Query 045388
Match_columns 214
No_of_seqs 153 out of 1250
Neff 9.4
Searched_HMMs 46136
Date Fri Mar 29 12:45:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045388.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045388hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1814 Predicted E3 ubiquitin 100.0 1.6E-33 3.5E-38 227.7 9.3 169 42-214 182-390 (445)
2 KOG1812 Predicted E3 ubiquitin 100.0 6.7E-32 1.5E-36 225.3 10.9 173 39-214 141-328 (384)
3 KOG0006 E3 ubiquitin-protein l 99.9 5E-26 1.1E-30 178.7 7.8 168 39-214 216-419 (446)
4 KOG1815 Predicted E3 ubiquitin 99.9 5.7E-25 1.2E-29 188.2 11.1 168 41-214 67-248 (444)
5 smart00647 IBR In Between Ring 99.2 1.5E-11 3.3E-16 77.4 4.8 60 116-177 1-61 (64)
6 PF01485 IBR: IBR domain; Int 99.2 6.7E-12 1.5E-16 79.0 0.6 60 116-177 1-61 (64)
7 PF15227 zf-C3HC4_4: zinc fing 98.8 2.2E-09 4.8E-14 61.4 1.1 41 47-94 1-41 (42)
8 PF13639 zf-RING_2: Ring finge 98.7 5.2E-09 1.1E-13 60.6 2.0 41 46-94 2-42 (44)
9 PF00097 zf-C3HC4: Zinc finger 98.7 2E-08 4.4E-13 57.2 3.0 40 47-94 1-40 (41)
10 PF13923 zf-C3HC4_2: Zinc fing 98.6 2.6E-08 5.5E-13 56.1 2.0 38 47-94 1-38 (39)
11 PLN03208 E3 ubiquitin-protein 98.6 4.7E-08 1E-12 73.6 3.1 63 43-111 17-88 (193)
12 PF14634 zf-RING_5: zinc-RING 98.5 6.1E-08 1.3E-12 56.1 2.5 43 46-98 1-43 (44)
13 KOG0320 Predicted E3 ubiquitin 98.5 1.2E-07 2.5E-12 69.9 3.3 59 38-107 125-183 (187)
14 PF13445 zf-RING_UBOX: RING-ty 98.4 1.6E-07 3.5E-12 53.7 2.5 42 47-93 1-43 (43)
15 cd00162 RING RING-finger (Real 98.4 3.9E-07 8.5E-12 52.4 3.3 44 46-100 1-44 (45)
16 KOG0823 Predicted E3 ubiquitin 98.2 3.7E-07 8E-12 70.1 1.4 60 41-110 44-103 (230)
17 PHA02926 zinc finger-like prot 98.2 1.3E-06 2.7E-11 66.9 3.7 55 43-101 169-229 (242)
18 PF13920 zf-C3HC4_3: Zinc fing 98.2 1.1E-06 2.3E-11 52.3 2.7 46 44-102 2-48 (50)
19 PHA02929 N1R/p28-like protein; 98.2 3.6E-06 7.7E-11 66.1 5.4 50 42-101 172-226 (238)
20 KOG0317 Predicted E3 ubiquitin 98.1 1.8E-06 3.9E-11 68.4 2.4 53 41-106 236-288 (293)
21 KOG2177 Predicted E3 ubiquitin 98.0 2.6E-06 5.5E-11 69.7 2.3 46 41-99 10-55 (386)
22 KOG2164 Predicted E3 ubiquitin 98.0 2.4E-06 5.2E-11 72.6 1.7 60 44-111 186-245 (513)
23 smart00184 RING Ring finger. E 98.0 5.8E-06 1.2E-10 45.7 2.6 38 47-94 1-38 (39)
24 smart00504 Ubox Modified RING 97.9 1.3E-05 2.8E-10 49.9 3.4 51 45-108 2-52 (63)
25 TIGR00599 rad18 DNA repair pro 97.9 1.1E-05 2.4E-10 67.9 4.0 66 42-120 24-90 (397)
26 KOG4628 Predicted E3 ubiquitin 97.8 1.8E-05 3.9E-10 65.1 4.0 46 45-99 230-275 (348)
27 KOG0287 Postreplication repair 97.7 2E-05 4.3E-10 63.8 2.7 65 43-120 22-87 (442)
28 TIGR00570 cdk7 CDK-activating 97.7 6.8E-05 1.5E-09 60.8 5.6 53 45-107 4-59 (309)
29 COG5540 RING-finger-containing 97.6 2.8E-05 6.1E-10 62.1 2.1 52 43-103 322-373 (374)
30 PF12678 zf-rbx1: RING-H2 zinc 97.4 0.00013 2.7E-09 46.9 2.1 42 45-94 20-71 (73)
31 KOG1002 Nucleotide excision re 97.3 0.00015 3.3E-09 62.1 2.9 62 36-105 528-589 (791)
32 PF11793 FANCL_C: FANCL C-term 97.3 0.00014 2.9E-09 46.4 1.6 58 44-103 2-67 (70)
33 KOG0978 E3 ubiquitin ligase in 97.2 0.0001 2.3E-09 65.7 1.1 55 43-109 642-696 (698)
34 PF11789 zf-Nse: Zinc-finger o 97.0 0.00052 1.1E-08 41.7 2.4 49 42-98 9-57 (57)
35 COG5574 PEX10 RING-finger-cont 97.0 0.00066 1.4E-08 53.4 3.0 52 43-106 214-266 (271)
36 COG5243 HRD1 HRD ubiquitin lig 96.8 0.0033 7.3E-08 51.9 5.9 54 41-104 284-347 (491)
37 KOG1039 Predicted E3 ubiquitin 96.8 0.0012 2.5E-08 54.8 3.2 56 41-99 158-218 (344)
38 PF14835 zf-RING_6: zf-RING of 96.7 0.00023 5E-09 43.8 -1.1 49 43-105 6-54 (65)
39 COG5432 RAD18 RING-finger-cont 96.5 0.0019 4.1E-08 51.6 2.6 65 42-119 23-88 (391)
40 PF04564 U-box: U-box domain; 96.3 0.0023 5.1E-08 41.0 1.8 51 43-105 3-53 (73)
41 KOG1814 Predicted E3 ubiquitin 96.3 0.0085 1.8E-07 50.2 5.2 111 44-175 273-405 (445)
42 KOG0006 E3 ubiquitin-protein l 95.9 0.008 1.7E-07 48.7 3.2 98 62-177 339-438 (446)
43 KOG2879 Predicted E3 ubiquitin 95.9 0.019 4E-07 45.7 5.1 55 38-102 233-287 (298)
44 KOG1812 Predicted E3 ubiquitin 95.8 0.0023 5.1E-08 54.3 -0.2 102 44-177 238-344 (384)
45 KOG0804 Cytoplasmic Zn-finger 95.3 0.011 2.3E-07 50.1 2.1 52 36-99 167-219 (493)
46 KOG1645 RING-finger-containing 95.3 0.014 3E-07 48.9 2.6 48 44-99 4-53 (463)
47 KOG4185 Predicted E3 ubiquitin 95.2 0.09 2E-06 43.0 7.3 120 44-177 3-130 (296)
48 KOG2660 Locus-specific chromos 95.1 0.01 2.2E-07 48.4 1.3 47 43-101 14-60 (331)
49 KOG0802 E3 ubiquitin ligase [P 95.0 0.018 3.9E-07 51.3 2.7 46 43-96 290-337 (543)
50 PF12861 zf-Apc11: Anaphase-pr 94.9 0.016 3.4E-07 38.0 1.7 52 44-102 21-82 (85)
51 KOG4367 Predicted Zn-finger pr 94.8 0.014 2.9E-07 49.4 1.4 34 43-79 3-36 (699)
52 PF07975 C1_4: TFIIH C1-like d 94.6 0.0092 2E-07 35.2 0.0 32 154-199 19-50 (51)
53 COG5152 Uncharacterized conser 94.6 0.019 4.1E-07 43.5 1.6 38 38-78 190-227 (259)
54 KOG1428 Inhibitor of type V ad 94.6 0.061 1.3E-06 52.1 5.1 67 44-112 3486-3554(3738)
55 PF14570 zf-RING_4: RING/Ubox 94.5 0.042 9E-07 32.0 2.5 44 47-100 1-46 (48)
56 KOG0824 Predicted E3 ubiquitin 94.4 0.029 6.3E-07 45.2 2.2 52 41-104 4-55 (324)
57 KOG0828 Predicted E3 ubiquitin 94.3 0.027 5.8E-07 48.4 2.1 53 41-102 568-634 (636)
58 smart00744 RINGv The RING-vari 94.0 0.055 1.2E-06 31.7 2.4 42 46-94 1-47 (49)
59 KOG4692 Predicted E3 ubiquitin 94.0 0.088 1.9E-06 43.5 4.3 53 37-102 415-467 (489)
60 PF10571 UPF0547: Uncharacteri 93.7 0.037 7.9E-07 27.8 1.1 23 134-166 2-24 (26)
61 KOG1734 Predicted RING-contain 93.6 0.068 1.5E-06 42.5 2.9 56 43-106 223-285 (328)
62 KOG1815 Predicted E3 ubiquitin 93.6 0.062 1.3E-06 46.7 3.0 38 131-174 225-264 (444)
63 PF14569 zf-UDP: Zinc-binding 93.5 0.062 1.3E-06 34.3 2.1 63 131-211 8-70 (80)
64 KOG1952 Transcription factor N 93.4 0.13 2.9E-06 47.1 4.7 56 41-99 188-244 (950)
65 KOG0827 Predicted E3 ubiquitin 93.4 0.039 8.4E-07 46.0 1.3 48 44-98 4-52 (465)
66 KOG4159 Predicted E3 ubiquitin 93.3 0.16 3.4E-06 43.3 5.0 48 42-102 82-129 (398)
67 KOG1785 Tyrosine kinase negati 93.2 0.042 9E-07 46.0 1.3 46 44-98 369-414 (563)
68 PF05883 Baculo_RING: Baculovi 93.2 0.033 7.2E-07 39.7 0.6 36 43-78 25-66 (134)
69 TIGR00622 ssl1 transcription f 93.1 0.11 2.4E-06 35.9 3.1 52 133-200 56-111 (112)
70 PHA03096 p28-like protein; Pro 93.1 0.18 3.9E-06 41.1 4.8 39 45-83 179-222 (284)
71 PF13719 zinc_ribbon_5: zinc-r 93.0 0.059 1.3E-06 29.6 1.3 32 133-166 3-35 (37)
72 KOG4739 Uncharacterized protei 93.0 0.036 7.7E-07 43.4 0.6 47 44-103 3-49 (233)
73 KOG0311 Predicted E3 ubiquitin 93.0 0.011 2.4E-07 48.5 -2.2 46 43-99 42-87 (381)
74 smart00647 IBR In Between Ring 92.8 0.2 4.3E-06 30.7 3.7 26 189-214 15-44 (64)
75 PF13717 zinc_ribbon_4: zinc-r 92.5 0.085 1.8E-06 28.8 1.5 32 133-166 3-35 (36)
76 KOG3039 Uncharacterized conser 92.4 0.072 1.6E-06 41.8 1.5 56 43-108 220-276 (303)
77 PF09788 Tmemb_55A: Transmembr 91.6 0.17 3.6E-06 40.1 2.8 78 41-149 62-140 (256)
78 KOG1941 Acetylcholine receptor 91.3 0.12 2.6E-06 43.3 1.7 76 9-98 336-412 (518)
79 COG2888 Predicted Zn-ribbon RN 91.2 0.2 4.3E-06 30.3 2.2 49 133-200 10-58 (61)
80 KOG0297 TNF receptor-associate 90.6 0.28 6E-06 42.0 3.4 38 41-80 18-55 (391)
81 PF01485 IBR: IBR domain; Int 90.3 0.16 3.6E-06 31.0 1.4 26 189-214 15-44 (64)
82 KOG3800 Predicted E3 ubiquitin 90.0 0.42 9E-06 38.5 3.7 52 46-106 2-55 (300)
83 PF04641 Rtf2: Rtf2 RING-finge 89.9 0.45 9.8E-06 38.3 3.9 71 41-122 110-182 (260)
84 KOG4172 Predicted E3 ubiquitin 89.9 0.1 2.2E-06 31.0 0.1 45 45-101 8-53 (62)
85 KOG4265 Predicted E3 ubiquitin 89.7 0.26 5.7E-06 40.8 2.5 47 42-101 288-335 (349)
86 COG5220 TFB3 Cdk activating ki 89.2 0.073 1.6E-06 41.6 -1.0 50 45-101 11-63 (314)
87 PRK14890 putative Zn-ribbon RN 88.9 0.46 9.9E-06 28.8 2.4 45 134-200 9-56 (59)
88 PRK00398 rpoP DNA-directed RNA 88.2 0.47 1E-05 27.3 2.2 28 133-166 4-31 (46)
89 TIGR02098 MJ0042_CXXC MJ0042 f 88.2 0.26 5.6E-06 27.0 1.0 32 133-166 3-35 (38)
90 KOG0825 PHD Zn-finger protein 88.0 0.12 2.6E-06 47.0 -0.7 41 43-83 95-139 (1134)
91 PRK14714 DNA polymerase II lar 87.9 0.52 1.1E-05 45.4 3.4 48 133-203 668-720 (1337)
92 PF05290 Baculo_IE-1: Baculovi 87.7 3.3 7.2E-05 29.5 6.5 56 40-102 76-132 (140)
93 KOG4445 Uncharacterized conser 87.6 0.39 8.5E-06 38.9 2.1 45 38-82 109-153 (368)
94 KOG2034 Vacuolar sorting prote 87.6 0.64 1.4E-05 43.0 3.6 46 36-82 809-854 (911)
95 COG5219 Uncharacterized conser 87.5 0.28 6.1E-06 45.7 1.4 51 43-101 1468-1522(1525)
96 PF02150 RNA_POL_M_15KD: RNA p 87.3 0.32 6.9E-06 26.3 1.0 28 133-165 2-29 (35)
97 KOG3579 Predicted E3 ubiquitin 87.3 0.59 1.3E-05 37.6 2.9 57 39-98 263-321 (352)
98 KOG2807 RNA polymerase II tran 87.2 0.11 2.3E-06 42.5 -1.2 32 154-199 343-374 (378)
99 PF14803 Nudix_N_2: Nudix N-te 86.8 0.36 7.9E-06 25.9 1.0 31 133-165 1-31 (34)
100 KOG0826 Predicted E3 ubiquitin 86.6 0.99 2.1E-05 37.1 3.9 62 36-109 292-353 (357)
101 COG5175 MOT2 Transcriptional r 86.2 1 2.3E-05 37.1 3.8 53 45-107 15-69 (480)
102 KOG1940 Zn-finger protein [Gen 85.8 0.55 1.2E-05 37.9 2.1 46 44-99 158-204 (276)
103 PLN02189 cellulose synthase 85.3 0.74 1.6E-05 43.7 2.8 63 131-211 33-95 (1040)
104 PF13240 zinc_ribbon_2: zinc-r 85.2 0.4 8.7E-06 23.3 0.6 22 134-165 1-22 (23)
105 PF13248 zf-ribbon_3: zinc-rib 84.8 0.44 9.4E-06 23.8 0.7 23 133-165 3-25 (26)
106 PRK04023 DNA polymerase II lar 84.7 0.89 1.9E-05 42.9 3.1 45 131-203 625-674 (1121)
107 KOG0823 Predicted E3 ubiquitin 84.7 0.26 5.5E-06 38.4 -0.3 37 155-204 60-96 (230)
108 smart00661 RPOL9 RNA polymeras 84.6 0.69 1.5E-05 27.1 1.6 28 134-165 2-29 (52)
109 PLN02638 cellulose synthase A 84.6 0.75 1.6E-05 43.8 2.6 63 131-211 16-78 (1079)
110 PRK14559 putative protein seri 84.4 0.83 1.8E-05 41.6 2.8 13 191-203 40-52 (645)
111 PF09297 zf-NADH-PPase: NADH p 84.1 0.96 2.1E-05 23.7 1.9 28 132-165 3-30 (32)
112 KOG2817 Predicted E3 ubiquitin 83.9 3.6 7.8E-05 34.8 6.0 59 43-108 333-391 (394)
113 PLN03208 E3 ubiquitin-protein 83.9 0.15 3.3E-06 38.8 -1.8 63 130-204 16-80 (193)
114 PF08746 zf-RING-like: RING-li 82.9 0.73 1.6E-05 26.1 1.2 42 47-94 1-42 (43)
115 PF14447 Prok-RING_4: Prokaryo 82.7 0.39 8.4E-06 28.7 -0.0 46 44-104 7-52 (55)
116 KOG0320 Predicted E3 ubiquitin 82.5 0.73 1.6E-05 34.5 1.4 30 161-204 150-179 (187)
117 KOG3268 Predicted E3 ubiquitin 82.2 2.2 4.8E-05 32.0 3.7 57 44-102 165-228 (234)
118 PF10367 Vps39_2: Vacuolar sor 82.0 1.7 3.6E-05 29.6 3.0 32 43-75 77-108 (109)
119 KOG3053 Uncharacterized conser 82.0 1.8 3.9E-05 34.4 3.3 58 41-100 17-80 (293)
120 KOG3002 Zn finger protein [Gen 81.9 1.3 2.9E-05 36.3 2.8 49 39-102 43-91 (299)
121 PF05605 zf-Di19: Drought indu 81.1 1.7 3.6E-05 25.8 2.4 41 44-102 2-42 (54)
122 PLN02436 cellulose synthase A 80.9 1.4 3.1E-05 42.0 2.9 63 131-211 35-97 (1094)
123 PF06844 DUF1244: Protein of u 80.9 1.3 2.8E-05 27.4 1.8 19 68-86 11-29 (68)
124 KOG1813 Predicted E3 ubiquitin 80.7 0.63 1.4E-05 37.7 0.5 45 44-101 241-285 (313)
125 COG5222 Uncharacterized conser 80.2 2.5 5.4E-05 34.4 3.7 44 45-99 275-318 (427)
126 PF12773 DZR: Double zinc ribb 80.0 1.3 2.7E-05 25.8 1.6 28 130-164 10-37 (50)
127 PF01599 Ribosomal_S27: Riboso 79.5 1.1 2.4E-05 25.9 1.1 29 132-164 18-46 (47)
128 KOG2114 Vacuolar assembly/sort 79.3 5.1 0.00011 37.3 5.7 41 44-99 840-880 (933)
129 PF14446 Prok-RING_1: Prokaryo 79.1 2 4.2E-05 25.7 2.1 35 43-77 4-39 (54)
130 PF12906 RINGv: RING-variant d 78.9 1.6 3.4E-05 25.2 1.7 33 47-80 1-38 (47)
131 KOG1001 Helicase-like transcri 78.6 0.69 1.5E-05 42.3 0.2 51 45-107 455-505 (674)
132 PLN02400 cellulose synthase 78.5 1.4 3.1E-05 42.0 2.1 63 131-211 35-97 (1085)
133 PRK00420 hypothetical protein; 77.7 5.5 0.00012 27.7 4.4 25 133-164 24-48 (112)
134 KOG0978 E3 ubiquitin ligase in 77.5 0.74 1.6E-05 41.9 0.0 29 161-202 660-688 (698)
135 PF14445 Prok-RING_2: Prokaryo 77.3 0.51 1.1E-05 27.5 -0.7 36 43-78 6-41 (57)
136 KOG2164 Predicted E3 ubiquitin 76.9 1.3 2.9E-05 38.6 1.3 35 161-204 203-237 (513)
137 KOG3970 Predicted E3 ubiquitin 76.3 2.4 5.2E-05 33.1 2.5 55 44-101 50-104 (299)
138 PF03119 DNA_ligase_ZBD: NAD-d 76.1 2.6 5.6E-05 21.5 1.8 14 194-207 1-14 (28)
139 PHA00626 hypothetical protein 75.7 2.7 5.9E-05 25.1 2.0 31 134-166 2-33 (59)
140 PLN02915 cellulose synthase A 75.3 2.1 4.5E-05 40.8 2.3 61 133-211 16-76 (1044)
141 smart00531 TFIIE Transcription 74.5 3.5 7.6E-05 30.1 2.9 62 101-165 67-132 (147)
142 smart00834 CxxC_CXXC_SSSS Puta 74.1 3.4 7.4E-05 22.6 2.2 28 134-164 7-34 (41)
143 TIGR00570 cdk7 CDK-activating 73.8 3 6.6E-05 34.3 2.6 52 134-205 5-56 (309)
144 PRK06266 transcription initiat 73.7 4 8.8E-05 30.9 3.1 58 101-164 85-144 (178)
145 PF07754 DUF1610: Domain of un 73.6 2.7 5.9E-05 20.6 1.4 9 155-163 15-23 (24)
146 PF14952 zf-tcix: Putative tre 73.5 1.8 3.9E-05 24.5 0.9 13 190-202 9-21 (44)
147 TIGR00373 conserved hypothetic 73.3 4.2 9E-05 30.1 3.1 59 101-165 77-137 (158)
148 KOG2932 E3 ubiquitin ligase in 73.2 1.6 3.4E-05 35.7 0.8 32 44-77 90-121 (389)
149 TIGR01206 lysW lysine biosynth 71.9 3.6 7.9E-05 24.6 2.0 30 133-166 3-32 (54)
150 PF03604 DNA_RNApol_7kD: DNA d 71.8 4 8.6E-05 21.5 1.9 22 139-165 5-26 (32)
151 PF08274 PhnA_Zn_Ribbon: PhnA 71.7 1.8 3.9E-05 22.5 0.6 25 134-165 4-28 (30)
152 PRK14892 putative transcriptio 70.4 4.2 9.1E-05 27.6 2.3 37 129-168 18-54 (99)
153 COG3492 Uncharacterized protei 70.1 4.1 8.8E-05 26.9 2.1 18 67-84 41-58 (104)
154 PF09538 FYDLN_acid: Protein o 69.9 3 6.5E-05 28.8 1.5 31 132-169 9-39 (108)
155 PRK14559 putative protein seri 69.8 4.2 9.1E-05 37.2 2.8 34 130-175 13-52 (645)
156 KOG2691 RNA polymerase II subu 69.3 4.5 9.6E-05 27.7 2.2 34 131-166 3-36 (113)
157 PF09723 Zn-ribbon_8: Zinc rib 68.9 4.9 0.00011 22.5 2.0 28 134-164 7-34 (42)
158 TIGR00686 phnA alkylphosphonat 68.8 3.3 7.1E-05 28.4 1.5 25 134-165 4-28 (109)
159 PRK03824 hypA hydrogenase nick 68.5 6.1 0.00013 28.4 3.0 13 133-147 71-83 (135)
160 PRK00432 30S ribosomal protein 67.8 3.6 7.8E-05 24.1 1.4 27 132-166 20-47 (50)
161 KOG0317 Predicted E3 ubiquitin 67.7 0.87 1.9E-05 36.8 -1.7 34 158-205 253-286 (293)
162 PF06524 NOA36: NOA36 protein; 67.1 3.2 6.8E-05 33.1 1.3 68 133-203 143-220 (314)
163 PF02318 FYVE_2: FYVE-type zin 66.9 9.1 0.0002 26.8 3.5 32 43-74 53-86 (118)
164 COG1594 RPB9 DNA-directed RNA 66.5 5.2 0.00011 27.9 2.2 32 132-167 2-33 (113)
165 smart00659 RPOLCX RNA polymera 66.3 5.6 0.00012 22.6 1.9 21 139-164 7-27 (44)
166 PRK10220 hypothetical protein; 66.2 4.4 9.4E-05 27.8 1.7 25 134-165 5-29 (111)
167 KOG0825 PHD Zn-finger protein 66.2 5.8 0.00013 36.7 2.9 50 44-103 123-172 (1134)
168 PHA02825 LAP/PHD finger-like p 65.8 8.1 0.00018 28.5 3.1 52 43-104 7-61 (162)
169 PHA02926 zinc finger-like prot 65.7 19 0.00042 28.2 5.3 36 160-203 195-230 (242)
170 PF06677 Auto_anti-p27: Sjogre 65.7 6.6 0.00014 22.0 2.1 24 133-163 18-41 (41)
171 KOG2906 RNA polymerase III sub 65.7 4.5 9.7E-05 27.2 1.6 33 133-169 2-34 (105)
172 PF01396 zf-C4_Topoisom: Topoi 65.5 5.6 0.00012 21.9 1.8 13 193-205 2-15 (39)
173 PRK03681 hypA hydrogenase nick 64.6 8.7 0.00019 26.8 3.1 25 133-164 71-95 (114)
174 PF01363 FYVE: FYVE zinc finge 64.4 2.4 5.3E-05 26.4 0.2 37 41-77 6-43 (69)
175 PF02891 zf-MIZ: MIZ/SP-RING z 64.1 6.3 0.00014 23.0 1.9 47 45-99 3-49 (50)
176 PF07503 zf-HYPF: HypF finger; 63.9 3.5 7.6E-05 22.2 0.7 31 69-101 1-31 (35)
177 KOG1493 Anaphase-promoting com 63.5 1.3 2.8E-05 28.3 -1.1 49 46-101 22-80 (84)
178 PF08792 A2L_zn_ribbon: A2L zi 63.1 7 0.00015 20.7 1.8 28 132-166 3-31 (33)
179 PF06467 zf-FCS: MYM-type Zinc 62.9 8.3 0.00018 21.3 2.2 36 42-77 4-43 (43)
180 KOG3161 Predicted E3 ubiquitin 62.7 2.6 5.6E-05 38.0 0.1 37 42-78 9-46 (861)
181 PF14369 zf-RING_3: zinc-finge 62.7 9.9 0.00022 20.4 2.4 30 132-166 2-31 (35)
182 smart00734 ZnF_Rad18 Rad18-lik 62.6 4.7 0.0001 20.1 1.0 20 90-111 2-21 (26)
183 PF14149 YhfH: YhfH-like prote 62.5 0.98 2.1E-05 24.6 -1.6 31 183-213 4-34 (37)
184 COG1579 Zn-ribbon protein, pos 62.4 9.5 0.00021 30.3 3.2 60 104-165 166-230 (239)
185 PLN02195 cellulose synthase A 62.3 5.2 0.00011 38.0 2.0 52 134-203 8-59 (977)
186 COG5236 Uncharacterized conser 61.9 4.7 0.0001 33.6 1.4 53 38-101 55-107 (493)
187 KOG2932 E3 ubiquitin ligase in 61.8 2.3 5.1E-05 34.7 -0.3 48 134-208 92-139 (389)
188 COG1198 PriA Primosomal protei 61.6 8 0.00017 35.9 3.0 34 134-173 446-484 (730)
189 PF14353 CpXC: CpXC protein 61.4 3.3 7.1E-05 29.3 0.5 46 89-146 1-50 (128)
190 COG3677 Transposase and inacti 61.4 17 0.00036 26.0 4.1 41 130-172 28-69 (129)
191 COG4647 AcxC Acetone carboxyla 61.0 33 0.00071 24.4 5.3 97 101-205 17-133 (165)
192 COG1998 RPS31 Ribosomal protei 61.0 5.1 0.00011 23.3 1.1 27 132-164 19-45 (51)
193 KOG4275 Predicted E3 ubiquitin 61.0 5.4 0.00012 32.4 1.6 27 44-73 300-327 (350)
194 TIGR03037 anthran_nbaC 3-hydro 60.9 4.2 9E-05 30.2 0.9 38 163-200 113-159 (159)
195 PF07191 zinc-ribbons_6: zinc- 60.8 1 2.2E-05 28.4 -1.9 39 45-101 2-40 (70)
196 PRK13264 3-hydroxyanthranilate 60.8 4 8.7E-05 30.8 0.8 43 162-204 118-169 (177)
197 KOG2930 SCF ubiquitin ligase, 60.5 7.7 0.00017 26.4 2.0 24 64-95 80-103 (114)
198 PF06827 zf-FPG_IleRS: Zinc fi 59.4 5.1 0.00011 20.5 0.9 13 193-205 2-14 (30)
199 KOG3039 Uncharacterized conser 59.3 10 0.00022 30.1 2.9 39 42-83 41-79 (303)
200 PLN03086 PRLI-interacting fact 58.8 12 0.00027 33.6 3.6 58 88-166 406-463 (567)
201 COG5151 SSL1 RNA polymerase II 57.6 2.8 6E-05 34.3 -0.5 91 66-175 307-407 (421)
202 PF02318 FYVE_2: FYVE-type zin 57.6 24 0.00052 24.6 4.3 36 131-173 53-88 (118)
203 KOG0309 Conserved WD40 repeat- 56.9 10 0.00022 35.0 2.8 54 38-100 1022-1076(1081)
204 COG5194 APC11 Component of SCF 56.4 7.9 0.00017 25.0 1.5 17 64-80 53-69 (88)
205 smart00249 PHD PHD zinc finger 56.4 4.1 8.8E-05 22.5 0.2 33 46-78 1-33 (47)
206 TIGR01053 LSD1 zinc finger dom 56.3 12 0.00026 19.5 1.9 27 133-165 2-28 (31)
207 PF11809 DUF3330: Domain of un 55.7 4.6 9.9E-05 25.1 0.3 42 40-81 7-51 (70)
208 TIGR02300 FYDLN_acid conserved 55.2 8.8 0.00019 27.2 1.7 29 132-167 9-37 (129)
209 PRK00564 hypA hydrogenase nick 55.2 13 0.00027 26.1 2.5 14 111-124 40-53 (117)
210 smart00064 FYVE Protein presen 55.1 11 0.00025 23.2 2.1 37 43-79 9-46 (68)
211 PLN00209 ribosomal protein S27 55.0 8.1 0.00018 25.3 1.4 30 133-167 37-66 (86)
212 PHA02862 5L protein; Provision 54.8 15 0.00033 26.7 2.9 48 45-102 3-53 (156)
213 PF10426 zf-RAG1: Recombinatio 54.3 3.1 6.7E-05 21.5 -0.5 21 89-109 2-22 (30)
214 TIGR00595 priA primosomal prot 54.0 14 0.0003 32.9 3.2 33 135-173 225-262 (505)
215 PF02591 DUF164: Putative zinc 53.9 9.9 0.00021 22.6 1.6 19 183-201 37-55 (56)
216 PF03854 zf-P11: P-11 zinc fin 53.7 5.1 0.00011 23.2 0.3 44 45-103 3-47 (50)
217 COG1675 TFA1 Transcription ini 53.6 13 0.00028 28.1 2.5 32 128-164 109-140 (176)
218 PRK12380 hydrogenase nickel in 53.2 18 0.00039 25.1 3.1 11 134-146 72-82 (113)
219 TIGR00100 hypA hydrogenase nic 52.2 19 0.00042 25.0 3.1 11 134-146 72-82 (115)
220 PTZ00083 40S ribosomal protein 52.1 11 0.00024 24.7 1.7 30 133-167 36-65 (85)
221 PF03833 PolC_DP2: DNA polymer 51.6 4.9 0.00011 37.5 0.0 10 132-143 655-664 (900)
222 COG2051 RPS27A Ribosomal prote 51.3 9.7 0.00021 23.7 1.3 30 133-167 20-49 (67)
223 PF01428 zf-AN1: AN1-like Zinc 49.5 6 0.00013 22.2 0.2 19 155-173 12-30 (43)
224 TIGR02605 CxxC_CxxC_SSSS putat 49.2 17 0.00037 21.1 2.1 8 157-164 27-34 (52)
225 PF08271 TF_Zn_Ribbon: TFIIB z 49.1 10 0.00023 21.2 1.1 27 134-165 2-28 (43)
226 PF06906 DUF1272: Protein of u 48.2 20 0.00043 21.5 2.2 46 44-102 5-52 (57)
227 COG5109 Uncharacterized conser 48.1 20 0.00044 29.6 2.9 58 42-106 334-391 (396)
228 KOG1039 Predicted E3 ubiquitin 48.0 6.7 0.00014 32.9 0.3 40 158-204 183-222 (344)
229 COG5220 TFB3 Cdk activating ki 47.6 12 0.00027 29.5 1.6 54 90-147 11-66 (314)
230 PRK14873 primosome assembly pr 47.1 19 0.0004 33.3 3.0 31 139-173 397-431 (665)
231 cd00065 FYVE FYVE domain; Zinc 47.1 14 0.0003 21.8 1.5 35 45-79 3-38 (57)
232 PF11023 DUF2614: Protein of u 47.0 12 0.00027 25.8 1.4 23 155-177 68-98 (114)
233 PF13453 zf-TFIIB: Transcripti 46.7 8.8 0.00019 21.2 0.6 11 135-147 2-12 (41)
234 TIGR01562 FdhE formate dehydro 46.6 14 0.00031 30.4 2.0 12 192-203 252-263 (305)
235 PF14205 Cys_rich_KTR: Cystein 46.3 14 0.00031 22.0 1.4 11 131-143 3-13 (55)
236 PRK03564 formate dehydrogenase 46.3 15 0.00033 30.3 2.1 13 191-203 251-263 (309)
237 KOG2807 RNA polymerase II tran 46.2 8.3 0.00018 31.9 0.5 29 46-74 332-360 (378)
238 PF00643 zf-B_box: B-box zinc 46.1 3.3 7.1E-05 22.9 -1.3 23 155-177 14-36 (42)
239 KOG0801 Predicted E3 ubiquitin 45.7 8 0.00017 28.6 0.3 29 42-70 175-203 (205)
240 cd00021 BBOX B-Box-type zinc f 45.3 11 0.00024 20.1 0.8 24 154-177 10-33 (39)
241 PF00628 PHD: PHD-finger; Int 45.1 8.1 0.00018 22.2 0.2 34 46-79 1-34 (51)
242 PF09151 DUF1936: Domain of un 45.0 11 0.00024 19.5 0.7 9 194-202 3-11 (36)
243 TIGR01384 TFS_arch transcripti 44.7 13 0.00028 25.2 1.2 26 134-167 2-27 (104)
244 PF10083 DUF2321: Uncharacteri 44.6 4.6 9.9E-05 29.7 -1.1 10 193-202 40-49 (158)
245 smart00154 ZnF_AN1 AN1-like Zi 44.4 13 0.00028 20.5 1.0 18 156-173 12-29 (39)
246 COG2176 PolC DNA polymerase II 43.9 24 0.00053 34.6 3.2 43 153-206 911-953 (1444)
247 COG2816 NPY1 NTP pyrophosphohy 43.2 52 0.0011 26.8 4.6 54 103-164 83-137 (279)
248 KOG1571 Predicted E3 ubiquitin 42.7 32 0.00069 28.9 3.4 43 43-101 304-346 (355)
249 PF06943 zf-LSD1: LSD1 zinc fi 42.4 33 0.00071 17.0 2.1 22 139-164 3-24 (25)
250 PRK05580 primosome assembly pr 41.5 25 0.00055 32.5 3.0 34 134-173 392-430 (679)
251 PF11682 DUF3279: Protein of u 41.4 19 0.00042 25.6 1.7 15 193-207 111-125 (128)
252 COG1645 Uncharacterized Zn-fin 41.3 14 0.00031 26.4 1.0 16 192-207 28-43 (131)
253 smart00336 BBOX B-Box-type zin 41.1 17 0.00036 19.7 1.1 23 155-177 14-36 (42)
254 COG1996 RPC10 DNA-directed RNA 40.9 16 0.00035 21.3 1.0 14 189-202 21-34 (49)
255 PF07282 OrfB_Zn_ribbon: Putat 40.2 32 0.0007 21.2 2.5 26 133-164 29-54 (69)
256 PF04423 Rad50_zn_hook: Rad50 39.5 36 0.00078 20.0 2.5 17 91-109 22-38 (54)
257 PF14169 YdjO: Cold-inducible 39.3 28 0.00061 21.2 1.9 28 134-164 20-47 (59)
258 PRK14714 DNA polymerase II lar 38.8 20 0.00044 35.2 1.9 35 156-205 667-705 (1337)
259 PRK09710 lar restriction allev 38.5 21 0.00046 22.1 1.3 15 190-204 4-18 (64)
260 COG4357 Zinc finger domain con 38.1 15 0.00033 24.6 0.8 19 155-173 25-44 (105)
261 PF01155 HypA: Hydrogenase exp 37.9 20 0.00044 24.8 1.4 13 134-148 72-84 (113)
262 PF10497 zf-4CXXC_R1: Zinc-fin 37.7 51 0.0011 22.6 3.3 32 63-94 31-66 (105)
263 PF02148 zf-UBP: Zn-finger in 37.5 28 0.0006 21.2 1.8 31 47-79 1-35 (63)
264 PF09889 DUF2116: Uncharacteri 36.6 18 0.00038 22.1 0.8 14 192-205 3-16 (59)
265 PRK00415 rps27e 30S ribosomal 36.5 30 0.00064 21.1 1.7 30 133-167 12-41 (59)
266 PRK13130 H/ACA RNA-protein com 36.4 21 0.00046 21.5 1.1 37 89-127 17-53 (56)
267 cd00350 rubredoxin_like Rubred 36.4 34 0.00073 17.9 1.8 22 135-164 4-25 (33)
268 KOG2979 Protein involved in DN 36.4 49 0.0011 26.5 3.4 47 45-99 177-223 (262)
269 PF10272 Tmpp129: Putative tra 36.3 71 0.0015 27.1 4.5 64 41-106 268-355 (358)
270 PF12760 Zn_Tnp_IS1595: Transp 36.0 46 0.00099 18.8 2.5 13 189-201 15-27 (46)
271 COG3024 Uncharacterized protei 35.3 20 0.00043 22.2 0.8 15 190-204 5-19 (65)
272 PF13913 zf-C2HC_2: zinc-finge 34.9 27 0.00059 17.0 1.2 18 90-109 3-20 (25)
273 COG0375 HybF Zn finger protein 34.7 44 0.00095 23.4 2.6 11 134-146 72-82 (115)
274 PF15135 UPF0515: Uncharacteri 34.5 52 0.0011 26.3 3.2 34 111-146 91-124 (278)
275 COG0266 Nei Formamidopyrimidin 34.5 33 0.00071 27.9 2.2 23 191-213 244-268 (273)
276 PRK12286 rpmF 50S ribosomal pr 34.4 30 0.00066 20.8 1.6 25 129-164 24-48 (57)
277 COG3357 Predicted transcriptio 34.3 1E+02 0.0022 20.6 4.1 25 134-164 60-84 (97)
278 PF01667 Ribosomal_S27e: Ribos 34.2 33 0.00072 20.5 1.7 30 133-167 8-37 (55)
279 PF14471 DUF4428: Domain of un 33.8 36 0.00078 19.9 1.8 30 46-77 1-30 (51)
280 KOG4362 Transcriptional regula 33.7 9 0.00019 35.0 -1.2 55 42-106 19-73 (684)
281 cd00729 rubredoxin_SM Rubredox 33.0 46 0.00099 17.6 2.0 23 134-164 4-26 (34)
282 PF07649 C1_3: C1-like domain; 33.0 27 0.00059 17.7 1.1 28 46-73 2-29 (30)
283 PF00096 zf-C2H2: Zinc finger, 32.9 13 0.00028 17.2 -0.2 6 159-164 3-8 (23)
284 COG5175 MOT2 Transcriptional r 32.0 18 0.00039 30.2 0.4 31 133-171 15-45 (480)
285 KOG3799 Rab3 effector RIM1 and 32.0 73 0.0016 22.9 3.4 24 39-68 60-83 (169)
286 PRK08665 ribonucleotide-diphos 31.7 29 0.00062 32.6 1.7 17 193-209 725-741 (752)
287 PF09986 DUF2225: Uncharacteri 31.5 61 0.0013 25.2 3.3 19 43-61 4-22 (214)
288 PF06044 DRP: Dam-replacing fa 31.3 7.2 0.00016 30.9 -1.9 35 133-169 32-66 (254)
289 COG3809 Uncharacterized protei 30.5 36 0.00077 22.0 1.5 32 134-177 3-34 (88)
290 PLN02189 cellulose synthase 29.4 39 0.00084 32.7 2.1 51 43-102 33-87 (1040)
291 PRK12495 hypothetical protein; 29.4 92 0.002 24.4 3.8 15 130-146 40-54 (226)
292 COG1656 Uncharacterized conser 29.1 51 0.0011 24.6 2.3 17 131-149 96-112 (165)
293 PF12172 DUF35_N: Rubredoxin-l 29.0 34 0.00073 18.3 1.1 21 134-164 13-33 (37)
294 cd02335 ZZ_ADA2 Zinc finger, Z 28.9 46 0.00099 19.2 1.7 32 46-77 2-34 (49)
295 KOG3623 Homeobox transcription 28.9 18 0.00039 33.4 -0.1 69 129-207 237-324 (1007)
296 PLN02436 cellulose synthase A 28.7 55 0.0012 31.9 3.0 51 43-102 35-89 (1094)
297 PRK00241 nudC NADH pyrophospha 28.6 1.2E+02 0.0026 24.4 4.6 29 130-164 97-125 (256)
298 COG2260 Predicted Zn-ribbon RN 28.5 53 0.0011 19.9 1.9 36 91-128 19-54 (59)
299 TIGR03655 anti_R_Lar restricti 28.2 29 0.00063 20.4 0.8 11 193-203 2-12 (53)
300 PF01927 Mut7-C: Mut7-C RNAse 28.0 30 0.00065 25.1 1.0 43 90-147 92-137 (147)
301 PRK11827 hypothetical protein; 28.0 46 0.001 20.3 1.6 29 132-166 8-36 (60)
302 COG3813 Uncharacterized protei 27.9 57 0.0012 20.7 2.0 59 44-118 5-65 (84)
303 KOG2041 WD40 repeat protein [G 27.7 59 0.0013 30.3 2.9 21 108-128 1087-1107(1189)
304 KOG1729 FYVE finger containing 27.5 19 0.0004 29.5 -0.2 54 38-94 162-219 (288)
305 PF09943 DUF2175: Uncharacteri 27.2 60 0.0013 22.1 2.2 41 44-85 2-42 (101)
306 PLN02638 cellulose synthase A 26.9 69 0.0015 31.2 3.3 50 43-101 16-69 (1079)
307 KOG2923 Uncharacterized conser 26.9 38 0.00082 20.9 1.1 17 187-203 39-55 (67)
308 COG1997 RPL43A Ribosomal prote 26.8 94 0.002 20.6 2.9 35 130-170 33-67 (89)
309 PRK14811 formamidopyrimidine-D 26.6 55 0.0012 26.5 2.4 15 191-205 234-248 (269)
310 TIGR00577 fpg formamidopyrimid 26.3 58 0.0013 26.4 2.4 15 191-205 244-258 (272)
311 PRK14810 formamidopyrimidine-D 26.2 57 0.0012 26.4 2.4 14 192-205 244-257 (272)
312 PRK01103 formamidopyrimidine/5 26.0 58 0.0013 26.4 2.4 14 192-205 245-258 (274)
313 KOG3816 Cell differentiation r 25.9 72 0.0016 27.3 2.9 15 187-201 495-509 (526)
314 PF13894 zf-C2H2_4: C2H2-type 25.8 27 0.00058 15.8 0.3 6 159-164 3-8 (24)
315 PF03966 Trm112p: Trm112p-like 25.6 1.3E+02 0.0028 18.5 3.4 12 88-101 6-17 (68)
316 KOG3183 Predicted Zn-finger pr 25.0 32 0.0007 27.2 0.7 57 133-204 9-67 (250)
317 COG4416 Com Mu-like prophage p 25.0 33 0.00072 20.4 0.6 11 193-203 25-35 (60)
318 PF08209 Sgf11: Sgf11 (transcr 25.0 33 0.00072 18.2 0.5 13 192-204 4-16 (33)
319 KOG3005 GIY-YIG type nuclease 24.9 1.3E+02 0.0029 24.3 4.1 61 45-108 183-249 (276)
320 PF01530 zf-C2HC: Zinc finger, 24.7 41 0.00089 17.6 0.8 15 133-147 2-16 (31)
321 PRK10445 endonuclease VIII; Pr 24.6 65 0.0014 25.9 2.4 15 191-205 234-248 (263)
322 PRK09678 DNA-binding transcrip 24.5 21 0.00044 22.7 -0.4 15 132-146 27-41 (72)
323 COG1096 Predicted RNA-binding 24.4 51 0.0011 25.1 1.6 30 134-171 151-180 (188)
324 PF01783 Ribosomal_L32p: Ribos 24.4 69 0.0015 19.1 1.9 24 130-164 24-47 (56)
325 TIGR01031 rpmF_bact ribosomal 24.4 50 0.0011 19.7 1.3 14 129-144 23-36 (55)
326 PRK13945 formamidopyrimidine-D 24.3 65 0.0014 26.3 2.4 14 192-205 254-267 (282)
327 PF10764 Gin: Inhibitor of sig 24.0 40 0.00087 19.3 0.8 36 46-85 1-36 (46)
328 PF03884 DUF329: Domain of unk 24.0 28 0.0006 21.0 0.1 13 192-204 2-14 (57)
329 PF14690 zf-ISL3: zinc-finger 23.9 51 0.0011 18.4 1.3 12 193-204 3-14 (47)
330 PF10058 DUF2296: Predicted in 23.9 80 0.0017 18.7 2.1 10 155-164 43-52 (54)
331 PRK02935 hypothetical protein; 23.6 39 0.00084 23.2 0.8 15 191-205 85-99 (110)
332 PF09862 DUF2089: Protein of u 23.4 45 0.00099 23.2 1.1 33 135-177 1-33 (113)
333 PF02748 PyrI_C: Aspartate car 23.3 39 0.00085 19.9 0.7 33 131-166 5-45 (52)
334 PF00412 LIM: LIM domain; Int 23.2 60 0.0013 18.8 1.5 32 44-77 26-57 (58)
335 COG1885 Uncharacterized protei 22.7 46 0.001 22.7 1.0 13 191-203 48-60 (115)
336 PF01194 RNA_pol_N: RNA polyme 22.5 82 0.0018 19.2 2.0 13 88-102 3-15 (60)
337 KOG1779 40s ribosomal protein 22.5 87 0.0019 20.2 2.1 31 133-168 35-65 (84)
338 PLN02195 cellulose synthase A 22.3 68 0.0015 30.9 2.3 50 44-102 6-59 (977)
339 COG2824 PhnA Uncharacterized Z 22.0 60 0.0013 22.3 1.4 29 134-177 5-33 (112)
340 PF01214 CK_II_beta: Casein ki 21.9 1E+02 0.0022 23.5 2.8 9 134-142 101-109 (184)
341 PF13465 zf-H2C2_2: Zinc-finge 21.9 36 0.00077 16.6 0.3 11 156-166 14-24 (26)
342 PRK00418 DNA gyrase inhibitor; 21.8 50 0.0011 20.3 1.0 13 191-203 5-17 (62)
343 PTZ00396 Casein kinase II subu 21.8 1.3E+02 0.0028 24.2 3.5 10 134-143 122-131 (251)
344 PF13834 DUF4193: Domain of un 21.7 44 0.00095 22.6 0.8 31 42-73 68-98 (99)
345 PF00569 ZZ: Zinc finger, ZZ t 21.6 82 0.0018 17.8 1.8 33 44-76 4-37 (46)
346 COG4306 Uncharacterized protei 21.5 29 0.00064 24.5 -0.1 8 157-164 29-36 (160)
347 COG4888 Uncharacterized Zn rib 21.3 55 0.0012 22.2 1.1 33 130-166 20-56 (104)
348 PRK12496 hypothetical protein; 21.3 48 0.001 24.7 1.0 8 135-144 130-137 (164)
349 PF10122 Mu-like_Com: Mu-like 21.2 29 0.00064 20.4 -0.1 6 195-200 27-32 (51)
350 PF08882 Acetone_carb_G: Aceto 21.0 47 0.001 23.0 0.8 49 155-205 23-87 (112)
351 PF05129 Elf1: Transcription e 21.0 42 0.00092 21.8 0.6 35 130-166 20-56 (81)
352 KOG4537 Zn-ribbon-containing p 20.9 48 0.001 24.4 0.8 15 133-149 41-55 (178)
353 PHA02325 hypothetical protein 20.9 51 0.0011 20.3 0.8 12 191-202 2-14 (72)
354 cd02249 ZZ Zinc finger, ZZ typ 20.8 81 0.0018 17.7 1.7 31 46-77 2-33 (46)
355 PRK00893 aspartate carbamoyltr 20.6 71 0.0015 23.5 1.7 33 131-166 104-144 (152)
356 KOG2462 C2H2-type Zn-finger pr 20.3 1.1E+02 0.0023 24.9 2.8 15 42-56 128-142 (279)
357 PF14255 Cys_rich_CPXG: Cystei 20.2 56 0.0012 19.3 0.9 11 194-204 2-12 (52)
No 1
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.6e-33 Score=227.71 Aligned_cols=169 Identities=29% Similarity=0.645 Sum_probs=145.5
Q ss_pred cccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHhhcCCHHHHHHHHHH
Q 045388 42 PSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKSVLSKNVLELWEKA 121 (214)
Q Consensus 42 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~~~l~~~~~~~~~~~ 121 (214)
.+.+.|.|||++.....-+..++|+|.||+.|++.|++..|++|.+..++||+.+|+..-....|+.+++.+++++|++.
