y 51 (99)
T PRK14892 19 PKIFECPRCGKVSISVKI--KK----NIAIITCGNCGLY 51 (99)
T ss_pred CcEeECCCCCCeEeeeec--CC----CcceEECCCCCCc
Confidence 5688888888 3333333 12 5667889999987
No 227
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=27.68 E-value=37 Score=24.28 Aligned_cols=20 Identities=25% Similarity=0.693 Sum_probs=12.8
Q ss_pred EeCCCCccccccccCCCCCCC
Q 027385 67 ICSVCDTEQPVAQVCTNCGVN 87 (224)
Q Consensus 67 lC~~C~~~q~~~~~C~~Cg~~ 87 (224)
.|..|+..++ .+.||+||..
T Consensus 5 AC~~C~~i~~-~~~CP~Cgs~ 24 (61)
T PRK08351 5 ACRHCHYITT-EDRCPVCGSR 24 (61)
T ss_pred hhhhCCcccC-CCcCCCCcCC
Confidence 4666766653 3468888764
No 228
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=27.55 E-value=42 Score=19.93 Aligned_cols=16 Identities=19% Similarity=0.617 Sum_probs=12.9
Q ss_pred cCCCCCCccccccchH
Q 027385 189 KYCCPICSKSVIDMSR 204 (224)
Q Consensus 189 ~~~CPiCrksi~dm~~ 204 (224)
.+.|.+|.+++.+...
T Consensus 3 ~~~C~~C~~~~~~~~~ 18 (35)
T smart00451 3 GFYCKLCNVTFTDEIS 18 (35)
T ss_pred CeEccccCCccCCHHH
Confidence 5789999999996544
No 229
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=27.54 E-value=39 Score=27.13 Aligned_cols=27 Identities=22% Similarity=0.618 Sum_probs=18.9
Q ss_pred ccCeeEeCCCCccccc---cccCCCCCCCc
Q 027385 62 DVKQVICSVCDTEQPV---AQVCTNCGVNM 88 (224)
Q Consensus 62 ~~~~vlC~~C~~~q~~---~~~C~~Cg~~f 88 (224)
.+..|.|..|+++-.. .+.|.+|++++
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 4567888888876433 46788888776
No 230
>PRK10445 endonuclease VIII; Provisional
Probab=27.54 E-value=36 Score=30.48 Aligned_cols=20 Identities=30% Similarity=0.894 Sum_probs=15.1
Q ss_pred cccCCCCCCCc--------ceeecCccc
Q 027385 78 AQVCTNCGVNM--------GEYFCDICK 97 (224)
Q Consensus 78 ~~~C~~Cg~~f--------~~Y~C~~C~ 97 (224)
++.|+.||... +.|||+.|.
T Consensus 235 g~~Cp~Cg~~I~~~~~~gR~t~~CP~CQ 262 (263)
T PRK10445 235 GEACERCGGIIEKTTLSSRPFYWCPGCQ 262 (263)
T ss_pred CCCCCCCCCEeEEEEECCCCcEECCCCc
Confidence 56899999887 567777763
No 231
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=27.51 E-value=21 Score=35.91 Aligned_cols=26 Identities=27% Similarity=0.775 Sum_probs=19.7
Q ss_pred eeEeccCCccCHHHHHHHHhcCcCCCCCCc
Q 027385 167 TTVMKCGHTMHCECYHEMIKRDKYCCPICS 196 (224)
Q Consensus 167 v~~LpCGH~~H~~C~~~~l~~~~~~CPiCr 196 (224)
.+-..||++||+.|+.. .+..||.|-
T Consensus 532 ~rC~~C~avfH~~C~~r----~s~~CPrC~ 557 (580)
T KOG1829|consen 532 RRCSTCLAVFHKKCLRR----KSPCCPRCE 557 (580)
T ss_pred eeHHHHHHHHHHHHHhc----cCCCCCchH
Confidence 34578999999999853 345599985
No 232
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=27.35 E-value=36 Score=30.60 Aligned_cols=20 Identities=40% Similarity=1.102 Sum_probs=15.5
Q ss_pred cccCCCCCCCc--------ceeecCccc
Q 027385 78 AQVCTNCGVNM--------GEYFCDICK 97 (224)
Q Consensus 78 ~~~C~~Cg~~f--------~~Y~C~~C~ 97 (224)
++.|+.||..+ +.|||+.|.
