Query 026787
Match_columns 233
No_of_seqs 229 out of 737
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 12:42:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026787.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026787hhsearch_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 7.1E-60 1.5E-64 423.5 5.5 217 4-231 21-237 (276)
2 PF05495 zf-CHY: CHY zinc fing 99.9 1.8E-24 3.9E-29 159.2 3.7 70 18-100 1-71 (71)
3 COG4357 Zinc finger domain con 99.7 2.7E-17 5.9E-22 126.9 2.0 73 15-90 12-92 (105)
4 PF13639 zf-RING_2: Ring finge 99.4 3.9E-14 8.4E-19 94.2 1.0 44 151-196 1-44 (44)
5 PF12678 zf-rbx1: RING-H2 zinc 99.1 6.7E-11 1.4E-15 87.3 3.5 48 148-196 17-73 (73)
6 PF14599 zinc_ribbon_6: Zinc-r 99.1 2.7E-11 6E-16 87.0 1.3 33 199-231 1-33 (61)
7 cd00162 RING RING-finger (Real 99.0 2.2E-10 4.8E-15 73.6 3.5 45 152-199 1-45 (45)
8 COG5243 HRD1 HRD ubiquitin lig 99.0 1.5E-10 3.3E-15 108.2 1.8 57 147-204 284-350 (491)
9 KOG4628 Predicted E3 ubiquitin 98.9 3.1E-10 6.7E-15 105.7 2.6 50 151-201 230-279 (348)
10 PF13923 zf-C3HC4_2: Zinc fing 98.9 8.2E-10 1.8E-14 71.7 2.1 39 153-195 1-39 (39)
11 PHA02929 N1R/p28-like protein; 98.9 1.7E-09 3.7E-14 96.4 4.1 55 146-201 170-228 (238)
12 PF13920 zf-C3HC4_3: Zinc fing 98.8 2.7E-09 5.8E-14 72.7 2.3 47 150-201 2-49 (50)
13 smart00184 RING Ring finger. E 98.7 8.6E-09 1.9E-13 63.8 2.6 39 153-195 1-39 (39)
14 PF12861 zf-Apc11: Anaphase-pr 98.7 1.1E-08 2.4E-13 77.9 3.4 33 167-199 47-81 (85)
15 PF00097 zf-C3HC4: Zinc finger 98.7 7.4E-09 1.6E-13 67.3 1.7 40 153-195 1-41 (41)
16 PF14634 zf-RING_5: zinc-RING 98.7 1.4E-08 3.1E-13 67.7 3.1 44 152-197 1-44 (44)
17 COG5540 RING-finger-containing 98.6 1.7E-08 3.8E-13 92.5 3.0 53 146-199 319-371 (374)
18 PF15227 zf-C3HC4_4: zinc fing 98.5 5.2E-08 1.1E-12 64.8 2.8 39 153-195 1-42 (42)
19 PF13445 zf-RING_UBOX: RING-ty 98.5 5.9E-08 1.3E-12 65.1 2.0 40 153-193 1-43 (43)
20 PLN03208 E3 ubiquitin-protein 98.4 1.8E-07 4E-12 81.0 4.0 57 141-201 9-80 (193)
21 KOG0802 E3 ubiquitin ligase [P 98.4 7.1E-08 1.5E-12 94.6 1.1 53 146-199 287-340 (543)
22 PHA02926 zinc finger-like prot 98.2 6.2E-07 1.3E-11 79.3 2.9 68 133-200 153-230 (242)
23 KOG0320 Predicted E3 ubiquitin 98.1 1.1E-06 2.5E-11 75.2 1.8 46 151-200 132-178 (187)
24 smart00504 Ubox Modified RING 98.1 3.6E-06 7.8E-11 58.8 3.3 45 151-200 2-46 (63)
25 smart00744 RINGv The RING-vari 98.0 3E-06 6.4E-11 58.2 2.4 43 152-196 1-49 (49)
26 KOG0804 Cytoplasmic Zn-finger 98.0 3.4E-06 7.4E-11 80.8 2.3 47 151-200 176-222 (493)
27 PF11793 FANCL_C: FANCL C-term 97.9 2.9E-06 6.3E-11 62.2 0.4 51 150-200 2-66 (70)
28 TIGR00599 rad18 DNA repair pro 97.8 1.4E-05 3E-10 76.2 3.7 46 150-200 26-71 (397)
29 COG5194 APC11 Component of SCF 97.7 2.4E-05 5.1E-10 59.2 3.0 29 171-200 53-81 (88)
30 KOG2177 Predicted E3 ubiquitin 97.7 2.2E-05 4.7E-10 66.6 2.4 44 149-197 12-55 (386)
31 KOG0827 Predicted E3 ubiquitin 97.7 1.6E-05 3.5E-10 75.3 1.7 46 150-196 4-52 (465)
32 TIGR00570 cdk7 CDK-activating 97.7 3.7E-05 7.9E-10 71.1 3.9 51 150-200 3-54 (309)
33 KOG0317 Predicted E3 ubiquitin 97.6 2.7E-05 5.7E-10 71.1 1.4 45 151-200 240-284 (293)
34 KOG0287 Postreplication repair 97.6 8.4E-05 1.8E-09 69.6 4.5 75 152-231 25-116 (442)
35 KOG2164 Predicted E3 ubiquitin 97.5 4.9E-05 1.1E-09 74.0 2.4 50 148-201 184-237 (513)
36 KOG0828 Predicted E3 ubiquitin 97.3 6.6E-05 1.4E-09 73.0 0.7 51 150-200 571-634 (636)
37 KOG1734 Predicted RING-contain 97.3 6.6E-05 1.4E-09 68.3 0.5 52 149-200 223-281 (328)
38 KOG0823 Predicted E3 ubiquitin 97.2 0.00017 3.7E-09 64.1 2.5 50 148-201 45-96 (230)
39 PF04564 U-box: U-box domain; 97.2 0.00037 8E-09 51.1 3.8 47 151-201 5-51 (73)
40 KOG1493 Anaphase-promoting com 97.2 0.00014 3E-09 54.7 0.8 29 171-199 50-80 (84)
41 PF14835 zf-RING_6: zf-RING of 97.1 0.00023 5E-09 51.8 1.6 56 151-213 8-65 (65)
42 KOG1941 Acetylcholine receptor 97.0 0.00019 4.2E-09 68.3 0.0 63 141-204 357-420 (518)
43 KOG4265 Predicted E3 ubiquitin 96.9 0.00061 1.3E-08 63.9 2.6 52 146-202 286-338 (349)
44 COG5574 PEX10 RING-finger-cont 96.6 0.00084 1.8E-08 60.8 1.6 47 150-200 215-262 (271)
45 PF14570 zf-RING_4: RING/Ubox 96.5 0.002 4.4E-08 44.3 2.5 44 153-198 1-46 (48)
46 COG5219 Uncharacterized conser 96.5 0.0014 3E-08 68.2 2.2 52 148-199 1467-1522(1525)
47 KOG2930 SCF ubiquitin ligase, 96.5 0.0017 3.6E-08 51.5 2.0 28 171-199 80-107 (114)
48 KOG4172 Predicted E3 ubiquitin 96.4 0.00086 1.9E-08 47.6 0.1 54 148-205 5-59 (62)
49 KOG0311 Predicted E3 ubiquitin 96.3 0.001 2.2E-08 62.5 -0.2 49 150-201 43-91 (381)
50 KOG1039 Predicted E3 ubiquitin 96.3 0.0014 3.1E-08 61.6 0.8 77 147-225 158-246 (344)
51 KOG0825 PHD Zn-finger protein 96.2 0.0017 3.8E-08 66.3 0.8 76 124-201 96-172 (1134)
52 PF11789 zf-Nse: Zinc-finger o 96.1 0.0041 8.9E-08 44.0 2.1 44 148-194 9-53 (57)
53 PF10367 Vps39_2: Vacuolar sor 96.0 0.003 6.4E-08 48.1 1.3 37 144-182 72-108 (109)
54 KOG3002 Zn finger protein [Gen 95.8 0.008 1.7E-07 55.6 3.5 63 151-224 49-113 (299)
55 KOG0978 E3 ubiquitin ligase in 95.7 0.0027 5.9E-08 64.4 0.1 46 151-200 644-689 (698)
56 KOG1645 RING-finger-containing 95.6 0.0071 1.5E-07 58.0 2.4 50 150-199 4-55 (463)
57 COG5432 RAD18 RING-finger-cont 95.6 0.0065 1.4E-07 56.2 2.1 45 151-200 26-70 (391)
58 PRK14890 putative Zn-ribbon RN 95.6 0.01 2.2E-07 42.4 2.5 46 63-115 5-56 (59)
59 PF12906 RINGv: RING-variant d 95.5 0.0066 1.4E-07 41.2 1.4 41 153-195 1-47 (47)
60 KOG1785 Tyrosine kinase negati 95.5 0.0041 8.9E-08 59.6 0.3 56 144-203 363-419 (563)
61 KOG1428 Inhibitor of type V ad 95.3 0.017 3.7E-07 62.8 4.0 74 119-200 3462-3544(3738)
62 KOG3970 Predicted E3 ubiquitin 95.1 0.019 4.1E-07 51.5 3.2 52 148-201 48-106 (299)
63 KOG4739 Uncharacterized protei 95.1 0.015 3.3E-07 52.0 2.6 37 161-200 12-48 (233)
64 KOG2879 Predicted E3 ubiquitin 94.1 0.041 8.9E-07 50.4 3.1 53 148-203 237-290 (298)
65 PF05883 Baculo_RING: Baculovi 94.1 0.022 4.8E-07 47.0 1.2 36 150-186 26-67 (134)
66 KOG0824 Predicted E3 ubiquitin 93.9 0.031 6.7E-07 51.8 1.9 50 147-200 4-53 (324)
67 PHA02862 5L protein; Provision 93.4 0.039 8.5E-07 46.3 1.5 60 149-214 1-66 (156)
68 KOG4185 Predicted E3 ubiquitin 93.4 0.052 1.1E-06 49.0 2.3 49 151-199 4-54 (296)
69 KOG3800 Predicted E3 ubiquitin 93.1 0.065 1.4E-06 49.4 2.5 49 152-200 2-51 (300)
70 KOG1571 Predicted E3 ubiquitin 93.1 0.051 1.1E-06 51.3 1.8 48 146-201 301-348 (355)
71 PF14447 Prok-RING_4: Prokaryo 93.0 0.038 8.2E-07 39.1 0.6 32 166-200 19-50 (55)
72 KOG3268 Predicted E3 ubiquitin 92.4 0.072 1.6E-06 46.3 1.8 35 169-203 187-232 (234)
73 PF12773 DZR: Double zinc ribb 92.4 0.14 3.1E-06 34.3 2.9 22 68-89 1-23 (50)
74 COG5175 MOT2 Transcriptional r 92.3 0.042 9.2E-07 51.9 0.3 59 150-208 14-72 (480)
75 KOG4445 Uncharacterized conser 91.7 0.07 1.5E-06 49.7 0.9 54 147-201 112-187 (368)
76 KOG2660 Locus-specific chromos 91.7 0.044 9.4E-07 51.2 -0.4 64 149-216 14-78 (331)
77 PF07800 DUF1644: Protein of u 91.6 0.21 4.7E-06 42.4 3.7 48 150-201 2-92 (162)
78 PF04641 Rtf2: Rtf2 RING-finge 91.5 0.15 3.2E-06 45.9 2.8 50 148-200 111-161 (260)
79 KOG1814 Predicted E3 ubiquitin 91.4 0.095 2.1E-06 50.5 1.5 46 150-196 184-236 (445)
80 KOG4275 Predicted E3 ubiquitin 91.4 0.034 7.5E-07 51.4 -1.5 60 139-207 286-349 (350)
81 COG2888 Predicted Zn-ribbon RN 91.2 0.15 3.3E-06 36.6 2.0 45 65-115 9-58 (61)
82 KOG0297 TNF receptor-associate 91.1 0.18 4E-06 48.0 3.1 54 148-205 19-72 (391)
83 KOG3161 Predicted E3 ubiquitin 90.5 0.13 2.7E-06 52.2 1.4 67 151-221 12-89 (861)
84 PF07191 zinc-ribbons_6: zinc- 90.4 0.16 3.5E-06 37.6 1.6 36 64-99 16-59 (70)
85 KOG0309 Conserved WD40 repeat- 89.9 0.17 3.8E-06 52.1 1.8 42 150-194 1028-1069(1081)
86 KOG1813 Predicted E3 ubiquitin 89.1 0.2 4.4E-06 46.4 1.6 67 151-222 242-308 (313)
87 KOG2114 Vacuolar assembly/sort 88.2 0.31 6.7E-06 50.7 2.3 47 151-204 841-890 (933)
88 KOG1002 Nucleotide excision re 87.8 0.19 4E-06 50.2 0.4 52 145-200 531-586 (791)
89 KOG3039 Uncharacterized conser 87.7 0.54 1.2E-05 42.9 3.3 54 147-202 218-272 (303)
90 COG5152 Uncharacterized conser 87.5 0.31 6.8E-06 43.1 1.6 58 152-214 198-255 (259)
91 PF13248 zf-ribbon_3: zinc-rib 87.1 0.31 6.7E-06 29.0 1.0 24 65-88 2-26 (26)
92 KOG4159 Predicted E3 ubiquitin 87.1 0.68 1.5E-05 44.6 3.8 49 148-201 82-130 (398)
93 KOG2817 Predicted E3 ubiquitin 87.1 0.56 1.2E-05 45.0 3.2 45 152-197 336-382 (394)
94 COG5236 Uncharacterized conser 86.8 0.51 1.1E-05 45.0 2.7 65 131-199 42-107 (493)
95 KOG2034 Vacuolar sorting prote 86.4 0.36 7.8E-06 50.4 1.6 43 142-186 809-851 (911)
96 PF03854 zf-P11: P-11 zinc fin 86.4 0.39 8.4E-06 33.2 1.3 32 168-200 14-46 (50)
97 PHA02825 LAP/PHD finger-like p 85.8 0.65 1.4E-05 39.5 2.6 48 148-200 6-59 (162)
98 PRK04023 DNA polymerase II lar 85.6 0.74 1.6E-05 48.9 3.4 31 80-114 628-658 (1121)
99 KOG2462 C2H2-type Zn-finger pr 85.5 0.75 1.6E-05 42.3 3.0 41 88-135 128-172 (279)
100 PF10571 UPF0547: Uncharacteri 84.7 0.68 1.5E-05 27.8 1.6 23 67-89 2-25 (26)
101 KOG0801 Predicted E3 ubiquitin 84.2 0.42 9.2E-06 41.1 0.8 31 147-178 174-204 (205)
102 PF09538 FYDLN_acid: Protein o 83.6 0.85 1.8E-05 36.3 2.2 28 76-115 7-34 (108)
103 PF13240 zinc_ribbon_2: zinc-r 83.1 0.7 1.5E-05 26.9 1.2 21 68-88 2-23 (23)
104 KOG1952 Transcription factor N 82.7 0.58 1.3E-05 48.8 1.2 50 150-200 191-247 (950)
105 PRK14559 putative protein seri 82.7 0.94 2E-05 46.1 2.7 32 66-97 2-34 (645)
106 smart00734 ZnF_Rad18 Rad18-lik 81.1 1.2 2.6E-05 26.6 1.7 21 190-211 2-22 (26)
107 PHA00626 hypothetical protein 80.9 1.3 2.7E-05 31.7 2.0 7 80-86 2-8 (59)
108 PF14446 Prok-RING_1: Prokaryo 80.2 1.6 3.5E-05 30.7 2.4 36 149-184 4-39 (54)
109 PRK14714 DNA polymerase II lar 78.5 2.2 4.9E-05 46.4 3.9 33 65-98 667-700 (1337)
110 TIGR00595 priA primosomal prot 78.4 1.8 3.9E-05 42.6 3.0 50 26-87 213-262 (505)
111 smart00132 LIM Zinc-binding do 78.3 1.3 2.8E-05 27.0 1.3 37 153-200 2-38 (39)
112 KOG4692 Predicted E3 ubiquitin 78.0 1.3 2.8E-05 42.4 1.8 51 146-201 418-468 (489)
113 PF02891 zf-MIZ: MIZ/SP-RING z 77.5 2 4.2E-05 29.4 2.1 41 152-198 4-50 (50)
114 PF08746 zf-RING-like: RING-li 77.1 1.6 3.5E-05 29.0 1.6 25 171-195 18-43 (43)
115 COG5220 TFB3 Cdk activating ki 76.4 0.93 2E-05 41.3 0.3 51 149-200 9-64 (314)
116 KOG0827 Predicted E3 ubiquitin 76.0 0.26 5.5E-06 47.4 -3.5 50 150-200 196-245 (465)
117 PF13894 zf-C2H2_4: C2H2-type 74.9 2 4.3E-05 23.4 1.3 20 190-209 1-20 (24)
118 COG1198 PriA Primosomal protei 74.2 3.1 6.7E-05 43.1 3.5 54 26-91 435-488 (730)
119 KOG0269 WD40 repeat-containing 73.6 3.1 6.6E-05 43.2 3.2 80 105-204 751-837 (839)
120 PHA03096 p28-like protein; Pro 72.1 1.8 3.8E-05 39.9 1.1 47 151-197 179-231 (284)
121 smart00249 PHD PHD zinc finger 72.0 1.5 3.3E-05 27.5 0.4 42 153-195 2-47 (47)
122 KOG3053 Uncharacterized conser 70.7 1.6 3.5E-05 39.9 0.5 67 149-215 19-104 (293)
123 COG1198 PriA Primosomal protei 70.7 4.3 9.3E-05 42.1 3.5 43 64-114 434-482 (730)
124 KOG1940 Zn-finger protein [Gen 70.4 2.7 5.8E-05 38.7 1.8 30 13-43 175-204 (276)
125 KOG2066 Vacuolar assembly/sort 69.8 1.7 3.7E-05 45.1 0.5 45 150-196 784-831 (846)
126 PRK14714 DNA polymerase II lar 69.8 3.9 8.4E-05 44.7 3.0 33 79-115 668-700 (1337)
127 PF07282 OrfB_Zn_ribbon: Putat 69.4 3.7 8E-05 29.1 2.0 27 78-115 28-54 (69)
128 PRK04023 DNA polymerase II lar 69.1 3.9 8.5E-05 43.8 2.9 49 64-118 625-674 (1121)
129 TIGR02300 FYDLN_acid conserved 68.7 3.5 7.7E-05 33.9 2.0 28 77-116 8-35 (129)
130 PF05605 zf-Di19: Drought indu 68.4 4.7 0.0001 27.5 2.3 10 190-199 32-41 (54)
131 PLN03086 PRLI-interacting fact 67.8 2.6 5.7E-05 42.4 1.3 84 62-160 404-514 (567)
132 PF03107 C1_2: C1 domain; Int 67.8 4 8.7E-05 24.8 1.7 20 112-131 2-22 (30)
133 PF07754 DUF1610: Domain of un 67.3 4.7 0.0001 23.9 1.8 9 106-114 15-23 (24)
134 PRK05580 primosome assembly pr 66.6 4.8 0.0001 41.1 2.9 51 26-88 381-431 (679)
135 PF05502 Dynactin_p62: Dynacti 66.3 3.2 7E-05 40.8 1.6 100 90-212 5-109 (483)
136 KOG2068 MOT2 transcription fac 64.9 5.1 0.00011 37.7 2.5 51 149-200 248-298 (327)
137 PRK14873 primosome assembly pr 64.7 5.3 0.00011 40.9 2.8 49 26-87 383-431 (665)
138 KOG1311 DHHC-type Zn-finger pr 62.6 5.2 0.00011 36.3 2.1 48 82-135 105-152 (299)
139 KOG1001 Helicase-like transcri 62.4 3.4 7.3E-05 42.4 0.9 45 151-200 455-500 (674)
140 PF06524 NOA36: NOA36 protein; 60.8 3 6.4E-05 38.4 0.2 51 33-98 140-190 (314)
141 PRK14559 putative protein seri 60.1 4.8 0.0001 41.1 1.5 34 65-99 15-50 (645)
142 PF13453 zf-TFIIB: Transcripti 59.9 7.3 0.00016 25.2 1.9 26 80-114 1-26 (41)
143 COG5109 Uncharacterized conser 59.7 7.8 0.00017 36.7 2.7 44 152-196 338-383 (396)
144 PF04216 FdhE: Protein involve 57.8 6.9 0.00015 35.5 2.0 48 63-114 195-245 (290)
145 COG5222 Uncharacterized conser 57.4 7.9 0.00017 36.4 2.3 44 151-197 275-318 (427)
146 KOG0298 DEAD box-containing he 57.3 5.3 0.00011 43.7 1.3 53 148-204 1151-1203(1394)
147 PF05191 ADK_lid: Adenylate ki 57.2 2.7 5.8E-05 27.0 -0.5 27 80-115 3-29 (36)
148 PF00096 zf-C2H2: Zinc finger, 56.7 6.9 0.00015 21.5 1.2 16 190-205 1-16 (23)
149 PRK00398 rpoP DNA-directed RNA 56.2 10 0.00022 25.1 2.1 8 107-114 21-28 (46)
150 PF08271 TF_Zn_Ribbon: TFIIB z 56.1 9.6 0.00021 24.8 2.0 8 80-87 2-9 (43)
151 PRK14890 putative Zn-ribbon RN 56.0 7.8 0.00017 27.8 1.6 34 63-98 23-56 (59)
152 PRK00415 rps27e 30S ribosomal 55.7 6.6 0.00014 28.2 1.2 35 64-98 10-50 (59)
153 PF07191 zinc-ribbons_6: zinc- 55.7 1.7 3.8E-05 32.1 -1.8 41 151-201 2-42 (70)
154 KOG1812 Predicted E3 ubiquitin 55.2 5.2 0.00011 38.2 0.8 37 150-186 146-182 (384)
155 KOG1609 Protein involved in mR 55.1 5.2 0.00011 35.7 0.7 51 150-200 78-134 (323)
156 KOG4185 Predicted E3 ubiquitin 54.0 2.8 6E-05 37.8 -1.2 50 151-200 208-267 (296)
157 KOG4367 Predicted Zn-finger pr 53.6 6.6 0.00014 38.7 1.2 33 150-186 4-36 (699)
158 PF15353 HECA: Headcase protei 53.2 6.6 0.00014 31.3 1.0 15 172-186 40-54 (107)
159 smart00659 RPOLCX RNA polymera 53.0 7.9 0.00017 25.9 1.2 21 67-87 4-28 (44)
160 PF14569 zf-UDP: Zinc-binding 50.4 17 0.00038 27.5 2.8 52 148-199 7-61 (80)
161 PF04423 Rad50_zn_hook: Rad50 50.4 11 0.00024 25.7 1.7 26 189-214 20-47 (54)
162 PF05290 Baculo_IE-1: Baculovi 49.4 9.1 0.0002 31.9 1.2 47 151-201 81-133 (140)
163 PHA00626 hypothetical protein 48.9 11 0.00025 26.9 1.5 34 66-101 1-34 (59)
164 PF07649 C1_3: C1-like domain; 47.5 11 0.00023 22.8 1.0 21 113-133 3-24 (30)
165 PF01096 TFIIS_C: Transcriptio 47.5 16 0.00035 23.6 2.0 34 80-114 2-35 (39)
166 KOG1312 DHHC-type Zn-finger pr 46.0 6.9 0.00015 36.6 0.0 32 111-145 149-180 (341)
167 PF14353 CpXC: CpXC protein 44.9 20 0.00044 28.3 2.6 11 80-90 3-13 (128)
168 PF13717 zinc_ribbon_4: zinc-r 44.7 15 0.00033 23.4 1.5 10 64-73 24-33 (36)
169 PRK00432 30S ribosomal protein 44.6 15 0.00033 25.1 1.6 9 106-114 36-44 (50)
170 cd00350 rubredoxin_like Rubred 44.4 17 0.00037 22.5 1.7 24 91-115 2-25 (33)
171 COG2051 RPS27A Ribosomal prote 42.8 11 0.00024 27.7 0.7 28 64-91 18-51 (67)
172 PF00412 LIM: LIM domain; Int 42.5 11 0.00023 25.2 0.6 40 153-203 1-40 (58)
173 PLN02189 cellulose synthase 41.9 24 0.00053 38.1 3.3 56 145-200 29-87 (1040)
174 PF01529 zf-DHHC: DHHC palmito 41.8 15 0.00032 30.0 1.4 49 83-137 41-89 (174)
175 PF03833 PolC_DP2: DNA polymer 41.2 8.9 0.00019 40.4 0.0 44 80-132 657-700 (900)
176 PF04438 zf-HIT: HIT zinc fing 40.9 13 0.00029 22.8 0.8 16 81-97 5-20 (30)
177 PF13719 zinc_ribbon_5: zinc-r 40.8 18 0.00039 23.0 1.4 9 65-73 25-33 (37)
178 TIGR00595 priA primosomal prot 39.7 32 0.00069 33.9 3.6 46 63-116 211-262 (505)
179 COG1996 RPC10 DNA-directed RNA 39.7 20 0.00044 24.7 1.6 26 90-115 6-32 (49)
180 PF01667 Ribosomal_S27e: Ribos 39.5 15 0.00033 25.9 1.0 34 65-98 7-46 (55)
181 PF08274 PhnA_Zn_Ribbon: PhnA 39.4 17 0.00037 22.5 1.1 23 80-114 4-26 (30)
182 cd02337 ZZ_CBP Zinc finger, ZZ 39.2 23 0.00049 23.3 1.7 20 108-131 1-20 (41)
183 PF01529 zf-DHHC: DHHC palmito 38.9 24 0.00052 28.7 2.2 29 114-145 52-80 (174)
184 KOG4399 C2HC-type Zn-finger pr 38.0 6.5 0.00014 36.2 -1.4 72 85-159 199-270 (325)
185 KOG3362 Predicted BBOX Zn-fing 37.5 11 0.00025 31.7 0.1 25 89-119 117-143 (156)
186 smart00661 RPOL9 RNA polymeras 36.8 27 0.00059 23.0 1.9 8 107-114 20-27 (52)
187 PF06827 zf-FPG_IleRS: Zinc fi 36.7 26 0.00056 21.0 1.6 10 79-88 2-11 (30)
188 KOG2272 Focal adhesion protein 36.7 22 0.00048 32.8 1.8 94 36-158 100-200 (332)
189 TIGR00100 hypA hydrogenase nic 36.6 16 0.00035 29.0 0.8 11 78-88 70-80 (115)
190 PLN02436 cellulose synthase A 36.3 32 0.0007 37.3 3.2 56 145-200 31-89 (1094)
191 PF12874 zf-met: Zinc-finger o 36.1 19 0.00041 20.1 0.9 16 190-205 1-16 (25)
192 PF03604 DNA_RNApol_7kD: DNA d 35.7 23 0.00051 22.2 1.3 10 105-114 15-24 (32)
193 PF12760 Zn_Tnp_IS1595: Transp 35.7 46 0.001 21.9 2.8 9 79-87 19-27 (46)
194 PF15616 TerY-C: TerY-C metal 35.5 37 0.00081 28.0 2.8 33 79-114 78-112 (131)
195 PF00643 zf-B_box: B-box zinc 35.1 32 0.0007 21.7 1.9 21 79-99 4-24 (42)
196 cd02249 ZZ Zinc finger, ZZ typ 34.7 28 0.00062 22.9 1.7 21 108-131 1-21 (46)
197 COG1645 Uncharacterized Zn-fin 34.2 24 0.00051 29.2 1.4 19 79-97 29-51 (131)
198 COG2888 Predicted Zn-ribbon RN 34.0 24 0.00052 25.5 1.3 33 64-98 26-58 (61)
199 PRK00420 hypothetical protein; 33.9 29 0.00062 27.9 1.9 19 79-97 24-47 (112)
200 PRK03564 formate dehydrogenase 33.7 46 0.001 31.1 3.5 25 63-87 210-235 (309)
201 PRK04136 rpl40e 50S ribosomal 33.5 28 0.0006 24.0 1.4 24 63-86 12-36 (48)
202 KOG4443 Putative transcription 33.2 46 0.00099 34.3 3.5 79 144-227 139-227 (694)
203 PRK14892 putative transcriptio 32.9 40 0.00086 26.5 2.4 32 122-159 19-51 (99)
204 KOG1100 Predicted E3 ubiquitin 32.4 27 0.00058 30.7 1.6 39 153-200 161-200 (207)
205 PF03833 PolC_DP2: DNA polymer 32.4 15 0.00032 38.8 0.0 46 64-115 654-700 (900)
206 KOG0802 E3 ubiquitin ligase [P 31.4 30 0.00066 34.3 2.0 44 148-200 477-520 (543)
207 COG3809 Uncharacterized protei 31.1 34 0.00074 26.1 1.7 50 152-224 3-54 (88)
208 TIGR02098 MJ0042_CXXC MJ0042 f 30.0 38 0.00082 21.1 1.6 10 65-74 25-34 (38)
209 KOG4317 Predicted Zn-finger pr 29.8 24 0.00052 33.5 0.9 20 80-99 9-28 (383)
210 COG5183 SSM4 Protein involved 29.7 29 0.00064 36.8 1.6 49 150-200 12-66 (1175)
211 smart00355 ZnF_C2H2 zinc finge 29.6 43 0.00094 17.8 1.7 16 190-205 1-16 (26)
212 PF11023 DUF2614: Protein of u 29.2 35 0.00076 27.6 1.6 27 62-88 66-95 (114)
213 PF12171 zf-C2H2_jaz: Zinc-fin 29.2 42 0.00091 19.4 1.6 16 189-204 1-16 (27)
214 PRK08351 DNA-directed RNA poly 29.1 34 0.00074 24.6 1.4 20 67-87 5-24 (61)
215 cd07973 Spt4 Transcription elo 28.9 31 0.00066 27.0 1.2 20 67-86 5-28 (98)
216 PF12172 DUF35_N: Rubredoxin-l 28.8 25 0.00055 22.0 0.6 23 64-86 10-33 (37)
217 PLN00209 ribosomal protein S27 28.7 36 0.00077 26.2 1.5 37 64-100 35-77 (86)
218 cd02341 ZZ_ZZZ3 Zinc finger, Z 28.7 40 0.00086 22.9 1.6 22 108-131 1-22 (48)
219 PTZ00083 40S ribosomal protein 28.6 30 0.00065 26.6 1.1 36 64-99 34-75 (85)
220 COG5273 Uncharacterized protei 28.3 27 0.00059 32.4 1.0 44 79-145 98-141 (309)
221 PF13913 zf-C2HC_2: zinc-finge 28.1 25 0.00055 20.5 0.5 12 79-90 3-14 (25)
222 PRK14873 primosome assembly pr 28.1 52 0.0011 33.8 3.0 23 64-90 382-404 (665)
223 PF11781 RRN7: RNA polymerase 27.1 38 0.00083 21.6 1.2 25 152-176 10-35 (36)
224 PF06677 Auto_anti-p27: Sjogre 27.1 44 0.00096 22.1 1.6 12 79-90 18-29 (41)
225 KOG0006 E3 ubiquitin-protein l 26.7 53 0.0012 31.4 2.6 88 90-186 149-255 (446)
226 PF01599 Ribosomal_S27: Riboso 26.5 38 0.00081 23.2 1.2 21 78-98 18-46 (47)
227 PRK14810 formamidopyrimidine-D 26.4 37 0.0008 30.7 1.5 20 78-97 244-271 (272)
228 COG5273 Uncharacterized protei 26.4 39 0.00086 31.3 1.7 33 59-91 103-136 (309)
229 KOG4399 C2HC-type Zn-finger pr 25.7 16 0.00035 33.7 -1.0 53 79-135 250-302 (325)
230 PF06220 zf-U1: U1 zinc finger 25.4 27 0.00058 22.5 0.3 13 88-100 1-13 (38)
231 PF00628 PHD: PHD-finger; Int 25.2 28 0.00062 22.8 0.4 43 153-196 2-49 (51)
232 PRK10445 endonuclease VIII; Pr 25.0 42 0.0009 30.3 1.5 20 78-97 235-262 (263)
233 COG1998 RPS31 Ribosomal protei 25.0 46 0.00099 23.2 1.4 8 79-86 20-27 (51)
234 PRK14811 formamidopyrimidine-D 24.9 42 0.0009 30.4 1.5 20 78-97 235-262 (269)
235 PLN02638 cellulose synthase A 24.7 65 0.0014 35.1 3.1 56 145-200 12-70 (1079)
236 smart00451 ZnF_U1 U1-like zinc 24.6 50 0.0011 19.7 1.4 17 188-204 2-18 (35)
237 PF00130 C1_1: Phorbol esters/ 24.5 59 0.0013 21.4 1.9 11 104-114 25-35 (53)
238 PF05458 Siva: Cd27 binding pr 24.5 59 0.0013 27.9 2.3 23 66-88 112-134 (175)
239 COG1144 Pyruvate:ferredoxin ox 24.4 39 0.00084 26.3 1.0 15 122-136 63-77 (91)
240 PRK00564 hypA hydrogenase nick 24.1 50 0.0011 26.3 1.7 11 78-88 71-81 (117)
241 PRK12380 hydrogenase nickel in 23.7 36 0.00079 26.9 0.8 10 79-88 71-80 (113)
242 PRK00464 nrdR transcriptional 23.6 48 0.001 27.9 1.6 12 80-91 30-41 (154)
243 TIGR00244 transcriptional regu 23.1 52 0.0011 27.7 1.7 13 80-92 30-42 (147)
244 PRK01103 formamidopyrimidine/5 23.0 48 0.001 29.9 1.6 20 78-97 245-272 (274)
245 KOG1815 Predicted E3 ubiquitin 23.0 42 0.00092 32.4 1.3 39 146-187 66-104 (444)
246 PF11331 DUF3133: Protein of u 22.8 72 0.0016 21.7 2.0 37 37-78 8-44 (46)
247 PF10272 Tmpp129: Putative tra 22.8 45 0.00098 31.9 1.4 36 153-200 316-351 (358)
248 PF12675 DUF3795: Protein of u 22.8 45 0.00099 24.5 1.1 37 78-114 34-70 (78)
249 KOG1829 Uncharacterized conser 22.7 28 0.00061 35.3 -0.0 26 167-196 532-557 (580)
250 PRK06266 transcription initiat 22.7 88 0.0019 26.7 3.0 27 188-214 135-163 (178)
251 KOG0269 WD40 repeat-containing 22.6 44 0.00096 35.0 1.3 50 79-137 754-806 (839)
252 PF13912 zf-C2H2_6: C2H2-type 22.6 45 0.00097 18.9 0.9 17 190-206 2-18 (27)
253 PF12756 zf-C2H2_2: C2H2 type 22.5 57 0.0012 23.5 1.6 22 189-210 50-71 (100)
254 PRK00418 DNA gyrase inhibitor; 22.4 45 0.00097 24.1 1.0 12 189-200 6-17 (62)
255 TIGR01384 TFS_arch transcripti 22.1 66 0.0014 24.5 1.9 8 81-88 3-10 (104)
256 TIGR01562 FdhE formate dehydro 21.9 1E+02 0.0022 28.8 3.4 25 63-87 208-233 (305)
257 PF09297 zf-NADH-PPase: NADH p 21.7 33 0.00072 20.9 0.2 20 67-86 5-29 (32)
258 KOG3005 GIY-YIG type nuclease 21.5 1.1E+02 0.0023 28.4 3.5 64 151-221 183-259 (276)
259 PF14445 Prok-RING_2: Prokaryo 21.5 5.8 0.00013 27.9 -3.6 46 86-136 3-53 (57)
260 KOG2593 Transcription initiati 21.3 46 0.00099 32.6 1.1 10 123-132 152-161 (436)
261 smart00440 ZnF_C2C2 C2C2 Zinc 21.1 1E+02 0.0022 19.9 2.4 33 80-114 2-35 (40)
262 PF00301 Rubredoxin: Rubredoxi 21.1 72 0.0016 21.6 1.7 10 90-99 1-10 (47)
263 KOG4275 Predicted E3 ubiquitin 21.1 30 0.00064 32.6 -0.2 19 79-99 322-340 (350)
264 PRK13945 formamidopyrimidine-D 21.1 56 0.0012 29.7 1.6 19 78-96 254-280 (282)
265 PF13824 zf-Mss51: Zinc-finger 21.0 69 0.0015 22.6 1.7 11 105-115 12-22 (55)
266 smart00064 FYVE Protein presen 21.0 48 0.001 23.1 0.9 38 149-186 9-46 (68)
267 TIGR00577 fpg formamidopyrimid 21.0 56 0.0012 29.5 1.5 19 78-96 245-271 (272)
268 smart00531 TFIIE Transcription 20.9 33 0.00072 28.1 0.1 8 125-132 124-131 (147)
269 smart00154 ZnF_AN1 AN1-like Zi 20.7 82 0.0018 20.3 1.9 23 124-146 12-36 (39)
270 PRK03681 hypA hydrogenase nick 20.7 63 0.0014 25.5 1.6 13 76-88 68-80 (114)
271 PF03884 DUF329: Domain of unk 20.4 37 0.0008 24.1 0.2 12 190-201 3-14 (57)
272 PRK05580 primosome assembly pr 20.4 1E+02 0.0022 31.6 3.4 45 63-115 379-429 (679)
273 PRK01343 zinc-binding protein; 20.2 54 0.0012 23.4 1.0 12 189-200 9-20 (57)
No 1
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=100.00 E-value=7.1e-60 Score=423.54 Aligned_cols=217 Identities=48% Similarity=1.039 Sum_probs=210.1
Q ss_pred CccccccCCCCccCCccccccceeecCCCCCcccCchhHHhhhcCCCCCCCcccccccccceeecCCCCccccccCcCCC
Q 026787 4 SANERITFGKMGYGCKHYRRRCRIRAPCCNEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVAQVCTN 83 (233)
Q Consensus 4 ~~~~~~~~~~~~~gC~HY~r~c~l~~pCC~~~y~Cr~CHde~~~~~~~~~~~H~~~r~~v~~v~C~~C~~~q~~~~~C~~ 83 (233)
..+++.|++.+++||+||+|++++++|+|+++|+|++||+++. +|.++|+.|.+|+|+.|+++|++++.|.+
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 3566789999999999999999999999999999999999974 69999999999999999999999999999
Q ss_pred CCCCcceeecCccccccCCCCcCeeccCCCCcceeCCccceeeccccCccccccccccceeecCCCCCCCcchhhhhccc
Q 026787 84 CGVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYSTSLRNNHLCIENSMHHHCPICYEYLFDS 163 (233)
Q Consensus 84 Cg~~f~~Y~C~~C~l~d~~~~k~~yHC~~CgiCR~G~~~~~fHC~~C~~C~s~~l~~~H~C~e~~~~~~CpICle~lf~s 163 (233)
|+..+|+|||++|+||||+++ .||||+.|||||+|++++||||++|+.|++..+.+.|+|+|++++.|||||.|+||++
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 CCceeEeccCCccChhhHHHHhccCCCcCCCCCccccchhHHhhhhHHHHHhCCCChhhhcceeEEEE
Q 026787 164 LRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRTWKRIDEEIEATVMPEDYRHKKVSSCL 231 (233)
Q Consensus 164 ~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrksi~dm~~~~~~lD~~i~~~pmP~~y~~~~~~i~~ 231 (233)
...+.+|+|||.+|..||+++...+ |+||+|.| +.||+.+|+++|.+|+++|||++|++++++|++
T Consensus 172 ~~~~~~~~CgH~~h~~cf~e~~~~~-y~CP~C~~-~~d~~~~~~~~d~~l~~~~~p~~y~~~~~~i~c 237 (276)
T KOG1940|consen 172 FEDAGVLKCGHYMHSRCFEEMICEG-YTCPICSK-PGDMSHYFRKLDKELAGSPMPEEYKNKTQDILC 237 (276)
T ss_pred cccCCccCcccchHHHHHHHHhccC-CCCCcccc-hHHHHHHHHHHHHHHhcCCCCchhhchhheeec
Confidence 9999999999999999999999865 99999999 999999999999999999999999999999986
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=1.8e-24 Score=159.20 Aligned_cols=70 Identities=51% Similarity=1.212 Sum_probs=53.0
Q ss_pred Ccccccc-ceeecCCCCCcccCchhHHhhhcCCCCCCCcccccccccceeecCCCCccccccCcCCCCCCCcceeecCcc
Q 026787 18 CKHYRRR-CRIRAPCCNEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVAQVCTNCGVNMGEYFCDIC 96 (233)
Q Consensus 18 C~HY~r~-c~l~~pCC~~~y~Cr~CHde~~~~~~~~~~~H~~~r~~v~~v~C~~C~~~q~~~~~C~~Cg~~f~~Y~C~~C 96 (233)
|+||+|+ ++|+||||++|||||+||||++ +|+++|+++++|+||.|+++|++++. +|+ |+|+|++|
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 9999999999999999999974 69999999999999999999999988 777 99999999
Q ss_pred cccc
Q 026787 97 KFYD 100 (233)
Q Consensus 97 ~l~d 100 (233)
++||
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=99.66 E-value=2.7e-17 Score=126.93 Aligned_cols=73 Identities=26% Similarity=0.611 Sum_probs=66.2
Q ss_pred ccCCccccc---cceeecCCCCCcccCchhHHhhhcCCCCCCCcccccccccceeecCCCCcccccc-----CcCCCCCC
Q 026787 15 GYGCKHYRR---RCRIRAPCCNEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVA-----QVCTNCGV 86 (233)
Q Consensus 15 ~~gC~HY~r---~c~l~~pCC~~~y~Cr~CHde~~~~~~~~~~~H~~~r~~v~~v~C~~C~~~q~~~-----~~C~~Cg~ 86 (233)
++||.||++ +++|||.+|+|||+|++||||+++|++ +.+.++.+..+.||||.|.++++++ ..|++|.+
T Consensus 12 etRC~Hyht~~Diialkc~~C~kyYaCy~CHdel~~Hpf---~p~~~~~~~~~~iiCGvC~~~LT~~EY~~~~~Cp~C~s 88 (105)
T COG4357 12 ETRCLHYHTPLDIIALKCKCCQKYYACYHCHDELEDHPF---EPWGLQEFNPKAIICGVCRKLLTRAEYGMCGSCPYCQS 88 (105)
T ss_pred cceeeEecCccceEeeeechhhhhhhHHHHHhHHhcCCC---ccCChhhcCCccEEhhhhhhhhhHHHHhhcCCCCCcCC
Confidence 579999999 789999999999999999999998875 6777788888899999999999884 57999999
Q ss_pred Ccce
Q 026787 87 NMGE 90 (233)
Q Consensus 87 ~f~~ 90 (233)
+||.
