Query 043604
Match_columns 268
No_of_seqs 253 out of 1360
Neff 9.1
Searched_HMMs 46136
Date Fri Mar 29 06:33:46 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043604.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043604hhsearch_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 8.7E-40 1.9E-44 279.4 10.1 210 29-244 176-416 (445)
2 KOG1812 Predicted E3 ubiquitin 100.0 2.7E-38 5.8E-43 280.1 11.9 201 36-240 145-349 (384)
3 KOG1815 Predicted E3 ubiquitin 100.0 5.1E-30 1.1E-34 233.1 10.5 193 35-236 68-268 (444)
4 KOG0006 E3 ubiquitin-protein l 99.9 5.1E-28 1.1E-32 200.6 8.4 191 33-235 217-438 (446)
5 smart00647 IBR In Between Ring 99.3 1.9E-12 4.1E-17 86.3 5.3 63 110-175 1-64 (64)
6 PF01485 IBR: IBR domain; Int 99.3 4.7E-13 1E-17 89.2 0.9 63 110-175 1-64 (64)
7 PF13445 zf-RING_UBOX: RING-ty 98.5 6.3E-08 1.4E-12 58.4 2.3 43 40-87 1-43 (43)
8 smart00647 IBR In Between Ring 98.5 2.4E-07 5.2E-12 61.3 5.0 47 188-234 7-60 (64)
9 PF13639 zf-RING_2: Ring finge 98.5 5.9E-08 1.3E-12 59.3 1.2 41 39-88 2-42 (44)
10 PLN03208 E3 ubiquitin-protein 98.4 2E-07 4.4E-12 74.3 4.0 66 34-105 15-88 (193)
11 PF15227 zf-C3HC4_4: zinc fing 98.4 5.7E-08 1.2E-12 58.6 0.4 41 40-88 1-41 (42)
12 PF00097 zf-C3HC4: Zinc finger 98.4 2.6E-07 5.7E-12 55.5 2.5 40 40-88 1-40 (41)
13 PF14634 zf-RING_5: zinc-RING 98.3 6.8E-07 1.5E-11 54.6 3.2 43 39-92 1-43 (44)
14 PF01485 IBR: IBR domain; Int 98.3 2.7E-07 5.8E-12 61.1 1.0 40 195-234 15-60 (64)
15 PF13923 zf-C3HC4_2: Zinc fing 98.2 3.8E-07 8.3E-12 54.1 1.1 38 40-88 1-38 (39)
16 KOG0320 Predicted E3 ubiquitin 98.2 1.6E-06 3.4E-11 67.6 3.5 57 34-102 128-184 (187)
17 PHA02926 zinc finger-like prot 98.1 3.9E-06 8.5E-11 67.8 4.3 59 34-96 167-230 (242)
18 cd00162 RING RING-finger (Real 98.0 5.2E-06 1.1E-10 50.3 3.3 44 39-94 1-44 (45)
19 PF13920 zf-C3HC4_3: Zinc fing 98.0 2.8E-06 6.1E-11 53.3 1.9 46 37-96 2-48 (50)
20 KOG0823 Predicted E3 ubiquitin 98.0 3.2E-06 6.9E-11 68.8 1.6 61 34-105 44-104 (230)
21 KOG0317 Predicted E3 ubiquitin 97.8 9.7E-06 2.1E-10 68.0 1.5 52 35-100 237-288 (293)
22 smart00184 RING Ring finger. E 97.8 3.1E-05 6.8E-10 45.1 3.3 30 40-73 1-30 (39)
23 PHA02929 N1R/p28-like protein; 97.7 2.6E-05 5.7E-10 64.9 3.7 52 35-96 172-227 (238)
24 KOG2164 Predicted E3 ubiquitin 97.7 1.8E-05 3.9E-10 71.4 2.4 60 37-105 186-245 (513)
25 smart00504 Ubox Modified RING 97.7 5.6E-05 1.2E-09 49.7 3.7 51 38-102 2-52 (63)
26 KOG2177 Predicted E3 ubiquitin 97.5 7.6E-05 1.6E-09 64.8 3.2 108 34-174 10-121 (386)
27 COG5540 RING-finger-containing 97.5 6.8E-05 1.5E-09 63.3 2.4 54 34-97 320-373 (374)
28 KOG4628 Predicted E3 ubiquitin 97.5 9.6E-05 2.1E-09 64.5 3.3 48 38-95 230-277 (348)
29 TIGR00599 rad18 DNA repair pro 97.3 0.0002 4.3E-09 64.1 3.8 66 34-113 23-89 (397)
30 TIGR00570 cdk7 CDK-activating 97.3 0.00033 7.2E-09 60.2 4.9 55 38-101 4-59 (309)
31 KOG1002 Nucleotide excision re 97.2 0.00028 6.1E-09 63.9 2.9 58 33-99 532-589 (791)
32 KOG0287 Postreplication repair 97.0 0.00041 8.8E-09 59.5 2.5 65 35-113 21-86 (442)
33 KOG0978 E3 ubiquitin ligase in 96.8 0.0006 1.3E-08 64.6 1.7 56 35-103 641-696 (698)
34 PF12678 zf-rbx1: RING-H2 zinc 96.7 0.0008 1.7E-08 45.7 1.6 44 37-88 19-71 (73)
35 PF11793 FANCL_C: FANCL C-term 96.7 0.00066 1.4E-08 45.7 1.0 59 37-97 2-67 (70)
36 COG5574 PEX10 RING-finger-cont 96.7 0.0014 3E-08 54.7 2.9 52 37-100 215-266 (271)
37 PF11789 zf-Nse: Zinc-finger o 96.4 0.0024 5.1E-08 41.0 2.1 49 35-92 9-57 (57)
38 COG5243 HRD1 HRD ubiquitin lig 96.0 0.0061 1.3E-07 53.2 3.4 55 34-98 284-347 (491)
39 KOG1039 Predicted E3 ubiquitin 95.9 0.0069 1.5E-07 53.3 3.3 94 35-131 159-264 (344)
40 KOG1814 Predicted E3 ubiquitin 95.7 0.021 4.5E-07 50.7 5.4 115 33-169 269-404 (445)
41 KOG4367 Predicted Zn-finger pr 95.6 0.0081 1.7E-07 53.5 2.6 85 150-242 175-263 (699)
42 PF14835 zf-RING_6: zf-RING of 95.6 0.00091 2E-08 43.4 -2.5 50 37-101 7-56 (65)
43 COG5432 RAD18 RING-finger-cont 95.4 0.012 2.7E-07 49.6 2.8 52 35-100 23-74 (391)
44 KOG4185 Predicted E3 ubiquitin 95.1 0.065 1.4E-06 46.6 6.4 58 37-103 3-64 (296)
45 PF10571 UPF0547: Uncharacteri 95.0 0.0091 2E-07 31.7 0.7 22 199-224 1-24 (26)
46 PF04564 U-box: U-box domain; 94.8 0.0099 2.1E-07 40.3 0.5 51 37-100 4-54 (73)
47 KOG0824 Predicted E3 ubiquitin 94.6 0.018 3.8E-07 49.0 1.6 53 36-101 6-58 (324)
48 KOG1812 Predicted E3 ubiquitin 94.6 0.0081 1.7E-07 54.1 -0.5 66 95-173 280-345 (384)
49 PF13719 zinc_ribbon_5: zinc-r 94.5 0.03 6.4E-07 32.5 2.0 33 127-161 3-35 (37)
50 PF14570 zf-RING_4: RING/Ubox 94.4 0.025 5.4E-07 34.7 1.6 46 40-94 1-46 (48)
51 PF12861 zf-Apc11: Anaphase-pr 94.4 0.026 5.6E-07 39.1 1.8 53 37-96 21-82 (85)
52 PF13717 zinc_ribbon_4: zinc-r 94.1 0.043 9.3E-07 31.6 2.1 33 127-161 3-35 (36)
53 COG5152 Uncharacterized conser 94.1 0.027 5.9E-07 45.0 1.5 35 34-72 193-227 (259)
54 KOG0006 E3 ubiquitin-protein l 94.0 0.07 1.5E-06 45.8 4.0 95 57-172 340-438 (446)
55 KOG0828 Predicted E3 ubiquitin 93.9 0.033 7.2E-07 50.5 1.9 58 31-97 565-635 (636)
56 COG5175 MOT2 Transcriptional r 93.9 0.092 2E-06 45.5 4.4 54 39-101 16-69 (480)
57 KOG2879 Predicted E3 ubiquitin 93.7 0.059 1.3E-06 45.4 2.9 52 34-96 236-287 (298)
58 KOG1428 Inhibitor of type V ad 93.6 0.093 2E-06 53.6 4.5 77 34-113 3483-3563(3738)
59 KOG4159 Predicted E3 ubiquitin 93.4 0.095 2.1E-06 47.2 4.1 48 35-96 82-129 (398)
60 smart00744 RINGv The RING-vari 93.4 0.12 2.7E-06 31.9 3.3 42 39-88 1-47 (49)
61 KOG4445 Uncharacterized conser 93.2 0.036 7.8E-07 47.2 1.0 63 33-98 111-188 (368)
62 PF05883 Baculo_RING: Baculovi 93.2 0.067 1.4E-06 40.3 2.2 47 31-78 20-72 (134)
63 KOG1952 Transcription factor N 93.0 0.06 1.3E-06 52.0 2.2 59 31-92 185-243 (950)
64 KOG4265 Predicted E3 ubiquitin 92.8 0.063 1.4E-06 46.9 1.8 49 34-96 287-336 (349)
65 TIGR02098 MJ0042_CXXC MJ0042 f 92.4 0.12 2.5E-06 30.0 2.2 33 127-161 3-35 (38)
66 PF04641 Rtf2: Rtf2 RING-finge 92.2 0.15 3.3E-06 43.5 3.5 72 34-116 110-182 (260)
67 KOG2660 Locus-specific chromos 92.0 0.12 2.6E-06 44.7 2.6 50 34-96 12-61 (331)
68 smart00661 RPOL9 RNA polymeras 91.9 0.13 2.8E-06 32.0 2.1 26 199-224 1-30 (52)
69 KOG0802 E3 ubiquitin ligase [P 91.7 0.11 2.3E-06 49.3 2.1 49 35-93 289-338 (543)
70 KOG4172 Predicted E3 ubiquitin 91.5 0.059 1.3E-06 33.7 0.1 45 38-95 8-53 (62)
71 KOG4739 Uncharacterized protei 91.2 0.063 1.4E-06 44.5 0.0 46 37-96 3-48 (233)
72 PHA00626 hypothetical protein 90.6 0.22 4.8E-06 31.3 2.1 26 200-225 2-34 (59)
73 KOG4692 Predicted E3 ubiquitin 90.5 0.21 4.6E-06 43.6 2.6 37 34-74 419-455 (489)
74 COG5220 TFB3 Cdk activating ki 90.2 0.11 2.4E-06 42.9 0.6 51 37-94 10-62 (314)
75 PF13240 zinc_ribbon_2: zinc-r 90.0 0.16 3.4E-06 26.1 0.9 9 201-209 2-10 (23)
76 KOG0317 Predicted E3 ubiquitin 89.9 0.081 1.8E-06 44.9 -0.4 26 216-241 251-278 (293)
77 PRK00398 rpoP DNA-directed RNA 89.8 0.33 7.1E-06 29.5 2.4 27 199-225 4-32 (46)
78 PF13248 zf-ribbon_3: zinc-rib 89.3 0.19 4.1E-06 26.6 0.9 11 199-209 3-13 (26)
79 KOG1734 Predicted RING-contain 88.6 0.11 2.4E-06 43.6 -0.5 58 36-102 223-287 (328)
80 PF09297 zf-NADH-PPase: NADH p 88.5 0.69 1.5E-05 25.7 2.9 26 198-223 3-29 (32)
81 KOG0311 Predicted E3 ubiquitin 88.3 0.077 1.7E-06 46.3 -1.6 49 34-94 40-88 (381)
82 KOG0827 Predicted E3 ubiquitin 88.1 0.32 6.9E-06 43.0 2.0 49 37-92 4-52 (465)
83 PHA03096 p28-like protein; Pro 88.0 0.37 8E-06 41.5 2.3 40 38-77 179-222 (284)
84 KOG1645 RING-finger-containing 87.9 0.32 6.9E-06 43.3 1.9 51 37-95 4-55 (463)
85 smart00661 RPOL9 RNA polymeras 87.7 0.49 1.1E-05 29.4 2.2 28 128-160 2-29 (52)
86 PRK00432 30S ribosomal protein 87.6 0.4 8.7E-06 29.8 1.7 24 198-223 20-45 (50)
87 PF14952 zf-tcix: Putative tre 87.4 0.32 7E-06 28.9 1.1 26 195-224 8-37 (44)
88 KOG2906 RNA polymerase III sub 87.0 0.55 1.2E-05 33.2 2.3 28 200-227 3-34 (105)
89 PF02150 RNA_POL_M_15KD: RNA p 86.9 0.42 9.1E-06 27.3 1.4 28 127-160 2-29 (35)
90 KOG3039 Uncharacterized conser 86.7 0.3 6.4E-06 40.6 1.0 59 35-103 219-277 (303)
91 PRK14559 putative protein seri 86.7 0.46 9.9E-06 45.8 2.4 25 199-234 28-53 (645)
92 PLN03086 PRLI-interacting fact 86.6 0.95 2.1E-05 42.7 4.3 59 81-161 405-463 (567)
93 KOG1785 Tyrosine kinase negati 85.9 0.29 6.3E-06 43.4 0.6 45 34-88 366-410 (563)
94 KOG3002 Zn finger protein [Gen 85.3 0.49 1.1E-05 41.1 1.7 45 34-96 45-91 (299)
95 KOG0825 PHD Zn-finger protein 85.0 0.57 1.2E-05 45.2 2.0 21 58-78 120-140 (1134)
96 PRK14890 putative Zn-ribbon RN 84.4 0.93 2E-05 29.0 2.2 30 127-163 8-37 (59)
97 PF14803 Nudix_N_2: Nudix N-te 84.3 1 2.3E-05 25.5 2.2 25 199-223 1-30 (34)
98 KOG1940 Zn-finger protein [Gen 84.3 0.87 1.9E-05 38.9 2.7 50 34-93 155-204 (276)
99 KOG1815 Predicted E3 ubiquitin 84.1 0.71 1.5E-05 42.6 2.3 40 197-236 157-200 (444)
100 KOG3800 Predicted E3 ubiquitin 83.5 1.8 3.9E-05 37.0 4.2 50 39-97 2-52 (300)
101 PF06677 Auto_anti-p27: Sjogre 82.7 1.2 2.7E-05 26.3 2.1 23 198-222 17-41 (41)
102 PRK00398 rpoP DNA-directed RNA 82.2 1.5 3.2E-05 26.6 2.5 28 127-161 4-31 (46)
103 COG2888 Predicted Zn-ribbon RN 82.2 1.7 3.8E-05 27.7 2.8 34 126-166 9-42 (61)
104 COG5236 Uncharacterized conser 81.6 0.95 2.1E-05 39.5 1.9 51 34-96 58-108 (493)
105 PF14353 CpXC: CpXC protein 81.1 1.1 2.5E-05 33.6 2.0 26 186-211 24-51 (128)
106 KOG3053 Uncharacterized conser 80.4 2.4 5.1E-05 35.6 3.7 57 35-93 18-79 (293)
107 KOG2817 Predicted E3 ubiquitin 80.4 1.3 2.9E-05 39.4 2.5 61 35-103 332-392 (394)
108 PF05290 Baculo_IE-1: Baculovi 80.1 3.8 8.3E-05 30.9 4.4 54 34-95 77-131 (140)
109 COG5219 Uncharacterized conser 79.8 0.99 2.1E-05 44.6 1.6 54 35-96 1467-1523(1525)
110 PF14447 Prok-RING_4: Prokaryo 79.7 0.53 1.1E-05 29.7 -0.2 48 36-99 6-53 (55)
111 KOG0297 TNF receptor-associate 79.7 1.8 3.9E-05 39.3 3.1 38 34-74 18-55 (391)
112 PF03119 DNA_ligase_ZBD: NAD-d 79.4 2.2 4.9E-05 22.9 2.3 21 200-220 1-21 (28)
113 COG1998 RPS31 Ribosomal protei 79.1 1.5 3.2E-05 27.0 1.6 26 198-223 19-45 (51)
114 KOG2034 Vacuolar sorting prote 79.0 0.68 1.5E-05 45.3 0.2 42 35-78 815-856 (911)
115 PF09788 Tmemb_55A: Transmembr 78.9 1.8 3.9E-05 36.3 2.7 38 124-161 121-167 (256)
116 COG1198 PriA Primosomal protei 77.9 7.4 0.00016 38.2 6.8 32 200-231 446-484 (730)
117 TIGR01384 TFS_arch transcripti 77.7 1.5 3.2E-05 31.7 1.7 25 199-225 1-27 (104)
118 PF14569 zf-UDP: Zinc-binding 77.4 1.5 3.3E-05 29.6 1.5 56 133-216 14-69 (80)
119 KOG1813 Predicted E3 ubiquitin 77.3 0.72 1.6E-05 39.4 -0.1 47 34-94 238-284 (313)
120 PF08274 PhnA_Zn_Ribbon: PhnA 77.2 2.1 4.6E-05 23.5 1.8 24 199-223 3-27 (30)
121 PF10367 Vps39_2: Vacuolar sor 77.1 0.71 1.5E-05 33.3 -0.2 33 35-69 76-108 (109)
122 PRK14714 DNA polymerase II lar 76.8 2.1 4.6E-05 43.9 2.9 9 127-137 668-676 (1337)
123 KOG1001 Helicase-like transcri 76.2 1 2.2E-05 43.7 0.5 52 38-102 455-506 (674)
124 PRK08665 ribonucleotide-diphos 75.1 1.7 3.7E-05 42.8 1.8 25 199-225 725-751 (752)
125 KOG0823 Predicted E3 ubiquitin 75.0 0.76 1.6E-05 37.9 -0.6 19 217-236 62-81 (230)
126 PF07191 zinc-ribbons_6: zinc- 74.6 2.9 6.3E-05 27.8 2.2 33 200-234 3-42 (70)
127 PRK00420 hypothetical protein; 74.6 2.4 5.1E-05 31.2 2.0 25 197-223 22-48 (112)
128 PF09538 FYDLN_acid: Protein o 74.4 1.7 3.7E-05 31.7 1.2 25 199-224 10-36 (108)
129 PF07975 C1_4: TFIIH C1-like d 74.1 1.2 2.5E-05 27.8 0.3 25 149-173 19-43 (51)
130 PRK04023 DNA polymerase II lar 73.9 1.8 3.9E-05 43.2 1.6 65 197-267 625-697 (1121)
131 PRK14873 primosome assembly pr 73.6 9.6 0.00021 37.1 6.4 24 200-223 394-418 (665)
132 PRK14559 putative protein seri 73.1 2.7 5.9E-05 40.6 2.6 14 196-209 39-52 (645)
133 COG1997 RPL43A Ribosomal prote 72.3 3.3 7.2E-05 28.7 2.1 28 197-224 34-63 (89)
134 PF12773 DZR: Double zinc ribb 72.1 2.4 5.1E-05 26.0 1.3 12 198-209 12-23 (50)
135 COG1645 Uncharacterized Zn-fin 71.8 3.6 7.9E-05 31.0 2.4 25 196-229 26-51 (131)
136 PLN00209 ribosomal protein S27 71.2 5.5 0.00012 27.6 3.0 31 127-163 37-67 (86)
137 COG1594 RPB9 DNA-directed RNA 71.1 3.8 8.3E-05 30.2 2.4 31 126-161 2-32 (113)
138 PLN03208 E3 ubiquitin-protein 71.0 2.4 5.3E-05 34.2 1.5 36 193-233 13-49 (193)
139 KOG1493 Anaphase-promoting com 71.0 0.96 2.1E-05 30.5 -0.7 52 38-96 21-81 (84)
140 PF12906 RINGv: RING-variant d 70.8 1.9 4.1E-05 26.3 0.6 34 40-75 1-39 (47)
141 KOG4684 Uncharacterized conser 70.5 5.2 0.00011 32.7 3.2 38 124-161 136-180 (275)
142 PF13453 zf-TFIIB: Transcripti 70.0 3.4 7.4E-05 24.3 1.6 12 200-211 1-12 (41)
143 PF14149 YhfH: YhfH-like prote 69.5 0.48 1E-05 27.3 -2.0 31 190-220 5-35 (37)
144 PF08792 A2L_zn_ribbon: A2L zi 69.4 5.8 0.00013 22.3 2.4 26 198-223 3-29 (33)
145 COG5194 APC11 Component of SCF 69.3 4.5 9.8E-05 27.6 2.2 28 58-95 53-80 (88)
146 KOG3970 Predicted E3 ubiquitin 69.1 8 0.00017 31.9 4.0 59 34-96 47-105 (299)
147 PRK11827 hypothetical protein; 68.1 6 0.00013 25.6 2.5 26 198-223 8-34 (60)
148 KOG0804 Cytoplasmic Zn-finger 68.1 2.4 5.2E-05 38.4 1.0 39 35-73 173-211 (493)
149 PRK14714 DNA polymerase II lar 67.7 2.5 5.5E-05 43.3 1.1 30 199-234 668-704 (1337)
150 PF14446 Prok-RING_1: Prokaryo 67.7 6.6 0.00014 24.8 2.6 36 35-70 3-38 (54)
151 KOG1941 Acetylcholine receptor 67.4 2.7 5.9E-05 37.4 1.1 50 35-92 363-412 (518)
152 PF01363 FYVE: FYVE zinc finge 67.4 2.6 5.6E-05 27.8 0.8 36 196-233 7-44 (69)
153 PF07282 OrfB_Zn_ribbon: Putat 66.7 4.8 0.0001 26.5 2.0 26 198-223 28-54 (69)
154 PF08271 TF_Zn_Ribbon: TFIIB z 66.7 7.2 0.00016 23.1 2.6 8 200-207 2-9 (43)
155 TIGR02443 conserved hypothetic 66.4 7.2 0.00016 25.0 2.6 25 199-223 10-39 (59)
156 PF01599 Ribosomal_S27: Riboso 66.2 4.2 9.2E-05 24.8 1.5 30 125-159 17-46 (47)
157 PRK05654 acetyl-CoA carboxylas 65.7 1.3 2.8E-05 38.5 -1.2 29 196-224 25-56 (292)
158 KOG2906 RNA polymerase III sub 65.3 5.7 0.00012 28.2 2.2 29 127-160 2-30 (105)
159 PTZ00083 40S ribosomal protein 64.4 10 0.00022 26.2 3.2 31 127-163 36-66 (85)
160 KOG3579 Predicted E3 ubiquitin 63.9 4.9 0.00011 34.3 2.0 67 34-107 265-343 (352)
161 KOG0801 Predicted E3 ubiquitin 63.2 2.2 4.8E-05 33.2 -0.2 30 34-64 174-203 (205)
162 PF12760 Zn_Tnp_IS1595: Transp 62.8 21 0.00045 21.4 4.2 33 190-222 7-44 (46)
163 COG1594 RPB9 DNA-directed RNA 62.6 7.3 0.00016 28.7 2.5 27 198-224 2-32 (113)
164 KOG3268 Predicted E3 ubiquitin 62.2 14 0.0003 29.3 4.0 62 34-97 162-229 (234)
165 CHL00174 accD acetyl-CoA carbo 62.0 1.6 3.4E-05 37.9 -1.3 29 197-225 37-68 (296)
166 PHA02926 zinc finger-like prot 62.0 5.2 0.00011 33.1 1.7 44 193-236 165-213 (242)
167 PF09723 Zn-ribbon_8: Zinc rib 61.7 1.6 3.5E-05 25.9 -0.9 16 196-211 24-40 (42)
168 PF09526 DUF2387: Probable met 61.5 9.2 0.0002 25.6 2.6 24 200-223 10-38 (71)
169 KOG2114 Vacuolar assembly/sort 61.4 5.8 0.00013 39.0 2.2 41 37-93 840-880 (933)
170 PRK14892 putative transcriptio 61.3 7.3 0.00016 28.0 2.2 31 196-226 19-54 (99)
171 PF06827 zf-FPG_IleRS: Zinc fi 60.9 7.5 0.00016 21.0 1.8 22 199-220 2-25 (30)
172 smart00659 RPOLCX RNA polymera 60.9 8.2 0.00018 23.2 2.1 13 197-209 18-30 (44)
173 PRK09710 lar restriction allev 59.5 11 0.00024 24.6 2.6 28 196-223 4-35 (64)
174 PF06844 DUF1244: Protein of u 59.5 8.4 0.00018 25.2 2.0 17 62-78 11-27 (68)
175 COG1579 Zn-ribbon protein, pos 59.4 19 0.00042 30.2 4.7 21 98-118 166-186 (239)
176 TIGR01053 LSD1 zinc finger dom 59.3 12 0.00026 20.6 2.4 24 200-223 3-27 (31)
177 COG2051 RPS27A Ribosomal prote 59.3 8.8 0.00019 25.2 2.1 32 126-163 19-50 (67)
178 TIGR00515 accD acetyl-CoA carb 58.7 2.1 4.4E-05 37.1 -1.2 30 196-225 24-56 (285)
179 smart00531 TFIIE Transcription 58.6 9.8 0.00021 29.4 2.7 36 124-161 97-133 (147)
180 PF01428 zf-AN1: AN1-like Zinc 58.3 9.3 0.0002 22.7 2.0 27 150-178 12-38 (43)
181 PHA02929 N1R/p28-like protein; 58.0 7.5 0.00016 32.6 2.1 47 196-242 172-222 (238)
182 COG5574 PEX10 RING-finger-cont 58.0 2.7 5.9E-05 35.4 -0.5 40 35-74 93-133 (271)
183 TIGR00570 cdk7 CDK-activating 57.7 5.8 0.00013 34.6 1.4 53 127-211 4-56 (309)
184 KOG3161 Predicted E3 ubiquitin 57.6 3.6 7.7E-05 39.1 0.1 38 37-74 11-48 (861)
185 TIGR01206 lysW lysine biosynth 57.5 13 0.00027 23.5 2.6 30 127-161 3-32 (54)
186 PF07754 DUF1610: Domain of un 57.2 9.6 0.00021 19.7 1.6 22 133-159 3-24 (24)
187 PF10122 Mu-like_Com: Mu-like 57.1 4.3 9.3E-05 25.2 0.4 24 200-223 6-32 (51)
188 smart00064 FYVE Protein presen 56.8 4.9 0.00011 26.3 0.6 38 37-74 10-47 (68)
189 PF14369 zf-RING_3: zinc-finge 56.2 13 0.00027 21.1 2.2 30 126-161 2-31 (35)
190 PF02748 PyrI_C: Aspartate car 56.1 10 0.00023 23.7 2.0 36 125-161 5-45 (52)
191 PF08746 zf-RING-like: RING-li 56.0 6 0.00013 23.6 0.9 42 40-88 1-42 (43)
192 PF06943 zf-LSD1: LSD1 zinc fi 55.7 15 0.00032 19.2 2.2 23 201-223 1-24 (25)
193 PLN02189 cellulose synthase 55.0 10 0.00022 38.4 2.8 62 126-217 34-95 (1040)
194 TIGR03655 anti_R_Lar restricti 54.1 12 0.00025 23.4 2.0 28 199-226 2-38 (53)
195 PF05129 Elf1: Transcription e 53.5 9.8 0.00021 26.2 1.7 30 197-226 21-58 (81)
196 COG0777 AccD Acetyl-CoA carbox 53.4 4.8 0.0001 34.3 0.2 31 195-225 25-58 (294)
197 PF14354 Lar_restr_allev: Rest 53.1 13 0.00029 23.7 2.3 13 197-209 2-14 (61)
198 cd00065 FYVE FYVE domain; Zinc 53.0 11 0.00024 23.5 1.9 37 38-74 3-39 (57)
199 TIGR00373 conserved hypothetic 52.7 12 0.00027 29.2 2.4 31 124-160 107-137 (158)
200 COG5432 RAD18 RING-finger-cont 52.5 4.5 9.8E-05 34.6 -0.1 36 199-241 26-64 (391)
201 PRK06266 transcription initiat 51.7 14 0.0003 29.6 2.6 31 124-160 115-145 (178)
202 PF12861 zf-Apc11: Anaphase-pr 51.5 9.3 0.0002 26.5 1.4 34 199-235 33-67 (85)
203 PF14569 zf-UDP: Zinc-binding 51.2 14 0.0003 25.1 2.1 50 36-94 8-60 (80)
204 COG3478 Predicted nucleic-acid 51.0 18 0.00038 23.6 2.4 9 215-223 39-48 (68)
205 TIGR02300 FYDLN_acid conserved 50.8 9 0.0002 28.7 1.3 24 199-223 10-34 (129)
206 KOG4275 Predicted E3 ubiquitin 50.6 5.7 0.00012 34.1 0.3 30 37-70 300-330 (350)
207 TIGR00686 phnA alkylphosphonat 50.3 13 0.00027 27.0 1.9 26 199-225 3-30 (109)
208 COG5222 Uncharacterized conser 49.1 42 0.00091 29.0 5.1 45 37-93 274-318 (427)
209 PF07503 zf-HYPF: HypF finger; 47.6 8.3 0.00018 22.0 0.5 31 63-95 1-31 (35)
210 PRK00415 rps27e 30S ribosomal 47.3 20 0.00044 23.0 2.3 30 127-162 12-41 (59)
211 PF07800 DUF1644: Protein of u 47.2 24 0.00052 27.6 3.1 83 37-143 2-124 (162)
212 PF03833 PolC_DP2: DNA polymer 46.5 6.6 0.00014 38.7 0.0 65 197-267 654-726 (900)
213 PLN02638 cellulose synthase A 46.3 15 0.00033 37.4 2.4 61 127-217 18-78 (1079)
214 KOG0978 E3 ubiquitin ligase in 46.0 5.9 0.00013 38.3 -0.4 29 156-208 660-688 (698)
215 COG0266 Nei Formamidopyrimidin 45.6 17 0.00037 31.2 2.4 24 199-222 246-272 (273)
216 PF13821 DUF4187: Domain of un 45.3 8.1 0.00018 24.5 0.3 15 221-235 25-40 (55)
217 PRK09521 exosome complex RNA-b 45.2 17 0.00037 29.3 2.2 24 199-223 150-174 (189)
218 PLN02400 cellulose synthase 45.1 16 0.00034 37.3 2.4 61 127-217 37-97 (1085)
219 cd00021 BBOX B-Box-type zinc f 44.6 15 0.00032 20.7 1.3 26 149-174 10-35 (39)
220 PF11023 DUF2614: Protein of u 44.5 14 0.0003 27.1 1.4 23 149-171 67-97 (114)
221 PF06524 NOA36: NOA36 protein; 44.3 13 0.00028 31.4 1.4 51 149-211 169-222 (314)
222 PF00643 zf-B_box: B-box zinc 44.2 7.9 0.00017 22.6 0.1 24 150-173 14-37 (42)
223 COG3492 Uncharacterized protei 43.4 41 0.00089 23.6 3.5 17 62-78 42-58 (104)
224 TIGR00622 ssl1 transcription f 42.9 14 0.00031 27.1 1.3 44 127-172 56-102 (112)
225 PRK04023 DNA polymerase II lar 42.3 19 0.00041 36.4 2.4 17 152-168 639-660 (1121)
226 PRK14811 formamidopyrimidine-D 42.2 21 0.00045 30.6 2.4 22 199-220 236-259 (269)
227 PF03604 DNA_RNApol_7kD: DNA d 42.0 15 0.00032 20.4 1.0 23 133-161 5-27 (32)
228 PF05605 zf-Di19: Drought indu 41.5 58 0.0013 20.1 3.8 41 37-96 2-42 (54)
229 KOG4218 Nuclear hormone recept 40.2 19 0.00042 31.7 1.8 9 198-206 67-75 (475)
230 PHA02825 LAP/PHD finger-like p 40.1 52 0.0011 25.8 4.0 52 35-97 6-60 (162)
231 KOG2691 RNA polymerase II subu 39.8 42 0.00092 24.3 3.2 33 125-160 3-35 (113)
232 PF01667 Ribosomal_S27e: Ribos 39.4 28 0.00061 22.0 2.0 31 127-163 8-38 (55)
233 PLN02436 cellulose synthase A 38.9 27 0.00058 35.7 2.9 61 127-217 37-97 (1094)
234 TIGR00595 priA primosomal prot 38.8 46 0.001 31.3 4.3 33 129-168 225-262 (505)
235 PF10426 zf-RAG1: Recombinatio 38.4 6.5 0.00014 21.5 -0.8 20 83-102 2-21 (30)
236 COG5220 TFB3 Cdk activating ki 38.3 18 0.0004 30.2 1.4 56 84-142 11-67 (314)
237 KOG3113 Uncharacterized conser 38.1 34 0.00074 28.9 2.9 73 34-118 108-181 (293)
238 TIGR00100 hypA hydrogenase nic 38.1 47 0.001 24.4 3.5 26 125-159 69-94 (115)
239 PLN02915 cellulose synthase A 37.7 23 0.0005 36.1 2.2 57 133-217 20-76 (1044)
240 COG1096 Predicted RNA-binding 37.6 25 0.00053 28.3 2.0 23 199-223 150-173 (188)
241 PRK01103 formamidopyrimidine/5 37.6 26 0.00057 30.0 2.3 22 199-220 246-269 (274)
242 TIGR00595 priA primosomal prot 37.4 29 0.00064 32.6 2.8 32 200-231 224-262 (505)
243 PF02891 zf-MIZ: MIZ/SP-RING z 37.2 18 0.0004 22.3 1.0 47 38-93 3-49 (50)
244 smart00734 ZnF_Rad18 Rad18-lik 37.1 18 0.00038 19.0 0.8 20 84-105 2-21 (26)
245 PRK10220 hypothetical protein; 37.1 30 0.00065 25.2 2.1 27 127-161 4-30 (111)
246 PRK03681 hypA hydrogenase nick 36.9 49 0.0011 24.3 3.4 27 125-159 69-95 (114)
247 smart00336 BBOX B-Box-type zin 36.8 29 0.00063 19.8 1.8 24 150-173 14-37 (42)
248 smart00834 CxxC_CXXC_SSSS Puta 36.8 20 0.00044 20.5 1.1 15 197-211 25-39 (41)
249 KOG2807 RNA polymerase II tran 36.7 24 0.00051 30.9 1.9 24 149-172 343-366 (378)
250 PRK03824 hypA hydrogenase nick 36.7 50 0.0011 25.1 3.5 15 125-141 69-83 (135)
251 PRK14810 formamidopyrimidine-D 36.4 28 0.0006 29.9 2.3 22 199-220 245-268 (272)
252 PLN02436 cellulose synthase A 35.9 26 0.00056 35.8 2.2 51 35-94 34-87 (1094)
253 TIGR00577 fpg formamidopyrimid 35.8 29 0.00063 29.8 2.3 22 199-220 246-269 (272)
254 PRK10445 endonuclease VIII; Pr 35.7 30 0.00065 29.5 2.4 24 199-222 236-262 (263)
255 KOG2041 WD40 repeat protein [G 35.6 42 0.00092 32.8 3.5 48 103-161 1088-1141(1189)
256 COG1996 RPC10 DNA-directed RNA 35.3 22 0.00048 21.9 1.1 15 195-209 21-35 (49)
257 COG5151 SSL1 RNA polymerase II 35.1 18 0.00038 31.5 0.8 43 127-171 363-408 (421)
258 PRK12380 hydrogenase nickel in 34.5 59 0.0013 23.8 3.5 26 125-159 69-94 (113)
259 KOG3799 Rab3 effector RIM1 and 34.4 18 0.0004 27.3 0.7 20 35-61 63-82 (169)
260 PF04216 FdhE: Protein involve 34.2 25 0.00054 30.4 1.7 35 199-233 173-222 (290)
261 PRK13945 formamidopyrimidine-D 34.1 31 0.00068 29.7 2.2 24 199-222 255-281 (282)
262 KOG2932 E3 ubiquitin ligase in 34.1 22 0.00048 30.9 1.3 33 37-72 90-122 (389)
263 PF02591 DUF164: Putative zinc 33.5 32 0.0007 21.6 1.7 21 188-208 36-56 (56)
264 KOG2930 SCF ubiquitin ligase, 33.3 34 0.00075 24.6 1.9 23 58-88 80-102 (114)
265 PF02318 FYVE_2: FYVE-type zin 33.2 73 0.0016 23.4 3.8 36 125-168 53-88 (118)
266 KOG4362 Transcriptional regula 33.1 9.1 0.0002 37.0 -1.3 57 34-101 18-74 (684)
267 PF02318 FYVE_2: FYVE-type zin 32.9 60 0.0013 23.9 3.3 34 197-231 53-88 (118)
268 PRK05580 primosome assembly pr 32.8 37 0.0008 33.3 2.8 32 200-231 392-430 (679)
269 KOG2932 E3 ubiquitin ligase in 32.8 21 0.00046 31.0 1.0 26 197-229 89-118 (389)
270 COG3677 Transposase and inacti 32.4 59 0.0013 24.5 3.2 35 125-161 29-63 (129)
271 PLN02195 cellulose synthase A 32.4 33 0.00071 34.8 2.3 30 133-166 11-40 (977)
272 PF10497 zf-4CXXC_R1: Zinc-fin 32.2 98 0.0021 22.4 4.3 29 60-88 37-66 (105)
273 TIGR01031 rpmF_bact ribosomal 32.2 28 0.00061 22.0 1.2 22 196-222 24-46 (55)
274 TIGR03826 YvyF flagellar opero 32.0 33 0.00072 26.2 1.8 24 199-233 82-105 (137)
275 PRK02935 hypothetical protein; 32.0 31 0.00066 24.9 1.5 22 149-170 68-97 (110)
276 PF01396 zf-C4_Topoisom: Topoi 32.0 32 0.0007 19.9 1.4 20 199-219 2-24 (39)
277 PRK00241 nudC NADH pyrophospha 31.9 33 0.00072 29.1 2.0 27 197-223 98-125 (256)
278 PRK12286 rpmF 50S ribosomal pr 31.6 44 0.00095 21.3 2.1 27 121-159 22-48 (57)
279 COG5204 SPT4 Transcription elo 31.6 26 0.00057 24.8 1.1 22 247-268 22-43 (112)
280 COG5216 Uncharacterized conser 31.4 34 0.00073 21.9 1.5 34 127-163 23-56 (67)
281 KOG3039 Uncharacterized conser 31.3 42 0.00091 28.2 2.4 41 34-78 39-80 (303)
282 PF01873 eIF-5_eIF-2B: Domain 31.3 81 0.0018 23.6 3.8 28 196-223 91-122 (125)
283 PRK12495 hypothetical protein; 31.1 39 0.00085 27.9 2.2 31 196-234 40-70 (226)
284 PF14445 Prok-RING_2: Prokaryo 31.0 12 0.00027 23.0 -0.5 36 36-72 6-41 (57)
285 PF14471 DUF4428: Domain of un 30.6 48 0.001 20.6 2.1 30 39-71 1-30 (51)
286 PHA02862 5L protein; Provision 30.3 84 0.0018 24.2 3.7 46 38-96 3-53 (156)
287 PF01780 Ribosomal_L37ae: Ribo 30.1 32 0.0007 24.2 1.4 27 198-224 35-63 (90)
288 PF03854 zf-P11: P-11 zinc fin 29.9 23 0.00049 21.7 0.5 44 38-97 3-47 (50)
289 COG1198 PriA Primosomal protei 29.8 44 0.00096 33.0 2.7 58 104-168 405-484 (730)
290 PF07227 DUF1423: Protein of u 29.8 35 0.00077 31.3 1.9 29 202-230 132-162 (446)
291 smart00249 PHD PHD zinc finger 29.5 33 0.00071 19.7 1.2 34 39-73 1-34 (47)
292 PF00098 zf-CCHC: Zinc knuckle 29.3 38 0.00083 16.0 1.2 16 161-176 2-17 (18)
293 KOG0309 Conserved WD40 repeat- 29.3 38 0.00082 33.2 2.1 38 35-74 1026-1063(1081)
294 COG3024 Uncharacterized protei 29.2 31 0.00067 22.5 1.0 16 197-212 6-21 (65)
295 COG2816 NPY1 NTP pyrophosphohy 29.2 60 0.0013 28.0 3.1 28 196-223 109-137 (279)
296 PRK00893 aspartate carbamoyltr 28.9 50 0.0011 25.7 2.4 33 125-161 104-144 (152)
297 PLN03086 PRLI-interacting fact 28.9 52 0.0011 31.4 2.9 29 196-224 431-463 (567)
298 KOG2164 Predicted E3 ubiquitin 28.6 39 0.00084 31.5 2.0 35 156-210 203-237 (513)
299 KOG0825 PHD Zn-finger protein 27.2 54 0.0012 32.4 2.7 45 39-94 125-169 (1134)
300 COG4647 AcxC Acetone carboxyla 27.1 2.8E+02 0.006 20.9 6.2 62 94-163 16-81 (165)
301 PRK13264 3-hydroxyanthranilate 26.8 24 0.00053 28.2 0.3 50 159-211 120-170 (177)
302 PRK08115 ribonucleotide-diphos 26.5 33 0.00072 34.4 1.2 23 199-223 828-852 (858)
303 COG1781 PyrI Aspartate carbamo 26.4 54 0.0012 25.4 2.1 37 125-161 105-145 (153)
304 PF01927 Mut7-C: Mut7-C RNAse 26.1 19 0.0004 27.8 -0.5 42 84-140 92-136 (147)
305 PF04981 NMD3: NMD3 family ; 25.8 40 0.00086 28.2 1.5 12 198-209 35-46 (236)
306 TIGR03037 anthran_nbaC 3-hydro 25.2 28 0.00061 27.3 0.4 44 160-206 115-159 (159)
307 PF08882 Acetone_carb_G: Aceto 25.1 56 0.0012 23.9 1.9 48 215-263 23-86 (112)
308 COG1656 Uncharacterized conser 24.9 48 0.001 26.1 1.6 25 84-110 98-125 (165)
309 PRK03564 formate dehydrogenase 24.8 75 0.0016 27.9 3.0 32 199-230 188-234 (309)
310 PLN02189 cellulose synthase 24.7 52 0.0011 33.7 2.2 51 35-94 32-85 (1040)
311 PF03811 Zn_Tnp_IS1: InsA N-te 24.6 73 0.0016 18.2 1.9 29 127-157 6-35 (36)
312 KOG2979 Protein involved in DN 24.6 1.1E+02 0.0024 26.0 3.8 71 38-119 177-248 (262)
313 PF01214 CK_II_beta: Casein ki 24.5 1.8E+02 0.004 23.4 5.0 35 124-158 97-134 (184)
314 COG5109 Uncharacterized conser 24.0 72 0.0016 27.9 2.6 58 35-100 334-391 (396)
315 COG2824 PhnA Uncharacterized Z 23.9 80 0.0017 22.9 2.4 26 198-225 3-31 (112)
316 cd04476 RPA1_DBD_C RPA1_DBD_C: 23.8 54 0.0012 25.6 1.8 25 198-223 34-59 (166)
317 smart00154 ZnF_AN1 AN1-like Zi 23.8 50 0.0011 19.1 1.2 18 151-168 12-29 (39)
318 PF01783 Ribosomal_L32p: Ribos 23.7 71 0.0015 20.1 2.0 15 123-139 23-37 (56)
319 PLN02638 cellulose synthase A 23.2 69 0.0015 33.0 2.7 50 36-94 16-68 (1079)
320 PRK08332 ribonucleotide-diphos 23.1 52 0.0011 35.8 2.0 26 199-226 1705-1738(1740)
321 PRK00564 hypA hydrogenase nick 22.8 93 0.002 22.9 2.8 26 126-159 71-96 (117)
322 PF00096 zf-C2H2: Zinc finger, 22.8 35 0.00077 16.6 0.4 9 153-161 2-10 (23)
323 KOG2807 RNA polymerase II tran 22.7 38 0.00083 29.7 0.8 39 38-78 331-369 (378)
324 TIGR00280 L37a ribosomal prote 22.5 58 0.0013 22.9 1.5 28 197-224 34-63 (91)
325 KOG2923 Uncharacterized conser 22.5 64 0.0014 21.0 1.6 20 191-210 37-56 (67)
326 PF08209 Sgf11: Sgf11 (transcr 22.3 49 0.0011 18.5 0.9 14 198-211 4-17 (33)
327 PRK03976 rpl37ae 50S ribosomal 22.2 58 0.0013 22.9 1.5 27 198-224 36-64 (90)
328 COG2816 NPY1 NTP pyrophosphohy 22.1 82 0.0018 27.2 2.6 30 124-160 109-138 (279)
329 PF13465 zf-H2C2_2: Zinc-finge 21.8 49 0.0011 17.0 0.8 12 150-161 13-24 (26)
330 PF03884 DUF329: Domain of unk 21.7 43 0.00094 21.4 0.7 16 198-213 2-17 (57)
331 PF01194 RNA_pol_N: RNA polyme 21.7 1.3E+02 0.0027 19.5 2.8 14 81-96 2-15 (60)
332 KOG1779 40s ribosomal protein 21.7 1.7E+02 0.0036 20.0 3.4 32 127-164 35-66 (84)
333 PTZ00255 60S ribosomal protein 21.3 67 0.0014 22.6 1.6 28 197-224 35-64 (90)
334 PF01155 HypA: Hydrogenase exp 21.2 59 0.0013 23.8 1.5 46 105-159 40-94 (113)
335 PF09151 DUF1936: Domain of un 21.0 45 0.00097 18.3 0.6 9 200-208 3-11 (36)
336 cd00350 rubredoxin_like Rubred 20.9 77 0.0017 17.4 1.5 20 133-159 6-25 (33)
337 PF14205 Cys_rich_KTR: Cystein 20.9 72 0.0016 20.1 1.5 34 125-160 3-37 (55)
338 PF13963 Transpos_assoc: Trans 20.7 1.2E+02 0.0027 20.4 2.8 35 68-102 21-58 (77)
339 PRK00423 tfb transcription ini 20.7 97 0.0021 27.1 2.9 28 195-222 8-37 (310)
340 KOG0826 Predicted E3 ubiquitin 20.4 1E+02 0.0022 27.1 2.9 55 36-103 299-353 (357)
341 PF13913 zf-C2HC_2: zinc-finge 20.1 54 0.0012 16.8 0.8 18 84-103 3-20 (25)
342 COG0777 AccD Acetyl-CoA carbox 20.0 42 0.0009 28.8 0.5 30 126-161 28-57 (294)
No 1
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=8.7e-40 Score=279.37 Aligned_cols=210 Identities=25% Similarity=0.530 Sum_probs=176.4
Q ss_pred hhhhcCCCcccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCCHHHHhhcCChhH
Q 043604 29 IELEDTNGIFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLDPFSCKLMIPSNL 108 (268)
Q Consensus 29 ~~~~~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~~l~~~~ 108 (268)
....+....+.|.|||++......| ..++|+|+||+.|++.|++..|++|.+..++||+++|+...++..++.+|+.++
T Consensus 176 ~~~~F~~slf~C~ICf~e~~G~~c~-~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C~~~a~~g~vKelvg~EL 254 (445)
T KOG1814|consen 176 TLEKFVNSLFDCCICFEEQMGQHCF-KFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCGSVAPPGQVKELVGDEL 254 (445)
T ss_pred HHHHHHhhcccceeeehhhcCccee-eecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCCcccCCchHHHHHHHHHH
Confidence 3455678899999999999776766 689999999999999999999999989999999999999999999999999999
Q ss_pred HHHHHHHHHhhhhcC-CCcccCCccccCceeeeccccccCCcCeeeCcccccccccccccccCCCCCcchhhc-------
Q 043604 109 FSKWCDVLFEDYVLG-FERSYCPNRNCMALVVNGCEINYGTLKKARCPNCTQWFCFQCKLAWHAGYRCEESGN------- 180 (268)
Q Consensus 109 ~~~~~~~~~~~~~~~-~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~tC~~~~~------- 180 (268)
+++|++++.+.++.. .+.+|||++.|+.++..++.. ..+.|.+|+..||+.|+..||+...|.--..
