Query 024566
Match_columns 265
No_of_seqs 249 out of 1463
Neff 9.2
Searched_HMMs 46136
Date Fri Mar 29 05:37:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024566.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024566hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1812 Predicted E3 ubiquitin 100.0 1.1E-38 2.3E-43 281.5 9.8 197 19-219 144-344 (384)
2 KOG1814 Predicted E3 ubiquitin 100.0 1.6E-38 3.5E-43 270.5 6.8 214 16-235 179-426 (445)
3 KOG1815 Predicted E3 ubiquitin 100.0 7.3E-30 1.6E-34 231.1 14.9 193 18-217 67-265 (444)
4 KOG0006 E3 ubiquitin-protein l 99.9 9E-28 2E-32 198.3 7.8 195 16-221 216-440 (446)
5 smart00647 IBR In Between Ring 99.3 4.1E-12 8.8E-17 84.3 5.2 63 94-158 1-64 (64)
6 PF01485 IBR: IBR domain; Int 99.2 1.4E-12 2.9E-17 86.6 0.4 63 94-158 1-64 (64)
7 smart00647 IBR In Between Ring 98.7 2.8E-08 6.1E-13 65.6 5.2 49 172-220 8-62 (64)
8 PF15227 zf-C3HC4_4: zinc fing 98.7 5.8E-09 1.3E-13 62.7 0.7 41 24-72 1-41 (42)
9 PLN03208 E3 ubiquitin-protein 98.6 5.3E-08 1.1E-12 77.3 4.9 71 13-89 10-88 (193)
10 PF00097 zf-C3HC4: Zinc finger 98.6 4.6E-08 1E-12 58.6 2.5 40 24-72 1-40 (41)
11 PF01485 IBR: IBR domain; Int 98.5 2.3E-08 5E-13 66.0 0.9 42 179-220 16-62 (64)
12 PF13445 zf-RING_UBOX: RING-ty 98.5 5.3E-08 1.1E-12 58.5 2.0 43 24-71 1-43 (43)
13 PF13639 zf-RING_2: Ring finge 98.5 3.7E-08 8E-13 60.0 0.4 41 23-72 2-42 (44)
14 PF13923 zf-C3HC4_2: Zinc fing 98.5 9.3E-08 2E-12 56.6 2.1 38 24-72 1-38 (39)
15 PF14634 zf-RING_5: zinc-RING 98.3 4.2E-07 9E-12 55.3 3.1 43 23-76 1-43 (44)
16 KOG0320 Predicted E3 ubiquitin 98.3 4.8E-07 1E-11 70.1 3.3 57 18-86 128-184 (187)
17 cd00162 RING RING-finger (Real 98.2 1.6E-06 3.5E-11 52.4 3.4 44 23-78 1-44 (45)
18 PF13920 zf-C3HC4_3: Zinc fing 98.1 1.3E-06 2.9E-11 54.6 2.1 46 21-80 2-48 (50)
19 PHA02926 zinc finger-like prot 98.1 3.3E-06 7.3E-11 67.9 4.2 58 18-79 167-229 (242)
20 KOG2177 Predicted E3 ubiquitin 98.0 4E-06 8.6E-11 72.6 3.6 112 17-160 9-124 (386)
21 PHA02929 N1R/p28-like protein; 98.0 6.3E-06 1.4E-10 68.3 3.3 52 19-80 172-227 (238)
22 KOG0823 Predicted E3 ubiquitin 98.0 7.5E-06 1.6E-10 66.4 3.7 61 18-89 44-104 (230)
23 smart00184 RING Ring finger. E 97.9 1.3E-05 2.9E-10 46.5 3.3 38 24-72 1-38 (39)
24 KOG2164 Predicted E3 ubiquitin 97.9 6.5E-06 1.4E-10 73.8 2.4 61 21-90 186-246 (513)
25 smart00504 Ubox Modified RING 97.8 2.4E-05 5.1E-10 51.3 3.7 50 22-85 2-51 (63)
26 KOG0317 Predicted E3 ubiquitin 97.8 2.2E-05 4.8E-10 65.6 3.9 52 19-84 237-288 (293)
27 COG5540 RING-finger-containing 97.7 2E-05 4.3E-10 66.2 2.7 55 17-81 319-373 (374)
28 TIGR00599 rad18 DNA repair pro 97.7 4.7E-05 1E-09 67.7 4.6 67 18-98 23-90 (397)
29 KOG4628 Predicted E3 ubiquitin 97.7 3.5E-05 7.5E-10 66.9 3.2 49 22-80 230-278 (348)
30 TIGR00570 cdk7 CDK-activating 97.5 0.00023 5E-09 60.9 6.1 55 22-86 4-60 (309)
31 KOG0287 Postreplication repair 97.4 7.5E-05 1.6E-09 63.7 2.4 66 18-97 20-86 (442)
32 PF11789 zf-Nse: Zinc-finger o 97.4 0.00011 2.5E-09 47.0 2.4 52 16-76 6-57 (57)
33 KOG1002 Nucleotide excision re 97.4 0.00016 3.6E-09 65.1 4.0 72 17-97 532-603 (791)
34 COG5574 PEX10 RING-finger-cont 97.0 0.00078 1.7E-08 55.8 4.0 52 21-84 215-266 (271)
35 KOG0978 E3 ubiquitin ligase in 97.0 0.00047 1E-08 65.0 2.7 56 19-87 641-696 (698)
36 PF12678 zf-rbx1: RING-H2 zinc 97.0 0.00041 9E-09 46.9 1.7 46 21-76 19-73 (73)
37 KOG4367 Predicted Zn-finger pr 96.9 0.00052 1.1E-08 60.6 2.6 82 132-220 174-257 (699)
38 PF11793 FANCL_C: FANCL C-term 96.8 0.00041 8.9E-09 46.5 0.8 59 21-81 2-67 (70)
39 PF14835 zf-RING_6: zf-RING of 96.8 0.0003 6.6E-09 45.4 -0.1 51 20-85 6-56 (65)
40 COG5432 RAD18 RING-finger-cont 96.4 0.0018 3.9E-08 54.3 2.1 68 17-98 21-89 (391)
41 KOG1814 Predicted E3 ubiquitin 96.4 0.005 1.1E-07 54.2 4.8 47 179-225 271-320 (445)
42 COG5243 HRD1 HRD ubiquitin lig 95.7 0.0085 1.8E-07 52.1 3.0 54 18-81 284-346 (491)
43 KOG2660 Locus-specific chromos 95.7 0.0092 2E-07 51.2 3.0 53 18-83 12-64 (331)
44 PF04564 U-box: U-box domain; 95.7 0.0057 1.2E-07 41.3 1.4 52 20-84 3-54 (73)
45 PF14570 zf-RING_4: RING/Ubox 95.6 0.012 2.6E-07 36.0 2.4 47 24-79 1-47 (48)
46 KOG0006 E3 ubiquitin-protein l 95.6 0.02 4.4E-07 48.8 4.6 93 42-154 341-437 (446)
47 KOG0824 Predicted E3 ubiquitin 95.4 0.012 2.7E-07 49.8 2.9 54 18-84 4-57 (324)
48 KOG1039 Predicted E3 ubiquitin 95.4 0.016 3.4E-07 50.8 3.6 95 18-115 158-264 (344)
49 KOG2879 Predicted E3 ubiquitin 94.7 0.034 7.4E-07 46.5 3.5 52 18-80 236-287 (298)
50 PF10571 UPF0547: Uncharacteri 94.7 0.013 2.9E-07 31.0 0.7 23 182-208 1-24 (26)
51 KOG4185 Predicted E3 ubiquitin 94.7 0.05 1.1E-06 47.1 4.7 50 21-79 3-54 (296)
52 COG5175 MOT2 Transcriptional r 94.6 0.07 1.5E-06 46.0 5.2 65 19-92 12-77 (480)
53 smart00744 RINGv The RING-vari 94.5 0.052 1.1E-06 33.5 3.2 42 23-72 1-47 (49)
54 COG5152 Uncharacterized conser 94.3 0.028 6.2E-07 44.7 2.0 36 17-56 192-227 (259)
55 KOG0802 E3 ubiquitin ligase [P 94.2 0.032 7E-07 52.5 2.7 49 19-77 289-338 (543)
56 KOG1812 Predicted E3 ubiquitin 93.7 0.007 1.5E-07 54.3 -2.6 42 108-156 304-345 (384)
57 KOG1428 Inhibitor of type V ad 93.6 0.059 1.3E-06 54.7 3.1 71 17-90 3482-3554(3738)
58 PF12861 zf-Apc11: Anaphase-pr 93.6 0.088 1.9E-06 36.3 3.1 54 21-81 21-83 (85)
59 KOG0828 Predicted E3 ubiquitin 93.5 0.061 1.3E-06 48.6 2.8 54 19-81 569-635 (636)
60 PF13240 zinc_ribbon_2: zinc-r 93.3 0.039 8.5E-07 28.2 0.8 11 183-193 1-11 (23)
61 KOG4159 Predicted E3 ubiquitin 93.3 0.073 1.6E-06 47.7 3.0 50 18-81 81-130 (398)
62 KOG3039 Uncharacterized conser 93.0 0.068 1.5E-06 44.1 2.3 57 19-85 219-275 (303)
63 PF13248 zf-ribbon_3: zinc-rib 93.0 0.047 1E-06 28.8 0.9 23 182-215 3-25 (26)
64 smart00661 RPOL9 RNA polymeras 92.7 0.099 2.1E-06 32.5 2.2 27 182-208 1-30 (52)
65 KOG0311 Predicted E3 ubiquitin 92.5 0.022 4.8E-07 49.3 -1.3 49 19-79 41-89 (381)
66 KOG4172 Predicted E3 ubiquitin 92.4 0.062 1.3E-06 33.4 1.0 46 21-79 7-53 (62)
67 KOG4739 Uncharacterized protei 92.3 0.049 1.1E-06 44.9 0.6 57 21-91 3-59 (233)
68 COG5220 TFB3 Cdk activating ki 92.3 0.038 8.2E-07 45.3 -0.1 54 19-79 8-63 (314)
69 KOG1734 Predicted RING-contain 92.3 0.025 5.4E-07 47.2 -1.2 56 19-83 222-284 (328)
70 PF04641 Rtf2: Rtf2 RING-finge 92.3 0.26 5.6E-06 41.9 5.0 72 18-100 110-182 (260)
71 KOG0827 Predicted E3 ubiquitin 92.0 0.14 2.9E-06 45.1 2.9 54 21-81 4-57 (465)
72 KOG1952 Transcription factor N 91.7 0.1 2.2E-06 50.2 2.0 57 17-76 187-243 (950)
73 PHA00626 hypothetical protein 91.6 0.14 3.1E-06 32.0 1.9 26 183-208 2-33 (59)
74 KOG1815 Predicted E3 ubiquitin 91.3 0.14 3E-06 47.1 2.4 43 180-222 157-202 (444)
75 KOG4265 Predicted E3 ubiquitin 91.2 0.19 4E-06 43.9 2.9 49 18-80 287-336 (349)
76 PF13719 zinc_ribbon_5: zinc-r 91.1 0.2 4.3E-06 28.9 2.1 32 111-144 3-35 (37)
77 KOG0804 Cytoplasmic Zn-finger 91.0 0.089 1.9E-06 47.1 0.8 53 16-80 170-222 (493)
78 KOG0297 TNF receptor-associate 91.0 0.32 6.9E-06 43.9 4.3 51 18-81 18-68 (391)
79 KOG1645 RING-finger-containing 90.9 0.099 2.1E-06 46.3 1.0 50 21-78 4-54 (463)
80 KOG3053 Uncharacterized conser 90.4 0.72 1.6E-05 38.4 5.5 62 16-79 15-81 (293)
81 PF05883 Baculo_RING: Baculovi 90.2 0.14 3.1E-06 38.4 1.2 39 18-57 23-67 (134)
82 PRK00432 30S ribosomal protein 90.1 0.22 4.8E-06 30.8 1.8 27 180-208 19-47 (50)
83 KOG3800 Predicted E3 ubiquitin 90.0 0.65 1.4E-05 39.4 5.0 53 23-84 2-55 (300)
84 PHA03096 p28-like protein; Pro 89.8 0.23 5E-06 42.6 2.3 40 22-61 179-222 (284)
85 KOG1940 Zn-finger protein [Gen 89.7 0.62 1.3E-05 39.6 4.8 50 18-77 155-204 (276)
86 KOG4445 Uncharacterized conser 89.3 0.3 6.6E-06 41.5 2.5 64 16-82 110-188 (368)
87 PF13717 zinc_ribbon_4: zinc-r 89.1 0.43 9.4E-06 27.3 2.4 32 111-144 3-35 (36)
88 PRK00398 rpoP DNA-directed RNA 89.0 0.44 9.4E-06 28.8 2.5 29 182-210 4-33 (46)
89 PF14803 Nudix_N_2: Nudix N-te 88.6 0.36 7.9E-06 27.2 1.8 31 111-143 1-31 (34)
90 KOG1785 Tyrosine kinase negati 88.5 0.18 4E-06 44.5 0.8 48 18-77 366-413 (563)
91 PF12773 DZR: Double zinc ribb 88.5 0.39 8.5E-06 29.5 2.1 15 179-193 27-41 (50)
92 PF07975 C1_4: TFIIH C1-like d 88.1 0.22 4.7E-06 30.9 0.7 38 118-155 5-42 (51)
93 PRK14890 putative Zn-ribbon RN 88.0 0.51 1.1E-05 30.0 2.4 33 111-149 8-43 (59)
94 PLN03086 PRLI-interacting fact 88.0 0.68 1.5E-05 43.5 4.2 59 65-144 405-463 (567)
95 PRK14559 putative protein seri 87.8 0.29 6.2E-06 46.9 1.7 10 206-215 41-50 (645)
96 COG5236 Uncharacterized conser 87.1 0.91 2E-05 39.5 4.1 69 18-98 58-126 (493)
97 KOG1493 Anaphase-promoting com 86.3 0.19 4.1E-06 33.6 -0.3 52 22-80 21-81 (84)
98 COG2888 Predicted Zn-ribbon RN 86.3 0.65 1.4E-05 29.5 2.1 32 111-148 10-41 (61)
99 COG1998 RPS31 Ribosomal protei 85.7 0.58 1.2E-05 28.6 1.6 27 180-206 18-45 (51)
100 PF09297 zf-NADH-PPase: NADH p 85.6 1.1 2.4E-05 24.7 2.7 27 181-207 3-30 (32)
101 PF14952 zf-tcix: Putative tre 85.2 0.46 9.9E-06 28.2 1.0 26 179-208 9-37 (44)
102 PF02150 RNA_POL_M_15KD: RNA p 85.1 0.61 1.3E-05 26.5 1.5 28 111-143 2-29 (35)
103 PF10083 DUF2321: Uncharacteri 84.9 1.4 3E-05 33.9 3.7 63 180-260 38-107 (158)
104 COG5219 Uncharacterized conser 84.5 0.61 1.3E-05 45.8 2.0 53 20-80 1468-1523(1525)
105 TIGR02098 MJ0042_CXXC MJ0042 f 84.5 0.95 2.1E-05 26.0 2.2 32 111-144 3-35 (38)
106 KOG1813 Predicted E3 ubiquitin 84.1 0.34 7.4E-06 41.2 0.2 47 19-79 239-285 (313)
107 PF05290 Baculo_IE-1: Baculovi 83.4 2.1 4.6E-05 32.1 4.0 55 19-81 78-133 (140)
108 KOG1941 Acetylcholine receptor 82.9 0.58 1.2E-05 41.4 1.1 51 19-77 363-413 (518)
109 smart00661 RPOL9 RNA polymeras 82.8 1.2 2.6E-05 27.4 2.3 28 112-143 2-29 (52)
110 KOG4692 Predicted E3 ubiquitin 82.5 1.1 2.3E-05 39.2 2.6 49 18-80 419-467 (489)
111 PRK05654 acetyl-CoA carboxylas 82.3 0.27 5.8E-06 42.4 -1.1 30 179-208 25-56 (292)
112 KOG2817 Predicted E3 ubiquitin 82.1 1.3 2.8E-05 39.3 3.0 60 19-86 332-391 (394)
113 PF09538 FYDLN_acid: Protein o 81.1 0.84 1.8E-05 33.2 1.3 26 182-208 10-36 (108)
114 PF14569 zf-UDP: Zinc-binding 80.0 1.5 3.2E-05 29.6 2.0 55 118-199 15-69 (80)
115 PF14447 Prok-RING_4: Prokaryo 79.9 1.1 2.3E-05 28.2 1.2 47 21-83 7-53 (55)
116 CHL00174 accD acetyl-CoA carbo 79.9 0.33 7.2E-06 41.8 -1.4 29 180-208 37-67 (296)
117 TIGR00515 accD acetyl-CoA carb 79.8 0.35 7.6E-06 41.6 -1.3 30 179-208 24-55 (285)
118 KOG2906 RNA polymerase III sub 79.4 1.6 3.4E-05 30.8 2.0 29 183-211 3-34 (105)
119 PF06677 Auto_anti-p27: Sjogre 79.0 1.8 3.9E-05 25.5 2.0 23 181-205 17-41 (41)
120 TIGR00622 ssl1 transcription f 78.6 2.1 4.6E-05 31.2 2.6 42 111-154 56-101 (112)
121 KOG0825 PHD Zn-finger protein 77.7 2.5 5.5E-05 40.9 3.5 19 43-61 121-139 (1134)
122 PF08274 PhnA_Zn_Ribbon: PhnA 77.4 1.6 3.5E-05 23.8 1.3 25 183-208 4-29 (30)
123 PRK14892 putative transcriptio 76.6 2.1 4.5E-05 30.6 2.1 29 180-208 20-52 (99)
124 KOG1001 Helicase-like transcri 76.5 0.74 1.6E-05 44.4 -0.3 48 22-82 455-502 (674)
125 COG0777 AccD Acetyl-CoA carbox 76.0 0.97 2.1E-05 38.2 0.3 32 178-209 25-58 (294)
126 PF01599 Ribosomal_S27: Riboso 75.2 2 4.3E-05 26.2 1.4 26 181-206 18-46 (47)
127 PF07282 OrfB_Zn_ribbon: Putat 75.2 2.5 5.5E-05 27.7 2.1 28 180-207 27-55 (69)
128 PF07191 zinc-ribbons_6: zinc- 74.8 2.6 5.5E-05 28.0 2.0 32 183-216 3-40 (70)
129 COG5222 Uncharacterized conser 74.7 5 0.00011 34.3 4.2 44 22-77 275-318 (427)
130 KOG2034 Vacuolar sorting prote 74.6 1.8 3.9E-05 42.3 1.8 41 19-61 815-855 (911)
131 COG5194 APC11 Component of SCF 74.4 3.7 8E-05 27.9 2.7 28 42-79 53-80 (88)
132 PF09788 Tmemb_55A: Transmembr 74.1 2.9 6.3E-05 35.0 2.6 37 108-144 121-167 (256)
133 COG1198 PriA Primosomal protei 73.7 2.7 5.7E-05 41.0 2.7 34 182-215 445-484 (730)
134 TIGR01384 TFS_arch transcripti 73.7 2.2 4.8E-05 30.6 1.7 24 182-207 1-25 (104)
135 PRK14714 DNA polymerase II lar 72.8 3.2 6.9E-05 42.5 3.0 11 181-191 709-719 (1337)
136 PF03119 DNA_ligase_ZBD: NAD-d 72.5 4.3 9.2E-05 21.7 2.2 20 183-202 1-20 (28)
137 KOG3002 Zn finger protein [Gen 72.4 3.7 8E-05 35.6 3.0 45 18-80 45-91 (299)
138 PF12906 RINGv: RING-variant d 72.0 2.4 5.2E-05 25.7 1.3 34 24-59 1-39 (47)
139 PF08746 zf-RING-like: RING-li 71.7 3.3 7.2E-05 24.6 1.8 42 24-72 1-42 (43)
140 PRK14559 putative protein seri 71.5 3 6.6E-05 40.1 2.5 12 180-191 40-51 (645)
141 PF14149 YhfH: YhfH-like prote 71.0 0.37 8E-06 27.6 -2.3 30 173-202 5-34 (37)
142 PF10122 Mu-like_Com: Mu-like 70.8 1.8 3.8E-05 26.7 0.5 25 182-206 5-32 (51)
143 PF14446 Prok-RING_1: Prokaryo 70.0 4.6 9.9E-05 25.4 2.2 36 19-54 3-38 (54)
144 KOG3161 Predicted E3 ubiquitin 69.5 1.9 4.2E-05 40.7 0.7 39 19-57 9-47 (861)
145 PRK00420 hypothetical protein; 69.5 3.8 8.2E-05 30.0 2.1 29 180-217 22-51 (112)
146 PHA02825 LAP/PHD finger-like p 69.1 8.5 0.00019 29.9 4.0 53 19-82 6-61 (162)
147 cd00021 BBOX B-Box-type zinc f 68.8 3.4 7.3E-05 23.5 1.4 26 132-157 10-35 (39)
148 KOG0320 Predicted E3 ubiquitin 68.7 2.4 5.3E-05 33.5 1.0 31 138-193 149-179 (187)
149 PF14569 zf-UDP: Zinc-binding 68.6 10 0.00022 25.7 3.8 52 19-79 7-61 (80)
150 PRK08665 ribonucleotide-diphos 68.4 2.8 6.1E-05 41.2 1.6 26 182-209 725-751 (752)
151 COG1645 Uncharacterized Zn-fin 68.4 2.9 6.4E-05 31.3 1.3 27 180-215 27-53 (131)
152 KOG2807 RNA polymerase II tran 68.3 1.1 2.4E-05 38.7 -1.0 24 132-155 343-366 (378)
153 KOG2691 RNA polymerase II subu 68.3 8.5 0.00018 27.7 3.5 34 109-144 3-36 (113)
154 KOG3579 Predicted E3 ubiquitin 67.1 2.8 6E-05 35.6 1.1 52 18-76 265-321 (352)
155 PLN03208 E3 ubiquitin-protein 66.7 1 2.2E-05 36.2 -1.4 37 176-217 13-49 (193)
156 TIGR03655 anti_R_Lar restricti 66.6 5.3 0.00012 24.8 2.1 27 182-208 2-36 (53)
157 COG1997 RPL43A Ribosomal prote 66.5 9.2 0.0002 26.5 3.3 29 180-208 34-63 (89)
158 PF06827 zf-FPG_IleRS: Zinc fi 66.4 4.1 8.9E-05 22.0 1.4 24 182-205 2-28 (30)
159 PF00643 zf-B_box: B-box zinc 66.3 2.5 5.5E-05 24.7 0.5 26 132-157 13-38 (42)
160 PF01428 zf-AN1: AN1-like Zinc 66.0 5.2 0.00011 23.7 1.9 19 133-151 12-30 (43)
161 KOG0317 Predicted E3 ubiquitin 66.0 0.84 1.8E-05 38.8 -2.2 19 199-217 251-270 (293)
162 KOG0823 Predicted E3 ubiquitin 65.9 1.6 3.5E-05 35.9 -0.5 16 204-219 65-80 (230)
163 PRK09710 lar restriction allev 65.6 5.7 0.00012 25.8 2.1 28 180-207 5-36 (64)
164 PF12760 Zn_Tnp_IS1595: Transp 65.2 15 0.00032 22.0 3.8 34 173-206 7-45 (46)
165 KOG3268 Predicted E3 ubiquitin 64.4 12 0.00025 29.7 3.9 63 18-82 162-230 (234)
166 smart00336 BBOX B-Box-type zin 63.9 6.5 0.00014 22.6 2.0 26 132-157 13-38 (42)
167 TIGR02443 conserved hypothetic 63.9 8.2 0.00018 24.6 2.5 26 182-207 10-40 (59)
168 PF10367 Vps39_2: Vacuolar sor 63.9 1.8 3.8E-05 31.0 -0.6 33 19-53 76-108 (109)
169 PF08271 TF_Zn_Ribbon: TFIIB z 63.2 7 0.00015 23.1 2.1 23 183-205 2-26 (43)
170 COG1594 RPB9 DNA-directed RNA 63.1 6.6 0.00014 28.8 2.3 28 181-208 2-32 (113)
171 PF09526 DUF2387: Probable met 62.8 8 0.00017 25.8 2.5 26 182-207 9-39 (71)
172 TIGR01206 lysW lysine biosynth 62.2 9.6 0.00021 24.0 2.6 27 182-208 3-32 (54)
173 PF08792 A2L_zn_ribbon: A2L zi 61.6 10 0.00022 21.2 2.4 27 181-207 3-30 (33)
174 PF05129 Elf1: Transcription e 61.2 5.4 0.00012 27.4 1.5 29 180-208 21-56 (81)
175 PLN00209 ribosomal protein S27 61.1 13 0.00028 25.7 3.3 31 111-146 37-67 (86)
176 TIGR02300 FYDLN_acid conserved 60.7 5 0.00011 29.9 1.3 26 182-208 10-36 (129)
177 COG1594 RPB9 DNA-directed RNA 60.4 7.8 0.00017 28.4 2.3 31 110-144 2-32 (113)
178 KOG4275 Predicted E3 ubiquitin 60.2 1.5 3.2E-05 37.4 -1.7 28 21-52 300-328 (350)
179 smart00064 FYVE Protein presen 59.9 7.6 0.00017 25.3 2.0 38 20-57 9-46 (68)
180 PF07754 DUF1610: Domain of un 58.9 8.1 0.00018 19.9 1.5 21 118-142 4-24 (24)
181 PF02891 zf-MIZ: MIZ/SP-RING z 58.5 6.3 0.00014 24.2 1.3 47 22-77 3-49 (50)
182 PF14354 Lar_restr_allev: Rest 58.1 9.3 0.0002 24.3 2.1 13 180-192 2-14 (61)
183 PF13453 zf-TFIIB: Transcripti 57.9 7 0.00015 22.8 1.4 12 183-194 1-12 (41)
184 PLN02638 cellulose synthase A 57.8 8.3 0.00018 39.0 2.7 56 118-200 23-78 (1079)
185 COG5220 TFB3 Cdk activating ki 57.7 9.9 0.00022 31.6 2.6 54 68-124 11-65 (314)
186 PHA02862 5L protein; Provision 57.6 15 0.00033 28.1 3.4 47 22-81 3-54 (156)
187 PF01363 FYVE: FYVE zinc finge 57.4 2 4.4E-05 28.2 -1.2 37 18-54 6-42 (69)
188 KOG3970 Predicted E3 ubiquitin 56.5 20 0.00044 29.5 4.2 60 18-81 47-106 (299)
189 PF15135 UPF0515: Uncharacteri 55.7 11 0.00023 31.6 2.5 37 179-215 130-183 (278)
190 PF06844 DUF1244: Protein of u 55.3 10 0.00022 24.7 1.9 16 47-62 12-27 (68)
191 cd00065 FYVE FYVE domain; Zinc 55.2 8.3 0.00018 24.0 1.5 36 22-57 3-38 (57)
192 PLN02189 cellulose synthase 55.0 13 0.00028 37.6 3.4 64 109-201 33-96 (1040)
193 PTZ00083 40S ribosomal protein 54.1 16 0.00035 25.1 2.8 31 111-146 36-66 (85)
194 PF07503 zf-HYPF: HypF finger; 53.2 8.8 0.00019 21.8 1.2 32 47-80 1-32 (35)
195 TIGR00686 phnA alkylphosphonat 53.2 9.9 0.00022 27.5 1.7 26 112-144 4-29 (109)
196 KOG0978 E3 ubiquitin ligase in 53.0 4.8 0.0001 38.8 0.2 29 139-191 660-688 (698)
197 KOG2906 RNA polymerase III sub 52.4 12 0.00025 26.5 2.0 28 111-142 2-29 (105)
198 PLN02436 cellulose synthase A 52.4 12 0.00026 37.9 2.8 53 19-80 34-89 (1094)
199 TIGR00595 priA primosomal prot 51.7 11 0.00025 35.2 2.4 34 182-215 223-262 (505)
200 COG0266 Nei Formamidopyrimidin 51.2 11 0.00024 32.1 2.1 25 182-206 246-273 (273)
201 PF07800 DUF1644: Protein of u 50.9 49 0.0011 25.8 5.3 90 21-126 2-123 (162)
202 TIGR00570 cdk7 CDK-activating 50.6 15 0.00032 32.0 2.7 53 111-194 4-56 (309)
203 KOG3039 Uncharacterized conser 50.4 12 0.00027 31.2 2.1 40 19-62 41-80 (303)
204 PRK10220 hypothetical protein; 49.3 14 0.00031 26.7 2.0 26 112-144 5-30 (111)
205 PHA02929 N1R/p28-like protein; 49.0 8 0.00017 32.4 0.9 41 178-218 171-214 (238)
206 PF02591 DUF164: Putative zinc 49.0 15 0.00033 23.0 2.0 22 170-191 35-56 (56)
207 PRK11827 hypothetical protein; 48.3 17 0.00036 23.4 2.1 28 180-207 7-35 (60)
208 PF02318 FYVE_2: FYVE-type zin 47.7 41 0.00088 24.7 4.4 36 109-151 53-88 (118)
209 PRK14811 formamidopyrimidine-D 47.5 14 0.0003 31.6 2.1 26 181-206 235-263 (269)
210 PLN02400 cellulose synthase 47.4 14 0.00031 37.5 2.4 61 111-200 37-97 (1085)
211 COG5151 SSL1 RNA polymerase II 46.7 4.5 9.8E-05 34.8 -0.9 78 66-154 321-408 (421)
212 PRK14714 DNA polymerase II lar 46.6 13 0.00028 38.4 2.0 30 182-217 668-703 (1337)
213 TIGR03826 YvyF flagellar opero 46.4 18 0.00038 27.6 2.3 11 182-192 82-92 (137)
214 PLN02436 cellulose synthase A 46.3 19 0.0004 36.7 3.0 62 111-201 37-98 (1094)
215 PRK14873 primosome assembly pr 45.6 15 0.00033 35.6 2.3 34 182-215 393-431 (665)
216 PRK01103 formamidopyrimidine/5 45.2 17 0.00036 31.2 2.3 25 182-206 246-273 (274)
217 PRK10445 endonuclease VIII; Pr 45.0 17 0.00036 31.0 2.2 25 181-205 235-262 (263)
218 PRK14810 formamidopyrimidine-D 44.5 17 0.00036 31.1 2.2 25 181-205 244-271 (272)
219 PHA02926 zinc finger-like prot 44.4 8.6 0.00019 31.7 0.4 46 173-218 162-211 (242)
220 smart00659 RPOLCX RNA polymera 43.6 22 0.00049 21.2 2.0 14 179-192 17-30 (44)
221 TIGR00577 fpg formamidopyrimid 43.1 18 0.00039 30.9 2.1 25 181-205 245-272 (272)
222 PLN02915 cellulose synthase A 43.0 22 0.00049 36.0 3.0 55 17-80 11-68 (1044)
223 PRK13945 formamidopyrimidine-D 42.5 18 0.0004 31.0 2.2 25 181-205 254-281 (282)
224 COG2051 RPS27A Ribosomal prote 42.4 21 0.00045 23.4 1.8 31 111-146 20-50 (67)
225 KOG2979 Protein involved in DN 42.4 43 0.00092 28.3 4.1 52 18-78 173-224 (262)
226 PLN02638 cellulose synthase A 42.2 26 0.00057 35.7 3.4 53 18-79 14-69 (1079)
227 PF14353 CpXC: CpXC protein 42.0 15 0.00033 27.3 1.4 15 67-83 1-15 (128)
228 smart00834 CxxC_CXXC_SSSS Puta 41.5 21 0.00046 20.4 1.7 29 111-142 6-34 (41)
229 PRK12286 rpmF 50S ribosomal pr 41.3 18 0.0004 22.9 1.5 24 178-206 24-48 (57)
230 KOG4362 Transcriptional regula 41.3 7 0.00015 37.5 -0.6 58 18-86 18-75 (684)
231 KOG0826 Predicted E3 ubiquitin 40.9 12 0.00026 32.6 0.7 49 19-78 298-346 (357)
232 PLN02915 cellulose synthase A 40.6 24 0.00053 35.8 2.9 55 118-199 21-75 (1044)
233 PRK09521 exosome complex RNA-b 40.6 22 0.00047 28.6 2.2 25 182-207 150-175 (189)
234 PRK05580 primosome assembly pr 40.1 21 0.00046 34.8 2.4 34 182-215 391-430 (679)
235 COG3492 Uncharacterized protei 40.0 30 0.00066 24.1 2.4 17 46-62 42-58 (104)
236 PF15616 TerY-C: TerY-C metal 40.0 24 0.00053 26.6 2.2 35 181-215 77-114 (131)
237 PF03604 DNA_RNApol_7kD: DNA d 39.6 19 0.00042 19.9 1.2 23 117-144 5-27 (32)
238 KOG2164 Predicted E3 ubiquitin 39.4 24 0.00052 32.7 2.4 35 139-193 203-237 (513)
239 PRK12495 hypothetical protein; 39.1 34 0.00075 28.1 3.0 29 180-217 41-69 (226)
240 PRK04023 DNA polymerase II lar 38.9 20 0.00044 36.1 2.0 32 180-217 625-662 (1121)
241 PLN02189 cellulose synthase 38.0 22 0.00048 36.0 2.2 53 19-80 32-87 (1040)
242 KOG2930 SCF ubiquitin ligase, 37.9 35 0.00076 24.5 2.5 28 41-78 79-106 (114)
243 PF06906 DUF1272: Protein of u 37.8 39 0.00084 21.3 2.4 46 22-81 6-53 (57)
244 PF05605 zf-Di19: Drought indu 36.8 16 0.00034 22.7 0.6 38 21-77 2-39 (54)
245 PF02748 PyrI_C: Aspartate car 36.6 35 0.00075 21.2 2.1 35 109-144 5-45 (52)
246 PF09723 Zn-ribbon_8: Zinc rib 36.6 28 0.0006 20.4 1.6 28 112-142 7-34 (42)
247 PF10497 zf-4CXXC_R1: Zinc-fin 36.4 58 0.0013 23.5 3.6 56 20-77 6-69 (105)
248 PRK13130 H/ACA RNA-protein com 36.3 78 0.0017 20.0 3.7 35 68-104 18-52 (56)
249 PF08882 Acetone_carb_G: Aceto 36.1 26 0.00057 25.5 1.7 13 198-210 23-35 (112)
250 PF11023 DUF2614: Protein of u 35.9 24 0.00053 25.7 1.6 23 131-153 66-96 (114)
251 smart00154 ZnF_AN1 AN1-like Zi 35.3 24 0.00052 20.4 1.2 18 134-151 12-29 (39)
252 PF00098 zf-CCHC: Zinc knuckle 35.2 23 0.0005 16.7 0.9 16 144-159 2-17 (18)
253 KOG2807 RNA polymerase II tran 34.9 17 0.00037 31.7 0.7 48 19-77 328-375 (378)
254 TIGR01053 LSD1 zinc finger dom 33.4 52 0.0011 18.0 2.3 24 183-206 3-27 (31)
255 smart00249 PHD PHD zinc finger 33.0 22 0.00047 20.5 0.8 33 23-56 1-33 (47)
256 KOG0309 Conserved WD40 repeat- 32.9 42 0.0009 32.9 3.0 39 18-58 1025-1063(1081)
257 PF09862 DUF2089: Protein of u 32.9 61 0.0013 23.8 3.2 31 228-258 29-59 (113)
258 KOG2041 WD40 repeat protein [G 32.8 71 0.0015 31.3 4.4 20 87-106 1088-1107(1189)
259 PLN02195 cellulose synthase A 32.7 41 0.00089 34.0 3.0 53 19-80 4-59 (977)
260 KOG2114 Vacuolar assembly/sort 32.4 28 0.00061 34.3 1.8 41 21-77 840-880 (933)
261 KOG2932 E3 ubiquitin ligase in 32.3 28 0.00061 30.1 1.6 31 21-54 90-120 (389)
262 TIGR01031 rpmF_bact ribosomal 32.3 30 0.00065 21.7 1.4 14 179-192 24-37 (55)
263 PRK03681 hypA hydrogenase nick 32.3 47 0.001 24.3 2.6 46 89-141 40-94 (114)
264 PRK02935 hypothetical protein; 31.9 34 0.00073 24.6 1.7 23 131-153 67-97 (110)
265 PRK04023 DNA polymerase II lar 31.5 34 0.00074 34.6 2.2 13 47-59 424-436 (1121)
266 PLN02400 cellulose synthase 31.4 34 0.00074 34.9 2.3 53 19-80 34-89 (1085)
267 PF13913 zf-C2HC_2: zinc-finge 31.3 22 0.00048 18.3 0.6 10 135-144 3-12 (25)
268 PF04216 FdhE: Protein involve 31.3 16 0.00034 31.5 -0.0 11 110-122 172-182 (290)
269 PRK00415 rps27e 30S ribosomal 31.1 48 0.001 21.2 2.1 31 111-146 12-42 (59)
270 smart00531 TFIIE Transcription 31.0 24 0.00051 27.1 0.9 34 108-143 97-132 (147)
271 PLN03086 PRLI-interacting fact 30.6 29 0.00063 32.9 1.6 30 179-208 431-463 (567)
272 PRK03824 hypA hydrogenase nick 30.4 50 0.0011 25.0 2.6 15 109-125 69-83 (135)
273 PRK00241 nudC NADH pyrophospha 30.3 40 0.00086 28.6 2.2 28 180-207 98-126 (256)
274 PF08209 Sgf11: Sgf11 (transcr 30.0 28 0.0006 19.5 0.8 14 180-193 3-16 (33)
275 PF06044 DRP: Dam-replacing fa 29.7 11 0.00024 31.5 -1.2 36 109-146 30-65 (254)
276 PF01783 Ribosomal_L32p: Ribos 29.7 22 0.00047 22.4 0.4 14 179-192 24-37 (56)
277 KOG0825 PHD Zn-finger protein 29.3 53 0.0011 32.4 3.0 48 23-81 125-172 (1134)
278 COG1096 Predicted RNA-binding 29.2 41 0.00088 27.0 1.9 23 182-206 150-173 (188)
279 PF01873 eIF-5_eIF-2B: Domain 29.0 66 0.0014 24.0 3.0 35 171-207 85-123 (125)
280 KOG1571 Predicted E3 ubiquitin 28.5 26 0.00056 31.0 0.8 46 17-79 301-346 (355)
281 TIGR00100 hypA hydrogenase nic 28.2 60 0.0013 23.8 2.6 24 110-141 70-93 (115)
282 PLN02195 cellulose synthase A 27.6 53 0.0011 33.3 2.8 28 118-148 12-39 (977)
283 COG5216 Uncharacterized conser 27.6 35 0.00075 21.7 1.0 21 172-192 35-55 (67)
284 PF06943 zf-LSD1: LSD1 zinc fi 27.5 77 0.0017 16.5 2.2 23 184-206 1-24 (25)
285 PF10426 zf-RAG1: Recombinatio 27.3 19 0.00041 19.6 -0.1 13 67-79 2-14 (30)
286 KOG2923 Uncharacterized conser 27.2 47 0.001 21.6 1.6 21 172-192 35-55 (67)
287 PRK12380 hydrogenase nickel in 27.2 64 0.0014 23.5 2.6 45 89-141 40-93 (113)
288 COG2816 NPY1 NTP pyrophosphohy 26.8 89 0.0019 26.8 3.7 30 108-143 109-138 (279)
289 PRK05978 hypothetical protein; 26.8 35 0.00076 26.3 1.2 33 180-219 32-65 (148)
290 KOG2932 E3 ubiquitin ligase in 26.7 16 0.00035 31.6 -0.7 18 180-197 122-139 (389)
291 smart00734 ZnF_Rad18 Rad18-lik 26.4 9.9 0.00022 19.9 -1.3 16 68-85 2-17 (26)
292 PF02318 FYVE_2: FYVE-type zin 26.1 97 0.0021 22.7 3.4 35 180-215 53-88 (118)
293 COG1198 PriA Primosomal protei 26.1 52 0.0011 32.4 2.4 35 111-151 445-484 (730)
294 PF01396 zf-C4_Topoisom: Topoi 26.0 43 0.00093 19.3 1.2 20 182-202 2-24 (39)
295 TIGR00373 conserved hypothetic 25.9 26 0.00057 27.3 0.4 31 108-143 107-137 (158)
296 PTZ00368 universal minicircle 25.8 83 0.0018 23.9 3.2 17 144-160 79-95 (148)
297 PF01667 Ribosomal_S27e: Ribos 25.8 60 0.0013 20.5 1.9 31 111-146 8-38 (55)
298 PF01214 CK_II_beta: Casein ki 25.8 1.2E+02 0.0025 24.4 4.0 36 108-143 97-136 (184)
299 cd04476 RPA1_DBD_C RPA1_DBD_C: 25.7 45 0.00097 25.9 1.7 26 181-207 34-60 (166)
300 PF04216 FdhE: Protein involve 25.7 36 0.00078 29.3 1.2 34 182-215 173-220 (290)
301 PF00096 zf-C2H2: Zinc finger, 25.3 32 0.0007 16.6 0.5 9 136-144 2-10 (23)
302 smart00653 eIF2B_5 domain pres 25.2 1.1E+02 0.0023 22.4 3.4 35 171-207 72-110 (110)
303 KOG1701 Focal adhesion adaptor 25.2 62 0.0013 29.4 2.5 11 22-32 275-285 (468)
304 PRK13264 3-hydroxyanthranilate 25.1 31 0.00067 27.5 0.6 24 170-193 146-169 (177)
305 PRK06266 transcription initiat 24.9 29 0.00064 27.6 0.5 30 108-142 115-144 (178)
306 PF01096 TFIIS_C: Transcriptio 24.9 60 0.0013 18.7 1.7 13 132-144 26-38 (39)
307 PF09889 DUF2116: Uncharacteri 24.9 93 0.002 19.9 2.7 31 21-61 3-34 (59)
308 PF04981 NMD3: NMD3 family ; 24.9 48 0.001 27.6 1.8 12 180-191 34-45 (236)
309 COG3813 Uncharacterized protei 24.7 65 0.0014 21.4 2.0 58 23-97 7-66 (84)
310 PF14471 DUF4428: Domain of un 24.6 72 0.0016 19.7 2.1 30 23-55 1-30 (51)
311 PF01780 Ribosomal_L37ae: Ribo 24.4 34 0.00075 23.9 0.7 29 180-208 34-63 (90)
312 PF04236 Transp_Tc5_C: Tc5 tra 24.4 81 0.0017 20.5 2.4 32 108-150 25-56 (63)
313 COG4888 Uncharacterized Zn rib 24.4 67 0.0015 22.9 2.1 28 181-208 22-56 (104)
314 COG2260 Predicted Zn-ribbon RN 23.9 1.7E+02 0.0037 18.7 3.7 34 69-104 19-52 (59)
315 PRK14873 primosome assembly pr 23.9 77 0.0017 30.9 3.2 30 117-150 397-430 (665)
316 KOG2789 Putative Zn-finger pro 23.8 32 0.00069 30.9 0.5 35 20-56 73-107 (482)
317 TIGR00311 aIF-2beta translatio 23.8 1E+02 0.0022 23.3 3.2 35 171-207 89-127 (133)
318 COG3357 Predicted transcriptio 23.7 32 0.0007 24.0 0.4 8 117-124 63-70 (97)
319 COG3677 Transposase and inacti 23.7 1.1E+02 0.0025 22.9 3.4 34 109-144 29-63 (129)
320 PF03833 PolC_DP2: DNA polymer 23.6 27 0.00058 34.6 0.0 34 180-219 654-693 (900)
321 PF01530 zf-C2HC: Zinc finger, 23.5 45 0.00099 18.3 0.9 11 68-78 2-12 (31)
322 PF05715 zf-piccolo: Piccolo Z 23.4 27 0.00059 22.3 0.0 34 182-215 3-39 (61)
323 TIGR03037 anthran_nbaC 3-hydro 23.3 37 0.0008 26.6 0.7 20 170-189 140-159 (159)
324 PRK08115 ribonucleotide-diphos 23.3 39 0.00085 33.8 1.1 24 182-207 828-853 (858)
325 PF13821 DUF4187: Domain of un 23.1 50 0.0011 20.8 1.2 14 205-218 26-39 (55)
326 PF14445 Prok-RING_2: Prokaryo 23.0 17 0.00038 22.3 -0.9 37 19-56 5-41 (57)
327 PRK03988 translation initiatio 22.9 1.2E+02 0.0025 23.1 3.4 34 172-207 95-132 (138)
328 PF09151 DUF1936: Domain of un 22.4 42 0.00092 18.3 0.6 9 183-191 3-11 (36)
329 KOG4684 Uncharacterized conser 22.3 85 0.0018 25.8 2.6 37 108-144 136-180 (275)
330 PHA02325 hypothetical protein 22.3 50 0.0011 21.4 1.1 12 180-191 2-13 (72)
331 PF01927 Mut7-C: Mut7-C RNAse 22.3 1.7E+02 0.0037 22.3 4.3 54 89-144 67-134 (147)
332 TIGR00595 priA primosomal prot 22.2 71 0.0015 30.0 2.5 33 113-151 225-262 (505)
333 COG3024 Uncharacterized protei 22.2 49 0.0011 21.5 1.0 15 179-193 5-19 (65)
334 smart00440 ZnF_C2C2 C2C2 Zinc 22.1 88 0.0019 18.1 2.0 12 132-143 26-37 (40)
335 PF03854 zf-P11: P-11 zinc fin 21.9 24 0.00051 21.5 -0.4 44 22-81 3-47 (50)
336 PRK03976 rpl37ae 50S ribosomal 21.7 56 0.0012 22.9 1.3 29 180-208 35-64 (90)
337 PF13465 zf-H2C2_2: Zinc-finge 21.6 52 0.0011 16.9 0.9 13 132-144 12-24 (26)
338 COG4416 Com Mu-like prophage p 21.5 47 0.001 20.7 0.8 12 181-192 24-35 (60)
339 PRK00564 hypA hydrogenase nick 21.5 83 0.0018 23.1 2.3 47 88-141 39-95 (117)
340 PF01194 RNA_pol_N: RNA polyme 21.4 1.2E+02 0.0026 19.5 2.7 24 66-101 3-26 (60)
341 PRK09678 DNA-binding transcrip 21.4 47 0.001 22.2 0.8 17 110-126 27-43 (72)
342 COG2824 PhnA Uncharacterized Z 21.2 75 0.0016 22.9 1.9 27 181-208 3-30 (112)
343 PF06221 zf-C2HC5: Putative zi 21.2 66 0.0014 20.4 1.5 12 135-146 19-30 (57)
344 COG5109 Uncharacterized conser 20.9 78 0.0017 27.6 2.2 55 19-81 334-388 (396)
345 PF08646 Rep_fac-A_C: Replicat 20.9 70 0.0015 24.2 1.9 26 181-207 18-46 (146)
346 KOG4218 Nuclear hormone recept 20.8 73 0.0016 28.2 2.1 20 229-248 102-121 (475)
347 PF14787 zf-CCHC_5: GAG-polypr 20.7 56 0.0012 18.6 0.9 18 143-160 3-20 (36)
348 COG1579 Zn-ribbon protein, pos 20.7 67 0.0014 27.0 1.8 59 83-143 167-230 (239)
349 PF13451 zf-trcl: Probable zin 20.6 66 0.0014 19.7 1.3 17 199-215 4-21 (49)
350 PF09986 DUF2225: Uncharacteri 20.4 75 0.0016 26.1 2.0 18 67-86 5-22 (214)
351 TIGR02605 CxxC_CxxC_SSSS putat 20.3 75 0.0016 19.2 1.6 28 112-142 7-34 (52)
352 COG2816 NPY1 NTP pyrophosphohy 20.1 69 0.0015 27.5 1.8 29 180-208 110-139 (279)
353 PF07295 DUF1451: Protein of u 20.1 60 0.0013 25.0 1.3 13 180-192 129-141 (146)
No 1
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.1e-38 Score=281.46 Aligned_cols=197 Identities=31% Similarity=0.744 Sum_probs=168.3
Q ss_pred Cccccccccccccccc-ccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCCccCccCCCChhHHHHHH
Q 024566 19 GSSFTCEICIEPMAAS-KKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFACEPVIPASLFSKWC 97 (265)
Q Consensus 19 ~~~~~C~IC~~~~~~~-~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~ 97 (265)
....+|.||+.+.+.. .+|. ...|+|.||.+|+++|++++.. ....++||..+|...++.+....+|++.+.++|.
