Query 000878
Match_columns 1241
No_of_seqs 596 out of 2174
Neff 5.5
Searched_HMMs 46136
Date Tue Apr 2 00:32:54 2013
Command hhsearch -i /work/01045/syshi/lefta3m/000878.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/leftcdd/000878hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1940 Zn-finger protein [Gen 100.0 3.8E-61 8.1E-66 526.8 6.6 253 977-1235 20-274 (276)
2 PF14599 zinc_ribbon_6: Zinc-r 99.9 5.2E-24 1.1E-28 185.5 0.5 61 1166-1226 1-61 (61)
3 PF05495 zf-CHY: CHY zinc fing 99.8 3.9E-21 8.5E-26 173.9 1.6 70 992-1069 1-71 (71)
4 PF01814 Hemerythrin: Hemeryth 99.4 2E-12 4.3E-17 126.7 10.3 129 41-172 2-133 (133)
5 COG3945 Uncharacterized conser 99.3 1.7E-11 3.6E-16 126.9 14.0 149 41-191 9-162 (189)
6 PRK10992 iron-sulfur cluster r 99.2 2.2E-10 4.8E-15 125.4 13.6 134 41-174 75-218 (220)
7 PF13639 zf-RING_2: Ring finge 99.1 3.6E-11 7.8E-16 99.0 2.0 44 1119-1163 1-44 (44)
8 TIGR03652 FeS_repair_RIC iron- 99.1 6.3E-10 1.4E-14 121.6 12.0 130 43-172 74-216 (216)
9 COG2846 Regulator of cell morp 99.0 3.5E-09 7.6E-14 111.4 12.1 131 43-173 79-218 (221)
10 PRK13276 cell wall biosynthesi 99.0 4.3E-09 9.3E-14 114.9 13.0 130 43-172 81-223 (224)
11 COG4357 Zinc finger domain con 98.9 1.4E-10 3E-15 108.3 -0.4 55 989-1043 12-74 (105)
12 PF12861 zf-Apc11: Anaphase-pr 98.9 8E-10 1.7E-14 102.8 4.0 57 1078-1166 22-81 (85)
13 KOG4628 Predicted E3 ubiquitin 98.8 1.2E-09 2.6E-14 125.0 2.7 55 1113-1169 225-280 (348)
14 PF01814 Hemerythrin: Hemeryth 98.8 9E-08 1.9E-12 93.8 14.1 129 302-435 1-133 (133)
15 COG5243 HRD1 HRD ubiquitin lig 98.8 3.5E-09 7.6E-14 119.2 3.2 57 1115-1171 284-350 (491)
16 PF12678 zf-rbx1: RING-H2 zinc 98.7 7.9E-09 1.7E-13 94.6 4.1 47 1117-1163 18-73 (73)
17 COG5194 APC11 Component of SCF 98.6 2.4E-08 5.2E-13 90.8 3.5 59 1078-1166 21-80 (88)
18 KOG0804 Cytoplasmic Zn-finger 98.6 1.4E-08 3E-13 117.3 2.3 81 1119-1226 176-258 (493)
19 KOG1493 Anaphase-promoting com 98.5 2.6E-08 5.6E-13 89.8 0.2 56 1079-1166 22-80 (84)
20 cd00162 RING RING-finger (Real 98.4 2E-07 4.3E-12 75.1 3.7 44 1120-1166 1-45 (45)
21 PHA02929 N1R/p28-like protein; 98.4 2.2E-07 4.7E-12 102.7 4.5 53 1115-1167 171-227 (238)
22 COG5540 RING-finger-containing 98.4 1.9E-07 4.2E-12 103.3 3.4 53 1114-1167 319-372 (374)
23 PF13923 zf-C3HC4_2: Zinc fing 98.3 4.8E-07 1E-11 72.8 3.0 39 1121-1162 1-39 (39)
24 PRK10992 iron-sulfur cluster r 98.2 1.6E-05 3.6E-10 87.5 14.7 133 302-437 74-218 (220)
25 PF13920 zf-C3HC4_3: Zinc fing 98.2 9E-07 2E-11 75.0 3.3 47 1118-1168 2-49 (50)
26 TIGR03652 FeS_repair_RIC iron- 98.1 9.3E-06 2E-10 89.1 8.1 135 651-809 72-216 (216)
27 KOG2930 SCF ubiquitin ligase, 98.0 1.1E-06 2.3E-11 83.8 0.5 61 1075-1165 44-106 (114)
28 PF14634 zf-RING_5: zinc-RING 98.0 3.6E-06 7.8E-11 69.6 3.5 44 1120-1164 1-44 (44)
29 smart00184 RING Ring finger. E 98.0 5.1E-06 1.1E-10 64.5 3.3 38 1121-1162 1-39 (39)
30 PF00097 zf-C3HC4: Zinc finger 97.9 8.1E-06 1.8E-10 66.0 3.3 39 1121-1162 1-41 (41)
31 PLN03208 E3 ubiquitin-protein 97.9 1.1E-05 2.4E-10 86.2 4.6 55 1110-1168 10-80 (193)
32 KOG0802 E3 ubiquitin ligase [P 97.8 6E-06 1.3E-10 102.0 1.7 53 1114-1166 287-340 (543)
33 PHA02926 zinc finger-like prot 97.8 1.6E-05 3.5E-10 85.8 3.4 53 1115-1167 167-230 (242)
34 PF15227 zf-C3HC4_4: zinc fing 97.8 2.1E-05 4.6E-10 64.7 3.2 38 1121-1162 1-42 (42)
35 KOG0320 Predicted E3 ubiquitin 97.8 1.4E-05 3.1E-10 83.5 2.9 48 1118-1167 131-178 (187)
36 PRK13276 cell wall biosynthesi 97.7 0.00015 3.3E-09 79.8 10.2 131 302-435 77-223 (224)
37 PF13445 zf-RING_UBOX: RING-ty 97.6 3.8E-05 8.2E-10 63.6 2.9 39 1121-1160 1-43 (43)
38 smart00504 Ubox Modified RING 97.5 7.7E-05 1.7E-09 65.6 3.9 44 1120-1167 3-46 (63)
39 COG2846 Regulator of cell morp 97.5 0.00062 1.3E-08 72.7 10.4 133 301-436 74-218 (221)
40 KOG0825 PHD Zn-finger protein 97.4 2.9E-05 6.2E-10 94.7 -0.3 52 1116-1168 121-172 (1134)
41 COG3945 Uncharacterized conser 97.4 0.002 4.4E-08 67.9 12.2 142 651-821 10-155 (189)
42 KOG0317 Predicted E3 ubiquitin 97.3 8.5E-05 1.8E-09 83.0 2.1 45 1119-1167 240-284 (293)
43 KOG0823 Predicted E3 ubiquitin 97.3 0.00015 3.2E-09 79.1 3.3 51 1115-1169 44-97 (230)
44 KOG1428 Inhibitor of type V ad 97.3 0.0001 2.2E-09 93.5 1.8 115 1029-1167 3415-3544(3738)
45 KOG0828 Predicted E3 ubiquitin 97.2 0.00012 2.6E-09 86.0 1.8 50 1118-1167 571-634 (636)
46 TIGR00570 cdk7 CDK-activating 97.2 0.00029 6.2E-09 80.5 4.0 50 1118-1167 3-54 (309)
47 TIGR00599 rad18 DNA repair pro 97.2 0.00024 5.3E-09 84.0 3.3 46 1118-1167 26-71 (397)
48 KOG2164 Predicted E3 ubiquitin 97.1 0.00023 5E-09 84.9 2.6 53 1112-1168 180-237 (513)
49 smart00744 RINGv The RING-vari 97.1 0.00037 7.9E-09 59.3 3.1 42 1120-1163 1-49 (49)
50 KOG0287 Postreplication repair 97.0 0.00039 8.5E-09 78.7 2.5 45 1120-1168 25-69 (442)
51 PF11793 FANCL_C: FANCL C-term 96.9 0.00025 5.5E-09 64.7 0.3 50 1118-1167 2-66 (70)
52 KOG2177 Predicted E3 ubiquitin 96.9 0.001 2.2E-08 73.5 4.7 43 1118-1164 13-55 (386)
53 KOG0827 Predicted E3 ubiquitin 96.8 0.00058 1.3E-08 78.7 2.2 45 1119-1164 5-53 (465)
54 KOG1940 Zn-finger protein [Gen 96.7 0.00021 4.5E-09 80.6 -2.1 143 679-857 7-149 (276)
55 KOG1734 Predicted RING-contain 96.7 0.00051 1.1E-08 75.9 0.4 49 1118-1166 224-280 (328)
56 COG5574 PEX10 RING-finger-cont 96.6 0.001 2.2E-08 73.9 2.1 46 1118-1167 215-262 (271)
57 COG2461 Uncharacterized conser 96.6 0.014 3E-07 68.3 11.0 138 38-187 84-222 (409)
58 KOG4172 Predicted E3 ubiquitin 96.3 0.001 2.2E-08 57.1 -0.1 50 1118-1171 7-58 (62)
59 KOG4265 Predicted E3 ubiquitin 96.1 0.0033 7.1E-08 72.7 3.0 48 1116-1167 288-336 (349)
60 KOG1039 Predicted E3 ubiquitin 96.1 0.0032 6.8E-08 73.5 2.6 82 1116-1199 159-253 (344)
61 PF04564 U-box: U-box domain; 96.1 0.0068 1.5E-07 55.7 4.1 47 1119-1169 5-52 (73)
62 COG5219 Uncharacterized conser 95.8 0.0038 8.3E-08 78.1 1.5 52 1115-1166 1466-1522(1525)
63 COG5432 RAD18 RING-finger-cont 95.6 0.0064 1.4E-07 68.0 2.4 44 1119-1166 26-69 (391)
64 KOG1941 Acetylcholine receptor 95.6 0.0037 8E-08 72.2 0.3 61 1109-1170 357-419 (518)
65 PF14835 zf-RING_6: zf-RING of 95.3 0.008 1.7E-07 53.8 1.6 43 1120-1167 9-51 (65)
66 KOG1785 Tyrosine kinase negati 94.6 0.012 2.5E-07 68.3 0.6 53 1111-1167 362-416 (563)
67 KOG1645 RING-finger-containing 94.5 0.024 5.3E-07 66.3 2.9 48 1119-1166 5-55 (463)
68 KOG2879 Predicted E3 ubiquitin 94.5 0.03 6.5E-07 62.7 3.5 51 1117-1170 238-290 (298)
69 KOG4445 Uncharacterized conser 94.2 0.016 3.4E-07 65.4 0.6 53 1115-1168 112-187 (368)
70 KOG0978 E3 ubiquitin ligase in 94.0 0.017 3.6E-07 72.5 0.5 46 1119-1168 644-690 (698)
71 PF14570 zf-RING_4: RING/Ubox 93.5 0.054 1.2E-06 46.1 2.5 45 1121-1165 1-46 (48)
72 KOG0311 Predicted E3 ubiquitin 93.5 0.017 3.7E-07 66.6 -0.8 47 1118-1167 43-90 (381)
73 KOG1701 Focal adhesion adaptor 93.3 0.0096 2.1E-07 69.9 -3.1 71 1072-1167 295-371 (468)
74 KOG0824 Predicted E3 ubiquitin 93.0 0.05 1.1E-06 61.8 1.9 47 1117-1167 6-53 (324)
75 KOG0297 TNF receptor-associate 93.0 0.053 1.2E-06 65.0 2.3 107 1118-1236 21-138 (391)
76 KOG3970 Predicted E3 ubiquitin 92.8 0.095 2.1E-06 57.1 3.6 51 1116-1168 48-106 (299)
77 PF11789 zf-Nse: Zinc-finger o 92.5 0.082 1.8E-06 46.6 2.2 41 1118-1161 11-53 (57)
78 PF10367 Vps39_2: Vacuolar sor 92.5 0.061 1.3E-06 52.0 1.6 38 1111-1150 71-108 (109)
79 PF12906 RINGv: RING-variant d 91.7 0.12 2.6E-06 43.8 2.3 40 1121-1162 1-47 (47)
80 KOG3268 Predicted E3 ubiquitin 91.6 0.13 2.7E-06 54.4 2.7 30 1138-1167 188-228 (234)
81 KOG3039 Uncharacterized conser 91.5 0.15 3.3E-06 56.4 3.3 57 1113-1170 216-273 (303)
82 KOG0309 Conserved WD40 repeat- 90.5 0.16 3.4E-06 63.3 2.5 41 1119-1161 1029-1069(1081)
83 COG5175 MOT2 Transcriptional r 90.0 0.15 3.3E-06 58.4 1.8 56 1119-1174 15-71 (480)
84 COG5152 Uncharacterized conser 89.8 0.17 3.7E-06 54.3 1.8 44 1120-1167 198-241 (259)
85 KOG2272 Focal adhesion protein 89.4 0.11 2.4E-06 57.5 0.0 145 991-1172 63-237 (332)
86 KOG3800 Predicted E3 ubiquitin 89.3 0.26 5.7E-06 56.0 2.9 48 1120-1167 2-51 (300)
87 KOG4739 Uncharacterized protei 89.2 0.16 3.5E-06 56.5 1.2 36 1129-1166 12-47 (233)
88 PF14447 Prok-RING_4: Prokaryo 89.1 0.18 3.9E-06 44.1 1.1 43 1119-1167 8-50 (55)
89 KOG1002 Nucleotide excision re 89.0 0.16 3.5E-06 61.0 1.0 52 1112-1167 530-586 (791)
90 PF04641 Rtf2: Rtf2 RING-finge 88.8 0.34 7.4E-06 55.1 3.4 51 1115-1167 110-161 (260)
91 KOG4275 Predicted E3 ubiquitin 87.7 0.11 2.3E-06 58.8 -1.3 47 1118-1172 300-347 (350)
92 KOG1571 Predicted E3 ubiquitin 87.1 0.34 7.5E-06 56.6 2.2 47 1114-1167 301-347 (355)
93 KOG2034 Vacuolar sorting prote 86.8 0.35 7.5E-06 61.9 2.1 43 1109-1153 808-850 (911)
94 PF05883 Baculo_RING: Baculovi 86.8 0.35 7.6E-06 49.6 1.8 42 1118-1160 26-73 (134)
95 KOG0269 WD40 repeat-containing 85.7 0.63 1.4E-05 58.6 3.5 74 1072-1165 751-826 (839)
96 PRK00808 hypothetical protein; 85.6 13 0.00027 38.9 12.6 112 312-439 15-131 (150)
97 KOG1813 Predicted E3 ubiquitin 84.8 0.46 1E-05 54.1 1.7 46 1119-1168 242-287 (313)
98 KOG4692 Predicted E3 ubiquitin 84.8 0.54 1.2E-05 54.4 2.2 51 1114-1168 418-468 (489)
99 KOG2660 Locus-specific chromos 84.7 0.29 6.2E-06 56.6 -0.0 48 1118-1168 15-62 (331)
100 PRK14890 putative Zn-ribbon RN 84.2 0.83 1.8E-05 40.6 2.6 47 1029-1082 5-56 (59)
101 TIGR00100 hypA hydrogenase nic 83.9 0.65 1.4E-05 46.6 2.1 35 1192-1228 67-101 (115)
102 PHA02862 5L protein; Provision 83.8 0.7 1.5E-05 47.8 2.3 44 1118-1166 2-52 (156)
103 PRK00564 hypA hydrogenase nick 83.6 0.68 1.5E-05 46.6 2.1 36 1192-1228 68-103 (117)
104 TIGR02481 hemeryth_dom hemeryt 82.5 13 0.00028 37.2 10.8 112 42-171 10-125 (126)
105 PF07800 DUF1644: Protein of u 82.2 1.2 2.5E-05 47.0 3.2 32 1118-1153 2-46 (162)
106 PRK04023 DNA polymerase II lar 82.1 1.1 2.3E-05 58.5 3.5 47 1031-1083 626-672 (1121)
107 KOG2114 Vacuolar assembly/sort 81.9 0.81 1.7E-05 58.4 2.3 82 625-706 306-390 (933)
108 COG5592 Uncharacterized conser 81.6 3.4 7.5E-05 43.6 6.3 75 312-397 74-148 (171)
109 PRK12380 hydrogenase nickel in 80.9 0.92 2E-05 45.4 1.9 35 1192-1228 67-101 (113)
110 PF03854 zf-P11: P-11 zinc fin 80.8 0.69 1.5E-05 39.3 0.8 43 1119-1167 3-46 (50)
111 KOG2807 RNA polymerase II tran 80.4 0.67 1.4E-05 53.4 0.8 22 1195-1220 353-374 (378)
112 KOG4159 Predicted E3 ubiquitin 79.9 1.1 2.3E-05 54.0 2.3 49 1116-1168 82-130 (398)
113 PRK03681 hypA hydrogenase nick 79.7 1.1 2.4E-05 45.0 2.0 35 1193-1228 68-102 (114)
114 PRK03824 hypA hydrogenase nick 79.4 1.1 2.4E-05 46.2 2.0 35 1194-1228 69-122 (135)
115 PHA02825 LAP/PHD finger-like p 79.4 1.5 3.3E-05 46.2 2.9 45 1117-1166 7-58 (162)
116 COG2888 Predicted Zn-ribbon RN 79.3 1.4 3E-05 39.2 2.2 45 1031-1082 9-58 (61)
117 KOG1814 Predicted E3 ubiquitin 78.5 1.3 2.8E-05 52.7 2.3 53 1109-1163 176-236 (445)
118 PRK00808 hypothetical protein; 77.9 28 0.00061 36.4 11.8 114 41-175 13-130 (150)
119 COG5592 Uncharacterized conser 77.9 12 0.00027 39.7 8.9 100 75-183 28-136 (171)
120 KOG3002 Zn finger protein [Gen 77.8 1.9 4.2E-05 50.1 3.5 62 1119-1190 49-112 (299)
121 TIGR02481 hemeryth_dom hemeryt 76.6 20 0.00044 35.8 10.0 108 312-433 11-124 (126)
122 PF01529 zf-DHHC: DHHC palmito 76.5 1.7 3.7E-05 45.7 2.4 47 1054-1106 43-89 (174)
123 KOG3161 Predicted E3 ubiquitin 74.6 1.1 2.4E-05 55.4 0.5 43 1120-1165 13-55 (861)
124 PF01155 HypA: Hydrogenase exp 74.4 1.1 2.4E-05 44.9 0.3 35 1192-1228 67-101 (113)
125 KOG4185 Predicted E3 ubiquitin 74.3 2.6 5.7E-05 48.5 3.4 47 1119-1166 4-54 (296)
126 cd00522 Hemerythrin Hemerythri 73.5 8.9 0.00019 38.1 6.4 46 112-169 13-58 (113)
127 PF05502 Dynactin_p62: Dynacti 73.3 2.3 5.1E-05 52.6 2.8 19 1108-1128 44-62 (483)
128 PF08746 zf-RING-like: RING-li 72.8 2 4.3E-05 35.9 1.4 24 1139-1162 18-43 (43)
129 PF07191 zinc-ribbons_6: zinc- 70.6 0.83 1.8E-05 42.0 -1.4 64 1119-1210 2-68 (70)
130 COG2461 Uncharacterized conser 70.0 36 0.00078 40.9 11.2 137 648-823 85-221 (409)
131 COG5236 Uncharacterized conser 69.9 4.3 9.4E-05 47.2 3.7 48 1115-1166 58-107 (493)
132 PF06524 NOA36: NOA36 protein; 69.9 2.1 4.6E-05 48.1 1.2 73 999-1082 121-217 (314)
133 KOG0801 Predicted E3 ubiquitin 69.9 2.2 4.7E-05 44.9 1.2 29 1117-1146 176-204 (205)
134 PRK00762 hypA hydrogenase nick 69.6 2.8 6E-05 42.7 1.9 35 1193-1228 68-107 (124)
135 smart00132 LIM Zinc-binding do 69.4 3 6.5E-05 32.5 1.7 37 1121-1167 2-38 (39)
136 PRK01917 cation-binding hemery 68.7 59 0.0013 33.6 11.4 109 312-438 15-128 (139)
137 COG5220 TFB3 Cdk activating ki 67.8 2 4.4E-05 47.6 0.6 50 1118-1167 10-64 (314)
138 PRK03564 formate dehydrogenase 67.8 2.5 5.4E-05 49.4 1.3 42 1118-1164 187-234 (309)
139 KOG2068 MOT2 transcription fac 65.8 3.9 8.5E-05 47.7 2.3 51 1117-1167 248-298 (327)
140 KOG1044 Actin-binding LIM Zn-f 65.5 4.9 0.00011 49.7 3.2 127 1072-1224 84-229 (670)
141 TIGR00595 priA primosomal prot 64.9 5.1 0.00011 49.9 3.3 45 1001-1049 214-258 (505)
142 KOG0827 Predicted E3 ubiquitin 64.9 0.58 1.2E-05 55.0 -4.5 52 1116-1167 194-245 (465)
143 KOG2817 Predicted E3 ubiquitin 64.1 5.2 0.00011 47.7 2.9 46 1119-1165 335-383 (394)
144 COG1198 PriA Primosomal protei 63.9 5.7 0.00012 51.4 3.5 53 1001-1060 436-488 (730)
145 PF14357 DUF4404: Domain of un 63.5 33 0.00072 32.9 7.7 81 52-134 2-82 (85)
146 PRK14714 DNA polymerase II lar 62.9 6.2 0.00013 53.1 3.6 51 1031-1085 667-720 (1337)
147 PHA03096 p28-like protein; Pro 62.1 4.3 9.3E-05 47.0 1.8 47 1119-1165 179-232 (284)
148 KOG4443 Putative transcription 61.5 3.7 8E-05 51.5 1.2 69 1119-1192 146-225 (694)
149 PF05290 Baculo_IE-1: Baculovi 61.4 5.5 0.00012 41.0 2.2 47 1117-1167 79-132 (140)
150 KOG0298 DEAD box-containing he 61.1 1.2 2.6E-05 59.1 -3.1 50 1118-1170 1153-1202(1394)
151 KOG1044 Actin-binding LIM Zn-f 60.8 7.9 0.00017 48.0 3.7 138 1072-1223 14-170 (670)
152 cd00522 Hemerythrin Hemerythri 60.6 62 0.0013 32.2 9.5 96 42-170 12-111 (113)
153 PF09538 FYDLN_acid: Protein o 60.3 5.5 0.00012 39.8 1.9 18 1066-1083 18-35 (108)
154 COG0375 HybF Zn finger protein 59.5 5.6 0.00012 40.1 1.9 37 1191-1229 66-102 (115)
155 PRK01917 cation-binding hemery 59.2 83 0.0018 32.5 10.4 111 42-175 14-128 (139)
156 TIGR02300 FYDLN_acid conserved 58.9 5 0.00011 41.0 1.4 18 1066-1083 18-35 (129)
157 KOG1952 Transcription factor N 58.4 5.6 0.00012 51.2 2.0 47 1117-1164 190-244 (950)
158 PF14446 Prok-RING_1: Prokaryo 58.4 10 0.00022 33.5 3.0 35 1117-1152 4-39 (54)
159 PRK14873 primosome assembly pr 57.8 7 0.00015 50.3 2.8 44 1001-1049 384-427 (665)
160 TIGR01562 FdhE formate dehydro 57.2 4.4 9.5E-05 47.3 0.8 43 1118-1165 184-233 (305)
161 PF02891 zf-MIZ: MIZ/SP-RING z 56.9 11 0.00024 32.4 3.0 40 1120-1165 4-50 (50)
162 PF12773 DZR: Double zinc ribb 55.2 8.8 0.00019 32.5 2.1 36 1034-1082 1-37 (50)
163 TIGR01562 FdhE formate dehydro 55.0 7.4 0.00016 45.5 2.1 23 1195-1221 210-232 (305)
164 PLN03086 PRLI-interacting fact 54.9 6.9 0.00015 49.2 2.0 103 1028-1166 404-551 (567)
165 PRK05580 primosome assembly pr 54.7 9.3 0.0002 49.4 3.2 45 1001-1049 382-426 (679)
166 PRK12286 rpmF 50S ribosomal pr 53.4 9.6 0.00021 33.9 2.1 30 1193-1227 25-54 (57)
167 PF14353 CpXC: CpXC protein 53.0 3.7 8.1E-05 41.6 -0.6 56 1157-1214 2-57 (128)
168 PF07191 zinc-ribbons_6: zinc- 52.7 6.5 0.00014 36.3 1.0 10 1057-1066 48-57 (70)
169 PF09538 FYDLN_acid: Protein o 52.4 7.7 0.00017 38.8 1.5 32 999-1044 8-39 (108)
170 COG5183 SSM4 Protein involved 52.4 9.4 0.0002 48.9 2.5 48 1118-1167 12-66 (1175)
171 KOG0826 Predicted E3 ubiquitin 52.0 12 0.00027 43.6 3.3 46 1118-1166 300-345 (357)
172 TIGR02605 CxxC_CxxC_SSSS putat 51.4 9.4 0.0002 32.6 1.7 34 1195-1228 5-42 (52)
173 COG5222 Uncharacterized conser 50.7 11 0.00024 43.2 2.5 43 1119-1164 275-318 (427)
174 KOG1001 Helicase-like transcri 50.5 7.9 0.00017 49.9 1.6 43 1119-1166 455-499 (674)
175 PRK04023 DNA polymerase II lar 50.3 12 0.00026 49.5 3.0 47 1045-1103 627-673 (1121)
176 COG1198 PriA Primosomal protei 49.8 13 0.00028 48.3 3.4 45 1030-1083 434-484 (730)
177 cd00350 rubredoxin_like Rubred 49.1 11 0.00024 29.6 1.7 24 1059-1082 1-25 (33)
178 KOG2462 C2H2-type Zn-finger pr 48.6 17 0.00037 41.7 3.6 78 1092-1205 160-253 (279)
179 KOG1311 DHHC-type Zn-finger pr 48.5 14 0.0003 42.8 3.1 47 1054-1106 108-154 (299)
180 TIGR01031 rpmF_bact ribosomal 47.1 11 0.00023 33.3 1.4 29 1194-1227 25-53 (55)
181 PRK07219 DNA topoisomerase I; 46.7 26 0.00057 46.4 5.5 63 1062-1129 672-744 (822)
182 PHA00626 hypothetical protein 46.7 17 0.00036 32.3 2.4 19 1061-1082 13-31 (59)
183 COG4888 Uncharacterized Zn rib 46.6 9.1 0.0002 37.6 1.0 30 1072-1101 20-54 (104)
184 PRK14559 putative protein seri 45.8 13 0.00028 47.8 2.4 32 1032-1066 2-34 (645)
185 COG0143 MetG Methionyl-tRNA sy 45.7 14 0.0003 46.8 2.6 45 1056-1106 123-168 (558)
186 COG5109 Uncharacterized conser 45.0 15 0.00032 42.7 2.4 43 1120-1163 338-383 (396)
187 PF01783 Ribosomal_L32p: Ribos 44.8 16 0.00034 32.3 2.1 29 1194-1227 25-53 (56)
188 PRK00398 rpoP DNA-directed RNA 43.6 15 0.00032 30.9 1.6 30 1195-1224 3-32 (46)
189 COG3058 FdhE Uncharacterized p 43.0 8.3 0.00018 44.1 0.1 43 1118-1165 185-234 (308)
190 PRK00398 rpoP DNA-directed RNA 43.0 19 0.00041 30.3 2.2 23 1059-1081 3-28 (46)
191 KOG1280 Uncharacterized conser 42.8 19 0.00042 42.4 2.9 26 1054-1082 60-87 (381)
192 PF09788 Tmemb_55A: Transmembr 42.8 24 0.00053 40.1 3.7 114 1091-1222 63-186 (256)
193 TIGR00058 Hemerythrin hemeryth 42.2 88 0.0019 31.3 7.2 44 112-168 16-59 (115)
194 COG5151 SSL1 RNA polymerase II 41.6 7.6 0.00016 44.8 -0.5 21 1197-1221 398-418 (421)
195 COG1656 Uncharacterized conser 40.7 22 0.00048 38.1 2.8 50 1156-1212 97-147 (165)
196 PRK03564 formate dehydrogenase 40.6 21 0.00045 42.0 2.9 23 1195-1221 212-234 (309)
197 COG1996 RPC10 DNA-directed RNA 40.4 15 0.00033 31.8 1.3 28 1194-1221 5-32 (49)
198 TIGR00373 conserved hypothetic 40.1 10 0.00022 40.2 0.3 41 821-863 7-47 (158)
199 PF00412 LIM: LIM domain; Int 39.9 15 0.00032 31.6 1.2 40 1121-1170 1-40 (58)
200 PF04216 FdhE: Protein involve 39.5 9.6 0.00021 44.1 -0.1 16 1208-1223 206-221 (290)
201 KOG2066 Vacuolar assembly/sort 39.5 12 0.00026 48.2 0.7 60 815-875 423-482 (846)
202 PF05502 Dynactin_p62: Dynacti 39.4 14 0.0003 46.0 1.3 13 1055-1067 22-34 (483)
203 PRK06266 transcription initiat 39.2 11 0.00024 40.7 0.4 22 1060-1081 118-143 (178)
204 smart00659 RPOLCX RNA polymera 39.2 19 0.00042 30.3 1.7 26 1195-1221 2-27 (44)
205 KOG4399 C2HC-type Zn-finger pr 38.6 7.6 0.00016 43.8 -1.0 63 1033-1104 240-302 (325)
206 PF13901 DUF4206: Domain of un 38.5 17 0.00038 40.0 1.7 31 1129-1164 167-197 (202)
207 PF07227 DUF1423: Protein of u 37.8 22 0.00048 43.3 2.6 46 1120-1166 130-193 (446)
208 PF01907 Ribosomal_L37e: Ribos 37.5 17 0.00037 32.1 1.2 27 1191-1220 11-37 (55)
209 COG2703 Hemerythrin [Inorganic 37.3 5.4E+02 0.012 27.4 12.3 124 41-183 12-140 (144)
210 KOG2593 Transcription initiati 37.2 14 0.0003 44.8 0.7 20 914-933 50-69 (436)
211 KOG1100 Predicted E3 ubiquitin 36.6 18 0.00039 40.1 1.5 38 1121-1166 161-199 (207)
212 PF00301 Rubredoxin: Rubredoxi 36.5 24 0.00051 30.3 1.8 9 1059-1067 1-9 (47)
213 KOG3362 Predicted BBOX Zn-fing 36.0 12 0.00025 39.0 -0.1 26 1057-1086 116-143 (156)
214 KOG1829 Uncharacterized conser 35.8 14 0.00031 46.5 0.6 29 991-1020 345-377 (580)
215 PF03833 PolC_DP2: DNA polymer 35.6 12 0.00027 48.6 0.0 45 1031-1081 655-699 (900)
216 PRK00420 hypothetical protein; 35.1 22 0.00047 35.9 1.6 30 1117-1167 22-51 (112)
217 KOG2272 Focal adhesion protein 34.7 22 0.00047 40.2 1.7 80 994-1087 114-205 (332)
218 PRK14714 DNA polymerase II lar 34.5 31 0.00068 46.9 3.3 19 926-944 588-606 (1337)
219 KOG4718 Non-SMC (structural ma 34.3 20 0.00042 39.7 1.3 41 1120-1163 183-223 (235)
220 cd00729 rubredoxin_SM Rubredox 34.2 30 0.00066 27.5 2.0 24 1059-1082 2-26 (34)
221 PRK07219 DNA topoisomerase I; 33.2 47 0.001 44.1 4.7 11 1074-1084 733-743 (822)
222 PF08271 TF_Zn_Ribbon: TFIIB z 33.1 20 0.00044 29.7 0.9 13 1069-1081 14-26 (43)
223 COG5273 Uncharacterized protei 32.5 26 0.00056 41.2 2.0 47 1054-1106 104-150 (309)
224 PF04216 FdhE: Protein involve 32.1 16 0.00035 42.2 0.2 43 1118-1165 172-220 (290)
225 KOG1609 Protein involved in mR 32.0 21 0.00046 41.0 1.2 50 1118-1167 78-134 (323)
226 TIGR00058 Hemerythrin hemeryth 31.6 3.9E+02 0.0085 26.7 9.9 90 312-430 16-110 (115)
227 KOG1313 DHHC-type Zn-finger pr 31.5 20 0.00044 41.0 0.9 46 1055-1106 98-143 (309)
228 PF06220 zf-U1: U1 zinc finger 31.5 17 0.00036 29.8 0.1 13 1057-1069 1-13 (38)
229 COG5243 HRD1 HRD ubiquitin lig 31.2 15 0.00032 43.6 -0.3 33 1098-1135 317-352 (491)
230 KOG3850 Predicted membrane pro 30.4 5.8E+02 0.013 31.1 12.2 61 300-367 251-312 (455)
231 KOG1812 Predicted E3 ubiquitin 29.7 23 0.00049 42.9 0.9 37 1118-1154 146-182 (384)
232 PF00628 PHD: PHD-finger; Int 29.2 11 0.00023 31.9 -1.4 42 1121-1163 2-49 (51)
233 PF01599 Ribosomal_S27: Riboso 28.7 24 0.00053 30.3 0.7 29 1039-1067 13-46 (47)
234 cd01675 RNR_III Class III ribo 28.4 29 0.00064 43.9 1.6 29 1197-1229 520-548 (555)
235 TIGR02300 FYDLN_acid conserved 28.2 32 0.0007 35.3 1.6 32 999-1044 8-39 (129)
236 PF09577 Spore_YpjB: Sporulati 27.9 4.1E+02 0.009 30.3 10.3 96 307-428 96-191 (232)
237 COG2888 Predicted Zn-ribbon RN 27.9 30 0.00065 31.1 1.1 10 1072-1081 25-34 (61)
238 KOG4684 Uncharacterized conser 27.8 32 0.0007 38.0 1.5 81 1131-1224 117-200 (275)
239 KOG2906 RNA polymerase III sub 27.6 36 0.00077 33.5 1.6 39 1154-1203 63-101 (105)
240 PRK00564 hypA hydrogenase nick 27.0 37 0.00081 34.3 1.8 25 1058-1082 70-96 (117)
241 COG1996 RPC10 DNA-directed RNA 26.9 39 0.00085 29.4 1.6 28 1056-1083 3-33 (49)
242 KOG4443 Putative transcription 26.3 34 0.00073 43.5 1.5 46 1120-1167 20-73 (694)
243 PRK03824 hypA hydrogenase nick 25.8 40 0.00086 35.0 1.8 10 1073-1082 106-115 (135)
244 PF14445 Prok-RING_2: Prokaryo 25.7 5.9 0.00013 34.2 -3.4 49 1055-1105 3-53 (57)
245 PF06524 NOA36: NOA36 protein; 25.7 64 0.0014 36.9 3.4 107 1032-1167 98-220 (314)
246 PF06937 EURL: EURL protein; 25.1 44 0.00094 38.3 2.0 42 1117-1161 29-75 (285)
247 PF05129 Elf1: Transcription e 25.0 29 0.00062 33.0 0.5 31 1073-1103 21-56 (81)
248 PRK00432 30S ribosomal protein 24.7 39 0.00085 29.3 1.2 23 1076-1100 22-44 (50)
249 smart00451 ZnF_U1 U1-like zinc 24.6 34 0.00073 26.5 0.7 11 1058-1068 2-12 (35)
250 PF09723 Zn-ribbon_8: Zinc rib 24.5 45 0.00098 27.6 1.5 31 1195-1225 5-38 (42)
251 PF07227 DUF1423: Protein of u 24.4 53 0.0011 40.3 2.7 31 922-954 21-51 (446)
252 PF03107 C1_2: C1 domain; Int 24.4 47 0.001 25.6 1.5 20 1079-1100 2-22 (30)
253 smart00249 PHD PHD zinc finger 24.2 33 0.00073 27.4 0.7 30 1121-1151 2-31 (47)
254 smart00531 TFIIE Transcription 24.0 28 0.00061 36.4 0.3 7 1075-1081 124-130 (147)
255 smart00734 ZnF_Rad18 Rad18-lik 23.9 45 0.00098 25.1 1.2 20 1157-1177 2-21 (26)
256 PRK01110 rpmF 50S ribosomal pr 23.8 48 0.001 29.9 1.6 29 1194-1228 26-54 (60)
257 PF01927 Mut7-C: Mut7-C RNAse 23.4 54 0.0012 34.3 2.2 48 1157-1211 92-140 (147)
258 TIGR00622 ssl1 transcription f 23.1 1.6E+02 0.0034 30.0 5.2 45 1118-1163 55-110 (112)
259 PRK00464 nrdR transcriptional 23.1 43 0.00093 35.6 1.4 27 1075-1101 1-36 (154)
260 KOG1703 Adaptor protein Enigma 23.1 31 0.00068 42.8 0.5 98 1109-1226 354-463 (479)
261 PF14952 zf-tcix: Putative tre 23.0 38 0.00082 28.7 0.8 12 1215-1226 13-24 (44)
262 PF13597 NRDD: Anaerobic ribon 23.0 38 0.00082 42.9 1.2 30 1195-1229 491-520 (546)
263 PF09332 Mcm10: Mcm10 replicat 22.9 21 0.00046 42.4 -1.0 34 1193-1226 283-316 (344)
264 KOG2462 C2H2-type Zn-finger pr 22.5 51 0.0011 38.0 1.9 29 1196-1224 216-254 (279)
265 PF13212 DUF4020: Domain of un 22.3 1.2E+02 0.0027 33.0 4.6 42 837-878 21-69 (180)
266 PRK14559 putative protein seri 22.1 56 0.0012 42.2 2.5 34 1031-1068 15-50 (645)
267 PF10272 Tmpp129: Putative tra 21.9 85 0.0018 37.8 3.7 16 1151-1166 335-350 (358)
268 KOG0006 E3 ubiquitin-protein l 21.7 84 0.0018 36.8 3.4 76 1068-1153 169-254 (446)
269 PRK14892 putative transcriptio 21.5 66 0.0014 31.9 2.2 38 1194-1235 20-64 (99)
270 smart00659 RPOLCX RNA polymera 21.4 70 0.0015 27.1 2.1 23 1059-1081 2-26 (44)
271 PF13824 zf-Mss51: Zinc-finger 21.2 57 0.0012 29.1 1.5 12 1072-1083 12-23 (55)
272 KOG0802 E3 ubiquitin ligase [P 21.1 43 0.00094 42.3 1.1 43 1117-1167 478-520 (543)
273 cd02341 ZZ_ZZZ3 Zinc finger, Z 21.0 56 0.0012 28.1 1.4 21 1075-1100 1-22 (48)
274 COG4913 Uncharacterized protei 20.8 3.9E+02 0.0084 35.0 8.9 63 803-865 464-530 (1104)
275 PHA00626 hypothetical protein 20.7 57 0.0012 29.1 1.4 33 1032-1069 1-33 (59)
276 PF15353 HECA: Headcase protei 20.7 51 0.0011 32.9 1.3 16 1139-1154 39-54 (107)
277 PLN02189 cellulose synthase 20.6 73 0.0016 42.9 3.0 52 1114-1166 30-86 (1040)
278 cd07170 NR_DBD_ERR DNA-binding 20.4 62 0.0013 31.8 1.8 44 1054-1100 16-63 (97)
279 KOG2231 Predicted E3 ubiquitin 20.3 85 0.0018 40.5 3.4 44 1120-1167 2-52 (669)
280 KOG1312 DHHC-type Zn-finger pr 20.2 32 0.0007 39.7 -0.2 33 1078-1114 149-181 (341)
281 PF03604 DNA_RNApol_7kD: DNA d 20.2 61 0.0013 25.7 1.4 22 1060-1081 1-24 (32)
282 PRK12775 putative trifunctiona 20.2 46 0.00099 45.2 1.1 53 1155-1222 795-847 (1006)
No 1
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=100.00 E-value=3.8e-61 Score=526.81 Aligned_cols=253 Identities=50% Similarity=1.084 Sum_probs=241.0
Q ss_pred CCCCCCCCccCCcCCCccccccccccccccCCcccCchhhcccCCCCCCcccccceeccccccccccCCCCCCCCCCCCc
Q 000878 977 DCYASYRDPEKQVFGCEHYKRNCKIRAACCGKLFTCRFCHDKASDHSMDRKATSEMMCMHCLKIQAIGPNCTTPSCNGLS 1056 (1241)
Q Consensus 977 ~~~~~~~~~~~~~~gC~HY~r~ckl~~pcC~k~y~Cr~CHde~~~H~~~r~~~~~~~C~~C~~~q~~~~~C~~~~Cc~~~ 1056 (1241)
+..+++.|++...+||+||+|+|++++|||+++|+|++||++..+|.++|+.+.+|+||.|.++|++++.|.+ |+..
T Consensus 20 ~~~~~~~d~~~~~~~c~hy~r~~~~~a~ccd~~~~C~hCH~~s~~h~~~r~~v~~~~C~~C~~~q~~~~~c~~---c~~~ 96 (276)
T KOG1940|consen 20 SIHSDAEDEIAFPYGCPHYRRNCKSRAPCCDREITCRHCHNESEDHDLDRKTVYELLCMKCRKIQPVGQICSN---CHVE 96 (276)
T ss_pred hcccccccccccccCCchhhhccccccccccceeeeEEecChhhhcccchhhhhhhhhhhHHhhhhhhhcccc---chhh
Confidence 3467889999999999999999999999999999999999999999999999999999999999999999999 4788
Q ss_pred ceeEeccccccccCC-CCcccCCCCCccccCCCCCccccccCCccccccccc-ccccccccccCCcccccccccccCCCc
Q 000878 1057 MAKYYCNICKFFDDE-RTVYHCPFCNLCRVGGGLGVDFFHCMTCNCCLGLKL-LNHKCLEKCLETNCPICCDFLFTSSET 1134 (1241)
Q Consensus 1057 ~a~y~C~~C~~~d~~-k~~yHC~~CgiCRvg~~l~~~~fhC~~C~~C~s~~l-~~H~C~e~~~~~~CpICle~lf~s~~~ 1134 (1241)
+|+|||.+||+|||+ ..||||+.|||||+|.++ +||||++|+.|+++.+ +.|+|+|++++.|||||.|+||++...
T Consensus 97 ~g~~~c~~C~l~dd~~~~~~hC~~C~icr~g~~~--~~fhc~~c~~c~~~~~~~~H~c~e~~~~~ncPic~e~l~~s~~~ 174 (276)
T KOG1940|consen 97 LGEYYCLICKLFDDDPSKQYHCDLCGICREGLGL--DFFHCKKCKACLSAYLSNWHKCVERSSEFNCPICKEYLFLSFED 174 (276)
T ss_pred hhhhcCcccccccccccceecccccccccccccc--chhHHhhhHhHHhhhcccccchhhhcccCCCchhHHHhcccccc
Confidence 999999999999988 699999999999999875 9999999999999999 669999999999999999999999999
Q ss_pred eEEcCCCCccchhhHHHHHhcCCCCCCCCcccccchhhhhhhHHHHhccCCCHhhhcccceEEcCCCCCCCCccchhhcc
Q 000878 1135 VRALPCGHYMHLACFQAYTCSHYTCPICSKSLGDMAIYFGMIDALLAAEELPEEYRNQVQDILCNDCEQKGAARFHWLYH 1214 (1241)
Q Consensus 1135 ~~~lpCgH~fH~~C~~~wl~~~~~CPiCrk~~~dm~~~~~~lD~~i~~~~~P~ey~~~~~~i~CnDC~~~s~~~fh~lg~ 1214 (1241)
+..++|||++|..||.++...+|+||+|.+ ++||..+|+++|.+|+.+|||++|.+++++|+||||+.+++++|||||+
T Consensus 175 ~~~~~CgH~~h~~cf~e~~~~~y~CP~C~~-~~d~~~~~~~~d~~l~~~~~p~~y~~~~~~i~cndC~~~~~~k~~~l~~ 253 (276)
T KOG1940|consen 175 AGVLKCGHYMHSRCFEEMICEGYTCPICSK-PGDMSHYFRKLDKELAGSPMPEEYKNKTQDILCNDCGSGTNVKYHILYH 253 (276)
T ss_pred CCccCcccchHHHHHHHHhccCCCCCcccc-hHHHHHHHHHHHHHHhcCCCCchhhchhheeeccCCCCCCccceehhhh
Confidence 999999999999999999988899999999 9999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCCccccccccCCCCCC
Q 000878 1215 KCGFCGSYNTRLIKNDTTVSN 1235 (1241)
Q Consensus 1215 kC~~CgsYNT~~~~~~~~~~~ 1235 (1241)
||+.|+|||||+++.+.....
T Consensus 254 kc~~c~~~~~r~~~~~~~~~~ 274 (276)
T KOG1940|consen 254 KCGKCGSYNTRMISDPSKYDP 274 (276)
T ss_pred hCCCcccceeeeccCCCccCC
Confidence 999999999999985544433
No 2
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=99.88 E-value=5.2e-24 Score=185.48 Aligned_cols=61 Identities=56% Similarity=0.992 Sum_probs=22.4
Q ss_pred cccchhhhhhhHHHHhccCCCHhhhcccceEEcCCCCCCCCccchhhcccCCCCCCccccc
Q 000878 1166 LGDMAIYFGMIDALLAAEELPEEYRNQVQDILCNDCEQKGAARFHWLYHKCGFCGSYNTRL 1226 (1241)
Q Consensus 1166 ~~dm~~~~~~lD~~i~~~~~P~ey~~~~~~i~CnDC~~~s~~~fh~lg~kC~~CgsYNT~~ 1226 (1241)
|.||+.+|++||++|+++|||++|++++++|+||||+++|.++||||||||++||||||||
T Consensus 1 v~dM~~~w~~LD~~i~~~pmP~~Y~~~~v~IlCNDC~~~s~v~fH~lg~KC~~C~SYNT~q 61 (61)
T PF14599_consen 1 VVDMSAYWRMLDAEIAATPMPEEYRNKKVWILCNDCNAKSEVPFHFLGHKCSHCGSYNTRQ 61 (61)
T ss_dssp ---------------------------EEEEEESSS--EEEEE--TT----TTTS---EEE
T ss_pred CCCHHHHHHHHHHHHHhCCCCHHHhCCEEEEECCCCCCccceeeeHhhhcCCCCCCcccCC
Confidence 5799999999999999999999999999999999999999999999999999999999986
No 3
>PF05495 zf-CHY: CHY zinc finger; InterPro: IPR008913 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. Pirh2 is an eukaryotic ubiquitin protein ligase, which has been shown to promote p53 degradation in mammals. Pirh2 physically interacts with p53 and promotes ubiquitination of p53 independently of MDM2. Like MDM2, Pirh2 is thought to participate in an autoregulatory feedback loop that controls p53 function. Pirh2 proteins contain three distinct zinc fingers, the CHY-type, the CTCHY-type which is C-terminal to the CHY-type zinc finger and a RING finger. The CHY-type zinc finger has no currently known function []. As well as Pirh2, the CHY-type zinc finger is also found in the following proteins: Yeast helper of Tim protein 13. Hot13 may have a role in the assembly and recycling of the small Tims, a complex of the mitochondrial intermembrane space that participates in the TIM22 import pathway for assembly of the inner membrane [] Several plant hypothetical proteins that also contain haemerythrin cation binding domains Several protozoan hypothetical proteins that also contain a Myb domain The solution structure of this zinc finger has been solved and binds 3 zinc atoms as shown in the following schematic representation: ++---------+-----+ || | | CXHYxxxxxxxxxCCxxxxxCxxCHxxxxxHxxxxxxxxxxxCxxCxxxxxxxxxCxxC | | | | | | | | +-+-----------------+--+ +--+---------+--+ 'C': conserved cysteine involved in the binding of one zinc atom. 'H': conserved histidine involved in the binding of one zinc atom. More information about these proteins can be found at Protein of the Month: Zinc Fingers []; GO: 0008270 zinc ion binding; PDB: 2DKT_A 2K2C_A.
Probab=99.81 E-value=3.9e-21 Score=173.90 Aligned_cols=70 Identities=46% Similarity=1.147 Sum_probs=53.8
Q ss_pred Ccccccc-ccccccccCCcccCchhhcccCCCCCCcccccceeccccccccccCCCCCCCCCCCCcceeEecccccccc
Q 000878 992 CEHYKRN-CKIRAACCGKLFTCRFCHDKASDHSMDRKATSEMMCMHCLKIQAIGPNCTTPSCNGLSMAKYYCNICKFFD 1069 (1241)
Q Consensus 992 C~HY~r~-ckl~~pcC~k~y~Cr~CHde~~~H~~~r~~~~~~~C~~C~~~q~~~~~C~~~~Cc~~~~a~y~C~~C~~~d 1069 (1241)
|+||+|+ |+|+||||++|||||+|||+.++|+++|..+++|+||.|+++|+++++ + | + |+|+|++|++||
T Consensus 1 C~HY~~~~~~~~~~cC~~~y~C~~CHde~~~H~~~~~~~~~v~Cg~C~~~~~~~~~--~--c-~---~~~~C~~C~~~~ 71 (71)
T PF05495_consen 1 CKHYHRSLCAIRFPCCGKYYPCRFCHDELEDHPFDRWPVKRVICGKCRTEQPIDEY--S--C-G---ADYFCPICGLYF 71 (71)
T ss_dssp -SS---S-EEEEETTTTEEESSHHHHHHCSSS---TTT--EEEETTT--EEES-SB--T--T------SEEETTTTEEE
T ss_pred CCCCCCCcEEEECCcccCeecHHHHHHHhccCccccccccCeECCCCCCccChhhh--h--c-C---CCccCcCcCCCC
Confidence 8999999 999999999999999999999999999999999999999999999988 4 4 5 999999999986
No 4
>PF01814 Hemerythrin: Hemerythrin HHE cation binding domain; InterPro: IPR012312 The haemerythrin family is composed of haemerythrin proteins found in invertebrates, and a broader collection of bacterial and archaeal homologues. Haemerythrin is an oxygen-binding protein found in the vascular system and coelemic fluid, or in muscles (myohaemerythrin) in invertebrates []. Many of the homologous proteins found in prokaryotes are multi-domain proteins with signal-transducing domains such as the GGDEF diguanylate cyclase domain (IPR000160 from INTERPRO) and methyl-accepting chemotaxis protein (MCP) signalling domain (IPR004089 from INTERPRO). Most haemerythrins are oxygen-carriers with a bound non-haem iron, but at least one example is a cadmium-binding protein, apparently with a role in sequestering toxic metals rather than in binding oxygen. The prokaryote with the most instances of this domain is Magnetococcus sp. MC-1, a magnetotactic bacterium. Haemerythrins and myohaemerythrins [, ] are small proteins of about 110 to 129 amino acid residues that bind two iron atoms. They are left-twisted 4-alpha-helical bundles, which provide a hydrophobic pocket where dioxygen binds as a peroxo species, interacting with adjacent aliphatic side chains via van der Waals forces []. In both haemerythrins and myohaemerythrins, the active centre is a binuclear iron complex, bound directly to the protein via 7 amino acid side chains [], 5 His, 1 Glu and 1 Asp []. Ovohaemerythrin [], a yolk protein from the leech Theromyzon tessulatum seems to belong to this family of proteins, it may play a role in the detoxification of free iron after a blood meal []. This entry represents a haemerythrin/HHE cation-binding motif that occurs as a duplicated domain in haemerythrin and related proteins. This domain binds iron in haemerythrin, but can bind other metals in related proteins, such as cadmium in a Nereis diversicolor protein (P80255 from SWISSPROT). A bacterial protein, Q7WX96 from SWISSPROT, is a regulator of response to NO, which suggests a different set-up for its metal ligands. A protein from Cryptococcus neoformans (Filobasidiella neoformans) that contains haemerythrin/HHE cation-binding motifs is also involved in NO response []. A Staphylococcus aureus protein (P72360 from SWISSPROT) has been noted to be important when the organism switches to living in environments with low oxygen concentrations; perhaps this protein acts as an oxygen store or scavenger.; PDB: 3CAX_A 3V5Z_B 3U9M_G 3V5Y_A 3U9J_B 3V5X_A 2MHR_A 1A7E_A 1A7D_A 2IGF_P ....