T Consensus 89 pFNp 92 (105)
T COG4357 89 PFNP 92 (105)
T ss_pred CCCc
Confidence 9985
No 4
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=99.42 E-value=3.9e-14 Score=94.16 Aligned_cols=44 Identities=39% Similarity=0.937 Sum_probs=37.7
Q ss_pred CCCcchhhhhcccCCceeEeccCCccChhhHHHHhccCCCcCCCCC
Q 026787 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICS 196 (233)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCr 196 (233)
++||||+|++.+ .+.+..|+|||.||.+|+.+|++. +.+||+||
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 479999999755 478889999999999999999985 68999996
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=99.09 E-value=6.7e-11 Score=87.27 Aligned_cols=48 Identities=31% Similarity=0.688 Sum_probs=37.0
Q ss_pred CCCCCCcchhhhhccc---------CCceeEeccCCccChhhHHHHhccCCCcCCCCC
Q 026787 148 SMHHHCPICYEYLFDS---------LRNTTVMKCGHTMHCECYHEMIKRDKYCCPICS 196 (233)
Q Consensus 148 ~~~~~CpICle~lf~s---------~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCr 196 (233)
..+++|+||++.|.+. ..++...+|||.||..||.+||+. +.+||+||
T Consensus 17 ~~~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~-~~~CP~CR 73 (73)
T PF12678_consen 17 IADDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQ-NNTCPLCR 73 (73)
T ss_dssp SCCSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTT-SSB-TTSS
T ss_pred CcCCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhc-CCcCCCCC
Confidence 3466799999998443 234566689999999999999985 67999997
No 6
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=99.09 E-value=2.7e-11 Score=86.97 Aligned_cols=33 Identities=55% Similarity=0.830 Sum_probs=5.6
Q ss_pred ccchhHHhhhhHHHHHhCCCChhhhcceeEEEE
Q 026787 199 VIDMSRTWKRIDEEIEATVMPEDYRHKKVSSCL 231 (233)
Q Consensus 199 i~dm~~~~~~lD~~i~~~pmP~~y~~~~~~i~~ 231 (233)
|+||+.+|++||++|+++|||++|++++|||+|
T Consensus 1 v~dM~~~w~~LD~~i~~~pmP~~Y~~~~v~IlC 33 (61)
T PF14599_consen 1 VVDMSAYWRMLDAEIAATPMPEEYRNKKVWILC 33 (61)
T ss_dssp ---------------------------EEEEEE
T ss_pred CCCHHHHHHHHHHHHHhCCCCHHHhCCEEEEEC
Confidence 579999999999999999999999999999997
No 7
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=99.02 E-value=2.2e-10 Score=73.58 Aligned_cols=45 Identities=31% Similarity=0.866 Sum_probs=37.8
Q ss_pred CCcchhhhhcccCCceeEeccCCccChhhHHHHhccCCCcCCCCCccc
Q 026787 152 HCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSV 199 (233)
Q Consensus 152 ~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrksi 199 (233)
.|+||++.+ ..++..++|||.||..|++.|++..+.+||+|++.+
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 245666779999999999999985578899999764
No 8
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=98.98 E-value=1.5e-10 Score=108.22 Aligned_cols=57 Identities=28% Similarity=0.771 Sum_probs=48.8
Q ss_pred CCCCCCCcchhhhhcccC---------CceeEeccCCccChhhHHHHhccCCCcCCCCCcc-ccchhH
Q 026787 147 NSMHHHCPICYEYLFDSL---------RNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKS-VIDMSR 204 (233)
Q Consensus 147 ~~~~~~CpICle~lf~s~---------~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrks-i~dm~~ 204 (233)
.+.+..|.||+|+|+.+. ...+.|||||.+|-+|++.|++. +.+|||||.+ +.||+.
T Consensus 284 ~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ER-qQTCPICr~p~ifd~~~ 350 (491)
T COG5243 284 TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLER-QQTCPICRRPVIFDQSS 350 (491)
T ss_pred cCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHh-ccCCCcccCccccccCC
Confidence 566788999999998775 23488999999999999999984 7899999999 678764
No 9
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.95 E-value=3.1e-10 Score=105.72 Aligned_cols=50 Identities=22% Similarity=0.762 Sum_probs=44.1
Q ss_pred CCCcchhhhhcccCCceeEeccCCccChhhHHHHhccCCCcCCCCCccccc
Q 026787 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID 201 (233)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrksi~d 201 (233)
..|.||||+ |..++.+++|||+|.||..|++.||......||+|+..+..
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 67779999999999999999999998544559999998864
No 10
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=98.88 E-value=8.2e-10 Score=71.69 Aligned_cols=39 Identities=38% Similarity=0.987 Sum_probs=33.3
Q ss_pred CcchhhhhcccCCceeEeccCCccChhhHHHHhccCCCcCCCC
Q 026787 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPIC 195 (233)
Q Consensus 153 CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiC 195 (233)
||||++.+.+ ++++++|||+|+..|+.+|++. +.+||+|
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 8999998653 6789999999999999999996 7999998
No 11
>PHA02929 N1R/p28-like protein; Provisional
Probab=98.86 E-value=1.7e-09 Score=96.38 Aligned_cols=55 Identities=29% Similarity=0.658 Sum_probs=43.1
Q ss_pred cCCCCCCCcchhhhhcccCC---c-eeEeccCCccChhhHHHHhccCCCcCCCCCccccc
Q 026787 146 ENSMHHHCPICYEYLFDSLR---N-TTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID 201 (233)
Q Consensus 146 e~~~~~~CpICle~lf~s~~---~-v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrksi~d 201 (233)
+.+.+..||||+|.+.+... . ...++|||.||..|+.+|++ .+.+||+||+.+..
T Consensus 170 ~~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~-~~~tCPlCR~~~~~ 228 (238)
T PHA02929 170 NRSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKK-EKNTCPVCRTPFIS 228 (238)
T ss_pred cCCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHh-cCCCCCCCCCEeeE
Confidence 34557899999999765321 1 23457999999999999998 57899999998874
No 12
>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=98.79 E-value=2.7e-09 Score=72.67 Aligned_cols=47 Identities=36% Similarity=0.918 Sum_probs=39.1
Q ss_pred CCCCcchhhhhcccCCceeEeccCCc-cChhhHHHHhccCCCcCCCCCccccc
Q 026787 150 HHHCPICYEYLFDSLRNTTVMKCGHT-MHCECYHEMIKRDKYCCPICSKSVID 201 (233)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCGH~-~H~~C~~~~~~~~~~~CPiCrksi~d 201 (233)
+..|+||++.. ..+.++||||. |...|+.+|++ ...+||+||++|.+
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 45799999973 35788999999 99999999998 57999999999864
No 13
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=98.71 E-value=8.6e-09 Score=63.82 Aligned_cols=39 Identities=44% Similarity=1.076 Sum_probs=33.6
Q ss_pred CcchhhhhcccCCceeEeccCCccChhhHHHHhccCCCcCCCC
Q 026787 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPIC 195 (233)
Q Consensus 153 CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiC 195 (233)
|+||++. .+....++|||.||..|++.|++....+||+|
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 24678899999999999999997556789987
No 14
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=98.70 E-value=1.1e-08 Score=77.94 Aligned_cols=33 Identities=27% Similarity=0.633 Sum_probs=27.3
Q ss_pred eeEeccCCccChhhHHHHhcc--CCCcCCCCCccc
Q 026787 167 TTVMKCGHTMHCECYHEMIKR--DKYCCPICSKSV 199 (233)
Q Consensus 167 v~~LpCGH~~H~~C~~~~~~~--~~~~CPiCrksi 199 (233)
+..-.|||.||..||.+|+.. ++.+||+||+..
T Consensus 47 lv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w 81 (85)
T PF12861_consen 47 LVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPW 81 (85)
T ss_pred eeeccCccHHHHHHHHHHHccccCCCCCCCcCCee
Confidence 344469999999999999985 367899999865
No 15
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=98.68 E-value=7.4e-09 Score=67.26 Aligned_cols=40 Identities=33% Similarity=0.938 Sum_probs=34.5
Q ss_pred CcchhhhhcccCCceeEeccCCccChhhHHHHhc-cCCCcCCCC
Q 026787 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIK-RDKYCCPIC 195 (233)
Q Consensus 153 CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~-~~~~~CPiC 195 (233)
||||++.+.+ ++..++|||.|+..|+.+|++ .+..+||+|
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 567899998
No 16
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.68 E-value=1.4e-08 Score=67.65 Aligned_cols=44 Identities=34% Similarity=0.848 Sum_probs=38.0
Q ss_pred CCcchhhhhcccCCceeEeccCCccChhhHHHHhccCCCcCCCCCc
Q 026787 152 HCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSK 197 (233)
Q Consensus 152 ~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrk 197 (233)
.|+||++.+ +......+|+|||+|...|+..+.. ....||+|+|
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 17
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.63 E-value=1.7e-08 Score=92.48 Aligned_cols=53 Identities=25% Similarity=0.601 Sum_probs=45.3
Q ss_pred cCCCCCCCcchhhhhcccCCceeEeccCCccChhhHHHHhccCCCcCCCCCccc
Q 026787 146 ENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSV 199 (233)
Q Consensus 146 e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrksi 199 (233)
|....-+|.|||++ |...+.+++|||.|.||..|+++|+.....+||+||..+
T Consensus 319 ea~~GveCaICms~-fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~i 371 (374)
T COG5540 319 EADKGVECAICMSN-FIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAI 371 (374)
T ss_pred hcCCCceEEEEhhh-hcccceEEEeccCceechhHHHHHHhhhcccCCccCCCC
Confidence 33445689999999 567788999999999999999999985678999999665
No 18
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.55 E-value=5.2e-08 Score=64.77 Aligned_cols=39 Identities=31% Similarity=0.963 Sum_probs=28.4
Q ss_pred CcchhhhhcccCCceeEeccCCccChhhHHHHhccCC---CcCCCC
Q 026787 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDK---YCCPIC 195 (233)
Q Consensus 153 CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~---~~CPiC 195 (233)
||||++.|. ..+.|+|||+|-..|+.+|.+... +.||+|
T Consensus 1 CpiC~~~~~----~Pv~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDLFK----DPVSLPCGHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB-S----SEEE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCccchhhC----CccccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 899999864 345699999999999999987532 579987
No 19
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.49 E-value=5.9e-08 Score=65.10 Aligned_cols=40 Identities=33% Similarity=0.890 Sum_probs=23.9
Q ss_pred CcchhhhhcccCCceeEeccCCccChhhHHHHhccC---CCcCC
Q 026787 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRD---KYCCP 193 (233)
Q Consensus 153 CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~---~~~CP 193 (233)
||||.| +.+...+.++|+|||+|-++|+++|++.+ ..+||
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 55545567889999999999999999843 56777
No 20
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.43 E-value=1.8e-07 Score=81.04 Aligned_cols=57 Identities=23% Similarity=0.599 Sum_probs=43.2
Q ss_pred cceeecCCCCCCCcchhhhhcccCCceeEeccCCccChhhHHHHhcc---------------CCCcCCCCCccccc
Q 026787 141 NHLCIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR---------------DKYCCPICSKSVID 201 (233)
Q Consensus 141 ~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~---------------~~~~CPiCrksi~d 201 (233)
+-+=++...+..||||++.+. ..++++|||.|+..|+.+|+.. +..+||+|+..+..
T Consensus 9 ~~~~~~~~~~~~CpICld~~~----dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~ 80 (193)
T PLN03208 9 DTTLVDSGGDFDCNICLDQVR----DPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE 80 (193)
T ss_pred cceeccCCCccCCccCCCcCC----CcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence 334445556789999999742 3456899999999999999842 23589999999864
No 21
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.41 E-value=7.1e-08 Score=94.60 Aligned_cols=53 Identities=26% Similarity=0.600 Sum_probs=43.9
Q ss_pred cCCCCCCCcchhhhhcccC-CceeEeccCCccChhhHHHHhccCCCcCCCCCccc
Q 026787 146 ENSMHHHCPICYEYLFDSL-RNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSV 199 (233)
Q Consensus 146 e~~~~~~CpICle~lf~s~-~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrksi 199 (233)
....+..|+||+|.|+.+. ....+|+|||.||..|+..|++. ..+||+||..+
T Consensus 287 ~~~~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er-~qtCP~CR~~~ 340 (543)
T KOG0802|consen 287 LALSDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFER-QQTCPTCRTVL 340 (543)
T ss_pred hhhcCCeeeeechhhccccccccceeecccchHHHHHHHHHHH-hCcCCcchhhh
Confidence 3455788999999997642 22678999999999999999984 79999999943
No 22
>PHA02926 zinc finger-like protein; Provisional
Probab=98.24 E-value=6.2e-07 Score=79.33 Aligned_cols=68 Identities=21% Similarity=0.377 Sum_probs=47.3
Q ss_pred cccccccccceeecCCCCCCCcchhhhhcccC-----CceeEeccCCccChhhHHHHhccC-----CCcCCCCCcccc
Q 026787 133 CYSTSLRNNHLCIENSMHHHCPICYEYLFDSL-----RNTTVMKCGHTMHCECYHEMIKRD-----KYCCPICSKSVI 200 (233)
Q Consensus 133 C~s~~l~~~H~C~e~~~~~~CpICle~lf~s~-----~~v~~LpCGH~~H~~C~~~~~~~~-----~~~CPiCrksi~ 200 (233)
+++.-|.+-..=...+.+..|+||+|.+++.. ......+|+|.|+..|+.+|.+.. ..+||+||..+.
T Consensus 153 ~i~~il~~ye~~~~~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~ 230 (242)
T PHA02926 153 DIIKILDKYEDVYRVSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFR 230 (242)
T ss_pred chhHHHHHHHHHHhccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceee
Confidence 44444433333345677889999999876531 123445899999999999999742 346999998875
No 23
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.11 E-value=1.1e-06 Score=75.18 Aligned_cols=46 Identities=30% Similarity=0.856 Sum_probs=37.8
Q ss_pred CCCcchhhhhcccCCce-eEeccCCccChhhHHHHhccCCCcCCCCCcccc
Q 026787 151 HHCPICYEYLFDSLRNT-TVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (233)
Q Consensus 151 ~~CpICle~lf~s~~~v-~~LpCGH~~H~~C~~~~~~~~~~~CPiCrksi~ 200 (233)
-.|||||+.. + +.+ ..-.|||.|.+.|++.-++ ...+||+|+|.|.
T Consensus 132 ~~CPiCl~~~-s--ek~~vsTkCGHvFC~~Cik~alk-~~~~CP~C~kkIt 178 (187)
T KOG0320|consen 132 YKCPICLDSV-S--EKVPVSTKCGHVFCSQCIKDALK-NTNKCPTCRKKIT 178 (187)
T ss_pred cCCCceecch-h--hccccccccchhHHHHHHHHHHH-hCCCCCCcccccc
Confidence 6899999984 3 233 3478999999999999998 4789999999664
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=98.06 E-value=3.6e-06 Score=58.84 Aligned_cols=45 Identities=18% Similarity=0.361 Sum_probs=38.0
Q ss_pred CCCcchhhhhcccCCceeEeccCCccChhhHHHHhccCCCcCCCCCcccc
Q 026787 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (233)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrksi~ 200 (233)
-.||||++.|.+ + .+++|||+|-+.|+.+|++. +.+||+|++.+.
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 369999998643 3 56799999999999999985 789999999873
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=98.04 E-value=3e-06 Score=58.16 Aligned_cols=43 Identities=28% Similarity=0.617 Sum_probs=33.6
Q ss_pred CCcchhhhhcccCCceeEeccC-----CccChhhHHHHhccC-CCcCCCCC
Q 026787 152 HCPICYEYLFDSLRNTTVMKCG-----HTMHCECYHEMIKRD-KYCCPICS 196 (233)
Q Consensus 152 ~CpICle~lf~s~~~v~~LpCG-----H~~H~~C~~~~~~~~-~~~CPiCr 196 (233)
.|-||++ +++.+...++||. |++|..|+.+|+..+ +.+||+|+
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 3344566688984 999999999999653 56899995
No 26
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=97.97 E-value=3.4e-06 Score=80.80 Aligned_cols=47 Identities=28% Similarity=0.757 Sum_probs=41.9
Q ss_pred CCCcchhhhhcccCCceeEeccCCccChhhHHHHhccCCCcCCCCCcccc
Q 026787 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (233)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrksi~ 200 (233)
..||||||.|.+|+..+....|.|+||..|+..|. ..+||+||-...
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 47999999999998888999999999999999995 479999996554
No 27
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=97.90 E-value=2.9e-06 Score=62.19 Aligned_cols=51 Identities=31% Similarity=0.656 Sum_probs=24.0
Q ss_pred CCCCcchhhhhc-ccCCceeEe---ccCCccChhhHHHHhcc--C--------CCcCCCCCcccc
Q 026787 150 HHHCPICYEYLF-DSLRNTTVM---KCGHTMHCECYHEMIKR--D--------KYCCPICSKSVI 200 (233)
Q Consensus 150 ~~~CpICle~lf-~s~~~v~~L---pCGH~~H~~C~~~~~~~--~--------~~~CPiCrksi~ 200 (233)
+.+|+||.+++. +...+..+- .|+..||..||.+|+.. + ..+||.|++.|.
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~ 66 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPIS 66 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEE
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeee
Confidence 457999999876 333333333 59999999999999873 1 246999999884
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=97.82 E-value=1.4e-05 Score=76.21 Aligned_cols=46 Identities=22% Similarity=0.587 Sum_probs=38.5
Q ss_pred CCCCcchhhhhcccCCceeEeccCCccChhhHHHHhccCCCcCCCCCcccc
Q 026787 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (233)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrksi~ 200 (233)
...|+||++.+.. ++ +++|||.|+..|+..|+.. ...||+|+..+.
T Consensus 26 ~l~C~IC~d~~~~---Pv-itpCgH~FCs~CI~~~l~~-~~~CP~Cr~~~~ 71 (397)
T TIGR00599 26 SLRCHICKDFFDV---PV-LTSCSHTFCSLCIRRCLSN-QPKCPLCRAEDQ 71 (397)
T ss_pred ccCCCcCchhhhC---cc-CCCCCCchhHHHHHHHHhC-CCCCCCCCCccc
Confidence 4589999998643 33 6899999999999999974 568999999876
No 29
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=97.74 E-value=2.4e-05 Score=59.24 Aligned_cols=29 Identities=24% Similarity=0.620 Sum_probs=26.0
Q ss_pred ccCCccChhhHHHHhccCCCcCCCCCcccc
Q 026787 171 KCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (233)
Q Consensus 171 pCGH~~H~~C~~~~~~~~~~~CPiCrksi~ 200 (233)
-|.|.||.+|+..||.+ ...||+++++..
T Consensus 53 ~CnHaFH~HCI~rWL~T-k~~CPld~q~w~ 81 (88)
T COG5194 53 VCNHAFHDHCIYRWLDT-KGVCPLDRQTWV 81 (88)
T ss_pred ecchHHHHHHHHHHHhh-CCCCCCCCceeE
Confidence 59999999999999985 789999998764
No 30
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.68 E-value=2.2e-05 Score=66.60 Aligned_cols=44 Identities=30% Similarity=0.845 Sum_probs=38.0
Q ss_pred CCCCCcchhhhhcccCCceeEeccCCccChhhHHHHhccCCCcCCCCCc
Q 026787 149 MHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSK 197 (233)
Q Consensus 149 ~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrk 197 (233)
....||||++++.. + .+|||||+|-..|+..++. ....||.||.
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 45689999999644 2 8899999999999999987 6799999994
No 31
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.68 E-value=1.6e-05 Score=75.25 Aligned_cols=46 Identities=26% Similarity=0.594 Sum_probs=39.7
Q ss_pred CCCCcchhhhhcccCCceeEec-cCCccChhhHHHHhcc--CCCcCCCCC
Q 026787 150 HHHCPICYEYLFDSLRNTTVMK-CGHTMHCECYHEMIKR--DKYCCPICS 196 (233)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~Lp-CGH~~H~~C~~~~~~~--~~~~CPiCr 196 (233)
...|.|| ++++.....+..+. |||+||..|+.+|+.. ++.+||||+
T Consensus 4 ~A~C~Ic-~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ 52 (465)
T KOG0827|consen 4 MAECHIC-IDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQ 52 (465)
T ss_pred cceeeEe-ccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCcee
Confidence 4579999 77888888888886 9999999999999985 346899999
No 32
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.67 E-value=3.7e-05 Score=71.10 Aligned_cols=51 Identities=25% Similarity=0.554 Sum_probs=38.9
Q ss_pred CCCCcchhhhhcccCCc-eeEeccCCccChhhHHHHhccCCCcCCCCCcccc
Q 026787 150 HHHCPICYEYLFDSLRN-TTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (233)
Q Consensus 150 ~~~CpICle~lf~s~~~-v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrksi~ 200 (233)
+..||||+.+...+.+. +.+.+|||.|..+|++.++..+...||+|++++-
T Consensus 3 ~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lr 54 (309)
T TIGR00570 3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLR 54 (309)
T ss_pred CCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCccc
Confidence 35799999965544332 1222799999999999977666789999998875
No 33
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=97.57 E-value=2.7e-05 Score=71.14 Aligned_cols=45 Identities=29% Similarity=0.693 Sum_probs=37.8
Q ss_pred CCCcchhhhhcccCCceeEeccCCccChhhHHHHhccCCCcCCCCCcccc
Q 026787 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (233)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrksi~ 200 (233)
..|.+|||... .....||||.|.-+|+.+|... .-.||+||..+-
T Consensus 240 ~kC~LCLe~~~----~pSaTpCGHiFCWsCI~~w~~e-k~eCPlCR~~~~ 284 (293)
T KOG0317|consen 240 RKCSLCLENRS----NPSATPCGHIFCWSCILEWCSE-KAECPLCREKFQ 284 (293)
T ss_pred CceEEEecCCC----CCCcCcCcchHHHHHHHHHHcc-ccCCCcccccCC
Confidence 47999999853 3457899999999999999985 577999997664
No 34
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=97.56 E-value=8.4e-05 Score=69.56 Aligned_cols=75 Identities=24% Similarity=0.534 Sum_probs=52.3
Q ss_pred CCcchhhhhcccCCceeEeccCCccChhhHHHHhccCCCcCCCCCccccc-hhHHhhhhHHHHHh---------------
Q 026787 152 HCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID-MSRTWKRIDEEIEA--------------- 215 (233)
Q Consensus 152 ~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrksi~d-m~~~~~~lD~~i~~--------------- 215 (233)
.|-||.|+|. ...+.||||+|.+-||..+|. .+-.||.|..++.. ..+--+.||++|++
T Consensus 25 RC~IC~eyf~----ip~itpCsHtfCSlCIR~~L~-~~p~CP~C~~~~~Es~Lr~n~il~Eiv~S~~~~R~~Ll~fl~~~ 99 (442)
T KOG0287|consen 25 RCGICFEYFN----IPMITPCSHTFCSLCIRKFLS-YKPQCPTCCVTVTESDLRNNRILDEIVKSLNFARNHLLQFLLES 99 (442)
T ss_pred HHhHHHHHhc----CceeccccchHHHHHHHHHhc-cCCCCCceecccchhhhhhhhHHHHHHHHHHHHHHHHHHHHhcC
Confidence 6999999953 345668999999999999998 58899999998863 12233445554433
Q ss_pred -CCCChhhhcceeEEEE
Q 026787 216 -TVMPEDYRHKKVSSCL 231 (233)
Q Consensus 216 -~pmP~~y~~~~~~i~~ 231 (233)
+|.|+.-.....||=.