T Consensus 182 ~slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C~~~a~~g~vKelvg~EL~arYe~l 261 (445)
T KOG1814|consen 182 NSLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCGSVAPPGQVKELVGDELFARYEKL 261 (445)
T ss_pred hhcccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCCcccCCchHHHHHHHHHHHHHHHHH
Confidence 35789999999998877777899999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhcC-CCCcccCccCCCceeeecCCCCCCcCcccCCCCChhhccccCCCCCCC------hH------------HHH
Q 045388 122 LSQELIDA-SQGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWHPG------RE------------ELM 182 (214)
Q Consensus 122 ~~~~~~~~-~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~h~~------~~------------~~~ 182 (214)
+.++.+.. .+.++||++.|....-.+++. ..+.|..|+..||..|+..||.. .+ |.+
T Consensus 262 ~lqk~l~~msdv~yCPr~~Cq~p~~~d~~~----~l~~CskCnFaFCtlCk~t~HG~s~Ck~~~~~~~~l~~~~~~~d~a 337 (445)
T KOG1814|consen 262 MLQKTLELMSDVVYCPRACCQLPVKQDPGR----ALAICSKCNFAFCTLCKLTWHGVSPCKVKAEKLIELYLEYLEADEA 337 (445)
T ss_pred HHHHHHHhhcccccCChhhccCccccCchh----hhhhhccCccHHHHHHHHhhcCCCcccCchHHHHHHHHHHhhcCHH
Confidence 99988876 678999999999998555443 67889999999999999999997 00 000
Q ss_pred H-----HH----------------HHHhCCCccCCCCCccceecCCCCCeecC
Q 045388 183 M-----RE----------------LVKKKQLRKCPNCKYHIERTGGCLHMTCL 214 (214)
Q Consensus 183 ~-----~~----------------~~~~~~~k~CP~C~~~iek~~GCnhm~C~ 214 (214)
- ++ -+-..+.|+||+|+++|+|.+|||||+|.
T Consensus 338 ~k~ele~Ryg~rvve~~vn~~lsekwl~~N~krCP~C~v~IEr~eGCnKM~C~ 390 (445)
T KOG1814|consen 338 RKRELEKRYGKRVVEELVNDFLSEKWLESNSKRCPKCKVVIERSEGCNKMHCT 390 (445)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHHHHHHHhcCCCCCcccceeecCCCccceeec
Confidence 0 00 01135779999999999999999999995
No 2
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.97 E-value=6.7e-32 Score=225.30 Aligned_cols=173 Identities=34% Similarity=0.829 Sum_probs=143.6
Q ss_pred CCCcccccccccccccc-cccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHhhcCCHHHHHH
Q 045388 39 SSPPSRSSCEICRERRE-NDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKSVLSKNVLEL 117 (214)
Q Consensus 39 ~~~~~~~~C~iC~~~~~-~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~~~l~~~~~~~ 117 (214)
+......+|.||+.+.+ .+.++....|+|.||.+|++.|++.+...+ ..++||..+|...+..+....+|++++.++
T Consensus 141 ~~~~~~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~~~~~--~~~~C~~~~C~~~l~~~~c~~llt~kl~e~ 218 (384)
T KOG1812|consen 141 PSKLPKEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVKLLSG--TVIRCPHDGCESRLTLESCRKLLTPKLREM 218 (384)
T ss_pred ccccccccCccCccccccHhhhHHHhcccchhhhHHhHHHhhhhhccC--CCccCCCCCCCccCCHHHHhhhcCHHHHHH
Confidence 34445789999995544 447777889999999999999999995444 489999999999999999999999999999
Q ss_pred HHHHHHHHHhcCCCCcccCccCCCceeeecCCCC-CCcCcccCCCCChhhccccCCCCCCChHHHHHH------------
Q 045388 118 WEKALSQELIDASQGIYCPFKDCSAKLVYENDGE-DVLSESECPYCHRLFCAHCYVPWHPGREELMMR------------ 184 (214)
Q Consensus 118 ~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~-~~~~~~~C~~C~~~~C~~C~~~~h~~~~~~~~~------------ 184 (214)
|+.++.+.++...+.+|||+|+|...+....... .......|+.|+..||..|+.+||++.....++
T Consensus 219 ~e~~~~e~~i~~~~~~ycp~~~C~~l~~~~el~~~~~~~~~~C~~C~~~fCv~C~~~wh~~~sC~eykk~~~~~~~d~~~ 298 (384)
T KOG1812|consen 219 WEQRLKEEVIPSLDRVYCPYPRCSSLMSKTELSSEVKSKRRPCVKCHELFCVKCKVPWHANLSCEEYKKLNPEEYVDDIT 298 (384)
T ss_pred HHHHHHHHhhhhhhcccCCCCCchHhhhhhhhccchhhcccccccCCCceeecCCCcCCCCCCHHHHHHhCCcccccHHH
Confidence 9999999999987777999999999988776421 233556799999999999999999982222222
Q ss_pred -HHHHhCCCccCCCCCccceecCCCCCeecC
Q 045388 185 -ELVKKKQLRKCPNCKYHIERTGGCLHMTCL 214 (214)
Q Consensus 185 -~~~~~~~~k~CP~C~~~iek~~GCnhm~C~ 214 (214)
.++. .+||+||+|+..|++++|||||+|+
T Consensus 299 ~~~la-~~wr~CpkC~~~ie~~~GCnhm~Cr 328 (384)
T KOG1812|consen 299 LKYLA-KRWRQCPKCKFMIELSEGCNHMTCR 328 (384)
T ss_pred HHHHH-HhcCcCcccceeeeecCCcceEEee
Confidence 2222 7899999999999999999999996
No 3
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=99.93 E-value=5e-26 Score=178.75 Aligned_cols=168 Identities=26% Similarity=0.571 Sum_probs=134.9
Q ss_pred CCCcccccccccccccccccccccCCCC--ccccHHHHHHHHHHHhhCCCc-------ccccCCCCCCCCcC-cHHHHhh
Q 045388 39 SSPPSRSSCEICRERRENDQMFKIESCI--HSFCSDCINKHVATKIQGGII-------TPVTCPGPDCKSVL-KFDACKS 108 (214)
Q Consensus 39 ~~~~~~~~C~iC~~~~~~~~~~~~~~C~--H~fC~~Cl~~~~~~~i~~~~~-------~~i~CP~~~C~~~l-~~~~~~~ 108 (214)
..+....+|..|.+.-.. ++ ..+|. |..|.+|++.|....+.+.++ +.+.||+ +|...| ..-+...
T Consensus 216 ~~N~~ni~C~~Ctdv~~~--vl-vf~Cns~HvtC~dCFr~yc~~Rl~~rqf~~~p~~gyslpc~a-gc~~s~i~e~HHF~ 291 (446)
T KOG0006|consen 216 ATNSRNITCITCTDVRSP--VL-VFQCNSRHVTCLDCFRLYCVTRLNDRQFVHDPQLGYSLPCVA-GCPNSLIKELHHFR 291 (446)
T ss_pred hcccccceeEEecCCccc--eE-EEecCCceeehHHhhhhHhhhcccccccccCccccccccccC-CCchHHHHhhhhhe
Confidence 345668899999885332 22 46787 999999999999999987764 6789987 677655 3334467
Q ss_pred cCCHHHHHHHHHHHHHHHhcCCCCcccCccCCCceeeecCCCCCCcCcccCCC-CChhhccccCCCCCCCh---------
Q 045388 109 VLSKNVLELWEKALSQELIDASQGIYCPFKDCSAKLVYENDGEDVLSESECPY-CHRLFCAHCYVPWHPGR--------- 178 (214)
Q Consensus 109 ~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~-C~~~~C~~C~~~~h~~~--------- 178 (214)
+|..+.|.+|+++..++.+...+.+.||.|+|+..+..+++. ..++|+. |+..||..|+..+|.+.
T Consensus 292 ilg~e~Y~rYQr~atEe~vlq~gGVlCP~pgCG~gll~EPD~----rkvtC~~gCgf~FCR~C~e~yh~geC~~~~~as~ 367 (446)
T KOG0006|consen 292 ILGEEQYNRYQRYATEECVLQMGGVLCPRPGCGAGLLPEPDQ----RKVTCEGGCGFAFCRECKEAYHEGECSAVFEASG 367 (446)
T ss_pred ecchhHHHHHHHhhhhhheeecCCEecCCCCCCcccccCCCC----CcccCCCCchhHhHHHHHhhhccccceeeecccc
Confidence 899999999999999999999999999999999999988765 7889986 99999999999999980
Q ss_pred -------HHHHHH---HH------HHhCCCccCCCCCccceecCCCCCeecC
Q 045388 179 -------EELMMR---EL------VKKKQLRKCPNCKYHIERTGGCLHMTCL 214 (214)
Q Consensus 179 -------~~~~~~---~~------~~~~~~k~CP~C~~~iek~~GCnhm~C~ 214 (214)
.|.... .| .....+|+||+|.++.||+|||.||.|+
T Consensus 368 t~tc~y~vde~~a~~arwd~as~~TIk~tTkpCPkChvptErnGGCmHm~Ct 419 (446)
T KOG0006|consen 368 TTTCAYRVDERAAEQARWDAASKETIKKTTKPCPKCHVPTERNGGCMHMKCT 419 (446)
T ss_pred ccceeeecChhhhhhhhhhhhhhhhhhhccCCCCCccCccccCCceEEeecC
Confidence 011111 11 1235679999999999999999999996
No 4
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.92 E-value=5.7e-25 Score=188.19 Aligned_cols=168 Identities=25% Similarity=0.533 Sum_probs=138.3
Q ss_pred CcccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHhhcCCH-HHHHHHH
Q 045388 41 PPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKSVLSK-NVLELWE 119 (214)
Q Consensus 41 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~~~l~~-~~~~~~~ 119 (214)
.....+|+||++.++. . ...+.|+|.||..||..|+..+|.++....|+||..+|...+..+.|..++++ +..++|.
T Consensus 67 ~~~~~~c~ic~~~~~~-~-~~~~~c~H~~c~~cw~~yl~~kI~~~~~~~i~cp~~~C~a~v~~~~i~~~~s~~~~~~ky~ 144 (444)
T KOG1815|consen 67 KKGDVQCGICVESYDG-E-IIGLGCGHPFCPPCWTGYLGTKIHEGEEAKIKCPAHGCPALVGEDTVEKLVSDKEDKEKYQ 144 (444)
T ss_pred CCccccCCcccCCCcc-h-hhhcCCCcHHHHHHHHHHhhheeeccccccccCCCCCccccCCCceeeeecCCHHHHHHHH
Confidence 3456899999999876 3 33689999999999999999999988744499999999999999999999888 5999999
Q ss_pred HHHHHHHhcCC-CCcccCccCCCceeeecCCCCCCcCcccCCCCChhhccccCCCCCCChHHHHHHHH------------
Q 045388 120 KALSQELIDAS-QGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWHPGREELMMREL------------ 186 (214)
Q Consensus 120 ~~~~~~~~~~~-~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~h~~~~~~~~~~~------------ 186 (214)
+.+.++++..+ ...|||+|+|+..+.... .....+.| .|++.||+.|..+||.+........|
T Consensus 145 ~~i~~syve~~~~lkwCP~~~C~~av~~~~---~~~~~v~C-~~g~~FC~~C~~~~H~p~~C~~~~~wl~k~~~~se~~~ 220 (444)
T KOG1815|consen 145 RYILRSYVEDNVPLKWCPAPGCGLAVKFGS---LESVEVDC-GCGHEFCFACGEESHSPVSCPGAKKWLKKCRDDSETIN 220 (444)
T ss_pred HHHHHHHHhcCCccccCCCCCCCceeeccC---CCccceeC-CCCchhHhhccccccCCCcccchHHHHHhhhhhhhhhh
Confidence 99999999874 568999999999887631 22477889 57779999999999999322211111
Q ss_pred HHhCCCccCCCCCccceecCCCCCeecC
Q 045388 187 VKKKQLRKCPNCKYHIERTGGCLHMTCL 214 (214)
Q Consensus 187 ~~~~~~k~CP~C~~~iek~~GCnhm~C~ 214 (214)
+...++++||+|.++|+|++|||||+|.
T Consensus 221 wi~~ntk~CP~c~~~iek~~gc~~~~~~ 248 (444)
T KOG1815|consen 221 WILANTKECPKCKVPIEKDGGCNHMTCK 248 (444)
T ss_pred hhhccCccCCCcccchhccCCccccccc
Confidence 2356789999999999999999999884
No 5
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=99.23 E-value=1.5e-11 Score=77.37 Aligned_cols=60 Identities=32% Similarity=0.785 Sum_probs=50.8
Q ss_pred HHHHHHHHHHHhcC-CCCcccCccCCCceeeecCCCCCCcCcccCCCCChhhccccCCCCCCC
Q 045388 116 ELWEKALSQELIDA-SQGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWHPG 177 (214)
Q Consensus 116 ~~~~~~~~~~~~~~-~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~h~~ 177 (214)
++|++++.++++.. .+.+|||+|+|+.++...+. .....+.|+.|+..||+.|+.+||.+
T Consensus 1 ~~y~~~~~~~~i~~~~~~~~CP~~~C~~~~~~~~~--~~~~~v~C~~C~~~fC~~C~~~~H~~ 61 (64)
T smart00647 1 EKYERLLLESYVESNPDLKWCPAPDCSAAIIVTEE--EGCNRVTCPKCGFSFCFRCKVPWHSP 61 (64)
T ss_pred ChHHHHHHHHHHhcCCCccCCCCCCCcceEEecCC--CCCCeeECCCCCCeECCCCCCcCCCC
Confidence 47888888888887 57889999999999988741 12378899999999999999999987
No 6
>PF01485 IBR: IBR domain; InterPro: IPR002867 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 cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=99.16 E-value=6.7e-12 Score=79.01 Aligned_cols=60 Identities=28% Similarity=0.679 Sum_probs=39.2
Q ss_pred HHHHHHHHHHHhcC-CCCcccCccCCCceeeecCCCCCCcCcccCCCCChhhccccCCCCCCC
Q 045388 116 ELWEKALSQELIDA-SQGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWHPG 177 (214)
Q Consensus 116 ~~~~~~~~~~~~~~-~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~h~~ 177 (214)
++|++++.+.++.. .+.+|||+|+|+.++..++... ...+.|+.|+..||+.|+.+||.+
T Consensus 1 eky~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~--~~~~~C~~C~~~fC~~C~~~~H~~ 61 (64)
T PF01485_consen 1 EKYQKFLLKRYLESDPNIRWCPNPDCEYIIEKDDGCN--SPIVTCPSCGTEFCFKCGEPWHEG 61 (64)
T ss_dssp HCHHHCCCHS---S---CC--TTSST---ECS-SSTT--S--CCTTSCCSEECSSSTSESCTT
T ss_pred ChHHHHHHHHHHHCCCCccCCCCCCCcccEEecCCCC--CCeeECCCCCCcCccccCcccCCC
Confidence 45777777777765 4668999999999999988741 124899999999999999999987
No 7
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.77 E-value=2.2e-09 Score=61.36 Aligned_cols=41 Identities=27% Similarity=0.666 Sum_probs=28.5
Q ss_pred ccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCC
Q 045388 47 CEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPG 94 (214)
Q Consensus 47 C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~ 94 (214)
|+||++.+..+. .+.|||+||..||..++...-. ..+.||.
T Consensus 1 CpiC~~~~~~Pv---~l~CGH~FC~~Cl~~~~~~~~~----~~~~CP~ 41 (42)
T PF15227_consen 1 CPICLDLFKDPV---SLPCGHSFCRSCLERLWKEPSG----SGFSCPE 41 (42)
T ss_dssp ETTTTSB-SSEE---E-SSSSEEEHHHHHHHHCCSSS----ST---SS
T ss_pred CCccchhhCCcc---ccCCcCHHHHHHHHHHHHccCC----cCCCCcC
Confidence 899999988765 5899999999999999854321 2378987
No 8
>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=98.74 E-value=5.2e-09 Score=60.64 Aligned_cols=41 Identities=29% Similarity=0.628 Sum_probs=33.0
Q ss_pred cccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCC
Q 045388 46 SCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPG 94 (214)
Q Consensus 46 ~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~ 94 (214)
+|+||++++...+.+..+.|+|.||.+||..|++.. .+||.
T Consensus 2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~--------~~CP~ 42 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRN--------NSCPV 42 (44)
T ss_dssp CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHS--------SB-TT
T ss_pred CCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhC--------CcCCc
Confidence 699999999765555567899999999999999652 27887
No 9
>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=98.66 E-value=2e-08 Score=57.19 Aligned_cols=40 Identities=40% Similarity=0.842 Sum_probs=33.2
Q ss_pred ccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCC
Q 045388 47 CEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPG 94 (214)
Q Consensus 47 C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~ 94 (214)
|+||++.+..+. ..++|+|.||..||.+|+.. . ..++||.
T Consensus 1 C~iC~~~~~~~~--~~~~C~H~fC~~C~~~~~~~---~---~~~~CP~ 40 (41)
T PF00097_consen 1 CPICLEPFEDPV--ILLPCGHSFCRDCLRKWLEN---S---GSVKCPL 40 (41)
T ss_dssp ETTTSSBCSSEE--EETTTSEEEEHHHHHHHHHH---T---SSSBTTT
T ss_pred CCcCCccccCCC--EEecCCCcchHHHHHHHHHh---c---CCccCCc
Confidence 899999887665 25899999999999999987 2 3567987
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=98.59 E-value=2.6e-08 Score=56.13 Aligned_cols=38 Identities=34% Similarity=0.859 Sum_probs=29.1
Q ss_pred ccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCC
Q 045388 47 CEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPG 94 (214)
Q Consensus 47 C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~ 94 (214)
|+||++.+..+. ..+.|||.||.+||..|++.. .+||.
T Consensus 1 C~iC~~~~~~~~--~~~~CGH~fC~~C~~~~~~~~--------~~CP~ 38 (39)
T PF13923_consen 1 CPICLDELRDPV--VVTPCGHSFCKECIEKYLEKN--------PKCPV 38 (39)
T ss_dssp ETTTTSB-SSEE--EECTTSEEEEHHHHHHHHHCT--------SB-TT
T ss_pred CCCCCCcccCcC--EECCCCCchhHHHHHHHHHCc--------CCCcC
Confidence 899999887642 268999999999999998742 47876
No 11
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.56 E-value=4.7e-08 Score=73.60 Aligned_cols=63 Identities=25% Similarity=0.517 Sum_probs=47.2
Q ss_pred ccccccccccccccccccccCCCCccccHHHHHHHHHHHhh---------CCCcccccCCCCCCCCcCcHHHHhhcCC
Q 045388 43 SRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQ---------GGIITPVTCPGPDCKSVLKFDACKSVLS 111 (214)
Q Consensus 43 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~---------~~~~~~i~CP~~~C~~~l~~~~~~~~l~ 111 (214)
+.++|+||++.+..+. .+.|+|.||..||..|+...-. ... ...+||. |...+....+..+..
T Consensus 17 ~~~~CpICld~~~dPV---vT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k-~~~~CPv--CR~~Is~~~LvPiyg 88 (193)
T PLN03208 17 GDFDCNICLDQVRDPV---VTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKR-EPPKCPV--CKSDVSEATLVPIYG 88 (193)
T ss_pred CccCCccCCCcCCCcE---EcCCCchhHHHHHHHHHHhccccccccccccccC-CCCcCCC--CCCcCChhcEEEeec
Confidence 4689999999876553 4689999999999999764321 112 4679999 999998777666543
No 12
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.53 E-value=6.1e-08 Score=56.09 Aligned_cols=43 Identities=35% Similarity=0.851 Sum_probs=35.3
Q ss_pred cccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCC
Q 045388 46 SCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCK 98 (214)
Q Consensus 46 ~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~ 98 (214)
.|++|++.+.....+.+++|||.||..|+.... . ..+.||. |+
T Consensus 1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~-------~-~~~~CP~--C~ 43 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLK-------G-KSVKCPI--CR 43 (44)
T ss_pred CCcCcCccccCCCCeEEcccCCHHHHHHHHhhc-------C-CCCCCcC--CC
Confidence 489999999555556689999999999999987 2 4689998 64
No 13
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.48 E-value=1.2e-07 Score=69.85 Aligned_cols=59 Identities=24% Similarity=0.602 Sum_probs=43.8
Q ss_pred CCCCcccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHh
Q 045388 38 PSSPPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACK 107 (214)
Q Consensus 38 ~~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~ 107 (214)
+..+...+.|+||++.+.....+ ...|||.||..|++.-+. ..-+||. |...+...++.
T Consensus 125 ~~~~~~~~~CPiCl~~~sek~~v-sTkCGHvFC~~Cik~alk--------~~~~CP~--C~kkIt~k~~~ 183 (187)
T KOG0320|consen 125 PLRKEGTYKCPICLDSVSEKVPV-STKCGHVFCSQCIKDALK--------NTNKCPT--CRKKITHKQFH 183 (187)
T ss_pred ccccccccCCCceecchhhcccc-ccccchhHHHHHHHHHHH--------hCCCCCC--cccccchhhhe
Confidence 33445678999999999876544 479999999999988765 2458999 66566555443
No 14
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.43 E-value=1.6e-07 Score=53.67 Aligned_cols=42 Identities=31% Similarity=0.714 Sum_probs=22.5
Q ss_pred cccccccccc-ccccccCCCCccccHHHHHHHHHHHhhCCCcccccCC
Q 045388 47 CEICRERREN-DQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCP 93 (214)
Q Consensus 47 C~iC~~~~~~-~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP 93 (214)
|+||.+ +.. ......+.|||.||++|+.++..... . ..++||
T Consensus 1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~~---~-~~~kCP 43 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKSD---R-NRFKCP 43 (43)
T ss_dssp -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH-S-----S-B--T
T ss_pred CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcCC---C-CeeeCc
Confidence 899999 644 33334688999999999999987543 1 367887
No 15
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=98.37 E-value=3.9e-07 Score=52.42 Aligned_cols=44 Identities=34% Similarity=0.788 Sum_probs=33.2
Q ss_pred cccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCc
Q 045388 46 SCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSV 100 (214)
Q Consensus 46 ~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~ 100 (214)
+|+||++.+.. .+....|+|.||..|+..|+.. ...+||. |+..
T Consensus 1 ~C~iC~~~~~~--~~~~~~C~H~~c~~C~~~~~~~-------~~~~Cp~--C~~~ 44 (45)
T cd00162 1 ECPICLEEFRE--PVVLLPCGHVFCRSCIDKWLKS-------GKNTCPL--CRTP 44 (45)
T ss_pred CCCcCchhhhC--ceEecCCCChhcHHHHHHHHHh-------CcCCCCC--CCCc
Confidence 58999998733 2335669999999999999875 2457998 7654
No 16
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.25 E-value=3.7e-07 Score=70.12 Aligned_cols=60 Identities=23% Similarity=0.563 Sum_probs=46.4
Q ss_pred CcccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHhhcC
Q 045388 41 PPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKSVL 110 (214)
Q Consensus 41 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~~~l 110 (214)
+...++|.||+|....+. +.-|||-||+.||.+|+..+... -.||. |+..+..+.|-.|.
T Consensus 44 ~~~~FdCNICLd~akdPV---vTlCGHLFCWpClyqWl~~~~~~-----~~cPV--CK~~Vs~~~vvPlY 103 (230)
T KOG0823|consen 44 DGGFFDCNICLDLAKDPV---VTLCGHLFCWPCLYQWLQTRPNS-----KECPV--CKAEVSIDTVVPLY 103 (230)
T ss_pred CCCceeeeeeccccCCCE---EeecccceehHHHHHHHhhcCCC-----eeCCc--cccccccceEEeee
Confidence 567899999999866553 46799999999999999776542 35899 88877776665443
No 17
>PHA02926 zinc finger-like protein; Provisional
Probab=98.21 E-value=1.3e-06 Score=66.87 Aligned_cols=55 Identities=33% Similarity=0.680 Sum_probs=39.7
Q ss_pred cccccccccccccc-----cc-ccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcC
Q 045388 43 SRSSCEICRERREN-----DQ-MFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVL 101 (214)
Q Consensus 43 ~~~~C~iC~~~~~~-----~~-~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 101 (214)
+..+|+||++.... +. +..+.+|+|.||..|++.|.......|. .-.||. |...+
T Consensus 169 kE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~--~rsCPi--CR~~f 229 (242)
T PHA02926 169 KEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGA--SDNCPI--CRTRF 229 (242)
T ss_pred CCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCc--CCcCCC--Cccee
Confidence 45899999998632 11 2226799999999999999986543332 458999 87654
No 18
>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=98.21 E-value=1.1e-06 Score=52.28 Aligned_cols=46 Identities=26% Similarity=0.722 Sum_probs=34.9
Q ss_pred cccccccccccccccccccCCCCcc-ccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCc
Q 045388 44 RSSCEICRERRENDQMFKIESCIHS-FCSDCINKHVATKIQGGIITPVTCPGPDCKSVLK 102 (214)
Q Consensus 44 ~~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 102 (214)
...|.||++..... ...+|+|. ||..|+..++. ...+||. |...+.
T Consensus 2 ~~~C~iC~~~~~~~---~~~pCgH~~~C~~C~~~~~~--------~~~~CP~--Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFENPRDV---VLLPCGHLCFCEECAERLLK--------RKKKCPI--CRQPIE 48 (50)
T ss_dssp HSB-TTTSSSBSSE---EEETTCEEEEEHHHHHHHHH--------TTSBBTT--TTBB-S
T ss_pred cCCCccCCccCCce---EEeCCCChHHHHHHhHHhcc--------cCCCCCc--CChhhc
Confidence 46899999985442 25799999 99999999987 2468999 887653
No 19
>PHA02929 N1R/p28-like protein; Provisional
Probab=98.16 E-value=3.6e-06 Score=66.12 Aligned_cols=50 Identities=28% Similarity=0.720 Sum_probs=37.5
Q ss_pred cccccccccccccccccc-----cccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcC
Q 045388 42 PSRSSCEICRERRENDQM-----FKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVL 101 (214)
Q Consensus 42 ~~~~~C~iC~~~~~~~~~-----~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 101 (214)
....+|+||++.+..+.. ....+|+|.||.+|+..|+.. ...||. |...+
T Consensus 172 ~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~--------~~tCPl--CR~~~ 226 (238)
T PHA02929 172 SKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKE--------KNTCPV--CRTPF 226 (238)
T ss_pred CCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhc--------CCCCCC--CCCEe
Confidence 346899999998765431 235689999999999999752 247999 87655
No 20
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=98.09 E-value=1.8e-06 Score=68.37 Aligned_cols=53 Identities=30% Similarity=0.714 Sum_probs=41.7
Q ss_pred CcccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHH
Q 045388 41 PPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDAC 106 (214)
Q Consensus 41 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~ 106 (214)
......|.+|++....+. .++|||.||..|+.+|..++- .||. |...+.+..+
T Consensus 236 ~~a~~kC~LCLe~~~~pS---aTpCGHiFCWsCI~~w~~ek~--------eCPl--CR~~~~pskv 288 (293)
T KOG0317|consen 236 PEATRKCSLCLENRSNPS---ATPCGHIFCWSCILEWCSEKA--------ECPL--CREKFQPSKV 288 (293)
T ss_pred CCCCCceEEEecCCCCCC---cCcCcchHHHHHHHHHHcccc--------CCCc--ccccCCCcce
Confidence 344688999999876655 689999999999999986433 3999 8877766544
No 21
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.03 E-value=2.6e-06 Score=69.68 Aligned_cols=46 Identities=28% Similarity=0.772 Sum_probs=39.0
Q ss_pred CcccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCC
Q 045388 41 PPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKS 99 (214)
Q Consensus 41 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~ 99 (214)
..+..+|+||++.+..+ ..++|+|.||..|+..++. ..+.||. |..
T Consensus 10 ~~~~~~C~iC~~~~~~p---~~l~C~H~~c~~C~~~~~~--------~~~~Cp~--cr~ 55 (386)
T KOG2177|consen 10 LQEELTCPICLEYFREP---VLLPCGHNFCRACLTRSWE--------GPLSCPV--CRP 55 (386)
T ss_pred ccccccChhhHHHhhcC---ccccccchHhHHHHHHhcC--------CCcCCcc--cCC
Confidence 44678999999999887 3689999999999999987 3589999 763
No 22
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.00 E-value=2.4e-06 Score=72.64 Aligned_cols=60 Identities=27% Similarity=0.534 Sum_probs=47.5
Q ss_pred cccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHhhcCC
Q 045388 44 RSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKSVLS 111 (214)
Q Consensus 44 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~~~l~ 111 (214)
...|+||++..+.+. .+.|||.||..||-.|+...... ...+||. |...+.+.+++.+.-
T Consensus 186 ~~~CPICL~~~~~p~---~t~CGHiFC~~CiLqy~~~s~~~---~~~~CPi--C~s~I~~kdl~pv~~ 245 (513)
T KOG2164|consen 186 DMQCPICLEPPSVPV---RTNCGHIFCGPCILQYWNYSAIK---GPCSCPI--CRSTITLKDLLPVFI 245 (513)
T ss_pred CCcCCcccCCCCccc---ccccCceeeHHHHHHHHhhhccc---CCccCCc--hhhhccccceeeeee
Confidence 678999999876655 45699999999999999876221 4579999 988888877766543
No 23
>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=97.98 E-value=5.8e-06 Score=45.72 Aligned_cols=38 Identities=37% Similarity=0.797 Sum_probs=28.5
Q ss_pred ccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCC
Q 045388 47 CEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPG 94 (214)
Q Consensus 47 C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~ 94 (214)
|+||++.... ...+.|+|.||..|+..|+. . ...+||.
T Consensus 1 C~iC~~~~~~---~~~~~C~H~~c~~C~~~~~~----~---~~~~CP~ 38 (39)
T smart00184 1 CPICLEELKD---PVVLPCGHTFCRSCIRKWLK----S---GNNTCPI 38 (39)
T ss_pred CCcCccCCCC---cEEecCCChHHHHHHHHHHH----h---CcCCCCC
Confidence 7899987332 23578999999999999987 1 2356876
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=97.91 E-value=1.3e-05 Score=49.92 Aligned_cols=51 Identities=18% Similarity=0.131 Sum_probs=40.0
Q ss_pred ccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHhh
Q 045388 45 SSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKS 108 (214)
Q Consensus 45 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~~ 108 (214)
+.|+||++.+..+. ...|||.||+.|+..|+.. ...||. |+..+..+++..
T Consensus 2 ~~Cpi~~~~~~~Pv---~~~~G~v~~~~~i~~~~~~--------~~~cP~--~~~~~~~~~l~~ 52 (63)
T smart00504 2 FLCPISLEVMKDPV---ILPSGQTYERRAIEKWLLS--------HGTDPV--TGQPLTHEDLIP 52 (63)
T ss_pred cCCcCCCCcCCCCE---ECCCCCEEeHHHHHHHHHH--------CCCCCC--CcCCCChhhcee
Confidence 57999999887653 4689999999999999975 136999 777776655443
No 25
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.90 E-value=1.1e-05 Score=67.85 Aligned_cols=66 Identities=24% Similarity=0.582 Sum_probs=47.5
Q ss_pred cccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHH-hhcCCHHHHHHHHH
Q 045388 42 PSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDAC-KSVLSKNVLELWEK 120 (214)
Q Consensus 42 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~-~~~l~~~~~~~~~~ 120 (214)
...+.|+||++.+..+. .+.|+|.||..|+..|+.. ...||. |...+....+ .+.+..++++.|..
T Consensus 24 e~~l~C~IC~d~~~~Pv---itpCgH~FCs~CI~~~l~~--------~~~CP~--Cr~~~~~~~Lr~N~~L~~iVe~~~~ 90 (397)
T TIGR00599 24 DTSLRCHICKDFFDVPV---LTSCSHTFCSLCIRRCLSN--------QPKCPL--CRAEDQESKLRSNWLVSEIVESFKN 90 (397)
T ss_pred ccccCCCcCchhhhCcc---CCCCCCchhHHHHHHHHhC--------CCCCCC--CCCccccccCccchHHHHHHHHHHH
Confidence 35689999999887653 5799999999999999853 137998 8877765433 33444556666643
No 26
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.83 E-value=1.8e-05 Score=65.11 Aligned_cols=46 Identities=33% Similarity=0.772 Sum_probs=39.6
Q ss_pred ccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCC
Q 045388 45 SSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKS 99 (214)
Q Consensus 45 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~ 99 (214)
.+|.||+|+|...+-...++|.|.|...|+..|+... +. .||. |+.
T Consensus 230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~---r~----~CPv--CK~ 275 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQT---RT----FCPV--CKR 275 (348)
T ss_pred ceEEEeecccccCCeeeEecCCCchhhccchhhHhhc---Cc----cCCC--CCC
Confidence 6999999999988888889999999999999999754 22 5999 554
No 27
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=97.73 E-value=2e-05 Score=63.82 Aligned_cols=65 Identities=25% Similarity=0.497 Sum_probs=51.2
Q ss_pred ccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHh-hcCCHHHHHHHHH
Q 045388 43 SRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACK-SVLSKNVLELWEK 120 (214)
Q Consensus 43 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~-~~l~~~~~~~~~~ 120 (214)
....|.||++-|..+- ..+|+|.||.-||+.|+. +...||. |...+...+++ +.+..++++.|.-
T Consensus 22 ~lLRC~IC~eyf~ip~---itpCsHtfCSlCIR~~L~--------~~p~CP~--C~~~~~Es~Lr~n~il~Eiv~S~~~ 87 (442)
T KOG0287|consen 22 DLLRCGICFEYFNIPM---ITPCSHTFCSLCIRKFLS--------YKPQCPT--CCVTVTESDLRNNRILDEIVKSLNF 87 (442)
T ss_pred HHHHHhHHHHHhcCce---eccccchHHHHHHHHHhc--------cCCCCCc--eecccchhhhhhhhHHHHHHHHHHH
Confidence 4678999999987764 467999999999999986 4567998 98888777775 4556777777754
No 28
>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=97.72 E-value=6.8e-05 Score=60.81 Aligned_cols=53 Identities=23% Similarity=0.682 Sum_probs=38.0
Q ss_pred ccccccccccc-cccc--cccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHh
Q 045388 45 SSCEICRERRE-NDQM--FKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACK 107 (214)
Q Consensus 45 ~~C~iC~~~~~-~~~~--~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~ 107 (214)
..||+|..+.. .+++ +.. .|||.||..|+...+. .+ +..||. |+..+....++
T Consensus 4 ~~CP~Ck~~~y~np~~kl~i~-~CGH~~C~sCv~~l~~----~~---~~~CP~--C~~~lrk~~fr 59 (309)
T TIGR00570 4 QGCPRCKTTKYRNPSLKLMVN-VCGHTLCESCVDLLFV----RG---SGSCPE--CDTPLRKNNFR 59 (309)
T ss_pred CCCCcCCCCCccCcccccccC-CCCCcccHHHHHHHhc----CC---CCCCCC--CCCccchhhcc
Confidence 57999999733 3332 222 8999999999999863 22 358997 98877766544
No 29
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.63 E-value=2.8e-05 Score=62.07 Aligned_cols=52 Identities=21% Similarity=0.572 Sum_probs=43.1
Q ss_pred ccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcH
Q 045388 43 SRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKF 103 (214)
Q Consensus 43 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~ 103 (214)
...+|.||++++...+-+..++|.|.|...|+.+|+.. +...||. |...+++
T Consensus 322 ~GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~-------y~~~CPv--Crt~iPP 373 (374)
T COG5540 322 KGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLG-------YSNKCPV--CRTAIPP 373 (374)
T ss_pred CCceEEEEhhhhcccceEEEeccCceechhHHHHHHhh-------hcccCCc--cCCCCCC
Confidence 34899999999976666668999999999999999852 4678999 8877753
No 30
>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=97.35 E-value=0.00013 Score=46.94 Aligned_cols=42 Identities=33% Similarity=0.620 Sum_probs=29.4
Q ss_pred ccccccccccccc----------cccccCCCCccccHHHHHHHHHHHhhCCCcccccCCC
Q 045388 45 SSCEICRERREND----------QMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPG 94 (214)
Q Consensus 45 ~~C~iC~~~~~~~----------~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~ 94 (214)
..|.||++.+... -.+....|+|.|...||..|+.. .-.||.
T Consensus 20 d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~--------~~~CP~ 71 (73)
T PF12678_consen 20 DNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQ--------NNTCPL 71 (73)
T ss_dssp SBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTT--------SSB-TT
T ss_pred CcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhc--------CCcCCC
Confidence 3499999998321 11224589999999999999842 227888
No 31
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=97.33 E-value=0.00015 Score=62.12 Aligned_cols=62 Identities=31% Similarity=0.675 Sum_probs=46.2
Q ss_pred CCCCCCcccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHH
Q 045388 36 ASPSSPPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDA 105 (214)
Q Consensus 36 ~~~~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~ 105 (214)
.....+.....|++|-+.-.. .+ ...|-|.||+-|+..|+.....+. .+.||. |...|..++
T Consensus 528 n~~~enk~~~~C~lc~d~aed--~i-~s~ChH~FCrlCi~eyv~~f~~~~---nvtCP~--C~i~LsiDl 589 (791)
T KOG1002|consen 528 NLPDENKGEVECGLCHDPAED--YI-ESSCHHKFCRLCIKEYVESFMENN---NVTCPV--CHIGLSIDL 589 (791)
T ss_pred CCCccccCceeecccCChhhh--hH-hhhhhHHHHHHHHHHHHHhhhccc---CCCCcc--ccccccccc
Confidence 345556678999999886433 22 479999999999999998766543 389999 877666553
No 32
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=97.28 E-value=0.00014 Score=46.37 Aligned_cols=58 Identities=22% Similarity=0.445 Sum_probs=27.5
Q ss_pred cccccccccccc-cccc---cc-cCCCCccccHHHHHHHHHHHhhCCCcc-c--ccCCCCCCCCcCcH
Q 045388 44 RSSCEICRERRE-NDQM---FK-IESCIHSFCSDCINKHVATKIQGGIIT-P--VTCPGPDCKSVLKF 103 (214)
Q Consensus 44 ~~~C~iC~~~~~-~~~~---~~-~~~C~H~fC~~Cl~~~~~~~i~~~~~~-~--i~CP~~~C~~~l~~ 103 (214)
..+|+||++.+. .... +. ...|+..|...||..|+...-.....+ + =.||. |...|..
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~--C~~~i~~ 67 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPY--CSSPISW 67 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TT--T-SEEEG
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcC--CCCeeeE
Confidence 468999999865 2222 11 358899999999999998766554322 2 26999 8877653
No 33
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=97.24 E-value=0.0001 Score=65.72 Aligned_cols=55 Identities=24% Similarity=0.705 Sum_probs=42.8
Q ss_pred ccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHhhc
Q 045388 43 SRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKSV 109 (214)
Q Consensus 43 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~~~ 109 (214)
...+|++|.+... +++ ...|+|.||.+|++..+...- =+||. |+..|+..+|..+
T Consensus 642 ~~LkCs~Cn~R~K--d~v-I~kC~H~FC~~Cvq~r~etRq-------RKCP~--Cn~aFganDv~~I 696 (698)
T KOG0978|consen 642 ELLKCSVCNTRWK--DAV-ITKCGHVFCEECVQTRYETRQ-------RKCPK--CNAAFGANDVHRI 696 (698)
T ss_pred hceeCCCccCchh--hHH-HHhcchHHHHHHHHHHHHHhc-------CCCCC--CCCCCCccccccc
Confidence 4678999985432 222 579999999999999987543 37998 9999998888754
No 34
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=97.04 E-value=0.00052 Score=41.73 Aligned_cols=49 Identities=24% Similarity=0.425 Sum_probs=31.7
Q ss_pred cccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCC
Q 045388 42 PSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCK 98 (214)
Q Consensus 42 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~ 98 (214)
...+.|+|-+..+..+- ....|+|.|-++-+..|+ + +. ..+.||..||.
T Consensus 9 ~~~~~CPiT~~~~~~PV--~s~~C~H~fek~aI~~~i----~-~~-~~~~CPv~GC~ 57 (57)
T PF11789_consen 9 TISLKCPITLQPFEDPV--KSKKCGHTFEKEAILQYI----Q-RN-GSKRCPVAGCN 57 (57)
T ss_dssp B--SB-TTTSSB-SSEE--EESSS--EEEHHHHHHHC----T-TT-S-EE-SCCC-S
T ss_pred EeccCCCCcCChhhCCc--CcCCCCCeecHHHHHHHH----H-hc-CCCCCCCCCCC
Confidence 34689999999887653 356999999999999999 2 22 47899998884
No 35
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.96 E-value=0.00066 Score=53.42 Aligned_cols=52 Identities=23% Similarity=0.481 Sum_probs=38.2
Q ss_pred ccccccccccccccccccccCCCCccccHHHHHH-HHHHHhhCCCcccccCCCCCCCCcCcHHHH
Q 045388 43 SRSSCEICRERRENDQMFKIESCIHSFCSDCINK-HVATKIQGGIITPVTCPGPDCKSVLKFDAC 106 (214)
Q Consensus 43 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~-~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~ 106 (214)
..+.|.||++....+ ..+.|||.||..||-. |-.. ..-.||. |.....+..+
T Consensus 214 ~d~kC~lC~e~~~~p---s~t~CgHlFC~~Cl~~~~t~~-------k~~~Cpl--CRak~~pk~v 266 (271)
T COG5574 214 ADYKCFLCLEEPEVP---SCTPCGHLFCLSCLLISWTKK-------KYEFCPL--CRAKVYPKKV 266 (271)
T ss_pred cccceeeeecccCCc---ccccccchhhHHHHHHHHHhh-------ccccCch--hhhhccchhh
Confidence 456799999975544 3689999999999998 4332 2346999 8876666655
No 36
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=96.80 E-value=0.0033 Score=51.87 Aligned_cols=54 Identities=26% Similarity=0.534 Sum_probs=39.3
Q ss_pred Cccccccccccccccccc----------ccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHH
Q 045388 41 PPSRSSCEICRERRENDQ----------MFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFD 104 (214)
Q Consensus 41 ~~~~~~C~iC~~~~~~~~----------~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~ 104 (214)
......|.||+|+.-.++ -+..++|||.+...|++.|++. .=.||. |..++-.+
T Consensus 284 ~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ER--------qQTCPI--Cr~p~ifd 347 (491)
T COG5243 284 TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLER--------QQTCPI--CRRPVIFD 347 (491)
T ss_pred cCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHh--------ccCCCc--ccCccccc
Confidence 455689999999942211 2237899999999999999873 237999 87765433
No 37
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.78 E-value=0.0012 Score=54.81 Aligned_cols=56 Identities=30% Similarity=0.612 Sum_probs=40.5
Q ss_pred Cccccccccccccccccc-----ccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCC
Q 045388 41 PPSRSSCEICRERRENDQ-----MFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKS 99 (214)
Q Consensus 41 ~~~~~~C~iC~~~~~~~~-----~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~ 99 (214)
..+..+|+||++...... +-.+..|.|.||..|++.|-...-.+.. ..-.||+ |..
T Consensus 158 ~s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~-~sksCP~--CRv 218 (344)
T KOG1039|consen 158 KSSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESK-TSKSCPF--CRV 218 (344)
T ss_pred ccccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccc-cccCCCc--ccC
Confidence 356789999999986654 3235789999999999999744332222 3568999 654
No 38
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=96.69 E-value=0.00023 Score=43.77 Aligned_cols=49 Identities=27% Similarity=0.622 Sum_probs=23.0
Q ss_pred ccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHH
Q 045388 43 SRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDA 105 (214)
Q Consensus 43 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~ 105 (214)
+...|.+|.+.+..+. .+..|.|.||..|+...+ .-.||. |..+--..+
T Consensus 6 ~lLrCs~C~~~l~~pv--~l~~CeH~fCs~Ci~~~~----------~~~CPv--C~~Paw~qD 54 (65)
T PF14835_consen 6 ELLRCSICFDILKEPV--CLGGCEHIFCSSCIRDCI----------GSECPV--CHTPAWIQD 54 (65)
T ss_dssp HTTS-SSS-S--SS-B-----SSS--B-TTTGGGGT----------TTB-SS--S--B-S-SS
T ss_pred HhcCCcHHHHHhcCCc--eeccCccHHHHHHhHHhc----------CCCCCC--cCChHHHHH
Confidence 3567999999876653 357999999999986643 124999 775443333
No 39
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=96.51 E-value=0.0019 Score=51.57 Aligned_cols=65 Identities=31% Similarity=0.493 Sum_probs=45.7
Q ss_pred cccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHh-hcCCHHHHHHHH
Q 045388 42 PSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACK-SVLSKNVLELWE 119 (214)
Q Consensus 42 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~-~~l~~~~~~~~~ 119 (214)
.....|-||-+-+..+- ...|||.||.-||+.|+.+ ...||. |........++ ..+..++.+.|.
