Query 026541
Match_columns 237
No_of_seqs 137 out of 1314
Neff 9.1
Searched_HMMs 46136
Date Fri Mar 29 09:21:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026541.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026541hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1812 Predicted E3 ubiquitin 100.0 1.1E-36 2.4E-41 263.0 10.5 208 19-230 128-338 (384)
2 KOG1814 Predicted E3 ubiquitin 100.0 2.1E-35 4.5E-40 246.8 10.0 197 30-231 176-402 (445)
3 KOG1815 Predicted E3 ubiquitin 100.0 3.2E-28 7E-33 215.6 10.9 193 36-235 68-268 (444)
4 KOG0006 E3 ubiquitin-protein l 99.9 7.2E-26 1.6E-30 183.8 8.9 189 32-230 215-432 (446)
5 smart00647 IBR In Between Ring 99.3 1.8E-12 4E-17 84.3 5.1 63 111-175 1-64 (64)
6 PF01485 IBR: IBR domain; Int 99.3 6.5E-13 1.4E-17 86.4 -0.1 63 111-175 1-64 (64)
7 PF15227 zf-C3HC4_4: zinc fing 98.6 2.1E-08 4.5E-13 59.2 2.3 41 41-89 1-41 (42)
8 PF13445 zf-RING_UBOX: RING-ty 98.5 9.1E-08 2E-12 56.6 2.4 43 41-88 1-43 (43)
9 PLN03208 E3 ubiquitin-protein 98.5 1.1E-07 2.3E-12 74.2 2.7 67 35-107 15-89 (193)
10 PF13639 zf-RING_2: Ring finge 98.4 8.2E-08 1.8E-12 57.4 1.3 41 40-89 2-42 (44)
11 PF00097 zf-C3HC4: Zinc finger 98.4 2.4E-07 5.3E-12 54.4 2.7 40 41-89 1-40 (41)
12 PF13923 zf-C3HC4_2: Zinc fing 98.3 3.5E-07 7.6E-12 53.1 2.2 38 41-89 1-38 (39)
13 PF14634 zf-RING_5: zinc-RING 98.2 8E-07 1.7E-11 53.1 2.4 43 40-93 1-43 (44)
14 KOG0320 Predicted E3 ubiquitin 98.2 1.6E-06 3.4E-11 66.1 3.4 57 35-103 128-184 (187)
15 PHA02926 zinc finger-like prot 98.1 3.9E-06 8.5E-11 66.3 4.3 59 35-97 167-230 (242)
16 cd00162 RING RING-finger (Real 98.1 3.7E-06 8.1E-11 49.8 3.1 44 40-95 1-44 (45)
17 PF13920 zf-C3HC4_3: Zinc fing 98.1 2.1E-06 4.5E-11 52.7 1.8 46 38-97 2-48 (50)
18 PHA02929 N1R/p28-like protein; 97.9 1.4E-05 3E-10 65.0 4.1 53 35-97 171-227 (238)
19 KOG2164 Predicted E3 ubiquitin 97.9 7E-06 1.5E-10 72.2 2.4 61 38-107 186-246 (513)
20 KOG0823 Predicted E3 ubiquitin 97.8 1E-05 2.3E-10 64.3 2.5 61 34-105 43-103 (230)
21 KOG2177 Predicted E3 ubiquitin 97.8 1.1E-05 2.4E-10 68.1 2.9 110 35-176 10-123 (386)
22 smart00647 IBR In Between Ring 97.8 3.4E-05 7.3E-10 49.7 4.4 40 196-235 16-60 (64)
23 smart00504 Ubox Modified RING 97.7 5.7E-05 1.2E-09 48.5 3.9 51 39-103 2-52 (63)
24 smart00184 RING Ring finger. E 97.7 3.6E-05 7.7E-10 43.8 2.7 30 41-74 1-30 (39)
25 TIGR00599 rad18 DNA repair pro 97.7 4.1E-05 8.8E-10 66.7 3.9 71 31-115 19-90 (397)
26 KOG0317 Predicted E3 ubiquitin 97.6 2.6E-05 5.7E-10 64.0 1.9 54 35-102 236-289 (293)
27 TIGR00570 cdk7 CDK-activating 97.6 0.00015 3.3E-09 60.8 6.5 57 39-104 4-61 (309)
28 PF01485 IBR: IBR domain; Int 97.6 3.1E-05 6.8E-10 49.8 1.4 41 195-235 15-60 (64)
29 COG5540 RING-finger-containing 97.5 7.8E-05 1.7E-09 61.6 2.8 54 35-98 320-373 (374)
30 KOG4628 Predicted E3 ubiquitin 97.5 7.5E-05 1.6E-09 63.6 2.7 52 36-97 227-278 (348)
31 KOG0287 Postreplication repair 97.4 6.9E-05 1.5E-09 62.8 1.5 66 35-114 20-86 (442)
32 KOG1814 Predicted E3 ubiquitin 97.1 0.0015 3.1E-08 56.4 6.4 120 29-169 264-404 (445)
33 PF12678 zf-rbx1: RING-H2 zinc 97.0 0.00065 1.4E-08 45.1 3.0 44 38-89 19-71 (73)
34 KOG1002 Nucleotide excision re 97.0 0.0004 8.8E-09 61.5 2.4 59 33-100 531-589 (791)
35 PF11793 FANCL_C: FANCL C-term 97.0 0.00028 6E-09 46.5 1.0 59 38-98 2-67 (70)
36 PF11789 zf-Nse: Zinc-finger o 96.7 0.0015 3.2E-08 41.1 2.4 50 35-93 8-57 (57)
37 KOG0978 E3 ubiquitin ligase in 96.6 0.0007 1.5E-08 62.6 1.1 57 35-104 640-696 (698)
38 COG5432 RAD18 RING-finger-cont 96.4 0.0017 3.6E-08 53.6 1.8 69 32-114 19-88 (391)
39 COG5243 HRD1 HRD ubiquitin lig 96.4 0.0045 9.8E-08 52.8 4.2 53 35-97 284-345 (491)
40 PF14835 zf-RING_6: zf-RING of 96.2 0.0008 1.7E-08 42.8 -0.8 50 38-102 7-56 (65)
41 COG5574 PEX10 RING-finger-cont 96.1 0.0048 1E-07 50.3 2.8 52 38-101 215-266 (271)
42 KOG4185 Predicted E3 ubiquitin 95.9 0.02 4.4E-07 48.4 6.3 123 38-173 3-131 (296)
43 KOG1812 Predicted E3 ubiquitin 95.9 0.0079 1.7E-07 52.8 3.6 106 37-174 237-346 (384)
44 PF04564 U-box: U-box domain; 95.8 0.01 2.2E-07 39.3 3.1 53 36-101 2-54 (73)
45 KOG0006 E3 ubiquitin-protein l 95.8 0.019 4E-07 48.1 5.0 144 7-171 285-437 (446)
46 KOG1785 Tyrosine kinase negati 95.6 0.0078 1.7E-07 51.8 2.2 67 5-89 344-410 (563)
47 KOG1039 Predicted E3 ubiquitin 95.5 0.011 2.4E-07 50.7 3.0 94 36-132 159-264 (344)
48 PF14570 zf-RING_4: RING/Ubox 95.4 0.018 3.9E-07 34.6 2.7 47 41-96 1-47 (48)
49 PF12861 zf-Apc11: Anaphase-pr 95.3 0.016 3.6E-07 39.2 2.7 55 36-97 19-82 (85)
50 KOG2660 Locus-specific chromos 95.0 0.013 2.7E-07 49.4 1.7 50 35-97 12-61 (331)
51 KOG1952 Transcription factor N 94.2 0.049 1.1E-06 51.3 3.7 57 34-93 187-243 (950)
52 smart00744 RINGv The RING-vari 94.0 0.074 1.6E-06 32.2 3.1 42 40-89 1-47 (49)
53 KOG4265 Predicted E3 ubiquitin 93.9 0.045 9.7E-07 46.7 2.7 49 35-97 287-336 (349)
54 KOG0802 E3 ubiquitin ligase [P 93.5 0.046 1E-06 50.4 2.3 49 36-94 289-338 (543)
55 KOG4159 Predicted E3 ubiquitin 93.3 0.14 3E-06 45.0 4.8 50 34-97 80-129 (398)
56 KOG0828 Predicted E3 ubiquitin 93.3 0.049 1.1E-06 48.3 1.8 54 35-97 568-634 (636)
57 KOG1428 Inhibitor of type V ad 93.1 0.15 3.2E-06 51.1 4.8 76 36-114 3484-3563(3738)
58 KOG2879 Predicted E3 ubiquitin 92.9 0.11 2.4E-06 42.8 3.2 51 36-97 237-287 (298)
59 COG5220 TFB3 Cdk activating ki 92.8 0.027 5.9E-07 45.3 -0.2 51 39-96 11-63 (314)
60 KOG4739 Uncharacterized protei 92.8 0.033 7.2E-07 45.0 0.2 55 38-106 3-57 (233)
61 smart00661 RPOL9 RNA polymeras 92.8 0.099 2.2E-06 31.8 2.3 28 199-226 1-31 (52)
62 COG5175 MOT2 Transcriptional r 92.7 0.16 3.4E-06 43.1 4.0 63 38-109 14-77 (480)
63 KOG0824 Predicted E3 ubiquitin 92.5 0.096 2.1E-06 43.7 2.5 53 36-101 5-57 (324)
64 KOG3039 Uncharacterized conser 92.1 0.11 2.4E-06 42.1 2.2 90 5-104 177-277 (303)
65 KOG4172 Predicted E3 ubiquitin 91.7 0.055 1.2E-06 33.1 0.1 46 39-97 8-54 (62)
66 PRK00432 30S ribosomal protein 91.5 0.19 4.1E-06 30.6 2.4 27 197-225 19-47 (50)
67 PF04641 Rtf2: Rtf2 RING-finge 91.5 0.26 5.7E-06 41.0 4.0 72 35-117 110-182 (260)
68 KOG0827 Predicted E3 ubiquitin 91.2 0.18 3.9E-06 43.6 2.8 50 37-93 3-52 (465)
69 KOG4445 Uncharacterized conser 91.2 0.1 2.3E-06 43.5 1.3 64 33-99 110-188 (368)
70 COG5152 Uncharacterized conser 91.1 0.099 2.2E-06 40.9 1.0 34 36-73 194-227 (259)
71 PHA00626 hypothetical protein 91.0 0.21 4.5E-06 30.8 2.2 26 200-225 2-33 (59)
72 KOG0804 Cytoplasmic Zn-finger 90.0 0.15 3.3E-06 44.8 1.3 48 36-95 173-220 (493)
73 PF05883 Baculo_RING: Baculovi 89.5 0.18 4E-06 37.2 1.3 40 36-76 24-69 (134)
74 KOG3002 Zn finger protein [Gen 88.8 0.26 5.5E-06 41.8 1.8 45 35-97 45-91 (299)
75 PF13719 zinc_ribbon_5: zinc-r 88.7 0.29 6.3E-06 27.7 1.4 32 128-161 3-35 (37)
76 PF10571 UPF0547: Uncharacteri 88.7 0.24 5.3E-06 25.7 1.0 23 129-161 2-24 (26)
77 KOG1645 RING-finger-containing 88.5 0.35 7.5E-06 42.2 2.4 51 37-95 3-54 (463)
78 PF13717 zinc_ribbon_4: zinc-r 88.4 0.39 8.5E-06 27.0 1.8 32 128-161 3-35 (36)
79 PRK00398 rpoP DNA-directed RNA 88.1 0.79 1.7E-05 27.2 3.2 29 199-227 4-33 (46)
80 PF05290 Baculo_IE-1: Baculovi 87.9 1.4 3E-05 32.5 4.8 58 32-97 74-132 (140)
81 KOG1493 Anaphase-promoting com 87.8 0.14 3E-06 33.7 -0.3 54 37-97 19-81 (84)
82 PF14447 Prok-RING_4: Prokaryo 87.6 0.23 5E-06 30.6 0.6 48 37-100 6-53 (55)
83 KOG0311 Predicted E3 ubiquitin 87.1 0.08 1.7E-06 45.1 -2.2 49 35-95 40-88 (381)
84 KOG3053 Uncharacterized conser 86.7 0.8 1.7E-05 37.5 3.4 61 33-95 15-80 (293)
85 PF09297 zf-NADH-PPase: NADH p 86.7 1.2 2.6E-05 24.1 3.2 27 198-224 3-30 (32)
86 PF14569 zf-UDP: Zinc-binding 86.3 0.45 9.8E-06 31.5 1.5 60 128-216 10-69 (80)
87 KOG3970 Predicted E3 ubiquitin 86.3 1.5 3.3E-05 35.2 4.7 63 30-96 42-104 (299)
88 PLN03086 PRLI-interacting fact 86.0 2.4 5.2E-05 39.1 6.5 103 83-209 406-515 (567)
89 KOG3800 Predicted E3 ubiquitin 85.8 1.1 2.4E-05 37.3 3.9 52 40-100 2-54 (300)
90 PHA03096 p28-like protein; Pro 85.7 0.61 1.3E-05 39.2 2.4 49 39-89 179-231 (284)
91 KOG1815 Predicted E3 ubiquitin 85.7 0.77 1.7E-05 41.3 3.2 39 125-169 224-264 (444)
92 KOG1940 Zn-finger protein [Gen 85.5 0.6 1.3E-05 38.9 2.2 50 35-94 155-204 (276)
93 KOG4692 Predicted E3 ubiquitin 85.4 0.87 1.9E-05 39.0 3.1 36 35-74 419-454 (489)
94 COG1998 RPS31 Ribosomal protei 85.4 0.72 1.6E-05 27.7 1.9 28 196-223 17-45 (51)
95 KOG2906 RNA polymerase III sub 85.2 0.69 1.5E-05 32.0 2.0 27 200-226 3-32 (105)
96 KOG4367 Predicted Zn-finger pr 85.2 0.72 1.6E-05 40.6 2.6 36 36-75 2-37 (699)
97 KOG1941 Acetylcholine receptor 85.1 0.31 6.6E-06 42.3 0.3 53 36-96 363-415 (518)
98 COG5219 Uncharacterized conser 84.4 0.8 1.7E-05 44.3 2.7 55 35-97 1466-1523(1525)
99 KOG1734 Predicted RING-contain 84.4 0.34 7.3E-06 39.9 0.3 59 36-103 222-287 (328)
100 KOG0297 TNF receptor-associate 84.2 1.2 2.6E-05 39.3 3.7 50 35-97 18-67 (391)
101 KOG1813 Predicted E3 ubiquitin 83.4 0.43 9.2E-06 39.9 0.5 47 36-96 239-285 (313)
102 COG5194 APC11 Component of SCF 82.2 1.5 3.3E-05 29.2 2.6 29 59-97 53-81 (88)
103 PRK00398 rpoP DNA-directed RNA 82.1 1.3 2.9E-05 26.2 2.2 28 128-161 4-31 (46)
104 COG5236 Uncharacterized conser 81.9 1.1 2.3E-05 38.4 2.2 69 33-113 56-124 (493)
105 PF12906 RINGv: RING-variant d 81.7 1.4 3E-05 26.4 2.1 33 41-75 1-38 (47)
106 KOG2817 Predicted E3 ubiquitin 81.6 2 4.3E-05 37.5 3.8 61 36-104 332-392 (394)
107 TIGR02098 MJ0042_CXXC MJ0042 f 81.2 1.2 2.5E-05 25.1 1.6 32 128-161 3-35 (38)
108 PF07975 C1_4: TFIIH C1-like d 81.2 0.39 8.5E-06 29.3 -0.4 39 134-172 4-42 (51)
109 PF14952 zf-tcix: Putative tre 80.1 0.85 1.8E-05 26.6 0.8 26 196-225 9-37 (44)
110 PF02150 RNA_POL_M_15KD: RNA p 80.1 1.1 2.3E-05 25.0 1.2 28 128-160 2-29 (35)
111 PF03119 DNA_ligase_ZBD: NAD-d 79.7 2.2 4.7E-05 22.5 2.2 20 200-219 1-20 (28)
112 KOG0825 PHD Zn-finger protein 79.5 1.3 2.9E-05 41.9 2.2 43 35-77 93-138 (1134)
113 PRK05654 acetyl-CoA carboxylas 79.1 0.51 1.1E-05 39.9 -0.5 32 195-226 24-57 (292)
114 PF10367 Vps39_2: Vacuolar sor 78.0 1.3 2.8E-05 31.1 1.4 34 35-70 75-108 (109)
115 TIGR00622 ssl1 transcription f 77.8 2.2 4.8E-05 30.5 2.5 78 83-171 14-101 (112)
116 PF14803 Nudix_N_2: Nudix N-te 77.7 1.6 3.4E-05 24.2 1.4 31 128-160 1-31 (34)
117 PF08274 PhnA_Zn_Ribbon: PhnA 77.0 2.6 5.6E-05 22.7 2.0 26 199-225 3-29 (30)
118 PF06677 Auto_anti-p27: Sjogre 76.5 2.6 5.6E-05 24.5 2.1 23 198-222 17-41 (41)
119 PF14446 Prok-RING_1: Prokaryo 76.0 3.4 7.4E-05 25.5 2.6 37 35-71 2-38 (54)
120 COG0777 AccD Acetyl-CoA carbox 75.9 1 2.2E-05 37.5 0.3 31 195-225 25-57 (294)
121 PRK00420 hypothetical protein; 75.9 2.1 4.6E-05 30.7 2.0 28 197-226 22-51 (112)
122 PRK14714 DNA polymerase II lar 75.8 2.4 5.3E-05 42.4 2.9 12 198-209 709-720 (1337)
123 KOG3268 Predicted E3 ubiquitin 75.1 4.1 8.8E-05 31.6 3.4 62 35-98 162-229 (234)
124 KOG2034 Vacuolar sorting prote 74.8 1.7 3.6E-05 41.8 1.5 43 35-79 814-856 (911)
125 COG2888 Predicted Zn-ribbon RN 74.7 2.7 5.9E-05 26.3 2.0 32 128-165 10-41 (61)
126 TIGR00515 accD acetyl-CoA carb 74.3 0.76 1.6E-05 38.8 -0.7 31 195-225 23-55 (285)
127 PF13240 zinc_ribbon_2: zinc-r 74.3 1.4 3.1E-05 22.0 0.6 22 129-160 1-22 (23)
128 CHL00174 accD acetyl-CoA carbo 74.3 0.71 1.5E-05 39.0 -0.9 31 195-225 35-67 (296)
129 TIGR01384 TFS_arch transcripti 74.3 2 4.4E-05 30.2 1.6 24 200-225 2-26 (104)
130 COG1645 Uncharacterized Zn-fin 73.9 3 6.4E-05 30.8 2.3 28 196-225 26-54 (131)
131 PF01599 Ribosomal_S27: Riboso 73.6 2.7 5.9E-05 25.1 1.7 27 197-223 17-46 (47)
132 PRK14559 putative protein seri 72.5 2.9 6.3E-05 39.4 2.5 13 197-209 40-52 (645)
133 PF13248 zf-ribbon_3: zinc-rib 72.5 1.8 4E-05 22.2 0.7 23 128-160 3-25 (26)
134 KOG1001 Helicase-like transcri 72.1 1.5 3.3E-05 41.5 0.6 52 39-103 455-506 (674)
135 KOG2691 RNA polymerase II subu 71.8 4.3 9.4E-05 28.6 2.7 34 126-161 3-36 (113)
136 PF09538 FYDLN_acid: Protein o 71.6 2.2 4.8E-05 30.4 1.2 26 199-225 10-36 (108)
137 COG5222 Uncharacterized conser 71.4 11 0.00023 31.8 5.3 44 38-93 274-317 (427)
138 PRK08665 ribonucleotide-diphos 71.1 2.5 5.4E-05 40.7 1.8 24 199-224 725-749 (752)
139 PF07282 OrfB_Zn_ribbon: Putat 71.0 3.8 8.2E-05 26.3 2.2 29 197-225 27-56 (69)
140 PF14149 YhfH: YhfH-like prote 69.7 0.5 1.1E-05 26.6 -1.9 29 191-219 6-34 (37)
141 PF07191 zinc-ribbons_6: zinc- 69.0 5 0.00011 26.2 2.3 24 200-225 3-27 (70)
142 PRK14890 putative Zn-ribbon RN 68.0 5.2 0.00011 25.1 2.1 32 128-165 8-39 (59)
143 PF07503 zf-HYPF: HypF finger; 67.7 3.5 7.6E-05 23.0 1.3 32 64-97 1-32 (35)
144 PF06827 zf-FPG_IleRS: Zinc fi 67.6 3.7 8.1E-05 21.7 1.3 24 199-222 2-28 (30)
145 KOG0823 Predicted E3 ubiquitin 67.4 4.1 9E-05 32.9 2.1 38 149-210 59-96 (230)
146 TIGR01053 LSD1 zinc finger dom 67.3 5.8 0.00013 21.4 2.0 27 128-160 2-28 (31)
147 PLN02189 cellulose synthase 66.9 5 0.00011 39.6 2.9 62 127-217 34-95 (1040)
148 COG3813 Uncharacterized protei 66.4 5.4 0.00012 26.0 2.1 60 39-115 6-67 (84)
149 PF01363 FYVE: FYVE zinc finge 66.2 1.4 3.1E-05 28.4 -0.6 39 35-73 6-44 (69)
150 PLN02638 cellulose synthase A 63.7 5.6 0.00012 39.4 2.6 61 128-217 18-78 (1079)
151 COG1997 RPL43A Ribosomal prote 63.5 6.7 0.00015 26.7 2.2 29 197-225 34-63 (89)
152 smart00064 FYVE Protein presen 63.4 7.1 0.00015 24.9 2.3 39 37-75 9-47 (68)
153 PF12773 DZR: Double zinc ribb 63.3 4.6 0.0001 24.1 1.3 28 125-159 10-37 (50)
154 TIGR00373 conserved hypothetic 63.1 7.3 0.00016 29.8 2.7 60 96-160 77-137 (158)
155 PHA02825 LAP/PHD finger-like p 63.0 7.1 0.00015 29.8 2.5 54 35-99 5-61 (162)
156 KOG2807 RNA polymerase II tran 62.6 4 8.7E-05 34.7 1.2 71 83-171 289-365 (378)
157 cd00065 FYVE FYVE domain; Zinc 62.2 6.7 0.00014 24.0 1.9 37 39-75 3-39 (57)
158 PHA02926 zinc finger-like prot 61.8 8.3 0.00018 31.2 2.8 75 108-209 156-230 (242)
159 KOG3161 Predicted E3 ubiquitin 61.7 2.7 5.9E-05 39.0 0.1 37 38-74 11-47 (861)
160 smart00531 TFIIE Transcription 61.7 8.3 0.00018 29.0 2.7 34 125-160 97-132 (147)
161 PRK14892 putative transcriptio 60.3 6.8 0.00015 27.5 1.9 30 196-225 19-52 (99)
162 PF08271 TF_Zn_Ribbon: TFIIB z 60.3 10 0.00022 21.9 2.4 10 200-209 21-30 (43)
163 PRK09710 lar restriction allev 60.2 8.1 0.00018 24.7 2.0 29 196-224 4-36 (64)
164 smart00659 RPOLCX RNA polymera 60.0 8.7 0.00019 22.6 2.0 11 198-208 19-29 (44)
165 PRK06266 transcription initiat 59.9 9 0.0002 29.9 2.7 30 125-159 115-144 (178)
166 cd00021 BBOX B-Box-type zinc f 59.8 6 0.00013 21.9 1.3 26 149-174 10-35 (39)
167 PF08746 zf-RING-like: RING-li 59.5 8.8 0.00019 22.4 2.0 25 59-89 18-42 (43)
168 KOG0801 Predicted E3 ubiquitin 58.1 3.7 8.1E-05 31.3 0.3 31 35-66 174-204 (205)
169 PF01428 zf-AN1: AN1-like Zinc 56.9 7.9 0.00017 22.5 1.5 27 150-178 12-38 (43)
170 KOG3579 Predicted E3 ubiquitin 56.9 7.2 0.00016 32.6 1.7 67 35-108 265-343 (352)
171 COG0266 Nei Formamidopyrimidin 56.6 8.1 0.00018 32.3 2.0 24 199-222 246-272 (273)
172 COG5151 SSL1 RNA polymerase II 56.6 4.5 9.8E-05 34.2 0.6 92 61-171 307-408 (421)
173 PF14353 CpXC: CpXC protein 56.3 4.7 0.0001 29.5 0.6 46 85-141 2-50 (128)
174 PLN02400 cellulose synthase 56.3 9.7 0.00021 37.8 2.8 61 128-217 37-97 (1085)
175 KOG4275 Predicted E3 ubiquitin 56.1 2.4 5.2E-05 35.5 -1.1 40 38-95 300-340 (350)
176 KOG1701 Focal adhesion adaptor 56.0 14 0.00031 32.7 3.5 68 149-222 380-459 (468)
177 PF10426 zf-RAG1: Recombinatio 55.3 1.9 4.1E-05 23.1 -1.2 19 84-102 2-20 (30)
178 PLN02436 cellulose synthase A 55.3 11 0.00024 37.4 3.0 61 128-217 37-97 (1094)
179 PF12760 Zn_Tnp_IS1595: Transp 55.1 26 0.00056 20.5 3.6 25 199-223 19-45 (46)
180 PHA02862 5L protein; Provision 54.4 16 0.00034 27.5 3.0 47 39-98 3-54 (156)
181 PF06844 DUF1244: Protein of u 53.8 9.7 0.00021 24.4 1.6 17 63-79 11-27 (68)
182 PF06906 DUF1272: Protein of u 53.4 11 0.00025 23.3 1.8 45 39-97 6-52 (57)
183 PRK03681 hypA hydrogenase nick 53.2 19 0.00041 25.9 3.3 47 106-159 40-95 (114)
184 PRK00420 hypothetical protein; 53.0 31 0.00068 24.7 4.3 43 108-159 6-48 (112)
185 PF05605 zf-Di19: Drought indu 52.9 20 0.00043 21.8 2.9 42 37-97 1-42 (54)
186 TIGR00686 phnA alkylphosphonat 52.8 10 0.00022 26.9 1.7 26 129-161 4-29 (109)
187 PF10122 Mu-like_Com: Mu-like 52.3 6 0.00013 24.0 0.5 9 199-207 25-33 (51)
188 PF09526 DUF2387: Probable met 52.3 15 0.00032 24.1 2.4 26 199-224 9-39 (71)
189 PRK14559 putative protein seri 52.2 12 0.00026 35.4 2.7 32 125-168 13-50 (645)
190 TIGR03655 anti_R_Lar restricti 52.1 13 0.00027 22.7 1.9 26 199-224 2-35 (53)
191 KOG2906 RNA polymerase III sub 51.5 13 0.00028 25.9 2.0 30 128-161 2-31 (105)
192 PF03604 DNA_RNApol_7kD: DNA d 51.5 9.2 0.0002 20.8 1.1 22 134-160 5-26 (32)
193 smart00336 BBOX B-Box-type zin 51.4 12 0.00026 21.0 1.7 26 149-174 13-38 (42)
194 PF05129 Elf1: Transcription e 51.3 11 0.00024 25.3 1.7 32 196-227 20-58 (81)
195 KOG0826 Predicted E3 ubiquitin 51.3 17 0.00036 31.1 3.1 57 34-103 296-352 (357)
196 PF07754 DUF1610: Domain of un 51.2 13 0.00028 18.8 1.5 22 134-159 3-24 (24)
197 COG1594 RPB9 DNA-directed RNA 50.7 16 0.00034 26.3 2.5 31 127-161 2-32 (113)
198 COG5220 TFB3 Cdk activating ki 50.7 12 0.00025 30.6 2.0 56 85-143 11-67 (314)
199 TIGR02443 conserved hypothetic 49.8 17 0.00037 22.8 2.2 26 199-224 10-40 (59)
200 PF02591 DUF164: Putative zinc 49.8 15 0.00032 22.6 2.0 22 187-208 35-56 (56)
201 PF00643 zf-B_box: B-box zinc 49.8 4.2 9.2E-05 23.2 -0.5 24 150-173 14-37 (42)
202 TIGR02300 FYDLN_acid conserved 49.7 10 0.00022 27.8 1.4 26 199-225 10-36 (129)
203 PRK01103 formamidopyrimidine/5 49.5 13 0.00028 31.2 2.2 24 199-222 246-272 (274)
204 smart00734 ZnF_Rad18 Rad18-lik 49.3 8 0.00017 19.9 0.6 20 85-106 2-21 (26)
205 PRK14811 formamidopyrimidine-D 49.1 13 0.00027 31.2 2.1 25 198-222 235-262 (269)
206 TIGR01206 lysW lysine biosynth 48.9 18 0.00038 22.3 2.2 30 128-161 3-32 (54)
207 PRK10445 endonuclease VIII; Pr 48.8 13 0.00029 30.9 2.2 25 198-222 235-262 (263)
208 smart00834 CxxC_CXXC_SSSS Puta 48.6 17 0.00037 20.4 2.0 29 128-159 6-34 (41)
209 PRK14810 formamidopyrimidine-D 48.6 13 0.00029 31.1 2.2 25 198-222 244-271 (272)
210 KOG2930 SCF ubiquitin ligase, 48.5 15 0.00034 25.8 2.0 29 58-96 79-107 (114)
211 KOG1571 Predicted E3 ubiquitin 48.4 7.2 0.00016 33.7 0.5 46 35-97 302-347 (355)
212 TIGR00577 fpg formamidopyrimid 48.3 14 0.0003 31.0 2.2 25 198-222 245-272 (272)
213 PF07800 DUF1644: Protein of u 48.3 24 0.00051 27.0 3.2 87 38-144 2-124 (162)
214 PRK10220 hypothetical protein; 47.8 15 0.00032 26.1 1.9 27 128-161 4-30 (111)
215 PRK13945 formamidopyrimidine-D 46.9 14 0.00031 31.0 2.1 25 198-222 254-281 (282)
216 PLN02915 cellulose synthase A 46.6 14 0.00031 36.6 2.3 57 134-217 20-76 (1044)
217 PF10497 zf-4CXXC_R1: Zinc-fin 46.3 35 0.00075 24.2 3.7 63 36-100 5-75 (105)
218 PLN02195 cellulose synthase A 46.2 16 0.00036 35.9 2.6 53 128-209 7-59 (977)
219 PLN00209 ribosomal protein S27 45.8 24 0.00051 24.0 2.6 31 128-163 37-67 (86)
220 PRK14714 DNA polymerase II lar 45.7 17 0.00037 36.8 2.6 22 200-223 694-717 (1337)
221 PRK03824 hypA hydrogenase nick 45.1 27 0.00059 25.9 3.1 15 126-142 69-83 (135)
222 PF13453 zf-TFIIB: Transcripti 44.7 18 0.0004 20.6 1.7 12 200-211 1-12 (41)
223 TIGR00570 cdk7 CDK-activating 44.1 17 0.00036 31.0 2.1 54 128-212 4-57 (309)
224 KOG2114 Vacuolar assembly/sort 43.6 22 0.00047 34.4 2.8 41 38-94 840-880 (933)
225 PF06943 zf-LSD1: LSD1 zinc fi 43.3 29 0.00063 17.7 2.1 22 134-159 3-24 (25)
226 PF14369 zf-RING_3: zinc-finge 42.6 26 0.00055 19.4 2.0 30 127-161 2-31 (35)
227 PRK11827 hypothetical protein; 42.6 24 0.00053 22.3 2.1 29 197-225 7-36 (60)
228 KOG2979 Protein involved in DN 42.5 36 0.00079 28.1 3.6 71 38-119 176-247 (262)
229 PF04216 FdhE: Protein involve 41.7 16 0.00034 30.9 1.6 36 199-234 173-222 (290)
230 PF08792 A2L_zn_ribbon: A2L zi 41.5 28 0.00062 19.0 2.1 29 127-161 3-31 (33)
231 PLN02436 cellulose synthase A 40.9 24 0.00052 35.2 2.8 53 36-97 34-89 (1094)
232 COG1579 Zn-ribbon protein, pos 40.4 20 0.00043 29.4 1.9 60 99-160 166-230 (239)
233 PF09889 DUF2116: Uncharacteri 40.4 13 0.00028 23.4 0.6 18 198-219 3-20 (59)
234 PTZ00083 40S ribosomal protein 40.0 35 0.00076 23.1 2.7 31 128-163 36-66 (85)
235 PF09723 Zn-ribbon_8: Zinc rib 40.0 27 0.00058 20.1 1.9 29 128-159 6-34 (42)
236 PF11023 DUF2614: Protein of u 39.8 23 0.00049 25.4 1.9 23 148-170 66-96 (114)
237 PRK12495 hypothetical protein; 39.4 45 0.00099 26.9 3.7 28 125-160 40-67 (226)
238 PF09788 Tmemb_55A: Transmembr 39.0 33 0.00072 28.3 2.9 93 35-161 62-167 (256)
239 PF02318 FYVE_2: FYVE-type zin 38.2 54 0.0012 23.5 3.8 36 126-168 53-88 (118)
240 TIGR00100 hypA hydrogenase nic 38.1 45 0.00098 23.9 3.3 27 125-159 68-94 (115)
241 COG3492 Uncharacterized protei 38.0 34 0.00073 23.5 2.4 17 63-79 42-58 (104)
242 PRK00564 hypA hydrogenase nick 37.8 35 0.00077 24.6 2.7 48 105-159 39-96 (117)
243 PRK12380 hydrogenase nickel in 37.0 48 0.001 23.7 3.3 47 105-159 39-94 (113)
244 PF02748 PyrI_C: Aspartate car 36.9 19 0.00042 21.9 1.0 35 126-161 5-45 (52)
245 TIGR00595 priA primosomal prot 36.3 49 0.0011 30.4 4.0 34 129-168 224-262 (505)
246 KOG4362 Transcriptional regula 36.2 11 0.00025 35.5 -0.1 60 33-103 16-75 (684)
247 PRK13130 H/ACA RNA-protein com 35.5 39 0.00084 21.0 2.2 36 85-122 18-53 (56)
248 PRK04023 DNA polymerase II lar 35.1 31 0.00066 34.3 2.5 16 152-167 639-659 (1121)
249 KOG3039 Uncharacterized conser 34.8 46 0.00099 27.4 3.1 43 33-79 38-80 (303)
250 COG2816 NPY1 NTP pyrophosphohy 34.3 78 0.0017 26.6 4.5 55 98-160 83-138 (279)
251 PRK09521 exosome complex RNA-b 33.9 32 0.00069 27.0 2.1 25 199-224 150-175 (189)
252 KOG0825 PHD Zn-finger protein 33.6 35 0.00076 32.9 2.5 50 37-97 122-171 (1134)
253 PF01927 Mut7-C: Mut7-C RNAse 33.1 15 0.00033 27.6 0.1 43 84-141 91-136 (147)
254 PF01194 RNA_pol_N: RNA polyme 32.9 53 0.0011 20.7 2.5 14 82-97 2-15 (60)
255 COG3024 Uncharacterized protei 32.7 18 0.0004 23.0 0.4 17 196-212 5-21 (65)
256 PF02891 zf-MIZ: MIZ/SP-RING z 32.5 28 0.0006 21.0 1.2 47 39-94 3-49 (50)
257 COG1675 TFA1 Transcription ini 32.3 35 0.00075 26.7 2.0 31 124-159 110-140 (176)
258 PRK00241 nudC NADH pyrophospha 32.0 37 0.0008 28.1 2.3 28 196-223 97-125 (256)
259 smart00154 ZnF_AN1 AN1-like Zi 32.0 28 0.0006 19.8 1.1 18 151-168 12-29 (39)
260 COG2051 RPS27A Ribosomal prote 31.8 37 0.0008 21.9 1.7 30 128-162 20-49 (67)
261 COG3677 Transposase and inacti 31.8 62 0.0013 23.8 3.2 36 126-163 29-65 (129)
262 PF03966 Trm112p: Trm112p-like 31.6 71 0.0015 20.4 3.1 17 125-143 51-67 (68)
263 PF06524 NOA36: NOA36 protein; 31.3 33 0.00071 28.5 1.8 69 128-210 143-221 (314)
264 PF08209 Sgf11: Sgf11 (transcr 31.0 29 0.00063 19.0 1.0 15 197-211 3-17 (33)
265 PLN02189 cellulose synthase 30.9 43 0.00093 33.4 2.8 53 36-97 32-87 (1040)
266 PRK12286 rpmF 50S ribosomal pr 30.5 46 0.001 20.7 2.0 27 123-160 23-49 (57)
267 smart00249 PHD PHD zinc finger 29.3 26 0.00057 19.7 0.7 34 40-74 1-34 (47)
268 PF03854 zf-P11: P-11 zinc fin 29.1 18 0.00039 21.7 -0.1 44 39-98 3-47 (50)
269 COG1198 PriA Primosomal protei 28.8 46 0.001 32.0 2.6 58 105-168 405-484 (730)
270 COG1996 RPC10 DNA-directed RNA 28.7 34 0.00074 20.6 1.1 15 195-209 21-35 (49)
271 PLN02638 cellulose synthase A 28.1 54 0.0012 32.9 2.9 52 36-96 15-69 (1079)
272 KOG2923 Uncharacterized conser 28.0 43 0.00093 21.4 1.5 21 190-210 36-56 (67)
273 PF13451 zf-trcl: Probable zin 28.0 43 0.00094 20.2 1.5 15 216-230 4-19 (49)
274 PF00098 zf-CCHC: Zinc knuckle 27.6 41 0.0009 15.5 1.1 16 161-176 2-17 (18)
275 KOG2932 E3 ubiquitin ligase in 27.4 33 0.00071 29.2 1.2 32 38-72 90-121 (389)
276 KOG2041 WD40 repeat protein [G 27.3 67 0.0014 30.9 3.2 48 104-161 1088-1141(1189)
277 PF10764 Gin: Inhibitor of sig 26.7 38 0.00082 20.1 1.1 35 40-79 1-35 (46)
278 KOG4684 Uncharacterized conser 26.2 57 0.0012 26.3 2.2 21 124-144 135-155 (275)
279 COG1096 Predicted RNA-binding 26.2 49 0.0011 26.0 1.9 23 199-223 150-173 (188)
280 COG5216 Uncharacterized conser 26.0 38 0.00082 21.2 1.0 19 190-208 36-54 (67)
281 KOG1100 Predicted E3 ubiquitin 26.0 32 0.00069 27.6 0.9 39 41-97 161-200 (207)
282 PF01873 eIF-5_eIF-2B: Domain 25.6 77 0.0017 23.2 2.7 27 197-223 92-122 (125)
283 PF14471 DUF4428: Domain of un 25.4 61 0.0013 19.6 1.9 30 40-72 1-30 (51)
284 PF03884 DUF329: Domain of unk 25.3 40 0.00087 21.0 1.0 19 198-216 2-20 (57)
285 COG2824 PhnA Uncharacterized Z 25.1 54 0.0012 23.2 1.7 26 199-226 4-31 (112)
286 KOG2857 Predicted MYND Zn-fing 25.0 37 0.0008 25.4 1.0 33 38-74 5-38 (157)
287 COG1656 Uncharacterized conser 24.9 48 0.001 25.5 1.6 42 85-141 98-142 (165)
288 PF01155 HypA: Hydrogenase exp 24.6 53 0.0011 23.5 1.7 47 105-159 39-94 (113)
289 PF14445 Prok-RING_2: Prokaryo 24.4 20 0.00044 21.6 -0.4 36 37-73 6-41 (57)
290 PF01530 zf-C2HC: Zinc finger, 24.4 35 0.00076 18.4 0.6 17 128-144 2-18 (31)
291 PRK02935 hypothetical protein; 24.3 64 0.0014 22.8 2.0 23 148-170 67-97 (110)
292 cd04476 RPA1_DBD_C RPA1_DBD_C: 24.3 51 0.0011 25.1 1.7 25 198-223 34-59 (166)
293 TIGR01031 rpmF_bact ribosomal 24.1 62 0.0013 20.0 1.7 25 124-159 23-47 (55)
294 COG1198 PriA Primosomal protei 24.1 55 0.0012 31.6 2.2 26 199-224 445-471 (730)
295 PF01396 zf-C4_Topoisom: Topoi 24.0 46 0.001 18.8 1.1 20 199-219 2-24 (39)
296 TIGR02605 CxxC_CxxC_SSSS putat 23.9 68 0.0015 19.0 1.9 29 128-159 6-34 (52)
297 COG5109 Uncharacterized conser 22.9 65 0.0014 27.6 2.1 55 36-98 334-388 (396)
298 KOG2789 Putative Zn-finger pro 22.6 1.2E+02 0.0025 27.0 3.6 37 35-73 71-107 (482)
299 PLN03086 PRLI-interacting fact 22.5 50 0.0011 30.8 1.5 30 196-225 431-463 (567)
300 PRK00241 nudC NADH pyrophospha 22.4 1.2E+02 0.0026 25.1 3.7 30 125-160 97-126 (256)
301 COG5175 MOT2 Transcriptional r 22.4 35 0.00076 29.4 0.5 32 128-167 15-46 (480)
302 PF01780 Ribosomal_L37ae: Ribo 22.2 60 0.0013 22.3 1.5 27 199-225 36-63 (90)
303 PF06467 zf-FCS: MYM-type Zinc 22.1 56 0.0012 18.5 1.2 37 36-72 4-43 (43)
304 PLN02915 cellulose synthase A 21.9 71 0.0015 32.0 2.5 54 35-97 12-68 (1044)
305 PF15616 TerY-C: TerY-C metal 21.8 90 0.0019 23.1 2.5 12 197-208 76-87 (131)
306 PRK06386 replication factor A; 21.8 42 0.0009 29.4 0.8 14 197-210 235-248 (358)
307 PF14169 YdjO: Cold-inducible 21.7 67 0.0014 20.2 1.5 29 128-159 19-47 (59)
308 PF04810 zf-Sec23_Sec24: Sec23 21.7 44 0.00096 19.0 0.7 30 128-159 3-32 (40)
309 PRK00415 rps27e 30S ribosomal 21.5 92 0.002 19.6 2.1 30 128-162 12-41 (59)
310 PF04981 NMD3: NMD3 family ; 21.0 59 0.0013 26.5 1.5 14 197-210 34-47 (236)
311 PF10013 DUF2256: Uncharacteri 20.9 54 0.0012 19.1 0.9 14 196-209 6-19 (42)
312 PRK03564 formate dehydrogenase 20.9 61 0.0013 27.8 1.6 28 199-226 188-223 (309)
313 COG2260 Predicted Zn-ribbon RN 20.6 1.1E+02 0.0024 19.2 2.3 35 86-122 19-53 (59)
314 KOG4718 Non-SMC (structural ma 20.4 1.2E+02 0.0025 24.5 3.0 47 37-96 180-226 (235)
315 PF01214 CK_II_beta: Casein ki 20.4 1.9E+02 0.0041 22.7 4.2 13 125-137 97-109 (184)
316 smart00653 eIF2B_5 domain pres 20.0 1.4E+02 0.0031 21.3 3.1 27 197-223 79-109 (110)
No 1
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.1e-36 Score=263.03 Aligned_cols=208 Identities=31% Similarity=0.591 Sum_probs=170.5
Q ss_pred hHHHHHHHHHhhhhhcCCCCccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCCH
Q 026541 19 KENLRQEEIKEEELEDIDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLDP 98 (237)
Q Consensus 19 ~~~~~~~~~~~~~~~~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~ 98 (237)
.+.++.+.+.+ ......+..+|.||+.+....+.+..+..|+|.||.+|+++|++++. .....|+||..+|...++.