Probab=99.37 E-value=2e-12 Score=126.72 Aligned_cols=129 Identities=33% Similarity=0.454 Sum_probs=116.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhcCCcccHHHHHHHHHHHHHHhhccCccccccccHHHhhhh---hhHHHHHHHh
Q 000878 41 PILIFCFFHKAVRNELDALHQLAMNFATGHRVDILSLSERYRFLHSVYKHHSNAEDEVIFPALDIRV---KNVARKYSLE 117 (1241)
Q Consensus 41 PId~l~~~H~AIRreL~~L~~la~~l~~gd~~dl~~L~~~l~fL~~~L~~HH~aEDevLFPaL~~R~---p~vl~~le~E 117 (1241)
+++.|...|+.|++.++.+...+... +...+...+...+.+|...+..|+..||.++||.|..+. +..+..+..|
T Consensus 2 ~i~~l~~~H~~~~~~~~~l~~~~~~~--~~~~~~~~l~~~~~~l~~~l~~H~~~EE~~l~p~l~~~~~~~~~~~~~~~~e 79 (133)
T PF01814_consen 2 PIDELRRDHRALRRLLAELEEALDEL--PDDEDLRALRELLDELRRELRHHHAREEEYLFPALERRDPRGDALIAELRRE 79 (133)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHH--CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHHHH-CCCHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhC--cCchhHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhccccchhhHHHH
Confidence 78999999999999999999999998 566789999999999999999999999999999999553 3788999999
Q ss_pred HHHHHHHHHHHHHHHhhhccCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhHHHHH
Q 000878 118 HEGESNLFDHLFQLLNSYTQNDESFPKELASCSRALQTSINQHMSKEEQQVFPLL 172 (1241)
Q Consensus 118 H~~id~lL~~L~~lL~~~~~~~~~~~~eLa~al~~L~~~L~~HL~~EE~eVfPLa 172 (1241)
|..+...++.+...+.... ........+...+..|...+..|+..||+.+||++
T Consensus 80 H~~~~~~l~~l~~~~~~~~-~~~~~~~~~~~~~~~l~~~l~~H~~~Ee~~l~P~~ 133 (133)
T PF01814_consen 80 HEEIRALLDELEEALARYS-GDEEDAEELREALRALAEWLRRHIAKEEEVLFPLL 133 (133)
T ss_dssp HHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHTHGGGHHHH
T ss_pred HHHHHHHHHHHHHHHhhCc-cccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 9999999999999998887 22345678999999999999999999999999986
No 5
>COG3945 Uncharacterized conserved protein [Function unknown]
Probab=99.32 E-value=1.7e-11 Score=126.89 Aligned_cols=149 Identities=18% Similarity=0.255 Sum_probs=135.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhcCCcccHHHHHHHHHHHHHHh-hccCccccccccHHHhhhhh----hHHHHHH
Q 000878 41 PILIFCFFHKAVRNELDALHQLAMNFATGHRVDILSLSERYRFLHSVY-KHHSNAEDEVIFPALDIRVK----NVARKYS 115 (1241)
Q Consensus 41 PId~l~~~H~AIRreL~~L~~la~~l~~gd~~dl~~L~~~l~fL~~~L-~~HH~aEDevLFPaL~~R~p----~vl~~le 115 (1241)
-+..|+..|..|.+.|..|+..+..+..| +-+...+-..++|+..+. .+||.+||.++||.+..+.. .++..|.
T Consensus 9 ~i~~lvEeH~yIlraL~iLr~~~~~~~~g-~i~y~~v~~iidFi~nfaDkcHH~KEE~~LF~~m~~~g~~~~~~~i~~m~ 87 (189)
T COG3945 9 SIKLLVEEHTYILRALSILRKALDLIKNG-PIDYSDVKEIIDFIRNFADKCHHGKEEKLLFNYMEHEGGPFEEGPIYVMT 87 (189)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcccCC-CCCHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHhCCCcccCceeeeh
Confidence 46789999999999999999999998887 788888898999998885 88999999999999988852 6788999
Q ss_pred HhHHHHHHHHHHHHHHHhhhccCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHhccCCHHHHHHHHHHHHhc
Q 000878 116 LEHEGESNLFDHLFQLLNSYTQNDESFPKELASCSRALQTSINQHMSKEEQQVFPLLTQHFSLEEQASLVWQFFCS 191 (1241)
Q Consensus 116 ~EH~~id~lL~~L~~lL~~~~~~~~~~~~eLa~al~~L~~~L~~HL~~EE~eVfPLa~~~lS~eEwaeL~~~~l~s 191 (1241)
.||.....++..|.++++.+..++..+...+...+..|...+.+|+++|+.++||+|.+.||.+ |..+..+....
T Consensus 88 ~EH~~~R~i~r~lee~~~~~kngd~~~~~~~i~~A~~y~~likrHIdkEdnvlfp~a~~~~s~e-~~~v~~e~~~~ 162 (189)
T COG3945 88 VEHGEGRYIIRDLEEAYERLKNGDEDSKDDVIDYAVAYLNLIKRHIDKEDNVLFPFAESTLSEE-LNEVNSECFRF 162 (189)
T ss_pred hhhhhHHHHHHHHHHHHHHHHccccchHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHH-HHHHHHHHHHh
Confidence 9999999999999999999998888888899999999999999999999999999999999999 88887765543
No 6
>PRK10992 iron-sulfur cluster repair di-iron protein; Provisional
Probab=99.17 E-value=2.2e-10 Score=125.43 Aligned_cols=134 Identities=21% Similarity=0.255 Sum_probs=115.7
Q ss_pred HHH-HHHHHHHHHHHHHHHHHHHHHhhh---cCCcccHHHHHHHHHHHHHHhhccCccccccccHHHhhhh----hhHHH
Q 000878 41 PIL-IFCFFHKAVRNELDALHQLAMNFA---TGHRVDILSLSERYRFLHSVYKHHSNAEDEVIFPALDIRV----KNVAR 112 (1241)
Q Consensus 41 PId-~l~~~H~AIRreL~~L~~la~~l~---~gd~~dl~~L~~~l~fL~~~L~~HH~aEDevLFPaL~~R~----p~vl~ 112 (1241)
-|+ ++...|..+|+++..|..++.++. ..+.+....+...+.+|...+..||.+||++|||+|++.. ..++.
T Consensus 75 LidyI~~~~H~~~r~~lp~L~~l~~kv~~vhg~~~~~~~~~~~l~~~~~~el~~H~~kEE~~LFP~l~~~~~~~~~~pi~ 154 (220)
T PRK10992 75 LIDHIIVRYHDRHREQLPELILLATKVERVHGDKPDCPRGLAKYLTALHEELSSHMMKEEQILFPMIKQGMGSQAMGPIS 154 (220)
T ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHhcccccccchHH
Confidence 344 558999999999999999998876 4456778889999999999999999999999999998732 36789
Q ss_pred HHHHhHHHHHHHHHHHHHHHhhhccCCC--CcHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHhc
Q 000878 113 KYSLEHEGESNLFDHLFQLLNSYTQNDE--SFPKELASCSRALQTSINQHMSKEEQQVFPLLTQ 174 (1241)
Q Consensus 113 ~le~EH~~id~lL~~L~~lL~~~~~~~~--~~~~eLa~al~~L~~~L~~HL~~EE~eVfPLa~~ 174 (1241)
.|..||..+...+.+|..+++.+....+ .....++..+..|...|.+|+.+||.++||.+..
T Consensus 155 vm~~EHd~~~~~l~~L~~lt~~~~~p~~ac~~~~~l~~~l~~~~~dL~~HI~~EnniLFP~a~~ 218 (220)
T PRK10992 155 VMESEHDEAGELLEVIKHLTNNVTPPPEACTTWRALYNGINELIDDLMEHIHLENNVLFPRALA 218 (220)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCChhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Confidence 9999999999999999999988754322 3577888999999999999999999999998864
No 7
>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=99.08 E-value=3.6e-11 Score=99.01 Aligned_cols=44 Identities=39% Similarity=1.022 Sum_probs=39.1
Q ss_pred CcccccccccccCCCceEEcCCCCccchhhHHHHHhcCCCCCCCC
Q 000878 1119 TNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICS 1163 (1241)
Q Consensus 1119 ~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~~~~~CPiCr 1163 (1241)
++||||++. |..++.+..++|||.||.+|+.+|++.+++||+||
T Consensus 1 d~C~IC~~~-~~~~~~~~~l~C~H~fh~~Ci~~~~~~~~~CP~CR 44 (44)
T PF13639_consen 1 DECPICLEE-FEDGEKVVKLPCGHVFHRSCIKEWLKRNNSCPVCR 44 (44)
T ss_dssp -CETTTTCB-HHTTSCEEEETTSEEEEHHHHHHHHHHSSB-TTTH
T ss_pred CCCcCCChh-hcCCCeEEEccCCCeeCHHHHHHHHHhCCcCCccC
Confidence 479999999 67778889999999999999999999999999997
No 8
>TIGR03652 FeS_repair_RIC iron-sulfur cluster repair di-iron protein. Members of this protein family, designated variously as YftE, NorA, DrnN, and NipC, are di-iron proteins involved in the repair of iron-sulfur clusters. Previously assigned names reflect pleiotropic effects of damage from NO or other oxidative stress when this protein is mutated. The suggested name now is RIC, for Repair of Iron Centers.
Probab=99.08 E-value=6.3e-10 Score=121.63 Aligned_cols=130 Identities=27% Similarity=0.402 Sum_probs=111.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhh---cCCcccHHHHHHHHHHHHHHhhccCccccccccHHHhh--hh-h-----hHH
Q 000878 43 LIFCFFHKAVRNELDALHQLAMNFA---TGHRVDILSLSERYRFLHSVYKHHSNAEDEVIFPALDI--RV-K-----NVA 111 (1241)
Q Consensus 43 d~l~~~H~AIRreL~~L~~la~~l~---~gd~~dl~~L~~~l~fL~~~L~~HH~aEDevLFPaL~~--R~-p-----~vl 111 (1241)
.++...|..||+++..|..++.++. ..+.+.+..+.+.++.|.+.+..|+..||++|||+|++ +. + .++
T Consensus 74 ~i~~~hH~~i~~~l~~L~~l~~kv~~~hg~~~~~l~~l~~~~~~~~~eL~~H~~kEE~~LFP~l~~~~~g~~~~~~~~pi 153 (216)
T TIGR03652 74 HIVDRHHEYLREELPELIPLATKVARVHGDHHPELIGLAELFRELKAELEQHLMKEEQILFPAIIEYKRGNPAQAIGTPI 153 (216)
T ss_pred HHHHHHhHHHHHHHHHHHHHHHHHHHHhCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHccCccccccchH
Confidence 4778899999999999999888865 33456778889999999999999999999999999985 21 1 278
Q ss_pred HHHHHhHHHHHHHHHHHHHHHhhhccCCC--CcHHHHHHHHHHHHHHHHHHHHHHHHhHHHHH
Q 000878 112 RKYSLEHEGESNLFDHLFQLLNSYTQNDE--SFPKELASCSRALQTSINQHMSKEEQQVFPLL 172 (1241)
Q Consensus 112 ~~le~EH~~id~lL~~L~~lL~~~~~~~~--~~~~eLa~al~~L~~~L~~HL~~EE~eVfPLa 172 (1241)
..|..||.++...+.+|+.+++.+....+ .....++..+..|...|.+|+.+||..+||.+
T Consensus 154 ~~m~~EH~~~~~~l~~L~~l~~~~~~p~~ac~~~~~~~~~l~~~~~~L~~HI~~En~iLFP~~ 216 (216)
T TIGR03652 154 SVMESEHDEAGDLLKELRELTNDYTPPEDACNTWRALYSGLEELEDDLHEHIHLENNILFPRA 216 (216)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCC
Confidence 99999999999999999999988764332 35678888899999999999999999999953
No 9
>COG2846 Regulator of cell morphogenesis and NO signaling [Cell division and chromosome partitioning]
Probab=98.98 E-value=3.5e-09 Score=111.36 Aligned_cols=131 Identities=22% Similarity=0.304 Sum_probs=116.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhh---cCCcccHHHHHHHHHHHHHHhhccCccccccccHHHhhh----hhhHHHHHH
Q 000878 43 LIFCFFHKAVRNELDALHQLAMNFA---TGHRVDILSLSERYRFLHSVYKHHSNAEDEVIFPALDIR----VKNVARKYS 115 (1241)
Q Consensus 43 d~l~~~H~AIRreL~~L~~la~~l~---~gd~~dl~~L~~~l~fL~~~L~~HH~aEDevLFPaL~~R----~p~vl~~le 115 (1241)
.++...|+..|.+|..|-.++.++. ++.++-...+.+.+..|.+.+..|-.+||+++||.+.+- +..++..|+
T Consensus 79 hIi~ryH~~hReqlpeLi~latKverVHgd~p~~p~gl~~~L~~l~~eL~~HMmKEEqIlFPmi~~G~g~~a~~pI~vm~ 158 (221)
T COG2846 79 HIIVRYHERHREQLPELIPLATKVERVHGDKPSCPAGLAELLEALKEELESHMMKEEQILFPMIKQGMGSQAAGPISVME 158 (221)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHhhHHHHhccCcccCcchHHHH
Confidence 5889999999999999999998875 444677888999999999999999999999999999763 226899999
Q ss_pred HhHHHHHHHHHHHHHHHhhhccCCC--CcHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHh
Q 000878 116 LEHEGESNLFDHLFQLLNSYTQNDE--SFPKELASCSRALQTSINQHMSKEEQQVFPLLT 173 (1241)
Q Consensus 116 ~EH~~id~lL~~L~~lL~~~~~~~~--~~~~eLa~al~~L~~~L~~HL~~EE~eVfPLa~ 173 (1241)
.||.+..++++.+.++.+.++-.++ ....+++.-+..|.+.+.+|++.|..++||-+.
T Consensus 159 ~EHde~g~~l~~lk~lT~n~tpP~~AC~tWkalY~gl~~~~dDl~~HIHLENnvLFpr~~ 218 (221)
T COG2846 159 SEHDEAGELLEVLKHLTNNYTPPEEACGTWKALYNGLNEFIDDLMEHIHLENNVLFPRVL 218 (221)
T ss_pred HHHHHHHHHHHHHHHHhcCCCCChHHHhHHHHHHHHHHHHHHHHHHHHHhhhccccchhc
Confidence 9999999999999999999876544 578899999999999999999999999999765
No 10
>PRK13276 cell wall biosynthesis protein ScdA; Provisional
Probab=98.97 E-value=4.3e-09 Score=114.95 Aligned_cols=130 Identities=21% Similarity=0.282 Sum_probs=116.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhh---cCCcccHHHHHHHHHHHHHHhhccCccccccccHHHhhhh--------hhHH
Q 000878 43 LIFCFFHKAVRNELDALHQLAMNFA---TGHRVDILSLSERYRFLHSVYKHHSNAEDEVIFPALDIRV--------KNVA 111 (1241)
Q Consensus 43 d~l~~~H~AIRreL~~L~~la~~l~---~gd~~dl~~L~~~l~fL~~~L~~HH~aEDevLFPaL~~R~--------p~vl 111 (1241)
.++...|+.+|+++..|..++.++. .++.+.+..+.+.+..+...+..|-.+||.++||++.+.. ..++
T Consensus 81 ~I~~~hH~~~r~~lp~l~~l~~kV~~VHg~~~p~l~~l~~lf~~l~~eL~~H~~KEE~ilFP~i~~~~~~~~~~~~~~pI 160 (224)
T PRK13276 81 YIQSAYHEPLREEFKNLTPYVTKLSKVHGPNHPYLVELKETYDTFKNGMLEHMQKEDDVDFPKLIKYEQGEVVDDINTVI 160 (224)
T ss_pred HHHHHHhHHHHHHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHhhccccchhhhhHH
Confidence 4778899999999999999998875 4567789999999999999999999999999999997732 2478
Q ss_pred HHHHHhHHHHHHHHHHHHHHHhhhccCCC--CcHHHHHHHHHHHHHHHHHHHHHHHHhHHHHH
Q 000878 112 RKYSLEHEGESNLFDHLFQLLNSYTQNDE--SFPKELASCSRALQTSINQHMSKEEQQVFPLL 172 (1241)
Q Consensus 112 ~~le~EH~~id~lL~~L~~lL~~~~~~~~--~~~~eLa~al~~L~~~L~~HL~~EE~eVfPLa 172 (1241)
..|+.||+...+.+.+|+++.+.++...+ ..++.++..+..|...|.+|++.|...+||-+
T Consensus 161 ~~m~~EH~~~g~~l~~i~~lTn~yt~P~~AC~t~r~ly~~L~~fe~dL~~HIhLENnILFPr~ 223 (224)
T PRK13276 161 DDLVSDHIATGQLLVKMSELTSSYEPPIEACGTWRLVYQRLKALEVLTHEHVHLENHVLFKKV 223 (224)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHcccCC
Confidence 99999999999999999999999987654 57889999999999999999999999999953
No 11
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=98.93 E-value=1.4e-10 Score=108.32 Aligned_cols=55 Identities=27% Similarity=0.715 Sum_probs=47.8
Q ss_pred cCCCcccccc---ccccccccCCcccCchhhcccCCCCCCc-----ccccceecccccccccc
Q 000878 989 VFGCEHYKRN---CKIRAACCGKLFTCRFCHDKASDHSMDR-----KATSEMMCMHCLKIQAI 1043 (1241)
Q Consensus 989 ~~gC~HY~r~---ckl~~pcC~k~y~Cr~CHde~~~H~~~r-----~~~~~~~C~~C~~~q~~ 1043 (1241)
..-|.||+.. ++|+|.||+|+|+|..|||+.++||+.+ ...+.|+||.|.++..+
T Consensus 12 etRC~Hyht~~Diialkc~~C~kyYaCy~CHdel~~Hpf~p~~~~~~~~~~iiCGvC~~~LT~ 74 (105)
T COG4357 12 ETRCLHYHTPLDIIALKCKCCQKYYACYHCHDELEDHPFEPWGLQEFNPKAIICGVCRKLLTR 74 (105)
T ss_pred cceeeEecCccceEeeeechhhhhhhHHHHHhHHhcCCCccCChhhcCCccEEhhhhhhhhhH
Confidence 3469999999 8899999999999999999999999877 34567999999987443
No 12
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=98.91 E-value=8e-10 Score=102.78 Aligned_cols=57 Identities=23% Similarity=0.588 Sum_probs=48.6
Q ss_pred CCCCccccCCCCCccccccCCcccccccccccccccccccCCcccccccccccCCCceEEcCCCCccchhhHHHHHhc--
Q 000878 1078 PFCNLCRVGGGLGVDFFHCMTCNCCLGLKLLNHKCLEKCLETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCS-- 1155 (1241)
Q Consensus 1078 ~~CgiCRvg~~l~~~~fhC~~C~~C~s~~l~~H~C~e~~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~~-- 1155 (1241)
+.|||||+.+ ++.||.|..+ +...++....|||.||.+||.+|+.+
T Consensus 22 d~CgICr~~f------------------------------dg~Cp~Ck~P--gd~Cplv~g~C~H~FH~hCI~kWl~~~~ 69 (85)
T PF12861_consen 22 DVCGICRMPF------------------------------DGCCPDCKFP--GDDCPLVWGKCSHNFHMHCILKWLSTQS 69 (85)
T ss_pred CceeeEeccc------------------------------ccCCCCccCC--CCCCceeeccCccHHHHHHHHHHHcccc
Confidence 5799999997 4779999987 56668888889999999999999964
Q ss_pred -CCCCCCCCccc
Q 000878 1156 -HYTCPICSKSL 1166 (1241)
Q Consensus 1156 -~~~CPiCrk~~ 1166 (1241)
+.+||+||+..
T Consensus 70 ~~~~CPmCR~~w 81 (85)
T PF12861_consen 70 SKGQCPMCRQPW 81 (85)
T ss_pred CCCCCCCcCCee
Confidence 58899999863
No 13
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.83 E-value=1.2e-09 Score=125.04 Aligned_cols=55 Identities=25% Similarity=0.739 Sum_probs=47.5
Q ss_pred cccccCCcccccccccccCCCceEEcCCCCccchhhHHHHHhcC-CCCCCCCcccccc
Q 000878 1113 LEKCLETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSH-YTCPICSKSLGDM 1169 (1241)
Q Consensus 1113 ~e~~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~~~-~~CPiCrk~~~dm 1169 (1241)
.++++ ..|+||+|+ |..++++++|||+|.||..|++.|+..+ ..||+|+.++..-
T Consensus 225 ~~~~~-~~CaIClEd-Y~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~di~~~ 280 (348)
T KOG4628|consen 225 DEDAT-DTCAICLED-YEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRDIRTD 280 (348)
T ss_pred ccCCC-ceEEEeecc-cccCCeeeEecCCCchhhccchhhHhhcCccCCCCCCcCCCC
Confidence 34444 589999999 9999999999999999999999999766 4599999988643
No 14
>PF01814 Hemerythrin: Hemerythrin HHE cation binding domain; InterPro: IPR012312 The haemerythrin family is composed of haemerythrin proteins found in invertebrates, and a broader collection of bacterial and archaeal homologues. Haemerythrin is an oxygen-binding protein found in the vascular system and coelemic fluid, or in muscles (myohaemerythrin) in invertebrates []. Many of the homologous proteins found in prokaryotes are multi-domain proteins with signal-transducing domains such as the GGDEF diguanylate cyclase domain (IPR000160 from INTERPRO) and methyl-accepting chemotaxis protein (MCP) signalling domain (IPR004089 from INTERPRO). Most haemerythrins are oxygen-carriers with a bound non-haem iron, but at least one example is a cadmium-binding protein, apparently with a role in sequestering toxic metals rather than in binding oxygen. The prokaryote with the most instances of this domain is Magnetococcus sp. MC-1, a magnetotactic bacterium. Haemerythrins and myohaemerythrins [, ] are small proteins of about 110 to 129 amino acid residues that bind two iron atoms. They are left-twisted 4-alpha-helical bundles, which provide a hydrophobic pocket where dioxygen binds as a peroxo species, interacting with adjacent aliphatic side chains via van der Waals forces []. In both haemerythrins and myohaemerythrins, the active centre is a binuclear iron complex, bound directly to the protein via 7 amino acid side chains [], 5 His, 1 Glu and 1 Asp []. Ovohaemerythrin [], a yolk protein from the leech Theromyzon tessulatum seems to belong to this family of proteins, it may play a role in the detoxification of free iron after a blood meal []. This entry represents a haemerythrin/HHE cation-binding motif that occurs as a duplicated domain in haemerythrin and related proteins. This domain binds iron in haemerythrin, but can bind other metals in related proteins, such as cadmium in a Nereis diversicolor protein (P80255 from SWISSPROT). A bacterial protein, Q7WX96 from SWISSPROT, is a regulator of response to NO, which suggests a different set-up for its metal ligands. A protein from Cryptococcus neoformans (Filobasidiella neoformans) that contains haemerythrin/HHE cation-binding motifs is also involved in NO response []. A Staphylococcus aureus protein (P72360 from SWISSPROT) has been noted to be important when the organism switches to living in environments with low oxygen concentrations; perhaps this protein acts as an oxygen store or scavenger.; PDB: 3CAX_A 3V5Z_B 3U9M_G 3V5Y_A 3U9J_B 3V5X_A 2MHR_A 1A7E_A 1A7D_A 2IGF_P ....
Probab=98.79 E-value=9e-08 Score=93.81 Aligned_cols=129 Identities=26% Similarity=0.327 Sum_probs=95.7
Q ss_pred CChhHHHHHHHHHHHHHHHHHHHHHhhhcCCChhhHHHHHHHHHHHHHHHHHHHhhhhhcccccccc---cccchhhhhH
Q 000878 302 YPIDEILLWHNAIRQELNEIAEESRKIQLSGDFTNLLAFNERLQFIAEVLIFHCIAEVNVIFPAVDG---ASSFSQKHAE 378 (1241)
Q Consensus 302 ~PId~If~~HkAIRkDh~el~~~~~kl~~~~d~~~l~~~~~r~qfL~el~r~HS~AEe~vVyPALE~---~~s~~~dh~~ 378 (1241)
.||+.|...|+.|+.-+..+...+.+. .+..+...+...+.++...+..|...||.++||.|+. ......+.-.
T Consensus 1 ~~i~~l~~~H~~~~~~~~~l~~~~~~~---~~~~~~~~l~~~~~~l~~~l~~H~~~EE~~l~p~l~~~~~~~~~~~~~~~ 77 (133)
T PF01814_consen 1 MPIDELRRDHRALRRLLAELEEALDEL---PDDEDLRALRELLDELRRELRHHHAREEEYLFPALERRDPRGDALIAELR 77 (133)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHHHHHHH---CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHHHH-CCCHHHHHHHH
T ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHhC---cCchhHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhccccchhhHH
Confidence 379999999999999999999999998 4677788888889999999999999999999999982 2222222222
Q ss_pred HhhhHHHHHHHHHHHHhcCCCC-CcHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHH
Q 000878 379 EESQFNDFRLLIESIQNEGAIS-TSAEFYAKLCSHADQIMETIERHFHKVEVQVLPLA 435 (1241)
Q Consensus 379 eeh~~eei~~LL~~lq~~~~~~-~~~~f~~kL~~~l~~l~~~l~~Hi~eEE~E~lPll 435 (1241)
.+| ++++.++..+...-... ........+...++.|...+.+||..||..++|++
T Consensus 78 ~eH--~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~H~~~Ee~~l~P~~ 133 (133)
T PF01814_consen 78 REH--EEIRALLDELEEALARYSGDEEDAEELREALRALAEWLRRHIAKEEEVLFPLL 133 (133)
T ss_dssp HHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHGGGHHHH
T ss_pred HHH--HHHHHHHHHHHHHHhhCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 222 22444444333221111 12345667788899999999999999999999986
No 15
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=98.76 E-value=3.5e-09 Score=119.16 Aligned_cols=57 Identities=35% Similarity=0.811 Sum_probs=49.4
Q ss_pred cccCCcccccccccccCC---------CceEEcCCCCccchhhHHHHHhcCCCCCCCCcc-cccchh
Q 000878 1115 KCLETNCPICCDFLFTSS---------ETVRALPCGHYMHLACFQAYTCSHYTCPICSKS-LGDMAI 1171 (1241)
Q Consensus 1115 ~~~~~~CpICle~lf~s~---------~~~~~lpCgH~fH~~C~~~wl~~~~~CPiCrk~-~~dm~~ 1171 (1241)
...++.|.||+|.||.++ .+.+.|||||.+|.+|++.|+..+.+|||||.+ ++|+..
T Consensus 284 ~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERqQTCPICr~p~ifd~~~ 350 (491)
T COG5243 284 TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQTCPICRRPVIFDQSS 350 (491)
T ss_pred cCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhccCCCcccCccccccCC
Confidence 556889999999998776 344789999999999999999999999999999 567754
No 16
>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=98.73 E-value=7.9e-09 Score=94.55 Aligned_cols=47 Identities=32% Similarity=0.767 Sum_probs=37.8
Q ss_pred cCCcccccccccccC---------CCceEEcCCCCccchhhHHHHHhcCCCCCCCC
Q 000878 1117 LETNCPICCDFLFTS---------SETVRALPCGHYMHLACFQAYTCSHYTCPICS 1163 (1241)
Q Consensus 1117 ~~~~CpICle~lf~s---------~~~~~~lpCgH~fH~~C~~~wl~~~~~CPiCr 1163 (1241)
.+++|+||+++|.+. ..++..++|||.||.+||.+|++.+.+||+||
T Consensus 18 ~~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR 73 (73)
T PF12678_consen 18 ADDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQNNTCPLCR 73 (73)
T ss_dssp CCSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred cCCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcCCcCCCCC
Confidence 356799999996332 35667789999999999999999999999997
No 17
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=98.62 E-value=2.4e-08 Score=90.77 Aligned_cols=59 Identities=22% Similarity=0.408 Sum_probs=49.9
Q ss_pred CCCCccccCCCCCccccccCCcccccccccccccccccccCCccccccccccc-CCCceEEcCCCCccchhhHHHHHhcC
Q 000878 1078 PFCNLCRVGGGLGVDFFHCMTCNCCLGLKLLNHKCLEKCLETNCPICCDFLFT-SSETVRALPCGHYMHLACFQAYTCSH 1156 (1241)
Q Consensus 1078 ~~CgiCRvg~~l~~~~fhC~~C~~C~s~~l~~H~C~e~~~~~~CpICle~lf~-s~~~~~~lpCgH~fH~~C~~~wl~~~ 1156 (1241)
|.|||||+.. .+.||-|...+-. +..++.+.-|.|.||.+||..|+..+
T Consensus 21 d~CaICRnhi------------------------------m~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~Tk 70 (88)
T COG5194 21 DVCAICRNHI------------------------------MGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTK 70 (88)
T ss_pred chhhhhhccc------------------------------cCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhhC
Confidence 8899999986 3679999986522 33477788899999999999999999
Q ss_pred CCCCCCCccc
Q 000878 1157 YTCPICSKSL 1166 (1241)
Q Consensus 1157 ~~CPiCrk~~ 1166 (1241)
..||+++++.
T Consensus 71 ~~CPld~q~w 80 (88)
T COG5194 71 GVCPLDRQTW 80 (88)
T ss_pred CCCCCCCcee
Confidence 9999999874
No 18
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=98.61 E-value=1.4e-08 Score=117.32 Aligned_cols=81 Identities=26% Similarity=0.693 Sum_probs=66.5
Q ss_pred CcccccccccccCCCceEEcCCCCccchhhHHHHHhcCCCCCCCCcccccchhhhhhhHHHHhccCCCHhhhcccceEEc
Q 000878 1119 TNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSLGDMAIYFGMIDALLAAEELPEEYRNQVQDILC 1198 (1241)
Q Consensus 1119 ~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~~~~~CPiCrk~~~dm~~~~~~lD~~i~~~~~P~ey~~~~~~i~C 1198 (1241)
.+||||+|.|-.+...+....|.|.||..|+..| ...+||+||.... |-+.+ .-.|
T Consensus 176 PTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w--~~~scpvcR~~q~----------------p~~ve------~~~c 231 (493)
T KOG0804|consen 176 PTCPVCLERMDSSTTGILTILCNHSFHCSCLMKW--WDSSCPVCRYCQS----------------PSVVE------SSLC 231 (493)
T ss_pred CCcchhHhhcCccccceeeeecccccchHHHhhc--ccCcChhhhhhcC----------------cchhh------hhhh
Confidence 5799999999889888999999999999999999 4778999996522 11111 2369
Q ss_pred CCCCCCCCccchhhcccCCC--CCCccccc
Q 000878 1199 NDCEQKGAARFHWLYHKCGF--CGSYNTRL 1226 (1241)
Q Consensus 1199 nDC~~~s~~~fh~lg~kC~~--CgsYNT~~ 1226 (1241)
++|+...+. |+++.|++ ||.|+-.-
T Consensus 232 ~~c~~~~~L---wicliCg~vgcgrY~egh 258 (493)
T KOG0804|consen 232 LACGCTEDL---WICLICGNVGCGRYKEGH 258 (493)
T ss_pred hhhcccccE---EEEEEccceecccccchh
Confidence 999988776 99999987 99999754
No 19
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=98.49 E-value=2.6e-08 Score=89.82 Aligned_cols=56 Identities=25% Similarity=0.523 Sum_probs=47.2
Q ss_pred CCCccccCCCCCccccccCCcccccccccccccccccccCCcccccccccccCCCceEEcCCCCccchhhHHHHHh---c
Q 000878 1079 FCNLCRVGGGLGVDFFHCMTCNCCLGLKLLNHKCLEKCLETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTC---S 1155 (1241)
Q Consensus 1079 ~CgiCRvg~~l~~~~fhC~~C~~C~s~~l~~H~C~e~~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~---~ 1155 (1241)
.|||||+.+ ++.||-|.-+ ++..++.+.-|.|.||.+|+.+|+. +
T Consensus 22 ~CGiCRm~F------------------------------dg~Cp~Ck~P--gDdCPLv~G~C~h~fh~hCI~~wl~~~ts 69 (84)
T KOG1493|consen 22 TCGICRMPF------------------------------DGCCPDCKLP--GDDCPLVWGYCLHAFHAHCILKWLNTPTS 69 (84)
T ss_pred ccceEeccc------------------------------CCcCCCCcCC--CCCCccHHHHHHHHHHHHHHHHHhcCccc
Confidence 799999997 4679999877 6667887778999999999999983 4
Q ss_pred CCCCCCCCccc
Q 000878 1156 HYTCPICSKSL 1166 (1241)
Q Consensus 1156 ~~~CPiCrk~~ 1166 (1241)
...||+||++.
T Consensus 70 q~~CPmcRq~~ 80 (84)
T KOG1493|consen 70 QGQCPMCRQTW 80 (84)
T ss_pred cccCCcchhee
Confidence 57899999863
No 20
>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=98.41 E-value=2e-07 Score=75.10 Aligned_cols=44 Identities=39% Similarity=0.951 Sum_probs=37.5
Q ss_pred cccccccccccCCCceEEcCCCCccchhhHHHHHhc-CCCCCCCCccc
Q 000878 1120 NCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCS-HYTCPICSKSL 1166 (1241)
Q Consensus 1120 ~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~~-~~~CPiCrk~~ 1166 (1241)
.|+||++.+ ..++...+|||.||..|+..|+.. +.+||+|++.+
T Consensus 1 ~C~iC~~~~---~~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~~ 45 (45)
T cd00162 1 ECPICLEEF---REPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45 (45)
T ss_pred CCCcCchhh---hCceEecCCCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence 499999994 456677789999999999999976 78899999763
No 21
>PHA02929 N1R/p28-like protein; Provisional
Probab=98.39 E-value=2.2e-07 Score=102.66 Aligned_cols=53 Identities=19% Similarity=0.580 Sum_probs=41.9
Q ss_pred cccCCcccccccccccCCCc----eEEcCCCCccchhhHHHHHhcCCCCCCCCcccc
Q 000878 1115 KCLETNCPICCDFLFTSSET----VRALPCGHYMHLACFQAYTCSHYTCPICSKSLG 1167 (1241)
Q Consensus 1115 ~~~~~~CpICle~lf~s~~~----~~~lpCgH~fH~~C~~~wl~~~~~CPiCrk~~~ 1167 (1241)
.+.+..||||++.++..... ....+|||.||..|+.+|+..+.+||+||..+.
T Consensus 171 ~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~ 227 (238)
T PHA02929 171 RSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFI 227 (238)
T ss_pred CCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEee
Confidence 34467899999995543211 234579999999999999999999999999875
No 22
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.37 E-value=1.9e-07 Score=103.34 Aligned_cols=53 Identities=28% Similarity=0.764 Sum_probs=45.8
Q ss_pred ccccCCcccccccccccCCCceEEcCCCCccchhhHHHHHh-cCCCCCCCCcccc
Q 000878 1114 EKCLETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTC-SHYTCPICSKSLG 1167 (1241)
Q Consensus 1114 e~~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~-~~~~CPiCrk~~~ 1167 (1241)
|.....+|+|||++ |...+.++++||.|.||..|+++|+. .+..||+||..++
T Consensus 319 ea~~GveCaICms~-fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iP 372 (374)
T COG5540 319 EADKGVECAICMSN-FIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIP 372 (374)
T ss_pred hcCCCceEEEEhhh-hcccceEEEeccCceechhHHHHHHhhhcccCCccCCCCC
Confidence 33344689999999 78888899999999999999999996 6789999998765
No 23
>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=98.28 E-value=4.8e-07 Score=72.80 Aligned_cols=39 Identities=41% Similarity=1.008 Sum_probs=33.5
Q ss_pred ccccccccccCCCceEEcCCCCccchhhHHHHHhcCCCCCCC
Q 000878 1121 CPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPIC 1162 (1241)
Q Consensus 1121 CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~~~~~CPiC 1162 (1241)
||||++.+ .+++..++|||.|+..|+..|++.+.+||+|
T Consensus 1 C~iC~~~~---~~~~~~~~CGH~fC~~C~~~~~~~~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDEL---RDPVVVTPCGHSFCKECIEKYLEKNPKCPVC 39 (39)
T ss_dssp ETTTTSB----SSEEEECTTSEEEEHHHHHHHHHCTSB-TTT
T ss_pred CCCCCCcc---cCcCEECCCCCchhHHHHHHHHHCcCCCcCC
Confidence 89999984 2367889999999999999999889999998
No 24
>PRK10992 iron-sulfur cluster repair di-iron protein; Provisional
Probab=98.24 E-value=1.6e-05 Score=87.48 Aligned_cols=133 Identities=17% Similarity=0.266 Sum_probs=95.2
Q ss_pred CChhHH-HHHHHHHHHHHHHHHHHHHhhhc--CCChhhHHHHHHHHHHHHHHHHHHHhhhhhcccccccccc----cc--
Q 000878 302 YPIDEI-LLWHNAIRQELNEIAEESRKIQL--SGDFTNLLAFNERLQFIAEVLIFHCIAEVNVIFPAVDGAS----SF-- 372 (1241)
Q Consensus 302 ~PId~I-f~~HkAIRkDh~el~~~~~kl~~--~~d~~~l~~~~~r~qfL~el~r~HS~AEe~vVyPALE~~~----s~-- 372 (1241)
--||.| -..|.-+|+.+.+|...+.++.. -.+...+......|.-+...+..|...||.++||+|++.. ..
T Consensus 74 ~LidyI~~~~H~~~r~~lp~L~~l~~kv~~vhg~~~~~~~~~~~l~~~~~~el~~H~~kEE~~LFP~l~~~~~~~~~~pi 153 (220)
T PRK10992 74 ELIDHIIVRYHDRHREQLPELILLATKVERVHGDKPDCPRGLAKYLTALHEELSSHMMKEEQILFPMIKQGMGSQAMGPI 153 (220)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHhcccccccchH
Confidence 358999 78899999999999999988852 2244667777777888888888899999999999999622 11
Q ss_pred ---hhhhhHHhhhHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHhc
Q 000878 373 ---SQKHAEEESQFNDFRLLIESIQNEGAISTSAEFYAKLCSHADQIMETIERHFHKVEVQVLPLARN 437 (1241)
Q Consensus 373 ---~~dh~~eeh~~eei~~LL~~lq~~~~~~~~~~f~~kL~~~l~~l~~~l~~Hi~eEE~E~lPll~k 437 (1241)
..+|+.....+.+++.+..+. ..+......+..||..++.+..+|.+||+.||..+||.+..
T Consensus 154 ~vm~~EHd~~~~~l~~L~~lt~~~---~~p~~ac~~~~~l~~~l~~~~~dL~~HI~~EnniLFP~a~~ 218 (220)
T PRK10992 154 SVMESEHDEAGELLEVIKHLTNNV---TPPPEACTTWRALYNGINELIDDLMEHIHLENNVLFPRALA 218 (220)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcC---CCChhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Confidence 124444333333333333221 11111234466788889999999999999999999998764
No 25
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=98.21 E-value=9e-07 Score=74.99 Aligned_cols=47 Identities=32% Similarity=0.812 Sum_probs=39.2
Q ss_pred CCcccccccccccCCCceEEcCCCCc-cchhhHHHHHhcCCCCCCCCccccc
Q 000878 1118 ETNCPICCDFLFTSSETVRALPCGHY-MHLACFQAYTCSHYTCPICSKSLGD 1168 (1241)
Q Consensus 1118 ~~~CpICle~lf~s~~~~~~lpCgH~-fH~~C~~~wl~~~~~CPiCrk~~~d 1168 (1241)
+..|+||++. ...+..+||||. |...|+..|.+...+||+||++|.+
T Consensus 2 ~~~C~iC~~~----~~~~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~~ 49 (50)
T PF13920_consen 2 DEECPICFEN----PRDVVLLPCGHLCFCEECAERLLKRKKKCPICRQPIES 49 (50)
T ss_dssp HSB-TTTSSS----BSSEEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-SE
T ss_pred cCCCccCCcc----CCceEEeCCCChHHHHHHhHHhcccCCCCCcCChhhcC
Confidence 3579999988 234788999999 9999999999999999999998753
No 26
>TIGR03652 FeS_repair_RIC iron-sulfur cluster repair di-iron protein. Members of this protein family, designated variously as YftE, NorA, DrnN, and NipC, are di-iron proteins involved in the repair of iron-sulfur clusters. Previously assigned names reflect pleiotropic effects of damage from NO or other oxidative stress when this protein is mutated. The suggested name now is RIC, for Repair of Iron Centers.
Probab=98.06 E-value=9.3e-06 Score=89.11 Aligned_cols=135 Identities=21% Similarity=0.263 Sum_probs=94.0
Q ss_pred hhHH-HHHHHHHHHhHhhHHHhhccCC---CCChHHHHHHHHHHHHHHHHHhhhccCccccccccccc--cccc----cc
Q 000878 651 IDTI-FKFHKAISKDLEYLDMESAKLS---DCDETFLRQFIGRFRLLWGLYRAHSNAEDEIVFPALES--KEAL----HN 720 (1241)
Q Consensus 651 id~~-~~~H~A~RrdL~~L~~~~~~~~---~~d~~~~~~~~~rf~~l~~~l~~Hh~aEDeivwPaLe~--r~~l----~n 720 (1241)
||.| ..-|+.+|+.|..|..++.++. ..+...+..+..-|+-|..-+..|+.-|.++|||+|+. ++.. .+
T Consensus 72 id~i~~~hH~~i~~~l~~L~~l~~kv~~~hg~~~~~l~~l~~~~~~~~~eL~~H~~kEE~~LFP~l~~~~~g~~~~~~~~ 151 (216)
T TIGR03652 72 IDHIVDRHHEYLREELPELIPLATKVARVHGDHHPELIGLAELFRELKAELEQHLMKEEQILFPAIIEYKRGNPAQAIGT 151 (216)
T ss_pred HHHHHHHHhHHHHHHHHHHHHHHHHHHHHhCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHccCccccccc
Confidence 7777 6678899999999998877653 34667789999999999999999999999999999984 3211 22
Q ss_pred cccccccchhHHHHHHHHHHHHHHhhhhhhccCCCCCCcccccccccCCCchhhhHHHHHHHHHHHHHHHHHHHhHhhHh
Q 000878 721 VSHSYTLDHKQEEKLFEDISCVLSEVSQLHESLPNADSEKEDKFSADYGSDNRRKYNELATKLQGMCKSIKVTLDQHILG 800 (1241)
Q Consensus 721 vs~s~~ldH~~e~~lf~~I~~~L~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~L~~~~~~l~~~L~~Hl~~ 800 (1241)
....|..+|.....++.++....... +... +....+..+...| ..+..-|.+|+..
T Consensus 152 pi~~m~~EH~~~~~~l~~L~~l~~~~------------------~~p~--~ac~~~~~~~~~l----~~~~~~L~~HI~~ 207 (216)
T TIGR03652 152 PISVMESEHDEAGDLLKELRELTNDY------------------TPPE--DACNTWRALYSGL----EELEDDLHEHIHL 207 (216)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHcCC------------------CCCc--chhHHHHHHHHHH----HHHHHHHHHHHHH
Confidence 34445556666655555444333321 1011 1122344555556 7777889999999
Q ss_pred hhhhhhhhh
Q 000878 801 EELELWPLF 809 (1241)
Q Consensus 801 EE~el~PL~ 809 (1241)
||.-|+|.+
T Consensus 208 En~iLFP~~ 216 (216)
T TIGR03652 208 ENNILFPRA 216 (216)
T ss_pred HHhhcccCC
Confidence 999999963
No 27
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=98.05 E-value=1.1e-06 Score=83.82 Aligned_cols=61 Identities=23% Similarity=0.394 Sum_probs=47.7
Q ss_pred ccCCCCCccccCCCCCccccccCCcccccccccccccccccccCCccccccccc--ccCCCceEEcCCCCccchhhHHHH
Q 000878 1075 YHCPFCNLCRVGGGLGVDFFHCMTCNCCLGLKLLNHKCLEKCLETNCPICCDFL--FTSSETVRALPCGHYMHLACFQAY 1152 (1241)
Q Consensus 1075 yHC~~CgiCRvg~~l~~~~fhC~~C~~C~s~~l~~H~C~e~~~~~~CpICle~l--f~s~~~~~~lpCgH~fH~~C~~~w 1152 (1241)
.-||.|.|||+..- ..|.-|+-.. -.....+.+.-|.|.||.+|+..|
T Consensus 44 i~vDnCAICRnHIM------------------------------d~CieCQa~~~~~~~EC~VaWG~CNHaFH~hCisrW 93 (114)
T KOG2930|consen 44 IVVDNCAICRNHIM------------------------------DLCIECQANQSATSEECTVAWGVCNHAFHFHCISRW 93 (114)
T ss_pred eeechhHHHHHHHH------------------------------HHHHhhccCCCCCCCceEEEeeecchHHHHHHHHHH
Confidence 35899999999852 3466666553 122335677889999999999999
Q ss_pred HhcCCCCCCCCcc
Q 000878 1153 TCSHYTCPICSKS 1165 (1241)
Q Consensus 1153 l~~~~~CPiCrk~ 1165 (1241)
++++..||+|.+.
T Consensus 94 lktr~vCPLdn~e 106 (114)
T KOG2930|consen 94 LKTRNVCPLDNKE 106 (114)
T ss_pred HhhcCcCCCcCcc
Confidence 9999999999986
No 28
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.04 E-value=3.6e-06 Score=69.62 Aligned_cols=44 Identities=30% Similarity=0.785 Sum_probs=38.9
Q ss_pred cccccccccccCCCceEEcCCCCccchhhHHHHHhcCCCCCCCCc
Q 000878 1120 NCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSK 1164 (1241)
Q Consensus 1120 ~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~~~~~CPiCrk 1164 (1241)
.|+||.+. |+......+++|||+|...|+..+......||+|++
T Consensus 1 ~C~~C~~~-~~~~~~~~l~~CgH~~C~~C~~~~~~~~~~CP~C~k 44 (44)
T PF14634_consen 1 HCNICFEK-YSEERRPRLTSCGHIFCEKCLKKLKGKSVKCPICRK 44 (44)
T ss_pred CCcCcCcc-ccCCCCeEEcccCCHHHHHHHHhhcCCCCCCcCCCC
Confidence 49999999 666677889999999999999999866789999986
No 29
>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=97.99 E-value=5.1e-06 Score=64.54 Aligned_cols=38 Identities=39% Similarity=0.975 Sum_probs=33.2
Q ss_pred ccccccccccCCCceEEcCCCCccchhhHHHHHh-cCCCCCCC
Q 000878 1121 CPICCDFLFTSSETVRALPCGHYMHLACFQAYTC-SHYTCPIC 1162 (1241)
Q Consensus 1121 CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~-~~~~CPiC 1162 (1241)
|+||++. ......++|||.||..|+..|+. .+.+||+|
T Consensus 1 C~iC~~~----~~~~~~~~C~H~~c~~C~~~~~~~~~~~CP~C 39 (39)
T smart00184 1 CPICLEE----LKDPVVLPCGHTFCRSCIRKWLKSGNNTCPIC 39 (39)
T ss_pred CCcCccC----CCCcEEecCCChHHHHHHHHHHHhCcCCCCCC
Confidence 8999988 45678899999999999999997 66889998
No 30
>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=97.91 E-value=8.1e-06 Score=66.04 Aligned_cols=39 Identities=36% Similarity=0.985 Sum_probs=33.3
Q ss_pred ccccccccccCCCceEEcCCCCccchhhHHHHHh--cCCCCCCC
Q 000878 1121 CPICCDFLFTSSETVRALPCGHYMHLACFQAYTC--SHYTCPIC 1162 (1241)
Q Consensus 1121 CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~--~~~~CPiC 1162 (1241)
|+||++.+ ..++..++|||.|+..|+.+|+. ...+||+|
T Consensus 1 C~iC~~~~---~~~~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEPF---EDPVILLPCGHSFCRDCLRKWLENSGSVKCPLC 41 (41)
T ss_dssp ETTTSSBC---SSEEEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred CCcCCccc---cCCCEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence 89999983 33447899999999999999987 56889998
No 31
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=97.89 E-value=1.1e-05 Score=86.25 Aligned_cols=55 Identities=22% Similarity=0.612 Sum_probs=41.6
Q ss_pred ccccccccCCcccccccccccCCCceEEcCCCCccchhhHHHHHhc----------------CCCCCCCCccccc
Q 000878 1110 HKCLEKCLETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCS----------------HYTCPICSKSLGD 1168 (1241)
Q Consensus 1110 H~C~e~~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~~----------------~~~CPiCrk~~~d 1168 (1241)
-+-++...+-.||||++. +. + ..+++|||.|+..|+.+|+.. ..+||+||..+..
