Query 000895
Match_columns 1235
No_of_seqs 554 out of 1579
Neff 5.3
Searched_HMMs 46136
Date Tue Apr 2 00:33:12 2013
Command hhsearch -i /work/01045/syshi/lefta3m/000895.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/leftcdd/000895hhsearch_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 2.1E-62 4.6E-67 536.2 7.4 273 945-1230 1-275 (276)
2 PF14599 zinc_ribbon_6: Zinc-r 99.9 1.7E-25 3.7E-30 195.1 -0.9 61 1160-1220 1-61 (61)
3 PF05495 zf-CHY: CHY zinc fing 99.8 4.9E-21 1.1E-25 173.3 0.8 70 986-1063 1-71 (71)
4 PF01814 Hemerythrin: Hemeryth 99.2 3.9E-10 8.4E-15 110.0 14.6 124 293-425 2-133 (133)
5 PF01814 Hemerythrin: Hemeryth 99.2 2.2E-10 4.9E-15 111.7 12.3 129 43-176 2-133 (133)
6 PF13639 zf-RING_2: Ring finge 99.1 8.9E-12 1.9E-16 102.6 0.9 44 1113-1157 1-44 (44)
7 COG4357 Zinc finger domain con 98.9 1.6E-10 3.5E-15 108.1 -1.3 58 982-1039 11-76 (105)
8 KOG0804 Cytoplasmic Zn-finger 98.8 9E-10 2E-14 126.9 2.4 82 1112-1220 175-258 (493)
9 COG5243 HRD1 HRD ubiquitin lig 98.8 1E-09 2.2E-14 123.4 2.8 57 1109-1165 284-350 (491)
10 KOG4628 Predicted E3 ubiquitin 98.8 1E-09 2.2E-14 125.5 2.6 74 1088-1163 204-280 (348)
11 PF12678 zf-rbx1: RING-H2 zinc 98.8 2.7E-09 5.8E-14 97.6 3.3 47 1111-1157 18-73 (73)
12 PRK10992 iron-sulfur cluster r 98.8 6.5E-08 1.4E-12 106.0 14.6 131 294-427 76-218 (220)
13 TIGR03652 FeS_repair_RIC iron- 98.7 1.4E-07 3.1E-12 103.0 12.9 129 294-425 72-216 (216)
14 PRK10992 iron-sulfur cluster r 98.6 5.9E-07 1.3E-11 98.6 14.4 129 49-178 82-218 (220)
15 PF12861 zf-Apc11: Anaphase-pr 98.6 3.6E-08 7.8E-13 92.1 3.2 46 1113-1160 33-81 (85)
16 PHA02929 N1R/p28-like protein; 98.5 4.7E-08 1E-12 107.7 4.1 53 1109-1161 171-227 (238)
17 COG3945 Uncharacterized conser 98.5 2E-06 4.4E-11 89.9 14.7 140 292-440 8-158 (189)
18 cd00162 RING RING-finger (Real 98.5 7E-08 1.5E-12 77.6 3.1 44 1114-1160 1-45 (45)
19 COG5540 RING-finger-containing 98.5 7.3E-08 1.6E-12 106.7 3.0 54 1107-1161 318-372 (374)
20 TIGR03652 FeS_repair_RIC iron- 98.4 2.1E-06 4.6E-11 93.9 13.4 127 49-175 78-215 (216)
21 PF13923 zf-C3HC4_2: Zinc fing 98.4 1.1E-07 2.5E-12 76.5 2.1 39 1115-1156 1-39 (39)
22 PRK13276 cell wall biosynthesi 98.4 3.4E-06 7.5E-11 92.5 13.3 125 297-424 83-222 (224)
23 PRK13276 cell wall biosynthesi 98.3 7.8E-06 1.7E-10 89.8 13.8 125 49-174 85-221 (224)
24 PF13920 zf-C3HC4_3: Zinc fing 98.2 5.7E-07 1.2E-11 76.2 2.2 47 1112-1162 2-49 (50)
25 COG5194 APC11 Component of SCF 98.2 7.4E-07 1.6E-11 81.5 2.6 48 1113-1160 32-80 (88)
26 smart00184 RING Ring finger. E 98.1 1.5E-06 3.3E-11 67.4 2.6 38 1115-1156 1-39 (39)
27 COG2846 Regulator of cell morp 98.1 2.6E-05 5.6E-10 82.9 12.0 128 295-425 79-217 (221)
28 PF14634 zf-RING_5: zinc-RING 98.1 2.4E-06 5.3E-11 70.7 2.9 44 1114-1158 1-44 (44)
29 PF00097 zf-C3HC4: Zinc finger 98.0 3.1E-06 6.8E-11 68.4 2.4 39 1115-1156 1-41 (41)
30 KOG0802 E3 ubiquitin ligase [P 98.0 1.7E-06 3.7E-11 106.5 1.0 53 1108-1160 287-340 (543)
31 PLN03208 E3 ubiquitin-protein 98.0 4.9E-06 1.1E-10 88.9 4.1 51 1108-1162 14-80 (193)
32 PF15227 zf-C3HC4_4: zinc fing 98.0 4E-06 8.6E-11 69.0 2.4 38 1115-1156 1-42 (42)
33 KOG0320 Predicted E3 ubiquitin 97.8 6.5E-06 1.4E-10 86.1 1.9 46 1113-1161 132-178 (187)
34 PHA02926 zinc finger-like prot 97.8 9.6E-06 2.1E-10 87.6 3.0 53 1109-1161 167-230 (242)
35 KOG1493 Anaphase-promoting com 97.8 4.7E-06 1E-10 75.8 -0.4 46 1113-1160 32-80 (84)
36 PF13445 zf-RING_UBOX: RING-ty 97.7 1.3E-05 2.9E-10 66.4 2.0 39 1115-1154 1-43 (43)
37 smart00504 Ubox Modified RING 97.7 2.3E-05 5E-10 68.8 3.6 45 1113-1161 2-46 (63)
38 KOG1428 Inhibitor of type V ad 97.6 2E-05 4.4E-10 99.4 1.4 115 1023-1161 3415-3544(3738)
39 TIGR00599 rad18 DNA repair pro 97.6 5E-05 1.1E-09 89.7 4.0 47 1112-1162 26-72 (397)
40 COG3945 Uncharacterized conser 97.6 0.00082 1.8E-08 70.9 12.3 140 44-190 10-157 (189)
41 KOG0825 PHD Zn-finger protein 97.6 1.3E-05 2.8E-10 97.7 -1.2 75 1087-1162 96-172 (1134)
42 COG2846 Regulator of cell morp 97.5 0.00094 2E-08 71.4 12.2 132 45-176 79-217 (221)
43 KOG0317 Predicted E3 ubiquitin 97.5 4.7E-05 1E-09 85.1 1.8 47 1112-1162 239-285 (293)
44 KOG2930 SCF ubiquitin ligase, 97.5 2.4E-05 5.2E-10 75.1 -0.4 31 1130-1160 77-107 (114)
45 smart00744 RINGv The RING-vari 97.3 0.00011 2.3E-09 62.7 2.2 42 1114-1157 1-49 (49)
46 KOG0827 Predicted E3 ubiquitin 97.3 7.6E-05 1.6E-09 85.7 1.6 66 1113-1179 5-75 (465)
47 PF11793 FANCL_C: FANCL C-term 97.3 7.8E-05 1.7E-09 68.0 0.8 50 1112-1161 2-66 (70)
48 KOG2177 Predicted E3 ubiquitin 97.2 0.00036 7.9E-09 76.4 4.8 44 1111-1158 12-55 (386)
49 KOG0287 Postreplication repair 97.2 0.00018 3.9E-09 81.4 2.5 59 1113-1175 24-83 (442)
50 TIGR00570 cdk7 CDK-activating 97.2 0.0003 6.5E-09 80.4 3.9 51 1112-1162 3-55 (309)
51 KOG2164 Predicted E3 ubiquitin 97.1 0.00023 5E-09 84.9 2.4 48 1111-1162 185-237 (513)
52 KOG0828 Predicted E3 ubiquitin 97.1 0.00019 4.2E-09 84.4 1.1 31 1131-1161 603-634 (636)
53 KOG0823 Predicted E3 ubiquitin 96.9 0.00048 1E-08 75.3 2.7 52 1109-1164 44-98 (230)
54 KOG1734 Predicted RING-contain 96.9 0.00026 5.6E-09 78.2 0.1 49 1112-1160 224-280 (328)
55 PF04564 U-box: U-box domain; 96.6 0.0017 3.6E-08 59.6 3.3 47 1112-1162 4-51 (73)
56 COG5574 PEX10 RING-finger-cont 96.5 0.0011 2.4E-08 73.6 1.7 46 1112-1161 215-262 (271)
57 PF14835 zf-RING_6: zf-RING of 96.4 0.0025 5.4E-08 57.1 2.8 56 1113-1174 8-65 (65)
58 KOG1039 Predicted E3 ubiquitin 96.3 0.0017 3.7E-08 75.7 2.1 82 1109-1192 158-252 (344)
59 KOG1941 Acetylcholine receptor 96.0 0.0015 3.2E-08 75.3 -0.7 61 1103-1164 357-419 (518)
60 COG5432 RAD18 RING-finger-cont 96.0 0.0033 7.1E-08 70.3 1.9 45 1112-1160 25-69 (391)
61 KOG1645 RING-finger-containing 95.6 0.0071 1.5E-07 70.6 2.6 49 1112-1160 4-55 (463)
62 COG2461 Uncharacterized conser 95.5 0.08 1.7E-06 62.3 11.0 131 291-440 85-222 (409)
63 COG5219 Uncharacterized conser 95.5 0.0041 8.9E-08 77.9 0.5 52 1109-1160 1466-1522(1525)
64 KOG4265 Predicted E3 ubiquitin 95.2 0.011 2.4E-07 68.5 2.6 51 1108-1162 286-337 (349)
65 KOG0311 Predicted E3 ubiquitin 95.2 0.0035 7.6E-08 72.1 -1.4 47 1112-1161 43-90 (381)
66 KOG1940 Zn-finger protein [Gen 94.9 0.0042 9.1E-08 70.3 -1.9 133 690-854 17-149 (276)
67 KOG4172 Predicted E3 ubiquitin 94.7 0.0075 1.6E-07 52.2 -0.4 52 1111-1166 6-59 (62)
68 KOG1785 Tyrosine kinase negati 94.6 0.0098 2.1E-07 69.0 0.1 53 1105-1161 362-416 (563)
69 KOG0978 E3 ubiquitin ligase in 94.5 0.012 2.5E-07 73.8 0.4 46 1113-1162 644-690 (698)
70 KOG4445 Uncharacterized conser 94.4 0.011 2.5E-07 66.5 0.0 54 1108-1162 111-187 (368)
71 KOG2879 Predicted E3 ubiquitin 94.3 0.032 7E-07 62.6 3.2 52 1110-1164 237-290 (298)
72 KOG1701 Focal adhesion adaptor 93.7 0.0091 2E-07 70.1 -2.6 71 1066-1161 295-371 (468)
73 KOG3970 Predicted E3 ubiquitin 93.6 0.047 1E-06 59.5 2.8 51 1110-1162 48-106 (299)
74 PF14570 zf-RING_4: RING/Ubox 93.6 0.051 1.1E-06 46.4 2.4 45 1115-1159 1-46 (48)
75 KOG0309 Conserved WD40 repeat- 93.5 0.043 9.3E-07 68.0 2.7 50 1104-1155 1020-1069(1081)
76 PF10367 Vps39_2: Vacuolar sor 93.1 0.042 9.2E-07 53.0 1.4 38 1105-1144 71-108 (109)
77 PF11789 zf-Nse: Zinc-finger o 92.8 0.06 1.3E-06 47.5 1.8 42 1111-1155 10-53 (57)
78 PF12906 RINGv: RING-variant d 92.0 0.1 2.2E-06 44.3 2.1 40 1115-1156 1-47 (47)
79 KOG3268 Predicted E3 ubiquitin 92.0 0.083 1.8E-06 55.8 1.9 31 1131-1161 187-228 (234)
80 KOG0824 Predicted E3 ubiquitin 91.8 0.091 2E-06 59.8 2.1 49 1109-1161 4-53 (324)
81 KOG4739 Uncharacterized protei 91.8 0.086 1.9E-06 58.6 1.9 37 1123-1161 12-48 (233)
82 KOG3039 Uncharacterized conser 91.6 0.12 2.6E-06 57.2 2.8 54 1110-1164 219-273 (303)
83 KOG0297 TNF receptor-associate 91.6 0.11 2.3E-06 62.4 2.5 54 1110-1166 19-72 (391)
84 KOG2272 Focal adhesion protein 91.2 0.075 1.6E-06 58.8 0.7 140 985-1165 63-236 (332)
85 COG5152 Uncharacterized conser 91.0 0.11 2.3E-06 55.9 1.5 58 1113-1174 197-254 (259)
86 PF05883 Baculo_RING: Baculovi 90.8 0.089 1.9E-06 53.9 0.7 43 1112-1155 26-74 (134)
87 KOG2660 Locus-specific chromos 90.4 0.067 1.4E-06 61.6 -0.6 49 1111-1162 14-62 (331)
88 KOG3800 Predicted E3 ubiquitin 88.5 0.26 5.6E-06 56.0 2.2 48 1114-1161 2-51 (300)
89 KOG1571 Predicted E3 ubiquitin 87.8 0.27 5.8E-06 57.4 1.8 47 1108-1161 301-347 (355)
90 COG5592 Uncharacterized conser 87.6 1.6 3.5E-05 46.0 7.1 102 679-817 28-136 (171)
91 COG5175 MOT2 Transcriptional r 87.0 0.22 4.8E-06 57.2 0.5 56 1112-1167 14-70 (480)
92 PF04641 Rtf2: Rtf2 RING-finge 86.6 0.46 1E-05 53.9 2.8 51 1109-1161 110-161 (260)
93 KOG2114 Vacuolar assembly/sort 86.4 0.38 8.2E-06 61.2 2.1 42 1113-1160 841-882 (933)
94 KOG1813 Predicted E3 ubiquitin 86.3 0.41 8.8E-06 54.6 2.1 63 1112-1178 241-303 (313)
95 KOG1002 Nucleotide excision re 86.1 0.26 5.6E-06 59.4 0.5 51 1107-1161 531-586 (791)
96 COG2461 Uncharacterized conser 85.6 3.6 7.9E-05 49.0 9.4 138 40-191 84-222 (409)
97 KOG4275 Predicted E3 ubiquitin 85.0 0.18 3.8E-06 57.2 -1.5 48 1112-1167 300-348 (350)
98 PF14447 Prok-RING_4: Prokaryo 84.6 0.47 1E-05 41.7 1.2 31 1129-1161 20-50 (55)
99 COG5592 Uncharacterized conser 84.2 3 6.6E-05 44.1 7.1 73 645-734 72-144 (171)
100 KOG3002 Zn finger protein [Gen 83.8 0.98 2.1E-05 52.4 3.8 62 1112-1183 48-111 (299)
101 TIGR00100 hypA hydrogenase nic 83.8 0.63 1.4E-05 46.7 1.9 34 1186-1221 67-100 (115)
102 PRK00564 hypA hydrogenase nick 83.6 0.69 1.5E-05 46.6 2.1 35 1185-1221 67-102 (117)
103 PHA02862 5L protein; Provision 83.2 0.7 1.5E-05 47.9 2.0 46 1111-1161 1-53 (156)
104 KOG4159 Predicted E3 ubiquitin 82.3 1.1 2.4E-05 53.9 3.4 49 1110-1162 82-130 (398)
105 KOG1814 Predicted E3 ubiquitin 81.9 0.68 1.5E-05 55.0 1.5 54 1103-1158 176-237 (445)
106 KOG4692 Predicted E3 ubiquitin 81.6 0.84 1.8E-05 53.0 2.1 54 1105-1162 415-468 (489)
107 PRK03824 hypA hydrogenase nick 81.1 0.86 1.9E-05 47.0 1.8 34 1188-1221 69-121 (135)
108 PF07800 DUF1644: Protein of u 81.0 1.2 2.5E-05 47.0 2.7 33 1112-1148 2-47 (162)
109 PRK12380 hydrogenase nickel in 80.8 0.88 1.9E-05 45.6 1.7 33 1187-1221 68-100 (113)
110 TIGR02481 hemeryth_dom hemeryt 80.6 5.9 0.00013 39.5 7.6 51 361-421 12-62 (126)
111 PRK03681 hypA hydrogenase nick 80.5 0.99 2.1E-05 45.3 1.9 34 1187-1221 68-101 (114)
112 KOG0827 Predicted E3 ubiquitin 79.7 0.15 3.2E-06 59.7 -4.6 52 1111-1162 195-246 (465)
113 KOG0269 WD40 repeat-containing 78.3 1.6 3.4E-05 55.3 3.1 70 1066-1155 751-820 (839)
114 COG5236 Uncharacterized conser 78.1 1.8 3.8E-05 50.3 3.2 64 1093-1160 41-107 (493)
115 KOG4185 Predicted E3 ubiquitin 77.1 2.1 4.5E-05 49.2 3.5 47 1113-1160 4-54 (296)
116 PHA02825 LAP/PHD finger-like p 75.5 2 4.2E-05 45.5 2.4 45 1111-1160 7-58 (162)
117 KOG4443 Putative transcription 75.4 2.4 5.1E-05 53.1 3.5 70 1112-1186 145-225 (694)
118 KOG2034 Vacuolar sorting prote 74.5 1.2 2.6E-05 57.3 0.7 44 1103-1148 808-851 (911)
119 PF03854 zf-P11: P-11 zinc fin 74.4 1 2.3E-05 38.4 0.1 43 1113-1161 3-46 (50)
120 PRK04023 DNA polymerase II lar 73.9 2.8 6E-05 54.9 3.7 23 297-319 5-27 (1121)
121 PF01155 HypA: Hydrogenase exp 73.3 1 2.2E-05 45.1 -0.3 34 1186-1221 67-100 (113)
122 PF07191 zinc-ribbons_6: zinc- 73.3 0.67 1.5E-05 42.7 -1.4 65 1113-1205 2-69 (70)
123 KOG1952 Transcription factor N 72.1 1.7 3.7E-05 55.6 1.2 49 1111-1160 190-246 (950)
124 KOG3161 Predicted E3 ubiquitin 71.8 1.3 2.8E-05 54.9 0.1 43 1113-1158 12-54 (861)
125 COG5220 TFB3 Cdk activating ki 69.3 1.3 2.7E-05 49.3 -0.6 50 1112-1161 10-64 (314)
126 PF14446 Prok-RING_1: Prokaryo 69.1 3.8 8.3E-05 36.1 2.4 37 1110-1146 3-39 (54)
127 PRK00762 hypA hydrogenase nick 68.9 2.8 6E-05 42.8 1.7 34 1187-1221 68-106 (124)
128 PF02084 Bindin: Bindin; Inte 68.7 14 0.0003 41.1 7.1 45 72-127 124-169 (238)
129 KOG1044 Actin-binding LIM Zn-f 68.4 5.6 0.00012 49.3 4.4 79 1130-1216 79-169 (670)
130 smart00132 LIM Zinc-binding do 68.1 3.5 7.5E-05 32.1 1.8 38 1114-1161 1-38 (39)
131 PRK14890 putative Zn-ribbon RN 68.1 4 8.8E-05 36.5 2.3 46 1024-1076 6-56 (59)
132 TIGR02481 hemeryth_dom hemeryt 66.3 90 0.0019 31.1 11.9 109 297-424 13-125 (126)
133 KOG2817 Predicted E3 ubiquitin 66.2 4 8.7E-05 48.6 2.6 47 1113-1160 335-384 (394)
134 PF08746 zf-RING-like: RING-li 65.1 3.6 7.8E-05 34.4 1.4 41 1115-1156 1-43 (43)
135 PF01529 zf-DHHC: DHHC palmito 64.7 4.7 0.0001 42.2 2.6 47 1048-1100 43-89 (174)
136 PRK00808 hypothetical protein; 63.7 23 0.0005 37.0 7.4 95 361-466 16-121 (150)
137 PF06524 NOA36: NOA36 protein; 62.1 3.5 7.7E-05 46.5 1.1 50 1001-1061 140-190 (314)
138 COG0375 HybF Zn finger protein 61.8 5 0.00011 40.5 2.0 35 1186-1222 67-101 (115)
139 KOG2068 MOT2 transcription fac 60.1 6.5 0.00014 46.0 2.7 52 1110-1161 247-298 (327)
140 KOG0801 Predicted E3 ubiquitin 58.1 5.3 0.00011 42.2 1.4 31 1109-1140 174-204 (205)
141 KOG2462 C2H2-type Zn-finger pr 57.4 9 0.0002 43.9 3.2 78 1086-1199 160-253 (279)
142 COG5222 Uncharacterized conser 56.8 6.6 0.00014 45.0 2.0 43 1113-1158 275-318 (427)
143 TIGR00595 priA primosomal prot 56.3 8 0.00017 48.2 2.9 45 995-1043 214-258 (505)
144 PF05502 Dynactin_p62: Dynacti 55.7 8.1 0.00018 47.9 2.7 13 1049-1061 22-34 (483)
145 PHA03096 p28-like protein; Pro 54.7 6 0.00013 45.8 1.3 46 1113-1158 179-231 (284)
146 PF14357 DUF4404: Domain of un 54.4 87 0.0019 30.1 8.8 82 54-139 2-83 (85)
147 PF02891 zf-MIZ: MIZ/SP-RING z 54.3 5.5 0.00012 34.4 0.7 41 1113-1159 3-50 (50)
148 cd00350 rubredoxin_like Rubred 53.4 9.4 0.0002 30.1 1.8 24 1053-1076 1-25 (33)
149 KOG2066 Vacuolar assembly/sort 53.3 5.2 0.00011 51.2 0.6 88 405-496 393-485 (846)
150 cd00522 Hemerythrin Hemerythri 52.7 71 0.0015 31.7 8.4 51 361-428 14-68 (113)
151 KOG0298 DEAD box-containing he 51.0 4 8.7E-05 54.6 -0.9 50 1112-1164 1153-1202(1394)
152 COG5183 SSM4 Protein involved 50.9 7.8 0.00017 49.6 1.6 50 1110-1161 10-66 (1175)
153 PF14353 CpXC: CpXC protein 49.7 4.2 9.2E-05 41.1 -0.8 56 1151-1208 2-57 (128)
154 KOG1044 Actin-binding LIM Zn-f 49.5 14 0.0003 46.0 3.3 188 994-1218 16-229 (670)
155 PF09538 FYDLN_acid: Protein o 49.0 9.8 0.00021 38.1 1.6 32 993-1038 8-39 (108)
156 KOG1001 Helicase-like transcri 48.8 7.6 0.00016 50.0 1.1 43 1113-1160 455-499 (674)
157 COG2888 Predicted Zn-ribbon RN 48.5 12 0.00026 33.6 1.9 45 1025-1076 9-58 (61)
158 PRK01917 cation-binding hemery 48.4 41 0.0009 34.7 6.2 68 398-465 38-118 (139)
159 PF09538 FYDLN_acid: Protein o 48.3 13 0.00028 37.3 2.4 27 1037-1076 8-34 (108)
160 TIGR02605 CxxC_CxxC_SSSS putat 48.2 9.5 0.00021 32.6 1.2 31 1189-1219 5-38 (52)
161 COG1198 PriA Primosomal protei 47.9 14 0.00031 47.8 3.3 54 995-1055 436-489 (730)
162 KOG3850 Predicted membrane pro 47.4 5.5E+02 0.012 31.4 15.4 129 301-445 262-396 (455)
163 PRK14714 DNA polymerase II lar 47.2 16 0.00036 49.3 3.7 24 296-319 6-29 (1337)
164 PRK05580 primosome assembly pr 46.2 14 0.00029 47.8 2.7 46 994-1043 381-426 (679)
165 PF12773 DZR: Double zinc ribb 45.3 17 0.00037 30.7 2.4 22 1028-1052 1-23 (50)
166 COG5109 Uncharacterized conser 45.2 13 0.00029 43.1 2.1 45 1113-1158 337-384 (396)
167 TIGR01562 FdhE formate dehydro 45.2 16 0.00035 42.8 2.9 23 1189-1215 210-232 (305)
168 PRK12286 rpmF 50S ribosomal pr 44.9 15 0.00033 32.8 2.0 29 1188-1221 26-54 (57)
169 KOG1609 Protein involved in mR 44.6 9.3 0.0002 43.8 0.8 50 1112-1161 78-134 (323)
170 COG4888 Uncharacterized Zn rib 44.3 9.9 0.00021 37.5 0.8 33 1066-1098 20-57 (104)
171 KOG1829 Uncharacterized conser 43.1 8.6 0.00019 48.4 0.3 29 985-1014 345-377 (580)
172 PRK04023 DNA polymerase II lar 42.9 21 0.00045 47.4 3.5 48 1023-1076 624-671 (1121)
173 PRK14873 primosome assembly pr 42.0 17 0.00037 46.9 2.6 44 995-1043 384-427 (665)
174 PRK00398 rpoP DNA-directed RNA 41.6 15 0.00033 30.9 1.4 30 1189-1218 3-32 (46)
175 PRK00808 hypothetical protein; 41.4 4.4E+02 0.0095 27.5 13.2 110 297-428 17-130 (150)
176 PF13597 NRDD: Anaerobic ribon 41.3 14 0.00029 46.7 1.6 57 1162-1224 465-521 (546)
177 TIGR01562 FdhE formate dehydro 41.2 17 0.00036 42.6 2.2 28 1127-1159 206-233 (305)
178 PF14631 FancD2: Fanconi anaem 40.2 5E+02 0.011 37.0 16.0 99 127-228 192-306 (1426)
179 COG1996 RPC10 DNA-directed RNA 39.8 14 0.0003 32.1 1.0 28 1188-1215 5-32 (49)
180 PRK14559 putative protein seri 39.7 21 0.00045 46.0 2.8 32 1026-1060 2-34 (645)
181 PF00628 PHD: PHD-finger; Int 39.7 6.4 0.00014 33.2 -1.1 42 1115-1157 2-49 (51)
182 PLN03086 PRLI-interacting fact 39.4 18 0.0004 45.5 2.3 118 1021-1166 403-559 (567)
183 smart00734 ZnF_Rad18 Rad18-lik 39.2 21 0.00046 26.9 1.7 21 1151-1172 2-22 (26)
184 TIGR01031 rpmF_bact ribosomal 39.2 18 0.00038 32.1 1.5 29 1188-1221 25-53 (55)
185 COG1656 Uncharacterized conser 39.1 21 0.00047 38.2 2.4 50 1150-1206 97-147 (165)
186 PRK03564 formate dehydrogenase 39.0 20 0.00044 42.1 2.4 26 1128-1158 209-234 (309)
187 cd01675 RNR_III Class III ribo 38.3 26 0.00057 44.3 3.5 56 1162-1223 493-548 (555)
188 KOG1280 Uncharacterized conser 38.1 25 0.00055 41.4 3.0 26 1048-1076 60-87 (381)
189 KOG0826 Predicted E3 ubiquitin 37.4 22 0.00047 41.8 2.3 47 1112-1161 300-346 (357)
190 smart00659 RPOLCX RNA polymera 37.0 21 0.00045 30.3 1.5 26 1189-1215 2-27 (44)
191 KOG2932 E3 ubiquitin ligase in 36.9 18 0.00039 42.0 1.5 31 1130-1162 105-135 (389)
192 KOG3576 Ovo and related transc 35.8 9.1 0.0002 42.1 -0.9 100 1086-1201 116-224 (267)
193 cd00522 Hemerythrin Hemerythri 35.3 1.9E+02 0.0041 28.7 8.3 61 117-195 14-78 (113)
194 KOG4399 C2HC-type Zn-finger pr 35.2 9.8 0.00021 43.1 -0.8 63 1027-1098 240-302 (325)
195 KOG3053 Uncharacterized conser 35.0 16 0.00035 41.5 0.8 53 1108-1160 16-81 (293)
196 PF01783 Ribosomal_L32p: Ribos 34.7 27 0.00058 30.9 2.0 29 1188-1221 25-53 (56)
197 TIGR02300 FYDLN_acid conserved 34.3 25 0.00054 36.2 1.9 18 1060-1077 18-35 (129)
198 smart00249 PHD PHD zinc finger 33.1 19 0.00042 28.8 0.8 32 1114-1146 1-32 (47)
199 KOG3362 Predicted BBOX Zn-fing 32.3 15 0.00032 38.5 -0.1 26 1051-1080 116-143 (156)
200 PF07227 DUF1423: Protein of u 32.1 33 0.00072 41.9 2.8 31 916-948 21-51 (446)
201 TIGR00373 conserved hypothetic 32.0 16 0.00034 38.9 0.0 22 1054-1075 110-135 (158)
202 KOG4654 Uncharacterized conser 31.9 7.5E+02 0.016 27.5 12.4 55 43-103 41-99 (252)
203 PF00539 Tat: Transactivating 31.7 44 0.00095 31.0 2.8 18 1068-1088 36-53 (68)
204 PRK06266 transcription initiat 30.9 17 0.00037 39.3 0.2 23 1053-1075 117-143 (178)
205 KOG4443 Putative transcription 30.8 27 0.00059 44.2 1.9 47 1113-1161 19-73 (694)
206 PRK14892 putative transcriptio 30.4 32 0.00069 34.1 1.9 31 1086-1121 20-51 (99)
207 PRK00398 rpoP DNA-directed RNA 30.3 40 0.00087 28.4 2.2 8 1068-1075 21-28 (46)
208 PF01907 Ribosomal_L37e: Ribos 30.3 19 0.00042 31.9 0.3 28 1184-1214 10-37 (55)
209 KOG2593 Transcription initiati 30.2 21 0.00045 43.3 0.7 20 908-927 50-69 (436)
210 PRK08271 anaerobic ribonucleos 29.8 40 0.00086 43.3 3.1 54 1162-1221 541-594 (623)
211 KOG1812 Predicted E3 ubiquitin 29.7 23 0.0005 42.8 1.0 37 1112-1148 146-182 (384)
212 PF05290 Baculo_IE-1: Baculovi 29.7 30 0.00065 35.9 1.6 47 1112-1162 80-133 (140)
213 PRK07219 DNA topoisomerase I; 29.3 76 0.0017 42.2 5.6 63 1056-1123 672-744 (822)
214 cd00729 rubredoxin_SM Rubredox 29.2 39 0.00084 27.0 1.8 23 1053-1075 2-25 (34)
215 PF04216 FdhE: Protein involve 28.8 19 0.00041 41.6 0.1 24 1138-1161 199-222 (290)
216 PF00412 LIM: LIM domain; Int 28.7 27 0.00059 29.9 1.0 40 1115-1164 1-40 (58)
217 PF07191 zinc-ribbons_6: zinc- 28.4 23 0.0005 33.0 0.5 10 1051-1060 48-57 (70)
218 PLN02189 cellulose synthase 27.7 46 0.001 44.7 3.2 53 1108-1161 30-87 (1040)
219 PF13901 DUF4206: Domain of un 27.0 34 0.00073 37.7 1.6 31 1123-1158 167-197 (202)
220 COG3809 Uncharacterized protei 26.7 40 0.00086 32.0 1.7 51 1113-1185 2-54 (88)
221 PLN02436 cellulose synthase A 26.2 51 0.0011 44.4 3.2 53 1108-1161 32-89 (1094)
222 PF00301 Rubredoxin: Rubredoxi 25.7 46 0.001 28.7 1.8 9 1053-1061 1-9 (47)
223 TIGR02300 FYDLN_acid conserved 25.7 40 0.00087 34.8 1.7 33 993-1039 8-40 (129)
224 TIGR02487 NrdD anaerobic ribon 25.5 58 0.0013 41.5 3.4 54 1162-1221 499-552 (579)
225 COG0143 MetG Methionyl-tRNA sy 25.3 44 0.00095 42.4 2.3 44 1050-1099 123-167 (558)
226 KOG1311 DHHC-type Zn-finger pr 25.1 58 0.0012 37.7 3.1 48 1047-1100 107-154 (299)
227 KOG4399 C2HC-type Zn-finger pr 24.9 21 0.00046 40.5 -0.4 71 1048-1121 199-270 (325)
228 PF03833 PolC_DP2: DNA polymer 24.6 25 0.00053 46.0 0.0 33 1026-1061 656-688 (900)
229 COG1144 Pyruvate:ferredoxin ox 24.2 32 0.0007 33.5 0.7 14 1085-1098 63-76 (91)
230 PRK00420 hypothetical protein; 23.6 45 0.00098 33.8 1.6 30 1111-1161 22-51 (112)
231 PF01780 Ribosomal_L37ae: Ribo 23.5 30 0.00065 33.7 0.3 27 1066-1096 33-62 (90)
232 KOG1100 Predicted E3 ubiquitin 23.2 42 0.00091 37.3 1.4 39 1115-1161 161-200 (207)
233 PF14952 zf-tcix: Putative tre 23.2 38 0.00082 28.9 0.8 22 1209-1231 13-34 (44)
234 KOG2231 Predicted E3 ubiquitin 23.2 53 0.0012 42.2 2.5 45 1113-1161 1-52 (669)
235 PRK14559 putative protein seri 22.9 57 0.0012 42.1 2.7 32 1026-1061 16-49 (645)
236 KOG4367 Predicted Zn-finger pr 22.7 32 0.0007 41.4 0.5 32 1112-1147 4-35 (699)
237 KOG2272 Focal adhesion protein 22.6 43 0.00093 38.0 1.4 77 989-1079 115-203 (332)
238 KOG0802 E3 ubiquitin ligase [P 22.4 36 0.00079 42.9 0.9 43 1111-1161 478-520 (543)
239 KOG0006 E3 ubiquitin-protein l 22.4 66 0.0014 37.7 2.8 74 1062-1146 169-253 (446)
240 PRK01917 cation-binding hemery 22.3 3.2E+02 0.0069 28.3 7.6 53 117-172 9-61 (139)
241 PF11229 DUF3028: Protein of u 22.3 3.7E+02 0.008 34.0 9.0 97 775-871 313-436 (589)
242 TIGR00622 ssl1 transcription f 22.2 1.9E+02 0.0041 29.5 5.6 45 1113-1157 56-110 (112)
243 PF08271 TF_Zn_Ribbon: TFIIB z 22.2 40 0.00086 28.0 0.8 10 1088-1097 20-29 (43)
244 PRK12775 putative trifunctiona 22.2 42 0.0009 45.5 1.4 52 1150-1216 796-847 (1006)
245 smart00451 ZnF_U1 U1-like zinc 22.1 43 0.00093 25.9 0.9 11 1052-1062 2-12 (35)
246 PF02701 zf-Dof: Dof domain, z 22.1 43 0.00094 30.5 1.0 15 1207-1221 5-19 (63)
247 PRK09263 anaerobic ribonucleos 21.9 50 0.0011 43.1 2.0 29 1189-1217 641-669 (711)
248 KOG3842 Adaptor protein Pellin 21.7 51 0.0011 38.5 1.7 34 1131-1164 375-417 (429)
249 PF09723 Zn-ribbon_8: Zinc rib 21.7 46 0.00099 27.7 1.0 31 1189-1219 5-38 (42)
250 PF06524 NOA36: NOA36 protein; 21.7 78 0.0017 36.3 3.1 10 1088-1097 183-192 (314)
251 PF13824 zf-Mss51: Zinc-finger 21.4 56 0.0012 29.2 1.5 11 1066-1076 12-22 (55)
252 PF13894 zf-C2H2_4: C2H2-type 21.4 50 0.0011 22.7 1.1 19 1151-1169 1-19 (24)
253 PF06220 zf-U1: U1 zinc finger 21.4 35 0.00076 28.0 0.3 13 1051-1063 1-13 (38)
254 PF06937 EURL: EURL protein; 21.3 57 0.0012 37.5 1.9 44 1110-1154 28-74 (285)
255 PRK00432 30S ribosomal protein 21.3 50 0.0011 28.8 1.2 24 1070-1095 22-45 (50)
256 KOG4718 Non-SMC (structural ma 21.2 42 0.00091 37.3 0.9 26 1132-1157 198-223 (235)
257 KOG2129 Uncharacterized conser 20.8 5.3E+02 0.012 31.7 9.6 15 182-196 196-210 (552)
258 PF09332 Mcm10: Mcm10 replicat 20.7 19 0.00042 42.8 -1.9 34 1187-1220 283-316 (344)
259 PF15353 HECA: Headcase protei 20.6 43 0.00092 33.5 0.7 16 1133-1148 39-54 (107)
260 PRK01110 rpmF 50S ribosomal pr 20.6 64 0.0014 29.2 1.7 28 1189-1222 27-54 (60)
261 PHA00626 hypothetical protein 20.5 62 0.0013 29.0 1.6 11 1052-1062 22-32 (59)
262 PF12126 DUF3583: Protein of u 20.4 5E+02 0.011 30.6 9.0 132 46-197 14-152 (324)
263 cd06960 NR_DBD_HNF4A DNA-bindi 20.3 93 0.002 29.0 2.9 45 1048-1095 10-58 (76)
264 PRK07111 anaerobic ribonucleos 20.2 90 0.002 41.0 3.7 53 1162-1221 655-707 (735)
265 PF05502 Dynactin_p62: Dynacti 20.1 78 0.0017 39.6 3.0 10 1003-1012 5-14 (483)
266 TIGR00058 Hemerythrin hemeryth 20.1 5.1E+02 0.011 25.9 8.3 69 117-194 10-79 (115)
No 1
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=100.00 E-value=2.1e-62 Score=536.23 Aligned_cols=273 Identities=48% Similarity=1.014 Sum_probs=249.3
Q ss_pred HHHHHHHHhhhcccccccCCCCCCCCCCCCCccccccCccCcccccccccccccccCCcccCcccccccCCCCCcccccc
Q 000895 945 TSRWIASQQKSLQARDSEISNGEDLFGCSPSFRDAEKQVFGCEHYKRNCKLRAACCGKLFTCRFCHDKVSDHSMDRKATT 1024 (1235)
Q Consensus 945 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gC~HY~r~c~l~~~cC~~~y~Cr~CHde~~~H~~~r~~~~ 1024 (1235)
|+||++.|+....... ......+++.|+...++||+||+|+|++++|||+++|+|++||++..+|.++|+.+.
T Consensus 1 ~~~~~~~~~~~~~~~~-------~~~~~~~~~~d~~~~~~~c~hy~r~~~~~a~ccd~~~~C~hCH~~s~~h~~~r~~v~ 73 (276)
T KOG1940|consen 1 MSRLAADQSFLEEFAQ-------ALSSIHSDAEDEIAFPYGCPHYRRNCKSRAPCCDREITCRHCHNESEDHDLDRKTVY 73 (276)
T ss_pred CccchhhhhhhHHHHh-------hhhhcccccccccccccCCchhhhccccccccccceeeeEEecChhhhcccchhhhh
Confidence 4566666655432222 112335678899999999999999999999999999999999999999999999999
Q ss_pred ccccccccccccCCCCCCCcCCCCCccceEecccccCcCCC-CccccCCCCCccccCCCCCccccccCCccccccccc-c
Q 000895 1025 EMMCMRCLKVQPVGPVCTTLSCSGLSMAKYYCGICKFFDDE-RVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLAKKL-V 1102 (1235)
Q Consensus 1025 ~v~C~~C~~~q~~~~~C~~~~C~~~~~a~y~C~iC~l~d~~-k~~yHC~~CgiCR~g~gl~~~~fHC~~C~~C~~~~l-~ 1102 (1235)
+++|+.|.++||++++|.+ | +..+|+|||.+|+||||+ ..||||+.|||||+|+++ |||||++|+.|+++.+ +
T Consensus 74 ~~~C~~C~~~q~~~~~c~~--c-~~~~g~~~c~~C~l~dd~~~~~~hC~~C~icr~g~~~--~~fhc~~c~~c~~~~~~~ 148 (276)
T KOG1940|consen 74 ELLCMKCRKIQPVGQICSN--C-HVELGEYYCLICKLFDDDPSKQYHCDLCGICREGLGL--DFFHCKKCKACLSAYLSN 148 (276)
T ss_pred hhhhhhHHhhhhhhhcccc--c-hhhhhhhcCcccccccccccceecccccccccccccc--chhHHhhhHhHHhhhccc
Confidence 9999999999999999999 4 778999999999999988 599999999999999875 9999999999999999 5
Q ss_pred cccccCCCCCCCccccccccccCCCcceecCCCCccChhhHHhhhhCCCCCCCCCcCcCchhhhhhhHHHHHhhcCCChh
Q 000895 1103 DHKCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGDMAVYFGMLDALLASEQLPEE 1182 (1235)
Q Consensus 1103 ~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrksv~dm~~~~~~lD~~i~~~pmP~e 1182 (1235)
.|+|+|+++..+||||.|++|++...+..++|||++|..|+.++...+|+||+|.+ ++||..+|+++|.+|+.+|||++
T Consensus 149 ~H~c~e~~~~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~~y~CP~C~~-~~d~~~~~~~~d~~l~~~~~p~~ 227 (276)
T KOG1940|consen 149 WHKCVERSSEFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICEGYTCPICSK-PGDMSHYFRKLDKELAGSPMPEE 227 (276)
T ss_pred ccchhhhcccCCCchhHHHhccccccCCccCcccchHHHHHHHHhccCCCCCcccc-hHHHHHHHHHHHHHHhcCCCCch
Confidence 69999999999999999999999999999999999999999999988899999999 99999999999999999999999
Q ss_pred hhccCCcEeccCCCCCCCCCceeeeccCCCCCCCccccccccCCCCcc
Q 000895 1183 YRDRCQEILCNDCDKKGSAPFHWLYHKCGFCGSYNTRVIKVESTNTYC 1230 (1235)
Q Consensus 1183 y~~~~~~i~CnDC~~~s~~~~h~lg~kC~~C~SYNT~~~~~~~~~~~~ 1230 (1235)
|.+++++|+||||+.+++++|||||+||+.|+|||||+++.+.....|
T Consensus 228 y~~~~~~i~cndC~~~~~~k~~~l~~kc~~c~~~~~r~~~~~~~~~~~ 275 (276)
T KOG1940|consen 228 YKNKTQDILCNDCGSGTNVKYHILYHKCGKCGSYNTRMISDPSKYDPQ 275 (276)
T ss_pred hhchhheeeccCCCCCCccceehhhhhCCCcccceeeeccCCCccCCC
Confidence 999999999999999999999999999999999999999855444433
No 2
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=99.90 E-value=1.7e-25 Score=195.06 Aligned_cols=61 Identities=56% Similarity=1.049 Sum_probs=22.5
Q ss_pred cCchhhhhhhHHHHHhhcCCChhhhccCCcEeccCCCCCCCCCceeeeccCCCCCCCcccc
Q 000895 1160 LGDMAVYFGMLDALLASEQLPEEYRDRCQEILCNDCDKKGSAPFHWLYHKCGFCGSYNTRV 1220 (1235)
Q Consensus 1160 v~dm~~~~~~lD~~i~~~pmP~ey~~~~~~i~CnDC~~~s~~~~h~lg~kC~~C~SYNT~~ 1220 (1235)
|+||+.+|++||++|+++|||++|++++++|+||||+++|.++||||||||++|+||||||
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=99.80 E-value=4.9e-21 Score=173.30 Aligned_cols=70 Identities=44% Similarity=1.197 Sum_probs=53.8
Q ss_pred ccccccc-ccccccccCCcccCcccccccCCCCCccccccccccccccccccCCCCCCCcCCCCCccceEecccccCcC
Q 000895 986 CEHYKRN-CKLRAACCGKLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVGPVCTTLSCSGLSMAKYYCGICKFFD 1063 (1235)
Q Consensus 986 C~HY~r~-c~l~~~cC~~~y~Cr~CHde~~~H~~~r~~~~~v~C~~C~~~q~~~~~C~~~~C~~~~~a~y~C~iC~l~d 1063 (1235)
|+||+|+ |+|+||||++|||||+|||+.++|+++|+.+++|+||.|+++|++++. + | + |+|+|++|++||
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 999999999999999999999999999999999999999999999998 4 5 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=99.18 E-value=3.9e-10 Score=110.00 Aligned_cols=124 Identities=26% Similarity=0.366 Sum_probs=109.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcccHHHHHHHHHHHHHHHHhhhhccccchhhhhhhHh--------hhHH
Q 000895 293 PIDEIMLWHNAIKRELNDIAEAARKIQLSGDFSDLSAFNKRLQFIAEVCIFHSIAEDKVIFPAVDVEL--------SFAQ 364 (1235)
Q Consensus 293 pid~l~~~HkALRrEL~~L~~~a~~i~~~gd~~~L~~L~~r~~fl~~vl~~Hs~aEDevlFPaL~~r~--------sme~ 364 (1235)
+++.|...|+.||+.++.+...+... ++..++..+...+.+|...+..|+..||.++||.|..+. .+..