T Consensus 144 ~~~~~C~iC~~e~~~~~~~f~-~~~C~H~fC~~C~k~~iev~~~--~~~~~~C~~~~C~~~l~~~~c~~llt~kl~e~~e 220 (384)
T KOG1812|consen 144 LPKEECGICFVEDPEAEDMFS-VLKCGHRFCKDCVKQHIEVKLL--SGTVIRCPHDGCESRLTLESCRKLLTPKLREMWE 220 (384)
T ss_pred cccccCccCccccccHhhhHH-HhcccchhhhHHhHHHhhhhhc--cCCCccCCCCCCCccCCHHHHhhhcCHHHHHHHH
Confidence 4578999999655555 4444 7889999999999999999943 4678999999999999999999999999999999
Q ss_pred HHHHHHhhcCCCccccCCcCcccceecccccc-CCcCeeeCCCcccccccccccccCCCCCChhHHhchhh--chHHHHH
Q 024566 98 DVLCEDYVLGFERSYCPNTNCMALVVNECERS-GKVKKTQCPNCKQWFCFQCKLKWHAGYRCEESRNLRDQ--NDIVFGQ 174 (265)
Q Consensus 98 ~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~-~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~--~d~~~~~ 174 (265)
+++.+.++...+..|||+|+|...+......+ .+.....|+.|+..||.+|+.+||.+.+|++|+++... .|....+
T Consensus 221 ~~~~e~~i~~~~~~ycp~~~C~~l~~~~el~~~~~~~~~~C~~C~~~fCv~C~~~wh~~~sC~eykk~~~~~~~d~~~~~ 300 (384)
T KOG1812|consen 221 QRLKEEVIPSLDRVYCPYPRCSSLMSKTELSSEVKSKRRPCVKCHELFCVKCKVPWHANLSCEEYKKLNPEEYVDDITLK 300 (384)
T ss_pred HHHHHHhhhhhhcccCCCCCchHhhhhhhhccchhhcccccccCCCceeecCCCcCCCCCCHHHHHHhCCcccccHHHHH
Confidence 99999999766666999999999988665322 33567789999999999999999999999999998754 3333444
Q ss_pred HHhcCCcccCCCCCceeeecCCCceeEeecCCceeeccCccccCC
Q 024566 175 LVERMKWARCPACGHCVERKDGCSVVMCRCNTRFCYECGRKISSG 219 (265)
Q Consensus 175 ~~~~~~~k~CP~C~~~iek~~GCnhm~C~C~~~FC~~C~~~~~~g 219 (265)
.+. ..|++||+|+..|++++|||||+|+||++|||.|+++|..+
T Consensus 301 ~la-~~wr~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~~~~~~~ 344 (384)
T KOG1812|consen 301 YLA-KRWRQCPKCKFMIELSEGCNHMTCRCGHQFCYMCGGDWKTH 344 (384)
T ss_pred HHH-HhcCcCcccceeeeecCCcceEEeeccccchhhcCcchhhC
Confidence 444 78999999999999999999999999999999999998654
No 2
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.6e-38 Score=270.48 Aligned_cols=214 Identities=25% Similarity=0.569 Sum_probs=173.3
Q ss_pred CCCCcccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCCccCccCCCChhHHHH
Q 024566 16 GGGGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFACEPVIPASLFSK 95 (265)
Q Consensus 16 ~~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~ 95 (265)
......+.|.|||++......| ..++|+|.||+.|++.|++..|++|....++||+++|+...++..++.+|+.++++|
T Consensus 179 ~F~~slf~C~ICf~e~~G~~c~-~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C~~~a~~g~vKelvg~EL~ar 257 (445)
T KOG1814|consen 179 KFVNSLFDCCICFEEQMGQHCF-KFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCGSVAPPGQVKELVGDELFAR 257 (445)
T ss_pred HHHhhcccceeeehhhcCccee-eecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCCcccCCchHHHHHHHHHHHHH
Confidence 3457789999999998654544 589999999999999999999999889999999999999999999999999999999
Q ss_pred HHHHHHHHhh-cCCCccccCCcCcccceeccccccCCcCeeeCCCcccccccccccccCCCCCChhHH--------hchh
Q 024566 96 WCDVLCEDYV-LGFERSYCPNTNCMALVVNECERSGKVKKTQCPNCKQWFCFQCKLKWHAGYRCEESR--------NLRD 166 (265)
Q Consensus 96 ~~~~~~~~~~-~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~--------~~~~ 166 (265)
|++.+.++.+ ...+++|||++.|..+...+++ ...+.|.+|++.||+.|+..||++..|.--. +|.+
T Consensus 258 Ye~l~lqk~l~~msdv~yCPr~~Cq~p~~~d~~----~~l~~CskCnFaFCtlCk~t~HG~s~Ck~~~~~~~~l~~~~~~ 333 (445)
T KOG1814|consen 258 YEKLMLQKTLELMSDVVYCPRACCQLPVKQDPG----RALAICSKCNFAFCTLCKLTWHGVSPCKVKAEKLIELYLEYLE 333 (445)
T ss_pred HHHHHHHHHHHhhcccccCChhhccCccccCch----hhhhhhccCccHHHHHHHHhhcCCCcccCchHHHHHHHHHHhh
Confidence 9999998888 4688999999999999865555 5789999999999999999999999896421 1111
Q ss_pred h---------------------chHHHHHHHhcCCcccCCCCCceeeecCCCceeEe-ecCCceeeccCccccCCCC--C
Q 024566 167 Q---------------------NDIVFGQLVERMKWARCPACGHCVERKDGCSVVMC-RCNTRFCYECGRKISSGCS--C 222 (265)
Q Consensus 167 ~---------------------~d~~~~~~~~~~~~k~CP~C~~~iek~~GCnhm~C-~C~~~FC~~C~~~~~~g~~--~ 222 (265)
. ++.+..+++ ..+.|+||+|+++|+|++|||+|+| .|++.|||+|+.....+.| |
T Consensus 334 ~d~a~k~ele~Ryg~rvve~~vn~~lsekwl-~~N~krCP~C~v~IEr~eGCnKM~C~~c~~~fc~~c~~~l~~~nPYkH 412 (445)
T KOG1814|consen 334 ADEARKRELEKRYGKRVVEELVNDFLSEKWL-ESNSKRCPKCKVVIERSEGCNKMHCTKCGTYFCWICAELLYPENPYKH 412 (445)
T ss_pred cCHHHHHHHHHHhhHHHHHHHHHHHHHHHHH-HhcCCCCCcccceeecCCCccceeeccccccceeehhhhcCCCChhhh
Confidence 0 111111222 2467999999999999999999999 7999999999999775533 4
Q ss_pred CCc-ccchhhhHHH
Q 024566 223 QTI-GFCQLTILTI 235 (265)
Q Consensus 223 ~~~-~~C~~~~~~~ 235 (265)
++. +++....+..
T Consensus 413 F~e~~s~c~~~~~~ 426 (445)
T KOG1814|consen 413 FSEPGSECYGQFFG 426 (445)
T ss_pred hcCCcCccccchhh
Confidence 443 3444444333
No 3
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.97 E-value=7.3e-30 Score=231.13 Aligned_cols=193 Identities=24% Similarity=0.534 Sum_probs=162.6
Q ss_pred CCcccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCCccCccCCCCh-hHHHHH
Q 024566 18 GGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFACEPVIPA-SLFSKW 96 (265)
Q Consensus 18 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~~l~~-~~~~~~ 96 (265)
.....+|.||++..+. ....+.|+|.||..||..|+..+|.++....|+||.++|...+..+.|..++++ +..++|
T Consensus 67 ~~~~~~c~ic~~~~~~---~~~~~~c~H~~c~~cw~~yl~~kI~~~~~~~i~cp~~~C~a~v~~~~i~~~~s~~~~~~ky 143 (444)
T KOG1815|consen 67 KKGDVQCGICVESYDG---EIIGLGCGHPFCPPCWTGYLGTKIHEGEEAKIKCPAHGCPALVGEDTVEKLVSDKEDKEKY 143 (444)
T ss_pred CCccccCCcccCCCcc---hhhhcCCCcHHHHHHHHHHhhheeeccccccccCCCCCccccCCCceeeeecCCHHHHHHH
Confidence 3456899999999864 234689999999999999999999986555599999999999999999999998 499999
Q ss_pred HHHHHHHhhcC-CCccccCCcCcccceeccccccCCcCeeeCCCcccccccccccccCCCCCChhHHhchhhchHHHHHH
Q 024566 97 CDVLCEDYVLG-FERSYCPNTNCMALVVNECERSGKVKKTQCPNCKQWFCFQCKLKWHAGYRCEESRNLRDQNDIVFGQL 175 (265)
Q Consensus 97 ~~~~~~~~~~~-~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~d~~~~~~ 175 (265)
.+++..+++.. ....|||+|+|+..+.... .....+.|. |+..||+.|+.+||.+.+|.....|..+.......+
T Consensus 144 ~~~i~~syve~~~~lkwCP~~~C~~av~~~~---~~~~~v~C~-~g~~FC~~C~~~~H~p~~C~~~~~wl~k~~~~se~~ 219 (444)
T KOG1815|consen 144 QRYILRSYVEDNVPLKWCPAPGCGLAVKFGS---LESVEVDCG-CGHEFCFACGEESHSPVSCPGAKKWLKKCRDDSETI 219 (444)
T ss_pred HHHHHHHHHhcCCccccCCCCCCCceeeccC---CCccceeCC-CCchhHhhccccccCCCcccchHHHHHhhhhhhhhh
Confidence 99999999964 4479999999999988641 226889995 677999999999999999999999887633222221
Q ss_pred H-hcCCcccCCCCCceeeecCCCceeEe-e--cCCceeeccCcccc
Q 024566 176 V-ERMKWARCPACGHCVERKDGCSVVMC-R--CNTRFCYECGRKIS 217 (265)
Q Consensus 176 ~-~~~~~k~CP~C~~~iek~~GCnhm~C-~--C~~~FC~~C~~~~~ 217 (265)
. ...++++||+|.++|+|++|||||+| . |+++|||.|++.|.
T Consensus 220 ~wi~~ntk~CP~c~~~iek~~gc~~~~~~~~~c~~~FCw~Cl~~~~ 265 (444)
T KOG1815|consen 220 NWILANTKECPKCKVPIEKDGGCNHMTCKSASCKHEFCWVCLASLS 265 (444)
T ss_pred hhhhccCccCCCcccchhccCCccccccccCCcCCeeceeeecccc
Confidence 1 24578999999999999999999999 4 99999999999986
No 4
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=99.94 E-value=9e-28 Score=198.32 Aligned_cols=195 Identities=24% Similarity=0.575 Sum_probs=153.2
Q ss_pred CCCCcccccccccccccccccccccCCCC--ChhHHHHHHHHHHHHhhCCC-------CCcccCCCCCCCCCC-CccCcc
Q 024566 16 GGGGSSFTCEICIEPMAASKKFKNRNLCT--HPFCQDCIARYIQVKVQDDN-------TAKIDCPGLDCKHNL-DPFACE 85 (265)
Q Consensus 16 ~~~~~~~~C~IC~~~~~~~~~~~~~~~C~--H~fC~~Cl~~~~~~~i~~~~-------~~~i~CP~~~C~~~l-~~~~i~ 85 (265)
+.+....+|..|.+... +. + .++|. |..|.+|++.|..+.+++.+ .+.+.||. +|...+ ..-.-.
T Consensus 216 ~~N~~ni~C~~Ctdv~~-~v-l--vf~Cns~HvtC~dCFr~yc~~Rl~~rqf~~~p~~gyslpc~a-gc~~s~i~e~HHF 290 (446)
T KOG0006|consen 216 ATNSRNITCITCTDVRS-PV-L--VFQCNSRHVTCLDCFRLYCVTRLNDRQFVHDPQLGYSLPCVA-GCPNSLIKELHHF 290 (446)
T ss_pred hcccccceeEEecCCcc-ce-E--EEecCCceeehHHhhhhHhhhcccccccccCccccccccccC-CCchHHHHhhhhh
Confidence 45788899999988663 22 2 47887 99999999999999998653 34588886 777554 333456
Q ss_pred CCCChhHHHHHHHHHHHHhhcCCCccccCCcCcccceeccccccCCcCeeeCCC-cccccccccccccCCCCCChhHHhc
Q 024566 86 PVIPASLFSKWCDVLCEDYVLGFERSYCPNTNCMALVVNECERSGKVKKTQCPN-CKQWFCFQCKLKWHAGYRCEESRNL 164 (265)
Q Consensus 86 ~~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~-C~~~~C~~C~~~~H~~~~C~~~~~~ 164 (265)
++|..+.+++|+++..+.++...+-+.||+|+|+..+.++++ ..++.|+. |++.||..|...+|.|. |.+.-..
T Consensus 291 ~ilg~e~Y~rYQr~atEe~vlq~gGVlCP~pgCG~gll~EPD----~rkvtC~~gCgf~FCR~C~e~yh~ge-C~~~~~a 365 (446)
T KOG0006|consen 291 RILGEEQYNRYQRYATEECVLQMGGVLCPRPGCGAGLLPEPD----QRKVTCEGGCGFAFCRECKEAYHEGE-CSAVFEA 365 (446)
T ss_pred eecchhHHHHHHHhhhhhheeecCCEecCCCCCCcccccCCC----CCcccCCCCchhHhHHHHHhhhcccc-ceeeecc
Confidence 789999999999999999997778899999999999999886 68999987 99999999999999875 3311110
Q ss_pred --------hhh----c----hHHHHHHHhcCCcccCCCCCceeeecCCCceeEe-e--cCCceeeccCccccCCCC
Q 024566 165 --------RDQ----N----DIVFGQLVERMKWARCPACGHCVERKDGCSVVMC-R--CNTRFCYECGRKISSGCS 221 (265)
Q Consensus 165 --------~~~----~----d~~~~~~~~~~~~k~CP~C~~~iek~~GCnhm~C-~--C~~~FC~~C~~~~~~g~~ 221 (265)
.-+ + |....+.+ +..+|+||+|+++.||+|||.||.| + ||.+|||.|+..|+..|.
T Consensus 366 s~t~tc~y~vde~~a~~arwd~as~~TI-k~tTkpCPkChvptErnGGCmHm~Ct~~~Cg~eWCw~C~tEW~r~Cm 440 (446)
T KOG0006|consen 366 SGTTTCAYRVDERAAEQARWDAASKETI-KKTTKPCPKCHVPTERNGGCMHMKCTQPQCGLEWCWNCGTEWNRVCM 440 (446)
T ss_pred ccccceeeecChhhhhhhhhhhhhhhhh-hhccCCCCCccCccccCCceEEeecCCCCCCceeEeccCChhhhhhc
Confidence 000 1 11222222 3567999999999999999999999 6 999999999999987654
No 5
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=99.30 E-value=4.1e-12 Score=84.30 Aligned_cols=63 Identities=33% Similarity=0.836 Sum_probs=54.1
Q ss_pred HHHHHHHHHHhhcC-CCccccCCcCcccceeccccccCCcCeeeCCCcccccccccccccCCCCCC
Q 024566 94 SKWCDVLCEDYVLG-FERSYCPNTNCMALVVNECERSGKVKKTQCPNCKQWFCFQCKLKWHAGYRC 158 (265)
Q Consensus 94 ~~~~~~~~~~~~~~-~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C 158 (265)
++|++++.+.+++. ++.+|||+|+|+.++...+. .....+.|+.|+..||+.|+.+||.+.+|
T Consensus 1 ~~y~~~~~~~~i~~~~~~~~CP~~~C~~~~~~~~~--~~~~~v~C~~C~~~fC~~C~~~~H~~~~C 64 (64)
T smart00647 1 EKYERLLLESYVESNPDLKWCPAPDCSAAIIVTEE--EGCNRVTCPKCGFSFCFRCKVPWHSPVSC 64 (64)
T ss_pred ChHHHHHHHHHHhcCCCccCCCCCCCcceEEecCC--CCCCeeECCCCCCeECCCCCCcCCCCCCC
Confidence 47888888888864 68899999999999988641 13579999999999999999999999987
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=99.24 E-value=1.4e-12 Score=86.60 Aligned_cols=63 Identities=29% Similarity=0.755 Sum_probs=41.0
Q ss_pred HHHHHHHHHHhhc-CCCccccCCcCcccceeccccccCCcCeeeCCCcccccccccccccCCCCCC
Q 024566 94 SKWCDVLCEDYVL-GFERSYCPNTNCMALVVNECERSGKVKKTQCPNCKQWFCFQCKLKWHAGYRC 158 (265)
Q Consensus 94 ~~~~~~~~~~~~~-~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C 158 (265)
++|++++.+.++. +++++|||+|+|+.++....... ...+.|+.|+..||+.|+.+||.|.+|
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 4677777777774 45678999999999999887632 224999999999999999999999886
No 7
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=98.71 E-value=2.8e-08 Score=65.64 Aligned_cols=49 Identities=29% Similarity=0.742 Sum_probs=41.0
Q ss_pred HHHHHhc-CCcccCC--CCCceeeecC--CCceeEe-ecCCceeeccCccccCCC
Q 024566 172 FGQLVER-MKWARCP--ACGHCVERKD--GCSVVMC-RCNTRFCYECGRKISSGC 220 (265)
Q Consensus 172 ~~~~~~~-~~~k~CP--~C~~~iek~~--GCnhm~C-~C~~~FC~~C~~~~~~g~ 220 (265)
+..++.. ..++.|| +|...|+..+ |.++|+| .|++.|||.|+.+||.+.
T Consensus 8 ~~~~i~~~~~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H~~~ 62 (64)
T smart00647 8 LESYVESNPDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWHSPV 62 (64)
T ss_pred HHHHHhcCCCccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcCCCCC
Confidence 3344443 5789999 9999999975 9999999 899999999999998764
No 8
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.66 E-value=5.8e-09 Score=62.68 Aligned_cols=41 Identities=27% Similarity=0.775 Sum_probs=29.0
Q ss_pred cccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCC
Q 024566 24 CEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPG 72 (265)
Q Consensus 24 C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~ 72 (265)
|+||++.+.++.. ++|||.||.+|+.+++...- ...+.||.
T Consensus 1 CpiC~~~~~~Pv~----l~CGH~FC~~Cl~~~~~~~~----~~~~~CP~ 41 (42)
T PF15227_consen 1 CPICLDLFKDPVS----LPCGHSFCRSCLERLWKEPS----GSGFSCPE 41 (42)
T ss_dssp ETTTTSB-SSEEE-----SSSSEEEHHHHHHHHCCSS----SST---SS
T ss_pred CCccchhhCCccc----cCCcCHHHHHHHHHHHHccC----CcCCCCcC
Confidence 8999999987764 99999999999999986432 22378987
No 9
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.61 E-value=5.3e-08 Score=77.28 Aligned_cols=71 Identities=24% Similarity=0.596 Sum_probs=51.9
Q ss_pred cccCCCCcccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhC--------CCCCcccCCCCCCCCCCCccCc
Q 024566 13 LEKGGGGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQD--------DNTAKIDCPGLDCKHNLDPFAC 84 (265)
Q Consensus 13 ~~~~~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~--------~~~~~i~CP~~~C~~~l~~~~i 84 (265)
...-...+.++|+||++.+.++. .+.|||.||..|+..|+...-.. ......+||. |+..++...+
T Consensus 10 ~~~~~~~~~~~CpICld~~~dPV----vT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPv--CR~~Is~~~L 83 (193)
T PLN03208 10 TTLVDSGGDFDCNICLDQVRDPV----VTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPV--CKSDVSEATL 83 (193)
T ss_pred ceeccCCCccCCccCCCcCCCcE----EcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCC--CCCcCChhcE
Confidence 33444556799999999886553 48899999999999997643110 0234579999 9999988777
Q ss_pred cCCCC
Q 024566 85 EPVIP 89 (265)
Q Consensus 85 ~~~l~ 89 (265)
..+..
T Consensus 84 vPiyg 88 (193)
T PLN03208 84 VPIYG 88 (193)
T ss_pred EEeec
Confidence 66654
No 10
>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=98.55 E-value=4.6e-08 Score=58.59 Aligned_cols=40 Identities=33% Similarity=0.962 Sum_probs=33.4
Q ss_pred cccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCC
Q 024566 24 CEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPG 72 (265)
Q Consensus 24 C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~ 72 (265)
|+||++.+..+.. .++|+|.||.+|+.++++. ...++||.
T Consensus 1 C~iC~~~~~~~~~---~~~C~H~fC~~C~~~~~~~------~~~~~CP~ 40 (41)
T PF00097_consen 1 CPICLEPFEDPVI---LLPCGHSFCRDCLRKWLEN------SGSVKCPL 40 (41)
T ss_dssp ETTTSSBCSSEEE---ETTTSEEEEHHHHHHHHHH------TSSSBTTT
T ss_pred CCcCCccccCCCE---EecCCCcchHHHHHHHHHh------cCCccCCc
Confidence 8999999876652 5999999999999999997 24567987
No 11
>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=98.54 E-value=2.3e-08 Score=66.04 Aligned_cols=42 Identities=38% Similarity=1.022 Sum_probs=30.9
Q ss_pred CCcccCCC--CCceeeecCCCce--eEee-cCCceeeccCccccCCC
Q 024566 179 MKWARCPA--CGHCVERKDGCSV--VMCR-CNTRFCYECGRKISSGC 220 (265)
Q Consensus 179 ~~~k~CP~--C~~~iek~~GCnh--m~C~-C~~~FC~~C~~~~~~g~ 220 (265)
...+.||+ |...|.+.+|.++ |+|. |++.|||.|+.+||.+-
T Consensus 16 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~~~ 62 (64)
T PF01485_consen 16 PNIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPWHEGV 62 (64)
T ss_dssp --CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSESCTTS
T ss_pred CCccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCcccCCCC
Confidence 45689988 9999999999999 9995 99999999999998653
No 12
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.51 E-value=5.3e-08 Score=58.53 Aligned_cols=43 Identities=28% Similarity=0.726 Sum_probs=24.3
Q ss_pred cccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCC
Q 024566 24 CEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCP 71 (265)
Q Consensus 24 C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP 71 (265)
|+||.+ +...++...+++|||.||++|+.+...... ...++||
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 766555555689999999999999998543 3568887
No 13
>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=98.46 E-value=3.7e-08 Score=60.01 Aligned_cols=41 Identities=29% Similarity=0.754 Sum_probs=32.4
Q ss_pred ccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCC
Q 024566 23 TCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPG 72 (265)
Q Consensus 23 ~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~ 72 (265)
+|+||++++.+.+..+ .++|+|.||.+|+..|++.. .+||.
T Consensus 2 ~C~IC~~~~~~~~~~~-~l~C~H~fh~~Ci~~~~~~~--------~~CP~ 42 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVV-KLPCGHVFHRSCIKEWLKRN--------NSCPV 42 (44)
T ss_dssp CETTTTCBHHTTSCEE-EETTSEEEEHHHHHHHHHHS--------SB-TT
T ss_pred CCcCCChhhcCCCeEE-EccCCCeeCHHHHHHHHHhC--------CcCCc
Confidence 6999999997655443 57799999999999999752 28987
No 14
>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=98.46 E-value=9.3e-08 Score=56.60 Aligned_cols=38 Identities=32% Similarity=0.959 Sum_probs=29.3
Q ss_pred cccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCC
Q 024566 24 CEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPG 72 (265)
Q Consensus 24 C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~ 72 (265)
|+||++...++.. .++|||.||.+|+.+|++. ..+||.
T Consensus 1 C~iC~~~~~~~~~---~~~CGH~fC~~C~~~~~~~--------~~~CP~ 38 (39)
T PF13923_consen 1 CPICLDELRDPVV---VTPCGHSFCKECIEKYLEK--------NPKCPV 38 (39)
T ss_dssp ETTTTSB-SSEEE---ECTTSEEEEHHHHHHHHHC--------TSB-TT
T ss_pred CCCCCCcccCcCE---ECCCCCchhHHHHHHHHHC--------cCCCcC
Confidence 8999998876432 5999999999999999873 257886
No 15
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.35 E-value=4.2e-07 Score=55.28 Aligned_cols=43 Identities=28% Similarity=0.883 Sum_probs=33.7
Q ss_pred ccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCC
Q 024566 23 TCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCK 76 (265)
Q Consensus 23 ~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~ 76 (265)
.|+||++.+.+... +.+++|||.||.+|+.... ...+.||. |+
T Consensus 1 ~C~~C~~~~~~~~~-~~l~~CgH~~C~~C~~~~~--------~~~~~CP~--C~ 43 (44)
T PF14634_consen 1 HCNICFEKYSEERR-PRLTSCGHIFCEKCLKKLK--------GKSVKCPI--CR 43 (44)
T ss_pred CCcCcCccccCCCC-eEEcccCCHHHHHHHHhhc--------CCCCCCcC--CC
Confidence 48999999943333 3479999999999999877 24578998 76
No 16
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.31 E-value=4.8e-07 Score=70.10 Aligned_cols=57 Identities=21% Similarity=0.651 Sum_probs=43.5
Q ss_pred CCcccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCCccCccC
Q 024566 18 GGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFACEP 86 (265)
Q Consensus 18 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~ 86 (265)
......|+||++.+..... ....|||.||+.|++..+.. ..+||. |...|+..++-.
T Consensus 128 ~~~~~~CPiCl~~~sek~~--vsTkCGHvFC~~Cik~alk~--------~~~CP~--C~kkIt~k~~~r 184 (187)
T KOG0320|consen 128 KEGTYKCPICLDSVSEKVP--VSTKCGHVFCSQCIKDALKN--------TNKCPT--CRKKITHKQFHR 184 (187)
T ss_pred cccccCCCceecchhhccc--cccccchhHHHHHHHHHHHh--------CCCCCC--cccccchhhhee
Confidence 4556899999999864433 35899999999999987762 358999 887777665543
No 17
>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=98.20 E-value=1.6e-06 Score=52.42 Aligned_cols=44 Identities=32% Similarity=0.843 Sum_probs=33.4
Q ss_pred ccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCC
Q 024566 23 TCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHN 78 (265)
Q Consensus 23 ~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~ 78 (265)
+|+||++.+.... ...+|+|.||.+|+..|++. ...+||. |+..
T Consensus 1 ~C~iC~~~~~~~~---~~~~C~H~~c~~C~~~~~~~-------~~~~Cp~--C~~~ 44 (45)
T cd00162 1 ECPICLEEFREPV---VLLPCGHVFCRSCIDKWLKS-------GKNTCPL--CRTP 44 (45)
T ss_pred CCCcCchhhhCce---EecCCCChhcHHHHHHHHHh-------CcCCCCC--CCCc
Confidence 5899999883322 24669999999999999874 2357998 8764
No 18
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=98.14 E-value=1.3e-06 Score=54.63 Aligned_cols=46 Identities=30% Similarity=0.761 Sum_probs=35.6
Q ss_pred ccccccccccccccccccccCCCCCh-hHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCC
Q 024566 21 SFTCEICIEPMAASKKFKNRNLCTHP-FCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLD 80 (265)
Q Consensus 21 ~~~C~IC~~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 80 (265)
...|.||++...+. .+.+|||. ||.+|+.+++. ...+||. |+..+.
T Consensus 2 ~~~C~iC~~~~~~~----~~~pCgH~~~C~~C~~~~~~--------~~~~CP~--Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFENPRDV----VLLPCGHLCFCEECAERLLK--------RKKKCPI--CRQPIE 48 (50)
T ss_dssp HSB-TTTSSSBSSE----EEETTCEEEEEHHHHHHHHH--------TTSBBTT--TTBB-S
T ss_pred cCCCccCCccCCce----EEeCCCChHHHHHHhHHhcc--------cCCCCCc--CChhhc
Confidence 56899999986432 25899999 99999999998 2458999 998764
No 19
>PHA02926 zinc finger-like protein; Provisional
Probab=98.10 E-value=3.3e-06 Score=67.95 Aligned_cols=58 Identities=26% Similarity=0.606 Sum_probs=42.5
Q ss_pred CCcccccccccccccc-----cccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCC
Q 024566 18 GGSSFTCEICIEPMAA-----SKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNL 79 (265)
Q Consensus 18 ~~~~~~C~IC~~~~~~-----~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 79 (265)
.++..+|+||+|.... ...|-.+.+|+|.||..|++.|....-. ....-.||. |+..+
T Consensus 167 ~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~--~~~~rsCPi--CR~~f 229 (242)
T PHA02926 167 VSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRE--TGASDNCPI--CRTRF 229 (242)
T ss_pred ccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccc--cCcCCcCCC--Cccee
Confidence 4566899999997532 2234446789999999999999986532 233457999 99765
No 20
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.02 E-value=4e-06 Score=72.62 Aligned_cols=112 Identities=22% Similarity=0.484 Sum_probs=71.4
Q ss_pred CCCcccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCCccCccCCCChhHHHHH
Q 024566 17 GGGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFACEPVIPASLFSKW 96 (265)
Q Consensus 17 ~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~ 96 (265)
...+...|+||++.+..+ .+++|+|.||..|+...+. ..+.||. |.. ... .+...-.+...
T Consensus 9 ~~~~~~~C~iC~~~~~~p----~~l~C~H~~c~~C~~~~~~--------~~~~Cp~--cr~-~~~----~~~~n~~l~~~ 69 (386)
T KOG2177|consen 9 VLQEELTCPICLEYFREP----VLLPCGHNFCRACLTRSWE--------GPLSCPV--CRP-PSR----NLRPNVLLANL 69 (386)
T ss_pred hccccccChhhHHHhhcC----ccccccchHhHHHHHHhcC--------CCcCCcc--cCC-chh----ccCccHHHHHH
Confidence 346789999999999776 2699999999999999998 3489999 884 222 22222233333
Q ss_pred HHHHHHHhhcC-C--CccccCCcCcccceeccccccCCcCeeeCCCcccccccccc-cccCCCCCChh
Q 024566 97 CDVLCEDYVLG-F--ERSYCPNTNCMALVVNECERSGKVKKTQCPNCKQWFCFQCK-LKWHAGYRCEE 160 (265)
Q Consensus 97 ~~~~~~~~~~~-~--~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~-~~~H~~~~C~~ 160 (265)
........... . ....|+. ......+.|..|....|..|. ...|.++.-..
T Consensus 70 ~~~~~~~~~~~~~~~~~~~c~~-------------~~~~~~~~c~~~~~~~c~~c~~~~~h~~h~~~~ 124 (386)
T KOG2177|consen 70 VERLRQLRLSRPLGSKEELCEK-------------HGEELKLFCEEDEKLLCVLCRESGEHRGHPVLP 124 (386)
T ss_pred HHHHHhcCCcccccccchhhhh-------------cCCcceEEecccccccCCCCCCcccccCCcccc
Confidence 33222211110 0 0112331 111267899999999999998 67788775443
No 21
>PHA02929 N1R/p28-like protein; Provisional
Probab=97.95 E-value=6.3e-06 Score=68.29 Aligned_cols=52 Identities=29% Similarity=0.670 Sum_probs=38.7
Q ss_pred Ccccccccccccccccc----cccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCC
Q 024566 19 GSSFTCEICIEPMAASK----KFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLD 80 (265)
Q Consensus 19 ~~~~~C~IC~~~~~~~~----~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 80 (265)
.+..+|+||++.+.+.. .+..+.+|+|.||.+|+..|... ...||. |+..+.
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 45689999999865432 12235789999999999998752 237999 997654
No 22
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.95 E-value=7.5e-06 Score=66.37 Aligned_cols=61 Identities=28% Similarity=0.704 Sum_probs=49.9
Q ss_pred CCcccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCCccCccCCCC
Q 024566 18 GGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFACEPVIP 89 (265)
Q Consensus 18 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~~l~ 89 (265)
+...++|-||+|...++. +..|||.||=-||-+|+..+.+. -.||. |+..++.+.|-.|..
T Consensus 44 ~~~~FdCNICLd~akdPV----vTlCGHLFCWpClyqWl~~~~~~-----~~cPV--CK~~Vs~~~vvPlYG 104 (230)
T KOG0823|consen 44 DGGFFDCNICLDLAKDPV----VTLCGHLFCWPCLYQWLQTRPNS-----KECPV--CKAEVSIDTVVPLYG 104 (230)
T ss_pred CCCceeeeeeccccCCCE----EeecccceehHHHHHHHhhcCCC-----eeCCc--cccccccceEEeeec
Confidence 577899999999887665 58999999999999999976543 36899 999998877655543
No 23
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=97.90 E-value=1.3e-05 Score=46.51 Aligned_cols=38 Identities=32% Similarity=0.891 Sum_probs=28.4
Q ss_pred cccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCC
Q 024566 24 CEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPG 72 (265)
Q Consensus 24 C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~ 72 (265)
|+||++..... ..++|+|.||.+|+..|+. . ...+||.
T Consensus 1 C~iC~~~~~~~----~~~~C~H~~c~~C~~~~~~---~----~~~~CP~ 38 (39)
T smart00184 1 CPICLEELKDP----VVLPCGHTFCRSCIRKWLK---S----GNNTCPI 38 (39)
T ss_pred CCcCccCCCCc----EEecCCChHHHHHHHHHHH---h----CcCCCCC
Confidence 78999884322 2588999999999999987 1 2346876
No 24
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.88 E-value=6.5e-06 Score=73.84 Aligned_cols=61 Identities=30% Similarity=0.673 Sum_probs=48.9
Q ss_pred ccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCCccCccCCCCh
Q 024566 21 SFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFACEPVIPA 90 (265)
Q Consensus 21 ~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~~l~~ 90 (265)
...|+||+++..-+. .+.|||.||-.|+-+||..... ..+..||. |...|.+.++..+.-.
T Consensus 186 ~~~CPICL~~~~~p~----~t~CGHiFC~~CiLqy~~~s~~---~~~~~CPi--C~s~I~~kdl~pv~~e 246 (513)
T KOG2164|consen 186 DMQCPICLEPPSVPV----RTNCGHIFCGPCILQYWNYSAI---KGPCSCPI--CRSTITLKDLLPVFIE 246 (513)
T ss_pred CCcCCcccCCCCccc----ccccCceeeHHHHHHHHhhhcc---cCCccCCc--hhhhccccceeeeeec
Confidence 789999999875433 4679999999999999998732 34678999 9999988777666543
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=97.82 E-value=2.4e-05 Score=51.31 Aligned_cols=50 Identities=16% Similarity=0.172 Sum_probs=40.0
Q ss_pred cccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCCccCcc
Q 024566 22 FTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFACE 85 (265)
Q Consensus 22 ~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~ 85 (265)
+.|+||.+.+.++. .++|||.||++|+.+|+.. ...||. |+..++.+++.
T Consensus 2 ~~Cpi~~~~~~~Pv----~~~~G~v~~~~~i~~~~~~--------~~~cP~--~~~~~~~~~l~ 51 (63)
T smart00504 2 FLCPISLEVMKDPV----ILPSGQTYERRAIEKWLLS--------HGTDPV--TGQPLTHEDLI 51 (63)
T ss_pred cCCcCCCCcCCCCE----ECCCCCEEeHHHHHHHHHH--------CCCCCC--CcCCCChhhce
Confidence 57999999987653 4799999999999999975 237998 88887665543
No 26
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=97.79 E-value=2.2e-05 Score=65.60 Aligned_cols=52 Identities=27% Similarity=0.749 Sum_probs=42.2
Q ss_pred CcccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCCccCc
Q 024566 19 GSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFAC 84 (265)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i 84 (265)
.....|.+|++...++. .++|||.||-+|+..|...+- .||. |+..+.+..+
T Consensus 237 ~a~~kC~LCLe~~~~pS----aTpCGHiFCWsCI~~w~~ek~--------eCPl--CR~~~~pskv 288 (293)
T KOG0317|consen 237 EATRKCSLCLENRSNPS----ATPCGHIFCWSCILEWCSEKA--------ECPL--CREKFQPSKV 288 (293)
T ss_pred CCCCceEEEecCCCCCC----cCcCcchHHHHHHHHHHcccc--------CCCc--ccccCCCcce
Confidence 34578999999886554 599999999999999997432 3999 9998887654
No 27
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.73 E-value=2e-05 Score=66.17 Aligned_cols=55 Identities=20% Similarity=0.639 Sum_probs=45.2
Q ss_pred CCCcccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCCc
Q 024566 17 GGGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDP 81 (265)
Q Consensus 17 ~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~ 81 (265)
+.....+|.||++++...+.+ ..++|.|.|...|+.+|+. .+..+||. |+..+++
T Consensus 319 ea~~GveCaICms~fiK~d~~-~vlPC~H~FH~~Cv~kW~~-------~y~~~CPv--Crt~iPP 373 (374)
T COG5540 319 EADKGVECAICMSNFIKNDRL-RVLPCDHRFHVGCVDKWLL-------GYSNKCPV--CRTAIPP 373 (374)
T ss_pred hcCCCceEEEEhhhhcccceE-EEeccCceechhHHHHHHh-------hhcccCCc--cCCCCCC
Confidence 345558999999999766654 4799999999999999996 35678999 9988875
No 28
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.68 E-value=4.7e-05 Score=67.71 Aligned_cols=67 Identities=21% Similarity=0.503 Sum_probs=48.5
Q ss_pred CCcccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCCccCcc-CCCChhHHHHH
Q 024566 18 GGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFACE-PVIPASLFSKW 96 (265)
Q Consensus 18 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~-~~l~~~~~~~~ 96 (265)
-...+.|+||.+.+..+. .++|+|.||..|+..|+.. ...||. |+..+....+. ..+-.++++.|
T Consensus 23 Le~~l~C~IC~d~~~~Pv----itpCgH~FCs~CI~~~l~~--------~~~CP~--Cr~~~~~~~Lr~N~~L~~iVe~~ 88 (397)
T TIGR00599 23 LDTSLRCHICKDFFDVPV----LTSCSHTFCSLCIRRCLSN--------QPKCPL--CRAEDQESKLRSNWLVSEIVESF 88 (397)
T ss_pred cccccCCCcCchhhhCcc----CCCCCCchhHHHHHHHHhC--------CCCCCC--CCCccccccCccchHHHHHHHHH
Confidence 355789999999886553 4899999999999998863 137998 99887665432 22233566666
Q ss_pred HH
Q 024566 97 CD 98 (265)
Q Consensus 97 ~~ 98 (265)
..
T Consensus 89 ~~ 90 (397)
T TIGR00599 89 KN 90 (397)
T ss_pred HH
Confidence 54
No 29
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.65 E-value=3.5e-05 Score=66.93 Aligned_cols=49 Identities=31% Similarity=0.743 Sum_probs=41.3
Q ss_pred cccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCC
Q 024566 22 FTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLD 80 (265)
Q Consensus 22 ~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 80 (265)
.+|.||+|++...+.++ .++|+|.|...|+..|+... .-.||. |+..+.
T Consensus 230 ~~CaIClEdY~~GdklR-iLPC~H~FH~~CIDpWL~~~-------r~~CPv--CK~di~ 278 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLR-ILPCSHKFHVNCIDPWLTQT-------RTFCPV--CKRDIR 278 (348)
T ss_pred ceEEEeecccccCCeee-EecCCCchhhccchhhHhhc-------CccCCC--CCCcCC
Confidence 79999999999887765 69999999999999999854 235999 987543
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=97.50 E-value=0.00023 Score=60.90 Aligned_cols=55 Identities=20% Similarity=0.495 Sum_probs=38.8
Q ss_pred ccccccccccccccc--ccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCCccCccC
Q 024566 22 FTCEICIEPMAASKK--FKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFACEP 86 (265)
Q Consensus 22 ~~C~IC~~~~~~~~~--~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~ 86 (265)
..|++|..+...... +. +..|||.||.+|+...+. ..+..||. |+..+....++.
T Consensus 4 ~~CP~Ck~~~y~np~~kl~-i~~CGH~~C~sCv~~l~~-------~~~~~CP~--C~~~lrk~~fr~ 60 (309)
T TIGR00570 4 QGCPRCKTTKYRNPSLKLM-VNVCGHTLCESCVDLLFV-------RGSGSCPE--CDTPLRKNNFRV 60 (309)
T ss_pred CCCCcCCCCCccCcccccc-cCCCCCcccHHHHHHHhc-------CCCCCCCC--CCCccchhhccc
Confidence 579999996432222 22 237999999999999874 12358998 998887765544
No 31
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=97.44 E-value=7.5e-05 Score=63.66 Aligned_cols=66 Identities=23% Similarity=0.502 Sum_probs=50.4
Q ss_pred CCcccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCCccCccC-CCChhHHHHH
Q 024566 18 GGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFACEP-VIPASLFSKW 96 (265)
Q Consensus 18 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~-~l~~~~~~~~ 96 (265)
-...+.|.||++.+..+. +.+|+|.||.-|++.|+. +...||. |...+....++. .+-.++++.|
T Consensus 20 lD~lLRC~IC~eyf~ip~----itpCsHtfCSlCIR~~L~--------~~p~CP~--C~~~~~Es~Lr~n~il~Eiv~S~ 85 (442)
T KOG0287|consen 20 LDDLLRCGICFEYFNIPM----ITPCSHTFCSLCIRKFLS--------YKPQCPT--CCVTVTESDLRNNRILDEIVKSL 85 (442)
T ss_pred hHHHHHHhHHHHHhcCce----eccccchHHHHHHHHHhc--------cCCCCCc--eecccchhhhhhhhHHHHHHHHH
Confidence 456789999999996443 488999999999999996 4568999 998888877654 2233566655
Q ss_pred H
Q 024566 97 C 97 (265)
Q Consensus 97 ~ 97 (265)
.
T Consensus 86 ~ 86 (442)
T KOG0287|consen 86 N 86 (442)
T ss_pred H
Confidence 4
No 32
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=97.41 E-value=0.00011 Score=46.99 Aligned_cols=52 Identities=31% Similarity=0.707 Sum_probs=34.6
Q ss_pred CCCCcccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCC
Q 024566 16 GGGGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCK 76 (265)
Q Consensus 16 ~~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~ 76 (265)
.+....+.|+|-...+.++.. ...|+|.|-++-+..|+ ++...++||..||.