T Consensus 10 ~~~~~~~~~~~CpICld~-~~--d-PVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~ 80 (193)
T PLN03208 10 TTLVDSGGDFDCNICLDQ-VR--D-PVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE 80 (193)
T ss_pred ceeccCCCccCCccCCCc-CC--C-cEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence 334444557789999998 32 3 355789999999999999742 3579999999854
No 32
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.83 E-value=6e-06 Score=102.04 Aligned_cols=53 Identities=32% Similarity=0.712 Sum_probs=44.5
Q ss_pred ccccCCcccccccccccCCC-ceEEcCCCCccchhhHHHHHhcCCCCCCCCccc
Q 000878 1114 EKCLETNCPICCDFLFTSSE-TVRALPCGHYMHLACFQAYTCSHYTCPICSKSL 1166 (1241)
Q Consensus 1114 e~~~~~~CpICle~lf~s~~-~~~~lpCgH~fH~~C~~~wl~~~~~CPiCrk~~ 1166 (1241)
.......|+||.|.|+.... ....|||||.||..|+..|++..++||+||..+
T Consensus 287 ~~~~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~qtCP~CR~~~ 340 (543)
T KOG0802|consen 287 LALSDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQQTCPTCRTVL 340 (543)
T ss_pred hhhcCCeeeeechhhccccccccceeecccchHHHHHHHHHHHhCcCCcchhhh
Confidence 34457889999999876433 357799999999999999999999999999843
No 33
>PHA02926 zinc finger-like protein; Provisional
Probab=97.76 E-value=1.6e-05 Score=85.81 Aligned_cols=53 Identities=21% Similarity=0.627 Sum_probs=40.0
Q ss_pred cccCCcccccccccccCC----CceEE-cCCCCccchhhHHHHHhcC------CCCCCCCcccc
Q 000878 1115 KCLETNCPICCDFLFTSS----ETVRA-LPCGHYMHLACFQAYTCSH------YTCPICSKSLG 1167 (1241)
Q Consensus 1115 ~~~~~~CpICle~lf~s~----~~~~~-lpCgH~fH~~C~~~wl~~~------~~CPiCrk~~~ 1167 (1241)
.+.+..|+||+|.++... ....+ .+|+|.|+..|+..|.+.+ .+||+||....
T Consensus 167 ~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~ 230 (242)
T PHA02926 167 VSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFR 230 (242)
T ss_pred ccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceee
Confidence 455789999999976532 12234 4799999999999998642 45999998764
No 34
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=97.76 E-value=2.1e-05 Score=64.69 Aligned_cols=38 Identities=37% Similarity=1.000 Sum_probs=27.5
Q ss_pred ccccccccccCCCceEEcCCCCccchhhHHHHHhcC----CCCCCC
Q 000878 1121 CPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSH----YTCPIC 1162 (1241)
Q Consensus 1121 CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~~~----~~CPiC 1162 (1241)
||||++.| + ..+.|+|||.|...|+..|.+.. +.||+|
T Consensus 1 CpiC~~~~-~---~Pv~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDLF-K---DPVSLPCGHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB--S---SEEE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCccchhh-C---CccccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 89999994 3 34669999999999999987432 689998
No 35
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.76 E-value=1.4e-05 Score=83.49 Aligned_cols=48 Identities=27% Similarity=0.650 Sum_probs=39.2
Q ss_pred CCcccccccccccCCCceEEcCCCCccchhhHHHHHhcCCCCCCCCcccc
Q 000878 1118 ETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSLG 1167 (1241)
Q Consensus 1118 ~~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~~~~~CPiCrk~~~ 1167 (1241)
...|||||+. |....+ ....|||.|...|++.-++...+||+|+|-|.
T Consensus 131 ~~~CPiCl~~-~sek~~-vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt 178 (187)
T KOG0320|consen 131 TYKCPICLDS-VSEKVP-VSTKCGHVFCSQCIKDALKNTNKCPTCRKKIT 178 (187)
T ss_pred ccCCCceecc-hhhccc-cccccchhHHHHHHHHHHHhCCCCCCcccccc
Confidence 3789999999 443222 33789999999999999999999999998653
No 36
>PRK13276 cell wall biosynthesis protein ScdA; Provisional
Probab=97.72 E-value=0.00015 Score=79.79 Aligned_cols=131 Identities=14% Similarity=0.161 Sum_probs=96.2
Q ss_pred CChhHHHH-HHHHHHHHHHHHHHHHHhhhcC--CChhhHHHHHHHHHHHHHHHHHHHhhhhhccccccccc--c------
Q 000878 302 YPIDEILL-WHNAIRQELNEIAEESRKIQLS--GDFTNLLAFNERLQFIAEVLIFHCIAEVNVIFPAVDGA--S------ 370 (1241)
Q Consensus 302 ~PId~If~-~HkAIRkDh~el~~~~~kl~~~--~d~~~l~~~~~r~qfL~el~r~HS~AEe~vVyPALE~~--~------ 370 (1241)
--||.|.. .|.-+|+.+-+|..++.|+... .+...+......|..++..+..|..-||.++||++..- +
T Consensus 77 ~Lid~I~~~hH~~~r~~lp~l~~l~~kV~~VHg~~~p~l~~l~~lf~~l~~eL~~H~~KEE~ilFP~i~~~~~~~~~~~~ 156 (224)
T PRK13276 77 SLIQYIQSAYHEPLREEFKNLTPYVTKLSKVHGPNHPYLVELKETYDTFKNGMLEHMQKEDDVDFPKLIKYEQGEVVDDI 156 (224)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHhhccccchhh
Confidence 35888875 6789999999999999998642 35568888999999999999999999999999999641 1
Q ss_pred -----cchhhhhHHhhhHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHH
Q 000878 371 -----SFSQKHAEEESQFNDFRLLIESIQNEGAISTSAEFYAKLCSHADQIMETIERHFHKVEVQVLPLA 435 (1241)
Q Consensus 371 -----s~~~dh~~eeh~~eei~~LL~~lq~~~~~~~~~~f~~kL~~~l~~l~~~l~~Hi~eEE~E~lPll 435 (1241)
..+.||+.....+.+|++|-..+ ..+.....-+..||..|+.|-++|.+||+-|-.-+||.+
T Consensus 157 ~~pI~~m~~EH~~~g~~l~~i~~lTn~y---t~P~~AC~t~r~ly~~L~~fe~dL~~HIhLENnILFPr~ 223 (224)
T PRK13276 157 NTVIDDLVSDHIATGQLLVKMSELTSSY---EPPIEACGTWRLVYQRLKALEVLTHEHVHLENHVLFKKV 223 (224)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHhCCC---CCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHcccCC
Confidence 11224443333333333333222 122223556778899999999999999999999999954
No 37
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=97.62 E-value=3.8e-05 Score=63.56 Aligned_cols=39 Identities=36% Similarity=0.907 Sum_probs=23.4
Q ss_pred ccccccccccCCCceEEcCCCCccchhhHHHHHhc----CCCCC
Q 000878 1121 CPICCDFLFTSSETVRALPCGHYMHLACFQAYTCS----HYTCP 1160 (1241)
Q Consensus 1121 CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~~----~~~CP 1160 (1241)
||||.| +-+...+.++|+|||+|-.+|++.+++. ..+||
T Consensus 1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~~~~~~kCP 43 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKSDRNRFKCP 43 (43)
T ss_dssp -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcCCCCeeeCc
Confidence 999999 4444556788999999999999999863 35677
No 38
>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=97.54 E-value=7.7e-05 Score=65.56 Aligned_cols=44 Identities=25% Similarity=0.457 Sum_probs=37.8
Q ss_pred cccccccccccCCCceEEcCCCCccchhhHHHHHhcCCCCCCCCcccc
Q 000878 1120 NCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSLG 1167 (1241)
Q Consensus 1120 ~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~~~~~CPiCrk~~~ 1167 (1241)
.||||++.| ++ + ..+||||.|...|+.+|+..+.+||+|++.+.
T Consensus 3 ~Cpi~~~~~-~~--P-v~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~ 46 (63)
T smart00504 3 LCPISLEVM-KD--P-VILPSGQTYERRAIEKWLLSHGTDPVTGQPLT 46 (63)
T ss_pred CCcCCCCcC-CC--C-EECCCCCEEeHHHHHHHHHHCCCCCCCcCCCC
Confidence 599999984 33 4 55799999999999999988899999998873
No 39
>COG2846 Regulator of cell morphogenesis and NO signaling [Cell division and chromosome partitioning]
Probab=97.49 E-value=0.00062 Score=72.66 Aligned_cols=133 Identities=17% Similarity=0.287 Sum_probs=97.2
Q ss_pred CCChhHHH-HHHHHHHHHHHHHHHHHHhhhcC--CChhhHHHHHHHHHHHHHHHHHHHhhhhhcccccccccc-------
Q 000878 301 TYPIDEIL-LWHNAIRQELNEIAEESRKIQLS--GDFTNLLAFNERLQFIAEVLIFHCIAEVNVIFPAVDGAS------- 370 (1241)
Q Consensus 301 ~~PId~If-~~HkAIRkDh~el~~~~~kl~~~--~d~~~l~~~~~r~qfL~el~r~HS~AEe~vVyPALE~~~------- 370 (1241)
..-||+|+ .+|+..|..+.+|-....|+... ...+....+.+.+.-+++.+-.|..-||.|+||.+..-.
T Consensus 74 s~lIdhIi~ryH~~hReqlpeLi~latKverVHgd~p~~p~gl~~~L~~l~~eL~~HMmKEEqIlFPmi~~G~g~~a~~p 153 (221)
T COG2846 74 SELIDHIIVRYHERHREQLPELIPLATKVERVHGDKPSCPAGLAELLEALKEELESHMMKEEQILFPMIKQGMGSQAAGP 153 (221)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHhhHHHHhccCcccCcc
Confidence 34789886 69999999999999999988642 234667777778888999999999999999999997511
Q ss_pred --cchhhhhHHhhhHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHh
Q 000878 371 --SFSQKHAEEESQFNDFRLLIESIQNEGAISTSAEFYAKLCSHADQIMETIERHFHKVEVQVLPLAR 436 (1241)
Q Consensus 371 --s~~~dh~~eeh~~eei~~LL~~lq~~~~~~~~~~f~~kL~~~l~~l~~~l~~Hi~eEE~E~lPll~ 436 (1241)
....+|+...++++.++.+-..+. .+.....-+..||.-++.|.+++.+||+-|-.-+||.+-
T Consensus 154 I~vm~~EHde~g~~l~~lk~lT~n~t---pP~~AC~tWkalY~gl~~~~dDl~~HIHLENnvLFpr~~ 218 (221)
T COG2846 154 ISVMESEHDEAGELLEVLKHLTNNYT---PPEEACGTWKALYNGLNEFIDDLMEHIHLENNVLFPRVL 218 (221)
T ss_pred hHHHHHHHHHHHHHHHHHHHHhcCCC---CChHHHhHHHHHHHHHHHHHHHHHHHHHhhhccccchhc
Confidence 222345544444444444433221 222224456778999999999999999999999998753
No 40
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.43 E-value=2.9e-05 Score=94.70 Aligned_cols=52 Identities=21% Similarity=0.496 Sum_probs=43.0
Q ss_pred ccCCcccccccccccCCCceEEcCCCCccchhhHHHHHhcCCCCCCCCccccc
Q 000878 1116 CLETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSLGD 1168 (1241)
Q Consensus 1116 ~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~~~~~CPiCrk~~~d 1168 (1241)
.....||+|+.. |.........+|+|+||.+||..|.+.-.+||+||+.+..
T Consensus 121 ~~~~~CP~Ci~s-~~DqL~~~~k~c~H~FC~~Ci~sWsR~aqTCPiDR~EF~~ 172 (1134)
T KOG0825|consen 121 HVENQCPNCLKS-CNDQLEESEKHTAHYFCEECVGSWSRCAQTCPVDRGEFGE 172 (1134)
T ss_pred hhhhhhhHHHHH-HHHHhhccccccccccHHHHhhhhhhhcccCchhhhhhhe
Confidence 346679999988 5555544557899999999999999999999999998753
No 41
>COG3945 Uncharacterized conserved protein [Function unknown]
Probab=97.36 E-value=0.002 Score=67.93 Aligned_cols=142 Identities=16% Similarity=0.229 Sum_probs=105.2
Q ss_pred hhHHHHHHHHHHHhHhhHHHhhccCCCC--ChHHHHHHHHHHHHHHHHHhhhccCcccccccccccccc--ccccccccc
Q 000878 651 IDTIFKFHKAISKDLEYLDMESAKLSDC--DETFLRQFIGRFRLLWGLYRAHSNAEDEIVFPALESKEA--LHNVSHSYT 726 (1241)
Q Consensus 651 id~~~~~H~A~RrdL~~L~~~~~~~~~~--d~~~~~~~~~rf~~l~~~l~~Hh~aEDeivwPaLe~r~~--l~nvs~s~~ 726 (1241)
|++|.-=|+-|.|-|.-|....--...| |++.+..+++..+-+.. .+||--||-++||-++.++. ....-..|+
T Consensus 10 i~~lvEeH~yIlraL~iLr~~~~~~~~g~i~y~~v~~iidFi~nfaD--kcHH~KEE~~LF~~m~~~g~~~~~~~i~~m~ 87 (189)
T COG3945 10 IKLLVEEHTYILRALSILRKALDLIKNGPIDYSDVKEIIDFIRNFAD--KCHHGKEEKLLFNYMEHEGGPFEEGPIYVMT 87 (189)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcccCCCCCHHHHHHHHHHHHHHHH--hccchHHHHHHHHHHHHhCCCcccCceeeeh
Confidence 6777888999999999998876555543 56555555554444433 68999999999999998854 566667788
Q ss_pred cchhHHHHHHHHHHHHHHhhhhhhccCCCCCCcccccccccCCCchhhhHHHHHHHHHHHHHHHHHHHhHhhHhhhhhhh
Q 000878 727 LDHKQEEKLFEDISCVLSEVSQLHESLPNADSEKEDKFSADYGSDNRRKYNELATKLQGMCKSIKVTLDQHILGEELELW 806 (1241)
Q Consensus 727 ldH~~e~~lf~~I~~~L~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~L~~~~~~l~~~L~~Hl~~EE~el~ 806 (1241)
.+|-.-..+..++..++.++-.. +. + ....++..+ ++-...+.+|++.|+..++
T Consensus 88 ~EH~~~R~i~r~lee~~~~~kng------------------d~-~---~~~~~i~~A----~~y~~likrHIdkEdnvlf 141 (189)
T COG3945 88 VEHGEGRYIIRDLEEAYERLKNG------------------DE-D---SKDDVIDYA----VAYLNLIKRHIDKEDNVLF 141 (189)
T ss_pred hhhhhHHHHHHHHHHHHHHHHcc------------------cc-c---hHHHHHHHH----HHHHHHHHHHHhhhhhHHH
Confidence 99999999999999999886553 11 1 112222333 4445668999999999999
Q ss_pred hhhhccCCHHHHHHH
Q 000878 807 PLFGRHFSVEEQDKI 821 (1241)
Q Consensus 807 PL~~~~~t~~Ew~~i 821 (1241)
|++.+.||.+ |.+|
T Consensus 142 p~a~~~~s~e-~~~v 155 (189)
T COG3945 142 PFAESTLSEE-LNEV 155 (189)
T ss_pred HHHHHHHHHH-HHHH
Confidence 9999999999 4443
No 42
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=97.35 E-value=8.5e-05 Score=83.04 Aligned_cols=45 Identities=24% Similarity=0.761 Sum_probs=38.4
Q ss_pred CcccccccccccCCCceEEcCCCCccchhhHHHHHhcCCCCCCCCcccc
Q 000878 1119 TNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSLG 1167 (1241)
Q Consensus 1119 ~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~~~~~CPiCrk~~~ 1167 (1241)
..|.+|+|.. ......||||.|...|+.+|.....-||+||....
T Consensus 240 ~kC~LCLe~~----~~pSaTpCGHiFCWsCI~~w~~ek~eCPlCR~~~~ 284 (293)
T KOG0317|consen 240 RKCSLCLENR----SNPSATPCGHIFCWSCILEWCSEKAECPLCREKFQ 284 (293)
T ss_pred CceEEEecCC----CCCCcCcCcchHHHHHHHHHHccccCCCcccccCC
Confidence 4699999983 34566899999999999999988888999997753
No 43
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.30 E-value=0.00015 Score=79.07 Aligned_cols=51 Identities=24% Similarity=0.584 Sum_probs=39.2
Q ss_pred cccCCcccccccccccCCCceEEcCCCCccchhhHHHHHhc---CCCCCCCCcccccc
Q 000878 1115 KCLETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCS---HYTCPICSKSLGDM 1169 (1241)
Q Consensus 1115 ~~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~~---~~~CPiCrk~~~dm 1169 (1241)
....-+|.||+|- ..++|.. .|||+|...||.+|+.. ...||+|+-.|..-
T Consensus 44 ~~~~FdCNICLd~---akdPVvT-lCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~ 97 (230)
T KOG0823|consen 44 DGGFFDCNICLDL---AKDPVVT-LCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSID 97 (230)
T ss_pred CCCceeeeeeccc---cCCCEEe-ecccceehHHHHHHHhhcCCCeeCCccccccccc
Confidence 3456789999977 5555554 59999999999999853 35589999888543
No 44
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=97.27 E-value=0.0001 Score=93.45 Aligned_cols=115 Identities=26% Similarity=0.547 Sum_probs=77.9
Q ss_pred ccceeccccccc-----cccCCCCCCCCCCCCcceeEeccccccccCCCCcccCCCCCccccCCCCCccccccCCccccc
Q 000878 1029 TSEMMCMHCLKI-----QAIGPNCTTPSCNGLSMAKYYCNICKFFDDERTVYHCPFCNLCRVGGGLGVDFFHCMTCNCCL 1103 (1241)
Q Consensus 1029 ~~~~~C~~C~~~-----q~~~~~C~~~~Cc~~~~a~y~C~~C~~~d~~k~~yHC~~CgiCRvg~~l~~~~fhC~~C~~C~ 1103 (1241)
+..--|.+|+.. |.++..|....| ...|+--|++-+-... .|| |. .|--||..|=.|-
T Consensus 3415 sS~~aCRFCGs~~~tE~sav~~vCs~aDC--~eYAK~ACs~~H~C~H--------~CG----Gv---kNEE~CLPCl~Cd 3477 (3738)
T KOG1428|consen 3415 SSSEACRFCGSRSGTELSAVGSVCSDADC--QEYAKIACSKTHPCGH--------PCG----GV---KNEEHCLPCLHCD 3477 (3738)
T ss_pred cchhHhhhccCCCCcchhcccCccccHHH--HHHHHHHHhccCcCCC--------ccc----Cc---cchhhcccccccC
Confidence 334478888754 677888988777 5677777776433221 244 22 3556777776664
Q ss_pred ccccccccccccccCCcccccccccccCCCceEEcCCCCccchhhHHHHHhcC----------CCCCCCCcccc
Q 000878 1104 GLKLLNHKCLEKCLETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSH----------YTCPICSKSLG 1167 (1241)
Q Consensus 1104 s~~l~~H~C~e~~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~~~----------~~CPiCrk~~~ 1167 (1241)
.-.. ....++.|.||.-. --+..+...|.|||.||.+|...-+.++ ..||||...|.
T Consensus 3478 ks~t------kQD~DDmCmICFTE-~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~In 3544 (3738)
T KOG1428|consen 3478 KSAT------KQDADDMCMICFTE-ALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKIN 3544 (3738)
T ss_pred hhhh------hcccCceEEEEehh-hhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchhh
Confidence 3111 23346789999977 4567788999999999999987655332 57999998873
No 45
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.24 E-value=0.00012 Score=86.04 Aligned_cols=50 Identities=26% Similarity=0.598 Sum_probs=38.0
Q ss_pred CCcccccccccc----cC---------CCceEEcCCCCccchhhHHHHHh-cCCCCCCCCcccc
Q 000878 1118 ETNCPICCDFLF----TS---------SETVRALPCGHYMHLACFQAYTC-SHYTCPICSKSLG 1167 (1241)
Q Consensus 1118 ~~~CpICle~lf----~s---------~~~~~~lpCgH~fH~~C~~~wl~-~~~~CPiCrk~~~ 1167 (1241)
..+|+|||.++- ++ ...++..||.|.||..|+..|+. .+..||+||.++.
T Consensus 571 t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLP 634 (636)
T KOG0828|consen 571 TNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLP 634 (636)
T ss_pred cccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCCC
Confidence 467999988751 11 11345669999999999999997 4568999998875
No 46
>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=97.17 E-value=0.00029 Score=80.52 Aligned_cols=50 Identities=22% Similarity=0.565 Sum_probs=39.3
Q ss_pred CCcccccccccccCCC-ceEEcCCCCccchhhHHHHH-hcCCCCCCCCcccc
Q 000878 1118 ETNCPICCDFLFTSSE-TVRALPCGHYMHLACFQAYT-CSHYTCPICSKSLG 1167 (1241)
Q Consensus 1118 ~~~CpICle~lf~s~~-~~~~lpCgH~fH~~C~~~wl-~~~~~CPiCrk~~~ 1167 (1241)
+..||||+...+.+.. .+.+.+|||.|+.+|++..+ .....||.|++++-
T Consensus 3 ~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lr 54 (309)
T TIGR00570 3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLR 54 (309)
T ss_pred CCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCccc
Confidence 4679999997655554 44455899999999999954 55678999999874
No 47
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.16 E-value=0.00024 Score=84.04 Aligned_cols=46 Identities=26% Similarity=0.630 Sum_probs=39.1
Q ss_pred CCcccccccccccCCCceEEcCCCCccchhhHHHHHhcCCCCCCCCcccc
Q 000878 1118 ETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSLG 1167 (1241)
Q Consensus 1118 ~~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~~~~~CPiCrk~~~ 1167 (1241)
...|+||++. |. .+ .++||||.|+..|+..|+.....||+|+..+.
T Consensus 26 ~l~C~IC~d~-~~--~P-vitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~ 71 (397)
T TIGR00599 26 SLRCHICKDF-FD--VP-VLTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQ 71 (397)
T ss_pred ccCCCcCchh-hh--Cc-cCCCCCCchhHHHHHHHHhCCCCCCCCCCccc
Confidence 4579999998 43 23 36899999999999999988889999999875
No 48
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.12 E-value=0.00023 Score=84.89 Aligned_cols=53 Identities=30% Similarity=0.631 Sum_probs=39.8
Q ss_pred ccccccCCcccccccccccCCCceEEcCCCCccchhhHHHHHhc-----CCCCCCCCccccc
Q 000878 1112 CLEKCLETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCS-----HYTCPICSKSLGD 1168 (1241)
Q Consensus 1112 C~e~~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~~-----~~~CPiCrk~~~d 1168 (1241)
++..+++..||||+++ ...+++.. |||.|+..|+-+|+.. ...||||+..|.-
T Consensus 180 qv~~~t~~~CPICL~~---~~~p~~t~-CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~ 237 (513)
T KOG2164|consen 180 QVYGSTDMQCPICLEP---PSVPVRTN-CGHIFCGPCILQYWNYSAIKGPCSCPICRSTITL 237 (513)
T ss_pred hhhcCcCCcCCcccCC---CCcccccc-cCceeeHHHHHHHHhhhcccCCccCCchhhhccc
Confidence 3334447899999998 33444544 9999999999998633 3779999998864
No 49
>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=97.12 E-value=0.00037 Score=59.35 Aligned_cols=42 Identities=31% Similarity=0.738 Sum_probs=33.0
Q ss_pred cccccccccccCCCceEEcCCC-----CccchhhHHHHHh--cCCCCCCCC
Q 000878 1120 NCPICCDFLFTSSETVRALPCG-----HYMHLACFQAYTC--SHYTCPICS 1163 (1241)
Q Consensus 1120 ~CpICle~lf~s~~~~~~lpCg-----H~fH~~C~~~wl~--~~~~CPiCr 1163 (1241)
.|-||++. .+.....+.||. |++|..|+..|+. .+.+||+|+
T Consensus 1 ~CrIC~~~--~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~ 49 (49)
T smart00744 1 ICRICHDE--GDEGDPLVSPCRCKGSLKYVHQECLERWINESGNKTCEICK 49 (49)
T ss_pred CccCCCCC--CCCCCeeEeccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence 38899983 344555688985 9999999999994 346899996
No 50
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=96.96 E-value=0.00039 Score=78.69 Aligned_cols=45 Identities=24% Similarity=0.748 Sum_probs=39.3
Q ss_pred cccccccccccCCCceEEcCCCCccchhhHHHHHhcCCCCCCCCccccc
Q 000878 1120 NCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSLGD 1168 (1241)
Q Consensus 1120 ~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~~~~~CPiCrk~~~d 1168 (1241)
.|-||.|+ |. ..++.||||+|+.-||..++..+..||.|+.++..
T Consensus 25 RC~IC~ey-f~---ip~itpCsHtfCSlCIR~~L~~~p~CP~C~~~~~E 69 (442)
T KOG0287|consen 25 RCGICFEY-FN---IPMITPCSHTFCSLCIRKFLSYKPQCPTCCVTVTE 69 (442)
T ss_pred HHhHHHHH-hc---CceeccccchHHHHHHHHHhccCCCCCceecccch
Confidence 49999999 43 34678999999999999999999999999998853
No 51
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=96.91 E-value=0.00025 Score=64.69 Aligned_cols=50 Identities=28% Similarity=0.672 Sum_probs=23.1
Q ss_pred CCcccccccccccCC-CceEEc---CCCCccchhhHHHHHhc-----------CCCCCCCCcccc
Q 000878 1118 ETNCPICCDFLFTSS-ETVRAL---PCGHYMHLACFQAYTCS-----------HYTCPICSKSLG 1167 (1241)
Q Consensus 1118 ~~~CpICle~lf~s~-~~~~~l---pCgH~fH~~C~~~wl~~-----------~~~CPiCrk~~~ 1167 (1241)
+..|+||++++.+.+ .+..+- .|+..||..|+.+|+.. ..+||.|+++|.
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~ 66 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPIS 66 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEE
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeee
Confidence 357999999966333 334433 59999999999999742 146999998863
No 52
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.87 E-value=0.001 Score=73.50 Aligned_cols=43 Identities=37% Similarity=0.936 Sum_probs=37.1
Q ss_pred CCcccccccccccCCCceEEcCCCCccchhhHHHHHhcCCCCCCCCc
Q 000878 1118 ETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSK 1164 (1241)
Q Consensus 1118 ~~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~~~~~CPiCrk 1164 (1241)
.-.||||+++ |... .++||||.|...|+..+......||.||.
T Consensus 13 ~~~C~iC~~~-~~~p---~~l~C~H~~c~~C~~~~~~~~~~Cp~cr~ 55 (386)
T KOG2177|consen 13 ELTCPICLEY-FREP---VLLPCGHNFCRACLTRSWEGPLSCPVCRP 55 (386)
T ss_pred cccChhhHHH-hhcC---ccccccchHhHHHHHHhcCCCcCCcccCC
Confidence 5679999999 5544 88999999999999998776688999994
No 53
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.80 E-value=0.00058 Score=78.68 Aligned_cols=45 Identities=27% Similarity=0.663 Sum_probs=37.5
Q ss_pred CcccccccccccCCCceEEcC-CCCccchhhHHHHHhc---CCCCCCCCc
Q 000878 1119 TNCPICCDFLFTSSETVRALP-CGHYMHLACFQAYTCS---HYTCPICSK 1164 (1241)
Q Consensus 1119 ~~CpICle~lf~s~~~~~~lp-CgH~fH~~C~~~wl~~---~~~CPiCrk 1164 (1241)
-.|.|| +++|.....+..+. |||+||..|+.+|... +.+||||+-
T Consensus 5 A~C~Ic-~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~i 53 (465)
T KOG0827|consen 5 AECHIC-IDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQI 53 (465)
T ss_pred ceeeEe-ccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceee
Confidence 469999 67688888787665 9999999999999854 468999993
No 54
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=96.72 E-value=0.00021 Score=80.57 Aligned_cols=143 Identities=21% Similarity=0.196 Sum_probs=112.8
Q ss_pred ChHHHHHHHHHHHHHHHHHhhhccCccccccccccccccccccccccccchhHHHHHHHHHHHHHHhhhhhhccCCCCCC
Q 000878 679 DETFLRQFIGRFRLLWGLYRAHSNAEDEIVFPALESKEALHNVSHSYTLDHKQEEKLFEDISCVLSEVSQLHESLPNADS 758 (1241)
Q Consensus 679 d~~~~~~~~~rf~~l~~~l~~Hh~aEDeivwPaLe~r~~l~nvs~s~~ldH~~e~~lf~~I~~~L~~l~~~~~~~~~~~~ 758 (1241)
+.++...++. ..|..|+.++|++-||++.+.....+++++...||--.-.|.+..+..+..
T Consensus 7 ~~~~~~~~~~------~~~~~~~~~~d~~~~~~~c~hy~r~~~~~a~ccd~~~~C~hCH~~s~~h~~------------- 67 (276)
T KOG1940|consen 7 DQSFLEEFAQ------ALSSIHSDAEDEIAFPYGCPHYRRNCKSRAPCCDREITCRHCHNESEDHDL------------- 67 (276)
T ss_pred hhhhhHHHHh------hhhhcccccccccccccCCchhhhccccccccccceeeeEEecChhhhccc-------------
Confidence 4445555554 889999999999999999999888898888888887777777666652221
Q ss_pred cccccccccCCCchhhhHHHHHHHHHHHHHHHHHHHhHhhHhhhhhhhhhhhccCCHHHHHHHHhHHhcCCCHHHHHHHh
Q 000878 759 EKEDKFSADYGSDNRRKYNELATKLQGMCKSIKVTLDQHILGEELELWPLFGRHFSVEEQDKIVGRIIGSTGAEVLQSML 838 (1241)
Q Consensus 759 ~~~~~~~~~~~~~~~~~~~~L~~~L~~~~~~l~~~L~~Hl~~EE~el~PL~~~~~t~~Ew~~i~~~~~~~~~~~~l~~~l 838 (1241)
++-..++-++...+...+...+.+..|+. +.++|=++-+.|.++++ ++...+.+.+--+..+.
T Consensus 68 ------------~r~~v~~~~C~~C~~~q~~~~~c~~c~~~--~g~~~c~~C~l~dd~~~-~~~hC~~C~icr~g~~~-- 130 (276)
T KOG1940|consen 68 ------------DRKTVYELLCMKCRKIQPVGQICSNCHVE--LGEYYCLICKLFDDDPS-KQYHCDLCGICREGLGL-- 130 (276)
T ss_pred ------------chhhhhhhhhhhHHhhhhhhhccccchhh--hhhhcCccccccccccc-ceecccccccccccccc--
Confidence 12245677788888888899999999998 99999999999999999 98888866554443443
Q ss_pred hHHhccCCHHHHHHHHHhc
Q 000878 839 PWVTSALTQDEQSKLIDTW 857 (1241)
Q Consensus 839 pwv~~~l~~~eq~~ml~~~ 857 (1241)
+|+......+++.+.|..|
T Consensus 131 ~~fhc~~c~~c~~~~~~~~ 149 (276)
T KOG1940|consen 131 DFFHCKKCKACLSAYLSNW 149 (276)
T ss_pred chhHHhhhHhHHhhhcccc
Confidence 9999888888888777766
No 55
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.66 E-value=0.00051 Score=75.88 Aligned_cols=49 Identities=24% Similarity=0.678 Sum_probs=40.2
Q ss_pred CCcccccccccccCCC------ceEEcCCCCccchhhHHHHH--hcCCCCCCCCccc
Q 000878 1118 ETNCPICCDFLFTSSE------TVRALPCGHYMHLACFQAYT--CSHYTCPICSKSL 1166 (1241)
Q Consensus 1118 ~~~CpICle~lf~s~~------~~~~lpCgH~fH~~C~~~wl--~~~~~CPiCrk~~ 1166 (1241)
++.|+||...++.+.+ +.-.|.|+|.||..|+..|- ....+||-|++.+
T Consensus 224 d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekV 280 (328)
T KOG1734|consen 224 DSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKV 280 (328)
T ss_pred cchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHh
Confidence 5679999999766552 45678999999999999995 5568999999875
No 56
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.58 E-value=0.001 Score=73.86 Aligned_cols=46 Identities=30% Similarity=0.800 Sum_probs=38.2
Q ss_pred CCcccccccccccCCCceEEcCCCCccchhhHHH-HHhcCCC-CCCCCcccc
Q 000878 1118 ETNCPICCDFLFTSSETVRALPCGHYMHLACFQA-YTCSHYT-CPICSKSLG 1167 (1241)
Q Consensus 1118 ~~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~-wl~~~~~-CPiCrk~~~ 1167 (1241)
+..|+||++.+ ......||||.|...|+.. |++..+- ||+||.-+.
T Consensus 215 d~kC~lC~e~~----~~ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~ 262 (271)
T COG5574 215 DYKCFLCLEEP----EVPSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVY 262 (271)
T ss_pred ccceeeeeccc----CCcccccccchhhHHHHHHHHHhhccccCchhhhhcc
Confidence 56799999984 3456689999999999999 9988877 999997643
No 57
>COG2461 Uncharacterized conserved protein [Function unknown]
Probab=96.55 E-value=0.014 Score=68.33 Aligned_cols=138 Identities=21% Similarity=0.214 Sum_probs=107.2
Q ss_pred CccHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCcccHHHHHHHHHHHHHHhhccCccccccccHHHhhhhh-hHHHHHHH
Q 000878 38 DDSPILIFCFFHKAVRNELDALHQLAMNFATGHRVDILSLSERYRFLHSVYKHHSNAEDEVIFPALDIRVK-NVARKYSL 116 (1241)
Q Consensus 38 ~~~PId~l~~~H~AIRreL~~L~~la~~l~~gd~~dl~~L~~~l~fL~~~L~~HH~aEDevLFPaL~~R~p-~vl~~le~ 116 (1241)
..+|+..|...-++|+ ..|...+..... ..-...+...+.++..+-+ |-..++..|||.++++.- .+...|-.
T Consensus 84 ~gHPv~tl~~EN~~i~---~ll~~~l~~~~~--~~ik~~l~~lv~~L~~vg~-Hy~RKe~lIfp~~Er~GitapptVmW~ 157 (409)
T COG2461 84 PGHPVRTLKRENKAIR---SLLANLLQFPPK--KEIKEKLVELVSELDKIGK-HYTRKEMLIFPYIERRGITAPPTVMWV 157 (409)
T ss_pred CCCcHHHHhcccHHHH---HHHHHHhhcccc--HHHHHHHHHHHHHHHHhcc-ccccccccchhHHHHcCCCCCCeeeec
Confidence 6789999999999999 444444444322 2223334444555555555 999999999999999843 44456778
Q ss_pred hHHHHHHHHHHHHHHHhhhccCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHhccCCHHHHHHHHHH
Q 000878 117 EHEGESNLFDHLFQLLNSYTQNDESFPKELASCSRALQTSINQHMSKEEQQVFPLLTQHFSLEEQASLVWQ 187 (1241)
Q Consensus 117 EH~~id~lL~~L~~lL~~~~~~~~~~~~eLa~al~~L~~~L~~HL~~EE~eVfPLa~~~lS~eEwaeL~~~ 187 (1241)
.|.++...+..+..++. +....++.+....+.+.+..=+-+||..+.|.....||..||.++..+
T Consensus 158 ~dDeiRe~lk~~~~~l~------~~s~~~~ve~~~~~~t~i~dmIFkEe~Ilypt~~d~~te~ew~~i~~~ 222 (409)
T COG2461 158 KDDEIREALKELLKLLK------EVSIEEFVEKAESVLTEIEDMIFKEENILYPTLLDLLTEGEWEAIKEQ 222 (409)
T ss_pred cCcHHHHHHHHHHHHhh------ccChHHHHHHHHHHHHHHHHHHHhhhhhHHhHHHHhcCHHHHHHHHhc
Confidence 99999999999998887 234578888999999999999999999999999999999999998665
No 58
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.28 E-value=0.001 Score=57.12 Aligned_cols=50 Identities=32% Similarity=0.695 Sum_probs=36.3
Q ss_pred CCcccccccccccCCCceEEcCCCCc-cchhhHHH-HHhcCCCCCCCCcccccchh
Q 000878 1118 ETNCPICCDFLFTSSETVRALPCGHY-MHLACFQA-YTCSHYTCPICSKSLGDMAI 1171 (1241)
Q Consensus 1118 ~~~CpICle~lf~s~~~~~~lpCgH~-fH~~C~~~-wl~~~~~CPiCrk~~~dm~~ 1171 (1241)
...|.||+|.- .+.| .--|||. |...|-.+ |...+..|||||.+|-+.-.
T Consensus 7 ~dECTICye~p---vdsV-lYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~dvIk 58 (62)
T KOG4172|consen 7 SDECTICYEHP---VDSV-LYTCGHMCMCYACGLRLKKALHGCCPICRAPIKDVIK 58 (62)
T ss_pred ccceeeeccCc---chHH-HHHcchHHhHHHHHHHHHHccCCcCcchhhHHHHHHH
Confidence 47899999882 2222 2359997 88888555 55578999999998876543
No 59
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.15 E-value=0.0033 Score=72.66 Aligned_cols=48 Identities=27% Similarity=0.643 Sum_probs=40.6
Q ss_pred ccCCcccccccccccCCCceEEcCCCCc-cchhhHHHHHhcCCCCCCCCcccc
Q 000878 1116 CLETNCPICCDFLFTSSETVRALPCGHY-MHLACFQAYTCSHYTCPICSKSLG 1167 (1241)
Q Consensus 1116 ~~~~~CpICle~lf~s~~~~~~lpCgH~-fH~~C~~~wl~~~~~CPiCrk~~~ 1167 (1241)
.....|.||+.. .....+|||-|+ +...|.+...-+...|||||..+.
T Consensus 288 ~~gkeCVIClse----~rdt~vLPCRHLCLCs~Ca~~Lr~q~n~CPICRqpi~ 336 (349)
T KOG4265|consen 288 ESGKECVICLSE----SRDTVVLPCRHLCLCSGCAKSLRYQTNNCPICRQPIE 336 (349)
T ss_pred cCCCeeEEEecC----CcceEEecchhhehhHhHHHHHHHhhcCCCccccchH
Confidence 335679999977 456789999998 999999998777889999999874
No 60
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.08 E-value=0.0032 Score=73.54 Aligned_cols=82 Identities=22% Similarity=0.546 Sum_probs=57.4
Q ss_pred ccCCcccccccccccCC---CceEEcC-CCCccchhhHHHHH--hc-----CCCCCCCCcccc--cchhhhhhhHHHHhc
Q 000878 1116 CLETNCPICCDFLFTSS---ETVRALP-CGHYMHLACFQAYT--CS-----HYTCPICSKSLG--DMAIYFGMIDALLAA 1182 (1241)
Q Consensus 1116 ~~~~~CpICle~lf~s~---~~~~~lp-CgH~fH~~C~~~wl--~~-----~~~CPiCrk~~~--dm~~~~~~lD~~i~~ 1182 (1241)
+.+..|-||+|.+.... ....+|| |.|.|...|+..|- .+ ...||+||.+.- .-+.+|-.-.. +.
T Consensus 159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~~v~pS~~Wv~t~~--~k 236 (344)
T KOG1039|consen 159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSSFVNPSSFWVETKE--EK 236 (344)
T ss_pred cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccccccccceeeeecc--cc
Confidence 55779999999965433 1134555 99999999999997 33 478999998874 33445544333 67
Q ss_pred cCCCHhhhcccceEEcC
Q 000878 1183 EELPEEYRNQVQDILCN 1199 (1241)
Q Consensus 1183 ~~~P~ey~~~~~~i~Cn 1199 (1241)
+.++++|........|+
T Consensus 237 ~~li~e~~~~~s~~~c~ 253 (344)
T KOG1039|consen 237 QKLIEEYEAEMSAKDCK 253 (344)
T ss_pred cccHHHHHHHhhccchh
Confidence 88888887766554443
No 61
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=96.07 E-value=0.0068 Score=55.67 Aligned_cols=47 Identities=21% Similarity=0.386 Sum_probs=35.0
Q ss_pred CcccccccccccCCCceEEcCCCCccchhhHHHHHhc-CCCCCCCCcccccc
Q 000878 1119 TNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCS-HYTCPICSKSLGDM 1169 (1241)
Q Consensus 1119 ~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~~-~~~CPiCrk~~~dm 1169 (1241)
-.|||+.+-| .+ .+++|+||+|-..|+..|+.. +.+||+|+..+...
T Consensus 5 f~CpIt~~lM---~d-PVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~ 52 (73)
T PF04564_consen 5 FLCPITGELM---RD-PVILPSGHTYERSAIERWLEQNGGTDPFTRQPLSES 52 (73)
T ss_dssp GB-TTTSSB----SS-EEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SGG
T ss_pred cCCcCcCcHh---hC-ceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCcc
Confidence 4699999886 23 346899999999999999987 89999999887643
No 62
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=95.76 E-value=0.0038 Score=78.14 Aligned_cols=52 Identities=21% Similarity=0.548 Sum_probs=37.9
Q ss_pred cccCCcccccccccc--cCCCceEE-cCCCCccchhhHHHHHh--cCCCCCCCCccc
Q 000878 1115 KCLETNCPICCDFLF--TSSETVRA-LPCGHYMHLACFQAYTC--SHYTCPICSKSL 1166 (1241)
Q Consensus 1115 ~~~~~~CpICle~lf--~s~~~~~~-lpCgH~fH~~C~~~wl~--~~~~CPiCrk~~ 1166 (1241)
=++...||||+.-|. +..-|... ..|.|.||..|+.+|.+ .+.+||+||..+
T Consensus 1466 fsG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRsei 1522 (1525)
T COG5219 1466 FSGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEI 1522 (1525)
T ss_pred cCCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCcccccc
Confidence 356788999997753 12222222 34889999999999984 468999999665
No 63
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=95.63 E-value=0.0064 Score=67.97 Aligned_cols=44 Identities=23% Similarity=0.541 Sum_probs=37.0
Q ss_pred CcccccccccccCCCceEEcCCCCccchhhHHHHHhcCCCCCCCCccc
Q 000878 1119 TNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSL 1166 (1241)
Q Consensus 1119 ~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~~~~~CPiCrk~~ 1166 (1241)
.-|-||.+++ . .....+|||+|..-||..++..+..||+||.+.
T Consensus 26 lrC~IC~~~i-~---ip~~TtCgHtFCslCIR~hL~~qp~CP~Cr~~~ 69 (391)
T COG5432 26 LRCRICDCRI-S---IPCETTCGHTFCSLCIRRHLGTQPFCPVCREDP 69 (391)
T ss_pred HHhhhhhhee-e---cceecccccchhHHHHHHHhcCCCCCccccccH
Confidence 3599999993 2 224568999999999999999999999999875
No 64
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=95.57 E-value=0.0037 Score=72.19 Aligned_cols=61 Identities=34% Similarity=0.750 Sum_probs=47.1
Q ss_pred cccccccccCCcccccccccccCCCceEEcCCCCccchhhHHHHHhcC--CCCCCCCcccccch
Q 000878 1109 NHKCLEKCLETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSH--YTCPICSKSLGDMA 1170 (1241)
Q Consensus 1109 ~H~C~e~~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~~~--~~CPiCrk~~~dm~ 1170 (1241)
.|.|++. ++-+|-.|.|.+=...+.+..|||.|.||..|+.+++.++ .+||-|||-...|.
T Consensus 357 a~~~~~e-~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~CrklrSs~~ 419 (518)
T KOG1941|consen 357 AHECVEE-TELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRKLRSSMK 419 (518)
T ss_pred HHHHHHH-HhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHHHHhhcc
Confidence 4556543 5678999999954455577889999999999999999665 77999996554443
No 65
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=95.34 E-value=0.008 Score=53.79 Aligned_cols=43 Identities=30% Similarity=0.680 Sum_probs=22.4
Q ss_pred cccccccccccCCCceEEcCCCCccchhhHHHHHhcCCCCCCCCcccc
Q 000878 1120 NCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSLG 1167 (1241)
Q Consensus 1120 ~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~~~~~CPiCrk~~~ 1167 (1241)
-|++|.+.| +.++....|.|.|...|+..-+ .+.||+|+.+.-
T Consensus 9 rCs~C~~~l---~~pv~l~~CeH~fCs~Ci~~~~--~~~CPvC~~Paw 51 (65)
T PF14835_consen 9 RCSICFDIL---KEPVCLGGCEHIFCSSCIRDCI--GSECPVCHTPAW 51 (65)
T ss_dssp S-SSS-S-----SS-B---SSS--B-TTTGGGGT--TTB-SSS--B-S
T ss_pred CCcHHHHHh---cCCceeccCccHHHHHHhHHhc--CCCCCCcCChHH
Confidence 499999885 5567778899999999998754 356999998874
No 66
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=94.55 E-value=0.012 Score=68.30 Aligned_cols=53 Identities=28% Similarity=0.667 Sum_probs=44.0
Q ss_pred cccccccCCcccccccccccCCCceEEcCCCCccchhhHHHHHh-c-CCCCCCCCcccc
Q 000878 1111 KCLEKCLETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTC-S-HYTCPICSKSLG 1167 (1241)
Q Consensus 1111 ~C~e~~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~-~-~~~CPiCrk~~~ 1167 (1241)
.|.-.++-.-|-||-|. .+.+++=||||.++..|+..|.. . ..+||.||-.|-
T Consensus 362 YceMgsTFeLCKICaen----dKdvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIK 416 (563)
T KOG1785|consen 362 YCEMGSTFELCKICAEN----DKDVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIK 416 (563)
T ss_pred HHHccchHHHHHHhhcc----CCCcccccccchHHHHHHHhhcccCCCCCCCceeeEec
Confidence 35556667789999977 67789999999999999999973 3 689999998873
No 67
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.46 E-value=0.024 Score=66.31 Aligned_cols=48 Identities=33% Similarity=0.812 Sum_probs=37.8
Q ss_pred CcccccccccccCCC-ceEEcCCCCccchhhHHHHHhc--CCCCCCCCccc
Q 000878 1119 TNCPICCDFLFTSSE-TVRALPCGHYMHLACFQAYTCS--HYTCPICSKSL 1166 (1241)
Q Consensus 1119 ~~CpICle~lf~s~~-~~~~lpCgH~fH~~C~~~wl~~--~~~CPiCrk~~ 1166 (1241)
.+||||++..-.+++ -+..+.|||.|=.+|+..|+-. ...||.|....
T Consensus 5 ~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~ka 55 (463)
T KOG1645|consen 5 TTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKA 55 (463)
T ss_pred ccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChh
Confidence 579999998655555 3455779999999999999943 47799998543
No 68
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.46 E-value=0.03 Score=62.73 Aligned_cols=51 Identities=24% Similarity=0.656 Sum_probs=42.2
Q ss_pred cCCcccccccccccCCCceEEcCCCCccchhhHHHHHh--cCCCCCCCCcccccch
Q 000878 1117 LETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTC--SHYTCPICSKSLGDMA 1170 (1241)
Q Consensus 1117 ~~~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~--~~~~CPiCrk~~~dm~ 1170 (1241)
...+||+|.++ +.-|..+.+|||.|.--|+..=.. ...+||.|+.++..|.
T Consensus 238 ~~~~C~~Cg~~---PtiP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~~lq 290 (298)
T KOG2879|consen 238 SDTECPVCGEP---PTIPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVEPLQ 290 (298)
T ss_pred CCceeeccCCC---CCCCeeeccccceeehhhhhhhhcchhhcccCccCCCCcchh
Confidence 35789999998 777888899999999999987543 4589999998876554
No 69
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=94.20 E-value=0.016 Score=65.39 Aligned_cols=53 Identities=32% Similarity=0.710 Sum_probs=43.4
Q ss_pred cccCCcccccccccccCCCceEEcCCCCccchhhHHHHHh-----------------------cCCCCCCCCccccc
Q 000878 1115 KCLETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTC-----------------------SHYTCPICSKSLGD 1168 (1241)
Q Consensus 1115 ~~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~-----------------------~~~~CPiCrk~~~d 1168 (1241)
+--.+.|.||+-- |.+.......+|-|+||..|+..|+. ..-.|||||..|.+
T Consensus 112 n~p~gqCvICLyg-fa~~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~ 187 (368)
T KOG4445|consen 112 NHPNGQCVICLYG-FASSPAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKI 187 (368)
T ss_pred CCCCCceEEEEEe-ecCCCceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccc
Confidence 3346789999988 88888889999999999999988862 12459999998864
No 70
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=94.02 E-value=0.017 Score=72.46 Aligned_cols=46 Identities=24% Similarity=0.585 Sum_probs=37.3
Q ss_pred CcccccccccccCCCceEEcCCCCccchhhHHHHHh-cCCCCCCCCccccc
Q 000878 1119 TNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTC-SHYTCPICSKSLGD 1168 (1241)
Q Consensus 1119 ~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~-~~~~CPiCrk~~~d 1168 (1241)
-.||+|-.. .+.+.+..|||.|+..|+..... ...+||.|+..++.
T Consensus 644 LkCs~Cn~R----~Kd~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFga 690 (698)
T KOG0978|consen 644 LKCSVCNTR----WKDAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGA 690 (698)
T ss_pred eeCCCccCc----hhhHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCc
Confidence 459999855 45567778999999999999774 45889999999764
No 71
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=93.53 E-value=0.054 Score=46.11 Aligned_cols=45 Identities=22% Similarity=0.562 Sum_probs=24.7
Q ss_pred ccccccccccCCCceEEcCCCCccchhhHHHHHh-cCCCCCCCCcc
Q 000878 1121 CPICCDFLFTSSETVRALPCGHYMHLACFQAYTC-SHYTCPICSKS 1165 (1241)
Q Consensus 1121 CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~-~~~~CPiCrk~ 1165 (1241)
||+|.++|..++....-=+||+-+...|+..-+. .+..||-||++
T Consensus 1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~ 46 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILENEGGRCPGCREP 46 (48)
T ss_dssp -TTTS-B--CCCTT--SSTTS----HHHHHHHTTSS-SB-TTT--B
T ss_pred CCCcccccccCCCccccCcCCCcHHHHHHHHHHhccCCCCCCCCCC
Confidence 8999999744444444446899999999999886 57999999976
No 72
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.45 E-value=0.017 Score=66.59 Aligned_cols=47 Identities=30% Similarity=0.673 Sum_probs=36.9
Q ss_pred CCcccccccccccCCCceEEcCCCCccchhhHHHHH-hcCCCCCCCCcccc
Q 000878 1118 ETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYT-CSHYTCPICSKSLG 1167 (1241)
Q Consensus 1118 ~~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl-~~~~~CPiCrk~~~ 1167 (1241)
+-.||||++-| + .......|+|-|..+||..-+ ..+..||.|||.+.
