Query 026529
Match_columns 237
No_of_seqs 200 out of 1317
Neff 9.3
Searched_HMMs 46136
Date Fri Mar 29 09:13:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026529.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026529hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1814 Predicted E3 ubiquitin 100.0 6.3E-38 1.4E-42 259.5 7.1 196 31-232 177-405 (445)
2 KOG1812 Predicted E3 ubiquitin 100.0 4.3E-37 9.3E-42 263.3 9.0 192 36-230 144-338 (384)
3 KOG1815 Predicted E3 ubiquitin 100.0 4.7E-29 1E-33 219.2 12.2 191 36-234 68-267 (444)
4 KOG0006 E3 ubiquitin-protein l 99.9 2.2E-26 4.7E-31 185.1 8.2 195 33-236 216-440 (446)
5 smart00647 IBR In Between Ring 99.3 1.5E-12 3.2E-17 84.1 4.8 63 111-175 1-64 (64)
6 PF01485 IBR: IBR domain; Int 99.3 5.5E-13 1.2E-17 86.1 0.5 63 111-175 1-64 (64)
7 PF15227 zf-C3HC4_4: zinc fing 98.8 2.3E-09 5.1E-14 62.7 2.2 41 41-89 1-41 (42)
8 PLN03208 E3 ubiquitin-protein 98.7 1.6E-08 3.5E-13 78.0 3.8 67 35-107 15-89 (193)
9 PF13445 zf-RING_UBOX: RING-ty 98.6 2.2E-08 4.7E-13 58.6 2.4 43 41-88 1-43 (43)
10 PF13639 zf-RING_2: Ring finge 98.6 1.5E-08 3.3E-13 60.1 0.9 41 40-89 2-42 (44)
11 PF13923 zf-C3HC4_2: Zinc fing 98.6 3.5E-08 7.6E-13 56.9 2.2 38 41-89 1-38 (39)
12 PF00097 zf-C3HC4: Zinc finger 98.5 5.3E-08 1.1E-12 56.8 2.6 40 41-89 1-40 (41)
13 KOG0320 Predicted E3 ubiquitin 98.5 1.2E-07 2.7E-12 71.4 4.0 56 35-102 128-183 (187)
14 KOG0317 Predicted E3 ubiquitin 98.4 2.3E-07 5.1E-12 75.1 4.3 71 17-101 218-288 (293)
15 PF14634 zf-RING_5: zinc-RING 98.4 2.3E-07 5E-12 54.9 2.9 44 40-94 1-44 (44)
16 PHA02926 zinc finger-like prot 98.3 8.3E-07 1.8E-11 69.5 5.0 62 31-96 163-229 (242)
17 cd00162 RING RING-finger (Real 98.2 1.3E-06 2.8E-11 51.4 3.2 44 40-95 1-44 (45)
18 PF13920 zf-C3HC4_3: Zinc fing 98.2 1.1E-06 2.3E-11 53.5 2.3 46 38-97 2-48 (50)
19 KOG0823 Predicted E3 ubiquitin 98.2 1.3E-06 2.9E-11 68.8 2.9 61 35-106 44-104 (230)
20 PHA02929 N1R/p28-like protein; 98.0 5.7E-06 1.2E-10 66.6 4.5 53 35-97 171-227 (238)
21 KOG2177 Predicted E3 ubiquitin 98.0 3.7E-06 7.9E-11 70.7 3.3 109 35-175 10-122 (386)
22 KOG2164 Predicted E3 ubiquitin 98.0 5E-06 1.1E-10 72.5 3.6 60 38-106 186-245 (513)
23 smart00504 Ubox Modified RING 98.0 1.3E-05 2.8E-10 51.1 4.1 51 39-103 2-52 (63)
24 smart00184 RING Ring finger. E 97.9 1E-05 2.2E-10 45.8 3.0 30 41-74 1-30 (39)
25 TIGR00599 rad18 DNA repair pro 97.9 1.7E-05 3.6E-10 68.6 4.6 70 32-115 20-90 (397)
26 smart00647 IBR In Between Ring 97.7 6.5E-05 1.4E-09 47.9 4.3 46 189-234 8-59 (64)
27 TIGR00570 cdk7 CDK-activating 97.7 0.00011 2.5E-09 61.0 6.6 55 39-103 4-60 (309)
28 COG5540 RING-finger-containing 97.6 3.7E-05 8E-10 62.8 3.1 56 33-98 318-373 (374)
29 KOG0287 Postreplication repair 97.6 2.6E-05 5.6E-10 64.7 1.6 65 36-114 21-86 (442)
30 KOG4628 Predicted E3 ubiquitin 97.5 6.2E-05 1.3E-09 63.6 2.8 49 38-96 229-277 (348)
31 PF01485 IBR: IBR domain; Int 97.3 0.00011 2.4E-09 46.8 1.6 40 195-234 15-59 (64)
32 PF11789 zf-Nse: Zinc-finger o 97.3 0.00016 3.4E-09 45.1 2.1 50 35-93 8-57 (57)
33 PF12678 zf-rbx1: RING-H2 zinc 97.3 0.00024 5.2E-09 46.7 2.9 44 38-89 19-71 (73)
34 KOG1002 Nucleotide excision re 97.2 0.00023 5E-09 62.5 3.2 65 33-106 531-595 (791)
35 COG5574 PEX10 RING-finger-cont 97.0 0.00068 1.5E-08 54.7 3.5 53 37-101 214-266 (271)
36 PF14835 zf-RING_6: zf-RING of 97.0 0.00013 2.9E-09 45.9 -0.6 50 38-102 7-56 (65)
37 KOG0978 E3 ubiquitin ligase in 96.9 0.00046 9.9E-09 63.3 2.2 56 36-104 641-696 (698)
38 PF11793 FANCL_C: FANCL C-term 96.9 0.00039 8.5E-09 45.3 1.1 59 38-98 2-67 (70)
39 KOG1039 Predicted E3 ubiquitin 96.6 0.0023 4.9E-08 54.5 3.6 95 35-132 158-264 (344)
40 PF04564 U-box: U-box domain; 96.5 0.0025 5.3E-08 41.9 2.7 52 37-101 3-54 (73)
41 COG5432 RAD18 RING-finger-cont 96.4 0.0026 5.5E-08 52.0 2.5 66 34-113 21-87 (391)
42 COG5243 HRD1 HRD ubiquitin lig 96.3 0.0055 1.2E-07 51.8 4.1 52 35-96 284-344 (491)
43 KOG1814 Predicted E3 ubiquitin 96.0 0.012 2.6E-07 50.5 4.9 120 30-170 265-405 (445)
44 COG5152 Uncharacterized conser 95.8 0.0043 9.4E-08 47.9 1.3 37 34-74 192-228 (259)
45 PF14570 zf-RING_4: RING/Ubox 95.6 0.014 3E-07 34.7 2.7 46 41-95 1-46 (48)
46 PF12861 zf-Apc11: Anaphase-pr 95.5 0.019 4.1E-07 38.5 3.5 53 38-97 21-82 (85)
47 KOG4185 Predicted E3 ubiquitin 95.5 0.03 6.5E-07 47.1 5.6 50 38-96 3-54 (296)
48 KOG2660 Locus-specific chromos 95.3 0.013 2.8E-07 49.0 2.5 52 35-99 12-63 (331)
49 KOG0006 E3 ubiquitin-protein l 94.9 0.047 1E-06 45.4 4.6 93 59-171 341-437 (446)
50 KOG2879 Predicted E3 ubiquitin 94.6 0.034 7.5E-07 45.3 3.2 51 36-97 237-287 (298)
51 KOG3039 Uncharacterized conser 94.4 0.035 7.5E-07 44.5 2.6 59 35-103 218-276 (303)
52 KOG4159 Predicted E3 ubiquitin 94.3 0.04 8.7E-07 48.0 3.2 48 36-97 82-129 (398)
53 KOG0824 Predicted E3 ubiquitin 94.2 0.038 8.3E-07 45.6 2.7 53 36-101 5-57 (324)
54 PF04641 Rtf2: Rtf2 RING-finge 94.2 0.089 1.9E-06 43.5 5.0 73 34-117 109-182 (260)
55 KOG1952 Transcription factor N 94.2 0.041 8.8E-07 51.5 3.0 57 34-93 187-243 (950)
56 PF07975 C1_4: TFIIH C1-like d 94.0 0.022 4.7E-07 34.4 0.6 39 134-172 4-42 (51)
57 KOG0802 E3 ubiquitin ligase [P 93.8 0.039 8.5E-07 50.4 2.2 49 36-94 289-338 (543)
58 PF10571 UPF0547: Uncharacteri 93.6 0.036 7.8E-07 28.5 1.0 23 129-161 2-24 (26)
59 smart00661 RPOL9 RNA polymeras 93.6 0.063 1.4E-06 32.4 2.3 28 199-226 1-31 (52)
60 KOG1812 Predicted E3 ubiquitin 93.5 0.055 1.2E-06 47.2 2.5 43 125-174 304-346 (384)
61 KOG4739 Uncharacterized protei 93.4 0.034 7.5E-07 44.5 1.1 55 38-106 3-57 (233)
62 smart00744 RINGv The RING-vari 93.3 0.12 2.6E-06 31.0 3.2 42 40-89 1-47 (49)
63 KOG0828 Predicted E3 ubiquitin 93.2 0.065 1.4E-06 47.2 2.5 55 35-98 568-635 (636)
64 PF13719 zinc_ribbon_5: zinc-r 93.2 0.065 1.4E-06 30.1 1.7 32 128-161 3-35 (37)
65 COG5175 MOT2 Transcriptional r 93.2 0.17 3.8E-06 42.5 4.8 60 40-108 16-76 (480)
66 COG5220 TFB3 Cdk activating ki 93.0 0.02 4.4E-07 45.6 -0.8 51 39-96 11-63 (314)
67 PF05883 Baculo_RING: Baculovi 92.8 0.037 8E-07 40.4 0.4 42 33-75 21-68 (134)
68 KOG0804 Cytoplasmic Zn-finger 92.8 0.035 7.6E-07 48.3 0.3 40 36-75 173-212 (493)
69 KOG1428 Inhibitor of type V ad 92.5 0.15 3.3E-06 50.7 4.0 69 36-107 3484-3554(3738)
70 PF13717 zinc_ribbon_4: zinc-r 92.4 0.11 2.3E-06 29.0 1.8 32 128-161 3-35 (36)
71 KOG1645 RING-finger-containing 91.6 0.094 2E-06 45.2 1.5 50 38-95 4-54 (463)
72 KOG0311 Predicted E3 ubiquitin 91.6 0.027 5.9E-07 47.5 -1.7 49 35-95 40-88 (381)
73 KOG0297 TNF receptor-associate 91.4 0.24 5.2E-06 43.4 3.9 48 35-95 18-65 (391)
74 TIGR00622 ssl1 transcription f 91.2 0.2 4.3E-06 35.6 2.5 42 128-171 56-101 (112)
75 KOG3800 Predicted E3 ubiquitin 91.2 0.42 9.1E-06 39.4 4.7 54 40-102 2-56 (300)
76 KOG0827 Predicted E3 ubiquitin 91.1 0.23 5E-06 42.6 3.3 50 37-93 3-52 (465)
77 PRK00432 30S ribosomal protein 91.0 0.23 4.9E-06 29.9 2.3 27 197-225 19-47 (50)
78 KOG4265 Predicted E3 ubiquitin 90.9 0.19 4.1E-06 42.7 2.6 49 35-97 287-336 (349)
79 KOG0825 PHD Zn-finger protein 90.6 0.24 5.1E-06 46.3 3.1 19 150-168 229-248 (1134)
80 KOG4445 Uncharacterized conser 90.5 0.14 3E-06 42.4 1.5 62 34-98 111-187 (368)
81 PF05290 Baculo_IE-1: Baculovi 90.2 0.57 1.2E-05 34.1 4.1 59 31-97 73-132 (140)
82 KOG3002 Zn finger protein [Gen 89.9 0.16 3.5E-06 42.6 1.4 45 35-97 45-91 (299)
83 PHA03096 p28-like protein; Pro 89.8 0.2 4.3E-06 41.8 1.9 53 39-95 179-235 (284)
84 KOG4172 Predicted E3 ubiquitin 89.8 0.11 2.4E-06 31.5 0.3 45 39-96 8-53 (62)
85 PF14569 zf-UDP: Zinc-binding 89.7 0.36 7.7E-06 31.6 2.6 61 128-217 10-70 (80)
86 KOG4692 Predicted E3 ubiquitin 89.4 0.31 6.6E-06 41.3 2.6 35 36-74 420-454 (489)
87 PF08274 PhnA_Zn_Ribbon: PhnA 89.4 0.31 6.8E-06 25.9 1.8 26 199-225 3-29 (30)
88 TIGR02098 MJ0042_CXXC MJ0042 f 89.0 0.32 6.9E-06 27.3 1.8 32 128-161 3-35 (38)
89 PHA00626 hypothetical protein 88.8 0.36 7.9E-06 29.4 1.9 27 200-226 2-34 (59)
90 KOG2817 Predicted E3 ubiquitin 88.7 0.48 1E-05 40.8 3.3 60 36-103 332-391 (394)
91 KOG1785 Tyrosine kinase negati 88.6 0.22 4.8E-06 42.8 1.3 45 35-89 366-410 (563)
92 PF02150 RNA_POL_M_15KD: RNA p 88.4 0.28 6.2E-06 27.1 1.3 29 128-161 2-30 (35)
93 PF14803 Nudix_N_2: Nudix N-te 88.4 0.26 5.7E-06 27.1 1.1 31 128-160 1-31 (34)
94 KOG1734 Predicted RING-contain 88.4 0.12 2.6E-06 42.1 -0.4 55 38-101 224-285 (328)
95 KOG1815 Predicted E3 ubiquitin 88.0 0.67 1.4E-05 41.4 4.1 38 126-169 225-264 (444)
96 KOG1813 Predicted E3 ubiquitin 88.0 0.14 3.1E-06 42.2 -0.2 48 34-95 237-284 (313)
97 smart00661 RPOL9 RNA polymeras 87.9 0.36 7.8E-06 29.1 1.6 29 129-161 2-30 (52)
98 PF14447 Prok-RING_4: Prokaryo 87.3 0.37 8.1E-06 29.4 1.4 49 37-101 6-54 (55)
99 KOG1940 Zn-finger protein [Gen 86.5 1.8 3.8E-05 35.9 5.3 50 35-94 155-204 (276)
100 PRK00398 rpoP DNA-directed RNA 86.3 1 2.2E-05 26.4 2.9 28 199-226 4-32 (46)
101 COG5236 Uncharacterized conser 86.3 0.87 1.9E-05 38.6 3.5 66 36-113 59-124 (493)
102 KOG2979 Protein involved in DN 85.5 2.1 4.6E-05 34.9 5.2 72 36-119 174-247 (262)
103 KOG1941 Acetylcholine receptor 85.1 0.43 9.4E-06 41.0 1.2 52 36-95 363-414 (518)
104 KOG2906 RNA polymerase III sub 84.9 0.71 1.5E-05 31.7 1.9 28 199-226 2-32 (105)
105 COG1998 RPS31 Ribosomal protei 84.5 0.88 1.9E-05 27.0 1.9 27 197-223 18-45 (51)
106 PRK00398 rpoP DNA-directed RNA 84.1 0.87 1.9E-05 26.7 1.9 29 128-162 4-32 (46)
107 PF14952 zf-tcix: Putative tre 84.0 0.49 1.1E-05 27.3 0.7 26 196-225 9-37 (44)
108 PF13240 zinc_ribbon_2: zinc-r 83.2 0.56 1.2E-05 23.3 0.7 22 129-160 1-22 (23)
109 PF09297 zf-NADH-PPase: NADH p 83.2 2 4.2E-05 23.1 2.9 27 198-224 3-30 (32)
110 COG5219 Uncharacterized conser 82.1 0.7 1.5E-05 44.3 1.4 54 36-97 1467-1523(1525)
111 KOG3053 Uncharacterized conser 81.7 2.5 5.4E-05 34.4 4.1 58 36-95 18-80 (293)
112 PF06677 Auto_anti-p27: Sjogre 81.5 1.3 2.8E-05 25.5 1.9 22 199-222 18-41 (41)
113 PF13248 zf-ribbon_3: zinc-rib 81.4 0.74 1.6E-05 23.5 0.8 23 128-160 3-25 (26)
114 PRK14559 putative protein seri 80.9 1.2 2.6E-05 41.6 2.5 13 197-209 40-52 (645)
115 KOG2807 RNA polymerase II tran 80.8 0.91 2E-05 38.2 1.5 23 149-171 343-365 (378)
116 KOG1001 Helicase-like transcri 80.0 0.6 1.3E-05 43.8 0.2 49 39-100 455-503 (674)
117 KOG1493 Anaphase-promoting com 80.0 0.59 1.3E-05 30.5 0.1 53 38-97 20-81 (84)
118 COG1645 Uncharacterized Zn-fin 80.0 1.2 2.6E-05 32.5 1.7 26 197-224 27-53 (131)
119 PRK05654 acetyl-CoA carboxylas 79.4 0.47 1E-05 39.8 -0.6 32 195-226 24-57 (292)
120 PRK14714 DNA polymerase II lar 79.3 1.8 3.8E-05 43.1 3.0 30 127-168 667-701 (1337)
121 PRK08665 ribonucleotide-diphos 78.6 1.2 2.6E-05 42.5 1.7 24 199-224 725-749 (752)
122 PF09788 Tmemb_55A: Transmembr 78.3 3 6.6E-05 33.9 3.7 37 125-161 121-167 (256)
123 COG5194 APC11 Component of SCF 78.3 2.8 6E-05 27.7 2.8 47 40-96 33-80 (88)
124 KOG2034 Vacuolar sorting prote 77.8 1.5 3.2E-05 41.8 2.0 42 36-79 815-856 (911)
125 COG5222 Uncharacterized conser 77.7 3.6 7.7E-05 34.3 4.0 44 39-94 275-318 (427)
126 PF09538 FYDLN_acid: Protein o 77.4 1.3 2.9E-05 31.3 1.3 26 199-225 10-36 (108)
127 PRK14559 putative protein seri 77.1 1.9 4.1E-05 40.3 2.5 11 201-211 30-40 (645)
128 TIGR01384 TFS_arch transcripti 77.0 1.6 3.4E-05 30.5 1.6 24 200-225 2-26 (104)
129 PF08746 zf-RING-like: RING-li 76.9 2.6 5.6E-05 24.4 2.2 42 41-89 1-42 (43)
130 PF03119 DNA_ligase_ZBD: NAD-d 75.9 2.8 6E-05 21.8 1.9 20 200-219 1-20 (28)
131 PF12906 RINGv: RING-variant d 75.8 1.8 4E-05 25.6 1.4 33 41-75 1-38 (47)
132 PF07282 OrfB_Zn_ribbon: Putat 75.5 2.8 6E-05 26.8 2.3 29 197-225 27-56 (69)
133 COG0777 AccD Acetyl-CoA carbox 75.4 1 2.3E-05 37.0 0.3 32 195-226 25-58 (294)
134 CHL00174 accD acetyl-CoA carbo 75.1 0.63 1.4E-05 39.0 -1.0 31 196-226 36-68 (296)
135 PRK00420 hypothetical protein; 75.1 2.2 4.7E-05 30.4 1.9 29 197-227 22-52 (112)
136 PLN02189 cellulose synthase 73.7 2.9 6.3E-05 40.9 2.8 63 126-217 33-95 (1040)
137 TIGR00515 accD acetyl-CoA carb 73.7 0.77 1.7E-05 38.4 -0.8 32 195-226 23-56 (285)
138 KOG3970 Predicted E3 ubiquitin 73.2 10 0.00022 30.4 5.3 63 33-99 45-108 (299)
139 PLN00209 ribosomal protein S27 73.1 4.1 8.9E-05 27.3 2.7 31 128-163 37-67 (86)
140 KOG3799 Rab3 effector RIM1 and 73.1 0.32 7E-06 35.3 -2.7 43 11-63 41-83 (169)
141 KOG3161 Predicted E3 ubiquitin 73.0 1.3 2.8E-05 40.7 0.4 38 38-75 11-48 (861)
142 PLN03208 E3 ubiquitin-protein 73.0 1 2.3E-05 35.2 -0.2 65 125-210 16-80 (193)
143 PF07503 zf-HYPF: HypF finger; 72.7 3.4 7.3E-05 22.8 1.9 32 64-97 1-32 (35)
144 TIGR00686 phnA alkylphosphonat 71.3 2.9 6.3E-05 29.3 1.7 27 199-226 3-30 (109)
145 KOG2164 Predicted E3 ubiquitin 70.0 3 6.5E-05 37.3 1.9 35 156-210 203-237 (513)
146 PF10367 Vps39_2: Vacuolar sor 69.4 1.6 3.5E-05 30.3 0.2 33 36-70 76-108 (109)
147 KOG2691 RNA polymerase II subu 68.4 3.9 8.4E-05 28.6 1.8 34 126-161 3-36 (113)
148 PLN02638 cellulose synthase A 68.0 4 8.7E-05 40.1 2.5 61 128-217 18-78 (1079)
149 PF01599 Ribosomal_S27: Riboso 68.0 3.2 6.9E-05 24.6 1.2 29 127-159 18-46 (47)
150 PF12773 DZR: Double zinc ribb 67.7 3.5 7.6E-05 24.4 1.4 28 125-159 10-37 (50)
151 COG1594 RPB9 DNA-directed RNA 67.6 3.9 8.5E-05 29.2 1.8 31 127-161 2-32 (113)
152 TIGR00686 phnA alkylphosphonat 67.6 3.2 7E-05 29.1 1.3 26 129-161 4-29 (109)
153 TIGR00570 cdk7 CDK-activating 67.4 4.4 9.5E-05 34.2 2.3 33 128-167 4-36 (309)
154 PF14446 Prok-RING_1: Prokaryo 67.2 7.5 0.00016 23.7 2.7 36 37-72 4-39 (54)
155 PRK14890 putative Zn-ribbon RN 66.7 4.4 9.6E-05 25.2 1.6 11 150-160 24-34 (59)
156 PTZ00083 40S ribosomal protein 65.7 6.3 0.00014 26.4 2.3 31 128-163 36-66 (85)
157 PHA02926 zinc finger-like prot 64.5 1.7 3.7E-05 34.7 -0.6 61 128-210 171-231 (242)
158 PF07754 DUF1610: Domain of un 64.1 4.9 0.00011 20.1 1.2 22 134-159 3-24 (24)
159 KOG0978 E3 ubiquitin ligase in 64.0 2.8 6E-05 39.3 0.6 29 156-208 660-688 (698)
160 TIGR02443 conserved hypothetic 63.6 6.6 0.00014 24.4 2.0 26 199-224 10-40 (59)
161 COG5220 TFB3 Cdk activating ki 63.2 6.6 0.00014 31.7 2.5 55 85-142 11-66 (314)
162 PF06844 DUF1244: Protein of u 63.2 5.1 0.00011 25.4 1.5 17 63-79 11-27 (68)
163 KOG4367 Predicted Zn-finger pr 63.1 3.8 8.3E-05 35.9 1.2 35 37-75 3-37 (699)
164 PHA02825 LAP/PHD finger-like p 63.1 14 0.00031 27.9 4.1 53 36-99 6-61 (162)
165 KOG3579 Predicted E3 ubiquitin 63.0 3.8 8.2E-05 33.9 1.1 52 35-93 265-321 (352)
166 TIGR00373 conserved hypothetic 62.8 5.1 0.00011 30.4 1.7 31 125-160 107-137 (158)
167 COG1997 RPL43A Ribosomal prote 62.2 6.8 0.00015 26.4 2.0 31 196-226 33-64 (89)
168 COG5151 SSL1 RNA polymerase II 62.2 1.9 4.2E-05 36.0 -0.7 78 83-171 321-408 (421)
169 PRK10220 hypothetical protein; 62.1 5.2 0.00011 28.1 1.5 26 129-161 5-30 (111)
170 PLN02436 cellulose synthase A 62.0 7.1 0.00015 38.4 2.9 62 127-217 36-97 (1094)
171 PRK06266 transcription initiat 61.7 5.6 0.00012 30.9 1.8 32 125-161 115-146 (178)
172 PF14369 zf-RING_3: zinc-finge 61.2 8.2 0.00018 21.2 1.9 29 128-161 3-31 (35)
173 smart00834 CxxC_CXXC_SSSS Puta 61.0 7.9 0.00017 21.6 2.0 30 128-160 6-35 (41)
174 PF03604 DNA_RNApol_7kD: DNA d 61.0 6.4 0.00014 21.2 1.4 23 134-161 5-27 (32)
175 smart00659 RPOLCX RNA polymera 60.9 8.1 0.00018 22.5 2.0 11 198-208 19-29 (44)
176 smart00531 TFIIE Transcription 60.9 5.4 0.00012 29.8 1.6 35 125-161 97-133 (147)
177 PF09526 DUF2387: Probable met 60.8 7.3 0.00016 25.3 2.0 26 199-224 9-39 (71)
178 KOG3268 Predicted E3 ubiquitin 60.6 13 0.00027 28.7 3.4 62 35-98 162-229 (234)
179 PRK03681 hypA hydrogenase nick 60.5 11 0.00024 26.9 3.1 29 125-160 68-96 (114)
180 PRK00420 hypothetical protein; 60.3 17 0.00037 25.9 3.9 44 108-160 6-49 (112)
181 PF14353 CpXC: CpXC protein 60.1 5.8 0.00013 28.8 1.6 15 85-101 2-16 (128)
182 KOG2906 RNA polymerase III sub 59.9 6.1 0.00013 27.2 1.5 30 128-161 2-31 (105)
183 smart00064 FYVE Protein presen 59.6 4.3 9.4E-05 25.7 0.7 39 38-76 10-48 (68)
184 TIGR03655 anti_R_Lar restricti 59.2 8.8 0.00019 23.2 2.0 27 198-224 1-35 (53)
185 PF05129 Elf1: Transcription e 58.8 7.6 0.00017 25.9 1.8 31 197-227 21-58 (81)
186 PF06827 zf-FPG_IleRS: Zinc fi 58.7 6.3 0.00014 20.6 1.2 21 199-219 2-24 (30)
187 PHA02929 N1R/p28-like protein; 58.7 7.2 0.00016 31.7 2.0 40 127-170 174-213 (238)
188 COG2051 RPS27A Ribosomal prote 58.4 6.7 0.00015 24.9 1.4 32 127-163 19-50 (67)
189 PLN02400 cellulose synthase 58.4 7.3 0.00016 38.4 2.3 61 128-217 37-97 (1085)
190 PF07191 zinc-ribbons_6: zinc- 57.9 10 0.00022 24.5 2.2 21 200-222 3-24 (70)
191 PF08792 A2L_zn_ribbon: A2L zi 57.6 9.3 0.0002 20.7 1.7 29 127-161 3-31 (33)
192 TIGR02300 FYDLN_acid conserved 57.3 6.6 0.00014 28.5 1.4 26 199-225 10-36 (129)
193 KOG0801 Predicted E3 ubiquitin 57.2 3.7 8E-05 31.0 0.1 29 36-65 175-203 (205)
194 cd00065 FYVE FYVE domain; Zinc 57.2 8.1 0.00018 23.4 1.7 37 39-75 3-39 (57)
195 KOG0317 Predicted E3 ubiquitin 56.8 3.1 6.7E-05 34.5 -0.3 21 151-171 251-271 (293)
196 TIGR01206 lysW lysine biosynth 56.8 10 0.00022 23.2 2.0 31 128-162 3-33 (54)
197 PF14149 YhfH: YhfH-like prote 55.5 1.6 3.4E-05 24.4 -1.6 28 192-219 7-34 (37)
198 PHA02862 5L protein; Provision 55.1 17 0.00036 27.1 3.2 47 39-98 3-54 (156)
199 TIGR01053 LSD1 zinc finger dom 54.8 12 0.00026 20.0 1.8 27 128-160 2-28 (31)
200 PF14354 Lar_restr_allev: Rest 54.8 9.8 0.00021 23.5 1.8 27 197-223 2-37 (61)
201 PF09723 Zn-ribbon_8: Zinc rib 54.3 12 0.00025 21.5 1.9 29 128-159 6-34 (42)
202 PF12760 Zn_Tnp_IS1595: Transp 53.8 29 0.00062 20.2 3.6 32 191-222 8-44 (46)
203 PF01363 FYVE: FYVE zinc finge 53.8 2.7 5.8E-05 26.8 -1.0 38 36-73 7-44 (69)
204 TIGR03826 YvyF flagellar opero 53.3 12 0.00026 27.7 2.2 13 199-211 82-94 (137)
205 PRK12380 hydrogenase nickel in 52.9 18 0.0004 25.7 3.1 27 125-159 68-94 (113)
206 KOG4684 Uncharacterized conser 52.9 19 0.00042 28.6 3.4 20 125-144 136-155 (275)
207 TIGR00100 hypA hydrogenase nic 52.5 19 0.00041 25.7 3.1 28 125-160 68-95 (115)
208 PRK14892 putative transcriptio 52.5 14 0.0003 25.7 2.3 35 124-161 18-52 (99)
209 PLN02915 cellulose synthase A 52.4 10 0.00022 37.3 2.3 57 134-217 20-76 (1044)
210 PF10497 zf-4CXXC_R1: Zinc-fin 52.3 26 0.00056 24.6 3.8 57 36-94 5-69 (105)
211 PF03854 zf-P11: P-11 zinc fin 52.3 4.7 0.0001 23.8 -0.0 44 38-97 2-46 (50)
212 PF00643 zf-B_box: B-box zinc 51.9 4.4 9.6E-05 22.9 -0.1 24 150-173 14-37 (42)
213 KOG3039 Uncharacterized conser 51.8 14 0.00031 30.0 2.6 40 36-79 41-80 (303)
214 COG3492 Uncharacterized protei 51.8 11 0.00024 25.5 1.7 17 63-79 42-58 (104)
215 PRK09710 lar restriction allev 51.6 13 0.00027 23.6 1.8 28 196-223 4-35 (64)
216 KOG4362 Transcriptional regula 51.0 4.5 9.7E-05 37.8 -0.3 59 34-103 17-75 (684)
217 cd00021 BBOX B-Box-type zinc f 50.3 7.9 0.00017 21.2 0.8 26 149-174 10-35 (39)
218 PRK03824 hypA hydrogenase nick 49.9 21 0.00046 26.3 3.1 16 125-142 68-83 (135)
219 COG1096 Predicted RNA-binding 49.7 11 0.00024 29.3 1.6 22 199-222 150-172 (188)
220 KOG4275 Predicted E3 ubiquitin 49.4 5.8 0.00013 33.0 0.1 31 38-72 300-331 (350)
221 PF08271 TF_Zn_Ribbon: TFIIB z 49.3 12 0.00025 21.5 1.4 27 129-160 2-28 (43)
222 KOG2041 WD40 repeat protein [G 48.9 15 0.00033 34.7 2.6 60 92-161 1076-1141(1189)
223 PF02748 PyrI_C: Aspartate car 48.2 13 0.00027 22.6 1.4 35 126-161 5-45 (52)
224 PRK00415 rps27e 30S ribosomal 48.1 14 0.00031 22.9 1.7 30 128-162 12-41 (59)
225 PRK00564 hypA hydrogenase nick 47.6 20 0.00044 25.7 2.7 28 125-159 69-96 (117)
226 PRK14714 DNA polymerase II lar 47.3 15 0.00032 37.0 2.4 50 151-209 667-720 (1337)
227 smart00336 BBOX B-Box-type zin 47.0 14 0.0003 20.6 1.4 25 149-173 13-37 (42)
228 KOG0825 PHD Zn-finger protein 46.5 16 0.00034 34.9 2.3 41 38-78 96-139 (1134)
229 PF02318 FYVE_2: FYVE-type zin 45.9 38 0.00082 24.2 3.9 36 126-168 53-88 (118)
230 PRK13130 H/ACA RNA-protein com 45.6 32 0.0007 21.2 2.9 36 84-121 17-52 (56)
231 PRK11827 hypothetical protein; 45.4 20 0.00043 22.4 2.0 27 197-223 7-34 (60)
232 PF13913 zf-C2HC_2: zinc-finge 45.2 11 0.00023 19.0 0.7 11 151-161 2-12 (25)
233 PF01428 zf-AN1: AN1-like Zinc 43.9 12 0.00025 21.5 0.8 27 150-178 12-38 (43)
234 PF06906 DUF1272: Protein of u 43.8 30 0.00065 21.3 2.5 45 40-98 7-53 (57)
235 PLN02195 cellulose synthase A 43.7 18 0.00039 35.4 2.4 34 128-166 7-40 (977)
236 PF13453 zf-TFIIB: Transcripti 43.4 13 0.00029 21.0 1.0 27 129-159 1-27 (41)
237 COG0266 Nei Formamidopyrimidin 43.1 16 0.00035 30.3 1.8 24 199-222 246-272 (273)
238 KOG1039 Predicted E3 ubiquitin 42.4 9.1 0.0002 33.0 0.2 42 151-210 181-222 (344)
239 COG1579 Zn-ribbon protein, pos 42.2 16 0.00035 29.7 1.6 59 100-160 167-230 (239)
240 PF04216 FdhE: Protein involve 42.0 15 0.00033 30.8 1.5 30 199-228 173-210 (290)
241 PF02591 DUF164: Putative zinc 41.7 23 0.00051 21.5 2.0 22 187-208 35-56 (56)
242 KOG1571 Predicted E3 ubiquitin 41.6 14 0.00031 31.7 1.2 45 35-96 302-346 (355)
243 PF01667 Ribosomal_S27e: Ribos 41.5 19 0.00042 22.1 1.5 31 128-163 8-38 (55)
244 PRK04023 DNA polymerase II lar 41.1 21 0.00045 35.1 2.4 7 152-158 639-645 (1121)
245 PF11023 DUF2614: Protein of u 40.7 15 0.00032 26.1 1.0 23 149-171 67-97 (114)
246 COG2888 Predicted Zn-ribbon RN 40.2 17 0.00036 22.6 1.1 34 127-166 9-42 (61)
247 KOG2930 SCF ubiquitin ligase, 40.0 20 0.00043 25.0 1.5 25 57-89 78-102 (114)
248 PF01927 Mut7-C: Mut7-C RNAse 40.0 49 0.0011 24.6 3.9 53 107-161 68-134 (147)
249 PRK09521 exosome complex RNA-b 39.7 28 0.00061 27.1 2.6 35 199-236 150-185 (189)
250 KOG1701 Focal adhesion adaptor 39.5 40 0.00088 29.8 3.7 68 149-222 380-459 (468)
251 PRK08115 ribonucleotide-diphos 39.1 14 0.00031 35.8 1.0 28 199-228 828-857 (858)
252 KOG0826 Predicted E3 ubiquitin 38.9 23 0.0005 30.1 2.1 48 35-93 297-344 (357)
253 PF05605 zf-Di19: Drought indu 38.8 25 0.00053 21.2 1.7 38 38-94 2-39 (54)
254 TIGR00515 accD acetyl-CoA carb 38.8 14 0.0003 31.0 0.8 32 125-161 24-55 (285)
255 PRK12286 rpmF 50S ribosomal pr 38.2 24 0.00051 21.8 1.6 27 123-160 23-49 (57)
256 PRK13264 3-hydroxyanthranilate 38.1 12 0.00026 29.0 0.3 52 157-211 118-170 (177)
257 KOG2114 Vacuolar assembly/sort 37.9 11 0.00025 36.0 0.2 40 39-94 841-880 (933)
258 PLN03086 PRLI-interacting fact 37.8 17 0.00036 33.6 1.2 59 82-161 405-463 (567)
259 COG2260 Predicted Zn-ribbon RN 37.3 63 0.0014 20.0 3.3 34 86-121 19-52 (59)
260 PLN02436 cellulose synthase A 37.1 30 0.00064 34.4 2.8 52 36-96 34-88 (1094)
261 PF01155 HypA: Hydrogenase exp 36.8 19 0.00042 25.5 1.2 28 125-160 68-95 (113)
262 TIGR02605 CxxC_CxxC_SSSS putat 36.7 30 0.00065 20.5 1.9 29 128-159 6-34 (52)
263 PF07800 DUF1644: Protein of u 36.7 35 0.00076 25.8 2.5 19 125-143 105-123 (162)
264 KOG0309 Conserved WD40 repeat- 36.3 31 0.00066 32.9 2.6 39 35-75 1025-1063(1081)
265 PF10426 zf-RAG1: Recombinatio 36.2 9.1 0.0002 20.3 -0.4 15 84-98 2-16 (30)
266 COG3058 FdhE Uncharacterized p 35.7 12 0.00026 31.0 0.0 43 126-170 184-236 (308)
267 PF03966 Trm112p: Trm112p-like 35.6 46 0.001 21.1 2.7 13 197-209 52-64 (68)
268 PRK05654 acetyl-CoA carboxylas 35.3 16 0.00036 30.7 0.7 32 125-161 25-56 (292)
269 PF04810 zf-Sec23_Sec24: Sec23 35.3 23 0.00051 19.9 1.1 31 128-160 3-33 (40)
270 COG2824 PhnA Uncharacterized Z 35.0 27 0.00059 24.5 1.6 26 199-226 4-31 (112)
271 TIGR03037 anthran_nbaC 3-hydro 34.9 15 0.00032 27.9 0.3 46 158-206 113-159 (159)
272 PRK01103 formamidopyrimidine/5 34.9 27 0.00059 29.0 1.9 24 199-222 246-272 (274)
273 COG1656 Uncharacterized conser 34.7 50 0.0011 25.2 3.1 35 125-161 95-140 (165)
274 PRK14811 formamidopyrimidine-D 34.7 27 0.00058 29.0 1.8 25 198-222 235-262 (269)
275 COG1996 RPC10 DNA-directed RNA 34.6 24 0.00051 21.1 1.1 15 195-209 21-35 (49)
276 PF14471 DUF4428: Domain of un 34.6 38 0.00082 20.3 2.0 30 40-72 1-30 (51)
277 PF00098 zf-CCHC: Zinc knuckle 34.2 25 0.00054 16.1 0.9 16 161-176 2-17 (18)
278 PRK14810 formamidopyrimidine-D 34.1 28 0.00061 28.9 1.9 25 198-222 244-271 (272)
279 TIGR00577 fpg formamidopyrimid 33.9 29 0.00063 28.8 2.0 23 199-221 246-271 (272)
280 CHL00174 accD acetyl-CoA carbo 33.8 18 0.00038 30.5 0.6 30 127-161 38-67 (296)
281 TIGR00595 priA primosomal prot 33.7 46 0.00099 30.4 3.3 34 129-168 224-262 (505)
282 COG3357 Predicted transcriptio 33.7 17 0.00037 24.7 0.4 13 95-107 18-30 (97)
283 PF02891 zf-MIZ: MIZ/SP-RING z 33.6 21 0.00045 21.3 0.8 47 39-94 3-49 (50)
284 PRK10445 endonuclease VIII; Pr 33.6 29 0.00064 28.6 1.9 24 199-222 236-262 (263)
285 PRK09678 DNA-binding transcrip 33.5 37 0.00081 22.1 2.0 17 127-143 27-43 (72)
286 PRK13945 formamidopyrimidine-D 33.1 30 0.00064 28.9 1.9 24 199-222 255-281 (282)
287 PF09151 DUF1936: Domain of un 33.1 22 0.00048 18.9 0.7 9 200-208 3-11 (36)
288 PF06524 NOA36: NOA36 protein; 33.0 21 0.00046 29.3 1.0 50 150-211 170-222 (314)
289 TIGR01031 rpmF_bact ribosomal 33.0 31 0.00067 21.1 1.5 27 123-160 22-48 (55)
290 COG5109 Uncharacterized conser 32.7 41 0.00089 28.5 2.6 55 36-98 334-388 (396)
291 PRK02935 hypothetical protein; 32.1 30 0.00066 24.2 1.5 21 150-170 69-97 (110)
292 PF06943 zf-LSD1: LSD1 zinc fi 32.1 48 0.001 16.8 1.8 22 134-159 3-24 (25)
293 PF01096 TFIIS_C: Transcriptio 31.9 28 0.00061 19.5 1.1 14 148-161 25-38 (39)
294 COG0777 AccD Acetyl-CoA carbox 31.9 22 0.00049 29.5 0.9 34 125-163 26-59 (294)
295 PF10764 Gin: Inhibitor of sig 31.8 29 0.00062 20.4 1.1 35 40-79 1-35 (46)
296 cd00350 rubredoxin_like Rubred 31.7 38 0.00082 18.1 1.5 22 130-159 4-25 (33)
297 PRK00241 nudC NADH pyrophospha 31.6 37 0.0008 27.9 2.2 28 196-223 97-125 (256)
298 COG3677 Transposase and inacti 31.6 81 0.0018 23.0 3.8 36 125-162 28-64 (129)
299 KOG2932 E3 ubiquitin ligase in 30.7 27 0.00059 29.5 1.2 33 38-73 90-122 (389)
300 smart00440 ZnF_C2C2 C2C2 Zinc 30.0 39 0.00085 19.0 1.5 14 148-161 25-38 (40)
301 KOG1779 40s ribosomal protein 29.6 80 0.0017 20.9 3.0 32 128-164 35-66 (84)
302 smart00734 ZnF_Rad18 Rad18-lik 29.4 12 0.00026 19.0 -0.7 19 85-105 2-20 (26)
303 PF10122 Mu-like_Com: Mu-like 29.2 25 0.00053 21.2 0.6 10 199-208 25-34 (51)
304 PRK12495 hypothetical protein; 29.1 74 0.0016 25.5 3.4 28 125-160 40-67 (226)
305 PF01783 Ribosomal_L32p: Ribos 28.9 53 0.0011 20.1 2.0 25 124-159 23-47 (56)
306 PF00096 zf-C2H2: Zinc finger, 28.6 21 0.00045 16.9 0.2 9 153-161 2-10 (23)
307 PF01396 zf-C4_Topoisom: Topoi 28.6 30 0.00065 19.4 0.8 21 199-220 2-25 (39)
308 COG0375 HybF Zn finger protein 28.3 65 0.0014 23.1 2.6 47 105-159 39-94 (115)
309 PF14169 YdjO: Cold-inducible 28.1 46 0.00099 20.8 1.6 30 128-160 19-48 (59)
310 PF04981 NMD3: NMD3 family ; 28.0 35 0.00076 27.6 1.5 14 197-210 34-47 (236)
311 PLN02189 cellulose synthase 27.9 51 0.0011 32.7 2.7 52 36-96 32-86 (1040)
312 PRK08332 ribonucleotide-diphos 27.8 34 0.00074 36.0 1.6 25 199-225 1705-1736(1740)
313 PF02146 SIR2: Sir2 family; I 27.2 56 0.0012 25.0 2.4 16 193-208 124-139 (178)
314 PF14205 Cys_rich_KTR: Cystein 27.2 45 0.00098 20.3 1.4 34 126-161 3-38 (55)
315 PF11682 DUF3279: Protein of u 27.1 44 0.00095 24.4 1.6 15 199-213 111-125 (128)
316 PF14768 RPA_interact_C: Repli 26.8 58 0.0013 21.6 2.1 24 201-225 2-25 (82)
317 COG3024 Uncharacterized protei 26.8 39 0.00083 21.4 1.1 17 196-212 5-21 (65)
318 PF03884 DUF329: Domain of unk 26.5 29 0.00063 21.5 0.6 16 198-213 2-17 (57)
319 PF13465 zf-H2C2_2: Zinc-finge 26.3 32 0.0007 17.2 0.6 13 149-161 12-24 (26)
320 smart00154 ZnF_AN1 AN1-like Zi 26.0 35 0.00077 19.1 0.8 18 151-168 12-29 (39)
321 COG4416 Com Mu-like prophage p 26.0 32 0.0007 20.9 0.7 11 199-209 25-35 (60)
322 smart00249 PHD PHD zinc finger 26.0 37 0.0008 18.8 1.0 34 40-74 1-34 (47)
323 PLN02638 cellulose synthase A 25.7 63 0.0014 32.2 2.9 51 37-96 16-69 (1079)
324 COG1198 PriA Primosomal protei 24.8 50 0.0011 31.6 2.0 35 128-168 445-484 (730)
325 COG1675 TFA1 Transcription ini 24.8 45 0.00097 25.8 1.4 32 124-160 110-141 (176)
326 COG2816 NPY1 NTP pyrophosphohy 24.8 99 0.0022 25.8 3.5 31 125-161 109-139 (279)
327 PRK00464 nrdR transcriptional 24.4 54 0.0012 24.8 1.8 12 151-162 28-39 (154)
328 PF10272 Tmpp129: Putative tra 24.3 63 0.0014 28.1 2.4 63 36-100 269-354 (358)
329 PF01194 RNA_pol_N: RNA polyme 23.3 98 0.0021 19.4 2.5 13 83-97 3-15 (60)
330 PF01530 zf-C2HC: Zinc finger, 23.2 48 0.0011 17.7 0.9 11 85-95 2-12 (31)
331 KOG2789 Putative Zn-finger pro 23.0 29 0.00064 30.3 0.2 35 37-73 73-107 (482)
332 PF05715 zf-piccolo: Piccolo Z 22.9 47 0.001 20.7 1.0 38 129-170 4-41 (61)
333 PF14445 Prok-RING_2: Prokaryo 22.8 23 0.00049 21.2 -0.4 35 37-72 6-40 (57)
334 COG1781 PyrI Aspartate carbamo 22.5 55 0.0012 24.6 1.4 37 125-161 104-145 (153)
335 PF13894 zf-C2H2_4: C2H2-type 22.4 36 0.00078 15.7 0.4 9 153-161 2-10 (24)
336 PRK00893 aspartate carbamoyltr 22.1 66 0.0014 24.3 1.8 34 125-161 103-144 (152)
337 PRK06386 replication factor A; 21.9 42 0.00092 29.1 0.9 13 198-210 236-248 (358)
338 COG4391 Uncharacterized protei 21.9 69 0.0015 20.1 1.6 35 127-161 24-58 (62)
339 PF15616 TerY-C: TerY-C metal 21.4 97 0.0021 22.8 2.5 23 197-219 76-99 (131)
340 PF03563 Bunya_G2: Bunyavirus 21.3 84 0.0018 26.0 2.4 31 194-225 230-260 (285)
341 PF04135 Nop10p: Nucleolar RNA 21.3 79 0.0017 19.2 1.7 33 86-120 19-51 (53)
342 PF08209 Sgf11: Sgf11 (transcr 21.2 46 0.00099 18.1 0.6 14 197-210 3-16 (33)
343 PRK03564 formate dehydrogenase 21.1 63 0.0014 27.5 1.7 29 199-227 188-224 (309)
344 PRK14873 primosome assembly pr 21.0 62 0.0013 30.7 1.9 25 199-223 393-418 (665)
345 COG3813 Uncharacterized protei 20.9 92 0.002 20.2 2.0 57 40-113 7-65 (84)
346 PRK04023 DNA polymerase II lar 20.8 74 0.0016 31.5 2.3 17 152-168 627-647 (1121)
347 KOG4218 Nuclear hormone recept 20.3 20 0.00043 30.7 -1.3 10 197-206 66-75 (475)
348 KOG3084 NADH pyrophosphatase I 20.1 91 0.002 26.6 2.4 29 196-224 148-182 (345)
No 1
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=6.3e-38 Score=259.50 Aligned_cols=196 Identities=27% Similarity=0.588 Sum_probs=163.4
Q ss_pred hhhcCCCCcccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCCCccccccCCChhHH
Q 026529 31 ELEDIDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFLDPLACKPTIPSSLF 110 (237)
Q Consensus 31 ~~~~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~~~~i~~~l~~~~~ 110 (237)
...+....+.|.|||++......| ..++|+|.||+.|++.|+++.|++|....++||+++|++..++..++.+|+.+++
T Consensus 177 ~~~F~~slf~C~ICf~e~~G~~c~-~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C~~~a~~g~vKelvg~EL~ 255 (445)
T KOG1814|consen 177 LEKFVNSLFDCCICFEEQMGQHCF-KFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCGSVAPPGQVKELVGDELF 255 (445)
T ss_pred HHHHHhhcccceeeehhhcCccee-eecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCCcccCCchHHHHHHHHHHH
Confidence 344567899999999999664555 5899999999999999999999999899999999999999999999999999999
Q ss_pred HHHHHHHHHHhhc-CCCcccCCCCCCCceeeccccccCCcCcccCcccccccccccccccCCCCCChhhhh--------c
Q 026529 111 IKWCDHLCEDYVL-GLERSYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQWFCFQCKLAWHAGYRCEESGN--------L 181 (237)
Q Consensus 111 ~~~~~~~~~~~~~-~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~--------~ 181 (237)
++|++++.++++. ..+.+|||.+.|..+...+++. ..+.|..|+.+||..|+..||++..|+--.. |
T Consensus 256 arYe~l~lqk~l~~msdv~yCPr~~Cq~p~~~d~~~----~l~~CskCnFaFCtlCk~t~HG~s~Ck~~~~~~~~l~~~~ 331 (445)
T KOG1814|consen 256 ARYEKLMLQKTLELMSDVVYCPRACCQLPVKQDPGR----ALAICSKCNFAFCTLCKLTWHGVSPCKVKAEKLIELYLEY 331 (445)
T ss_pred HHHHHHHHHHHHHhhcccccCChhhccCccccCchh----hhhhhccCccHHHHHHHHhhcCCCcccCchHHHHHHHHHH
Confidence 9999999998884 5889999999999998666654 8999999999999999999999999974211 1
Q ss_pred ccc---------------------chHHHHHHHHhCCcccCCCCCcceeccCCCCceeec-Cc--cEEEecccCC
Q 026529 182 RDR---------------------NDIAFGKLLEKMNWTRCPGCGNCIERKKGCRIMFCR-FI--FLSLCLCIFS 232 (237)
Q Consensus 182 ~~~---------------------~~~~~~~~~~~~~~k~CP~C~~~iek~~GCnhm~C~-C~--~cf~c~~~~~ 232 (237)
... ++....+|+ ..+.|+||+|+++|+|.+|||||+|. |+ |||+|...+.