T Consensus 255 ~arYe~l~lqk~l~~msdv~yCPr~~Cq~p~~~d~~~-----~l~~CskCnFaFCtlCk~t~HG~s~Ck~~~~~~~~l~~ 329 (445)
T KOG1814|consen 255 FARYEKLMLQKTLELMSDVVYCPRACCQLPVKQDPGR-----ALAICSKCNFAFCTLCKLTWHGVSPCKVKAEKLIELYL 329 (445)
T ss_pred HHHHHHHHHHHHHHhhcccccCChhhccCccccCchh-----hhhhhccCccHHHHHHHHhhcCCCcccCchHHHHHHHH
Confidence 999999999999985 889999999999998555544 7889999999999999999999999984311
Q ss_pred -ccch------------hhHHHHHH--------HHhCCcccCCCCCceeeecCCcCeEEec-CCc-ccccccccccCCCC
Q 043604 181 -LRDW------------NDIAFGKL--------VERMHWARCPACGSCVERKEGCRVMYCS-CHS-VTYSRAKHISLRKH 237 (268)
Q Consensus 181 -~~~~------------~~~~~~~~--------~~~~~~k~CP~C~~~iek~~GCnhm~C~-C~~-FC~~C~~~~~~~~~ 237 (268)
|... +...+.++ ....+.|+||+|+++|||++|||+|+|. |++ |||.|+....+.+.
T Consensus 330 ~~~~~d~a~k~ele~Ryg~rvve~~vn~~lsekwl~~N~krCP~C~v~IEr~eGCnKM~C~~c~~~fc~~c~~~l~~~nP 409 (445)
T KOG1814|consen 330 EYLEADEARKRELEKRYGKRVVEELVNDFLSEKWLESNSKRCPKCKVVIERSEGCNKMHCTKCGTYFCWICAELLYPENP 409 (445)
T ss_pred HHhhcCHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhcCCCCCcccceeecCCCccceeeccccccceeehhhhcCCCCh
Confidence 1100 10011111 1134569999999999999999999998 999 99999999988777
Q ss_pred CCCCCCC
Q 043604 238 STRGDNK 244 (268)
Q Consensus 238 ~~~~~~~ 244 (268)
|-|+.++
T Consensus 410 YkHF~e~ 416 (445)
T KOG1814|consen 410 YKHFSEP 416 (445)
T ss_pred hhhhcCC
Confidence 7776643
No 2
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2.7e-38 Score=280.10 Aligned_cols=201 Identities=29% Similarity=0.610 Sum_probs=171.4
Q ss_pred CcccccccccCCcCC-cCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCCHHHHhhcCChhHHHHHHH
Q 043604 36 GIFTCEICIEPISAN-DKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLDPFSCKLMIPSNLFSKWCD 114 (268)
Q Consensus 36 ~~~~C~IC~~~~~~~-~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~~l~~~~~~~~~~ 114 (268)
...+|.||+.+.+.. +.| .+..|+|.||.+|+++|++.+.. ....++||..+|...++.+....+|++++.++|+.
T Consensus 145 ~~~~C~iC~~e~~~~~~~f-~~~~C~H~fC~~C~k~~iev~~~--~~~~~~C~~~~C~~~l~~~~c~~llt~kl~e~~e~ 221 (384)
T KOG1812|consen 145 PKEECGICFVEDPEAEDMF-SVLKCGHRFCKDCVKQHIEVKLL--SGTVIRCPHDGCESRLTLESCRKLLTPKLREMWEQ 221 (384)
T ss_pred ccccCccCccccccHhhhH-HHhcccchhhhHHhHHHhhhhhc--cCCCccCCCCCCCccCCHHHHhhhcCHHHHHHHHH
Confidence 467999999655555 455 47899999999999999999843 57789999999999999999999999999999999
Q ss_pred HHHhhhhcCCCcccCCccccCceeeeccccccCCcCeeeCcccccccccccccccCCCCCcchhhcccch--hhHHHHHH
Q 043604 115 VLFEDYVLGFERSYCPNRNCMALVVNGCEINYGTLKKARCPNCTQWFCFQCKLAWHAGYRCEESGNLRDW--NDIAFGKL 192 (268)
Q Consensus 115 ~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~tC~~~~~~~~~--~~~~~~~~ 192 (268)
++.+.++...+.+|||+|+|...+...............|+.|+..||.+|+.+||.+.+|++++++... .|....+.
T Consensus 222 ~~~e~~i~~~~~~ycp~~~C~~l~~~~el~~~~~~~~~~C~~C~~~fCv~C~~~wh~~~sC~eykk~~~~~~~d~~~~~~ 301 (384)
T KOG1812|consen 222 RLKEEVIPSLDRVYCPYPRCSSLMSKTELSSEVKSKRRPCVKCHELFCVKCKVPWHANLSCEEYKKLNPEEYVDDITLKY 301 (384)
T ss_pred HHHHHhhhhhhcccCCCCCchHhhhhhhhccchhhcccccccCCCceeecCCCcCCCCCCHHHHHHhCCcccccHHHHHH
Confidence 9999999876656999999999988766432123566789999999999999999999999999998864 33344444
Q ss_pred HHhCCcccCCCCCceeeecCCcCeEEecCCc-ccccccccccCCCCCCC
Q 043604 193 VERMHWARCPACGSCVERKEGCRVMYCSCHS-VTYSRAKHISLRKHSTR 240 (268)
Q Consensus 193 ~~~~~~k~CP~C~~~iek~~GCnhm~C~C~~-FC~~C~~~~~~~~~~~~ 240 (268)
+. ..|++||+|+..|++.+|||||+|+||+ |||.|+.+|..+.+.+.
T Consensus 302 la-~~wr~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~~~~~~~~~~~~ 349 (384)
T KOG1812|consen 302 LA-KRWRQCPKCKFMIELSEGCNHMTCRCGHQFCYMCGGDWKTHNGECY 349 (384)
T ss_pred HH-HhcCcCcccceeeeecCCcceEEeeccccchhhcCcchhhCCcccc
Confidence 44 8999999999999999999999999999 99999999988766443
No 3
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.96 E-value=5.1e-30 Score=233.14 Aligned_cols=193 Identities=23% Similarity=0.486 Sum_probs=164.7
Q ss_pred CCcccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCCHHHHhhcCCh-hHHHHHH
Q 043604 35 NGIFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLDPFSCKLMIPS-NLFSKWC 113 (268)
Q Consensus 35 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~~l~~-~~~~~~~ 113 (268)
....+|.||++.++. . ...+.|+|.||..|+..|+..+|.++....|+||..+|.+.+..+.|..++++ +..++|.
T Consensus 68 ~~~~~c~ic~~~~~~--~-~~~~~c~H~~c~~cw~~yl~~kI~~~~~~~i~cp~~~C~a~v~~~~i~~~~s~~~~~~ky~ 144 (444)
T KOG1815|consen 68 KGDVQCGICVESYDG--E-IIGLGCGHPFCPPCWTGYLGTKIHEGEEAKIKCPAHGCPALVGEDTVEKLVSDKEDKEKYQ 144 (444)
T ss_pred CccccCCcccCCCcc--h-hhhcCCCcHHHHHHHHHHhhheeeccccccccCCCCCccccCCCceeeeecCCHHHHHHHH
Confidence 456899999999865 2 25789999999999999999999996555599999999999999999999998 5999999
Q ss_pred HHHHhhhhcC-CCcccCCccccCceeeeccccccCCcCeeeCcccccccccccccccCCCCCcchhhcccchhhHH--HH
Q 043604 114 DVLFEDYVLG-FERSYCPNRNCMALVVNGCEINYGTLKKARCPNCTQWFCFQCKLAWHAGYRCEESGNLRDWNDIA--FG 190 (268)
Q Consensus 114 ~~~~~~~~~~-~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~tC~~~~~~~~~~~~~--~~ 190 (268)
+.+..+++.. ..+.|||.|+|+..+..... ....+.|. |+..||+.|..+||.|.+|.....|....... ..
T Consensus 145 ~~i~~syve~~~~lkwCP~~~C~~av~~~~~----~~~~v~C~-~g~~FC~~C~~~~H~p~~C~~~~~wl~k~~~~se~~ 219 (444)
T KOG1815|consen 145 RYILRSYVEDNVPLKWCPAPGCGLAVKFGSL----ESVEVDCG-CGHEFCFACGEESHSPVSCPGAKKWLKKCRDDSETI 219 (444)
T ss_pred HHHHHHHHhcCCccccCCCCCCCceeeccCC----CccceeCC-CCchhHhhccccccCCCcccchHHHHHhhhhhhhhh
Confidence 9999999996 55899999999999987522 25789994 77799999999999999999998887652221 11
Q ss_pred HHHHhCCcccCCCCCceeeecCCcCeEEec---CCc-ccccccccccCCC
Q 043604 191 KLVERMHWARCPACGSCVERKEGCRVMYCS---CHS-VTYSRAKHISLRK 236 (268)
Q Consensus 191 ~~~~~~~~k~CP~C~~~iek~~GCnhm~C~---C~~-FC~~C~~~~~~~~ 236 (268)
.+ ...+++.||+|..+|||++|||||+|. |++ |||+|++.|..+.
T Consensus 220 ~w-i~~ntk~CP~c~~~iek~~gc~~~~~~~~~c~~~FCw~Cl~~~~~h~ 268 (444)
T KOG1815|consen 220 NW-ILANTKECPKCKVPIEKDGGCNHMTCKSASCKHEFCWVCLASLSDHG 268 (444)
T ss_pred hh-hhccCccCCCcccchhccCCccccccccCCcCCeeceeeeccccccc
Confidence 22 367789999999999999999999995 999 9999999999874
No 4
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=99.95 E-value=5.1e-28 Score=200.60 Aligned_cols=191 Identities=24% Similarity=0.472 Sum_probs=150.9
Q ss_pred cCCCcccccccccCCcCCcCccccCCCC--ChhhHHHHHHHHHHHhhcC-------CCceeccCCCCCCC-CCCHHHHhh
Q 043604 33 DTNGIFTCEICIEPISANDKFRNKDLCS--HHFCQDCIAKYIEAKVQDN-------NTAKIECPGVHCDQ-FLDPFSCKL 102 (268)
Q Consensus 33 ~~~~~~~C~IC~~~~~~~~~~~~~~~C~--H~fC~~Cl~~~~~~~i~~~-------~~~~i~CP~~~C~~-~i~~~~i~~ 102 (268)
.+....+|..|.+.-.+ + .+++|. |+.|.+|++.|..+.+.+. -.+.+.||. +|.. .|..-....
T Consensus 217 ~N~~ni~C~~Ctdv~~~---v-lvf~Cns~HvtC~dCFr~yc~~Rl~~rqf~~~p~~gyslpc~a-gc~~s~i~e~HHF~ 291 (446)
T KOG0006|consen 217 TNSRNITCITCTDVRSP---V-LVFQCNSRHVTCLDCFRLYCVTRLNDRQFVHDPQLGYSLPCVA-GCPNSLIKELHHFR 291 (446)
T ss_pred cccccceeEEecCCccc---e-EEEecCCceeehHHhhhhHhhhcccccccccCccccccccccC-CCchHHHHhhhhhe
Confidence 36778999999986632 2 367887 9999999999999999772 234678886 6764 344445578
Q ss_pred cCChhHHHHHHHHHHhhhhcCCCcccCCccccCceeeeccccccCCcCeeeCcc-cccccccccccccCCCCCcchhhcc
Q 043604 103 MIPSNLFSKWCDVLFEDYVLGFERSYCPNRNCMALVVNGCEINYGTLKKARCPN-CTQWFCFQCKLAWHAGYRCEESGNL 181 (268)
Q Consensus 103 ~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~-C~~~~C~~C~~~~H~~~tC~~~~~~ 181 (268)
+|..+.|++|+++..+..+...+-+.||+|+|+..+.+++.. .+++|+. |++.||..|...||.|. |.+.-..
T Consensus 292 ilg~e~Y~rYQr~atEe~vlq~gGVlCP~pgCG~gll~EPD~-----rkvtC~~gCgf~FCR~C~e~yh~ge-C~~~~~a 365 (446)
T KOG0006|consen 292 ILGEEQYNRYQRYATEECVLQMGGVLCPRPGCGAGLLPEPDQ-----RKVTCEGGCGFAFCRECKEAYHEGE-CSAVFEA 365 (446)
T ss_pred ecchhHHHHHHHhhhhhheeecCCEecCCCCCCcccccCCCC-----CcccCCCCchhHhHHHHHhhhcccc-ceeeecc
Confidence 999999999999999999998889999999999999988865 7899986 99999999999999874 5421100
Q ss_pred --------c-ch---h----hHHHHHHHHhCCcccCCCCCceeeecCCcCeEEec---CCc-ccccccccccCC
Q 043604 182 --------R-DW---N----DIAFGKLVERMHWARCPACGSCVERKEGCRVMYCS---CHS-VTYSRAKHISLR 235 (268)
Q Consensus 182 --------~-~~---~----~~~~~~~~~~~~~k~CP~C~~~iek~~GCnhm~C~---C~~-FC~~C~~~~~~~ 235 (268)
. ++ + |.+ .+...+..+|+||+|.++.||+|||.||.|. ||. |||.|+-+|+..
T Consensus 366 s~t~tc~y~vde~~a~~arwd~a-s~~TIk~tTkpCPkChvptErnGGCmHm~Ct~~~Cg~eWCw~C~tEW~r~ 438 (446)
T KOG0006|consen 366 SGTTTCAYRVDERAAEQARWDAA-SKETIKKTTKPCPKCHVPTERNGGCMHMKCTQPQCGLEWCWNCGTEWNRV 438 (446)
T ss_pred ccccceeeecChhhhhhhhhhhh-hhhhhhhccCCCCCccCccccCCceEEeecCCCCCCceeEeccCChhhhh
Confidence 0 00 0 111 2223356779999999999999999999994 999 999999999874
No 5
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=99.34 E-value=1.9e-12 Score=86.28 Aligned_cols=63 Identities=33% Similarity=0.830 Sum_probs=55.0
Q ss_pred HHHHHHHHhhhhcC-CCcccCCccccCceeeeccccccCCcCeeeCcccccccccccccccCCCCCc
Q 043604 110 SKWCDVLFEDYVLG-FERSYCPNRNCMALVVNGCEINYGTLKKARCPNCTQWFCFQCKLAWHAGYRC 175 (268)
Q Consensus 110 ~~~~~~~~~~~~~~-~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~tC 175 (268)
++|++++.+.+|.. ++++|||+|+|+.++...... ....+.|+.|+..||+.|+.+||.|.+|
T Consensus 1 ~~y~~~~~~~~i~~~~~~~~CP~~~C~~~~~~~~~~---~~~~v~C~~C~~~fC~~C~~~~H~~~~C 64 (64)
T smart00647 1 EKYERLLLESYVESNPDLKWCPAPDCSAAIIVTEEE---GCNRVTCPKCGFSFCFRCKVPWHSPVSC 64 (64)
T ss_pred ChHHHHHHHHHHhcCCCccCCCCCCCcceEEecCCC---CCCeeECCCCCCeECCCCCCcCCCCCCC
Confidence 47889999999886 789999999999999887411 2478999999999999999999999987
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=99.30 E-value=4.7e-13 Score=89.20 Aligned_cols=63 Identities=30% Similarity=0.776 Sum_probs=43.2
Q ss_pred HHHHHHHHhhhhcC-CCcccCCccccCceeeeccccccCCcCeeeCcccccccccccccccCCCCCc
Q 043604 110 SKWCDVLFEDYVLG-FERSYCPNRNCMALVVNGCEINYGTLKKARCPNCTQWFCFQCKLAWHAGYRC 175 (268)
Q Consensus 110 ~~~~~~~~~~~~~~-~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~tC 175 (268)
++|++++++.+|.. ++++|||+|+|+.++....... ...++|+.|+..||+.|+.+||.|.+|
T Consensus 1 eky~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~---~~~~~C~~C~~~fC~~C~~~~H~~~~C 64 (64)
T PF01485_consen 1 EKYQKFLLKRYLESDPNIRWCPNPDCEYIIEKDDGCN---SPIVTCPSCGTEFCFKCGEPWHEGVTC 64 (64)
T ss_dssp HCHHHCCCHS---S---CC--TTSST---ECS-SSTT---S--CCTTSCCSEECSSSTSESCTTS-H
T ss_pred ChHHHHHHHHHHHCCCCccCCCCCCCcccEEecCCCC---CCeeECCCCCCcCccccCcccCCCCCC
Confidence 57888888888875 6789999999999999988762 224999999999999999999999887
No 7
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.51 E-value=6.3e-08 Score=58.43 Aligned_cols=43 Identities=33% Similarity=0.767 Sum_probs=25.0
Q ss_pred ccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccC
Q 043604 40 CEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECP 87 (268)
Q Consensus 40 C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP 87 (268)
|+||.+ +...++...+++|||.||++|+.+.+.... ...|+||
T Consensus 1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~~----~~~~kCP 43 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKSD----RNRFKCP 43 (43)
T ss_dssp -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH-S-----S-B--T
T ss_pred CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcCC----CCeeeCc
Confidence 899999 766566667799999999999999998543 3468887
No 8
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=98.49 E-value=2.4e-07 Score=61.34 Aligned_cols=47 Identities=21% Similarity=0.475 Sum_probs=38.7
Q ss_pred HHHHHHHh-CCcccCC--CCCceeeecC--CcCeEEec-CCc-ccccccccccC
Q 043604 188 AFGKLVER-MHWARCP--ACGSCVERKE--GCRVMYCS-CHS-VTYSRAKHISL 234 (268)
Q Consensus 188 ~~~~~~~~-~~~k~CP--~C~~~iek~~--GCnhm~C~-C~~-FC~~C~~~~~~ 234 (268)
++..+++. .+++.|| +|+..|+..+ |..+|+|. |++ |||.|+.+|..
T Consensus 7 ~~~~~i~~~~~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H~ 60 (64)
T smart00647 7 LLESYVESNPDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWHS 60 (64)
T ss_pred HHHHHHhcCCCccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcCCC
Confidence 34444544 5789999 9999999975 99999995 999 99999999843
No 9
>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=98.45 E-value=5.9e-08 Score=59.33 Aligned_cols=41 Identities=32% Similarity=0.778 Sum_probs=33.0
Q ss_pred cccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCC
Q 043604 39 TCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPG 88 (268)
Q Consensus 39 ~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~ 88 (268)
+|+||++++...+.+ ..++|+|.||.+|+..|++.. ..||.
T Consensus 2 ~C~IC~~~~~~~~~~-~~l~C~H~fh~~Ci~~~~~~~--------~~CP~ 42 (44)
T PF13639_consen 2 ECPICLEEFEDGEKV-VKLPCGHVFHRSCIKEWLKRN--------NSCPV 42 (44)
T ss_dssp CETTTTCBHHTTSCE-EEETTSEEEEHHHHHHHHHHS--------SB-TT
T ss_pred CCcCCChhhcCCCeE-EEccCCCeeCHHHHHHHHHhC--------CcCCc
Confidence 699999999766665 467899999999999999763 27887
No 10
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.43 E-value=2e-07 Score=74.31 Aligned_cols=66 Identities=26% Similarity=0.591 Sum_probs=49.5
Q ss_pred CCCcccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhc--------CCCceeccCCCCCCCCCCHHHHhhcCC
Q 043604 34 TNGIFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQD--------NNTAKIECPGVHCDQFLDPFSCKLMIP 105 (268)
Q Consensus 34 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~--------~~~~~i~CP~~~C~~~i~~~~i~~~l~ 105 (268)
..+.++|+||++.+... +++.|||.||..|+..|+...-.. .......||. |+..|....+..+.+
T Consensus 15 ~~~~~~CpICld~~~dP----VvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPv--CR~~Is~~~LvPiyg 88 (193)
T PLN03208 15 SGGDFDCNICLDQVRDP----VVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPV--CKSDVSEATLVPIYG 88 (193)
T ss_pred CCCccCCccCCCcCCCc----EEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCC--CCCcCChhcEEEeec
Confidence 34578999999987533 467899999999999997643110 1234679999 999998887776654
No 11
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.41 E-value=5.7e-08 Score=58.57 Aligned_cols=41 Identities=24% Similarity=0.754 Sum_probs=28.0
Q ss_pred ccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCC
Q 043604 40 CEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPG 88 (268)
Q Consensus 40 C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~ 88 (268)
|+||++.+..+ +.++|||.||..||..+.+..-. ..+.||.
T Consensus 1 CpiC~~~~~~P----v~l~CGH~FC~~Cl~~~~~~~~~----~~~~CP~ 41 (42)
T PF15227_consen 1 CPICLDLFKDP----VSLPCGHSFCRSCLERLWKEPSG----SGFSCPE 41 (42)
T ss_dssp ETTTTSB-SSE----EE-SSSSEEEHHHHHHHHCCSSS----ST---SS
T ss_pred CCccchhhCCc----cccCCcCHHHHHHHHHHHHccCC----cCCCCcC
Confidence 89999998654 57999999999999999864322 2288886
No 12
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=98.37 E-value=2.6e-07 Score=55.49 Aligned_cols=40 Identities=38% Similarity=0.974 Sum_probs=32.3
Q ss_pred ccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCC
Q 043604 40 CEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPG 88 (268)
Q Consensus 40 C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~ 88 (268)
|+||++.+.... .+++|+|.||..|+.++++. ...+.||.
T Consensus 1 C~iC~~~~~~~~---~~~~C~H~fC~~C~~~~~~~------~~~~~CP~ 40 (41)
T PF00097_consen 1 CPICLEPFEDPV---ILLPCGHSFCRDCLRKWLEN------SGSVKCPL 40 (41)
T ss_dssp ETTTSSBCSSEE---EETTTSEEEEHHHHHHHHHH------TSSSBTTT
T ss_pred CCcCCccccCCC---EEecCCCcchHHHHHHHHHh------cCCccCCc
Confidence 789999885442 36999999999999999998 23467886
No 13
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.30 E-value=6.8e-07 Score=54.56 Aligned_cols=43 Identities=33% Similarity=0.843 Sum_probs=34.3
Q ss_pred cccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCC
Q 043604 39 TCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCD 92 (268)
Q Consensus 39 ~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~ 92 (268)
.|.||++.+.....+ .+++|||.||..|+.... ...+.||. |+
T Consensus 1 ~C~~C~~~~~~~~~~-~l~~CgH~~C~~C~~~~~--------~~~~~CP~--C~ 43 (44)
T PF14634_consen 1 HCNICFEKYSEERRP-RLTSCGHIFCEKCLKKLK--------GKSVKCPI--CR 43 (44)
T ss_pred CCcCcCccccCCCCe-EEcccCCHHHHHHHHhhc--------CCCCCCcC--CC
Confidence 489999999444444 689999999999999988 23578998 75
No 14
>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=98.26 E-value=2.7e-07 Score=61.10 Aligned_cols=40 Identities=20% Similarity=0.606 Sum_probs=28.4
Q ss_pred hCCcccCCC--CCceeeecCCcCe--EEec-CCc-ccccccccccC
Q 043604 195 RMHWARCPA--CGSCVERKEGCRV--MYCS-CHS-VTYSRAKHISL 234 (268)
Q Consensus 195 ~~~~k~CP~--C~~~iek~~GCnh--m~C~-C~~-FC~~C~~~~~~ 234 (268)
..+.+.||+ |...|++.+|.++ |+|. |++ |||.|+.+|..
T Consensus 15 ~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~ 60 (64)
T PF01485_consen 15 DPNIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPWHE 60 (64)
T ss_dssp ---CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSESCT
T ss_pred CCCccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCcccCC
Confidence 345689988 9999999999999 9998 999 99999999943
No 15
>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=98.24 E-value=3.8e-07 Score=54.13 Aligned_cols=38 Identities=37% Similarity=1.010 Sum_probs=28.6
Q ss_pred ccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCC
Q 043604 40 CEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPG 88 (268)
Q Consensus 40 C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~ 88 (268)
|+||++.+.. .+ ..++|||.||.+|+.+|++.. .+||.
T Consensus 1 C~iC~~~~~~--~~-~~~~CGH~fC~~C~~~~~~~~--------~~CP~ 38 (39)
T PF13923_consen 1 CPICLDELRD--PV-VVTPCGHSFCKECIEKYLEKN--------PKCPV 38 (39)
T ss_dssp ETTTTSB-SS--EE-EECTTSEEEEHHHHHHHHHCT--------SB-TT
T ss_pred CCCCCCcccC--cC-EECCCCCchhHHHHHHHHHCc--------CCCcC
Confidence 7899998854 22 479999999999999998752 56775
No 16
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.17 E-value=1.6e-06 Score=67.57 Aligned_cols=57 Identities=26% Similarity=0.718 Sum_probs=43.5
Q ss_pred CCCcccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCCHHHHhh
Q 043604 34 TNGIFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLDPFSCKL 102 (268)
Q Consensus 34 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~ 102 (268)
+.+.+.|+||++.+.. ..++...|||.||..|++.-+... .+||. |...|+..++..
T Consensus 128 ~~~~~~CPiCl~~~se--k~~vsTkCGHvFC~~Cik~alk~~--------~~CP~--C~kkIt~k~~~r 184 (187)
T KOG0320|consen 128 KEGTYKCPICLDSVSE--KVPVSTKCGHVFCSQCIKDALKNT--------NKCPT--CRKKITHKQFHR 184 (187)
T ss_pred cccccCCCceecchhh--ccccccccchhHHHHHHHHHHHhC--------CCCCC--cccccchhhhee
Confidence 4566899999999853 333468999999999999887643 57998 887777665543
No 17
>PHA02926 zinc finger-like protein; Provisional
Probab=98.09 E-value=3.9e-06 Score=67.82 Aligned_cols=59 Identities=27% Similarity=0.564 Sum_probs=42.9
Q ss_pred CCCcccccccccCCc-----CCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCC
Q 043604 34 TNGIFTCEICIEPIS-----ANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLD 96 (268)
Q Consensus 34 ~~~~~~C~IC~~~~~-----~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~ 96 (268)
.+...+|+||+|... ....|-.+.+|+|.||..|++.|..+... ....-.||. |+..+.
T Consensus 167 ~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~--~~~~rsCPi--CR~~f~ 230 (242)
T PHA02926 167 VSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRE--TGASDNCPI--CRTRFR 230 (242)
T ss_pred ccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccc--cCcCCcCCC--Ccceee
Confidence 345688999999762 22345556789999999999999987532 234467999 987543
No 18
>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=98.04 E-value=5.2e-06 Score=50.32 Aligned_cols=44 Identities=34% Similarity=0.845 Sum_probs=33.2
Q ss_pred cccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCC
Q 043604 39 TCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQF 94 (268)
Q Consensus 39 ~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~ 94 (268)
+|.||++.+. +.+ ...+|+|.||.+|+..|++. ....||. |+..
T Consensus 1 ~C~iC~~~~~--~~~-~~~~C~H~~c~~C~~~~~~~-------~~~~Cp~--C~~~ 44 (45)
T cd00162 1 ECPICLEEFR--EPV-VLLPCGHVFCRSCIDKWLKS-------GKNTCPL--CRTP 44 (45)
T ss_pred CCCcCchhhh--Cce-EecCCCChhcHHHHHHHHHh-------CcCCCCC--CCCc
Confidence 5899999882 222 35669999999999999875 2356887 8754
No 19
>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=98.02 E-value=2.8e-06 Score=53.33 Aligned_cols=46 Identities=30% Similarity=0.703 Sum_probs=35.4
Q ss_pred cccccccccCCcCCcCccccCCCCCh-hhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCC
Q 043604 37 IFTCEICIEPISANDKFRNKDLCSHH-FCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLD 96 (268)
Q Consensus 37 ~~~C~IC~~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~ 96 (268)
...|.||++.... . .+++|||. ||.+|+..++. ...+||. |+.+|.
T Consensus 2 ~~~C~iC~~~~~~---~-~~~pCgH~~~C~~C~~~~~~--------~~~~CP~--Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFENPRD---V-VLLPCGHLCFCEECAERLLK--------RKKKCPI--CRQPIE 48 (50)
T ss_dssp HSB-TTTSSSBSS---E-EEETTCEEEEEHHHHHHHHH--------TTSBBTT--TTBB-S
T ss_pred cCCCccCCccCCc---e-EEeCCCChHHHHHHhHHhcc--------cCCCCCc--CChhhc
Confidence 4579999998632 2 57899999 99999999998 2467998 988764
No 20
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.96 E-value=3.2e-06 Score=68.79 Aligned_cols=61 Identities=25% Similarity=0.649 Sum_probs=49.5
Q ss_pred CCCcccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCCHHHHhhcCC
Q 043604 34 TNGIFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLDPFSCKLMIP 105 (268)
Q Consensus 34 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~~l~ 105 (268)
....++|.||+|....+ ++..|||.||..||-+|+..+... -.||. |+..++.+.+--|..
T Consensus 44 ~~~~FdCNICLd~akdP----VvTlCGHLFCWpClyqWl~~~~~~-----~~cPV--CK~~Vs~~~vvPlYG 104 (230)
T KOG0823|consen 44 DGGFFDCNICLDLAKDP----VVTLCGHLFCWPCLYQWLQTRPNS-----KECPV--CKAEVSIDTVVPLYG 104 (230)
T ss_pred CCCceeeeeeccccCCC----EEeecccceehHHHHHHHhhcCCC-----eeCCc--cccccccceEEeeec
Confidence 46789999999987543 578999999999999999877654 46788 999888877766553
No 21
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=97.77 E-value=9.7e-06 Score=68.01 Aligned_cols=52 Identities=31% Similarity=0.742 Sum_probs=42.1
Q ss_pred CCcccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCCHHHH
Q 043604 35 NGIFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLDPFSC 100 (268)
Q Consensus 35 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i 100 (268)
.....|.+|+++...+ ...+|||.||.+|+..|...+- .||. |...+.+..+
T Consensus 237 ~a~~kC~LCLe~~~~p----SaTpCGHiFCWsCI~~w~~ek~--------eCPl--CR~~~~pskv 288 (293)
T KOG0317|consen 237 EATRKCSLCLENRSNP----SATPCGHIFCWSCILEWCSEKA--------ECPL--CREKFQPSKV 288 (293)
T ss_pred CCCCceEEEecCCCCC----CcCcCcchHHHHHHHHHHcccc--------CCCc--ccccCCCcce
Confidence 3457899999998544 5789999999999999997643 2999 9988877654
No 22
>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=97.76 E-value=3.1e-05 Score=45.07 Aligned_cols=30 Identities=37% Similarity=0.956 Sum_probs=24.6
Q ss_pred ccccccCCcCCcCccccCCCCChhhHHHHHHHHH
Q 043604 40 CEICIEPISANDKFRNKDLCSHHFCQDCIAKYIE 73 (268)
Q Consensus 40 C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~ 73 (268)
|+||++... .. ..++|+|.||..|+..|+.
T Consensus 1 C~iC~~~~~---~~-~~~~C~H~~c~~C~~~~~~ 30 (39)
T smart00184 1 CPICLEELK---DP-VVLPCGHTFCRSCIRKWLK 30 (39)
T ss_pred CCcCccCCC---Cc-EEecCCChHHHHHHHHHHH
Confidence 789998842 22 4689999999999999987
No 23
>PHA02929 N1R/p28-like protein; Provisional
Probab=97.75 E-value=2.6e-05 Score=64.91 Aligned_cols=52 Identities=29% Similarity=0.639 Sum_probs=38.4
Q ss_pred CCcccccccccCCcCCc----CccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCC
Q 043604 35 NGIFTCEICIEPISAND----KFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLD 96 (268)
Q Consensus 35 ~~~~~C~IC~~~~~~~~----~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~ 96 (268)
.+..+|+||++++...+ .+..+.+|+|.||.+|+..|+.. ...||. |+..+.
T Consensus 172 ~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~--------~~tCPl--CR~~~~ 227 (238)
T PHA02929 172 SKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKE--------KNTCPV--CRTPFI 227 (238)
T ss_pred CCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhc--------CCCCCC--CCCEee
Confidence 45689999999874432 13346789999999999999753 237999 987654
No 24
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.71 E-value=1.8e-05 Score=71.36 Aligned_cols=60 Identities=27% Similarity=0.554 Sum_probs=47.7
Q ss_pred cccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCCHHHHhhcCC
Q 043604 37 IFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLDPFSCKLMIP 105 (268)
Q Consensus 37 ~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~~l~ 105 (268)
...|+||+++.+. .....|||.||-.||-+|+.... ...+-.||. |...|.+.++..+.-
T Consensus 186 ~~~CPICL~~~~~----p~~t~CGHiFC~~CiLqy~~~s~---~~~~~~CPi--C~s~I~~kdl~pv~~ 245 (513)
T KOG2164|consen 186 DMQCPICLEPPSV----PVRTNCGHIFCGPCILQYWNYSA---IKGPCSCPI--CRSTITLKDLLPVFI 245 (513)
T ss_pred CCcCCcccCCCCc----ccccccCceeeHHHHHHHHhhhc---ccCCccCCc--hhhhccccceeeeee
Confidence 7889999998753 34677999999999999999872 244678999 998888877665443
No 25
>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=97.66 E-value=5.6e-05 Score=49.67 Aligned_cols=51 Identities=18% Similarity=0.151 Sum_probs=40.4
Q ss_pred ccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCCHHHHhh
Q 043604 38 FTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLDPFSCKL 102 (268)
Q Consensus 38 ~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~ 102 (268)
+.|+||.+.+..+ +.++|||.||+.|+..|+.. . ..||. |+..++.+++..
T Consensus 2 ~~Cpi~~~~~~~P----v~~~~G~v~~~~~i~~~~~~---~-----~~cP~--~~~~~~~~~l~~ 52 (63)
T smart00504 2 FLCPISLEVMKDP----VILPSGQTYERRAIEKWLLS---H-----GTDPV--TGQPLTHEDLIP 52 (63)
T ss_pred cCCcCCCCcCCCC----EECCCCCEEeHHHHHHHHHH---C-----CCCCC--CcCCCChhhcee
Confidence 5799999988543 46799999999999999976 2 47898 888887665544
No 26
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.49 E-value=7.6e-05 Score=64.77 Aligned_cols=108 Identities=22% Similarity=0.469 Sum_probs=66.5
Q ss_pred CCCcccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCCHHHHhhcCChhHHHHHH
Q 043604 34 TNGIFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLDPFSCKLMIPSNLFSKWC 113 (268)
Q Consensus 34 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~~l~~~~~~~~~ 113 (268)
....+.|+||++.+..+ ..++|+|.||..|+...+. ..+.||. |.. ... .+...-.+....
T Consensus 10 ~~~~~~C~iC~~~~~~p----~~l~C~H~~c~~C~~~~~~--------~~~~Cp~--cr~-~~~----~~~~n~~l~~~~ 70 (386)
T KOG2177|consen 10 LQEELTCPICLEYFREP----VLLPCGHNFCRACLTRSWE--------GPLSCPV--CRP-PSR----NLRPNVLLANLV 70 (386)
T ss_pred ccccccChhhHHHhhcC----ccccccchHhHHHHHHhcC--------CCcCCcc--cCC-chh----ccCccHHHHHHH
Confidence 34678999999999655 4689999999999999998 3489999 884 222 222222222222
Q ss_pred HHHHhhhhcC-CC--cccCCccccCceeeeccccccCCcCeeeCcccccccccccc-cccCCCCC
Q 043604 114 DVLFEDYVLG-FE--RSYCPNRNCMALVVNGCEINYGTLKKARCPNCTQWFCFQCK-LAWHAGYR 174 (268)
Q Consensus 114 ~~~~~~~~~~-~~--~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~-~~~H~~~t 174 (268)
.......+.. .. ...|+ ... ....+.|..|....|..|. ...|.++.
T Consensus 71 ~~~~~~~~~~~~~~~~~~c~----------~~~----~~~~~~c~~~~~~~c~~c~~~~~h~~h~ 121 (386)
T KOG2177|consen 71 ERLRQLRLSRPLGSKEELCE----------KHG----EELKLFCEEDEKLLCVLCRESGEHRGHP 121 (386)
T ss_pred HHHHhcCCcccccccchhhh----------hcC----CcceEEecccccccCCCCCCcccccCCc
Confidence 2222211111 00 01222 011 1146789999999999998 66777664
No 27
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.47 E-value=6.8e-05 Score=63.27 Aligned_cols=54 Identities=26% Similarity=0.645 Sum_probs=45.2
Q ss_pred CCCcccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCCH
Q 043604 34 TNGIFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLDP 97 (268)
Q Consensus 34 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~ 97 (268)
.....+|.||++++...+.+ .+++|.|.|...|+.+|+. ....+||. |...+++
T Consensus 320 a~~GveCaICms~fiK~d~~-~vlPC~H~FH~~Cv~kW~~-------~y~~~CPv--Crt~iPP 373 (374)
T COG5540 320 ADKGVECAICMSNFIKNDRL-RVLPCDHRFHVGCVDKWLL-------GYSNKCPV--CRTAIPP 373 (374)
T ss_pred cCCCceEEEEhhhhcccceE-EEeccCceechhHHHHHHh-------hhcccCCc--cCCCCCC
Confidence 45568999999999877776 6899999999999999985 34568999 9988764
No 28
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.46 E-value=9.6e-05 Score=64.49 Aligned_cols=48 Identities=35% Similarity=0.757 Sum_probs=41.0
Q ss_pred ccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCC
Q 043604 38 FTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFL 95 (268)
Q Consensus 38 ~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i 95 (268)
.+|.||+|++...+.++ .|+|.|.|...|+..|+... + -.||. |+..+
T Consensus 230 ~~CaIClEdY~~GdklR-iLPC~H~FH~~CIDpWL~~~-r------~~CPv--CK~di 277 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLR-ILPCSHKFHVNCIDPWLTQT-R------TFCPV--CKRDI 277 (348)
T ss_pred ceEEEeecccccCCeee-EecCCCchhhccchhhHhhc-C------ccCCC--CCCcC
Confidence 79999999999988884 79999999999999999865 2 24998 88644
No 29
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.33 E-value=0.0002 Score=64.08 Aligned_cols=66 Identities=21% Similarity=0.471 Sum_probs=45.3
Q ss_pred CCCcccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCCHHHHh-hcCChhHHHHH
Q 043604 34 TNGIFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLDPFSCK-LMIPSNLFSKW 112 (268)
Q Consensus 34 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i~-~~l~~~~~~~~ 112 (268)
....+.|+||.+.+..+ ++++|+|.||..|+..++.. ...||. |...+....+. ..+-.++++.|
T Consensus 23 Le~~l~C~IC~d~~~~P----vitpCgH~FCs~CI~~~l~~--------~~~CP~--Cr~~~~~~~Lr~N~~L~~iVe~~ 88 (397)
T TIGR00599 23 LDTSLRCHICKDFFDVP----VLTSCSHTFCSLCIRRCLSN--------QPKCPL--CRAEDQESKLRSNWLVSEIVESF 88 (397)
T ss_pred cccccCCCcCchhhhCc----cCCCCCCchhHHHHHHHHhC--------CCCCCC--CCCccccccCccchHHHHHHHHH
Confidence 34578999999988543 46899999999999998853 137998 99877654332 22223444544
Q ss_pred H
Q 043604 113 C 113 (268)
Q Consensus 113 ~ 113 (268)
.
T Consensus 89 ~ 89 (397)
T TIGR00599 89 K 89 (397)
T ss_pred H
Confidence 3
No 30
>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=97.32 E-value=0.00033 Score=60.22 Aligned_cols=55 Identities=22% Similarity=0.558 Sum_probs=37.7
Q ss_pred ccccccccCCcCCcCcc-ccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCCHHHHh
Q 043604 38 FTCEICIEPISANDKFR-NKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLDPFSCK 101 (268)
Q Consensus 38 ~~C~IC~~~~~~~~~~~-~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i~ 101 (268)
..|+||..+...+.... .+..|||.||.+|+...+. ..+..||. |+..+....++
T Consensus 4 ~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~-------~~~~~CP~--C~~~lrk~~fr 59 (309)
T TIGR00570 4 QGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFV-------RGSGSCPE--CDTPLRKNNFR 59 (309)
T ss_pred CCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhc-------CCCCCCCC--CCCccchhhcc
Confidence 47999998644333211 1227999999999999872 12358997 99877765543
No 31
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=97.16 E-value=0.00028 Score=63.89 Aligned_cols=58 Identities=31% Similarity=0.796 Sum_probs=45.7
Q ss_pred cCCCcccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCCHHH
Q 043604 33 DTNGIFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLDPFS 99 (268)
Q Consensus 33 ~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~ 99 (268)
++....+|.+|-++-. + . ....|.|.||+-|++.|+.....+. .+.||. |...++.+.
T Consensus 532 enk~~~~C~lc~d~ae--d-~-i~s~ChH~FCrlCi~eyv~~f~~~~---nvtCP~--C~i~LsiDl 589 (791)
T KOG1002|consen 532 ENKGEVECGLCHDPAE--D-Y-IESSCHHKFCRLCIKEYVESFMENN---NVTCPV--CHIGLSIDL 589 (791)
T ss_pred cccCceeecccCChhh--h-h-HhhhhhHHHHHHHHHHHHHhhhccc---CCCCcc--ccccccccc
Confidence 3667789999998763 2 2 4689999999999999999877652 299999 987766553
No 32
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=97.02 E-value=0.00041 Score=59.53 Aligned_cols=65 Identities=26% Similarity=0.567 Sum_probs=48.0
Q ss_pred CCcccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCCHHHHhh-cCChhHHHHHH
Q 043604 35 NGIFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLDPFSCKL-MIPSNLFSKWC 113 (268)
Q Consensus 35 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~-~l~~~~~~~~~ 113 (268)
....-|.||++-|..+ ...+|+|.||.-|++.|+.. ...||. |..++....++. .+-.++++-|.
T Consensus 21 D~lLRC~IC~eyf~ip----~itpCsHtfCSlCIR~~L~~--------~p~CP~--C~~~~~Es~Lr~n~il~Eiv~S~~ 86 (442)
T KOG0287|consen 21 DDLLRCGICFEYFNIP----MITPCSHTFCSLCIRKFLSY--------KPQCPT--CCVTVTESDLRNNRILDEIVKSLN 86 (442)
T ss_pred HHHHHHhHHHHHhcCc----eeccccchHHHHHHHHHhcc--------CCCCCc--eecccchhhhhhhhHHHHHHHHHH
Confidence 3467899999998543 46789999999999999853 467998 998888877764 22234555443
No 33
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=96.77 E-value=0.0006 Score=64.61 Aligned_cols=56 Identities=21% Similarity=0.673 Sum_probs=44.8
Q ss_pred CCcccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCCHHHHhhc
Q 043604 35 NGIFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLDPFSCKLM 103 (268)
Q Consensus 35 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~~ 103 (268)
.....|++|.+.. .+. +...|+|.||.+|++..+.+.-+ +||. |+..+...+|..+
T Consensus 641 K~~LkCs~Cn~R~--Kd~--vI~kC~H~FC~~Cvq~r~etRqR-------KCP~--Cn~aFganDv~~I 696 (698)
T KOG0978|consen 641 KELLKCSVCNTRW--KDA--VITKCGHVFCEECVQTRYETRQR-------KCPK--CNAAFGANDVHRI 696 (698)
T ss_pred HhceeCCCccCch--hhH--HHHhcchHHHHHHHHHHHHHhcC-------CCCC--CCCCCCccccccc
Confidence 4578999999443 333 46899999999999999998765 5998 9999988877653
No 34
>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=96.73 E-value=0.0008 Score=45.68 Aligned_cols=44 Identities=27% Similarity=0.557 Sum_probs=30.1
Q ss_pred cccccccccCCcCC---------cCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCC
Q 043604 37 IFTCEICIEPISAN---------DKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPG 88 (268)
Q Consensus 37 ~~~C~IC~~~~~~~---------~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~ 88 (268)
.-.|.||++++... +..+....|+|.|...||..|++.+ -.||.