T Consensus 23 Ds~lrC~IC~~~i~ip~---~TtCgHtFCslCIR~hL~~--------qp~CP~--Cr~~~~esrlr~~s~~~ei~es~~ 88 (391)
T COG5432 23 DSMLRCRICDCRISIPC---ETTCGHTFCSLCIRRHLGT--------QPFCPV--CREDPCESRLRGSSGSREINESHA 88 (391)
T ss_pred hhHHHhhhhhheeecce---ecccccchhHHHHHHHhcC--------CCCCcc--ccccHHhhhcccchhHHHHHHhhh
Confidence 34678999999876653 5799999999999999853 456888 76555443332 344556666654
No 40
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=96.32 E-value=0.0023 Score=41.01 Aligned_cols=51 Identities=18% Similarity=0.160 Sum_probs=35.8
Q ss_pred ccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHH
Q 045388 43 SRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDA 105 (214)
Q Consensus 43 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~ 105 (214)
+.+.|+|+.+-+..+. .+++||.|.+.++..|+.. ....||. ++..+...+
T Consensus 3 ~~f~CpIt~~lM~dPV---i~~~G~tyer~~I~~~l~~-------~~~~~P~--t~~~l~~~~ 53 (73)
T PF04564_consen 3 DEFLCPITGELMRDPV---ILPSGHTYERSAIERWLEQ-------NGGTDPF--TRQPLSESD 53 (73)
T ss_dssp GGGB-TTTSSB-SSEE---EETTSEEEEHHHHHHHHCT-------TSSB-TT--T-SB-SGGG
T ss_pred cccCCcCcCcHhhCce---eCCcCCEEcHHHHHHHHHc-------CCCCCCC--CCCcCCccc
Confidence 4688999999887664 4678999999999999865 2457898 677776544
No 41
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.28 E-value=0.0085 Score=50.18 Aligned_cols=111 Identities=20% Similarity=0.442 Sum_probs=69.3
Q ss_pred cccccc--ccccc---ccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHhh---cC--C--
Q 045388 44 RSSCEI--CRERR---ENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKS---VL--S-- 111 (214)
Q Consensus 44 ~~~C~i--C~~~~---~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~~---~l--~-- 111 (214)
...||- |.... +...+.....|.-+||.-|...|- |. . + |+.... +.++- .+ +
T Consensus 273 v~yCPr~~Cq~p~~~d~~~~l~~CskCnFaFCtlCk~t~H------G~-s--~-----Ck~~~~-~~~~l~~~~~~~d~a 337 (445)
T KOG1814|consen 273 VVYCPRACCQLPVKQDPGRALAICSKCNFAFCTLCKLTWH------GV-S--P-----CKVKAE-KLIELYLEYLEADEA 337 (445)
T ss_pred cccCChhhccCccccCchhhhhhhccCccHHHHHHHHhhc------CC-C--c-----ccCchH-HHHHHHHHHhhcCHH
Confidence 356665 44331 123344466888999999998884 22 2 2 554322 22221 11 1
Q ss_pred --HHHHHHHHHHHHHHHhc--------CCCCcccCccCCCceeeecCCCCCCcCcccCCCCChhhccccCCCCC
Q 045388 112 --KNVLELWEKALSQELID--------ASQGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWH 175 (214)
Q Consensus 112 --~~~~~~~~~~~~~~~~~--------~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~h 175 (214)
.++.++|-+++.+..++ ..+...|| .|...+...++- +.+.|..|++.|||.|.....
T Consensus 338 ~k~ele~Ryg~rvve~~vn~~lsekwl~~N~krCP--~C~v~IEr~eGC----nKM~C~~c~~~fc~~c~~~l~ 405 (445)
T KOG1814|consen 338 RKRELEKRYGKRVVEELVNDFLSEKWLESNSKRCP--KCKVVIERSEGC----NKMHCTKCGTYFCWICAELLY 405 (445)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHHHHHHHhcCCCCC--cccceeecCCCc----cceeeccccccceeehhhhcC
Confidence 24455565444443332 23556899 999999999875 889999999999999987544
No 42
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=95.87 E-value=0.008 Score=48.69 Aligned_cols=98 Identities=16% Similarity=0.365 Sum_probs=58.0
Q ss_pred cCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHhhcCCHHHHHHHHHHHHHHHhcCCCCcccCccCCC
Q 045388 62 IESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKSVLSKNVLELWEKALSQELIDASQGIYCPFKDCS 141 (214)
Q Consensus 62 ~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~ 141 (214)
.-.|+-.||++|++.|-.-.-..+. ..+ --..|...++... ..-.+|+.....- .+...+.|| .|.
T Consensus 339 ~~gCgf~FCR~C~e~yh~geC~~~~--~as-~t~tc~y~vde~~-------a~~arwd~as~~T--Ik~tTkpCP--kCh 404 (446)
T KOG0006|consen 339 EGGCGFAFCRECKEAYHEGECSAVF--EAS-GTTTCAYRVDERA-------AEQARWDAASKET--IKKTTKPCP--KCH 404 (446)
T ss_pred CCCchhHhHHHHHhhhccccceeee--ccc-cccceeeecChhh-------hhhhhhhhhhhhh--hhhccCCCC--Ccc
Confidence 3459999999999998532111110 000 0012444443332 2334555544332 122345688 999
Q ss_pred ceeeecCCCCCCcCcccCC--CCChhhccccCCCCCCC
Q 045388 142 AKLVYENDGEDVLSESECP--YCHRLFCAHCYVPWHPG 177 (214)
Q Consensus 142 ~~~~~~~~~~~~~~~~~C~--~C~~~~C~~C~~~~h~~ 177 (214)
.....+.+- ..+.|+ .||-.+||.|+.+|...
T Consensus 405 vptErnGGC----mHm~Ct~~~Cg~eWCw~C~tEW~r~ 438 (446)
T KOG0006|consen 405 VPTERNGGC----MHMKCTQPQCGLEWCWNCGTEWNRV 438 (446)
T ss_pred CccccCCce----EEeecCCCCCCceeEeccCChhhhh
Confidence 888777663 667785 59999999999999643
No 43
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.85 E-value=0.019 Score=45.69 Aligned_cols=55 Identities=27% Similarity=0.587 Sum_probs=39.6
Q ss_pred CCCCcccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCc
Q 045388 38 PSSPPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLK 102 (214)
Q Consensus 38 ~~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 102 (214)
....+...+|++|.+.-+.+-+ ...|+|.||-.|++.-.... ..++||. |+....
T Consensus 233 ss~~t~~~~C~~Cg~~PtiP~~--~~~C~HiyCY~Ci~ts~~~~------asf~Cp~--Cg~~~~ 287 (298)
T KOG2879|consen 233 SSTGTSDTECPVCGEPPTIPHV--IGKCGHIYCYYCIATSRLWD------ASFTCPL--CGENVE 287 (298)
T ss_pred cccccCCceeeccCCCCCCCee--eccccceeehhhhhhhhcch------hhcccCc--cCCCCc
Confidence 3344567899999997665532 46799999999998875432 2479999 776553
No 44
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.77 E-value=0.0023 Score=54.25 Aligned_cols=102 Identities=17% Similarity=0.405 Sum_probs=64.0
Q ss_pred cccccccccccccc---cc--cccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHhhcCCHHHHHHH
Q 045388 44 RSSCEICRERREND---QM--FKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKSVLSKNVLELW 118 (214)
Q Consensus 44 ~~~C~iC~~~~~~~---~~--~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~~~l~~~~~~~~ 118 (214)
...|+.++...... +. .....|+-.||.+|-..|- .. ++-++++.+.+.....
T Consensus 238 ~~~C~~l~~~~el~~~~~~~~~~C~~C~~~fCv~C~~~wh---------~~-----------~sC~eykk~~~~~~~d-- 295 (384)
T KOG1812|consen 238 YPRCSSLMSKTELSSEVKSKRRPCVKCHELFCVKCKVPWH---------AN-----------LSCEEYKKLNPEEYVD-- 295 (384)
T ss_pred CCCchHhhhhhhhccchhhcccccccCCCceeecCCCcCC---------CC-----------CCHHHHHHhCCccccc--
Confidence 45677777754421 11 1144777788888844432 11 3345566655432222
Q ss_pred HHHHHHHHhcCCCCcccCccCCCceeeecCCCCCCcCcccCCCCChhhccccCCCCCCC
Q 045388 119 EKALSQELIDASQGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWHPG 177 (214)
Q Consensus 119 ~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~h~~ 177 (214)
..+..++. ..++.|| .|...+....+- +.++|. |+..||+.|...|..+
T Consensus 296 --~~~~~~la-~~wr~Cp--kC~~~ie~~~GC----nhm~Cr-C~~~fcy~C~~~~~~~ 344 (384)
T KOG1812|consen 296 --DITLKYLA-KRWRQCP--KCKFMIELSEGC----NHMTCR-CGHQFCYMCGGDWKTH 344 (384)
T ss_pred --HHHHHHHH-HhcCcCc--ccceeeeecCCc----ceEEee-ccccchhhcCcchhhC
Confidence 22222222 5778899 999999877764 889997 9999999999988654
No 45
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=95.30 E-value=0.011 Score=50.11 Aligned_cols=52 Identities=27% Similarity=0.607 Sum_probs=39.7
Q ss_pred CCCCCCccccccccccccccccc-ccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCC
Q 045388 36 ASPSSPPSRSSCEICRERRENDQ-MFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKS 99 (214)
Q Consensus 36 ~~~~~~~~~~~C~iC~~~~~~~~-~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~ 99 (214)
+.+.+..+..+|+||++..+.+. +.....|.|+|--.|+..|. ..+||. |..
T Consensus 167 ~~~~~~tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~----------~~scpv--cR~ 219 (493)
T KOG0804|consen 167 EPPTGLTELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWW----------DSSCPV--CRY 219 (493)
T ss_pred CCCCCcccCCCcchhHhhcCccccceeeeecccccchHHHhhcc----------cCcChh--hhh
Confidence 45667788999999999876543 22356899999999999984 467777 543
No 46
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.26 E-value=0.014 Score=48.92 Aligned_cols=48 Identities=29% Similarity=0.594 Sum_probs=37.2
Q ss_pred ccccccccccccccc--ccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCC
Q 045388 44 RSSCEICRERRENDQ--MFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKS 99 (214)
Q Consensus 44 ~~~C~iC~~~~~~~~--~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~ 99 (214)
..+|+||++.+..+- -...+.|+|-|=.+|+++|+. +.....||. |..
T Consensus 4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~------k~~~~~cp~--c~~ 53 (463)
T KOG1645|consen 4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLG------KKTKMQCPL--CSG 53 (463)
T ss_pred cccCceeeeeeeecCceEEeeecccccccHHHHHHHHh------hhhhhhCcc--cCC
Confidence 468999999986532 222689999999999999992 226789999 754
No 47
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.21 E-value=0.09 Score=43.04 Aligned_cols=120 Identities=22% Similarity=0.485 Sum_probs=65.4
Q ss_pred cccccccccccccc---cccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCc--CcHHHHhhcCCHHHHHHH
Q 045388 44 RSSCEICRERREND---QMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSV--LKFDACKSVLSKNVLELW 118 (214)
Q Consensus 44 ~~~C~iC~~~~~~~---~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~--l~~~~~~~~l~~~~~~~~ 118 (214)
...|.||-++|+.. ..+..+.|||.+|..|+...+.+ ..+.||. |... +....++.+- ..|...
T Consensus 3 ~~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~-------~~i~cpf--cR~~~~~~~~~~~~l~--kNf~ll 71 (296)
T KOG4185|consen 3 FPECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGN-------SRILCPF--CRETTEIPDGDVKSLQ--KNFALL 71 (296)
T ss_pred CCceeecCccccccCcccCCcccccCceehHhHHHHHhcC-------ceeeccC--CCCcccCCchhHhhhh--hhHHHH
Confidence 47899999998764 34447899999999999988643 4577888 7766 4444554442 222222
Q ss_pred HHHHH--HHHhcCCCCcccCccCCCceeeecCCCCCCcCcccCCCCChhhccccCCC-CCCC
Q 045388 119 EKALS--QELIDASQGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVP-WHPG 177 (214)
Q Consensus 119 ~~~~~--~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~-~h~~ 177 (214)
+.... ...+.......+| +.|.......... ....-.|+.....+|..|... .|.+
T Consensus 72 ~~~~~~~~~~~~~~~~~~~~-~~c~~~~~nl~~~--vc~~~~~~~~~~~~c~t~~~~~~~~~ 130 (296)
T KOG4185|consen 72 QAIEHMKKTTVEEKGEADSP-PKCKEHPYNLAEF--VCVEPDCSSKDKLMCRTCEEFGIHKG 130 (296)
T ss_pred HHHHHHhcccccccCcccCC-cccccCcccccce--eecCCCcchhhhhhhhhccchhhhhh
Confidence 22111 1112222222333 1244222111110 111223666678899999874 4555
No 48
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=95.06 E-value=0.01 Score=48.36 Aligned_cols=47 Identities=30% Similarity=0.793 Sum_probs=36.2
Q ss_pred ccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcC
Q 045388 43 SRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVL 101 (214)
Q Consensus 43 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 101 (214)
...+|.+|-.-+-+... ...|-|.||+.||-.|++. ...||. |+..+
T Consensus 14 ~~itC~LC~GYliDATT--I~eCLHTFCkSCivk~l~~--------~~~CP~--C~i~i 60 (331)
T KOG2660|consen 14 PHITCRLCGGYLIDATT--ITECLHTFCKSCIVKYLEE--------SKYCPT--CDIVI 60 (331)
T ss_pred cceehhhccceeecchh--HHHHHHHHHHHHHHHHHHH--------hccCCc--cceec
Confidence 46899999887655433 5799999999999999986 247998 65433
No 49
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.97 E-value=0.018 Score=51.27 Aligned_cols=46 Identities=28% Similarity=0.479 Sum_probs=35.5
Q ss_pred ccccccccccccccccc--cccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCC
Q 045388 43 SRSSCEICRERRENDQM--FKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPD 96 (214)
Q Consensus 43 ~~~~C~iC~~~~~~~~~--~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~ 96 (214)
....|.||.+.+....- ...+.|+|.|+..|++.|++. .-.||.+.
T Consensus 290 ~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er--------~qtCP~CR 337 (543)
T KOG0802|consen 290 SDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFER--------QQTCPTCR 337 (543)
T ss_pred cCCeeeeechhhccccccccceeecccchHHHHHHHHHHH--------hCcCCcch
Confidence 36789999999866311 236899999999999999986 23688833
No 50
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=94.94 E-value=0.016 Score=38.00 Aligned_cols=52 Identities=31% Similarity=0.628 Sum_probs=35.5
Q ss_pred ccccccccccccc---------ccc-cccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCc
Q 045388 44 RSSCEICRERREN---------DQM-FKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLK 102 (214)
Q Consensus 44 ~~~C~iC~~~~~~---------~~~-~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 102 (214)
...|+||...|.. ++- +..-.|+|.|...||.+|+.++-. .-.||. |...+.
T Consensus 21 dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~-----~~~CPm--CR~~w~ 82 (85)
T PF12861_consen 21 DDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSS-----KGQCPM--CRQPWK 82 (85)
T ss_pred CCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccC-----CCCCCC--cCCeee
Confidence 4578888877652 110 113479999999999999987522 237999 776553
No 51
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=94.79 E-value=0.014 Score=49.38 Aligned_cols=34 Identities=21% Similarity=0.591 Sum_probs=28.5
Q ss_pred ccccccccccccccccccccCCCCccccHHHHHHHHH
Q 045388 43 SRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVA 79 (214)
Q Consensus 43 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~ 79 (214)
+...|+||..-|..+- .+.|+|..|+.|.+..+.
T Consensus 3 eelkc~vc~~f~~epi---il~c~h~lc~~ca~~~~~ 36 (699)
T KOG4367|consen 3 EELKCPVCGSFYREPI---ILPCSHNLCQACARNILV 36 (699)
T ss_pred ccccCceehhhccCce---EeecccHHHHHHHHhhcc
Confidence 4678999999887765 589999999999997654
No 52
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=94.65 E-value=0.0092 Score=35.20 Aligned_cols=32 Identities=41% Similarity=0.969 Sum_probs=19.2
Q ss_pred cCcccCCCCChhhccccCCCCCCChHHHHHHHHHHhCCCccCCCCC
Q 045388 154 LSESECPYCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCK 199 (214)
Q Consensus 154 ~~~~~C~~C~~~~C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~ 199 (214)
....+|+.|+..||+.|..-.|+. ...||.|.
T Consensus 19 ~~~y~C~~C~~~FC~dCD~fiHE~--------------LH~CPGC~ 50 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCIDCDVFIHET--------------LHNCPGCE 50 (51)
T ss_dssp -EEE--TTTT--B-HHHHHTTTTT--------------S-SSSTT-
T ss_pred CCeEECCCCCCccccCcChhhhcc--------------ccCCcCCC
Confidence 367899999999999998877743 56788774
No 53
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=94.60 E-value=0.019 Score=43.45 Aligned_cols=38 Identities=29% Similarity=0.579 Sum_probs=29.7
Q ss_pred CCCCcccccccccccccccccccccCCCCccccHHHHHHHH
Q 045388 38 PSSPPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHV 78 (214)
Q Consensus 38 ~~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~ 78 (214)
.+++.-.+.|.||-.+|..+. ...|||.||..|+..-+
T Consensus 190 ~~~e~IPF~C~iCKkdy~spv---vt~CGH~FC~~Cai~~y 227 (259)
T COG5152 190 GPGEKIPFLCGICKKDYESPV---VTECGHSFCSLCAIRKY 227 (259)
T ss_pred CCCCCCceeehhchhhccchh---hhhcchhHHHHHHHHHh
Confidence 344445689999999998764 47899999999976544
No 54
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=94.57 E-value=0.061 Score=52.08 Aligned_cols=67 Identities=21% Similarity=0.388 Sum_probs=50.8
Q ss_pred cccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCC--cccccCCCCCCCCcCcHHHHhhcCCH
Q 045388 44 RSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGI--ITPVTCPGPDCKSVLKFDACKSVLSK 112 (214)
Q Consensus 44 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~--~~~i~CP~~~C~~~l~~~~~~~~l~~ 112 (214)
.--|-|||.+.-.......++|+|.|...|.+..+++.-..-. +.-|.||. |...++--.++++|++
T Consensus 3486 DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPi--C~n~InH~~LkDLldP 3554 (3738)
T KOG1428|consen 3486 DDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPI--CKNKINHIVLKDLLDP 3554 (3738)
T ss_pred CceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeeccc--ccchhhhHHHHHHHHH
Confidence 4569999988544333337899999999999998887665433 24589999 9998887777888764
No 55
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=94.47 E-value=0.042 Score=31.97 Aligned_cols=44 Identities=23% Similarity=0.700 Sum_probs=20.5
Q ss_pred ccccccccccc--cccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCc
Q 045388 47 CEICRERREND--QMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSV 100 (214)
Q Consensus 47 C~iC~~~~~~~--~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~ 100 (214)
|++|.+++... ++. --.|++++|+.|+..... ++ .=+||. |+..
T Consensus 1 cp~C~e~~d~~d~~~~-PC~Cgf~IC~~C~~~i~~----~~---~g~CPg--Cr~~ 46 (48)
T PF14570_consen 1 CPLCDEELDETDKDFY-PCECGFQICRFCYHDILE----NE---GGRCPG--CREP 46 (48)
T ss_dssp -TTTS-B--CCCTT---SSTTS----HHHHHHHTT----SS----SB-TT--T--B
T ss_pred CCCcccccccCCCccc-cCcCCCcHHHHHHHHHHh----cc---CCCCCC--CCCC
Confidence 68888887443 333 348899999999987754 11 237998 7654
No 56
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.36 E-value=0.029 Score=45.21 Aligned_cols=52 Identities=23% Similarity=0.500 Sum_probs=38.6
Q ss_pred CcccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHH
Q 045388 41 PPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFD 104 (214)
Q Consensus 41 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~ 104 (214)
.....+|.||+.+-..+ ..+.|+|.||.-|+++-+.. + ...|+. |..+++..
T Consensus 4 ~~~~~eC~IC~nt~n~P---v~l~C~HkFCyiCiKGsy~n----d---k~~Cav--CR~pids~ 55 (324)
T KOG0824|consen 4 RTKKKECLICYNTGNCP---VNLYCFHKFCYICIKGSYKN----D---KKTCAV--CRFPIDST 55 (324)
T ss_pred cccCCcceeeeccCCcC---ccccccchhhhhhhcchhhc----C---CCCCce--ecCCCCcc
Confidence 34567899999986554 26899999999999986542 1 235998 88777654
No 57
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.34 E-value=0.027 Score=48.36 Aligned_cols=53 Identities=25% Similarity=0.560 Sum_probs=38.2
Q ss_pred Ccccccccccccccccc----------ccc----ccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCc
Q 045388 41 PPSRSSCEICRERREND----------QMF----KIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLK 102 (214)
Q Consensus 41 ~~~~~~C~iC~~~~~~~----------~~~----~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 102 (214)
...+..|.||+.+++.- .++ -..+|.|.|.+.|+..|+.. +.+-||. |..+|+
T Consensus 568 ~~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~-------ykl~CPv--CR~pLP 634 (636)
T KOG0828|consen 568 VRRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDT-------YKLICPV--CRCPLP 634 (636)
T ss_pred hhccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhh-------hcccCCc--cCCCCC
Confidence 45678999999987531 111 14599999999999999853 3578999 555553
No 58
>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=94.03 E-value=0.055 Score=31.74 Aligned_cols=42 Identities=17% Similarity=0.536 Sum_probs=28.9
Q ss_pred cccccccccccccccccCCCC-----ccccHHHHHHHHHHHhhCCCcccccCCC
Q 045388 46 SCEICRERRENDQMFKIESCI-----HSFCSDCINKHVATKIQGGIITPVTCPG 94 (214)
Q Consensus 46 ~C~iC~~~~~~~~~~~~~~C~-----H~fC~~Cl~~~~~~~i~~~~~~~i~CP~ 94 (214)
.|-||++..+..+.+ ..+|. |.+..+||..|+...- ..+||.
T Consensus 1 ~CrIC~~~~~~~~~l-~~PC~C~G~~~~vH~~Cl~~W~~~~~------~~~C~i 47 (49)
T smart00744 1 ICRICHDEGDEGDPL-VSPCRCKGSLKYVHQECLERWINESG------NKTCEI 47 (49)
T ss_pred CccCCCCCCCCCCee-EeccccCCchhHHHHHHHHHHHHHcC------CCcCCC
Confidence 488999833333333 45674 7899999999997543 237887
No 59
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.96 E-value=0.088 Score=43.46 Aligned_cols=53 Identities=23% Similarity=0.516 Sum_probs=37.5
Q ss_pred CCCCCcccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCc
Q 045388 37 SPSSPPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLK 102 (214)
Q Consensus 37 ~~~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 102 (214)
......+...|+||+..- ...+ ..+|+|+-|..|+..|+.+ .-+|.. |+..+.
T Consensus 415 ~~lp~sEd~lCpICyA~p-i~Av--f~PC~H~SC~~CI~qHlmN--------~k~CFf--CktTv~ 467 (489)
T KOG4692|consen 415 KDLPDSEDNLCPICYAGP-INAV--FAPCSHRSCYGCITQHLMN--------CKRCFF--CKTTVI 467 (489)
T ss_pred CCCCCcccccCcceeccc-chhh--ccCCCCchHHHHHHHHHhc--------CCeeeE--ecceee
Confidence 334456678899999863 3334 4799999999999999753 235666 776653
No 60
>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=93.72 E-value=0.037 Score=27.85 Aligned_cols=23 Identities=35% Similarity=0.826 Sum_probs=16.5
Q ss_pred ccCccCCCceeeecCCCCCCcCcccCCCCChhh
Q 045388 134 YCPFKDCSAKLVYENDGEDVLSESECPYCHRLF 166 (214)
Q Consensus 134 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 166 (214)
.|| +|+..+.... ..||.||+.|
T Consensus 2 ~CP--~C~~~V~~~~--------~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCP--ECGAEVPESA--------KFCPHCGYDF 24 (26)
T ss_pred cCC--CCcCCchhhc--------CcCCCCCCCC
Confidence 477 8888775543 3499999876
No 61
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.60 E-value=0.068 Score=42.49 Aligned_cols=56 Identities=29% Similarity=0.501 Sum_probs=41.3
Q ss_pred cccccccccccccccc-------ccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHH
Q 045388 43 SRSSCEICRERRENDQ-------MFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDAC 106 (214)
Q Consensus 43 ~~~~C~iC~~~~~~~~-------~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~ 106 (214)
+...|.||...+..+. =...++|+|.|...|+++|... |+ .-.||- |+..++...+
T Consensus 223 ~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWciv----GK--kqtCPY--CKekVdl~rm 285 (328)
T KOG1734|consen 223 SDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIV----GK--KQTCPY--CKEKVDLKRM 285 (328)
T ss_pred CcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheee----cC--CCCCch--HHHHhhHhhh
Confidence 4577999998876543 1226899999999999999642 33 468998 9887766544
No 62
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.56 E-value=0.062 Score=46.70 Aligned_cols=38 Identities=21% Similarity=0.600 Sum_probs=29.3
Q ss_pred CCcccCccCCCceeeecCCCCCCcCcccCCC--CChhhccccCCCC
Q 045388 131 QGIYCPFKDCSAKLVYENDGEDVLSESECPY--CHRLFCAHCYVPW 174 (214)
Q Consensus 131 ~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~--C~~~~C~~C~~~~ 174 (214)
+...|| .|...+..+.+. +...|.. |+..||+.|...|
T Consensus 225 ntk~CP--~c~~~iek~~gc----~~~~~~~~~c~~~FCw~Cl~~~ 264 (444)
T KOG1815|consen 225 NTKECP--KCKVPIEKDGGC----NHMTCKSASCKHEFCWVCLASL 264 (444)
T ss_pred cCccCC--CcccchhccCCc----cccccccCCcCCeeceeeeccc
Confidence 444588 999998888764 5555654 9999999997776
No 63
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=93.48 E-value=0.062 Score=34.34 Aligned_cols=63 Identities=25% Similarity=0.575 Sum_probs=25.9
Q ss_pred CCcccCccCCCceeeecCCCCCCcCcccCCCCChhhccccCCCCCCChHHHHHHHHHHhCCCccCCCCCccceecCCCCC
Q 045388 131 QGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKYHIERTGGCLH 210 (214)
Q Consensus 131 ~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~~~iek~~GCnh 210 (214)
+...|. -|+--+-.+..+ ...+.|..|+.-.|..|.. +......+.||+|++...+.-|+..
T Consensus 8 ~~qiCq--iCGD~VGl~~~G---e~FVAC~eC~fPvCr~CyE-------------YErkeg~q~CpqCkt~ykr~kgsp~ 69 (80)
T PF14569_consen 8 NGQICQ--ICGDDVGLTENG---EVFVACHECAFPVCRPCYE-------------YERKEGNQVCPQCKTRYKRHKGSPR 69 (80)
T ss_dssp SS-B-S--SS--B--B-SSS---SB--S-SSS-----HHHHH-------------HHHHTS-SB-TTT--B----TT---
T ss_pred CCcccc--cccCccccCCCC---CEEEEEcccCCccchhHHH-------------HHhhcCcccccccCCCcccccCCCC
Confidence 444566 777666665544 3778899999999988853 5566788999999999988877654
Q ss_pred e
Q 045388 211 M 211 (214)
Q Consensus 211 m 211 (214)
+
T Consensus 70 V 70 (80)
T PF14569_consen 70 V 70 (80)
T ss_dssp -
T ss_pred C
Confidence 3
No 64
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=93.35 E-value=0.13 Score=47.06 Aligned_cols=56 Identities=30% Similarity=0.679 Sum_probs=43.6
Q ss_pred Ccccccccccccccccc-cccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCC
Q 045388 41 PPSRSSCEICRERREND-QMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKS 99 (214)
Q Consensus 41 ~~~~~~C~iC~~~~~~~-~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~ 99 (214)
....++|.||++.+... .++....|-|.|...||+.|.+..-.++. ..-+||. |+.
T Consensus 188 ~~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~-~~WrCP~--Cqs 244 (950)
T KOG1952|consen 188 SNRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQ-DGWRCPA--CQS 244 (950)
T ss_pred hcCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccC-ccccCCc--ccc
Confidence 34579999999998653 45556778999999999999988555555 5679998 763
No 65
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.35 E-value=0.039 Score=46.03 Aligned_cols=48 Identities=29% Similarity=0.693 Sum_probs=34.9
Q ss_pred cccccccccccccccccc-cCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCC
Q 045388 44 RSSCEICRERRENDQMFK-IESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCK 98 (214)
Q Consensus 44 ~~~C~iC~~~~~~~~~~~-~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~ 98 (214)
...|.||-+-++...-+. ...|||.|...|+..|++..-.. =.||. |+
T Consensus 4 ~A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~-----R~cpi--c~ 52 (465)
T KOG0827|consen 4 MAECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSN-----RGCPI--CQ 52 (465)
T ss_pred cceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCcc-----CCCCc--ee
Confidence 468999977666654333 34599999999999999754443 25888 65
No 66
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.34 E-value=0.16 Score=43.26 Aligned_cols=48 Identities=27% Similarity=0.720 Sum_probs=36.3
Q ss_pred cccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCc
Q 045388 42 PSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLK 102 (214)
Q Consensus 42 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 102 (214)
...+.|.||+..+..+. .++|||.||..|+.. .+. ....||. |...+.
T Consensus 82 ~sef~c~vc~~~l~~pv---~tpcghs~c~~Cl~r----~ld----~~~~cp~--Cr~~l~ 129 (398)
T KOG4159|consen 82 RSEFECCVCSRALYPPV---VTPCGHSFCLECLDR----SLD----QETECPL--CRDELV 129 (398)
T ss_pred cchhhhhhhHhhcCCCc---cccccccccHHHHHH----Hhc----cCCCCcc--cccccc
Confidence 56799999999887654 469999999999766 222 2457888 877665
No 67
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=93.23 E-value=0.042 Score=46.04 Aligned_cols=46 Identities=35% Similarity=0.798 Sum_probs=33.3
Q ss_pred cccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCC
Q 045388 44 RSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCK 98 (214)
Q Consensus 44 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~ 98 (214)
...|.||-+.-.. +...+|||..|..|+..|-.. .+|+ .||.+.|.
T Consensus 369 FeLCKICaendKd---vkIEPCGHLlCt~CLa~WQ~s--d~gq----~CPFCRcE 414 (563)
T KOG1785|consen 369 FELCKICAENDKD---VKIEPCGHLLCTSCLAAWQDS--DEGQ----TCPFCRCE 414 (563)
T ss_pred HHHHHHhhccCCC---cccccccchHHHHHHHhhccc--CCCC----CCCceeeE
Confidence 4569999986433 446899999999999999422 1244 79996664
No 68
>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=93.22 E-value=0.033 Score=39.68 Aligned_cols=36 Identities=25% Similarity=0.530 Sum_probs=27.3
Q ss_pred ccccccccccccccccccccCCCC------ccccHHHHHHHH
Q 045388 43 SRSSCEICRERRENDQMFKIESCI------HSFCSDCINKHV 78 (214)
Q Consensus 43 ~~~~C~iC~~~~~~~~~~~~~~C~------H~fC~~Cl~~~~ 78 (214)
...+|.||++.+...+-+....|+ |.||.+|++.|-
T Consensus 25 ~~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~ 66 (134)
T PF05883_consen 25 CTVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWR 66 (134)
T ss_pred cCeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHH
Confidence 368999999999873333334554 789999999994
No 69
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=93.15 E-value=0.11 Score=35.91 Aligned_cols=52 Identities=25% Similarity=0.570 Sum_probs=35.5
Q ss_pred cccCccCCCceeeecCC---C-CCCcCcccCCCCChhhccccCCCCCCChHHHHHHHHHHhCCCccCCCCCc
Q 045388 133 IYCPFKDCSAKLVYEND---G-EDVLSESECPYCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKY 200 (214)
Q Consensus 133 ~~Cp~~~C~~~~~~~~~---~-~~~~~~~~C~~C~~~~C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~~ 200 (214)
..|- .|...+..... + .....+..|+.|+..||..|..-+|+ ....||+|..
T Consensus 56 ~~C~--~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe--------------~Lh~CPGC~~ 111 (112)
T TIGR00622 56 RFCF--GCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHE--------------SLHCCPGCIH 111 (112)
T ss_pred Cccc--CcCCCCCCcccccccccccccceeCCCCCCccccccchhhhh--------------hccCCcCCCC
Confidence 4577 88876653211 0 12235678999999999999987774 3466888863
No 70
>PHA03096 p28-like protein; Provisional
Probab=93.12 E-value=0.18 Score=41.05 Aligned_cols=39 Identities=21% Similarity=0.448 Sum_probs=30.7
Q ss_pred ccccccccccccc----cccc-cCCCCccccHHHHHHHHHHHhh
Q 045388 45 SSCEICRERREND----QMFK-IESCIHSFCSDCINKHVATKIQ 83 (214)
Q Consensus 45 ~~C~iC~~~~~~~----~~~~-~~~C~H~fC~~Cl~~~~~~~i~ 83 (214)
..|+||++..... ..+. +..|.|.||..|++.|..+...
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~ 222 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLY 222 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhh
Confidence 7899999986543 1222 6699999999999999987764
No 71
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=93.03 E-value=0.059 Score=29.58 Aligned_cols=32 Identities=28% Similarity=0.740 Sum_probs=22.2
Q ss_pred cccCccCCCceeeecCCC-CCCcCcccCCCCChhh
Q 045388 133 IYCPFKDCSAKLVYENDG-EDVLSESECPYCHRLF 166 (214)
Q Consensus 133 ~~Cp~~~C~~~~~~~~~~-~~~~~~~~C~~C~~~~ 166 (214)
+.|| +|+..+..++.. ......++|+.|+..|
T Consensus 3 i~CP--~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 3 ITCP--NCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EECC--CCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 4688 999888776541 1334678888888765
No 72
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=93.01 E-value=0.036 Score=43.39 Aligned_cols=47 Identities=28% Similarity=0.747 Sum_probs=34.1
Q ss_pred cccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcH
Q 045388 44 RSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKF 103 (214)
Q Consensus 44 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~ 103 (214)
.+.|..|+---. .+-+.++.|.|.||..|...- .+-.||. |+..+..
T Consensus 3 ~VhCn~C~~~~~-~~~f~LTaC~HvfC~~C~k~~----------~~~~C~l--Ckk~ir~ 49 (233)
T KOG4739|consen 3 FVHCNKCFRFPS-QDPFFLTACRHVFCEPCLKAS----------SPDVCPL--CKKSIRI 49 (233)
T ss_pred eEEeccccccCC-CCceeeeechhhhhhhhcccC----------Ccccccc--ccceeee
Confidence 467999988766 444558999999999996543 2228999 8876543
No 73
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.01 E-value=0.011 Score=48.53 Aligned_cols=46 Identities=33% Similarity=0.812 Sum_probs=33.8
Q ss_pred ccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCC
Q 045388 43 SRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKS 99 (214)
Q Consensus 43 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~ 99 (214)
..+.|+||++-+...-+ ...|.|+||.+||..-+.. .+. .||- |..
T Consensus 42 ~~v~c~icl~llk~tmt--tkeClhrfc~~ci~~a~r~---gn~----ecpt--cRk 87 (381)
T KOG0311|consen 42 IQVICPICLSLLKKTMT--TKECLHRFCFDCIWKALRS---GNN----ECPT--CRK 87 (381)
T ss_pred hhhccHHHHHHHHhhcc--cHHHHHHHHHHHHHHHHHh---cCC----CCch--HHh
Confidence 46789999998876532 5799999999998876542 222 6887 654
No 74
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=92.82 E-value=0.2 Score=30.69 Aligned_cols=26 Identities=38% Similarity=0.823 Sum_probs=21.6
Q ss_pred hCCCccCC--CCCccceecC--CCCCeecC
Q 045388 189 KKQLRKCP--NCKYHIERTG--GCLHMTCL 214 (214)
Q Consensus 189 ~~~~k~CP--~C~~~iek~~--GCnhm~C~ 214 (214)
+.+++.|| +|+..|+..+ |.++++|+
T Consensus 15 ~~~~~~CP~~~C~~~~~~~~~~~~~~v~C~ 44 (64)
T smart00647 15 NPDLKWCPAPDCSAAIIVTEEEGCNRVTCP 44 (64)
T ss_pred CCCccCCCCCCCcceEEecCCCCCCeeECC
Confidence 36789999 9999999874 88888883
No 75
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=92.45 E-value=0.085 Score=28.75 Aligned_cols=32 Identities=28% Similarity=0.663 Sum_probs=22.0
Q ss_pred cccCccCCCceeeecCC-CCCCcCcccCCCCChhh
Q 045388 133 IYCPFKDCSAKLVYEND-GEDVLSESECPYCHRLF 166 (214)
Q Consensus 133 ~~Cp~~~C~~~~~~~~~-~~~~~~~~~C~~C~~~~ 166 (214)
+.|| +|...+..++. -......++|+.|+..|
T Consensus 3 i~Cp--~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCP--NCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECC--CCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 4688 99988777654 22344678888888765
No 76
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=92.40 E-value=0.072 Score=41.80 Aligned_cols=56 Identities=18% Similarity=0.255 Sum_probs=42.7
Q ss_pred ccccccccccccccccc-cccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHhh
Q 045388 43 SRSSCEICRERRENDQM-FKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKS 108 (214)
Q Consensus 43 ~~~~C~iC~~~~~~~~~-~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~~ 108 (214)
..+.|++|-+.+++..- ..+.+|||.||.+|....|. ..+.||. ++.++..++|..
T Consensus 220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir--------~D~v~pv--~d~plkdrdiI~ 276 (303)
T KOG3039|consen 220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIR--------KDMVDPV--TDKPLKDRDIIG 276 (303)
T ss_pred cceecccchhhhcCccceEEeccCCcEeeHHHHHHhcc--------ccccccC--CCCcCcccceEe
Confidence 67899999999876422 22679999999999999875 3567888 777777666543
No 77
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=91.64 E-value=0.17 Score=40.05 Aligned_cols=78 Identities=23% Similarity=0.457 Sum_probs=45.8
Q ss_pred CcccccccccccccccccccccCCCCcc-ccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHhhcCCHHHHHHHH
Q 045388 41 PPSRSSCEICRERRENDQMFKIESCIHS-FCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKSVLSKNVLELWE 119 (214)
Q Consensus 41 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~~~l~~~~~~~~~ 119 (214)
....++|.+|...+..+.-. =+|. -|..|-+..-...---|+ .-++|| |+-.|--
T Consensus 62 ~~p~v~CrVCq~~I~i~gk~----~QhVVkC~~CnEATPIr~aPpGK-KYVRCP---CNCLLIC---------------- 117 (256)
T PF09788_consen 62 GAPVVTCRVCQSLIDIEGKM----HQHVVKCSVCNEATPIRNAPPGK-KYVRCP---CNCLLIC---------------- 117 (256)
T ss_pred CCceEEeecCCceecccCcc----ceeeEECCCCCccccccCCCCCC-eeEecC---CceEEEe----------------
Confidence 33578999998877654311 1443 466665554322223344 457777 5543300
Q ss_pred HHHHHHHhcCCCCcccCccCCCceeeecCC
Q 045388 120 KALSQELIDASQGIYCPFKDCSAKLVYEND 149 (214)
Q Consensus 120 ~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~ 149 (214)
.....++.||.|+|..++.....
T Consensus 118 -------k~sS~rIaCPRp~CkRiI~L~~~ 140 (256)
T PF09788_consen 118 -------KSSSQRIACPRPNCKRIINLGPS 140 (256)
T ss_pred -------ecccccccCCCCCCcceEEeCCc
Confidence 02346778999999998877654
No 78
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=91.28 E-value=0.12 Score=43.28 Aligned_cols=76 Identities=18% Similarity=0.457 Sum_probs=51.7
Q ss_pred HHHHHHHHHHHHHHHHHhhhccccccCCCCCCCcccccccccccccccc-cccccCCCCccccHHHHHHHHHHHhhCCCc
Q 045388 9 AFATLAEELEIQEALMASTITSQMAKSASPSSPPSRSSCEICRERREND-QMFKIESCIHSFCSDCINKHVATKIQGGII 87 (214)
Q Consensus 9 ~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~C~iC~~~~~~~-~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~ 87 (214)
.++++++.+++++.+......+..- .......|+.|.+.+... +-.+.++|.|.|...|+..+++. +
T Consensus 336 rla~iYrs~gl~d~~~~h~~ra~~~------~~e~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~---n--- 403 (518)
T KOG1941|consen 336 RLASIYRSKGLQDELRAHVVRAHEC------VEETELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILEN---N--- 403 (518)
T ss_pred HHHHHHHhccchhHHHHHHHHHHHH------HHHHhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHh---C---
Confidence 3566677776666666555443322 234468899999987643 23447899999999999999842 2
Q ss_pred ccccCCCCCCC
Q 045388 88 TPVTCPGPDCK 98 (214)
Q Consensus 88 ~~i~CP~~~C~ 98 (214)
.+=+||. |.
T Consensus 404 ~~rsCP~--Cr 412 (518)
T KOG1941|consen 404 GTRSCPN--CR 412 (518)
T ss_pred CCCCCcc--HH
Confidence 2457998 65
No 79
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=91.23 E-value=0.2 Score=30.29 Aligned_cols=49 Identities=20% Similarity=0.537 Sum_probs=32.4
Q ss_pred cccCccCCCceeeecCCCCCCcCcccCCCCChhhccccCCCCCCChHHHHHHHHHHhCCCccCCCCCc
Q 045388 133 IYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKY 200 (214)
Q Consensus 133 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~~ 200 (214)
-.|. .|+..+...+.. ..+.||.||.+.=++|..= -+..+.=.||+|+.
T Consensus 10 ~~Ct--SCg~~i~p~e~~----v~F~CPnCGe~~I~Rc~~C-------------Rk~g~~Y~Cp~CGF 58 (61)
T COG2888 10 PVCT--SCGREIAPGETA----VKFPCPNCGEVEIYRCAKC-------------RKLGNPYRCPKCGF 58 (61)
T ss_pred ceec--cCCCEeccCCce----eEeeCCCCCceeeehhhhH-------------HHcCCceECCCcCc
Confidence 4577 888888555543 7888999996665555330 11345567999986
No 80
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=90.57 E-value=0.28 Score=41.96 Aligned_cols=38 Identities=21% Similarity=0.549 Sum_probs=30.9
Q ss_pred CcccccccccccccccccccccCCCCccccHHHHHHHHHH
Q 045388 41 PPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVAT 80 (214)
Q Consensus 41 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~ 80 (214)
......|++|...+..+.. ...|+|.||..|+..+...
T Consensus 18 ~~~~l~C~~C~~vl~~p~~--~~~cgh~fC~~C~~~~~~~ 55 (391)
T KOG0297|consen 18 LDENLLCPICMSVLRDPVQ--TTTCGHRFCAGCLLESLSN 55 (391)
T ss_pred CcccccCccccccccCCCC--CCCCCCcccccccchhhcc
Confidence 4567899999998876542 2599999999999999865
No 81
>PF01485 IBR: IBR domain; InterPro: IPR002867 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 cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=90.32 E-value=0.16 Score=31.02 Aligned_cols=26 Identities=46% Similarity=1.081 Sum_probs=14.9
Q ss_pred hCCCccCCC--CCccceecCCCCC--eecC
Q 045388 189 KKQLRKCPN--CKYHIERTGGCLH--MTCL 214 (214)
Q Consensus 189 ~~~~k~CP~--C~~~iek~~GCnh--m~C~ 214 (214)
+.+++.||+ |...|++.+|.++ |+|+
T Consensus 15 ~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~ 44 (64)
T PF01485_consen 15 DPNIRWCPNPDCEYIIEKDDGCNSPIVTCP 44 (64)
T ss_dssp ---CC--TTSST---ECS-SSTTS--CCTT
T ss_pred CCCccCCCCCCCcccEEecCCCCCCeeECC
Confidence 446689988 9999999999999 8885
No 82
>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=90.02 E-value=0.42 Score=38.55 Aligned_cols=52 Identities=27% Similarity=0.757 Sum_probs=35.0
Q ss_pred cccccccccc-cccccc-cCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHH
Q 045388 46 SCEICRERRE-NDQMFK-IESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDAC 106 (214)
Q Consensus 46 ~C~iC~~~~~-~~~~~~-~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~ 106 (214)
.|++|-.+.- .++++- ...|+|..|.+|+-..+.. .+-.||. |..+|-...+
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~-------g~~~Cpe--C~~iLRk~nf 55 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSL-------GPAQCPE--CMVILRKNNF 55 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHhc-------CCCCCCc--ccchhhhccc
Confidence 4888877643 333322 4599999999999887642 3456995 9877754433
No 83
>PF04641 Rtf2: Rtf2 RING-finger
Probab=89.91 E-value=0.45 Score=38.30 Aligned_cols=71 Identities=13% Similarity=0.284 Sum_probs=50.9
Q ss_pred Ccccccccccccccccc-cccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHhhcCC-HHHHHHH
Q 045388 41 PPSRSSCEICRERREND-QMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKSVLS-KNVLELW 118 (214)
Q Consensus 41 ~~~~~~C~iC~~~~~~~-~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~~~l~-~~~~~~~ 118 (214)
....+.|||....+... .++.+.+|||+|....|...- . .-.||. |+..+...+|-.|-+ .+.++.+
T Consensus 110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k-----~----~~~Cp~--c~~~f~~~DiI~Lnp~~ee~~~l 178 (260)
T PF04641_consen 110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK-----K----SKKCPV--CGKPFTEEDIIPLNPPEEELEKL 178 (260)
T ss_pred CCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc-----c----cccccc--cCCccccCCEEEecCCccHHHHH
Confidence 45678999999998543 455578999999999998871 1 234999 999998877766654 3344444
Q ss_pred HHHH
Q 045388 119 EKAL 122 (214)
Q Consensus 119 ~~~~ 122 (214)
...+
T Consensus 179 ~~~~ 182 (260)
T PF04641_consen 179 RERM 182 (260)
T ss_pred HHHH
Confidence 4443
No 84
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.86 E-value=0.1 Score=30.97 Aligned_cols=45 Identities=24% Similarity=0.574 Sum_probs=31.6
Q ss_pred ccccccccccccccccccCCCCcc-ccHHHHHHHHHHHhhCCCcccccCCCCCCCCcC
Q 045388 45 SSCEICRERRENDQMFKIESCIHS-FCSDCINKHVATKIQGGIITPVTCPGPDCKSVL 101 (214)
Q Consensus 45 ~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 101 (214)
.+|.||++.-.++. .-.|||. .|.+|-...+.. + .-.||. |..++
T Consensus 8 dECTICye~pvdsV---lYtCGHMCmCy~Cg~rl~~~----~---~g~CPi--CRapi 53 (62)
T KOG4172|consen 8 DECTICYEHPVDSV---LYTCGHMCMCYACGLRLKKA----L---HGCCPI--CRAPI 53 (62)
T ss_pred cceeeeccCcchHH---HHHcchHHhHHHHHHHHHHc----c---CCcCcc--hhhHH
Confidence 78999999744332 3579998 899997776543 1 235888 77654
No 85
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.74 E-value=0.26 Score=40.80 Aligned_cols=47 Identities=28% Similarity=0.651 Sum_probs=34.7
Q ss_pred cccccccccccccccccccccCCCCcc-ccHHHHHHHHHHHhhCCCcccccCCCCCCCCcC
Q 045388 42 PSRSSCEICRERRENDQMFKIESCIHS-FCSDCINKHVATKIQGGIITPVTCPGPDCKSVL 101 (214)
Q Consensus 42 ~~~~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 101 (214)
....+|.||+++..... .++|.|. .|.+|.+..- +.. =+||. |...+
T Consensus 288 ~~gkeCVIClse~rdt~---vLPCRHLCLCs~Ca~~Lr---~q~-----n~CPI--CRqpi 335 (349)
T KOG4265|consen 288 ESGKECVICLSESRDTV---VLPCRHLCLCSGCAKSLR---YQT-----NNCPI--CRQPI 335 (349)
T ss_pred cCCCeeEEEecCCcceE---EecchhhehhHhHHHHHH---Hhh-----cCCCc--cccch
Confidence 44789999999855432 6899998 9999987653 222 25999 87755
No 86
>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=89.21 E-value=0.073 Score=41.56 Aligned_cols=50 Identities=24% Similarity=0.759 Sum_probs=36.8
Q ss_pred cccccccccccc-ccc--cccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcC
Q 045388 45 SSCEICRERREN-DQM--FKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVL 101 (214)
Q Consensus 45 ~~C~iC~~~~~~-~~~--~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 101 (214)
.-||+|..+.-. +++ .....|-|.+|..|+...++. .+..||-.+|+..|
T Consensus 11 ~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~-------GpAqCP~~gC~kIL 63 (314)
T COG5220 11 RRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSR-------GPAQCPYKGCGKIL 63 (314)
T ss_pred ccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcC-------CCCCCCCccHHHHH
Confidence 469999988533 333 224569999999999887742 46789999998654
No 87
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=88.90 E-value=0.46 Score=28.81 Aligned_cols=45 Identities=22% Similarity=0.769 Sum_probs=30.2
Q ss_pred ccCccCCCceeeecCCCCCCcCcccCCCCChhh---ccccCCCCCCChHHHHHHHHHHhCCCccCCCCCc
Q 045388 134 YCPFKDCSAKLVYENDGEDVLSESECPYCHRLF---CAHCYVPWHPGREELMMRELVKKKQLRKCPNCKY 200 (214)
Q Consensus 134 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~---C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~~ 200 (214)
.|. .|+..+...+.. ..+.||.||... |.+|++ ..+.=.||+|+.