T Consensus 2 ~i~~l~~~H~~~~~~~~~l~~~~~~~---~~~~~~~~l~~~~~~l~~~l~~H~~~EE~~l~p~l~~~~~~~~~~~~~~~~ 78 (133)
T PF01814_consen 2 PIDELRRDHRALRRLLAELEEALDEL---PDDEDLRALRELLDELRRELRHHHAREEEYLFPALERRDPRGDALIAELRR 78 (133)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHH---CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHHHH-CCCHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhC---cCchhHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhccccchhhHHH
Confidence 78999999999999999999999987 455678999999999999999999999999999998332 8899
Q ss_pred hHHHHHHHHHHHHHHHHHHhhcCCCCCcHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 000895 365 EHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPLA 425 (1235)
Q Consensus 365 EH~~ie~l~e~l~~ll~~l~~~~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qvfPLl 425 (1235)
||..+...++.+...+...... ......+...+..+...+..|+.+||+.+||++
T Consensus 79 eH~~~~~~l~~l~~~~~~~~~~------~~~~~~~~~~~~~l~~~l~~H~~~Ee~~l~P~~ 133 (133)
T PF01814_consen 79 EHEEIRALLDELEEALARYSGD------EEDAEELREALRALAEWLRRHIAKEEEVLFPLL 133 (133)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHTHGGGHHHH
T ss_pred HHHHHHHHHHHHHHHHhhCccc------cchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 9999999999999999776511 255678888999999999999999999999986
No 5
>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=99.17 E-value=2.2e-10 Score=111.67 Aligned_cols=129 Identities=33% Similarity=0.413 Sum_probs=115.5
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHHhhccCCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHHHhh---hhHHHHHH
Q 000895 43 PILIFLFFHKAIKSELDVLHRAAMAFATNLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIRV---KNIARTYS 119 (1235)
Q Consensus 43 Pi~~~~~~HkAlR~eL~~l~~~~~~~~~~~gd~~~~~~l~~r~~fL~~~~~~H~~aEDevI~PaLd~Rv---~~v~~~~~ 119 (1235)
||+.+...|+.||+.+..+...+... ++......+...+.+|...+..|+..|++++||.|+.+. ++.+..+.
T Consensus 2 ~i~~l~~~H~~~~~~~~~l~~~~~~~----~~~~~~~~l~~~~~~l~~~l~~H~~~EE~~l~p~l~~~~~~~~~~~~~~~ 77 (133)
T PF01814_consen 2 PIDELRRDHRALRRLLAELEEALDEL----PDDEDLRALRELLDELRRELRHHHAREEEYLFPALERRDPRGDALIAELR 77 (133)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHH----CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHHHH-CCCHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhC----cCchhHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhccccchhhHH
Confidence 78899999999999999999998888 245578999999999999999999999999999999443 67889999
Q ss_pred hhhhhHHHHHHHHHHHHHhhhcCchHHHHHHHHHHHHHHHHHHHhHHHHHHHHhhHH
Q 000895 120 LEHEGESVLFDQLFELLNSSMRNEESYRRELASCTGALQTSISQHMSKEEEQVFPLL 176 (1235)
Q Consensus 120 ~EH~~~~~lf~~l~~~l~~~~~~~~~~~~eLa~~l~~l~~~l~qHm~~EE~qv~PLl 176 (1235)
.||..+...++.+...+..+. ........+...+..+...+.+||.+||+.++|++
T Consensus 78 ~eH~~~~~~l~~l~~~~~~~~-~~~~~~~~~~~~~~~l~~~l~~H~~~Ee~~l~P~~ 133 (133)
T PF01814_consen 78 REHEEIRALLDELEEALARYS-GDEEDAEELREALRALAEWLRRHIAKEEEVLFPLL 133 (133)
T ss_dssp HHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHTHGGGHHHH
T ss_pred HHHHHHHHHHHHHHHHHhhCc-cccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 999999999999999999997 33466788888888999999999999999999986
No 6
>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=99.14 E-value=8.9e-12 Score=102.59 Aligned_cols=44 Identities=34% Similarity=0.951 Sum_probs=38.1
Q ss_pred CCccccccccccCCCcceecCCCCccChhhHHhhhhCCCCCCCCC
Q 000895 1113 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICS 1157 (1235)
Q Consensus 1113 ~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCr 1157 (1235)
++||||++++ ..++.+..++|||.||.+|+.+|++.+++||+||
T Consensus 1 d~C~IC~~~~-~~~~~~~~l~C~H~fh~~Ci~~~~~~~~~CP~CR 44 (44)
T PF13639_consen 1 DECPICLEEF-EDGEKVVKLPCGHVFHRSCIKEWLKRNNSCPVCR 44 (44)
T ss_dssp -CETTTTCBH-HTTSCEEEETTSEEEEHHHHHHHHHHSSB-TTTH
T ss_pred CCCcCCChhh-cCCCeEEEccCCCeeCHHHHHHHHHhCCcCCccC
Confidence 4799999994 4467788999999999999999999999999997
No 7
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=98.89 E-value=1.6e-10 Score=108.12 Aligned_cols=58 Identities=29% Similarity=0.714 Sum_probs=50.8
Q ss_pred CccCccccccc---ccccccccCCcccCcccccccCCCCCcccc-----ccccccccccccccCCC
Q 000895 982 QVFGCEHYKRN---CKLRAACCGKLFTCRFCHDKVSDHSMDRKA-----TTEMMCMRCLKVQPVGP 1039 (1235)
Q Consensus 982 ~~~gC~HY~r~---c~l~~~cC~~~y~Cr~CHde~~~H~~~r~~-----~~~v~C~~C~~~q~~~~ 1039 (1235)
++++|.||+.. ++|+|.||+|||+|..|||+.++|++.++. .+.|+||.|.++..+++
T Consensus 11 ~etRC~Hyht~~Diialkc~~C~kyYaCy~CHdel~~Hpf~p~~~~~~~~~~iiCGvC~~~LT~~E 76 (105)
T COG4357 11 QETRCLHYHTPLDIIALKCKCCQKYYACYHCHDELEDHPFEPWGLQEFNPKAIICGVCRKLLTRAE 76 (105)
T ss_pred ccceeeEecCccceEeeeechhhhhhhHHHHHhHHhcCCCccCChhhcCCccEEhhhhhhhhhHHH
Confidence 57899999999 789999999999999999999999998653 46799999988776643
No 8
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=98.85 E-value=9e-10 Score=126.95 Aligned_cols=82 Identities=24% Similarity=0.659 Sum_probs=68.7
Q ss_pred CCCccccccccccCCCcceecCCCCccChhhHHhhhhCCCCCCCCCcCcCchhhhhhhHHHHHhhcCCChhhhccCCcEe
Q 000895 1112 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGDMAVYFGMLDALLASEQLPEEYRDRCQEIL 1191 (1235)
Q Consensus 1112 ~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrksv~dm~~~~~~lD~~i~~~pmP~ey~~~~~~i~ 1191 (1235)
-.+||||||.|..+.+.+....|.|.||..|+.+|- ..+||+||.... |-+. ..-+
T Consensus 175 LPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~--~~scpvcR~~q~----------------p~~v------e~~~ 230 (493)
T KOG0804|consen 175 LPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWW--DSSCPVCRYCQS----------------PSVV------ESSL 230 (493)
T ss_pred CCCcchhHhhcCccccceeeeecccccchHHHhhcc--cCcChhhhhhcC----------------cchh------hhhh
Confidence 478999999999999999999999999999999995 779999997532 1111 1346
Q ss_pred ccCCCCCCCCCceeeeccCCC--CCCCcccc
Q 000895 1192 CNDCDKKGSAPFHWLYHKCGF--CGSYNTRV 1220 (1235)
Q Consensus 1192 CnDC~~~s~~~~h~lg~kC~~--C~SYNT~~ 1220 (1235)
|++|+...+. |+++.|++ ||.|+-.-
T Consensus 231 c~~c~~~~~L---wicliCg~vgcgrY~egh 258 (493)
T KOG0804|consen 231 CLACGCTEDL---WICLICGNVGCGRYKEGH 258 (493)
T ss_pred hhhhcccccE---EEEEEccceecccccchh
Confidence 9999998887 99999997 99999754
No 9
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=98.85 E-value=1e-09 Score=123.43 Aligned_cols=57 Identities=32% Similarity=0.799 Sum_probs=49.1
Q ss_pred CCCCCCccccccccccCCC---------cceecCCCCccChhhHHhhhhCCCCCCCCCcC-cCchhh
Q 000895 1109 KGLETNCPICCDFLFTSSA---------TVRALPCGHFMHSDCFQAYTCSHYICPICSKS-LGDMAV 1165 (1235)
Q Consensus 1109 ~~~~~~CpICle~lf~s~~---------~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrks-v~dm~~ 1165 (1235)
...+..|.||+|+|+.++. ..+.|||||.+|.+|++.|++++.+|||||.+ +.|++.
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 4567889999999987762 34789999999999999999999999999999 567764
No 10
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.84 E-value=1e-09 Score=125.54 Aligned_cols=74 Identities=19% Similarity=0.495 Sum_probs=54.5
Q ss_pred cccCCccccccccc--ccccccCCCCCCCccccccccccCCCcceecCCCCccChhhHHhhhhCC-CCCCCCCcCcCch
Q 000895 1088 FHCMTCNCCLAKKL--VDHKCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSH-YICPICSKSLGDM 1163 (1235)
Q Consensus 1088 fHC~~C~~C~~~~l--~~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~-~~CPiCrksv~dm 1163 (1235)
+|.+.=+.+..+.. .+....++.. ..|.||+|+ |..++.++.|||+|.||..||++|+..+ ..||+|+..+...
T Consensus 204 ~~r~~k~~l~~~p~~~f~~~~~~~~~-~~CaIClEd-Y~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~di~~~ 280 (348)
T KOG4628|consen 204 RNRLIKRLLKKLPVRTFTKGDDEDAT-DTCAICLED-YEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRDIRTD 280 (348)
T ss_pred hhhhHHHHHhhCCcEEeccccccCCC-ceEEEeecc-cccCCeeeEecCCCchhhccchhhHhhcCccCCCCCCcCCCC
Confidence 44444444444443 2223333444 699999999 8999999999999999999999999766 4599999988643
No 11
>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=98.80 E-value=2.7e-09 Score=97.62 Aligned_cols=47 Identities=30% Similarity=0.757 Sum_probs=37.4
Q ss_pred CCCCccccccccccC---------CCcceecCCCCccChhhHHhhhhCCCCCCCCC
Q 000895 1111 LETNCPICCDFLFTS---------SATVRALPCGHFMHSDCFQAYTCSHYICPICS 1157 (1235)
Q Consensus 1111 ~~~~CpICle~lf~s---------~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCr 1157 (1235)
.+++|+||++.|.+. .-++...+|||.||..||.+|+..+.+||+||
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 356799999997433 23455679999999999999999999999998
No 12
>PRK10992 iron-sulfur cluster repair di-iron protein; Provisional
Probab=98.80 E-value=6.5e-08 Score=106.03 Aligned_cols=131 Identities=18% Similarity=0.315 Sum_probs=106.7
Q ss_pred HHHH-HHHHHHHHHHHHHHHHHHHHhcc--cCCcccHHHHHHHHHHHHHHHHhhhhccccchhhhhhhHh---------h
Q 000895 294 IDEI-MLWHNAIKRELNDIAEAARKIQL--SGDFSDLSAFNKRLQFIAEVCIFHSIAEDKVIFPAVDVEL---------S 361 (1235)
Q Consensus 294 id~l-~~~HkALRrEL~~L~~~a~~i~~--~gd~~~L~~L~~r~~fl~~vl~~Hs~aEDevlFPaL~~r~---------s 361 (1235)
||.+ ..-|..+|++|..|.+.+.++.. .++...+..+..-+..|...+..|+..|++++||+|.+.. .
T Consensus 76 idyI~~~~H~~~r~~lp~L~~l~~kv~~vhg~~~~~~~~~~~l~~~~~~el~~H~~kEE~~LFP~l~~~~~~~~~~pi~v 155 (220)
T PRK10992 76 IDHIIVRYHDRHREQLPELILLATKVERVHGDKPDCPRGLAKYLTALHEELSSHMMKEEQILFPMIKQGMGSQAMGPISV 155 (220)
T ss_pred HHHHHHHHhHHHHHHHHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHhcccccccchHHH
Confidence 5555 78899999999999999977642 2344567888889999999999999999999999999621 8
Q ss_pred hHHhHHHHHHHHHHHHHHHHHHhhcCCCCCcHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHh
Q 000895 362 FAQEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPLARR 427 (1235)
Q Consensus 362 me~EH~~ie~l~e~l~~ll~~l~~~~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qvfPLl~~ 427 (1235)
|..||+++...+.+|..++..... +..+...++.+-..+..+...|.+|..+||+.+||++..
T Consensus 156 m~~EHd~~~~~l~~L~~lt~~~~~---p~~ac~~~~~l~~~l~~~~~dL~~HI~~EnniLFP~a~~ 218 (220)
T PRK10992 156 MESEHDEAGELLEVIKHLTNNVTP---PPEACTTWRALYNGINELIDDLMEHIHLENNVLFPRALA 218 (220)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCC---ChhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Confidence 899999999999999988866431 111124577777888889999999999999999998864
No 13
>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=98.69 E-value=1.4e-07 Score=102.99 Aligned_cols=129 Identities=20% Similarity=0.309 Sum_probs=103.5
Q ss_pred HHHH-HHHHHHHHHHHHHHHHHHHHhcc--cCCcccHHHHHHHHHHHHHHHHhhhhccccchhhhhhhH-----------
Q 000895 294 IDEI-MLWHNAIKRELNDIAEAARKIQL--SGDFSDLSAFNKRLQFIAEVCIFHSIAEDKVIFPAVDVE----------- 359 (1235)
Q Consensus 294 id~l-~~~HkALRrEL~~L~~~a~~i~~--~gd~~~L~~L~~r~~fl~~vl~~Hs~aEDevlFPaL~~r----------- 359 (1235)
||.+ ...|..||++|..|...+.++.. ..+...+..+..-+..|..-+..|+..|+++|||+|...
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 4443 77899999999999998877642 233446788889999999999999999999999999741
Q ss_pred -h-hhHHhHHHHHHHHHHHHHHHHHHhhcCCCCCcHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 000895 360 -L-SFAQEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPLA 425 (1235)
Q Consensus 360 -~-sme~EH~~ie~l~e~l~~ll~~l~~~~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qvfPLl 425 (1235)
+ .|..||+++...+.+|..++..... +..+...++.+...+..+...|.+|..+||+.+||.+
T Consensus 152 pi~~m~~EH~~~~~~l~~L~~l~~~~~~---p~~ac~~~~~~~~~l~~~~~~L~~HI~~En~iLFP~~ 216 (216)
T TIGR03652 152 PISVMESEHDEAGDLLKELRELTNDYTP---PEDACNTWRALYSGLEELEDDLHEHIHLENNILFPRA 216 (216)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHcCCCC---CcchhHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCC
Confidence 1 7899999999999999988865432 1112345677778888899999999999999999963
No 14
>PRK10992 iron-sulfur cluster repair di-iron protein; Provisional
Probab=98.60 E-value=5.9e-07 Score=98.59 Aligned_cols=129 Identities=17% Similarity=0.222 Sum_probs=109.2
Q ss_pred HHHHHHHHHHHHHHHHHHhhcc--CCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHHHh----hhhHHHHHHhhh
Q 000895 49 FFHKAIKSELDVLHRAAMAFAT--NLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIR----VKNIARTYSLEH 122 (1235)
Q Consensus 49 ~~HkAlR~eL~~l~~~~~~~~~--~~gd~~~~~~l~~r~~fL~~~~~~H~~aEDevI~PaLd~R----v~~v~~~~~~EH 122 (1235)
.-|.-+|++|..|.+++..+.. + ++......+.+-++-|..-+..|+..|.+++||.|... +.+.+..|..||
T Consensus 82 ~~H~~~r~~lp~L~~l~~kv~~vhg-~~~~~~~~~~~l~~~~~~el~~H~~kEE~~LFP~l~~~~~~~~~~pi~vm~~EH 160 (220)
T PRK10992 82 RYHDRHREQLPELILLATKVERVHG-DKPDCPRGLAKYLTALHEELSSHMMKEEQILFPMIKQGMGSQAMGPISVMESEH 160 (220)
T ss_pred HHhHHHHHHHHHHHHHHHHHHHHhC-CCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHhcccccccchHHHHHHHH
Confidence 6699999999999999988773 2 45567788888899999999999999999999999962 356789999999
Q ss_pred hhHHHHHHHHHHHHHhhhcCch--HHHHHHHHHHHHHHHHHHHhHHHHHHHHhhHHhh
Q 000895 123 EGESVLFDQLFELLNSSMRNEE--SYRRELASCTGALQTSISQHMSKEEEQVFPLLIE 178 (1235)
Q Consensus 123 ~~~~~lf~~l~~~l~~~~~~~~--~~~~eLa~~l~~l~~~l~qHm~~EE~qv~PLl~~ 178 (1235)
.++..++..|..+.+......+ ..++.+...+..+..-|.+|.++|+..+||.+.+
T Consensus 161 d~~~~~l~~L~~lt~~~~~p~~ac~~~~~l~~~l~~~~~dL~~HI~~EnniLFP~a~~ 218 (220)
T PRK10992 161 DEAGELLEVIKHLTNNVTPPPEACTTWRALYNGINELIDDLMEHIHLENNVLFPRALA 218 (220)
T ss_pred HHHHHHHHHHHHHHhcCCCChhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Confidence 9999999999999988754332 5577777777778888999999999999998764
No 15
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=98.56 E-value=3.6e-08 Score=92.07 Aligned_cols=46 Identities=22% Similarity=0.442 Sum_probs=34.2
Q ss_pred CCccccccccccCCCcceecCCCCccChhhHHhhhhC---CCCCCCCCcCc
Q 000895 1113 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS---HYICPICSKSL 1160 (1235)
Q Consensus 1113 ~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~---~~~CPiCrksv 1160 (1235)
..||.|..+..+ -++..-.|||.||.+||.+|+.+ +.+||+||...
T Consensus 33 g~Cp~Ck~Pgd~--Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w 81 (85)
T PF12861_consen 33 GCCPDCKFPGDD--CPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPW 81 (85)
T ss_pred cCCCCccCCCCC--CceeeccCccHHHHHHHHHHHccccCCCCCCCcCCee
Confidence 456777654211 24555679999999999999974 58899999864
No 16
>PHA02929 N1R/p28-like protein; Provisional
Probab=98.54 E-value=4.7e-08 Score=107.72 Aligned_cols=53 Identities=17% Similarity=0.558 Sum_probs=42.4
Q ss_pred CCCCCCccccccccccCCC---c-ceecCCCCccChhhHHhhhhCCCCCCCCCcCcC
Q 000895 1109 KGLETNCPICCDFLFTSSA---T-VRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1161 (1235)
Q Consensus 1109 ~~~~~~CpICle~lf~s~~---~-v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrksv~ 1161 (1235)
.+.+..||||+|.+.+... . ....+|||.||..||.+|++.+.+||+||..+.
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 3456899999998654321 1 234589999999999999999999999999875
No 17
>COG3945 Uncharacterized conserved protein [Function unknown]
Probab=98.51 E-value=2e-06 Score=89.95 Aligned_cols=140 Identities=21% Similarity=0.284 Sum_probs=109.2
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHhcccC--CcccHHHHHHHHHHHHHHHHhhhhccccchhhhhhhHh---------
Q 000895 292 CPIDEIMLWHNAIKRELNDIAEAARKIQLSG--DFSDLSAFNKRLQFIAEVCIFHSIAEDKVIFPAVDVEL--------- 360 (1235)
Q Consensus 292 ~pid~l~~~HkALRrEL~~L~~~a~~i~~~g--d~~~L~~L~~r~~fl~~vl~~Hs~aEDevlFPaL~~r~--------- 360 (1235)
.-++.|+-.|+.|.+-|.-|...+-.+. .| +.+++..+.+-++-|++- .||..|+.++||-|..+.
T Consensus 8 ~~i~~lvEeH~yIlraL~iLr~~~~~~~-~g~i~y~~v~~iidFi~nfaDk--cHH~KEE~~LF~~m~~~g~~~~~~~i~ 84 (189)
T COG3945 8 DSIKLLVEEHTYILRALSILRKALDLIK-NGPIDYSDVKEIIDFIRNFADK--CHHGKEEKLLFNYMEHEGGPFEEGPIY 84 (189)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhccc-CCCCCHHHHHHHHHHHHHHHHh--ccchHHHHHHHHHHHHhCCCcccCcee
Confidence 3578889999999999999988887775 44 233444444444444443 578889999999998765
Q ss_pred hhHHhHHHHHHHHHHHHHHHHHHhhcCCCCCcHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhhCCHHHHHHHHHh
Q 000895 361 SFAQEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPLARRHFSPKRQRELLYQ 440 (1235)
Q Consensus 361 sme~EH~~ie~l~e~l~~ll~~l~~~~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qvfPLl~~~fS~eEq~~L~~~ 440 (1235)
.|..||...-.++..|.+++..+.+.+. +....++..+......+.+|+.+|+.++||++++.||.+ |.++..+
T Consensus 85 ~m~~EH~~~R~i~r~lee~~~~~kngd~-----~~~~~~i~~A~~y~~likrHIdkEdnvlfp~a~~~~s~e-~~~v~~e 158 (189)
T COG3945 85 VMTVEHGEGRYIIRDLEEAYERLKNGDE-----DSKDDVIDYAVAYLNLIKRHIDKEDNVLFPFAESTLSEE-LNEVNSE 158 (189)
T ss_pred eehhhhhhHHHHHHHHHHHHHHHHcccc-----chHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHH-HHHHHHH
Confidence 8999999999999999999999875322 223556666677788999999999999999999999999 6666544
No 18
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=98.50 E-value=7e-08 Score=77.63 Aligned_cols=44 Identities=34% Similarity=0.921 Sum_probs=37.2
Q ss_pred CccccccccccCCCcceecCCCCccChhhHHhhhhC-CCCCCCCCcCc
Q 000895 1114 NCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS-HYICPICSKSL 1160 (1235)
Q Consensus 1114 ~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~-~~~CPiCrksv 1160 (1235)
.|+||++.+ ..++...+|||.||..|+..|+.. +.+||+|++.+
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 599999985 345666789999999999999987 78899999864
No 19
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.46 E-value=7.3e-08 Score=106.70 Aligned_cols=54 Identities=28% Similarity=0.698 Sum_probs=46.5
Q ss_pred cCCCCCCCccccccccccCCCcceecCCCCccChhhHHhhhh-CCCCCCCCCcCcC
Q 000895 1107 REKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC-SHYICPICSKSLG 1161 (1235)
Q Consensus 1107 ~e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~-~~~~CPiCrksv~ 1161 (1235)
+|....-+|.||+++ |...+.+++|||.|.||..|+++|+. .+..||+||..+.
T Consensus 318 ~ea~~GveCaICms~-fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iP 372 (374)
T COG5540 318 VEADKGVECAICMSN-FIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIP 372 (374)
T ss_pred HhcCCCceEEEEhhh-hcccceEEEeccCceechhHHHHHHhhhcccCCccCCCCC
Confidence 344455789999999 67778899999999999999999986 6799999998765
No 20
>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=98.43 E-value=2.1e-06 Score=93.95 Aligned_cols=127 Identities=24% Similarity=0.300 Sum_probs=105.5
Q ss_pred HHHHHHHHHHHHHHHHHHhhcc-CCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHHH--hh------hhHHHHHH
Q 000895 49 FFHKAIKSELDVLHRAAMAFAT-NLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDI--RV------KNIARTYS 119 (1235)
Q Consensus 49 ~~HkAlR~eL~~l~~~~~~~~~-~~gd~~~~~~l~~r~~fL~~~~~~H~~aEDevI~PaLd~--Rv------~~v~~~~~ 119 (1235)
.-|..||++|..|..++..+.. .-.+...+..+.+-++.|..-+..|+..|.+++||+|.. +. .+.+..|.
T Consensus 78 ~hH~~i~~~l~~L~~l~~kv~~~hg~~~~~l~~l~~~~~~~~~eL~~H~~kEE~~LFP~l~~~~~g~~~~~~~~pi~~m~ 157 (216)
T TIGR03652 78 RHHEYLREELPELIPLATKVARVHGDHHPELIGLAELFRELKAELEQHLMKEEQILFPAIIEYKRGNPAQAIGTPISVME 157 (216)
T ss_pred HHhHHHHHHHHHHHHHHHHHHHHhCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHccCccccccchHHHHH
Confidence 7799999999999998888774 114456778999999999999999999999999999984 21 22889999
Q ss_pred hhhhhHHHHHHHHHHHHHhhhcCch--HHHHHHHHHHHHHHHHHHHhHHHHHHHHhhH
Q 000895 120 LEHEGESVLFDQLFELLNSSMRNEE--SYRRELASCTGALQTSISQHMSKEEEQVFPL 175 (1235)
Q Consensus 120 ~EH~~~~~lf~~l~~~l~~~~~~~~--~~~~eLa~~l~~l~~~l~qHm~~EE~qv~PL 175 (1235)
.||.++...+++|...++......+ ..++.+...+.++..-|.+|.++||..+||.
T Consensus 158 ~EH~~~~~~l~~L~~l~~~~~~p~~ac~~~~~~~~~l~~~~~~L~~HI~~En~iLFP~ 215 (216)
T TIGR03652 158 SEHDEAGDLLKELRELTNDYTPPEDACNTWRALYSGLEELEDDLHEHIHLENNILFPR 215 (216)
T ss_pred HHHHHHHHHHHHHHHHHcCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHhhcccC
Confidence 9999999999999999987654322 4566777777777777999999999999995
No 21
>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=98.41 E-value=1.1e-07 Score=76.46 Aligned_cols=39 Identities=41% Similarity=0.974 Sum_probs=33.6
Q ss_pred ccccccccccCCCcceecCCCCccChhhHHhhhhCCCCCCCC
Q 000895 1115 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPIC 1156 (1235)
Q Consensus 1115 CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiC 1156 (1235)
||||++.+.+ ++..++|||.|+..|+.+|++.+.+||+|
T Consensus 1 C~iC~~~~~~---~~~~~~CGH~fC~~C~~~~~~~~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDELRD---PVVVTPCGHSFCKECIEKYLEKNPKCPVC 39 (39)
T ss_dssp ETTTTSB-SS---EEEECTTSEEEEHHHHHHHHHCTSB-TTT
T ss_pred CCCCCCcccC---cCEECCCCCchhHHHHHHHHHCcCCCcCC
Confidence 8999998543 67889999999999999999889999998
No 22
>PRK13276 cell wall biosynthesis protein ScdA; Provisional
Probab=98.38 E-value=3.4e-06 Score=92.48 Aligned_cols=125 Identities=13% Similarity=0.183 Sum_probs=106.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcc--cCCcccHHHHHHHHHHHHHHHHhhhhccccchhhhhhhH------------h-h
Q 000895 297 IMLWHNAIKRELNDIAEAARKIQL--SGDFSDLSAFNKRLQFIAEVCIFHSIAEDKVIFPAVDVE------------L-S 361 (1235)
Q Consensus 297 l~~~HkALRrEL~~L~~~a~~i~~--~gd~~~L~~L~~r~~fl~~vl~~Hs~aEDevlFPaL~~r------------~-s 361 (1235)
+...|..+|++|..|...+.++.. .++...+..+...+..+..-|..|-..|+.++||++... + .
T Consensus 83 ~~~hH~~~r~~lp~l~~l~~kV~~VHg~~~p~l~~l~~lf~~l~~eL~~H~~KEE~ilFP~i~~~~~~~~~~~~~~pI~~ 162 (224)
T PRK13276 83 QSAYHEPLREEFKNLTPYVTKLSKVHGPNHPYLVELKETYDTFKNGMLEHMQKEDDVDFPKLIKYEQGEVVDDINTVIDD 162 (224)
T ss_pred HHHHhHHHHHHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHhhccccchhhhhHHHH
Confidence 467899999999999999988743 345557899999999999999999999999999999641 1 8
Q ss_pred hHHhHHHHHHHHHHHHHHHHHHhhcCCCCCcHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 000895 362 FAQEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPL 424 (1235)
Q Consensus 362 me~EH~~ie~l~e~l~~ll~~l~~~~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qvfPL 424 (1235)
|+.||+.+.+.+.+|++++..... |..+...|+.|=..+.++...|.+|.+.|-+.+||-
T Consensus 163 m~~EH~~~g~~l~~i~~lTn~yt~---P~~AC~t~r~ly~~L~~fe~dL~~HIhLENnILFPr 222 (224)
T PRK13276 163 LVSDHIATGQLLVKMSELTSSYEP---PIEACGTWRLVYQRLKALEVLTHEHVHLENHVLFKK 222 (224)
T ss_pred HHHHHHHHHHHHHHHHHHhCCCCC---CcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHcccC
Confidence 999999999999999999977742 222346688888888999999999999999999993
No 23
>PRK13276 cell wall biosynthesis protein ScdA; Provisional
Probab=98.30 E-value=7.8e-06 Score=89.76 Aligned_cols=125 Identities=21% Similarity=0.253 Sum_probs=109.8
Q ss_pred HHHHHHHHHHHHHHHHHHhhcc--CCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHHHh--------hhhHHHHH
Q 000895 49 FFHKAIKSELDVLHRAAMAFAT--NLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIR--------VKNIARTY 118 (1235)
Q Consensus 49 ~~HkAlR~eL~~l~~~~~~~~~--~~gd~~~~~~l~~r~~fL~~~~~~H~~aEDevI~PaLd~R--------v~~v~~~~ 118 (1235)
..|.-+|++|..|..++..|.. + ++......|.+.|..|+.=+..|..-|.+++||.+... +.+.+..|
T Consensus 85 ~hH~~~r~~lp~l~~l~~kV~~VHg-~~~p~l~~l~~lf~~l~~eL~~H~~KEE~ilFP~i~~~~~~~~~~~~~~pI~~m 163 (224)
T PRK13276 85 AYHEPLREEFKNLTPYVTKLSKVHG-PNHPYLVELKETYDTFKNGMLEHMQKEDDVDFPKLIKYEQGEVVDDINTVIDDL 163 (224)
T ss_pred HHhHHHHHHHHHHHHHHHHHHHHhC-CCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHhhccccchhhhhHHHHH
Confidence 7899999999999999999986 3 55668999999999999999999999999999999752 35578999
Q ss_pred HhhhhhHHHHHHHHHHHHHhhhcCch--HHHHHHHHHHHHHHHHHHHhHHHHHHHHhh
Q 000895 119 SLEHEGESVLFDQLFELLNSSMRNEE--SYRRELASCTGALQTSISQHMSKEEEQVFP 174 (1235)
Q Consensus 119 ~~EH~~~~~lf~~l~~~l~~~~~~~~--~~~~eLa~~l~~l~~~l~qHm~~EE~qv~P 174 (1235)
..||+++.+++.+|.++.+-++..++ ..|+.|=.-+.++..-|.+|.+.|-.-+||
T Consensus 164 ~~EH~~~g~~l~~i~~lTn~yt~P~~AC~t~r~ly~~L~~fe~dL~~HIhLENnILFP 221 (224)
T PRK13276 164 VSDHIATGQLLVKMSELTSSYEPPIEACGTWRLVYQRLKALEVLTHEHVHLENHVLFK 221 (224)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHccc
Confidence 99999999999999999998876544 677777777777777799999999999998
No 24
>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=98.22 E-value=5.7e-07 Score=76.21 Aligned_cols=47 Identities=32% Similarity=0.824 Sum_probs=38.9
Q ss_pred CCCccccccccccCCCcceecCCCCc-cChhhHHhhhhCCCCCCCCCcCcCc
Q 000895 1112 ETNCPICCDFLFTSSATVRALPCGHF-MHSDCFQAYTCSHYICPICSKSLGD 1162 (1235)
Q Consensus 1112 ~~~CpICle~lf~s~~~v~~LpCgH~-fH~~Ci~~wl~~~~~CPiCrksv~d 1162 (1235)
+..|+||++.. ..+..+||||. |...|+..|.....+||+||+++.+
T Consensus 2 ~~~C~iC~~~~----~~~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~~ 49 (50)
T PF13920_consen 2 DEECPICFENP----RDVVLLPCGHLCFCEECAERLLKRKKKCPICRQPIES 49 (50)
T ss_dssp HSB-TTTSSSB----SSEEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-SE
T ss_pred cCCCccCCccC----CceEEeCCCChHHHHHHhHHhcccCCCCCcCChhhcC
Confidence 46799999872 23778899999 9999999999999999999998753
No 25
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=98.20 E-value=7.4e-07 Score=81.51 Aligned_cols=48 Identities=21% Similarity=0.448 Sum_probs=37.1
Q ss_pred CCccccccccccCCC-cceecCCCCccChhhHHhhhhCCCCCCCCCcCc
Q 000895 1113 TNCPICCDFLFTSSA-TVRALPCGHFMHSDCFQAYTCSHYICPICSKSL 1160 (1235)
Q Consensus 1113 ~~CpICle~lf~s~~-~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrksv 1160 (1235)
..||-|.-.+....+ ++..--|.|.||.+||.+|+.+...||++|++.
T Consensus 32 ~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~Tk~~CPld~q~w 80 (88)
T COG5194 32 GTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQTW 80 (88)
T ss_pred CcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhhCCCCCCCCcee
Confidence 456777665533333 334458999999999999999999999999875
No 26
>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=98.12 E-value=1.5e-06 Score=67.41 Aligned_cols=38 Identities=37% Similarity=0.943 Sum_probs=32.9
Q ss_pred ccccccccccCCCcceecCCCCccChhhHHhhhh-CCCCCCCC
Q 000895 1115 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC-SHYICPIC 1156 (1235)
Q Consensus 1115 CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~-~~~~CPiC 1156 (1235)
|+||++. ......++|||.||..|++.|+. ...+||+|
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 8999987 24577889999999999999997 66889998
No 27
>COG2846 Regulator of cell morphogenesis and NO signaling [Cell division and chromosome partitioning]
Probab=98.10 E-value=2.6e-05 Score=82.94 Aligned_cols=128 Identities=18% Similarity=0.313 Sum_probs=104.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcc-cCC-cccHHHHHHHHHHHHHHHHhhhhccccchhhhhhhHh---------hhH
Q 000895 295 DEIMLWHNAIKRELNDIAEAARKIQL-SGD-FSDLSAFNKRLQFIAEVCIFHSIAEDKVIFPAVDVEL---------SFA 363 (1235)
Q Consensus 295 d~l~~~HkALRrEL~~L~~~a~~i~~-~gd-~~~L~~L~~r~~fl~~vl~~Hs~aEDevlFPaL~~r~---------sme 363 (1235)
.++..+|+-.|.+|.+|-..+.++.. -|| ++-...|.+-+..|...|.-|-..|++++||++..-. .|+
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 45688999999999999999988742 244 4456888888999999999999999999999997432 899
Q ss_pred HhHHHHHHHHHHHHHHHHHHhhcCCCCCcHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 000895 364 QEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPLA 425 (1235)
Q Consensus 364 ~EH~~ie~l~e~l~~ll~~l~~~~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qvfPLl 425 (1235)
.||++..++++.+..++..... |..+...++.|=.-+..+.+.+.+|++-|=..+||=+
T Consensus 159 ~EHde~g~~l~~lk~lT~n~tp---P~~AC~tWkalY~gl~~~~dDl~~HIHLENnvLFpr~ 217 (221)
T COG2846 159 SEHDEAGELLEVLKHLTNNYTP---PEEACGTWKALYNGLNEFIDDLMEHIHLENNVLFPRV 217 (221)
T ss_pred HHHHHHHHHHHHHHHHhcCCCC---ChHHHhHHHHHHHHHHHHHHHHHHHHHhhhccccchh
Confidence 9999999999999999977742 1122345666777778889999999999999999954
No 28
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.07 E-value=2.4e-06 Score=70.68 Aligned_cols=44 Identities=30% Similarity=0.803 Sum_probs=38.1
Q ss_pred CccccccccccCCCcceecCCCCccChhhHHhhhhCCCCCCCCCc
Q 000895 1114 NCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSK 1158 (1235)
Q Consensus 1114 ~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrk 1158 (1235)
.|+||.+. ++......+++|||+|...|+..+......||+||+
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 455566788999999999999999866789999996
No 29
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=98.00 E-value=3.1e-06 Score=68.45 Aligned_cols=39 Identities=38% Similarity=0.961 Sum_probs=33.3
Q ss_pred ccccccccccCCCcceecCCCCccChhhHHhhhh--CCCCCCCC
Q 000895 1115 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC--SHYICPIC 1156 (1235)
Q Consensus 1115 CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~--~~~~CPiC 1156 (1235)
||||++.+.. ++..++|||.|+..|+.+|+. ...+||+|
T Consensus 1 C~iC~~~~~~---~~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEPFED---PVILLPCGHSFCRDCLRKWLENSGSVKCPLC 41 (41)
T ss_dssp ETTTSSBCSS---EEEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred CCcCCccccC---CCEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence 8999998433 346899999999999999987 56889998
No 30
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.99 E-value=1.7e-06 Score=106.51 Aligned_cols=53 Identities=30% Similarity=0.702 Sum_probs=44.8
Q ss_pred CCCCCCCccccccccccCCC-cceecCCCCccChhhHHhhhhCCCCCCCCCcCc
Q 000895 1108 EKGLETNCPICCDFLFTSSA-TVRALPCGHFMHSDCFQAYTCSHYICPICSKSL 1160 (1235)
Q Consensus 1108 e~~~~~~CpICle~lf~s~~-~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrksv 1160 (1235)
....+..|+||.|.|+.+.. ..+.|||||.||..|+..|++..++||+||..+
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 34557899999999887432 357899999999999999999999999999944
No 31
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=97.98 E-value=4.9e-06 Score=88.86 Aligned_cols=51 Identities=25% Similarity=0.682 Sum_probs=39.8
Q ss_pred CCCCCCCccccccccccCCCcceecCCCCccChhhHHhhhhC----------------CCCCCCCCcCcCc
Q 000895 1108 EKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS----------------HYICPICSKSLGD 1162 (1235)
Q Consensus 1108 e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~----------------~~~CPiCrksv~d 1162 (1235)
+......||||++.+ . + .++.+|||.|+..||.+|+.. ..+||+||..+..
T Consensus 14 ~~~~~~~CpICld~~-~--d-PVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~ 80 (193)
T PLN03208 14 DSGGDFDCNICLDQV-R--D-PVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE 80 (193)
T ss_pred cCCCccCCccCCCcC-C--C-cEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence 334568899999973 2 2 355799999999999999742 3589999999864
No 32
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=97.97 E-value=4e-06 Score=69.04 Aligned_cols=38 Identities=37% Similarity=0.946 Sum_probs=27.7
Q ss_pred ccccccccccCCCcceecCCCCccChhhHHhhhhCC----CCCCCC
Q 000895 1115 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSH----YICPIC 1156 (1235)
Q Consensus 1115 CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~----~~CPiC 1156 (1235)
||||++.+.+ .+.|+|||.|-..||..|.+.. +.||+|
T Consensus 1 CpiC~~~~~~----Pv~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDLFKD----PVSLPCGHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB-SS----EEE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCccchhhCC----ccccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 8999998543 4669999999999999987542 689998
No 33
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.84 E-value=6.5e-06 Score=86.10 Aligned_cols=46 Identities=33% Similarity=0.748 Sum_probs=38.9
Q ss_pred CCccccccccccCCCcc-eecCCCCccChhhHHhhhhCCCCCCCCCcCcC
Q 000895 1113 TNCPICCDFLFTSSATV-RALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1161 (1235)
Q Consensus 1113 ~~CpICle~lf~s~~~v-~~LpCgH~fH~~Ci~~wl~~~~~CPiCrksv~ 1161 (1235)
-.|||||+. +.. .+ ..-.|||.|.+.||+.-++...+||+|+|-|.