T Consensus 100 ~~p~P~~~~~p~~~ve~ 116 (442)
T KOG0287|consen 100 PAPSPASSSSPNLAVEV 116 (442)
T ss_pred CCCCcccccCCccceee
Confidence 4666555555445533
No 35
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.51 E-value=4.9e-05 Score=73.97 Aligned_cols=50 Identities=28% Similarity=0.628 Sum_probs=38.9
Q ss_pred CCCCCCcchhhhhcccCCceeEeccCCccChhhHHHHhccC----CCcCCCCCccccc
Q 026787 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRD----KYCCPICSKSVID 201 (233)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~----~~~CPiCrksi~d 201 (233)
+++..|||||++- . ....+.|||+|.-.||-+|+..+ ...||||+.+|.-
T Consensus 184 ~t~~~CPICL~~~-~---~p~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~ 237 (513)
T KOG2164|consen 184 STDMQCPICLEPP-S---VPVRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITL 237 (513)
T ss_pred CcCCcCCcccCCC-C---cccccccCceeeHHHHHHHHhhhcccCCccCCchhhhccc
Confidence 4488999999982 1 23345699999999999988643 4679999999863
No 36
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.31 E-value=6.6e-05 Score=73.02 Aligned_cols=51 Identities=24% Similarity=0.533 Sum_probs=37.4
Q ss_pred CCCCcchhhhhcc--cCC-----------ceeEeccCCccChhhHHHHhccCCCcCCCCCcccc
Q 026787 150 HHHCPICYEYLFD--SLR-----------NTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (233)
Q Consensus 150 ~~~CpICle~lf~--s~~-----------~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrksi~ 200 (233)
..+|+||+.++-- ... ...+-||.|.||+.|+.+|+...+..||+||..+-
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 3579999876421 111 23344999999999999999866678999998763
No 37
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.30 E-value=6.6e-05 Score=68.33 Aligned_cols=52 Identities=27% Similarity=0.520 Sum_probs=42.2
Q ss_pred CCCCCcchhhhhcccC------CceeEeccCCccChhhHHHHhc-cCCCcCCCCCcccc
Q 026787 149 MHHHCPICYEYLFDSL------RNTTVMKCGHTMHCECYHEMIK-RDKYCCPICSKSVI 200 (233)
Q Consensus 149 ~~~~CpICle~lf~s~------~~v~~LpCGH~~H~~C~~~~~~-~~~~~CPiCrksi~ 200 (233)
+++.|.||...++.|. +....|.|+|.||+.|++-|-- ....+||.|++.+.
T Consensus 223 ~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVd 281 (328)
T KOG1734|consen 223 SDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVD 281 (328)
T ss_pred CcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhh
Confidence 4567999999987764 2457799999999999999953 34689999998774
No 38
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.25 E-value=0.00017 Score=64.05 Aligned_cols=50 Identities=24% Similarity=0.632 Sum_probs=38.9
Q ss_pred CCCCCCcchhhhhcccCCceeEeccCCccChhhHHHHhcc--CCCcCCCCCccccc
Q 026787 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR--DKYCCPICSKSVID 201 (233)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~--~~~~CPiCrksi~d 201 (233)
...-+|-||||-- ++.++-.|||.|.-.||.+||.. +...||+|+..|.+
T Consensus 45 ~~~FdCNICLd~a----kdPVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~ 96 (230)
T KOG0823|consen 45 GGFFDCNICLDLA----KDPVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSI 96 (230)
T ss_pred CCceeeeeecccc----CCCEEeecccceehHHHHHHHhhcCCCeeCCcccccccc
Confidence 4456899999852 34566779999999999999974 24558999988764
No 39
>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=97.24 E-value=0.00037 Score=51.07 Aligned_cols=47 Identities=17% Similarity=0.369 Sum_probs=35.6
Q ss_pred CCCcchhhhhcccCCceeEeccCCccChhhHHHHhccCCCcCCCCCccccc
Q 026787 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID 201 (233)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrksi~d 201 (233)
-.|||+++-|. +.+++|+||+|=+.++.+|+..++.+||++++.+..
T Consensus 5 f~CpIt~~lM~----dPVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~ 51 (73)
T PF04564_consen 5 FLCPITGELMR----DPVILPSGHTYERSAIERWLEQNGGTDPFTRQPLSE 51 (73)
T ss_dssp GB-TTTSSB-S----SEEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SG
T ss_pred cCCcCcCcHhh----CceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCc
Confidence 46999999764 345689999999999999998668999999988763
No 40
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=97.16 E-value=0.00014 Score=54.72 Aligned_cols=29 Identities=24% Similarity=0.707 Sum_probs=24.9
Q ss_pred ccCCccChhhHHHHhcc--CCCcCCCCCccc
Q 026787 171 KCGHTMHCECYHEMIKR--DKYCCPICSKSV 199 (233)
Q Consensus 171 pCGH~~H~~C~~~~~~~--~~~~CPiCrksi 199 (233)
-|.|.||..|+.+|+.. ++..||+||++.
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 467799999875
No 41
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=97.12 E-value=0.00023 Score=51.76 Aligned_cols=56 Identities=25% Similarity=0.640 Sum_probs=29.1
Q ss_pred CCCcchhhhhcccCCceeEeccCCccChhhHHHHhccCCCcCCCCCcccc--chhHHhhhhHHHH
Q 026787 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI--DMSRTWKRIDEEI 213 (233)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrksi~--dm~~~~~~lD~~i 213 (233)
..|++|.+.|. ++|..-.|.|.|.+.|+.+-+. ..||+|+.+.. |+. ..+.||.+|
T Consensus 8 LrCs~C~~~l~---~pv~l~~CeH~fCs~Ci~~~~~---~~CPvC~~Paw~qD~~-~NrqLd~~i 65 (65)
T PF14835_consen 8 LRCSICFDILK---EPVCLGGCEHIFCSSCIRDCIG---SECPVCHTPAWIQDIQ-INRQLDSMI 65 (65)
T ss_dssp TS-SSS-S--S---S-B---SSS--B-TTTGGGGTT---TB-SSS--B-S-SS-----HHHHHHH
T ss_pred cCCcHHHHHhc---CCceeccCccHHHHHHhHHhcC---CCCCCcCChHHHHHHH-hhhhhhccC
Confidence 36999999874 3666778999999999998774 46999999884 443 457787765
No 42
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=96.96 E-value=0.00019 Score=68.25 Aligned_cols=63 Identities=27% Similarity=0.589 Sum_probs=52.4
Q ss_pred cceeecCCCCCCCcchhhhhcccCCceeEeccCCccChhhHHHHhcc-CCCcCCCCCccccchhH
Q 026787 141 NHLCIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR-DKYCCPICSKSVIDMSR 204 (233)
Q Consensus 141 ~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~-~~~~CPiCrksi~dm~~ 204 (233)
.|.|++ .++-+|-.|.|-+-...+....|||.|+||..|+.++|.. ...+||-|||....|++
T Consensus 357 a~~~~~-e~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~CrklrSs~~r 420 (518)
T KOG1941|consen 357 AHECVE-ETELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRKLRSSMKR 420 (518)
T ss_pred HHHHHH-HHhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHHHHhhccC
Confidence 456665 4578999999999888888999999999999999999864 45789999987776663
No 43
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.88 E-value=0.00061 Score=63.87 Aligned_cols=52 Identities=27% Similarity=0.660 Sum_probs=41.8
Q ss_pred cCCCCCCCcchhhhhcccCCceeEeccCCc-cChhhHHHHhccCCCcCCCCCccccch
Q 026787 146 ENSMHHHCPICYEYLFDSLRNTTVMKCGHT-MHCECYHEMIKRDKYCCPICSKSVIDM 202 (233)
Q Consensus 146 e~~~~~~CpICle~lf~s~~~v~~LpCGH~-~H~~C~~~~~~~~~~~CPiCrksi~dm 202 (233)
++....+|.|||.+. +++.+|||.|. |.+.|-+.+.- .+.+|||||+.|...
T Consensus 286 ~~~~gkeCVIClse~----rdt~vLPCRHLCLCs~Ca~~Lr~-q~n~CPICRqpi~~l 338 (349)
T KOG4265|consen 286 ESESGKECVICLSES----RDTVVLPCRHLCLCSGCAKSLRY-QTNNCPICRQPIEEL 338 (349)
T ss_pred cccCCCeeEEEecCC----cceEEecchhhehhHhHHHHHHH-hhcCCCccccchHhh
Confidence 334466899999873 57889999997 89999998863 578999999998754
No 44
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.64 E-value=0.00084 Score=60.83 Aligned_cols=47 Identities=26% Similarity=0.548 Sum_probs=37.4
Q ss_pred CCCCcchhhhhcccCCceeEeccCCccChhhHHH-HhccCCCcCCCCCcccc
Q 026787 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHE-MIKRDKYCCPICSKSVI 200 (233)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~-~~~~~~~~CPiCrksi~ 200 (233)
+-.|+||+|... .....+|||.|.-.|+.. |.......||+||.-+.
T Consensus 215 d~kC~lC~e~~~----~ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~ 262 (271)
T COG5574 215 DYKCFLCLEEPE----VPSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVY 262 (271)
T ss_pred ccceeeeecccC----CcccccccchhhHHHHHHHHHhhccccCchhhhhcc
Confidence 456999999853 456789999999999999 88754344999997664
No 45
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=96.53 E-value=0.002 Score=44.30 Aligned_cols=44 Identities=30% Similarity=0.815 Sum_probs=24.5
Q ss_pred CcchhhhhcccCCceeEec--cCCccChhhHHHHhccCCCcCCCCCcc
Q 026787 153 CPICYEYLFDSLRNTTVMK--CGHTMHCECYHEMIKRDKYCCPICSKS 198 (233)
Q Consensus 153 CpICle~lf~s~~~v~~Lp--CGH~~H~~C~~~~~~~~~~~CPiCrks 198 (233)
||+|.|+|..+ ...++| ||.-+-+.|+..-++..+.+||-||+.
T Consensus 1 cp~C~e~~d~~--d~~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~ 46 (48)
T PF14570_consen 1 CPLCDEELDET--DKDFYPCECGFQICRFCYHDILENEGGRCPGCREP 46 (48)
T ss_dssp -TTTS-B--CC--CTT--SSTTS----HHHHHHHTTSS-SB-TTT--B
T ss_pred CCCcccccccC--CCccccCcCCCcHHHHHHHHHHhccCCCCCCCCCC
Confidence 79999998444 445555 799999999999987568999999975
No 46
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=96.48 E-value=0.0014 Score=68.17 Aligned_cols=52 Identities=27% Similarity=0.653 Sum_probs=37.9
Q ss_pred CCCCCCcchhhhhc--ccCCceeE-eccCCccChhhHHHHhcc-CCCcCCCCCccc
Q 026787 148 SMHHHCPICYEYLF--DSLRNTTV-MKCGHTMHCECYHEMIKR-DKYCCPICSKSV 199 (233)
Q Consensus 148 ~~~~~CpICle~lf--~s~~~v~~-LpCGH~~H~~C~~~~~~~-~~~~CPiCrksi 199 (233)
+...+|+||..-|. +..-|.+. -.|.|-||..|+.+|+++ ++.+||+||.++
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 45678999988765 22222222 237799999999999986 468899999765
No 47
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=96.46 E-value=0.0017 Score=51.54 Aligned_cols=28 Identities=29% Similarity=0.734 Sum_probs=24.9
Q ss_pred ccCCccChhhHHHHhccCCCcCCCCCccc
Q 026787 171 KCGHTMHCECYHEMIKRDKYCCPICSKSV 199 (233)
Q Consensus 171 pCGH~~H~~C~~~~~~~~~~~CPiCrksi 199 (233)
-|.|+||-.|+..||+ ++..|||+.|.-
T Consensus 80 ~CNHaFH~hCisrWlk-tr~vCPLdn~eW 107 (114)
T KOG2930|consen 80 VCNHAFHFHCISRWLK-TRNVCPLDNKEW 107 (114)
T ss_pred ecchHHHHHHHHHHHh-hcCcCCCcCcce
Confidence 5999999999999998 478999998753
No 48
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.40 E-value=0.00086 Score=47.56 Aligned_cols=54 Identities=37% Similarity=0.784 Sum_probs=39.3
Q ss_pred CCCCCCcchhhhhcccCCceeEeccCCc-cChhhHHHHhccCCCcCCCCCccccchhHH
Q 026787 148 SMHHHCPICYEYLFDSLRNTTVMKCGHT-MHCECYHEMIKRDKYCCPICSKSVIDMSRT 205 (233)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~-~H~~C~~~~~~~~~~~CPiCrksi~dm~~~ 205 (233)
+.+.+|.||.|.-.+| +.--|||+ |.-.|-.+.++..+..|||||.+|-|+-+.
T Consensus 5 ~~~dECTICye~pvds----VlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~dvIkT 59 (62)
T KOG4172|consen 5 QWSDECTICYEHPVDS----VLYTCGHMCMCYACGLRLKKALHGCCPICRAPIKDVIKT 59 (62)
T ss_pred ccccceeeeccCcchH----HHHHcchHHhHHHHHHHHHHccCCcCcchhhHHHHHHHh
Confidence 3457899999974433 33479997 566776666655688999999999876543
No 49
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.26 E-value=0.001 Score=62.54 Aligned_cols=49 Identities=27% Similarity=0.688 Sum_probs=41.7
Q ss_pred CCCCcchhhhhcccCCceeEeccCCccChhhHHHHhccCCCcCCCCCccccc
Q 026787 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID 201 (233)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrksi~d 201 (233)
+-.|||||+-|.. .+..+-|+|-|...||..-++.++..||.|||.+..
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 3479999997653 456778999999999999888889999999999973
No 50
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.26 E-value=0.0014 Score=61.56 Aligned_cols=77 Identities=23% Similarity=0.527 Sum_probs=54.3
Q ss_pred CCCCCCCcchhhhhcccC---CceeE-eccCCccChhhHHHHhccC------CCcCCCCCcccc--chhHHhhhhHHHHH
Q 026787 147 NSMHHHCPICYEYLFDSL---RNTTV-MKCGHTMHCECYHEMIKRD------KYCCPICSKSVI--DMSRTWKRIDEEIE 214 (233)
Q Consensus 147 ~~~~~~CpICle~lf~s~---~~v~~-LpCGH~~H~~C~~~~~~~~------~~~CPiCrksi~--dm~~~~~~lD~~i~ 214 (233)
++.+..|-||+|.+.+.. ..-.+ ++|-|+|...|+..|.... ...||+||.+.. .-+.+|..-.+ +
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 366789999999987653 11223 4599999999999998432 478999998874 44456755444 5
Q ss_pred hCCCChhhhcc
Q 026787 215 ATVMPEDYRHK 225 (233)
Q Consensus 215 ~~pmP~~y~~~ 225 (233)
.++.+++|+..
T Consensus 236 k~~li~e~~~~ 246 (344)
T KOG1039|consen 236 KQKLIEEYEAE 246 (344)
T ss_pred ccccHHHHHHH
Confidence 66667776654
No 51
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=96.15 E-value=0.0017 Score=66.34 Aligned_cols=76 Identities=16% Similarity=0.290 Sum_probs=53.5
Q ss_pred eeeccccCccccccccccceeec-CCCCCCCcchhhhhcccCCceeEeccCCccChhhHHHHhccCCCcCCCCCccccc
Q 026787 124 YFHCKRCGSCYSTSLRNNHLCIE-NSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID 201 (233)
Q Consensus 124 ~fHC~~C~~C~s~~l~~~H~C~e-~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrksi~d 201 (233)
-..|..|-.+.|...-+.-.|+- +-....||+|+....+ .......+|+|.||..||..|-+ ...+||+||+.++.
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 44566666666663333344432 2335579999987444 34556678999999999999998 47899999998763
No 52
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=96.06 E-value=0.0041 Score=43.97 Aligned_cols=44 Identities=27% Similarity=0.563 Sum_probs=30.4
Q ss_pred CCCCCCcchhhhhcccCCceeEeccCCccChhhHHHHhc-cCCCcCCC
Q 026787 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIK-RDKYCCPI 194 (233)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~-~~~~~CPi 194 (233)
.....|||-+..|. ++|+...|||+|=++-+.+|+. .+..+||+
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 5889999999999999999993 35678998
No 53
>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=96.02 E-value=0.003 Score=48.08 Aligned_cols=37 Identities=27% Similarity=0.583 Sum_probs=30.1
Q ss_pred eecCCCCCCCcchhhhhcccCCceeEeccCCccChhhHH
Q 026787 144 CIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYH 182 (233)
Q Consensus 144 C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~ 182 (233)
.+.-..+..|+||...|.++ ...+.||||.+|..|++
T Consensus 72 ~v~i~~~~~C~vC~k~l~~~--~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 72 SVVITESTKCSVCGKPLGNS--VFVVFPCGHVVHYSCIK 108 (109)
T ss_pred eEEECCCCCccCcCCcCCCc--eEEEeCCCeEEeccccc
Confidence 34445567899999998774 78899999999999975
No 54
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=95.83 E-value=0.008 Score=55.59 Aligned_cols=63 Identities=22% Similarity=0.636 Sum_probs=50.1
Q ss_pred CCCcchhhhhcccCCceeEecc--CCccChhhHHHHhccCCCcCCCCCccccchhHHhhhhHHHHHhCCCChhhhc
Q 026787 151 HHCPICYEYLFDSLRNTTVMKC--GHTMHCECYHEMIKRDKYCCPICSKSVIDMSRTWKRIDEEIEATVMPEDYRH 224 (233)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpC--GH~~H~~C~~~~~~~~~~~CPiCrksi~dm~~~~~~lD~~i~~~pmP~~y~~ 224 (233)
.+||||.++|.. -++.| ||....+|-.+. ..+||.|+..+++.. -+.++..+++...|=.|.+
T Consensus 49 leCPvC~~~l~~-----Pi~QC~nGHlaCssC~~~~----~~~CP~Cr~~~g~~R--~~amEkV~e~~~vpC~~~~ 113 (299)
T KOG3002|consen 49 LDCPVCFNPLSP-----PIFQCDNGHLACSSCRTKV----SNKCPTCRLPIGNIR--CRAMEKVAEAVLVPCKNAK 113 (299)
T ss_pred ccCchhhccCcc-----cceecCCCcEehhhhhhhh----cccCCccccccccHH--HHHHHHHHHhceecccccc
Confidence 489999999753 35778 899999998754 469999999999763 4678888888888766554
No 55
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=95.74 E-value=0.0027 Score=64.36 Aligned_cols=46 Identities=24% Similarity=0.651 Sum_probs=40.1
Q ss_pred CCCcchhhhhcccCCceeEeccCCccChhhHHHHhccCCCcCCCCCcccc
Q 026787 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (233)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrksi~ 200 (233)
-.||+|-.. ..++++..|||.|...|+...+...+.+||.|+.+++
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 479999854 3567778999999999999999888999999999987
No 56
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.64 E-value=0.0071 Score=57.98 Aligned_cols=50 Identities=26% Similarity=0.720 Sum_probs=38.6
Q ss_pred CCCCcchhhhhcccCCc-eeEeccCCccChhhHHHHhcc-CCCcCCCCCccc
Q 026787 150 HHHCPICYEYLFDSLRN-TTVMKCGHTMHCECYHEMIKR-DKYCCPICSKSV 199 (233)
Q Consensus 150 ~~~CpICle~lf~s~~~-v~~LpCGH~~H~~C~~~~~~~-~~~~CPiCrksi 199 (233)
...|||||+....+.+. +..|.|||.|=+.|++.||.. ....||.|.-..
T Consensus 4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~ka 55 (463)
T KOG1645|consen 4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKA 55 (463)
T ss_pred cccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChh
Confidence 35799999987655443 456789999999999999952 346799997544
No 57
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=95.63 E-value=0.0065 Score=56.20 Aligned_cols=45 Identities=24% Similarity=0.577 Sum_probs=36.7
Q ss_pred CCCcchhhhhcccCCceeEeccCCccChhhHHHHhccCCCcCCCCCcccc
Q 026787 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (233)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrksi~ 200 (233)
..|-||-++|. ....-+|||+|..-||..+|. .+-.||+|+...-
T Consensus 26 lrC~IC~~~i~----ip~~TtCgHtFCslCIR~hL~-~qp~CP~Cr~~~~ 70 (391)
T COG5432 26 LRCRICDCRIS----IPCETTCGHTFCSLCIRRHLG-TQPFCPVCREDPC 70 (391)
T ss_pred HHhhhhhheee----cceecccccchhHHHHHHHhc-CCCCCccccccHH
Confidence 46999999853 234458999999999999998 5899999997653
No 58
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=95.57 E-value=0.01 Score=42.45 Aligned_cols=46 Identities=26% Similarity=0.768 Sum_probs=33.6
Q ss_pred cceeecCCCCcccccc-----CcCCCCCCC-cceeecCccccccCCCCcCeeccCCCCc
Q 026787 63 VKQVICSVCDTEQPVA-----QVCTNCGVN-MGEYFCDICKFYDDDIEKGQFHCDDCGI 115 (233)
Q Consensus 63 v~~v~C~~C~~~q~~~-----~~C~~Cg~~-f~~Y~C~~C~l~d~~~~k~~yHC~~Cgi 115 (233)
++...|..|+.+.... -.||+||.. ..| |.+|+-+. ..|.|++||+
T Consensus 5 ~~~~~CtSCg~~i~~~~~~~~F~CPnCG~~~I~R--C~~CRk~~-----~~Y~CP~CGF 56 (59)
T PRK14890 5 MEPPKCTSCGIEIAPREKAVKFLCPNCGEVIIYR--CEKCRKQS-----NPYTCPKCGF 56 (59)
T ss_pred ccCccccCCCCcccCCCccCEeeCCCCCCeeEee--chhHHhcC-----CceECCCCCC
Confidence 3456788898776543 379999986 444 89998774 3799999985
No 59
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=95.54 E-value=0.0066 Score=41.18 Aligned_cols=41 Identities=29% Similarity=0.704 Sum_probs=27.2
Q ss_pred CcchhhhhcccCCceeEecc---C--CccChhhHHHHhcc-CCCcCCCC
Q 026787 153 CPICYEYLFDSLRNTTVMKC---G--HTMHCECYHEMIKR-DKYCCPIC 195 (233)
Q Consensus 153 CpICle~lf~s~~~v~~LpC---G--H~~H~~C~~~~~~~-~~~~CPiC 195 (233)
|-||++.-.++ +..+.|| | -..|.+|+.+|+.. ++.+|++|
T Consensus 1 CrIC~~~~~~~--~~li~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C 47 (47)
T PF12906_consen 1 CRICLEGEEED--EPLISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC 47 (47)
T ss_dssp ETTTTEE-SSS--S-EE-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred CeEeCCcCCCC--CceecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence 56898874433 3456787 3 68999999999974 46789987
No 60
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=95.51 E-value=0.0041 Score=59.62 Aligned_cols=56 Identities=25% Similarity=0.584 Sum_probs=45.3
Q ss_pred eecCCCCCCCcchhhhhcccCCceeEeccCCccChhhHHHHhccC-CCcCCCCCccccchh
Q 026787 144 CIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRD-KYCCPICSKSVIDMS 203 (233)
Q Consensus 144 C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~-~~~CPiCrksi~dm~ 203 (233)
|.=+++-.-|-||-|. ..+|++=||||.+...|+..|-.+. ..+||.||-.|-..+
T Consensus 363 ceMgsTFeLCKICaen----dKdvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKGte 419 (563)
T KOG1785|consen 363 CEMGSTFELCKICAEN----DKDVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIKGTE 419 (563)
T ss_pred HHccchHHHHHHhhcc----CCCcccccccchHHHHHHHhhcccCCCCCCCceeeEecccc
Confidence 3335777789999986 3678899999999999999998544 689999998886433
No 61
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=95.30 E-value=0.017 Score=62.79 Aligned_cols=74 Identities=26% Similarity=0.633 Sum_probs=56.0
Q ss_pred CCccceeeccccCccccccccccceeecCCCCCCCcchhhhhcccCCceeEeccCCccChhhHHHHhcc---------CC
Q 026787 119 GGRENYFHCKRCGSCYSTSLRNNHLCIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR---------DK 189 (233)
Q Consensus 119 G~~~~~fHC~~C~~C~s~~l~~~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~---------~~ 189 (233)
||.+|-.||--|-.|-.-.. ....++.|.||.-+- -+-.+.+.|.|||.||-.|....|.+ +-
T Consensus 3462 GGvkNEE~CLPCl~Cdks~t-------kQD~DDmCmICFTE~-L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~F 3533 (3738)
T KOG1428|consen 3462 GGVKNEEHCLPCLHCDKSAT-------KQDADDMCMICFTEA-LSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGF 3533 (3738)
T ss_pred cCccchhhcccccccChhhh-------hcccCceEEEEehhh-hCCCcceecCCccchhHHHHHHHHHhcccCCeeEEee
Confidence 56778889988877744321 234467899998773 34478999999999999999887763 23
Q ss_pred CcCCCCCcccc
Q 026787 190 YCCPICSKSVI 200 (233)
Q Consensus 190 ~~CPiCrksi~ 200 (233)
.+||||...|.
T Consensus 3534 isCPiC~n~In 3544 (3738)
T KOG1428|consen 3534 ISCPICKNKIN 3544 (3738)
T ss_pred eecccccchhh
Confidence 68999998886
No 62
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.10 E-value=0.019 Score=51.51 Aligned_cols=52 Identities=29% Similarity=0.675 Sum_probs=44.0
Q ss_pred CCCCCCcchhhhhcccCCceeEeccCCccChhhHHHHhcc-------CCCcCCCCCccccc
Q 026787 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR-------DKYCCPICSKSVID 201 (233)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~-------~~~~CPiCrksi~d 201 (233)
....||..|.-.|.+. +...|-|=|.||-.|+++|... ..|+||-|+..|+.
T Consensus 48 DY~pNC~LC~t~La~g--dt~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFP 106 (299)
T KOG3970|consen 48 DYNPNCRLCNTPLASG--DTTRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFP 106 (299)
T ss_pred CCCCCCceeCCccccC--cceeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCC
Confidence 4577999999997654 6778999999999999999763 36999999999973
No 63
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=95.10 E-value=0.015 Score=52.01 Aligned_cols=37 Identities=27% Similarity=0.546 Sum_probs=28.0
Q ss_pred cccCCceeEeccCCccChhhHHHHhccCCCcCCCCCcccc
Q 026787 161 FDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (233)
Q Consensus 161 f~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrksi~ 200 (233)
+.+.++.....|+|+|...|...=. ...||+|+|+|-
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 4444556677899999999997543 238999999974
No 64
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.13 E-value=0.041 Score=50.43 Aligned_cols=53 Identities=25% Similarity=0.589 Sum_probs=42.3
Q ss_pred CCCCCCcchhhhhcccCCceeEeccCCccChhhHHHHhcc-CCCcCCCCCccccchh
Q 026787 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR-DKYCCPICSKSVIDMS 203 (233)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~-~~~~CPiCrksi~dm~ 203 (233)
+.+..||+|.|+ ++-|.+..+|||.+.=-|+..-... ...+||.|+.++..|+
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 4467788899999999999875542 3589999999987664
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=94.11 E-value=0.022 Score=47.00 Aligned_cols=36 Identities=14% Similarity=0.418 Sum_probs=31.8
Q ss_pred CCCCcchhhhhcccCCceeEeccC------CccChhhHHHHhc
Q 026787 150 HHHCPICYEYLFDSLRNTTVMKCG------HTMHCECYHEMIK 186 (233)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCG------H~~H~~C~~~~~~ 186 (233)
..+|.||++.+.+ .+.|+.+++| |+||.+|+..|.+
T Consensus 26 ~~EC~IC~~~I~~-~~GvV~vt~~g~lnLEkmfc~~C~~rw~~ 67 (134)
T PF05883_consen 26 TVECQICFDRIDN-NDGVVYVTDGGTLNLEKMFCADCDKRWRR 67 (134)
T ss_pred Ceeehhhhhhhhc-CCCEEEEecCCeehHHHHHHHHHHHHHHh
Confidence 4689999999887 6789999997 9999999999954
No 66
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.94 E-value=0.031 Score=51.82 Aligned_cols=50 Identities=24% Similarity=0.473 Sum_probs=40.2
Q ss_pred CCCCCCCcchhhhhcccCCceeEeccCCccChhhHHHHhccCCCcCCCCCcccc
Q 026787 147 NSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (233)
Q Consensus 147 ~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrksi~ 200 (233)
+.+..+|+||+.... .+ ..|+|+|.|.-.|++--......+||+||..|-
T Consensus 4 ~~~~~eC~IC~nt~n---~P-v~l~C~HkFCyiCiKGsy~ndk~~CavCR~pid 53 (324)
T KOG0824|consen 4 RTKKKECLICYNTGN---CP-VNLYCFHKFCYICIKGSYKNDKKTCAVCRFPID 53 (324)
T ss_pred cccCCcceeeeccCC---cC-ccccccchhhhhhhcchhhcCCCCCceecCCCC
Confidence 345678999998643 34 679999999999998765556788999999885
No 67
>PHA02862 5L protein; Provisional
Probab=93.42 E-value=0.039 Score=46.28 Aligned_cols=60 Identities=22% Similarity=0.419 Sum_probs=43.2
Q ss_pred CCCCCcchhhhhcccCCceeEecc---C--CccChhhHHHHhccC-CCcCCCCCccccchhHHhhhhHHHHH
Q 026787 149 MHHHCPICYEYLFDSLRNTTVMKC---G--HTMHCECYHEMIKRD-KYCCPICSKSVIDMSRTWKRIDEEIE 214 (233)
Q Consensus 149 ~~~~CpICle~lf~s~~~v~~LpC---G--H~~H~~C~~~~~~~~-~~~CPiCrksi~dm~~~~~~lD~~i~ 214 (233)
|...|=||.+.= + +++ -|| | -..|++|+.+|+..+ +.+||+|+.... +...|+.+.+..-
T Consensus 1 ~~diCWIC~~~~-~--e~~--~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~-Ik~~yKpf~kW~~ 66 (156)
T PHA02862 1 MSDICWICNDVC-D--ERN--NFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYN-IKKTYVSFKKWNW 66 (156)
T ss_pred CCCEEEEecCcC-C--CCc--ccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEE-EEEccccHHHhhc
Confidence 346788999862 1 223 465 2 789999999999753 577999998875 6667777776654
No 68
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.35 E-value=0.052 Score=49.01 Aligned_cols=49 Identities=29% Similarity=0.699 Sum_probs=39.5
Q ss_pred CCCcchhhhhccc--CCceeEeccCCccChhhHHHHhccCCCcCCCCCccc
Q 026787 151 HHCPICYEYLFDS--LRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSV 199 (233)
Q Consensus 151 ~~CpICle~lf~s--~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrksi 199 (233)
..|-||-+++.+. ....++|.|||++-..|+..++..+...||.||.+.
T Consensus 4 ~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~~~i~cpfcR~~~ 54 (296)
T KOG4185|consen 4 PECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGNSRILCPFCRETT 54 (296)
T ss_pred CceeecCccccccCcccCCcccccCceehHhHHHHHhcCceeeccCCCCcc
Confidence 4688999885432 233467889999999999999988778899999994
No 69
>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=93.11 E-value=0.065 Score=49.38 Aligned_cols=49 Identities=20% Similarity=0.469 Sum_probs=38.8
Q ss_pred CCcchhhhhcccCCceeE-eccCCccChhhHHHHhccCCCcCCCCCcccc
Q 026787 152 HCPICYEYLFDSLRNTTV-MKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (233)
Q Consensus 152 ~CpICle~lf~s~~~v~~-LpCGH~~H~~C~~~~~~~~~~~CPiCrksi~ 200 (233)
.||+|.-+...+..-+.. =+|||.+..+|++..+..+.+.||.|.+.+.
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 588888776655332222 2899999999999999888999999998876
No 70
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.06 E-value=0.051 Score=51.29 Aligned_cols=48 Identities=21% Similarity=0.501 Sum_probs=35.6
Q ss_pred cCCCCCCCcchhhhhcccCCceeEeccCCccChhhHHHHhccCCCcCCCCCccccc
Q 026787 146 ENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID 201 (233)
Q Consensus 146 e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrksi~d 201 (233)
|.+..++|.||+++- .....+||||+-- |..-.. ...+||+||.+|.-
T Consensus 301 ~~~~p~lcVVcl~e~----~~~~fvpcGh~cc--ct~cs~--~l~~CPvCR~rI~~ 348 (355)
T KOG1571|consen 301 ELPQPDLCVVCLDEP----KSAVFVPCGHVCC--CTLCSK--HLPQCPVCRQRIRL 348 (355)
T ss_pred ccCCCCceEEecCCc----cceeeecCCcEEE--chHHHh--hCCCCchhHHHHHH
Confidence 456678999999973 3478999999954 554443 24669999988853
No 71
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=92.97 E-value=0.038 Score=39.07 Aligned_cols=32 Identities=28% Similarity=0.669 Sum_probs=25.8
Q ss_pred ceeEeccCCccChhhHHHHhccCCCcCCCCCcccc
Q 026787 166 NTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (233)
Q Consensus 166 ~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrksi~ 200 (233)
.-.+|||||.+-..|+.-+- -.-||+|.+.+.