T Consensus 332 ~~~d~a~k~ele~Ryg~rvve~~vn~~lsekwl-~~N~krCP~C~v~IEr~eGCnKM~C~~c~~~fc~~c~~~l~ 405 (445)
T KOG1814|consen 332 LEADEARKRELEKRYGKRVVEELVNDFLSEKWL-ESNSKRCPKCKVVIERSEGCNKMHCTKCGTYFCWICAELLY 405 (445)
T ss_pred hhcCHHHHHHHHHHhhHHHHHHHHHHHHHHHHH-HhcCCCCCcccceeecCCCccceeeccccccceeehhhhcC
Confidence 100 111122333 24669999999999999999999997 87 7777776665
No 2
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=4.3e-37 Score=263.31 Aligned_cols=192 Identities=32% Similarity=0.626 Sum_probs=161.8
Q ss_pred CCCcccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCCCccccccCCChhHHHHHHH
Q 026529 36 DGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFLDPLACKPTIPSSLFIKWCD 115 (237)
Q Consensus 36 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~~~~i~~~l~~~~~~~~~~ 115 (237)
.+..+|.||+.+.+..+.+..+..|+|.||.+|+++|++++.. +...++||..+|...++.+....+|++.+.++|.+
T Consensus 144 ~~~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~~~--~~~~~~C~~~~C~~~l~~~~c~~llt~kl~e~~e~ 221 (384)
T KOG1812|consen 144 LPKEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVKLL--SGTVIRCPHDGCESRLTLESCRKLLTPKLREMWEQ 221 (384)
T ss_pred cccccCccCccccccHhhhHHHhcccchhhhHHhHHHhhhhhc--cCCCccCCCCCCCccCCHHHHhhhcCHHHHHHHHH
Confidence 3577999999666666444448899999999999999999933 57889999999999999999999999999999999
Q ss_pred HHHHHhhcCCCcccCCCCCCCceeecccccc-CCcCcccCcccccccccccccccCCCCCChhhhhcccc--chHHHHHH
Q 026529 116 HLCEDYVLGLERSYCPNRNCMAVMVNECEEI-GRVKKAQCPKCKQWFCFQCKLAWHAGYRCEESGNLRDR--NDIAFGKL 192 (237)
Q Consensus 116 ~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~-~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~--~~~~~~~~ 192 (237)
.+.+.++...+.+|||+|+|...+....... .......|+.|+..||..|+.+||++.+|++++++... .+....++
T Consensus 222 ~~~e~~i~~~~~~ycp~~~C~~l~~~~el~~~~~~~~~~C~~C~~~fCv~C~~~wh~~~sC~eykk~~~~~~~d~~~~~~ 301 (384)
T KOG1812|consen 222 RLKEEVIPSLDRVYCPYPRCSSLMSKTELSSEVKSKRRPCVKCHELFCVKCKVPWHANLSCEEYKKLNPEEYVDDITLKY 301 (384)
T ss_pred HHHHHhhhhhhcccCCCCCchHhhhhhhhccchhhcccccccCCCceeecCCCcCCCCCCHHHHHHhCCcccccHHHHHH
Confidence 9999999877766999999998888665321 12466779999999999999999999999999998754 33444455
Q ss_pred HHhCCcccCCCCCcceeccCCCCceeecCccEEEeccc
Q 026529 193 LEKMNWTRCPGCGNCIERKKGCRIMFCRFIFLSLCLCI 230 (237)
Q Consensus 193 ~~~~~~k~CP~C~~~iek~~GCnhm~C~C~~cf~c~~~ 230 (237)
+. ..||.||+|+..|++.+|||||+|+||+.|||+|.
T Consensus 302 la-~~wr~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~ 338 (384)
T KOG1812|consen 302 LA-KRWRQCPKCKFMIELSEGCNHMTCRCGHQFCYMCG 338 (384)
T ss_pred HH-HhcCcCcccceeeeecCCcceEEeeccccchhhcC
Confidence 55 89999999999999999999999999965555554
No 3
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.96 E-value=4.7e-29 Score=219.17 Aligned_cols=191 Identities=25% Similarity=0.519 Sum_probs=161.2
Q ss_pred CCCcccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCCCccccccCCCh-hHHHHHH
Q 026529 36 DGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFLDPLACKPTIPS-SLFIKWC 114 (237)
Q Consensus 36 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~~~~i~~~l~~-~~~~~~~ 114 (237)
....+|.||++.+.. ....+.|+|.||..||..|+..+|.++....|+||..+|...+..+.|..++++ +..++|.
T Consensus 68 ~~~~~c~ic~~~~~~---~~~~~~c~H~~c~~cw~~yl~~kI~~~~~~~i~cp~~~C~a~v~~~~i~~~~s~~~~~~ky~ 144 (444)
T KOG1815|consen 68 KGDVQCGICVESYDG---EIIGLGCGHPFCPPCWTGYLGTKIHEGEEAKIKCPAHGCPALVGEDTVEKLVSDKEDKEKYQ 144 (444)
T ss_pred CccccCCcccCCCcc---hhhhcCCCcHHHHHHHHHHhhheeeccccccccCCCCCccccCCCceeeeecCCHHHHHHHH
Confidence 455899999999854 235789999999999999999999985444499999999999999999999998 5999999
Q ss_pred HHHHHHhhcC-CCcccCCCCCCCceeeccccccCCcCcccCcccccccccccccccCCCCCChhhhhccccchH--HHHH
Q 026529 115 DHLCEDYVLG-LERSYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQWFCFQCKLAWHAGYRCEESGNLRDRNDI--AFGK 191 (237)
Q Consensus 115 ~~~~~~~~~~-~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~--~~~~ 191 (237)
+.+..+++.. ....|||+|+|+..+..... ....+.| .|++.||+.|+.+||.+.+|.....|...... ....
T Consensus 145 ~~i~~syve~~~~lkwCP~~~C~~av~~~~~---~~~~v~C-~~g~~FC~~C~~~~H~p~~C~~~~~wl~k~~~~se~~~ 220 (444)
T KOG1815|consen 145 RYILRSYVEDNVPLKWCPAPGCGLAVKFGSL---ESVEVDC-GCGHEFCFACGEESHSPVSCPGAKKWLKKCRDDSETIN 220 (444)
T ss_pred HHHHHHHHhcCCccccCCCCCCCceeeccCC---CccceeC-CCCchhHhhccccccCCCcccchHHHHHhhhhhhhhhh
Confidence 9999999975 34799999999998887522 2588999 58889999999999999999999998765222 1122
Q ss_pred HHHhCCcccCCCCCcceeccCCCCceeec---Cc--cEEEecccCCCC
Q 026529 192 LLEKMNWTRCPGCGNCIERKKGCRIMFCR---FI--FLSLCLCIFSNR 234 (237)
Q Consensus 192 ~~~~~~~k~CP~C~~~iek~~GCnhm~C~---C~--~cf~c~~~~~~~ 234 (237)
|+ ..+++.||+|.++|+|++|||||+|. |+ |||.|+..|++|
T Consensus 221 wi-~~ntk~CP~c~~~iek~~gc~~~~~~~~~c~~~FCw~Cl~~~~~h 267 (444)
T KOG1815|consen 221 WI-LANTKECPKCKVPIEKDGGCNHMTCKSASCKHEFCWVCLASLSDH 267 (444)
T ss_pred hh-hccCccCCCcccchhccCCccccccccCCcCCeeceeeecccccc
Confidence 33 46779999999999999999999995 85 888888999988
No 4
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=99.93 E-value=2.2e-26 Score=185.12 Aligned_cols=195 Identities=24% Similarity=0.419 Sum_probs=146.2
Q ss_pred hcCCCCcccccccccCCCCccccccCCCC--CcchHHHHHHHHHhccccCC-------cccccCCCCcCCCC-CCccccc
Q 026529 33 EDIDGTFTCDICIEPMSVNNKFKNNNLCT--HPFCQDCTAKYIEVKVRDNN-------TAKIECPGLHCEQF-LDPLACK 102 (237)
Q Consensus 33 ~~~~~~~~C~IC~~~~~~~~~~~~~~~C~--H~fC~~Cl~~~~~~~i~~~~-------~~~i~CP~~~C~~~-~~~~~i~ 102 (237)
..+.+..+|..|-+.... +.+++|. |..|.+|++.|..+.+++.. ...+.||. +|... |..-.-.
T Consensus 216 ~~N~~ni~C~~Ctdv~~~----vlvf~Cns~HvtC~dCFr~yc~~Rl~~rqf~~~p~~gyslpc~a-gc~~s~i~e~HHF 290 (446)
T KOG0006|consen 216 ATNSRNITCITCTDVRSP----VLVFQCNSRHVTCLDCFRLYCVTRLNDRQFVHDPQLGYSLPCVA-GCPNSLIKELHHF 290 (446)
T ss_pred hcccccceeEEecCCccc----eEEEecCCceeehHHhhhhHhhhcccccccccCccccccccccC-CCchHHHHhhhhh
Confidence 346888999999876532 2357886 99999999999999997621 23678885 67754 3333446
Q ss_pred cCCChhHHHHHHHHHHHHhhcCCCcccCCCCCCCceeeccccccCCcCcccCcc-cccccccccccccCCCC--------
Q 026529 103 PTIPSSLFIKWCDHLCEDYVLGLERSYCPNRNCMAVMVNECEEIGRVKKAQCPK-CKQWFCFQCKLAWHAGY-------- 173 (237)
Q Consensus 103 ~~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~-C~~~~C~~C~~~~H~~~-------- 173 (237)
.+|..+.|.+|+++..+.++...+.+.||.|+|+..+.+++.. .+++|+. |++.||..|.+.+|.|.
T Consensus 291 ~ilg~e~Y~rYQr~atEe~vlq~gGVlCP~pgCG~gll~EPD~----rkvtC~~gCgf~FCR~C~e~yh~geC~~~~~as 366 (446)
T KOG0006|consen 291 RILGEEQYNRYQRYATEECVLQMGGVLCPRPGCGAGLLPEPDQ----RKVTCEGGCGFAFCRECKEAYHEGECSAVFEAS 366 (446)
T ss_pred eecchhHHHHHHHhhhhhheeecCCEecCCCCCCcccccCCCC----CcccCCCCchhHhHHHHHhhhccccceeeeccc
Confidence 7899999999999999999877778999999999999999864 8999986 99999999999999873
Q ss_pred ---CChhhhhccccch---HHHHHHHHhCCcccCCCCCcceeccCCCCceeec---CccEEE--ecccCCCCcc
Q 026529 174 ---RCEESGNLRDRND---IAFGKLLEKMNWTRCPGCGNCIERKKGCRIMFCR---FIFLSL--CLCIFSNRYL 236 (237)
Q Consensus 174 ---~C~~~~~~~~~~~---~~~~~~~~~~~~k~CP~C~~~iek~~GCnhm~C~---C~~cf~--c~~~~~~~~~ 236 (237)
+|........-+. ....+...+..+|+||+|.++.||+|||.||.|+ ||+.|| |..+|..++|
T Consensus 367 ~t~tc~y~vde~~a~~arwd~as~~TIk~tTkpCPkChvptErnGGCmHm~Ct~~~Cg~eWCw~C~tEW~r~Cm 440 (446)
T KOG0006|consen 367 GTTTCAYRVDERAAEQARWDAASKETIKKTTKPCPKCHVPTERNGGCMHMKCTQPQCGLEWCWNCGTEWNRVCM 440 (446)
T ss_pred cccceeeecChhhhhhhhhhhhhhhhhhhccCCCCCccCccccCCceEEeecCCCCCCceeEeccCChhhhhhc
Confidence 1321000000000 0111222346779999999999999999999995 996555 5667876654
No 5
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=99.34 E-value=1.5e-12 Score=84.06 Aligned_cols=63 Identities=37% Similarity=0.849 Sum_probs=54.0
Q ss_pred HHHHHHHHHHhhcC-CCcccCCCCCCCceeeccccccCCcCcccCcccccccccccccccCCCCCC
Q 026529 111 IKWCDHLCEDYVLG-LERSYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQWFCFQCKLAWHAGYRC 175 (237)
Q Consensus 111 ~~~~~~~~~~~~~~-~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C 175 (237)
++|++++.+.+|+. ++++|||+|+|+.++...... ....+.|+.|+..||+.|+.+||++.+|
T Consensus 1 ~~y~~~~~~~~i~~~~~~~~CP~~~C~~~~~~~~~~--~~~~v~C~~C~~~fC~~C~~~~H~~~~C 64 (64)
T smart00647 1 EKYERLLLESYVESNPDLKWCPAPDCSAAIIVTEEE--GCNRVTCPKCGFSFCFRCKVPWHSPVSC 64 (64)
T ss_pred ChHHHHHHHHHHhcCCCccCCCCCCCcceEEecCCC--CCCeeECCCCCCeECCCCCCcCCCCCCC
Confidence 47888999998865 678999999999998886411 2588999999999999999999999987
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=99.29 E-value=5.5e-13 Score=86.09 Aligned_cols=63 Identities=29% Similarity=0.717 Sum_probs=41.6
Q ss_pred HHHHHHHHHHhhc-CCCcccCCCCCCCceeeccccccCCcCcccCcccccccccccccccCCCCCC
Q 026529 111 IKWCDHLCEDYVL-GLERSYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQWFCFQCKLAWHAGYRC 175 (237)
Q Consensus 111 ~~~~~~~~~~~~~-~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C 175 (237)
++|++++++.++. +++++|||+|+|+.++....... ...++|+.|++.||+.|+.+||.+.+|
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 35678999999999999988752 124999999999999999999999886
No 7
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.81 E-value=2.3e-09 Score=62.69 Aligned_cols=41 Identities=24% Similarity=0.690 Sum_probs=29.2
Q ss_pred cccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCC
Q 026529 41 CDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPG 89 (237)
Q Consensus 41 C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~ 89 (237)
|+||++.+..+ ++++|||.||..||.++++..-.. .+.||.
T Consensus 1 CpiC~~~~~~P----v~l~CGH~FC~~Cl~~~~~~~~~~----~~~CP~ 41 (42)
T PF15227_consen 1 CPICLDLFKDP----VSLPCGHSFCRSCLERLWKEPSGS----GFSCPE 41 (42)
T ss_dssp ETTTTSB-SSE----EE-SSSSEEEHHHHHHHHCCSSSS----T---SS
T ss_pred CCccchhhCCc----cccCCcCHHHHHHHHHHHHccCCc----CCCCcC
Confidence 89999999654 589999999999999999764322 288987
No 8
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.68 E-value=1.6e-08 Score=77.97 Aligned_cols=67 Identities=24% Similarity=0.561 Sum_probs=50.0
Q ss_pred CCCCcccccccccCCCCccccccCCCCCcchHHHHHHHHHhcccc--------CCcccccCCCCcCCCCCCccccccCCC
Q 026529 35 IDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRD--------NNTAKIECPGLHCEQFLDPLACKPTIP 106 (237)
Q Consensus 35 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~--------~~~~~i~CP~~~C~~~~~~~~i~~~l~ 106 (237)
..+.++|+||++.+..+ +++.|||.||..|+..|+...-.. ......+||. |+..++...+..+.+
T Consensus 15 ~~~~~~CpICld~~~dP----VvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPv--CR~~Is~~~LvPiyg 88 (193)
T PLN03208 15 SGGDFDCNICLDQVRDP----VVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPV--CKSDVSEATLVPIYG 88 (193)
T ss_pred CCCccCCccCCCcCCCc----EEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCC--CCCcCChhcEEEeec
Confidence 35678999999988543 467899999999999997643110 1234689999 999998877776654
Q ss_pred h
Q 026529 107 S 107 (237)
Q Consensus 107 ~ 107 (237)
.
T Consensus 89 r 89 (193)
T PLN03208 89 R 89 (193)
T ss_pred c
Confidence 3
No 9
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.63 E-value=2.2e-08 Score=58.63 Aligned_cols=43 Identities=33% Similarity=0.706 Sum_probs=24.9
Q ss_pred cccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCC
Q 026529 41 CDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECP 88 (237)
Q Consensus 41 C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP 88 (237)
|+||.+ +...+....+++|||.||++|+.+...... ...++||
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 766566566789999999999999998532 3568887
No 10
>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=98.58 E-value=1.5e-08 Score=60.08 Aligned_cols=41 Identities=27% Similarity=0.675 Sum_probs=32.8
Q ss_pred ccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCC
Q 026529 40 TCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPG 89 (237)
Q Consensus 40 ~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~ 89 (237)
+|+||++++...+.+ ..++|+|.||.+|+..|++.. .+||.
T Consensus 2 ~C~IC~~~~~~~~~~-~~l~C~H~fh~~Ci~~~~~~~--------~~CP~ 42 (44)
T PF13639_consen 2 ECPICLEEFEDGEKV-VKLPCGHVFHRSCIKEWLKRN--------NSCPV 42 (44)
T ss_dssp CETTTTCBHHTTSCE-EEETTSEEEEHHHHHHHHHHS--------SB-TT
T ss_pred CCcCCChhhcCCCeE-EEccCCCeeCHHHHHHHHHhC--------CcCCc
Confidence 699999999665555 467799999999999999762 28887
No 11
>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=98.57 E-value=3.5e-08 Score=56.88 Aligned_cols=38 Identities=34% Similarity=0.907 Sum_probs=29.3
Q ss_pred cccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCC
Q 026529 41 CDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPG 89 (237)
Q Consensus 41 C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~ 89 (237)
|+||++.+..+ +++++|||.||.+|+.+|++.. .+||.
T Consensus 1 C~iC~~~~~~~---~~~~~CGH~fC~~C~~~~~~~~--------~~CP~ 38 (39)
T PF13923_consen 1 CPICLDELRDP---VVVTPCGHSFCKECIEKYLEKN--------PKCPV 38 (39)
T ss_dssp ETTTTSB-SSE---EEECTTSEEEEHHHHHHHHHCT--------SB-TT
T ss_pred CCCCCCcccCc---CEECCCCCchhHHHHHHHHHCc--------CCCcC
Confidence 89999988542 2478999999999999999852 57876
No 12
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=98.55 E-value=5.3e-08 Score=56.77 Aligned_cols=40 Identities=38% Similarity=0.905 Sum_probs=32.6
Q ss_pred cccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCC
Q 026529 41 CDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPG 89 (237)
Q Consensus 41 C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~ 89 (237)
|+||++.+..+. .+++|+|.||.+|+.+|++. ...++||.
T Consensus 1 C~iC~~~~~~~~---~~~~C~H~fC~~C~~~~~~~------~~~~~CP~ 40 (41)
T PF00097_consen 1 CPICLEPFEDPV---ILLPCGHSFCRDCLRKWLEN------SGSVKCPL 40 (41)
T ss_dssp ETTTSSBCSSEE---EETTTSEEEEHHHHHHHHHH------TSSSBTTT
T ss_pred CCcCCccccCCC---EEecCCCcchHHHHHHHHHh------cCCccCCc
Confidence 799999986542 37899999999999999997 23467886
No 13
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.50 E-value=1.2e-07 Score=71.39 Aligned_cols=56 Identities=27% Similarity=0.711 Sum_probs=43.3
Q ss_pred CCCCcccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCCCccccc
Q 026529 35 IDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFLDPLACK 102 (237)
Q Consensus 35 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~~~~i~ 102 (237)
....+.|+|||+.+.. ..++...|||.||+.|++..+.. ..+||. |...|+..++.
T Consensus 128 ~~~~~~CPiCl~~~se--k~~vsTkCGHvFC~~Cik~alk~--------~~~CP~--C~kkIt~k~~~ 183 (187)
T KOG0320|consen 128 KEGTYKCPICLDSVSE--KVPVSTKCGHVFCSQCIKDALKN--------TNKCPT--CRKKITHKQFH 183 (187)
T ss_pred cccccCCCceecchhh--ccccccccchhHHHHHHHHHHHh--------CCCCCC--cccccchhhhe
Confidence 3556899999999853 34457899999999999998874 358998 88777665543
No 14
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=98.43 E-value=2.3e-07 Score=75.11 Aligned_cols=71 Identities=27% Similarity=0.499 Sum_probs=52.9
Q ss_pred ccccCCChHHHhHHhhhcCCCCcccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCC
Q 026529 17 QEKENPRQEEIKEEELEDIDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFL 96 (237)
Q Consensus 17 ~~~~~~~~~~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~ 96 (237)
++++++.+.+.+............|.+|++....+ ...+|||.||-.|+..|...+- .||. |...+
T Consensus 218 e~~~~~~~~~~s~~~~~i~~a~~kC~LCLe~~~~p----SaTpCGHiFCWsCI~~w~~ek~--------eCPl--CR~~~ 283 (293)
T KOG0317|consen 218 ESKLNHSKLEDSNSLSSIPEATRKCSLCLENRSNP----SATPCGHIFCWSCILEWCSEKA--------ECPL--CREKF 283 (293)
T ss_pred cccccccchhhccCCccCCCCCCceEEEecCCCCC----CcCcCcchHHHHHHHHHHcccc--------CCCc--ccccC
Confidence 66666666444444333345668999999998554 4789999999999999998643 2999 99888
Q ss_pred Ccccc
Q 026529 97 DPLAC 101 (237)
Q Consensus 97 ~~~~i 101 (237)
.+..+
T Consensus 284 ~pskv 288 (293)
T KOG0317|consen 284 QPSKV 288 (293)
T ss_pred CCcce
Confidence 77655
No 15
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.41 E-value=2.3e-07 Score=54.92 Aligned_cols=44 Identities=32% Similarity=0.820 Sum_probs=34.6
Q ss_pred ccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCC
Q 026529 40 TCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQ 94 (237)
Q Consensus 40 ~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~ 94 (237)
.|+||++.+..... ..+++|||.||..|+.... ...+.||. |++
T Consensus 1 ~C~~C~~~~~~~~~-~~l~~CgH~~C~~C~~~~~--------~~~~~CP~--C~k 44 (44)
T PF14634_consen 1 HCNICFEKYSEERR-PRLTSCGHIFCEKCLKKLK--------GKSVKCPI--CRK 44 (44)
T ss_pred CCcCcCccccCCCC-eEEcccCCHHHHHHHHhhc--------CCCCCCcC--CCC
Confidence 48999999943333 4689999999999999888 24578998 763
No 16
>PHA02926 zinc finger-like protein; Provisional
Probab=98.33 E-value=8.3e-07 Score=69.46 Aligned_cols=62 Identities=23% Similarity=0.517 Sum_probs=45.4
Q ss_pred hhhcCCCCcccccccccCCC-----CccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCC
Q 026529 31 ELEDIDGTFTCDICIEPMSV-----NNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFL 96 (237)
Q Consensus 31 ~~~~~~~~~~C~IC~~~~~~-----~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~ 96 (237)
.+...+...+|+||++.... ...|-.+.+|+|.||..|++.|..+... ....-.||. |+..+
T Consensus 163 ~~~~~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~--~~~~rsCPi--CR~~f 229 (242)
T PHA02926 163 DVYRVSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRE--TGASDNCPI--CRTRF 229 (242)
T ss_pred HHHhccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccc--cCcCCcCCC--Cccee
Confidence 33345777899999998632 2235567899999999999999987542 234568999 99753
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=98.22 E-value=1.3e-06 Score=51.40 Aligned_cols=44 Identities=32% Similarity=0.745 Sum_probs=33.3
Q ss_pred ccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCC
Q 026529 40 TCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQF 95 (237)
Q Consensus 40 ~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~ 95 (237)
+|+||++.+.. . ....+|+|.||..|+..|++. ...+||. |+..
T Consensus 1 ~C~iC~~~~~~--~-~~~~~C~H~~c~~C~~~~~~~-------~~~~Cp~--C~~~ 44 (45)
T cd00162 1 ECPICLEEFRE--P-VVLLPCGHVFCRSCIDKWLKS-------GKNTCPL--CRTP 44 (45)
T ss_pred CCCcCchhhhC--c-eEecCCCChhcHHHHHHHHHh-------CcCCCCC--CCCc
Confidence 58999998832 2 235669999999999999885 2357988 8754
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=98.18 E-value=1.1e-06 Score=53.54 Aligned_cols=46 Identities=30% Similarity=0.701 Sum_probs=35.5
Q ss_pred CcccccccccCCCCccccccCCCCCc-chHHHHHHHHHhccccCCcccccCCCCcCCCCCC
Q 026529 38 TFTCDICIEPMSVNNKFKNNNLCTHP-FCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFLD 97 (237)
Q Consensus 38 ~~~C~IC~~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~ 97 (237)
...|.||++.... ..+.+|||. ||..|+.+++. ...+||. |++.+.
T Consensus 2 ~~~C~iC~~~~~~----~~~~pCgH~~~C~~C~~~~~~--------~~~~CP~--Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFENPRD----VVLLPCGHLCFCEECAERLLK--------RKKKCPI--CRQPIE 48 (50)
T ss_dssp HSB-TTTSSSBSS----EEEETTCEEEEEHHHHHHHHH--------TTSBBTT--TTBB-S
T ss_pred cCCCccCCccCCc----eEEeCCCChHHHHHHhHHhcc--------cCCCCCc--CChhhc
Confidence 3589999998643 247899999 99999999998 3468999 987664
No 19
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.16 E-value=1.3e-06 Score=68.77 Aligned_cols=61 Identities=26% Similarity=0.598 Sum_probs=49.1
Q ss_pred CCCCcccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCCCccccccCCC
Q 026529 35 IDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFLDPLACKPTIP 106 (237)
Q Consensus 35 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~~~~i~~~l~ 106 (237)
+...|+|.||+|...++ ++..|||.||-.||-+|+...... -.||. |+..++.+.+-.+..
T Consensus 44 ~~~~FdCNICLd~akdP----VvTlCGHLFCWpClyqWl~~~~~~-----~~cPV--CK~~Vs~~~vvPlYG 104 (230)
T KOG0823|consen 44 DGGFFDCNICLDLAKDP----VVTLCGHLFCWPCLYQWLQTRPNS-----KECPV--CKAEVSIDTVVPLYG 104 (230)
T ss_pred CCCceeeeeeccccCCC----EEeecccceehHHHHHHHhhcCCC-----eeCCc--cccccccceEEeeec
Confidence 57889999999987543 578999999999999999976543 46798 998888776665543
No 20
>PHA02929 N1R/p28-like protein; Provisional
Probab=98.04 E-value=5.7e-06 Score=66.62 Aligned_cols=53 Identities=26% Similarity=0.553 Sum_probs=39.4
Q ss_pred CCCCcccccccccCCCCc----cccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCCC
Q 026529 35 IDGTFTCDICIEPMSVNN----KFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFLD 97 (237)
Q Consensus 35 ~~~~~~C~IC~~~~~~~~----~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~ 97 (237)
.....+|+||++++...+ .+.++.+|+|.||.+|+..|... ...||. |+..+.
T Consensus 171 ~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~--------~~tCPl--CR~~~~ 227 (238)
T PHA02929 171 RSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKE--------KNTCPV--CRTPFI 227 (238)
T ss_pred CCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhc--------CCCCCC--CCCEee
Confidence 355689999999875432 12346789999999999999863 237999 987544
No 21
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.02 E-value=3.7e-06 Score=70.68 Aligned_cols=109 Identities=24% Similarity=0.506 Sum_probs=68.2
Q ss_pred CCCCcccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCCCccccccCCChhHHHHHH
Q 026529 35 IDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFLDPLACKPTIPSSLFIKWC 114 (237)
Q Consensus 35 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~~~~i~~~l~~~~~~~~~ 114 (237)
....+.|+||++.+..+ .+++|+|.||..|+...+. ..+.||. |.. ... .+.....+....
T Consensus 10 ~~~~~~C~iC~~~~~~p----~~l~C~H~~c~~C~~~~~~--------~~~~Cp~--cr~-~~~----~~~~n~~l~~~~ 70 (386)
T KOG2177|consen 10 LQEELTCPICLEYFREP----VLLPCGHNFCRACLTRSWE--------GPLSCPV--CRP-PSR----NLRPNVLLANLV 70 (386)
T ss_pred ccccccChhhHHHhhcC----ccccccchHhHHHHHHhcC--------CCcCCcc--cCC-chh----ccCccHHHHHHH
Confidence 45678999999999765 4789999999999999998 3489999 884 222 222222222222
Q ss_pred HHHHHHhhcC-CC--cccCCCCCCCceeeccccccCCcCcccCcccccccccccc-cccCCCCCC
Q 026529 115 DHLCEDYVLG-LE--RSYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQWFCFQCK-LAWHAGYRC 175 (237)
Q Consensus 115 ~~~~~~~~~~-~~--~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~-~~~H~~~~C 175 (237)
.......... .. ...|+. +.....+.|..|....|..|. ...|.++.-
T Consensus 71 ~~~~~~~~~~~~~~~~~~c~~-------------~~~~~~~~c~~~~~~~c~~c~~~~~h~~h~~ 122 (386)
T KOG2177|consen 71 ERLRQLRLSRPLGSKEELCEK-------------HGEELKLFCEEDEKLLCVLCRESGEHRGHPV 122 (386)
T ss_pred HHHHhcCCcccccccchhhhh-------------cCCcceEEecccccccCCCCCCcccccCCcc
Confidence 2222211110 00 112331 111256789999999999998 667877653
No 22
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.99 E-value=5e-06 Score=72.49 Aligned_cols=60 Identities=28% Similarity=0.605 Sum_probs=48.3
Q ss_pred CcccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCCCccccccCCC
Q 026529 38 TFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFLDPLACKPTIP 106 (237)
Q Consensus 38 ~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~~~~i~~~l~ 106 (237)
...|+||+++.+.+ ....|||.||-.||-+|+.... -..+..||. |...|.+.++..+.-
T Consensus 186 ~~~CPICL~~~~~p----~~t~CGHiFC~~CiLqy~~~s~---~~~~~~CPi--C~s~I~~kdl~pv~~ 245 (513)
T KOG2164|consen 186 DMQCPICLEPPSVP----VRTNCGHIFCGPCILQYWNYSA---IKGPCSCPI--CRSTITLKDLLPVFI 245 (513)
T ss_pred CCcCCcccCCCCcc----cccccCceeeHHHHHHHHhhhc---ccCCccCCc--hhhhccccceeeeee
Confidence 78999999987543 3567999999999999998872 235689999 999888877776544
No 23
>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=97.95 E-value=1.3e-05 Score=51.11 Aligned_cols=51 Identities=20% Similarity=0.157 Sum_probs=40.5
Q ss_pred cccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCCCcccccc
Q 026529 39 FTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFLDPLACKP 103 (237)
Q Consensus 39 ~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~~~~i~~ 103 (237)
+.|+||.+.+..+ ++.+|||.||+.|+.+|+.. ...||. |+..++.+++..
T Consensus 2 ~~Cpi~~~~~~~P----v~~~~G~v~~~~~i~~~~~~--------~~~cP~--~~~~~~~~~l~~ 52 (63)
T smart00504 2 FLCPISLEVMKDP----VILPSGQTYERRAIEKWLLS--------HGTDPV--TGQPLTHEDLIP 52 (63)
T ss_pred cCCcCCCCcCCCC----EECCCCCEEeHHHHHHHHHH--------CCCCCC--CcCCCChhhcee
Confidence 5799999998654 46799999999999999975 247998 888876655443
No 24
>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=97.93 E-value=1e-05 Score=45.80 Aligned_cols=30 Identities=33% Similarity=0.931 Sum_probs=24.6
Q ss_pred cccccccCCCCccccccCCCCCcchHHHHHHHHH
Q 026529 41 CDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIE 74 (237)
Q Consensus 41 C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~ 74 (237)
|+||++... . ...++|+|.||..|+..|+.
T Consensus 1 C~iC~~~~~---~-~~~~~C~H~~c~~C~~~~~~ 30 (39)
T smart00184 1 CPICLEELK---D-PVVLPCGHTFCRSCIRKWLK 30 (39)
T ss_pred CCcCccCCC---C-cEEecCCChHHHHHHHHHHH
Confidence 789998842 2 24679999999999999988
No 25
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.87 E-value=1.7e-05 Score=68.58 Aligned_cols=70 Identities=21% Similarity=0.474 Sum_probs=50.3
Q ss_pred hhcCCCCcccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCCCccccc-cCCChhHH
Q 026529 32 LEDIDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFLDPLACK-PTIPSSLF 110 (237)
Q Consensus 32 ~~~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~~~~i~-~~l~~~~~ 110 (237)
+......+.|+||++.+..+ ++++|+|.||..|+..|+... ..||. |+..+....++ +.+-.+++
T Consensus 20 l~~Le~~l~C~IC~d~~~~P----vitpCgH~FCs~CI~~~l~~~--------~~CP~--Cr~~~~~~~Lr~N~~L~~iV 85 (397)
T TIGR00599 20 LYPLDTSLRCHICKDFFDVP----VLTSCSHTFCSLCIRRCLSNQ--------PKCPL--CRAEDQESKLRSNWLVSEIV 85 (397)
T ss_pred ccccccccCCCcCchhhhCc----cCCCCCCchhHHHHHHHHhCC--------CCCCC--CCCccccccCccchHHHHHH
Confidence 34456678999999988543 468999999999999998641 27998 99877654443 34445566
Q ss_pred HHHHH
Q 026529 111 IKWCD 115 (237)
Q Consensus 111 ~~~~~ 115 (237)
+.|..
T Consensus 86 e~~~~ 90 (397)
T TIGR00599 86 ESFKN 90 (397)
T ss_pred HHHHH
Confidence 66643
No 26
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=97.70 E-value=6.5e-05 Score=47.91 Aligned_cols=46 Identities=22% Similarity=0.473 Sum_probs=34.0
Q ss_pred HHHHHHh-CCcccCC--CCCcceeccC--CCCceee-cCccEEEecccCCCC
Q 026529 189 FGKLLEK-MNWTRCP--GCGNCIERKK--GCRIMFC-RFIFLSLCLCIFSNR 234 (237)
Q Consensus 189 ~~~~~~~-~~~k~CP--~C~~~iek~~--GCnhm~C-~C~~cf~c~~~~~~~ 234 (237)
+..++.. .+++.|| +|...|+..+ |..+|+| .|++.||+.|.-..|
T Consensus 8 ~~~~i~~~~~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H 59 (64)
T smart00647 8 LESYVESNPDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWH 59 (64)
T ss_pred HHHHHhcCCCccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcCC
Confidence 3344444 5789999 9999999975 9999999 698666655554444
No 27
>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=97.69 E-value=0.00011 Score=61.02 Aligned_cols=55 Identities=20% Similarity=0.449 Sum_probs=39.5
Q ss_pred cccccccccCCC-Ccc-ccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCCCcccccc
Q 026529 39 FTCDICIEPMSV-NNK-FKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFLDPLACKP 103 (237)
Q Consensus 39 ~~C~IC~~~~~~-~~~-~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~~~~i~~ 103 (237)
..||+|..+... ++. +.+. .|||.||..|+...+.. .+..||. |+..+....++.
T Consensus 4 ~~CP~Ck~~~y~np~~kl~i~-~CGH~~C~sCv~~l~~~-------~~~~CP~--C~~~lrk~~fr~ 60 (309)
T TIGR00570 4 QGCPRCKTTKYRNPSLKLMVN-VCGHTLCESCVDLLFVR-------GSGSCPE--CDTPLRKNNFRV 60 (309)
T ss_pred CCCCcCCCCCccCcccccccC-CCCCcccHHHHHHHhcC-------CCCCCCC--CCCccchhhccc
Confidence 579999996332 232 2223 89999999999999742 2358997 998887776554
No 28
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.65 E-value=3.7e-05 Score=62.85 Aligned_cols=56 Identities=25% Similarity=0.609 Sum_probs=46.4
Q ss_pred hcCCCCcccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCCCc
Q 026529 33 EDIDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFLDP 98 (237)
Q Consensus 33 ~~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~~ 98 (237)
.......+|.||++.+...+.. .+++|.|.|.+.|+.+|+. ....+||. |...+++
T Consensus 318 ~ea~~GveCaICms~fiK~d~~-~vlPC~H~FH~~Cv~kW~~-------~y~~~CPv--Crt~iPP 373 (374)
T COG5540 318 VEADKGVECAICMSNFIKNDRL-RVLPCDHRFHVGCVDKWLL-------GYSNKCPV--CRTAIPP 373 (374)
T ss_pred HhcCCCceEEEEhhhhcccceE-EEeccCceechhHHHHHHh-------hhcccCCc--cCCCCCC
Confidence 3356679999999999776664 5899999999999999997 24578999 9988775
No 29
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=97.60 E-value=2.6e-05 Score=64.68 Aligned_cols=65 Identities=25% Similarity=0.570 Sum_probs=49.6
Q ss_pred CCCcccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCCCcccccc-CCChhHHHHHH
Q 026529 36 DGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFLDPLACKP-TIPSSLFIKWC 114 (237)
Q Consensus 36 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~~~~i~~-~l~~~~~~~~~ 114 (237)
...+-|.||++.+..+ .+.+|+|.||.-|++.|+.. ...||. |...+...+++. .+-+++++.|.
T Consensus 21 D~lLRC~IC~eyf~ip----~itpCsHtfCSlCIR~~L~~--------~p~CP~--C~~~~~Es~Lr~n~il~Eiv~S~~ 86 (442)
T KOG0287|consen 21 DDLLRCGICFEYFNIP----MITPCSHTFCSLCIRKFLSY--------KPQCPT--CCVTVTESDLRNNRILDEIVKSLN 86 (442)
T ss_pred HHHHHHhHHHHHhcCc----eeccccchHHHHHHHHHhcc--------CCCCCc--eecccchhhhhhhhHHHHHHHHHH
Confidence 4467899999999654 36789999999999999973 357998 988887777764 44456666553
No 30
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.52 E-value=6.2e-05 Score=63.58 Aligned_cols=49 Identities=29% Similarity=0.682 Sum_probs=41.3
Q ss_pred CcccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCC
Q 026529 38 TFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFL 96 (237)
Q Consensus 38 ~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~ 96 (237)
+.+|.||+|++...+.+. .++|.|.|...|+..|+... .-.||. |+..+
T Consensus 229 ~~~CaIClEdY~~GdklR-iLPC~H~FH~~CIDpWL~~~-------r~~CPv--CK~di 277 (348)
T KOG4628|consen 229 TDTCAICLEDYEKGDKLR-ILPCSHKFHVNCIDPWLTQT-------RTFCPV--CKRDI 277 (348)
T ss_pred CceEEEeecccccCCeee-EecCCCchhhccchhhHhhc-------CccCCC--CCCcC
Confidence 369999999998888875 69999999999999999864 235999 98743
No 31
>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=97.32 E-value=0.00011 Score=46.82 Aligned_cols=40 Identities=25% Similarity=0.392 Sum_probs=24.5
Q ss_pred hCCcccCCC--CCcceeccCCCCc--eeec-CccEEEecccCCCC
Q 026529 195 KMNWTRCPG--CGNCIERKKGCRI--MFCR-FIFLSLCLCIFSNR 234 (237)
Q Consensus 195 ~~~~k~CP~--C~~~iek~~GCnh--m~C~-C~~cf~c~~~~~~~ 234 (237)
...++.||+ |...|.+.+|.++ |+|. |++.||+.|.-..|
T Consensus 15 ~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H 59 (64)
T PF01485_consen 15 DPNIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPWH 59 (64)
T ss_dssp ---CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSESC
T ss_pred CCCccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCcccC
Confidence 345689987 9999999999999 9998 99666665554434
No 32
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=97.30 E-value=0.00016 Score=45.09 Aligned_cols=50 Identities=22% Similarity=0.543 Sum_probs=32.9
Q ss_pred CCCCcccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCC
Q 026529 35 IDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCE 93 (237)
Q Consensus 35 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~ 93 (237)
....+.|+|-...+..+ +....|+|.|-++-+..|+. ....++||..||.