T Consensus 132 ~~CPiCl~~-~se--k~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt 178 (187)
T KOG0320|consen 132 YKCPICLDS-VSE--KVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKIT 178 (187)
T ss_pred cCCCceecc-hhh--ccccccccchhHHHHHHHHHHHhCCCCCCcccccc
Confidence 789999998 443 23 34799999999999999999999999999654
No 34
>PHA02926 zinc finger-like protein; Provisional
Probab=97.83 E-value=9.6e-06 Score=87.61 Aligned_cols=53 Identities=21% Similarity=0.535 Sum_probs=40.3
Q ss_pred CCCCCCccccccccccCC-----CcceecCCCCccChhhHHhhhhC------CCCCCCCCcCcC
Q 000895 1109 KGLETNCPICCDFLFTSS-----ATVRALPCGHFMHSDCFQAYTCS------HYICPICSKSLG 1161 (1235)
Q Consensus 1109 ~~~~~~CpICle~lf~s~-----~~v~~LpCgH~fH~~Ci~~wl~~------~~~CPiCrksv~ 1161 (1235)
.+.+..|+||+|.++... ......+|+|.|+..||..|... ..+||+||....
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 455789999999876531 11234599999999999999864 245999999764
No 35
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=97.77 E-value=4.7e-06 Score=75.81 Aligned_cols=46 Identities=22% Similarity=0.418 Sum_probs=31.4
Q ss_pred CCccccccccccCCCcceecCCCCccChhhHHhhhhC---CCCCCCCCcCc
Q 000895 1113 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS---HYICPICSKSL 1160 (1235)
Q Consensus 1113 ~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~---~~~CPiCrksv 1160 (1235)
..||-|.-+-. .=++..--|.|.||.+||.+|+.. ...||+||...
T Consensus 32 g~Cp~Ck~PgD--dCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~ 80 (84)
T KOG1493|consen 32 GCCPDCKLPGD--DCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTW 80 (84)
T ss_pred CcCCCCcCCCC--CCccHHHHHHHHHHHHHHHHHhcCccccccCCcchhee
Confidence 34666653311 113333479999999999999853 47899999764
No 36
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=97.75 E-value=1.3e-05 Score=66.35 Aligned_cols=39 Identities=38% Similarity=0.950 Sum_probs=23.6
Q ss_pred ccccccccccCCCcceecCCCCccChhhHHhhhhC----CCCCC
Q 000895 1115 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS----HYICP 1154 (1235)
Q Consensus 1115 CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~----~~~CP 1154 (1235)
||||.| +.+...+.++|+|||+|-.+|++++... ..+||
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 4555556678999999999999999863 35687
No 37
>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=97.74 E-value=2.3e-05 Score=68.78 Aligned_cols=45 Identities=22% Similarity=0.394 Sum_probs=38.5
Q ss_pred CCccccccccccCCCcceecCCCCccChhhHHhhhhCCCCCCCCCcCcC
Q 000895 1113 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1161 (1235)
Q Consensus 1113 ~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrksv~ 1161 (1235)
..||||++.|.+ + ..++|||.|...||.+|+..+.+||+|++.+.
T Consensus 2 ~~Cpi~~~~~~~---P-v~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~ 46 (63)
T smart00504 2 FLCPISLEVMKD---P-VILPSGQTYERRAIEKWLLSHGTDPVTGQPLT 46 (63)
T ss_pred cCCcCCCCcCCC---C-EECCCCCEEeHHHHHHHHHHCCCCCCCcCCCC
Confidence 469999998543 3 55799999999999999988899999999874
No 38
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=97.60 E-value=2e-05 Score=99.37 Aligned_cols=115 Identities=26% Similarity=0.567 Sum_probs=78.4
Q ss_pred ccccccccccc-----cccCCCCCCCcCCCCCccceEecccccCcCCCCccccCCCCCccccCCCCCccccccCCccccc
Q 000895 1023 TTEMMCMRCLK-----VQPVGPVCTTLSCSGLSMAKYYCGICKFFDDERVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCL 1097 (1235)
Q Consensus 1023 ~~~v~C~~C~~-----~q~~~~~C~~~~C~~~~~a~y~C~iC~l~d~~k~~yHC~~CgiCR~g~gl~~~~fHC~~C~~C~ 1097 (1235)
+..--|..|+. .|.++.+|....| ++.|+--|.+=+--. ..|| | . +|--||.-|=.|-
T Consensus 3415 sS~~aCRFCGs~~~tE~sav~~vCs~aDC--~eYAK~ACs~~H~C~--------H~CG----G--v-kNEE~CLPCl~Cd 3477 (3738)
T KOG1428|consen 3415 SSSEACRFCGSRSGTELSAVGSVCSDADC--QEYAKIACSKTHPCG--------HPCG----G--V-KNEEHCLPCLHCD 3477 (3738)
T ss_pred cchhHhhhccCCCCcchhcccCccccHHH--HHHHHHHHhccCcCC--------Cccc----C--c-cchhhcccccccC
Confidence 34457999974 3667889998888 567777776522111 2344 2 1 3778888887774
Q ss_pred ccccccccccCCCCCCCccccccccccCCCcceecCCCCccChhhHHhhhhC----------CCCCCCCCcCcC
Q 000895 1098 AKKLVDHKCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS----------HYICPICSKSLG 1161 (1235)
Q Consensus 1098 ~~~l~~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~----------~~~CPiCrksv~ 1161 (1235)
.-.. ....++.|.||.-+ --+-.+.+.|.|||.||.+|...-+.+ -..||||...+.
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 3211 23456889999876 445567889999999999999764432 257999998874
No 39
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.57 E-value=5e-05 Score=89.66 Aligned_cols=47 Identities=26% Similarity=0.575 Sum_probs=39.8
Q ss_pred CCCccccccccccCCCcceecCCCCccChhhHHhhhhCCCCCCCCCcCcCc
Q 000895 1112 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1162 (1235)
Q Consensus 1112 ~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrksv~d 1162 (1235)
...|+||++.+.. + ++++|||.|+..||..|+.....||+|+..+..
T Consensus 26 ~l~C~IC~d~~~~---P-vitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~~ 72 (397)
T TIGR00599 26 SLRCHICKDFFDV---P-VLTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQE 72 (397)
T ss_pred ccCCCcCchhhhC---c-cCCCCCCchhHHHHHHHHhCCCCCCCCCCcccc
Confidence 5789999998432 3 368999999999999999888899999998863
No 40
>COG3945 Uncharacterized conserved protein [Function unknown]
Probab=97.56 E-value=0.00082 Score=70.93 Aligned_cols=140 Identities=18% Similarity=0.228 Sum_probs=109.3
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHhhccCCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHHHhh----hhHHHHHH
Q 000895 44 ILIFLFFHKAIKSELDVLHRAAMAFATNLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIRV----KNIARTYS 119 (1235)
Q Consensus 44 i~~~~~~HkAlR~eL~~l~~~~~~~~~~~gd~~~~~~l~~r~~fL~~~~~~H~~aEDevI~PaLd~Rv----~~v~~~~~ 119 (1235)
|..|+==|+-|-|-|.-|...+--+..+-=|.+++..+++-++-+.+ ++||.-|+.++||-+..+. ++....|.
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 56777789999999988887766666511245566666655555554 5688999999999999886 57899999
Q ss_pred hhhhhHHHHHHHHHHHHHhhhcCch----HHHHHHHHHHHHHHHHHHHhHHHHHHHHhhHHhhcCCHHHHHHHHH
Q 000895 120 LEHEGESVLFDQLFELLNSSMRNEE----SYRRELASCTGALQTSISQHMSKEEEQVFPLLIEKFSFEEQASLVW 190 (1235)
Q Consensus 120 ~EH~~~~~lf~~l~~~l~~~~~~~~----~~~~eLa~~l~~l~~~l~qHm~~EE~qv~PLl~~~fS~~Eq~~L~~ 190 (1235)
-||..--.++..+.+++.+|...++ .+...+++.+.- +.+|.++|+-.+||.+.+.||.+ |..+..
T Consensus 88 ~EH~~~R~i~r~lee~~~~~kngd~~~~~~~i~~A~~y~~l----ikrHIdkEdnvlfp~a~~~~s~e-~~~v~~ 157 (189)
T COG3945 88 VEHGEGRYIIRDLEEAYERLKNGDEDSKDDVIDYAVAYLNL----IKRHIDKEDNVLFPFAESTLSEE-LNEVNS 157 (189)
T ss_pred hhhhhHHHHHHHHHHHHHHHHccccchHHHHHHHHHHHHHH----HHHHHhhhhhHHHHHHHHHHHHH-HHHHHH
Confidence 9999999999999999999976554 444455555555 99999999999999999999999 555443
No 41
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.55 E-value=1.3e-05 Score=97.66 Aligned_cols=75 Identities=15% Similarity=0.389 Sum_probs=52.6
Q ss_pred ccccCCccccccccc-cccccc-CCCCCCCccccccccccCCCcceecCCCCccChhhHHhhhhCCCCCCCCCcCcCc
Q 000895 1087 FFHCMTCNCCLAKKL-VDHKCR-EKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1162 (1235)
Q Consensus 1087 ~fHC~~C~~C~~~~l-~~H~C~-e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrksv~d 1162 (1235)
--.|..|-.|.+-.. ..-.|+ .+.....||+|+-. +.........+|+|+||..||..|.+.-.+||+||+.+..
T Consensus 96 s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s-~~DqL~~~~k~c~H~FC~~Ci~sWsR~aqTCPiDR~EF~~ 172 (1134)
T KOG0825|consen 96 SDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKS-CNDQLEESEKHTAHYFCEECVGSWSRCAQTCPVDRGEFGE 172 (1134)
T ss_pred ccccchhheecCCcccccCcCchhhhhhhhhhHHHHH-HHHHhhccccccccccHHHHhhhhhhhcccCchhhhhhhe
Confidence 345555555555433 233343 23345689999977 4433434557999999999999999999999999998864
No 42
>COG2846 Regulator of cell morphogenesis and NO signaling [Cell division and chromosome partitioning]
Probab=97.52 E-value=0.00094 Score=71.41 Aligned_cols=132 Identities=18% Similarity=0.239 Sum_probs=107.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcc-CCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHHHh----hhhHHHHHH
Q 000895 45 LIFLFFHKAIKSELDVLHRAAMAFAT-NLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIR----VKNIARTYS 119 (1235)
Q Consensus 45 ~~~~~~HkAlR~eL~~l~~~~~~~~~-~~gd~~~~~~l~~r~~fL~~~~~~H~~aEDevI~PaLd~R----v~~v~~~~~ 119 (1235)
.|..-+|.-.|.+|..|..++..|.. -.+...-.+.|..-+.-|..-+.-|-.-|++++||.+..= +.+....|+
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 45568999999999999999998885 1145567888999999999999999999999999999743 256889999
Q ss_pred hhhhhHHHHHHHHHHHHHhhhcCch--HHHHHHHHHHHHHHHHHHHhHHHHHHHHhhHH
Q 000895 120 LEHEGESVLFDQLFELLNSSMRNEE--SYRRELASCTGALQTSISQHMSKEEEQVFPLL 176 (1235)
Q Consensus 120 ~EH~~~~~lf~~l~~~l~~~~~~~~--~~~~eLa~~l~~l~~~l~qHm~~EE~qv~PLl 176 (1235)
.||+++..+++.+.++.+..+-..+ ..++.|=.-+.++.+-+.+|++-|---+||=+
T Consensus 159 ~EHde~g~~l~~lk~lT~n~tpP~~AC~tWkalY~gl~~~~dDl~~HIHLENnvLFpr~ 217 (221)
T COG2846 159 SEHDEAGELLEVLKHLTNNYTPPEEACGTWKALYNGLNEFIDDLMEHIHLENNVLFPRV 217 (221)
T ss_pred HHHHHHHHHHHHHHHHhcCCCCChHHHhHHHHHHHHHHHHHHHHHHHHHhhhccccchh
Confidence 9999999999999999888865544 44555555555555559999999988888754
No 43
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=97.46 E-value=4.7e-05 Score=85.11 Aligned_cols=47 Identities=23% Similarity=0.673 Sum_probs=39.6
Q ss_pred CCCccccccccccCCCcceecCCCCccChhhHHhhhhCCCCCCCCCcCcCc
Q 000895 1112 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1162 (1235)
Q Consensus 1112 ~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrksv~d 1162 (1235)
...|.+|||...+ ....||||.|...||.+|.....-||+||.....
T Consensus 239 ~~kC~LCLe~~~~----pSaTpCGHiFCWsCI~~w~~ek~eCPlCR~~~~p 285 (293)
T KOG0317|consen 239 TRKCSLCLENRSN----PSATPCGHIFCWSCILEWCSEKAECPLCREKFQP 285 (293)
T ss_pred CCceEEEecCCCC----CCcCcCcchHHHHHHHHHHccccCCCcccccCCC
Confidence 3679999998533 4568999999999999999988889999987643
No 44
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=97.46 E-value=2.4e-05 Score=75.05 Aligned_cols=31 Identities=23% Similarity=0.523 Sum_probs=27.9
Q ss_pred eecCCCCccChhhHHhhhhCCCCCCCCCcCc
Q 000895 1130 RALPCGHFMHSDCFQAYTCSHYICPICSKSL 1160 (1235)
Q Consensus 1130 ~~LpCgH~fH~~Ci~~wl~~~~~CPiCrksv 1160 (1235)
.---|.|.||.+||.+|++++..||+|.+.-
T Consensus 77 aWG~CNHaFH~hCisrWlktr~vCPLdn~eW 107 (114)
T KOG2930|consen 77 AWGVCNHAFHFHCISRWLKTRNVCPLDNKEW 107 (114)
T ss_pred EeeecchHHHHHHHHHHHhhcCcCCCcCcce
Confidence 3457999999999999999999999999864
No 45
>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=97.34 E-value=0.00011 Score=62.69 Aligned_cols=42 Identities=26% Similarity=0.736 Sum_probs=32.5
Q ss_pred CccccccccccCCCcceecCCC-----CccChhhHHhhhhC--CCCCCCCC
Q 000895 1114 NCPICCDFLFTSSATVRALPCG-----HFMHSDCFQAYTCS--HYICPICS 1157 (1235)
Q Consensus 1114 ~CpICle~lf~s~~~v~~LpCg-----H~fH~~Ci~~wl~~--~~~CPiCr 1157 (1235)
.|-||+++ ...+...+.||. |++|..|+.+|+.. +.+||+|+
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 48999983 333445678985 99999999999854 46899995
No 46
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.34 E-value=7.6e-05 Score=85.71 Aligned_cols=66 Identities=23% Similarity=0.502 Sum_probs=45.6
Q ss_pred CCccccccccccCCCcceecC-CCCccChhhHHhhhhC---CCCCCCCCcCcCchhhh-hhhHHHHHhhcCC
Q 000895 1113 TNCPICCDFLFTSSATVRALP-CGHFMHSDCFQAYTCS---HYICPICSKSLGDMAVY-FGMLDALLASEQL 1179 (1235)
Q Consensus 1113 ~~CpICle~lf~s~~~v~~Lp-CgH~fH~~Ci~~wl~~---~~~CPiCrksv~dm~~~-~~~lD~~i~~~pm 1179 (1235)
..|.|| ++++.....+.... |||+||..|+.+|+.. +.+||+|+-.++..... --..|..++..++
T Consensus 5 A~C~Ic-~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~~~r~~~N~~~~d~vvEe~~V 75 (465)
T KOG0827|consen 5 AECHIC-IDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKLQERHVANPSTVDHVVEESVV 75 (465)
T ss_pred ceeeEe-ccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeecccceeeechhhhhhhhccchh
Confidence 569999 67788777777664 9999999999999975 36899999444332211 1233555555544
No 47
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=97.28 E-value=7.8e-05 Score=68.01 Aligned_cols=50 Identities=26% Similarity=0.594 Sum_probs=23.8
Q ss_pred CCCccccccccccC-CCccee---cCCCCccChhhHHhhhhC-----------CCCCCCCCcCcC
Q 000895 1112 ETNCPICCDFLFTS-SATVRA---LPCGHFMHSDCFQAYTCS-----------HYICPICSKSLG 1161 (1235)
Q Consensus 1112 ~~~CpICle~lf~s-~~~v~~---LpCgH~fH~~Ci~~wl~~-----------~~~CPiCrksv~ 1161 (1235)
+..|+||..++.+. ..+..+ -.|+..||..|+.+|+.. ..+||.|++.|.
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 46899999986633 233333 279999999999999752 146999999863
No 48
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.18 E-value=0.00036 Score=76.40 Aligned_cols=44 Identities=32% Similarity=0.786 Sum_probs=37.2
Q ss_pred CCCCccccccccccCCCcceecCCCCccChhhHHhhhhCCCCCCCCCc
Q 000895 1111 LETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSK 1158 (1235)
Q Consensus 1111 ~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrk 1158 (1235)
....||||++++.. + ..+||||.|...|+..+......||.||.
T Consensus 12 ~~~~C~iC~~~~~~---p-~~l~C~H~~c~~C~~~~~~~~~~Cp~cr~ 55 (386)
T KOG2177|consen 12 EELTCPICLEYFRE---P-VLLPCGHNFCRACLTRSWEGPLSCPVCRP 55 (386)
T ss_pred ccccChhhHHHhhc---C-ccccccchHhHHHHHHhcCCCcCCcccCC
Confidence 45789999999433 2 88999999999999998766689999994
No 49
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=97.18 E-value=0.00018 Score=81.38 Aligned_cols=59 Identities=24% Similarity=0.616 Sum_probs=45.8
Q ss_pred CCccccccccccCCCcceecCCCCccChhhHHhhhhCCCCCCCCCcCcCchhh-hhhhHHHHHh
Q 000895 1113 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGDMAV-YFGMLDALLA 1175 (1235)
Q Consensus 1113 ~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrksv~dm~~-~~~~lD~~i~ 1175 (1235)
..|-||.|| |. ...+.||||+|.+-||..++..+..||.|+.++..-.. .-+++|++|+
T Consensus 24 LRC~IC~ey-f~---ip~itpCsHtfCSlCIR~~L~~~p~CP~C~~~~~Es~Lr~n~il~Eiv~ 83 (442)
T KOG0287|consen 24 LRCGICFEY-FN---IPMITPCSHTFCSLCIRKFLSYKPQCPTCCVTVTESDLRNNRILDEIVK 83 (442)
T ss_pred HHHhHHHHH-hc---CceeccccchHHHHHHHHHhccCCCCCceecccchhhhhhhhHHHHHHH
Confidence 569999999 43 13556899999999999999999999999999864322 2456666654
No 50
>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=97.15 E-value=0.0003 Score=80.37 Aligned_cols=51 Identities=22% Similarity=0.537 Sum_probs=38.4
Q ss_pred CCCccccccccccCCCcc-eecCCCCccChhhHHhh-hhCCCCCCCCCcCcCc
Q 000895 1112 ETNCPICCDFLFTSSATV-RALPCGHFMHSDCFQAY-TCSHYICPICSKSLGD 1162 (1235)
Q Consensus 1112 ~~~CpICle~lf~s~~~v-~~LpCgH~fH~~Ci~~w-l~~~~~CPiCrksv~d 1162 (1235)
+..||||+.+.+.+.+.. .+.+|||.|+..|++.. ......||.|++++-.
T Consensus 3 ~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk 55 (309)
T TIGR00570 3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLRK 55 (309)
T ss_pred CCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCccch
Confidence 357999999765554422 22289999999999995 4556789999998753
No 51
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.10 E-value=0.00023 Score=84.87 Aligned_cols=48 Identities=29% Similarity=0.686 Sum_probs=36.9
Q ss_pred CCCCccccccccccCCCcceecCCCCccChhhHHhhhhC-----CCCCCCCCcCcCc
Q 000895 1111 LETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS-----HYICPICSKSLGD 1162 (1235)
Q Consensus 1111 ~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~-----~~~CPiCrksv~d 1162 (1235)
+...||||+++ .. -++ .+.|||.|+..||-+|+.. ...||||+..|.-
T Consensus 185 t~~~CPICL~~-~~--~p~-~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~ 237 (513)
T KOG2164|consen 185 TDMQCPICLEP-PS--VPV-RTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITL 237 (513)
T ss_pred cCCcCCcccCC-CC--ccc-ccccCceeeHHHHHHHHhhhcccCCccCCchhhhccc
Confidence 37899999988 22 223 3459999999999997543 3779999998864
No 52
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.05 E-value=0.00019 Score=84.36 Aligned_cols=31 Identities=32% Similarity=0.846 Sum_probs=27.2
Q ss_pred ecCCCCccChhhHHhhhh-CCCCCCCCCcCcC
Q 000895 1131 ALPCGHFMHSDCFQAYTC-SHYICPICSKSLG 1161 (1235)
Q Consensus 1131 ~LpCgH~fH~~Ci~~wl~-~~~~CPiCrksv~ 1161 (1235)
.-||.|.||..|+.+|.. .+..||+||.++.
T Consensus 603 ~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLP 634 (636)
T KOG0828|consen 603 LTPCHHIFHRQCLLQWMDTYKLICPVCRCPLP 634 (636)
T ss_pred ccchHHHHHHHHHHHHHhhhcccCCccCCCCC
Confidence 349999999999999997 5678999998875
No 53
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.93 E-value=0.00048 Score=75.31 Aligned_cols=52 Identities=23% Similarity=0.540 Sum_probs=39.9
Q ss_pred CCCCCCccccccccccCCCcceecCCCCccChhhHHhhhhC---CCCCCCCCcCcCchh
Q 000895 1109 KGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS---HYICPICSKSLGDMA 1164 (1235)
Q Consensus 1109 ~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~---~~~CPiCrksv~dm~ 1164 (1235)
.+..-+|-||||- ..+ .++-.|||.|...||.+|+.. +..||+|+-.|..-+
T Consensus 44 ~~~~FdCNICLd~---akd-PVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~ 98 (230)
T KOG0823|consen 44 DGGFFDCNICLDL---AKD-PVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDT 98 (230)
T ss_pred CCCceeeeeeccc---cCC-CEEeecccceehHHHHHHHhhcCCCeeCCccccccccce
Confidence 3456789999976 334 445679999999999999864 366899998886543
No 54
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.87 E-value=0.00026 Score=78.22 Aligned_cols=49 Identities=22% Similarity=0.652 Sum_probs=39.0
Q ss_pred CCCccccccccccCC------CcceecCCCCccChhhHHhhh--hCCCCCCCCCcCc
Q 000895 1112 ETNCPICCDFLFTSS------ATVRALPCGHFMHSDCFQAYT--CSHYICPICSKSL 1160 (1235)
Q Consensus 1112 ~~~CpICle~lf~s~------~~v~~LpCgH~fH~~Ci~~wl--~~~~~CPiCrksv 1160 (1235)
+.-|.||...++.+. +..-.|.|+|.||..||.-|- ....+||-|++.+
T Consensus 224 d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekV 280 (328)
T KOG1734|consen 224 DSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKV 280 (328)
T ss_pred cchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHh
Confidence 456888887766554 235679999999999999994 5679999999876
No 55
>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=96.60 E-value=0.0017 Score=59.63 Aligned_cols=47 Identities=21% Similarity=0.367 Sum_probs=35.6
Q ss_pred CCCccccccccccCCCcceecCCCCccChhhHHhhhhC-CCCCCCCCcCcCc
Q 000895 1112 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS-HYICPICSKSLGD 1162 (1235)
Q Consensus 1112 ~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~-~~~CPiCrksv~d 1162 (1235)
...|||+.+-|.+ .+++||||+|-..||.+|+.. +.+||+|+..+..
T Consensus 4 ~f~CpIt~~lM~d----PVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~ 51 (73)
T PF04564_consen 4 EFLCPITGELMRD----PVILPSGHTYERSAIERWLEQNGGTDPFTRQPLSE 51 (73)
T ss_dssp GGB-TTTSSB-SS----EEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SG
T ss_pred ccCCcCcCcHhhC----ceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCc
Confidence 3579999987644 356899999999999999988 8999999988764
No 56
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.50 E-value=0.0011 Score=73.61 Aligned_cols=46 Identities=26% Similarity=0.694 Sum_probs=38.3
Q ss_pred CCCccccccccccCCCcceecCCCCccChhhHHh-hhhCCCC-CCCCCcCcC
Q 000895 1112 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQA-YTCSHYI-CPICSKSLG 1161 (1235)
Q Consensus 1112 ~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~-wl~~~~~-CPiCrksv~ 1161 (1235)
+..|+||+|.... ....+|||.|...||.. |....+- ||+||.-+.
T Consensus 215 d~kC~lC~e~~~~----ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~ 262 (271)
T COG5574 215 DYKCFLCLEEPEV----PSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVY 262 (271)
T ss_pred ccceeeeecccCC----cccccccchhhHHHHHHHHHhhccccCchhhhhcc
Confidence 5669999998543 46689999999999999 9887766 999998654
No 57
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=96.37 E-value=0.0025 Score=57.10 Aligned_cols=56 Identities=29% Similarity=0.589 Sum_probs=28.1
Q ss_pred CCccccccccccCCCcceecCCCCccChhhHHhhhhCCCCCCCCCcCcC--chhhhhhhHHHHH
Q 000895 1113 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG--DMAVYFGMLDALL 1174 (1235)
Q Consensus 1113 ~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrksv~--dm~~~~~~lD~~i 1174 (1235)
..|++|.+.|. ++|..-.|.|.|.+.|+..-+ ++.||+|+.+.- |+. ..+.||.+|
T Consensus 8 LrCs~C~~~l~---~pv~l~~CeH~fCs~Ci~~~~--~~~CPvC~~Paw~qD~~-~NrqLd~~i 65 (65)
T PF14835_consen 8 LRCSICFDILK---EPVCLGGCEHIFCSSCIRDCI--GSECPVCHTPAWIQDIQ-INRQLDSMI 65 (65)
T ss_dssp TS-SSS-S--S---S-B---SSS--B-TTTGGGGT--TTB-SSS--B-S-SS-----HHHHHHH
T ss_pred cCCcHHHHHhc---CCceeccCccHHHHHHhHHhc--CCCCCCcCChHHHHHHH-hhhhhhccC
Confidence 46999998864 357778999999999998865 356999999884 433 246677654
No 58
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.34 E-value=0.0017 Score=75.65 Aligned_cols=82 Identities=21% Similarity=0.470 Sum_probs=58.1
Q ss_pred CCCCCCccccccccccCCCc---cee-cCCCCccChhhHHhhh--hC-----CCCCCCCCcCcC--chhhhhhhHHHHHh
Q 000895 1109 KGLETNCPICCDFLFTSSAT---VRA-LPCGHFMHSDCFQAYT--CS-----HYICPICSKSLG--DMAVYFGMLDALLA 1175 (1235)
Q Consensus 1109 ~~~~~~CpICle~lf~s~~~---v~~-LpCgH~fH~~Ci~~wl--~~-----~~~CPiCrksv~--dm~~~~~~lD~~i~ 1175 (1235)
++.+..|-||+|.+.+.... -.+ ++|.|.|...||..|- .. +..||+||...- .-+.+|-.-.+ +
T Consensus 158 ~s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~~v~pS~~Wv~t~~--~ 235 (344)
T KOG1039|consen 158 KSSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSSFVNPSSFWVETKE--E 235 (344)
T ss_pred ccccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccccccccceeeeecc--c
Confidence 46678999999987664311 122 4699999999999997 33 578999998764 34455644433 6
Q ss_pred hcCCChhhhccCCcEec
Q 000895 1176 SEQLPEEYRDRCQEILC 1192 (1235)
Q Consensus 1176 ~~pmP~ey~~~~~~i~C 1192 (1235)
.++.+++|........|
T Consensus 236 k~~li~e~~~~~s~~~c 252 (344)
T KOG1039|consen 236 KQKLIEEYEAEMSAKDC 252 (344)
T ss_pred ccccHHHHHHHhhccch
Confidence 77888998777655444
No 59
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=95.98 E-value=0.0015 Score=75.35 Aligned_cols=61 Identities=31% Similarity=0.658 Sum_probs=48.7
Q ss_pred cccccCCCCCCCccccccccccCCCcceecCCCCccChhhHHhhhhCC--CCCCCCCcCcCchh
Q 000895 1103 DHKCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSH--YICPICSKSLGDMA 1164 (1235)
Q Consensus 1103 ~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~--~~CPiCrksv~dm~ 1164 (1235)
.|.|++ .++.+|-.|.|-+--..+....|||.|.||..|+.+++..+ .+||-|||....|.
T Consensus 357 a~~~~~-e~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~CrklrSs~~ 419 (518)
T KOG1941|consen 357 AHECVE-ETELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRKLRSSMK 419 (518)
T ss_pred HHHHHH-HHhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHHHHhhcc
Confidence 456664 36689999999877677778899999999999999998654 78999996554443
No 60
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=95.96 E-value=0.0033 Score=70.25 Aligned_cols=45 Identities=24% Similarity=0.515 Sum_probs=38.0
Q ss_pred CCCccccccccccCCCcceecCCCCccChhhHHhhhhCCCCCCCCCcCc
Q 000895 1112 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSL 1160 (1235)
Q Consensus 1112 ~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrksv 1160 (1235)
...|-||.+++.. ...-+|||.|..-||..++..+..||+||...
T Consensus 25 ~lrC~IC~~~i~i----p~~TtCgHtFCslCIR~hL~~qp~CP~Cr~~~ 69 (391)
T COG5432 25 MLRCRICDCRISI----PCETTCGHTFCSLCIRRHLGTQPFCPVCREDP 69 (391)
T ss_pred HHHhhhhhheeec----ceecccccchhHHHHHHHhcCCCCCccccccH
Confidence 3579999998432 24469999999999999999999999999865
No 61
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.58 E-value=0.0071 Score=70.62 Aligned_cols=49 Identities=35% Similarity=0.819 Sum_probs=39.2
Q ss_pred CCCccccccccccCCC-cceecCCCCccChhhHHhhhhC--CCCCCCCCcCc
Q 000895 1112 ETNCPICCDFLFTSSA-TVRALPCGHFMHSDCFQAYTCS--HYICPICSKSL 1160 (1235)
Q Consensus 1112 ~~~CpICle~lf~s~~-~v~~LpCgH~fH~~Ci~~wl~~--~~~CPiCrksv 1160 (1235)
...||||++..-.+++ .+..|.|||.|-++||+.|+.. ...||.|.-..
T Consensus 4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~ka 55 (463)
T KOG1645|consen 4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKA 55 (463)
T ss_pred cccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChh
Confidence 4689999998755554 4556899999999999999953 36799998654
No 62
>COG2461 Uncharacterized conserved protein [Function unknown]
Probab=95.55 E-value=0.08 Score=62.25 Aligned_cols=131 Identities=13% Similarity=0.204 Sum_probs=102.9
Q ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcccH-HHHHHHHHHHHHHHHhhhhccccchhhhhhhHh------hhH
Q 000895 291 SCPIDEIMLWHNAIKRELNDIAEAARKIQLSGDFSDL-SAFNKRLQFIAEVCIFHSIAEDKVIFPAVDVEL------SFA 363 (1235)
Q Consensus 291 ~~pid~l~~~HkALRrEL~~L~~~a~~i~~~gd~~~L-~~L~~r~~fl~~vl~~Hs~aEDevlFPaL~~r~------sme 363 (1235)
-+|+..|+..-++||..|+.+.+. .. + ..+ -.+...+.++-.+=+ |=.++...|||.++.|- .|-
T Consensus 85 gHPv~tl~~EN~~i~~ll~~~l~~---~~---~-~~ik~~l~~lv~~L~~vg~-Hy~RKe~lIfp~~Er~GitapptVmW 156 (409)
T COG2461 85 GHPVRTLKRENKAIRSLLANLLQF---PP---K-KEIKEKLVELVSELDKIGK-HYTRKEMLIFPYIERRGITAPPTVMW 156 (409)
T ss_pred CCcHHHHhcccHHHHHHHHHHhhc---cc---c-HHHHHHHHHHHHHHHHhcc-ccccccccchhHHHHcCCCCCCeeee
Confidence 689999999999999554444333 21 2 233 556666677776666 88999999999999885 888
Q ss_pred HhHHHHHHHHHHHHHHHHHHhhcCCCCCcHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhhCCHHHHHHHHHh
Q 000895 364 QEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPLARRHFSPKRQRELLYQ 440 (1235)
Q Consensus 364 ~EH~~ie~l~e~l~~ll~~l~~~~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qvfPLl~~~fS~eEq~~L~~~ 440 (1235)
-.|+++-..|..+...+... + ..++...+..+.+.+..=+.+||+.+.|.+-..||..||.++-.+
T Consensus 157 ~~dDeiRe~lk~~~~~l~~~--s---------~~~~ve~~~~~~t~i~dmIFkEe~Ilypt~~d~~te~ew~~i~~~ 222 (409)
T COG2461 157 VKDDEIREALKELLKLLKEV--S---------IEEFVEKAESVLTEIEDMIFKEENILYPTLLDLLTEGEWEAIKEQ 222 (409)
T ss_pred ccCcHHHHHHHHHHHHhhcc--C---------hHHHHHHHHHHHHHHHHHHHhhhhhHHhHHHHhcCHHHHHHHHhc
Confidence 99999988888888887622 1 245666777788889999999999999999999999999998755
No 63
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=95.51 E-value=0.0041 Score=77.92 Aligned_cols=52 Identities=25% Similarity=0.578 Sum_probs=37.9
Q ss_pred CCCCCCccccccccc--cCCCcc-eecCCCCccChhhHHhhhhC--CCCCCCCCcCc
Q 000895 1109 KGLETNCPICCDFLF--TSSATV-RALPCGHFMHSDCFQAYTCS--HYICPICSKSL 1160 (1235)
Q Consensus 1109 ~~~~~~CpICle~lf--~s~~~v-~~LpCgH~fH~~Ci~~wl~~--~~~CPiCrksv 1160 (1235)
-+....|+||.--+. +..-|. +--.|.|.||..|+.+|.++ +.+||+||-++
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 355788999987654 221122 23458899999999999875 58999999765
No 64
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.22 E-value=0.011 Score=68.50 Aligned_cols=51 Identities=29% Similarity=0.671 Sum_probs=40.7
Q ss_pred CCCCCCCccccccccccCCCcceecCCCCc-cChhhHHhhhhCCCCCCCCCcCcCc
Q 000895 1108 EKGLETNCPICCDFLFTSSATVRALPCGHF-MHSDCFQAYTCSHYICPICSKSLGD 1162 (1235)
Q Consensus 1108 e~~~~~~CpICle~lf~s~~~v~~LpCgH~-fH~~Ci~~wl~~~~~CPiCrksv~d 1162 (1235)
++.....|.||+.+ + ..+.+|||-|. +.+.|-+...-....|||||..+..
T Consensus 286 ~~~~gkeCVIClse---~-rdt~vLPCRHLCLCs~Ca~~Lr~q~n~CPICRqpi~~ 337 (349)
T KOG4265|consen 286 ESESGKECVICLSE---S-RDTVVLPCRHLCLCSGCAKSLRYQTNNCPICRQPIEE 337 (349)
T ss_pred cccCCCeeEEEecC---C-cceEEecchhhehhHhHHHHHHHhhcCCCccccchHh
Confidence 33446789999977 3 34788999995 8999999887678899999998753
No 65
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.19 E-value=0.0035 Score=72.07 Aligned_cols=47 Identities=32% Similarity=0.598 Sum_probs=38.6
Q ss_pred CCCccccccccccCCCcceecCCCCccChhhHHhhhh-CCCCCCCCCcCcC
Q 000895 1112 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC-SHYICPICSKSLG 1161 (1235)
Q Consensus 1112 ~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~-~~~~CPiCrksv~ 1161 (1235)
+..|||||+-|.. .+...-|+|-|..+||..-++ .+..||.|||.+.
T Consensus 43 ~v~c~icl~llk~---tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~ 90 (381)
T KOG0311|consen 43 QVICPICLSLLKK---TMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLV 90 (381)
T ss_pred hhccHHHHHHHHh---hcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhcc
Confidence 4689999987544 256678999999999988765 5789999999986
No 66
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=94.87 E-value=0.0042 Score=70.30 Aligned_cols=133 Identities=17% Similarity=0.124 Sum_probs=90.6
Q ss_pred HHHHHHhhhhchhccccccccccccccccccchhhHHHHHHHHHHHHHHHhhhhhhhccccCcCCcccccccccccchhh
Q 000895 690 GLYRAHSNAEDDIVFPALESKETLSNVSHSYTLDHKQEEKLFEDISSALSELTELHECLSTDLTGDLTRNSLESCDQNET 769 (1235)
Q Consensus 690 ~v~~~HS~AEDeivfPALe~k~~~~nvshs~~~EH~~ee~lfedi~~~L~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 769 (1235)
.++..|+.++|++-||+..+.....+..++...||.-.=.+..+.+... +. .+
T Consensus 17 ~~~~~~~~~~d~~~~~~~c~hy~r~~~~~a~ccd~~~~C~hCH~~s~~h--------------------------~~-~r 69 (276)
T KOG1940|consen 17 ALSSIHSDAEDEIAFPYGCPHYRRNCKSRAPCCDREITCRHCHNESEDH--------------------------DL-DR 69 (276)
T ss_pred hhhhcccccccccccccCCchhhhccccccccccceeeeEEecChhhhc--------------------------cc-ch
Confidence 7899999999999999998877766666665444443333333331100 00 01
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHhhHhHHHhhhhHHhhhCCHHHHHHHHHHHHhccCHHHHHHhhhHHhhcCCHHHHHH
Q 000895 770 VRKYNEKATELQGMCKSIRVTLDQHVFREELELWPLFDRHFSVEEQDKIVGRIIGTTGAEVLQSMLPWVTSALTQEEQNT 849 (1235)
Q Consensus 770 ~~~~~e~~~kL~~~~ksl~~~L~~Hl~~EE~EvfPL~rk~fS~eeQ~~Lv~~~l~~~p~~~L~~~LPWl~~~Lte~E~~~ 849 (1235)
..++.-...+.....++.......|.. +.+.|=++.+.|+++++ +++.-+.+.+--+.++. |||.-.....+..+
T Consensus 70 ~~v~~~~C~~C~~~q~~~~~c~~c~~~--~g~~~c~~C~l~dd~~~-~~~hC~~C~icr~g~~~--~~fhc~~c~~c~~~ 144 (276)
T KOG1940|consen 70 KTVYELLCMKCRKIQPVGQICSNCHVE--LGEYYCLICKLFDDDPS-KQYHCDLCGICREGLGL--DFFHCKKCKACLSA 144 (276)
T ss_pred hhhhhhhhhhHHhhhhhhhccccchhh--hhhhcCccccccccccc-ceecccccccccccccc--chhHHhhhHhHHhh
Confidence 122233444444455555578888888 99999999999999999 88888877665544443 99998887777777
Q ss_pred HHHHh
Q 000895 850 MMDTW 854 (1235)
Q Consensus 850 ml~~~ 854 (1235)
-|.+|
T Consensus 145 ~~~~~ 149 (276)
T KOG1940|consen 145 YLSNW 149 (276)
T ss_pred hcccc
Confidence 66665
No 67
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.69 E-value=0.0075 Score=52.20 Aligned_cols=52 Identities=27% Similarity=0.572 Sum_probs=37.3
Q ss_pred CCCCccccccccccCCCcceecCCCCc-cChhhHHh-hhhCCCCCCCCCcCcCchhhh
Q 000895 1111 LETNCPICCDFLFTSSATVRALPCGHF-MHSDCFQA-YTCSHYICPICSKSLGDMAVY 1166 (1235)
Q Consensus 1111 ~~~~CpICle~lf~s~~~v~~LpCgH~-fH~~Ci~~-wl~~~~~CPiCrksv~dm~~~ 1166 (1235)
....|.||+|.-.+ .+.--|||. +...|-.+ |...+.+|||||.++.|.-..
T Consensus 6 ~~dECTICye~pvd----sVlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~dvIkT 59 (62)
T KOG4172|consen 6 WSDECTICYEHPVD----SVLYTCGHMCMCYACGLRLKKALHGCCPICRAPIKDVIKT 59 (62)
T ss_pred cccceeeeccCcch----HHHHHcchHHhHHHHHHHHHHccCCcCcchhhHHHHHHHh
Confidence 34789999987222 234589996 66777554 656789999999998775443
No 68
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=94.58 E-value=0.0098 Score=68.97 Aligned_cols=53 Identities=28% Similarity=0.696 Sum_probs=44.2
Q ss_pred cccCCCCCCCccccccccccCCCcceecCCCCccChhhHHhhhhC--CCCCCCCCcCcC
Q 000895 1105 KCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS--HYICPICSKSLG 1161 (1235)
Q Consensus 1105 ~C~e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~--~~~CPiCrksv~ 1161 (1235)
.|.-.++-.-|-||-|. ...|++=||||.+...|+..|-.. +.+||-||..|-
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 56667777889999875 446888999999999999999743 699999999874
No 69
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=94.50 E-value=0.012 Score=73.81 Aligned_cols=46 Identities=24% Similarity=0.608 Sum_probs=37.5
Q ss_pred CCccccccccccCCCcceecCCCCccChhhHHhhhh-CCCCCCCCCcCcCc
Q 000895 1113 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC-SHYICPICSKSLGD 1162 (1235)
Q Consensus 1113 ~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~-~~~~CPiCrksv~d 1162 (1235)
..||+|-.. ...+++..|||.|+..|+...+. +..+||.|..+++.
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 568999644 33467789999999999999875 46899999999874
No 70
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=94.38 E-value=0.011 Score=66.50 Aligned_cols=54 Identities=28% Similarity=0.663 Sum_probs=43.5
Q ss_pred CCCCCCCccccccccccCCCcceecCCCCccChhhHHhhhh-----------------------CCCCCCCCCcCcCc
Q 000895 1108 EKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC-----------------------SHYICPICSKSLGD 1162 (1235)
Q Consensus 1108 e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~-----------------------~~~~CPiCrksv~d 1162 (1235)
.+-..+.|.|||-- |.+.....+-+|-|+||..|+..|+. ....|||||-.|++
T Consensus 111 nn~p~gqCvICLyg-fa~~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~ 187 (368)
T KOG4445|consen 111 NNHPNGQCVICLYG-FASSPAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKI 187 (368)
T ss_pred CCCCCCceEEEEEe-ecCCCceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccc
Confidence 35567899999965 77777788999999999999988763 12459999998864
No 71
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.30 E-value=0.032 Score=62.59 Aligned_cols=52 Identities=21% Similarity=0.596 Sum_probs=42.1
Q ss_pred CCCCCccccccccccCCCcceecCCCCccChhhHHhhhhC--CCCCCCCCcCcCchh
Q 000895 1110 GLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS--HYICPICSKSLGDMA 1164 (1235)
Q Consensus 1110 ~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~--~~~CPiCrksv~dm~ 1164 (1235)
.....||+|.++ +..|....+|||.|.--|+..=... +.+||.|+.++..|.