T Consensus 43 ~v~c~icl~ll-k--~tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~ 90 (381)
T KOG0311|consen 43 QVICPICLSLL-K--KTMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLV 90 (381)
T ss_pred hhccHHHHHHH-H--hhcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhcc
Confidence 45699999875 2 223456799999999998755 67899999999985
No 73
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=93.31 E-value=0.0096 Score=69.94 Aligned_cols=71 Identities=31% Similarity=0.773 Sum_probs=40.4
Q ss_pred CCccc--CCCCCccccCCCCCccccccCC---cccccccccccccccccccCCcccccccccccCCCceEEc-CCCCccc
Q 000878 1072 RTVYH--CPFCNLCRVGGGLGVDFFHCMT---CNCCLGLKLLNHKCLEKCLETNCPICCDFLFTSSETVRAL-PCGHYMH 1145 (1241)
Q Consensus 1072 k~~yH--C~~CgiCRvg~~l~~~~fhC~~---C~~C~s~~l~~H~C~e~~~~~~CpICle~lf~s~~~~~~l-pCgH~fH 1145 (1241)
+.+|| |=.|+.||.-.. |..||.-+. |--|+--++ ..|..|.+.+.+ ++| .||-.||
T Consensus 295 ~~~fHv~CFtC~~C~r~L~-Gq~FY~v~~k~~CE~cyq~tl-----------ekC~~Cg~~I~d-----~iLrA~GkayH 357 (468)
T KOG1701|consen 295 DQLFHVQCFTCRTCRRQLA-GQSFYQVDGKPYCEGCYQDTL-----------EKCNKCGEPIMD-----RILRALGKAYH 357 (468)
T ss_pred hhhhcccceehHhhhhhhc-cccccccCCcccchHHHHHHH-----------HHHhhhhhHHHH-----HHHHhcccccC
Confidence 45666 667777776654 566665443 222332221 237777766321 233 3777788
Q ss_pred hhhHHHHHhcCCCCCCCCcccc
Q 000878 1146 LACFQAYTCSHYTCPICSKSLG 1167 (1241)
Q Consensus 1146 ~~C~~~wl~~~~~CPiCrk~~~ 1167 (1241)
..|| +|=+|.+.+.
T Consensus 358 p~CF--------~Cv~C~r~ld 371 (468)
T KOG1701|consen 358 PGCF--------TCVVCARCLD 371 (468)
T ss_pred CCce--------EEEEeccccC
Confidence 8777 6667777664
No 74
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.96 E-value=0.05 Score=61.77 Aligned_cols=47 Identities=23% Similarity=0.529 Sum_probs=37.6
Q ss_pred cCCcccccccccccCCCceEEcCCCCccchhhHHH-HHhcCCCCCCCCcccc
Q 000878 1117 LETNCPICCDFLFTSSETVRALPCGHYMHLACFQA-YTCSHYTCPICSKSLG 1167 (1241)
Q Consensus 1117 ~~~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~-wl~~~~~CPiCrk~~~ 1167 (1241)
+...|+||+... ..+ ..|+|+|.|...|++. +.....+||+||.+|.
T Consensus 6 ~~~eC~IC~nt~---n~P-v~l~C~HkFCyiCiKGsy~ndk~~CavCR~pid 53 (324)
T KOG0824|consen 6 KKKECLICYNTG---NCP-VNLYCFHKFCYICIKGSYKNDKKTCAVCRFPID 53 (324)
T ss_pred cCCcceeeeccC---CcC-ccccccchhhhhhhcchhhcCCCCCceecCCCC
Confidence 467899999773 444 6799999999999987 4445678999999984
No 75
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=92.95 E-value=0.053 Score=64.97 Aligned_cols=107 Identities=26% Similarity=0.488 Sum_probs=65.3
Q ss_pred CCcccccccccccCCCceEEcCCCCccchhhHHHHHhcCCCCCCCCcccccchhhhhhhHHHHhccCCCHhhhcccceEE
Q 000878 1118 ETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSLGDMAIYFGMIDALLAAEELPEEYRNQVQDIL 1197 (1241)
Q Consensus 1118 ~~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~~~~~CPiCrk~~~dm~~~~~~lD~~i~~~~~P~ey~~~~~~i~ 1197 (1241)
+..||+|...+ .+++....|||.|...|+..|+..+..||.|+..+..-..+. ....+..++.++ .|.
T Consensus 21 ~l~C~~C~~vl---~~p~~~~~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~~~~-------~~~~~~~~~~~l--~i~ 88 (391)
T KOG0297|consen 21 NLLCPICMSVL---RDPVQTTTCGHRFCAGCLLESLSNHQKCPVCRQELTQAEELP-------VPRALRRELLKL--PIR 88 (391)
T ss_pred cccCccccccc---cCCCCCCCCCCcccccccchhhccCcCCcccccccchhhccC-------chHHHHHHHHhc--ccc
Confidence 46799999873 455555789999999999999988999999998865443332 011111222222 245
Q ss_pred c----CCCCCCC---Cccchhh---cccCCC-CCCccccccccCCCCCCC
Q 000878 1198 C----NDCEQKG---AARFHWL---YHKCGF-CGSYNTRLIKNDTTVSNS 1236 (1241)
Q Consensus 1198 C----nDC~~~s---~~~fh~l---g~kC~~-CgsYNT~~~~~~~~~~~~ 1236 (1241)
| -+|..+. ...-|.- ..+|++ |+--+-+....+....+|
T Consensus 89 c~~~~~GC~~~~~l~~~~~Hl~~c~~~~C~~~C~~~~~~~d~~~hl~~~C 138 (391)
T KOG0297|consen 89 CIFASRGCRADLELEALQGHLSTCDPLKCPHRCGVQVPRDDLEDHLEAEC 138 (391)
T ss_pred cccCCCCccccccHHHHHhHhccCCcccCccccccccchHHHHHHHhccc
Confidence 5 3555443 2334432 357877 876655554433333344
No 76
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.79 E-value=0.095 Score=57.10 Aligned_cols=51 Identities=31% Similarity=0.693 Sum_probs=40.9
Q ss_pred ccCCcccccccccccCCCceEEcCCCCccchhhHHHHHh--------cCCCCCCCCccccc
Q 000878 1116 CLETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTC--------SHYTCPICSKSLGD 1168 (1241)
Q Consensus 1116 ~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~--------~~~~CPiCrk~~~d 1168 (1241)
....||-.|.-.| .+++. ..|-|-|.||..|+++|.. ..|+||-|+..|+.
T Consensus 48 DY~pNC~LC~t~L-a~gdt-~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFP 106 (299)
T KOG3970|consen 48 DYNPNCRLCNTPL-ASGDT-TRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFP 106 (299)
T ss_pred CCCCCCceeCCcc-ccCcc-eeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCC
Confidence 3467899999994 55554 4477999999999999963 35999999999964
No 77
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=92.51 E-value=0.082 Score=46.63 Aligned_cols=41 Identities=24% Similarity=0.603 Sum_probs=29.6
Q ss_pred CCcccccccccccCCCceEEcCCCCccchhhHHHHHh--cCCCCCC
Q 000878 1118 ETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTC--SHYTCPI 1161 (1241)
Q Consensus 1118 ~~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~--~~~~CPi 1161 (1241)
...|||.+..| .+|++-..|||+|=...+.+|++ ....||+
T Consensus 11 ~~~CPiT~~~~---~~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv 53 (57)
T PF11789_consen 11 SLKCPITLQPF---EDPVKSKKCGHTFEKEAILQYIQRNGSKRCPV 53 (57)
T ss_dssp -SB-TTTSSB----SSEEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred ccCCCCcCChh---hCCcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence 46799999984 46888889999999999999993 4577998
No 78
>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=92.50 E-value=0.061 Score=52.03 Aligned_cols=38 Identities=26% Similarity=0.658 Sum_probs=30.0
Q ss_pred cccccccCCcccccccccccCCCceEEcCCCCccchhhHH
Q 000878 1111 KCLEKCLETNCPICCDFLFTSSETVRALPCGHYMHLACFQ 1150 (1241)
Q Consensus 1111 ~C~e~~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~ 1150 (1241)
.++.-.....|++|...|+. ....+.||||.+|..|++
T Consensus 71 ~~v~i~~~~~C~vC~k~l~~--~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 71 RSVVITESTKCSVCGKPLGN--SVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred ceEEECCCCCccCcCCcCCC--ceEEEeCCCeEEeccccc
Confidence 44555557789999999654 567788999999999974
No 79
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=91.75 E-value=0.12 Score=43.78 Aligned_cols=40 Identities=28% Similarity=0.756 Sum_probs=26.6
Q ss_pred ccccccccccCCCceEEcCCC-----CccchhhHHHHHh--cCCCCCCC
Q 000878 1121 CPICCDFLFTSSETVRALPCG-----HYMHLACFQAYTC--SHYTCPIC 1162 (1241)
Q Consensus 1121 CpICle~lf~s~~~~~~lpCg-----H~fH~~C~~~wl~--~~~~CPiC 1162 (1241)
|=||++.- +.....+.||+ -+.|..|+..|+. .+.+|++|
T Consensus 1 CrIC~~~~--~~~~~li~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C 47 (47)
T PF12906_consen 1 CRICLEGE--EEDEPLISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC 47 (47)
T ss_dssp ETTTTEE---SSSS-EE-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred CeEeCCcC--CCCCceecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence 66899882 22235667875 4789999999984 56889998
No 80
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.61 E-value=0.13 Score=54.39 Aligned_cols=30 Identities=27% Similarity=0.773 Sum_probs=25.2
Q ss_pred cCCCCccchhhHHHHHhc------C-----CCCCCCCcccc
Q 000878 1138 LPCGHYMHLACFQAYTCS------H-----YTCPICSKSLG 1167 (1241)
Q Consensus 1138 lpCgH~fH~~C~~~wl~~------~-----~~CPiCrk~~~ 1167 (1241)
..||-.||.-|+..|++. + ..||.|++++.
T Consensus 188 ~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~Pia 228 (234)
T KOG3268|consen 188 IQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIA 228 (234)
T ss_pred cccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcce
Confidence 569999999999999842 1 67999999974
No 81
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=91.53 E-value=0.15 Score=56.41 Aligned_cols=57 Identities=23% Similarity=0.434 Sum_probs=48.9
Q ss_pred cccccCCcccccccccccCCCceEEc-CCCCccchhhHHHHHhcCCCCCCCCcccccch
Q 000878 1113 LEKCLETNCPICCDFLFTSSETVRAL-PCGHYMHLACFQAYTCSHYTCPICSKSLGDMA 1170 (1241)
Q Consensus 1113 ~e~~~~~~CpICle~lf~s~~~~~~l-pCgH~fH~~C~~~wl~~~~~CPiCrk~~~dm~ 1170 (1241)
+..+....||||.+. .++..+..+| ||||.+-..|...++.....||+|.+++-+.+
T Consensus 216 ~a~s~ryiCpvtrd~-LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdrd 273 (303)
T KOG3039|consen 216 IAASKRYICPVTRDT-LTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDRD 273 (303)
T ss_pred hhhccceecccchhh-hcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCcccc
Confidence 334457889999999 5888888887 79999999999999999999999999987654
No 82
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=90.46 E-value=0.16 Score=63.30 Aligned_cols=41 Identities=24% Similarity=0.488 Sum_probs=30.5
Q ss_pred CcccccccccccCCCceEEcCCCCccchhhHHHHHhcCCCCCC
Q 000878 1119 TNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPI 1161 (1241)
Q Consensus 1119 ~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~~~~~CPi 1161 (1241)
-.|.||.-.+-. .....+.|||.+|.+|+.+|.+....||.
T Consensus 1029 ~~C~~C~l~V~g--ss~~Cg~C~Hv~H~sc~~eWf~~gd~Cps 1069 (1081)
T KOG0309|consen 1029 FQCAICHLAVRG--SSNFCGTCGHVGHTSCMMEWFRTGDVCPS 1069 (1081)
T ss_pred eeeeeEeeEeec--cchhhccccccccHHHHHHHHhcCCcCCC
Confidence 347777655322 22345679999999999999999889984
No 83
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=90.01 E-value=0.15 Score=58.38 Aligned_cols=56 Identities=20% Similarity=0.552 Sum_probs=42.9
Q ss_pred CcccccccccccCCCceEEcCCCCccchhhHHHHHh-cCCCCCCCCcccccchhhhh
Q 000878 1119 TNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTC-SHYTCPICSKSLGDMAIYFG 1174 (1241)
Q Consensus 1119 ~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~-~~~~CPiCrk~~~dm~~~~~ 1174 (1241)
+-||.|+|+|--+++...--|||.-++.-|+...-. -+.+||-||+-..+-...|.
T Consensus 15 d~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~denv~~~ 71 (480)
T COG5175 15 DYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDENVRYV 71 (480)
T ss_pred ccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhccccceeEE
Confidence 349999999866666666678999999999877643 47899999998765544443
No 84
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=89.77 E-value=0.17 Score=54.30 Aligned_cols=44 Identities=25% Similarity=0.446 Sum_probs=36.7
Q ss_pred cccccccccccCCCceEEcCCCCccchhhHHHHHhcCCCCCCCCcccc
Q 000878 1120 NCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSLG 1167 (1241)
Q Consensus 1120 ~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~~~~~CPiCrk~~~ 1167 (1241)
.|-||.++ |.+. ++..|||.|...|+-.-.+...+|-+|.+...
T Consensus 198 ~C~iCKkd-y~sp---vvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~ 241 (259)
T COG5152 198 LCGICKKD-YESP---VVTECGHSFCSLCAIRKYQKGDECGVCGKATY 241 (259)
T ss_pred eehhchhh-ccch---hhhhcchhHHHHHHHHHhccCCcceecchhhc
Confidence 59999999 6654 55679999999998877778889999998764
No 85
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=89.36 E-value=0.11 Score=57.50 Aligned_cols=145 Identities=26% Similarity=0.524 Sum_probs=82.4
Q ss_pred CCccccccccccccccCC--------------------cccCchhhcccCCCCCCcccccceeccccccccccCCCCCCC
Q 000878 991 GCEHYKRNCKIRAACCGK--------------------LFTCRFCHDKASDHSMDRKATSEMMCMHCLKIQAIGPNCTTP 1050 (1241)
Q Consensus 991 gC~HY~r~ckl~~pcC~k--------------------~y~Cr~CHde~~~H~~~r~~~~~~~C~~C~~~q~~~~~C~~~ 1050 (1241)
=|+|=- =-|.+|||+| -|.|.+|.....|--+-|.+ .+.+|-.|+..-.+
T Consensus 63 YCEhDF--~~LfaPcC~kC~EFiiGrVikamnnSwHp~CF~Cd~Cn~~Lad~gf~rnq-gr~LC~~Cn~k~Ka------- 132 (332)
T KOG2272|consen 63 YCEHDF--HVLFAPCCGKCGEFIIGRVIKAMNNSWHPACFRCDLCNKHLADQGFYRNQ-GRALCRECNQKEKA------- 132 (332)
T ss_pred cccccc--hhhhchhhcccccchhhHHHHhhccccCcccchhHHHHHHHhhhhhHhhc-chHHhhhhhhhhcc-------
Confidence 477632 1377888876 36788887777776666654 47888888755322
Q ss_pred CCCCCcceeEeccccccc-cCC-----CCcccCCCCCccccCCCCCccccccCCcccccccccccccccccccCCccccc
Q 000878 1051 SCNGLSMAKYYCNICKFF-DDE-----RTVYHCPFCNLCRVGGGLGVDFFHCMTCNCCLGLKLLNHKCLEKCLETNCPIC 1124 (1241)
Q Consensus 1051 ~Cc~~~~a~y~C~~C~~~-d~~-----k~~yHC~~CgiCRvg~~l~~~~fhC~~C~~C~s~~l~~H~C~e~~~~~~CpIC 1124 (1241)
.--|+|-|.+|+-. |++ -++|| -..|.|.+||-=+...- .|-..+--|+-|
T Consensus 133 ----~~~g~YvC~KCh~~iD~~~l~fr~d~yH--------------~yHFkCt~C~keL~sda-----Revk~eLyClrC 189 (332)
T KOG2272|consen 133 ----KGRGRYVCQKCHAHIDEQPLTFRGDPYH--------------PYHFKCTTCGKELTSDA-----REVKGELYCLRC 189 (332)
T ss_pred ----cccceeehhhhhhhcccccccccCCCCC--------------ccceecccccccccchh-----hhhccceecccc
Confidence 23689999999964 555 56777 35688999987664321 111223334444
Q ss_pred ccccccCCCceEEcCCCCccchhhHH----HHHhcCCCCCCCCcccccchhh
Q 000878 1125 CDFLFTSSETVRALPCGHYMHLACFQ----AYTCSHYTCPICSKSLGDMAIY 1172 (1241)
Q Consensus 1125 le~lf~s~~~~~~lpCgH~fH~~C~~----~wl~~~~~CPiCrk~~~dm~~~ 1172 (1241)
.+.| . .+ +...|.-.+-..=+. .|--.++.|-.|-|+.+--..|
T Consensus 190 hD~m-g--ip-iCgaC~rpIeervi~amgKhWHveHFvCa~CekPFlGHrHY 237 (332)
T KOG2272|consen 190 HDKM-G--IP-ICGACRRPIEERVIFAMGKHWHVEHFVCAKCEKPFLGHRHY 237 (332)
T ss_pred cccc-C--Cc-ccccccCchHHHHHHHhccccchhheeehhcCCcccchhhh
Confidence 4432 0 00 001111111111121 2333578888898887655544
No 86
>KOG3800 consensus Predicted E3 ubiquitin ligase containing RING finger, subunit of transcription/repair factor TFIIH and CDK-activating kinase assembly factor [Posttranslational modification, protein turnover, chaperones]
Probab=89.27 E-value=0.26 Score=55.96 Aligned_cols=48 Identities=23% Similarity=0.522 Sum_probs=39.4
Q ss_pred cccccccccccCCC-ceEEcCCCCccchhhHHHHH-hcCCCCCCCCcccc
Q 000878 1120 NCPICCDFLFTSSE-TVRALPCGHYMHLACFQAYT-CSHYTCPICSKSLG 1167 (1241)
Q Consensus 1120 ~CpICle~lf~s~~-~~~~lpCgH~fH~~C~~~wl-~~~~~CPiCrk~~~ 1167 (1241)
.||+|..+.|.+.. ..++-||||.+..+|++... .+.+.||.|.+.+.
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iLR 51 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGPAQCPECMVILR 51 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHhcCCCCCCcccchhh
Confidence 59999998877766 34445899999999999965 56799999998874
No 87
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=89.24 E-value=0.16 Score=56.47 Aligned_cols=36 Identities=33% Similarity=0.701 Sum_probs=29.0
Q ss_pred ccCCCceEEcCCCCccchhhHHHHHhcCCCCCCCCccc
Q 000878 1129 FTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSL 1166 (1241)
Q Consensus 1129 f~s~~~~~~lpCgH~fH~~C~~~wl~~~~~CPiCrk~~ 1166 (1241)
|.+..+.....|+|.|...|...- ....||+|++++
T Consensus 12 ~~~~~~f~LTaC~HvfC~~C~k~~--~~~~C~lCkk~i 47 (233)
T KOG4739|consen 12 FPSQDPFFLTACRHVFCEPCLKAS--SPDVCPLCKKSI 47 (233)
T ss_pred cCCCCceeeeechhhhhhhhcccC--Ccccccccccee
Confidence 566677788899999999998653 234899999997
No 88
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=89.09 E-value=0.18 Score=44.09 Aligned_cols=43 Identities=28% Similarity=0.693 Sum_probs=30.4
Q ss_pred CcccccccccccCCCceEEcCCCCccchhhHHHHHhcCCCCCCCCcccc
Q 000878 1119 TNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSLG 1167 (1241)
Q Consensus 1119 ~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~~~~~CPiCrk~~~ 1167 (1241)
..|-.|... +..-.++||||.+-..|++-+ .-+-||+|.+.+.
T Consensus 8 ~~~~~~~~~----~~~~~~~pCgH~I~~~~f~~~--rYngCPfC~~~~~ 50 (55)
T PF14447_consen 8 QPCVFCGFV----GTKGTVLPCGHLICDNCFPGE--RYNGCPFCGTPFE 50 (55)
T ss_pred eeEEEcccc----ccccccccccceeeccccChh--hccCCCCCCCccc
Confidence 445555533 334567999999999998765 3345999998864
No 89
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=89.00 E-value=0.16 Score=61.04 Aligned_cols=52 Identities=29% Similarity=0.568 Sum_probs=42.6
Q ss_pred ccccccCCcccccccccccCCCceEEcCCCCccchhhHHHHH-----hcCCCCCCCCcccc
Q 000878 1112 CLEKCLETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYT-----CSHYTCPICSKSLG 1167 (1241)
Q Consensus 1112 C~e~~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl-----~~~~~CPiCrk~~~ 1167 (1241)
=.|+..+..|-+|.++ .+.+....|.|.|+.-|+.+|. ..+.+||+|...+.
T Consensus 530 ~~enk~~~~C~lc~d~----aed~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~Ls 586 (791)
T KOG1002|consen 530 PDENKGEVECGLCHDP----AEDYIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLS 586 (791)
T ss_pred CccccCceeecccCCh----hhhhHhhhhhHHHHHHHHHHHHHhhhcccCCCCcccccccc
Confidence 3467778899999988 4456778899999999999996 34689999998873
No 90
>PF04641 Rtf2: Rtf2 RING-finger
Probab=88.78 E-value=0.34 Score=55.08 Aligned_cols=51 Identities=22% Similarity=0.490 Sum_probs=41.0
Q ss_pred cccCCcccccccccccCCCceEEc-CCCCccchhhHHHHHhcCCCCCCCCcccc
Q 000878 1115 KCLETNCPICCDFLFTSSETVRAL-PCGHYMHLACFQAYTCSHYTCPICSKSLG 1167 (1241)
Q Consensus 1115 ~~~~~~CpICle~lf~s~~~~~~l-pCgH~fH~~C~~~wl~~~~~CPiCrk~~~ 1167 (1241)
......|||.... |++.....+| ||||.|-..++.+.- ....||+|.+++.
T Consensus 110 ~~~~~~CPvt~~~-~~~~~~fv~l~~cG~V~s~~alke~k-~~~~Cp~c~~~f~ 161 (260)
T PF04641_consen 110 SEGRFICPVTGKE-FNGKHKFVYLRPCGCVFSEKALKELK-KSKKCPVCGKPFT 161 (260)
T ss_pred CCceeECCCCCcc-cCCceeEEEEcCCCCEeeHHHHHhhc-ccccccccCCccc
Confidence 3456679999999 5666666665 899999999999984 4678999999974
No 91
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.75 E-value=0.11 Score=58.76 Aligned_cols=47 Identities=28% Similarity=0.609 Sum_probs=33.0
Q ss_pred CCcccccccccccCCCceEEcCCCCcc-chhhHHHHHhcCCCCCCCCcccccchhh
Q 000878 1118 ETNCPICCDFLFTSSETVRALPCGHYM-HLACFQAYTCSHYTCPICSKSLGDMAIY 1172 (1241)
Q Consensus 1118 ~~~CpICle~lf~s~~~~~~lpCgH~f-H~~C~~~wl~~~~~CPiCrk~~~dm~~~ 1172 (1241)
+..|.||++- ......|+|||.. ...|-..+ ..|||||+-|...-..
T Consensus 300 ~~LC~ICmDa----P~DCvfLeCGHmVtCt~CGkrm----~eCPICRqyi~rvvri 347 (350)
T KOG4275|consen 300 RRLCAICMDA----PRDCVFLECGHMVTCTKCGKRM----NECPICRQYIVRVVRI 347 (350)
T ss_pred HHHHHHHhcC----CcceEEeecCcEEeehhhcccc----ccCchHHHHHHHHHhh
Confidence 7789999976 5668999999974 33443222 3899999876544433
No 92
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.14 E-value=0.34 Score=56.57 Aligned_cols=47 Identities=26% Similarity=0.574 Sum_probs=34.2
Q ss_pred ccccCCcccccccccccCCCceEEcCCCCccchhhHHHHHhcCCCCCCCCcccc
Q 000878 1114 EKCLETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSLG 1167 (1241)
Q Consensus 1114 e~~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~~~~~CPiCrk~~~ 1167 (1241)
+.....+|.||++. ......+||||.-. |..-. +...+||+||..|-
T Consensus 301 ~~~~p~lcVVcl~e----~~~~~fvpcGh~cc--ct~cs-~~l~~CPvCR~rI~ 347 (355)
T KOG1571|consen 301 ELPQPDLCVVCLDE----PKSAVFVPCGHVCC--CTLCS-KHLPQCPVCRQRIR 347 (355)
T ss_pred ccCCCCceEEecCC----ccceeeecCCcEEE--chHHH-hhCCCCchhHHHHH
Confidence 45567899999988 33478999999954 55433 34466999998763
No 93
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=86.85 E-value=0.35 Score=61.93 Aligned_cols=43 Identities=21% Similarity=0.474 Sum_probs=32.4
Q ss_pred cccccccccCCcccccccccccCCCceEEcCCCCccchhhHHHHH
Q 000878 1109 NHKCLEKCLETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYT 1153 (1241)
Q Consensus 1109 ~H~C~e~~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl 1153 (1241)
.|.|.--.....|-+|.-+|+. ++-.+.||||.||.+|+..-.
T Consensus 808 ~~ry~v~ep~d~C~~C~~~ll~--~pF~vf~CgH~FH~~Cl~~~v 850 (911)
T KOG2034|consen 808 RQRYRVLEPQDSCDHCGRPLLI--KPFYVFPCGHCFHRDCLIRHV 850 (911)
T ss_pred hcceEEecCccchHHhcchhhc--CcceeeeccchHHHHHHHHHH
Confidence 4445444456789999999643 467778999999999997754
No 94
>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=86.81 E-value=0.35 Score=49.59 Aligned_cols=42 Identities=19% Similarity=0.370 Sum_probs=33.5
Q ss_pred CCcccccccccccCCCceEEcCCC------CccchhhHHHHHhcCCCCC
Q 000878 1118 ETNCPICCDFLFTSSETVRALPCG------HYMHLACFQAYTCSHYTCP 1160 (1241)
Q Consensus 1118 ~~~CpICle~lf~s~~~~~~lpCg------H~fH~~C~~~wl~~~~~CP 1160 (1241)
...|.||++.+-. ...++.++|| |.||.+|+..|.+.+.+=|
T Consensus 26 ~~EC~IC~~~I~~-~~GvV~vt~~g~lnLEkmfc~~C~~rw~~~~~rDP 73 (134)
T PF05883_consen 26 TVECQICFDRIDN-NDGVVYVTDGGTLNLEKMFCADCDKRWRRERNRDP 73 (134)
T ss_pred Ceeehhhhhhhhc-CCCEEEEecCCeehHHHHHHHHHHHHHHhhccCCC
Confidence 4579999999644 6788999998 8899999999965544444
No 95
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=85.66 E-value=0.63 Score=58.61 Aligned_cols=74 Identities=23% Similarity=0.490 Sum_probs=50.0
Q ss_pred CCcccCCCCCccccCCCCCccccccCCcccccccccccccccccccCCcccccccccccCCCceEEcCCCCccchhhHHH
Q 000878 1072 RTVYHCPFCNLCRVGGGLGVDFFHCMTCNCCLGLKLLNHKCLEKCLETNCPICCDFLFTSSETVRALPCGHYMHLACFQA 1151 (1241)
Q Consensus 1072 k~~yHC~~CgiCRvg~~l~~~~fhC~~C~~C~s~~l~~H~C~e~~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~ 1151 (1241)
-=+|-|+.|+---+++++ .-|++|-.|-+. .|.+|-..+- +..+..--|||..|.+|+..
T Consensus 751 ~i~~~~~nc~a~~~~~~~----~~c~rc~s~a~~--------------~CtVC~~vi~--G~~~~c~~C~H~gH~sh~~s 810 (839)
T KOG0269|consen 751 TIHYACPNCDAPMVLTKL----WQCDRCESRASA--------------KCTVCDLVIR--GVDVWCQVCGHGGHDSHLKS 810 (839)
T ss_pred eeeccccccCCccccccc----eeechHHHHhhc--------------Cceeecceee--eeEeecccccccccHHHHHH
Confidence 346777777776676653 456666666553 4999987631 11122234999999999999
Q ss_pred HHhcCCCCCC--CCcc
Q 000878 1152 YTCSHYTCPI--CSKS 1165 (1241)
Q Consensus 1152 wl~~~~~CPi--Crk~ 1165 (1241)
|...+.-||. |.+.
T Consensus 811 w~~~~s~ca~~~C~~~ 826 (839)
T KOG0269|consen 811 WFFKASPCAKSICPHL 826 (839)
T ss_pred HHhcCCCCccccCCcc
Confidence 9988877876 5543
No 96
>PRK00808 hypothetical protein; Provisional
Probab=85.60 E-value=13 Score=38.94 Aligned_cols=112 Identities=14% Similarity=0.189 Sum_probs=75.4
Q ss_pred HHHHHHHHHHHHHHHhhhcCCChhhHHHHHHHHHHHHHHHHHHHhhhhhc----ccccccccccchhhhhHHhhhH-HHH
Q 000878 312 NAIRQELNEIAEESRKIQLSGDFTNLLAFNERLQFIAEVLIFHCIAEVNV----IFPAVDGASSFSQKHAEEESQF-NDF 386 (1241)
Q Consensus 312 kAIRkDh~el~~~~~kl~~~~d~~~l~~~~~r~qfL~el~r~HS~AEe~v----VyPALE~~~s~~~dh~~eeh~~-eei 386 (1241)
..|=.+|++|-+.++++..+........+...+.+|.+-.+.|=..||.+ -||.++ .|..+-..| .+|
T Consensus 15 ~~ID~qH~~L~~lin~l~~a~~~~~~~~i~~~l~~L~~y~~~HF~~EE~lM~~~~Yp~~~-------~H~~~H~~fl~~l 87 (150)
T PRK00808 15 DVIDQQHKRIVDYINHLHDAQDSPDRLAVAEVIDELIDYTLSHFAFEESLMEEAGYPFLV-------PHKRVHELFIKRV 87 (150)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCHH-------HHHHHHHHHHHHH
Confidence 44556777777777776432111123456677899999999999999955 599997 666543333 346
Q ss_pred HHHHHHHHhcCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHhccC
Q 000878 387 RLLIESIQNEGAISTSAEFYAKLCSHADQIMETIERHFHKVEVQVLPLARNHF 439 (1241)
Q Consensus 387 ~~LL~~lq~~~~~~~~~~f~~kL~~~l~~l~~~l~~Hi~eEE~E~lPll~k~f 439 (1241)
..+...+.. + . ..... .+..|..-+..||..+-....+.+++.-
T Consensus 88 ~~l~~~~~~-g--~---~~~~~---l~~~L~~WL~~HI~~~D~~~~~~l~~~~ 131 (150)
T PRK00808 88 EEYRERFQA-G--E---DVADE---LHGMLSRWLFNHIRNDDAAYVDAVKANM 131 (150)
T ss_pred HHHHHHHHc-c--c---hHHHH---HHHHHHHHHHHHHHHHhHHHHHHHHHhh
Confidence 666666652 1 1 12222 3456888899999999999999988863
No 97
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=84.84 E-value=0.46 Score=54.14 Aligned_cols=46 Identities=26% Similarity=0.554 Sum_probs=37.3
Q ss_pred CcccccccccccCCCceEEcCCCCccchhhHHHHHhcCCCCCCCCccccc
Q 000878 1119 TNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSLGD 1168 (1241)
Q Consensus 1119 ~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~~~~~CPiCrk~~~d 1168 (1241)
-.|-||..+ |.+. ++..|||+|...|...-++.+..|++|.+.+-.
T Consensus 242 f~c~icr~~-f~~p---Vvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g 287 (313)
T KOG1813|consen 242 FKCFICRKY-FYRP---VVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHG 287 (313)
T ss_pred ccccccccc-cccc---hhhcCCceeehhhhccccccCCcceeccccccc
Confidence 359999999 4433 557899999999998777778899999998743
No 98
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=84.78 E-value=0.54 Score=54.40 Aligned_cols=51 Identities=22% Similarity=0.455 Sum_probs=43.1
Q ss_pred ccccCCcccccccccccCCCceEEcCCCCccchhhHHHHHhcCCCCCCCCccccc
Q 000878 1114 EKCLETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSLGD 1168 (1241)
Q Consensus 1114 e~~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~~~~~CPiCrk~~~d 1168 (1241)
..+.++.||||+.. .-..++-||||-=...||.+-+-++..|=.|+.++.+
T Consensus 418 p~sEd~lCpICyA~----pi~Avf~PC~H~SC~~CI~qHlmN~k~CFfCktTv~~ 468 (489)
T KOG4692|consen 418 PDSEDNLCPICYAG----PINAVFAPCSHRSCYGCITQHLMNCKRCFFCKTTVID 468 (489)
T ss_pred CCcccccCcceecc----cchhhccCCCCchHHHHHHHHHhcCCeeeEecceeee
Confidence 35667899999965 3445778999999999999999899999999999865
No 99
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=84.70 E-value=0.29 Score=56.57 Aligned_cols=48 Identities=21% Similarity=0.578 Sum_probs=39.7
Q ss_pred CCcccccccccccCCCceEEcCCCCccchhhHHHHHhcCCCCCCCCccccc
Q 000878 1118 ETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSLGD 1168 (1241)
Q Consensus 1118 ~~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~~~~~CPiCrk~~~d 1168 (1241)
.-.|.+|..+|.+.+ .+.-|=|+|+.+||..++..+.+||+|+-.|..
T Consensus 15 ~itC~LC~GYliDAT---TI~eCLHTFCkSCivk~l~~~~~CP~C~i~ih~ 62 (331)
T KOG2660|consen 15 HITCRLCGGYLIDAT---TITECLHTFCKSCIVKYLEESKYCPTCDIVIHK 62 (331)
T ss_pred ceehhhccceeecch---hHHHHHHHHHHHHHHHHHHHhccCCccceeccC
Confidence 457999999964443 455699999999999999889999999988753
No 100
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=84.18 E-value=0.83 Score=40.58 Aligned_cols=47 Identities=28% Similarity=0.607 Sum_probs=32.0
Q ss_pred ccceeccccccccccC-----CCCCCCCCCCCcceeEeccccccccCCCCcccCCCCCc
Q 000878 1029 TSEMMCMHCLKIQAIG-----PNCTTPSCNGLSMAKYYCNICKFFDDERTVYHCPFCNL 1082 (1241)
Q Consensus 1029 ~~~~~C~~C~~~q~~~-----~~C~~~~Cc~~~~a~y~C~~C~~~d~~k~~yHC~~Cgi 1082 (1241)
.....|..|+.+-... -.|+| | |. .--|-|.+|+-.. ..|.||+||+
T Consensus 5 ~~~~~CtSCg~~i~~~~~~~~F~CPn--C-G~-~~I~RC~~CRk~~---~~Y~CP~CGF 56 (59)
T PRK14890 5 MEPPKCTSCGIEIAPREKAVKFLCPN--C-GE-VIIYRCEKCRKQS---NPYTCPKCGF 56 (59)
T ss_pred ccCccccCCCCcccCCCccCEeeCCC--C-CC-eeEeechhHHhcC---CceECCCCCC
Confidence 3455788898664332 36888 4 64 3356689998775 4599999985
No 101
>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=83.87 E-value=0.65 Score=46.60 Aligned_cols=35 Identities=14% Similarity=0.408 Sum_probs=26.4
Q ss_pred ccceEEcCCCCCCCCccchhhcccCCCCCCccccccc
Q 000878 1192 QVQDILCNDCEQKGAARFHWLYHKCGFCGSYNTRLIK 1228 (1241)
Q Consensus 1192 ~~~~i~CnDC~~~s~~~fh~lg~kC~~CgsYNT~~~~ 1228 (1241)
......|++|+.......+ +..||.|||++++++.
T Consensus 67 ~p~~~~C~~Cg~~~~~~~~--~~~CP~Cgs~~~~i~~ 101 (115)
T TIGR00100 67 EPVECECEDCSEEVSPEID--LYRCPKCHGIMLQVRA 101 (115)
T ss_pred eCcEEEcccCCCEEecCCc--CccCcCCcCCCcEEec
Confidence 3456899999987665422 4579999999988864
No 102
>PHA02862 5L protein; Provisional
Probab=83.82 E-value=0.7 Score=47.79 Aligned_cols=44 Identities=27% Similarity=0.659 Sum_probs=33.1
Q ss_pred CCcccccccccccCCCceEEcCCC-----CccchhhHHHHHh--cCCCCCCCCccc
Q 000878 1118 ETNCPICCDFLFTSSETVRALPCG-----HYMHLACFQAYTC--SHYTCPICSKSL 1166 (1241)
Q Consensus 1118 ~~~CpICle~lf~s~~~~~~lpCg-----H~fH~~C~~~wl~--~~~~CPiCrk~~ 1166 (1241)
...|=||.+. .++. .-||. -..|..|+.+|+. .+..||+|+...
T Consensus 2 ~diCWIC~~~---~~e~--~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY 52 (156)
T PHA02862 2 SDICWICNDV---CDER--NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKY 52 (156)
T ss_pred CCEEEEecCc---CCCC--cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeE
Confidence 4679999987 2222 35775 4699999999984 457899999875
No 103
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=83.57 E-value=0.68 Score=46.65 Aligned_cols=36 Identities=22% Similarity=0.405 Sum_probs=26.4
Q ss_pred ccceEEcCCCCCCCCccchhhcccCCCCCCccccccc
Q 000878 1192 QVQDILCNDCEQKGAARFHWLYHKCGFCGSYNTRLIK 1228 (1241)
Q Consensus 1192 ~~~~i~CnDC~~~s~~~fh~lg~kC~~CgsYNT~~~~ 1228 (1241)
......|++||........ .+.+|+.|||++..+++
T Consensus 68 vp~~~~C~~Cg~~~~~~~~-~~~~CP~Cgs~~~~i~~ 103 (117)
T PRK00564 68 EKVELECKDCSHVFKPNAL-DYGVCEKCHSKNVIITQ 103 (117)
T ss_pred cCCEEEhhhCCCccccCCc-cCCcCcCCCCCceEEec
Confidence 4467899999987765421 23469999999988764
No 104
>TIGR02481 hemeryth_dom hemerythrin-like metal-binding domain. This model describes both members of the hemerythrin (TIGR00058) family of marine invertebrates and a broader collection of bacterial and archaeal homologs. Many of the latter group are multidomain proteins with signal-transducing domains such as the GGDEF diguanylate cyclase domain (TIGR00254, pfam00990) and methyl-accepting chemotaxis protein signaling domain (pfam00015). Most hemerythrins are oxygen-carriers with a bound non-heme iron, but at least one example is a cadmium-binding protein, apparently with a role in sequestering toxic metals rather than in binding oxygen. Patterns of conserved residues suggest that all prokaryotic instances of this domain bind iron or another heavy metal, but the exact function is unknown. Not surprisingly, the prokaryote with the most instances of this domain is Magnetococcus sp. MC-1, a magnetotactic bacterium.
Probab=82.53 E-value=13 Score=37.17 Aligned_cols=112 Identities=20% Similarity=0.206 Sum_probs=74.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhcCCcccHHHHHHHHHHHHHHhhccCccccccc----cHHHhhhhhhHHHHHHHh
Q 000878 42 ILIFCFFHKAVRNELDALHQLAMNFATGHRVDILSLSERYRFLHSVYKHHSNAEDEVI----FPALDIRVKNVARKYSLE 117 (1241)
Q Consensus 42 Id~l~~~H~AIRreL~~L~~la~~l~~gd~~dl~~L~~~l~fL~~~L~~HH~aEDevL----FPaL~~R~p~vl~~le~E 117 (1241)
+..|-.-|+.|-..++.|...+.. + .....+...+..|.++...|=..||.++ ||.+... ..+
T Consensus 10 ~~~ID~qH~~l~~~in~l~~a~~~---~--~~~~~~~~~l~~L~~y~~~HF~~EE~~M~~~~yp~~~~H--------~~~ 76 (126)
T TIGR02481 10 IEEIDAQHKELFELINELYDALSA---G--NGKDELKEILDELIDYTENHFADEEELMEEYGYPDLEEH--------KKE 76 (126)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHc---C--CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCHHHH--------HHH
Confidence 456667898888888888876643 2 2245778889999999999999999765 5554433 345
Q ss_pred HHHHHHHHHHHHHHHhhhccCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhHHHH
Q 000878 118 HEGESNLFDHLFQLLNSYTQNDESFPKELASCSRALQTSINQHMSKEEQQVFPL 171 (1241)
Q Consensus 118 H~~id~lL~~L~~lL~~~~~~~~~~~~eLa~al~~L~~~L~~HL~~EE~eVfPL 171 (1241)
|+..-..+..+.. .+..+.. .......+..+..-+..|+..+...+.+.
T Consensus 77 H~~~l~~l~~l~~---~~~~~~~--~~~~~~~~~~l~~Wl~~HI~~~D~~~~~~ 125 (126)
T TIGR02481 77 HEKFVKKIEELQE---AVAEGAD--ESLAEELLDFLKDWLVNHILKEDKKYAPY 125 (126)
T ss_pred HHHHHHHHHHHHH---HHHcCCc--hhHHHHHHHHHHHHHHHHhHHHhHHHHhh
Confidence 6655555555544 4433211 12333556778888999999998877653
No 105
>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=82.16 E-value=1.2 Score=46.96 Aligned_cols=32 Identities=28% Similarity=0.832 Sum_probs=21.4
Q ss_pred CCcccccccccccCCCceEEcCC------------C-CccchhhHHHHH
Q 000878 1118 ETNCPICCDFLFTSSETVRALPC------------G-HYMHLACFQAYT 1153 (1241)
Q Consensus 1118 ~~~CpICle~lf~s~~~~~~lpC------------g-H~fH~~C~~~wl 1153 (1241)
+-.||||||. .-..+.|-| + =+-|..|+++|-
T Consensus 2 d~~CpICme~----PHNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfk 46 (162)
T PF07800_consen 2 DVTCPICMEH----PHNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFK 46 (162)
T ss_pred CccCceeccC----CCceEEEEeccccCCccccccCCccchhHHHHHHH
Confidence 4579999998 222333333 3 346999999985
No 106
>PRK04023 DNA polymerase II large subunit; Validated
Probab=82.14 E-value=1.1 Score=58.49 Aligned_cols=47 Identities=23% Similarity=0.419 Sum_probs=27.0
Q ss_pred ceeccccccccccCCCCCCCCCCCCcceeEeccccccccCCCCcccCCCCCcc
Q 000878 1031 EMMCMHCLKIQAIGPNCTTPSCNGLSMAKYYCNICKFFDDERTVYHCPFCNLC 1083 (1241)
Q Consensus 1031 ~~~C~~C~~~q~~~~~C~~~~Cc~~~~a~y~C~~C~~~d~~k~~yHC~~CgiC 1083 (1241)
.-.|..|+++. +...|++ |+......|||..|. ..-..|.||.||.=
T Consensus 626 ~RfCpsCG~~t-~~frCP~--CG~~Te~i~fCP~CG---~~~~~y~CPKCG~E 672 (1121)
T PRK04023 626 RRKCPSCGKET-FYRRCPF--CGTHTEPVYRCPRCG---IEVEEDECEKCGRE 672 (1121)
T ss_pred CccCCCCCCcC-CcccCCC--CCCCCCcceeCcccc---CcCCCCcCCCCCCC
Confidence 34666666665 3347776 533345667777772 22334667777753
No 107
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=81.94 E-value=0.81 Score=58.41 Aligned_cols=82 Identities=22% Similarity=0.177 Sum_probs=52.8
Q ss_pred CCCccccccccccC---CCCCCCCCCCCchhHHHHHHHHHHHhHhhHHHhhccCCCCChHHHHHHHHHHHHHHHHHhhhc
Q 000878 625 APSLNSSLFMWETD---NSSYDVVSAERPIDTIFKFHKAISKDLEYLDMESAKLSDCDETFLRQFIGRFRLLWGLYRAHS 701 (1241)
Q Consensus 625 ~~~~~~~~~~~~~~---~~~~~~~~~~~Pid~~~~~H~A~RrdL~~L~~~~~~~~~~d~~~~~~~~~rf~~l~~~l~~Hh 701 (1241)
++.+.--|+-|+-+ -++.+.-..-.|+|+=.++-.-+.|.|--++.--|+---.|+..++.++.-+--....=--|.
T Consensus 306 l~~l~d~l~~w~~~~~vltsdg~~~~L~ek~le~kL~iL~kK~ly~~Ai~LAk~~~~d~d~~~~i~~kYgd~Ly~Kgdf~ 385 (933)
T KOG2114|consen 306 LEDLSDNLIEWSFDCLVLTSDGVVHELIEKDLETKLDILFKKNLYKVAINLAKSQHLDEDTLAEIHRKYGDYLYGKGDFD 385 (933)
T ss_pred HHHHHHHHHhcCCcEEEEecCCceeeeeeccHHHHHHHHHHhhhHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHhcCCHH
Confidence 44444446677711 123355556678888888888889999888888777655688888888766655444434444
Q ss_pred cCccc
Q 000878 702 NAEDE 706 (1241)
Q Consensus 702 ~aEDe 706 (1241)
+|=|.
T Consensus 386 ~A~~q 390 (933)
T KOG2114|consen 386 EATDQ 390 (933)
T ss_pred HHHHH
Confidence 44443
No 108
>COG5592 Uncharacterized conserved protein [Function unknown]
Probab=81.59 E-value=3.4 Score=43.65 Aligned_cols=75 Identities=23% Similarity=0.305 Sum_probs=56.1
Q ss_pred HHHHHHHHHHHHHHHhhhcCCChhhHHHHHHHHHHHHHHHHHHHhhhhhcccccccccccchhhhhHHhhhHHHHHHHHH
Q 000878 312 NAIRQELNEIAEESRKIQLSGDFTNLLAFNERLQFIAEVLIFHCIAEVNVIFPAVDGASSFSQKHAEEESQFNDFRLLIE 391 (1241)
Q Consensus 312 kAIRkDh~el~~~~~kl~~~~d~~~l~~~~~r~qfL~el~r~HS~AEe~vVyPALE~~~s~~~dh~~eeh~~eei~~LL~ 391 (1241)
+.|+.||+-+.-....++....++ .+..++..+...+-.|--|||+.+||-+++.. +.++ .++++.+|+
T Consensus 74 ~~i~~DHkliE~l~tnlik~kR~~---k~~e~~p~fyK~LtdHn~aEE~~IfPrvks~~----~E~~----~~~~kl~Le 142 (171)
T COG5592 74 DRIKNDHKLIETLATNLIKWKRPD---KIKERVPLFYKTLTDHNLAEEEYIFPRVKSLK----GEDE----QSALKLALE 142 (171)
T ss_pred hHhHhhHHHHHHHHHHHHhhccch---HHHHHHHHHHHHHHHccccccchhhHHHHhhc----chhh----HHHHHHHHH
Confidence 468899999998888887655553 67788888888888899999999999997321 1122 344778888
Q ss_pred HHHhcC
Q 000878 392 SIQNEG 397 (1241)
Q Consensus 392 ~lq~~~ 397 (1241)
.+...+
T Consensus 143 iI~~~~ 148 (171)
T COG5592 143 IIEQYG 148 (171)
T ss_pred HHHHhC
Confidence 887554
No 109
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=80.89 E-value=0.92 Score=45.43 Aligned_cols=35 Identities=20% Similarity=0.321 Sum_probs=25.7
Q ss_pred ccceEEcCCCCCCCCccchhhcccCCCCCCccccccc
Q 000878 1192 QVQDILCNDCEQKGAARFHWLYHKCGFCGSYNTRLIK 1228 (1241)
Q Consensus 1192 ~~~~i~CnDC~~~s~~~fh~lg~kC~~CgsYNT~~~~ 1228 (1241)
......|++|+....... ....||.|||++..+++
T Consensus 67 vp~~~~C~~Cg~~~~~~~--~~~~CP~Cgs~~~~i~~ 101 (113)
T PRK12380 67 KPAQAWCWDCSQVVEIHQ--HDAQCPHCHGERLRVDT 101 (113)
T ss_pred eCcEEEcccCCCEEecCC--cCccCcCCCCCCcEEcc
Confidence 345689999998766542 22359999999988764
No 110
>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=80.75 E-value=0.69 Score=39.29 Aligned_cols=43 Identities=35% Similarity=0.848 Sum_probs=25.9
Q ss_pred CcccccccccccCCCceEEcCCC-CccchhhHHHHHhcCCCCCCCCcccc
Q 000878 1119 TNCPICCDFLFTSSETVRALPCG-HYMHLACFQAYTCSHYTCPICSKSLG 1167 (1241)
Q Consensus 1119 ~~CpICle~lf~s~~~~~~lpCg-H~fH~~C~~~wl~~~~~CPiCrk~~~ 1167 (1241)
.+|--|. |... ..+.|. |+....|+.-++.....||||.++++
T Consensus 3 ~nCKsCW---f~~k---~Li~C~dHYLCl~CLt~ml~~s~~C~iC~~~LP 46 (50)
T PF03854_consen 3 YNCKSCW---FANK---GLIKCSDHYLCLNCLTLMLSRSDRCPICGKPLP 46 (50)
T ss_dssp ----SS----S--S---SEEE-SS-EEEHHHHHHT-SSSSEETTTTEE--
T ss_pred ccChhhh---hcCC---CeeeecchhHHHHHHHHHhccccCCCcccCcCc
Confidence 4566676 3333 235686 99999999999999999999999875
No 111
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=80.35 E-value=0.67 Score=53.40 Aligned_cols=22 Identities=32% Similarity=0.824 Sum_probs=14.8
Q ss_pred eEEcCCCCCCCCccchhhcccCCCCC
Q 000878 1195 DILCNDCEQKGAARFHWLYHKCGFCG 1220 (1241)
Q Consensus 1195 ~i~CnDC~~~s~~~fh~lg~kC~~Cg 1220 (1241)
.++|-||+ +-.|---|-|++|.