T Consensus 19 ~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~--------~~CP~ 71 (73)
T PF12678_consen 19 DDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQN--------NTCPL 71 (73)
T ss_dssp CSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTS--------SB-TT
T ss_pred CCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcC--------CcCCC
Confidence 33599999988332 1222345799999999999999532 17887
No 35
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=96.70 E-value=0.00066 Score=45.68 Aligned_cols=59 Identities=17% Similarity=0.373 Sum_probs=28.1
Q ss_pred cccccccccCCcCCcCc----cccCCCCChhhHHHHHHHHHHHhhcCC-Cce--eccCCCCCCCCCCH
Q 043604 37 IFTCEICIEPISANDKF----RNKDLCSHHFCQDCIAKYIEAKVQDNN-TAK--IECPGVHCDQFLDP 97 (268)
Q Consensus 37 ~~~C~IC~~~~~~~~~~----~~~~~C~H~fC~~Cl~~~~~~~i~~~~-~~~--i~CP~~~C~~~i~~ 97 (268)
..+|.|||+.....+.. -....|+..|...||..|+...-.... ..+ =.||. |+.+|..
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 46799999987522211 112368899999999999987665522 222 37998 9987754
No 36
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.67 E-value=0.0014 Score=54.65 Aligned_cols=52 Identities=25% Similarity=0.526 Sum_probs=38.8
Q ss_pred cccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCCHHHH
Q 043604 37 IFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLDPFSC 100 (268)
Q Consensus 37 ~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i 100 (268)
.+.|.||++..... ...+|||.||..||-.....+ ..-.||. |.+...+..+
T Consensus 215 d~kC~lC~e~~~~p----s~t~CgHlFC~~Cl~~~~t~~------k~~~Cpl--CRak~~pk~v 266 (271)
T COG5574 215 DYKCFLCLEEPEVP----SCTPCGHLFCLSCLLISWTKK------KYEFCPL--CRAKVYPKKV 266 (271)
T ss_pred ccceeeeecccCCc----ccccccchhhHHHHHHHHHhh------ccccCch--hhhhccchhh
Confidence 56799999987432 578999999999999853221 1235998 9988777665
No 37
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=96.38 E-value=0.0024 Score=41.05 Aligned_cols=49 Identities=24% Similarity=0.635 Sum_probs=31.7
Q ss_pred CCcccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCC
Q 043604 35 NGIFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCD 92 (268)
Q Consensus 35 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~ 92 (268)
...+.|+|-...+..+ + ....|+|.|-++-+.+|+ +....+.||..||.
T Consensus 9 ~~~~~CPiT~~~~~~P--V-~s~~C~H~fek~aI~~~i------~~~~~~~CPv~GC~ 57 (57)
T PF11789_consen 9 TISLKCPITLQPFEDP--V-KSKKCGHTFEKEAILQYI------QRNGSKRCPVAGCN 57 (57)
T ss_dssp B--SB-TTTSSB-SSE--E-EESSS--EEEHHHHHHHC------TTTS-EE-SCCC-S
T ss_pred EeccCCCCcCChhhCC--c-CcCCCCCeecHHHHHHHH------HhcCCCCCCCCCCC
Confidence 3467899999988544 3 356899999999999999 24567999999984
No 38
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=96.04 E-value=0.0061 Score=53.19 Aligned_cols=55 Identities=25% Similarity=0.496 Sum_probs=40.4
Q ss_pred CCCcccccccccCCcCCc---------CccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCCHH
Q 043604 34 TNGIFTCEICIEPISAND---------KFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLDPF 98 (268)
Q Consensus 34 ~~~~~~C~IC~~~~~~~~---------~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~ 98 (268)
......|.||+|+.-.++ .-+..++|||.+...|++.|++.+ -.||. |+.++-.+
T Consensus 284 ~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERq--------QTCPI--Cr~p~ifd 347 (491)
T COG5243 284 TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQ--------QTCPI--CRRPVIFD 347 (491)
T ss_pred cCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhc--------cCCCc--ccCccccc
Confidence 355678999999832222 223578999999999999999854 36898 98775443
No 39
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.91 E-value=0.0069 Score=53.28 Aligned_cols=94 Identities=23% Similarity=0.430 Sum_probs=56.9
Q ss_pred CCcccccccccCCcCCc----CccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCC---HHHH---hhcC
Q 043604 35 NGIFTCEICIEPISAND----KFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLD---PFSC---KLMI 104 (268)
Q Consensus 35 ~~~~~C~IC~~~~~~~~----~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~---~~~i---~~~l 104 (268)
....+|.||++.+.... .|..+.+|.|.||..|++.|-...-.+ ....-.||. |..... +..+ ..--
T Consensus 159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~-~~~sksCP~--CRv~s~~v~pS~~Wv~t~~~ 235 (344)
T KOG1039|consen 159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFE-SKTSKSCPF--CRVPSSFVNPSSFWVETKEE 235 (344)
T ss_pred cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccc-cccccCCCc--ccCccccccccceeeeeccc
Confidence 55789999999874431 143457799999999999998544433 556678998 875432 2211 1111
Q ss_pred ChhHHHHHHHHHHhhhhc--CCCcccCCc
Q 043604 105 PSNLFSKWCDVLFEDYVL--GFERSYCPN 131 (268)
Q Consensus 105 ~~~~~~~~~~~~~~~~~~--~~~~~~Cp~ 131 (268)
...+.+.|.+......-. ......||.
T Consensus 236 k~~li~e~~~~~s~~~c~yf~~~~g~cPf 264 (344)
T KOG1039|consen 236 KQKLIEEYEAEMSAKDCKYFSQGLGSCPF 264 (344)
T ss_pred ccccHHHHHHHhhccchhhhcCCCCCCCC
Confidence 233556666554433222 245677885
No 40
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.72 E-value=0.021 Score=50.67 Aligned_cols=115 Identities=19% Similarity=0.470 Sum_probs=74.3
Q ss_pred cCCCcccccc--cccCC--cCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCCHHHHhhcC----
Q 043604 33 DTNGIFTCEI--CIEPI--SANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLDPFSCKLMI---- 104 (268)
Q Consensus 33 ~~~~~~~C~I--C~~~~--~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~~l---- 104 (268)
..+....|+- |.... .+.+.+..-..|.-.||..|...|.- +. + |+.... +.++-++
T Consensus 269 ~msdv~yCPr~~Cq~p~~~d~~~~l~~CskCnFaFCtlCk~t~HG--~s-------~-----Ck~~~~-~~~~l~~~~~~ 333 (445)
T KOG1814|consen 269 LMSDVVYCPRACCQLPVKQDPGRALAICSKCNFAFCTLCKLTWHG--VS-------P-----CKVKAE-KLIELYLEYLE 333 (445)
T ss_pred hhcccccCChhhccCccccCchhhhhhhccCccHHHHHHHHhhcC--CC-------c-----ccCchH-HHHHHHHHHhh
Confidence 3555678887 55442 11233334557899999999998864 21 1 665433 2222111
Q ss_pred -C----hhHHHHHHHHHHhhhhcC--------CCcccCCccccCceeeeccccccCCcCeeeCccccccccccccccc
Q 043604 105 -P----SNLFSKWCDVLFEDYVLG--------FERSYCPNRNCMALVVNGCEINYGTLKKARCPNCTQWFCFQCKLAW 169 (268)
Q Consensus 105 -~----~~~~~~~~~~~~~~~~~~--------~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~ 169 (268)
+ .++.+||.++..+..+.. .+...|| .|..++....+- +++.|..|++.||+.|....
T Consensus 334 ~d~a~k~ele~Ryg~rvve~~vn~~lsekwl~~N~krCP--~C~v~IEr~eGC-----nKM~C~~c~~~fc~~c~~~l 404 (445)
T KOG1814|consen 334 ADEARKRELEKRYGKRVVEELVNDFLSEKWLESNSKRCP--KCKVVIERSEGC-----NKMHCTKCGTYFCWICAELL 404 (445)
T ss_pred cCHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhcCCCCC--cccceeecCCCc-----cceeeccccccceeehhhhc
Confidence 1 245677875555443321 3568899 899999888765 78999999999999998753
No 41
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=95.65 E-value=0.0081 Score=53.47 Aligned_cols=85 Identities=18% Similarity=0.346 Sum_probs=49.6
Q ss_pred CeeeCcccccccccccccccCCCCC-cchhhcccchhhHHHHHHHHhCCcccCCCCCceeeecCCcCe-EEec-CCc-cc
Q 043604 150 KKARCPNCTQWFCFQCKLAWHAGYR-CEESGNLRDWNDIAFGKLVERMHWARCPACGSCVERKEGCRV-MYCS-CHS-VT 225 (268)
Q Consensus 150 ~~~~C~~C~~~~C~~C~~~~H~~~t-C~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~~iek~~GCnh-m~C~-C~~-FC 225 (268)
..+.|..|...+|.-|+..-|++.- =...... ..++-.+.....-....+|.. -+|=|| |+|. |+. .|
T Consensus 175 a~v~ceqcdv~yc~pc~~~~hp~rgplakh~l~-~~~~grvs~~~s~r~~~~ct~-------h~~e~~smyc~~ck~pvc 246 (699)
T KOG4367|consen 175 ATVMCEQCDVFYCDPCRLRCHPPRGPLAKHRLV-PPAQGRVSRRLSPRKVSTCTD-------HELENHSMYCVQCKMPVC 246 (699)
T ss_pred hhhhHhhCceEEechHHhccCCCCCchhhcccC-CcccCceeeccchhhhhhccC-------CCCCCceEEEEecCChHH
Confidence 5678999999999999998888641 1111111 101111111111111223331 245566 9998 999 99
Q ss_pred ccccccccCCCCCCCCC
Q 043604 226 YSRAKHISLRKHSTRGD 242 (268)
Q Consensus 226 ~~C~~~~~~~~~~~~~~ 242 (268)
|.|+.......|.-...
T Consensus 247 ~~clee~khs~hevkal 263 (699)
T KOG4367|consen 247 YQCLEEGKHSSHEVKAL 263 (699)
T ss_pred HHHHHhhcccchhhhhH
Confidence 99999887766654433
No 42
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=95.62 E-value=0.00091 Score=43.44 Aligned_cols=50 Identities=28% Similarity=0.631 Sum_probs=22.6
Q ss_pred cccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCCHHHHh
Q 043604 37 IFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLDPFSCK 101 (268)
Q Consensus 37 ~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i~ 101 (268)
..-|++|++.+..+ + .+..|.|.||..|++..+. -.||. |..+....+++
T Consensus 7 lLrCs~C~~~l~~p--v-~l~~CeH~fCs~Ci~~~~~----------~~CPv--C~~Paw~qD~~ 56 (65)
T PF14835_consen 7 LLRCSICFDILKEP--V-CLGGCEHIFCSSCIRDCIG----------SECPV--CHTPAWIQDIQ 56 (65)
T ss_dssp TTS-SSS-S--SS---B----SSS--B-TTTGGGGTT----------TB-SS--S--B-S-SS--
T ss_pred hcCCcHHHHHhcCC--c-eeccCccHHHHHHhHHhcC----------CCCCC--cCChHHHHHHH
Confidence 46799999988543 2 3678999999999976332 24998 98766555443
No 43
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=95.39 E-value=0.012 Score=49.62 Aligned_cols=52 Identities=27% Similarity=0.566 Sum_probs=38.7
Q ss_pred CCcccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCCHHHH
Q 043604 35 NGIFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLDPFSC 100 (268)
Q Consensus 35 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i 100 (268)
....-|.||-+-+.. +...+|||.||.-|++.|+.+ ...||. |........+
T Consensus 23 Ds~lrC~IC~~~i~i----p~~TtCgHtFCslCIR~hL~~--------qp~CP~--Cr~~~~esrl 74 (391)
T COG5432 23 DSMLRCRICDCRISI----PCETTCGHTFCSLCIRRHLGT--------QPFCPV--CREDPCESRL 74 (391)
T ss_pred hhHHHhhhhhheeec----ceecccccchhHHHHHHHhcC--------CCCCcc--ccccHHhhhc
Confidence 445679999988843 356899999999999999854 356888 8765544433
No 44
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.05 E-value=0.065 Score=46.55 Aligned_cols=58 Identities=31% Similarity=0.643 Sum_probs=42.7
Q ss_pred cccccccccCCcCC--cCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCC--CCHHHHhhc
Q 043604 37 IFTCEICIEPISAN--DKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQF--LDPFSCKLM 103 (268)
Q Consensus 37 ~~~C~IC~~~~~~~--~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~--i~~~~i~~~ 103 (268)
...|.||-+++... +..+..+.|||.+|..|+...+. ...+.||. |..+ +....++.+
T Consensus 3 ~~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~-------~~~i~cpf--cR~~~~~~~~~~~~l 64 (296)
T KOG4185|consen 3 FPECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLG-------NSRILCPF--CRETTEIPDGDVKSL 64 (296)
T ss_pred CCceeecCccccccCcccCCcccccCceehHhHHHHHhc-------CceeeccC--CCCcccCCchhHhhh
Confidence 46899999999765 34456788999999999998874 34567787 8876 444445443
No 45
>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=95.05 E-value=0.0091 Score=31.71 Aligned_cols=22 Identities=32% Similarity=0.940 Sum_probs=14.1
Q ss_pred ccCCCCCceeeecCCcCeEEec-CCc-c
Q 043604 199 ARCPACGSCVERKEGCRVMYCS-CHS-V 224 (268)
Q Consensus 199 k~CP~C~~~iek~~GCnhm~C~-C~~-F 224 (268)
|.||.|+..|-.. -..|. ||+ |
T Consensus 1 K~CP~C~~~V~~~----~~~Cp~CG~~F 24 (26)
T PF10571_consen 1 KTCPECGAEVPES----AKFCPHCGYDF 24 (26)
T ss_pred CcCCCCcCCchhh----cCcCCCCCCCC
Confidence 5688888777532 25565 776 6
No 46
>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=94.80 E-value=0.0099 Score=40.28 Aligned_cols=51 Identities=20% Similarity=0.159 Sum_probs=35.8
Q ss_pred cccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCCHHHH
Q 043604 37 IFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLDPFSC 100 (268)
Q Consensus 37 ~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i 100 (268)
.+.|+|+.+-+..+ +.+++||.|.++++..|+.. ....||. ++..+...++
T Consensus 4 ~f~CpIt~~lM~dP----Vi~~~G~tyer~~I~~~l~~-------~~~~~P~--t~~~l~~~~l 54 (73)
T PF04564_consen 4 EFLCPITGELMRDP----VILPSGHTYERSAIERWLEQ-------NGGTDPF--TRQPLSESDL 54 (73)
T ss_dssp GGB-TTTSSB-SSE----EEETTSEEEEHHHHHHHHCT-------TSSB-TT--T-SB-SGGGS
T ss_pred ccCCcCcCcHhhCc----eeCCcCCEEcHHHHHHHHHc-------CCCCCCC--CCCcCCcccc
Confidence 57899999987543 46789999999999999975 3467888 7777776543
No 47
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.61 E-value=0.018 Score=49.03 Aligned_cols=53 Identities=23% Similarity=0.356 Sum_probs=40.2
Q ss_pred CcccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCCHHHHh
Q 043604 36 GIFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLDPFSCK 101 (268)
Q Consensus 36 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i~ 101 (268)
..-+|.||+.+-..+ +.+.|+|.||.-|++.-+.... ..|+. |..+|+...+.
T Consensus 6 ~~~eC~IC~nt~n~P----v~l~C~HkFCyiCiKGsy~ndk-------~~Cav--CR~pids~i~~ 58 (324)
T KOG0824|consen 6 KKKECLICYNTGNCP----VNLYCFHKFCYICIKGSYKNDK-------KTCAV--CRFPIDSTIDF 58 (324)
T ss_pred cCCcceeeeccCCcC----ccccccchhhhhhhcchhhcCC-------CCCce--ecCCCCcchhc
Confidence 456899999877433 5799999999999998775433 34888 99888765543
No 48
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.57 E-value=0.0081 Score=54.09 Aligned_cols=66 Identities=20% Similarity=0.450 Sum_probs=44.6
Q ss_pred CCHHHHhhcCChhHHHHHHHHHHhhhhcCCCcccCCccccCceeeeccccccCCcCeeeCcccccccccccccccCCCC
Q 043604 95 LDPFSCKLMIPSNLFSKWCDVLFEDYVLGFERSYCPNRNCMALVVNGCEINYGTLKKARCPNCTQWFCFQCKLAWHAGY 173 (268)
Q Consensus 95 i~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~ 173 (268)
++-++++.+.+++..+.- ...++. ..++.|| .|...+....+- +.++|. |+..||+.|..+|..+.
T Consensus 280 ~sC~eykk~~~~~~~d~~----~~~~la-~~wr~Cp--kC~~~ie~~~GC-----nhm~Cr-C~~~fcy~C~~~~~~~~ 345 (384)
T KOG1812|consen 280 LSCEEYKKLNPEEYVDDI----TLKYLA-KRWRQCP--KCKFMIELSEGC-----NHMTCR-CGHQFCYMCGGDWKTHN 345 (384)
T ss_pred CCHHHHHHhCCcccccHH----HHHHHH-HhcCcCc--ccceeeeecCCc-----ceEEee-ccccchhhcCcchhhCC
Confidence 455666666653322211 111122 4578999 999998766654 889998 99999999999996654
No 49
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=94.53 E-value=0.03 Score=32.52 Aligned_cols=33 Identities=30% Similarity=0.559 Sum_probs=25.9
Q ss_pred ccCCccccCceeeeccccccCCcCeeeCccccccc
Q 043604 127 SYCPNRNCMALVVNGCEINYGTLKKARCPNCTQWF 161 (268)
Q Consensus 127 ~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~ 161 (268)
+.|| +|+..+..++..-......++|+.|+..|
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 5688 89999988776444457899999998765
No 50
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=94.45 E-value=0.025 Score=34.74 Aligned_cols=46 Identities=28% Similarity=0.642 Sum_probs=21.8
Q ss_pred ccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCC
Q 043604 40 CEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQF 94 (268)
Q Consensus 40 C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~ 94 (268)
|++|.+++...+.-+.--.|++.+|+.|+..-.+. ..=+||. |+.+
T Consensus 1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~~-------~~g~CPg--Cr~~ 46 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILEN-------EGGRCPG--CREP 46 (48)
T ss_dssp -TTTS-B--CCCTT--SSTTS----HHHHHHHTTS-------S-SB-TT--T--B
T ss_pred CCCcccccccCCCccccCcCCCcHHHHHHHHHHhc-------cCCCCCC--CCCC
Confidence 78999988555432234568999999999876651 1246888 8764
No 51
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=94.44 E-value=0.026 Score=39.10 Aligned_cols=53 Identities=32% Similarity=0.589 Sum_probs=36.2
Q ss_pred cccccccccCCcCC--------cCc-cccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCC
Q 043604 37 IFTCEICIEPISAN--------DKF-RNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLD 96 (268)
Q Consensus 37 ~~~C~IC~~~~~~~--------~~~-~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~ 96 (268)
.-.|.||...|... +.- .+.-.|+|.|...||..++.++-. .-.||. |++.+.
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 45688887766521 111 123469999999999999987622 237998 987654
No 52
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=94.13 E-value=0.043 Score=31.63 Aligned_cols=33 Identities=33% Similarity=0.508 Sum_probs=26.5
Q ss_pred ccCCccccCceeeeccccccCCcCeeeCccccccc
Q 043604 127 SYCPNRNCMALVVNGCEINYGTLKKARCPNCTQWF 161 (268)
Q Consensus 127 ~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~ 161 (268)
+.|| +|+..+..++..-+.....++|+.|+..|
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 5688 89999988777555567889999998765
No 53
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=94.07 E-value=0.027 Score=44.96 Aligned_cols=35 Identities=26% Similarity=0.563 Sum_probs=28.1
Q ss_pred CCCcccccccccCCcCCcCccccCCCCChhhHHHHHHHH
Q 043604 34 TNGIFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYI 72 (268)
Q Consensus 34 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~ 72 (268)
..-+|.|.||-.++..+ ++..|||.||..|...-+
T Consensus 193 e~IPF~C~iCKkdy~sp----vvt~CGH~FC~~Cai~~y 227 (259)
T COG5152 193 EKIPFLCGICKKDYESP----VVTECGHSFCSLCAIRKY 227 (259)
T ss_pred CCCceeehhchhhccch----hhhhcchhHHHHHHHHHh
Confidence 34568999999999654 578999999999976544
No 54
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=94.02 E-value=0.07 Score=45.79 Aligned_cols=95 Identities=19% Similarity=0.504 Sum_probs=58.0
Q ss_pred CCCCChhhHHHHHHHHHHHhhc--CCCceeccCCCCCCCCCCHHHHhhcCChhHHHHHHHHHHhhhhcCCCcccCCcccc
Q 043604 57 DLCSHHFCQDCIAKYIEAKVQD--NNTAKIECPGVHCDQFLDPFSCKLMIPSNLFSKWCDVLFEDYVLGFERSYCPNRNC 134 (268)
Q Consensus 57 ~~C~H~fC~~Cl~~~~~~~i~~--~~~~~i~CP~~~C~~~i~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C 134 (268)
-.|+-.||++|+..|.+-.-.. +....- .|...++.... .-.+|+....+ .| ....+-|| .|
T Consensus 340 ~gCgf~FCR~C~e~yh~geC~~~~~as~t~-----tc~y~vde~~a-------~~arwd~as~~-TI-k~tTkpCP--kC 403 (446)
T KOG0006|consen 340 GGCGFAFCRECKEAYHEGECSAVFEASGTT-----TCAYRVDERAA-------EQARWDAASKE-TI-KKTTKPCP--KC 403 (446)
T ss_pred CCchhHhHHHHHhhhccccceeeecccccc-----ceeeecChhhh-------hhhhhhhhhhh-hh-hhccCCCC--Cc
Confidence 3489999999999987533222 111111 23333333222 22455544332 11 23456777 88
Q ss_pred CceeeeccccccCCcCeeeCcc--cccccccccccccCCC
Q 043604 135 MALVVNGCEINYGTLKKARCPN--CTQWFCFQCKLAWHAG 172 (268)
Q Consensus 135 ~~~~~~~~~~~~~~~~~~~C~~--C~~~~C~~C~~~~H~~ 172 (268)
.........- ..+.|+. |+..+|+.|+.+|...
T Consensus 404 hvptErnGGC-----mHm~Ct~~~Cg~eWCw~C~tEW~r~ 438 (446)
T KOG0006|consen 404 HVPTERNGGC-----MHMKCTQPQCGLEWCWNCGTEWNRV 438 (446)
T ss_pred cCccccCCce-----EEeecCCCCCCceeEeccCChhhhh
Confidence 8877766654 6788975 9999999999998653
No 55
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.89 E-value=0.033 Score=50.47 Aligned_cols=58 Identities=26% Similarity=0.583 Sum_probs=41.6
Q ss_pred hhcCCCcccccccccCCcCCcC----c---------cccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCCH
Q 043604 31 LEDTNGIFTCEICIEPISANDK----F---------RNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLDP 97 (268)
Q Consensus 31 ~~~~~~~~~C~IC~~~~~~~~~----~---------~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~ 97 (268)
..+......|.||+.+++.-.. . +.+.+|.|.|...||.+|+.. ..+.||. |..++++
T Consensus 565 ~~~~~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~-------ykl~CPv--CR~pLPp 635 (636)
T KOG0828|consen 565 EAFVRRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDT-------YKLICPV--CRCPLPP 635 (636)
T ss_pred cchhhccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhh-------hcccCCc--cCCCCCC
Confidence 3345567899999988754211 0 135699999999999999963 3477998 8877653
No 56
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=93.86 E-value=0.092 Score=45.47 Aligned_cols=54 Identities=30% Similarity=0.663 Sum_probs=39.0
Q ss_pred cccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCCHHHHh
Q 043604 39 TCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLDPFSCK 101 (268)
Q Consensus 39 ~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i~ 101 (268)
.|+.|+++.+..|.-+...+||-.+|+-|+.. |...+.. +||. |....+.+-++
T Consensus 16 ~cplcie~mditdknf~pc~cgy~ic~fc~~~-irq~lng------rcpa--crr~y~denv~ 69 (480)
T COG5175 16 YCPLCIEPMDITDKNFFPCPCGYQICQFCYNN-IRQNLNG------RCPA--CRRKYDDENVR 69 (480)
T ss_pred cCcccccccccccCCcccCCcccHHHHHHHHH-HHhhccC------CChH--hhhhcccccee
Confidence 49999999877765334677899999999865 3333433 7999 98776665554
No 57
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.71 E-value=0.059 Score=45.35 Aligned_cols=52 Identities=25% Similarity=0.532 Sum_probs=39.3
Q ss_pred CCCcccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCC
Q 043604 34 TNGIFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLD 96 (268)
Q Consensus 34 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~ 96 (268)
.....+|++|.+.-..+ + ....|+|.||--|+..-..... .+.||. |+....
T Consensus 236 ~t~~~~C~~Cg~~PtiP--~-~~~~C~HiyCY~Ci~ts~~~~a------sf~Cp~--Cg~~~~ 287 (298)
T KOG2879|consen 236 GTSDTECPVCGEPPTIP--H-VIGKCGHIYCYYCIATSRLWDA------SFTCPL--CGENVE 287 (298)
T ss_pred ccCCceeeccCCCCCCC--e-eeccccceeehhhhhhhhcchh------hcccCc--cCCCCc
Confidence 34567999999866444 3 3567999999999998876443 479998 997665
No 58
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=93.61 E-value=0.093 Score=53.60 Aligned_cols=77 Identities=19% Similarity=0.342 Sum_probs=57.4
Q ss_pred CCCcccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCC--CceeccCCCCCCCCCCHHHHhhcCCh--hHH
Q 043604 34 TNGIFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNN--TAKIECPGVHCDQFLDPFSCKLMIPS--NLF 109 (268)
Q Consensus 34 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~--~~~i~CP~~~C~~~i~~~~i~~~l~~--~~~ 109 (268)
.+..-.|.|||.+.....-. ..+.|+|.|...|.+.-++..-.... ..-|.||. |..+|..-.++.+|++ +++
T Consensus 3483 QD~DDmCmICFTE~L~AAP~-IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPi--C~n~InH~~LkDLldPiKel~ 3559 (3738)
T KOG1428|consen 3483 QDADDMCMICFTEALSAAPA-IQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPI--CKNKINHIVLKDLLDPIKELY 3559 (3738)
T ss_pred cccCceEEEEehhhhCCCcc-eecCCccchhHHHHHHHHHhcccCCeeEEeeeeccc--ccchhhhHHHHHHHHHHHHHH
Confidence 34556799999877544333 46899999999999999988766522 12478999 9999999999999884 444
Q ss_pred HHHH
Q 043604 110 SKWC 113 (268)
Q Consensus 110 ~~~~ 113 (268)
+.-.
T Consensus 3560 edV~ 3563 (3738)
T KOG1428|consen 3560 EDVR 3563 (3738)
T ss_pred HHHH
Confidence 4433
No 59
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.45 E-value=0.095 Score=47.19 Aligned_cols=48 Identities=27% Similarity=0.735 Sum_probs=36.2
Q ss_pred CCcccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCC
Q 043604 35 NGIFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLD 96 (268)
Q Consensus 35 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~ 96 (268)
...++|.||+..+..+ +.++|||.||..|+.+ .+. ..-.||. |...+.
T Consensus 82 ~sef~c~vc~~~l~~p----v~tpcghs~c~~Cl~r----~ld----~~~~cp~--Cr~~l~ 129 (398)
T KOG4159|consen 82 RSEFECCVCSRALYPP----VVTPCGHSFCLECLDR----SLD----QETECPL--CRDELV 129 (398)
T ss_pred cchhhhhhhHhhcCCC----ccccccccccHHHHHH----Hhc----cCCCCcc--cccccc
Confidence 5679999999988654 4679999999999776 222 2356887 886665
No 60
>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=93.36 E-value=0.12 Score=31.94 Aligned_cols=42 Identities=21% Similarity=0.536 Sum_probs=29.4
Q ss_pred cccccccCCcCCcCccccCCCC-----ChhhHHHHHHHHHHHhhcCCCceeccCC
Q 043604 39 TCEICIEPISANDKFRNKDLCS-----HHFCQDCIAKYIEAKVQDNNTAKIECPG 88 (268)
Q Consensus 39 ~C~IC~~~~~~~~~~~~~~~C~-----H~fC~~Cl~~~~~~~i~~~~~~~i~CP~ 88 (268)
.|-||++.....+.+ ..+|. |.+..+||..|+..+-. ..||.
T Consensus 1 ~CrIC~~~~~~~~~l--~~PC~C~G~~~~vH~~Cl~~W~~~~~~------~~C~i 47 (49)
T smart00744 1 ICRICHDEGDEGDPL--VSPCRCKGSLKYVHQECLERWINESGN------KTCEI 47 (49)
T ss_pred CccCCCCCCCCCCee--EeccccCCchhHHHHHHHHHHHHHcCC------CcCCC
Confidence 488999844333333 46774 88999999999986532 36776
No 61
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=93.25 E-value=0.036 Score=47.15 Aligned_cols=63 Identities=19% Similarity=0.479 Sum_probs=47.5
Q ss_pred cCCCcccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhc---------------CCCceeccCCCCCCCCCCH
Q 043604 33 DTNGIFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQD---------------NNTAKIECPGVHCDQFLDP 97 (268)
Q Consensus 33 ~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~---------------~~~~~i~CP~~~C~~~i~~ 97 (268)
.+.+...|.||+--|..++.| ....|.|+|...||..|+.....+ ...+.-.||. |...|.+
T Consensus 111 nn~p~gqCvICLygfa~~~~f-t~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpV--cre~i~~ 187 (368)
T KOG4445|consen 111 NNHPNGQCVICLYGFASSPAF-TVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPV--CRERIKI 187 (368)
T ss_pred CCCCCCceEEEEEeecCCCce-eeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhH--hhhhccc
Confidence 366788999999888777778 589999999999999999764433 1122345998 8877665
Q ss_pred H
Q 043604 98 F 98 (268)
Q Consensus 98 ~ 98 (268)
+
T Consensus 188 e 188 (368)
T KOG4445|consen 188 E 188 (368)
T ss_pred c
Confidence 4
No 62
>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=93.18 E-value=0.067 Score=40.33 Aligned_cols=47 Identities=23% Similarity=0.450 Sum_probs=33.3
Q ss_pred hhcCCCcccccccccCCcCCcCccccCCCC------ChhhHHHHHHHHHHHhhc
Q 043604 31 LEDTNGIFTCEICIEPISANDKFRNKDLCS------HHFCQDCIAKYIEAKVQD 78 (268)
Q Consensus 31 ~~~~~~~~~C~IC~~~~~~~~~~~~~~~C~------H~fC~~Cl~~~~~~~i~~ 78 (268)
........+|.||++.+...+.+ +..+|+ |.||.+|++.|-...-++
T Consensus 20 ~~w~~~~~EC~IC~~~I~~~~Gv-V~vt~~g~lnLEkmfc~~C~~rw~~~~~rD 72 (134)
T PF05883_consen 20 DQWPRCTVECQICFDRIDNNDGV-VYVTDGGTLNLEKMFCADCDKRWRRERNRD 72 (134)
T ss_pred HHccccCeeehhhhhhhhcCCCE-EEEecCCeehHHHHHHHHHHHHHHhhccCC
Confidence 33355588999999999763444 355664 899999999995444444
No 63
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=93.03 E-value=0.06 Score=51.96 Aligned_cols=59 Identities=25% Similarity=0.563 Sum_probs=45.6
Q ss_pred hhcCCCcccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCC
Q 043604 31 LEDTNGIFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCD 92 (268)
Q Consensus 31 ~~~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~ 92 (268)
.+.....++|.||++.+.....+..-..|=|+|...|++.|..+.-.+ +...-+||. |.
T Consensus 185 ~~l~~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~-~~~~WrCP~--Cq 243 (950)
T KOG1952|consen 185 EQLSNRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKT-GQDGWRCPA--CQ 243 (950)
T ss_pred HHHhcCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhc-cCccccCCc--cc
Confidence 334567899999999997776655566688999999999999984444 345578988 76
No 64
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.77 E-value=0.063 Score=46.92 Aligned_cols=49 Identities=24% Similarity=0.526 Sum_probs=36.3
Q ss_pred CCCcccccccccCCcCCcCccccCCCCCh-hhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCC
Q 043604 34 TNGIFTCEICIEPISANDKFRNKDLCSHH-FCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLD 96 (268)
Q Consensus 34 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~ 96 (268)
+....+|.||+++... . .+++|+|. .|.+|.+..- +.. =.||. |+.+|.
T Consensus 287 ~~~gkeCVIClse~rd--t--~vLPCRHLCLCs~Ca~~Lr---~q~-----n~CPI--CRqpi~ 336 (349)
T KOG4265|consen 287 SESGKECVICLSESRD--T--VVLPCRHLCLCSGCAKSLR---YQT-----NNCPI--CRQPIE 336 (349)
T ss_pred ccCCCeeEEEecCCcc--e--EEecchhhehhHhHHHHHH---Hhh-----cCCCc--cccchH
Confidence 4557899999998743 2 57999996 7999988766 222 24998 988754
No 65
>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=92.43 E-value=0.12 Score=30.03 Aligned_cols=33 Identities=24% Similarity=0.360 Sum_probs=23.7
Q ss_pred ccCCccccCceeeeccccccCCcCeeeCccccccc
Q 043604 127 SYCPNRNCMALVVNGCEINYGTLKKARCPNCTQWF 161 (268)
Q Consensus 127 ~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~ 161 (268)
+.|| .|+..+..+..........+.|+.|+..|
T Consensus 3 ~~CP--~C~~~~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCP--NCKTSFRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred EECC--CCCCEEEeCHHHcCCCCCEEECCCCCCEE
Confidence 4688 89998887765432234579999998765
No 66
>PF04641 Rtf2: Rtf2 RING-finger
Probab=92.22 E-value=0.15 Score=43.49 Aligned_cols=72 Identities=17% Similarity=0.368 Sum_probs=54.2
Q ss_pred CCCcccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCCHHHHhhcCCh-hHHHHH
Q 043604 34 TNGIFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLDPFSCKLMIPS-NLFSKW 112 (268)
Q Consensus 34 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~~l~~-~~~~~~ 112 (268)
....+.|+|...++.....|..+.+|||+|...+|+..- .+ -.||. |+.++...+|-.|-++ +.++.+
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----KS-----KKCPV--CGKPFTEEDIIPLNPPEEELEKL 178 (260)
T ss_pred CCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc----cc-----ccccc--cCCccccCCEEEecCCccHHHHH
Confidence 466799999999997666787788999999999998872 12 23998 9999998888776663 344444
Q ss_pred HHHH
Q 043604 113 CDVL 116 (268)
Q Consensus 113 ~~~~ 116 (268)
...+
T Consensus 179 ~~~~ 182 (260)
T PF04641_consen 179 RERM 182 (260)
T ss_pred HHHH
Confidence 4443
No 67
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=92.00 E-value=0.12 Score=44.68 Aligned_cols=50 Identities=34% Similarity=0.770 Sum_probs=38.1
Q ss_pred CCCcccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCC
Q 043604 34 TNGIFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLD 96 (268)
Q Consensus 34 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~ 96 (268)
-....+|.+|-.-+.... ....|-|.||++||-.|++.. ..||. |+..|.
T Consensus 12 ~n~~itC~LC~GYliDAT---TI~eCLHTFCkSCivk~l~~~--------~~CP~--C~i~ih 61 (331)
T KOG2660|consen 12 LNPHITCRLCGGYLIDAT---TITECLHTFCKSCIVKYLEES--------KYCPT--CDIVIH 61 (331)
T ss_pred cccceehhhccceeecch---hHHHHHHHHHHHHHHHHHHHh--------ccCCc--cceecc
Confidence 456789999988775443 356799999999999999871 46888 875543
No 68
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=91.86 E-value=0.13 Score=32.03 Aligned_cols=26 Identities=38% Similarity=0.805 Sum_probs=19.9
Q ss_pred ccCCCCCceeeecCC--cCeEEec-CCc-c
Q 043604 199 ARCPACGSCVERKEG--CRVMYCS-CHS-V 224 (268)
Q Consensus 199 k~CP~C~~~iek~~G--Cnhm~C~-C~~-F 224 (268)
+.||.|+.++...++ -+++.|+ ||+ +
T Consensus 1 ~FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~ 30 (52)
T smart00661 1 KFCPKCGNMLIPKEGKEKRRFVCRKCGYEE 30 (52)
T ss_pred CCCCCCCCccccccCCCCCEEECCcCCCeE
Confidence 369999998877644 4688897 987 5
No 69
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.72 E-value=0.11 Score=49.29 Aligned_cols=49 Identities=24% Similarity=0.644 Sum_probs=37.4
Q ss_pred CCcccccccccCCcCCcCc-cccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCC
Q 043604 35 NGIFTCEICIEPISANDKF-RNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQ 93 (268)
Q Consensus 35 ~~~~~C~IC~~~~~~~~~~-~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~ 93 (268)
.....|.||.|+....... ...++|+|.|+..|++.|++.+ -.||. |..
T Consensus 289 ~~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~--------qtCP~--CR~ 338 (543)
T KOG0802|consen 289 LSDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQ--------QTCPT--CRT 338 (543)
T ss_pred hcCCeeeeechhhccccccccceeecccchHHHHHHHHHHHh--------CcCCc--chh
Confidence 3467899999998653221 2578999999999999999972 35887 665
No 70
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.51 E-value=0.059 Score=33.69 Aligned_cols=45 Identities=27% Similarity=0.518 Sum_probs=32.4
Q ss_pred ccccccccCCcCCcCccccCCCCCh-hhHHHHHHHHHHHhhcCCCceeccCCCCCCCCC
Q 043604 38 FTCEICIEPISANDKFRNKDLCSHH-FCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFL 95 (268)
Q Consensus 38 ~~C~IC~~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i 95 (268)
-+|.||+|.-..+ ++..|||. +|.+|-....+. . .=.||. |..+|
T Consensus 8 dECTICye~pvds----VlYtCGHMCmCy~Cg~rl~~~-~------~g~CPi--CRapi 53 (62)
T KOG4172|consen 8 DECTICYEHPVDS----VLYTCGHMCMCYACGLRLKKA-L------HGCCPI--CRAPI 53 (62)
T ss_pred cceeeeccCcchH----HHHHcchHHhHHHHHHHHHHc-c------CCcCcc--hhhHH
Confidence 6799999965332 46789996 799998877654 2 235887 87654
No 71
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=91.15 E-value=0.063 Score=44.46 Aligned_cols=46 Identities=28% Similarity=0.662 Sum_probs=33.5
Q ss_pred cccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCC
Q 043604 37 IFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLD 96 (268)
Q Consensus 37 ~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~ 96 (268)
-+.|..|+---+ .+.| .++.|.|+||..|.+.-. +-.||. |+..|.
T Consensus 3 ~VhCn~C~~~~~-~~~f-~LTaC~HvfC~~C~k~~~----------~~~C~l--Ckk~ir 48 (233)
T KOG4739|consen 3 FVHCNKCFRFPS-QDPF-FLTACRHVFCEPCLKASS----------PDVCPL--CKKSIR 48 (233)
T ss_pred eEEeccccccCC-CCce-eeeechhhhhhhhcccCC----------cccccc--ccceee
Confidence 356888887554 6677 488999999999986432 227988 987654
No 72
>PHA00626 hypothetical protein
Probab=90.58 E-value=0.22 Score=31.30 Aligned_cols=26 Identities=31% Similarity=0.791 Sum_probs=19.9
Q ss_pred cCCCCCc-eeeecCCcCe----EEec-CCc-cc
Q 043604 200 RCPACGS-CVERKEGCRV----MYCS-CHS-VT 225 (268)
Q Consensus 200 ~CP~C~~-~iek~~GCnh----m~C~-C~~-FC 225 (268)
.||+|+. -|.|.+-|+. -.|. ||+ |=
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft 34 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDS 34 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCeec
Confidence 5999999 4888876644 7787 888 74
No 73
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.55 E-value=0.21 Score=43.58 Aligned_cols=37 Identities=27% Similarity=0.455 Sum_probs=28.2
Q ss_pred CCCcccccccccCCcCCcCccccCCCCChhhHHHHHHHHHH
Q 043604 34 TNGIFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEA 74 (268)
Q Consensus 34 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~ 74 (268)
.++...|+||+..-. +. +..+|+|.-|..|+.+|+-+
T Consensus 419 ~sEd~lCpICyA~pi-~A---vf~PC~H~SC~~CI~qHlmN 455 (489)
T KOG4692|consen 419 DSEDNLCPICYAGPI-NA---VFAPCSHRSCYGCITQHLMN 455 (489)
T ss_pred CcccccCcceecccc-hh---hccCCCCchHHHHHHHHHhc
Confidence 356678999997542 22 35899999999999999843
No 74
>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=90.19 E-value=0.11 Score=42.87 Aligned_cols=51 Identities=20% Similarity=0.543 Sum_probs=36.6
Q ss_pred cccccccccCCcCCcCc-cccCC-CCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCC
Q 043604 37 IFTCEICIEPISANDKF-RNKDL-CSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQF 94 (268)
Q Consensus 37 ~~~C~IC~~~~~~~~~~-~~~~~-C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~ 94 (268)
..-|+||..+...+..+ +...+ |-|.+|.+|+..-+. ..|-.||.++|+..
T Consensus 10 d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs-------~GpAqCP~~gC~kI 62 (314)
T COG5220 10 DRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFS-------RGPAQCPYKGCGKI 62 (314)
T ss_pred cccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhc-------CCCCCCCCccHHHH
Confidence 34699998765544332 22233 999999999988773 56788999999843
No 75
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=90.01 E-value=0.16 Score=26.09 Aligned_cols=9 Identities=56% Similarity=1.542 Sum_probs=5.6
Q ss_pred CCCCCceee
Q 043604 201 CPACGSCVE 209 (268)
Q Consensus 201 CP~C~~~ie 209 (268)
||+|+..|+
T Consensus 2 Cp~CG~~~~ 10 (23)
T PF13240_consen 2 CPNCGAEIE 10 (23)
T ss_pred CcccCCCCC
Confidence 666666665
No 76
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=89.91 E-value=0.081 Score=44.90 Aligned_cols=26 Identities=12% Similarity=0.002 Sum_probs=21.2
Q ss_pred eEEec-CCc-ccccccccccCCCCCCCC
Q 043604 216 VMYCS-CHS-VTYSRAKHISLRKHSTRG 241 (268)
Q Consensus 216 hm~C~-C~~-FC~~C~~~~~~~~~~~~~ 241 (268)
|-+|. ||| |||.|...|-.....|+-
T Consensus 251 ~pSaTpCGHiFCWsCI~~w~~ek~eCPl 278 (293)
T KOG0317|consen 251 NPSATPCGHIFCWSCILEWCSEKAECPL 278 (293)
T ss_pred CCCcCcCcchHHHHHHHHHHccccCCCc
Confidence 45787 999 999999999887666554
No 77
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=89.82 E-value=0.33 Score=29.53 Aligned_cols=27 Identities=30% Similarity=0.589 Sum_probs=18.6
Q ss_pred ccCCCCCceeeecCCcCeEEec-CCc-cc
Q 043604 199 ARCPACGSCVERKEGCRVMYCS-CHS-VT 225 (268)
Q Consensus 199 k~CP~C~~~iek~~GCnhm~C~-C~~-FC 225 (268)
-+||+|+..++-..+=..++|. ||. +=
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGYRIL 32 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCCeEE
Confidence 4688888887776544467786 776 53
No 78
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=89.31 E-value=0.19 Score=26.58 Aligned_cols=11 Identities=36% Similarity=1.117 Sum_probs=7.1
Q ss_pred ccCCCCCceee
Q 043604 199 ARCPACGSCVE 209 (268)
Q Consensus 199 k~CP~C~~~ie 209 (268)
+.||+|+..|.