T Consensus 237 t~~~~C~~Cg~~---PtiP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~~lq 290 (298)
T KOG2879|consen 237 TSDTECPVCGEP---PTIPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVEPLQ 290 (298)
T ss_pred cCCceeeccCCC---CCCCeeeccccceeehhhhhhhhcchhhcccCccCCCCcchh
Confidence 345789999987 5567778899999999999886543 589999999887664
No 72
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=93.66 E-value=0.0091 Score=70.15 Aligned_cols=71 Identities=30% Similarity=0.797 Sum_probs=39.8
Q ss_pred Ccccc--CCCCCccccCCCCCccccccCC---cccccccccccccccCCCCCCCccccccccccCCCcceec-CCCCccC
Q 000895 1066 RVVYH--CPFCNLCRVGRGLGVDFFHCMT---CNCCLAKKLVDHKCREKGLETNCPICCDFLFTSSATVRAL-PCGHFMH 1139 (1235)
Q Consensus 1066 k~~yH--C~~CgiCR~g~gl~~~~fHC~~---C~~C~~~~l~~H~C~e~~~~~~CpICle~lf~s~~~v~~L-pCgH~fH 1139 (1235)
+.+|| |=.|+.||.-.. |..||.=+. |--|+.-.+ ..|..|-+-+-+ ++| .||-.||
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 46777 777888877554 556655433 333333222 346666665332 233 5777777
Q ss_pred hhhHHhhhhCCCCCCCCCcCcC
Q 000895 1140 SDCFQAYTCSHYICPICSKSLG 1161 (1235)
Q Consensus 1140 ~~Ci~~wl~~~~~CPiCrksv~ 1161 (1235)
..|| +|=+|.+.+.
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 7776 5555555553
No 73
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.62 E-value=0.047 Score=59.48 Aligned_cols=51 Identities=27% Similarity=0.645 Sum_probs=41.6
Q ss_pred CCCCCccccccccccCCCcceecCCCCccChhhHHhhhh--------CCCCCCCCCcCcCc
Q 000895 1110 GLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC--------SHYICPICSKSLGD 1162 (1235)
Q Consensus 1110 ~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~--------~~~~CPiCrksv~d 1162 (1235)
....||..|.-.|-. ++ ...|-|=|.||..|+++|.. ..|.||.|...|..
T Consensus 48 DY~pNC~LC~t~La~-gd-t~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFP 106 (299)
T KOG3970|consen 48 DYNPNCRLCNTPLAS-GD-TTRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFP 106 (299)
T ss_pred CCCCCCceeCCcccc-Cc-ceeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCC
Confidence 457899999988654 44 46689999999999999963 26999999999863
No 74
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=93.59 E-value=0.051 Score=46.38 Aligned_cols=45 Identities=22% Similarity=0.526 Sum_probs=24.5
Q ss_pred ccccccccccCCCcceecCCCCccChhhHHhhhh-CCCCCCCCCcC
Q 000895 1115 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC-SHYICPICSKS 1159 (1235)
Q Consensus 1115 CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~-~~~~CPiCrks 1159 (1235)
||+|.++|..++....-=+||+-+...|+..-+. .+..||-||+.
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 8999999855544333346899999999999886 48999999986
No 75
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=93.54 E-value=0.043 Score=68.02 Aligned_cols=50 Identities=24% Similarity=0.484 Sum_probs=36.7
Q ss_pred ccccCCCCCCCccccccccccCCCcceecCCCCccChhhHHhhhhCCCCCCC
Q 000895 1104 HKCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPI 1155 (1235)
Q Consensus 1104 H~C~e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPi 1155 (1235)
.+|+-......|.||.--+.. ....-+.|||.+|..|..+|.+....||.
T Consensus 1020 ~~~~~~~~~~~C~~C~l~V~g--ss~~Cg~C~Hv~H~sc~~eWf~~gd~Cps 1069 (1081)
T KOG0309|consen 1020 QCAICKGFTFQCAICHLAVRG--SSNFCGTCGHVGHTSCMMEWFRTGDVCPS 1069 (1081)
T ss_pred eccccccceeeeeeEeeEeec--cchhhccccccccHHHHHHHHhcCCcCCC
Confidence 334444445569999755433 34566789999999999999999989984
No 76
>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=93.06 E-value=0.042 Score=53.00 Aligned_cols=38 Identities=26% Similarity=0.616 Sum_probs=29.8
Q ss_pred cccCCCCCCCccccccccccCCCcceecCCCCccChhhHH
Q 000895 1105 KCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQ 1144 (1235)
Q Consensus 1105 ~C~e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~ 1144 (1235)
.++.-.....|+||...+.. ....+.||||.||..|++
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 33434456789999999876 357788999999999985
No 77
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=92.83 E-value=0.06 Score=47.54 Aligned_cols=42 Identities=26% Similarity=0.643 Sum_probs=29.6
Q ss_pred CCCCccccccccccCCCcceecCCCCccChhhHHhhhh--CCCCCCC
Q 000895 1111 LETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC--SHYICPI 1155 (1235)
Q Consensus 1111 ~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~--~~~~CPi 1155 (1235)
....|||.+.. |. ++|+...|||+|=...|.+|++ ....||+
T Consensus 10 ~~~~CPiT~~~-~~--~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv 53 (57)
T PF11789_consen 10 ISLKCPITLQP-FE--DPVKSKKCGHTFEKEAILQYIQRNGSKRCPV 53 (57)
T ss_dssp --SB-TTTSSB--S--SEEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred eccCCCCcCCh-hh--CCcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence 45789999988 43 5789899999999999999994 3578999
No 78
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=91.99 E-value=0.1 Score=44.28 Aligned_cols=40 Identities=25% Similarity=0.674 Sum_probs=26.8
Q ss_pred ccccccccccCCCcceecCCC-----CccChhhHHhhhh--CCCCCCCC
Q 000895 1115 CPICCDFLFTSSATVRALPCG-----HFMHSDCFQAYTC--SHYICPIC 1156 (1235)
Q Consensus 1115 CpICle~lf~s~~~v~~LpCg-----H~fH~~Ci~~wl~--~~~~CPiC 1156 (1235)
|-||++.-.++. ..+.||+ -+.|..|+.+|+. .+.+|++|
T Consensus 1 CrIC~~~~~~~~--~li~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C 47 (47)
T PF12906_consen 1 CRICLEGEEEDE--PLISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC 47 (47)
T ss_dssp ETTTTEE-SSSS---EE-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred CeEeCCcCCCCC--ceecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence 679998733332 4456774 6899999999986 46889998
No 79
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.98 E-value=0.083 Score=55.82 Aligned_cols=31 Identities=26% Similarity=0.698 Sum_probs=26.1
Q ss_pred ecCCCCccChhhHHhhhhC-----------CCCCCCCCcCcC
Q 000895 1131 ALPCGHFMHSDCFQAYTCS-----------HYICPICSKSLG 1161 (1235)
Q Consensus 1131 ~LpCgH~fH~~Ci~~wl~~-----------~~~CPiCrksv~ 1161 (1235)
...||-.||+-|+..|++. -..||.|++++.
T Consensus 187 N~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~Pia 228 (234)
T KOG3268|consen 187 NIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIA 228 (234)
T ss_pred ccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcce
Confidence 3689999999999999863 257999999884
No 80
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.84 E-value=0.091 Score=59.82 Aligned_cols=49 Identities=18% Similarity=0.362 Sum_probs=38.2
Q ss_pred CCCCCCccccccccccCCCcceecCCCCccChhhHHhhhhC-CCCCCCCCcCcC
Q 000895 1109 KGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS-HYICPICSKSLG 1161 (1235)
Q Consensus 1109 ~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~-~~~CPiCrksv~ 1161 (1235)
..+...|+||+....- + ..|+|+|.|..-||+--... ..+||+||.++.
T Consensus 4 ~~~~~eC~IC~nt~n~---P-v~l~C~HkFCyiCiKGsy~ndk~~CavCR~pid 53 (324)
T KOG0824|consen 4 RTKKKECLICYNTGNC---P-VNLYCFHKFCYICIKGSYKNDKKTCAVCRFPID 53 (324)
T ss_pred cccCCcceeeeccCCc---C-ccccccchhhhhhhcchhhcCCCCCceecCCCC
Confidence 3456789999976432 3 67999999999999875444 477999999985
No 81
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=91.81 E-value=0.086 Score=58.57 Aligned_cols=37 Identities=30% Similarity=0.696 Sum_probs=28.1
Q ss_pred ccCCCcceecCCCCccChhhHHhhhhCCCCCCCCCcCcC
Q 000895 1123 FTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1161 (1235)
Q Consensus 1123 f~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrksv~ 1161 (1235)
+.+.++.....|+|+|...|...=. ...||+|++++-
T Consensus 12 ~~~~~~f~LTaC~HvfC~~C~k~~~--~~~C~lCkk~ir 48 (233)
T KOG4739|consen 12 FPSQDPFFLTACRHVFCEPCLKASS--PDVCPLCKKSIR 48 (233)
T ss_pred cCCCCceeeeechhhhhhhhcccCC--ccccccccceee
Confidence 4455556678999999999995532 239999999974
No 82
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=91.64 E-value=0.12 Score=57.19 Aligned_cols=54 Identities=24% Similarity=0.489 Sum_probs=45.4
Q ss_pred CCCCCccccccccccCCCcceec-CCCCccChhhHHhhhhCCCCCCCCCcCcCchh
Q 000895 1110 GLETNCPICCDFLFTSSATVRAL-PCGHFMHSDCFQAYTCSHYICPICSKSLGDMA 1164 (1235)
Q Consensus 1110 ~~~~~CpICle~lf~s~~~v~~L-pCgH~fH~~Ci~~wl~~~~~CPiCrksv~dm~ 1164 (1235)
+..-.||||.+.|- +..+..+| ||||.+-..|+.+.++....||+|.+.+-+.+
T Consensus 219 s~ryiCpvtrd~Lt-Nt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdrd 273 (303)
T KOG3039|consen 219 SKRYICPVTRDTLT-NTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDRD 273 (303)
T ss_pred ccceecccchhhhc-CccceEEeccCCcEeeHHHHHHhccccccccCCCCcCcccc
Confidence 35578999999954 45666666 99999999999999999999999999987643
No 83
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=91.58 E-value=0.11 Score=62.41 Aligned_cols=54 Identities=28% Similarity=0.641 Sum_probs=43.3
Q ss_pred CCCCCccccccccccCCCcceecCCCCccChhhHHhhhhCCCCCCCCCcCcCchhhh
Q 000895 1110 GLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGDMAVY 1166 (1235)
Q Consensus 1110 ~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrksv~dm~~~ 1166 (1235)
..+..||||..-+- +++....|||.|...|+.+|+..+..||.|+..+..-..+
T Consensus 19 ~~~l~C~~C~~vl~---~p~~~~~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~~~ 72 (391)
T KOG0297|consen 19 DENLLCPICMSVLR---DPVQTTTCGHRFCAGCLLESLSNHQKCPVCRQELTQAEEL 72 (391)
T ss_pred cccccCcccccccc---CCCCCCCCCCcccccccchhhccCcCCcccccccchhhcc
Confidence 44578999987643 3455579999999999999998899999999887654443
No 84
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=91.22 E-value=0.075 Score=58.81 Aligned_cols=140 Identities=25% Similarity=0.564 Sum_probs=86.2
Q ss_pred CcccccccccccccccCC--------------------cccCcccccccCCCCCccccccccccccccccccCCCCCCCc
Q 000895 985 GCEHYKRNCKLRAACCGK--------------------LFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVGPVCTTL 1044 (1235)
Q Consensus 985 gC~HY~r~c~l~~~cC~~--------------------~y~Cr~CHde~~~H~~~r~~~~~v~C~~C~~~q~~~~~C~~~ 1044 (1235)
-|.|=-. -|.+|||+| -|.|.+|.....|--+-|. ....+|..|+..-.+
T Consensus 63 YCEhDF~--~LfaPcC~kC~EFiiGrVikamnnSwHp~CF~Cd~Cn~~Lad~gf~rn-qgr~LC~~Cn~k~Ka------- 132 (332)
T KOG2272|consen 63 YCEHDFH--VLFAPCCGKCGEFIIGRVIKAMNNSWHPACFRCDLCNKHLADQGFYRN-QGRALCRECNQKEKA------- 132 (332)
T ss_pred cccccch--hhhchhhcccccchhhHHHHhhccccCcccchhHHHHHHHhhhhhHhh-cchHHhhhhhhhhcc-------
Confidence 3666321 377888876 3677788777777666665 347888888654322
Q ss_pred CCCCCccceEecccccC-cCCC-----CccccCCCCCccccCCCCCccccccCCccccccccc----ccccccCCCCCCC
Q 000895 1045 SCSGLSMAKYYCGICKF-FDDE-----RVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLAKKL----VDHKCREKGLETN 1114 (1235)
Q Consensus 1045 ~C~~~~~a~y~C~iC~l-~d~~-----k~~yHC~~CgiCR~g~gl~~~~fHC~~C~~C~~~~l----~~H~C~e~~~~~~ 1114 (1235)
.--|+|.|.+|+- +|++ .++|| -.-|.|.+||-=+...- +.--|..-...+-
T Consensus 133 ----~~~g~YvC~KCh~~iD~~~l~fr~d~yH--------------~yHFkCt~C~keL~sdaRevk~eLyClrChD~mg 194 (332)
T KOG2272|consen 133 ----KGRGRYVCQKCHAHIDEQPLTFRGDPYH--------------PYHFKCTTCGKELTSDAREVKGELYCLRCHDKMG 194 (332)
T ss_pred ----cccceeehhhhhhhcccccccccCCCCC--------------ccceecccccccccchhhhhccceeccccccccC
Confidence 1267999999995 5666 67888 26799999997764332 3334444444455
Q ss_pred ccccccccccCCCcceecCCCCccChhhH----HhhhhCCCCCCCCCcCcCchhh
Q 000895 1115 CPICCDFLFTSSATVRALPCGHFMHSDCF----QAYTCSHYICPICSKSLGDMAV 1165 (1235)
Q Consensus 1115 CpICle~lf~s~~~v~~LpCgH~fH~~Ci----~~wl~~~~~CPiCrksv~dm~~ 1165 (1235)
||||..= .-.+-..-| ..|--.+..|-.|-|++.--.-
T Consensus 195 ipiCgaC-------------~rpIeervi~amgKhWHveHFvCa~CekPFlGHrH 236 (332)
T KOG2272|consen 195 IPICGAC-------------RRPIEERVIFAMGKHWHVEHFVCAKCEKPFLGHRH 236 (332)
T ss_pred Ccccccc-------------cCchHHHHHHHhccccchhheeehhcCCcccchhh
Confidence 6666432 111111112 2355567889999998865443
No 85
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=90.99 E-value=0.11 Score=55.94 Aligned_cols=58 Identities=24% Similarity=0.309 Sum_probs=43.0
Q ss_pred CCccccccccccCCCcceecCCCCccChhhHHhhhhCCCCCCCCCcCcCchhhhhhhHHHHH
Q 000895 1113 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGDMAVYFGMLDALL 1174 (1235)
Q Consensus 1113 ~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrksv~dm~~~~~~lD~~i 1174 (1235)
..|.||.++ |.+ .++-.|||.|...|.-.=.+...+|-+|.+...-.-..-..+|.++
T Consensus 197 F~C~iCKkd-y~s---pvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~G~f~V~~d~~kmL 254 (259)
T COG5152 197 FLCGICKKD-YES---PVVTECGHSFCSLCAIRKYQKGDECGVCGKATYGRFWVVSDLQKML 254 (259)
T ss_pred eeehhchhh-ccc---hhhhhcchhHHHHHHHHHhccCCcceecchhhccceeHHhhHHHHH
Confidence 469999998 654 4567899999999998877788999999997653322234455544
No 86
>PF05883 Baculo_RING: Baculovirus U-box/Ring-like domain; InterPro: IPR008573 This family consists of several Baculovirus proteins of around 130 residues in length. The function of this family is unknown, but it appears to be related to the U-box and ring finger domain by profile-profile comparison.
Probab=90.83 E-value=0.089 Score=53.86 Aligned_cols=43 Identities=21% Similarity=0.400 Sum_probs=35.0
Q ss_pred CCCccccccccccCCCcceecCCC------CccChhhHHhhhhCCCCCCC
Q 000895 1112 ETNCPICCDFLFTSSATVRALPCG------HFMHSDCFQAYTCSHYICPI 1155 (1235)
Q Consensus 1112 ~~~CpICle~lf~s~~~v~~LpCg------H~fH~~Ci~~wl~~~~~CPi 1155 (1235)
...|.||++.+.+ ...|+.++|| |.||.+|+.+|.+...+=|-
T Consensus 26 ~~EC~IC~~~I~~-~~GvV~vt~~g~lnLEkmfc~~C~~rw~~~~~rDPf 74 (134)
T PF05883_consen 26 TVECQICFDRIDN-NDGVVYVTDGGTLNLEKMFCADCDKRWRRERNRDPF 74 (134)
T ss_pred Ceeehhhhhhhhc-CCCEEEEecCCeehHHHHHHHHHHHHHHhhccCCCc
Confidence 4689999999877 6779999998 99999999999655444443
No 87
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=90.44 E-value=0.067 Score=61.61 Aligned_cols=49 Identities=20% Similarity=0.567 Sum_probs=41.6
Q ss_pred CCCCccccccccccCCCcceecCCCCccChhhHHhhhhCCCCCCCCCcCcCc
Q 000895 1111 LETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1162 (1235)
Q Consensus 1111 ~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrksv~d 1162 (1235)
....|++|..||-+.+ .+.-|=|+|...||.+++..+.+||.|...+..
T Consensus 14 ~~itC~LC~GYliDAT---TI~eCLHTFCkSCivk~l~~~~~CP~C~i~ih~ 62 (331)
T KOG2660|consen 14 PHITCRLCGGYLIDAT---TITECLHTFCKSCIVKYLEESKYCPTCDIVIHK 62 (331)
T ss_pred cceehhhccceeecch---hHHHHHHHHHHHHHHHHHHHhccCCccceeccC
Confidence 4568999999976643 456799999999999999999999999998864
No 88
>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=88.55 E-value=0.26 Score=56.03 Aligned_cols=48 Identities=23% Similarity=0.470 Sum_probs=38.1
Q ss_pred CccccccccccCCCccee-cCCCCccChhhHHhhhh-CCCCCCCCCcCcC
Q 000895 1114 NCPICCDFLFTSSATVRA-LPCGHFMHSDCFQAYTC-SHYICPICSKSLG 1161 (1235)
Q Consensus 1114 ~CpICle~lf~s~~~v~~-LpCgH~fH~~Ci~~wl~-~~~~CPiCrksv~ 1161 (1235)
.||+|.-+.+.+.+-+.. =+|||.+...|++.-+. ..+.||.|.+.+.
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 599999887776553322 29999999999999864 5699999998874
No 89
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.77 E-value=0.27 Score=57.44 Aligned_cols=47 Identities=28% Similarity=0.547 Sum_probs=33.8
Q ss_pred CCCCCCCccccccccccCCCcceecCCCCccChhhHHhhhhCCCCCCCCCcCcC
Q 000895 1108 EKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1161 (1235)
Q Consensus 1108 e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrksv~ 1161 (1235)
+.+...+|.||++. +.+ ...+||||.-. |..-. +...+||+||.++.
T Consensus 301 ~~~~p~lcVVcl~e-~~~---~~fvpcGh~cc--ct~cs-~~l~~CPvCR~rI~ 347 (355)
T KOG1571|consen 301 ELPQPDLCVVCLDE-PKS---AVFVPCGHVCC--CTLCS-KHLPQCPVCRQRIR 347 (355)
T ss_pred ccCCCCceEEecCC-ccc---eeeecCCcEEE--chHHH-hhCCCCchhHHHHH
Confidence 34567899999988 332 78899999944 55443 23466999998874
No 90
>COG5592 Uncharacterized conserved protein [Function unknown]
Probab=87.60 E-value=1.6 Score=46.05 Aligned_cols=102 Identities=21% Similarity=0.231 Sum_probs=69.2
Q ss_pred HHHHHHHHHHHHHHHHHhhhhchhccccc-ccccc----cccc--ccccchhhHHHHHHHHHHHHHHHhhhhhhhccccC
Q 000895 679 RQFTGRFRLLWGLYRAHSNAEDDIVFPAL-ESKET----LSNV--SHSYTLDHKQEEKLFEDISSALSELTELHECLSTD 751 (1235)
Q Consensus 679 ~~f~~rf~~L~~v~~~HS~AEDeivfPAL-e~k~~----~~nv--shs~~~EH~~ee~lfedi~~~L~~~~~l~~~~~~~ 751 (1235)
....+...|+|.++..|---|+++.||+. ..+.. .... .--+..||+.++.|+..+- ..
T Consensus 28 ~e~le~~gf~~k~~k~h~e~Ee~ilF~v~Vd~~~ed~~~fkdt~~~~~i~~DHkliE~l~tnli-------------k~- 93 (171)
T COG5592 28 LEILEFEGFNEKLGKDHVELEEKILFPVIVDADMEDLYVFKDTPEVDRIKNDHKLIETLATNLI-------------KW- 93 (171)
T ss_pred HHHHhhcchHHHHhhhHHHHHHHhhhhhccchHHHHHHhhhccchhhHhHhhHHHHHHHHHHHH-------------hh-
Confidence 33444555899999999999999999987 32211 1111 1246689999999998871 10
Q ss_pred cCCcccccccccccchhhhhhHHHHHHHHHHHHHHHHHHHHHhhHhHHHhhhhHHhhhCCHHHHHH
Q 000895 752 LTGDLTRNSLESCDQNETVRKYNEKATELQGMCKSIRVTLDQHVFREELELWPLFDRHFSVEEQDK 817 (1235)
Q Consensus 752 ~~~~~~~~~~~~~~~~~~~~~~~e~~~kL~~~~ksl~~~L~~Hl~~EE~EvfPL~rk~fS~eeQ~~ 817 (1235)
.+..|+.++. -.+.++|..|=..||.-+||..++.=...+|.+
T Consensus 94 ----------------kR~~k~~e~~-------p~fyK~LtdHn~aEE~~IfPrvks~~~E~~~~~ 136 (171)
T COG5592 94 ----------------KRPDKIKERV-------PLFYKTLTDHNLAEEEYIFPRVKSLKGEDEQSA 136 (171)
T ss_pred ----------------ccchHHHHHH-------HHHHHHHHHccccccchhhHHHHhhcchhhHHH
Confidence 0112333333 556778899999999999999988776655554
No 91
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=86.96 E-value=0.22 Score=57.23 Aligned_cols=56 Identities=23% Similarity=0.564 Sum_probs=42.7
Q ss_pred CCCccccccccccCCCcceecCCCCccChhhHHhhhh-CCCCCCCCCcCcCchhhhh
Q 000895 1112 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC-SHYICPICSKSLGDMAVYF 1167 (1235)
Q Consensus 1112 ~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~-~~~~CPiCrksv~dm~~~~ 1167 (1235)
++.||.|+|+|.-++..-.--|||--+..-|+..--. -+.+||-||+-..+-...|
T Consensus 14 ed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~denv~~ 70 (480)
T COG5175 14 EDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDENVRY 70 (480)
T ss_pred cccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhccccceeE
Confidence 4559999999887766555568998888888876543 3799999999876654444
No 92
>PF04641 Rtf2: Rtf2 RING-finger
Probab=86.57 E-value=0.46 Score=53.93 Aligned_cols=51 Identities=20% Similarity=0.483 Sum_probs=40.4
Q ss_pred CCCCCCccccccccccCCCcceec-CCCCccChhhHHhhhhCCCCCCCCCcCcC
Q 000895 1109 KGLETNCPICCDFLFTSSATVRAL-PCGHFMHSDCFQAYTCSHYICPICSKSLG 1161 (1235)
Q Consensus 1109 ~~~~~~CpICle~lf~s~~~v~~L-pCgH~fH~~Ci~~wl~~~~~CPiCrksv~ 1161 (1235)
....-.|||....| ++....+.| ||||+|=..++.+.- ....||+|.+++.
T Consensus 110 ~~~~~~CPvt~~~~-~~~~~fv~l~~cG~V~s~~alke~k-~~~~Cp~c~~~f~ 161 (260)
T PF04641_consen 110 SEGRFICPVTGKEF-NGKHKFVYLRPCGCVFSEKALKELK-KSKKCPVCGKPFT 161 (260)
T ss_pred CCceeECCCCCccc-CCceeEEEEcCCCCEeeHHHHHhhc-ccccccccCCccc
Confidence 44567899999995 544555555 999999999999984 4678999999974
No 93
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=86.44 E-value=0.38 Score=61.21 Aligned_cols=42 Identities=29% Similarity=0.639 Sum_probs=33.2
Q ss_pred CCccccccccccCCCcceecCCCCccChhhHHhhhhCCCCCCCCCcCc
Q 000895 1113 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSL 1160 (1235)
Q Consensus 1113 ~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrksv 1160 (1235)
..|..|--.|. -|.+...|||.||.+|+. .....||-|+-..
T Consensus 841 skCs~C~~~Ld---lP~VhF~CgHsyHqhC~e---~~~~~CP~C~~e~ 882 (933)
T KOG2114|consen 841 SKCSACEGTLD---LPFVHFLCGHSYHQHCLE---DKEDKCPKCLPEL 882 (933)
T ss_pred eeecccCCccc---cceeeeecccHHHHHhhc---cCcccCCccchhh
Confidence 47888875543 367778999999999997 5568899999844
No 94
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=86.26 E-value=0.41 Score=54.62 Aligned_cols=63 Identities=21% Similarity=0.311 Sum_probs=44.7
Q ss_pred CCCccccccccccCCCcceecCCCCccChhhHHhhhhCCCCCCCCCcCcCchhhhhhhHHHHHhhcC
Q 000895 1112 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGDMAVYFGMLDALLASEQ 1178 (1235)
Q Consensus 1112 ~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrksv~dm~~~~~~lD~~i~~~p 1178 (1235)
-..|-||..+ |.+ .++-.|||+|...|...-++.+..|+||.+.+......-..|+..+..-+
T Consensus 241 Pf~c~icr~~-f~~---pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g~~~~akeL~~~L~~kk 303 (313)
T KOG1813|consen 241 PFKCFICRKY-FYR---PVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHGSFNVAKELLVSLKLKK 303 (313)
T ss_pred Cccccccccc-ccc---chhhcCCceeehhhhccccccCCcceecccccccccchHHHHHHHHHhhh
Confidence 3569999999 443 35679999999999988888889999999987543222233444444333
No 95
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=86.07 E-value=0.26 Score=59.39 Aligned_cols=51 Identities=25% Similarity=0.570 Sum_probs=41.3
Q ss_pred cCCCCCCCccccccccccCCCcceecCCCCccChhhHHhhhh-----CCCCCCCCCcCcC
Q 000895 1107 REKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC-----SHYICPICSKSLG 1161 (1235)
Q Consensus 1107 ~e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~-----~~~~CPiCrksv~ 1161 (1235)
.++..+..|-+|.|+ .+....-.|.|.|+.-|+.+|.. .+.+||+|.+.+.
T Consensus 531 ~enk~~~~C~lc~d~----aed~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~Ls 586 (791)
T KOG1002|consen 531 DENKGEVECGLCHDP----AEDYIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLS 586 (791)
T ss_pred ccccCceeecccCCh----hhhhHhhhhhHHHHHHHHHHHHHhhhcccCCCCcccccccc
Confidence 456677899999877 23456789999999999999974 3699999998774
No 96
>COG2461 Uncharacterized conserved protein [Function unknown]
Probab=85.60 E-value=3.6 Score=48.97 Aligned_cols=138 Identities=22% Similarity=0.214 Sum_probs=104.3
Q ss_pred cCCChHHHHHHHHHHHHHHHHHHHHHHhhccCCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHHHhh-hhHHHHH
Q 000895 40 LKSPILIFLFFHKAIKSELDVLHRAAMAFATNLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIRV-KNIARTY 118 (1235)
Q Consensus 40 ~~~Pi~~~~~~HkAlR~eL~~l~~~~~~~~~~~gd~~~~~~l~~r~~fL~~~~~~H~~aEDevI~PaLd~Rv-~~v~~~~ 118 (1235)
-.+|+..|..=-+++|..|+.+.+. . .+..-...+...+.+|..+=+ |-+-+-..|||-++.|- ..+.-.|
T Consensus 84 ~gHPv~tl~~EN~~i~~ll~~~l~~---~----~~~~ik~~l~~lv~~L~~vg~-Hy~RKe~lIfp~~Er~GitapptVm 155 (409)
T COG2461 84 PGHPVRTLKRENKAIRSLLANLLQF---P----PKKEIKEKLVELVSELDKIGK-HYTRKEMLIFPYIERRGITAPPTVM 155 (409)
T ss_pred CCCcHHHHhcccHHHHHHHHHHhhc---c----ccHHHHHHHHHHHHHHHHhcc-ccccccccchhHHHHcCCCCCCeee
Confidence 3569988888888999555555422 2 123344556667777777777 99999999999999886 4577778
Q ss_pred HhhhhhHHHHHHHHHHHHHhhhcCchHHHHHHHHHHHHHHHHHHHhHHHHHHHHhhHHhhcCCHHHHHHHHHH
Q 000895 119 SLEHEGESVLFDQLFELLNSSMRNEESYRRELASCTGALQTSISQHMSKEEEQVFPLLIEKFSFEEQASLVWQ 191 (1235)
Q Consensus 119 ~~EH~~~~~lf~~l~~~l~~~~~~~~~~~~eLa~~l~~l~~~l~qHm~~EE~qv~PLl~~~fS~~Eq~~L~~~ 191 (1235)
-.-|.++-..|..+...+. ..+. .+++.....+.+.+..=+.+||.-+.|-+..-||..||.++..+
T Consensus 156 W~~dDeiRe~lk~~~~~l~--~~s~----~~~ve~~~~~~t~i~dmIFkEe~Ilypt~~d~~te~ew~~i~~~ 222 (409)
T COG2461 156 WVKDDEIREALKELLKLLK--EVSI----EEFVEKAESVLTEIEDMIFKEENILYPTLLDLLTEGEWEAIKEQ 222 (409)
T ss_pred eccCcHHHHHHHHHHHHhh--ccCh----HHHHHHHHHHHHHHHHHHHhhhhhHHhHHHHhcCHHHHHHHHhc
Confidence 8899999999999888887 2222 33344444555568888999999999999999999999998876
No 97
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=84.99 E-value=0.18 Score=57.21 Aligned_cols=48 Identities=29% Similarity=0.653 Sum_probs=32.8
Q ss_pred CCCccccccccccCCCcceecCCCCcc-ChhhHHhhhhCCCCCCCCCcCcCchhhhh
Q 000895 1112 ETNCPICCDFLFTSSATVRALPCGHFM-HSDCFQAYTCSHYICPICSKSLGDMAVYF 1167 (1235)
Q Consensus 1112 ~~~CpICle~lf~s~~~v~~LpCgH~f-H~~Ci~~wl~~~~~CPiCrksv~dm~~~~ 1167 (1235)
+.-|.||++- ......|+|||.. ...|-.. -..|||||+-|......|
T Consensus 300 ~~LC~ICmDa----P~DCvfLeCGHmVtCt~CGkr----m~eCPICRqyi~rvvrif 348 (350)
T KOG4275|consen 300 RRLCAICMDA----PRDCVFLECGHMVTCTKCGKR----MNECPICRQYIVRVVRIF 348 (350)
T ss_pred HHHHHHHhcC----CcceEEeecCcEEeehhhccc----cccCchHHHHHHHHHhhh
Confidence 6789999864 3447889999974 2333322 248999998776655444
No 98
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=84.62 E-value=0.47 Score=41.69 Aligned_cols=31 Identities=32% Similarity=0.857 Sum_probs=25.1
Q ss_pred ceecCCCCccChhhHHhhhhCCCCCCCCCcCcC
Q 000895 1129 VRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1161 (1235)
Q Consensus 1129 v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrksv~ 1161 (1235)
-.++||||.+-..|++-+ +-+-||+|.+.+.
T Consensus 20 ~~~~pCgH~I~~~~f~~~--rYngCPfC~~~~~ 50 (55)
T PF14447_consen 20 GTVLPCGHLICDNCFPGE--RYNGCPFCGTPFE 50 (55)
T ss_pred cccccccceeeccccChh--hccCCCCCCCccc
Confidence 467899999999998765 3456999999875
No 99
>COG5592 Uncharacterized conserved protein [Function unknown]
Probab=84.21 E-value=3 Score=44.10 Aligned_cols=73 Identities=22% Similarity=0.245 Sum_probs=58.1
Q ss_pred hhhHHHHHHHHHHHHHHHHHHhhccCCCCChhhHHHHHHHHHHHHHHHHHHhhhhchhccccccccccccccccccchhh
Q 000895 645 PIDNIFKFHKAIRKDLEYLDGESGKLNDCNETFLRQFTGRFRLLWGLYRAHSNAEDDIVFPALESKETLSNVSHSYTLDH 724 (1235)
Q Consensus 645 PID~i~~~H~AIRkdL~~L~~ea~~l~~~d~~~L~~f~~rf~~L~~v~~~HS~AEDeivfPALe~k~~~~nvshs~~~EH 724 (1235)
..|.|..+||.|-+.-..+.... ++ +.+..|+..+...+..|--||++.+||-+++..+ +.+.
T Consensus 72 ~~~~i~~DHkliE~l~tnlik~k------R~---~k~~e~~p~fyK~LtdHn~aEE~~IfPrvks~~~--------E~~~ 134 (171)
T COG5592 72 EVDRIKNDHKLIETLATNLIKWK------RP---DKIKERVPLFYKTLTDHNLAEEEYIFPRVKSLKG--------EDEQ 134 (171)
T ss_pred hhhHhHhhHHHHHHHHHHHHhhc------cc---hHHHHHHHHHHHHHHHccccccchhhHHHHhhcc--------hhhH
Confidence 45999999999999888887531 22 3789999999999999999999999999987643 2455
Q ss_pred HHHHHHHHHH
Q 000895 725 KQEEKLFEDI 734 (1235)
Q Consensus 725 ~~ee~lfedi 734 (1235)
.+...+++.|
T Consensus 135 ~~~kl~LeiI 144 (171)
T COG5592 135 SALKLALEII 144 (171)
T ss_pred HHHHHHHHHH
Confidence 5566667777
No 100
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=83.82 E-value=0.98 Score=52.42 Aligned_cols=62 Identities=23% Similarity=0.580 Sum_probs=47.4
Q ss_pred CCCccccccccccCCCcceecCC--CCccChhhHHhhhhCCCCCCCCCcCcCchhhhhhhHHHHHhhcCCChhh
Q 000895 1112 ETNCPICCDFLFTSSATVRALPC--GHFMHSDCFQAYTCSHYICPICSKSLGDMAVYFGMLDALLASEQLPEEY 1183 (1235)
Q Consensus 1112 ~~~CpICle~lf~s~~~v~~LpC--gH~fH~~Ci~~wl~~~~~CPiCrksv~dm~~~~~~lD~~i~~~pmP~ey 1183 (1235)
-.+||||.++|.. -++.| ||.-...|-. +...+||.||.++++... +.++.+++....|=.|
T Consensus 48 lleCPvC~~~l~~-----Pi~QC~nGHlaCssC~~---~~~~~CP~Cr~~~g~~R~--~amEkV~e~~~vpC~~ 111 (299)
T KOG3002|consen 48 LLDCPVCFNPLSP-----PIFQCDNGHLACSSCRT---KVSNKCPTCRLPIGNIRC--RAMEKVAEAVLVPCKN 111 (299)
T ss_pred hccCchhhccCcc-----cceecCCCcEehhhhhh---hhcccCCccccccccHHH--HHHHHHHHhceecccc
Confidence 4789999999643 34667 7998888875 458999999999997533 5677778888777554
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=83.80 E-value=0.63 Score=46.73 Aligned_cols=34 Identities=24% Similarity=0.423 Sum_probs=25.9
Q ss_pred cCCcEeccCCCCCCCCCceeeeccCCCCCCCccccc
Q 000895 1186 RCQEILCNDCDKKGSAPFHWLYHKCGFCGSYNTRVI 1221 (1235)
Q Consensus 1186 ~~~~i~CnDC~~~s~~~~h~lg~kC~~C~SYNT~~~ 1221 (1235)
..+...|++|+.......+ +..||.|||++++++
T Consensus 67 ~p~~~~C~~Cg~~~~~~~~--~~~CP~Cgs~~~~i~ 100 (115)
T TIGR00100 67 EPVECECEDCSEEVSPEID--LYRCPKCHGIMLQVR 100 (115)
T ss_pred eCcEEEcccCCCEEecCCc--CccCcCCcCCCcEEe
Confidence 3467899999987765432 347999999998875
No 102
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=83.59 E-value=0.69 Score=46.59 Aligned_cols=35 Identities=26% Similarity=0.491 Sum_probs=26.6
Q ss_pred ccCCcEeccCCCCCCCCC-ceeeeccCCCCCCCccccc
Q 000895 1185 DRCQEILCNDCDKKGSAP-FHWLYHKCGFCGSYNTRVI 1221 (1235)
Q Consensus 1185 ~~~~~i~CnDC~~~s~~~-~h~lg~kC~~C~SYNT~~~ 1221 (1235)
...+...|++||...... +++ .+||.|||++..++
T Consensus 67 ~vp~~~~C~~Cg~~~~~~~~~~--~~CP~Cgs~~~~i~ 102 (117)
T PRK00564 67 DEKVELECKDCSHVFKPNALDY--GVCEKCHSKNVIIT 102 (117)
T ss_pred ecCCEEEhhhCCCccccCCccC--CcCcCCCCCceEEe
Confidence 344678999999877664 333 47999999998765
No 103
>PHA02862 5L protein; Provisional
Probab=83.22 E-value=0.7 Score=47.93 Aligned_cols=46 Identities=24% Similarity=0.569 Sum_probs=34.2
Q ss_pred CCCCccccccccccCCCcceecCCC-----CccChhhHHhhhhC--CCCCCCCCcCcC
Q 000895 1111 LETNCPICCDFLFTSSATVRALPCG-----HFMHSDCFQAYTCS--HYICPICSKSLG 1161 (1235)
Q Consensus 1111 ~~~~CpICle~lf~s~~~v~~LpCg-----H~fH~~Ci~~wl~~--~~~CPiCrksv~ 1161 (1235)
+...|=||.+. . ++. .-||. -..|..|+.+|+.. +.+||+|+....
T Consensus 1 ~~diCWIC~~~-~--~e~--~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~ 53 (156)
T PHA02862 1 MSDICWICNDV-C--DER--NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYN 53 (156)
T ss_pred CCCEEEEecCc-C--CCC--cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEE
Confidence 35679999987 2 222 34663 78999999999964 478999998763
No 104
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=82.29 E-value=1.1 Score=53.91 Aligned_cols=49 Identities=27% Similarity=0.642 Sum_probs=39.9
Q ss_pred CCCCCccccccccccCCCcceecCCCCccChhhHHhhhhCCCCCCCCCcCcCc
Q 000895 1110 GLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1162 (1235)
Q Consensus 1110 ~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrksv~d 1162 (1235)
..+-.|-||..-++. .+..||||.|...|+++-+....-||+||-.+..
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 456789999877554 3445999999999999977777889999998874
No 105
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=81.86 E-value=0.68 Score=54.95 Aligned_cols=54 Identities=22% Similarity=0.399 Sum_probs=40.1
Q ss_pred cccccCCCCCCCccccccccccCCCcceecCCCCccChhhHHhhhh--------CCCCCCCCCc
Q 000895 1103 DHKCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC--------SHYICPICSK 1158 (1235)
Q Consensus 1103 ~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~--------~~~~CPiCrk 1158 (1235)
.+.+.-+ .--.|-||.+. +....-...+||+|+|...|...|.. +..+||-|..