T Consensus 6 ~~~~~~~~CPiT~~~~~~PV~---s~~C~H~fek~aI~~~i------~~~~~~~CPv~GC~ 57 (57)
T PF11789_consen 6 EGGTISLKCPITLQPFEDPVK---SKKCGHTFEKEAILQYI------QRNGSKRCPVAGCN 57 (57)
T ss_dssp -SSB--SB-TTTSSB-SSEEE---ESSS--EEEHHHHHHHC------TTTS-EE-SCCC-S
T ss_pred eccEeccCCCCcCChhhCCcC---cCCCCCeecHHHHHHHH------HhcCCCCCCCCCCC
Confidence 345667899999999987764 47899999999999999 13567899999985
No 33
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=97.39 E-value=0.00016 Score=65.08 Aligned_cols=72 Identities=22% Similarity=0.588 Sum_probs=53.0
Q ss_pred CCCcccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCCccCccCCCChhHHHHH
Q 024566 17 GGGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFACEPVIPASLFSKW 96 (265)
Q Consensus 17 ~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~ 96 (265)
++....+|.+|-++-.+.. ...|.|.||+-|++.|+.....+ ..+.||. |...|+.+.-+..+..-.++.|
T Consensus 532 enk~~~~C~lc~d~aed~i----~s~ChH~FCrlCi~eyv~~f~~~---~nvtCP~--C~i~LsiDlse~alek~~l~~F 602 (791)
T KOG1002|consen 532 ENKGEVECGLCHDPAEDYI----ESSCHHKFCRLCIKEYVESFMEN---NNVTCPV--CHIGLSIDLSEPALEKTDLKGF 602 (791)
T ss_pred cccCceeecccCChhhhhH----hhhhhHHHHHHHHHHHHHhhhcc---cCCCCcc--ccccccccccchhhhhcchhhh
Confidence 4577889999988764332 48899999999999999987764 3389999 9988877755544443334444
Q ss_pred H
Q 024566 97 C 97 (265)
Q Consensus 97 ~ 97 (265)
.
T Consensus 603 k 603 (791)
T KOG1002|consen 603 K 603 (791)
T ss_pred h
Confidence 3
No 34
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.01 E-value=0.00078 Score=55.83 Aligned_cols=52 Identities=25% Similarity=0.576 Sum_probs=39.2
Q ss_pred ccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCCccCc
Q 024566 21 SFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFAC 84 (265)
Q Consensus 21 ~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i 84 (265)
...|.||++....+. .++|||.||-.|+-..++.+ ..-.||. |++...+..+
T Consensus 215 d~kC~lC~e~~~~ps----~t~CgHlFC~~Cl~~~~t~~------k~~~Cpl--CRak~~pk~v 266 (271)
T COG5574 215 DYKCFLCLEEPEVPS----CTPCGHLFCLSCLLISWTKK------KYEFCPL--CRAKVYPKKV 266 (271)
T ss_pred ccceeeeecccCCcc----cccccchhhHHHHHHHHHhh------ccccCch--hhhhccchhh
Confidence 566999999875443 59999999999999864432 2236999 9988777654
No 35
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=96.97 E-value=0.00047 Score=65.02 Aligned_cols=56 Identities=18% Similarity=0.585 Sum_probs=44.1
Q ss_pred CcccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCCccCccCC
Q 024566 19 GSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFACEPV 87 (265)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~~ 87 (265)
.....|++|.+-..+ . ++..|+|.||.+|++..+.+.-. +||. |+..+...+|..+
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 KELLKCSVCNTRWKD--A--VITKCGHVFCEECVQTRYETRQR-------KCPK--CNAAFGANDVHRI 696 (698)
T ss_pred HhceeCCCccCchhh--H--HHHhcchHHHHHHHHHHHHHhcC-------CCCC--CCCCCCccccccc
Confidence 457899999954432 2 25889999999999999986533 7999 9999998887654
No 36
>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=96.97 E-value=0.00041 Score=46.90 Aligned_cols=46 Identities=28% Similarity=0.632 Sum_probs=31.4
Q ss_pred ccccccccccccccc---------cccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCC
Q 024566 21 SFTCEICIEPMAASK---------KFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCK 76 (265)
Q Consensus 21 ~~~C~IC~~~~~~~~---------~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~ 76 (265)
...|.||++++.++. ..+....|+|.|...||.+|++.+ -.||. |+
T Consensus 19 ~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~--------~~CP~--CR 73 (73)
T PF12678_consen 19 DDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQN--------NTCPL--CR 73 (73)
T ss_dssp CSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTS--------SB-TT--SS
T ss_pred CCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcC--------CcCCC--CC
Confidence 445999999983221 122345799999999999999521 28998 64
No 37
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=96.95 E-value=0.00052 Score=60.55 Aligned_cols=82 Identities=17% Similarity=0.425 Sum_probs=48.0
Q ss_pred cCeeeCCCcccccccccccccCCCCCChhHHhchhhchHHHHHHHhcCCcccCCCCCceeeecCCCce-eEe-ecCCcee
Q 024566 132 VKKTQCPNCKQWFCFQCKLKWHAGYRCEESRNLRDQNDIVFGQLVERMKWARCPACGHCVERKDGCSV-VMC-RCNTRFC 209 (265)
Q Consensus 132 ~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~d~~~~~~~~~~~~k~CP~C~~~iek~~GCnh-m~C-~C~~~FC 209 (265)
...+.|..|...+|.-|+..-|++..=-.--++...++-.+.........-+|. -.+|=|| |+| .|+.-.|
T Consensus 174 ~a~v~ceqcdv~yc~pc~~~~hp~rgplakh~l~~~~~grvs~~~s~r~~~~ct-------~h~~e~~smyc~~ck~pvc 246 (699)
T KOG4367|consen 174 EATVMCEQCDVFYCDPCRLRCHPPRGPLAKHRLVPPAQGRVSRRLSPRKVSTCT-------DHELENHSMYCVQCKMPVC 246 (699)
T ss_pred hhhhhHhhCceEEechHHhccCCCCCchhhcccCCcccCceeeccchhhhhhcc-------CCCCCCceEEEEecCChHH
Confidence 467899999999999999999986421000001111111100000111112222 2355566 999 7999999
Q ss_pred eccCccccCCC
Q 024566 210 YECGRKISSGC 220 (265)
Q Consensus 210 ~~C~~~~~~g~ 220 (265)
|.|+....|..
T Consensus 247 ~~clee~khs~ 257 (699)
T KOG4367|consen 247 YQCLEEGKHSS 257 (699)
T ss_pred HHHHHhhcccc
Confidence 99999976653
No 38
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=96.84 E-value=0.00041 Score=46.49 Aligned_cols=59 Identities=15% Similarity=0.359 Sum_probs=28.0
Q ss_pred ccccccccccccccccc--ccc--CCCCChhHHHHHHHHHHHHhhCCCC-Cc--ccCCCCCCCCCCCc
Q 024566 21 SFTCEICIEPMAASKKF--KNR--NLCTHPFCQDCIARYIQVKVQDDNT-AK--IDCPGLDCKHNLDP 81 (265)
Q Consensus 21 ~~~C~IC~~~~~~~~~~--~~~--~~C~H~fC~~Cl~~~~~~~i~~~~~-~~--i~CP~~~C~~~l~~ 81 (265)
..+|.||+....+.... ... ..|+..|...||..|+...-+.... .+ -.||. |+.+|+.
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 56899999876422111 112 3689999999999999887664322 22 26999 9987754
No 39
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=96.79 E-value=0.0003 Score=45.43 Aligned_cols=51 Identities=25% Similarity=0.574 Sum_probs=24.3
Q ss_pred cccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCCccCcc
Q 024566 20 SSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFACE 85 (265)
Q Consensus 20 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~ 85 (265)
+...|++|.+.+..+.. +..|.|.||..|++..+. -.||. |..+--..+++
T Consensus 6 ~lLrCs~C~~~l~~pv~---l~~CeH~fCs~Ci~~~~~----------~~CPv--C~~Paw~qD~~ 56 (65)
T PF14835_consen 6 ELLRCSICFDILKEPVC---LGGCEHIFCSSCIRDCIG----------SECPV--CHTPAWIQDIQ 56 (65)
T ss_dssp HTTS-SSS-S--SS-B------SSS--B-TTTGGGGTT----------TB-SS--S--B-S-SS--
T ss_pred HhcCCcHHHHHhcCCce---eccCccHHHHHHhHHhcC----------CCCCC--cCChHHHHHHH
Confidence 45789999999876654 478999999999976332 24999 98765444443
No 40
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=96.42 E-value=0.0018 Score=54.31 Aligned_cols=68 Identities=22% Similarity=0.415 Sum_probs=47.5
Q ss_pred CCCcccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCCccCccC-CCChhHHHH
Q 024566 17 GGGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFACEP-VIPASLFSK 95 (265)
Q Consensus 17 ~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~-~l~~~~~~~ 95 (265)
+-.....|.||-+.+..+. ..+|||.||.-|++.|+. ....||. |........++. .+..++.+.
T Consensus 21 ~LDs~lrC~IC~~~i~ip~----~TtCgHtFCslCIR~hL~--------~qp~CP~--Cr~~~~esrlr~~s~~~ei~es 86 (391)
T COG5432 21 GLDSMLRCRICDCRISIPC----ETTCGHTFCSLCIRRHLG--------TQPFCPV--CREDPCESRLRGSSGSREINES 86 (391)
T ss_pred cchhHHHhhhhhheeecce----ecccccchhHHHHHHHhc--------CCCCCcc--ccccHHhhhcccchhHHHHHHh
Confidence 3466789999999885443 489999999999999985 3457998 886654443332 334455555
Q ss_pred HHH
Q 024566 96 WCD 98 (265)
Q Consensus 96 ~~~ 98 (265)
|..
T Consensus 87 ~~~ 89 (391)
T COG5432 87 HAR 89 (391)
T ss_pred hhh
Confidence 543
No 41
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.40 E-value=0.005 Score=54.24 Aligned_cols=47 Identities=26% Similarity=0.638 Sum_probs=41.2
Q ss_pred CCcccCCC--CCceeeecCCCceeEe-ecCCceeeccCccccCCCCCCCc
Q 024566 179 MKWARCPA--CGHCVERKDGCSVVMC-RCNTRFCYECGRKISSGCSCQTI 225 (265)
Q Consensus 179 ~~~k~CP~--C~~~iek~~GCnhm~C-~C~~~FC~~C~~~~~~g~~~~~~ 225 (265)
.++.-||+ |..++..+.|..-..| +|.+.||..|...||.+.++...
T Consensus 271 sdv~yCPr~~Cq~p~~~d~~~~l~~CskCnFaFCtlCk~t~HG~s~Ck~~ 320 (445)
T KOG1814|consen 271 SDVVYCPRACCQLPVKQDPGRALAICSKCNFAFCTLCKLTWHGVSPCKVK 320 (445)
T ss_pred cccccCChhhccCccccCchhhhhhhccCccHHHHHHHHhhcCCCcccCc
Confidence 35699998 9999988899999999 79999999999999987666554
No 42
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=95.73 E-value=0.0085 Score=52.09 Aligned_cols=54 Identities=24% Similarity=0.540 Sum_probs=39.4
Q ss_pred CCcccccccccccccccc---------cccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCCc
Q 024566 18 GGSSFTCEICIEPMAASK---------KFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDP 81 (265)
Q Consensus 18 ~~~~~~C~IC~~~~~~~~---------~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~ 81 (265)
......|.||+|+.-.+. .-+..++|||.+...|++.|.+.+ =.||. |+.++-.
T Consensus 284 ~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERq--------QTCPI--Cr~p~if 346 (491)
T COG5243 284 TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQ--------QTCPI--CRRPVIF 346 (491)
T ss_pred cCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhc--------cCCCc--ccCcccc
Confidence 455678999999832222 112358999999999999999842 27999 9987533
No 43
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=95.68 E-value=0.0092 Score=51.19 Aligned_cols=53 Identities=25% Similarity=0.640 Sum_probs=42.5
Q ss_pred CCcccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCCccC
Q 024566 18 GGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFA 83 (265)
Q Consensus 18 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~ 83 (265)
-...++|.+|--.+.+..+ +..|-|.||+.||-.|++. ...||. |+..+....
T Consensus 12 ~n~~itC~LC~GYliDATT---I~eCLHTFCkSCivk~l~~--------~~~CP~--C~i~ih~t~ 64 (331)
T KOG2660|consen 12 LNPHITCRLCGGYLIDATT---ITECLHTFCKSCIVKYLEE--------SKYCPT--CDIVIHKTH 64 (331)
T ss_pred cccceehhhccceeecchh---HHHHHHHHHHHHHHHHHHH--------hccCCc--cceeccCcc
Confidence 3567899999998876654 5889999999999999996 237999 987766553
No 44
>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=95.66 E-value=0.0057 Score=41.31 Aligned_cols=52 Identities=19% Similarity=0.214 Sum_probs=37.5
Q ss_pred cccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCCccCc
Q 024566 20 SSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFAC 84 (265)
Q Consensus 20 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i 84 (265)
+.+.|+|+.+-+.++.. +++||+|.++++.+|+.. ....||. ++..++..++
T Consensus 3 ~~f~CpIt~~lM~dPVi----~~~G~tyer~~I~~~l~~-------~~~~~P~--t~~~l~~~~l 54 (73)
T PF04564_consen 3 DEFLCPITGELMRDPVI----LPSGHTYERSAIERWLEQ-------NGGTDPF--TRQPLSESDL 54 (73)
T ss_dssp GGGB-TTTSSB-SSEEE----ETTSEEEEHHHHHHHHCT-------TSSB-TT--T-SB-SGGGS
T ss_pred cccCCcCcCcHhhCcee----CCcCCEEcHHHHHHHHHc-------CCCCCCC--CCCcCCcccc
Confidence 46889999999987763 789999999999999974 3457898 7877776543
No 45
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=95.58 E-value=0.012 Score=35.97 Aligned_cols=47 Identities=23% Similarity=0.613 Sum_probs=21.7
Q ss_pred cccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCC
Q 024566 24 CEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNL 79 (265)
Q Consensus 24 C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 79 (265)
|++|.++.+....-+.--+|++.+|+.|+.+..+ + ..=+||. |+.+.
T Consensus 1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~----~---~~g~CPg--Cr~~Y 47 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILE----N---EGGRCPG--CREPY 47 (48)
T ss_dssp -TTTS-B--CCCTT--SSTTS----HHHHHHHTT----S---S-SB-TT--T--B-
T ss_pred CCCcccccccCCCccccCcCCCcHHHHHHHHHHh----c---cCCCCCC--CCCCC
Confidence 7899998854433222356899999999887665 1 1237998 98754
No 46
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=95.58 E-value=0.02 Score=48.79 Aligned_cols=93 Identities=19% Similarity=0.516 Sum_probs=56.4
Q ss_pred CCCChhHHHHHHHHHHHHhhCC--CCCcccCCCCCCCCCCCccCccCCCChhHHHHHHHHHHHHhhcCCCccccCCcCcc
Q 024566 42 LCTHPFCQDCIARYIQVKVQDD--NTAKIDCPGLDCKHNLDPFACEPVIPASLFSKWCDVLCEDYVLGFERSYCPNTNCM 119 (265)
Q Consensus 42 ~C~H~fC~~Cl~~~~~~~i~~~--~~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~ 119 (265)
.|+-.||++|++.|-+-.-..+ ....- .|.-.+++. ....++|+....+ .| ....+.|| +|.
T Consensus 341 gCgf~FCR~C~e~yh~geC~~~~~as~t~-----tc~y~vde~-------~a~~arwd~as~~-TI-k~tTkpCP--kCh 404 (446)
T KOG0006|consen 341 GCGFAFCRECKEAYHEGECSAVFEASGTT-----TCAYRVDER-------AAEQARWDAASKE-TI-KKTTKPCP--KCH 404 (446)
T ss_pred CchhHhHHHHHhhhccccceeeecccccc-----ceeeecChh-------hhhhhhhhhhhhh-hh-hhccCCCC--Ccc
Confidence 4899999999998865221110 00001 122222111 1345677765432 22 24557788 587
Q ss_pred cceeccccccCCcCeeeCCC--cccccccccccccCC
Q 024566 120 ALVVNECERSGKVKKTQCPN--CKQWFCFQCKLKWHA 154 (265)
Q Consensus 120 ~~~~~~~~~~~~~~~~~C~~--C~~~~C~~C~~~~H~ 154 (265)
.....+.. ...+.|+. |+..+|+.|+-+|..
T Consensus 405 vptErnGG----CmHm~Ct~~~Cg~eWCw~C~tEW~r 437 (446)
T KOG0006|consen 405 VPTERNGG----CMHMKCTQPQCGLEWCWNCGTEWNR 437 (446)
T ss_pred CccccCCc----eEEeecCCCCCCceeEeccCChhhh
Confidence 76655444 78999976 999999999998854
No 47
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.44 E-value=0.012 Score=49.77 Aligned_cols=54 Identities=24% Similarity=0.461 Sum_probs=41.0
Q ss_pred CCcccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCCccCc
Q 024566 18 GGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFAC 84 (265)
Q Consensus 18 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i 84 (265)
.....+|+||+.+-.-+. .+.|+|.||.-|++.-+.. ....|+. |..+|+...+
T Consensus 4 ~~~~~eC~IC~nt~n~Pv----~l~C~HkFCyiCiKGsy~n-------dk~~Cav--CR~pids~i~ 57 (324)
T KOG0824|consen 4 RTKKKECLICYNTGNCPV----NLYCFHKFCYICIKGSYKN-------DKKTCAV--CRFPIDSTID 57 (324)
T ss_pred cccCCcceeeeccCCcCc----cccccchhhhhhhcchhhc-------CCCCCce--ecCCCCcchh
Confidence 345679999999875443 5999999999999986652 2345999 9988876543
No 48
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.39 E-value=0.016 Score=50.85 Aligned_cols=95 Identities=20% Similarity=0.419 Sum_probs=55.9
Q ss_pred CCcccccccccccccccc----cccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCCc---cCc---cCC
Q 024566 18 GGSSFTCEICIEPMAASK----KFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDP---FAC---EPV 87 (265)
Q Consensus 18 ~~~~~~C~IC~~~~~~~~----~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~---~~i---~~~ 87 (265)
..+..+|.||++...... .|-.+.+|.|.||..|++.|-...-. +....-.||. |+..... ..+ ..-
T Consensus 158 ~s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~-~~~~sksCP~--CRv~s~~v~pS~~Wv~t~~ 234 (344)
T KOG1039|consen 158 KSSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQF-ESKTSKSCPF--CRVPSSFVNPSSFWVETKE 234 (344)
T ss_pred ccccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhcc-ccccccCCCc--ccCccccccccceeeeecc
Confidence 466889999999875432 13334679999999999998754332 2344568999 8854322 111 111
Q ss_pred CChhHHHHHHHHHHHHhh--cCCCccccCC
Q 024566 88 IPASLFSKWCDVLCEDYV--LGFERSYCPN 115 (265)
Q Consensus 88 l~~~~~~~~~~~~~~~~~--~~~~~~~Cp~ 115 (265)
-+..+.+.|.+......- -....-.||.
T Consensus 235 ~k~~li~e~~~~~s~~~c~yf~~~~g~cPf 264 (344)
T KOG1039|consen 235 EKQKLIEEYEAEMSAKDCKYFSQGLGSCPF 264 (344)
T ss_pred cccccHHHHHHHhhccchhhhcCCCCCCCC
Confidence 222355666554332211 1244567886
No 49
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.70 E-value=0.034 Score=46.53 Aligned_cols=52 Identities=33% Similarity=0.662 Sum_probs=39.0
Q ss_pred CCcccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCC
Q 024566 18 GGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLD 80 (265)
Q Consensus 18 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 80 (265)
.....+|++|-+.-..+-. ...|+|.||--|+..-... ...+.||. |++...
T Consensus 236 ~t~~~~C~~Cg~~PtiP~~---~~~C~HiyCY~Ci~ts~~~------~asf~Cp~--Cg~~~~ 287 (298)
T KOG2879|consen 236 GTSDTECPVCGEPPTIPHV---IGKCGHIYCYYCIATSRLW------DASFTCPL--CGENVE 287 (298)
T ss_pred ccCCceeeccCCCCCCCee---eccccceeehhhhhhhhcc------hhhcccCc--cCCCCc
Confidence 4567899999986544432 4679999999999887653 24579999 997654
No 50
>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=94.70 E-value=0.013 Score=30.95 Aligned_cols=23 Identities=35% Similarity=0.941 Sum_probs=15.0
Q ss_pred ccCCCCCceeeecCCCceeEe-ecCCce
Q 024566 182 ARCPACGHCVERKDGCSVVMC-RCNTRF 208 (265)
Q Consensus 182 k~CP~C~~~iek~~GCnhm~C-~C~~~F 208 (265)
|.||.|+..|-.+ -..| .||+.|
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 5788888888432 2456 477665
No 51
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.67 E-value=0.05 Score=47.10 Aligned_cols=50 Identities=28% Similarity=0.687 Sum_probs=38.6
Q ss_pred cccccccccccccc--ccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCC
Q 024566 21 SFTCEICIEPMAAS--KKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNL 79 (265)
Q Consensus 21 ~~~C~IC~~~~~~~--~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 79 (265)
...|.||-+++... ...+..+.|||.+|..|+...+. ...+.||. |+...
T Consensus 3 ~~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~-------~~~i~cpf--cR~~~ 54 (296)
T KOG4185|consen 3 FPECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLG-------NSRILCPF--CRETT 54 (296)
T ss_pred CCceeecCccccccCcccCCcccccCceehHhHHHHHhc-------CceeeccC--CCCcc
Confidence 56899999999754 33445688999999999998875 34567788 98774
No 52
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=94.62 E-value=0.07 Score=46.00 Aligned_cols=65 Identities=25% Similarity=0.498 Sum_probs=45.1
Q ss_pred CcccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCCccCccCC-CChhH
Q 024566 19 GSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFACEPV-IPASL 92 (265)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~~-l~~~~ 92 (265)
++...|++|+|+.+-.+.-+.-.+||-.+|+-||... ...++. +||. |+...+++.++-. |+++.
T Consensus 12 deed~cplcie~mditdknf~pc~cgy~ic~fc~~~i-rq~lng------rcpa--crr~y~denv~~~~~s~ee 77 (480)
T COG5175 12 DEEDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNI-RQNLNG------RCPA--CRRKYDDENVRYVTLSPEE 77 (480)
T ss_pred cccccCcccccccccccCCcccCCcccHHHHHHHHHH-HhhccC------CChH--hhhhccccceeEEecCHHH
Confidence 3444599999988654432235778999999999764 434543 7999 9999888876543 44443
No 53
>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class
Probab=94.54 E-value=0.052 Score=33.51 Aligned_cols=42 Identities=21% Similarity=0.498 Sum_probs=29.6
Q ss_pred ccccccccccccccccccCCCC-----ChhHHHHHHHHHHHHhhCCCCCcccCCC
Q 024566 23 TCEICIEPMAASKKFKNRNLCT-----HPFCQDCIARYIQVKVQDDNTAKIDCPG 72 (265)
Q Consensus 23 ~C~IC~~~~~~~~~~~~~~~C~-----H~fC~~Cl~~~~~~~i~~~~~~~i~CP~ 72 (265)
.|-||++...+.+.+ ..+|. |.+..+||.+|+...-+ .+||.
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 488999833333333 46774 88999999999986532 37887
No 54
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=94.26 E-value=0.028 Score=44.67 Aligned_cols=36 Identities=31% Similarity=0.669 Sum_probs=28.8
Q ss_pred CCCcccccccccccccccccccccCCCCChhHHHHHHHHH
Q 024566 17 GGGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYI 56 (265)
Q Consensus 17 ~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~ 56 (265)
.+.-.+.|.||-.++..+. ...|||.||..|...-+
T Consensus 192 ~e~IPF~C~iCKkdy~spv----vt~CGH~FC~~Cai~~y 227 (259)
T COG5152 192 GEKIPFLCGICKKDYESPV----VTECGHSFCSLCAIRKY 227 (259)
T ss_pred CCCCceeehhchhhccchh----hhhcchhHHHHHHHHHh
Confidence 3455689999999997654 48999999999976544
No 55
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.23 E-value=0.032 Score=52.51 Aligned_cols=49 Identities=27% Similarity=0.655 Sum_probs=37.5
Q ss_pred Cccccccccccccccccc-ccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCC
Q 024566 19 GSSFTCEICIEPMAASKK-FKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKH 77 (265)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~-~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~ 77 (265)
.....|.||.|....... -...++|+|.|+..|++.|++.+ -.||. |+.
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 446899999999865311 02358999999999999999962 26988 876
No 56
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.74 E-value=0.007 Score=54.27 Aligned_cols=42 Identities=21% Similarity=0.641 Sum_probs=34.2
Q ss_pred CCccccCCcCcccceeccccccCCcCeeeCCCcccccccccccccCCCC
Q 024566 108 FERSYCPNTNCMALVVNECERSGKVKKTQCPNCKQWFCFQCKLKWHAGY 156 (265)
Q Consensus 108 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~ 156 (265)
...+.|| .|...+....+ -+.+.|. |++.||+.|..+|..+.
T Consensus 304 ~~wr~Cp--kC~~~ie~~~G----Cnhm~Cr-C~~~fcy~C~~~~~~~~ 345 (384)
T KOG1812|consen 304 KRWRQCP--KCKFMIELSEG----CNHMTCR-CGHQFCYMCGGDWKTHN 345 (384)
T ss_pred HhcCcCc--ccceeeeecCC----cceEEee-ccccchhhcCcchhhCC
Confidence 5668899 59988855444 7999998 99999999999986544
No 57
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=93.56 E-value=0.059 Score=54.73 Aligned_cols=71 Identities=18% Similarity=0.390 Sum_probs=54.3
Q ss_pred CCCcccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCC--CCcccCCCCCCCCCCCccCccCCCCh
Q 024566 17 GGGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDN--TAKIDCPGLDCKHNLDPFACEPVIPA 90 (265)
Q Consensus 17 ~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~--~~~i~CP~~~C~~~l~~~~i~~~l~~ 90 (265)
.++....|.|||.+.-..... ..+.|+|.|...|.+..++..-.... +.-|.||. |+.+|....++.+|++
T Consensus 3482 kQD~DDmCmICFTE~L~AAP~-IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPi--C~n~InH~~LkDLldP 3554 (3738)
T KOG1428|consen 3482 KQDADDMCMICFTEALSAAPA-IQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPI--CKNKINHIVLKDLLDP 3554 (3738)
T ss_pred hcccCceEEEEehhhhCCCcc-eecCCccchhHHHHHHHHHhcccCCeeEEeeeeccc--ccchhhhHHHHHHHHH
Confidence 445667899999876433222 25899999999999999987766432 23488999 9999999888888884
No 58
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=93.55 E-value=0.088 Score=36.33 Aligned_cols=54 Identities=24% Similarity=0.578 Sum_probs=36.9
Q ss_pred cccccccccccccc--------ccc-cccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCCc
Q 024566 21 SFTCEICIEPMAAS--------KKF-KNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDP 81 (265)
Q Consensus 21 ~~~C~IC~~~~~~~--------~~~-~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~ 81 (265)
...|+||...++.. +.- +..-.|+|.|...|+.+|++++-. .-.||. |++.+..
T Consensus 21 dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~-----~~~CPm--CR~~w~~ 83 (85)
T PF12861_consen 21 DDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSS-----KGQCPM--CRQPWKF 83 (85)
T ss_pred CCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccC-----CCCCCC--cCCeeee
Confidence 56788888777521 110 012469999999999999997521 238999 9987643
No 59
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.48 E-value=0.061 Score=48.63 Aligned_cols=54 Identities=26% Similarity=0.651 Sum_probs=40.0
Q ss_pred Cccccccccccccccccc-------------ccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCCc
Q 024566 19 GSSFTCEICIEPMAASKK-------------FKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDP 81 (265)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~-------------~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~ 81 (265)
.....|.||+.+.+-... -+.+.+|.|.|.+.|+.+|... ..+.||. |+.+|++
T Consensus 569 ~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~-------ykl~CPv--CR~pLPp 635 (636)
T KOG0828|consen 569 RRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDT-------YKLICPV--CRCPLPP 635 (636)
T ss_pred hccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhh-------hcccCCc--cCCCCCC
Confidence 456799999988752111 0125699999999999999972 4578999 9888764
No 60
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=93.30 E-value=0.039 Score=28.24 Aligned_cols=11 Identities=45% Similarity=1.141 Sum_probs=8.0
Q ss_pred cCCCCCceeee
Q 024566 183 RCPACGHCVER 193 (265)
Q Consensus 183 ~CP~C~~~iek 193 (265)
.||+|+..|+.
T Consensus 1 ~Cp~CG~~~~~ 11 (23)
T PF13240_consen 1 YCPNCGAEIED 11 (23)
T ss_pred CCcccCCCCCC
Confidence 47888887764
No 61
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.28 E-value=0.073 Score=47.74 Aligned_cols=50 Identities=28% Similarity=0.749 Sum_probs=38.6
Q ss_pred CCcccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCCc
Q 024566 18 GGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDP 81 (265)
Q Consensus 18 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~ 81 (265)
....++|.||+..+.++. .++|||.||..|+.+-.. ....||. |+..+..
T Consensus 81 ~~sef~c~vc~~~l~~pv----~tpcghs~c~~Cl~r~ld--------~~~~cp~--Cr~~l~e 130 (398)
T KOG4159|consen 81 IRSEFECCVCSRALYPPV----VTPCGHSFCLECLDRSLD--------QETECPL--CRDELVE 130 (398)
T ss_pred ccchhhhhhhHhhcCCCc----cccccccccHHHHHHHhc--------cCCCCcc--ccccccc
Confidence 367899999999987665 379999999999777222 3357888 9877654
No 62
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=93.05 E-value=0.068 Score=44.06 Aligned_cols=57 Identities=11% Similarity=0.248 Sum_probs=45.3
Q ss_pred CcccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCCccCcc
Q 024566 19 GSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFACE 85 (265)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~ 85 (265)
...+.|+||-+.+.+......+.+|||.||.+|+++++. ....||. |+.++.+.+|-
T Consensus 219 s~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir--------~D~v~pv--~d~plkdrdiI 275 (303)
T KOG3039|consen 219 SKRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIR--------KDMVDPV--TDKPLKDRDII 275 (303)
T ss_pred ccceecccchhhhcCccceEEeccCCcEeeHHHHHHhcc--------ccccccC--CCCcCcccceE
Confidence 478899999999977666666788999999999999886 2345788 88888776653
No 63
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=92.99 E-value=0.047 Score=28.82 Aligned_cols=23 Identities=39% Similarity=1.109 Sum_probs=14.7
Q ss_pred ccCCCCCceeeecCCCceeEeecCCceeeccCcc
Q 024566 182 ARCPACGHCVERKDGCSVVMCRCNTRFCYECGRK 215 (265)
Q Consensus 182 k~CP~C~~~iek~~GCnhm~C~C~~~FC~~C~~~ 215 (265)
+.||+|+..|.. +..||-.||.+
T Consensus 3 ~~Cp~Cg~~~~~-----------~~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGAEIDP-----------DAKFCPNCGAK 25 (26)
T ss_pred CCCcccCCcCCc-----------ccccChhhCCC
Confidence 578888886654 25566666554
No 64
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=92.69 E-value=0.099 Score=32.47 Aligned_cols=27 Identities=30% Similarity=0.760 Sum_probs=20.6
Q ss_pred ccCCCCCceeeecCC--CceeEe-ecCCce
Q 024566 182 ARCPACGHCVERKDG--CSVVMC-RCNTRF 208 (265)
Q Consensus 182 k~CP~C~~~iek~~G--Cnhm~C-~C~~~F 208 (265)
+.||.|+.++...++ -++..| .||+++
T Consensus 1 ~FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~ 30 (52)
T smart00661 1 KFCPKCGNMLIPKEGKEKRRFVCRKCGYEE 30 (52)
T ss_pred CCCCCCCCccccccCCCCCEEECCcCCCeE
Confidence 469999998876543 468999 699764
No 65
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.50 E-value=0.022 Score=49.34 Aligned_cols=49 Identities=31% Similarity=0.807 Sum_probs=35.2
Q ss_pred CcccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCC
Q 024566 19 GSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNL 79 (265)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 79 (265)
...+.|+||++-+...- +...|.|.||.+|+..-+.. ++ =.||. |+..+
T Consensus 41 ~~~v~c~icl~llk~tm---ttkeClhrfc~~ci~~a~r~----gn---~ecpt--cRk~l 89 (381)
T KOG0311|consen 41 DIQVICPICLSLLKKTM---TTKECLHRFCFDCIWKALRS----GN---NECPT--CRKKL 89 (381)
T ss_pred hhhhccHHHHHHHHhhc---ccHHHHHHHHHHHHHHHHHh----cC---CCCch--HHhhc
Confidence 55789999999885432 24679999999998766542 22 26888 88554
No 66
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.44 E-value=0.062 Score=33.45 Aligned_cols=46 Identities=30% Similarity=0.573 Sum_probs=34.1
Q ss_pred ccccccccccccccccccccCCCCCh-hHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCC
Q 024566 21 SFTCEICIEPMAASKKFKNRNLCTHP-FCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNL 79 (265)
Q Consensus 21 ~~~C~IC~~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 79 (265)
..+|.||+|.-.++. +..|||. .|.+|-.+.+.. . .=.||. |+.++
T Consensus 7 ~dECTICye~pvdsV----lYtCGHMCmCy~Cg~rl~~~-~------~g~CPi--CRapi 53 (62)
T KOG4172|consen 7 SDECTICYEHPVDSV----LYTCGHMCMCYACGLRLKKA-L------HGCCPI--CRAPI 53 (62)
T ss_pred ccceeeeccCcchHH----HHHcchHHhHHHHHHHHHHc-c------CCcCcc--hhhHH
Confidence 379999999654433 4689995 999998887763 2 237998 88765
No 67
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=92.33 E-value=0.049 Score=44.89 Aligned_cols=57 Identities=23% Similarity=0.550 Sum_probs=39.4
Q ss_pred ccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCCccCccCCCChh
Q 024566 21 SFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFACEPVIPAS 91 (265)
Q Consensus 21 ~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~~l~~~ 91 (265)
...|..|+.--. ...|+ ++.|.|+||..|.+.-. +-.||. |+..+....+..-|+.+
T Consensus 3 ~VhCn~C~~~~~-~~~f~-LTaC~HvfC~~C~k~~~----------~~~C~l--Ckk~ir~i~l~~slp~~ 59 (233)
T KOG4739|consen 3 FVHCNKCFRFPS-QDPFF-LTACRHVFCEPCLKASS----------PDVCPL--CKKSIRIIQLNRSLPTD 59 (233)
T ss_pred eEEeccccccCC-CCcee-eeechhhhhhhhcccCC----------cccccc--ccceeeeeecccccchh
Confidence 457888887654 55554 78999999999965421 228999 99877665555545543
No 68
>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=92.32 E-value=0.038 Score=45.31 Aligned_cols=54 Identities=20% Similarity=0.481 Sum_probs=38.6
Q ss_pred Ccccccccccccccc-ccc-ccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCC
Q 024566 19 GSSFTCEICIEPMAA-SKK-FKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNL 79 (265)
Q Consensus 19 ~~~~~C~IC~~~~~~-~~~-~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 79 (265)
....-|+||..+... +.. +.....|-|.+|.+|+.+.+. ..|-.||.++|+..|
T Consensus 8 ~~d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs-------~GpAqCP~~gC~kIL 63 (314)
T COG5220 8 MEDRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFS-------RGPAQCPYKGCGKIL 63 (314)
T ss_pred hhcccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhc-------CCCCCCCCccHHHHH
Confidence 344579999976542 222 222234999999999999885 457799999999654
No 69
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.30 E-value=0.025 Score=47.19 Aligned_cols=56 Identities=29% Similarity=0.506 Sum_probs=42.3
Q ss_pred Ccccccccccccccccc-------cccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCCccC
Q 024566 19 GSSFTCEICIEPMAASK-------KFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFA 83 (265)
Q Consensus 19 ~~~~~C~IC~~~~~~~~-------~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~ 83 (265)
.+...|.||-..+..++ +. ..++|+|.|...|++.|...- ..-.||- |++.++...
T Consensus 222 l~d~vCaVCg~~~~~s~~eegvient-y~LsCnHvFHEfCIrGWcivG------KkqtCPY--CKekVdl~r 284 (328)
T KOG1734|consen 222 LSDSVCAVCGQQIDVSVDEEGVIENT-YKLSCNHVFHEFCIRGWCIVG------KKQTCPY--CKEKVDLKR 284 (328)
T ss_pred CCcchhHhhcchheeecchhhhhhhh-eeeecccchHHHhhhhheeec------CCCCCch--HHHHhhHhh
Confidence 44678999998776544 22 358999999999999998642 3348999 998887643
No 70
>PF04641 Rtf2: Rtf2 RING-finger
Probab=92.30 E-value=0.26 Score=41.91 Aligned_cols=72 Identities=17% Similarity=0.357 Sum_probs=54.1
Q ss_pred CCcccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCCccCccCCCCh-hHHHHH
Q 024566 18 GGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFACEPVIPA-SLFSKW 96 (265)
Q Consensus 18 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~~l~~-~~~~~~ 96 (265)
....+.|||-..++.....|+.+.+|||+|....++..- .+ -.||. |+.++...+|-.|-+. +.++.+
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 567899999999997666777788999999999999872 12 24999 9999998887766554 344444
Q ss_pred HHHH
Q 024566 97 CDVL 100 (265)
Q Consensus 97 ~~~~ 100 (265)
...+
T Consensus 179 ~~~~ 182 (260)
T PF04641_consen 179 RERM 182 (260)
T ss_pred HHHH
Confidence 4443
No 71
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.04 E-value=0.14 Score=45.11 Aligned_cols=54 Identities=22% Similarity=0.586 Sum_probs=37.5
Q ss_pred ccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCCc
Q 024566 21 SFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDP 81 (265)
Q Consensus 21 ~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~ 81 (265)
.-.|.||-+-++....+-..-.|||.|...|+.+|++..-.+ -.||. |+-.+..
T Consensus 4 ~A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~-----R~cpi--c~ik~~~ 57 (465)
T KOG0827|consen 4 MAECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSN-----RGCPI--CQIKLQE 57 (465)
T ss_pred cceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCcc-----CCCCc--eeecccc
Confidence 357999966665555544344599999999999999854332 36888 7744433
No 72
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=91.72 E-value=0.1 Score=50.22 Aligned_cols=57 Identities=21% Similarity=0.558 Sum_probs=46.5
Q ss_pred CCCcccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCC
Q 024566 17 GGGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCK 76 (265)
Q Consensus 17 ~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~ 76 (265)
-+....+|.||++.+......+....|-|+|...|++.|..+.-++ +...-+||. |.
T Consensus 187 l~~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~-~~~~WrCP~--Cq 243 (950)
T KOG1952|consen 187 LSNRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKT-GQDGWRCPA--CQ 243 (950)
T ss_pred HhcCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhc-cCccccCCc--cc
Confidence 4567899999999998777777777899999999999999984444 345678998 77
No 73
>PHA00626 hypothetical protein
Probab=91.64 E-value=0.14 Score=32.00 Aligned_cols=26 Identities=23% Similarity=0.694 Sum_probs=19.7
Q ss_pred cCCCCCc-eeeecCCCce----eEe-ecCCce
Q 024566 183 RCPACGH-CVERKDGCSV----VMC-RCNTRF 208 (265)
Q Consensus 183 ~CP~C~~-~iek~~GCnh----m~C-~C~~~F 208 (265)
.||+|+. -|.|.+-|+. ..| .||+.|
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~f 33 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYND 33 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCee
Confidence 5999999 4878776554 778 588876
No 74
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.31 E-value=0.14 Score=47.08 Aligned_cols=43 Identities=35% Similarity=0.817 Sum_probs=36.1
Q ss_pred CcccCC--CCCceeee-cCCCceeEeecCCceeeccCccccCCCCC
Q 024566 180 KWARCP--ACGHCVER-KDGCSVVMCRCNTRFCYECGRKISSGCSC 222 (265)
Q Consensus 180 ~~k~CP--~C~~~iek-~~GCnhm~C~C~~~FC~~C~~~~~~g~~~ 222 (265)
..+-|| .|+..+.- .+...-+.|.|++.|||.|+.+||.+..+
T Consensus 157 ~lkwCP~~~C~~av~~~~~~~~~v~C~~g~~FC~~C~~~~H~p~~C 202 (444)
T KOG1815|consen 157 PLKWCPAPGCGLAVKFGSLESVEVDCGCGHEFCFACGEESHSPVSC 202 (444)
T ss_pred ccccCCCCCCCceeeccCCCccceeCCCCchhHhhccccccCCCcc
Confidence 356676 59999987 78899999999999999999999877533
No 75
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.16 E-value=0.19 Score=43.89 Aligned_cols=49 Identities=24% Similarity=0.604 Sum_probs=36.8
Q ss_pred CCcccccccccccccccccccccCCCCCh-hHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCC
Q 024566 18 GGSSFTCEICIEPMAASKKFKNRNLCTHP-FCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLD 80 (265)
Q Consensus 18 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 80 (265)
+....+|.||+.+..+.. +++|.|. .|.+|.+..- +.. =+||. |++.+.
T Consensus 287 ~~~gkeCVIClse~rdt~----vLPCRHLCLCs~Ca~~Lr---~q~-----n~CPI--CRqpi~ 336 (349)
T KOG4265|consen 287 SESGKECVICLSESRDTV----VLPCRHLCLCSGCAKSLR---YQT-----NNCPI--CRQPIE 336 (349)
T ss_pred ccCCCeeEEEecCCcceE----EecchhhehhHhHHHHHH---Hhh-----cCCCc--cccchH
Confidence 355789999999875432 6999996 9999988765 221 16999 998763
No 76
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=91.15 E-value=0.2 Score=28.89 Aligned_cols=32 Identities=28% Similarity=0.682 Sum_probs=23.6
Q ss_pred cccCCcCcccceeccccc-cCCcCeeeCCCccccc
Q 024566 111 SYCPNTNCMALVVNECER-SGKVKKTQCPNCKQWF 144 (265)
Q Consensus 111 ~~Cp~~~C~~~~~~~~~~-~~~~~~~~C~~C~~~~ 144 (265)
+.|| .|+..+...+.. ......+.|+.|+..|
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 499988876652 1236799999998765
No 77
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=91.02 E-value=0.089 Score=47.09 Aligned_cols=53 Identities=28% Similarity=0.575 Sum_probs=40.9
Q ss_pred CCCCcccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCC
Q 024566 16 GGGGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLD 80 (265)
Q Consensus 16 ~~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 80 (265)
..-.+..+|+||+|-.++....+....|.|.|.-.|+..|.. ..||. |+-...
T Consensus 170 ~~~tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~~----------~scpv--cR~~q~ 222 (493)
T KOG0804|consen 170 TGLTELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWWD----------SSCPV--CRYCQS 222 (493)
T ss_pred CCcccCCCcchhHhhcCccccceeeeecccccchHHHhhccc----------CcChh--hhhhcC
Confidence 345678899999999977665554577999999999988764 47888 875443
No 78
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=90.98 E-value=0.32 Score=43.91 Aligned_cols=51 Identities=24% Similarity=0.702 Sum_probs=38.8
Q ss_pred CCcccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCCc
Q 024566 18 GGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDP 81 (265)
Q Consensus 18 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~ 81 (265)
-++...|++|.....++.. ...|||.||..|+..+... ...||. |...+..
T Consensus 18 ~~~~l~C~~C~~vl~~p~~---~~~cgh~fC~~C~~~~~~~--------~~~cp~--~~~~~~~ 68 (391)
T KOG0297|consen 18 LDENLLCPICMSVLRDPVQ---TTTCGHRFCAGCLLESLSN--------HQKCPV--CRQELTQ 68 (391)
T ss_pred CcccccCccccccccCCCC---CCCCCCcccccccchhhcc--------CcCCcc--cccccch
Confidence 4677999999998876643 2589999999999998864 457887 7554433
No 79
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.89 E-value=0.099 Score=46.26 Aligned_cols=50 Identities=26% Similarity=0.672 Sum_probs=38.1
Q ss_pred cccccccccccccccc-ccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCC
Q 024566 21 SFTCEICIEPMAASKK-FKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHN 78 (265)
Q Consensus 21 ~~~C~IC~~~~~~~~~-~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~ 78 (265)
..+|+||++.+.-+.+ ....+.|+|.|=.+|+++|+- ......||. |+..
T Consensus 4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~------k~~~~~cp~--c~~k 54 (463)
T KOG1645|consen 4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLG------KKTKMQCPL--CSGK 54 (463)
T ss_pred cccCceeeeeeeecCceEEeeecccccccHHHHHHHHh------hhhhhhCcc--cCCh
Confidence 4689999998764433 234678999999999999993 235578999 8854
No 80
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=90.39 E-value=0.72 Score=38.43 Aligned_cols=62 Identities=19% Similarity=0.433 Sum_probs=44.9
Q ss_pred CCCCcccccccccccccccccccccCCCC-----ChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCC
Q 024566 16 GGGGSSFTCEICIEPMAASKKFKNRNLCT-----HPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNL 79 (265)
Q Consensus 16 ~~~~~~~~C~IC~~~~~~~~~~~~~~~C~-----H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 79 (265)
.+......|=|||...++...---+-||. |-...+|+..|+..+-..+...++.||+ |....