T Consensus 3 ~~Cp~Cg~~~~ 13 (26)
T PF13248_consen 3 MFCPNCGAEID 13 (26)
T ss_pred CCCcccCCcCC
Confidence 46777777555
No 79
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.59 E-value=0.11 Score=43.64 Aligned_cols=58 Identities=24% Similarity=0.386 Sum_probs=42.4
Q ss_pred CcccccccccCCcCCc-------CccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCCHHHHhh
Q 043604 36 GIFTCEICIEPISAND-------KFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLDPFSCKL 102 (268)
Q Consensus 36 ~~~~C~IC~~~~~~~~-------~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~ 102 (268)
....|.||-..+..+. +. ..++|+|.|...|++.|...- ..-.||- |++.++...+.+
T Consensus 223 ~d~vCaVCg~~~~~s~~eegvient-y~LsCnHvFHEfCIrGWcivG------KkqtCPY--CKekVdl~rmfs 287 (328)
T KOG1734|consen 223 SDSVCAVCGQQIDVSVDEEGVIENT-YKLSCNHVFHEFCIRGWCIVG------KKQTCPY--CKEKVDLKRMFS 287 (328)
T ss_pred CcchhHhhcchheeecchhhhhhhh-eeeecccchHHHhhhhheeec------CCCCCch--HHHHhhHhhhcc
Confidence 3567999987665432 22 468999999999999998532 2357998 999888765543
No 80
>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=88.53 E-value=0.69 Score=25.69 Aligned_cols=26 Identities=23% Similarity=0.534 Sum_probs=16.7
Q ss_pred cccCCCCCceeeecCCcCeEEec-CCc
Q 043604 198 WARCPACGSCVERKEGCRVMYCS-CHS 223 (268)
Q Consensus 198 ~k~CP~C~~~iek~~GCnhm~C~-C~~ 223 (268)
.+-||.|+.+.+...+=--|.|. |++
T Consensus 3 ~rfC~~CG~~t~~~~~g~~r~C~~Cg~ 29 (32)
T PF09297_consen 3 HRFCGRCGAPTKPAPGGWARRCPSCGH 29 (32)
T ss_dssp TSB-TTT--BEEE-SSSS-EEESSSS-
T ss_pred CcccCcCCccccCCCCcCEeECCCCcC
Confidence 47899999999999887788887 886
No 81
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.32 E-value=0.077 Score=46.26 Aligned_cols=49 Identities=31% Similarity=0.693 Sum_probs=34.9
Q ss_pred CCCcccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCC
Q 043604 34 TNGIFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQF 94 (268)
Q Consensus 34 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~ 94 (268)
-...+.|+||++-+... + ....|.|.||.+|+..-+...- =.||. |...
T Consensus 40 ~~~~v~c~icl~llk~t--m-ttkeClhrfc~~ci~~a~r~gn-------~ecpt--cRk~ 88 (381)
T KOG0311|consen 40 FDIQVICPICLSLLKKT--M-TTKECLHRFCFDCIWKALRSGN-------NECPT--CRKK 88 (381)
T ss_pred hhhhhccHHHHHHHHhh--c-ccHHHHHHHHHHHHHHHHHhcC-------CCCch--HHhh
Confidence 45568899999987543 2 3567999999999987665332 24887 7643
No 82
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.14 E-value=0.32 Score=43.03 Aligned_cols=49 Identities=24% Similarity=0.699 Sum_probs=35.7
Q ss_pred cccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCC
Q 043604 37 IFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCD 92 (268)
Q Consensus 37 ~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~ 92 (268)
...|.||-+-++....+...-.|||.|...|+..|++..-.+ -.||. |.
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 357999976666555554445599999999999999865442 35777 65
No 83
>PHA03096 p28-like protein; Provisional
Probab=88.00 E-value=0.37 Score=41.52 Aligned_cols=40 Identities=25% Similarity=0.453 Sum_probs=30.9
Q ss_pred ccccccccCCcCC----cCccccCCCCChhhHHHHHHHHHHHhh
Q 043604 38 FTCEICIEPISAN----DKFRNKDLCSHHFCQDCIAKYIEAKVQ 77 (268)
Q Consensus 38 ~~C~IC~~~~~~~----~~~~~~~~C~H~fC~~Cl~~~~~~~i~ 77 (268)
..|.||++..... ..|-.+..|.|.||..|++.|..+...
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 6799999876532 234345579999999999999988763
No 84
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.86 E-value=0.32 Score=43.34 Aligned_cols=51 Identities=27% Similarity=0.626 Sum_probs=38.5
Q ss_pred cccccccccCCcCC-cCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCC
Q 043604 37 IFTCEICIEPISAN-DKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFL 95 (268)
Q Consensus 37 ~~~C~IC~~~~~~~-~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i 95 (268)
-.+|+||++.+... +...+.+.|+|.|=.+|++.|+. ......||. |...-
T Consensus 4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~------k~~~~~cp~--c~~ka 55 (463)
T KOG1645|consen 4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLG------KKTKMQCPL--CSGKA 55 (463)
T ss_pred cccCceeeeeeeecCceEEeeecccccccHHHHHHHHh------hhhhhhCcc--cCChh
Confidence 35799999977543 33336788999999999999993 345578998 87543
No 85
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=87.66 E-value=0.49 Score=29.35 Aligned_cols=28 Identities=18% Similarity=0.562 Sum_probs=20.4
Q ss_pred cCCccccCceeeeccccccCCcCeeeCcccccc
Q 043604 128 YCPNRNCMALVVNGCEINYGTLKKARCPNCTQW 160 (268)
Q Consensus 128 ~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~ 160 (268)
+|| .|+.++...... ....+.|+.|++.
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 788 899988776543 1247889988864
No 86
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=87.60 E-value=0.4 Score=29.79 Aligned_cols=24 Identities=29% Similarity=0.628 Sum_probs=18.3
Q ss_pred cccCCCCCc-eeeecCCcCeEEec-CCc
Q 043604 198 WARCPACGS-CVERKEGCRVMYCS-CHS 223 (268)
Q Consensus 198 ~k~CP~C~~-~iek~~GCnhm~C~-C~~ 223 (268)
.+.||+|+. .+.... +.++|. ||+
T Consensus 20 ~~fCP~Cg~~~m~~~~--~r~~C~~Cgy 45 (50)
T PRK00432 20 NKFCPRCGSGFMAEHL--DRWHCGKCGY 45 (50)
T ss_pred cCcCcCCCcchheccC--CcEECCCcCC
Confidence 468999998 444444 789997 998
No 87
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=87.40 E-value=0.32 Score=28.93 Aligned_cols=26 Identities=31% Similarity=0.786 Sum_probs=20.5
Q ss_pred hCCcccCCCCCceeeecCCcCeEEec---CCc-c
Q 043604 195 RMHWARCPACGSCVERKEGCRVMYCS---CHS-V 224 (268)
Q Consensus 195 ~~~~k~CP~C~~~iek~~GCnhm~C~---C~~-F 224 (268)
..++++||+|++.- |+.-+.|+ |++ |
T Consensus 8 lRGirkCp~CGt~N----G~R~~~CKN~~C~~~~ 37 (44)
T PF14952_consen 8 LRGIRKCPKCGTYN----GTRGLSCKNKSCPQVF 37 (44)
T ss_pred HhccccCCcCcCcc----CcccccccCCccchhh
Confidence 45779999999976 77778885 776 5
No 88
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=86.98 E-value=0.55 Score=33.20 Aligned_cols=28 Identities=32% Similarity=0.808 Sum_probs=21.9
Q ss_pred cCCCCCceeeec--CCcCeEEec-CCc-cccc
Q 043604 200 RCPACGSCVERK--EGCRVMYCS-CHS-VTYS 227 (268)
Q Consensus 200 ~CP~C~~~iek~--~GCnhm~C~-C~~-FC~~ 227 (268)
-||.|+.++.-. +-||...|+ |++ |=-.
T Consensus 3 FCP~Cgn~Live~g~~~~rf~C~tCpY~~~I~ 34 (105)
T KOG2906|consen 3 FCPTCGNMLIVESGESCNRFSCRTCPYVFPIS 34 (105)
T ss_pred ccCCCCCEEEEecCCeEeeEEcCCCCceeeEe
Confidence 699999865444 459999998 999 7655
No 89
>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=86.91 E-value=0.42 Score=27.27 Aligned_cols=28 Identities=25% Similarity=0.651 Sum_probs=19.3
Q ss_pred ccCCccccCceeeeccccccCCcCeeeCcccccc
Q 043604 127 SYCPNRNCMALVVNGCEINYGTLKKARCPNCTQW 160 (268)
Q Consensus 127 ~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~ 160 (268)
++|| .|++++.+..... ..+.|+.|++.
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 6888 9999999877652 22378888764
No 90
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=86.74 E-value=0.3 Score=40.56 Aligned_cols=59 Identities=14% Similarity=0.239 Sum_probs=44.9
Q ss_pred CCcccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCCHHHHhhc
Q 043604 35 NGIFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLDPFSCKLM 103 (268)
Q Consensus 35 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~~ 103 (268)
+..+.|+||-+++.+.-...++.+|||+||.+|+..+|..- ..||. |+.++...+|-.|
T Consensus 219 s~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D--------~v~pv--~d~plkdrdiI~L 277 (303)
T KOG3039|consen 219 SKRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKD--------MVDPV--TDKPLKDRDIIGL 277 (303)
T ss_pred ccceecccchhhhcCccceEEeccCCcEeeHHHHHHhcccc--------ccccC--CCCcCcccceEee
Confidence 46789999999997654455677899999999999988532 34577 8888777766543
No 91
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=86.66 E-value=0.46 Score=45.76 Aligned_cols=25 Identities=20% Similarity=0.398 Sum_probs=16.5
Q ss_pred ccCCCCCceeeecCCcCeEEecCCc-ccccccccccC
Q 043604 199 ARCPACGSCVERKEGCRVMYCSCHS-VTYSRAKHISL 234 (268)
Q Consensus 199 k~CP~C~~~iek~~GCnhm~C~C~~-FC~~C~~~~~~ 234 (268)
+.||+|+..+. =+. ||-.||.+...
T Consensus 28 ~~Cp~CG~~~~-----------~~~~fC~~CG~~~~~ 53 (645)
T PRK14559 28 KPCPQCGTEVP-----------VDEAHCPNCGAETGT 53 (645)
T ss_pred CcCCCCCCCCC-----------cccccccccCCcccc
Confidence 35777777655 356 88888876544
No 92
>PLN03086 PRLI-interacting factor K; Provisional
Probab=86.59 E-value=0.95 Score=42.72 Aligned_cols=59 Identities=22% Similarity=0.560 Sum_probs=39.6
Q ss_pred CceeccCCCCCCCCCCHHHHhhcCChhHHHHHHHHHHhhhhcCCCcccCCccccCceeeeccccccCCcCeeeCcccccc
Q 043604 81 TAKIECPGVHCDQFLDPFSCKLMIPSNLFSKWCDVLFEDYVLGFERSYCPNRNCMALVVNGCEINYGTLKKARCPNCTQW 160 (268)
Q Consensus 81 ~~~i~CP~~~C~~~i~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~ 160 (268)
...+.||. |...++...+...+. +- ....+.||+.+|+..+...... ..+.|+.|+..
T Consensus 405 ~~~V~C~N--C~~~i~l~~l~lHe~------~C---------~r~~V~Cp~~~Cg~v~~r~el~-----~H~~C~~Cgk~ 462 (567)
T PLN03086 405 VDTVECRN--CKHYIPSRSIALHEA------YC---------SRHNVVCPHDGCGIVLRVEEAK-----NHVHCEKCGQA 462 (567)
T ss_pred CCeEECCC--CCCccchhHHHHHHh------hC---------CCcceeCCcccccceeeccccc-----cCccCCCCCCc
Confidence 34578998 988777665553221 00 1235779987899999766655 55789999877
Q ss_pred c
Q 043604 161 F 161 (268)
Q Consensus 161 ~ 161 (268)
|
T Consensus 463 f 463 (567)
T PLN03086 463 F 463 (567)
T ss_pred c
Confidence 6
No 93
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=85.92 E-value=0.29 Score=43.42 Aligned_cols=45 Identities=24% Similarity=0.604 Sum_probs=32.8
Q ss_pred CCCcccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCC
Q 043604 34 TNGIFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPG 88 (268)
Q Consensus 34 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~ 88 (268)
.+...-|.||.+.-.. + ..-+|||..|..||..|-.+.- .-.||.
T Consensus 366 gsTFeLCKICaendKd---v-kIEPCGHLlCt~CLa~WQ~sd~------gq~CPF 410 (563)
T KOG1785|consen 366 GSTFELCKICAENDKD---V-KIEPCGHLLCTSCLAAWQDSDE------GQTCPF 410 (563)
T ss_pred cchHHHHHHhhccCCC---c-ccccccchHHHHHHHhhcccCC------CCCCCc
Confidence 4455679999987643 2 4689999999999999864321 235888
No 94
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=85.31 E-value=0.49 Score=41.09 Aligned_cols=45 Identities=27% Similarity=0.721 Sum_probs=34.9
Q ss_pred CCCcccccccccCCcCCcCccccCCC--CChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCC
Q 043604 34 TNGIFTCEICIEPISANDKFRNKDLC--SHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLD 96 (268)
Q Consensus 34 ~~~~~~C~IC~~~~~~~~~~~~~~~C--~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~ 96 (268)
....++|+||++.+.++ ...| ||..|.+|-. . ..-+||. |..+|.
T Consensus 45 ~~~lleCPvC~~~l~~P-----i~QC~nGHlaCssC~~-----~------~~~~CP~--Cr~~~g 91 (299)
T KOG3002|consen 45 DLDLLDCPVCFNPLSPP-----IFQCDNGHLACSSCRT-----K------VSNKCPT--CRLPIG 91 (299)
T ss_pred chhhccCchhhccCccc-----ceecCCCcEehhhhhh-----h------hcccCCc--cccccc
Confidence 45678999999999654 3556 8999999976 2 2357999 988877
No 95
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=85.02 E-value=0.57 Score=45.22 Aligned_cols=21 Identities=10% Similarity=0.324 Sum_probs=15.1
Q ss_pred CCCChhhHHHHHHHHHHHhhc
Q 043604 58 LCSHHFCQDCIAKYIEAKVQD 78 (268)
Q Consensus 58 ~C~H~fC~~Cl~~~~~~~i~~ 78 (268)
.|+|.+|..||..+....+..
T Consensus 120 ~~~~~~CP~Ci~s~~DqL~~~ 140 (1134)
T KOG0825|consen 120 THVENQCPNCLKSCNDQLEES 140 (1134)
T ss_pred hhhhhhhhHHHHHHHHHhhcc
Confidence 477888888888777766654
No 96
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=84.37 E-value=0.93 Score=29.01 Aligned_cols=30 Identities=23% Similarity=0.533 Sum_probs=20.3
Q ss_pred ccCCccccCceeeeccccccCCcCeeeCccccccccc
Q 043604 127 SYCPNRNCMALVVNGCEINYGTLKKARCPNCTQWFCF 163 (268)
Q Consensus 127 ~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~C~ 163 (268)
..|. .|+..+..... ...+.||.||...=+
T Consensus 8 ~~Ct--SCg~~i~~~~~-----~~~F~CPnCG~~~I~ 37 (59)
T PRK14890 8 PKCT--SCGIEIAPREK-----AVKFLCPNCGEVIIY 37 (59)
T ss_pred cccc--CCCCcccCCCc-----cCEeeCCCCCCeeEe
Confidence 4565 78877765443 378999999977433
No 97
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=84.29 E-value=1 Score=25.48 Aligned_cols=25 Identities=32% Similarity=0.845 Sum_probs=13.1
Q ss_pred ccCCCCCceeeec----CCcCeEEec-CCc
Q 043604 199 ARCPACGSCVERK----EGCRVMYCS-CHS 223 (268)
Q Consensus 199 k~CP~C~~~iek~----~GCnhm~C~-C~~ 223 (268)
|-||.|+.+++.. ++=..+.|. ||+
T Consensus 1 kfC~~CG~~l~~~ip~gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 1 KFCPQCGGPLERRIPEGDDRERLVCPACGF 30 (34)
T ss_dssp -B-TTT--B-EEE--TT-SS-EEEETTTTE
T ss_pred CccccccChhhhhcCCCCCccceECCCCCC
Confidence 4688999888875 445567786 876
No 98
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=84.27 E-value=0.87 Score=38.91 Aligned_cols=50 Identities=24% Similarity=0.487 Sum_probs=38.8
Q ss_pred CCCcccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCC
Q 043604 34 TNGIFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQ 93 (268)
Q Consensus 34 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~ 93 (268)
......|+||.+.+..+......++|+|..-..|+..++.. . .+||. |..
T Consensus 155 ~~~~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~-------~-y~CP~--C~~ 204 (276)
T KOG1940|consen 155 RSSEFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICE-------G-YTCPI--CSK 204 (276)
T ss_pred hcccCCCchhHHHhccccccCCccCcccchHHHHHHHHhcc-------C-CCCCc--ccc
Confidence 34455699999988776555578899999999999988742 2 78998 876
No 99
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=84.05 E-value=0.71 Score=42.60 Aligned_cols=40 Identities=18% Similarity=0.385 Sum_probs=33.6
Q ss_pred CcccCC--CCCceeee-cCCcCeEEecCCc-ccccccccccCCC
Q 043604 197 HWARCP--ACGSCVER-KEGCRVMYCSCHS-VTYSRAKHISLRK 236 (268)
Q Consensus 197 ~~k~CP--~C~~~iek-~~GCnhm~C~C~~-FC~~C~~~~~~~~ 236 (268)
..+-|| .|+..+.- .+...-+.|.|++ |||.|+.+|....
T Consensus 157 ~lkwCP~~~C~~av~~~~~~~~~v~C~~g~~FC~~C~~~~H~p~ 200 (444)
T KOG1815|consen 157 PLKWCPAPGCGLAVKFGSLESVEVDCGCGHEFCFACGEESHSPV 200 (444)
T ss_pred ccccCCCCCCCceeeccCCCccceeCCCCchhHhhccccccCCC
Confidence 356676 69999988 7889999999999 9999998887643
No 100
>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=83.54 E-value=1.8 Score=36.98 Aligned_cols=50 Identities=22% Similarity=0.564 Sum_probs=34.4
Q ss_pred cccccccCCcC-CcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCCH
Q 043604 39 TCEICIEPISA-NDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLDP 97 (268)
Q Consensus 39 ~C~IC~~~~~~-~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~ 97 (268)
.|++|-.+... ++.+....+|+|..|.+|+-..+. ..+-.||. |...+-.
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~-------~g~~~Cpe--C~~iLRk 52 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFS-------LGPAQCPE--CMVILRK 52 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHh-------cCCCCCCc--ccchhhh
Confidence 48888664433 344434458999999999988774 44567995 9876543
No 101
>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=82.74 E-value=1.2 Score=26.35 Aligned_cols=23 Identities=43% Similarity=1.113 Sum_probs=18.1
Q ss_pred cccCCCCCceeee-cCCcCeEEec-CC
Q 043604 198 WARCPACGSCVER-KEGCRVMYCS-CH 222 (268)
Q Consensus 198 ~k~CP~C~~~iek-~~GCnhm~C~-C~ 222 (268)
...||.|++|+.+ .+| .+.|. |+
T Consensus 17 ~~~Cp~C~~PL~~~k~g--~~~Cv~C~ 41 (41)
T PF06677_consen 17 DEHCPDCGTPLMRDKDG--KIYCVSCG 41 (41)
T ss_pred cCccCCCCCeeEEecCC--CEECCCCC
Confidence 3789999999999 466 57786 74
No 102
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=82.21 E-value=1.5 Score=26.56 Aligned_cols=28 Identities=25% Similarity=0.367 Sum_probs=21.5
Q ss_pred ccCCccccCceeeeccccccCCcCeeeCccccccc
Q 043604 127 SYCPNRNCMALVVNGCEINYGTLKKARCPNCTQWF 161 (268)
Q Consensus 127 ~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~ 161 (268)
..|| +|+..+..+... ..+.||.||..+
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 4577 899988887654 378999998765
No 103
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=82.19 E-value=1.7 Score=27.74 Aligned_cols=34 Identities=26% Similarity=0.627 Sum_probs=23.5
Q ss_pred cccCCccccCceeeeccccccCCcCeeeCcccccccccccc
Q 043604 126 RSYCPNRNCMALVVNGCEINYGTLKKARCPNCTQWFCFQCK 166 (268)
Q Consensus 126 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~ 166 (268)
...|. .|+..+.+.... ..+.||.||...=.+|.
T Consensus 9 ~~~Ct--SCg~~i~p~e~~-----v~F~CPnCGe~~I~Rc~ 42 (61)
T COG2888 9 PPVCT--SCGREIAPGETA-----VKFPCPNCGEVEIYRCA 42 (61)
T ss_pred Cceec--cCCCEeccCCce-----eEeeCCCCCceeeehhh
Confidence 45666 788888665543 78999999966555444
No 104
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=81.55 E-value=0.95 Score=39.53 Aligned_cols=51 Identities=20% Similarity=0.614 Sum_probs=34.7
Q ss_pred CCCcccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCC
Q 043604 34 TNGIFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLD 96 (268)
Q Consensus 34 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~ 96 (268)
+.....|.||.+.+. +..+++|+|.+|.-|-...-..-. .-.||. |.....
T Consensus 58 DEen~~C~ICA~~~T----Ys~~~PC~H~~CH~Ca~RlRALY~------~K~C~~--CrTE~e 108 (493)
T COG5236 58 DEENMNCQICAGSTT----YSARYPCGHQICHACAVRLRALYM------QKGCPL--CRTETE 108 (493)
T ss_pred ccccceeEEecCCce----EEEeccCCchHHHHHHHHHHHHHh------ccCCCc--cccccc
Confidence 445678999998774 336799999999999765433222 234777 875433
No 105
>PF14353 CpXC: CpXC protein
Probab=81.15 E-value=1.1 Score=33.63 Aligned_cols=26 Identities=19% Similarity=0.436 Sum_probs=15.9
Q ss_pred hHHHHHHHH--hCCcccCCCCCceeeec
Q 043604 186 DIAFGKLVE--RMHWARCPACGSCVERK 211 (268)
Q Consensus 186 ~~~~~~~~~--~~~~k~CP~C~~~iek~ 211 (268)
+..+.+.+. +...-.||+|+..+.-.
T Consensus 24 ~p~l~e~il~g~l~~~~CP~Cg~~~~~~ 51 (128)
T PF14353_consen 24 DPELKEKILDGSLFSFTCPSCGHKFRLE 51 (128)
T ss_pred CHHHHHHHHcCCcCEEECCCCCCceecC
Confidence 444444443 33458999999877644
No 106
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=80.41 E-value=2.4 Score=35.62 Aligned_cols=57 Identities=23% Similarity=0.480 Sum_probs=41.3
Q ss_pred CCcccccccccCCcCCcCccccCCCC-----ChhhHHHHHHHHHHHhhcCCCceeccCCCCCCC
Q 043604 35 NGIFTCEICIEPISANDKFRNKDLCS-----HHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQ 93 (268)
Q Consensus 35 ~~~~~C~IC~~~~~~~~~~~~~~~C~-----H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~ 93 (268)
...-.|-|||.+......-.-+-+|. |....+||..|+..+-......++.||. |..
T Consensus 18 e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~Q--CqT 79 (293)
T KOG3053|consen 18 ELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQ--CQT 79 (293)
T ss_pred ccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechh--hcc
Confidence 34567999998775432211245663 7899999999998777654677899999 974
No 107
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=80.36 E-value=1.3 Score=39.40 Aligned_cols=61 Identities=20% Similarity=0.415 Sum_probs=42.4
Q ss_pred CCcccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCCHHHHhhc
Q 043604 35 NGIFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLDPFSCKLM 103 (268)
Q Consensus 35 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~~ 103 (268)
...|.|+|=-+.-. .++-+..+.|||+.+++=+..... ++...++||- |......+..+++
T Consensus 332 HSvF~CPVlKeqts-deNPPm~L~CGHVISkdAlnrLS~-----ng~~sfKCPY--CP~e~~~~~~kql 392 (394)
T KOG2817|consen 332 HSVFICPVLKEQTS-DENPPMMLICGHVISKDALNRLSK-----NGSQSFKCPY--CPVEQLASDTKQL 392 (394)
T ss_pred cceeecccchhhcc-CCCCCeeeeccceecHHHHHHHhh-----CCCeeeeCCC--CCcccCHHhcccc
Confidence 45789999655442 223345789999999997766553 3445799999 9887777666553
No 108
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=80.07 E-value=3.8 Score=30.86 Aligned_cols=54 Identities=22% Similarity=0.589 Sum_probs=39.6
Q ss_pred CCCcccccccccCCcCCcCccc-cCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCC
Q 043604 34 TNGIFTCEICIEPISANDKFRN-KDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFL 95 (268)
Q Consensus 34 ~~~~~~C~IC~~~~~~~~~~~~-~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i 95 (268)
+.+..+|.||.|.... +.|.. ..-||-..|..|....++..- ....||. |+..+
T Consensus 77 d~~lYeCnIC~etS~e-e~FLKPneCCgY~iCn~Cya~LWK~~~-----~ypvCPv--CkTSF 131 (140)
T PF05290_consen 77 DPKLYECNICKETSAE-ERFLKPNECCGYSICNACYANLWKFCN-----LYPVCPV--CKTSF 131 (140)
T ss_pred CCCceeccCcccccch-hhcCCcccccchHHHHHHHHHHHHHcc-----cCCCCCc--ccccc
Confidence 4478999999998743 44522 223899999999999998754 3478999 87543
No 109
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=79.76 E-value=0.99 Score=44.63 Aligned_cols=54 Identities=22% Similarity=0.597 Sum_probs=38.5
Q ss_pred CCcccccccccCCcCCc-Ccc--ccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCC
Q 043604 35 NGIFTCEICIEPISAND-KFR--NKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLD 96 (268)
Q Consensus 35 ~~~~~C~IC~~~~~~~~-~~~--~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~ 96 (268)
++..+|.|||.-+...+ .++ ....|.|.|...|+-.|+.+.-++ +||. |+..|+
T Consensus 1467 sG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s------~CPl--CRseit 1523 (1525)
T COG5219 1467 SGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARS------NCPL--CRSEIT 1523 (1525)
T ss_pred CCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCC------CCCc--cccccc
Confidence 45678999997664222 111 234689999999999999876544 7998 887654
No 110
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=79.68 E-value=0.53 Score=29.69 Aligned_cols=48 Identities=19% Similarity=0.339 Sum_probs=32.0
Q ss_pred CcccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCCHHH
Q 043604 36 GIFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLDPFS 99 (268)
Q Consensus 36 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~ 99 (268)
....|..|...... ..+++|+|.+|..|+-. ...-.||. |+.+++..+
T Consensus 6 ~~~~~~~~~~~~~~----~~~~pCgH~I~~~~f~~----------~rYngCPf--C~~~~~~~~ 53 (55)
T PF14447_consen 6 PEQPCVFCGFVGTK----GTVLPCGHLICDNCFPG----------ERYNGCPF--CGTPFEFDD 53 (55)
T ss_pred cceeEEEccccccc----cccccccceeeccccCh----------hhccCCCC--CCCcccCCC
Confidence 34566667655422 25799999999999853 12235998 998876543
No 111
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=79.65 E-value=1.8 Score=39.26 Aligned_cols=38 Identities=21% Similarity=0.688 Sum_probs=30.1
Q ss_pred CCCcccccccccCCcCCcCccccCCCCChhhHHHHHHHHHH
Q 043604 34 TNGIFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEA 74 (268)
Q Consensus 34 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~ 74 (268)
......|++|...+..+ + ....|||.||..|+..+...
T Consensus 18 ~~~~l~C~~C~~vl~~p--~-~~~~cgh~fC~~C~~~~~~~ 55 (391)
T KOG0297|consen 18 LDENLLCPICMSVLRDP--V-QTTTCGHRFCAGCLLESLSN 55 (391)
T ss_pred CcccccCccccccccCC--C-CCCCCCCcccccccchhhcc
Confidence 35578899999988644 2 12589999999999998875
No 112
>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=79.37 E-value=2.2 Score=22.93 Aligned_cols=21 Identities=43% Similarity=0.907 Sum_probs=13.5
Q ss_pred cCCCCCceeeecCCcCeEEec
Q 043604 200 RCPACGSCVERKEGCRVMYCS 220 (268)
Q Consensus 200 ~CP~C~~~iek~~GCnhm~C~ 220 (268)
.||.|+..+.+.+|=-.+.|.
T Consensus 1 ~CP~C~s~l~~~~~ev~~~C~ 21 (28)
T PF03119_consen 1 TCPVCGSKLVREEGEVDIRCP 21 (28)
T ss_dssp B-TTT--BEEE-CCTTCEEE-
T ss_pred CcCCCCCEeEcCCCCEeEECC
Confidence 499999999999887777773
No 113
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=79.12 E-value=1.5 Score=26.95 Aligned_cols=26 Identities=27% Similarity=0.489 Sum_probs=18.2
Q ss_pred cccCCCCCceeeecCCcCeEEec-CCc
Q 043604 198 WARCPACGSCVERKEGCRVMYCS-CHS 223 (268)
Q Consensus 198 ~k~CP~C~~~iek~~GCnhm~C~-C~~ 223 (268)
-+.||+|+.-+.-..-=+...|. ||+
T Consensus 19 ~~~CPrCG~gvfmA~H~dR~~CGkCgy 45 (51)
T COG1998 19 NRFCPRCGPGVFMADHKDRWACGKCGY 45 (51)
T ss_pred cccCCCCCCcchhhhcCceeEeccccc
Confidence 47899999655544444577885 886
No 114
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=78.96 E-value=0.68 Score=45.33 Aligned_cols=42 Identities=21% Similarity=0.499 Sum_probs=33.0
Q ss_pred CCcccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhc
Q 043604 35 NGIFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQD 78 (268)
Q Consensus 35 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~ 78 (268)
.+.-+|.+|.-.+. ...| .+.+|||.|..+|+..++......
T Consensus 815 ep~d~C~~C~~~ll-~~pF-~vf~CgH~FH~~Cl~~~v~~~~~~ 856 (911)
T KOG2034|consen 815 EPQDSCDHCGRPLL-IKPF-YVFPCGHCFHRDCLIRHVLSLLSE 856 (911)
T ss_pred cCccchHHhcchhh-cCcc-eeeeccchHHHHHHHHHHHccccH
Confidence 34568999999884 4466 489999999999999988755443
No 115
>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=78.87 E-value=1.8 Score=36.30 Aligned_cols=38 Identities=24% Similarity=0.472 Sum_probs=26.3
Q ss_pred CCcccCCccccCceeeeccccc---------cCCcCeeeCccccccc
Q 043604 124 FERSYCPNRNCMALVVNGCEIN---------YGTLKKARCPNCTQWF 161 (268)
Q Consensus 124 ~~~~~Cp~~~C~~~~~~~~~~~---------~~~~~~~~C~~C~~~~ 161 (268)
..++.||.++|+.++....... ......+.|..|...|
T Consensus 121 S~rIaCPRp~CkRiI~L~~~~~~p~~~~~~~~p~~~rv~CghC~~~F 167 (256)
T PF09788_consen 121 SQRIACPRPNCKRIINLGPSHQGPVTPPVPTQPGSCRVICGHCSNTF 167 (256)
T ss_pred cccccCCCCCCcceEEeCCccCCCCCCCCCCCCCceeEECCCCCCcE
Confidence 4579999999999998766521 1134567777776655
No 116
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=77.88 E-value=7.4 Score=38.18 Aligned_cols=32 Identities=19% Similarity=0.479 Sum_probs=19.0
Q ss_pred cCCCCCceeeecCCcCeEEec-CC-----c-cccccccc
Q 043604 200 RCPACGSCVERKEGCRVMYCS-CH-----S-VTYSRAKH 231 (268)
Q Consensus 200 ~CP~C~~~iek~~GCnhm~C~-C~-----~-FC~~C~~~ 231 (268)
.||+|..++.--..=+.|.|. || . .|..||..
T Consensus 446 ~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 446 ECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred cCCCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCC
Confidence 566666655555444666665 66 2 46666655
No 117
>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=77.72 E-value=1.5 Score=31.69 Aligned_cols=25 Identities=40% Similarity=0.874 Sum_probs=19.6
Q ss_pred ccCCCCCceeeecCCcCeEEec-CCc-cc
Q 043604 199 ARCPACGSCVERKEGCRVMYCS-CHS-VT 225 (268)
Q Consensus 199 k~CP~C~~~iek~~GCnhm~C~-C~~-FC 225 (268)
+.||+|+.++...+| .+.|. |++ +=
T Consensus 1 ~fC~~Cg~~l~~~~~--~~~C~~C~~~~~ 27 (104)
T TIGR01384 1 KFCPKCGSLMTPKNG--VYVCPSCGYEKE 27 (104)
T ss_pred CCCcccCcccccCCC--eEECcCCCCccc
Confidence 369999999977654 78887 887 64
No 118
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=77.44 E-value=1.5 Score=29.64 Aligned_cols=56 Identities=21% Similarity=0.308 Sum_probs=20.7
Q ss_pred ccCceeeeccccccCCcCeeeCcccccccccccccccCCCCCcchhhcccchhhHHHHHHHHhCCcccCCCCCceeeecC
Q 043604 133 NCMALVVNGCEINYGTLKKARCPNCTQWFCFQCKLAWHAGYRCEESGNLRDWNDIAFGKLVERMHWARCPACGSCVERKE 212 (268)
Q Consensus 133 ~C~~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~tC~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~~iek~~ 212 (268)
-|+--+..... ....+-|..|+...|..|. +| -.+.+.+.||.|+++..+..
T Consensus 14 iCGD~VGl~~~----Ge~FVAC~eC~fPvCr~Cy----------EY--------------Erkeg~q~CpqCkt~ykr~k 65 (80)
T PF14569_consen 14 ICGDDVGLTEN----GEVFVACHECAFPVCRPCY----------EY--------------ERKEGNQVCPQCKTRYKRHK 65 (80)
T ss_dssp SS--B--B-SS----SSB--S-SSS-----HHHH----------HH--------------HHHTS-SB-TTT--B----T
T ss_pred cccCccccCCC----CCEEEEEcccCCccchhHH----------HH--------------HhhcCcccccccCCCccccc
Confidence 46555544433 2477889999998888554 22 23567899999999999887
Q ss_pred CcCe
Q 043604 213 GCRV 216 (268)
Q Consensus 213 GCnh 216 (268)
|+..
T Consensus 66 gsp~ 69 (80)
T PF14569_consen 66 GSPR 69 (80)
T ss_dssp T---
T ss_pred CCCC
Confidence 7654
No 119
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=77.28 E-value=0.72 Score=39.42 Aligned_cols=47 Identities=28% Similarity=0.463 Sum_probs=34.0
Q ss_pred CCCcccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCC
Q 043604 34 TNGIFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQF 94 (268)
Q Consensus 34 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~ 94 (268)
..-.+.|.||-.++..+ ++..|+|.||..|....+.. .-+|+. |+..
T Consensus 238 ~~~Pf~c~icr~~f~~p----Vvt~c~h~fc~~ca~~~~qk--------~~~c~v--C~~~ 284 (313)
T KOG1813|consen 238 ELLPFKCFICRKYFYRP----VVTKCGHYFCEVCALKPYQK--------GEKCYV--CSQQ 284 (313)
T ss_pred ccCCccccccccccccc----hhhcCCceeehhhhcccccc--------CCccee--cccc
Confidence 34467899999999543 57899999999998766532 235666 7654
No 120
>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=77.21 E-value=2.1 Score=23.45 Aligned_cols=24 Identities=33% Similarity=0.888 Sum_probs=10.7
Q ss_pred ccCCCCCceeeecCCcCeEEec-CCc
Q 043604 199 ARCPACGSCVERKEGCRVMYCS-CHS 223 (268)
Q Consensus 199 k~CP~C~~~iek~~GCnhm~C~-C~~ 223 (268)
-+||.|+.-..-.+|.. |.|. |++
T Consensus 3 p~Cp~C~se~~y~D~~~-~vCp~C~~ 27 (30)
T PF08274_consen 3 PKCPLCGSEYTYEDGEL-LVCPECGH 27 (30)
T ss_dssp ---TTT-----EE-SSS-EEETTTTE
T ss_pred CCCCCCCCcceeccCCE-EeCCcccc
Confidence 36888888777777755 5676 776
No 121
>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=77.15 E-value=0.71 Score=33.30 Aligned_cols=33 Identities=24% Similarity=0.536 Sum_probs=26.4
Q ss_pred CCcccccccccCCcCCcCccccCCCCChhhHHHHH
Q 043604 35 NGIFTCEICIEPISANDKFRNKDLCSHHFCQDCIA 69 (268)
Q Consensus 35 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~ 69 (268)
.+...|.+|...+.. ..| .+.+|||.|...|++
T Consensus 76 ~~~~~C~vC~k~l~~-~~f-~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 76 TESTKCSVCGKPLGN-SVF-VVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCCCccCcCCcCCC-ceE-EEeCCCeEEeccccc
Confidence 445679999999954 456 688999999999975
No 122
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=76.78 E-value=2.1 Score=43.86 Aligned_cols=9 Identities=33% Similarity=0.881 Sum_probs=5.5
Q ss_pred ccCCccccCce
Q 043604 127 SYCPNRNCMAL 137 (268)
Q Consensus 127 ~~Cp~~~C~~~ 137 (268)
+.|| .|+..
T Consensus 668 rkCP--kCG~~ 676 (1337)
T PRK14714 668 RRCP--SCGTE 676 (1337)
T ss_pred EECC--CCCCc
Confidence 5666 66664
No 123
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=76.20 E-value=1 Score=43.70 Aligned_cols=52 Identities=31% Similarity=0.710 Sum_probs=38.0
Q ss_pred ccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCCHHHHhh
Q 043604 38 FTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLDPFSCKL 102 (268)
Q Consensus 38 ~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~ 102 (268)
++|.||.+ . +.+ ....|+|.||.+|+..++...-. -.||. |...+....+..
T Consensus 455 ~~c~ic~~-~---~~~-~it~c~h~~c~~c~~~~i~~~~~------~~~~~--cr~~l~~~~l~s 506 (674)
T KOG1001|consen 455 HWCHICCD-L---DSF-FITRCGHDFCVECLKKSIQQSEN------APCPL--CRNVLKEKKLLS 506 (674)
T ss_pred cccccccc-c---ccc-eeecccchHHHHHHHhccccccC------CCCcH--HHHHHHHHHHhh
Confidence 89999999 2 223 36899999999999999875332 16776 887766655544
No 124
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=75.08 E-value=1.7 Score=42.81 Aligned_cols=25 Identities=44% Similarity=1.083 Sum_probs=22.4
Q ss_pred ccCCCCCceeeecCCcCeEEec-CCc-cc
Q 043604 199 ARCPACGSCVERKEGCRVMYCS-CHS-VT 225 (268)
Q Consensus 199 k~CP~C~~~iek~~GCnhm~C~-C~~-FC 225 (268)
..||.|+..+...+||. +|+ ||+ =|
T Consensus 725 ~~Cp~Cg~~l~~~~GC~--~C~~CG~skC 751 (752)
T PRK08665 725 GACPECGSILEHEEGCV--VCHSCGYSKC 751 (752)
T ss_pred CCCCCCCcccEECCCCC--cCCCCCCCCC
Confidence 35999999999999997 998 998 66
No 125
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=74.95 E-value=0.76 Score=37.92 Aligned_cols=19 Identities=5% Similarity=0.088 Sum_probs=15.3
Q ss_pred EEecCCc-ccccccccccCCC
Q 043604 217 MYCSCHS-VTYSRAKHISLRK 236 (268)
Q Consensus 217 m~C~C~~-FC~~C~~~~~~~~ 236 (268)
+|+ ||| |||-|+-.|....
T Consensus 62 vTl-CGHLFCWpClyqWl~~~ 81 (230)
T KOG0823|consen 62 VTL-CGHLFCWPCLYQWLQTR 81 (230)
T ss_pred Eee-cccceehHHHHHHHhhc
Confidence 344 999 9999999997654
No 126
>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=74.63 E-value=2.9 Score=27.84 Aligned_cols=33 Identities=18% Similarity=0.510 Sum_probs=22.1
Q ss_pred cCCCCCceeeecCCcCeEEec-CC-----c-ccccccccccC
Q 043604 200 RCPACGSCVERKEGCRVMYCS-CH-----S-VTYSRAKHISL 234 (268)
Q Consensus 200 ~CP~C~~~iek~~GCnhm~C~-C~-----~-FC~~C~~~~~~ 234 (268)
.||.|+.+++..+ .+.+|. |. . +|-.|+.++..
T Consensus 3 ~CP~C~~~L~~~~--~~~~C~~C~~~~~~~a~CPdC~~~Le~ 42 (70)
T PF07191_consen 3 TCPKCQQELEWQG--GHYHCEACQKDYKKEAFCPDCGQPLEV 42 (70)
T ss_dssp B-SSS-SBEEEET--TEEEETTT--EEEEEEE-TTT-SB-EE
T ss_pred cCCCCCCccEEeC--CEEECccccccceecccCCCcccHHHH
Confidence 6999999999998 788897 87 4 68888887653
No 127
>PRK00420 hypothetical protein; Validated
Probab=74.62 E-value=2.4 Score=31.17 Aligned_cols=25 Identities=28% Similarity=0.611 Sum_probs=17.8
Q ss_pred CcccCCCCCceeee-cCCcCeEEec-CCc
Q 043604 197 HWARCPACGSCVER-KEGCRVMYCS-CHS 223 (268)
Q Consensus 197 ~~k~CP~C~~~iek-~~GCnhm~C~-C~~ 223 (268)
....||.|+.++.+ .+| ...|. ||.
T Consensus 22 l~~~CP~Cg~pLf~lk~g--~~~Cp~Cg~ 48 (112)
T PRK00420 22 LSKHCPVCGLPLFELKDG--EVVCPVHGK 48 (112)
T ss_pred ccCCCCCCCCcceecCCC--ceECCCCCC
Confidence 44899999999997 454 45554 553
No 128
>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=74.39 E-value=1.7 Score=31.73 Aligned_cols=25 Identities=24% Similarity=0.713 Sum_probs=15.3
Q ss_pred ccCCCCCceeeecCCcCeEEec-CCc-c
Q 043604 199 ARCPACGSCVERKEGCRVMYCS-CHS-V 224 (268)
Q Consensus 199 k~CP~C~~~iek~~GCnhm~C~-C~~-F 224 (268)
|.||+|++...=-.- +-++|. ||+ |
T Consensus 10 R~Cp~CG~kFYDLnk-~PivCP~CG~~~ 36 (108)
T PF09538_consen 10 RTCPSCGAKFYDLNK-DPIVCPKCGTEF 36 (108)
T ss_pred ccCCCCcchhccCCC-CCccCCCCCCcc
Confidence 567777776553333 566675 666 5
No 129
>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=74.11 E-value=1.2 Score=27.80 Aligned_cols=25 Identities=32% Similarity=0.927 Sum_probs=15.4
Q ss_pred cCeeeCcccccccccccccccCCCC
Q 043604 149 LKKARCPNCTQWFCFQCKLAWHAGY 173 (268)
Q Consensus 149 ~~~~~C~~C~~~~C~~C~~~~H~~~ 173 (268)
.....|+.|+..||..|..-.|+-+
T Consensus 19 ~~~y~C~~C~~~FC~dCD~fiHE~L 43 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCIDCDVFIHETL 43 (51)
T ss_dssp -EEE--TTTT--B-HHHHHTTTTTS
T ss_pred CCeEECCCCCCccccCcChhhhccc
Confidence 3678999999999999988777543
No 130
>PRK04023 DNA polymerase II large subunit; Validated
Probab=73.91 E-value=1.8 Score=43.24 Aligned_cols=65 Identities=18% Similarity=0.282 Sum_probs=38.7
Q ss_pred CcccCCCCCceeeecCCcCeEEec-CC-----c-ccccccccccCCC-CCCCCCCCCCcccceecccCccccccccccc
Q 043604 197 HWARCPACGSCVERKEGCRVMYCS-CH-----S-VTYSRAKHISLRK-HSTRGDNKGWRIYKVSGCRSTCRSLENFGVT 267 (268)
Q Consensus 197 ~~k~CP~C~~~iek~~GCnhm~C~-C~-----~-FC~~C~~~~~~~~-~~~~~~~~~~~~~~~~gc~~~~~~l~~~~~~ 267 (268)
..+.||.|+... ..-.|. || . ||-.|+....... ..|..-....+..++.==-...++|+++|+.
T Consensus 625 g~RfCpsCG~~t------~~frCP~CG~~Te~i~fCP~CG~~~~~y~CPKCG~El~~~s~~~i~l~~~~~~A~~~lg~~ 697 (1121)
T PRK04023 625 GRRKCPSCGKET------FYRRCPFCGTHTEPVYRCPRCGIEVEEDECEKCGREPTPYSKRKIDLKELYDRALENLGER 697 (1121)
T ss_pred cCccCCCCCCcC------CcccCCCCCCCCCcceeCccccCcCCCCcCCCCCCCCCccceEEecHHHHHHHHHHHhCCc
Confidence 348999999985 457897 98 6 9999987765432 1233322222222222222344577777764
No 131
>PRK14873 primosome assembly protein PriA; Provisional
Probab=73.58 E-value=9.6 Score=37.13 Aligned_cols=24 Identities=21% Similarity=0.488 Sum_probs=13.1
Q ss_pred cCCCCCceeeecCCcCeEEec-CCc
Q 043604 200 RCPACGSCVERKEGCRVMYCS-CHS 223 (268)
Q Consensus 200 ~CP~C~~~iek~~GCnhm~C~-C~~ 223 (268)
+||+|..++.--.+=+.+.|. ||+
T Consensus 394 ~C~~C~~~L~~h~~~~~l~Ch~CG~ 418 (665)
T PRK14873 394 RCRHCTGPLGLPSAGGTPRCRWCGR 418 (665)
T ss_pred ECCCCCCceeEecCCCeeECCCCcC
Confidence 566666555543333456665 664
No 132
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=73.14 E-value=2.7 Score=40.57 Aligned_cols=14 Identities=36% Similarity=0.831 Sum_probs=9.5
Q ss_pred CCcccCCCCCceee
Q 043604 196 MHWARCPACGSCVE 209 (268)
Q Consensus 196 ~~~k~CP~C~~~ie 209 (268)
.+.+.||+|+..+-
T Consensus 39 ~~~~fC~~CG~~~~ 52 (645)
T PRK14559 39 VDEAHCPNCGAETG 52 (645)
T ss_pred cccccccccCCccc
Confidence 34578888887654
No 133
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=72.32 E-value=3.3 Score=28.73 Aligned_cols=28 Identities=21% Similarity=0.590 Sum_probs=23.3
Q ss_pred CcccCCCCCceeeecCCcCeEEec-CCc-c
Q 043604 197 HWARCPACGSCVERKEGCRVMYCS-CHS-V 224 (268)
Q Consensus 197 ~~k~CP~C~~~iek~~GCnhm~C~-C~~-F 224 (268)
.--.||.|+...-|..+=---.|+ ||+ |
T Consensus 34 ~~~~Cp~C~~~~VkR~a~GIW~C~kCg~~f 63 (89)
T COG1997 34 AKHVCPFCGRTTVKRIATGIWKCRKCGAKF 63 (89)
T ss_pred cCCcCCCCCCcceeeeccCeEEcCCCCCee
Confidence 346899999999998887778887 887 7
No 134
>PF12773 DZR: Double zinc ribbon
Probab=72.05 E-value=2.4 Score=26.02 Aligned_cols=12 Identities=33% Similarity=0.802 Sum_probs=7.2
Q ss_pred cccCCCCCceee
Q 043604 198 WARCPACGSCVE 209 (268)
Q Consensus 198 ~k~CP~C~~~ie 209 (268)
.+.||.|++.+.