T Consensus 235 g~pC~~Cg~~I~~~~~~gR~ty~Cp~CQ 262 (269)
T PRK14811 235 GQPCPRCGTPIEKIVVGGRGTHFCPQCQ 262 (269)
T ss_pred cCCCCcCCCeeEEEEECCCCcEECCCCc
Confidence 45799998877 568888885
No 233
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=27.17 E-value=39 Score=21.09 Aligned_cols=11 Identities=27% Similarity=0.486 Sum_probs=5.2
Q ss_pred eEeCCCCcccc
Q 027385 66 VICSVCDTEQP 76 (224)
Q Consensus 66 vlC~~C~~~q~ 76 (224)
.+|..|+...-
T Consensus 4 ~~C~~C~~~~i 14 (33)
T PF08792_consen 4 KKCSKCGGNGI 14 (33)
T ss_pred eEcCCCCCCeE
Confidence 34555554443
No 234
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=26.99 E-value=24 Score=23.01 Aligned_cols=43 Identities=28% Similarity=0.574 Sum_probs=28.1
Q ss_pred CccchhhcccCCCceeEeccCCccCHHHHHHHHh-----cCcCCCCCCc
Q 027385 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIK-----RDKYCCPICS 196 (224)
Q Consensus 153 CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~-----~~~~~CPiCr 196 (224)
|+||... .+....+.=-.|+-.||..|+..-+. ...+.||.|+
T Consensus 2 C~vC~~~-~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~ 49 (51)
T PF00628_consen 2 CPVCGQS-DDDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCR 49 (51)
T ss_dssp BTTTTSS-CTTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHH
T ss_pred CcCCCCc-CCCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCc
Confidence 7888883 33223233347899999999976543 1267888775
No 235
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.38 E-value=35 Score=24.80 Aligned_cols=26 Identities=31% Similarity=0.658 Sum_probs=16.8
Q ss_pred cccccCCCCCCCcce-------eecC-ccccccC
Q 027385 76 PVAQVCTNCGVNMGE-------YFCD-ICKFYDD 101 (224)
Q Consensus 76 ~~~~~C~~Cg~~f~~-------Y~C~-~C~l~dd 101 (224)
..+..|+-||+.... -||+ -|++.|-
T Consensus 5 ~~~v~CP~Cgkpv~w~~~s~frPFCSkRCklIDL 38 (65)
T COG3024 5 RITVPCPTCGKPVVWGEESPFRPFCSKRCKLIDL 38 (65)
T ss_pred cccccCCCCCCcccccccCCcCcchhHhhhhcch
Confidence 345578888877643 4565 4888764
No 236
>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=26.15 E-value=31 Score=21.40 Aligned_cols=23 Identities=35% Similarity=0.752 Sum_probs=11.5
Q ss_pred CeeEeCCCCccc-cccccCCCCCC
Q 027385 64 KQVICSVCDTEQ-PVAQVCTNCGV 86 (224)
Q Consensus 64 ~~vlC~~C~~~q-~~~~~C~~Cg~ 86 (224)
..-.|..|++.+ |+...|++||.
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 455677787764 45677777764
No 237
>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=26.10 E-value=53 Score=27.97 Aligned_cols=36 Identities=33% Similarity=0.886 Sum_probs=21.5
Q ss_pred eeEeCCCCccccccccCCCCCCCc-----------ceeecCcccccc
Q 027385 65 QVICSVCDTEQPVAQVCTNCGVNM-----------GEYFCDICKFYD 100 (224)
Q Consensus 65 ~vlC~~C~~~q~~~~~C~~Cg~~f-----------~~Y~C~~C~l~d 100 (224)
...|..|...+.+...|.+|...+ +.+||+.|-+.|
T Consensus 111 ~~aCs~C~r~~~~~~~C~~Cdr~lC~~C~~~C~~C~~~~Cs~Cs~~~ 157 (175)
T PF05458_consen 111 SRACSVCQRTQRIKSVCSQCDRALCESCIRSCSSCSEVFCSLCSTVN 157 (175)
T ss_pred CccCcCCcCCCCCCccccccCcHHHHHHHhhhhchhhhhhcCccccc
Confidence 335777776666666777766554 445555555543
No 238
>smart00586 ZnF_DBF Zinc finger in DBF-like proteins.
Probab=26.08 E-value=39 Score=23.13 Aligned_cols=14 Identities=7% Similarity=0.347 Sum_probs=11.5
Q ss_pred hHHHHHHHHHHhcC
Q 027385 203 SRTWKRIDEEMNSS 216 (224)
Q Consensus 203 ~~~~~~lD~~i~~~ 216 (224)
+..|..||.+|+..