T Consensus 176 ~~~~F~~-slf~C~ICf~e-~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C 237 (445)
T KOG1814|consen 176 TLEKFVN-SLFDCCICFEE-QMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKC 237 (445)
T ss_pred HHHHHHh-hcccceeeehh-hcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCC
Confidence 3444433 34689999988 55556678899999999999999863 2478987764
No 106
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=81.60 E-value=0.84 Score=52.97 Aligned_cols=54 Identities=22% Similarity=0.394 Sum_probs=43.9
Q ss_pred cccCCCCCCCccccccccccCCCcceecCCCCccChhhHHhhhhCCCCCCCCCcCcCc
Q 000895 1105 KCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1162 (1235)
Q Consensus 1105 ~C~e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrksv~d 1162 (1235)
+-..++.+..||||.-. ....+.-||||--...||.+.+.++..|=-|+.++.+
T Consensus 415 ~~lp~sEd~lCpICyA~----pi~Avf~PC~H~SC~~CI~qHlmN~k~CFfCktTv~~ 468 (489)
T KOG4692|consen 415 KDLPDSEDNLCPICYAG----PINAVFAPCSHRSCYGCITQHLMNCKRCFFCKTTVID 468 (489)
T ss_pred CCCCCcccccCcceecc----cchhhccCCCCchHHHHHHHHHhcCCeeeEecceeee
Confidence 33456778899999754 2234556999999999999999999999999999876
No 107
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=81.06 E-value=0.86 Score=47.01 Aligned_cols=34 Identities=26% Similarity=0.687 Sum_probs=24.7
Q ss_pred CcEeccCCCCCCCCC-------------cee------eeccCCCCCCCccccc
Q 000895 1188 QEILCNDCDKKGSAP-------------FHW------LYHKCGFCGSYNTRVI 1221 (1235)
Q Consensus 1188 ~~i~CnDC~~~s~~~-------------~h~------lg~kC~~C~SYNT~~~ 1221 (1235)
....|++||...... +|+ .+.+|+.|||++..++
T Consensus 69 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~ 121 (135)
T PRK03824 69 AVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRDFEIV 121 (135)
T ss_pred eEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCCcEEe
Confidence 568899999776543 222 2367999999998764
No 108
>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=81.01 E-value=1.2 Score=47.04 Aligned_cols=33 Identities=27% Similarity=0.788 Sum_probs=22.5
Q ss_pred CCCccccccccccCCCcceecCC------------C-CccChhhHHhhhh
Q 000895 1112 ETNCPICCDFLFTSSATVRALPC------------G-HFMHSDCFQAYTC 1148 (1235)
Q Consensus 1112 ~~~CpICle~lf~s~~~v~~LpC------------g-H~fH~~Ci~~wl~ 1148 (1235)
+..||||||.=.+ .+.|-| + =+=|+.|++++-+
T Consensus 2 d~~CpICme~PHN----AVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkk 47 (162)
T PF07800_consen 2 DVTCPICMEHPHN----AVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKK 47 (162)
T ss_pred CccCceeccCCCc----eEEEEeccccCCccccccCCccchhHHHHHHHH
Confidence 4579999997322 344555 3 3569999999853
No 109
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=80.82 E-value=0.88 Score=45.56 Aligned_cols=33 Identities=24% Similarity=0.390 Sum_probs=24.8
Q ss_pred CCcEeccCCCCCCCCCceeeeccCCCCCCCccccc
Q 000895 1187 CQEILCNDCDKKGSAPFHWLYHKCGFCGSYNTRVI 1221 (1235)
Q Consensus 1187 ~~~i~CnDC~~~s~~~~h~lg~kC~~C~SYNT~~~ 1221 (1235)
.....|++||........ ...||.|||++..++
T Consensus 68 p~~~~C~~Cg~~~~~~~~--~~~CP~Cgs~~~~i~ 100 (113)
T PRK12380 68 PAQAWCWDCSQVVEIHQH--DAQCPHCHGERLRVD 100 (113)
T ss_pred CcEEEcccCCCEEecCCc--CccCcCCCCCCcEEc
Confidence 457899999987766422 225999999998775
No 110
>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=80.61 E-value=5.9 Score=39.54 Aligned_cols=51 Identities=18% Similarity=0.176 Sum_probs=36.8
Q ss_pred hhHHhHHHHHHHHHHHHHHHHHHhhcCCCCCcHHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 000895 361 SFAQEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQV 421 (1235)
Q Consensus 361 sme~EH~~ie~l~e~l~~ll~~l~~~~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qv 421 (1235)
.+..+|++.-++++.|..++..- .+ ..++...+..|..-+..||..||.-.
T Consensus 12 ~ID~qH~~l~~~in~l~~a~~~~----~~------~~~~~~~l~~L~~y~~~HF~~EE~~M 62 (126)
T TIGR02481 12 EIDAQHKELFELINELYDALSAG----NG------KDELKEILDELIDYTENHFADEEELM 62 (126)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcC----CC------HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56678888777777777665321 11 24667788888999999999999765
No 111
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=80.46 E-value=0.99 Score=45.28 Aligned_cols=34 Identities=18% Similarity=0.389 Sum_probs=25.2
Q ss_pred CCcEeccCCCCCCCCCceeeeccCCCCCCCccccc
Q 000895 1187 CQEILCNDCDKKGSAPFHWLYHKCGFCGSYNTRVI 1221 (1235)
Q Consensus 1187 ~~~i~CnDC~~~s~~~~h~lg~kC~~C~SYNT~~~ 1221 (1235)
.....|++|+.......+. ...||.|||+++.++
T Consensus 68 p~~~~C~~Cg~~~~~~~~~-~~~CP~Cgs~~~~i~ 101 (114)
T PRK03681 68 EAECWCETCQQYVTLLTQR-VRRCPQCHGDMLRIV 101 (114)
T ss_pred CcEEEcccCCCeeecCCcc-CCcCcCcCCCCcEEc
Confidence 4578999999876654332 246999999998775
No 112
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=79.74 E-value=0.15 Score=59.65 Aligned_cols=52 Identities=23% Similarity=0.475 Sum_probs=45.4
Q ss_pred CCCCccccccccccCCCcceecCCCCccChhhHHhhhhCCCCCCCCCcCcCc
Q 000895 1111 LETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1162 (1235)
Q Consensus 1111 ~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrksv~d 1162 (1235)
....|.||.+.+...-+.+..+.|||.+|..|+.+|+.....||-|++.+..
T Consensus 195 lv~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~~~~kl~~~~rel~~ 246 (465)
T KOG0827|consen 195 LVGSLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLATKRKLPSCRRELPK 246 (465)
T ss_pred HHhhhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHHHhHHHHhhhhh
Confidence 3568999999977665678889999999999999999989999999998853
No 113
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=78.28 E-value=1.6 Score=55.30 Aligned_cols=70 Identities=23% Similarity=0.505 Sum_probs=47.4
Q ss_pred CccccCCCCCccccCCCCCccccccCCcccccccccccccccCCCCCCCccccccccccCCCcceecCCCCccChhhHHh
Q 000895 1066 RVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLAKKLVDHKCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQA 1145 (1235)
Q Consensus 1066 k~~yHC~~CgiCR~g~gl~~~~fHC~~C~~C~~~~l~~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~ 1145 (1235)
--+|-|+.|+-=-+++++ .-|++|-.|-+ ..|.||-..+-. ..+.---|||..|.+|+.+
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----WQCDRCESRAS--------------AKCTVCDLVIRG--VDVWCQVCGHGGHDSHLKS 810 (839)
T ss_pred eeeccccccCCccccccc----eeechHHHHhh--------------cCceeecceeee--eEeecccccccccHHHHHH
Confidence 456778888755555442 55666666644 369999765322 2233346999999999999
Q ss_pred hhhCCCCCCC
Q 000895 1146 YTCSHYICPI 1155 (1235)
Q Consensus 1146 wl~~~~~CPi 1155 (1235)
|+..+..||.
T Consensus 811 w~~~~s~ca~ 820 (839)
T KOG0269|consen 811 WFFKASPCAK 820 (839)
T ss_pred HHhcCCCCcc
Confidence 9987766665
No 114
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=78.06 E-value=1.8 Score=50.31 Aligned_cols=64 Identities=22% Similarity=0.424 Sum_probs=45.4
Q ss_pred ccccccccc-ccccccCCCCCCCccccccccccCCCcceecCCCCccChhhHHhh--hhCCCCCCCCCcCc
Q 000895 1093 CNCCLAKKL-VDHKCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAY--TCSHYICPICSKSL 1160 (1235)
Q Consensus 1093 C~~C~~~~l-~~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~w--l~~~~~CPiCrksv 1160 (1235)
=+.|..-++ ..-+=..+..++.|-||-+.+ +-+.++||||-+.-.|--.. +.....||+||...
T Consensus 41 NnlsaEPnlttsSaddtDEen~~C~ICA~~~----TYs~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~ 107 (493)
T COG5236 41 NNLSAEPNLTTSSADDTDEENMNCQICAGST----TYSARYPCGHQICHACAVRLRALYMQKGCPLCRTET 107 (493)
T ss_pred cccccCCccccccccccccccceeEEecCCc----eEEEeccCCchHHHHHHHHHHHHHhccCCCcccccc
Confidence 356665555 333333344568999998763 34678999999999998664 55678899999865
No 115
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=77.06 E-value=2.1 Score=49.20 Aligned_cols=47 Identities=28% Similarity=0.742 Sum_probs=38.2
Q ss_pred CCccccccccccCCCc---ceecCCCCccChhhHHhhhhCC-CCCCCCCcCc
Q 000895 1113 TNCPICCDFLFTSSAT---VRALPCGHFMHSDCFQAYTCSH-YICPICSKSL 1160 (1235)
Q Consensus 1113 ~~CpICle~lf~s~~~---v~~LpCgH~fH~~Ci~~wl~~~-~~CPiCrksv 1160 (1235)
..|-||-++ |.+.+. .+.|.|||+|...|+.+.+..+ ..||-||...
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 569999999 666543 3678999999999999987654 6689999994
No 116
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=75.46 E-value=2 Score=45.49 Aligned_cols=45 Identities=22% Similarity=0.617 Sum_probs=32.9
Q ss_pred CCCCccccccccccCCCcceecCCC--C---ccChhhHHhhhhC--CCCCCCCCcCc
Q 000895 1111 LETNCPICCDFLFTSSATVRALPCG--H---FMHSDCFQAYTCS--HYICPICSKSL 1160 (1235)
Q Consensus 1111 ~~~~CpICle~lf~s~~~v~~LpCg--H---~fH~~Ci~~wl~~--~~~CPiCrksv 1160 (1235)
++..|-||.+.- + . ..-||. . ..|.+|++.|+.. ..+||+|+...
T Consensus 7 ~~~~CRIC~~~~-~--~--~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y 58 (162)
T PHA02825 7 MDKCCWICKDEY-D--V--VTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPY 58 (162)
T ss_pred CCCeeEecCCCC-C--C--ccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeE
Confidence 467899998772 1 2 224664 4 6799999999854 57899999875
No 117
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=75.39 E-value=2.4 Score=53.12 Aligned_cols=70 Identities=17% Similarity=0.397 Sum_probs=45.6
Q ss_pred CCCccccccccccCCCcceecC---CCCccChhhHHhhh--------hCCCCCCCCCcCcCchhhhhhhHHHHHhhcCCC
Q 000895 1112 ETNCPICCDFLFTSSATVRALP---CGHFMHSDCFQAYT--------CSHYICPICSKSLGDMAVYFGMLDALLASEQLP 1180 (1235)
Q Consensus 1112 ~~~CpICle~lf~s~~~v~~Lp---CgH~fH~~Ci~~wl--------~~~~~CPiCrksv~dm~~~~~~lD~~i~~~pmP 1180 (1235)
-..||||+-. |-..+....+. |.--.|..|..-.. ...|.|-+|| .....-+.+-..+...-+|
T Consensus 145 ~~~cPvc~~~-Y~~~e~~~~~~c~~c~rwsh~~c~~~sdd~~~q~~vD~~~~CS~CR----~es~qvKdi~~~vqe~~~~ 219 (694)
T KOG4443|consen 145 LSYCPVCLIV-YQDSESLPMVCCSICQRWSHGGCDGISDDKYMQAQVDLQYKCSTCR----GESYQVKDISDALQETWKA 219 (694)
T ss_pred cccCchHHHh-hhhccchhhHHHHHhcccccCCCCccchHHHHHHhhhhhcccceee----hhhhhhhhHHHHHHhhcch
Confidence 4689999865 44344443343 55568888874332 1369999999 2233456777778888888
Q ss_pred hhhhcc
Q 000895 1181 EEYRDR 1186 (1235)
Q Consensus 1181 ~ey~~~ 1186 (1235)
..|.+.
T Consensus 220 k~~~~~ 225 (694)
T KOG4443|consen 220 KDKPDK 225 (694)
T ss_pred hhcccc
Confidence 777544
No 118
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=74.49 E-value=1.2 Score=57.28 Aligned_cols=44 Identities=25% Similarity=0.554 Sum_probs=33.1
Q ss_pred cccccCCCCCCCccccccccccCCCcceecCCCCccChhhHHhhhh
Q 000895 1103 DHKCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC 1148 (1235)
Q Consensus 1103 ~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~ 1148 (1235)
.|.|+--.....|-+|.-.++. .+-.+.||||.||.+|+.+-..
T Consensus 808 ~~ry~v~ep~d~C~~C~~~ll~--~pF~vf~CgH~FH~~Cl~~~v~ 851 (911)
T KOG2034|consen 808 RQRYRVLEPQDSCDHCGRPLLI--KPFYVFPCGHCFHRDCLIRHVL 851 (911)
T ss_pred hcceEEecCccchHHhcchhhc--CcceeeeccchHHHHHHHHHHH
Confidence 4555444456789999888664 3667789999999999988653
No 119
>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=74.38 E-value=1 Score=38.42 Aligned_cols=43 Identities=30% Similarity=0.783 Sum_probs=26.2
Q ss_pred CCccccccccccCCCcceecCCC-CccChhhHHhhhhCCCCCCCCCcCcC
Q 000895 1113 TNCPICCDFLFTSSATVRALPCG-HFMHSDCFQAYTCSHYICPICSKSLG 1161 (1235)
Q Consensus 1113 ~~CpICle~lf~s~~~v~~LpCg-H~fH~~Ci~~wl~~~~~CPiCrksv~ 1161 (1235)
.+|--|. |... ....|. |+....|+..++..+..||||.+++.
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 3566665 4332 345786 99999999999999999999999875
No 120
>PRK04023 DNA polymerase II large subunit; Validated
Probab=73.85 E-value=2.8 Score=54.91 Aligned_cols=23 Identities=22% Similarity=0.437 Sum_probs=14.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhc
Q 000895 297 IMLWHNAIKRELNDIAEAARKIQ 319 (1235)
Q Consensus 297 l~~~HkALRrEL~~L~~~a~~i~ 319 (1235)
+..-++-|.+++.++.+.|.+.+
T Consensus 5 ~~~Yf~~L~~~~~~~~eiA~~AR 27 (1121)
T PRK04023 5 MEDYFERLEKELDELYEIAEKAR 27 (1121)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 44456667777777666666654
No 121
>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=73.33 E-value=1 Score=45.07 Aligned_cols=34 Identities=24% Similarity=0.403 Sum_probs=22.5
Q ss_pred cCCcEeccCCCCCCCCCceeeeccCCCCCCCccccc
Q 000895 1186 RCQEILCNDCDKKGSAPFHWLYHKCGFCGSYNTRVI 1221 (1235)
Q Consensus 1186 ~~~~i~CnDC~~~s~~~~h~lg~kC~~C~SYNT~~~ 1221 (1235)
......|++||..+....+. ..||.|||++..++
T Consensus 67 ~p~~~~C~~Cg~~~~~~~~~--~~CP~Cgs~~~~i~ 100 (113)
T PF01155_consen 67 VPARARCRDCGHEFEPDEFD--FSCPRCGSPDVEII 100 (113)
T ss_dssp E--EEEETTTS-EEECHHCC--HH-SSSSSS-EEEE
T ss_pred cCCcEECCCCCCEEecCCCC--CCCcCCcCCCcEEc
Confidence 34578999999988765443 47999999997765
No 122
>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=73.28 E-value=0.67 Score=42.68 Aligned_cols=65 Identities=26% Similarity=0.637 Sum_probs=36.7
Q ss_pred CCccccccccccCCCcceecCCCCccChhhHHhhhhCCCCCCCCCcCcCchhhhhhhHHHHHhhcCCChhhhccCCcEec
Q 000895 1113 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGDMAVYFGMLDALLASEQLPEEYRDRCQEILC 1192 (1235)
Q Consensus 1113 ~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrksv~dm~~~~~~lD~~i~~~pmP~ey~~~~~~i~C 1192 (1235)
..||+|..+|...+ ||++...|-..+. ....||-|..++..+.+ =-.++++|
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 47999998864432 7888888887654 35789999998754321 11268999
Q ss_pred cCCC---CCCCCCcee
Q 000895 1193 NDCD---KKGSAPFHW 1205 (1235)
Q Consensus 1193 nDC~---~~s~~~~h~ 1205 (1235)
|.|+ +|+.|.|.+
T Consensus 54 ~~c~gLiSKkrV~f~~ 69 (70)
T PF07191_consen 54 NHCHGLISKKRVRFEF 69 (70)
T ss_dssp TTTT-EE-TTTSEEEE
T ss_pred ccCCceeecceEEEEe
Confidence 9998 445565543
No 123
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=72.12 E-value=1.7 Score=55.65 Aligned_cols=49 Identities=27% Similarity=0.633 Sum_probs=35.9
Q ss_pred CCCCccccccccccCCCccee-cCCCCccChhhHHhhhhC-------CCCCCCCCcCc
Q 000895 1111 LETNCPICCDFLFTSSATVRA-LPCGHFMHSDCFQAYTCS-------HYICPICSKSL 1160 (1235)
Q Consensus 1111 ~~~~CpICle~lf~s~~~v~~-LpCgH~fH~~Ci~~wl~~-------~~~CPiCrksv 1160 (1235)
..-.|.||.|.+..+ .++-. -.|=|+||..||..|.+. .-+||-|+...
T Consensus 190 ~~yeCmIC~e~I~~t-~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv~ 246 (950)
T KOG1952|consen 190 RKYECMICTERIKRT-APVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSVS 246 (950)
T ss_pred CceEEEEeeeecccc-CCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccchh
Confidence 346899999996554 33322 357799999999999742 47899999543
No 124
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=71.82 E-value=1.3 Score=54.95 Aligned_cols=43 Identities=26% Similarity=0.623 Sum_probs=35.2
Q ss_pred CCccccccccccCCCcceecCCCCccChhhHHhhhhCCCCCCCCCc
Q 000895 1113 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSK 1158 (1235)
Q Consensus 1113 ~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrk 1158 (1235)
.+|+||+..++.+.-..+.|-|||++...|+..- .+.+|| |..
T Consensus 12 l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~l--yn~scp-~~~ 54 (861)
T KOG3161|consen 12 LLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLL--YNASCP-TKR 54 (861)
T ss_pred hhchHHHHHHHHHhcCcccccccchHHHHHHHhH--hhccCC-CCc
Confidence 5799998887777666778999999999999765 377899 664
No 125
>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=69.28 E-value=1.3 Score=49.27 Aligned_cols=50 Identities=26% Similarity=0.568 Sum_probs=39.3
Q ss_pred CCCccccccccccCCCcceec-C-CCCccChhhHHhhhhCC-CCCC--CCCcCcC
Q 000895 1112 ETNCPICCDFLFTSSATVRAL-P-CGHFMHSDCFQAYTCSH-YICP--ICSKSLG 1161 (1235)
Q Consensus 1112 ~~~CpICle~lf~s~~~v~~L-p-CgH~fH~~Ci~~wl~~~-~~CP--iCrksv~ 1161 (1235)
+..||||.-+.+-+.+-.... | |=|-|..+|++.-+..+ ..|| -|.|.+.
T Consensus 10 d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kILR 64 (314)
T COG5220 10 DRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKILR 64 (314)
T ss_pred cccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHHH
Confidence 458999999888776633332 6 99999999999987655 7799 8988764
No 126
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=69.08 E-value=3.8 Score=36.10 Aligned_cols=37 Identities=24% Similarity=0.518 Sum_probs=28.6
Q ss_pred CCCCCccccccccccCCCcceecCCCCccChhhHHhh
Q 000895 1110 GLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAY 1146 (1235)
Q Consensus 1110 ~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~w 1146 (1235)
.....|++|.+.+...++.|+--.||-.+|+.|.++-
T Consensus 3 ~~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~ 39 (54)
T PF14446_consen 3 YEGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKA 39 (54)
T ss_pred ccCccChhhCCcccCCCCEEECCCCCCcccHHHHhhC
Confidence 3567899999996555555555689999999998653
No 127
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=68.92 E-value=2.8 Score=42.75 Aligned_cols=34 Identities=26% Similarity=0.654 Sum_probs=23.7
Q ss_pred CCcEeccCCCCCCCCC-c---ee-eeccCCCCCCCccccc
Q 000895 1187 CQEILCNDCDKKGSAP-F---HW-LYHKCGFCGSYNTRVI 1221 (1235)
Q Consensus 1187 ~~~i~CnDC~~~s~~~-~---h~-lg~kC~~C~SYNT~~~ 1221 (1235)
.....| +||..+... + |+ .+..||.|||++..++
T Consensus 68 p~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~ 106 (124)
T PRK00762 68 PVEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKRAHIL 106 (124)
T ss_pred CeeEEe-eCcCcccccccchhccccCCcCcCCCCCCCEEe
Confidence 457889 999875432 1 22 1357999999998875
No 128
>PF02084 Bindin: Bindin; InterPro: IPR000775 Bindin, the major protein component of the acrosome granule of sea urchin sperm, mediates species-specific adhesion of sperm to the egg surface during fertilisation [, ]. The protein coats the acrosomal process after externalisation by the acrosome reaction; it binds to sulphated, fucose-containing polysaccharides on the vitelline-layer receptor proteoglycans that cover the egg plasma membrane. Bindins from different genera show high levels of sequence similarity in both the mature bindin domain and in the probindin precursor region. The most highly conserved region is a 42-residue segment in the central portion of the mature bindin protein. This domain may be responsible for conserved functions of bindin, while the more highly divergent flanking regions may be responsible for its species-specific properties [].; GO: 0007342 fusion of sperm to egg plasma membrane
Probab=68.71 E-value=14 Score=41.14 Aligned_cols=45 Identities=24% Similarity=0.336 Sum_probs=26.5
Q ss_pred CCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHHHhhh-hHHHHHHhhhhhHHH
Q 000895 72 LGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIRVK-NIARTYSLEHEGESV 127 (1235)
Q Consensus 72 ~gd~~~~~~l~~r~~fL~~~~~~H~~aEDevI~PaLd~Rv~-~v~~~~~~EH~~~~~ 127 (1235)
+.|.=++.-|++| ||||++ +|==.=|--|+ -|+.+|..|-++++.
T Consensus 124 INDPYDlGLLLRh-------LRHHSN----LLAnIgdP~VreqVLsAMqEeeeEEe~ 169 (238)
T PF02084_consen 124 INDPYDLGLLLRH-------LRHHSN----LLANIGDPEVREQVLSAMQEEEEEEEQ 169 (238)
T ss_pred cCChhhHHHHHHH-------HHHHHH----HHhhcCCHHHHHHHHHHHhhhHHHHHH
Confidence 4677777766655 578988 22111122234 488899877665554
No 129
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=68.40 E-value=5.6 Score=49.32 Aligned_cols=79 Identities=22% Similarity=0.478 Sum_probs=44.9
Q ss_pred eecCCCCccChhhHHhhhhCCCCCCCCCcCcCchh-hhhhhHH--HHHhhcCCChhhhccCCcEeccCCCCC---C----
Q 000895 1130 RALPCGHFMHSDCFQAYTCSHYICPICSKSLGDMA-VYFGMLD--ALLASEQLPEEYRDRCQEILCNDCDKK---G---- 1199 (1235)
Q Consensus 1130 ~~LpCgH~fH~~Ci~~wl~~~~~CPiCrksv~dm~-~~~~~lD--~~i~~~pmP~ey~~~~~~i~CnDC~~~---s---- 1199 (1235)
++..=|-+||..|+ +|-+|+++...-+ ..|.--+ -+.-.++||--=.....--.|--|+.. +
T Consensus 79 vvsa~gktyh~~cf--------~cs~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk~gq~ll 150 (670)
T KOG1044|consen 79 VVSTLGKTYHPKCF--------SCSTCKSPFKSGDKVTFSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELKNGQALL 150 (670)
T ss_pred eEecccceeccccc--------eecccCCCCCCCCeeeecchhhhhhhhcCcccCCcccccCCccccchhhhhhccceee
Confidence 44444899999987 6777777653111 1121111 122345555331222334568888744 2
Q ss_pred --CCCceeeeccCCCCCCC
Q 000895 1200 --SAPFHWLYHKCGFCGSY 1216 (1235)
Q Consensus 1200 --~~~~h~lg~kC~~C~SY 1216 (1235)
..++|+.+-||..|+--
T Consensus 151 ald~qwhv~cfkc~~c~~v 169 (670)
T KOG1044|consen 151 ALDKQWHVSCFKCKSCSAV 169 (670)
T ss_pred eeccceeeeeeehhhhccc
Confidence 35799999999987654
No 130
>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=68.10 E-value=3.5 Score=32.13 Aligned_cols=38 Identities=32% Similarity=0.747 Sum_probs=26.2
Q ss_pred CccccccccccCCCcceecCCCCccChhhHHhhhhCCCCCCCCCcCcC
Q 000895 1114 NCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1161 (1235)
Q Consensus 1114 ~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrksv~ 1161 (1235)
.|+.|.+.+......+. .=|..||.+|+ +|..|++++.
T Consensus 1 ~C~~C~~~i~~~~~~~~--~~~~~~H~~Cf--------~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLR--ALGKVWHPECF--------KCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEE--eCCccccccCC--------CCcccCCcCc
Confidence 37888888665422222 22789999987 7888988764
No 131
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=68.09 E-value=4 Score=36.52 Aligned_cols=46 Identities=26% Similarity=0.658 Sum_probs=25.6
Q ss_pred cccccccccccccCCC-----CCCCcCCCCCccceEecccccCcCCCCccccCCCCCc
Q 000895 1024 TEMMCMRCLKVQPVGP-----VCTTLSCSGLSMAKYYCGICKFFDDERVVYHCPFCNL 1076 (1235)
Q Consensus 1024 ~~v~C~~C~~~q~~~~-----~C~~~~C~~~~~a~y~C~iC~l~d~~k~~yHC~~Cgi 1076 (1235)
....|..|+..-.... .|-| | |.. -=|-|.+|+-..+ .|.|++||+
T Consensus 6 ~~~~CtSCg~~i~~~~~~~~F~CPn--C-G~~-~I~RC~~CRk~~~---~Y~CP~CGF 56 (59)
T PRK14890 6 EPPKCTSCGIEIAPREKAVKFLCPN--C-GEV-IIYRCEKCRKQSN---PYTCPKCGF 56 (59)
T ss_pred cCccccCCCCcccCCCccCEeeCCC--C-CCe-eEeechhHHhcCC---ceECCCCCC
Confidence 3446777765544322 4655 4 432 1344667765543 577777774
No 132
>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=66.33 E-value=90 Score=31.12 Aligned_cols=109 Identities=19% Similarity=0.317 Sum_probs=68.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcccCCcccHHHHHHHHHHHHHHHHhhhhccccch----hhhhhhHhhhHHhHHHHHHH
Q 000895 297 IMLWHNAIKRELNDIAEAARKIQLSGDFSDLSAFNKRLQFIAEVCIFHSIAEDKVI----FPAVDVELSFAQEHAEEEIQ 372 (1235)
Q Consensus 297 l~~~HkALRrEL~~L~~~a~~i~~~gd~~~L~~L~~r~~fl~~vl~~Hs~aEDevl----FPaL~~r~sme~EH~~ie~l 372 (1235)
+=.-|+.|=..++.+.+.+.. + .....+...+.+|.+....|-..|+.++ ||.+..+. .+| +..
T Consensus 13 ID~qH~~l~~~in~l~~a~~~----~--~~~~~~~~~l~~L~~y~~~HF~~EE~~M~~~~yp~~~~H~---~~H---~~~ 80 (126)
T TIGR02481 13 IDAQHKELFELINELYDALSA----G--NGKDELKEILDELIDYTENHFADEEELMEEYGYPDLEEHK---KEH---EKF 80 (126)
T ss_pred HHHHHHHHHHHHHHHHHHHHc----C--CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHH---HHH---HHH
Confidence 335688777777777776543 1 1245677788888999999999998765 77766443 344 444
Q ss_pred HHHHHHHHHHHhhcCCCCCcHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 000895 373 FDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPL 424 (1235)
Q Consensus 373 ~e~l~~ll~~l~~~~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qvfPL 424 (1235)
++.+..+...+.. +.. ..... ..+..+..-|..|+..+-..+.+.
T Consensus 81 l~~l~~l~~~~~~-~~~---~~~~~---~~~~~l~~Wl~~HI~~~D~~~~~~ 125 (126)
T TIGR02481 81 VKKIEELQEAVAE-GAD---ESLAE---ELLDFLKDWLVNHILKEDKKYAPY 125 (126)
T ss_pred HHHHHHHHHHHHc-CCc---hhHHH---HHHHHHHHHHHHHhHHHhHHHHhh
Confidence 5555555544432 211 12222 344556778999999888776553
No 133
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=66.22 E-value=4 Score=48.61 Aligned_cols=47 Identities=21% Similarity=0.513 Sum_probs=38.1
Q ss_pred CCccccccccccCCCcceecCCCCccChhhHHhhhhCC---CCCCCCCcCc
Q 000895 1113 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSH---YICPICSKSL 1160 (1235)
Q Consensus 1113 ~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~---~~CPiCrksv 1160 (1235)
-.|||=.+. -+...|...|.|||.+-.+=+++..+++ .+||-|-...
T Consensus 335 F~CPVlKeq-tsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~e~ 384 (394)
T KOG2817|consen 335 FICPVLKEQ-TSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPVEQ 384 (394)
T ss_pred eecccchhh-ccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCccc
Confidence 568888776 5556788999999999999999987653 7899997643
No 134
>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=65.09 E-value=3.6 Score=34.44 Aligned_cols=41 Identities=29% Similarity=0.745 Sum_probs=19.9
Q ss_pred ccccccccccCCCcceecCCCCccChhhHHhhhhCCC--CCCCC
Q 000895 1115 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHY--ICPIC 1156 (1235)
Q Consensus 1115 CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~--~CPiC 1156 (1235)
|.+|.+-. .-+..-..-.|+=.+|..|+..|++... +||.|
T Consensus 1 C~~C~~iv-~~G~~C~~~~C~~r~H~~C~~~y~r~~~~~~CP~C 43 (43)
T PF08746_consen 1 CEACKEIV-TQGQRCSNRDCNVRLHDDCFKKYFRHRSNPKCPNC 43 (43)
T ss_dssp -TTT-SB--SSSEE-SS--S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred CcccchhH-eeeccCCCCccCchHHHHHHHHHHhcCCCCCCcCC
Confidence 55666542 2221111225777899999999987643 79988
No 135
>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=64.66 E-value=4.7 Score=42.23 Aligned_cols=47 Identities=26% Similarity=0.579 Sum_probs=39.3
Q ss_pred CCccceEecccccCcCCCCccccCCCCCccccCCCCCccccccCCcccccccc
Q 000895 1048 GLSMAKYYCGICKFFDDERVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLAKK 1100 (1235)
Q Consensus 1048 ~~~~a~y~C~iC~l~d~~k~~yHC~~CgiCR~g~gl~~~~fHC~~C~~C~~~~ 1100 (1235)
+......||..|+.+... ..+||..||.|-.+- -.||.=-|.|+...
T Consensus 43 ~~~~~~~~C~~C~~~kp~-Rs~HC~~C~~CV~~~-----DHHC~w~~~cIG~~ 89 (174)
T PF01529_consen 43 DENGELKYCSTCKIIKPP-RSHHCRVCNRCVLRF-----DHHCPWLGNCIGRR 89 (174)
T ss_pred ccCCCCEECcccCCcCCC-cceeccccccccccc-----cccchhhccccccc
Confidence 456778899999999766 489999999999874 47999999998765
No 136
>PRK00808 hypothetical protein; Provisional
Probab=63.74 E-value=23 Score=36.95 Aligned_cols=95 Identities=19% Similarity=0.193 Sum_probs=56.1
Q ss_pred hhHHhHHHHHHHHHHHHHHHHHHhhcCCCCCcHHHHHHHHHHHHHHHHHHHHhHHHHHHHH----HHHHHhhCCH-----
Q 000895 361 SFAQEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQV----LPLARRHFSP----- 431 (1235)
Q Consensus 361 sme~EH~~ie~l~e~l~~ll~~l~~~~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qv----fPLl~~~fS~----- 431 (1235)
.+..+|++.-.+++.|..++.. +. ...+...+..|..-...||..||.-. +|-+..|--.
T Consensus 16 ~ID~qH~~L~~lin~l~~a~~~----~~-------~~~i~~~l~~L~~y~~~HF~~EE~lM~~~~Yp~~~~H~~~H~~fl 84 (150)
T PRK00808 16 VIDQQHKRIVDYINHLHDAQDS----PD-------RLAVAEVIDELIDYTLSHFAFEESLMEEAGYPFLVPHKRVHELFI 84 (150)
T ss_pred HHHHHHHHHHHHHHHHHHHHHc----Cc-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHH
Confidence 5667888777777776655421 11 24577778899999999999999753 4544443221
Q ss_pred HHHHHHHHhHhh--cCCHHHHHHHHhhhcCCCCHHHH
Q 000895 432 KRQRELLYQSLC--VMPLKLIECVLPWLVGSLSEEEA 466 (1235)
Q Consensus 432 eEq~~L~~~~l~--smPl~~l~~vLpWl~~~Ls~~E~ 466 (1235)
++..++..++.. .+...++..+..||+.++....+
T Consensus 85 ~~l~~l~~~~~~g~~~~~~l~~~L~~WL~~HI~~~D~ 121 (150)
T PRK00808 85 KRVEEYRERFQAGEDVADELHGMLSRWLFNHIRNDDA 121 (150)
T ss_pred HHHHHHHHHHHccchHHHHHHHHHHHHHHHHHHHHhH
Confidence 222223222211 12334555677788888754443
No 137
>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=62.06 E-value=3.5 Score=46.48 Aligned_cols=50 Identities=28% Similarity=0.824 Sum_probs=36.0
Q ss_pred CCcccCccccccc-CCCCCccccccccccccccccccCCCCCCCcCCCCCccceEecccccC
Q 000895 1001 GKLFTCRFCHDKV-SDHSMDRKATTEMMCMRCLKVQPVGPVCTTLSCSGLSMAKYYCGICKF 1061 (1235)
Q Consensus 1001 ~~~y~Cr~CHde~-~~H~~~r~~~~~v~C~~C~~~q~~~~~C~~~~C~~~~~a~y~C~iC~l 1061 (1235)
|+.|.|-+|++-. +|-.|.-.+ .|+....-+-.|.+ | + .+|.|.|-.||.
T Consensus 140 Grif~CsfC~~flCEDDQFEHQA-------sCQvLe~E~~KC~S--C-N-rlGq~sCLRCK~ 190 (314)
T PF06524_consen 140 GRIFKCSFCDNFLCEDDQFEHQA-------SCQVLESETFKCQS--C-N-RLGQYSCLRCKI 190 (314)
T ss_pred CeEEEeecCCCeeeccchhhhhh-------hhhhhhcccccccc--c-c-cccchhhhheee
Confidence 6799999999873 555555332 36666666777876 6 3 689999999985
No 138
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=61.85 E-value=5 Score=40.52 Aligned_cols=35 Identities=31% Similarity=0.460 Sum_probs=27.8
Q ss_pred cCCcEeccCCCCCCCCCceeeeccCCCCCCCcccccc
Q 000895 1186 RCQEILCNDCDKKGSAPFHWLYHKCGFCGSYNTRVIK 1222 (1235)
Q Consensus 1186 ~~~~i~CnDC~~~s~~~~h~lg~kC~~C~SYNT~~~~ 1222 (1235)
..+.+.|-||+......-|.++ ||.|||-|.+++.
T Consensus 67 ~p~~~~C~~C~~~~~~e~~~~~--CP~C~s~~~~i~~ 101 (115)
T COG0375 67 EPAECWCLDCGQEVELEELDYR--CPKCGSINLRIIG 101 (115)
T ss_pred eccEEEeccCCCeecchhheeE--CCCCCCCceEEec
Confidence 3467899999887766666544 9999999998863
No 139
>KOG2068 consensus MOT2 transcription factor [Transcription]
Probab=60.08 E-value=6.5 Score=46.03 Aligned_cols=52 Identities=25% Similarity=0.545 Sum_probs=40.4
Q ss_pred CCCCCccccccccccCCCcceecCCCCccChhhHHhhhhCCCCCCCCCcCcC
Q 000895 1110 GLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1161 (1235)
Q Consensus 1110 ~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrksv~ 1161 (1235)
+-...||||.+++...+....--|||+-++..|...-...+.+||.||+...
T Consensus 247 ~v~~s~p~~~~~~~~~d~~~lP~~~~~~~~l~~~~t~~~~~~~~~~~rk~~~ 298 (327)
T KOG2068|consen 247 SVPPSCPICYEDLDLTDSNFLPCPCGFRLCLFCHKTISDGDGRCPGCRKPYE 298 (327)
T ss_pred ccCCCCCCCCCcccccccccccccccccchhhhhhcccccCCCCCccCCccc
Confidence 4457899999997554444444578999999999888888999999997754
No 140
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=58.12 E-value=5.3 Score=42.25 Aligned_cols=31 Identities=32% Similarity=0.562 Sum_probs=24.9
Q ss_pred CCCCCCccccccccccCCCcceecCCCCccCh
Q 000895 1109 KGLETNCPICCDFLFTSSATVRALPCGHFMHS 1140 (1235)
Q Consensus 1109 ~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~ 1140 (1235)
+....+|.||||+|- .++.+..|||-=.||.
T Consensus 174 ~ddkGECvICLEdL~-~GdtIARLPCLCIYHK 204 (205)
T KOG0801|consen 174 KDDKGECVICLEDLE-AGDTIARLPCLCIYHK 204 (205)
T ss_pred cccCCcEEEEhhhcc-CCCceeccceEEEeec
Confidence 345688999999965 4567999999988886
No 141
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=57.44 E-value=9 Score=43.86 Aligned_cols=78 Identities=26% Similarity=0.548 Sum_probs=45.6
Q ss_pred cccccCCcccccc-cc-----cccccccCCCCCCCccccccccccCCCcceecCCCCccChhhHHhhh-----hC-----
Q 000895 1086 DFFHCMTCNCCLA-KK-----LVDHKCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYT-----CS----- 1149 (1235)
Q Consensus 1086 ~~fHC~~C~~C~~-~~-----l~~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl-----~~----- 1149 (1235)
.-|+|..|+-=|. +- +.+|. ....|+||.-. |. ..|| ++
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 4677777776552 21 24554 45679999766 54 1354 22
Q ss_pred CCCCCCCCcCcCchhhhhhhHHHHHhhcCCChhhhccCCcEeccCCCCCC
Q 000895 1150 HYICPICSKSLGDMAVYFGMLDALLASEQLPEEYRDRCQEILCNDCDKKG 1199 (1235)
Q Consensus 1150 ~~~CPiCrksv~dm~~~~~~lD~~i~~~pmP~ey~~~~~~i~CnDC~~~s 1199 (1235)
-+.||.|+|.+.|.+. |.+-++- -.+.+ ...|--|++.+
T Consensus 215 PF~C~hC~kAFADRSN----LRAHmQT------HS~~K-~~qC~~C~KsF 253 (279)
T KOG2462|consen 215 PFSCPHCGKAFADRSN----LRAHMQT------HSDVK-KHQCPRCGKSF 253 (279)
T ss_pred CccCCcccchhcchHH----HHHHHHh------hcCCc-cccCcchhhHH
Confidence 2889999999998763 3222211 12223 45677787653
No 142
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=56.84 E-value=6.6 Score=45.03 Aligned_cols=43 Identities=30% Similarity=0.772 Sum_probs=34.5
Q ss_pred CCccccccccccCCCcceecCCCCccChhhHHhhh-hCCCCCCCCCc
Q 000895 1113 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYT-CSHYICPICSK 1158 (1235)
Q Consensus 1113 ~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl-~~~~~CPiCrk 1158 (1235)
..||.|..-+. .+++.--|||.|..+||..-| .....||.|.+
T Consensus 275 LkCplc~~Llr---np~kT~cC~~~fc~eci~~al~dsDf~CpnC~r 318 (427)
T COG5222 275 LKCPLCHCLLR---NPMKTPCCGHTFCDECIGTALLDSDFKCPNCSR 318 (427)
T ss_pred ccCcchhhhhh---CcccCccccchHHHHHHhhhhhhccccCCCccc
Confidence 67999986543 456666789999999999764 66799999987
No 143
>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=56.28 E-value=8 Score=48.17 Aligned_cols=45 Identities=22% Similarity=0.583 Sum_probs=39.8
Q ss_pred ccccccCCcccCcccccccCCCCCccccccccccccccccccCCCCCCC
Q 000895 995 LRAACCGKLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVGPVCTT 1043 (1235)
Q Consensus 995 l~~~cC~~~y~Cr~CHde~~~H~~~r~~~~~v~C~~C~~~q~~~~~C~~ 1043 (1235)
+.|.-||....|..|.-...-|.- ...+.|-.|+..+++...|-+
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 789999999999999888777743 448999999999999999987
No 144
>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=55.68 E-value=8.1 Score=47.93 Aligned_cols=13 Identities=38% Similarity=0.994 Sum_probs=6.9
Q ss_pred CccceEecccccC
Q 000895 1049 LSMAKYYCGICKF 1061 (1235)
Q Consensus 1049 ~~~a~y~C~iC~l 1061 (1235)
.+.-.|||+.|-+
T Consensus 22 ~Ei~~~yCp~CL~ 34 (483)
T PF05502_consen 22 EEIDSYYCPNCLF 34 (483)
T ss_pred cccceeECccccc
Confidence 4455555555543
No 145
>PHA03096 p28-like protein; Provisional
Probab=54.69 E-value=6 Score=45.81 Aligned_cols=46 Identities=15% Similarity=0.220 Sum_probs=30.4
Q ss_pred CCccccccccccCC---Ccceec-CCCCccChhhHHhhhhC---CCCCCCCCc
Q 000895 1113 TNCPICCDFLFTSS---ATVRAL-PCGHFMHSDCFQAYTCS---HYICPICSK 1158 (1235)
Q Consensus 1113 ~~CpICle~lf~s~---~~v~~L-pCgH~fH~~Ci~~wl~~---~~~CPiCrk 1158 (1235)
-.|.||+|...... ..-..| .|.|.|...|+..|... .-+||.|+.