T Consensus 128 ~~~lA~e~i~s-~~~~~~~~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~~--~~~~~~~C~~~~C~~~l~~ 204 (384)
T KOG1812|consen 128 AYKLAREAIVS-QLPSKLPKEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVKL--LSGTVIRCPHDGCESRLTL 204 (384)
T ss_pred HHHHHHHhhcc-ccccccccccCccCccccccHhhhHHHhcccchhhhHHhHHHhhhhh--ccCCCccCCCCCCCccCCH
Confidence 34444444433 23333468899999966655533334789999999999999999993 3568899999999999999
Q ss_pred HHHhccCChhHHHHHHHHHHHHhhcCCCcccCCccccCceeeeccccC-CcccceeCcccchhhccccccCcCCCCCChh
Q 026541 99 FACKHTIPSSLFLKWCDHLCEDYVLGFERSYCPNRNCMAVMVNECEGI-GRVKKAQCPKCKQWFCFQCKLAWHAGYRCEE 177 (237)
Q Consensus 99 ~~i~~~l~~~~~~~y~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~-~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~ 177 (237)
+....+|++.+.++|.+.+.+.++...+.+|||+++|...+...+... .+.....|+.|+..||.+|+.+||++.+|++
T Consensus 205 ~~c~~llt~kl~e~~e~~~~e~~i~~~~~~ycp~~~C~~l~~~~el~~~~~~~~~~C~~C~~~fCv~C~~~wh~~~sC~e 284 (384)
T KOG1812|consen 205 ESCRKLLTPKLREMWEQRLKEEVIPSLDRVYCPYPRCSSLMSKTELSSEVKSKRRPCVKCHELFCVKCKVPWHANLSCEE 284 (384)
T ss_pred HHHhhhcCHHHHHHHHHHHHHHhhhhhhcccCCCCCchHhhhhhhhccchhhcccccccCCCceeecCCCcCCCCCCHHH
Confidence 999999999999999999999998866666999999999998766432 2356678999999999999999999999999
Q ss_pred hhccccc--chHHHHHHHhcCCcccCCCCCcceeecCCCcceEecCCcEEEeccc
Q 026541 178 SGNLRDR--NDIAFGKLLEKMNWTRCPGCGNCIERKKGCRIMFCRFIFLSLCLCI 230 (237)
Q Consensus 178 ~~~~~~~--~~~~~~~~~~~~~~k~CP~C~~~iek~~GCnhm~C~C~~~fc~~c~ 230 (237)
++++..+ .+......++ .+||+||+|+..|++++|||||+|+||+.|||.|.
T Consensus 285 ykk~~~~~~~d~~~~~~la-~~wr~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~ 338 (384)
T KOG1812|consen 285 YKKLNPEEYVDDITLKYLA-KRWRQCPKCKFMIELSEGCNHMTCRCGHQFCYMCG 338 (384)
T ss_pred HHHhCCcccccHHHHHHHH-HhcCcCcccceeeeecCCcceEEeeccccchhhcC
Confidence 9998754 3333333444 89999999999999999999999999999999998
No 2
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2.1e-35 Score=246.84 Aligned_cols=197 Identities=25% Similarity=0.548 Sum_probs=164.4
Q ss_pred hhhhcCCCCccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCCHHHHhccCChhH
Q 026541 30 EELEDIDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLDPFACKHTIPSSL 109 (237)
Q Consensus 30 ~~~~~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~~l~~~~ 109 (237)
..+......+.|.||+++.....-| ..++|+|+||+.|+++|++..|++|....++||+++|+...++..++.+|..++
T Consensus 176 ~~~~F~~slf~C~ICf~e~~G~~c~-~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C~~~a~~g~vKelvg~EL 254 (445)
T KOG1814|consen 176 TLEKFVNSLFDCCICFEEQMGQHCF-KFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCGSVAPPGQVKELVGDEL 254 (445)
T ss_pred HHHHHHhhcccceeeehhhcCccee-eecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCCcccCCchHHHHHHHHHH
Confidence 4445568899999999999654444 589999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhhc-CCCcccCCccccCceeeeccccCCcccceeCcccchhhccccccCcCCCCCChhhhc--------
Q 026541 110 FLKWCDHLCEDYVL-GFERSYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQWFCFQCKLAWHAGYRCEESGN-------- 180 (237)
Q Consensus 110 ~~~y~~~~~~~~~~-~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~-------- 180 (237)
+++|.+++.++++. ..+.+|||++.|..+...+++ ...+.|..|+..||..|+..||+...|.--..
T Consensus 255 ~arYe~l~lqk~l~~msdv~yCPr~~Cq~p~~~d~~----~~l~~CskCnFaFCtlCk~t~HG~s~Ck~~~~~~~~l~~~ 330 (445)
T KOG1814|consen 255 FARYEKLMLQKTLELMSDVVYCPRACCQLPVKQDPG----RALAICSKCNFAFCTLCKLTWHGVSPCKVKAEKLIELYLE 330 (445)
T ss_pred HHHHHHHHHHHHHHhhcccccCChhhccCccccCch----hhhhhhccCccHHHHHHHHhhcCCCcccCchHHHHHHHHH
Confidence 99999999999887 688899999999999976666 58999999999999999999999888964321
Q ss_pred cccc------------ch----HHHHHHHh----cCCcccCCCCCcceeecCCCcceEe-cCCcEEEecccc
Q 026541 181 LRDR------------ND----IAFGKLLE----KMNWTRCPGCGNCIERKKGCRIMFC-RFIFLSLCLCIF 231 (237)
Q Consensus 181 ~~~~------------~~----~~~~~~~~----~~~~k~CP~C~~~iek~~GCnhm~C-~C~~~fc~~c~~ 231 (237)
|... +. .++.+..+ ..+.|+||+|+++|||++|||+|.| .|++.|||.|..
T Consensus 331 ~~~~d~a~k~ele~Ryg~rvve~~vn~~lsekwl~~N~krCP~C~v~IEr~eGCnKM~C~~c~~~fc~~c~~ 402 (445)
T KOG1814|consen 331 YLEADEARKRELEKRYGKRVVEELVNDFLSEKWLESNSKRCPKCKVVIERSEGCNKMHCTKCGTYFCWICAE 402 (445)
T ss_pred HhhcCHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhcCCCCCcccceeecCCCccceeeccccccceeehhh
Confidence 1100 10 01111111 3466999999999999999999999 599889988864
No 3
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.95 E-value=3.2e-28 Score=215.57 Aligned_cols=193 Identities=23% Similarity=0.473 Sum_probs=160.0
Q ss_pred CCCccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCCHHHHhccCCh-hHHHHHH
Q 026541 36 DGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLDPFACKHTIPS-SLFLKWC 114 (237)
Q Consensus 36 ~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~~l~~-~~~~~y~ 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 456899999999854 235789999999999999999999996554599999999999999999999988 5999999
Q ss_pred HHHHHHhhcC-CCcccCCccccCceeeeccccCCcccceeCcccchhhccccccCcCCCCCChhhhcccccchHHHHHHH
Q 026541 115 DHLCEDYVLG-FERSYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQWFCFQCKLAWHAGYRCEESGNLRDRNDIAFGKLL 193 (237)
Q Consensus 115 ~~~~~~~~~~-~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~ 193 (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---ESVEVDCG-CGHEFCFACGEESHSPVSCPGAKKWLKKCRDDSETIN 220 (444)
T ss_pred HHHHHHHHhcCCccccCCCCCCCceeeccCC---CccceeCC-CCchhHhhccccccCCCcccchHHHHHhhhhhhhhhh
Confidence 9999999984 44789999999999987422 25889996 7779999999999999999999888755222222111
Q ss_pred -hcCCcccCCCCCcceeecCCCcceEec---CCcEEEecc--ccCCCc
Q 026541 194 -EKMNWTRCPGCGNCIERKKGCRIMFCR---FIFLSLCLC--IFSNRY 235 (237)
Q Consensus 194 -~~~~~k~CP~C~~~iek~~GCnhm~C~---C~~~fc~~c--~~~~~~ 235 (237)
...++++||+|..+|+|++|||||+|. |++.|||.| .|++|.
T Consensus 221 wi~~ntk~CP~c~~~iek~~gc~~~~~~~~~c~~~FCw~Cl~~~~~h~ 268 (444)
T KOG1815|consen 221 WILANTKECPKCKVPIEKDGGCNHMTCKSASCKHEFCWVCLASLSDHG 268 (444)
T ss_pred hhhccCccCCCcccchhccCCccccccccCCcCCeeceeeeccccccc
Confidence 246788999999999999999999994 998777766 666773
No 4
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=99.93 E-value=7.2e-26 Score=183.82 Aligned_cols=189 Identities=24% Similarity=0.429 Sum_probs=144.6
Q ss_pred hhcCCCCccccccccCCCccccccccCCCC--CcccHHHHHHHHHhhcccCC-------ceeecCCCCcCCCC-CCHHHH
Q 026541 32 LEDIDGTFTCDICIEPMSVNNKFKNNNLCT--HPFCQDCTVKYIEVKVRDNN-------TAKIECPGLHCEQF-LDPFAC 101 (237)
Q Consensus 32 ~~~~~~~~~C~iC~~~~~~~~~~~~~~~C~--H~~C~~Cl~~~~~~~i~~~~-------~~~i~CP~~~C~~~-i~~~~i 101 (237)
+..+....+|..|.+.... + .+++|. |+.|.+|++.|..+.+.+.. .+.+.||+ +|... |..-.-
T Consensus 215 i~~N~~ni~C~~Ctdv~~~---v-lvf~Cns~HvtC~dCFr~yc~~Rl~~rqf~~~p~~gyslpc~a-gc~~s~i~e~HH 289 (446)
T KOG0006|consen 215 IATNSRNITCITCTDVRSP---V-LVFQCNSRHVTCLDCFRLYCVTRLNDRQFVHDPQLGYSLPCVA-GCPNSLIKELHH 289 (446)
T ss_pred hhcccccceeEEecCCccc---e-EEEecCCceeehHHhhhhHhhhcccccccccCccccccccccC-CCchHHHHhhhh
Confidence 4457889999999986633 2 367886 99999999999999997632 34678886 58744 434445
Q ss_pred hccCChhHHHHHHHHHHHHhhcCCCcccCCccccCceeeeccccCCcccceeCcc-cchhhccccccCcCCCCCChhhhc
Q 026541 102 KHTIPSSLFLKWCDHLCEDYVLGFERSYCPNRNCMAVMVNECEGIGRVKKAQCPK-CKQWFCFQCKLAWHAGYRCEESGN 180 (237)
Q Consensus 102 ~~~l~~~~~~~y~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~-C~~~~C~~C~~~~H~~~~C~~~~~ 180 (237)
..+|..+.|++|+++..+.++...+-+-||+|+|+..+..++. ..+++|+. |++.||+.|+..||.| .|.+.-.
T Consensus 290 F~ilg~e~Y~rYQr~atEe~vlq~gGVlCP~pgCG~gll~EPD----~rkvtC~~gCgf~FCR~C~e~yh~g-eC~~~~~ 364 (446)
T KOG0006|consen 290 FRILGEEQYNRYQRYATEECVLQMGGVLCPRPGCGAGLLPEPD----QRKVTCEGGCGFAFCRECKEAYHEG-ECSAVFE 364 (446)
T ss_pred heecchhHHHHHHHhhhhhheeecCCEecCCCCCCcccccCCC----CCcccCCCCchhHhHHHHHhhhccc-cceeeec
Confidence 5689999999999999999988777899999999999998886 68999986 9999999999999976 3431110
Q ss_pred --------ccccc---h----HHHHHHHhcCCcccCCCCCcceeecCCCcceEe-c--CCcEEEeccc
Q 026541 181 --------LRDRN---D----IAFGKLLEKMNWTRCPGCGNCIERKKGCRIMFC-R--FIFLSLCLCI 230 (237)
Q Consensus 181 --------~~~~~---~----~~~~~~~~~~~~k~CP~C~~~iek~~GCnhm~C-~--C~~~fc~~c~ 230 (237)
+.-+. . +.+.....+..+|+||+|++++|||+||.||.| + ||+.|||.|.
T Consensus 365 as~t~tc~y~vde~~a~~arwd~as~~TIk~tTkpCPkChvptErnGGCmHm~Ct~~~Cg~eWCw~C~ 432 (446)
T KOG0006|consen 365 ASGTTTCAYRVDERAAEQARWDAASKETIKKTTKPCPKCHVPTERNGGCMHMKCTQPQCGLEWCWNCG 432 (446)
T ss_pred cccccceeeecChhhhhhhhhhhhhhhhhhhccCCCCCccCccccCCceEEeecCCCCCCceeEeccC
Confidence 00000 0 111222235677999999999999999999999 4 9999888664
No 5
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=99.34 E-value=1.8e-12 Score=84.31 Aligned_cols=63 Identities=35% Similarity=0.817 Sum_probs=54.5
Q ss_pred HHHHHHHHHHhhcC-CCcccCCccccCceeeeccccCCcccceeCcccchhhccccccCcCCCCCC
Q 026541 111 LKWCDHLCEDYVLG-FERSYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQWFCFQCKLAWHAGYRC 175 (237)
Q Consensus 111 ~~y~~~~~~~~~~~-~~~~~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 EKYERLLLESYVESNPDLKWCPAPDCSAAIIVTEE--EGCNRVTCPKCGFSFCFRCKVPWHSPVSC 64 (64)
T ss_pred ChHHHHHHHHHHhcCCCccCCCCCCCcceEEecCC--CCCCeeECCCCCCeECCCCCCcCCCCCCC
Confidence 47889999999884 67899999999999988741 12589999999999999999999999987
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=99.27 E-value=6.5e-13 Score=86.45 Aligned_cols=63 Identities=29% Similarity=0.714 Sum_probs=41.6
Q ss_pred HHHHHHHHHHhhc-CCCcccCCccccCceeeeccccCCcccceeCcccchhhccccccCcCCCCCC
Q 026541 111 LKWCDHLCEDYVL-GFERSYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQWFCFQCKLAWHAGYRC 175 (237)
Q Consensus 111 ~~y~~~~~~~~~~-~~~~~~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 4688888888776 45678999999999999988732 124999999999999999999999876
No 7
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.63 E-value=2.1e-08 Score=59.24 Aligned_cols=41 Identities=24% Similarity=0.674 Sum_probs=28.3
Q ss_pred ccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCC
Q 026541 41 CDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPG 89 (237)
Q Consensus 41 C~iC~~~~~~~~~~~~~~~C~H~~C~~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 89999998543 679999999999999998654322 288987
No 8
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.49 E-value=9.1e-08 Score=56.55 Aligned_cols=43 Identities=33% Similarity=0.695 Sum_probs=24.5
Q ss_pred ccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCC
Q 026541 41 CDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECP 88 (237)
Q Consensus 41 C~iC~~~~~~~~~~~~~~~C~H~~C~~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 756566667899999999999999887432 3467887
No 9
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.45 E-value=1.1e-07 Score=74.16 Aligned_cols=67 Identities=22% Similarity=0.507 Sum_probs=50.1
Q ss_pred CCCCccccccccCCCccccccccCCCCCcccHHHHHHHHHhhccc--------CCceeecCCCCcCCCCCCHHHHhccCC
Q 026541 35 IDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRD--------NNTAKIECPGLHCEQFLDPFACKHTIP 106 (237)
Q Consensus 35 ~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~--------~~~~~i~CP~~~C~~~i~~~~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 45679999999987432 567899999999999998643110 1234679999 999999887777644
Q ss_pred h
Q 026541 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 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=98.43 E-value=8.2e-08 Score=57.42 Aligned_cols=41 Identities=27% Similarity=0.664 Sum_probs=32.6
Q ss_pred cccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCC
Q 026541 40 TCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPG 89 (237)
Q Consensus 40 ~C~iC~~~~~~~~~~~~~~~C~H~~C~~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 699999999655554 467799999999999999753 18887
No 11
>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=98.39 E-value=2.4e-07 Score=54.41 Aligned_cols=40 Identities=38% Similarity=0.894 Sum_probs=32.2
Q ss_pred ccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCC
Q 026541 41 CDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPG 89 (237)
Q Consensus 41 C~iC~~~~~~~~~~~~~~~C~H~~C~~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 789999885432 37999999999999999987 24467886
No 12
>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=98.32 E-value=3.5e-07 Score=53.13 Aligned_cols=38 Identities=34% Similarity=0.893 Sum_probs=28.6
Q ss_pred ccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCC
Q 026541 41 CDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPG 89 (237)
Q Consensus 41 C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~ 89 (237)
|+||++.+.. . ...++|||.||.+|+.+|++.. .+||.
T Consensus 1 C~iC~~~~~~--~-~~~~~CGH~fC~~C~~~~~~~~--------~~CP~ 38 (39)
T PF13923_consen 1 CPICLDELRD--P-VVVTPCGHSFCKECIEKYLEKN--------PKCPV 38 (39)
T ss_dssp ETTTTSB-SS--E-EEECTTSEEEEHHHHHHHHHCT--------SB-TT
T ss_pred CCCCCCcccC--c-CEECCCCCchhHHHHHHHHHCc--------CCCcC
Confidence 7899998843 1 2479999999999999998742 57876
No 13
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.23 E-value=8e-07 Score=53.07 Aligned_cols=43 Identities=33% Similarity=0.817 Sum_probs=33.8
Q ss_pred cccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCC
Q 026541 40 TCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCE 93 (237)
Q Consensus 40 ~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~ 93 (237)
.|+||++.+..... +.+++|+|+||..|+.... ...+.||. |+
T Consensus 1 ~C~~C~~~~~~~~~-~~l~~CgH~~C~~C~~~~~--------~~~~~CP~--C~ 43 (44)
T PF14634_consen 1 HCNICFEKYSEERR-PRLTSCGHIFCEKCLKKLK--------GKSVKCPI--CR 43 (44)
T ss_pred CCcCcCccccCCCC-eEEcccCCHHHHHHHHhhc--------CCCCCCcC--CC
Confidence 48999999943333 4689999999999999866 24578998 75
No 14
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.17 E-value=1.6e-06 Score=66.13 Aligned_cols=57 Identities=26% Similarity=0.687 Sum_probs=43.2
Q ss_pred CCCCccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCCHHHHhc
Q 026541 35 IDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLDPFACKH 103 (237)
Q Consensus 35 ~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~ 103 (237)
..+.+.|+|||+.+.. ..++...|||.||+.|++..+.. ..+||. |+..|+..++-.
T Consensus 128 ~~~~~~CPiCl~~~se--k~~vsTkCGHvFC~~Cik~alk~--------~~~CP~--C~kkIt~k~~~r 184 (187)
T KOG0320|consen 128 KEGTYKCPICLDSVSE--KVPVSTKCGHVFCSQCIKDALKN--------TNKCPT--CRKKITHKQFHR 184 (187)
T ss_pred cccccCCCceecchhh--ccccccccchhHHHHHHHHHHHh--------CCCCCC--cccccchhhhee
Confidence 4567999999999853 33346889999999998886652 348999 888887665544
No 15
>PHA02926 zinc finger-like protein; Provisional
Probab=98.09 E-value=3.9e-06 Score=66.34 Aligned_cols=59 Identities=24% Similarity=0.513 Sum_probs=43.6
Q ss_pred CCCCccccccccCCC-----ccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCC
Q 026541 35 IDGTFTCDICIEPMS-----VNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLD 97 (237)
Q Consensus 35 ~~~~~~C~iC~~~~~-----~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~ 97 (237)
..+..+|+||++... ....|..+.+|+|.||..|+..|...+... ...-.||. |...+.
T Consensus 167 ~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~--~~~rsCPi--CR~~f~ 230 (242)
T PHA02926 167 VSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRET--GASDNCPI--CRTRFR 230 (242)
T ss_pred ccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhcccc--CcCCcCCC--Ccceee
Confidence 466799999999862 223455677999999999999999875422 23457999 986654
No 16
>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=98.07 E-value=3.7e-06 Score=49.78 Aligned_cols=44 Identities=32% Similarity=0.760 Sum_probs=33.0
Q ss_pred cccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCC
Q 026541 40 TCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQF 95 (237)
Q Consensus 40 ~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~ 95 (237)
+|.||++.+. +.+ ...+|+|.||..|+..++.. ...+||. |+..
T Consensus 1 ~C~iC~~~~~--~~~-~~~~C~H~~c~~C~~~~~~~-------~~~~Cp~--C~~~ 44 (45)
T cd00162 1 ECPICLEEFR--EPV-VLLPCGHVFCRSCIDKWLKS-------GKNTCPL--CRTP 44 (45)
T ss_pred CCCcCchhhh--Cce-EecCCCChhcHHHHHHHHHh-------CcCCCCC--CCCc
Confidence 5899999872 222 35669999999999999875 2357988 8754
No 17
>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=98.05 E-value=2.1e-06 Score=52.73 Aligned_cols=46 Identities=30% Similarity=0.700 Sum_probs=35.3
Q ss_pred CccccccccCCCccccccccCCCCCc-ccHHHHHHHHHhhcccCCceeecCCCCcCCCCCC
Q 026541 38 TFTCDICIEPMSVNNKFKNNNLCTHP-FCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLD 97 (237)
Q Consensus 38 ~~~C~iC~~~~~~~~~~~~~~~C~H~-~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~ 97 (237)
...|.||++.... . .+++|+|. ||.+|+.+++. ...+||. |+++|+
T Consensus 2 ~~~C~iC~~~~~~---~-~~~pCgH~~~C~~C~~~~~~--------~~~~CP~--Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFENPRD---V-VLLPCGHLCFCEECAERLLK--------RKKKCPI--CRQPIE 48 (50)
T ss_dssp HSB-TTTSSSBSS---E-EEETTCEEEEEHHHHHHHHH--------TTSBBTT--TTBB-S
T ss_pred cCCCccCCccCCc---e-EEeCCCChHHHHHHhHHhcc--------cCCCCCc--CChhhc
Confidence 3689999998632 2 57899999 99999999987 2358999 988775
No 18
>PHA02929 N1R/p28-like protein; Provisional
Probab=97.88 E-value=1.4e-05 Score=64.99 Aligned_cols=53 Identities=26% Similarity=0.537 Sum_probs=39.6
Q ss_pred CCCCccccccccCCCccc----cccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCC
Q 026541 35 IDGTFTCDICIEPMSVNN----KFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLD 97 (237)
Q Consensus 35 ~~~~~~C~iC~~~~~~~~----~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~ 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 355789999999874322 13346789999999999998853 238999 987664
No 19
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.87 E-value=7e-06 Score=72.23 Aligned_cols=61 Identities=26% Similarity=0.561 Sum_probs=49.3
Q ss_pred CccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCCHHHHhccCCh
Q 026541 38 TFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLDPFACKHTIPS 107 (237)
Q Consensus 38 ~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~~l~~ 107 (237)
...|+||+++... +..+.|||.||-.||.+|+.... ...+..||. |...|.+.++..+.-.
T Consensus 186 ~~~CPICL~~~~~----p~~t~CGHiFC~~CiLqy~~~s~---~~~~~~CPi--C~s~I~~kdl~pv~~e 246 (513)
T KOG2164|consen 186 DMQCPICLEPPSV----PVRTNCGHIFCGPCILQYWNYSA---IKGPCSCPI--CRSTITLKDLLPVFIE 246 (513)
T ss_pred CCcCCcccCCCCc----ccccccCceeeHHHHHHHHhhhc---ccCCccCCc--hhhhccccceeeeeec
Confidence 7899999998743 35677999999999999999873 235679999 9999998777775533
No 20
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.83 E-value=1e-05 Score=64.35 Aligned_cols=61 Identities=25% Similarity=0.561 Sum_probs=49.6
Q ss_pred cCCCCccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCCHHHHhccC
Q 026541 34 DIDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLDPFACKHTI 105 (237)
Q Consensus 34 ~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~~l 105 (237)
.+...++|.||++..... ++..|||.||=.||.+|+...... -.||. |+..++.+.|-.+.
T Consensus 43 ~~~~~FdCNICLd~akdP----VvTlCGHLFCWpClyqWl~~~~~~-----~~cPV--CK~~Vs~~~vvPlY 103 (230)
T KOG0823|consen 43 RDGGFFDCNICLDLAKDP----VVTLCGHLFCWPCLYQWLQTRPNS-----KECPV--CKAEVSIDTVVPLY 103 (230)
T ss_pred CCCCceeeeeeccccCCC----EEeecccceehHHHHHHHhhcCCC-----eeCCc--cccccccceEEeee
Confidence 367899999999987443 678899999999999999876544 36788 99999888776654
No 21
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.83 E-value=1.1e-05 Score=68.08 Aligned_cols=110 Identities=23% Similarity=0.496 Sum_probs=69.0
Q ss_pred CCCCccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCCHHHHhccCChhHHHHHH
Q 026541 35 IDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLDPFACKHTIPSSLFLKWC 114 (237)
Q Consensus 35 ~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~~l~~~~~~~y~ 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 46789999999999654 5799999999999999887 4489999 984 222 222222333222
Q ss_pred HHHHHHhhcC-C--CcccCCccccCceeeeccccCCcccceeCcccchhhccccc-cCcCCCCCCh
Q 026541 115 DHLCEDYVLG-F--ERSYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQWFCFQCK-LAWHAGYRCE 176 (237)
Q Consensus 115 ~~~~~~~~~~-~--~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~-~~~H~~~~C~ 176 (237)
.......... . ....|+. +.....+.|..|+...|..|. ...|.++.-.
T Consensus 71 ~~~~~~~~~~~~~~~~~~c~~-------------~~~~~~~~c~~~~~~~c~~c~~~~~h~~h~~~ 123 (386)
T KOG2177|consen 71 ERLRQLRLSRPLGSKEELCEK-------------HGEELKLFCEEDEKLLCVLCRESGEHRGHPVL 123 (386)
T ss_pred HHHHhcCCcccccccchhhhh-------------cCCcceEEecccccccCCCCCCcccccCCccc
Confidence 2222211110 0 0112331 111267889999999999998 5677776543
No 22
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=97.82 E-value=3.4e-05 Score=49.69 Aligned_cols=40 Identities=23% Similarity=0.471 Sum_probs=35.5
Q ss_pred CCcccCC--CCCcceeecC--CCcceEe-cCCcEEEeccccCCCc
Q 026541 196 MNWTRCP--GCGNCIERKK--GCRIMFC-RFIFLSLCLCIFSNRY 235 (237)
Q Consensus 196 ~~~k~CP--~C~~~iek~~--GCnhm~C-~C~~~fc~~c~~~~~~ 235 (237)
..++.|| +|+..|+..+ |..+|+| .|++.||+.|.-.-|.
T Consensus 16 ~~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H~ 60 (64)
T smart00647 16 PDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWHS 60 (64)
T ss_pred CCccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcCCC
Confidence 5789999 9999999975 9999999 6999999999877664
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=97.69 E-value=5.7e-05 Score=48.49 Aligned_cols=51 Identities=18% Similarity=0.081 Sum_probs=40.5
Q ss_pred ccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCCHHHHhc
Q 026541 39 FTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLDPFACKH 103 (237)
Q Consensus 39 ~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~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 5799999988542 56799999999999999975 237998 888887666554
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=97.69 E-value=3.6e-05 Score=43.79 Aligned_cols=30 Identities=33% Similarity=0.916 Sum_probs=24.3
Q ss_pred ccccccCCCccccccccCCCCCcccHHHHHHHHH
Q 026541 41 CDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIE 74 (237)
Q Consensus 41 C~iC~~~~~~~~~~~~~~~C~H~~C~~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 789988742 2 25688999999999999987
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=97.67 E-value=4.1e-05 Score=66.74 Aligned_cols=71 Identities=21% Similarity=0.461 Sum_probs=50.2
Q ss_pred hhhcCCCCccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCCHHHHhc-cCChhH
Q 026541 31 ELEDIDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLDPFACKH-TIPSSL 109 (237)
Q Consensus 31 ~~~~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~-~l~~~~ 109 (237)
.+......+.|+||.+.+... ++++|+|.||..|+..++... ..||. |...+....++. .+-.++
T Consensus 19 ~l~~Le~~l~C~IC~d~~~~P----vitpCgH~FCs~CI~~~l~~~--------~~CP~--Cr~~~~~~~Lr~N~~L~~i 84 (397)
T TIGR00599 19 SLYPLDTSLRCHICKDFFDVP----VLTSCSHTFCSLCIRRCLSNQ--------PKCPL--CRAEDQESKLRSNWLVSEI 84 (397)
T ss_pred cccccccccCCCcCchhhhCc----cCCCCCCchhHHHHHHHHhCC--------CCCCC--CCCccccccCccchHHHHH
Confidence 344556789999999988432 468999999999999988631 27998 998877544432 333456
Q ss_pred HHHHHH
Q 026541 110 FLKWCD 115 (237)
Q Consensus 110 ~~~y~~ 115 (237)
++.|..
T Consensus 85 Ve~~~~ 90 (397)
T TIGR00599 85 VESFKN 90 (397)
T ss_pred HHHHHH
Confidence 666653
No 26
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=97.62 E-value=2.6e-05 Score=63.97 Aligned_cols=54 Identities=30% Similarity=0.682 Sum_probs=43.6
Q ss_pred CCCCccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCCHHHHh
Q 026541 35 IDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLDPFACK 102 (237)
Q Consensus 35 ~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i~ 102 (237)
...+..|.+|++..... +..+|||.||-.|+..|...+- .||. |...+.+..+-
T Consensus 236 ~~a~~kC~LCLe~~~~p----SaTpCGHiFCWsCI~~w~~ek~--------eCPl--CR~~~~pskvi 289 (293)
T KOG0317|consen 236 PEATRKCSLCLENRSNP----SATPCGHIFCWSCILEWCSEKA--------ECPL--CREKFQPSKVI 289 (293)
T ss_pred CCCCCceEEEecCCCCC----CcCcCcchHHHHHHHHHHcccc--------CCCc--ccccCCCccee
Confidence 35668999999988443 6799999999999999997654 2999 99888776543
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=97.62 E-value=0.00015 Score=60.82 Aligned_cols=57 Identities=23% Similarity=0.470 Sum_probs=40.4
Q ss_pred ccccccccCCCcccccc-ccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCCHHHHhcc
Q 026541 39 FTCDICIEPMSVNNKFK-NNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLDPFACKHT 104 (237)
Q Consensus 39 ~~C~iC~~~~~~~~~~~-~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~~ 104 (237)
..|++|..+...+..+. .+..|||.||..|+...+. . .+..||. |+.++....++..
T Consensus 4 ~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~----~---~~~~CP~--C~~~lrk~~fr~q 61 (309)
T TIGR00570 4 QGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFV----R---GSGSCPE--CDTPLRKNNFRVQ 61 (309)
T ss_pred CCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhc----C---CCCCCCC--CCCccchhhcccc
Confidence 57999999754433221 1227999999999999873 1 2348997 9998887765543
No 28
>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=97.57 E-value=3.1e-05 Score=49.81 Aligned_cols=41 Identities=24% Similarity=0.361 Sum_probs=28.3
Q ss_pred cCCcccCCC--CCcceeecCCCcc--eEec-CCcEEEeccccCCCc
Q 026541 195 KMNWTRCPG--CGNCIERKKGCRI--MFCR-FIFLSLCLCIFSNRY 235 (237)
Q Consensus 195 ~~~~k~CP~--C~~~iek~~GCnh--m~C~-C~~~fc~~c~~~~~~ 235 (237)
....+.||+ |...|++..|.++ |+|. |++.||+.|.-.-|.
T Consensus 15 ~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~ 60 (64)
T PF01485_consen 15 DPNIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPWHE 60 (64)
T ss_dssp ---CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSESCT
T ss_pred CCCccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCcccCC
Confidence 455689988 9999999999999 9997 999999999876564
No 29
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.48 E-value=7.8e-05 Score=61.56 Aligned_cols=54 Identities=26% Similarity=0.611 Sum_probs=45.4
Q ss_pred CCCCccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCCH
Q 026541 35 IDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLDP 98 (237)
Q Consensus 35 ~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~ 98 (237)
.+...+|.||++.+...++. .+++|.|.|...|+.+|+. .....||. |..++++
T Consensus 320 a~~GveCaICms~fiK~d~~-~vlPC~H~FH~~Cv~kW~~-------~y~~~CPv--Crt~iPP 373 (374)
T COG5540 320 ADKGVECAICMSNFIKNDRL-RVLPCDHRFHVGCVDKWLL-------GYSNKCPV--CRTAIPP 373 (374)
T ss_pred cCCCceEEEEhhhhcccceE-EEeccCceechhHHHHHHh-------hhcccCCc--cCCCCCC
Confidence 46679999999999777764 5899999999999999995 35568999 9988764
No 30
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.47 E-value=7.5e-05 Score=63.62 Aligned_cols=52 Identities=31% Similarity=0.671 Sum_probs=42.5
Q ss_pred CCCccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCC
Q 026541 36 DGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLD 97 (237)
Q Consensus 36 ~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~ 97 (237)
..+.+|-||+|++...+..+ .++|.|.|+..|+..|+... + -.||. |+..+.
T Consensus 227 ~~~~~CaIClEdY~~GdklR-iLPC~H~FH~~CIDpWL~~~-r------~~CPv--CK~di~ 278 (348)
T KOG4628|consen 227 DATDTCAICLEDYEKGDKLR-ILPCSHKFHVNCIDPWLTQT-R------TFCPV--CKRDIR 278 (348)
T ss_pred CCCceEEEeecccccCCeee-EecCCCchhhccchhhHhhc-C------ccCCC--CCCcCC
Confidence 33479999999999888775 69999999999999999854 2 26999 886544
No 31
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=97.39 E-value=6.9e-05 Score=62.75 Aligned_cols=66 Identities=24% Similarity=0.570 Sum_probs=50.5
Q ss_pred CCCCccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCCHHHHhc-cCChhHHHHH
Q 026541 35 IDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLDPFACKH-TIPSSLFLKW 113 (237)
Q Consensus 35 ~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~-~l~~~~~~~y 113 (237)
.+..+.|.||.+.|... ...+|+|.||.-|++.|+. ....||. |..++....++. .+-.++++-|
T Consensus 20 lD~lLRC~IC~eyf~ip----~itpCsHtfCSlCIR~~L~--------~~p~CP~--C~~~~~Es~Lr~n~il~Eiv~S~ 85 (442)
T KOG0287|consen 20 LDDLLRCGICFEYFNIP----MITPCSHTFCSLCIRKFLS--------YKPQCPT--CCVTVTESDLRNNRILDEIVKSL 85 (442)
T ss_pred hHHHHHHhHHHHHhcCc----eeccccchHHHHHHHHHhc--------cCCCCCc--eecccchhhhhhhhHHHHHHHHH
Confidence 35578999999998443 5678999999999999996 3457999 999999888876 3344555555
Q ss_pred H
Q 026541 114 C 114 (237)
Q Consensus 114 ~ 114 (237)
.
T Consensus 86 ~ 86 (442)
T KOG0287|consen 86 N 86 (442)
T ss_pred H
Confidence 4
No 32
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.09 E-value=0.0015 Score=56.42 Aligned_cols=120 Identities=20% Similarity=0.471 Sum_probs=78.0
Q ss_pred hhhhhcCCCCccccc--cccCC--CccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCCHHHHhcc
Q 026541 29 EEELEDIDGTFTCDI--CIEPM--SVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLDPFACKHT 104 (237)
Q Consensus 29 ~~~~~~~~~~~~C~i--C~~~~--~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~~ 104 (237)
.+..+.......||- |..+. .+.+.+..-..|.-+||..|...|-- . . + |+.... +.++-+
T Consensus 264 qk~l~~msdv~yCPr~~Cq~p~~~d~~~~l~~CskCnFaFCtlCk~t~HG------~-s--~-----Ck~~~~-~~~~l~ 328 (445)
T KOG1814|consen 264 QKTLELMSDVVYCPRACCQLPVKQDPGRALAICSKCNFAFCTLCKLTWHG------V-S--P-----CKVKAE-KLIELY 328 (445)
T ss_pred HHHHHhhcccccCChhhccCccccCchhhhhhhccCccHHHHHHHHhhcC------C-C--c-----ccCchH-HHHHHH
Confidence 345556777889998 65542 12233444567899999999887642 1 1 1 665543 222221
Q ss_pred ---C--Ch----hHHHHHHHHHHHHhhc--------CCCcccCCccccCceeeeccccCCcccceeCcccchhhcccccc
Q 026541 105 ---I--PS----SLFLKWCDHLCEDYVL--------GFERSYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQWFCFQCKL 167 (237)
Q Consensus 105 ---l--~~----~~~~~y~~~~~~~~~~--------~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~ 167 (237)
+ +. ++..+|-+++.+..+. ..+...|| .|..++.+.++ .+++.|..|++.||+.|..