T Consensus 12 ~~fC~~CG~~l~ 23 (50)
T PF12773_consen 12 AKFCPHCGTPLP 23 (50)
T ss_pred ccCChhhcCChh
Confidence 456666666655
No 135
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=71.82 E-value=3.6 Score=31.00 Aligned_cols=25 Identities=32% Similarity=0.578 Sum_probs=18.6
Q ss_pred CCcccCCCCCceeeecCCcCeEEecCCc-cccccc
Q 043604 196 MHWARCPACGSCVERKEGCRVMYCSCHS-VTYSRA 229 (268)
Q Consensus 196 ~~~k~CP~C~~~iek~~GCnhm~C~C~~-FC~~C~ 229 (268)
+...-||.|+.|+.+..| . ||-+|+
T Consensus 26 ML~~hCp~Cg~PLF~KdG---------~v~CPvC~ 51 (131)
T COG1645 26 MLAKHCPKCGTPLFRKDG---------EVFCPVCG 51 (131)
T ss_pred HHHhhCcccCCcceeeCC---------eEECCCCC
Confidence 344899999999997654 5 666665
No 136
>PLN00209 ribosomal protein S27; Provisional
Probab=71.20 E-value=5.5 Score=27.56 Aligned_cols=31 Identities=16% Similarity=0.442 Sum_probs=24.4
Q ss_pred ccCCccccCceeeeccccccCCcCeeeCccccccccc
Q 043604 127 SYCPNRNCMALVVNGCEINYGTLKKARCPNCTQWFCF 163 (268)
Q Consensus 127 ~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~C~ 163 (268)
+.|| +|.+.-.+-... ...+.|..|+...|.
T Consensus 37 VkCp--~C~n~q~VFShA----~t~V~C~~Cg~~L~~ 67 (86)
T PLN00209 37 VKCQ--GCFNITTVFSHS----QTVVVCGSCQTVLCQ 67 (86)
T ss_pred EECC--CCCCeeEEEecC----ceEEEccccCCEeec
Confidence 7899 999887766554 578999999987764
No 137
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=71.08 E-value=3.8 Score=30.18 Aligned_cols=31 Identities=23% Similarity=0.402 Sum_probs=23.8
Q ss_pred cccCCccccCceeeeccccccCCcCeeeCccccccc
Q 043604 126 RSYCPNRNCMALVVNGCEINYGTLKKARCPNCTQWF 161 (268)
Q Consensus 126 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~ 161 (268)
..+|| .|+.++.+.... ....+.|+.|++..
T Consensus 2 m~FCp--~Cgsll~p~~~~---~~~~l~C~kCgye~ 32 (113)
T COG1594 2 MRFCP--KCGSLLYPKKDD---EGGKLVCRKCGYEE 32 (113)
T ss_pred ccccC--CccCeeEEeEcC---CCcEEECCCCCcch
Confidence 46899 999999987654 23578898888755
No 138
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=71.04 E-value=2.4 Score=34.22 Aligned_cols=36 Identities=14% Similarity=0.195 Sum_probs=25.2
Q ss_pred HHhCCcccCCCCCceeeecCCcCeEEecCCc-cccccccccc
Q 043604 193 VERMHWARCPACGSCVERKEGCRVMYCSCHS-VTYSRAKHIS 233 (268)
Q Consensus 193 ~~~~~~k~CP~C~~~iek~~GCnhm~C~C~~-FC~~C~~~~~ 233 (268)
+...+.-.||=|.-.+..- +.=.||| |||.|...|.
T Consensus 13 ~~~~~~~~CpICld~~~dP-----VvT~CGH~FC~~CI~~wl 49 (193)
T PLN03208 13 VDSGGDFDCNICLDQVRDP-----VVTLCGHLFCWPCIHKWT 49 (193)
T ss_pred ccCCCccCCccCCCcCCCc-----EEcCCCchhHHHHHHHHH
Confidence 3344557899998866421 2324999 9999999884
No 139
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=71.00 E-value=0.96 Score=30.46 Aligned_cols=52 Identities=31% Similarity=0.633 Sum_probs=34.7
Q ss_pred ccccccccCCcCC--------cCcccc-CCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCC
Q 043604 38 FTCEICIEPISAN--------DKFRNK-DLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLD 96 (268)
Q Consensus 38 ~~C~IC~~~~~~~--------~~~~~~-~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~ 96 (268)
.+|.||-.+|... |..+.+ -.|.|.|-.-|+.+++.+.-.. -.||. |++.+.
T Consensus 21 e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq-----~~CPm--cRq~~~ 81 (84)
T KOG1493|consen 21 ETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQ-----GQCPM--CRQTWQ 81 (84)
T ss_pred CccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCcccc-----ccCCc--chheeE
Confidence 3899997776432 222111 1378999999999998776544 46888 876543
No 140
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=70.77 E-value=1.9 Score=26.33 Aligned_cols=34 Identities=21% Similarity=0.649 Sum_probs=22.7
Q ss_pred ccccccCCcCCcCccccCCCC--C---hhhHHHHHHHHHHH
Q 043604 40 CEICIEPISANDKFRNKDLCS--H---HFCQDCIAKYIEAK 75 (268)
Q Consensus 40 C~IC~~~~~~~~~~~~~~~C~--H---~fC~~Cl~~~~~~~ 75 (268)
|-||+++....+.+ ..+|. - .+..+||..|+..+
T Consensus 1 CrIC~~~~~~~~~l--i~pC~C~Gs~~~vH~~CL~~W~~~~ 39 (47)
T PF12906_consen 1 CRICLEGEEEDEPL--ISPCRCKGSMKYVHRSCLERWIRES 39 (47)
T ss_dssp ETTTTEE-SSSS-E--E-SSS-SSCCGSEECCHHHHHHHHH
T ss_pred CeEeCCcCCCCCce--ecccccCCCcchhHHHHHHHHHHhc
Confidence 67999887554434 35553 3 77899999999873
No 141
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=70.53 E-value=5.2 Score=32.68 Aligned_cols=38 Identities=26% Similarity=0.497 Sum_probs=24.3
Q ss_pred CCcccCCccccCceeeecccccc-------CCcCeeeCccccccc
Q 043604 124 FERSYCPNRNCMALVVNGCEINY-------GTLKKARCPNCTQWF 161 (268)
Q Consensus 124 ~~~~~Cp~~~C~~~~~~~~~~~~-------~~~~~~~C~~C~~~~ 161 (268)
+.++-||.|+|..++..+...+. ...-.++|..|+..|
T Consensus 136 SqRIACPRpnCkRiInL~p~~~~p~~P~~~P~gcRV~CgHC~~tF 180 (275)
T KOG4684|consen 136 SQRIACPRPNCKRIINLDPLIEKPRDPGTAPTGCRVKCGHCNETF 180 (275)
T ss_pred cceeccCCCCcceeeecCCCCCCCCCCCCCCcceEEEecCcccee
Confidence 46789999999999876554321 123456666555444
No 142
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=69.96 E-value=3.4 Score=24.28 Aligned_cols=12 Identities=42% Similarity=1.126 Sum_probs=9.0
Q ss_pred cCCCCCceeeec
Q 043604 200 RCPACGSCVERK 211 (268)
Q Consensus 200 ~CP~C~~~iek~ 211 (268)
+||+|+..++..
T Consensus 1 ~CP~C~~~l~~~ 12 (41)
T PF13453_consen 1 KCPRCGTELEPV 12 (41)
T ss_pred CcCCCCcccceE
Confidence 588888877655
No 143
>PF14149 YhfH: YhfH-like protein
Probab=69.52 E-value=0.48 Score=27.26 Aligned_cols=31 Identities=19% Similarity=0.515 Sum_probs=24.1
Q ss_pred HHHHHhCCcccCCCCCceeeecCCcCeEEec
Q 043604 190 GKLVERMHWARCPACGSCVERKEGCRVMYCS 220 (268)
Q Consensus 190 ~~~~~~~~~k~CP~C~~~iek~~GCnhm~C~ 220 (268)
.++.++...|.||.||..|+-..-|-.++|.
T Consensus 5 ~eFfrnLp~K~C~~CG~~i~EQ~E~Y~n~C~ 35 (37)
T PF14149_consen 5 VEFFRNLPPKKCTECGKEIEEQAECYGNECD 35 (37)
T ss_pred HHHHHhCCCcccHHHHHHHHHHHHHHhCcCC
Confidence 4556778889999999999877777666663
No 144
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=69.42 E-value=5.8 Score=22.25 Aligned_cols=26 Identities=23% Similarity=0.479 Sum_probs=14.1
Q ss_pred cccCCCCCceeeecCCcCeEEec-CCc
Q 043604 198 WARCPACGSCVERKEGCRVMYCS-CHS 223 (268)
Q Consensus 198 ~k~CP~C~~~iek~~GCnhm~C~-C~~ 223 (268)
.+.|+.|+....-+.-=..+.|. |+.
T Consensus 3 ~~~C~~C~~~~i~~~~~~~~~C~~Cg~ 29 (33)
T PF08792_consen 3 LKKCSKCGGNGIVNKEDDYEVCIFCGS 29 (33)
T ss_pred ceEcCCCCCCeEEEecCCeEEcccCCc
Confidence 35677777655443333345565 554
No 145
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=69.30 E-value=4.5 Score=27.57 Aligned_cols=28 Identities=29% Similarity=0.753 Sum_probs=21.6
Q ss_pred CCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCC
Q 043604 58 LCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFL 95 (268)
Q Consensus 58 ~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i 95 (268)
.|.|.|...|+.+|+.+ ++ .||. +.+++
T Consensus 53 ~CnHaFH~HCI~rWL~T--k~------~CPl--d~q~w 80 (88)
T COG5194 53 VCNHAFHDHCIYRWLDT--KG------VCPL--DRQTW 80 (88)
T ss_pred ecchHHHHHHHHHHHhh--CC------CCCC--CCcee
Confidence 49999999999999987 22 4776 55543
No 146
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=69.07 E-value=8 Score=31.88 Aligned_cols=59 Identities=22% Similarity=0.521 Sum_probs=44.2
Q ss_pred CCCcccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCC
Q 043604 34 TNGIFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLD 96 (268)
Q Consensus 34 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~ 96 (268)
.+-.-.|..|-.++...+. ..+.|-|.|.-.||..+..+--.+-.-.-..||. |..+|-
T Consensus 47 sDY~pNC~LC~t~La~gdt--~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~--Cs~eiF 105 (299)
T KOG3970|consen 47 SDYNPNCRLCNTPLASGDT--TRLVCYHLFHWKCLNERAANLPANTAPAGYQCPC--CSQEIF 105 (299)
T ss_pred cCCCCCCceeCCccccCcc--eeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCC--CCCccC
Confidence 4445679999999977776 4699999999999999887655442333478998 987553
No 147
>PRK11827 hypothetical protein; Provisional
Probab=68.06 E-value=6 Score=25.57 Aligned_cols=26 Identities=15% Similarity=0.377 Sum_probs=20.3
Q ss_pred cccCCCCCceeeecCCcCeEEec-CCc
Q 043604 198 WARCPACGSCVERKEGCRVMYCS-CHS 223 (268)
Q Consensus 198 ~k~CP~C~~~iek~~GCnhm~C~-C~~ 223 (268)
+-.||.|+..++-..+=+.+.|. |+-
T Consensus 8 ILaCP~ckg~L~~~~~~~~Lic~~~~l 34 (60)
T PRK11827 8 IIACPVCNGKLWYNQEKQELICKLDNL 34 (60)
T ss_pred heECCCCCCcCeEcCCCCeEECCccCe
Confidence 35899999999877666778886 764
No 148
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=68.05 E-value=2.4 Score=38.44 Aligned_cols=39 Identities=26% Similarity=0.606 Sum_probs=29.9
Q ss_pred CCcccccccccCCcCCcCccccCCCCChhhHHHHHHHHH
Q 043604 35 NGIFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIE 73 (268)
Q Consensus 35 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~ 73 (268)
.+.-+|+||++-.+..-..+....|.|.|.-.|+..|..
T Consensus 173 tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~~ 211 (493)
T KOG0804|consen 173 TELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWWD 211 (493)
T ss_pred ccCCCcchhHhhcCccccceeeeecccccchHHHhhccc
Confidence 456799999998866544444567999999999987753
No 149
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=67.72 E-value=2.5 Score=43.29 Aligned_cols=30 Identities=23% Similarity=0.639 Sum_probs=23.6
Q ss_pred ccCCCCCceeeecCCcCeEEec-CCc-c-----cccccccccC
Q 043604 199 ARCPACGSCVERKEGCRVMYCS-CHS-V-----TYSRAKHISL 234 (268)
Q Consensus 199 k~CP~C~~~iek~~GCnhm~C~-C~~-F-----C~~C~~~~~~ 234 (268)
++||+|+..+... .|. ||. . |-.||.....
T Consensus 668 rkCPkCG~~t~~~------fCP~CGs~te~vy~CPsCGaev~~ 704 (1337)
T PRK14714 668 RRCPSCGTETYEN------RCPDCGTHTEPVYVCPDCGAEVPP 704 (1337)
T ss_pred EECCCCCCccccc------cCcccCCcCCCceeCccCCCccCC
Confidence 8999999987542 887 985 5 8888887654
No 150
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=67.66 E-value=6.6 Score=24.75 Aligned_cols=36 Identities=19% Similarity=0.410 Sum_probs=28.5
Q ss_pred CCcccccccccCCcCCcCccccCCCCChhhHHHHHH
Q 043604 35 NGIFTCEICIEPISANDKFRNKDLCSHHFCQDCIAK 70 (268)
Q Consensus 35 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~ 70 (268)
.....|.+|-+.+.+.+...+-..|+-.+.++|+..
T Consensus 3 ~~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~ 38 (54)
T PF14446_consen 3 YEGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK 38 (54)
T ss_pred ccCccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence 345679999999976766656677999999999865
No 151
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=67.45 E-value=2.7 Score=37.45 Aligned_cols=50 Identities=26% Similarity=0.596 Sum_probs=36.8
Q ss_pred CCcccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCC
Q 043604 35 NGIFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCD 92 (268)
Q Consensus 35 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~ 92 (268)
.....|..|-+.+-..+.--..++|.|.|...|+..+++. ..+-.||. |.
T Consensus 363 e~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~------n~~rsCP~--Cr 412 (518)
T KOG1941|consen 363 ETELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILEN------NGTRSCPN--CR 412 (518)
T ss_pred HHhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHh------CCCCCCcc--HH
Confidence 3467899999877543322257899999999999999953 33457887 76
No 152
>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=67.42 E-value=2.6 Score=27.80 Aligned_cols=36 Identities=22% Similarity=0.281 Sum_probs=19.3
Q ss_pred CCcccCCCCCceeeecCCcCeEEec-CCc-cccccccccc
Q 043604 196 MHWARCPACGSCVERKEGCRVMYCS-CHS-VTYSRAKHIS 233 (268)
Q Consensus 196 ~~~k~CP~C~~~iek~~GCnhm~C~-C~~-FC~~C~~~~~ 233 (268)
.....|+.|+...- --=..-.|+ ||. ||-.|.....
T Consensus 7 ~~~~~C~~C~~~F~--~~~rrhhCr~CG~~vC~~Cs~~~~ 44 (69)
T PF01363_consen 7 SEASNCMICGKKFS--LFRRRHHCRNCGRVVCSSCSSQRI 44 (69)
T ss_dssp GG-SB-TTT--B-B--SSS-EEE-TTT--EEECCCS-EEE
T ss_pred CCCCcCcCcCCcCC--CceeeEccCCCCCEECCchhCCEE
Confidence 34578999999883 345667898 999 9999987544
No 153
>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=66.66 E-value=4.8 Score=26.49 Aligned_cols=26 Identities=31% Similarity=0.778 Sum_probs=19.6
Q ss_pred cccCCCCCceeeecCCcCeEEec-CCc
Q 043604 198 WARCPACGSCVERKEGCRVMYCS-CHS 223 (268)
Q Consensus 198 ~k~CP~C~~~iek~~GCnhm~C~-C~~ 223 (268)
.+.||.|+....+...=..++|. ||+
T Consensus 28 Sq~C~~CG~~~~~~~~~r~~~C~~Cg~ 54 (69)
T PF07282_consen 28 SQTCPRCGHRNKKRRSGRVFTCPNCGF 54 (69)
T ss_pred ccCccCcccccccccccceEEcCCCCC
Confidence 47899999998885555567776 775
No 154
>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=66.66 E-value=7.2 Score=23.12 Aligned_cols=8 Identities=63% Similarity=1.622 Sum_probs=4.8
Q ss_pred cCCCCCce
Q 043604 200 RCPACGSC 207 (268)
Q Consensus 200 ~CP~C~~~ 207 (268)
.||.|+..
T Consensus 2 ~Cp~Cg~~ 9 (43)
T PF08271_consen 2 KCPNCGSK 9 (43)
T ss_dssp SBTTTSSS
T ss_pred CCcCCcCC
Confidence 46666664
No 155
>TIGR02443 conserved hypothetical metal-binding protein. Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various Proteobacteria.
Probab=66.42 E-value=7.2 Score=25.01 Aligned_cols=25 Identities=28% Similarity=0.755 Sum_probs=19.3
Q ss_pred ccCCCCCc----eeeecCCcCeEEec-CCc
Q 043604 199 ARCPACGS----CVERKEGCRVMYCS-CHS 223 (268)
Q Consensus 199 k~CP~C~~----~iek~~GCnhm~C~-C~~ 223 (268)
-.||+|+. .+-+..|=.++.|. ||+
T Consensus 10 A~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~ 39 (59)
T TIGR02443 10 AVCPACSAQDTLAMWKENNIELVECVECGY 39 (59)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEeccCCC
Confidence 37999987 34556777899997 997
No 156
>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=66.21 E-value=4.2 Score=24.82 Aligned_cols=30 Identities=27% Similarity=0.465 Sum_probs=18.6
Q ss_pred CcccCCccccCceeeeccccccCCcCeeeCccccc
Q 043604 125 ERSYCPNRNCMALVVNGCEINYGTLKKARCPNCTQ 159 (268)
Q Consensus 125 ~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~ 159 (268)
.+..||++.|+..+....-. ....|-.|+.
T Consensus 17 ~rk~CP~~~CG~GvFMA~H~-----dR~~CGKCg~ 46 (47)
T PF01599_consen 17 LRKECPSPRCGAGVFMAEHK-----DRHYCGKCGY 46 (47)
T ss_dssp SSEE-TSTTTTSSSEEEE-S-----SEEEETTTSS
T ss_pred hhhcCCCcccCCceEeeecC-----CCccCCCccc
Confidence 35899999999865433322 4667777764
No 157
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=65.75 E-value=1.3 Score=38.48 Aligned_cols=29 Identities=34% Similarity=0.954 Sum_probs=23.3
Q ss_pred CCcccCCCCCceeeecC-CcCeEEec-CCc-c
Q 043604 196 MHWARCPACGSCVERKE-GCRVMYCS-CHS-V 224 (268)
Q Consensus 196 ~~~k~CP~C~~~iek~~-GCnhm~C~-C~~-F 224 (268)
..|.+||+|+..|.+.+ .=|.+.|. |++ |
T Consensus 25 ~~~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 56 (292)
T PRK05654 25 GLWTKCPSCGQVLYRKELEANLNVCPKCGHHM 56 (292)
T ss_pred CCeeECCCccchhhHHHHHhcCCCCCCCCCCe
Confidence 35999999999888763 45678997 998 8
No 158
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=65.26 E-value=5.7 Score=28.18 Aligned_cols=29 Identities=17% Similarity=0.587 Sum_probs=20.4
Q ss_pred ccCCccccCceeeeccccccCCcCeeeCcccccc
Q 043604 127 SYCPNRNCMALVVNGCEINYGTLKKARCPNCTQW 160 (268)
Q Consensus 127 ~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~ 160 (268)
.+|| .|++.+++.... ....+.|+.|.+.
T Consensus 2 ~FCP--~Cgn~Live~g~---~~~rf~C~tCpY~ 30 (105)
T KOG2906|consen 2 LFCP--TCGNMLIVESGE---SCNRFSCRTCPYV 30 (105)
T ss_pred cccC--CCCCEEEEecCC---eEeeEEcCCCCce
Confidence 5788 899999998876 2355666655543
No 159
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=64.36 E-value=10 Score=26.20 Aligned_cols=31 Identities=19% Similarity=0.515 Sum_probs=24.6
Q ss_pred ccCCccccCceeeeccccccCCcCeeeCccccccccc
Q 043604 127 SYCPNRNCMALVVNGCEINYGTLKKARCPNCTQWFCF 163 (268)
Q Consensus 127 ~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~C~ 163 (268)
+.|| +|.+.-.+-... ...+.|..|+...|.
T Consensus 36 VkCp--~C~n~q~VFShA----~t~V~C~~Cg~~L~~ 66 (85)
T PTZ00083 36 VKCP--GCSQITTVFSHA----QTVVLCGGCSSQLCQ 66 (85)
T ss_pred EECC--CCCCeeEEEecC----ceEEEccccCCEeec
Confidence 7899 999887766554 578999999988765
No 160
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=63.86 E-value=4.9 Score=34.27 Aligned_cols=67 Identities=21% Similarity=0.533 Sum_probs=45.9
Q ss_pred CCCcccccccccCCcCCcCccccCCC----CChhhHHHHHHHHHHHhhcCCCceeccCC-CCCC---CCCCHH----HHh
Q 043604 34 TNGIFTCEICIEPISANDKFRNKDLC----SHHFCQDCIAKYIEAKVQDNNTAKIECPG-VHCD---QFLDPF----SCK 101 (268)
Q Consensus 34 ~~~~~~C~IC~~~~~~~~~~~~~~~C----~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~-~~C~---~~i~~~----~i~ 101 (268)
....+-|.+|.|-+.+. .| ..| .|.||..|-+..|+.+-.. ..+.||. ..|. ..+++. +|.
T Consensus 265 ~~apLcCTLC~ERLEDT-HF---VQCPSVp~HKFCFPCSResIK~Qg~s---gevYCPSGdkCPLvgS~vPWAFMQGEIa 337 (352)
T KOG3579|consen 265 PSAPLCCTLCHERLEDT-HF---VQCPSVPSHKFCFPCSRESIKQQGAS---GEVYCPSGDKCPLVGSNVPWAFMQGEIA 337 (352)
T ss_pred CCCceeehhhhhhhccC-ce---eecCCCcccceecccCHHHHHhhcCC---CceeCCCCCcCcccCCcccHHHhhhhHH
Confidence 45668999999988543 23 455 6999999999999987654 3688886 3454 334443 455
Q ss_pred hcCChh
Q 043604 102 LMIPSN 107 (268)
Q Consensus 102 ~~l~~~ 107 (268)
.+|..|
T Consensus 338 tILagd 343 (352)
T KOG3579|consen 338 TILAGD 343 (352)
T ss_pred HHhccc
Confidence 666544
No 161
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=63.24 E-value=2.2 Score=33.18 Aligned_cols=30 Identities=23% Similarity=0.481 Sum_probs=23.6
Q ss_pred CCCcccccccccCCcCCcCccccCCCCChhh
Q 043604 34 TNGIFTCEICIEPISANDKFRNKDLCSHHFC 64 (268)
Q Consensus 34 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC 64 (268)
.....+|.||+|++...+.+ ..++|-..|.
T Consensus 174 ~ddkGECvICLEdL~~GdtI-ARLPCLCIYH 203 (205)
T KOG0801|consen 174 KDDKGECVICLEDLEAGDTI-ARLPCLCIYH 203 (205)
T ss_pred cccCCcEEEEhhhccCCCce-eccceEEEee
Confidence 45567999999999888876 6889876654
No 162
>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=62.82 E-value=21 Score=21.45 Aligned_cols=33 Identities=30% Similarity=0.723 Sum_probs=18.1
Q ss_pred HHHHHhCCc---ccCCCCCce-eeecCCcCeEEec-CC
Q 043604 190 GKLVERMHW---ARCPACGSC-VERKEGCRVMYCS-CH 222 (268)
Q Consensus 190 ~~~~~~~~~---k~CP~C~~~-iek~~GCnhm~C~-C~ 222 (268)
.+++....| ..||+|+.. +-+..+=....|. |+
T Consensus 7 ~~~l~~~RW~~g~~CP~Cg~~~~~~~~~~~~~~C~~C~ 44 (46)
T PF12760_consen 7 REYLEEIRWPDGFVCPHCGSTKHYRLKTRGRYRCKACR 44 (46)
T ss_pred HHHHHHhcCCCCCCCCCCCCeeeEEeCCCCeEECCCCC
Confidence 334444444 569999984 3333443445554 54
No 163
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=62.62 E-value=7.3 Score=28.69 Aligned_cols=27 Identities=30% Similarity=0.625 Sum_probs=19.6
Q ss_pred cccCCCCCceeeec--CCcCeEEec-CCc-c
Q 043604 198 WARCPACGSCVERK--EGCRVMYCS-CHS-V 224 (268)
Q Consensus 198 ~k~CP~C~~~iek~--~GCnhm~C~-C~~-F 224 (268)
.+-||+|+.++.-. ++=+-+.|+ ||+ +
T Consensus 2 m~FCp~Cgsll~p~~~~~~~~l~C~kCgye~ 32 (113)
T COG1594 2 MRFCPKCGSLLYPKKDDEGGKLVCRKCGYEE 32 (113)
T ss_pred ccccCCccCeeEEeEcCCCcEEECCCCCcch
Confidence 46799999988762 122388897 997 5
No 164
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=62.19 E-value=14 Score=29.33 Aligned_cols=62 Identities=21% Similarity=0.483 Sum_probs=41.0
Q ss_pred CCCcccccccccCCcCC---cCccccCCCCChhhHHHHHHHHHHHhhcCCCcee---ccCCCCCCCCCCH
Q 043604 34 TNGIFTCEICIEPISAN---DKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKI---ECPGVHCDQFLDP 97 (268)
Q Consensus 34 ~~~~~~C~IC~~~~~~~---~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i---~CP~~~C~~~i~~ 97 (268)
......|.|||...... +..--...|+..|..-||..|+..-+.....+.| .||- |..+|..
T Consensus 162 dd~~~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPY--CS~Pial 229 (234)
T KOG3268|consen 162 DDELGACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPY--CSDPIAL 229 (234)
T ss_pred chhhhcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCC--CCCccee
Confidence 34567788887643221 2211345799999999999999887766333433 6888 8877653
No 165
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=62.02 E-value=1.6 Score=37.86 Aligned_cols=29 Identities=21% Similarity=0.579 Sum_probs=21.6
Q ss_pred CcccCCCCCceeeecC-CcCeEEec-CCc-cc
Q 043604 197 HWARCPACGSCVERKE-GCRVMYCS-CHS-VT 225 (268)
Q Consensus 197 ~~k~CP~C~~~iek~~-GCnhm~C~-C~~-FC 225 (268)
.|.+||+|+..|.+.+ .=|...|. |++ |=
T Consensus 37 lw~kc~~C~~~~~~~~l~~~~~vcp~c~~h~r 68 (296)
T CHL00174 37 LWVQCENCYGLNYKKFLKSKMNICEQCGYHLK 68 (296)
T ss_pred CeeECCCccchhhHHHHHHcCCCCCCCCCCcC
Confidence 4888999998887664 45667886 887 63
No 166
>PHA02926 zinc finger-like protein; Provisional
Probab=61.96 E-value=5.2 Score=33.05 Aligned_cols=44 Identities=16% Similarity=0.172 Sum_probs=27.9
Q ss_pred HHhCCcccCCCCCceeeecC--CcCe--EEecCCc-ccccccccccCCC
Q 043604 193 VERMHWARCPACGSCVERKE--GCRV--MYCSCHS-VTYSRAKHISLRK 236 (268)
Q Consensus 193 ~~~~~~k~CP~C~~~iek~~--GCnh--m~C~C~~-FC~~C~~~~~~~~ 236 (268)
.+...-+.|+=|-..+-+.. +... +.=.|+| ||+.|...|....
T Consensus 165 ~~~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r 213 (242)
T PHA02926 165 YRVSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTR 213 (242)
T ss_pred HhccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhc
Confidence 34445588999987663322 2211 1112999 9999999998743
No 167
>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=61.66 E-value=1.6 Score=25.92 Aligned_cols=16 Identities=44% Similarity=0.725 Sum_probs=11.5
Q ss_pred CCcccCCCCCc-eeeec
Q 043604 196 MHWARCPACGS-CVERK 211 (268)
Q Consensus 196 ~~~k~CP~C~~-~iek~ 211 (268)
.....||.|+. .++|.
T Consensus 24 ~~~~~CP~Cg~~~~~r~ 40 (42)
T PF09723_consen 24 DDPVPCPECGSTEVRRV 40 (42)
T ss_pred CCCCcCCCCCCCceEEe
Confidence 34578999998 66653
No 168
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=61.46 E-value=9.2 Score=25.63 Aligned_cols=24 Identities=29% Similarity=0.764 Sum_probs=19.1
Q ss_pred cCCCCCc----eeeecCCcCeEEec-CCc
Q 043604 200 RCPACGS----CVERKEGCRVMYCS-CHS 223 (268)
Q Consensus 200 ~CP~C~~----~iek~~GCnhm~C~-C~~ 223 (268)
.||+|+. .+-+..|=.++.|. |||
T Consensus 10 ~CP~C~~~D~i~~~~e~~ve~vECV~CGy 38 (71)
T PF09526_consen 10 VCPKCQAMDTIMMWRENGVEYVECVECGY 38 (71)
T ss_pred cCCCCcCccEEEEEEeCCceEEEecCCCC
Confidence 6999987 34456788889997 997
No 169
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=61.43 E-value=5.8 Score=38.98 Aligned_cols=41 Identities=27% Similarity=0.660 Sum_probs=31.7
Q ss_pred cccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCC
Q 043604 37 IFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQ 93 (268)
Q Consensus 37 ~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~ 93 (268)
...|..|--++..+- +...|+|.|...|+. + ....||. |..
T Consensus 840 ~skCs~C~~~LdlP~---VhF~CgHsyHqhC~e--------~---~~~~CP~--C~~ 880 (933)
T KOG2114|consen 840 VSKCSACEGTLDLPF---VHFLCGHSYHQHCLE--------D---KEDKCPK--CLP 880 (933)
T ss_pred eeeecccCCccccce---eeeecccHHHHHhhc--------c---CcccCCc--cch
Confidence 358999998886652 467999999999998 2 2367988 865
No 170
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=61.27 E-value=7.3 Score=27.96 Aligned_cols=31 Identities=23% Similarity=0.653 Sum_probs=21.2
Q ss_pred CCcccCCCCCcee---eecCCcCeEEec-CCc-ccc
Q 043604 196 MHWARCPACGSCV---ERKEGCRVMYCS-CHS-VTY 226 (268)
Q Consensus 196 ~~~k~CP~C~~~i---ek~~GCnhm~C~-C~~-FC~ 226 (268)
...-.||+|+... ...-|=-|+.|. ||+ +=.
T Consensus 19 pt~f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 19 PKIFECPRCGKVSISVKIKKNIAIITCGNCGLYTEF 54 (99)
T ss_pred CcEeECCCCCCeEeeeecCCCcceEECCCCCCccCE
Confidence 4557899999432 233467799997 997 643
No 171
>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=60.94 E-value=7.5 Score=20.99 Aligned_cols=22 Identities=27% Similarity=0.760 Sum_probs=11.8
Q ss_pred ccCCCCCceeeec--CCcCeEEec
Q 043604 199 ARCPACGSCVERK--EGCRVMYCS 220 (268)
Q Consensus 199 k~CP~C~~~iek~--~GCnhm~C~ 220 (268)
++||+|+..|++. +|=+...|.
T Consensus 2 ~~C~rC~~~~~~~~~~~r~~~~C~ 25 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGINGRSTYLCP 25 (30)
T ss_dssp SB-TTT--BBEEEEETTEEEEE-T
T ss_pred CcCccCCCcceEeEecCCCCeECc
Confidence 5799999988766 454445553
No 172
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=60.92 E-value=8.2 Score=23.19 Aligned_cols=13 Identities=31% Similarity=0.705 Sum_probs=8.0
Q ss_pred CcccCCCCCceee
Q 043604 197 HWARCPACGSCVE 209 (268)
Q Consensus 197 ~~k~CP~C~~~ie 209 (268)
...+||.|+..|.
T Consensus 18 ~~irC~~CG~rIl 30 (44)
T smart00659 18 DVVRCRECGYRIL 30 (44)
T ss_pred CceECCCCCceEE
Confidence 3457777776654
No 173
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=59.51 E-value=11 Score=24.61 Aligned_cols=28 Identities=29% Similarity=0.567 Sum_probs=17.7
Q ss_pred CCcccCCCCCceeeec---CCcCeEEec-CCc
Q 043604 196 MHWARCPACGSCVERK---EGCRVMYCS-CHS 223 (268)
Q Consensus 196 ~~~k~CP~C~~~iek~---~GCnhm~C~-C~~ 223 (268)
...|+||.|+..+.+. +|=-...|. |+.
T Consensus 4 d~lKPCPFCG~~~~~v~~~~g~~~v~C~~CgA 35 (64)
T PRK09710 4 DNVKPCPFCGCPSVTVKAISGYYRAKCNGCES 35 (64)
T ss_pred ccccCCCCCCCceeEEEecCceEEEEcCCCCc
Confidence 3569999999755544 554445554 554
No 174
>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=59.47 E-value=8.4 Score=25.22 Aligned_cols=17 Identities=24% Similarity=0.927 Sum_probs=13.2
Q ss_pred hhhHHHHHHHHHHHhhc
Q 043604 62 HFCQDCIAKYIEAKVQD 78 (268)
Q Consensus 62 ~fC~~Cl~~~~~~~i~~ 78 (268)
-||++||..|+.....+
T Consensus 11 gFCRNCLskWy~~aA~~ 27 (68)
T PF06844_consen 11 GFCRNCLSKWYREAAEE 27 (68)
T ss_dssp S--HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHh
Confidence 39999999999988876
No 175
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=59.38 E-value=19 Score=30.21 Aligned_cols=21 Identities=14% Similarity=0.096 Sum_probs=16.2
Q ss_pred HHHhhcCChhHHHHHHHHHHh
Q 043604 98 FSCKLMIPSNLFSKWCDVLFE 118 (268)
Q Consensus 98 ~~i~~~l~~~~~~~~~~~~~~ 118 (268)
+.+..-++++++..|++....
T Consensus 166 ~~L~~~l~~ell~~yeri~~~ 186 (239)
T COG1579 166 EELKEKLDPELLSEYERIRKN 186 (239)
T ss_pred HHHHHhcCHHHHHHHHHHHhc
Confidence 346667889999999988765
No 176
>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=59.32 E-value=12 Score=20.63 Aligned_cols=24 Identities=21% Similarity=0.683 Sum_probs=20.7
Q ss_pred cCCCCCceeeecCCcCeEEec-CCc
Q 043604 200 RCPACGSCVERKEGCRVMYCS-CHS 223 (268)
Q Consensus 200 ~CP~C~~~iek~~GCnhm~C~-C~~ 223 (268)
.|+.|++++.--.|=..+.|. |++
T Consensus 3 ~C~~C~t~L~yP~gA~~vrCs~C~~ 27 (31)
T TIGR01053 3 VCGGCRTLLMYPRGASSVRCALCQT 27 (31)
T ss_pred CcCCCCcEeecCCCCCeEECCCCCe
Confidence 689999999999999999997 864
No 177
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=59.28 E-value=8.8 Score=25.19 Aligned_cols=32 Identities=22% Similarity=0.315 Sum_probs=23.9
Q ss_pred cccCCccccCceeeeccccccCCcCeeeCccccccccc
Q 043604 126 RSYCPNRNCMALVVNGCEINYGTLKKARCPNCTQWFCF 163 (268)
Q Consensus 126 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~C~ 163 (268)
.+.|| +|++.-..-... +..++|..|+...+.
T Consensus 19 ~VkCp--dC~N~q~vFsha----st~V~C~~CG~~l~~ 50 (67)
T COG2051 19 RVKCP--DCGNEQVVFSHA----STVVTCLICGTTLAE 50 (67)
T ss_pred EEECC--CCCCEEEEeccC----ceEEEecccccEEEe
Confidence 47898 999877665554 578999999877643
No 178
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=58.70 E-value=2.1 Score=37.07 Aligned_cols=30 Identities=30% Similarity=0.841 Sum_probs=22.7
Q ss_pred CCcccCCCCCceeeecC-CcCeEEec-CCc-cc
Q 043604 196 MHWARCPACGSCVERKE-GCRVMYCS-CHS-VT 225 (268)
Q Consensus 196 ~~~k~CP~C~~~iek~~-GCnhm~C~-C~~-FC 225 (268)
..|.+||+|+..|.+.+ .=|.+.|. |++ |=
T Consensus 24 ~~~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~r 56 (285)
T TIGR00515 24 GVWTKCPKCGQVLYTKELERNLEVCPKCDHHMR 56 (285)
T ss_pred CCeeECCCCcchhhHHHHHhhCCCCCCCCCcCc
Confidence 35899999999888763 34667887 887 63
No 179
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=58.56 E-value=9.8 Score=29.35 Aligned_cols=36 Identities=19% Similarity=0.289 Sum_probs=21.4
Q ss_pred CCcccCCccccCceeeecccccc-CCcCeeeCccccccc
Q 043604 124 FERSYCPNRNCMALVVNGCEINY-GTLKKARCPNCTQWF 161 (268)
Q Consensus 124 ~~~~~Cp~~~C~~~~~~~~~~~~-~~~~~~~C~~C~~~~ 161 (268)
.....|| .|+..+........ .....+.||.||...
T Consensus 97 ~~~Y~Cp--~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l 133 (147)
T smart00531 97 NAYYKCP--NCQSKYTFLEANQLLDMDGTFTCPRCGEEL 133 (147)
T ss_pred CcEEECc--CCCCEeeHHHHHHhcCCCCcEECCCCCCEE
Confidence 4567898 79877765433210 012338899887643
No 180
>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=58.25 E-value=9.3 Score=22.67 Aligned_cols=27 Identities=22% Similarity=0.680 Sum_probs=15.9
Q ss_pred CeeeCcccccccccccccccCCCCCcchh
Q 043604 150 KKARCPNCTQWFCFQCKLAWHAGYRCEES 178 (268)
Q Consensus 150 ~~~~C~~C~~~~C~~C~~~~H~~~tC~~~ 178 (268)
..+.|+.|+..||...+.+ ..+.|...
T Consensus 12 ~~~~C~~C~~~FC~~Hr~~--e~H~C~~~ 38 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLKHRLP--EDHNCSKL 38 (43)
T ss_dssp SHEE-TTTS-EE-TTTHST--TTCT-SST
T ss_pred CCeECCCCCcccCccccCc--cccCCcch
Confidence 4578999999999988764 22356543
No 181
>PHA02929 N1R/p28-like protein; Provisional
Probab=58.01 E-value=7.5 Score=32.65 Aligned_cols=47 Identities=15% Similarity=0.090 Sum_probs=32.5
Q ss_pred CCcccCCCCCceeeecCCcC---eEEecCCc-ccccccccccCCCCCCCCC
Q 043604 196 MHWARCPACGSCVERKEGCR---VMYCSCHS-VTYSRAKHISLRKHSTRGD 242 (268)
Q Consensus 196 ~~~k~CP~C~~~iek~~GCn---hm~C~C~~-FC~~C~~~~~~~~~~~~~~ 242 (268)
.....||=|.-.+...+.-+ -+.-.|+| ||..|...|......|+.-
T Consensus 172 ~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlC 222 (238)
T PHA02929 172 SKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVC 222 (238)
T ss_pred CCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCC
Confidence 34578999999876554222 13335999 9999999998765555543
No 182
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=57.98 E-value=2.7 Score=35.43 Aligned_cols=40 Identities=18% Similarity=0.132 Sum_probs=27.3
Q ss_pred CCccccccccc-CCcCCcCccccCCCCChhhHHHHHHHHHH
Q 043604 35 NGIFTCEICIE-PISANDKFRNKDLCSHHFCQDCIAKYIEA 74 (268)
Q Consensus 35 ~~~~~C~IC~~-~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~ 74 (268)
....++.+++. +.........+..+++.|+..|-.-++..
T Consensus 93 ~~~~~ls~~~s~e~~~~~e~~~~y~~~~~f~i~~~~i~~~~ 133 (271)
T COG5574 93 NREETLSIEYSRETNIDKEGEVLYPCGIFFCIGCDYIWSID 133 (271)
T ss_pred ccccccccccCcccccccccceeeecccccchhhhHHHHHH
Confidence 34567888887 43332233356789999999998877763
No 183
>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=57.66 E-value=5.8 Score=34.55 Aligned_cols=53 Identities=17% Similarity=0.404 Sum_probs=30.8
Q ss_pred ccCCccccCceeeeccccccCCcCeeeCcccccccccccccccCCCCCcchhhcccchhhHHHHHHHHhCCcccCCCCCc
Q 043604 127 SYCPNRNCMALVVNGCEINYGTLKKARCPNCTQWFCFQCKLAWHAGYRCEESGNLRDWNDIAFGKLVERMHWARCPACGS 206 (268)
Q Consensus 127 ~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~tC~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~ 206 (268)
.-|| .|..-....+.. ...+. .||..||..|.... . ..+...||.|+.
T Consensus 4 ~~CP--~Ck~~~y~np~~----kl~i~--~CGH~~C~sCv~~l-----------------------~-~~~~~~CP~C~~ 51 (309)
T TIGR00570 4 QGCP--RCKTTKYRNPSL----KLMVN--VCGHTLCESCVDLL-----------------------F-VRGSGSCPECDT 51 (309)
T ss_pred CCCC--cCCCCCccCccc----ccccC--CCCCcccHHHHHHH-----------------------h-cCCCCCCCCCCC
Confidence 3577 777644333321 12233 68999999887531 0 123347888888
Q ss_pred eeeec
Q 043604 207 CVERK 211 (268)
Q Consensus 207 ~iek~ 211 (268)
.+.+.
T Consensus 52 ~lrk~ 56 (309)
T TIGR00570 52 PLRKN 56 (309)
T ss_pred ccchh
Confidence 77765
No 184
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=57.58 E-value=3.6 Score=39.12 Aligned_cols=38 Identities=21% Similarity=0.570 Sum_probs=29.2
Q ss_pred cccccccccCCcCCcCccccCCCCChhhHHHHHHHHHH
Q 043604 37 IFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEA 74 (268)
Q Consensus 37 ~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~ 74 (268)
...|.||...+.......+.+.|||..|.-|+......
T Consensus 11 ~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~lyn~ 48 (861)
T KOG3161|consen 11 LLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLYNA 48 (861)
T ss_pred HhhchHHHHHHHHHhcCcccccccchHHHHHHHhHhhc
Confidence 45799998877555444567889999999999876643
No 185
>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=57.55 E-value=13 Score=23.52 Aligned_cols=30 Identities=20% Similarity=0.296 Sum_probs=22.1
Q ss_pred ccCCccccCceeeeccccccCCcCeeeCccccccc
Q 043604 127 SYCPNRNCMALVVNGCEINYGTLKKARCPNCTQWF 161 (268)
Q Consensus 127 ~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~ 161 (268)
..|| .|+.-+...... ..-.+.|+.||..+
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 899988776544 35678999998765
No 186
>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=57.22 E-value=9.6 Score=19.71 Aligned_cols=22 Identities=23% Similarity=0.455 Sum_probs=13.2
Q ss_pred ccCceeeeccccccCCcCeeeCccccc
Q 043604 133 NCMALVVNGCEINYGTLKKARCPNCTQ 159 (268)
Q Consensus 133 ~C~~~~~~~~~~~~~~~~~~~C~~C~~ 159 (268)
.|+..+..... ...+.||.||.