T Consensus 15 ~~~e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~Q--CqTEY 81 (293)
T KOG3053|consen 15 DNQELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQ--CQTEY 81 (293)
T ss_pred CccccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechh--hcchh
Confidence 34556679999998765543211135664 5699999999999887755678899999 99754
No 81
>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=90.22 E-value=0.14 Score=38.41 Aligned_cols=39 Identities=21% Similarity=0.496 Sum_probs=28.2
Q ss_pred CCcccccccccccccccccccccCCCC------ChhHHHHHHHHHH
Q 024566 18 GGSSFTCEICIEPMAASKKFKNRNLCT------HPFCQDCIARYIQ 57 (265)
Q Consensus 18 ~~~~~~C~IC~~~~~~~~~~~~~~~C~------H~fC~~Cl~~~~~ 57 (265)
.....+|.||++........+ ...|+ |.||.+|+++|-.
T Consensus 23 ~~~~~EC~IC~~~I~~~~GvV-~vt~~g~lnLEkmfc~~C~~rw~~ 67 (134)
T PF05883_consen 23 PRCTVECQICFDRIDNNDGVV-YVTDGGTLNLEKMFCADCDKRWRR 67 (134)
T ss_pred cccCeeehhhhhhhhcCCCEE-EEecCCeehHHHHHHHHHHHHHHh
Confidence 345889999999997622222 35554 7899999999943
No 82
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=90.15 E-value=0.22 Score=30.84 Aligned_cols=27 Identities=26% Similarity=0.555 Sum_probs=19.9
Q ss_pred CcccCCCCCc-eeeecCCCceeEe-ecCCce
Q 024566 180 KWARCPACGH-CVERKDGCSVVMC-RCNTRF 208 (265)
Q Consensus 180 ~~k~CP~C~~-~iek~~GCnhm~C-~C~~~F 208 (265)
.-+.||+|+. .+.... +.++| +||+.+
T Consensus 19 ~~~fCP~Cg~~~m~~~~--~r~~C~~Cgyt~ 47 (50)
T PRK00432 19 KNKFCPRCGSGFMAEHL--DRWHCGKCGYTE 47 (50)
T ss_pred ccCcCcCCCcchheccC--CcEECCCcCCEE
Confidence 3468999998 444444 78999 799875
No 83
>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=89.99 E-value=0.65 Score=39.41 Aligned_cols=53 Identities=23% Similarity=0.476 Sum_probs=36.8
Q ss_pred cccccccccc-ccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCCccCc
Q 024566 23 TCEICIEPMA-ASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFAC 84 (265)
Q Consensus 23 ~C~IC~~~~~-~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i 84 (265)
.|++|-.+.. ++..+..+-+|+|..|.+|+...+. ..+-.||. |..++-..-+
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~-------~g~~~Cpe--C~~iLRk~nf 55 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFS-------LGPAQCPE--CMVILRKNNF 55 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHh-------cCCCCCCc--ccchhhhccc
Confidence 4888876543 3333333458999999999998885 34557995 9987755433
No 84
>PHA03096 p28-like protein; Provisional
Probab=89.76 E-value=0.23 Score=42.59 Aligned_cols=40 Identities=25% Similarity=0.430 Sum_probs=30.5
Q ss_pred ccccccccccccc---c-cccccCCCCChhHHHHHHHHHHHHhh
Q 024566 22 FTCEICIEPMAAS---K-KFKNRNLCTHPFCQDCIARYIQVKVQ 61 (265)
Q Consensus 22 ~~C~IC~~~~~~~---~-~~~~~~~C~H~fC~~Cl~~~~~~~i~ 61 (265)
..|.||++..... + .|-.+..|.|.||..|++.|..+...
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 7899999876531 2 23334569999999999999998764
No 85
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=89.73 E-value=0.62 Score=39.64 Aligned_cols=50 Identities=28% Similarity=0.497 Sum_probs=39.3
Q ss_pred CCcccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCC
Q 024566 18 GGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKH 77 (265)
Q Consensus 18 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~ 77 (265)
......|+||.+...........++|+|..-..|++.++-. . .+||. |..
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 44555699999988776666667899999999999988751 2 68999 876
No 86
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=89.29 E-value=0.3 Score=41.54 Aligned_cols=64 Identities=23% Similarity=0.499 Sum_probs=47.0
Q ss_pred CCCCcccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhC-------C--------CCCcccCCCCCCCCCCC
Q 024566 16 GGGGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQD-------D--------NTAKIDCPGLDCKHNLD 80 (265)
Q Consensus 16 ~~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~-------~--------~~~~i~CP~~~C~~~l~ 80 (265)
.++.+...|.||+--|.+...|. ...|.|.|...||.+|++....+ . ....-.||. |...|.
T Consensus 110 ~nn~p~gqCvICLygfa~~~~ft-~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpV--cre~i~ 186 (368)
T KOG4445|consen 110 ENNHPNGQCVICLYGFASSPAFT-VTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPV--CRERIK 186 (368)
T ss_pred cCCCCCCceEEEEEeecCCCcee-eehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhH--hhhhcc
Confidence 45677889999998887766654 79999999999999999875431 0 112234999 987665
Q ss_pred cc
Q 024566 81 PF 82 (265)
Q Consensus 81 ~~ 82 (265)
++
T Consensus 187 ~e 188 (368)
T KOG4445|consen 187 IE 188 (368)
T ss_pred cc
Confidence 44
No 87
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=89.07 E-value=0.43 Score=27.28 Aligned_cols=32 Identities=34% Similarity=0.675 Sum_probs=23.0
Q ss_pred cccCCcCcccceeccccc-cCCcCeeeCCCccccc
Q 024566 111 SYCPNTNCMALVVNECER-SGKVKKTQCPNCKQWF 144 (265)
Q Consensus 111 ~~Cp~~~C~~~~~~~~~~-~~~~~~~~C~~C~~~~ 144 (265)
+.|| .|+..+..++.. ..+...++|+.|+..|
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 499888766542 2346789999998765
No 88
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=88.99 E-value=0.44 Score=28.84 Aligned_cols=29 Identities=31% Similarity=0.670 Sum_probs=18.9
Q ss_pred ccCCCCCceeeecCCCceeEe-ecCCceee
Q 024566 182 ARCPACGHCVERKDGCSVVMC-RCNTRFCY 210 (265)
Q Consensus 182 k~CP~C~~~iek~~GCnhm~C-~C~~~FC~ 210 (265)
-+||+|+..++-+.+=..++| .||..+=+
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~ 33 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGYRILF 33 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCCeEEE
Confidence 368888887766654446777 47766543
No 89
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=88.58 E-value=0.36 Score=27.24 Aligned_cols=31 Identities=19% Similarity=0.597 Sum_probs=16.1
Q ss_pred cccCCcCcccceeccccccCCcCeeeCCCcccc
Q 024566 111 SYCPNTNCMALVVNECERSGKVKKTQCPNCKQW 143 (265)
Q Consensus 111 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 143 (265)
.+|| .|+..+.......+...+..|+.|+..
T Consensus 1 kfC~--~CG~~l~~~ip~gd~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 1 KFCP--QCGGPLERRIPEGDDRERLVCPACGFI 31 (34)
T ss_dssp -B-T--TT--B-EEE--TT-SS-EEEETTTTEE
T ss_pred Cccc--cccChhhhhcCCCCCccceECCCCCCE
Confidence 4788 599887654433344789999999864
No 90
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=88.48 E-value=0.18 Score=44.48 Aligned_cols=48 Identities=29% Similarity=0.653 Sum_probs=34.7
Q ss_pred CCcccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCC
Q 024566 18 GGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKH 77 (265)
Q Consensus 18 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~ 77 (265)
.+....|-||-|...+.. +.+|||..|..|+..|-.+.- .-.||. |+-
T Consensus 366 gsTFeLCKICaendKdvk----IEPCGHLlCt~CLa~WQ~sd~------gq~CPF--CRc 413 (563)
T KOG1785|consen 366 GSTFELCKICAENDKDVK----IEPCGHLLCTSCLAAWQDSDE------GQTCPF--CRC 413 (563)
T ss_pred cchHHHHHHhhccCCCcc----cccccchHHHHHHHhhcccCC------CCCCCc--eee
Confidence 355678999998765433 589999999999998864321 236888 653
No 91
>PF12773 DZR: Double zinc ribbon
Probab=88.46 E-value=0.39 Score=29.50 Aligned_cols=15 Identities=27% Similarity=0.496 Sum_probs=10.4
Q ss_pred CCcccCCCCCceeee
Q 024566 179 MKWARCPACGHCVER 193 (265)
Q Consensus 179 ~~~k~CP~C~~~iek 193 (265)
...+.||+|+..+..
T Consensus 27 ~~~~~C~~Cg~~~~~ 41 (50)
T PF12773_consen 27 QSKKICPNCGAENPP 41 (50)
T ss_pred CCCCCCcCCcCCCcC
Confidence 345778888887654
No 92
>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=88.09 E-value=0.22 Score=30.92 Aligned_cols=38 Identities=26% Similarity=0.717 Sum_probs=18.8
Q ss_pred cccceeccccccCCcCeeeCCCcccccccccccccCCC
Q 024566 118 CMALVVNECERSGKVKKTQCPNCKQWFCFQCKLKWHAG 155 (265)
Q Consensus 118 C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~ 155 (265)
|...+..............|++|+..||..|..-.|+.
T Consensus 5 C~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHE~ 42 (51)
T PF07975_consen 5 CQKPFPDGPEKKADSSRYRCPKCKNHFCIDCDVFIHET 42 (51)
T ss_dssp TTEE-TTS-------EEE--TTTT--B-HHHHHTTTTT
T ss_pred CCCCCCCcccccccCCeEECCCCCCccccCcChhhhcc
Confidence 55555443322222478999999999999998877764
No 93
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=88.00 E-value=0.51 Score=30.04 Aligned_cols=33 Identities=27% Similarity=0.713 Sum_probs=21.7
Q ss_pred cccCCcCcccceeccccccCCcCeeeCCCccccc---ccccc
Q 024566 111 SYCPNTNCMALVVNECERSGKVKKTQCPNCKQWF---CFQCK 149 (265)
Q Consensus 111 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~---C~~C~ 149 (265)
..|-+ |+..+..... ...|.||.||... |.+|+
T Consensus 8 ~~CtS--Cg~~i~~~~~----~~~F~CPnCG~~~I~RC~~CR 43 (59)
T PRK14890 8 PKCTS--CGIEIAPREK----AVKFLCPNCGEVIIYRCEKCR 43 (59)
T ss_pred ccccC--CCCcccCCCc----cCEeeCCCCCCeeEeechhHH
Confidence 34553 7777755443 5799999999874 44443
No 94
>PLN03086 PRLI-interacting factor K; Provisional
Probab=87.96 E-value=0.68 Score=43.50 Aligned_cols=59 Identities=20% Similarity=0.449 Sum_probs=37.2
Q ss_pred CCcccCCCCCCCCCCCccCccCCCChhHHHHHHHHHHHHhhcCCCccccCCcCcccceeccccccCCcCeeeCCCccccc
Q 024566 65 TAKIDCPGLDCKHNLDPFACEPVIPASLFSKWCDVLCEDYVLGFERSYCPNTNCMALVVNECERSGKVKKTQCPNCKQWF 144 (265)
Q Consensus 65 ~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 144 (265)
...+.||. |...++...+. .-.. .=....+.||..+|+..+..... ...+.|+.|+..|
T Consensus 405 ~~~V~C~N--C~~~i~l~~l~---------lHe~------~C~r~~V~Cp~~~Cg~v~~r~el----~~H~~C~~Cgk~f 463 (567)
T PLN03086 405 VDTVECRN--CKHYIPSRSIA---------LHEA------YCSRHNVVCPHDGCGIVLRVEEA----KNHVHCEKCGQAF 463 (567)
T ss_pred CCeEECCC--CCCccchhHHH---------HHHh------hCCCcceeCCcccccceeecccc----ccCccCCCCCCcc
Confidence 34578988 88776543221 1110 11134577998789999866555 4567899998776
No 95
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=87.83 E-value=0.29 Score=46.92 Aligned_cols=10 Identities=30% Similarity=0.906 Sum_probs=8.3
Q ss_pred CceeeccCcc
Q 024566 206 TRFCYECGRK 215 (265)
Q Consensus 206 ~~FC~~C~~~ 215 (265)
..||-.||.+
T Consensus 41 ~~fC~~CG~~ 50 (645)
T PRK14559 41 EAHCPNCGAE 50 (645)
T ss_pred cccccccCCc
Confidence 4599999988
No 96
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=87.07 E-value=0.91 Score=39.49 Aligned_cols=69 Identities=20% Similarity=0.532 Sum_probs=44.8
Q ss_pred CCcccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCCccCccCCCChhHHHHHH
Q 024566 18 GGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFACEPVIPASLFSKWC 97 (265)
Q Consensus 18 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~ 97 (265)
+.+...|.||.+... +...++|+|..|.-|-.+.-.-- ..-.||. |+.....-.+..-.+.++-++|.
T Consensus 58 DEen~~C~ICA~~~T----Ys~~~PC~H~~CH~Ca~RlRALY------~~K~C~~--CrTE~e~V~fT~~~~~DI~D~~~ 125 (493)
T COG5236 58 DEENMNCQICAGSTT----YSARYPCGHQICHACAVRLRALY------MQKGCPL--CRTETEAVVFTASSPADITDRRQ 125 (493)
T ss_pred ccccceeEEecCCce----EEEeccCCchHHHHHHHHHHHHH------hccCCCc--cccccceEEEecCCCCcchhHhh
Confidence 455688999998774 33469999999999976643322 2346888 98765544444444445545444
Q ss_pred H
Q 024566 98 D 98 (265)
Q Consensus 98 ~ 98 (265)
.
T Consensus 126 ~ 126 (493)
T COG5236 126 W 126 (493)
T ss_pred h
Confidence 3
No 97
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=86.35 E-value=0.19 Score=33.63 Aligned_cols=52 Identities=25% Similarity=0.645 Sum_probs=35.0
Q ss_pred ccccccccccccc--------cccccc-CCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCC
Q 024566 22 FTCEICIEPMAAS--------KKFKNR-NLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLD 80 (265)
Q Consensus 22 ~~C~IC~~~~~~~--------~~~~~~-~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 80 (265)
.+|.||..+|+.. +..+.+ -.|.|.|..-|+.+++...-++ -.||. |++.+.
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 3899999887521 111111 1378999999999999865544 37998 887653
No 98
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=86.25 E-value=0.65 Score=29.54 Aligned_cols=32 Identities=25% Similarity=0.620 Sum_probs=21.4
Q ss_pred cccCCcCcccceeccccccCCcCeeeCCCccccccccc
Q 024566 111 SYCPNTNCMALVVNECERSGKVKKTQCPNCKQWFCFQC 148 (265)
Q Consensus 111 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C 148 (265)
..|-+ |+..+.+... ...+.||.||...=.+|
T Consensus 10 ~~CtS--Cg~~i~p~e~----~v~F~CPnCGe~~I~Rc 41 (61)
T COG2888 10 PVCTS--CGREIAPGET----AVKFPCPNCGEVEIYRC 41 (61)
T ss_pred ceecc--CCCEeccCCc----eeEeeCCCCCceeeehh
Confidence 45653 7877755544 57899999996554444
No 99
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=85.67 E-value=0.58 Score=28.56 Aligned_cols=27 Identities=33% Similarity=0.576 Sum_probs=19.6
Q ss_pred CcccCCCCCceeeecCCCceeEe-ecCC
Q 024566 180 KWARCPACGHCVERKDGCSVVMC-RCNT 206 (265)
Q Consensus 180 ~~k~CP~C~~~iek~~GCnhm~C-~C~~ 206 (265)
.-+.||+|+--+.-..-=+...| +||+
T Consensus 18 k~~~CPrCG~gvfmA~H~dR~~CGkCgy 45 (51)
T COG1998 18 KNRFCPRCGPGVFMADHKDRWACGKCGY 45 (51)
T ss_pred ccccCCCCCCcchhhhcCceeEeccccc
Confidence 34789999976665554557888 7886
No 100
>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=85.58 E-value=1.1 Score=24.69 Aligned_cols=27 Identities=22% Similarity=0.484 Sum_probs=16.1
Q ss_pred cccCCCCCceeeecCCCceeEe-ecCCc
Q 024566 181 WARCPACGHCVERKDGCSVVMC-RCNTR 207 (265)
Q Consensus 181 ~k~CP~C~~~iek~~GCnhm~C-~C~~~ 207 (265)
.+-||.|+.+.+...+=-.|.| .|+.+
T Consensus 3 ~rfC~~CG~~t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 3 HRFCGRCGAPTKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp TSB-TTT--BEEE-SSSS-EEESSSS-E
T ss_pred CcccCcCCccccCCCCcCEeECCCCcCE
Confidence 4678888888888877667888 58765
No 101
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=85.21 E-value=0.46 Score=28.20 Aligned_cols=26 Identities=31% Similarity=0.822 Sum_probs=19.8
Q ss_pred CCcccCCCCCceeeecCCCceeEee---cCCce
Q 024566 179 MKWARCPACGHCVERKDGCSVVMCR---CNTRF 208 (265)
Q Consensus 179 ~~~k~CP~C~~~iek~~GCnhm~C~---C~~~F 208 (265)
..+|+||+|+..- |+.-+.|+ |++.|
T Consensus 9 RGirkCp~CGt~N----G~R~~~CKN~~C~~~~ 37 (44)
T PF14952_consen 9 RGIRKCPKCGTYN----GTRGLSCKNKSCPQVF 37 (44)
T ss_pred hccccCCcCcCcc----CcccccccCCccchhh
Confidence 4689999999876 77777773 76654
No 102
>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=85.14 E-value=0.61 Score=26.50 Aligned_cols=28 Identities=25% Similarity=0.731 Sum_probs=18.7
Q ss_pred cccCCcCcccceeccccccCCcCeeeCCCcccc
Q 024566 111 SYCPNTNCMALVVNECERSGKVKKTQCPNCKQW 143 (265)
Q Consensus 111 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 143 (265)
++|| +|++.+.+..... ..+.|..|++.
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 5788 6999998877643 22278888764
No 103
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=84.86 E-value=1.4 Score=33.95 Aligned_cols=63 Identities=17% Similarity=0.378 Sum_probs=41.0
Q ss_pred CcccCCCCCceeeec---CCC----ceeEeecCCceeeccCccccCCCCCCCcccchhhhHHHHHHHHHHHHHHhhhhhh
Q 024566 180 KWARCPACGHCVERK---DGC----SVVMCRCNTRFCYECGRKISSGCSCQTIGFCQLTILTIAMMVIFHVIVLAGMKIS 252 (265)
Q Consensus 180 ~~k~CP~C~~~iek~---~GC----nhm~C~C~~~FC~~C~~~~~~g~~~~~~~~C~~~~~~~~~~~~~~~~~~~~~~~~ 252 (265)
.+..||+|+.+|.-. +|= -|.. --.||+.||++ |.|+...+-..+.++..-+.++
T Consensus 38 tI~~Cp~C~~~IrG~y~v~gv~~~g~~~~---~PsYC~~CGkp---------------yPWt~~~L~aa~el~ee~eeLs 99 (158)
T PF10083_consen 38 TITSCPNCSTPIRGDYHVEGVFGLGGHYE---APSYCHNCGKP---------------YPWTENALEAANELIEEDEELS 99 (158)
T ss_pred HHHHCcCCCCCCCCceecCCeeeeCCCCC---CChhHHhCCCC---------------CchHHHHHHHHHHHHHHhhcCC
Confidence 457899999999733 110 0000 23466677666 4567777777777777777777
Q ss_pred hhhhhhhh
Q 024566 253 KYEKNVLA 260 (265)
Q Consensus 253 ~~~~~~~~ 260 (265)
-.|++.|+
T Consensus 100 ~deke~~~ 107 (158)
T PF10083_consen 100 PDEKEQFK 107 (158)
T ss_pred HHHHHHHH
Confidence 77777664
No 104
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=84.51 E-value=0.61 Score=45.85 Aligned_cols=53 Identities=17% Similarity=0.594 Sum_probs=37.3
Q ss_pred ccccccccccccccc-cccc--ccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCC
Q 024566 20 SSFTCEICIEPMAAS-KKFK--NRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLD 80 (265)
Q Consensus 20 ~~~~C~IC~~~~~~~-~~~~--~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 80 (265)
...+|+|||.-.... ..++ ....|.|.|...|+-+|+.+.- .-+||. |+..++
T Consensus 1468 G~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~------~s~CPl--CRseit 1523 (1525)
T COG5219 1468 GHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSA------RSNCPL--CRSEIT 1523 (1525)
T ss_pred CcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcC------CCCCCc--cccccc
Confidence 456899999765411 1111 1355899999999999998643 348999 987664
No 105
>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=84.48 E-value=0.95 Score=25.98 Aligned_cols=32 Identities=22% Similarity=0.452 Sum_probs=21.7
Q ss_pred cccCCcCcccceecccccc-CCcCeeeCCCccccc
Q 024566 111 SYCPNTNCMALVVNECERS-GKVKKTQCPNCKQWF 144 (265)
Q Consensus 111 ~~Cp~~~C~~~~~~~~~~~-~~~~~~~C~~C~~~~ 144 (265)
+.|| .|+..+...+... .....+.|+.|+..|
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 5998877665322 224589999998764
No 106
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=84.15 E-value=0.34 Score=41.16 Aligned_cols=47 Identities=26% Similarity=0.490 Sum_probs=35.4
Q ss_pred CcccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCC
Q 024566 19 GSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNL 79 (265)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 79 (265)
.-.+-|.||-.++..+. ...|+|.||..|....++ ..-+|+. |.+.+
T Consensus 239 ~~Pf~c~icr~~f~~pV----vt~c~h~fc~~ca~~~~q--------k~~~c~v--C~~~t 285 (313)
T KOG1813|consen 239 LLPFKCFICRKYFYRPV----VTKCGHYFCEVCALKPYQ--------KGEKCYV--CSQQT 285 (313)
T ss_pred cCCccccccccccccch----hhcCCceeehhhhccccc--------cCCccee--ccccc
Confidence 33567999999997664 489999999999776654 2247887 88654
No 107
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=83.37 E-value=2.1 Score=32.08 Aligned_cols=55 Identities=25% Similarity=0.577 Sum_probs=40.7
Q ss_pred Ccccccccccccccccccccc-cCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCCc
Q 024566 19 GSSFTCEICIEPMAASKKFKN-RNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDP 81 (265)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~~~~-~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~ 81 (265)
....+|.||.|...+. .|.. -.-||=.+|..|....|+..- ....||. |+..+..
T Consensus 78 ~~lYeCnIC~etS~ee-~FLKPneCCgY~iCn~Cya~LWK~~~-----~ypvCPv--CkTSFKs 133 (140)
T PF05290_consen 78 PKLYECNICKETSAEE-RFLKPNECCGYSICNACYANLWKFCN-----LYPVCPV--CKTSFKS 133 (140)
T ss_pred CCceeccCcccccchh-hcCCcccccchHHHHHHHHHHHHHcc-----cCCCCCc--ccccccc
Confidence 4778999999987543 3422 122899999999999998653 4568999 9976643
No 108
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=82.86 E-value=0.58 Score=41.37 Aligned_cols=51 Identities=22% Similarity=0.619 Sum_probs=38.8
Q ss_pred CcccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCC
Q 024566 19 GSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKH 77 (265)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~ 77 (265)
.....|..|-+.+.....-...++|.|.|...|+..+++ +..+-.||. |+.
T Consensus 363 e~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~------~n~~rsCP~--Crk 413 (518)
T KOG1941|consen 363 ETELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILE------NNGTRSCPN--CRK 413 (518)
T ss_pred HHhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHH------hCCCCCCcc--HHH
Confidence 446789999998754333334699999999999999995 235568998 884
No 109
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=82.77 E-value=1.2 Score=27.42 Aligned_cols=28 Identities=18% Similarity=0.674 Sum_probs=19.5
Q ss_pred ccCCcCcccceeccccccCCcCeeeCCCcccc
Q 024566 112 YCPNTNCMALVVNECERSGKVKKTQCPNCKQW 143 (265)
Q Consensus 112 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 143 (265)
+|| .|+..+...... ....+.|+.|++.
T Consensus 2 FCp--~Cg~~l~~~~~~--~~~~~vC~~Cg~~ 29 (52)
T smart00661 2 FCP--KCGNMLIPKEGK--EKRRFVCRKCGYE 29 (52)
T ss_pred CCC--CCCCccccccCC--CCCEEECCcCCCe
Confidence 688 599988766442 1247889988853
No 110
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=82.54 E-value=1.1 Score=39.17 Aligned_cols=49 Identities=22% Similarity=0.417 Sum_probs=34.9
Q ss_pred CCcccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCC
Q 024566 18 GGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLD 80 (265)
Q Consensus 18 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 80 (265)
+.+...|+||+-.-. ... +.+|+|.-|..|+.+|+-. .-.|-. |+..+.
T Consensus 419 ~sEd~lCpICyA~pi-~Av---f~PC~H~SC~~CI~qHlmN--------~k~CFf--CktTv~ 467 (489)
T KOG4692|consen 419 DSEDNLCPICYAGPI-NAV---FAPCSHRSCYGCITQHLMN--------CKRCFF--CKTTVI 467 (489)
T ss_pred CcccccCcceecccc-hhh---ccCCCCchHHHHHHHHHhc--------CCeeeE--ecceee
Confidence 366789999997542 222 4899999999999988752 225666 776554
No 111
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=82.31 E-value=0.27 Score=42.44 Aligned_cols=30 Identities=30% Similarity=0.935 Sum_probs=24.4
Q ss_pred CCcccCCCCCceeeec-CCCceeEe-ecCCce
Q 024566 179 MKWARCPACGHCVERK-DGCSVVMC-RCNTRF 208 (265)
Q Consensus 179 ~~~k~CP~C~~~iek~-~GCnhm~C-~C~~~F 208 (265)
..|.+||+|+..|.+. -.=|.+.| +|++||
T Consensus 25 ~~~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 56 (292)
T PRK05654 25 GLWTKCPSCGQVLYRKELEANLNVCPKCGHHM 56 (292)
T ss_pred CCeeECCCccchhhHHHHHhcCCCCCCCCCCe
Confidence 3599999999988754 45577899 699988
No 112
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=82.08 E-value=1.3 Score=39.29 Aligned_cols=60 Identities=18% Similarity=0.366 Sum_probs=41.5
Q ss_pred CcccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCCccCccC
Q 024566 19 GSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFACEP 86 (265)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~ 86 (265)
-+.+.|||=-+...+ ++-+..+.|||.++++=+.+... ++...++||- |......+..++
T Consensus 332 HSvF~CPVlKeqtsd-eNPPm~L~CGHVISkdAlnrLS~-----ng~~sfKCPY--CP~e~~~~~~kq 391 (394)
T KOG2817|consen 332 HSVFICPVLKEQTSD-ENPPMMLICGHVISKDALNRLSK-----NGSQSFKCPY--CPVEQLASDTKQ 391 (394)
T ss_pred cceeecccchhhccC-CCCCeeeeccceecHHHHHHHhh-----CCCeeeeCCC--CCcccCHHhccc
Confidence 456889986655432 22233689999999998877665 3445799999 987766655544
No 113
>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=81.14 E-value=0.84 Score=33.22 Aligned_cols=26 Identities=31% Similarity=0.889 Sum_probs=18.3
Q ss_pred ccCCCCCceeeecCCCceeEe-ecCCce
Q 024566 182 ARCPACGHCVERKDGCSVVMC-RCNTRF 208 (265)
Q Consensus 182 k~CP~C~~~iek~~GCnhm~C-~C~~~F 208 (265)
+.||+|+...---.- +.++| .||+.|
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 668888887653333 77888 687765
No 114
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=79.98 E-value=1.5 Score=29.60 Aligned_cols=55 Identities=22% Similarity=0.342 Sum_probs=20.4
Q ss_pred cccceeccccccCCcCeeeCCCcccccccccccccCCCCCChhHHhchhhchHHHHHHHhcCCcccCCCCCceeeecCCC
Q 024566 118 CMALVVNECERSGKVKKTQCPNCKQWFCFQCKLKWHAGYRCEESRNLRDQNDIVFGQLVERMKWARCPACGHCVERKDGC 197 (265)
Q Consensus 118 C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~d~~~~~~~~~~~~k~CP~C~~~iek~~GC 197 (265)
|+.-+-.... ....+.|..|++-.|..| .+|.. +...+.||.|+.+..+..|+
T Consensus 15 CGD~VGl~~~---Ge~FVAC~eC~fPvCr~C----------yEYEr--------------keg~q~CpqCkt~ykr~kgs 67 (80)
T PF14569_consen 15 CGDDVGLTEN---GEVFVACHECAFPVCRPC----------YEYER--------------KEGNQVCPQCKTRYKRHKGS 67 (80)
T ss_dssp S--B--B-SS---SSB--S-SSS-----HHH----------HHHHH--------------HTS-SB-TTT--B----TT-
T ss_pred ccCccccCCC---CCEEEEEcccCCccchhH----------HHHHh--------------hcCcccccccCCCcccccCC
Confidence 6555544332 258899999999998865 34332 45789999999999887776
Q ss_pred ce
Q 024566 198 SV 199 (265)
Q Consensus 198 nh 199 (265)
..
T Consensus 68 p~ 69 (80)
T PF14569_consen 68 PR 69 (80)
T ss_dssp --
T ss_pred CC
Confidence 43
No 115
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=79.91 E-value=1.1 Score=28.21 Aligned_cols=47 Identities=19% Similarity=0.374 Sum_probs=31.3
Q ss_pred ccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCCccC
Q 024566 21 SFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFA 83 (265)
Q Consensus 21 ~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~ 83 (265)
...|-.|....... .+++|+|.+|..||... ..-.||. |...++...
T Consensus 7 ~~~~~~~~~~~~~~----~~~pCgH~I~~~~f~~~----------rYngCPf--C~~~~~~~~ 53 (55)
T PF14447_consen 7 EQPCVFCGFVGTKG----TVLPCGHLICDNCFPGE----------RYNGCPF--CGTPFEFDD 53 (55)
T ss_pred ceeEEEcccccccc----ccccccceeeccccChh----------hccCCCC--CCCcccCCC
Confidence 44555665543222 36999999999997642 1226999 998887654
No 116
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=79.89 E-value=0.33 Score=41.78 Aligned_cols=29 Identities=21% Similarity=0.605 Sum_probs=23.1
Q ss_pred CcccCCCCCceeeec-CCCceeEe-ecCCce
Q 024566 180 KWARCPACGHCVERK-DGCSVVMC-RCNTRF 208 (265)
Q Consensus 180 ~~k~CP~C~~~iek~-~GCnhm~C-~C~~~F 208 (265)
.|.+||+|+..+.+. -.=|...| .|++||
T Consensus 37 lw~kc~~C~~~~~~~~l~~~~~vcp~c~~h~ 67 (296)
T CHL00174 37 LWVQCENCYGLNYKKFLKSKMNICEQCGYHL 67 (296)
T ss_pred CeeECCCccchhhHHHHHHcCCCCCCCCCCc
Confidence 599999999988754 44677889 698876
No 117
>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=79.80 E-value=0.35 Score=41.57 Aligned_cols=30 Identities=27% Similarity=0.862 Sum_probs=24.0
Q ss_pred CCcccCCCCCceeeec-CCCceeEe-ecCCce
Q 024566 179 MKWARCPACGHCVERK-DGCSVVMC-RCNTRF 208 (265)
Q Consensus 179 ~~~k~CP~C~~~iek~-~GCnhm~C-~C~~~F 208 (265)
..|.+||+|+..|.+. -.=|.+.| .|++||
T Consensus 24 ~~~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 55 (285)
T TIGR00515 24 GVWTKCPKCGQVLYTKELERNLEVCPKCDHHM 55 (285)
T ss_pred CCeeECCCCcchhhHHHHHhhCCCCCCCCCcC
Confidence 3599999999999765 44677899 699875
No 118
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=79.38 E-value=1.6 Score=30.84 Aligned_cols=29 Identities=31% Similarity=0.834 Sum_probs=21.9
Q ss_pred cCCCCCcee--eecCCCceeEe-ecCCceeec
Q 024566 183 RCPACGHCV--ERKDGCSVVMC-RCNTRFCYE 211 (265)
Q Consensus 183 ~CP~C~~~i--ek~~GCnhm~C-~C~~~FC~~ 211 (265)
-||.|+..+ ++.+.||...| .|.|.|=-.
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 599999855 44455999999 599987544
No 119
>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=79.02 E-value=1.8 Score=25.53 Aligned_cols=23 Identities=43% Similarity=1.047 Sum_probs=17.4
Q ss_pred cccCCCCCceeee-cCCCceeEe-ecC
Q 024566 181 WARCPACGHCVER-KDGCSVVMC-RCN 205 (265)
Q Consensus 181 ~k~CP~C~~~iek-~~GCnhm~C-~C~ 205 (265)
...||.|+.++.+ ..| .+.| .|+
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 4789999999998 455 5677 464
No 120
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=78.58 E-value=2.1 Score=31.24 Aligned_cols=42 Identities=21% Similarity=0.533 Sum_probs=28.6
Q ss_pred cccCCcCcccceeccccc----cCCcCeeeCCCcccccccccccccCC
Q 024566 111 SYCPNTNCMALVVNECER----SGKVKKTQCPNCKQWFCFQCKLKWHA 154 (265)
Q Consensus 111 ~~Cp~~~C~~~~~~~~~~----~~~~~~~~C~~C~~~~C~~C~~~~H~ 154 (265)
..|- .|...+...... ........|++|+..||..|..-+|+
T Consensus 56 ~~C~--~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe 101 (112)
T TIGR00622 56 RFCF--GCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHE 101 (112)
T ss_pred Cccc--CcCCCCCCcccccccccccccceeCCCCCCccccccchhhhh
Confidence 4576 487776543210 11245788999999999999887775
No 121
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=77.72 E-value=2.5 Score=40.87 Aligned_cols=19 Identities=11% Similarity=0.293 Sum_probs=10.7
Q ss_pred CCChhHHHHHHHHHHHHhh
Q 024566 43 CTHPFCQDCIARYIQVKVQ 61 (265)
Q Consensus 43 C~H~fC~~Cl~~~~~~~i~ 61 (265)
|+|.+|..||..+....+.
T Consensus 121 ~~~~~CP~Ci~s~~DqL~~ 139 (1134)
T KOG0825|consen 121 HVENQCPNCLKSCNDQLEE 139 (1134)
T ss_pred hhhhhhhHHHHHHHHHhhc
Confidence 5566666666655554443
No 122
>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=77.38 E-value=1.6 Score=23.83 Aligned_cols=25 Identities=32% Similarity=0.943 Sum_probs=12.1
Q ss_pred cCCCCCceeeecCCCceeEe-ecCCce
Q 024566 183 RCPACGHCVERKDGCSVVMC-RCNTRF 208 (265)
Q Consensus 183 ~CP~C~~~iek~~GCnhm~C-~C~~~F 208 (265)
+||.|+.-..-.+|.. |.| .|+++|
T Consensus 4 ~Cp~C~se~~y~D~~~-~vCp~C~~ew 29 (30)
T PF08274_consen 4 KCPLCGSEYTYEDGEL-LVCPECGHEW 29 (30)
T ss_dssp --TTT-----EE-SSS-EEETTTTEEE
T ss_pred CCCCCCCcceeccCCE-EeCCcccccC
Confidence 6899998887777654 667 588765
No 123
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=76.57 E-value=2.1 Score=30.60 Aligned_cols=29 Identities=28% Similarity=0.720 Sum_probs=20.8
Q ss_pred CcccCCCCCcee---eecCCCceeEe-ecCCce
Q 024566 180 KWARCPACGHCV---ERKDGCSVVMC-RCNTRF 208 (265)
Q Consensus 180 ~~k~CP~C~~~i---ek~~GCnhm~C-~C~~~F 208 (265)
..-.||+|+... .+..|=-|+.| .||+.+
T Consensus 20 t~f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y~ 52 (99)
T PRK14892 20 KIFECPRCGKVSISVKIKKNIAIITCGNCGLYT 52 (99)
T ss_pred cEeECCCCCCeEeeeecCCCcceEECCCCCCcc
Confidence 457899999432 33457789999 699874
No 124
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=76.54 E-value=0.74 Score=44.43 Aligned_cols=48 Identities=31% Similarity=0.764 Sum_probs=35.0
Q ss_pred cccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCCcc
Q 024566 22 FTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPF 82 (265)
Q Consensus 22 ~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~ 82 (265)
..|.||.+ ... .+ ...|+|.||.+|+...++..- .-.||. |...+...
T Consensus 455 ~~c~ic~~-~~~--~~--it~c~h~~c~~c~~~~i~~~~------~~~~~~--cr~~l~~~ 502 (674)
T KOG1001|consen 455 HWCHICCD-LDS--FF--ITRCGHDFCVECLKKSIQQSE------NAPCPL--CRNVLKEK 502 (674)
T ss_pred cccccccc-ccc--ce--eecccchHHHHHHHhcccccc------CCCCcH--HHHHHHHH
Confidence 89999999 221 22 589999999999999987432 227887 88665544
No 125
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=76.02 E-value=0.97 Score=38.23 Aligned_cols=32 Identities=28% Similarity=0.841 Sum_probs=26.1
Q ss_pred cCCcccCCCCCceeeec-CCCceeEe-ecCCcee
Q 024566 178 RMKWARCPACGHCVERK-DGCSVVMC-RCNTRFC 209 (265)
Q Consensus 178 ~~~~k~CP~C~~~iek~-~GCnhm~C-~C~~~FC 209 (265)
...|.+||+|+..+-+. -+=|...| +|+++|=
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 45799999999988754 67788899 6998873
No 126
>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=75.25 E-value=2 Score=26.16 Aligned_cols=26 Identities=27% Similarity=0.624 Sum_probs=19.8
Q ss_pred cccCC--CCCceeeecCCCceeEe-ecCC
Q 024566 181 WARCP--ACGHCVERKDGCSVVMC-RCNT 206 (265)
Q Consensus 181 ~k~CP--~C~~~iek~~GCnhm~C-~C~~ 206 (265)
-+.|| .|+.-|.-..--|..+| +|++
T Consensus 18 rk~CP~~~CG~GvFMA~H~dR~~CGKCg~ 46 (47)
T PF01599_consen 18 RKECPSPRCGAGVFMAEHKDRHYCGKCGY 46 (47)
T ss_dssp SEE-TSTTTTSSSEEEE-SSEEEETTTSS
T ss_pred hhcCCCcccCCceEeeecCCCccCCCccc
Confidence 47899 99998877766788999 7885
No 127
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=75.23 E-value=2.5 Score=27.75 Aligned_cols=28 Identities=29% Similarity=0.761 Sum_probs=21.1
Q ss_pred CcccCCCCCceeeecCCCceeEe-ecCCc
Q 024566 180 KWARCPACGHCVERKDGCSVVMC-RCNTR 207 (265)
Q Consensus 180 ~~k~CP~C~~~iek~~GCnhm~C-~C~~~ 207 (265)
..+.||.|+....+...=..++| .||+.
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred CccCccCcccccccccccceEEcCCCCCE
Confidence 45889999999988555556778 47765
No 128
>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=74.83 E-value=2.6 Score=28.00 Aligned_cols=32 Identities=31% Similarity=0.951 Sum_probs=21.2
Q ss_pred cCCCCCceeeecCCCceeEe-ecCCc-----eeeccCccc
Q 024566 183 RCPACGHCVERKDGCSVVMC-RCNTR-----FCYECGRKI 216 (265)
Q Consensus 183 ~CP~C~~~iek~~GCnhm~C-~C~~~-----FC~~C~~~~ 216 (265)
.||.|+..++..+ .+.+| .|+.+ +|-.|+.+.
T Consensus 3 ~CP~C~~~L~~~~--~~~~C~~C~~~~~~~a~CPdC~~~L 40 (70)
T PF07191_consen 3 TCPKCQQELEWQG--GHYHCEACQKDYKKEAFCPDCGQPL 40 (70)
T ss_dssp B-SSS-SBEEEET--TEEEETTT--EEEEEEE-TTT-SB-
T ss_pred cCCCCCCccEEeC--CEEECccccccceecccCCCcccHH
Confidence 6999999999888 78999 69865 688888885
No 129
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=74.70 E-value=5 Score=34.34 Aligned_cols=44 Identities=30% Similarity=0.865 Sum_probs=32.3
Q ss_pred cccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCC
Q 024566 22 FTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKH 77 (265)
Q Consensus 22 ~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~ 77 (265)
+-|+.|---...+.. ...|+|.||.+|+..-+. + ..+.||. |..
T Consensus 275 LkCplc~~Llrnp~k---T~cC~~~fc~eci~~al~----d---sDf~Cpn--C~r 318 (427)
T COG5222 275 LKCPLCHCLLRNPMK---TPCCGHTFCDECIGTALL----D---SDFKCPN--CSR 318 (427)
T ss_pred ccCcchhhhhhCccc---CccccchHHHHHHhhhhh----h---ccccCCC--ccc
Confidence 789999877654432 256999999999876553 2 3468998 875
No 130
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=74.61 E-value=1.8 Score=42.34 Aligned_cols=41 Identities=27% Similarity=0.532 Sum_probs=32.1
Q ss_pred CcccccccccccccccccccccCCCCChhHHHHHHHHHHHHhh
Q 024566 19 GSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQ 61 (265)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~ 61 (265)
.+...|.+|...+. ...|+ +.+|||.|..+|+.+++.....
T Consensus 815 ep~d~C~~C~~~ll-~~pF~-vf~CgH~FH~~Cl~~~v~~~~~ 855 (911)
T KOG2034|consen 815 EPQDSCDHCGRPLL-IKPFY-VFPCGHCFHRDCLIRHVLSLLS 855 (911)
T ss_pred cCccchHHhcchhh-cCcce-eeeccchHHHHHHHHHHHcccc
Confidence 45678999999885 34443 6899999999999998776543
No 131
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=74.39 E-value=3.7 Score=27.86 Aligned_cols=28 Identities=29% Similarity=0.795 Sum_probs=22.0
Q ss_pred CCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCC
Q 024566 42 LCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNL 79 (265)
Q Consensus 42 ~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 79 (265)
.|.|.|..-|+.+|+.+ ++ .||. +++.+
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 48999999999999987 21 5887 66554
No 132
>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=74.14 E-value=2.9 Score=34.97 Aligned_cols=37 Identities=22% Similarity=0.464 Sum_probs=24.6
Q ss_pred CCccccCCcCcccceecccccc----------CCcCeeeCCCccccc
Q 024566 108 FERSYCPNTNCMALVVNECERS----------GKVKKTQCPNCKQWF 144 (265)
Q Consensus 108 ~~~~~Cp~~~C~~~~~~~~~~~----------~~~~~~~C~~C~~~~ 144 (265)
..++.||.|+|.+++....... ....++.|..|...|
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 5678999999999987654411 123467777666544
No 133
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=73.70 E-value=2.7 Score=41.02 Aligned_cols=34 Identities=29% Similarity=0.774 Sum_probs=29.9
Q ss_pred ccCCCCCceeeecCCCceeEe-ecCCc-----eeeccCcc
Q 024566 182 ARCPACGHCVERKDGCSVVMC-RCNTR-----FCYECGRK 215 (265)
Q Consensus 182 k~CP~C~~~iek~~GCnhm~C-~C~~~-----FC~~C~~~ 215 (265)
-+||+|..+..-...=|.|.| .||++ .|..||..
T Consensus 445 ~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 445 AECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred ccCCCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCC
Confidence 479999999887777799999 69988 89999998
No 134
>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=73.69 E-value=2.2 Score=30.63 Aligned_cols=24 Identities=33% Similarity=0.881 Sum_probs=18.5
Q ss_pred ccCCCCCceeeecCCCceeEe-ecCCc
Q 024566 182 ARCPACGHCVERKDGCSVVMC-RCNTR 207 (265)
Q Consensus 182 k~CP~C~~~iek~~GCnhm~C-~C~~~ 207 (265)
+.||+|+.++...+ +.+.| .|++.
T Consensus 1 ~fC~~Cg~~l~~~~--~~~~C~~C~~~ 25 (104)
T TIGR01384 1 KFCPKCGSLMTPKN--GVYVCPSCGYE 25 (104)
T ss_pred CCCcccCcccccCC--CeEECcCCCCc
Confidence 36999999997765 47888 58876
No 135
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=72.81 E-value=3.2 Score=42.46 Aligned_cols=11 Identities=27% Similarity=0.782 Sum_probs=5.5
Q ss_pred cccCCCCCcee
Q 024566 181 WARCPACGHCV 191 (265)
Q Consensus 181 ~k~CP~C~~~i 191 (265)
+..||+|+.++
T Consensus 709 a~~CP~CGtpl 719 (1337)
T PRK14714 709 RVECPRCDVEL 719 (1337)
T ss_pred cccCCCCCCcc
Confidence 33455555544
No 136
>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=72.51 E-value=4.3 Score=21.73 Aligned_cols=20 Identities=35% Similarity=0.919 Sum_probs=12.8
Q ss_pred cCCCCCceeeecCCCceeEe
Q 024566 183 RCPACGHCVERKDGCSVVMC 202 (265)
Q Consensus 183 ~CP~C~~~iek~~GCnhm~C 202 (265)
.||.|+..+.+.+|=-.+.|
T Consensus 1 ~CP~C~s~l~~~~~ev~~~C 20 (28)
T PF03119_consen 1 TCPVCGSKLVREEGEVDIRC 20 (28)
T ss_dssp B-TTT--BEEE-CCTTCEEE
T ss_pred CcCCCCCEeEcCCCCEeEEC
Confidence 49999999999888666666
No 137
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=72.40 E-value=3.7 Score=35.62 Aligned_cols=45 Identities=22% Similarity=0.708 Sum_probs=32.9
Q ss_pred CCcccccccccccccccccccccCCC--CChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCC
Q 024566 18 GGSSFTCEICIEPMAASKKFKNRNLC--THPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLD 80 (265)
Q Consensus 18 ~~~~~~C~IC~~~~~~~~~~~~~~~C--~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 80 (265)
....++|+||++.+.++. ..| ||..|.+|-.. ..-+||. |..+++
T Consensus 45 ~~~lleCPvC~~~l~~Pi-----~QC~nGHlaCssC~~~-----------~~~~CP~--Cr~~~g 91 (299)
T KOG3002|consen 45 DLDLLDCPVCFNPLSPPI-----FQCDNGHLACSSCRTK-----------VSNKCPT--CRLPIG 91 (299)
T ss_pred chhhccCchhhccCcccc-----eecCCCcEehhhhhhh-----------hcccCCc--cccccc
Confidence 456789999999996553 556 89999999641 2236777 776665
No 138
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=71.95 E-value=2.4 Score=25.74 Aligned_cols=34 Identities=24% Similarity=0.627 Sum_probs=22.7
Q ss_pred cccccccccccccccccCCCC--C---hhHHHHHHHHHHHH
Q 024566 24 CEICIEPMAASKKFKNRNLCT--H---PFCQDCIARYIQVK 59 (265)
Q Consensus 24 C~IC~~~~~~~~~~~~~~~C~--H---~fC~~Cl~~~~~~~ 59 (265)
|-||+++......+ ..+|. - ....+||.+|+...