T Consensus 329 ~~~~~~d~a~k~ele~Ryg~rvve~~vn~~lsekwl~~N~krCP--~C~v~IEr~eG----CnKM~C~~c~~~fc~~c~~ 402 (445)
T KOG1814|consen 329 LEYLEADEARKRELEKRYGKRVVEELVNDFLSEKWLESNSKRCP--KCKVVIERSEG----CNKMHCTKCGTYFCWICAE 402 (445)
T ss_pred HHHhhcCHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhcCCCCC--cccceeecCCC----ccceeeccccccceeehhh
Confidence 1 11 3556666444333321 24568899 99999999888 7999999999999999997
Q ss_pred Cc
Q 026541 168 AW 169 (237)
Q Consensus 168 ~~ 169 (237)
..
T Consensus 403 ~l 404 (445)
T KOG1814|consen 403 LL 404 (445)
T ss_pred hc
Confidence 54
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=97.03 E-value=0.00065 Score=45.10 Aligned_cols=44 Identities=25% Similarity=0.483 Sum_probs=30.4
Q ss_pred CccccccccCCCcc---------ccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCC
Q 026541 38 TFTCDICIEPMSVN---------NKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPG 89 (237)
Q Consensus 38 ~~~C~iC~~~~~~~---------~~~~~~~~C~H~~C~~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 44599999998322 11223457999999999999996321 8887
No 34
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=97.00 E-value=0.0004 Score=61.52 Aligned_cols=59 Identities=25% Similarity=0.637 Sum_probs=47.2
Q ss_pred hcCCCCccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCCHHH
Q 026541 33 EDIDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLDPFA 100 (237)
Q Consensus 33 ~~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~ 100 (237)
..+.....|.+|-++... - ...+|.|.||+-|++.|+.....+ ..+.||. |...++.+.
T Consensus 531 ~enk~~~~C~lc~d~aed--~--i~s~ChH~FCrlCi~eyv~~f~~~---~nvtCP~--C~i~LsiDl 589 (791)
T KOG1002|consen 531 DENKGEVECGLCHDPAED--Y--IESSCHHKFCRLCIKEYVESFMEN---NNVTCPV--CHIGLSIDL 589 (791)
T ss_pred ccccCceeecccCChhhh--h--HhhhhhHHHHHHHHHHHHHhhhcc---cCCCCcc--ccccccccc
Confidence 446778999999987632 2 478999999999999999987765 2399999 998877653
No 35
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=97.00 E-value=0.00028 Score=46.46 Aligned_cols=59 Identities=19% Similarity=0.342 Sum_probs=28.4
Q ss_pred CccccccccCCCcccccc-c---cCCCCCcccHHHHHHHHHhhcccCCce---eecCCCCcCCCCCCH
Q 026541 38 TFTCDICIEPMSVNNKFK-N---NNLCTHPFCQDCTVKYIEVKVRDNNTA---KIECPGLHCEQFLDP 98 (237)
Q Consensus 38 ~~~C~iC~~~~~~~~~~~-~---~~~C~H~~C~~Cl~~~~~~~i~~~~~~---~i~CP~~~C~~~i~~ 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 468999998874222211 1 136899999999999998765542222 247999 9988764
No 36
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=96.68 E-value=0.0015 Score=41.12 Aligned_cols=50 Identities=22% Similarity=0.569 Sum_probs=32.1
Q ss_pred CCCCccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCC
Q 026541 35 IDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCE 93 (237)
Q Consensus 35 ~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~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--V-KSKKCGHTFEKEAILQYI------QRNGSKRCPVAGCN 57 (57)
T ss_dssp SB--SB-TTTSSB-SSE--E-EESSS--EEEHHHHHHHC------TTTS-EE-SCCC-S
T ss_pred cEeccCCCCcCChhhCC--c-CcCCCCCeecHHHHHHHH------HhcCCCCCCCCCCC
Confidence 45578999999988533 2 456899999999999999 24567899999985
No 37
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=96.64 E-value=0.0007 Score=62.63 Aligned_cols=57 Identities=19% Similarity=0.549 Sum_probs=45.1
Q ss_pred CCCCccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCCHHHHhcc
Q 026541 35 IDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLDPFACKHT 104 (237)
Q Consensus 35 ~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~~ 104 (237)
-....+|++|-+.. .+. +...|+|.||..|++..+.... =+||. |+..|...+|..+
T Consensus 640 yK~~LkCs~Cn~R~--Kd~--vI~kC~H~FC~~Cvq~r~etRq-------RKCP~--Cn~aFganDv~~I 696 (698)
T KOG0978|consen 640 YKELLKCSVCNTRW--KDA--VITKCGHVFCEECVQTRYETRQ-------RKCPK--CNAAFGANDVHRI 696 (698)
T ss_pred HHhceeCCCccCch--hhH--HHHhcchHHHHHHHHHHHHHhc-------CCCCC--CCCCCCccccccc
Confidence 46789999999544 333 4688999999999998886542 37999 9999998888764
No 38
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=96.42 E-value=0.0017 Score=53.57 Aligned_cols=69 Identities=20% Similarity=0.416 Sum_probs=48.3
Q ss_pred hhcCCCCccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCCHHHHhc-cCChhHH
Q 026541 32 LEDIDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLDPFACKH-TIPSSLF 110 (237)
Q Consensus 32 ~~~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~-~l~~~~~ 110 (237)
+..-+....|.||-+.+.. +...+|||.||.-|++.|+.. ...||. |..+.....++. .+..+..
T Consensus 19 L~~LDs~lrC~IC~~~i~i----p~~TtCgHtFCslCIR~hL~~--------qp~CP~--Cr~~~~esrlr~~s~~~ei~ 84 (391)
T COG5432 19 LKGLDSMLRCRICDCRISI----PCETTCGHTFCSLCIRRHLGT--------QPFCPV--CREDPCESRLRGSSGSREIN 84 (391)
T ss_pred hhcchhHHHhhhhhheeec----ceecccccchhHHHHHHHhcC--------CCCCcc--ccccHHhhhcccchhHHHHH
Confidence 3334567889999988843 367899999999999999853 347898 887766555544 3344455
Q ss_pred HHHH
Q 026541 111 LKWC 114 (237)
Q Consensus 111 ~~y~ 114 (237)
+-|.
T Consensus 85 es~~ 88 (391)
T COG5432 85 ESHA 88 (391)
T ss_pred Hhhh
Confidence 5554
No 39
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=96.38 E-value=0.0045 Score=52.77 Aligned_cols=53 Identities=23% Similarity=0.493 Sum_probs=39.7
Q ss_pred CCCCccccccccCCCccc---------cccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCC
Q 026541 35 IDGTFTCDICIEPMSVNN---------KFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLD 97 (237)
Q Consensus 35 ~~~~~~C~iC~~~~~~~~---------~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~ 97 (237)
...--.|.||+++.-..+ +-++.++|||.+...|++.|++.+ =.||. |+.++-
T Consensus 284 ~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERq--------QTCPI--Cr~p~i 345 (491)
T COG5243 284 TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQ--------QTCPI--CRRPVI 345 (491)
T ss_pred cCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhc--------cCCCc--ccCccc
Confidence 455678999999942222 334578999999999999999743 27898 987744
No 40
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=96.20 E-value=0.0008 Score=42.81 Aligned_cols=50 Identities=26% Similarity=0.555 Sum_probs=22.4
Q ss_pred CccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCCHHHHh
Q 026541 38 TFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLDPFACK 102 (237)
Q Consensus 38 ~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~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--V-CLGGCEHIFCSSCIRDCIG----S------ECPV--CHTPAWIQDIQ 56 (65)
T ss_dssp TTS-SSS-S--SS---B----SSS--B-TTTGGGGTT----T------B-SS--S--B-S-SS--
T ss_pred hcCCcHHHHHhcCC--c-eeccCccHHHHHHhHHhcC----C------CCCC--cCChHHHHHHH
Confidence 67899999987432 2 3678999999999866332 1 4999 98665444433
No 41
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.07 E-value=0.0048 Score=50.31 Aligned_cols=52 Identities=27% Similarity=0.552 Sum_probs=38.7
Q ss_pred CccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCCHHHH
Q 026541 38 TFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLDPFAC 101 (237)
Q Consensus 38 ~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i 101 (237)
...|.||++..... ...+|||.||..||...++.+ ..-.||. |.+...+..+
T Consensus 215 d~kC~lC~e~~~~p----s~t~CgHlFC~~Cl~~~~t~~------k~~~Cpl--CRak~~pk~v 266 (271)
T COG5574 215 DYKCFLCLEEPEVP----SCTPCGHLFCLSCLLISWTKK------KYEFCPL--CRAKVYPKKV 266 (271)
T ss_pred ccceeeeecccCCc----ccccccchhhHHHHHHHHHhh------ccccCch--hhhhccchhh
Confidence 67799999987432 678999999999999854322 2236998 9877766655
No 42
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.95 E-value=0.02 Score=48.43 Aligned_cols=123 Identities=22% Similarity=0.370 Sum_probs=67.8
Q ss_pred CccccccccCCCcc--ccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCC--CCHHHHhccCCh-hHHHH
Q 026541 38 TFTCDICIEPMSVN--NKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQF--LDPFACKHTIPS-SLFLK 112 (237)
Q Consensus 38 ~~~C~iC~~~~~~~--~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~--i~~~~i~~~l~~-~~~~~ 112 (237)
...|.||-+++++. +..+..+.|||.+|..|+...+. ...+.||. |..+ +....++.+-.. .+++.
T Consensus 3 ~~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~-------~~~i~cpf--cR~~~~~~~~~~~~l~kNf~ll~~ 73 (296)
T KOG4185|consen 3 FPECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLG-------NSRILCPF--CRETTEIPDGDVKSLQKNFALLQA 73 (296)
T ss_pred CCceeecCccccccCcccCCcccccCceehHhHHHHHhc-------CceeeccC--CCCcccCCchhHhhhhhhHHHHHH
Confidence 56899999999765 45566788999999999888763 35567787 9866 555555554332 23333
Q ss_pred HHHHHHHHhhcCCCcccCCccccCceeeeccccCCcccceeCcccchhhccccccC-cCCCC
Q 026541 113 WCDHLCEDYVLGFERSYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQWFCFQCKLA-WHAGY 173 (237)
Q Consensus 113 y~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~-~H~~~ 173 (237)
.... ....+.......+|. +|.......... ....-.|+.....+|..|... .|.++
T Consensus 74 ~~~~-~~~~~~~~~~~~~~~-~c~~~~~nl~~~--vc~~~~~~~~~~~~c~t~~~~~~~~~~ 131 (296)
T KOG4185|consen 74 IEHM-KKTTVEEKGEADSPP-KCKEHPYNLAEF--VCVEPDCSSKDKLMCRTCEEFGIHKGH 131 (296)
T ss_pred HHHH-hcccccccCcccCCc-ccccCcccccce--eecCCCcchhhhhhhhhccchhhhhhh
Confidence 3332 121222222333441 243322211110 011223555566788877764 34444
No 43
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.90 E-value=0.0079 Score=52.79 Aligned_cols=106 Identities=19% Similarity=0.419 Sum_probs=66.0
Q ss_pred CCccccccccCCCcc----ccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCCHHHHhccCChhHHHH
Q 026541 37 GTFTCDICIEPMSVN----NKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLDPFACKHTIPSSLFLK 112 (237)
Q Consensus 37 ~~~~C~iC~~~~~~~----~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~~l~~~~~~~ 112 (237)
+...|+.++...... .....-..|+-.||.+|-..|-. + ++-++++.+.++.....
T Consensus 237 p~~~C~~l~~~~el~~~~~~~~~~C~~C~~~fCv~C~~~wh~---------~-----------~sC~eykk~~~~~~~d~ 296 (384)
T KOG1812|consen 237 PYPRCSSLMSKTELSSEVKSKRRPCVKCHELFCVKCKVPWHA---------N-----------LSCEEYKKLNPEEYVDD 296 (384)
T ss_pred CCCCchHhhhhhhhccchhhcccccccCCCceeecCCCcCCC---------C-----------CCHHHHHHhCCcccccH
Confidence 677888888766432 11112336777888888332211 1 33367776655332211
Q ss_pred HHHHHHHHhhcCCCcccCCccccCceeeeccccCCcccceeCcccchhhccccccCcCCCCC
Q 026541 113 WCDHLCEDYVLGFERSYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQWFCFQCKLAWHAGYR 174 (237)
Q Consensus 113 y~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~ 174 (237)
....++. ...+.|| .|+..+....+ .+.++|. |++.||..|..+|..+..
T Consensus 297 ----~~~~~la-~~wr~Cp--kC~~~ie~~~G----Cnhm~Cr-C~~~fcy~C~~~~~~~~~ 346 (384)
T KOG1812|consen 297 ----ITLKYLA-KRWRQCP--KCKFMIELSEG----CNHMTCR-CGHQFCYMCGGDWKTHNG 346 (384)
T ss_pred ----HHHHHHH-HhcCcCc--ccceeeeecCC----cceEEee-ccccchhhcCcchhhCCc
Confidence 1111112 3468899 99999977666 7999998 999999999999865443
No 44
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=95.83 E-value=0.01 Score=39.28 Aligned_cols=53 Identities=19% Similarity=0.105 Sum_probs=37.0
Q ss_pred CCCccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCCHHHH
Q 026541 36 DGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLDPFAC 101 (237)
Q Consensus 36 ~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i 101 (237)
.+.+.|+|+.+-.... +.+++||+|.+.++.+|+.. ....||. ++.+++..++
T Consensus 2 P~~f~CpIt~~lM~dP----Vi~~~G~tyer~~I~~~l~~-------~~~~~P~--t~~~l~~~~l 54 (73)
T PF04564_consen 2 PDEFLCPITGELMRDP----VILPSGHTYERSAIERWLEQ-------NGGTDPF--TRQPLSESDL 54 (73)
T ss_dssp SGGGB-TTTSSB-SSE----EEETTSEEEEHHHHHHHHCT-------TSSB-TT--T-SB-SGGGS
T ss_pred CcccCCcCcCcHhhCc----eeCCcCCEEcHHHHHHHHHc-------CCCCCCC--CCCcCCcccc
Confidence 3568899999887543 56789999999999999975 3357888 7888876544
No 45
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=95.76 E-value=0.019 Score=48.14 Aligned_cols=144 Identities=20% Similarity=0.393 Sum_probs=85.9
Q ss_pred CCCCccccchhhhHHHHHHHHHhhhhhcCCCCccccc--cccCCCc---cccccccCCCCCcccHHHHHHHHHhhccc--
Q 026541 7 KPIENRECPRQEKENLRQEEIKEEELEDIDGTFTCDI--CIEPMSV---NNKFKNNNLCTHPFCQDCTVKYIEVKVRD-- 79 (237)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~i--C~~~~~~---~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~-- 79 (237)
|..-..++..++++..+|.--.++-+.. .....|+- |-.-+-+ ...+...-.|+-.||+.|+..|-.-.-..
T Consensus 285 ~e~HHF~ilg~e~Y~rYQr~atEe~vlq-~gGVlCP~pgCG~gll~EPD~rkvtC~~gCgf~FCR~C~e~yh~geC~~~~ 363 (446)
T KOG0006|consen 285 KELHHFRILGEEQYNRYQRYATEECVLQ-MGGVLCPRPGCGAGLLPEPDQRKVTCEGGCGFAFCRECKEAYHEGECSAVF 363 (446)
T ss_pred HhhhhheecchhHHHHHHHhhhhhheee-cCCEecCCCCCCcccccCCCCCcccCCCCchhHhHHHHHhhhccccceeee
Confidence 3344567778889988887444433333 33666653 5332211 12222233589999999999876533222
Q ss_pred CCceeecCCCCcCCCCCCHHHHhccCChhHHHHHHHHHHHHhhcCCCcccCCccccCceeeeccccCCcccceeCcc--c
Q 026541 80 NNTAKIECPGLHCEQFLDPFACKHTIPSSLFLKWCDHLCEDYVLGFERSYCPNRNCMAVMVNECEGIGRVKKAQCPK--C 157 (237)
Q Consensus 80 ~~~~~i~CP~~~C~~~i~~~~i~~~l~~~~~~~y~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~--C 157 (237)
+....- .|...+++.. ..-.+|+.+..+. +. .....|| +|.....++.+ ...+.|+. |
T Consensus 364 ~as~t~-----tc~y~vde~~-------a~~arwd~as~~T-Ik-~tTkpCP--kChvptErnGG----CmHm~Ct~~~C 423 (446)
T KOG0006|consen 364 EASGTT-----TCAYRVDERA-------AEQARWDAASKET-IK-KTTKPCP--KCHVPTERNGG----CMHMKCTQPQC 423 (446)
T ss_pred cccccc-----ceeeecChhh-------hhhhhhhhhhhhh-hh-hccCCCC--CccCccccCCc----eEEeecCCCCC
Confidence 111111 1333333221 2345666654332 22 3457898 89888887776 78999975 9
Q ss_pred chhhccccccCcCC
Q 026541 158 KQWFCFQCKLAWHA 171 (237)
Q Consensus 158 ~~~~C~~C~~~~H~ 171 (237)
+..+|+.|+-.|..
T Consensus 424 g~eWCw~C~tEW~r 437 (446)
T KOG0006|consen 424 GLEWCWNCGTEWNR 437 (446)
T ss_pred CceeEeccCChhhh
Confidence 99999999999864
No 46
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=95.56 E-value=0.0078 Score=51.82 Aligned_cols=67 Identities=25% Similarity=0.365 Sum_probs=50.1
Q ss_pred CCCCCCccccchhhhHHHHHHHHHhhhhhcCCCCccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCcee
Q 026541 5 LQKPIENRECPRQEKENLRQEEIKEEELEDIDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAK 84 (237)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~ 84 (237)
.|-+..++.-.++|+++|+-++- ....-|.||-+.... + ...+|||..|..||..|-.+.- .
T Consensus 344 ~~~~p~d~i~VtqEQyeLYceMg--------sTFeLCKICaendKd---v-kIEPCGHLlCt~CLa~WQ~sd~------g 405 (563)
T KOG1785|consen 344 CQPPPQDRIKVTQEQYELYCEMG--------STFELCKICAENDKD---V-KIEPCGHLLCTSCLAAWQDSDE------G 405 (563)
T ss_pred cCCCcccceeeeHHHHHHHHHcc--------chHHHHHHhhccCCC---c-ccccccchHHHHHHHhhcccCC------C
Confidence 56677788888999999998632 446789999986532 2 5789999999999999864321 2
Q ss_pred ecCCC
Q 026541 85 IECPG 89 (237)
Q Consensus 85 i~CP~ 89 (237)
-.||.
T Consensus 406 q~CPF 410 (563)
T KOG1785|consen 406 QTCPF 410 (563)
T ss_pred CCCCc
Confidence 36887
No 47
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.51 E-value=0.011 Score=50.72 Aligned_cols=94 Identities=19% Similarity=0.408 Sum_probs=56.9
Q ss_pred CCCccccccccCCCccc----cccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCC---HHHH---hccC
Q 026541 36 DGTFTCDICIEPMSVNN----KFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLD---PFAC---KHTI 105 (237)
Q Consensus 36 ~~~~~C~iC~~~~~~~~----~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~---~~~i---~~~l 105 (237)
....+|.||++...... .|..+.+|.|.||..|++.|-...-. +....-.||. |..... +..+ ..--
T Consensus 159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~-~~~~sksCP~--CRv~s~~v~pS~~Wv~t~~~ 235 (344)
T KOG1039|consen 159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQF-ESKTSKSCPF--CRVPSSFVNPSSFWVETKEE 235 (344)
T ss_pred cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhcc-ccccccCCCc--ccCccccccccceeeeeccc
Confidence 66899999999884321 13345779999999999998754433 3555678999 885533 2211 1112
Q ss_pred ChhHHHHHHHHHHHHhhc--CCCcccCCc
Q 026541 106 PSSLFLKWCDHLCEDYVL--GFERSYCPN 132 (237)
Q Consensus 106 ~~~~~~~y~~~~~~~~~~--~~~~~~Cp~ 132 (237)
+..+.+.|.+.+...... ......||.
T Consensus 236 k~~li~e~~~~~s~~~c~yf~~~~g~cPf 264 (344)
T KOG1039|consen 236 KQKLIEEYEAEMSAKDCKYFSQGLGSCPF 264 (344)
T ss_pred ccccHHHHHHHhhccchhhhcCCCCCCCC
Confidence 233556665554433221 244567885
No 48
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=95.39 E-value=0.018 Score=34.60 Aligned_cols=47 Identities=26% Similarity=0.588 Sum_probs=22.1
Q ss_pred ccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCC
Q 026541 41 CDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFL 96 (237)
Q Consensus 41 C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i 96 (237)
|++|.++....+.-+..-+|++.+|+.|+.+-.+ + ..-+||. |+.+.
T Consensus 1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~----~---~~g~CPg--Cr~~Y 47 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILE----N---EGGRCPG--CREPY 47 (48)
T ss_dssp -TTTS-B--CCCTT--SSTTS----HHHHHHHTT----S---S-SB-TT--T--B-
T ss_pred CCCcccccccCCCccccCcCCCcHHHHHHHHHHh----c---cCCCCCC--CCCCC
Confidence 7899998855443223557899999999988654 1 1238998 87653
No 49
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=95.33 E-value=0.016 Score=39.19 Aligned_cols=55 Identities=25% Similarity=0.518 Sum_probs=38.0
Q ss_pred CCCccccccccCCCcc--------cc-ccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCC
Q 026541 36 DGTFTCDICIEPMSVN--------NK-FKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLD 97 (237)
Q Consensus 36 ~~~~~C~iC~~~~~~~--------~~-~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~ 97 (237)
.....|+||...|... +. -++...|+|.|...||.+++.++-. .-.||. |.+++.
T Consensus 19 ~~dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~-----~~~CPm--CR~~w~ 82 (85)
T PF12861_consen 19 ANDDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSS-----KGQCPM--CRQPWK 82 (85)
T ss_pred CCCCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccC-----CCCCCC--cCCeee
Confidence 3466788888777421 11 1123479999999999999987522 238999 987764
No 50
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=95.01 E-value=0.013 Score=49.42 Aligned_cols=50 Identities=30% Similarity=0.750 Sum_probs=39.3
Q ss_pred CCCCccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCC
Q 026541 35 IDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLD 97 (237)
Q Consensus 35 ~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~ 97 (237)
..+..+|.+|-..+-.. ++...|-|+||+.||..|++. ...||. |+..|.
T Consensus 12 ~n~~itC~LC~GYliDA---TTI~eCLHTFCkSCivk~l~~--------~~~CP~--C~i~ih 61 (331)
T KOG2660|consen 12 LNPHITCRLCGGYLIDA---TTITECLHTFCKSCIVKYLEE--------SKYCPT--CDIVIH 61 (331)
T ss_pred cccceehhhccceeecc---hhHHHHHHHHHHHHHHHHHHH--------hccCCc--cceecc
Confidence 36689999999888443 246789999999999999986 237998 875544
No 51
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=94.22 E-value=0.049 Score=51.32 Aligned_cols=57 Identities=21% Similarity=0.514 Sum_probs=45.0
Q ss_pred cCCCCccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCC
Q 026541 34 DIDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCE 93 (237)
Q Consensus 34 ~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~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 3577899999999997766554556789999999999999984444 345678997 76
No 52
>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class
Probab=94.05 E-value=0.074 Score=32.24 Aligned_cols=42 Identities=19% Similarity=0.391 Sum_probs=29.1
Q ss_pred cccccccCCCccccccccCCCC-----CcccHHHHHHHHHhhcccCCceeecCCC
Q 026541 40 TCDICIEPMSVNNKFKNNNLCT-----HPFCQDCTVKYIEVKVRDNNTAKIECPG 89 (237)
Q Consensus 40 ~C~iC~~~~~~~~~~~~~~~C~-----H~~C~~Cl~~~~~~~i~~~~~~~i~CP~ 89 (237)
.|.||++.....+. ...+|. |.+..+||.+|+..+-. .+||.
T Consensus 1 ~CrIC~~~~~~~~~--l~~PC~C~G~~~~vH~~Cl~~W~~~~~~------~~C~i 47 (49)
T smart00744 1 ICRICHDEGDEGDP--LVSPCRCKGSLKYVHQECLERWINESGN------KTCEI 47 (49)
T ss_pred CccCCCCCCCCCCe--eEeccccCCchhHHHHHHHHHHHHHcCC------CcCCC
Confidence 48899984333333 246774 78999999999986532 27776
No 53
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.93 E-value=0.045 Score=46.70 Aligned_cols=49 Identities=22% Similarity=0.518 Sum_probs=37.1
Q ss_pred CCCCccccccccCCCccccccccCCCCCc-ccHHHHHHHHHhhcccCCceeecCCCCcCCCCCC
Q 026541 35 IDGTFTCDICIEPMSVNNKFKNNNLCTHP-FCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLD 97 (237)
Q Consensus 35 ~~~~~~C~iC~~~~~~~~~~~~~~~C~H~-~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~ 97 (237)
++...+|.||+.+.... .+++|+|. .|.+|.+..- +.. =+||. |.++|.
T Consensus 287 ~~~gkeCVIClse~rdt----~vLPCRHLCLCs~Ca~~Lr---~q~-----n~CPI--CRqpi~ 336 (349)
T KOG4265|consen 287 SESGKECVICLSESRDT----VVLPCRHLCLCSGCAKSLR---YQT-----NNCPI--CRQPIE 336 (349)
T ss_pred ccCCCeeEEEecCCcce----EEecchhhehhHhHHHHHH---Hhh-----cCCCc--cccchH
Confidence 35688999999887432 68999998 9999977643 112 26999 998875
No 54
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.54 E-value=0.046 Score=50.36 Aligned_cols=49 Identities=24% Similarity=0.562 Sum_probs=38.2
Q ss_pred CCCccccccccCCCcccc-ccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCC
Q 026541 36 DGTFTCDICIEPMSVNNK-FKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQ 94 (237)
Q Consensus 36 ~~~~~C~iC~~~~~~~~~-~~~~~~C~H~~C~~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 LSDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQ--------QTCPT--CRT 338 (543)
T ss_pred hcCCeeeeechhhccccccccceeecccchHHHHHHHHHHHh--------CcCCc--chh
Confidence 457899999999865322 13578999999999999999872 27887 765
No 55
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.30 E-value=0.14 Score=45.02 Aligned_cols=50 Identities=28% Similarity=0.707 Sum_probs=38.1
Q ss_pred cCCCCccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCC
Q 026541 34 DIDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLD 97 (237)
Q Consensus 34 ~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~ 97 (237)
.....+.|.||+..+... +.++|||.||..|+.+-+. ....||. |...+.
T Consensus 80 ~~~sef~c~vc~~~l~~p----v~tpcghs~c~~Cl~r~ld--------~~~~cp~--Cr~~l~ 129 (398)
T KOG4159|consen 80 EIRSEFECCVCSRALYPP----VVTPCGHSFCLECLDRSLD--------QETECPL--CRDELV 129 (398)
T ss_pred cccchhhhhhhHhhcCCC----ccccccccccHHHHHHHhc--------cCCCCcc--cccccc
Confidence 347899999999988554 5679999999999877222 2357888 886665
No 56
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.25 E-value=0.049 Score=48.35 Aligned_cols=54 Identities=28% Similarity=0.655 Sum_probs=39.8
Q ss_pred CCCCccccccccCCCcc----c-cc--------cccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCC
Q 026541 35 IDGTFTCDICIEPMSVN----N-KF--------KNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLD 97 (237)
Q Consensus 35 ~~~~~~C~iC~~~~~~~----~-~~--------~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~ 97 (237)
...+.+|.||+.+++.- + ++ +.+.+|.|.|.+.||.+|+. ...+.||. |..+++
T Consensus 568 ~~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd-------~ykl~CPv--CR~pLP 634 (636)
T KOG0828|consen 568 VRRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMD-------TYKLICPV--CRCPLP 634 (636)
T ss_pred hhccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHh-------hhcccCCc--cCCCCC
Confidence 46788999999988521 1 11 12458999999999999985 24478998 887765
No 57
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=93.09 E-value=0.15 Score=51.15 Aligned_cols=76 Identities=20% Similarity=0.342 Sum_probs=55.9
Q ss_pred CCCccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCc--eeecCCCCcCCCCCCHHHHhccCCh--hHHH
Q 026541 36 DGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNT--AKIECPGLHCEQFLDPFACKHTIPS--SLFL 111 (237)
Q Consensus 36 ~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~--~~i~CP~~~C~~~i~~~~i~~~l~~--~~~~ 111 (237)
+..-.|.||+.+.-..... ..+.|+|.|...|.+.-++..-....+ .-|.||. |.++|+-..++.+|++ ++++
T Consensus 3484 D~DDmCmICFTE~L~AAP~-IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPi--C~n~InH~~LkDLldPiKel~e 3560 (3738)
T KOG1428|consen 3484 DADDMCMICFTEALSAAPA-IQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPI--CKNKINHIVLKDLLDPIKELYE 3560 (3738)
T ss_pred ccCceEEEEehhhhCCCcc-eecCCccchhHHHHHHHHHhcccCCeeEEeeeeccc--ccchhhhHHHHHHHHHHHHHHH
Confidence 4456799999887443322 468999999999999988765544222 2589999 9999999999988876 4444
Q ss_pred HHH
Q 026541 112 KWC 114 (237)
Q Consensus 112 ~y~ 114 (237)
...
T Consensus 3561 dV~ 3563 (3738)
T KOG1428|consen 3561 DVR 3563 (3738)
T ss_pred HHH
Confidence 433
No 58
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.88 E-value=0.11 Score=42.82 Aligned_cols=51 Identities=24% Similarity=0.549 Sum_probs=37.8
Q ss_pred CCCccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCC
Q 026541 36 DGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLD 97 (237)
Q Consensus 36 ~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~ 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 5678999998764222 2 45679999999998876642 24689999 997665
No 59
>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=92.84 E-value=0.027 Score=45.29 Aligned_cols=51 Identities=24% Similarity=0.568 Sum_probs=37.5
Q ss_pred ccccccccCCCccccc-cccCC-CCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCC
Q 026541 39 FTCDICIEPMSVNNKF-KNNNL-CTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFL 96 (237)
Q Consensus 39 ~~C~iC~~~~~~~~~~-~~~~~-C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i 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 4699998887654333 22234 999999999998774 356789999998553
No 60
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=92.78 E-value=0.033 Score=45.00 Aligned_cols=55 Identities=24% Similarity=0.559 Sum_probs=37.5
Q ss_pred CccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCCHHHHhccCC
Q 026541 38 TFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLDPFACKHTIP 106 (237)
Q Consensus 38 ~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~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-LTACRHVFCEPCLKASS----------PDVCPL--CKKSIRIIQLNRSLP 57 (233)
T ss_pred eEEeccccccCC-CCcee-eeechhhhhhhhcccCC----------cccccc--ccceeeeeecccccc
Confidence 357888887664 55664 78999999999965421 128998 997766544444343
No 61
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=92.76 E-value=0.099 Score=31.84 Aligned_cols=28 Identities=36% Similarity=0.695 Sum_probs=21.2
Q ss_pred ccCCCCCcceeecCC--CcceEec-CCcEEE
Q 026541 199 TRCPGCGNCIERKKG--CRIMFCR-FIFLSL 226 (237)
Q Consensus 199 k~CP~C~~~iek~~G--Cnhm~C~-C~~~fc 226 (237)
+.||.|+.++...++ -+++.|+ ||+++-
T Consensus 1 ~FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~~ 31 (52)
T smart00661 1 KFCPKCGNMLIPKEGKEKRRFVCRKCGYEEP 31 (52)
T ss_pred CCCCCCCCccccccCCCCCEEECCcCCCeEE
Confidence 469999998876543 4689995 998764
No 62
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=92.73 E-value=0.16 Score=43.13 Aligned_cols=63 Identities=27% Similarity=0.529 Sum_probs=43.5
Q ss_pred CccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCCHHHHhc-cCChhH
Q 026541 38 TFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLDPFACKH-TIPSSL 109 (237)
Q Consensus 38 ~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~-~l~~~~ 109 (237)
.-.|++|+++....+.-+...+||-.+|+-||.. |.+.+.. +||+ |....+.+.++- -|+++.
T Consensus 14 ed~cplcie~mditdknf~pc~cgy~ic~fc~~~-irq~lng------rcpa--crr~y~denv~~~~~s~ee 77 (480)
T COG5175 14 EDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNN-IRQNLNG------RCPA--CRRKYDDENVRYVTLSPEE 77 (480)
T ss_pred cccCcccccccccccCCcccCCcccHHHHHHHHH-HHhhccC------CChH--hhhhccccceeEEecCHHH
Confidence 3349999999976554234678899999999875 5444433 8999 997777665553 344443
No 63
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.49 E-value=0.096 Score=43.70 Aligned_cols=53 Identities=25% Similarity=0.397 Sum_probs=39.4
Q ss_pred CCCccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCCHHHH
Q 026541 36 DGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLDPFAC 101 (237)
Q Consensus 36 ~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i 101 (237)
....+|.||+.+-.. ++.+.|.|.||--|++..+.. .-..|+. |..+|+...+
T Consensus 5 ~~~~eC~IC~nt~n~----Pv~l~C~HkFCyiCiKGsy~n-------dk~~Cav--CR~pids~i~ 57 (324)
T KOG0824|consen 5 TKKKECLICYNTGNC----PVNLYCFHKFCYICIKGSYKN-------DKKTCAV--CRFPIDSTID 57 (324)
T ss_pred ccCCcceeeeccCCc----Cccccccchhhhhhhcchhhc-------CCCCCce--ecCCCCcchh
Confidence 457789999988633 368999999999998875532 1235988 9988885543
No 64
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=92.08 E-value=0.11 Score=42.13 Aligned_cols=90 Identities=17% Similarity=0.231 Sum_probs=60.3
Q ss_pred CCCCCCccccchhhhHHHHHHHHH-----------hhhhhcCCCCccccccccCCCccccccccCCCCCcccHHHHHHHH
Q 026541 5 LQKPIENRECPRQEKENLRQEEIK-----------EEELEDIDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYI 73 (237)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~-----------~~~~~~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~ 73 (237)
++||+-+-+|+..-+.-.+.+.+. +..+......+.|++|.+++...-....+.+++|+|+.+|+...|
T Consensus 177 lekP~~~v~CP~s~kplklkdL~~VkFT~l~s~~~et~l~a~s~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEkli 256 (303)
T KOG3039|consen 177 LEKPSTTVVCPVSGKPLKLKDLFAVKFTPLNSEETETKLIAASKRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLI 256 (303)
T ss_pred ccCCCceeeccCCCCccchhhcceeeeeecCCchhhhhhhhhccceecccchhhhcCccceEEeccCCcEeeHHHHHHhc
Confidence 578888888876544333333221 122233457899999999986543334567899999999999877
Q ss_pred HhhcccCCceeecCCCCcCCCCCCHHHHhcc
Q 026541 74 EVKVRDNNTAKIECPGLHCEQFLDPFACKHT 104 (237)
Q Consensus 74 ~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~~ 104 (237)
. ..+.||. |+.++...+|-.+
T Consensus 257 r--------~D~v~pv--~d~plkdrdiI~L 277 (303)
T KOG3039|consen 257 R--------KDMVDPV--TDKPLKDRDIIGL 277 (303)
T ss_pred c--------ccccccC--CCCcCcccceEee
Confidence 5 2356787 8888887766553
No 65
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.68 E-value=0.055 Score=33.15 Aligned_cols=46 Identities=24% Similarity=0.508 Sum_probs=33.4
Q ss_pred ccccccccCCCccccccccCCCCCc-ccHHHHHHHHHhhcccCCceeecCCCCcCCCCCC
Q 026541 39 FTCDICIEPMSVNNKFKNNNLCTHP-FCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLD 97 (237)
Q Consensus 39 ~~C~iC~~~~~~~~~~~~~~~C~H~-~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~ 97 (237)
-+|.||++.--. . ++..|||. +|-+|-.+..+. .. -.||. |..+|.
T Consensus 8 dECTICye~pvd--s--VlYtCGHMCmCy~Cg~rl~~~-~~------g~CPi--CRapi~ 54 (62)
T KOG4172|consen 8 DECTICYEHPVD--S--VLYTCGHMCMCYACGLRLKKA-LH------GCCPI--CRAPIK 54 (62)
T ss_pred cceeeeccCcch--H--HHHHcchHHhHHHHHHHHHHc-cC------CcCcc--hhhHHH
Confidence 689999986532 2 46789998 999998876653 21 26888 887764
No 66
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=91.49 E-value=0.19 Score=30.59 Aligned_cols=27 Identities=19% Similarity=0.506 Sum_probs=19.9
Q ss_pred CcccCCCCCc-ceeecCCCcceEe-cCCcEE
Q 026541 197 NWTRCPGCGN-CIERKKGCRIMFC-RFIFLS 225 (237)
Q Consensus 197 ~~k~CP~C~~-~iek~~GCnhm~C-~C~~~f 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 79999 599865
No 67
>PF04641 Rtf2: Rtf2 RING-finger
Probab=91.47 E-value=0.26 Score=40.98 Aligned_cols=72 Identities=17% Similarity=0.308 Sum_probs=53.7
Q ss_pred CCCCccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCCHHHHhccCCh-hHHHHH
Q 026541 35 IDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLDPFACKHTIPS-SLFLKW 113 (237)
Q Consensus 35 ~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~~l~~-~~~~~y 113 (237)
....+.|||-..++...-.|..+.+|||+|....|...- .+ -.||. |+.++...+|-.+-+. +.++..
T Consensus 110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k----~~-----~~Cp~--c~~~f~~~DiI~Lnp~~ee~~~l 178 (260)
T PF04641_consen 110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK----KS-----KKCPV--CGKPFTEEDIIPLNPPEEELEKL 178 (260)
T ss_pred CCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc----cc-----ccccc--cCCccccCCEEEecCCccHHHHH
Confidence 477899999999996655676788999999999998851 12 24999 9999998887776554 344444
Q ss_pred HHHH
Q 026541 114 CDHL 117 (237)
Q Consensus 114 ~~~~ 117 (237)
...+
T Consensus 179 ~~~~ 182 (260)
T PF04641_consen 179 RERM 182 (260)
T ss_pred HHHH
Confidence 4443
No 68
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.20 E-value=0.18 Score=43.57 Aligned_cols=50 Identities=24% Similarity=0.563 Sum_probs=36.4
Q ss_pred CCccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCC
Q 026541 37 GTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCE 93 (237)
Q Consensus 37 ~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~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 3568999966665555554455699999999999999854432 36776 65
No 69
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=91.16 E-value=0.1 Score=43.46 Aligned_cols=64 Identities=19% Similarity=0.424 Sum_probs=47.7
Q ss_pred hcCCCCccccccccCCCccccccccCCCCCcccHHHHHHHHHhhccc---------------CCceeecCCCCcCCCCCC
Q 026541 33 EDIDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRD---------------NNTAKIECPGLHCEQFLD 97 (237)
Q Consensus 33 ~~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~---------------~~~~~i~CP~~~C~~~i~ 97 (237)
.++-+...|.||+--|.+++.| ....|.|.|...||.+|++.-+.+ .....-.||. |...|.