T Consensus 9 ~Ct--SCg~~i~~~~~~----~~F~CPnCG~~~I~RC~~CRk----------------~~~~Y~CP~CGF 56 (59)
T PRK14890 9 KCT--SCGIEIAPREKA----VKFLCPNCGEVIIYRCEKCRK----------------QSNPYTCPKCGF 56 (59)
T ss_pred ccc--CCCCcccCCCcc----CEeeCCCCCCeeEeechhHHh----------------cCCceECCCCCC
Confidence 566 788777655432 788899999874 555543 234567898885
No 88
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=88.25 E-value=0.47 Score=27.25 Aligned_cols=28 Identities=25% Similarity=0.745 Sum_probs=19.8
Q ss_pred cccCccCCCceeeecCCCCCCcCcccCCCCChhh
Q 045388 133 IYCPFKDCSAKLVYENDGEDVLSESECPYCHRLF 166 (214)
Q Consensus 133 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 166 (214)
+.|+ +|+..+..++.. ..++||.||..+
T Consensus 4 y~C~--~CG~~~~~~~~~----~~~~Cp~CG~~~ 31 (46)
T PRK00398 4 YKCA--RCGREVELDEYG----TGVRCPYCGYRI 31 (46)
T ss_pred EECC--CCCCEEEECCCC----CceECCCCCCeE
Confidence 4578 888888777653 267788887654
No 89
>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=88.22 E-value=0.26 Score=26.99 Aligned_cols=32 Identities=19% Similarity=0.519 Sum_probs=18.3
Q ss_pred cccCccCCCceeeecCCCC-CCcCcccCCCCChhh
Q 045388 133 IYCPFKDCSAKLVYENDGE-DVLSESECPYCHRLF 166 (214)
Q Consensus 133 ~~Cp~~~C~~~~~~~~~~~-~~~~~~~C~~C~~~~ 166 (214)
+.|| .|+..+..++... .....++|+.|+..|
T Consensus 3 ~~CP--~C~~~~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCP--NCKTSFRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred EECC--CCCCEEEeCHHHcCCCCCEEECCCCCCEE
Confidence 4577 8887766654311 122356777777643
No 90
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=87.95 E-value=0.12 Score=47.01 Aligned_cols=41 Identities=7% Similarity=0.404 Sum_probs=22.4
Q ss_pred cccccccccccccc----ccccccCCCCccccHHHHHHHHHHHhh
Q 045388 43 SRSSCEICRERREN----DQMFKIESCIHSFCSDCINKHVATKIQ 83 (214)
Q Consensus 43 ~~~~C~iC~~~~~~----~~~~~~~~C~H~fC~~Cl~~~~~~~i~ 83 (214)
...+|.+|.-++.. ..+.....|+|.+|..||..|....+.
T Consensus 95 ~s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~ 139 (1134)
T KOG0825|consen 95 ESDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEE 139 (1134)
T ss_pred cccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhc
Confidence 34555555555443 111113347777777777777655544
No 91
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=87.94 E-value=0.52 Score=45.44 Aligned_cols=48 Identities=27% Similarity=0.748 Sum_probs=32.5
Q ss_pred cccCccCCCceeeecCCCCCCcCcccCCCCChhh-----ccccCCCCCCChHHHHHHHHHHhCCCccCCCCCccce
Q 045388 133 IYCPFKDCSAKLVYENDGEDVLSESECPYCHRLF-----CAHCYVPWHPGREELMMRELVKKKQLRKCPNCKYHIE 203 (214)
Q Consensus 133 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~-----C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~~~ie 203 (214)
+.|| +|+.... ..+||.||... |..|+.....+ ......||+|++.+.
T Consensus 668 rkCP--kCG~~t~----------~~fCP~CGs~te~vy~CPsCGaev~~d-----------es~a~~CP~CGtplv 720 (1337)
T PRK14714 668 RRCP--SCGTETY----------ENRCPDCGTHTEPVYVCPDCGAEVPPD-----------ESGRVECPRCDVELT 720 (1337)
T ss_pred EECC--CCCCccc----------cccCcccCCcCCCceeCccCCCccCCC-----------ccccccCCCCCCccc
Confidence 5899 9997532 23699998664 99998864433 122567999998653
No 92
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=87.72 E-value=3.3 Score=29.54 Aligned_cols=56 Identities=29% Similarity=0.574 Sum_probs=42.5
Q ss_pred CCcccccccccccccccccccc-cCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCc
Q 045388 40 SPPSRSSCEICRERRENDQMFK-IESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLK 102 (214)
Q Consensus 40 ~~~~~~~C~iC~~~~~~~~~~~-~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 102 (214)
.+...++|.||.+.-.++.+.. ..-||-+.|..|....|...- .-.+||+ |+..+.
T Consensus 76 ~d~~lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~-----~ypvCPv--CkTSFK 132 (140)
T PF05290_consen 76 LDPKLYECNICKETSAEERFLKPNECCGYSICNACYANLWKFCN-----LYPVCPV--CKTSFK 132 (140)
T ss_pred cCCCceeccCcccccchhhcCCcccccchHHHHHHHHHHHHHcc-----cCCCCCc--cccccc
Confidence 3447899999999877766554 456899999999999886543 2468999 876653
No 93
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=87.65 E-value=0.39 Score=38.90 Aligned_cols=45 Identities=16% Similarity=0.401 Sum_probs=36.3
Q ss_pred CCCCcccccccccccccccccccccCCCCccccHHHHHHHHHHHh
Q 045388 38 PSSPPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKI 82 (214)
Q Consensus 38 ~~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i 82 (214)
+..+.....|.||+--|...+-|....|.|.|...||..|+...+
T Consensus 109 T~nn~p~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~ 153 (368)
T KOG4445|consen 109 TENNHPNGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTECL 153 (368)
T ss_pred ccCCCCCCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHHH
Confidence 334555678999998888877666789999999999999986554
No 94
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=87.56 E-value=0.64 Score=43.05 Aligned_cols=46 Identities=22% Similarity=0.478 Sum_probs=34.9
Q ss_pred CCCCCCcccccccccccccccccccccCCCCccccHHHHHHHHHHHh
Q 045388 36 ASPSSPPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKI 82 (214)
Q Consensus 36 ~~~~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i 82 (214)
+....-...-.|.+|.-.+-...++ ..+|||.|.++|+..++....
T Consensus 809 ~ry~v~ep~d~C~~C~~~ll~~pF~-vf~CgH~FH~~Cl~~~v~~~~ 854 (911)
T KOG2034|consen 809 QRYRVLEPQDSCDHCGRPLLIKPFY-VFPCGHCFHRDCLIRHVLSLL 854 (911)
T ss_pred cceEEecCccchHHhcchhhcCcce-eeeccchHHHHHHHHHHHccc
Confidence 3344445567899999988777655 579999999999999875433
No 95
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=87.54 E-value=0.28 Score=45.74 Aligned_cols=51 Identities=25% Similarity=0.634 Sum_probs=36.6
Q ss_pred cccccccccccccc-c-ccc--ccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcC
Q 045388 43 SRSSCEICRERREN-D-QMF--KIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVL 101 (214)
Q Consensus 43 ~~~~C~iC~~~~~~-~-~~~--~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 101 (214)
...+|+|||.-+.. + ..+ ....|.|.|...|+-+|+...- .-+||. |...+
T Consensus 1468 G~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~------~s~CPl--CRsei 1522 (1525)
T COG5219 1468 GHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSA------RSNCPL--CRSEI 1522 (1525)
T ss_pred CcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcC------CCCCCc--ccccc
Confidence 35689999987652 1 111 1678999999999999997533 247999 77654
No 96
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=87.35 E-value=0.32 Score=26.30 Aligned_cols=28 Identities=29% Similarity=0.676 Sum_probs=18.2
Q ss_pred cccCccCCCceeeecCCCCCCcCcccCCCCChh
Q 045388 133 IYCPFKDCSAKLVYENDGEDVLSESECPYCHRL 165 (214)
Q Consensus 133 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 165 (214)
++|| .|+..+....+.. ....|..|++.
T Consensus 2 ~FCp--~C~nlL~p~~~~~---~~~~C~~C~Y~ 29 (35)
T PF02150_consen 2 RFCP--ECGNLLYPKEDKE---KRVACRTCGYE 29 (35)
T ss_dssp -BET--TTTSBEEEEEETT---TTEEESSSS-E
T ss_pred eeCC--CCCccceEcCCCc---cCcCCCCCCCc
Confidence 5799 9999998876532 11268878764
No 97
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.27 E-value=0.59 Score=37.58 Aligned_cols=57 Identities=28% Similarity=0.681 Sum_probs=42.3
Q ss_pred CCCcccccccccccccccccccccCC-CCccccHHHHHHHHHHHhhCCCcccccCCC-CCCC
Q 045388 39 SSPPSRSSCEICRERRENDQMFKIES-CIHSFCSDCINKHVATKIQGGIITPVTCPG-PDCK 98 (214)
Q Consensus 39 ~~~~~~~~C~iC~~~~~~~~~~~~~~-C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~-~~C~ 98 (214)
.......-|.+|.+.+++..+++... =.|.||..|-+..|..+-..| .++||. ..|.
T Consensus 263 ~A~~apLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSResIK~Qg~sg---evYCPSGdkCP 321 (352)
T KOG3579|consen 263 AAPSAPLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSRESIKQQGASG---EVYCPSGDKCP 321 (352)
T ss_pred cCCCCceeehhhhhhhccCceeecCCCcccceecccCHHHHHhhcCCC---ceeCCCCCcCc
Confidence 33445689999999998887665221 169999999999998876655 478888 3564
No 98
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=87.24 E-value=0.11 Score=42.47 Aligned_cols=32 Identities=34% Similarity=0.918 Sum_probs=24.9
Q ss_pred cCcccCCCCChhhccccCCCCCCChHHHHHHHHHHhCCCccCCCCC
Q 045388 154 LSESECPYCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCK 199 (214)
Q Consensus 154 ~~~~~C~~C~~~~C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~ 199 (214)
...++|..|+.+||..|..-.|+. ...||.|.
T Consensus 343 ~~~y~C~~Ck~~FCldCDv~iHes--------------Lh~CpgCe 374 (378)
T KOG2807|consen 343 SGRYRCESCKNVFCLDCDVFIHES--------------LHNCPGCE 374 (378)
T ss_pred CCcEEchhccceeeccchHHHHhh--------------hhcCCCcC
Confidence 367889999999999998866632 35688776
No 99
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=86.76 E-value=0.36 Score=25.90 Aligned_cols=31 Identities=26% Similarity=0.573 Sum_probs=14.9
Q ss_pred cccCccCCCceeeecCCCCCCcCcccCCCCChh
Q 045388 133 IYCPFKDCSAKLVYENDGEDVLSESECPYCHRL 165 (214)
Q Consensus 133 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 165 (214)
++|| .|+..+...-...+...+..|+.|+..
T Consensus 1 kfC~--~CG~~l~~~ip~gd~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 1 KFCP--QCGGPLERRIPEGDDRERLVCPACGFI 31 (34)
T ss_dssp -B-T--TT--B-EEE--TT-SS-EEEETTTTEE
T ss_pred Cccc--cccChhhhhcCCCCCccceECCCCCCE
Confidence 3788 899776554222234577889988863
No 100
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=86.63 E-value=0.99 Score=37.10 Aligned_cols=62 Identities=29% Similarity=0.544 Sum_probs=43.6
Q ss_pred CCCCCCcccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHhhc
Q 045388 36 ASPSSPPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKSV 109 (214)
Q Consensus 36 ~~~~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~~~ 109 (214)
+.+........|++|+....++.+. ..-|-.||-.|+..|+. +.| +||..++. ...+++.++
T Consensus 292 e~e~l~~~~~~CpvClk~r~Nptvl--~vSGyVfCY~Ci~~Yv~---~~~-----~CPVT~~p--~~v~~l~rl 353 (357)
T KOG0826|consen 292 ESELLPPDREVCPVCLKKRQNPTVL--EVSGYVFCYPCIFSYVV---NYG-----HCPVTGYP--ASVDHLIRL 353 (357)
T ss_pred ccccCCCccccChhHHhccCCCceE--EecceEEeHHHHHHHHH---hcC-----CCCccCCc--chHHHHHHH
Confidence 5566666788999999988776543 33488999999999986 222 59996554 444555443
No 101
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=86.18 E-value=1 Score=37.14 Aligned_cols=53 Identities=21% Similarity=0.536 Sum_probs=37.1
Q ss_pred cccccccccccc--ccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHh
Q 045388 45 SSCEICRERREN--DQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACK 107 (214)
Q Consensus 45 ~~C~iC~~~~~~--~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~ 107 (214)
-.|++|.+++.. ..++. -+||-++|+-||...-+. + .=+||+ |......+.|+
T Consensus 15 d~cplcie~mditdknf~p-c~cgy~ic~fc~~~irq~-l------ngrcpa--crr~y~denv~ 69 (480)
T COG5175 15 DYCPLCIEPMDITDKNFFP-CPCGYQICQFCYNNIRQN-L------NGRCPA--CRRKYDDENVR 69 (480)
T ss_pred ccCcccccccccccCCccc-CCcccHHHHHHHHHHHhh-c------cCCChH--hhhhcccccee
Confidence 349999998653 45554 589999999998765332 3 237999 88766665554
No 102
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=85.80 E-value=0.55 Score=37.90 Aligned_cols=46 Identities=26% Similarity=0.532 Sum_probs=34.4
Q ss_pred cccccccccccccc-cccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCC
Q 045388 44 RSSCEICRERREND-QMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKS 99 (214)
Q Consensus 44 ~~~C~iC~~~~~~~-~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~ 99 (214)
...||+|.+.+... ..+..+.|+|..-..|++.++.. . .+||. |..
T Consensus 158 ~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~-------~-y~CP~--C~~ 204 (276)
T KOG1940|consen 158 EFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICE-------G-YTCPI--CSK 204 (276)
T ss_pred cCCCchhHHHhccccccCCccCcccchHHHHHHHHhcc-------C-CCCCc--ccc
Confidence 34499999986543 22337899999999999998642 2 68999 877
No 103
>PLN02189 cellulose synthase
Probab=85.26 E-value=0.74 Score=43.68 Aligned_cols=63 Identities=25% Similarity=0.578 Sum_probs=48.7
Q ss_pred CCcccCccCCCceeeecCCCCCCcCcccCCCCChhhccccCCCCCCChHHHHHHHHHHhCCCccCCCCCccceecCCCCC
Q 045388 131 QGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKYHIERTGGCLH 210 (214)
Q Consensus 131 ~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~~~iek~~GCnh 210 (214)
+...|. -|+..+-.+..+ ...+-|..|+.-.|.-|.. +.++...+.||+|++...+.-|++.
T Consensus 33 ~~~~C~--iCgd~vg~~~~g---~~fvaC~~C~fpvCr~Cye-------------yer~eg~q~CpqCkt~Y~r~kgs~~ 94 (1040)
T PLN02189 33 DGQVCE--ICGDEIGLTVDG---DLFVACNECGFPVCRPCYE-------------YERREGTQNCPQCKTRYKRLKGSPR 94 (1040)
T ss_pred cCcccc--ccccccCcCCCC---CEEEeeccCCCccccchhh-------------hhhhcCCccCcccCCchhhccCCCC
Confidence 444677 788777766554 2778999999999999974 3456678999999999987777765
Q ss_pred e
Q 045388 211 M 211 (214)
Q Consensus 211 m 211 (214)
+
T Consensus 95 v 95 (1040)
T PLN02189 95 V 95 (1040)
T ss_pred c
Confidence 4
No 104
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=85.16 E-value=0.4 Score=23.26 Aligned_cols=22 Identities=36% Similarity=1.008 Sum_probs=12.1
Q ss_pred ccCccCCCceeeecCCCCCCcCcccCCCCChh
Q 045388 134 YCPFKDCSAKLVYENDGEDVLSESECPYCHRL 165 (214)
Q Consensus 134 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 165 (214)
+|| .|+.-+..+. ..|+.||..
T Consensus 1 ~Cp--~CG~~~~~~~--------~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCP--NCGAEIEDDA--------KFCPNCGTP 22 (23)
T ss_pred CCc--ccCCCCCCcC--------cchhhhCCc
Confidence 466 7776664322 236666653
No 105
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=84.79 E-value=0.44 Score=23.82 Aligned_cols=23 Identities=30% Similarity=0.940 Sum_probs=13.1
Q ss_pred cccCccCCCceeeecCCCCCCcCcccCCCCChh
Q 045388 133 IYCPFKDCSAKLVYENDGEDVLSESECPYCHRL 165 (214)
Q Consensus 133 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 165 (214)
+.|| +|+..+..+. ..|+.||+.
T Consensus 3 ~~Cp--~Cg~~~~~~~--------~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCP--NCGAEIDPDA--------KFCPNCGAK 25 (26)
T ss_pred CCCc--ccCCcCCccc--------ccChhhCCC
Confidence 4577 8887443322 237777653
No 106
>PRK04023 DNA polymerase II large subunit; Validated
Probab=84.72 E-value=0.89 Score=42.91 Aligned_cols=45 Identities=22% Similarity=0.642 Sum_probs=30.1
Q ss_pred CCcccCccCCCceeeecCCCCCCcCcccCCCCCh-----hhccccCCCCCCChHHHHHHHHHHhCCCccCCCCCccce
Q 045388 131 QGIYCPFKDCSAKLVYENDGEDVLSESECPYCHR-----LFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKYHIE 203 (214)
Q Consensus 131 ~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~-----~~C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~~~ie 203 (214)
..++|| .|+... ..++||.||. .||..|..... ...||+|+..+.
T Consensus 625 g~RfCp--sCG~~t----------~~frCP~CG~~Te~i~fCP~CG~~~~----------------~y~CPKCG~El~ 674 (1121)
T PRK04023 625 GRRKCP--SCGKET----------FYRRCPFCGTHTEPVYRCPRCGIEVE----------------EDECEKCGREPT 674 (1121)
T ss_pred cCccCC--CCCCcC----------CcccCCCCCCCCCcceeCccccCcCC----------------CCcCCCCCCCCC
Confidence 456899 888663 4456999984 58888865322 245888887553
No 107
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=84.71 E-value=0.26 Score=38.44 Aligned_cols=37 Identities=27% Similarity=0.728 Sum_probs=27.3
Q ss_pred CcccCCCCChhhccccCCCCCCChHHHHHHHHHHhCCCccCCCCCcccee
Q 045388 155 SESECPYCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKYHIER 204 (214)
Q Consensus 155 ~~~~C~~C~~~~C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~~~iek 204 (214)
+.+++ ||+.|||-|.-.|- ....+.+.||-|+..|..
T Consensus 60 PVvTl--CGHLFCWpClyqWl-----------~~~~~~~~cPVCK~~Vs~ 96 (230)
T KOG0823|consen 60 PVVTL--CGHLFCWPCLYQWL-----------QTRPNSKECPVCKAEVSI 96 (230)
T ss_pred CEEee--cccceehHHHHHHH-----------hhcCCCeeCCcccccccc
Confidence 66665 99999999986552 224567889999986643
No 108
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=84.61 E-value=0.69 Score=27.08 Aligned_cols=28 Identities=21% Similarity=0.542 Sum_probs=18.3
Q ss_pred ccCccCCCceeeecCCCCCCcCcccCCCCChh
Q 045388 134 YCPFKDCSAKLVYENDGEDVLSESECPYCHRL 165 (214)
Q Consensus 134 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 165 (214)
+|| .|+..+...+.. ....+.|+.|++.
T Consensus 2 FCp--~Cg~~l~~~~~~--~~~~~vC~~Cg~~ 29 (52)
T smart00661 2 FCP--KCGNMLIPKEGK--EKRRFVCRKCGYE 29 (52)
T ss_pred CCC--CCCCccccccCC--CCCEEECCcCCCe
Confidence 688 898877666432 1136678888753
No 109
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=84.59 E-value=0.75 Score=43.77 Aligned_cols=63 Identities=27% Similarity=0.572 Sum_probs=48.7
Q ss_pred CCcccCccCCCceeeecCCCCCCcCcccCCCCChhhccccCCCCCCChHHHHHHHHHHhCCCccCCCCCccceecCCCCC
Q 045388 131 QGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKYHIERTGGCLH 210 (214)
Q Consensus 131 ~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~~~iek~~GCnh 210 (214)
+..-|. -|+..+-.+..+ ...+-|..|+.-.|.-|.. +.+....+.||+|++...+.-|++.
T Consensus 16 ~~qiCq--ICGD~vg~~~~G---e~FVAC~eC~FPVCrpCYE-------------YEr~eG~q~CPqCktrYkr~kgspr 77 (1079)
T PLN02638 16 GGQVCQ--ICGDNVGKTVDG---EPFVACDVCAFPVCRPCYE-------------YERKDGNQSCPQCKTKYKRHKGSPA 77 (1079)
T ss_pred CCceee--ecccccCcCCCC---CEEEEeccCCCccccchhh-------------hhhhcCCccCCccCCchhhhcCCCC
Confidence 334577 788777666555 3778999999999999974 4456778999999999988778775
Q ss_pred e
Q 045388 211 M 211 (214)
Q Consensus 211 m 211 (214)
+
T Consensus 78 v 78 (1079)
T PLN02638 78 I 78 (1079)
T ss_pred c
Confidence 4
No 110
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=84.41 E-value=0.83 Score=41.57 Aligned_cols=13 Identities=31% Similarity=0.723 Sum_probs=8.1
Q ss_pred CCccCCCCCccce
Q 045388 191 QLRKCPNCKYHIE 203 (214)
Q Consensus 191 ~~k~CP~C~~~ie 203 (214)
+.+.||+||..+.
T Consensus 40 ~~~fC~~CG~~~~ 52 (645)
T PRK14559 40 DEAHCPNCGAETG 52 (645)
T ss_pred ccccccccCCccc
Confidence 4567777776543
No 111
>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=84.09 E-value=0.96 Score=23.72 Aligned_cols=28 Identities=25% Similarity=0.552 Sum_probs=15.7
Q ss_pred CcccCccCCCceeeecCCCCCCcCcccCCCCChh
Q 045388 132 GIYCPFKDCSAKLVYENDGEDVLSESECPYCHRL 165 (214)
Q Consensus 132 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 165 (214)
..+|+ .|+........+ ....|+.|+..
T Consensus 3 ~rfC~--~CG~~t~~~~~g----~~r~C~~Cg~~ 30 (32)
T PF09297_consen 3 HRFCG--RCGAPTKPAPGG----WARRCPSCGHE 30 (32)
T ss_dssp TSB-T--TT--BEEE-SSS----S-EEESSSS-E
T ss_pred CcccC--cCCccccCCCCc----CEeECCCCcCE
Confidence 45788 888888777664 56678888753
No 112
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=83.91 E-value=3.6 Score=34.81 Aligned_cols=59 Identities=20% Similarity=0.353 Sum_probs=43.2
Q ss_pred ccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHhh
Q 045388 43 SRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKS 108 (214)
Q Consensus 43 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~~ 108 (214)
+.+.|||=-+.-+.++.+..+.|||..+++=+..... +|. ..++||= |+..-...+.+.
T Consensus 333 SvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~----ng~-~sfKCPY--CP~e~~~~~~kq 391 (394)
T KOG2817|consen 333 SVFICPVLKEQTSDENPPMMLICGHVISKDALNRLSK----NGS-QSFKCPY--CPVEQLASDTKQ 391 (394)
T ss_pred ceeecccchhhccCCCCCeeeeccceecHHHHHHHhh----CCC-eeeeCCC--CCcccCHHhccc
Confidence 4678999777666666556899999999998877653 444 4789998 887666655443
No 113
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=83.87 E-value=0.15 Score=38.81 Aligned_cols=63 Identities=22% Similarity=0.517 Sum_probs=35.5
Q ss_pred CCCcccCccCCCceeeecCCCCCCcCcccCCCCChhhccccCCCCCCChH--HHHHHHHHHhCCCccCCCCCcccee
Q 045388 130 SQGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWHPGRE--ELMMRELVKKKQLRKCPNCKYHIER 204 (214)
Q Consensus 130 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~h~~~~--~~~~~~~~~~~~~k~CP~C~~~iek 204 (214)
.+.+.|| =|...+.. +.+ ..||+.||+.|...|..... ......+....+...||.|+..|..
T Consensus 16 ~~~~~Cp--ICld~~~d--------PVv--T~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~ 80 (193)
T PLN03208 16 GGDFDCN--ICLDQVRD--------PVV--TLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE 80 (193)
T ss_pred CCccCCc--cCCCcCCC--------cEE--cCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence 3456777 66654311 222 26899999999887742100 0001111123445789999998854
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=82.86 E-value=0.73 Score=26.12 Aligned_cols=42 Identities=26% Similarity=0.560 Sum_probs=20.6
Q ss_pred ccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCC
Q 045388 47 CEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPG 94 (214)
Q Consensus 47 C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~ 94 (214)
|.+|.+-+.....-...+|+-++...|++.|++.+- ..+||.
T Consensus 1 C~~C~~iv~~G~~C~~~~C~~r~H~~C~~~y~r~~~------~~~CP~ 42 (43)
T PF08746_consen 1 CEACKEIVTQGQRCSNRDCNVRLHDDCFKKYFRHRS------NPKCPN 42 (43)
T ss_dssp -TTT-SB-SSSEE-SS--S--EE-HHHHHHHTTT-S------S-B-TT
T ss_pred CcccchhHeeeccCCCCccCchHHHHHHHHHHhcCC------CCCCcC
Confidence 566766655444333457899999999999986432 227886
No 115
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=82.66 E-value=0.39 Score=28.70 Aligned_cols=46 Identities=24% Similarity=0.586 Sum_probs=29.8
Q ss_pred cccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHH
Q 045388 44 RSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFD 104 (214)
Q Consensus 44 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~ 104 (214)
...|-.|...-.. -..++|+|.+|..||... .---||. |+..+...
T Consensus 7 ~~~~~~~~~~~~~---~~~~pCgH~I~~~~f~~~----------rYngCPf--C~~~~~~~ 52 (55)
T PF14447_consen 7 EQPCVFCGFVGTK---GTVLPCGHLICDNCFPGE----------RYNGCPF--CGTPFEFD 52 (55)
T ss_pred ceeEEEccccccc---cccccccceeeccccChh----------hccCCCC--CCCcccCC
Confidence 3455555443222 226899999999998654 1236999 88877644
No 116
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=82.55 E-value=0.73 Score=34.51 Aligned_cols=30 Identities=33% Similarity=0.960 Sum_probs=22.3
Q ss_pred CCChhhccccCCCCCCChHHHHHHHHHHhCCCccCCCCCcccee
Q 045388 161 YCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKYHIER 204 (214)
Q Consensus 161 ~C~~~~C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~~~iek 204 (214)
+||++||..|-+ ... .+...||-|+..|.+
T Consensus 150 kCGHvFC~~Cik------------~al--k~~~~CP~C~kkIt~ 179 (187)
T KOG0320|consen 150 KCGHVFCSQCIK------------DAL--KNTNKCPTCRKKITH 179 (187)
T ss_pred ccchhHHHHHHH------------HHH--HhCCCCCCcccccch
Confidence 789999999953 222 356899999987643
No 117
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=82.17 E-value=2.2 Score=31.96 Aligned_cols=57 Identities=19% Similarity=0.428 Sum_probs=36.6
Q ss_pred ccccccccccccc----ccccccCCCCccccHHHHHHHHHHHhhCCCcccc---cCCCCCCCCcCc
Q 045388 44 RSSCEICRERREN----DQMFKIESCIHSFCSDCINKHVATKIQGGIITPV---TCPGPDCKSVLK 102 (214)
Q Consensus 44 ~~~C~iC~~~~~~----~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i---~CP~~~C~~~l~ 102 (214)
...|+|||.---. +......+|+..|..-||..|++.-+-.++.+.| .||- |..++.
T Consensus 165 ~~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPY--CS~Pia 228 (234)
T KOG3268|consen 165 LGACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPY--CSDPIA 228 (234)
T ss_pred hhcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCC--CCCcce
Confidence 4456666653211 1122256899999999999999887766554443 6777 766553
No 118
>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=82.02 E-value=1.7 Score=29.55 Aligned_cols=32 Identities=25% Similarity=0.600 Sum_probs=25.9
Q ss_pred ccccccccccccccccccccCCCCccccHHHHH
Q 045388 43 SRSSCEICRERRENDQMFKIESCIHSFCSDCIN 75 (214)
Q Consensus 43 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~ 75 (214)
....|.+|...+..+. |...+|||.|...|++
T Consensus 77 ~~~~C~vC~k~l~~~~-f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 77 ESTKCSVCGKPLGNSV-FVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCCccCcCCcCCCce-EEEeCCCeEEeccccc
Confidence 3566999999998755 4467999999999975
No 119
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=81.97 E-value=1.8 Score=34.42 Aligned_cols=58 Identities=21% Similarity=0.583 Sum_probs=41.0
Q ss_pred Ccccccccccccccccccccc-cCCCC-----ccccHHHHHHHHHHHhhCCCcccccCCCCCCCCc
Q 045388 41 PPSRSSCEICRERRENDQMFK-IESCI-----HSFCSDCINKHVATKIQGGIITPVTCPGPDCKSV 100 (214)
Q Consensus 41 ~~~~~~C~iC~~~~~~~~~~~-~~~C~-----H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~ 100 (214)
......|-|||.+-++...-. .-+|. |-+...|+..|+.++-.....-++.||+ |+..
T Consensus 17 ~e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~Q--CqTE 80 (293)
T KOG3053|consen 17 QELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQ--CQTE 80 (293)
T ss_pred cccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechh--hcch
Confidence 344578999999865543211 33553 6699999999998877655557899999 8753
No 120
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=81.87 E-value=1.3 Score=36.30 Aligned_cols=49 Identities=22% Similarity=0.430 Sum_probs=33.7
Q ss_pred CCCcccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCc
Q 045388 39 SSPPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLK 102 (214)
Q Consensus 39 ~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 102 (214)
....+.++||||++.+..+. ++ -+=||..|..|-.. ..-+||. |...+.
T Consensus 43 ~~~~~lleCPvC~~~l~~Pi-~Q-C~nGHlaCssC~~~-----------~~~~CP~--Cr~~~g 91 (299)
T KOG3002|consen 43 LLDLDLLDCPVCFNPLSPPI-FQ-CDNGHLACSSCRTK-----------VSNKCPT--CRLPIG 91 (299)
T ss_pred ccchhhccCchhhccCcccc-ee-cCCCcEehhhhhhh-----------hcccCCc--cccccc
Confidence 34556899999999988764 32 23489999999641 2346777 665554
No 121
>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=81.10 E-value=1.7 Score=25.81 Aligned_cols=41 Identities=20% Similarity=0.449 Sum_probs=23.5
Q ss_pred cccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCc
Q 045388 44 RSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLK 102 (214)
Q Consensus 44 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 102 (214)
.++||.|...++... |..++...=.... ..+.||. |...+.
T Consensus 2 ~f~CP~C~~~~~~~~---------------L~~H~~~~H~~~~-~~v~CPi--C~~~~~ 42 (54)
T PF05605_consen 2 SFTCPYCGKGFSESS---------------LVEHCEDEHRSES-KNVVCPI--CSSRVT 42 (54)
T ss_pred CcCCCCCCCccCHHH---------------HHHHHHhHCcCCC-CCccCCC--chhhhh
Confidence 578999988544322 3444433322333 4689999 876443
No 122
>PLN02436 cellulose synthase A
Probab=80.95 E-value=1.4 Score=42.00 Aligned_cols=63 Identities=25% Similarity=0.590 Sum_probs=47.7
Q ss_pred CCcccCccCCCceeeecCCCCCCcCcccCCCCChhhccccCCCCCCChHHHHHHHHHHhCCCccCCCCCccceecCCCCC
Q 045388 131 QGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKYHIERTGGCLH 210 (214)
Q Consensus 131 ~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~~~iek~~GCnh 210 (214)
+..-|. =|+-.+-.+..+ ...+-|..|+.-.|.-|.. +.++...+.||+|++...+.-|++.
T Consensus 35 ~~~iCq--ICGD~Vg~t~dG---e~FVACn~C~fpvCr~Cye-------------yer~eg~~~Cpqckt~Y~r~kgs~~ 96 (1094)
T PLN02436 35 SGQTCQ--ICGDEIELTVDG---EPFVACNECAFPVCRPCYE-------------YERREGNQACPQCKTRYKRIKGSPR 96 (1094)
T ss_pred CCcccc--ccccccCcCCCC---CEEEeeccCCCccccchhh-------------hhhhcCCccCcccCCchhhccCCCC
Confidence 334677 788776665554 2788999999999999974 3456678999999999887777765
Q ss_pred e
Q 045388 211 M 211 (214)
Q Consensus 211 m 211 (214)
+
T Consensus 97 ~ 97 (1094)
T PLN02436 97 V 97 (1094)
T ss_pred c
Confidence 4
No 123
>PF06844 DUF1244: Protein of unknown function (DUF1244); InterPro: IPR009654 This family consists of several short bacterial proteins of around 100 residues in length. The function of this family is unknown.; PDB: 2O35_A 3FYB_B.
Probab=80.89 E-value=1.3 Score=27.41 Aligned_cols=19 Identities=21% Similarity=0.543 Sum_probs=13.4
Q ss_pred cccHHHHHHHHHHHhhCCC
Q 045388 68 SFCSDCINKHVATKIQGGI 86 (214)
Q Consensus 68 ~fC~~Cl~~~~~~~i~~~~ 86 (214)
-||++||..|+...-.+..
T Consensus 11 gFCRNCLskWy~~aA~~~g 29 (68)
T PF06844_consen 11 GFCRNCLSKWYREAAEERG 29 (68)
T ss_dssp S--HHHHHHHHHHHHHHCT
T ss_pred HHHHHHHHHHHHHHHHhcC
Confidence 4999999999988776543
No 124
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=80.68 E-value=0.63 Score=37.66 Aligned_cols=45 Identities=27% Similarity=0.483 Sum_probs=33.6
Q ss_pred cccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcC
Q 045388 44 RSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVL 101 (214)
Q Consensus 44 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 101 (214)
.+-|.||-..|..+. ...|+|.||..|....++ ..-+|++ |+...
T Consensus 241 Pf~c~icr~~f~~pV---vt~c~h~fc~~ca~~~~q--------k~~~c~v--C~~~t 285 (313)
T KOG1813|consen 241 PFKCFICRKYFYRPV---VTKCGHYFCEVCALKPYQ--------KGEKCYV--CSQQT 285 (313)
T ss_pred Cccccccccccccch---hhcCCceeehhhhccccc--------cCCccee--ccccc
Confidence 467999999987764 478999999999776653 2347887 76533
No 125
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=80.22 E-value=2.5 Score=34.37 Aligned_cols=44 Identities=30% Similarity=0.816 Sum_probs=32.6
Q ss_pred ccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCC
Q 045388 45 SSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKS 99 (214)
Q Consensus 45 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~ 99 (214)
..|++|..-+..+ +....|+|.||.+||..-+. + ..+.||. |..
T Consensus 275 LkCplc~~Llrnp--~kT~cC~~~fc~eci~~al~----d---sDf~Cpn--C~r 318 (427)
T COG5222 275 LKCPLCHCLLRNP--MKTPCCGHTFCDECIGTALL----D---SDFKCPN--CSR 318 (427)
T ss_pred ccCcchhhhhhCc--ccCccccchHHHHHHhhhhh----h---ccccCCC--ccc
Confidence 7899998876544 23468999999999876543 2 4579999 753
No 126
>PF12773 DZR: Double zinc ribbon
Probab=79.98 E-value=1.3 Score=25.76 Aligned_cols=28 Identities=29% Similarity=0.756 Sum_probs=16.0
Q ss_pred CCCcccCccCCCceeeecCCCCCCcCcccCCCCCh
Q 045388 130 SQGIYCPFKDCSAKLVYENDGEDVLSESECPYCHR 164 (214)
Q Consensus 130 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 164 (214)
.+..+|| .|+..+.... ...+.|+.|+.
T Consensus 10 ~~~~fC~--~CG~~l~~~~-----~~~~~C~~Cg~ 37 (50)
T PF12773_consen 10 DDAKFCP--HCGTPLPPPD-----QSKKICPNCGA 37 (50)
T ss_pred ccccCCh--hhcCChhhcc-----CCCCCCcCCcC
Confidence 3456777 7777766211 13455666654
No 127
>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=79.47 E-value=1.1 Score=25.92 Aligned_cols=29 Identities=21% Similarity=0.447 Sum_probs=18.9
Q ss_pred CcccCccCCCceeeecCCCCCCcCcccCCCCCh
Q 045388 132 GIYCPFKDCSAKLVYENDGEDVLSESECPYCHR 164 (214)
Q Consensus 132 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 164 (214)
...||++.|+..++-.... .+..|..|+.
T Consensus 18 rk~CP~~~CG~GvFMA~H~----dR~~CGKCg~ 46 (47)
T PF01599_consen 18 RKECPSPRCGAGVFMAEHK----DRHYCGKCGY 46 (47)
T ss_dssp SEE-TSTTTTSSSEEEE-S----SEEEETTTSS
T ss_pred hhcCCCcccCCceEeeecC----CCccCCCccc
Confidence 4589999999866554432 5677877764
No 128
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=79.31 E-value=5.1 Score=37.29 Aligned_cols=41 Identities=24% Similarity=0.580 Sum_probs=32.4
Q ss_pred cccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCC
Q 045388 44 RSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKS 99 (214)
Q Consensus 44 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~ 99 (214)
...|..|--++..+-+. ..|+|.|...|+. + ..-.||. |..
T Consensus 840 ~skCs~C~~~LdlP~Vh--F~CgHsyHqhC~e--------~---~~~~CP~--C~~ 880 (933)
T KOG2114|consen 840 VSKCSACEGTLDLPFVH--FLCGHSYHQHCLE--------D---KEDKCPK--CLP 880 (933)
T ss_pred eeeecccCCccccceee--eecccHHHHHhhc--------c---CcccCCc--cch
Confidence 46899999888877543 5899999999988 2 3468998 765
No 129
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=79.12 E-value=2 Score=25.66 Aligned_cols=35 Identities=20% Similarity=0.565 Sum_probs=28.3
Q ss_pred ccccccccccccc-cccccccCCCCccccHHHHHHH
Q 045388 43 SRSSCEICRERRE-NDQMFKIESCIHSFCSDCINKH 77 (214)
Q Consensus 43 ~~~~C~iC~~~~~-~~~~~~~~~C~H~fC~~Cl~~~ 77 (214)
....|++|-+.+. ..+++....|+-.+.++||...
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~ 39 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKA 39 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCCCcccHHHHhhC
Confidence 3567999999995 5566778899999999998653
No 130
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=78.94 E-value=1.6 Score=25.22 Aligned_cols=33 Identities=27% Similarity=0.687 Sum_probs=22.1
Q ss_pred ccccccccccccccccCCC--Cc---cccHHHHHHHHHH
Q 045388 47 CEICRERRENDQMFKIESC--IH---SFCSDCINKHVAT 80 (214)
Q Consensus 47 C~iC~~~~~~~~~~~~~~C--~H---~fC~~Cl~~~~~~ 80 (214)
|-||+++...+..+ ..+| .- .+..+||..|+..
T Consensus 1 CrIC~~~~~~~~~l-i~pC~C~Gs~~~vH~~CL~~W~~~ 38 (47)
T PF12906_consen 1 CRICLEGEEEDEPL-ISPCRCKGSMKYVHRSCLERWIRE 38 (47)
T ss_dssp ETTTTEE-SSSS-E-E-SSS-SSCCGSEECCHHHHHHHH
T ss_pred CeEeCCcCCCCCce-ecccccCCCcchhHHHHHHHHHHh
Confidence 67899887655412 2344 43 6889999999987
No 131
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=78.62 E-value=0.69 Score=42.31 Aligned_cols=51 Identities=35% Similarity=0.809 Sum_probs=36.6
Q ss_pred ccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHh
Q 045388 45 SSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACK 107 (214)
Q Consensus 45 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~ 107 (214)
..|.+|.+ . ...+ ...|+|.||.+|+...+...- ...||. |...+....+.
T Consensus 455 ~~c~ic~~-~--~~~~-it~c~h~~c~~c~~~~i~~~~------~~~~~~--cr~~l~~~~l~ 505 (674)
T KOG1001|consen 455 HWCHICCD-L--DSFF-ITRCGHDFCVECLKKSIQQSE------NAPCPL--CRNVLKEKKLL 505 (674)
T ss_pred cccccccc-c--ccce-eecccchHHHHHHHhcccccc------CCCCcH--HHHHHHHHHHh
Confidence 79999999 2 2223 579999999999999885322 226777 87766655544
No 132
>PLN02400 cellulose synthase
Probab=78.52 E-value=1.4 Score=42.04 Aligned_cols=63 Identities=25% Similarity=0.547 Sum_probs=48.4
Q ss_pred CCcccCccCCCceeeecCCCCCCcCcccCCCCChhhccccCCCCCCChHHHHHHHHHHhCCCccCCCCCccceecCCCCC
Q 045388 131 QGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKYHIERTGGCLH 210 (214)
Q Consensus 131 ~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~~~iek~~GCnh 210 (214)
+..-|. -|+-.+-.+..+ ...+-|..|+.-.|.-|.. +.+....+.||+|++...+.-|+..
T Consensus 35 ~gqiCq--ICGD~VG~t~dG---e~FVAC~eCaFPVCRpCYE-------------YERkeGnq~CPQCkTrYkR~Kgspr 96 (1085)
T PLN02400 35 NGQICQ--ICGDDVGVTETG---DVFVACNECAFPVCRPCYE-------------YERKDGTQCCPQCKTRYRRHKGSPR 96 (1085)
T ss_pred CCceee--ecccccCcCCCC---CEEEEEccCCCccccchhh-------------eecccCCccCcccCCccccccCCCC
Confidence 334677 788777666555 3788999999999999975 3345678999999999988878775
Q ss_pred e
Q 045388 211 M 211 (214)
Q Consensus 211 m 211 (214)
+
T Consensus 97 V 97 (1085)
T PLN02400 97 V 97 (1085)
T ss_pred C
Confidence 4
No 133
>PRK00420 hypothetical protein; Validated
Probab=77.74 E-value=5.5 Score=27.68 Aligned_cols=25 Identities=32% Similarity=0.603 Sum_probs=17.1
Q ss_pred cccCccCCCceeeecCCCCCCcCcccCCCCCh
Q 045388 133 IYCPFKDCSAKLVYENDGEDVLSESECPYCHR 164 (214)
Q Consensus 133 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 164 (214)
..|| .|+..++.... ....||.||.
T Consensus 24 ~~CP--~Cg~pLf~lk~-----g~~~Cp~Cg~ 48 (112)
T PRK00420 24 KHCP--VCGLPLFELKD-----GEVVCPVHGK 48 (112)
T ss_pred CCCC--CCCCcceecCC-----CceECCCCCC
Confidence 6799 89988887443 3445666665
No 134
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=77.51 E-value=0.74 Score=41.86 Aligned_cols=29 Identities=31% Similarity=0.844 Sum_probs=22.1
Q ss_pred CCChhhccccCCCCCCChHHHHHHHHHHhCCCccCCCCCccc
Q 045388 161 YCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKYHI 202 (214)
Q Consensus 161 ~C~~~~C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~~~i 202 (214)
.|++.||..|-.. .-+..-+.||+|+..+
T Consensus 660 kC~H~FC~~Cvq~-------------r~etRqRKCP~Cn~aF 688 (698)
T KOG0978|consen 660 KCGHVFCEECVQT-------------RYETRQRKCPKCNAAF 688 (698)
T ss_pred hcchHHHHHHHHH-------------HHHHhcCCCCCCCCCC
Confidence 6899999999652 1244569999999865
No 135
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=77.30 E-value=0.51 Score=27.47 Aligned_cols=36 Identities=22% Similarity=0.525 Sum_probs=30.9
Q ss_pred ccccccccccccccccccccCCCCccccHHHHHHHH
Q 045388 43 SRSSCEICRERRENDQMFKIESCIHSFCSDCINKHV 78 (214)
Q Consensus 43 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~ 78 (214)
.+++|.+|-+.++..+..+..-||...|..||+.-.