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~ 231 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRR 231 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCccccc
Confidence 46888888765431 111234 79999999999999642 345666554
No 146
>PF14357 DUF4404: Domain of unknown function (DUF4404)
Probab=54.37 E-value=87 Score=30.11 Aligned_cols=82 Identities=13% Similarity=0.095 Sum_probs=63.6
Q ss_pred HHHHHHHHHHHHHhhccCCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHHHhhhhHHHHHHhhhhhHHHHHHHHH
Q 000895 54 IKSELDVLHRAAMAFATNLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIRVKNIARTYSLEHEGESVLFDQLF 133 (1235)
Q Consensus 54 lR~eL~~l~~~~~~~~~~~gd~~~~~~l~~r~~fL~~~~~~H~~aEDevI~PaLd~Rv~~v~~~~~~EH~~~~~lf~~l~ 133 (1235)
||..|..|+.-+...++ -|......|..=-+.+...+.. ..|...--+.|..|+...+.+|+.+|=.....+..|-
T Consensus 2 L~~~L~~L~~eL~~~~~--ld~~~~~~L~~l~~dIe~~L~~--~~~~~~~~~~l~d~l~~av~~FE~~HP~l~~~lr~i~ 77 (85)
T PF14357_consen 2 LQELLEKLHQELEQNPP--LDEETRAELSSLDDDIEAQLAE--EDEAEAEDESLVDRLNEAVERFEASHPKLAGILRNIM 77 (85)
T ss_pred HHHHHHHHHHHHhcCCC--CCHHHHHHHHHHHHHHHHHHhc--CCcccccchhHHHHHHHHHHHHHHhCCcHHHHHHHHH
Confidence 67888889988888777 5666666655555555655554 5677788899999999999999999999998888887
Q ss_pred HHHHhh
Q 000895 134 ELLNSS 139 (1235)
Q Consensus 134 ~~l~~~ 139 (1235)
..|..+
T Consensus 78 ~sLa~M 83 (85)
T PF14357_consen 78 DSLANM 83 (85)
T ss_pred HHHHHC
Confidence 776543
No 147
>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=54.31 E-value=5.5 Score=34.36 Aligned_cols=41 Identities=32% Similarity=0.835 Sum_probs=20.2
Q ss_pred CCccccccccccCCCcceecCCCCccChhhHHh--hhh-----CCCCCCCCCcC
Q 000895 1113 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQA--YTC-----SHYICPICSKS 1159 (1235)
Q Consensus 1113 ~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~--wl~-----~~~~CPiCrks 1159 (1235)
..|||....|. .+++...|.|. +|++- |+. ....||+|+++
T Consensus 3 L~CPls~~~i~---~P~Rg~~C~H~---~CFDl~~fl~~~~~~~~W~CPiC~~~ 50 (50)
T PF02891_consen 3 LRCPLSFQRIR---IPVRGKNCKHL---QCFDLESFLESNQRTPKWKCPICNKP 50 (50)
T ss_dssp SB-TTTSSB-S---SEEEETT--SS-----EEHHHHHHHHHHS---B-TTT---
T ss_pred eeCCCCCCEEE---eCccCCcCccc---ceECHHHHHHHhhccCCeECcCCcCc
Confidence 46999887753 37888888866 57754 553 24789999874
No 148
>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=53.41 E-value=9.4 Score=30.11 Aligned_cols=24 Identities=38% Similarity=1.089 Sum_probs=19.0
Q ss_pred eEecccccCc-CCCCccccCCCCCc
Q 000895 1053 KYYCGICKFF-DDERVVYHCPFCNL 1076 (1235)
Q Consensus 1053 ~y~C~iC~l~-d~~k~~yHC~~Cgi 1076 (1235)
.|-|.+|.+. |.++.++.||.||.
T Consensus 1 ~~~C~~CGy~y~~~~~~~~CP~Cg~ 25 (33)
T cd00350 1 KYVCPVCGYIYDGEEAPWVCPVCGA 25 (33)
T ss_pred CEECCCCCCEECCCcCCCcCcCCCC
Confidence 4788999886 55578999999984
No 149
>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]
Probab=53.26 E-value=5.2 Score=51.18 Aligned_cols=88 Identities=13% Similarity=0.053 Sum_probs=61.1
Q ss_pred HHHHHHHHhHHHHHH-----HHHHHHHhhCCHHHHHHHHHhHhhcCCHHHHHHHHhhhcCCCCHHHHHHHHHHhhhhCCC
Q 000895 405 LIMASIQKHFRNEEV-----QVLPLARRHFSPKRQRELLYQSLCVMPLKLIECVLPWLVGSLSEEEARSFLQNIYMAAPA 479 (1235)
Q Consensus 405 ~L~~~L~~Hf~~EE~-----qvfPLl~~~fS~eEq~~L~~~~l~smPl~~l~~vLpWl~~~Ls~~E~~~~L~~l~~~aP~ 479 (1235)
.+-...-.|+..|++ -+.|.+=.. +.+||+..+.+|.-.--+..+.-+||=.-+.|.|.-...+|...=. |-
T Consensus 393 kv~~~yI~HLl~~~~y~~Aas~~p~m~gn-~~~eWe~~V~~f~e~~~l~~Ia~~lPt~~~rL~p~vYemvLve~L~--~~ 469 (846)
T KOG2066|consen 393 KVGKTYIDHLLFEGKYDEAASLCPKMLGN-NAAEWELWVFKFAELDQLTDIAPYLPTGPPRLKPLVYEMVLVEFLA--SD 469 (846)
T ss_pred HHHHHHHHHHHhcchHHHHHhhhHHHhcc-hHHHHHHHHHHhccccccchhhccCCCCCcccCchHHHHHHHHHHH--HH
Confidence 334445666654443 344444433 4578999999988777777888889988999999999999887443 54
Q ss_pred CchHHHHHHHHHhhcCC
Q 000895 480 SDSALITLFAGWACKGH 496 (1235)
Q Consensus 480 ~~~~~~~l~~~w~~~~~ 496 (1235)
... |-.+++.|-+.-|
T Consensus 470 ~~~-F~e~i~~Wp~~Ly 485 (846)
T KOG2066|consen 470 VKG-FLELIKEWPGHLY 485 (846)
T ss_pred HHH-HHHHHHhCChhhh
Confidence 444 8888999954444
No 150
>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=52.71 E-value=71 Score=31.74 Aligned_cols=51 Identities=20% Similarity=0.232 Sum_probs=31.8
Q ss_pred hhHHhHHHHHHHHHHHHHHHHHHhhcCCCCCcHHHHHHHHHHHHHHHHHHHHhHHHHHHHH----HHHHHhh
Q 000895 361 SFAQEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQV----LPLARRH 428 (1235)
Q Consensus 361 sme~EH~~ie~l~e~l~~ll~~l~~~~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qv----fPLl~~~ 428 (1235)
.+..+|++.-.+++.|..++.. ...+..|..-...||..||.-. +|-+..|
T Consensus 14 ~ID~qH~~L~~l~n~l~~a~~~-----------------~~~l~~L~~y~~~HF~~EE~~M~~~~yp~~~~H 68 (113)
T cd00522 14 VIDDEHKTLFNGINDLSEANNR-----------------ADNLKELVDYTVKHFKDEEALMEAAGYPDYEEH 68 (113)
T ss_pred HHHHHHHHHHHHHHHHHHHHhH-----------------HHHHHHHHHHHHHHHHHHHHHHHHcCCCCHHHH
Confidence 4456666655555555544422 2356677778899999999764 4555544
No 151
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=51.05 E-value=4 Score=54.57 Aligned_cols=50 Identities=30% Similarity=0.582 Sum_probs=40.7
Q ss_pred CCCccccccccccCCCcceecCCCCccChhhHHhhhhCCCCCCCCCcCcCchh
Q 000895 1112 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGDMA 1164 (1235)
Q Consensus 1112 ~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrksv~dm~ 1164 (1235)
...|+||++-+..- -.+.-|||.+...|+..|+..+..||+|....++..
T Consensus 1153 ~~~c~ic~dil~~~---~~I~~cgh~~c~~c~~~~l~~~s~~~~~ksi~~dfg 1202 (1394)
T KOG0298|consen 1153 HFVCEICLDILRNQ---GGIAGCGHEPCCRCDELWLYASSRCPICKSIKGDFG 1202 (1394)
T ss_pred ccchHHHHHHHHhc---CCeeeechhHhhhHHHHHHHHhccCcchhhhhhhhc
Confidence 34899999986532 245689999999999999999999999997766643
No 152
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=50.87 E-value=7.8 Score=49.55 Aligned_cols=50 Identities=20% Similarity=0.469 Sum_probs=35.5
Q ss_pred CCCCCccccccccccCCCcceecCCC-----CccChhhHHhhhhC--CCCCCCCCcCcC
Q 000895 1110 GLETNCPICCDFLFTSSATVRALPCG-----HFMHSDCFQAYTCS--HYICPICSKSLG 1161 (1235)
Q Consensus 1110 ~~~~~CpICle~lf~s~~~v~~LpCg-----H~fH~~Ci~~wl~~--~~~CPiCrksv~ 1161 (1235)
.....|-||..+ ...++ .-.-||. -++|.+|+-+|+.. ..+|-+|...+.
T Consensus 10 ~d~~~CRICr~e-~~~d~-pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~ 66 (1175)
T COG5183 10 EDKRSCRICRTE-DIRDD-PLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYK 66 (1175)
T ss_pred ccchhceeecCC-CCCCC-cCcccccccchhHHHHHHHHHHHHhcCCCcceeeecceee
Confidence 345789999866 33333 2334663 78999999999965 477999998764
No 153
>PF14353 CpXC: CpXC protein
Probab=49.73 E-value=4.2 Score=41.15 Aligned_cols=56 Identities=20% Similarity=0.344 Sum_probs=31.4
Q ss_pred CCCCCCCcCcCchhhhhhhHHHHHhhcCCChhhhccCCcEeccCCCCCCCCCceeeec
Q 000895 1151 YICPICSKSLGDMAVYFGMLDALLASEQLPEEYRDRCQEILCNDCDKKGSAPFHWLYH 1208 (1235)
Q Consensus 1151 ~~CPiCrksv~dm~~~~~~lD~~i~~~pmP~ey~~~~~~i~CnDC~~~s~~~~h~lg~ 1208 (1235)
.+||.|++...- ..|..+|......-...-..+..-.+.|..||.+..+.|=++||
T Consensus 2 itCP~C~~~~~~--~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~~p~lY~ 57 (128)
T PF14353_consen 2 ITCPHCGHEFEF--EVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLEYPLLYH 57 (128)
T ss_pred cCCCCCCCeeEE--EEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecCCCEEEE
Confidence 589999987641 12333322111000111123444578899999998877777765
No 154
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=49.55 E-value=14 Score=46.05 Aligned_cols=188 Identities=23% Similarity=0.466 Sum_probs=98.0
Q ss_pred cccccccCCcccCcccccccCCCCCccccccccccccccccccCCCCCCCcCCCCCccceEec-ccccCcCCC------C
Q 000895 994 KLRAACCGKLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVGPVCTTLSCSGLSMAKYYC-GICKFFDDE------R 1066 (1235)
Q Consensus 994 ~l~~~cC~~~y~Cr~CHde~~~H~~~r~~~~~v~C~~C~~~q~~~~~C~~~~C~~~~~a~y~C-~iC~l~d~~------k 1066 (1235)
.++|.-|++ .|-.++-.-.-.-+-+.-..|-.|+.--..+..|.. | +. +||| ..|.-|-.. -
T Consensus 16 ~i~c~~c~~-----kc~gevlrv~d~~fhi~cf~c~~cg~~la~~gff~k--~-~~---~~ygt~~c~~~~~gevvsa~g 84 (670)
T KOG1044|consen 16 GIKCDKCRK-----KCSGEVLRVNDNHFHINCFQCKKCGRNLAEGGFFTK--P-EN---RLYGTDDCRAFVEGEVVSTLG 84 (670)
T ss_pred ceehhhhCC-----ccccceeEeeccccceeeeeccccCCCcccccceec--c-cc---eeecccchhhhccceeEeccc
Confidence 466666655 454442111011122335556666665555566665 2 32 6776 445444221 5
Q ss_pred cccc--CCCCCccccCCCCCcc------ccccCCcccccccccccccccCCCCCCCccccccccccCCCcceecCCCCcc
Q 000895 1067 VVYH--CPFCNLCRVGRGLGVD------FFHCMTCNCCLAKKLVDHKCREKGLETNCPICCDFLFTSSATVRALPCGHFM 1138 (1235)
Q Consensus 1067 ~~yH--C~~CgiCR~g~gl~~~------~fHC~~C~~C~~~~l~~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCgH~f 1138 (1235)
+.|| |-.|-+|+..-.-|.. +--|.+|-.=+++. =.+...-.+|.-|.+.+... +....| +
T Consensus 85 ktyh~~cf~cs~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~-----p~~~~~ps~cagc~~~lk~g-q~llal--d--- 153 (670)
T KOG1044|consen 85 KTYHPKCFSCSTCKSPFKSGDKVTFSGKECLCQTCSQPMPVS-----PAESYGPSTCAGCGEELKNG-QALLAL--D--- 153 (670)
T ss_pred ceeccccceecccCCCCCCCCeeeecchhhhhhhhcCcccCC-----cccccCCccccchhhhhhcc-ceeeee--c---
Confidence 6677 6667777654322221 22233333322222 11223457899999996654 434444 2
Q ss_pred ChhhHHhhhhCCCCCCCCCcCcCchhhhhhhHHHHHhhcCCC---hhhhccCCcEeccCCCCC--------CCCCceeee
Q 000895 1139 HSDCFQAYTCSHYICPICSKSLGDMAVYFGMLDALLASEQLP---EEYRDRCQEILCNDCDKK--------GSAPFHWLY 1207 (1235)
Q Consensus 1139 H~~Ci~~wl~~~~~CPiCrksv~dm~~~~~~lD~~i~~~pmP---~ey~~~~~~i~CnDC~~~--------s~~~~h~lg 1207 (1235)
++|--...+|--|.+.+.- .| |...-.| ..|.... -|.|..|.+- +.-.||--+
T Consensus 154 -----~qwhv~cfkc~~c~~vL~g--ey-------~skdg~pyce~dy~~~f-gvkc~~c~~fisgkvLqag~kh~HPtC 218 (670)
T KOG1044|consen 154 -----KQWHVSCFKCKSCSAVLNG--EY-------MSKDGVPYCEKDYQAKF-GVKCEECEKFISGKVLQAGDKHFHPTC 218 (670)
T ss_pred -----cceeeeeeehhhhcccccc--ee-------eccCCCcchhhhhhhhc-CeehHHhhhhhhhhhhhccCcccCcch
Confidence 3444344578888877642 11 1111222 2355554 6789999853 335688878
Q ss_pred ccCCCCCCCcc
Q 000895 1208 HKCGFCGSYNT 1218 (1235)
Q Consensus 1208 ~kC~~C~SYNT 1218 (1235)
-+|..||+-=|
T Consensus 219 ARCsRCgqmF~ 229 (670)
T KOG1044|consen 219 ARCSRCGQMFG 229 (670)
T ss_pred hhhhhhccccc
Confidence 88888887544
No 155
>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=48.97 E-value=9.8 Score=38.11 Aligned_cols=32 Identities=25% Similarity=0.517 Sum_probs=23.8
Q ss_pred ccccccccCCcccCcccccccCCCCCccccccccccccccccccCC
Q 000895 993 CKLRAACCGKLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVG 1038 (1235)
Q Consensus 993 c~l~~~cC~~~y~Cr~CHde~~~H~~~r~~~~~v~C~~C~~~q~~~ 1038 (1235)
-|-.||-||+-| .+... ..++|.+|+++|++.
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 466789998744 23332 579999999999987
No 156
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=48.83 E-value=7.6 Score=49.96 Aligned_cols=43 Identities=30% Similarity=0.745 Sum_probs=34.5
Q ss_pred CCccccccccccCCCcceecCCCCccChhhHHhhhhC--CCCCCCCCcCc
Q 000895 1113 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS--HYICPICSKSL 1160 (1235)
Q Consensus 1113 ~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~--~~~CPiCrksv 1160 (1235)
..|+||++ .+.....+|||.|...|+.+.+.. ...||+||..+
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 78999998 234677899999999999997643 35699999654
No 157
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=48.48 E-value=12 Score=33.64 Aligned_cols=45 Identities=29% Similarity=0.808 Sum_probs=28.1
Q ss_pred ccccccccccccCC-----CCCCCcCCCCCccceEecccccCcCCCCccccCCCCCc
Q 000895 1025 EMMCMRCLKVQPVG-----PVCTTLSCSGLSMAKYYCGICKFFDDERVVYHCPFCNL 1076 (1235)
Q Consensus 1025 ~v~C~~C~~~q~~~-----~~C~~~~C~~~~~a~y~C~iC~l~d~~k~~yHC~~Cgi 1076 (1235)
...|..|+.+-.+. -.|-| | |. .-=|-|..|+-..+ .|.|++||+
T Consensus 9 ~~~CtSCg~~i~p~e~~v~F~CPn--C-Ge-~~I~Rc~~CRk~g~---~Y~Cp~CGF 58 (61)
T COG2888 9 PPVCTSCGREIAPGETAVKFPCPN--C-GE-VEIYRCAKCRKLGN---PYRCPKCGF 58 (61)
T ss_pred CceeccCCCEeccCCceeEeeCCC--C-Cc-eeeehhhhHHHcCC---ceECCCcCc
Confidence 45788888776443 24665 4 52 23466777776644 688888875
No 158
>PRK01917 cation-binding hemerythrin HHE family protein; Provisional
Probab=48.39 E-value=41 Score=34.73 Aligned_cols=68 Identities=12% Similarity=0.160 Sum_probs=38.1
Q ss_pred HHHHHHHHHHHHHHHhHHHHHHHH----HHHHHhhCCH-----HHHHHHHHhHhh----cCCHHHHHHHHhhhcCCCCHH
Q 000895 398 KLCSQADLIMASIQKHFRNEEVQV----LPLARRHFSP-----KRQRELLYQSLC----VMPLKLIECVLPWLVGSLSEE 464 (1235)
Q Consensus 398 eLa~~le~L~~~L~~Hf~~EE~qv----fPLl~~~fS~-----eEq~~L~~~~l~----smPl~~l~~vLpWl~~~Ls~~ 464 (1235)
.+...++.|..-...||..||.-. +|-+..|--. ++..++..+... .+...++..+..||+.++.-.
T Consensus 38 ~i~~~l~~L~~y~~~HF~~EE~lM~~~~YP~~~~H~~eH~~fl~~v~~l~~~~~~~g~~~~~~~l~~~L~~Wl~~HI~~~ 117 (139)
T PRK01917 38 DFLQALDAWIDHTRHHFAQEERWMEATKFGPRHCHRAEHDEVLAVAADVREKVARDGDFELGRRLVAELPEWFDQHVRTM 117 (139)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 356778888999999999999653 3434333211 122222222221 233445556667888877443
Q ss_pred H
Q 000895 465 E 465 (1235)
Q Consensus 465 E 465 (1235)
.
T Consensus 118 D 118 (139)
T PRK01917 118 D 118 (139)
T ss_pred H
Confidence 3
No 159
>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=48.34 E-value=13 Score=37.25 Aligned_cols=27 Identities=33% Similarity=0.822 Sum_probs=20.9
Q ss_pred CCCCCCCcCCCCCccceEecccccCcCCCCccccCCCCCc
Q 000895 1037 VGPVCTTLSCSGLSMAKYYCGICKFFDDERVVYHCPFCNL 1076 (1235)
Q Consensus 1037 ~~~~C~~~~C~~~~~a~y~C~iC~l~d~~k~~yHC~~Cgi 1076 (1235)
...+|-+ | |. ||||-+|.+-.||+||.
T Consensus 8 tKR~Cp~--C-G~----------kFYDLnk~PivCP~CG~ 34 (108)
T PF09538_consen 8 TKRTCPS--C-GA----------KFYDLNKDPIVCPKCGT 34 (108)
T ss_pred CcccCCC--C-cc----------hhccCCCCCccCCCCCC
Confidence 3457866 5 65 78899999999999984
No 160
>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=48.16 E-value=9.5 Score=32.60 Aligned_cols=31 Identities=23% Similarity=0.432 Sum_probs=21.0
Q ss_pred cEeccCCCCCCCCCcee---eeccCCCCCCCccc
Q 000895 1189 EILCNDCDKKGSAPFHW---LYHKCGFCGSYNTR 1219 (1235)
Q Consensus 1189 ~i~CnDC~~~s~~~~h~---lg~kC~~C~SYNT~ 1219 (1235)
.+.|++||....+-..+ -...|+.||+-+.+
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~ 38 (52)
T TIGR02605 5 EYRCTACGHRFEVLQKMSDDPLATCPECGGEKLR 38 (52)
T ss_pred EEEeCCCCCEeEEEEecCCCCCCCCCCCCCCcee
Confidence 46799999876643221 12379999998763
No 161
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=47.88 E-value=14 Score=47.85 Aligned_cols=54 Identities=24% Similarity=0.551 Sum_probs=43.3
Q ss_pred ccccccCCcccCcccccccCCCCCccccccccccccccccccCCCCCCCcCCCCCccceEe
Q 000895 995 LRAACCGKLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVGPVCTTLSCSGLSMAKYY 1055 (1235)
Q Consensus 995 l~~~cC~~~y~Cr~CHde~~~H~~~r~~~~~v~C~~C~~~q~~~~~C~~~~C~~~~~a~y~ 1055 (1235)
+.|.-||-.+.|++|=.-..=|.- +..+.|-+|+..+++-..|-+ | |...=+|+
T Consensus 436 l~C~~Cg~v~~Cp~Cd~~lt~H~~----~~~L~CH~Cg~~~~~p~~Cp~--C-gs~~L~~~ 489 (730)
T COG1198 436 LLCRDCGYIAECPNCDSPLTLHKA----TGQLRCHYCGYQEPIPQSCPE--C-GSEHLRAV 489 (730)
T ss_pred eecccCCCcccCCCCCcceEEecC----CCeeEeCCCCCCCCCCCCCCC--C-CCCeeEEe
Confidence 899999999999999666555533 369999999999999999987 6 65544444
No 162
>KOG3850 consensus Predicted membrane protein [Function unknown]
Probab=47.38 E-value=5.5e+02 Score=31.35 Aligned_cols=129 Identities=19% Similarity=0.247 Sum_probs=74.5
Q ss_pred HHHHHHHHHHHHHHHHHhcccCCcccH-HHHHHHHHHHHHHHHhhhhccccchhhhhhhHh--hhHHhHHHHHHHHHHHH
Q 000895 301 HNAIKRELNDIAEAARKIQLSGDFSDL-SAFNKRLQFIAEVCIFHSIAEDKVIFPAVDVEL--SFAQEHAEEEIQFDKLR 377 (1235)
Q Consensus 301 HkALRrEL~~L~~~a~~i~~~gd~~~L-~~L~~r~~fl~~vl~~Hs~aEDevlFPaL~~r~--sme~EH~~ie~l~e~l~ 377 (1235)
=+||..||++|.+.-..++ .+..+| .++..-+.|+.+.|. |+.+-.-.|++.+ ..+....+|..+=-++.
T Consensus 262 l~aileeL~eIk~~q~~Le--esye~Lke~~krdy~fi~etLQ-----EERyR~erLEEqLNdlteLqQnEi~nLKqEla 334 (455)
T KOG3850|consen 262 LDAILEELREIKETQALLE--ESYERLKEQIKRDYKFIAETLQ-----EERYRYERLEEQLNDLTELQQNEIANLKQELA 334 (455)
T ss_pred HHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHH
Confidence 4677788888888777764 334456 666777778887776 7766666666555 44444444433322222
Q ss_pred HHHHHHhhcCCCCCcHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH---HHHHhhCCHHHHHHHHHhHhhcC
Q 000895 378 CLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVL---PLARRHFSPKRQRELLYQSLCVM 445 (1235)
Q Consensus 378 ~ll~~l~~~~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qvf---PLl~~~fS~eEq~~L~~~~l~sm 445 (1235)
..-..++= .-| +=+..+.+.+++...|+.+=|.+.- -+--++++++-|..|+.+++-.+
T Consensus 335 smeervaY--------Qsy-ERaRdIqEalEscqtrisKlEl~qq~qqv~Q~e~~~na~a~~llgk~iNii 396 (455)
T KOG3850|consen 335 SMEERVAY--------QSY-ERARDIQEALESCQTRISKLELQQQQQQVVQLEGLENAVARRLLGKFINII 396 (455)
T ss_pred HHHHHHHH--------HHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccHHHHHHHHHHHH
Confidence 11111110 001 1234555666777777777665544 22345677778888888877643
No 163
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=47.24 E-value=16 Score=49.33 Aligned_cols=24 Identities=25% Similarity=0.404 Sum_probs=16.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhc
Q 000895 296 EIMLWHNAIKRELNDIAEAARKIQ 319 (1235)
Q Consensus 296 ~l~~~HkALRrEL~~L~~~a~~i~ 319 (1235)
.+..-++-|.+++.++.+.|.+.+
T Consensus 6 ~~~~Yf~~l~~~~~~~~~iA~~ar 29 (1337)
T PRK14714 6 EMERYFERLERELDKAYEVAEAAR 29 (1337)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344567778888888777777664
No 164
>PRK05580 primosome assembly protein PriA; Validated
Probab=46.21 E-value=14 Score=47.84 Aligned_cols=46 Identities=22% Similarity=0.548 Sum_probs=40.2
Q ss_pred cccccccCCcccCcccccccCCCCCccccccccccccccccccCCCCCCC
Q 000895 994 KLRAACCGKLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVGPVCTT 1043 (1235)
Q Consensus 994 ~l~~~cC~~~y~Cr~CHde~~~H~~~r~~~~~v~C~~C~~~q~~~~~C~~ 1043 (1235)
-+.|.-||....|..|.-...-|.. ...+.|-.|+..+++...|-+
T Consensus 381 ~~~C~~Cg~~~~C~~C~~~l~~h~~----~~~l~Ch~Cg~~~~~~~~Cp~ 426 (679)
T PRK05580 381 FLLCRDCGWVAECPHCDASLTLHRF----QRRLRCHHCGYQEPIPKACPE 426 (679)
T ss_pred ceEhhhCcCccCCCCCCCceeEECC----CCeEECCCCcCCCCCCCCCCC
Confidence 3889999999999999988777753 457999999999999999987
No 165
>PF12773 DZR: Double zinc ribbon
Probab=45.35 E-value=17 Score=30.71 Aligned_cols=22 Identities=27% Similarity=0.789 Sum_probs=12.6
Q ss_pred cccccccccC-CCCCCCcCCCCCccc
Q 000895 1028 CMRCLKVQPV-GPVCTTLSCSGLSMA 1052 (1235)
Q Consensus 1028 C~~C~~~q~~-~~~C~~~~C~~~~~a 1052 (1235)
|..|+++.+. +..|.+ | |..+.
T Consensus 1 Cp~Cg~~~~~~~~fC~~--C-G~~l~ 23 (50)
T PF12773_consen 1 CPHCGTPNPDDAKFCPH--C-GTPLP 23 (50)
T ss_pred CCCcCCcCCccccCChh--h-cCChh
Confidence 5566666554 356766 3 65544
No 166
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=45.24 E-value=13 Score=43.14 Aligned_cols=45 Identities=22% Similarity=0.631 Sum_probs=35.5
Q ss_pred CCccccccccccCCCcceecCCCCccChhhHHhhhhC---CCCCCCCCc
Q 000895 1113 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS---HYICPICSK 1158 (1235)
Q Consensus 1113 ~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~---~~~CPiCrk 1158 (1235)
-.|||=.|. -+...+...|.|||.+-..=++..-++ ..+||-|-.
T Consensus 337 FiCPVlKe~-~t~ENpP~ml~CgHVIskeal~~LS~nG~~~FKCPYCP~ 384 (396)
T COG5109 337 FICPVLKEL-CTDENPPVMLECGHVISKEALSVLSQNGVLSFKCPYCPE 384 (396)
T ss_pred eeccccHhh-hcccCCCeeeeccceeeHHHHHHHhhcCcEEeeCCCCCc
Confidence 457877765 566677888999999999999887654 488999963
No 167
>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=45.22 E-value=16 Score=42.81 Aligned_cols=23 Identities=26% Similarity=0.801 Sum_probs=13.9
Q ss_pred cEeccCCCCCCCCCceeeeccCCCCCC
Q 000895 1189 EILCNDCDKKGSAPFHWLYHKCGFCGS 1215 (1235)
Q Consensus 1189 ~i~CnDC~~~s~~~~h~lg~kC~~C~S 1215 (1235)
.-.|+-|+ ..+|+.-.||++||+
T Consensus 210 yL~CslC~----teW~~~R~~C~~Cg~ 232 (305)
T TIGR01562 210 YLSCSLCA----TEWHYVRVKCSHCEE 232 (305)
T ss_pred EEEcCCCC----CcccccCccCCCCCC
Confidence 45566666 356666666666664
No 168
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=44.91 E-value=15 Score=32.75 Aligned_cols=29 Identities=28% Similarity=0.651 Sum_probs=22.3
Q ss_pred CcEeccCCCCCCCCCceeeeccCCCCCCCccccc
Q 000895 1188 QEILCNDCDKKGSAPFHWLYHKCGFCGSYNTRVI 1221 (1235)
Q Consensus 1188 ~~i~CnDC~~~s~~~~h~lg~kC~~C~SYNT~~~ 1221 (1235)
..+.|-.||.. ...| +-|++||.||.+++
T Consensus 26 ~l~~C~~CG~~--~~~H---~vC~~CG~Y~gr~v 54 (57)
T PRK12286 26 GLVECPNCGEP--KLPH---RVCPSCGYYKGREV 54 (57)
T ss_pred cceECCCCCCc--cCCe---EECCCCCcCCCEEe
Confidence 45789999974 3345 46999999999885
No 169
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=44.62 E-value=9.3 Score=43.83 Aligned_cols=50 Identities=22% Similarity=0.543 Sum_probs=37.8
Q ss_pred CCCccccccccccCCCcceecCCC-----CccChhhHHhhhh--CCCCCCCCCcCcC
Q 000895 1112 ETNCPICCDFLFTSSATVRALPCG-----HFMHSDCFQAYTC--SHYICPICSKSLG 1161 (1235)
Q Consensus 1112 ~~~CpICle~lf~s~~~v~~LpCg-----H~fH~~Ci~~wl~--~~~~CPiCrksv~ 1161 (1235)
...|-||.++.+.........||. ++.|..|++.|.. .+.+|.+|.....
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 468999999865543323456773 8889999999986 5688999998654
No 170
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=44.29 E-value=9.9 Score=37.47 Aligned_cols=33 Identities=21% Similarity=0.637 Sum_probs=26.0
Q ss_pred CccccCCCCC-----ccccCCCCCccccccCCcccccc
Q 000895 1066 RVVYHCPFCN-----LCRVGRGLGVDFFHCMTCNCCLA 1098 (1235)
Q Consensus 1066 k~~yHC~~Cg-----iCR~g~gl~~~~fHC~~C~~C~~ 1098 (1235)
+..|-|+.|| +|-|-+++++-+-||..||.-..
T Consensus 20 ~k~FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e 57 (104)
T COG4888 20 PKTFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSFE 57 (104)
T ss_pred CceEecCccCCeeeeEEEEEecCceeEEEcccCcceEE
Confidence 4678899998 78888877777888888886543
No 171
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=43.05 E-value=8.6 Score=48.36 Aligned_cols=29 Identities=31% Similarity=0.595 Sum_probs=22.8
Q ss_pred Cccccccc----ccccccccCCcccCcccccccC
Q 000895 985 GCEHYKRN----CKLRAACCGKLFTCRFCHDKVS 1014 (1235)
Q Consensus 985 gC~HY~r~----c~l~~~cC~~~y~Cr~CHde~~ 1014 (1235)
||.|+--. ..-.|.-+|+|| |..||....
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 78887762 456788899987 999998854
No 172
>PRK04023 DNA polymerase II large subunit; Validated
Probab=42.87 E-value=21 Score=47.40 Aligned_cols=48 Identities=23% Similarity=0.386 Sum_probs=31.7
Q ss_pred ccccccccccccccCCCCCCCcCCCCCccceEecccccCcCCCCccccCCCCCc
Q 000895 1023 TTEMMCMRCLKVQPVGPVCTTLSCSGLSMAKYYCGICKFFDDERVVYHCPFCNL 1076 (1235)
Q Consensus 1023 ~~~v~C~~C~~~q~~~~~C~~~~C~~~~~a~y~C~iC~l~d~~k~~yHC~~Cgi 1076 (1235)
+..-.|..|+++. +...|.+ |....-.-|||+.|. ..-..|.|+.||.
T Consensus 624 Vg~RfCpsCG~~t-~~frCP~--CG~~Te~i~fCP~CG---~~~~~y~CPKCG~ 671 (1121)
T PRK04023 624 IGRRKCPSCGKET-FYRRCPF--CGTHTEPVYRCPRCG---IEVEEDECEKCGR 671 (1121)
T ss_pred ccCccCCCCCCcC-CcccCCC--CCCCCCcceeCcccc---CcCCCCcCCCCCC
Confidence 3455788898886 5578877 643445667888883 2233577888874
No 173
>PRK14873 primosome assembly protein PriA; Provisional
Probab=42.02 E-value=17 Score=46.92 Aligned_cols=44 Identities=25% Similarity=0.400 Sum_probs=36.9
Q ss_pred ccccccCCcccCcccccccCCCCCccccccccccccccccccCCCCCCC
Q 000895 995 LRAACCGKLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVGPVCTT 1043 (1235)
Q Consensus 995 l~~~cC~~~y~Cr~CHde~~~H~~~r~~~~~v~C~~C~~~q~~~~~C~~ 1043 (1235)
+.|.-||....|..|.--..=|. ....+.|-.|+..+ +...|-+
T Consensus 384 l~C~~Cg~~~~C~~C~~~L~~h~----~~~~l~Ch~CG~~~-~p~~Cp~ 427 (665)
T PRK14873 384 LACARCRTPARCRHCTGPLGLPS----AGGTPRCRWCGRAA-PDWRCPR 427 (665)
T ss_pred eEhhhCcCeeECCCCCCceeEec----CCCeeECCCCcCCC-cCccCCC
Confidence 89999999999999988877664 24578999999976 5788977
No 174
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=41.61 E-value=15 Score=30.87 Aligned_cols=30 Identities=20% Similarity=0.366 Sum_probs=19.7
Q ss_pred cEeccCCCCCCCCCceeeeccCCCCCCCcc
Q 000895 1189 EILCNDCDKKGSAPFHWLYHKCGFCGSYNT 1218 (1235)
Q Consensus 1189 ~i~CnDC~~~s~~~~h~lg~kC~~C~SYNT 1218 (1235)
.+.|.+||......-..-..+|+.||+.-.
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCGYRIL 32 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCCCeEE
Confidence 467999998653322222568999997543
No 175
>PRK00808 hypothetical protein; Provisional
Probab=41.39 E-value=4.4e+02 Score=27.55 Aligned_cols=110 Identities=16% Similarity=0.228 Sum_probs=71.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcccCCcccHHHHHHHHHHHHHHHHhhhhccccch----hhhhhhHhhhHHhHHHHHHH
Q 000895 297 IMLWHNAIKRELNDIAEAARKIQLSGDFSDLSAFNKRLQFIAEVCIFHSIAEDKVI----FPAVDVELSFAQEHAEEEIQ 372 (1235)
Q Consensus 297 l~~~HkALRrEL~~L~~~a~~i~~~gd~~~L~~L~~r~~fl~~vl~~Hs~aEDevl----FPaL~~r~sme~EH~~ie~l 372 (1235)
+=.-|+.|=.-++.|...+. .++ ...+..-+.+|.+....|=..|+.++ ||.++.+. .+++..
T Consensus 17 ID~qH~~L~~lin~l~~a~~----~~~---~~~i~~~l~~L~~y~~~HF~~EE~lM~~~~Yp~~~~H~------~~H~~f 83 (150)
T PRK00808 17 IDQQHKRIVDYINHLHDAQD----SPD---RLAVAEVIDELIDYTLSHFAFEESLMEEAGYPFLVPHK------RVHELF 83 (150)
T ss_pred HHHHHHHHHHHHHHHHHHHH----cCc---HHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHH------HHHHHH
Confidence 33467777666666665542 222 24566678888999999999898764 77776444 334444
Q ss_pred HHHHHHHHHHHhhcCCCCCcHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhh
Q 000895 373 FDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPLARRH 428 (1235)
Q Consensus 373 ~e~l~~ll~~l~~~~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qvfPLl~~~ 428 (1235)
++.+..+...... +. ... ...+.-|..-|.+|+..+-....+.+.+.
T Consensus 84 l~~l~~l~~~~~~-g~-----~~~---~~l~~~L~~WL~~HI~~~D~~~~~~l~~~ 130 (150)
T PRK00808 84 IKRVEEYRERFQA-GE-----DVA---DELHGMLSRWLFNHIRNDDAAYVDAVKAN 130 (150)
T ss_pred HHHHHHHHHHHHc-cc-----hHH---HHHHHHHHHHHHHHHHHHhHHHHHHHHHh
Confidence 5555555544432 21 122 23445678889999999999999998885
No 176
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=41.30 E-value=14 Score=46.69 Aligned_cols=57 Identities=21% Similarity=0.289 Sum_probs=26.6
Q ss_pred chhhhhhhHHHHHhhcCCChhhhccCCcEeccCCCCCCCCCceeeeccCCCCCCCcccccccc
Q 000895 1162 DMAVYFGMLDALLASEQLPEEYRDRCQEILCNDCDKKGSAPFHWLYHKCGFCGSYNTRVIKVE 1224 (1235)
Q Consensus 1162 dm~~~~~~lD~~i~~~pmP~ey~~~~~~i~CnDC~~~s~~~~h~lg~kC~~C~SYNT~~~~~~ 1224 (1235)
+.+.....++.......+|----+ ...-.|++||....- +-+|+.|||-|+.+++..
T Consensus 465 n~~al~~lv~~~~~~~~i~Y~~in-~~~~~C~~CG~~~~~-----~~~CP~CGs~~~~~~~Rv 521 (546)
T PF13597_consen 465 NPEALEKLVRYAMENTGIPYFTIN-PPIDICPDCGYIGGE-----GDKCPKCGSENIEVYSRV 521 (546)
T ss_dssp -HHHHHHHHHHHHH--H-SEEEEE---EEEETTT---S-------EEE-CCC----EEEEB-S
T ss_pred CHHHHHHHHHHHHHhCCCCeEEEe-cCcccccCCCcCCCC-----CCCCCCCCCcccceEEEe
Confidence 566667777777765666532112 234579999987653 448999999998776543
No 177
>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=41.16 E-value=17 Score=42.64 Aligned_cols=28 Identities=25% Similarity=0.593 Sum_probs=21.0
Q ss_pred CcceecCCCCccChhhHHhhhhCCCCCCCCCcC
Q 000895 1127 ATVRALPCGHFMHSDCFQAYTCSHYICPICSKS 1159 (1235)
Q Consensus 1127 ~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrks 1159 (1235)
+..+.|.|+ -|-.+|-....+||.|..+
T Consensus 206 ~G~RyL~Cs-----lC~teW~~~R~~C~~Cg~~ 233 (305)
T TIGR01562 206 TGLRYLSCS-----LCATEWHYVRVKCSHCEES 233 (305)
T ss_pred CCceEEEcC-----CCCCcccccCccCCCCCCC
Confidence 345666665 5777898788999999964
No 178
>PF14631 FancD2: Fanconi anaemia protein FancD2 nuclease; PDB: 3S4W_B.
Probab=40.23 E-value=5e+02 Score=37.02 Aligned_cols=99 Identities=20% Similarity=0.278 Sum_probs=58.8
Q ss_pred HHHHHHHHHHHhhhcCchHHHHHHHHHHHHH---------HHHHHHhHHHHHHHHhhHHhh----cCCHHHH---HHHHH
Q 000895 127 VLFDQLFELLNSSMRNEESYRRELASCTGAL---------QTSISQHMSKEEEQVFPLLIE----KFSFEEQ---ASLVW 190 (1235)
Q Consensus 127 ~lf~~l~~~l~~~~~~~~~~~~eLa~~l~~l---------~~~l~qHm~~EE~qv~PLl~~----~fS~~Eq---~~L~~ 190 (1235)
.++++|++.++.. +..+-+++...+-+| -..|.+=|..++.-+.|.|.. .++++.+ ...+-
T Consensus 192 ~l~~kl~~~l~~a---p~~lq~eiI~~LPeIl~ds~h~~v~~~L~~ll~~~~~L~~~iLd~Ls~L~Ls~~~l~~vr~~vl 268 (1426)
T PF14631_consen 192 ELTDKLFEVLSIA---PVELQKEIISSLPEILDDSQHDEVVEELLELLQENPELTVPILDALSNLNLSPELLEEVREKVL 268 (1426)
T ss_dssp HHHHHHHHHHHHS----TTTHHHHHHTHHHHS-GGGHHHHHHHHHHHHHH-STTHHHHHHHHHHS---HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhC---CHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHhcCCchhhhHHHHHhcCCCCHHHHHHHHHHHH
Confidence 5556666655543 223334444444322 222333344444445566543 3345544 44555
Q ss_pred HHhcccCHHHHHHHHhhhcCCCCHHHHHHHHHHHhhhC
Q 000895 191 QFLCSIPVNMMAEFLPWLSSSISSDEHQDMRKCLCKII 228 (1235)
Q Consensus 191 ~~i~siP~~~m~~~LpWm~~~lsp~Er~~~l~~l~~~~ 228 (1235)
..+.+++++.|..++..++.++++.+...+...||+..
T Consensus 269 ~~L~s~~~e~LP~lirFLL~s~t~~da~evI~~LR~~L 306 (1426)
T PF14631_consen 269 EKLSSVDLEDLPVLIRFLLQSITPSDAVEVISELRENL 306 (1426)
T ss_dssp HSTTSS-TTHHHHHHHHHHHS-SSTTHHHHHHHHHHHH
T ss_pred HHHhcCChhhhHHHHHHHHHhCCcccHHHHHHHHHHHc
Confidence 67788999999999999999999999999999999864
No 179
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=39.77 E-value=14 Score=32.09 Aligned_cols=28 Identities=25% Similarity=0.538 Sum_probs=20.9
Q ss_pred CcEeccCCCCCCCCCceeeeccCCCCCC
Q 000895 1188 QEILCNDCDKKGSAPFHWLYHKCGFCGS 1215 (1235)
Q Consensus 1188 ~~i~CnDC~~~s~~~~h~lg~kC~~C~S 1215 (1235)
..+.|.+||+.-....---+.+|++||+
T Consensus 5 ~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~ 32 (49)
T COG1996 5 MEYKCARCGREVELDQETRGIRCPYCGS 32 (49)
T ss_pred EEEEhhhcCCeeehhhccCceeCCCCCc
Confidence 4678999998765444456788999987
No 180
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=39.68 E-value=21 Score=45.97 Aligned_cols=32 Identities=28% Similarity=0.772 Sum_probs=17.4
Q ss_pred cccccccccccCC-CCCCCcCCCCCccceEeccccc
Q 000895 1026 MMCMRCLKVQPVG-PVCTTLSCSGLSMAKYYCGICK 1060 (1235)
Q Consensus 1026 v~C~~C~~~q~~~-~~C~~~~C~~~~~a~y~C~iC~ 1060 (1235)
++|..|+.+-|.+ ..|.+ | |..+..-.|..|.