T Consensus 34 ~~Nf~~lD~Li~~l 47 (49)
T smart00586 34 NDNFQALDDLISQL 47 (49)
T ss_pred chhHHHHHHHHHHh
Confidence 44899999999864
No 239
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=25.58 E-value=59 Score=21.97 Aligned_cols=38 Identities=13% Similarity=0.454 Sum_probs=25.4
Q ss_pred ccChhhHHhhhcCCCCCCCcccccccccCeeEeCCCCcccccc
Q 027385 36 FDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVA 78 (224)
Q Consensus 36 y~Cr~CHde~~~~~~~~~~~H~~~r~~~~~vlC~~C~~~q~~~ 78 (224)
-.|..|-+-+. -| .+..+.++....+.||.|++...++
T Consensus 7 v~C~~C~~lLq-lP----~~~~~~~k~~~klrCGaCs~vl~~s 44 (46)
T PF11331_consen 7 VVCSSCFELLQ-LP----AKFSLSKKNQQKLRCGACSEVLSFS 44 (46)
T ss_pred eECccHHHHHc-CC----CccCCCccceeEEeCCCCceeEEEe
Confidence 35667766543 12 3456666678899999999886653
No 240
>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=25.56 E-value=26 Score=21.26 Aligned_cols=20 Identities=30% Similarity=0.845 Sum_probs=9.1
Q ss_pred EeCCCCccccc-----cccCCCCCC
Q 027385 67 ICSVCDTEQPV-----AQVCTNCGV 86 (224)
Q Consensus 67 lC~~C~~~q~~-----~~~C~~Cg~ 86 (224)
.|+.|+.+..+ +..|++||.
T Consensus 5 fC~~CG~~t~~~~~g~~r~C~~Cg~ 29 (32)
T PF09297_consen 5 FCGRCGAPTKPAPGGWARRCPSCGH 29 (32)
T ss_dssp B-TTT--BEEE-SSSS-EEESSSS-
T ss_pred ccCcCCccccCCCCcCEeECCCCcC
Confidence 46777766443 236777765
No 241
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=25.41 E-value=63 Score=34.93 Aligned_cols=56 Identities=18% Similarity=0.444 Sum_probs=40.5
Q ss_pred ecCCCCCCCccchhhcccCCCceeEe---ccCCccCHHHHHHHHhcCcCCCCCCccccc
Q 027385 145 IENSMHHHCPICYEYLFDSLRNTTVM---KCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (224)
Q Consensus 145 ~e~~~~~~CpICle~lf~s~~~v~~L---pCGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (224)
+++...+.|-||.|++--+.+.-... -||=-..+.|++-=.+..+..||.|+...-
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 44556778999999965443333333 577789999996656667889999997654
No 242
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=25.31 E-value=41 Score=30.12 Aligned_cols=20 Identities=30% Similarity=1.090 Sum_probs=14.9
Q ss_pred cccCCCCCCCc--------ceeecCccc
Q 027385 78 AQVCTNCGVNM--------GEYFCDICK 97 (224)
Q Consensus 78 ~~~C~~Cg~~f--------~~Y~C~~C~ 97 (224)
++.|+.||... +.|||+.|.
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 272 (274)
T PRK01103 245 GEPCRRCGTPIEKIKQGGRSTFFCPRCQ 272 (274)
T ss_pred CCCCCCCCCeeEEEEECCCCcEECcCCC
Confidence 45799999877 567777773
No 243
>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=25.08 E-value=58 Score=21.33 Aligned_cols=11 Identities=36% Similarity=0.939 Sum_probs=5.1
Q ss_pred CcCeeccCCCC
Q 027385 104 EKGQFHCDDCG 114 (224)
Q Consensus 104 ~k~~yHC~~Cg 114 (224)
.+.-|.|..|+
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 244
>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=25.00 E-value=98 Score=25.64 Aligned_cols=28 Identities=21% Similarity=0.540 Sum_probs=22.2
Q ss_pred CcCCCCCCccccc--cchHHHHHHHHHHhc
Q 027385 188 DKYCCPICSKSVI--DMSRTWKRIDEEMNS 215 (224)
Q Consensus 188 ~~~~CPiCrksi~--dm~~~~~~lD~~i~~ 215 (224)
..++||.|+..+. |-+..-+.|++.|+.
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 455677888888764
No 245
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=24.92 E-value=22 Score=33.13 Aligned_cols=20 Identities=45% Similarity=1.019 Sum_probs=17.3
Q ss_pred ccCCCCCCCcceeecCcccccc
Q 027385 79 QVCTNCGVNMGEYFCDICKFYD 100 (224)
Q Consensus 79 ~~C~~Cg~~f~~Y~C~~C~l~d 100 (224)
.+|..||+.|| +|+||+-|-
T Consensus 322 VtCt~CGkrm~--eCPICRqyi 341 (350)
T KOG4275|consen 322 VTCTKCGKRMN--ECPICRQYI 341 (350)
T ss_pred Eeehhhccccc--cCchHHHHH
Confidence 47999999999 999998663
No 246
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=24.82 E-value=35 Score=33.17 Aligned_cols=10 Identities=50% Similarity=1.404 Sum_probs=5.6
Q ss_pred ceeecCccCc
Q 027385 123 NYFHCKRCGS 132 (224)
Q Consensus 123 ~~fHC~~C~~ 132 (224)
..|||..||.