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 67899887654434 35553 3 68899999999973
No 139
>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=71.69 E-value=3.3 Score=24.63 Aligned_cols=42 Identities=24% Similarity=0.702 Sum_probs=20.2
Q ss_pred cccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCC
Q 024566 24 CEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPG 72 (265)
Q Consensus 24 C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~ 72 (265)
|.+|.+-......- ....|+=.+...|++.|+..+ ...+||.
T Consensus 1 C~~C~~iv~~G~~C-~~~~C~~r~H~~C~~~y~r~~------~~~~CP~ 42 (43)
T PF08746_consen 1 CEACKEIVTQGQRC-SNRDCNVRLHDDCFKKYFRHR------SNPKCPN 42 (43)
T ss_dssp -TTT-SB-SSSEE--SS--S--EE-HHHHHHHTTT-------SS-B-TT
T ss_pred CcccchhHeeeccC-CCCccCchHHHHHHHHHHhcC------CCCCCcC
Confidence 56777665444331 123588899999999999743 2227886
No 140
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=71.48 E-value=3 Score=40.12 Aligned_cols=12 Identities=42% Similarity=0.897 Sum_probs=6.4
Q ss_pred CcccCCCCCcee
Q 024566 180 KWARCPACGHCV 191 (265)
Q Consensus 180 ~~k~CP~C~~~i 191 (265)
..+.||+|+..+
T Consensus 40 ~~~fC~~CG~~~ 51 (645)
T PRK14559 40 DEAHCPNCGAET 51 (645)
T ss_pred ccccccccCCcc
Confidence 345555555554
No 141
>PF14149 YhfH: YhfH-like protein
Probab=71.02 E-value=0.37 Score=27.61 Aligned_cols=30 Identities=20% Similarity=0.546 Sum_probs=22.8
Q ss_pred HHHHhcCCcccCCCCCceeeecCCCceeEe
Q 024566 173 GQLVERMKWARCPACGHCVERKDGCSVVMC 202 (265)
Q Consensus 173 ~~~~~~~~~k~CP~C~~~iek~~GCnhm~C 202 (265)
.++.+....|.||.|+..|+--.-|-.++|
T Consensus 5 ~eFfrnLp~K~C~~CG~~i~EQ~E~Y~n~C 34 (37)
T PF14149_consen 5 VEFFRNLPPKKCTECGKEIEEQAECYGNEC 34 (37)
T ss_pred HHHHHhCCCcccHHHHHHHHHHHHHHhCcC
Confidence 456667788999999999886666666666
No 142
>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=70.82 E-value=1.8 Score=26.74 Aligned_cols=25 Identities=28% Similarity=0.752 Sum_probs=11.8
Q ss_pred ccCCCCCceeeecCCCc--eeEe-ecCC
Q 024566 182 ARCPACGHCVERKDGCS--VVMC-RCNT 206 (265)
Q Consensus 182 k~CP~C~~~iek~~GCn--hm~C-~C~~ 206 (265)
.+|++|+.++.+.++=. .|.| +|++
T Consensus 5 iRC~~CnklLa~~g~~~~leIKCpRC~t 32 (51)
T PF10122_consen 5 IRCGHCNKLLAKAGEVIELEIKCPRCKT 32 (51)
T ss_pred eeccchhHHHhhhcCccEEEEECCCCCc
Confidence 34555555555543322 3455 4543
No 143
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=69.96 E-value=4.6 Score=25.36 Aligned_cols=36 Identities=17% Similarity=0.470 Sum_probs=29.0
Q ss_pred CcccccccccccccccccccccCCCCChhHHHHHHH
Q 024566 19 GSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIAR 54 (265)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~ 54 (265)
....-|.+|-+.+.+....+....|+-.+.++||..
T Consensus 3 ~~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~ 38 (54)
T PF14446_consen 3 YEGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK 38 (54)
T ss_pred ccCccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence 345679999999976666666788999999999865
No 144
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=69.46 E-value=1.9 Score=40.66 Aligned_cols=39 Identities=18% Similarity=0.479 Sum_probs=30.8
Q ss_pred CcccccccccccccccccccccCCCCChhHHHHHHHHHH
Q 024566 19 GSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQ 57 (265)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~ 57 (265)
.....|.||+..+.........+.|||.+|.-|+.....
T Consensus 9 ~~~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~lyn 47 (861)
T KOG3161|consen 9 VLLLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLYN 47 (861)
T ss_pred HHHhhchHHHHHHHHHhcCcccccccchHHHHHHHhHhh
Confidence 345789999988866555556789999999999987654
No 145
>PRK00420 hypothetical protein; Validated
Probab=69.46 E-value=3.8 Score=29.98 Aligned_cols=29 Identities=31% Similarity=0.555 Sum_probs=22.2
Q ss_pred CcccCCCCCceeee-cCCCceeEeecCCceeeccCcccc
Q 024566 180 KWARCPACGHCVER-KDGCSVVMCRCNTRFCYECGRKIS 217 (265)
Q Consensus 180 ~~k~CP~C~~~iek-~~GCnhm~C~C~~~FC~~C~~~~~ 217 (265)
....||.|+.++.+ ..| ..||-.||..+.
T Consensus 22 l~~~CP~Cg~pLf~lk~g---------~~~Cp~Cg~~~~ 51 (112)
T PRK00420 22 LSKHCPVCGLPLFELKDG---------EVVCPVHGKVYI 51 (112)
T ss_pred ccCCCCCCCCcceecCCC---------ceECCCCCCeee
Confidence 45899999999997 454 667777777644
No 146
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=69.07 E-value=8.5 Score=29.89 Aligned_cols=53 Identities=17% Similarity=0.354 Sum_probs=36.9
Q ss_pred CcccccccccccccccccccccCCCCC---hhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCCcc
Q 024566 19 GSSFTCEICIEPMAASKKFKNRNLCTH---PFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPF 82 (265)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~~~~~~~C~H---~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~ 82 (265)
.....|=||+++.. ... ....|.. ....+|+++|+... ....|+. |+..+...
T Consensus 6 ~~~~~CRIC~~~~~-~~~--~PC~CkGs~k~VH~sCL~rWi~~s------~~~~Cei--C~~~Y~i~ 61 (162)
T PHA02825 6 LMDKCCWICKDEYD-VVT--NYCNCKNENKIVHKECLEEWINTS------KNKSCKI--CNGPYNIK 61 (162)
T ss_pred CCCCeeEecCCCCC-Ccc--CCcccCCCchHHHHHHHHHHHhcC------CCCcccc--cCCeEEEE
Confidence 45678999998864 222 1234444 67999999999842 4568999 99876554
No 147
>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=68.82 E-value=3.4 Score=23.46 Aligned_cols=26 Identities=27% Similarity=0.598 Sum_probs=22.1
Q ss_pred cCeeeCCCcccccccccccccCCCCC
Q 024566 132 VKKTQCPNCKQWFCFQCKLKWHAGYR 157 (265)
Q Consensus 132 ~~~~~C~~C~~~~C~~C~~~~H~~~~ 157 (265)
...++|..|+..+|..|....|.++.
T Consensus 10 ~~~~fC~~~~~~iC~~C~~~~H~~H~ 35 (39)
T cd00021 10 PLSLFCETDRALLCVDCDLSVHSGHR 35 (39)
T ss_pred ceEEEeCccChhhhhhcChhhcCCCC
Confidence 46899999999999999876687764
No 148
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=68.68 E-value=2.4 Score=33.46 Aligned_cols=31 Identities=26% Similarity=0.721 Sum_probs=21.6
Q ss_pred CCcccccccccccccCCCCCChhHHhchhhchHHHHHHHhcCCcccCCCCCceeee
Q 024566 138 PNCKQWFCFQCKLKWHAGYRCEESRNLRDQNDIVFGQLVERMKWARCPACGHCVER 193 (265)
Q Consensus 138 ~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~d~~~~~~~~~~~~k~CP~C~~~iek 193 (265)
.+||+.||..|-+ +++ ..+.+||-|+..|.+
T Consensus 149 TkCGHvFC~~Cik-----------------------~al--k~~~~CP~C~kkIt~ 179 (187)
T KOG0320|consen 149 TKCGHVFCSQCIK-----------------------DAL--KNTNKCPTCRKKITH 179 (187)
T ss_pred cccchhHHHHHHH-----------------------HHH--HhCCCCCCcccccch
Confidence 3689999988843 222 257899999976653
No 149
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=68.63 E-value=10 Score=25.65 Aligned_cols=52 Identities=25% Similarity=0.605 Sum_probs=21.7
Q ss_pred Ccccccccccccccc---cccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCC
Q 024566 19 GSSFTCEICIEPMAA---SKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNL 79 (265)
Q Consensus 19 ~~~~~C~IC~~~~~~---~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 79 (265)
.....|.||-+++.. .+.|++...|+-..|+.|+..- .++|+ -.||. |+...
T Consensus 7 ~~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYE----rkeg~---q~Cpq--Ckt~y 61 (80)
T PF14569_consen 7 LNGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYE----RKEGN---QVCPQ--CKTRY 61 (80)
T ss_dssp -SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHH----HHTS----SB-TT--T--B-
T ss_pred cCCcccccccCccccCCCCCEEEEEcccCCccchhHHHHH----hhcCc---ccccc--cCCCc
Confidence 456789999998753 3457667789999999997644 34433 36888 88654
No 150
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=68.37 E-value=2.8 Score=41.19 Aligned_cols=26 Identities=38% Similarity=1.200 Sum_probs=22.8
Q ss_pred ccCCCCCceeeecCCCceeEe-ecCCcee
Q 024566 182 ARCPACGHCVERKDGCSVVMC-RCNTRFC 209 (265)
Q Consensus 182 k~CP~C~~~iek~~GCnhm~C-~C~~~FC 209 (265)
..||.|+..+...+||. +| .||+.=|
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 36999999999999998 99 5999765
No 151
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=68.37 E-value=2.9 Score=31.35 Aligned_cols=27 Identities=44% Similarity=0.930 Sum_probs=21.6
Q ss_pred CcccCCCCCceeeecCCCceeEeecCCceeeccCcc
Q 024566 180 KWARCPACGHCVERKDGCSVVMCRCNTRFCYECGRK 215 (265)
Q Consensus 180 ~~k~CP~C~~~iek~~GCnhm~C~C~~~FC~~C~~~ 215 (265)
..+.||.|+.++++.+| .-||-+|+..
T Consensus 27 L~~hCp~Cg~PLF~KdG---------~v~CPvC~~~ 53 (131)
T COG1645 27 LAKHCPKCGTPLFRKDG---------EVFCPVCGYR 53 (131)
T ss_pred HHhhCcccCCcceeeCC---------eEECCCCCce
Confidence 44899999999998776 7788888733
No 152
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=68.32 E-value=1.1 Score=38.67 Aligned_cols=24 Identities=29% Similarity=0.852 Sum_probs=20.4
Q ss_pred cCeeeCCCcccccccccccccCCC
Q 024566 132 VKKTQCPNCKQWFCFQCKLKWHAG 155 (265)
Q Consensus 132 ~~~~~C~~C~~~~C~~C~~~~H~~ 155 (265)
...++|..|+..||..|..-.|..
T Consensus 343 ~~~y~C~~Ck~~FCldCDv~iHes 366 (378)
T KOG2807|consen 343 SGRYRCESCKNVFCLDCDVFIHES 366 (378)
T ss_pred CCcEEchhccceeeccchHHHHhh
Confidence 578999999999999998777653
No 153
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=68.30 E-value=8.5 Score=27.71 Aligned_cols=34 Identities=15% Similarity=0.462 Sum_probs=24.4
Q ss_pred CccccCCcCcccceeccccccCCcCeeeCCCccccc
Q 024566 109 ERSYCPNTNCMALVVNECERSGKVKKTQCPNCKQWF 144 (265)
Q Consensus 109 ~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 144 (265)
..++|+ .|++.+.+..+.+++.....|..|.+.+
T Consensus 3 ~~rfC~--eCNNmLYPkEDked~~L~laCrnCd~ve 36 (113)
T KOG2691|consen 3 GIRFCR--ECNNMLYPKEDKEDRILLLACRNCDYVE 36 (113)
T ss_pred ccchhh--hhhccccccccccccEEEEEecCCcceE
Confidence 356787 6999988877655566777887776543
No 154
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=67.13 E-value=2.8 Score=35.58 Aligned_cols=52 Identities=23% Similarity=0.623 Sum_probs=38.6
Q ss_pred CCcccccccccccccccccccccCCC----CChhHHHHHHHHHHHHhhCCCCCcccCCCC-CCC
Q 024566 18 GGSSFTCEICIEPMAASKKFKNRNLC----THPFCQDCIARYIQVKVQDDNTAKIDCPGL-DCK 76 (265)
Q Consensus 18 ~~~~~~C~IC~~~~~~~~~~~~~~~C----~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~-~C~ 76 (265)
....+.|.+|-|-+.+. + +..| .|.||.-|-+..|+.+-.. ..+.||.. .|.
T Consensus 265 ~~apLcCTLC~ERLEDT--H--FVQCPSVp~HKFCFPCSResIK~Qg~s---gevYCPSGdkCP 321 (352)
T KOG3579|consen 265 PSAPLCCTLCHERLEDT--H--FVQCPSVPSHKFCFPCSRESIKQQGAS---GEVYCPSGDKCP 321 (352)
T ss_pred CCCceeehhhhhhhccC--c--eeecCCCcccceecccCHHHHHhhcCC---CceeCCCCCcCc
Confidence 45569999999988643 2 2566 6999999999999977554 36788853 454
No 155
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=66.75 E-value=1 Score=36.18 Aligned_cols=37 Identities=27% Similarity=0.491 Sum_probs=26.4
Q ss_pred HhcCCcccCCCCCceeeecCCCceeEeecCCceeeccCcccc
Q 024566 176 VERMKWARCPACGHCVERKDGCSVVMCRCNTRFCYECGRKIS 217 (265)
Q Consensus 176 ~~~~~~k~CP~C~~~iek~~GCnhm~C~C~~~FC~~C~~~~~ 217 (265)
+.....-.||-|.-.+.. -+.=.|||.|||.|...|.
T Consensus 13 ~~~~~~~~CpICld~~~d-----PVvT~CGH~FC~~CI~~wl 49 (193)
T PLN03208 13 VDSGGDFDCNICLDQVRD-----PVVTLCGHLFCWPCIHKWT 49 (193)
T ss_pred ccCCCccCCccCCCcCCC-----cEEcCCCchhHHHHHHHHH
Confidence 333456789999886632 1333699999999999874
No 156
>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=66.64 E-value=5.3 Score=24.85 Aligned_cols=27 Identities=26% Similarity=0.503 Sum_probs=16.3
Q ss_pred ccCCCCCceee------ecCCCceeE-e-ecCCce
Q 024566 182 ARCPACGHCVE------RKDGCSVVM-C-RCNTRF 208 (265)
Q Consensus 182 k~CP~C~~~ie------k~~GCnhm~-C-~C~~~F 208 (265)
|+||.|+-.-+ .+.+..++. | .||+..
T Consensus 2 kPCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~~ 36 (53)
T TIGR03655 2 KPCPFCGGADVYLRRGFDPLDLSHYFECSTCGASG 36 (53)
T ss_pred CCCCCCCCcceeeEeccCCCCCEEEEECCCCCCCc
Confidence 79999987555 123455554 5 365553
No 157
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=66.50 E-value=9.2 Score=26.47 Aligned_cols=29 Identities=24% Similarity=0.735 Sum_probs=22.0
Q ss_pred CcccCCCCCceeeecCCCceeEe-ecCCce
Q 024566 180 KWARCPACGHCVERKDGCSVVMC-RCNTRF 208 (265)
Q Consensus 180 ~~k~CP~C~~~iek~~GCnhm~C-~C~~~F 208 (265)
.--.||.|+....|-.+=---.| +||+.|
T Consensus 34 ~~~~Cp~C~~~~VkR~a~GIW~C~kCg~~f 63 (89)
T COG1997 34 AKHVCPFCGRTTVKRIATGIWKCRKCGAKF 63 (89)
T ss_pred cCCcCCCCCCcceeeeccCeEEcCCCCCee
Confidence 45689999999988877666677 466655
No 158
>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=66.42 E-value=4.1 Score=21.96 Aligned_cols=24 Identities=38% Similarity=1.007 Sum_probs=13.6
Q ss_pred ccCCCCCceeeec--CCCceeEe-ecC
Q 024566 182 ARCPACGHCVERK--DGCSVVMC-RCN 205 (265)
Q Consensus 182 k~CP~C~~~iek~--~GCnhm~C-~C~ 205 (265)
++||.|+..|++. +|=+...| +|.
T Consensus 2 ~~C~rC~~~~~~~~~~~r~~~~C~rCq 28 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGINGRSTYLCPRCQ 28 (30)
T ss_dssp SB-TTT--BBEEEEETTEEEEE-TTTC
T ss_pred CcCccCCCcceEeEecCCCCeECcCCc
Confidence 5799999998654 56666666 564
No 159
>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=66.32 E-value=2.5 Score=24.66 Aligned_cols=26 Identities=23% Similarity=0.630 Sum_probs=22.7
Q ss_pred cCeeeCCCcccccccccccccCCCCC
Q 024566 132 VKKTQCPNCKQWFCFQCKLKWHAGYR 157 (265)
Q Consensus 132 ~~~~~C~~C~~~~C~~C~~~~H~~~~ 157 (265)
...++|..|+..+|..|....|.++.
T Consensus 13 ~~~~~C~~C~~~~C~~C~~~~H~~H~ 38 (42)
T PF00643_consen 13 PLSLFCEDCNEPLCSECTVSGHKGHK 38 (42)
T ss_dssp BEEEEETTTTEEEEHHHHHTSTTTSE
T ss_pred ceEEEecCCCCccCccCCCCCCCCCE
Confidence 37899999999999999988898753
No 160
>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=66.04 E-value=5.2 Score=23.69 Aligned_cols=19 Identities=26% Similarity=0.773 Sum_probs=13.4
Q ss_pred CeeeCCCcccccccccccc
Q 024566 133 KKTQCPNCKQWFCFQCKLK 151 (265)
Q Consensus 133 ~~~~C~~C~~~~C~~C~~~ 151 (265)
..+.|+.|+..||...+.+
T Consensus 12 ~~~~C~~C~~~FC~~Hr~~ 30 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLKHRLP 30 (43)
T ss_dssp SHEE-TTTS-EE-TTTHST
T ss_pred CCeECCCCCcccCccccCc
Confidence 4678999999999998764
No 161
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=65.99 E-value=0.84 Score=38.76 Aligned_cols=19 Identities=21% Similarity=0.536 Sum_probs=16.6
Q ss_pred eeEe-ecCCceeeccCcccc
Q 024566 199 VVMC-RCNTRFCYECGRKIS 217 (265)
Q Consensus 199 hm~C-~C~~~FC~~C~~~~~ 217 (265)
|-+| .|||-|||.|...|-
T Consensus 251 ~pSaTpCGHiFCWsCI~~w~ 270 (293)
T KOG0317|consen 251 NPSATPCGHIFCWSCILEWC 270 (293)
T ss_pred CCCcCcCcchHHHHHHHHHH
Confidence 5678 599999999999985
No 162
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=65.90 E-value=1.6 Score=35.87 Aligned_cols=16 Identities=25% Similarity=0.698 Sum_probs=14.2
Q ss_pred cCCceeeccCccccCC
Q 024566 204 CNTRFCYECGRKISSG 219 (265)
Q Consensus 204 C~~~FC~~C~~~~~~g 219 (265)
|||-|||-|+-.|.+.
T Consensus 65 CGHLFCWpClyqWl~~ 80 (230)
T KOG0823|consen 65 CGHLFCWPCLYQWLQT 80 (230)
T ss_pred cccceehHHHHHHHhh
Confidence 9999999999999753
No 163
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=65.65 E-value=5.7 Score=25.81 Aligned_cols=28 Identities=29% Similarity=0.628 Sum_probs=18.2
Q ss_pred CcccCCCCCceeee---cCCCceeEe-ecCCc
Q 024566 180 KWARCPACGHCVER---KDGCSVVMC-RCNTR 207 (265)
Q Consensus 180 ~~k~CP~C~~~iek---~~GCnhm~C-~C~~~ 207 (265)
.+|+||.|+-.+.+ .+|=-...| .|+..
T Consensus 5 ~lKPCPFCG~~~~~v~~~~g~~~v~C~~CgA~ 36 (64)
T PRK09710 5 NVKPCPFCGCPSVTVKAISGYYRAKCNGCESR 36 (64)
T ss_pred cccCCCCCCCceeEEEecCceEEEEcCCCCcC
Confidence 57999999876543 355444556 46664
No 164
>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=65.23 E-value=15 Score=22.03 Aligned_cols=34 Identities=26% Similarity=0.694 Sum_probs=19.6
Q ss_pred HHHHhcCCc---ccCCCCCce-eeecCCCceeEe-ecCC
Q 024566 173 GQLVERMKW---ARCPACGHC-VERKDGCSVVMC-RCNT 206 (265)
Q Consensus 173 ~~~~~~~~~---k~CP~C~~~-iek~~GCnhm~C-~C~~ 206 (265)
.+++....| -.||+|+.. +-+..+=....| .|++
T Consensus 7 ~~~l~~~RW~~g~~CP~Cg~~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 7 REYLEEIRWPDGFVCPHCGSTKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred HHHHHHhcCCCCCCCCCCCCeeeEEeCCCCeEECCCCCC
Confidence 344444445 569999984 333344455666 4665
No 165
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=64.36 E-value=12 Score=29.67 Aligned_cols=63 Identities=19% Similarity=0.433 Sum_probs=40.0
Q ss_pred CCcccccccccccccccc---cccccCCCCChhHHHHHHHHHHHHhhCCCCCcc---cCCCCCCCCCCCcc
Q 024566 18 GGSSFTCEICIEPMAASK---KFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKI---DCPGLDCKHNLDPF 82 (265)
Q Consensus 18 ~~~~~~C~IC~~~~~~~~---~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i---~CP~~~C~~~l~~~ 82 (265)
+.....|.|||..--+.. ..--...|+..|..-|+..|+..-+..++.+.| .||. |..++...
T Consensus 162 dd~~~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPY--CS~PialK 230 (234)
T KOG3268|consen 162 DDELGACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPY--CSDPIALK 230 (234)
T ss_pred chhhhcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCC--CCCcceee
Confidence 455667777775332211 111135699999999999999877765443333 5998 98877543
No 166
>smart00336 BBOX B-Box-type zinc finger.
Probab=63.92 E-value=6.5 Score=22.61 Aligned_cols=26 Identities=23% Similarity=0.514 Sum_probs=21.8
Q ss_pred cCeeeCCCcccccccccccccCCCCC
Q 024566 132 VKKTQCPNCKQWFCFQCKLKWHAGYR 157 (265)
Q Consensus 132 ~~~~~C~~C~~~~C~~C~~~~H~~~~ 157 (265)
...++|..|+..+|..|....|.++.
T Consensus 13 ~~~~~C~~c~~~iC~~C~~~~H~~H~ 38 (42)
T smart00336 13 PAEFFCEECGALLCRTCDEAEHRGHT 38 (42)
T ss_pred ceEEECCCCCcccccccChhhcCCCc
Confidence 46889999999999999977787653
No 167
>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=63.89 E-value=8.2 Score=24.64 Aligned_cols=26 Identities=31% Similarity=0.808 Sum_probs=20.1
Q ss_pred ccCCCCCc----eeeecCCCceeEe-ecCCc
Q 024566 182 ARCPACGH----CVERKDGCSVVMC-RCNTR 207 (265)
Q Consensus 182 k~CP~C~~----~iek~~GCnhm~C-~C~~~ 207 (265)
-.||+|+. .+-+..|=.++.| .|||.
T Consensus 10 A~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~ 40 (59)
T TIGR02443 10 AVCPACSAQDTLAMWKENNIELVECVECGYQ 40 (59)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEeccCCCc
Confidence 46999986 3446677899999 69985
No 168
>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=63.87 E-value=1.8 Score=31.04 Aligned_cols=33 Identities=27% Similarity=0.565 Sum_probs=25.6
Q ss_pred CcccccccccccccccccccccCCCCChhHHHHHH
Q 024566 19 GSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIA 53 (265)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~ 53 (265)
.+...|++|...+.. ..| ...+|||.|+..|++
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 445679999999965 333 478999999999975
No 169
>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=63.24 E-value=7 Score=23.06 Aligned_cols=23 Identities=26% Similarity=0.754 Sum_probs=10.3
Q ss_pred cCCCCCcee-eecCCCceeEe-ecC
Q 024566 183 RCPACGHCV-ERKDGCSVVMC-RCN 205 (265)
Q Consensus 183 ~CP~C~~~i-ek~~GCnhm~C-~C~ 205 (265)
.||+|+..- .-+..=..+.| .||
T Consensus 2 ~Cp~Cg~~~~~~D~~~g~~vC~~CG 26 (43)
T PF08271_consen 2 KCPNCGSKEIVFDPERGELVCPNCG 26 (43)
T ss_dssp SBTTTSSSEEEEETTTTEEEETTT-
T ss_pred CCcCCcCCceEEcCCCCeEECCCCC
Confidence 466666642 33333334455 344
No 170
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=63.08 E-value=6.6 Score=28.80 Aligned_cols=28 Identities=25% Similarity=0.640 Sum_probs=19.7
Q ss_pred cccCCCCCceeee--cCCCceeEe-ecCCce
Q 024566 181 WARCPACGHCVER--KDGCSVVMC-RCNTRF 208 (265)
Q Consensus 181 ~k~CP~C~~~iek--~~GCnhm~C-~C~~~F 208 (265)
.+-||+|+.++.. .++=+-+.| +||+++
T Consensus 2 m~FCp~Cgsll~p~~~~~~~~l~C~kCgye~ 32 (113)
T COG1594 2 MRFCPKCGSLLYPKKDDEGGKLVCRKCGYEE 32 (113)
T ss_pred ccccCCccCeeEEeEcCCCcEEECCCCCcch
Confidence 4679999998865 223338889 588864
No 171
>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=62.81 E-value=8 Score=25.83 Aligned_cols=26 Identities=35% Similarity=0.796 Sum_probs=20.3
Q ss_pred ccCCCCCce----eeecCCCceeEe-ecCCc
Q 024566 182 ARCPACGHC----VERKDGCSVVMC-RCNTR 207 (265)
Q Consensus 182 k~CP~C~~~----iek~~GCnhm~C-~C~~~ 207 (265)
-.||+|+.. +-+..|=.++.| .|||.
T Consensus 9 a~CP~C~~~D~i~~~~e~~ve~vECV~CGy~ 39 (71)
T PF09526_consen 9 AVCPKCQAMDTIMMWRENGVEYVECVECGYT 39 (71)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEecCCCCe
Confidence 469999873 446688999999 69985
No 172
>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=62.19 E-value=9.6 Score=23.95 Aligned_cols=27 Identities=30% Similarity=0.854 Sum_probs=16.3
Q ss_pred ccCCCCCceeeecCCC--ceeEe-ecCCce
Q 024566 182 ARCPACGHCVERKDGC--SVVMC-RCNTRF 208 (265)
Q Consensus 182 k~CP~C~~~iek~~GC--nhm~C-~C~~~F 208 (265)
..||.|+..|+-.+.= -.+.| .||+.|
T Consensus 3 ~~CP~CG~~iev~~~~~GeiV~Cp~CGael 32 (54)
T TIGR01206 3 FECPDCGAEIELENPELGELVICDECGAEL 32 (54)
T ss_pred cCCCCCCCEEecCCCccCCEEeCCCCCCEE
Confidence 3688888877765321 24666 476654
No 173
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=61.64 E-value=10 Score=21.18 Aligned_cols=27 Identities=19% Similarity=0.469 Sum_probs=13.9
Q ss_pred cccCCCCCceeeecCCCceeEe-ecCCc
Q 024566 181 WARCPACGHCVERKDGCSVVMC-RCNTR 207 (265)
Q Consensus 181 ~k~CP~C~~~iek~~GCnhm~C-~C~~~ 207 (265)
.+.|+.|+....-..-=..+.| .||..
T Consensus 3 ~~~C~~C~~~~i~~~~~~~~~C~~Cg~~ 30 (33)
T PF08792_consen 3 LKKCSKCGGNGIVNKEDDYEVCIFCGSS 30 (33)
T ss_pred ceEcCCCCCCeEEEecCCeEEcccCCcE
Confidence 4677777765543222234555 35543
No 174
>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=61.25 E-value=5.4 Score=27.36 Aligned_cols=29 Identities=31% Similarity=0.848 Sum_probs=16.3
Q ss_pred CcccCCCCC------ceeeecCCCceeEe-ecCCce
Q 024566 180 KWARCPACG------HCVERKDGCSVVMC-RCNTRF 208 (265)
Q Consensus 180 ~~k~CP~C~------~~iek~~GCnhm~C-~C~~~F 208 (265)
..-.||.|+ +.|.|..|=-+++| .||..|
T Consensus 21 ~~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~ 56 (81)
T PF05129_consen 21 KVFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESF 56 (81)
T ss_dssp S----TTT--SS-EEEEEETTTTEEEEEESSS--EE
T ss_pred ceEcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeE
Confidence 457899999 23456788888999 597776
No 175
>PLN00209 ribosomal protein S27; Provisional
Probab=61.11 E-value=13 Score=25.66 Aligned_cols=31 Identities=16% Similarity=0.498 Sum_probs=23.1
Q ss_pred cccCCcCcccceeccccccCCcCeeeCCCccccccc
Q 024566 111 SYCPNTNCMALVVNECERSGKVKKTQCPNCKQWFCF 146 (265)
Q Consensus 111 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~ 146 (265)
+.|| +|.+.-..-+- ....+.|..|+..+|.
T Consensus 37 VkCp--~C~n~q~VFSh---A~t~V~C~~Cg~~L~~ 67 (86)
T PLN00209 37 VKCQ--GCFNITTVFSH---SQTVVVCGSCQTVLCQ 67 (86)
T ss_pred EECC--CCCCeeEEEec---CceEEEccccCCEeec
Confidence 7799 69887665443 2578999999988765
No 176
>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=60.73 E-value=5 Score=29.90 Aligned_cols=26 Identities=15% Similarity=0.276 Sum_probs=17.6
Q ss_pred ccCCCCCceeeecCCCceeEe-ecCCce
Q 024566 182 ARCPACGHCVERKDGCSVVMC-RCNTRF 208 (265)
Q Consensus 182 k~CP~C~~~iek~~GCnhm~C-~C~~~F 208 (265)
+.||+|+...---.- +-++| .||+.|
T Consensus 10 r~Cp~cg~kFYDLnk-~p~vcP~cg~~~ 36 (129)
T TIGR02300 10 RICPNTGSKFYDLNR-RPAVSPYTGEQF 36 (129)
T ss_pred ccCCCcCccccccCC-CCccCCCcCCcc
Confidence 679999887653332 67788 577664
No 177
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=60.37 E-value=7.8 Score=28.43 Aligned_cols=31 Identities=23% Similarity=0.484 Sum_probs=22.5
Q ss_pred ccccCCcCcccceeccccccCCcCeeeCCCccccc
Q 024566 110 RSYCPNTNCMALVVNECERSGKVKKTQCPNCKQWF 144 (265)
Q Consensus 110 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 144 (265)
.++|| +|++.+.+..... ...+.|+.|++..
T Consensus 2 m~FCp--~Cgsll~p~~~~~--~~~l~C~kCgye~ 32 (113)
T COG1594 2 MRFCP--KCGSLLYPKKDDE--GGKLVCRKCGYEE 32 (113)
T ss_pred ccccC--CccCeeEEeEcCC--CcEEECCCCCcch
Confidence 36898 6999999866433 3488898888644
No 178
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=60.20 E-value=1.5 Score=37.37 Aligned_cols=28 Identities=25% Similarity=0.536 Sum_probs=21.1
Q ss_pred ccccccccccccccccccccCCCCC-hhHHHHH
Q 024566 21 SFTCEICIEPMAASKKFKNRNLCTH-PFCQDCI 52 (265)
Q Consensus 21 ~~~C~IC~~~~~~~~~~~~~~~C~H-~fC~~Cl 52 (265)
...|.||++.-. +-| +++||| .-|..|-
T Consensus 300 ~~LC~ICmDaP~--DCv--fLeCGHmVtCt~CG 328 (350)
T KOG4275|consen 300 RRLCAICMDAPR--DCV--FLECGHMVTCTKCG 328 (350)
T ss_pred HHHHHHHhcCCc--ceE--EeecCcEEeehhhc
Confidence 678999999643 333 599999 5788883
No 179
>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 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=58.86 E-value=8.1 Score=19.91 Aligned_cols=21 Identities=24% Similarity=0.518 Sum_probs=13.2
Q ss_pred cccceeccccccCCcCeeeCCCccc
Q 024566 118 CMALVVNECERSGKVKKTQCPNCKQ 142 (265)
Q Consensus 118 C~~~~~~~~~~~~~~~~~~C~~C~~ 142 (265)
|+..+..... ...+.||+||.
T Consensus 4 C~~~i~~r~~----~v~f~CPnCG~ 24 (24)
T PF07754_consen 4 CGRPIAPREQ----AVPFPCPNCGF 24 (24)
T ss_pred CCCcccCccc----CceEeCCCCCC
Confidence 5555544332 57889999874
No 181
>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=58.48 E-value=6.3 Score=24.24 Aligned_cols=47 Identities=19% Similarity=0.595 Sum_probs=24.8
Q ss_pred cccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCC
Q 024566 22 FTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKH 77 (265)
Q Consensus 22 ~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~ 77 (265)
+.|+|-+.....+.. ...|.|.-|.| +..|++...+.+ .-+||. |++
T Consensus 3 L~CPls~~~i~~P~R---g~~C~H~~CFD-l~~fl~~~~~~~---~W~CPi--C~~ 49 (50)
T PF02891_consen 3 LRCPLSFQRIRIPVR---GKNCKHLQCFD-LESFLESNQRTP---KWKCPI--CNK 49 (50)
T ss_dssp SB-TTTSSB-SSEEE---ETT--SS--EE-HHHHHHHHHHS------B-TT--T--
T ss_pred eeCCCCCCEEEeCcc---CCcCcccceEC-HHHHHHHhhccC---CeECcC--CcC
Confidence 568888877755543 57899997754 667887777652 378998 865
No 182
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=58.13 E-value=9.3 Score=24.30 Aligned_cols=13 Identities=31% Similarity=0.759 Sum_probs=9.7
Q ss_pred CcccCCCCCceee
Q 024566 180 KWARCPACGHCVE 192 (265)
Q Consensus 180 ~~k~CP~C~~~ie 192 (265)
..|+||.|+....
T Consensus 2 ~LkPCPFCG~~~~ 14 (61)
T PF14354_consen 2 ELKPCPFCGSADV 14 (61)
T ss_pred CCcCCCCCCCcce
Confidence 4689999986443
No 183
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=57.94 E-value=7 Score=22.82 Aligned_cols=12 Identities=42% Similarity=1.077 Sum_probs=8.8
Q ss_pred cCCCCCceeeec
Q 024566 183 RCPACGHCVERK 194 (265)
Q Consensus 183 ~CP~C~~~iek~ 194 (265)
+||+|+..++..
T Consensus 1 ~CP~C~~~l~~~ 12 (41)
T PF13453_consen 1 KCPRCGTELEPV 12 (41)
T ss_pred CcCCCCcccceE
Confidence 588888876644
No 184
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=57.84 E-value=8.3 Score=39.05 Aligned_cols=56 Identities=21% Similarity=0.415 Sum_probs=39.2
Q ss_pred cccceeccccccCCcCeeeCCCcccccccccccccCCCCCChhHHhchhhchHHHHHHHhcCCcccCCCCCceeeecCCC
Q 024566 118 CMALVVNECERSGKVKKTQCPNCKQWFCFQCKLKWHAGYRCEESRNLRDQNDIVFGQLVERMKWARCPACGHCVERKDGC 197 (265)
Q Consensus 118 C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~d~~~~~~~~~~~~k~CP~C~~~iek~~GC 197 (265)
|+.-+-.... ....|.|..|++-.|.-| .+|++ ....+-||.|+.+..+--|+
T Consensus 23 CGD~vg~~~~---Ge~FVAC~eC~FPVCrpC----------YEYEr--------------~eG~q~CPqCktrYkr~kgs 75 (1079)
T PLN02638 23 CGDNVGKTVD---GEPFVACDVCAFPVCRPC----------YEYER--------------KDGNQSCPQCKTKYKRHKGS 75 (1079)
T ss_pred cccccCcCCC---CCEEEEeccCCCccccch----------hhhhh--------------hcCCccCCccCCchhhhcCC
Confidence 6665554433 258899999999999865 44443 34678899999988866665
Q ss_pred cee
Q 024566 198 SVV 200 (265)
Q Consensus 198 nhm 200 (265)
..+
T Consensus 76 prv 78 (1079)
T PLN02638 76 PAI 78 (1079)
T ss_pred CCc
Confidence 544
No 185
>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=57.70 E-value=9.9 Score=31.55 Aligned_cols=54 Identities=17% Similarity=0.411 Sum_probs=38.2
Q ss_pred ccCCCCCCCCC-CCccCccCCCChhHHHHHHHHHHHHhhcCCCccccCCcCcccceec
Q 024566 68 IDCPGLDCKHN-LDPFACEPVIPASLFSKWCDVLCEDYVLGFERSYCPNTNCMALVVN 124 (265)
Q Consensus 68 i~CP~~~C~~~-l~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~ 124 (265)
-+||. |+.- ....+++-+++++-+.+.-+.-....+ ......||.++|+.++..
T Consensus 11 ~~CPv--CksDrYLnPdik~linPECyHrmCESCvdRIF-s~GpAqCP~~gC~kILRK 65 (314)
T COG5220 11 RRCPV--CKSDRYLNPDIKILINPECYHRMCESCVDRIF-SRGPAQCPYKGCGKILRK 65 (314)
T ss_pred ccCCc--cccccccCCCeEEEECHHHHHHHHHHHHHHHh-cCCCCCCCCccHHHHHHH
Confidence 37999 9853 444577888999988877665444333 245578999999987643
No 186
>PHA02862 5L protein; Provisional
Probab=57.61 E-value=15 Score=28.07 Aligned_cols=47 Identities=23% Similarity=0.513 Sum_probs=34.3
Q ss_pred cccccccccccccccccccCCCC-----ChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCCc
Q 024566 22 FTCEICIEPMAASKKFKNRNLCT-----HPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDP 81 (265)
Q Consensus 22 ~~C~IC~~~~~~~~~~~~~~~C~-----H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~ 81 (265)
..|=||+++.++. ..+|. .....+||.+|+.. ..+..||. |+.++..
T Consensus 3 diCWIC~~~~~e~-----~~PC~C~GS~K~VHq~CL~~WIn~------S~k~~CeL--CkteY~I 54 (156)
T PHA02862 3 DICWICNDVCDER-----NNFCGCNEEYKVVHIKCMQLWINY------SKKKECNL--CKTKYNI 54 (156)
T ss_pred CEEEEecCcCCCC-----cccccccCcchhHHHHHHHHHHhc------CCCcCccC--CCCeEEE
Confidence 4689999986432 24553 46899999999953 35679999 9987654
No 187
>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=57.36 E-value=2 Score=28.21 Aligned_cols=37 Identities=16% Similarity=0.471 Sum_probs=18.2
Q ss_pred CCcccccccccccccccccccccCCCCChhHHHHHHH
Q 024566 18 GGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIAR 54 (265)
Q Consensus 18 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~ 54 (265)
+.+...|.+|...|.....-...-.||+.||.+|...
T Consensus 6 d~~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~ 42 (69)
T PF01363_consen 6 DSEASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQ 42 (69)
T ss_dssp GGG-SB-TTT--B-BSSS-EEE-TTT--EEECCCS-E
T ss_pred CCCCCcCcCcCCcCCCceeeEccCCCCCEECCchhCC
Confidence 4567899999999853322223466999999888643
No 188
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=56.48 E-value=20 Score=29.46 Aligned_cols=60 Identities=23% Similarity=0.545 Sum_probs=43.4
Q ss_pred CCcccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCCc
Q 024566 18 GGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDP 81 (265)
Q Consensus 18 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~ 81 (265)
++-.-.|..|-.+....+.. .+.|-|.|.-+|+..+...--.+-.-...+||. |...|-+
T Consensus 47 sDY~pNC~LC~t~La~gdt~--RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~--Cs~eiFP 106 (299)
T KOG3970|consen 47 SDYNPNCRLCNTPLASGDTT--RLVCYHLFHWKCLNERAANLPANTAPAGYQCPC--CSQEIFP 106 (299)
T ss_pred cCCCCCCceeCCccccCcce--eehhhhhHHHHHhhHHHhhCCCcCCCCcccCCC--CCCccCC
Confidence 34456899999988776664 489999999999998876544432223468998 9976543
No 189
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=55.66 E-value=11 Score=31.56 Aligned_cols=37 Identities=30% Similarity=0.834 Sum_probs=27.1
Q ss_pred CCcccCCCCCceee-----ecCCCceeEe-ecCCce-----------eeccCcc
Q 024566 179 MKWARCPACGHCVE-----RKDGCSVVMC-RCNTRF-----------CYECGRK 215 (265)
Q Consensus 179 ~~~k~CP~C~~~ie-----k~~GCnhm~C-~C~~~F-----------C~~C~~~ 215 (265)
+.+-+|-+|+...+ |..|=-...| .|++.| ||.|+.+
T Consensus 130 KeVSRCr~C~~rYDPVP~dkmwG~aef~C~~C~h~F~G~~qm~v~sPCy~C~~~ 183 (278)
T PF15135_consen 130 KEVSRCRKCRKRYDPVPCDKMWGIAEFHCPKCRHNFRGFAQMGVPSPCYGCGNP 183 (278)
T ss_pred cccccccccccccCCCccccccceeeeecccccccchhhhhcCCCCCccCCCCc
Confidence 45667777777653 5577777788 688877 8888887
No 190
>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=55.28 E-value=10 Score=24.73 Aligned_cols=16 Identities=19% Similarity=0.987 Sum_probs=12.3
Q ss_pred hHHHHHHHHHHHHhhC
Q 024566 47 FCQDCIARYIQVKVQD 62 (265)
Q Consensus 47 fC~~Cl~~~~~~~i~~ 62 (265)
||+.||.+|+...-.+
T Consensus 12 FCRNCLskWy~~aA~~ 27 (68)
T PF06844_consen 12 FCRNCLSKWYREAAEE 27 (68)
T ss_dssp --HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHh
Confidence 9999999999988765
No 191
>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=55.16 E-value=8.3 Score=24.02 Aligned_cols=36 Identities=22% Similarity=0.573 Sum_probs=24.9
Q ss_pred cccccccccccccccccccCCCCChhHHHHHHHHHH
Q 024566 22 FTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQ 57 (265)
Q Consensus 22 ~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~ 57 (265)
..|.+|-..+.....-.....||+.||.+|......
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~~ 38 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRIP 38 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCcChHHcCCeee
Confidence 468888877754322223467999999999887654
No 192
>PLN02189 cellulose synthase
Probab=55.03 E-value=13 Score=37.62 Aligned_cols=64 Identities=22% Similarity=0.377 Sum_probs=44.7
Q ss_pred CccccCCcCcccceeccccccCCcCeeeCCCcccccccccccccCCCCCChhHHhchhhchHHHHHHHhcCCcccCCCCC
Q 024566 109 ERSYCPNTNCMALVVNECERSGKVKKTQCPNCKQWFCFQCKLKWHAGYRCEESRNLRDQNDIVFGQLVERMKWARCPACG 188 (265)
Q Consensus 109 ~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~d~~~~~~~~~~~~k~CP~C~ 188 (265)
+...|.- |+..+-.... ....+.|..|++-.|..| .+|.+ +...+.||.|+
T Consensus 33 ~~~~C~i--Cgd~vg~~~~---g~~fvaC~~C~fpvCr~C----------yeyer--------------~eg~q~CpqCk 83 (1040)
T PLN02189 33 DGQVCEI--CGDEIGLTVD---GDLFVACNECGFPVCRPC----------YEYER--------------REGTQNCPQCK 83 (1040)
T ss_pred cCccccc--cccccCcCCC---CCEEEeeccCCCccccch----------hhhhh--------------hcCCccCcccC
Confidence 3346663 7776655433 257899999999999866 34432 35678999999
Q ss_pred ceeeecCCCceeE
Q 024566 189 HCVERKDGCSVVM 201 (265)
Q Consensus 189 ~~iek~~GCnhm~ 201 (265)
....+--|++.+.