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 3577777665543 45666 3 6655433444443
No 181
>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=39.68 E-value=6.4 Score=33.24 Aligned_cols=42 Identities=21% Similarity=0.701 Sum_probs=29.1
Q ss_pred ccccccccccCCCcceecCCCCccChhhHHhhhh------CCCCCCCCC
Q 000895 1115 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC------SHYICPICS 1157 (1235)
Q Consensus 1115 CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~------~~~~CPiCr 1157 (1235)
|+||... .....-+.=-.|+-.||..|+..-.. ..+.||.|+
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 8899884 33333333358999999999976532 268888885
No 182
>PLN03086 PRLI-interacting factor K; Provisional
Probab=39.41 E-value=18 Score=45.54 Aligned_cols=118 Identities=23% Similarity=0.514 Sum_probs=0.0
Q ss_pred ccccccccccccccccCCC-CCCCcCCCCCccceEeccc--ccCcCCC---CccccCCCCCccccCCCCCccccc-----
Q 000895 1021 KATTEMMCMRCLKVQPVGP-VCTTLSCSGLSMAKYYCGI--CKFFDDE---RVVYHCPFCNLCRVGRGLGVDFFH----- 1089 (1235)
Q Consensus 1021 ~~~~~v~C~~C~~~q~~~~-~C~~~~C~~~~~a~y~C~i--C~l~d~~---k~~yHC~~CgiCR~g~gl~~~~fH----- 1089 (1235)
..+..+.|..|....|..+ .-.-..| .+..--|+. |+..=.- +..+||+.|| ..|.
T Consensus 403 ~~~~~V~C~NC~~~i~l~~l~lHe~~C---~r~~V~Cp~~~Cg~v~~r~el~~H~~C~~Cg----------k~f~~s~Le 469 (567)
T PLN03086 403 MDVDTVECRNCKHYIPSRSIALHEAYC---SRHNVVCPHDGCGIVLRVEEAKNHVHCEKCG----------QAFQQGEME 469 (567)
T ss_pred CCCCeEECCCCCCccchhHHHHHHhhC---CCcceeCCcccccceeeccccccCccCCCCC----------CccchHHHH
Q ss_pred -----------cCCccccccccc-ccc---cccCCCCCCCccccccccccC-----------CCcceecCCCCccChhhH
Q 000895 1090 -----------CMTCNCCLAKKL-VDH---KCREKGLETNCPICCDFLFTS-----------SATVRALPCGHFMHSDCF 1143 (1235)
Q Consensus 1090 -----------C~~C~~C~~~~l-~~H---~C~e~~~~~~CpICle~lf~s-----------~~~v~~LpCgH~fH~~Ci 1143 (1235)
|. ||..+.... ..| .|.++ ...|+.|...+-.. .-.....-||
T Consensus 470 kH~~~~Hkpv~Cp-Cg~~~~R~~L~~H~~thCp~K--pi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~CG-------- 538 (567)
T PLN03086 470 KHMKVFHEPLQCP-CGVVLEKEQMVQHQASTCPLR--LITCRFCGDMVQAGGSAMDVRDRLRGMSEHESICG-------- 538 (567)
T ss_pred HHHHhcCCCccCC-CCCCcchhHHHhhhhccCCCC--ceeCCCCCCccccCccccchhhhhhhHHHHHHhcC--------
Q ss_pred HhhhhCCCCCCCCCcCcC--chhhh
Q 000895 1144 QAYTCSHYICPICSKSLG--DMAVY 1166 (1235)
Q Consensus 1144 ~~wl~~~~~CPiCrksv~--dm~~~ 1166 (1235)
...+.|..|++.+. ||..+
T Consensus 539 ----~rt~~C~~Cgk~Vrlrdm~~H 559 (567)
T PLN03086 539 ----SRTAPCDSCGRSVMLKEMDIH 559 (567)
T ss_pred ----CcceEccccCCeeeehhHHHH
No 183
>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=39.21 E-value=21 Score=26.87 Aligned_cols=21 Identities=24% Similarity=0.580 Sum_probs=15.1
Q ss_pred CCCCCCCcCcCchhhhhhhHHH
Q 000895 1151 YICPICSKSLGDMAVYFGMLDA 1172 (1235)
Q Consensus 1151 ~~CPiCrksv~dm~~~~~~lD~ 1172 (1235)
..||||.+.+ .+....+.+|.
T Consensus 2 v~CPiC~~~v-~~~~in~HLD~ 22 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLDS 22 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHHH
Confidence 3699999998 55555677773
No 184
>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=39.17 E-value=18 Score=32.09 Aligned_cols=29 Identities=28% Similarity=0.689 Sum_probs=22.0
Q ss_pred CcEeccCCCCCCCCCceeeeccCCCCCCCccccc
Q 000895 1188 QEILCNDCDKKGSAPFHWLYHKCGFCGSYNTRVI 1221 (1235)
Q Consensus 1188 ~~i~CnDC~~~s~~~~h~lg~kC~~C~SYNT~~~ 1221 (1235)
..+.|..||.- ...| +-|+.||.|+-+++
T Consensus 25 ~l~~C~~cG~~--~~~H---~vc~~cG~Y~gr~v 53 (55)
T TIGR01031 25 TLVVCPNCGEF--KLPH---RVCPSCGYYKGRQV 53 (55)
T ss_pred cceECCCCCCc--ccCe---eECCccCeECCEEc
Confidence 45779999963 3344 46999999999875
No 185
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=39.06 E-value=21 Score=38.18 Aligned_cols=50 Identities=28% Similarity=0.489 Sum_probs=36.3
Q ss_pred CCCCCCCCcCcCchhhhhhhHHHHHhhcCCCh-hhhccCCcEeccCCCCCCCCCceee
Q 000895 1150 HYICPICSKSLGDMAVYFGMLDALLASEQLPE-EYRDRCQEILCNDCDKKGSAPFHWL 1206 (1235)
Q Consensus 1150 ~~~CPiCrksv~dm~~~~~~lD~~i~~~pmP~-ey~~~~~~i~CnDC~~~s~~~~h~l 1206 (1235)
-.+||.|+.++...+. +.....+|+ .|.+......|.-||+.....-||=
T Consensus 97 ~~RCp~CN~~L~~vs~-------eev~~~Vp~~~~~~~~~f~~C~~CgkiYW~GsHw~ 147 (165)
T COG1656 97 FSRCPECNGELEKVSR-------EEVKEKVPEKVYRNYEEFYRCPKCGKIYWKGSHWR 147 (165)
T ss_pred cccCcccCCEeccCcH-------HHHhhccchhhhhcccceeECCCCcccccCchHHH
Confidence 5789999999876543 333344444 5777777788999999988888873
No 186
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=38.99 E-value=20 Score=42.07 Aligned_cols=26 Identities=23% Similarity=0.568 Sum_probs=19.7
Q ss_pred cceecCCCCccChhhHHhhhhCCCCCCCCCc
Q 000895 1128 TVRALPCGHFMHSDCFQAYTCSHYICPICSK 1158 (1235)
Q Consensus 1128 ~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrk 1158 (1235)
..+.|.|+ -|-.+|-.....||.|..
T Consensus 209 G~RyL~Cs-----lC~teW~~~R~~C~~Cg~ 234 (309)
T PRK03564 209 GLRYLHCN-----LCESEWHVVRVKCSNCEQ 234 (309)
T ss_pred CceEEEcC-----CCCCcccccCccCCCCCC
Confidence 34566665 577789878899999996
No 187
>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=38.31 E-value=26 Score=44.27 Aligned_cols=56 Identities=21% Similarity=0.279 Sum_probs=35.0
Q ss_pred chhhhhhhHHHHHhhcCCChhhhccCCcEeccCCCCCCCCCceeeeccCCCCCCCccccccc
Q 000895 1162 DMAVYFGMLDALLASEQLPEEYRDRCQEILCNDCDKKGSAPFHWLYHKCGFCGSYNTRVIKV 1223 (1235)
Q Consensus 1162 dm~~~~~~lD~~i~~~pmP~ey~~~~~~i~CnDC~~~s~~~~h~lg~kC~~C~SYNT~~~~~ 1223 (1235)
|.+.....++......-++- .-+.... .|++||.... -.+.+|+.|||-|+.+++.
T Consensus 493 n~~al~~lv~~a~~~~~~y~-~~~~p~~-~C~~CG~~~~----~~~~~CP~CGs~~~~~~~R 548 (555)
T cd01675 493 NPEALEALVKKAAKRGVIYF-GINTPID-ICNDCGYIGE----GEGFKCPKCGSEDVEVISR 548 (555)
T ss_pred CHHHHHHHHHHHHHcCCceE-EEecCCc-cCCCCCCCCc----CCCCCCcCCCCcCceEEEe
Confidence 55666666666654433331 1233334 8999997553 2357999999998766543
No 188
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=38.09 E-value=25 Score=41.45 Aligned_cols=26 Identities=19% Similarity=0.734 Sum_probs=19.9
Q ss_pred CCccceEe--cccccCcCCCCccccCCCCCc
Q 000895 1048 GLSMAKYY--CGICKFFDDERVVYHCPFCNL 1076 (1235)
Q Consensus 1048 ~~~~a~y~--C~iC~l~d~~k~~yHC~~Cgi 1076 (1235)
.+.|--|| |.||++++. .|.|+.||+
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 34676677 788887765 899999995
No 189
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=37.45 E-value=22 Score=41.75 Aligned_cols=47 Identities=17% Similarity=0.347 Sum_probs=35.1
Q ss_pred CCCccccccccccCCCcceecCCCCccChhhHHhhhhCCCCCCCCCcCcC
Q 000895 1112 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1161 (1235)
Q Consensus 1112 ~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrksv~ 1161 (1235)
...||||+-..-+ +...--=|=.|+-.|+..++.+..+||+=.+++.
T Consensus 300 ~~~CpvClk~r~N---ptvl~vSGyVfCY~Ci~~Yv~~~~~CPVT~~p~~ 346 (357)
T KOG0826|consen 300 REVCPVCLKKRQN---PTVLEVSGYVFCYPCIFSYVVNYGHCPVTGYPAS 346 (357)
T ss_pred cccChhHHhccCC---CceEEecceEEeHHHHHHHHHhcCCCCccCCcch
Confidence 4679999865221 2222234999999999999999999999887753
No 190
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=37.00 E-value=21 Score=30.26 Aligned_cols=26 Identities=19% Similarity=0.524 Sum_probs=17.2
Q ss_pred cEeccCCCCCCCCCceeeeccCCCCCC
Q 000895 1189 EILCNDCDKKGSAPFHWLYHKCGFCGS 1215 (1235)
Q Consensus 1189 ~i~CnDC~~~s~~~~h~lg~kC~~C~S 1215 (1235)
.+.|.+||....... --..+|+.||+
T Consensus 2 ~Y~C~~Cg~~~~~~~-~~~irC~~CG~ 27 (44)
T smart00659 2 IYICGECGRENEIKS-KDVVRCRECGY 27 (44)
T ss_pred EEECCCCCCEeecCC-CCceECCCCCc
Confidence 467888887655442 23567888886
No 191
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=36.95 E-value=18 Score=42.05 Aligned_cols=31 Identities=32% Similarity=0.855 Sum_probs=23.1
Q ss_pred eecCCCCccChhhHHhhhhCCCCCCCCCcCcCc
Q 000895 1130 RALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1162 (1235)
Q Consensus 1130 ~~LpCgH~fH~~Ci~~wl~~~~~CPiCrksv~d 1162 (1235)
+.+||.|+|..+|-.. .....||.|.-.|..
T Consensus 105 RmIPCkHvFCl~CAr~--~~dK~Cp~C~d~Vqr 135 (389)
T KOG2932|consen 105 RMIPCKHVFCLECARS--DSDKICPLCDDRVQR 135 (389)
T ss_pred cccccchhhhhhhhhc--CccccCcCcccHHHH
Confidence 5689999999999743 224689999877643
No 192
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=35.81 E-value=9.1 Score=42.06 Aligned_cols=100 Identities=22% Similarity=0.445 Sum_probs=56.3
Q ss_pred cccccCCccccccccc--ccc-cccCCCCCCCccccccccccCCCcceecCCCCccChhhHHhhhh-----CCCCCCCCC
Q 000895 1086 DFFHCMTCNCCLAKKL--VDH-KCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC-----SHYICPICS 1157 (1235)
Q Consensus 1086 ~~fHC~~C~~C~~~~l--~~H-~C~e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~-----~~~~CPiCr 1157 (1235)
|.|.|..|+-=.+.+- ..| +|-...-..-|..|... |...-. +...++ .-|+|-+|.
T Consensus 116 d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkg-fndtfd--------------lkrh~rthtgvrpykc~~c~ 180 (267)
T KOG3576|consen 116 DSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKG-FNDTFD--------------LKRHTRTHTGVRPYKCSLCE 180 (267)
T ss_pred CeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCc-ccchhh--------------hhhhhccccCccccchhhhh
Confidence 5677777766666552 444 67666666778888766 332111 112222 249999999
Q ss_pred cCcCchhhhhhhHHHHHhhcCCChhhhccCC-cEeccCCCCCCCC
Q 000895 1158 KSLGDMAVYFGMLDALLASEQLPEEYRDRCQ-EILCNDCDKKGSA 1201 (1235)
Q Consensus 1158 ksv~dm~~~~~~lD~~i~~~pmP~ey~~~~~-~i~CnDC~~~s~~ 1201 (1235)
|.+....+.-..+.. |-..+---.|+.++. ...|-|||-++..
T Consensus 181 kaftqrcsleshl~k-vhgv~~~yaykerr~kl~vcedcg~t~~~ 224 (267)
T KOG3576|consen 181 KAFTQRCSLESHLKK-VHGVQHQYAYKERRAKLYVCEDCGYTSER 224 (267)
T ss_pred HHHHhhccHHHHHHH-HcCchHHHHHHHhhhheeeecccCCCCCC
Confidence 988643332222221 222222234555554 4789999987753
No 193
>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=35.25 E-value=1.9e+02 Score=28.69 Aligned_cols=61 Identities=21% Similarity=0.114 Sum_probs=34.8
Q ss_pred HHHhhhhhHHHHHHHHHHHHHhhhcCchHHHHHHHHHHHHHHHHHHHhHHHHHHHHh----hHHhhcCCHHHHHHHHHHH
Q 000895 117 TYSLEHEGESVLFDQLFELLNSSMRNEESYRRELASCTGALQTSISQHMSKEEEQVF----PLLIEKFSFEEQASLVWQF 192 (1235)
Q Consensus 117 ~~~~EH~~~~~lf~~l~~~l~~~~~~~~~~~~eLa~~l~~l~~~l~qHm~~EE~qv~----PLl~~~fS~~Eq~~L~~~~ 192 (1235)
.+..||++.=+++++|..++.. ...+..|..-...|+..||.-.- |-+..| .+.+.+|
T Consensus 14 ~ID~qH~~L~~l~n~l~~a~~~------------~~~l~~L~~y~~~HF~~EE~~M~~~~yp~~~~H------~~~H~~f 75 (113)
T cd00522 14 VIDDEHKTLFNGINDLSEANNR------------ADNLKELVDYTVKHFKDEEALMEAAGYPDYEEH------KKIHEDF 75 (113)
T ss_pred HHHHHHHHHHHHHHHHHHHHhH------------HHHHHHHHHHHHHHHHHHHHHHHHcCCCCHHHH------HHHHHHH
Confidence 3455555444444444444332 34567777778889999998653 433333 5555555
Q ss_pred hcc
Q 000895 193 LCS 195 (1235)
Q Consensus 193 i~s 195 (1235)
+..
T Consensus 76 ~~~ 78 (113)
T cd00522 76 VEK 78 (113)
T ss_pred HHH
Confidence 443
No 194
>KOG4399 consensus C2HC-type Zn-finger protein [General function prediction only]
Probab=35.19 E-value=9.8 Score=43.05 Aligned_cols=63 Identities=22% Similarity=0.348 Sum_probs=43.8
Q ss_pred ccccccccccCCCCCCCcCCCCCccceEecccccCcCCCCccccCCCCCccccCCCCCccccccCCcccccc
Q 000895 1027 MCMRCLKVQPVGPVCTTLSCSGLSMAKYYCGICKFFDDERVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLA 1098 (1235)
Q Consensus 1027 ~C~~C~~~q~~~~~C~~~~C~~~~~a~y~C~iC~l~d~~k~~yHC~~CgiCR~g~gl~~~~fHC~~C~~C~~ 1098 (1235)
+|..|....- -.|+- | +...+.-+|.||.=+|.++ -|||.|.-||--+. ...-||.+|..|..
T Consensus 240 ~~~~~~~~~~--i~C~~--~-~~~A~~~~C~iC~~~~~~R--~~C~~~kA~~~~~Q--~K~N~~~~~~~~~q 302 (325)
T KOG4399|consen 240 LCKKCVKPSW--IHCSI--C-NHCAVKHGCFICGELDHKR--STCPNIKAVRKQKQ--RKSNKMKMETTKGQ 302 (325)
T ss_pred Hhhhhcccce--eeeec--c-cchhhhcceeecccccccc--ccCccHHHHHHHHh--cccchhhhhhhhhh
Confidence 4444444333 24544 3 3346677899999998877 89999999997543 25679998888875
No 195
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=35.04 E-value=16 Score=41.48 Aligned_cols=53 Identities=23% Similarity=0.535 Sum_probs=36.0
Q ss_pred CCCCCCCccccccccccCCCcceecCC-----CCccChhhHHhhhhC--------CCCCCCCCcCc
Q 000895 1108 EKGLETNCPICCDFLFTSSATVRALPC-----GHFMHSDCFQAYTCS--------HYICPICSKSL 1160 (1235)
Q Consensus 1108 e~~~~~~CpICle~lf~s~~~v~~LpC-----gH~fH~~Ci~~wl~~--------~~~CPiCrksv 1160 (1235)
+...+..|=||...=-++....-+-|| .|-.|..|+..|+.. .-+||-|+...
T Consensus 16 ~~e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEY 81 (293)
T KOG3053|consen 16 NQELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEY 81 (293)
T ss_pred ccccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchh
Confidence 345577899998652222222234577 299999999999732 25699999865
No 196
>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=34.71 E-value=27 Score=30.92 Aligned_cols=29 Identities=28% Similarity=0.683 Sum_probs=21.8
Q ss_pred CcEeccCCCCCCCCCceeeeccCCCCCCCccccc
Q 000895 1188 QEILCNDCDKKGSAPFHWLYHKCGFCGSYNTRVI 1221 (1235)
Q Consensus 1188 ~~i~CnDC~~~s~~~~h~lg~kC~~C~SYNT~~~ 1221 (1235)
..+.|..||.. ...| +-|++||-|+.+++
T Consensus 25 ~l~~c~~cg~~--~~~H---~vc~~cG~y~~r~v 53 (56)
T PF01783_consen 25 NLVKCPNCGEP--KLPH---RVCPSCGYYKGRQV 53 (56)
T ss_dssp SEEESSSSSSE--ESTT---SBCTTTBBSSSSSS
T ss_pred ceeeeccCCCE--eccc---EeeCCCCeECCEEE
Confidence 45789999953 2233 56999999999985
No 197
>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=34.29 E-value=25 Score=36.24 Aligned_cols=18 Identities=28% Similarity=0.392 Sum_probs=15.6
Q ss_pred cCcCCCCccccCCCCCcc
Q 000895 1060 KFFDDERVVYHCPFCNLC 1077 (1235)
Q Consensus 1060 ~l~d~~k~~yHC~~CgiC 1077 (1235)
||||-.|.+-.||+||.=
T Consensus 18 kFYDLnk~p~vcP~cg~~ 35 (129)
T TIGR02300 18 KFYDLNRRPAVSPYTGEQ 35 (129)
T ss_pred cccccCCCCccCCCcCCc
Confidence 788988999999999954
No 198
>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 KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=32.34 E-value=15 Score=38.46 Aligned_cols=26 Identities=27% Similarity=0.837 Sum_probs=17.6
Q ss_pred cceEecccccCcCCCCccccCCCCC--ccccC
Q 000895 1051 MAKYYCGICKFFDDERVVYHCPFCN--LCRVG 1080 (1235)
Q Consensus 1051 ~a~y~C~iC~l~d~~k~~yHC~~Cg--iCR~g 1080 (1235)
-.+-||.||.+| ++|-|-.|| +|-|+
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 345577777755 577788887 66665
No 200
>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=32.14 E-value=33 Score=41.93 Aligned_cols=31 Identities=23% Similarity=0.356 Sum_probs=18.4
Q ss_pred HHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHH
Q 000895 916 NELEAEIRKVSRDSTLDPRRKAYLIQNLMTSRW 948 (1235)
Q Consensus 916 ~~l~~~ir~i~~~~~l~~~~k~~~~q~l~~~~~ 948 (1235)
..|+..||.|--. .+.+..-...|+++-.|-
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 3566777777643 444445556677765553
No 201
>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=31.95 E-value=16 Score=38.87 Aligned_cols=22 Identities=23% Similarity=0.794 Sum_probs=11.0
Q ss_pred EecccccC---cCCC-CccccCCCCC
Q 000895 1054 YYCGICKF---FDDE-RVVYHCPFCN 1075 (1235)
Q Consensus 1054 y~C~iC~l---~d~~-k~~yHC~~Cg 1075 (1235)
|+|+.|+. |++. ..-|+||.||
T Consensus 110 Y~Cp~c~~r~tf~eA~~~~F~Cp~Cg 135 (158)
T TIGR00373 110 FICPNMCVRFTFNEAMELNFTCPRCG 135 (158)
T ss_pred EECCCCCcEeeHHHHHHcCCcCCCCC
Confidence 55555552 3333 4456666665
No 202
>KOG4654 consensus Uncharacterized conserved protein [Function unknown]
Probab=31.93 E-value=7.5e+02 Score=27.47 Aligned_cols=55 Identities=18% Similarity=0.097 Sum_probs=33.8
Q ss_pred ChHHHH----HHHHHHHHHHHHHHHHHHhhccCCCCcchHHHHHHHHHHHHHHHHHhhccccccc
Q 000895 43 PILIFL----FFHKAIKSELDVLHRAAMAFATNLGGGGDINKLLERYHFFRAIYKHHCNAEDEVI 103 (1235)
Q Consensus 43 Pi~~~~----~~HkAlR~eL~~l~~~~~~~~~~~gd~~~~~~l~~r~~fL~~~~~~H~~aEDevI 103 (1235)
|+|+|. ++|||+-..-..= -|+-- -=...|++|..-++|+.+....-+..||.+-
T Consensus 41 p~dlY~~c~q~Vhk~lc~~kkc~----iRl~Y--~W~ELW~aL~n~L~Flmsne~~llak~dif~ 99 (252)
T KOG4654|consen 41 PADLYFLCFQFVHKALCSLKKCG----IRLEY--HWLELWRALFNFLDFLMSNEINLLAKEDIFR 99 (252)
T ss_pred ChhHHHHHHHHHHHHHHHHHhhc----ceeee--HHHHHHHHHHHHHHHHHHhHhhhcchhhHHH
Confidence 777776 7888865432111 11111 1123677888888888888888888888653
No 203
>PF00539 Tat: Transactivating regulatory protein (Tat); InterPro: IPR001831 Like other lentiviruses, Human immunodeficiency virus 1 (HIV-1) encodes a trans-activating regulatory protein (Tat), which is essential for efficient transcription of the viral genome [, ]. Tat acts by binding to an RNA stem-loop structure, the trans-activating response element (TAR), found at the 5' ends of nascent HIV-1 transcripts. In binding to TAR, Tat alters the properties of the transcription complex, recruits a positive transcription elongation complex (P-TEFb) and hence increases the production of full-length viral RNA []. Tat protein also associates with RNA polymerase II complexes during early transcription elongation after the promoter clearance and before the synthesis of full-length TAR RNA transcript. This interaction of Tat with RNA polymerase II elongation complexes is P-TEFb-independent. There are two Tat binding sites on each transcription elongation complex; one is located on TAR RNA and the other one on RNA polymerase II near the exit site for nascent mRNA transcripts which suggests that two Tat molecules are involved in performing various functions during a single round of HIV-1 mRNA synthesis []. The minimum Tat sequence that can mediate specific TAR binding in vitro has been mapped to a basic domain of 10 amino acids, comprising mostly Arg and Lys residues. Regulatory activity, however, also requires the 47 N-terminal residues, which interact with components of the transcription complex and function as a transcriptional activation domain [, , ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0042025 host cell nucleus; PDB: 2W2H_D 1ZBN_B 1TVS_A 1TVT_A 3O6L_C 3O6M_C 3MI9_C 3MIA_C 1JFW_A 1TBC_A ....
Probab=31.74 E-value=44 Score=31.03 Aligned_cols=18 Identities=44% Similarity=1.139 Sum_probs=13.4
Q ss_pred cccCCCCCccccCCCCCcccc
Q 000895 1068 VYHCPFCNLCRVGRGLGVDFF 1088 (1235)
Q Consensus 1068 ~yHC~~CgiCR~g~gl~~~~f 1088 (1235)
-|||. +|-+-+|||+.|.
T Consensus 36 cyHCq---lCFl~KgLGI~Y~ 53 (68)
T PF00539_consen 36 CYHCQ---LCFLQKGLGISYG 53 (68)
T ss_dssp TSSSS---CCCCCTSSSTSSS
T ss_pred eeece---eeeeeCCCccccc
Confidence 46655 7788899998763
No 204
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=30.91 E-value=17 Score=39.34 Aligned_cols=23 Identities=30% Similarity=1.037 Sum_probs=11.6
Q ss_pred eEecccccC---cCCC-CccccCCCCC
Q 000895 1053 KYYCGICKF---FDDE-RVVYHCPFCN 1075 (1235)
Q Consensus 1053 ~y~C~iC~l---~d~~-k~~yHC~~Cg 1075 (1235)
.|+|+.|+. |++. ...|+||.||
T Consensus 117 ~Y~Cp~C~~rytf~eA~~~~F~Cp~Cg 143 (178)
T PRK06266 117 FFFCPNCHIRFTFDEAMEYGFRCPQCG 143 (178)
T ss_pred EEECCCCCcEEeHHHHhhcCCcCCCCC
Confidence 355655553 3332 4456666665
No 205
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=30.82 E-value=27 Score=44.23 Aligned_cols=47 Identities=26% Similarity=0.627 Sum_probs=32.4
Q ss_pred CCccccccccccCCCcceec---CCCCccChhhHHhhhh-----CCCCCCCCCcCcC
Q 000895 1113 TNCPICCDFLFTSSATVRAL---PCGHFMHSDCFQAYTC-----SHYICPICSKSLG 1161 (1235)
Q Consensus 1113 ~~CpICle~lf~s~~~v~~L---pCgH~fH~~Ci~~wl~-----~~~~CPiCrksv~ 1161 (1235)
..|+||--. .....-..+ .||-.||..|+.-|+. ...+||-||+..+
T Consensus 19 ~mc~l~~s~--G~~~ag~m~ac~~c~~~yH~~cvt~~~~~~~l~~gWrC~~crvCe~ 73 (694)
T KOG4443|consen 19 LMCPLCGSS--GKGRAGRLLACSDCGQKYHPYCVTSWAQHAVLSGGWRCPSCRVCEA 73 (694)
T ss_pred hhhhhhccc--cccccCcchhhhhhcccCCcchhhHHHhHHHhcCCcccCCceeeee
Confidence 468888643 222323333 6899999999999974 3478999998753
No 206
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=30.36 E-value=32 Score=34.09 Aligned_cols=31 Identities=19% Similarity=0.504 Sum_probs=18.3
Q ss_pred cccccCCcc-cccccccccccccCCCCCCCccccccc
Q 000895 1086 DFFHCMTCN-CCLAKKLVDHKCREKGLETNCPICCDF 1121 (1235)
Q Consensus 1086 ~~fHC~~C~-~C~~~~l~~H~C~e~~~~~~CpICle~ 1121 (1235)
.+|+|..|| ..+++.++. +..+..||+|..+
T Consensus 20 t~f~CP~Cge~~v~v~~~k-----~~~h~~C~~CG~y 51 (99)
T PRK14892 20 KIFECPRCGKVSISVKIKK-----NIAIITCGNCGLY 51 (99)
T ss_pred cEeECCCCCCeEeeeecCC-----CcceEECCCCCCc
Confidence 467777777 333333322 4556778888766
No 207
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=30.31 E-value=40 Score=28.36 Aligned_cols=8 Identities=38% Similarity=1.344 Sum_probs=4.0
Q ss_pred cccCCCCC
Q 000895 1068 VYHCPFCN 1075 (1235)
Q Consensus 1068 ~yHC~~Cg 1075 (1235)
..+|+.||
T Consensus 21 ~~~Cp~CG 28 (46)
T PRK00398 21 GVRCPYCG 28 (46)
T ss_pred ceECCCCC
Confidence 44555554
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=30.25 E-value=19 Score=31.92 Aligned_cols=28 Identities=29% Similarity=0.820 Sum_probs=20.8
Q ss_pred hccCCcEeccCCCCCCCCCceeeeccCCCCC
Q 000895 1184 RDRCQEILCNDCDKKGSAPFHWLYHKCGFCG 1214 (1235)
Q Consensus 1184 ~~~~~~i~CnDC~~~s~~~~h~lg~kC~~C~ 1214 (1235)
++.+..|+|.-||.+ .||+--..|..||
T Consensus 10 r~~ktH~~CrRCG~~---syH~qK~~CasCG 37 (55)
T PF01907_consen 10 RHNKTHTLCRRCGRR---SYHIQKKTCASCG 37 (55)
T ss_dssp S-S-SEEE-TTTSSE---EEETTTTEETTTB
T ss_pred cCCccEeeecccCCe---eeecCCCcccccC
Confidence 345678999999985 6888777899999
No 209
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=30.16 E-value=21 Score=43.34 Aligned_cols=20 Identities=15% Similarity=0.453 Sum_probs=15.3
Q ss_pred hHHHhcCHHHHHHHHhhhcc
Q 000895 908 NDIFRMNQNELEAEIRKVSR 927 (1235)
Q Consensus 908 ~~~~~~~q~~l~~~ir~i~~ 927 (1235)
...+++|+.+||..|++.-.
T Consensus 50 ~~llk~~~KqLR~li~~Lre 69 (436)
T KOG2593|consen 50 KELLKFNKKQLRKLIASLRE 69 (436)
T ss_pred HHHhcccHHHHHHHHHHhhh
Confidence 34567889999888887765
No 210
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=29.78 E-value=40 Score=43.29 Aligned_cols=54 Identities=20% Similarity=0.292 Sum_probs=32.4
Q ss_pred chhhhhhhHHHHHhhcCCChhhhccCCcEeccCCCCCCCCCceeeeccCCCCCCCccccc
Q 000895 1162 DMAVYFGMLDALLASEQLPEEYRDRCQEILCNDCDKKGSAPFHWLYHKCGFCGSYNTRVI 1221 (1235)
Q Consensus 1162 dm~~~~~~lD~~i~~~pmP~ey~~~~~~i~CnDC~~~s~~~~h~lg~kC~~C~SYNT~~~ 1221 (1235)
|.+...+.++.... +.+|----+. ..-.|++||.... . .+..||.|||-|+.++
T Consensus 541 n~eal~~lv~~~~~-~~i~Yf~in~-~~~iC~~CG~~~~-g---~~~~CP~CGs~~~ev~ 594 (623)
T PRK08271 541 SEEGYRKLLNIAAK-TGCNYFAFNV-KITICNDCHHIDK-R---TGKRCPICGSENIDYY 594 (623)
T ss_pred CHHHHHHHHHHHHH-cCCceEEeCC-CCccCCCCCCcCC-C---CCcCCcCCCCcchhHH
Confidence 45555555555543 5555322222 3446999997532 2 3469999999886554
No 211
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=29.73 E-value=23 Score=42.77 Aligned_cols=37 Identities=24% Similarity=0.441 Sum_probs=27.0
Q ss_pred CCCccccccccccCCCcceecCCCCccChhhHHhhhh
Q 000895 1112 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC 1148 (1235)
Q Consensus 1112 ~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~ 1148 (1235)
...|.||..+.........+..|||.|..+|..+++.
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 4679999943233333334679999999999999875
No 212
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=29.69 E-value=30 Score=35.92 Aligned_cols=47 Identities=30% Similarity=0.723 Sum_probs=34.4
Q ss_pred CCCccccccccccCCCcceec-C---CCCccChhhHHh-hh--hCCCCCCCCCcCcCc
Q 000895 1112 ETNCPICCDFLFTSSATVRAL-P---CGHFMHSDCFQA-YT--CSHYICPICSKSLGD 1162 (1235)
Q Consensus 1112 ~~~CpICle~lf~s~~~v~~L-p---CgH~fH~~Ci~~-wl--~~~~~CPiCrksv~d 1162 (1235)
--.|-||.|- |.+ -+.| | ||=.+...|+.. |- ..+..||+|+.|.-.
T Consensus 80 lYeCnIC~et---S~e-e~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKs 133 (140)
T PF05290_consen 80 LYECNICKET---SAE-ERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKS 133 (140)
T ss_pred ceeccCcccc---cch-hhcCCcccccchHHHHHHHHHHHHHcccCCCCCcccccccc
Confidence 4579999876 333 3445 3 899999999877 74 246889999998753
No 213
>PRK07219 DNA topoisomerase I; Validated
Probab=29.32 E-value=76 Score=42.16 Aligned_cols=63 Identities=25% Similarity=0.495 Sum_probs=34.2
Q ss_pred cccccCcCCC----CccccCCCCCcc---ccCCCCCccccccCC---cccccccccccccccCCCCCCCccccccccc
Q 000895 1056 CGICKFFDDE----RVVYHCPFCNLC---RVGRGLGVDFFHCMT---CNCCLAKKLVDHKCREKGLETNCPICCDFLF 1123 (1235)
Q Consensus 1056 C~iC~l~d~~----k~~yHC~~CgiC---R~g~gl~~~~fHC~~---C~~C~~~~l~~H~C~e~~~~~~CpICle~lf 1123 (1235)
|+.|+..... .....|+.||-- |.|+. | .|+-|.+ |+.-..+.-..+. ......||-|...+.
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 7888766432 346889999821 22332 3 3888865 6543332211111 123467888876543
No 214
>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=29.22 E-value=39 Score=27.04 Aligned_cols=23 Identities=26% Similarity=0.953 Sum_probs=16.6
Q ss_pred eEecccccCc-CCCCccccCCCCC
Q 000895 1053 KYYCGICKFF-DDERVVYHCPFCN 1075 (1235)
Q Consensus 1053 ~y~C~iC~l~-d~~k~~yHC~~Cg 1075 (1235)
.|-|.+|.+. +.++.+..||-||
T Consensus 2 ~~~C~~CG~i~~g~~~p~~CP~Cg 25 (34)
T cd00729 2 VWVCPVCGYIHEGEEAPEKCPICG 25 (34)
T ss_pred eEECCCCCCEeECCcCCCcCcCCC
Confidence 4778888876 4446777787777
No 215
>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=28.80 E-value=19 Score=41.60 Aligned_cols=24 Identities=21% Similarity=0.404 Sum_probs=11.8
Q ss_pred cChhhHHhhhhCCCCCCCCCcCcC
Q 000895 1138 MHSDCFQAYTCSHYICPICSKSLG 1161 (1235)
Q Consensus 1138 fH~~Ci~~wl~~~~~CPiCrksv~ 1161 (1235)
+.+-|-.+|.....+||.|...=.
T Consensus 199 ~Cs~C~t~W~~~R~~Cp~Cg~~~~ 222 (290)
T PF04216_consen 199 HCSLCGTEWRFVRIKCPYCGNTDH 222 (290)
T ss_dssp EETTT--EEE--TTS-TTT---SS
T ss_pred EcCCCCCeeeecCCCCcCCCCCCC
Confidence 344688889877889999997643
No 216
>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=28.74 E-value=27 Score=29.89 Aligned_cols=40 Identities=30% Similarity=0.756 Sum_probs=29.0
Q ss_pred ccccccccccCCCcceecCCCCccChhhHHhhhhCCCCCCCCCcCcCchh
Q 000895 1115 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGDMA 1164 (1235)
Q Consensus 1115 CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrksv~dm~ 1164 (1235)
|+.|...+... .+.+..=|..||..|+ +|-.|++++.+..
T Consensus 1 C~~C~~~I~~~--~~~~~~~~~~~H~~Cf--------~C~~C~~~l~~~~ 40 (58)
T PF00412_consen 1 CARCGKPIYGT--EIVIKAMGKFWHPECF--------KCSKCGKPLNDGD 40 (58)
T ss_dssp BTTTSSBESSS--SEEEEETTEEEETTTS--------BETTTTCBTTTSS
T ss_pred CCCCCCCccCc--EEEEEeCCcEEEcccc--------ccCCCCCccCCCe
Confidence 77888886633 2333356899999987 8999999987643
No 217
>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=28.43 E-value=23 Score=32.98 Aligned_cols=10 Identities=30% Similarity=1.152 Sum_probs=6.3
Q ss_pred cceEeccccc
Q 000895 1051 MAKYYCGICK 1060 (1235)
Q Consensus 1051 ~a~y~C~iC~ 1060 (1235)
.+.|||..|+
T Consensus 48 AvdYFC~~c~ 57 (70)
T PF07191_consen 48 AVDYFCNHCH 57 (70)
T ss_dssp EEEEE-TTTT
T ss_pred ccceeeccCC
Confidence 3578887776
No 218
>PLN02189 cellulose synthase
Probab=27.65 E-value=46 Score=44.67 Aligned_cols=53 Identities=21% Similarity=0.399 Sum_probs=36.4
Q ss_pred CCCCCCCccccccccccCCCcceec---CCCCccChhhHHhhhh--CCCCCCCCCcCcC
Q 000895 1108 EKGLETNCPICCDFLFTSSATVRAL---PCGHFMHSDCFQAYTC--SHYICPICSKSLG 1161 (1235)
Q Consensus 1108 e~~~~~~CpICle~lf~s~~~v~~L---pCgH~fH~~Ci~~wl~--~~~~CPiCrksv~ 1161 (1235)
++.....|.||.|++-...+.-... -||--.+..|+ ++-+ .+..||-|+...-
T Consensus 30 ~~~~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cy-eyer~eg~q~CpqCkt~Y~ 87 (1040)
T PLN02189 30 RNLDGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCY-EYERREGTQNCPQCKTRYK 87 (1040)
T ss_pred ccccCccccccccccCcCCCCCEEEeeccCCCccccchh-hhhhhcCCccCcccCCchh
Confidence 3345568999999975333322223 37777999999 5543 4688999998764
No 219
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=27.00 E-value=34 Score=37.74 Aligned_cols=31 Identities=35% Similarity=0.870 Sum_probs=22.4
Q ss_pred ccCCCcceecCCCCccChhhHHhhhhCCCCCCCCCc
Q 000895 1123 FTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSK 1158 (1235)
Q Consensus 1123 f~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrk 1158 (1235)
|+....++--.|+-.||..|+.+ ..||-|.+
T Consensus 167 F~~~~~~~C~~C~~v~H~~C~~~-----~~CpkC~R 197 (202)
T PF13901_consen 167 FQIDTTVRCPKCKSVFHKSCFRK-----KSCPKCAR 197 (202)
T ss_pred CCCCCeeeCCcCccccchhhcCC-----CCCCCcHh
Confidence 34333445568999999999962 66999965
No 220
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.73 E-value=40 Score=32.03 Aligned_cols=51 Identities=33% Similarity=0.509 Sum_probs=32.9
Q ss_pred CCccccccccccCCCcceecCCCCccChhhHHhhhhCCCCCCCCCcCcCchhhhhhhHHHHHhhc--CCChhhhc
Q 000895 1113 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGDMAVYFGMLDALLASE--QLPEEYRD 1185 (1235)
Q Consensus 1113 ~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrksv~dm~~~~~~lD~~i~~~--pmP~ey~~ 1185 (1235)
..||||--+|-.+...-+ .-..||-||-...|. ..||.+|+.. |-|.+|+.
T Consensus 2 llCP~C~v~l~~~~rs~v------------------EiD~CPrCrGVWLDr----GELdKli~r~r~pqpa~ys~ 54 (88)
T COG3809 2 LLCPICGVELVMSVRSGV------------------EIDYCPRCRGVWLDR----GELDKLIERSRYPQPAEYSQ 54 (88)
T ss_pred cccCcCCceeeeeeecCc------------------eeeeCCccccEeecc----hhHHHHHHHhcCCCCcccCC
Confidence 369999877654422111 125699999988875 5788888865 44555643
No 221
>PLN02436 cellulose synthase A
Probab=26.22 E-value=51 Score=44.40 Aligned_cols=53 Identities=19% Similarity=0.452 Sum_probs=36.5
Q ss_pred CCCCCCCccccccccccCCCcceecC---CCCccChhhHHhhhh--CCCCCCCCCcCcC
Q 000895 1108 EKGLETNCPICCDFLFTSSATVRALP---CGHFMHSDCFQAYTC--SHYICPICSKSLG 1161 (1235)
Q Consensus 1108 e~~~~~~CpICle~lf~s~~~v~~Lp---CgH~fH~~Ci~~wl~--~~~~CPiCrksv~ 1161 (1235)
.......|.||.|++-.+.+.-.... ||--.+..|+ ++-+ .+..||-|+...-
T Consensus 32 ~~~~~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cy-eyer~eg~~~Cpqckt~Y~ 89 (1094)
T PLN02436 32 QELSGQTCQICGDEIELTVDGEPFVACNECAFPVCRPCY-EYERREGNQACPQCKTRYK 89 (1094)
T ss_pred cccCCccccccccccCcCCCCCEEEeeccCCCccccchh-hhhhhcCCccCcccCCchh
Confidence 34455689999999754443333343 6666999999 5543 4688999998764
No 222
>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=25.71 E-value=46 Score=28.68 Aligned_cols=9 Identities=44% Similarity=1.397 Sum_probs=6.7
Q ss_pred eEecccccC
Q 000895 1053 KYYCGICKF 1061 (1235)
Q Consensus 1053 ~y~C~iC~l 1061 (1235)
+|.|.+|.+
T Consensus 1 ky~C~~Cgy 9 (47)
T PF00301_consen 1 KYQCPVCGY 9 (47)
T ss_dssp EEEETTTSB
T ss_pred CcCCCCCCE
Confidence 577888876
No 223
>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=25.69 E-value=40 Score=34.79 Aligned_cols=33 Identities=15% Similarity=0.096 Sum_probs=23.4
Q ss_pred ccccccccCCcccCcccccccCCCCCccccccccccccccccccCCC
Q 000895 993 CKLRAACCGKLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVGP 1039 (1235)
Q Consensus 993 c~l~~~cC~~~y~Cr~CHde~~~H~~~r~~~~~v~C~~C~~~q~~~~ 1039 (1235)
-|-.||-||+-|= .+.| ..++|.+|++.+++..