T Consensus 19 ~~~~~pCgH~I~~~~f~~~r---YngCPfC~~~~~ 50 (55)
T PF14447_consen 19 KGTVLPCGHLICDNCFPGER---YNGCPFCGTPFE 50 (55)
T ss_pred ccccccccceeeccccChhh---ccCCCCCCCccc
Confidence 45679999999999997653 246999998875
No 72
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.44 E-value=0.072 Score=46.35 Aligned_cols=35 Identities=29% Similarity=0.655 Sum_probs=27.9
Q ss_pred EeccCCccChhhHHHHhccC----------CCcCCCCCcccc-chh
Q 026787 169 VMKCGHTMHCECYHEMIKRD----------KYCCPICSKSVI-DMS 203 (233)
Q Consensus 169 ~LpCGH~~H~~C~~~~~~~~----------~~~CPiCrksi~-dm~ 203 (233)
-..||-.||+-|+.+||+.- -..||.|+++|. .|+
T Consensus 187 N~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialKmS 232 (234)
T KOG3268|consen 187 NIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALKMS 232 (234)
T ss_pred ccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceeecc
Confidence 46799999999999999831 246999999984 443
No 73
>PF12773 DZR: Double zinc ribbon
Probab=92.38 E-value=0.14 Score=34.28 Aligned_cols=22 Identities=36% Similarity=0.970 Sum_probs=14.3
Q ss_pred cCCCCccccc-cCcCCCCCCCcc
Q 026787 68 CSVCDTEQPV-AQVCTNCGVNMG 89 (233)
Q Consensus 68 C~~C~~~q~~-~~~C~~Cg~~f~ 89 (233)
|..|+++.+. +..|++||+.+.
T Consensus 1 Cp~Cg~~~~~~~~fC~~CG~~l~ 23 (50)
T PF12773_consen 1 CPHCGTPNPDDAKFCPHCGTPLP 23 (50)
T ss_pred CCCcCCcCCccccCChhhcCChh
Confidence 4566666555 456777777776
No 74
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=92.33 E-value=0.042 Score=51.91 Aligned_cols=59 Identities=22% Similarity=0.444 Sum_probs=45.8
Q ss_pred CCCCcchhhhhcccCCceeEeccCCccChhhHHHHhccCCCcCCCCCccccchhHHhhh
Q 026787 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRTWKR 208 (233)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrksi~dm~~~~~~ 208 (233)
++-||.|+|+|.-+......-|||=-+.+-|+......-+.+||-||+...|-...|+.
T Consensus 14 ed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~denv~~~~ 72 (480)
T COG5175 14 EDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDENVRYVT 72 (480)
T ss_pred cccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhccccceeEEe
Confidence 44599999998766555555578999999999887665578999999988875556643
No 75
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=91.74 E-value=0.07 Score=49.68 Aligned_cols=54 Identities=30% Similarity=0.594 Sum_probs=42.2
Q ss_pred CCCCCCCcchhhhhcccCCceeEeccCCccChhhHHHHhcc----------------------CCCcCCCCCccccc
Q 026787 147 NSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR----------------------DKYCCPICSKSVID 201 (233)
Q Consensus 147 ~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~----------------------~~~~CPiCrksi~d 201 (233)
+-..++|.|||-- |.+.....+.+|-|+||..||..||.. ..--|||||-.|.+
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 3456799999988 555567889999999999999988762 02349999988874
No 76
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=91.70 E-value=0.044 Score=51.24 Aligned_cols=64 Identities=25% Similarity=0.522 Sum_probs=47.9
Q ss_pred CCCCCcchhhhhcccCCceeEeccCCccChhhHHHHhccCCCcCCCCCccccchh-HHhhhhHHHHHhC
Q 026787 149 MHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMS-RTWKRIDEEIEAT 216 (233)
Q Consensus 149 ~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrksi~dm~-~~~~~lD~~i~~~ 216 (233)
....|++|..+|.+.+ .+.-|=|+|.++||-.+|.. +.+||.|+-.|...- .+.-+.|..++++
T Consensus 14 ~~itC~LC~GYliDAT---TI~eCLHTFCkSCivk~l~~-~~~CP~C~i~ih~t~pl~ni~~Drtlqdi 78 (331)
T KOG2660|consen 14 PHITCRLCGGYLIDAT---TITECLHTFCKSCIVKYLEE-SKYCPTCDIVIHKTHPLLNIRSDRTLQDI 78 (331)
T ss_pred cceehhhccceeecch---hHHHHHHHHHHHHHHHHHHH-hccCCccceeccCccccccCCcchHHHHH
Confidence 4558999999987653 45679999999999999985 789999998887532 2334455555443
No 77
>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=91.62 E-value=0.21 Score=42.38 Aligned_cols=48 Identities=29% Similarity=0.726 Sum_probs=35.2
Q ss_pred CCCCcchhhhhcccCCceeEeccC-------------CccChhhHHHHhcc-----------------------------
Q 026787 150 HHHCPICYEYLFDSLRNTTVMKCG-------------HTMHCECYHEMIKR----------------------------- 187 (233)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCG-------------H~~H~~C~~~~~~~----------------------------- 187 (233)
+..||||||.= ...+.|-|. =.-|+.||++|-+.
T Consensus 2 d~~CpICme~P----HNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkka~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 77 (162)
T PF07800_consen 2 DVTCPICMEHP----HNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKKAYGKSSSSSSQSSSSAPSDSSSSESSESQE 77 (162)
T ss_pred CccCceeccCC----CceEEEEeccccCCccccccCCccchhHHHHHHHHHhcCCCCccccccccCcCCCcccccccccc
Confidence 45799999973 355667662 24699999999762
Q ss_pred -CCCcCCCCCccccc
Q 026787 188 -DKYCCPICSKSVID 201 (233)
Q Consensus 188 -~~~~CPiCrksi~d 201 (233)
....||+||-.|..
T Consensus 78 ~~~L~CPLCRG~V~G 92 (162)
T PF07800_consen 78 QPELACPLCRGEVKG 92 (162)
T ss_pred cccccCccccCceec
Confidence 14679999988874
No 78
>PF04641 Rtf2: Rtf2 RING-finger
Probab=91.48 E-value=0.15 Score=45.87 Aligned_cols=50 Identities=18% Similarity=0.436 Sum_probs=39.2
Q ss_pred CCCCCCcchhhhhcccCCceeEe-ccCCccChhhHHHHhccCCCcCCCCCcccc
Q 026787 148 SMHHHCPICYEYLFDSLRNTTVM-KCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (233)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~L-pCGH~~H~~C~~~~~~~~~~~CPiCrksi~ 200 (233)
...-.|||-...|... ...+.| ||||+|=...+.+.- ....||+|.+++.
T Consensus 111 ~~~~~CPvt~~~~~~~-~~fv~l~~cG~V~s~~alke~k--~~~~Cp~c~~~f~ 161 (260)
T PF04641_consen 111 EGRFICPVTGKEFNGK-HKFVYLRPCGCVFSEKALKELK--KSKKCPVCGKPFT 161 (260)
T ss_pred CceeECCCCCcccCCc-eeEEEEcCCCCEeeHHHHHhhc--ccccccccCCccc
Confidence 4455799999997444 445544 999999999999984 3568999999976
No 79
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.42 E-value=0.095 Score=50.47 Aligned_cols=46 Identities=20% Similarity=0.411 Sum_probs=37.7
Q ss_pred CCCCcchhhhhcccCCceeEeccCCccChhhHHHHhcc-------CCCcCCCCC
Q 026787 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR-------DKYCCPICS 196 (233)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~-------~~~~CPiCr 196 (233)
--+|.||.+. +....-.+.|||+|+|.++|+..|... +..+||-++
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 555578899999999999999998762 367898765
No 80
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.36 E-value=0.034 Score=51.45 Aligned_cols=60 Identities=23% Similarity=0.622 Sum_probs=41.9
Q ss_pred cccceeecCCC---CCCCcchhhhhcccCCceeEeccCCccC-hhhHHHHhccCCCcCCCCCccccchhHHhh
Q 026787 139 RNNHLCIENSM---HHHCPICYEYLFDSLRNTTVMKCGHTMH-CECYHEMIKRDKYCCPICSKSVIDMSRTWK 207 (233)
Q Consensus 139 ~~~H~C~e~~~---~~~CpICle~lf~s~~~v~~LpCGH~~H-~~C~~~~~~~~~~~CPiCrksi~dm~~~~~ 207 (233)
++.+.+--... +.-|.||++- ..+-.+|+|||..= .+|-.. -..|||||+-|.....+|+
T Consensus 286 k~~~g~~~~~s~~~~~LC~ICmDa----P~DCvfLeCGHmVtCt~CGkr-----m~eCPICRqyi~rvvrif~ 349 (350)
T KOG4275|consen 286 KGNDGEQHSRSLATRRLCAICMDA----PRDCVFLECGHMVTCTKCGKR-----MNECPICRQYIVRVVRIFR 349 (350)
T ss_pred hcccccccccchhHHHHHHHHhcC----CcceEEeecCcEEeehhhccc-----cccCchHHHHHHHHHhhhc
Confidence 45555544444 7789999975 46789999999752 234322 2389999999987776664
No 81
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=91.21 E-value=0.15 Score=36.61 Aligned_cols=45 Identities=29% Similarity=0.802 Sum_probs=33.4
Q ss_pred eeecCCCCcccccc-----CcCCCCCCCcceeecCccccccCCCCcCeeccCCCCc
Q 026787 65 QVICSVCDTEQPVA-----QVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGI 115 (233)
Q Consensus 65 ~v~C~~C~~~q~~~-----~~C~~Cg~~f~~Y~C~~C~l~d~~~~k~~yHC~~Cgi 115 (233)
...|..|+.+..+. -.|||||... =|-|.+|+...+ +|.|++||+
T Consensus 9 ~~~CtSCg~~i~p~e~~v~F~CPnCGe~~-I~Rc~~CRk~g~-----~Y~Cp~CGF 58 (61)
T COG2888 9 PPVCTSCGREIAPGETAVKFPCPNCGEVE-IYRCAKCRKLGN-----PYRCPKCGF 58 (61)
T ss_pred CceeccCCCEeccCCceeEeeCCCCCcee-eehhhhHHHcCC-----ceECCCcCc
Confidence 56889999887553 4699999543 366888887744 788999885
No 82
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=91.10 E-value=0.18 Score=48.03 Aligned_cols=54 Identities=26% Similarity=0.645 Sum_probs=43.1
Q ss_pred CCCCCCcchhhhhcccCCceeEeccCCccChhhHHHHhccCCCcCCCCCccccchhHH
Q 026787 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRT 205 (233)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrksi~dm~~~ 205 (233)
..+..||||..-|-+ ++....|||.|...|+.+|+.. +..||.|+..+..-..+
T Consensus 19 ~~~l~C~~C~~vl~~---p~~~~~cgh~fC~~C~~~~~~~-~~~cp~~~~~~~~~~~~ 72 (391)
T KOG0297|consen 19 DENLLCPICMSVLRD---PVQTTTCGHRFCAGCLLESLSN-HQKCPVCRQELTQAEEL 72 (391)
T ss_pred cccccCccccccccC---CCCCCCCCCcccccccchhhcc-CcCCcccccccchhhcc
Confidence 445689999988644 4444789999999999999985 88999999888754444
No 83
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.49 E-value=0.13 Score=52.21 Aligned_cols=67 Identities=21% Similarity=0.486 Sum_probs=47.0
Q ss_pred CCCcchhhhhcccCCceeEeccCCccChhhHHHHhccCCCcCCCCCc----cccchhHHh-------hhhHHHHHhCCCC
Q 026787 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSK----SVIDMSRTW-------KRIDEEIEATVMP 219 (233)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrk----si~dm~~~~-------~~lD~~i~~~pmP 219 (233)
..|+||+..++.++...+.|-|||++.+.|+...- +.+|| |.. ++.+.+.++ +..|++|-...|+
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 37999988888888888889999999999998764 57899 543 344444443 3345555555554
Q ss_pred hh
Q 026787 220 ED 221 (233)
Q Consensus 220 ~~ 221 (233)
+.
T Consensus 88 ~g 89 (861)
T KOG3161|consen 88 AG 89 (861)
T ss_pred Cc
Confidence 43
No 84
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=90.37 E-value=0.16 Score=37.58 Aligned_cols=36 Identities=25% Similarity=0.783 Sum_probs=22.5
Q ss_pred ceeecCCCCccccccCcCCCCCCCc--------ceeecCccccc
Q 026787 64 KQVICSVCDTEQPVAQVCTNCGVNM--------GEYFCDICKFY 99 (233)
Q Consensus 64 ~~v~C~~C~~~q~~~~~C~~Cg~~f--------~~Y~C~~C~l~ 99 (233)
....|..|...-.....||.|+..+ +.|||..|+=.
T Consensus 16 ~~~~C~~C~~~~~~~a~CPdC~~~Le~LkACGAvdYFC~~c~gL 59 (70)
T PF07191_consen 16 GHYHCEACQKDYKKEAFCPDCGQPLEVLKACGAVDYFCNHCHGL 59 (70)
T ss_dssp TEEEETTT--EEEEEEE-TTT-SB-EEEEETTEEEEE-TTTT-E
T ss_pred CEEECccccccceecccCCCcccHHHHHHHhcccceeeccCCce
Confidence 5778888887766677888888877 68899888733
No 85
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=89.86 E-value=0.17 Score=52.10 Aligned_cols=42 Identities=29% Similarity=0.583 Sum_probs=31.5
Q ss_pred CCCCcchhhhhcccCCceeEeccCCccChhhHHHHhccCCCcCCC
Q 026787 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPI 194 (233)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPi 194 (233)
...|.||--.+..+ ...-+.|||.+|.+|+.+|++. ...||.
T Consensus 1028 ~~~C~~C~l~V~gs--s~~Cg~C~Hv~H~sc~~eWf~~-gd~Cps 1069 (1081)
T KOG0309|consen 1028 TFQCAICHLAVRGS--SNFCGTCGHVGHTSCMMEWFRT-GDVCPS 1069 (1081)
T ss_pred eeeeeeEeeEeecc--chhhccccccccHHHHHHHHhc-CCcCCC
Confidence 34588887654433 4556789999999999999985 568884
No 86
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.12 E-value=0.2 Score=46.36 Aligned_cols=67 Identities=22% Similarity=0.452 Sum_probs=50.9
Q ss_pred CCCcchhhhhcccCCceeEeccCCccChhhHHHHhccCCCcCCCCCccccchhHHhhhhHHHHHhCCCChhh
Q 026787 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRTWKRIDEEIEATVMPEDY 222 (233)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrksi~dm~~~~~~lD~~i~~~pmP~~y 222 (233)
..|-||-+++. ..++-.|||+|...|...-++ ..-+|+||.+.+-.....-..|...+..-++-.+|
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 FKCFICRKYFY----RPVVTKCGHYFCEVCALKPYQ-KGEKCYVCSQQTHGSFNVAKELLVSLKLKKSDSEY 308 (313)
T ss_pred ccccccccccc----cchhhcCCceeehhhhccccc-cCCcceecccccccccchHHHHHHHHHhhhhhccc
Confidence 45999999953 345678999999999988776 35899999999977665556677777666655544
No 87
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=88.24 E-value=0.31 Score=50.73 Aligned_cols=47 Identities=30% Similarity=0.650 Sum_probs=35.7
Q ss_pred CCCcchhhhhcccCCceeEeccCCccChhhHHHHhccCCCcCCCCCc---cccchhH
Q 026787 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSK---SVIDMSR 204 (233)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrk---si~dm~~ 204 (233)
+.|..|--.|- -|++-..|||.||+.|+. . +...||-|+- ++++|.+
T Consensus 841 skCs~C~~~Ld---lP~VhF~CgHsyHqhC~e---~-~~~~CP~C~~e~~~~m~l~~ 890 (933)
T KOG2114|consen 841 SKCSACEGTLD---LPFVHFLCGHSYHQHCLE---D-KEDKCPKCLPELRGVMDLKR 890 (933)
T ss_pred eeecccCCccc---cceeeeecccHHHHHhhc---c-CcccCCccchhhhhhHHHHH
Confidence 36778876653 477888999999999998 3 5689999998 5555543
No 88
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=87.80 E-value=0.19 Score=50.15 Aligned_cols=52 Identities=21% Similarity=0.513 Sum_probs=42.9
Q ss_pred ecCCCCCCCcchhhhhcccCCceeEeccCCccChhhHHHHhcc----CCCcCCCCCcccc
Q 026787 145 IENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR----DKYCCPICSKSVI 200 (233)
Q Consensus 145 ~e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~----~~~~CPiCrksi~ 200 (233)
.|+..+..|-+|.+.- ++..+-+|-|.|.+.|+.+|+.. .+.+||+|.+.+.
T Consensus 531 ~enk~~~~C~lc~d~a----ed~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~Ls 586 (791)
T KOG1002|consen 531 DENKGEVECGLCHDPA----EDYIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLS 586 (791)
T ss_pred ccccCceeecccCChh----hhhHhhhhhHHHHHHHHHHHHHhhhcccCCCCcccccccc
Confidence 4677788999999873 45677899999999999888753 4799999998874
No 89
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=87.71 E-value=0.54 Score=42.87 Aligned_cols=54 Identities=24% Similarity=0.485 Sum_probs=44.9
Q ss_pred CCCCCCCcchhhhhcccCCceeEe-ccCCccChhhHHHHhccCCCcCCCCCccccch
Q 026787 147 NSMHHHCPICYEYLFDSLRNTTVM-KCGHTMHCECYHEMIKRDKYCCPICSKSVIDM 202 (233)
Q Consensus 147 ~~~~~~CpICle~lf~s~~~v~~L-pCGH~~H~~C~~~~~~~~~~~CPiCrksi~dm 202 (233)
.+..-.|||+.+.|... .+..+| |+||++-..|.+.+++ ...-+||+.+.+-|-
T Consensus 218 ~s~ryiCpvtrd~LtNt-~~ca~Lr~sg~Vv~~ecvEklir-~D~v~pv~d~plkdr 272 (303)
T KOG3039|consen 218 ASKRYICPVTRDTLTNT-TPCAVLRPSGHVVTKECVEKLIR-KDMVDPVTDKPLKDR 272 (303)
T ss_pred hccceecccchhhhcCc-cceEEeccCCcEeeHHHHHHhcc-ccccccCCCCcCccc
Confidence 34566899999998655 567777 7999999999999998 468899999998763
No 90
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=87.55 E-value=0.31 Score=43.13 Aligned_cols=58 Identities=21% Similarity=0.454 Sum_probs=43.4
Q ss_pred CCcchhhhhcccCCceeEeccCCccChhhHHHHhccCCCcCCCCCccccchhHHhhhhHHHHH
Q 026787 152 HCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRTWKRIDEEIE 214 (233)
Q Consensus 152 ~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrksi~dm~~~~~~lD~~i~ 214 (233)
.|-||-+++ .| .++..|||.|...|+-.=.+ ...+|-+|.|..-....+-..||.++.
T Consensus 198 ~C~iCKkdy-~s---pvvt~CGH~FC~~Cai~~y~-kg~~C~~Cgk~t~G~f~V~~d~~kmL~ 255 (259)
T COG5152 198 LCGICKKDY-ES---PVVTECGHSFCSLCAIRKYQ-KGDECGVCGKATYGRFWVVSDLQKMLN 255 (259)
T ss_pred eehhchhhc-cc---hhhhhcchhHHHHHHHHHhc-cCCcceecchhhccceeHHhhHHHHHh
Confidence 799999994 33 45678999999999877555 358999999988655444456666554
No 91
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=87.13 E-value=0.31 Score=28.95 Aligned_cols=24 Identities=33% Similarity=0.924 Sum_probs=17.6
Q ss_pred eeecCCCCccccc-cCcCCCCCCCc
Q 026787 65 QVICSVCDTEQPV-AQVCTNCGVNM 88 (233)
Q Consensus 65 ~v~C~~C~~~q~~-~~~C~~Cg~~f 88 (233)
.+.|..|+++.+. +..|++||+.+
T Consensus 2 ~~~Cp~Cg~~~~~~~~fC~~CG~~L 26 (26)
T PF13248_consen 2 EMFCPNCGAEIDPDAKFCPNCGAKL 26 (26)
T ss_pred cCCCcccCCcCCcccccChhhCCCC
Confidence 4678888886444 46899998864
No 92
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.11 E-value=0.68 Score=44.57 Aligned_cols=49 Identities=24% Similarity=0.748 Sum_probs=39.4
Q ss_pred CCCCCCcchhhhhcccCCceeEeccCCccChhhHHHHhccCCCcCCCCCccccc
Q 026787 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID 201 (233)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrksi~d 201 (233)
..+-.|-||..-|.. .+.+||||+|-..|+..-+. ....||+||-.+..
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 556789999887653 34569999999999999776 46789999998874
No 93
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.08 E-value=0.56 Score=44.98 Aligned_cols=45 Identities=22% Similarity=0.589 Sum_probs=37.4
Q ss_pred CCcchhhhhcccCCceeEeccCCccChhhHHHHhccCC--CcCCCCCc
Q 026787 152 HCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDK--YCCPICSK 197 (233)
Q Consensus 152 ~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~--~~CPiCrk 197 (233)
.|||=-|. .+...|...|.|||++-+.=++.+.+++. ++||.|-.
T Consensus 336 ~CPVlKeq-tsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~ 382 (394)
T KOG2817|consen 336 ICPVLKEQ-TSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPV 382 (394)
T ss_pred ecccchhh-ccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCc
Confidence 68887776 44446788899999999999999998766 89999974
No 94
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=86.80 E-value=0.51 Score=44.97 Aligned_cols=65 Identities=17% Similarity=0.369 Sum_probs=45.9
Q ss_pred CccccccccccceeecCCCCCCCcchhhhhcccCCceeEeccCCccChhhHHHHhc-cCCCcCCCCCccc
Q 026787 131 GSCYSTSLRNNHLCIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIK-RDKYCCPICSKSV 199 (233)
Q Consensus 131 ~~C~s~~l~~~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~-~~~~~CPiCrksi 199 (233)
|.|....+.++-+=.....+++|.||.+.+ +-+.++||||-|.-.|--.... ...-.||+||..-
T Consensus 42 nlsaEPnlttsSaddtDEen~~C~ICA~~~----TYs~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~ 107 (493)
T COG5236 42 NLSAEPNLTTSSADDTDEENMNCQICAGST----TYSARYPCGHQICHACAVRLRALYMQKGCPLCRTET 107 (493)
T ss_pred ccccCCccccccccccccccceeEEecCCc----eEEEeccCCchHHHHHHHHHHHHHhccCCCcccccc
Confidence 456655555555444455677899999975 4567899999999999765432 2357899999643
No 95
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=86.39 E-value=0.36 Score=50.38 Aligned_cols=43 Identities=21% Similarity=0.382 Sum_probs=33.3
Q ss_pred ceeecCCCCCCCcchhhhhcccCCceeEeccCCccChhhHHHHhc
Q 026787 142 HLCIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIK 186 (233)
Q Consensus 142 H~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~ 186 (233)
+.+.--..+..|-+|.-.|+. ++-.+.||||.||+.|+.+-..
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 344333446789999998765 5888899999999999987654
No 96
>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.
Probab=86.36 E-value=0.39 Score=33.17 Aligned_cols=32 Identities=31% Similarity=0.745 Sum_probs=23.2
Q ss_pred eEeccC-CccChhhHHHHhccCCCcCCCCCcccc
Q 026787 168 TVMKCG-HTMHCECYHEMIKRDKYCCPICSKSVI 200 (233)
Q Consensus 168 ~~LpCG-H~~H~~C~~~~~~~~~~~CPiCrksi~ 200 (233)
..+.|. |++...|+..++. .+..||||.+++-
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 356795 9999999999998 4789999998763
No 97
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=85.83 E-value=0.65 Score=39.53 Aligned_cols=48 Identities=29% Similarity=0.561 Sum_probs=34.5
Q ss_pred CCCCCCcchhhhhcccCCceeEecc--CC---ccChhhHHHHhccC-CCcCCCCCcccc
Q 026787 148 SMHHHCPICYEYLFDSLRNTTVMKC--GH---TMHCECYHEMIKRD-KYCCPICSKSVI 200 (233)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpC--GH---~~H~~C~~~~~~~~-~~~CPiCrksi~ 200 (233)
.++..|=||.++- + . ..-|| .. +.|++|++.|+..+ ..+||+|+....
T Consensus 6 ~~~~~CRIC~~~~-~--~--~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~ 59 (162)
T PHA02825 6 LMDKCCWICKDEY-D--V--VTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYN 59 (162)
T ss_pred CCCCeeEecCCCC-C--C--ccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEE
Confidence 3456799998872 1 1 23465 34 67999999999753 678999998764
No 98
>PRK04023 DNA polymerase II large subunit; Validated
Probab=85.58 E-value=0.74 Score=48.94 Aligned_cols=31 Identities=26% Similarity=0.696 Sum_probs=13.9
Q ss_pred cCCCCCCCcceeecCccccccCCCCcCeeccCCCC
Q 026787 80 VCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCG 114 (233)
Q Consensus 80 ~C~~Cg~~f~~Y~C~~C~l~d~~~~k~~yHC~~Cg 114 (233)
.|++||.....-+|+.|.-- ...+|.|++||
T Consensus 628 fCpsCG~~t~~frCP~CG~~----Te~i~fCP~CG 658 (1121)
T PRK04023 628 KCPSCGKETFYRRCPFCGTH----TEPVYRCPRCG 658 (1121)
T ss_pred cCCCCCCcCCcccCCCCCCC----CCcceeCcccc
Confidence 34444444444444444322 34455555553
No 99
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=85.51 E-value=0.75 Score=42.25 Aligned_cols=41 Identities=32% Similarity=0.603 Sum_probs=20.0
Q ss_pred cceeecCcc-ccccCCC---CcCeeccCCCCcceeCCccceeeccccCcccc
Q 026787 88 MGEYFCDIC-KFYDDDI---EKGQFHCDDCGICRIGGRENYFHCKRCGSCYS 135 (233)
Q Consensus 88 f~~Y~C~~C-~l~d~~~---~k~~yHC~~CgiCR~G~~~~~fHC~~C~~C~s 135 (233)
-++|-|+.| |-|.... .-+|+||+- .-...|.|+.||-=|.
T Consensus 128 ~~r~~c~eCgk~ysT~snLsrHkQ~H~~~-------~s~ka~~C~~C~K~Yv 172 (279)
T KOG2462|consen 128 HPRYKCPECGKSYSTSSNLSRHKQTHRSL-------DSKKAFSCKYCGKVYV 172 (279)
T ss_pred CCceeccccccccccccccchhhcccccc-------cccccccCCCCCceee
Confidence 345555555 4443322 225666642 1134566666665543
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=84.66 E-value=0.68 Score=27.80 Aligned_cols=23 Identities=35% Similarity=0.959 Sum_probs=18.2
Q ss_pred ecCCCCccccc-cCcCCCCCCCcc
Q 026787 67 ICSVCDTEQPV-AQVCTNCGVNMG 89 (233)
Q Consensus 67 ~C~~C~~~q~~-~~~C~~Cg~~f~ 89 (233)
.|..|+.+-+. +..|++||..|.
T Consensus 2 ~CP~C~~~V~~~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCPHCGYDFE 25 (26)
T ss_pred cCCCCcCCchhhcCcCCCCCCCCc
Confidence 37778887766 468999999986
No 101
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=84.20 E-value=0.42 Score=41.06 Aligned_cols=31 Identities=23% Similarity=0.353 Sum_probs=25.3
Q ss_pred CCCCCCCcchhhhhcccCCceeEeccCCccCh
Q 026787 147 NSMHHHCPICYEYLFDSLRNTTVMKCGHTMHC 178 (233)
Q Consensus 147 ~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~ 178 (233)
+....+|.||||+|... +.+..|||-=++|+
T Consensus 174 ~ddkGECvICLEdL~~G-dtIARLPCLCIYHK 204 (205)
T KOG0801|consen 174 KDDKGECVICLEDLEAG-DTIARLPCLCIYHK 204 (205)
T ss_pred cccCCcEEEEhhhccCC-CceeccceEEEeec
Confidence 34567999999998655 78999999877776
No 102
>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=83.61 E-value=0.85 Score=36.28 Aligned_cols=28 Identities=32% Similarity=0.948 Sum_probs=20.9
Q ss_pred cccCcCCCCCCCcceeecCccccccCCCCcCeeccCCCCc
Q 026787 76 PVAQVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGI 115 (233)
Q Consensus 76 ~~~~~C~~Cg~~f~~Y~C~~C~l~d~~~~k~~yHC~~Cgi 115 (233)
....+|++||+.| | +.+|.+-.|++||.
T Consensus 7 GtKR~Cp~CG~kF----------Y--DLnk~PivCP~CG~ 34 (108)
T PF09538_consen 7 GTKRTCPSCGAKF----------Y--DLNKDPIVCPKCGT 34 (108)
T ss_pred CCcccCCCCcchh----------c--cCCCCCccCCCCCC
Confidence 3446799999854 6 45788999999984
No 103
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=83.07 E-value=0.7 Score=26.89 Aligned_cols=21 Identities=38% Similarity=0.945 Sum_probs=14.7
Q ss_pred cCCCCccccc-cCcCCCCCCCc
Q 026787 68 CSVCDTEQPV-AQVCTNCGVNM 88 (233)
Q Consensus 68 C~~C~~~q~~-~~~C~~Cg~~f 88 (233)
|..|+++.+. +..|++||+.|
T Consensus 2 Cp~CG~~~~~~~~fC~~CG~~l 23 (23)
T PF13240_consen 2 CPNCGAEIEDDAKFCPNCGTPL 23 (23)
T ss_pred CcccCCCCCCcCcchhhhCCcC
Confidence 6677777655 46788888764
No 104
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=82.71 E-value=0.58 Score=48.77 Aligned_cols=50 Identities=24% Similarity=0.547 Sum_probs=36.9
Q ss_pred CCCCcchhhhhcccCCceeE-eccCCccChhhHHHHhcc------CCCcCCCCCcccc
Q 026787 150 HHHCPICYEYLFDSLRNTTV-MKCGHTMHCECYHEMIKR------DKYCCPICSKSVI 200 (233)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~-LpCGH~~H~~C~~~~~~~------~~~~CPiCrksi~ 200 (233)
.-.|.||.|.+..+ .++.. -.|=|+||-.||..|.+. ...+||-|.....
T Consensus 191 ~yeCmIC~e~I~~t-~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv~~ 247 (950)
T KOG1952|consen 191 KYECMICTERIKRT-APVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSVSK 247 (950)
T ss_pred ceEEEEeeeecccc-CCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccchhc
Confidence 45899999997654 34432 246799999999999874 3578999984443
No 105
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=82.66 E-value=0.94 Score=46.14 Aligned_cols=32 Identities=31% Similarity=0.877 Sum_probs=18.4
Q ss_pred eecCCCCccccc-cCcCCCCCCCcceeecCccc
Q 026787 66 VICSVCDTEQPV-AQVCTNCGVNMGEYFCDICK 97 (233)
Q Consensus 66 v~C~~C~~~q~~-~~~C~~Cg~~f~~Y~C~~C~ 97 (233)
++|..|+.+-+. +..|++||..+..-.|+.|.
T Consensus 2 ~~Cp~Cg~~n~~~akFC~~CG~~l~~~~Cp~CG 34 (645)
T PRK14559 2 LICPQCQFENPNNNRFCQKCGTSLTHKPCPQCG 34 (645)
T ss_pred CcCCCCCCcCCCCCccccccCCCCCCCcCCCCC
Confidence 356666666444 34566666666544555554
No 106
>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=81.14 E-value=1.2 Score=26.57 Aligned_cols=21 Identities=24% Similarity=0.539 Sum_probs=16.7
Q ss_pred CcCCCCCccccchhHHhhhhHH
Q 026787 190 YCCPICSKSVIDMSRTWKRIDE 211 (233)
Q Consensus 190 ~~CPiCrksi~dm~~~~~~lD~ 211 (233)
..||||.+.+ .+..+.+.||.
T Consensus 2 v~CPiC~~~v-~~~~in~HLD~ 22 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLDS 22 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHHH
Confidence 3699999998 66677788884
No 107
>PHA00626 hypothetical protein
Probab=80.93 E-value=1.3 Score=31.67 Aligned_cols=7 Identities=43% Similarity=1.355 Sum_probs=3.9
Q ss_pred cCCCCCC
Q 026787 80 VCTNCGV 86 (233)
Q Consensus 80 ~C~~Cg~ 86 (233)
.||+||+
T Consensus 2 ~CP~CGS 8 (59)
T PHA00626 2 SCPKCGS 8 (59)
T ss_pred CCCCCCC
Confidence 3566655
No 108
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=80.21 E-value=1.6 Score=30.75 Aligned_cols=36 Identities=22% Similarity=0.560 Sum_probs=27.3
Q ss_pred CCCCCcchhhhhcccCCceeEeccCCccChhhHHHH
Q 026787 149 MHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEM 184 (233)
Q Consensus 149 ~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~ 184 (233)
+...|++|.+.|.+..+.|+---||=..|+.|++..
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~ 39 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKA 39 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCCCcccHHHHhhC
Confidence 457899999997655444444569999999998654
No 109
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=78.46 E-value=2.2 Score=46.41 Aligned_cols=33 Identities=30% Similarity=0.761 Sum_probs=19.9
Q ss_pred eeecCCCCccccccCcCCCCCCCc-ceeecCcccc
Q 026787 65 QVICSVCDTEQPVAQVCTNCGVNM-GEYFCDICKF 98 (233)
Q Consensus 65 ~v~C~~C~~~q~~~~~C~~Cg~~f-~~Y~C~~C~l 98 (233)
...|..|+++- +...|+.||... ..|+|+.|..