T Consensus 152 ~~F~C~~C~g 161 (436)
T KOG2593|consen 152 GEFHCENCGG 161 (436)
T ss_pred ceEEEecCCC
Confidence 3566666654
No 247
>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=24.59 E-value=40 Score=18.97 Aligned_cols=17 Identities=24% Similarity=0.532 Sum_probs=13.2
Q ss_pred CCCCCCccccccchHHH
Q 027385 190 YCCPICSKSVIDMSRTW 206 (224)
Q Consensus 190 ~~CPiCrksi~dm~~~~ 206 (224)
++|.+|++.+.+.+.+.
T Consensus 2 ~~C~~C~~~F~~~~~l~ 18 (27)
T PF13912_consen 2 FECDECGKTFSSLSALR 18 (27)
T ss_dssp EEETTTTEEESSHHHHH
T ss_pred CCCCccCCccCChhHHH
Confidence 57999999998866543
No 248
>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=24.05 E-value=42 Score=24.46 Aligned_cols=37 Identities=30% Similarity=0.644 Sum_probs=23.8
Q ss_pred cccCCCCCCCcceeecCccccccCCCCcCeeccCCCC
Q 027385 78 AQVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCG 114 (224)
Q Consensus 78 ~~~C~~Cg~~f~~Y~C~~C~l~dd~~~k~~yHC~~Cg 114 (224)
...|+.|...=....+..|.+.+=-.+|.+-||-.|.
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 3457777655444677777777665667777776653
No 249
>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=24.04 E-value=87 Score=29.06 Aligned_cols=25 Identities=28% Similarity=0.687 Sum_probs=21.2
Q ss_pred cCeeEeCCCCcccccc-ccCCCCCCC
Q 027385 63 VKQVICSVCDTEQPVA-QVCTNCGVN 87 (224)
Q Consensus 63 ~~~vlC~~C~~~q~~~-~~C~~Cg~~ 87 (224)
.+-..|+.|.++-.+. ..|++||..
T Consensus 208 ~RyL~CslC~teW~~~R~~C~~Cg~~ 233 (305)
T TIGR01562 208 LRYLSCSLCATEWHYVRVKCSHCEES 233 (305)
T ss_pred ceEEEcCCCCCcccccCccCCCCCCC
Confidence 4688999999998874 689999975
No 250
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=23.60 E-value=73 Score=30.15 Aligned_cols=48 Identities=17% Similarity=0.372 Sum_probs=35.3
Q ss_pred CCCCCccchhhcccCCCceeEeccCCccCHHHHHHHHhcCcCCCCCCccccc
Q 027385 149 MHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (224)
Q Consensus 149 ~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi~ 200 (224)
....||||+...- .+.+.--=|=.|.-.|+-.++. +..+||+=.+++.
T Consensus 299 ~~~~CpvClk~r~---Nptvl~vSGyVfCY~Ci~~Yv~-~~~~CPVT~~p~~ 346 (357)
T KOG0826|consen 299 DREVCPVCLKKRQ---NPTVLEVSGYVFCYPCIFSYVV-NYGHCPVTGYPAS 346 (357)
T ss_pred ccccChhHHhccC---CCceEEecceEEeHHHHHHHHH-hcCCCCccCCcch
Confidence 3567999997632 2233334499999999999998 5789998777664
No 251
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=23.56 E-value=46 Score=31.99 Aligned_cols=38 Identities=21% Similarity=0.469 Sum_probs=30.6
Q ss_pred CCCCCCCccchhhcccCCCceeEeccCCccCHHHHHHHHhc
Q 027385 147 NSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR 187 (224)
Q Consensus 147 ~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~l~~ 187 (224)
......|.||.+.+-. ....+.|||-|-..|...+|..