T Consensus 6 sry~CDLCn~~~p~~~LRQCvlCGRWaC~sCW~deY 41 (57)
T PF14445_consen 6 SRYSCDLCNSSHPISELRQCVLCGRWACNSCWQDEY 41 (57)
T ss_pred hhHhHHhhcccCcHHHHHHHhhhchhhhhhhhhhhH
Confidence 468999999999988877777899999999998743
No 136
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=76.92 E-value=1.3 Score=38.56 Aligned_cols=35 Identities=26% Similarity=0.627 Sum_probs=26.2
Q ss_pred CCChhhccccCCCCCCChHHHHHHHHHHhCCCccCCCCCcccee
Q 045388 161 YCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKYHIER 204 (214)
Q Consensus 161 ~C~~~~C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~~~iek 204 (214)
.||+.||+.|... +..+.....++.||-|+..|-.
T Consensus 203 ~CGHiFC~~CiLq---------y~~~s~~~~~~~CPiC~s~I~~ 237 (513)
T KOG2164|consen 203 NCGHIFCGPCILQ---------YWNYSAIKGPCSCPICRSTITL 237 (513)
T ss_pred ccCceeeHHHHHH---------HHhhhcccCCccCCchhhhccc
Confidence 5899999999642 2333356788999999998854
No 137
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=76.34 E-value=2.4 Score=33.05 Aligned_cols=55 Identities=20% Similarity=0.468 Sum_probs=40.4
Q ss_pred cccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcC
Q 045388 44 RSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVL 101 (214)
Q Consensus 44 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 101 (214)
...|.+|-.++...+.+ .+-|-|.|..+|+..+..+--.+.--....||. |...+
T Consensus 50 ~pNC~LC~t~La~gdt~-RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~--Cs~ei 104 (299)
T KOG3970|consen 50 NPNCRLCNTPLASGDTT-RLVCYHLFHWKCLNERAANLPANTAPAGYQCPC--CSQEI 104 (299)
T ss_pred CCCCceeCCccccCcce-eehhhhhHHHHHhhHHHhhCCCcCCCCcccCCC--CCCcc
Confidence 35799999998887766 489999999999999875444332213458998 76544
No 138
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 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 zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=76.06 E-value=2.6 Score=21.47 Aligned_cols=14 Identities=36% Similarity=0.890 Sum_probs=8.3
Q ss_pred cCCCCCccceecCC
Q 045388 194 KCPNCKYHIERTGG 207 (214)
Q Consensus 194 ~CP~C~~~iek~~G 207 (214)
.||.|+..+.+.+|
T Consensus 1 ~CP~C~s~l~~~~~ 14 (28)
T PF03119_consen 1 TCPVCGSKLVREEG 14 (28)
T ss_dssp B-TTT--BEEE-CC
T ss_pred CcCCCCCEeEcCCC
Confidence 49999999988766
No 139
>PHA00626 hypothetical protein
Probab=75.67 E-value=2.7 Score=25.12 Aligned_cols=31 Identities=19% Similarity=0.355 Sum_probs=15.9
Q ss_pred ccCccCCCce-eeecCCCCCCcCcccCCCCChhh
Q 045388 134 YCPFKDCSAK-LVYENDGEDVLSESECPYCHRLF 166 (214)
Q Consensus 134 ~Cp~~~C~~~-~~~~~~~~~~~~~~~C~~C~~~~ 166 (214)
.|| +|+.. +.....-........|+.||+.|
T Consensus 2 ~CP--~CGS~~Ivrcg~cr~~snrYkCkdCGY~f 33 (59)
T PHA00626 2 SCP--KCGSGNIAKEKTMRGWSDDYVCCDCGYND 33 (59)
T ss_pred CCC--CCCCceeeeeceecccCcceEcCCCCCee
Confidence 377 78763 33322111113556677777655
No 140
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=75.26 E-value=2.1 Score=40.81 Aligned_cols=61 Identities=25% Similarity=0.612 Sum_probs=45.7
Q ss_pred cccCccCCCceeeecCCCCCCcCcccCCCCChhhccccCCCCCCChHHHHHHHHHHhCCCccCCCCCccceecCCCCCe
Q 045388 133 IYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKYHIERTGGCLHM 211 (214)
Q Consensus 133 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~~~iek~~GCnhm 211 (214)
.-|. -|+..+-.+..+ .+.+.|..|+.-.|..|.. +.+....+.||+|++...+.-|.+.+
T Consensus 16 ~~c~--iCGd~vg~~~~G---e~FVAC~eC~fpvCr~cye-------------ye~~~g~~~cp~c~t~y~~~~~~~~~ 76 (1044)
T PLN02915 16 KTCR--VCGDEVGVKEDG---QPFVACHVCGFPVCKPCYE-------------YERSEGNQCCPQCNTRYKRHKGCPRV 76 (1044)
T ss_pred chhh--ccccccCcCCCC---CEEEEeccCCCccccchhh-------------hhhhcCCccCCccCCchhhhcCCCCc
Confidence 3455 677666665554 2778999999999999974 34456789999999998877677654
No 141
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=74.48 E-value=3.5 Score=30.09 Aligned_cols=62 Identities=23% Similarity=0.462 Sum_probs=29.4
Q ss_pred CcHHHHhhcCCHHHHHHHHHHHHHHHhcC--CCCcccCccCCCceeeecCCCC--CCcCcccCCCCChh
Q 045388 101 LKFDACKSVLSKNVLELWEKALSQELIDA--SQGIYCPFKDCSAKLVYENDGE--DVLSESECPYCHRL 165 (214)
Q Consensus 101 l~~~~~~~~l~~~~~~~~~~~~~~~~~~~--~~~~~Cp~~~C~~~~~~~~~~~--~~~~~~~C~~C~~~ 165 (214)
++++.+..++...+. +..+.+..+.... .....|| .|+..+...+... +....+.||.||..
T Consensus 67 i~y~~~~~vik~r~~-~~~~~L~~~l~~e~~~~~Y~Cp--~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~ 132 (147)
T smart00531 67 INYDTLLDVVKYKLD-KMRKRLEDKLEDETNNAYYKCP--NCQSKYTFLEANQLLDMDGTFTCPRCGEE 132 (147)
T ss_pred ecHHHHHHHHHHHHH-HHHHHHHHHHhcccCCcEEECc--CCCCEeeHHHHHHhcCCCCcEECCCCCCE
Confidence 445555555433322 2223333332222 3456798 8987766543210 11233677777653
No 142
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=74.08 E-value=3.4 Score=22.62 Aligned_cols=28 Identities=25% Similarity=0.513 Sum_probs=12.5
Q ss_pred ccCccCCCceeeecCCCCCCcCcccCCCCCh
Q 045388 134 YCPFKDCSAKLVYENDGEDVLSESECPYCHR 164 (214)
Q Consensus 134 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 164 (214)
.|+ .|+..+.......+ .....||.||.
T Consensus 7 ~C~--~Cg~~fe~~~~~~~-~~~~~CP~Cg~ 34 (41)
T smart00834 7 RCE--DCGHTFEVLQKISD-DPLATCPECGG 34 (41)
T ss_pred EcC--CCCCEEEEEEecCC-CCCCCCCCCCC
Confidence 465 66665443322111 23444555554
No 143
>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=73.84 E-value=3 Score=34.29 Aligned_cols=52 Identities=19% Similarity=0.483 Sum_probs=32.2
Q ss_pred ccCccCCCceeeecCCCCCCcCcccCCCCChhhccccCCCCCCChHHHHHHHHHHhCCCccCCCCCccceec
Q 045388 134 YCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKYHIERT 205 (214)
Q Consensus 134 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~~~iek~ 205 (214)
.|| .|.......+.- ...+. .||+.||..|... +.. .+..+||.|+..+.|.
T Consensus 5 ~CP--~Ck~~~y~np~~---kl~i~--~CGH~~C~sCv~~------------l~~-~~~~~CP~C~~~lrk~ 56 (309)
T TIGR00570 5 GCP--RCKTTKYRNPSL---KLMVN--VCGHTLCESCVDL------------LFV-RGSGSCPECDTPLRKN 56 (309)
T ss_pred CCC--cCCCCCccCccc---ccccC--CCCCcccHHHHHH------------Hhc-CCCCCCCCCCCccchh
Confidence 477 777644333321 12222 6899999999642 111 2345899999988765
No 144
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=73.65 E-value=4 Score=30.87 Aligned_cols=58 Identities=17% Similarity=0.455 Sum_probs=32.5
Q ss_pred CcHHHHhhcCCHHHHHHHHHHHHHHHhcC--CCCcccCccCCCceeeecCCCCCCcCcccCCCCCh
Q 045388 101 LKFDACKSVLSKNVLELWEKALSQELIDA--SQGIYCPFKDCSAKLVYENDGEDVLSESECPYCHR 164 (214)
Q Consensus 101 l~~~~~~~~l~~~~~~~~~~~~~~~~~~~--~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 164 (214)
++.+.+..++..+.. +..+.+.++.-.. +....|| +|+.-+...+.. ...+.||.||.
T Consensus 85 l~~~~i~d~ik~~~~-~~~~klk~~l~~e~~~~~Y~Cp--~C~~rytf~eA~---~~~F~Cp~Cg~ 144 (178)
T PRK06266 85 PELEKLPEIIKKKKM-EELKKLKEQLEEEENNMFFFCP--NCHIRFTFDEAM---EYGFRCPQCGE 144 (178)
T ss_pred eCHHHHHHHHHHHHH-HHHHHHHHHhhhccCCCEEECC--CCCcEEeHHHHh---hcCCcCCCCCC
Confidence 455666666554433 2333333333322 3456799 799777766542 25677877765
No 145
>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=73.61 E-value=2.7 Score=20.59 Aligned_cols=9 Identities=33% Similarity=0.851 Sum_probs=6.3
Q ss_pred CcccCCCCC
Q 045388 155 SESECPYCH 163 (214)
Q Consensus 155 ~~~~C~~C~ 163 (214)
..+.||.||
T Consensus 15 v~f~CPnCG 23 (24)
T PF07754_consen 15 VPFPCPNCG 23 (24)
T ss_pred ceEeCCCCC
Confidence 566777776
No 146
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=73.51 E-value=1.8 Score=24.48 Aligned_cols=13 Identities=38% Similarity=0.917 Sum_probs=10.7
Q ss_pred CCCccCCCCCccc
Q 045388 190 KQLRKCPNCKYHI 202 (214)
Q Consensus 190 ~~~k~CP~C~~~i 202 (214)
..+|.||+|+++-
T Consensus 9 RGirkCp~CGt~N 21 (44)
T PF14952_consen 9 RGIRKCPKCGTYN 21 (44)
T ss_pred hccccCCcCcCcc
Confidence 4689999999854
No 147
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=73.29 E-value=4.2 Score=30.13 Aligned_cols=59 Identities=19% Similarity=0.400 Sum_probs=32.2
Q ss_pred CcHHHHhhcCCHHHHHHHHHHHHHHHhc--CCCCcccCccCCCceeeecCCCCCCcCcccCCCCChh
Q 045388 101 LKFDACKSVLSKNVLELWEKALSQELID--ASQGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRL 165 (214)
Q Consensus 101 l~~~~~~~~l~~~~~~~~~~~~~~~~~~--~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 165 (214)
++.+.+...+..++.... +.+....-. .+....|| +|+.-+...+.. ...+.||.||..
T Consensus 77 i~~~~i~d~Ik~~~~~~~-~~lk~~l~~e~~~~~Y~Cp--~c~~r~tf~eA~---~~~F~Cp~Cg~~ 137 (158)
T TIGR00373 77 INYEKALDVLKRKLEETA-KKLREKLEFETNNMFFICP--NMCVRFTFNEAM---ELNFTCPRCGAM 137 (158)
T ss_pred eCHHHHHHHHHHHHHHHH-HHHHHHHhhccCCCeEECC--CCCcEeeHHHHH---HcCCcCCCCCCE
Confidence 455666655544433222 223333222 23456798 898777666542 256788888764
No 148
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=73.18 E-value=1.6 Score=35.72 Aligned_cols=32 Identities=22% Similarity=0.540 Sum_probs=22.0
Q ss_pred cccccccccccccccccccCCCCccccHHHHHHH
Q 045388 44 RSSCEICRERRENDQMFKIESCIHSFCSDCINKH 77 (214)
Q Consensus 44 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~ 77 (214)
...|.-|- ++...--.+..|.|.||.+|.+..
T Consensus 90 VHfCd~Cd--~PI~IYGRmIPCkHvFCl~CAr~~ 121 (389)
T KOG2932|consen 90 VHFCDRCD--FPIAIYGRMIPCKHVFCLECARSD 121 (389)
T ss_pred eEeecccC--CcceeeecccccchhhhhhhhhcC
Confidence 45688883 333222237899999999997764
No 149
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=71.91 E-value=3.6 Score=24.56 Aligned_cols=30 Identities=30% Similarity=0.582 Sum_probs=18.8
Q ss_pred cccCccCCCceeeecCCCCCCcCcccCCCCChhh
Q 045388 133 IYCPFKDCSAKLVYENDGEDVLSESECPYCHRLF 166 (214)
Q Consensus 133 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 166 (214)
+.|| .|+..+...+.. ....+.|+.||..+
T Consensus 3 ~~CP--~CG~~iev~~~~--~GeiV~Cp~CGael 32 (54)
T TIGR01206 3 FECP--DCGAEIELENPE--LGELVICDECGAEL 32 (54)
T ss_pred cCCC--CCCCEEecCCCc--cCCEEeCCCCCCEE
Confidence 3577 888777665432 24566777777654
No 150
>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=71.79 E-value=4 Score=21.53 Aligned_cols=22 Identities=23% Similarity=0.637 Sum_probs=11.6
Q ss_pred CCCceeeecCCCCCCcCcccCCCCChh
Q 045388 139 DCSAKLVYENDGEDVLSESECPYCHRL 165 (214)
Q Consensus 139 ~C~~~~~~~~~~~~~~~~~~C~~C~~~ 165 (214)
+|+..+..... ..++|+.||..
T Consensus 5 ~Cg~~~~~~~~-----~~irC~~CG~R 26 (32)
T PF03604_consen 5 ECGAEVELKPG-----DPIRCPECGHR 26 (32)
T ss_dssp SSSSSE-BSTS-----STSSBSSSS-S
T ss_pred cCCCeeEcCCC-----CcEECCcCCCe
Confidence 66666654333 44567777753
No 151
>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=71.71 E-value=1.8 Score=22.49 Aligned_cols=25 Identities=32% Similarity=0.781 Sum_probs=11.6
Q ss_pred ccCccCCCceeeecCCCCCCcCcccCCCCChh
Q 045388 134 YCPFKDCSAKLVYENDGEDVLSESECPYCHRL 165 (214)
Q Consensus 134 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 165 (214)
.|| .|+.-....++ ..+.||.|+..
T Consensus 4 ~Cp--~C~se~~y~D~-----~~~vCp~C~~e 28 (30)
T PF08274_consen 4 KCP--LCGSEYTYEDG-----ELLVCPECGHE 28 (30)
T ss_dssp --T--TT-----EE-S-----SSEEETTTTEE
T ss_pred CCC--CCCCcceeccC-----CEEeCCccccc
Confidence 366 77776666554 56678888764
No 152
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=70.36 E-value=4.2 Score=27.61 Aligned_cols=37 Identities=14% Similarity=0.206 Sum_probs=23.1
Q ss_pred CCCCcccCccCCCceeeecCCCCCCcCcccCCCCChhhcc
Q 045388 129 ASQGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCA 168 (214)
Q Consensus 129 ~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~ 168 (214)
.+..+.|| +|+........+ .....+.|+.||.++=.
T Consensus 18 lpt~f~CP--~Cge~~v~v~~~-k~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 18 LPKIFECP--RCGKVSISVKIK-KNIAIITCGNCGLYTEF 54 (99)
T ss_pred CCcEeECC--CCCCeEeeeecC-CCcceEECCCCCCccCE
Confidence 35678899 898544332222 13467788888887544
No 153
>COG3492 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=70.11 E-value=4.1 Score=26.95 Aligned_cols=18 Identities=17% Similarity=0.639 Sum_probs=15.1
Q ss_pred ccccHHHHHHHHHHHhhC
Q 045388 67 HSFCSDCINKHVATKIQG 84 (214)
Q Consensus 67 H~fC~~Cl~~~~~~~i~~ 84 (214)
--||++||.+|+....+.
T Consensus 41 AgFCRNCLs~Wy~eaae~ 58 (104)
T COG3492 41 AGFCRNCLSNWYREAAEA 58 (104)
T ss_pred HHHHHHHHHHHHHHHHhc
Confidence 359999999999887764
No 154
>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=69.93 E-value=3 Score=28.83 Aligned_cols=31 Identities=32% Similarity=0.606 Sum_probs=19.1
Q ss_pred CcccCccCCCceeeecCCCCCCcCcccCCCCChhhccc
Q 045388 132 GIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAH 169 (214)
Q Consensus 132 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~ 169 (214)
.+.|| .|+.-|.--+. .-+.||+||..|=..
T Consensus 9 KR~Cp--~CG~kFYDLnk-----~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 9 KRTCP--SCGAKFYDLNK-----DPIVCPKCGTEFPPE 39 (108)
T ss_pred cccCC--CCcchhccCCC-----CCccCCCCCCccCcc
Confidence 35788 88866554332 335588888776444
No 155
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=69.76 E-value=4.2 Score=37.17 Aligned_cols=34 Identities=24% Similarity=0.687 Sum_probs=24.1
Q ss_pred CCCcccCccCCCceeeecCCCCCCcCcccCCCCChh------hccccCCCCC
Q 045388 130 SQGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRL------FCAHCYVPWH 175 (214)
Q Consensus 130 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~------~C~~C~~~~h 175 (214)
.+.++|+ .|+..+.. ..|+.||+. ||..|+....
T Consensus 13 ~~akFC~--~CG~~l~~----------~~Cp~CG~~~~~~~~fC~~CG~~~~ 52 (645)
T PRK14559 13 NNNRFCQ--KCGTSLTH----------KPCPQCGTEVPVDEAHCPNCGAETG 52 (645)
T ss_pred CCCcccc--ccCCCCCC----------CcCCCCCCCCCcccccccccCCccc
Confidence 5667888 88876521 249999855 9999987543
No 156
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=69.27 E-value=4.5 Score=27.69 Aligned_cols=34 Identities=24% Similarity=0.452 Sum_probs=23.0
Q ss_pred CCcccCccCCCceeeecCCCCCCcCcccCCCCChhh
Q 045388 131 QGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLF 166 (214)
Q Consensus 131 ~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 166 (214)
+.++|+ .|++.+....+..++.....|..|.+.+
T Consensus 3 ~~rfC~--eCNNmLYPkEDked~~L~laCrnCd~ve 36 (113)
T KOG2691|consen 3 GIRFCR--ECNNMLYPKEDKEDRILLLACRNCDYVE 36 (113)
T ss_pred ccchhh--hhhccccccccccccEEEEEecCCcceE
Confidence 356788 8888877766644555666777776554
No 157
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=68.89 E-value=4.9 Score=22.50 Aligned_cols=28 Identities=18% Similarity=0.487 Sum_probs=12.1
Q ss_pred ccCccCCCceeeecCCCCCCcCcccCCCCCh
Q 045388 134 YCPFKDCSAKLVYENDGEDVLSESECPYCHR 164 (214)
Q Consensus 134 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 164 (214)
.|+ +|+..+.......+ .....||.||.
T Consensus 7 ~C~--~Cg~~fe~~~~~~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 7 RCE--ECGHEFEVLQSISE-DDPVPCPECGS 34 (42)
T ss_pred EeC--CCCCEEEEEEEcCC-CCCCcCCCCCC
Confidence 455 66644433322111 24445555554
No 158
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=68.76 E-value=3.3 Score=28.41 Aligned_cols=25 Identities=28% Similarity=0.830 Sum_probs=17.0
Q ss_pred ccCccCCCceeeecCCCCCCcCcccCCCCChh
Q 045388 134 YCPFKDCSAKLVYENDGEDVLSESECPYCHRL 165 (214)
Q Consensus 134 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 165 (214)
.|| .|+.-+.+.++ ..+.||.|+++
T Consensus 4 ~CP--~C~seytY~dg-----~~~iCpeC~~E 28 (109)
T TIGR00686 4 PCP--KCNSEYTYHDG-----TQLICPSCLYE 28 (109)
T ss_pred cCC--cCCCcceEecC-----CeeECcccccc
Confidence 477 88888888776 44566666553
No 159
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=68.46 E-value=6.1 Score=28.44 Aligned_cols=13 Identities=15% Similarity=0.662 Sum_probs=7.8
Q ss_pred cccCccCCCceeeec
Q 045388 133 IYCPFKDCSAKLVYE 147 (214)
Q Consensus 133 ~~Cp~~~C~~~~~~~ 147 (214)
.+|+ +|+..+...
T Consensus 71 ~~C~--~CG~~~~~~ 83 (135)
T PRK03824 71 LKCR--NCGNEWSLK 83 (135)
T ss_pred EECC--CCCCEEecc
Confidence 3666 777665554
No 160
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=67.84 E-value=3.6 Score=24.13 Aligned_cols=27 Identities=19% Similarity=0.475 Sum_probs=17.5
Q ss_pred CcccCccCCCc-eeeecCCCCCCcCcccCCCCChhh
Q 045388 132 GIYCPFKDCSA-KLVYENDGEDVLSESECPYCHRLF 166 (214)
Q Consensus 132 ~~~Cp~~~C~~-~~~~~~~~~~~~~~~~C~~C~~~~ 166 (214)
..+|| .|+. ++.... ..+.|..|+..+
T Consensus 20 ~~fCP--~Cg~~~m~~~~------~r~~C~~Cgyt~ 47 (50)
T PRK00432 20 NKFCP--RCGSGFMAEHL------DRWHCGKCGYTE 47 (50)
T ss_pred cCcCc--CCCcchheccC------CcEECCCcCCEE
Confidence 34899 8887 443322 567788888654
No 161
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=67.67 E-value=0.87 Score=36.75 Aligned_cols=34 Identities=24% Similarity=0.789 Sum_probs=24.0
Q ss_pred cCCCCChhhccccCCCCCCChHHHHHHHHHHhCCCccCCCCCccceec
Q 045388 158 ECPYCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKYHIERT 205 (214)
Q Consensus 158 ~C~~C~~~~C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~~~iek~ 205 (214)
.|.-||+.|||.|-.+|-.. ...||-|+......
T Consensus 253 SaTpCGHiFCWsCI~~w~~e--------------k~eCPlCR~~~~ps 286 (293)
T KOG0317|consen 253 SATPCGHIFCWSCILEWCSE--------------KAECPLCREKFQPS 286 (293)
T ss_pred CcCcCcchHHHHHHHHHHcc--------------ccCCCcccccCCCc
Confidence 36679999999997654322 22399999877654
No 162
>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=67.15 E-value=3.2 Score=33.14 Aligned_cols=68 Identities=19% Similarity=0.378 Sum_probs=37.5
Q ss_pred cccCccCCCceeeecCCCC-------CCcCcccCCCC---ChhhccccCCCCCCChHHHHHHHHHHhCCCccCCCCCccc
Q 045388 133 IYCPFKDCSAKLVYENDGE-------DVLSESECPYC---HRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKYHI 202 (214)
Q Consensus 133 ~~Cp~~~C~~~~~~~~~~~-------~~~~~~~C~~C---~~~~C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~~~i 202 (214)
+.|. .|..++--+++.+ -....+.|..| |+..|++|+.-+=+.+.......+. .....+||+|+..+
T Consensus 143 f~Cs--fC~~flCEDDQFEHQAsCQvLe~E~~KC~SCNrlGq~sCLRCK~cfCddHvrrKg~ky~-k~k~~PCPKCg~et 219 (314)
T PF06524_consen 143 FKCS--FCDNFLCEDDQFEHQASCQVLESETFKCQSCNRLGQYSCLRCKICFCDDHVRRKGFKYE-KGKPIPCPKCGYET 219 (314)
T ss_pred EEee--cCCCeeeccchhhhhhhhhhhhcccccccccccccchhhhheeeeehhhhhhhcccccc-cCCCCCCCCCCCcc
Confidence 4566 7777776555421 01244567666 5778888877543221111111111 23568999999866
Q ss_pred e
Q 045388 203 E 203 (214)
Q Consensus 203 e 203 (214)
.
T Consensus 220 ~ 220 (314)
T PF06524_consen 220 Q 220 (314)
T ss_pred c
Confidence 4
No 163
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=66.94 E-value=9.1 Score=26.76 Aligned_cols=32 Identities=19% Similarity=0.358 Sum_probs=21.1
Q ss_pred ccccccccccccccc--cccccCCCCccccHHHH
Q 045388 43 SRSSCEICRERREND--QMFKIESCIHSFCSDCI 74 (214)
Q Consensus 43 ~~~~C~iC~~~~~~~--~~~~~~~C~H~fC~~Cl 74 (214)
....|.+|..++..- .-.....|+|.+|..|-
T Consensus 53 ~~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~ 86 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCG 86 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTCEEETTTTEEEETTSE
T ss_pred CCcchhhhCCcccccCCCCCcCCcCCccccCccC
Confidence 456899999876432 11226799999999993
No 164
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=66.55 E-value=5.2 Score=27.88 Aligned_cols=32 Identities=25% Similarity=0.420 Sum_probs=22.3
Q ss_pred CcccCccCCCceeeecCCCCCCcCcccCCCCChhhc
Q 045388 132 GIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFC 167 (214)
Q Consensus 132 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C 167 (214)
..+|| .|+..+....... ...+.|+.||+.+=
T Consensus 2 m~FCp--~Cgsll~p~~~~~--~~~l~C~kCgye~~ 33 (113)
T COG1594 2 MRFCP--KCGSLLYPKKDDE--GGKLVCRKCGYEEE 33 (113)
T ss_pred ccccC--CccCeeEEeEcCC--CcEEECCCCCcchh
Confidence 35799 9999998875431 23677888877543
No 165
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=66.29 E-value=5.6 Score=22.62 Aligned_cols=21 Identities=14% Similarity=0.420 Sum_probs=9.8
Q ss_pred CCCceeeecCCCCCCcCcccCCCCCh
Q 045388 139 DCSAKLVYENDGEDVLSESECPYCHR 164 (214)
Q Consensus 139 ~C~~~~~~~~~~~~~~~~~~C~~C~~ 164 (214)
+|+.-+..+.. ..++||.||.
T Consensus 7 ~Cg~~~~~~~~-----~~irC~~CG~ 27 (44)
T smart00659 7 ECGRENEIKSK-----DVVRCRECGY 27 (44)
T ss_pred CCCCEeecCCC-----CceECCCCCc
Confidence 55554444322 3455555554
No 166
>PRK10220 hypothetical protein; Provisional
Probab=66.16 E-value=4.4 Score=27.85 Aligned_cols=25 Identities=32% Similarity=0.887 Sum_probs=17.1
Q ss_pred ccCccCCCceeeecCCCCCCcCcccCCCCChh
Q 045388 134 YCPFKDCSAKLVYENDGEDVLSESECPYCHRL 165 (214)
Q Consensus 134 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 165 (214)
.|| .|+.-+.+.++ ..+.||.|+++
T Consensus 5 ~CP--~C~seytY~d~-----~~~vCpeC~hE 29 (111)
T PRK10220 5 HCP--KCNSEYTYEDN-----GMYICPECAHE 29 (111)
T ss_pred cCC--CCCCcceEcCC-----CeEECCcccCc
Confidence 477 88888888776 44566665553
No 167
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=66.15 E-value=5.8 Score=36.71 Aligned_cols=50 Identities=18% Similarity=0.409 Sum_probs=36.6
Q ss_pred cccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcH
Q 045388 44 RSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKF 103 (214)
Q Consensus 44 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~ 103 (214)
...|++|+..+....+..-..|+|.||..||..|-.. .=.||. |...+..
T Consensus 123 ~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~--------aqTCPi--DR~EF~~ 172 (1134)
T KOG0825|consen 123 ENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRC--------AQTCPV--DRGEFGE 172 (1134)
T ss_pred hhhhhHHHHHHHHHhhccccccccccHHHHhhhhhhh--------cccCch--hhhhhhe
Confidence 4568888887766555446799999999999999752 347888 7665543
No 168
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=65.84 E-value=8.1 Score=28.54 Aligned_cols=52 Identities=15% Similarity=0.441 Sum_probs=35.0
Q ss_pred ccccccccccccccccccccCCCCc---cccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHH
Q 045388 43 SRSSCEICRERRENDQMFKIESCIH---SFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFD 104 (214)
Q Consensus 43 ~~~~C~iC~~~~~~~~~~~~~~C~H---~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~ 104 (214)
....|-||+++.... ..--.|.. ...++|++.|+... ...+|+. |+..+...
T Consensus 7 ~~~~CRIC~~~~~~~--~~PC~CkGs~k~VH~sCL~rWi~~s------~~~~Cei--C~~~Y~i~ 61 (162)
T PHA02825 7 MDKCCWICKDEYDVV--TNYCNCKNENKIVHKECLEEWINTS------KNKSCKI--CNGPYNIK 61 (162)
T ss_pred CCCeeEecCCCCCCc--cCCcccCCCchHHHHHHHHHHHhcC------CCCcccc--cCCeEEEE
Confidence 457899999986432 22234444 57999999999742 3578999 87655433
No 169
>PHA02926 zinc finger-like protein; Provisional
Probab=65.72 E-value=19 Score=28.22 Aligned_cols=36 Identities=28% Similarity=0.826 Sum_probs=25.2
Q ss_pred CCCChhhccccCCCCCCChHHHHHHHHHHhCCCccCCCCCccce
Q 045388 160 PYCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKYHIE 203 (214)
Q Consensus 160 ~~C~~~~C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~~~ie 203 (214)
+.|++.||+.|-..|..... .....+.||-|+..+.
T Consensus 195 ~~CnHsFCl~CIr~Wr~~r~--------~~~~~rsCPiCR~~f~ 230 (242)
T PHA02926 195 DSCNHIFCITCINIWHRTRR--------ETGASDNCPICRTRFR 230 (242)
T ss_pred CCCCchHHHHHHHHHHHhcc--------ccCcCCcCCCCcceee
Confidence 47999999999876653210 1234578999998764
No 170
>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=65.71 E-value=6.6 Score=21.98 Aligned_cols=24 Identities=33% Similarity=0.802 Sum_probs=16.6
Q ss_pred cccCccCCCceeeecCCCCCCcCcccCCCCC
Q 045388 133 IYCPFKDCSAKLVYENDGEDVLSESECPYCH 163 (214)
Q Consensus 133 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~ 163 (214)
..|| .|+..+..+.. ..+.|+.|+
T Consensus 18 ~~Cp--~C~~PL~~~k~-----g~~~Cv~C~ 41 (41)
T PF06677_consen 18 EHCP--DCGTPLMRDKD-----GKIYCVSCG 41 (41)
T ss_pred CccC--CCCCeeEEecC-----CCEECCCCC
Confidence 4699 89988877544 345677664
No 171
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=65.69 E-value=4.5 Score=27.21 Aligned_cols=33 Identities=24% Similarity=0.659 Sum_probs=22.9
Q ss_pred cccCccCCCceeeecCCCCCCcCcccCCCCChhhccc
Q 045388 133 IYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAH 169 (214)
Q Consensus 133 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~ 169 (214)
.+|| .|+..++...+. ....+.|..|.+.+=..
T Consensus 2 ~FCP--~Cgn~Live~g~--~~~rf~C~tCpY~~~I~ 34 (105)
T KOG2906|consen 2 LFCP--TCGNMLIVESGE--SCNRFSCRTCPYVFPIS 34 (105)
T ss_pred cccC--CCCCEEEEecCC--eEeeEEcCCCCceeeEe
Confidence 4799 999999998875 24566666666655443
No 172
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=65.50 E-value=5.6 Score=21.91 Aligned_cols=13 Identities=38% Similarity=0.841 Sum_probs=9.2
Q ss_pred ccCCCCCc-cceec
Q 045388 193 RKCPNCKY-HIERT 205 (214)
Q Consensus 193 k~CP~C~~-~iek~ 205 (214)
+.||.|+. +|+|.
T Consensus 2 ~~CP~Cg~~lv~r~ 15 (39)
T PF01396_consen 2 EKCPKCGGPLVLRR 15 (39)
T ss_pred cCCCCCCceeEEEE
Confidence 67999998 44444
No 173
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=64.65 E-value=8.7 Score=26.76 Aligned_cols=25 Identities=24% Similarity=0.744 Sum_probs=12.9
Q ss_pred cccCccCCCceeeecCCCCCCcCcccCCCCCh
Q 045388 133 IYCPFKDCSAKLVYENDGEDVLSESECPYCHR 164 (214)
Q Consensus 133 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 164 (214)
.+|+ +|+..+..... ..+.||.||.
T Consensus 71 ~~C~--~Cg~~~~~~~~-----~~~~CP~Cgs 95 (114)
T PRK03681 71 CWCE--TCQQYVTLLTQ-----RVRRCPQCHG 95 (114)
T ss_pred EEcc--cCCCeeecCCc-----cCCcCcCcCC
Confidence 3677 77765544322 2244666653
No 174
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=64.44 E-value=2.4 Score=26.36 Aligned_cols=37 Identities=22% Similarity=0.486 Sum_probs=18.7
Q ss_pred Cccccccccccccccccc-ccccCCCCccccHHHHHHH
Q 045388 41 PPSRSSCEICRERRENDQ-MFKIESCIHSFCSDCINKH 77 (214)
Q Consensus 41 ~~~~~~C~iC~~~~~~~~-~~~~~~C~H~fC~~Cl~~~ 77 (214)
+.+...|.+|...|.... -.....||+.||.+|....
T Consensus 6 d~~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~~ 43 (69)
T PF01363_consen 6 DSEASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQR 43 (69)
T ss_dssp GGG-SB-TTT--B-BSSS-EEE-TTT--EEECCCS-EE
T ss_pred CCCCCcCcCcCCcCCCceeeEccCCCCCEECCchhCCE
Confidence 345688999999985421 1116689999999997544
No 175
>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=64.14 E-value=6.3 Score=23.03 Aligned_cols=47 Identities=19% Similarity=0.433 Sum_probs=24.1
Q ss_pred ccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCC
Q 045388 45 SSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKS 99 (214)
Q Consensus 45 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~ 99 (214)
..|++-+..+..+ .....|.|.-|.+ +..|+....+.+. .+||. |+.
T Consensus 3 L~CPls~~~i~~P--~Rg~~C~H~~CFD-l~~fl~~~~~~~~---W~CPi--C~~ 49 (50)
T PF02891_consen 3 LRCPLSFQRIRIP--VRGKNCKHLQCFD-LESFLESNQRTPK---WKCPI--CNK 49 (50)
T ss_dssp SB-TTTSSB-SSE--EEETT--SS--EE-HHHHHHHHHHS------B-TT--T--
T ss_pred eeCCCCCCEEEeC--ccCCcCcccceEC-HHHHHHHhhccCC---eECcC--CcC
Confidence 4678877766554 2357899997755 6677777766544 68998 754
No 176
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 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. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=63.93 E-value=3.5 Score=22.24 Aligned_cols=31 Identities=16% Similarity=0.474 Sum_probs=15.6
Q ss_pred ccHHHHHHHHHHHhhCCCcccccCCCCCCCCcC
Q 045388 69 FCSDCINKHVATKIQGGIITPVTCPGPDCKSVL 101 (214)
Q Consensus 69 fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 101 (214)
+|.+|+++|....-+.-....+.|+. |+-.+
T Consensus 1 lC~~C~~Ey~~p~~RR~~~~~isC~~--CGPr~ 31 (35)
T PF07503_consen 1 LCDDCLKEYFDPSNRRFHYQFISCTN--CGPRY 31 (35)
T ss_dssp --HHHHHHHCSTTSTTTT-TT--BTT--CC-SC
T ss_pred CCHHHHHHHcCCCCCcccCcCccCCC--CCCCE
Confidence 48889998864332222225789988 76544
No 177
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=63.45 E-value=1.3 Score=28.28 Aligned_cols=49 Identities=33% Similarity=0.702 Sum_probs=33.4
Q ss_pred ccccccccccc---------ccccc-cCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcC
Q 045388 46 SCEICRERREN---------DQMFK-IESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVL 101 (214)
Q Consensus 46 ~C~iC~~~~~~---------~~~~~-~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 101 (214)
+|+||--.|.. ++-.- .--|.|.|-.-|+.+|+...-.++. ||. |...+
T Consensus 22 ~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~-----CPm--cRq~~ 80 (84)
T KOG1493|consen 22 TCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQ-----CPM--CRQTW 80 (84)
T ss_pred ccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCcccccc-----CCc--chhee
Confidence 89999877643 11111 2257899999999999877665544 888 66544
No 178
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=63.06 E-value=7 Score=20.72 Aligned_cols=28 Identities=21% Similarity=0.552 Sum_probs=17.4
Q ss_pred CcccCccCCCceeee-cCCCCCCcCcccCCCCChhh
Q 045388 132 GIYCPFKDCSAKLVY-ENDGEDVLSESECPYCHRLF 166 (214)
Q Consensus 132 ~~~Cp~~~C~~~~~~-~~~~~~~~~~~~C~~C~~~~ 166 (214)
...|+ .|++..+. .+. ....|+.|+..|
T Consensus 3 ~~~C~--~C~~~~i~~~~~-----~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 3 LKKCS--KCGGNGIVNKED-----DYEVCIFCGSSF 31 (33)
T ss_pred ceEcC--CCCCCeEEEecC-----CeEEcccCCcEe
Confidence 45677 78876666 433 445577777643
No 179
>PF06467 zf-FCS: MYM-type Zinc finger with FCS sequence motif; InterPro: IPR010507 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. MYM-type zinc fingers were identified in MYM family proteins []. Human protein Q14202 from SWISSPROT is involved in a chromosomal translocation and may be responsible for X-linked retardation in XQ13.1 []. Q9UBW7 from SWISSPROT is also involved in disease. In myeloproliferative disorders it is fused to FGF receptor 1 []; in atypical myeloproliferative disorders it is rearranged []. Members of the family generally are involved in development. This Zn-finger domain functions as a transcriptional trans-activator of late vaccinia viral genes, and orthologues are also found in all nucleocytoplasmic large DNA viruses, NCLDV. This domain is also found fused to the C termini of recombinases from certain prokaryotic transposons []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2L8E_A 2DAS_A.
Probab=62.88 E-value=8.3 Score=21.34 Aligned_cols=36 Identities=17% Similarity=0.553 Sum_probs=21.7
Q ss_pred cccccccccccccccccc---cccCCCCcccc-HHHHHHH
Q 045388 42 PSRSSCEICRERRENDQM---FKIESCIHSFC-SDCINKH 77 (214)
Q Consensus 42 ~~~~~C~iC~~~~~~~~~---~~~~~C~H~fC-~~Cl~~~ 77 (214)
.....|..|...+..... +....-.|.|| ..|+..|
T Consensus 4 ~~~~~C~~C~~~~~~~~~~~~~~~~g~~~~FCS~~C~~~y 43 (43)
T PF06467_consen 4 LKMKTCSYCKKYIPNKPTMIEVQYDGKMKQFCSQSCLSSY 43 (43)
T ss_dssp -SCEE-TTT--EEECCC----EE-TTTTSCCSSHHHHHHH
T ss_pred CcCCcCcccCCcccCCCccccccccCcccChhCHHHHhhC
Confidence 456789999999876552 33446678899 7787765
No 180
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=62.73 E-value=2.6 Score=37.96 Aligned_cols=37 Identities=19% Similarity=0.388 Sum_probs=28.7
Q ss_pred cccccccccccccccccccc-cCCCCccccHHHHHHHH
Q 045388 42 PSRSSCEICRERRENDQMFK-IESCIHSFCSDCINKHV 78 (214)
Q Consensus 42 ~~~~~C~iC~~~~~~~~~~~-~~~C~H~fC~~Cl~~~~ 78 (214)
.....|.||+..|....+.. .+.|||..|+.|+....
T Consensus 9 ~~~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~ly 46 (861)
T KOG3161|consen 9 VLLLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLY 46 (861)
T ss_pred HHHhhchHHHHHHHHHhcCcccccccchHHHHHHHhHh
Confidence 34678999988876554322 78999999999998764
No 181
>PF14369 zf-RING_3: zinc-finger
Probab=62.72 E-value=9.9 Score=20.41 Aligned_cols=30 Identities=27% Similarity=0.692 Sum_probs=17.7
Q ss_pred CcccCccCCCceeeecCCCCCCcCcccCCCCChhh
Q 045388 132 GIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLF 166 (214)
Q Consensus 132 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 166 (214)
..||- .|...+....... ..+.||.|+..|
T Consensus 2 ~ywCh--~C~~~V~~~~~~~---~~~~CP~C~~gF 31 (35)
T PF14369_consen 2 RYWCH--QCNRFVRIAPSPD---SDVACPRCHGGF 31 (35)
T ss_pred CEeCc--cCCCEeEeCcCCC---CCcCCcCCCCcE
Confidence 35777 8887777653321 223588777544
No 182
>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=62.63 E-value=4.7 Score=20.08 Aligned_cols=20 Identities=30% Similarity=0.468 Sum_probs=15.3
Q ss_pred ccCCCCCCCCcCcHHHHhhcCC
Q 045388 90 VTCPGPDCKSVLKFDACKSVLS 111 (214)
Q Consensus 90 i~CP~~~C~~~l~~~~~~~~l~ 111 (214)
+.||. |+..+....+..+|+
T Consensus 2 v~CPi--C~~~v~~~~in~HLD 21 (26)
T smart00734 2 VQCPV--CFREVPENLINSHLD 21 (26)
T ss_pred CcCCC--CcCcccHHHHHHHHH
Confidence 57998 888887777776665
No 183
>PF14149 YhfH: YhfH-like protein
Probab=62.53 E-value=0.98 Score=24.63 Aligned_cols=31 Identities=26% Similarity=0.637 Sum_probs=21.5
Q ss_pred HHHHHHhCCCccCCCCCccceecCCCCCeec
Q 045388 183 MRELVKKKQLRKCPNCKYHIERTGGCLHMTC 213 (214)
Q Consensus 183 ~~~~~~~~~~k~CP~C~~~iek~~GCnhm~C 213 (214)
..++.++...|.|+.||..|+--.-|..++|
T Consensus 4 ~~eFfrnLp~K~C~~CG~~i~EQ~E~Y~n~C 34 (37)
T PF14149_consen 4 IVEFFRNLPPKKCTECGKEIEEQAECYGNEC 34 (37)
T ss_pred HHHHHHhCCCcccHHHHHHHHHHHHHHhCcC
Confidence 3456778888999999998875444444433
No 184
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=62.35 E-value=9.5 Score=30.30 Aligned_cols=60 Identities=23% Similarity=0.429 Sum_probs=35.2
Q ss_pred HHHhhcCCHHHHHHHHHHHHHH-Hhc--CCCCcccCccCCCceeeecCCC--CCCcCcccCCCCChh
Q 045388 104 DACKSVLSKNVLELWEKALSQE-LID--ASQGIYCPFKDCSAKLVYENDG--EDVLSESECPYCHRL 165 (214)
Q Consensus 104 ~~~~~~l~~~~~~~~~~~~~~~-~~~--~~~~~~Cp~~~C~~~~~~~~~~--~~~~~~~~C~~C~~~ 165 (214)
..+..-++++++..|++..... -+. .-....|. +|...+...... ......++||.||..
T Consensus 166 ~~L~~~l~~ell~~yeri~~~~kg~gvvpl~g~~C~--GC~m~l~~~~~~~V~~~d~iv~CP~CgRI 230 (239)
T COG1579 166 EELKEKLDPELLSEYERIRKNKKGVGVVPLEGRVCG--GCHMKLPSQTLSKVRKKDEIVFCPYCGRI 230 (239)
T ss_pred HHHHHhcCHHHHHHHHHHHhcCCCceEEeecCCccc--CCeeeecHHHHHHHhcCCCCccCCccchH
Confidence 3566778999999998886653 111 11233677 787665433110 012366788888864
No 185
>PLN02195 cellulose synthase A
Probab=62.30 E-value=5.2 Score=38.01 Aligned_cols=52 Identities=19% Similarity=0.508 Sum_probs=40.4
Q ss_pred ccCccCCCceeeecCCCCCCcCcccCCCCChhhccccCCCCCCChHHHHHHHHHHhCCCccCCCCCccce
Q 045388 134 YCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKYHIE 203 (214)
Q Consensus 134 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~~~ie 203 (214)
.|. -|+..+-.+..+ .+.+-|..|+.-.|.-|.. +.+..+.+.||+|++...
T Consensus 8 ~c~--~cgd~~~~~~~g---~~fvaC~eC~~pvCrpCye-------------yer~eg~q~CpqCkt~Yk 59 (977)
T PLN02195 8 ICA--TCGEEVGVDSNG---EAFVACHECSYPLCKACLE-------------YEIKEGRKVCLRCGGPYD 59 (977)
T ss_pred cce--ecccccCcCCCC---CeEEEeccCCCccccchhh-------------hhhhcCCccCCccCCccc
Confidence 455 677777666555 3778999999999999974 445677899999999765
No 186
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=61.88 E-value=4.7 Score=33.59 Aligned_cols=53 Identities=19% Similarity=0.491 Sum_probs=35.5
Q ss_pred CCCCcccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcC
Q 045388 38 PSSPPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVL 101 (214)
Q Consensus 38 ~~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 101 (214)
...+++...|.||...++-.. .++|+|..|.-|--..- ++- ..-.||. |....
T Consensus 55 ddtDEen~~C~ICA~~~TYs~---~~PC~H~~CH~Ca~RlR--ALY----~~K~C~~--CrTE~ 107 (493)
T COG5236 55 DDTDEENMNCQICAGSTTYSA---RYPCGHQICHACAVRLR--ALY----MQKGCPL--CRTET 107 (493)
T ss_pred cccccccceeEEecCCceEEE---eccCCchHHHHHHHHHH--HHH----hccCCCc--ccccc
Confidence 344556788999999876544 68999999999965431 121 2346888 66433
No 187
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=61.82 E-value=2.3 Score=34.73 Aligned_cols=48 Identities=21% Similarity=0.601 Sum_probs=33.5
Q ss_pred ccCccCCCceeeecCCCCCCcCcccCCCCChhhccccCCCCCCChHHHHHHHHHHhCCCccCCCCCccceecCCC
Q 045388 134 YCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKYHIERTGGC 208 (214)
Q Consensus 134 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~~~iek~~GC 208 (214)
+|- .|+..|..-.. .+ -|+.+||+.|... ...|.||.|.-.|+|.+-|
T Consensus 92 fCd--~Cd~PI~IYGR------mI---PCkHvFCl~CAr~----------------~~dK~Cp~C~d~VqrIeq~ 139 (389)
T KOG2932|consen 92 FCD--RCDFPIAIYGR------MI---PCKHVFCLECARS----------------DSDKICPLCDDRVQRIEQI 139 (389)
T ss_pred eec--ccCCcceeeec------cc---ccchhhhhhhhhc----------------CccccCcCcccHHHHHHHh
Confidence 677 78865544322 11 4799999999652 2368999999998887554
No 188
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=61.56 E-value=8 Score=35.87 Aligned_cols=34 Identities=26% Similarity=0.741 Sum_probs=22.1
Q ss_pred ccCccCCCceeeecCCCCCCcCcccCCCCChh-----hccccCCC
Q 045388 134 YCPFKDCSAKLVYENDGEDVLSESECPYCHRL-----FCAHCYVP 173 (214)
Q Consensus 134 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~-----~C~~C~~~ 173 (214)
.|| +|+..+..-... ....|..||+. .|..|+..