T Consensus 353 ~~FCldCD----v~iHesLh~CpgCe 374 (378)
T KOG2807|consen 353 NVFCLDCD----VFIHESLHNCPGCE 374 (378)
T ss_pred ceeeccch----HHHHhhhhcCCCcC
Confidence 45777776 44566666788776
No 112
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=79.93 E-value=1.1 Score=54.00 Aligned_cols=49 Identities=29% Similarity=0.681 Sum_probs=39.7
Q ss_pred ccCCcccccccccccCCCceEEcCCCCccchhhHHHHHhcCCCCCCCCccccc
Q 000878 1116 CLETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSLGD 1168 (1241)
Q Consensus 1116 ~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~~~~~CPiCrk~~~d 1168 (1241)
..+..|.||+.-++. ...+||||.|...|+..-+....-||+||..+..
T Consensus 82 ~sef~c~vc~~~l~~----pv~tpcghs~c~~Cl~r~ld~~~~cp~Cr~~l~e 130 (398)
T KOG4159|consen 82 RSEFECCVCSRALYP----PVVTPCGHSFCLECLDRSLDQETECPLCRDELVE 130 (398)
T ss_pred cchhhhhhhHhhcCC----CccccccccccHHHHHHHhccCCCCccccccccc
Confidence 457789999877543 2345999999999999977778889999998863
No 113
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=79.71 E-value=1.1 Score=44.98 Aligned_cols=35 Identities=17% Similarity=0.384 Sum_probs=25.5
Q ss_pred cceEEcCCCCCCCCccchhhcccCCCCCCccccccc
Q 000878 1193 VQDILCNDCEQKGAARFHWLYHKCGFCGSYNTRLIK 1228 (1241)
Q Consensus 1193 ~~~i~CnDC~~~s~~~fh~lg~kC~~CgsYNT~~~~ 1228 (1241)
.....|++|+.......+. +..||.|||+++.++.
T Consensus 68 p~~~~C~~Cg~~~~~~~~~-~~~CP~Cgs~~~~i~~ 102 (114)
T PRK03681 68 EAECWCETCQQYVTLLTQR-VRRCPQCHGDMLRIVA 102 (114)
T ss_pred CcEEEcccCCCeeecCCcc-CCcCcCcCCCCcEEcc
Confidence 4568999999876553221 2469999999988764
No 114
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=79.42 E-value=1.1 Score=46.17 Aligned_cols=35 Identities=26% Similarity=0.655 Sum_probs=25.3
Q ss_pred ceEEcCCCCCCCCcc-------------ch------hhcccCCCCCCccccccc
Q 000878 1194 QDILCNDCEQKGAAR-------------FH------WLYHKCGFCGSYNTRLIK 1228 (1241)
Q Consensus 1194 ~~i~CnDC~~~s~~~-------------fh------~lg~kC~~CgsYNT~~~~ 1228 (1241)
....|++||...... +| ..+.+|+.|||++.+++.
T Consensus 69 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~ 122 (135)
T PRK03824 69 AVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRDFEIVK 122 (135)
T ss_pred eEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCCcEEec
Confidence 568899999776443 22 234679999999988754
No 115
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=79.36 E-value=1.5 Score=46.23 Aligned_cols=45 Identities=22% Similarity=0.590 Sum_probs=33.0
Q ss_pred cCCcccccccccccCCCceEEcCCCC-----ccchhhHHHHHh--cCCCCCCCCccc
Q 000878 1117 LETNCPICCDFLFTSSETVRALPCGH-----YMHLACFQAYTC--SHYTCPICSKSL 1166 (1241)
Q Consensus 1117 ~~~~CpICle~lf~s~~~~~~lpCgH-----~fH~~C~~~wl~--~~~~CPiCrk~~ 1166 (1241)
++..|=||.+. - +. ..-||.. ..|.+|+..|+. ...+||+|+...
T Consensus 7 ~~~~CRIC~~~-~--~~--~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y 58 (162)
T PHA02825 7 MDKCCWICKDE-Y--DV--VTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPY 58 (162)
T ss_pred CCCeeEecCCC-C--CC--ccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeE
Confidence 45679999887 1 11 2357754 579999999984 457899999874
No 116
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=79.26 E-value=1.4 Score=39.16 Aligned_cols=45 Identities=31% Similarity=0.822 Sum_probs=33.3
Q ss_pred ceeccccccccccC-----CCCCCCCCCCCcceeEeccccccccCCCCcccCCCCCc
Q 000878 1031 EMMCMHCLKIQAIG-----PNCTTPSCNGLSMAKYYCNICKFFDDERTVYHCPFCNL 1082 (1241)
Q Consensus 1031 ~~~C~~C~~~q~~~-----~~C~~~~Cc~~~~a~y~C~~C~~~d~~k~~yHC~~Cgi 1082 (1241)
...|..|+.+-.++ -.|+| | | ..--|-|..|+-.. ..|.||+||+
T Consensus 9 ~~~CtSCg~~i~p~e~~v~F~CPn--C-G-e~~I~Rc~~CRk~g---~~Y~Cp~CGF 58 (61)
T COG2888 9 PPVCTSCGREIAPGETAVKFPCPN--C-G-EVEIYRCAKCRKLG---NPYRCPKCGF 58 (61)
T ss_pred CceeccCCCEeccCCceeEeeCCC--C-C-ceeeehhhhHHHcC---CceECCCcCc
Confidence 56899999876443 34888 4 6 34578899998775 4699999986
No 117
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=78.46 E-value=1.3 Score=52.68 Aligned_cols=53 Identities=23% Similarity=0.477 Sum_probs=38.7
Q ss_pred cccccccccCCcccccccccccCCCceEEcCCCCccchhhHHHHHh--------cCCCCCCCC
Q 000878 1109 NHKCLEKCLETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTC--------SHYTCPICS 1163 (1241)
Q Consensus 1109 ~H~C~e~~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~--------~~~~CPiCr 1163 (1241)
+|.+.-++ -..|.||++. +....-...+||+|.|...|...|.. +..+||-++
T Consensus 176 ~~~~F~~s-lf~C~ICf~e-~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~ 236 (445)
T KOG1814|consen 176 TLEKFVNS-LFDCCICFEE-QMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPK 236 (445)
T ss_pred HHHHHHhh-cccceeeehh-hcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCC
Confidence 44444443 3579999998 55556678899999999999999852 236788654
No 118
>PRK00808 hypothetical protein; Provisional
Probab=77.91 E-value=28 Score=36.35 Aligned_cols=114 Identities=14% Similarity=0.133 Sum_probs=77.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhcCCcccHHHHHHHHHHHHHHhhccCccccccc----cHHHhhhhhhHHHHHHH
Q 000878 41 PILIFCFFHKAVRNELDALHQLAMNFATGHRVDILSLSERYRFLHSVYKHHSNAEDEVI----FPALDIRVKNVARKYSL 116 (1241)
Q Consensus 41 PId~l~~~H~AIRreL~~L~~la~~l~~gd~~dl~~L~~~l~fL~~~L~~HH~aEDevL----FPaL~~R~p~vl~~le~ 116 (1241)
-+..|-.-|+.|=..++.|...+. .++ ...+...+..|.++...|=..||.++ ||.+.... .
T Consensus 13 G~~~ID~qH~~L~~lin~l~~a~~---~~~---~~~i~~~l~~L~~y~~~HF~~EE~lM~~~~Yp~~~~H~--------~ 78 (150)
T PRK00808 13 GIDVIDQQHKRIVDYINHLHDAQD---SPD---RLAVAEVIDELIDYTLSHFAFEESLMEEAGYPFLVPHK--------R 78 (150)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHH---cCc---HHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHH--------H
Confidence 345666789888888777776653 232 45677889999999999999999765 66554332 3
Q ss_pred hHHHHHHHHHHHHHHHhhhccCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHhcc
Q 000878 117 EHEGESNLFDHLFQLLNSYTQNDESFPKELASCSRALQTSINQHMSKEEQQVFPLLTQH 175 (1241)
Q Consensus 117 EH~~id~lL~~L~~lL~~~~~~~~~~~~eLa~al~~L~~~L~~HL~~EE~eVfPLa~~~ 175 (1241)
+|+..-. .+..+...+..++ ......+.-+..-+..|+..+.....+.+++.
T Consensus 79 ~H~~fl~---~l~~l~~~~~~g~----~~~~~l~~~L~~WL~~HI~~~D~~~~~~l~~~ 130 (150)
T PRK00808 79 VHELFIK---RVEEYRERFQAGE----DVADELHGMLSRWLFNHIRNDDAAYVDAVKAN 130 (150)
T ss_pred HHHHHHH---HHHHHHHHHHccc----hHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHh
Confidence 5555444 4444444443322 12234567788899999999999999998874
No 119
>COG5592 Uncharacterized conserved protein [Function unknown]
Probab=77.89 E-value=12 Score=39.69 Aligned_cols=100 Identities=19% Similarity=0.268 Sum_probs=73.3
Q ss_pred HHHHHHHHHHHHHhhccCccccccccHHHhhh-------hh--hHHHHHHHhHHHHHHHHHHHHHHHhhhccCCCCcHHH
Q 000878 75 LSLSERYRFLHSVYKHHSNAEDEVIFPALDIR-------VK--NVARKYSLEHEGESNLFDHLFQLLNSYTQNDESFPKE 145 (1241)
Q Consensus 75 ~~L~~~l~fL~~~L~~HH~aEDevLFPaL~~R-------~p--~vl~~le~EH~~id~lL~~L~~lL~~~~~~~~~~~~e 145 (1241)
..+.+...|.......|-.-|+..+||..-.. .. +..+.+..+|.-++-+...+...-. + +.
T Consensus 28 ~e~le~~gf~~k~~k~h~e~Ee~ilF~v~Vd~~~ed~~~fkdt~~~~~i~~DHkliE~l~tnlik~kR------~---~k 98 (171)
T COG5592 28 LEILEFEGFNEKLGKDHVELEEKILFPVIVDADMEDLYVFKDTPEVDRIKNDHKLIETLATNLIKWKR------P---DK 98 (171)
T ss_pred HHHHhhcchHHHHhhhHHHHHHHhhhhhccchHHHHHHhhhccchhhHhHhhHHHHHHHHHHHHhhcc------c---hH
Confidence 33445555777778999999999999986322 11 3467888899988887777643221 1 47
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhHHHHHhccCCHHHHHH
Q 000878 146 LASCSRALQTSINQHMSKEEQQVFPLLTQHFSLEEQAS 183 (1241)
Q Consensus 146 La~al~~L~~~L~~HL~~EE~eVfPLa~~~lS~eEwae 183 (1241)
+...+..|...|..|=..||..+||.++..-...++.+
T Consensus 99 ~~e~~p~fyK~LtdHn~aEE~~IfPrvks~~~E~~~~~ 136 (171)
T COG5592 99 IKERVPLFYKTLTDHNLAEEEYIFPRVKSLKGEDEQSA 136 (171)
T ss_pred HHHHHHHHHHHHHHccccccchhhHHHHhhcchhhHHH
Confidence 77899999999999999999999999986554434433
No 120
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=77.77 E-value=1.9 Score=50.07 Aligned_cols=62 Identities=23% Similarity=0.558 Sum_probs=44.5
Q ss_pred CcccccccccccCCCceEEcCC--CCccchhhHHHHHhcCCCCCCCCcccccchhhhhhhHHHHhccCCCHhhh
Q 000878 1119 TNCPICCDFLFTSSETVRALPC--GHYMHLACFQAYTCSHYTCPICSKSLGDMAIYFGMIDALLAAEELPEEYR 1190 (1241)
Q Consensus 1119 ~~CpICle~lf~s~~~~~~lpC--gH~fH~~C~~~wl~~~~~CPiCrk~~~dm~~~~~~lD~~i~~~~~P~ey~ 1190 (1241)
-+||||.++|. .-++.| ||+....|-. +....||.|+.++++.- -+.++..+++...|=.|.
T Consensus 49 leCPvC~~~l~-----~Pi~QC~nGHlaCssC~~---~~~~~CP~Cr~~~g~~R--~~amEkV~e~~~vpC~~~ 112 (299)
T KOG3002|consen 49 LDCPVCFNPLS-----PPIFQCDNGHLACSSCRT---KVSNKCPTCRLPIGNIR--CRAMEKVAEAVLVPCKNA 112 (299)
T ss_pred ccCchhhccCc-----ccceecCCCcEehhhhhh---hhcccCCccccccccHH--HHHHHHHHHhceeccccc
Confidence 47999999952 233455 8999999985 45789999999999653 245667777776664443
No 121
>TIGR02481 hemeryth_dom hemerythrin-like metal-binding domain. This model describes both members of the hemerythrin (TIGR00058) family of marine invertebrates and a broader collection of bacterial and archaeal homologs. Many of the latter group are multidomain proteins with signal-transducing domains such as the GGDEF diguanylate cyclase domain (TIGR00254, pfam00990) and methyl-accepting chemotaxis protein signaling domain (pfam00015). Most hemerythrins are oxygen-carriers with a bound non-heme iron, but at least one example is a cadmium-binding protein, apparently with a role in sequestering toxic metals rather than in binding oxygen. Patterns of conserved residues suggest that all prokaryotic instances of this domain bind iron or another heavy metal, but the exact function is unknown. Not surprisingly, the prokaryote with the most instances of this domain is Magnetococcus sp. MC-1, a magnetotactic bacterium.
Probab=76.57 E-value=20 Score=35.77 Aligned_cols=108 Identities=15% Similarity=0.179 Sum_probs=68.3
Q ss_pred HHHHHHHHHHHHHHHhhhcCC-ChhhHHHHHHHHHHHHHHHHHHHhhhhhcc----cccccccccchhhhhHHhh-hHHH
Q 000878 312 NAIRQELNEIAEESRKIQLSG-DFTNLLAFNERLQFIAEVLIFHCIAEVNVI----FPAVDGASSFSQKHAEEES-QFND 385 (1241)
Q Consensus 312 kAIRkDh~el~~~~~kl~~~~-d~~~l~~~~~r~qfL~el~r~HS~AEe~vV----yPALE~~~s~~~dh~~eeh-~~ee 385 (1241)
..|=.+|++|-+.++++..+. .......+...+.+|.+-.+.|=..||.+. ||.++ .|..+-. .+.+
T Consensus 11 ~~ID~qH~~l~~~in~l~~a~~~~~~~~~~~~~l~~L~~y~~~HF~~EE~~M~~~~yp~~~-------~H~~~H~~~l~~ 83 (126)
T TIGR02481 11 EEIDAQHKELFELINELYDALSAGNGKDELKEILDELIDYTENHFADEEELMEEYGYPDLE-------EHKKEHEKFVKK 83 (126)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCHH-------HHHHHHHHHHHH
Confidence 456677888888887775321 122345677888999999999999999654 99887 5544322 2333
Q ss_pred HHHHHHHHHhcCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHH
Q 000878 386 FRLLIESIQNEGAISTSAEFYAKLCSHADQIMETIERHFHKVEVQVLP 433 (1241)
Q Consensus 386 i~~LL~~lq~~~~~~~~~~f~~kL~~~l~~l~~~l~~Hi~eEE~E~lP 433 (1241)
+..+...+... .. ...... ..+.+..-+.+||..+-...-+
T Consensus 84 l~~l~~~~~~~--~~--~~~~~~---~~~~l~~Wl~~HI~~~D~~~~~ 124 (126)
T TIGR02481 84 IEELQEAVAEG--AD--ESLAEE---LLDFLKDWLVNHILKEDKKYAP 124 (126)
T ss_pred HHHHHHHHHcC--Cc--hhHHHH---HHHHHHHHHHHHhHHHhHHHHh
Confidence 66666655421 11 122222 2456778888999887655443
No 122
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 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 DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=76.52 E-value=1.7 Score=45.67 Aligned_cols=47 Identities=30% Similarity=0.624 Sum_probs=40.1
Q ss_pred CCcceeEeccccccccCCCCcccCCCCCccccCCCCCccccccCCcccccccc
Q 000878 1054 GLSMAKYYCNICKFFDDERTVYHCPFCNLCRVGGGLGVDFFHCMTCNCCLGLK 1106 (1241)
Q Consensus 1054 ~~~~a~y~C~~C~~~d~~k~~yHC~~CgiCRvg~~l~~~~fhC~~C~~C~s~~ 1106 (1241)
+......||..|+.+...| .+||..||.|-.+. ..||.=-|.|++..
T Consensus 43 ~~~~~~~~C~~C~~~kp~R-s~HC~~C~~CV~~~-----DHHC~w~~~cIG~~ 89 (174)
T PF01529_consen 43 DENGELKYCSTCKIIKPPR-SHHCRVCNRCVLRF-----DHHCPWLGNCIGRR 89 (174)
T ss_pred ccCCCCEECcccCCcCCCc-ceeccccccccccc-----cccchhhccccccc
Confidence 4567888999999997774 88999999999985 47999999998855
No 123
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=74.62 E-value=1.1 Score=55.44 Aligned_cols=43 Identities=26% Similarity=0.606 Sum_probs=35.1
Q ss_pred cccccccccccCCCceEEcCCCCccchhhHHHHHhcCCCCCCCCcc
Q 000878 1120 NCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKS 1165 (1241)
Q Consensus 1120 ~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~~~~~CPiCrk~ 1165 (1241)
+|+||+..+|.+.-..+.+-|||++..+|.... .+.+|| |+++
T Consensus 13 ~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~l--yn~scp-~~~D 55 (861)
T KOG3161|consen 13 LCDICLNLFVVQRLEPVSLQCGHTICGHCVQLL--YNASCP-TKRD 55 (861)
T ss_pred hchHHHHHHHHHhcCcccccccchHHHHHHHhH--hhccCC-CCcc
Confidence 699998886777776777889999999999765 467899 7765
No 124
>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=74.36 E-value=1.1 Score=44.85 Aligned_cols=35 Identities=23% Similarity=0.399 Sum_probs=22.6
Q ss_pred ccceEEcCCCCCCCCccchhhcccCCCCCCccccccc
Q 000878 1192 QVQDILCNDCEQKGAARFHWLYHKCGFCGSYNTRLIK 1228 (1241)
Q Consensus 1192 ~~~~i~CnDC~~~s~~~fh~lg~kC~~CgsYNT~~~~ 1228 (1241)
......|++||..+....+. ..||.|||++..+++
T Consensus 67 ~p~~~~C~~Cg~~~~~~~~~--~~CP~Cgs~~~~i~~ 101 (113)
T PF01155_consen 67 VPARARCRDCGHEFEPDEFD--FSCPRCGSPDVEIIS 101 (113)
T ss_dssp E--EEEETTTS-EEECHHCC--HH-SSSSSS-EEEEE
T ss_pred cCCcEECCCCCCEEecCCCC--CCCcCCcCCCcEEcc
Confidence 34568999999988655332 459999999987754
No 125
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=74.27 E-value=2.6 Score=48.50 Aligned_cols=47 Identities=28% Similarity=0.699 Sum_probs=38.5
Q ss_pred CcccccccccccCCCce---EEcCCCCccchhhHHHHHhcC-CCCCCCCccc
Q 000878 1119 TNCPICCDFLFTSSETV---RALPCGHYMHLACFQAYTCSH-YTCPICSKSL 1166 (1241)
Q Consensus 1119 ~~CpICle~lf~s~~~~---~~lpCgH~fH~~C~~~wl~~~-~~CPiCrk~~ 1166 (1241)
..|-||-++ |.+.+.. +.|.|||++...|+...+.+. ..||-||.+.
T Consensus 4 ~~c~~c~~~-~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~~~i~cpfcR~~~ 54 (296)
T KOG4185|consen 4 PECEICNED-YSSEDGDHIPRVLKCGHTICQNCASKLLGNSRILCPFCRETT 54 (296)
T ss_pred CceeecCcc-ccccCcccCCcccccCceehHhHHHHHhcCceeeccCCCCcc
Confidence 469999999 8877543 567899999999999987554 6699999994
No 126
>cd00522 Hemerythrin Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the muscle tissue of sipunculids as well as in polycheate and oligocheate annelids. In addition to oxygen transport, Mhr proteins are involved in cadmium fixation and host anti-bacterial defense. Hr and Mhr proteins have the same "four alpha helix bundle" motif and active site structure. Hr forms oligomers, the octameric form being most prevalent, while Mhr is monomeric.
Probab=73.48 E-value=8.9 Score=38.11 Aligned_cols=46 Identities=22% Similarity=0.120 Sum_probs=37.8
Q ss_pred HHHHHhHHHHHHHHHHHHHHHhhhccCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhHH
Q 000878 112 RKYSLEHEGESNLFDHLFQLLNSYTQNDESFPKELASCSRALQTSINQHMSKEEQQVF 169 (1241)
Q Consensus 112 ~~le~EH~~id~lL~~L~~lL~~~~~~~~~~~~eLa~al~~L~~~L~~HL~~EE~eVf 169 (1241)
..+..+|+.+=.++++|..++.. ...+..|......||..||...-
T Consensus 13 ~~ID~qH~~L~~l~n~l~~a~~~------------~~~l~~L~~y~~~HF~~EE~~M~ 58 (113)
T cd00522 13 EVIDDEHKTLFNGINDLSEANNR------------ADNLKELVDYTVKHFKDEEALME 58 (113)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhH------------HHHHHHHHHHHHHHHHHHHHHHH
Confidence 46778999998888888877754 46789999999999999998753
No 127
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=73.33 E-value=2.3 Score=52.56 Aligned_cols=19 Identities=32% Similarity=0.772 Sum_probs=10.5
Q ss_pred ccccccccccCCccccccccc
Q 000878 1108 LNHKCLEKCLETNCPICCDFL 1128 (1241)
Q Consensus 1108 ~~H~C~e~~~~~~CpICle~l 1128 (1241)
.+.+|..+ .-+||+|.-.|
T Consensus 44 ~~nrC~r~--Cf~CP~C~~~L 62 (483)
T PF05502_consen 44 EKNRCSRN--CFDCPICFSPL 62 (483)
T ss_pred ccceeccc--cccCCCCCCcc
Confidence 34555443 34577777665
No 128
>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=72.85 E-value=2 Score=35.91 Aligned_cols=24 Identities=33% Similarity=0.851 Sum_probs=15.5
Q ss_pred CCCCccchhhHHHHHhcCC--CCCCC
Q 000878 1139 PCGHYMHLACFQAYTCSHY--TCPIC 1162 (1241)
Q Consensus 1139 pCgH~fH~~C~~~wl~~~~--~CPiC 1162 (1241)
.|+=-||..|+..|++... +||.|
T Consensus 18 ~C~~r~H~~C~~~y~r~~~~~~CP~C 43 (43)
T PF08746_consen 18 DCNVRLHDDCFKKYFRHRSNPKCPNC 43 (43)
T ss_dssp -S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred ccCchHHHHHHHHHHhcCCCCCCcCC
Confidence 4777899999999986654 79988
No 129
>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=70.59 E-value=0.83 Score=42.01 Aligned_cols=64 Identities=33% Similarity=0.662 Sum_probs=33.5
Q ss_pred CcccccccccccCCCceEEcCCCCccchhhHHHHHhcCCCCCCCCcccccchhhhhhhHHHHhccCCCHhhhcccceEEc
Q 000878 1119 TNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSLGDMAIYFGMIDALLAAEELPEEYRNQVQDILC 1198 (1241)
Q Consensus 1119 ~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~~~~~CPiCrk~~~dm~~~~~~lD~~i~~~~~P~ey~~~~~~i~C 1198 (1241)
..||.|..+|-..+ ||+....|-..+. ....||-|..++-.... =-.++++|
T Consensus 2 ~~CP~C~~~L~~~~--------~~~~C~~C~~~~~-~~a~CPdC~~~Le~LkA-------------------CGAvdYFC 53 (70)
T PF07191_consen 2 NTCPKCQQELEWQG--------GHYHCEACQKDYK-KEAFCPDCGQPLEVLKA-------------------CGAVDYFC 53 (70)
T ss_dssp -B-SSS-SBEEEET--------TEEEETTT--EEE-EEEE-TTT-SB-EEEEE-------------------TTEEEEE-
T ss_pred CcCCCCCCccEEeC--------CEEECccccccce-ecccCCCcccHHHHHHH-------------------hcccceee
Confidence 57999999852222 7777888877654 34579999987632211 11257899
Q ss_pred CCCC---CCCCccch
Q 000878 1199 NDCE---QKGAARFH 1210 (1241)
Q Consensus 1199 nDC~---~~s~~~fh 1210 (1241)
|.|+ +|+.+.|.
T Consensus 54 ~~c~gLiSKkrV~f~ 68 (70)
T PF07191_consen 54 NHCHGLISKKRVRFE 68 (70)
T ss_dssp TTTT-EE-TTTSEEE
T ss_pred ccCCceeecceEEEE
Confidence 9997 34455553
No 130
>COG2461 Uncharacterized conserved protein [Function unknown]
Probab=69.98 E-value=36 Score=40.94 Aligned_cols=137 Identities=18% Similarity=0.247 Sum_probs=92.3
Q ss_pred CCchhHHHHHHHHHHHhHhhHHHhhccCCCCChHHHHHHHHHHHHHHHHHhhhccCcccccccccccccccccccccccc
Q 000878 648 ERPIDTIFKFHKAISKDLEYLDMESAKLSDCDETFLRQFIGRFRLLWGLYRAHSNAEDEIVFPALESKEALHNVSHSYTL 727 (1241)
Q Consensus 648 ~~Pid~~~~~H~A~RrdL~~L~~~~~~~~~~d~~~~~~~~~rf~~l~~~l~~Hh~aEDeivwPaLe~r~~l~nvs~s~~l 727 (1241)
--||-.+|.=-+++|..|+.+-. .+. +......+.....++..+=. |=+-+-..+||-+|.+ ....++--|-.
T Consensus 85 gHPv~tl~~EN~~i~~ll~~~l~---~~~--~~~ik~~l~~lv~~L~~vg~-Hy~RKe~lIfp~~Er~-GitapptVmW~ 157 (409)
T COG2461 85 GHPVRTLKRENKAIRSLLANLLQ---FPP--KKEIKEKLVELVSELDKIGK-HYTRKEMLIFPYIERR-GITAPPTVMWV 157 (409)
T ss_pred CCcHHHHhcccHHHHHHHHHHhh---ccc--cHHHHHHHHHHHHHHHHhcc-ccccccccchhHHHHc-CCCCCCeeeec
Confidence 56888888888888844444332 222 12222223333333433334 9999999999999987 45666666777
Q ss_pred chhHHHHHHHHHHHHHHhhhhhhccCCCCCCcccccccccCCCchhhhHHHHHHHHHHHHHHHHHHHhHhhHhhhhhhhh
Q 000878 728 DHKQEEKLFEDISCVLSEVSQLHESLPNADSEKEDKFSADYGSDNRRKYNELATKLQGMCKSIKVTLDQHILGEELELWP 807 (1241)
Q Consensus 728 dH~~e~~lf~~I~~~L~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~L~~~~~~l~~~L~~Hl~~EE~el~P 807 (1241)
+|....+.|..+-..|.+ . ..+++..+. .++.+.+..=+.+||.=+.|
T Consensus 158 ~dDeiRe~lk~~~~~l~~-------~---------------------s~~~~ve~~----~~~~t~i~dmIFkEe~Ilyp 205 (409)
T COG2461 158 KDDEIREALKELLKLLKE-------V---------------------SIEEFVEKA----ESVLTEIEDMIFKEENILYP 205 (409)
T ss_pred cCcHHHHHHHHHHHHhhc-------c---------------------ChHHHHHHH----HHHHHHHHHHHHhhhhhHHh
Confidence 898887777777666663 1 122333333 55566677789999999999
Q ss_pred hhhccCCHHHHHHHHh
Q 000878 808 LFGRHFSVEEQDKIVG 823 (1241)
Q Consensus 808 L~~~~~t~~Ew~~i~~ 823 (1241)
....-||..||.+|..
T Consensus 206 t~~d~~te~ew~~i~~ 221 (409)
T COG2461 206 TLLDLLTEGEWEAIKE 221 (409)
T ss_pred HHHHhcCHHHHHHHHh
Confidence 9999999999999743
No 131
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=69.93 E-value=4.3 Score=47.20 Aligned_cols=48 Identities=27% Similarity=0.601 Sum_probs=36.8
Q ss_pred cccCCcccccccccccCCCceEEcCCCCccchhhHHHH--HhcCCCCCCCCccc
Q 000878 1115 KCLETNCPICCDFLFTSSETVRALPCGHYMHLACFQAY--TCSHYTCPICSKSL 1166 (1241)
Q Consensus 1115 ~~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~w--l~~~~~CPiCrk~~ 1166 (1241)
+..+.+|-||-+. .+-+-.+||||-+.-.|-... +.....||+||..-
T Consensus 58 DEen~~C~ICA~~----~TYs~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~ 107 (493)
T COG5236 58 DEENMNCQICAGS----TTYSARYPCGHQICHACAVRLRALYMQKGCPLCRTET 107 (493)
T ss_pred ccccceeEEecCC----ceEEEeccCCchHHHHHHHHHHHHHhccCCCcccccc
Confidence 3446789999987 345677999999999996654 45667899999753
No 132
>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=69.91 E-value=2.1 Score=48.08 Aligned_cols=73 Identities=30% Similarity=0.845 Sum_probs=46.6
Q ss_pred cccccccc-----------CCcccCchhhccc-CCCCCCcccccceeccccccccccCCCCCCCCCCCCcceeEeccccc
Q 000878 999 CKIRAACC-----------GKLFTCRFCHDKA-SDHSMDRKATSEMMCMHCLKIQAIGPNCTTPSCNGLSMAKYYCNICK 1066 (1241)
Q Consensus 999 ckl~~pcC-----------~k~y~Cr~CHde~-~~H~~~r~~~~~~~C~~C~~~q~~~~~C~~~~Cc~~~~a~y~C~~C~ 1066 (1241)
|+|+=+.| |+.|.|-||++-. +|-.++-.+ .|+....-.-.|.. | ..+|.|-|-.||
T Consensus 121 Cpl~da~C~EC~R~vw~hGGrif~CsfC~~flCEDDQFEHQA-------sCQvLe~E~~KC~S--C--NrlGq~sCLRCK 189 (314)
T PF06524_consen 121 CPLQDAVCIECERGVWDHGGRIFKCSFCDNFLCEDDQFEHQA-------SCQVLESETFKCQS--C--NRLGQYSCLRCK 189 (314)
T ss_pred CcCCCcEeeeeecccccCCCeEEEeecCCCeeeccchhhhhh-------hhhhhhcccccccc--c--ccccchhhhhee
Confidence 66665555 6689999998873 444444422 35555555556876 6 379999999999
Q ss_pred c-ccCC-----------CCcccCCCCCc
Q 000878 1067 F-FDDE-----------RTVYHCPFCNL 1082 (1241)
Q Consensus 1067 ~-~d~~-----------k~~yHC~~Cgi 1082 (1241)
. |-|| .+++-||+||.
T Consensus 190 ~cfCddHvrrKg~ky~k~k~~PCPKCg~ 217 (314)
T PF06524_consen 190 ICFCDDHVRRKGFKYEKGKPIPCPKCGY 217 (314)
T ss_pred eeehhhhhhhcccccccCCCCCCCCCCC
Confidence 6 3333 24566666664
No 133
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=69.90 E-value=2.2 Score=44.90 Aligned_cols=29 Identities=28% Similarity=0.573 Sum_probs=24.7
Q ss_pred cCCcccccccccccCCCceEEcCCCCccch
Q 000878 1117 LETNCPICCDFLFTSSETVRALPCGHYMHL 1146 (1241)
Q Consensus 1117 ~~~~CpICle~lf~s~~~~~~lpCgH~fH~ 1146 (1241)
....|.||+|+ +..++.+..|||=..||.
T Consensus 176 dkGECvICLEd-L~~GdtIARLPCLCIYHK 204 (205)
T KOG0801|consen 176 DKGECVICLED-LEAGDTIARLPCLCIYHK 204 (205)
T ss_pred cCCcEEEEhhh-ccCCCceeccceEEEeec
Confidence 35789999999 577788899999999986
No 134
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=69.55 E-value=2.8 Score=42.75 Aligned_cols=35 Identities=23% Similarity=0.636 Sum_probs=24.1
Q ss_pred cceEEcCCCCCCCCcc-c---hh-hcccCCCCCCccccccc
Q 000878 1193 VQDILCNDCEQKGAAR-F---HW-LYHKCGFCGSYNTRLIK 1228 (1241)
Q Consensus 1193 ~~~i~CnDC~~~s~~~-f---h~-lg~kC~~CgsYNT~~~~ 1228 (1241)
.....| +||..+... + |+ .+..||.|||++..++.
T Consensus 68 p~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~ 107 (124)
T PRK00762 68 PVEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKRAHILG 107 (124)
T ss_pred CeeEEe-eCcCcccccccchhccccCCcCcCCCCCCCEEec
Confidence 356799 999875422 1 11 23569999999988753
No 135
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=69.39 E-value=3 Score=32.48 Aligned_cols=37 Identities=35% Similarity=0.725 Sum_probs=26.1
Q ss_pred ccccccccccCCCceEEcCCCCccchhhHHHHHhcCCCCCCCCcccc
Q 000878 1121 CPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSLG 1167 (1241)
Q Consensus 1121 CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~~~~~CPiCrk~~~ 1167 (1241)
|+.|.+.+..+...+.. =|..||.+|| +|..|++++.
T Consensus 2 C~~C~~~i~~~~~~~~~--~~~~~H~~Cf--------~C~~C~~~L~ 38 (39)
T smart00132 2 CAGCGKPIRGGELVLRA--LGKVWHPECF--------KCSKCGKPLG 38 (39)
T ss_pred ccccCCcccCCcEEEEe--CCccccccCC--------CCcccCCcCc
Confidence 88898886544232222 3889999988 7888888764
No 136
>PRK01917 cation-binding hemerythrin HHE family protein; Provisional
Probab=68.66 E-value=59 Score=33.63 Aligned_cols=109 Identities=13% Similarity=0.110 Sum_probs=73.6
Q ss_pred HHHHHHHHHHHHHHHhhhcCCChhhHHHHHHHHHHHHHHHHHHHhhhhh----cccccccccccchhhhhHHhh-hHHHH
Q 000878 312 NAIRQELNEIAEESRKIQLSGDFTNLLAFNERLQFIAEVLIFHCIAEVN----VIFPAVDGASSFSQKHAEEES-QFNDF 386 (1241)
Q Consensus 312 kAIRkDh~el~~~~~kl~~~~d~~~l~~~~~r~qfL~el~r~HS~AEe~----vVyPALE~~~s~~~dh~~eeh-~~eei 386 (1241)
..|=.+|++|-+.++++..+ .. ..+...+.+|.+-.+.|=..||. +=||.++ .|..+-. .+++|
T Consensus 15 ~~ID~qH~~Lf~lin~l~~~-~~---~~i~~~l~~L~~y~~~HF~~EE~lM~~~~YP~~~-------~H~~eH~~fl~~v 83 (139)
T PRK01917 15 PFTDATHAEFVQLLNAVARA-DD---ADFLQALDAWIDHTRHHFAQEERWMEATKFGPRH-------CHRAEHDEVLAVA 83 (139)
T ss_pred hhhhHHHHHHHHHHHHHHcC-CH---HHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCChH-------HHHHHHHHHHHHH
Confidence 34567889999999998643 22 23566788999999999999994 5699997 5555422 23446
Q ss_pred HHHHHHHHhcCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHhcc
Q 000878 387 RLLIESIQNEGAISTSAEFYAKLCSHADQIMETIERHFHKVEVQVLPLARNH 438 (1241)
Q Consensus 387 ~~LL~~lq~~~~~~~~~~f~~kL~~~l~~l~~~l~~Hi~eEE~E~lPll~k~ 438 (1241)
..+...+...+ +..+... ....|..-+..||..+-...-+.+.+.
T Consensus 84 ~~l~~~~~~~g----~~~~~~~---l~~~L~~Wl~~HI~~~D~~~~~~l~~~ 128 (139)
T PRK01917 84 ADVREKVARDG----DFELGRR---LVAELPEWFDQHVRTMDAMMVSHLKML 128 (139)
T ss_pred HHHHHHHHhcC----CHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 66666664321 1122222 245688889999999988887777654
No 137
>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=67.83 E-value=2 Score=47.63 Aligned_cols=50 Identities=26% Similarity=0.597 Sum_probs=39.2
Q ss_pred CCcccccccccccCCCc-eEEcC-CCCccchhhHHHHHh-cCCCCC--CCCcccc
Q 000878 1118 ETNCPICCDFLFTSSET-VRALP-CGHYMHLACFQAYTC-SHYTCP--ICSKSLG 1167 (1241)
Q Consensus 1118 ~~~CpICle~lf~s~~~-~~~lp-CgH~fH~~C~~~wl~-~~~~CP--iCrk~~~ 1167 (1241)
+..||||..+.|-+.+- +.+-| |=|-|+.+|.+.-.+ .--.|| -|.|.+-
T Consensus 10 d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kILR 64 (314)
T COG5220 10 DRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKILR 64 (314)
T ss_pred cccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHHH
Confidence 44799999998887773 33446 999999999999764 457799 8988763
No 138
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=67.75 E-value=2.5 Score=49.35 Aligned_cols=42 Identities=21% Similarity=0.657 Sum_probs=26.9
Q ss_pred CCccccccccc------ccCCCceEEcCCCCccchhhHHHHHhcCCCCCCCCc
Q 000878 1118 ETNCPICCDFL------FTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSK 1164 (1241)
Q Consensus 1118 ~~~CpICle~l------f~s~~~~~~lpCgH~fH~~C~~~wl~~~~~CPiCrk 1164 (1241)
.+.||||...= .......++|-|+ -|-.+|--....||-|..
T Consensus 187 ~~~CPvCGs~P~~s~v~~~~~~G~RyL~Cs-----lC~teW~~~R~~C~~Cg~ 234 (309)
T PRK03564 187 RQFCPVCGSMPVSSVVQIGTTQGLRYLHCN-----LCESEWHVVRVKCSNCEQ 234 (309)
T ss_pred CCCCCCCCCcchhheeeccCCCCceEEEcC-----CCCCcccccCccCCCCCC
Confidence 45677777651 1122345666554 466778767889999995
No 139
>KOG2068 consensus MOT2 transcription factor [Transcription]
Probab=65.78 E-value=3.9 Score=47.73 Aligned_cols=51 Identities=27% Similarity=0.625 Sum_probs=39.9
Q ss_pred cCCcccccccccccCCCceEEcCCCCccchhhHHHHHhcCCCCCCCCcccc
Q 000878 1117 LETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSLG 1167 (1241)
Q Consensus 1117 ~~~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~~~~~CPiCrk~~~ 1167 (1241)
-...||||.+++-..+....-.|||+.++..|...-...+.+||.||++..
T Consensus 248 v~~s~p~~~~~~~~~d~~~lP~~~~~~~~l~~~~t~~~~~~~~~~~rk~~~ 298 (327)
T KOG2068|consen 248 VPPSCPICYEDLDLTDSNFLPCPCGFRLCLFCHKTISDGDGRCPGCRKPYE 298 (327)
T ss_pred cCCCCCCCCCcccccccccccccccccchhhhhhcccccCCCCCccCCccc
Confidence 356799999996444444444568999999999888888999999998753
No 140
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=65.55 E-value=4.9 Score=49.71 Aligned_cols=127 Identities=26% Similarity=0.593 Sum_probs=71.9
Q ss_pred CCccc--CCCCCccccCCCCCccc------cccCCcccccccccccccccccccCCcccccccccccCCCceEEcCCCCc
Q 000878 1072 RTVYH--CPFCNLCRVGGGLGVDF------FHCMTCNCCLGLKLLNHKCLEKCLETNCPICCDFLFTSSETVRALPCGHY 1143 (1241)
Q Consensus 1072 k~~yH--C~~CgiCRvg~~l~~~~------fhC~~C~~C~s~~l~~H~C~e~~~~~~CpICle~lf~s~~~~~~lpCgH~ 1143 (1241)
-+.|| |-.|.+|+..+.-|... --|.+|-.=+++. =.+...-.+|+-|.+.| .++..+..| +--
T Consensus 84 gktyh~~cf~cs~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~-----p~~~~~ps~cagc~~~l-k~gq~llal--d~q 155 (670)
T KOG1044|consen 84 GKTYHPKCFSCSTCKSPFKSGDKVTFSGKECLCQTCSQPMPVS-----PAESYGPSTCAGCGEEL-KNGQALLAL--DKQ 155 (670)
T ss_pred cceeccccceecccCCCCCCCCeeeecchhhhhhhhcCcccCC-----cccccCCccccchhhhh-hccceeeee--ccc
Confidence 45666 77777777776555332 2333333333322 12234567899999994 555545444 566
Q ss_pred cchhhHHHHHhcCCCCCCCCcccccchhhhhhhHHHHhccCCC---HhhhcccceEEcCCCCCC--------CCccchhh
Q 000878 1144 MHLACFQAYTCSHYTCPICSKSLGDMAIYFGMIDALLAAEELP---EEYRNQVQDILCNDCEQK--------GAARFHWL 1212 (1241)
Q Consensus 1144 fH~~C~~~wl~~~~~CPiCrk~~~dm~~~~~~lD~~i~~~~~P---~ey~~~~~~i~CnDC~~~--------s~~~fh~l 1212 (1241)
+|..|| +|--|.+-+. - +.+...-.| ..|...+ -|.|-.|.+- +.--||--
T Consensus 156 whv~cf--------kc~~c~~vL~-g--------ey~skdg~pyce~dy~~~f-gvkc~~c~~fisgkvLqag~kh~HPt 217 (670)
T KOG1044|consen 156 WHVSCF--------KCKSCSAVLN-G--------EYMSKDGVPYCEKDYQAKF-GVKCEECEKFISGKVLQAGDKHFHPT 217 (670)
T ss_pred eeeeee--------ehhhhccccc-c--------eeeccCCCcchhhhhhhhc-CeehHHhhhhhhhhhhhccCcccCcc
Confidence 777776 5666765442 1 111222333 2355554 4789999643 22347777
Q ss_pred cccCCCCCCccc
Q 000878 1213 YHKCGFCGSYNT 1224 (1241)
Q Consensus 1213 g~kC~~CgsYNT 1224 (1241)
+-+|.-||.-=|
T Consensus 218 CARCsRCgqmF~ 229 (670)
T KOG1044|consen 218 CARCSRCGQMFG 229 (670)
T ss_pred hhhhhhhccccc
Confidence 888888887544
No 141
>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=64.93 E-value=5.1 Score=49.95 Aligned_cols=45 Identities=20% Similarity=0.514 Sum_probs=39.6
Q ss_pred ccccccCCcccCchhhcccCCCCCCcccccceeccccccccccCCCCCC
Q 000878 1001 IRAACCGKLFTCRFCHDKASDHSMDRKATSEMMCMHCLKIQAIGPNCTT 1049 (1241)
Q Consensus 1001 l~~pcC~k~y~Cr~CHde~~~H~~~r~~~~~~~C~~C~~~q~~~~~C~~ 1049 (1241)
+.|.-||....|..|.-...-|.. ...+.|-.|+..+++...|++
T Consensus 214 ~~C~~Cg~~~~C~~C~~~l~~h~~----~~~l~Ch~Cg~~~~~~~~Cp~ 258 (505)
T TIGR00595 214 LLCRSCGYILCCPNCDVSLTYHKK----EGKLRCHYCGYQEPIPKTCPQ 258 (505)
T ss_pred eEhhhCcCccCCCCCCCceEEecC----CCeEEcCCCcCcCCCCCCCCC
Confidence 789999999999999887777754 348999999999999999988
No 142
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=64.91 E-value=0.58 Score=54.95 Aligned_cols=52 Identities=23% Similarity=0.486 Sum_probs=44.4
Q ss_pred ccCCcccccccccccCCCceEEcCCCCccchhhHHHHHhcCCCCCCCCcccc
Q 000878 1116 CLETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSLG 1167 (1241)
Q Consensus 1116 ~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~~~~~CPiCrk~~~ 1167 (1241)
+.-..|.||.+.|-..-.++..+-|||.+|..|+.+|+.....||.|++.+.
T Consensus 194 slv~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~~~~kl~~~~rel~ 245 (465)
T KOG0827|consen 194 SLVGSLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLATKRKLPSCRRELP 245 (465)
T ss_pred HHHhhhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHHHhHHHHhhhh
Confidence 4456799999996555467788899999999999999988999999999885
No 143
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=64.06 E-value=5.2 Score=47.72 Aligned_cols=46 Identities=20% Similarity=0.500 Sum_probs=37.4
Q ss_pred CcccccccccccCCCceEEcCCCCccchhhHHHHHhcC---CCCCCCCcc
Q 000878 1119 TNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSH---YTCPICSKS 1165 (1241)
Q Consensus 1119 ~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~~~---~~CPiCrk~ 1165 (1241)
-.|||=.+- -+...|.+.|.|||.+-.+-++...+++ .+||.|-..
T Consensus 335 F~CPVlKeq-tsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~e 383 (394)
T KOG2817|consen 335 FICPVLKEQ-TSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPVE 383 (394)
T ss_pred eecccchhh-ccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCcc
Confidence 469998877 4555688899999999999999998654 689999754
No 144
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=63.95 E-value=5.7 Score=51.44 Aligned_cols=53 Identities=21% Similarity=0.503 Sum_probs=42.2
Q ss_pred ccccccCCcccCchhhcccCCCCCCcccccceeccccccccccCCCCCCCCCCCCcceeE
Q 000878 1001 IRAACCGKLFTCRFCHDKASDHSMDRKATSEMMCMHCLKIQAIGPNCTTPSCNGLSMAKY 1060 (1241)
Q Consensus 1001 l~~pcC~k~y~Cr~CHde~~~H~~~r~~~~~~~C~~C~~~q~~~~~C~~~~Cc~~~~a~y 1060 (1241)
+.|..||-.+.|.+|=.-..=|.-. ..+.|-+|+..+++-..|++ | |...=+|
T Consensus 436 l~C~~Cg~v~~Cp~Cd~~lt~H~~~----~~L~CH~Cg~~~~~p~~Cp~--C-gs~~L~~ 488 (730)
T COG1198 436 LLCRDCGYIAECPNCDSPLTLHKAT----GQLRCHYCGYQEPIPQSCPE--C-GSEHLRA 488 (730)
T ss_pred eecccCCCcccCCCCCcceEEecCC----CeeEeCCCCCCCCCCCCCCC--C-CCCeeEE
Confidence 8899999999999996555545433 59999999999999999988 5 6554444
No 145
>PF14357 DUF4404: Domain of unknown function (DUF4404)
Probab=63.54 E-value=33 Score=32.86 Aligned_cols=81 Identities=15% Similarity=0.140 Sum_probs=62.9
Q ss_pred HHHHHHHHHHHHHhhhcCCcccHHHHHHHHHHHHHHhhccCccccccccHHHhhhhhhHHHHHHHhHHHHHHHHHHHHHH
Q 000878 52 VRNELDALHQLAMNFATGHRVDILSLSERYRFLHSVYKHHSNAEDEVIFPALDIRVKNVARKYSLEHEGESNLFDHLFQL 131 (1241)
Q Consensus 52 IRreL~~L~~la~~l~~gd~~dl~~L~~~l~fL~~~L~~HH~aEDevLFPaL~~R~p~vl~~le~EH~~id~lL~~L~~l 131 (1241)
|+..|+.|+..+.+..+-|......+....+-+...+.. ..+...-=+.|..++...+.+++.+|=.+...+..|-..
T Consensus 2 L~~~L~~L~~eL~~~~~ld~~~~~~L~~l~~dIe~~L~~--~~~~~~~~~~l~d~l~~av~~FE~~HP~l~~~lr~i~~s 79 (85)
T PF14357_consen 2 LQELLEKLHQELEQNPPLDEETRAELSSLDDDIEAQLAE--EDEAEAEDESLVDRLNEAVERFEASHPKLAGILRNIMDS 79 (85)
T ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHhc--CCcccccchhHHHHHHHHHHHHHHhCCcHHHHHHHHHHH
Confidence 678899999999987766666666777766777777744 445556667788888888899999999999999988877
Q ss_pred Hhh
Q 000878 132 LNS 134 (1241)
Q Consensus 132 L~~ 134 (1241)
|..
T Consensus 80 La~ 82 (85)
T PF14357_consen 80 LAN 82 (85)
T ss_pred HHH
Confidence 754
No 146
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=62.85 E-value=6.2 Score=53.11 Aligned_cols=51 Identities=25% Similarity=0.505 Sum_probs=26.6
Q ss_pred ceeccccccccccCCCCCCCCCCCCc-ceeEeccccccc--cCCCCcccCCCCCcccc
Q 000878 1031 EMMCMHCLKIQAIGPNCTTPSCNGLS-MAKYYCNICKFF--DDERTVYHCPFCNLCRV 1085 (1241)
Q Consensus 1031 ~~~C~~C~~~q~~~~~C~~~~Cc~~~-~a~y~C~~C~~~--d~~k~~yHC~~CgiCRv 1085 (1241)
...|..|+++-+. ..|++ | |.+ -..|+|..|..- .|+.....||+||.=-+
T Consensus 667 ~rkCPkCG~~t~~-~fCP~--C-Gs~te~vy~CPsCGaev~~des~a~~CP~CGtplv 720 (1337)
T PRK14714 667 RRRCPSCGTETYE-NRCPD--C-GTHTEPVYVCPDCGAEVPPDESGRVECPRCDVELT 720 (1337)
T ss_pred EEECCCCCCcccc-ccCcc--c-CCcCCCceeCccCCCccCCCccccccCCCCCCccc
Confidence 3455555554332 25655 3 333 245666666652 12223668999985443
No 147
>PHA03096 p28-like protein; Provisional
Probab=62.10 E-value=4.3 Score=46.97 Aligned_cols=47 Identities=17% Similarity=0.311 Sum_probs=32.2
Q ss_pred CcccccccccccC---CCceEEcC-CCCccchhhHHHHHhc---CCCCCCCCcc
Q 000878 1119 TNCPICCDFLFTS---SETVRALP-CGHYMHLACFQAYTCS---HYTCPICSKS 1165 (1241)
Q Consensus 1119 ~~CpICle~lf~s---~~~~~~lp-CgH~fH~~C~~~wl~~---~~~CPiCrk~ 1165 (1241)
-.|-||+|..... ...-.+|+ |.|.|...|+..|... ..+||.|+..