T Consensus 8 ~~~~~~CPiT~~~~~~P---V~s~~C~H~fek~aI~~~i~------~~~~~~CPv~GC~ 57 (57)
T PF11789_consen 8 GTISLKCPITLQPFEDP---VKSKKCGHTFEKEAILQYIQ------RNGSKRCPVAGCN 57 (57)
T ss_dssp SB--SB-TTTSSB-SSE---EEESSS--EEEHHHHHHHCT------TTS-EE-SCCC-S
T ss_pred cEeccCCCCcCChhhCC---cCcCCCCCeecHHHHHHHHH------hcCCCCCCCCCCC
Confidence 45678999999988644 34679999999999999992 4567899999984
No 33
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=97.29 E-value=0.00024 Score=46.74 Aligned_cols=44 Identities=25% Similarity=0.499 Sum_probs=31.1
Q ss_pred CcccccccccCCCC---------ccccccCCCCCcchHHHHHHHHHhccccCCcccccCCC
Q 026529 38 TFTCDICIEPMSVN---------NKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPG 89 (237)
Q Consensus 38 ~~~C~IC~~~~~~~---------~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~ 89 (237)
...|.||++.+..+ +..+....|+|.|...||.+|++.+- .||.
T Consensus 19 ~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~~--------~CP~ 71 (73)
T PF12678_consen 19 DDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQNN--------TCPL 71 (73)
T ss_dssp CSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTSS--------B-TT
T ss_pred CCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcCC--------cCCC
Confidence 34599999998332 12234568999999999999997421 7887
No 34
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=97.25 E-value=0.00023 Score=62.50 Aligned_cols=65 Identities=25% Similarity=0.711 Sum_probs=48.6
Q ss_pred hcCCCCcccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCCCccccccCCC
Q 026529 33 EDIDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFLDPLACKPTIP 106 (237)
Q Consensus 33 ~~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~~~~i~~~l~ 106 (237)
+++.....|.+|-++-. + . ....|-|.||+-|++.|+.+...+ ..+.||. |...++.+.-+..+.
T Consensus 531 ~enk~~~~C~lc~d~ae--d-~-i~s~ChH~FCrlCi~eyv~~f~~~---~nvtCP~--C~i~LsiDlse~ale 595 (791)
T KOG1002|consen 531 DENKGEVECGLCHDPAE--D-Y-IESSCHHKFCRLCIKEYVESFMEN---NNVTCPV--CHIGLSIDLSEPALE 595 (791)
T ss_pred ccccCceeecccCChhh--h-h-HhhhhhHHHHHHHHHHHHHhhhcc---cCCCCcc--ccccccccccchhhh
Confidence 34567789999987763 2 2 367999999999999999987654 2399999 998777664444443
No 35
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.01 E-value=0.00068 Score=54.68 Aligned_cols=53 Identities=26% Similarity=0.533 Sum_probs=39.1
Q ss_pred CCcccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCCCcccc
Q 026529 37 GTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFLDPLAC 101 (237)
Q Consensus 37 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~~~~i 101 (237)
..+.|.||++....+ ...+|||.||..||-..+..+ ..-.||. |.....+..+
T Consensus 214 ~d~kC~lC~e~~~~p----s~t~CgHlFC~~Cl~~~~t~~------k~~~Cpl--CRak~~pk~v 266 (271)
T COG5574 214 ADYKCFLCLEEPEVP----SCTPCGHLFCLSCLLISWTKK------KYEFCPL--CRAKVYPKKV 266 (271)
T ss_pred cccceeeeecccCCc----ccccccchhhHHHHHHHHHhh------ccccCch--hhhhccchhh
Confidence 367899999887443 578999999999999954322 2335998 9987666554
No 36
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=96.99 E-value=0.00013 Score=45.87 Aligned_cols=50 Identities=26% Similarity=0.543 Sum_probs=22.9
Q ss_pred CcccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCCCccccc
Q 026529 38 TFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFLDPLACK 102 (237)
Q Consensus 38 ~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~~~~i~ 102 (237)
...|++|.+.+..+ +.+..|.|.||..|++..+. -.||. |..+....+++
T Consensus 7 lLrCs~C~~~l~~p---v~l~~CeH~fCs~Ci~~~~~----------~~CPv--C~~Paw~qD~~ 56 (65)
T PF14835_consen 7 LLRCSICFDILKEP---VCLGGCEHIFCSSCIRDCIG----------SECPV--CHTPAWIQDIQ 56 (65)
T ss_dssp TTS-SSS-S--SS----B---SSS--B-TTTGGGGTT----------TB-SS--S--B-S-SS--
T ss_pred hcCCcHHHHHhcCC---ceeccCccHHHHHHhHHhcC----------CCCCC--cCChHHHHHHH
Confidence 46899999998654 23679999999999976333 14999 98765555444
No 37
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=96.93 E-value=0.00046 Score=63.31 Aligned_cols=56 Identities=20% Similarity=0.562 Sum_probs=44.9
Q ss_pred CCCcccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCCCccccccC
Q 026529 36 DGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFLDPLACKPT 104 (237)
Q Consensus 36 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~~~~i~~~ 104 (237)
.....|++|.+.. .+. +...|+|.||..|++..+.+.- =+||. |+..|++.+|..+
T Consensus 641 K~~LkCs~Cn~R~--Kd~--vI~kC~H~FC~~Cvq~r~etRq-------RKCP~--Cn~aFganDv~~I 696 (698)
T KOG0978|consen 641 KELLKCSVCNTRW--KDA--VITKCGHVFCEECVQTRYETRQ-------RKCPK--CNAAFGANDVHRI 696 (698)
T ss_pred HhceeCCCccCch--hhH--HHHhcchHHHHHHHHHHHHHhc-------CCCCC--CCCCCCccccccc
Confidence 5678999999443 233 4689999999999999998654 37998 9999999888754
No 38
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=96.90 E-value=0.00039 Score=45.32 Aligned_cols=59 Identities=19% Similarity=0.383 Sum_probs=27.5
Q ss_pred CcccccccccCCCCccc-c---ccCCCCCcchHHHHHHHHHhccccCCcc-c--ccCCCCcCCCCCCc
Q 026529 38 TFTCDICIEPMSVNNKF-K---NNNLCTHPFCQDCTAKYIEVKVRDNNTA-K--IECPGLHCEQFLDP 98 (237)
Q Consensus 38 ~~~C~IC~~~~~~~~~~-~---~~~~C~H~fC~~Cl~~~~~~~i~~~~~~-~--i~CP~~~C~~~~~~ 98 (237)
..+|+||++.....+.. . ....|+..|...||.+|+.+.-.....+ + -.||. |+..|..
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 46899999986422211 1 1236899999999999998765542222 2 36998 9987653
No 39
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.57 E-value=0.0023 Score=54.50 Aligned_cols=95 Identities=19% Similarity=0.423 Sum_probs=58.0
Q ss_pred CCCCcccccccccCCCCc----cccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCC---Ccc--cccc-C
Q 026529 35 IDGTFTCDICIEPMSVNN----KFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFL---DPL--ACKP-T 104 (237)
Q Consensus 35 ~~~~~~C~IC~~~~~~~~----~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~---~~~--~i~~-~ 104 (237)
......|.||++...... .|-++.+|.|.||..|+++|-...-.+ ....-.||. |.... .+. .+.. -
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 KSSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFE-SKTSKSCPF--CRVPSSFVNPSSFWVETKE 234 (344)
T ss_pred ccccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccc-cccccCCCc--ccCccccccccceeeeecc
Confidence 466889999999985432 133457899999999999998554433 556678999 88532 111 1111 1
Q ss_pred CChhHHHHHHHHHHHHhh--cCCCcccCCC
Q 026529 105 IPSSLFIKWCDHLCEDYV--LGLERSYCPN 132 (237)
Q Consensus 105 l~~~~~~~~~~~~~~~~~--~~~~~~~Cp~ 132 (237)
-...+.+.|.+.+....- -......||.
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 223355666555443311 2355678886
No 40
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=96.49 E-value=0.0025 Score=41.92 Aligned_cols=52 Identities=19% Similarity=0.128 Sum_probs=37.2
Q ss_pred CCcccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCCCcccc
Q 026529 37 GTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFLDPLAC 101 (237)
Q Consensus 37 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~~~~i 101 (237)
..+.|+|+.+-+.++ +.+++||.|.+.++.+|+.. ....||. ++..++..++
T Consensus 3 ~~f~CpIt~~lM~dP----Vi~~~G~tyer~~I~~~l~~-------~~~~~P~--t~~~l~~~~l 54 (73)
T PF04564_consen 3 DEFLCPITGELMRDP----VILPSGHTYERSAIERWLEQ-------NGGTDPF--TRQPLSESDL 54 (73)
T ss_dssp GGGB-TTTSSB-SSE----EEETTSEEEEHHHHHHHHCT-------TSSB-TT--T-SB-SGGGS
T ss_pred cccCCcCcCcHhhCc----eeCCcCCEEcHHHHHHHHHc-------CCCCCCC--CCCcCCcccc
Confidence 468999999988654 46789999999999999986 3457888 7777776544
No 41
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=96.35 E-value=0.0026 Score=52.02 Aligned_cols=66 Identities=20% Similarity=0.415 Sum_probs=45.0
Q ss_pred cCCCCcccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCCCcccccc-CCChhHHHH
Q 026529 34 DIDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFLDPLACKP-TIPSSLFIK 112 (237)
Q Consensus 34 ~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~~~~i~~-~l~~~~~~~ 112 (237)
......-|.||-+.+..+ ....|||.||.-|++.|+..+ ..||. |....-...++. .+..++.+.
T Consensus 21 ~LDs~lrC~IC~~~i~ip----~~TtCgHtFCslCIR~hL~~q--------p~CP~--Cr~~~~esrlr~~s~~~ei~es 86 (391)
T COG5432 21 GLDSMLRCRICDCRISIP----CETTCGHTFCSLCIRRHLGTQ--------PFCPV--CREDPCESRLRGSSGSREINES 86 (391)
T ss_pred cchhHHHhhhhhheeecc----eecccccchhHHHHHHHhcCC--------CCCcc--ccccHHhhhcccchhHHHHHHh
Confidence 345667899999888543 578999999999999998742 46887 875443333332 333455555
Q ss_pred H
Q 026529 113 W 113 (237)
Q Consensus 113 ~ 113 (237)
|
T Consensus 87 ~ 87 (391)
T COG5432 87 H 87 (391)
T ss_pred h
Confidence 5
No 42
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=96.27 E-value=0.0055 Score=51.84 Aligned_cols=52 Identities=23% Similarity=0.537 Sum_probs=39.0
Q ss_pred CCCCcccccccccCCCCc---------cccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCC
Q 026529 35 IDGTFTCDICIEPMSVNN---------KFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFL 96 (237)
Q Consensus 35 ~~~~~~C~IC~~~~~~~~---------~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~ 96 (237)
......|.||+|+.-.++ +-+..++|||.+...|++.|.+.+- .||. |+.++
T Consensus 284 ~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERqQ--------TCPI--Cr~p~ 344 (491)
T COG5243 284 TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQ--------TCPI--CRRPV 344 (491)
T ss_pred cCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhcc--------CCCc--ccCcc
Confidence 345678999999943322 2235789999999999999999642 6888 88764
No 43
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.99 E-value=0.012 Score=50.51 Aligned_cols=120 Identities=21% Similarity=0.458 Sum_probs=74.8
Q ss_pred HhhhcCCCCccccc--ccccC-C-CCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCCCccccccCC
Q 026529 30 EELEDIDGTFTCDI--CIEPM-S-VNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFLDPLACKPTI 105 (237)
Q Consensus 30 ~~~~~~~~~~~C~I--C~~~~-~-~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~~~~i~~~l 105 (237)
+..+..+....||- |-... . +.+.+..-..|.-+||..|...|-- +. + |+.... +.++.++
T Consensus 265 k~l~~msdv~yCPr~~Cq~p~~~d~~~~l~~CskCnFaFCtlCk~t~HG--~s-------~-----Ck~~~~-~~~~l~~ 329 (445)
T KOG1814|consen 265 KTLELMSDVVYCPRACCQLPVKQDPGRALAICSKCNFAFCTLCKLTWHG--VS-------P-----CKVKAE-KLIELYL 329 (445)
T ss_pred HHHHhhcccccCChhhccCccccCchhhhhhhccCccHHHHHHHHhhcC--CC-------c-----ccCchH-HHHHHHH
Confidence 34455566788987 54442 1 1233333456888999999988865 11 1 665432 1122111
Q ss_pred ---C------hhHHHHHHHHHHHHhhc--------CCCcccCCCCCCCceeeccccccCCcCcccCcccccccccccccc
Q 026529 106 ---P------SSLFIKWCDHLCEDYVL--------GLERSYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQWFCFQCKLA 168 (237)
Q Consensus 106 ---~------~~~~~~~~~~~~~~~~~--------~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~ 168 (237)
. .++.+||-++..+..++ ..+...|| .|..++...++- +.+.|..|++.||+.|...
T Consensus 330 ~~~~~d~a~k~ele~Ryg~rvve~~vn~~lsekwl~~N~krCP--~C~v~IEr~eGC----nKM~C~~c~~~fc~~c~~~ 403 (445)
T KOG1814|consen 330 EYLEADEARKRELEKRYGKRVVEELVNDFLSEKWLESNSKRCP--KCKVVIERSEGC----NKMHCTKCGTYFCWICAEL 403 (445)
T ss_pred HHhhcCHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhcCCCCC--cccceeecCCCc----cceeeccccccceeehhhh
Confidence 1 12445665443333221 24568899 999999988875 8999999999999999876
Q ss_pred cC
Q 026529 169 WH 170 (237)
Q Consensus 169 ~H 170 (237)
..
T Consensus 404 l~ 405 (445)
T KOG1814|consen 404 LY 405 (445)
T ss_pred cC
Confidence 44
No 44
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=95.76 E-value=0.0043 Score=47.89 Aligned_cols=37 Identities=24% Similarity=0.546 Sum_probs=29.5
Q ss_pred cCCCCcccccccccCCCCccccccCCCCCcchHHHHHHHHH
Q 026529 34 DIDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIE 74 (237)
Q Consensus 34 ~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~ 74 (237)
...-+|.|.||-.++.++ ++..|||.||..|..+-+.
T Consensus 192 ~e~IPF~C~iCKkdy~sp----vvt~CGH~FC~~Cai~~y~ 228 (259)
T COG5152 192 GEKIPFLCGICKKDYESP----VVTECGHSFCSLCAIRKYQ 228 (259)
T ss_pred CCCCceeehhchhhccch----hhhhcchhHHHHHHHHHhc
Confidence 345578999999999654 5789999999999876554
No 45
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=95.61 E-value=0.014 Score=34.73 Aligned_cols=46 Identities=26% Similarity=0.578 Sum_probs=22.3
Q ss_pred cccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCC
Q 026529 41 CDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQF 95 (237)
Q Consensus 41 C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~ 95 (237)
|++|.+++...+.-+.-.+|++.+|+.|+.+-.+. ..=+||. |+.+
T Consensus 1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~~-------~~g~CPg--Cr~~ 46 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILEN-------EGGRCPG--CREP 46 (48)
T ss_dssp -TTTS-B--CCCTT--SSTTS----HHHHHHHTTS-------S-SB-TT--T--B
T ss_pred CCCcccccccCCCccccCcCCCcHHHHHHHHHHhc-------cCCCCCC--CCCC
Confidence 78999998544432234578999999999887762 1237987 8865
No 46
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=95.54 E-value=0.019 Score=38.52 Aligned_cols=53 Identities=26% Similarity=0.518 Sum_probs=36.7
Q ss_pred CcccccccccCCCC--------cc-ccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCCC
Q 026529 38 TFTCDICIEPMSVN--------NK-FKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFLD 97 (237)
Q Consensus 38 ~~~C~IC~~~~~~~--------~~-~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~ 97 (237)
...|+||...+... +. -++...|+|.|...||.+|++++-. .-.||. |++.+.
T Consensus 21 dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~-----~~~CPm--CR~~w~ 82 (85)
T PF12861_consen 21 DDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSS-----KGQCPM--CRQPWK 82 (85)
T ss_pred CCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccC-----CCCCCC--cCCeee
Confidence 45788887766411 11 1235579999999999999997522 238998 987654
No 47
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.53 E-value=0.03 Score=47.08 Aligned_cols=50 Identities=30% Similarity=0.673 Sum_probs=39.0
Q ss_pred CcccccccccCCCC--ccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCC
Q 026529 38 TFTCDICIEPMSVN--NKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFL 96 (237)
Q Consensus 38 ~~~C~IC~~~~~~~--~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~ 96 (237)
...|.||-+++++. +..+..+.|||.+|..|+...+.. ..+.||. |....
T Consensus 3 ~~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~-------~~i~cpf--cR~~~ 54 (296)
T KOG4185|consen 3 FPECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGN-------SRILCPF--CRETT 54 (296)
T ss_pred CCceeecCccccccCcccCCcccccCceehHhHHHHHhcC-------ceeeccC--CCCcc
Confidence 46899999999765 334557889999999999988773 4466788 88763
No 48
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=95.30 E-value=0.013 Score=48.97 Aligned_cols=52 Identities=27% Similarity=0.690 Sum_probs=40.6
Q ss_pred CCCCcccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCCCcc
Q 026529 35 IDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFLDPL 99 (237)
Q Consensus 35 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~~~ 99 (237)
....++|.+|-..+.+.. .+..|-|.||+.||-+|++. ...||. |+-.+.-.
T Consensus 12 ~n~~itC~LC~GYliDAT---TI~eCLHTFCkSCivk~l~~--------~~~CP~--C~i~ih~t 63 (331)
T KOG2660|consen 12 LNPHITCRLCGGYLIDAT---TITECLHTFCKSCIVKYLEE--------SKYCPT--CDIVIHKT 63 (331)
T ss_pred cccceehhhccceeecch---hHHHHHHHHHHHHHHHHHHH--------hccCCc--cceeccCc
Confidence 467789999998886543 35689999999999999996 247998 88655433
No 49
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=94.89 E-value=0.047 Score=45.42 Aligned_cols=93 Identities=19% Similarity=0.504 Sum_probs=58.0
Q ss_pred CCCCcchHHHHHHHHHhcccc--CCcccccCCCCcCCCCCCccccccCCChhHHHHHHHHHHHHhhcCCCcccCCCCCCC
Q 026529 59 LCTHPFCQDCTAKYIEVKVRD--NNTAKIECPGLHCEQFLDPLACKPTIPSSLFIKWCDHLCEDYVLGLERSYCPNRNCM 136 (237)
Q Consensus 59 ~C~H~fC~~Cl~~~~~~~i~~--~~~~~i~CP~~~C~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~ 136 (237)
.|+-.||++|+..|-+-.-.. +....-. |.-.+++. .....+|+.+..... . ...+.|| .|.
T Consensus 341 gCgf~FCR~C~e~yh~geC~~~~~as~t~t-----c~y~vde~-------~a~~arwd~as~~TI-k-~tTkpCP--kCh 404 (446)
T KOG0006|consen 341 GCGFAFCRECKEAYHEGECSAVFEASGTTT-----CAYRVDER-------AAEQARWDAASKETI-K-KTTKPCP--KCH 404 (446)
T ss_pred CchhHhHHHHHhhhccccceeeeccccccc-----eeeecChh-------hhhhhhhhhhhhhhh-h-hccCCCC--Ccc
Confidence 499999999999887532221 1111111 22222221 234567776654432 1 2346788 898
Q ss_pred ceeeccccccCCcCcccCcc--cccccccccccccCC
Q 026529 137 AVMVNECEEIGRVKKAQCPK--CKQWFCFQCKLAWHA 171 (237)
Q Consensus 137 ~~~~~~~~~~~~~~~~~C~~--C~~~~C~~C~~~~H~ 171 (237)
.....+.+- ..+.|+. |+..+|+.|+-.|..
T Consensus 405 vptErnGGC----mHm~Ct~~~Cg~eWCw~C~tEW~r 437 (446)
T KOG0006|consen 405 VPTERNGGC----MHMKCTQPQCGLEWCWNCGTEWNR 437 (446)
T ss_pred CccccCCce----EEeecCCCCCCceeEeccCChhhh
Confidence 777666553 7788965 999999999999975
No 50
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.62 E-value=0.034 Score=45.28 Aligned_cols=51 Identities=25% Similarity=0.564 Sum_probs=38.4
Q ss_pred CCCcccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCCC
Q 026529 36 DGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFLD 97 (237)
Q Consensus 36 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~ 97 (237)
+...+|++|-+.-..+ + +...|+|.||--|+..-... ...+.||. |+....
T Consensus 237 t~~~~C~~Cg~~PtiP--~-~~~~C~HiyCY~Ci~ts~~~------~asf~Cp~--Cg~~~~ 287 (298)
T KOG2879|consen 237 TSDTECPVCGEPPTIP--H-VIGKCGHIYCYYCIATSRLW------DASFTCPL--CGENVE 287 (298)
T ss_pred cCCceeeccCCCCCCC--e-eeccccceeehhhhhhhhcc------hhhcccCc--cCCCCc
Confidence 4467999998775443 2 35679999999999987764 34579998 997655
No 51
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=94.36 E-value=0.035 Score=44.54 Aligned_cols=59 Identities=12% Similarity=0.193 Sum_probs=45.8
Q ss_pred CCCCcccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCCCcccccc
Q 026529 35 IDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFLDPLACKP 103 (237)
Q Consensus 35 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~~~~i~~ 103 (237)
....+.|+||-+++...-...++.++||+||.+|+.+.|.. ...||. |+.++...+|-.
T Consensus 218 ~s~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~--------D~v~pv--~d~plkdrdiI~ 276 (303)
T KOG3039|consen 218 ASKRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRK--------DMVDPV--TDKPLKDRDIIG 276 (303)
T ss_pred hccceecccchhhhcCccceEEeccCCcEeeHHHHHHhccc--------cccccC--CCCcCcccceEe
Confidence 35789999999999765555567789999999999999873 345777 888777666543
No 52
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.34 E-value=0.04 Score=48.00 Aligned_cols=48 Identities=27% Similarity=0.708 Sum_probs=36.6
Q ss_pred CCCcccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCCC
Q 026529 36 DGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFLD 97 (237)
Q Consensus 36 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~ 97 (237)
...++|.||+..+..+ ++++|||.||..|+.+-.. ....||. |...+.
T Consensus 82 ~sef~c~vc~~~l~~p----v~tpcghs~c~~Cl~r~ld--------~~~~cp~--Cr~~l~ 129 (398)
T KOG4159|consen 82 RSEFECCVCSRALYPP----VVTPCGHSFCLECLDRSLD--------QETECPL--CRDELV 129 (398)
T ss_pred cchhhhhhhHhhcCCC----ccccccccccHHHHHHHhc--------cCCCCcc--cccccc
Confidence 6789999999998654 4679999999999777222 2356887 886655
No 53
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.24 E-value=0.038 Score=45.62 Aligned_cols=53 Identities=25% Similarity=0.414 Sum_probs=39.9
Q ss_pred CCCcccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCCCcccc
Q 026529 36 DGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFLDPLAC 101 (237)
Q Consensus 36 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~~~~i 101 (237)
...-+|.||+.+-..+ +.+.|+|.||--|++.-+... ...|+. |..+|+...+
T Consensus 5 ~~~~eC~IC~nt~n~P----v~l~C~HkFCyiCiKGsy~nd-------k~~Cav--CR~pids~i~ 57 (324)
T KOG0824|consen 5 TKKKECLICYNTGNCP----VNLYCFHKFCYICIKGSYKND-------KKTCAV--CRFPIDSTID 57 (324)
T ss_pred ccCCcceeeeccCCcC----ccccccchhhhhhhcchhhcC-------CCCCce--ecCCCCcchh
Confidence 4456899999887543 578999999999999766532 235888 9988776533
No 54
>PF04641 Rtf2: Rtf2 RING-finger
Probab=94.23 E-value=0.089 Score=43.46 Aligned_cols=73 Identities=18% Similarity=0.365 Sum_probs=54.8
Q ss_pred cCCCCcccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCCCccccccCCCh-hHHHH
Q 026529 34 DIDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFLDPLACKPTIPS-SLFIK 112 (237)
Q Consensus 34 ~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~~~~i~~~l~~-~~~~~ 112 (237)
.....+.|||-..++.....|+.+.+|||+|....++..- .+ -.||. |+..+...+|-.+-+. +.++.
T Consensus 109 ~~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k----~~-----~~Cp~--c~~~f~~~DiI~Lnp~~ee~~~ 177 (260)
T PF04641_consen 109 NSEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK----KS-----KKCPV--CGKPFTEEDIIPLNPPEEELEK 177 (260)
T ss_pred cCCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc----cc-----ccccc--cCCccccCCEEEecCCccHHHH
Confidence 3577899999999997666787788999999999999872 12 24999 9999998877766553 34444
Q ss_pred HHHHH
Q 026529 113 WCDHL 117 (237)
Q Consensus 113 ~~~~~ 117 (237)
+...+
T Consensus 178 l~~~~ 182 (260)
T PF04641_consen 178 LRERM 182 (260)
T ss_pred HHHHH
Confidence 44443
No 55
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=94.16 E-value=0.041 Score=51.46 Aligned_cols=57 Identities=21% Similarity=0.521 Sum_probs=45.8
Q ss_pred cCCCCcccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCC
Q 026529 34 DIDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCE 93 (237)
Q Consensus 34 ~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~ 93 (237)
.....++|.||++.+.....++.-..|-|+|-..|+++|..+.-++ +...-+||. |.
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 3467899999999998777666667799999999999999884444 346678987 76
No 56
>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=93.98 E-value=0.022 Score=34.43 Aligned_cols=39 Identities=28% Similarity=0.707 Sum_probs=18.9
Q ss_pred CCCceeeccccccCCcCcccCcccccccccccccccCCC
Q 026529 134 NCMAVMVNECEEIGRVKKAQCPKCKQWFCFQCKLAWHAG 172 (237)
Q Consensus 134 ~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~ 172 (237)
+|...+..............||.|+..||..|-.-.|..
T Consensus 4 gC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHE~ 42 (51)
T PF07975_consen 4 GCQKPFPDGPEKKADSSRYRCPKCKNHFCIDCDVFIHET 42 (51)
T ss_dssp TTTEE-TTS-------EEE--TTTT--B-HHHHHTTTTT
T ss_pred cCCCCCCCcccccccCCeEECCCCCCccccCcChhhhcc
Confidence 455555443322112468899999999999998777754
No 57
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.77 E-value=0.039 Score=50.44 Aligned_cols=49 Identities=24% Similarity=0.572 Sum_probs=37.4
Q ss_pred CCCcccccccccCCCCcc-ccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCC
Q 026529 36 DGTFTCDICIEPMSVNNK-FKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQ 94 (237)
Q Consensus 36 ~~~~~C~IC~~~~~~~~~-~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~ 94 (237)
.....|.||.|++..... -...++|+|.|+..|++.|++. .-.||. |+.
T Consensus 289 ~~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er--------~qtCP~--CR~ 338 (543)
T KOG0802|consen 289 LSDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFER--------QQTCPT--CRT 338 (543)
T ss_pred hcCCeeeeechhhccccccccceeecccchHHHHHHHHHHH--------hCcCCc--chh
Confidence 446699999999865322 1247899999999999999997 236887 775
No 58
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=93.64 E-value=0.036 Score=28.51 Aligned_cols=23 Identities=35% Similarity=0.800 Sum_probs=17.1
Q ss_pred cCCCCCCCceeeccccccCCcCcccCccccccc
Q 026529 129 YCPNRNCMAVMVNECEEIGRVKKAQCPKCKQWF 161 (237)
Q Consensus 129 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 161 (237)
.|| .|+..+.... ..||.||+.|
T Consensus 2 ~CP--~C~~~V~~~~--------~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCP--ECGAEVPESA--------KFCPHCGYDF 24 (26)
T ss_pred cCC--CCcCCchhhc--------CcCCCCCCCC
Confidence 577 8888885544 4599999876
No 59
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=93.64 E-value=0.063 Score=32.45 Aligned_cols=28 Identities=32% Similarity=0.608 Sum_probs=21.4
Q ss_pred ccCCCCCcceeccC--CCCceeec-CccEEE
Q 026529 199 TRCPGCGNCIERKK--GCRIMFCR-FIFLSL 226 (237)
Q Consensus 199 k~CP~C~~~iek~~--GCnhm~C~-C~~cf~ 226 (237)
+.||.|+.++...+ +-+++.|. |||.+.
T Consensus 1 ~FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~~ 31 (52)
T smart00661 1 KFCPKCGNMLIPKEGKEKRRFVCRKCGYEEP 31 (52)
T ss_pred CCCCCCCCccccccCCCCCEEECCcCCCeEE
Confidence 46999999887764 34689997 998764
No 60
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.46 E-value=0.055 Score=47.19 Aligned_cols=43 Identities=21% Similarity=0.583 Sum_probs=35.7
Q ss_pred CCcccCCCCCCCceeeccccccCCcCcccCcccccccccccccccCCCCC
Q 026529 125 LERSYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQWFCFQCKLAWHAGYR 174 (237)
Q Consensus 125 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~ 174 (237)
...+.|| .|...+....+- +.++|. |++.||+.|...|..+..
T Consensus 304 ~~wr~Cp--kC~~~ie~~~GC----nhm~Cr-C~~~fcy~C~~~~~~~~~ 346 (384)
T KOG1812|consen 304 KRWRQCP--KCKFMIELSEGC----NHMTCR-CGHQFCYMCGGDWKTHNG 346 (384)
T ss_pred HhcCcCc--ccceeeeecCCc----ceEEee-ccccchhhcCcchhhCCc
Confidence 5578999 999998766664 899998 999999999999966443
No 61
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=93.40 E-value=0.034 Score=44.54 Aligned_cols=55 Identities=24% Similarity=0.569 Sum_probs=37.4
Q ss_pred CcccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCCCccccccCCC
Q 026529 38 TFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFLDPLACKPTIP 106 (237)
Q Consensus 38 ~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~~~~i~~~l~ 106 (237)
.+.|..|+---+ .+.|+ ++.|+|+||..|.+.-.. -.||. |++.+....+-.-|+
T Consensus 3 ~VhCn~C~~~~~-~~~f~-LTaC~HvfC~~C~k~~~~----------~~C~l--Ckk~ir~i~l~~slp 57 (233)
T KOG4739|consen 3 FVHCNKCFRFPS-QDPFF-LTACRHVFCEPCLKASSP----------DVCPL--CKKSIRIIQLNRSLP 57 (233)
T ss_pred eEEeccccccCC-CCcee-eeechhhhhhhhcccCCc----------ccccc--ccceeeeeecccccc
Confidence 357888886654 56664 889999999999763222 28998 998765444433343
No 62
>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class
Probab=93.35 E-value=0.12 Score=30.98 Aligned_cols=42 Identities=19% Similarity=0.445 Sum_probs=29.2
Q ss_pred ccccccccCCCCccccccCCCC-----CcchHHHHHHHHHhccccCCcccccCCC
Q 026529 40 TCDICIEPMSVNNKFKNNNLCT-----HPFCQDCTAKYIEVKVRDNNTAKIECPG 89 (237)
Q Consensus 40 ~C~IC~~~~~~~~~~~~~~~C~-----H~fC~~Cl~~~~~~~i~~~~~~~i~CP~ 89 (237)
.|-||++...+.+.+ ..+|. |.+...||.+|+...-. .+||.
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 388999843333333 46774 78999999999986432 37876
No 63
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.22 E-value=0.065 Score=47.19 Aligned_cols=55 Identities=27% Similarity=0.649 Sum_probs=40.4
Q ss_pred CCCCcccccccccCCCCc----cc---------cccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCCCc
Q 026529 35 IDGTFTCDICIEPMSVNN----KF---------KNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFLDP 98 (237)
Q Consensus 35 ~~~~~~C~IC~~~~~~~~----~~---------~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~~ 98 (237)
...+..|.||+.+++.-. .+ +.+.+|.|.|-+.||.+|... ..+.||. |+.++++
T Consensus 568 ~~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~-------ykl~CPv--CR~pLPp 635 (636)
T KOG0828|consen 568 VRRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDT-------YKLICPV--CRCPLPP 635 (636)
T ss_pred hhccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhh-------hcccCCc--cCCCCCC
Confidence 355779999999874211 00 125699999999999999983 3478998 8887764
No 64
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=93.19 E-value=0.065 Score=30.10 Aligned_cols=32 Identities=31% Similarity=0.736 Sum_probs=24.8
Q ss_pred ccCCCCCCCceeecccccc-CCcCcccCccccccc
Q 026529 128 SYCPNRNCMAVMVNECEEI-GRVKKAQCPKCKQWF 161 (237)
Q Consensus 128 ~~Cp~~~C~~~~~~~~~~~-~~~~~~~C~~C~~~~ 161 (237)
+.|| .|+..+...+... .....++|+.|++.|
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 5799 9999888877532 235799999999876
No 65
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=93.16 E-value=0.17 Score=42.52 Aligned_cols=60 Identities=27% Similarity=0.558 Sum_probs=42.6
Q ss_pred ccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCCCcccccc-CCChh
Q 026529 40 TCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFLDPLACKP-TIPSS 108 (237)
Q Consensus 40 ~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~~~~i~~-~l~~~ 108 (237)
.|++|+++....+.-+.-.+||-.+|..||...-+ .++ =+||. |+...+.+.++= -|+++
T Consensus 16 ~cplcie~mditdknf~pc~cgy~ic~fc~~~irq-~ln------grcpa--crr~y~denv~~~~~s~e 76 (480)
T COG5175 16 YCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQ-NLN------GRCPA--CRRKYDDENVRYVTLSPE 76 (480)
T ss_pred cCcccccccccccCCcccCCcccHHHHHHHHHHHh-hcc------CCChH--hhhhccccceeEEecCHH
Confidence 59999999866554334678899999999975433 343 37998 998887776652 34444
No 66
>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=92.99 E-value=0.02 Score=45.64 Aligned_cols=51 Identities=22% Similarity=0.542 Sum_probs=37.4
Q ss_pred cccccccccCC-CCcc-ccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCC
Q 026529 39 FTCDICIEPMS-VNNK-FKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFL 96 (237)
Q Consensus 39 ~~C~IC~~~~~-~~~~-~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~ 96 (237)
--||||-.+.. .++. +.+...|-|.+|.+|+.+.|. ..|-.||.++|+.+|
T Consensus 11 ~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs-------~GpAqCP~~gC~kIL 63 (314)
T COG5220 11 RRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFS-------RGPAQCPYKGCGKIL 63 (314)
T ss_pred ccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhc-------CCCCCCCCccHHHHH
Confidence 37999987743 3333 223334999999999999887 356789999999654
No 67
>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=92.78 E-value=0.037 Score=40.41 Aligned_cols=42 Identities=21% Similarity=0.426 Sum_probs=30.4
Q ss_pred hcCCCCcccccccccCCCCccccccCCC------CCcchHHHHHHHHHh
Q 026529 33 EDIDGTFTCDICIEPMSVNNKFKNNNLC------THPFCQDCTAKYIEV 75 (237)
Q Consensus 33 ~~~~~~~~C~IC~~~~~~~~~~~~~~~C------~H~fC~~Cl~~~~~~ 75 (237)
.-.....+|.||++.+...+. ++...| .|.||.+|+++|-..
T Consensus 21 ~w~~~~~EC~IC~~~I~~~~G-vV~vt~~g~lnLEkmfc~~C~~rw~~~ 68 (134)
T PF05883_consen 21 QWPRCTVECQICFDRIDNNDG-VVYVTDGGTLNLEKMFCADCDKRWRRE 68 (134)
T ss_pred HccccCeeehhhhhhhhcCCC-EEEEecCCeehHHHHHHHHHHHHHHhh
Confidence 344558999999999976233 344555 477999999999533
No 68
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=92.77 E-value=0.035 Score=48.27 Aligned_cols=40 Identities=28% Similarity=0.527 Sum_probs=32.7
Q ss_pred CCCcccccccccCCCCccccccCCCCCcchHHHHHHHHHh
Q 026529 36 DGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEV 75 (237)
Q Consensus 36 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~ 75 (237)
...-+|+||++..++.-..+....|.|+|--.|+..|..+
T Consensus 173 tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~~~ 212 (493)
T KOG0804|consen 173 TELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWWDS 212 (493)
T ss_pred ccCCCcchhHhhcCccccceeeeecccccchHHHhhcccC
Confidence 4456999999999766556667899999999999988764
No 69
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=92.50 E-value=0.15 Score=50.73 Aligned_cols=69 Identities=20% Similarity=0.376 Sum_probs=53.3
Q ss_pred CCCcccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCc--ccccCCCCcCCCCCCccccccCCCh
Q 026529 36 DGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNT--AKIECPGLHCEQFLDPLACKPTIPS 107 (237)
Q Consensus 36 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~--~~i~CP~~~C~~~~~~~~i~~~l~~ 107 (237)
+..--|.|||.+--..... ..+.|+|.|-..|.+.-++..-....+ .-|.||. |.+.+..-.++.+|++
T Consensus 3484 D~DDmCmICFTE~L~AAP~-IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPi--C~n~InH~~LkDLldP 3554 (3738)
T KOG1428|consen 3484 DADDMCMICFTEALSAAPA-IQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPI--CKNKINHIVLKDLLDP 3554 (3738)
T ss_pred ccCceEEEEehhhhCCCcc-eecCCccchhHHHHHHHHHhcccCCeeEEeeeeccc--ccchhhhHHHHHHHHH
Confidence 4556899999886443333 368999999999999999877665222 3589999 9999998888888874
No 70
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=92.36 E-value=0.11 Score=29.03 Aligned_cols=32 Identities=34% Similarity=0.663 Sum_probs=24.6
Q ss_pred ccCCCCCCCceeeccccc-cCCcCcccCccccccc
Q 026529 128 SYCPNRNCMAVMVNECEE-IGRVKKAQCPKCKQWF 161 (237)
Q Consensus 128 ~~Cp~~~C~~~~~~~~~~-~~~~~~~~C~~C~~~~ 161 (237)
+.|| .|+..+..++.. ......++|+.|++.|
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 5788 999888877653 2346789999999875
No 71
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.59 E-value=0.094 Score=45.16 Aligned_cols=50 Identities=28% Similarity=0.647 Sum_probs=39.1
Q ss_pred CcccccccccCCCC-ccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCC
Q 026529 38 TFTCDICIEPMSVN-NKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQF 95 (237)
Q Consensus 38 ~~~C~IC~~~~~~~-~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~ 95 (237)
..+|+||++.+..+ +..++++.|+|.|=.+|+++|+. ......||. |+..
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 46899999986432 34456899999999999999993 345689998 8853
No 72
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.58 E-value=0.027 Score=47.48 Aligned_cols=49 Identities=33% Similarity=0.735 Sum_probs=35.8
Q ss_pred CCCCcccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCC
Q 026529 35 IDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQF 95 (237)
Q Consensus 35 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~ 95 (237)
....+.|+||++-+... + ....|.|.||.+|+..-+... + -.||. |++.
T Consensus 40 ~~~~v~c~icl~llk~t--m-ttkeClhrfc~~ci~~a~r~g----n---~ecpt--cRk~ 88 (381)
T KOG0311|consen 40 FDIQVICPICLSLLKKT--M-TTKECLHRFCFDCIWKALRSG----N---NECPT--CRKK 88 (381)
T ss_pred hhhhhccHHHHHHHHhh--c-ccHHHHHHHHHHHHHHHHHhc----C---CCCch--HHhh
Confidence 35678999999887432 2 367899999999998776642 2 36887 8754
No 73
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=91.41 E-value=0.24 Score=43.42 Aligned_cols=48 Identities=27% Similarity=0.705 Sum_probs=36.2
Q ss_pred CCCCcccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCC
Q 026529 35 IDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQF 95 (237)
Q Consensus 35 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~ 95 (237)
......|++|...+.++- .+..|||.||..|+..+... ...||. |...
T Consensus 18 ~~~~l~C~~C~~vl~~p~---~~~~cgh~fC~~C~~~~~~~--------~~~cp~--~~~~ 65 (391)
T KOG0297|consen 18 LDENLLCPICMSVLRDPV---QTTTCGHRFCAGCLLESLSN--------HQKCPV--CRQE 65 (391)
T ss_pred CcccccCccccccccCCC---CCCCCCCcccccccchhhcc--------CcCCcc--cccc
Confidence 456789999999986542 23699999999999999885 346776 6443
No 74
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=91.17 E-value=0.2 Score=35.56 Aligned_cols=42 Identities=21% Similarity=0.594 Sum_probs=28.8
Q ss_pred ccCCCCCCCceeeccccc----cCCcCcccCcccccccccccccccCC
Q 026529 128 SYCPNRNCMAVMVNECEE----IGRVKKAQCPKCKQWFCFQCKLAWHA 171 (237)
Q Consensus 128 ~~Cp~~~C~~~~~~~~~~----~~~~~~~~C~~C~~~~C~~C~~~~H~ 171 (237)
..|- +|...+...... ........|+.|+..||..|..-+|.
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 4577 888766543211 01245778999999999999877775
No 75
>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=91.16 E-value=0.42 Score=39.45 Aligned_cols=54 Identities=20% Similarity=0.488 Sum_probs=37.9
Q ss_pred ccccccccC-CCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCCCccccc
Q 026529 40 TCDICIEPM-SVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFLDPLACK 102 (237)
Q Consensus 40 ~C~IC~~~~-~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~~~~i~ 102 (237)
.|++|-.+. ..++.+..+.+|+|..|.+|+...+.. .+-.||. |..++-..-++
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~-------g~~~Cpe--C~~iLRk~nfr 56 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSL-------GPAQCPE--CMVILRKNNFR 56 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHhc-------CCCCCCc--ccchhhhcccc
Confidence 588887664 234444345599999999999998873 4557996 99876554443
No 76
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.08 E-value=0.23 Score=42.55 Aligned_cols=50 Identities=24% Similarity=0.567 Sum_probs=35.9
Q ss_pred CCcccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCC
Q 026529 37 GTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCE 93 (237)
Q Consensus 37 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~ 93 (237)
....|.||-+-++....+-....|||.|...|+..|++..-.. -.||. |+
T Consensus 3 i~A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~-----R~cpi--c~ 52 (465)
T KOG0827|consen 3 IMAECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSN-----RGCPI--CQ 52 (465)
T ss_pred ccceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCcc-----CCCCc--ee
Confidence 3568999966665555554444599999999999999954321 36787 76
No 77
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=90.98 E-value=0.23 Score=29.95 Aligned_cols=27 Identities=19% Similarity=0.460 Sum_probs=19.9
Q ss_pred CcccCCCCCc-ceeccCCCCceeec-CccEE
Q 026529 197 NWTRCPGCGN-CIERKKGCRIMFCR-FIFLS 225 (237)
Q Consensus 197 ~~k~CP~C~~-~iek~~GCnhm~C~-C~~cf 225 (237)
..+.||+|+. .+.... +.++|. |||.+
T Consensus 19 ~~~fCP~Cg~~~m~~~~--~r~~C~~Cgyt~ 47 (50)
T PRK00432 19 KNKFCPRCGSGFMAEHL--DRWHCGKCGYTE 47 (50)
T ss_pred ccCcCcCCCcchheccC--CcEECCCcCCEE
Confidence 4479999998 444444 689996 99765
No 78
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.85 E-value=0.19 Score=42.65 Aligned_cols=49 Identities=22% Similarity=0.524 Sum_probs=36.6
Q ss_pred CCCCcccccccccCCCCccccccCCCCCc-chHHHHHHHHHhccccCCcccccCCCCcCCCCCC
Q 026529 35 IDGTFTCDICIEPMSVNNKFKNNNLCTHP-FCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFLD 97 (237)
Q Consensus 35 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~ 97 (237)
+....+|.||+++..+ +.+++|+|. .|.+|.+..- +.. -+||. |++.+.