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 3456789999987422 5777899999999999999974
No 252
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=23.41 E-value=52 Score=25.96 Aligned_cols=11 Identities=18% Similarity=0.594 Sum_probs=5.6
Q ss_pred cccCCCCCCCc
Q 027385 78 AQVCTNCGVNM 88 (224)
Q Consensus 78 ~~~C~~Cg~~f 88 (224)
...|..||..|
T Consensus 71 ~~~C~~Cg~~~ 81 (117)
T PRK00564 71 ELECKDCSHVF 81 (117)
T ss_pred EEEhhhCCCcc
Confidence 34555555444
No 253
>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=23.37 E-value=47 Score=29.80 Aligned_cols=19 Identities=37% Similarity=1.111 Sum_probs=14.0
Q ss_pred cccCCCCCCCc--------ceeecCcc
Q 027385 78 AQVCTNCGVNM--------GEYFCDIC 96 (224)
Q Consensus 78 ~~~C~~Cg~~f--------~~Y~C~~C 96 (224)
++.|+.||... +.|||+.|
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~CP~C 271 (272)
T TIGR00577 245 GEPCRRCGTPIEKIKVGGRGTHFCPQC 271 (272)
T ss_pred CCCCCCCCCeeEEEEECCCCCEECCCC
Confidence 46899998877 45777766
No 254
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=23.11 E-value=49 Score=29.88 Aligned_cols=19 Identities=26% Similarity=0.933 Sum_probs=14.0
Q ss_pred cccCCCCCCCc--------ceeecCcc
Q 027385 78 AQVCTNCGVNM--------GEYFCDIC 96 (224)
Q Consensus 78 ~~~C~~Cg~~f--------~~Y~C~~C 96 (224)
++.|+.||... +.|||+.|
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 45677666
No 255
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=23.09 E-value=39 Score=26.53 Aligned_cols=10 Identities=20% Similarity=0.574 Sum_probs=4.9
Q ss_pred ccCCCCCCCc
Q 027385 79 QVCTNCGVNM 88 (224)
Q Consensus 79 ~~C~~Cg~~f 88 (224)
..|..||..|
T Consensus 71 ~~C~~Cg~~~ 80 (113)
T PRK12380 71 AWCWDCSQVV 80 (113)
T ss_pred EEcccCCCEE
Confidence 3455555444
No 256
>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=22.79 E-value=33 Score=21.97 Aligned_cols=13 Identities=54% Similarity=1.196 Sum_probs=5.4
Q ss_pred cceeecCcccccc
Q 027385 88 MGEYFCDICKFYD 100 (224)
Q Consensus 88 f~~Y~C~~C~l~d 100 (224)
|-+|||+-|+.|-
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 3589999998774
No 257
>PRK05580 primosome assembly protein PriA; Validated
Probab=22.72 E-value=85 Score=31.93 Aligned_cols=45 Identities=22% Similarity=0.596 Sum_probs=28.1
Q ss_pred cCeeEeCCCCccccccccCCCCCCCccee------ecCccccccCCCCcCeeccCCCCc
Q 027385 63 VKQVICSVCDTEQPVAQVCTNCGVNMGEY------FCDICKFYDDDIEKGQFHCDDCGI 115 (224)
Q Consensus 63 ~~~vlC~~C~~~q~~~~~C~~Cg~~f~~Y------~C~~C~l~dd~~~k~~yHC~~Cgi 115 (224)
...++|..|+.. ..|++|+..+.-. .|.-|..- ...+..|+.||-
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 5799999877433 35555432 223445666654
No 258
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=22.68 E-value=30 Score=27.11 Aligned_cols=40 Identities=23% Similarity=0.664 Sum_probs=22.9
Q ss_pred eeEeCCCCccccc----cccCCCCCCCcceeecCccccccCCCCcCeecc
Q 027385 65 QVICSVCDTEQPV----AQVCTNCGVNMGEYFCDICKFYDDDIEKGQFHC 110 (224)
Q Consensus 65 ~vlC~~C~~~q~~----~~~C~~Cg~~f~~Y~C~~C~l~dd~~~k~~yHC 110 (224)
.-.|+.|+....+ +..|..|+. +.|..|..+ ..++..+.|
T Consensus 54 ~~~C~~C~~~fg~l~~~~~~C~~C~~----~VC~~C~~~--~~~~~~WlC 97 (118)
T PF02318_consen 54 ERHCARCGKPFGFLFNRGRVCVDCKH----RVCKKCGVY--SKKEPIWLC 97 (118)
T ss_dssp CSB-TTTS-BCSCTSTTCEEETTTTE----EEETTSEEE--TSSSCCEEE
T ss_pred CcchhhhCCcccccCCCCCcCCcCCc----cccCccCCc--CCCCCCEEC
Confidence 3467777765322 456777765 568888887 233455554
No 259
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=22.65 E-value=54 Score=22.48 Aligned_cols=24 Identities=33% Similarity=0.875 Sum_probs=19.7
Q ss_pred cCeeEeCCCCccccc-cccCCCCCC
Q 027385 63 VKQVICSVCDTEQPV-AQVCTNCGV 86 (224)
Q Consensus 63 ~~~vlC~~C~~~q~~-~~~C~~Cg~ 86 (224)
...+||+.|+...++ +..|-.||.