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~~ 232 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRRL 232 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCccccch
Confidence 5699999986543 22334564 9999999999999732 3456655543
No 148
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=61.50 E-value=3.7 Score=51.47 Aligned_cols=69 Identities=20% Similarity=0.457 Sum_probs=41.4
Q ss_pred CcccccccccccCCCceEEcCCC---CccchhhHHH----HH----hcCCCCCCCCcccccchhhhhhhHHHHhccCCCH
Q 000878 1119 TNCPICCDFLFTSSETVRALPCG---HYMHLACFQA----YT----CSHYTCPICSKSLGDMAIYFGMIDALLAAEELPE 1187 (1241)
Q Consensus 1119 ~~CpICle~lf~s~~~~~~lpCg---H~fH~~C~~~----wl----~~~~~CPiCrk~~~dm~~~~~~lD~~i~~~~~P~ 1187 (1241)
..||+|+-. |-..+....+-|. --.|..|..- +. ...|.|-+|| ....+-..+...+...-+|.
T Consensus 146 ~~cPvc~~~-Y~~~e~~~~~~c~~c~rwsh~~c~~~sdd~~~q~~vD~~~~CS~CR----~es~qvKdi~~~vqe~~~~k 220 (694)
T KOG4443|consen 146 SYCPVCLIV-YQDSESLPMVCCSICQRWSHGGCDGISDDKYMQAQVDLQYKCSTCR----GESYQVKDISDALQETWKAK 220 (694)
T ss_pred ccCchHHHh-hhhccchhhHHHHHhcccccCCCCccchHHHHHHhhhhhcccceee----hhhhhhhhHHHHHHhhcchh
Confidence 579999966 6555555444444 4478888533 22 1369999999 22223445555566666666
Q ss_pred hhhcc
Q 000878 1188 EYRNQ 1192 (1241)
Q Consensus 1188 ey~~~ 1192 (1241)
.|.+.
T Consensus 221 ~~~~~ 225 (694)
T KOG4443|consen 221 DKPDK 225 (694)
T ss_pred hcccc
Confidence 55443
No 149
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=61.42 E-value=5.5 Score=40.98 Aligned_cols=47 Identities=34% Similarity=0.706 Sum_probs=34.9
Q ss_pred cCCcccccccccccCCCceEEc-C---CCCccchhhHHH-HH--hcCCCCCCCCcccc
Q 000878 1117 LETNCPICCDFLFTSSETVRAL-P---CGHYMHLACFQA-YT--CSHYTCPICSKSLG 1167 (1241)
Q Consensus 1117 ~~~~CpICle~lf~s~~~~~~l-p---CgH~fH~~C~~~-wl--~~~~~CPiCrk~~~ 1167 (1241)
.-..|.||.|- |.+ -+.| | ||-.+...|+.. |- .....||+|+.|.-
T Consensus 79 ~lYeCnIC~et---S~e-e~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFK 132 (140)
T PF05290_consen 79 KLYECNICKET---SAE-ERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFK 132 (140)
T ss_pred CceeccCcccc---cch-hhcCCcccccchHHHHHHHHHHHHHcccCCCCCccccccc
Confidence 34679999987 443 3444 4 999999999887 43 34588999998853
No 150
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=61.08 E-value=1.2 Score=59.14 Aligned_cols=50 Identities=30% Similarity=0.594 Sum_probs=40.4
Q ss_pred CCcccccccccccCCCceEEcCCCCccchhhHHHHHhcCCCCCCCCcccccch
Q 000878 1118 ETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSLGDMA 1170 (1241)
Q Consensus 1118 ~~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~~~~~CPiCrk~~~dm~ 1170 (1241)
.-.|+||++-|- ..-.+..|||.+...|+..|+..+..||+|+...++..
T Consensus 1153 ~~~c~ic~dil~---~~~~I~~cgh~~c~~c~~~~l~~~s~~~~~ksi~~dfg 1202 (1394)
T KOG0298|consen 1153 HFVCEICLDILR---NQGGIAGCGHEPCCRCDELWLYASSRCPICKSIKGDFG 1202 (1394)
T ss_pred ccchHHHHHHHH---hcCCeeeechhHhhhHHHHHHHHhccCcchhhhhhhhc
Confidence 348999998852 12345679999999999999999999999997766554
No 151
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=60.84 E-value=7.9 Score=48.03 Aligned_cols=138 Identities=20% Similarity=0.336 Sum_probs=68.3
Q ss_pred CCcccCCCCCccccCCCC--Cccccc-----cCCcccccccccccccccccccCCcccccccccccCCCceEEcCCCCcc
Q 000878 1072 RTVYHCPFCNLCRVGGGL--GVDFFH-----CMTCNCCLGLKLLNHKCLEKCLETNCPICCDFLFTSSETVRALPCGHYM 1144 (1241)
Q Consensus 1072 k~~yHC~~CgiCRvg~~l--~~~~fh-----C~~C~~C~s~~l~~H~C~e~~~~~~CpICle~lf~s~~~~~~lpCgH~f 1144 (1241)
+.+.||++|+-==-|.-| ..++|| |.+||.=+.-...-+|+.|.-. ++ .-|.+. .+...+..=|-+|
T Consensus 14 ~~~i~c~~c~~kc~gevlrv~d~~fhi~cf~c~~cg~~la~~gff~k~~~~~y-gt-~~c~~~----~~gevvsa~gkty 87 (670)
T KOG1044|consen 14 KQGIKCDKCRKKCSGEVLRVNDNHFHINCFQCKKCGRNLAEGGFFTKPENRLY-GT-DDCRAF----VEGEVVSTLGKTY 87 (670)
T ss_pred ccceehhhhCCccccceeEeeccccceeeeeccccCCCcccccceecccceee-cc-cchhhh----ccceeEeccccee
Confidence 566677777632112111 123333 4444443333334556655311 11 223332 1223444458999
Q ss_pred chhhHHHHHhcCCCCCCCCcccccchh-hhh--hhHHHHhccCCCHhhhcccceEEcCCCCCCC---------Cccchhh
Q 000878 1145 HLACFQAYTCSHYTCPICSKSLGDMAI-YFG--MIDALLAAEELPEEYRNQVQDILCNDCEQKG---------AARFHWL 1212 (1241)
Q Consensus 1145 H~~C~~~wl~~~~~CPiCrk~~~dm~~-~~~--~lD~~i~~~~~P~ey~~~~~~i~CnDC~~~s---------~~~fh~l 1212 (1241)
|..|+ +|-+|+++...-+. .+. ..--+.-.++||-.=.....--.|-.|+..- ..++|+.
T Consensus 88 h~~cf--------~cs~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk~gq~llald~qwhv~ 159 (670)
T KOG1044|consen 88 HPKCF--------SCSTCKSPFKSGDKVTFSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELKNGQALLALDKQWHVS 159 (670)
T ss_pred ccccc--------eecccCCCCCCCCeeeecchhhhhhhhcCcccCCcccccCCccccchhhhhhccceeeeeccceeee
Confidence 99987 57777777532111 111 1111223455554312222334688887542 3568999
Q ss_pred cccCCCCCCcc
Q 000878 1213 YHKCGFCGSYN 1223 (1241)
Q Consensus 1213 g~kC~~CgsYN 1223 (1241)
+-||..|+.-=
T Consensus 160 cfkc~~c~~vL 170 (670)
T KOG1044|consen 160 CFKCKSCSAVL 170 (670)
T ss_pred eeehhhhcccc
Confidence 99999876543
No 152
>cd00522 Hemerythrin Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the muscle tissue of sipunculids as well as in polycheate and oligocheate annelids. In addition to oxygen transport, Mhr proteins are involved in cadmium fixation and host anti-bacterial defense. Hr and Mhr proteins have the same "four alpha helix bundle" motif and active site structure. Hr forms oligomers, the octameric form being most prevalent, while Mhr is monomeric.
Probab=60.63 E-value=62 Score=32.16 Aligned_cols=96 Identities=15% Similarity=0.129 Sum_probs=63.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhcCCcccHHHHHHHHHHHHHHhhccCccccccc----cHHHhhhhhhHHHHHHHh
Q 000878 42 ILIFCFFHKAVRNELDALHQLAMNFATGHRVDILSLSERYRFLHSVYKHHSNAEDEVI----FPALDIRVKNVARKYSLE 117 (1241)
Q Consensus 42 Id~l~~~H~AIRreL~~L~~la~~l~~gd~~dl~~L~~~l~fL~~~L~~HH~aEDevL----FPaL~~R~p~vl~~le~E 117 (1241)
+..|-..|+.|=..++.|..+... ...+.+|.++...|=..||.++ ||.+... ..+
T Consensus 12 ~~~ID~qH~~L~~l~n~l~~a~~~------------~~~l~~L~~y~~~HF~~EE~~M~~~~yp~~~~H--------~~~ 71 (113)
T cd00522 12 YEVIDDEHKTLFNGINDLSEANNR------------ADNLKELVDYTVKHFKDEEALMEAAGYPDYEEH--------KKI 71 (113)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHhH------------HHHHHHHHHHHHHHHHHHHHHHHHcCCCCHHHH--------HHH
Confidence 345567888888887777776543 4567888888888988898765 5554433 345
Q ss_pred HHHHHHHHHHHHHHHhhhccCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhHHH
Q 000878 118 HEGESNLFDHLFQLLNSYTQNDESFPKELASCSRALQTSINQHMSKEEQQVFP 170 (1241)
Q Consensus 118 H~~id~lL~~L~~lL~~~~~~~~~~~~eLa~al~~L~~~L~~HL~~EE~eVfP 170 (1241)
|+..-..+.++...+ ....+.-+..-+..|+..+...+.+
T Consensus 72 H~~f~~~~~~~~~~~-------------~~~~~~~l~~Wl~~HI~~~D~~~~~ 111 (113)
T cd00522 72 HEDFVEKVGGLKAPV-------------GQADLKYLKDWLVNHIKTEDFKYKG 111 (113)
T ss_pred HHHHHHHHHHHHHHH-------------HHHHHHHHHHHHHHHhHhHHHHhhh
Confidence 655544444443322 1234556788899999988876654
No 153
>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=60.29 E-value=5.5 Score=39.81 Aligned_cols=18 Identities=33% Similarity=0.713 Sum_probs=15.7
Q ss_pred ccccCCCCcccCCCCCcc
Q 000878 1066 KFFDDERTVYHCPFCNLC 1083 (1241)
Q Consensus 1066 ~~~d~~k~~yHC~~CgiC 1083 (1241)
||||=.|.+..||+||-=
T Consensus 18 kFYDLnk~PivCP~CG~~ 35 (108)
T PF09538_consen 18 KFYDLNKDPIVCPKCGTE 35 (108)
T ss_pred hhccCCCCCccCCCCCCc
Confidence 788999999999999953
No 154
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=59.55 E-value=5.6 Score=40.14 Aligned_cols=37 Identities=30% Similarity=0.469 Sum_probs=28.3
Q ss_pred cccceEEcCCCCCCCCccchhhcccCCCCCCcccccccc
Q 000878 1191 NQVQDILCNDCEQKGAARFHWLYHKCGFCGSYNTRLIKN 1229 (1241)
Q Consensus 1191 ~~~~~i~CnDC~~~s~~~fh~lg~kC~~CgsYNT~~~~~ 1229 (1241)
.....+.|-+|+......-|.++ ||.|||-|.+++.-
T Consensus 66 ~~p~~~~C~~C~~~~~~e~~~~~--CP~C~s~~~~i~~G 102 (115)
T COG0375 66 EEPAECWCLDCGQEVELEELDYR--CPKCGSINLRIIGG 102 (115)
T ss_pred EeccEEEeccCCCeecchhheeE--CCCCCCCceEEecC
Confidence 34567899999887765555545 99999999998743
No 155
>PRK01917 cation-binding hemerythrin HHE family protein; Provisional
Probab=59.18 E-value=83 Score=32.53 Aligned_cols=111 Identities=12% Similarity=0.050 Sum_probs=71.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhcCCcccHHHHHHHHHHHHHHhhccCccccccc----cHHHhhhhhhHHHHHHHh
Q 000878 42 ILIFCFFHKAVRNELDALHQLAMNFATGHRVDILSLSERYRFLHSVYKHHSNAEDEVI----FPALDIRVKNVARKYSLE 117 (1241)
Q Consensus 42 Id~l~~~H~AIRreL~~L~~la~~l~~gd~~dl~~L~~~l~fL~~~L~~HH~aEDevL----FPaL~~R~p~vl~~le~E 117 (1241)
+..|-.-|+.|=..++.|.... ...+...+.+|.++...|=..||.++ ||.+... ..+
T Consensus 14 i~~ID~qH~~Lf~lin~l~~~~----------~~~i~~~l~~L~~y~~~HF~~EE~lM~~~~YP~~~~H--------~~e 75 (139)
T PRK01917 14 DPFTDATHAEFVQLLNAVARAD----------DADFLQALDAWIDHTRHHFAQEERWMEATKFGPRHCH--------RAE 75 (139)
T ss_pred ChhhhHHHHHHHHHHHHHHcCC----------HHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCChHHH--------HHH
Confidence 4566677887776666665431 12367788999999999999998664 5544332 245
Q ss_pred HHHHHHHHHHHHHHHhhhccCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHhcc
Q 000878 118 HEGESNLFDHLFQLLNSYTQNDESFPKELASCSRALQTSINQHMSKEEQQVFPLLTQH 175 (1241)
Q Consensus 118 H~~id~lL~~L~~lL~~~~~~~~~~~~eLa~al~~L~~~L~~HL~~EE~eVfPLa~~~ 175 (1241)
|+..-..+.++... +...+. .......+..+..-+..|+..+-..+.+.+.+.
T Consensus 76 H~~fl~~v~~l~~~---~~~~g~--~~~~~~l~~~L~~Wl~~HI~~~D~~~~~~l~~~ 128 (139)
T PRK01917 76 HDEVLAVAADVREK---VARDGD--FELGRRLVAELPEWFDQHVRTMDAMMVSHLKML 128 (139)
T ss_pred HHHHHHHHHHHHHH---HHhcCC--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 55555555554443 333111 123345667788899999999999988877654
No 156
>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=58.93 E-value=5 Score=41.02 Aligned_cols=18 Identities=28% Similarity=0.425 Sum_probs=16.0
Q ss_pred ccccCCCCcccCCCCCcc
Q 000878 1066 KFFDDERTVYHCPFCNLC 1083 (1241)
Q Consensus 1066 ~~~d~~k~~yHC~~CgiC 1083 (1241)
||||-.|.+..||+||.=
T Consensus 18 kFYDLnk~p~vcP~cg~~ 35 (129)
T TIGR02300 18 KFYDLNRRPAVSPYTGEQ 35 (129)
T ss_pred cccccCCCCccCCCcCCc
Confidence 788989999999999964
No 157
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=58.42 E-value=5.6 Score=51.24 Aligned_cols=47 Identities=28% Similarity=0.721 Sum_probs=34.9
Q ss_pred cCCcccccccccccCCCceEE-cCCCCccchhhHHHHHhc-------CCCCCCCCc
Q 000878 1117 LETNCPICCDFLFTSSETVRA-LPCGHYMHLACFQAYTCS-------HYTCPICSK 1164 (1241)
Q Consensus 1117 ~~~~CpICle~lf~s~~~~~~-lpCgH~fH~~C~~~wl~~-------~~~CPiCrk 1164 (1241)
....|.||.+.| +...++-- -.|=|.||..||..|.++ .-+||-|+.
T Consensus 190 ~~yeCmIC~e~I-~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqs 244 (950)
T KOG1952|consen 190 RKYECMICTERI-KRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQS 244 (950)
T ss_pred CceEEEEeeeec-cccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccc
Confidence 456899999995 44444322 348899999999999742 378999993
No 158
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=58.36 E-value=10 Score=33.45 Aligned_cols=35 Identities=23% Similarity=0.633 Sum_probs=26.4
Q ss_pred cCCcccccccccccCCCceEE-cCCCCccchhhHHHH
Q 000878 1117 LETNCPICCDFLFTSSETVRA-LPCGHYMHLACFQAY 1152 (1241)
Q Consensus 1117 ~~~~CpICle~lf~s~~~~~~-lpCgH~fH~~C~~~w 1152 (1241)
....|++|.+. |++.+.+.+ --||=.+|..|...-
T Consensus 4 ~~~~C~~Cg~~-~~~~dDiVvCp~CgapyHR~C~~~~ 39 (54)
T PF14446_consen 4 EGCKCPVCGKK-FKDGDDIVVCPECGAPYHRDCWEKA 39 (54)
T ss_pred cCccChhhCCc-ccCCCCEEECCCCCCcccHHHHhhC
Confidence 34679999999 555555555 459999999998654
No 159
>PRK14873 primosome assembly protein PriA; Provisional
Probab=57.83 E-value=7 Score=50.33 Aligned_cols=44 Identities=20% Similarity=0.366 Sum_probs=36.8
Q ss_pred ccccccCCcccCchhhcccCCCCCCcccccceeccccccccccCCCCCC
Q 000878 1001 IRAACCGKLFTCRFCHDKASDHSMDRKATSEMMCMHCLKIQAIGPNCTT 1049 (1241)
Q Consensus 1001 l~~pcC~k~y~Cr~CHde~~~H~~~r~~~~~~~C~~C~~~q~~~~~C~~ 1049 (1241)
+.|..||....|..|.--..=|.- ...+.|-+|+..+ ....|++
T Consensus 384 l~C~~Cg~~~~C~~C~~~L~~h~~----~~~l~Ch~CG~~~-~p~~Cp~ 427 (665)
T PRK14873 384 LACARCRTPARCRHCTGPLGLPSA----GGTPRCRWCGRAA-PDWRCPR 427 (665)
T ss_pred eEhhhCcCeeECCCCCCceeEecC----CCeeECCCCcCCC-cCccCCC
Confidence 799999999999999888776642 3479999999977 4679988
No 160
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=57.17 E-value=4.4 Score=47.35 Aligned_cols=43 Identities=26% Similarity=0.593 Sum_probs=28.0
Q ss_pred CCcccccccccc----c---CCCceEEcCCCCccchhhHHHHHhcCCCCCCCCcc
Q 000878 1118 ETNCPICCDFLF----T---SSETVRALPCGHYMHLACFQAYTCSHYTCPICSKS 1165 (1241)
Q Consensus 1118 ~~~CpICle~lf----~---s~~~~~~lpCgH~fH~~C~~~wl~~~~~CPiCrk~ 1165 (1241)
.+.||||...=. . .....++|-|+ -|-.+|--....||.|..+
T Consensus 184 ~~~CPvCGs~P~~s~~~~~~~~~G~RyL~Cs-----lC~teW~~~R~~C~~Cg~~ 233 (305)
T TIGR01562 184 RTLCPACGSPPVASMVRQGGKETGLRYLSCS-----LCATEWHYVRVKCSHCEES 233 (305)
T ss_pred CCcCCCCCChhhhhhhcccCCCCCceEEEcC-----CCCCcccccCccCCCCCCC
Confidence 457888876511 1 12345666655 4777787778899999964
No 161
>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=56.94 E-value=11 Score=32.44 Aligned_cols=40 Identities=33% Similarity=0.869 Sum_probs=20.0
Q ss_pred cccccccccccCCCceEEcCCCCccchhhHHH--HHh-----cCCCCCCCCcc
Q 000878 1120 NCPICCDFLFTSSETVRALPCGHYMHLACFQA--YTC-----SHYTCPICSKS 1165 (1241)
Q Consensus 1120 ~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~--wl~-----~~~~CPiCrk~ 1165 (1241)
.|||....| ..+++...|.|. +||+- |+. ....||+|+++
T Consensus 4 ~CPls~~~i---~~P~Rg~~C~H~---~CFDl~~fl~~~~~~~~W~CPiC~~~ 50 (50)
T PF02891_consen 4 RCPLSFQRI---RIPVRGKNCKHL---QCFDLESFLESNQRTPKWKCPICNKP 50 (50)
T ss_dssp B-TTTSSB----SSEEEETT--SS-----EEHHHHHHHHHHS---B-TTT---
T ss_pred eCCCCCCEE---EeCccCCcCccc---ceECHHHHHHHhhccCCeECcCCcCc
Confidence 599998885 558888889976 57553 542 34679999974
No 162
>PF12773 DZR: Double zinc ribbon
Probab=55.23 E-value=8.8 Score=32.47 Aligned_cols=36 Identities=22% Similarity=0.529 Sum_probs=20.4
Q ss_pred cccccccccc-CCCCCCCCCCCCcceeEeccccccccCCCCcccCCCCCc
Q 000878 1034 CMHCLKIQAI-GPNCTTPSCNGLSMAKYYCNICKFFDDERTVYHCPFCNL 1082 (1241)
Q Consensus 1034 C~~C~~~q~~-~~~C~~~~Cc~~~~a~y~C~~C~~~d~~k~~yHC~~Cgi 1082 (1241)
|..|+++.+. ..+|.+ ||..+. ..+...+.|+.||-
T Consensus 1 Cp~Cg~~~~~~~~fC~~---CG~~l~----------~~~~~~~~C~~Cg~ 37 (50)
T PF12773_consen 1 CPHCGTPNPDDAKFCPH---CGTPLP----------PPDQSKKICPNCGA 37 (50)
T ss_pred CCCcCCcCCccccCChh---hcCChh----------hccCCCCCCcCCcC
Confidence 5667766544 456777 366655 22345556666663
No 163
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=55.05 E-value=7.4 Score=45.53 Aligned_cols=23 Identities=26% Similarity=0.817 Sum_probs=17.1
Q ss_pred eEEcCCCCCCCCccchhhcccCCCCCC
Q 000878 1195 DILCNDCEQKGAARFHWLYHKCGFCGS 1221 (1241)
Q Consensus 1195 ~i~CnDC~~~s~~~fh~lg~kC~~Cgs 1221 (1241)
...|+=|+ ..+|+.-.||++||+
T Consensus 210 yL~CslC~----teW~~~R~~C~~Cg~ 232 (305)
T TIGR01562 210 YLSCSLCA----TEWHYVRVKCSHCEE 232 (305)
T ss_pred EEEcCCCC----CcccccCccCCCCCC
Confidence 45688777 567777888888885
No 164
>PLN03086 PRLI-interacting factor K; Provisional
Probab=54.92 E-value=6.9 Score=49.20 Aligned_cols=103 Identities=21% Similarity=0.572 Sum_probs=0.0
Q ss_pred cccceeccccccccccCCC-------------CCCCCCCCCcceeEeccccccccCCCCcccCCCCCccccCCCCCcccc
Q 000878 1028 ATSEMMCMHCLKIQAIGPN-------------CTTPSCNGLSMAKYYCNICKFFDDERTVYHCPFCNLCRVGGGLGVDFF 1094 (1241)
Q Consensus 1028 ~~~~~~C~~C~~~q~~~~~-------------C~~~~Cc~~~~a~y~C~~C~~~d~~k~~yHC~~CgiCRvg~~l~~~~f 1094 (1241)
.+..+.|..|....+.... |++..| |..|.+- +-+..+||+.|| ..|
T Consensus 404 ~~~~V~C~NC~~~i~l~~l~lHe~~C~r~~V~Cp~~~C-g~v~~r~---------el~~H~~C~~Cg----------k~f 463 (567)
T PLN03086 404 DVDTVECRNCKHYIPSRSIALHEAYCSRHNVVCPHDGC-GIVLRVE---------EAKNHVHCEKCG----------QAF 463 (567)
T ss_pred CCCeEECCCCCCccchhHHHHHHhhCCCcceeCCcccc-cceeecc---------ccccCccCCCCC----------Ccc
Q ss_pred c----------------cCCccccccccc-ccc---cccccccCCcccccccccc------------cCCCceEEcCCCC
Q 000878 1095 H----------------CMTCNCCLGLKL-LNH---KCLEKCLETNCPICCDFLF------------TSSETVRALPCGH 1142 (1241)
Q Consensus 1095 h----------------C~~C~~C~s~~l-~~H---~C~e~~~~~~CpICle~lf------------~s~~~~~~lpCgH 1142 (1241)
. |. ||..+.... ..| .|-++ ...|+.|... | .+.-.....-||
T Consensus 464 ~~s~LekH~~~~Hkpv~Cp-Cg~~~~R~~L~~H~~thCp~K--pi~C~fC~~~-v~~g~~~~d~~d~~s~Lt~HE~~CG- 538 (567)
T PLN03086 464 QQGEMEKHMKVFHEPLQCP-CGVVLEKEQMVQHQASTCPLR--LITCRFCGDM-VQAGGSAMDVRDRLRGMSEHESICG- 538 (567)
T ss_pred chHHHHHHHHhcCCCccCC-CCCCcchhHHHhhhhccCCCC--ceeCCCCCCc-cccCccccchhhhhhhHHHHHHhcC-
Q ss_pred ccchhhHHHHHhcCCCCCCCCccc
Q 000878 1143 YMHLACFQAYTCSHYTCPICSKSL 1166 (1241)
Q Consensus 1143 ~fH~~C~~~wl~~~~~CPiCrk~~ 1166 (1241)
...+.|..|++.+
T Consensus 539 -----------~rt~~C~~Cgk~V 551 (567)
T PLN03086 539 -----------SRTAPCDSCGRSV 551 (567)
T ss_pred -----------CcceEccccCCee
No 165
>PRK05580 primosome assembly protein PriA; Validated
Probab=54.66 E-value=9.3 Score=49.40 Aligned_cols=45 Identities=22% Similarity=0.540 Sum_probs=39.6
Q ss_pred ccccccCCcccCchhhcccCCCCCCcccccceeccccccccccCCCCCC
Q 000878 1001 IRAACCGKLFTCRFCHDKASDHSMDRKATSEMMCMHCLKIQAIGPNCTT 1049 (1241)
Q Consensus 1001 l~~pcC~k~y~Cr~CHde~~~H~~~r~~~~~~~C~~C~~~q~~~~~C~~ 1049 (1241)
+.|.-||....|..|.-...-|.. ...+.|-.|+..++....|++
T Consensus 382 ~~C~~Cg~~~~C~~C~~~l~~h~~----~~~l~Ch~Cg~~~~~~~~Cp~ 426 (679)
T PRK05580 382 LLCRDCGWVAECPHCDASLTLHRF----QRRLRCHHCGYQEPIPKACPE 426 (679)
T ss_pred eEhhhCcCccCCCCCCCceeEECC----CCeEECCCCcCCCCCCCCCCC
Confidence 889999999999999888776753 358999999999998899998
No 166
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=53.44 E-value=9.6 Score=33.91 Aligned_cols=30 Identities=27% Similarity=0.586 Sum_probs=22.5
Q ss_pred cceEEcCCCCCCCCccchhhcccCCCCCCcccccc
Q 000878 1193 VQDILCNDCEQKGAARFHWLYHKCGFCGSYNTRLI 1227 (1241)
Q Consensus 1193 ~~~i~CnDC~~~s~~~fh~lg~kC~~CgsYNT~~~ 1227 (1241)
...+.|..||..-. .| +-|++||.||-+++
T Consensus 25 ~~l~~C~~CG~~~~--~H---~vC~~CG~Y~gr~v 54 (57)
T PRK12286 25 PGLVECPNCGEPKL--PH---RVCPSCGYYKGREV 54 (57)
T ss_pred CcceECCCCCCccC--Ce---EECCCCCcCCCEEe
Confidence 34678999997432 23 46999999999986
No 167
>PF14353 CpXC: CpXC protein
Probab=53.03 E-value=3.7 Score=41.59 Aligned_cols=56 Identities=23% Similarity=0.436 Sum_probs=29.9
Q ss_pred CCCCCCCcccccchhhhhhhHHHHhccCCCHhhhcccceEEcCCCCCCCCccchhhcc
Q 000878 1157 YTCPICSKSLGDMAIYFGMIDALLAAEELPEEYRNQVQDILCNDCEQKGAARFHWLYH 1214 (1241)
Q Consensus 1157 ~~CPiCrk~~~dm~~~~~~lD~~i~~~~~P~ey~~~~~~i~CnDC~~~s~~~fh~lg~ 1214 (1241)
.+||.|++... .+ .|..+|.....+-...-..+..-.+.|..||.+..+.|=++||
T Consensus 2 itCP~C~~~~~-~~-v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~~p~lY~ 57 (128)
T PF14353_consen 2 ITCPHCGHEFE-FE-VWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLEYPLLYH 57 (128)
T ss_pred cCCCCCCCeeE-EE-EEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecCCCEEEE
Confidence 48999998752 11 1233222111100111123445578899999988776555554
No 168
>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=52.75 E-value=6.5 Score=36.34 Aligned_cols=10 Identities=40% Similarity=1.265 Sum_probs=6.6
Q ss_pred ceeEeccccc
Q 000878 1057 MAKYYCNICK 1066 (1241)
Q Consensus 1057 ~a~y~C~~C~ 1066 (1241)
.+.|||..|+
T Consensus 48 AvdYFC~~c~ 57 (70)
T PF07191_consen 48 AVDYFCNHCH 57 (70)
T ss_dssp EEEEE-TTTT
T ss_pred ccceeeccCC
Confidence 4678888876
No 169
>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=52.41 E-value=7.7 Score=38.79 Aligned_cols=32 Identities=22% Similarity=0.406 Sum_probs=24.4
Q ss_pred ccccccccCCcccCchhhcccCCCCCCcccccceeccccccccccC
Q 000878 999 CKIRAACCGKLFTCRFCHDKASDHSMDRKATSEMMCMHCLKIQAIG 1044 (1241)
Q Consensus 999 ckl~~pcC~k~y~Cr~CHde~~~H~~~r~~~~~~~C~~C~~~q~~~ 1044 (1241)
-|-.||-||+-| .+... ..|+|.+|+++|++.
T Consensus 8 tKR~Cp~CG~kF-------------YDLnk-~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 8 TKRTCPSCGAKF-------------YDLNK-DPIVCPKCGTEFPPE 39 (108)
T ss_pred CcccCCCCcchh-------------ccCCC-CCccCCCCCCccCcc
Confidence 466889998855 34443 578999999999876
No 170
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=52.37 E-value=9.4 Score=48.85 Aligned_cols=48 Identities=23% Similarity=0.563 Sum_probs=34.3
Q ss_pred CCcccccccccccCCCceEEcCCC-----CccchhhHHHHHhc--CCCCCCCCcccc
Q 000878 1118 ETNCPICCDFLFTSSETVRALPCG-----HYMHLACFQAYTCS--HYTCPICSKSLG 1167 (1241)
Q Consensus 1118 ~~~CpICle~lf~s~~~~~~lpCg-----H~fH~~C~~~wl~~--~~~CPiCrk~~~ 1167 (1241)
...|-||.-. +..+....-||. -++|.+|+.+|+.. ...|-+|...+-
T Consensus 12 ~~~CRICr~e--~~~d~pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~ 66 (1175)
T COG5183 12 KRSCRICRTE--DIRDDPLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYK 66 (1175)
T ss_pred chhceeecCC--CCCCCcCcccccccchhHHHHHHHHHHHHhcCCCcceeeecceee
Confidence 4578899866 233334455765 46999999999954 467999998763
No 171
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=51.96 E-value=12 Score=43.59 Aligned_cols=46 Identities=17% Similarity=0.393 Sum_probs=34.9
Q ss_pred CCcccccccccccCCCceEEcCCCCccchhhHHHHHhcCCCCCCCCccc
Q 000878 1118 ETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSL 1166 (1241)
Q Consensus 1118 ~~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~~~~~CPiCrk~~ 1166 (1241)
.+.||||+.. -.+.+ ..--=|-.|+-.|+..|+.+..+||+=..++
T Consensus 300 ~~~CpvClk~-r~Npt--vl~vSGyVfCY~Ci~~Yv~~~~~CPVT~~p~ 345 (357)
T KOG0826|consen 300 REVCPVCLKK-RQNPT--VLEVSGYVFCYPCIFSYVVNYGHCPVTGYPA 345 (357)
T ss_pred cccChhHHhc-cCCCc--eEEecceEEeHHHHHHHHHhcCCCCccCCcc
Confidence 4679999977 22222 2222499999999999999999999988775
No 172
>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=51.36 E-value=9.4 Score=32.61 Aligned_cols=34 Identities=21% Similarity=0.449 Sum_probs=22.3
Q ss_pred eEEcCCCCCCCCccchh---hcccCCCCCCccc-cccc
Q 000878 1195 DILCNDCEQKGAARFHW---LYHKCGFCGSYNT-RLIK 1228 (1241)
Q Consensus 1195 ~i~CnDC~~~s~~~fh~---lg~kC~~CgsYNT-~~~~ 1228 (1241)
...|++|+....+-..+ -...|+.||+-+. |++.
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~r~~s 42 (52)
T TIGR02605 5 EYRCTACGHRFEVLQKMSDDPLATCPECGGEKLRRLLS 42 (52)
T ss_pred EEEeCCCCCEeEEEEecCCCCCCCCCCCCCCceeEEec
Confidence 35799999876543211 1347999999886 4443
No 173
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=50.65 E-value=11 Score=43.21 Aligned_cols=43 Identities=30% Similarity=0.768 Sum_probs=33.3
Q ss_pred CcccccccccccCCCceEEcCCCCccchhhHHHH-HhcCCCCCCCCc
Q 000878 1119 TNCPICCDFLFTSSETVRALPCGHYMHLACFQAY-TCSHYTCPICSK 1164 (1241)
Q Consensus 1119 ~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~w-l~~~~~CPiCrk 1164 (1241)
-.||.|.--| +.+++.--|||.|..+|+..- +...+.||.|.+
T Consensus 275 LkCplc~~Ll---rnp~kT~cC~~~fc~eci~~al~dsDf~CpnC~r 318 (427)
T COG5222 275 LKCPLCHCLL---RNPMKTPCCGHTFCDECIGTALLDSDFKCPNCSR 318 (427)
T ss_pred ccCcchhhhh---hCcccCccccchHHHHHHhhhhhhccccCCCccc
Confidence 4599998653 445566448999999999865 567899999987
No 174
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=50.49 E-value=7.9 Score=49.88 Aligned_cols=43 Identities=30% Similarity=0.803 Sum_probs=34.5
Q ss_pred CcccccccccccCCCceEEcCCCCccchhhHHHHHhc--CCCCCCCCccc
Q 000878 1119 TNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCS--HYTCPICSKSL 1166 (1241)
Q Consensus 1119 ~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~~--~~~CPiCrk~~ 1166 (1241)
..|+||++ .+...+.+|||.|...|+.+.... ...||+|+..+
T Consensus 455 ~~c~ic~~-----~~~~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l 499 (674)
T KOG1001|consen 455 HWCHICCD-----LDSFFITRCGHDFCVECLKKSIQQSENAPCPLCRNVL 499 (674)
T ss_pred cccccccc-----cccceeecccchHHHHHHHhccccccCCCCcHHHHHH
Confidence 67999998 355778899999999999997632 34699999654
No 175
>PRK04023 DNA polymerase II large subunit; Validated
Probab=50.34 E-value=12 Score=49.49 Aligned_cols=47 Identities=26% Similarity=0.605 Sum_probs=28.6
Q ss_pred CCCCCCCCCCCcceeEeccccccccCCCCcccCCCCCccccCCCCCccccccCCccccc
Q 000878 1045 PNCTTPSCNGLSMAKYYCNICKFFDDERTVYHCPFCNLCRVGGGLGVDFFHCMTCNCCL 1103 (1241)
Q Consensus 1045 ~~C~~~~Cc~~~~a~y~C~~C~~~d~~k~~yHC~~CgiCRvg~~l~~~~fhC~~C~~C~ 1103 (1241)
..|+. | |......+|..|.-- ...+|.|+.||..-.+ +.|.+||.=.
T Consensus 627 RfCps--C-G~~t~~frCP~CG~~--Te~i~fCP~CG~~~~~-------y~CPKCG~El 673 (1121)
T PRK04023 627 RKCPS--C-GKETFYRRCPFCGTH--TEPVYRCPRCGIEVEE-------DECEKCGREP 673 (1121)
T ss_pred ccCCC--C-CCcCCcccCCCCCCC--CCcceeCccccCcCCC-------CcCCCCCCCC
Confidence 46766 4 666666677777543 3567777777654332 3477776543
No 176
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=49.82 E-value=13 Score=48.26 Aligned_cols=45 Identities=24% Similarity=0.693 Sum_probs=28.0
Q ss_pred cceeccccccccccCCCCCCCCCCCCcce------eEeccccccccCCCCcccCCCCCcc
Q 000878 1030 SEMMCMHCLKIQAIGPNCTTPSCNGLSMA------KYYCNICKFFDDERTVYHCPFCNLC 1083 (1241)
Q Consensus 1030 ~~~~C~~C~~~q~~~~~C~~~~Cc~~~~a------~y~C~~C~~~d~~k~~yHC~~CgiC 1083 (1241)
+.++|..|+.+- .|+| | ...+. ...|-.|..= .+.+.+||.||-=
T Consensus 434 ~~l~C~~Cg~v~----~Cp~--C-d~~lt~H~~~~~L~CH~Cg~~--~~~p~~Cp~Cgs~ 484 (730)
T COG1198 434 PLLLCRDCGYIA----ECPN--C-DSPLTLHKATGQLRCHYCGYQ--EPIPQSCPECGSE 484 (730)
T ss_pred ceeecccCCCcc----cCCC--C-CcceEEecCCCeeEeCCCCCC--CCCCCCCCCCCCC
Confidence 489999999876 7888 4 54442 3444444332 2556666666643
No 177
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=49.14 E-value=11 Score=29.58 Aligned_cols=24 Identities=38% Similarity=1.106 Sum_probs=19.2
Q ss_pred eEeccccccc-cCCCCcccCCCCCc
Q 000878 1059 KYYCNICKFF-DDERTVYHCPFCNL 1082 (1241)
Q Consensus 1059 ~y~C~~C~~~-d~~k~~yHC~~Cgi 1082 (1241)
.|-|.+|-+. +.++..+.||.||.
T Consensus 1 ~~~C~~CGy~y~~~~~~~~CP~Cg~ 25 (33)
T cd00350 1 KYVCPVCGYIYDGEEAPWVCPVCGA 25 (33)
T ss_pred CEECCCCCCEECCCcCCCcCcCCCC
Confidence 4789999875 55589999999985
No 178
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=48.55 E-value=17 Score=41.70 Aligned_cols=78 Identities=22% Similarity=0.523 Sum_probs=44.0
Q ss_pred cccccCCcccccc-cc-----cccccccccccCCcccccccccccCCCceEEcCCCCccchhhHHHHHhc----------
Q 000878 1092 DFFHCMTCNCCLG-LK-----LLNHKCLEKCLETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCS---------- 1155 (1241)
Q Consensus 1092 ~~fhC~~C~~C~s-~~-----l~~H~C~e~~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~~---------- 1155 (1241)
.-|+|..||--|. +. +.+|. +...|+||.-. |. ..||.+
T Consensus 160 ka~~C~~C~K~YvSmpALkMHirTH~-----l~c~C~iCGKa-FS-------------------RPWLLQGHiRTHTGEK 214 (279)
T KOG2462|consen 160 KAFSCKYCGKVYVSMPALKMHIRTHT-----LPCECGICGKA-FS-------------------RPWLLQGHIRTHTGEK 214 (279)
T ss_pred ccccCCCCCceeeehHHHhhHhhccC-----CCccccccccc-cc-------------------chHHhhcccccccCCC
Confidence 4566666665542 22 24665 34568898876 43 235421
Q ss_pred CCCCCCCCcccccchhhhhhhHHHHhccCCCHhhhcccceEEcCCCCCCC
Q 000878 1156 HYTCPICSKSLGDMAIYFGMIDALLAAEELPEEYRNQVQDILCNDCEQKG 1205 (1241)
Q Consensus 1156 ~~~CPiCrk~~~dm~~~~~~lD~~i~~~~~P~ey~~~~~~i~CnDC~~~s 1205 (1241)
=+.||.|+|.+.|.+.. .+-++- -.+.+ ...|--|++.+
T Consensus 215 PF~C~hC~kAFADRSNL----RAHmQT------HS~~K-~~qC~~C~KsF 253 (279)
T KOG2462|consen 215 PFSCPHCGKAFADRSNL----RAHMQT------HSDVK-KHQCPRCGKSF 253 (279)
T ss_pred CccCCcccchhcchHHH----HHHHHh------hcCCc-cccCcchhhHH
Confidence 28899999988776543 222111 12223 46788888765
No 179
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=48.53 E-value=14 Score=42.78 Aligned_cols=47 Identities=30% Similarity=0.750 Sum_probs=39.7
Q ss_pred CCcceeEeccccccccCCCCcccCCCCCccccCCCCCccccccCCcccccccc
Q 000878 1054 GLSMAKYYCNICKFFDDERTVYHCPFCNLCRVGGGLGVDFFHCMTCNCCLGLK 1106 (1241)
Q Consensus 1054 ~~~~a~y~C~~C~~~d~~k~~yHC~~CgiCRvg~~l~~~~fhC~~C~~C~s~~ 1106 (1241)
|....-+||..|+++-.. .-.||.-||.|-.+. --||.==|.|++..
T Consensus 108 ~~~~~~~~C~~C~~~rPp-Rs~HCsvC~~CV~rf-----DHHC~WvnnCVG~r 154 (299)
T KOG1311|consen 108 GIQVEWKYCDTCQLYRPP-RSSHCSVCNNCVLRF-----DHHCPWLNNCIGER 154 (299)
T ss_pred CcccceEEcCcCcccCCC-Ccccchhhccccccc-----CCCCCCccceECCC
Confidence 677888999999999655 578999999999886 47999999998754
No 180
>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=47.11 E-value=11 Score=33.32 Aligned_cols=29 Identities=24% Similarity=0.611 Sum_probs=21.8
Q ss_pred ceEEcCCCCCCCCccchhhcccCCCCCCcccccc
Q 000878 1194 QDILCNDCEQKGAARFHWLYHKCGFCGSYNTRLI 1227 (1241)
Q Consensus 1194 ~~i~CnDC~~~s~~~fh~lg~kC~~CgsYNT~~~ 1227 (1241)
..+.|..||+- . .--+-|+.||.|+-+++
T Consensus 25 ~l~~C~~cG~~--~---~~H~vc~~cG~Y~gr~v 53 (55)
T TIGR01031 25 TLVVCPNCGEF--K---LPHRVCPSCGYYKGRQV 53 (55)
T ss_pred cceECCCCCCc--c---cCeeECCccCeECCEEc
Confidence 46789999973 2 22346999999999886
No 181
>PRK07219 DNA topoisomerase I; Validated
Probab=46.73 E-value=26 Score=46.38 Aligned_cols=63 Identities=25% Similarity=0.501 Sum_probs=34.2
Q ss_pred ccccccccCC----CCcccCCCCCcc---ccCCCCCccccccCC---cccccccccccccccccccCCcccccccccc
Q 000878 1062 CNICKFFDDE----RTVYHCPFCNLC---RVGGGLGVDFFHCMT---CNCCLGLKLLNHKCLEKCLETNCPICCDFLF 1129 (1241)
Q Consensus 1062 C~~C~~~d~~----k~~yHC~~CgiC---Rvg~~l~~~~fhC~~---C~~C~s~~l~~H~C~e~~~~~~CpICle~lf 1129 (1241)
|..|+..... .....||.||-- |.|.. | .|+-|.+ |+.-..+.-..+. ......||-|..+|+
T Consensus 672 CP~C~~~~~~~~~~~~~~~CP~Cg~~l~~k~gr~-G-~F~~Cs~yp~C~~~~~l~~~~~~---~~~~~~CpkCg~~l~ 744 (822)
T PRK07219 672 CPDCEAEKEEEDPDEVIGPCPKCGGELAIKQLKY-G-SFLGCTNYPKCKYTLPLPRRGKI---TVTDEKCPECGLPLL 744 (822)
T ss_pred CCCCCCCccccccccccccCCCCCCeeEEEcCCC-C-CeeeCCCCCCCCceeeccccccc---ccccCCCCCCCCeEE
Confidence 7778765432 346899999822 22322 3 3888875 6543332211111 123467888877654
No 182
>PHA00626 hypothetical protein
Probab=46.72 E-value=17 Score=32.29 Aligned_cols=19 Identities=16% Similarity=0.243 Sum_probs=10.2
Q ss_pred eccccccccCCCCcccCCCCCc
Q 000878 1061 YCNICKFFDDERTVYHCPFCNL 1082 (1241)
Q Consensus 1061 ~C~~C~~~d~~k~~yHC~~Cgi 1082 (1241)
-|.+|+-+ +..|.|++||.
T Consensus 13 rcg~cr~~---snrYkCkdCGY 31 (59)
T PHA00626 13 KEKTMRGW---SDDYVCCDCGY 31 (59)
T ss_pred eeceeccc---CcceEcCCCCC
Confidence 45555544 33466666663
No 183
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=46.60 E-value=9.1 Score=37.62 Aligned_cols=30 Identities=23% Similarity=0.655 Sum_probs=23.0
Q ss_pred CCcccCCCCC-----ccccCCCCCccccccCCccc
Q 000878 1072 RTVYHCPFCN-----LCRVGGGLGVDFFHCMTCNC 1101 (1241)
Q Consensus 1072 k~~yHC~~Cg-----iCRvg~~l~~~~fhC~~C~~ 1101 (1241)
+..|-||.|| +|-|-++++..+-+|..||.
T Consensus 20 ~k~FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGl 54 (104)
T COG4888 20 PKTFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGL 54 (104)
T ss_pred CceEecCccCCeeeeEEEEEecCceeEEEcccCcc
Confidence 4568888888 78888877777788777775
No 184
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=45.77 E-value=13 Score=47.77 Aligned_cols=32 Identities=25% Similarity=0.652 Sum_probs=15.7
Q ss_pred eeccccccccccC-CCCCCCCCCCCcceeEeccccc
Q 000878 1032 MMCMHCLKIQAIG-PNCTTPSCNGLSMAKYYCNICK 1066 (1241)
Q Consensus 1032 ~~C~~C~~~q~~~-~~C~~~~Cc~~~~a~y~C~~C~ 1066 (1241)
++|..|+.+-+.+ ..|.+ | |..+..-.|..|.
T Consensus 2 ~~Cp~Cg~~n~~~akFC~~--C-G~~l~~~~Cp~CG 34 (645)
T PRK14559 2 LICPQCQFENPNNNRFCQK--C-GTSLTHKPCPQCG 34 (645)
T ss_pred CcCCCCCCcCCCCCccccc--c-CCCCCCCcCCCCC
Confidence 3566666664433 45655 3 5555433344443
No 185
>COG0143 MetG Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=45.72 E-value=14 Score=46.75 Aligned_cols=45 Identities=24% Similarity=0.510 Sum_probs=36.0
Q ss_pred cceeEeccccccccCC-CCcccCCCCCccccCCCCCccccccCCcccccccc
Q 000878 1056 SMAKYYCNICKFFDDE-RTVYHCPFCNLCRVGGGLGVDFFHCMTCNCCLGLK 1106 (1241)
Q Consensus 1056 ~~a~y~C~~C~~~d~~-k~~yHC~~CgiCRvg~~l~~~~fhC~~C~~C~s~~ 1106 (1241)
....+||..|.-|=.| .-.=.||+||.+..++. +|+.||.++.-.
T Consensus 123 ~~~~~Yc~~~e~fl~dr~v~g~cp~cg~~~arGD------~Ce~Cg~~~~P~ 168 (558)
T COG0143 123 EYEGLYCVSCERFLPDRYVEGTCPKCGGEDARGD------QCENCGRTLDPT 168 (558)
T ss_pred ceeeeEcccccccccchheeccCCCcCccccCcc------hhhhccCcCCch
Confidence 4667789999887666 55568999999999863 899999998743
No 186
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=44.99 E-value=15 Score=42.68 Aligned_cols=43 Identities=23% Similarity=0.638 Sum_probs=33.3
Q ss_pred cccccccccccCCCceEEcCCCCccchhhHHHHHhcC---CCCCCCC
Q 000878 1120 NCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSH---YTCPICS 1163 (1241)
Q Consensus 1120 ~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~~~---~~CPiCr 1163 (1241)
.|||=.|. -+...+...|.|||.+-..-++...+++ +.||.|-
T Consensus 338 iCPVlKe~-~t~ENpP~ml~CgHVIskeal~~LS~nG~~~FKCPYCP 383 (396)
T COG5109 338 ICPVLKEL-CTDENPPVMLECGHVISKEALSVLSQNGVLSFKCPYCP 383 (396)
T ss_pred eccccHhh-hcccCCCeeeeccceeeHHHHHHHhhcCcEEeeCCCCC
Confidence 47776666 4566677888999999999988887553 7899996
No 187
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=44.83 E-value=16 Score=32.27 Aligned_cols=29 Identities=24% Similarity=0.597 Sum_probs=22.1
Q ss_pred ceEEcCCCCCCCCccchhhcccCCCCCCcccccc
Q 000878 1194 QDILCNDCEQKGAARFHWLYHKCGFCGSYNTRLI 1227 (1241)
Q Consensus 1194 ~~i~CnDC~~~s~~~fh~lg~kC~~CgsYNT~~~ 1227 (1241)
..+.|..||.-. .-.+.|++||-|+.+++
T Consensus 25 ~l~~c~~cg~~~-----~~H~vc~~cG~y~~r~v 53 (56)
T PF01783_consen 25 NLVKCPNCGEPK-----LPHRVCPSCGYYKGRQV 53 (56)
T ss_dssp SEEESSSSSSEE-----STTSBCTTTBBSSSSSS
T ss_pred ceeeeccCCCEe-----cccEeeCCCCeECCEEE
Confidence 568899999632 22356999999999986
No 188
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=43.57 E-value=15 Score=30.91 Aligned_cols=30 Identities=17% Similarity=0.335 Sum_probs=19.4
Q ss_pred eEEcCCCCCCCCccchhhcccCCCCCCccc
Q 000878 1195 DILCNDCEQKGAARFHWLYHKCGFCGSYNT 1224 (1241)
Q Consensus 1195 ~i~CnDC~~~s~~~fh~lg~kC~~CgsYNT 1224 (1241)
.+.|.+||......-.....+|+.||+.-.