T Consensus 446 ~Cp--~Cd~~lt~H~~~----~~L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 446 ECP--NCDSPLTLHKAT----GQLRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred cCC--CCCcceEEecCC----CeeEeCCCCCCCCCCCCCCCCCCC
Confidence 466 777666665443 67778888764 56666665
No 189
>PF14353 CpXC: CpXC protein
Probab=61.41 E-value=3.3 Score=29.34 Aligned_cols=46 Identities=26% Similarity=0.656 Sum_probs=25.5
Q ss_pred cccCCCCCCCCcCcHHHHhhc---CCHHHHHHHHHHHHHHHhcC-CCCcccCccCCCceeee
Q 045388 89 PVTCPGPDCKSVLKFDACKSV---LSKNVLELWEKALSQELIDA-SQGIYCPFKDCSAKLVY 146 (214)
Q Consensus 89 ~i~CP~~~C~~~l~~~~~~~~---l~~~~~~~~~~~~~~~~~~~-~~~~~Cp~~~C~~~~~~ 146 (214)
.|+||. |+..+..+....+ .++++.+ ..++. -..+.|| .|+..+..
T Consensus 1 ~itCP~--C~~~~~~~v~~~I~~~~~p~l~e--------~il~g~l~~~~CP--~Cg~~~~~ 50 (128)
T PF14353_consen 1 EITCPH--CGHEFEFEVWTSINADEDPELKE--------KILDGSLFSFTCP--SCGHKFRL 50 (128)
T ss_pred CcCCCC--CCCeeEEEEEeEEcCcCCHHHHH--------HHHcCCcCEEECC--CCCCceec
Confidence 378999 8877765433222 2333333 22322 3456888 88876544
No 190
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=61.39 E-value=17 Score=25.97 Aligned_cols=41 Identities=20% Similarity=0.382 Sum_probs=25.2
Q ss_pred CCCcccCccCCCceeeecCCCCCC-cCcccCCCCChhhccccCC
Q 045388 130 SQGIYCPFKDCSAKLVYENDGEDV-LSESECPYCHRLFCAHCYV 172 (214)
Q Consensus 130 ~~~~~Cp~~~C~~~~~~~~~~~~~-~~~~~C~~C~~~~C~~C~~ 172 (214)
.....|| .|........+.... ....+|+.|+..|=..=+.
T Consensus 28 ~~~~~cP--~C~s~~~~k~g~~~~~~qRyrC~~C~~tf~~~~~~ 69 (129)
T COG3677 28 ITKVNCP--RCKSSNVVKIGGIRRGHQRYKCKSCGSTFTVETGS 69 (129)
T ss_pred cccCcCC--CCCccceeeECCccccccccccCCcCcceeeeccC
Confidence 4557899 888776333322222 4678899888776544433
No 191
>COG4647 AcxC Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=61.04 E-value=33 Score=24.40 Aligned_cols=97 Identities=16% Similarity=0.269 Sum_probs=49.1
Q ss_pred CcHHHHhhcC----CHHHHHHHHHHHHHHHhcCCCCcccCccCCCceeeecCCCCCCcCcccCCCCChhhccccCCCC--
Q 045388 101 LKFDACKSVL----SKNVLELWEKALSQELIDASQGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPW-- 174 (214)
Q Consensus 101 l~~~~~~~~l----~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~-- 174 (214)
|+...++.++ +.+-|.+|.+.+..+.--.+.... | -=...++....+ ....+| .||..||.-=. .|
T Consensus 17 l~w~qt~r~msa~kdhdrf~kylavlqdrv~~~dpill-p--vg~hlfi~qs~~---~rv~rc-ecghsf~d~r~-nwkl 88 (165)
T COG4647 17 LPWPQTRRMMSAYKDHDRFFKYLAVLQDRVDWDDPILL-P--VGDHLFICQSAQ---KRVIRC-ECGHSFGDYRE-NWKL 88 (165)
T ss_pred CCcHHHHHHHhccccHHHHHHHHHHHHhhcccCCCeee-e--cCCcEEEEeccc---ccEEEE-eccccccChhh-Ccee
Confidence 3434444443 456677776665554333232221 3 223334433332 246688 79999986432 23
Q ss_pred CCC----hHHHHHHHHHH-----hCCC-----ccCCCCCccceec
Q 045388 175 HPG----REELMMRELVK-----KKQL-----RKCPNCKYHIERT 205 (214)
Q Consensus 175 h~~----~~~~~~~~~~~-----~~~~-----k~CP~C~~~iek~ 205 (214)
|.. ...+.+++.-. +.+| --||.|+++.+-.
T Consensus 89 ~a~i~vrdtee~lreiyp~s~ipdp~wme~reficpecg~l~eve 133 (165)
T COG4647 89 HANIYVRDTEEKLREIYPKSDIPDPQWMEIREFICPECGILHEVE 133 (165)
T ss_pred eeEEEEcchHHHHHHhCcccCCCCchHHHHHHhhCccccceeeec
Confidence 443 33334444321 1222 4699999977643
No 192
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=60.97 E-value=5.1 Score=23.35 Aligned_cols=27 Identities=19% Similarity=0.616 Sum_probs=17.8
Q ss_pred CcccCccCCCceeeecCCCCCCcCcccCCCCCh
Q 045388 132 GIYCPFKDCSAKLVYENDGEDVLSESECPYCHR 164 (214)
Q Consensus 132 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 164 (214)
...|| +|+...+-.+.. .+..|..||+
T Consensus 19 ~~~CP--rCG~gvfmA~H~----dR~~CGkCgy 45 (51)
T COG1998 19 NRFCP--RCGPGVFMADHK----DRWACGKCGY 45 (51)
T ss_pred cccCC--CCCCcchhhhcC----ceeEeccccc
Confidence 34799 899655554443 5677877775
No 193
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=60.97 E-value=5.4 Score=32.43 Aligned_cols=27 Identities=30% Similarity=0.759 Sum_probs=20.8
Q ss_pred cccccccccccccccccccCCCCcc-ccHHH
Q 045388 44 RSSCEICRERRENDQMFKIESCIHS-FCSDC 73 (214)
Q Consensus 44 ~~~C~iC~~~~~~~~~~~~~~C~H~-fC~~C 73 (214)
...|.||+|-. .+-+ +++|||. -|..|
T Consensus 300 ~~LC~ICmDaP--~DCv-fLeCGHmVtCt~C 327 (350)
T KOG4275|consen 300 RRLCAICMDAP--RDCV-FLECGHMVTCTKC 327 (350)
T ss_pred HHHHHHHhcCC--cceE-EeecCcEEeehhh
Confidence 78899999953 2333 6899996 78888
No 194
>TIGR03037 anthran_nbaC 3-hydroxyanthranilate 3,4-dioxygenase. Members of this protein family, from both bacteria and eukaryotes, are the enzyme 3-hydroxyanthranilate 3,4-dioxygenase. This enzyme acts on the tryptophan metabolite 3-hydroxyanthranilate and produces 2-amino-3-carboxymuconate semialdehyde, which can rearrange spontaneously to quinolinic acid and feed into nicotinamide biosynthesis, or undergo further enzymatic degradation.
Probab=60.95 E-value=4.2 Score=30.16 Aligned_cols=38 Identities=21% Similarity=0.518 Sum_probs=23.5
Q ss_pred ChhhccccCCCCCCC---------hHHHHHHHHHHhCCCccCCCCCc
Q 045388 163 HRLFCAHCYVPWHPG---------REELMMRELVKKKQLRKCPNCKY 200 (214)
Q Consensus 163 ~~~~C~~C~~~~h~~---------~~~~~~~~~~~~~~~k~CP~C~~ 200 (214)
-..||..|....|.. +-...+.++..+...|+|++|++
T Consensus 113 ~~wyc~~c~~~~~e~~f~~~d~~~~~~~~~~~f~~~~~~rtC~~Cg~ 159 (159)
T TIGR03037 113 FQWFCPQCGHKLHRAEVQLENIVTDLPPVFEHFYSNEDARTCKNCGH 159 (159)
T ss_pred eEEECCCCCCeEEEEEEEecChhhhhHHHHHHHhCChhhccCCccCC
Confidence 345555665555543 22224456666778899999985
No 195
>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=60.79 E-value=1 Score=28.38 Aligned_cols=39 Identities=26% Similarity=0.611 Sum_probs=22.4
Q ss_pred ccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcC
Q 045388 45 SSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVL 101 (214)
Q Consensus 45 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 101 (214)
..||.|..++.... +|..|..|-..|. ....||. |+..|
T Consensus 2 ~~CP~C~~~L~~~~-------~~~~C~~C~~~~~---------~~a~CPd--C~~~L 40 (70)
T PF07191_consen 2 NTCPKCQQELEWQG-------GHYHCEACQKDYK---------KEAFCPD--CGQPL 40 (70)
T ss_dssp -B-SSS-SBEEEET-------TEEEETTT--EEE---------EEEE-TT--T-SB-
T ss_pred CcCCCCCCccEEeC-------CEEECccccccce---------ecccCCC--cccHH
Confidence 57999988765432 8889999966442 4578998 88766
No 196
>PRK13264 3-hydroxyanthranilate 3,4-dioxygenase; Provisional
Probab=60.79 E-value=4 Score=30.78 Aligned_cols=43 Identities=19% Similarity=0.380 Sum_probs=27.0
Q ss_pred CChhhccccCCCCCCC---------hHHHHHHHHHHhCCCccCCCCCcccee
Q 045388 162 CHRLFCAHCYVPWHPG---------REELMMRELVKKKQLRKCPNCKYHIER 204 (214)
Q Consensus 162 C~~~~C~~C~~~~h~~---------~~~~~~~~~~~~~~~k~CP~C~~~iek 204 (214)
.-..||..|....|.. +-...+.++..+...|+|++|++.-..
T Consensus 118 ~~~wyc~~c~~~~~e~~f~~~d~~~~~~~~~~~f~~~~e~rtC~~CG~v~~~ 169 (177)
T PRK13264 118 GFQWYCDECNHKVHEVEVQLTDIETDLPPVFAAFYASEELRTCDNCGTVHPG 169 (177)
T ss_pred ceEEECCCCCCeEEEEEEEecChhhhhHHHHHHHhcCHhhccCCcCCcccCc
Confidence 3455566666655543 222345566667788999999996543
No 197
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=60.50 E-value=7.7 Score=26.39 Aligned_cols=24 Identities=33% Similarity=0.711 Sum_probs=19.8
Q ss_pred CCCccccHHHHHHHHHHHhhCCCcccccCCCC
Q 045388 64 SCIHSFCSDCINKHVATKIQGGIITPVTCPGP 95 (214)
Q Consensus 64 ~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~ 95 (214)
.|.|.|..-|+..|+.+ .-+||..
T Consensus 80 ~CNHaFH~hCisrWlkt--------r~vCPLd 103 (114)
T KOG2930|consen 80 VCNHAFHFHCISRWLKT--------RNVCPLD 103 (114)
T ss_pred ecchHHHHHHHHHHHhh--------cCcCCCc
Confidence 68999999999999874 3478983
No 198
>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=59.41 E-value=5.1 Score=20.49 Aligned_cols=13 Identities=46% Similarity=0.874 Sum_probs=8.0
Q ss_pred ccCCCCCccceec
Q 045388 193 RKCPNCKYHIERT 205 (214)
Q Consensus 193 k~CP~C~~~iek~ 205 (214)
++||+|+..|++.
T Consensus 2 ~~C~rC~~~~~~~ 14 (30)
T PF06827_consen 2 EKCPRCWNYIEDI 14 (30)
T ss_dssp SB-TTT--BBEEE
T ss_pred CcCccCCCcceEe
Confidence 6899999998764
No 199
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=59.34 E-value=10 Score=30.08 Aligned_cols=39 Identities=8% Similarity=0.079 Sum_probs=30.8
Q ss_pred cccccccccccccccccccccCCCCccccHHHHHHHHHHHhh
Q 045388 42 PSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQ 83 (214)
Q Consensus 42 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~ 83 (214)
...--|.+|+.....+.+ .+=||.||++||-.||..+-+
T Consensus 41 K~FdcCsLtLqPc~dPvi---t~~GylfdrEaILe~ilaqKk 79 (303)
T KOG3039|consen 41 KPFDCCSLTLQPCRDPVI---TPDGYLFDREAILEYILAQKK 79 (303)
T ss_pred CCcceeeeecccccCCcc---CCCCeeeeHHHHHHHHHHHHH
Confidence 345679999998877653 455999999999999977664
No 200
>PLN03086 PRLI-interacting factor K; Provisional
Probab=58.76 E-value=12 Score=33.57 Aligned_cols=58 Identities=21% Similarity=0.460 Sum_probs=37.3
Q ss_pred ccccCCCCCCCCcCcHHHHhhcCCHHHHHHHHHHHHHHHhcCCCCcccCccCCCceeeecCCCCCCcCcccCCCCChhh
Q 045388 88 TPVTCPGPDCKSVLKFDACKSVLSKNVLELWEKALSQELIDASQGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLF 166 (214)
Q Consensus 88 ~~i~CP~~~C~~~l~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 166 (214)
..+.||. |...+....+..++.. =..+.+.||..+|+..+...+.. ..+.|+.|+..|
T Consensus 406 ~~V~C~N--C~~~i~l~~l~lHe~~---------------C~r~~V~Cp~~~Cg~v~~r~el~----~H~~C~~Cgk~f 463 (567)
T PLN03086 406 DTVECRN--CKHYIPSRSIALHEAY---------------CSRHNVVCPHDGCGIVLRVEEAK----NHVHCEKCGQAF 463 (567)
T ss_pred CeEECCC--CCCccchhHHHHHHhh---------------CCCcceeCCcccccceeeccccc----cCccCCCCCCcc
Confidence 4578998 9887776665433210 11355678876799888665543 556788887654
No 201
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=57.60 E-value=2.8 Score=34.33 Aligned_cols=91 Identities=21% Similarity=0.481 Sum_probs=47.6
Q ss_pred CccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHhhcCCHHHHHHHHHHHH-HHHhcC-----CCCcccCccC
Q 045388 66 IHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKSVLSKNVLELWEKALS-QELIDA-----SQGIYCPFKD 139 (214)
Q Consensus 66 ~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~~~l~~~~~~~~~~~~~-~~~~~~-----~~~~~Cp~~~ 139 (214)
+..+|..|-..-.. .|+.||. |...| +|+-.+-+.|..+.- +.+... +....|- -
T Consensus 307 gGy~CP~CktkVCs--------LPi~CP~--Csl~L-------ilsthLarSyhhL~PLk~f~E~p~~~~~ks~~Cf--~ 367 (421)
T COG5151 307 GGYECPVCKTKVCS--------LPISCPI--CSLQL-------ILSTHLARSYHHLYPLKPFVEKPEGTNPKSTHCF--V 367 (421)
T ss_pred CceeCCcccceeec--------CCccCcc--hhHHH-------HHHHHHHHHHHhhccCcccccccCCCCCCCccce--e
Confidence 45577777333221 6888988 65322 233333344443321 111221 1222455 5
Q ss_pred CCceeeecCCC----CCCcCcccCCCCChhhccccCCCCC
Q 045388 140 CSAKLVYENDG----EDVLSESECPYCHRLFCAHCYVPWH 175 (214)
Q Consensus 140 C~~~~~~~~~~----~~~~~~~~C~~C~~~~C~~C~~~~h 175 (214)
|...|...+.. .......+|+.|+..||..|..-.|
T Consensus 368 CQ~~fp~~~~~~~~~~~ss~rY~Ce~CK~~FC~dCdvfiH 407 (421)
T COG5151 368 CQGPFPKPPVSPFDESTSSGRYQCELCKSTFCSDCDVFIH 407 (421)
T ss_pred ccCCCCCCCCCcccccccccceechhhhhhhhhhhHHHHH
Confidence 66544333211 1123567899999999999987544
No 202
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=57.57 E-value=24 Score=24.61 Aligned_cols=36 Identities=19% Similarity=0.464 Sum_probs=24.6
Q ss_pred CCcccCccCCCceeeecCCCCCCcCcccCCCCChhhccccCCC
Q 045388 131 QGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVP 173 (214)
Q Consensus 131 ~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~ 173 (214)
+...|. .|...+..-.. ....|..|+..+|..|...
T Consensus 53 ~~~~C~--~C~~~fg~l~~-----~~~~C~~C~~~VC~~C~~~ 88 (118)
T PF02318_consen 53 GERHCA--RCGKPFGFLFN-----RGRVCVDCKHRVCKKCGVY 88 (118)
T ss_dssp CCSB-T--TTS-BCSCTST-----TCEEETTTTEEEETTSEEE
T ss_pred CCcchh--hhCCcccccCC-----CCCcCCcCCccccCccCCc
Confidence 445788 88765543322 3467999999999999885
No 203
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=56.86 E-value=10 Score=35.01 Aligned_cols=54 Identities=22% Similarity=0.457 Sum_probs=38.4
Q ss_pred CCCCcccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCC-CCCCCc
Q 045388 38 PSSPPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPG-PDCKSV 100 (214)
Q Consensus 38 ~~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~-~~C~~~ 100 (214)
......++.|.+|--.+....++ ...|+|....+|+..|+++ |. .||. ++|...
T Consensus 1022 ~~~~~~~~~C~~C~l~V~gss~~-Cg~C~Hv~H~sc~~eWf~~----gd----~CpsGCGC~C~ 1076 (1081)
T KOG0309|consen 1022 AICKGFTFQCAICHLAVRGSSNF-CGTCGHVGHTSCMMEWFRT----GD----VCPSGCGCHCL 1076 (1081)
T ss_pred cccccceeeeeeEeeEeeccchh-hccccccccHHHHHHHHhc----CC----cCCCCCCcCch
Confidence 33444566788887776666655 5799999999999999974 33 6887 455543
No 204
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=56.37 E-value=7.9 Score=25.04 Aligned_cols=17 Identities=35% Similarity=0.812 Sum_probs=15.7
Q ss_pred CCCccccHHHHHHHHHH
Q 045388 64 SCIHSFCSDCINKHVAT 80 (214)
Q Consensus 64 ~C~H~fC~~Cl~~~~~~ 80 (214)
.|.|.|...|+..|+.+
T Consensus 53 ~CnHaFH~HCI~rWL~T 69 (88)
T COG5194 53 VCNHAFHDHCIYRWLDT 69 (88)
T ss_pred ecchHHHHHHHHHHHhh
Confidence 68999999999999976
No 205
>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 TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=56.28 E-value=12 Score=19.54 Aligned_cols=27 Identities=26% Similarity=0.784 Sum_probs=20.4
Q ss_pred cccCccCCCceeeecCCCCCCcCcccCCCCChh
Q 045388 133 IYCPFKDCSAKLVYENDGEDVLSESECPYCHRL 165 (214)
Q Consensus 133 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 165 (214)
+.|. .|+..+.+..+. ..++|..|+..
T Consensus 2 ~~C~--~C~t~L~yP~gA----~~vrCs~C~~v 28 (31)
T TIGR01053 2 VVCG--GCRTLLMYPRGA----SSVRCALCQTV 28 (31)
T ss_pred cCcC--CCCcEeecCCCC----CeEECCCCCeE
Confidence 3577 899888887764 78889888753
No 207
>PF11809 DUF3330: Domain of unknown function (DUF3330); InterPro: IPR021767 This family of proteins are functionally uncharacterised. This family is only found in bacteria.
Probab=55.71 E-value=4.6 Score=25.10 Aligned_cols=42 Identities=24% Similarity=0.573 Sum_probs=29.6
Q ss_pred CCccccccccccccccccccccc--CCCCcccc-HHHHHHHHHHH
Q 045388 40 SPPSRSSCEICRERRENDQMFKI--ESCIHSFC-SDCINKHVATK 81 (214)
Q Consensus 40 ~~~~~~~C~iC~~~~~~~~~~~~--~~C~H~fC-~~Cl~~~~~~~ 81 (214)
...+...|.+|+.+++.+..+.- ..=-+.|| .+|...|....
T Consensus 7 ~~~~~~sC~vC~KEIPl~~a~t~E~~eYV~hFCGLeCY~~w~a~~ 51 (70)
T PF11809_consen 7 NDPKTTSCCVCCKEIPLDAAFTPEAAEYVEHFCGLECYQRWQARA 51 (70)
T ss_pred cccccchHHHHhhhCChhhccCcchHHHHHHHhhHHHHHHHHHHH
Confidence 34557899999999998776541 11125688 89999997544
No 208
>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=55.23 E-value=8.8 Score=27.22 Aligned_cols=29 Identities=24% Similarity=0.402 Sum_probs=18.7
Q ss_pred CcccCccCCCceeeecCCCCCCcCcccCCCCChhhc
Q 045388 132 GIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFC 167 (214)
Q Consensus 132 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C 167 (214)
.+.|| +|+.-|.--+. .-+.||+||..|=
T Consensus 9 Kr~Cp--~cg~kFYDLnk-----~p~vcP~cg~~~~ 37 (129)
T TIGR02300 9 KRICP--NTGSKFYDLNR-----RPAVSPYTGEQFP 37 (129)
T ss_pred cccCC--CcCccccccCC-----CCccCCCcCCccC
Confidence 35788 88866654333 4456888887653
No 209
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=55.19 E-value=13 Score=26.08 Aligned_cols=14 Identities=7% Similarity=0.055 Sum_probs=6.1
Q ss_pred CHHHHHHHHHHHHH
Q 045388 111 SKNVLELWEKALSQ 124 (214)
Q Consensus 111 ~~~~~~~~~~~~~~ 124 (214)
.++.++-.-..+.+
T Consensus 40 ~pe~L~faf~~~~~ 53 (117)
T PRK00564 40 DKSLFVSAFETFRE 53 (117)
T ss_pred CHHHHHHHHHHHhc
Confidence 34445444444443
No 210
>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 PLN00209 ribosomal protein S27; Provisional
Probab=54.98 E-value=8.1 Score=25.34 Aligned_cols=30 Identities=17% Similarity=0.485 Sum_probs=18.9
Q ss_pred cccCccCCCceeeecCCCCCCcCcccCCCCChhhc
Q 045388 133 IYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFC 167 (214)
Q Consensus 133 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C 167 (214)
+.|| +|...-..=.. ....+.|..|+..+|
T Consensus 37 VkCp--~C~n~q~VFSh---A~t~V~C~~Cg~~L~ 66 (86)
T PLN00209 37 VKCQ--GCFNITTVFSH---SQTVVVCGSCQTVLC 66 (86)
T ss_pred EECC--CCCCeeEEEec---CceEEEccccCCEee
Confidence 4799 99965433222 125677888887665
No 212
>PHA02862 5L protein; Provisional
Probab=54.84 E-value=15 Score=26.67 Aligned_cols=48 Identities=17% Similarity=0.401 Sum_probs=32.2
Q ss_pred ccccccccccccccccccCCC---CccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCc
Q 045388 45 SSCEICRERRENDQMFKIESC---IHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLK 102 (214)
Q Consensus 45 ~~C~iC~~~~~~~~~~~~~~C---~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 102 (214)
..|-||+++-... ..--.| .....++||..|+.. . .+..|+. |+....
T Consensus 3 diCWIC~~~~~e~--~~PC~C~GS~K~VHq~CL~~WIn~-----S-~k~~CeL--CkteY~ 53 (156)
T PHA02862 3 DICWICNDVCDER--NNFCGCNEEYKVVHIKCMQLWINY-----S-KKKECNL--CKTKYN 53 (156)
T ss_pred CEEEEecCcCCCC--cccccccCcchhHHHHHHHHHHhc-----C-CCcCccC--CCCeEE
Confidence 4699999985433 211233 235899999999942 1 4679999 887664
No 213
>PF10426 zf-RAG1: Recombination-activating protein 1 zinc-finger domain; InterPro: IPR019485 During lymphocyte development, the genes encoding immunoglobulins and T-cell receptors are assembled from variable (V), diversity (D), and joining (J) gene segments. This combinatorial process, known as V(D)J recombination, allows the generation of an enormous range of binding specificities from a limited amount of genetic information. The V(D)J recombination-activating proteins 1 and 2 (RAG1 and RAG2) form a complex that initiates this process by binding to the conserved recombination signal sequences (RSS) and introducing a double-strand break between the RSS and the adjacent coding segment. These breaks are generated in two steps, nicking of one strand (hydrolysis), followed by hairpin formation (transesterification). RAG1/2 has also been shown to function as a transposase in vitro, and to possess RSS-independent endonuclease activity (end processing) and hairpin opening. RAG1 alone can bind to RSS but stable, efficient binding requires RAG2. All known catalytic activities require the presence of both proteins. For more information see []. 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 domain found in the RAG1 protein. The structure contains the characteristic two-stranded beta-sheet and alpha-helix of a classical zinc-finger. The domain binds one zinc and, in complex with an adjacent RING-type zinc finger domain, helps to stabilise the whole of the dimerisation region of recombination activating protein 1 (RAG1) []. The function of the whole is to bind double-stranded DNA. ; GO: 0016788 hydrolase activity, acting on ester bonds, 0016881 acid-amino acid ligase activity; PDB: 1RMD_A.
Probab=54.27 E-value=3.1 Score=21.53 Aligned_cols=21 Identities=24% Similarity=0.518 Sum_probs=11.2
Q ss_pred cccCCCCCCCCcCcHHHHhhc
Q 045388 89 PVTCPGPDCKSVLKFDACKSV 109 (214)
Q Consensus 89 ~i~CP~~~C~~~l~~~~~~~~ 109 (214)
.++||.-+|...+.......+
T Consensus 2 ~vrCPvkdC~EEv~lgKY~~H 22 (30)
T PF10426_consen 2 VVRCPVKDCDEEVSLGKYSHH 22 (30)
T ss_dssp EEE--STT---EEEHHHHHHH
T ss_pred ccccccccCcchhhhhhhccc
Confidence 479999999988876655443
No 214
>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=54.04 E-value=14 Score=32.89 Aligned_cols=33 Identities=30% Similarity=0.886 Sum_probs=23.1
Q ss_pred cCccCCCceeeecCCCCCCcCcccCCCCChh-----hccccCCC
Q 045388 135 CPFKDCSAKLVYENDGEDVLSESECPYCHRL-----FCAHCYVP 173 (214)
Q Consensus 135 Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~-----~C~~C~~~ 173 (214)
|| .|+..+...... ....|+.||.. .|..|...
T Consensus 225 C~--~C~~~l~~h~~~----~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 225 CP--NCDVSLTYHKKE----GKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred CC--CCCCceEEecCC----CeEEcCCCcCcCCCCCCCCCCCCC
Confidence 66 777777665443 67789999865 58888764
No 215
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=53.92 E-value=9.9 Score=22.63 Aligned_cols=19 Identities=32% Similarity=0.677 Sum_probs=11.3
Q ss_pred HHHHHHhCCCccCCCCCcc
Q 045388 183 MRELVKKKQLRKCPNCKYH 201 (214)
Q Consensus 183 ~~~~~~~~~~k~CP~C~~~ 201 (214)
+.++..+..+..||+|+..
T Consensus 37 ~~~i~~~~~i~~Cp~CgRi 55 (56)
T PF02591_consen 37 LNEIRKGDEIVFCPNCGRI 55 (56)
T ss_pred HHHHHcCCCeEECcCCCcc
Confidence 3444444566777777754
No 216
>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=53.74 E-value=5.1 Score=23.15 Aligned_cols=44 Identities=25% Similarity=0.612 Sum_probs=21.4
Q ss_pred ccccccccccccccccccCCC-CccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcH
Q 045388 45 SSCEICRERRENDQMFKIESC-IHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKF 103 (214)
Q Consensus 45 ~~C~iC~~~~~~~~~~~~~~C-~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~ 103 (214)
+.|..|+- ..... ..| .|..|..|+...+. ..-.||. |+.+|+.
T Consensus 3 ~nCKsCWf--~~k~L---i~C~dHYLCl~CLt~ml~--------~s~~C~i--C~~~LPt 47 (50)
T PF03854_consen 3 YNCKSCWF--ANKGL---IKCSDHYLCLNCLTLMLS--------RSDRCPI--CGKPLPT 47 (50)
T ss_dssp ----SS-S----SSE---EE-SS-EEEHHHHHHT-S--------SSSEETT--TTEE---
T ss_pred ccChhhhh--cCCCe---eeecchhHHHHHHHHHhc--------cccCCCc--ccCcCcc
Confidence 45777744 33332 344 59999999988763 1347999 8877753
No 217
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=53.56 E-value=13 Score=28.11 Aligned_cols=32 Identities=22% Similarity=0.568 Sum_probs=21.4
Q ss_pred cCCCCcccCccCCCceeeecCCCCCCcCcccCCCCCh
Q 045388 128 DASQGIYCPFKDCSAKLVYENDGEDVLSESECPYCHR 164 (214)
Q Consensus 128 ~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 164 (214)
..+..+.|| .|...+..+... ...+.||.||.
T Consensus 109 ~~~~~y~C~--~~~~r~sfdeA~---~~~F~Cp~Cg~ 140 (176)
T COG1675 109 TENNYYVCP--NCHVKYSFDEAM---ELGFTCPKCGE 140 (176)
T ss_pred ccCCceeCC--CCCCcccHHHHH---HhCCCCCCCCc
Confidence 345677897 888877776543 24567777765
No 218
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=53.22 E-value=18 Score=25.11 Aligned_cols=11 Identities=36% Similarity=0.797 Sum_probs=6.2
Q ss_pred ccCccCCCceeee
Q 045388 134 YCPFKDCSAKLVY 146 (214)
Q Consensus 134 ~Cp~~~C~~~~~~ 146 (214)
+|+ +|+..+..
T Consensus 72 ~C~--~Cg~~~~~ 82 (113)
T PRK12380 72 WCW--DCSQVVEI 82 (113)
T ss_pred Ecc--cCCCEEec
Confidence 666 66655444
No 219
>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=52.21 E-value=19 Score=25.04 Aligned_cols=11 Identities=36% Similarity=0.776 Sum_probs=6.0
Q ss_pred ccCccCCCceeee
Q 045388 134 YCPFKDCSAKLVY 146 (214)
Q Consensus 134 ~Cp~~~C~~~~~~ 146 (214)
+|+ +|+..+..
T Consensus 72 ~C~--~Cg~~~~~ 82 (115)
T TIGR00100 72 ECE--DCSEEVSP 82 (115)
T ss_pred Ecc--cCCCEEec
Confidence 566 66654444
No 220
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=52.12 E-value=11 Score=24.67 Aligned_cols=30 Identities=23% Similarity=0.554 Sum_probs=19.0
Q ss_pred cccCccCCCceeeecCCCCCCcCcccCCCCChhhc
Q 045388 133 IYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFC 167 (214)
Q Consensus 133 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C 167 (214)
+.|| +|...-..=.. ....+.|..|+..+|
T Consensus 36 VkCp--~C~n~q~VFSh---A~t~V~C~~Cg~~L~ 65 (85)
T PTZ00083 36 VKCP--GCSQITTVFSH---AQTVVLCGGCSSQLC 65 (85)
T ss_pred EECC--CCCCeeEEEec---CceEEEccccCCEee
Confidence 4799 99965433222 125677888887765
No 221
>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=51.57 E-value=4.9 Score=37.50 Aligned_cols=10 Identities=30% Similarity=0.903 Sum_probs=0.0
Q ss_pred CcccCccCCCce
Q 045388 132 GIYCPFKDCSAK 143 (214)
Q Consensus 132 ~~~Cp~~~C~~~ 143 (214)
.+.|| .|+..
T Consensus 655 ~r~Cp--~Cg~~ 664 (900)
T PF03833_consen 655 RRRCP--KCGKE 664 (900)
T ss_dssp ------------
T ss_pred cccCc--ccCCc
Confidence 34676 66643
No 222
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=51.32 E-value=9.7 Score=23.69 Aligned_cols=30 Identities=23% Similarity=0.576 Sum_probs=18.1
Q ss_pred cccCccCCCceeeecCCCCCCcCcccCCCCChhhc
Q 045388 133 IYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFC 167 (214)
Q Consensus 133 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C 167 (214)
+.|| +|++....=.. ....++|..||...+
T Consensus 20 VkCp--dC~N~q~vFsh---ast~V~C~~CG~~l~ 49 (67)
T COG2051 20 VKCP--DCGNEQVVFSH---ASTVVTCLICGTTLA 49 (67)
T ss_pred EECC--CCCCEEEEecc---CceEEEecccccEEE
Confidence 4788 88865433222 125677887877654
No 223
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 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 AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=49.53 E-value=6 Score=22.22 Aligned_cols=19 Identities=26% Similarity=0.691 Sum_probs=12.9
Q ss_pred CcccCCCCChhhccccCCC
Q 045388 155 SESECPYCHRLFCAHCYVP 173 (214)
Q Consensus 155 ~~~~C~~C~~~~C~~C~~~ 173 (214)
..+.|+.|+..||...+.+
T Consensus 12 ~~~~C~~C~~~FC~~Hr~~ 30 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLKHRLP 30 (43)
T ss_dssp SHEE-TTTS-EE-TTTHST
T ss_pred CCeECCCCCcccCccccCc
Confidence 3467999999999998774
No 224
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=49.24 E-value=17 Score=21.07 Aligned_cols=8 Identities=38% Similarity=1.103 Sum_probs=3.7
Q ss_pred ccCCCCCh
Q 045388 157 SECPYCHR 164 (214)
Q Consensus 157 ~~C~~C~~ 164 (214)
..||.||.
T Consensus 27 ~~CP~Cg~ 34 (52)
T TIGR02605 27 ATCPECGG 34 (52)
T ss_pred CCCCCCCC
Confidence 34555543
No 225
>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=49.12 E-value=10 Score=21.17 Aligned_cols=27 Identities=30% Similarity=0.699 Sum_probs=12.7
Q ss_pred ccCccCCCceeeecCCCCCCcCcccCCCCChh
Q 045388 134 YCPFKDCSAKLVYENDGEDVLSESECPYCHRL 165 (214)
Q Consensus 134 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 165 (214)
.|| .|+...+..+.. ...+.|+.||.+
T Consensus 2 ~Cp--~Cg~~~~~~D~~---~g~~vC~~CG~V 28 (43)
T PF08271_consen 2 KCP--NCGSKEIVFDPE---RGELVCPNCGLV 28 (43)
T ss_dssp SBT--TTSSSEEEEETT---TTEEEETTT-BB
T ss_pred CCc--CCcCCceEEcCC---CCeEECCCCCCE
Confidence 477 777644322211 244456666643
No 226
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=48.20 E-value=20 Score=21.53 Aligned_cols=46 Identities=30% Similarity=0.686 Sum_probs=31.1
Q ss_pred cccccccccccccccccccCCCC--ccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCc
Q 045388 44 RSSCEICRERRENDQMFKIESCI--HSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLK 102 (214)
Q Consensus 44 ~~~C~iC~~~~~~~~~~~~~~C~--H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 102 (214)
+..|..|-.+++.+..- ..-|. ..||.+|....+ .=.||. |+..|.
T Consensus 5 rpnCE~C~~dLp~~s~~-A~ICSfECTFC~~C~e~~l----------~~~CPN--CgGelv 52 (57)
T PF06906_consen 5 RPNCECCDKDLPPDSPE-AYICSFECTFCADCAETML----------NGVCPN--CGGELV 52 (57)
T ss_pred CCCccccCCCCCCCCCc-ceEEeEeCcccHHHHHHHh----------cCcCcC--CCCccc
Confidence 46788998888765411 22344 479999987764 236998 887663
No 227
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=48.05 E-value=20 Score=29.60 Aligned_cols=58 Identities=19% Similarity=0.393 Sum_probs=39.8
Q ss_pred cccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHH
Q 045388 42 PSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDAC 106 (214)
Q Consensus 42 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~ 106 (214)
-..+.||+=-+.-+.+..+.++.|||..=.+=+.. ..++|. ..++||- |...-.+..+
T Consensus 334 Hs~FiCPVlKe~~t~ENpP~ml~CgHVIskeal~~----LS~nG~-~~FKCPY--CP~~~~~~~~ 391 (396)
T COG5109 334 HSLFICPVLKELCTDENPPVMLECGHVISKEALSV----LSQNGV-LSFKCPY--CPEMSKYENI 391 (396)
T ss_pred cceeeccccHhhhcccCCCeeeeccceeeHHHHHH----HhhcCc-EEeeCCC--CCcchhhhhh
Confidence 35688998777666666666899999986655443 345666 6899998 8765444443
No 228
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=47.95 E-value=6.7 Score=32.93 Aligned_cols=40 Identities=25% Similarity=0.675 Sum_probs=28.9
Q ss_pred cCCCCChhhccccCCCCCCChHHHHHHHHHHhCCCccCCCCCcccee
Q 045388 158 ECPYCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKYHIER 204 (214)
Q Consensus 158 ~C~~C~~~~C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~~~iek 204 (214)
.=|.|.+.||+.|...|...... .....+.||-|++....
T Consensus 183 ilpnC~H~~Cl~Cir~wr~~~q~-------~~~~sksCP~CRv~s~~ 222 (344)
T KOG1039|consen 183 ILPNCNHSFCLNCIRKWRQATQF-------ESKTSKSCPFCRVPSSF 222 (344)
T ss_pred cCCCcchhhhhcHhHhhhhhhcc-------ccccccCCCcccCcccc
Confidence 44689999999999888633111 23457999999997654
No 229
>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=47.56 E-value=12 Score=29.52 Aligned_cols=54 Identities=22% Similarity=0.400 Sum_probs=38.0
Q ss_pred ccCCCCCCCC--cCcHHHHhhcCCHHHHHHHHHHHHHHHhcCCCCcccCccCCCceeeec
Q 045388 90 VTCPGPDCKS--VLKFDACKSVLSKNVLELWEKALSQELIDASQGIYCPFKDCSAKLVYE 147 (214)
Q Consensus 90 i~CP~~~C~~--~l~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~ 147 (214)
-+||. |+. -|++ +++-+++++-|.++-..-..+.+. .+--.||+++|+.++...
T Consensus 11 ~~CPv--CksDrYLnP-dik~linPECyHrmCESCvdRIFs-~GpAqCP~~gC~kILRK~ 66 (314)
T COG5220 11 RRCPV--CKSDRYLNP-DIKILINPECYHRMCESCVDRIFS-RGPAQCPYKGCGKILRKI 66 (314)
T ss_pred ccCCc--cccccccCC-CeEEEECHHHHHHHHHHHHHHHhc-CCCCCCCCccHHHHHHHh
Confidence 47999 764 3333 477888998888887766665554 444579999999876543
No 230
>PRK14873 primosome assembly protein PriA; Provisional
Probab=47.14 E-value=19 Score=33.27 Aligned_cols=31 Identities=26% Similarity=0.700 Sum_probs=17.3
Q ss_pred CCCceeeecCCCCCCcCcccCCCCChh----hccccCCC
Q 045388 139 DCSAKLVYENDGEDVLSESECPYCHRL----FCAHCYVP 173 (214)
Q Consensus 139 ~C~~~~~~~~~~~~~~~~~~C~~C~~~----~C~~C~~~ 173 (214)
+|+..+...... ....|..||+. .|..|+..
T Consensus 397 ~C~~~L~~h~~~----~~l~Ch~CG~~~~p~~Cp~Cgs~ 431 (665)
T PRK14873 397 HCTGPLGLPSAG----GTPRCRWCGRAAPDWRCPRCGSD 431 (665)
T ss_pred CCCCceeEecCC----CeeECCCCcCCCcCccCCCCcCC
Confidence 666655553322 45667777642 36666553
No 231
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=47.07 E-value=14 Score=21.78 Aligned_cols=35 Identities=26% Similarity=0.542 Sum_probs=24.3
Q ss_pred cccccccccccccc-ccccCCCCccccHHHHHHHHH
Q 045388 45 SSCEICRERRENDQ-MFKIESCIHSFCSDCINKHVA 79 (214)
Q Consensus 45 ~~C~iC~~~~~~~~-~~~~~~C~H~fC~~Cl~~~~~ 79 (214)
..|.+|...|.... -.....||+.||.+|......
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~~ 38 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRIP 38 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCcChHHcCCeee
Confidence 46888877665421 122568999999999887754
No 232
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=47.04 E-value=12 Score=25.83 Aligned_cols=23 Identities=35% Similarity=0.849 Sum_probs=12.2
Q ss_pred CcccCCCCChh--------hccccCCCCCCC
Q 045388 155 SESECPYCHRL--------FCAHCYVPWHPG 177 (214)
Q Consensus 155 ~~~~C~~C~~~--------~C~~C~~~~h~~ 177 (214)
..+.||.|++. .|..|+.+.+-+
T Consensus 68 v~V~CP~C~K~TKmLGr~D~CM~C~~pLTLd 98 (114)
T PF11023_consen 68 VQVECPNCGKQTKMLGRVDACMHCKEPLTLD 98 (114)
T ss_pred eeeECCCCCChHhhhchhhccCcCCCcCccC
Confidence 34455555543 366666665443
No 233
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=46.75 E-value=8.8 Score=21.23 Aligned_cols=11 Identities=36% Similarity=0.896 Sum_probs=6.8
Q ss_pred cCccCCCceeeec
Q 045388 135 CPFKDCSAKLVYE 147 (214)
Q Consensus 135 Cp~~~C~~~~~~~ 147 (214)
|| .|+..+...
T Consensus 2 CP--~C~~~l~~~ 12 (41)
T PF13453_consen 2 CP--RCGTELEPV 12 (41)
T ss_pred cC--CCCcccceE
Confidence 66 777655443
No 234
>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=46.62 E-value=14 Score=30.44 Aligned_cols=12 Identities=17% Similarity=0.606 Sum_probs=9.1
Q ss_pred CccCCCCCccce
Q 045388 192 LRKCPNCKYHIE 203 (214)
Q Consensus 192 ~k~CP~C~~~ie 203 (214)
+-.|-.|+.++.
T Consensus 252 ~e~C~~C~~YlK 263 (305)
T TIGR01562 252 AETCDSCQGYLK 263 (305)
T ss_pred Eeeccccccchh
Confidence 447999998774
No 235
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=46.35 E-value=14 Score=21.97 Aligned_cols=11 Identities=45% Similarity=0.963 Sum_probs=6.8
Q ss_pred CCcccCccCCCce
Q 045388 131 QGIYCPFKDCSAK 143 (214)
Q Consensus 131 ~~~~Cp~~~C~~~ 143 (214)
.++.|| -|++-
T Consensus 3 ~Wi~CP--~CgnK 13 (55)
T PF14205_consen 3 EWILCP--ICGNK 13 (55)
T ss_pred eEEECC--CCCCc
Confidence 356677 77743
No 236
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=46.34 E-value=15 Score=30.33 Aligned_cols=13 Identities=15% Similarity=0.595 Sum_probs=9.8
Q ss_pred CCccCCCCCccce
Q 045388 191 QLRKCPNCKYHIE 203 (214)
Q Consensus 191 ~~k~CP~C~~~ie 203 (214)
.+-.|-.|+.++.
T Consensus 251 r~e~C~~C~~YlK 263 (309)
T PRK03564 251 KAESCGDCGTYLK 263 (309)
T ss_pred Eeeecccccccce
Confidence 4567999998774
No 237
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=46.18 E-value=8.3 Score=31.88 Aligned_cols=29 Identities=31% Similarity=0.704 Sum_probs=23.2
Q ss_pred cccccccccccccccccCCCCccccHHHH
Q 045388 46 SCEICRERRENDQMFKIESCIHSFCSDCI 74 (214)
Q Consensus 46 ~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl 74 (214)
.|-.|+++......+....|++.||.+|=
T Consensus 332 ~Cf~C~~~~~~~~~y~C~~Ck~~FCldCD 360 (378)
T KOG2807|consen 332 FCFACQGELLSSGRYRCESCKNVFCLDCD 360 (378)
T ss_pred ceeeeccccCCCCcEEchhccceeeccch
Confidence 38888777776666778889999999993
No 238
>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=46.06 E-value=3.3 Score=22.90 Aligned_cols=23 Identities=30% Similarity=0.688 Sum_probs=19.5
Q ss_pred CcccCCCCChhhccccCCCCCCC
Q 045388 155 SESECPYCHRLFCAHCYVPWHPG 177 (214)
Q Consensus 155 ~~~~C~~C~~~~C~~C~~~~h~~ 177 (214)
..++|..|+..+|..|...-|.+
T Consensus 14 ~~~~C~~C~~~~C~~C~~~~H~~ 36 (42)
T PF00643_consen 14 LSLFCEDCNEPLCSECTVSGHKG 36 (42)
T ss_dssp EEEEETTTTEEEEHHHHHTSTTT
T ss_pred eEEEecCCCCccCccCCCCCCCC
Confidence 66789999999999998876765
No 239
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=45.74 E-value=8 Score=28.60 Aligned_cols=29 Identities=21% Similarity=0.479 Sum_probs=20.7
Q ss_pred cccccccccccccccccccccCCCCcccc
Q 045388 42 PSRSSCEICRERRENDQMFKIESCIHSFC 70 (214)
Q Consensus 42 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC 70 (214)
...-+|.||++++...+....++|...|.
T Consensus 175 ddkGECvICLEdL~~GdtIARLPCLCIYH 203 (205)
T KOG0801|consen 175 DDKGECVICLEDLEAGDTIARLPCLCIYH 203 (205)
T ss_pred ccCCcEEEEhhhccCCCceeccceEEEee
Confidence 34678999999887766666677765553
No 240
>cd00021 BBOX B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
Probab=45.27 E-value=11 Score=20.08 Aligned_cols=24 Identities=25% Similarity=0.487 Sum_probs=19.2
Q ss_pred cCcccCCCCChhhccccCCCCCCC
Q 045388 154 LSESECPYCHRLFCAHCYVPWHPG 177 (214)
Q Consensus 154 ~~~~~C~~C~~~~C~~C~~~~h~~ 177 (214)
...++|..|+..+|..|....|.+
T Consensus 10 ~~~~fC~~~~~~iC~~C~~~~H~~ 33 (39)
T cd00021 10 PLSLFCETDRALLCVDCDLSVHSG 33 (39)
T ss_pred ceEEEeCccChhhhhhcChhhcCC
Confidence 356789999999999998765654
No 241
>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=45.09 E-value=8.1 Score=22.23 Aligned_cols=34 Identities=18% Similarity=0.629 Sum_probs=24.6
Q ss_pred cccccccccccccccccCCCCccccHHHHHHHHH
Q 045388 46 SCEICRERRENDQMFKIESCIHSFCSDCINKHVA 79 (214)
Q Consensus 46 ~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~ 79 (214)
.|.||........++....|+..|...|+.....