T Consensus 12 ~~k~ICrkC~ARnp~~A~~CRKCg~ 36 (48)
T PRK04136 12 FNKKICMRCNARNPWRATKCRKCGY 36 (48)
T ss_pred hcccchhcccCCCCccccccccCCC
Confidence 357899999999887 467888886
No 260
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=22.41 E-value=43 Score=31.86 Aligned_cols=65 Identities=18% Similarity=0.300 Sum_probs=36.5
Q ss_pred CCCCccchhhcccCCC-ceeEeccCCccCHHHHHHHHhcCcCCCCCCcccc--ccchHHHHHHHHHHhc
Q 027385 150 HHHCPICYEYLFDSLR-NTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSV--IDMSRTWKRIDEEMNS 215 (224)
Q Consensus 150 ~~~CpICle~lf~s~~-~v~~LpCGH~~H~~C~~~~l~~~~~~CPiCrksi--~dm~~~~~~lD~~i~~ 215 (224)
-..||+|.-.+.-+.- ....-+|||-|--.|..+|... +..|.-+.... ......|...|..+..
T Consensus 306 wr~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~~~~~~~-~~~~~~~~r~~~~~~~~~~~~~~~~~~~~ 373 (384)
T KOG1812|consen 306 WRQCPKCKFMIELSEGCNHMTCRCGHQFCYMCGGDWKTH-NGECYECCRYKESTHYFEDDENHDKSIQL 373 (384)
T ss_pred cCcCcccceeeeecCCcceEEeeccccchhhcCcchhhC-CccccCccccccccccccccccccccccc
Confidence 3457777655432222 1223368999999999999864 44555444433 3334445555444433
No 261
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=22.27 E-value=56 Score=34.61 Aligned_cols=49 Identities=24% Similarity=0.467 Sum_probs=32.6
Q ss_pred CCCCccchhhcccCCCceeEecc---C--CccCHHHHHHHHhcC-cCCCCCCccccc
Q 027385 150 HHHCPICYEYLFDSLRNTTVMKC---G--HTMHCECYHEMIKRD-KYCCPICSKSVI 200 (224)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpC---G--H~~H~~C~~~~l~~~-~~~CPiCrksi~ 200 (224)
+..|-||.-+ -. ++..-.=|| | -.+|++|+.+|+..+ .-+|-||...+.
T Consensus 12 ~~~CRICr~e-~~-~d~pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~ 66 (1175)
T COG5183 12 KRSCRICRTE-DI-RDDPLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYK 66 (1175)
T ss_pred chhceeecCC-CC-CCCcCcccccccchhHHHHHHHHHHHHhcCCCcceeeecceee
Confidence 4567788754 11 122223355 3 679999999999864 556999997664
No 262
>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=22.26 E-value=58 Score=27.27 Aligned_cols=12 Identities=17% Similarity=0.645 Sum_probs=11.2
Q ss_pred cCCCCCCCccee
Q 027385 80 VCTNCGVNMGEY 91 (224)
Q Consensus 80 ~C~~Cg~~f~~Y 91 (224)
.|++||..|..|
T Consensus 30 eC~~C~~RFTTy 41 (147)
T TIGR00244 30 ECLECHERFTTF 41 (147)
T ss_pred cCCccCCcccee
Confidence 799999999998
No 263
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=22.20 E-value=94 Score=19.93 Aligned_cols=33 Identities=24% Similarity=0.691 Sum_probs=16.7
Q ss_pred cCCCCCCCcceeecCccccc-cCCCCcCeeccCCCC
Q 027385 80 VCTNCGVNMGEYFCDICKFY-DDDIEKGQFHCDDCG 114 (224)
Q Consensus 80 ~C~~Cg~~f~~Y~C~~C~l~-dd~~~k~~yHC~~Cg 114 (224)
.|++||..-+.|| .+ ..- -|++..-.|-|.+||
T Consensus 2 ~Cp~C~~~~a~~~-q~-Q~RsaDE~mT~fy~C~~C~ 35 (40)
T smart00440 2 PCPKCGNREATFF-QL-QTRSADEPMTVFYVCTKCG 35 (40)
T ss_pred cCCCCCCCeEEEE-EE-cccCCCCCCeEEEEeCCCC
Confidence 4777777666654 10 111 223444556665555
No 264
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=22.06 E-value=32 Score=27.98 Aligned_cols=9 Identities=33% Similarity=0.881 Sum_probs=4.9
Q ss_pred cCCCCCCCc
Q 027385 80 VCTNCGVNM 88 (224)
Q Consensus 80 ~C~~Cg~~f 88 (224)
.||+||..|
T Consensus 101 ~Cp~C~~~y 109 (147)
T smart00531 101 KCPNCQSKY 109 (147)
T ss_pred ECcCCCCEe
Confidence 455555544
No 265
>COG1144 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, delta subunit [Energy production and conversion]
Probab=21.73 E-value=47 Score=25.65 Aligned_cols=15 Identities=40% Similarity=0.906 Sum_probs=12.3
Q ss_pred cceeecCccCccccc
Q 027385 122 ENYFHCKRCGSCYST 136 (224)
Q Consensus 122 ~~~fHC~~C~~C~s~ 136 (224)
.||-.|+.||.|...