T Consensus 84 t~Y~r~kgs~~v~ 96 (1040)
T PLN02189 84 TRYKRLKGSPRVE 96 (1040)
T ss_pred CchhhccCCCCcC
Confidence 9998766766553
No 193
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=54.11 E-value=16 Score=25.13 Aligned_cols=31 Identities=19% Similarity=0.524 Sum_probs=23.3
Q ss_pred cccCCcCcccceeccccccCCcCeeeCCCccccccc
Q 024566 111 SYCPNTNCMALVVNECERSGKVKKTQCPNCKQWFCF 146 (265)
Q Consensus 111 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~ 146 (265)
+.|| +|.+.-..-+- ....+.|..|+..+|.
T Consensus 36 VkCp--~C~n~q~VFSh---A~t~V~C~~Cg~~L~~ 66 (85)
T PTZ00083 36 VKCP--GCSQITTVFSH---AQTVVLCGGCSSQLCQ 66 (85)
T ss_pred EECC--CCCCeeEEEec---CceEEEccccCCEeec
Confidence 6798 69887665443 2578999999988875
No 194
>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=53.25 E-value=8.8 Score=21.75 Aligned_cols=32 Identities=22% Similarity=0.608 Sum_probs=15.8
Q ss_pred hHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCC
Q 024566 47 FCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLD 80 (265)
Q Consensus 47 fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 80 (265)
+|.+|++.|..-.-..-....+.|+. |+-.++
T Consensus 1 lC~~C~~Ey~~p~~RR~~~~~isC~~--CGPr~~ 32 (35)
T PF07503_consen 1 LCDDCLKEYFDPSNRRFHYQFISCTN--CGPRYS 32 (35)
T ss_dssp --HHHHHHHCSTTSTTTT-TT--BTT--CC-SCC
T ss_pred CCHHHHHHHcCCCCCcccCcCccCCC--CCCCEE
Confidence 48888888765332211345688988 885543
No 195
>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=53.16 E-value=9.9 Score=27.45 Aligned_cols=26 Identities=23% Similarity=0.561 Sum_probs=18.3
Q ss_pred ccCCcCcccceeccccccCCcCeeeCCCccccc
Q 024566 112 YCPNTNCMALVVNECERSGKVKKTQCPNCKQWF 144 (265)
Q Consensus 112 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 144 (265)
.|| .|+.-+.+++. ..+.||.|+++|
T Consensus 4 ~CP--~C~seytY~dg-----~~~iCpeC~~EW 29 (109)
T TIGR00686 4 PCP--KCNSEYTYHDG-----TQLICPSCLYEW 29 (109)
T ss_pred cCC--cCCCcceEecC-----CeeECccccccc
Confidence 466 58887777665 568888887644
No 196
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=52.98 E-value=4.8 Score=38.81 Aligned_cols=29 Identities=24% Similarity=0.710 Sum_probs=20.4
Q ss_pred CcccccccccccccCCCCCChhHHhchhhchHHHHHHHhcCCcccCCCCCcee
Q 024566 139 NCKQWFCFQCKLKWHAGYRCEESRNLRDQNDIVFGQLVERMKWARCPACGHCV 191 (265)
Q Consensus 139 ~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~d~~~~~~~~~~~~k~CP~C~~~i 191 (265)
.|++.||..|-.. . .....++||+|+...
T Consensus 660 kC~H~FC~~Cvq~-----------------------r-~etRqRKCP~Cn~aF 688 (698)
T KOG0978|consen 660 KCGHVFCEECVQT-----------------------R-YETRQRKCPKCNAAF 688 (698)
T ss_pred hcchHHHHHHHHH-----------------------H-HHHhcCCCCCCCCCC
Confidence 6788899888431 1 124579999999765
No 197
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=52.43 E-value=12 Score=26.54 Aligned_cols=28 Identities=25% Similarity=0.751 Sum_probs=19.9
Q ss_pred cccCCcCcccceeccccccCCcCeeeCCCccc
Q 024566 111 SYCPNTNCMALVVNECERSGKVKKTQCPNCKQ 142 (265)
Q Consensus 111 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 142 (265)
.+|| .|++.++++.+.. ..++.|..|.+
T Consensus 2 ~FCP--~Cgn~Live~g~~--~~rf~C~tCpY 29 (105)
T KOG2906|consen 2 LFCP--TCGNMLIVESGES--CNRFSCRTCPY 29 (105)
T ss_pred cccC--CCCCEEEEecCCe--EeeEEcCCCCc
Confidence 4788 4999999887632 46677766654
No 198
>PLN02436 cellulose synthase A
Probab=52.38 E-value=12 Score=37.93 Aligned_cols=53 Identities=32% Similarity=0.736 Sum_probs=37.2
Q ss_pred Cccccccccccccc---ccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCC
Q 024566 19 GSSFTCEICIEPMA---ASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLD 80 (265)
Q Consensus 19 ~~~~~C~IC~~~~~---~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 80 (265)
.....|+||-|++. +.+.|++.-.|+-..|+.|. .|- .++|+ -.||. |+....
T Consensus 34 ~~~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cy-eye---r~eg~---~~Cpq--ckt~Y~ 89 (1094)
T PLN02436 34 LSGQTCQICGDEIELTVDGEPFVACNECAFPVCRPCY-EYE---RREGN---QACPQ--CKTRYK 89 (1094)
T ss_pred cCCccccccccccCcCCCCCEEEeeccCCCccccchh-hhh---hhcCC---ccCcc--cCCchh
Confidence 34559999999853 45567777779999999998 332 33332 37998 986553
No 199
>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=51.71 E-value=11 Score=35.24 Aligned_cols=34 Identities=24% Similarity=0.677 Sum_probs=26.6
Q ss_pred ccCCCCCceeeecCCCceeEe-ecCCc-----eeeccCcc
Q 024566 182 ARCPACGHCVERKDGCSVVMC-RCNTR-----FCYECGRK 215 (265)
Q Consensus 182 k~CP~C~~~iek~~GCnhm~C-~C~~~-----FC~~C~~~ 215 (265)
-+||+|..+..-...=|.+.| .||+. .|-.|+..
T Consensus 223 ~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 223 LCCPNCDVSLTYHKKEGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred cCCCCCCCceEEecCCCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 469999988875555668999 69977 68888875
No 200
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=51.23 E-value=11 Score=32.14 Aligned_cols=25 Identities=32% Similarity=0.793 Sum_probs=21.4
Q ss_pred ccCCCCCceeeec--CCCceeEe-ecCC
Q 024566 182 ARCPACGHCVERK--DGCSVVMC-RCNT 206 (265)
Q Consensus 182 k~CP~C~~~iek~--~GCnhm~C-~C~~ 206 (265)
++|+.|+.+|+|. +|-+-..| .|+.
T Consensus 246 epC~~CGt~I~k~~~~gR~t~~CP~CQ~ 273 (273)
T COG0266 246 EPCRRCGTPIEKIKLGGRSTFYCPVCQK 273 (273)
T ss_pred CCCCccCCEeEEEEEcCCcCEeCCCCCC
Confidence 7899999999986 89888888 5863
No 201
>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=50.91 E-value=49 Score=25.76 Aligned_cols=90 Identities=14% Similarity=0.424 Sum_probs=47.5
Q ss_pred cccccccccccccccccc---ccCCCCChhH------HHHHHHHHHHHhhCC-----------------------CCCcc
Q 024566 21 SFTCEICIEPMAASKKFK---NRNLCTHPFC------QDCIARYIQVKVQDD-----------------------NTAKI 68 (265)
Q Consensus 21 ~~~C~IC~~~~~~~~~~~---~~~~C~H~fC------~~Cl~~~~~~~i~~~-----------------------~~~~i 68 (265)
...|+||+|---+.+.+. .--+|.-.+| ..||.+|-....+.. ....+
T Consensus 2 d~~CpICme~PHNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkka~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L 81 (162)
T PF07800_consen 2 DVTCPICMEHPHNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKKAYGKSSSSSSQSSSSAPSDSSSSESSESQEQPEL 81 (162)
T ss_pred CccCceeccCCCceEEEEeccccCCccccccCCccchhHHHHHHHHHhcCCCCccccccccCcCCCcccccccccccccc
Confidence 468999999543322110 0112333333 578888887765421 12357
Q ss_pred cCCCCCCCCCCCccCccCCCChhHHHHHHHHHHHHhhcCCCccccCCcCcccceeccc
Q 024566 69 DCPGLDCKHNLDPFACEPVIPASLFSKWCDVLCEDYVLGFERSYCPNTNCMALVVNEC 126 (265)
Q Consensus 69 ~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~ 126 (265)
.||. |...+..-.+- +...+|. +...+.|+..+|...-.+..
T Consensus 82 ~CPL--CRG~V~GWtvv-----e~AR~~L---------N~K~RsC~~e~C~F~GtY~e 123 (162)
T PF07800_consen 82 ACPL--CRGEVKGWTVV-----EPARRFL---------NAKKRSCSQESCSFSGTYSE 123 (162)
T ss_pred cCcc--ccCceeceEEc-----hHHHHHh---------ccCCccCcccccccccCHHH
Confidence 8888 88665332211 2222222 24457788777776655443
No 202
>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=50.57 E-value=15 Score=31.96 Aligned_cols=53 Identities=19% Similarity=0.394 Sum_probs=31.1
Q ss_pred cccCCcCcccceeccccccCCcCeeeCCCcccccccccccccCCCCCChhHHhchhhchHHHHHHHhcCCcccCCCCCce
Q 024566 111 SYCPNTNCMALVVNECERSGKVKKTQCPNCKQWFCFQCKLKWHAGYRCEESRNLRDQNDIVFGQLVERMKWARCPACGHC 190 (265)
Q Consensus 111 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~d~~~~~~~~~~~~k~CP~C~~~ 190 (265)
..||. |.......+.- ...+. .||+.||..|-.. +. .....+||.|+..
T Consensus 4 ~~CP~--Ck~~~y~np~~---kl~i~--~CGH~~C~sCv~~-----------------------l~-~~~~~~CP~C~~~ 52 (309)
T TIGR00570 4 QGCPR--CKTTKYRNPSL---KLMVN--VCGHTLCESCVDL-----------------------LF-VRGSGSCPECDTP 52 (309)
T ss_pred CCCCc--CCCCCccCccc---ccccC--CCCCcccHHHHHH-----------------------Hh-cCCCCCCCCCCCc
Confidence 35774 76643333220 12233 6899999988431 11 1234589999998
Q ss_pred eeec
Q 024566 191 VERK 194 (265)
Q Consensus 191 iek~ 194 (265)
+.|.
T Consensus 53 lrk~ 56 (309)
T TIGR00570 53 LRKN 56 (309)
T ss_pred cchh
Confidence 8765
No 203
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=50.39 E-value=12 Score=31.16 Aligned_cols=40 Identities=15% Similarity=0.231 Sum_probs=32.7
Q ss_pred CcccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhC
Q 024566 19 GSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQD 62 (265)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~ 62 (265)
.+..-|.+|+.+..++. +.+=||.||++|+..||..+-++
T Consensus 41 K~FdcCsLtLqPc~dPv----it~~GylfdrEaILe~ilaqKke 80 (303)
T KOG3039|consen 41 KPFDCCSLTLQPCRDPV----ITPDGYLFDREAILEYILAQKKE 80 (303)
T ss_pred CCcceeeeecccccCCc----cCCCCeeeeHHHHHHHHHHHHHH
Confidence 45568899999987665 47889999999999999887653
No 204
>PRK10220 hypothetical protein; Provisional
Probab=49.35 E-value=14 Score=26.69 Aligned_cols=26 Identities=27% Similarity=0.634 Sum_probs=18.4
Q ss_pred ccCCcCcccceeccccccCCcCeeeCCCccccc
Q 024566 112 YCPNTNCMALVVNECERSGKVKKTQCPNCKQWF 144 (265)
Q Consensus 112 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 144 (265)
.|| .|+.-+.+++. ..+.||.|+++|
T Consensus 5 ~CP--~C~seytY~d~-----~~~vCpeC~hEW 30 (111)
T PRK10220 5 HCP--KCNSEYTYEDN-----GMYICPECAHEW 30 (111)
T ss_pred cCC--CCCCcceEcCC-----CeEECCcccCcC
Confidence 466 58887777665 568888877654
No 205
>PHA02929 N1R/p28-like protein; Provisional
Probab=49.04 E-value=8 Score=32.37 Aligned_cols=41 Identities=29% Similarity=0.474 Sum_probs=28.8
Q ss_pred cCCcccCCCCCceeeecCCCc---eeEeecCCceeeccCccccC
Q 024566 178 RMKWARCPACGHCVERKDGCS---VVMCRCNTRFCYECGRKISS 218 (265)
Q Consensus 178 ~~~~k~CP~C~~~iek~~GCn---hm~C~C~~~FC~~C~~~~~~ 218 (265)
......||=|.-.+.....-+ -+.-.|+|.||..|...|..
T Consensus 171 ~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~ 214 (238)
T PHA02929 171 RSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKK 214 (238)
T ss_pred CCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHh
Confidence 344578999999876544222 13336999999999999864
No 206
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=49.01 E-value=15 Score=23.01 Aligned_cols=22 Identities=18% Similarity=0.498 Sum_probs=15.9
Q ss_pred HHHHHHHhcCCcccCCCCCcee
Q 024566 170 IVFGQLVERMKWARCPACGHCV 191 (265)
Q Consensus 170 ~~~~~~~~~~~~k~CP~C~~~i 191 (265)
+.+.++........||+|+..+
T Consensus 35 ~~~~~i~~~~~i~~Cp~CgRiL 56 (56)
T PF02591_consen 35 QELNEIRKGDEIVFCPNCGRIL 56 (56)
T ss_pred HHHHHHHcCCCeEECcCCCccC
Confidence 3455665666789999999763
No 207
>PRK11827 hypothetical protein; Provisional
Probab=48.35 E-value=17 Score=23.43 Aligned_cols=28 Identities=18% Similarity=0.350 Sum_probs=20.4
Q ss_pred CcccCCCCCceeeecCCCceeEe-ecCCc
Q 024566 180 KWARCPACGHCVERKDGCSVVMC-RCNTR 207 (265)
Q Consensus 180 ~~k~CP~C~~~iek~~GCnhm~C-~C~~~ 207 (265)
.+-.||.|+-.++-+.+=+...| .|+-.
T Consensus 7 eILaCP~ckg~L~~~~~~~~Lic~~~~la 35 (60)
T PRK11827 7 EIIACPVCNGKLWYNQEKQELICKLDNLA 35 (60)
T ss_pred hheECCCCCCcCeEcCCCCeEECCccCee
Confidence 35689999998887666667777 46643
No 208
>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=47.69 E-value=41 Score=24.72 Aligned_cols=36 Identities=19% Similarity=0.450 Sum_probs=24.8
Q ss_pred CccccCCcCcccceeccccccCCcCeeeCCCcccccccccccc
Q 024566 109 ERSYCPNTNCMALVVNECERSGKVKKTQCPNCKQWFCFQCKLK 151 (265)
Q Consensus 109 ~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~ 151 (265)
+...|. .|...+..-. .....|..|+..+|..|+..
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 346777 4877554332 24589999999999999886
No 209
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=47.47 E-value=14 Score=31.62 Aligned_cols=26 Identities=31% Similarity=0.835 Sum_probs=20.1
Q ss_pred cccCCCCCceeeec--CCCceeEe-ecCC
Q 024566 181 WARCPACGHCVERK--DGCSVVMC-RCNT 206 (265)
Q Consensus 181 ~k~CP~C~~~iek~--~GCnhm~C-~C~~ 206 (265)
-++||.|+..|+|. +|-.-..| .|+.
T Consensus 235 g~pC~~Cg~~I~~~~~~gR~ty~Cp~CQ~ 263 (269)
T PRK14811 235 GQPCPRCGTPIEKIVVGGRGTHFCPQCQP 263 (269)
T ss_pred cCCCCcCCCeeEEEEECCCCcEECCCCcC
Confidence 47899999999865 77776777 5664
No 210
>PLN02400 cellulose synthase
Probab=47.39 E-value=14 Score=37.47 Aligned_cols=61 Identities=23% Similarity=0.358 Sum_probs=37.8
Q ss_pred cccCCcCcccceeccccccCCcCeeeCCCcccccccccccccCCCCCChhHHhchhhchHHHHHHHhcCCcccCCCCCce
Q 024566 111 SYCPNTNCMALVVNECERSGKVKKTQCPNCKQWFCFQCKLKWHAGYRCEESRNLRDQNDIVFGQLVERMKWARCPACGHC 190 (265)
Q Consensus 111 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~d~~~~~~~~~~~~k~CP~C~~~ 190 (265)
..|-- |+.-+-.... ....+-|..|++-.|.-|- +|++ +...+-||.|+.+
T Consensus 37 qiCqI--CGD~VG~t~d---Ge~FVAC~eCaFPVCRpCY----------EYER--------------keGnq~CPQCkTr 87 (1085)
T PLN02400 37 QICQI--CGDDVGVTET---GDVFVACNECAFPVCRPCY----------EYER--------------KDGTQCCPQCKTR 87 (1085)
T ss_pred ceeee--cccccCcCCC---CCEEEEEccCCCccccchh----------heec--------------ccCCccCcccCCc
Confidence 34542 6665554433 2588999999999998663 3332 3356677777777
Q ss_pred eeecCCCcee
Q 024566 191 VERKDGCSVV 200 (265)
Q Consensus 191 iek~~GCnhm 200 (265)
..+.-|+..+
T Consensus 88 YkR~KgsprV 97 (1085)
T PLN02400 88 YRRHKGSPRV 97 (1085)
T ss_pred cccccCCCCC
Confidence 7655454433
No 211
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=46.73 E-value=4.5 Score=34.81 Aligned_cols=78 Identities=22% Similarity=0.384 Sum_probs=44.6
Q ss_pred CcccCCCCCCCCCCCccCccCCCChhHHHHHHHHHHHHh-hc-----CCCccccCCcCcccceeccccc----cCCcCee
Q 024566 66 AKIDCPGLDCKHNLDPFACEPVIPASLFSKWCDVLCEDY-VL-----GFERSYCPNTNCMALVVNECER----SGKVKKT 135 (265)
Q Consensus 66 ~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~~~~~~~-~~-----~~~~~~Cp~~~C~~~~~~~~~~----~~~~~~~ 135 (265)
.|+.||. |.. .-+|+..+...|..+.--.. .+ .+....|-. |+..++..+.. .....+.
T Consensus 321 LPi~CP~--Csl-------~LilsthLarSyhhL~PLk~f~E~p~~~~~ks~~Cf~--CQ~~fp~~~~~~~~~~~ss~rY 389 (421)
T COG5151 321 LPISCPI--CSL-------QLILSTHLARSYHHLYPLKPFVEKPEGTNPKSTHCFV--CQGPFPKPPVSPFDESTSSGRY 389 (421)
T ss_pred CCccCcc--hhH-------HHHHHHHHHHHHHhhccCcccccccCCCCCCCcccee--ccCCCCCCCCCcccccccccce
Confidence 3556665 542 33445556666665432211 11 123355653 77766543321 1225689
Q ss_pred eCCCcccccccccccccCC
Q 024566 136 QCPNCKQWFCFQCKLKWHA 154 (265)
Q Consensus 136 ~C~~C~~~~C~~C~~~~H~ 154 (265)
.|+.|+..||..|..-.|.
T Consensus 390 ~Ce~CK~~FC~dCdvfiHe 408 (421)
T COG5151 390 QCELCKSTFCSDCDVFIHE 408 (421)
T ss_pred echhhhhhhhhhhHHHHHH
Confidence 9999999999999876664
No 212
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=46.55 E-value=13 Score=38.39 Aligned_cols=30 Identities=37% Similarity=1.034 Sum_probs=22.9
Q ss_pred ccCCCCCceeeecCCCceeEe-ecCCce-----eeccCcccc
Q 024566 182 ARCPACGHCVERKDGCSVVMC-RCNTRF-----CYECGRKIS 217 (265)
Q Consensus 182 k~CP~C~~~iek~~GCnhm~C-~C~~~F-----C~~C~~~~~ 217 (265)
++||+|+..+... .| .||.+. |-.||....
T Consensus 668 rkCPkCG~~t~~~------fCP~CGs~te~vy~CPsCGaev~ 703 (1337)
T PRK14714 668 RRCPSCGTETYEN------RCPDCGTHTEPVYVCPDCGAEVP 703 (1337)
T ss_pred EECCCCCCccccc------cCcccCCcCCCceeCccCCCccC
Confidence 8999999987542 88 588664 888888754
No 213
>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=46.45 E-value=18 Score=27.57 Aligned_cols=11 Identities=27% Similarity=0.869 Sum_probs=8.2
Q ss_pred ccCCCCCceee
Q 024566 182 ARCPACGHCVE 192 (265)
Q Consensus 182 k~CP~C~~~ie 192 (265)
-+|.+|+.+|.
T Consensus 82 ~~CE~CG~~I~ 92 (137)
T TIGR03826 82 YPCERCGTSIR 92 (137)
T ss_pred CcccccCCcCC
Confidence 57888887775
No 214
>PLN02436 cellulose synthase A
Probab=46.26 E-value=19 Score=36.67 Aligned_cols=62 Identities=23% Similarity=0.396 Sum_probs=42.4
Q ss_pred cccCCcCcccceeccccccCCcCeeeCCCcccccccccccccCCCCCChhHHhchhhchHHHHHHHhcCCcccCCCCCce
Q 024566 111 SYCPNTNCMALVVNECERSGKVKKTQCPNCKQWFCFQCKLKWHAGYRCEESRNLRDQNDIVFGQLVERMKWARCPACGHC 190 (265)
Q Consensus 111 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~d~~~~~~~~~~~~k~CP~C~~~ 190 (265)
..|.- |+.-+-.... ....+.|..|++-.|..| .+|.+ +...+.||.|+..
T Consensus 37 ~iCqI--CGD~Vg~t~d---Ge~FVACn~C~fpvCr~C----------yeyer--------------~eg~~~Cpqckt~ 87 (1094)
T PLN02436 37 QTCQI--CGDEIELTVD---GEPFVACNECAFPVCRPC----------YEYER--------------REGNQACPQCKTR 87 (1094)
T ss_pred ccccc--cccccCcCCC---CCEEEeeccCCCccccch----------hhhhh--------------hcCCccCcccCCc
Confidence 45553 6666544433 258899999999999866 34332 3467899999999
Q ss_pred eeecCCCceeE
Q 024566 191 VERKDGCSVVM 201 (265)
Q Consensus 191 iek~~GCnhm~ 201 (265)
..+--|++.+.
T Consensus 88 Y~r~kgs~~~~ 98 (1094)
T PLN02436 88 YKRIKGSPRVE 98 (1094)
T ss_pred hhhccCCCCcC
Confidence 88766666543
No 215
>PRK14873 primosome assembly protein PriA; Provisional
Probab=45.60 E-value=15 Score=35.64 Aligned_cols=34 Identities=26% Similarity=0.607 Sum_probs=25.9
Q ss_pred ccCCCCCceeeecCCCceeEe-ecCCc----eeeccCcc
Q 024566 182 ARCPACGHCVERKDGCSVVMC-RCNTR----FCYECGRK 215 (265)
Q Consensus 182 k~CP~C~~~iek~~GCnhm~C-~C~~~----FC~~C~~~ 215 (265)
-+||+|..+..-..+=+.+.| .||+. .|-.|+..
T Consensus 393 ~~C~~C~~~L~~h~~~~~l~Ch~CG~~~~p~~Cp~Cgs~ 431 (665)
T PRK14873 393 ARCRHCTGPLGLPSAGGTPRCRWCGRAAPDWRCPRCGSD 431 (665)
T ss_pred eECCCCCCceeEecCCCeeECCCCcCCCcCccCCCCcCC
Confidence 479999988886556678999 69974 57777665
No 216
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=45.23 E-value=17 Score=31.16 Aligned_cols=25 Identities=36% Similarity=0.906 Sum_probs=19.8
Q ss_pred ccCCCCCceeeec--CCCceeEe-ecCC
Q 024566 182 ARCPACGHCVERK--DGCSVVMC-RCNT 206 (265)
Q Consensus 182 k~CP~C~~~iek~--~GCnhm~C-~C~~ 206 (265)
++||.|+..|+|. +|-.-..| .|+.
T Consensus 246 ~pC~~Cg~~I~~~~~~gR~t~~CP~CQ~ 273 (274)
T PRK01103 246 EPCRRCGTPIEKIKQGGRSTFFCPRCQK 273 (274)
T ss_pred CCCCCCCCeeEEEEECCCCcEECcCCCC
Confidence 6899999999875 77777777 5753
No 217
>PRK10445 endonuclease VIII; Provisional
Probab=45.03 E-value=17 Score=30.98 Aligned_cols=25 Identities=24% Similarity=0.676 Sum_probs=19.9
Q ss_pred cccCCCCCceeeec--CCCceeEe-ecC
Q 024566 181 WARCPACGHCVERK--DGCSVVMC-RCN 205 (265)
Q Consensus 181 ~k~CP~C~~~iek~--~GCnhm~C-~C~ 205 (265)
-++||.|+..|++. +|-.-..| .|+
T Consensus 235 g~~Cp~Cg~~I~~~~~~gR~t~~CP~CQ 262 (263)
T PRK10445 235 GEACERCGGIIEKTTLSSRPFYWCPGCQ 262 (263)
T ss_pred CCCCCCCCCEeEEEEECCCCcEECCCCc
Confidence 37899999999865 88777777 575
No 218
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=44.55 E-value=17 Score=31.11 Aligned_cols=25 Identities=28% Similarity=0.599 Sum_probs=19.6
Q ss_pred cccCCCCCceeeec--CCCceeEe-ecC
Q 024566 181 WARCPACGHCVERK--DGCSVVMC-RCN 205 (265)
Q Consensus 181 ~k~CP~C~~~iek~--~GCnhm~C-~C~ 205 (265)
-++||.|+..|++. +|-.-..| .|+
T Consensus 244 g~pCprCG~~I~~~~~~gR~t~~CP~CQ 271 (272)
T PRK14810 244 GEPCLNCKTPIRRVVVAGRSSHYCPHCQ 271 (272)
T ss_pred CCcCCCCCCeeEEEEECCCccEECcCCc
Confidence 47999999999865 77776777 565
No 219
>PHA02926 zinc finger-like protein; Provisional
Probab=44.44 E-value=8.6 Score=31.66 Aligned_cols=46 Identities=22% Similarity=0.307 Sum_probs=29.2
Q ss_pred HHHHhcCCcccCCCCCceeeecCCCce----eEeecCCceeeccCccccC
Q 024566 173 GQLVERMKWARCPACGHCVERKDGCSV----VMCRCNTRFCYECGRKISS 218 (265)
Q Consensus 173 ~~~~~~~~~k~CP~C~~~iek~~GCnh----m~C~C~~~FC~~C~~~~~~ 218 (265)
+.+.+....+.|+=|--.+-+...-+. +.=.|+|.||+.|...|..
T Consensus 162 e~~~~~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~ 211 (242)
T PHA02926 162 EDVYRVSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHR 211 (242)
T ss_pred HHHHhccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHH
Confidence 344455566899999977643221111 1113888899999999874
No 220
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=43.63 E-value=22 Score=21.19 Aligned_cols=14 Identities=29% Similarity=0.617 Sum_probs=9.8
Q ss_pred CCcccCCCCCceee
Q 024566 179 MKWARCPACGHCVE 192 (265)
Q Consensus 179 ~~~k~CP~C~~~ie 192 (265)
....+||.|+..|.
T Consensus 17 ~~~irC~~CG~rIl 30 (44)
T smart00659 17 KDVVRCRECGYRIL 30 (44)
T ss_pred CCceECCCCCceEE
Confidence 34577888887764
No 221
>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=43.15 E-value=18 Score=30.94 Aligned_cols=25 Identities=28% Similarity=0.757 Sum_probs=19.3
Q ss_pred cccCCCCCceeeec--CCCceeEe-ecC
Q 024566 181 WARCPACGHCVERK--DGCSVVMC-RCN 205 (265)
Q Consensus 181 ~k~CP~C~~~iek~--~GCnhm~C-~C~ 205 (265)
-++||.|+..|+|. +|-+-..| .|+
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 272 (272)
T TIGR00577 245 GEPCRRCGTPIEKIKVGGRGTHFCPQCQ 272 (272)
T ss_pred CCCCCCCCCeeEEEEECCCCCEECCCCC
Confidence 36999999999875 77776777 464
No 222
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=42.97 E-value=22 Score=36.01 Aligned_cols=55 Identities=22% Similarity=0.653 Sum_probs=38.8
Q ss_pred CCCcccccccccccccc---cccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCC
Q 024566 17 GGGSSFTCEICIEPMAA---SKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLD 80 (265)
Q Consensus 17 ~~~~~~~C~IC~~~~~~---~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 80 (265)
..-....|.||-+++.. .+.|++.-.|+-..|+.|. +...++|+ -.||. |+....
T Consensus 11 ~~~~~~~c~iCGd~vg~~~~Ge~FVAC~eC~fpvCr~cy----eye~~~g~---~~cp~--c~t~y~ 68 (1044)
T PLN02915 11 QSADAKTCRVCGDEVGVKEDGQPFVACHVCGFPVCKPCY----EYERSEGN---QCCPQ--CNTRYK 68 (1044)
T ss_pred cCCCcchhhccccccCcCCCCCEEEEeccCCCccccchh----hhhhhcCC---ccCCc--cCCchh
Confidence 34567889999998653 3457677789999999997 33334433 37998 987654
No 223
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=42.52 E-value=18 Score=31.03 Aligned_cols=25 Identities=36% Similarity=0.749 Sum_probs=20.2
Q ss_pred cccCCCCCceeeec--CCCceeEe-ecC
Q 024566 181 WARCPACGHCVERK--DGCSVVMC-RCN 205 (265)
Q Consensus 181 ~k~CP~C~~~iek~--~GCnhm~C-~C~ 205 (265)
-++||.|+..|.|. +|-+-..| .|+
T Consensus 254 g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 281 (282)
T PRK13945 254 GKPCRKCGTPIERIKLAGRSTHWCPNCQ 281 (282)
T ss_pred cCCCCcCCCeeEEEEECCCccEECCCCc
Confidence 37999999999865 88777777 575
No 224
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=42.45 E-value=21 Score=23.37 Aligned_cols=31 Identities=19% Similarity=0.304 Sum_probs=22.6
Q ss_pred cccCCcCcccceeccccccCCcCeeeCCCccccccc
Q 024566 111 SYCPNTNCMALVVNECERSGKVKKTQCPNCKQWFCF 146 (265)
Q Consensus 111 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~ 146 (265)
+.|| +|++....-+.. ...+.|..|+..++.
T Consensus 20 VkCp--dC~N~q~vFsha---st~V~C~~CG~~l~~ 50 (67)
T COG2051 20 VKCP--DCGNEQVVFSHA---STVVTCLICGTTLAE 50 (67)
T ss_pred EECC--CCCCEEEEeccC---ceEEEecccccEEEe
Confidence 6788 698876654432 578999999887754
No 225
>KOG2979 consensus Protein involved in DNA repair [General function prediction only]
Probab=42.38 E-value=43 Score=28.26 Aligned_cols=52 Identities=23% Similarity=0.397 Sum_probs=37.8
Q ss_pred CCcccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCC
Q 024566 18 GGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHN 78 (265)
Q Consensus 18 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~ 78 (265)
..-...|+|=+.++..+.. ...|+|.|=++=+..++. ....++||..+|..+
T Consensus 173 e~fs~rdPis~~~I~nPvi---SkkC~HvydrDsI~~~l~------~~~~i~CPv~gC~~~ 224 (262)
T KOG2979|consen 173 EVFSNRDPISKKPIVNPVI---SKKCGHVYDRDSIMQILC------DEITIRCPVLGCENP 224 (262)
T ss_pred hhhcccCchhhhhhhchhh---hcCcCcchhhhhHHHHhc------cCceeecccccCCcc
Confidence 3445678877666655543 578999999888877775 356789999999943
No 226
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=42.24 E-value=26 Score=35.67 Aligned_cols=53 Identities=28% Similarity=0.789 Sum_probs=37.6
Q ss_pred CCccccccccccccc---ccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCC
Q 024566 18 GGSSFTCEICIEPMA---ASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNL 79 (265)
Q Consensus 18 ~~~~~~C~IC~~~~~---~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 79 (265)
+.....|.||-+++. +.+.|++.-.|+-..|+.|. +...++|+. .||. |+...
T Consensus 14 ~~~~qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCY----EYEr~eG~q---~CPq--CktrY 69 (1079)
T PLN02638 14 HGGGQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCY----EYERKDGNQ---SCPQ--CKTKY 69 (1079)
T ss_pred ccCCceeeecccccCcCCCCCEEEEeccCCCccccchh----hhhhhcCCc---cCCc--cCCch
Confidence 344569999999865 34457777789999999997 333344433 7998 98654
No 227
>PF14353 CpXC: CpXC protein
Probab=42.04 E-value=15 Score=27.32 Aligned_cols=15 Identities=33% Similarity=0.829 Sum_probs=11.0
Q ss_pred cccCCCCCCCCCCCccC
Q 024566 67 KIDCPGLDCKHNLDPFA 83 (265)
Q Consensus 67 ~i~CP~~~C~~~l~~~~ 83 (265)
.|+||. |+..+..+.
T Consensus 1 ~itCP~--C~~~~~~~v 15 (128)
T PF14353_consen 1 EITCPH--CGHEFEFEV 15 (128)
T ss_pred CcCCCC--CCCeeEEEE
Confidence 378999 998766543
No 228
>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=41.53 E-value=21 Score=20.38 Aligned_cols=29 Identities=21% Similarity=0.366 Sum_probs=18.0
Q ss_pred cccCCcCcccceeccccccCCcCeeeCCCccc
Q 024566 111 SYCPNTNCMALVVNECERSGKVKKTQCPNCKQ 142 (265)
Q Consensus 111 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 142 (265)
..|+ .|+..+........ ...+.||.|+.
T Consensus 6 y~C~--~Cg~~fe~~~~~~~-~~~~~CP~Cg~ 34 (41)
T smart00834 6 YRCE--DCGHTFEVLQKISD-DPLATCPECGG 34 (41)
T ss_pred EEcC--CCCCEEEEEEecCC-CCCCCCCCCCC
Confidence 3576 58887654433221 46778988875
No 229
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=41.34 E-value=18 Score=22.95 Aligned_cols=24 Identities=25% Similarity=0.603 Sum_probs=16.8
Q ss_pred cCCcccCCCCCceeeecCCCceeEe-ecCC
Q 024566 178 RMKWARCPACGHCVERKDGCSVVMC-RCNT 206 (265)
Q Consensus 178 ~~~~k~CP~C~~~iek~~GCnhm~C-~C~~ 206 (265)
....-.||+|+.+... |-.| .||+
T Consensus 24 ~~~l~~C~~CG~~~~~-----H~vC~~CG~ 48 (57)
T PRK12286 24 APGLVECPNCGEPKLP-----HRVCPSCGY 48 (57)
T ss_pred CCcceECCCCCCccCC-----eEECCCCCc
Confidence 3456789999999873 5555 4554
No 230
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=41.29 E-value=7 Score=37.54 Aligned_cols=58 Identities=21% Similarity=0.479 Sum_probs=43.9
Q ss_pred CCcccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCCccCccC
Q 024566 18 GGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFACEP 86 (265)
Q Consensus 18 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~ 86 (265)
.....+|+||+..+..+. .+.|.|.||..|+-.-+...- ....||. |+..+....++.
T Consensus 18 ~~k~lEc~ic~~~~~~p~----~~kc~~~~l~~~~n~~f~~~~-----~~~~~~l--c~~~~eK~s~~E 75 (684)
T KOG4362|consen 18 MQKILECPICLEHVKEPS----LLKCDHIFLKFCLNKLFESKK-----GPKQCAL--CKSDIEKRSLRE 75 (684)
T ss_pred HhhhccCCceeEEeeccc----hhhhhHHHHhhhhhceeeccC-----ccccchh--hhhhhhhhhccc
Confidence 356789999999886552 589999999999988776432 2678888 887766655554
No 231
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=40.93 E-value=12 Score=32.58 Aligned_cols=49 Identities=18% Similarity=0.402 Sum_probs=35.3
Q ss_pred CcccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCC
Q 024566 19 GSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHN 78 (265)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~ 78 (265)
.....|+||.....++.. +.-=|-.||-.|+-+|+.. . =+||..++...
T Consensus 298 ~~~~~CpvClk~r~Nptv---l~vSGyVfCY~Ci~~Yv~~---~-----~~CPVT~~p~~ 346 (357)
T KOG0826|consen 298 PDREVCPVCLKKRQNPTV---LEVSGYVFCYPCIFSYVVN---Y-----GHCPVTGYPAS 346 (357)
T ss_pred CccccChhHHhccCCCce---EEecceEEeHHHHHHHHHh---c-----CCCCccCCcch
Confidence 345689999998765443 2334789999999999972 2 27998777654
No 232
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=40.63 E-value=24 Score=35.75 Aligned_cols=55 Identities=24% Similarity=0.417 Sum_probs=37.2
Q ss_pred cccceeccccccCCcCeeeCCCcccccccccccccCCCCCChhHHhchhhchHHHHHHHhcCCcccCCCCCceeeecCCC
Q 024566 118 CMALVVNECERSGKVKKTQCPNCKQWFCFQCKLKWHAGYRCEESRNLRDQNDIVFGQLVERMKWARCPACGHCVERKDGC 197 (265)
Q Consensus 118 C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~d~~~~~~~~~~~~k~CP~C~~~iek~~GC 197 (265)
|+.-+-.... ..+.+.|..|++-.|..| .+|.+ +...+.||.|+.+..+--|.
T Consensus 21 CGd~vg~~~~---Ge~FVAC~eC~fpvCr~c----------yeye~--------------~~g~~~cp~c~t~y~~~~~~ 73 (1044)
T PLN02915 21 CGDEVGVKED---GQPFVACHVCGFPVCKPC----------YEYER--------------SEGNQCCPQCNTRYKRHKGC 73 (1044)
T ss_pred cccccCcCCC---CCEEEEeccCCCccccch----------hhhhh--------------hcCCccCCccCCchhhhcCC
Confidence 5555544433 258899999999999866 33332 34678899998888765554
Q ss_pred ce
Q 024566 198 SV 199 (265)
Q Consensus 198 nh 199 (265)
+.
T Consensus 74 ~~ 75 (1044)
T PLN02915 74 PR 75 (1044)
T ss_pred CC
Confidence 44
No 233
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=40.58 E-value=22 Score=28.57 Aligned_cols=25 Identities=24% Similarity=0.606 Sum_probs=20.6
Q ss_pred ccCCCCCceeeecCCCceeEe-ecCCc
Q 024566 182 ARCPACGHCVERKDGCSVVMC-RCNTR 207 (265)
Q Consensus 182 k~CP~C~~~iek~~GCnhm~C-~C~~~ 207 (265)
-.||.|+.+..+... |+|.| .|++.
T Consensus 150 a~~~~~g~~~~~~~~-~~~~c~~~~~~ 175 (189)
T PRK09521 150 AMCSRCRTPLVKKGE-NELKCPNCGNI 175 (189)
T ss_pred EEccccCCceEECCC-CEEECCCCCCE
Confidence 469999999988555 99999 69864
No 234
>PRK05580 primosome assembly protein PriA; Validated
Probab=40.12 E-value=21 Score=34.80 Aligned_cols=34 Identities=29% Similarity=0.720 Sum_probs=26.5
Q ss_pred ccCCCCCceeeecCCCceeEe-ecCCc-----eeeccCcc
Q 024566 182 ARCPACGHCVERKDGCSVVMC-RCNTR-----FCYECGRK 215 (265)
Q Consensus 182 k~CP~C~~~iek~~GCnhm~C-~C~~~-----FC~~C~~~ 215 (265)
-+||+|..+..-...=|.+.| .||+. .|-.|++.
T Consensus 391 ~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 391 AECPHCDASLTLHRFQRRLRCHHCGYQEPIPKACPECGST 430 (679)
T ss_pred cCCCCCCCceeEECCCCeEECCCCcCCCCCCCCCCCCcCC
Confidence 369999998875545578999 69986 58888776
No 235
>COG3492 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=40.04 E-value=30 Score=24.09 Aligned_cols=17 Identities=18% Similarity=0.792 Sum_probs=14.8
Q ss_pred hhHHHHHHHHHHHHhhC
Q 024566 46 PFCQDCIARYIQVKVQD 62 (265)
Q Consensus 46 ~fC~~Cl~~~~~~~i~~ 62 (265)
-||+.||.+|+...-..
T Consensus 42 gFCRNCLs~Wy~eaae~ 58 (104)
T COG3492 42 GFCRNCLSNWYREAAEA 58 (104)
T ss_pred HHHHHHHHHHHHHHHhc
Confidence 49999999999988764
No 236
>PF15616 TerY-C: TerY-C metal binding domain
Probab=39.99 E-value=24 Score=26.56 Aligned_cols=35 Identities=29% Similarity=0.634 Sum_probs=18.6
Q ss_pred cccCCCCCcee-eecCCCceeEee--cCCceeeccCcc
Q 024566 181 WARCPACGHCV-ERKDGCSVVMCR--CNTRFCYECGRK 215 (265)
Q Consensus 181 ~k~CP~C~~~i-ek~~GCnhm~C~--C~~~FC~~C~~~ 215 (265)
.--||.|+... .-.-+|.++.|. =+..-|-.|+..
T Consensus 77 ~PgCP~CGn~~~fa~C~CGkl~Ci~g~~~~~CPwCg~~ 114 (131)
T PF15616_consen 77 APGCPHCGNQYAFAVCGCGKLFCIDGEGEVTCPWCGNE 114 (131)
T ss_pred CCCCCCCcChhcEEEecCCCEEEeCCCCCEECCCCCCe
Confidence 46899999874 222344444441 333344445444
No 237
>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=39.57 E-value=19 Score=19.90 Aligned_cols=23 Identities=26% Similarity=0.524 Sum_probs=13.4
Q ss_pred CcccceeccccccCCcCeeeCCCccccc
Q 024566 117 NCMALVVNECERSGKVKKTQCPNCKQWF 144 (265)
Q Consensus 117 ~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 144 (265)
+|+..+..... ..+.|+.||..+
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 57776664432 457888888643
No 238
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=39.41 E-value=24 Score=32.71 Aligned_cols=35 Identities=26% Similarity=0.579 Sum_probs=24.6
Q ss_pred CcccccccccccccCCCCCChhHHhchhhchHHHHHHHhcCCcccCCCCCceeee
Q 024566 139 NCKQWFCFQCKLKWHAGYRCEESRNLRDQNDIVFGQLVERMKWARCPACGHCVER 193 (265)
Q Consensus 139 ~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~d~~~~~~~~~~~~k~CP~C~~~iek 193 (265)
.||+.||+.|-..+ ..+.....++.||=|...|-.
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 58999999995421 111134578999999988864
No 239
>PRK12495 hypothetical protein; Provisional
Probab=39.09 E-value=34 Score=28.10 Aligned_cols=29 Identities=34% Similarity=0.841 Sum_probs=21.6
Q ss_pred CcccCCCCCceeeecCCCceeEeecCCceeeccCcccc
Q 024566 180 KWARCPACGHCVERKDGCSVVMCRCNTRFCYECGRKIS 217 (265)
Q Consensus 180 ~~k~CP~C~~~iek~~GCnhm~C~C~~~FC~~C~~~~~ 217 (265)
..+.||.|+.+|.+..| ..||-.|...+.
T Consensus 41 sa~hC~~CG~PIpa~pG---------~~~Cp~CQ~~~~ 69 (226)
T PRK12495 41 TNAHCDECGDPIFRHDG---------QEFCPTCQQPVT 69 (226)
T ss_pred chhhcccccCcccCCCC---------eeECCCCCCccc
Confidence 44899999999997766 456666666643
No 240
>PRK04023 DNA polymerase II large subunit; Validated
Probab=38.90 E-value=20 Score=36.10 Aligned_cols=32 Identities=31% Similarity=0.775 Sum_probs=25.6
Q ss_pred CcccCCCCCceeeecCCCceeEe-ecCC-----ceeeccCcccc
Q 024566 180 KWARCPACGHCVERKDGCSVVMC-RCNT-----RFCYECGRKIS 217 (265)
Q Consensus 180 ~~k~CP~C~~~iek~~GCnhm~C-~C~~-----~FC~~C~~~~~ 217 (265)
..+.||.|+... ..-.| .||. .||-.|+....