T Consensus 287 ~~~gkeCVIClse~rd----t~vLPCRHLCLCs~Ca~~Lr---~q~-----n~CPI--CRqpi~ 336 (349)
T KOG4265|consen 287 SESGKECVICLSESRD----TVVLPCRHLCLCSGCAKSLR---YQT-----NNCPI--CRQPIE 336 (349)
T ss_pred ccCCCeeEEEecCCcc----eEEecchhhehhHhHHHHHH---Hhh-----cCCCc--cccchH
Confidence 3557799999998753 258999997 7999988765 222 26999 998654
No 79
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=90.64 E-value=0.24 Score=46.29 Aligned_cols=19 Identities=16% Similarity=0.412 Sum_probs=12.5
Q ss_pred CcccCcccccc-cccccccc
Q 026529 150 KKAQCPKCKQW-FCFQCKLA 168 (237)
Q Consensus 150 ~~~~C~~C~~~-~C~~C~~~ 168 (237)
..+.|..|+.. +=..|..+
T Consensus 229 VLLLCDsCN~~~YH~YCLDP 248 (1134)
T KOG0825|consen 229 VLLLCDSCNKVYYHVYCLDP 248 (1134)
T ss_pred hheeecccccceeeccccCc
Confidence 78889888877 43444443
No 80
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=90.55 E-value=0.14 Score=42.37 Aligned_cols=62 Identities=19% Similarity=0.449 Sum_probs=46.3
Q ss_pred cCCCCcccccccccCCCCccccccCCCCCcchHHHHHHHHHhcccc---------------CCcccccCCCCcCCCCCCc
Q 026529 34 DIDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRD---------------NNTAKIECPGLHCEQFLDP 98 (237)
Q Consensus 34 ~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~---------------~~~~~i~CP~~~C~~~~~~ 98 (237)
++.+...|.||+--|.+.+.|+ ...|.|.|-..||.+|+.....+ .....-.||. |...|.+
T Consensus 111 nn~p~gqCvICLygfa~~~~ft-~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpV--cre~i~~ 187 (368)
T KOG4445|consen 111 NNHPNGQCVICLYGFASSPAFT-VTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPV--CRERIKI 187 (368)
T ss_pred CCCCCCceEEEEEeecCCCcee-eehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhH--hhhhccc
Confidence 4567889999999998877774 78999999999999999765432 0122345998 8865544
No 81
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=90.16 E-value=0.57 Score=34.11 Aligned_cols=59 Identities=22% Similarity=0.477 Sum_probs=43.2
Q ss_pred hhhcCCCCcccccccccCCCCcccc-ccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCCC
Q 026529 31 ELEDIDGTFTCDICIEPMSVNNKFK-NNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFLD 97 (237)
Q Consensus 31 ~~~~~~~~~~C~IC~~~~~~~~~~~-~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~ 97 (237)
.+-.+.+..+|.||-|...+ +.|. ...-||-.+|-.|....|+.. .....||. |+..+.
T Consensus 73 nvF~d~~lYeCnIC~etS~e-e~FLKPneCCgY~iCn~Cya~LWK~~-----~~ypvCPv--CkTSFK 132 (140)
T PF05290_consen 73 NVFLDPKLYECNICKETSAE-ERFLKPNECCGYSICNACYANLWKFC-----NLYPVCPV--CKTSFK 132 (140)
T ss_pred eeecCCCceeccCcccccch-hhcCCcccccchHHHHHHHHHHHHHc-----ccCCCCCc--cccccc
Confidence 33344578899999999865 3442 233489999999999999874 35678999 986543
No 82
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=89.91 E-value=0.16 Score=42.63 Aligned_cols=45 Identities=24% Similarity=0.628 Sum_probs=34.5
Q ss_pred CCCCcccccccccCCCCccccccCCC--CCcchHHHHHHHHHhccccCCcccccCCCCcCCCCCC
Q 026529 35 IDGTFTCDICIEPMSVNNKFKNNNLC--THPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFLD 97 (237)
Q Consensus 35 ~~~~~~C~IC~~~~~~~~~~~~~~~C--~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~ 97 (237)
....++||||++.+..+ ...| ||..|..|-. ...-+||. |...+.
T Consensus 45 ~~~lleCPvC~~~l~~P-----i~QC~nGHlaCssC~~-----------~~~~~CP~--Cr~~~g 91 (299)
T KOG3002|consen 45 DLDLLDCPVCFNPLSPP-----IFQCDNGHLACSSCRT-----------KVSNKCPT--CRLPIG 91 (299)
T ss_pred chhhccCchhhccCccc-----ceecCCCcEehhhhhh-----------hhcccCCc--cccccc
Confidence 45678999999999654 3455 8999999976 12348998 988776
No 83
>PHA03096 p28-like protein; Provisional
Probab=89.85 E-value=0.2 Score=41.80 Aligned_cols=53 Identities=15% Similarity=0.271 Sum_probs=36.9
Q ss_pred cccccccccCCCC----ccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCC
Q 026529 39 FTCDICIEPMSVN----NKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQF 95 (237)
Q Consensus 39 ~~C~IC~~~~~~~----~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~ 95 (237)
..|.||++..... ..|-.+..|.|.||..|++.|..+... ......||. |...
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~--~e~~~~c~~--~~~~ 235 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLY--KETEPENRR--LNTV 235 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhh--cccCccccc--hhhH
Confidence 7899999987432 233346689999999999999987653 233445554 5543
No 84
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.83 E-value=0.11 Score=31.47 Aligned_cols=45 Identities=24% Similarity=0.531 Sum_probs=32.7
Q ss_pred cccccccccCCCCccccccCCCCCc-chHHHHHHHHHhccccCCcccccCCCCcCCCCC
Q 026529 39 FTCDICIEPMSVNNKFKNNNLCTHP-FCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFL 96 (237)
Q Consensus 39 ~~C~IC~~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~ 96 (237)
.+|.||+|--- +. ++..|||. .|-+|-.+.+.. . .=.||. |..++
T Consensus 8 dECTICye~pv--ds--VlYtCGHMCmCy~Cg~rl~~~-~------~g~CPi--CRapi 53 (62)
T KOG4172|consen 8 DECTICYEHPV--DS--VLYTCGHMCMCYACGLRLKKA-L------HGCCPI--CRAPI 53 (62)
T ss_pred cceeeeccCcc--hH--HHHHcchHHhHHHHHHHHHHc-c------CCcCcc--hhhHH
Confidence 68999998653 22 36789997 799999888875 2 125887 77653
No 85
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=89.74 E-value=0.36 Score=31.63 Aligned_cols=61 Identities=23% Similarity=0.367 Sum_probs=22.3
Q ss_pred ccCCCCCCCceeeccccccCCcCcccCcccccccccccccccCCCCCChhhhhccccchHHHHHHHHhCCcccCCCCCcc
Q 026529 128 SYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQWFCFQCKLAWHAGYRCEESGNLRDRNDIAFGKLLEKMNWTRCPGCGNC 207 (237)
Q Consensus 128 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~~ 207 (237)
..|- -|+--+-..... ...+.|..|+.-.|..|. +| -.+.+.+.||+|++.
T Consensus 10 qiCq--iCGD~VGl~~~G---e~FVAC~eC~fPvCr~Cy----------EY--------------Erkeg~q~CpqCkt~ 60 (80)
T PF14569_consen 10 QICQ--ICGDDVGLTENG---EVFVACHECAFPVCRPCY----------EY--------------ERKEGNQVCPQCKTR 60 (80)
T ss_dssp -B-S--SS--B--B-SSS---SB--S-SSS-----HHHH----------HH--------------HHHTS-SB-TTT--B
T ss_pred cccc--cccCccccCCCC---CEEEEEcccCCccchhHH----------HH--------------HhhcCcccccccCCC
Confidence 4455 666554444332 488899999999987553 33 235677999999999
Q ss_pred eeccCCCCce
Q 026529 208 IERKKGCRIM 217 (237)
Q Consensus 208 iek~~GCnhm 217 (237)
..+..|+..+
T Consensus 61 ykr~kgsp~V 70 (80)
T PF14569_consen 61 YKRHKGSPRV 70 (80)
T ss_dssp ----TT----
T ss_pred cccccCCCCC
Confidence 9988886543
No 86
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.42 E-value=0.31 Score=41.34 Aligned_cols=35 Identities=20% Similarity=0.395 Sum_probs=27.3
Q ss_pred CCCcccccccccCCCCccccccCCCCCcchHHHHHHHHH
Q 026529 36 DGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIE 74 (237)
Q Consensus 36 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~ 74 (237)
+....|+||+..-.. . +..+|+|.-|.+|+.+|+-
T Consensus 420 sEd~lCpICyA~pi~--A--vf~PC~H~SC~~CI~qHlm 454 (489)
T KOG4692|consen 420 SEDNLCPICYAGPIN--A--VFAPCSHRSCYGCITQHLM 454 (489)
T ss_pred cccccCcceecccch--h--hccCCCCchHHHHHHHHHh
Confidence 455689999865422 2 3679999999999999986
No 87
>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=89.37 E-value=0.31 Score=25.93 Aligned_cols=26 Identities=23% Similarity=0.570 Sum_probs=13.9
Q ss_pred ccCCCCCcceeccCCCCceeec-CccEE
Q 026529 199 TRCPGCGNCIERKKGCRIMFCR-FIFLS 225 (237)
Q Consensus 199 k~CP~C~~~iek~~GCnhm~C~-C~~cf 225 (237)
-+||.|+.-..-.+| ..|.|. |++.|
T Consensus 3 p~Cp~C~se~~y~D~-~~~vCp~C~~ew 29 (30)
T PF08274_consen 3 PKCPLCGSEYTYEDG-ELLVCPECGHEW 29 (30)
T ss_dssp ---TTT-----EE-S-SSEEETTTTEEE
T ss_pred CCCCCCCCcceeccC-CEEeCCcccccC
Confidence 479999998888777 467896 99887
No 88
>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=89.01 E-value=0.32 Score=27.26 Aligned_cols=32 Identities=28% Similarity=0.616 Sum_probs=22.9
Q ss_pred ccCCCCCCCceeeccccccC-CcCcccCccccccc
Q 026529 128 SYCPNRNCMAVMVNECEEIG-RVKKAQCPKCKQWF 161 (237)
Q Consensus 128 ~~Cp~~~C~~~~~~~~~~~~-~~~~~~C~~C~~~~ 161 (237)
+.|| .|+..+..++.... ....+.|+.|+..|
T Consensus 3 ~~CP--~C~~~~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCP--NCKTSFRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred EECC--CCCCEEEeCHHHcCCCCCEEECCCCCCEE
Confidence 5688 99998887764321 23479999998865
No 89
>PHA00626 hypothetical protein
Probab=88.76 E-value=0.36 Score=29.44 Aligned_cols=27 Identities=30% Similarity=0.602 Sum_probs=19.8
Q ss_pred cCCCCCc-ceeccCCCCc----eeec-CccEEE
Q 026529 200 RCPGCGN-CIERKKGCRI----MFCR-FIFLSL 226 (237)
Q Consensus 200 ~CP~C~~-~iek~~GCnh----m~C~-C~~cf~ 226 (237)
.||+|+. -|.|.+-|+. -.|. |||-|.
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft 34 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDS 34 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCeec
Confidence 5899998 4778776654 6786 887764
No 90
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.66 E-value=0.48 Score=40.84 Aligned_cols=60 Identities=18% Similarity=0.293 Sum_probs=44.7
Q ss_pred CCCcccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCCCcccccc
Q 026529 36 DGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFLDPLACKP 103 (237)
Q Consensus 36 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~~~~i~~ 103 (237)
...|.|||=-+.-.. ++.+..+.|||+++++=+.+.... +...++||- |......++.++
T Consensus 332 HSvF~CPVlKeqtsd-eNPPm~L~CGHVISkdAlnrLS~n-----g~~sfKCPY--CP~e~~~~~~kq 391 (394)
T KOG2817|consen 332 HSVFICPVLKEQTSD-ENPPMMLICGHVISKDALNRLSKN-----GSQSFKCPY--CPVEQLASDTKQ 391 (394)
T ss_pred cceeecccchhhccC-CCCCeeeeccceecHHHHHHHhhC-----CCeeeeCCC--CCcccCHHhccc
Confidence 567899997776643 445568999999999988877763 445799998 987666655544
No 91
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=88.61 E-value=0.22 Score=42.83 Aligned_cols=45 Identities=24% Similarity=0.442 Sum_probs=32.9
Q ss_pred CCCCcccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCC
Q 026529 35 IDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPG 89 (237)
Q Consensus 35 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~ 89 (237)
.+....|.||.+.-.+ +...+|||..|..||..|-.+.- .-.||.
T Consensus 366 gsTFeLCKICaendKd----vkIEPCGHLlCt~CLa~WQ~sd~------gq~CPF 410 (563)
T KOG1785|consen 366 GSTFELCKICAENDKD----VKIEPCGHLLCTSCLAAWQDSDE------GQTCPF 410 (563)
T ss_pred cchHHHHHHhhccCCC----cccccccchHHHHHHHhhcccCC------CCCCCc
Confidence 3455689999876532 25789999999999999975432 235887
No 92
>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=88.44 E-value=0.28 Score=27.12 Aligned_cols=29 Identities=21% Similarity=0.594 Sum_probs=20.0
Q ss_pred ccCCCCCCCceeeccccccCCcCcccCccccccc
Q 026529 128 SYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQWF 161 (237)
Q Consensus 128 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 161 (237)
.+|| .|+..+.+..... ....|+.|++.+
T Consensus 2 ~FCp--~C~nlL~p~~~~~---~~~~C~~C~Y~~ 30 (35)
T PF02150_consen 2 RFCP--ECGNLLYPKEDKE---KRVACRTCGYEE 30 (35)
T ss_dssp -BET--TTTSBEEEEEETT---TTEEESSSS-EE
T ss_pred eeCC--CCCccceEcCCCc---cCcCCCCCCCcc
Confidence 5788 9999999887652 223788888753
No 93
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=88.39 E-value=0.26 Score=27.06 Aligned_cols=31 Identities=23% Similarity=0.587 Sum_probs=15.9
Q ss_pred ccCCCCCCCceeeccccccCCcCcccCcccccc
Q 026529 128 SYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQW 160 (237)
Q Consensus 128 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 160 (237)
.+|| .|+..+...........+..|+.|+..
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 999877654332223688999999874
No 94
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.36 E-value=0.12 Score=42.11 Aligned_cols=55 Identities=24% Similarity=0.478 Sum_probs=40.0
Q ss_pred CcccccccccCCCCc-------cccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCCCcccc
Q 026529 38 TFTCDICIEPMSVNN-------KFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFLDPLAC 101 (237)
Q Consensus 38 ~~~C~IC~~~~~~~~-------~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~~~~i 101 (237)
...|.||-..+.... + +..+.|+|+|...|++.|... ...-.||- |+..++...+
T Consensus 224 d~vCaVCg~~~~~s~~eegvien-ty~LsCnHvFHEfCIrGWciv------GKkqtCPY--CKekVdl~rm 285 (328)
T KOG1734|consen 224 DSVCAVCGQQIDVSVDEEGVIEN-TYKLSCNHVFHEFCIRGWCIV------GKKQTCPY--CKEKVDLKRM 285 (328)
T ss_pred cchhHhhcchheeecchhhhhhh-heeeecccchHHHhhhhheee------cCCCCCch--HHHHhhHhhh
Confidence 346999977664332 2 236899999999999999875 23458998 9987765443
No 95
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.03 E-value=0.67 Score=41.40 Aligned_cols=38 Identities=24% Similarity=0.677 Sum_probs=28.8
Q ss_pred CcccCCCCCCCceeeccccccCCcCcccCcc--ccccccccccccc
Q 026529 126 ERSYCPNRNCMAVMVNECEEIGRVKKAQCPK--CKQWFCFQCKLAW 169 (237)
Q Consensus 126 ~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~--C~~~~C~~C~~~~ 169 (237)
+...|| .|...+...... +...|.. |++.||+.|..+|
T Consensus 225 ntk~CP--~c~~~iek~~gc----~~~~~~~~~c~~~FCw~Cl~~~ 264 (444)
T KOG1815|consen 225 NTKECP--KCKVPIEKDGGC----NHMTCKSASCKHEFCWVCLASL 264 (444)
T ss_pred cCccCC--CcccchhccCCc----cccccccCCcCCeeceeeeccc
Confidence 345588 998888877764 5556644 9999999997776
No 96
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.98 E-value=0.14 Score=42.21 Aligned_cols=48 Identities=27% Similarity=0.393 Sum_probs=36.1
Q ss_pred cCCCCcccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCC
Q 026529 34 DIDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQF 95 (237)
Q Consensus 34 ~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~ 95 (237)
...-++-|.||-.++..+ ++..|+|.||..|....+.. .-+|+. |.+.
T Consensus 237 ~~~~Pf~c~icr~~f~~p----Vvt~c~h~fc~~ca~~~~qk--------~~~c~v--C~~~ 284 (313)
T KOG1813|consen 237 IELLPFKCFICRKYFYRP----VVTKCGHYFCEVCALKPYQK--------GEKCYV--CSQQ 284 (313)
T ss_pred cccCCccccccccccccc----hhhcCCceeehhhhcccccc--------CCccee--cccc
Confidence 345678899999998654 57899999999998776652 235666 7753
No 97
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=87.90 E-value=0.36 Score=29.05 Aligned_cols=29 Identities=21% Similarity=0.604 Sum_probs=21.0
Q ss_pred cCCCCCCCceeeccccccCCcCcccCccccccc
Q 026529 129 YCPNRNCMAVMVNECEEIGRVKKAQCPKCKQWF 161 (237)
Q Consensus 129 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 161 (237)
+|| .|+..+...... ....+.|+.|++.+
T Consensus 2 FCp--~Cg~~l~~~~~~--~~~~~vC~~Cg~~~ 30 (52)
T smart00661 2 FCP--KCGNMLIPKEGK--EKRRFVCRKCGYEE 30 (52)
T ss_pred CCC--CCCCccccccCC--CCCEEECCcCCCeE
Confidence 688 999988776543 12478899998753
No 98
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=87.28 E-value=0.37 Score=29.44 Aligned_cols=49 Identities=18% Similarity=0.263 Sum_probs=32.7
Q ss_pred CCcccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCCCcccc
Q 026529 37 GTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFLDPLAC 101 (237)
Q Consensus 37 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~~~~i 101 (237)
....|..|...... ..+++|+|.+|..|+-.. ..--||. |+..++..++
T Consensus 6 ~~~~~~~~~~~~~~----~~~~pCgH~I~~~~f~~~----------rYngCPf--C~~~~~~~~~ 54 (55)
T PF14447_consen 6 PEQPCVFCGFVGTK----GTVLPCGHLICDNCFPGE----------RYNGCPF--CGTPFEFDDP 54 (55)
T ss_pred cceeEEEccccccc----cccccccceeeccccChh----------hccCCCC--CCCcccCCCC
Confidence 34566666655422 247899999999998532 2235998 9988876543
No 99
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=86.51 E-value=1.8 Score=35.95 Aligned_cols=50 Identities=24% Similarity=0.467 Sum_probs=39.7
Q ss_pred CCCCcccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCC
Q 026529 35 IDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQ 94 (237)
Q Consensus 35 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~ 94 (237)
....+.||||.+.+.........+.|+|..-..|++.++-. . ..||. |..
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 45556699999998766655668899999999999988873 2 78998 876
No 100
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=86.33 E-value=1 Score=26.43 Aligned_cols=28 Identities=21% Similarity=0.374 Sum_probs=17.9
Q ss_pred ccCCCCCcceeccCCCCceeec-CccEEE
Q 026529 199 TRCPGCGNCIERKKGCRIMFCR-FIFLSL 226 (237)
Q Consensus 199 k~CP~C~~~iek~~GCnhm~C~-C~~cf~ 226 (237)
-+||+|+..++.+.+=..++|. ||.-+.
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGYRIL 32 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCCeEE
Confidence 3677888777666443367776 775444
No 101
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=86.27 E-value=0.87 Score=38.60 Aligned_cols=66 Identities=17% Similarity=0.506 Sum_probs=42.7
Q ss_pred CCCcccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCCCccccccCCChhHHHHH
Q 026529 36 DGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFLDPLACKPTIPSSLFIKW 113 (237)
Q Consensus 36 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~~~~i~~~l~~~~~~~~ 113 (237)
.....|.||.+.+.- ..+++|+|.+|..|-.+.-.- ...-.||. |+.....-.+..-.+.++-+++
T Consensus 59 Een~~C~ICA~~~TY----s~~~PC~H~~CH~Ca~RlRAL------Y~~K~C~~--CrTE~e~V~fT~~~~~DI~D~~ 124 (493)
T COG5236 59 EENMNCQICAGSTTY----SARYPCGHQICHACAVRLRAL------YMQKGCPL--CRTETEAVVFTASSPADITDRR 124 (493)
T ss_pred cccceeEEecCCceE----EEeccCCchHHHHHHHHHHHH------HhccCCCc--cccccceEEEecCCCCcchhHh
Confidence 446789999988753 257899999999998765442 23456888 8865444333333344444444
No 102
>KOG2979 consensus Protein involved in DNA repair [General function prediction only]
Probab=85.50 E-value=2.1 Score=34.86 Aligned_cols=72 Identities=17% Similarity=0.194 Sum_probs=45.3
Q ss_pred CCCcccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCCCccccc-cCCC-hhHHHHH
Q 026529 36 DGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFLDPLACK-PTIP-SSLFIKW 113 (237)
Q Consensus 36 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~~~~i~-~~l~-~~~~~~~ 113 (237)
.-...|||=+-.+..+ +.+..|+|+|=++=+..++. ....++||..+|..+.. ++ .++. +..+.++
T Consensus 174 ~fs~rdPis~~~I~nP---viSkkC~HvydrDsI~~~l~------~~~~i~CPv~gC~~~~~---~~~~~l~~d~el~~k 241 (262)
T KOG2979|consen 174 VFSNRDPISKKPIVNP---VISKKCGHVYDRDSIMQILC------DEITIRCPVLGCENPYY---IQPGHLDEDKELQQK 241 (262)
T ss_pred hhcccCchhhhhhhch---hhhcCcCcchhhhhHHHHhc------cCceeecccccCCcccc---ccccccCchHHHHHH
Confidence 3345677766665333 24789999999988877776 35679999999994322 22 2233 3355555
Q ss_pred HHHHHH
Q 026529 114 CDHLCE 119 (237)
Q Consensus 114 ~~~~~~ 119 (237)
.+.+.+
T Consensus 242 Ir~~qe 247 (262)
T KOG2979|consen 242 IRQSQE 247 (262)
T ss_pred HHHhcc
Confidence 555444
No 103
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=85.05 E-value=0.43 Score=41.02 Aligned_cols=52 Identities=25% Similarity=0.654 Sum_probs=40.0
Q ss_pred CCCcccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCC
Q 026529 36 DGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQF 95 (237)
Q Consensus 36 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~ 95 (237)
.-...|..|-+.+...+.-...++|.|+|...|+..+++ ...+-.||. |.+.
T Consensus 363 e~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~------~n~~rsCP~--Crkl 414 (518)
T KOG1941|consen 363 ETELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILE------NNGTRSCPN--CRKL 414 (518)
T ss_pred HHhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHH------hCCCCCCcc--HHHH
Confidence 346789999888754443346789999999999999995 345678998 8854
No 104
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=84.93 E-value=0.71 Score=31.66 Aligned_cols=28 Identities=29% Similarity=0.666 Sum_probs=21.2
Q ss_pred ccCCCCCcceec--cCCCCceeec-CccEEE
Q 026529 199 TRCPGCGNCIER--KKGCRIMFCR-FIFLSL 226 (237)
Q Consensus 199 k~CP~C~~~iek--~~GCnhm~C~-C~~cf~ 226 (237)
..||.|+.++.- .+-||...|+ |+|.|-
T Consensus 2 ~FCP~Cgn~Live~g~~~~rf~C~tCpY~~~ 32 (105)
T KOG2906|consen 2 LFCPTCGNMLIVESGESCNRFSCRTCPYVFP 32 (105)
T ss_pred cccCCCCCEEEEecCCeEeeEEcCCCCceee
Confidence 369999986544 4559999997 997664
No 105
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=84.45 E-value=0.88 Score=27.05 Aligned_cols=27 Identities=19% Similarity=0.353 Sum_probs=18.2
Q ss_pred CcccCCCCCcceeccCCCCceee-cCcc
Q 026529 197 NWTRCPGCGNCIERKKGCRIMFC-RFIF 223 (237)
Q Consensus 197 ~~k~CP~C~~~iek~~GCnhm~C-~C~~ 223 (237)
.-+.||+|+-.+....-=+...| +||+
T Consensus 18 k~~~CPrCG~gvfmA~H~dR~~CGkCgy 45 (51)
T COG1998 18 KNRFCPRCGPGVFMADHKDRWACGKCGY 45 (51)
T ss_pred ccccCCCCCCcchhhhcCceeEeccccc
Confidence 33899999975555443357788 4873
No 106
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=84.13 E-value=0.87 Score=26.73 Aligned_cols=29 Identities=17% Similarity=0.354 Sum_probs=22.4
Q ss_pred ccCCCCCCCceeeccccccCCcCcccCcccccccc
Q 026529 128 SYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQWFC 162 (237)
Q Consensus 128 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C 162 (237)
..|| +|+..+..++.. ..+.||.||..+=
T Consensus 4 y~C~--~CG~~~~~~~~~----~~~~Cp~CG~~~~ 32 (46)
T PRK00398 4 YKCA--RCGREVELDEYG----TGVRCPYCGYRIL 32 (46)
T ss_pred EECC--CCCCEEEECCCC----CceECCCCCCeEE
Confidence 4688 999988887654 3789999988653
No 107
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=84.04 E-value=0.49 Score=27.33 Aligned_cols=26 Identities=27% Similarity=0.593 Sum_probs=20.0
Q ss_pred CCcccCCCCCcceeccCCCCceeec---CccEE
Q 026529 196 MNWTRCPGCGNCIERKKGCRIMFCR---FIFLS 225 (237)
Q Consensus 196 ~~~k~CP~C~~~iek~~GCnhm~C~---C~~cf 225 (237)
.++|+||+|++.- |+--+.|+ |+..|
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 5789999999876 77778885 76543
No 108
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=83.18 E-value=0.56 Score=23.28 Aligned_cols=22 Identities=41% Similarity=1.008 Sum_probs=12.8
Q ss_pred cCCCCCCCceeeccccccCCcCcccCcccccc
Q 026529 129 YCPNRNCMAVMVNECEEIGRVKKAQCPKCKQW 160 (237)
Q Consensus 129 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 160 (237)
+|| .|+.-+... ...|+.||+.
T Consensus 1 ~Cp--~CG~~~~~~--------~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCP--NCGAEIEDD--------AKFCPNCGTP 22 (23)
T ss_pred CCc--ccCCCCCCc--------CcchhhhCCc
Confidence 466 777666433 2337777764
No 109
>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=83.17 E-value=2 Score=23.07 Aligned_cols=27 Identities=19% Similarity=0.222 Sum_probs=15.4
Q ss_pred cccCCCCCcceeccCCCCceeec-CccE
Q 026529 198 WTRCPGCGNCIERKKGCRIMFCR-FIFL 224 (237)
Q Consensus 198 ~k~CP~C~~~iek~~GCnhm~C~-C~~c 224 (237)
.+.||+|+.+.....+=-.|.|. ||..
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 47888888888888664558886 8743
No 110
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=82.11 E-value=0.7 Score=44.30 Aligned_cols=54 Identities=20% Similarity=0.563 Sum_probs=38.9
Q ss_pred CCCcccccccccCCCCc-ccc--ccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCCC
Q 026529 36 DGTFTCDICIEPMSVNN-KFK--NNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFLD 97 (237)
Q Consensus 36 ~~~~~C~IC~~~~~~~~-~~~--~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~ 97 (237)
.+..+|+||+..+...+ .++ .-..|.|.|...|+-+|+.+.- .-+||. |+..++
T Consensus 1467 sG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~------~s~CPl--CRseit 1523 (1525)
T COG5219 1467 SGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSA------RSNCPL--CRSEIT 1523 (1525)
T ss_pred CCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcC------CCCCCc--cccccc
Confidence 56779999998765222 111 1346899999999999999643 347999 987654
No 111
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=81.70 E-value=2.5 Score=34.43 Aligned_cols=58 Identities=24% Similarity=0.430 Sum_probs=40.6
Q ss_pred CCCcccccccccCCCCccccccCCCC-----CcchHHHHHHHHHhccccCCcccccCCCCcCCCC
Q 026529 36 DGTFTCDICIEPMSVNNKFKNNNLCT-----HPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQF 95 (237)
Q Consensus 36 ~~~~~C~IC~~~~~~~~~~~~~~~C~-----H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~ 95 (237)
...-.|-|||.+-.+...---+-+|+ |.....|+..|+..+-......++.||+ |...
T Consensus 18 e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~Q--CqTE 80 (293)
T KOG3053|consen 18 ELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQ--CQTE 80 (293)
T ss_pred ccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechh--hcch
Confidence 44568999998874432110134563 5689999999998776654677899999 9853
No 112
>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=81.54 E-value=1.3 Score=25.46 Aligned_cols=22 Identities=36% Similarity=0.919 Sum_probs=17.9
Q ss_pred ccCCCCCcceec-cCCCCceeec-Cc
Q 026529 199 TRCPGCGNCIER-KKGCRIMFCR-FI 222 (237)
Q Consensus 199 k~CP~C~~~iek-~~GCnhm~C~-C~ 222 (237)
..||.|++++.+ ..| .+.|. |+
T Consensus 18 ~~Cp~C~~PL~~~k~g--~~~Cv~C~ 41 (41)
T PF06677_consen 18 EHCPDCGTPLMRDKDG--KIYCVSCG 41 (41)
T ss_pred CccCCCCCeeEEecCC--CEECCCCC
Confidence 799999999999 466 67885 64
No 113
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=81.44 E-value=0.74 Score=23.51 Aligned_cols=23 Identities=35% Similarity=0.865 Sum_probs=13.3
Q ss_pred ccCCCCCCCceeeccccccCCcCcccCcccccc
Q 026529 128 SYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQW 160 (237)
Q Consensus 128 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 160 (237)
+.|| .|+..+..+ ...|+.||+.
T Consensus 3 ~~Cp--~Cg~~~~~~--------~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCP--NCGAEIDPD--------AKFCPNCGAK 25 (26)
T ss_pred CCCc--ccCCcCCcc--------cccChhhCCC
Confidence 4677 787744322 3347777653
No 114
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=80.91 E-value=1.2 Score=41.62 Aligned_cols=13 Identities=31% Similarity=0.820 Sum_probs=8.0
Q ss_pred CcccCCCCCccee
Q 026529 197 NWTRCPGCGNCIE 209 (237)
Q Consensus 197 ~~k~CP~C~~~ie 209 (237)
+.+.||+|+..+.
T Consensus 40 ~~~fC~~CG~~~~ 52 (645)
T PRK14559 40 DEAHCPNCGAETG 52 (645)
T ss_pred ccccccccCCccc
Confidence 4467777776553
No 115
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=80.82 E-value=0.91 Score=38.17 Aligned_cols=23 Identities=30% Similarity=0.882 Sum_probs=19.3
Q ss_pred cCcccCcccccccccccccccCC
Q 026529 149 VKKAQCPKCKQWFCFQCKLAWHA 171 (237)
Q Consensus 149 ~~~~~C~~C~~~~C~~C~~~~H~ 171 (237)
...++|..|+..||..|..-.|.
T Consensus 343 ~~~y~C~~Ck~~FCldCDv~iHe 365 (378)
T KOG2807|consen 343 SGRYRCESCKNVFCLDCDVFIHE 365 (378)
T ss_pred CCcEEchhccceeeccchHHHHh
Confidence 46789999999999999776664
No 116
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=79.99 E-value=0.6 Score=43.78 Aligned_cols=49 Identities=31% Similarity=0.729 Sum_probs=35.8
Q ss_pred cccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCCCccc
Q 026529 39 FTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFLDPLA 100 (237)
Q Consensus 39 ~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~~~~ 100 (237)
+.|.||.+ . +.+ ....|+|.||.+|+...+...- .-.||. |...+....
T Consensus 455 ~~c~ic~~-~---~~~-~it~c~h~~c~~c~~~~i~~~~------~~~~~~--cr~~l~~~~ 503 (674)
T KOG1001|consen 455 HWCHICCD-L---DSF-FITRCGHDFCVECLKKSIQQSE------NAPCPL--CRNVLKEKK 503 (674)
T ss_pred cccccccc-c---ccc-eeecccchHHHHHHHhcccccc------CCCCcH--HHHHHHHHH
Confidence 89999998 2 222 3679999999999999988432 227777 886554443
No 117
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=79.99 E-value=0.59 Score=30.50 Aligned_cols=53 Identities=26% Similarity=0.569 Sum_probs=36.0
Q ss_pred CcccccccccCCCC--------cccc-ccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCCC
Q 026529 38 TFTCDICIEPMSVN--------NKFK-NNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFLD 97 (237)
Q Consensus 38 ~~~C~IC~~~~~~~--------~~~~-~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~ 97 (237)
..+|+||...+... +..+ +...|.|.|-..|+.+|+.+.-.. -.||. |++.+.
T Consensus 20 ~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq-----~~CPm--cRq~~~ 81 (84)
T KOG1493|consen 20 DETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQ-----GQCPM--CRQTWQ 81 (84)
T ss_pred CCccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCcccc-----ccCCc--chheeE
Confidence 34899997776321 2211 233589999999999999876554 46888 876543
No 118
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=79.96 E-value=1.2 Score=32.54 Aligned_cols=26 Identities=35% Similarity=0.713 Sum_probs=22.2
Q ss_pred CcccCCCCCcceeccCCCCceeec-CccE
Q 026529 197 NWTRCPGCGNCIERKKGCRIMFCR-FIFL 224 (237)
Q Consensus 197 ~~k~CP~C~~~iek~~GCnhm~C~-C~~c 224 (237)
..+-||.|+.++++..| .+.|. ||+-
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 33899999999999988 89996 9853
No 119
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=79.39 E-value=0.47 Score=39.83 Aligned_cols=32 Identities=28% Similarity=0.646 Sum_probs=25.1
Q ss_pred hCCcccCCCCCcceeccC-CCCceeec-CccEEE
Q 026529 195 KMNWTRCPGCGNCIERKK-GCRIMFCR-FIFLSL 226 (237)
Q Consensus 195 ~~~~k~CP~C~~~iek~~-GCnhm~C~-C~~cf~ 226 (237)
+..|.+||+|+..|.+.+ .=|.+.|. |+++|-
T Consensus 24 ~~~~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~r 57 (292)
T PRK05654 24 EGLWTKCPSCGQVLYRKELEANLNVCPKCGHHMR 57 (292)
T ss_pred CCCeeECCCccchhhHHHHHhcCCCCCCCCCCee
Confidence 346999999999888763 44678996 998875
No 120
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=79.28 E-value=1.8 Score=43.05 Aligned_cols=30 Identities=30% Similarity=0.832 Sum_probs=17.7
Q ss_pred cccCCCCCCCceeeccccccCCcCcccCccccccc-----ccccccc
Q 026529 127 RSYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQWF-----CFQCKLA 168 (237)
Q Consensus 127 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~-----C~~C~~~ 168 (237)
.+.|| .|+.... ..+||.||... |..|+..
T Consensus 667 ~rkCP--kCG~~t~----------~~fCP~CGs~te~vy~CPsCGae 701 (1337)
T PRK14714 667 RRRCP--SCGTETY----------ENRCPDCGTHTEPVYVCPDCGAE 701 (1337)
T ss_pred EEECC--CCCCccc----------cccCcccCCcCCCceeCccCCCc
Confidence 36787 7776431 12577777554 6666554
No 121
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=78.60 E-value=1.2 Score=42.52 Aligned_cols=24 Identities=33% Similarity=0.970 Sum_probs=21.1
Q ss_pred ccCCCCCcceeccCCCCceeec-CccE
Q 026529 199 TRCPGCGNCIERKKGCRIMFCR-FIFL 224 (237)
Q Consensus 199 k~CP~C~~~iek~~GCnhm~C~-C~~c 224 (237)
..||.|+..+...+||. +|+ |||.
T Consensus 725 ~~Cp~Cg~~l~~~~GC~--~C~~CG~s 749 (752)
T PRK08665 725 GACPECGSILEHEEGCV--VCHSCGYS 749 (752)
T ss_pred CCCCCCCcccEECCCCC--cCCCCCCC
Confidence 36999999999999998 897 9974
No 122
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=78.31 E-value=3 Score=33.93 Aligned_cols=37 Identities=24% Similarity=0.508 Sum_probs=25.2
Q ss_pred CCcccCCCCCCCceeeccccccC----------CcCcccCccccccc
Q 026529 125 LERSYCPNRNCMAVMVNECEEIG----------RVKKAQCPKCKQWF 161 (237)
Q Consensus 125 ~~~~~Cp~~~C~~~~~~~~~~~~----------~~~~~~C~~C~~~~ 161 (237)
..++.||.|+|..++...+...+ ...++.|..|...|
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 45689999999998886655210 13456777776666
No 123
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=78.28 E-value=2.8 Score=27.70 Aligned_cols=47 Identities=23% Similarity=0.510 Sum_probs=28.6
Q ss_pred ccccccccCCCCcccc-ccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCC
Q 026529 40 TCDICIEPMSVNNKFK-NNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFL 96 (237)
Q Consensus 40 ~C~IC~~~~~~~~~~~-~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~ 96 (237)
.|+-|.....+.+..+ +-.-|.|.|-..|+.+|+.+ + =.||. +.+.+
T Consensus 33 ~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~T--k------~~CPl--d~q~w 80 (88)
T COG5194 33 TCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDT--K------GVCPL--DRQTW 80 (88)
T ss_pred cCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhh--C------CCCCC--CCcee
Confidence 4444443332333322 23359999999999999997 2 25776 55543
No 124
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=77.77 E-value=1.5 Score=41.78 Aligned_cols=42 Identities=24% Similarity=0.522 Sum_probs=33.0
Q ss_pred CCCcccccccccCCCCccccccCCCCCcchHHHHHHHHHhcccc
Q 026529 36 DGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRD 79 (237)
Q Consensus 36 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~ 79 (237)
.+.-+|.+|...+.. ..| .+.+|||.|.++|+.+++......
T Consensus 815 ep~d~C~~C~~~ll~-~pF-~vf~CgH~FH~~Cl~~~v~~~~~~ 856 (911)
T KOG2034|consen 815 EPQDSCDHCGRPLLI-KPF-YVFPCGHCFHRDCLIRHVLSLLSE 856 (911)
T ss_pred cCccchHHhcchhhc-Ccc-eeeeccchHHHHHHHHHHHccccH
Confidence 456689999988854 455 478999999999999998765543
No 125
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=77.68 E-value=3.6 Score=34.29 Aligned_cols=44 Identities=23% Similarity=0.767 Sum_probs=32.9
Q ss_pred cccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCC
Q 026529 39 FTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQ 94 (237)
Q Consensus 39 ~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~ 94 (237)
+.|+.|-.-+..+ + ...-|+|.||.+|+..-+.. ..+.||. |..
T Consensus 275 LkCplc~~Llrnp--~-kT~cC~~~fc~eci~~al~d-------sDf~Cpn--C~r 318 (427)
T COG5222 275 LKCPLCHCLLRNP--M-KTPCCGHTFCDECIGTALLD-------SDFKCPN--CSR 318 (427)
T ss_pred ccCcchhhhhhCc--c-cCccccchHHHHHHhhhhhh-------ccccCCC--ccc
Confidence 7899998776443 2 34579999999999876542 4578998 874
No 126
>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=77.43 E-value=1.3 Score=31.29 Aligned_cols=26 Identities=19% Similarity=0.346 Sum_probs=17.4
Q ss_pred ccCCCCCcceeccCCCCceeec-CccEE
Q 026529 199 TRCPGCGNCIERKKGCRIMFCR-FIFLS 225 (237)
Q Consensus 199 k~CP~C~~~iek~~GCnhm~C~-C~~cf 225 (237)
|.||+|+..+.--.- +.++|. ||..|
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 678888876655444 677785 77554
No 127
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=77.13 E-value=1.9 Score=40.34 Aligned_cols=11 Identities=36% Similarity=1.053 Sum_probs=4.3
Q ss_pred CCCCCcceecc
Q 026529 201 CPGCGNCIERK 211 (237)
Q Consensus 201 CP~C~~~iek~ 211 (237)
||+|+..+...
T Consensus 30 Cp~CG~~~~~~ 40 (645)
T PRK14559 30 CPQCGTEVPVD 40 (645)
T ss_pred CCCCCCCCCcc
Confidence 44444433333
No 128
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=77.05 E-value=1.6 Score=30.54 Aligned_cols=24 Identities=29% Similarity=0.765 Sum_probs=17.8
Q ss_pred cCCCCCcceeccCCCCceeec-CccEE
Q 026529 200 RCPGCGNCIERKKGCRIMFCR-FIFLS 225 (237)
Q Consensus 200 ~CP~C~~~iek~~GCnhm~C~-C~~cf 225 (237)
.||.|+.++...+| .+.|. |++.+
T Consensus 2 fC~~Cg~~l~~~~~--~~~C~~C~~~~ 26 (104)
T TIGR01384 2 FCPKCGSLMTPKNG--VYVCPSCGYEK 26 (104)
T ss_pred CCcccCcccccCCC--eEECcCCCCcc
Confidence 68888888876654 78886 88653
No 129
>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=76.92 E-value=2.6 Score=24.42 Aligned_cols=42 Identities=26% Similarity=0.672 Sum_probs=20.1
Q ss_pred cccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCC
Q 026529 41 CDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPG 89 (237)
Q Consensus 41 C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~ 89 (237)
|.+|.+-+.....- ....|+=.+...|+.+|+...- ..+||.
T Consensus 1 C~~C~~iv~~G~~C-~~~~C~~r~H~~C~~~y~r~~~------~~~CP~ 42 (43)
T PF08746_consen 1 CEACKEIVTQGQRC-SNRDCNVRLHDDCFKKYFRHRS------NPKCPN 42 (43)
T ss_dssp -TTT-SB-SSSEE--SS--S--EE-HHHHHHHTTT-S------S-B-TT
T ss_pred CcccchhHeeeccC-CCCccCchHHHHHHHHHHhcCC------CCCCcC
Confidence 56676665433222 1335888999999999998532 227886
No 130
>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=75.86 E-value=2.8 Score=21.85 Aligned_cols=20 Identities=35% Similarity=0.806 Sum_probs=12.5
Q ss_pred cCCCCCcceeccCCCCceee
Q 026529 200 RCPGCGNCIERKKGCRIMFC 219 (237)
Q Consensus 200 ~CP~C~~~iek~~GCnhm~C 219 (237)
.||.|+..+.+.+|=-.++|
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 59999999999887556666
No 131
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=75.78 E-value=1.8 Score=25.55 Aligned_cols=33 Identities=21% Similarity=0.558 Sum_probs=22.0
Q ss_pred cccccccCCCCccccccCCCC--C---cchHHHHHHHHHh
Q 026529 41 CDICIEPMSVNNKFKNNNLCT--H---PFCQDCTAKYIEV 75 (237)
Q Consensus 41 C~IC~~~~~~~~~~~~~~~C~--H---~fC~~Cl~~~~~~ 75 (237)
|-||+++....+.+ ..+|. - ....+||.+|+..
T Consensus 1 CrIC~~~~~~~~~l--i~pC~C~Gs~~~vH~~CL~~W~~~ 38 (47)
T PF12906_consen 1 CRICLEGEEEDEPL--ISPCRCKGSMKYVHRSCLERWIRE 38 (47)
T ss_dssp ETTTTEE-SSSS-E--E-SSS-SSCCGSEECCHHHHHHHH
T ss_pred CeEeCCcCCCCCce--ecccccCCCcchhHHHHHHHHHHh
Confidence 67999887654434 34553 3 5789999999987
No 132
>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=75.49 E-value=2.8 Score=26.78 Aligned_cols=29 Identities=24% Similarity=0.603 Sum_probs=21.7
Q ss_pred CcccCCCCCcceeccCCCCceeec-CccEE
Q 026529 197 NWTRCPGCGNCIERKKGCRIMFCR-FIFLS 225 (237)
Q Consensus 197 ~~k~CP~C~~~iek~~GCnhm~C~-C~~cf 225 (237)
..+.||.|+....+...=..++|. ||+.+
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCGFEM 56 (69)
T ss_pred CccCccCcccccccccccceEEcCCCCCEE
Confidence 448999999999884333468887 88763
No 133
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=75.35 E-value=1 Score=37.04 Aligned_cols=32 Identities=28% Similarity=0.643 Sum_probs=26.1
Q ss_pred hCCcccCCCCCcceeccC-CCCceeec-CccEEE
Q 026529 195 KMNWTRCPGCGNCIERKK-GCRIMFCR-FIFLSL 226 (237)
Q Consensus 195 ~~~~k~CP~C~~~iek~~-GCnhm~C~-C~~cf~ 226 (237)
...|.+||+|+.++.+.+ +=|...|. |++++-
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 568999999999998874 66788886 988763
No 134
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=75.09 E-value=0.63 Score=38.98 Aligned_cols=31 Identities=16% Similarity=0.376 Sum_probs=21.7
Q ss_pred CCcccCCCCCcceeccC-CCCceeec-CccEEE
Q 026529 196 MNWTRCPGCGNCIERKK-GCRIMFCR-FIFLSL 226 (237)
Q Consensus 196 ~~~k~CP~C~~~iek~~-GCnhm~C~-C~~cf~ 226 (237)
..|.+||+|+..|.+.+ .=|...|. |+++|.