T Consensus 63 idYdyCKGCGICa~v 77 (91)
T COG1144 63 IDYDYCKGCGICANV 77 (91)
T ss_pred eEcccccCceechhh
Confidence 488899999999764
No 266
>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=21.52 E-value=80 Score=19.43 Aligned_cols=7 Identities=43% Similarity=1.298 Sum_probs=3.6
Q ss_pred cCCCCCC
Q 027385 80 VCTNCGV 86 (224)
Q Consensus 80 ~C~~Cg~ 86 (224)
.||.||+
T Consensus 28 ~CP~Cg~ 34 (41)
T smart00834 28 TCPECGG 34 (41)
T ss_pred CCCCCCC
Confidence 4555554
No 267
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=21.33 E-value=70 Score=24.15 Aligned_cols=8 Identities=50% Similarity=1.281 Sum_probs=4.3
Q ss_pred CCCCCCCc
Q 027385 81 CTNCGVNM 88 (224)
Q Consensus 81 C~~Cg~~f 88 (224)
|++||..|
T Consensus 3 C~~Cg~~l 10 (104)
T TIGR01384 3 CPKCGSLM 10 (104)
T ss_pred CcccCccc
Confidence 55555554
No 268
>PHA00616 hypothetical protein
Probab=20.95 E-value=62 Score=21.68 Aligned_cols=29 Identities=10% Similarity=0.187 Sum_probs=19.6
Q ss_pred CCCCCCccccccchHHHHHHHHHHhcCCC
Q 027385 190 YCCPICSKSVIDMSRTWKRIDEEMNSSIF 218 (224)
Q Consensus 190 ~~CPiCrksi~dm~~~~~~lD~~i~~~pm 218 (224)
|+||.|++.+.+-+.+-+.+-..-...|.
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~~hg~~~~ 30 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLSVHKQNKL 30 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHHhcCCCcc
Confidence 78999999998876665555443333333
No 269
>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=20.69 E-value=77 Score=21.34 Aligned_cols=10 Identities=30% Similarity=1.155 Sum_probs=6.6
Q ss_pred eeecCccccc
Q 027385 90 EYFCDICKFY 99 (224)
Q Consensus 90 ~Y~C~~C~l~ 99 (224)
+|.|.+|.+.
T Consensus 1 ky~C~~Cgyv 10 (47)
T PF00301_consen 1 KYQCPVCGYV 10 (47)
T ss_dssp EEEETTTSBE
T ss_pred CcCCCCCCEE
Confidence 5777788543
No 270
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=20.49 E-value=79 Score=28.35 Aligned_cols=48 Identities=25% Similarity=0.645 Sum_probs=31.8
Q ss_pred CCCCCcceeecCccccccCCCCcCeeccCCCCcceeCCccceeecCccCccccc
Q 027385 83 NCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYST 136 (224)
Q Consensus 83 ~Cg~~f~~Y~C~~C~l~dd~~~k~~yHC~~CgiCR~G~~~~~fHC~~C~~C~s~ 136 (224)
.=|......||+.|+++- .+...||.-||.|-.+- =-||.==|.|+..
T Consensus 106 ~~~~~~~~~~C~~C~~~r---PpRs~HCsvC~~CV~rf---DHHC~WvnnCVG~ 153 (299)
T KOG1311|consen 106 VNGIQVEWKYCDTCQLYR---PPRSSHCSVCNNCVLRF---DHHCPWLNNCIGE 153 (299)
T ss_pred cCCcccceEEcCcCcccC---CCCcccchhhccccccc---CCCCCCccceECC
Confidence 335566789999999993 33466888888776651 2366666666554
No 271
>PRK12496 hypothetical protein; Provisional
Probab=20.47 E-value=48 Score=27.75 Aligned_cols=22 Identities=32% Similarity=0.896 Sum_probs=10.0
Q ss_pred EeCCCCcccc---ccccCCCCCCCc
Q 027385 67 ICSVCDTEQP---VAQVCTNCGVNM 88 (224)
Q Consensus 67 lC~~C~~~q~---~~~~C~~Cg~~f 88 (224)
.|..|+++-+ ..+.|+.||.+.