T Consensus 110 ~nn~p~gqCvICLygfa~~~~f-t~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpV--cre~i~ 186 (368)
T KOG4445|consen 110 ENNHPNGQCVICLYGFASSPAF-TVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPV--CRERIK 186 (368)
T ss_pred cCCCCCCceEEEEEeecCCCce-eeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhH--hhhhcc
Confidence 4567889999999999877767 589999999999999999764432 0011235998 886655
Q ss_pred HH
Q 026541 98 PF 99 (237)
Q Consensus 98 ~~ 99 (237)
++
T Consensus 187 ~e 188 (368)
T KOG4445|consen 187 IE 188 (368)
T ss_pred cc
Confidence 44
No 70
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=91.05 E-value=0.099 Score=40.94 Aligned_cols=34 Identities=26% Similarity=0.640 Sum_probs=27.5
Q ss_pred CCCccccccccCCCccccccccCCCCCcccHHHHHHHH
Q 026541 36 DGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYI 73 (237)
Q Consensus 36 ~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~ 73 (237)
.-.+.|.||-.++.+. ++..|||.||..|...-+
T Consensus 194 ~IPF~C~iCKkdy~sp----vvt~CGH~FC~~Cai~~y 227 (259)
T COG5152 194 KIPFLCGICKKDYESP----VVTECGHSFCSLCAIRKY 227 (259)
T ss_pred CCceeehhchhhccch----hhhhcchhHHHHHHHHHh
Confidence 4467999999999654 578999999999976644
No 71
>PHA00626 hypothetical protein
Probab=91.01 E-value=0.21 Score=30.79 Aligned_cols=26 Identities=31% Similarity=0.651 Sum_probs=19.9
Q ss_pred cCCCCCc-ceeecCCCcc----eEec-CCcEE
Q 026541 200 RCPGCGN-CIERKKGCRI----MFCR-FIFLS 225 (237)
Q Consensus 200 ~CP~C~~-~iek~~GCnh----m~C~-C~~~f 225 (237)
.||+|+. -|.|.+-|+. ..|+ |||.|
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~f 33 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYND 33 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCee
Confidence 5999999 4888776654 7785 99876
No 72
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=89.98 E-value=0.15 Score=44.83 Aligned_cols=48 Identities=29% Similarity=0.598 Sum_probs=36.8
Q ss_pred CCCccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCC
Q 026541 36 DGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQF 95 (237)
Q Consensus 36 ~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~ 95 (237)
.+..+|+||++...+.-..+....|.|+|...|+..| ....||. |...
T Consensus 173 tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w----------~~~scpv--cR~~ 220 (493)
T KOG0804|consen 173 TELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKW----------WDSSCPV--CRYC 220 (493)
T ss_pred ccCCCcchhHhhcCccccceeeeecccccchHHHhhc----------ccCcChh--hhhh
Confidence 6688999999998665444456789999999998764 4467887 7633
No 73
>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=89.52 E-value=0.18 Score=37.17 Aligned_cols=40 Identities=23% Similarity=0.525 Sum_probs=29.7
Q ss_pred CCCccccccccCCCccccccccCCC------CCcccHHHHHHHHHhh
Q 026541 36 DGTFTCDICIEPMSVNNKFKNNNLC------THPFCQDCTVKYIEVK 76 (237)
Q Consensus 36 ~~~~~C~iC~~~~~~~~~~~~~~~C------~H~~C~~Cl~~~~~~~ 76 (237)
....+|.||++.+...+.+ +..++ .|.||.+|+++|-...
T Consensus 24 ~~~~EC~IC~~~I~~~~Gv-V~vt~~g~lnLEkmfc~~C~~rw~~~~ 69 (134)
T PF05883_consen 24 RCTVECQICFDRIDNNDGV-VYVTDGGTLNLEKMFCADCDKRWRRER 69 (134)
T ss_pred ccCeeehhhhhhhhcCCCE-EEEecCCeehHHHHHHHHHHHHHHhhc
Confidence 4589999999999663333 45566 4789999999995443
No 74
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=88.82 E-value=0.26 Score=41.80 Aligned_cols=45 Identities=24% Similarity=0.623 Sum_probs=35.3
Q ss_pred CCCCccccccccCCCccccccccCCC--CCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCC
Q 026541 35 IDGTFTCDICIEPMSVNNKFKNNNLC--THPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLD 97 (237)
Q Consensus 35 ~~~~~~C~iC~~~~~~~~~~~~~~~C--~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~ 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 56789999999999553 4566 8999999955 23348999 998887
No 75
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=88.67 E-value=0.29 Score=27.70 Aligned_cols=32 Identities=31% Similarity=0.657 Sum_probs=23.9
Q ss_pred ccCCccccCceeeecccc-CCcccceeCcccchhh
Q 026541 128 SYCPNRNCMAVMVNECEG-IGRVKKAQCPKCKQWF 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 899988887652 1235699999998765
No 76
>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=88.66 E-value=0.24 Score=25.69 Aligned_cols=23 Identities=35% Similarity=0.785 Sum_probs=16.4
Q ss_pred cCCccccCceeeeccccCCcccceeCcccchhh
Q 026541 129 YCPNRNCMAVMVNECEGIGRVKKAQCPKCKQWF 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--ECGAEVPE--------SAKFCPHCGYDF 24 (26)
T ss_pred cCC--CCcCCchh--------hcCcCCCCCCCC
Confidence 577 78887744 344788888876
No 77
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.45 E-value=0.35 Score=42.15 Aligned_cols=51 Identities=27% Similarity=0.609 Sum_probs=39.8
Q ss_pred CCccccccccCCCcc-ccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCC
Q 026541 37 GTFTCDICIEPMSVN-NKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQF 95 (237)
Q Consensus 37 ~~~~C~iC~~~~~~~-~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~ 95 (237)
-..+|+||++.+... +.....+.|+|.|=.+|++.|+. ......||. |...
T Consensus 3 ~g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~------k~~~~~cp~--c~~k 54 (463)
T KOG1645|consen 3 CGTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLG------KKTKMQCPL--CSGK 54 (463)
T ss_pred ccccCceeeeeeeecCceEEeeecccccccHHHHHHHHh------hhhhhhCcc--cCCh
Confidence 357899999988643 33345788999999999999993 446689999 8854
No 78
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=88.39 E-value=0.39 Score=27.00 Aligned_cols=32 Identities=34% Similarity=0.639 Sum_probs=23.9
Q ss_pred ccCCccccCceeeecccc-CCcccceeCcccchhh
Q 026541 128 SYCPNRNCMAVMVNECEG-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 899988877652 2346789999998765
No 79
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=88.07 E-value=0.79 Score=27.17 Aligned_cols=29 Identities=21% Similarity=0.352 Sum_probs=20.2
Q ss_pred ccCCCCCcceeecCCCcceEec-CCcEEEe
Q 026541 199 TRCPGCGNCIERKKGCRIMFCR-FIFLSLC 227 (237)
Q Consensus 199 k~CP~C~~~iek~~GCnhm~C~-C~~~fc~ 227 (237)
-+||+|+..++-+.+=..++|. ||..+.+
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~ 33 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGYRILF 33 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCCeEEE
Confidence 4688888888766544478885 8876554
No 80
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=87.89 E-value=1.4 Score=32.45 Aligned_cols=58 Identities=21% Similarity=0.459 Sum_probs=42.2
Q ss_pred hhcCCCCccccccccCCCccccccccCC-CCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCC
Q 026541 32 LEDIDGTFTCDICIEPMSVNNKFKNNNL-CTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLD 97 (237)
Q Consensus 32 ~~~~~~~~~C~iC~~~~~~~~~~~~~~~-C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~ 97 (237)
+..+++..+|.||.+.-. .+.|...-. ||-.+|..|-...+...- ....||. |+..+-
T Consensus 74 vF~d~~lYeCnIC~etS~-ee~FLKPneCCgY~iCn~Cya~LWK~~~-----~ypvCPv--CkTSFK 132 (140)
T PF05290_consen 74 VFLDPKLYECNICKETSA-EERFLKPNECCGYSICNACYANLWKFCN-----LYPVCPV--CKTSFK 132 (140)
T ss_pred eecCCCceeccCcccccc-hhhcCCcccccchHHHHHHHHHHHHHcc-----cCCCCCc--cccccc
Confidence 334569999999998863 345543333 799999999998887543 4568999 986653
No 81
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=87.76 E-value=0.14 Score=33.74 Aligned_cols=54 Identities=26% Similarity=0.576 Sum_probs=37.1
Q ss_pred CCccccccccCCCc--------cccccc-cCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCC
Q 026541 37 GTFTCDICIEPMSV--------NNKFKN-NNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLD 97 (237)
Q Consensus 37 ~~~~C~iC~~~~~~--------~~~~~~-~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~ 97 (237)
+..+|.||.-+|.. .+.-+. .-.|.|.|..-|+.+++.+.-.. -.||. |.+.+.
T Consensus 19 ~~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq-----~~CPm--cRq~~~ 81 (84)
T KOG1493|consen 19 PDETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQ-----GQCPM--CRQTWQ 81 (84)
T ss_pred CCCccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCcccc-----ccCCc--chheeE
Confidence 34499999877742 122111 22589999999999999877655 36888 877654
No 82
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=87.61 E-value=0.23 Score=30.63 Aligned_cols=48 Identities=19% Similarity=0.279 Sum_probs=32.8
Q ss_pred CCccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCCHHH
Q 026541 37 GTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLDPFA 100 (237)
Q Consensus 37 ~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~ 100 (237)
+...|..|..... ...+++|+|.+|..||-. ..--.||. |+.+++...
T Consensus 6 ~~~~~~~~~~~~~----~~~~~pCgH~I~~~~f~~----------~rYngCPf--C~~~~~~~~ 53 (55)
T PF14447_consen 6 PEQPCVFCGFVGT----KGTVLPCGHLICDNCFPG----------ERYNGCPF--CGTPFEFDD 53 (55)
T ss_pred cceeEEEcccccc----ccccccccceeeccccCh----------hhccCCCC--CCCcccCCC
Confidence 4556667765542 226899999999999753 12237999 998887543
No 83
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.09 E-value=0.08 Score=45.12 Aligned_cols=49 Identities=31% Similarity=0.741 Sum_probs=35.5
Q ss_pred CCCCccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCC
Q 026541 35 IDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQF 95 (237)
Q Consensus 35 ~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~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-TTKECLHRFCFDCIWKALR----SG---NNECPT--CRKK 88 (381)
T ss_pred hhhhhccHHHHHHHHhh--c-ccHHHHHHHHHHHHHHHHH----hc---CCCCch--HHhh
Confidence 45678999999887432 2 4678999999999887664 22 236887 8744
No 84
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=86.75 E-value=0.8 Score=37.48 Aligned_cols=61 Identities=25% Similarity=0.428 Sum_probs=44.8
Q ss_pred hcCCCCccccccccCCCccccccccCCC-----CCcccHHHHHHHHHhhcccCCceeecCCCCcCCCC
Q 026541 33 EDIDGTFTCDICIEPMSVNNKFKNNNLC-----THPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQF 95 (237)
Q Consensus 33 ~~~~~~~~C~iC~~~~~~~~~~~~~~~C-----~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~ 95 (237)
.+....-.|-||+.+.+++..-.=+.+| .|-+...||..|+..+-......++.||. |...
T Consensus 15 ~~~e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~Q--CqTE 80 (293)
T KOG3053|consen 15 DNQELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQ--CQTE 80 (293)
T ss_pred CccccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechh--hcch
Confidence 3345677899999987654321124566 35699999999999888765677999999 9844
No 85
>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=86.66 E-value=1.2 Score=24.12 Aligned_cols=27 Identities=19% Similarity=0.222 Sum_probs=16.8
Q ss_pred cccCCCCCcceeecCCCcceEec-CCcE
Q 026541 198 WTRCPGCGNCIERKKGCRIMFCR-FIFL 224 (237)
Q Consensus 198 ~k~CP~C~~~iek~~GCnhm~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 47899999999998886678894 8864
No 86
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=86.33 E-value=0.45 Score=31.47 Aligned_cols=60 Identities=25% Similarity=0.413 Sum_probs=21.6
Q ss_pred ccCCccccCceeeeccccCCcccceeCcccchhhccccccCcCCCCCChhhhcccccchHHHHHHHhcCCcccCCCCCcc
Q 026541 128 SYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQWFCFQCKLAWHAGYRCEESGNLRDRNDIAFGKLLEKMNWTRCPGCGNC 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~----------CyEYE--------------rkeg~q~CpqCkt~ 60 (80)
T PF14569_consen 10 QICQ--ICGDDVGLTENG---EVFVACHECAFPVCRP----------CYEYE--------------RKEGNQVCPQCKTR 60 (80)
T ss_dssp -B-S--SS--B--B-SSS---SB--S-SSS-----HH----------HHHHH--------------HHTS-SB-TTT--B
T ss_pred cccc--cccCccccCCCC---CEEEEEcccCCccchh----------HHHHH--------------hhcCcccccccCCC
Confidence 3455 455544433322 5889999999999864 44433 35678999999999
Q ss_pred eeecCCCcc
Q 026541 208 IERKKGCRI 216 (237)
Q Consensus 208 iek~~GCnh 216 (237)
..+..|+..
T Consensus 61 ykr~kgsp~ 69 (80)
T PF14569_consen 61 YKRHKGSPR 69 (80)
T ss_dssp ----TT---
T ss_pred cccccCCCC
Confidence 988877654
No 87
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=86.31 E-value=1.5 Score=35.17 Aligned_cols=63 Identities=24% Similarity=0.483 Sum_probs=50.2
Q ss_pred hhhhcCCCCccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCC
Q 026541 30 EELEDIDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFL 96 (237)
Q Consensus 30 ~~~~~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i 96 (237)
+++.+.+=...|.+|-.++...+. +.+.|-|.|.-+||......--.+-.-....||. |.++|
T Consensus 42 qWL~DsDY~pNC~LC~t~La~gdt--~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~--Cs~ei 104 (299)
T KOG3970|consen 42 QWLQDSDYNPNCRLCNTPLASGDT--TRLVCYHLFHWKCLNERAANLPANTAPAGYQCPC--CSQEI 104 (299)
T ss_pred HHHhhcCCCCCCceeCCccccCcc--eeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCC--CCCcc
Confidence 677777778899999999977766 5699999999999999877655553445679998 99654
No 88
>PLN03086 PRLI-interacting factor K; Provisional
Probab=86.04 E-value=2.4 Score=39.14 Aligned_cols=103 Identities=21% Similarity=0.495 Sum_probs=58.6
Q ss_pred eeecCCCCcCCCCCCHHHHhccCChhHHHHHHHHHHHHhhcCCCcccCCccccCceeeeccccCCcccceeCcccchhhc
Q 026541 83 AKIECPGLHCEQFLDPFACKHTIPSSLFLKWCDHLCEDYVLGFERSYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQWFC 162 (237)
Q Consensus 83 ~~i~CP~~~C~~~i~~~~i~~~l~~~~~~~y~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C 162 (237)
..+.||. |...++...+... +.+- .-+.+.||+.+|+..+..... ...+.|+.|+..|
T Consensus 406 ~~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 406 DTVECRN--CKHYIPSRSIALH--------------EAYC-SRHNVVCPHDGCGIVLRVEEA----KNHVHCEKCGQAF- 463 (567)
T ss_pred CeEECCC--CCCccchhHHHHH--------------HhhC-CCcceeCCcccccceeecccc----ccCccCCCCCCcc-
Confidence 4678998 9988875554421 1111 123578998789999987777 4667899998776
Q ss_pred ccc-----ccCcCCCCCChhhhcccccchHHHHHHHh--cCCcccCCCCCccee
Q 026541 163 FQC-----KLAWHAGYRCEESGNLRDRNDIAFGKLLE--KMNWTRCPGCGNCIE 209 (237)
Q Consensus 163 ~~C-----~~~~H~~~~C~~~~~~~~~~~~~~~~~~~--~~~~k~CP~C~~~ie 209 (237)
..- ....|.+..|. -..... ...+...+.. ......|+.|+..+.
T Consensus 464 ~~s~LekH~~~~Hkpv~Cp-Cg~~~~-R~~L~~H~~thCp~Kpi~C~fC~~~v~ 515 (567)
T PLN03086 464 QQGEMEKHMKVFHEPLQCP-CGVVLE-KEQMVQHQASTCPLRLITCRFCGDMVQ 515 (567)
T ss_pred chHHHHHHHHhcCCCccCC-CCCCcc-hhHHHhhhhccCCCCceeCCCCCCccc
Confidence 211 11124555664 211111 1111112211 234468999998874
No 89
>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=85.83 E-value=1.1 Score=37.33 Aligned_cols=52 Identities=23% Similarity=0.514 Sum_probs=35.7
Q ss_pred cccccccCCCcc-ccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCCHHH
Q 026541 40 TCDICIEPMSVN-NKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLDPFA 100 (237)
Q Consensus 40 ~C~iC~~~~~~~-~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~ 100 (237)
.|++|-.+...+ +.+....+|+|..|.+|+-.-+. ..+-.||. |..++--.-
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~-------~g~~~Cpe--C~~iLRk~n 54 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFS-------LGPAQCPE--CMVILRKNN 54 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHh-------cCCCCCCc--ccchhhhcc
Confidence 488886665443 33334458999999999988764 33457896 997766443
No 90
>PHA03096 p28-like protein; Provisional
Probab=85.71 E-value=0.61 Score=39.25 Aligned_cols=49 Identities=16% Similarity=0.286 Sum_probs=34.8
Q ss_pred ccccccccCCCcc----ccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCC
Q 026541 39 FTCDICIEPMSVN----NKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPG 89 (237)
Q Consensus 39 ~~C~iC~~~~~~~----~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~ 89 (237)
..|.||++..... ..|..+..|.|.||..|++.|..++... .....||.
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~--e~~~~c~~ 231 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYK--ETEPENRR 231 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhc--ccCccccc
Confidence 8899999887432 2344456799999999999999987633 33334444
No 91
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.71 E-value=0.77 Score=41.31 Aligned_cols=39 Identities=23% Similarity=0.666 Sum_probs=31.4
Q ss_pred CCcccCCccccCceeeeccccCCcccceeCcc--cchhhccccccCc
Q 026541 125 FERSYCPNRNCMAVMVNECEGIGRVKKAQCPK--CKQWFCFQCKLAW 169 (237)
Q Consensus 125 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~--C~~~~C~~C~~~~ 169 (237)
.+...|| .|...+..+.+ .+.+.|.. |...||+.|..+|
T Consensus 224 ~ntk~CP--~c~~~iek~~g----c~~~~~~~~~c~~~FCw~Cl~~~ 264 (444)
T KOG1815|consen 224 ANTKECP--KCKVPIEKDGG----CNHMTCKSASCKHEFCWVCLASL 264 (444)
T ss_pred ccCccCC--CcccchhccCC----ccccccccCCcCCeeceeeeccc
Confidence 4456699 89998888777 57777766 9999999997777
No 92
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=85.50 E-value=0.6 Score=38.93 Aligned_cols=50 Identities=24% Similarity=0.485 Sum_probs=39.3
Q ss_pred CCCCccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCC
Q 026541 35 IDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQ 94 (237)
Q Consensus 35 ~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~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 RSSEFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMIC----E---G-YTCPI--CSK 204 (276)
T ss_pred hcccCCCchhHHHhccccccCCccCcccchHHHHHHHHhc----c---C-CCCCc--ccc
Confidence 3445559999998877665567899999999999988774 2 2 79999 977
No 93
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.39 E-value=0.87 Score=39.01 Aligned_cols=36 Identities=22% Similarity=0.399 Sum_probs=27.7
Q ss_pred CCCCccccccccCCCccccccccCCCCCcccHHHHHHHHH
Q 026541 35 IDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIE 74 (237)
Q Consensus 35 ~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~ 74 (237)
+.+...|+||+-.-- + .+..+|+|.-|.+|+.+|+.
T Consensus 419 ~sEd~lCpICyA~pi-~---Avf~PC~H~SC~~CI~qHlm 454 (489)
T KOG4692|consen 419 DSEDNLCPICYAGPI-N---AVFAPCSHRSCYGCITQHLM 454 (489)
T ss_pred CcccccCcceecccc-h---hhccCCCCchHHHHHHHHHh
Confidence 456678999996431 1 14689999999999999885
No 94
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=85.36 E-value=0.72 Score=27.69 Aligned_cols=28 Identities=18% Similarity=0.320 Sum_probs=20.1
Q ss_pred CCcccCCCCCcceeecCCCcceEe-cCCc
Q 026541 196 MNWTRCPGCGNCIERKKGCRIMFC-RFIF 223 (237)
Q Consensus 196 ~~~k~CP~C~~~iek~~GCnhm~C-~C~~ 223 (237)
...+.||+|+--+...+-=+...| +||+
T Consensus 17 rk~~~CPrCG~gvfmA~H~dR~~CGkCgy 45 (51)
T COG1998 17 RKNRFCPRCGPGVFMADHKDRWACGKCGY 45 (51)
T ss_pred EccccCCCCCCcchhhhcCceeEeccccc
Confidence 345899999975555544458889 6986
No 95
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=85.19 E-value=0.69 Score=32.01 Aligned_cols=27 Identities=33% Similarity=0.810 Sum_probs=21.4
Q ss_pred cCCCCCcc--eeecCCCcceEec-CCcEEE
Q 026541 200 RCPGCGNC--IERKKGCRIMFCR-FIFLSL 226 (237)
Q Consensus 200 ~CP~C~~~--iek~~GCnhm~C~-C~~~fc 226 (237)
-||.|+.. |+..+-||.+.|+ |.|.|-
T Consensus 3 FCP~Cgn~Live~g~~~~rf~C~tCpY~~~ 32 (105)
T KOG2906|consen 3 FCPTCGNMLIVESGESCNRFSCRTCPYVFP 32 (105)
T ss_pred ccCCCCCEEEEecCCeEeeEEcCCCCceee
Confidence 59999985 5555669999996 998773
No 96
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=85.16 E-value=0.72 Score=40.60 Aligned_cols=36 Identities=19% Similarity=0.470 Sum_probs=28.3
Q ss_pred CCCccccccccCCCccccccccCCCCCcccHHHHHHHHHh
Q 026541 36 DGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEV 75 (237)
Q Consensus 36 ~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~ 75 (237)
.+...|+||..-+... ..++|+|..|+.|.+..+.+
T Consensus 2 eeelkc~vc~~f~~ep----iil~c~h~lc~~ca~~~~~~ 37 (699)
T KOG4367|consen 2 EEELKCPVCGSFYREP----IILPCSHNLCQACARNILVQ 37 (699)
T ss_pred cccccCceehhhccCc----eEeecccHHHHHHHHhhccc
Confidence 3467899998877432 57999999999999876654
No 97
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=85.09 E-value=0.31 Score=42.25 Aligned_cols=53 Identities=25% Similarity=0.620 Sum_probs=40.4
Q ss_pred CCCccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCC
Q 026541 36 DGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFL 96 (237)
Q Consensus 36 ~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i 96 (237)
.-...|..|-+.+...+.-...++|.|+|...|+..++. +..+-.||. |+..+
T Consensus 363 e~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~------~n~~rsCP~--Crklr 415 (518)
T KOG1941|consen 363 ETELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILE------NNGTRSCPN--CRKLR 415 (518)
T ss_pred HHhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHH------hCCCCCCcc--HHHHH
Confidence 346789999988865443346789999999999999994 345668998 87443
No 98
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=84.45 E-value=0.8 Score=44.26 Aligned_cols=55 Identities=22% Similarity=0.580 Sum_probs=39.9
Q ss_pred CCCCccccccccCCCcc-cccc--ccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCC
Q 026541 35 IDGTFTCDICIEPMSVN-NKFK--NNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLD 97 (237)
Q Consensus 35 ~~~~~~C~iC~~~~~~~-~~~~--~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~ 97 (237)
-.+..+|.||+.-.... +.++ ....|.|.|...|+.+|+++.-.+ +||. |...|+
T Consensus 1466 fsG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s------~CPl--CRseit 1523 (1525)
T COG5219 1466 FSGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARS------NCPL--CRSEIT 1523 (1525)
T ss_pred cCCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCC------CCCc--cccccc
Confidence 47788999998766421 1111 234689999999999999865444 8999 987665
No 99
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=84.42 E-value=0.34 Score=39.92 Aligned_cols=59 Identities=22% Similarity=0.371 Sum_probs=42.6
Q ss_pred CCCccccccccCCCccc-------cccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCCHHHHhc
Q 026541 36 DGTFTCDICIEPMSVNN-------KFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLDPFACKH 103 (237)
Q Consensus 36 ~~~~~C~iC~~~~~~~~-------~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~ 103 (237)
.....|-||-..+..+. +. ..++|+|+|...|++.|...-- .-.||- |+..++...+.+
T Consensus 222 l~d~vCaVCg~~~~~s~~eegvient-y~LsCnHvFHEfCIrGWcivGK------kqtCPY--CKekVdl~rmfs 287 (328)
T KOG1734|consen 222 LSDSVCAVCGQQIDVSVDEEGVIENT-YKLSCNHVFHEFCIRGWCIVGK------KQTCPY--CKEKVDLKRMFS 287 (328)
T ss_pred CCcchhHhhcchheeecchhhhhhhh-eeeecccchHHHhhhhheeecC------CCCCch--HHHHhhHhhhcc
Confidence 34567999987765432 22 3689999999999999986432 248998 998887665544
No 100
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=84.21 E-value=1.2 Score=39.33 Aligned_cols=50 Identities=28% Similarity=0.739 Sum_probs=36.8
Q ss_pred CCCCccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCC
Q 026541 35 IDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLD 97 (237)
Q Consensus 35 ~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~ 97 (237)
.+....|++|....... + ....|+|.||..|+..+.+. ...||. |...+.
T Consensus 18 ~~~~l~C~~C~~vl~~p--~-~~~~cgh~fC~~C~~~~~~~--------~~~cp~--~~~~~~ 67 (391)
T KOG0297|consen 18 LDENLLCPICMSVLRDP--V-QTTTCGHRFCAGCLLESLSN--------HQKCPV--CRQELT 67 (391)
T ss_pred CcccccCccccccccCC--C-CCCCCCCcccccccchhhcc--------CcCCcc--cccccc
Confidence 46679999999988543 2 23699999999999988764 346776 654444
No 101
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=83.42 E-value=0.43 Score=39.85 Aligned_cols=47 Identities=28% Similarity=0.469 Sum_probs=34.5
Q ss_pred CCCccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCC
Q 026541 36 DGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFL 96 (237)
Q Consensus 36 ~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i 96 (237)
.-.+.|.||-.++... ++..|+|.||..|....++ ..-+|+. |++.+
T Consensus 239 ~~Pf~c~icr~~f~~p----Vvt~c~h~fc~~ca~~~~q--------k~~~c~v--C~~~t 285 (313)
T KOG1813|consen 239 LLPFKCFICRKYFYRP----VVTKCGHYFCEVCALKPYQ--------KGEKCYV--CSQQT 285 (313)
T ss_pred cCCccccccccccccc----hhhcCCceeehhhhccccc--------cCCccee--ccccc
Confidence 4467799999999543 6789999999999766554 1236666 77544
No 102
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=82.19 E-value=1.5 Score=29.20 Aligned_cols=29 Identities=24% Similarity=0.677 Sum_probs=22.5
Q ss_pred CCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCC
Q 026541 59 LCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLD 97 (237)
Q Consensus 59 ~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~ 97 (237)
.|.|.|..-|+.+++.+ ++ .||. +.+++.
T Consensus 53 ~CnHaFH~HCI~rWL~T--k~------~CPl--d~q~w~ 81 (88)
T COG5194 53 VCNHAFHDHCIYRWLDT--KG------VCPL--DRQTWV 81 (88)
T ss_pred ecchHHHHHHHHHHHhh--CC------CCCC--CCceeE
Confidence 59999999999999987 22 6787 665543
No 103
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=82.07 E-value=1.3 Score=26.18 Aligned_cols=28 Identities=18% Similarity=0.355 Sum_probs=21.7
Q ss_pred ccCCccccCceeeeccccCCcccceeCcccchhh
Q 026541 128 SYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQWF 161 (237)
Q Consensus 128 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 161 (237)
..|| +|+..+..++. ...++||.||..+
T Consensus 4 y~C~--~CG~~~~~~~~----~~~~~Cp~CG~~~ 31 (46)
T PRK00398 4 YKCA--RCGREVELDEY----GTGVRCPYCGYRI 31 (46)
T ss_pred EECC--CCCCEEEECCC----CCceECCCCCCeE
Confidence 4688 89998888766 3478999998755
No 104
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=81.86 E-value=1.1 Score=38.42 Aligned_cols=69 Identities=17% Similarity=0.484 Sum_probs=43.9
Q ss_pred hcCCCCccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCCHHHHhccCChhHHHH
Q 026541 33 EDIDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLDPFACKHTIPSSLFLK 112 (237)
Q Consensus 33 ~~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~~l~~~~~~~ 112 (237)
+.+.+...|.||-+.+... .+++|+|.+|..|-.+.-.. ...-.||. |......-.+-.-.+.++-++
T Consensus 56 dtDEen~~C~ICA~~~TYs----~~~PC~H~~CH~Ca~RlRAL------Y~~K~C~~--CrTE~e~V~fT~~~~~DI~D~ 123 (493)
T COG5236 56 DTDEENMNCQICAGSTTYS----ARYPCGHQICHACAVRLRAL------YMQKGCPL--CRTETEAVVFTASSPADITDR 123 (493)
T ss_pred ccccccceeEEecCCceEE----EeccCCchHHHHHHHHHHHH------HhccCCCc--cccccceEEEecCCCCcchhH
Confidence 4457788999999887543 68999999999997653321 12336887 886654333333333344444
Q ss_pred H
Q 026541 113 W 113 (237)
Q Consensus 113 y 113 (237)
|
T Consensus 124 ~ 124 (493)
T COG5236 124 R 124 (493)
T ss_pred h
Confidence 3
No 105
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=81.68 E-value=1.4 Score=26.36 Aligned_cols=33 Identities=21% Similarity=0.542 Sum_probs=22.4
Q ss_pred ccccccCCCccccccccCCC--CC---cccHHHHHHHHHh
Q 026541 41 CDICIEPMSVNNKFKNNNLC--TH---PFCQDCTVKYIEV 75 (237)
Q Consensus 41 C~iC~~~~~~~~~~~~~~~C--~H---~~C~~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 67999887554422 3455 33 6899999999987
No 106
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=81.58 E-value=2 Score=37.49 Aligned_cols=61 Identities=18% Similarity=0.318 Sum_probs=42.8
Q ss_pred CCCccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCCHHHHhcc
Q 026541 36 DGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLDPFACKHT 104 (237)
Q Consensus 36 ~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~~ 104 (237)
-..+.|||=-+.. ..++.+..+.|||+++++=+.+..+ |+...++||- |......+..+++
T Consensus 332 HSvF~CPVlKeqt-sdeNPPm~L~CGHVISkdAlnrLS~-----ng~~sfKCPY--CP~e~~~~~~kql 392 (394)
T KOG2817|consen 332 HSVFICPVLKEQT-SDENPPMMLICGHVISKDALNRLSK-----NGSQSFKCPY--CPVEQLASDTKQL 392 (394)
T ss_pred cceeecccchhhc-cCCCCCeeeeccceecHHHHHHHhh-----CCCeeeeCCC--CCcccCHHhcccc
Confidence 3467888854444 3345556899999999997766443 3556899998 9877776665553
No 107
>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=81.20 E-value=1.2 Score=25.12 Aligned_cols=32 Identities=25% Similarity=0.525 Sum_probs=22.0
Q ss_pred ccCCccccCceeeeccccC-CcccceeCcccchhh
Q 026541 128 SYCPNRNCMAVMVNECEGI-GRVKKAQCPKCKQWF 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 8999887765422 123478999998754
No 108
>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=81.15 E-value=0.39 Score=29.28 Aligned_cols=39 Identities=28% Similarity=0.687 Sum_probs=19.0
Q ss_pred ccCceeeeccccCCcccceeCcccchhhccccccCcCCC
Q 026541 134 NCMAVMVNECEGIGRVKKAQCPKCKQWFCFQCKLAWHAG 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 455544443322122478899999999999998877753
No 109
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=80.08 E-value=0.85 Score=26.63 Aligned_cols=26 Identities=27% Similarity=0.593 Sum_probs=20.2
Q ss_pred CCcccCCCCCcceeecCCCcceEec---CCcEE
Q 026541 196 MNWTRCPGCGNCIERKKGCRIMFCR---FIFLS 225 (237)
Q Consensus 196 ~~~k~CP~C~~~iek~~GCnhm~C~---C~~~f 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 4679999999975 77778884 77654
No 110
>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=80.05 E-value=1.1 Score=25.05 Aligned_cols=28 Identities=21% Similarity=0.634 Sum_probs=18.5
Q ss_pred ccCCccccCceeeeccccCCcccceeCcccchh
Q 026541 128 SYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQW 160 (237)
Q Consensus 128 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 160 (237)
+.|| .|++.+....... ..+.|..|++.
T Consensus 2 ~FCp--~C~nlL~p~~~~~---~~~~C~~C~Y~ 29 (35)
T PF02150_consen 2 RFCP--ECGNLLYPKEDKE---KRVACRTCGYE 29 (35)
T ss_dssp -BET--TTTSBEEEEEETT---TTEEESSSS-E
T ss_pred eeCC--CCCccceEcCCCc---cCcCCCCCCCc
Confidence 5798 9999998877642 22278777764
No 111
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=79.71 E-value=2.2 Score=22.50 Aligned_cols=20 Identities=35% Similarity=0.806 Sum_probs=13.6
Q ss_pred cCCCCCcceeecCCCcceEe
Q 026541 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 49999999999988777777
No 112
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=79.45 E-value=1.3 Score=41.90 Aligned_cols=43 Identities=12% Similarity=0.121 Sum_probs=21.8
Q ss_pred CCCCccccccccCCCcccc-cc--ccCCCCCcccHHHHHHHHHhhc
Q 026541 35 IDGTFTCDICIEPMSVNNK-FK--NNNLCTHPFCQDCTVKYIEVKV 77 (237)
Q Consensus 35 ~~~~~~C~iC~~~~~~~~~-~~--~~~~C~H~~C~~Cl~~~~~~~i 77 (237)
..++.+|.+|..++.+.+. +. .+-.|.|.+|..||..+....+
T Consensus 93 ~a~s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~ 138 (1134)
T KOG0825|consen 93 TAESDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLE 138 (1134)
T ss_pred cccccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhh
Confidence 4556677777766654111 10 1122556666666655554444
No 113
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=79.12 E-value=0.51 Score=39.94 Aligned_cols=32 Identities=28% Similarity=0.684 Sum_probs=25.4
Q ss_pred cCCcccCCCCCcceeecC-CCcceEe-cCCcEEE
Q 026541 195 KMNWTRCPGCGNCIERKK-GCRIMFC-RFIFLSL 226 (237)
Q Consensus 195 ~~~~k~CP~C~~~iek~~-GCnhm~C-~C~~~fc 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 456999999999887653 5567899 4999884
No 114
>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=78.00 E-value=1.3 Score=31.10 Aligned_cols=34 Identities=24% Similarity=0.513 Sum_probs=27.2
Q ss_pred CCCCccccccccCCCccccccccCCCCCcccHHHHH
Q 026541 35 IDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTV 70 (237)
Q Consensus 35 ~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~ 70 (237)
.++...|.+|...+.. ..| ...+|+|.|+..|++
T Consensus 75 i~~~~~C~vC~k~l~~-~~f-~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 75 ITESTKCSVCGKPLGN-SVF-VVFPCGHVVHYSCIK 108 (109)
T ss_pred ECCCCCccCcCCcCCC-ceE-EEeCCCeEEeccccc
Confidence 3667779999999954 444 588999999999975
No 115
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=77.76 E-value=2.2 Score=30.54 Aligned_cols=78 Identities=19% Similarity=0.446 Sum_probs=44.7
Q ss_pred eeecCCCCcCCCCCCHHHHhccCChhHHHHHHHHHHHH-h--h--c-CCCcccCCccccCceeeecccc----CCcccce
Q 026541 83 AKIECPGLHCEQFLDPFACKHTIPSSLFLKWCDHLCED-Y--V--L-GFERSYCPNRNCMAVMVNECEG----IGRVKKA 152 (237)
Q Consensus 83 ~~i~CP~~~C~~~i~~~~i~~~l~~~~~~~y~~~~~~~-~--~--~-~~~~~~Cp~~~C~~~~~~~~~~----~~~~~~~ 152 (237)
.|+.||. |+..| +++..+.+.|..+.--. + + . ......|- +|...+...... .......
T Consensus 14 LP~~Cpi--CgLtL-------Vss~HLARSyHHLfPl~~f~ev~~~~~~~~~~C~--~C~~~f~~~~~~~~~~~~~~~~y 82 (112)
T TIGR00622 14 LPVECPI--CGLTL-------ILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCF--GCQGPFPKPPVSPFDELKDSHRY 82 (112)
T ss_pred CCCcCCc--CCCEE-------eccchHHHhhhccCCCcccccccccccCCCCccc--CcCCCCCCcccccccccccccce
Confidence 5788988 87443 24444444454431111 1 1 1 11224577 788766543210 0113577
Q ss_pred eCcccchhhccccccCcCC
Q 026541 153 QCPKCKQWFCFQCKLAWHA 171 (237)
Q Consensus 153 ~C~~C~~~~C~~C~~~~H~ 171 (237)
.|+.|+..||..|..-+|.
T Consensus 83 ~C~~C~~~FC~dCD~fiHe 101 (112)
T TIGR00622 83 VCAVCKNVFCVDCDVFVHE 101 (112)
T ss_pred eCCCCCCccccccchhhhh
Confidence 8999999999999888775
No 116
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=77.73 E-value=1.6 Score=24.21 Aligned_cols=31 Identities=19% Similarity=0.539 Sum_probs=15.2
Q ss_pred ccCCccccCceeeeccccCCcccceeCcccchh
Q 026541 128 SYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQW 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 3788 788877654332223678899988863
No 117
>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=76.97 E-value=2.6 Score=22.65 Aligned_cols=26 Identities=23% Similarity=0.526 Sum_probs=13.1
Q ss_pred ccCCCCCcceeecCCCcceEec-CCcEE
Q 026541 199 TRCPGCGNCIERKKGCRIMFCR-FIFLS 225 (237)
Q Consensus 199 k~CP~C~~~iek~~GCnhm~C~-C~~~f 225 (237)
-+||.|+.-..-.+|. .|.|. |++.|
T Consensus 3 p~Cp~C~se~~y~D~~-~~vCp~C~~ew 29 (30)
T PF08274_consen 3 PKCPLCGSEYTYEDGE-LLVCPECGHEW 29 (30)
T ss_dssp ---TTT-----EE-SS-SEEETTTTEEE
T ss_pred CCCCCCCCcceeccCC-EEeCCcccccC
Confidence 3799999988877765 57784 99887
No 118
>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=76.45 E-value=2.6 Score=24.45 Aligned_cols=23 Identities=35% Similarity=0.804 Sum_probs=17.8
Q ss_pred cccCCCCCcceee-cCCCcceEec-CC
Q 026541 198 WTRCPGCGNCIER-KKGCRIMFCR-FI 222 (237)
Q Consensus 198 ~k~CP~C~~~iek-~~GCnhm~C~-C~ 222 (237)
...||.|+.++.+ ..| .+.|. |+
T Consensus 17 ~~~Cp~C~~PL~~~k~g--~~~Cv~C~ 41 (41)
T PF06677_consen 17 DEHCPDCGTPLMRDKDG--KIYCVSCG 41 (41)
T ss_pred cCccCCCCCeeEEecCC--CEECCCCC
Confidence 3799999999998 466 57774 64
No 119
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=76.01 E-value=3.4 Score=25.46 Aligned_cols=37 Identities=19% Similarity=0.391 Sum_probs=29.5
Q ss_pred CCCCccccccccCCCccccccccCCCCCcccHHHHHH
Q 026541 35 IDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVK 71 (237)
Q Consensus 35 ~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~ 71 (237)
+.....|.+|-+++.+.+.+.+-..|+-.+.++||..
T Consensus 2 ~~~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~ 38 (54)
T PF14446_consen 2 NYEGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK 38 (54)
T ss_pred CccCccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence 3456789999999976666555667999999999865
No 120
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=75.88 E-value=1 Score=37.46 Aligned_cols=31 Identities=29% Similarity=0.726 Sum_probs=26.4
Q ss_pred cCCcccCCCCCcceeecC-CCcceEe-cCCcEE
Q 026541 195 KMNWTRCPGCGNCIERKK-GCRIMFC-RFIFLS 225 (237)
Q Consensus 195 ~~~~k~CP~C~~~iek~~-GCnhm~C-~C~~~f 225 (237)
...|.+||.|+..+-+.+ +=|...| .|++|+
T Consensus 25 e~lw~KCp~c~~~~y~~eL~~n~~vcp~c~~h~ 57 (294)
T COG0777 25 EGLWTKCPSCGEMLYRKELESNLKVCPKCGHHM 57 (294)
T ss_pred CCceeECCCccceeeHHHHHhhhhcccccCccc
Confidence 678999999999988775 7788889 499886
No 121
>PRK00420 hypothetical protein; Validated
Probab=75.87 E-value=2.1 Score=30.72 Aligned_cols=28 Identities=25% Similarity=0.432 Sum_probs=22.6
Q ss_pred CcccCCCCCcceee-cCCCcceEec-CCcEEE
Q 026541 197 NWTRCPGCGNCIER-KKGCRIMFCR-FIFLSL 226 (237)
Q Consensus 197 ~~k~CP~C~~~iek-~~GCnhm~C~-C~~~fc 226 (237)
....||.|+.++.+ +.| +..|. ||.-..