T Consensus 667 ~rkCPkCG~~t-~~~fCP~CGs~te~vy~CPsCGa 700 (1337)
T PRK14714 667 RRRCPSCGTET-YENRCPDCGTHTEPVYVCPDCGA 700 (1337)
T ss_pred EEECCCCCCcc-ccccCcccCCcCCCceeCccCCC
Confidence 46777777653 334777777665 2445666654
No 110
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=78.38 E-value=1.8 Score=42.57 Aligned_cols=50 Identities=22% Similarity=0.690 Sum_probs=41.6
Q ss_pred eeecCCCCCcccCchhHHhhhcCCCCCCCcccccccccceeecCCCCccccccCcCCCCCCC
Q 026787 26 RIRAPCCNEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVAQVCTNCGVN 87 (233)
Q Consensus 26 ~l~~pCC~~~y~Cr~CHde~~~~~~~~~~~H~~~r~~v~~v~C~~C~~~q~~~~~C~~Cg~~ 87 (233)
.+.|.-||....|..|.-...- |. ....+.|-.|+..+++...|++||..
T Consensus 213 ~~~C~~Cg~~~~C~~C~~~l~~--------h~----~~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 213 NLLCRSCGYILCCPNCDVSLTY--------HK----KEGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred eeEhhhCcCccCCCCCCCceEE--------ec----CCCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 3789999999999999766543 32 24589999999999999999999885
No 111
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=78.30 E-value=1.3 Score=27.00 Aligned_cols=37 Identities=24% Similarity=0.499 Sum_probs=23.4
Q ss_pred CcchhhhhcccCCceeEeccCCccChhhHHHHhccCCCcCCCCCcccc
Q 026787 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (233)
Q Consensus 153 CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrksi~ 200 (233)
|+.|.+.+.++.. .+..=|..||..|| +|..|++++.
T Consensus 2 C~~C~~~i~~~~~--~~~~~~~~~H~~Cf---------~C~~C~~~L~ 38 (39)
T smart00132 2 CAGCGKPIRGGEL--VLRALGKVWHPECF---------KCSKCGKPLG 38 (39)
T ss_pred ccccCCcccCCcE--EEEeCCccccccCC---------CCcccCCcCc
Confidence 6778887655411 22222788888876 6777887764
No 112
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=78.03 E-value=1.3 Score=42.38 Aligned_cols=51 Identities=29% Similarity=0.612 Sum_probs=42.3
Q ss_pred cCCCCCCCcchhhhhcccCCceeEeccCCccChhhHHHHhccCCCcCCCCCccccc
Q 026787 146 ENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID 201 (233)
Q Consensus 146 e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrksi~d 201 (233)
..+.++.||||... ....++-||||--...||.+.+. ++..|=.|+.++.|
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 44778899999864 23456779999999999999998 57899999999986
No 113
>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=77.50 E-value=2 Score=29.40 Aligned_cols=41 Identities=27% Similarity=0.805 Sum_probs=19.8
Q ss_pred CCcchhhhhcccCCceeEeccCCccChhhHHH--Hhc----cCCCcCCCCCcc
Q 026787 152 HCPICYEYLFDSLRNTTVMKCGHTMHCECYHE--MIK----RDKYCCPICSKS 198 (233)
Q Consensus 152 ~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~--~~~----~~~~~CPiCrks 198 (233)
.|||-...|. .+++-..|.|. .||+. ||. ....+||+|+++
T Consensus 4 ~CPls~~~i~---~P~Rg~~C~H~---~CFDl~~fl~~~~~~~~W~CPiC~~~ 50 (50)
T PF02891_consen 4 RCPLSFQRIR---IPVRGKNCKHL---QCFDLESFLESNQRTPKWKCPICNKP 50 (50)
T ss_dssp B-TTTSSB-S---SEEEETT--SS-----EEHHHHHHHHHHS---B-TTT---
T ss_pred eCCCCCCEEE---eCccCCcCccc---ceECHHHHHHHhhccCCeECcCCcCc
Confidence 5888887764 47888889977 46543 444 245789999974
No 114
>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=77.14 E-value=1.6 Score=28.98 Aligned_cols=25 Identities=24% Similarity=0.858 Sum_probs=15.6
Q ss_pred ccCCccChhhHHHHhccCCC-cCCCC
Q 026787 171 KCGHTMHCECYHEMIKRDKY-CCPIC 195 (233)
Q Consensus 171 pCGH~~H~~C~~~~~~~~~~-~CPiC 195 (233)
.|+=.||..|++.|+++... +||.|
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 36668999999999986433 69987
No 115
>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=76.44 E-value=0.93 Score=41.26 Aligned_cols=51 Identities=24% Similarity=0.561 Sum_probs=41.5
Q ss_pred CCCCCcchhhhhcccCCceeEe--c-cCCccChhhHHHHhccCCCcCC--CCCcccc
Q 026787 149 MHHHCPICYEYLFDSLRNTTVM--K-CGHTMHCECYHEMIKRDKYCCP--ICSKSVI 200 (233)
Q Consensus 149 ~~~~CpICle~lf~s~~~v~~L--p-CGH~~H~~C~~~~~~~~~~~CP--iCrksi~ 200 (233)
.+..||||..+.+-+.+ ++.| | |=|-|..+|.+..+..+.-.|| -|.|.+-
T Consensus 9 ~d~~CPvCksDrYLnPd-ik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kILR 64 (314)
T COG5220 9 EDRRCPVCKSDRYLNPD-IKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKILR 64 (314)
T ss_pred hcccCCccccccccCCC-eEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHHH
Confidence 35589999999887754 4444 5 9999999999999988888999 7887665
No 116
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=75.95 E-value=0.26 Score=47.40 Aligned_cols=50 Identities=22% Similarity=0.436 Sum_probs=44.1
Q ss_pred CCCCcchhhhhcccCCceeEeccCCccChhhHHHHhccCCCcCCCCCcccc
Q 026787 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (233)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrksi~ 200 (233)
-..+.||.+.|...-+....+.|||..|..++.+||.. ..++|.|+..+-
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 45799999999876677888999999999999999985 789999998885
No 117
>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=74.86 E-value=2 Score=23.35 Aligned_cols=20 Identities=35% Similarity=0.737 Sum_probs=14.1
Q ss_pred CcCCCCCccccchhHHhhhh
Q 026787 190 YCCPICSKSVIDMSRTWKRI 209 (233)
Q Consensus 190 ~~CPiCrksi~dm~~~~~~l 209 (233)
+.||+|.+++.+...+++-+
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~ 20 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHM 20 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHH
Confidence 47999999999887776554
No 118
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=74.21 E-value=3.1 Score=43.08 Aligned_cols=54 Identities=22% Similarity=0.532 Sum_probs=42.5
Q ss_pred eeecCCCCCcccCchhHHhhhcCCCCCCCcccccccccceeecCCCCccccccCcCCCCCCCccee
Q 026787 26 RIRAPCCNEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVAQVCTNCGVNMGEY 91 (233)
Q Consensus 26 ~l~~pCC~~~y~Cr~CHde~~~~~~~~~~~H~~~r~~v~~v~C~~C~~~q~~~~~C~~Cg~~f~~Y 91 (233)
.+.|.-||..+.|++|=.-..-|. .+..+.|-.|+.++++...|++||...=+|
T Consensus 435 ~l~C~~Cg~v~~Cp~Cd~~lt~H~------------~~~~L~CH~Cg~~~~~p~~Cp~Cgs~~L~~ 488 (730)
T COG1198 435 LLLCRDCGYIAECPNCDSPLTLHK------------ATGQLRCHYCGYQEPIPQSCPECGSEHLRA 488 (730)
T ss_pred eeecccCCCcccCCCCCcceEEec------------CCCeeEeCCCCCCCCCCCCCCCCCCCeeEE
Confidence 388999999999999965544322 237899999999999999999999884343
No 119
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=73.64 E-value=3.1 Score=43.17 Aligned_cols=80 Identities=20% Similarity=0.386 Sum_probs=48.8
Q ss_pred cCeeccCCCCcceeCCccceeeccccCccccccccccceeecCCCCCCCcchhhhhcccCCceeEeccCCccChhhHHHH
Q 026787 105 KGQFHCDDCGICRIGGRENYFHCKRCGSCYSTSLRNNHLCIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEM 184 (233)
Q Consensus 105 k~~yHC~~CgiCR~G~~~~~fHC~~C~~C~s~~l~~~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~ 184 (233)
.-+|-|+.|+-=-++++. --|++ |-+.+ ...|.+|-..+.. ..+.---|||..|.+++.+|
T Consensus 751 ~i~~~~~nc~a~~~~~~~--~~c~r---c~s~a------------~~~CtVC~~vi~G--~~~~c~~C~H~gH~sh~~sw 811 (839)
T KOG0269|consen 751 TIHYACPNCDAPMVLTKL--WQCDR---CESRA------------SAKCTVCDLVIRG--VDVWCQVCGHGGHDSHLKSW 811 (839)
T ss_pred eeeccccccCCccccccc--eeech---HHHHh------------hcCceeecceeee--eEeecccccccccHHHHHHH
Confidence 346667776654444433 33444 43333 2358888766532 22333459999999999999
Q ss_pred hccCCCcCCC-------CCccccchhH
Q 026787 185 IKRDKYCCPI-------CSKSVIDMSR 204 (233)
Q Consensus 185 ~~~~~~~CPi-------Crksi~dm~~ 204 (233)
+.. +..||. +++++.||..
T Consensus 812 ~~~-~s~ca~~~C~~~c~~~~~~D~~~ 837 (839)
T KOG0269|consen 812 FFK-ASPCAKSICPHLCHYSSFIDTFM 837 (839)
T ss_pred Hhc-CCCCccccCCccccccccchhhh
Confidence 974 566665 4566667654
No 120
>PHA03096 p28-like protein; Provisional
Probab=72.12 E-value=1.8 Score=39.94 Aligned_cols=47 Identities=17% Similarity=0.328 Sum_probs=31.8
Q ss_pred CCCcchhhhhcccC---CceeEe-ccCCccChhhHHHHhccC--CCcCCCCCc
Q 026787 151 HHCPICYEYLFDSL---RNTTVM-KCGHTMHCECYHEMIKRD--KYCCPICSK 197 (233)
Q Consensus 151 ~~CpICle~lf~s~---~~v~~L-pCGH~~H~~C~~~~~~~~--~~~CPiCrk 197 (233)
-.|.||+|...... ..-..| .|-|.|...|+..|.... ..+||.|+.
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 46889998876531 222345 499999999999998643 334555554
No 121
>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 KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=70.69 E-value=1.6 Score=39.95 Aligned_cols=67 Identities=25% Similarity=0.445 Sum_probs=45.1
Q ss_pred CCCCCcchhhhhcccCCceeEecc-----CCccChhhHHHHhccC-------CCcCCCCCccccc-------hhHHhhhh
Q 026787 149 MHHHCPICYEYLFDSLRNTTVMKC-----GHTMHCECYHEMIKRD-------KYCCPICSKSVID-------MSRTWKRI 209 (233)
Q Consensus 149 ~~~~CpICle~lf~s~~~v~~LpC-----GH~~H~~C~~~~~~~~-------~~~CPiCrksi~d-------m~~~~~~l 209 (233)
.+.-|=||.+.=.+.....-+=|| .|+.|.+|+..|+.+. .-+||.|+....- .....+++
T Consensus 19 ~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYiiv~P~l~~~~~~Le~~ 98 (293)
T KOG3053|consen 19 LERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYIIVFPQLGPFDRVLERL 98 (293)
T ss_pred cceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchheeeccccChHHHHHHHh
Confidence 355699999863443333345577 3999999999999753 3479999976542 22344666
Q ss_pred HHHHHh
Q 026787 210 DEEIEA 215 (233)
Q Consensus 210 D~~i~~ 215 (233)
|..|..
T Consensus 99 d~~i~r 104 (293)
T KOG3053|consen 99 DILIFR 104 (293)
T ss_pred hhHHhh
Confidence 766665
No 123
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=70.65 E-value=4.3 Score=42.06 Aligned_cols=43 Identities=28% Similarity=0.781 Sum_probs=29.6
Q ss_pred ceeecCCCCccccccCcCCCCCCCc------ceeecCccccccCCCCcCeeccCCCC
Q 026787 64 KQVICSVCDTEQPVAQVCTNCGVNM------GEYFCDICKFYDDDIEKGQFHCDDCG 114 (233)
Q Consensus 64 ~~v~C~~C~~~q~~~~~C~~Cg~~f------~~Y~C~~C~l~d~~~~k~~yHC~~Cg 114 (233)
+.++|..|+.. ..|++|...+ +...|--|..= ++.+.+|++||
T Consensus 434 ~~l~C~~Cg~v----~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~----~~~p~~Cp~Cg 482 (730)
T COG1198 434 PLLLCRDCGYI----AECPNCDSPLTLHKATGQLRCHYCGYQ----EPIPQSCPECG 482 (730)
T ss_pred ceeecccCCCc----ccCCCCCcceEEecCCCeeEeCCCCCC----CCCCCCCCCCC
Confidence 58999999966 5799998887 44555555432 34566666666
No 124
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=70.39 E-value=2.7 Score=38.74 Aligned_cols=30 Identities=20% Similarity=0.504 Sum_probs=26.2
Q ss_pred CCccCCccccccceeecCCCCCcccCchhHH
Q 026787 13 KMGYGCKHYRRRCRIRAPCCNEIFDCRHCHN 43 (233)
Q Consensus 13 ~~~~gC~HY~r~c~l~~pCC~~~y~Cr~CHd 43 (233)
...+.|.||...=.++.++|.. |+|..||+
T Consensus 175 ~~~~~CgH~~h~~cf~e~~~~~-y~CP~C~~ 204 (276)
T KOG1940|consen 175 AGVLKCGHYMHSRCFEEMICEG-YTCPICSK 204 (276)
T ss_pred CCccCcccchHHHHHHHHhccC-CCCCcccc
Confidence 3456899999866699999999 99999999
No 125
>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]
Probab=69.76 E-value=1.7 Score=45.08 Aligned_cols=45 Identities=33% Similarity=0.620 Sum_probs=31.7
Q ss_pred CCCCcchhhhhcccC---CceeEeccCCccChhhHHHHhccCCCcCCCCC
Q 026787 150 HHHCPICYEYLFDSL---RNTTVMKCGHTMHCECYHEMIKRDKYCCPICS 196 (233)
Q Consensus 150 ~~~CpICle~lf~s~---~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCr 196 (233)
++.|.-|.+....+. ..+.++.|||.||+.|+.....+++ |-+|.
T Consensus 784 e~rc~~c~~~~l~~~~~~~~~~v~~c~h~yhk~c~~~~~~~~~--~~~~~ 831 (846)
T KOG2066|consen 784 EERCSSCFEPNLPSGAAFDSVVVFHCGHMYHKECLMMESLRNA--CNIES 831 (846)
T ss_pred hhhhhhhcccccccCcccceeeEEEccchhhhcccccHHHhcc--cChhh
Confidence 346777777665444 5789999999999999987655332 55554
No 126
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=69.76 E-value=3.9 Score=44.70 Aligned_cols=33 Identities=30% Similarity=0.730 Sum_probs=24.9
Q ss_pred CcCCCCCCCcceeecCccccccCCCCcCeeccCCCCc
Q 026787 79 QVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGI 115 (233)
Q Consensus 79 ~~C~~Cg~~f~~Y~C~~C~l~d~~~~k~~yHC~~Cgi 115 (233)
..|++||......||+.|.-. .+.+|+|+.||.
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 479999987777799999644 245678877776
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=69.37 E-value=3.7 Score=29.06 Aligned_cols=27 Identities=30% Similarity=0.774 Sum_probs=17.1
Q ss_pred cCcCCCCCCCcceeecCccccccCCCCcCeeccCCCCc
Q 026787 78 AQVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGI 115 (233)
Q Consensus 78 ~~~C~~Cg~~f~~Y~C~~C~l~d~~~~k~~yHC~~Cgi 115 (233)
++.|+.||..... ......|.|+.||.
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 5678888877765 23445666666654
No 128
>PRK04023 DNA polymerase II large subunit; Validated
Probab=69.10 E-value=3.9 Score=43.75 Aligned_cols=49 Identities=24% Similarity=0.578 Sum_probs=36.3
Q ss_pred ceeecCCCCccccccCcCCCCCCC-cceeecCccccccCCCCcCeeccCCCCccee
Q 026787 64 KQVICSVCDTEQPVAQVCTNCGVN-MGEYFCDICKFYDDDIEKGQFHCDDCGICRI 118 (233)
Q Consensus 64 ~~v~C~~C~~~q~~~~~C~~Cg~~-f~~Y~C~~C~l~d~~~~k~~yHC~~CgiCR~ 118 (233)
..-.|..|+++. +...|++||.. -..|||+.|.-- -..|.|++||.=..
T Consensus 625 g~RfCpsCG~~t-~~frCP~CG~~Te~i~fCP~CG~~-----~~~y~CPKCG~El~ 674 (1121)
T PRK04023 625 GRRKCPSCGKET-FYRRCPFCGTHTEPVYRCPRCGIE-----VEEDECEKCGREPT 674 (1121)
T ss_pred cCccCCCCCCcC-CcccCCCCCCCCCcceeCccccCc-----CCCCcCCCCCCCCC
Confidence 455899999984 66899999974 577899999432 23477999986433
No 129
>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=68.69 E-value=3.5 Score=33.89 Aligned_cols=28 Identities=21% Similarity=0.455 Sum_probs=20.8
Q ss_pred ccCcCCCCCCCcceeecCccccccCCCCcCeeccCCCCcc
Q 026787 77 VAQVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGIC 116 (233)
Q Consensus 77 ~~~~C~~Cg~~f~~Y~C~~C~l~d~~~~k~~yHC~~CgiC 116 (233)
....|++||+.| | +.+|.+-.|++||.=
T Consensus 8 tKr~Cp~cg~kF----------Y--DLnk~p~vcP~cg~~ 35 (129)
T TIGR02300 8 TKRICPNTGSKF----------Y--DLNRRPAVSPYTGEQ 35 (129)
T ss_pred ccccCCCcCccc----------c--ccCCCCccCCCcCCc
Confidence 345788888854 5 457889999998853
No 130
>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=68.42 E-value=4.7 Score=27.51 Aligned_cols=10 Identities=60% Similarity=1.298 Sum_probs=5.6
Q ss_pred CcCCCCCccc
Q 026787 190 YCCPICSKSV 199 (233)
Q Consensus 190 ~~CPiCrksi 199 (233)
+.||||.+.+
T Consensus 32 v~CPiC~~~~ 41 (54)
T PF05605_consen 32 VVCPICSSRV 41 (54)
T ss_pred ccCCCchhhh
Confidence 3466666543
No 131
>PLN03086 PRLI-interacting factor K; Provisional
Probab=67.84 E-value=2.6 Score=42.37 Aligned_cols=84 Identities=26% Similarity=0.611 Sum_probs=48.8
Q ss_pred ccceeecCCCCcccccc-------------CcCCC--CCCCcceeecCccccccCCCCcCeeccCCCCcceeCCc-----
Q 026787 62 DVKQVICSVCDTEQPVA-------------QVCTN--CGVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGR----- 121 (233)
Q Consensus 62 ~v~~v~C~~C~~~q~~~-------------~~C~~--Cg~~f~~Y~C~~C~l~d~~~~k~~yHC~~CgiCR~G~~----- 121 (233)
.+..|.|..|....+.. ..|++ ||..|.+- .-+..+||+.||- ..+..
T Consensus 404 ~~~~V~C~NC~~~i~l~~l~lHe~~C~r~~V~Cp~~~Cg~v~~r~-----------el~~H~~C~~Cgk-~f~~s~LekH 471 (567)
T PLN03086 404 DVDTVECRNCKHYIPSRSIALHEAYCSRHNVVCPHDGCGIVLRVE-----------EAKNHVHCEKCGQ-AFQQGEMEKH 471 (567)
T ss_pred CCCeEECCCCCCccchhHHHHHHhhCCCcceeCCcccccceeecc-----------ccccCccCCCCCC-ccchHHHHHH
Confidence 45688999998776553 24663 77766332 2344578888864 22211
Q ss_pred ----cceeeccccCccccccccccce---eecCCCCCCCcchhhhh
Q 026787 122 ----ENYFHCKRCGSCYSTSLRNNHL---CIENSMHHHCPICYEYL 160 (233)
Q Consensus 122 ----~~~fHC~~C~~C~s~~l~~~H~---C~e~~~~~~CpICle~l 160 (233)
..-+-|. ||.-+.......|. |.++ ...|+.|...+
T Consensus 472 ~~~~Hkpv~Cp-Cg~~~~R~~L~~H~~thCp~K--pi~C~fC~~~v 514 (567)
T PLN03086 472 MKVFHEPLQCP-CGVVLEKEQMVQHQASTCPLR--LITCRFCGDMV 514 (567)
T ss_pred HHhcCCCccCC-CCCCcchhHHHhhhhccCCCC--ceeCCCCCCcc
Confidence 1124576 77655444445664 4433 35799998764
No 132
>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=67.81 E-value=4 Score=24.84 Aligned_cols=20 Identities=30% Similarity=0.853 Sum_probs=13.9
Q ss_pred CCCcceeCCccc-eeeccccC
Q 026787 112 DCGICRIGGREN-YFHCKRCG 131 (233)
Q Consensus 112 ~CgiCR~G~~~~-~fHC~~C~ 131 (233)
.|++|+.-.... +++|+.|+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~ 22 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECC 22 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCC
Confidence 467776654434 88888887
No 133
>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=67.34 E-value=4.7 Score=23.91 Aligned_cols=9 Identities=44% Similarity=1.239 Sum_probs=5.0
Q ss_pred CeeccCCCC
Q 026787 106 GQFHCDDCG 114 (233)
Q Consensus 106 ~~yHC~~Cg 114 (233)
..|.|++||
T Consensus 15 v~f~CPnCG 23 (24)
T PF07754_consen 15 VPFPCPNCG 23 (24)
T ss_pred ceEeCCCCC
Confidence 455555555
No 134
>PRK05580 primosome assembly protein PriA; Validated
Probab=66.63 E-value=4.8 Score=41.07 Aligned_cols=51 Identities=22% Similarity=0.632 Sum_probs=41.7
Q ss_pred eeecCCCCCcccCchhHHhhhcCCCCCCCcccccccccceeecCCCCccccccCcCCCCCCCc
Q 026787 26 RIRAPCCNEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVAQVCTNCGVNM 88 (233)
Q Consensus 26 ~l~~pCC~~~y~Cr~CHde~~~~~~~~~~~H~~~r~~v~~v~C~~C~~~q~~~~~C~~Cg~~f 88 (233)
.+.|.-||....|..|.-...- |. ....+.|-.|+..+++...|++||...
T Consensus 381 ~~~C~~Cg~~~~C~~C~~~l~~--------h~----~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~ 431 (679)
T PRK05580 381 FLLCRDCGWVAECPHCDASLTL--------HR----FQRRLRCHHCGYQEPIPKACPECGSTD 431 (679)
T ss_pred ceEhhhCcCccCCCCCCCceeE--------EC----CCCeEECCCCcCCCCCCCCCCCCcCCe
Confidence 3789999999999999875542 22 246899999999999999999998863
No 135
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=66.32 E-value=3.2 Score=40.81 Aligned_cols=100 Identities=22% Similarity=0.408 Sum_probs=54.2
Q ss_pred eeecCccccccCCCCcCeeccCCCCcceeCCccceeeccccCccccccc--cccceeecCCCCCCCcchhhhhcccCCce
Q 026787 90 EYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYSTSL--RNNHLCIENSMHHHCPICYEYLFDSLRNT 167 (233)
Q Consensus 90 ~Y~C~~C~l~d~~~~k~~yHC~~CgiCR~G~~~~~fHC~~C~~C~s~~l--~~~H~C~e~~~~~~CpICle~lf~s~~~v 167 (233)
-|||..|+-.- |+-|-.... +.+=|..|-.=++.+. .+..+|..+- -+||+|.-.|.......
T Consensus 5 L~fC~~C~~ir------------c~~c~~~Ei-~~~yCp~CL~~~p~~e~~~~~nrC~r~C--f~CP~C~~~L~~~~~~~ 69 (483)
T PF05502_consen 5 LYFCEHCHKIR------------CPRCVSEEI-DSYYCPNCLFEVPSSEARSEKNRCSRNC--FDCPICFSPLSVRASDT 69 (483)
T ss_pred ceecccccccC------------Chhhccccc-ceeECccccccCChhhheeccceecccc--ccCCCCCCcceeEeccc
Confidence 38888887661 333444433 3455666665555432 3566776443 47999998886543332
Q ss_pred eE---eccCCccChhhHHHHhccCCCcCCCCCccccchhHHhhhhHHH
Q 026787 168 TV---MKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRTWKRIDEE 212 (233)
Q Consensus 168 ~~---LpCGH~~H~~C~~~~~~~~~~~CPiCrksi~dm~~~~~~lD~~ 212 (233)
.. -+-+=.- -......|+.|+=+-.++...|.+.+.+
T Consensus 70 ~~~~~~~~~~~~--------~~~~~l~C~~C~Wss~~igi~Fdkpt~l 109 (483)
T PF05502_consen 70 PPSPPDPSSDSG--------GKPYYLSCSYCRWSSRDIGIKFDKPTGL 109 (483)
T ss_pred ccccccccccCC--------CCCEEEECCCceeeccccCccccCchhH
Confidence 11 0000000 0001358999998877665555554443
No 136
>KOG2068 consensus MOT2 transcription factor [Transcription]
Probab=64.91 E-value=5.1 Score=37.73 Aligned_cols=51 Identities=29% Similarity=0.505 Sum_probs=39.0
Q ss_pred CCCCCcchhhhhcccCCceeEeccCCccChhhHHHHhccCCCcCCCCCcccc
Q 026787 149 MHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (233)
Q Consensus 149 ~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrksi~ 200 (233)
-...||||-+++.........-|||+-++..|+..-.. .+.+||.|||...
T Consensus 248 v~~s~p~~~~~~~~~d~~~lP~~~~~~~~l~~~~t~~~-~~~~~~~~rk~~~ 298 (327)
T KOG2068|consen 248 VPPSCPICYEDLDLTDSNFLPCPCGFRLCLFCHKTISD-GDGRCPGCRKPYE 298 (327)
T ss_pred cCCCCCCCCCcccccccccccccccccchhhhhhcccc-cCCCCCccCCccc
Confidence 34689999999744433444446799999999988876 5899999998775
No 137
>PRK14873 primosome assembly protein PriA; Provisional
Probab=64.66 E-value=5.3 Score=40.88 Aligned_cols=49 Identities=20% Similarity=0.491 Sum_probs=39.0
Q ss_pred eeecCCCCCcccCchhHHhhhcCCCCCCCcccccccccceeecCCCCccccccCcCCCCCCC
Q 026787 26 RIRAPCCNEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVAQVCTNCGVN 87 (233)
Q Consensus 26 ~l~~pCC~~~y~Cr~CHde~~~~~~~~~~~H~~~r~~v~~v~C~~C~~~q~~~~~C~~Cg~~ 87 (233)
.+.|.-||...-|..|.-.+.- |. ....+.|-.|+..+ +...|++||..
T Consensus 383 ~l~C~~Cg~~~~C~~C~~~L~~--------h~----~~~~l~Ch~CG~~~-~p~~Cp~Cgs~ 431 (665)
T PRK14873 383 SLACARCRTPARCRHCTGPLGL--------PS----AGGTPRCRWCGRAA-PDWRCPRCGSD 431 (665)
T ss_pred eeEhhhCcCeeECCCCCCceeE--------ec----CCCeeECCCCcCCC-cCccCCCCcCC
Confidence 4899999999999999876542 22 23578999999876 57899999886
No 138
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=62.61 E-value=5.2 Score=36.25 Aligned_cols=48 Identities=25% Similarity=0.645 Sum_probs=27.8
Q ss_pred CCCCCCcceeecCccccccCCCCcCeeccCCCCcceeCCccceeeccccCcccc
Q 026787 82 TNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYS 135 (233)
Q Consensus 82 ~~Cg~~f~~Y~C~~C~l~d~~~~k~~yHC~~CgiCR~G~~~~~fHC~~C~~C~s 135 (233)
..=|......||+.|+++-- +...||.-||.|-.+- ==||.==|.|+.
T Consensus 105 ~~~~~~~~~~~C~~C~~~rP---pRs~HCsvC~~CV~rf---DHHC~WvnnCVG 152 (299)
T KOG1311|consen 105 DVNGIQVEWKYCDTCQLYRP---PRSSHCSVCNNCVLRF---DHHCPWLNNCIG 152 (299)
T ss_pred ccCCcccceEEcCcCcccCC---CCcccchhhccccccc---CCCCCCccceEC
Confidence 33455667789999999932 3345666666665441 134544455544
No 139
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=62.38 E-value=3.4 Score=42.40 Aligned_cols=45 Identities=31% Similarity=0.855 Sum_probs=36.4
Q ss_pred CCCcchhhhhcccCCceeEeccCCccChhhHHHHhccCCC-cCCCCCcccc
Q 026787 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKY-CCPICSKSVI 200 (233)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~-~CPiCrksi~ 200 (233)
..|+||++ .+...+-+|||.|-..|+.+.+..... .||+|+..+.
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 246677899999999999998875433 5999996654
No 140
>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=60.80 E-value=3 Score=38.42 Aligned_cols=51 Identities=27% Similarity=0.735 Sum_probs=31.1
Q ss_pred CCcccCchhHHhhhcCCCCCCCcccccccccceeecCCCCccccccCcCCCCCCCcceeecCcccc
Q 026787 33 NEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVAQVCTNCGVNMGEYFCDICKF 98 (233)
Q Consensus 33 ~~~y~Cr~CHde~~~~~~~~~~~H~~~r~~v~~v~C~~C~~~q~~~~~C~~Cg~~f~~Y~C~~C~l 98 (233)
|++|.|-+|++-+... |+++ |.. .|+....-+-.|.+|+. +|.|.|..||.
T Consensus 140 Grif~CsfC~~flCED--DQFE-HQA-----------sCQvLe~E~~KC~SCNr-lGq~sCLRCK~ 190 (314)
T PF06524_consen 140 GRIFKCSFCDNFLCED--DQFE-HQA-----------SCQVLESETFKCQSCNR-LGQYSCLRCKI 190 (314)
T ss_pred CeEEEeecCCCeeecc--chhh-hhh-----------hhhhhhccccccccccc-ccchhhhheee
Confidence 5678888887765421 1112 222 15555555667888764 78888888874
No 141
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=60.12 E-value=4.8 Score=41.15 Aligned_cols=34 Identities=26% Similarity=0.666 Sum_probs=21.1
Q ss_pred eeecCCCCccccccCcCCCCCCCc--ceeecCccccc
Q 026787 65 QVICSVCDTEQPVAQVCTNCGVNM--GEYFCDICKFY 99 (233)
Q Consensus 65 ~v~C~~C~~~q~~~~~C~~Cg~~f--~~Y~C~~C~l~ 99 (233)
.-.|..|++.++. ..|++||+.. +.-||+.|-..
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 4467777776543 4677777654 55566666543
No 142
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=59.95 E-value=7.3 Score=25.19 Aligned_cols=26 Identities=23% Similarity=0.579 Sum_probs=15.4
Q ss_pred cCCCCCCCcceeecCccccccCCCCcCeeccCCCC
Q 026787 80 VCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCG 114 (233)
Q Consensus 80 ~C~~Cg~~f~~Y~C~~C~l~d~~~~k~~yHC~~Cg 114 (233)
+||.|+..|..+. + .+-.++.|+.||
T Consensus 1 ~CP~C~~~l~~~~-----~----~~~~id~C~~C~ 26 (41)
T PF13453_consen 1 KCPRCGTELEPVR-----L----GDVEIDVCPSCG 26 (41)
T ss_pred CcCCCCcccceEE-----E----CCEEEEECCCCC
Confidence 4777777776553 1 224566676665
No 143
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=59.67 E-value=7.8 Score=36.65 Aligned_cols=44 Identities=23% Similarity=0.631 Sum_probs=35.1
Q ss_pred CCcchhhhhcccCCceeEeccCCccChhhHHHHhccC--CCcCCCCC
Q 026787 152 HCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRD--KYCCPICS 196 (233)
Q Consensus 152 ~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~--~~~CPiCr 196 (233)
.|||=-|. -+...+...|.|||.+=+.=++++-+++ .++||.|-
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 4555677889999999999999987754 57899996
No 144
>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=57.84 E-value=6.9 Score=35.53 Aligned_cols=48 Identities=25% Similarity=0.607 Sum_probs=22.4
Q ss_pred cceeecCCCCcccccc-CcCCCCCCCcceeecCccccc--cCCCCcCeeccCCCC
Q 026787 63 VKQVICSVCDTEQPVA-QVCTNCGVNMGEYFCDICKFY--DDDIEKGQFHCDDCG 114 (233)
Q Consensus 63 v~~v~C~~C~~~q~~~-~~C~~Cg~~f~~Y~C~~C~l~--d~~~~k~~yHC~~Cg 114 (233)
.+-..|+.|+++-.+. ..|++||..-..-+ .+| ++++.-.++-|+.||
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 3688999999998775 68999998765543 333 333344455555544
No 145
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=57.44 E-value=7.9 Score=36.44 Aligned_cols=44 Identities=32% Similarity=0.710 Sum_probs=35.0
Q ss_pred CCCcchhhhhcccCCceeEeccCCccChhhHHHHhccCCCcCCCCCc
Q 026787 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSK 197 (233)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrk 197 (233)
..||.|.--|. .+++.--|||.|...|+..-|..+.+.||.|..