T Consensus 3 sC~~~i~~r~~-----~v~f~CPnCG~ 24 (24)
T PF07754_consen 3 SCGRPIAPREQ-----AVPFPCPNCGF 24 (24)
T ss_pred cCCCcccCccc-----CceEeCCCCCC
Confidence 45555543332 46788998873
No 187
>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=57.12 E-value=4.3 Score=25.16 Aligned_cols=24 Identities=21% Similarity=0.675 Sum_probs=11.1
Q ss_pred cCCCCCceeeecCCc--CeEEec-CCc
Q 043604 200 RCPACGSCVERKEGC--RVMYCS-CHS 223 (268)
Q Consensus 200 ~CP~C~~~iek~~GC--nhm~C~-C~~ 223 (268)
+|++|+.++-+.++= -.|+|. |++
T Consensus 6 RC~~CnklLa~~g~~~~leIKCpRC~t 32 (51)
T PF10122_consen 6 RCGHCNKLLAKAGEVIELEIKCPRCKT 32 (51)
T ss_pred eccchhHHHhhhcCccEEEEECCCCCc
Confidence 455555555553222 234553 554
No 188
>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 PF14369 zf-RING_3: zinc-finger
Probab=56.18 E-value=13 Score=21.15 Aligned_cols=30 Identities=27% Similarity=0.567 Sum_probs=19.6
Q ss_pred cccCCccccCceeeeccccccCCcCeeeCccccccc
Q 043604 126 RSYCPNRNCMALVVNGCEINYGTLKKARCPNCTQWF 161 (268)
Q Consensus 126 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~ 161 (268)
..||= .|...+...... ...+.||.|+..|
T Consensus 2 ~ywCh--~C~~~V~~~~~~----~~~~~CP~C~~gF 31 (35)
T PF14369_consen 2 RYWCH--QCNRFVRIAPSP----DSDVACPRCHGGF 31 (35)
T ss_pred CEeCc--cCCCEeEeCcCC----CCCcCCcCCCCcE
Confidence 35776 799888875443 1334699887654
No 190
>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=56.08 E-value=10 Score=23.66 Aligned_cols=36 Identities=28% Similarity=0.384 Sum_probs=18.2
Q ss_pred CcccCCccccCceeeecccc-----ccCCcCeeeCccccccc
Q 043604 125 ERSYCPNRNCMALVVNGCEI-----NYGTLKKARCPNCTQWF 161 (268)
Q Consensus 125 ~~~~Cp~~~C~~~~~~~~~~-----~~~~~~~~~C~~C~~~~ 161 (268)
+++.||||+|-.- ...... .......++|..|...+
T Consensus 5 gvl~C~Np~CITn-~~E~v~~~F~v~~~~~~~~rC~YCe~~~ 45 (52)
T PF02748_consen 5 GVLKCPNPNCITN-SNEPVESRFYVIDKEPIKLRCHYCERII 45 (52)
T ss_dssp SSSE-SSTTBTTT--TSSS--EEEEEETTTCEEEETTT--EE
T ss_pred eEEEcCCCCcccC-CCCCCCceEEEEeCCCCEEEeeCCCCEe
Confidence 5688999999654 111100 01134678888776543
No 191
>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=56.04 E-value=6 Score=23.60 Aligned_cols=42 Identities=26% Similarity=0.724 Sum_probs=19.6
Q ss_pred ccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCC
Q 043604 40 CEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPG 88 (268)
Q Consensus 40 C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~ 88 (268)
|.+|-+-+.....- ....|+=.+...|+..|+...-. .+||.
T Consensus 1 C~~C~~iv~~G~~C-~~~~C~~r~H~~C~~~y~r~~~~------~~CP~ 42 (43)
T PF08746_consen 1 CEACKEIVTQGQRC-SNRDCNVRLHDDCFKKYFRHRSN------PKCPN 42 (43)
T ss_dssp -TTT-SB-SSSEE--SS--S--EE-HHHHHHHTTT-SS-------B-TT
T ss_pred CcccchhHeeeccC-CCCccCchHHHHHHHHHHhcCCC------CCCcC
Confidence 56777665433222 22358888999999999875421 26875
No 192
>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=55.74 E-value=15 Score=19.24 Aligned_cols=23 Identities=26% Similarity=0.801 Sum_probs=18.7
Q ss_pred CCCCCceeeecCCcCeEEec-CCc
Q 043604 201 CPACGSCVERKEGCRVMYCS-CHS 223 (268)
Q Consensus 201 CP~C~~~iek~~GCnhm~C~-C~~ 223 (268)
|-+|++++.--.|=.++.|. |++
T Consensus 1 C~~Cr~~L~yp~GA~sVrCa~C~~ 24 (25)
T PF06943_consen 1 CGGCRTLLMYPRGAPSVRCACCHT 24 (25)
T ss_pred CCCCCceEEcCCCCCCeECCccCc
Confidence 56788888888888888887 764
No 193
>PLN02189 cellulose synthase
Probab=55.05 E-value=10 Score=38.40 Aligned_cols=62 Identities=19% Similarity=0.312 Sum_probs=43.2
Q ss_pred cccCCccccCceeeeccccccCCcCeeeCcccccccccccccccCCCCCcchhhcccchhhHHHHHHHHhCCcccCCCCC
Q 043604 126 RSYCPNRNCMALVVNGCEINYGTLKKARCPNCTQWFCFQCKLAWHAGYRCEESGNLRDWNDIAFGKLVERMHWARCPACG 205 (268)
Q Consensus 126 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~tC~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~ 205 (268)
..-|. -|+--+..+... ...+-|..|++..|..|.+ |. .+.+.+.||.|+
T Consensus 34 ~~~C~--iCgd~vg~~~~g----~~fvaC~~C~fpvCr~Cye----------ye--------------r~eg~q~CpqCk 83 (1040)
T PLN02189 34 GQVCE--ICGDEIGLTVDG----DLFVACNECGFPVCRPCYE----------YE--------------RREGTQNCPQCK 83 (1040)
T ss_pred Ccccc--ccccccCcCCCC----CEEEeeccCCCccccchhh----------hh--------------hhcCCccCcccC
Confidence 44666 687777665443 4779999999999996653 21 245667888888
Q ss_pred ceeeecCCcCeE
Q 043604 206 SCVERKEGCRVM 217 (268)
Q Consensus 206 ~~iek~~GCnhm 217 (268)
+...+--|++.+
T Consensus 84 t~Y~r~kgs~~v 95 (1040)
T PLN02189 84 TRYKRLKGSPRV 95 (1040)
T ss_pred CchhhccCCCCc
Confidence 888866666554
No 194
>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=54.06 E-value=12 Score=23.40 Aligned_cols=28 Identities=25% Similarity=0.571 Sum_probs=16.6
Q ss_pred ccCCCCCceee------ecCCcCeEE-ec-CCc-ccc
Q 043604 199 ARCPACGSCVE------RKEGCRVMY-CS-CHS-VTY 226 (268)
Q Consensus 199 k~CP~C~~~ie------k~~GCnhm~-C~-C~~-FC~ 226 (268)
|+||.|+-.-+ .+.+..++. |. |++ .-+
T Consensus 2 kPCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~~~~ 38 (53)
T TIGR03655 2 KPCPFCGGADVYLRRGFDPLDLSHYFECSTCGASGPV 38 (53)
T ss_pred CCCCCCCCcceeeEeccCCCCCEEEEECCCCCCCccc
Confidence 78999987555 123444443 65 665 543
No 195
>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=53.54 E-value=9.8 Score=26.20 Aligned_cols=30 Identities=27% Similarity=0.719 Sum_probs=16.6
Q ss_pred CcccCCCCCc------eeeecCCcCeEEec-CCc-ccc
Q 043604 197 HWARCPACGS------CVERKEGCRVMYCS-CHS-VTY 226 (268)
Q Consensus 197 ~~k~CP~C~~------~iek~~GCnhm~C~-C~~-FC~ 226 (268)
..-.||.|+. -|.+..|=-+++|+ ||. |=+
T Consensus 21 ~~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~~ 58 (81)
T PF05129_consen 21 KVFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQT 58 (81)
T ss_dssp S----TTT--SS-EEEEEETTTTEEEEEESSS--EEEE
T ss_pred ceEcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeEEE
Confidence 4568999992 45566888899998 987 743
No 196
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=53.43 E-value=4.8 Score=34.32 Aligned_cols=31 Identities=32% Similarity=0.890 Sum_probs=25.1
Q ss_pred hCCcccCCCCCceeeecC-CcCeEEec-CCc-cc
Q 043604 195 RMHWARCPACGSCVERKE-GCRVMYCS-CHS-VT 225 (268)
Q Consensus 195 ~~~~k~CP~C~~~iek~~-GCnhm~C~-C~~-FC 225 (268)
...|-+||.|+.++.+.+ +=|...|. |++ |=
T Consensus 25 e~lw~KCp~c~~~~y~~eL~~n~~vcp~c~~h~r 58 (294)
T COG0777 25 EGLWTKCPSCGEMLYRKELESNLKVCPKCGHHMR 58 (294)
T ss_pred CCceeECCCccceeeHHHHHhhhhcccccCcccc
Confidence 567899999999988774 66788887 988 63
No 197
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=53.06 E-value=13 Score=23.66 Aligned_cols=13 Identities=38% Similarity=0.800 Sum_probs=9.3
Q ss_pred CcccCCCCCceee
Q 043604 197 HWARCPACGSCVE 209 (268)
Q Consensus 197 ~~k~CP~C~~~ie 209 (268)
..|+||-|+....
T Consensus 2 ~LkPCPFCG~~~~ 14 (61)
T PF14354_consen 2 ELKPCPFCGSADV 14 (61)
T ss_pred CCcCCCCCCCcce
Confidence 3589999986443
No 198
>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=53.03 E-value=11 Score=23.51 Aligned_cols=37 Identities=22% Similarity=0.521 Sum_probs=25.5
Q ss_pred ccccccccCCcCCcCccccCCCCChhhHHHHHHHHHH
Q 043604 38 FTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEA 74 (268)
Q Consensus 38 ~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~ 74 (268)
..|.+|-..+.....-..-..||+.||.+|.......
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~~~ 39 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRIPL 39 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCcChHHcCCeeec
Confidence 4688898777543222234579999999999877543
No 199
>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=52.71 E-value=12 Score=29.22 Aligned_cols=31 Identities=19% Similarity=0.282 Sum_probs=21.3
Q ss_pred CCcccCCccccCceeeeccccccCCcCeeeCcccccc
Q 043604 124 FERSYCPNRNCMALVVNGCEINYGTLKKARCPNCTQW 160 (268)
Q Consensus 124 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~ 160 (268)
+....|| .|..-+...... ...+.||.||..
T Consensus 107 ~~~Y~Cp--~c~~r~tf~eA~----~~~F~Cp~Cg~~ 137 (158)
T TIGR00373 107 NMFFICP--NMCVRFTFNEAM----ELNFTCPRCGAM 137 (158)
T ss_pred CCeEECC--CCCcEeeHHHHH----HcCCcCCCCCCE
Confidence 4567798 688766655544 256889988764
No 200
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=52.52 E-value=4.5 Score=34.61 Aligned_cols=36 Identities=14% Similarity=0.252 Sum_probs=27.7
Q ss_pred ccCCCCCceeeecCCcCeEEec--CCc-ccccccccccCCCCCCCC
Q 043604 199 ARCPACGSCVERKEGCRVMYCS--CHS-VTYSRAKHISLRKHSTRG 241 (268)
Q Consensus 199 k~CP~C~~~iek~~GCnhm~C~--C~~-FC~~C~~~~~~~~~~~~~ 241 (268)
-+|-=|.-.|. +-|. ||| ||++|-..+-+.+..|+.
T Consensus 26 lrC~IC~~~i~-------ip~~TtCgHtFCslCIR~hL~~qp~CP~ 64 (391)
T COG5432 26 LRCRICDCRIS-------IPCETTCGHTFCSLCIRRHLGTQPFCPV 64 (391)
T ss_pred HHhhhhhheee-------cceecccccchhHHHHHHHhcCCCCCcc
Confidence 46776777776 7783 999 999999887776766654
No 201
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=51.69 E-value=14 Score=29.60 Aligned_cols=31 Identities=26% Similarity=0.517 Sum_probs=21.2
Q ss_pred CCcccCCccccCceeeeccccccCCcCeeeCcccccc
Q 043604 124 FERSYCPNRNCMALVVNGCEINYGTLKKARCPNCTQW 160 (268)
Q Consensus 124 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~ 160 (268)
+....|| .|+.-+...... ...+.||.||..
T Consensus 115 ~~~Y~Cp--~C~~rytf~eA~----~~~F~Cp~Cg~~ 145 (178)
T PRK06266 115 NMFFFCP--NCHIRFTFDEAM----EYGFRCPQCGEM 145 (178)
T ss_pred CCEEECC--CCCcEEeHHHHh----hcCCcCCCCCCC
Confidence 4567898 688777665544 356889888753
No 202
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=51.53 E-value=9.3 Score=26.54 Aligned_cols=34 Identities=15% Similarity=0.386 Sum_probs=27.1
Q ss_pred ccCCCCCceeeecCCcCeEEecCCc-ccccccccccCC
Q 043604 199 ARCPACGSCVERKEGCRVMYCSCHS-VTYSRAKHISLR 235 (268)
Q Consensus 199 k~CP~C~~~iek~~GCnhm~C~C~~-FC~~C~~~~~~~ 235 (268)
.-||.|+.+ .+.|.-+...|++ |=..|..+|-..
T Consensus 33 g~Cp~Ck~P---gd~Cplv~g~C~H~FH~hCI~kWl~~ 67 (85)
T PF12861_consen 33 GCCPDCKFP---GDDCPLVWGKCSHNFHMHCILKWLST 67 (85)
T ss_pred cCCCCccCC---CCCCceeeccCccHHHHHHHHHHHcc
Confidence 367888887 4678778888999 999999998763
No 203
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=51.24 E-value=14 Score=25.15 Aligned_cols=50 Identities=22% Similarity=0.570 Sum_probs=20.2
Q ss_pred CcccccccccCCcCC---cCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCC
Q 043604 36 GIFTCEICIEPISAN---DKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQF 94 (268)
Q Consensus 36 ~~~~C~IC~~~~~~~---~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~ 94 (268)
....|.||-+++-.. +.|.....|+-..|+.|+.- ..++|+ -.||. |+..
T Consensus 8 ~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEY----Erkeg~---q~Cpq--Ckt~ 60 (80)
T PF14569_consen 8 NGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEY----ERKEGN---QVCPQ--CKTR 60 (80)
T ss_dssp SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHH----HHHTS----SB-TT--T--B
T ss_pred CCcccccccCccccCCCCCEEEEEcccCCccchhHHHH----HhhcCc---ccccc--cCCC
Confidence 456799999987543 45655667899999999754 344433 35787 7743
No 204
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=51.02 E-value=18 Score=23.64 Aligned_cols=9 Identities=33% Similarity=0.792 Sum_probs=7.0
Q ss_pred CeEEec-CCc
Q 043604 215 RVMYCS-CHS 223 (268)
Q Consensus 215 nhm~C~-C~~ 223 (268)
-+++|. ||+
T Consensus 39 ~~itCk~CgY 48 (68)
T COG3478 39 IVITCKNCGY 48 (68)
T ss_pred EEEEeccCCc
Confidence 468897 987
No 205
>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=50.80 E-value=9 Score=28.68 Aligned_cols=24 Identities=21% Similarity=0.225 Sum_probs=14.8
Q ss_pred ccCCCCCceeeecCCcCeEEec-CCc
Q 043604 199 ARCPACGSCVERKEGCRVMYCS-CHS 223 (268)
Q Consensus 199 k~CP~C~~~iek~~GCnhm~C~-C~~ 223 (268)
+.||+|++...--.- +-++|. ||+
T Consensus 10 r~Cp~cg~kFYDLnk-~p~vcP~cg~ 34 (129)
T TIGR02300 10 RICPNTGSKFYDLNR-RPAVSPYTGE 34 (129)
T ss_pred ccCCCcCccccccCC-CCccCCCcCC
Confidence 568888776553333 556665 665
No 206
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=50.58 E-value=5.7 Score=34.06 Aligned_cols=30 Identities=27% Similarity=0.566 Sum_probs=22.2
Q ss_pred cccccccccCCcCCcCccccCCCCCh-hhHHHHHH
Q 043604 37 IFTCEICIEPISANDKFRNKDLCSHH-FCQDCIAK 70 (268)
Q Consensus 37 ~~~C~IC~~~~~~~~~~~~~~~C~H~-fC~~Cl~~ 70 (268)
..-|.|||+.- .+.| ++.|||. .|..|=+.
T Consensus 300 ~~LC~ICmDaP--~DCv--fLeCGHmVtCt~CGkr 330 (350)
T KOG4275|consen 300 RRLCAICMDAP--RDCV--FLECGHMVTCTKCGKR 330 (350)
T ss_pred HHHHHHHhcCC--cceE--EeecCcEEeehhhccc
Confidence 56799999864 2444 7999995 58888554
No 207
>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=50.29 E-value=13 Score=27.04 Aligned_cols=26 Identities=27% Similarity=0.727 Sum_probs=19.0
Q ss_pred ccCCCCCceeeecCCcCeEEec-CCc-cc
Q 043604 199 ARCPACGSCVERKEGCRVMYCS-CHS-VT 225 (268)
Q Consensus 199 k~CP~C~~~iek~~GCnhm~C~-C~~-FC 225 (268)
-.||+|..-..-.+|=+ +.|. |++ |=
T Consensus 3 p~CP~C~seytY~dg~~-~iCpeC~~EW~ 30 (109)
T TIGR00686 3 PPCPKCNSEYTYHDGTQ-LICPSCLYEWN 30 (109)
T ss_pred CcCCcCCCcceEecCCe-eECcccccccc
Confidence 47999998877777754 6676 776 63
No 208
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=49.11 E-value=42 Score=29.03 Aligned_cols=45 Identities=24% Similarity=0.814 Sum_probs=31.7
Q ss_pred cccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCC
Q 043604 37 IFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQ 93 (268)
Q Consensus 37 ~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~ 93 (268)
.+.|+.|-.-+... + ....|+|.||.+|+..-+.. ..+.||. |..
T Consensus 274 ~LkCplc~~Llrnp--~-kT~cC~~~fc~eci~~al~d-------sDf~Cpn--C~r 318 (427)
T COG5222 274 SLKCPLCHCLLRNP--M-KTPCCGHTFCDECIGTALLD-------SDFKCPN--CSR 318 (427)
T ss_pred cccCcchhhhhhCc--c-cCccccchHHHHHHhhhhhh-------ccccCCC--ccc
Confidence 37899998755332 2 23568999999999866532 3578998 874
No 209
>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=47.57 E-value=8.3 Score=21.96 Aligned_cols=31 Identities=23% Similarity=0.669 Sum_probs=15.7
Q ss_pred hhHHHHHHHHHHHhhcCCCceeccCCCCCCCCC
Q 043604 63 FCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFL 95 (268)
Q Consensus 63 fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i 95 (268)
+|.+|++.|....-+.-....+.|+. |+-.+
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 47888888865432222345688988 87544
No 210
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=47.33 E-value=20 Score=23.00 Aligned_cols=30 Identities=23% Similarity=0.404 Sum_probs=22.2
Q ss_pred ccCCccccCceeeeccccccCCcCeeeCcccccccc
Q 043604 127 SYCPNRNCMALVVNGCEINYGTLKKARCPNCTQWFC 162 (268)
Q Consensus 127 ~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~C 162 (268)
+.|| +|.+....-... ...+.|..|+...+
T Consensus 12 VkCp--~C~n~q~vFsha----~t~V~C~~Cg~~L~ 41 (59)
T PRK00415 12 VKCP--DCGNEQVVFSHA----STVVRCLVCGKTLA 41 (59)
T ss_pred EECC--CCCCeEEEEecC----CcEEECcccCCCcc
Confidence 6788 898877665554 47888988887664
No 211
>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.
Probab=47.15 E-value=24 Score=27.57 Aligned_cols=83 Identities=18% Similarity=0.448 Sum_probs=47.5
Q ss_pred cccccccccCCcCCcCccccCCC-------CChhh------HHHHHHHHHHHhhcC-----------------------C
Q 043604 37 IFTCEICIEPISANDKFRNKDLC-------SHHFC------QDCIAKYIEAKVQDN-----------------------N 80 (268)
Q Consensus 37 ~~~C~IC~~~~~~~~~~~~~~~C-------~H~fC------~~Cl~~~~~~~i~~~-----------------------~ 80 (268)
..+|+||+|--... ++|.| .-++| .+||.+|-++..+.. .
T Consensus 2 d~~CpICme~PHNA----VLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkka~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 77 (162)
T PF07800_consen 2 DVTCPICMEHPHNA----VLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKKAYGKSSSSSSQSSSSAPSDSSSSESSESQE 77 (162)
T ss_pred CccCceeccCCCce----EEEEeccccCCccccccCCccchhHHHHHHHHHhcCCCCccccccccCcCCCcccccccccc
Confidence 46799999865332 23433 33333 578888887655441 1
Q ss_pred CceeccCCCCCCCCCCHH----HHhhcCChhHHHHHHHHHHhhhhcCCCcccCCccccCceeeeccc
Q 043604 81 TAKIECPGVHCDQFLDPF----SCKLMIPSNLFSKWCDVLFEDYVLGFERSYCPNRNCMALVVNGCE 143 (268)
Q Consensus 81 ~~~i~CP~~~C~~~i~~~----~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~ 143 (268)
...+.||. |...|.-- ..+.+| +...+.|+..+|.+...+...
T Consensus 78 ~~~L~CPL--CRG~V~GWtvve~AR~~L------------------N~K~RsC~~e~C~F~GtY~eL 124 (162)
T PF07800_consen 78 QPELACPL--CRGEVKGWTVVEPARRFL------------------NAKKRSCSQESCSFSGTYSEL 124 (162)
T ss_pred cccccCcc--ccCceeceEEchHHHHHh------------------ccCCccCcccccccccCHHHH
Confidence 23578988 88654321 122222 124577887788776655443
No 212
>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=46.45 E-value=6.6 Score=38.75 Aligned_cols=65 Identities=22% Similarity=0.327 Sum_probs=0.0
Q ss_pred CcccCCCCCceeeecCCcCeEEec-CC-----c-ccccccccccCCCC-CCCCCCCCCcccceecccCccccccccccc
Q 043604 197 HWARCPACGSCVERKEGCRVMYCS-CH-----S-VTYSRAKHISLRKH-STRGDNKGWRIYKVSGCRSTCRSLENFGVT 267 (268)
Q Consensus 197 ~~k~CP~C~~~iek~~GCnhm~C~-C~-----~-FC~~C~~~~~~~~~-~~~~~~~~~~~~~~~gc~~~~~~l~~~~~~ 267 (268)
..++||+|+..... .+|. || . +|..|+........ .|...-......++.==....++|+++|+.
T Consensus 654 ~~r~Cp~Cg~~t~~------~~Cp~CG~~T~~~~~Cp~C~~~~~~~~C~~C~~~~~~~~~~~i~l~~~~~~A~e~lg~r 726 (900)
T PF03833_consen 654 GRRRCPKCGKETFY------NRCPECGSHTEPVYVCPDCGIEVEEDECPKCGRETTSYSKQKIDLKEEYDRALENLGER 726 (900)
T ss_dssp -------------------------------------------------------------------------------
T ss_pred ecccCcccCCcchh------hcCcccCCccccceeccccccccCccccccccccCcccceeecCHHHHHHHHHHhhccc
Confidence 45899999987653 4575 76 4 67777777654321 111111111122222223355688888864
No 213
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=46.30 E-value=15 Score=37.42 Aligned_cols=61 Identities=20% Similarity=0.362 Sum_probs=39.9
Q ss_pred ccCCccccCceeeeccccccCCcCeeeCcccccccccccccccCCCCCcchhhcccchhhHHHHHHHHhCCcccCCCCCc
Q 043604 127 SYCPNRNCMALVVNGCEINYGTLKKARCPNCTQWFCFQCKLAWHAGYRCEESGNLRDWNDIAFGKLVERMHWARCPACGS 206 (268)
Q Consensus 127 ~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~tC~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~ 206 (268)
.-|- -|+--+.....- ...|-|..|+.-.|.-|.+ |. .+.+.+-||.|++
T Consensus 18 qiCq--ICGD~vg~~~~G----e~FVAC~eC~FPVCrpCYE----------YE--------------r~eG~q~CPqCkt 67 (1079)
T PLN02638 18 QVCQ--ICGDNVGKTVDG----EPFVACDVCAFPVCRPCYE----------YE--------------RKDGNQSCPQCKT 67 (1079)
T ss_pred ceee--ecccccCcCCCC----CEEEEeccCCCccccchhh----------hh--------------hhcCCccCCccCC
Confidence 3454 577666555432 4789999999999996653 22 2455677888888
Q ss_pred eeeecCCcCeE
Q 043604 207 CVERKEGCRVM 217 (268)
Q Consensus 207 ~iek~~GCnhm 217 (268)
+..+--|+..+
T Consensus 68 rYkr~kgsprv 78 (1079)
T PLN02638 68 KYKRHKGSPAI 78 (1079)
T ss_pred chhhhcCCCCc
Confidence 77765555444
No 214
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=46.05 E-value=5.9 Score=38.34 Aligned_cols=29 Identities=24% Similarity=0.716 Sum_probs=20.1
Q ss_pred ccccccccccccccCCCCCcchhhcccchhhHHHHHHHHhCCcccCCCCCcee
Q 043604 156 NCTQWFCFQCKLAWHAGYRCEESGNLRDWNDIAFGKLVERMHWARCPACGSCV 208 (268)
Q Consensus 156 ~C~~~~C~~C~~~~H~~~tC~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~~i 208 (268)
.|+..||..|..+ .-....++||+|+...
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 5788888887753 1133458999998764
No 215
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=45.60 E-value=17 Score=31.16 Aligned_cols=24 Identities=33% Similarity=0.975 Sum_probs=20.9
Q ss_pred ccCCCCCceeeec--CCcCeEEec-CC
Q 043604 199 ARCPACGSCVERK--EGCRVMYCS-CH 222 (268)
Q Consensus 199 k~CP~C~~~iek~--~GCnhm~C~-C~ 222 (268)
++|+.|+.+|+|. +|=+...|. |.
T Consensus 246 epC~~CGt~I~k~~~~gR~t~~CP~CQ 272 (273)
T COG0266 246 EPCRRCGTPIEKIKLGGRSTFYCPVCQ 272 (273)
T ss_pred CCCCccCCEeEEEEEcCCcCEeCCCCC
Confidence 7999999999998 888888886 75
No 216
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=45.25 E-value=8.1 Score=24.47 Aligned_cols=15 Identities=0% Similarity=-0.162 Sum_probs=12.0
Q ss_pred CCc-ccccccccccCC
Q 043604 221 CHS-VTYSRAKHISLR 235 (268)
Q Consensus 221 C~~-FC~~C~~~~~~~ 235 (268)
=.+ |||.||..|...
T Consensus 25 ~~~~YC~~Cg~~Y~d~ 40 (55)
T PF13821_consen 25 EEHNYCFWCGTKYDDE 40 (55)
T ss_pred hhCceeeeeCCccCCH
Confidence 357 999999998774
No 217
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=45.18 E-value=17 Score=29.27 Aligned_cols=24 Identities=25% Similarity=0.654 Sum_probs=20.2
Q ss_pred ccCCCCCceeeecCCcCeEEec-CCc
Q 043604 199 ARCPACGSCVERKEGCRVMYCS-CHS 223 (268)
Q Consensus 199 k~CP~C~~~iek~~GCnhm~C~-C~~ 223 (268)
-.||+|+.++.+.+. |+|.|. |++
T Consensus 150 a~~~~~g~~~~~~~~-~~~~c~~~~~ 174 (189)
T PRK09521 150 AMCSRCRTPLVKKGE-NELKCPNCGN 174 (189)
T ss_pred EEccccCCceEECCC-CEEECCCCCC
Confidence 479999999988544 999998 987
No 218
>PLN02400 cellulose synthase
Probab=45.11 E-value=16 Score=37.31 Aligned_cols=61 Identities=20% Similarity=0.304 Sum_probs=40.1
Q ss_pred ccCCccccCceeeeccccccCCcCeeeCcccccccccccccccCCCCCcchhhcccchhhHHHHHHHHhCCcccCCCCCc
Q 043604 127 SYCPNRNCMALVVNGCEINYGTLKKARCPNCTQWFCFQCKLAWHAGYRCEESGNLRDWNDIAFGKLVERMHWARCPACGS 206 (268)
Q Consensus 127 ~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~tC~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~ 206 (268)
.-|- -|+--+..... ....+-|..|+.-.|.-|.+ |.+ +.+.+-||.|++
T Consensus 37 qiCq--ICGD~VG~t~d----Ge~FVAC~eCaFPVCRpCYE----------YER--------------keGnq~CPQCkT 86 (1085)
T PLN02400 37 QICQ--ICGDDVGVTET----GDVFVACNECAFPVCRPCYE----------YER--------------KDGTQCCPQCKT 86 (1085)
T ss_pred ceee--ecccccCcCCC----CCEEEEEccCCCccccchhh----------eec--------------ccCCccCcccCC
Confidence 3454 57666655433 24789999999999996653 221 345677888888
Q ss_pred eeeecCCcCeE
Q 043604 207 CVERKEGCRVM 217 (268)
Q Consensus 207 ~iek~~GCnhm 217 (268)
...+--|+..+
T Consensus 87 rYkR~KgsprV 97 (1085)
T PLN02400 87 RYRRHKGSPRV 97 (1085)
T ss_pred ccccccCCCCC
Confidence 77766665544
No 219
>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=44.62 E-value=15 Score=20.75 Aligned_cols=26 Identities=27% Similarity=0.561 Sum_probs=21.2
Q ss_pred cCeeeCcccccccccccccccCCCCC
Q 043604 149 LKKARCPNCTQWFCFQCKLAWHAGYR 174 (268)
Q Consensus 149 ~~~~~C~~C~~~~C~~C~~~~H~~~t 174 (268)
...+.|..|+...|..|....|.++.
T Consensus 10 ~~~~fC~~~~~~iC~~C~~~~H~~H~ 35 (39)
T cd00021 10 PLSLFCETDRALLCVDCDLSVHSGHR 35 (39)
T ss_pred ceEEEeCccChhhhhhcChhhcCCCC
Confidence 45789999999999999876687653
No 220
>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=44.47 E-value=14 Score=27.05 Aligned_cols=23 Identities=30% Similarity=0.772 Sum_probs=15.0
Q ss_pred cCeeeCccccccc--------ccccccccCC
Q 043604 149 LKKARCPNCTQWF--------CFQCKLAWHA 171 (268)
Q Consensus 149 ~~~~~C~~C~~~~--------C~~C~~~~H~ 171 (268)
...+.||.|++.+ |..|+.+.+-
T Consensus 67 av~V~CP~C~K~TKmLGr~D~CM~C~~pLTL 97 (114)
T PF11023_consen 67 AVQVECPNCGKQTKMLGRVDACMHCKEPLTL 97 (114)
T ss_pred ceeeECCCCCChHhhhchhhccCcCCCcCcc
Confidence 4667788776544 7777776543
No 221
>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=44.33 E-value=13 Score=31.43 Aligned_cols=51 Identities=27% Similarity=0.723 Sum_probs=28.6
Q ss_pred cCeeeCccc---ccccccccccccCCCCCcchhhcccchhhHHHHHHHHhCCcccCCCCCceeeec
Q 043604 149 LKKARCPNC---TQWFCFQCKLAWHAGYRCEESGNLRDWNDIAFGKLVERMHWARCPACGSCVERK 211 (268)
Q Consensus 149 ~~~~~C~~C---~~~~C~~C~~~~H~~~tC~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~~iek~ 211 (268)
.-.+.|.+| |...|++|+.- -|+++-+.. .+ + .......+||+|+..+.-.
T Consensus 169 ~E~~KC~SCNrlGq~sCLRCK~c-----fCddHvrrK-----g~-k-y~k~k~~PCPKCg~et~eT 222 (314)
T PF06524_consen 169 SETFKCQSCNRLGQYSCLRCKIC-----FCDDHVRRK-----GF-K-YEKGKPIPCPKCGYETQET 222 (314)
T ss_pred cccccccccccccchhhhheeee-----ehhhhhhhc-----cc-c-cccCCCCCCCCCCCccccc
Confidence 345566666 56778888764 344332210 11 1 1233557999999887644
No 222
>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=44.19 E-value=7.9 Score=22.56 Aligned_cols=24 Identities=25% Similarity=0.672 Sum_probs=21.1
Q ss_pred CeeeCcccccccccccccccCCCC
Q 043604 150 KKARCPNCTQWFCFQCKLAWHAGY 173 (268)
Q Consensus 150 ~~~~C~~C~~~~C~~C~~~~H~~~ 173 (268)
..+.|..|+..+|..|...-|.++
T Consensus 14 ~~~~C~~C~~~~C~~C~~~~H~~H 37 (42)
T PF00643_consen 14 LSLFCEDCNEPLCSECTVSGHKGH 37 (42)
T ss_dssp EEEEETTTTEEEEHHHHHTSTTTS
T ss_pred eEEEecCCCCccCccCCCCCCCCC
Confidence 678999999999999999878774
No 223
>COG3492 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=43.44 E-value=41 Score=23.56 Aligned_cols=17 Identities=18% Similarity=0.821 Sum_probs=15.1
Q ss_pred hhhHHHHHHHHHHHhhc
Q 043604 62 HFCQDCIAKYIEAKVQD 78 (268)
Q Consensus 62 ~fC~~Cl~~~~~~~i~~ 78 (268)
-||++||..|+......
T Consensus 42 gFCRNCLs~Wy~eaae~ 58 (104)
T COG3492 42 GFCRNCLSNWYREAAEA 58 (104)
T ss_pred HHHHHHHHHHHHHHHhc
Confidence 59999999999988766
No 224
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=42.93 E-value=14 Score=27.09 Aligned_cols=44 Identities=18% Similarity=0.467 Sum_probs=29.6
Q ss_pred ccCCccccCceeeeccccc---cCCcCeeeCcccccccccccccccCCC
Q 043604 127 SYCPNRNCMALVVNGCEIN---YGTLKKARCPNCTQWFCFQCKLAWHAG 172 (268)
Q Consensus 127 ~~Cp~~~C~~~~~~~~~~~---~~~~~~~~C~~C~~~~C~~C~~~~H~~ 172 (268)
..|- +|...+....... ........|+.|+..||..|..-+|+-
T Consensus 56 ~~C~--~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~ 102 (112)
T TIGR00622 56 RFCF--GCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHES 102 (112)
T ss_pred Cccc--CcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhh
Confidence 4576 7887775432110 112457889999999999998877753
No 225
>PRK04023 DNA polymerase II large subunit; Validated
Probab=42.31 E-value=19 Score=36.45 Aligned_cols=17 Identities=35% Similarity=1.054 Sum_probs=9.2
Q ss_pred eeCccccc-----ccccccccc
Q 043604 152 ARCPNCTQ-----WFCFQCKLA 168 (268)
Q Consensus 152 ~~C~~C~~-----~~C~~C~~~ 168 (268)
..||.||. .+|..|+..
T Consensus 639 frCP~CG~~Te~i~fCP~CG~~ 660 (1121)
T PRK04023 639 RRCPFCGTHTEPVYRCPRCGIE 660 (1121)
T ss_pred ccCCCCCCCCCcceeCccccCc
Confidence 45666653 356666544
No 226
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=42.18 E-value=21 Score=30.63 Aligned_cols=22 Identities=32% Similarity=0.901 Sum_probs=16.2
Q ss_pred ccCCCCCceeeec--CCcCeEEec
Q 043604 199 ARCPACGSCVERK--EGCRVMYCS 220 (268)
Q Consensus 199 k~CP~C~~~iek~--~GCnhm~C~ 220 (268)
++||.|+..|++. +|=.--.|.
T Consensus 236 ~pC~~Cg~~I~~~~~~gR~ty~Cp 259 (269)
T PRK14811 236 QPCPRCGTPIEKIVVGGRGTHFCP 259 (269)
T ss_pred CCCCcCCCeeEEEEECCCCcEECC
Confidence 7899999999987 664444443
No 227
>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=42.00 E-value=15 Score=20.43 Aligned_cols=23 Identities=30% Similarity=0.534 Sum_probs=13.6
Q ss_pred ccCceeeeccccccCCcCeeeCccccccc
Q 043604 133 NCMALVVNGCEINYGTLKKARCPNCTQWF 161 (268)
Q Consensus 133 ~C~~~~~~~~~~~~~~~~~~~C~~C~~~~ 161 (268)
+|+..+..... ..++|+.||..+
T Consensus 5 ~Cg~~~~~~~~------~~irC~~CG~RI 27 (32)
T PF03604_consen 5 ECGAEVELKPG------DPIRCPECGHRI 27 (32)
T ss_dssp SSSSSE-BSTS------STSSBSSSS-SE
T ss_pred cCCCeeEcCCC------CcEECCcCCCeE
Confidence 67777664433 457888888653
No 228
>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=41.53 E-value=58 Score=20.14 Aligned_cols=41 Identities=22% Similarity=0.514 Sum_probs=24.0
Q ss_pred cccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCC
Q 043604 37 IFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLD 96 (268)
Q Consensus 37 ~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~ 96 (268)
.+.|+.|...+.. .=|..++...=.. ....+.||. |...+.
T Consensus 2 ~f~CP~C~~~~~~----------------~~L~~H~~~~H~~-~~~~v~CPi--C~~~~~ 42 (54)
T PF05605_consen 2 SFTCPYCGKGFSE----------------SSLVEHCEDEHRS-ESKNVVCPI--CSSRVT 42 (54)
T ss_pred CcCCCCCCCccCH----------------HHHHHHHHhHCcC-CCCCccCCC--chhhhh
Confidence 5789999885421 1234444443333 344699999 876433
No 229
>KOG4218 consensus Nuclear hormone receptor betaFTZ-F1 [Transcription]
Probab=40.16 E-value=19 Score=31.72 Aligned_cols=9 Identities=44% Similarity=1.132 Sum_probs=5.9
Q ss_pred cccCCCCCc
Q 043604 198 WARCPACGS 206 (268)
Q Consensus 198 ~k~CP~C~~ 206 (268)
.|+||.|+.
T Consensus 67 RKRCP~CRF 75 (475)
T KOG4218|consen 67 RKRCPSCRF 75 (475)
T ss_pred hccCCchhH
Confidence 378887653
No 230
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=40.08 E-value=52 Score=25.75 Aligned_cols=52 Identities=17% Similarity=0.342 Sum_probs=34.7
Q ss_pred CCcccccccccCCcCCcCccccCCCCC---hhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCCH
Q 043604 35 NGIFTCEICIEPISANDKFRNKDLCSH---HFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLDP 97 (268)
Q Consensus 35 ~~~~~C~IC~~~~~~~~~~~~~~~C~H---~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~ 97 (268)
.....|-||+++... . .....|.. ....+|+..|+... ....|+. |+.+...
T Consensus 6 ~~~~~CRIC~~~~~~-~--~~PC~CkGs~k~VH~sCL~rWi~~s------~~~~Cei--C~~~Y~i 60 (162)
T PHA02825 6 LMDKCCWICKDEYDV-V--TNYCNCKNENKIVHKECLEEWINTS------KNKSCKI--CNGPYNI 60 (162)
T ss_pred CCCCeeEecCCCCCC-c--cCCcccCCCchHHHHHHHHHHHhcC------CCCcccc--cCCeEEE
Confidence 345689999998632 1 12233433 67999999999843 3567988 8866543
No 231
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=39.83 E-value=42 Score=24.32 Aligned_cols=33 Identities=15% Similarity=0.410 Sum_probs=20.5
Q ss_pred CcccCCccccCceeeeccccccCCcCeeeCcccccc
Q 043604 125 ERSYCPNRNCMALVVNGCEINYGTLKKARCPNCTQW 160 (268)
Q Consensus 125 ~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~ 160 (268)
..++|+ .|++.+.+..... .+...+.|..|.+.
T Consensus 3 ~~rfC~--eCNNmLYPkEDke-d~~L~laCrnCd~v 35 (113)
T KOG2691|consen 3 GIRFCR--ECNNMLYPKEDKE-DRILLLACRNCDYV 35 (113)
T ss_pred ccchhh--hhhcccccccccc-ccEEEEEecCCcce
Confidence 357887 8999888766532 12344567666543
No 232
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=39.37 E-value=28 Score=22.04 Aligned_cols=31 Identities=16% Similarity=0.386 Sum_probs=19.6
Q ss_pred ccCCccccCceeeeccccccCCcCeeeCccccccccc
Q 043604 127 SYCPNRNCMALVVNGCEINYGTLKKARCPNCTQWFCF 163 (268)
Q Consensus 127 ~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~C~ 163 (268)
+.|| +|.+.-..-... ...+.|..|+...|.
T Consensus 8 VkCp--~C~~~q~vFSha----~t~V~C~~Cg~~L~~ 38 (55)
T PF01667_consen 8 VKCP--GCYNIQTVFSHA----QTVVKCVVCGTVLAQ 38 (55)
T ss_dssp EE-T--TT-SEEEEETT-----SS-EE-SSSTSEEEE
T ss_pred EECC--CCCCeeEEEecC----CeEEEcccCCCEecC
Confidence 6788 898877765544 578999999887764
No 233
>PLN02436 cellulose synthase A
Probab=38.87 E-value=27 Score=35.70 Aligned_cols=61 Identities=20% Similarity=0.346 Sum_probs=40.7
Q ss_pred ccCCccccCceeeeccccccCCcCeeeCcccccccccccccccCCCCCcchhhcccchhhHHHHHHHHhCCcccCCCCCc
Q 043604 127 SYCPNRNCMALVVNGCEINYGTLKKARCPNCTQWFCFQCKLAWHAGYRCEESGNLRDWNDIAFGKLVERMHWARCPACGS 206 (268)
Q Consensus 127 ~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~tC~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~ 206 (268)
.-|. -|+--+.....- ...+-|..|++..|..|.+ |. .+.+.+.||.|++
T Consensus 37 ~iCq--ICGD~Vg~t~dG----e~FVACn~C~fpvCr~Cye----------ye--------------r~eg~~~Cpqckt 86 (1094)
T PLN02436 37 QTCQ--ICGDEIELTVDG----EPFVACNECAFPVCRPCYE----------YE--------------RREGNQACPQCKT 86 (1094)
T ss_pred cccc--ccccccCcCCCC----CEEEeeccCCCccccchhh----------hh--------------hhcCCccCcccCC
Confidence 4555 677666555332 4789999999999996653 21 2455678888888
Q ss_pred eeeecCCcCeE
Q 043604 207 CVERKEGCRVM 217 (268)
Q Consensus 207 ~iek~~GCnhm 217 (268)
...+--|++.+
T Consensus 87 ~Y~r~kgs~~~ 97 (1094)
T PLN02436 87 RYKRIKGSPRV 97 (1094)
T ss_pred chhhccCCCCc
Confidence 87765555544
No 234
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=38.85 E-value=46 Score=31.34 Aligned_cols=33 Identities=33% Similarity=0.619 Sum_probs=24.0
Q ss_pred CCccccCceeeeccccccCCcCeeeCcccccc-----cccccccc
Q 043604 129 CPNRNCMALVVNGCEINYGTLKKARCPNCTQW-----FCFQCKLA 168 (268)
Q Consensus 129 Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~-----~C~~C~~~ 168 (268)
|| .|+..+...... ..+.|+.||+. .|..|+..
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 65 777777766543 67899999875 58888764
No 235
>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=38.44 E-value=6.5 Score=21.46 Aligned_cols=20 Identities=20% Similarity=0.383 Sum_probs=10.3
Q ss_pred eeccCCCCCCCCCCHHHHhh
Q 043604 83 KIECPGVHCDQFLDPFSCKL 102 (268)
Q Consensus 83 ~i~CP~~~C~~~i~~~~i~~ 102 (268)
.++||..+|...+.......
T Consensus 2 ~vrCPvkdC~EEv~lgKY~~ 21 (30)
T PF10426_consen 2 VVRCPVKDCDEEVSLGKYSH 21 (30)
T ss_dssp EEE--STT---EEEHHHHHH
T ss_pred ccccccccCcchhhhhhhcc
Confidence 47999999998877655443
No 236
>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=38.27 E-value=18 Score=30.16 Aligned_cols=56 Identities=16% Similarity=0.373 Sum_probs=39.2
Q ss_pred eccCCCCCCCCCC-HHHHhhcCChhHHHHHHHHHHhhhhcCCCcccCCccccCceeeecc
Q 043604 84 IECPGVHCDQFLD-PFSCKLMIPSNLFSKWCDVLFEDYVLGFERSYCPNRNCMALVVNGC 142 (268)
Q Consensus 84 i~CP~~~C~~~i~-~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~ 142 (268)
-+||. |+...- ..+++-+++++-|.+...--..... +.+...||.++|+.++....