T Consensus 22 l~~~CP~Cg~pLf~lk~g--~~~Cp~Cg~~~~ 51 (112)
T PRK00420 22 LSKHCPVCGLPLFELKDG--EVVCPVHGKVYI 51 (112)
T ss_pred ccCCCCCCCCcceecCCC--ceECCCCCCeee
Confidence 44899999999998 677 89995 997543
No 122
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=75.76 E-value=2.4 Score=42.42 Aligned_cols=12 Identities=25% Similarity=0.722 Sum_probs=7.7
Q ss_pred cccCCCCCccee
Q 026541 198 WTRCPGCGNCIE 209 (237)
Q Consensus 198 ~k~CP~C~~~ie 209 (237)
+..||+|+.++.
T Consensus 709 a~~CP~CGtplv 720 (1337)
T PRK14714 709 RVECPRCDVELT 720 (1337)
T ss_pred cccCCCCCCccc
Confidence 456777776543
No 123
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=75.06 E-value=4.1 Score=31.58 Aligned_cols=62 Identities=23% Similarity=0.399 Sum_probs=42.4
Q ss_pred CCCCccccccccCCCcc---ccccccCCCCCcccHHHHHHHHHhhcccCCcee---ecCCCCcCCCCCCH
Q 026541 35 IDGTFTCDICIEPMSVN---NKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAK---IECPGLHCEQFLDP 98 (237)
Q Consensus 35 ~~~~~~C~iC~~~~~~~---~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~---i~CP~~~C~~~i~~ 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 56677888887654221 221124579999999999999987766644443 37988 9887753
No 124
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=74.76 E-value=1.7 Score=41.77 Aligned_cols=43 Identities=23% Similarity=0.562 Sum_probs=34.5
Q ss_pred CCCCccccccccCCCccccccccCCCCCcccHHHHHHHHHhhccc
Q 026541 35 IDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRD 79 (237)
Q Consensus 35 ~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~ 79 (237)
..+...|.+|...+.. ..| .+.+|||.|..+|+..++......
T Consensus 814 ~ep~d~C~~C~~~ll~-~pF-~vf~CgH~FH~~Cl~~~v~~~~~~ 856 (911)
T KOG2034|consen 814 LEPQDSCDHCGRPLLI-KPF-YVFPCGHCFHRDCLIRHVLSLLSE 856 (911)
T ss_pred ecCccchHHhcchhhc-Ccc-eeeeccchHHHHHHHHHHHccccH
Confidence 3678899999998844 445 478999999999999988765544
No 125
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=74.70 E-value=2.7 Score=26.33 Aligned_cols=32 Identities=22% Similarity=0.591 Sum_probs=22.8
Q ss_pred ccCCccccCceeeeccccCCcccceeCcccchhhcccc
Q 026541 128 SYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQWFCFQC 165 (237)
Q Consensus 128 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C 165 (237)
..|. .|+..+...+. ...+.||.||...-.+|
T Consensus 10 ~~Ct--SCg~~i~p~e~----~v~F~CPnCGe~~I~Rc 41 (61)
T COG2888 10 PVCT--SCGREIAPGET----AVKFPCPNCGEVEIYRC 41 (61)
T ss_pred ceec--cCCCEeccCCc----eeEeeCCCCCceeeehh
Confidence 4566 78887755555 58899999996665544
No 126
>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=74.35 E-value=0.76 Score=38.75 Aligned_cols=31 Identities=26% Similarity=0.611 Sum_probs=24.6
Q ss_pred cCCcccCCCCCcceeecC-CCcceEec-CCcEE
Q 026541 195 KMNWTRCPGCGNCIERKK-GCRIMFCR-FIFLS 225 (237)
Q Consensus 195 ~~~~k~CP~C~~~iek~~-GCnhm~C~-C~~~f 225 (237)
+..|.+||+|+..|.+.+ .=|.+.|. |++||
T Consensus 23 ~~~~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 55 (285)
T TIGR00515 23 EGVWTKCPKCGQVLYTKELERNLEVCPKCDHHM 55 (285)
T ss_pred CCCeeECCCCcchhhHHHHHhhCCCCCCCCCcC
Confidence 456999999999988763 45678994 99887
No 127
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=74.29 E-value=1.4 Score=22.00 Aligned_cols=22 Identities=41% Similarity=0.975 Sum_probs=12.3
Q ss_pred cCCccccCceeeeccccCCcccceeCcccchh
Q 026541 129 YCPNRNCMAVMVNECEGIGRVKKAQCPKCKQW 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--NCGAEIED--------DAKFCPNCGTP 22 (23)
T ss_pred CCc--ccCCCCCC--------cCcchhhhCCc
Confidence 466 67666532 23357777654
No 128
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=74.27 E-value=0.71 Score=39.01 Aligned_cols=31 Identities=19% Similarity=0.433 Sum_probs=24.7
Q ss_pred cCCcccCCCCCcceeecC-CCcceEec-CCcEE
Q 026541 195 KMNWTRCPGCGNCIERKK-GCRIMFCR-FIFLS 225 (237)
Q Consensus 195 ~~~~k~CP~C~~~iek~~-GCnhm~C~-C~~~f 225 (237)
+..|.+||+|+..|.+.+ .=|...|. |++||
T Consensus 35 ~~lw~kc~~C~~~~~~~~l~~~~~vcp~c~~h~ 67 (296)
T CHL00174 35 KHLWVQCENCYGLNYKKFLKSKMNICEQCGYHL 67 (296)
T ss_pred CCCeeECCCccchhhHHHHHHcCCCCCCCCCCc
Confidence 346999999999887664 56778995 99887
No 129
>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=74.25 E-value=2 Score=30.23 Aligned_cols=24 Identities=29% Similarity=0.765 Sum_probs=17.5
Q ss_pred cCCCCCcceeecCCCcceEec-CCcEE
Q 026541 200 RCPGCGNCIERKKGCRIMFCR-FIFLS 225 (237)
Q Consensus 200 ~CP~C~~~iek~~GCnhm~C~-C~~~f 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 58888888866553 78884 88654
No 130
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=73.93 E-value=3 Score=30.76 Aligned_cols=28 Identities=36% Similarity=0.715 Sum_probs=22.7
Q ss_pred CCcccCCCCCcceeecCCCcceEec-CCcEE
Q 026541 196 MNWTRCPGCGNCIERKKGCRIMFCR-FIFLS 225 (237)
Q Consensus 196 ~~~k~CP~C~~~iek~~GCnhm~C~-C~~~f 225 (237)
...+.||.||.|.++..| .++|. |++.+
T Consensus 26 ML~~hCp~Cg~PLF~KdG--~v~CPvC~~~~ 54 (131)
T COG1645 26 MLAKHCPKCGTPLFRKDG--EVFCPVCGYRE 54 (131)
T ss_pred HHHhhCcccCCcceeeCC--eEECCCCCceE
Confidence 344899999999999877 79995 98654
No 131
>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=73.56 E-value=2.7 Score=25.10 Aligned_cols=27 Identities=19% Similarity=0.482 Sum_probs=20.5
Q ss_pred CcccCC--CCCcceeecCCCcceEe-cCCc
Q 026541 197 NWTRCP--GCGNCIERKKGCRIMFC-RFIF 223 (237)
Q Consensus 197 ~~k~CP--~C~~~iek~~GCnhm~C-~C~~ 223 (237)
.-+.|| .|+.-+....--+..+| +||+
T Consensus 17 ~rk~CP~~~CG~GvFMA~H~dR~~CGKCg~ 46 (47)
T PF01599_consen 17 LRKECPSPRCGAGVFMAEHKDRHYCGKCGY 46 (47)
T ss_dssp SSEE-TSTTTTSSSEEEE-SSEEEETTTSS
T ss_pred hhhcCCCcccCCceEeeecCCCccCCCccc
Confidence 458999 99998877777789999 6885
No 132
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=72.53 E-value=2.9 Score=39.41 Aligned_cols=13 Identities=31% Similarity=0.820 Sum_probs=7.7
Q ss_pred CcccCCCCCccee
Q 026541 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 4466777766543
No 133
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=72.51 E-value=1.8 Score=22.23 Aligned_cols=23 Identities=35% Similarity=0.833 Sum_probs=13.1
Q ss_pred ccCCccccCceeeeccccCCcccceeCcccchh
Q 026541 128 SYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQW 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--NCGAEIDP--------DAKFCPNCGAK 25 (26)
T ss_pred CCCc--ccCCcCCc--------ccccChhhCCC
Confidence 4677 77774422 23467666653
No 134
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=72.09 E-value=1.5 Score=41.49 Aligned_cols=52 Identities=29% Similarity=0.644 Sum_probs=38.0
Q ss_pred ccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCCHHHHhc
Q 026541 39 FTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLDPFACKH 103 (237)
Q Consensus 39 ~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~ 103 (237)
.+|.+|.+ . +.+ ....|+|.||.+|+...+...-. -.||. |...+....+..
T Consensus 455 ~~c~ic~~-~---~~~-~it~c~h~~c~~c~~~~i~~~~~------~~~~~--cr~~l~~~~l~s 506 (674)
T KOG1001|consen 455 HWCHICCD-L---DSF-FITRCGHDFCVECLKKSIQQSEN------APCPL--CRNVLKEKKLLS 506 (674)
T ss_pred cccccccc-c---ccc-eeecccchHHHHHHHhccccccC------CCCcH--HHHHHHHHHHhh
Confidence 99999999 2 222 46889999999999998864321 16776 887777665554
No 135
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=71.83 E-value=4.3 Score=28.65 Aligned_cols=34 Identities=15% Similarity=0.386 Sum_probs=24.4
Q ss_pred CcccCCccccCceeeeccccCCcccceeCcccchhh
Q 026541 126 ERSYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQWF 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 356888 8998888776655556777887776654
No 136
>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=71.61 E-value=2.2 Score=30.44 Aligned_cols=26 Identities=19% Similarity=0.392 Sum_probs=16.1
Q ss_pred ccCCCCCcceeecCCCcceEe-cCCcEE
Q 026541 199 TRCPGCGNCIERKKGCRIMFC-RFIFLS 225 (237)
Q Consensus 199 k~CP~C~~~iek~~GCnhm~C-~C~~~f 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 567777776543322 66777 477655
No 137
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=71.42 E-value=11 Score=31.84 Aligned_cols=44 Identities=25% Similarity=0.795 Sum_probs=32.1
Q ss_pred CccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCC
Q 026541 38 TFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCE 93 (237)
Q Consensus 38 ~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~ 93 (237)
.+.|+.|-..+... + ....|+|.||..|+..-+. + ..+.||. |.
T Consensus 274 ~LkCplc~~Llrnp--~-kT~cC~~~fc~eci~~al~----d---sDf~Cpn--C~ 317 (427)
T COG5222 274 SLKCPLCHCLLRNP--M-KTPCCGHTFCDECIGTALL----D---SDFKCPN--CS 317 (427)
T ss_pred cccCcchhhhhhCc--c-cCccccchHHHHHHhhhhh----h---ccccCCC--cc
Confidence 38899998766322 2 3457999999999876553 2 5689998 87
No 138
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=71.12 E-value=2.5 Score=40.66 Aligned_cols=24 Identities=33% Similarity=0.970 Sum_probs=20.7
Q ss_pred ccCCCCCcceeecCCCcceEec-CCcE
Q 026541 199 TRCPGCGNCIERKKGCRIMFCR-FIFL 224 (237)
Q Consensus 199 k~CP~C~~~iek~~GCnhm~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 35999999999999998 895 8863
No 139
>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=70.98 E-value=3.8 Score=26.35 Aligned_cols=29 Identities=24% Similarity=0.603 Sum_probs=21.6
Q ss_pred CcccCCCCCcceeecCCCcceEec-CCcEE
Q 026541 197 NWTRCPGCGNCIERKKGCRIMFCR-FIFLS 225 (237)
Q Consensus 197 ~~k~CP~C~~~iek~~GCnhm~C~-C~~~f 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 347899999999885555568885 88763
No 140
>PF14149 YhfH: YhfH-like protein
Probab=69.71 E-value=0.5 Score=26.65 Aligned_cols=29 Identities=24% Similarity=0.595 Sum_probs=22.6
Q ss_pred HHHhcCCcccCCCCCcceeecCCCcceEe
Q 026541 191 KLLEKMNWTRCPGCGNCIERKKGCRIMFC 219 (237)
Q Consensus 191 ~~~~~~~~k~CP~C~~~iek~~GCnhm~C 219 (237)
+.......|.||.||..|+--.-|..+.|
T Consensus 6 eFfrnLp~K~C~~CG~~i~EQ~E~Y~n~C 34 (37)
T PF14149_consen 6 EFFRNLPPKKCTECGKEIEEQAECYGNEC 34 (37)
T ss_pred HHHHhCCCcccHHHHHHHHHHHHHHhCcC
Confidence 34456778999999999987777777776
No 141
>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=69.03 E-value=5 Score=26.17 Aligned_cols=24 Identities=21% Similarity=0.386 Sum_probs=15.1
Q ss_pred cCCCCCcceeecCCCcceEec-CCcEE
Q 026541 200 RCPGCGNCIERKKGCRIMFCR-FIFLS 225 (237)
Q Consensus 200 ~CP~C~~~iek~~GCnhm~C~-C~~~f 225 (237)
.||.|+..++..+ .+..|. |+..|
T Consensus 3 ~CP~C~~~L~~~~--~~~~C~~C~~~~ 27 (70)
T PF07191_consen 3 TCPKCQQELEWQG--GHYHCEACQKDY 27 (70)
T ss_dssp B-SSS-SBEEEET--TEEEETTT--EE
T ss_pred cCCCCCCccEEeC--CEEECccccccc
Confidence 5889999888887 577774 77544
No 142
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=68.04 E-value=5.2 Score=25.10 Aligned_cols=32 Identities=22% Similarity=0.641 Sum_probs=21.4
Q ss_pred ccCCccccCceeeeccccCCcccceeCcccchhhcccc
Q 026541 128 SYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQWFCFQC 165 (237)
Q Consensus 128 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C 165 (237)
..|. .|+..+...+. ...+.||.|+...=++|
T Consensus 8 ~~Ct--SCg~~i~~~~~----~~~F~CPnCG~~~I~RC 39 (59)
T PRK14890 8 PKCT--SCGIEIAPREK----AVKFLCPNCGEVIIYRC 39 (59)
T ss_pred cccc--CCCCcccCCCc----cCEeeCCCCCCeeEeec
Confidence 3566 67777755543 58899999988744433
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=67.70 E-value=3.5 Score=22.97 Aligned_cols=32 Identities=25% Similarity=0.599 Sum_probs=17.3
Q ss_pred ccHHHHHHHHHhhcccCCceeecCCCCcCCCCCC
Q 026541 64 FCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLD 97 (237)
Q Consensus 64 ~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~ 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 58899998875443332455789988 885543
No 144
>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=67.58 E-value=3.7 Score=21.73 Aligned_cols=24 Identities=38% Similarity=0.783 Sum_probs=13.8
Q ss_pred ccCCCCCcceeec--CCCcceEe-cCC
Q 026541 199 TRCPGCGNCIERK--KGCRIMFC-RFI 222 (237)
Q Consensus 199 k~CP~C~~~iek~--~GCnhm~C-~C~ 222 (237)
++||+|+..|++. +|=+...| +|.
T Consensus 2 ~~C~rC~~~~~~~~~~~r~~~~C~rCq 28 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGINGRSTYLCPRCQ 28 (30)
T ss_dssp SB-TTT--BBEEEEETTEEEEE-TTTC
T ss_pred CcCccCCCcceEeEecCCCCeECcCCc
Confidence 5799999998765 56666667 363
No 145
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=67.38 E-value=4.1 Score=32.93 Aligned_cols=38 Identities=26% Similarity=0.676 Sum_probs=26.3
Q ss_pred ccceeCcccchhhccccccCcCCCCCChhhhcccccchHHHHHHHhcCCcccCCCCCcceee
Q 026541 149 VKKAQCPKCKQWFCFQCKLAWHAGYRCEESGNLRDRNDIAFGKLLEKMNWTRCPGCGNCIER 210 (237)
Q Consensus 149 ~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~~iek 210 (237)
.+.+++ ||+.|||-|-..| +......+.||-|+..|..
T Consensus 59 dPVvTl--CGHLFCWpClyqW----------------------l~~~~~~~~cPVCK~~Vs~ 96 (230)
T KOG0823|consen 59 DPVVTL--CGHLFCWPCLYQW----------------------LQTRPNSKECPVCKAEVSI 96 (230)
T ss_pred CCEEee--cccceehHHHHHH----------------------HhhcCCCeeCCcccccccc
Confidence 467777 9999999887655 2233455677888876654
No 146
>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=67.32 E-value=5.8 Score=21.45 Aligned_cols=27 Identities=15% Similarity=0.518 Sum_probs=21.9
Q ss_pred ccCCccccCceeeeccccCCcccceeCcccchh
Q 026541 128 SYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQW 160 (237)
Q Consensus 128 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 160 (237)
+.|. +|+..+....+ ...++|..|+..
T Consensus 2 ~~C~--~C~t~L~yP~g----A~~vrCs~C~~v 28 (31)
T TIGR01053 2 VVCG--GCRTLLMYPRG----ASSVRCALCQTV 28 (31)
T ss_pred cCcC--CCCcEeecCCC----CCeEECCCCCeE
Confidence 4677 89998888887 789999988753
No 147
>PLN02189 cellulose synthase
Probab=66.87 E-value=5 Score=39.56 Aligned_cols=62 Identities=23% Similarity=0.416 Sum_probs=43.8
Q ss_pred cccCCccccCceeeeccccCCcccceeCcccchhhccccccCcCCCCCChhhhcccccchHHHHHHHhcCCcccCCCCCc
Q 026541 127 RSYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQWFCFQCKLAWHAGYRCEESGNLRDRNDIAFGKLLEKMNWTRCPGCGN 206 (237)
Q Consensus 127 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~ 206 (237)
...|. -|+.-+...... .+.+.|..|+..+|. +|-+|.. +.+.+.||.|++
T Consensus 34 ~~~C~--iCgd~vg~~~~g---~~fvaC~~C~fpvCr----------~Cyeyer--------------~eg~q~CpqCkt 84 (1040)
T PLN02189 34 GQVCE--ICGDEIGLTVDG---DLFVACNECGFPVCR----------PCYEYER--------------REGTQNCPQCKT 84 (1040)
T ss_pred Ccccc--ccccccCcCCCC---CEEEeeccCCCcccc----------chhhhhh--------------hcCCccCcccCC
Confidence 34677 677666554432 488999999999997 4544432 456789999999
Q ss_pred ceeecCCCcce
Q 026541 207 CIERKKGCRIM 217 (237)
Q Consensus 207 ~iek~~GCnhm 217 (237)
.+.+--|+..+
T Consensus 85 ~Y~r~kgs~~v 95 (1040)
T PLN02189 85 RYKRLKGSPRV 95 (1040)
T ss_pred chhhccCCCCc
Confidence 99877676654
No 148
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=66.36 E-value=5.4 Score=26.01 Aligned_cols=60 Identities=20% Similarity=0.568 Sum_probs=37.3
Q ss_pred ccccccccCCCccccccccCCC--CCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCCHHHHhccCChhHHHHHHH
Q 026541 39 FTCDICIEPMSVNNKFKNNNLC--THPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLDPFACKHTIPSSLFLKWCD 115 (237)
Q Consensus 39 ~~C~iC~~~~~~~~~~~~~~~C--~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~~l~~~~~~~y~~ 115 (237)
..|..|-.++++... ..+.| .|.||.+|...-+ .+ .||. |+..+.-.-+ -+.+.+.+|-.
T Consensus 6 PnCECCDrDLpp~s~--dA~ICtfEcTFCadCae~~l----~g------~CPn--CGGelv~RP~---RPaa~L~r~PA 67 (84)
T COG3813 6 PNCECCDRDLPPDST--DARICTFECTFCADCAENRL----HG------LCPN--CGGELVARPI---RPAAKLARYPA 67 (84)
T ss_pred CCCcccCCCCCCCCC--ceeEEEEeeehhHhHHHHhh----cC------cCCC--CCchhhcCcC---ChHHHHhhCch
Confidence 468888888866433 34556 6899999966533 22 6888 9876643322 23455555543
No 149
>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=66.20 E-value=1.4 Score=28.37 Aligned_cols=39 Identities=21% Similarity=0.438 Sum_probs=19.7
Q ss_pred CCCCccccccccCCCccccccccCCCCCcccHHHHHHHH
Q 026541 35 IDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYI 73 (237)
Q Consensus 35 ~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~ 73 (237)
+.....|.+|...|.....-..-..||++||.+|....+
T Consensus 6 d~~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~~~ 44 (69)
T PF01363_consen 6 DSEASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQRI 44 (69)
T ss_dssp GGG-SB-TTT--B-BSSS-EEE-TTT--EEECCCS-EEE
T ss_pred CCCCCcCcCcCCcCCCceeeEccCCCCCEECCchhCCEE
Confidence 355788999999995433222345789999999976544
No 150
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=63.71 E-value=5.6 Score=39.40 Aligned_cols=61 Identities=25% Similarity=0.466 Sum_probs=42.5
Q ss_pred ccCCccccCceeeeccccCCcccceeCcccchhhccccccCcCCCCCChhhhcccccchHHHHHHHhcCCcccCCCCCcc
Q 026541 128 SYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQWFCFQCKLAWHAGYRCEESGNLRDRNDIAFGKLLEKMNWTRCPGCGNC 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~FPVCr----------pCYEYEr--------------~eG~q~CPqCktr 68 (1079)
T PLN02638 18 QVCQ--ICGDNVGKTVDG---EPFVACDVCAFPVCR----------PCYEYER--------------KDGNQSCPQCKTK 68 (1079)
T ss_pred ceee--ecccccCcCCCC---CEEEEeccCCCcccc----------chhhhhh--------------hcCCccCCccCCc
Confidence 3565 566555444332 588999999999996 5555433 4577899999999
Q ss_pred eeecCCCcce
Q 026541 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 9877676543
No 151
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=63.54 E-value=6.7 Score=26.67 Aligned_cols=29 Identities=24% Similarity=0.334 Sum_probs=23.8
Q ss_pred CcccCCCCCcceeecCCCcceEec-CCcEE
Q 026541 197 NWTRCPGCGNCIERKKGCRIMFCR-FIFLS 225 (237)
Q Consensus 197 ~~k~CP~C~~~iek~~GCnhm~C~-C~~~f 225 (237)
.--.||.|+....|..+=---.|+ ||+.|
T Consensus 34 ~~~~Cp~C~~~~VkR~a~GIW~C~kCg~~f 63 (89)
T COG1997 34 AKHVCPFCGRTTVKRIATGIWKCRKCGAKF 63 (89)
T ss_pred cCCcCCCCCCcceeeeccCeEEcCCCCCee
Confidence 335899999999888887788884 99876
No 152
>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 PF12773 DZR: Double zinc ribbon
Probab=63.27 E-value=4.6 Score=24.10 Aligned_cols=28 Identities=25% Similarity=0.666 Sum_probs=15.0
Q ss_pred CCcccCCccccCceeeeccccCCcccceeCcccch
Q 026541 125 FERSYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQ 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 3456677 6776665111 24556665544
No 154
>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=63.05 E-value=7.3 Score=29.79 Aligned_cols=60 Identities=12% Similarity=0.007 Sum_probs=32.0
Q ss_pred CCHHHHhccCChhHHHHHHHHHHHHhhc-CCCcccCCccccCceeeeccccCCcccceeCcccchh
Q 026541 96 LDPFACKHTIPSSLFLKWCDHLCEDYVL-GFERSYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQW 160 (237)
Q Consensus 96 i~~~~i~~~l~~~~~~~y~~~~~~~~~~-~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 160 (237)
++++.+...+..++.....++..+-... ++.+..|| .|+.-+...+.- ...+.||.||..
T Consensus 77 i~~~~i~d~Ik~~~~~~~~~lk~~l~~e~~~~~Y~Cp--~c~~r~tf~eA~---~~~F~Cp~Cg~~ 137 (158)
T TIGR00373 77 INYEKALDVLKRKLEETAKKLREKLEFETNNMFFICP--NMCVRFTFNEAM---ELNFTCPRCGAM 137 (158)
T ss_pred eCHHHHHHHHHHHHHHHHHHHHHHHhhccCCCeEECC--CCCcEeeHHHHH---HcCCcCCCCCCE
Confidence 4555555544444333222222111112 35567898 688766665542 357888888764
No 155
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=62.97 E-value=7.1 Score=29.78 Aligned_cols=54 Identities=19% Similarity=0.301 Sum_probs=37.1
Q ss_pred CCCCccccccccCCCccccccccCCCCC---cccHHHHHHHHHhhcccCCceeecCCCCcCCCCCCHH
Q 026541 35 IDGTFTCDICIEPMSVNNKFKNNNLCTH---PFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLDPF 99 (237)
Q Consensus 35 ~~~~~~C~iC~~~~~~~~~~~~~~~C~H---~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~ 99 (237)
......|-||.++... . ...-.|.. ....+|+.+|+..+ ...+|+. |+.+....
T Consensus 5 s~~~~~CRIC~~~~~~-~--~~PC~CkGs~k~VH~sCL~rWi~~s------~~~~Cei--C~~~Y~i~ 61 (162)
T PHA02825 5 SLMDKCCWICKDEYDV-V--TNYCNCKNENKIVHKECLEEWINTS------KNKSCKI--CNGPYNIK 61 (162)
T ss_pred CCCCCeeEecCCCCCC-c--cCCcccCCCchHHHHHHHHHHHhcC------CCCcccc--cCCeEEEE
Confidence 3556789999988632 1 12334444 57999999999843 4568998 99776644
No 156
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=62.58 E-value=4 Score=34.73 Aligned_cols=71 Identities=23% Similarity=0.417 Sum_probs=42.0
Q ss_pred eeecCCCCcCCCCCCHHHHhccCChhHHHHHHHHHHHHhh------cCCCcccCCccccCceeeeccccCCcccceeCcc
Q 026541 83 AKIECPGLHCEQFLDPFACKHTIPSSLFLKWCDHLCEDYV------LGFERSYCPNRNCMAVMVNECEGIGRVKKAQCPK 156 (237)
Q Consensus 83 ~~i~CP~~~C~~~i~~~~i~~~l~~~~~~~y~~~~~~~~~------~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~ 156 (237)
.|+.||. |+..+ ++++.+.+.|..+.--+.+ ..++...|- .|.. .. ......+|+.
T Consensus 289 LP~eCpi--C~ltL-------Vss~hLARSyhhL~PL~~F~Eip~~~~~~~~~Cf--~C~~-----~~--~~~~~y~C~~ 350 (378)
T KOG2807|consen 289 LPIECPI--CSLTL-------VSSPHLARSYHHLFPLKPFVEIPETEYNGSRFCF--ACQG-----EL--LSSGRYRCES 350 (378)
T ss_pred CCccCCc--cceeE-------ecchHHHHHHHhhcCCcchhhccccccCCCccee--eecc-----cc--CCCCcEEchh
Confidence 5777877 76332 3455555556554222111 123345576 5611 11 1257889999
Q ss_pred cchhhccccccCcCC
Q 026541 157 CKQWFCFQCKLAWHA 171 (237)
Q Consensus 157 C~~~~C~~C~~~~H~ 171 (237)
|+..||..|..-.|.
T Consensus 351 Ck~~FCldCDv~iHe 365 (378)
T KOG2807|consen 351 CKNVFCLDCDVFIHE 365 (378)
T ss_pred ccceeeccchHHHHh
Confidence 999999999887775
No 157
>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=62.18 E-value=6.7 Score=23.99 Aligned_cols=37 Identities=22% Similarity=0.585 Sum_probs=26.1
Q ss_pred ccccccccCCCccccccccCCCCCcccHHHHHHHHHh
Q 026541 39 FTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEV 75 (237)
Q Consensus 39 ~~C~iC~~~~~~~~~~~~~~~C~H~~C~~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 4688898877553322235679999999998876543
No 158
>PHA02926 zinc finger-like protein; Provisional
Probab=61.81 E-value=8.3 Score=31.17 Aligned_cols=75 Identities=21% Similarity=0.380 Sum_probs=42.5
Q ss_pred hHHHHHHHHHHHHhhcCCCcccCCccccCceeeeccccCCcccceeCcccchhhccccccCcCCCCCChhhhcccccchH
Q 026541 108 SLFLKWCDHLCEDYVLGFERSYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQWFCFQCKLAWHAGYRCEESGNLRDRNDI 187 (237)
Q Consensus 108 ~~~~~y~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~ 187 (237)
..+.+|+..... +.-..|+ -|...+........ .....=+.|++.||+.|-..|.....
T Consensus 156 ~il~~ye~~~~~-----SkE~eCg--ICmE~I~eK~~~~e-RrFGIL~~CnHsFCl~CIr~Wr~~r~------------- 214 (242)
T PHA02926 156 KILDKYEDVYRV-----SKEKECG--ICYEVVYSKRLEND-RYFGLLDSCNHIFCITCINIWHRTRR------------- 214 (242)
T ss_pred HHHHHHHHHHhc-----cCCCCCc--cCcccccccccccc-ccccccCCCCchHHHHHHHHHHHhcc-------------
Confidence 455555554332 2335677 67665543321100 11222346999999999988865321
Q ss_pred HHHHHHhcCCcccCCCCCccee
Q 026541 188 AFGKLLEKMNWTRCPGCGNCIE 209 (237)
Q Consensus 188 ~~~~~~~~~~~k~CP~C~~~ie 209 (237)
.....+.||-|+....
T Consensus 215 ------~~~~~rsCPiCR~~f~ 230 (242)
T PHA02926 215 ------ETGASDNCPICRTRFR 230 (242)
T ss_pred ------ccCcCCcCCCCcceee
Confidence 0234578999998765
No 159
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=61.74 E-value=2.7 Score=38.99 Aligned_cols=37 Identities=24% Similarity=0.555 Sum_probs=29.1
Q ss_pred CccccccccCCCccccccccCCCCCcccHHHHHHHHH
Q 026541 38 TFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIE 74 (237)
Q Consensus 38 ~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~ 74 (237)
...|.||+..+......++.+.|+|++|.-|+..-..
T Consensus 11 ~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~lyn 47 (861)
T KOG3161|consen 11 LLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLYN 47 (861)
T ss_pred HhhchHHHHHHHHHhcCcccccccchHHHHHHHhHhh
Confidence 5679999988865544456789999999999887554
No 160
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=61.74 E-value=8.3 Score=29.03 Aligned_cols=34 Identities=21% Similarity=0.346 Sum_probs=20.5
Q ss_pred CCcccCCccccCceeeeccccC--CcccceeCcccchh
Q 026541 125 FERSYCPNRNCMAVMVNECEGI--GRVKKAQCPKCKQW 160 (237)
Q Consensus 125 ~~~~~Cp~~~C~~~~~~~~~~~--~~~~~~~C~~C~~~ 160 (237)
+....|| .|+.-+...+... +....+.||.||..
T Consensus 97 ~~~Y~Cp--~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~ 132 (147)
T smart00531 97 NAYYKCP--NCQSKYTFLEANQLLDMDGTFTCPRCGEE 132 (147)
T ss_pred CcEEECc--CCCCEeeHHHHHHhcCCCCcEECCCCCCE
Confidence 4567899 7887776644311 00223888877763
No 161
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=60.33 E-value=6.8 Score=27.49 Aligned_cols=30 Identities=27% Similarity=0.576 Sum_probs=21.0
Q ss_pred CCcccCCCCCcc---eeecCCCcceEec-CCcEE
Q 026541 196 MNWTRCPGCGNC---IERKKGCRIMFCR-FIFLS 225 (237)
Q Consensus 196 ~~~k~CP~C~~~---iek~~GCnhm~C~-C~~~f 225 (237)
...-.||+|+.. |.+..|=-|..|. ||+.+
T Consensus 19 pt~f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y~ 52 (99)
T PRK14892 19 PKIFECPRCGKVSISVKIKKNIAIITCGNCGLYT 52 (99)
T ss_pred CcEeECCCCCCeEeeeecCCCcceEECCCCCCcc
Confidence 455789999943 2334477799995 99754
No 162
>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=60.26 E-value=10 Score=21.91 Aligned_cols=10 Identities=50% Similarity=1.298 Sum_probs=4.3
Q ss_pred cCCCCCccee
Q 026541 200 RCPGCGNCIE 209 (237)
Q Consensus 200 ~CP~C~~~ie 209 (237)
.|++||.+|+
T Consensus 21 vC~~CG~Vl~ 30 (43)
T PF08271_consen 21 VCPNCGLVLE 30 (43)
T ss_dssp EETTT-BBEE
T ss_pred ECCCCCCEee
Confidence 4555554444
No 163
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=60.22 E-value=8.1 Score=24.67 Aligned_cols=29 Identities=24% Similarity=0.214 Sum_probs=19.5
Q ss_pred CCcccCCCCCcceee---cCCCcceEe-cCCcE
Q 026541 196 MNWTRCPGCGNCIER---KKGCRIMFC-RFIFL 224 (237)
Q Consensus 196 ~~~k~CP~C~~~iek---~~GCnhm~C-~C~~~ 224 (237)
...|+||.|+..+.+ .+|=-...| .|+..
T Consensus 4 d~lKPCPFCG~~~~~v~~~~g~~~v~C~~CgA~ 36 (64)
T PRK09710 4 DNVKPCPFCGCPSVTVKAISGYYRAKCNGCESR 36 (64)
T ss_pred ccccCCCCCCCceeEEEecCceEEEEcCCCCcC
Confidence 457999999986544 456555667 47753
No 164
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=59.96 E-value=8.7 Score=22.58 Aligned_cols=11 Identities=45% Similarity=0.921 Sum_probs=6.3
Q ss_pred cccCCCCCcce
Q 026541 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 34666666554
No 165
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=59.95 E-value=9 Score=29.94 Aligned_cols=30 Identities=23% Similarity=0.510 Sum_probs=20.6
Q ss_pred CCcccCCccccCceeeeccccCCcccceeCcccch
Q 026541 125 FERSYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQ 159 (237)
Q Consensus 125 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 159 (237)
+.+..|| .|+.-+...+.- ...+.||.||.
T Consensus 115 ~~~Y~Cp--~C~~rytf~eA~---~~~F~Cp~Cg~ 144 (178)
T PRK06266 115 NMFFFCP--NCHIRFTFDEAM---EYGFRCPQCGE 144 (178)
T ss_pred CCEEECC--CCCcEEeHHHHh---hcCCcCCCCCC
Confidence 4578899 688777665542 35688887765
No 166
>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=59.75 E-value=6 Score=21.92 Aligned_cols=26 Identities=27% Similarity=0.607 Sum_probs=21.7
Q ss_pred ccceeCcccchhhccccccCcCCCCC
Q 026541 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 46889999999999999876687664
No 167
>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=59.52 E-value=8.8 Score=22.36 Aligned_cols=25 Identities=28% Similarity=0.667 Sum_probs=14.3
Q ss_pred CCCCcccHHHHHHHHHhhcccCCceeecCCC
Q 026541 59 LCTHPFCQDCTVKYIEVKVRDNNTAKIECPG 89 (237)
Q Consensus 59 ~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~ 89 (237)
.|+-.+...|+..|++..- ..+||.
T Consensus 18 ~C~~r~H~~C~~~y~r~~~------~~~CP~ 42 (43)
T PF08746_consen 18 DCNVRLHDDCFKKYFRHRS------NPKCPN 42 (43)
T ss_dssp -S--EE-HHHHHHHTTT-S------S-B-TT
T ss_pred ccCchHHHHHHHHHHhcCC------CCCCcC
Confidence 5888899999999997432 227886
No 168
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=58.08 E-value=3.7 Score=31.27 Aligned_cols=31 Identities=19% Similarity=0.435 Sum_probs=24.1
Q ss_pred CCCCccccccccCCCccccccccCCCCCcccH
Q 026541 35 IDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQ 66 (237)
Q Consensus 35 ~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~ 66 (237)
.+..-+|.||++++...+.+ ..++|-.+|.+
T Consensus 174 ~ddkGECvICLEdL~~GdtI-ARLPCLCIYHK 204 (205)
T KOG0801|consen 174 KDDKGECVICLEDLEAGDTI-ARLPCLCIYHK 204 (205)
T ss_pred cccCCcEEEEhhhccCCCce-eccceEEEeec
Confidence 46678999999999877765 57888777653
No 169
>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=56.94 E-value=7.9 Score=22.47 Aligned_cols=27 Identities=22% Similarity=0.605 Sum_probs=16.3
Q ss_pred cceeCcccchhhccccccCcCCCCCChhh
Q 026541 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 56789999999999888652 3456543
No 170
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=56.88 E-value=7.2 Score=32.59 Aligned_cols=67 Identities=18% Similarity=0.431 Sum_probs=43.6
Q ss_pred CCCCccccccccCCCccccccccCCC----CCcccHHHHHHHHHhhcccCCceeecCCCC-cCC---CCCCHH----HHh
Q 026541 35 IDGTFTCDICIEPMSVNNKFKNNNLC----THPFCQDCTVKYIEVKVRDNNTAKIECPGL-HCE---QFLDPF----ACK 102 (237)
Q Consensus 35 ~~~~~~C~iC~~~~~~~~~~~~~~~C----~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~-~C~---~~i~~~----~i~ 102 (237)
....+.|.+|.+.+.+ .+ +..| .|.||..|-+..|+.+-.. ..+.||.. .|. ..+++. +|.
T Consensus 265 ~~apLcCTLC~ERLED--TH--FVQCPSVp~HKFCFPCSResIK~Qg~s---gevYCPSGdkCPLvgS~vPWAFMQGEIa 337 (352)
T KOG3579|consen 265 PSAPLCCTLCHERLED--TH--FVQCPSVPSHKFCFPCSRESIKQQGAS---GEVYCPSGDKCPLVGSNVPWAFMQGEIA 337 (352)
T ss_pred CCCceeehhhhhhhcc--Cc--eeecCCCcccceecccCHHHHHhhcCC---CceeCCCCCcCcccCCcccHHHhhhhHH
Confidence 3455899999998843 22 3445 8999999999999876544 46778743 354 334433 455
Q ss_pred ccCChh
Q 026541 103 HTIPSS 108 (237)
Q Consensus 103 ~~l~~~ 108 (237)
.+|..+
T Consensus 338 tILagd 343 (352)
T KOG3579|consen 338 TILAGD 343 (352)
T ss_pred HHhccc
Confidence 555544
No 171
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=56.65 E-value=8.1 Score=32.34 Aligned_cols=24 Identities=29% Similarity=0.686 Sum_probs=21.7
Q ss_pred ccCCCCCcceeec--CCCcceEec-CC
Q 026541 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 6999999999987 899999995 85
No 172
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=56.58 E-value=4.5 Score=34.19 Aligned_cols=92 Identities=22% Similarity=0.387 Sum_probs=52.7
Q ss_pred CCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCCHHHHhccCChhHHHHHHHHHHHH-hhc-----CCCcccCCccc
Q 026541 61 THPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLDPFACKHTIPSSLFLKWCDHLCED-YVL-----GFERSYCPNRN 134 (237)
Q Consensus 61 ~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~~l~~~~~~~y~~~~~~~-~~~-----~~~~~~Cp~~~ 134 (237)
+-.+|..|-.. + -..||.||. |. +.-+|+..+.+.|..+.--+ +.+ ++..-.|- .