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 47999997654 355655589999999999766557899999987
No 146
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=57.33 E-value=5.3 Score=43.71 Aligned_cols=53 Identities=30% Similarity=0.636 Sum_probs=42.6
Q ss_pred CCCCCCcchhhhhcccCCceeEeccCCccChhhHHHHhccCCCcCCCCCccccchhH
Q 026787 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSR 204 (233)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrksi~dm~~ 204 (233)
+....|+||++.|.. .-.+..|||.+-..|+..|+. .+..||+|+...+|...
T Consensus 1151 ~~~~~c~ic~dil~~---~~~I~~cgh~~c~~c~~~~l~-~~s~~~~~ksi~~dfg~ 1203 (1394)
T KOG0298|consen 1151 SGHFVCEICLDILRN---QGGIAGCGHEPCCRCDELWLY-ASSRCPICKSIKGDFGT 1203 (1394)
T ss_pred hcccchHHHHHHHHh---cCCeeeechhHhhhHHHHHHH-HhccCcchhhhhhhhcc
Confidence 445589999998853 334668999999999999998 47899999977776544
No 147
>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=57.21 E-value=2.7 Score=27.03 Aligned_cols=27 Identities=33% Similarity=0.671 Sum_probs=15.0
Q ss_pred cCCCCCCCcceeecCccccccCCCCcCeeccCCCCc
Q 026787 80 VCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGI 115 (233)
Q Consensus 80 ~C~~Cg~~f~~Y~C~~C~l~d~~~~k~~yHC~~Cgi 115 (233)
.|++||+.++.+| ++.|..=-||.||-
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 34455556666664
No 148
>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=56.74 E-value=6.9 Score=21.54 Aligned_cols=16 Identities=50% Similarity=0.916 Sum_probs=12.4
Q ss_pred CcCCCCCccccchhHH
Q 026787 190 YCCPICSKSVIDMSRT 205 (233)
Q Consensus 190 ~~CPiCrksi~dm~~~ 205 (233)
|+||+|.+++.+.+.+
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 5799999999875543
No 149
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=56.24 E-value=10 Score=25.06 Aligned_cols=8 Identities=38% Similarity=1.074 Sum_probs=4.1
Q ss_pred eeccCCCC
Q 026787 107 QFHCDDCG 114 (233)
Q Consensus 107 ~yHC~~Cg 114 (233)
..+|+.||
T Consensus 21 ~~~Cp~CG 28 (46)
T PRK00398 21 GVRCPYCG 28 (46)
T ss_pred ceECCCCC
Confidence 44555554
No 150
>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=56.06 E-value=9.6 Score=24.84 Aligned_cols=8 Identities=50% Similarity=1.315 Sum_probs=4.1
Q ss_pred cCCCCCCC
Q 026787 80 VCTNCGVN 87 (233)
Q Consensus 80 ~C~~Cg~~ 87 (233)
.||+||+.
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 151
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=56.03 E-value=7.8 Score=27.81 Aligned_cols=34 Identities=24% Similarity=0.712 Sum_probs=25.1
Q ss_pred cceeecCCCCccccccCcCCCCCCCcceeecCcccc
Q 026787 63 VKQVICSVCDTEQPVAQVCTNCGVNMGEYFCDICKF 98 (233)
Q Consensus 63 v~~v~C~~C~~~q~~~~~C~~Cg~~f~~Y~C~~C~l 98 (233)
...-.|..|+.+ +-..|..|....+.|-|++|.|
T Consensus 23 ~~~F~CPnCG~~--~I~RC~~CRk~~~~Y~CP~CGF 56 (59)
T PRK14890 23 AVKFLCPNCGEV--IIYRCEKCRKQSNPYTCPKCGF 56 (59)
T ss_pred cCEeeCCCCCCe--eEeechhHHhcCCceECCCCCC
Confidence 357788888754 1235888888888888888876
No 152
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=55.68 E-value=6.6 Score=28.18 Aligned_cols=35 Identities=31% Similarity=0.510 Sum_probs=25.6
Q ss_pred ceeecCCCCccccc------cCcCCCCCCCcceeecCcccc
Q 026787 64 KQVICSVCDTEQPV------AQVCTNCGVNMGEYFCDICKF 98 (233)
Q Consensus 64 ~~v~C~~C~~~q~~------~~~C~~Cg~~f~~Y~C~~C~l 98 (233)
-.|.|..|+.+|.+ ...|..||..+++-.=.+-+|
T Consensus 10 ~~VkCp~C~n~q~vFsha~t~V~C~~Cg~~L~~PtGGKa~i 50 (59)
T PRK00415 10 LKVKCPDCGNEQVVFSHASTVVRCLVCGKTLAEPTGGKAKI 50 (59)
T ss_pred EEEECCCCCCeEEEEecCCcEEECcccCCCcccCCCcceee
Confidence 47899999999966 247999999887655444443
No 153
>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=55.66 E-value=1.7 Score=32.13 Aligned_cols=41 Identities=27% Similarity=0.489 Sum_probs=25.0
Q ss_pred CCCcchhhhhcccCCceeEeccCCccChhhHHHHhccCCCcCCCCCccccc
Q 026787 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID 201 (233)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrksi~d 201 (233)
..||.|..+|.... ||+....|-..+.. ...||-|.+.+.-
T Consensus 2 ~~CP~C~~~L~~~~--------~~~~C~~C~~~~~~--~a~CPdC~~~Le~ 42 (70)
T PF07191_consen 2 NTCPKCQQELEWQG--------GHYHCEACQKDYKK--EAFCPDCGQPLEV 42 (70)
T ss_dssp -B-SSS-SBEEEET--------TEEEETTT--EEEE--EEE-TTT-SB-EE
T ss_pred CcCCCCCCccEEeC--------CEEECcccccccee--cccCCCcccHHHH
Confidence 46999999875432 77888888888875 4789999998863
No 154
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=55.18 E-value=5.2 Score=38.23 Aligned_cols=37 Identities=27% Similarity=0.608 Sum_probs=27.7
Q ss_pred CCCCcchhhhhcccCCceeEeccCCccChhhHHHHhc
Q 026787 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIK 186 (233)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~ 186 (233)
...|.||..+..+......++.|||.|...|..+++.
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 5689999933333323344788999999999999987
No 155
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=55.06 E-value=5.2 Score=35.73 Aligned_cols=51 Identities=24% Similarity=0.374 Sum_probs=38.7
Q ss_pred CCCCcchhhhhcccCCceeEecc-----CCccChhhHHHHhcc-CCCcCCCCCcccc
Q 026787 150 HHHCPICYEYLFDSLRNTTVMKC-----GHTMHCECYHEMIKR-DKYCCPICSKSVI 200 (233)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpC-----GH~~H~~C~~~~~~~-~~~~CPiCrksi~ 200 (233)
+..|=||.+..+++.......|| ....|+.|+..|+.. ++..|.+|.....
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 35799999987665433455677 278899999999973 4678999998665
No 156
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=53.98 E-value=2.8 Score=37.79 Aligned_cols=50 Identities=28% Similarity=0.547 Sum_probs=38.6
Q ss_pred CCCcchhhhhcc--cCCceeEec--------cCCccChhhHHHHhccCCCcCCCCCcccc
Q 026787 151 HHCPICYEYLFD--SLRNTTVMK--------CGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (233)
Q Consensus 151 ~~CpICle~lf~--s~~~v~~Lp--------CGH~~H~~C~~~~~~~~~~~CPiCrksi~ 200 (233)
..|.||...+.. ......++. |||++-..|.+..+.....+||.|++...
T Consensus 208 ~~c~ic~~~~~~n~~~~~p~vl~~~~~~~~~c~htlc~~c~~~~l~~~~~~cp~~~~~~~ 267 (296)
T KOG4185|consen 208 KLCEICERIYSENDEKLAPLVLSLSRLKEKIEGHTLCKECIDTILLQAGIKCPFCTWSHI 267 (296)
T ss_pred HHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcchHHHHHHhhhcCCcccceee
Confidence 469999988652 333445667 99999999999998765689999998643
No 157
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=53.56 E-value=6.6 Score=38.70 Aligned_cols=33 Identities=21% Similarity=0.772 Sum_probs=27.0
Q ss_pred CCCCcchhhhhcccCCceeEeccCCccChhhHHHHhc
Q 026787 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIK 186 (233)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~ 186 (233)
+..||||..++ ++.++|||||.+.+.|...-+.
T Consensus 4 elkc~vc~~f~----~epiil~c~h~lc~~ca~~~~~ 36 (699)
T KOG4367|consen 4 ELKCPVCGSFY----REPIILPCSHNLCQACARNILV 36 (699)
T ss_pred cccCceehhhc----cCceEeecccHHHHHHHHhhcc
Confidence 56799999874 3567899999999999987664
No 158
>PF15353 HECA: Headcase protein family homologue
Probab=53.21 E-value=6.6 Score=31.33 Aligned_cols=15 Identities=33% Similarity=0.707 Sum_probs=13.3
Q ss_pred cCCccChhhHHHHhc
Q 026787 172 CGHTMHCECYHEMIK 186 (233)
Q Consensus 172 CGH~~H~~C~~~~~~ 186 (233)
-|++||+.||++|-.
T Consensus 40 ~~~~MH~~CF~~wE~ 54 (107)
T PF15353_consen 40 FGQYMHRECFEKWED 54 (107)
T ss_pred CCCchHHHHHHHHHH
Confidence 489999999999965
No 159
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=53.01 E-value=7.9 Score=25.92 Aligned_cols=21 Identities=33% Similarity=0.918 Sum_probs=10.3
Q ss_pred ecCCCCcccccc----CcCCCCCCC
Q 026787 67 ICSVCDTEQPVA----QVCTNCGVN 87 (233)
Q Consensus 67 ~C~~C~~~q~~~----~~C~~Cg~~ 87 (233)
+|+.|+.+.+.. ..|++||..
T Consensus 4 ~C~~Cg~~~~~~~~~~irC~~CG~r 28 (44)
T smart00659 4 ICGECGRENEIKSKDVVRCRECGYR 28 (44)
T ss_pred ECCCCCCEeecCCCCceECCCCCce
Confidence 455555544332 345555554
No 160
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=50.44 E-value=17 Score=27.52 Aligned_cols=52 Identities=19% Similarity=0.389 Sum_probs=24.9
Q ss_pred CCCCCCcchhhhhcccCCceeE---eccCCccChhhHHHHhccCCCcCCCCCccc
Q 026787 148 SMHHHCPICYEYLFDSLRNTTV---MKCGHTMHCECYHEMIKRDKYCCPICSKSV 199 (233)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~---LpCGH~~H~~C~~~~~~~~~~~CPiCrksi 199 (233)
...+.|-||.|++-.+.+.-.+ .-|+-.+.+.|++--.+.++..||-|+...
T Consensus 7 ~~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg~q~CpqCkt~y 61 (80)
T PF14569_consen 7 LNGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEGNQVCPQCKTRY 61 (80)
T ss_dssp -SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS-SB-TTT--B-
T ss_pred cCCcccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcCcccccccCCCc
Confidence 3456799999997554433333 358999999999988888889999999443
No 161
>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=50.36 E-value=11 Score=25.65 Aligned_cols=26 Identities=38% Similarity=0.831 Sum_probs=12.2
Q ss_pred CCcCCCCCccccchhH--HhhhhHHHHH
Q 026787 189 KYCCPICSKSVIDMSR--TWKRIDEEIE 214 (233)
Q Consensus 189 ~~~CPiCrksi~dm~~--~~~~lD~~i~ 214 (233)
...||+|.+++.+-.. +-+.+...|.
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 3499999999985332 3344444443
No 162
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=49.45 E-value=9.1 Score=31.87 Aligned_cols=47 Identities=32% Similarity=0.678 Sum_probs=35.1
Q ss_pred CCCcchhhhhcccCCceeEec----cCCccChhhHHHHhccC--CCcCCCCCccccc
Q 026787 151 HHCPICYEYLFDSLRNTTVMK----CGHTMHCECYHEMIKRD--KYCCPICSKSVID 201 (233)
Q Consensus 151 ~~CpICle~lf~s~~~v~~Lp----CGH~~H~~C~~~~~~~~--~~~CPiCrksi~d 201 (233)
-+|-||.|. | .+.++|. ||=.+...|+.++.+.. .-.||+|+.|+-.
T Consensus 81 YeCnIC~et---S-~ee~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKs 133 (140)
T PF05290_consen 81 YECNICKET---S-AEERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKS 133 (140)
T ss_pred eeccCcccc---c-chhhcCCcccccchHHHHHHHHHHHHHcccCCCCCcccccccc
Confidence 368888875 2 2445663 89999999999977643 4679999988864
No 163
>PHA00626 hypothetical protein
Probab=48.90 E-value=11 Score=26.87 Aligned_cols=34 Identities=18% Similarity=0.400 Sum_probs=22.0
Q ss_pred eecCCCCccccccCcCCCCCCCcceeecCccccccC
Q 026787 66 VICSVCDTEQPVAQVCTNCGVNMGEYFCDICKFYDD 101 (233)
Q Consensus 66 v~C~~C~~~q~~~~~C~~Cg~~f~~Y~C~~C~l~d~ 101 (233)
|.|..|+..+-+ .|.-|...-++|-|..|.+++.
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 456677665444 5555666667788888877644
No 164
>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=47.53 E-value=11 Score=22.77 Aligned_cols=21 Identities=19% Similarity=0.585 Sum_probs=6.3
Q ss_pred CCcceeCCc-cceeeccccCcc
Q 026787 113 CGICRIGGR-ENYFHCKRCGSC 133 (233)
Q Consensus 113 CgiCR~G~~-~~~fHC~~C~~C 133 (233)
|++|+..+. ..+++|..|+.=
T Consensus 3 C~~C~~~~~~~~~Y~C~~Cdf~ 24 (30)
T PF07649_consen 3 CDACGKPIDGGWFYRCSECDFD 24 (30)
T ss_dssp -TTTS----S--EEE-TTT---
T ss_pred CCcCCCcCCCCceEECccCCCc
Confidence 445555433 256777776643
No 165
>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=47.52 E-value=16 Score=23.56 Aligned_cols=34 Identities=29% Similarity=0.629 Sum_probs=15.9
Q ss_pred cCCCCCCCcceeecCccccccCCCCcCeeccCCCC
Q 026787 80 VCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCG 114 (233)
Q Consensus 80 ~C~~Cg~~f~~Y~C~~C~l~d~~~~k~~yHC~~Cg 114 (233)
.|++||+.-+-|+ .+=--=-|++..-.|.|-+||
T Consensus 2 ~Cp~Cg~~~a~~~-~~Q~rsaDE~~T~fy~C~~C~ 35 (39)
T PF01096_consen 2 KCPKCGHNEAVFF-QIQTRSADEPMTLFYVCCNCG 35 (39)
T ss_dssp --SSS-SSEEEEE-EESSSSSSSSSEEEEEESSST
T ss_pred CCcCCCCCeEEEE-EeeccCCCCCCeEEEEeCCCC
Confidence 5788888777665 100000233455566666655
No 166
>KOG1312 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=46.05 E-value=6.9 Score=36.60 Aligned_cols=32 Identities=31% Similarity=0.782 Sum_probs=28.1
Q ss_pred CCCCcceeCCccceeeccccCccccccccccceee
Q 026787 111 DDCGICRIGGRENYFHCKRCGSCYSTSLRNNHLCI 145 (233)
Q Consensus 111 ~~CgiCR~G~~~~~fHC~~C~~C~s~~l~~~H~C~ 145 (233)
.+|..|++.+.--..||..||.|+..- +|.|+
T Consensus 149 ~kCSTCki~KPARSKHCsiCNrCV~rf---DHHCi 180 (341)
T KOG1312|consen 149 VKCSTCKIRKPARSKHCSICNRCVHRF---DHHCI 180 (341)
T ss_pred CccccccCCCccccccchHHHHHHHHh---ccceE
Confidence 679999999888899999999999864 78886
No 167
>PF14353 CpXC: CpXC protein
Probab=44.94 E-value=20 Score=28.33 Aligned_cols=11 Identities=27% Similarity=0.809 Sum_probs=7.5
Q ss_pred cCCCCCCCcce
Q 026787 80 VCTNCGVNMGE 90 (233)
Q Consensus 80 ~C~~Cg~~f~~ 90 (233)
+||+||+.|..
T Consensus 3 tCP~C~~~~~~ 13 (128)
T PF14353_consen 3 TCPHCGHEFEF 13 (128)
T ss_pred CCCCCCCeeEE
Confidence 57777777744
No 168
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=44.73 E-value=15 Score=23.36 Aligned_cols=10 Identities=40% Similarity=0.949 Sum_probs=5.0
Q ss_pred ceeecCCCCc
Q 026787 64 KQVICSVCDT 73 (233)
Q Consensus 64 ~~v~C~~C~~ 73 (233)
..|.|+.|++
T Consensus 24 ~~v~C~~C~~ 33 (36)
T PF13717_consen 24 RKVRCSKCGH 33 (36)
T ss_pred cEEECCCCCC
Confidence 3555555543
No 169
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=44.64 E-value=15 Score=25.13 Aligned_cols=9 Identities=44% Similarity=1.531 Sum_probs=4.9
Q ss_pred CeeccCCCC
Q 026787 106 GQFHCDDCG 114 (233)
Q Consensus 106 ~~yHC~~Cg 114 (233)
+.|+|..||
T Consensus 36 ~r~~C~~Cg 44 (50)
T PRK00432 36 DRWHCGKCG 44 (50)
T ss_pred CcEECCCcC
Confidence 455555555
No 170
>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=44.37 E-value=17 Score=22.49 Aligned_cols=24 Identities=33% Similarity=0.915 Sum_probs=15.7
Q ss_pred eecCccccccCCCCcCeeccCCCCc
Q 026787 91 YFCDICKFYDDDIEKGQFHCDDCGI 115 (233)
Q Consensus 91 Y~C~~C~l~d~~~~k~~yHC~~Cgi 115 (233)
|-|.+|-+.-+ +.+.++.|+.||.
T Consensus 2 ~~C~~CGy~y~-~~~~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYD-GEEAPWVCPVCGA 25 (33)
T ss_pred EECCCCCCEEC-CCcCCCcCcCCCC
Confidence 66777765422 2457788888875
No 171
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=42.83 E-value=11 Score=27.66 Aligned_cols=28 Identities=36% Similarity=0.692 Sum_probs=22.0
Q ss_pred ceeecCCCCccccc------cCcCCCCCCCccee
Q 026787 64 KQVICSVCDTEQPV------AQVCTNCGVNMGEY 91 (233)
Q Consensus 64 ~~v~C~~C~~~q~~------~~~C~~Cg~~f~~Y 91 (233)
-.|.|..|+.+|.+ ...|..||..+++-
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 48999999999977 24799999877653
No 172
>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=42.48 E-value=11 Score=25.20 Aligned_cols=40 Identities=25% Similarity=0.629 Sum_probs=27.3
Q ss_pred CcchhhhhcccCCceeEeccCCccChhhHHHHhccCCCcCCCCCccccchh
Q 026787 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMS 203 (233)
Q Consensus 153 CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrksi~dm~ 203 (233)
|+.|.+.+... .+.+..=|..+|..|| +|-.|+++|.+..
T Consensus 1 C~~C~~~I~~~--~~~~~~~~~~~H~~Cf---------~C~~C~~~l~~~~ 40 (58)
T PF00412_consen 1 CARCGKPIYGT--EIVIKAMGKFWHPECF---------KCSKCGKPLNDGD 40 (58)
T ss_dssp BTTTSSBESSS--SEEEEETTEEEETTTS---------BETTTTCBTTTSS
T ss_pred CCCCCCCccCc--EEEEEeCCcEEEcccc---------ccCCCCCccCCCe
Confidence 56777776532 3333356889998765 7888999887644
No 173
>PLN02189 cellulose synthase
Probab=41.94 E-value=24 Score=38.06 Aligned_cols=56 Identities=20% Similarity=0.434 Sum_probs=41.0
Q ss_pred ecCCCCCCCcchhhhhcccCCceeEec---cCCccChhhHHHHhccCCCcCCCCCcccc
Q 026787 145 IENSMHHHCPICYEYLFDSLRNTTVMK---CGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (233)
Q Consensus 145 ~e~~~~~~CpICle~lf~s~~~v~~Lp---CGH~~H~~C~~~~~~~~~~~CPiCrksi~ 200 (233)
+++...+.|.||.|++-.+.+.-.+.. ||=.+.+.|++-=.++++..||-|+...-
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 445566789999999764433333333 78889999996556667899999997665
No 174
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=41.75 E-value=15 Score=30.01 Aligned_cols=49 Identities=24% Similarity=0.541 Sum_probs=36.2
Q ss_pred CCCCCcceeecCccccccCCCCcCeeccCCCCcceeCCccceeeccccCcccccc
Q 026787 83 NCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYSTS 137 (233)
Q Consensus 83 ~Cg~~f~~Y~C~~C~l~d~~~~k~~yHC~~CgiCR~G~~~~~fHC~~C~~C~s~~ 137 (233)
.-+......+|..|+.+-- . ...||..||.|..+- -.||.-=|.|+...
T Consensus 41 ~~~~~~~~~~C~~C~~~kp--~-Rs~HC~~C~~CV~~~---DHHC~w~~~cIG~~ 89 (174)
T PF01529_consen 41 EDDENGELKYCSTCKIIKP--P-RSHHCRVCNRCVLRF---DHHCPWLGNCIGRR 89 (174)
T ss_pred ccccCCCCEECcccCCcCC--C-cceeccccccccccc---cccchhhccccccc
Confidence 3457778889999999833 2 477888888888773 45888878887653
No 175
>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=41.16 E-value=8.9 Score=40.42 Aligned_cols=44 Identities=30% Similarity=0.728 Sum_probs=0.0
Q ss_pred cCCCCCCCcceeecCccccccCCCCcCeeccCCCCcceeCCccceeeccccCc
Q 026787 80 VCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGS 132 (233)
Q Consensus 80 ~C~~Cg~~f~~Y~C~~C~l~d~~~~k~~yHC~~CgiCR~G~~~~~fHC~~C~~ 132 (233)
.|++||..--.-.|+.|.-. +...|.|+.||+ .+.. .+|.+||.
T Consensus 657 ~Cp~Cg~~t~~~~Cp~CG~~----T~~~~~Cp~C~~-~~~~----~~C~~C~~ 700 (900)
T PF03833_consen 657 RCPKCGKETFYNRCPECGSH----TEPVYVCPDCGI-EVEE----DECPKCGR 700 (900)
T ss_dssp -----------------------------------------------------
T ss_pred cCcccCCcchhhcCcccCCc----cccceecccccc-ccCc----cccccccc
Confidence 46666666555556666544 345677777776 2221 16777765
No 176
>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=40.86 E-value=13 Score=22.82 Aligned_cols=16 Identities=38% Similarity=1.028 Sum_probs=7.6
Q ss_pred CCCCCCCcceeecCccc
Q 026787 81 CTNCGVNMGEYFCDICK 97 (233)
Q Consensus 81 C~~Cg~~f~~Y~C~~C~ 97 (233)
|.-||. .++|-|+.|.
T Consensus 5 C~vC~~-~~kY~Cp~C~ 20 (30)
T PF04438_consen 5 CSVCGN-PAKYRCPRCG 20 (30)
T ss_dssp ETSSSS-EESEE-TTT-
T ss_pred CccCcC-CCEEECCCcC
Confidence 444555 5555555554
No 177
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=40.80 E-value=18 Score=23.02 Aligned_cols=9 Identities=33% Similarity=0.888 Sum_probs=4.3
Q ss_pred eeecCCCCc
Q 026787 65 QVICSVCDT 73 (233)
Q Consensus 65 ~v~C~~C~~ 73 (233)
.|.|+.|++
T Consensus 25 ~vrC~~C~~ 33 (37)
T PF13719_consen 25 KVRCPKCGH 33 (37)
T ss_pred EEECCCCCc
Confidence 455444443
No 178
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=39.74 E-value=32 Score=33.94 Aligned_cols=46 Identities=28% Similarity=0.717 Sum_probs=29.9
Q ss_pred cceeecCCCCccccccCcCCCCCCCcc------eeecCccccccCCCCcCeeccCCCCcc
Q 026787 63 VKQVICSVCDTEQPVAQVCTNCGVNMG------EYFCDICKFYDDDIEKGQFHCDDCGIC 116 (233)
Q Consensus 63 v~~v~C~~C~~~q~~~~~C~~Cg~~f~------~Y~C~~C~l~d~~~~k~~yHC~~CgiC 116 (233)
.+.++|..|+.. ..|++|+..+. .-.|.-|.+- .+.+..|+.||-=
T Consensus 211 a~~~~C~~Cg~~----~~C~~C~~~l~~h~~~~~l~Ch~Cg~~----~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 211 SKNLLCRSCGYI----LCCPNCDVSLTYHKKEGKLRCHYCGYQ----EPIPKTCPQCGSE 262 (505)
T ss_pred CCeeEhhhCcCc----cCCCCCCCceEEecCCCeEEcCCCcCc----CCCCCCCCCCCCC
Confidence 357889999865 57999997774 3446655532 3345567777653
No 179
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=39.73 E-value=20 Score=24.74 Aligned_cols=26 Identities=35% Similarity=0.708 Sum_probs=13.7
Q ss_pred eeecCcc-ccccCCCCcCeeccCCCCc
Q 026787 90 EYFCDIC-KFYDDDIEKGQFHCDDCGI 115 (233)
Q Consensus 90 ~Y~C~~C-~l~d~~~~k~~yHC~~Cgi 115 (233)
.|-|..| +.++.+....-.-|+.||.
T Consensus 6 ~Y~C~~Cg~~~~~~~~~~~irCp~Cg~ 32 (49)
T COG1996 6 EYKCARCGREVELDQETRGIRCPYCGS 32 (49)
T ss_pred EEEhhhcCCeeehhhccCceeCCCCCc
Confidence 4444444 2334444556666666664
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=39.49 E-value=15 Score=25.92 Aligned_cols=34 Identities=24% Similarity=0.457 Sum_probs=19.6
Q ss_pred eeecCCCCccccc------cCcCCCCCCCcceeecCcccc
Q 026787 65 QVICSVCDTEQPV------AQVCTNCGVNMGEYFCDICKF 98 (233)
Q Consensus 65 ~v~C~~C~~~q~~------~~~C~~Cg~~f~~Y~C~~C~l 98 (233)
.|.|..|..+|.+ ...|..||..+++-.=.+-+|
T Consensus 7 ~VkCp~C~~~q~vFSha~t~V~C~~Cg~~L~~PtGGKa~l 46 (55)
T PF01667_consen 7 DVKCPGCYNIQTVFSHAQTVVKCVVCGTVLAQPTGGKARL 46 (55)
T ss_dssp EEE-TTT-SEEEEETT-SS-EE-SSSTSEEEEE-SSSEEE
T ss_pred EEECCCCCCeeEEEecCCeEEEcccCCCEecCCCCcCeEE
Confidence 6788888888866 136888888777654444333
No 181
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=39.38 E-value=17 Score=22.53 Aligned_cols=23 Identities=26% Similarity=0.710 Sum_probs=10.5
Q ss_pred cCCCCCCCcceeecCccccccCCCCcCeeccCCCC
Q 026787 80 VCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCG 114 (233)
Q Consensus 80 ~C~~Cg~~f~~Y~C~~C~l~d~~~~k~~yHC~~Cg 114 (233)
.|+.|+..++- .+..+|-|+.||
T Consensus 4 ~Cp~C~se~~y------------~D~~~~vCp~C~ 26 (30)
T PF08274_consen 4 KCPLCGSEYTY------------EDGELLVCPECG 26 (30)
T ss_dssp --TTT-----E------------E-SSSEEETTTT
T ss_pred CCCCCCCccee------------ccCCEEeCCccc
Confidence 57777777653 234678888876
No 182
>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=39.18 E-value=23 Score=23.27 Aligned_cols=20 Identities=25% Similarity=0.861 Sum_probs=11.7
Q ss_pred eccCCCCcceeCCccceeeccccC
Q 026787 108 FHCDDCGICRIGGRENYFHCKRCG 131 (233)
Q Consensus 108 yHC~~CgiCR~G~~~~~fHC~~C~ 131 (233)
|+|+.|+. +++ ..+||..|.
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 56666655 332 567777664
No 183
>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=38.93 E-value=24 Score=28.71 Aligned_cols=29 Identities=28% Similarity=0.686 Sum_probs=19.2
Q ss_pred CcceeCCccceeeccccCccccccccccceee
Q 026787 114 GICRIGGRENYFHCKRCGSCYSTSLRNNHLCI 145 (233)
Q Consensus 114 giCR~G~~~~~fHC~~C~~C~s~~l~~~H~C~ 145 (233)
-.|++-......||..||.|+..- +|-|.
T Consensus 52 ~~C~~~kp~Rs~HC~~C~~CV~~~---DHHC~ 80 (174)
T PF01529_consen 52 STCKIIKPPRSHHCRVCNRCVLRF---DHHCP 80 (174)
T ss_pred cccCCcCCCcceeccccccccccc---cccch
Confidence 334455555688888888887754 56654
No 184
>KOG4399 consensus C2HC-type Zn-finger protein [General function prediction only]
Probab=38.01 E-value=6.5 Score=36.24 Aligned_cols=72 Identities=28% Similarity=0.669 Sum_probs=54.0
Q ss_pred CCCcceeecCccccccCCCCcCeeccCCCCcceeCCccceeeccccCccccccccccceeecCCCCCCCcchhhh
Q 026787 85 GVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYSTSLRNNHLCIENSMHHHCPICYEY 159 (233)
Q Consensus 85 g~~f~~Y~C~~C~l~d~~~~k~~yHC~~CgiCR~G~~~~~fHC~~C~~C~s~~l~~~H~C~e~~~~~~CpICle~ 159 (233)
|..=+-.||+.|..| ..+-.-||+.|+.|..-.++.|-||..|-.|+-.++-.--.|-.-+..--|-||.|.
T Consensus 199 ~~EE~~~~~~~~~~Y---v~~~~~H~~~~~S~~~~~~~~~~H~~~~~~~~~~~~i~C~~~~~~A~~~~C~iC~~~ 270 (325)
T KOG4399|consen 199 PTEEGYRFCSPCQRY---VSLENQHCEHCNSCTSKDGRKWNHCFLCKKCVKPSWIHCSICNHCAVKHGCFICGEL 270 (325)
T ss_pred ccccceEEEeehHHH---HHHHhhhchhhcccccchhHHHhHhHHhhhhcccceeeeecccchhhhcceeecccc
Confidence 444466779999988 446778999999998877778999999999998887433333334555678888886
No 185
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=37.54 E-value=11 Score=31.72 Aligned_cols=25 Identities=28% Similarity=1.016 Sum_probs=18.9
Q ss_pred ceeecCccccccCCCCcCeeccCCCC--cceeC
Q 026787 89 GEYFCDICKFYDDDIEKGQFHCDDCG--ICRIG 119 (233)
Q Consensus 89 ~~Y~C~~C~l~d~~~~k~~yHC~~Cg--iCR~G 119 (233)
.+-||++|-+| ++|-|-.|| +|-|+
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 186
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=36.83 E-value=27 Score=23.02 Aligned_cols=8 Identities=50% Similarity=1.510 Sum_probs=3.9
Q ss_pred eeccCCCC
Q 026787 107 QFHCDDCG 114 (233)
Q Consensus 107 ~yHC~~Cg 114 (233)
.|-|+.||
T Consensus 20 ~~vC~~Cg 27 (52)
T smart00661 20 RFVCRKCG 27 (52)
T ss_pred EEECCcCC
Confidence 44454444
No 187
>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=36.74 E-value=26 Score=20.98 Aligned_cols=10 Identities=20% Similarity=0.610 Sum_probs=3.8
Q ss_pred CcCCCCCCCc
Q 026787 79 QVCTNCGVNM 88 (233)
Q Consensus 79 ~~C~~Cg~~f 88 (233)
+.|+.|+..+
T Consensus 2 ~~C~rC~~~~ 11 (30)
T PF06827_consen 2 EKCPRCWNYI 11 (30)
T ss_dssp SB-TTT--BB
T ss_pred CcCccCCCcc
Confidence 3566665554
No 188
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=36.66 E-value=22 Score=32.78 Aligned_cols=94 Identities=22% Similarity=0.630 Sum_probs=0.0
Q ss_pred ccCchhHHhhhcCCCCCCCcccccccccceeecCCCCccccccCcCCCCCCCcceeecCccc-cccCCC---CcCeeccC
Q 026787 36 FDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVAQVCTNCGVNMGEYFCDICK-FYDDDI---EKGQFHCD 111 (233)
Q Consensus 36 y~Cr~CHde~~~~~~~~~~~H~~~r~~v~~v~C~~C~~~q~~~~~C~~Cg~~f~~Y~C~~C~-l~d~~~---~k~~yHC~ 111 (233)
|.|.+|-..+++ --..|.+ .+++|-.|+..-.+ .-.|+|-|.+|+ +.|+++ .-++||=
T Consensus 100 F~Cd~Cn~~Lad--------~gf~rnq-gr~LC~~Cn~k~Ka--------~~~g~YvC~KCh~~iD~~~l~fr~d~yH~- 161 (332)
T KOG2272|consen 100 FRCDLCNKHLAD--------QGFYRNQ-GRALCRECNQKEKA--------KGRGRYVCQKCHAHIDEQPLTFRGDPYHP- 161 (332)
T ss_pred chhHHHHHHHhh--------hhhHhhc-chHHhhhhhhhhcc--------cccceeehhhhhhhcccccccccCCCCCc-
Q ss_pred CCCcceeCCccceeeccccCccccc---cccccceeecCCCCCCCcchhh
Q 026787 112 DCGICRIGGRENYFHCKRCGSCYST---SLRNNHLCIENSMHHHCPICYE 158 (233)
Q Consensus 112 ~CgiCR~G~~~~~fHC~~C~~C~s~---~l~~~H~C~e~~~~~~CpICle 158 (233)
.-|.|.+||-=+.. ++++.--|..=-...-+|||..