T Consensus 11 ~~CPv--CksDrYLnPdik~linPECyHrmCESCvdRIF-s~GpAqCP~~gC~kILRK~k 67 (314)
T COG5220 11 RRCPV--CKSDRYLNPDIKILINPECYHRMCESCVDRIF-SRGPAQCPYKGCGKILRKIK 67 (314)
T ss_pred ccCCc--cccccccCCCeEEEECHHHHHHHHHHHHHHHh-cCCCCCCCCccHHHHHHHhc
Confidence 47998 986433 3578888999988887665444322 34568899999998876433
No 237
>KOG3113 consensus Uncharacterized conserved protein [Function unknown]
Probab=38.11 E-value=34 Score=28.86 Aligned_cols=73 Identities=11% Similarity=0.189 Sum_probs=47.8
Q ss_pred CCCcccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCCHHHHhhcCC-hhHHHHH
Q 043604 34 TNGIFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLDPFSCKLMIP-SNLFSKW 112 (268)
Q Consensus 34 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~~l~-~~~~~~~ 112 (268)
+...|.|+|=--++.....|..+..|||+|=..=| .+|.. -.|+. |++.+..+++--|=+ +|.++.|
T Consensus 108 ~~a~fiCPvtgleMng~~~F~~l~~CGcV~SerAl-----Keika-----s~C~~--C~a~y~~~dvIvlNg~~E~~dll 175 (293)
T KOG3113|consen 108 QRARFICPVTGLEMNGKYRFCALRCCGCVFSERAL-----KEIKA-----SVCHV--CGAAYQEDDVIVLNGTEEDVDLL 175 (293)
T ss_pred ccceeecccccceecceEEEEEEeccceeccHHHH-----HHhhh-----ccccc--cCCcccccCeEeeCCCHHHHHHH
Confidence 35678999987777666667777899999844433 23332 45888 998888777655443 4556555
Q ss_pred HHHHHh
Q 043604 113 CDVLFE 118 (268)
Q Consensus 113 ~~~~~~ 118 (268)
..++.+
T Consensus 176 k~rme~ 181 (293)
T KOG3113|consen 176 KTRMEE 181 (293)
T ss_pred HHHHHH
Confidence 554443
No 238
>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=38.10 E-value=47 Score=24.42 Aligned_cols=26 Identities=27% Similarity=0.631 Sum_probs=16.7
Q ss_pred CcccCCccccCceeeeccccccCCcCeeeCccccc
Q 043604 125 ERSYCPNRNCMALVVNGCEINYGTLKKARCPNCTQ 159 (268)
Q Consensus 125 ~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~ 159 (268)
-..+|+ +|+..+..... .+.||.|+.
T Consensus 69 ~~~~C~--~Cg~~~~~~~~-------~~~CP~Cgs 94 (115)
T TIGR00100 69 VECECE--DCSEEVSPEID-------LYRCPKCHG 94 (115)
T ss_pred cEEEcc--cCCCEEecCCc-------CccCcCCcC
Confidence 357888 88877665432 355887764
No 239
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=37.67 E-value=23 Score=36.06 Aligned_cols=57 Identities=21% Similarity=0.349 Sum_probs=38.0
Q ss_pred ccCceeeeccccccCCcCeeeCcccccccccccccccCCCCCcchhhcccchhhHHHHHHHHhCCcccCCCCCceeeecC
Q 043604 133 NCMALVVNGCEINYGTLKKARCPNCTQWFCFQCKLAWHAGYRCEESGNLRDWNDIAFGKLVERMHWARCPACGSCVERKE 212 (268)
Q Consensus 133 ~C~~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~tC~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~~iek~~ 212 (268)
-|+--+..... ....+-|..|+...|..|.. |. .+.+.+.||.|+++..+--
T Consensus 20 iCGd~vg~~~~----Ge~FVAC~eC~fpvCr~cye----------ye--------------~~~g~~~cp~c~t~y~~~~ 71 (1044)
T PLN02915 20 VCGDEVGVKED----GQPFVACHVCGFPVCKPCYE----------YE--------------RSEGNQCCPQCNTRYKRHK 71 (1044)
T ss_pred ccccccCcCCC----CCEEEEeccCCCccccchhh----------hh--------------hhcCCccCCccCCchhhhc
Confidence 56666555433 24789999999999996653 21 2455678888888887655
Q ss_pred CcCeE
Q 043604 213 GCRVM 217 (268)
Q Consensus 213 GCnhm 217 (268)
|++.+
T Consensus 72 ~~~~~ 76 (1044)
T PLN02915 72 GCPRV 76 (1044)
T ss_pred CCCCc
Confidence 55443
No 240
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=37.65 E-value=25 Score=28.29 Aligned_cols=23 Identities=26% Similarity=0.752 Sum_probs=19.4
Q ss_pred ccCCCCCceeeecCCcCeEEec-CCc
Q 043604 199 ARCPACGSCVERKEGCRVMYCS-CHS 223 (268)
Q Consensus 199 k~CP~C~~~iek~~GCnhm~C~-C~~ 223 (268)
-+|++|+.++++ .=+.|+|. ||.
T Consensus 150 A~CsrC~~~L~~--~~~~l~Cp~Cg~ 173 (188)
T COG1096 150 ARCSRCRAPLVK--KGNMLKCPNCGN 173 (188)
T ss_pred EEccCCCcceEE--cCcEEECCCCCC
Confidence 589999999999 44788997 986
No 241
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=37.60 E-value=26 Score=30.04 Aligned_cols=22 Identities=27% Similarity=0.831 Sum_probs=16.5
Q ss_pred ccCCCCCceeeec--CCcCeEEec
Q 043604 199 ARCPACGSCVERK--EGCRVMYCS 220 (268)
Q Consensus 199 k~CP~C~~~iek~--~GCnhm~C~ 220 (268)
++||.|+..|+|. +|=.-..|.
T Consensus 246 ~pC~~Cg~~I~~~~~~gR~t~~CP 269 (274)
T PRK01103 246 EPCRRCGTPIEKIKQGGRSTFFCP 269 (274)
T ss_pred CCCCCCCCeeEEEEECCCCcEECc
Confidence 6899999999987 664444454
No 242
>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=37.40 E-value=29 Score=32.64 Aligned_cols=32 Identities=16% Similarity=0.378 Sum_probs=19.3
Q ss_pred cCCCCCceeeecCCcCeEEec-CCc-c-----ccccccc
Q 043604 200 RCPACGSCVERKEGCRVMYCS-CHS-V-----TYSRAKH 231 (268)
Q Consensus 200 ~CP~C~~~iek~~GCnhm~C~-C~~-F-----C~~C~~~ 231 (268)
+||+|..++.--..=+.+.|. ||+ . |-.|+..
T Consensus 224 ~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 224 CCPNCDVSLTYHKKEGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred CCCCCCCceEEecCCCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 577777666544344467776 774 3 6666653
No 243
>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=37.15 E-value=18 Score=22.26 Aligned_cols=47 Identities=23% Similarity=0.624 Sum_probs=23.9
Q ss_pred ccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCC
Q 043604 38 FTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQ 93 (268)
Q Consensus 38 ~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~ 93 (268)
..|+|-+..+..+- ....|.|.-|.| +..|++...+.+ ...||. |++
T Consensus 3 L~CPls~~~i~~P~---Rg~~C~H~~CFD-l~~fl~~~~~~~---~W~CPi--C~~ 49 (50)
T PF02891_consen 3 LRCPLSFQRIRIPV---RGKNCKHLQCFD-LESFLESNQRTP---KWKCPI--CNK 49 (50)
T ss_dssp SB-TTTSSB-SSEE---EETT--SS--EE-HHHHHHHHHHS------B-TT--T--
T ss_pred eeCCCCCCEEEeCc---cCCcCcccceEC-HHHHHHHhhccC---CeECcC--CcC
Confidence 45777777664331 356899998855 778888777652 378998 864
No 244
>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=37.14 E-value=18 Score=18.98 Aligned_cols=20 Identities=15% Similarity=0.318 Sum_probs=14.9
Q ss_pred eccCCCCCCCCCCHHHHhhcCC
Q 043604 84 IECPGVHCDQFLDPFSCKLMIP 105 (268)
Q Consensus 84 i~CP~~~C~~~i~~~~i~~~l~ 105 (268)
+.||. |...+....+...|+
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 988887777766655
No 245
>PRK10220 hypothetical protein; Provisional
Probab=37.08 E-value=30 Score=25.17 Aligned_cols=27 Identities=22% Similarity=0.564 Sum_probs=17.6
Q ss_pred ccCCccccCceeeeccccccCCcCeeeCccccccc
Q 043604 127 SYCPNRNCMALVVNGCEINYGTLKKARCPNCTQWF 161 (268)
Q Consensus 127 ~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~ 161 (268)
-.|| .|+.-+.+... ..+.||.|+..|
T Consensus 4 P~CP--~C~seytY~d~------~~~vCpeC~hEW 30 (111)
T PRK10220 4 PHCP--KCNSEYTYEDN------GMYICPECAHEW 30 (111)
T ss_pred CcCC--CCCCcceEcCC------CeEECCcccCcC
Confidence 3566 78776666554 357788777654
No 246
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=36.87 E-value=49 Score=24.28 Aligned_cols=27 Identities=26% Similarity=0.725 Sum_probs=17.3
Q ss_pred CcccCCccccCceeeeccccccCCcCeeeCccccc
Q 043604 125 ERSYCPNRNCMALVVNGCEINYGTLKKARCPNCTQ 159 (268)
Q Consensus 125 ~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~ 159 (268)
-..+|+ +|+..+..... ..+.||.||.
T Consensus 69 ~~~~C~--~Cg~~~~~~~~------~~~~CP~Cgs 95 (114)
T PRK03681 69 AECWCE--TCQQYVTLLTQ------RVRRCPQCHG 95 (114)
T ss_pred cEEEcc--cCCCeeecCCc------cCCcCcCcCC
Confidence 357888 88877655432 2356888774
No 247
>smart00336 BBOX B-Box-type zinc finger.
Probab=36.78 E-value=29 Score=19.81 Aligned_cols=24 Identities=29% Similarity=0.613 Sum_probs=20.0
Q ss_pred CeeeCcccccccccccccccCCCC
Q 043604 150 KKARCPNCTQWFCFQCKLAWHAGY 173 (268)
Q Consensus 150 ~~~~C~~C~~~~C~~C~~~~H~~~ 173 (268)
..+.|..|....|..|....|.+.
T Consensus 14 ~~~~C~~c~~~iC~~C~~~~H~~H 37 (42)
T smart00336 14 AEFFCEECGALLCRTCDEAEHRGH 37 (42)
T ss_pred eEEECCCCCcccccccChhhcCCC
Confidence 567899999999999997777654
No 248
>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=36.77 E-value=20 Score=20.53 Aligned_cols=15 Identities=47% Similarity=0.915 Sum_probs=11.8
Q ss_pred CcccCCCCCceeeec
Q 043604 197 HWARCPACGSCVERK 211 (268)
Q Consensus 197 ~~k~CP~C~~~iek~ 211 (268)
....||.|+..++|.
T Consensus 25 ~~~~CP~Cg~~~~r~ 39 (41)
T smart00834 25 PLATCPECGGDVRRL 39 (41)
T ss_pred CCCCCCCCCCcceec
Confidence 456899999988764
No 249
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=36.72 E-value=24 Score=30.93 Aligned_cols=24 Identities=29% Similarity=0.848 Sum_probs=20.0
Q ss_pred cCeeeCcccccccccccccccCCC
Q 043604 149 LKKARCPNCTQWFCFQCKLAWHAG 172 (268)
Q Consensus 149 ~~~~~C~~C~~~~C~~C~~~~H~~ 172 (268)
...++|+.|+..||..|..-.|..
T Consensus 343 ~~~y~C~~Ck~~FCldCDv~iHes 366 (378)
T KOG2807|consen 343 SGRYRCESCKNVFCLDCDVFIHES 366 (378)
T ss_pred CCcEEchhccceeeccchHHHHhh
Confidence 567899999999999998766643
No 250
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=36.68 E-value=50 Score=25.09 Aligned_cols=15 Identities=20% Similarity=0.122 Sum_probs=11.5
Q ss_pred CcccCCccccCceeeec
Q 043604 125 ERSYCPNRNCMALVVNG 141 (268)
Q Consensus 125 ~~~~Cp~~~C~~~~~~~ 141 (268)
...+|+ +|+..+...
T Consensus 69 ~~~~C~--~CG~~~~~~ 83 (135)
T PRK03824 69 AVLKCR--NCGNEWSLK 83 (135)
T ss_pred eEEECC--CCCCEEecc
Confidence 457898 899887765
No 251
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=36.40 E-value=28 Score=29.88 Aligned_cols=22 Identities=27% Similarity=0.680 Sum_probs=16.7
Q ss_pred ccCCCCCceeeec--CCcCeEEec
Q 043604 199 ARCPACGSCVERK--EGCRVMYCS 220 (268)
Q Consensus 199 k~CP~C~~~iek~--~GCnhm~C~ 220 (268)
++||+|+.+|++. +|=.--.|.
T Consensus 245 ~pCprCG~~I~~~~~~gR~t~~CP 268 (272)
T PRK14810 245 EPCLNCKTPIRRVVVAGRSSHYCP 268 (272)
T ss_pred CcCCCCCCeeEEEEECCCccEECc
Confidence 7999999999987 664444454
No 252
>PLN02436 cellulose synthase A
Probab=35.91 E-value=26 Score=35.85 Aligned_cols=51 Identities=27% Similarity=0.658 Sum_probs=34.3
Q ss_pred CCcccccccccCCcC---CcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCC
Q 043604 35 NGIFTCEICIEPISA---NDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQF 94 (268)
Q Consensus 35 ~~~~~C~IC~~~~~~---~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~ 94 (268)
.....|+||-|++.. .+.|+..-.|+-..|+.|. .|-. ++|+ -.||. |+..
T Consensus 34 ~~~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cy-eyer---~eg~---~~Cpq--ckt~ 87 (1094)
T PLN02436 34 LSGQTCQICGDEIELTVDGEPFVACNECAFPVCRPCY-EYER---REGN---QACPQ--CKTR 87 (1094)
T ss_pred cCCccccccccccCcCCCCCEEEeeccCCCccccchh-hhhh---hcCC---ccCcc--cCCc
Confidence 345589999998633 3556555568999999999 4443 3333 35887 7754
No 253
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=35.75 E-value=29 Score=29.76 Aligned_cols=22 Identities=27% Similarity=0.776 Sum_probs=17.0
Q ss_pred ccCCCCCceeeec--CCcCeEEec
Q 043604 199 ARCPACGSCVERK--EGCRVMYCS 220 (268)
Q Consensus 199 k~CP~C~~~iek~--~GCnhm~C~ 220 (268)
++||.|+..|++. +|=.-..|.
T Consensus 246 ~pC~~Cg~~I~~~~~~gR~t~~CP 269 (272)
T TIGR00577 246 EPCRRCGTPIEKIKVGGRGTHFCP 269 (272)
T ss_pred CCCCCCCCeeEEEEECCCCCEECC
Confidence 6999999999987 665555554
No 254
>PRK10445 endonuclease VIII; Provisional
Probab=35.67 E-value=30 Score=29.54 Aligned_cols=24 Identities=25% Similarity=0.872 Sum_probs=18.2
Q ss_pred ccCCCCCceeeec--CCcCeEEec-CC
Q 043604 199 ARCPACGSCVERK--EGCRVMYCS-CH 222 (268)
Q Consensus 199 k~CP~C~~~iek~--~GCnhm~C~-C~ 222 (268)
+.||.|+..|++. +|=.-..|. |.
T Consensus 236 ~~Cp~Cg~~I~~~~~~gR~t~~CP~CQ 262 (263)
T PRK10445 236 EACERCGGIIEKTTLSSRPFYWCPGCQ 262 (263)
T ss_pred CCCCCCCCEeEEEEECCCCcEECCCCc
Confidence 7899999999987 775555554 53
No 255
>KOG2041 consensus WD40 repeat protein [General function prediction only]
Probab=35.56 E-value=42 Score=32.83 Aligned_cols=48 Identities=15% Similarity=0.271 Sum_probs=29.4
Q ss_pred cCChhHHHHHHHHHHhhhhcCC------CcccCCccccCceeeeccccccCCcCeeeCccccccc
Q 043604 103 MIPSNLFSKWCDVLFEDYVLGF------ERSYCPNRNCMALVVNGCEINYGTLKKARCPNCTQWF 161 (268)
Q Consensus 103 ~l~~~~~~~~~~~~~~~~~~~~------~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~ 161 (268)
-|+++..++|+.+.++.+...+ ..+-|. .|+..+.+.+ ..|+.|...|
T Consensus 1088 ~l~~a~kq~ye~La~~iFsk~~p~d~~~~~vdc~--~cg~~i~~~~---------~~c~ec~~kf 1141 (1189)
T KOG2041|consen 1088 ELDDAEKQEYENLAFRIFSKNPPVDPNSAKVDCS--VCGAKIDPYD---------LQCSECQTKF 1141 (1189)
T ss_pred hCCHHHHHHHHHHHHHHhccCCCCCCCccceeee--ecCCcCCccC---------CCChhhcCcC
Confidence 4677888899998887665431 134554 5666554333 3477776554
No 256
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=35.31 E-value=22 Score=21.92 Aligned_cols=15 Identities=40% Similarity=0.791 Sum_probs=10.6
Q ss_pred hCCcccCCCCCceee
Q 043604 195 RMHWARCPACGSCVE 209 (268)
Q Consensus 195 ~~~~k~CP~C~~~ie 209 (268)
.....+||.|+..|-
T Consensus 21 ~~~~irCp~Cg~rIl 35 (49)
T COG1996 21 ETRGIRCPYCGSRIL 35 (49)
T ss_pred ccCceeCCCCCcEEE
Confidence 344578888888764
No 257
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=35.05 E-value=18 Score=31.47 Aligned_cols=43 Identities=19% Similarity=0.396 Sum_probs=28.9
Q ss_pred ccCCccccCceeeecccc---ccCCcCeeeCcccccccccccccccCC
Q 043604 127 SYCPNRNCMALVVNGCEI---NYGTLKKARCPNCTQWFCFQCKLAWHA 171 (268)
Q Consensus 127 ~~Cp~~~C~~~~~~~~~~---~~~~~~~~~C~~C~~~~C~~C~~~~H~ 171 (268)
..|- .|+..++..+.. +........|+.|+..||..|..-.|.
T Consensus 363 ~~Cf--~CQ~~fp~~~~~~~~~~~ss~rY~Ce~CK~~FC~dCdvfiHe 408 (421)
T COG5151 363 THCF--VCQGPFPKPPVSPFDESTSSGRYQCELCKSTFCSDCDVFIHE 408 (421)
T ss_pred ccce--eccCCCCCCCCCcccccccccceechhhhhhhhhhhHHHHHH
Confidence 4454 577665543322 122467889999999999999876554
No 258
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=34.48 E-value=59 Score=23.84 Aligned_cols=26 Identities=27% Similarity=0.737 Sum_probs=16.2
Q ss_pred CcccCCccccCceeeeccccccCCcCeeeCccccc
Q 043604 125 ERSYCPNRNCMALVVNGCEINYGTLKKARCPNCTQ 159 (268)
Q Consensus 125 ~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~ 159 (268)
-..+|+ +|+..+.... ..+.||.|+.
T Consensus 69 ~~~~C~--~Cg~~~~~~~-------~~~~CP~Cgs 94 (113)
T PRK12380 69 AQAWCW--DCSQVVEIHQ-------HDAQCPHCHG 94 (113)
T ss_pred cEEEcc--cCCCEEecCC-------cCccCcCCCC
Confidence 346887 7887666543 2344887763
No 259
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=34.36 E-value=18 Score=27.27 Aligned_cols=20 Identities=40% Similarity=0.748 Sum_probs=14.3
Q ss_pred CCcccccccccCCcCCcCccccCCCCC
Q 043604 35 NGIFTCEICIEPISANDKFRNKDLCSH 61 (268)
Q Consensus 35 ~~~~~C~IC~~~~~~~~~~~~~~~C~H 61 (268)
....+|.||..+. | ...|||
T Consensus 63 ~ddatC~IC~KTK-----F--ADG~GH 82 (169)
T KOG3799|consen 63 GDDATCGICHKTK-----F--ADGCGH 82 (169)
T ss_pred CcCcchhhhhhcc-----c--ccccCc
Confidence 4457899999765 3 466777
No 260
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=34.23 E-value=25 Score=30.43 Aligned_cols=35 Identities=31% Similarity=0.561 Sum_probs=16.3
Q ss_pred ccCCCCCce-----eeecC--CcCeEEec-CCc-c------ccccccccc
Q 043604 199 ARCPACGSC-----VERKE--GCRVMYCS-CHS-V------TYSRAKHIS 233 (268)
Q Consensus 199 k~CP~C~~~-----iek~~--GCnhm~C~-C~~-F------C~~C~~~~~ 233 (268)
..||-||.. |...+ |=.+++|. |++ | |-.||..-.
T Consensus 173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R~~Cp~Cg~~~~ 222 (290)
T PF04216_consen 173 GYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVRIKCPYCGNTDH 222 (290)
T ss_dssp SS-TTT---EEEEEEE------EEEEEETTT--EEE--TTS-TTT---SS
T ss_pred CcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecCCCCcCCCCCCC
Confidence 689999984 44444 88999997 997 7 666876533
No 261
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=34.08 E-value=31 Score=29.75 Aligned_cols=24 Identities=33% Similarity=0.920 Sum_probs=18.3
Q ss_pred ccCCCCCceeeec--CCcCeEEec-CC
Q 043604 199 ARCPACGSCVERK--EGCRVMYCS-CH 222 (268)
Q Consensus 199 k~CP~C~~~iek~--~GCnhm~C~-C~ 222 (268)
++||.|+..|+|. +|=.-..|. |.
T Consensus 255 ~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 281 (282)
T PRK13945 255 KPCRKCGTPIERIKLAGRSTHWCPNCQ 281 (282)
T ss_pred CCCCcCCCeeEEEEECCCccEECCCCc
Confidence 7999999999987 775555564 53
No 262
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=34.07 E-value=22 Score=30.87 Aligned_cols=33 Identities=27% Similarity=0.601 Sum_probs=24.1
Q ss_pred cccccccccCCcCCcCccccCCCCChhhHHHHHHHH
Q 043604 37 IFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYI 72 (268)
Q Consensus 37 ~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~ 72 (268)
...|.-|--.+... -.+.+|.|+||.+|-+..-
T Consensus 90 VHfCd~Cd~PI~IY---GRmIPCkHvFCl~CAr~~~ 122 (389)
T KOG2932|consen 90 VHFCDRCDFPIAIY---GRMIPCKHVFCLECARSDS 122 (389)
T ss_pred eEeecccCCcceee---ecccccchhhhhhhhhcCc
Confidence 57788887666432 2467999999999987643
No 263
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=33.52 E-value=32 Score=21.55 Aligned_cols=21 Identities=19% Similarity=0.548 Sum_probs=14.9
Q ss_pred HHHHHHHhCCcccCCCCCcee
Q 043604 188 AFGKLVERMHWARCPACGSCV 208 (268)
Q Consensus 188 ~~~~~~~~~~~k~CP~C~~~i 208 (268)
.+.++........||+|+..+
T Consensus 36 ~~~~i~~~~~i~~Cp~CgRiL 56 (56)
T PF02591_consen 36 ELNEIRKGDEIVFCPNCGRIL 56 (56)
T ss_pred HHHHHHcCCCeEECcCCCccC
Confidence 455555556789999999753
No 264
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=33.33 E-value=34 Score=24.60 Aligned_cols=23 Identities=30% Similarity=0.921 Sum_probs=19.5
Q ss_pred CCCChhhHHHHHHHHHHHhhcCCCceeccCC
Q 043604 58 LCSHHFCQDCIAKYIEAKVQDNNTAKIECPG 88 (268)
Q Consensus 58 ~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~ 88 (268)
.|.|.|..-|+..|+++. -.||.
T Consensus 80 ~CNHaFH~hCisrWlktr--------~vCPL 102 (114)
T KOG2930|consen 80 VCNHAFHFHCISRWLKTR--------NVCPL 102 (114)
T ss_pred ecchHHHHHHHHHHHhhc--------CcCCC
Confidence 599999999999999864 35787
No 265
>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=33.18 E-value=73 Score=23.45 Aligned_cols=36 Identities=17% Similarity=0.390 Sum_probs=24.8
Q ss_pred CcccCCccccCceeeeccccccCCcCeeeCcccccccccccccc
Q 043604 125 ERSYCPNRNCMALVVNGCEINYGTLKKARCPNCTQWFCFQCKLA 168 (268)
Q Consensus 125 ~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~ 168 (268)
+...|. .|...+..-. .....|..|+..+|..|...
T Consensus 53 ~~~~C~--~C~~~fg~l~------~~~~~C~~C~~~VC~~C~~~ 88 (118)
T PF02318_consen 53 GERHCA--RCGKPFGFLF------NRGRVCVDCKHRVCKKCGVY 88 (118)
T ss_dssp CCSB-T--TTS-BCSCTS------TTCEEETTTTEEEETTSEEE
T ss_pred CCcchh--hhCCcccccC------CCCCcCCcCCccccCccCCc
Confidence 456787 7876553222 24578999999999999986
No 266
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=33.06 E-value=9.1 Score=36.97 Aligned_cols=57 Identities=26% Similarity=0.542 Sum_probs=41.1
Q ss_pred CCCcccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCCHHHHh
Q 043604 34 TNGIFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLDPFSCK 101 (268)
Q Consensus 34 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i~ 101 (268)
.....+|+||+..+..+ ..+.|.|.||..|+..-+...-. ...||. |+..++-..++
T Consensus 18 ~~k~lEc~ic~~~~~~p----~~~kc~~~~l~~~~n~~f~~~~~-----~~~~~l--c~~~~eK~s~~ 74 (684)
T KOG4362|consen 18 MQKILECPICLEHVKEP----SLLKCDHIFLKFCLNKLFESKKG-----PKQCAL--CKSDIEKRSLR 74 (684)
T ss_pred HhhhccCCceeEEeecc----chhhhhHHHHhhhhhceeeccCc-----cccchh--hhhhhhhhhcc
Confidence 34578999999988543 47899999999999887765432 567777 77555544433
No 267
>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=32.86 E-value=60 Score=23.91 Aligned_cols=34 Identities=18% Similarity=0.225 Sum_probs=25.9
Q ss_pred CcccCCCCCceeeecCCcCeEEec-CCc-cccccccc
Q 043604 197 HWARCPACGSCVERKEGCRVMYCS-CHS-VTYSRAKH 231 (268)
Q Consensus 197 ~~k~CP~C~~~iek~~GCnhm~C~-C~~-FC~~C~~~ 231 (268)
+.+.|..|+.+.-...+.. ..|. |++ +|-.|+..
T Consensus 53 ~~~~C~~C~~~fg~l~~~~-~~C~~C~~~VC~~C~~~ 88 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRG-RVCVDCKHRVCKKCGVY 88 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTC-EEETTTTEEEETTSEEE
T ss_pred CCcchhhhCCcccccCCCC-CcCCcCCccccCccCCc
Confidence 5589999998876665555 8897 999 99999877
No 268
>PRK05580 primosome assembly protein PriA; Validated
Probab=32.78 E-value=37 Score=33.28 Aligned_cols=32 Identities=19% Similarity=0.422 Sum_probs=20.3
Q ss_pred cCCCCCceeeecCCcCeEEec-CCc-c-----ccccccc
Q 043604 200 RCPACGSCVERKEGCRVMYCS-CHS-V-----TYSRAKH 231 (268)
Q Consensus 200 ~CP~C~~~iek~~GCnhm~C~-C~~-F-----C~~C~~~ 231 (268)
+||+|..++.--..=+.+.|. ||+ . |-.|+..
T Consensus 392 ~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 392 ECPHCDASLTLHRFQRRLRCHHCGYQEPIPKACPECGST 430 (679)
T ss_pred CCCCCCCceeEECCCCeEECCCCcCCCCCCCCCCCCcCC
Confidence 577777766543344667776 775 3 7777654
No 269
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=32.75 E-value=21 Score=30.98 Aligned_cols=26 Identities=19% Similarity=0.424 Sum_probs=18.2
Q ss_pred CcccCCCCCceeeecCCcCeEEec---CCc-cccccc
Q 043604 197 HWARCPACGSCVERKEGCRVMYCS---CHS-VTYSRA 229 (268)
Q Consensus 197 ~~k~CP~C~~~iek~~GCnhm~C~---C~~-FC~~C~ 229 (268)
.+--|-+|..+|- |+=+ |++ ||+.|-
T Consensus 89 ~VHfCd~Cd~PI~-------IYGRmIPCkHvFCl~CA 118 (389)
T KOG2932|consen 89 RVHFCDRCDFPIA-------IYGRMIPCKHVFCLECA 118 (389)
T ss_pred ceEeecccCCcce-------eeecccccchhhhhhhh
Confidence 3567999999998 4443 666 666664
No 270
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=32.41 E-value=59 Score=24.52 Aligned_cols=35 Identities=20% Similarity=0.403 Sum_probs=21.2
Q ss_pred CcccCCccccCceeeeccccccCCcCeeeCccccccc
Q 043604 125 ERSYCPNRNCMALVVNGCEINYGTLKKARCPNCTQWF 161 (268)
Q Consensus 125 ~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~ 161 (268)
....|| .|+..................|+.|+..|
T Consensus 29 ~~~~cP--~C~s~~~~k~g~~~~~~qRyrC~~C~~tf 63 (129)
T COG3677 29 TKVNCP--RCKSSNVVKIGGIRRGHQRYKCKSCGSTF 63 (129)
T ss_pred ccCcCC--CCCccceeeECCccccccccccCCcCcce
Confidence 348898 77766522222111235778899998877
No 271
>PLN02195 cellulose synthase A
Probab=32.40 E-value=33 Score=34.77 Aligned_cols=30 Identities=20% Similarity=0.337 Sum_probs=22.5
Q ss_pred ccCceeeeccccccCCcCeeeCcccccccccccc
Q 043604 133 NCMALVVNGCEINYGTLKKARCPNCTQWFCFQCK 166 (268)
Q Consensus 133 ~C~~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~ 166 (268)
-|+..+..+..- ...+-|..|+...|.-|.
T Consensus 11 ~cgd~~~~~~~g----~~fvaC~eC~~pvCrpCy 40 (977)
T PLN02195 11 TCGEEVGVDSNG----EAFVACHECSYPLCKACL 40 (977)
T ss_pred ecccccCcCCCC----CeEEEeccCCCccccchh
Confidence 577766655443 478999999999999665
No 272
>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=32.19 E-value=98 Score=22.38 Aligned_cols=29 Identities=21% Similarity=0.607 Sum_probs=21.6
Q ss_pred CChhhHHHHHHHHHHHhhc-CCCceeccCC
Q 043604 60 SHHFCQDCIAKYIEAKVQD-NNTAKIECPG 88 (268)
Q Consensus 60 ~H~fC~~Cl~~~~~~~i~~-~~~~~i~CP~ 88 (268)
.=.||..||...+...+.+ .....-.||.
T Consensus 37 ~~~fC~~CL~~ryge~~~ev~~~~~W~CP~ 66 (105)
T PF10497_consen 37 RGKFCGGCLRNRYGENVEEVLEDPNWKCPK 66 (105)
T ss_pred cceehHhHHHHHHhhhHHHHhcCCceECCC
Confidence 6689999999998877655 1233477887
No 273
>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=32.16 E-value=28 Score=21.99 Aligned_cols=22 Identities=27% Similarity=0.649 Sum_probs=14.8
Q ss_pred CCcccCCCCCceeeecCCcCeEEec-CC
Q 043604 196 MHWARCPACGSCVERKEGCRVMYCS-CH 222 (268)
Q Consensus 196 ~~~k~CP~C~~~iek~~GCnhm~C~-C~ 222 (268)
.....||+|+.+.. .|-.|. ||
T Consensus 24 p~l~~C~~cG~~~~-----~H~vc~~cG 46 (55)
T TIGR01031 24 PTLVVCPNCGEFKL-----PHRVCPSCG 46 (55)
T ss_pred CcceECCCCCCccc-----CeeECCccC
Confidence 45567999998877 455554 55
No 274
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=32.05 E-value=33 Score=26.20 Aligned_cols=24 Identities=21% Similarity=0.451 Sum_probs=17.2
Q ss_pred ccCCCCCceeeecCCcCeEEecCCccccccccccc
Q 043604 199 ARCPACGSCVERKEGCRVMYCSCHSVTYSRAKHIS 233 (268)
Q Consensus 199 k~CP~C~~~iek~~GCnhm~C~C~~FC~~C~~~~~ 233 (268)
-+|.+||.+|.. |.||-.|...+.
T Consensus 82 ~~CE~CG~~I~~-----------Gr~C~~C~~~l~ 105 (137)
T TIGR03826 82 YPCERCGTSIRE-----------GRLCDSCAGELK 105 (137)
T ss_pred CcccccCCcCCC-----------CCccHHHHHHHH
Confidence 689999999971 227777776554
No 275
>PRK02935 hypothetical protein; Provisional
Probab=32.02 E-value=31 Score=24.95 Aligned_cols=22 Identities=23% Similarity=0.697 Sum_probs=13.0
Q ss_pred cCeeeCccccc--------ccccccccccC
Q 043604 149 LKKARCPNCTQ--------WFCFQCKLAWH 170 (268)
Q Consensus 149 ~~~~~C~~C~~--------~~C~~C~~~~H 170 (268)
...+.||.|++ ..|..|++|-+
T Consensus 68 avqV~CP~C~K~TKmLGrvD~CM~C~~PLT 97 (110)
T PRK02935 68 AVQVICPSCEKPTKMLGRVDACMHCNQPLT 97 (110)
T ss_pred ceeeECCCCCchhhhccceeecCcCCCcCC
Confidence 45666776654 34666666544
No 276
>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=32.01 E-value=32 Score=19.91 Aligned_cols=20 Identities=30% Similarity=0.967 Sum_probs=13.1
Q ss_pred ccCCCCCceeeec---CCcCeEEe
Q 043604 199 ARCPACGSCVERK---EGCRVMYC 219 (268)
Q Consensus 199 k~CP~C~~~iek~---~GCnhm~C 219 (268)
+.||.|+..+... .| ..+-|
T Consensus 2 ~~CP~Cg~~lv~r~~k~g-~F~~C 24 (39)
T PF01396_consen 2 EKCPKCGGPLVLRRGKKG-KFLGC 24 (39)
T ss_pred cCCCCCCceeEEEECCCC-CEEEC
Confidence 5799998755543 44 55656
No 277
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=31.85 E-value=33 Score=29.13 Aligned_cols=27 Identities=22% Similarity=0.532 Sum_probs=22.5
Q ss_pred CcccCCCCCceeeecCCcCeEEec-CCc
Q 043604 197 HWARCPACGSCVERKEGCRVMYCS-CHS 223 (268)
Q Consensus 197 ~~k~CP~C~~~iek~~GCnhm~C~-C~~ 223 (268)
..+.||.|+.+++...|=..+.|. |+.
T Consensus 98 ~~~fC~~CG~~~~~~~~~~~~~C~~c~~ 125 (256)
T PRK00241 98 SHRFCGYCGHPMHPSKTEWAMLCPHCRE 125 (256)
T ss_pred cCccccccCCCCeecCCceeEECCCCCC
Confidence 458999999998877666778997 997
No 278
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=31.63 E-value=44 Score=21.30 Aligned_cols=27 Identities=26% Similarity=0.546 Sum_probs=16.9
Q ss_pred hcCCCcccCCccccCceeeeccccccCCcCeeeCccccc
Q 043604 121 VLGFERSYCPNRNCMALVVNGCEINYGTLKKARCPNCTQ 159 (268)
Q Consensus 121 ~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~ 159 (268)
+..+.+..|| .|+.+... ...|+.||+
T Consensus 22 l~~~~l~~C~--~CG~~~~~----------H~vC~~CG~ 48 (57)
T PRK12286 22 LKAPGLVECP--NCGEPKLP----------HRVCPSCGY 48 (57)
T ss_pred ccCCcceECC--CCCCccCC----------eEECCCCCc
Confidence 3346677787 77776643 345777764
No 279
>COG5204 SPT4 Transcription elongation factor SPT4 [Transcription]
Probab=31.59 E-value=26 Score=24.76 Aligned_cols=22 Identities=23% Similarity=0.259 Sum_probs=16.2
Q ss_pred cccceecccCcccccccccccC
Q 043604 247 RIYKVSGCRSTCRSLENFGVTK 268 (268)
Q Consensus 247 ~~~~~~gc~~~~~~l~~~~~~~ 268 (268)
+.++..|||+-+.--+..|||+
T Consensus 22 n~F~~dGCpNc~~l~~~~gV~~ 43 (112)
T COG5204 22 NGFRKDGCPNCPMLNMKGGVTN 43 (112)
T ss_pred ccccccCCCCCcccccccCccc
Confidence 5667889999777666677764
No 280
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=31.45 E-value=34 Score=21.86 Aligned_cols=34 Identities=29% Similarity=0.495 Sum_probs=21.8
Q ss_pred ccCCccccCceeeeccccccCCcCeeeCccccccccc
Q 043604 127 SYCPNRNCMALVVNGCEINYGTLKKARCPNCTQWFCF 163 (268)
Q Consensus 127 ~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~C~ 163 (268)
.-|| |+--+.....+.......++||+|.-..|.
T Consensus 23 yPCP---CGDRFeIsLeDl~~GE~VArCPSCSLiv~v 56 (67)
T COG5216 23 YPCP---CGDRFEISLEDLRNGEVVARCPSCSLIVCV 56 (67)
T ss_pred ecCC---CCCEeEEEHHHhhCCceEEEcCCceEEEEE
Confidence 4576 776665544433234577899999877765
No 281
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=31.29 E-value=42 Score=28.24 Aligned_cols=41 Identities=20% Similarity=0.323 Sum_probs=30.4
Q ss_pred CCCcc-cccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhc
Q 043604 34 TNGIF-TCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQD 78 (268)
Q Consensus 34 ~~~~~-~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~ 78 (268)
..+.| -|..|+.+...+ +..+=||.||++|+..||..+-++
T Consensus 39 siK~FdcCsLtLqPc~dP----vit~~GylfdrEaILe~ilaqKke 80 (303)
T KOG3039|consen 39 SIKPFDCCSLTLQPCRDP----VITPDGYLFDREAILEYILAQKKE 80 (303)
T ss_pred ccCCcceeeeecccccCC----ccCCCCeeeeHHHHHHHHHHHHHH
Confidence 44444 567788777543 356779999999999999887765
No 282
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=31.28 E-value=81 Score=23.63 Aligned_cols=28 Identities=25% Similarity=0.693 Sum_probs=22.8
Q ss_pred CCcccCCCCCce---eeecCCcCeEEec-CCc
Q 043604 196 MHWARCPACGSC---VERKEGCRVMYCS-CHS 223 (268)
Q Consensus 196 ~~~k~CP~C~~~---iek~~GCnhm~C~-C~~ 223 (268)
..+..||.|+.| +.+.++=-.|.|. ||+
T Consensus 91 ~~yVlC~~C~spdT~l~k~~r~~~l~C~aCGa 122 (125)
T PF01873_consen 91 KEYVLCPECGSPDTELIKEGRLIFLKCKACGA 122 (125)
T ss_dssp CHHSSCTSTSSSSEEEEEETTCCEEEETTTSC
T ss_pred HHEEEcCCCCCCccEEEEcCCEEEEEecccCC
Confidence 346899999974 6677888999998 986
No 283
>PRK12495 hypothetical protein; Provisional
Probab=31.05 E-value=39 Score=27.89 Aligned_cols=31 Identities=23% Similarity=0.398 Sum_probs=21.2
Q ss_pred CCcccCCCCCceeeecCCcCeEEecCCcccccccccccC
Q 043604 196 MHWARCPACGSCVERKEGCRVMYCSCHSVTYSRAKHISL 234 (268)
Q Consensus 196 ~~~k~CP~C~~~iek~~GCnhm~C~C~~FC~~C~~~~~~ 234 (268)
+..+.||.|+.+|.+..|+ . ||-.|...+..
T Consensus 40 msa~hC~~CG~PIpa~pG~--~------~Cp~CQ~~~~~ 70 (226)
T PRK12495 40 MTNAHCDECGDPIFRHDGQ--E------FCPTCQQPVTE 70 (226)
T ss_pred cchhhcccccCcccCCCCe--e------ECCCCCCcccc
Confidence 3458999999999965553 2 56666655443
No 284
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=30.97 E-value=12 Score=23.03 Aligned_cols=36 Identities=19% Similarity=0.614 Sum_probs=27.7
Q ss_pred CcccccccccCCcCCcCccccCCCCChhhHHHHHHHH
Q 043604 36 GIFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYI 72 (268)
Q Consensus 36 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~ 72 (268)
..++|..|-+..+..+ ++...-||-..|.+||+.-.
T Consensus 6 sry~CDLCn~~~p~~~-LRQCvlCGRWaC~sCW~deY 41 (57)
T PF14445_consen 6 SRYSCDLCNSSHPISE-LRQCVLCGRWACNSCWQDEY 41 (57)
T ss_pred hhHhHHhhcccCcHHH-HHHHhhhchhhhhhhhhhhH
Confidence 3578999999986654 33456799999999998643
No 285
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=30.60 E-value=48 Score=20.55 Aligned_cols=30 Identities=33% Similarity=0.685 Sum_probs=21.4
Q ss_pred cccccccCCcCCcCccccCCCCChhhHHHHHHH
Q 043604 39 TCEICIEPISANDKFRNKDLCSHHFCQDCIAKY 71 (268)
Q Consensus 39 ~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~ 71 (268)
.|.||-.++.....+ -+.=| ..|.+|+...
T Consensus 1 ~C~iCg~kigl~~~~--k~~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRF--KIKDG-YICKDCLKKL 30 (51)
T ss_pred CCCccccccccccce--eccCc-cchHHHHHHh
Confidence 489999988543322 34555 8999999876
No 286
>PHA02862 5L protein; Provisional
Probab=30.25 E-value=84 Score=24.22 Aligned_cols=46 Identities=22% Similarity=0.523 Sum_probs=32.9
Q ss_pred ccccccccCCcCCcCccccCCCC-----ChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCC
Q 043604 38 FTCEICIEPISANDKFRNKDLCS-----HHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLD 96 (268)
Q Consensus 38 ~~C~IC~~~~~~~~~~~~~~~C~-----H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~ 96 (268)
..|-||+++-.. . ..+|. .....+||.+|+.. ..+..||. |+.+..
T Consensus 3 diCWIC~~~~~e--~---~~PC~C~GS~K~VHq~CL~~WIn~------S~k~~CeL--CkteY~ 53 (156)
T PHA02862 3 DICWICNDVCDE--R---NNFCGCNEEYKVVHIKCMQLWINY------SKKKECNL--CKTKYN 53 (156)
T ss_pred CEEEEecCcCCC--C---cccccccCcchhHHHHHHHHHHhc------CCCcCccC--CCCeEE
Confidence 369999998632 2 24553 47899999999943 34678998 987654
No 287
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 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 ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=30.07 E-value=32 Score=24.17 Aligned_cols=27 Identities=22% Similarity=0.619 Sum_probs=21.5
Q ss_pred cccCCCCCceeeecCCcCeEEec-CCc-c
Q 043604 198 WARCPACGSCVERKEGCRVMYCS-CHS-V 224 (268)
Q Consensus 198 ~k~CP~C~~~iek~~GCnhm~C~-C~~-F 224 (268)
--.||.|+..-.|..+----.|. |+. |
T Consensus 35 ky~Cp~Cgk~~vkR~a~GIW~C~~C~~~~ 63 (90)
T PF01780_consen 35 KYTCPFCGKTSVKRVATGIWKCKKCGKKF 63 (90)
T ss_dssp -BEESSSSSSEEEEEETTEEEETTTTEEE
T ss_pred CCcCCCCCCceeEEeeeEEeecCCCCCEE
Confidence 35899999998888777777887 887 6
No 288
>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=29.90 E-value=23 Score=21.69 Aligned_cols=44 Identities=23% Similarity=0.616 Sum_probs=21.5
Q ss_pred ccccccccCCcCCcCccccCCC-CChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCCH
Q 043604 38 FTCEICIEPISANDKFRNKDLC-SHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLDP 97 (268)
Q Consensus 38 ~~C~IC~~~~~~~~~~~~~~~C-~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~ 97 (268)
+.|..|.-... .+..| .|+.|..|+..++. ..-.||. |+.+++.
T Consensus 3 ~nCKsCWf~~k------~Li~C~dHYLCl~CLt~ml~--------~s~~C~i--C~~~LPt 47 (50)
T PF03854_consen 3 YNCKSCWFANK------GLIKCSDHYLCLNCLTLMLS--------RSDRCPI--CGKPLPT 47 (50)
T ss_dssp ----SS-S--S------SEEE-SS-EEEHHHHHHT-S--------SSSEETT--TTEE---
T ss_pred ccChhhhhcCC------CeeeecchhHHHHHHHHHhc--------cccCCCc--ccCcCcc
Confidence 45677764331 24566 69999999988763 2246888 8877654
No 289
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=29.79 E-value=44 Score=32.98 Aligned_cols=58 Identities=19% Similarity=0.305 Sum_probs=36.2
Q ss_pred CChhHHHHHHHHHHhh--hh---cCCC------------cccCCccccCceeeeccccccCCcCeeeCcccccc-----c
Q 043604 104 IPSNLFSKWCDVLFED--YV---LGFE------------RSYCPNRNCMALVVNGCEINYGTLKKARCPNCTQW-----F 161 (268)
Q Consensus 104 l~~~~~~~~~~~~~~~--~~---~~~~------------~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~-----~ 161 (268)
|++.+++...+.+... .+ .... +..|| +|+..+...... ..+.|..||+. .
T Consensus 405 lS~~Ll~~i~~~l~~geQ~llflnRRGys~~l~C~~Cg~v~~Cp--~Cd~~lt~H~~~-----~~L~CH~Cg~~~~~p~~ 477 (730)
T COG1198 405 LSPALLEAIRKTLERGEQVLLFLNRRGYAPLLLCRDCGYIAECP--NCDSPLTLHKAT-----GQLRCHYCGYQEPIPQS 477 (730)
T ss_pred CCHHHHHHHHHHHhcCCeEEEEEccCCccceeecccCCCcccCC--CCCcceEEecCC-----CeeEeCCCCCCCCCCCC
Confidence 6777888777666542 11 1111 23455 677777666554 77888888875 6
Q ss_pred ccccccc
Q 043604 162 CFQCKLA 168 (268)
Q Consensus 162 C~~C~~~ 168 (268)
|..|+..