T Consensus 36 ~lw~kc~~C~~~~~~~~l~~~~~vcp~c~~h~r 68 (296)
T CHL00174 36 HLWVQCENCYGLNYKKFLKSKMNICEQCGYHLK 68 (296)
T ss_pred CCeeECCCccchhhHHHHHHcCCCCCCCCCCcC
Confidence 35788888888877763 34667886 887653
No 135
>PRK00420 hypothetical protein; Validated
Probab=75.06 E-value=2.2 Score=30.37 Aligned_cols=29 Identities=24% Similarity=0.417 Sum_probs=23.0
Q ss_pred CcccCCCCCcceec-cCCCCceeec-CccEEEe
Q 026529 197 NWTRCPGCGNCIER-KKGCRIMFCR-FIFLSLC 227 (237)
Q Consensus 197 ~~k~CP~C~~~iek-~~GCnhm~C~-C~~cf~c 227 (237)
....||.|+.++.+ ..| +..|. ||.-..+
T Consensus 22 l~~~CP~Cg~pLf~lk~g--~~~Cp~Cg~~~~v 52 (112)
T PRK00420 22 LSKHCPVCGLPLFELKDG--EVVCPVHGKVYIV 52 (112)
T ss_pred ccCCCCCCCCcceecCCC--ceECCCCCCeeee
Confidence 34899999999998 677 88997 9865443
No 136
>PLN02189 cellulose synthase
Probab=73.68 E-value=2.9 Score=40.87 Aligned_cols=63 Identities=21% Similarity=0.392 Sum_probs=45.8
Q ss_pred CcccCCCCCCCceeeccccccCCcCcccCcccccccccccccccCCCCCChhhhhccccchHHHHHHHHhCCcccCCCCC
Q 026529 126 ERSYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQWFCFQCKLAWHAGYRCEESGNLRDRNDIAFGKLLEKMNWTRCPGCG 205 (237)
Q Consensus 126 ~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~ 205 (237)
....|. -|+..+-..... ...+.|..|+.-.|..|- ||. .+.+.+.||.|+
T Consensus 33 ~~~~C~--iCgd~vg~~~~g---~~fvaC~~C~fpvCr~Cy----------eye--------------r~eg~q~CpqCk 83 (1040)
T PLN02189 33 DGQVCE--ICGDEIGLTVDG---DLFVACNECGFPVCRPCY----------EYE--------------RREGTQNCPQCK 83 (1040)
T ss_pred cCcccc--ccccccCcCCCC---CEEEeeccCCCccccchh----------hhh--------------hhcCCccCcccC
Confidence 345677 788776665443 478999999999998553 332 245669999999
Q ss_pred cceeccCCCCce
Q 026529 206 NCIERKKGCRIM 217 (237)
Q Consensus 206 ~~iek~~GCnhm 217 (237)
+...+.-|+..+
T Consensus 84 t~Y~r~kgs~~v 95 (1040)
T PLN02189 84 TRYKRLKGSPRV 95 (1040)
T ss_pred CchhhccCCCCc
Confidence 999887777654
No 137
>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=73.66 E-value=0.77 Score=38.41 Aligned_cols=32 Identities=25% Similarity=0.569 Sum_probs=24.0
Q ss_pred hCCcccCCCCCcceeccC-CCCceeec-CccEEE
Q 026529 195 KMNWTRCPGCGNCIERKK-GCRIMFCR-FIFLSL 226 (237)
Q Consensus 195 ~~~~k~CP~C~~~iek~~-GCnhm~C~-C~~cf~ 226 (237)
+..|.+||+|+..|.+.+ .=|.+.|. ||++|-
T Consensus 23 ~~~~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~r 56 (285)
T TIGR00515 23 EGVWTKCPKCGQVLYTKELERNLEVCPKCDHHMR 56 (285)
T ss_pred CCCeeECCCCcchhhHHHHHhhCCCCCCCCCcCc
Confidence 346999999999888763 34668896 988764
No 138
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=73.23 E-value=10 Score=30.37 Aligned_cols=63 Identities=24% Similarity=0.533 Sum_probs=45.2
Q ss_pred hcCCCCcccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCC-CCcc
Q 026529 33 EDIDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQF-LDPL 99 (237)
Q Consensus 33 ~~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~-~~~~ 99 (237)
.+.+-.-.|.+|-.++...+. +.+.|-|.|--+|+..+...--.+..-....||. |.+. +++.
T Consensus 45 ~DsDY~pNC~LC~t~La~gdt--~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~--Cs~eiFPp~ 108 (299)
T KOG3970|consen 45 QDSDYNPNCRLCNTPLASGDT--TRLVCYHLFHWKCLNERAANLPANTAPAGYQCPC--CSQEIFPPI 108 (299)
T ss_pred hhcCCCCCCceeCCccccCcc--eeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCC--CCCccCCCc
Confidence 334445689999999977665 4689999999999998876544432334578998 8874 4443
No 139
>PLN00209 ribosomal protein S27; Provisional
Probab=73.14 E-value=4.1 Score=27.32 Aligned_cols=31 Identities=16% Similarity=0.488 Sum_probs=23.4
Q ss_pred ccCCCCCCCceeeccccccCCcCcccCccccccccc
Q 026529 128 SYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQWFCF 163 (237)
Q Consensus 128 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~ 163 (237)
+.|| +|...-..-... ...+.|..|+...+.
T Consensus 37 VkCp--~C~n~q~VFShA---~t~V~C~~Cg~~L~~ 67 (86)
T PLN00209 37 VKCQ--GCFNITTVFSHS---QTVVVCGSCQTVLCQ 67 (86)
T ss_pred EECC--CCCCeeEEEecC---ceEEEccccCCEeec
Confidence 8899 998765554443 578999999998874
No 140
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=73.11 E-value=0.32 Score=35.33 Aligned_cols=43 Identities=21% Similarity=0.383 Sum_probs=24.3
Q ss_pred cCCCCcccccCCChHHHhHHhhhcCCCCcccccccccCCCCccccccCCCCCc
Q 026529 11 NRQSPRQEKENPRQEEIKEEELEDIDGTFTCDICIEPMSVNNKFKNNNLCTHP 63 (237)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~ 63 (237)
..++..+.+++++++..+...+ ....+|.||..+.. .-.|||.
T Consensus 41 ~e~~el~~Qi~erkEqqKKaGv---~ddatC~IC~KTKF-------ADG~GH~ 83 (169)
T KOG3799|consen 41 KEMGELSQQIQERKEQQKKAGV---GDDATCGICHKTKF-------ADGCGHN 83 (169)
T ss_pred HHHHHHHHHHHHHHHHhhcccc---CcCcchhhhhhccc-------ccccCcc
Confidence 3344444555555555554322 44569999987752 3466774
No 141
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=73.02 E-value=1.3 Score=40.66 Aligned_cols=38 Identities=24% Similarity=0.552 Sum_probs=30.3
Q ss_pred CcccccccccCCCCccccccCCCCCcchHHHHHHHHHh
Q 026529 38 TFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEV 75 (237)
Q Consensus 38 ~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~ 75 (237)
...|.||+..+.......+++.|||.+|..|+......
T Consensus 11 ~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~lyn~ 48 (861)
T KOG3161|consen 11 LLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLYNA 48 (861)
T ss_pred HhhchHHHHHHHHHhcCcccccccchHHHHHHHhHhhc
Confidence 45799998887655555678999999999999887654
No 142
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=72.98 E-value=1 Score=35.18 Aligned_cols=65 Identities=18% Similarity=0.426 Sum_probs=36.5
Q ss_pred CCcccCCCCCCCceeeccccccCCcCcccCcccccccccccccccCCCCCChhhhhccccchHHHHHHHHhCCcccCCCC
Q 026529 125 LERSYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQWFCFQCKLAWHAGYRCEESGNLRDRNDIAFGKLLEKMNWTRCPGC 204 (237)
Q Consensus 125 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~k~CP~C 204 (237)
.+...|| -|...+.. ..+ ..||+.||+.|-..|....+ ... .....+....+..+||.|
T Consensus 16 ~~~~~Cp--ICld~~~d--------PVv--T~CGH~FC~~CI~~wl~~s~--~s~-------~~~~~~~~~k~~~~CPvC 74 (193)
T PLN03208 16 GGDFDCN--ICLDQVRD--------PVV--TLCGHLFCWPCIHKWTYASN--NSR-------QRVDQYDHKREPPKCPVC 74 (193)
T ss_pred CCccCCc--cCCCcCCC--------cEE--cCCCchhHHHHHHHHHHhcc--ccc-------cccccccccCCCCcCCCC
Confidence 4456788 77654311 122 36999999999988743110 000 000011112345799999
Q ss_pred Ccceec
Q 026529 205 GNCIER 210 (237)
Q Consensus 205 ~~~iek 210 (237)
+..|..
T Consensus 75 R~~Is~ 80 (193)
T PLN03208 75 KSDVSE 80 (193)
T ss_pred CCcCCh
Confidence 998865
No 143
>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=72.72 E-value=3.4 Score=22.82 Aligned_cols=32 Identities=25% Similarity=0.613 Sum_probs=17.6
Q ss_pred chHHHHHHHHHhccccCCcccccCCCCcCCCCCC
Q 026529 64 FCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFLD 97 (237)
Q Consensus 64 fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~ 97 (237)
+|.+|++.|....-..-....+.|+. |+-.+.
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 58899999876443322456899998 885543
No 144
>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=71.33 E-value=2.9 Score=29.35 Aligned_cols=27 Identities=19% Similarity=0.524 Sum_probs=22.2
Q ss_pred ccCCCCCcceeccCCCCceeec-CccEEE
Q 026529 199 TRCPGCGNCIERKKGCRIMFCR-FIFLSL 226 (237)
Q Consensus 199 k~CP~C~~~iek~~GCnhm~C~-C~~cf~ 226 (237)
-.||+|..-.--..| +.+.|. |++.|-
T Consensus 3 p~CP~C~seytY~dg-~~~iCpeC~~EW~ 30 (109)
T TIGR00686 3 PPCPKCNSEYTYHDG-TQLICPSCLYEWN 30 (109)
T ss_pred CcCCcCCCcceEecC-CeeECcccccccc
Confidence 479999998877777 468997 999885
No 145
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=70.03 E-value=3 Score=37.33 Aligned_cols=35 Identities=26% Similarity=0.525 Sum_probs=25.0
Q ss_pred ccccccccccccccCCCCCChhhhhccccchHHHHHHHHhCCcccCCCCCcceec
Q 026529 156 KCKQWFCFQCKLAWHAGYRCEESGNLRDRNDIAFGKLLEKMNWTRCPGCGNCIER 210 (237)
Q Consensus 156 ~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~~iek 210 (237)
.||+.||+.|--. +....+..+++.||=|+..|-.
T Consensus 203 ~CGHiFC~~CiLq--------------------y~~~s~~~~~~~CPiC~s~I~~ 237 (513)
T KOG2164|consen 203 NCGHIFCGPCILQ--------------------YWNYSAIKGPCSCPICRSTITL 237 (513)
T ss_pred ccCceeeHHHHHH--------------------HHhhhcccCCccCCchhhhccc
Confidence 5999999988632 1122235688999999988855
No 146
>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=69.36 E-value=1.6 Score=30.34 Aligned_cols=33 Identities=21% Similarity=0.502 Sum_probs=26.2
Q ss_pred CCCcccccccccCCCCccccccCCCCCcchHHHHH
Q 026529 36 DGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTA 70 (237)
Q Consensus 36 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~ 70 (237)
.....|.+|...+.. ..| ...+|||.|...|++
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 455679999999854 444 678999999999975
No 147
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=68.44 E-value=3.9 Score=28.63 Aligned_cols=34 Identities=15% Similarity=0.408 Sum_probs=24.0
Q ss_pred CcccCCCCCCCceeeccccccCCcCcccCccccccc
Q 026529 126 ERSYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQWF 161 (237)
Q Consensus 126 ~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 161 (237)
.+++|+ .|+..+.+......+.....|..|.+.+
T Consensus 3 ~~rfC~--eCNNmLYPkEDked~~L~laCrnCd~ve 36 (113)
T KOG2691|consen 3 GIRFCR--ECNNMLYPKEDKEDRILLLACRNCDYVE 36 (113)
T ss_pred ccchhh--hhhccccccccccccEEEEEecCCcceE
Confidence 357888 9998888766544345677787777665
No 148
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=68.01 E-value=4 Score=40.07 Aligned_cols=61 Identities=23% Similarity=0.430 Sum_probs=43.6
Q ss_pred ccCCCCCCCceeeccccccCCcCcccCcccccccccccccccCCCCCChhhhhccccchHHHHHHHHhCCcccCCCCCcc
Q 026529 128 SYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQWFCFQCKLAWHAGYRCEESGNLRDRNDIAFGKLLEKMNWTRCPGCGNC 207 (237)
Q Consensus 128 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~~ 207 (237)
.-|- -|+--+-..... ...+.|..|+.-.|..| -||. .+.+.+.||+|++.
T Consensus 18 qiCq--ICGD~vg~~~~G---e~FVAC~eC~FPVCrpC----------YEYE--------------r~eG~q~CPqCktr 68 (1079)
T PLN02638 18 QVCQ--ICGDNVGKTVDG---EPFVACDVCAFPVCRPC----------YEYE--------------RKDGNQSCPQCKTK 68 (1079)
T ss_pred ceee--ecccccCcCCCC---CEEEEeccCCCccccch----------hhhh--------------hhcCCccCCccCCc
Confidence 4555 677655555433 48899999999999855 4443 24567999999999
Q ss_pred eeccCCCCce
Q 026529 208 IERKKGCRIM 217 (237)
Q Consensus 208 iek~~GCnhm 217 (237)
..+--|+..+
T Consensus 69 Ykr~kgsprv 78 (1079)
T PLN02638 69 YKRHKGSPAI 78 (1079)
T ss_pred hhhhcCCCCc
Confidence 9888787654
No 149
>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=67.98 E-value=3.2 Score=24.58 Aligned_cols=29 Identities=28% Similarity=0.566 Sum_probs=18.0
Q ss_pred cccCCCCCCCceeeccccccCCcCcccCccccc
Q 026529 127 RSYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQ 159 (237)
Q Consensus 127 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 159 (237)
...||++.|+..+....-. .+..|-.|+.
T Consensus 18 rk~CP~~~CG~GvFMA~H~----dR~~CGKCg~ 46 (47)
T PF01599_consen 18 RKECPSPRCGAGVFMAEHK----DRHYCGKCGY 46 (47)
T ss_dssp SEE-TSTTTTSSSEEEE-S----SEEEETTTSS
T ss_pred hhcCCCcccCCceEeeecC----CCccCCCccc
Confidence 5889999999855444332 4666766664
No 150
>PF12773 DZR: Double zinc ribbon
Probab=67.71 E-value=3.5 Score=24.40 Aligned_cols=28 Identities=25% Similarity=0.672 Sum_probs=16.2
Q ss_pred CCcccCCCCCCCceeeccccccCCcCcccCccccc
Q 026529 125 LERSYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQ 159 (237)
Q Consensus 125 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 159 (237)
.+..+|| .|+..+.... ...+.|+.|++
T Consensus 10 ~~~~fC~--~CG~~l~~~~-----~~~~~C~~Cg~ 37 (50)
T PF12773_consen 10 DDAKFCP--HCGTPLPPPD-----QSKKICPNCGA 37 (50)
T ss_pred ccccCCh--hhcCChhhcc-----CCCCCCcCCcC
Confidence 3456777 7777666111 24566776655
No 151
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=67.64 E-value=3.9 Score=29.19 Aligned_cols=31 Identities=23% Similarity=0.499 Sum_probs=24.0
Q ss_pred cccCCCCCCCceeeccccccCCcCcccCccccccc
Q 026529 127 RSYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQWF 161 (237)
Q Consensus 127 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 161 (237)
..+|| .|+.++.+..... ...+.|+.|++..
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 36799 9999999876542 3588899998876
No 152
>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=67.63 E-value=3.2 Score=29.10 Aligned_cols=26 Identities=23% Similarity=0.575 Sum_probs=20.0
Q ss_pred cCCCCCCCceeeccccccCCcCcccCccccccc
Q 026529 129 YCPNRNCMAVMVNECEEIGRVKKAQCPKCKQWF 161 (237)
Q Consensus 129 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 161 (237)
.|| .|+.-+.+++. ..+.||.|++.|
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 477 88888777765 568899888876
No 153
>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=67.40 E-value=4.4 Score=34.20 Aligned_cols=33 Identities=18% Similarity=0.374 Sum_probs=20.3
Q ss_pred ccCCCCCCCceeeccccccCCcCcccCccccccccccccc
Q 026529 128 SYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQWFCFQCKL 167 (237)
Q Consensus 128 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~ 167 (237)
..|| .|..-....+.. ...+. .||+.||..|-.
T Consensus 4 ~~CP--~Ck~~~y~np~~---kl~i~--~CGH~~C~sCv~ 36 (309)
T TIGR00570 4 QGCP--RCKTTKYRNPSL---KLMVN--VCGHTLCESCVD 36 (309)
T ss_pred CCCC--cCCCCCccCccc---ccccC--CCCCcccHHHHH
Confidence 3588 887654444331 12333 699999998864
No 154
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=67.24 E-value=7.5 Score=23.74 Aligned_cols=36 Identities=19% Similarity=0.451 Sum_probs=29.3
Q ss_pred CCcccccccccCCCCccccccCCCCCcchHHHHHHH
Q 026529 37 GTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKY 72 (237)
Q Consensus 37 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~ 72 (237)
....|.+|-+.+.+.+..++-..|+-.+.++|+...
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~ 39 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKA 39 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCCCcccHHHHhhC
Confidence 445799999999766777667789999999999754
No 155
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=66.65 E-value=4.4 Score=25.16 Aligned_cols=11 Identities=36% Similarity=0.818 Sum_probs=6.0
Q ss_pred CcccCcccccc
Q 026529 150 KKAQCPKCKQW 160 (237)
Q Consensus 150 ~~~~C~~C~~~ 160 (237)
..+.||.||..
T Consensus 24 ~~F~CPnCG~~ 34 (59)
T PRK14890 24 VKFLCPNCGEV 34 (59)
T ss_pred CEeeCCCCCCe
Confidence 45555555554
No 156
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=65.65 E-value=6.3 Score=26.41 Aligned_cols=31 Identities=19% Similarity=0.510 Sum_probs=23.5
Q ss_pred ccCCCCCCCceeeccccccCCcCcccCccccccccc
Q 026529 128 SYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQWFCF 163 (237)
Q Consensus 128 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~ 163 (237)
+.|| +|...-..-... ...+.|..|+...|.
T Consensus 36 VkCp--~C~n~q~VFShA---~t~V~C~~Cg~~L~~ 66 (85)
T PTZ00083 36 VKCP--GCSQITTVFSHA---QTVVLCGGCSSQLCQ 66 (85)
T ss_pred EECC--CCCCeeEEEecC---ceEEEccccCCEeec
Confidence 8899 998765554443 578999999998874
No 157
>PHA02926 zinc finger-like protein; Provisional
Probab=64.54 E-value=1.7 Score=34.71 Aligned_cols=61 Identities=25% Similarity=0.493 Sum_probs=35.8
Q ss_pred ccCCCCCCCceeeccccccCCcCcccCcccccccccccccccCCCCCChhhhhccccchHHHHHHHHhCCcccCCCCCcc
Q 026529 128 SYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQWFCFQCKLAWHAGYRCEESGNLRDRNDIAFGKLLEKMNWTRCPGCGNC 207 (237)
Q Consensus 128 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~~ 207 (237)
..|+ -|-..+...... +......=+.|++.||+.|-..|..... .....+.||-|+..
T Consensus 171 ~eCg--ICmE~I~eK~~~-~eRrFGIL~~CnHsFCl~CIr~Wr~~r~-------------------~~~~~rsCPiCR~~ 228 (242)
T PHA02926 171 KECG--ICYEVVYSKRLE-NDRYFGLLDSCNHIFCITCINIWHRTRR-------------------ETGASDNCPICRTR 228 (242)
T ss_pred CCCc--cCcccccccccc-ccccccccCCCCchHHHHHHHHHHHhcc-------------------ccCcCCcCCCCcce
Confidence 4566 666554332110 0012233357999999999988875320 02345789999987
Q ss_pred eec
Q 026529 208 IER 210 (237)
Q Consensus 208 iek 210 (237)
+..
T Consensus 229 f~~ 231 (242)
T PHA02926 229 FRN 231 (242)
T ss_pred eee
Confidence 653
No 158
>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=64.09 E-value=4.9 Score=20.14 Aligned_cols=22 Identities=18% Similarity=0.460 Sum_probs=13.1
Q ss_pred CCCceeeccccccCCcCcccCccccc
Q 026529 134 NCMAVMVNECEEIGRVKKAQCPKCKQ 159 (237)
Q Consensus 134 ~C~~~~~~~~~~~~~~~~~~C~~C~~ 159 (237)
.|+..+..... ...+.||.||.
T Consensus 3 sC~~~i~~r~~----~v~f~CPnCG~ 24 (24)
T PF07754_consen 3 SCGRPIAPREQ----AVPFPCPNCGF 24 (24)
T ss_pred cCCCcccCccc----CceEeCCCCCC
Confidence 45555544432 36788888873
No 159
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=63.95 E-value=2.8 Score=39.25 Aligned_cols=29 Identities=28% Similarity=0.769 Sum_probs=21.0
Q ss_pred ccccccccccccccCCCCCChhhhhccccchHHHHHHHHhCCcccCCCCCcce
Q 026529 156 KCKQWFCFQCKLAWHAGYRCEESGNLRDRNDIAFGKLLEKMNWTRCPGCGNCI 208 (237)
Q Consensus 156 ~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~~i 208 (237)
.|++.||..|-++ .. ....++||.|+..+
T Consensus 660 kC~H~FC~~Cvq~-----------------------r~-etRqRKCP~Cn~aF 688 (698)
T KOG0978|consen 660 KCGHVFCEECVQT-----------------------RY-ETRQRKCPKCNAAF 688 (698)
T ss_pred hcchHHHHHHHHH-----------------------HH-HHhcCCCCCCCCCC
Confidence 7899999988532 11 23559999999876
No 160
>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=63.57 E-value=6.6 Score=24.39 Aligned_cols=26 Identities=15% Similarity=0.528 Sum_probs=19.1
Q ss_pred ccCCCCCc----ceeccCCCCceeec-CccE
Q 026529 199 TRCPGCGN----CIERKKGCRIMFCR-FIFL 224 (237)
Q Consensus 199 k~CP~C~~----~iek~~GCnhm~C~-C~~c 224 (237)
-.||+|+. .+.+..|=.++.|. |||.
T Consensus 10 A~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~ 40 (59)
T TIGR02443 10 AVCPACSAQDTLAMWKENNIELVECVECGYQ 40 (59)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEeccCCCc
Confidence 47999986 34456666889997 9874
No 161
>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=63.20 E-value=6.6 Score=31.71 Aligned_cols=55 Identities=16% Similarity=0.352 Sum_probs=39.3
Q ss_pred ccCCCCcCCCC-CCccccccCCChhHHHHHHHHHHHHhhcCCCcccCCCCCCCceeecc
Q 026529 85 IECPGLHCEQF-LDPLACKPTIPSSLFIKWCDHLCEDYVLGLERSYCPNRNCMAVMVNE 142 (237)
Q Consensus 85 i~CP~~~C~~~-~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~ 142 (237)
-+||. |+.- .-..++.-+++++-+.++-+.-..+.+. .+...||.++|+.++...
T Consensus 11 ~~CPv--CksDrYLnPdik~linPECyHrmCESCvdRIFs-~GpAqCP~~gC~kILRK~ 66 (314)
T COG5220 11 RRCPV--CKSDRYLNPDIKILINPECYHRMCESCVDRIFS-RGPAQCPYKGCGKILRKI 66 (314)
T ss_pred ccCCc--cccccccCCCeEEEECHHHHHHHHHHHHHHHhc-CCCCCCCCccHHHHHHHh
Confidence 48999 9863 2234588888999888887665555443 455789999999876643
No 162
>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=63.16 E-value=5.1 Score=25.40 Aligned_cols=17 Identities=24% Similarity=0.780 Sum_probs=12.8
Q ss_pred cchHHHHHHHHHhcccc
Q 026529 63 PFCQDCTAKYIEVKVRD 79 (237)
Q Consensus 63 ~fC~~Cl~~~~~~~i~~ 79 (237)
-||+.||.+|+..+-.+
T Consensus 11 gFCRNCLskWy~~aA~~ 27 (68)
T PF06844_consen 11 GFCRNCLSKWYREAAEE 27 (68)
T ss_dssp S--HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHh
Confidence 49999999999887765
No 163
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=63.11 E-value=3.8 Score=35.93 Aligned_cols=35 Identities=20% Similarity=0.471 Sum_probs=27.7
Q ss_pred CCcccccccccCCCCccccccCCCCCcchHHHHHHHHHh
Q 026529 37 GTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEV 75 (237)
Q Consensus 37 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~ 75 (237)
..+.|+||..-+..+ +.++|+|..|..|.++...+
T Consensus 3 eelkc~vc~~f~~ep----iil~c~h~lc~~ca~~~~~~ 37 (699)
T KOG4367|consen 3 EELKCPVCGSFYREP----IILPCSHNLCQACARNILVQ 37 (699)
T ss_pred ccccCceehhhccCc----eEeecccHHHHHHHHhhccc
Confidence 356899999887543 47899999999999976544
No 164
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=63.10 E-value=14 Score=27.93 Aligned_cols=53 Identities=19% Similarity=0.338 Sum_probs=36.4
Q ss_pred CCCcccccccccCCCCccccccCCCCC---cchHHHHHHHHHhccccCCcccccCCCCcCCCCCCcc
Q 026529 36 DGTFTCDICIEPMSVNNKFKNNNLCTH---PFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFLDPL 99 (237)
Q Consensus 36 ~~~~~C~IC~~~~~~~~~~~~~~~C~H---~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~~~ 99 (237)
.....|-||+++... . .....|.. ....+|+.+|+... ...+|+. |+..+...
T Consensus 6 ~~~~~CRIC~~~~~~-~--~~PC~CkGs~k~VH~sCL~rWi~~s------~~~~Cei--C~~~Y~i~ 61 (162)
T PHA02825 6 LMDKCCWICKDEYDV-V--TNYCNCKNENKIVHKECLEEWINTS------KNKSCKI--CNGPYNIK 61 (162)
T ss_pred CCCCeeEecCCCCCC-c--cCCcccCCCchHHHHHHHHHHHhcC------CCCcccc--cCCeEEEE
Confidence 445689999988642 2 12334444 46999999999942 4578998 99765544
No 165
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=63.03 E-value=3.8 Score=33.91 Aligned_cols=52 Identities=23% Similarity=0.619 Sum_probs=38.2
Q ss_pred CCCCcccccccccCCCCccccccCCC----CCcchHHHHHHHHHhccccCCcccccCCCC-cCC
Q 026529 35 IDGTFTCDICIEPMSVNNKFKNNNLC----THPFCQDCTAKYIEVKVRDNNTAKIECPGL-HCE 93 (237)
Q Consensus 35 ~~~~~~C~IC~~~~~~~~~~~~~~~C----~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~-~C~ 93 (237)
....+.|.+|.|.+.+ .. ...| .|.||..|-+..|+.+=.. ..+.||.. .|.
T Consensus 265 ~~apLcCTLC~ERLED-TH---FVQCPSVp~HKFCFPCSResIK~Qg~s---gevYCPSGdkCP 321 (352)
T KOG3579|consen 265 PSAPLCCTLCHERLED-TH---FVQCPSVPSHKFCFPCSRESIKQQGAS---GEVYCPSGDKCP 321 (352)
T ss_pred CCCceeehhhhhhhcc-Cc---eeecCCCcccceecccCHHHHHhhcCC---CceeCCCCCcCc
Confidence 3456899999998843 22 3355 7999999999999987554 37889854 465
No 166
>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=62.76 E-value=5.1 Score=30.43 Aligned_cols=31 Identities=19% Similarity=0.296 Sum_probs=23.4
Q ss_pred CCcccCCCCCCCceeeccccccCCcCcccCcccccc
Q 026529 125 LERSYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQW 160 (237)
Q Consensus 125 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 160 (237)
+....|| .|+.-+...+.. ...+.||.||..
T Consensus 107 ~~~Y~Cp--~c~~r~tf~eA~---~~~F~Cp~Cg~~ 137 (158)
T TIGR00373 107 NMFFICP--NMCVRFTFNEAM---ELNFTCPRCGAM 137 (158)
T ss_pred CCeEECC--CCCcEeeHHHHH---HcCCcCCCCCCE
Confidence 4567898 798777776654 367999999875
No 167
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=62.24 E-value=6.8 Score=26.38 Aligned_cols=31 Identities=23% Similarity=0.281 Sum_probs=24.2
Q ss_pred CCcccCCCCCcceeccCCCCceeec-CccEEE
Q 026529 196 MNWTRCPGCGNCIERKKGCRIMFCR-FIFLSL 226 (237)
Q Consensus 196 ~~~k~CP~C~~~iek~~GCnhm~C~-C~~cf~ 226 (237)
..--.||.|+....|..+=---.|+ ||+-|-
T Consensus 33 ~~~~~Cp~C~~~~VkR~a~GIW~C~kCg~~fA 64 (89)
T COG1997 33 RAKHVCPFCGRTTVKRIATGIWKCRKCGAKFA 64 (89)
T ss_pred hcCCcCCCCCCcceeeeccCeEEcCCCCCeec
Confidence 3447999999998888776667786 987764
No 168
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=62.19 E-value=1.9 Score=36.01 Aligned_cols=78 Identities=21% Similarity=0.384 Sum_probs=43.7
Q ss_pred ccccCCCCcCCCCCCccccccCCChhHHHHHHHHHHHH-hhc-----CCCcccCCCCCCCceeecccccc----CCcCcc
Q 026529 83 AKIECPGLHCEQFLDPLACKPTIPSSLFIKWCDHLCED-YVL-----GLERSYCPNRNCMAVMVNECEEI----GRVKKA 152 (237)
Q Consensus 83 ~~i~CP~~~C~~~~~~~~i~~~l~~~~~~~~~~~~~~~-~~~-----~~~~~~Cp~~~C~~~~~~~~~~~----~~~~~~ 152 (237)
.||.||. |. +..+|+..+...|..++--. +.+ .+....|- .|...++..+... ......
T Consensus 321 LPi~CP~--Cs-------l~LilsthLarSyhhL~PLk~f~E~p~~~~~ks~~Cf--~CQ~~fp~~~~~~~~~~~ss~rY 389 (421)
T COG5151 321 LPISCPI--CS-------LQLILSTHLARSYHHLYPLKPFVEKPEGTNPKSTHCF--VCQGPFPKPPVSPFDESTSSGRY 389 (421)
T ss_pred CCccCcc--hh-------HHHHHHHHHHHHHHhhccCcccccccCCCCCCCccce--eccCCCCCCCCCcccccccccce
Confidence 4666665 54 22334444455555443221 222 12334565 6777665443321 125678
Q ss_pred cCcccccccccccccccCC
Q 026529 153 QCPKCKQWFCFQCKLAWHA 171 (237)
Q Consensus 153 ~C~~C~~~~C~~C~~~~H~ 171 (237)
+|+.|+..||..|..-.|.
T Consensus 390 ~Ce~CK~~FC~dCdvfiHe 408 (421)
T COG5151 390 QCELCKSTFCSDCDVFIHE 408 (421)
T ss_pred echhhhhhhhhhhHHHHHH
Confidence 8999999999999766553
No 169
>PRK10220 hypothetical protein; Provisional
Probab=62.10 E-value=5.2 Score=28.13 Aligned_cols=26 Identities=27% Similarity=0.657 Sum_probs=19.9
Q ss_pred cCCCCCCCceeeccccccCCcCcccCccccccc
Q 026529 129 YCPNRNCMAVMVNECEEIGRVKKAQCPKCKQWF 161 (237)
Q Consensus 129 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 161 (237)
-|| .|+.-+.+++. ..+.||.|++.|
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 477 88888777765 468898888866
No 170
>PLN02436 cellulose synthase A
Probab=61.96 E-value=7.1 Score=38.43 Aligned_cols=62 Identities=21% Similarity=0.401 Sum_probs=43.6
Q ss_pred cccCCCCCCCceeeccccccCCcCcccCcccccccccccccccCCCCCChhhhhccccchHHHHHHHHhCCcccCCCCCc
Q 026529 127 RSYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQWFCFQCKLAWHAGYRCEESGNLRDRNDIAFGKLLEKMNWTRCPGCGN 206 (237)
Q Consensus 127 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~ 206 (237)
..-|. -|+--+-..... ...+.|..|++-.|..|- ||. .+.+.+.||.|++
T Consensus 36 ~~iCq--ICGD~Vg~t~dG---e~FVACn~C~fpvCr~Cy----------eye--------------r~eg~~~Cpqckt 86 (1094)
T PLN02436 36 GQTCQ--ICGDEIELTVDG---EPFVACNECAFPVCRPCY----------EYE--------------RREGNQACPQCKT 86 (1094)
T ss_pred Ccccc--ccccccCcCCCC---CEEEeeccCCCccccchh----------hhh--------------hhcCCccCcccCC
Confidence 34566 777665544332 488999999999998554 332 2456689999999
Q ss_pred ceeccCCCCce
Q 026529 207 CIERKKGCRIM 217 (237)
Q Consensus 207 ~iek~~GCnhm 217 (237)
...+--|+..+
T Consensus 87 ~Y~r~kgs~~~ 97 (1094)
T PLN02436 87 RYKRIKGSPRV 97 (1094)
T ss_pred chhhccCCCCc
Confidence 99877777654
No 171
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=61.67 E-value=5.6 Score=30.87 Aligned_cols=32 Identities=22% Similarity=0.505 Sum_probs=23.6
Q ss_pred CCcccCCCCCCCceeeccccccCCcCcccCccccccc
Q 026529 125 LERSYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQWF 161 (237)
Q Consensus 125 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 161 (237)
+.+..|| .|+.-+...+.. ...+.||.||...
T Consensus 115 ~~~Y~Cp--~C~~rytf~eA~---~~~F~Cp~Cg~~L 146 (178)
T PRK06266 115 NMFFFCP--NCHIRFTFDEAM---EYGFRCPQCGEML 146 (178)
T ss_pred CCEEECC--CCCcEEeHHHHh---hcCCcCCCCCCCC
Confidence 4567898 798877776654 4678999888754
No 172
>PF14369 zf-RING_3: zinc-finger
Probab=61.15 E-value=8.2 Score=21.23 Aligned_cols=29 Identities=21% Similarity=0.564 Sum_probs=19.6
Q ss_pred ccCCCCCCCceeeccccccCCcCcccCccccccc
Q 026529 128 SYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQWF 161 (237)
Q Consensus 128 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 161 (237)
.||= .|...+...... ...+.||.|+..|
T Consensus 3 ywCh--~C~~~V~~~~~~---~~~~~CP~C~~gF 31 (35)
T PF14369_consen 3 YWCH--QCNRFVRIAPSP---DSDVACPRCHGGF 31 (35)
T ss_pred EeCc--cCCCEeEeCcCC---CCCcCCcCCCCcE
Confidence 4777 888888876443 1334699887655
No 173
>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=61.01 E-value=7.9 Score=21.63 Aligned_cols=30 Identities=20% Similarity=0.298 Sum_probs=19.6
Q ss_pred ccCCCCCCCceeeccccccCCcCcccCcccccc
Q 026529 128 SYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQW 160 (237)
Q Consensus 128 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 160 (237)
..|+ .|+..+....... ......||.||..
T Consensus 6 y~C~--~Cg~~fe~~~~~~-~~~~~~CP~Cg~~ 35 (41)
T smart00834 6 YRCE--DCGHTFEVLQKIS-DDPLATCPECGGD 35 (41)
T ss_pred EEcC--CCCCEEEEEEecC-CCCCCCCCCCCCc
Confidence 4687 8998766544321 1467789988873
No 174
>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=60.99 E-value=6.4 Score=21.24 Aligned_cols=23 Identities=22% Similarity=0.512 Sum_probs=14.2
Q ss_pred CCCceeeccccccCCcCcccCccccccc
Q 026529 134 NCMAVMVNECEEIGRVKKAQCPKCKQWF 161 (237)
Q Consensus 134 ~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 161 (237)
+|+..+..... ..++|+.||+.+
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 77777664433 567898888754
No 175
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=60.90 E-value=8.1 Score=22.48 Aligned_cols=11 Identities=45% Similarity=0.921 Sum_probs=6.5
Q ss_pred cccCCCCCcce
Q 026529 198 WTRCPGCGNCI 208 (237)
Q Consensus 198 ~k~CP~C~~~i 208 (237)
..+||.|+..|
T Consensus 19 ~irC~~CG~rI 29 (44)
T smart00659 19 VVRCRECGYRI 29 (44)
T ss_pred ceECCCCCceE
Confidence 35666666654
No 176
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=60.87 E-value=5.4 Score=29.84 Aligned_cols=35 Identities=20% Similarity=0.360 Sum_probs=22.3
Q ss_pred CCcccCCCCCCCceeecccccc--CCcCcccCccccccc
Q 026529 125 LERSYCPNRNCMAVMVNECEEI--GRVKKAQCPKCKQWF 161 (237)
Q Consensus 125 ~~~~~Cp~~~C~~~~~~~~~~~--~~~~~~~C~~C~~~~ 161 (237)
.....|| .|+..+...+... .....+.||.||...
T Consensus 97 ~~~Y~Cp--~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l 133 (147)
T smart00531 97 NAYYKCP--NCQSKYTFLEANQLLDMDGTFTCPRCGEEL 133 (147)
T ss_pred CcEEECc--CCCCEeeHHHHHHhcCCCCcEECCCCCCEE
Confidence 4467899 8998777644321 012338899888754
No 177
>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=60.84 E-value=7.3 Score=25.30 Aligned_cols=26 Identities=23% Similarity=0.549 Sum_probs=19.6
Q ss_pred ccCCCCCc----ceeccCCCCceeec-CccE
Q 026529 199 TRCPGCGN----CIERKKGCRIMFCR-FIFL 224 (237)
Q Consensus 199 k~CP~C~~----~iek~~GCnhm~C~-C~~c 224 (237)
-.||+|+. ++.+..|=.++.|. |||.
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 47999987 34456777889997 9975
No 178
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=60.56 E-value=13 Score=28.70 Aligned_cols=62 Identities=23% Similarity=0.402 Sum_probs=40.1
Q ss_pred CCCCcccccccccCCCC---ccccccCCCCCcchHHHHHHHHHhccccCCccc---ccCCCCcCCCCCCc
Q 026529 35 IDGTFTCDICIEPMSVN---NKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAK---IECPGLHCEQFLDP 98 (237)
Q Consensus 35 ~~~~~~C~IC~~~~~~~---~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~---i~CP~~~C~~~~~~ 98 (237)
+.....|.||+..-.+. +..-....|+..|..-||..|+..-+.....+. =.||. |..++..
T Consensus 162 dd~~~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPY--CS~Pial 229 (234)
T KOG3268|consen 162 DDELGACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPY--CSDPIAL 229 (234)
T ss_pred chhhhcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCC--CCCccee
Confidence 45566888887653221 221235679999999999999987665433333 36887 8876653
No 179
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=60.49 E-value=11 Score=26.86 Aligned_cols=29 Identities=17% Similarity=0.551 Sum_probs=19.6
Q ss_pred CCcccCCCCCCCceeeccccccCCcCcccCcccccc
Q 026529 125 LERSYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQW 160 (237)
Q Consensus 125 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 160 (237)
+...+|+ +|+..+..... ..+.||.||..
T Consensus 68 p~~~~C~--~Cg~~~~~~~~-----~~~~CP~Cgs~ 96 (114)
T PRK03681 68 EAECWCE--TCQQYVTLLTQ-----RVRRCPQCHGD 96 (114)
T ss_pred CcEEEcc--cCCCeeecCCc-----cCCcCcCcCCC
Confidence 4568999 99976665432 23668888753
No 180
>PRK00420 hypothetical protein; Validated
Probab=60.32 E-value=17 Score=25.90 Aligned_cols=44 Identities=16% Similarity=0.268 Sum_probs=24.9
Q ss_pred hHHHHHHHHHHHHhhcCCCcccCCCCCCCceeeccccccCCcCcccCcccccc
Q 026529 108 SLFIKWCDHLCEDYVLGLERSYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQW 160 (237)
Q Consensus 108 ~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 160 (237)
+...+.-+++..-+.. -...|| .|+..+..... ....||.||..
T Consensus 6 ~~~k~~a~~Ll~Ga~m--l~~~CP--~Cg~pLf~lk~-----g~~~Cp~Cg~~ 49 (112)
T PRK00420 6 DIVKKAAELLLKGAKM--LSKHCP--VCGLPLFELKD-----GEVVCPVHGKV 49 (112)
T ss_pred HHHHHHHHHHHhHHHH--ccCCCC--CCCCcceecCC-----CceECCCCCCe
Confidence 3444444444443322 126899 89987776422 45677777664
No 181
>PF14353 CpXC: CpXC protein
Probab=60.07 E-value=5.8 Score=28.78 Aligned_cols=15 Identities=27% Similarity=0.596 Sum_probs=11.1
Q ss_pred ccCCCCcCCCCCCcccc
Q 026529 85 IECPGLHCEQFLDPLAC 101 (237)
Q Consensus 85 i~CP~~~C~~~~~~~~i 101 (237)
|.||. |+..+..+..
T Consensus 2 itCP~--C~~~~~~~v~ 16 (128)
T PF14353_consen 2 ITCPH--CGHEFEFEVW 16 (128)
T ss_pred cCCCC--CCCeeEEEEE
Confidence 78998 9987665543
No 182
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=59.88 E-value=6.1 Score=27.21 Aligned_cols=30 Identities=27% Similarity=0.733 Sum_probs=22.3
Q ss_pred ccCCCCCCCceeeccccccCCcCcccCccccccc
Q 026529 128 SYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQWF 161 (237)
Q Consensus 128 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 161 (237)
.+|| .|+..+++..+.. .+.+.|+.|.+.+
T Consensus 2 ~FCP--~Cgn~Live~g~~--~~rf~C~tCpY~~ 31 (105)
T KOG2906|consen 2 LFCP--TCGNMLIVESGES--CNRFSCRTCPYVF 31 (105)
T ss_pred cccC--CCCCEEEEecCCe--EeeEEcCCCCcee
Confidence 4688 9999999887762 4677777776655
No 183
>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 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=59.16 E-value=8.8 Score=23.17 Aligned_cols=27 Identities=22% Similarity=0.338 Sum_probs=16.7
Q ss_pred cccCCCCCccee------ccCCCCcee-ec-CccE
Q 026529 198 WTRCPGCGNCIE------RKKGCRIMF-CR-FIFL 224 (237)
Q Consensus 198 ~k~CP~C~~~ie------k~~GCnhm~-C~-C~~c 224 (237)
.|+||.|+-.-+ .+.+..++. |. ||+.
T Consensus 1 LkPCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~ 35 (53)
T TIGR03655 1 LKPCPFCGGADVYLRRGFDPLDLSHYFECSTCGAS 35 (53)
T ss_pred CCCCCCCCCcceeeEeccCCCCCEEEEECCCCCCC
Confidence 378999987555 123455554 76 7643
No 185
>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=58.80 E-value=7.6 Score=25.90 Aligned_cols=31 Identities=29% Similarity=0.418 Sum_probs=17.4
Q ss_pred CcccCCCCC------cceeccCCCCceeec-CccEEEe
Q 026529 197 NWTRCPGCG------NCIERKKGCRIMFCR-FIFLSLC 227 (237)
Q Consensus 197 ~~k~CP~C~------~~iek~~GCnhm~C~-C~~cf~c 227 (237)
..-.||.|+ +.|.+..|=-+++|+ ||..|-.
T Consensus 21 ~~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~~ 58 (81)
T PF05129_consen 21 KVFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQT 58 (81)
T ss_dssp S----TTT--SS-EEEEEETTTTEEEEEESSS--EEEE
T ss_pred ceEcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeEEE
Confidence 556899999 245556788899997 9865543
No 186
>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=58.73 E-value=6.3 Score=20.61 Aligned_cols=21 Identities=38% Similarity=0.863 Sum_probs=11.4
Q ss_pred ccCCCCCcceecc--CCCCceee
Q 026529 199 TRCPGCGNCIERK--KGCRIMFC 219 (237)
Q Consensus 199 k~CP~C~~~iek~--~GCnhm~C 219 (237)
++||+|+..|++. +|=+...|
T Consensus 2 ~~C~rC~~~~~~~~~~~r~~~~C 24 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGINGRSTYLC 24 (30)
T ss_dssp SB-TTT--BBEEEEETTEEEEE-
T ss_pred CcCccCCCcceEeEecCCCCeEC
Confidence 5799999988765 45444555
No 187
>PHA02929 N1R/p28-like protein; Provisional
Probab=58.69 E-value=7.2 Score=31.75 Aligned_cols=40 Identities=20% Similarity=0.550 Sum_probs=23.7
Q ss_pred cccCCCCCCCceeeccccccCCcCcccCcccccccccccccccC
Q 026529 127 RSYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQWFCFQCKLAWH 170 (237)
Q Consensus 127 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H 170 (237)
...|| -|...+...... ......=+.|++.||..|-..|.