T Consensus 307 gGy~CP~Cktk-----V---CsLPi~CP~--Cs-------l~LilsthLarSyhhL~PLk~f~E~p~~~~~ks~~Cf--~ 367 (421)
T COG5151 307 GGYECPVCKTK-----V---CSLPISCPI--CS-------LQLILSTHLARSYHHLYPLKPFVEKPEGTNPKSTHCF--V 367 (421)
T ss_pred CceeCCcccce-----e---ecCCccCcc--hh-------HHHHHHHHHHHHHHhhccCcccccccCCCCCCCccce--e
Confidence 44577777221 1 235788887 63 33345555666665553222 222 12234565 5
Q ss_pred cCceeeecccc----CCcccceeCcccchhhccccccCcCC
Q 026541 135 CMAVMVNECEG----IGRVKKAQCPKCKQWFCFQCKLAWHA 171 (237)
Q Consensus 135 C~~~~~~~~~~----~~~~~~~~C~~C~~~~C~~C~~~~H~ 171 (237)
|...++..+.. .......+|+.|...||..|.+..|.
T Consensus 368 CQ~~fp~~~~~~~~~~~ss~rY~Ce~CK~~FC~dCdvfiHe 408 (421)
T COG5151 368 CQGPFPKPPVSPFDESTSSGRYQCELCKSTFCSDCDVFIHE 408 (421)
T ss_pred ccCCCCCCCCCcccccccccceechhhhhhhhhhhHHHHHH
Confidence 66655544331 11256788999999999999887764
No 173
>PF14353 CpXC: CpXC protein
Probab=56.32 E-value=4.7 Score=29.48 Aligned_cols=46 Identities=20% Similarity=0.280 Sum_probs=24.8
Q ss_pred ecCCCCcCCCCCCHHHHhcc---CChhHHHHHHHHHHHHhhcCCCcccCCccccCceeee
Q 026541 85 IECPGLHCEQFLDPFACKHT---IPSSLFLKWCDHLCEDYVLGFERSYCPNRNCMAVMVN 141 (237)
Q Consensus 85 i~CP~~~C~~~i~~~~i~~~---l~~~~~~~y~~~~~~~~~~~~~~~~Cp~~~C~~~~~~ 141 (237)
|+||. |+..+..+....+ .++++.++.. +. .-....|| .|+..+..
T Consensus 2 itCP~--C~~~~~~~v~~~I~~~~~p~l~e~il----~g---~l~~~~CP--~Cg~~~~~ 50 (128)
T PF14353_consen 2 ITCPH--CGHEFEFEVWTSINADEDPELKEKIL----DG---SLFSFTCP--SCGHKFRL 50 (128)
T ss_pred cCCCC--CCCeeEEEEEeEEcCcCCHHHHHHHH----cC---CcCEEECC--CCCCceec
Confidence 78999 9988775443332 2333333221 11 12246788 77765554
No 174
>PLN02400 cellulose synthase
Probab=56.26 E-value=9.7 Score=37.84 Aligned_cols=61 Identities=25% Similarity=0.395 Sum_probs=42.1
Q ss_pred ccCCccccCceeeeccccCCcccceeCcccchhhccccccCcCCCCCChhhhcccccchHHHHHHHhcCCcccCCCCCcc
Q 026541 128 SYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQWFCFQCKLAWHAGYRCEESGNLRDRNDIAFGKLLEKMNWTRCPGCGNC 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~eCaFPVCR----------pCYEYER--------------keGnq~CPQCkTr 87 (1085)
T PLN02400 37 QICQ--ICGDDVGVTETG---DVFVACNECAFPVCR----------PCYEYER--------------KDGTQCCPQCKTR 87 (1085)
T ss_pred ceee--ecccccCcCCCC---CEEEEEccCCCcccc----------chhheec--------------ccCCccCcccCCc
Confidence 3565 566554443332 588999999999997 4555443 4567899999999
Q ss_pred eeecCCCcce
Q 026541 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 8877676554
No 175
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=56.08 E-value=2.4 Score=35.47 Aligned_cols=40 Identities=30% Similarity=0.733 Sum_probs=27.9
Q ss_pred CccccccccCCCccccccccCCCCCc-ccHHHHHHHHHhhcccCCceeecCCCCcCCCC
Q 026541 38 TFTCDICIEPMSVNNKFKNNNLCTHP-FCQDCTVKYIEVKVRDNNTAKIECPGLHCEQF 95 (237)
Q Consensus 38 ~~~C~iC~~~~~~~~~~~~~~~C~H~-~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~ 95 (237)
..-|.||++-- .+- .+++|||. .|..| |.... .||. |.+.
T Consensus 300 ~~LC~ICmDaP--~DC--vfLeCGHmVtCt~C-----------Gkrm~-eCPI--CRqy 340 (350)
T KOG4275|consen 300 RRLCAICMDAP--RDC--VFLECGHMVTCTKC-----------GKRMN-ECPI--CRQY 340 (350)
T ss_pred HHHHHHHhcCC--cce--EEeecCcEEeehhh-----------ccccc-cCch--HHHH
Confidence 56799999864 233 47999996 78888 33333 7887 7543
No 176
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=56.05 E-value=14 Score=32.68 Aligned_cols=68 Identities=16% Similarity=0.336 Sum_probs=37.9
Q ss_pred ccceeCcccch----hhccccccCcCCCCCChhhhcccccchHHHHHHHhcCCcccCCCCCccee-ec--CCC----cce
Q 026541 149 VKKAQCPKCKQ----WFCFQCKLAWHAGYRCEESGNLRDRNDIAFGKLLEKMNWTRCPGCGNCIE-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~~etvRvvamdr~----f--Hv~CY~CEDCg~~LS~e~e~qgCyPld~Hl 453 (468)
T KOG1701|consen 380 QNNVYCVPDFHKKFAPRCSVCGNPILPRDGKDETVRVVAMDRD----F--HVNCYKCEDCGLLLSSEEEGQGCYPLDGHL 453 (468)
T ss_pred CCceeeehhhhhhcCcchhhccCCccCCCCCcceEEEEEcccc----c--cccceehhhcCccccccCCCCcceeccCce
Confidence 47777765532 2477777765544444433332111000 0 123357788999887 44 356 799
Q ss_pred Eec-CC
Q 026541 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 995 86
No 177
>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=55.31 E-value=1.9 Score=23.07 Aligned_cols=19 Identities=16% Similarity=0.385 Sum_probs=9.6
Q ss_pred eecCCCCcCCCCCCHHHHh
Q 026541 84 KIECPGLHCEQFLDPFACK 102 (237)
Q Consensus 84 ~i~CP~~~C~~~i~~~~i~ 102 (237)
.++||..+|...+..+...
T Consensus 2 ~vrCPvkdC~EEv~lgKY~ 20 (30)
T PF10426_consen 2 VVRCPVKDCDEEVSLGKYS 20 (30)
T ss_dssp EEE--STT---EEEHHHHH
T ss_pred ccccccccCcchhhhhhhc
Confidence 4799999998887755433
No 178
>PLN02436 cellulose synthase A
Probab=55.28 E-value=11 Score=37.40 Aligned_cols=61 Identities=23% Similarity=0.449 Sum_probs=41.6
Q ss_pred ccCCccccCceeeeccccCCcccceeCcccchhhccccccCcCCCCCChhhhcccccchHHHHHHHhcCCcccCCCCCcc
Q 026541 128 SYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQWFCFQCKLAWHAGYRCEESGNLRDRNDIAFGKLLEKMNWTRCPGCGNC 207 (237)
Q Consensus 128 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~~ 207 (237)
..|. -|+--+-..... .+.+.|..|+..+|.- |-+|.. +...+.||.|++.
T Consensus 37 ~iCq--ICGD~Vg~t~dG---e~FVACn~C~fpvCr~----------Cyeyer--------------~eg~~~Cpqckt~ 87 (1094)
T PLN02436 37 QTCQ--ICGDEIELTVDG---EPFVACNECAFPVCRP----------CYEYER--------------REGNQACPQCKTR 87 (1094)
T ss_pred cccc--ccccccCcCCCC---CEEEeeccCCCccccc----------hhhhhh--------------hcCCccCcccCCc
Confidence 4566 566655443332 5889999999999974 444432 4567899999999
Q ss_pred eeecCCCcce
Q 026541 208 IERKKGCRIM 217 (237)
Q Consensus 208 iek~~GCnhm 217 (237)
+.+--|+..+
T Consensus 88 Y~r~kgs~~~ 97 (1094)
T PLN02436 88 YKRIKGSPRV 97 (1094)
T ss_pred hhhccCCCCc
Confidence 8876666544
No 179
>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=55.08 E-value=26 Score=20.55 Aligned_cols=25 Identities=28% Similarity=0.408 Sum_probs=14.9
Q ss_pred ccCCCCCcc-eeecCCCcceEec-CCc
Q 026541 199 TRCPGCGNC-IERKKGCRIMFCR-FIF 223 (237)
Q Consensus 199 k~CP~C~~~-iek~~GCnhm~C~-C~~ 223 (237)
..||.|+.. +-+..+=....|+ |++
T Consensus 19 ~~CP~Cg~~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGSTKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCeeeEEeCCCCeEECCCCCC
Confidence 579999984 3333444445664 653
No 180
>PHA02862 5L protein; Provisional
Probab=54.45 E-value=16 Score=27.46 Aligned_cols=47 Identities=26% Similarity=0.480 Sum_probs=33.9
Q ss_pred ccccccccCCCccccccccCCCC-----CcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCCH
Q 026541 39 FTCDICIEPMSVNNKFKNNNLCT-----HPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLDP 98 (237)
Q Consensus 39 ~~C~iC~~~~~~~~~~~~~~~C~-----H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~ 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---NNFCGCNEEYKVVHIKCMQLWINY------SKKKECNL--CKTKYNI 54 (156)
T ss_pred CEEEEecCcCCC--C---cccccccCcchhHHHHHHHHHHhc------CCCcCccC--CCCeEEE
Confidence 579999998632 1 34553 35999999999953 35679999 9877653
No 181
>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=53.83 E-value=9.7 Score=24.40 Aligned_cols=17 Identities=24% Similarity=0.739 Sum_probs=13.0
Q ss_pred cccHHHHHHHHHhhccc
Q 026541 63 PFCQDCTVKYIEVKVRD 79 (237)
Q Consensus 63 ~~C~~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 49999999999988766
No 182
>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=53.45 E-value=11 Score=23.29 Aligned_cols=45 Identities=24% Similarity=0.674 Sum_probs=30.9
Q ss_pred ccccccccCCCccccccccCCC--CCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCC
Q 026541 39 FTCDICIEPMSVNNKFKNNNLC--THPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLD 97 (237)
Q Consensus 39 ~~C~iC~~~~~~~~~~~~~~~C--~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~ 97 (237)
..|..|-.++++... ....| ...||.+|....+. -.||. |+..+.
T Consensus 6 pnCE~C~~dLp~~s~--~A~ICSfECTFC~~C~e~~l~----------~~CPN--CgGelv 52 (57)
T PF06906_consen 6 PNCECCDKDLPPDSP--EAYICSFECTFCADCAETMLN----------GVCPN--CGGELV 52 (57)
T ss_pred CCccccCCCCCCCCC--cceEEeEeCcccHHHHHHHhc----------CcCcC--CCCccc
Confidence 468889888866432 23456 56899999776542 27888 987664
No 183
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=53.22 E-value=19 Score=25.89 Aligned_cols=47 Identities=19% Similarity=0.460 Sum_probs=26.7
Q ss_pred ChhHHHHHHHHHHHHhhc---------CCCcccCCccccCceeeeccccCCcccceeCcccch
Q 026541 106 PSSLFLKWCDHLCEDYVL---------GFERSYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQ 159 (237)
Q Consensus 106 ~~~~~~~y~~~~~~~~~~---------~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 159 (237)
.++.++-....+.+..+. .+...+|+ +|+..+..... ..+.||.|+.
T Consensus 40 ~p~~L~f~f~~~~~~t~~egA~L~i~~~p~~~~C~--~Cg~~~~~~~~-----~~~~CP~Cgs 95 (114)
T PRK03681 40 ETSSLAFCFDLVCRGTVAEGCKLHLEEQEAECWCE--TCQQYVTLLTQ-----RVRRCPQCHG 95 (114)
T ss_pred CHHHHHHHHHHHhCCCccCCCEEEEEeeCcEEEcc--cCCCeeecCCc-----cCCcCcCcCC
Confidence 445555444444444332 24468898 88876655432 3356887774
No 184
>PRK00420 hypothetical protein; Validated
Probab=53.03 E-value=31 Score=24.75 Aligned_cols=43 Identities=16% Similarity=0.295 Sum_probs=24.8
Q ss_pred hHHHHHHHHHHHHhhcCCCcccCCccccCceeeeccccCCcccceeCcccch
Q 026541 108 SLFLKWCDHLCEDYVLGFERSYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQ 159 (237)
Q Consensus 108 ~~~~~y~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 159 (237)
+...+..+++...+.. -...|| .|+..+..-.. -...||.|+.
T Consensus 6 ~~~k~~a~~Ll~Ga~m--l~~~CP--~Cg~pLf~lk~-----g~~~Cp~Cg~ 48 (112)
T PRK00420 6 DIVKKAAELLLKGAKM--LSKHCP--VCGLPLFELKD-----GEVVCPVHGK 48 (112)
T ss_pred HHHHHHHHHHHhHHHH--ccCCCC--CCCCcceecCC-----CceECCCCCC
Confidence 3444555555554333 126899 79987776332 3566776665
No 185
>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=52.85 E-value=20 Score=21.79 Aligned_cols=42 Identities=26% Similarity=0.513 Sum_probs=25.4
Q ss_pred CCccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCC
Q 026541 37 GTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLD 97 (237)
Q Consensus 37 ~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~ 97 (237)
+++.||.|...+.. .=|..++...=.. ....+.||. |...+.
T Consensus 1 ~~f~CP~C~~~~~~----------------~~L~~H~~~~H~~-~~~~v~CPi--C~~~~~ 42 (54)
T PF05605_consen 1 DSFTCPYCGKGFSE----------------SSLVEHCEDEHRS-ESKNVVCPI--CSSRVT 42 (54)
T ss_pred CCcCCCCCCCccCH----------------HHHHHHHHhHCcC-CCCCccCCC--chhhhh
Confidence 36889999985421 2355555543333 334689999 976433
No 186
>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=52.76 E-value=10 Score=26.89 Aligned_cols=26 Identities=23% Similarity=0.575 Sum_probs=18.9
Q ss_pred cCCccccCceeeeccccCCcccceeCcccchhh
Q 026541 129 YCPNRNCMAVMVNECEGIGRVKKAQCPKCKQWF 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 577 88887777766 567888777654
No 187
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=52.35 E-value=6 Score=24.00 Aligned_cols=9 Identities=33% Similarity=1.110 Sum_probs=4.5
Q ss_pred ccCCCCCcc
Q 026541 199 TRCPGCGNC 207 (237)
Q Consensus 199 k~CP~C~~~ 207 (237)
..||+|+..
T Consensus 25 IKCpRC~ti 33 (51)
T PF10122_consen 25 IKCPRCKTI 33 (51)
T ss_pred EECCCCCcc
Confidence 455555543
No 188
>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=52.28 E-value=15 Score=24.07 Aligned_cols=26 Identities=23% Similarity=0.580 Sum_probs=20.1
Q ss_pred ccCCCCCcc----eeecCCCcceEe-cCCcE
Q 026541 199 TRCPGCGNC----IERKKGCRIMFC-RFIFL 224 (237)
Q Consensus 199 k~CP~C~~~----iek~~GCnhm~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 479999874 445678889999 49985
No 189
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=52.15 E-value=12 Score=35.37 Aligned_cols=32 Identities=22% Similarity=0.726 Sum_probs=21.6
Q ss_pred CCcccCCccccCceeeeccccCCcccceeCcccchh------hccccccC
Q 026541 125 FERSYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQW------FCFQCKLA 168 (237)
Q Consensus 125 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~------~C~~C~~~ 168 (237)
.+.++|+ .|+..+. ...|+.||+. ||..|+..
T Consensus 13 ~~akFC~--~CG~~l~----------~~~Cp~CG~~~~~~~~fC~~CG~~ 50 (645)
T PRK14559 13 NNNRFCQ--KCGTSLT----------HKPCPQCGTEVPVDEAHCPNCGAE 50 (645)
T ss_pred CCCcccc--ccCCCCC----------CCcCCCCCCCCCcccccccccCCc
Confidence 3456788 7766552 1258888766 89988865
No 190
>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=52.14 E-value=13 Score=22.69 Aligned_cols=26 Identities=23% Similarity=0.360 Sum_probs=16.8
Q ss_pred ccCCCCCccee------ecCCCcceE-ec-CCcE
Q 026541 199 TRCPGCGNCIE------RKKGCRIMF-CR-FIFL 224 (237)
Q Consensus 199 k~CP~C~~~ie------k~~GCnhm~-C~-C~~~ 224 (237)
|+||.|+-.-+ .+.+..++. |. ||..
T Consensus 2 kPCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~ 35 (53)
T TIGR03655 2 KPCPFCGGADVYLRRGFDPLDLSHYFECSTCGAS 35 (53)
T ss_pred CCCCCCCCcceeeEeccCCCCCEEEEECCCCCCC
Confidence 78999998554 223555554 74 8754
No 191
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=51.52 E-value=13 Score=25.85 Aligned_cols=30 Identities=23% Similarity=0.684 Sum_probs=22.1
Q ss_pred ccCCccccCceeeeccccCCcccceeCcccchhh
Q 026541 128 SYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQWF 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 4799 8999888887743 5777787776644
No 192
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=51.52 E-value=9.2 Score=20.83 Aligned_cols=22 Identities=23% Similarity=0.520 Sum_probs=12.7
Q ss_pred ccCceeeeccccCCcccceeCcccchh
Q 026541 134 NCMAVMVNECEGIGRVKKAQCPKCKQW 160 (237)
Q Consensus 134 ~C~~~~~~~~~~~~~~~~~~C~~C~~~ 160 (237)
+|+..+..... ..++|+.||..
T Consensus 5 ~Cg~~~~~~~~-----~~irC~~CG~R 26 (32)
T PF03604_consen 5 ECGAEVELKPG-----DPIRCPECGHR 26 (32)
T ss_dssp SSSSSE-BSTS-----STSSBSSSS-S
T ss_pred cCCCeeEcCCC-----CcEECCcCCCe
Confidence 66666654433 56788888764
No 193
>smart00336 BBOX B-Box-type zinc finger.
Probab=51.43 E-value=12 Score=20.97 Aligned_cols=26 Identities=27% Similarity=0.552 Sum_probs=21.3
Q ss_pred ccceeCcccchhhccccccCcCCCCC
Q 026541 149 VKKAQCPKCKQWFCFQCKLAWHAGYR 174 (237)
Q Consensus 149 ~~~~~C~~C~~~~C~~C~~~~H~~~~ 174 (237)
...++|..|+...|..|....|.++.
T Consensus 13 ~~~~~C~~c~~~iC~~C~~~~H~~H~ 38 (42)
T smart00336 13 PAEFFCEECGALLCRTCDEAEHRGHT 38 (42)
T ss_pred ceEEECCCCCcccccccChhhcCCCc
Confidence 46788999999999999977776653
No 194
>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=51.30 E-value=11 Score=25.35 Aligned_cols=32 Identities=28% Similarity=0.416 Sum_probs=18.0
Q ss_pred CCcccCCCCCc------ceeecCCCcceEec-CCcEEEe
Q 026541 196 MNWTRCPGCGN------CIERKKGCRIMFCR-FIFLSLC 227 (237)
Q Consensus 196 ~~~k~CP~C~~------~iek~~GCnhm~C~-C~~~fc~ 227 (237)
...-.||.|+. -|.+..|=.++.|+ ||..|-+
T Consensus 20 ~~~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~~ 58 (81)
T PF05129_consen 20 PKVFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQT 58 (81)
T ss_dssp SS----TTT--SS-EEEEEETTTTEEEEEESSS--EEEE
T ss_pred CceEcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeEEE
Confidence 45579999992 35566888999995 9977754
No 195
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=51.26 E-value=17 Score=31.14 Aligned_cols=57 Identities=14% Similarity=0.249 Sum_probs=38.1
Q ss_pred cCCCCccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCCHHHHhc
Q 026541 34 DIDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLDPFACKH 103 (237)
Q Consensus 34 ~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~ 103 (237)
-......|++|+.+... +. ++..=|-+||-.|+.+|+. +.| +||..++.. +.+++.+
T Consensus 296 l~~~~~~CpvClk~r~N-pt--vl~vSGyVfCY~Ci~~Yv~---~~~-----~CPVT~~p~--~v~~l~r 352 (357)
T KOG0826|consen 296 LPPDREVCPVCLKKRQN-PT--VLEVSGYVFCYPCIFSYVV---NYG-----HCPVTGYPA--SVDHLIR 352 (357)
T ss_pred CCCccccChhHHhccCC-Cc--eEEecceEEeHHHHHHHHH---hcC-----CCCccCCcc--hHHHHHH
Confidence 34667899999988733 22 2344588999999999997 222 789865543 3344443
No 196
>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=51.20 E-value=13 Score=18.84 Aligned_cols=22 Identities=18% Similarity=0.460 Sum_probs=12.7
Q ss_pred ccCceeeeccccCCcccceeCcccch
Q 026541 134 NCMAVMVNECEGIGRVKKAQCPKCKQ 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 34444443332 57788888863
No 197
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=50.73 E-value=16 Score=26.32 Aligned_cols=31 Identities=23% Similarity=0.471 Sum_probs=22.6
Q ss_pred cccCCccccCceeeeccccCCcccceeCcccchhh
Q 026541 127 RSYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQWF 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 36899 9999998865422 3488888887754
No 198
>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=50.69 E-value=12 Score=30.61 Aligned_cols=56 Identities=16% Similarity=0.304 Sum_probs=38.2
Q ss_pred ecCCCCcCCCCCCH-HHHhccCChhHHHHHHHHHHHHhhcCCCcccCCccccCceeeecc
Q 026541 85 IECPGLHCEQFLDP-FACKHTIPSSLFLKWCDHLCEDYVLGFERSYCPNRNCMAVMVNEC 143 (237)
Q Consensus 85 i~CP~~~C~~~i~~-~~i~~~l~~~~~~~y~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~ 143 (237)
-+||. |....-+ -++.-+++++-|.+.-.--..+.+. .+...||+++|+.++....
T Consensus 11 ~~CPv--CksDrYLnPdik~linPECyHrmCESCvdRIFs-~GpAqCP~~gC~kILRK~k 67 (314)
T COG5220 11 RRCPV--CKSDRYLNPDIKILINPECYHRMCESCVDRIFS-RGPAQCPYKGCGKILRKIK 67 (314)
T ss_pred ccCCc--cccccccCCCeEEEECHHHHHHHHHHHHHHHhc-CCCCCCCCccHHHHHHHhc
Confidence 48999 9854332 3566678888887776554444443 4568999999998876543
No 199
>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=49.83 E-value=17 Score=22.82 Aligned_cols=26 Identities=15% Similarity=0.491 Sum_probs=19.5
Q ss_pred ccCCCCCcc----eeecCCCcceEec-CCcE
Q 026541 199 TRCPGCGNC----IERKKGCRIMFCR-FIFL 224 (237)
Q Consensus 199 k~CP~C~~~----iek~~GCnhm~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 479999874 4456777899994 9974
No 200
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=49.81 E-value=15 Score=22.59 Aligned_cols=22 Identities=18% Similarity=0.530 Sum_probs=16.1
Q ss_pred HHHHHHHhcCCcccCCCCCcce
Q 026541 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 4455666667889999999753
No 201
>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=49.76 E-value=4.2 Score=23.21 Aligned_cols=24 Identities=25% Similarity=0.661 Sum_probs=21.5
Q ss_pred cceeCcccchhhccccccCcCCCC
Q 026541 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 788999999999999999878775
No 202
>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=49.67 E-value=10 Score=27.78 Aligned_cols=26 Identities=15% Similarity=0.023 Sum_probs=16.2
Q ss_pred ccCCCCCcceeecCCCcceEe-cCCcEE
Q 026541 199 TRCPGCGNCIERKKGCRIMFC-RFIFLS 225 (237)
Q Consensus 199 k~CP~C~~~iek~~GCnhm~C-~C~~~f 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 578888776543322 66777 477654
No 203
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=49.51 E-value=13 Score=31.17 Aligned_cols=24 Identities=33% Similarity=0.713 Sum_probs=20.3
Q ss_pred ccCCCCCcceeec--CCCcceEec-CC
Q 026541 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 6899999999976 788888884 75
No 204
>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=49.35 E-value=8 Score=19.89 Aligned_cols=20 Identities=15% Similarity=0.391 Sum_probs=15.4
Q ss_pred ecCCCCcCCCCCCHHHHhccCC
Q 026541 85 IECPGLHCEQFLDPFACKHTIP 106 (237)
Q Consensus 85 i~CP~~~C~~~i~~~~i~~~l~ 106 (237)
+.||. |...++...+...|+
T Consensus 2 v~CPi--C~~~v~~~~in~HLD 21 (26)
T smart00734 2 VQCPV--CFREVPENLINSHLD 21 (26)
T ss_pred CcCCC--CcCcccHHHHHHHHH
Confidence 57998 998887777776665
No 205
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=49.11 E-value=13 Score=31.16 Aligned_cols=25 Identities=36% Similarity=0.696 Sum_probs=21.2
Q ss_pred cccCCCCCcceeec--CCCcceEec-CC
Q 026541 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 47999999999975 788888894 86
No 206
>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=48.89 E-value=18 Score=22.34 Aligned_cols=30 Identities=23% Similarity=0.436 Sum_probs=22.1
Q ss_pred ccCCccccCceeeeccccCCcccceeCcccchhh
Q 026541 128 SYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQWF 161 (237)
Q Consensus 128 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 161 (237)
+.|| .|+.-+....... ...+.|+.|+..+
T Consensus 3 ~~CP--~CG~~iev~~~~~--GeiV~Cp~CGael 32 (54)
T TIGR01206 3 FECP--DCGAEIELENPEL--GELVICDECGAEL 32 (54)
T ss_pred cCCC--CCCCEEecCCCcc--CCEEeCCCCCCEE
Confidence 4688 8999887765422 5688999888765
No 207
>PRK10445 endonuclease VIII; Provisional
Probab=48.81 E-value=13 Score=30.90 Aligned_cols=25 Identities=24% Similarity=0.571 Sum_probs=20.9
Q ss_pred cccCCCCCcceeec--CCCcceEec-CC
Q 026541 198 WTRCPGCGNCIERK--KGCRIMFCR-FI 222 (237)
Q Consensus 198 ~k~CP~C~~~iek~--~GCnhm~C~-C~ 222 (237)
-++||+|+..|++. +|=.-.+|. |.
T Consensus 235 g~~Cp~Cg~~I~~~~~~gR~t~~CP~CQ 262 (263)
T PRK10445 235 GEACERCGGIIEKTTLSSRPFYWCPGCQ 262 (263)
T ss_pred CCCCCCCCCEeEEEEECCCCcEECCCCc
Confidence 47999999999975 888888884 75
No 208
>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=48.63 E-value=17 Score=20.38 Aligned_cols=29 Identities=21% Similarity=0.352 Sum_probs=18.8
Q ss_pred ccCCccccCceeeeccccCCcccceeCcccch
Q 026541 128 SYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQ 159 (237)
Q Consensus 128 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 159 (237)
..|+ .|+..+........ .....||.|+.
T Consensus 6 y~C~--~Cg~~fe~~~~~~~-~~~~~CP~Cg~ 34 (41)
T smart00834 6 YRCE--DCGHTFEVLQKISD-DPLATCPECGG 34 (41)
T ss_pred EEcC--CCCCEEEEEEecCC-CCCCCCCCCCC
Confidence 4687 88886665443211 46777888876
No 209
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=48.58 E-value=13 Score=31.05 Aligned_cols=25 Identities=24% Similarity=0.448 Sum_probs=20.7
Q ss_pred cccCCCCCcceeec--CCCcceEec-CC
Q 026541 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 47999999999975 788888884 75
No 210
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=48.45 E-value=15 Score=25.78 Aligned_cols=29 Identities=21% Similarity=0.598 Sum_probs=22.2
Q ss_pred CCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCC
Q 026541 58 NLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFL 96 (237)
Q Consensus 58 ~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i 96 (237)
..|.|.|..-|+.+++.+. -+||. +....
T Consensus 79 G~CNHaFH~hCisrWlktr--------~vCPL--dn~eW 107 (114)
T KOG2930|consen 79 GVCNHAFHFHCISRWLKTR--------NVCPL--DNKEW 107 (114)
T ss_pred eecchHHHHHHHHHHHhhc--------CcCCC--cCcce
Confidence 3699999999999999753 27887 55443
No 211
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=48.41 E-value=7.2 Score=33.66 Aligned_cols=46 Identities=24% Similarity=0.532 Sum_probs=30.4
Q ss_pred CCCCccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCC
Q 026541 35 IDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLD 97 (237)
Q Consensus 35 ~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~ 97 (237)
.+....|.||.++..+ + ...+|||.-| |..- ....+.||. |...|.
T Consensus 302 ~~~p~lcVVcl~e~~~---~-~fvpcGh~cc--ct~c---------s~~l~~CPv--CR~rI~ 347 (355)
T KOG1571|consen 302 LPQPDLCVVCLDEPKS---A-VFVPCGHVCC--CTLC---------SKHLPQCPV--CRQRIR 347 (355)
T ss_pred cCCCCceEEecCCccc---e-eeecCCcEEE--chHH---------HhhCCCCch--hHHHHH
Confidence 4667789999998744 2 5799999965 4221 112345998 876553
No 212
>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=48.34 E-value=14 Score=30.96 Aligned_cols=25 Identities=32% Similarity=0.582 Sum_probs=20.4
Q ss_pred cccCCCCCcceeec--CCCcceEec-CC
Q 026541 198 WTRCPGCGNCIERK--KGCRIMFCR-FI 222 (237)
Q Consensus 198 ~k~CP~C~~~iek~--~GCnhm~C~-C~ 222 (237)
-++||+|+..|++. +|=.-.+|. |.
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 272 (272)
T TIGR00577 245 GEPCRRCGTPIEKIKVGGRGTHFCPQCQ 272 (272)
T ss_pred CCCCCCCCCeeEEEEECCCCCEECCCCC
Confidence 36999999999986 788888884 74
No 213
>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=48.33 E-value=24 Score=26.96 Aligned_cols=87 Identities=17% Similarity=0.408 Sum_probs=47.5
Q ss_pred CccccccccCCCccccccccCC-------CCCccc------HHHHHHHHHhhcccC-----------------------C
Q 026541 38 TFTCDICIEPMSVNNKFKNNNL-------CTHPFC------QDCTVKYIEVKVRDN-----------------------N 81 (237)
Q Consensus 38 ~~~C~iC~~~~~~~~~~~~~~~-------C~H~~C------~~Cl~~~~~~~i~~~-----------------------~ 81 (237)
..+|+||++-- .+ . +++- |+-.+| ..||.+|-.+..+.. .
T Consensus 2 d~~CpICme~P-HN-A--VLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkka~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 77 (162)
T PF07800_consen 2 DVTCPICMEHP-HN-A--VLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKKAYGKSSSSSSQSSSSAPSDSSSSESSESQE 77 (162)
T ss_pred CccCceeccCC-Cc-e--EEEEeccccCCccccccCCccchhHHHHHHHHHhcCCCCccccccccCcCCCcccccccccc
Confidence 46899999864 32 1 3333 333333 578888776544431 1
Q ss_pred ceeecCCCCcCCCCCCHHHHhccCChhHHHHHHHHHHHHhhcCCCcccCCccccCceeeeccc
Q 026541 82 TAKIECPGLHCEQFLDPFACKHTIPSSLFLKWCDHLCEDYVLGFERSYCPNRNCMAVMVNECE 144 (237)
Q Consensus 82 ~~~i~CP~~~C~~~i~~~~i~~~l~~~~~~~y~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~ 144 (237)
...+.||. |.+.|.--.+.. .. +.++ +...+-|+.-+|.....+.+.
T Consensus 78 ~~~L~CPL--CRG~V~GWtvve-----~A--------R~~L-N~K~RsC~~e~C~F~GtY~eL 124 (162)
T PF07800_consen 78 QPELACPL--CRGEVKGWTVVE-----PA--------RRFL-NAKKRSCSQESCSFSGTYSEL 124 (162)
T ss_pred cccccCcc--ccCceeceEEch-----HH--------HHHh-ccCCccCcccccccccCHHHH
Confidence 23678888 886654221111 01 1222 234567777777776666554
No 214
>PRK10220 hypothetical protein; Provisional
Probab=47.75 E-value=15 Score=26.12 Aligned_cols=27 Identities=26% Similarity=0.637 Sum_probs=19.1
Q ss_pred ccCCccccCceeeeccccCCcccceeCcccchhh
Q 026541 128 SYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQWF 161 (237)
Q Consensus 128 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 161 (237)
--|| .|..-+.+++. ..+.||.|++.+
T Consensus 4 P~CP--~C~seytY~d~-----~~~vCpeC~hEW 30 (111)
T PRK10220 4 PHCP--KCNSEYTYEDN-----GMYICPECAHEW 30 (111)
T ss_pred CcCC--CCCCcceEcCC-----CeEECCcccCcC
Confidence 3577 88887777766 567788776644
No 215
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=46.91 E-value=14 Score=31.02 Aligned_cols=25 Identities=32% Similarity=0.584 Sum_probs=20.9
Q ss_pred cccCCCCCcceeec--CCCcceEec-CC
Q 026541 198 WTRCPGCGNCIERK--KGCRIMFCR-FI 222 (237)
Q Consensus 198 ~k~CP~C~~~iek~--~GCnhm~C~-C~ 222 (237)
-++||.|+..|++. +|=.-.+|. |.
T Consensus 254 g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 281 (282)
T PRK13945 254 GKPCRKCGTPIERIKLAGRSTHWCPNCQ 281 (282)
T ss_pred cCCCCcCCCeeEEEEECCCccEECCCCc
Confidence 37999999999975 788888884 75
No 216
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=46.62 E-value=14 Score=36.56 Aligned_cols=57 Identities=25% Similarity=0.455 Sum_probs=38.0
Q ss_pred ccCceeeeccccCCcccceeCcccchhhccccccCcCCCCCChhhhcccccchHHHHHHHhcCCcccCCCCCcceeecCC
Q 026541 134 NCMAVMVNECEGIGRVKKAQCPKCKQWFCFQCKLAWHAGYRCEESGNLRDRNDIAFGKLLEKMNWTRCPGCGNCIERKKG 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~----------cyeye~--------------~~g~~~cp~c~t~y~~~~~ 72 (1044)
T PLN02915 20 VCGDEVGVKEDG---QPFVACHVCGFPVCKP----------CYEYER--------------SEGNQCCPQCNTRYKRHKG 72 (1044)
T ss_pred ccccccCcCCCC---CEEEEeccCCCccccc----------hhhhhh--------------hcCCccCCccCCchhhhcC
Confidence 455544443332 5889999999999974 444432 4566889999998886556
Q ss_pred Ccce
Q 026541 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 5543
No 217
>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=46.26 E-value=35 Score=24.16 Aligned_cols=63 Identities=19% Similarity=0.359 Sum_probs=37.1
Q ss_pred CCCccccccccCCCccccc----cccCCC---CCcccHHHHHHHHHhhccc-CCceeecCCCCcCCCCCCHHH
Q 026541 36 DGTFTCDICIEPMSVNNKF----KNNNLC---THPFCQDCTVKYIEVKVRD-NNTAKIECPGLHCEQFLDPFA 100 (237)
Q Consensus 36 ~~~~~C~iC~~~~~~~~~~----~~~~~C---~H~~C~~Cl~~~~~~~i~~-~~~~~i~CP~~~C~~~i~~~~ 100 (237)
....+|-.|.......... .....| .-.||..||...+...+.+ .....-.||. |...-+=..
T Consensus 5 ~~g~~CHqCrqKt~~~~~~C~~~~~~~~C~~~~~~fC~~CL~~ryge~~~ev~~~~~W~CP~--CrgiCnCs~ 75 (105)
T PF10497_consen 5 VNGKTCHQCRQKTLDFKTICTGHWKNSSCRGCRGKFCGGCLRNRYGENVEEVLEDPNWKCPK--CRGICNCSF 75 (105)
T ss_pred CCCCCchhhcCCCCCCceEcCCCCCCCCCccCcceehHhHHHHHHhhhHHHHhcCCceECCC--CCCeeCCHh
Confidence 3456677776654322110 012455 6779999999888776654 1234578997 766544333
No 218
>PLN02195 cellulose synthase A
Probab=46.23 E-value=16 Score=35.93 Aligned_cols=53 Identities=23% Similarity=0.478 Sum_probs=35.1
Q ss_pred ccCCccccCceeeeccccCCcccceeCcccchhhccccccCcCCCCCChhhhcccccchHHHHHHHhcCCcccCCCCCcc
Q 026541 128 SYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQWFCFQCKLAWHAGYRCEESGNLRDRNDIAFGKLLEKMNWTRCPGCGNC 207 (237)
Q Consensus 128 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~~ 207 (237)
..|. -|+..+-..... .+.+.|..|+...|.- |-+|.+ +.+.+.||.|+++
T Consensus 7 ~~c~--~cgd~~~~~~~g---~~fvaC~eC~~pvCrp----------Cyeyer--------------~eg~q~CpqCkt~ 57 (977)
T PLN02195 7 PICA--TCGEEVGVDSNG---EAFVACHECSYPLCKA----------CLEYEI--------------KEGRKVCLRCGGP 57 (977)
T ss_pred ccce--ecccccCcCCCC---CeEEEeccCCCccccc----------hhhhhh--------------hcCCccCCccCCc
Confidence 3455 566655554432 5889999999999974 444432 3466778888777
Q ss_pred ee
Q 026541 208 IE 209 (237)
Q Consensus 208 ie 209 (237)
+.
T Consensus 58 Yk 59 (977)
T PLN02195 58 YD 59 (977)
T ss_pred cc
Confidence 65
No 219
>PLN00209 ribosomal protein S27; Provisional
Probab=45.84 E-value=24 Score=23.97 Aligned_cols=31 Identities=16% Similarity=0.484 Sum_probs=21.5
Q ss_pred ccCCccccCceeeeccccCCcccceeCcccchhhcc
Q 026541 128 SYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQWFCF 163 (237)
Q Consensus 128 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~ 163 (237)
+.|| +|...-..=.. ....+.|..|+...+.
T Consensus 37 VkCp--~C~n~q~VFSh---A~t~V~C~~Cg~~L~~ 67 (86)
T PLN00209 37 VKCQ--GCFNITTVFSH---SQTVVVCGSCQTVLCQ 67 (86)
T ss_pred EECC--CCCCeeEEEec---CceEEEccccCCEeec
Confidence 7899 88875443221 1578999999988763
No 220
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=45.66 E-value=17 Score=36.78 Aligned_cols=22 Identities=32% Similarity=0.726 Sum_probs=16.0
Q ss_pred cCCCCCcceeec-CCCcceEe-cCCc
Q 026541 200 RCPGCGNCIERK-KGCRIMFC-RFIF 223 (237)
Q Consensus 200 ~CP~C~~~iek~-~GCnhm~C-~C~~ 223 (237)
.||+|+..+.-. .| ..+| .|+.
T Consensus 694 ~CPsCGaev~~des~--a~~CP~CGt 717 (1337)
T PRK14714 694 VCPDCGAEVPPDESG--RVECPRCDV 717 (1337)
T ss_pred eCccCCCccCCCccc--cccCCCCCC
Confidence 899999987654 35 5578 4874
No 221
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=45.11 E-value=27 Score=25.89 Aligned_cols=15 Identities=20% Similarity=0.228 Sum_probs=11.5
Q ss_pred CcccCCccccCceeeec
Q 026541 126 ERSYCPNRNCMAVMVNE 142 (237)
Q Consensus 126 ~~~~Cp~~~C~~~~~~~ 142 (237)
...+|+ +|+......