T Consensus 625 g~RfCpsCG~~t------~~frCP~CG~~Te~i~fCP~CG~~~~ 662 (1121)
T PRK04023 625 GRRKCPSCGKET------FYRRCPFCGTHTEPVYRCPRCGIEVE 662 (1121)
T ss_pred cCccCCCCCCcC------CcccCCCCCCCCCcceeCccccCcCC
Confidence 448999999985 55789 5996 49999988854
No 241
>PLN02189 cellulose synthase
Probab=37.97 E-value=22 Score=36.01 Aligned_cols=53 Identities=28% Similarity=0.695 Sum_probs=36.6
Q ss_pred Cccccccccccccc---ccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCC
Q 024566 19 GSSFTCEICIEPMA---ASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLD 80 (265)
Q Consensus 19 ~~~~~C~IC~~~~~---~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 80 (265)
.....|.||-+++. +.+.|++.-.|+-..|+.|. .|- .++|+ -.||. |+....
T Consensus 32 ~~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cy-eye---r~eg~---q~Cpq--Ckt~Y~ 87 (1040)
T PLN02189 32 LDGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCY-EYE---RREGT---QNCPQ--CKTRYK 87 (1040)
T ss_pred ccCccccccccccCcCCCCCEEEeeccCCCccccchh-hhh---hhcCC---ccCcc--cCCchh
Confidence 34559999999864 34456666779999999998 332 33333 37998 986553
No 242
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=37.88 E-value=35 Score=24.47 Aligned_cols=28 Identities=29% Similarity=0.768 Sum_probs=21.6
Q ss_pred CCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCC
Q 024566 41 NLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHN 78 (265)
Q Consensus 41 ~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~ 78 (265)
-.|.|.|..-|+.+|+.+. -.||. +...
T Consensus 79 G~CNHaFH~hCisrWlktr--------~vCPL--dn~e 106 (114)
T KOG2930|consen 79 GVCNHAFHFHCISRWLKTR--------NVCPL--DNKE 106 (114)
T ss_pred eecchHHHHHHHHHHHhhc--------CcCCC--cCcc
Confidence 3589999999999999853 26888 5543
No 243
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=37.80 E-value=39 Score=21.35 Aligned_cols=46 Identities=26% Similarity=0.652 Sum_probs=30.5
Q ss_pred cccccccccccccccccccCCCC--ChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCCc
Q 024566 22 FTCEICIEPMAASKKFKNRNLCT--HPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDP 81 (265)
Q Consensus 22 ~~C~IC~~~~~~~~~~~~~~~C~--H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~ 81 (265)
-.|..|-.++++...- ..-|. ..||.+|....+. =.||. |+..|..
T Consensus 6 pnCE~C~~dLp~~s~~--A~ICSfECTFC~~C~e~~l~----------~~CPN--CgGelv~ 53 (57)
T PF06906_consen 6 PNCECCDKDLPPDSPE--AYICSFECTFCADCAETMLN----------GVCPN--CGGELVR 53 (57)
T ss_pred CCccccCCCCCCCCCc--ceEEeEeCcccHHHHHHHhc----------CcCcC--CCCcccc
Confidence 4688888888654411 23454 4799999877653 16998 9876644
No 244
>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=36.78 E-value=16 Score=22.71 Aligned_cols=38 Identities=21% Similarity=0.533 Sum_probs=21.9
Q ss_pred ccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCC
Q 024566 21 SFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKH 77 (265)
Q Consensus 21 ~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~ 77 (265)
.+.||.|.+.++ ... |..++...=.. ....+.||. |..
T Consensus 2 ~f~CP~C~~~~~-~~~---------------L~~H~~~~H~~-~~~~v~CPi--C~~ 39 (54)
T PF05605_consen 2 SFTCPYCGKGFS-ESS---------------LVEHCEDEHRS-ESKNVVCPI--CSS 39 (54)
T ss_pred CcCCCCCCCccC-HHH---------------HHHHHHhHCcC-CCCCccCCC--chh
Confidence 578999988543 222 33344332222 234689999 975
No 245
>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=36.64 E-value=35 Score=21.22 Aligned_cols=35 Identities=29% Similarity=0.505 Sum_probs=18.9
Q ss_pred CccccCCcCcccceecccc------ccCCcCeeeCCCccccc
Q 024566 109 ERSYCPNTNCMALVVNECE------RSGKVKKTQCPNCKQWF 144 (265)
Q Consensus 109 ~~~~Cp~~~C~~~~~~~~~------~~~~~~~~~C~~C~~~~ 144 (265)
+.+.||+|+|-.- ..++. .+.....++|..|++.+
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 4578999999765 11111 11235678888887543
No 246
>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=36.63 E-value=28 Score=20.43 Aligned_cols=28 Identities=21% Similarity=0.381 Sum_probs=17.3
Q ss_pred ccCCcCcccceeccccccCCcCeeeCCCccc
Q 024566 112 YCPNTNCMALVVNECERSGKVKKTQCPNCKQ 142 (265)
Q Consensus 112 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 142 (265)
.|+ +|+..+......++ ...+.||.|+.
T Consensus 7 ~C~--~Cg~~fe~~~~~~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 7 RCE--ECGHEFEVLQSISE-DDPVPCPECGS 34 (42)
T ss_pred EeC--CCCCEEEEEEEcCC-CCCCcCCCCCC
Confidence 466 58866654433322 56788888875
No 247
>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=36.42 E-value=58 Score=23.50 Aligned_cols=56 Identities=21% Similarity=0.536 Sum_probs=32.8
Q ss_pred ccccccccccccccccccc----ccCCC---CChhHHHHHHHHHHHHhhCC-CCCcccCCCCCCCC
Q 024566 20 SSFTCEICIEPMAASKKFK----NRNLC---THPFCQDCIARYIQVKVQDD-NTAKIDCPGLDCKH 77 (265)
Q Consensus 20 ~~~~C~IC~~~~~~~~~~~----~~~~C---~H~fC~~Cl~~~~~~~i~~~-~~~~i~CP~~~C~~ 77 (265)
....|..|.....+....- ....| .-.||..||...+...+.+. ....-.||. |..
T Consensus 6 ~g~~CHqCrqKt~~~~~~C~~~~~~~~C~~~~~~fC~~CL~~ryge~~~ev~~~~~W~CP~--Crg 69 (105)
T PF10497_consen 6 NGKTCHQCRQKTLDFKTICTGHWKNSSCRGCRGKFCGGCLRNRYGENVEEVLEDPNWKCPK--CRG 69 (105)
T ss_pred CCCCchhhcCCCCCCceEcCCCCCCCCCccCcceehHhHHHHHHhhhHHHHhcCCceECCC--CCC
Confidence 3455666666443222210 12456 67899999998877766431 123467987 654
No 248
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=36.30 E-value=78 Score=20.03 Aligned_cols=35 Identities=17% Similarity=0.224 Sum_probs=26.2
Q ss_pred ccCCCCCCCCCCCccCccCCCChhHHHHHHHHHHHHh
Q 024566 68 IDCPGLDCKHNLDPFACEPVIPASLFSKWCDVLCEDY 104 (265)
Q Consensus 68 i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~~~~~~~ 104 (265)
..||. |+.......-...-+.|-+.+|...+....
T Consensus 18 ~~CP~--CG~~t~~~~P~rfSp~D~y~~yR~~~kk~~ 52 (56)
T PRK13130 18 EICPV--CGGKTKNPHPPRFSPEDKYGKYRRALKKRR 52 (56)
T ss_pred ccCcC--CCCCCCCCCCCCCCCCCccHHHHHHHHHHh
Confidence 45888 998777666666677788999988776554
No 249
>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=36.13 E-value=26 Score=25.46 Aligned_cols=13 Identities=46% Similarity=1.137 Sum_probs=11.0
Q ss_pred ceeEeecCCceee
Q 024566 198 SVVMCRCNTRFCY 210 (265)
Q Consensus 198 nhm~C~C~~~FC~ 210 (265)
.-+.|.||++||-
T Consensus 23 k~vkc~CGh~f~d 35 (112)
T PF08882_consen 23 KVVKCDCGHEFCD 35 (112)
T ss_pred ceeeccCCCeecC
Confidence 4788999999984
No 250
>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=35.93 E-value=24 Score=25.67 Aligned_cols=23 Identities=35% Similarity=0.859 Sum_probs=15.5
Q ss_pred CcCeeeCCCccccc--------ccccccccC
Q 024566 131 KVKKTQCPNCKQWF--------CFQCKLKWH 153 (265)
Q Consensus 131 ~~~~~~C~~C~~~~--------C~~C~~~~H 153 (265)
+...+.||.|++.+ |..|+.+-+
T Consensus 66 kav~V~CP~C~K~TKmLGr~D~CM~C~~pLT 96 (114)
T PF11023_consen 66 KAVQVECPNCGKQTKMLGRVDACMHCKEPLT 96 (114)
T ss_pred cceeeECCCCCChHhhhchhhccCcCCCcCc
Confidence 35678888887543 777766654
No 251
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=35.33 E-value=24 Score=20.42 Aligned_cols=18 Identities=28% Similarity=0.744 Sum_probs=15.7
Q ss_pred eeeCCCcccccccccccc
Q 024566 134 KTQCPNCKQWFCFQCKLK 151 (265)
Q Consensus 134 ~~~C~~C~~~~C~~C~~~ 151 (265)
.+.|..|+..||...+.+
T Consensus 12 ~f~C~~C~~~FC~~HR~~ 29 (39)
T smart00154 12 GFKCRHCGNLFCGEHRLP 29 (39)
T ss_pred CeECCccCCccccccCCc
Confidence 678999999999988764
No 252
>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=35.17 E-value=23 Score=16.67 Aligned_cols=16 Identities=31% Similarity=0.698 Sum_probs=12.1
Q ss_pred cccccccccCCCCCCh
Q 024566 144 FCFQCKLKWHAGYRCE 159 (265)
Q Consensus 144 ~C~~C~~~~H~~~~C~ 159 (265)
.|+.|+..-|....|.
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 4888888888766664
No 253
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=34.90 E-value=17 Score=31.68 Aligned_cols=48 Identities=31% Similarity=0.831 Sum_probs=31.5
Q ss_pred CcccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCC
Q 024566 19 GSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKH 77 (265)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~ 77 (265)
.....|-.|.++..+...+ ....|.+.||.+|=. ++-..+. .||. |..
T Consensus 328 ~~~~~Cf~C~~~~~~~~~y-~C~~Ck~~FCldCDv-~iHesLh-------~Cpg--Ceh 375 (378)
T KOG2807|consen 328 NGSRFCFACQGELLSSGRY-RCESCKNVFCLDCDV-FIHESLH-------NCPG--CEH 375 (378)
T ss_pred CCCcceeeeccccCCCCcE-EchhccceeeccchH-HHHhhhh-------cCCC--cCC
Confidence 3444599998777655443 477899999999943 3333333 4776 653
No 254
>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=33.45 E-value=52 Score=18.01 Aligned_cols=24 Identities=33% Similarity=0.670 Sum_probs=18.6
Q ss_pred cCCCCCceeeecCCCceeEe-ecCC
Q 024566 183 RCPACGHCVERKDGCSVVMC-RCNT 206 (265)
Q Consensus 183 ~CP~C~~~iek~~GCnhm~C-~C~~ 206 (265)
.|+.|+.++.--.|=..+.| .|++
T Consensus 3 ~C~~C~t~L~yP~gA~~vrCs~C~~ 27 (31)
T TIGR01053 3 VCGGCRTLLMYPRGASSVRCALCQT 27 (31)
T ss_pred CcCCCCcEeecCCCCCeEECCCCCe
Confidence 58888888888888888888 4754
No 255
>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 KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=32.91 E-value=42 Score=32.86 Aligned_cols=39 Identities=26% Similarity=0.606 Sum_probs=30.1
Q ss_pred CCcccccccccccccccccccccCCCCChhHHHHHHHHHHH
Q 024566 18 GGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQV 58 (265)
Q Consensus 18 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~ 58 (265)
....+.|.||--.+.....+ ...|+|....+|+..|++.
T Consensus 1025 ~~~~~~C~~C~l~V~gss~~--Cg~C~Hv~H~sc~~eWf~~ 1063 (1081)
T KOG0309|consen 1025 KGFTFQCAICHLAVRGSSNF--CGTCGHVGHTSCMMEWFRT 1063 (1081)
T ss_pred ccceeeeeeEeeEeeccchh--hccccccccHHHHHHHHhc
Confidence 35567799987776544433 6789999999999999984
No 257
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=32.89 E-value=61 Score=23.77 Aligned_cols=31 Identities=10% Similarity=0.142 Sum_probs=22.1
Q ss_pred chhhhHHHHHHHHHHHHHHhhhhhhhhhhhh
Q 024566 228 CQLTILTIAMMVIFHVIVLAGMKISKYEKNV 258 (265)
Q Consensus 228 C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 258 (265)
+.+...+...+.|...++.+.-++.++|..+
T Consensus 29 ~~~~~L~~E~~~Fi~~Fi~~rGnlKe~e~~l 59 (113)
T PF09862_consen 29 PWFARLSPEQLEFIKLFIKNRGNLKEMEKEL 59 (113)
T ss_pred chhhcCCHHHHHHHHHHHHhcCCHHHHHHHH
Confidence 4555566677777778888888888777653
No 258
>KOG2041 consensus WD40 repeat protein [General function prediction only]
Probab=32.81 E-value=71 Score=31.29 Aligned_cols=20 Identities=0% Similarity=-0.031 Sum_probs=14.4
Q ss_pred CCChhHHHHHHHHHHHHhhc
Q 024566 87 VIPASLFSKWCDVLCEDYVL 106 (265)
Q Consensus 87 ~l~~~~~~~~~~~~~~~~~~ 106 (265)
-|++...++|+++.++-+.+
T Consensus 1088 ~l~~a~kq~ye~La~~iFsk 1107 (1189)
T KOG2041|consen 1088 ELDDAEKQEYENLAFRIFSK 1107 (1189)
T ss_pred hCCHHHHHHHHHHHHHHhcc
Confidence 46777888898887765543
No 259
>PLN02195 cellulose synthase A
Probab=32.71 E-value=41 Score=33.97 Aligned_cols=53 Identities=21% Similarity=0.604 Sum_probs=38.3
Q ss_pred Ccccccccccccccc---cccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCC
Q 024566 19 GSSFTCEICIEPMAA---SKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLD 80 (265)
Q Consensus 19 ~~~~~C~IC~~~~~~---~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 80 (265)
.....|.||-++... .+.|++.-.|+-..|+.|. +...++|+ =.||. |+....
T Consensus 4 ~~~~~c~~cgd~~~~~~~g~~fvaC~eC~~pvCrpCy----eyer~eg~---q~Cpq--Ckt~Yk 59 (977)
T PLN02195 4 SGAPICATCGEEVGVDSNGEAFVACHECSYPLCKACL----EYEIKEGR---KVCLR--CGGPYD 59 (977)
T ss_pred CCCccceecccccCcCCCCCeEEEeccCCCccccchh----hhhhhcCC---ccCCc--cCCccc
Confidence 345589999997643 3457777789999999997 33334443 37999 998877
No 260
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=32.38 E-value=28 Score=34.34 Aligned_cols=41 Identities=27% Similarity=0.651 Sum_probs=31.9
Q ss_pred ccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCC
Q 024566 21 SFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKH 77 (265)
Q Consensus 21 ~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~ 77 (265)
...|..|--+.+-|.. ...|+|.|.+.|+. + ..-.||. |..
T Consensus 840 ~skCs~C~~~LdlP~V---hF~CgHsyHqhC~e--------~---~~~~CP~--C~~ 880 (933)
T KOG2114|consen 840 VSKCSACEGTLDLPFV---HFLCGHSYHQHCLE--------D---KEDKCPK--CLP 880 (933)
T ss_pred eeeecccCCcccccee---eeecccHHHHHhhc--------c---CcccCCc--cch
Confidence 3589999988866554 37899999999998 2 2358998 875
No 261
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=32.33 E-value=28 Score=30.14 Aligned_cols=31 Identities=29% Similarity=0.704 Sum_probs=21.6
Q ss_pred ccccccccccccccccccccCCCCChhHHHHHHH
Q 024566 21 SFTCEICIEPMAASKKFKNRNLCTHPFCQDCIAR 54 (265)
Q Consensus 21 ~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~ 54 (265)
...|.-|--.+. .+-.+.+|.|.||.+|.+.
T Consensus 90 VHfCd~Cd~PI~---IYGRmIPCkHvFCl~CAr~ 120 (389)
T KOG2932|consen 90 VHFCDRCDFPIA---IYGRMIPCKHVFCLECARS 120 (389)
T ss_pred eEeecccCCcce---eeecccccchhhhhhhhhc
Confidence 467777755442 2223689999999999764
No 262
>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=32.31 E-value=30 Score=21.75 Aligned_cols=14 Identities=29% Similarity=0.645 Sum_probs=11.2
Q ss_pred CCcccCCCCCceee
Q 024566 179 MKWARCPACGHCVE 192 (265)
Q Consensus 179 ~~~k~CP~C~~~ie 192 (265)
.....||+|+.+..
T Consensus 24 p~l~~C~~cG~~~~ 37 (55)
T TIGR01031 24 PTLVVCPNCGEFKL 37 (55)
T ss_pred CcceECCCCCCccc
Confidence 45677999999886
No 263
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=32.31 E-value=47 Score=24.32 Aligned_cols=46 Identities=22% Similarity=0.520 Sum_probs=24.1
Q ss_pred ChhHHHHHHHHHHHHhh-c--------CCCccccCCcCcccceeccccccCCcCeeeCCCcc
Q 024566 89 PASLFSKWCDVLCEDYV-L--------GFERSYCPNTNCMALVVNECERSGKVKKTQCPNCK 141 (265)
Q Consensus 89 ~~~~~~~~~~~~~~~~~-~--------~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~ 141 (265)
.++.++-....+.+..+ . .+-..+|+ +|+..+..... ..+.||.||
T Consensus 40 ~p~~L~f~f~~~~~~t~~egA~L~i~~~p~~~~C~--~Cg~~~~~~~~-----~~~~CP~Cg 94 (114)
T PRK03681 40 ETSSLAFCFDLVCRGTVAEGCKLHLEEQEAECWCE--TCQQYVTLLTQ-----RVRRCPQCH 94 (114)
T ss_pred CHHHHHHHHHHHhCCCccCCCEEEEEeeCcEEEcc--cCCCeeecCCc-----cCCcCcCcC
Confidence 44555555555544433 1 12346787 58766654322 235677776
No 264
>PRK02935 hypothetical protein; Provisional
Probab=31.91 E-value=34 Score=24.64 Aligned_cols=23 Identities=26% Similarity=0.746 Sum_probs=14.3
Q ss_pred CcCeeeCCCcccc--------cccccccccC
Q 024566 131 KVKKTQCPNCKQW--------FCFQCKLKWH 153 (265)
Q Consensus 131 ~~~~~~C~~C~~~--------~C~~C~~~~H 153 (265)
+...+.||.|++. .|..|+.|-+
T Consensus 67 kavqV~CP~C~K~TKmLGrvD~CM~C~~PLT 97 (110)
T PRK02935 67 KAVQVICPSCEKPTKMLGRVDACMHCNQPLT 97 (110)
T ss_pred cceeeECCCCCchhhhccceeecCcCCCcCC
Confidence 3567788888643 3666666543
No 265
>PRK04023 DNA polymerase II large subunit; Validated
Probab=31.53 E-value=34 Score=34.63 Aligned_cols=13 Identities=8% Similarity=0.524 Sum_probs=7.2
Q ss_pred hHHHHHHHHHHHH
Q 024566 47 FCQDCIARYIQVK 59 (265)
Q Consensus 47 fC~~Cl~~~~~~~ 59 (265)
||.+-|.+.+...
T Consensus 424 y~~EWW~qe~~~~ 436 (1121)
T PRK04023 424 YCEEWWIQELEAA 436 (1121)
T ss_pred ccHHHHHHHHHhc
Confidence 5666665555543
No 266
>PLN02400 cellulose synthase
Probab=31.36 E-value=34 Score=34.92 Aligned_cols=53 Identities=26% Similarity=0.644 Sum_probs=37.6
Q ss_pred Cccccccccccccc---ccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCC
Q 024566 19 GSSFTCEICIEPMA---ASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLD 80 (265)
Q Consensus 19 ~~~~~C~IC~~~~~---~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~ 80 (265)
.....|+||-|++. +.+.|++.-.|+-..|+.|. +...++|+ =.||. |+....
T Consensus 34 ~~gqiCqICGD~VG~t~dGe~FVAC~eCaFPVCRpCY----EYERkeGn---q~CPQ--CkTrYk 89 (1085)
T PLN02400 34 LNGQICQICGDDVGVTETGDVFVACNECAFPVCRPCY----EYERKDGT---QCCPQ--CKTRYR 89 (1085)
T ss_pred cCCceeeecccccCcCCCCCEEEEEccCCCccccchh----heecccCC---ccCcc--cCCccc
Confidence 34559999999865 34457777889999999997 33344433 37999 986553
No 267
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=31.29 E-value=22 Score=18.26 Aligned_cols=10 Identities=40% Similarity=1.049 Sum_probs=6.8
Q ss_pred eeCCCccccc
Q 024566 135 TQCPNCKQWF 144 (265)
Q Consensus 135 ~~C~~C~~~~ 144 (265)
+.|+.|+..|
T Consensus 3 ~~C~~CgR~F 12 (25)
T PF13913_consen 3 VPCPICGRKF 12 (25)
T ss_pred CcCCCCCCEE
Confidence 5677777665
No 268
>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=31.29 E-value=16 Score=31.55 Aligned_cols=11 Identities=45% Similarity=1.053 Sum_probs=4.3
Q ss_pred ccccCCcCcccce
Q 024566 110 RSYCPNTNCMALV 122 (265)
Q Consensus 110 ~~~Cp~~~C~~~~ 122 (265)
..+||. |+..-
T Consensus 172 ~g~CPv--CGs~P 182 (290)
T PF04216_consen 172 RGYCPV--CGSPP 182 (290)
T ss_dssp -SS-TT--T---E
T ss_pred CCcCCC--CCCcC
Confidence 368995 88753
No 269
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=31.08 E-value=48 Score=21.23 Aligned_cols=31 Identities=19% Similarity=0.342 Sum_probs=21.3
Q ss_pred cccCCcCcccceeccccccCCcCeeeCCCccccccc
Q 024566 111 SYCPNTNCMALVVNECERSGKVKKTQCPNCKQWFCF 146 (265)
Q Consensus 111 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~ 146 (265)
+.|| +|++....-+.. ...+.|..|+...+.
T Consensus 12 VkCp--~C~n~q~vFsha---~t~V~C~~Cg~~L~~ 42 (59)
T PRK00415 12 VKCP--DCGNEQVVFSHA---STVVRCLVCGKTLAE 42 (59)
T ss_pred EECC--CCCCeEEEEecC---CcEEECcccCCCccc
Confidence 6788 688876554432 478889888876653
No 270
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=31.00 E-value=24 Score=27.12 Aligned_cols=34 Identities=21% Similarity=0.333 Sum_probs=20.5
Q ss_pred CCccccCCcCcccceecccccc--CCcCeeeCCCcccc
Q 024566 108 FERSYCPNTNCMALVVNECERS--GKVKKTQCPNCKQW 143 (265)
Q Consensus 108 ~~~~~Cp~~~C~~~~~~~~~~~--~~~~~~~C~~C~~~ 143 (265)
.....||+ |+..+...+... +....+.||.||..
T Consensus 97 ~~~Y~Cp~--C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~ 132 (147)
T smart00531 97 NAYYKCPN--CQSKYTFLEANQLLDMDGTFTCPRCGEE 132 (147)
T ss_pred CcEEECcC--CCCEeeHHHHHHhcCCCCcEECCCCCCE
Confidence 34577995 988776543211 11234899988854
No 271
>PLN03086 PRLI-interacting factor K; Provisional
Probab=30.57 E-value=29 Score=32.92 Aligned_cols=30 Identities=27% Similarity=0.699 Sum_probs=25.5
Q ss_pred CCcccCCC--CCceeeecCCCceeEe-ecCCce
Q 024566 179 MKWARCPA--CGHCVERKDGCSVVMC-RCNTRF 208 (265)
Q Consensus 179 ~~~k~CP~--C~~~iek~~GCnhm~C-~C~~~F 208 (265)
.+...||+ |+..+.+...=+|..| .|+..|
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 35678995 9999999999999999 698765
No 272
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=30.37 E-value=50 Score=24.97 Aligned_cols=15 Identities=20% Similarity=0.173 Sum_probs=10.6
Q ss_pred CccccCCcCcccceecc
Q 024566 109 ERSYCPNTNCMALVVNE 125 (265)
Q Consensus 109 ~~~~Cp~~~C~~~~~~~ 125 (265)
...+|+ +|+..+...
T Consensus 69 ~~~~C~--~CG~~~~~~ 83 (135)
T PRK03824 69 AVLKCR--NCGNEWSLK 83 (135)
T ss_pred eEEECC--CCCCEEecc
Confidence 347888 598777664
No 273
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=30.25 E-value=40 Score=28.57 Aligned_cols=28 Identities=25% Similarity=0.613 Sum_probs=21.8
Q ss_pred CcccCCCCCceeeecCCCceeEe-ecCCc
Q 024566 180 KWARCPACGHCVERKDGCSVVMC-RCNTR 207 (265)
Q Consensus 180 ~~k~CP~C~~~iek~~GCnhm~C-~C~~~ 207 (265)
..+-||.|+.++....+=..+.| .|+..
T Consensus 98 ~~~fC~~CG~~~~~~~~~~~~~C~~c~~~ 126 (256)
T PRK00241 98 SHRFCGYCGHPMHPSKTEWAMLCPHCRER 126 (256)
T ss_pred cCccccccCCCCeecCCceeEECCCCCCE
Confidence 45899999999887666577888 68743
No 274
>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=29.98 E-value=28 Score=19.46 Aligned_cols=14 Identities=36% Similarity=0.980 Sum_probs=9.3
Q ss_pred CcccCCCCCceeee
Q 024566 180 KWARCPACGHCVER 193 (265)
Q Consensus 180 ~~k~CP~C~~~iek 193 (265)
.+-.||+|+..|.-
T Consensus 3 ~~~~C~nC~R~v~a 16 (33)
T PF08209_consen 3 PYVECPNCGRPVAA 16 (33)
T ss_dssp -EEE-TTTSSEEEG
T ss_pred CeEECCCCcCCcch
Confidence 35679999998863
No 275
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=29.70 E-value=11 Score=31.47 Aligned_cols=36 Identities=33% Similarity=0.750 Sum_probs=12.2
Q ss_pred CccccCCcCcccceeccccccCCcCeeeCCCccccccc
Q 024566 109 ERSYCPNTNCMALVVNECERSGKVKKTQCPNCKQWFCF 146 (265)
Q Consensus 109 ~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~ 146 (265)
...+||+ |+..-...-....-...+.|+.|+..|=+
T Consensus 30 ~n~yCP~--Cg~~~L~~f~NN~PVaDF~C~~C~eeyEL 65 (254)
T PF06044_consen 30 ENMYCPN--CGSKPLSKFENNRPVADFYCPNCNEEYEL 65 (254)
T ss_dssp HH---TT--T--SS-EE--------EEE-TTT--EEEE
T ss_pred HCCcCCC--CCChhHhhccCCCccceeECCCCchHHhh
Confidence 3478995 88763222111112578999999866633
No 276
>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=29.69 E-value=22 Score=22.44 Aligned_cols=14 Identities=29% Similarity=0.719 Sum_probs=11.2
Q ss_pred CCcccCCCCCceee
Q 024566 179 MKWARCPACGHCVE 192 (265)
Q Consensus 179 ~~~k~CP~C~~~ie 192 (265)
.+...||+|+.+..
T Consensus 24 ~~l~~c~~cg~~~~ 37 (56)
T PF01783_consen 24 PNLVKCPNCGEPKL 37 (56)
T ss_dssp TSEEESSSSSSEES
T ss_pred cceeeeccCCCEec
Confidence 36688999998876
No 277
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=29.33 E-value=53 Score=32.36 Aligned_cols=48 Identities=17% Similarity=0.535 Sum_probs=30.5
Q ss_pred ccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCCc
Q 024566 23 TCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDP 81 (265)
Q Consensus 23 ~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~ 81 (265)
.|++|+..+.+.. ...-..|+|.||..|+..|-... =.||. |...+..
T Consensus 125 ~CP~Ci~s~~DqL-~~~~k~c~H~FC~~Ci~sWsR~a--------qTCPi--DR~EF~~ 172 (1134)
T KOG0825|consen 125 QCPNCLKSCNDQL-EESEKHTAHYFCEECVGSWSRCA--------QTCPV--DRGEFGE 172 (1134)
T ss_pred hhhHHHHHHHHHh-hccccccccccHHHHhhhhhhhc--------ccCch--hhhhhhe
Confidence 4555555443222 12246799999999999987632 26888 7765544
No 278
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=29.16 E-value=41 Score=26.98 Aligned_cols=23 Identities=26% Similarity=0.748 Sum_probs=18.3
Q ss_pred ccCCCCCceeeecCCCceeEe-ecCC
Q 024566 182 ARCPACGHCVERKDGCSVVMC-RCNT 206 (265)
Q Consensus 182 k~CP~C~~~iek~~GCnhm~C-~C~~ 206 (265)
-.|++|+...++ .=+.|+| .||+
T Consensus 150 A~CsrC~~~L~~--~~~~l~Cp~Cg~ 173 (188)
T COG1096 150 ARCSRCRAPLVK--KGNMLKCPNCGN 173 (188)
T ss_pred EEccCCCcceEE--cCcEEECCCCCC
Confidence 579999999999 4477888 6875
No 279
>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=28.96 E-value=66 Score=24.04 Aligned_cols=35 Identities=17% Similarity=0.679 Sum_probs=25.7
Q ss_pred HHHHHHhcCCcccCCCCCce---eeecCCCceeEe-ecCCc
Q 024566 171 VFGQLVERMKWARCPACGHC---VERKDGCSVVMC-RCNTR 207 (265)
Q Consensus 171 ~~~~~~~~~~~k~CP~C~~~---iek~~GCnhm~C-~C~~~ 207 (265)
.+..++. ..-.||.|+.+ +.|.++=-.+.| .||+.
T Consensus 85 ~L~~fI~--~yVlC~~C~spdT~l~k~~r~~~l~C~aCGa~ 123 (125)
T PF01873_consen 85 LLDKFIK--EYVLCPECGSPDTELIKEGRLIFLKCKACGAS 123 (125)
T ss_dssp HHHHHHC--HHSSCTSTSSSSEEEEEETTCCEEEETTTSCE
T ss_pred HHHHHHH--HEEEcCCCCCCccEEEEcCCEEEEEecccCCc
Confidence 3444443 46899999985 556788889999 59974
No 280
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=28.46 E-value=26 Score=30.96 Aligned_cols=46 Identities=20% Similarity=0.473 Sum_probs=30.0
Q ss_pred CCCcccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCC
Q 024566 17 GGGSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNL 79 (265)
Q Consensus 17 ~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l 79 (265)
+......|.||.++..+. ...+|||.-| |..-+- ..+.||. |.+.|
T Consensus 301 ~~~~p~lcVVcl~e~~~~----~fvpcGh~cc--ct~cs~---------~l~~CPv--CR~rI 346 (355)
T KOG1571|consen 301 ELPQPDLCVVCLDEPKSA----VFVPCGHVCC--CTLCSK---------HLPQCPV--CRQRI 346 (355)
T ss_pred ccCCCCceEEecCCccce----eeecCCcEEE--chHHHh---------hCCCCch--hHHHH
Confidence 345678899999987542 2599999855 432211 2245999 88654
No 281
>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=28.20 E-value=60 Score=23.77 Aligned_cols=24 Identities=29% Similarity=0.726 Sum_probs=13.0
Q ss_pred ccccCCcCcccceeccccccCCcCeeeCCCcc
Q 024566 110 RSYCPNTNCMALVVNECERSGKVKKTQCPNCK 141 (265)
Q Consensus 110 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~ 141 (265)
..+|+ +|+..+.... ..+.||.|+
T Consensus 70 ~~~C~--~Cg~~~~~~~------~~~~CP~Cg 93 (115)
T TIGR00100 70 ECECE--DCSEEVSPEI------DLYRCPKCH 93 (115)
T ss_pred EEEcc--cCCCEEecCC------cCccCcCCc
Confidence 36676 4775554432 234566665
No 282
>PLN02195 cellulose synthase A
Probab=27.62 E-value=53 Score=33.26 Aligned_cols=28 Identities=21% Similarity=0.449 Sum_probs=20.8
Q ss_pred cccceeccccccCCcCeeeCCCccccccccc
Q 024566 118 CMALVVNECERSGKVKKTQCPNCKQWFCFQC 148 (265)
Q Consensus 118 C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C 148 (265)
|+..+-.... ..+.+.|..|++-.|..|
T Consensus 12 cgd~~~~~~~---g~~fvaC~eC~~pvCrpC 39 (977)
T PLN02195 12 CGEEVGVDSN---GEAFVACHECSYPLCKAC 39 (977)
T ss_pred cccccCcCCC---CCeEEEeccCCCccccch
Confidence 6666655433 258899999999999866
No 283
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=27.59 E-value=35 Score=21.73 Aligned_cols=21 Identities=33% Similarity=0.545 Sum_probs=15.7
Q ss_pred HHHHHhcCCcccCCCCCceee
Q 024566 172 FGQLVERMKWARCPACGHCVE 192 (265)
Q Consensus 172 ~~~~~~~~~~k~CP~C~~~ie 192 (265)
+.++......-+||+|...|-
T Consensus 35 LeDl~~GE~VArCPSCSLiv~ 55 (67)
T COG5216 35 LEDLRNGEVVARCPSCSLIVC 55 (67)
T ss_pred HHHhhCCceEEEcCCceEEEE
Confidence 455666677899999988763
No 284
>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=27.51 E-value=77 Score=16.47 Aligned_cols=23 Identities=30% Similarity=0.709 Sum_probs=16.2
Q ss_pred CCCCCceeeecCCCceeEe-ecCC
Q 024566 184 CPACGHCVERKDGCSVVMC-RCNT 206 (265)
Q Consensus 184 CP~C~~~iek~~GCnhm~C-~C~~ 206 (265)
|-+|+.++.--.|=.++.| .|++
T Consensus 1 C~~Cr~~L~yp~GA~sVrCa~C~~ 24 (25)
T PF06943_consen 1 CGGCRTLLMYPRGAPSVRCACCHT 24 (25)
T ss_pred CCCCCceEEcCCCCCCeECCccCc
Confidence 4567777777777777777 4654
No 285
>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=27.28 E-value=19 Score=19.59 Aligned_cols=13 Identities=31% Similarity=0.887 Sum_probs=5.9
Q ss_pred cccCCCCCCCCCC
Q 024566 67 KIDCPGLDCKHNL 79 (265)
Q Consensus 67 ~i~CP~~~C~~~l 79 (265)
.++||..+|...+
T Consensus 2 ~vrCPvkdC~EEv 14 (30)
T PF10426_consen 2 VVRCPVKDCDEEV 14 (30)
T ss_dssp EEE--STT---EE
T ss_pred ccccccccCcchh
Confidence 3789999998665
No 286
>KOG2923 consensus Uncharacterized conserved protein [Function unknown]
Probab=27.21 E-value=47 Score=21.56 Aligned_cols=21 Identities=29% Similarity=0.631 Sum_probs=16.4
Q ss_pred HHHHHhcCCcccCCCCCceee
Q 024566 172 FGQLVERMKWARCPACGHCVE 192 (265)
Q Consensus 172 ~~~~~~~~~~k~CP~C~~~ie 192 (265)
..++.....+-+||+|...|.
T Consensus 35 ~edL~~ge~Va~CpsCSL~I~ 55 (67)
T KOG2923|consen 35 LEDLENGEDVARCPSCSLIIR 55 (67)
T ss_pred HHHHhCCCeeecCCCceEEEE
Confidence 345666778899999998885
No 287
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=27.15 E-value=64 Score=23.54 Aligned_cols=45 Identities=24% Similarity=0.563 Sum_probs=21.9
Q ss_pred ChhHHHHHHHHHHHHhh-cC--------CCccccCCcCcccceeccccccCCcCeeeCCCcc
Q 024566 89 PASLFSKWCDVLCEDYV-LG--------FERSYCPNTNCMALVVNECERSGKVKKTQCPNCK 141 (265)
Q Consensus 89 ~~~~~~~~~~~~~~~~~-~~--------~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~ 141 (265)
.++.++-....+.+..+ .. +-..+|+ +|+..+.... ..+.||.||
T Consensus 40 ~pe~L~f~f~~~~~~T~~egA~L~I~~vp~~~~C~--~Cg~~~~~~~------~~~~CP~Cg 93 (113)
T PRK12380 40 EESAVRFSFEIVCHGTVAQGCDLHIVYKPAQAWCW--DCSQVVEIHQ------HDAQCPHCH 93 (113)
T ss_pred CHHHHHHHHHHHhCCCccCCCEEEEEeeCcEEEcc--cCCCEEecCC------cCccCcCCC
Confidence 44555555555444433 11 2336676 4765554432 233466665
No 288
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=26.82 E-value=89 Score=26.84 Aligned_cols=30 Identities=17% Similarity=0.358 Sum_probs=23.0
Q ss_pred CCccccCCcCcccceeccccccCCcCeeeCCCcccc
Q 024566 108 FERSYCPNTNCMALVVNECERSGKVKKTQCPNCKQW 143 (265)
Q Consensus 108 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 143 (265)
...++|+ .|+........ .....|+.|+..
T Consensus 109 ~~~RFCg--~CG~~~~~~~~----g~~~~C~~cg~~ 138 (279)
T COG2816 109 RSHRFCG--RCGTKTYPREG----GWARVCPKCGHE 138 (279)
T ss_pred hhCcCCC--CCCCcCccccC----ceeeeCCCCCCc
Confidence 4568999 59998877665 578899998754
No 289
>PRK05978 hypothetical protein; Provisional
Probab=26.80 E-value=35 Score=26.34 Aligned_cols=33 Identities=30% Similarity=0.654 Sum_probs=18.4
Q ss_pred CcccCCCCCce-eeecCCCceeEeecCCceeeccCccccCC
Q 024566 180 KWARCPACGHC-VERKDGCSVVMCRCNTRFCYECGRKISSG 219 (265)
Q Consensus 180 ~~k~CP~C~~~-iek~~GCnhm~C~C~~~FC~~C~~~~~~g 219 (265)
-.-+||+|+.- +.+ |=-. -..-|-.||.++.+.
T Consensus 32 l~grCP~CG~G~LF~--g~Lk-----v~~~C~~CG~~~~~~ 65 (148)
T PRK05978 32 FRGRCPACGEGKLFR--AFLK-----PVDHCAACGEDFTHH 65 (148)
T ss_pred HcCcCCCCCCCcccc--cccc-----cCCCccccCCccccC
Confidence 34789999873 222 1111 134566777777654
No 290
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=26.65 E-value=16 Score=31.56 Aligned_cols=18 Identities=28% Similarity=0.521 Sum_probs=15.0
Q ss_pred CcccCCCCCceeeecCCC
Q 024566 180 KWARCPACGHCVERKDGC 197 (265)
Q Consensus 180 ~~k~CP~C~~~iek~~GC 197 (265)
..|.||.|.-.|+|.+-|
T Consensus 122 ~dK~Cp~C~d~VqrIeq~ 139 (389)
T KOG2932|consen 122 SDKICPLCDDRVQRIEQI 139 (389)
T ss_pred ccccCcCcccHHHHHHHh
Confidence 378999999999988765
No 291
>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=26.39 E-value=9.9 Score=19.87 Aligned_cols=16 Identities=19% Similarity=0.534 Sum_probs=10.6
Q ss_pred ccCCCCCCCCCCCccCcc
Q 024566 68 IDCPGLDCKHNLDPFACE 85 (265)
Q Consensus 68 i~CP~~~C~~~l~~~~i~ 85 (265)
+.||. |...++...+.
T Consensus 2 v~CPi--C~~~v~~~~in 17 (26)
T smart00734 2 VQCPV--CFREVPENLIN 17 (26)
T ss_pred CcCCC--CcCcccHHHHH
Confidence 57998 88776544443
No 292
>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=26.08 E-value=97 Score=22.67 Aligned_cols=35 Identities=26% Similarity=0.588 Sum_probs=26.3
Q ss_pred CcccCCCCCceeeecCCCceeEe-ecCCceeeccCcc
Q 024566 180 KWARCPACGHCVERKDGCSVVMC-RCNTRFCYECGRK 215 (265)
Q Consensus 180 ~~k~CP~C~~~iek~~GCnhm~C-~C~~~FC~~C~~~ 215 (265)
..+.|..|+.+.-...+.. ..| .|++.+|-.|+..
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 5589999998765555555 888 6999999999887
No 293
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=26.06 E-value=52 Score=32.41 Aligned_cols=35 Identities=23% Similarity=0.541 Sum_probs=25.1
Q ss_pred cccCCcCcccceeccccccCCcCeeeCCCcccc-----cccccccc
Q 024566 111 SYCPNTNCMALVVNECERSGKVKKTQCPNCKQW-----FCFQCKLK 151 (265)
Q Consensus 111 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~-----~C~~C~~~ 151 (265)
..|| +|+..+..+.. .....|..||+. .|..|+..
T Consensus 445 ~~Cp--~Cd~~lt~H~~----~~~L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 445 AECP--NCDSPLTLHKA----TGQLRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred ccCC--CCCcceEEecC----CCeeEeCCCCCCCCCCCCCCCCCCC
Confidence 3455 47777776655 578889888876 58888776
No 294
>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=25.96 E-value=43 Score=19.30 Aligned_cols=20 Identities=30% Similarity=0.874 Sum_probs=12.7
Q ss_pred ccCCCCCceeeec---CCCceeEe
Q 024566 182 ARCPACGHCVERK---DGCSVVMC 202 (265)
Q Consensus 182 k~CP~C~~~iek~---~GCnhm~C 202 (265)
+.||.|+..+... .| ..+.|
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 5799999866533 33 44555
No 295
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=25.94 E-value=26 Score=27.28 Aligned_cols=31 Identities=19% Similarity=0.255 Sum_probs=20.8
Q ss_pred CCccccCCcCcccceeccccccCCcCeeeCCCcccc
Q 024566 108 FERSYCPNTNCMALVVNECERSGKVKKTQCPNCKQW 143 (265)
Q Consensus 108 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 143 (265)
+..-.||+ |+.-+...+.- ...|.||.||..
T Consensus 107 ~~~Y~Cp~--c~~r~tf~eA~---~~~F~Cp~Cg~~ 137 (158)
T TIGR00373 107 NMFFICPN--MCVRFTFNEAM---ELNFTCPRCGAM 137 (158)
T ss_pred CCeEECCC--CCcEeeHHHHH---HcCCcCCCCCCE
Confidence 44577985 88766655442 357899988854
No 296
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=25.80 E-value=83 Score=23.93 Aligned_cols=17 Identities=24% Similarity=0.696 Sum_probs=8.3
Q ss_pred cccccccccCCCCCChh
Q 024566 144 FCFQCKLKWHAGYRCEE 160 (265)
Q Consensus 144 ~C~~C~~~~H~~~~C~~ 160 (265)
+|+.|...-|....|.+
T Consensus 79 ~C~~Cg~~GH~~~~C~~ 95 (148)
T PTZ00368 79 SCYNCGQTGHISRECPN 95 (148)
T ss_pred ccCcCCCCCcccccCCC
Confidence 45555555555444443
No 297
>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=25.80 E-value=60 Score=20.48 Aligned_cols=31 Identities=16% Similarity=0.391 Sum_probs=18.7
Q ss_pred cccCCcCcccceeccccccCCcCeeeCCCccccccc
Q 024566 111 SYCPNTNCMALVVNECERSGKVKKTQCPNCKQWFCF 146 (265)
Q Consensus 111 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~ 146 (265)
+.|| +|.+.-..-+. ....+.|..|+..+|.
T Consensus 8 VkCp--~C~~~q~vFSh---a~t~V~C~~Cg~~L~~ 38 (55)
T PF01667_consen 8 VKCP--GCYNIQTVFSH---AQTVVKCVVCGTVLAQ 38 (55)
T ss_dssp EE-T--TT-SEEEEETT----SS-EE-SSSTSEEEE
T ss_pred EECC--CCCCeeEEEec---CCeEEEcccCCCEecC
Confidence 5688 68887665433 2578999999988765
No 298
>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=25.75 E-value=1.2e+02 Score=24.39 Aligned_cols=36 Identities=25% Similarity=0.475 Sum_probs=18.6
Q ss_pred CCccccCCcCccc--ceecccccc--CCcCeeeCCCcccc
Q 024566 108 FERSYCPNTNCMA--LVVNECERS--GKVKKTQCPNCKQW 143 (265)
Q Consensus 108 ~~~~~Cp~~~C~~--~~~~~~~~~--~~~~~~~C~~C~~~ 143 (265)
..+-.||+-.|++ .++....+. ....++.||.|+..