T Consensus 174 ~~eC~--ICle~~~~~~~~--~~~~~vl~~C~H~FC~~CI~~Wl 213 (238)
T PHA02929 174 DKECA--ICMEKVYDKEIK--NMYFGILSNCNHVFCIECIDIWK 213 (238)
T ss_pred CCCCc--cCCcccccCccc--cccceecCCCCCcccHHHHHHHH
Confidence 46788 787765433211 01122334799999999976654
No 188
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=58.45 E-value=6.7 Score=24.94 Aligned_cols=32 Identities=22% Similarity=0.372 Sum_probs=23.0
Q ss_pred cccCCCCCCCceeeccccccCCcCcccCccccccccc
Q 026529 127 RSYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQWFCF 163 (237)
Q Consensus 127 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~ 163 (237)
.+.|| +|++....-... ...++|..||...+.
T Consensus 19 ~VkCp--dC~N~q~vFsha---st~V~C~~CG~~l~~ 50 (67)
T COG2051 19 RVKCP--DCGNEQVVFSHA---STVVTCLICGTTLAE 50 (67)
T ss_pred EEECC--CCCCEEEEeccC---ceEEEecccccEEEe
Confidence 37899 998765544433 478999999987753
No 189
>PLN02400 cellulose synthase
Probab=58.41 E-value=7.3 Score=38.39 Aligned_cols=61 Identities=23% Similarity=0.361 Sum_probs=43.2
Q ss_pred ccCCCCCCCceeeccccccCCcCcccCcccccccccccccccCCCCCChhhhhccccchHHHHHHHHhCCcccCCCCCcc
Q 026529 128 SYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQWFCFQCKLAWHAGYRCEESGNLRDRNDIAFGKLLEKMNWTRCPGCGNC 207 (237)
Q Consensus 128 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~~ 207 (237)
.-|- -|+--+-..... ...+.|..|+.-.|..|. ||.+ +.+.+.||+|++.
T Consensus 37 qiCq--ICGD~VG~t~dG---e~FVAC~eCaFPVCRpCY----------EYER--------------keGnq~CPQCkTr 87 (1085)
T PLN02400 37 QICQ--ICGDDVGVTETG---DVFVACNECAFPVCRPCY----------EYER--------------KDGTQCCPQCKTR 87 (1085)
T ss_pred ceee--ecccccCcCCCC---CEEEEEccCCCccccchh----------heec--------------ccCCccCcccCCc
Confidence 4565 677655554433 488999999999998554 3332 3566899999999
Q ss_pred eeccCCCCce
Q 026529 208 IERKKGCRIM 217 (237)
Q Consensus 208 iek~~GCnhm 217 (237)
..+.-|+..+
T Consensus 88 YkR~KgsprV 97 (1085)
T PLN02400 88 YRRHKGSPRV 97 (1085)
T ss_pred cccccCCCCC
Confidence 9888787654
No 190
>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=57.92 E-value=10 Score=24.54 Aligned_cols=21 Identities=24% Similarity=0.586 Sum_probs=14.0
Q ss_pred cCCCCCcceeccCCCCceeec-Cc
Q 026529 200 RCPGCGNCIERKKGCRIMFCR-FI 222 (237)
Q Consensus 200 ~CP~C~~~iek~~GCnhm~C~-C~ 222 (237)
.||.|+..++..+ .+.+|. |+
T Consensus 3 ~CP~C~~~L~~~~--~~~~C~~C~ 24 (70)
T PF07191_consen 3 TCPKCQQELEWQG--GHYHCEACQ 24 (70)
T ss_dssp B-SSS-SBEEEET--TEEEETTT-
T ss_pred cCCCCCCccEEeC--CEEECcccc
Confidence 5888988888887 477775 75
No 191
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=57.62 E-value=9.3 Score=20.73 Aligned_cols=29 Identities=21% Similarity=0.385 Sum_probs=18.6
Q ss_pred cccCCCCCCCceeeccccccCCcCcccCccccccc
Q 026529 127 RSYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQWF 161 (237)
Q Consensus 127 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 161 (237)
...|+ .|++.......+ ....|+.|+..|
T Consensus 3 ~~~C~--~C~~~~i~~~~~----~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 3 LKKCS--KCGGNGIVNKED----DYEVCIFCGSSF 31 (33)
T ss_pred ceEcC--CCCCCeEEEecC----CeEEcccCCcEe
Confidence 35677 788777664332 567788787654
No 192
>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=57.30 E-value=6.6 Score=28.48 Aligned_cols=26 Identities=15% Similarity=0.034 Sum_probs=17.3
Q ss_pred ccCCCCCcceeccCCCCceeec-CccEE
Q 026529 199 TRCPGCGNCIERKKGCRIMFCR-FIFLS 225 (237)
Q Consensus 199 k~CP~C~~~iek~~GCnhm~C~-C~~cf 225 (237)
|.||+|+..+.--.- +-++|. ||..|
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 678888876654433 667885 77654
No 193
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=57.24 E-value=3.7 Score=31.01 Aligned_cols=29 Identities=21% Similarity=0.472 Sum_probs=21.5
Q ss_pred CCCcccccccccCCCCccccccCCCCCcch
Q 026529 36 DGTFTCDICIEPMSVNNKFKNNNLCTHPFC 65 (237)
Q Consensus 36 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC 65 (237)
....+|.||+|++...+.+ ..++|-.+|-
T Consensus 175 ddkGECvICLEdL~~GdtI-ARLPCLCIYH 203 (205)
T KOG0801|consen 175 DDKGECVICLEDLEAGDTI-ARLPCLCIYH 203 (205)
T ss_pred ccCCcEEEEhhhccCCCce-eccceEEEee
Confidence 5567899999999776654 6788866553
No 194
>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=57.16 E-value=8.1 Score=23.40 Aligned_cols=37 Identities=22% Similarity=0.604 Sum_probs=25.5
Q ss_pred cccccccccCCCCccccccCCCCCcchHHHHHHHHHh
Q 026529 39 FTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEV 75 (237)
Q Consensus 39 ~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~ 75 (237)
..|.+|-..+.....-..-..||+.||.+|.......
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~~~ 39 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRIPL 39 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCcChHHcCCeeec
Confidence 3688887776543222234579999999999977554
No 195
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=56.83 E-value=3.1 Score=34.47 Aligned_cols=21 Identities=29% Similarity=0.964 Sum_probs=16.0
Q ss_pred cccCcccccccccccccccCC
Q 026529 151 KAQCPKCKQWFCFQCKLAWHA 171 (237)
Q Consensus 151 ~~~C~~C~~~~C~~C~~~~H~ 171 (237)
.-.|.-||+.||+.|-..|-.
T Consensus 251 ~pSaTpCGHiFCWsCI~~w~~ 271 (293)
T KOG0317|consen 251 NPSATPCGHIFCWSCILEWCS 271 (293)
T ss_pred CCCcCcCcchHHHHHHHHHHc
Confidence 344678999999999876653
No 196
>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=56.79 E-value=10 Score=23.15 Aligned_cols=31 Identities=26% Similarity=0.437 Sum_probs=22.9
Q ss_pred ccCCCCCCCceeeccccccCCcCcccCcccccccc
Q 026529 128 SYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQWFC 162 (237)
Q Consensus 128 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C 162 (237)
+.|| .|+..+....... ...+.||.||..+=
T Consensus 3 ~~CP--~CG~~iev~~~~~--GeiV~Cp~CGaele 33 (54)
T TIGR01206 3 FECP--DCGAEIELENPEL--GELVICDECGAELE 33 (54)
T ss_pred cCCC--CCCCEEecCCCcc--CCEEeCCCCCCEEE
Confidence 4688 9999888765443 46789999998763
No 197
>PF14149 YhfH: YhfH-like protein
Probab=55.52 E-value=1.6 Score=24.41 Aligned_cols=28 Identities=25% Similarity=0.602 Sum_probs=20.6
Q ss_pred HHHhCCcccCCCCCcceeccCCCCceee
Q 026529 192 LLEKMNWTRCPGCGNCIERKKGCRIMFC 219 (237)
Q Consensus 192 ~~~~~~~k~CP~C~~~iek~~GCnhm~C 219 (237)
.......|.||.||..|+--.-|-.++|
T Consensus 7 FfrnLp~K~C~~CG~~i~EQ~E~Y~n~C 34 (37)
T PF14149_consen 7 FFRNLPPKKCTECGKEIEEQAECYGNEC 34 (37)
T ss_pred HHHhCCCcccHHHHHHHHHHHHHHhCcC
Confidence 4445677999999999987666655555
No 198
>PHA02862 5L protein; Provisional
Probab=55.05 E-value=17 Score=27.10 Aligned_cols=47 Identities=26% Similarity=0.457 Sum_probs=33.6
Q ss_pred cccccccccCCCCccccccCCCCC-----cchHHHHHHHHHhccccCCcccccCCCCcCCCCCCc
Q 026529 39 FTCDICIEPMSVNNKFKNNNLCTH-----PFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFLDP 98 (237)
Q Consensus 39 ~~C~IC~~~~~~~~~~~~~~~C~H-----~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~~ 98 (237)
..|-||+++-.. + ..+|.. ....+||.+|+. ...+..||. |+.....
T Consensus 3 diCWIC~~~~~e-~----~~PC~C~GS~K~VHq~CL~~WIn------~S~k~~CeL--CkteY~I 54 (156)
T PHA02862 3 DICWICNDVCDE-R----NNFCGCNEEYKVVHIKCMQLWIN------YSKKKECNL--CKTKYNI 54 (156)
T ss_pred CEEEEecCcCCC-C----cccccccCcchhHHHHHHHHHHh------cCCCcCccC--CCCeEEE
Confidence 369999998632 2 245533 479999999995 345679999 9976543
No 199
>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=54.83 E-value=12 Score=19.99 Aligned_cols=27 Identities=15% Similarity=0.517 Sum_probs=21.1
Q ss_pred ccCCCCCCCceeeccccccCCcCcccCcccccc
Q 026529 128 SYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQW 160 (237)
Q Consensus 128 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 160 (237)
+.|. .|+..+....+. ..++|..|+..
T Consensus 2 ~~C~--~C~t~L~yP~gA----~~vrCs~C~~v 28 (31)
T TIGR01053 2 VVCG--GCRTLLMYPRGA----SSVRCALCQTV 28 (31)
T ss_pred cCcC--CCCcEeecCCCC----CeEECCCCCeE
Confidence 3577 888888888774 89999988764
No 200
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=54.81 E-value=9.8 Score=23.51 Aligned_cols=27 Identities=22% Similarity=0.359 Sum_probs=17.0
Q ss_pred CcccCCCCCcceecc---CC--C---Cceeec-Ccc
Q 026529 197 NWTRCPGCGNCIERK---KG--C---RIMFCR-FIF 223 (237)
Q Consensus 197 ~~k~CP~C~~~iek~---~G--C---nhm~C~-C~~ 223 (237)
..|+||.|+...... .+ - ..|.|. ||.
T Consensus 2 ~LkPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 2 ELKPCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCcCCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 468999998644332 22 1 457786 875
No 201
>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=54.26 E-value=12 Score=21.46 Aligned_cols=29 Identities=17% Similarity=0.329 Sum_probs=18.5
Q ss_pred ccCCCCCCCceeeccccccCCcCcccCccccc
Q 026529 128 SYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQ 159 (237)
Q Consensus 128 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 159 (237)
..|+ +|+..+........ ...+.||.||.
T Consensus 6 y~C~--~Cg~~fe~~~~~~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCE--ECGHEFEVLQSISE-DDPVPCPECGS 34 (42)
T ss_pred EEeC--CCCCEEEEEEEcCC-CCCCcCCCCCC
Confidence 4577 88866554433222 46788988886
No 202
>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=53.78 E-value=29 Score=20.16 Aligned_cols=32 Identities=31% Similarity=0.634 Sum_probs=17.0
Q ss_pred HHHHhCCc---ccCCCCCcc-eeccCCCCceeec-Cc
Q 026529 191 KLLEKMNW---TRCPGCGNC-IERKKGCRIMFCR-FI 222 (237)
Q Consensus 191 ~~~~~~~~---k~CP~C~~~-iek~~GCnhm~C~-C~ 222 (237)
+++....| -.||+|+.. +.+..+=....|+ |+
T Consensus 8 ~~l~~~RW~~g~~CP~Cg~~~~~~~~~~~~~~C~~C~ 44 (46)
T PF12760_consen 8 EYLEEIRWPDGFVCPHCGSTKHYRLKTRGRYRCKACR 44 (46)
T ss_pred HHHHHhcCCCCCCCCCCCCeeeEEeCCCCeEECCCCC
Confidence 34444444 569999973 3333333345554 54
No 203
>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=53.78 E-value=2.7 Score=26.83 Aligned_cols=38 Identities=21% Similarity=0.501 Sum_probs=18.7
Q ss_pred CCCcccccccccCCCCccccccCCCCCcchHHHHHHHH
Q 026529 36 DGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYI 73 (237)
Q Consensus 36 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~ 73 (237)
.....|.+|...|.....-..-..||+.||.+|....+
T Consensus 7 ~~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~~~ 44 (69)
T PF01363_consen 7 SEASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQRI 44 (69)
T ss_dssp GG-SB-TTT--B-BSSS-EEE-TTT--EEECCCS-EEE
T ss_pred CCCCcCcCcCCcCCCceeeEccCCCCCEECCchhCCEE
Confidence 34568999998885433222345699999999986544
No 204
>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=53.29 E-value=12 Score=27.72 Aligned_cols=13 Identities=31% Similarity=0.759 Sum_probs=10.7
Q ss_pred ccCCCCCcceecc
Q 026529 199 TRCPGCGNCIERK 211 (237)
Q Consensus 199 k~CP~C~~~iek~ 211 (237)
-+|.+||.+|...
T Consensus 82 ~~CE~CG~~I~~G 94 (137)
T TIGR03826 82 YPCERCGTSIREG 94 (137)
T ss_pred CcccccCCcCCCC
Confidence 6899999999554
No 205
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=52.91 E-value=18 Score=25.69 Aligned_cols=27 Identities=30% Similarity=0.720 Sum_probs=18.3
Q ss_pred CCcccCCCCCCCceeeccccccCCcCcccCccccc
Q 026529 125 LERSYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQ 159 (237)
Q Consensus 125 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 159 (237)
+...+|+ +|+..+.... ..+.||.||.
T Consensus 68 p~~~~C~--~Cg~~~~~~~------~~~~CP~Cgs 94 (113)
T PRK12380 68 PAQAWCW--DCSQVVEIHQ------HDAQCPHCHG 94 (113)
T ss_pred CcEEEcc--cCCCEEecCC------cCccCcCCCC
Confidence 4568898 8987766653 3345888874
No 206
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=52.89 E-value=19 Score=28.60 Aligned_cols=20 Identities=25% Similarity=0.489 Sum_probs=15.5
Q ss_pred CCcccCCCCCCCceeecccc
Q 026529 125 LERSYCPNRNCMAVMVNECE 144 (237)
Q Consensus 125 ~~~~~Cp~~~C~~~~~~~~~ 144 (237)
..++-||.|+|..++..+..
T Consensus 136 SqRIACPRpnCkRiInL~p~ 155 (275)
T KOG4684|consen 136 SQRIACPRPNCKRIINLDPL 155 (275)
T ss_pred cceeccCCCCcceeeecCCC
Confidence 45688999999988876543
No 207
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=52.50 E-value=19 Score=25.73 Aligned_cols=28 Identities=25% Similarity=0.554 Sum_probs=18.9
Q ss_pred CCcccCCCCCCCceeeccccccCCcCcccCcccccc
Q 026529 125 LERSYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQW 160 (237)
Q Consensus 125 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 160 (237)
+...+|+ +|+..+.... ..+.||.||..
T Consensus 68 p~~~~C~--~Cg~~~~~~~------~~~~CP~Cgs~ 95 (115)
T TIGR00100 68 PVECECE--DCSEEVSPEI------DLYRCPKCHGI 95 (115)
T ss_pred CcEEEcc--cCCCEEecCC------cCccCcCCcCC
Confidence 4468898 8987766653 24568877753
No 208
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=52.49 E-value=14 Score=25.74 Aligned_cols=35 Identities=17% Similarity=0.314 Sum_probs=22.5
Q ss_pred CCCcccCCCCCCCceeeccccccCCcCcccCccccccc
Q 026529 124 GLERSYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQWF 161 (237)
Q Consensus 124 ~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 161 (237)
.+..+.|| .|+.....-.... ....+.|+.||+++
T Consensus 18 lpt~f~CP--~Cge~~v~v~~~k-~~~h~~C~~CG~y~ 52 (99)
T PRK14892 18 LPKIFECP--RCGKVSISVKIKK-NIAIITCGNCGLYT 52 (99)
T ss_pred CCcEeECC--CCCCeEeeeecCC-CcceEECCCCCCcc
Confidence 46678899 8885443322221 24678899898876
No 209
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=52.38 E-value=10 Score=37.27 Aligned_cols=57 Identities=23% Similarity=0.416 Sum_probs=39.8
Q ss_pred CCCceeeccccccCCcCcccCcccccccccccccccCCCCCChhhhhccccchHHHHHHHHhCCcccCCCCCcceeccCC
Q 026529 134 NCMAVMVNECEEIGRVKKAQCPKCKQWFCFQCKLAWHAGYRCEESGNLRDRNDIAFGKLLEKMNWTRCPGCGNCIERKKG 213 (237)
Q Consensus 134 ~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~~iek~~G 213 (237)
-|+.-+-..... ...+.|..|+...|..|- +|. .+.+.+.||+|++...+.-|
T Consensus 20 iCGd~vg~~~~G---e~FVAC~eC~fpvCr~cy----------eye--------------~~~g~~~cp~c~t~y~~~~~ 72 (1044)
T PLN02915 20 VCGDEVGVKEDG---QPFVACHVCGFPVCKPCY----------EYE--------------RSEGNQCCPQCNTRYKRHKG 72 (1044)
T ss_pred ccccccCcCCCC---CEEEEeccCCCccccchh----------hhh--------------hhcCCccCCccCCchhhhcC
Confidence 566555544333 488999999999998554 332 24566899999999987767
Q ss_pred CCce
Q 026529 214 CRIM 217 (237)
Q Consensus 214 Cnhm 217 (237)
.+.+
T Consensus 73 ~~~~ 76 (1044)
T PLN02915 73 CPRV 76 (1044)
T ss_pred CCCc
Confidence 6654
No 210
>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=52.34 E-value=26 Score=24.60 Aligned_cols=57 Identities=21% Similarity=0.443 Sum_probs=33.6
Q ss_pred CCCcccccccccCCCCccc----cccCCC---CCcchHHHHHHHHHhcccc-CCcccccCCCCcCCC
Q 026529 36 DGTFTCDICIEPMSVNNKF----KNNNLC---THPFCQDCTAKYIEVKVRD-NNTAKIECPGLHCEQ 94 (237)
Q Consensus 36 ~~~~~C~IC~~~~~~~~~~----~~~~~C---~H~fC~~Cl~~~~~~~i~~-~~~~~i~CP~~~C~~ 94 (237)
....+|..|.......... .....| .=.||..||...+...+.+ .....-.||. |..
T Consensus 5 ~~g~~CHqCrqKt~~~~~~C~~~~~~~~C~~~~~~fC~~CL~~ryge~~~ev~~~~~W~CP~--Crg 69 (105)
T PF10497_consen 5 VNGKTCHQCRQKTLDFKTICTGHWKNSSCRGCRGKFCGGCLRNRYGENVEEVLEDPNWKCPK--CRG 69 (105)
T ss_pred CCCCCchhhcCCCCCCceEcCCCCCCCCCccCcceehHhHHHHHHhhhHHHHhcCCceECCC--CCC
Confidence 3445677776644321110 012456 6679999999888766654 1234567887 664
No 211
>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=52.29 E-value=4.7 Score=23.85 Aligned_cols=44 Identities=23% Similarity=0.554 Sum_probs=21.6
Q ss_pred CcccccccccCCCCccccccCCC-CCcchHHHHHHHHHhccccCCcccccCCCCcCCCCCC
Q 026529 38 TFTCDICIEPMSVNNKFKNNNLC-THPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFLD 97 (237)
Q Consensus 38 ~~~C~IC~~~~~~~~~~~~~~~C-~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~ 97 (237)
.+.|..|+-... .+..| .|..|..|+...+.. .-.||. |+.+++
T Consensus 2 r~nCKsCWf~~k------~Li~C~dHYLCl~CLt~ml~~--------s~~C~i--C~~~LP 46 (50)
T PF03854_consen 2 RYNCKSCWFANK------GLIKCSDHYLCLNCLTLMLSR--------SDRCPI--CGKPLP 46 (50)
T ss_dssp -----SS-S--S------SEEE-SS-EEEHHHHHHT-SS--------SSEETT--TTEE--
T ss_pred CccChhhhhcCC------CeeeecchhHHHHHHHHHhcc--------ccCCCc--ccCcCc
Confidence 356777875442 14466 589999999887763 236887 887665
No 212
>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=51.95 E-value=4.4 Score=22.91 Aligned_cols=24 Identities=25% Similarity=0.661 Sum_probs=21.4
Q ss_pred CcccCcccccccccccccccCCCC
Q 026529 150 KKAQCPKCKQWFCFQCKLAWHAGY 173 (237)
Q Consensus 150 ~~~~C~~C~~~~C~~C~~~~H~~~ 173 (237)
..+.|..|+..+|..|....|.++
T Consensus 14 ~~~~C~~C~~~~C~~C~~~~H~~H 37 (42)
T PF00643_consen 14 LSLFCEDCNEPLCSECTVSGHKGH 37 (42)
T ss_dssp EEEEETTTTEEEEHHHHHTSTTTS
T ss_pred eEEEecCCCCccCccCCCCCCCCC
Confidence 678899999999999998888875
No 213
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=51.84 E-value=14 Score=30.05 Aligned_cols=40 Identities=13% Similarity=0.167 Sum_probs=32.1
Q ss_pred CCCcccccccccCCCCccccccCCCCCcchHHHHHHHHHhcccc
Q 026529 36 DGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRD 79 (237)
Q Consensus 36 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~ 79 (237)
.+...|.+|+.+...+ +..+=||.||++|+..||..+-++
T Consensus 41 K~FdcCsLtLqPc~dP----vit~~GylfdrEaILe~ilaqKke 80 (303)
T KOG3039|consen 41 KPFDCCSLTLQPCRDP----VITPDGYLFDREAILEYILAQKKE 80 (303)
T ss_pred CCcceeeeecccccCC----ccCCCCeeeeHHHHHHHHHHHHHH
Confidence 4456789999888654 467889999999999999887655
No 214
>COG3492 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=51.80 E-value=11 Score=25.51 Aligned_cols=17 Identities=18% Similarity=0.675 Sum_probs=14.7
Q ss_pred cchHHHHHHHHHhcccc
Q 026529 63 PFCQDCTAKYIEVKVRD 79 (237)
Q Consensus 63 ~fC~~Cl~~~~~~~i~~ 79 (237)
-||+.||.+|+..+...
T Consensus 42 gFCRNCLs~Wy~eaae~ 58 (104)
T COG3492 42 GFCRNCLSNWYREAAEA 58 (104)
T ss_pred HHHHHHHHHHHHHHHhc
Confidence 49999999999887765
No 215
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=51.59 E-value=13 Score=23.57 Aligned_cols=28 Identities=25% Similarity=0.268 Sum_probs=18.2
Q ss_pred CCcccCCCCCcceecc---CCCCceeec-Ccc
Q 026529 196 MNWTRCPGCGNCIERK---KGCRIMFCR-FIF 223 (237)
Q Consensus 196 ~~~k~CP~C~~~iek~---~GCnhm~C~-C~~ 223 (237)
..+|+||.|+..+.+. +|=-...|. |+.
T Consensus 4 d~lKPCPFCG~~~~~v~~~~g~~~v~C~~CgA 35 (64)
T PRK09710 4 DNVKPCPFCGCPSVTVKAISGYYRAKCNGCES 35 (64)
T ss_pred ccccCCCCCCCceeEEEecCceEEEEcCCCCc
Confidence 3579999999865553 554445664 764
No 216
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=51.04 E-value=4.5 Score=37.79 Aligned_cols=59 Identities=22% Similarity=0.464 Sum_probs=44.4
Q ss_pred cCCCCcccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCCCcccccc
Q 026529 34 DIDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFLDPLACKP 103 (237)
Q Consensus 34 ~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~~~~i~~ 103 (237)
......+|+||+..+..+ +++.|.|.||..|+..-+...- ....||. |+..+....++.
T Consensus 17 ~~~k~lEc~ic~~~~~~p----~~~kc~~~~l~~~~n~~f~~~~-----~~~~~~l--c~~~~eK~s~~E 75 (684)
T KOG4362|consen 17 AMQKILECPICLEHVKEP----SLLKCDHIFLKFCLNKLFESKK-----GPKQCAL--CKSDIEKRSLRE 75 (684)
T ss_pred HHhhhccCCceeEEeecc----chhhhhHHHHhhhhhceeeccC-----ccccchh--hhhhhhhhhccc
Confidence 346678999999998654 4789999999999998777532 2678888 886665555544
No 217
>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=50.25 E-value=7.9 Score=21.21 Aligned_cols=26 Identities=27% Similarity=0.607 Sum_probs=21.2
Q ss_pred cCcccCcccccccccccccccCCCCC
Q 026529 149 VKKAQCPKCKQWFCFQCKLAWHAGYR 174 (237)
Q Consensus 149 ~~~~~C~~C~~~~C~~C~~~~H~~~~ 174 (237)
...+.|..|+...|..|....|.++.
T Consensus 10 ~~~~fC~~~~~~iC~~C~~~~H~~H~ 35 (39)
T cd00021 10 PLSLFCETDRALLCVDCDLSVHSGHR 35 (39)
T ss_pred ceEEEeCccChhhhhhcChhhcCCCC
Confidence 45788999999999999877687653
No 218
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=49.93 E-value=21 Score=26.29 Aligned_cols=16 Identities=19% Similarity=0.156 Sum_probs=12.3
Q ss_pred CCcccCCCCCCCceeecc
Q 026529 125 LERSYCPNRNCMAVMVNE 142 (237)
Q Consensus 125 ~~~~~Cp~~~C~~~~~~~ 142 (237)
+...+|+ +|+..+...
T Consensus 68 p~~~~C~--~CG~~~~~~ 83 (135)
T PRK03824 68 EAVLKCR--NCGNEWSLK 83 (135)
T ss_pred ceEEECC--CCCCEEecc
Confidence 3468899 999887765
No 219
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=49.72 E-value=11 Score=29.33 Aligned_cols=22 Identities=27% Similarity=0.671 Sum_probs=18.6
Q ss_pred ccCCCCCcceeccCCCCceeec-Cc
Q 026529 199 TRCPGCGNCIERKKGCRIMFCR-FI 222 (237)
Q Consensus 199 k~CP~C~~~iek~~GCnhm~C~-C~ 222 (237)
-.|++|+..+++ .| +.|+|. ||
T Consensus 150 A~CsrC~~~L~~-~~-~~l~Cp~Cg 172 (188)
T COG1096 150 ARCSRCRAPLVK-KG-NMLKCPNCG 172 (188)
T ss_pred EEccCCCcceEE-cC-cEEECCCCC
Confidence 589999999999 55 788996 87
No 220
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=49.43 E-value=5.8 Score=33.02 Aligned_cols=31 Identities=23% Similarity=0.533 Sum_probs=22.7
Q ss_pred CcccccccccCCCCccccccCCCCCc-chHHHHHHH
Q 026529 38 TFTCDICIEPMSVNNKFKNNNLCTHP-FCQDCTAKY 72 (237)
Q Consensus 38 ~~~C~IC~~~~~~~~~~~~~~~C~H~-fC~~Cl~~~ 72 (237)
...|.|||+.-. +- +++.|||. .|..|-+.+
T Consensus 300 ~~LC~ICmDaP~--DC--vfLeCGHmVtCt~CGkrm 331 (350)
T KOG4275|consen 300 RRLCAICMDAPR--DC--VFLECGHMVTCTKCGKRM 331 (350)
T ss_pred HHHHHHHhcCCc--ce--EEeecCcEEeehhhcccc
Confidence 457999998753 33 37999997 598886543
No 221
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=49.26 E-value=12 Score=21.48 Aligned_cols=27 Identities=30% Similarity=0.551 Sum_probs=14.5
Q ss_pred cCCCCCCCceeeccccccCCcCcccCcccccc
Q 026529 129 YCPNRNCMAVMVNECEEIGRVKKAQCPKCKQW 160 (237)
Q Consensus 129 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 160 (237)
.|| .|+......+.. ...+.|+.||..
T Consensus 2 ~Cp--~Cg~~~~~~D~~---~g~~vC~~CG~V 28 (43)
T PF08271_consen 2 KCP--NCGSKEIVFDPE---RGELVCPNCGLV 28 (43)
T ss_dssp SBT--TTSSSEEEEETT---TTEEEETTT-BB
T ss_pred CCc--CCcCCceEEcCC---CCeEECCCCCCE
Confidence 477 787654333322 355677777654
No 222
>KOG2041 consensus WD40 repeat protein [General function prediction only]
Probab=48.94 E-value=15 Score=34.72 Aligned_cols=60 Identities=15% Similarity=0.248 Sum_probs=34.8
Q ss_pred CCCCCCccccccCCChhHHHHHHHHHHHHhhcC------CCcccCCCCCCCceeeccccccCCcCcccCccccccc
Q 026529 92 CEQFLDPLACKPTIPSSLFIKWCDHLCEDYVLG------LERSYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQWF 161 (237)
Q Consensus 92 C~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~------~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 161 (237)
|.+.+-.-.-...|+++..++|+.+.++-+... ...+-|. .|+..+.+.+ ..|+.|...|
T Consensus 1076 CSKAfmkLe~~e~l~~a~kq~ye~La~~iFsk~~p~d~~~~~vdc~--~cg~~i~~~~--------~~c~ec~~kf 1141 (1189)
T KOG2041|consen 1076 CSKAFMKLEAFEELDDAEKQEYENLAFRIFSKNPPVDPNSAKVDCS--VCGAKIDPYD--------LQCSECQTKF 1141 (1189)
T ss_pred hHHHHHHHHhhhhCCHHHHHHHHHHHHHHhccCCCCCCCccceeee--ecCCcCCccC--------CCChhhcCcC
Confidence 554333223334567788899999888766532 1235555 5665554433 3477776665
No 223
>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=48.18 E-value=13 Score=22.57 Aligned_cols=35 Identities=29% Similarity=0.446 Sum_probs=17.7
Q ss_pred CcccCCCCCCCceeecccc------ccCCcCcccCccccccc
Q 026529 126 ERSYCPNRNCMAVMVNECE------EIGRVKKAQCPKCKQWF 161 (237)
Q Consensus 126 ~~~~Cp~~~C~~~~~~~~~------~~~~~~~~~C~~C~~~~ 161 (237)
+.+.||||+|-.- ..++. .+.....++|.-|.+.+
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 4578999999654 11111 11124677787776643
No 224
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=48.05 E-value=14 Score=22.94 Aligned_cols=30 Identities=20% Similarity=0.425 Sum_probs=21.7
Q ss_pred ccCCCCCCCceeeccccccCCcCcccCcccccccc
Q 026529 128 SYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQWFC 162 (237)
Q Consensus 128 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C 162 (237)
+.|| +|+.....-... ...+.|..|+...+
T Consensus 12 VkCp--~C~n~q~vFsha---~t~V~C~~Cg~~L~ 41 (59)
T PRK00415 12 VKCP--DCGNEQVVFSHA---STVVRCLVCGKTLA 41 (59)
T ss_pred EECC--CCCCeEEEEecC---CcEEECcccCCCcc
Confidence 7798 998765544433 47888988888765
No 225
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=47.59 E-value=20 Score=25.66 Aligned_cols=28 Identities=21% Similarity=0.464 Sum_probs=17.9
Q ss_pred CCcccCCCCCCCceeeccccccCCcCcccCccccc
Q 026529 125 LERSYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQ 159 (237)
Q Consensus 125 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 159 (237)
+...+|. +|+..+..... ....||.||.
T Consensus 69 p~~~~C~--~Cg~~~~~~~~-----~~~~CP~Cgs 96 (117)
T PRK00564 69 KVELECK--DCSHVFKPNAL-----DYGVCEKCHS 96 (117)
T ss_pred CCEEEhh--hCCCccccCCc-----cCCcCcCCCC
Confidence 4458888 88866655432 2345887775
No 226
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=47.28 E-value=15 Score=36.98 Aligned_cols=50 Identities=22% Similarity=0.571 Sum_probs=28.9
Q ss_pred cccCccccc----ccccccccccCCCCCChhhhhccccchHHHHHHHHhCCcccCCCCCccee
Q 026529 151 KAQCPKCKQ----WFCFQCKLAWHAGYRCEESGNLRDRNDIAFGKLLEKMNWTRCPGCGNCIE 209 (237)
Q Consensus 151 ~~~C~~C~~----~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~~ie 209 (237)
..+||.||. .||..|+........|..-..... . ....+..||.|+.++.
T Consensus 667 ~rkCPkCG~~t~~~fCP~CGs~te~vy~CPsCGaev~-~--------des~a~~CP~CGtplv 720 (1337)
T PRK14714 667 RRRCPSCGTETYENRCPDCGTHTEPVYVCPDCGAEVP-P--------DESGRVECPRCDVELT 720 (1337)
T ss_pred EEECCCCCCccccccCcccCCcCCCceeCccCCCccC-C--------CccccccCCCCCCccc
Confidence 478999986 479999877544445543322100 0 0112457777776553
No 227
>smart00336 BBOX B-Box-type zinc finger.
Probab=47.01 E-value=14 Score=20.56 Aligned_cols=25 Identities=28% Similarity=0.577 Sum_probs=20.6
Q ss_pred cCcccCcccccccccccccccCCCC
Q 026529 149 VKKAQCPKCKQWFCFQCKLAWHAGY 173 (237)
Q Consensus 149 ~~~~~C~~C~~~~C~~C~~~~H~~~ 173 (237)
...+.|..|....|..|....|.++
T Consensus 13 ~~~~~C~~c~~~iC~~C~~~~H~~H 37 (42)
T smart00336 13 PAEFFCEECGALLCRTCDEAEHRGH 37 (42)
T ss_pred ceEEECCCCCcccccccChhhcCCC
Confidence 3577899999999999997777665
No 228
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=46.45 E-value=16 Score=34.88 Aligned_cols=41 Identities=15% Similarity=0.186 Sum_probs=18.7
Q ss_pred CcccccccccCCCCccccc---cCCCCCcchHHHHHHHHHhccc
Q 026529 38 TFTCDICIEPMSVNNKFKN---NNLCTHPFCQDCTAKYIEVKVR 78 (237)
Q Consensus 38 ~~~C~IC~~~~~~~~~~~~---~~~C~H~fC~~Cl~~~~~~~i~ 78 (237)
..+|.+|..++.+++.-.. +-.|+|.+|..||..+....+.
T Consensus 96 s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~ 139 (1134)
T KOG0825|consen 96 SDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEE 139 (1134)
T ss_pred ccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhc
Confidence 3455555555543211111 2225555666666555554443
No 229
>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=45.88 E-value=38 Score=24.18 Aligned_cols=36 Identities=19% Similarity=0.448 Sum_probs=25.0
Q ss_pred CcccCCCCCCCceeeccccccCCcCcccCcccccccccccccc
Q 026529 126 ERSYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQWFCFQCKLA 168 (237)
Q Consensus 126 ~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~ 168 (237)
+...|. .|...+..-. +....|..|++.+|..|+..
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 346787 8876544332 24588999999999999976
No 230
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=45.59 E-value=32 Score=21.17 Aligned_cols=36 Identities=19% Similarity=0.166 Sum_probs=27.6
Q ss_pred cccCCCCcCCCCCCccccccCCChhHHHHHHHHHHHHh
Q 026529 84 KIECPGLHCEQFLDPLACKPTIPSSLFIKWCDHLCEDY 121 (237)
Q Consensus 84 ~i~CP~~~C~~~~~~~~i~~~l~~~~~~~~~~~~~~~~ 121 (237)
...||. |+.......=..+-++|-+.+|...+....
T Consensus 17 k~~CP~--CG~~t~~~~P~rfSp~D~y~~yR~~~kk~~ 52 (56)
T PRK13130 17 KEICPV--CGGKTKNPHPPRFSPEDKYGKYRRALKKRR 52 (56)
T ss_pred cccCcC--CCCCCCCCCCCCCCCCCccHHHHHHHHHHh
Confidence 456888 998777666677778889999988877654
No 231
>PRK11827 hypothetical protein; Provisional
Probab=45.35 E-value=20 Score=22.43 Aligned_cols=27 Identities=15% Similarity=0.373 Sum_probs=20.6
Q ss_pred CcccCCCCCcceeccCCCCceeec-Ccc
Q 026529 197 NWTRCPGCGNCIERKKGCRIMFCR-FIF 223 (237)
Q Consensus 197 ~~k~CP~C~~~iek~~GCnhm~C~-C~~ 223 (237)
.+-.||.|+..++-+.+=+.++|+ |+-
T Consensus 7 eILaCP~ckg~L~~~~~~~~Lic~~~~l 34 (60)
T PRK11827 7 EIIACPVCNGKLWYNQEKQELICKLDNL 34 (60)
T ss_pred hheECCCCCCcCeEcCCCCeEECCccCe
Confidence 346899999988877655678886 764
No 232
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=45.23 E-value=11 Score=18.95 Aligned_cols=11 Identities=36% Similarity=0.915 Sum_probs=8.0
Q ss_pred cccCccccccc
Q 026529 151 KAQCPKCKQWF 161 (237)
Q Consensus 151 ~~~C~~C~~~~ 161 (237)
.+.|+.||..|
T Consensus 2 l~~C~~CgR~F 12 (25)
T PF13913_consen 2 LVPCPICGRKF 12 (25)
T ss_pred CCcCCCCCCEE
Confidence 45688888777
No 233
>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=43.88 E-value=12 Score=21.53 Aligned_cols=27 Identities=22% Similarity=0.605 Sum_probs=15.3
Q ss_pred CcccCcccccccccccccccCCCCCChhh
Q 026529 150 KKAQCPKCKQWFCFQCKLAWHAGYRCEES 178 (237)
Q Consensus 150 ~~~~C~~C~~~~C~~C~~~~H~~~~C~~~ 178 (237)
..+.|+.|+..||...+.+. .+.|...
T Consensus 12 ~~~~C~~C~~~FC~~Hr~~e--~H~C~~~ 38 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLKHRLPE--DHNCSKL 38 (43)
T ss_dssp SHEE-TTTS-EE-TTTHSTT--TCT-SST
T ss_pred CCeECCCCCcccCccccCcc--ccCCcch
Confidence 34679999999999887642 2355543
No 234
>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=43.83 E-value=30 Score=21.27 Aligned_cols=45 Identities=24% Similarity=0.721 Sum_probs=29.7
Q ss_pred ccccccccCCCCccccccCCCC--CcchHHHHHHHHHhccccCCcccccCCCCcCCCCCCc
Q 026529 40 TCDICIEPMSVNNKFKNNNLCT--HPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFLDP 98 (237)
Q Consensus 40 ~C~IC~~~~~~~~~~~~~~~C~--H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~~ 98 (237)
.|..|-.+++.... ....|. ..||.+|....+. -.||. |+..|..
T Consensus 7 nCE~C~~dLp~~s~--~A~ICSfECTFC~~C~e~~l~----------~~CPN--CgGelv~ 53 (57)
T PF06906_consen 7 NCECCDKDLPPDSP--EAYICSFECTFCADCAETMLN----------GVCPN--CGGELVR 53 (57)
T ss_pred CccccCCCCCCCCC--cceEEeEeCcccHHHHHHHhc----------CcCcC--CCCcccc
Confidence 68888888865431 123343 4799999987764 26888 9876543
No 235
>PLN02195 cellulose synthase A
Probab=43.68 E-value=18 Score=35.40 Aligned_cols=34 Identities=18% Similarity=0.465 Sum_probs=24.2
Q ss_pred ccCCCCCCCceeeccccccCCcCcccCcccccccccccc
Q 026529 128 SYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQWFCFQCK 166 (237)
Q Consensus 128 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~ 166 (237)
..|- -|+..+-..... ...+.|..|+.-.|..|-
T Consensus 7 ~~c~--~cgd~~~~~~~g---~~fvaC~eC~~pvCrpCy 40 (977)
T PLN02195 7 PICA--TCGEEVGVDSNG---EAFVACHECSYPLCKACL 40 (977)
T ss_pred ccce--ecccccCcCCCC---CeEEEeccCCCccccchh
Confidence 3455 677666655443 488999999999998664
No 236
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=43.42 E-value=13 Score=21.00 Aligned_cols=27 Identities=26% Similarity=0.560 Sum_probs=13.8
Q ss_pred cCCCCCCCceeeccccccCCcCcccCccccc
Q 026529 129 YCPNRNCMAVMVNECEEIGRVKKAQCPKCKQ 159 (237)
Q Consensus 129 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 159 (237)
.|| .|+..+...... ....-.|+.|+-
T Consensus 1 ~CP--~C~~~l~~~~~~--~~~id~C~~C~G 27 (41)
T PF13453_consen 1 KCP--RCGTELEPVRLG--DVEIDVCPSCGG 27 (41)
T ss_pred CcC--CCCcccceEEEC--CEEEEECCCCCe
Confidence 367 787755544332 234445655544
No 237
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=43.09 E-value=16 Score=30.35 Aligned_cols=24 Identities=29% Similarity=0.686 Sum_probs=21.0
Q ss_pred ccCCCCCcceecc--CCCCceeec-Cc
Q 026529 199 TRCPGCGNCIERK--KGCRIMFCR-FI 222 (237)
Q Consensus 199 k~CP~C~~~iek~--~GCnhm~C~-C~ 222 (237)
.+|+.|+.+|+|. +|-+-..|. |.
T Consensus 246 epC~~CGt~I~k~~~~gR~t~~CP~CQ 272 (273)
T COG0266 246 EPCRRCGTPIEKIKLGGRSTFYCPVCQ 272 (273)
T ss_pred CCCCccCCEeEEEEEcCCcCEeCCCCC
Confidence 6999999999997 888888886 74
No 238
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=42.39 E-value=9.1 Score=32.95 Aligned_cols=42 Identities=24% Similarity=0.505 Sum_probs=27.9
Q ss_pred cccCcccccccccccccccCCCCCChhhhhccccchHHHHHHHHhCCcccCCCCCcceec
Q 026529 151 KAQCPKCKQWFCFQCKLAWHAGYRCEESGNLRDRNDIAFGKLLEKMNWTRCPGCGNCIER 210 (237)
Q Consensus 151 ~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~~iek 210 (237)
...=|.|.+.||++|...|..-. .. .....+.||-|++....
T Consensus 181 fgilpnC~H~~Cl~Cir~wr~~~-----------q~-------~~~~sksCP~CRv~s~~ 222 (344)
T KOG1039|consen 181 FGILPNCNHSFCLNCIRKWRQAT-----------QF-------ESKTSKSCPFCRVPSSF 222 (344)
T ss_pred cccCCCcchhhhhcHhHhhhhhh-----------cc-------ccccccCCCcccCcccc
Confidence 34447899999999999887321 00 12345788888876654
No 239
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=42.16 E-value=16 Score=29.69 Aligned_cols=59 Identities=17% Similarity=0.237 Sum_probs=37.7
Q ss_pred ccccCCChhHHHHHHHHHHHH-hhc--CCCcccCCCCCCCceeeccccc--cCCcCcccCcccccc
Q 026529 100 ACKPTIPSSLFIKWCDHLCED-YVL--GLERSYCPNRNCMAVMVNECEE--IGRVKKAQCPKCKQW 160 (237)
Q Consensus 100 ~i~~~l~~~~~~~~~~~~~~~-~~~--~~~~~~Cp~~~C~~~~~~~~~~--~~~~~~~~C~~C~~~ 160 (237)
.+..-++++++..|.+..... -+. .-....|. +|...++..... ......++||.||..
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 455667889999998887654 211 12235677 888777654321 112578999999875
No 240
>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=42.03 E-value=15 Score=30.76 Aligned_cols=30 Identities=23% Similarity=0.424 Sum_probs=15.2
Q ss_pred ccCCCCCcc-----eeccC--CCCceeec-CccEEEec
Q 026529 199 TRCPGCGNC-----IERKK--GCRIMFCR-FIFLSLCL 228 (237)
Q Consensus 199 k~CP~C~~~-----iek~~--GCnhm~C~-C~~cf~c~ 228 (237)
..||-||.. |...+ |=-+++|. |++.|-..