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCGYRIL 32 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCCCeEE
Confidence 467999987653332222568999997543
No 189
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=42.99 E-value=8.3 Score=44.12 Aligned_cols=43 Identities=23% Similarity=0.616 Sum_probs=25.8
Q ss_pred CCccccccccc-------ccCCCceEEcCCCCccchhhHHHHHhcCCCCCCCCcc
Q 000878 1118 ETNCPICCDFL-------FTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKS 1165 (1241)
Q Consensus 1118 ~~~CpICle~l-------f~s~~~~~~lpCgH~fH~~C~~~wl~~~~~CPiCrk~ 1165 (1241)
.+.||+|...= +...+..++|.|. -|..+|...+.+|--|..+
T Consensus 185 ~~~CPvCGS~PvaSmV~~g~~~~GlRYL~Cs-----lC~teW~~VR~KC~nC~~t 234 (308)
T COG3058 185 RQYCPVCGSMPVASMVQIGETEQGLRYLHCS-----LCETEWHYVRVKCSNCEQS 234 (308)
T ss_pred cccCCCcCCCCcceeeeecCccccchhhhhh-----hHHHHHHHHHHHhcccccc
Confidence 44577776431 1133445555553 5788887777777777755
No 190
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=42.97 E-value=19 Score=30.25 Aligned_cols=23 Identities=35% Similarity=0.918 Sum_probs=11.2
Q ss_pred eEecccccc---ccCCCCcccCCCCC
Q 000878 1059 KYYCNICKF---FDDERTVYHCPFCN 1081 (1241)
Q Consensus 1059 ~y~C~~C~~---~d~~k~~yHC~~Cg 1081 (1241)
.|-|..|.- +++.....+||+||
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG 28 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCG 28 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCC
Confidence 344555542 22223356666666
No 191
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=42.82 E-value=19 Score=42.37 Aligned_cols=26 Identities=19% Similarity=0.743 Sum_probs=20.3
Q ss_pred CCcceeEe--ccccccccCCCCcccCCCCCc
Q 000878 1054 GLSMAKYY--CNICKFFDDERTVYHCPFCNL 1082 (1241)
Q Consensus 1054 ~~~~a~y~--C~~C~~~d~~k~~yHC~~Cgi 1082 (1241)
...|--|| |.||++++. -|-||+||+
T Consensus 60 ~~dfeL~f~Ge~i~~y~~q---SftCPyC~~ 87 (381)
T KOG1280|consen 60 RVDFELYFGGEPISHYDPQ---SFTCPYCGI 87 (381)
T ss_pred ccceeeEecCccccccccc---cccCCcccc
Confidence 34577777 889988765 799999995
No 192
>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=42.81 E-value=24 Score=40.09 Aligned_cols=114 Identities=13% Similarity=0.388 Sum_probs=63.6
Q ss_pred ccccccCCcccccccccccccccccccCCccccccccc----ccCCCceEEcCCCCccchhhHHHHHhcCCCCCC--CCc
Q 000878 1091 VDFFHCMTCNCCLGLKLLNHKCLEKCLETNCPICCDFL----FTSSETVRALPCGHYMHLACFQAYTCSHYTCPI--CSK 1164 (1241)
Q Consensus 1091 ~~~fhC~~C~~C~s~~l~~H~C~e~~~~~~CpICle~l----f~s~~~~~~lpCgH~fH~~C~~~wl~~~~~CPi--Crk 1164 (1241)
.....|..|+.=+.++...|.-+ -.|+.|-|-- =-.++++..-||+.+.= | +-..+.-.||. |++
T Consensus 63 ~p~v~CrVCq~~I~i~gk~~QhV-----VkC~~CnEATPIr~aPpGKKYVRCPCNCLLI--C--k~sS~rIaCPRp~CkR 133 (256)
T PF09788_consen 63 APVVTCRVCQSLIDIEGKMHQHV-----VKCSVCNEATPIRNAPPGKKYVRCPCNCLLI--C--KSSSQRIACPRPNCKR 133 (256)
T ss_pred CceEEeecCCceecccCccceee-----EECCCCCccccccCCCCCCeeEecCCceEEE--e--ecccccccCCCCCCcc
Confidence 35677888888777776333333 2388888761 11445566678873321 1 12345677998 998
Q ss_pred ccccchhhhhhhHHHHhccCCCHhh--hcccceEEcCCCCCCCCc-cch-hhcccCCCCCCc
Q 000878 1165 SLGDMAIYFGMIDALLAAEELPEEY--RNQVQDILCNDCEQKGAA-RFH-WLYHKCGFCGSY 1222 (1241)
Q Consensus 1165 ~~~dm~~~~~~lD~~i~~~~~P~ey--~~~~~~i~CnDC~~~s~~-~fh-~lg~kC~~CgsY 1222 (1241)
.|.--.. ...|..++- .....-+.|.-|+..+-- .+. ---.+|++|..+
T Consensus 134 iI~L~~~---------~~~p~~~~~~~~p~~~rv~CghC~~~Fl~~~~~~~tlARCPHCrKv 186 (256)
T PF09788_consen 134 IINLGPS---------HQGPVTPPVPTQPGSCRVICGHCSNTFLFNTLTSNTLARCPHCRKV 186 (256)
T ss_pred eEEeCCc---------cCCCCCCCCCCCCCceeEECCCCCCcEeccCCCCCccccCCCCcee
Confidence 7632111 112221111 223445889999987632 222 123599999843
No 193
>TIGR00058 Hemerythrin hemerythrin family non-heme iron proteins. This family includes oxygen carrier proteins of various oligomeric states from the vascular fluid (hemerythrin) and muscle (myohemerythrin) of some marine invertebrates. Each unit binds 2 non-heme Fe using 5 H, one E and one D. One member of this family,from the sandworm Nereis diversicolor, is an unusual (non-metallothionein) cadmium-binding protein. Homologous proteins, excluded from this narrowly defined family, are found in archaea and bacteria (see pfam01814).
Probab=42.15 E-value=88 Score=31.33 Aligned_cols=44 Identities=20% Similarity=0.058 Sum_probs=33.4
Q ss_pred HHHHHhHHHHHHHHHHHHHHHhhhccCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhH
Q 000878 112 RKYSLEHEGESNLFDHLFQLLNSYTQNDESFPKELASCSRALQTSINQHMSKEEQQV 168 (1241)
Q Consensus 112 ~~le~EH~~id~lL~~L~~lL~~~~~~~~~~~~eLa~al~~L~~~L~~HL~~EE~eV 168 (1241)
..+..||+++=.++++|.... . ...++.|......||..||.-.
T Consensus 16 ~~ID~qH~~L~~lin~l~~~~-----------~--~~~l~~L~~y~~~HF~~EE~lM 59 (115)
T TIGR00058 16 DNLDEEHKTLFNGIFALAADN-----------S--ATALKELIDVTVLHFLDEEAMM 59 (115)
T ss_pred HHHHHHHHHHHHHHHHHHhcc-----------h--HHHHHHHHHHHHHHHHHHHHHH
Confidence 467789998888777765321 0 3678999999999999999754
No 194
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=41.57 E-value=7.6 Score=44.75 Aligned_cols=21 Identities=33% Similarity=0.710 Sum_probs=15.4
Q ss_pred EcCCCCCCCCccchhhcccCCCCCC
Q 000878 1197 LCNDCEQKGAARFHWLYHKCGFCGS 1221 (1241)
Q Consensus 1197 ~CnDC~~~s~~~fh~lg~kC~~Cgs 1221 (1241)
+|.||+ +-.|-.-|-|.+|.+
T Consensus 398 FC~dCd----vfiHe~Lh~C~gCe~ 418 (421)
T COG5151 398 FCSDCD----VFIHETLHFCIGCEL 418 (421)
T ss_pred hhhhhH----HHHHHHHhhCCCCcC
Confidence 577776 556777778988865
No 195
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=40.68 E-value=22 Score=38.06 Aligned_cols=50 Identities=28% Similarity=0.507 Sum_probs=35.9
Q ss_pred CCCCCCCCcccccchhhhhhhHHHHhccCCCH-hhhcccceEEcCCCCCCCCccchhh
Q 000878 1156 HYTCPICSKSLGDMAIYFGMIDALLAAEELPE-EYRNQVQDILCNDCEQKGAARFHWL 1212 (1241)
Q Consensus 1156 ~~~CPiCrk~~~dm~~~~~~lD~~i~~~~~P~-ey~~~~~~i~CnDC~~~s~~~fh~l 1212 (1241)
..+||.|+..+...+ ++.....+|+ .|.+......|..|++.-...-||=
T Consensus 97 ~~RCp~CN~~L~~vs-------~eev~~~Vp~~~~~~~~~f~~C~~CgkiYW~GsHw~ 147 (165)
T COG1656 97 FSRCPECNGELEKVS-------REEVKEKVPEKVYRNYEEFYRCPKCGKIYWKGSHWR 147 (165)
T ss_pred cccCcccCCEeccCc-------HHHHhhccchhhhhcccceeECCCCcccccCchHHH
Confidence 478999999876443 3444445554 4677777788999999888777773
No 196
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=40.61 E-value=21 Score=41.96 Aligned_cols=23 Identities=35% Similarity=0.781 Sum_probs=16.3
Q ss_pred eEEcCCCCCCCCccchhhcccCCCCCC
Q 000878 1195 DILCNDCEQKGAARFHWLYHKCGFCGS 1221 (1241)
Q Consensus 1195 ~i~CnDC~~~s~~~fh~lg~kC~~Cgs 1221 (1241)
...|+=|+ ..+|+.-.+|++||+
T Consensus 212 yL~CslC~----teW~~~R~~C~~Cg~ 234 (309)
T PRK03564 212 YLHCNLCE----SEWHVVRVKCSNCEQ 234 (309)
T ss_pred EEEcCCCC----CcccccCccCCCCCC
Confidence 45677777 567777777877774
No 197
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=40.37 E-value=15 Score=31.77 Aligned_cols=28 Identities=21% Similarity=0.504 Sum_probs=20.7
Q ss_pred ceEEcCCCCCCCCccchhhcccCCCCCC
Q 000878 1194 QDILCNDCEQKGAARFHWLYHKCGFCGS 1221 (1241)
Q Consensus 1194 ~~i~CnDC~~~s~~~fh~lg~kC~~Cgs 1221 (1241)
..+.|..||+......---+.+|+.||+
T Consensus 5 ~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~ 32 (49)
T COG1996 5 MEYKCARCGREVELDQETRGIRCPYCGS 32 (49)
T ss_pred EEEEhhhcCCeeehhhccCceeCCCCCc
Confidence 3577889988776444456788999987
No 198
>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=40.14 E-value=10 Score=40.22 Aligned_cols=41 Identities=22% Similarity=0.225 Sum_probs=17.5
Q ss_pred HHhHHhcCCCHHHHHHHhhHHhccCCHHHHHHHHHhchHHHhh
Q 000878 821 IVGRIIGSTGAEVLQSMLPWVTSALTQDEQSKLIDTWKHATKN 863 (1241)
Q Consensus 821 i~~~~~~~~~~~~l~~~lpwv~~~l~~~eq~~ml~~~~~a~r~ 863 (1241)
++..++|..+..++..++ --+.+|+++-+..|+.=....|.
T Consensus 7 ~~~~~~g~~~v~Vl~aL~--~~~~~tdEeLa~~Lgi~~~~VRk 47 (158)
T TIGR00373 7 VVGRAAEEEVGLVLFSLG--IKGEFTDEEISLELGIKLNEVRK 47 (158)
T ss_pred HHHHHcChhHHHHHHHHh--ccCCCCHHHHHHHHCCCHHHHHH
Confidence 444555555544443222 11234555555554443333333
No 199
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=39.92 E-value=15 Score=31.56 Aligned_cols=40 Identities=30% Similarity=0.744 Sum_probs=28.7
Q ss_pred ccccccccccCCCceEEcCCCCccchhhHHHHHhcCCCCCCCCcccccch
Q 000878 1121 CPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSLGDMA 1170 (1241)
Q Consensus 1121 CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~~~~~CPiCrk~~~dm~ 1170 (1241)
|+.|...+.. .. +.+..-|..||..|| +|=.|++++.+..
T Consensus 1 C~~C~~~I~~-~~-~~~~~~~~~~H~~Cf--------~C~~C~~~l~~~~ 40 (58)
T PF00412_consen 1 CARCGKPIYG-TE-IVIKAMGKFWHPECF--------KCSKCGKPLNDGD 40 (58)
T ss_dssp BTTTSSBESS-SS-EEEEETTEEEETTTS--------BETTTTCBTTTSS
T ss_pred CCCCCCCccC-cE-EEEEeCCcEEEcccc--------ccCCCCCccCCCe
Confidence 7788888542 22 332346899999988 7999999886554
No 200
>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=39.53 E-value=9.6 Score=44.07 Aligned_cols=16 Identities=25% Similarity=0.906 Sum_probs=4.3
Q ss_pred cchhhcccCCCCCCcc
Q 000878 1208 RFHWLYHKCGFCGSYN 1223 (1241)
Q Consensus 1208 ~fh~lg~kC~~CgsYN 1223 (1241)
.+|+.-.+|++||+-+
T Consensus 206 ~W~~~R~~Cp~Cg~~~ 221 (290)
T PF04216_consen 206 EWRFVRIKCPYCGNTD 221 (290)
T ss_dssp EEE--TTS-TTT---S
T ss_pred eeeecCCCCcCCCCCC
Confidence 3444444444444333
No 201
>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]
Probab=39.45 E-value=12 Score=48.17 Aligned_cols=60 Identities=13% Similarity=0.007 Sum_probs=39.7
Q ss_pred HHHHHHHHhHHhcCCCHHHHHHHhhHHhccCCHHHHHHHHHhchHHHhhhhHHHHHHhhhc
Q 000878 815 VEEQDKIVGRIIGSTGAEVLQSMLPWVTSALTQDEQSKLIDTWKHATKNTMFNEWLDECWK 875 (1241)
Q Consensus 815 ~~Ew~~i~~~~~~~~~~~~l~~~lpwv~~~l~~~eq~~ml~~~~~a~r~t~f~~Wl~~~~~ 875 (1241)
.+||+..|....-.---.++..++|==-.-|.|.-...++--.-. .=.--|.+-+.+|-.
T Consensus 423 ~~eWe~~V~~f~e~~~l~~Ia~~lPt~~~rL~p~vYemvLve~L~-~~~~~F~e~i~~Wp~ 482 (846)
T KOG2066|consen 423 AAEWELWVFKFAELDQLTDIAPYLPTGPPRLKPLVYEMVLVEFLA-SDVKGFLELIKEWPG 482 (846)
T ss_pred HHHHHHHHHHhccccccchhhccCCCCCcccCchHHHHHHHHHHH-HHHHHHHHHHHhCCh
Confidence 567888777775544445566677776677888888777775544 333346677777754
No 202
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=39.44 E-value=14 Score=45.97 Aligned_cols=13 Identities=38% Similarity=1.012 Sum_probs=7.1
Q ss_pred CcceeEecccccc
Q 000878 1055 LSMAKYYCNICKF 1067 (1241)
Q Consensus 1055 ~~~a~y~C~~C~~ 1067 (1241)
..+-.|||+.|-+
T Consensus 22 ~Ei~~~yCp~CL~ 34 (483)
T PF05502_consen 22 EEIDSYYCPNCLF 34 (483)
T ss_pred cccceeECccccc
Confidence 4455566666643
No 203
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=39.21 E-value=11 Score=40.74 Aligned_cols=22 Identities=32% Similarity=1.132 Sum_probs=11.4
Q ss_pred Eecccccc---ccCC-CCcccCCCCC
Q 000878 1060 YYCNICKF---FDDE-RTVYHCPFCN 1081 (1241)
Q Consensus 1060 y~C~~C~~---~d~~-k~~yHC~~Cg 1081 (1241)
|+|+.|+. |++. -..|+||.||
T Consensus 118 Y~Cp~C~~rytf~eA~~~~F~Cp~Cg 143 (178)
T PRK06266 118 FFCPNCHIRFTFDEAMEYGFRCPQCG 143 (178)
T ss_pred EECCCCCcEEeHHHHhhcCCcCCCCC
Confidence 44544442 3333 4457777776
No 204
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=39.20 E-value=19 Score=30.34 Aligned_cols=26 Identities=19% Similarity=0.556 Sum_probs=17.0
Q ss_pred eEEcCCCCCCCCccchhhcccCCCCCC
Q 000878 1195 DILCNDCEQKGAARFHWLYHKCGFCGS 1221 (1241)
Q Consensus 1195 ~i~CnDC~~~s~~~fh~lg~kC~~Cgs 1221 (1241)
...|.+||...... ---..+|+.||+
T Consensus 2 ~Y~C~~Cg~~~~~~-~~~~irC~~CG~ 27 (44)
T smart00659 2 IYICGECGRENEIK-SKDVVRCRECGY 27 (44)
T ss_pred EEECCCCCCEeecC-CCCceECCCCCc
Confidence 45688888765543 134567888886
No 205
>KOG4399 consensus C2HC-type Zn-finger protein [General function prediction only]
Probab=38.63 E-value=7.6 Score=43.81 Aligned_cols=63 Identities=24% Similarity=0.378 Sum_probs=43.6
Q ss_pred eccccccccccCCCCCCCCCCCCcceeEeccccccccCCCCcccCCCCCccccCCCCCccccccCCcccccc
Q 000878 1033 MCMHCLKIQAIGPNCTTPSCNGLSMAKYYCNICKFFDDERTVYHCPFCNLCRVGGGLGVDFFHCMTCNCCLG 1104 (1241)
Q Consensus 1033 ~C~~C~~~q~~~~~C~~~~Cc~~~~a~y~C~~C~~~d~~k~~yHC~~CgiCRvg~~l~~~~fhC~~C~~C~s 1104 (1241)
+|..|....-+ .|+- | +...+.-+|.||-=||-++ -|||.|.-||--+. ...-||..|..|..
T Consensus 240 ~~~~~~~~~~i--~C~~--~-~~~A~~~~C~iC~~~~~~R--~~C~~~kA~~~~~Q--~K~N~~~~~~~~~q 302 (325)
T KOG4399|consen 240 LCKKCVKPSWI--HCSI--C-NHCAVKHGCFICGELDHKR--STCPNIKAVRKQKQ--RKSNKMKMETTKGQ 302 (325)
T ss_pred Hhhhhccccee--eeec--c-cchhhhcceeecccccccc--ccCccHHHHHHHHh--cccchhhhhhhhhh
Confidence 44444444332 3544 2 4456677899999998877 89999999996653 35678888887765
No 206
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=38.54 E-value=17 Score=40.00 Aligned_cols=31 Identities=35% Similarity=0.879 Sum_probs=23.4
Q ss_pred ccCCCceEEcCCCCccchhhHHHHHhcCCCCCCCCc
Q 000878 1129 FTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSK 1164 (1241)
Q Consensus 1129 f~s~~~~~~lpCgH~fH~~C~~~wl~~~~~CPiCrk 1164 (1241)
|.....++--.|+-.||..|+. ...||.|.+
T Consensus 167 F~~~~~~~C~~C~~v~H~~C~~-----~~~CpkC~R 197 (202)
T PF13901_consen 167 FQIDTTVRCPKCKSVFHKSCFR-----KKSCPKCAR 197 (202)
T ss_pred CCCCCeeeCCcCccccchhhcC-----CCCCCCcHh
Confidence 4554555666799999999996 266999975
No 207
>PF07227 DUF1423: Protein of unknown function (DUF1423); InterPro: IPR004082 A total of 715 potential protein-coding genes have been identified in the nucleotide sequence of Arabidopsis thaliana chromosome 5, with an average gene density of 1 gene per 4001 bp []. Amongst the gene products is a well-conserved family of 130.7kDa proteins that share no sequence similarity with any other known proteins, other than in plants. The sequences are characterised by an N-terminal domain of variable length, a central cysteine-rich region and a relatively acidic C-terminal domain. The sequences may possess a PHD finger.
Probab=37.80 E-value=22 Score=43.32 Aligned_cols=46 Identities=30% Similarity=0.669 Sum_probs=31.7
Q ss_pred cccccccccccCCCceEEcC---CCCccchhhHHH-HH--------------hcCCCCCCCCccc
Q 000878 1120 NCPICCDFLFTSSETVRALP---CGHYMHLACFQA-YT--------------CSHYTCPICSKSL 1166 (1241)
Q Consensus 1120 ~CpICle~lf~s~~~~~~lp---CgH~fH~~C~~~-wl--------------~~~~~CPiCrk~~ 1166 (1241)
.|+||.-+ -.+..+..++. |||.-|..|--. .+ ...|.|--|.+.-
T Consensus 130 ~C~iC~kf-D~~~n~~~Wi~Cd~CgH~cH~dCALr~~~i~~G~s~~g~~g~~d~~f~C~~C~~~s 193 (446)
T PF07227_consen 130 MCCICSKF-DDNKNTCSWIGCDVCGHWCHLDCALRHELIGTGPSVKGSIGTLDMQFHCRACGKTS 193 (446)
T ss_pred CccccCCc-ccCCCCeeEEeccCCCceehhhhhcccccccCCccCCCCCccCceEEEccCCCChh
Confidence 49999765 34456777775 799999999543 32 1137788888764
No 208
>PF01907 Ribosomal_L37e: Ribosomal protein L37e; InterPro: IPR001569 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families consists of proteins of 56 to 96 amino-acid residues that share a highly conserved region located in the N-terminal part.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A19_A 4A1D_A 4A18_A 4A1B_A 1S1I_Y 3O5H_d 3IZS_l 3O58_d 2ZKR_2 3IZR_l ....
Probab=37.49 E-value=17 Score=32.11 Aligned_cols=27 Identities=26% Similarity=0.747 Sum_probs=21.2
Q ss_pred cccceEEcCCCCCCCCccchhhcccCCCCC
Q 000878 1191 NQVQDILCNDCEQKGAARFHWLYHKCGFCG 1220 (1241)
Q Consensus 1191 ~~~~~i~CnDC~~~s~~~fh~lg~kC~~Cg 1220 (1241)
+.+..|+|.-||+ ..||+--..|..||
T Consensus 11 ~~ktH~~CrRCG~---~syH~qK~~CasCG 37 (55)
T PF01907_consen 11 HNKTHTLCRRCGR---RSYHIQKKTCASCG 37 (55)
T ss_dssp -S-SEEE-TTTSS---EEEETTTTEETTTB
T ss_pred CCccEeeecccCC---eeeecCCCcccccC
Confidence 4557899999998 56898889999999
No 209
>COG2703 Hemerythrin [Inorganic ion transport and metabolism]
Probab=37.28 E-value=5.4e+02 Score=27.39 Aligned_cols=124 Identities=19% Similarity=0.164 Sum_probs=78.9
Q ss_pred HHHHHHHHHHHHHHHHH-HHHHHHHhhhcCCcccHHHHHHHHHHHHHHhhccCccccccc----cHHHhhhhhhHHHHHH
Q 000878 41 PILIFCFFHKAVRNELD-ALHQLAMNFATGHRVDILSLSERYRFLHSVYKHHSNAEDEVI----FPALDIRVKNVARKYS 115 (1241)
Q Consensus 41 PId~l~~~H~AIRreL~-~L~~la~~l~~gd~~dl~~L~~~l~fL~~~L~~HH~aEDevL----FPaL~~R~p~vl~~le 115 (1241)
-++.+-..|+.|=+.++ .+.-.+ ........+...+..|..+...|=..|++++ ||.|...-
T Consensus 12 gn~~iD~qHk~l~ei~N~~~~~~~-----~~~~~~~~i~~~l~el~~y~e~HF~~EE~~Me~igyp~l~~Hk-------- 78 (144)
T COG2703 12 GNAAIDNQHKELFEILNKKLLLDA-----QNHKSKAEIKQLLDELLNYTEDHFKEEEKLMEEIGYPPLEEHK-------- 78 (144)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHH-----HccccHHHHHHHHHHHHHHHHHHHhhHHHHHHHcCCCcHHHHH--------
Confidence 34567778888888776 221111 1233566777788888888888999998776 77665432
Q ss_pred HhHHHHHHHHHHHHHHHhhhccCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHhccCCHHHHHH
Q 000878 116 LEHEGESNLFDHLFQLLNSYTQNDESFPKELASCSRALQTSINQHMSKEEQQVFPLLTQHFSLEEQAS 183 (1241)
Q Consensus 116 ~EH~~id~lL~~L~~lL~~~~~~~~~~~~eLa~al~~L~~~L~~HL~~EE~eVfPLa~~~lS~eEwae 183 (1241)
.+|+.+-..+.++ +.....++. .-....+..+..-|..|+..|....--.+.+.++..+-.+
T Consensus 79 k~H~~~i~~v~e~---~~~~~~~~~---~~~~~L~~~l~~Wl~~Hia~~D~~~~~~~~~~~~~~~~e~ 140 (144)
T COG2703 79 KEHDTFIKRVKEV---LRKIAKGDE---KLGRELLEFLVDWLAEHIAKEDRKYADWLKEKGSDAEEEA 140 (144)
T ss_pred HHHHHHHHHHHHH---HHHHHhcHH---HHHHHHHHHHHHHHHHHHhHHhHHHHHHHHHhcchhhhhh
Confidence 2444444444443 323322221 2223456778889999999999988888888877665443
No 210
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=37.20 E-value=14 Score=44.79 Aligned_cols=20 Identities=20% Similarity=0.466 Sum_probs=15.2
Q ss_pred hHHHhcCHHHHHHHHhhhcC
Q 000878 914 KDIFRMNQNELEAEIRKVYR 933 (1241)
Q Consensus 914 ~~~~~~~~~~l~~~i~~~~~ 933 (1241)
...+.+|+.+||..|+++-.
T Consensus 50 ~~llk~~~KqLR~li~~Lre 69 (436)
T KOG2593|consen 50 KELLKFNKKQLRKLIASLRE 69 (436)
T ss_pred HHHhcccHHHHHHHHHHhhh
Confidence 34567899999888887765
No 211
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=36.57 E-value=18 Score=40.14 Aligned_cols=38 Identities=34% Similarity=0.695 Sum_probs=27.6
Q ss_pred ccccccccccCCCceEEcCCCCcc-chhhHHHHHhcCCCCCCCCccc
Q 000878 1121 CPICCDFLFTSSETVRALPCGHYM-HLACFQAYTCSHYTCPICSKSL 1166 (1241)
Q Consensus 1121 CpICle~lf~s~~~~~~lpCgH~f-H~~C~~~wl~~~~~CPiCrk~~ 1166 (1241)
|-.|.+. ...|..+||-|.. ...|-.. -.+||+|+...
T Consensus 161 Cr~C~~~----~~~VlllPCrHl~lC~~C~~~----~~~CPiC~~~~ 199 (207)
T KOG1100|consen 161 CRKCGER----EATVLLLPCRHLCLCGICDES----LRICPICRSPK 199 (207)
T ss_pred ceecCcC----CceEEeecccceEeccccccc----CccCCCCcChh
Confidence 8888877 4458889999874 4556532 35699999764
No 212
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=36.52 E-value=24 Score=30.31 Aligned_cols=9 Identities=44% Similarity=1.423 Sum_probs=6.6
Q ss_pred eEecccccc
Q 000878 1059 KYYCNICKF 1067 (1241)
Q Consensus 1059 ~y~C~~C~~ 1067 (1241)
+|.|.+|.+
T Consensus 1 ky~C~~Cgy 9 (47)
T PF00301_consen 1 KYQCPVCGY 9 (47)
T ss_dssp EEEETTTSB
T ss_pred CcCCCCCCE
Confidence 577777775
No 213
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=36.04 E-value=12 Score=39.05 Aligned_cols=26 Identities=27% Similarity=0.858 Sum_probs=18.3
Q ss_pred ceeEeccccccccCCCCcccCCCCC--ccccC
Q 000878 1057 MAKYYCNICKFFDDERTVYHCPFCN--LCRVG 1086 (1241)
Q Consensus 1057 ~a~y~C~~C~~~d~~k~~yHC~~Cg--iCRvg 1086 (1241)
-.+-||.+|-+| ++|-|-.|| +|-|+
T Consensus 116 P~r~fCaVCG~~----S~ysC~~CG~kyCsv~ 143 (156)
T KOG3362|consen 116 PLRKFCAVCGYD----SKYSCVNCGTKYCSVR 143 (156)
T ss_pred CcchhhhhcCCC----chhHHHhcCCceeech
Confidence 345678888765 678888887 56665
No 214
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=35.79 E-value=14 Score=46.47 Aligned_cols=29 Identities=31% Similarity=0.622 Sum_probs=23.6
Q ss_pred CCcccccc----ccccccccCCcccCchhhcccC
Q 000878 991 GCEHYKRN----CKIRAACCGKLFTCRFCHDKAS 1020 (1241)
Q Consensus 991 gC~HY~r~----ckl~~pcC~k~y~Cr~CHde~~ 1020 (1241)
||.|+--. +.-.|.-+|+|| |..||....
T Consensus 345 gC~~~i~~~~~~~~R~C~y~G~y~-C~~Ch~~~~ 377 (580)
T KOG1829|consen 345 GCGHTIGPDLEQRPRLCRYLGKYF-CDCCHQNDK 377 (580)
T ss_pred ccCCCcccccccchhHhhhhhhhh-CchhcccCc
Confidence 89988773 557788999988 999998754
No 215
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=35.63 E-value=12 Score=48.57 Aligned_cols=45 Identities=27% Similarity=0.590 Sum_probs=0.0
Q ss_pred ceeccccccccccCCCCCCCCCCCCcceeEeccccccccCCCCcccCCCCC
Q 000878 1031 EMMCMHCLKIQAIGPNCTTPSCNGLSMAKYYCNICKFFDDERTVYHCPFCN 1081 (1241)
Q Consensus 1031 ~~~C~~C~~~q~~~~~C~~~~Cc~~~~a~y~C~~C~~~d~~k~~yHC~~Cg 1081 (1241)
.-.|..|+++.. ...|+. |.+...-.|+|..|+.=-++. +||.||
T Consensus 655 ~r~Cp~Cg~~t~-~~~Cp~--CG~~T~~~~~Cp~C~~~~~~~---~C~~C~ 699 (900)
T PF03833_consen 655 RRRCPKCGKETF-YNRCPE--CGSHTEPVYVCPDCGIEVEED---ECPKCG 699 (900)
T ss_dssp ---------------------------------------------------
T ss_pred cccCcccCCcch-hhcCcc--cCCccccceeccccccccCcc---cccccc
Confidence 345666665542 235655 433335566666665421111 566666
No 216
>PRK00420 hypothetical protein; Validated
Probab=35.07 E-value=22 Score=35.93 Aligned_cols=30 Identities=30% Similarity=0.664 Sum_probs=21.4
Q ss_pred cCCcccccccccccCCCceEEcCCCCccchhhHHHHHhcCCCCCCCCcccc
Q 000878 1117 LETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSLG 1167 (1241)
Q Consensus 1117 ~~~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~~~~~CPiCrk~~~ 1167 (1241)
+...||+|..+||.... +...||.|+..+.
T Consensus 22 l~~~CP~Cg~pLf~lk~---------------------g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 22 LSKHCPVCGLPLFELKD---------------------GEVVCPVHGKVYI 51 (112)
T ss_pred ccCCCCCCCCcceecCC---------------------CceECCCCCCeee
Confidence 34679999999876332 3566998888653
No 217
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=34.71 E-value=22 Score=40.16 Aligned_cols=80 Identities=20% Similarity=0.487 Sum_probs=51.7
Q ss_pred cccccccccccccCC--------cccCchhhcccCCCCC----CcccccceeccccccccccCCCCCCCCCCCCcceeEe
Q 000878 994 HYKRNCKIRAACCGK--------LFTCRFCHDKASDHSM----DRKATSEMMCMHCLKIQAIGPNCTTPSCNGLSMAKYY 1061 (1241)
Q Consensus 994 HY~r~ckl~~pcC~k--------~y~Cr~CHde~~~H~~----~r~~~~~~~C~~C~~~q~~~~~C~~~~Cc~~~~a~y~ 1061 (1241)
-|+..=...|.-|+. .|.|..||.-..+.|+ |-+-.-...|..|+++..... ...-+.-|
T Consensus 114 f~rnqgr~LC~~Cn~k~Ka~~~g~YvC~KCh~~iD~~~l~fr~d~yH~yHFkCt~C~keL~sda--------Revk~eLy 185 (332)
T KOG2272|consen 114 FYRNQGRALCRECNQKEKAKGRGRYVCQKCHAHIDEQPLTFRGDPYHPYHFKCTTCGKELTSDA--------REVKGELY 185 (332)
T ss_pred hHhhcchHHhhhhhhhhcccccceeehhhhhhhcccccccccCCCCCccceecccccccccchh--------hhhcccee
Confidence 344444556666654 6999999977654333 334445788999988865431 33456777
Q ss_pred ccccccccCCCCcccCCCCCccccCC
Q 000878 1062 CNICKFFDDERTVYHCPFCNLCRVGG 1087 (1241)
Q Consensus 1062 C~~C~~~d~~k~~yHC~~CgiCRvg~ 1087 (1241)
|.-|. +.+-||-||-||...
T Consensus 186 ClrCh------D~mgipiCgaC~rpI 205 (332)
T KOG2272|consen 186 CLRCH------DKMGIPICGACRRPI 205 (332)
T ss_pred ccccc------cccCCcccccccCch
Confidence 77775 346688899998653
No 218
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=34.54 E-value=31 Score=46.87 Aligned_cols=19 Identities=16% Similarity=0.135 Sum_probs=12.3
Q ss_pred HHHhhhcCCCCCCHHHHHH
Q 000878 926 AEIRKVYRDPTLDPRRKAY 944 (1241)
Q Consensus 926 ~~i~~~~~~~~l~~~~k~~ 944 (1241)
..|.-|+..+.+.=++||.
T Consensus 588 ~~~~~vn~~s~~~ir~ra~ 606 (1337)
T PRK14714 588 NAIDLINELAPFKVRERAP 606 (1337)
T ss_pred cHHHHHHhhCCcEEeccCc
Confidence 4466666667777666664
No 219
>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]
Probab=34.34 E-value=20 Score=39.72 Aligned_cols=41 Identities=29% Similarity=0.723 Sum_probs=28.8
Q ss_pred cccccccccccCCCceEEcCCCCccchhhHHHHHhcCCCCCCCC
Q 000878 1120 NCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICS 1163 (1241)
Q Consensus 1120 ~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~~~~~CPiCr 1163 (1241)
+|.+|..-+ ...++.-.||=-||..|+..|+.....||-|+
T Consensus 183 ~Cn~Ch~Lv---Iqg~rCg~c~i~~h~~c~qty~q~~~~cphc~ 223 (235)
T KOG4718|consen 183 NCNLCHCLV---IQGIRCGSCNIQYHRGCIQTYLQRRDICPHCG 223 (235)
T ss_pred HHhHhHHHh---heeeccCcccchhhhHHHHHHhcccCcCCchh
Confidence 466666542 12234455777789999999998888899885
No 220
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=34.16 E-value=30 Score=27.53 Aligned_cols=24 Identities=25% Similarity=0.913 Sum_probs=17.5
Q ss_pred eEeccccccc-cCCCCcccCCCCCc
Q 000878 1059 KYYCNICKFF-DDERTVYHCPFCNL 1082 (1241)
Q Consensus 1059 ~y~C~~C~~~-d~~k~~yHC~~Cgi 1082 (1241)
.|-|.+|-+. +.++.+..||.||-
T Consensus 2 ~~~C~~CG~i~~g~~~p~~CP~Cg~ 26 (34)
T cd00729 2 VWVCPVCGYIHEGEEAPEKCPICGA 26 (34)
T ss_pred eEECCCCCCEeECCcCCCcCcCCCC
Confidence 4778888876 44467778888874
No 221
>PRK07219 DNA topoisomerase I; Validated
Probab=33.23 E-value=47 Score=44.10 Aligned_cols=11 Identities=36% Similarity=0.630 Sum_probs=7.5
Q ss_pred cccCCCCCccc
Q 000878 1074 VYHCPFCNLCR 1084 (1241)
Q Consensus 1074 ~yHC~~CgiCR 1084 (1241)
...||.||---
T Consensus 733 ~~~CpkCg~~l 743 (822)
T PRK07219 733 DEKCPECGLPL 743 (822)
T ss_pred cCCCCCCCCeE
Confidence 36788888643
No 222
>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=33.10 E-value=20 Score=29.65 Aligned_cols=13 Identities=46% Similarity=0.902 Sum_probs=5.7
Q ss_pred cCCCCcccCCCCC
Q 000878 1069 DDERTVYHCPFCN 1081 (1241)
Q Consensus 1069 d~~k~~yHC~~Cg 1081 (1241)
|...+.+-|..||
T Consensus 14 D~~~g~~vC~~CG 26 (43)
T PF08271_consen 14 DPERGELVCPNCG 26 (43)
T ss_dssp ETTTTEEEETTT-
T ss_pred cCCCCeEECCCCC
Confidence 3334455555554
No 223
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=32.54 E-value=26 Score=41.18 Aligned_cols=47 Identities=30% Similarity=0.739 Sum_probs=37.4
Q ss_pred CCcceeEeccccccccCCCCcccCCCCCccccCCCCCccccccCCcccccccc
Q 000878 1054 GLSMAKYYCNICKFFDDERTVYHCPFCNLCRVGGGLGVDFFHCMTCNCCLGLK 1106 (1241)
Q Consensus 1054 ~~~~a~y~C~~C~~~d~~k~~yHC~~CgiCRvg~~l~~~~fhC~~C~~C~s~~ 1106 (1241)
+....+=||.+|+.|..+| ..||.-||.|-... --||.==|-|++..
T Consensus 104 ~~~~~~~~C~~C~~~KP~R-S~HC~~Cn~CV~k~-----DHHC~Wi~nCVG~~ 150 (309)
T COG5273 104 GKFGTENFCSTCNIYKPPR-SHHCSICNRCVLKF-----DHHCPWINNCVGFR 150 (309)
T ss_pred CccccceeccccccccCCC-Cccchhhcchhhcc-----CccCcccccccCcc
Confidence 5556667899999998884 56999999998874 47888888888755
No 224
>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=32.13 E-value=16 Score=42.24 Aligned_cols=43 Identities=23% Similarity=0.537 Sum_probs=15.8
Q ss_pred CCccccccccc----ccCCC--ceEEcCCCCccchhhHHHHHhcCCCCCCCCcc
Q 000878 1118 ETNCPICCDFL----FTSSE--TVRALPCGHYMHLACFQAYTCSHYTCPICSKS 1165 (1241)
Q Consensus 1118 ~~~CpICle~l----f~s~~--~~~~lpCgH~fH~~C~~~wl~~~~~CPiCrk~ 1165 (1241)
.+.||||...= ..... ..++|- +.-|-.+|--...+||.|..+
T Consensus 172 ~g~CPvCGs~P~~s~l~~~~~~G~R~L~-----Cs~C~t~W~~~R~~Cp~Cg~~ 220 (290)
T PF04216_consen 172 RGYCPVCGSPPVLSVLRGGEREGKRYLH-----CSLCGTEWRFVRIKCPYCGNT 220 (290)
T ss_dssp -SS-TTT---EEEEEEE------EEEEE-----ETTT--EEE--TTS-TTT---
T ss_pred CCcCCCCCCcCceEEEecCCCCccEEEE-----cCCCCCeeeecCCCCcCCCCC
Confidence 46688887551 11111 224443 345667776678899999976
No 225
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=32.00 E-value=21 Score=41.04 Aligned_cols=50 Identities=26% Similarity=0.563 Sum_probs=37.4
Q ss_pred CCcccccccccccCCCceEEcCCC-----CccchhhHHHHHh--cCCCCCCCCcccc
Q 000878 1118 ETNCPICCDFLFTSSETVRALPCG-----HYMHLACFQAYTC--SHYTCPICSKSLG 1167 (1241)
Q Consensus 1118 ~~~CpICle~lf~s~~~~~~lpCg-----H~fH~~C~~~wl~--~~~~CPiCrk~~~ 1167 (1241)
...|=||.+..+.........||. .+.|..|+..|.. .+.+|.+|.....
T Consensus 78 ~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~ 134 (323)
T KOG1609|consen 78 GPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFI 134 (323)
T ss_pred CCcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhccccCeeeecccccce
Confidence 357999999854433324567874 6789999999985 6788999998653
No 226
>TIGR00058 Hemerythrin hemerythrin family non-heme iron proteins. This family includes oxygen carrier proteins of various oligomeric states from the vascular fluid (hemerythrin) and muscle (myohemerythrin) of some marine invertebrates. Each unit binds 2 non-heme Fe using 5 H, one E and one D. One member of this family,from the sandworm Nereis diversicolor, is an unusual (non-metallothionein) cadmium-binding protein. Homologous proteins, excluded from this narrowly defined family, are found in archaea and bacteria (see pfam01814).
Probab=31.63 E-value=3.9e+02 Score=26.74 Aligned_cols=90 Identities=12% Similarity=0.211 Sum_probs=57.2
Q ss_pred HHHHHHHHHHHHHHHhhhcCCChhhHHHHHHHHHHHHHHHHHHHhhhh----hcccccccccccchhhhhHHhhhH-HHH
Q 000878 312 NAIRQELNEIAEESRKIQLSGDFTNLLAFNERLQFIAEVLIFHCIAEV----NVIFPAVDGASSFSQKHAEEESQF-NDF 386 (1241)
Q Consensus 312 kAIRkDh~el~~~~~kl~~~~d~~~l~~~~~r~qfL~el~r~HS~AEe----~vVyPALE~~~s~~~dh~~eeh~~-eei 386 (1241)
..|=.+|++|-+.++++..+.+ ...+.+|.+-.+.|=..|| .+-||.++ .|..+-..| +++
T Consensus 16 ~~ID~qH~~L~~lin~l~~~~~-------~~~l~~L~~y~~~HF~~EE~lM~~~~yp~~~-------~H~~~H~~f~~~l 81 (115)
T TIGR00058 16 DNLDEEHKTLFNGIFALAADNS-------ATALKELIDVTVLHFLDEEAMMIAANYSDYD-------EHKKAHDDFLAVL 81 (115)
T ss_pred HHHHHHHHHHHHHHHHHHhcch-------HHHHHHHHHHHHHHHHHHHHHHHHcCCCChH-------HHHHHHHHHHHHH
Confidence 3456788899999988853221 2467889999999999999 56799887 555542323 223
Q ss_pred HHHHHHHHhcCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 000878 387 RLLIESIQNEGAISTSAEFYAKLCSHADQIMETIERHFHKVEVQ 430 (1241)
Q Consensus 387 ~~LL~~lq~~~~~~~~~~f~~kL~~~l~~l~~~l~~Hi~eEE~E 430 (1241)
..+...+ ... .++.|..-+..||..+-..
T Consensus 82 ~~~~~~~------------~~~---~~~~l~~Wl~~HI~~~D~~ 110 (115)
T TIGR00058 82 RGLKAPV------------PQD---DLLYAKDWLVNHIKTTDFK 110 (115)
T ss_pred HHHHHHh------------hHH---HHHHHHHHHHHHhHHHHHH
Confidence 3332211 111 2456778888888766543
No 227
>KOG1313 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=31.49 E-value=20 Score=41.04 Aligned_cols=46 Identities=28% Similarity=0.626 Sum_probs=37.2
Q ss_pred CcceeEeccccccccCCCCcccCCCCCccccCCCCCccccccCCcccccccc
Q 000878 1055 LSMAKYYCNICKFFDDERTVYHCPFCNLCRVGGGLGVDFFHCMTCNCCLGLK 1106 (1241)
Q Consensus 1055 ~~~a~y~C~~C~~~d~~k~~yHC~~CgiCRvg~~l~~~~fhC~~C~~C~s~~ 1106 (1241)
..-+--||.+|+.|..+ ..-||--||-|..+ ..-||.-=|-|+...
T Consensus 98 ~~~~~SfC~KC~~pK~p-rTHHCsiC~kCVL~-----MDHHCPwinnCVG~~ 143 (309)
T KOG1313|consen 98 GLENDSFCNKCNYPKSP-RTHHCSICNKCVLK-----MDHHCPWINNCVGAH 143 (309)
T ss_pred CCccccHHhhcCCCCCC-CcchhhHHhhHhhc-----cccCCchhhcccccc
Confidence 34556689999999777 46799999999987 358999999998754
No 228
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 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 motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=31.46 E-value=17 Score=29.78 Aligned_cols=13 Identities=46% Similarity=1.239 Sum_probs=5.5
Q ss_pred ceeEecccccccc
Q 000878 1057 MAKYYCNICKFFD 1069 (1241)
Q Consensus 1057 ~a~y~C~~C~~~d 1069 (1241)
|.+|||+.|+.|=
T Consensus 1 m~ryyCdyC~~~~ 13 (38)
T PF06220_consen 1 MPRYYCDYCKKYL 13 (38)
T ss_dssp --S-B-TTT--B-
T ss_pred CcCeeccccccee
Confidence 4689999999874
No 229
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=31.22 E-value=15 Score=43.56 Aligned_cols=33 Identities=36% Similarity=0.811 Sum_probs=22.0
Q ss_pred Cccccccccccccccccccc--CCcccccccc-cccCCCce
Q 000878 1098 TCNCCLGLKLLNHKCLEKCL--ETNCPICCDF-LFTSSETV 1135 (1241)
Q Consensus 1098 ~C~~C~s~~l~~H~C~e~~~--~~~CpICle~-lf~s~~~~ 1135 (1241)
.||-|+-.. |..+|+ .++||||.-+ .|+...++
T Consensus 317 pCGHilHl~-----CLknW~ERqQTCPICr~p~ifd~~~~~ 352 (491)
T COG5243 317 PCGHILHLH-----CLKNWLERQQTCPICRRPVIFDQSSPT 352 (491)
T ss_pred cccceeeHH-----HHHHHHHhccCCCcccCccccccCCCC
Confidence 466665432 666666 4689999999 56655544
No 230
>KOG3850 consensus Predicted membrane protein [Function unknown]
Probab=30.40 E-value=5.8e+02 Score=31.09 Aligned_cols=61 Identities=25% Similarity=0.292 Sum_probs=42.7
Q ss_pred CCCChhHHHHHHHHHHHHHHHHHHHHHhhhcCCChh-hHHHHHHHHHHHHHHHHHHHhhhhhccccccc
Q 000878 300 GTYPIDEILLWHNAIRQELNEIAEESRKIQLSGDFT-NLLAFNERLQFIAEVLIFHCIAEVNVIFPAVD 367 (1241)
Q Consensus 300 ~~~PId~If~~HkAIRkDh~el~~~~~kl~~~~d~~-~l~~~~~r~qfL~el~r~HS~AEe~vVyPALE 367 (1241)
+++|.+.=-..-+||..++++|++....|.. +.. -..++..-++|+.+-+. ||++-|--||
T Consensus 251 ~~n~~~s~~~~l~aileeL~eIk~~q~~Lee--sye~Lke~~krdy~fi~etLQ-----EERyR~erLE 312 (455)
T KOG3850|consen 251 GANPYHSQGAALDAILEELREIKETQALLEE--SYERLKEQIKRDYKFIAETLQ-----EERYRYERLE 312 (455)
T ss_pred CCCcccccchHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHH
Confidence 3556655555567888899998888888842 233 33445555678877777 9999998887
No 231
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=29.67 E-value=23 Score=42.88 Aligned_cols=37 Identities=22% Similarity=0.415 Sum_probs=26.2
Q ss_pred CCcccccccccccCCCceEEcCCCCccchhhHHHHHh
Q 000878 1118 ETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTC 1154 (1241)
Q Consensus 1118 ~~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~ 1154 (1241)
..+|.||............+..|||.|..+|..++..
T Consensus 146 ~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~ie 182 (384)
T KOG1812|consen 146 KEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIE 182 (384)
T ss_pred cccCccCccccccHhhhHHHhcccchhhhHHhHHHhh
Confidence 3579999933233323233678999999999999874
No 232
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=29.19 E-value=11 Score=31.88 Aligned_cols=42 Identities=21% Similarity=0.706 Sum_probs=28.5
Q ss_pred ccccccccccCCCceEEcCCCCccchhhHHHHH------hcCCCCCCCC
Q 000878 1121 CPICCDFLFTSSETVRALPCGHYMHLACFQAYT------CSHYTCPICS 1163 (1241)
Q Consensus 1121 CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl------~~~~~CPiCr 1163 (1241)
|+||... ...+.-+.--.|+-.||..|+..-. ...+.||.|+
T Consensus 2 C~vC~~~-~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~ 49 (51)
T PF00628_consen 2 CPVCGQS-DDDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCR 49 (51)
T ss_dssp BTTTTSS-CTTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHH
T ss_pred CcCCCCc-CCCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCc
Confidence 8899984 3333333445799999999986542 2357888775
No 233
>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=28.67 E-value=24 Score=30.31 Aligned_cols=29 Identities=24% Similarity=0.817 Sum_probs=15.5
Q ss_pred cccccCCCCCCCCCCC-----CcceeEecccccc
Q 000878 1039 KIQAIGPNCTTPSCNG-----LSMAKYYCNICKF 1067 (1241)
Q Consensus 1039 ~~q~~~~~C~~~~Cc~-----~~~a~y~C~~C~~ 1067 (1241)
+++.....|+++.|+. .++.++||.+|.+
T Consensus 13 kv~r~rk~CP~~~CG~GvFMA~H~dR~~CGKCg~ 46 (47)
T PF01599_consen 13 KVKRLRKECPSPRCGAGVFMAEHKDRHYCGKCGY 46 (47)
T ss_dssp EEEESSEE-TSTTTTSSSEEEE-SSEEEETTTSS
T ss_pred cEEEhhhcCCCcccCCceEeeecCCCccCCCccc
Confidence 3444556787666742 2345677777754
No 234
>cd01675 RNR_III Class III ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit w
Probab=28.43 E-value=29 Score=43.93 Aligned_cols=29 Identities=38% Similarity=0.708 Sum_probs=21.8
Q ss_pred EcCCCCCCCCccchhhcccCCCCCCcccccccc
Q 000878 1197 LCNDCEQKGAARFHWLYHKCGFCGSYNTRLIKN 1229 (1241)
Q Consensus 1197 ~CnDC~~~s~~~fh~lg~kC~~CgsYNT~~~~~ 1229 (1241)
.|++||.... ..+.+|+.|||-|+.+++.
T Consensus 520 ~C~~CG~~~~----~~~~~CP~CGs~~~~~~~R 548 (555)
T cd01675 520 ICNDCGYIGE----GEGFKCPKCGSEDVEVISR 548 (555)
T ss_pred cCCCCCCCCc----CCCCCCcCCCCcCceEEEe
Confidence 8999997553 3457999999988666543
No 235
>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=28.22 E-value=32 Score=35.35 Aligned_cols=32 Identities=13% Similarity=-0.050 Sum_probs=23.1
Q ss_pred ccccccccCCcccCchhhcccCCCCCCcccccceeccccccccccC
Q 000878 999 CKIRAACCGKLFTCRFCHDKASDHSMDRKATSEMMCMHCLKIQAIG 1044 (1241)
Q Consensus 999 ckl~~pcC~k~y~Cr~CHde~~~H~~~r~~~~~~~C~~C~~~q~~~ 1044 (1241)
-|-.||.||+-| .+... ..++|.+|++.+++.