T Consensus 69 ~~~~C~--~CG~~~~~~ 83 (135)
T PRK03824 69 AVLKCR--NCGNEWSLK 83 (135)
T ss_pred eEEECC--CCCCEEecc
Confidence 467899 899877665
No 222
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=44.70 E-value=18 Score=20.59 Aligned_cols=12 Identities=42% Similarity=1.115 Sum_probs=8.5
Q ss_pred cCCCCCcceeec
Q 026541 200 RCPGCGNCIERK 211 (237)
Q Consensus 200 ~CP~C~~~iek~ 211 (237)
.||+|+..++..
T Consensus 1 ~CP~C~~~l~~~ 12 (41)
T PF13453_consen 1 KCPRCGTELEPV 12 (41)
T ss_pred CcCCCCcccceE
Confidence 488888876654
No 223
>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=44.08 E-value=17 Score=31.02 Aligned_cols=54 Identities=17% Similarity=0.375 Sum_probs=31.7
Q ss_pred ccCCccccCceeeeccccCCcccceeCcccchhhccccccCcCCCCCChhhhcccccchHHHHHHHhcCCcccCCCCCcc
Q 026541 128 SYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQWFCFQCKLAWHAGYRCEESGNLRDRNDIAFGKLLEKMNWTRCPGCGNC 207 (237)
Q Consensus 128 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~~ 207 (237)
..|| .|..-....+.- ...+. .||+.||..|-...- ..+..+||.|+..
T Consensus 4 ~~CP--~Ck~~~y~np~~---kl~i~--~CGH~~C~sCv~~l~------------------------~~~~~~CP~C~~~ 52 (309)
T TIGR00570 4 QGCP--RCKTTKYRNPSL---KLMVN--VCGHTLCESCVDLLF------------------------VRGSGSCPECDTP 52 (309)
T ss_pred CCCC--cCCCCCccCccc---ccccC--CCCCcccHHHHHHHh------------------------cCCCCCCCCCCCc
Confidence 3588 777754443330 12333 689999987754210 1123489999888
Q ss_pred eeecC
Q 026541 208 IERKK 212 (237)
Q Consensus 208 iek~~ 212 (237)
+.++.
T Consensus 53 lrk~~ 57 (309)
T TIGR00570 53 LRKNN 57 (309)
T ss_pred cchhh
Confidence 87753
No 224
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=43.57 E-value=22 Score=34.44 Aligned_cols=41 Identities=27% Similarity=0.641 Sum_probs=30.8
Q ss_pred CccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCC
Q 026541 38 TFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQ 94 (237)
Q Consensus 38 ~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~ 94 (237)
...|..|--++..+ .+-..|+|.|...|+. + ..-.||. |..
T Consensus 840 ~skCs~C~~~LdlP---~VhF~CgHsyHqhC~e--------~---~~~~CP~--C~~ 880 (933)
T KOG2114|consen 840 VSKCSACEGTLDLP---FVHFLCGHSYHQHCLE--------D---KEDKCPK--CLP 880 (933)
T ss_pred eeeecccCCccccc---eeeeecccHHHHHhhc--------c---CcccCCc--cch
Confidence 45899999888443 2457899999999987 2 2348998 865
No 225
>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=43.28 E-value=29 Score=17.73 Aligned_cols=22 Identities=14% Similarity=0.522 Sum_probs=17.4
Q ss_pred ccCceeeeccccCCcccceeCcccch
Q 026541 134 NCMAVMVNECEGIGRVKKAQCPKCKQ 159 (237)
Q Consensus 134 ~C~~~~~~~~~~~~~~~~~~C~~C~~ 159 (237)
+|...+....+ +..++|..|++
T Consensus 3 ~Cr~~L~yp~G----A~sVrCa~C~~ 24 (25)
T PF06943_consen 3 GCRTLLMYPRG----APSVRCACCHT 24 (25)
T ss_pred CCCceEEcCCC----CCCeECCccCc
Confidence 67777877777 68899988865
No 226
>PF14369 zf-RING_3: zinc-finger
Probab=42.61 E-value=26 Score=19.43 Aligned_cols=30 Identities=23% Similarity=0.585 Sum_probs=19.3
Q ss_pred cccCCccccCceeeeccccCCcccceeCcccchhh
Q 026541 127 RSYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQWF 161 (237)
Q Consensus 127 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 161 (237)
+.||- .|...+...... ...+.||.|+..|
T Consensus 2 ~ywCh--~C~~~V~~~~~~---~~~~~CP~C~~gF 31 (35)
T PF14369_consen 2 RYWCH--QCNRFVRIAPSP---DSDVACPRCHGGF 31 (35)
T ss_pred CEeCc--cCCCEeEeCcCC---CCCcCCcCCCCcE
Confidence 35787 788888875432 2334688887544
No 227
>PRK11827 hypothetical protein; Provisional
Probab=42.55 E-value=24 Score=22.26 Aligned_cols=29 Identities=14% Similarity=0.302 Sum_probs=21.6
Q ss_pred CcccCCCCCcceeecCCCcceEec-CCcEE
Q 026541 197 NWTRCPGCGNCIERKKGCRIMFCR-FIFLS 225 (237)
Q Consensus 197 ~~k~CP~C~~~iek~~GCnhm~C~-C~~~f 225 (237)
.+-.||.|+-..+-+.+=+.+.|+ |+--|
T Consensus 7 eILaCP~ckg~L~~~~~~~~Lic~~~~laY 36 (60)
T PRK11827 7 EIIACPVCNGKLWYNQEKQELICKLDNLAF 36 (60)
T ss_pred hheECCCCCCcCeEcCCCCeEECCccCeec
Confidence 346899999998877666678885 87543
No 228
>KOG2979 consensus Protein involved in DNA repair [General function prediction only]
Probab=42.46 E-value=36 Score=28.13 Aligned_cols=71 Identities=17% Similarity=0.226 Sum_probs=41.7
Q ss_pred CccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCCHHHHhccCCh-hHHHHHHHH
Q 026541 38 TFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLDPFACKHTIPS-SLFLKWCDH 116 (237)
Q Consensus 38 ~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~~l~~-~~~~~y~~~ 116 (237)
...|+|=.-++..+ + ....|+|+|=++=+..++. ....++||..+|..+... ...++++ ..+.++.+.
T Consensus 176 s~rdPis~~~I~nP--v-iSkkC~HvydrDsI~~~l~------~~~~i~CPv~gC~~~~~~--~~~~l~~d~el~~kIr~ 244 (262)
T KOG2979|consen 176 SNRDPISKKPIVNP--V-ISKKCGHVYDRDSIMQILC------DEITIRCPVLGCENPYYI--QPGHLDEDKELQQKIRQ 244 (262)
T ss_pred cccCchhhhhhhch--h-hhcCcCcchhhhhHHHHhc------cCceeecccccCCccccc--cccccCchHHHHHHHHH
Confidence 34455544444221 1 4568999999988777764 356899999999833321 1223333 355555554
Q ss_pred HHH
Q 026541 117 LCE 119 (237)
Q Consensus 117 ~~~ 119 (237)
..+
T Consensus 245 ~qe 247 (262)
T KOG2979|consen 245 SQE 247 (262)
T ss_pred hcc
Confidence 443
No 229
>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=41.74 E-value=16 Score=30.90 Aligned_cols=36 Identities=22% Similarity=0.413 Sum_probs=16.8
Q ss_pred ccCCCCCcc-----eeecC--CCcceEec-CCcEEEe------ccccCCC
Q 026541 199 TRCPGCGNC-----IERKK--GCRIMFCR-FIFLSLC------LCIFSNR 234 (237)
Q Consensus 199 k~CP~C~~~-----iek~~--GCnhm~C~-C~~~fc~------~c~~~~~ 234 (237)
-.||-||.. |...+ |=-++.|. |++.|-+ .|..+++
T Consensus 173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R~~Cp~Cg~~~~ 222 (290)
T PF04216_consen 173 GYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVRIKCPYCGNTDH 222 (290)
T ss_dssp SS-TTT---EEEEEEE------EEEEEETTT--EEE--TTS-TTT---SS
T ss_pred CcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecCCCCcCCCCCCC
Confidence 699999985 34444 88999995 9999843 4555544
No 230
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=41.55 E-value=28 Score=19.00 Aligned_cols=29 Identities=21% Similarity=0.321 Sum_probs=17.7
Q ss_pred cccCCccccCceeeeccccCCcccceeCcccchhh
Q 026541 127 RSYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQWF 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--KCGGNGIVNKE----DDYEVCIFCGSSF 31 (33)
T ss_pred ceEcC--CCCCCeEEEec----CCeEEcccCCcEe
Confidence 35677 68876666322 2566777777643
No 231
>PLN02436 cellulose synthase A
Probab=40.90 E-value=24 Score=35.20 Aligned_cols=53 Identities=28% Similarity=0.713 Sum_probs=35.6
Q ss_pred CCCccccccccCCCc---cccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCC
Q 026541 36 DGTFTCDICIEPMSV---NNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLD 97 (237)
Q Consensus 36 ~~~~~C~iC~~~~~~---~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~ 97 (237)
.....|.||-++... .+.|.....|+-.+|+.|. .|-. ++| .-.||. |+....
T Consensus 34 ~~~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cy-eyer---~eg---~~~Cpq--ckt~Y~ 89 (1094)
T PLN02436 34 LSGQTCQICGDEIELTVDGEPFVACNECAFPVCRPCY-EYER---REG---NQACPQ--CKTRYK 89 (1094)
T ss_pred cCCccccccccccCcCCCCCEEEeeccCCCccccchh-hhhh---hcC---CccCcc--cCCchh
Confidence 445699999998643 3455555569999999998 3333 333 237888 885543
No 232
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=40.45 E-value=20 Score=29.44 Aligned_cols=60 Identities=15% Similarity=0.205 Sum_probs=39.1
Q ss_pred HHHhccCChhHHHHHHHHHHHH-hhc--CCCcccCCccccCceeeecccc--CCcccceeCcccchh
Q 026541 99 FACKHTIPSSLFLKWCDHLCED-YVL--GFERSYCPNRNCMAVMVNECEG--IGRVKKAQCPKCKQW 160 (237)
Q Consensus 99 ~~i~~~l~~~~~~~y~~~~~~~-~~~--~~~~~~Cp~~~C~~~~~~~~~~--~~~~~~~~C~~C~~~ 160 (237)
..+..-++++++..|.+..... -+. .-.-..|. +|...++..... ..+...++||.||..
T Consensus 166 ~~L~~~l~~ell~~yeri~~~~kg~gvvpl~g~~C~--GC~m~l~~~~~~~V~~~d~iv~CP~CgRI 230 (239)
T COG1579 166 EELKEKLDPELLSEYERIRKNKKGVGVVPLEGRVCG--GCHMKLPSQTLSKVRKKDEIVFCPYCGRI 230 (239)
T ss_pred HHHHHhcCHHHHHHHHHHHhcCCCceEEeecCCccc--CCeeeecHHHHHHHhcCCCCccCCccchH
Confidence 3566678999999999887654 221 11225687 888877764431 113678899988864
No 233
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=40.41 E-value=13 Score=23.44 Aligned_cols=18 Identities=39% Similarity=0.907 Sum_probs=14.1
Q ss_pred cccCCCCCcceeecCCCcceEe
Q 026541 198 WTRCPGCGNCIERKKGCRIMFC 219 (237)
Q Consensus 198 ~k~CP~C~~~iek~~GCnhm~C 219 (237)
-|-||.||.+|.-+ ..+|
T Consensus 3 HkHC~~CG~~Ip~~----~~fC 20 (59)
T PF09889_consen 3 HKHCPVCGKPIPPD----ESFC 20 (59)
T ss_pred CCcCCcCCCcCCcc----hhhh
Confidence 47899999999864 4555
No 234
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=40.01 E-value=35 Score=23.12 Aligned_cols=31 Identities=19% Similarity=0.504 Sum_probs=21.6
Q ss_pred ccCCccccCceeeeccccCCcccceeCcccchhhcc
Q 026541 128 SYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQWFCF 163 (237)
Q Consensus 128 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~ 163 (237)
+.|| +|...-..=.. ....+.|..|+...|.
T Consensus 36 VkCp--~C~n~q~VFSh---A~t~V~C~~Cg~~L~~ 66 (85)
T PTZ00083 36 VKCP--GCSQITTVFSH---AQTVVLCGGCSSQLCQ 66 (85)
T ss_pred EECC--CCCCeeEEEec---CceEEEccccCCEeec
Confidence 7899 88875443221 2578999999988764
No 235
>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=39.98 E-value=27 Score=20.12 Aligned_cols=29 Identities=17% Similarity=0.308 Sum_probs=18.3
Q ss_pred ccCCccccCceeeeccccCCcccceeCcccch
Q 026541 128 SYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQ 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 4677 78865554433222 56788888876
No 236
>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=39.77 E-value=23 Score=25.37 Aligned_cols=23 Identities=26% Similarity=0.823 Sum_probs=14.2
Q ss_pred cccceeCcccchhh--------ccccccCcC
Q 026541 148 RVKKAQCPKCKQWF--------CFQCKLAWH 170 (237)
Q Consensus 148 ~~~~~~C~~C~~~~--------C~~C~~~~H 170 (237)
++..+.||.|++.+ |..|+.|.+
T Consensus 66 kav~V~CP~C~K~TKmLGr~D~CM~C~~pLT 96 (114)
T PF11023_consen 66 KAVQVECPNCGKQTKMLGRVDACMHCKEPLT 96 (114)
T ss_pred cceeeECCCCCChHhhhchhhccCcCCCcCc
Confidence 35666677776543 777776654
No 237
>PRK12495 hypothetical protein; Provisional
Probab=39.41 E-value=45 Score=26.91 Aligned_cols=28 Identities=21% Similarity=0.549 Sum_probs=17.8
Q ss_pred CCcccCCccccCceeeeccccCCcccceeCcccchh
Q 026541 125 FERSYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQW 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 8999888432 24556655543
No 238
>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=39.01 E-value=33 Score=28.30 Aligned_cols=93 Identities=22% Similarity=0.472 Sum_probs=52.8
Q ss_pred CCCCccccccccCCCccccccccCCCCCc-ccHHHHHHHHHhhccc--CCceeecCCCCcCCCCCCHHHHhccCChhHHH
Q 026541 35 IDGTFTCDICIEPMSVNNKFKNNNLCTHP-FCQDCTVKYIEVKVRD--NNTAKIECPGLHCEQFLDPFACKHTIPSSLFL 111 (237)
Q Consensus 35 ~~~~~~C~iC~~~~~~~~~~~~~~~C~H~-~C~~Cl~~~~~~~i~~--~~~~~i~CP~~~C~~~i~~~~i~~~l~~~~~~ 111 (237)
..+..+|.+|...+...... =+|+ -|..|-+. +-|++ .+..-++|| |+-.|-
T Consensus 62 ~~p~v~CrVCq~~I~i~gk~-----~QhVVkC~~CnEA---TPIr~aPpGKKYVRCP---CNCLLI-------------- 116 (256)
T PF09788_consen 62 GAPVVTCRVCQSLIDIEGKM-----HQHVVKCSVCNEA---TPIRNAPPGKKYVRCP---CNCLLI-------------- 116 (256)
T ss_pred CCceEEeecCCceecccCcc-----ceeeEECCCCCcc---ccccCCCCCCeeEecC---CceEEE--------------
Confidence 45788999998877443211 1332 45556332 22333 234457888 543221
Q ss_pred HHHHHHHHHhhcCCCcccCCccccCceeeeccccC----------CcccceeCcccchhh
Q 026541 112 KWCDHLCEDYVLGFERSYCPNRNCMAVMVNECEGI----------GRVKKAQCPKCKQWF 161 (237)
Q Consensus 112 ~y~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~----------~~~~~~~C~~C~~~~ 161 (237)
-.....++-||+++|+.++...+... .....+.|..|+..|
T Consensus 117 ---------Ck~sS~rIaCPRp~CkRiI~L~~~~~~p~~~~~~~~p~~~rv~CghC~~~F 167 (256)
T PF09788_consen 117 ---------CKSSSQRIACPRPNCKRIINLGPSHQGPVTPPVPTQPGSCRVICGHCSNTF 167 (256)
T ss_pred ---------eecccccccCCCCCCcceEEeCCccCCCCCCCCCCCCCceeEECCCCCCcE
Confidence 01235679999999999998876511 123456666665554
No 239
>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=38.20 E-value=54 Score=23.55 Aligned_cols=36 Identities=19% Similarity=0.448 Sum_probs=24.2
Q ss_pred CcccCCccccCceeeeccccCCcccceeCcccchhhccccccC
Q 026541 126 ERSYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQWFCFQCKLA 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 7776443222 24589999999999999875
No 240
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=38.09 E-value=45 Score=23.94 Aligned_cols=27 Identities=26% Similarity=0.605 Sum_probs=16.9
Q ss_pred CCcccCCccccCceeeeccccCCcccceeCcccch
Q 026541 125 FERSYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQ 159 (237)
Q Consensus 125 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 159 (237)
+...+|+ +|+..+..... .+.||.|+.
T Consensus 68 p~~~~C~--~Cg~~~~~~~~------~~~CP~Cgs 94 (115)
T TIGR00100 68 PVECECE--DCSEEVSPEID------LYRCPKCHG 94 (115)
T ss_pred CcEEEcc--cCCCEEecCCc------CccCcCCcC
Confidence 4457888 78866655432 355776664
No 241
>COG3492 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.95 E-value=34 Score=23.45 Aligned_cols=17 Identities=18% Similarity=0.634 Sum_probs=14.9
Q ss_pred cccHHHHHHHHHhhccc
Q 026541 63 PFCQDCTVKYIEVKVRD 79 (237)
Q Consensus 63 ~~C~~Cl~~~~~~~i~~ 79 (237)
-||+.||.+|+..+-..
T Consensus 42 gFCRNCLs~Wy~eaae~ 58 (104)
T COG3492 42 GFCRNCLSNWYREAAEA 58 (104)
T ss_pred HHHHHHHHHHHHHHHhc
Confidence 49999999999988766
No 242
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=37.81 E-value=35 Score=24.59 Aligned_cols=48 Identities=23% Similarity=0.410 Sum_probs=25.3
Q ss_pred CChhHHHHHHHHHHHHh-hc-C--------CCcccCCccccCceeeeccccCCcccceeCcccch
Q 026541 105 IPSSLFLKWCDHLCEDY-VL-G--------FERSYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQ 159 (237)
Q Consensus 105 l~~~~~~~y~~~~~~~~-~~-~--------~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 159 (237)
+.++.++-....+.+.. +. . +-..+|. +|+..+..... ....||.|+.
T Consensus 39 V~pe~L~faf~~~~~~T~~~ega~L~Ie~vp~~~~C~--~Cg~~~~~~~~-----~~~~CP~Cgs 96 (117)
T PRK00564 39 MDKSLFVSAFETFREESLVCKDAILDIVDEKVELECK--DCSHVFKPNAL-----DYGVCEKCHS 96 (117)
T ss_pred cCHHHHHHHHHHHhcCCcccCCCEEEEEecCCEEEhh--hCCCccccCCc-----cCCcCcCCCC
Confidence 34455544444455544 32 1 3457888 78866554432 2335776664
No 243
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=37.03 E-value=48 Score=23.72 Aligned_cols=47 Identities=23% Similarity=0.459 Sum_probs=25.3
Q ss_pred CChhHHHHHHHHHHHHhhc---------CCCcccCCccccCceeeeccccCCcccceeCcccch
Q 026541 105 IPSSLFLKWCDHLCEDYVL---------GFERSYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQ 159 (237)
Q Consensus 105 l~~~~~~~y~~~~~~~~~~---------~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 159 (237)
+.++.++-....+.+..+. .+-..+|+ .|+..+.... ..+.||.|+.
T Consensus 39 v~pe~L~f~f~~~~~~T~~egA~L~I~~vp~~~~C~--~Cg~~~~~~~------~~~~CP~Cgs 94 (113)
T PRK12380 39 VEESAVRFSFEIVCHGTVAQGCDLHIVYKPAQAWCW--DCSQVVEIHQ------HDAQCPHCHG 94 (113)
T ss_pred cCHHHHHHHHHHHhCCCccCCCEEEEEeeCcEEEcc--cCCCEEecCC------cCccCcCCCC
Confidence 3445555444444444331 14457888 7886665543 2344777664
No 244
>PF02748 PyrI_C: Aspartate carbamoyltransferase regulatory chain, metal binding domain; InterPro: IPR020542 Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) 2.1.3.2 from EC is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity []. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme []. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies. A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme []. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold. ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation []. This entry represents the C-terminal domain.; PDB: 2YWW_B 1SKU_D 1Q95_L 8ATC_B 3AT1_D 1RAI_D 4E2F_D 1NBE_B 6AT1_B 2FZC_D ....
Probab=36.89 E-value=19 Score=21.94 Aligned_cols=35 Identities=29% Similarity=0.429 Sum_probs=18.7
Q ss_pred CcccCCccccCceeeeccc------cCCcccceeCcccchhh
Q 026541 126 ERSYCPNRNCMAVMVNECE------GIGRVKKAQCPKCKQWF 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 4578999999766 11111 01125678888887643
No 245
>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=36.27 E-value=49 Score=30.41 Aligned_cols=34 Identities=29% Similarity=0.603 Sum_probs=25.2
Q ss_pred cCCccccCceeeeccccCCcccceeCcccchh-----hccccccC
Q 026541 129 YCPNRNCMAVMVNECEGIGRVKKAQCPKCKQW-----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 466 78777776654 468899999876 58888764
No 246
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=36.18 E-value=11 Score=35.46 Aligned_cols=60 Identities=22% Similarity=0.450 Sum_probs=44.0
Q ss_pred hcCCCCccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCCHHHHhc
Q 026541 33 EDIDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLDPFACKH 103 (237)
Q Consensus 33 ~~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~~~i~~ 103 (237)
..+....+|+||+..+... +.+.|.|.||..|+..-+...- ....||. |...+.-...+.
T Consensus 16 ~~~~k~lEc~ic~~~~~~p----~~~kc~~~~l~~~~n~~f~~~~-----~~~~~~l--c~~~~eK~s~~E 75 (684)
T KOG4362|consen 16 NAMQKILECPICLEHVKEP----SLLKCDHIFLKFCLNKLFESKK-----GPKQCAL--CKSDIEKRSLRE 75 (684)
T ss_pred HHHhhhccCCceeEEeecc----chhhhhHHHHhhhhhceeeccC-----ccccchh--hhhhhhhhhccc
Confidence 3457789999999988543 5789999999999887665432 2667887 876666554444
No 247
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=35.45 E-value=39 Score=21.02 Aligned_cols=36 Identities=17% Similarity=0.121 Sum_probs=26.3
Q ss_pred ecCCCCcCCCCCCHHHHhccCChhHHHHHHHHHHHHhh
Q 026541 85 IECPGLHCEQFLDPFACKHTIPSSLFLKWCDHLCEDYV 122 (237)
Q Consensus 85 i~CP~~~C~~~i~~~~i~~~l~~~~~~~y~~~~~~~~~ 122 (237)
..||. |+.+.....=..+-++|-+.+|...+.+...
T Consensus 18 ~~CP~--CG~~t~~~~P~rfSp~D~y~~yR~~~kk~~~ 53 (56)
T PRK13130 18 EICPV--CGGKTKNPHPPRFSPEDKYGKYRRALKKRRK 53 (56)
T ss_pred ccCcC--CCCCCCCCCCCCCCCCCccHHHHHHHHHHhh
Confidence 46888 9877665555566677899999988876643
No 248
>PRK04023 DNA polymerase II large subunit; Validated
Probab=35.08 E-value=31 Score=34.26 Aligned_cols=16 Identities=31% Similarity=1.049 Sum_probs=8.1
Q ss_pred eeCcccch-----hhcccccc
Q 026541 152 AQCPKCKQ-----WFCFQCKL 167 (237)
Q Consensus 152 ~~C~~C~~-----~~C~~C~~ 167 (237)
+.||.||. .+|..|+.
T Consensus 639 frCP~CG~~Te~i~fCP~CG~ 659 (1121)
T PRK04023 639 RRCPFCGTHTEPVYRCPRCGI 659 (1121)
T ss_pred ccCCCCCCCCCcceeCccccC
Confidence 45555553 35555543
No 249
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=34.81 E-value=46 Score=27.42 Aligned_cols=43 Identities=14% Similarity=0.234 Sum_probs=32.9
Q ss_pred hcCCCCccccccccCCCccccccccCCCCCcccHHHHHHHHHhhccc
Q 026541 33 EDIDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRD 79 (237)
Q Consensus 33 ~~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~ 79 (237)
+...+..-|.+|+.+.... +..+=||.||++|+..||..+-++
T Consensus 38 DsiK~FdcCsLtLqPc~dP----vit~~GylfdrEaILe~ilaqKke 80 (303)
T KOG3039|consen 38 DSIKPFDCCSLTLQPCRDP----VITPDGYLFDREAILEYILAQKKE 80 (303)
T ss_pred cccCCcceeeeecccccCC----ccCCCCeeeeHHHHHHHHHHHHHH
Confidence 3446677789999888443 456779999999999999876554
No 250
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=34.28 E-value=78 Score=26.64 Aligned_cols=55 Identities=15% Similarity=0.124 Sum_probs=33.7
Q ss_pred HHHHhccCChhHHHHHHHHHHHHhhc-CCCcccCCccccCceeeeccccCCcccceeCcccchh
Q 026541 98 PFACKHTIPSSLFLKWCDHLCEDYVL-GFERSYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQW 160 (237)
Q Consensus 98 ~~~i~~~l~~~~~~~y~~~~~~~~~~-~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 160 (237)
...+...++.+.+..+.+...- +. ....++|+ .|+.-...... .....|+.|+..
T Consensus 83 lR~l~~~~~~~~~~~~~~a~~l--~~w~~~~RFCg--~CG~~~~~~~~----g~~~~C~~cg~~ 138 (279)
T COG2816 83 LRSLLTELDEGLFGLAARAVQL--LEWYRSHRFCG--RCGTKTYPREG----GWARVCPKCGHE 138 (279)
T ss_pred HHHHhccCCHHHHHHHHHHHHH--HHHHhhCcCCC--CCCCcCccccC----ceeeeCCCCCCc
Confidence 3444444566666666554321 11 23457899 89988877666 577888887654
No 251
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=33.93 E-value=32 Score=27.00 Aligned_cols=25 Identities=16% Similarity=0.331 Sum_probs=20.4
Q ss_pred ccCCCCCcceeecCCCcceEec-CCcE
Q 026541 199 TRCPGCGNCIERKKGCRIMFCR-FIFL 224 (237)
Q Consensus 199 k~CP~C~~~iek~~GCnhm~C~-C~~~ 224 (237)
-.||.|+.++.+.++ +.|.|. |++-
T Consensus 150 a~~~~~g~~~~~~~~-~~~~c~~~~~~ 175 (189)
T PRK09521 150 AMCSRCRTPLVKKGE-NELKCPNCGNI 175 (189)
T ss_pred EEccccCCceEECCC-CEEECCCCCCE
Confidence 479999999988555 999995 9854
No 252
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=33.55 E-value=35 Score=32.89 Aligned_cols=50 Identities=16% Similarity=0.392 Sum_probs=35.0
Q ss_pred CCccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCC
Q 026541 37 GTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLD 97 (237)
Q Consensus 37 ~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~ 97 (237)
....|++|+..+... .......|+|.||..||..|-..+ + +||. |...+.
T Consensus 122 ~~~~CP~Ci~s~~Dq-L~~~~k~c~H~FC~~Ci~sWsR~a--q------TCPi--DR~EF~ 171 (1134)
T KOG0825|consen 122 VENQCPNCLKSCNDQ-LEESEKHTAHYFCEECVGSWSRCA--Q------TCPV--DRGEFG 171 (1134)
T ss_pred hhhhhhHHHHHHHHH-hhccccccccccHHHHhhhhhhhc--c------cCch--hhhhhh
Confidence 345688888777432 233467899999999999987643 2 6887 776554
No 253
>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=33.14 E-value=15 Score=27.59 Aligned_cols=43 Identities=23% Similarity=0.473 Sum_probs=25.9
Q ss_pred eecCCCCcCCCCC---CHHHHhccCChhHHHHHHHHHHHHhhcCCCcccCCccccCceeee
Q 026541 84 KIECPGLHCEQFL---DPFACKHTIPSSLFLKWCDHLCEDYVLGFERSYCPNRNCMAVMVN 141 (237)
Q Consensus 84 ~i~CP~~~C~~~i---~~~~i~~~l~~~~~~~y~~~~~~~~~~~~~~~~Cp~~~C~~~~~~ 141 (237)
.-+||. |+..+ +.+++...+++..++.| ..+..|| +|+.++-.
T Consensus 91 ~sRC~~--CN~~L~~v~~~~v~~~vp~~v~~~~-----------~~f~~C~--~C~kiyW~ 136 (147)
T PF01927_consen 91 FSRCPK--CNGPLRPVSKEEVKDRVPPYVYETY-----------DEFWRCP--GCGKIYWE 136 (147)
T ss_pred CCccCC--CCcEeeechhhccccccCccccccC-----------CeEEECC--CCCCEecc
Confidence 469999 99654 44455555554444322 2357888 78776644
No 254
>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=32.86 E-value=53 Score=20.74 Aligned_cols=14 Identities=14% Similarity=0.555 Sum_probs=9.8
Q ss_pred ceeecCCCCcCCCCCC
Q 026541 82 TAKIECPGLHCEQFLD 97 (237)
Q Consensus 82 ~~~i~CP~~~C~~~i~ 97 (237)
..|++|+. |+..+.
T Consensus 2 iiPVRCFT--CGkvi~ 15 (60)
T PF01194_consen 2 IIPVRCFT--CGKVIG 15 (60)
T ss_dssp --SSS-ST--TTSBTC
T ss_pred CCceecCC--CCCChh
Confidence 36899998 999886
No 255
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.70 E-value=18 Score=23.03 Aligned_cols=17 Identities=24% Similarity=0.483 Sum_probs=13.8
Q ss_pred CCcccCCCCCcceeecC
Q 026541 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 45689999999998754
No 256
>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=32.53 E-value=28 Score=20.96 Aligned_cols=47 Identities=23% Similarity=0.614 Sum_probs=23.1
Q ss_pred ccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCC
Q 026541 39 FTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQ 94 (237)
Q Consensus 39 ~~C~iC~~~~~~~~~~~~~~~C~H~~C~~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-LESFLESNQRTP---KWKCPI--CNK 49 (50)
T ss_dssp SB-TTTSSB-SSE---EEETT--SS--EE-HHHHHHHHHHS------B-TT--T--
T ss_pred eeCCCCCCEEEeC---ccCCcCcccceEC-HHHHHHHhhccC---CeECcC--CcC
Confidence 4677776665332 2467899998744 777777776552 378998 875
No 257
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=32.27 E-value=35 Score=26.66 Aligned_cols=31 Identities=26% Similarity=0.459 Sum_probs=20.2
Q ss_pred CCCcccCCccccCceeeeccccCCcccceeCcccch
Q 026541 124 GFERSYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQ 159 (237)
Q Consensus 124 ~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 159 (237)
.+.+..|| .|...+..+... ...+.||.||.
T Consensus 110 ~~~~y~C~--~~~~r~sfdeA~---~~~F~Cp~Cg~ 140 (176)
T COG1675 110 ENNYYVCP--NCHVKYSFDEAM---ELGFTCPKCGE 140 (176)
T ss_pred cCCceeCC--CCCCcccHHHHH---HhCCCCCCCCc
Confidence 45578897 677766665543 24577887765
No 258
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=32.02 E-value=37 Score=28.15 Aligned_cols=28 Identities=21% Similarity=0.307 Sum_probs=22.3
Q ss_pred CCcccCCCCCcceeecCCCcceEec-CCc
Q 026541 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 4569999999998877655778994 985
No 259
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=32.00 E-value=28 Score=19.78 Aligned_cols=18 Identities=28% Similarity=0.748 Sum_probs=15.6
Q ss_pred ceeCcccchhhccccccC
Q 026541 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 678999999999988765
No 260
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=31.77 E-value=37 Score=21.85 Aligned_cols=30 Identities=20% Similarity=0.381 Sum_probs=20.2
Q ss_pred ccCCccccCceeeeccccCCcccceeCcccchhhc
Q 026541 128 SYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQWFC 162 (237)
Q Consensus 128 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C 162 (237)
+.|| +|++....=.. ....++|..|+...+
T Consensus 20 VkCp--dC~N~q~vFsh---ast~V~C~~CG~~l~ 49 (67)
T COG2051 20 VKCP--DCGNEQVVFSH---ASTVVTCLICGTTLA 49 (67)
T ss_pred EECC--CCCCEEEEecc---CceEEEecccccEEE
Confidence 6899 88874433221 147889988888765
No 261
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=31.77 E-value=62 Score=23.82 Aligned_cols=36 Identities=19% Similarity=0.421 Sum_probs=22.2
Q ss_pred CcccCCccccCceeeeccc-cCCcccceeCcccchhhcc
Q 026541 126 ERSYCPNRNCMAVMVNECE-GIGRVKKAQCPKCKQWFCF 163 (237)
Q Consensus 126 ~~~~Cp~~~C~~~~~~~~~-~~~~~~~~~C~~C~~~~C~ 163 (237)
....|| -|........+ ...+.....|+.|+..|=.
T Consensus 29 ~~~~cP--~C~s~~~~k~g~~~~~~qRyrC~~C~~tf~~ 65 (129)
T COG3677 29 TKVNCP--RCKSSNVVKIGGIRRGHQRYKCKSCGSTFTV 65 (129)
T ss_pred ccCcCC--CCCccceeeECCccccccccccCCcCcceee
Confidence 347899 78776633222 2222567888888877643
No 262
>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=31.60 E-value=71 Score=20.39 Aligned_cols=17 Identities=18% Similarity=0.213 Sum_probs=11.3
Q ss_pred CCcccCCccccCceeeecc
Q 026541 125 FERSYCPNRNCMAVMVNEC 143 (237)
Q Consensus 125 ~~~~~Cp~~~C~~~~~~~~ 143 (237)
.+...|| .|+.++...+
T Consensus 51 eg~L~Cp--~c~r~YPI~d 67 (68)
T PF03966_consen 51 EGELICP--ECGREYPIRD 67 (68)
T ss_dssp TTEEEET--TTTEEEEEET
T ss_pred CCEEEcC--CCCCEEeCCC
Confidence 4456787 7777776654
No 263
>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=31.34 E-value=33 Score=28.46 Aligned_cols=69 Identities=23% Similarity=0.588 Sum_probs=37.0
Q ss_pred ccCCccccCceeeeccccCCc-------ccceeCccc---chhhccccccCcCCCCCChhhhcccccchHHHHHHHhcCC
Q 026541 128 SYCPNRNCMAVMVNECEGIGR-------VKKAQCPKC---KQWFCFQCKLAWHAGYRCEESGNLRDRNDIAFGKLLEKMN 197 (237)
Q Consensus 128 ~~Cp~~~C~~~~~~~~~~~~~-------~~~~~C~~C---~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~~~~~~ 197 (237)
+.|. -|..|+--++.-++. +..+.|..| |...|++|+.-+ |++..+.. .+ -..+..
T Consensus 143 f~Cs--fC~~flCEDDQFEHQAsCQvLe~E~~KC~SCNrlGq~sCLRCK~cf-----CddHvrrK-----g~--ky~k~k 208 (314)
T PF06524_consen 143 FKCS--FCDNFLCEDDQFEHQASCQVLESETFKCQSCNRLGQYSCLRCKICF-----CDDHVRRK-----GF--KYEKGK 208 (314)
T ss_pred EEee--cCCCeeeccchhhhhhhhhhhhcccccccccccccchhhhheeeee-----hhhhhhhc-----cc--ccccCC
Confidence 4565 566666655543221 345556666 466788887543 33222110 00 112345
Q ss_pred cccCCCCCcceee
Q 026541 198 WTRCPGCGNCIER 210 (237)
Q Consensus 198 ~k~CP~C~~~iek 210 (237)
..+||+|+..+.-
T Consensus 209 ~~PCPKCg~et~e 221 (314)
T PF06524_consen 209 PIPCPKCGYETQE 221 (314)
T ss_pred CCCCCCCCCcccc
Confidence 6799999987653
No 264
>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=30.99 E-value=29 Score=19.03 Aligned_cols=15 Identities=27% Similarity=0.910 Sum_probs=10.0
Q ss_pred CcccCCCCCcceeec
Q 026541 197 NWTRCPGCGNCIERK 211 (237)
Q Consensus 197 ~~k~CP~C~~~iek~ 211 (237)
.+-.||+|+..|.-+
T Consensus 3 ~~~~C~nC~R~v~a~ 17 (33)
T PF08209_consen 3 PYVECPNCGRPVAAS 17 (33)
T ss_dssp -EEE-TTTSSEEEGG
T ss_pred CeEECCCCcCCcchh
Confidence 346899999988654
No 265
>PLN02189 cellulose synthase
Probab=30.89 E-value=43 Score=33.42 Aligned_cols=53 Identities=26% Similarity=0.700 Sum_probs=35.3
Q ss_pred CCCccccccccCCCc---cccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCC
Q 026541 36 DGTFTCDICIEPMSV---NNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLD 97 (237)
Q Consensus 36 ~~~~~C~iC~~~~~~---~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~ 97 (237)
.....|.||.++... .+.|.....|+-.+|+.|. .|-. ++|+ =.||. |+....
T Consensus 32 ~~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cy-eyer---~eg~---q~Cpq--Ckt~Y~ 87 (1040)
T PLN02189 32 LDGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCY-EYER---REGT---QNCPQ--CKTRYK 87 (1040)
T ss_pred ccCccccccccccCcCCCCCEEEeeccCCCccccchh-hhhh---hcCC---ccCcc--cCCchh
Confidence 445699999999753 2345445568999999998 3333 3432 37888 885543
No 266
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=30.48 E-value=46 Score=20.71 Aligned_cols=27 Identities=26% Similarity=0.584 Sum_probs=16.5
Q ss_pred cCCCcccCCccccCceeeeccccCCcccceeCcccchh
Q 026541 123 LGFERSYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQW 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--NCGEPKL---------PHRVCPSCGYY 49 (57)
T ss_pred cCCcceECC--CCCCccC---------CeEECCCCCcC
Confidence 346667788 6766653 34457767653
No 267
>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 PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.
Probab=29.14 E-value=18 Score=21.66 Aligned_cols=44 Identities=23% Similarity=0.557 Sum_probs=21.4
Q ss_pred ccccccccCCCccccccccCCC-CCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCCH
Q 026541 39 FTCDICIEPMSVNNKFKNNNLC-THPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLDP 98 (237)
Q Consensus 39 ~~C~iC~~~~~~~~~~~~~~~C-~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~ 98 (237)
+.|..|+-.. + .+..| .|..|..|+...+.. .-.||. |+.+++.
T Consensus 3 ~nCKsCWf~~---k---~Li~C~dHYLCl~CLt~ml~~--------s~~C~i--C~~~LPt 47 (50)
T PF03854_consen 3 YNCKSCWFAN---K---GLIKCSDHYLCLNCLTLMLSR--------SDRCPI--CGKPLPT 47 (50)
T ss_dssp ----SS-S-----S---SEEE-SS-EEEHHHHHHT-SS--------SSEETT--TTEE---
T ss_pred ccChhhhhcC---C---CeeeecchhHHHHHHHHHhcc--------ccCCCc--ccCcCcc
Confidence 4566776433 1 35567 699999998876642 227888 8877653
No 269
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=28.82 E-value=46 Score=32.04 Aligned_cols=58 Identities=17% Similarity=0.268 Sum_probs=37.0
Q ss_pred CChhHHHHHHHHHHHHh--h---cC------------CCcccCCccccCceeeeccccCCcccceeCcccchh-----hc
Q 026541 105 IPSSLFLKWCDHLCEDY--V---LG------------FERSYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQW-----FC 162 (237)
Q Consensus 105 l~~~~~~~y~~~~~~~~--~---~~------------~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~-----~C 162 (237)
|++.+++...+.+.+.. + .- .....|| .|+.++..... .....|..|++. .|
T Consensus 405 lS~~Ll~~i~~~l~~geQ~llflnRRGys~~l~C~~Cg~v~~Cp--~Cd~~lt~H~~----~~~L~CH~Cg~~~~~p~~C 478 (730)
T COG1198 405 LSPALLEAIRKTLERGEQVLLFLNRRGYAPLLLCRDCGYIAECP--NCDSPLTLHKA----TGQLRCHYCGYQEPIPQSC 478 (730)
T ss_pred CCHHHHHHHHHHHhcCCeEEEEEccCCccceeecccCCCcccCC--CCCcceEEecC----CCeeEeCCCCCCCCCCCCC
Confidence 66778887776655432 1 00 1124566 67777776665 578888888776 67
Q ss_pred cccccC
Q 026541 163 FQCKLA 168 (237)
Q Consensus 163 ~~C~~~ 168 (237)
..|+..