T Consensus 173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~ 210 (290)
T PF04216_consen 173 GYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFV 210 (290)
T ss_dssp SS-TTT---EEEEEEE------EEEEEETTT--EEE--
T ss_pred CcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeec
Confidence 799999984 33344 88899997 99988754
No 241
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=41.74 E-value=23 Score=21.50 Aligned_cols=22 Identities=18% Similarity=0.530 Sum_probs=15.3
Q ss_pred HHHHHHHHhCCcccCCCCCcce
Q 026529 187 IAFGKLLEKMNWTRCPGCGNCI 208 (237)
Q Consensus 187 ~~~~~~~~~~~~k~CP~C~~~i 208 (237)
..+.++........||+|+..+
T Consensus 35 ~~~~~i~~~~~i~~Cp~CgRiL 56 (56)
T PF02591_consen 35 QELNEIRKGDEIVFCPNCGRIL 56 (56)
T ss_pred HHHHHHHcCCCeEECcCCCccC
Confidence 3444555556889999999753
No 242
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=41.64 E-value=14 Score=31.69 Aligned_cols=45 Identities=24% Similarity=0.487 Sum_probs=29.5
Q ss_pred CCCCcccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCC
Q 026529 35 IDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFL 96 (237)
Q Consensus 35 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~ 96 (237)
......|.||.++..+ + +..+|||.-| |..-+- .-+.||. |.+.+
T Consensus 302 ~~~p~lcVVcl~e~~~---~-~fvpcGh~cc--ct~cs~---------~l~~CPv--CR~rI 346 (355)
T KOG1571|consen 302 LPQPDLCVVCLDEPKS---A-VFVPCGHVCC--CTLCSK---------HLPQCPV--CRQRI 346 (355)
T ss_pred cCCCCceEEecCCccc---e-eeecCCcEEE--chHHHh---------hCCCCch--hHHHH
Confidence 4556789999998854 2 4689999965 433221 1234998 87644
No 243
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=41.49 E-value=19 Score=22.08 Aligned_cols=31 Identities=16% Similarity=0.411 Sum_probs=18.9
Q ss_pred ccCCCCCCCceeeccccccCCcCcccCccccccccc
Q 026529 128 SYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQWFCF 163 (237)
Q Consensus 128 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~ 163 (237)
+.|| +|...-..-... ...+.|..|+...|.
T Consensus 8 VkCp--~C~~~q~vFSha---~t~V~C~~Cg~~L~~ 38 (55)
T PF01667_consen 8 VKCP--GCYNIQTVFSHA---QTVVKCVVCGTVLAQ 38 (55)
T ss_dssp EE-T--TT-SEEEEETT----SS-EE-SSSTSEEEE
T ss_pred EECC--CCCCeeEEEecC---CeEEEcccCCCEecC
Confidence 6788 998765554333 578899999988874
No 244
>PRK04023 DNA polymerase II large subunit; Validated
Probab=41.15 E-value=21 Score=35.10 Aligned_cols=7 Identities=43% Similarity=1.288 Sum_probs=3.4
Q ss_pred ccCcccc
Q 026529 152 AQCPKCK 158 (237)
Q Consensus 152 ~~C~~C~ 158 (237)
+.||.||
T Consensus 639 frCP~CG 645 (1121)
T PRK04023 639 RRCPFCG 645 (1121)
T ss_pred ccCCCCC
Confidence 3455554
No 245
>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=40.73 E-value=15 Score=26.09 Aligned_cols=23 Identities=26% Similarity=0.767 Sum_probs=14.2
Q ss_pred cCcccCccccccc--------ccccccccCC
Q 026529 149 VKKAQCPKCKQWF--------CFQCKLAWHA 171 (237)
Q Consensus 149 ~~~~~C~~C~~~~--------C~~C~~~~H~ 171 (237)
...+.||.|++.+ |..|+.+.+-
T Consensus 67 av~V~CP~C~K~TKmLGr~D~CM~C~~pLTL 97 (114)
T PF11023_consen 67 AVQVECPNCGKQTKMLGRVDACMHCKEPLTL 97 (114)
T ss_pred ceeeECCCCCChHhhhchhhccCcCCCcCcc
Confidence 4556677776554 7777766553
No 246
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=40.22 E-value=17 Score=22.63 Aligned_cols=34 Identities=21% Similarity=0.544 Sum_probs=23.6
Q ss_pred cccCCCCCCCceeeccccccCCcCcccCcccccccccccc
Q 026529 127 RSYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQWFCFQCK 166 (237)
Q Consensus 127 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~ 166 (237)
.-.|. .|+..+.+... ...+.||.||...-.+|.
T Consensus 9 ~~~Ct--SCg~~i~p~e~----~v~F~CPnCGe~~I~Rc~ 42 (61)
T COG2888 9 PPVCT--SCGREIAPGET----AVKFPCPNCGEVEIYRCA 42 (61)
T ss_pred Cceec--cCCCEeccCCc----eeEeeCCCCCceeeehhh
Confidence 34666 78888866655 378899999976655443
No 247
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=40.04 E-value=20 Score=25.03 Aligned_cols=25 Identities=24% Similarity=0.745 Sum_probs=20.5
Q ss_pred cCCCCCcchHHHHHHHHHhccccCCcccccCCC
Q 026529 57 NNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPG 89 (237)
Q Consensus 57 ~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~ 89 (237)
=..|.|.|-..|+.+|+++. -.||.
T Consensus 78 WG~CNHaFH~hCisrWlktr--------~vCPL 102 (114)
T KOG2930|consen 78 WGVCNHAFHFHCISRWLKTR--------NVCPL 102 (114)
T ss_pred eeecchHHHHHHHHHHHhhc--------CcCCC
Confidence 34699999999999999863 36887
No 248
>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=39.99 E-value=49 Score=24.61 Aligned_cols=53 Identities=17% Similarity=0.175 Sum_probs=30.6
Q ss_pred hhHHHHHHHHHHHHhhc---CCCcccCCCCCCCceeecccccc-----------CCcCcccCccccccc
Q 026529 107 SSLFIKWCDHLCEDYVL---GLERSYCPNRNCMAVMVNECEEI-----------GRVKKAQCPKCKQWF 161 (237)
Q Consensus 107 ~~~~~~~~~~~~~~~~~---~~~~~~Cp~~~C~~~~~~~~~~~-----------~~~~~~~C~~C~~~~ 161 (237)
.+..+++.+.+...-+. .+....|+ .|++.+...+..+ .......|+.|++.|
T Consensus 68 ~~~~~QL~ev~~~~~l~~~~~~~~sRC~--~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiy 134 (147)
T PF01927_consen 68 DDPEEQLREVLERFGLKLRLDPIFSRCP--KCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIY 134 (147)
T ss_pred CCHHHHHHHHHHHcCCccccCCCCCccC--CCCcEeeechhhccccccCccccccCCeEEECCCCCCEe
Confidence 34455555554443332 23368899 9998776654321 013466788887766
No 249
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=39.71 E-value=28 Score=27.11 Aligned_cols=35 Identities=17% Similarity=0.249 Sum_probs=24.3
Q ss_pred ccCCCCCcceeccCCCCceeec-CccEEEecccCCCCcc
Q 026529 199 TRCPGCGNCIERKKGCRIMFCR-FIFLSLCLCIFSNRYL 236 (237)
Q Consensus 199 k~CP~C~~~iek~~GCnhm~C~-C~~cf~c~~~~~~~~~ 236 (237)
-.||.|+.+..+.+. +.|.|. ||+-.- ...+..|+
T Consensus 150 a~~~~~g~~~~~~~~-~~~~c~~~~~~e~--rkva~~~~ 185 (189)
T PRK09521 150 AMCSRCRTPLVKKGE-NELKCPNCGNIET--RKLSSYYG 185 (189)
T ss_pred EEccccCCceEECCC-CEEECCCCCCEEe--eccchhhc
Confidence 479999999888554 999997 984332 44444443
No 250
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=39.49 E-value=40 Score=29.76 Aligned_cols=68 Identities=21% Similarity=0.454 Sum_probs=37.3
Q ss_pred cCcccCccc-cccc---ccccccccCCCCCChhhhhccccchHHHHHHHHhCCcccCCCCCccee-cc--CCC----Cce
Q 026529 149 VKKAQCPKC-KQWF---CFQCKLAWHAGYRCEESGNLRDRNDIAFGKLLEKMNWTRCPGCGNCIE-RK--KGC----RIM 217 (237)
Q Consensus 149 ~~~~~C~~C-~~~~---C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~~ie-k~--~GC----nhm 217 (237)
.+.+.|..+ ++.| |..|..+.-+.-.+++..++.. .|..| -.+--+|-.|+..+. +. .|| ||+
T Consensus 380 ~n~v~Cv~dfh~kfAPrCs~C~~PI~P~~G~~etvRvva-mdr~f-----Hv~CY~CEDCg~~LS~e~e~qgCyPld~Hl 453 (468)
T KOG1701|consen 380 QNNVYCVPDFHKKFAPRCSVCGNPILPRDGKDETVRVVA-MDRDF-----HVNCYKCEDCGLLLSSEEEGQGCYPLDGHL 453 (468)
T ss_pred CCceeeehhhhhhcCcchhhccCCccCCCCCcceEEEEE-ccccc-----cccceehhhcCccccccCCCCcceeccCce
Confidence 577888655 2333 7777776655444554333221 11111 123356778888877 43 355 688
Q ss_pred eec-Cc
Q 026529 218 FCR-FI 222 (237)
Q Consensus 218 ~C~-C~ 222 (237)
.|+ |.
T Consensus 454 lCk~Ch 459 (468)
T KOG1701|consen 454 LCKTCH 459 (468)
T ss_pred eechhh
Confidence 886 73
No 251
>PRK08115 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=39.07 E-value=14 Score=35.77 Aligned_cols=28 Identities=29% Similarity=0.621 Sum_probs=21.8
Q ss_pred ccCCCCCc-ceeccCCCCceeec-CccEEEec
Q 026529 199 TRCPGCGN-CIERKKGCRIMFCR-FIFLSLCL 228 (237)
Q Consensus 199 k~CP~C~~-~iek~~GCnhm~C~-C~~cf~c~ 228 (237)
-.||-|+. -|+..|||| ||+ ||...-|+
T Consensus 828 ~~cp~c~~~~~~~~~~c~--~c~~c~~~~~~~ 857 (858)
T PRK08115 828 NTCPVCREGTVEEIGGCN--TCTNCGAQLKCG 857 (858)
T ss_pred CCCCccCCCceeecCCCc--cccchhhhhccC
Confidence 48999998 567779999 787 87666554
No 252
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=38.90 E-value=23 Score=30.07 Aligned_cols=48 Identities=17% Similarity=0.326 Sum_probs=33.9
Q ss_pred CCCCcccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCC
Q 026529 35 IDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCE 93 (237)
Q Consensus 35 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~ 93 (237)
......|+||+.....+. ++.-=|-+||-.|+.+|+.. . =.||.-++.
T Consensus 297 ~~~~~~CpvClk~r~Npt---vl~vSGyVfCY~Ci~~Yv~~---~-----~~CPVT~~p 344 (357)
T KOG0826|consen 297 PPDREVCPVCLKKRQNPT---VLEVSGYVFCYPCIFSYVVN---Y-----GHCPVTGYP 344 (357)
T ss_pred CCccccChhHHhccCCCc---eEEecceEEeHHHHHHHHHh---c-----CCCCccCCc
Confidence 355678999998875432 23334889999999999982 2 268875554
No 253
>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=38.79 E-value=25 Score=21.19 Aligned_cols=38 Identities=26% Similarity=0.549 Sum_probs=22.3
Q ss_pred CcccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCC
Q 026529 38 TFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQ 94 (237)
Q Consensus 38 ~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~ 94 (237)
.+.||.|...++. .=|..++...=.. ....+.||. |..
T Consensus 2 ~f~CP~C~~~~~~----------------~~L~~H~~~~H~~-~~~~v~CPi--C~~ 39 (54)
T PF05605_consen 2 SFTCPYCGKGFSE----------------SSLVEHCEDEHRS-ESKNVVCPI--CSS 39 (54)
T ss_pred CcCCCCCCCccCH----------------HHHHHHHHhHCcC-CCCCccCCC--chh
Confidence 5789999885522 1133444332222 234689999 875
No 254
>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=38.77 E-value=14 Score=31.03 Aligned_cols=32 Identities=28% Similarity=0.577 Sum_probs=25.0
Q ss_pred CCcccCCCCCCCceeeccccccCCcCcccCccccccc
Q 026529 125 LERSYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQWF 161 (237)
Q Consensus 125 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 161 (237)
.-+..|| .|+..+...+.. .+...||.|++.+
T Consensus 24 ~~~~~c~--~c~~~~~~~~l~---~~~~vc~~c~~h~ 55 (285)
T TIGR00515 24 GVWTKCP--KCGQVLYTKELE---RNLEVCPKCDHHM 55 (285)
T ss_pred CCeeECC--CCcchhhHHHHH---hhCCCCCCCCCcC
Confidence 3368899 999998887664 4678999999865
No 255
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=38.16 E-value=24 Score=21.83 Aligned_cols=27 Identities=26% Similarity=0.597 Sum_probs=17.0
Q ss_pred cCCCcccCCCCCCCceeeccccccCCcCcccCcccccc
Q 026529 123 LGLERSYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQW 160 (237)
Q Consensus 123 ~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 160 (237)
..+.+..|| .|+.+..+. ..|+.||++
T Consensus 23 ~~~~l~~C~--~CG~~~~~H---------~vC~~CG~Y 49 (57)
T PRK12286 23 KAPGLVECP--NCGEPKLPH---------RVCPSCGYY 49 (57)
T ss_pred cCCcceECC--CCCCccCCe---------EECCCCCcC
Confidence 446677788 777766543 346677653
No 256
>PRK13264 3-hydroxyanthranilate 3,4-dioxygenase; Provisional
Probab=38.08 E-value=12 Score=28.97 Aligned_cols=52 Identities=19% Similarity=0.392 Sum_probs=30.0
Q ss_pred cccccccccccccCCC-CCChhhhhccccchHHHHHHHHhCCcccCCCCCcceecc
Q 026529 157 CKQWFCFQCKLAWHAG-YRCEESGNLRDRNDIAFGKLLEKMNWTRCPGCGNCIERK 211 (237)
Q Consensus 157 C~~~~C~~C~~~~H~~-~~C~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~~iek~ 211 (237)
.-.-||..|....|.. ..|.+.... -...+.++......|+|++|+++....
T Consensus 118 ~~~wyc~~c~~~~~e~~f~~~d~~~~---~~~~~~~f~~~~e~rtC~~CG~v~~~~ 170 (177)
T PRK13264 118 GFQWYCDECNHKVHEVEVQLTDIETD---LPPVFAAFYASEELRTCDNCGTVHPGK 170 (177)
T ss_pred ceEEECCCCCCeEEEEEEEecChhhh---hHHHHHHHhcCHhhccCCcCCcccCcc
Confidence 3444555565555532 234443221 123555666677889999999976543
No 257
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=37.89 E-value=11 Score=35.95 Aligned_cols=40 Identities=28% Similarity=0.673 Sum_probs=30.7
Q ss_pred cccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCC
Q 026529 39 FTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQ 94 (237)
Q Consensus 39 ~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~ 94 (237)
-.|..|-.++..| .+...|+|.|...|+. + ..-.||. |.-
T Consensus 841 skCs~C~~~LdlP---~VhF~CgHsyHqhC~e--------~---~~~~CP~--C~~ 880 (933)
T KOG2114|consen 841 SKCSACEGTLDLP---FVHFLCGHSYHQHCLE--------D---KEDKCPK--CLP 880 (933)
T ss_pred eeecccCCccccc---eeeeecccHHHHHhhc--------c---CcccCCc--cch
Confidence 3799998888554 2567899999999998 2 2357887 874
No 258
>PLN03086 PRLI-interacting factor K; Provisional
Probab=37.77 E-value=17 Score=33.57 Aligned_cols=59 Identities=25% Similarity=0.588 Sum_probs=37.0
Q ss_pred cccccCCCCcCCCCCCccccccCCChhHHHHHHHHHHHHhhcCCCcccCCCCCCCceeeccccccCCcCcccCccccccc
Q 026529 82 TAKIECPGLHCEQFLDPLACKPTIPSSLFIKWCDHLCEDYVLGLERSYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQWF 161 (237)
Q Consensus 82 ~~~i~CP~~~C~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 161 (237)
...+.||. |...++...+... +.+-. -..+.||+.+|+..+...... ..+.|+.|+..|
T Consensus 405 ~~~V~C~N--C~~~i~l~~l~lH--------------e~~C~-r~~V~Cp~~~Cg~v~~r~el~----~H~~C~~Cgk~f 463 (567)
T PLN03086 405 VDTVECRN--CKHYIPSRSIALH--------------EAYCS-RHNVVCPHDGCGIVLRVEEAK----NHVHCEKCGQAF 463 (567)
T ss_pred CCeEECCC--CCCccchhHHHHH--------------HhhCC-CcceeCCcccccceeeccccc----cCccCCCCCCcc
Confidence 34578887 8876664433211 11111 224679977899988766654 567899998876
No 259
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=37.28 E-value=63 Score=20.04 Aligned_cols=34 Identities=18% Similarity=0.217 Sum_probs=25.0
Q ss_pred cCCCCcCCCCCCccccccCCChhHHHHHHHHHHHHh
Q 026529 86 ECPGLHCEQFLDPLACKPTIPSSLFIKWCDHLCEDY 121 (237)
Q Consensus 86 ~CP~~~C~~~~~~~~i~~~l~~~~~~~~~~~~~~~~ 121 (237)
+||. |+.......=..+-+.|-+.+|...+.+..
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 6988 997655555556667788999988877654
No 260
>PLN02436 cellulose synthase A
Probab=37.11 E-value=30 Score=34.36 Aligned_cols=52 Identities=29% Similarity=0.693 Sum_probs=35.6
Q ss_pred CCCcccccccccCC---CCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCC
Q 026529 36 DGTFTCDICIEPMS---VNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFL 96 (237)
Q Consensus 36 ~~~~~C~IC~~~~~---~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~ 96 (237)
.....|.||-|++. +.+.|++--.|+-..|+.|. .|-. ++| .-.||+ |+...
T Consensus 34 ~~~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cy-eyer---~eg---~~~Cpq--ckt~Y 88 (1094)
T PLN02436 34 LSGQTCQICGDEIELTVDGEPFVACNECAFPVCRPCY-EYER---REG---NQACPQ--CKTRY 88 (1094)
T ss_pred cCCccccccccccCcCCCCCEEEeeccCCCccccchh-hhhh---hcC---CccCcc--cCCch
Confidence 34558999999963 34556655669999999999 4443 222 247998 88643
No 261
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=36.79 E-value=19 Score=25.55 Aligned_cols=28 Identities=21% Similarity=0.479 Sum_probs=17.2
Q ss_pred CCcccCCCCCCCceeeccccccCCcCcccCcccccc
Q 026529 125 LERSYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQW 160 (237)
Q Consensus 125 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 160 (237)
+...+|. +|+..+.++.. ...||.|+..
T Consensus 68 p~~~~C~--~Cg~~~~~~~~------~~~CP~Cgs~ 95 (113)
T PF01155_consen 68 PARARCR--DCGHEFEPDEF------DFSCPRCGSP 95 (113)
T ss_dssp --EEEET--TTS-EEECHHC------CHH-SSSSSS
T ss_pred CCcEECC--CCCCEEecCCC------CCCCcCCcCC
Confidence 4458888 89888877754 2568877754
No 262
>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=36.70 E-value=30 Score=20.48 Aligned_cols=29 Identities=21% Similarity=0.331 Sum_probs=17.4
Q ss_pred ccCCCCCCCceeeccccccCCcCcccCccccc
Q 026529 128 SYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQ 159 (237)
Q Consensus 128 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 159 (237)
..|+ +|+..+....... ....+.||.|+.
T Consensus 6 y~C~--~Cg~~fe~~~~~~-~~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCT--ACGHRFEVLQKMS-DDPLATCPECGG 34 (52)
T ss_pred EEeC--CCCCEeEEEEecC-CCCCCCCCCCCC
Confidence 4577 8887555443221 135677888886
No 263
>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=36.67 E-value=35 Score=25.84 Aligned_cols=19 Identities=11% Similarity=0.240 Sum_probs=12.3
Q ss_pred CCcccCCCCCCCceeeccc
Q 026529 125 LERSYCPNRNCMAVMVNEC 143 (237)
Q Consensus 125 ~~~~~Cp~~~C~~~~~~~~ 143 (237)
...+.|+..+|.....+..
T Consensus 105 ~K~RsC~~e~C~F~GtY~e 123 (162)
T PF07800_consen 105 AKKRSCSQESCSFSGTYSE 123 (162)
T ss_pred cCCccCcccccccccCHHH
Confidence 3456788778876655544
No 264
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=36.31 E-value=31 Score=32.88 Aligned_cols=39 Identities=21% Similarity=0.383 Sum_probs=30.0
Q ss_pred CCCCcccccccccCCCCccccccCCCCCcchHHHHHHHHHh
Q 026529 35 IDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEV 75 (237)
Q Consensus 35 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~ 75 (237)
....+.|.||--.+..... .-..|+|....+|+..|++.
T Consensus 1025 ~~~~~~C~~C~l~V~gss~--~Cg~C~Hv~H~sc~~eWf~~ 1063 (1081)
T KOG0309|consen 1025 KGFTFQCAICHLAVRGSSN--FCGTCGHVGHTSCMMEWFRT 1063 (1081)
T ss_pred ccceeeeeeEeeEeeccch--hhccccccccHHHHHHHHhc
Confidence 3556789999766644333 36789999999999999985
No 265
>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=36.18 E-value=9.1 Score=20.26 Aligned_cols=15 Identities=20% Similarity=0.620 Sum_probs=7.0
Q ss_pred cccCCCCcCCCCCCc
Q 026529 84 KIECPGLHCEQFLDP 98 (237)
Q Consensus 84 ~i~CP~~~C~~~~~~ 98 (237)
.++||..+|...+..
T Consensus 2 ~vrCPvkdC~EEv~l 16 (30)
T PF10426_consen 2 VVRCPVKDCDEEVSL 16 (30)
T ss_dssp EEE--STT---EEEH
T ss_pred ccccccccCcchhhh
Confidence 479999999876543
No 266
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=35.75 E-value=12 Score=30.98 Aligned_cols=43 Identities=28% Similarity=0.666 Sum_probs=23.3
Q ss_pred CcccCCCCCCCce----eeccccccCCcCcccCccccccc------ccccccccC
Q 026529 126 ERSYCPNRNCMAV----MVNECEEIGRVKKAQCPKCKQWF------CFQCKLAWH 170 (237)
Q Consensus 126 ~~~~Cp~~~C~~~----~~~~~~~~~~~~~~~C~~C~~~~------C~~C~~~~H 170 (237)
.+.+|| -|++. ++.........+...|..|-+.+ |.+|.+.-|
T Consensus 184 ~~~~CP--vCGS~PvaSmV~~g~~~~GlRYL~CslC~teW~~VR~KC~nC~~t~~ 236 (308)
T COG3058 184 SRQYCP--VCGSMPVASMVQIGETEQGLRYLHCSLCETEWHYVRVKCSNCEQSKK 236 (308)
T ss_pred ccccCC--CcCCCCcceeeeecCccccchhhhhhhHHHHHHHHHHHhccccccCC
Confidence 457999 89853 22222122235677777666554 555554433
No 267
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=35.56 E-value=46 Score=21.10 Aligned_cols=13 Identities=31% Similarity=0.639 Sum_probs=6.6
Q ss_pred CcccCCCCCccee
Q 026529 197 NWTRCPGCGNCIE 209 (237)
Q Consensus 197 ~~k~CP~C~~~ie 209 (237)
+.-.||+|+..+-
T Consensus 52 g~L~Cp~c~r~YP 64 (68)
T PF03966_consen 52 GELICPECGREYP 64 (68)
T ss_dssp TEEEETTTTEEEE
T ss_pred CEEEcCCCCCEEe
Confidence 4445555555443
No 268
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=35.33 E-value=16 Score=30.69 Aligned_cols=32 Identities=28% Similarity=0.568 Sum_probs=24.9
Q ss_pred CCcccCCCCCCCceeeccccccCCcCcccCccccccc
Q 026529 125 LERSYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQWF 161 (237)
Q Consensus 125 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 161 (237)
.-+..|| .|+..+...+-. .+...||.|++.+
T Consensus 25 ~~~~~c~--~c~~~~~~~~l~---~~~~vc~~c~~h~ 56 (292)
T PRK05654 25 GLWTKCP--SCGQVLYRKELE---ANLNVCPKCGHHM 56 (292)
T ss_pred CCeeECC--CccchhhHHHHH---hcCCCCCCCCCCe
Confidence 3368899 999988877765 3567999999866
No 269
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 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. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=35.33 E-value=23 Score=19.94 Aligned_cols=31 Identities=23% Similarity=0.306 Sum_probs=15.2
Q ss_pred ccCCCCCCCceeeccccccCCcCcccCcccccc
Q 026529 128 SYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQW 160 (237)
Q Consensus 128 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 160 (237)
+.|. .|++++-+--.-+.....++|+-|+..
T Consensus 3 ~rC~--~C~aylNp~~~~~~~~~~w~C~~C~~~ 33 (40)
T PF04810_consen 3 VRCR--RCRAYLNPFCQFDDGGKTWICNFCGTK 33 (40)
T ss_dssp -B-T--TT--BS-TTSEEETTTTEEEETTT--E
T ss_pred cccC--CCCCEECCcceEcCCCCEEECcCCCCc
Confidence 4566 787777665444333567888877764
No 270
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=34.99 E-value=27 Score=24.49 Aligned_cols=26 Identities=19% Similarity=0.441 Sum_probs=19.6
Q ss_pred ccCCCCCc-ceeccCCCCceeec-CccEEE
Q 026529 199 TRCPGCGN-CIERKKGCRIMFCR-FIFLSL 226 (237)
Q Consensus 199 k~CP~C~~-~iek~~GCnhm~C~-C~~cf~ 226 (237)
-.||.|.. .+..+++ +|.|. |++.|.
T Consensus 4 p~cp~c~sEytYed~~--~~~cpec~~ew~ 31 (112)
T COG2824 4 PPCPKCNSEYTYEDGG--QLICPECAHEWN 31 (112)
T ss_pred CCCCccCCceEEecCc--eEeCchhccccc
Confidence 57999966 4445566 99997 998885
No 271
>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=34.95 E-value=15 Score=27.95 Aligned_cols=46 Identities=26% Similarity=0.504 Sum_probs=25.2
Q ss_pred ccccccccccccCCC-CCChhhhhccccchHHHHHHHHhCCcccCCCCCc
Q 026529 158 KQWFCFQCKLAWHAG-YRCEESGNLRDRNDIAFGKLLEKMNWTRCPGCGN 206 (237)
Q Consensus 158 ~~~~C~~C~~~~H~~-~~C~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~ 206 (237)
-.-||..|....|.. ..|.+.... -...+.++......|+|++|++
T Consensus 113 ~~wyc~~c~~~~~e~~f~~~d~~~~---~~~~~~~f~~~~~~rtC~~Cg~ 159 (159)
T TIGR03037 113 FQWFCPQCGHKLHRAEVQLENIVTD---LPPVFEHFYSNEDARTCKNCGH 159 (159)
T ss_pred eEEECCCCCCeEEEEEEEecChhhh---hHHHHHHHhCChhhccCCccCC
Confidence 334444555554532 234433221 1234556666778899999985
No 272
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=34.94 E-value=27 Score=29.01 Aligned_cols=24 Identities=33% Similarity=0.713 Sum_probs=18.6
Q ss_pred ccCCCCCcceecc--CCCCceeec-Cc
Q 026529 199 TRCPGCGNCIERK--KGCRIMFCR-FI 222 (237)
Q Consensus 199 k~CP~C~~~iek~--~GCnhm~C~-C~ 222 (237)
++||.|+..|.+. +|=.-..|. |.
T Consensus 246 ~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 272 (274)
T PRK01103 246 EPCRRCGTPIEKIKQGGRSTFFCPRCQ 272 (274)
T ss_pred CCCCCCCCeeEEEEECCCCcEECcCCC
Confidence 6899999999986 676666664 63
No 273
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=34.75 E-value=50 Score=25.22 Aligned_cols=35 Identities=29% Similarity=0.551 Sum_probs=22.6
Q ss_pred CCcccCCCCCCCceeecccccc--C---------CcCcccCccccccc
Q 026529 125 LERSYCPNRNCMAVMVNECEEI--G---------RVKKAQCPKCKQWF 161 (237)
Q Consensus 125 ~~~~~Cp~~~C~~~~~~~~~~~--~---------~~~~~~C~~C~~~~ 161 (237)
+....|| .|++.+......+ + ......||.|++.|
T Consensus 95 ~e~~RCp--~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiY 140 (165)
T COG1656 95 PEFSRCP--ECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIY 140 (165)
T ss_pred cccccCc--ccCCEeccCcHHHHhhccchhhhhcccceeECCCCcccc
Confidence 5578899 9999887655432 0 12344587777765
No 274
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=34.67 E-value=27 Score=29.01 Aligned_cols=25 Identities=36% Similarity=0.696 Sum_probs=19.8
Q ss_pred cccCCCCCcceecc--CCCCceeec-Cc
Q 026529 198 WTRCPGCGNCIERK--KGCRIMFCR-FI 222 (237)
Q Consensus 198 ~k~CP~C~~~iek~--~GCnhm~C~-C~ 222 (237)
-+.||.|+..|++. +|=.--.|. |.
T Consensus 235 g~pC~~Cg~~I~~~~~~gR~ty~Cp~CQ 262 (269)
T PRK14811 235 GQPCPRCGTPIEKIVVGGRGTHFCPQCQ 262 (269)
T ss_pred cCCCCcCCCeeEEEEECCCCcEECCCCc
Confidence 37999999999986 776767775 74
No 275
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=34.61 E-value=24 Score=21.11 Aligned_cols=15 Identities=40% Similarity=0.758 Sum_probs=10.4
Q ss_pred hCCcccCCCCCccee
Q 026529 195 KMNWTRCPGCGNCIE 209 (237)
Q Consensus 195 ~~~~k~CP~C~~~ie 209 (237)
.....+||.|+..|.
T Consensus 21 ~~~~irCp~Cg~rIl 35 (49)
T COG1996 21 ETRGIRCPYCGSRIL 35 (49)
T ss_pred ccCceeCCCCCcEEE
Confidence 345578888887664
No 276
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=34.58 E-value=38 Score=20.33 Aligned_cols=30 Identities=27% Similarity=0.614 Sum_probs=21.3
Q ss_pred ccccccccCCCCccccccCCCCCcchHHHHHHH
Q 026529 40 TCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKY 72 (237)
Q Consensus 40 ~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~ 72 (237)
.|.||-.++.....+ .+.=| ..|.+|+.+.
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 489999887543322 34556 7999999886
No 277
>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=34.19 E-value=25 Score=16.09 Aligned_cols=16 Identities=31% Similarity=0.717 Sum_probs=11.8
Q ss_pred cccccccccCCCCCCh
Q 026529 161 FCFQCKLAWHAGYRCE 176 (237)
Q Consensus 161 ~C~~C~~~~H~~~~C~ 176 (237)
.|+.|++.-|....|.
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 4788888888766664
No 278
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=34.10 E-value=28 Score=28.92 Aligned_cols=25 Identities=24% Similarity=0.448 Sum_probs=18.9
Q ss_pred cccCCCCCcceecc--CCCCceeec-Cc
Q 026529 198 WTRCPGCGNCIERK--KGCRIMFCR-FI 222 (237)
Q Consensus 198 ~k~CP~C~~~iek~--~GCnhm~C~-C~ 222 (237)
-+.||+|+..|++. +|=.--.|. |.
T Consensus 244 g~pCprCG~~I~~~~~~gR~t~~CP~CQ 271 (272)
T PRK14810 244 GEPCLNCKTPIRRVVVAGRSSHYCPHCQ 271 (272)
T ss_pred CCcCCCCCCeeEEEEECCCccEECcCCc
Confidence 37999999999986 676656664 53
No 279
>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=33.87 E-value=29 Score=28.81 Aligned_cols=23 Identities=35% Similarity=0.717 Sum_probs=18.3
Q ss_pred ccCCCCCcceecc--CCCCceeec-C
Q 026529 199 TRCPGCGNCIERK--KGCRIMFCR-F 221 (237)
Q Consensus 199 k~CP~C~~~iek~--~GCnhm~C~-C 221 (237)
+.||.|+..|.+. +|=.-..|. |
T Consensus 246 ~pC~~Cg~~I~~~~~~gR~t~~CP~C 271 (272)
T TIGR00577 246 EPCRRCGTPIEKIKVGGRGTHFCPQC 271 (272)
T ss_pred CCCCCCCCeeEEEEECCCCCEECCCC
Confidence 6999999999986 676666664 5
No 280
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=33.82 E-value=18 Score=30.52 Aligned_cols=30 Identities=20% Similarity=0.461 Sum_probs=23.7
Q ss_pred cccCCCCCCCceeeccccccCCcCcccCccccccc
Q 026529 127 RSYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQWF 161 (237)
Q Consensus 127 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 161 (237)
+..|| .|+..+....-. .+...||.|++.+
T Consensus 38 w~kc~--~C~~~~~~~~l~---~~~~vcp~c~~h~ 67 (296)
T CHL00174 38 WVQCE--NCYGLNYKKFLK---SKMNICEQCGYHL 67 (296)
T ss_pred eeECC--CccchhhHHHHH---HcCCCCCCCCCCc
Confidence 57788 999988887764 4678899999855
No 281
>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=33.71 E-value=46 Score=30.38 Aligned_cols=34 Identities=29% Similarity=0.603 Sum_probs=24.2
Q ss_pred cCCCCCCCceeeccccccCCcCcccCcccccc-----cccccccc
Q 026529 129 YCPNRNCMAVMVNECEEIGRVKKAQCPKCKQW-----FCFQCKLA 168 (237)
Q Consensus 129 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~-----~C~~C~~~ 168 (237)
.|| .|+..+..... ...+.|..||+. .|..|+..
T Consensus 224 ~C~--~C~~~l~~h~~----~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 224 CCP--NCDVSLTYHKK----EGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred CCC--CCCCceEEecC----CCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 366 77777766654 367889999877 48888764
No 282
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=33.68 E-value=17 Score=24.69 Aligned_cols=13 Identities=8% Similarity=-0.169 Sum_probs=6.3
Q ss_pred CCCccccccCCCh
Q 026529 95 FLDPLACKPTIPS 107 (237)
Q Consensus 95 ~~~~~~i~~~l~~ 107 (237)
++....+..+++.
T Consensus 18 plt~~ei~~~~~~ 30 (97)
T COG3357 18 PLTVAEIFELLNG 30 (97)
T ss_pred cchHHHHHHHHcC
Confidence 3444555555553
No 283
>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=33.62 E-value=21 Score=21.33 Aligned_cols=47 Identities=23% Similarity=0.636 Sum_probs=24.1
Q ss_pred cccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCC
Q 026529 39 FTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQ 94 (237)
Q Consensus 39 ~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~ 94 (237)
+.|+|-+..+..+ .....|.|.-|.| +..|++..... ...+||. |++
T Consensus 3 L~CPls~~~i~~P---~Rg~~C~H~~CFD-l~~fl~~~~~~---~~W~CPi--C~~ 49 (50)
T PF02891_consen 3 LRCPLSFQRIRIP---VRGKNCKHLQCFD-LESFLESNQRT---PKWKCPI--CNK 49 (50)
T ss_dssp SB-TTTSSB-SSE---EEETT--SS--EE-HHHHHHHHHHS------B-TT--T--
T ss_pred eeCCCCCCEEEeC---ccCCcCcccceEC-HHHHHHHhhcc---CCeECcC--CcC
Confidence 4688887776443 2367899998744 67788777654 2378998 875
No 284
>PRK10445 endonuclease VIII; Provisional
Probab=33.57 E-value=29 Score=28.64 Aligned_cols=24 Identities=25% Similarity=0.650 Sum_probs=18.9
Q ss_pred ccCCCCCcceecc--CCCCceeec-Cc
Q 026529 199 TRCPGCGNCIERK--KGCRIMFCR-FI 222 (237)
Q Consensus 199 k~CP~C~~~iek~--~GCnhm~C~-C~ 222 (237)
+.||.|+..|++. +|=.-..|. |.
T Consensus 236 ~~Cp~Cg~~I~~~~~~gR~t~~CP~CQ 262 (263)
T PRK10445 236 EACERCGGIIEKTTLSSRPFYWCPGCQ 262 (263)
T ss_pred CCCCCCCCEeEEEEECCCCcEECCCCc
Confidence 7999999999986 776666664 63
No 285
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=33.45 E-value=37 Score=22.09 Aligned_cols=17 Identities=29% Similarity=0.495 Sum_probs=12.5
Q ss_pred cccCCCCCCCceeeccc
Q 026529 127 RSYCPNRNCMAVMVNEC 143 (237)
Q Consensus 127 ~~~Cp~~~C~~~~~~~~ 143 (237)
+..|.|..|+..+....
T Consensus 27 Y~qC~N~eCg~tF~t~e 43 (72)
T PRK09678 27 YHQCQNVNCSATFITYE 43 (72)
T ss_pred eeecCCCCCCCEEEEEE
Confidence 46799999997766544
No 286
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=33.12 E-value=30 Score=28.95 Aligned_cols=24 Identities=33% Similarity=0.664 Sum_probs=19.1
Q ss_pred ccCCCCCcceecc--CCCCceeec-Cc
Q 026529 199 TRCPGCGNCIERK--KGCRIMFCR-FI 222 (237)
Q Consensus 199 k~CP~C~~~iek~--~GCnhm~C~-C~ 222 (237)
+.||.|+..|.+. +|=.-..|. |.
T Consensus 255 ~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 281 (282)
T PRK13945 255 KPCRKCGTPIERIKLAGRSTHWCPNCQ 281 (282)
T ss_pred CCCCcCCCeeEEEEECCCccEECCCCc
Confidence 7999999999986 776666774 63
No 287
>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=33.09 E-value=22 Score=18.86 Aligned_cols=9 Identities=44% Similarity=1.213 Sum_probs=6.3
Q ss_pred cCCCCCcce
Q 026529 200 RCPGCGNCI 208 (237)
Q Consensus 200 ~CP~C~~~i 208 (237)
-||+|++.+
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 288
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=33.05 E-value=21 Score=29.27 Aligned_cols=50 Identities=30% Similarity=0.772 Sum_probs=26.9
Q ss_pred CcccCccc---ccccccccccccCCCCCChhhhhccccchHHHHHHHHhCCcccCCCCCcceecc
Q 026529 150 KKAQCPKC---KQWFCFQCKLAWHAGYRCEESGNLRDRNDIAFGKLLEKMNWTRCPGCGNCIERK 211 (237)
Q Consensus 150 ~~~~C~~C---~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~~iek~ 211 (237)
..+.|.+| |...|++|+.-+ |.+..+ ...+ ++ .+....+||+|+..+.-.
T Consensus 170 E~~KC~SCNrlGq~sCLRCK~cf-----CddHvr-----rKg~-ky-~k~k~~PCPKCg~et~eT 222 (314)
T PF06524_consen 170 ETFKCQSCNRLGQYSCLRCKICF-----CDDHVR-----RKGF-KY-EKGKPIPCPKCGYETQET 222 (314)
T ss_pred ccccccccccccchhhhheeeee-----hhhhhh-----hccc-cc-ccCCCCCCCCCCCccccc
Confidence 45556666 566777777543 222221 0111 11 133557999999877543
No 289
>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=32.96 E-value=31 Score=21.10 Aligned_cols=27 Identities=26% Similarity=0.658 Sum_probs=15.9
Q ss_pred cCCCcccCCCCCCCceeeccccccCCcCcccCcccccc
Q 026529 123 LGLERSYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQW 160 (237)
Q Consensus 123 ~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 160 (237)
..+.+..|| .|+.+..+. ..|+.||++
T Consensus 22 ~~p~l~~C~--~cG~~~~~H---------~vc~~cG~Y 48 (55)
T TIGR01031 22 TAPTLVVCP--NCGEFKLPH---------RVCPSCGYY 48 (55)
T ss_pred cCCcceECC--CCCCcccCe---------eECCccCeE
Confidence 345667777 777665443 336666643
No 290
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=32.70 E-value=41 Score=28.50 Aligned_cols=55 Identities=15% Similarity=0.299 Sum_probs=36.7
Q ss_pred CCCcccccccccCCCCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCCCc
Q 026529 36 DGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFLDP 98 (237)
Q Consensus 36 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~~ 98 (237)
.+.|.||+=-+.-.. ++.+.++.|||++=++=++..-+ + +...++||- |...-..
T Consensus 334 Hs~FiCPVlKe~~t~-ENpP~ml~CgHVIskeal~~LS~----n-G~~~FKCPY--CP~~~~~ 388 (396)
T COG5109 334 HSLFICPVLKELCTD-ENPPVMLECGHVISKEALSVLSQ----N-GVLSFKCPY--CPEMSKY 388 (396)
T ss_pred cceeeccccHhhhcc-cCCCeeeeccceeeHHHHHHHhh----c-CcEEeeCCC--CCcchhh
Confidence 556789986655433 34456899999987766554433 2 455899998 8864333
No 291
>PRK02935 hypothetical protein; Provisional
Probab=32.11 E-value=30 Score=24.22 Aligned_cols=21 Identities=24% Similarity=0.768 Sum_probs=11.1
Q ss_pred CcccCcccccc--------cccccccccC
Q 026529 150 KKAQCPKCKQW--------FCFQCKLAWH 170 (237)
Q Consensus 150 ~~~~C~~C~~~--------~C~~C~~~~H 170 (237)
..+.||.|++. .|..|++|.+
T Consensus 69 vqV~CP~C~K~TKmLGrvD~CM~C~~PLT 97 (110)
T PRK02935 69 VQVICPSCEKPTKMLGRVDACMHCNQPLT 97 (110)
T ss_pred eeeECCCCCchhhhccceeecCcCCCcCC
Confidence 44555555443 3666666554
No 292
>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=32.11 E-value=48 Score=16.76 Aligned_cols=22 Identities=14% Similarity=0.520 Sum_probs=16.5
Q ss_pred CCCceeeccccccCCcCcccCccccc
Q 026529 134 NCMAVMVNECEEIGRVKKAQCPKCKQ 159 (237)
Q Consensus 134 ~C~~~~~~~~~~~~~~~~~~C~~C~~ 159 (237)
+|...+....+. ..++|..|++
T Consensus 3 ~Cr~~L~yp~GA----~sVrCa~C~~ 24 (25)
T PF06943_consen 3 GCRTLLMYPRGA----PSVRCACCHT 24 (25)
T ss_pred CCCceEEcCCCC----CCeECCccCc
Confidence 677777777664 7889988865
No 293
>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=31.94 E-value=28 Score=19.52 Aligned_cols=14 Identities=14% Similarity=0.287 Sum_probs=9.5
Q ss_pred CcCcccCccccccc
Q 026529 148 RVKKAQCPKCKQWF 161 (237)
Q Consensus 148 ~~~~~~C~~C~~~~ 161 (237)
....+.|..|++.|
T Consensus 25 ~T~fy~C~~C~~~w 38 (39)
T PF01096_consen 25 MTLFYVCCNCGHRW 38 (39)
T ss_dssp SEEEEEESSSTEEE
T ss_pred CeEEEEeCCCCCee
Confidence 35667788887754
No 294
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=31.91 E-value=22 Score=29.48 Aligned_cols=34 Identities=24% Similarity=0.496 Sum_probs=26.5
Q ss_pred CCcccCCCCCCCceeeccccccCCcCcccCccccccccc
Q 026529 125 LERSYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQWFCF 163 (237)
Q Consensus 125 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~ 163 (237)
.-+..|| .|+..+...+.. .+...||.|++.+=.
T Consensus 26 ~lw~KCp--~c~~~~y~~eL~---~n~~vcp~c~~h~ri 59 (294)
T COG0777 26 GLWTKCP--SCGEMLYRKELE---SNLKVCPKCGHHMRI 59 (294)
T ss_pred CceeECC--CccceeeHHHHH---hhhhcccccCccccc
Confidence 3357798 999999888765 578899999886633
No 295
>PF10764 Gin: Inhibitor of sigma-G Gin; InterPro: IPR019700 Gin allows sigma-F to delay late forespore transcription by preventing sigma-G to take over before the cell has reached a critical stage of development. Gin is also known as CsfB [].