T Consensus 1 ~C~vC~~~~~~~~~i~C~~C~~~~H~~C~~~~~~ 34 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDSCNRWYHQECVGPPEK 34 (51)
T ss_dssp EBTTTTSSCTTSSEEEBSTTSCEEETTTSTSSHS
T ss_pred eCcCCCCcCCCCCeEEcCCCChhhCcccCCCChh
Confidence 3778888666666666778888888888776554
No 242
>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins. Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.
Probab=45.05 E-value=11 Score=19.53 Aligned_cols=9 Identities=33% Similarity=1.065 Sum_probs=6.1
Q ss_pred cCCCCCccc
Q 045388 194 KCPNCKYHI 202 (214)
Q Consensus 194 ~CP~C~~~i 202 (214)
-||+|++-+
T Consensus 3 lcpkcgvgv 11 (36)
T PF09151_consen 3 LCPKCGVGV 11 (36)
T ss_dssp B-TTTSSSB
T ss_pred cCCccCceE
Confidence 599999844
No 243
>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=44.74 E-value=13 Score=25.23 Aligned_cols=26 Identities=27% Similarity=0.659 Sum_probs=18.6
Q ss_pred ccCccCCCceeeecCCCCCCcCcccCCCCChhhc
Q 045388 134 YCPFKDCSAKLVYENDGEDVLSESECPYCHRLFC 167 (214)
Q Consensus 134 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C 167 (214)
+|| +|+..+.... ..+.|+.|++.+=
T Consensus 2 fC~--~Cg~~l~~~~------~~~~C~~C~~~~~ 27 (104)
T TIGR01384 2 FCP--KCGSLMTPKN------GVYVCPSCGYEKE 27 (104)
T ss_pred CCc--ccCcccccCC------CeEECcCCCCccc
Confidence 688 9999886532 3577888887643
No 244
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=44.56 E-value=4.6 Score=29.65 Aligned_cols=10 Identities=50% Similarity=1.178 Sum_probs=4.8
Q ss_pred ccCCCCCccc
Q 045388 193 RKCPNCKYHI 202 (214)
Q Consensus 193 k~CP~C~~~i 202 (214)
..||+|+.+|
T Consensus 40 ~~Cp~C~~~I 49 (158)
T PF10083_consen 40 TSCPNCSTPI 49 (158)
T ss_pred HHCcCCCCCC
Confidence 3455554444
No 245
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=44.42 E-value=13 Score=20.49 Aligned_cols=18 Identities=33% Similarity=0.853 Sum_probs=15.4
Q ss_pred cccCCCCChhhccccCCC
Q 045388 156 ESECPYCHRLFCAHCYVP 173 (214)
Q Consensus 156 ~~~C~~C~~~~C~~C~~~ 173 (214)
.+.|..|+..||...+.+
T Consensus 12 ~f~C~~C~~~FC~~HR~~ 29 (39)
T smart00154 12 GFKCRHCGNLFCGEHRLP 29 (39)
T ss_pred CeECCccCCccccccCCc
Confidence 567999999999998764
No 246
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=43.91 E-value=24 Score=34.56 Aligned_cols=43 Identities=19% Similarity=0.347 Sum_probs=25.6
Q ss_pred CcCcccCCCCChhhccccCCCCCCChHHHHHHHHHHhCCCccCCCCCccceecC
Q 045388 153 VLSESECPYCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKYHIERTG 206 (214)
Q Consensus 153 ~~~~~~C~~C~~~~C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~~~iek~~ 206 (214)
-.+...||.|++.-...=.. ...| -+..-|.||+|+.++.|.|
T Consensus 911 L~PHY~Cp~Cky~Ef~~d~s-vgsG----------fDLpdK~CPkCg~pl~kDG 953 (1444)
T COG2176 911 LPPHYLCPECKYSEFIDDGS-VGSG----------FDLPDKDCPKCGTPLKKDG 953 (1444)
T ss_pred CCccccCCCCceeeeecCCC-cCCC----------CCCCCCCCCcCCCccccCC
Confidence 35777888887643332111 0001 0234599999999988876
No 247
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=43.16 E-value=52 Score=26.82 Aligned_cols=54 Identities=20% Similarity=0.458 Sum_probs=32.1
Q ss_pred HHHHhhcCCHHHHHHHHHHHHHHHhc-CCCCcccCccCCCceeeecCCCCCCcCcccCCCCCh
Q 045388 103 FDACKSVLSKNVLELWEKALSQELID-ASQGIYCPFKDCSAKLVYENDGEDVLSESECPYCHR 164 (214)
Q Consensus 103 ~~~~~~~l~~~~~~~~~~~~~~~~~~-~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 164 (214)
.+.+...++...+..+-.... ++. ....++|+ .|+.-.....++ ....|+.|+.
T Consensus 83 lR~l~~~~~~~~~~~~~~a~~--l~~w~~~~RFCg--~CG~~~~~~~~g----~~~~C~~cg~ 137 (279)
T COG2816 83 LRSLLTELDEGLFGLAARAVQ--LLEWYRSHRFCG--RCGTKTYPREGG----WARVCPKCGH 137 (279)
T ss_pred HHHHhccCCHHHHHHHHHHHH--HHHHHhhCcCCC--CCCCcCccccCc----eeeeCCCCCC
Confidence 333444455666655433321 111 24567899 999888877765 5566888874
No 248
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=42.72 E-value=32 Score=28.93 Aligned_cols=43 Identities=21% Similarity=0.576 Sum_probs=28.1
Q ss_pred ccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcC
Q 045388 43 SRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVL 101 (214)
Q Consensus 43 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 101 (214)
....|.||.++...-. ..+|||.-| |..-+- ....||. |...+
T Consensus 304 ~p~lcVVcl~e~~~~~---fvpcGh~cc--ct~cs~---------~l~~CPv--CR~rI 346 (355)
T KOG1571|consen 304 QPDLCVVCLDEPKSAV---FVPCGHVCC--CTLCSK---------HLPQCPV--CRQRI 346 (355)
T ss_pred CCCceEEecCCcccee---eecCCcEEE--chHHHh---------hCCCCch--hHHHH
Confidence 3567999999876533 579999966 533221 1345998 76544
No 249
>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 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 model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=42.45 E-value=33 Score=16.96 Aligned_cols=22 Identities=27% Similarity=0.792 Sum_probs=16.2
Q ss_pred CCCceeeecCCCCCCcCcccCCCCCh
Q 045388 139 DCSAKLVYENDGEDVLSESECPYCHR 164 (214)
Q Consensus 139 ~C~~~~~~~~~~~~~~~~~~C~~C~~ 164 (214)
+|...+.+..+. ..++|..|+.
T Consensus 3 ~Cr~~L~yp~GA----~sVrCa~C~~ 24 (25)
T PF06943_consen 3 GCRTLLMYPRGA----PSVRCACCHT 24 (25)
T ss_pred CCCceEEcCCCC----CCeECCccCc
Confidence 677777777664 7788888765
No 250
>PRK05580 primosome assembly protein PriA; Validated
Probab=41.51 E-value=25 Score=32.47 Aligned_cols=34 Identities=26% Similarity=0.593 Sum_probs=21.1
Q ss_pred ccCccCCCceeeecCCCCCCcCcccCCCCChh-----hccccCCC
Q 045388 134 YCPFKDCSAKLVYENDGEDVLSESECPYCHRL-----FCAHCYVP 173 (214)
Q Consensus 134 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~-----~C~~C~~~ 173 (214)
.|| +|+..+...... ....|+.||.. .|..|+..
T Consensus 392 ~C~--~C~~~l~~h~~~----~~l~Ch~Cg~~~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 392 ECP--HCDASLTLHRFQ----RRLRCHHCGYQEPIPKACPECGST 430 (679)
T ss_pred CCC--CCCCceeEECCC----CeEECCCCcCCCCCCCCCCCCcCC
Confidence 355 677666554332 56678888764 47777653
No 251
>PF11682 DUF3279: Protein of unknown function (DUF3279); InterPro: IPR021696 This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.
Probab=41.42 E-value=19 Score=25.63 Aligned_cols=15 Identities=27% Similarity=0.534 Sum_probs=11.1
Q ss_pred ccCCCCCccceecCC
Q 045388 193 RKCPNCKYHIERTGG 207 (214)
Q Consensus 193 k~CP~C~~~iek~~G 207 (214)
|.||+|++.|.-.++
T Consensus 111 K~C~~C~tGiYS~e~ 125 (128)
T PF11682_consen 111 KYCPKCGTGIYSIEV 125 (128)
T ss_pred EecCCCCCcccceec
Confidence 889999987765443
No 252
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=41.27 E-value=14 Score=26.39 Aligned_cols=16 Identities=31% Similarity=0.829 Sum_probs=12.9
Q ss_pred CccCCCCCccceecCC
Q 045388 192 LRKCPNCKYHIERTGG 207 (214)
Q Consensus 192 ~k~CP~C~~~iek~~G 207 (214)
.+.||.||.++.+..|
T Consensus 28 ~~hCp~Cg~PLF~KdG 43 (131)
T COG1645 28 AKHCPKCGTPLFRKDG 43 (131)
T ss_pred HhhCcccCCcceeeCC
Confidence 4789999998877655
No 253
>smart00336 BBOX B-Box-type zinc finger.
Probab=41.09 E-value=17 Score=19.70 Aligned_cols=23 Identities=35% Similarity=0.680 Sum_probs=18.5
Q ss_pred CcccCCCCChhhccccCCCCCCC
Q 045388 155 SESECPYCHRLFCAHCYVPWHPG 177 (214)
Q Consensus 155 ~~~~C~~C~~~~C~~C~~~~h~~ 177 (214)
..++|..|+..+|..|....|.+
T Consensus 14 ~~~~C~~c~~~iC~~C~~~~H~~ 36 (42)
T smart00336 14 AEFFCEECGALLCRTCDEAEHRG 36 (42)
T ss_pred eEEECCCCCcccccccChhhcCC
Confidence 56789999999999998765644
No 254
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=40.93 E-value=16 Score=21.32 Aligned_cols=14 Identities=29% Similarity=0.702 Sum_probs=7.3
Q ss_pred hCCCccCCCCCccc
Q 045388 189 KKQLRKCPNCKYHI 202 (214)
Q Consensus 189 ~~~~k~CP~C~~~i 202 (214)
.....+||.|+..|
T Consensus 21 ~~~~irCp~Cg~rI 34 (49)
T COG1996 21 ETRGIRCPYCGSRI 34 (49)
T ss_pred ccCceeCCCCCcEE
Confidence 34445566665544
No 255
>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=40.23 E-value=32 Score=21.15 Aligned_cols=26 Identities=23% Similarity=0.493 Sum_probs=15.8
Q ss_pred cccCccCCCceeeecCCCCCCcCcccCCCCCh
Q 045388 133 IYCPFKDCSAKLVYENDGEDVLSESECPYCHR 164 (214)
Q Consensus 133 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 164 (214)
..|| .|+........ ...+.|+.||.
T Consensus 29 q~C~--~CG~~~~~~~~----~r~~~C~~Cg~ 54 (69)
T PF07282_consen 29 QTCP--RCGHRNKKRRS----GRVFTCPNCGF 54 (69)
T ss_pred cCcc--Ccccccccccc----cceEEcCCCCC
Confidence 4677 78777666222 25667776665
No 256
>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=39.48 E-value=36 Score=19.96 Aligned_cols=17 Identities=24% Similarity=0.518 Sum_probs=10.3
Q ss_pred cCCCCCCCCcCcHHHHhhc
Q 045388 91 TCPGPDCKSVLKFDACKSV 109 (214)
Q Consensus 91 ~CP~~~C~~~l~~~~~~~~ 109 (214)
.||. |+..|+.++-..+
T Consensus 22 ~CPl--C~r~l~~e~~~~l 38 (54)
T PF04423_consen 22 CCPL--CGRPLDEEHRQEL 38 (54)
T ss_dssp E-TT--T--EE-HHHHHHH
T ss_pred cCCC--CCCCCCHHHHHHH
Confidence 8999 9999988876444
No 257
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=39.28 E-value=28 Score=21.19 Aligned_cols=28 Identities=29% Similarity=0.589 Sum_probs=18.7
Q ss_pred ccCccCCCceeeecCCCCCCcCcccCCCCCh
Q 045388 134 YCPFKDCSAKLVYENDGEDVLSESECPYCHR 164 (214)
Q Consensus 134 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 164 (214)
.|.+.+|.+++..+-... ..-.||.|+.
T Consensus 20 ~Ct~e~C~gWmR~nFs~~---~~p~CPlC~s 47 (59)
T PF14169_consen 20 ECTSEDCNGWMRDNFSFE---EEPVCPLCKS 47 (59)
T ss_pred EeCCCCCCcccccccccC---CCccCCCcCC
Confidence 599999999998765432 2234776654
No 258
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=38.78 E-value=20 Score=35.25 Aligned_cols=35 Identities=23% Similarity=0.643 Sum_probs=25.7
Q ss_pred cccCCCCCh----hhccccCCCCCCChHHHHHHHHHHhCCCccCCCCCccceec
Q 045388 156 ESECPYCHR----LFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKYHIERT 205 (214)
Q Consensus 156 ~~~C~~C~~----~~C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~~~iek~ 205 (214)
..+||.||. .||..|+... ...-.||+|+..+.-.
T Consensus 667 ~rkCPkCG~~t~~~fCP~CGs~t---------------e~vy~CPsCGaev~~d 705 (1337)
T PRK14714 667 RRRCPSCGTETYENRCPDCGTHT---------------EPVYVCPDCGAEVPPD 705 (1337)
T ss_pred EEECCCCCCccccccCcccCCcC---------------CCceeCccCCCccCCC
Confidence 478999995 5899998742 1134899999977543
No 259
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=38.55 E-value=21 Score=22.07 Aligned_cols=15 Identities=20% Similarity=0.578 Sum_probs=11.3
Q ss_pred CCCccCCCCCcccee
Q 045388 190 KQLRKCPNCKYHIER 204 (214)
Q Consensus 190 ~~~k~CP~C~~~iek 204 (214)
..+|+||-|+..+.+
T Consensus 4 d~lKPCPFCG~~~~~ 18 (64)
T PRK09710 4 DNVKPCPFCGCPSVT 18 (64)
T ss_pred ccccCCCCCCCceeE
Confidence 467999999985543
No 260
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=38.07 E-value=15 Score=24.59 Aligned_cols=19 Identities=26% Similarity=0.866 Sum_probs=13.5
Q ss_pred CcccCCCCChhh-ccccCCC
Q 045388 155 SESECPYCHRLF-CAHCYVP 173 (214)
Q Consensus 155 ~~~~C~~C~~~~-C~~C~~~ 173 (214)
.-++|..|.+.+ |+.|..+
T Consensus 25 ialkc~~C~kyYaCy~CHde 44 (105)
T COG4357 25 IALKCKCCQKYYACYHCHDE 44 (105)
T ss_pred EeeeechhhhhhhHHHHHhH
Confidence 445677787665 9999764
No 261
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=37.85 E-value=20 Score=24.81 Aligned_cols=13 Identities=23% Similarity=0.677 Sum_probs=6.8
Q ss_pred ccCccCCCceeeecC
Q 045388 134 YCPFKDCSAKLVYEN 148 (214)
Q Consensus 134 ~Cp~~~C~~~~~~~~ 148 (214)
+|. +|+..+..+.
T Consensus 72 ~C~--~Cg~~~~~~~ 84 (113)
T PF01155_consen 72 RCR--DCGHEFEPDE 84 (113)
T ss_dssp EET--TTS-EEECHH
T ss_pred ECC--CCCCEEecCC
Confidence 566 6666555543
No 262
>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type [].
Probab=37.72 E-value=51 Score=22.57 Aligned_cols=32 Identities=22% Similarity=0.622 Sum_probs=22.3
Q ss_pred CCC---CccccHHHHHHHHHHHhhCCC-cccccCCC
Q 045388 63 ESC---IHSFCSDCINKHVATKIQGGI-ITPVTCPG 94 (214)
Q Consensus 63 ~~C---~H~fC~~Cl~~~~~~~i~~~~-~~~i~CP~ 94 (214)
..| .-.||..||...+.+.+.+-. ...-.||.
T Consensus 31 ~~C~~~~~~fC~~CL~~ryge~~~ev~~~~~W~CP~ 66 (105)
T PF10497_consen 31 SSCRGCRGKFCGGCLRNRYGENVEEVLEDPNWKCPK 66 (105)
T ss_pred CCCccCcceehHhHHHHHHhhhHHHHhcCCceECCC
Confidence 456 778999999998876664321 13467887
No 263
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 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 UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=37.49 E-value=28 Score=21.22 Aligned_cols=31 Identities=23% Similarity=0.485 Sum_probs=18.5
Q ss_pred ccccccccccccccccCCCCccccHH----HHHHHHH
Q 045388 47 CEICRERRENDQMFKIESCIHSFCSD----CINKHVA 79 (214)
Q Consensus 47 C~iC~~~~~~~~~~~~~~C~H~fC~~----Cl~~~~~ 79 (214)
|..|... ...+...+.|++.+|.. -...+++
T Consensus 1 C~~C~~~--~~~lw~CL~Cg~~~C~~~~~~Ha~~H~~ 35 (63)
T PF02148_consen 1 CSVCGST--NSNLWLCLTCGYVGCGRYSNGHALKHYK 35 (63)
T ss_dssp -SSSHTC--SSSEEEETTTS-EEETTTSTSHHHHHHH
T ss_pred CCCCCCc--CCceEEeCCCCcccccCCcCcHHHHhhc
Confidence 4556544 23445578889988885 6666665
No 264
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=36.65 E-value=18 Score=22.05 Aligned_cols=14 Identities=29% Similarity=0.669 Sum_probs=11.2
Q ss_pred CccCCCCCccceec
Q 045388 192 LRKCPNCKYHIERT 205 (214)
Q Consensus 192 ~k~CP~C~~~iek~ 205 (214)
-|-||.||.+|.-+
T Consensus 3 HkHC~~CG~~Ip~~ 16 (59)
T PF09889_consen 3 HKHCPVCGKPIPPD 16 (59)
T ss_pred CCcCCcCCCcCCcc
Confidence 47899999998754
No 265
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=36.46 E-value=30 Score=21.08 Aligned_cols=30 Identities=23% Similarity=0.609 Sum_probs=17.0
Q ss_pred cccCccCCCceeeecCCCCCCcCcccCCCCChhhc
Q 045388 133 IYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFC 167 (214)
Q Consensus 133 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C 167 (214)
+.|| +|......=.. ....+.|..|+...+
T Consensus 12 VkCp--~C~n~q~vFsh---a~t~V~C~~Cg~~L~ 41 (59)
T PRK00415 12 VKCP--DCGNEQVVFSH---ASTVVRCLVCGKTLA 41 (59)
T ss_pred EECC--CCCCeEEEEec---CCcEEECcccCCCcc
Confidence 4788 88865433221 125566777776544
No 266
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=36.42 E-value=21 Score=21.46 Aligned_cols=37 Identities=16% Similarity=0.215 Sum_probs=25.8
Q ss_pred cccCCCCCCCCcCcHHHHhhcCCHHHHHHHHHHHHHHHh
Q 045388 89 PVTCPGPDCKSVLKFDACKSVLSKNVLELWEKALSQELI 127 (214)
Q Consensus 89 ~i~CP~~~C~~~l~~~~~~~~l~~~~~~~~~~~~~~~~~ 127 (214)
...||. |+......+=..+-++|.+.+|...+..+..
T Consensus 17 k~~CP~--CG~~t~~~~P~rfSp~D~y~~yR~~~kk~~~ 53 (56)
T PRK13130 17 KEICPV--CGGKTKNPHPPRFSPEDKYGKYRRALKKRRK 53 (56)
T ss_pred cccCcC--CCCCCCCCCCCCCCCCCccHHHHHHHHHHhh
Confidence 346888 8876655544566678889999888776543
No 267
>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=36.39 E-value=34 Score=17.87 Aligned_cols=22 Identities=32% Similarity=0.671 Sum_probs=12.8
Q ss_pred cCccCCCceeeecCCCCCCcCcccCCCCCh
Q 045388 135 CPFKDCSAKLVYENDGEDVLSESECPYCHR 164 (214)
Q Consensus 135 Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 164 (214)
|+ .|++.+.... ....||.|+.
T Consensus 4 C~--~CGy~y~~~~------~~~~CP~Cg~ 25 (33)
T cd00350 4 CP--VCGYIYDGEE------APWVCPVCGA 25 (33)
T ss_pred CC--CCCCEECCCc------CCCcCcCCCC
Confidence 55 7776664432 3345777764
No 268
>KOG2979 consensus Protein involved in DNA repair [General function prediction only]
Probab=36.37 E-value=49 Score=26.54 Aligned_cols=47 Identities=19% Similarity=0.371 Sum_probs=35.7
Q ss_pred ccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCC
Q 045388 45 SSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKS 99 (214)
Q Consensus 45 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~ 99 (214)
..||+=+..+..+.+ ...|+|.|=++=+..++.. . ..++||..+|..
T Consensus 177 ~rdPis~~~I~nPvi--SkkC~HvydrDsI~~~l~~-----~-~~i~CPv~gC~~ 223 (262)
T KOG2979|consen 177 NRDPISKKPIVNPVI--SKKCGHVYDRDSIMQILCD-----E-ITIRCPVLGCEN 223 (262)
T ss_pred ccCchhhhhhhchhh--hcCcCcchhhhhHHHHhcc-----C-ceeecccccCCc
Confidence 468877777766643 5789999999888877643 2 478999999983
No 269
>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=36.28 E-value=71 Score=27.11 Aligned_cols=64 Identities=19% Similarity=0.437 Sum_probs=38.9
Q ss_pred Cccccccccccccccccccccc--------------CC-----CCccccHHHHHHHHHHHhhCCC---c--ccccCCCCC
Q 045388 41 PPSRSSCEICRERRENDQMFKI--------------ES-----CIHSFCSDCINKHVATKIQGGI---I--TPVTCPGPD 96 (214)
Q Consensus 41 ~~~~~~C~iC~~~~~~~~~~~~--------------~~-----C~H~fC~~Cl~~~~~~~i~~~~---~--~~i~CP~~~ 96 (214)
..+...|--|+..-++-++.+. .. |.-..|.+|+.+|+..+=.+.. | ....||-
T Consensus 268 ~~e~e~CigC~~~~~~vkl~k~C~~~~~~g~~~~~~~~C~~C~CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPt-- 345 (358)
T PF10272_consen 268 GQELEPCIGCMQAQPNVKLVKRCADEEQEGSPLPNEPPCQQCYCRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPT-- 345 (358)
T ss_pred ccccCCccccccCCCCcEEEeccCCcccCCcccccCCCCccccccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCC--
Confidence 3567779999887654443321 12 2335799999999865443221 2 4566776
Q ss_pred CCCcCcHHHH
Q 045388 97 CKSVLKFDAC 106 (214)
Q Consensus 97 C~~~l~~~~~ 106 (214)
|...+-..||
T Consensus 346 CRa~FCilDV 355 (358)
T PF10272_consen 346 CRAKFCILDV 355 (358)
T ss_pred Ccccceeeee
Confidence 8887755443
No 270
>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=36.04 E-value=46 Score=18.81 Aligned_cols=13 Identities=23% Similarity=0.411 Sum_probs=9.1
Q ss_pred hCCCccCCCCCcc
Q 045388 189 KKQLRKCPNCKYH 201 (214)
Q Consensus 189 ~~~~k~CP~C~~~ 201 (214)
-.+...||+|+..
T Consensus 15 W~~g~~CP~Cg~~ 27 (46)
T PF12760_consen 15 WPDGFVCPHCGST 27 (46)
T ss_pred CCCCCCCCCCCCe
Confidence 3444669999973
No 271
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.25 E-value=20 Score=22.15 Aligned_cols=15 Identities=20% Similarity=0.519 Sum_probs=11.8
Q ss_pred CCCccCCCCCcccee
Q 045388 190 KQLRKCPNCKYHIER 204 (214)
Q Consensus 190 ~~~k~CP~C~~~iek 204 (214)
.....||.|+++++.
T Consensus 5 ~~~v~CP~Cgkpv~w 19 (65)
T COG3024 5 RITVPCPTCGKPVVW 19 (65)
T ss_pred cccccCCCCCCcccc
Confidence 446789999998875
No 272
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=34.94 E-value=27 Score=17.01 Aligned_cols=18 Identities=28% Similarity=0.510 Sum_probs=13.8
Q ss_pred ccCCCCCCCCcCcHHHHhhc
Q 045388 90 VTCPGPDCKSVLKFDACKSV 109 (214)
Q Consensus 90 i~CP~~~C~~~l~~~~~~~~ 109 (214)
+.||. |+..+..+.+..+
T Consensus 3 ~~C~~--CgR~F~~~~l~~H 20 (25)
T PF13913_consen 3 VPCPI--CGRKFNPDRLEKH 20 (25)
T ss_pred CcCCC--CCCEECHHHHHHH
Confidence 57888 9988887776554
No 273
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=34.75 E-value=44 Score=23.36 Aligned_cols=11 Identities=27% Similarity=0.933 Sum_probs=5.3
Q ss_pred ccCccCCCceeee
Q 045388 134 YCPFKDCSAKLVY 146 (214)
Q Consensus 134 ~Cp~~~C~~~~~~ 146 (214)
||. +|+..+..
T Consensus 72 ~C~--~C~~~~~~ 82 (115)
T COG0375 72 WCL--DCGQEVEL 82 (115)
T ss_pred Eec--cCCCeecc
Confidence 555 55444443
No 274
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=34.55 E-value=52 Score=26.30 Aligned_cols=34 Identities=12% Similarity=0.315 Sum_probs=19.1
Q ss_pred CHHHHHHHHHHHHHHHhcCCCCcccCccCCCceeee
Q 045388 111 SKNVLELWEKALSQELIDASQGIYCPFKDCSAKLVY 146 (214)
Q Consensus 111 ~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~ 146 (214)
+.+.+.+|++...+.....+-.|-|. .|+.....
T Consensus 91 Te~Nlrm~d~a~~~~ip~~drqFaC~--~Cd~~WwR 124 (278)
T PF15135_consen 91 TEENLRMFDDAQENLIPSVDRQFACS--SCDHMWWR 124 (278)
T ss_pred hHHHHHHhhhhhhccccccceeeecc--ccchHHHh
Confidence 45666666666443332334456788 88765433
No 275
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=34.53 E-value=33 Score=27.90 Aligned_cols=23 Identities=30% Similarity=0.624 Sum_probs=16.7
Q ss_pred CCccCCCCCccceec--CCCCCeec
Q 045388 191 QLRKCPNCKYHIERT--GGCLHMTC 213 (214)
Q Consensus 191 ~~k~CP~C~~~iek~--~GCnhm~C 213 (214)
..++|+.|+..|+|. +|=+...|
T Consensus 244 ~GepC~~CGt~I~k~~~~gR~t~~C 268 (273)
T COG0266 244 AGEPCRRCGTPIEKIKLGGRSTFYC 268 (273)
T ss_pred CCCCCCccCCEeEEEEEcCCcCEeC
Confidence 458999999999986 56444444
No 276
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=34.38 E-value=30 Score=20.83 Aligned_cols=25 Identities=28% Similarity=0.724 Sum_probs=14.7
Q ss_pred CCCCcccCccCCCceeeecCCCCCCcCcccCCCCCh
Q 045388 129 ASQGIYCPFKDCSAKLVYENDGEDVLSESECPYCHR 164 (214)
Q Consensus 129 ~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 164 (214)
.++...|| .|+.+.. +...|+.||.
T Consensus 24 ~~~l~~C~--~CG~~~~---------~H~vC~~CG~ 48 (57)
T PRK12286 24 APGLVECP--NCGEPKL---------PHRVCPSCGY 48 (57)
T ss_pred CCcceECC--CCCCccC---------CeEECCCCCc
Confidence 35566777 7775553 3344666664
No 277
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=34.35 E-value=1e+02 Score=20.57 Aligned_cols=25 Identities=24% Similarity=0.631 Sum_probs=14.7
Q ss_pred ccCccCCCceeeecCCCCCCcCcccCCCCCh
Q 045388 134 YCPFKDCSAKLVYENDGEDVLSESECPYCHR 164 (214)
Q Consensus 134 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 164 (214)
.|- +|++.+..+... .--+||.|+.
T Consensus 60 ~Ck--kCGfef~~~~ik----~pSRCP~CKS 84 (97)
T COG3357 60 RCK--KCGFEFRDDKIK----KPSRCPKCKS 84 (97)
T ss_pred hhc--ccCccccccccC----CcccCCcchh
Confidence 577 888887764431 2345765543
No 278
>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=34.24 E-value=33 Score=20.55 Aligned_cols=30 Identities=17% Similarity=0.481 Sum_probs=15.4
Q ss_pred cccCccCCCceeeecCCCCCCcCcccCCCCChhhc
Q 045388 133 IYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFC 167 (214)
Q Consensus 133 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C 167 (214)
+.|| +|...-..=.. ....+.|..|+..+|
T Consensus 8 VkCp--~C~~~q~vFSh---a~t~V~C~~Cg~~L~ 37 (55)
T PF01667_consen 8 VKCP--GCYNIQTVFSH---AQTVVKCVVCGTVLA 37 (55)
T ss_dssp EE-T--TT-SEEEEETT----SS-EE-SSSTSEEE
T ss_pred EECC--CCCCeeEEEec---CCeEEEcccCCCEec
Confidence 4788 88865433221 125677888887765
No 279
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=33.78 E-value=36 Score=19.94 Aligned_cols=30 Identities=30% Similarity=0.565 Sum_probs=21.0
Q ss_pred cccccccccccccccccCCCCccccHHHHHHH
Q 045388 46 SCEICRERRENDQMFKIESCIHSFCSDCINKH 77 (214)
Q Consensus 46 ~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~ 77 (214)
.|.||..++..-..+. +.=| ..|.+|+...
T Consensus 1 ~C~iCg~kigl~~~~k-~~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFK-IKDG-YICKDCLKKL 30 (51)
T ss_pred CCCcccccccccccee-ccCc-cchHHHHHHh
Confidence 4899999876644332 3335 7999999776
No 280
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=33.68 E-value=9 Score=35.02 Aligned_cols=55 Identities=29% Similarity=0.516 Sum_probs=39.6
Q ss_pred cccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHH
Q 045388 42 PSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDAC 106 (214)
Q Consensus 42 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~ 106 (214)
....+|+||+..+-.+ ..+.|.|.||..|+..-+...-. ...||. |...+.....
T Consensus 19 ~k~lEc~ic~~~~~~p---~~~kc~~~~l~~~~n~~f~~~~~-----~~~~~l--c~~~~eK~s~ 73 (684)
T KOG4362|consen 19 QKILECPICLEHVKEP---SLLKCDHIFLKFCLNKLFESKKG-----PKQCAL--CKSDIEKRSL 73 (684)
T ss_pred hhhccCCceeEEeecc---chhhhhHHHHhhhhhceeeccCc-----cccchh--hhhhhhhhhc
Confidence 3468999999998766 26899999999999887653322 456787 7655544433
No 281
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=33.03 E-value=46 Score=17.59 Aligned_cols=23 Identities=30% Similarity=0.694 Sum_probs=13.6
Q ss_pred ccCccCCCceeeecCCCCCCcCcccCCCCCh
Q 045388 134 YCPFKDCSAKLVYENDGEDVLSESECPYCHR 164 (214)
Q Consensus 134 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 164 (214)
.|+ .|++++..+.. --.||.|+.
T Consensus 4 ~C~--~CG~i~~g~~~------p~~CP~Cg~ 26 (34)
T cd00729 4 VCP--VCGYIHEGEEA------PEKCPICGA 26 (34)
T ss_pred ECC--CCCCEeECCcC------CCcCcCCCC
Confidence 366 78877654321 225887775
No 282
>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=33.02 E-value=27 Score=17.67 Aligned_cols=28 Identities=14% Similarity=0.643 Sum_probs=8.6
Q ss_pred cccccccccccccccccCCCCccccHHH
Q 045388 46 SCEICRERRENDQMFKIESCIHSFCSDC 73 (214)
Q Consensus 46 ~C~iC~~~~~~~~~~~~~~C~H~fC~~C 73 (214)
.|.+|........++....|.-.+..+|
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~Cdf~lH~~C 29 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSECDFDLHEEC 29 (30)
T ss_dssp --TTTS----S--EEE-TTT-----HHH
T ss_pred cCCcCCCcCCCCceEECccCCCccChhc
Confidence 5777777665533344566666666665
No 283
>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=32.88 E-value=13 Score=17.23 Aligned_cols=6 Identities=50% Similarity=1.730 Sum_probs=2.5
Q ss_pred CCCCCh
Q 045388 159 CPYCHR 164 (214)
Q Consensus 159 C~~C~~ 164 (214)
|+.|+.
T Consensus 3 C~~C~~ 8 (23)
T PF00096_consen 3 CPICGK 8 (23)
T ss_dssp ETTTTE
T ss_pred CCCCCC
Confidence 444443
No 284
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=32.04 E-value=18 Score=30.17 Aligned_cols=31 Identities=29% Similarity=0.756 Sum_probs=22.0
Q ss_pred cccCccCCCceeeecCCCCCCcCcccCCCCChhhccccC
Q 045388 133 IYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCY 171 (214)
Q Consensus 133 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~ 171 (214)
-+|| -|-..+-..+. +.+-| .||+.+|.-|.
T Consensus 15 d~cp--lcie~mditdk-----nf~pc-~cgy~ic~fc~ 45 (480)
T COG5175 15 DYCP--LCIEPMDITDK-----NFFPC-PCGYQICQFCY 45 (480)
T ss_pred ccCc--ccccccccccC-----CcccC-CcccHHHHHHH
Confidence 3588 77765544443 67779 49999999884
No 285
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=31.96 E-value=73 Score=22.87 Aligned_cols=24 Identities=21% Similarity=0.607 Sum_probs=16.2
Q ss_pred CCCcccccccccccccccccccccCCCCcc
Q 045388 39 SSPPSRSSCEICRERRENDQMFKIESCIHS 68 (214)
Q Consensus 39 ~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~ 68 (214)
.+.....+|.||..+.- .-.|||.
T Consensus 60 aGv~ddatC~IC~KTKF------ADG~GH~ 83 (169)
T KOG3799|consen 60 AGVGDDATCGICHKTKF------ADGCGHN 83 (169)
T ss_pred cccCcCcchhhhhhccc------ccccCcc
Confidence 45566789999988632 2467774
No 286
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=31.67 E-value=29 Score=32.56 Aligned_cols=17 Identities=35% Similarity=0.997 Sum_probs=15.2
Q ss_pred ccCCCCCccceecCCCC
Q 045388 193 RKCPNCKYHIERTGGCL 209 (214)
Q Consensus 193 k~CP~C~~~iek~~GCn 209 (214)
..||.|+..+...+||.
T Consensus 725 ~~Cp~Cg~~l~~~~GC~ 741 (752)
T PRK08665 725 GACPECGSILEHEEGCV 741 (752)
T ss_pred CCCCCCCcccEECCCCC
Confidence 35999999999999997
No 287
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=31.48 E-value=61 Score=25.23 Aligned_cols=19 Identities=11% Similarity=0.487 Sum_probs=15.1
Q ss_pred ccccccccccccccccccc
Q 045388 43 SRSSCEICRERRENDQMFK 61 (214)
Q Consensus 43 ~~~~C~iC~~~~~~~~~~~ 61 (214)
+..+||+|..+|....+..
T Consensus 4 k~~~CPvC~~~F~~~~vrs 22 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRS 22 (214)
T ss_pred CceECCCCCCeeeeeEEEc
Confidence 4689999999998776543
No 288
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=31.34 E-value=7.2 Score=30.88 Aligned_cols=35 Identities=23% Similarity=0.714 Sum_probs=11.4
Q ss_pred cccCccCCCceeeecCCCCCCcCcccCCCCChhhccc
Q 045388 133 IYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAH 169 (214)
Q Consensus 133 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~ 169 (214)
.+|| +|+..-...-.......-+.|+.|+..|=+.
T Consensus 32 ~yCP--~Cg~~~L~~f~NN~PVaDF~C~~C~eeyELK 66 (254)
T PF06044_consen 32 MYCP--NCGSKPLSKFENNRPVADFYCPNCNEEYELK 66 (254)
T ss_dssp ---T--TT--SS-EE--------EEE-TTT--EEEEE
T ss_pred CcCC--CCCChhHhhccCCCccceeECCCCchHHhhh
Confidence 4799 8987622221111334557788887666444
No 289
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.48 E-value=36 Score=21.98 Aligned_cols=32 Identities=25% Similarity=0.615 Sum_probs=17.2
Q ss_pred ccCccCCCceeeecCCCCCCcCcccCCCCChhhccccCCCCCCC
Q 045388 134 YCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWHPG 177 (214)
Q Consensus 134 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~h~~ 177 (214)
.|| .|+..+...... .. ...+|..|+.-|-++
T Consensus 3 lCP--~C~v~l~~~~rs--~v--------EiD~CPrCrGVWLDr 34 (88)
T COG3809 3 LCP--ICGVELVMSVRS--GV--------EIDYCPRCRGVWLDR 34 (88)
T ss_pred ccC--cCCceeeeeeec--Cc--------eeeeCCccccEeecc
Confidence 477 787666554331 11 233455666667554
No 290
>PLN02189 cellulose synthase
Probab=29.41 E-value=39 Score=32.69 Aligned_cols=51 Identities=27% Similarity=0.617 Sum_probs=34.6
Q ss_pred cccccccccccccc----ccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCc
Q 045388 43 SRSSCEICRERREN----DQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLK 102 (214)
Q Consensus 43 ~~~~C~iC~~~~~~----~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 102 (214)
....|+||.|++.. +.++..-.|+-..|+.|+ +|- .++|. =.||. |+....
T Consensus 33 ~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cy-eye---r~eg~---q~Cpq--Ckt~Y~ 87 (1040)
T PLN02189 33 DGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCY-EYE---RREGT---QNCPQ--CKTRYK 87 (1040)
T ss_pred cCccccccccccCcCCCCCEEEeeccCCCccccchh-hhh---hhcCC---ccCcc--cCCchh
Confidence 34589999999653 333446679999999998 443 33444 47998 765443
No 291
>PRK12495 hypothetical protein; Provisional
Probab=29.36 E-value=92 Score=24.43 Aligned_cols=15 Identities=13% Similarity=0.481 Sum_probs=11.4
Q ss_pred CCCcccCccCCCceeee
Q 045388 130 SQGIYCPFKDCSAKLVY 146 (214)
Q Consensus 130 ~~~~~Cp~~~C~~~~~~ 146 (214)
...++|+ .|+..|+.
T Consensus 40 msa~hC~--~CG~PIpa 54 (226)
T PRK12495 40 MTNAHCD--ECGDPIFR 54 (226)
T ss_pred cchhhcc--cccCcccC
Confidence 3457999 99988873
No 292
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=29.11 E-value=51 Score=24.57 Aligned_cols=17 Identities=24% Similarity=0.540 Sum_probs=12.4
Q ss_pred CCcccCccCCCceeeecCC
Q 045388 131 QGIYCPFKDCSAKLVYEND 149 (214)
Q Consensus 131 ~~~~Cp~~~C~~~~~~~~~ 149 (214)
..-.|| .|++.+.....
T Consensus 96 e~~RCp--~CN~~L~~vs~ 112 (165)
T COG1656 96 EFSRCP--ECNGELEKVSR 112 (165)
T ss_pred ccccCc--ccCCEeccCcH
Confidence 355799 99998876643
No 293
>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=28.99 E-value=34 Score=18.26 Aligned_cols=21 Identities=29% Similarity=0.694 Sum_probs=10.3
Q ss_pred ccCccCCCceeeecCCCCCCcCcccCCCCCh
Q 045388 134 YCPFKDCSAKLVYENDGEDVLSESECPYCHR 164 (214)
Q Consensus 134 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 164 (214)
.|. +|+.++... ...|+.|+.
T Consensus 13 rC~--~Cg~~~~pP--------r~~Cp~C~s 33 (37)
T PF12172_consen 13 RCR--DCGRVQFPP--------RPVCPHCGS 33 (37)
T ss_dssp E-T--TT--EEES----------SEETTTT-
T ss_pred EcC--CCCCEecCC--------CcCCCCcCc
Confidence 677 888877653 344777753
No 294
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=28.93 E-value=46 Score=19.16 Aligned_cols=32 Identities=19% Similarity=0.611 Sum_probs=21.0
Q ss_pred cccccccccccccccccCCCCc-cccHHHHHHH
Q 045388 46 SCEICRERRENDQMFKIESCIH-SFCSDCINKH 77 (214)
Q Consensus 46 ~C~iC~~~~~~~~~~~~~~C~H-~fC~~Cl~~~ 77 (214)
+|..|..++.....+..+.|.. -.|.+|+..-
T Consensus 2 ~Cd~C~~~~~~g~r~~C~~C~d~dLC~~Cf~~g 34 (49)
T cd02335 2 HCDYCSKDITGTIRIKCAECPDFDLCLECFSAG 34 (49)
T ss_pred CCCCcCCCCCCCcEEECCCCCCcchhHHhhhCc
Confidence 5778877665544444667744 4888888744
No 295
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=28.86 E-value=18 Score=33.40 Aligned_cols=69 Identities=23% Similarity=0.514 Sum_probs=41.0
Q ss_pred CCCCcccCccCCCceeeecC-----------CCC--------CCcCcccCCCCChhhccccCCCCCCChHHHHHHHHHHh
Q 045388 129 ASQGIYCPFKDCSAKLVYEN-----------DGE--------DVLSESECPYCHRLFCAHCYVPWHPGREELMMRELVKK 189 (214)
Q Consensus 129 ~~~~~~Cp~~~C~~~~~~~~-----------~~~--------~~~~~~~C~~C~~~~C~~C~~~~h~~~~~~~~~~~~~~ 189 (214)
..+.+.|+ -|.+.|-+.. .+. .....+.|+.|++.|=+......| .++..+
T Consensus 237 ne~nfsC~--lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgKAFKfKHHLKEH--------lRIHSG 306 (1007)
T KOG3623|consen 237 NEPNFSCM--LCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGKAFKFKHHLKEH--------LRIHSG 306 (1007)
T ss_pred CCCCCcch--hhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccchhhhhHHHHHhh--------heeecC
Confidence 45667888 8987763321 111 124678898888887555433211 112223
Q ss_pred CCCccCCCCCccceecCC
Q 045388 190 KQLRKCPNCKYHIERTGG 207 (214)
Q Consensus 190 ~~~k~CP~C~~~iek~~G 207 (214)
.+--.||+|+..+-..|.
T Consensus 307 EKPfeCpnCkKRFSHSGS 324 (1007)
T KOG3623|consen 307 EKPFECPNCKKRFSHSGS 324 (1007)
T ss_pred CCCcCCcccccccccCCc
Confidence 344579999999887764
No 296
>PLN02436 cellulose synthase A
Probab=28.72 E-value=55 Score=31.85 Aligned_cols=51 Identities=27% Similarity=0.667 Sum_probs=34.5
Q ss_pred cccccccccccccc----ccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCc
Q 045388 43 SRSSCEICRERREN----DQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLK 102 (214)
Q Consensus 43 ~~~~C~iC~~~~~~----~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 102 (214)
....|+||.|++.. +.++..-.|+-..|+.|+ +|- .++|. -.||. |+....
T Consensus 35 ~~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cy-eye---r~eg~---~~Cpq--ckt~Y~ 89 (1094)
T PLN02436 35 SGQTCQICGDEIELTVDGEPFVACNECAFPVCRPCY-EYE---RREGN---QACPQ--CKTRYK 89 (1094)
T ss_pred CCccccccccccCcCCCCCEEEeeccCCCccccchh-hhh---hhcCC---ccCcc--cCCchh
Confidence 34589999999743 233336689999999998 443 33444 47998 765443
No 297
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=28.62 E-value=1.2e+02 Score=24.38 Aligned_cols=29 Identities=17% Similarity=0.446 Sum_probs=20.4
Q ss_pred CCCcccCccCCCceeeecCCCCCCcCcccCCCCCh
Q 045388 130 SQGIYCPFKDCSAKLVYENDGEDVLSESECPYCHR 164 (214)
Q Consensus 130 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 164 (214)
...++|| .|+..+.....+ ....|+.|+.
T Consensus 97 ~~~~fC~--~CG~~~~~~~~~----~~~~C~~c~~ 125 (256)
T PRK00241 97 RSHRFCG--YCGHPMHPSKTE----WAMLCPHCRE 125 (256)
T ss_pred hcCcccc--ccCCCCeecCCc----eeEECCCCCC
Confidence 4567999 999877665443 5567888874
No 298
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=28.49 E-value=53 Score=19.90 Aligned_cols=36 Identities=17% Similarity=0.245 Sum_probs=23.7
Q ss_pred cCCCCCCCCcCcHHHHhhcCCHHHHHHHHHHHHHHHhc
Q 045388 91 TCPGPDCKSVLKFDACKSVLSKNVLELWEKALSQELID 128 (214)
Q Consensus 91 ~CP~~~C~~~l~~~~~~~~l~~~~~~~~~~~~~~~~~~ 128 (214)
+||. |+.......=-.+-+++-|.+|...+......
T Consensus 19 ~Cp~--CG~~t~~~~PprFSPeD~y~kYR~~lkk~~~~ 54 (59)
T COG2260 19 KCPV--CGGDTKVPHPPRFSPEDKYGKYRRELKKRLGL 54 (59)
T ss_pred cCCC--CCCccccCCCCCCCccchHHHHHHHHHHHhcc
Confidence 5888 77654333334455678899998887766443
No 299
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=28.19 E-value=29 Score=20.36 Aligned_cols=11 Identities=27% Similarity=0.546 Sum_probs=8.7
Q ss_pred ccCCCCCccce
Q 045388 193 RKCPNCKYHIE 203 (214)
Q Consensus 193 k~CP~C~~~ie 203 (214)
|+||.|+-.-+
T Consensus 2 kPCPfCGg~~~ 12 (53)
T TIGR03655 2 KPCPFCGGADV 12 (53)
T ss_pred CCCCCCCCcce
Confidence 79999998444
No 300
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=28.01 E-value=30 Score=25.12 Aligned_cols=43 Identities=23% Similarity=0.457 Sum_probs=22.9
Q ss_pred ccCCCCCCCCcC---cHHHHhhcCCHHHHHHHHHHHHHHHhcCCCCcccCccCCCceeeec
Q 045388 90 VTCPGPDCKSVL---KFDACKSVLSKNVLELWEKALSQELIDASQGIYCPFKDCSAKLVYE 147 (214)
Q Consensus 90 i~CP~~~C~~~l---~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~ 147 (214)
-+||. |+..| +.++++..+++.+++.+ .....|| +|+.++...