T Consensus 478 Cp~Cgs~ 484 (730)
T COG1198 478 CPECGSE 484 (730)
T ss_pred CCCCCCC
Confidence 7777765
No 290
>PF07227 DUF1423: Protein of unknown function (DUF1423); InterPro: IPR004082 A total of 715 potential protein-coding genes have been identified in the nucleotide sequence of Arabidopsis thaliana chromosome 5, with an average gene density of 1 gene per 4001 bp []. Amongst the gene products is a well-conserved family of 130.7kDa proteins that share no sequence similarity with any other known proteins, other than in plants. The sequences are characterised by an N-terminal domain of variable length, a central cysteine-rich region and a relatively acidic C-terminal domain. The sequences may possess a PHD finger.
Probab=29.77 E-value=35 Score=31.27 Aligned_cols=29 Identities=21% Similarity=0.378 Sum_probs=17.2
Q ss_pred CCCCceeeecCCcCeEEec-CCcccc-cccc
Q 043604 202 PACGSCVERKEGCRVMYCS-CHSVTY-SRAK 230 (268)
Q Consensus 202 P~C~~~iek~~GCnhm~C~-C~~FC~-~C~~ 230 (268)
+-|...=.-.+||..+.|- ||+||- .|+-
T Consensus 132 ~iC~kfD~~~n~~~Wi~Cd~CgH~cH~dCAL 162 (446)
T PF07227_consen 132 CICSKFDDNKNTCSWIGCDVCGHWCHLDCAL 162 (446)
T ss_pred cccCCcccCCCCeeEEeccCCCceehhhhhc
Confidence 3344433334678888886 888664 3544
No 291
>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 PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 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 (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=29.27 E-value=38 Score=15.96 Aligned_cols=16 Identities=31% Similarity=0.717 Sum_probs=11.8
Q ss_pred cccccccccCCCCCcc
Q 043604 161 FCFQCKLAWHAGYRCE 176 (268)
Q Consensus 161 ~C~~C~~~~H~~~tC~ 176 (268)
.|+.|++.-|.-..|.
T Consensus 2 ~C~~C~~~GH~~~~Cp 17 (18)
T PF00098_consen 2 KCFNCGEPGHIARDCP 17 (18)
T ss_dssp BCTTTSCSSSCGCTSS
T ss_pred cCcCCCCcCcccccCc
Confidence 5788888888766664
No 293
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=29.25 E-value=38 Score=33.24 Aligned_cols=38 Identities=21% Similarity=0.553 Sum_probs=29.1
Q ss_pred CCcccccccccCCcCCcCccccCCCCChhhHHHHHHHHHH
Q 043604 35 NGIFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEA 74 (268)
Q Consensus 35 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~ 74 (268)
...+.|.||--.+.....| ...|+|....+|++.|+.+
T Consensus 1026 ~~~~~C~~C~l~V~gss~~--Cg~C~Hv~H~sc~~eWf~~ 1063 (1081)
T KOG0309|consen 1026 GFTFQCAICHLAVRGSSNF--CGTCGHVGHTSCMMEWFRT 1063 (1081)
T ss_pred cceeeeeeEeeEeeccchh--hccccccccHHHHHHHHhc
Confidence 4456788887766554433 6789999999999999975
No 294
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.21 E-value=31 Score=22.50 Aligned_cols=16 Identities=38% Similarity=0.640 Sum_probs=12.9
Q ss_pred CcccCCCCCceeeecC
Q 043604 197 HWARCPACGSCVERKE 212 (268)
Q Consensus 197 ~~k~CP~C~~~iek~~ 212 (268)
...+||.|+++++...
T Consensus 6 ~~v~CP~Cgkpv~w~~ 21 (65)
T COG3024 6 ITVPCPTCGKPVVWGE 21 (65)
T ss_pred ccccCCCCCCcccccc
Confidence 4579999999999643
No 295
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=29.18 E-value=60 Score=27.98 Aligned_cols=28 Identities=25% Similarity=0.529 Sum_probs=25.1
Q ss_pred CCcccCCCCCceeeecCCcCeEEec-CCc
Q 043604 196 MHWARCPACGSCVERKEGCRVMYCS-CHS 223 (268)
Q Consensus 196 ~~~k~CP~C~~~iek~~GCnhm~C~-C~~ 223 (268)
...|-||+|+.+.+-..|=-.+.|. ||+
T Consensus 109 ~~~RFCg~CG~~~~~~~~g~~~~C~~cg~ 137 (279)
T COG2816 109 RSHRFCGRCGTKTYPREGGWARVCPKCGH 137 (279)
T ss_pred hhCcCCCCCCCcCccccCceeeeCCCCCC
Confidence 3459999999999999999999997 998
No 296
>PRK00893 aspartate carbamoyltransferase regulatory subunit; Reviewed
Probab=28.94 E-value=50 Score=25.66 Aligned_cols=33 Identities=30% Similarity=0.474 Sum_probs=20.5
Q ss_pred CcccCCccccCcee--------eeccccccCCcCeeeCccccccc
Q 043604 125 ERSYCPNRNCMALV--------VNGCEINYGTLKKARCPNCTQWF 161 (268)
Q Consensus 125 ~~~~Cp~~~C~~~~--------~~~~~~~~~~~~~~~C~~C~~~~ 161 (268)
+...||||+|-.-. .... .....++|..|...+
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 46789999995431 1111 124678888877654
No 297
>PLN03086 PRLI-interacting factor K; Provisional
Probab=28.86 E-value=52 Score=31.43 Aligned_cols=29 Identities=28% Similarity=0.643 Sum_probs=25.3
Q ss_pred CCcccCCC--CCceeeecCCcCeEEec-CCc-c
Q 043604 196 MHWARCPA--CGSCVERKEGCRVMYCS-CHS-V 224 (268)
Q Consensus 196 ~~~k~CP~--C~~~iek~~GCnhm~C~-C~~-F 224 (268)
.+...||+ |+..+.+.+.=+|..|. |+. |
T Consensus 431 r~~V~Cp~~~Cg~v~~r~el~~H~~C~~Cgk~f 463 (567)
T PLN03086 431 RHNVVCPHDGCGIVLRVEEAKNHVHCEKCGQAF 463 (567)
T ss_pred CcceeCCcccccceeeccccccCccCCCCCCcc
Confidence 34578995 99999999999999997 988 7
No 298
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=28.59 E-value=39 Score=31.50 Aligned_cols=35 Identities=29% Similarity=0.583 Sum_probs=23.4
Q ss_pred ccccccccccccccCCCCCcchhhcccchhhHHHHHHHHhCCcccCCCCCceeee
Q 043604 156 NCTQWFCFQCKLAWHAGYRCEESGNLRDWNDIAFGKLVERMHWARCPACGSCVER 210 (268)
Q Consensus 156 ~C~~~~C~~C~~~~H~~~tC~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~~iek 210 (268)
.||..||+.|.-.+ ........++.||=|+..|-.
T Consensus 203 ~CGHiFC~~CiLqy--------------------~~~s~~~~~~~CPiC~s~I~~ 237 (513)
T KOG2164|consen 203 NCGHIFCGPCILQY--------------------WNYSAIKGPCSCPICRSTITL 237 (513)
T ss_pred ccCceeeHHHHHHH--------------------HhhhcccCCccCCchhhhccc
Confidence 48999999886431 111234677899988887764
No 299
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=27.25 E-value=54 Score=32.40 Aligned_cols=45 Identities=18% Similarity=0.520 Sum_probs=27.7
Q ss_pred cccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCC
Q 043604 39 TCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQF 94 (268)
Q Consensus 39 ~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~ 94 (268)
.|++|+..+... .......|+|+||..||..|-... -.||. |...
T Consensus 125 ~CP~Ci~s~~Dq-L~~~~k~c~H~FC~~Ci~sWsR~a--------qTCPi--DR~E 169 (1134)
T KOG0825|consen 125 QCPNCLKSCNDQ-LEESEKHTAHYFCEECVGSWSRCA--------QTCPV--DRGE 169 (1134)
T ss_pred hhhHHHHHHHHH-hhccccccccccHHHHhhhhhhhc--------ccCch--hhhh
Confidence 455554443221 122345799999999999997643 25777 6543
No 300
>COG4647 AcxC Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=27.14 E-value=2.8e+02 Score=20.94 Aligned_cols=62 Identities=19% Similarity=0.150 Sum_probs=31.7
Q ss_pred CCCHHHHhhcCC----hhHHHHHHHHHHhhhhcCCCcccCCccccCceeeeccccccCCcCeeeCccccccccc
Q 043604 94 FLDPFSCKLMIP----SNLFSKWCDVLFEDYVLGFERSYCPNRNCMALVVNGCEINYGTLKKARCPNCTQWFCF 163 (268)
Q Consensus 94 ~i~~~~i~~~l~----~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~C~ 163 (268)
.++....+.+++ .+-|.+|...+.+.. .-.+.+.=| --...++..... ...++| .||..||-
T Consensus 16 tl~w~qt~r~msa~kdhdrf~kylavlqdrv-~~~dpillp--vg~hlfi~qs~~----~rv~rc-ecghsf~d 81 (165)
T COG4647 16 TLPWPQTRRMMSAYKDHDRFFKYLAVLQDRV-DWDDPILLP--VGDHLFICQSAQ----KRVIRC-ECGHSFGD 81 (165)
T ss_pred CCCcHHHHHHHhccccHHHHHHHHHHHHhhc-ccCCCeeee--cCCcEEEEeccc----ccEEEE-eccccccC
Confidence 345555555443 456667766655432 112222222 223344433333 357889 69999975
No 301
>PRK13264 3-hydroxyanthranilate 3,4-dioxygenase; Provisional
Probab=26.79 E-value=24 Score=28.15 Aligned_cols=50 Identities=20% Similarity=0.423 Sum_probs=28.2
Q ss_pred cccccccccccCCC-CCcchhhcccchhhHHHHHHHHhCCcccCCCCCceeeec
Q 043604 159 QWFCFQCKLAWHAG-YRCEESGNLRDWNDIAFGKLVERMHWARCPACGSCVERK 211 (268)
Q Consensus 159 ~~~C~~C~~~~H~~-~tC~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~~iek~ 211 (268)
.-+|..|...-|.- ..|.+... .-...+.++..+...|.|++|++.....
T Consensus 120 ~wyc~~c~~~~~e~~f~~~d~~~---~~~~~~~~f~~~~e~rtC~~CG~v~~~~ 170 (177)
T PRK13264 120 QWYCDECNHKVHEVEVQLTDIET---DLPPVFAAFYASEELRTCDNCGTVHPGK 170 (177)
T ss_pred EEECCCCCCeEEEEEEEecChhh---hhHHHHHHHhcCHhhccCCcCCcccCcc
Confidence 34445555554532 24443322 1123455666677789999999876543
No 302
>PRK08115 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=26.55 E-value=33 Score=34.41 Aligned_cols=23 Identities=39% Similarity=1.073 Sum_probs=18.8
Q ss_pred ccCCCCCc-eeeecCCcCeEEec-CCc
Q 043604 199 ARCPACGS-CVERKEGCRVMYCS-CHS 223 (268)
Q Consensus 199 k~CP~C~~-~iek~~GCnhm~C~-C~~ 223 (268)
-.||-|+. .|+..|||| +|. |+.
T Consensus 828 ~~cp~c~~~~~~~~~~c~--~c~~c~~ 852 (858)
T PRK08115 828 NTCPVCREGTVEEIGGCN--TCTNCGA 852 (858)
T ss_pred CCCCccCCCceeecCCCc--cccchhh
Confidence 48999998 678889998 576 765
No 303
>COG1781 PyrI Aspartate carbamoyltransferase, regulatory subunit [Nucleotide transport and metabolism]
Probab=26.40 E-value=54 Score=25.39 Aligned_cols=37 Identities=24% Similarity=0.476 Sum_probs=20.0
Q ss_pred CcccCCccccCceeee--ccc--cccCCcCeeeCccccccc
Q 043604 125 ERSYCPNRNCMALVVN--GCE--INYGTLKKARCPNCTQWF 161 (268)
Q Consensus 125 ~~~~Cp~~~C~~~~~~--~~~--~~~~~~~~~~C~~C~~~~ 161 (268)
++..||||+|-.--.. ... ........++|..|...+
T Consensus 105 gvlkCpN~nCITn~e~pv~s~F~~~~~~~~~lrC~YCe~~~ 145 (153)
T COG1781 105 GVLRCPNPNCITNAEEPVESKFYVVSKEPLALRCKYCEKTF 145 (153)
T ss_pred cEEEcCCCCcccCCCccCCccEEEEecCCcEEEEEecCcEe
Confidence 4578999999543221 000 000123568888777544
No 304
>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=26.07 E-value=19 Score=27.79 Aligned_cols=42 Identities=24% Similarity=0.504 Sum_probs=25.9
Q ss_pred eccCCCCCCCCC---CHHHHhhcCChhHHHHHHHHHHhhhhcCCCcccCCccccCceeee
Q 043604 84 IECPGVHCDQFL---DPFSCKLMIPSNLFSKWCDVLFEDYVLGFERSYCPNRNCMALVVN 140 (268)
Q Consensus 84 i~CP~~~C~~~i---~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~ 140 (268)
-+||. |+..+ +.++++..+++..++.|. .+..|| .|+.++..
T Consensus 92 sRC~~--CN~~L~~v~~~~v~~~vp~~v~~~~~-----------~f~~C~--~C~kiyW~ 136 (147)
T PF01927_consen 92 SRCPK--CNGPLRPVSKEEVKDRVPPYVYETYD-----------EFWRCP--GCGKIYWE 136 (147)
T ss_pred CccCC--CCcEeeechhhccccccCccccccCC-----------eEEECC--CCCCEecc
Confidence 58988 88644 455666666655554332 246777 77776654
No 305
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=25.84 E-value=40 Score=28.22 Aligned_cols=12 Identities=33% Similarity=0.750 Sum_probs=5.7
Q ss_pred cccCCCCCceee
Q 043604 198 WARCPACGSCVE 209 (268)
Q Consensus 198 ~k~CP~C~~~ie 209 (268)
...||.|+....
T Consensus 35 v~~C~~Cg~~~~ 46 (236)
T PF04981_consen 35 VTICPKCGRYRI 46 (236)
T ss_pred ceECCCCCCEEC
Confidence 345555554433
No 306
>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=25.24 E-value=28 Score=27.30 Aligned_cols=44 Identities=25% Similarity=0.478 Sum_probs=24.0
Q ss_pred ccccccccccCCC-CCcchhhcccchhhHHHHHHHHhCCcccCCCCCc
Q 043604 160 WFCFQCKLAWHAG-YRCEESGNLRDWNDIAFGKLVERMHWARCPACGS 206 (268)
Q Consensus 160 ~~C~~C~~~~H~~-~tC~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~ 206 (268)
-+|..|...-|.- ..|.+... .-...+.++..+...|.|++|++
T Consensus 115 wyc~~c~~~~~e~~f~~~d~~~---~~~~~~~~f~~~~~~rtC~~Cg~ 159 (159)
T TIGR03037 115 WFCPQCGHKLHRAEVQLENIVT---DLPPVFEHFYSNEDARTCKNCGH 159 (159)
T ss_pred EECCCCCCeEEEEEEEecChhh---hhHHHHHHHhCChhhccCCccCC
Confidence 3444555554532 24443322 11234556666777899999984
No 307
>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=25.09 E-value=56 Score=23.89 Aligned_cols=48 Identities=21% Similarity=0.403 Sum_probs=32.2
Q ss_pred CeEEecCCc-ccccccccccCCC---------------CCCCCCCCCCcccceecccCccccccc
Q 043604 215 RVMYCSCHS-VTYSRAKHISLRK---------------HSTRGDNKGWRIYKVSGCRSTCRSLEN 263 (268)
Q Consensus 215 nhm~C~C~~-FC~~C~~~~~~~~---------------~~~~~~~~~~~~~~~~gc~~~~~~l~~ 263 (268)
.-+.|.||+ ||-.= ..|+.+. .+.-..+++|.-..-+=||+=+..||.
T Consensus 23 k~vkc~CGh~f~d~r-~NwK~~alv~vRd~~E~~~~iYp~~~aPdp~w~~irEyyCP~Cgt~lev 86 (112)
T PF08882_consen 23 KVVKCDCGHEFCDAR-ENWKLGALVYVRDPEEIHPEIYPFTMAPDPEWQVIREYYCPGCGTQLEV 86 (112)
T ss_pred ceeeccCCCeecChh-cChhhCcEEEecChHHhhhhhcccccCCCCCcEEEEEEECCCCcceeEE
Confidence 478999999 99542 3333221 123344789999999999997776653
No 308
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=24.94 E-value=48 Score=26.12 Aligned_cols=25 Identities=20% Similarity=0.545 Sum_probs=16.6
Q ss_pred eccCCCCCCCC---CCHHHHhhcCChhHHH
Q 043604 84 IECPGVHCDQF---LDPFSCKLMIPSNLFS 110 (268)
Q Consensus 84 i~CP~~~C~~~---i~~~~i~~~l~~~~~~ 110 (268)
-+||. |+.. ++-++++.-+++..+.
T Consensus 98 ~RCp~--CN~~L~~vs~eev~~~Vp~~~~~ 125 (165)
T COG1656 98 SRCPE--CNGELEKVSREEVKEKVPEKVYR 125 (165)
T ss_pred ccCcc--cCCEeccCcHHHHhhccchhhhh
Confidence 47988 8854 4566777777765444
No 309
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=24.82 E-value=75 Score=27.87 Aligned_cols=32 Identities=34% Similarity=0.759 Sum_probs=24.6
Q ss_pred ccCCCCCce-----ee--ecCCcCeEEec-CCc-c------cccccc
Q 043604 199 ARCPACGSC-----VE--RKEGCRVMYCS-CHS-V------TYSRAK 230 (268)
Q Consensus 199 k~CP~C~~~-----ie--k~~GCnhm~C~-C~~-F------C~~C~~ 230 (268)
..||-||.. |. -.+|=.++.|. |++ | |-.|+.
T Consensus 188 ~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~ 234 (309)
T PRK03564 188 QFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVVRVKCSNCEQ 234 (309)
T ss_pred CCCCCCCCcchhheeeccCCCCceEEEcCCCCCcccccCccCCCCCC
Confidence 689999985 21 23788999998 998 7 667886
No 310
>PLN02189 cellulose synthase
Probab=24.66 E-value=52 Score=33.67 Aligned_cols=51 Identities=27% Similarity=0.637 Sum_probs=34.0
Q ss_pred CCcccccccccCCcC---CcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCC
Q 043604 35 NGIFTCEICIEPISA---NDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQF 94 (268)
Q Consensus 35 ~~~~~C~IC~~~~~~---~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~ 94 (268)
.....|.||-|++.. .+.|+..-.|+-..|+.|. .|-. ++|+ -.||. |+..
T Consensus 32 ~~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cy-eyer---~eg~---q~Cpq--Ckt~ 85 (1040)
T PLN02189 32 LDGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCY-EYER---REGT---QNCPQ--CKTR 85 (1040)
T ss_pred ccCccccccccccCcCCCCCEEEeeccCCCccccchh-hhhh---hcCC---ccCcc--cCCc
Confidence 345589999998643 3456545558999999999 4433 3333 35887 7754
No 311
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=24.61 E-value=73 Score=18.18 Aligned_cols=29 Identities=24% Similarity=0.569 Sum_probs=15.0
Q ss_pred ccCCccccCcee-eeccccccCCcCeeeCccc
Q 043604 127 SYCPNRNCMALV-VNGCEINYGTLKKARCPNC 157 (268)
Q Consensus 127 ~~Cp~~~C~~~~-~~~~~~~~~~~~~~~C~~C 157 (268)
+.|| .|+..- .............+.|..|
T Consensus 6 v~CP--~C~s~~~v~k~G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 6 VHCP--RCQSTEGVKKNGKSPSGHQRYRCKDC 35 (36)
T ss_pred eeCC--CCCCCCcceeCCCCCCCCEeEecCcC
Confidence 6787 666544 3222222224466777665
No 312
>KOG2979 consensus Protein involved in DNA repair [General function prediction only]
Probab=24.59 E-value=1.1e+02 Score=25.95 Aligned_cols=71 Identities=17% Similarity=0.211 Sum_probs=43.3
Q ss_pred ccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCCHHHHhhcCC-hhHHHHHHHHH
Q 043604 38 FTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLDPFSCKLMIP-SNLFSKWCDVL 116 (268)
Q Consensus 38 ~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~~l~-~~~~~~~~~~~ 116 (268)
..|+|=+-.+..+ + ....|+|+|=++=+..++. ....+.||..+|..+... ...+|. +..+.++.+..
T Consensus 177 ~rdPis~~~I~nP--v-iSkkC~HvydrDsI~~~l~------~~~~i~CPv~gC~~~~~~--~~~~l~~d~el~~kIr~~ 245 (262)
T KOG2979|consen 177 NRDPISKKPIVNP--V-ISKKCGHVYDRDSIMQILC------DEITIRCPVLGCENPYYI--QPGHLDEDKELQQKIRQS 245 (262)
T ss_pred ccCchhhhhhhch--h-hhcCcCcchhhhhHHHHhc------cCceeecccccCCccccc--cccccCchHHHHHHHHHh
Confidence 5677766655443 2 3568999998877666654 345799999999832211 123343 33566666555
Q ss_pred Hhh
Q 043604 117 FED 119 (268)
Q Consensus 117 ~~~ 119 (268)
.+.
T Consensus 246 qe~ 248 (262)
T KOG2979|consen 246 QEP 248 (262)
T ss_pred ccc
Confidence 543
No 313
>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=24.55 E-value=1.8e+02 Score=23.36 Aligned_cols=35 Identities=26% Similarity=0.447 Sum_probs=17.0
Q ss_pred CCcccCCccccCc--eeeeccccc-cCCcCeeeCcccc
Q 043604 124 FERSYCPNRNCMA--LVVNGCEIN-YGTLKKARCPNCT 158 (268)
Q Consensus 124 ~~~~~Cp~~~C~~--~~~~~~~~~-~~~~~~~~C~~C~ 158 (268)
.++..||+-.|+. .++....+. .....++.||.|+
T Consensus 97 g~FG~CPRv~C~~~~lLPiGlsd~~g~~~vKlyCP~C~ 134 (184)
T PF01214_consen 97 GDFGRCPRVYCNGQPLLPIGLSDTPGESTVKLYCPRCK 134 (184)
T ss_dssp TTT-B-SBGGGTT-B-EEEBS-SSTTS-BBEEEETTTT
T ss_pred CcCCcCCcccCCCCceeCccCCCCCCccceeEECCCCc
Confidence 4567899999985 344433322 1234555565554
No 314
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=23.96 E-value=72 Score=27.92 Aligned_cols=58 Identities=16% Similarity=0.367 Sum_probs=36.2
Q ss_pred CCcccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCCHHHH
Q 043604 35 NGIFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLDPFSC 100 (268)
Q Consensus 35 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i 100 (268)
.+.|.|++=-+.-.. ++-+.++.|||++=++=+.. +...+...++||- |...-..+.+
T Consensus 334 Hs~FiCPVlKe~~t~-ENpP~ml~CgHVIskeal~~-----LS~nG~~~FKCPY--CP~~~~~~~~ 391 (396)
T COG5109 334 HSLFICPVLKELCTD-ENPPVMLECGHVISKEALSV-----LSQNGVLSFKCPY--CPEMSKYENI 391 (396)
T ss_pred cceeeccccHhhhcc-cCCCeeeeccceeeHHHHHH-----HhhcCcEEeeCCC--CCcchhhhhh
Confidence 456889985443322 23346789999986665443 3333566899998 8765444443
No 315
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=23.90 E-value=80 Score=22.90 Aligned_cols=26 Identities=27% Similarity=0.704 Sum_probs=17.5
Q ss_pred cccCCCCCceee-ecCCcCeEEec-CCc-cc
Q 043604 198 WARCPACGSCVE-RKEGCRVMYCS-CHS-VT 225 (268)
Q Consensus 198 ~k~CP~C~~~ie-k~~GCnhm~C~-C~~-FC 225 (268)
...||+|..-.. .+++ .|.|. |.+ |=
T Consensus 3 lp~cp~c~sEytYed~~--~~~cpec~~ew~ 31 (112)
T COG2824 3 LPPCPKCNSEYTYEDGG--QLICPECAHEWN 31 (112)
T ss_pred CCCCCccCCceEEecCc--eEeCchhccccc
Confidence 357999976444 4455 88887 776 63
No 316
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=23.81 E-value=54 Score=25.56 Aligned_cols=25 Identities=24% Similarity=0.757 Sum_probs=17.2
Q ss_pred cccCCCCCceeeecCCcCeEEec-CCc
Q 043604 198 WARCPACGSCVERKEGCRVMYCS-CHS 223 (268)
Q Consensus 198 ~k~CP~C~~~iek~~GCnhm~C~-C~~ 223 (268)
+..||.|+..+...+. ....|. |+.
T Consensus 34 Y~aC~~C~kkv~~~~~-~~~~C~~C~~ 59 (166)
T cd04476 34 YPACPGCNKKVVEEGN-GTYRCEKCNK 59 (166)
T ss_pred EccccccCcccEeCCC-CcEECCCCCC
Confidence 4899999999987765 344443 443
No 317
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=23.77 E-value=50 Score=19.15 Aligned_cols=18 Identities=28% Similarity=0.781 Sum_probs=15.2
Q ss_pred eeeCcccccccccccccc
Q 043604 151 KARCPNCTQWFCFQCKLA 168 (268)
Q Consensus 151 ~~~C~~C~~~~C~~C~~~ 168 (268)
.+.|..|+..||..-+.+
T Consensus 12 ~f~C~~C~~~FC~~HR~~ 29 (39)
T smart00154 12 GFKCRHCGNLFCGEHRLP 29 (39)
T ss_pred CeECCccCCccccccCCc
Confidence 578999999999987764
No 318
>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=23.70 E-value=71 Score=20.12 Aligned_cols=15 Identities=27% Similarity=0.468 Sum_probs=9.7
Q ss_pred CCCcccCCccccCceee
Q 043604 123 GFERSYCPNRNCMALVV 139 (268)
Q Consensus 123 ~~~~~~Cp~~~C~~~~~ 139 (268)
.+++..|| .|+.+..
T Consensus 23 ~~~l~~c~--~cg~~~~ 37 (56)
T PF01783_consen 23 APNLVKCP--NCGEPKL 37 (56)
T ss_dssp TTSEEESS--SSSSEES
T ss_pred ccceeeec--cCCCEec
Confidence 35667777 6776553
No 319
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=23.20 E-value=69 Score=32.97 Aligned_cols=50 Identities=30% Similarity=0.786 Sum_probs=34.3
Q ss_pred CcccccccccCCcCC---cCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCC
Q 043604 36 GIFTCEICIEPISAN---DKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQF 94 (268)
Q Consensus 36 ~~~~C~IC~~~~~~~---~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~ 94 (268)
....|.||-|++... +.|+..-.|+-..|+.|. .| ..++|+ -.||. |+..
T Consensus 16 ~~qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCY-EY---Er~eG~---q~CPq--Cktr 68 (1079)
T PLN02638 16 GGQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCY-EY---ERKDGN---QSCPQ--CKTK 68 (1079)
T ss_pred CCceeeecccccCcCCCCCEEEEeccCCCccccchh-hh---hhhcCC---ccCCc--cCCc
Confidence 345899999987543 456556678999999998 33 344443 35887 7743
No 320
>PRK08332 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=23.12 E-value=52 Score=35.75 Aligned_cols=26 Identities=27% Similarity=0.709 Sum_probs=22.1
Q ss_pred ccCCCCCce------eeecCCcCeEEec-CCc-ccc
Q 043604 199 ARCPACGSC------VERKEGCRVMYCS-CHS-VTY 226 (268)
Q Consensus 199 k~CP~C~~~------iek~~GCnhm~C~-C~~-FC~ 226 (268)
..||.|+.. +...+||. +|+ ||+ =|-
T Consensus 1705 ~~cp~c~~~~~~~~~~~~~~gc~--~c~~cg~s~c~ 1738 (1740)
T PRK08332 1705 VYCPVCYEKEGKLVELRMESGCA--TCPVCGWSKCV 1738 (1740)
T ss_pred CCCCCCCCCCCcceeeEecCCce--eCCCCCCcccc
Confidence 459999999 88889996 998 998 763
No 321
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=22.84 E-value=93 Score=22.92 Aligned_cols=26 Identities=15% Similarity=0.456 Sum_probs=15.2
Q ss_pred cccCCccccCceeeeccccccCCcCeeeCccccc
Q 043604 126 RSYCPNRNCMALVVNGCEINYGTLKKARCPNCTQ 159 (268)
Q Consensus 126 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~ 159 (268)
..+|+ +|+..+..... ....||.|+.
T Consensus 71 ~~~C~--~Cg~~~~~~~~------~~~~CP~Cgs 96 (117)
T PRK00564 71 ELECK--DCSHVFKPNAL------DYGVCEKCHS 96 (117)
T ss_pred EEEhh--hCCCccccCCc------cCCcCcCCCC
Confidence 46787 78866654432 2234777764
No 322
>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=22.80 E-value=35 Score=16.57 Aligned_cols=9 Identities=44% Similarity=1.279 Sum_probs=4.9
Q ss_pred eCccccccc
Q 043604 153 RCPNCTQWF 161 (268)
Q Consensus 153 ~C~~C~~~~ 161 (268)
.|+.|+..|
T Consensus 2 ~C~~C~~~f 10 (23)
T PF00096_consen 2 KCPICGKSF 10 (23)
T ss_dssp EETTTTEEE
T ss_pred CCCCCCCcc
Confidence 466665544
No 323
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=22.67 E-value=38 Score=29.69 Aligned_cols=39 Identities=21% Similarity=0.628 Sum_probs=28.0
Q ss_pred ccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhc
Q 043604 38 FTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQD 78 (268)
Q Consensus 38 ~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~ 78 (268)
..|-.|+++..+...+ .-..|.+.||.+|=. ++-..+..
T Consensus 331 ~~Cf~C~~~~~~~~~y-~C~~Ck~~FCldCDv-~iHesLh~ 369 (378)
T KOG2807|consen 331 RFCFACQGELLSSGRY-RCESCKNVFCLDCDV-FIHESLHN 369 (378)
T ss_pred cceeeeccccCCCCcE-EchhccceeeccchH-HHHhhhhc
Confidence 3499998887666555 467899999999953 55555544
No 324
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=22.48 E-value=58 Score=22.93 Aligned_cols=28 Identities=21% Similarity=0.573 Sum_probs=21.4
Q ss_pred CcccCCCCCceeeecCCcCeEEec-CCc-c
Q 043604 197 HWARCPACGSCVERKEGCRVMYCS-CHS-V 224 (268)
Q Consensus 197 ~~k~CP~C~~~iek~~GCnhm~C~-C~~-F 224 (268)
..-.||.|+..-.|..+----.|. |+. |
T Consensus 34 a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~ 63 (91)
T TIGR00280 34 AKYVCPFCGKKTVKRGSTGIWTCRKCGAKF 63 (91)
T ss_pred cCccCCCCCCCceEEEeeEEEEcCCCCCEE
Confidence 346899998887777777777786 877 6
No 325
>KOG2923 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.47 E-value=64 Score=21.02 Aligned_cols=20 Identities=30% Similarity=0.597 Sum_probs=15.1
Q ss_pred HHHHhCCcccCCCCCceeee
Q 043604 191 KLVERMHWARCPACGSCVER 210 (268)
Q Consensus 191 ~~~~~~~~k~CP~C~~~iek 210 (268)
.+.....+-+||.|...|.-
T Consensus 37 dL~~ge~Va~CpsCSL~I~V 56 (67)
T KOG2923|consen 37 DLENGEDVARCPSCSLIIRV 56 (67)
T ss_pred HHhCCCeeecCCCceEEEEE
Confidence 34456678899999988864
No 326
>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=22.27 E-value=49 Score=18.54 Aligned_cols=14 Identities=36% Similarity=0.978 Sum_probs=9.7
Q ss_pred cccCCCCCceeeec
Q 043604 198 WARCPACGSCVERK 211 (268)
Q Consensus 198 ~k~CP~C~~~iek~ 211 (268)
+-.||+|+..|.-+
T Consensus 4 ~~~C~nC~R~v~a~ 17 (33)
T PF08209_consen 4 YVECPNCGRPVAAS 17 (33)
T ss_dssp EEE-TTTSSEEEGG
T ss_pred eEECCCCcCCcchh
Confidence 45799999988643
No 327
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=22.19 E-value=58 Score=22.89 Aligned_cols=27 Identities=26% Similarity=0.676 Sum_probs=21.6
Q ss_pred cccCCCCCceeeecCCcCeEEec-CCc-c
Q 043604 198 WARCPACGSCVERKEGCRVMYCS-CHS-V 224 (268)
Q Consensus 198 ~k~CP~C~~~iek~~GCnhm~C~-C~~-F 224 (268)
.-.||.|+..-.|..+----.|. |+. |
T Consensus 36 ~y~CpfCgk~~vkR~a~GIW~C~~C~~~~ 64 (90)
T PRK03976 36 KHVCPVCGRPKVKRVGTGIWECRKCGAKF 64 (90)
T ss_pred CccCCCCCCCceEEEEEEEEEcCCCCCEE
Confidence 46899999888887777777786 887 6
No 328
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=22.10 E-value=82 Score=27.16 Aligned_cols=30 Identities=17% Similarity=0.319 Sum_probs=22.2
Q ss_pred CCcccCCccccCceeeeccccccCCcCeeeCcccccc
Q 043604 124 FERSYCPNRNCMALVVNGCEINYGTLKKARCPNCTQW 160 (268)
Q Consensus 124 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~ 160 (268)
...++|+ .|+......... ....|+.|+..
T Consensus 109 ~~~RFCg--~CG~~~~~~~~g-----~~~~C~~cg~~ 138 (279)
T COG2816 109 RSHRFCG--RCGTKTYPREGG-----WARVCPKCGHE 138 (279)
T ss_pred hhCcCCC--CCCCcCccccCc-----eeeeCCCCCCc
Confidence 4568999 899887766543 67889988754
No 329
>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=21.78 E-value=49 Score=17.05 Aligned_cols=12 Identities=42% Similarity=1.010 Sum_probs=8.4
Q ss_pred CeeeCccccccc
Q 043604 150 KKARCPNCTQWF 161 (268)
Q Consensus 150 ~~~~C~~C~~~~ 161 (268)
..+.|+.|++.|
T Consensus 13 k~~~C~~C~k~F 24 (26)
T PF13465_consen 13 KPYKCPYCGKSF 24 (26)
T ss_dssp SSEEESSSSEEE
T ss_pred CCCCCCCCcCee
Confidence 457788887665
No 330
>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=21.70 E-value=43 Score=21.36 Aligned_cols=16 Identities=38% Similarity=0.769 Sum_probs=8.3
Q ss_pred cccCCCCCceeeecCC
Q 043604 198 WARCPACGSCVERKEG 213 (268)
Q Consensus 198 ~k~CP~C~~~iek~~G 213 (268)
...||.|+..++-..+
T Consensus 2 ~v~CP~C~k~~~~~~~ 17 (57)
T PF03884_consen 2 TVKCPICGKPVEWSPE 17 (57)
T ss_dssp EEE-TTT--EEE-SSS
T ss_pred cccCCCCCCeecccCC
Confidence 3579999998886433
No 331
>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=21.69 E-value=1.3e+02 Score=19.50 Aligned_cols=14 Identities=14% Similarity=0.577 Sum_probs=9.4
Q ss_pred CceeccCCCCCCCCCC
Q 043604 81 TAKIECPGVHCDQFLD 96 (268)
Q Consensus 81 ~~~i~CP~~~C~~~i~ 96 (268)
..||+|+. |+..|.
T Consensus 2 iiPVRCFT--CGkvi~ 15 (60)
T PF01194_consen 2 IIPVRCFT--CGKVIG 15 (60)
T ss_dssp --SSS-ST--TTSBTC
T ss_pred CCceecCC--CCCChh
Confidence 36899998 998875
No 332
>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=21.68 E-value=1.7e+02 Score=20.02 Aligned_cols=32 Identities=19% Similarity=0.546 Sum_probs=22.2
Q ss_pred ccCCccccCceeeeccccccCCcCeeeCcccccccccc
Q 043604 127 SYCPNRNCMALVVNGCEINYGTLKKARCPNCTQWFCFQ 164 (268)
Q Consensus 127 ~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~C~~ 164 (268)
+.|| +|-.+--.-.-. ...+.|+.|+...|.-
T Consensus 35 VkC~--gc~~iT~vfSHa----qtvVvc~~c~~il~~~ 66 (84)
T KOG1779|consen 35 VKCP--GCFKITTVFSHA----QTVVVCEGCSTILCQP 66 (84)
T ss_pred EEcC--CceEEEEEeecC----ceEEEcCCCceEEEEe
Confidence 6787 777665544433 4778999998887764
No 333
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=21.35 E-value=67 Score=22.61 Aligned_cols=28 Identities=25% Similarity=0.671 Sum_probs=21.1
Q ss_pred CcccCCCCCceeeecCCcCeEEec-CCc-c
Q 043604 197 HWARCPACGSCVERKEGCRVMYCS-CHS-V 224 (268)
Q Consensus 197 ~~k~CP~C~~~iek~~GCnhm~C~-C~~-F 224 (268)
..-.||.|+..-.|..+----.|+ |+. |
T Consensus 35 a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~ 64 (90)
T PTZ00255 35 AKYFCPFCGKHAVKRQAVGIWRCKGCKKTV 64 (90)
T ss_pred CCccCCCCCCCceeeeeeEEEEcCCCCCEE
Confidence 346899998877777776667776 776 6
No 334
>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=21.21 E-value=59 Score=23.77 Aligned_cols=46 Identities=22% Similarity=0.300 Sum_probs=22.6
Q ss_pred ChhHHHHHHHHHHhhhhcC---------CCcccCCccccCceeeeccccccCCcCeeeCccccc
Q 043604 105 PSNLFSKWCDVLFEDYVLG---------FERSYCPNRNCMALVVNGCEINYGTLKKARCPNCTQ 159 (268)
Q Consensus 105 ~~~~~~~~~~~~~~~~~~~---------~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~ 159 (268)
.++.++.....+.+..+.. +-..+|. +|+.-+..+... ..||.|+.
T Consensus 40 ~pe~L~f~f~~~~~~T~~e~a~L~Ie~~p~~~~C~--~Cg~~~~~~~~~-------~~CP~Cgs 94 (113)
T PF01155_consen 40 EPEALRFAFEVLAEGTILEGAELEIEEVPARARCR--DCGHEFEPDEFD-------FSCPRCGS 94 (113)
T ss_dssp -HHHHHHHHHHHHCCSTTTT-EEEEEEE--EEEET--TTS-EEECHHCC-------HH-SSSSS
T ss_pred CHHHHHHHHHHHhCCCCccCCEEEEEecCCcEECC--CCCCEEecCCCC-------CCCcCCcC
Confidence 4555555444444433321 2346777 788877665432 45777764
No 335
>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=20.99 E-value=45 Score=18.27 Aligned_cols=9 Identities=56% Similarity=1.294 Sum_probs=5.6
Q ss_pred cCCCCCcee
Q 043604 200 RCPACGSCV 208 (268)
Q Consensus 200 ~CP~C~~~i 208 (268)
.||+|++-+
T Consensus 3 lcpkcgvgv 11 (36)
T PF09151_consen 3 LCPKCGVGV 11 (36)
T ss_dssp B-TTTSSSB
T ss_pred cCCccCceE
Confidence 588888743
No 336
>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=20.87 E-value=77 Score=17.45 Aligned_cols=20 Identities=20% Similarity=0.326 Sum_probs=11.7
Q ss_pred ccCceeeeccccccCCcCeeeCccccc
Q 043604 133 NCMALVVNGCEINYGTLKKARCPNCTQ 159 (268)
Q Consensus 133 ~C~~~~~~~~~~~~~~~~~~~C~~C~~ 159 (268)
.|+.++.... ....||.|+.
T Consensus 6 ~CGy~y~~~~-------~~~~CP~Cg~ 25 (33)
T cd00350 6 VCGYIYDGEE-------APWVCPVCGA 25 (33)
T ss_pred CCCCEECCCc-------CCCcCcCCCC
Confidence 6777665432 2346887764
No 337
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=20.86 E-value=72 Score=20.11 Aligned_cols=34 Identities=24% Similarity=0.282 Sum_probs=15.1
Q ss_pred CcccCCccccCceeeecccccc-CCcCeeeCcccccc
Q 043604 125 ERSYCPNRNCMALVVNGCEINY-GTLKKARCPNCTQW 160 (268)
Q Consensus 125 ~~~~Cp~~~C~~~~~~~~~~~~-~~~~~~~C~~C~~~ 160 (268)
.++.|| .|++--...-..+. -...-+.||.|.+.
T Consensus 3 ~Wi~CP--~CgnKTR~kir~DT~LkNfPlyCpKCK~E 37 (55)
T PF14205_consen 3 EWILCP--ICGNKTRLKIREDTVLKNFPLYCPKCKQE 37 (55)
T ss_pred eEEECC--CCCCccceeeecCceeccccccCCCCCce
Confidence 356777 67643322111110 02344566666543
No 338
>PF13963 Transpos_assoc: Transposase-associated domain
Probab=20.69 E-value=1.2e+02 Score=20.35 Aligned_cols=35 Identities=17% Similarity=0.361 Sum_probs=20.7
Q ss_pred HHHHHHHHhhcC-CCceeccCCCCCCCC--CCHHHHhh
Q 043604 68 IAKYIEAKVQDN-NTAKIECPGVHCDQF--LDPFSCKL 102 (268)
Q Consensus 68 l~~~~~~~i~~~-~~~~i~CP~~~C~~~--i~~~~i~~ 102 (268)
+..++..+.... ....|.||-..|+.. .+..+|..
T Consensus 21 v~~Fi~~A~~~~~~~~~i~CPC~~C~N~~~~~~~~V~~ 58 (77)
T PF13963_consen 21 VEEFIDFAFSNPSNDNMIRCPCRKCKNEKRQSRDDVHE 58 (77)
T ss_pred HHHHHHHHHhcccCCCceECCchhhccCccCCHHHHHH
Confidence 355666666552 223799998888743 34444443
No 339
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=20.68 E-value=97 Score=27.11 Aligned_cols=28 Identities=25% Similarity=0.501 Sum_probs=15.3
Q ss_pred hCCcccCCCCCc-eeeecCCcCeEEec-CC
Q 043604 195 RMHWARCPACGS-CVERKEGCRVMYCS-CH 222 (268)
Q Consensus 195 ~~~~k~CP~C~~-~iek~~GCnhm~C~-C~ 222 (268)
......||.|+. .|.-+..=.-+.|. ||
T Consensus 8 ~~~~~~Cp~Cg~~~iv~d~~~Ge~vC~~CG 37 (310)
T PRK00423 8 EEEKLVCPECGSDKLIYDYERGEIVCADCG 37 (310)
T ss_pred cccCCcCcCCCCCCeeEECCCCeEeecccC
Confidence 344568999987 44333333334454 44
No 340
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=20.39 E-value=1e+02 Score=27.13 Aligned_cols=55 Identities=16% Similarity=0.287 Sum_probs=36.4
Q ss_pred CcccccccccCCcCCcCccccCCCCChhhHHHHHHHHHHHhhcCCCceeccCCCCCCCCCCHHHHhhc
Q 043604 36 GIFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLDPFSCKLM 103 (268)
Q Consensus 36 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~~ 103 (268)
....|+||.....++ . ++..=|-+||-.|+-.|+.+ . =+||.-++ ++..+++.++
T Consensus 299 ~~~~CpvClk~r~Np-t--vl~vSGyVfCY~Ci~~Yv~~---~-----~~CPVT~~--p~~v~~l~rl 353 (357)
T KOG0826|consen 299 DREVCPVCLKKRQNP-T--VLEVSGYVFCYPCIFSYVVN---Y-----GHCPVTGY--PASVDHLIRL 353 (357)
T ss_pred ccccChhHHhccCCC-c--eEEecceEEeHHHHHHHHHh---c-----CCCCccCC--cchHHHHHHH
Confidence 446899999887443 2 23445889999999999972 2 25887554 3444444443
No 341
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=20.11 E-value=54 Score=16.85 Aligned_cols=18 Identities=22% Similarity=0.563 Sum_probs=13.4
Q ss_pred eccCCCCCCCCCCHHHHhhc
Q 043604 84 IECPGVHCDQFLDPFSCKLM 103 (268)
Q Consensus 84 i~CP~~~C~~~i~~~~i~~~ 103 (268)
+.||. |+..+..+.+...
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 9988877776553
No 342
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=20.00 E-value=42 Score=28.82 Aligned_cols=30 Identities=20% Similarity=0.517 Sum_probs=23.6
Q ss_pred cccCCccccCceeeeccccccCCcCeeeCccccccc
Q 043604 126 RSYCPNRNCMALVVNGCEINYGTLKKARCPNCTQWF 161 (268)
Q Consensus 126 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~ 161 (268)
+..|| .|+..+...+.. .+...||.|++.+
T Consensus 28 w~KCp--~c~~~~y~~eL~----~n~~vcp~c~~h~ 57 (294)
T COG0777 28 WTKCP--SCGEMLYRKELE----SNLKVCPKCGHHM 57 (294)
T ss_pred eeECC--CccceeeHHHHH----hhhhcccccCccc
Confidence 57788 999999887775 4677899888655
Done!