Probab=31.81 E-value=29 Score=20.42 Aligned_cols=35 Identities=20% Similarity=0.515 Sum_probs=25.9
Q ss_pred ccccccccCCCCccccccCCCCCcchHHHHHHHHHhcccc
Q 026529 40 TCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYIEVKVRD 79 (237)
Q Consensus 40 ~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~ 79 (237)
.|.||-..... .+ .--+..+|.+|-+..+.....+
T Consensus 1 ~CiiC~~~~~~--GI---~I~~~fIC~~CE~~iv~~~~~d 35 (46)
T PF10764_consen 1 KCIICGKEKEE--GI---HIYGKFICSDCEKEIVNTETDD 35 (46)
T ss_pred CeEeCCCcCCC--CE---EEECeEehHHHHHHhccCCCCC
Confidence 38888877743 22 2347889999999999887765
No 296
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=31.72 E-value=38 Score=18.13 Aligned_cols=22 Identities=32% Similarity=0.685 Sum_probs=13.5
Q ss_pred CCCCCCCceeeccccccCCcCcccCccccc
Q 026529 130 CPNRNCMAVMVNECEEIGRVKKAQCPKCKQ 159 (237)
Q Consensus 130 Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 159 (237)
|+ .|+.++.... ....||.|+.
T Consensus 4 C~--~CGy~y~~~~------~~~~CP~Cg~ 25 (33)
T cd00350 4 CP--VCGYIYDGEE------APWVCPVCGA 25 (33)
T ss_pred CC--CCCCEECCCc------CCCcCcCCCC
Confidence 55 6776665432 3457887775
No 297
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=31.61 E-value=37 Score=27.94 Aligned_cols=28 Identities=21% Similarity=0.307 Sum_probs=21.5
Q ss_pred CCcccCCCCCcceeccCCCCceeec-Ccc
Q 026529 196 MNWTRCPGCGNCIERKKGCRIMFCR-FIF 223 (237)
Q Consensus 196 ~~~k~CP~C~~~iek~~GCnhm~C~-C~~ 223 (237)
...+.||.|+..+....|=..+.|. ||+
T Consensus 97 ~~~~fC~~CG~~~~~~~~~~~~~C~~c~~ 125 (256)
T PRK00241 97 RSHRFCGYCGHPMHPSKTEWAMLCPHCRE 125 (256)
T ss_pred hcCccccccCCCCeecCCceeEECCCCCC
Confidence 3569999999998776544678896 973
No 298
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=31.57 E-value=81 Score=23.01 Aligned_cols=36 Identities=19% Similarity=0.419 Sum_probs=22.8
Q ss_pred CCcccCCCCCCCceeec-cccccCCcCcccCcccccccc
Q 026529 125 LERSYCPNRNCMAVMVN-ECEEIGRVKKAQCPKCKQWFC 162 (237)
Q Consensus 125 ~~~~~Cp~~~C~~~~~~-~~~~~~~~~~~~C~~C~~~~C 162 (237)
....+|| .|...... ...........+|+.|+..|=
T Consensus 28 ~~~~~cP--~C~s~~~~k~g~~~~~~qRyrC~~C~~tf~ 64 (129)
T COG3677 28 ITKVNCP--RCKSSNVVKIGGIRRGHQRYKCKSCGSTFT 64 (129)
T ss_pred cccCcCC--CCCccceeeECCccccccccccCCcCccee
Confidence 3347899 88876622 222222257889999998873
No 299
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=30.72 E-value=27 Score=29.47 Aligned_cols=33 Identities=27% Similarity=0.631 Sum_probs=21.7
Q ss_pred CcccccccccCCCCccccccCCCCCcchHHHHHHHH
Q 026529 38 TFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYI 73 (237)
Q Consensus 38 ~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~ 73 (237)
...|.-|--.+ ..+-.+.+|.|+||.+|.+..-
T Consensus 90 VHfCd~Cd~PI---~IYGRmIPCkHvFCl~CAr~~~ 122 (389)
T KOG2932|consen 90 VHFCDRCDFPI---AIYGRMIPCKHVFCLECARSDS 122 (389)
T ss_pred eEeecccCCcc---eeeecccccchhhhhhhhhcCc
Confidence 45677774333 1222477999999999987543
No 300
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=30.03 E-value=39 Score=19.05 Aligned_cols=14 Identities=21% Similarity=0.430 Sum_probs=8.8
Q ss_pred CcCcccCccccccc
Q 026529 148 RVKKAQCPKCKQWF 161 (237)
Q Consensus 148 ~~~~~~C~~C~~~~ 161 (237)
....+.|..|++.|
T Consensus 25 mT~fy~C~~C~~~w 38 (40)
T smart00440 25 MTVFYVCTKCGHRW 38 (40)
T ss_pred CeEEEEeCCCCCEe
Confidence 35667777776643
No 301
>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=29.57 E-value=80 Score=20.86 Aligned_cols=32 Identities=19% Similarity=0.541 Sum_probs=21.9
Q ss_pred ccCCCCCCCceeeccccccCCcCcccCcccccccccc
Q 026529 128 SYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQWFCFQ 164 (237)
Q Consensus 128 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~ 164 (237)
+.|| +|-.+-..-... ...+.|+.|+...|..
T Consensus 35 VkC~--gc~~iT~vfSHa---qtvVvc~~c~~il~~~ 66 (84)
T KOG1779|consen 35 VKCP--GCFKITTVFSHA---QTVVVCEGCSTILCQP 66 (84)
T ss_pred EEcC--CceEEEEEeecC---ceEEEcCCCceEEEEe
Confidence 7788 776554433322 5788999999988853
No 302
>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=29.45 E-value=12 Score=19.01 Aligned_cols=19 Identities=16% Similarity=0.436 Sum_probs=12.3
Q ss_pred ccCCCCcCCCCCCccccccCC
Q 026529 85 IECPGLHCEQFLDPLACKPTI 105 (237)
Q Consensus 85 i~CP~~~C~~~~~~~~i~~~l 105 (237)
+.||. |.+.++...+...|
T Consensus 2 v~CPi--C~~~v~~~~in~HL 20 (26)
T smart00734 2 VQCPV--CFREVPENLINSHL 20 (26)
T ss_pred CcCCC--CcCcccHHHHHHHH
Confidence 57888 88877555554443
No 303
>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=29.24 E-value=25 Score=21.18 Aligned_cols=10 Identities=30% Similarity=0.906 Sum_probs=5.9
Q ss_pred ccCCCCCcce
Q 026529 199 TRCPGCGNCI 208 (237)
Q Consensus 199 k~CP~C~~~i 208 (237)
.+||+|++.-
T Consensus 25 IKCpRC~tiN 34 (51)
T PF10122_consen 25 IKCPRCKTIN 34 (51)
T ss_pred EECCCCCccc
Confidence 5666666543
No 304
>PRK12495 hypothetical protein; Provisional
Probab=29.13 E-value=74 Score=25.52 Aligned_cols=28 Identities=21% Similarity=0.564 Sum_probs=18.0
Q ss_pred CCcccCCCCCCCceeeccccccCCcCcccCcccccc
Q 026529 125 LERSYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQW 160 (237)
Q Consensus 125 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 160 (237)
....+|+ .|+..|+..+ -.++|+.|+..
T Consensus 40 msa~hC~--~CG~PIpa~p------G~~~Cp~CQ~~ 67 (226)
T PRK12495 40 MTNAHCD--ECGDPIFRHD------GQEFCPTCQQP 67 (226)
T ss_pred cchhhcc--cccCcccCCC------CeeECCCCCCc
Confidence 3458999 9999888332 34556655543
No 305
>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=28.91 E-value=53 Score=20.07 Aligned_cols=25 Identities=28% Similarity=0.648 Sum_probs=15.4
Q ss_pred CCCcccCCCCCCCceeeccccccCCcCcccCccccc
Q 026529 124 GLERSYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQ 159 (237)
Q Consensus 124 ~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 159 (237)
.+....|| .|+.+..+. ..|+.||+
T Consensus 23 ~~~l~~c~--~cg~~~~~H---------~vc~~cG~ 47 (56)
T PF01783_consen 23 APNLVKCP--NCGEPKLPH---------RVCPSCGY 47 (56)
T ss_dssp TTSEEESS--SSSSEESTT---------SBCTTTBB
T ss_pred ccceeeec--cCCCEeccc---------EeeCCCCe
Confidence 35667888 777665443 34666664
No 306
>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=28.59 E-value=21 Score=16.88 Aligned_cols=9 Identities=44% Similarity=1.261 Sum_probs=5.3
Q ss_pred cCccccccc
Q 026529 153 QCPKCKQWF 161 (237)
Q Consensus 153 ~C~~C~~~~ 161 (237)
.|+.|+..|
T Consensus 2 ~C~~C~~~f 10 (23)
T PF00096_consen 2 KCPICGKSF 10 (23)
T ss_dssp EETTTTEEE
T ss_pred CCCCCCCcc
Confidence 466666655
No 307
>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=28.59 E-value=30 Score=19.41 Aligned_cols=21 Identities=33% Similarity=0.948 Sum_probs=14.3
Q ss_pred ccCCCCCcceecc---CCCCceeec
Q 026529 199 TRCPGCGNCIERK---KGCRIMFCR 220 (237)
Q Consensus 199 k~CP~C~~~iek~---~GCnhm~C~ 220 (237)
+.||.|+..+... .| ..+.|+
T Consensus 2 ~~CP~Cg~~lv~r~~k~g-~F~~Cs 25 (39)
T PF01396_consen 2 EKCPKCGGPLVLRRGKKG-KFLGCS 25 (39)
T ss_pred cCCCCCCceeEEEECCCC-CEEECC
Confidence 5799999755443 45 667773
No 308
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=28.27 E-value=65 Score=23.07 Aligned_cols=47 Identities=17% Similarity=0.332 Sum_probs=28.5
Q ss_pred CChhHHHHHHHHHHHHhhc---------CCCcccCCCCCCCceeeccccccCCcCcccCccccc
Q 026529 105 IPSSLFIKWCDHLCEDYVL---------GLERSYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQ 159 (237)
Q Consensus 105 l~~~~~~~~~~~~~~~~~~---------~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 159 (237)
+.+++++.-.+...+.++. .+...||. +|+..+..... .+.||.|+.
T Consensus 39 v~~~~l~FaFev~~egT~aega~l~Ie~~p~~~~C~--~C~~~~~~e~~------~~~CP~C~s 94 (115)
T COG0375 39 VEPEALRFAFEVVAEGTIAEGAELHIEEEPAECWCL--DCGQEVELEEL------DYRCPKCGS 94 (115)
T ss_pred cCHHHHHHHHHHHhccCcccCCEEEEEEeccEEEec--cCCCeecchhh------eeECCCCCC
Confidence 3455555544544444332 24458899 99888777754 344888874
No 309
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=28.07 E-value=46 Score=20.75 Aligned_cols=30 Identities=23% Similarity=0.483 Sum_probs=21.0
Q ss_pred ccCCCCCCCceeeccccccCCcCcccCcccccc
Q 026529 128 SYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQW 160 (237)
Q Consensus 128 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 160 (237)
=.|.+.+|++++..+-.. ...-.||-|+..
T Consensus 19 W~Ct~e~C~gWmR~nFs~---~~~p~CPlC~s~ 48 (59)
T PF14169_consen 19 WECTSEDCNGWMRDNFSF---EEEPVCPLCKSP 48 (59)
T ss_pred EEeCCCCCCccccccccc---CCCccCCCcCCc
Confidence 459999999999866554 345567777653
No 310
>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=28.04 E-value=35 Score=27.65 Aligned_cols=14 Identities=36% Similarity=0.672 Sum_probs=8.0
Q ss_pred CcccCCCCCcceec
Q 026529 197 NWTRCPGCGNCIER 210 (237)
Q Consensus 197 ~~k~CP~C~~~iek 210 (237)
....||.|+....+
T Consensus 34 ~v~~C~~Cg~~~~~ 47 (236)
T PF04981_consen 34 EVTICPKCGRYRIG 47 (236)
T ss_pred CceECCCCCCEECC
Confidence 44666666665544
No 311
>PLN02189 cellulose synthase
Probab=27.91 E-value=51 Score=32.70 Aligned_cols=52 Identities=27% Similarity=0.677 Sum_probs=35.2
Q ss_pred CCCcccccccccCC---CCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCC
Q 026529 36 DGTFTCDICIEPMS---VNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFL 96 (237)
Q Consensus 36 ~~~~~C~IC~~~~~---~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~ 96 (237)
.....|.||-|++. ..+.|+..-.|+-..|+.|. .|-. ++| .-.||+ |+...
T Consensus 32 ~~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cy-eyer---~eg---~q~Cpq--Ckt~Y 86 (1040)
T PLN02189 32 LDGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCY-EYER---REG---TQNCPQ--CKTRY 86 (1040)
T ss_pred ccCccccccccccCcCCCCCEEEeeccCCCccccchh-hhhh---hcC---CccCcc--cCCch
Confidence 34558999999964 23456555569999999999 4443 232 247998 88643
No 312
>PRK08332 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=27.84 E-value=34 Score=35.95 Aligned_cols=25 Identities=24% Similarity=0.595 Sum_probs=21.0
Q ss_pred ccCCCCCcc------eeccCCCCceeec-CccEE
Q 026529 199 TRCPGCGNC------IERKKGCRIMFCR-FIFLS 225 (237)
Q Consensus 199 k~CP~C~~~------iek~~GCnhm~C~-C~~cf 225 (237)
..||.|+.. +...+||. +|. |||.=
T Consensus 1705 ~~cp~c~~~~~~~~~~~~~~gc~--~c~~cg~s~ 1736 (1740)
T PRK08332 1705 VYCPVCYEKEGKLVELRMESGCA--TCPVCGWSK 1736 (1740)
T ss_pred CCCCCCCCCCCcceeeEecCCce--eCCCCCCcc
Confidence 449999999 88899997 897 99753
No 313
>PF02146 SIR2: Sir2 family; InterPro: IPR003000 These sequences represent the Sirtuin (Sir2-related) family of NAD+-dependent deacetylases. This family of enzymes is broadly conserved from bacteria to humans. In yeast, Sir2 proteins form complexes with other proteins to silence chromatin by accessing histones and deacetylating them. Sir2 proteins have been proposed to play a role in silencing, chromosome stability and ageing []. The bacterial enzyme CobB, an homologue of Sir2, is a phosphoribosyltransferase []. An in vitro ADP ribosyltransferase activity has also been associated with human members of this family []. Sir2-like enzymes employ NAD+ as a cosubstrate in deacetylation reactions [] and catalyse a reaction in which the cleavage of NAD(+)and histone and/or protein deacetylation are coupled to the formation of O-acetyl-ADP-ribose, a novel metabolite. The dependence of the reaction on both NAD(+) and the generation of this potential second messenger offers new clues to understanding the function and regulation of nuclear, cytoplasmic and mitochondrial Sir2-like enzymes []. Silent Information Regulator protein of Saccharomyces cerevisiae (Sir2) is one of several factors critical for silencing at least three loci. Among them, it is unique because it silences the rDNA as well as the mating type loci and telomeres []. Sir2 interacts in a complex with itself and with Sir3 and Sir4, two proteins that are able to interact with nucleosomes. In addition Sir2 also interacts with ubiquitination factors and/or complexes []. Homologues of Sir2 share a core domain including the GAG and NID motifs and a putative C4 Zinc finger. The regions containing these three conserved motifs are individually essential for Sir2 silencing function, as are the four cysteins []. In addition, the conserved residues HG next to the putative Zn finger have been shown to be essential for the ADP ribosyltransferase activity []. ; GO: 0008270 zinc ion binding, 0070403 NAD+ binding, 0006476 protein deacetylation; PDB: 1S5P_A 3PKI_E 3PKJ_F 3K35_A 1ICI_A 1M2K_A 1M2G_A 1M2N_B 1M2H_A 1M2J_A ....
Probab=27.23 E-value=56 Score=25.02 Aligned_cols=16 Identities=31% Similarity=0.899 Sum_probs=11.1
Q ss_pred HHhCCcccCCCCCcce
Q 026529 193 LEKMNWTRCPGCGNCI 208 (237)
Q Consensus 193 ~~~~~~k~CP~C~~~i 208 (237)
.......+||.|+..+
T Consensus 124 ~~~~~~~~C~~C~~~l 139 (178)
T PF02146_consen 124 IDEEEPPRCPKCGGLL 139 (178)
T ss_dssp HHTTSSCBCTTTSCBE
T ss_pred ccccccccccccCccC
Confidence 3445567999998765
No 314
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=27.18 E-value=45 Score=20.35 Aligned_cols=34 Identities=29% Similarity=0.426 Sum_probs=17.5
Q ss_pred CcccCCCCCCCceeecc--ccccCCcCcccCccccccc
Q 026529 126 ERSYCPNRNCMAVMVNE--CEEIGRVKKAQCPKCKQWF 161 (237)
Q Consensus 126 ~~~~Cp~~~C~~~~~~~--~~~~~~~~~~~C~~C~~~~ 161 (237)
.++.|| .|++--... ....-...-+.||.|.+.+
T Consensus 3 ~Wi~CP--~CgnKTR~kir~DT~LkNfPlyCpKCK~Et 38 (55)
T PF14205_consen 3 EWILCP--ICGNKTRLKIREDTVLKNFPLYCPKCKQET 38 (55)
T ss_pred eEEECC--CCCCccceeeecCceeccccccCCCCCceE
Confidence 356788 787532221 1111124556677776654
No 315
>PF11682 DUF3279: Protein of unknown function (DUF3279); InterPro: IPR021696 This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.
Probab=27.05 E-value=44 Score=24.43 Aligned_cols=15 Identities=33% Similarity=0.662 Sum_probs=11.0
Q ss_pred ccCCCCCcceeccCC
Q 026529 199 TRCPGCGNCIERKKG 213 (237)
Q Consensus 199 k~CP~C~~~iek~~G 213 (237)
|.||.|+..|.-.++
T Consensus 111 K~C~~C~tGiYS~e~ 125 (128)
T PF11682_consen 111 KYCPKCGTGIYSIEV 125 (128)
T ss_pred EecCCCCCcccceec
Confidence 788888887765544
No 316
>PF14768 RPA_interact_C: Replication protein A interacting C-terminal
Probab=26.84 E-value=58 Score=21.62 Aligned_cols=24 Identities=21% Similarity=0.465 Sum_probs=15.9
Q ss_pred CCCCCcceeccCCCCceeecCccEE
Q 026529 201 CPGCGNCIERKKGCRIMFCRFIFLS 225 (237)
Q Consensus 201 CP~C~~~iek~~GCnhm~C~C~~cf 225 (237)
||-|+...-+..+ +.++|.||+.+
T Consensus 2 CPVC~~~~L~~~~-~~i~C~Cgl~l 25 (82)
T PF14768_consen 2 CPVCQKGNLRENS-NVISCSCGLRL 25 (82)
T ss_pred CCccCCCcccccC-CeEECCCccEE
Confidence 7888876666533 45888887543
No 317
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.81 E-value=39 Score=21.38 Aligned_cols=17 Identities=24% Similarity=0.483 Sum_probs=13.6
Q ss_pred CCcccCCCCCcceeccC
Q 026529 196 MNWTRCPGCGNCIERKK 212 (237)
Q Consensus 196 ~~~k~CP~C~~~iek~~ 212 (237)
....+||.|+.+++...
T Consensus 5 ~~~v~CP~Cgkpv~w~~ 21 (65)
T COG3024 5 RITVPCPTCGKPVVWGE 21 (65)
T ss_pred cccccCCCCCCcccccc
Confidence 34589999999998753
No 318
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=26.54 E-value=29 Score=21.47 Aligned_cols=16 Identities=31% Similarity=0.696 Sum_probs=9.0
Q ss_pred cccCCCCCcceeccCC
Q 026529 198 WTRCPGCGNCIERKKG 213 (237)
Q Consensus 198 ~k~CP~C~~~iek~~G 213 (237)
..+||.|+..++-..+
T Consensus 2 ~v~CP~C~k~~~~~~~ 17 (57)
T PF03884_consen 2 TVKCPICGKPVEWSPE 17 (57)
T ss_dssp EEE-TTT--EEE-SSS
T ss_pred cccCCCCCCeecccCC
Confidence 4689999999987544
No 319
>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=26.25 E-value=32 Score=17.17 Aligned_cols=13 Identities=38% Similarity=0.835 Sum_probs=9.0
Q ss_pred cCcccCccccccc
Q 026529 149 VKKAQCPKCKQWF 161 (237)
Q Consensus 149 ~~~~~C~~C~~~~ 161 (237)
...+.|+.|++.|
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 3557788887765
No 320
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=26.05 E-value=35 Score=19.14 Aligned_cols=18 Identities=28% Similarity=0.748 Sum_probs=14.9
Q ss_pred cccCcccccccccccccc
Q 026529 151 KAQCPKCKQWFCFQCKLA 168 (237)
Q Consensus 151 ~~~C~~C~~~~C~~C~~~ 168 (237)
.+.|..|+..||..-+.+
T Consensus 12 ~f~C~~C~~~FC~~HR~~ 29 (39)
T smart00154 12 GFKCRHCGNLFCGEHRLP 29 (39)
T ss_pred CeECCccCCccccccCCc
Confidence 577999999999877654
No 321
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=26.02 E-value=32 Score=20.89 Aligned_cols=11 Identities=36% Similarity=0.999 Sum_probs=9.1
Q ss_pred ccCCCCCccee
Q 026529 199 TRCPGCGNCIE 209 (237)
Q Consensus 199 k~CP~C~~~ie 209 (237)
++||+|+.+-+
T Consensus 25 ~KCPrCK~vN~ 35 (60)
T COG4416 25 KKCPRCKEVNE 35 (60)
T ss_pred ecCCccceeee
Confidence 89999998654
No 322
>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 PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=25.71 E-value=63 Score=32.24 Aligned_cols=51 Identities=29% Similarity=0.789 Sum_probs=35.2
Q ss_pred CCcccccccccCC---CCccccccCCCCCcchHHHHHHHHHhccccCCcccccCCCCcCCCCC
Q 026529 37 GTFTCDICIEPMS---VNNKFKNNNLCTHPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFL 96 (237)
Q Consensus 37 ~~~~C~IC~~~~~---~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~ 96 (237)
....|.||-|++. +.+.|++-..|+-..|+.|. .|-. ++|+ =.||+ |+...
T Consensus 16 ~~qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCY-EYEr---~eG~---q~CPq--CktrY 69 (1079)
T PLN02638 16 GGQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCY-EYER---KDGN---QSCPQ--CKTKY 69 (1079)
T ss_pred CCceeeecccccCcCCCCCEEEEeccCCCccccchh-hhhh---hcCC---ccCCc--cCCch
Confidence 3458999999963 23456666679999999999 4433 2333 37998 88543
No 324
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=24.85 E-value=50 Score=31.64 Aligned_cols=35 Identities=23% Similarity=0.538 Sum_probs=22.4
Q ss_pred ccCCCCCCCceeeccccccCCcCcccCcccccc-----cccccccc
Q 026529 128 SYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQW-----FCFQCKLA 168 (237)
Q Consensus 128 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~-----~C~~C~~~ 168 (237)
..|| +|...+..... .....|..||+. .|..|+..
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 66666665554 367778888776 47777665
No 325
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=24.77 E-value=45 Score=25.84 Aligned_cols=32 Identities=25% Similarity=0.407 Sum_probs=22.3
Q ss_pred CCCcccCCCCCCCceeeccccccCCcCcccCcccccc
Q 026529 124 GLERSYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQW 160 (237)
Q Consensus 124 ~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 160 (237)
.+.+..|| .|...+..+..- ...+.||.||..
T Consensus 110 ~~~~y~C~--~~~~r~sfdeA~---~~~F~Cp~Cg~~ 141 (176)
T COG1675 110 ENNYYVCP--NCHVKYSFDEAM---ELGFTCPKCGED 141 (176)
T ss_pred cCCceeCC--CCCCcccHHHHH---HhCCCCCCCCch
Confidence 45578896 887777766554 356888888764
No 326
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=24.76 E-value=99 Score=25.85 Aligned_cols=31 Identities=19% Similarity=0.402 Sum_probs=23.4
Q ss_pred CCcccCCCCCCCceeeccccccCCcCcccCccccccc
Q 026529 125 LERSYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQWF 161 (237)
Q Consensus 125 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 161 (237)
...++|+ .|+.-....... ....|+.|+..+
T Consensus 109 ~~~RFCg--~CG~~~~~~~~g----~~~~C~~cg~~~ 139 (279)
T COG2816 109 RSHRFCG--RCGTKTYPREGG----WARVCPKCGHEH 139 (279)
T ss_pred hhCcCCC--CCCCcCccccCc----eeeeCCCCCCcc
Confidence 3357899 999888777664 778899887654
No 327
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=24.43 E-value=54 Score=24.80 Aligned_cols=12 Identities=25% Similarity=0.816 Sum_probs=9.3
Q ss_pred cccCcccccccc
Q 026529 151 KAQCPKCKQWFC 162 (237)
Q Consensus 151 ~~~C~~C~~~~C 162 (237)
...|+.||..|=
T Consensus 28 ~~~c~~c~~~f~ 39 (154)
T PRK00464 28 RRECLACGKRFT 39 (154)
T ss_pred eeeccccCCcce
Confidence 477998888873
No 328
>PF10272 Tmpp129: Putative transmembrane protein precursor; InterPro: IPR018801 This entry consists of proteins conserved from worms to humans. They are purported to be transmembrane protein-precursors but their function is unknown.
Probab=24.32 E-value=63 Score=28.07 Aligned_cols=63 Identities=19% Similarity=0.420 Sum_probs=37.5
Q ss_pred CCCcccccccccCCCCccc-------------cc-----cCCCCCcchHHHHHHHHHhcccc---CCcc--cccCCCCcC
Q 026529 36 DGTFTCDICIEPMSVNNKF-------------KN-----NNLCTHPFCQDCTAKYIEVKVRD---NNTA--KIECPGLHC 92 (237)
Q Consensus 36 ~~~~~C~IC~~~~~~~~~~-------------~~-----~~~C~H~fC~~Cl~~~~~~~i~~---~~~~--~i~CP~~~C 92 (237)
.....|.-|+..-+.-... .. ..-|+-..|.+|+.+|+.++-.+ ..+. ...||. |
T Consensus 269 ~e~e~CigC~~~~~~vkl~k~C~~~~~~g~~~~~~~~C~~C~CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPt--C 346 (358)
T PF10272_consen 269 QELEPCIGCMQAQPNVKLVKRCADEEQEGSPLPNEPPCQQCYCRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPT--C 346 (358)
T ss_pred cccCCccccccCCCCcEEEeccCCcccCCcccccCCCCccccccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCC--C
Confidence 4556799998775432110 00 11234457999999999887754 1222 456666 9
Q ss_pred CCCCCccc
Q 026529 93 EQFLDPLA 100 (237)
Q Consensus 93 ~~~~~~~~ 100 (237)
+..+-.-+
T Consensus 347 Ra~FCilD 354 (358)
T PF10272_consen 347 RAKFCILD 354 (358)
T ss_pred cccceeee
Confidence 98665433
No 329
>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=23.28 E-value=98 Score=19.36 Aligned_cols=13 Identities=15% Similarity=0.613 Sum_probs=9.6
Q ss_pred ccccCCCCcCCCCCC
Q 026529 83 AKIECPGLHCEQFLD 97 (237)
Q Consensus 83 ~~i~CP~~~C~~~~~ 97 (237)
.|++|+. |+.++.
T Consensus 3 iPVRCFT--CGkvi~ 15 (60)
T PF01194_consen 3 IPVRCFT--CGKVIG 15 (60)
T ss_dssp -SSS-ST--TTSBTC
T ss_pred CceecCC--CCCChh
Confidence 5899998 998876
No 330
>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=23.20 E-value=48 Score=17.71 Aligned_cols=11 Identities=27% Similarity=0.869 Sum_probs=7.2
Q ss_pred ccCCCCcCCCC
Q 026529 85 IECPGLHCEQF 95 (237)
Q Consensus 85 i~CP~~~C~~~ 95 (237)
++||.++|...
T Consensus 2 ~~CPtpGCdg~ 12 (31)
T PF01530_consen 2 LKCPTPGCDGS 12 (31)
T ss_dssp TSSSSTT--SC
T ss_pred CcCCCCCCCcc
Confidence 58999999864
No 331
>KOG2789 consensus Putative Zn-finger protein [General function prediction only]
Probab=23.02 E-value=29 Score=30.27 Aligned_cols=35 Identities=20% Similarity=0.541 Sum_probs=27.0
Q ss_pred CCcccccccccCCCCccccccCCCCCcchHHHHHHHH
Q 026529 37 GTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKYI 73 (237)
Q Consensus 37 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~~ 73 (237)
++.+|+|||-.++..... +.-|.-.+|.+|+..+-
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 456999999988764332 56789999999998653
No 332
>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=22.93 E-value=47 Score=20.66 Aligned_cols=38 Identities=21% Similarity=0.551 Sum_probs=27.2
Q ss_pred cCCCCCCCceeeccccccCCcCcccCcccccccccccccccC
Q 026529 129 YCPNRNCMAVMVNECEEIGRVKKAQCPKCKQWFCFQCKLAWH 170 (237)
Q Consensus 129 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H 170 (237)
.|| -|.........+ ..+.-.|..|+...|..|+-...
T Consensus 4 ~CP--lCkt~~n~gsk~--~pNyntCT~Ck~~VCnlCGFNP~ 41 (61)
T PF05715_consen 4 LCP--LCKTTLNVGSKD--PPNYNTCTECKSQVCNLCGFNPT 41 (61)
T ss_pred cCC--cccchhhcCCCC--CCCccHHHHHhhhhhcccCCCCC
Confidence 466 777655443333 35788899999999999997643
No 333
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=22.78 E-value=23 Score=21.22 Aligned_cols=35 Identities=20% Similarity=0.637 Sum_probs=26.7
Q ss_pred CCcccccccccCCCCccccccCCCCCcchHHHHHHH
Q 026529 37 GTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTAKY 72 (237)
Q Consensus 37 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fC~~Cl~~~ 72 (237)
..++|.+|-+..+.. .+..-.-||-.-|..||+.-
T Consensus 6 sry~CDLCn~~~p~~-~LRQCvlCGRWaC~sCW~de 40 (57)
T PF14445_consen 6 SRYSCDLCNSSHPIS-ELRQCVLCGRWACNSCWQDE 40 (57)
T ss_pred hhHhHHhhcccCcHH-HHHHHhhhchhhhhhhhhhh
Confidence 457899999988654 33445679999999999853
No 334
>COG1781 PyrI Aspartate carbamoyltransferase, regulatory subunit [Nucleotide transport and metabolism]
Probab=22.50 E-value=55 Score=24.60 Aligned_cols=37 Identities=22% Similarity=0.377 Sum_probs=19.8
Q ss_pred CCcccCCCCCCCceee-ccccc----cCCcCcccCccccccc
Q 026529 125 LERSYCPNRNCMAVMV-NECEE----IGRVKKAQCPKCKQWF 161 (237)
Q Consensus 125 ~~~~~Cp~~~C~~~~~-~~~~~----~~~~~~~~C~~C~~~~ 161 (237)
.+...||||+|-.--. +.... +.....++|..|.+.+
T Consensus 104 ~gvlkCpN~nCITn~e~pv~s~F~~~~~~~~~lrC~YCe~~~ 145 (153)
T COG1781 104 EGVLRCPNPNCITNAEEPVESKFYVVSKEPLALRCKYCEKTF 145 (153)
T ss_pred ccEEEcCCCCcccCCCccCCccEEEEecCCcEEEEEecCcEe
Confidence 3468999999953222 11000 0013567787776654
No 335
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=22.39 E-value=36 Score=15.74 Aligned_cols=9 Identities=56% Similarity=1.305 Sum_probs=3.8
Q ss_pred cCccccccc
Q 026529 153 QCPKCKQWF 161 (237)
Q Consensus 153 ~C~~C~~~~ 161 (237)
.|+.|+..|
T Consensus 2 ~C~~C~~~~ 10 (24)
T PF13894_consen 2 QCPICGKSF 10 (24)
T ss_dssp E-SSTS-EE
T ss_pred CCcCCCCcC
Confidence 455665554
No 336
>PRK00893 aspartate carbamoyltransferase regulatory subunit; Reviewed
Probab=22.09 E-value=66 Score=24.26 Aligned_cols=34 Identities=26% Similarity=0.476 Sum_probs=20.3
Q ss_pred CCcccCCCCCCCce--------eeccccccCCcCcccCccccccc
Q 026529 125 LERSYCPNRNCMAV--------MVNECEEIGRVKKAQCPKCKQWF 161 (237)
Q Consensus 125 ~~~~~Cp~~~C~~~--------~~~~~~~~~~~~~~~C~~C~~~~ 161 (237)
.+.+.||||+|-.- |...+. .....+|..|...+
T Consensus 103 ~gi~kC~Np~CITn~~E~v~~~F~v~~~---~~~~~rC~YCe~~~ 144 (152)
T PRK00893 103 EGVLKCPNPNCITNTNEPVESRFYVVDK---EPIKLRCKYCEKEF 144 (152)
T ss_pred cceEECCCCCCcCCCCcCcCcEEEEEeC---CCCEEEeeCCCCEe
Confidence 34688999999543 111111 24577787776654
No 337
>PRK06386 replication factor A; Reviewed
Probab=21.94 E-value=42 Score=29.13 Aligned_cols=13 Identities=38% Similarity=0.930 Sum_probs=11.6
Q ss_pred cccCCCCCcceec
Q 026529 198 WTRCPGCGNCIER 210 (237)
Q Consensus 198 ~k~CP~C~~~iek 210 (237)
+++||.|+..+++
T Consensus 236 i~rCP~C~R~l~~ 248 (358)
T PRK06386 236 FTKCSVCNKIIED 248 (358)
T ss_pred EecCcCCCeEccC
Confidence 3899999999996
No 338
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.91 E-value=69 Score=20.09 Aligned_cols=35 Identities=17% Similarity=0.379 Sum_probs=19.0
Q ss_pred cccCCCCCCCceeeccccccCCcCcccCccccccc
Q 026529 127 RSYCPNRNCMAVMVNECEEIGRVKKAQCPKCKQWF 161 (237)
Q Consensus 127 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 161 (237)
.+.|+.++=...-...-.+.+....+.||-|++.|
T Consensus 24 ~l~C~g~~~p~~HPrV~L~mg~~gev~CPYC~t~y 58 (62)
T COG4391 24 PLMCPGPEPPNDHPRVFLDMGDEGEVVCPYCSTRY 58 (62)
T ss_pred eEEcCCCCCCCCCCEEEEEcCCCCcEecCccccEE
Confidence 57888654321111000011236789999999876
No 339
>PF15616 TerY-C: TerY-C metal binding domain
Probab=21.36 E-value=97 Score=22.76 Aligned_cols=23 Identities=39% Similarity=0.883 Sum_probs=15.4
Q ss_pred CcccCCCCCcceec-cCCCCceee
Q 026529 197 NWTRCPGCGNCIER-KKGCRIMFC 219 (237)
Q Consensus 197 ~~k~CP~C~~~iek-~~GCnhm~C 219 (237)
+.--||.|+...-- .-+|.++.|
T Consensus 76 g~PgCP~CGn~~~fa~C~CGkl~C 99 (131)
T PF15616_consen 76 GAPGCPHCGNQYAFAVCGCGKLFC 99 (131)
T ss_pred CCCCCCCCcChhcEEEecCCCEEE
Confidence 45799999998422 245666666
No 340
>PF03563 Bunya_G2: Bunyavirus glycoprotein G2; InterPro: IPR005168 Bunyavirus has three genomic segments: small (S), middle-sized (M), and large (L). The S segment encodes the nucleocapsid and a non-structural protein. The M segment codes for two glycoproteins, G1 and G2, and another non-structural protein (NSm). The L segment codes for an RNA polymerase. This entry represents the polyprotein region forming the G2 glycoprotein, which interacts with the IPR005167 from INTERPRO G1 glycoprotein [].
Probab=21.32 E-value=84 Score=25.97 Aligned_cols=31 Identities=16% Similarity=0.343 Sum_probs=23.0
Q ss_pred HhCCcccCCCCCcceeccCCCCceeecCccEE
Q 026529 194 EKMNWTRCPGCGNCIERKKGCRIMFCRFIFLS 225 (237)
Q Consensus 194 ~~~~~k~CP~C~~~iek~~GCnhm~C~C~~cf 225 (237)
-.+-.|.||+|+-.+.--.-|-. +|.||.-|
T Consensus 230 ynk~ck~C~nC~La~HPFtnC~s-~CvCG~~f 260 (285)
T PF03563_consen 230 YNKSCKKCKNCGLAYHPFTNCGS-HCVCGMKF 260 (285)
T ss_pred HHHHhhhCcccCeeccCCCCCCC-eeeccccc
Confidence 34456999999999977777665 67777544
No 341
>PF04135 Nop10p: Nucleolar RNA-binding protein, Nop10p family; InterPro: IPR007264 H/ACA ribonucleoprotein particles (RNPs) are a family of RNA pseudouridine synthases that specify modification sites through guide RNAs. More than 100 mammalian H/ACA RNAs form an equal number of ribonucleoproteins (RNPs) by associating with the same four core proteins: Cbf5, Gar1, Nhp2 and Nop10. The function of these H/ACA RNPs is essential for biogenesis of the ribosome, splicing of precursor mRNAs (pre-mRNAs), maintenance of telomeres and probably for additional cellular processes []. Recent crystal structures of archaeal H/ACA protein complexes show how the same four proteins accommodate >100 distinct but related H/ACA RNAs []. The complex contains a stable core composed of Cbf5 and Nop10, to which Gar1 and Nhp2 subsequently bind, the complex interacts with snoRNAs []. In eukaryotes Nop10 is a nucleolar protein that is specifically associated with H/ACA snoRNAs. It is essential for normal 18S rRNA production and rRNA pseudouridylation by the ribonucleoprotein particles containing H/ACA snoRNAs (H/ACA snoRNPs). Nop10 is probably necessary for the stability of these RNPs [].; PDB: 2RFK_B 3LWR_B 2HVY_C 3HAX_C 3MQK_B 3LWO_B 3LWV_B 3HAY_C 3HJY_B 2EY4_E ....
Probab=21.29 E-value=79 Score=19.22 Aligned_cols=33 Identities=18% Similarity=0.288 Sum_probs=22.6
Q ss_pred cCCCCcCCCCCCccccccCCChhHHHHHHHHHHHH
Q 026529 86 ECPGLHCEQFLDPLACKPTIPSSLFIKWCDHLCED 120 (237)
Q Consensus 86 ~CP~~~C~~~~~~~~i~~~l~~~~~~~~~~~~~~~ 120 (237)
+||. |+.......=..+-++|-+.+|...+...
T Consensus 19 ~cp~--cG~~T~~ahPaRFSPdDky~~yRi~lKkr 51 (53)
T PF04135_consen 19 KCPP--CGGPTESAHPARFSPDDKYSKYRIALKKR 51 (53)
T ss_dssp BBTT--TSSBSEESSSSSS-TTTTTCHHHHHHHHH
T ss_pred ccCC--CCCCCcCCcCCCCCCCCccHHHHHHHHhh
Confidence 4887 88766555556667778888887776554
No 342
>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=21.25 E-value=46 Score=18.06 Aligned_cols=14 Identities=29% Similarity=0.973 Sum_probs=9.3
Q ss_pred CcccCCCCCcceec
Q 026529 197 NWTRCPGCGNCIER 210 (237)
Q Consensus 197 ~~k~CP~C~~~iek 210 (237)
.+-.||+|+..|.-
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 34689999988854
No 343
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=21.06 E-value=63 Score=27.49 Aligned_cols=29 Identities=24% Similarity=0.532 Sum_probs=20.7
Q ss_pred ccCCCCCcc-----ee--ccCCCCceeec-CccEEEe
Q 026529 199 TRCPGCGNC-----IE--RKKGCRIMFCR-FIFLSLC 227 (237)
Q Consensus 199 k~CP~C~~~-----ie--k~~GCnhm~C~-C~~cf~c 227 (237)
..||-||.. |. -.+|=-++.|. |++.|-.
T Consensus 188 ~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~ 224 (309)
T PRK03564 188 QFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHV 224 (309)
T ss_pred CCCCCCCCcchhheeeccCCCCceEEEcCCCCCcccc
Confidence 689999975 21 13677889997 9877653
No 344
>PRK14873 primosome assembly protein PriA; Provisional
Probab=21.01 E-value=62 Score=30.69 Aligned_cols=25 Identities=20% Similarity=0.275 Sum_probs=19.2
Q ss_pred ccCCCCCcceeccCCCCceeec-Ccc
Q 026529 199 TRCPGCGNCIERKKGCRIMFCR-FIF 223 (237)
Q Consensus 199 k~CP~C~~~iek~~GCnhm~C~-C~~ 223 (237)
-+||+|..++.-..+=+.+.|. ||+
T Consensus 393 ~~C~~C~~~L~~h~~~~~l~Ch~CG~ 418 (665)
T PRK14873 393 ARCRHCTGPLGLPSAGGTPRCRWCGR 418 (665)
T ss_pred eECCCCCCceeEecCCCeeECCCCcC
Confidence 3899999887765455689996 985
No 345
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.90 E-value=92 Score=20.20 Aligned_cols=57 Identities=21% Similarity=0.660 Sum_probs=34.0
Q ss_pred ccccccccCCCCccccccCCC--CCcchHHHHHHHHHhccccCCcccccCCCCcCCCCCCccccccCCChhHHHHH
Q 026529 40 TCDICIEPMSVNNKFKNNNLC--THPFCQDCTAKYIEVKVRDNNTAKIECPGLHCEQFLDPLACKPTIPSSLFIKW 113 (237)
Q Consensus 40 ~C~IC~~~~~~~~~~~~~~~C--~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~~~~i~~~l~~~~~~~~ 113 (237)
.|..|-.++++... ...-| .|.||.+|...-+. =.||. |+..+...-++ +...+.+|
T Consensus 7 nCECCDrDLpp~s~--dA~ICtfEcTFCadCae~~l~----------g~CPn--CGGelv~RP~R---Paa~L~r~ 65 (84)
T COG3813 7 NCECCDRDLPPDST--DARICTFECTFCADCAENRLH----------GLCPN--CGGELVARPIR---PAAKLARY 65 (84)
T ss_pred CCcccCCCCCCCCC--ceeEEEEeeehhHhHHHHhhc----------CcCCC--CCchhhcCcCC---hHHHHhhC
Confidence 57778777754322 12334 58999999876554 15888 99765433332 33444444
No 346
>PRK04023 DNA polymerase II large subunit; Validated
Probab=20.83 E-value=74 Score=31.54 Aligned_cols=17 Identities=29% Similarity=0.743 Sum_probs=7.9
Q ss_pred ccCcccccc----cccccccc
Q 026529 152 AQCPKCKQW----FCFQCKLA 168 (237)
Q Consensus 152 ~~C~~C~~~----~C~~C~~~ 168 (237)
.+|+.||.. .|..|+..
T Consensus 627 RfCpsCG~~t~~frCP~CG~~ 647 (1121)
T PRK04023 627 RKCPSCGKETFYRRCPFCGTH 647 (1121)
T ss_pred ccCCCCCCcCCcccCCCCCCC
Confidence 345555543 34455443
No 347
>KOG4218 consensus Nuclear hormone receptor betaFTZ-F1 [Transcription]
Probab=20.33 E-value=20 Score=30.68 Aligned_cols=10 Identities=40% Similarity=1.026 Sum_probs=7.6
Q ss_pred CcccCCCCCc
Q 026529 197 NWTRCPGCGN 206 (237)
Q Consensus 197 ~~k~CP~C~~ 206 (237)
.-|+||.|+.
T Consensus 66 qRKRCP~CRF 75 (475)
T KOG4218|consen 66 QRKRCPSCRF 75 (475)
T ss_pred hhccCCchhH
Confidence 3489999874
No 348
>KOG3084 consensus NADH pyrophosphatase I of the Nudix family of hydrolases [Replication, recombination and repair]
Probab=20.13 E-value=91 Score=26.58 Aligned_cols=29 Identities=24% Similarity=0.665 Sum_probs=18.9
Q ss_pred CCcccCCCCCcceeccCC-----CCceeec-CccE
Q 026529 196 MNWTRCPGCGNCIERKKG-----CRIMFCR-FIFL 224 (237)
Q Consensus 196 ~~~k~CP~C~~~iek~~G-----Cnhm~C~-C~~c 224 (237)
..+|.||.|+.+..-.+| |..-+|. ++.+
T Consensus 148 skykFCp~CG~~tkp~e~g~k~~Cs~~~C~~~n~~ 182 (345)
T KOG3084|consen 148 SKYKFCPGCGSPTKPEEAGTKLQCSDETCPSCNVI 182 (345)
T ss_pred HHhccCcccCCCcccccCCccceeecccCCcCCee
Confidence 367999999998766543 4444554 4433
Done!