T Consensus 162 -----------yHFkCt~C~keL~sdaRevk~eLyClrChD~mgipiCga 200 (332)
T KOG2272|consen 162 -----------YHFKCTTCGKELTSDAREVKGELYCLRCHDKMGIPICGA 200 (332)
T ss_pred -----------cceecccccccccchhhhhccceeccccccccCCccccc
No 189
>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=36.57 E-value=16 Score=28.95 Aligned_cols=11 Identities=18% Similarity=0.661 Sum_probs=5.6
Q ss_pred cCcCCCCCCCc
Q 026787 78 AQVCTNCGVNM 88 (233)
Q Consensus 78 ~~~C~~Cg~~f 88 (233)
...|.+||..|
T Consensus 70 ~~~C~~Cg~~~ 80 (115)
T TIGR00100 70 ECECEDCSEEV 80 (115)
T ss_pred EEEcccCCCEE
Confidence 34555555444
No 190
>PLN02436 cellulose synthase A
Probab=36.27 E-value=32 Score=37.32 Aligned_cols=56 Identities=16% Similarity=0.445 Sum_probs=41.1
Q ss_pred ecCCCCCCCcchhhhhcccCCceeEec---cCCccChhhHHHHhccCCCcCCCCCcccc
Q 026787 145 IENSMHHHCPICYEYLFDSLRNTTVMK---CGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (233)
Q Consensus 145 ~e~~~~~~CpICle~lf~s~~~v~~Lp---CGH~~H~~C~~~~~~~~~~~CPiCrksi~ 200 (233)
+.....+.|.||.|++-.+.+.-.+.. ||=.+.+.|++-=.++++..||-|+...-
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 444556789999999855544444444 67889999996556667899999997664
No 191
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=36.09 E-value=19 Score=20.13 Aligned_cols=16 Identities=31% Similarity=0.696 Sum_probs=12.2
Q ss_pred CcCCCCCccccchhHH
Q 026787 190 YCCPICSKSVIDMSRT 205 (233)
Q Consensus 190 ~~CPiCrksi~dm~~~ 205 (233)
+.|.+|.+++.+...+
T Consensus 1 ~~C~~C~~~f~s~~~~ 16 (25)
T PF12874_consen 1 FYCDICNKSFSSENSL 16 (25)
T ss_dssp EEETTTTEEESSHHHH
T ss_pred CCCCCCCCCcCCHHHH
Confidence 4699999999876543
No 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=35.68 E-value=23 Score=22.18 Aligned_cols=10 Identities=30% Similarity=1.066 Sum_probs=5.4
Q ss_pred cCeeccCCCC
Q 026787 105 KGQFHCDDCG 114 (233)
Q Consensus 105 k~~yHC~~Cg 114 (233)
.++-.|..||
T Consensus 15 ~~~irC~~CG 24 (32)
T PF03604_consen 15 GDPIRCPECG 24 (32)
T ss_dssp SSTSSBSSSS
T ss_pred CCcEECCcCC
Confidence 3444566665
No 193
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=35.67 E-value=46 Score=21.90 Aligned_cols=9 Identities=44% Similarity=1.154 Sum_probs=5.3
Q ss_pred CcCCCCCCC
Q 026787 79 QVCTNCGVN 87 (233)
Q Consensus 79 ~~C~~Cg~~ 87 (233)
..||.||..
T Consensus 19 ~~CP~Cg~~ 27 (46)
T PF12760_consen 19 FVCPHCGST 27 (46)
T ss_pred CCCCCCCCe
Confidence 456666665
No 194
>PF15616 TerY-C: TerY-C metal binding domain
Probab=35.46 E-value=37 Score=27.97 Aligned_cols=33 Identities=33% Similarity=0.805 Sum_probs=21.8
Q ss_pred CcCCCCCCCcceeecCcc-cccc-CCCCcCeeccCCCC
Q 026787 79 QVCTNCGVNMGEYFCDIC-KFYD-DDIEKGQFHCDDCG 114 (233)
Q Consensus 79 ~~C~~Cg~~f~~Y~C~~C-~l~d-~~~~k~~yHC~~Cg 114 (233)
..||.||..+|---| .| ||+- +++ ....|+-||
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 689999999998888 58 4552 211 244555554
No 195
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=35.13 E-value=32 Score=21.69 Aligned_cols=21 Identities=19% Similarity=0.363 Sum_probs=15.4
Q ss_pred CcCCCCCCCcceeecCccccc
Q 026787 79 QVCTNCGVNMGEYFCDICKFY 99 (233)
Q Consensus 79 ~~C~~Cg~~f~~Y~C~~C~l~ 99 (233)
..|..++...+.|||..|+.+
T Consensus 4 ~~C~~H~~~~~~~~C~~C~~~ 24 (42)
T PF00643_consen 4 PKCPEHPEEPLSLFCEDCNEP 24 (42)
T ss_dssp SB-SSTTTSBEEEEETTTTEE
T ss_pred ccCccCCccceEEEecCCCCc
Confidence 467788887788888888754
No 196
>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=34.72 E-value=28 Score=22.90 Aligned_cols=21 Identities=38% Similarity=0.917 Sum_probs=10.2
Q ss_pred eccCCCCcceeCCccceeeccccC
Q 026787 108 FHCDDCGICRIGGRENYFHCKRCG 131 (233)
Q Consensus 108 yHC~~CgiCR~G~~~~~fHC~~C~ 131 (233)
|.|+.|+. -+-| ..|||.+|.
T Consensus 1 ~~C~~C~~-~i~g--~r~~C~~C~ 21 (46)
T cd02249 1 YSCDGCLK-PIVG--VRYHCLVCE 21 (46)
T ss_pred CCCcCCCC-CCcC--CEEECCCCC
Confidence 34555555 2222 466666554
No 197
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=34.16 E-value=24 Score=29.18 Aligned_cols=19 Identities=42% Similarity=1.267 Sum_probs=13.8
Q ss_pred CcCCCCCCCc----ceeecCccc
Q 026787 79 QVCTNCGVNM----GEYFCDICK 97 (233)
Q Consensus 79 ~~C~~Cg~~f----~~Y~C~~C~ 97 (233)
..|+.||.++ |+-||++|-
T Consensus 29 ~hCp~Cg~PLF~KdG~v~CPvC~ 51 (131)
T COG1645 29 KHCPKCGTPLFRKDGEVFCPVCG 51 (131)
T ss_pred hhCcccCCcceeeCCeEECCCCC
Confidence 5788888887 555677774
No 198
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=33.97 E-value=24 Score=25.48 Aligned_cols=33 Identities=24% Similarity=0.590 Sum_probs=20.1
Q ss_pred ceeecCCCCccccccCcCCCCCCCcceeecCcccc
Q 026787 64 KQVICSVCDTEQPVAQVCTNCGVNMGEYFCDICKF 98 (233)
Q Consensus 64 ~~v~C~~C~~~q~~~~~C~~Cg~~f~~Y~C~~C~l 98 (233)
..-.|..|+.++-. .|..|-..=+.|-|++|-|
T Consensus 26 v~F~CPnCGe~~I~--Rc~~CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 26 VKFPCPNCGEVEIY--RCAKCRKLGNPYRCPKCGF 58 (61)
T ss_pred eEeeCCCCCceeee--hhhhHHHcCCceECCCcCc
Confidence 45566666654332 5666666666777776655
No 199
>PRK00420 hypothetical protein; Validated
Probab=33.94 E-value=29 Score=27.88 Aligned_cols=19 Identities=26% Similarity=0.695 Sum_probs=12.1
Q ss_pred CcCCCCCCCcce-----eecCccc
Q 026787 79 QVCTNCGVNMGE-----YFCDICK 97 (233)
Q Consensus 79 ~~C~~Cg~~f~~-----Y~C~~C~ 97 (233)
..||.||.+|.+ .||+.|.
T Consensus 24 ~~CP~Cg~pLf~lk~g~~~Cp~Cg 47 (112)
T PRK00420 24 KHCPVCGLPLFELKDGEVVCPVHG 47 (112)
T ss_pred CCCCCCCCcceecCCCceECCCCC
Confidence 578888887643 5555554
No 200
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=33.70 E-value=46 Score=31.13 Aligned_cols=25 Identities=28% Similarity=0.790 Sum_probs=20.8
Q ss_pred cceeecCCCCcccccc-CcCCCCCCC
Q 026787 63 VKQVICSVCDTEQPVA-QVCTNCGVN 87 (233)
Q Consensus 63 v~~v~C~~C~~~q~~~-~~C~~Cg~~ 87 (233)
.+-..|+.|+++-.+. ..|++||..
T Consensus 210 ~RyL~CslC~teW~~~R~~C~~Cg~~ 235 (309)
T PRK03564 210 LRYLHCNLCESEWHVVRVKCSNCEQS 235 (309)
T ss_pred ceEEEcCCCCCcccccCccCCCCCCC
Confidence 4688999999998775 689999974
No 201
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=33.52 E-value=28 Score=24.04 Aligned_cols=24 Identities=33% Similarity=0.875 Sum_probs=20.0
Q ss_pred cceeecCCCCccccc-cCcCCCCCC
Q 026787 63 VKQVICSVCDTEQPV-AQVCTNCGV 86 (233)
Q Consensus 63 v~~v~C~~C~~~q~~-~~~C~~Cg~ 86 (233)
...+||+.|+...++ +..|..||.
T Consensus 12 ~~k~ICrkC~ARnp~~A~~CRKCg~ 36 (48)
T PRK04136 12 FNKKICMRCNARNPWRATKCRKCGY 36 (48)
T ss_pred hcccchhcccCCCCccccccccCCC
Confidence 357899999999888 568998886
No 202
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=33.16 E-value=46 Score=34.32 Aligned_cols=79 Identities=23% Similarity=0.364 Sum_probs=53.7
Q ss_pred eecCCCCCCCcchhhhhcccCCceeEec---cCCccChhhHHHHh-------ccCCCcCCCCCccccchhHHhhhhHHHH
Q 026787 144 CIENSMHHHCPICYEYLFDSLRNTTVMK---CGHTMHCECYHEMI-------KRDKYCCPICSKSVIDMSRTWKRIDEEI 213 (233)
Q Consensus 144 C~e~~~~~~CpICle~lf~s~~~v~~Lp---CGH~~H~~C~~~~~-------~~~~~~CPiCrksi~dm~~~~~~lD~~i 213 (233)
|...+.-..||||+-..-++ +....+. |.=+.|..|..-+- ....|+|-+|| ..+.+-+.|...+
T Consensus 139 ~~~c~s~~~cPvc~~~Y~~~-e~~~~~~c~~c~rwsh~~c~~~sdd~~~q~~vD~~~~CS~CR----~es~qvKdi~~~v 213 (694)
T KOG4443|consen 139 CAPCASLSYCPVCLIVYQDS-ESLPMVCCSICQRWSHGGCDGISDDKYMQAQVDLQYKCSTCR----GESYQVKDISDAL 213 (694)
T ss_pred cccccccccCchHHHhhhhc-cchhhHHHHHhcccccCCCCccchHHHHHHhhhhhcccceee----hhhhhhhhHHHHH
Confidence 33344457899999876554 3343333 55678888864321 11379999999 5555778888889
Q ss_pred HhCCCChhhhccee
Q 026787 214 EATVMPEDYRHKKV 227 (233)
Q Consensus 214 ~~~pmP~~y~~~~~ 227 (233)
+.+-||..|.++.+
T Consensus 214 qe~~~~k~~~~~~~ 227 (694)
T KOG4443|consen 214 QETWKAKDKPDKIL 227 (694)
T ss_pred Hhhcchhhccccce
Confidence 99999999887654
No 203
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=32.87 E-value=40 Score=26.47 Aligned_cols=32 Identities=31% Similarity=0.664 Sum_probs=21.6
Q ss_pred cceeeccccC-ccccccccccceeecCCCCCCCcchhhh
Q 026787 122 ENYFHCKRCG-SCYSTSLRNNHLCIENSMHHHCPICYEY 159 (233)
Q Consensus 122 ~~~fHC~~C~-~C~s~~l~~~H~C~e~~~~~~CpICle~ 159 (233)
..+|+|..|| .-+++.+. + +..+..||+|..+
T Consensus 19 pt~f~CP~Cge~~v~v~~~--k----~~~h~~C~~CG~y 51 (99)
T PRK14892 19 PKIFECPRCGKVSISVKIK--K----NIAIITCGNCGLY 51 (99)
T ss_pred CcEeECCCCCCeEeeeecC--C----CcceEECCCCCCc
Confidence 4788888888 33333332 1 4667889999987
No 204
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=32.42 E-value=27 Score=30.71 Aligned_cols=39 Identities=26% Similarity=0.579 Sum_probs=28.1
Q ss_pred CcchhhhhcccCCceeEeccCCccC-hhhHHHHhccCCCcCCCCCcccc
Q 026787 153 CPICYEYLFDSLRNTTVMKCGHTMH-CECYHEMIKRDKYCCPICSKSVI 200 (233)
Q Consensus 153 CpICle~lf~s~~~v~~LpCGH~~H-~~C~~~~~~~~~~~CPiCrksi~ 200 (233)
|-+|.+. + ..|..|||.|..+ ..|-.. ...||||+....
T Consensus 161 Cr~C~~~--~--~~VlllPCrHl~lC~~C~~~-----~~~CPiC~~~~~ 200 (207)
T KOG1100|consen 161 CRKCGER--E--ATVLLLPCRHLCLCGICDES-----LRICPICRSPKT 200 (207)
T ss_pred ceecCcC--C--ceEEeecccceEeccccccc-----CccCCCCcChhh
Confidence 9999886 2 3588899997654 466533 456999997653
No 205
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=32.37 E-value=15 Score=38.83 Aligned_cols=46 Identities=26% Similarity=0.686 Sum_probs=0.0
Q ss_pred ceeecCCCCccccccCcCCCCCCCc-ceeecCccccccCCCCcCeeccCCCCc
Q 026787 64 KQVICSVCDTEQPVAQVCTNCGVNM-GEYFCDICKFYDDDIEKGQFHCDDCGI 115 (233)
Q Consensus 64 ~~v~C~~C~~~q~~~~~C~~Cg~~f-~~Y~C~~C~l~d~~~~k~~yHC~~Cgi 115 (233)
-.-.|..|+++ ++...|+.||..- -.|+|+.|+.--++. +|+.||.
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 34567777766 5666777777653 456677776532211 6777663
No 206
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=31.38 E-value=30 Score=34.31 Aligned_cols=44 Identities=23% Similarity=0.704 Sum_probs=34.6
Q ss_pred CCCCCCcchhhhhcccCCceeEeccCCccChhhHHHHhccCCCcCCCCCcccc
Q 026787 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (233)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrksi~ 200 (233)
..+++|.||.+.+ ..++-+|- |..|+.+|+. .+-.||+|++.+.
T Consensus 477 ~~~~~~~~~~~~~-----~~~~~~~~---~~~~l~~~~~-~~~~~pl~~~~~~ 520 (543)
T KOG0802|consen 477 EPNDVCAICYQEM-----SARITPCS---HALCLRKWLY-VQEVCPLCHTYMK 520 (543)
T ss_pred cccCcchHHHHHH-----Hhcccccc---chhHHHhhhh-hccccCCCchhhh
Confidence 4578999999997 23344555 9999999997 4688999998875
No 207
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.12 E-value=34 Score=26.14 Aligned_cols=50 Identities=32% Similarity=0.601 Sum_probs=33.0
Q ss_pred CCcchhhhhcccCCceeEeccCCccChhhHHHHhccCCCcCCCCCccccchhHHhhhhHHHHHhC--CCChhhhc
Q 026787 152 HCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRTWKRIDEEIEAT--VMPEDYRH 224 (233)
Q Consensus 152 ~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrksi~dm~~~~~~lD~~i~~~--pmP~~y~~ 224 (233)
.||||.-+|-.+...-+ .-..||-||-.-+|- ..||.+|+.. |-|.+|+.
T Consensus 3 lCP~C~v~l~~~~rs~v-------------------EiD~CPrCrGVWLDr----GELdKli~r~r~pqpa~ys~ 54 (88)
T COG3809 3 LCPICGVELVMSVRSGV-------------------EIDYCPRCRGVWLDR----GELDKLIERSRYPQPAEYSQ 54 (88)
T ss_pred ccCcCCceeeeeeecCc-------------------eeeeCCccccEeecc----hhHHHHHHHhcCCCCcccCC
Confidence 59999988866532211 135799999777765 4567777665 56666764
No 208
>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=30.02 E-value=38 Score=21.13 Aligned_cols=10 Identities=30% Similarity=0.737 Sum_probs=5.3
Q ss_pred eeecCCCCcc
Q 026787 65 QVICSVCDTE 74 (233)
Q Consensus 65 ~v~C~~C~~~ 74 (233)
.+.|+.|++.
T Consensus 25 ~v~C~~C~~~ 34 (38)
T TIGR02098 25 KVRCGKCGHV 34 (38)
T ss_pred EEECCCCCCE
Confidence 4555555543
No 209
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=29.82 E-value=24 Score=33.46 Aligned_cols=20 Identities=40% Similarity=0.989 Sum_probs=15.7
Q ss_pred cCCCCCCCcceeecCccccc
Q 026787 80 VCTNCGVNMGEYFCDICKFY 99 (233)
Q Consensus 80 ~C~~Cg~~f~~Y~C~~C~l~ 99 (233)
.|+-||+.+++|.|+-|+|-
T Consensus 9 ~C~ic~vq~~~YtCPRCn~~ 28 (383)
T KOG4317|consen 9 ACGICGVQKREYTCPRCNLL 28 (383)
T ss_pred eccccccccccccCCCCCcc
Confidence 57777888888888888764
No 210
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=29.71 E-value=29 Score=36.80 Aligned_cols=49 Identities=27% Similarity=0.543 Sum_probs=34.1
Q ss_pred CCCCcchhhhhcccCCceeEecc---C--CccChhhHHHHhccC-CCcCCCCCcccc
Q 026787 150 HHHCPICYEYLFDSLRNTTVMKC---G--HTMHCECYHEMIKRD-KYCCPICSKSVI 200 (233)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpC---G--H~~H~~C~~~~~~~~-~~~CPiCrksi~ 200 (233)
+..|-||.-+ +.++..-.=|| | -.+|++|+.+|+..+ .-+|-||...+.
T Consensus 12 ~~~CRICr~e--~~~d~pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~ 66 (1175)
T COG5183 12 KRSCRICRTE--DIRDDPLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYK 66 (1175)
T ss_pred chhceeecCC--CCCCCcCcccccccchhHHHHHHHHHHHHhcCCCcceeeecceee
Confidence 4568888765 22233334466 3 689999999999864 567999997764
No 211
>smart00355 ZnF_C2H2 zinc finger.
Probab=29.58 E-value=43 Score=17.76 Aligned_cols=16 Identities=38% Similarity=0.698 Sum_probs=12.0
Q ss_pred CcCCCCCccccchhHH
Q 026787 190 YCCPICSKSVIDMSRT 205 (233)
Q Consensus 190 ~~CPiCrksi~dm~~~ 205 (233)
+.|+.|.+++...+..
T Consensus 1 ~~C~~C~~~f~~~~~l 16 (26)
T smart00355 1 YRCPECGKVFKSKSAL 16 (26)
T ss_pred CCCCCCcchhCCHHHH
Confidence 5799999998765443
No 212
>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=29.16 E-value=35 Score=27.57 Aligned_cols=27 Identities=22% Similarity=0.618 Sum_probs=19.1
Q ss_pred ccceeecCCCCccccc---cCcCCCCCCCc
Q 026787 62 DVKQVICSVCDTEQPV---AQVCTNCGVNM 88 (233)
Q Consensus 62 ~v~~v~C~~C~~~q~~---~~~C~~Cg~~f 88 (233)
++..|.|..|+++-.. .+.|.+|++++
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 213
>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=29.15 E-value=42 Score=19.36 Aligned_cols=16 Identities=19% Similarity=0.596 Sum_probs=12.3
Q ss_pred CCcCCCCCccccchhH
Q 026787 189 KYCCPICSKSVIDMSR 204 (233)
Q Consensus 189 ~~~CPiCrksi~dm~~ 204 (233)
++.|++|.+.+.+...
T Consensus 1 q~~C~~C~k~f~~~~~ 16 (27)
T PF12171_consen 1 QFYCDACDKYFSSENQ 16 (27)
T ss_dssp -CBBTTTTBBBSSHHH
T ss_pred CCCcccCCCCcCCHHH
Confidence 3689999999987543
No 214
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=29.14 E-value=34 Score=24.63 Aligned_cols=20 Identities=25% Similarity=0.693 Sum_probs=13.3
Q ss_pred ecCCCCccccccCcCCCCCCC
Q 026787 67 ICSVCDTEQPVAQVCTNCGVN 87 (233)
Q Consensus 67 ~C~~C~~~q~~~~~C~~Cg~~ 87 (233)
-|..|+..++ .+.||+||..
T Consensus 5 AC~~C~~i~~-~~~CP~Cgs~ 24 (61)
T PRK08351 5 ACRHCHYITT-EDRCPVCGSR 24 (61)
T ss_pred hhhhCCcccC-CCcCCCCcCC
Confidence 5677776663 3468888774
No 215
>cd07973 Spt4 Transcription elongation factor Spt4. Spt4 is a transcription elongation factor. Three transcription-elongation factors Spt4, Spt5, and Spt6, are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles. Spt4 functions entirely in the context of the Spt4-Spt5 heterodimer and it has been found only as a complex to Spt5 in Yeast and Human. Spt4 is a small protein that has zinc finger at the N-terminus. Spt5 is a large protein that has several interesting structural features of an acidic N-terminus, a single NGN domain, five or six KOW domains, and a set of simple C-termianl repeats. Spt4 binds to Spt5 NGN domain. Unlike Spt5, Spt4 is not essential for viability in yeast, however Spt4 is critical for normal function of the Spt4-Spt5 compl
Probab=28.88 E-value=31 Score=27.04 Aligned_cols=20 Identities=25% Similarity=0.637 Sum_probs=14.6
Q ss_pred ecCCCCcccccc----CcCCCCCC
Q 026787 67 ICSVCDTEQPVA----QVCTNCGV 86 (233)
Q Consensus 67 ~C~~C~~~q~~~----~~C~~Cg~ 86 (233)
-|+.|+..++.. +.|+||+.
T Consensus 5 AC~~C~~I~~~~qf~~~gCpnC~~ 28 (98)
T cd07973 5 ACLLCSLIKTEDQFERDGCPNCEG 28 (98)
T ss_pred hhccCCcccccccccCCCCCCCcc
Confidence 588888887764 47888863
No 216
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=28.83 E-value=25 Score=21.99 Aligned_cols=23 Identities=35% Similarity=0.752 Sum_probs=11.9
Q ss_pred ceeecCCCCccc-cccCcCCCCCC
Q 026787 64 KQVICSVCDTEQ-PVAQVCTNCGV 86 (233)
Q Consensus 64 ~~v~C~~C~~~q-~~~~~C~~Cg~ 86 (233)
..-.|..|++.+ |+...|++|+.
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 355688887775 55677888864
No 217
>PLN00209 ribosomal protein S27; Provisional
Probab=28.69 E-value=36 Score=26.24 Aligned_cols=37 Identities=19% Similarity=0.346 Sum_probs=27.9
Q ss_pred ceeecCCCCccccc------cCcCCCCCCCcceeecCcccccc
Q 026787 64 KQVICSVCDTEQPV------AQVCTNCGVNMGEYFCDICKFYD 100 (233)
Q Consensus 64 ~~v~C~~C~~~q~~------~~~C~~Cg~~f~~Y~C~~C~l~d 100 (233)
-.|.|..|..+|.+ ...|..||..+++-.=.+.+|-+
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 24799999988876655555543
No 218
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=28.69 E-value=40 Score=22.92 Aligned_cols=22 Identities=50% Similarity=1.284 Sum_probs=10.5
Q ss_pred eccCCCCcceeCCccceeeccccC
Q 026787 108 FHCDDCGICRIGGRENYFHCKRCG 131 (233)
Q Consensus 108 yHC~~CgiCR~G~~~~~fHC~~C~ 131 (233)
|.|+.||.--+-| --|||..|.
T Consensus 1 y~Cd~C~~~pI~G--~R~~C~~C~ 22 (48)
T cd02341 1 FKCDSCGIEPIPG--TRYHCSECD 22 (48)
T ss_pred CCCCCCCCCcccc--ceEECCCCC
Confidence 4455555433332 245555554
No 219
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=28.65 E-value=30 Score=26.58 Aligned_cols=36 Identities=19% Similarity=0.390 Sum_probs=26.7
Q ss_pred ceeecCCCCccccc------cCcCCCCCCCcceeecCccccc
Q 026787 64 KQVICSVCDTEQPV------AQVCTNCGVNMGEYFCDICKFY 99 (233)
Q Consensus 64 ~~v~C~~C~~~q~~------~~~C~~Cg~~f~~Y~C~~C~l~ 99 (233)
-.|.|..|..+|.+ ...|..||..+++-.=.+.+|-
T Consensus 34 m~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~~PTGGKa~l~ 75 (85)
T PTZ00083 34 MDVKCPGCSQITTVFSHAQTVVLCGGCSSQLCQPTGGKAKLT 75 (85)
T ss_pred EEEECCCCCCeeEEEecCceEEEccccCCEeeccCCCCeEec
Confidence 37899999999877 2469999988877655555544
No 220
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=28.32 E-value=27 Score=32.41 Aligned_cols=44 Identities=27% Similarity=0.594 Sum_probs=30.5
Q ss_pred CcCCCCCCCcceeecCccccccCCCCcCeeccCCCCcceeCCccceeeccccCccccccccccceee
Q 026787 79 QVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYSTSLRNNHLCI 145 (233)
Q Consensus 79 ~~C~~Cg~~f~~Y~C~~C~l~d~~~~k~~yHC~~CgiCR~G~~~~~fHC~~C~~C~s~~l~~~H~C~ 145 (233)
..+...+....+-||.+|+.|--+ -.-||..||.|+-.- +|.|+
T Consensus 98 ~~~~~~~~~~~~~~C~~C~~~KP~--------------------RS~HC~~Cn~CV~k~---DHHC~ 141 (309)
T COG5273 98 SRLLDDGKFGTENFCSTCNIYKPP--------------------RSHHCSICNRCVLKF---DHHCP 141 (309)
T ss_pred hhhhhcCccccceeccccccccCC--------------------CCccchhhcchhhcc---CccCc
Confidence 566677888888999999999332 356777777776543 56554
No 221
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=28.08 E-value=25 Score=20.49 Aligned_cols=12 Identities=25% Similarity=0.664 Sum_probs=9.3
Q ss_pred CcCCCCCCCcce
Q 026787 79 QVCTNCGVNMGE 90 (233)
Q Consensus 79 ~~C~~Cg~~f~~ 90 (233)
..|+.||..|+.
T Consensus 3 ~~C~~CgR~F~~ 14 (25)
T PF13913_consen 3 VPCPICGRKFNP 14 (25)
T ss_pred CcCCCCCCEECH
Confidence 368899998864
No 222
>PRK14873 primosome assembly protein PriA; Provisional
Probab=28.06 E-value=52 Score=33.83 Aligned_cols=23 Identities=26% Similarity=0.689 Sum_probs=17.6
Q ss_pred ceeecCCCCccccccCcCCCCCCCcce
Q 026787 64 KQVICSVCDTEQPVAQVCTNCGVNMGE 90 (233)
Q Consensus 64 ~~v~C~~C~~~q~~~~~C~~Cg~~f~~ 90 (233)
..++|..|+.. ..|++|+..+.-
T Consensus 382 p~l~C~~Cg~~----~~C~~C~~~L~~ 404 (665)
T PRK14873 382 PSLACARCRTP----ARCRHCTGPLGL 404 (665)
T ss_pred CeeEhhhCcCe----eECCCCCCceeE
Confidence 57788888865 578889888753
No 223
>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=27.13 E-value=38 Score=21.63 Aligned_cols=25 Identities=32% Similarity=0.642 Sum_probs=18.4
Q ss_pred CCcchhhhhcccCCceeEe-ccCCcc
Q 026787 152 HCPICYEYLFDSLRNTTVM-KCGHTM 176 (233)
Q Consensus 152 ~CpICle~lf~s~~~v~~L-pCGH~~ 176 (233)
.|++|.+.++.+.+....= .|||.+
T Consensus 10 ~C~~C~~~~~~~~dG~~yC~~cG~~~ 35 (36)
T PF11781_consen 10 PCPVCGSRWFYSDDGFYYCDRCGHQS 35 (36)
T ss_pred cCCCCCCeEeEccCCEEEhhhCceEc
Confidence 3999999877776666554 788864
No 224
>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=27.06 E-value=44 Score=22.07 Aligned_cols=12 Identities=25% Similarity=0.844 Sum_probs=7.6
Q ss_pred CcCCCCCCCcce
Q 026787 79 QVCTNCGVNMGE 90 (233)
Q Consensus 79 ~~C~~Cg~~f~~ 90 (233)
..|+.||.++-+
T Consensus 18 ~~Cp~C~~PL~~ 29 (41)
T PF06677_consen 18 EHCPDCGTPLMR 29 (41)
T ss_pred CccCCCCCeeEE
Confidence 567777766643
No 225
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=26.73 E-value=53 Score=31.36 Aligned_cols=88 Identities=25% Similarity=0.590 Sum_probs=57.7
Q ss_pred eeecCccc-----------cccC--CCCcCeeccCCCCcceeCC-ccceeeccccCcccccc---ccccceeecCCCCCC
Q 026787 90 EYFCDICK-----------FYDD--DIEKGQFHCDDCGICRIGG-RENYFHCKRCGSCYSTS---LRNNHLCIENSMHHH 152 (233)
Q Consensus 90 ~Y~C~~C~-----------l~d~--~~~k~~yHC~~CgiCR~G~-~~~~fHC~~C~~C~s~~---l~~~H~C~e~~~~~~ 152 (233)
+-+|.+|+ -||| .+.+-+-||+.| |--|. .|=|| +|+++.+.. -...|.=..++-...
T Consensus 149 RV~C~~C~~~s~tv~~~P~cWdDVLks~Ripg~Ces~--~~pg~fAEFfF---KC~ah~~~~k~~aa~lhli~~N~~ni~ 223 (446)
T KOG0006|consen 149 RVYCQKCSSTSVTVKSEPQCWDDVLKSKRIPGVCESC--CTPGLFAEFFF---KCGAHPTSDKETAAALHLIATNSRNIT 223 (446)
T ss_pred EEEeecccCceEEEecCccchhhhhhcccCccccccc--cCCcchHhhee---hhccCCCccccchhHHHHhhcccccce
Confidence 45566665 3776 246678888875 33343 35566 566666551 112344445666778
Q ss_pred CcchhhhhcccCCceeEeccC--CccChhhHHHHhc
Q 026787 153 CPICYEYLFDSLRNTTVMKCG--HTMHCECYHEMIK 186 (233)
Q Consensus 153 CpICle~lf~s~~~v~~LpCG--H~~H~~C~~~~~~ 186 (233)
|-.|-+- +++|.+++|. |.....||.-|-.
T Consensus 224 C~~Ctdv----~~~vlvf~Cns~HvtC~dCFr~yc~ 255 (446)
T KOG0006|consen 224 CITCTDV----RSPVLVFQCNSRHVTCLDCFRLYCV 255 (446)
T ss_pred eEEecCC----ccceEEEecCCceeehHHhhhhHhh
Confidence 9999864 3588999998 9999999986654
No 226
>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=26.51 E-value=38 Score=23.22 Aligned_cols=21 Identities=24% Similarity=0.896 Sum_probs=12.4
Q ss_pred cCcCC--CCCCC------cceeecCcccc
Q 026787 78 AQVCT--NCGVN------MGEYFCDICKF 98 (233)
Q Consensus 78 ~~~C~--~Cg~~------f~~Y~C~~C~l 98 (233)
...|| .||.- ++|+||.+|.+
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 34677 68763 36677777654
No 227
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=26.43 E-value=37 Score=30.73 Aligned_cols=20 Identities=25% Similarity=0.858 Sum_probs=15.2
Q ss_pred cCcCCCCCCCc--------ceeecCccc
Q 026787 78 AQVCTNCGVNM--------GEYFCDICK 97 (233)
Q Consensus 78 ~~~C~~Cg~~f--------~~Y~C~~C~ 97 (233)
++.|+.||..+ +.|||+.|.