T Consensus 97 g~FG~CPRv~C~~~~lLPiGlsd~~g~~~vKlyCP~C~dv 136 (184)
T PF01214_consen 97 GDFGRCPRVYCNGQPLLPIGLSDTPGESTVKLYCPRCKDV 136 (184)
T ss_dssp TTT-B-SBGGGTT-B-EEEBS-SSTTS-BBEEEETTTTEE
T ss_pred CcCCcCCcccCCCCceeCccCCCCCCccceeEECCCCccc
Confidence 5667899999986 333322211 22567777766543
No 299
>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=25.69 E-value=45 Score=25.94 Aligned_cols=26 Identities=27% Similarity=0.816 Sum_probs=17.5
Q ss_pred cccCCCCCceeeecCCCceeEe-ecCCc
Q 024566 181 WARCPACGHCVERKDGCSVVMC-RCNTR 207 (265)
Q Consensus 181 ~k~CP~C~~~iek~~GCnhm~C-~C~~~ 207 (265)
+..||.|+..+...+. ....| +|+..
T Consensus 34 Y~aC~~C~kkv~~~~~-~~~~C~~C~~~ 60 (166)
T cd04476 34 YPACPGCNKKVVEEGN-GTYRCEKCNKS 60 (166)
T ss_pred EccccccCcccEeCCC-CcEECCCCCCc
Confidence 4889999999987765 34444 34433
No 300
>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=25.66 E-value=36 Score=29.31 Aligned_cols=34 Identities=32% Similarity=0.886 Sum_probs=16.6
Q ss_pred ccCCCCCce-----eeecC--CCceeEe-ecCCce------eeccCcc
Q 024566 182 ARCPACGHC-----VERKD--GCSVVMC-RCNTRF------CYECGRK 215 (265)
Q Consensus 182 k~CP~C~~~-----iek~~--GCnhm~C-~C~~~F------C~~C~~~ 215 (265)
..||-|+.. |...+ |=.+++| .|+++| |-.||..
T Consensus 173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R~~Cp~Cg~~ 220 (290)
T PF04216_consen 173 GYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVRIKCPYCGNT 220 (290)
T ss_dssp SS-TTT---EEEEEEE------EEEEEETTT--EEE--TTS-TTT---
T ss_pred CcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecCCCCcCCCCC
Confidence 689999985 33334 8899999 699886 8889888
No 301
>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=25.33 E-value=32 Score=16.64 Aligned_cols=9 Identities=44% Similarity=1.235 Sum_probs=5.0
Q ss_pred eCCCccccc
Q 024566 136 QCPNCKQWF 144 (265)
Q Consensus 136 ~C~~C~~~~ 144 (265)
.|+.|++.|
T Consensus 2 ~C~~C~~~f 10 (23)
T PF00096_consen 2 KCPICGKSF 10 (23)
T ss_dssp EETTTTEEE
T ss_pred CCCCCCCcc
Confidence 466666544
No 302
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=25.19 E-value=1.1e+02 Score=22.38 Aligned_cols=35 Identities=20% Similarity=0.707 Sum_probs=24.5
Q ss_pred HHHHHHhcCCcccCCCCCce---eeecCCCceeEe-ecCCc
Q 024566 171 VFGQLVERMKWARCPACGHC---VERKDGCSVVMC-RCNTR 207 (265)
Q Consensus 171 ~~~~~~~~~~~k~CP~C~~~---iek~~GCnhm~C-~C~~~ 207 (265)
.+..++. ..-.||.|+.+ +.|.++=-.+.| .||+.
T Consensus 72 ~l~~yI~--~yVlC~~C~spdT~l~k~~r~~~l~C~aCGa~ 110 (110)
T smart00653 72 LLRRYIK--EYVLCPECGSPDTELIKENRLFFLKCEACGAR 110 (110)
T ss_pred HHHHHHH--hcEECCCCCCCCcEEEEeCCeEEEEccccCCC
Confidence 3444554 57899999985 556666667889 59863
No 303
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=25.17 E-value=62 Score=29.43 Aligned_cols=11 Identities=18% Similarity=0.606 Sum_probs=7.8
Q ss_pred ccccccccccc
Q 024566 22 FTCEICIEPMA 32 (265)
Q Consensus 22 ~~C~IC~~~~~ 32 (265)
..|.-|-.++.
T Consensus 275 ~iC~~C~K~V~ 285 (468)
T KOG1701|consen 275 GICAFCHKTVS 285 (468)
T ss_pred hhhhhcCCccc
Confidence 37888877764
No 304
>PRK13264 3-hydroxyanthranilate 3,4-dioxygenase; Provisional
Probab=25.12 E-value=31 Score=27.45 Aligned_cols=24 Identities=21% Similarity=0.436 Sum_probs=18.4
Q ss_pred HHHHHHHhcCCcccCCCCCceeee
Q 024566 170 IVFGQLVERMKWARCPACGHCVER 193 (265)
Q Consensus 170 ~~~~~~~~~~~~k~CP~C~~~iek 193 (265)
..+.++..+...|.|++|+..-..
T Consensus 146 ~~~~~f~~~~e~rtC~~CG~v~~~ 169 (177)
T PRK13264 146 PVFAAFYASEELRTCDNCGTVHPG 169 (177)
T ss_pred HHHHHHhcCHhhccCCcCCcccCc
Confidence 456667777788999999987653
No 305
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=24.93 E-value=29 Score=27.62 Aligned_cols=30 Identities=23% Similarity=0.503 Sum_probs=20.5
Q ss_pred CCccccCCcCcccceeccccccCCcCeeeCCCccc
Q 024566 108 FERSYCPNTNCMALVVNECERSGKVKKTQCPNCKQ 142 (265)
Q Consensus 108 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 142 (265)
.....||+ |+.-+...+.- ...|.||.||.
T Consensus 115 ~~~Y~Cp~--C~~rytf~eA~---~~~F~Cp~Cg~ 144 (178)
T PRK06266 115 NMFFFCPN--CHIRFTFDEAM---EYGFRCPQCGE 144 (178)
T ss_pred CCEEECCC--CCcEEeHHHHh---hcCCcCCCCCC
Confidence 34577985 88777665542 35788988875
No 306
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=24.92 E-value=60 Score=18.67 Aligned_cols=13 Identities=23% Similarity=0.437 Sum_probs=8.7
Q ss_pred cCeeeCCCccccc
Q 024566 132 VKKTQCPNCKQWF 144 (265)
Q Consensus 132 ~~~~~C~~C~~~~ 144 (265)
...+.|..|++.|
T Consensus 26 T~fy~C~~C~~~w 38 (39)
T PF01096_consen 26 TLFYVCCNCGHRW 38 (39)
T ss_dssp EEEEEESSSTEEE
T ss_pred eEEEEeCCCCCee
Confidence 5567787777653
No 307
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=24.87 E-value=93 Score=19.91 Aligned_cols=31 Identities=23% Similarity=0.708 Sum_probs=22.3
Q ss_pred ccccccccccccccccccccCCCCChhH-HHHHHHHHHHHhh
Q 024566 21 SFTCEICIEPMAASKKFKNRNLCTHPFC-QDCIARYIQVKVQ 61 (265)
Q Consensus 21 ~~~C~IC~~~~~~~~~~~~~~~C~H~fC-~~Cl~~~~~~~i~ 61 (265)
-..|++|-.+.++++ .|| .+|=+.|...+-+
T Consensus 3 HkHC~~CG~~Ip~~~----------~fCS~~C~~~~~k~qk~ 34 (59)
T PF09889_consen 3 HKHCPVCGKPIPPDE----------SFCSPKCREEYRKRQKR 34 (59)
T ss_pred CCcCCcCCCcCCcch----------hhhCHHHHHHHHHHHHH
Confidence 357999988886543 378 5898888876543
No 308
>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=24.86 E-value=48 Score=27.63 Aligned_cols=12 Identities=33% Similarity=0.880 Sum_probs=6.0
Q ss_pred CcccCCCCCcee
Q 024566 180 KWARCPACGHCV 191 (265)
Q Consensus 180 ~~k~CP~C~~~i 191 (265)
....||.|+...
T Consensus 34 ~v~~C~~Cg~~~ 45 (236)
T PF04981_consen 34 EVTICPKCGRYR 45 (236)
T ss_pred CceECCCCCCEE
Confidence 345555555544
No 309
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.67 E-value=65 Score=21.45 Aligned_cols=58 Identities=24% Similarity=0.668 Sum_probs=35.2
Q ss_pred ccccccccccccccccccCCC--CChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCCccCccCCCChhHHHHHH
Q 024566 23 TCEICIEPMAASKKFKNRNLC--THPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDPFACEPVIPASLFSKWC 97 (265)
Q Consensus 23 ~C~IC~~~~~~~~~~~~~~~C--~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~ 97 (265)
.|.-|-.++++... ..+-| .|.||.+|...-+. + .||. |+..|...-++ +...+.+|-
T Consensus 7 nCECCDrDLpp~s~--dA~ICtfEcTFCadCae~~l~----g------~CPn--CGGelv~RP~R---Paa~L~r~P 66 (84)
T COG3813 7 NCECCDRDLPPDST--DARICTFECTFCADCAENRLH----G------LCPN--CGGELVARPIR---PAAKLARYP 66 (84)
T ss_pred CCcccCCCCCCCCC--ceeEEEEeeehhHhHHHHhhc----C------cCCC--CCchhhcCcCC---hHHHHhhCc
Confidence 57777777765432 12445 58999999765442 1 6998 99776543332 444555554
No 310
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=24.60 E-value=72 Score=19.66 Aligned_cols=30 Identities=27% Similarity=0.676 Sum_probs=20.6
Q ss_pred ccccccccccccccccccCCCCChhHHHHHHHH
Q 024566 23 TCEICIEPMAASKKFKNRNLCTHPFCQDCIARY 55 (265)
Q Consensus 23 ~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~ 55 (265)
.|.||-++......+ -+.=| ..|.+|+.+.
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 489998887533222 24455 7999999876
No 311
>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=24.45 E-value=34 Score=23.93 Aligned_cols=29 Identities=24% Similarity=0.732 Sum_probs=19.0
Q ss_pred CcccCCCCCceeeecCCCceeEe-ecCCce
Q 024566 180 KWARCPACGHCVERKDGCSVVMC-RCNTRF 208 (265)
Q Consensus 180 ~~k~CP~C~~~iek~~GCnhm~C-~C~~~F 208 (265)
.--.||.|+..-.|..+----.| +|+..|
T Consensus 34 ~ky~Cp~Cgk~~vkR~a~GIW~C~~C~~~~ 63 (90)
T PF01780_consen 34 AKYTCPFCGKTSVKRVATGIWKCKKCGKKF 63 (90)
T ss_dssp S-BEESSSSSSEEEEEETTEEEETTTTEEE
T ss_pred CCCcCCCCCCceeEEeeeEEeecCCCCCEE
Confidence 34679999998877655555566 465544
No 312
>PF04236 Transp_Tc5_C: Tc5 transposase C-terminal domain; InterPro: IPR007350 This domain corresponds to a C-terminal cysteine rich region that probably binds to a metal ion and could be DNA-binding. It is found in association with the DDE superfamily (IPR004875 from INTERPRO) and the Tc5 transposase family (IPR004906 from INTERPRO). More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=24.40 E-value=81 Score=20.48 Aligned_cols=32 Identities=25% Similarity=0.545 Sum_probs=23.8
Q ss_pred CCccccCCcCcccceeccccccCCcCeeeCCCccccccccccc
Q 024566 108 FERSYCPNTNCMALVVNECERSGKVKKTQCPNCKQWFCFQCKL 150 (265)
Q Consensus 108 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~ 150 (265)
.....|+.++|+. ...+.|..|.+.+|+.+-.
T Consensus 25 ~~~~~C~~~gC~~-----------~s~I~C~~Ckk~~Cf~Hfi 56 (63)
T PF04236_consen 25 NVAGDCDITGCNN-----------TSFIRCAYCKKSLCFNHFI 56 (63)
T ss_pred CCcCcCCCCCCCC-----------cCEEEccccCCccccccee
Confidence 3446677777755 4578999999999998765
No 313
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=24.39 E-value=67 Score=22.93 Aligned_cols=28 Identities=32% Similarity=0.818 Sum_probs=17.6
Q ss_pred cccCCCCCce------eeecCCCceeEe-ecCCce
Q 024566 181 WARCPACGHC------VERKDGCSVVMC-RCNTRF 208 (265)
Q Consensus 181 ~k~CP~C~~~------iek~~GCnhm~C-~C~~~F 208 (265)
+-.||.|+.. +.|..+=--++| .||..|
T Consensus 22 ~FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~ 56 (104)
T COG4888 22 TFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSF 56 (104)
T ss_pred eEecCccCCeeeeEEEEEecCceeEEEcccCcceE
Confidence 4569999874 345555556666 466554
No 314
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=23.93 E-value=1.7e+02 Score=18.66 Aligned_cols=34 Identities=18% Similarity=0.301 Sum_probs=23.6
Q ss_pred cCCCCCCCCCCCccCccCCCChhHHHHHHHHHHHHh
Q 024566 69 DCPGLDCKHNLDPFACEPVIPASLFSKWCDVLCEDY 104 (265)
Q Consensus 69 ~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~~~~~~~ 104 (265)
+||. |+...-...--..-+.|-+.+|...+.+..
T Consensus 19 ~Cp~--CG~~t~~~~PprFSPeD~y~kYR~~lkk~~ 52 (59)
T COG2260 19 KCPV--CGGDTKVPHPPRFSPEDKYGKYRRELKKRL 52 (59)
T ss_pred cCCC--CCCccccCCCCCCCccchHHHHHHHHHHHh
Confidence 5998 887655554455556678889988776654
No 315
>PRK14873 primosome assembly protein PriA; Provisional
Probab=23.93 E-value=77 Score=30.93 Aligned_cols=30 Identities=17% Similarity=0.360 Sum_probs=16.5
Q ss_pred CcccceeccccccCCcCeeeCCCcccc----ccccccc
Q 024566 117 NCMALVVNECERSGKVKKTQCPNCKQW----FCFQCKL 150 (265)
Q Consensus 117 ~C~~~~~~~~~~~~~~~~~~C~~C~~~----~C~~C~~ 150 (265)
.|+..+..+.. .....|..||+. .|..|+.
T Consensus 397 ~C~~~L~~h~~----~~~l~Ch~CG~~~~p~~Cp~Cgs 430 (665)
T PRK14873 397 HCTGPLGLPSA----GGTPRCRWCGRAAPDWRCPRCGS 430 (665)
T ss_pred CCCCceeEecC----CCeeECCCCcCCCcCccCCCCcC
Confidence 36666655433 346777777653 2555544
No 316
>KOG2789 consensus Putative Zn-finger protein [General function prediction only]
Probab=23.81 E-value=32 Score=30.86 Aligned_cols=35 Identities=23% Similarity=0.635 Sum_probs=27.4
Q ss_pred cccccccccccccccccccccCCCCChhHHHHHHHHH
Q 024566 20 SSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYI 56 (265)
Q Consensus 20 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~ 56 (265)
...+|+|||-.++...++ ..-|.-.+|.+|+..+-
T Consensus 73 r~~ecpicflyyps~~n~--~rcC~~~Ic~ecf~~~~ 107 (482)
T KOG2789|consen 73 RKTECPICFLYYPSAKNL--VRCCSETICGECFAPFG 107 (482)
T ss_pred ccccCceeeeecccccch--hhhhccchhhhheeccc
Confidence 458999999998654553 35689999999998753
No 317
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=23.79 E-value=1e+02 Score=23.30 Aligned_cols=35 Identities=20% Similarity=0.589 Sum_probs=23.9
Q ss_pred HHHHHHhcCCcccCCCCCce---eeecCCCceeEe-ecCCc
Q 024566 171 VFGQLVERMKWARCPACGHC---VERKDGCSVVMC-RCNTR 207 (265)
Q Consensus 171 ~~~~~~~~~~~k~CP~C~~~---iek~~GCnhm~C-~C~~~ 207 (265)
.+..++. ..-.||.|+.+ +.|.+.=..+.| .||+.
T Consensus 89 ~L~~yI~--~yVlC~~C~sPdT~l~k~~r~~~l~C~ACGa~ 127 (133)
T TIGR00311 89 RIEDYVR--KYVICRECNRPDTRIIKEGRVSLLKCEACGAK 127 (133)
T ss_pred HHHHHHh--heEECCCCCCCCcEEEEeCCeEEEecccCCCC
Confidence 3444443 57899999985 456665556899 59875
No 318
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=23.74 E-value=32 Score=24.03 Aligned_cols=8 Identities=13% Similarity=0.169 Sum_probs=4.0
Q ss_pred Ccccceec
Q 024566 117 NCMALVVN 124 (265)
Q Consensus 117 ~C~~~~~~ 124 (265)
+||+.+..
T Consensus 63 kCGfef~~ 70 (97)
T COG3357 63 KCGFEFRD 70 (97)
T ss_pred ccCccccc
Confidence 35555544
No 319
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=23.67 E-value=1.1e+02 Score=22.86 Aligned_cols=34 Identities=21% Similarity=0.473 Sum_probs=21.0
Q ss_pred CccccCCcCccccee-ccccccCCcCeeeCCCccccc
Q 024566 109 ERSYCPNTNCMALVV-NECERSGKVKKTQCPNCKQWF 144 (265)
Q Consensus 109 ~~~~Cp~~~C~~~~~-~~~~~~~~~~~~~C~~C~~~~ 144 (265)
.-..||. |..... .......+.++..|+.|+..|
T Consensus 29 ~~~~cP~--C~s~~~~k~g~~~~~~qRyrC~~C~~tf 63 (129)
T COG3677 29 TKVNCPR--CKSSNVVKIGGIRRGHQRYKCKSCGSTF 63 (129)
T ss_pred ccCcCCC--CCccceeeECCccccccccccCCcCcce
Confidence 3478985 776662 222222236788999888766
No 320
>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=23.60 E-value=27 Score=34.62 Aligned_cols=34 Identities=29% Similarity=0.821 Sum_probs=0.0
Q ss_pred CcccCCCCCceeeecCCCceeEe-ecCCc-----eeeccCccccCC
Q 024566 180 KWARCPACGHCVERKDGCSVVMC-RCNTR-----FCYECGRKISSG 219 (265)
Q Consensus 180 ~~k~CP~C~~~iek~~GCnhm~C-~C~~~-----FC~~C~~~~~~g 219 (265)
..++||+|+..... -+| .||.+ +|..|+......
T Consensus 654 ~~r~Cp~Cg~~t~~------~~Cp~CG~~T~~~~~Cp~C~~~~~~~ 693 (900)
T PF03833_consen 654 GRRRCPKCGKETFY------NRCPECGSHTEPVYVCPDCGIEVEED 693 (900)
T ss_dssp ----------------------------------------------
T ss_pred ecccCcccCCcchh------hcCcccCCccccceeccccccccCcc
Confidence 34899999998653 678 58876 899998886543
No 321
>PF01530 zf-C2HC: Zinc finger, C2HC type; InterPro: IPR002515 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (C2HC) type zinc finger domain found in eukaryotes. Proteins containing these domains include: MYST family histone acetyltransferases [, [] Myelin transcription factor Myt1 [] Suppressor of tumourigenicity protein 18 (ST18) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2CS8_A 1PXE_A 2JX1_A 2JYD_A.
Probab=23.54 E-value=45 Score=18.31 Aligned_cols=11 Identities=27% Similarity=0.927 Sum_probs=6.9
Q ss_pred ccCCCCCCCCC
Q 024566 68 IDCPGLDCKHN 78 (265)
Q Consensus 68 i~CP~~~C~~~ 78 (265)
.+||.++|...
T Consensus 2 ~~CPtpGCdg~ 12 (31)
T PF01530_consen 2 LKCPTPGCDGS 12 (31)
T ss_dssp TSSSSTT--SC
T ss_pred CcCCCCCCCcc
Confidence 57999999853
No 322
>PF05715 zf-piccolo: Piccolo Zn-finger; InterPro: IPR008899 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 (predicted) zinc finger is found in the bassoon and piccolo proteins, both of which are components of the presynaptic cytoskeletal matrix (PCM) assembled at the active zone of neurotransmitter release, where Piccolo plays a role in the trafficking of synaptic vesicles (SVs) [, , ]. The Piccolo zinc fingers were found to interact with the dual prenylated rab3A and VAMP2/Synaptobrevin II receptor PRA1. There are eight conserved cysteines in Piccolo-type zinc fingers, suggesting that they coordinates two zinc ligands. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding, 0045202 synapse
Probab=23.36 E-value=27 Score=22.29 Aligned_cols=34 Identities=29% Similarity=0.761 Sum_probs=26.1
Q ss_pred ccCCCCCceeee--cCCCceeEe-ecCCceeeccCcc
Q 024566 182 ARCPACGHCVER--KDGCSVVMC-RCNTRFCYECGRK 215 (265)
Q Consensus 182 k~CP~C~~~iek--~~GCnhm~C-~C~~~FC~~C~~~ 215 (265)
..||-|+.-..- .+-=|+=+| .|+...|-.||-.
T Consensus 3 ~~CPlCkt~~n~gsk~~pNyntCT~Ck~~VCnlCGFN 39 (61)
T PF05715_consen 3 SLCPLCKTTLNVGSKDPPNYNTCTECKSQVCNLCGFN 39 (61)
T ss_pred ccCCcccchhhcCCCCCCCccHHHHHhhhhhcccCCC
Confidence 468888886622 244688999 7999999999866
No 323
>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=23.32 E-value=37 Score=26.56 Aligned_cols=20 Identities=30% Similarity=0.640 Sum_probs=15.4
Q ss_pred HHHHHHHhcCCcccCCCCCc
Q 024566 170 IVFGQLVERMKWARCPACGH 189 (265)
Q Consensus 170 ~~~~~~~~~~~~k~CP~C~~ 189 (265)
..+.++..+...|.|++|+.
T Consensus 140 ~~~~~f~~~~~~rtC~~Cg~ 159 (159)
T TIGR03037 140 PVFEHFYSNEDARTCKNCGH 159 (159)
T ss_pred HHHHHHhCChhhccCCccCC
Confidence 35666777778899999984
No 324
>PRK08115 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=23.31 E-value=39 Score=33.78 Aligned_cols=24 Identities=38% Similarity=1.092 Sum_probs=18.9
Q ss_pred ccCCCCCc-eeeecCCCceeEe-ecCCc
Q 024566 182 ARCPACGH-CVERKDGCSVVMC-RCNTR 207 (265)
Q Consensus 182 k~CP~C~~-~iek~~GCnhm~C-~C~~~ 207 (265)
-.||-|+. .|+..|||| +| .||++
T Consensus 828 ~~cp~c~~~~~~~~~~c~--~c~~c~~~ 853 (858)
T PRK08115 828 NTCPVCREGTVEEIGGCN--TCTNCGAQ 853 (858)
T ss_pred CCCCccCCCceeecCCCc--cccchhhh
Confidence 48999998 567889998 67 47665
No 325
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=23.07 E-value=50 Score=20.75 Aligned_cols=14 Identities=29% Similarity=0.945 Sum_probs=11.3
Q ss_pred CCceeeccCccccC
Q 024566 205 NTRFCYECGRKISS 218 (265)
Q Consensus 205 ~~~FC~~C~~~~~~ 218 (265)
.+.|||-||..+..
T Consensus 26 ~~~YC~~Cg~~Y~d 39 (55)
T PF13821_consen 26 EHNYCFWCGTKYDD 39 (55)
T ss_pred hCceeeeeCCccCC
Confidence 47899999998763
No 326
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=22.97 E-value=17 Score=22.29 Aligned_cols=37 Identities=19% Similarity=0.509 Sum_probs=28.5
Q ss_pred CcccccccccccccccccccccCCCCChhHHHHHHHHH
Q 024566 19 GSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYI 56 (265)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~ 56 (265)
...++|..|-+.++. ..++...-||.--|..||+.-.
T Consensus 5 Fsry~CDLCn~~~p~-~~LRQCvlCGRWaC~sCW~deY 41 (57)
T PF14445_consen 5 FSRYSCDLCNSSHPI-SELRQCVLCGRWACNSCWQDEY 41 (57)
T ss_pred HhhHhHHhhcccCcH-HHHHHHhhhchhhhhhhhhhhH
Confidence 457899999998854 3455567799999999998643
No 327
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=22.92 E-value=1.2e+02 Score=23.15 Aligned_cols=34 Identities=24% Similarity=0.680 Sum_probs=23.8
Q ss_pred HHHHHhcCCcccCCCCCce---eeecCCCceeEe-ecCCc
Q 024566 172 FGQLVERMKWARCPACGHC---VERKDGCSVVMC-RCNTR 207 (265)
Q Consensus 172 ~~~~~~~~~~k~CP~C~~~---iek~~GCnhm~C-~C~~~ 207 (265)
+..++. ..-.||.|+.+ +.|.+.=-.+.| .||+.
T Consensus 95 L~~yI~--~yVlC~~C~spdT~l~k~~r~~~l~C~ACGa~ 132 (138)
T PRK03988 95 IDRYVK--EYVICPECGSPDTKLIKEGRIWVLKCEACGAE 132 (138)
T ss_pred HHHHHH--hcEECCCCCCCCcEEEEcCCeEEEEcccCCCC
Confidence 344444 57899999985 556666567889 59875
No 328
>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=22.36 E-value=42 Score=18.28 Aligned_cols=9 Identities=56% Similarity=1.257 Sum_probs=6.2
Q ss_pred cCCCCCcee
Q 024566 183 RCPACGHCV 191 (265)
Q Consensus 183 ~CP~C~~~i 191 (265)
.||+|++-+
T Consensus 3 lcpkcgvgv 11 (36)
T PF09151_consen 3 LCPKCGVGV 11 (36)
T ss_dssp B-TTTSSSB
T ss_pred cCCccCceE
Confidence 599999855
No 329
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=22.31 E-value=85 Score=25.76 Aligned_cols=37 Identities=22% Similarity=0.482 Sum_probs=23.2
Q ss_pred CCccccCCcCcccceeccccccC--------CcCeeeCCCccccc
Q 024566 108 FERSYCPNTNCMALVVNECERSG--------KVKKTQCPNCKQWF 144 (265)
Q Consensus 108 ~~~~~Cp~~~C~~~~~~~~~~~~--------~~~~~~C~~C~~~~ 144 (265)
..++-||.|+|..++........ ..-++.|..|+..|
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 56788999999998865443211 12356776665443
No 330
>PHA02325 hypothetical protein
Probab=22.31 E-value=50 Score=21.39 Aligned_cols=12 Identities=33% Similarity=0.706 Sum_probs=8.1
Q ss_pred CcccCCCCCcee
Q 024566 180 KWARCPACGHCV 191 (265)
Q Consensus 180 ~~k~CP~C~~~i 191 (265)
..|.||+|+.+-
T Consensus 2 ~~k~CPkC~A~W 13 (72)
T PHA02325 2 DTKICPKCGARW 13 (72)
T ss_pred CccccCccCCEe
Confidence 457788887653
No 331
>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=22.31 E-value=1.7e+02 Score=22.26 Aligned_cols=54 Identities=17% Similarity=0.209 Sum_probs=29.4
Q ss_pred ChhHHHHHHHHHHHHhhc---CCCccccCCcCcccceecccccc-----------CCcCeeeCCCccccc
Q 024566 89 PASLFSKWCDVLCEDYVL---GFERSYCPNTNCMALVVNECERS-----------GKVKKTQCPNCKQWF 144 (265)
Q Consensus 89 ~~~~~~~~~~~~~~~~~~---~~~~~~Cp~~~C~~~~~~~~~~~-----------~~~~~~~C~~C~~~~ 144 (265)
+.+..+++.+.+..--+. .+....|| .|+..+...+..+ .......|+.|++.|
T Consensus 67 ~~~~~~QL~ev~~~~~l~~~~~~~~sRC~--~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiy 134 (147)
T PF01927_consen 67 SDDPEEQLREVLERFGLKLRLDPIFSRCP--KCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIY 134 (147)
T ss_pred CCCHHHHHHHHHHHcCCccccCCCCCccC--CCCcEeeechhhccccccCccccccCCeEEECCCCCCEe
Confidence 334555555554433332 23368899 5988775443221 012367788777655
No 332
>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=22.23 E-value=71 Score=29.97 Aligned_cols=33 Identities=30% Similarity=0.624 Sum_probs=24.7
Q ss_pred cCCcCcccceeccccccCCcCeeeCCCcccc-----cccccccc
Q 024566 113 CPNTNCMALVVNECERSGKVKKTQCPNCKQW-----FCFQCKLK 151 (265)
Q Consensus 113 Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~-----~C~~C~~~ 151 (265)
|| .|+..+..+.. ...+.|..||+. .|..|+..
T Consensus 225 C~--~C~~~l~~h~~----~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 225 CP--NCDVSLTYHKK----EGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred CC--CCCCceEEecC----CCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 66 48877776654 568899999876 59999764
No 333
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.21 E-value=49 Score=21.50 Aligned_cols=15 Identities=33% Similarity=0.603 Sum_probs=11.7
Q ss_pred CCcccCCCCCceeee
Q 024566 179 MKWARCPACGHCVER 193 (265)
Q Consensus 179 ~~~k~CP~C~~~iek 193 (265)
..+.+||.|+.+++.
T Consensus 5 ~~~v~CP~Cgkpv~w 19 (65)
T COG3024 5 RITVPCPTCGKPVVW 19 (65)
T ss_pred cccccCCCCCCcccc
Confidence 356789999999873
No 334
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=22.10 E-value=88 Score=18.08 Aligned_cols=12 Identities=17% Similarity=0.390 Sum_probs=7.8
Q ss_pred cCeeeCCCcccc
Q 024566 132 VKKTQCPNCKQW 143 (265)
Q Consensus 132 ~~~~~C~~C~~~ 143 (265)
...+.|..|++.
T Consensus 26 T~fy~C~~C~~~ 37 (40)
T smart00440 26 TVFYVCTKCGHR 37 (40)
T ss_pred eEEEEeCCCCCE
Confidence 456777777654
No 335
>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=21.90 E-value=24 Score=21.50 Aligned_cols=44 Identities=23% Similarity=0.601 Sum_probs=21.5
Q ss_pred cccccccccccccccccccCCC-CChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCCc
Q 024566 22 FTCEICIEPMAASKKFKNRNLC-THPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDP 81 (265)
Q Consensus 22 ~~C~IC~~~~~~~~~~~~~~~C-~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~ 81 (265)
..|--|+-... . +..| .|..|..|+...+. ..-.||. |+.+++.
T Consensus 3 ~nCKsCWf~~k---~---Li~C~dHYLCl~CLt~ml~--------~s~~C~i--C~~~LPt 47 (50)
T PF03854_consen 3 YNCKSCWFANK---G---LIKCSDHYLCLNCLTLMLS--------RSDRCPI--CGKPLPT 47 (50)
T ss_dssp ----SS-S--S---S---EEE-SS-EEEHHHHHHT-S--------SSSEETT--TTEE---
T ss_pred ccChhhhhcCC---C---eeeecchhHHHHHHHHHhc--------cccCCCc--ccCcCcc
Confidence 34556655432 2 3556 69999999987664 2337998 9887654
No 336
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=21.74 E-value=56 Score=22.89 Aligned_cols=29 Identities=28% Similarity=0.786 Sum_probs=20.5
Q ss_pred CcccCCCCCceeeecCCCceeEe-ecCCce
Q 024566 180 KWARCPACGHCVERKDGCSVVMC-RCNTRF 208 (265)
Q Consensus 180 ~~k~CP~C~~~iek~~GCnhm~C-~C~~~F 208 (265)
..-.||.|+..-.|..+----.| .|+..|
T Consensus 35 a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~ 64 (90)
T PRK03976 35 AKHVCPVCGRPKVKRVGTGIWECRKCGAKF 64 (90)
T ss_pred cCccCCCCCCCceEEEEEEEEEcCCCCCEE
Confidence 44689999888777766666666 466654
No 337
>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=21.64 E-value=52 Score=16.87 Aligned_cols=13 Identities=38% Similarity=0.861 Sum_probs=8.7
Q ss_pred cCeeeCCCccccc
Q 024566 132 VKKTQCPNCKQWF 144 (265)
Q Consensus 132 ~~~~~C~~C~~~~ 144 (265)
...+.|+.|++.|
T Consensus 12 ~k~~~C~~C~k~F 24 (26)
T PF13465_consen 12 EKPYKCPYCGKSF 24 (26)
T ss_dssp SSSEEESSSSEEE
T ss_pred CCCCCCCCCcCee
Confidence 3457788887655
No 338
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=21.50 E-value=47 Score=20.75 Aligned_cols=12 Identities=33% Similarity=0.797 Sum_probs=9.9
Q ss_pred cccCCCCCceee
Q 024566 181 WARCPACGHCVE 192 (265)
Q Consensus 181 ~k~CP~C~~~ie 192 (265)
-++||+|+..-+
T Consensus 24 e~KCPrCK~vN~ 35 (60)
T COG4416 24 EKKCPRCKEVNE 35 (60)
T ss_pred eecCCccceeee
Confidence 389999998765
No 339
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=21.49 E-value=83 Score=23.11 Aligned_cols=47 Identities=19% Similarity=0.342 Sum_probs=22.8
Q ss_pred CChhHHHHHHHHHHHHh-h-cC--------CCccccCCcCcccceeccccccCCcCeeeCCCcc
Q 024566 88 IPASLFSKWCDVLCEDY-V-LG--------FERSYCPNTNCMALVVNECERSGKVKKTQCPNCK 141 (265)
Q Consensus 88 l~~~~~~~~~~~~~~~~-~-~~--------~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~ 141 (265)
+.++.++-....+.+.. + .. +-..+|+ +|+..+..... ....||.|+
T Consensus 39 V~pe~L~faf~~~~~~T~~~ega~L~Ie~vp~~~~C~--~Cg~~~~~~~~-----~~~~CP~Cg 95 (117)
T PRK00564 39 MDKSLFVSAFETFREESLVCKDAILDIVDEKVELECK--DCSHVFKPNAL-----DYGVCEKCH 95 (117)
T ss_pred cCHHHHHHHHHHHhcCCcccCCCEEEEEecCCEEEhh--hCCCccccCCc-----cCCcCcCCC
Confidence 34455555555555554 3 21 2235676 47755544321 123466665
No 340
>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=21.39 E-value=1.2e+02 Score=19.48 Aligned_cols=24 Identities=13% Similarity=0.387 Sum_probs=15.9
Q ss_pred CcccCCCCCCCCCCCccCccCCCChhHHHHHHHHHH
Q 024566 66 AKIDCPGLDCKHNLDPFACEPVIPASLFSKWCDVLC 101 (265)
Q Consensus 66 ~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~~~~ 101 (265)
.||+|+. |+.++. +.++.|.+.+.
T Consensus 3 iPVRCFT--CGkvi~----------~~~e~y~~~~~ 26 (60)
T PF01194_consen 3 IPVRCFT--CGKVIG----------NKWEEYLERLE 26 (60)
T ss_dssp -SSS-ST--TTSBTC----------GHHHHHHHHHH
T ss_pred CceecCC--CCCChh----------HhHHHHHHHHH
Confidence 5899998 998774 45666766654
No 341
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=21.39 E-value=47 Score=22.23 Aligned_cols=17 Identities=29% Similarity=0.479 Sum_probs=12.4
Q ss_pred ccccCCcCcccceeccc
Q 024566 110 RSYCPNTNCMALVVNEC 126 (265)
Q Consensus 110 ~~~Cp~~~C~~~~~~~~ 126 (265)
+..|.+++|+.-+....
T Consensus 27 Y~qC~N~eCg~tF~t~e 43 (72)
T PRK09678 27 YHQCQNVNCSATFITYE 43 (72)
T ss_pred eeecCCCCCCCEEEEEE
Confidence 35699889998776543
No 342
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=21.23 E-value=75 Score=22.95 Aligned_cols=27 Identities=26% Similarity=0.780 Sum_probs=17.3
Q ss_pred cccCCCCCceeeecCCCceeEe-ecCCce
Q 024566 181 WARCPACGHCVERKDGCSVVMC-RCNTRF 208 (265)
Q Consensus 181 ~k~CP~C~~~iek~~GCnhm~C-~C~~~F 208 (265)
.-.||+|..-..=.+|= +|.| .|.++|
T Consensus 3 lp~cp~c~sEytYed~~-~~~cpec~~ew 30 (112)
T COG2824 3 LPPCPKCNSEYTYEDGG-QLICPECAHEW 30 (112)
T ss_pred CCCCCccCCceEEecCc-eEeCchhcccc
Confidence 35799997755443332 7888 477665
No 343
>PF06221 zf-C2HC5: Putative zinc finger motif, C2HC5-type; InterPro: IPR009349 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 zinc finger appears to be common in activating signal cointegrator 1/thyroid receptor interacting protein 4. 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, 0005634 nucleus
Probab=21.20 E-value=66 Score=20.43 Aligned_cols=12 Identities=33% Similarity=0.902 Sum_probs=7.8
Q ss_pred eeCCCccccccc
Q 024566 135 TQCPNCKQWFCF 146 (265)
Q Consensus 135 ~~C~~C~~~~C~ 146 (265)
-.|..||+.+|.
T Consensus 19 ~NCl~CGkIiC~ 30 (57)
T PF06221_consen 19 PNCLNCGKIICE 30 (57)
T ss_pred ccccccChhhcc
Confidence 356677776665
No 344
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=20.90 E-value=78 Score=27.62 Aligned_cols=55 Identities=18% Similarity=0.309 Sum_probs=34.3
Q ss_pred CcccccccccccccccccccccCCCCChhHHHHHHHHHHHHhhCCCCCcccCCCCCCCCCCCc
Q 024566 19 GSSFTCEICIEPMAASKKFKNRNLCTHPFCQDCIARYIQVKVQDDNTAKIDCPGLDCKHNLDP 81 (265)
Q Consensus 19 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~ 81 (265)
.+.+.||+=-+... .++-+.++.|||.+=++=+...-+ ++...++||- |...-..
T Consensus 334 Hs~FiCPVlKe~~t-~ENpP~ml~CgHVIskeal~~LS~-----nG~~~FKCPY--CP~~~~~ 388 (396)
T COG5109 334 HSLFICPVLKELCT-DENPPVMLECGHVISKEALSVLSQ-----NGVLSFKCPY--CPEMSKY 388 (396)
T ss_pred cceeeccccHhhhc-ccCCCeeeeccceeeHHHHHHHhh-----cCcEEeeCCC--CCcchhh
Confidence 45678887544332 122233699999987776554332 3456899998 8754333
No 345
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=20.86 E-value=70 Score=24.23 Aligned_cols=26 Identities=27% Similarity=0.764 Sum_probs=15.7
Q ss_pred cccCC--CCCceeeecCCCceeEe-ecCCc
Q 024566 181 WARCP--ACGHCVERKDGCSVVMC-RCNTR 207 (265)
Q Consensus 181 ~k~CP--~C~~~iek~~GCnhm~C-~C~~~ 207 (265)
+..|| .|+..+...+ =+...| +|+..
T Consensus 18 Y~aC~~~~C~kKv~~~~-~~~y~C~~C~~~ 46 (146)
T PF08646_consen 18 YPACPNEKCNKKVTENG-DGSYRCEKCNKT 46 (146)
T ss_dssp EEE-TSTTTS-B-EEET-TTEEEETTTTEE
T ss_pred ECCCCCccCCCEeecCC-CcEEECCCCCCc
Confidence 47899 9999888773 355666 56644
No 346
>KOG4218 consensus Nuclear hormone receptor betaFTZ-F1 [Transcription]
Probab=20.84 E-value=73 Score=28.15 Aligned_cols=20 Identities=10% Similarity=-0.104 Sum_probs=10.9
Q ss_pred hhhhHHHHHHHHHHHHHHhh
Q 024566 229 QLTILTIAMMVIFHVIVLAG 248 (265)
Q Consensus 229 ~~~~~~~~~~~~~~~~~~~~ 248 (265)
.||-.+++....-++.+.|.
T Consensus 102 pmYKrDRAlkqQkkAqirAn 121 (475)
T KOG4218|consen 102 PMYKRDRALKQQKKAQIRAN 121 (475)
T ss_pred chhhhhHHHHHHHHHHhhhc
Confidence 56666666555555444443
No 347
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=20.72 E-value=56 Score=18.60 Aligned_cols=18 Identities=22% Similarity=0.584 Sum_probs=10.3
Q ss_pred ccccccccccCCCCCChh
Q 024566 143 WFCFQCKLKWHAGYRCEE 160 (265)
Q Consensus 143 ~~C~~C~~~~H~~~~C~~ 160 (265)
..|++|++..|....|..
T Consensus 3 ~~CprC~kg~Hwa~~C~s 20 (36)
T PF14787_consen 3 GLCPRCGKGFHWASECRS 20 (36)
T ss_dssp -C-TTTSSSCS-TTT---
T ss_pred ccCcccCCCcchhhhhhh
Confidence 357888899999888864
No 348
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=20.71 E-value=67 Score=26.95 Aligned_cols=59 Identities=17% Similarity=0.265 Sum_probs=35.1
Q ss_pred CccCCCChhHHHHHHHHHHHH-hhc--CCCccccCCcCcccceeccccc--cCCcCeeeCCCcccc
Q 024566 83 ACEPVIPASLFSKWCDVLCED-YVL--GFERSYCPNTNCMALVVNECER--SGKVKKTQCPNCKQW 143 (265)
Q Consensus 83 ~i~~~l~~~~~~~~~~~~~~~-~~~--~~~~~~Cp~~~C~~~~~~~~~~--~~~~~~~~C~~C~~~ 143 (265)
.+..-++++++..|.+..... -+. .-.-..|. +|.-.++..... ......++||.||..
T Consensus 167 ~L~~~l~~ell~~yeri~~~~kg~gvvpl~g~~C~--GC~m~l~~~~~~~V~~~d~iv~CP~CgRI 230 (239)
T COG1579 167 ELKEKLDPELLSEYERIRKNKKGVGVVPLEGRVCG--GCHMKLPSQTLSKVRKKDEIVFCPYCGRI 230 (239)
T ss_pred HHHHhcCHHHHHHHHHHHhcCCCceEEeecCCccc--CCeeeecHHHHHHHhcCCCCccCCccchH
Confidence 345567889999999876544 111 11235566 577666543221 113567899999854
No 349
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=20.56 E-value=66 Score=19.74 Aligned_cols=17 Identities=24% Similarity=0.966 Sum_probs=12.5
Q ss_pred eeEee-cCCceeeccCcc
Q 024566 199 VVMCR-CNTRFCYECGRK 215 (265)
Q Consensus 199 hm~C~-C~~~FC~~C~~~ 215 (265)
+++|+ ||.+|=|.=+..
T Consensus 4 ~l~C~dCg~~FvfTa~EQ 21 (49)
T PF13451_consen 4 TLTCKDCGAEFVFTAGEQ 21 (49)
T ss_pred eEEcccCCCeEEEehhHH
Confidence 47784 888888876665
No 350
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=20.39 E-value=75 Score=26.09 Aligned_cols=18 Identities=28% Similarity=0.641 Sum_probs=14.1
Q ss_pred cccCCCCCCCCCCCccCccC
Q 024566 67 KIDCPGLDCKHNLDPFACEP 86 (265)
Q Consensus 67 ~i~CP~~~C~~~l~~~~i~~ 86 (265)
.++||. |+..+....|+.
T Consensus 5 ~~~CPv--C~~~F~~~~vrs 22 (214)
T PF09986_consen 5 KITCPV--CGKEFKTKKVRS 22 (214)
T ss_pred ceECCC--CCCeeeeeEEEc
Confidence 579999 999887766554
No 351
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=20.32 E-value=75 Score=19.23 Aligned_cols=28 Identities=21% Similarity=0.376 Sum_probs=15.5
Q ss_pred ccCCcCcccceeccccccCCcCeeeCCCccc
Q 024566 112 YCPNTNCMALVVNECERSGKVKKTQCPNCKQ 142 (265)
Q Consensus 112 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 142 (265)
.|+ +|+..+......++ ...+.||.|+.
T Consensus 7 ~C~--~Cg~~fe~~~~~~~-~~~~~CP~Cg~ 34 (52)
T TIGR02605 7 RCT--ACGHRFEVLQKMSD-DPLATCPECGG 34 (52)
T ss_pred EeC--CCCCEeEEEEecCC-CCCCCCCCCCC
Confidence 466 58875554322111 34567888875
No 352
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=20.14 E-value=69 Score=27.50 Aligned_cols=29 Identities=21% Similarity=0.560 Sum_probs=22.6
Q ss_pred CcccCCCCCceeeecCCCceeEe-ecCCce
Q 024566 180 KWARCPACGHCVERKDGCSVVMC-RCNTRF 208 (265)
Q Consensus 180 ~~k~CP~C~~~iek~~GCnhm~C-~C~~~F 208 (265)
..|-||+|+...+-..|=-.+.| .||+.+
T Consensus 110 ~~RFCg~CG~~~~~~~~g~~~~C~~cg~~~ 139 (279)
T COG2816 110 SHRFCGRCGTKTYPREGGWARVCPKCGHEH 139 (279)
T ss_pred hCcCCCCCCCcCccccCceeeeCCCCCCcc
Confidence 45889999999988888777888 577543
No 353
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=20.09 E-value=60 Score=24.99 Aligned_cols=13 Identities=38% Similarity=0.971 Sum_probs=9.3
Q ss_pred CcccCCCCCceee
Q 024566 180 KWARCPACGHCVE 192 (265)
Q Consensus 180 ~~k~CP~C~~~ie 192 (265)
..-+||+|+..-.
T Consensus 129 ~l~~Cp~C~~~~F 141 (146)
T PF07295_consen 129 RLPPCPKCGHTEF 141 (146)
T ss_pred cCCCCCCCCCCee
Confidence 4678999986543
Done!