T Consensus 92 sRC~~--CN~~L~~v~~~~v~~~vp~~v~~~~-----------~~f~~C~--~C~kiyW~G 137 (147)
T PF01927_consen 92 SRCPK--CNGPLRPVSKEEVKDRVPPYVYETY-----------DEFWRCP--GCGKIYWEG 137 (147)
T ss_pred CccCC--CCcEeeechhhccccccCccccccC-----------CeEEECC--CCCCEeccc
Confidence 58988 77655 33444444444333321 1233577 777666543
No 301
>PRK11827 hypothetical protein; Provisional
Probab=27.97 E-value=46 Score=20.32 Aligned_cols=29 Identities=34% Similarity=0.615 Sum_probs=17.6
Q ss_pred CcccCccCCCceeeecCCCCCCcCcccCCCCChhh
Q 045388 132 GIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLF 166 (214)
Q Consensus 132 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 166 (214)
..-|| .|.+.+..+... ....|..|+..|
T Consensus 8 ILaCP--~ckg~L~~~~~~----~~Lic~~~~laY 36 (60)
T PRK11827 8 IIACP--VCNGKLWYNQEK----QELICKLDNLAF 36 (60)
T ss_pred heECC--CCCCcCeEcCCC----CeEECCccCeec
Confidence 34588 888877776542 345566555443
No 302
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.89 E-value=57 Score=20.68 Aligned_cols=59 Identities=27% Similarity=0.625 Sum_probs=35.1
Q ss_pred cccccccccccccccccccCCC--CccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHhhcCCHHHHHHH
Q 045388 44 RSSCEICRERRENDQMFKIESC--IHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKSVLSKNVLELW 118 (214)
Q Consensus 44 ~~~C~iC~~~~~~~~~~~~~~C--~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~~~l~~~~~~~~ 118 (214)
...|..|-.+++....- .+-| .|.||.+|...-+ +| .||. |+..|.... +-+...+.+|
T Consensus 5 RPnCECCDrDLpp~s~d-A~ICtfEcTFCadCae~~l-----~g-----~CPn--CGGelv~RP---~RPaa~L~r~ 65 (84)
T COG3813 5 RPNCECCDRDLPPDSTD-ARICTFECTFCADCAENRL-----HG-----LCPN--CGGELVARP---IRPAAKLARY 65 (84)
T ss_pred cCCCcccCCCCCCCCCc-eeEEEEeeehhHhHHHHhh-----cC-----cCCC--CCchhhcCc---CChHHHHhhC
Confidence 45688887777654321 2334 5789999977553 22 5898 887663322 3334445554
No 303
>KOG2041 consensus WD40 repeat protein [General function prediction only]
Probab=27.71 E-value=59 Score=30.31 Aligned_cols=21 Identities=10% Similarity=0.014 Sum_probs=14.8
Q ss_pred hcCCHHHHHHHHHHHHHHHhc
Q 045388 108 SVLSKNVLELWEKALSQELID 128 (214)
Q Consensus 108 ~~l~~~~~~~~~~~~~~~~~~ 128 (214)
..|++...++|+.+..+-+..
T Consensus 1087 e~l~~a~kq~ye~La~~iFsk 1107 (1189)
T KOG2041|consen 1087 EELDDAEKQEYENLAFRIFSK 1107 (1189)
T ss_pred hhCCHHHHHHHHHHHHHHhcc
Confidence 446778888888887765443
No 304
>KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=27.51 E-value=19 Score=29.55 Aligned_cols=54 Identities=13% Similarity=0.359 Sum_probs=33.6
Q ss_pred CCCCccccccccccc-ccccccc-cccCCCCccccHHHHHHH-HHHHhhCCCcccc-cCCC
Q 045388 38 PSSPPSRSSCEICRE-RRENDQM-FKIESCIHSFCSDCINKH-VATKIQGGIITPV-TCPG 94 (214)
Q Consensus 38 ~~~~~~~~~C~iC~~-~~~~~~~-~~~~~C~H~fC~~Cl~~~-~~~~i~~~~~~~i-~CP~ 94 (214)
-.++.+...|.+|.. +|+...- .-...||+.||..|-..- +......+ ++ .|+.
T Consensus 162 W~PD~ea~~C~~C~~~~Ftl~~RRHHCR~CG~ivC~~Cs~n~~~l~~~~~k---~~rvC~~ 219 (288)
T KOG1729|consen 162 WLPDSEATECMVCGCTEFTLSERRHHCRNCGDIVCAPCSRNRFLLPNLSTK---PIRVCDI 219 (288)
T ss_pred ccCcccceecccCCCccccHHHHHHHHHhcchHhhhhhhcCcccccccCCC---CceecHH
Confidence 334456788999999 5544211 115689999999998873 33333332 33 5655
No 305
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=27.18 E-value=60 Score=22.11 Aligned_cols=41 Identities=20% Similarity=0.456 Sum_probs=32.4
Q ss_pred cccccccccccccccccccCCCCccccHHHHHHHHHHHhhCC
Q 045388 44 RSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGG 85 (214)
Q Consensus 44 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~ 85 (214)
.+.|.||.+++-....|.+.. +-.+..+||+.-+...+...
T Consensus 2 kWkC~iCg~~I~~gqlFTF~~-kG~VH~~C~~~~~~~k~~~~ 42 (101)
T PF09943_consen 2 KWKCYICGKPIYEGQLFTFTK-KGPVHYECFREKASKKLYGD 42 (101)
T ss_pred ceEEEecCCeeeecceEEEec-CCcEeHHHHHHHHhhhcccC
Confidence 578999999988888777544 48899999999887666543
No 306
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=26.90 E-value=69 Score=31.22 Aligned_cols=50 Identities=22% Similarity=0.649 Sum_probs=34.7
Q ss_pred ccccccccccccccc----cccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcC
Q 045388 43 SRSSCEICRERREND----QMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVL 101 (214)
Q Consensus 43 ~~~~C~iC~~~~~~~----~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 101 (214)
....|.||.|++... .++..-.|+-..|+.|. +| ..++|. =.||+ |+...
T Consensus 16 ~~qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCY-EY---Er~eG~---q~CPq--CktrY 69 (1079)
T PLN02638 16 GGQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCY-EY---ERKDGN---QSCPQ--CKTKY 69 (1079)
T ss_pred CCceeeecccccCcCCCCCEEEEeccCCCccccchh-hh---hhhcCC---ccCCc--cCCch
Confidence 356899999997542 33446789999999998 44 334554 37998 76543
No 307
>KOG2923 consensus Uncharacterized conserved protein [Function unknown]
Probab=26.90 E-value=38 Score=20.90 Aligned_cols=17 Identities=24% Similarity=0.737 Sum_probs=12.3
Q ss_pred HHhCCCccCCCCCccce
Q 045388 187 VKKKQLRKCPNCKYHIE 203 (214)
Q Consensus 187 ~~~~~~k~CP~C~~~ie 203 (214)
..+..+-+||+|...|.
T Consensus 39 ~~ge~Va~CpsCSL~I~ 55 (67)
T KOG2923|consen 39 ENGEDVARCPSCSLIIR 55 (67)
T ss_pred hCCCeeecCCCceEEEE
Confidence 34567788888887764
No 308
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=26.77 E-value=94 Score=20.56 Aligned_cols=35 Identities=20% Similarity=0.342 Sum_probs=20.0
Q ss_pred CCCcccCccCCCceeeecCCCCCCcCcccCCCCChhhcccc
Q 045388 130 SQGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHC 170 (214)
Q Consensus 130 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C 170 (214)
.+.-.|| .|+........ .-+..|..|+..|=--.
T Consensus 33 ~~~~~Cp--~C~~~~VkR~a----~GIW~C~kCg~~fAGga 67 (89)
T COG1997 33 RAKHVCP--FCGRTTVKRIA----TGIWKCRKCGAKFAGGA 67 (89)
T ss_pred hcCCcCC--CCCCcceeeec----cCeEEcCCCCCeecccc
Confidence 3445688 89876433322 25667777766554333
No 309
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=26.64 E-value=55 Score=26.47 Aligned_cols=15 Identities=33% Similarity=0.771 Sum_probs=11.7
Q ss_pred CCccCCCCCccceec
Q 045388 191 QLRKCPNCKYHIERT 205 (214)
Q Consensus 191 ~~k~CP~C~~~iek~ 205 (214)
..++||.|+..|+|.
T Consensus 234 ~g~pC~~Cg~~I~~~ 248 (269)
T PRK14811 234 EGQPCPRCGTPIEKI 248 (269)
T ss_pred CcCCCCcCCCeeEEE
Confidence 357899999988765
No 310
>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=26.25 E-value=58 Score=26.35 Aligned_cols=15 Identities=27% Similarity=0.554 Sum_probs=12.5
Q ss_pred CCccCCCCCccceec
Q 045388 191 QLRKCPNCKYHIERT 205 (214)
Q Consensus 191 ~~k~CP~C~~~iek~ 205 (214)
..++||+|+..|+|.
T Consensus 244 ~g~pC~~Cg~~I~~~ 258 (272)
T TIGR00577 244 KGEPCRRCGTPIEKI 258 (272)
T ss_pred CCCCCCCCCCeeEEE
Confidence 357999999999875
No 311
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=26.25 E-value=57 Score=26.43 Aligned_cols=14 Identities=43% Similarity=0.695 Sum_probs=12.1
Q ss_pred CccCCCCCccceec
Q 045388 192 LRKCPNCKYHIERT 205 (214)
Q Consensus 192 ~k~CP~C~~~iek~ 205 (214)
.++||+|+..|++.
T Consensus 244 g~pCprCG~~I~~~ 257 (272)
T PRK14810 244 GEPCLNCKTPIRRV 257 (272)
T ss_pred CCcCCCCCCeeEEE
Confidence 57999999999875
No 312
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=25.98 E-value=58 Score=26.36 Aligned_cols=14 Identities=29% Similarity=0.558 Sum_probs=11.8
Q ss_pred CccCCCCCccceec
Q 045388 192 LRKCPNCKYHIERT 205 (214)
Q Consensus 192 ~k~CP~C~~~iek~ 205 (214)
.++||.|+..|+|.
T Consensus 245 g~pC~~Cg~~I~~~ 258 (274)
T PRK01103 245 GEPCRRCGTPIEKI 258 (274)
T ss_pred CCCCCCCCCeeEEE
Confidence 47899999999875
No 313
>KOG3816 consensus Cell differentiation regulator of the Headcase family [Signal transduction mechanisms]
Probab=25.91 E-value=72 Score=27.29 Aligned_cols=15 Identities=40% Similarity=0.846 Sum_probs=10.7
Q ss_pred HHhCCCccCCCCCcc
Q 045388 187 VKKKQLRKCPNCKYH 201 (214)
Q Consensus 187 ~~~~~~k~CP~C~~~ 201 (214)
..=...+.||.|+..
T Consensus 495 s~ys~~~~cP~c~~~ 509 (526)
T KOG3816|consen 495 SNYSALRICPSCKLA 509 (526)
T ss_pred hhhhcccccCCcCcc
Confidence 333567999999873
No 314
>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=25.83 E-value=27 Score=15.81 Aligned_cols=6 Identities=50% Similarity=1.730 Sum_probs=1.7
Q ss_pred CCCCCh
Q 045388 159 CPYCHR 164 (214)
Q Consensus 159 C~~C~~ 164 (214)
|+.|+.
T Consensus 3 C~~C~~ 8 (24)
T PF13894_consen 3 CPICGK 8 (24)
T ss_dssp -SSTS-
T ss_pred CcCCCC
Confidence 444443
No 315
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=25.64 E-value=1.3e+02 Score=18.55 Aligned_cols=12 Identities=42% Similarity=0.927 Sum_probs=8.2
Q ss_pred ccccCCCCCCCCcC
Q 045388 88 TPVTCPGPDCKSVL 101 (214)
Q Consensus 88 ~~i~CP~~~C~~~l 101 (214)
.-+.||. |+.+|
T Consensus 6 niL~Cp~--ck~pL 17 (68)
T PF03966_consen 6 NILACPV--CKGPL 17 (68)
T ss_dssp GTBB-TT--TSSBE
T ss_pred hhhcCCC--CCCcc
Confidence 3578998 88866
No 316
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=25.05 E-value=32 Score=27.22 Aligned_cols=57 Identities=21% Similarity=0.381 Sum_probs=35.8
Q ss_pred cccCccCCCceeeecCCCCCCcCcccCCCCChhhccccCCC-CCC-ChHHHHHHHHHHhCCCccCCCCCcccee
Q 045388 133 IYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVP-WHP-GREELMMRELVKKKQLRKCPNCKYHIER 204 (214)
Q Consensus 133 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~-~h~-~~~~~~~~~~~~~~~~k~CP~C~~~iek 204 (214)
.+|..+.|...=+ .-+.|..|+..||...... .|. +. .+-.+..++.||.|.++|.-
T Consensus 9 kHCs~~~CkqlDF---------LPf~Cd~C~~~FC~eHrsye~H~Cp~------~~~~~~~v~icp~cs~pv~~ 67 (250)
T KOG3183|consen 9 KHCSVPYCKQLDF---------LPFKCDGCSGIFCLEHRSYESHHCPK------GLRIDVQVPICPLCSKPVPT 67 (250)
T ss_pred cccCcchhhhccc---------cceeeCCccchhhhccchHhhcCCCc------ccccceeecccCCCCCCCCC
Confidence 4566556653221 3467999999999998762 222 21 11234567889999988753
No 317
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=25.04 E-value=33 Score=20.35 Aligned_cols=11 Identities=55% Similarity=1.093 Sum_probs=8.6
Q ss_pred ccCCCCCccce
Q 045388 193 RKCPNCKYHIE 203 (214)
Q Consensus 193 k~CP~C~~~ie 203 (214)
+.||+|+..-+
T Consensus 25 ~KCPrCK~vN~ 35 (60)
T COG4416 25 KKCPRCKEVNE 35 (60)
T ss_pred ecCCccceeee
Confidence 78999998543
No 318
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=25.02 E-value=33 Score=18.16 Aligned_cols=13 Identities=31% Similarity=0.823 Sum_probs=7.9
Q ss_pred CccCCCCCcccee
Q 045388 192 LRKCPNCKYHIER 204 (214)
Q Consensus 192 ~k~CP~C~~~iek 204 (214)
+-.||+|+..|..
T Consensus 4 ~~~C~nC~R~v~a 16 (33)
T PF08209_consen 4 YVECPNCGRPVAA 16 (33)
T ss_dssp EEE-TTTSSEEEG
T ss_pred eEECCCCcCCcch
Confidence 3468888877653
No 319
>KOG3005 consensus GIY-YIG type nuclease [General function prediction only]
Probab=24.89 E-value=1.3e+02 Score=24.34 Aligned_cols=61 Identities=18% Similarity=0.520 Sum_probs=38.8
Q ss_pred ccccccccccccccccc----cCCCCccccHHHHHHHHHHHhhCCCcccc--cCCCCCCCCcCcHHHHhh
Q 045388 45 SSCEICRERRENDQMFK----IESCIHSFCSDCINKHVATKIQGGIITPV--TCPGPDCKSVLKFDACKS 108 (214)
Q Consensus 45 ~~C~iC~~~~~~~~~~~----~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i--~CP~~~C~~~l~~~~~~~ 108 (214)
..|.+|.+++...+-.. ...|+-.+...||..+.. ....|++.++ .||. |...+.-.++..
T Consensus 183 ~~celc~~ei~e~~~~~a~c~~~~c~~~~h~~CLa~~~~-~~e~g~~~p~eg~cp~--C~~~~~w~~lv~ 249 (276)
T KOG3005|consen 183 VECELCEKEILETDWSRATCPNPDCDSLNHLTCLAEELL-EVEPGQLIPLEGMCPK--CEKFLSWTTLVD 249 (276)
T ss_pred hhhHHHHHHhccccceeccCCCCCCCchhhhhhhhHHHh-ccCCCceeccCCCCCc--hhceeeHHHHHH
Confidence 58999999984322221 345666677889988432 2334444444 7888 998887666554
No 320
>PF01530 zf-C2HC: Zinc finger, C2HC type; InterPro: IPR002515 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 CysCysHisCys (C2HC) type zinc finger domain found in eukaryotes. Proteins containing these domains include: MYST family histone acetyltransferases [, [] Myelin transcription factor Myt1 [] Suppressor of tumourigenicity protein 18 (ST18) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2CS8_A 1PXE_A 2JX1_A 2JYD_A.
Probab=24.68 E-value=41 Score=17.56 Aligned_cols=15 Identities=20% Similarity=0.501 Sum_probs=8.8
Q ss_pred cccCccCCCceeeec
Q 045388 133 IYCPFKDCSAKLVYE 147 (214)
Q Consensus 133 ~~Cp~~~C~~~~~~~ 147 (214)
..||+|+|+..-...
T Consensus 2 ~~CPtpGCdg~GHi~ 16 (31)
T PF01530_consen 2 LKCPTPGCDGSGHIT 16 (31)
T ss_dssp TSSSSTT--SCSTTT
T ss_pred CcCCCCCCCcccccc
Confidence 359999999764443
No 321
>PRK10445 endonuclease VIII; Provisional
Probab=24.61 E-value=65 Score=25.93 Aligned_cols=15 Identities=33% Similarity=0.552 Sum_probs=12.0
Q ss_pred CCccCCCCCccceec
Q 045388 191 QLRKCPNCKYHIERT 205 (214)
Q Consensus 191 ~~k~CP~C~~~iek~ 205 (214)
..++||.|+..|++.
T Consensus 234 ~g~~Cp~Cg~~I~~~ 248 (263)
T PRK10445 234 DGEACERCGGIIEKT 248 (263)
T ss_pred CCCCCCCCCCEeEEE
Confidence 357899999999875
No 322
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=24.47 E-value=21 Score=22.74 Aligned_cols=15 Identities=27% Similarity=0.450 Sum_probs=10.9
Q ss_pred CcccCccCCCceeee
Q 045388 132 GIYCPFKDCSAKLVY 146 (214)
Q Consensus 132 ~~~Cp~~~C~~~~~~ 146 (214)
+..|.+++|+..|..
T Consensus 27 Y~qC~N~eCg~tF~t 41 (72)
T PRK09678 27 YHQCQNVNCSATFIT 41 (72)
T ss_pred eeecCCCCCCCEEEE
Confidence 346999999976643
No 323
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=24.40 E-value=51 Score=25.14 Aligned_cols=30 Identities=27% Similarity=0.489 Sum_probs=21.8
Q ss_pred ccCccCCCceeeecCCCCCCcCcccCCCCChhhccccC
Q 045388 134 YCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCY 171 (214)
Q Consensus 134 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~ 171 (214)
.|+ +|...+.. .. ..++||.||..-=..|.
T Consensus 151 ~Cs--rC~~~L~~-~~-----~~l~Cp~Cg~tEkRKia 180 (188)
T COG1096 151 RCS--RCRAPLVK-KG-----NMLKCPNCGNTEKRKIA 180 (188)
T ss_pred Ecc--CCCcceEE-cC-----cEEECCCCCCEEeeeec
Confidence 688 99999988 32 67889999875444443
No 324
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 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 [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=24.37 E-value=69 Score=19.09 Aligned_cols=24 Identities=25% Similarity=0.753 Sum_probs=14.2
Q ss_pred CCCcccCccCCCceeeecCCCCCCcCcccCCCCCh
Q 045388 130 SQGIYCPFKDCSAKLVYENDGEDVLSESECPYCHR 164 (214)
Q Consensus 130 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 164 (214)
.+...|| .|+.+.. +...|+.||+
T Consensus 24 ~~l~~c~--~cg~~~~---------~H~vc~~cG~ 47 (56)
T PF01783_consen 24 PNLVKCP--NCGEPKL---------PHRVCPSCGY 47 (56)
T ss_dssp TSEEESS--SSSSEES---------TTSBCTTTBB
T ss_pred cceeeec--cCCCEec---------ccEeeCCCCe
Confidence 4556788 7775543 3344777763
No 325
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=24.35 E-value=50 Score=19.70 Aligned_cols=14 Identities=29% Similarity=0.672 Sum_probs=8.1
Q ss_pred CCCCcccCccCCCcee
Q 045388 129 ASQGIYCPFKDCSAKL 144 (214)
Q Consensus 129 ~~~~~~Cp~~~C~~~~ 144 (214)
.++...|| .|+.+.
T Consensus 23 ~p~l~~C~--~cG~~~ 36 (55)
T TIGR01031 23 APTLVVCP--NCGEFK 36 (55)
T ss_pred CCcceECC--CCCCcc
Confidence 34555677 666544
No 326
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=24.28 E-value=65 Score=26.25 Aligned_cols=14 Identities=36% Similarity=0.672 Sum_probs=12.0
Q ss_pred CccCCCCCccceec
Q 045388 192 LRKCPNCKYHIERT 205 (214)
Q Consensus 192 ~k~CP~C~~~iek~ 205 (214)
.++||.|+..|+|.
T Consensus 254 g~pC~~Cg~~I~~~ 267 (282)
T PRK13945 254 GKPCRKCGTPIERI 267 (282)
T ss_pred cCCCCcCCCeeEEE
Confidence 47999999999875
No 327
>PF10764 Gin: Inhibitor of sigma-G Gin; InterPro: IPR019700 Gin allows sigma-F to delay late forespore transcription by preventing sigma-G to take over before the cell has reached a critical stage of development. Gin is also known as CsfB [].
Probab=24.01 E-value=40 Score=19.33 Aligned_cols=36 Identities=28% Similarity=0.514 Sum_probs=24.6
Q ss_pred cccccccccccccccccCCCCccccHHHHHHHHHHHhhCC
Q 045388 46 SCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGG 85 (214)
Q Consensus 46 ~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~ 85 (214)
.|.||-......- .--+..+|.+|-+..+.....+.
T Consensus 1 ~CiiC~~~~~~GI----~I~~~fIC~~CE~~iv~~~~~d~ 36 (46)
T PF10764_consen 1 KCIICGKEKEEGI----HIYGKFICSDCEKEIVNTETDDP 36 (46)
T ss_pred CeEeCCCcCCCCE----EEECeEehHHHHHHhccCCCCCC
Confidence 3778877655432 22488999999988887665543
No 328
>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=23.97 E-value=28 Score=21.03 Aligned_cols=13 Identities=38% Similarity=0.731 Sum_probs=6.7
Q ss_pred CccCCCCCcccee
Q 045388 192 LRKCPNCKYHIER 204 (214)
Q Consensus 192 ~k~CP~C~~~iek 204 (214)
...||.|+..++-
T Consensus 2 ~v~CP~C~k~~~~ 14 (57)
T PF03884_consen 2 TVKCPICGKPVEW 14 (57)
T ss_dssp EEE-TTT--EEE-
T ss_pred cccCCCCCCeecc
Confidence 3579999988765
No 329
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=23.91 E-value=51 Score=18.39 Aligned_cols=12 Identities=25% Similarity=0.733 Sum_probs=7.7
Q ss_pred ccCCCCCcccee
Q 045388 193 RKCPNCKYHIER 204 (214)
Q Consensus 193 k~CP~C~~~iek 204 (214)
..||.|+....+
T Consensus 3 ~~Cp~Cg~~~~~ 14 (47)
T PF14690_consen 3 PRCPHCGSPSVH 14 (47)
T ss_pred ccCCCcCCCceE
Confidence 358888875433
No 330
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=23.87 E-value=80 Score=18.74 Aligned_cols=10 Identities=40% Similarity=1.158 Sum_probs=5.7
Q ss_pred CcccCCCCCh
Q 045388 155 SESECPYCHR 164 (214)
Q Consensus 155 ~~~~C~~C~~ 164 (214)
..++|+.|+.
T Consensus 43 i~y~C~~Cg~ 52 (54)
T PF10058_consen 43 IQYRCPYCGA 52 (54)
T ss_pred eEEEcCCCCC
Confidence 3556666654
No 331
>PRK02935 hypothetical protein; Provisional
Probab=23.58 E-value=39 Score=23.15 Aligned_cols=15 Identities=13% Similarity=0.510 Sum_probs=9.9
Q ss_pred CCccCCCCCccceec
Q 045388 191 QLRKCPNCKYHIERT 205 (214)
Q Consensus 191 ~~k~CP~C~~~iek~ 205 (214)
++-.|..|+.++...
T Consensus 85 rvD~CM~C~~PLTLd 99 (110)
T PRK02935 85 RVDACMHCNQPLTLD 99 (110)
T ss_pred ceeecCcCCCcCCcC
Confidence 445788888776543
No 332
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=23.42 E-value=45 Score=23.21 Aligned_cols=33 Identities=30% Similarity=0.788 Sum_probs=22.7
Q ss_pred cCccCCCceeeecCCCCCCcCcccCCCCChhhccccCCCCCCC
Q 045388 135 CPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWHPG 177 (214)
Q Consensus 135 Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~h~~ 177 (214)
|| .|+.-+..+ .+.|+.|+..+=..=..+|-..
T Consensus 1 CP--vCg~~l~vt--------~l~C~~C~t~i~G~F~l~~~~~ 33 (113)
T PF09862_consen 1 CP--VCGGELVVT--------RLKCPSCGTEIEGEFELPWFAR 33 (113)
T ss_pred CC--CCCCceEEE--------EEEcCCCCCEEEeeeccchhhc
Confidence 66 788777664 4569999887766666666444
No 333
>PF02748 PyrI_C: Aspartate carbamoyltransferase regulatory chain, metal binding domain; InterPro: IPR020542 Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) 2.1.3.2 from EC is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity []. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme []. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies. A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme []. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold. ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation []. This entry represents the C-terminal domain.; PDB: 2YWW_B 1SKU_D 1Q95_L 8ATC_B 3AT1_D 1RAI_D 4E2F_D 1NBE_B 6AT1_B 2FZC_D ....
Probab=23.33 E-value=39 Score=19.91 Aligned_cols=33 Identities=21% Similarity=0.576 Sum_probs=17.6
Q ss_pred CCcccCccCCCce--------eeecCCCCCCcCcccCCCCChhh
Q 045388 131 QGIYCPFKDCSAK--------LVYENDGEDVLSESECPYCHRLF 166 (214)
Q Consensus 131 ~~~~Cp~~~C~~~--------~~~~~~~~~~~~~~~C~~C~~~~ 166 (214)
+.+.||+|+|=.- |...+ .....++|..|++.+
T Consensus 5 gvl~C~Np~CITn~~E~v~~~F~v~~---~~~~~~rC~YCe~~~ 45 (52)
T PF02748_consen 5 GVLKCPNPNCITNSNEPVESRFYVID---KEPIKLRCHYCERII 45 (52)
T ss_dssp SSSE-SSTTBTTT-TSSS--EEEEEE---TTTCEEEETTT--EE
T ss_pred eEEEcCCCCcccCCCCCCCceEEEEe---CCCCEEEeeCCCCEe
Confidence 5578999999654 11111 123667888887643
No 334
>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=23.18 E-value=60 Score=18.81 Aligned_cols=32 Identities=19% Similarity=0.578 Sum_probs=22.9
Q ss_pred cccccccccccccccccccCCCCccccHHHHHHH
Q 045388 44 RSSCEICRERRENDQMFKIESCIHSFCSDCINKH 77 (214)
Q Consensus 44 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~ 77 (214)
=+.|..|...+.....+. .=+..||..|..+.
T Consensus 26 Cf~C~~C~~~l~~~~~~~--~~~~~~C~~c~~~~ 57 (58)
T PF00412_consen 26 CFKCSKCGKPLNDGDFYE--KDGKPYCKDCYQKR 57 (58)
T ss_dssp TSBETTTTCBTTTSSEEE--ETTEEEEHHHHHHH
T ss_pred ccccCCCCCccCCCeeEe--ECCEEECHHHHhhh
Confidence 367999998887766332 33688999998653
No 335
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=22.74 E-value=46 Score=22.69 Aligned_cols=13 Identities=31% Similarity=0.715 Sum_probs=10.5
Q ss_pred CCccCCCCCccce
Q 045388 191 QLRKCPNCKYHIE 203 (214)
Q Consensus 191 ~~k~CP~C~~~ie 203 (214)
+...||+|+..++
T Consensus 48 G~t~CP~Cg~~~e 60 (115)
T COG1885 48 GSTSCPKCGEPFE 60 (115)
T ss_pred ccccCCCCCCccc
Confidence 4588999998775
No 336
>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....
Probab=22.46 E-value=82 Score=19.25 Aligned_cols=13 Identities=38% Similarity=0.830 Sum_probs=9.4
Q ss_pred ccccCCCCCCCCcCc
Q 045388 88 TPVTCPGPDCKSVLK 102 (214)
Q Consensus 88 ~~i~CP~~~C~~~l~ 102 (214)
.|++|+. |+.++.
T Consensus 3 iPVRCFT--CGkvi~ 15 (60)
T PF01194_consen 3 IPVRCFT--CGKVIG 15 (60)
T ss_dssp -SSS-ST--TTSBTC
T ss_pred CceecCC--CCCChh
Confidence 5899988 999885
No 337
>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=22.45 E-value=87 Score=20.21 Aligned_cols=31 Identities=19% Similarity=0.547 Sum_probs=18.1
Q ss_pred cccCccCCCceeeecCCCCCCcCcccCCCCChhhcc
Q 045388 133 IYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCA 168 (214)
Q Consensus 133 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~ 168 (214)
+.|| +|..+-..=.. ....+.|+.|+...|.
T Consensus 35 VkC~--gc~~iT~vfSH---aqtvVvc~~c~~il~~ 65 (84)
T KOG1779|consen 35 VKCP--GCFKITTVFSH---AQTVVVCEGCSTILCQ 65 (84)
T ss_pred EEcC--CceEEEEEeec---CceEEEcCCCceEEEE
Confidence 3788 77754322211 1255678888877774
No 338
>PLN02195 cellulose synthase A
Probab=22.30 E-value=68 Score=30.93 Aligned_cols=50 Identities=22% Similarity=0.563 Sum_probs=36.0
Q ss_pred cccccccccccccc----cccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCc
Q 045388 44 RSSCEICRERREND----QMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLK 102 (214)
Q Consensus 44 ~~~C~iC~~~~~~~----~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 102 (214)
...|.||.+++... .++..-.|+-..|+.|. +| ..++|. =.||+ |+....
T Consensus 6 ~~~c~~cgd~~~~~~~g~~fvaC~eC~~pvCrpCy-ey---er~eg~---q~Cpq--Ckt~Yk 59 (977)
T PLN02195 6 APICATCGEEVGVDSNGEAFVACHECSYPLCKACL-EY---EIKEGR---KVCLR--CGGPYD 59 (977)
T ss_pred CccceecccccCcCCCCCeEEEeccCCCccccchh-hh---hhhcCC---ccCCc--cCCccc
Confidence 45799999987543 33346789999999998 44 334554 47999 887776
No 339
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=21.97 E-value=60 Score=22.29 Aligned_cols=29 Identities=28% Similarity=0.921 Sum_probs=17.4
Q ss_pred ccCccCCCceeeecCCCCCCcCcccCCCCChhhccccCCCCCCC
Q 045388 134 YCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWHPG 177 (214)
Q Consensus 134 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~h~~ 177 (214)
.|| .|+.-+.+.+. ..+ +|..|..+|.+.
T Consensus 5 ~cp--~c~sEytYed~-----~~~--------~cpec~~ew~~~ 33 (112)
T COG2824 5 PCP--KCNSEYTYEDG-----GQL--------ICPECAHEWNEN 33 (112)
T ss_pred CCC--ccCCceEEecC-----ceE--------eCchhccccccc
Confidence 366 78777777665 233 455566677644
No 340
>PF01214 CK_II_beta: Casein kinase II regulatory subunit; InterPro: IPR000704 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. Casein kinase, a ubiquitous, well-conserved protein kinase involved in cell metabolism and differentiation, is characterised by its preference for Ser or Thr in acidic stretches of amino acids. The enzyme is a tetramer of 2 alpha- and 2 beta-subunits [, ]. However, some species (e.g., mammals) possess 2 related forms of the alpha-subunit (alpha and alpha'), while others (e.g., fungi) possess 2 related beta-subunits (beta and beta') []. The alpha-subunit is the catalytic unit and contains regions characteristic of serine/threonine protein kinases. The beta-subunit is believed to be regulatory, possessing an N-terminal auto-phosphorylation site, an internal acidic domain, and a potential metal-binding motif []. The beta subunit is a highly conserved protein of about 25kDa that contains, in its central section, a cysteine-rich motif, CX(n)C, that could be involved in binding a metal such as zinc []. The mammalian beta-subunit gene promoter shares common features with those of other mammalian protein kinases and is closely related to the promoter of the regulatory subunit of cAMP-dependent protein kinase [].; GO: 0019887 protein kinase regulator activity, 0005956 protein kinase CK2 complex; PDB: 2R6M_B 1RQF_K 1DS5_G 1QF8_B 3EED_A 4DGL_A 1JWH_D.
Probab=21.90 E-value=1e+02 Score=23.49 Aligned_cols=9 Identities=33% Similarity=0.833 Sum_probs=6.7
Q ss_pred ccCccCCCc
Q 045388 134 YCPFKDCSA 142 (214)
Q Consensus 134 ~Cp~~~C~~ 142 (214)
.||.-.|.+
T Consensus 101 ~CPRv~C~~ 109 (184)
T PF01214_consen 101 RCPRVYCNG 109 (184)
T ss_dssp B-SBGGGTT
T ss_pred cCCcccCCC
Confidence 699888985
No 341
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=21.88 E-value=36 Score=16.59 Aligned_cols=11 Identities=45% Similarity=1.313 Sum_probs=5.8
Q ss_pred cccCCCCChhh
Q 045388 156 ESECPYCHRLF 166 (214)
Q Consensus 156 ~~~C~~C~~~~ 166 (214)
.+.|+.|++.|
T Consensus 14 ~~~C~~C~k~F 24 (26)
T PF13465_consen 14 PYKCPYCGKSF 24 (26)
T ss_dssp SEEESSSSEEE
T ss_pred CCCCCCCcCee
Confidence 34566665543
No 342
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=21.79 E-value=50 Score=20.31 Aligned_cols=13 Identities=31% Similarity=0.746 Sum_probs=9.8
Q ss_pred CCccCCCCCccce
Q 045388 191 QLRKCPNCKYHIE 203 (214)
Q Consensus 191 ~~k~CP~C~~~ie 203 (214)
....||.|+..++
T Consensus 5 ~~v~CP~C~k~~~ 17 (62)
T PRK00418 5 ITVNCPTCGKPVE 17 (62)
T ss_pred ccccCCCCCCccc
Confidence 4567999998764
No 343
>PTZ00396 Casein kinase II subunit beta; Provisional
Probab=21.76 E-value=1.3e+02 Score=24.19 Aligned_cols=10 Identities=30% Similarity=0.723 Sum_probs=7.8
Q ss_pred ccCccCCCce
Q 045388 134 YCPFKDCSAK 143 (214)
Q Consensus 134 ~Cp~~~C~~~ 143 (214)
.||.-.|.+.
T Consensus 122 ~CPRv~C~~q 131 (251)
T PTZ00396 122 HCPRVLCEGQ 131 (251)
T ss_pred CCCCccCCCC
Confidence 7998888854
No 344
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=21.75 E-value=44 Score=22.62 Aligned_cols=31 Identities=23% Similarity=0.507 Sum_probs=18.9
Q ss_pred cccccccccccccccccccccCCCCccccHHH
Q 045388 42 PSRSSCEICRERRENDQMFKIESCIHSFCSDC 73 (214)
Q Consensus 42 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~C 73 (214)
...++|..||=-.-.+.+-. ..=|+.+|++|
T Consensus 68 ~DEFTCssCFLV~HRSqLa~-~~~g~~iC~DC 98 (99)
T PF13834_consen 68 ADEFTCSSCFLVHHRSQLAR-EKDGQPICRDC 98 (99)
T ss_pred CCceeeeeeeeEechhhhcc-ccCCCEecccc
Confidence 34678888876554443322 23367788777
No 345
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 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 ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=21.58 E-value=82 Score=17.78 Aligned_cols=33 Identities=21% Similarity=0.527 Sum_probs=19.8
Q ss_pred cccccccccccccccccccCCCCcc-ccHHHHHH
Q 045388 44 RSSCEICRERRENDQMFKIESCIHS-FCSDCINK 76 (214)
Q Consensus 44 ~~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~ 76 (214)
.+.|..|..+......+..+.|... +|.+|+..
T Consensus 4 ~~~C~~C~~~~i~g~Ry~C~~C~d~dLC~~C~~~ 37 (46)
T PF00569_consen 4 GYTCDGCGTDPIIGVRYHCLVCPDYDLCEDCFSK 37 (46)
T ss_dssp SCE-SSS-SSSEESSEEEESSSSS-EEEHHHHHH
T ss_pred CeECcCCCCCcCcCCeEECCCCCCCchhhHHHhC
Confidence 4678888873222333446677754 99999876
No 346
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.53 E-value=29 Score=24.52 Aligned_cols=8 Identities=25% Similarity=0.729 Sum_probs=3.7
Q ss_pred ccCCCCCh
Q 045388 157 SECPYCHR 164 (214)
Q Consensus 157 ~~C~~C~~ 164 (214)
..|.+||.
T Consensus 29 afcskcge 36 (160)
T COG4306 29 AFCSKCGE 36 (160)
T ss_pred HHHhhhch
Confidence 34555543
No 347
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=21.26 E-value=55 Score=22.21 Aligned_cols=33 Identities=21% Similarity=0.515 Sum_probs=20.7
Q ss_pred CCCcccCccCCCceeee----cCCCCCCcCcccCCCCChhh
Q 045388 130 SQGIYCPFKDCSAKLVY----ENDGEDVLSESECPYCHRLF 166 (214)
Q Consensus 130 ~~~~~Cp~~~C~~~~~~----~~~~~~~~~~~~C~~C~~~~ 166 (214)
+..|.|| .|+.--.. +.. .....+.|..||..|
T Consensus 20 ~k~FtCp--~Cghe~vs~ctvkk~--~~~g~~~Cg~CGls~ 56 (104)
T COG4888 20 PKTFTCP--RCGHEKVSSCTVKKT--VNIGTAVCGNCGLSF 56 (104)
T ss_pred CceEecC--ccCCeeeeEEEEEec--CceeEEEcccCcceE
Confidence 4567899 99975444 221 223566788888765
No 348
>PRK12496 hypothetical protein; Provisional
Probab=21.26 E-value=48 Score=24.69 Aligned_cols=8 Identities=38% Similarity=1.057 Sum_probs=4.4
Q ss_pred cCccCCCcee
Q 045388 135 CPFKDCSAKL 144 (214)
Q Consensus 135 Cp~~~C~~~~ 144 (214)
|+ +|+..+
T Consensus 130 C~--gC~~~~ 137 (164)
T PRK12496 130 CK--GCKKKY 137 (164)
T ss_pred CC--CCCccc
Confidence 55 555444
No 349
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=21.22 E-value=29 Score=20.38 Aligned_cols=6 Identities=67% Similarity=1.785 Sum_probs=2.5
Q ss_pred CCCCCc
Q 045388 195 CPNCKY 200 (214)
Q Consensus 195 CP~C~~ 200 (214)
||+|++
T Consensus 27 CpRC~t 32 (51)
T PF10122_consen 27 CPRCKT 32 (51)
T ss_pred CCCCCc
Confidence 444443
No 350
>PF08882 Acetone_carb_G: Acetone carboxylase gamma subunit; InterPro: IPR014979 Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO2 to form acetoacetate [] according to the following reaction: CH3COCH3 + CO2 + ATP = CH3COCH2COO- + AMP + 2P(i) + H+ It has the subunit composition: (alpha(2)beta(2)gamma(2) multimers of 85kDa, 78kDa, and 20kDa subunits). It is expressed to high levels (17 to 25% of soluble protein) in cells grown with acetone as the carbon source but are not present at detectable levels in cells grown with other carbon sources []. Acetone carboxylase may enable Helicobacter pylori to survive off acetone in the stomach of humans and other mammals where it is the etiological agent of peptic ulcer disease []. This entry represents the family of gamma subunit-related acetone carboxylase proteins.
Probab=21.02 E-value=47 Score=23.01 Aligned_cols=49 Identities=24% Similarity=0.552 Sum_probs=26.8
Q ss_pred CcccCCCCChhhccccCCCCCCC------hHHHHHHHH-----HHhCCC-----ccCCCCCccceec
Q 045388 155 SESECPYCHRLFCAHCYVPWHPG------REELMMREL-----VKKKQL-----RKCPNCKYHIERT 205 (214)
Q Consensus 155 ~~~~C~~C~~~~C~~C~~~~h~~------~~~~~~~~~-----~~~~~~-----k~CP~C~~~iek~ 205 (214)
..++| .||+.||.-=.. |..+ .......++ +....| =-||+|++.++-.
T Consensus 23 k~vkc-~CGh~f~d~r~N-wK~~alv~vRd~~E~~~~iYp~~~aPdp~w~~irEyyCP~Cgt~levE 87 (112)
T PF08882_consen 23 KVVKC-DCGHEFCDAREN-WKLGALVYVRDPEEIHPEIYPFTMAPDPEWQVIREYYCPGCGTQLEVE 87 (112)
T ss_pred ceeec-cCCCeecChhcC-hhhCcEEEecChHHhhhhhcccccCCCCCcEEEEEEECCCCcceeEEc
Confidence 36778 799999864322 3322 222222222 222333 3599999988753
No 351
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=21.01 E-value=42 Score=21.78 Aligned_cols=35 Identities=20% Similarity=0.477 Sum_probs=13.9
Q ss_pred CCCcccCccCCCce--eeecCCCCCCcCcccCCCCChhh
Q 045388 130 SQGIYCPFKDCSAK--LVYENDGEDVLSESECPYCHRLF 166 (214)
Q Consensus 130 ~~~~~Cp~~~C~~~--~~~~~~~~~~~~~~~C~~C~~~~ 166 (214)
+..|.|| .|+.. +..+-........+.|..|+..|
T Consensus 20 ~~~F~CP--fC~~~~sV~v~idkk~~~~~~~C~~Cg~~~ 56 (81)
T PF05129_consen 20 PKVFDCP--FCNHEKSVSVKIDKKEGIGILSCRVCGESF 56 (81)
T ss_dssp SS----T--TT--SS-EEEEEETTTTEEEEEESSS--EE
T ss_pred CceEcCC--cCCCCCeEEEEEEccCCEEEEEecCCCCeE
Confidence 4667899 88832 22222111234566777777665
No 352
>KOG4537 consensus Zn-ribbon-containing protein implicated in mitosis [Cell cycle control, cell division, chromosome partitioning; Defense mechanisms]
Probab=20.86 E-value=48 Score=24.40 Aligned_cols=15 Identities=33% Similarity=0.820 Sum_probs=11.6
Q ss_pred cccCccCCCceeeecCC
Q 045388 133 IYCPFKDCSAKLVYEND 149 (214)
Q Consensus 133 ~~Cp~~~C~~~~~~~~~ 149 (214)
-+|| +|+.++..+..
T Consensus 41 e~Cp--~C~~Ilm~dr~ 55 (178)
T KOG4537|consen 41 EICP--KCEKILMRDRD 55 (178)
T ss_pred hhcc--hHHHHHHhhcc
Confidence 4799 99999776654
No 353
>PHA02325 hypothetical protein
Probab=20.86 E-value=51 Score=20.34 Aligned_cols=12 Identities=25% Similarity=0.841 Sum_probs=9.3
Q ss_pred CCccCCCCCc-cc
Q 045388 191 QLRKCPNCKY-HI 202 (214)
Q Consensus 191 ~~k~CP~C~~-~i 202 (214)
+.|.||+|+. +|
T Consensus 2 ~~k~CPkC~A~Wl 14 (72)
T PHA02325 2 DTKICPKCGARWL 14 (72)
T ss_pred CccccCccCCEeE
Confidence 4688999998 44
No 354
>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=20.84 E-value=81 Score=17.73 Aligned_cols=31 Identities=26% Similarity=0.575 Sum_probs=20.8
Q ss_pred cccccccccccccccccCCCCc-cccHHHHHHH
Q 045388 46 SCEICRERRENDQMFKIESCIH-SFCSDCINKH 77 (214)
Q Consensus 46 ~C~iC~~~~~~~~~~~~~~C~H-~fC~~Cl~~~ 77 (214)
.|..|..++.. ..+....|.. .+|.+|+..-
T Consensus 2 ~C~~C~~~i~g-~r~~C~~C~d~dLC~~Cf~~~ 33 (46)
T cd02249 2 SCDGCLKPIVG-VRYHCLVCEDFDLCSSCYAKG 33 (46)
T ss_pred CCcCCCCCCcC-CEEECCCCCCCcCHHHHHCcC
Confidence 57888886654 3444667764 5899998754
No 355
>PRK00893 aspartate carbamoyltransferase regulatory subunit; Reviewed
Probab=20.60 E-value=71 Score=23.52 Aligned_cols=33 Identities=21% Similarity=0.573 Sum_probs=20.3
Q ss_pred CCcccCccCCCce--------eeecCCCCCCcCcccCCCCChhh
Q 045388 131 QGIYCPFKDCSAK--------LVYENDGEDVLSESECPYCHRLF 166 (214)
Q Consensus 131 ~~~~Cp~~~C~~~--------~~~~~~~~~~~~~~~C~~C~~~~ 166 (214)
+.+.||+|+|=.- |...+ ......+|..|++.+
T Consensus 104 gi~kC~Np~CITn~~E~v~~~F~v~~---~~~~~~rC~YCe~~~ 144 (152)
T PRK00893 104 GVLKCPNPNCITNTNEPVESRFYVVD---KEPIKLRCKYCEKEF 144 (152)
T ss_pred ceEECCCCCCcCCCCcCcCcEEEEEe---CCCCEEEeeCCCCEe
Confidence 4468999999643 22211 123577888887654
No 356
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=20.27 E-value=1.1e+02 Score=24.94 Aligned_cols=15 Identities=20% Similarity=0.465 Sum_probs=9.2
Q ss_pred ccccccccccccccc
Q 045388 42 PSRSSCEICRERREN 56 (214)
Q Consensus 42 ~~~~~C~iC~~~~~~ 56 (214)
.....|+-|...|..
T Consensus 128 ~~r~~c~eCgk~ysT 142 (279)
T KOG2462|consen 128 HPRYKCPECGKSYST 142 (279)
T ss_pred CCceecccccccccc
Confidence 345667777666654
No 357
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=20.22 E-value=56 Score=19.29 Aligned_cols=11 Identities=45% Similarity=0.939 Sum_probs=8.3
Q ss_pred cCCCCCcccee
Q 045388 194 KCPNCKYHIER 204 (214)
Q Consensus 194 ~CP~C~~~iek 204 (214)
.||.|+..|+-
T Consensus 2 ~CPyCge~~~~ 12 (52)
T PF14255_consen 2 QCPYCGEPIEI 12 (52)
T ss_pred CCCCCCCeeEE
Confidence 68888887754
Done!