T Consensus 129 ~C~gC~~~~~~~~~~~~C~~CG~~~ 153 (164)
T PRK12496 129 VCKGCKKKYPEDYPDDVCEICGSPV 153 (164)
T ss_pred ECCCCCccccCCCCCCcCCCCCChh
Confidence 3555554442 123455555443
No 272
>PRK00366 ispG 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed
Probab=20.44 E-value=85 Score=29.91 Aligned_cols=31 Identities=13% Similarity=0.452 Sum_probs=28.4
Q ss_pred cCCCCCCccccccchHHHHHHHHHHhcCCCC
Q 027385 189 KYCCPICSKSVIDMSRTWKRIDEEMNSSIFF 219 (224)
Q Consensus 189 ~~~CPiCrksi~dm~~~~~~lD~~i~~~pmp 219 (224)
-..||-|++...|+-..-..+|+.+...++|
T Consensus 268 IisCPgCgR~~~D~~~la~~vee~~~~~~~P 298 (360)
T PRK00366 268 VISCPTCGRTEFDVIQELAEVEQRLEHIKMP 298 (360)
T ss_pred EEECCCCCCCcccHHHHHHHHHHHhcCCCCC
Confidence 4579999999999999999999999999888
No 273
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=20.26 E-value=66 Score=25.28 Aligned_cols=13 Identities=15% Similarity=0.404 Sum_probs=7.9
Q ss_pred cccccCCCCCCCc
Q 027385 76 PVAQVCTNCGVNM 88 (224)
Q Consensus 76 ~~~~~C~~Cg~~f 88 (224)
|+...|..||..|
T Consensus 68 p~~~~C~~Cg~~~ 80 (114)
T PRK03681 68 EAECWCETCQQYV 80 (114)
T ss_pred CcEEEcccCCCee
Confidence 4445677777654
No 274
>KOG3990 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.18 E-value=9.3 Score=34.84 Aligned_cols=63 Identities=24% Similarity=0.613 Sum_probs=35.1
Q ss_pred cccChhhHHhhhcCCCCCCCccccc------------ccccCeeEeCCCCcc-ccc---cccCCCCCCCcceeecCcccc
Q 027385 35 IFDCRHCHNEAASMLRNPYDRHELV------------RQDVKQVICSVCDTE-QPV---AQVCTNCGVNMGEYFCDICKF 98 (224)
Q Consensus 35 ~y~Cr~CHde~~~~~~~~~~~H~~~------------r~~~~~vlC~~C~~~-q~~---~~~C~~Cg~~f~~Y~C~~C~l 98 (224)
.|+|..||... |.+ |-+.+.+.|+.|+.+ |+. ...|..|.+....|
T Consensus 6 L~aCtkC~~r~-----------p~eals~gQqlCk~Cr~a~~vgKctyCrse~q~askt~t~CkkCah~~~kf------- 67 (305)
T KOG3990|consen 6 LYACTKCRQRL-----------PFEALSQGQQLCKECRIAHPVGKCTYCRSEFQQASKTNTICKKCAHNVRKF------- 67 (305)
T ss_pred HHHHHhHhhhC-----------cHHHHHHHHHHHHHhcccCCccccchhHHHhhhhhhhhhHHHHHHHHHHhc-------
Confidence 68899998653 322 334556666666655 222 23455555544444
Q ss_pred ccCCCCcCeeccCCCCc-ceeCCc
Q 027385 99 YDDDIEKGQFHCDDCGI-CRIGGR 121 (224)
Q Consensus 99 ~dd~~~k~~yHC~~Cgi-CR~G~~ 121 (224)
-.|+-|..|+| +-.+|+
T Consensus 68 ------G~P~pC~~CkiiaAF~g~ 85 (305)
T KOG3990|consen 68 ------GTPKPCQYCKIIAAFIGR 85 (305)
T ss_pred ------CCCCcchhhhhhhhhccc
Confidence 24667777773 444444
No 275
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=20.13 E-value=51 Score=23.70 Aligned_cols=12 Identities=42% Similarity=0.886 Sum_probs=10.1
Q ss_pred cCCCCCCccccc
Q 027385 189 KYCCPICSKSVI 200 (224)
Q Consensus 189 ~~~CPiCrksi~ 200 (224)
..+||+|+|.+.
T Consensus 6 ~v~CP~C~k~~~ 17 (62)
T PRK00418 6 TVNCPTCGKPVE 17 (62)
T ss_pred cccCCCCCCccc
Confidence 468999999974
Done!