T Consensus 8 tKr~Cp~cg~kF-------------YDLnk-~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 8 TKRICPNTGSKF-------------YDLNR-RPAVSPYTGEQFPPE 39 (129)
T ss_pred ccccCCCcCccc-------------cccCC-CCccCCCcCCccCcc
Confidence 456789998754 23322 589999999998776
No 236
>PF09577 Spore_YpjB: Sporulation protein YpjB (SpoYpjB); InterPro: IPR014231 Proteins in thie entry, typified by YpjB, are restricted to a subset of the endospore-forming bacteria which includes Bacillus species, but not species. In Bacillus subtilis, ypjB was found to be part of the sigma-E regulon []. Sigma-E is a sporulation sigma factor that regulates expression in the mother cell compartment. Null mutants of ypjB show a sporulation defect, but this gene is not, however, a part of the endospore formation minimal gene set.
Probab=27.94 E-value=4.1e+02 Score=30.27 Aligned_cols=96 Identities=16% Similarity=0.203 Sum_probs=57.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhcCCChhhHHHHHHHHHHHHHHHHHHHhhhhhcccccccccccchhhhhHHhhhHHHH
Q 000878 307 ILLWHNAIRQELNEIAEESRKIQLSGDFTNLLAFNERLQFIAEVLIFHCIAEVNVIFPAVDGASSFSQKHAEEESQFNDF 386 (1241)
Q Consensus 307 If~~HkAIRkDh~el~~~~~kl~~~~d~~~l~~~~~r~qfL~el~r~HS~AEe~vVyPALE~~~s~~~dh~~eeh~~eei 386 (1241)
+...=+.|..|+..+.....+= +. ..|...++-+...|- +|+|++- ++... +.++.|
T Consensus 96 W~~~e~~i~~~~~~mk~a~~~~----~~---~~f~~~~n~f~~~y~--------~I~Psl~------I~~~~--~~v~~v 152 (232)
T PF09577_consen 96 WLQYEKPIMEDFQRMKQAAQKG----DK---EAFRASLNEFLSHYE--------LIRPSLT------IDRPP--EQVQRV 152 (232)
T ss_pred HHHHHHHHHHHHHHHHHHHHhC----CH---HHHHHHHHHHHHHHH--------Hhcchhh------ccCCH--HHHHHH
Confidence 6677788888888888776532 23 344554455555444 7899994 33333 446667
Q ss_pred HHHHHHHHhcCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 000878 387 RLLIESIQNEGAISTSAEFYAKLCSHADQIMETIERHFHKVE 428 (1241)
Q Consensus 387 ~~LL~~lq~~~~~~~~~~f~~kL~~~l~~l~~~l~~Hi~eEE 428 (1241)
+..+..++.......+ ......++..+-.++...|...+
T Consensus 153 ~s~i~yl~~~~~~~~~---~~~~~~~l~~le~~l~~lF~~~k 191 (232)
T PF09577_consen 153 DSHISYLERLRFQQLD---QKEVQEALEQLEEDLQKLFDGVK 191 (232)
T ss_pred HHHHHHHHHhhhcccC---hHHHHHHHHHHHHHHHHHhCccc
Confidence 7777777644322222 12344557777777777776633
No 237
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=27.92 E-value=30 Score=31.14 Aligned_cols=10 Identities=30% Similarity=0.986 Sum_probs=6.3
Q ss_pred CCcccCCCCC
Q 000878 1072 RTVYHCPFCN 1081 (1241)
Q Consensus 1072 k~~yHC~~Cg 1081 (1241)
...|-||+||
T Consensus 25 ~v~F~CPnCG 34 (61)
T COG2888 25 AVKFPCPNCG 34 (61)
T ss_pred eeEeeCCCCC
Confidence 4556666666
No 238
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=27.79 E-value=32 Score=38.04 Aligned_cols=81 Identities=16% Similarity=0.440 Sum_probs=50.5
Q ss_pred CCCceEEcCCCCccchhhHHHHHhcCCCCC--CCCcccccchhhhhhhHHHHhccCCCHhhhcccceEEcCCCCCCCC-c
Q 000878 1131 SSETVRALPCGHYMHLACFQAYTCSHYTCP--ICSKSLGDMAIYFGMIDALLAAEELPEEYRNQVQDILCNDCEQKGA-A 1207 (1241)
Q Consensus 1131 s~~~~~~lpCgH~fH~~C~~~wl~~~~~CP--iCrk~~~dm~~~~~~lD~~i~~~~~P~ey~~~~~~i~CnDC~~~s~-~ 1207 (1241)
.++++..-||..+.= | +-.++.-.|| -|++.| .||-.+...+.|.. +-..+-+.|+-|+...- .
T Consensus 117 pGKKYVRCPCNCLLI--C--K~sSqRIACPRpnCkRiI--------nL~p~~~~p~~P~~-~P~gcRV~CgHC~~tFLfn 183 (275)
T KOG4684|consen 117 PGKKYVRCPCNCLLI--C--KASSQRIACPRPNCKRII--------NLDPLIEKPRDPGT-APTGCRVKCGHCNETFLFN 183 (275)
T ss_pred CCCceeecCCcEEEE--E--ecccceeccCCCCcceee--------ecCCCCCCCCCCCC-CCcceEEEecCccceeehh
Confidence 345566667763321 1 1224456686 587664 34444555555544 33446789999998863 5
Q ss_pred cchhhcccCCCCCCccc
Q 000878 1208 RFHWLYHKCGFCGSYNT 1224 (1241)
Q Consensus 1208 ~fh~lg~kC~~CgsYNT 1224 (1241)
.||----+|++|..|-+
T Consensus 184 t~tnaLArCPHCrKvSs 200 (275)
T KOG4684|consen 184 TLTNALARCPHCRKVSS 200 (275)
T ss_pred hHHHHHhcCCcccchhh
Confidence 57777789999988765
No 239
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=27.57 E-value=36 Score=33.52 Aligned_cols=39 Identities=28% Similarity=0.672 Sum_probs=28.5
Q ss_pred hcCCCCCCCCcccccchhhhhhhHHHHhccCCCHhhhcccceEEcCCCCC
Q 000878 1154 CSHYTCPICSKSLGDMAIYFGMIDALLAAEELPEEYRNQVQDILCNDCEQ 1203 (1241)
Q Consensus 1154 ~~~~~CPiCrk~~~dm~~~~~~lD~~i~~~~~P~ey~~~~~~i~CnDC~~ 1203 (1241)
+..-+||.|.+. .+||-.|.-..+.+||..-|+ |-+|+.
T Consensus 63 ~t~~~Cp~Cgh~----rayF~qlQtRSADEPmT~FYk-------C~~C~~ 101 (105)
T KOG2906|consen 63 QTEATCPTCGHE----RAYFMQLQTRSADEPMTTFYK-------CCKCKH 101 (105)
T ss_pred hccCcCCCCCCC----ceEEEEeeeccCCCcHhHhhh-------hhcccc
Confidence 345789999976 567777777778888887663 555764
No 240
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=26.96 E-value=37 Score=34.31 Aligned_cols=25 Identities=20% Similarity=0.471 Sum_probs=11.6
Q ss_pred eeEecccccc-ccCC-CCcccCCCCCc
Q 000878 1058 AKYYCNICKF-FDDE-RTVYHCPFCNL 1082 (1241)
Q Consensus 1058 a~y~C~~C~~-~d~~-k~~yHC~~Cgi 1082 (1241)
++.+|..|.. |.-+ ...++||.||-
T Consensus 70 ~~~~C~~Cg~~~~~~~~~~~~CP~Cgs 96 (117)
T PRK00564 70 VELECKDCSHVFKPNALDYGVCEKCHS 96 (117)
T ss_pred CEEEhhhCCCccccCCccCCcCcCCCC
Confidence 4445555542 2222 22335777774
No 241
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=26.95 E-value=39 Score=29.36 Aligned_cols=28 Identities=25% Similarity=0.680 Sum_probs=21.0
Q ss_pred cceeEecccccc-ccCC--CCcccCCCCCcc
Q 000878 1056 SMAKYYCNICKF-FDDE--RTVYHCPFCNLC 1083 (1241)
Q Consensus 1056 ~~a~y~C~~C~~-~d~~--k~~yHC~~CgiC 1083 (1241)
.+..|-|..|.= ++.+ ..-+.|++||.=
T Consensus 3 ~~~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~r 33 (49)
T COG1996 3 AMMEYKCARCGREVELDQETRGIRCPYCGSR 33 (49)
T ss_pred ceEEEEhhhcCCeeehhhccCceeCCCCCcE
Confidence 467899999973 4533 788999999953
No 242
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=26.27 E-value=34 Score=43.46 Aligned_cols=46 Identities=26% Similarity=0.666 Sum_probs=31.8
Q ss_pred cccccccccccCCCceEEc---CCCCccchhhHHHHHh-----cCCCCCCCCcccc
Q 000878 1120 NCPICCDFLFTSSETVRAL---PCGHYMHLACFQAYTC-----SHYTCPICSKSLG 1167 (1241)
Q Consensus 1120 ~CpICle~lf~s~~~~~~l---pCgH~fH~~C~~~wl~-----~~~~CPiCrk~~~ 1167 (1241)
-|++|-.. ....+-+.+ .||-++|..|..-|+. +.-+||-|++...
T Consensus 20 mc~l~~s~--G~~~ag~m~ac~~c~~~yH~~cvt~~~~~~~l~~gWrC~~crvCe~ 73 (694)
T KOG4443|consen 20 MCPLCGSS--GKGRAGRLLACSDCGQKYHPYCVTSWAQHAVLSGGWRCPSCRVCEA 73 (694)
T ss_pred hhhhhccc--cccccCcchhhhhhcccCCcchhhHHHhHHHhcCCcccCCceeeee
Confidence 47777643 333333333 4899999999999974 3467999998753
No 243
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=25.85 E-value=40 Score=34.97 Aligned_cols=10 Identities=30% Similarity=0.896 Sum_probs=6.3
Q ss_pred CcccCCCCCc
Q 000878 1073 TVYHCPFCNL 1082 (1241)
Q Consensus 1073 ~~yHC~~Cgi 1082 (1241)
..|.||.||-
T Consensus 106 ~~~~CP~Cgs 115 (135)
T PRK03824 106 AFLKCPKCGS 115 (135)
T ss_pred cCcCCcCCCC
Confidence 3456777773
No 244
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=25.71 E-value=5.9 Score=34.21 Aligned_cols=49 Identities=22% Similarity=0.693 Sum_probs=29.9
Q ss_pred CcceeEeccccccccCCCCcccCCCCCc--cccCCCCCccccccCCccccccc
Q 000878 1055 LSMAKYYCNICKFFDDERTVYHCPFCNL--CRVGGGLGVDFFHCMTCNCCLGL 1105 (1241)
Q Consensus 1055 ~~~a~y~C~~C~~~d~~k~~yHC~~Cgi--CRvg~~l~~~~fhC~~C~~C~s~ 1105 (1241)
..|++|.|+.|+--..-++.-.|--||- |-.- -.+.||.|..||.-+.+
T Consensus 3 ~SFsry~CDLCn~~~p~~~LRQCvlCGRWaC~sC--W~deYY~CksC~Gii~l 53 (57)
T PF14445_consen 3 HSFSRYSCDLCNSSHPISELRQCVLCGRWACNSC--WQDEYYTCKSCNGIINL 53 (57)
T ss_pred hHHhhHhHHhhcccCcHHHHHHHhhhchhhhhhh--hhhhHhHHHhhhchhhh
Confidence 3688899988885444355555666551 1111 12578888888865543
No 245
>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=25.68 E-value=64 Score=36.89 Aligned_cols=107 Identities=24% Similarity=0.599 Sum_probs=57.0
Q ss_pred eeccccccccccCCCCCCCCCCCCcceeEeccccc--cccCCCCcccCCCCC-------------ccccCCCCCcccccc
Q 000878 1032 MMCMHCLKIQAIGPNCTTPSCNGLSMAKYYCNICK--FFDDERTVYHCPFCN-------------LCRVGGGLGVDFFHC 1096 (1241)
Q Consensus 1032 ~~C~~C~~~q~~~~~C~~~~Cc~~~~a~y~C~~C~--~~d~~k~~yHC~~Cg-------------iCRvg~~l~~~~fhC 1096 (1241)
-||-+|..--=-+..|....-|.-++..-.|-.|. .||..-.+|.|.+|+ .|.|-. ...|.|
T Consensus 98 aiCDfCEawvCHgrkCl~~HaC~Cpl~da~C~EC~R~vw~hGGrif~CsfC~~flCEDDQFEHQAsCQvLe---~E~~KC 174 (314)
T PF06524_consen 98 AICDFCEAWVCHGRKCLSTHACTCPLQDAVCIECERGVWDHGGRIFKCSFCDNFLCEDDQFEHQASCQVLE---SETFKC 174 (314)
T ss_pred hhhccchhheeccccccccccccCcCCCcEeeeeecccccCCCeEEEeecCCCeeeccchhhhhhhhhhhh---cccccc
Confidence 35666654433334443333345566666677775 577667778887776 344432 355666
Q ss_pred CCcccccccccccccccccccCCcccccccccccCCCceEEcCCCCccchhhHHHHH-hcCCCCCCCCcccc
Q 000878 1097 MTCNCCLGLKLLNHKCLEKCLETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYT-CSHYTCPICSKSLG 1167 (1241)
Q Consensus 1097 ~~C~~C~s~~l~~H~C~e~~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl-~~~~~CPiCrk~~~ 1167 (1241)
..||- +.+|.|. .|-||.=+-...++.+ .+- ...+-||-|...+.
T Consensus 175 ~SCNr-----lGq~sCL------RCK~cfCddHvrrKg~---------------ky~k~k~~PCPKCg~et~ 220 (314)
T PF06524_consen 175 QSCNR-----LGQYSCL------RCKICFCDDHVRRKGF---------------KYEKGKPIPCPKCGYETQ 220 (314)
T ss_pred ccccc-----ccchhhh------heeeeehhhhhhhccc---------------ccccCCCCCCCCCCCccc
Confidence 66652 3455554 3666654421111111 122 23577888888774
No 246
>PF06937 EURL: EURL protein; InterPro: IPR009704 This family consists of several animal EURL proteins. EURL is preferentially expressed in chick retinal precursor cells as well as in the anterior epithelial cells of the lens at early stages of development. EURL transcripts are found primarily in the peripheral dorsal retina, i.e., the most undifferentiated part of the dorsal retina. EURL transcripts are also detected in the lens at stage 18 and remain abundant in the proliferating epithelial cells of the lens until at least day 11. The distribution pattern of EURL in the developing retina and lens suggest a role before the events leading to cell determination and differentiation [].
Probab=25.10 E-value=44 Score=38.35 Aligned_cols=42 Identities=26% Similarity=0.505 Sum_probs=25.4
Q ss_pred cCCcccccccccccCCCceEEcCCCCc----cchhhHHHH-HhcCCCCCC
Q 000878 1117 LETNCPICCDFLFTSSETVRALPCGHY----MHLACFQAY-TCSHYTCPI 1161 (1241)
Q Consensus 1117 ~~~~CpICle~lf~s~~~~~~lpCgH~----fH~~C~~~w-l~~~~~CPi 1161 (1241)
+-.-|+||.|- .-.+.+-.-| =|+ =|..||.+| +-.+..||.
T Consensus 29 tLsfChiCfEl-~iegvpks~l--lHtkSlRGHrdCFEK~HlIanQ~~pr 75 (285)
T PF06937_consen 29 TLSFCHICFEL-SIEGVPKSNL--LHTKSLRGHRDCFEKYHLIANQDCPR 75 (285)
T ss_pred ceeecceeecc-ccccCccccc--cccccccchHHHHHHHHHHHcCCCCc
Confidence 34569999987 2222211111 132 489999999 456788983
No 247
>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=24.95 E-value=29 Score=33.02 Aligned_cols=31 Identities=29% Similarity=0.888 Sum_probs=10.7
Q ss_pred CcccCCCCC-----ccccCCCCCccccccCCccccc
Q 000878 1073 TVYHCPFCN-----LCRVGGGLGVDFFHCMTCNCCL 1103 (1241)
Q Consensus 1073 ~~yHC~~Cg-----iCRvg~~l~~~~fhC~~C~~C~ 1103 (1241)
..|.||+|| .|.+-...|...-+|..||.-+
T Consensus 21 ~~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~ 56 (81)
T PF05129_consen 21 KVFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESF 56 (81)
T ss_dssp S----TTT--SS-EEEEEETTTTEEEEEESSS--EE
T ss_pred ceEcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeE
Confidence 456666666 3444333333344444444433
No 248
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=24.75 E-value=39 Score=29.31 Aligned_cols=23 Identities=30% Similarity=0.742 Sum_probs=10.6
Q ss_pred cCCCCCccccCCCCCccccccCCcc
Q 000878 1076 HCPFCNLCRVGGGLGVDFFHCMTCN 1100 (1241)
Q Consensus 1076 HC~~CgiCRvg~~l~~~~fhC~~C~ 1100 (1241)
.||.||---.. ...+.|+|.+||
T Consensus 22 fCP~Cg~~~m~--~~~~r~~C~~Cg 44 (50)
T PRK00432 22 FCPRCGSGFMA--EHLDRWHCGKCG 44 (50)
T ss_pred cCcCCCcchhe--ccCCcEECCCcC
Confidence 55555543111 123456666665
No 249
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=24.59 E-value=34 Score=26.45 Aligned_cols=11 Identities=27% Similarity=1.138 Sum_probs=8.6
Q ss_pred eeEeccccccc
Q 000878 1058 AKYYCNICKFF 1068 (1241)
Q Consensus 1058 a~y~C~~C~~~ 1068 (1241)
+.|||++|+.+
T Consensus 2 ~~~~C~~C~~~ 12 (35)
T smart00451 2 GGFYCKLCNVT 12 (35)
T ss_pred cCeEccccCCc
Confidence 57888888865
No 250
>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=24.51 E-value=45 Score=27.65 Aligned_cols=31 Identities=23% Similarity=0.356 Sum_probs=19.3
Q ss_pred eEEcCCCCCCCCccch---hhcccCCCCCCcccc
Q 000878 1195 DILCNDCEQKGAARFH---WLYHKCGFCGSYNTR 1225 (1241)
Q Consensus 1195 ~i~CnDC~~~s~~~fh---~lg~kC~~CgsYNT~ 1225 (1241)
...|.+||....+-.. -....|+.||+-+.+
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~ 38 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSISEDDPVPCPECGSTEVR 38 (42)
T ss_pred EEEeCCCCCEEEEEEEcCCCCCCcCCCCCCCceE
Confidence 3578889866542211 245679999985443
No 251
>PF07227 DUF1423: Protein of unknown function (DUF1423); InterPro: IPR004082 A total of 715 potential protein-coding genes have been identified in the nucleotide sequence of Arabidopsis thaliana chromosome 5, with an average gene density of 1 gene per 4001 bp []. Amongst the gene products is a well-conserved family of 130.7kDa proteins that share no sequence similarity with any other known proteins, other than in plants. The sequences are characterised by an N-terminal domain of variable length, a central cysteine-rich region and a relatively acidic C-terminal domain. The sequences may possess a PHD finger.
Probab=24.41 E-value=53 Score=40.25 Aligned_cols=31 Identities=23% Similarity=0.336 Sum_probs=18.9
Q ss_pred HHHHHHHhhhcCCCCCCHHHHHHHHHHHHHHHH
Q 000878 922 NELEAEIRKVYRDPTLDPRRKAYLAQNLMTSRW 954 (1241)
Q Consensus 922 ~~l~~~i~~~~~~~~l~~~~k~~~~q~l~~~~~ 954 (1241)
..|+..||.|--. .+.+..-...|+++-.|-
T Consensus 21 ~~lk~~lr~i~~~--~~~r~e~~~lQ~~l~~Rs 51 (446)
T PF07227_consen 21 EELKEYLREILEG--PEKREEFVALQKLLQRRS 51 (446)
T ss_pred HHHHHHHHHHHhC--cchHHHHHHHHHHHhccc
Confidence 3567778877754 444455566677765543
No 252
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=24.39 E-value=47 Score=25.58 Aligned_cols=20 Identities=35% Similarity=0.963 Sum_probs=12.3
Q ss_pred CCCccccCCCCCcc-ccccCCcc
Q 000878 1079 FCNLCRVGGGLGVD-FFHCMTCN 1100 (1241)
Q Consensus 1079 ~CgiCRvg~~l~~~-~fhC~~C~ 1100 (1241)
.|++|+.-.. .. +|+|..|+
T Consensus 2 ~C~~C~~~~~--~~~~Y~C~~c~ 22 (30)
T PF03107_consen 2 WCDVCRRKID--GFYFYHCSECC 22 (30)
T ss_pred CCCCCCCCcC--CCEeEEeCCCC
Confidence 3666654432 23 78888887
No 253
>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 smart00531 TFIIE Transcription initiation factor IIE.
Probab=23.98 E-value=28 Score=36.38 Aligned_cols=7 Identities=43% Similarity=1.549 Sum_probs=5.1
Q ss_pred ccCCCCC
Q 000878 1075 YHCPFCN 1081 (1241)
Q Consensus 1075 yHC~~Cg 1081 (1241)
|.||.||
T Consensus 124 f~Cp~Cg 130 (147)
T smart00531 124 FTCPRCG 130 (147)
T ss_pred EECCCCC
Confidence 7777776
No 255
>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=23.86 E-value=45 Score=25.07 Aligned_cols=20 Identities=20% Similarity=0.619 Sum_probs=12.4
Q ss_pred CCCCCCCcccccchhhhhhhH
Q 000878 1157 YTCPICSKSLGDMAIYFGMID 1177 (1241)
Q Consensus 1157 ~~CPiCrk~~~dm~~~~~~lD 1177 (1241)
..||||.+.+ .+....+.+|
T Consensus 2 v~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLD 21 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHH
Confidence 3699999887 3333334444
No 256
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=23.79 E-value=48 Score=29.89 Aligned_cols=29 Identities=17% Similarity=0.075 Sum_probs=21.1
Q ss_pred ceEEcCCCCCCCCccchhhcccCCCCCCccccccc
Q 000878 1194 QDILCNDCEQKGAARFHWLYHKCGFCGSYNTRLIK 1228 (1241)
Q Consensus 1194 ~~i~CnDC~~~s~~~fh~lg~kC~~CgsYNT~~~~ 1228 (1241)
..+.|..||..- ..| +.|. ||.||.+++-
T Consensus 26 ~~~~c~~cg~~~--~pH---~vc~-cG~Y~gr~v~ 54 (60)
T PRK01110 26 TLSVDKTTGEYH--LPH---HVSP-KGYYKGRKVL 54 (60)
T ss_pred ceeEcCCCCcee--ccc---eecC-CcccCCeEee
Confidence 357899999742 223 3499 9999999874
No 257
>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=23.36 E-value=54 Score=34.29 Aligned_cols=48 Identities=21% Similarity=0.428 Sum_probs=30.6
Q ss_pred CCCCCCCcccccchhhhhhhHHHHhccCCCHh-hhcccceEEcCCCCCCCCccchh
Q 000878 1157 YTCPICSKSLGDMAIYFGMIDALLAAEELPEE-YRNQVQDILCNDCEQKGAARFHW 1211 (1241)
Q Consensus 1157 ~~CPiCrk~~~dm~~~~~~lD~~i~~~~~P~e-y~~~~~~i~CnDC~~~s~~~fh~ 1211 (1241)
.+||.|+..+...+ .+-....+|+. |........|..||+.-...-||
T Consensus 92 sRC~~CN~~L~~v~-------~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~GsH~ 140 (147)
T PF01927_consen 92 SRCPKCNGPLRPVS-------KEEVKDRVPPYVYETYDEFWRCPGCGKIYWEGSHW 140 (147)
T ss_pred CccCCCCcEeeech-------hhccccccCccccccCCeEEECCCCCCEecccccH
Confidence 68999999765443 22223335554 44444567899999876665565
No 258
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=23.15 E-value=1.6e+02 Score=30.00 Aligned_cols=45 Identities=20% Similarity=0.296 Sum_probs=23.8
Q ss_pred CCcccccccccccCCC-----------ceEEcCCCCccchhhHHHHHhcCCCCCCCC
Q 000878 1118 ETNCPICCDFLFTSSE-----------TVRALPCGHYMHLACFQAYTCSHYTCPICS 1163 (1241)
Q Consensus 1118 ~~~CpICle~lf~s~~-----------~~~~lpCgH~fH~~C~~~wl~~~~~CPiCr 1163 (1241)
...|--|+.. |.... .+.--.|++.|..+|-.-+-..=..||-|.
T Consensus 55 ~~~C~~C~~~-f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~CPGC~ 110 (112)
T TIGR00622 55 SRFCFGCQGP-FPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHESLHCCPGCI 110 (112)
T ss_pred CCcccCcCCC-CCCcccccccccccccceeCCCCCCccccccchhhhhhccCCcCCC
Confidence 3469999988 54321 122234666666666433323334466664
No 259
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=23.11 E-value=43 Score=35.65 Aligned_cols=27 Identities=22% Similarity=0.513 Sum_probs=0.0
Q ss_pred ccCCCCC----ccccCCCCCc-----cccccCCccc
Q 000878 1075 YHCPFCN----LCRVGGGLGV-----DFFHCMTCNC 1101 (1241)
Q Consensus 1075 yHC~~Cg----iCRvg~~l~~-----~~fhC~~C~~ 1101 (1241)
++||+|| .=+-...+.+ .+++|..||.
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~ 36 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGK 36 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCC
No 260
>KOG1703 consensus Adaptor protein Enigma and related PDZ-LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=23.06 E-value=31 Score=42.83 Aligned_cols=98 Identities=24% Similarity=0.456 Sum_probs=60.8
Q ss_pred cccccccccCCcccccccccccCCCceEEcCCCCccchhhHHHHHhcCCCCCCCCcccccchhhhhhhHHHHhccCCC--
Q 000878 1109 NHKCLEKCLETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSLGDMAIYFGMIDALLAAEELP-- 1186 (1241)
Q Consensus 1109 ~H~C~e~~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~~~~~CPiCrk~~~dm~~~~~~lD~~i~~~~~P-- 1186 (1241)
-|.|.......+|.-|..++.+.. +..+ ++.||..|| +|-.|.+++.+-..++.. .+|
T Consensus 354 c~~~~~~~~~p~C~~C~~~i~~~~--v~a~--~~~wH~~cf--------~C~~C~~~~~~~~~~~~~--------~~pyc 413 (479)
T KOG1703|consen 354 CHECFHAPFRPNCKRCLLPILEEG--VCAL--GRLWHPECF--------VCADCGKPLKNSSFFESD--------GEPYC 413 (479)
T ss_pred HHHHHHHhhCccccccCCchHHhH--hhhc--cCeechhce--------eeecccCCCCCCcccccC--------Cccch
Confidence 566777788889999998864433 3344 999999998 566887776554433211 111
Q ss_pred H-hhhccc---------ceEEcCCCCCCCCccchhhcccCCCCCCccccc
Q 000878 1187 E-EYRNQV---------QDILCNDCEQKGAARFHWLYHKCGFCGSYNTRL 1226 (1241)
Q Consensus 1187 ~-ey~~~~---------~~i~CnDC~~~s~~~fh~lg~kC~~CgsYNT~~ 1226 (1241)
+ .|.... -...|-.+-+.....||--+-+|..|.--++..
T Consensus 414 e~~~~~~~~~~~~~~~~p~~~~~~~ie~~~~~~h~~~F~c~~c~~~l~~~ 463 (479)
T KOG1703|consen 414 EDHYKKLFTTKCDYCKKPVEFGSRQIEADGSPFHGDCFRCANCMKKLTKK 463 (479)
T ss_pred hhhHhhhccccchhccchhHhhhhHhhccCccccccceehhhhhccccCC
Confidence 0 111111 112233344445678999999999998877744
No 261
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=22.99 E-value=38 Score=28.70 Aligned_cols=12 Identities=50% Similarity=1.041 Sum_probs=10.3
Q ss_pred cCCCCCCccccc
Q 000878 1215 KCGFCGSYNTRL 1226 (1241)
Q Consensus 1215 kC~~CgsYNT~~ 1226 (1241)
||+.||-||-..
T Consensus 13 kCp~CGt~NG~R 24 (44)
T PF14952_consen 13 KCPKCGTYNGTR 24 (44)
T ss_pred cCCcCcCccCcc
Confidence 899999999654
No 262
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=22.99 E-value=38 Score=42.87 Aligned_cols=30 Identities=33% Similarity=0.594 Sum_probs=11.9
Q ss_pred eEEcCCCCCCCCccchhhcccCCCCCCcccccccc
Q 000878 1195 DILCNDCEQKGAARFHWLYHKCGFCGSYNTRLIKN 1229 (1241)
Q Consensus 1195 ~i~CnDC~~~s~~~fh~lg~kC~~CgsYNT~~~~~ 1229 (1241)
.-.|++||....- +.+|+.|||-|+.+++.
T Consensus 491 ~~~C~~CG~~~~~-----~~~CP~CGs~~~~~~~R 520 (546)
T PF13597_consen 491 IDICPDCGYIGGE-----GDKCPKCGSENIEVYSR 520 (546)
T ss_dssp EEEETTT---S-------EEE-CCC----EEEEB-
T ss_pred cccccCCCcCCCC-----CCCCCCCCCcccceEEE
Confidence 3457777765542 34677777777666543
No 263
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=22.87 E-value=21 Score=42.44 Aligned_cols=34 Identities=21% Similarity=0.372 Sum_probs=15.4
Q ss_pred cceEEcCCCCCCCCccchhhcccCCCCCCccccc
Q 000878 1193 VQDILCNDCEQKGAARFHWLYHKCGFCGSYNTRL 1226 (1241)
Q Consensus 1193 ~~~i~CnDC~~~s~~~fh~lg~kC~~CgsYNT~~ 1226 (1241)
+-...|-+|+.+...-.-+=...|.+||++|-..
T Consensus 283 KRFFkC~~C~~Rt~sl~r~P~~~C~~Cg~~~wer 316 (344)
T PF09332_consen 283 KRFFKCKDCGNRTISLERLPKKHCSNCGSSKWER 316 (344)
T ss_dssp -EEEE-T-TS-EEEESSSS--S--TTT-S---EE
T ss_pred eeeEECCCCCCeeeecccCCCCCCCcCCcCceee
Confidence 3467899999986644334457899999987543
No 264
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=22.53 E-value=51 Score=38.01 Aligned_cols=29 Identities=28% Similarity=0.602 Sum_probs=18.7
Q ss_pred EEcCCCCCC----CCccchhh------cccCCCCCCccc
Q 000878 1196 ILCNDCEQK----GAARFHWL------YHKCGFCGSYNT 1224 (1241)
Q Consensus 1196 i~CnDC~~~----s~~~fh~l------g~kC~~CgsYNT 1224 (1241)
..|-.|++. |+..-|.- -++|+.|+.+=.
T Consensus 216 F~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFs 254 (279)
T KOG2462|consen 216 FSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFA 254 (279)
T ss_pred ccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHH
Confidence 469999975 44444443 457999986533
No 265
>PF13212 DUF4020: Domain of unknown function (DUF4020)
Probab=22.31 E-value=1.2e+02 Score=33.03 Aligned_cols=42 Identities=14% Similarity=0.272 Sum_probs=37.7
Q ss_pred HhhHHhccCCHHHHHHHHH-------hchHHHhhhhHHHHHHhhhcCCC
Q 000878 837 MLPWVTSALTQDEQSKLID-------TWKHATKNTMFNEWLDECWKGPH 878 (1241)
Q Consensus 837 ~lpwv~~~l~~~eq~~ml~-------~~~~a~r~t~f~~Wl~~~~~~~~ 878 (1241)
.||-++...+++++-++|. +++...+...++.||...|+.-+
T Consensus 21 wL~~l~~~~~e~~rikF~~~L~~~v~~L~~~~qqe~W~~WL~~fl~~r~ 69 (180)
T PF13212_consen 21 WLYPLFIQESEEERIKFMFHLSYYVKTLSKEEQQEFWDAWLSQFLRNRP 69 (180)
T ss_pred HHHHHHhccCHHHHHHHHHHHHHHHhccCHHHHHHHHHHHHHHHHhcCc
Confidence 8899999999999987875 88999999999999999998744
No 266
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=22.15 E-value=56 Score=42.18 Aligned_cols=34 Identities=21% Similarity=0.504 Sum_probs=18.5
Q ss_pred ceeccccccccccCCCCCCCCCCCCc--ceeEeccccccc
Q 000878 1031 EMMCMHCLKIQAIGPNCTTPSCNGLS--MAKYYCNICKFF 1068 (1241)
Q Consensus 1031 ~~~C~~C~~~q~~~~~C~~~~Cc~~~--~a~y~C~~C~~~ 1068 (1241)
.-.|..|++.... ..|++ | |.. .+.-||..|-..
T Consensus 15 akFC~~CG~~l~~-~~Cp~--C-G~~~~~~~~fC~~CG~~ 50 (645)
T PRK14559 15 NRFCQKCGTSLTH-KPCPQ--C-GTEVPVDEAHCPNCGAE 50 (645)
T ss_pred CccccccCCCCCC-CcCCC--C-CCCCCcccccccccCCc
Confidence 3467777666543 35666 3 333 555566666543
No 267
>PF10272 Tmpp129: Putative transmembrane protein precursor; InterPro: IPR018801 This entry consists of proteins conserved from worms to humans. They are purported to be transmembrane protein-precursors but their function is unknown.
Probab=21.94 E-value=85 Score=37.78 Aligned_cols=16 Identities=19% Similarity=0.742 Sum_probs=12.1
Q ss_pred HHHhcCCCCCCCCccc
Q 000878 1151 AYTCSHYTCPICSKSL 1166 (1241)
Q Consensus 1151 ~wl~~~~~CPiCrk~~ 1166 (1241)
.|+.++-+||.||+..
T Consensus 335 ~Wl~~~~~CPtCRa~F 350 (358)
T PF10272_consen 335 TWLSGKCPCPTCRAKF 350 (358)
T ss_pred hhhcCCCCCCCCcccc
Confidence 4555668899999875
No 268
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=21.70 E-value=84 Score=36.77 Aligned_cols=76 Identities=26% Similarity=0.484 Sum_probs=49.4
Q ss_pred ccCC----CCcccCCCCCccccCCCCCccccccCCcccccccc--c--ccccccccccCCcccccccccccCCCceEEcC
Q 000878 1068 FDDE----RTVYHCPFCNLCRVGGGLGVDFFHCMTCNCCLGLK--L--LNHKCLEKCLETNCPICCDFLFTSSETVRALP 1139 (1241)
Q Consensus 1068 ~d~~----k~~yHC~~CgiCRvg~~l~~~~fhC~~C~~C~s~~--l--~~H~C~e~~~~~~CpICle~lf~s~~~~~~lp 1139 (1241)
|||- +-+=||..|- +.+-.-+-||.| +.|.+-. . -.|-=..++-.-.|-.|-+. .+++.+++
T Consensus 169 WdDVLks~Ripg~Ces~~---~pg~fAEFfFKC---~ah~~~~k~~aa~lhli~~N~~ni~C~~Ctdv----~~~vlvf~ 238 (446)
T KOG0006|consen 169 WDDVLKSKRIPGVCESCC---TPGLFAEFFFKC---GAHPTSDKETAAALHLIATNSRNITCITCTDV----RSPVLVFQ 238 (446)
T ss_pred hhhhhhcccCcccccccc---CCcchHhheehh---ccCCCccccchhHHHHhhcccccceeEEecCC----ccceEEEe
Confidence 7764 5566777663 222122445654 4555432 1 35544556667789999866 67889999
Q ss_pred CC--CccchhhHHHHH
Q 000878 1140 CG--HYMHLACFQAYT 1153 (1241)
Q Consensus 1140 Cg--H~fH~~C~~~wl 1153 (1241)
|. |.....||.-|-
T Consensus 239 Cns~HvtC~dCFr~yc 254 (446)
T KOG0006|consen 239 CNSRHVTCLDCFRLYC 254 (446)
T ss_pred cCCceeehHHhhhhHh
Confidence 99 999999998773
No 269
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=21.48 E-value=66 Score=31.86 Aligned_cols=38 Identities=18% Similarity=0.380 Sum_probs=0.0
Q ss_pred ceEEcCCCCCCCCc-------cchhhcccCCCCCCccccccccCCCCCC
Q 000878 1194 QDILCNDCEQKGAA-------RFHWLYHKCGFCGSYNTRLIKNDTTVSN 1235 (1241)
Q Consensus 1194 ~~i~CnDC~~~s~~-------~fh~lg~kC~~CgsYNT~~~~~~~~~~~ 1235 (1241)
....|..|+..+.. ..+. |+.||-|+.+++.....+-|
T Consensus 20 t~f~CP~Cge~~v~v~~~k~~~h~~----C~~CG~y~~~~V~~l~epID 64 (99)
T PRK14892 20 KIFECPRCGKVSISVKIKKNIAIIT----CGNCGLYTEFEVPSVYDEVD 64 (99)
T ss_pred cEeECCCCCCeEeeeecCCCcceEE----CCCCCCccCEECCccccchh
No 270
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=21.38 E-value=70 Score=27.07 Aligned_cols=23 Identities=26% Similarity=0.618 Sum_probs=15.5
Q ss_pred eEecccccc-ccCC-CCcccCCCCC
Q 000878 1059 KYYCNICKF-FDDE-RTVYHCPFCN 1081 (1241)
Q Consensus 1059 ~y~C~~C~~-~d~~-k~~yHC~~Cg 1081 (1241)
.|-|..|.- ++-+ ++...|++||
T Consensus 2 ~Y~C~~Cg~~~~~~~~~~irC~~CG 26 (44)
T smart00659 2 IYICGECGRENEIKSKDVVRCRECG 26 (44)
T ss_pred EEECCCCCCEeecCCCCceECCCCC
Confidence 466777764 3333 6788888888
No 271
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=21.23 E-value=57 Score=29.06 Aligned_cols=12 Identities=25% Similarity=0.835 Sum_probs=9.1
Q ss_pred CCcccCCCCCcc
Q 000878 1072 RTVYHCPFCNLC 1083 (1241)
Q Consensus 1072 k~~yHC~~CgiC 1083 (1241)
...|-||+|||-
T Consensus 12 ~v~~~Cp~cGip 23 (55)
T PF13824_consen 12 HVNFECPDCGIP 23 (55)
T ss_pred ccCCcCCCCCCc
Confidence 567888888863
No 272
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.06 E-value=43 Score=42.28 Aligned_cols=43 Identities=26% Similarity=0.758 Sum_probs=36.4
Q ss_pred cCCcccccccccccCCCceEEcCCCCccchhhHHHHHhcCCCCCCCCcccc
Q 000878 1117 LETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSLG 1167 (1241)
Q Consensus 1117 ~~~~CpICle~lf~s~~~~~~lpCgH~fH~~C~~~wl~~~~~CPiCrk~~~ 1167 (1241)
.+++|.||.+.+ ..++.+|- |..|+.+|+....+||.|++.+.
T Consensus 478 ~~~~~~~~~~~~-----~~~~~~~~---~~~~l~~~~~~~~~~pl~~~~~~ 520 (543)
T KOG0802|consen 478 PNDVCAICYQEM-----SARITPCS---HALCLRKWLYVQEVCPLCHTYMK 520 (543)
T ss_pred ccCcchHHHHHH-----Hhcccccc---chhHHHhhhhhccccCCCchhhh
Confidence 367899999995 44566777 99999999999999999998764
No 273
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=20.97 E-value=56 Score=28.15 Aligned_cols=21 Identities=29% Similarity=0.942 Sum_probs=14.2
Q ss_pred ccCCCCCcc-ccCCCCCccccccCCcc
Q 000878 1075 YHCPFCNLC-RVGGGLGVDFFHCMTCN 1100 (1241)
Q Consensus 1075 yHC~~CgiC-Rvg~~l~~~~fhC~~C~ 1100 (1241)
|.|+.|+.. .+| -.|||..|.
T Consensus 1 y~Cd~C~~~pI~G-----~R~~C~~C~ 22 (48)
T cd02341 1 FKCDSCGIEPIPG-----TRYHCSECD 22 (48)
T ss_pred CCCCCCCCCcccc-----ceEECCCCC
Confidence 678888873 343 358888765
No 274
>COG4913 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.83 E-value=3.9e+02 Score=35.03 Aligned_cols=63 Identities=24% Similarity=0.304 Sum_probs=41.4
Q ss_pred hhhhhhhhccC--CHHHHHHHHhHHhcCCCHHHHHH--HhhHHhccCCHHHHHHHHHhchHHHhhhh
Q 000878 803 LELWPLFGRHF--SVEEQDKIVGRIIGSTGAEVLQS--MLPWVTSALTQDEQSKLIDTWKHATKNTM 865 (1241)
Q Consensus 803 ~el~PL~~~~~--t~~Ew~~i~~~~~~~~~~~~l~~--~lpwv~~~l~~~eq~~ml~~~~~a~r~t~ 865 (1241)
-+.||...+-+ ...||+-.+.+|+|..+++.|.- .+|-|.+-.....-++.|..--..+++||
T Consensus 464 ~~~mPFAGELI~~~~~~WE~~~qRiL~GF~~~mLVP~~~~~~V~~WVN~k~L~~~L~~~~~~~~~~~ 530 (1104)
T COG4913 464 PRDMPFAGELIDPNNAEWEPVVQRILGGFAAEMLVPHGLLPRVRDWVNAKHLAALLKFNGVVTTGEY 530 (1104)
T ss_pred hhhCCccccccCCCcccchHHHHHHhhhchhhhcccccchHHHHHHHhHHHHHHHHHhcceeecCcc
Confidence 35677766654 57899999999999999975532 45555554555555555554444555555
No 275
>PHA00626 hypothetical protein
Probab=20.72 E-value=57 Score=29.12 Aligned_cols=33 Identities=24% Similarity=0.342 Sum_probs=19.9
Q ss_pred eeccccccccccCCCCCCCCCCCCcceeEecccccccc
Q 000878 1032 MMCMHCLKIQAIGPNCTTPSCNGLSMAKYYCNICKFFD 1069 (1241)
Q Consensus 1032 ~~C~~C~~~q~~~~~C~~~~Cc~~~~a~y~C~~C~~~d 1069 (1241)
|.|..|+..+-+ .|.. | ..+-.+|-|..|.+++
T Consensus 1 m~CP~CGS~~Iv--rcg~--c-r~~snrYkCkdCGY~f 33 (59)
T PHA00626 1 MSCPKCGSGNIA--KEKT--M-RGWSDDYVCCDCGYND 33 (59)
T ss_pred CCCCCCCCceee--eece--e-cccCcceEcCCCCCee
Confidence 457777665533 3433 2 3456678888888764
No 276
>PF15353 HECA: Headcase protein family homologue
Probab=20.70 E-value=51 Score=32.92 Aligned_cols=16 Identities=44% Similarity=1.063 Sum_probs=13.8
Q ss_pred CCCCccchhhHHHHHh
Q 000878 1139 PCGHYMHLACFQAYTC 1154 (1241)
Q Consensus 1139 pCgH~fH~~C~~~wl~ 1154 (1241)
|.|++||.+||+.|-.
T Consensus 39 p~~~~MH~~CF~~wE~ 54 (107)
T PF15353_consen 39 PFGQYMHRECFEKWED 54 (107)
T ss_pred CCCCchHHHHHHHHHH
Confidence 5689999999999953
No 277
>PLN02189 cellulose synthase
Probab=20.59 E-value=73 Score=42.92 Aligned_cols=52 Identities=23% Similarity=0.494 Sum_probs=35.4
Q ss_pred ccccCCccccccccccc--CCCceEEcC-CCCccchhhHHHHH--hcCCCCCCCCccc
Q 000878 1114 EKCLETNCPICCDFLFT--SSETVRALP-CGHYMHLACFQAYT--CSHYTCPICSKSL 1166 (1241)
Q Consensus 1114 e~~~~~~CpICle~lf~--s~~~~~~lp-CgH~fH~~C~~~wl--~~~~~CPiCrk~~ 1166 (1241)
++...+.|.||.+++=. +++.-+.-. ||--.+..|+ +|- ..+..||-|+...
T Consensus 30 ~~~~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cy-eyer~eg~q~CpqCkt~Y 86 (1040)
T PLN02189 30 RNLDGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCY-EYERREGTQNCPQCKTRY 86 (1040)
T ss_pred ccccCccccccccccCcCCCCCEEEeeccCCCccccchh-hhhhhcCCccCcccCCch
Confidence 34445689999999632 222222223 7778999999 664 4568899999875
No 278
>cd07170 NR_DBD_ERR DNA-binding domain of estrogen related receptors (ERR) is composed of two C4-type zinc fingers. DNA-binding domain of estrogen related receptors (ERRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ERR interacts with the palindromic inverted repeat, 5'GGTCAnnnTGACC-3', upstream of the target gene and modulates the rate of transcriptional initiation. The estrogen receptor-related receptors (ERRs) are transcriptional regulators, which are closely related to the estrogen receptor (ER) family. Although ERRs lack the ability to bind to estrogen and are so-called orphan receptors, they share target genes, co-regulators and promoters with the estrogen receptor (ER) family. By targeting the same set of genes, ERRs seem to interfere with the classic ER-mediated estrogen response in various ways. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription
Probab=20.41 E-value=62 Score=31.82 Aligned_cols=44 Identities=27% Similarity=0.619 Sum_probs=31.5
Q ss_pred CCcceeEeccccccc-cC---CCCcccCCCCCccccCCCCCccccccCCcc
Q 000878 1054 GLSMAKYYCNICKFF-DD---ERTVYHCPFCNLCRVGGGLGVDFFHCMTCN 1100 (1241)
Q Consensus 1054 ~~~~a~y~C~~C~~~-d~---~k~~yHC~~CgiCRvg~~l~~~~fhC~~C~ 1100 (1241)
|.+||-+.|.-|+-| -- .+..|.|..-+-|.+... ....|..|.
T Consensus 16 g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~---~r~~Cr~CR 63 (97)
T cd07170 16 GYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKR---RRKSCQACR 63 (97)
T ss_pred ceEECceeehhhhHHHHHHhccCCceeecCCCccccCcc---cCccCCccc
Confidence 678999999999955 32 257899998888887642 345555554
No 279
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=20.30 E-value=85 Score=40.53 Aligned_cols=44 Identities=25% Similarity=0.649 Sum_probs=32.5
Q ss_pred cccccccccccCCCceEEcCCCC-ccchhhHHHHH--hc----CCCCCCCCcccc
Q 000878 1120 NCPICCDFLFTSSETVRALPCGH-YMHLACFQAYT--CS----HYTCPICSKSLG 1167 (1241)
Q Consensus 1120 ~CpICle~lf~s~~~~~~lpCgH-~fH~~C~~~wl--~~----~~~CPiCrk~~~ 1167 (1241)
.|+||-.. .+-+..-.||| -....|..... .. ...||+|+..+.
T Consensus 2 ~c~ic~~s----~~~~~~~s~~h~~v~~~~~~R~~~~~~~~~~~~~~~vcr~~~~ 52 (669)
T KOG2231|consen 2 SCAICAFS----PDFVGRGSCGHNEVCATCVVRLRFELNNRKCSNECPVCRREVE 52 (669)
T ss_pred CcceeecC----ccccccccccccccchhhhhhhhhhcccccccccCccccccee
Confidence 69999866 34456667999 89999987763 33 466799999663
No 280
>KOG1312 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=20.24 E-value=32 Score=39.72 Aligned_cols=33 Identities=27% Similarity=0.731 Sum_probs=23.5
Q ss_pred CCCCccccCCCCCccccccCCcccccccccccccccc
Q 000878 1078 PFCNLCRVGGGLGVDFFHCMTCNCCLGLKLLNHKCLE 1114 (1241)
Q Consensus 1078 ~~CgiCRvg~~l~~~~fhC~~C~~C~s~~l~~H~C~e 1114 (1241)
-+|..|+..+- -...||..||-|+.. ..|.|+=
T Consensus 149 ~kCSTCki~KP--ARSKHCsiCNrCV~r--fDHHCiW 181 (341)
T KOG1312|consen 149 VKCSTCKIRKP--ARSKHCSICNRCVHR--FDHHCIW 181 (341)
T ss_pred CccccccCCCc--cccccchHHHHHHHH--hccceEe
Confidence 46777777763 567888888888753 3677774
No 281
>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=20.23 E-value=61 Score=25.74 Aligned_cols=22 Identities=27% Similarity=0.676 Sum_probs=13.4
Q ss_pred Eeccccccc-cCC-CCcccCCCCC
Q 000878 1060 YYCNICKFF-DDE-RTVYHCPFCN 1081 (1241)
Q Consensus 1060 y~C~~C~~~-d~~-k~~yHC~~Cg 1081 (1241)
|.|..|..- +.. .+...|++||
T Consensus 1 Y~C~~Cg~~~~~~~~~~irC~~CG 24 (32)
T PF03604_consen 1 YICGECGAEVELKPGDPIRCPECG 24 (32)
T ss_dssp EBESSSSSSE-BSTSSTSSBSSSS
T ss_pred CCCCcCCCeeEcCCCCcEECCcCC
Confidence 556666542 222 6677888888
No 282
>PRK12775 putative trifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta/ferritin domain-containing protein; Provisional
Probab=20.15 E-value=46 Score=45.24 Aligned_cols=53 Identities=26% Similarity=0.573 Sum_probs=35.9
Q ss_pred cCCCCCCCCcccccchhhhhhhHHHHhccCCCHhhhcccceEEcCCCCCCCCccchhhcccCCCCCCc
Q 000878 1155 SHYTCPICSKSLGDMAIYFGMIDALLAAEELPEEYRNQVQDILCNDCEQKGAARFHWLYHKCGFCGSY 1222 (1241)
Q Consensus 1155 ~~~~CPiCrk~~~dm~~~~~~lD~~i~~~~~P~ey~~~~~~i~CnDC~~~s~~~fh~lg~kC~~CgsY 1222 (1241)
..-+||.|.+++.-.+.|.-- .+..-...|.||++.+. .|-+-|-.|+.||..
T Consensus 795 ~~~~~~~~~~~~~~~~~~~~~--------------~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~ 847 (1006)
T PRK12775 795 GVATCPKCHRPLEGDEEYVCC--------------ATSELQWRCDDCGKVSE-GFAFPYGMCPACGGK 847 (1006)
T ss_pred CCccCcccCCCCCCCceeEEe--------------cCcceeeehhhhccccc-cccCCcCcCcccccc
Confidence 347899999988654444211 11222457999998875 355667899999986
Done!