T Consensus 244 g~pCprCG~~I~~~~~~gR~t~~CP~CQ 271 (272)
T PRK14810 244 GEPCLNCKTPIRRVVVAGRSSHYCPHCQ 271 (272)
T ss_pred CCcCCCCCCeeEEEEECCCccEECcCCc
Confidence 46799998887 568888774
No 228
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=26.41 E-value=39 Score=31.33 Aligned_cols=33 Identities=18% Similarity=0.444 Sum_probs=21.6
Q ss_pred cccccceeecCCCCccccc-cCcCCCCCCCccee
Q 026787 59 VRQDVKQVICSVCDTEQPV-AQVCTNCGVNMGEY 91 (233)
Q Consensus 59 ~r~~v~~v~C~~C~~~q~~-~~~C~~Cg~~f~~Y 91 (233)
+-...++..|..|+..-|. +-.|..|++...++
T Consensus 103 ~~~~~~~~~C~~C~~~KP~RS~HC~~Cn~CV~k~ 136 (309)
T COG5273 103 DGKFGTENFCSTCNIYKPPRSHHCSICNRCVLKF 136 (309)
T ss_pred cCccccceeccccccccCCCCccchhhcchhhcc
Confidence 3345678899999877666 45566666555443
No 229
>KOG4399 consensus C2HC-type Zn-finger protein [General function prediction only]
Probab=25.66 E-value=16 Score=33.73 Aligned_cols=53 Identities=17% Similarity=0.172 Sum_probs=40.5
Q ss_pred CcCCCCCCCcceeecCccccccCCCCcCeeccCCCCcceeCCccceeeccccCcccc
Q 026787 79 QVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYS 135 (233)
Q Consensus 79 ~~C~~Cg~~f~~Y~C~~C~l~d~~~~k~~yHC~~CgiCR~G~~~~~fHC~~C~~C~s 135 (233)
..|+-|+..-+.-||.||--+|.. + -|||.|.-||--....+-||+.|..|..
T Consensus 250 i~C~~~~~~A~~~~C~iC~~~~~~--R--~~C~~~kA~~~~~Q~K~N~~~~~~~~~q 302 (325)
T KOG4399|consen 250 IHCSICNHCAVKHGCFICGELDHK--R--STCPNIKAVRKQKQRKSNKMKMETTKGQ 302 (325)
T ss_pred eeeecccchhhhcceeeccccccc--c--ccCccHHHHHHHHhcccchhhhhhhhhh
Confidence 357777777788899999888663 2 7999999998876556778887777755
No 230
>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=25.42 E-value=27 Score=22.55 Aligned_cols=13 Identities=54% Similarity=1.196 Sum_probs=5.5
Q ss_pred cceeecCcccccc
Q 026787 88 MGEYFCDICKFYD 100 (233)
Q Consensus 88 f~~Y~C~~C~l~d 100 (233)
|-+|||+-|+.|-
T Consensus 1 m~ryyCdyC~~~~ 13 (38)
T PF06220_consen 1 MPRYYCDYCKKYL 13 (38)
T ss_dssp --S-B-TTT--B-
T ss_pred CcCeeccccccee
Confidence 4589999998775
No 231
>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=25.24 E-value=28 Score=22.78 Aligned_cols=43 Identities=28% Similarity=0.574 Sum_probs=27.8
Q ss_pred CcchhhhhcccCCceeEeccCCccChhhHHHHhc-----cCCCcCCCCC
Q 026787 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIK-----RDKYCCPICS 196 (233)
Q Consensus 153 CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~-----~~~~~CPiCr 196 (233)
|+||... .+....+.=-.|+-+||..|+..-+. ...+.||.|+
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 23323333346899999999976543 1267888775
No 232
>PRK10445 endonuclease VIII; Provisional
Probab=25.02 E-value=42 Score=30.25 Aligned_cols=20 Identities=30% Similarity=0.894 Sum_probs=14.8
Q ss_pred cCcCCCCCCCc--------ceeecCccc
Q 026787 78 AQVCTNCGVNM--------GEYFCDICK 97 (233)
Q Consensus 78 ~~~C~~Cg~~f--------~~Y~C~~C~ 97 (233)
++.|+.||... +.|||+.|.
T Consensus 235 g~~Cp~Cg~~I~~~~~~gR~t~~CP~CQ 262 (263)
T PRK10445 235 GEACERCGGIIEKTTLSSRPFYWCPGCQ 262 (263)
T ss_pred CCCCCCCCCEeEEEEECCCCcEECCCCc
Confidence 46799999887 467777663
No 233
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=24.96 E-value=46 Score=23.22 Aligned_cols=8 Identities=38% Similarity=1.240 Sum_probs=5.8
Q ss_pred CcCCCCCC
Q 026787 79 QVCTNCGV 86 (233)
Q Consensus 79 ~~C~~Cg~ 86 (233)
..||+||.
T Consensus 20 ~~CPrCG~ 27 (51)
T COG1998 20 RFCPRCGP 27 (51)
T ss_pred ccCCCCCC
Confidence 46888883
No 234
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=24.94 E-value=42 Score=30.39 Aligned_cols=20 Identities=40% Similarity=1.102 Sum_probs=15.2
Q ss_pred cCcCCCCCCCc--------ceeecCccc
Q 026787 78 AQVCTNCGVNM--------GEYFCDICK 97 (233)
Q Consensus 78 ~~~C~~Cg~~f--------~~Y~C~~C~ 97 (233)
++.|+.||..+ +.|||+.|.
T Consensus 235 g~pC~~Cg~~I~~~~~~gR~ty~Cp~CQ 262 (269)
T PRK14811 235 GQPCPRCGTPIEKIVVGGRGTHFCPQCQ 262 (269)
T ss_pred cCCCCcCCCeeEEEEECCCCcEECCCCc
Confidence 35788888877 568888884
No 235
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=24.73 E-value=65 Score=35.07 Aligned_cols=56 Identities=18% Similarity=0.444 Sum_probs=40.4
Q ss_pred ecCCCCCCCcchhhhhcccCCceeEe---ccCCccChhhHHHHhccCCCcCCCCCcccc
Q 026787 145 IENSMHHHCPICYEYLFDSLRNTTVM---KCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (233)
Q Consensus 145 ~e~~~~~~CpICle~lf~s~~~v~~L---pCGH~~H~~C~~~~~~~~~~~CPiCrksi~ 200 (233)
+++...+.|-||.|++--+.+.-.+. -||=-..+.|++-=.+.++..||-|+...-
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 44556678999999975544443333 477889999996556667899999986543
No 236
>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=24.58 E-value=50 Score=19.72 Aligned_cols=17 Identities=18% Similarity=0.583 Sum_probs=13.2
Q ss_pred CCCcCCCCCccccchhH
Q 026787 188 DKYCCPICSKSVIDMSR 204 (233)
Q Consensus 188 ~~~~CPiCrksi~dm~~ 204 (233)
+.+.|.+|.+++.+...
T Consensus 2 ~~~~C~~C~~~~~~~~~ 18 (35)
T smart00451 2 GGFYCKLCNVTFTDEIS 18 (35)
T ss_pred cCeEccccCCccCCHHH
Confidence 35789999999986543
No 237
>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=24.53 E-value=59 Score=21.45 Aligned_cols=11 Identities=36% Similarity=0.939 Sum_probs=4.9
Q ss_pred CcCeeccCCCC
Q 026787 104 EKGQFHCDDCG 114 (233)
Q Consensus 104 ~k~~yHC~~Cg 114 (233)
.++-|+|..|+
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 238
>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=24.52 E-value=59 Score=27.89 Aligned_cols=23 Identities=35% Similarity=0.873 Sum_probs=14.8
Q ss_pred eecCCCCccccccCcCCCCCCCc
Q 026787 66 VICSVCDTEQPVAQVCTNCGVNM 88 (233)
Q Consensus 66 v~C~~C~~~q~~~~~C~~Cg~~f 88 (233)
..|..|...+.+...|.+|...+
T Consensus 112 ~aCs~C~r~~~~~~~C~~Cdr~l 134 (175)
T PF05458_consen 112 RACSVCQRTQRIKSVCSQCDRAL 134 (175)
T ss_pred ccCcCCcCCCCCCccccccCcHH
Confidence 34777776666666676665544
No 239
>COG1144 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, delta subunit [Energy production and conversion]
Probab=24.37 E-value=39 Score=26.30 Aligned_cols=15 Identities=40% Similarity=0.906 Sum_probs=12.5
Q ss_pred cceeeccccCccccc
Q 026787 122 ENYFHCKRCGSCYST 136 (233)
Q Consensus 122 ~~~fHC~~C~~C~s~ 136 (233)
.||-+|+.||.|.+.
T Consensus 63 idYdyCKGCGICa~v 77 (91)
T COG1144 63 IDYDYCKGCGICANV 77 (91)
T ss_pred eEcccccCceechhh
Confidence 488999999999764
No 240
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=24.06 E-value=50 Score=26.26 Aligned_cols=11 Identities=18% Similarity=0.594 Sum_probs=5.4
Q ss_pred cCcCCCCCCCc
Q 026787 78 AQVCTNCGVNM 88 (233)
Q Consensus 78 ~~~C~~Cg~~f 88 (233)
...|..||..|
T Consensus 71 ~~~C~~Cg~~~ 81 (117)
T PRK00564 71 ELECKDCSHVF 81 (117)
T ss_pred EEEhhhCCCcc
Confidence 34555555443
No 241
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=23.73 E-value=36 Score=26.90 Aligned_cols=10 Identities=20% Similarity=0.574 Sum_probs=4.9
Q ss_pred CcCCCCCCCc
Q 026787 79 QVCTNCGVNM 88 (233)
Q Consensus 79 ~~C~~Cg~~f 88 (233)
..|..||..|
T Consensus 71 ~~C~~Cg~~~ 80 (113)
T PRK12380 71 AWCWDCSQVV 80 (113)
T ss_pred EEcccCCCEE
Confidence 3455555444
No 242
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=23.62 E-value=48 Score=27.90 Aligned_cols=12 Identities=25% Similarity=0.839 Sum_probs=5.9
Q ss_pred cCCCCCCCccee
Q 026787 80 VCTNCGVNMGEY 91 (233)
Q Consensus 80 ~C~~Cg~~f~~Y 91 (233)
.|++||..|+.|
T Consensus 30 ~c~~c~~~f~~~ 41 (154)
T PRK00464 30 ECLACGKRFTTF 41 (154)
T ss_pred eccccCCcceEe
Confidence 344555555444
No 243
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=23.10 E-value=52 Score=27.69 Aligned_cols=13 Identities=15% Similarity=0.496 Sum_probs=11.4
Q ss_pred cCCCCCCCcceee
Q 026787 80 VCTNCGVNMGEYF 92 (233)
Q Consensus 80 ~C~~Cg~~f~~Y~ 92 (233)
.|.+||..|..|=
T Consensus 30 eC~~C~~RFTTyE 42 (147)
T TIGR00244 30 ECLECHERFTTFE 42 (147)
T ss_pred cCCccCCccceee
Confidence 6999999999983
No 244
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=23.02 E-value=48 Score=29.91 Aligned_cols=20 Identities=30% Similarity=1.090 Sum_probs=14.6
Q ss_pred cCcCCCCCCCc--------ceeecCccc
Q 026787 78 AQVCTNCGVNM--------GEYFCDICK 97 (233)
Q Consensus 78 ~~~C~~Cg~~f--------~~Y~C~~C~ 97 (233)
++.|+.||... +.|||+.|.
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 272 (274)
T PRK01103 245 GEPCRRCGTPIEKIKQGGRSTFFCPRCQ 272 (274)
T ss_pred CCCCCCCCCeeEEEEECCCCcEECcCCC
Confidence 35799999887 567777763
No 245
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=22.96 E-value=42 Score=32.43 Aligned_cols=39 Identities=21% Similarity=0.468 Sum_probs=31.1
Q ss_pred cCCCCCCCcchhhhhcccCCceeEeccCCccChhhHHHHhcc
Q 026787 146 ENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR 187 (233)
Q Consensus 146 e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~ 187 (233)
.......|.||.+.+-. ....+.|||.|-..|...++..
T Consensus 66 ~~~~~~~c~ic~~~~~~---~~~~~~c~H~~c~~cw~~yl~~ 104 (444)
T KOG1815|consen 66 KKKGDVQCGICVESYDG---EIIGLGCGHPFCPPCWTGYLGT 104 (444)
T ss_pred CCCccccCCcccCCCcc---hhhhcCCCcHHHHHHHHHHhhh
Confidence 34556789999987432 5677899999999999999974
No 246
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=22.85 E-value=72 Score=21.72 Aligned_cols=37 Identities=14% Similarity=0.422 Sum_probs=24.8
Q ss_pred cCchhHHhhhcCCCCCCCcccccccccceeecCCCCcccccc
Q 026787 37 DCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVA 78 (233)
Q Consensus 37 ~Cr~CHde~~~~~~~~~~~H~~~r~~v~~v~C~~C~~~q~~~ 78 (233)
.|..|-+-+.- | .+..+.++....+.||.|+....++
T Consensus 8 ~C~~C~~lLql-P----~~~~~~~k~~~klrCGaCs~vl~~s 44 (46)
T PF11331_consen 8 VCSSCFELLQL-P----AKFSLSKKNQQKLRCGACSEVLSFS 44 (46)
T ss_pred ECccHHHHHcC-C----CccCCCccceeEEeCCCCceeEEEe
Confidence 56666655431 2 3456666678899999999876553
No 247
>PF10272 Tmpp129: Putative transmembrane protein precursor; InterPro: IPR018801 This entry consists of proteins conserved from worms to humans. They are purported to be transmembrane protein-precursors but their function is unknown.
Probab=22.84 E-value=45 Score=31.86 Aligned_cols=36 Identities=25% Similarity=0.537 Sum_probs=26.9
Q ss_pred CcchhhhhcccCCceeEeccCCccChhhHHHHhccCCCcCCCCCcccc
Q 026787 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (233)
Q Consensus 153 CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrksi~ 200 (233)
|--||...|.|+++-. |. +.||. +.-+||.||+.+-
T Consensus 316 C~~Cm~kwFasrQd~~--------~~---~~Wl~-~~~~CPtCRa~FC 351 (358)
T PF10272_consen 316 CLECMGKWFASRQDQQ--------HP---ETWLS-GKCPCPTCRAKFC 351 (358)
T ss_pred HHHHHHHHhhhcCCCC--------Ch---hhhhc-CCCCCCCCcccce
Confidence 6778888888876433 33 67987 5789999999863
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=22.83 E-value=45 Score=24.45 Aligned_cols=37 Identities=30% Similarity=0.644 Sum_probs=23.0
Q ss_pred cCcCCCCCCCcceeecCccccccCCCCcCeeccCCCC
Q 026787 78 AQVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCG 114 (233)
Q Consensus 78 ~~~C~~Cg~~f~~Y~C~~C~l~d~~~~k~~yHC~~Cg 114 (233)
...|+.|...=....+..|.+.+=-.+|++-||-+|.
T Consensus 34 ~~~C~GCr~~~~~~~~~~C~i~~C~~ekgv~~C~eC~ 70 (78)
T PF12675_consen 34 KIRCPGCRSGGGKCCCKSCKIRQCAKEKGVDFCGECP 70 (78)
T ss_pred CCcCcCCcCCCCCcCCCCCCcCcHHhhCCCCeeecCC
Confidence 3457777555444667777776555566676666553
No 249
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=22.73 E-value=28 Score=35.29 Aligned_cols=26 Identities=27% Similarity=0.775 Sum_probs=19.6
Q ss_pred eeEeccCCccChhhHHHHhccCCCcCCCCC
Q 026787 167 TTVMKCGHTMHCECYHEMIKRDKYCCPICS 196 (233)
Q Consensus 167 v~~LpCGH~~H~~C~~~~~~~~~~~CPiCr 196 (233)
.+-..||+.||+.|+.. .+..||.|-
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 44567999999999864 344599985
No 250
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=22.66 E-value=88 Score=26.72 Aligned_cols=27 Identities=26% Similarity=0.573 Sum_probs=17.3
Q ss_pred CCCcCCCCCccccch--hHHhhhhHHHHH
Q 026787 188 DKYCCPICSKSVIDM--SRTWKRIDEEIE 214 (233)
Q Consensus 188 ~~~~CPiCrksi~dm--~~~~~~lD~~i~ 214 (233)
..++||.|+..+..+ +...+.|++.|+
T Consensus 135 ~~F~Cp~Cg~~L~~~dn~~~~~~l~~~I~ 163 (178)
T PRK06266 135 YGFRCPQCGEMLEEYDNSELIKELKEQIK 163 (178)
T ss_pred cCCcCCCCCCCCeecccHHHHHHHHHHHH
Confidence 479999999999732 234444444443
No 251
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=22.62 E-value=44 Score=35.04 Aligned_cols=50 Identities=28% Similarity=0.557 Sum_probs=40.2
Q ss_pred CcCCCCCCCccee---ecCccccccCCCCcCeeccCCCCcceeCCccceeeccccCcccccc
Q 026787 79 QVCTNCGVNMGEY---FCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYSTS 137 (233)
Q Consensus 79 ~~C~~Cg~~f~~Y---~C~~C~l~d~~~~k~~yHC~~CgiCR~G~~~~~fHC~~C~~C~s~~ 137 (233)
-.|++|++.++.- +|++|.--.. .+|-+|+.+-+.-+++|..|+-+.-.+
T Consensus 754 ~~~~nc~a~~~~~~~~~c~rc~s~a~---------~~CtVC~~vi~G~~~~c~~C~H~gH~s 806 (839)
T KOG0269|consen 754 YACPNCDAPMVLTKLWQCDRCESRAS---------AKCTVCDLVIRGVDVWCQVCGHGGHDS 806 (839)
T ss_pred ccccccCCccccccceeechHHHHhh---------cCceeecceeeeeEeecccccccccHH
Confidence 4799999998765 8888876533 268899999888899999999886554
No 252
>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=22.60 E-value=45 Score=18.89 Aligned_cols=17 Identities=24% Similarity=0.532 Sum_probs=13.2
Q ss_pred CcCCCCCccccchhHHh
Q 026787 190 YCCPICSKSVIDMSRTW 206 (233)
Q Consensus 190 ~~CPiCrksi~dm~~~~ 206 (233)
++|.+|++++.+.+.+.
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 57999999988766543
No 253
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=22.49 E-value=57 Score=23.47 Aligned_cols=22 Identities=18% Similarity=0.525 Sum_probs=15.7
Q ss_pred CCcCCCCCccccchhHHhhhhH
Q 026787 189 KYCCPICSKSVIDMSRTWKRID 210 (233)
Q Consensus 189 ~~~CPiCrksi~dm~~~~~~lD 210 (233)
.++|++|.+.+.+.+.+.+-|.
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~ 71 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMR 71 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHH
T ss_pred CCCCCccCCCCcCHHHHHHHHc
Confidence 4899999999887666555444
No 254
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=22.40 E-value=45 Score=24.14 Aligned_cols=12 Identities=42% Similarity=0.886 Sum_probs=10.2
Q ss_pred CCcCCCCCcccc
Q 026787 189 KYCCPICSKSVI 200 (233)
Q Consensus 189 ~~~CPiCrksi~ 200 (233)
..+||+|+|.+.
T Consensus 6 ~v~CP~C~k~~~ 17 (62)
T PRK00418 6 TVNCPTCGKPVE 17 (62)
T ss_pred cccCCCCCCccc
Confidence 478999999974
No 255
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=22.06 E-value=66 Score=24.48 Aligned_cols=8 Identities=50% Similarity=1.281 Sum_probs=4.2
Q ss_pred CCCCCCCc
Q 026787 81 CTNCGVNM 88 (233)
Q Consensus 81 C~~Cg~~f 88 (233)
|++||..|
T Consensus 3 C~~Cg~~l 10 (104)
T TIGR01384 3 CPKCGSLM 10 (104)
T ss_pred CcccCccc
Confidence 55555544
No 256
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=21.85 E-value=1e+02 Score=28.82 Aligned_cols=25 Identities=28% Similarity=0.687 Sum_probs=21.1
Q ss_pred cceeecCCCCcccccc-CcCCCCCCC
Q 026787 63 VKQVICSVCDTEQPVA-QVCTNCGVN 87 (233)
Q Consensus 63 v~~v~C~~C~~~q~~~-~~C~~Cg~~ 87 (233)
.+-..|+.|+++-.+. ..|++||..
T Consensus 208 ~RyL~CslC~teW~~~R~~C~~Cg~~ 233 (305)
T TIGR01562 208 LRYLSCSLCATEWHYVRVKCSHCEES 233 (305)
T ss_pred ceEEEcCCCCCcccccCccCCCCCCC
Confidence 4588999999998775 689999985
No 257
>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=21.68 E-value=33 Score=20.90 Aligned_cols=20 Identities=30% Similarity=0.845 Sum_probs=8.7
Q ss_pred ecCCCCccccc-----cCcCCCCCC
Q 026787 67 ICSVCDTEQPV-----AQVCTNCGV 86 (233)
Q Consensus 67 ~C~~C~~~q~~-----~~~C~~Cg~ 86 (233)
.|+.|+.+..+ +..|++||.
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 46667655433 235666665
No 258
>KOG3005 consensus GIY-YIG type nuclease [General function prediction only]
Probab=21.50 E-value=1.1e+02 Score=28.36 Aligned_cols=64 Identities=19% Similarity=0.381 Sum_probs=41.9
Q ss_pred CCCcchhhhhcccCCceeEe-----ccCCccChhhHHHHhcc--------CCCcCCCCCccccchhHHhhhhHHHHHhCC
Q 026787 151 HHCPICYEYLFDSLRNTTVM-----KCGHTMHCECYHEMIKR--------DKYCCPICSKSVIDMSRTWKRIDEEIEATV 217 (233)
Q Consensus 151 ~~CpICle~lf~s~~~v~~L-----pCGH~~H~~C~~~~~~~--------~~~~CPiCrksi~dm~~~~~~lD~~i~~~p 217 (233)
..|-+|.+++.+. +. .++ -|+=..|..|+.+.+.. ....||.|++.+. |..|=.++-.+|
T Consensus 183 ~~celc~~ei~e~-~~-~~a~c~~~~c~~~~h~~CLa~~~~~~e~g~~~p~eg~cp~C~~~~~-----w~~lv~~~~~t~ 255 (276)
T KOG3005|consen 183 VECELCEKEILET-DW-SRATCPNPDCDSLNHLTCLAEELLEVEPGQLIPLEGMCPKCEKFLS-----WTTLVDLDFMTP 255 (276)
T ss_pred hhhHHHHHHhccc-cc-eeccCCCCCCCchhhhhhhhHHHhccCCCceeccCCCCCchhceee-----HHHHHHHHhcCc
Confidence 5799999987543 22 222 27888999999984331 1468999999664 544444555666
Q ss_pred CChh
Q 026787 218 MPED 221 (233)
Q Consensus 218 mP~~ 221 (233)
++-.
T Consensus 256 ~e~~ 259 (276)
T KOG3005|consen 256 TELA 259 (276)
T ss_pred hhhh
Confidence 6544
No 259
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=21.46 E-value=5.8 Score=27.86 Aligned_cols=46 Identities=22% Similarity=0.592 Sum_probs=26.6
Q ss_pred CCcceeecCccccccCCCCcCeeccCCCCcceeCC-----ccceeeccccCccccc
Q 026787 86 VNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGG-----RENYFHCKRCGSCYST 136 (233)
Q Consensus 86 ~~f~~Y~C~~C~l~d~~~~k~~yHC~~CgiCR~G~-----~~~~fHC~~C~~C~s~ 136 (233)
++|++|.|+.|+-- -+.+.-=.| -+|-+.+ .+.|+-|+.||.=+.+
T Consensus 3 ~SFsry~CDLCn~~--~p~~~LRQC---vlCGRWaC~sCW~deYY~CksC~Gii~l 53 (57)
T PF14445_consen 3 HSFSRYSCDLCNSS--HPISELRQC---VLCGRWACNSCWQDEYYTCKSCNGIINL 53 (57)
T ss_pred hHHhhHhHHhhccc--CcHHHHHHH---hhhchhhhhhhhhhhHhHHHhhhchhhh
Confidence 46788888888733 222323233 3343332 5778888888865554
No 260
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=21.26 E-value=46 Score=32.64 Aligned_cols=10 Identities=50% Similarity=1.404 Sum_probs=6.3
Q ss_pred ceeeccccCc
Q 026787 123 NYFHCKRCGS 132 (233)
Q Consensus 123 ~~fHC~~C~~ 132 (233)
..|||..||.
T Consensus 152 ~~F~C~~C~g 161 (436)
T KOG2593|consen 152 GEFHCENCGG 161 (436)
T ss_pred ceEEEecCCC
Confidence 4666666664
No 261
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=21.14 E-value=1e+02 Score=19.94 Aligned_cols=33 Identities=24% Similarity=0.691 Sum_probs=16.8
Q ss_pred cCCCCCCCcceeecCccccc-cCCCCcCeeccCCCC
Q 026787 80 VCTNCGVNMGEYFCDICKFY-DDDIEKGQFHCDDCG 114 (233)
Q Consensus 80 ~C~~Cg~~f~~Y~C~~C~l~-d~~~~k~~yHC~~Cg 114 (233)
.|++||..-+.|| .+ ..- -|++..-.|-|.+||
T Consensus 2 ~Cp~C~~~~a~~~-q~-Q~RsaDE~mT~fy~C~~C~ 35 (40)
T smart00440 2 PCPKCGNREATFF-QL-QTRSADEPMTVFYVCTKCG 35 (40)
T ss_pred cCCCCCCCeEEEE-EE-cccCCCCCCeEEEEeCCCC
Confidence 4777877766665 10 111 223344555565555
No 262
>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=21.10 E-value=72 Score=21.62 Aligned_cols=10 Identities=30% Similarity=1.155 Sum_probs=6.7
Q ss_pred eeecCccccc
Q 026787 90 EYFCDICKFY 99 (233)
Q Consensus 90 ~Y~C~~C~l~ 99 (233)
+|.|.+|...
T Consensus 1 ky~C~~Cgyv 10 (47)
T PF00301_consen 1 KYQCPVCGYV 10 (47)
T ss_dssp EEEETTTSBE
T ss_pred CcCCCCCCEE
Confidence 5778888643
No 263
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.09 E-value=30 Score=32.56 Aligned_cols=19 Identities=47% Similarity=1.139 Sum_probs=16.9
Q ss_pred CcCCCCCCCcceeecCccccc
Q 026787 79 QVCTNCGVNMGEYFCDICKFY 99 (233)
Q Consensus 79 ~~C~~Cg~~f~~Y~C~~C~l~ 99 (233)
.+|..||+.|+ +|+||+-|
T Consensus 322 VtCt~CGkrm~--eCPICRqy 340 (350)
T KOG4275|consen 322 VTCTKCGKRMN--ECPICRQY 340 (350)
T ss_pred Eeehhhccccc--cCchHHHH
Confidence 47999999999 99999866
No 264
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=21.06 E-value=56 Score=29.68 Aligned_cols=19 Identities=26% Similarity=0.933 Sum_probs=13.7
Q ss_pred cCcCCCCCCCc--------ceeecCcc
Q 026787 78 AQVCTNCGVNM--------GEYFCDIC 96 (233)
Q Consensus 78 ~~~C~~Cg~~f--------~~Y~C~~C 96 (233)
++.|+.||... +.|||+.|
T Consensus 254 g~pC~~Cg~~I~~~~~~gR~t~~CP~C 280 (282)
T PRK13945 254 GKPCRKCGTPIERIKLAGRSTHWCPNC 280 (282)
T ss_pred cCCCCcCCCeeEEEEECCCccEECCCC
Confidence 46799998887 45666666
No 265
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=21.02 E-value=69 Score=22.65 Aligned_cols=11 Identities=55% Similarity=1.301 Sum_probs=5.6
Q ss_pred cCeeccCCCCc
Q 026787 105 KGQFHCDDCGI 115 (233)
Q Consensus 105 k~~yHC~~Cgi 115 (233)
...|-|++|||
T Consensus 12 ~v~~~Cp~cGi 22 (55)
T PF13824_consen 12 HVNFECPDCGI 22 (55)
T ss_pred ccCCcCCCCCC
Confidence 34455555554
No 266
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the 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=20.95 E-value=56 Score=29.54 Aligned_cols=19 Identities=37% Similarity=1.111 Sum_probs=13.6
Q ss_pred cCcCCCCCCCc--------ceeecCcc
Q 026787 78 AQVCTNCGVNM--------GEYFCDIC 96 (233)
Q Consensus 78 ~~~C~~Cg~~f--------~~Y~C~~C 96 (233)
++.|+.||... +.|||+.|
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~CP~C 271 (272)
T TIGR00577 245 GEPCRRCGTPIEKIKVGGRGTHFCPQC 271 (272)
T ss_pred CCCCCCCCCeeEEEEECCCCCEECCCC
Confidence 45799998877 45666666
No 268
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=20.94 E-value=33 Score=28.09 Aligned_cols=8 Identities=63% Similarity=1.688 Sum_probs=4.1
Q ss_pred eeccccCc
Q 026787 125 FHCKRCGS 132 (233)
Q Consensus 125 fHC~~C~~ 132 (233)
|.|..||.
T Consensus 124 f~Cp~Cg~ 131 (147)
T smart00531 124 FTCPRCGE 131 (147)
T ss_pred EECCCCCC
Confidence 55555554
No 269
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=20.72 E-value=82 Score=20.32 Aligned_cols=23 Identities=35% Similarity=0.829 Sum_probs=16.1
Q ss_pred eeeccccC--ccccccccccceeec
Q 026787 124 YFHCKRCG--SCYSTSLRNNHLCIE 146 (233)
Q Consensus 124 ~fHC~~C~--~C~s~~l~~~H~C~e 146 (233)
-|.|..|+ .|.+-.+.++|.|..
T Consensus 12 ~f~C~~C~~~FC~~HR~~e~H~C~~ 36 (39)
T smart00154 12 GFKCRHCGNLFCGEHRLPEDHDCPG 36 (39)
T ss_pred CeECCccCCccccccCCccccCCcc
Confidence 46666665 677777778888753
No 270
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=20.66 E-value=63 Score=25.54 Aligned_cols=13 Identities=15% Similarity=0.404 Sum_probs=7.7
Q ss_pred cccCcCCCCCCCc
Q 026787 76 PVAQVCTNCGVNM 88 (233)
Q Consensus 76 ~~~~~C~~Cg~~f 88 (233)
|+...|..||..|
T Consensus 68 p~~~~C~~Cg~~~ 80 (114)
T PRK03681 68 EAECWCETCQQYV 80 (114)
T ss_pred CcEEEcccCCCee
Confidence 4445677777544
No 271
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=20.45 E-value=37 Score=24.10 Aligned_cols=12 Identities=50% Similarity=0.839 Sum_probs=6.8
Q ss_pred CcCCCCCccccc
Q 026787 190 YCCPICSKSVID 201 (233)
Q Consensus 190 ~~CPiCrksi~d 201 (233)
.+||+|+|.+.-
T Consensus 3 v~CP~C~k~~~~ 14 (57)
T PF03884_consen 3 VKCPICGKPVEW 14 (57)
T ss_dssp EE-TTT--EEE-
T ss_pred ccCCCCCCeecc
Confidence 589999999873
No 272
>PRK05580 primosome assembly protein PriA; Validated
Probab=20.43 E-value=1e+02 Score=31.62 Aligned_cols=45 Identities=22% Similarity=0.596 Sum_probs=27.7
Q ss_pred cceeecCCCCccccccCcCCCCCCCccee------ecCccccccCCCCcCeeccCCCCc
Q 026787 63 VKQVICSVCDTEQPVAQVCTNCGVNMGEY------FCDICKFYDDDIEKGQFHCDDCGI 115 (233)
Q Consensus 63 v~~v~C~~C~~~q~~~~~C~~Cg~~f~~Y------~C~~C~l~d~~~~k~~yHC~~Cgi 115 (233)
...+.|..|+.. ..|++|+..+.-. .|.-|..- ...+..|+.||-
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 357889999865 4799998877432 35555432 223345666654
No 273
>PRK01343 zinc-binding protein; Provisional
Probab=20.21 E-value=54 Score=23.35 Aligned_cols=12 Identities=33% Similarity=0.708 Sum_probs=10.1
Q ss_pred CCcCCCCCcccc
Q 026787 189 KYCCPICSKSVI 200 (233)
Q Consensus 189 ~~~CPiCrksi~ 200 (233)
..+||+|+|.+.
T Consensus 9 ~~~CP~C~k~~~ 20 (57)
T PRK01343 9 TRPCPECGKPST 20 (57)
T ss_pred CCcCCCCCCcCc
Confidence 578999999876
Done!