T Consensus 479 p~Cgs~ 484 (730)
T COG1198 479 PECGSE 484 (730)
T ss_pred CCCCCC
Confidence 777765
No 270
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=28.74 E-value=34 Score=20.64 Aligned_cols=15 Identities=40% Similarity=0.758 Sum_probs=10.3
Q ss_pred cCCcccCCCCCccee
Q 026541 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 345568888887664
No 271
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=28.13 E-value=54 Score=32.91 Aligned_cols=52 Identities=29% Similarity=0.793 Sum_probs=35.3
Q ss_pred CCCccccccccCCCcc---ccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCC
Q 026541 36 DGTFTCDICIEPMSVN---NKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFL 96 (237)
Q Consensus 36 ~~~~~C~iC~~~~~~~---~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i 96 (237)
.....|.||-++.... +.|.....|+-.+|+.|. .| ..++|+ =.||. |+...
T Consensus 15 ~~~qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCY-EY---Er~eG~---q~CPq--CktrY 69 (1079)
T PLN02638 15 GGGQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCY-EY---ERKDGN---QSCPQ--CKTKY 69 (1079)
T ss_pred cCCceeeecccccCcCCCCCEEEEeccCCCccccchh-hh---hhhcCC---ccCCc--cCCch
Confidence 3456999999987543 445556679999999997 33 234433 37888 87554
No 272
>KOG2923 consensus Uncharacterized conserved protein [Function unknown]
Probab=27.96 E-value=43 Score=21.35 Aligned_cols=21 Identities=29% Similarity=0.529 Sum_probs=16.0
Q ss_pred HHHHhcCCcccCCCCCcceee
Q 026541 190 GKLLEKMNWTRCPGCGNCIER 210 (237)
Q Consensus 190 ~~~~~~~~~k~CP~C~~~iek 210 (237)
..|.......+||+|...|.-
T Consensus 36 edL~~ge~Va~CpsCSL~I~V 56 (67)
T KOG2923|consen 36 EDLENGEDVARCPSCSLIIRV 56 (67)
T ss_pred HHHhCCCeeecCCCceEEEEE
Confidence 345667788999999988753
No 273
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=27.95 E-value=43 Score=20.19 Aligned_cols=15 Identities=7% Similarity=-0.071 Sum_probs=11.8
Q ss_pred ceEec-CCcEEEeccc
Q 026541 216 IMFCR-FIFLSLCLCI 230 (237)
Q Consensus 216 hm~C~-C~~~fc~~c~ 230 (237)
+++|+ ||..|.|...
T Consensus 4 ~l~C~dCg~~FvfTa~ 19 (49)
T PF13451_consen 4 TLTCKDCGAEFVFTAG 19 (49)
T ss_pred eEEcccCCCeEEEehh
Confidence 57896 9999988653
No 274
>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=27.63 E-value=41 Score=15.50 Aligned_cols=16 Identities=31% Similarity=0.717 Sum_probs=11.5
Q ss_pred hccccccCcCCCCCCh
Q 026541 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 275
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=27.35 E-value=33 Score=29.24 Aligned_cols=32 Identities=28% Similarity=0.669 Sum_probs=22.8
Q ss_pred CccccccccCCCccccccccCCCCCcccHHHHHHH
Q 026541 38 TFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKY 72 (237)
Q Consensus 38 ~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~ 72 (237)
...|.-|--.+. ..-.+.+|.|+||.+|.+..
T Consensus 90 VHfCd~Cd~PI~---IYGRmIPCkHvFCl~CAr~~ 121 (389)
T KOG2932|consen 90 VHFCDRCDFPIA---IYGRMIPCKHVFCLECARSD 121 (389)
T ss_pred eEeecccCCcce---eeecccccchhhhhhhhhcC
Confidence 667888865552 22247899999999997653
No 276
>KOG2041 consensus WD40 repeat protein [General function prediction only]
Probab=27.31 E-value=67 Score=30.89 Aligned_cols=48 Identities=15% Similarity=0.260 Sum_probs=28.5
Q ss_pred cCChhHHHHHHHHHHHHhhcCC------CcccCCccccCceeeeccccCCcccceeCcccchhh
Q 026541 104 TIPSSLFLKWCDHLCEDYVLGF------ERSYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQWF 161 (237)
Q Consensus 104 ~l~~~~~~~y~~~~~~~~~~~~------~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~ 161 (237)
-|+++..+.|+.+.++-+.+++ ..+-|. -|+..+.. -...|+.|+..|
T Consensus 1088 ~l~~a~kq~ye~La~~iFsk~~p~d~~~~~vdc~--~cg~~i~~--------~~~~c~ec~~kf 1141 (1189)
T KOG2041|consen 1088 ELDDAEKQEYENLAFRIFSKNPPVDPNSAKVDCS--VCGAKIDP--------YDLQCSECQTKF 1141 (1189)
T ss_pred hCCHHHHHHHHHHHHHHhccCCCCCCCccceeee--ecCCcCCc--------cCCCChhhcCcC
Confidence 4788899999998887665431 124454 45544432 233576666543
No 277
>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=26.69 E-value=38 Score=20.10 Aligned_cols=35 Identities=20% Similarity=0.481 Sum_probs=26.1
Q ss_pred cccccccCCCccccccccCCCCCcccHHHHHHHHHhhccc
Q 026541 40 TCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRD 79 (237)
Q Consensus 40 ~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~ 79 (237)
.|.||-.+.... ..--+..+|.+|-+..+.....+
T Consensus 1 ~CiiC~~~~~~G-----I~I~~~fIC~~CE~~iv~~~~~d 35 (46)
T PF10764_consen 1 KCIICGKEKEEG-----IHIYGKFICSDCEKEIVNTETDD 35 (46)
T ss_pred CeEeCCCcCCCC-----EEEECeEehHHHHHHhccCCCCC
Confidence 478888776432 24458899999999988877766
No 278
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=26.18 E-value=57 Score=26.27 Aligned_cols=21 Identities=24% Similarity=0.461 Sum_probs=17.5
Q ss_pred CCCcccCCccccCceeeeccc
Q 026541 124 GFERSYCPNRNCMAVMVNECE 144 (237)
Q Consensus 124 ~~~~~~Cp~~~C~~~~~~~~~ 144 (237)
.+.++-||.|.|..+|..++.
T Consensus 135 sSqRIACPRpnCkRiInL~p~ 155 (275)
T KOG4684|consen 135 SSQRIACPRPNCKRIINLDPL 155 (275)
T ss_pred ccceeccCCCCcceeeecCCC
Confidence 366789999999999987665
No 279
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=26.15 E-value=49 Score=26.05 Aligned_cols=23 Identities=17% Similarity=0.411 Sum_probs=19.2
Q ss_pred ccCCCCCcceeecCCCcceEec-CCc
Q 026541 199 TRCPGCGNCIERKKGCRIMFCR-FIF 223 (237)
Q Consensus 199 k~CP~C~~~iek~~GCnhm~C~-C~~ 223 (237)
-+|++|+.++++ .=+.|+|. ||.
T Consensus 150 A~CsrC~~~L~~--~~~~l~Cp~Cg~ 173 (188)
T COG1096 150 ARCSRCRAPLVK--KGNMLKCPNCGN 173 (188)
T ss_pred EEccCCCcceEE--cCcEEECCCCCC
Confidence 599999999999 44789994 984
No 280
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=26.04 E-value=38 Score=21.19 Aligned_cols=19 Identities=26% Similarity=0.531 Sum_probs=14.1
Q ss_pred HHHHhcCCcccCCCCCcce
Q 026541 190 GKLLEKMNWTRCPGCGNCI 208 (237)
Q Consensus 190 ~~~~~~~~~k~CP~C~~~i 208 (237)
..+.......+||+|...|
T Consensus 36 eDl~~GE~VArCPSCSLiv 54 (67)
T COG5216 36 EDLRNGEVVARCPSCSLIV 54 (67)
T ss_pred HHhhCCceEEEcCCceEEE
Confidence 3455566778999998876
No 281
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=25.98 E-value=32 Score=27.60 Aligned_cols=39 Identities=26% Similarity=0.484 Sum_probs=27.0
Q ss_pred ccccccCCCccccccccCCCCCc-ccHHHHHHHHHhhcccCCceeecCCCCcCCCCCC
Q 026541 41 CDICIEPMSVNNKFKNNNLCTHP-FCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLD 97 (237)
Q Consensus 41 C~iC~~~~~~~~~~~~~~~C~H~-~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~ 97 (237)
|..|.+.-.. + .+++|+|. +|..|= ..--.||. |..+..
T Consensus 161 Cr~C~~~~~~---V-lllPCrHl~lC~~C~------------~~~~~CPi--C~~~~~ 200 (207)
T KOG1100|consen 161 CRKCGEREAT---V-LLLPCRHLCLCGICD------------ESLRICPI--CRSPKT 200 (207)
T ss_pred ceecCcCCce---E-EeecccceEeccccc------------ccCccCCC--CcChhh
Confidence 9999876522 3 57899985 999992 11335998 876543
No 282
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=25.57 E-value=77 Score=23.21 Aligned_cols=27 Identities=19% Similarity=0.520 Sum_probs=22.1
Q ss_pred CcccCCCCCcc---eeecCCCcceEec-CCc
Q 026541 197 NWTRCPGCGNC---IERKKGCRIMFCR-FIF 223 (237)
Q Consensus 197 ~~k~CP~C~~~---iek~~GCnhm~C~-C~~ 223 (237)
.+-.||.|+.+ +.+.++=-.+.|. ||.
T Consensus 92 ~yVlC~~C~spdT~l~k~~r~~~l~C~aCGa 122 (125)
T PF01873_consen 92 EYVLCPECGSPDTELIKEGRLIFLKCKACGA 122 (125)
T ss_dssp HHSSCTSTSSSSEEEEEETTCCEEEETTTSC
T ss_pred HEEEcCCCCCCccEEEEcCCEEEEEecccCC
Confidence 55799999986 6677888889996 985
No 283
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=25.40 E-value=61 Score=19.60 Aligned_cols=30 Identities=23% Similarity=0.487 Sum_probs=20.9
Q ss_pred cccccccCCCccccccccCCCCCcccHHHHHHH
Q 026541 40 TCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKY 72 (237)
Q Consensus 40 ~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~ 72 (237)
.|.||-.+...... ..+.=+ .+|.+|+...
T Consensus 1 ~C~iCg~kigl~~~--~k~~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKR--FKIKDG-YICKDCLKKL 30 (51)
T ss_pred CCCccccccccccc--eeccCc-cchHHHHHHh
Confidence 48899988854322 234556 8999999875
No 284
>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=25.28 E-value=40 Score=21.04 Aligned_cols=19 Identities=26% Similarity=0.557 Sum_probs=9.7
Q ss_pred cccCCCCCcceeecCCCcc
Q 026541 198 WTRCPGCGNCIERKKGCRI 216 (237)
Q Consensus 198 ~k~CP~C~~~iek~~GCnh 216 (237)
..+||.|+..++-..+=.+
T Consensus 2 ~v~CP~C~k~~~~~~~n~~ 20 (57)
T PF03884_consen 2 TVKCPICGKPVEWSPENPF 20 (57)
T ss_dssp EEE-TTT--EEE-SSSSS-
T ss_pred cccCCCCCCeecccCCCCc
Confidence 3689999999988544333
No 285
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=25.09 E-value=54 Score=23.25 Aligned_cols=26 Identities=19% Similarity=0.441 Sum_probs=19.6
Q ss_pred ccCCCCCccee-ecCCCcceEec-CCcEEE
Q 026541 199 TRCPGCGNCIE-RKKGCRIMFCR-FIFLSL 226 (237)
Q Consensus 199 k~CP~C~~~ie-k~~GCnhm~C~-C~~~fc 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 57999977544 4555 99996 999885
No 286
>KOG2857 consensus Predicted MYND Zn-finger protein/hormone receptor interactor [Transcription]
Probab=24.98 E-value=37 Score=25.37 Aligned_cols=33 Identities=30% Similarity=0.572 Sum_probs=25.0
Q ss_pred CccccccccCCCccccccccCCCCCcccH-HHHHHHHH
Q 026541 38 TFTCDICIEPMSVNNKFKNNNLCTHPFCQ-DCTVKYIE 74 (237)
Q Consensus 38 ~~~C~iC~~~~~~~~~~~~~~~C~H~~C~-~Cl~~~~~ 74 (237)
+.+|.||++.-. .+....|.-.||. .||+.|-.
T Consensus 5 t~tC~ic~e~~~----KYKCpkC~vPYCSl~CfKiHk~ 38 (157)
T KOG2857|consen 5 TTTCVICLESEI----KYKCPKCSVPYCSLPCFKIHKS 38 (157)
T ss_pred eeeehhhhcchh----hccCCCCCCccccchhhhhccC
Confidence 679999997431 1246789999998 89998765
No 287
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=24.93 E-value=48 Score=25.53 Aligned_cols=42 Identities=24% Similarity=0.554 Sum_probs=24.2
Q ss_pred ecCCCCcCCCCC---CHHHHhccCChhHHHHHHHHHHHHhhcCCCcccCCccccCceeee
Q 026541 85 IECPGLHCEQFL---DPFACKHTIPSSLFLKWCDHLCEDYVLGFERSYCPNRNCMAVMVN 141 (237)
Q Consensus 85 i~CP~~~C~~~i---~~~~i~~~l~~~~~~~y~~~~~~~~~~~~~~~~Cp~~~C~~~~~~ 141 (237)
-+||. |+.++ +-+.++..+++..+..+ .++-.|| +|+.++-.
T Consensus 98 ~RCp~--CN~~L~~vs~eev~~~Vp~~~~~~~-----------~~f~~C~--~CgkiYW~ 142 (165)
T COG1656 98 SRCPE--CNGELEKVSREEVKEKVPEKVYRNY-----------EEFYRCP--KCGKIYWK 142 (165)
T ss_pred ccCcc--cCCEeccCcHHHHhhccchhhhhcc-----------cceeECC--CCcccccC
Confidence 58999 99554 45556655555433321 3345688 67665543
No 288
>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=24.64 E-value=53 Score=23.46 Aligned_cols=47 Identities=21% Similarity=0.416 Sum_probs=24.1
Q ss_pred CChhHHHHHHHHHHHHhhc-C--------CCcccCCccccCceeeeccccCCcccceeCcccch
Q 026541 105 IPSSLFLKWCDHLCEDYVL-G--------FERSYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQ 159 (237)
Q Consensus 105 l~~~~~~~y~~~~~~~~~~-~--------~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 159 (237)
+.++.++-....+.+..+. . +-..+|. .|+.-+..... ...||.|+.
T Consensus 39 V~pe~L~f~f~~~~~~T~~e~a~L~Ie~~p~~~~C~--~Cg~~~~~~~~------~~~CP~Cgs 94 (113)
T PF01155_consen 39 VEPEALRFAFEVLAEGTILEGAELEIEEVPARARCR--DCGHEFEPDEF------DFSCPRCGS 94 (113)
T ss_dssp --HHHHHHHHHHHHCCSTTTT-EEEEEEE--EEEET--TTS-EEECHHC------CHH-SSSSS
T ss_pred CCHHHHHHHHHHHhCCCCccCCEEEEEecCCcEECC--CCCCEEecCCC------CCCCcCCcC
Confidence 4455555555555544332 1 3457888 78887776654 255776664
No 289
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=24.42 E-value=20 Score=21.63 Aligned_cols=36 Identities=19% Similarity=0.598 Sum_probs=27.2
Q ss_pred CCccccccccCCCccccccccCCCCCcccHHHHHHHH
Q 026541 37 GTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYI 73 (237)
Q Consensus 37 ~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~ 73 (237)
..++|.+|-+..+..+ .+...-||..-|..||++-.
T Consensus 6 sry~CDLCn~~~p~~~-LRQCvlCGRWaC~sCW~deY 41 (57)
T PF14445_consen 6 SRYSCDLCNSSHPISE-LRQCVLCGRWACNSCWQDEY 41 (57)
T ss_pred hhHhHHhhcccCcHHH-HHHHhhhchhhhhhhhhhhH
Confidence 3578999999885543 34566799999999998643
No 290
>PF01530 zf-C2HC: Zinc finger, C2HC type; InterPro: IPR002515 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (C2HC) type zinc finger domain found in eukaryotes. Proteins containing these domains include: MYST family histone acetyltransferases [, [] Myelin transcription factor Myt1 [] Suppressor of tumourigenicity protein 18 (ST18) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2CS8_A 1PXE_A 2JX1_A 2JYD_A.
Probab=24.41 E-value=35 Score=18.42 Aligned_cols=17 Identities=18% Similarity=0.270 Sum_probs=10.7
Q ss_pred ccCCccccCceeeeccc
Q 026541 128 SYCPNRNCMAVMVNECE 144 (237)
Q Consensus 128 ~~Cp~~~C~~~~~~~~~ 144 (237)
..||.|+|....-....
T Consensus 2 ~~CPtpGCdg~GHi~G~ 18 (31)
T PF01530_consen 2 LKCPTPGCDGSGHITGK 18 (31)
T ss_dssp TSSSSTT--SCSTTTSS
T ss_pred CcCCCCCCCccccccCC
Confidence 46999999887665554
No 291
>PRK02935 hypothetical protein; Provisional
Probab=24.29 E-value=64 Score=22.84 Aligned_cols=23 Identities=22% Similarity=0.742 Sum_probs=11.8
Q ss_pred cccceeCcccchh--------hccccccCcC
Q 026541 148 RVKKAQCPKCKQW--------FCFQCKLAWH 170 (237)
Q Consensus 148 ~~~~~~C~~C~~~--------~C~~C~~~~H 170 (237)
+...+.||.|++. .|..|+.|-+
T Consensus 67 kavqV~CP~C~K~TKmLGrvD~CM~C~~PLT 97 (110)
T PRK02935 67 KAVQVICPSCEKPTKMLGRVDACMHCNQPLT 97 (110)
T ss_pred cceeeECCCCCchhhhccceeecCcCCCcCC
Confidence 3455566655432 4555555543
No 292
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=24.27 E-value=51 Score=25.06 Aligned_cols=25 Identities=20% Similarity=0.582 Sum_probs=18.1
Q ss_pred cccCCCCCcceeecCCCcceEe-cCCc
Q 026541 198 WTRCPGCGNCIERKKGCRIMFC-RFIF 223 (237)
Q Consensus 198 ~k~CP~C~~~iek~~GCnhm~C-~C~~ 223 (237)
+..||.|+..+..++. ....| +|+.
T Consensus 34 Y~aC~~C~kkv~~~~~-~~~~C~~C~~ 59 (166)
T cd04476 34 YPACPGCNKKVVEEGN-GTYRCEKCNK 59 (166)
T ss_pred EccccccCcccEeCCC-CcEECCCCCC
Confidence 4789999998887654 56777 4763
No 293
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=24.09 E-value=62 Score=19.95 Aligned_cols=25 Identities=28% Similarity=0.660 Sum_probs=14.6
Q ss_pred CCCcccCCccccCceeeeccccCCcccceeCcccch
Q 026541 124 GFERSYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQ 159 (237)
Q Consensus 124 ~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 159 (237)
.+++..|| .|+.+.. +...|+.||+
T Consensus 23 ~p~l~~C~--~cG~~~~---------~H~vc~~cG~ 47 (55)
T TIGR01031 23 APTLVVCP--NCGEFKL---------PHRVCPSCGY 47 (55)
T ss_pred CCcceECC--CCCCccc---------CeeECCccCe
Confidence 45666777 6666553 3345666664
No 294
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=24.07 E-value=55 Score=31.56 Aligned_cols=26 Identities=19% Similarity=0.529 Sum_probs=20.8
Q ss_pred ccCCCCCcceeecCCCcceEec-CCcE
Q 026541 199 TRCPGCGNCIERKKGCRIMFCR-FIFL 224 (237)
Q Consensus 199 k~CP~C~~~iek~~GCnhm~C~-C~~~ 224 (237)
-.||+|..+..--..=+.|.|. ||+.
T Consensus 445 ~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~ 471 (730)
T COG1198 445 AECPNCDSPLTLHKATGQLRCHYCGYQ 471 (730)
T ss_pred ccCCCCCcceEEecCCCeeEeCCCCCC
Confidence 3899999988766655999995 9864
No 295
>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=24.01 E-value=46 Score=18.81 Aligned_cols=20 Identities=35% Similarity=0.999 Sum_probs=13.8
Q ss_pred ccCCCCCcceee-c--CCCcceEe
Q 026541 199 TRCPGCGNCIER-K--KGCRIMFC 219 (237)
Q Consensus 199 k~CP~C~~~iek-~--~GCnhm~C 219 (237)
+.||.|+..+.. . .| ..+.|
T Consensus 2 ~~CP~Cg~~lv~r~~k~g-~F~~C 24 (39)
T PF01396_consen 2 EKCPKCGGPLVLRRGKKG-KFLGC 24 (39)
T ss_pred cCCCCCCceeEEEECCCC-CEEEC
Confidence 579999986543 2 45 66777
No 296
>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=23.94 E-value=68 Score=19.03 Aligned_cols=29 Identities=21% Similarity=0.319 Sum_probs=16.7
Q ss_pred ccCCccccCceeeeccccCCcccceeCcccch
Q 026541 128 SYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQ 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--ACGHRFEVLQKMSD-DPLATCPECGG 34 (52)
T ss_pred EEeC--CCCCEeEEEEecCC-CCCCCCCCCCC
Confidence 4677 78875554322111 34567887776
No 297
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=22.94 E-value=65 Score=27.56 Aligned_cols=55 Identities=16% Similarity=0.333 Sum_probs=33.6
Q ss_pred CCCccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCCH
Q 026541 36 DGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLDP 98 (237)
Q Consensus 36 ~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~~ 98 (237)
-+.+.||+=-+.. ..++.+.++.|||++=+.=+.. +..++...++||- |...-..
T Consensus 334 Hs~FiCPVlKe~~-t~ENpP~ml~CgHVIskeal~~-----LS~nG~~~FKCPY--CP~~~~~ 388 (396)
T COG5109 334 HSLFICPVLKELC-TDENPPVMLECGHVISKEALSV-----LSQNGVLSFKCPY--CPEMSKY 388 (396)
T ss_pred cceeeccccHhhh-cccCCCeeeeccceeeHHHHHH-----HhhcCcEEeeCCC--CCcchhh
Confidence 3567888743333 2233446899999986654433 3333566899998 8754333
No 298
>KOG2789 consensus Putative Zn-finger protein [General function prediction only]
Probab=22.62 E-value=1.2e+02 Score=26.98 Aligned_cols=37 Identities=16% Similarity=0.427 Sum_probs=28.3
Q ss_pred CCCCccccccccCCCccccccccCCCCCcccHHHHHHHH
Q 026541 35 IDGTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYI 73 (237)
Q Consensus 35 ~~~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~ 73 (237)
+..+.+|+||+-.+++..+ .+.-|.-.+|..||...-
T Consensus 71 ~rr~~ecpicflyyps~~n--~~rcC~~~Ic~ecf~~~~ 107 (482)
T KOG2789|consen 71 SRRKTECPICFLYYPSAKN--LVRCCSETICGECFAPFG 107 (482)
T ss_pred ccccccCceeeeecccccc--hhhhhccchhhhheeccc
Confidence 3456799999999876444 356789999999997643
No 299
>PLN03086 PRLI-interacting factor K; Provisional
Probab=22.53 E-value=50 Score=30.76 Aligned_cols=30 Identities=17% Similarity=0.310 Sum_probs=24.3
Q ss_pred CCcccCCC--CCcceeecCCCcceEec-CCcEE
Q 026541 196 MNWTRCPG--CGNCIERKKGCRIMFCR-FIFLS 225 (237)
Q Consensus 196 ~~~k~CP~--C~~~iek~~GCnhm~C~-C~~~f 225 (237)
.....||+ |+..+.+.+.=+|..|. |+..|
T Consensus 431 r~~V~Cp~~~Cg~v~~r~el~~H~~C~~Cgk~f 463 (567)
T PLN03086 431 RHNVVCPHDGCGIVLRVEEAKNHVHCEKCGQAF 463 (567)
T ss_pred CcceeCCcccccceeeccccccCccCCCCCCcc
Confidence 45578995 99999999999999994 97654
No 300
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=22.43 E-value=1.2e+02 Score=25.10 Aligned_cols=30 Identities=20% Similarity=0.457 Sum_probs=21.7
Q ss_pred CCcccCCccccCceeeeccccCCcccceeCcccchh
Q 026541 125 FERSYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQW 160 (237)
Q Consensus 125 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~ 160 (237)
....+|| .|+........ .....|+.|+..
T Consensus 97 ~~~~fC~--~CG~~~~~~~~----~~~~~C~~c~~~ 126 (256)
T PRK00241 97 RSHRFCG--YCGHPMHPSKT----EWAMLCPHCRER 126 (256)
T ss_pred hcCcccc--ccCCCCeecCC----ceeEECCCCCCE
Confidence 4568999 88887766544 466789888754
No 301
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=22.42 E-value=35 Score=29.42 Aligned_cols=32 Identities=31% Similarity=0.697 Sum_probs=24.4
Q ss_pred ccCCccccCceeeeccccCCcccceeCcccchhhcccccc
Q 026541 128 SYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQWFCFQCKL 167 (237)
Q Consensus 128 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~ 167 (237)
-+|| -|...|...+. +.+.|+ ||+.+|..|-.
T Consensus 15 d~cp--lcie~mditdk-----nf~pc~-cgy~ic~fc~~ 46 (480)
T COG5175 15 DYCP--LCIEPMDITDK-----NFFPCP-CGYQICQFCYN 46 (480)
T ss_pred ccCc--ccccccccccC-----CcccCC-cccHHHHHHHH
Confidence 4599 78776665554 788997 99999988854
No 302
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=22.16 E-value=60 Score=22.34 Aligned_cols=27 Identities=22% Similarity=0.367 Sum_probs=22.3
Q ss_pred ccCCCCCcceeecCCCcceEec-CCcEE
Q 026541 199 TRCPGCGNCIERKKGCRIMFCR-FIFLS 225 (237)
Q Consensus 199 k~CP~C~~~iek~~GCnhm~C~-C~~~f 225 (237)
-.||.|+..-.+..+----.|+ |++.|
T Consensus 36 y~Cp~Cgk~~vkR~a~GIW~C~~C~~~~ 63 (90)
T PF01780_consen 36 YTCPFCGKTSVKRVATGIWKCKKCGKKF 63 (90)
T ss_dssp BEESSSSSSEEEEEETTEEEETTTTEEE
T ss_pred CcCCCCCCceeEEeeeEEeecCCCCCEE
Confidence 5899999998888777788894 98766
No 303
>PF06467 zf-FCS: MYM-type Zinc finger with FCS sequence motif; InterPro: IPR010507 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. MYM-type zinc fingers were identified in MYM family proteins []. Human protein Q14202 from SWISSPROT is involved in a chromosomal translocation and may be responsible for X-linked retardation in XQ13.1 []. Q9UBW7 from SWISSPROT is also involved in disease. In myeloproliferative disorders it is fused to FGF receptor 1 []; in atypical myeloproliferative disorders it is rearranged []. Members of the family generally are involved in development. This Zn-finger domain functions as a transcriptional trans-activator of late vaccinia viral genes, and orthologues are also found in all nucleocytoplasmic large DNA viruses, NCLDV. This domain is also found fused to the C termini of recombinases from certain prokaryotic transposons []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2L8E_A 2DAS_A.
Probab=22.15 E-value=56 Score=18.45 Aligned_cols=37 Identities=19% Similarity=0.342 Sum_probs=19.2
Q ss_pred CCCccccccccCCCcccc--ccccCCCCCcccH-HHHHHH
Q 026541 36 DGTFTCDICIEPMSVNNK--FKNNNLCTHPFCQ-DCTVKY 72 (237)
Q Consensus 36 ~~~~~C~iC~~~~~~~~~--~~~~~~C~H~~C~-~Cl~~~ 72 (237)
.....|..|-.++..... ....-.-.+.||. .|+..|
T Consensus 4 ~~~~~C~~C~~~~~~~~~~~~~~~~g~~~~FCS~~C~~~y 43 (43)
T PF06467_consen 4 LKMKTCSYCKKYIPNKPTMIEVQYDGKMKQFCSQSCLSSY 43 (43)
T ss_dssp -SCEE-TTT--EEECCC----EE-TTTTSCCSSHHHHHHH
T ss_pred CcCCcCcccCCcccCCCccccccccCcccChhCHHHHhhC
Confidence 456789999888854432 1123345677886 676654
No 304
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=21.95 E-value=71 Score=31.99 Aligned_cols=54 Identities=26% Similarity=0.688 Sum_probs=36.9
Q ss_pred CCCCccccccccCCCcc---ccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCCC
Q 026541 35 IDGTFTCDICIEPMSVN---NKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFLD 97 (237)
Q Consensus 35 ~~~~~~C~iC~~~~~~~---~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i~ 97 (237)
......|.||-++.... +.|.....|+-.+|+.|. .| ..++|+ -.||. |+....
T Consensus 12 ~~~~~~c~iCGd~vg~~~~Ge~FVAC~eC~fpvCr~cy-ey---e~~~g~---~~cp~--c~t~y~ 68 (1044)
T PLN02915 12 SADAKTCRVCGDEVGVKEDGQPFVACHVCGFPVCKPCY-EY---ERSEGN---QCCPQ--CNTRYK 68 (1044)
T ss_pred CCCcchhhccccccCcCCCCCEEEEeccCCCccccchh-hh---hhhcCC---ccCCc--cCCchh
Confidence 34678899999987543 445556678999999997 33 234432 37888 886654
No 305
>PF15616 TerY-C: TerY-C metal binding domain
Probab=21.79 E-value=90 Score=23.11 Aligned_cols=12 Identities=42% Similarity=0.899 Sum_probs=9.8
Q ss_pred CcccCCCCCcce
Q 026541 197 NWTRCPGCGNCI 208 (237)
Q Consensus 197 ~~k~CP~C~~~i 208 (237)
..-.||.|+...
T Consensus 76 g~PgCP~CGn~~ 87 (131)
T PF15616_consen 76 GAPGCPHCGNQY 87 (131)
T ss_pred CCCCCCCCcChh
Confidence 447999999985
No 306
>PRK06386 replication factor A; Reviewed
Probab=21.78 E-value=42 Score=29.38 Aligned_cols=14 Identities=36% Similarity=0.797 Sum_probs=12.1
Q ss_pred CcccCCCCCcceee
Q 026541 197 NWTRCPGCGNCIER 210 (237)
Q Consensus 197 ~~k~CP~C~~~iek 210 (237)
.+++||.|+..+++
T Consensus 235 li~rCP~C~R~l~~ 248 (358)
T PRK06386 235 IFTKCSVCNKIIED 248 (358)
T ss_pred eEecCcCCCeEccC
Confidence 33899999999996
No 307
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=21.69 E-value=67 Score=20.21 Aligned_cols=29 Identities=24% Similarity=0.533 Sum_probs=19.5
Q ss_pred ccCCccccCceeeeccccCCcccceeCcccch
Q 026541 128 SYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQ 159 (237)
Q Consensus 128 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 159 (237)
=.|.+.+|.+|+..+...+ ..-.||.|+.
T Consensus 19 W~Ct~e~C~gWmR~nFs~~---~~p~CPlC~s 47 (59)
T PF14169_consen 19 WECTSEDCNGWMRDNFSFE---EEPVCPLCKS 47 (59)
T ss_pred EEeCCCCCCcccccccccC---CCccCCCcCC
Confidence 3588899999998776532 3345665554
No 308
>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=21.68 E-value=44 Score=18.96 Aligned_cols=30 Identities=23% Similarity=0.340 Sum_probs=12.5
Q ss_pred ccCCccccCceeeeccccCCcccceeCcccch
Q 026541 128 SYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQ 159 (237)
Q Consensus 128 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~ 159 (237)
+.|. .|++++..--.-......++|+.|+.
T Consensus 3 ~rC~--~C~aylNp~~~~~~~~~~w~C~~C~~ 32 (40)
T PF04810_consen 3 VRCR--RCRAYLNPFCQFDDGGKTWICNFCGT 32 (40)
T ss_dssp -B-T--TT--BS-TTSEEETTTTEEEETTT--
T ss_pred cccC--CCCCEECCcceEcCCCCEEECcCCCC
Confidence 4565 67666654322222246777877765
No 309
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=21.50 E-value=92 Score=19.59 Aligned_cols=30 Identities=20% Similarity=0.419 Sum_probs=19.5
Q ss_pred ccCCccccCceeeeccccCCcccceeCcccchhhc
Q 026541 128 SYCPNRNCMAVMVNECEGIGRVKKAQCPKCKQWFC 162 (237)
Q Consensus 128 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C 162 (237)
+.|| +|++....=.. ....+.|..|+...+
T Consensus 12 VkCp--~C~n~q~vFsh---a~t~V~C~~Cg~~L~ 41 (59)
T PRK00415 12 VKCP--DCGNEQVVFSH---ASTVVRCLVCGKTLA 41 (59)
T ss_pred EECC--CCCCeEEEEec---CCcEEECcccCCCcc
Confidence 6888 88875433221 147888888887665
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=20.97 E-value=59 Score=26.53 Aligned_cols=14 Identities=36% Similarity=0.672 Sum_probs=7.9
Q ss_pred CcccCCCCCcceee
Q 026541 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 44566666665443
No 311
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=20.91 E-value=54 Score=19.06 Aligned_cols=14 Identities=29% Similarity=0.674 Sum_probs=11.0
Q ss_pred CCcccCCCCCccee
Q 026541 196 MNWTRCPGCGNCIE 209 (237)
Q Consensus 196 ~~~k~CP~C~~~ie 209 (237)
...|.||.|+.++.
T Consensus 6 lp~K~C~~C~rpf~ 19 (42)
T PF10013_consen 6 LPSKICPVCGRPFT 19 (42)
T ss_pred CCCCcCcccCCcch
Confidence 45689999998875
No 312
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=20.89 E-value=61 Score=27.76 Aligned_cols=28 Identities=25% Similarity=0.550 Sum_probs=19.6
Q ss_pred ccCCCCCcc-----ee--ecCCCcceEec-CCcEEE
Q 026541 199 TRCPGCGNC-----IE--RKKGCRIMFCR-FIFLSL 226 (237)
Q Consensus 199 k~CP~C~~~-----ie--k~~GCnhm~C~-C~~~fc 226 (237)
..||-||.. |. -.+|=-++.|. |++.|-
T Consensus 188 ~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~ 223 (309)
T PRK03564 188 QFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWH 223 (309)
T ss_pred CCCCCCCCcchhheeeccCCCCceEEEcCCCCCccc
Confidence 578888875 21 23677888885 887773
No 313
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=20.64 E-value=1.1e+02 Score=19.19 Aligned_cols=35 Identities=17% Similarity=0.181 Sum_probs=23.8
Q ss_pred cCCCCcCCCCCCHHHHhccCChhHHHHHHHHHHHHhh
Q 026541 86 ECPGLHCEQFLDPFACKHTIPSSLFLKWCDHLCEDYV 122 (237)
Q Consensus 86 ~CP~~~C~~~i~~~~i~~~l~~~~~~~y~~~~~~~~~ 122 (237)
+||. |+...-...=..+.++|-+.+|...+.+...
T Consensus 19 ~Cp~--CG~~t~~~~PprFSPeD~y~kYR~~lkk~~~ 53 (59)
T COG2260 19 KCPV--CGGDTKVPHPPRFSPEDKYGKYRRELKKRLG 53 (59)
T ss_pred cCCC--CCCccccCCCCCCCccchHHHHHHHHHHHhc
Confidence 5888 8855443343445567889999988877643
No 314
>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]
Probab=20.45 E-value=1.2e+02 Score=24.50 Aligned_cols=47 Identities=17% Similarity=0.470 Sum_probs=33.0
Q ss_pred CCccccccccCCCccccccccCCCCCcccHHHHHHHHHhhcccCCceeecCCCCcCCCCC
Q 026541 37 GTFTCDICIEPMSVNNKFKNNNLCTHPFCQDCTVKYIEVKVRDNNTAKIECPGLHCEQFL 96 (237)
Q Consensus 37 ~~~~C~iC~~~~~~~~~~~~~~~C~H~~C~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~i 96 (237)
...+|.+|-.-.-. .....+|+=.+...|+..|+.. --.||+ |+..+
T Consensus 180 nlk~Cn~Ch~LvIq---g~rCg~c~i~~h~~c~qty~q~--------~~~cph--c~d~w 226 (235)
T KOG4718|consen 180 NLKNCNLCHCLVIQ---GIRCGSCNIQYHRGCIQTYLQR--------RDICPH--CGDLW 226 (235)
T ss_pred HHHHHhHhHHHhhe---eeccCcccchhhhHHHHHHhcc--------cCcCCc--hhccc
Confidence 46789999866522 1235677888999999999975 237888 75443
No 315
>PF01214 CK_II_beta: Casein kinase II regulatory subunit; InterPro: IPR000704 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. Casein kinase, a ubiquitous, well-conserved protein kinase involved in cell metabolism and differentiation, is characterised by its preference for Ser or Thr in acidic stretches of amino acids. The enzyme is a tetramer of 2 alpha- and 2 beta-subunits [, ]. However, some species (e.g., mammals) possess 2 related forms of the alpha-subunit (alpha and alpha'), while others (e.g., fungi) possess 2 related beta-subunits (beta and beta') []. The alpha-subunit is the catalytic unit and contains regions characteristic of serine/threonine protein kinases. The beta-subunit is believed to be regulatory, possessing an N-terminal auto-phosphorylation site, an internal acidic domain, and a potential metal-binding motif []. The beta subunit is a highly conserved protein of about 25kDa that contains, in its central section, a cysteine-rich motif, CX(n)C, that could be involved in binding a metal such as zinc []. The mammalian beta-subunit gene promoter shares common features with those of other mammalian protein kinases and is closely related to the promoter of the regulatory subunit of cAMP-dependent protein kinase [].; GO: 0019887 protein kinase regulator activity, 0005956 protein kinase CK2 complex; PDB: 2R6M_B 1RQF_K 1DS5_G 1QF8_B 3EED_A 4DGL_A 1JWH_D.
Probab=20.41 E-value=1.9e+02 Score=22.74 Aligned_cols=13 Identities=23% Similarity=0.480 Sum_probs=9.2
Q ss_pred CCcccCCccccCc
Q 026541 125 FERSYCPNRNCMA 137 (237)
Q Consensus 125 ~~~~~Cp~~~C~~ 137 (237)
..+..||+..|.+
T Consensus 97 g~FG~CPRv~C~~ 109 (184)
T PF01214_consen 97 GDFGRCPRVYCNG 109 (184)
T ss_dssp TTT-B-SBGGGTT
T ss_pred CcCCcCCcccCCC
Confidence 5678999999996
No 316
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=20.03 E-value=1.4e+02 Score=21.27 Aligned_cols=27 Identities=19% Similarity=0.506 Sum_probs=20.4
Q ss_pred CcccCCCCCcc---eeecCCCcceEec-CCc
Q 026541 197 NWTRCPGCGNC---IERKKGCRIMFCR-FIF 223 (237)
Q Consensus 197 ~~k~CP~C~~~---iek~~GCnhm~C~-C~~ 223 (237)
.+-.||.|+.| +.|.++=-.|.|. ||.
T Consensus 79 ~yVlC~~C~spdT~l~k~~r~~~l~C~aCGa 109 (110)
T smart00653 79 EYVLCPECGSPDTELIKENRLFFLKCEACGA 109 (110)
T ss_pred hcEECCCCCCCCcEEEEeCCeEEEEccccCC
Confidence 56799999986 6666665567885 875
Done!