T Consensus 8 tKr~Cp~cg~kFY-----------DLnk---~p~vcP~cg~~~~~~~ 40 (129)
T TIGR02300 8 TKRICPNTGSKFY-----------DLNR---RPAVSPYTGEQFPPEE 40 (129)
T ss_pred ccccCCCcCcccc-----------ccCC---CCccCCCcCCccCcch
Confidence 3567889987441 1333 6899999999998863
No 224
>TIGR02487 NrdD anaerobic ribonucleoside-triphosphate reductase. This model represents the oxygen-sensitive (anaerobic, class III) ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centered radical, a C-terminal zinc binding site, and a set of conserved active site cysteines and asparagines. This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (TIGR02491). Together the two form an alpha-2/beta-2 heterodimer.
Probab=25.52 E-value=58 Score=41.53 Aligned_cols=54 Identities=24% Similarity=0.381 Sum_probs=31.7
Q ss_pred chhhhhhhHHHHHhhcCCChhhhccCCcEeccCCCCCCCCCceeeeccCCCCCCCccccc
Q 000895 1162 DMAVYFGMLDALLASEQLPEEYRDRCQEILCNDCDKKGSAPFHWLYHKCGFCGSYNTRVI 1221 (1235)
Q Consensus 1162 dm~~~~~~lD~~i~~~pmP~ey~~~~~~i~CnDC~~~s~~~~h~lg~kC~~C~SYNT~~~ 1221 (1235)
|.+.....++...... +|----+. ..-.|++||..+.- +..+|+.|||-|..++
T Consensus 499 n~eal~~lv~~a~~~~-i~Y~~~n~-~~~~C~~CG~~g~~----~~~~CP~Cgs~~~~~~ 552 (579)
T TIGR02487 499 DPEALKDITKKAMKNG-IGYFGINP-PVDVCEDCGYTGEG----LNDKCPKCGSHDIEVI 552 (579)
T ss_pred CHHHHHHHHHHHHhcC-CceEEecc-CCccCCCCCCCCCC----CCCcCcCCCCccceeh
Confidence 4455555555554433 54322222 34469999974332 1358999999886555
No 225
>COG0143 MetG Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=25.28 E-value=44 Score=42.39 Aligned_cols=44 Identities=25% Similarity=0.456 Sum_probs=34.2
Q ss_pred ccceEecccccCcCCC-CccccCCCCCccccCCCCCccccccCCccccccc
Q 000895 1050 SMAKYYCGICKFFDDE-RVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLAK 1099 (1235)
Q Consensus 1050 ~~a~y~C~iC~l~d~~-k~~yHC~~CgiCR~g~gl~~~~fHC~~C~~C~~~ 1099 (1235)
...-+||..|.-|=.| .-.=.|++||.+..++ -||+.||.++.-
T Consensus 123 ~~~~~Yc~~~e~fl~dr~v~g~cp~cg~~~arG------D~Ce~Cg~~~~P 167 (558)
T COG0143 123 EYEGLYCVSCERFLPDRYVEGTCPKCGGEDARG------DQCENCGRTLDP 167 (558)
T ss_pred ceeeeEcccccccccchheeccCCCcCccccCc------chhhhccCcCCc
Confidence 3556789999877666 4445699999999884 489999999875
No 226
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=25.09 E-value=58 Score=37.71 Aligned_cols=48 Identities=29% Similarity=0.773 Sum_probs=38.4
Q ss_pred CCCccceEecccccCcCCCCccccCCCCCccccCCCCCccccccCCcccccccc
Q 000895 1047 SGLSMAKYYCGICKFFDDERVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLAKK 1100 (1235)
Q Consensus 1047 ~~~~~a~y~C~iC~l~d~~k~~yHC~~CgiCR~g~gl~~~~fHC~~C~~C~~~~ 1100 (1235)
.|....-+||..|+++-. +...||.-||.|-.+- | -||.=-|.|+...
T Consensus 107 ~~~~~~~~~C~~C~~~rP-pRs~HCsvC~~CV~rf----D-HHC~WvnnCVG~r 154 (299)
T KOG1311|consen 107 NGIQVEWKYCDTCQLYRP-PRSSHCSVCNNCVLRF----D-HHCPWLNNCIGER 154 (299)
T ss_pred CCcccceEEcCcCcccCC-CCcccchhhccccccc----C-CCCCCccceECCC
Confidence 366778899999999955 4678999999998763 3 7999999998754
No 227
>KOG4399 consensus C2HC-type Zn-finger protein [General function prediction only]
Probab=24.94 E-value=21 Score=40.52 Aligned_cols=71 Identities=23% Similarity=0.591 Sum_probs=47.6
Q ss_pred CCccceEecccccCcCCCCccccCCCCCccccCCCCCccccccCCccccccccc-ccccccCCCCCCCccccccc
Q 000895 1048 GLSMAKYYCGICKFFDDERVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLAKKL-VDHKCREKGLETNCPICCDF 1121 (1235)
Q Consensus 1048 ~~~~a~y~C~iC~l~d~~k~~yHC~~CgiCR~g~gl~~~~fHC~~C~~C~~~~l-~~H~C~e~~~~~~CpICle~ 1121 (1235)
|..-+-+||..|-.|=. +..-||..|+-|..-.| +-|-||.+|-.|+-.++ .--.|..-+...-|-||-++
T Consensus 199 ~~EE~~~~~~~~~~Yv~-~~~~H~~~~~S~~~~~~--~~~~H~~~~~~~~~~~~i~C~~~~~~A~~~~C~iC~~~ 270 (325)
T KOG4399|consen 199 PTEEGYRFCSPCQRYVS-LENQHCEHCNSCTSKDG--RKWNHCFLCKKCVKPSWIHCSICNHCAVKHGCFICGEL 270 (325)
T ss_pred ccccceEEEeehHHHHH-HHhhhchhhcccccchh--HHHhHhHHhhhhcccceeeeecccchhhhcceeecccc
Confidence 45566677999987743 45679999999987653 57999999999987765 11112212223456677655
No 228
>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=24.64 E-value=25 Score=45.97 Aligned_cols=33 Identities=24% Similarity=0.548 Sum_probs=0.0
Q ss_pred cccccccccccCCCCCCCcCCCCCccceEecccccC
Q 000895 1026 MMCMRCLKVQPVGPVCTTLSCSGLSMAKYYCGICKF 1061 (1235)
Q Consensus 1026 v~C~~C~~~q~~~~~C~~~~C~~~~~a~y~C~iC~l 1061 (1235)
-.|..|+++. ....|.. |.+...-.|+|..|+.
T Consensus 656 r~Cp~Cg~~t-~~~~Cp~--CG~~T~~~~~Cp~C~~ 688 (900)
T PF03833_consen 656 RRCPKCGKET-FYNRCPE--CGSHTEPVYVCPDCGI 688 (900)
T ss_dssp ------------------------------------
T ss_pred ccCcccCCcc-hhhcCcc--cCCccccceecccccc
Confidence 3455555542 2234433 4333344555555554
No 229
>COG1144 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, delta subunit [Energy production and conversion]
Probab=24.23 E-value=32 Score=33.51 Aligned_cols=14 Identities=29% Similarity=0.857 Sum_probs=12.5
Q ss_pred ccccccCCcccccc
Q 000895 1085 VDFFHCMTCNCCLA 1098 (1235)
Q Consensus 1085 ~~~fHC~~C~~C~~ 1098 (1235)
.||-+|+.||.|..
T Consensus 63 idYdyCKGCGICa~ 76 (91)
T COG1144 63 IDYDYCKGCGICAN 76 (91)
T ss_pred eEcccccCceechh
Confidence 58999999999976
No 230
>PRK00420 hypothetical protein; Validated
Probab=23.56 E-value=45 Score=33.75 Aligned_cols=30 Identities=30% Similarity=0.665 Sum_probs=21.4
Q ss_pred CCCCccccccccccCCCcceecCCCCccChhhHHhhhhCCCCCCCCCcCcC
Q 000895 1111 LETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1161 (1235)
Q Consensus 1111 ~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrksv~ 1161 (1235)
....||+|.-+||...+ ....||.|+..+.
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 34789999988876211 3567999998664
No 231
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=23.46 E-value=30 Score=33.73 Aligned_cols=27 Identities=37% Similarity=0.941 Sum_probs=15.6
Q ss_pred CccccCCCCCc---cccCCCCCccccccCCcccc
Q 000895 1066 RVVYHCPFCNL---CRVGRGLGVDFFHCMTCNCC 1096 (1235)
Q Consensus 1066 k~~yHC~~Cgi---CR~g~gl~~~~fHC~~C~~C 1096 (1235)
+.-|.|++||- =|++-| ..+|.+|+.=
T Consensus 33 ~~ky~Cp~Cgk~~vkR~a~G----IW~C~~C~~~ 62 (90)
T PF01780_consen 33 HAKYTCPFCGKTSVKRVATG----IWKCKKCGKK 62 (90)
T ss_dssp HS-BEESSSSSSEEEEEETT----EEEETTTTEE
T ss_pred hCCCcCCCCCCceeEEeeeE----EeecCCCCCE
Confidence 45577777773 334433 5777777643
No 232
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=23.21 E-value=42 Score=37.34 Aligned_cols=39 Identities=38% Similarity=0.760 Sum_probs=26.7
Q ss_pred ccccccccccCCCcceecCCCCcc-ChhhHHhhhhCCCCCCCCCcCcC
Q 000895 1115 CPICCDFLFTSSATVRALPCGHFM-HSDCFQAYTCSHYICPICSKSLG 1161 (1235)
Q Consensus 1115 CpICle~lf~s~~~v~~LpCgH~f-H~~Ci~~wl~~~~~CPiCrksv~ 1161 (1235)
|-+|.+. ...|..+||.|.. ...|-.. -.+||+|+....
T Consensus 161 Cr~C~~~----~~~VlllPCrHl~lC~~C~~~----~~~CPiC~~~~~ 200 (207)
T KOG1100|consen 161 CRKCGER----EATVLLLPCRHLCLCGICDES----LRICPICRSPKT 200 (207)
T ss_pred ceecCcC----CceEEeecccceEeccccccc----CccCCCCcChhh
Confidence 8888765 2347889999764 4556532 456999997653
No 233
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=23.20 E-value=38 Score=28.85 Aligned_cols=22 Identities=36% Similarity=0.747 Sum_probs=14.9
Q ss_pred cCCCCCCCccccccccCCCCccC
Q 000895 1209 KCGFCGSYNTRVIKVESTNTYCS 1231 (1235)
Q Consensus 1209 kC~~C~SYNT~~~~~~~~~~~~~ 1231 (1235)
||+.||-||-..- +.=.+.+|+
T Consensus 13 kCp~CGt~NG~R~-~~CKN~~C~ 34 (44)
T PF14952_consen 13 KCPKCGTYNGTRG-LSCKNKSCP 34 (44)
T ss_pred cCCcCcCccCccc-ccccCCccc
Confidence 7999999996653 333455554
No 234
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=23.19 E-value=53 Score=42.25 Aligned_cols=45 Identities=24% Similarity=0.597 Sum_probs=33.3
Q ss_pred CCccccccccccCCCcceecCCCC-ccChhhHHhhh--hC----CCCCCCCCcCcC
Q 000895 1113 TNCPICCDFLFTSSATVRALPCGH-FMHSDCFQAYT--CS----HYICPICSKSLG 1161 (1235)
Q Consensus 1113 ~~CpICle~lf~s~~~v~~LpCgH-~fH~~Ci~~wl--~~----~~~CPiCrksv~ 1161 (1235)
..|+||-.. .+-+..-.||| -....|..... .. ...||+||..+.
T Consensus 1 ~~c~ic~~s----~~~~~~~s~~h~~v~~~~~~R~~~~~~~~~~~~~~~vcr~~~~ 52 (669)
T KOG2231|consen 1 DSCAICAFS----PDFVGRGSCGHNEVCATCVVRLRFELNNRKCSNECPVCRREVE 52 (669)
T ss_pred CCcceeecC----ccccccccccccccchhhhhhhhhhcccccccccCccccccee
Confidence 369999765 23355668999 89999998863 23 466899999764
No 235
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=22.94 E-value=57 Score=42.09 Aligned_cols=32 Identities=22% Similarity=0.579 Sum_probs=15.6
Q ss_pred cccccccccccCCCCCCCcCCCCC--ccceEecccccC
Q 000895 1026 MMCMRCLKVQPVGPVCTTLSCSGL--SMAKYYCGICKF 1061 (1235)
Q Consensus 1026 v~C~~C~~~q~~~~~C~~~~C~~~--~~a~y~C~iC~l 1061 (1235)
-.|..|++..+. ..|.+ | |. ..+.-||+.|..
T Consensus 16 kFC~~CG~~l~~-~~Cp~--C-G~~~~~~~~fC~~CG~ 49 (645)
T PRK14559 16 RFCQKCGTSLTH-KPCPQ--C-GTEVPVDEAHCPNCGA 49 (645)
T ss_pred ccccccCCCCCC-CcCCC--C-CCCCCcccccccccCC
Confidence 356666655432 35655 3 33 244445555543
No 236
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=22.73 E-value=32 Score=41.42 Aligned_cols=32 Identities=31% Similarity=0.815 Sum_probs=25.8
Q ss_pred CCCccccccccccCCCcceecCCCCccChhhHHhhh
Q 000895 1112 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYT 1147 (1235)
Q Consensus 1112 ~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl 1147 (1235)
+..||||..+ |. ..++|||||.....|-..-+
T Consensus 4 elkc~vc~~f-~~---epiil~c~h~lc~~ca~~~~ 35 (699)
T KOG4367|consen 4 ELKCPVCGSF-YR---EPIILPCSHNLCQACARNIL 35 (699)
T ss_pred cccCceehhh-cc---CceEeecccHHHHHHHHhhc
Confidence 5679999976 54 25789999999999987654
No 237
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=22.63 E-value=43 Score=38.01 Aligned_cols=77 Identities=19% Similarity=0.509 Sum_probs=49.2
Q ss_pred ccccccccccccCC--------cccCcccccccCCCCCc----cccccccccccccccccCCCCCCCcCCCCCccceEec
Q 000895 989 YKRNCKLRAACCGK--------LFTCRFCHDKVSDHSMD----RKATTEMMCMRCLKVQPVGPVCTTLSCSGLSMAKYYC 1056 (1235)
Q Consensus 989 Y~r~c~l~~~cC~~--------~y~Cr~CHde~~~H~~~----r~~~~~v~C~~C~~~q~~~~~C~~~~C~~~~~a~y~C 1056 (1235)
|+..=...|.-|+. .|.|..||.-..+.++. -+-.-...|..|+++......= .-++-||
T Consensus 115 ~rnqgr~LC~~Cn~k~Ka~~~g~YvC~KCh~~iD~~~l~fr~d~yH~yHFkCt~C~keL~sdaRe--------vk~eLyC 186 (332)
T KOG2272|consen 115 YRNQGRALCRECNQKEKAKGRGRYVCQKCHAHIDEQPLTFRGDPYHPYHFKCTTCGKELTSDARE--------VKGELYC 186 (332)
T ss_pred HhhcchHHhhhhhhhhcccccceeehhhhhhhcccccccccCCCCCccceecccccccccchhhh--------hccceec
Confidence 33333455555643 79999999876654433 2233477899998887754322 2457788
Q ss_pred ccccCcCCCCccccCCCCCcccc
Q 000895 1057 GICKFFDDERVVYHCPFCNLCRV 1079 (1235)
Q Consensus 1057 ~iC~l~d~~k~~yHC~~CgiCR~ 1079 (1235)
.-|. +.+-|+-||-||.
T Consensus 187 lrCh------D~mgipiCgaC~r 203 (332)
T KOG2272|consen 187 LRCH------DKMGIPICGACRR 203 (332)
T ss_pred cccc------cccCCcccccccC
Confidence 8885 2355788888885
No 238
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=22.42 E-value=36 Score=42.87 Aligned_cols=43 Identities=26% Similarity=0.778 Sum_probs=35.9
Q ss_pred CCCCccccccccccCCCcceecCCCCccChhhHHhhhhCCCCCCCCCcCcC
Q 000895 1111 LETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1161 (1235)
Q Consensus 1111 ~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrksv~ 1161 (1235)
.+++|.||.+.+ ..+.-+|- |..|+.+|+.....||.|++.+.
T Consensus 478 ~~~~~~~~~~~~-----~~~~~~~~---~~~~l~~~~~~~~~~pl~~~~~~ 520 (543)
T KOG0802|consen 478 PNDVCAICYQEM-----SARITPCS---HALCLRKWLYVQEVCPLCHTYMK 520 (543)
T ss_pred ccCcchHHHHHH-----Hhcccccc---chhHHHhhhhhccccCCCchhhh
Confidence 468999999996 24555677 99999999999999999998764
No 239
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=22.36 E-value=66 Score=37.65 Aligned_cols=74 Identities=28% Similarity=0.554 Sum_probs=48.6
Q ss_pred cCCC----CccccCCCCCccccCCCCCc-cccccCCcccccccc--c--ccccccCCCCCCCccccccccccCCCcceec
Q 000895 1062 FDDE----RVVYHCPFCNLCRVGRGLGV-DFFHCMTCNCCLAKK--L--VDHKCREKGLETNCPICCDFLFTSSATVRAL 1132 (1235)
Q Consensus 1062 ~d~~----k~~yHC~~CgiCR~g~gl~~-~~fHC~~C~~C~~~~--l--~~H~C~e~~~~~~CpICle~lf~s~~~v~~L 1132 (1235)
|||= +-+=||..|- --| |-- =||. |+.|.+-. . ..|-=.-+.....|-.|-+- .++|.++
T Consensus 169 WdDVLks~Ripg~Ces~~--~pg--~fAEFfFK---C~ah~~~~k~~aa~lhli~~N~~ni~C~~Ctdv----~~~vlvf 237 (446)
T KOG0006|consen 169 WDDVLKSKRIPGVCESCC--TPG--LFAEFFFK---CGAHPTSDKETAAALHLIATNSRNITCITCTDV----RSPVLVF 237 (446)
T ss_pred hhhhhhcccCcccccccc--CCc--chHhheeh---hccCCCccccchhHHHHhhcccccceeEEecCC----ccceEEE
Confidence 6664 6677887763 222 333 4554 55555432 2 35555556777889999754 4568889
Q ss_pred CCC--CccChhhHHhh
Q 000895 1133 PCG--HFMHSDCFQAY 1146 (1235)
Q Consensus 1133 pCg--H~fH~~Ci~~w 1146 (1235)
+|. |.....|+.-|
T Consensus 238 ~Cns~HvtC~dCFr~y 253 (446)
T KOG0006|consen 238 QCNSRHVTCLDCFRLY 253 (446)
T ss_pred ecCCceeehHHhhhhH
Confidence 999 99999999866
No 240
>PRK01917 cation-binding hemerythrin HHE family protein; Provisional
Probab=22.32 E-value=3.2e+02 Score=28.27 Aligned_cols=53 Identities=17% Similarity=0.247 Sum_probs=34.8
Q ss_pred HHHhhhhhHHHHHHHHHHHHHhhhcCchHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 000895 117 TYSLEHEGESVLFDQLFELLNSSMRNEESYRRELASCTGALQTSISQHMSKEEEQV 172 (1235)
Q Consensus 117 ~~~~EH~~~~~lf~~l~~~l~~~~~~~~~~~~eLa~~l~~l~~~l~qHm~~EE~qv 172 (1235)
.|+.-+..+|+.=..|+++++.+.... ..++...+..|..-...|+..||.-.
T Consensus 9 ~l~vGi~~ID~qH~~Lf~lin~l~~~~---~~~i~~~l~~L~~y~~~HF~~EE~lM 61 (139)
T PRK01917 9 ELHLGDPFTDATHAEFVQLLNAVARAD---DADFLQALDAWIDHTRHHFAQEERWM 61 (139)
T ss_pred HhhcCChhhhHHHHHHHHHHHHHHcCC---HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444455555555556666666664332 23466777888888999999999754
No 241
>PF11229 DUF3028: Protein of unknown function (DUF3028); InterPro: IPR021392 This eukaryotic family of proteins has no known function.
Probab=22.31 E-value=3.7e+02 Score=34.00 Aligned_cols=97 Identities=23% Similarity=0.179 Sum_probs=71.8
Q ss_pred HHHHHHHHHHHHHHHHHHHhhHhHHHhhhhHHhhhCC---HHHHHHHHHH----------------HHhccCHHHHHHhh
Q 000895 775 EKATELQGMCKSIRVTLDQHVFREELELWPLFDRHFS---VEEQDKIVGR----------------IIGTTGAEVLQSML 835 (1235)
Q Consensus 775 e~~~kL~~~~ksl~~~L~~Hl~~EE~EvfPL~rk~fS---~eeQ~~Lv~~----------------~l~~~p~~~L~~~L 835 (1235)
..++-||..++.|-+.|-+-+.+.|.|++=-+-|++| .+|.++|... +.|+.|+.-|..+|
T Consensus 313 h~Ws~Lc~ttekIF~lLPn~i~~~eveLYi~vAkCLSEMtd~eidrItqitK~nieKa~FVr~yLVSQGR~PL~~LnDvL 392 (589)
T PF11229_consen 313 HCWSLLCETTEKIFDLLPNKIQRNEVELYIGVAKCLSEMTDTEIDRITQITKDNIEKAIFVRLYLVSQGRLPLMGLNDVL 392 (589)
T ss_pred HHHHHHHHHHHHHHHhCcccccHHHHHHHHHHHHHHhhcCHHHHHHHHHhhhccchhhhhhhheehhcccccHhHHHHHH
Confidence 5778899999999999999999999999977777654 5666776552 46789999999999
Q ss_pred hHHhhcCCHHHH-HHHHHHhhhhh----hh---hhHHHHHHHhh
Q 000895 836 PWVTSALTQEEQ-NTMMDTWKQAT----KN---TMFSEWLNEWW 871 (1235)
Q Consensus 836 PWl~~~Lte~E~-~~ml~~~~~a~----~~---t~f~~WL~eW~ 871 (1235)
+|++..-..+-. -.+|....++- .| .-.-+||.|=+
T Consensus 393 ~~a~~~~eket~~WmlL~sfyqarivSh~nTGV~KRmEWLLELM 436 (589)
T PF11229_consen 393 STAMQHHEKETVAWMLLHSFYQARIVSHSNTGVLKRMEWLLELM 436 (589)
T ss_pred HHHHhcchHHHHHHHHHHHHHHheeecccccchHHHHHHHHHHH
Confidence 999996544443 46677666632 22 22338888743
No 242
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=22.23 E-value=1.9e+02 Score=29.49 Aligned_cols=45 Identities=20% Similarity=0.257 Sum_probs=25.9
Q ss_pred CCccccccccccCCC----------cceecCCCCccChhhHHhhhhCCCCCCCCC
Q 000895 1113 TNCPICCDFLFTSSA----------TVRALPCGHFMHSDCFQAYTCSHYICPICS 1157 (1235)
Q Consensus 1113 ~~CpICle~lf~s~~----------~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCr 1157 (1235)
..|--|+..+-+... ...--.|++.|..+|-.-+-..-..||-|.
T Consensus 56 ~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~CPGC~ 110 (112)
T TIGR00622 56 RFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHESLHCCPGCI 110 (112)
T ss_pred CcccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhhccCCcCCC
Confidence 469999887432100 112245777777777655544445677775
No 243
>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=22.19 E-value=40 Score=28.00 Aligned_cols=10 Identities=30% Similarity=0.799 Sum_probs=4.0
Q ss_pred cccCCccccc
Q 000895 1088 FHCMTCNCCL 1097 (1235)
Q Consensus 1088 fHC~~C~~C~ 1097 (1235)
+-|..||.-+
T Consensus 20 ~vC~~CG~Vl 29 (43)
T PF08271_consen 20 LVCPNCGLVL 29 (43)
T ss_dssp EEETTT-BBE
T ss_pred EECCCCCCEe
Confidence 3444444443
No 244
>PRK12775 putative trifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta/ferritin domain-containing protein; Provisional
Probab=22.18 E-value=42 Score=45.51 Aligned_cols=52 Identities=27% Similarity=0.586 Sum_probs=36.1
Q ss_pred CCCCCCCCcCcCchhhhhhhHHHHHhhcCCChhhhccCCcEeccCCCCCCCCCceeeeccCCCCCCC
Q 000895 1150 HYICPICSKSLGDMAVYFGMLDALLASEQLPEEYRDRCQEILCNDCDKKGSAPFHWLYHKCGFCGSY 1216 (1235)
Q Consensus 1150 ~~~CPiCrksv~dm~~~~~~lD~~i~~~pmP~ey~~~~~~i~CnDC~~~s~~~~h~lg~kC~~C~SY 1216 (1235)
..+||-|.+++.-.+.|.-- .+..-...|.||++.|.- |-|-|-.|++||..
T Consensus 796 ~~~~~~~~~~~~~~~~~~~~--------------~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~ 847 (1006)
T PRK12775 796 VATCPKCHRPLEGDEEYVCC--------------ATSELQWRCDDCGKVSEG-FAFPYGMCPACGGK 847 (1006)
T ss_pred CccCcccCCCCCCCceeEEe--------------cCcceeeehhhhcccccc-ccCCcCcCcccccc
Confidence 47899999998654444211 122234579999998753 55567799999986
No 245
>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=22.13 E-value=43 Score=25.90 Aligned_cols=11 Identities=27% Similarity=1.081 Sum_probs=8.6
Q ss_pred ceEecccccCc
Q 000895 1052 AKYYCGICKFF 1062 (1235)
Q Consensus 1052 a~y~C~iC~l~ 1062 (1235)
+.|||++|+.+
T Consensus 2 ~~~~C~~C~~~ 12 (35)
T smart00451 2 GGFYCKLCNVT 12 (35)
T ss_pred cCeEccccCCc
Confidence 57888888865
No 246
>PF02701 zf-Dof: Dof domain, zinc finger; InterPro: IPR003851 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 consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved []. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent
Probab=22.13 E-value=43 Score=30.48 Aligned_cols=15 Identities=33% Similarity=0.467 Sum_probs=12.9
Q ss_pred eccCCCCCCCccccc
Q 000895 1207 YHKCGFCGSYNTRVI 1221 (1235)
Q Consensus 1207 g~kC~~C~SYNT~~~ 1221 (1235)
.++|+.|+|+||+.-
T Consensus 5 ~~~CPRC~S~nTKFc 19 (63)
T PF02701_consen 5 PLPCPRCDSTNTKFC 19 (63)
T ss_pred CCCCCCcCCCCCEEE
Confidence 368999999999874
No 247
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=21.91 E-value=50 Score=43.08 Aligned_cols=29 Identities=21% Similarity=0.346 Sum_probs=20.1
Q ss_pred cEeccCCCCCCCCCceeeeccCCCCCCCc
Q 000895 1189 EILCNDCDKKGSAPFHWLYHKCGFCGSYN 1217 (1235)
Q Consensus 1189 ~i~CnDC~~~s~~~~h~lg~kC~~C~SYN 1217 (1235)
.-.|++||..+.....-.|..|+.|||-|
T Consensus 641 ~~~C~~CG~~Ge~~~~~~~~~CP~CG~~~ 669 (711)
T PRK09263 641 IDECYECGFTGEFECTEKGFTCPKCGNHD 669 (711)
T ss_pred CcccCCCCCCccccCCCCCCcCcCCCCCC
Confidence 34699999865543333356899999977
No 248
>KOG3842 consensus Adaptor protein Pellino [Signal transduction mechanisms]
Probab=21.70 E-value=51 Score=38.55 Aligned_cols=34 Identities=26% Similarity=0.626 Sum_probs=25.3
Q ss_pred ecCCCCccChhhHHhhhh---------CCCCCCCCCcCcCchh
Q 000895 1131 ALPCGHFMHSDCFQAYTC---------SHYICPICSKSLGDMA 1164 (1235)
Q Consensus 1131 ~LpCgH~fH~~Ci~~wl~---------~~~~CPiCrksv~dm~ 1164 (1235)
.-||||.--..=..-|-. .+..||.|-..+..-.
T Consensus 375 F~PCGHv~sekt~~YWs~iplPhGT~~f~a~CPFC~~~L~ge~ 417 (429)
T KOG3842|consen 375 FNPCGHVCSEKTVKYWSQIPLPHGTHAFHAACPFCATQLAGEQ 417 (429)
T ss_pred cCCcccccchhhhhHhhcCcCCCccccccccCcchhhhhccCC
Confidence 459999988888888854 2577999988765433
No 249
>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=21.67 E-value=46 Score=27.69 Aligned_cols=31 Identities=26% Similarity=0.370 Sum_probs=19.8
Q ss_pred cEeccCCCCCCCCCce---eeeccCCCCCCCccc
Q 000895 1189 EILCNDCDKKGSAPFH---WLYHKCGFCGSYNTR 1219 (1235)
Q Consensus 1189 ~i~CnDC~~~s~~~~h---~lg~kC~~C~SYNT~ 1219 (1235)
.+.|.+||....+-.. -....|+.||+-+.+
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~ 38 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSISEDDPVPCPECGSTEVR 38 (42)
T ss_pred EEEeCCCCCEEEEEEEcCCCCCCcCCCCCCCceE
Confidence 4679999976543222 235679999995443
No 250
>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=21.66 E-value=78 Score=36.29 Aligned_cols=10 Identities=30% Similarity=1.454 Sum_probs=5.2
Q ss_pred cccCCccccc
Q 000895 1088 FHCMTCNCCL 1097 (1235)
Q Consensus 1088 fHC~~C~~C~ 1097 (1235)
+.|.+|.+|+
T Consensus 183 ~sCLRCK~cf 192 (314)
T PF06524_consen 183 YSCLRCKICF 192 (314)
T ss_pred hhhhheeeee
Confidence 4455555554
No 251
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=21.44 E-value=56 Score=29.18 Aligned_cols=11 Identities=36% Similarity=1.108 Sum_probs=8.0
Q ss_pred CccccCCCCCc
Q 000895 1066 RVVYHCPFCNL 1076 (1235)
Q Consensus 1066 k~~yHC~~Cgi 1076 (1235)
...|-|++|||
T Consensus 12 ~v~~~Cp~cGi 22 (55)
T PF13824_consen 12 HVNFECPDCGI 22 (55)
T ss_pred ccCCcCCCCCC
Confidence 56677888875
No 252
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=21.41 E-value=50 Score=22.70 Aligned_cols=19 Identities=32% Similarity=0.656 Sum_probs=11.9
Q ss_pred CCCCCCCcCcCchhhhhhh
Q 000895 1151 YICPICSKSLGDMAVYFGM 1169 (1235)
Q Consensus 1151 ~~CPiCrksv~dm~~~~~~ 1169 (1235)
+.||+|.+...+...+..-
T Consensus 1 ~~C~~C~~~~~~~~~l~~H 19 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQH 19 (24)
T ss_dssp EE-SSTS-EESSHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHH
Confidence 4699999988876655443
No 253
>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=21.41 E-value=35 Score=28.00 Aligned_cols=13 Identities=46% Similarity=1.185 Sum_probs=5.5
Q ss_pred cceEecccccCcC
Q 000895 1051 MAKYYCGICKFFD 1063 (1235)
Q Consensus 1051 ~a~y~C~iC~l~d 1063 (1235)
|.+|||+-|+.|=
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 5689999999874
No 254
>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=21.26 E-value=57 Score=37.53 Aligned_cols=44 Identities=25% Similarity=0.468 Sum_probs=25.6
Q ss_pred CCCCCccccccccccCCCcceecC-CC-CccChhhHHhh-hhCCCCCC
Q 000895 1110 GLETNCPICCDFLFTSSATVRALP-CG-HFMHSDCFQAY-TCSHYICP 1154 (1235)
Q Consensus 1110 ~~~~~CpICle~lf~s~~~v~~Lp-Cg-H~fH~~Ci~~w-l~~~~~CP 1154 (1235)
.+-.-|+||.|- ...+.+-..|. =. =-=|.+||.+| +--+..||
T Consensus 28 ~tLsfChiCfEl-~iegvpks~llHtkSlRGHrdCFEK~HlIanQ~~p 74 (285)
T PF06937_consen 28 ETLSFCHICFEL-SIEGVPKSNLLHTKSLRGHRDCFEKYHLIANQDCP 74 (285)
T ss_pred cceeecceeecc-ccccCccccccccccccchHHHHHHHHHHHcCCCC
Confidence 344568888865 33332222221 00 12389999999 55688999
No 255
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=21.25 E-value=50 Score=28.76 Aligned_cols=24 Identities=29% Similarity=0.664 Sum_probs=14.9
Q ss_pred cCCCCCccccCCCCCccccccCCccc
Q 000895 1070 HCPFCNLCRVGRGLGVDFFHCMTCNC 1095 (1235)
Q Consensus 1070 HC~~CgiCR~g~gl~~~~fHC~~C~~ 1095 (1235)
.||.||-. +-. ...+.++|.+||.
T Consensus 22 fCP~Cg~~-~m~-~~~~r~~C~~Cgy 45 (50)
T PRK00432 22 FCPRCGSG-FMA-EHLDRWHCGKCGY 45 (50)
T ss_pred cCcCCCcc-hhe-ccCCcEECCCcCC
Confidence 68888764 221 1246788888874
No 256
>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]
Probab=21.15 E-value=42 Score=37.32 Aligned_cols=26 Identities=35% Similarity=0.758 Sum_probs=17.0
Q ss_pred cCCCCccChhhHHhhhhCCCCCCCCC
Q 000895 1132 LPCGHFMHSDCFQAYTCSHYICPICS 1157 (1235)
Q Consensus 1132 LpCgH~fH~~Ci~~wl~~~~~CPiCr 1157 (1235)
-.||=-||..|+..++.....||-|.
T Consensus 198 g~c~i~~h~~c~qty~q~~~~cphc~ 223 (235)
T KOG4718|consen 198 GSCNIQYHRGCIQTYLQRRDICPHCG 223 (235)
T ss_pred CcccchhhhHHHHHHhcccCcCCchh
Confidence 34555567777777776666777764
No 257
>KOG2129 consensus Uncharacterized conserved protein H4 [Function unknown]
Probab=20.79 E-value=5.3e+02 Score=31.71 Aligned_cols=15 Identities=27% Similarity=0.224 Sum_probs=9.1
Q ss_pred HHHHHHHHHHHhccc
Q 000895 182 FEEQASLVWQFLCSI 196 (1235)
Q Consensus 182 ~~Eq~~L~~~~i~si 196 (1235)
..||.+|+..++.-|
T Consensus 196 EQEqEalvN~LwKrm 210 (552)
T KOG2129|consen 196 EQEQEALVNSLWKRM 210 (552)
T ss_pred HHHHHHHHHHHHHHH
Confidence 346667777666544
No 258
>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=20.68 E-value=19 Score=42.79 Aligned_cols=34 Identities=21% Similarity=0.368 Sum_probs=14.3
Q ss_pred CCcEeccCCCCCCCCCceeeeccCCCCCCCcccc
Q 000895 1187 CQEILCNDCDKKGSAPFHWLYHKCGFCGSYNTRV 1220 (1235)
Q Consensus 1187 ~~~i~CnDC~~~s~~~~h~lg~kC~~C~SYNT~~ 1220 (1235)
+-...|-||+.++..-.-+=...|.+||++|-..
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 3467899999886533333346799999887543
No 259
>PF15353 HECA: Headcase protein family homologue
Probab=20.63 E-value=43 Score=33.55 Aligned_cols=16 Identities=38% Similarity=1.105 Sum_probs=13.8
Q ss_pred CCCCccChhhHHhhhh
Q 000895 1133 PCGHFMHSDCFQAYTC 1148 (1235)
Q Consensus 1133 pCgH~fH~~Ci~~wl~ 1148 (1235)
|.|++||.+||++|-.
T Consensus 39 p~~~~MH~~CF~~wE~ 54 (107)
T PF15353_consen 39 PFGQYMHRECFEKWED 54 (107)
T ss_pred CCCCchHHHHHHHHHH
Confidence 5589999999999953
No 260
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=20.56 E-value=64 Score=29.18 Aligned_cols=28 Identities=18% Similarity=0.107 Sum_probs=20.7
Q ss_pred cEeccCCCCCCCCCceeeeccCCCCCCCcccccc
Q 000895 1189 EILCNDCDKKGSAPFHWLYHKCGFCGSYNTRVIK 1222 (1235)
Q Consensus 1189 ~i~CnDC~~~s~~~~h~lg~kC~~C~SYNT~~~~ 1222 (1235)
.+.|..||.. ...| +.|. ||.||.+++-
T Consensus 27 ~~~c~~cg~~--~~pH---~vc~-cG~Y~gr~v~ 54 (60)
T PRK01110 27 LSVDKTTGEY--HLPH---HVSP-KGYYKGRKVL 54 (60)
T ss_pred eeEcCCCCce--eccc---eecC-CcccCCeEee
Confidence 5789999964 3334 3499 9999999863
No 261
>PHA00626 hypothetical protein
Probab=20.47 E-value=62 Score=29.03 Aligned_cols=11 Identities=27% Similarity=0.758 Sum_probs=5.3
Q ss_pred ceEecccccCc
Q 000895 1052 AKYYCGICKFF 1062 (1235)
Q Consensus 1052 a~y~C~iC~l~ 1062 (1235)
.+|-|..|.++
T Consensus 22 nrYkCkdCGY~ 32 (59)
T PHA00626 22 DDYVCCDCGYN 32 (59)
T ss_pred cceEcCCCCCe
Confidence 34555555544
No 262
>PF12126 DUF3583: Protein of unknown function (DUF3583); InterPro: IPR021978 This domain is found in eukaryotes, and is typically between 302 and 338 amino acids in length. It is found in association with PF00097 from PFAM and PF00643 from PFAM. Most members are promyelocytic leukemia proteins, and this family lies towards the C terminus.
Probab=20.36 E-value=5e+02 Score=30.62 Aligned_cols=132 Identities=14% Similarity=0.150 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhccCCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHHHhhhhHHHHHHhhhhhH
Q 000895 46 IFLFFHKAIKSELDVLHRAAMAFATNLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIRVKNIARTYSLEHEGE 125 (1235)
Q Consensus 46 ~~~~~HkAlR~eL~~l~~~~~~~~~~~gd~~~~~~l~~r~~fL~~~~~~H~~aEDevI~PaLd~Rv~~v~~~~~~EH~~~ 125 (1235)
.|--.|..+|.-...|-+.-..+.. -=.++++++.+++ .+.-..|.-+++ . +|+.+|+++
T Consensus 14 ~F~aahaqm~sav~qL~~~r~~tee--lIr~rVrq~V~hV-----------qaqEreLLe~v~--~-----rYqR~y~em 73 (324)
T PF12126_consen 14 AFGAAHAQMRSAVSQLGRARADTEE--LIRARVRQVVAHV-----------QAQERELLEAVE--A-----RYQRDYEEM 73 (324)
T ss_pred hHHHHHHHHHHHHHHHHHHHhhHHH--HHHHHHHHHHHHH-----------HHHHHHHHHHHH--H-----HHHHHHHHH
Q ss_pred HHHHHHHHHHHHhhhcCch-----HHH--HHHHHHHHHHHHHHHHhHHHHHHHHhhHHhhcCCHHHHHHHHHHHhcccC
Q 000895 126 SVLFDQLFELLNSSMRNEE-----SYR--RELASCTGALQTSISQHMSKEEEQVFPLLIEKFSFEEQASLVWQFLCSIP 197 (1235)
Q Consensus 126 ~~lf~~l~~~l~~~~~~~~-----~~~--~eLa~~l~~l~~~l~qHm~~EE~qv~PLl~~~fS~~Eq~~L~~~~i~siP 197 (1235)
..-+.+|.+-|.+++.... ..| ++=+.-..-+..-...+|..||=+.+-.+.++=.++|-+.=...++..|.
T Consensus 74 a~~L~~LeavLqRir~G~~LVekM~~YASDQEVLdMh~FlreAL~rLrqeePq~lqa~V~td~F~E~k~rLQ~L~scIt 152 (324)
T PF12126_consen 74 AGQLGRLEAVLQRIRTGGALVEKMKLYASDQEVLDMHGFLREALERLRQEEPQNLQAAVRTDGFDEFKARLQDLVSCIT 152 (324)
T ss_pred HHHHhHHHHHHHHHHhHHHHHHHHHHhcchHHHHHHHHHHHHHHHHhhhhcCcccccceecccHHHHHHHHHHHHHHHh
No 263
>cd06960 NR_DBD_HNF4A DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers. DNA-binding domain of hepatocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. HNF4 interacts with a DNA site, composed of two direct repeats of AGTTCA with 1 bp spacer, which is upstream of target genes and modulates the rate of transcriptional initiation. HNF4 is a member of the nuclear receptor superfamily. HNF4 plays a key role in establishing and maintenance of hepatocyte differentiation in the liver. It is also expressed in gut, kidney, and pancreatic beta cells. HNF4 was originally classified as an orphan receptor, but later it is found that HNF4 binds with very high affinity to a variety of fatty acids. However, unlike other nuclear receptors, the ligands do not act as a molecular switch for HNF4. They seem to constantly bind to the receptor, which is
Probab=20.29 E-value=93 Score=29.01 Aligned_cols=45 Identities=27% Similarity=0.530 Sum_probs=31.9
Q ss_pred CCccceEecccccCc-CCC---CccccCCCCCccccCCCCCccccccCCccc
Q 000895 1048 GLSMAKYYCGICKFF-DDE---RVVYHCPFCNLCRVGRGLGVDFFHCMTCNC 1095 (1235)
Q Consensus 1048 ~~~~a~y~C~iC~l~-d~~---k~~yHC~~CgiCR~g~gl~~~~fHC~~C~~ 1095 (1235)
|..+|-+-|.-|+-| -.. +..|.|..-+-|.+... ....|..|..
T Consensus 10 ~~hygv~~C~aC~~FFrR~~~~~~~~~C~~~~~C~i~~~---~r~~C~~CR~ 58 (76)
T cd06960 10 GKHYGVLSCNGCKGFFRRSVRKNRTYTCRFGGNCVVDKD---KRNACRYCRF 58 (76)
T ss_pred ccEECcceeeeehheeCccccCCCceeCCCCCcccccCc---ccccCccchh
Confidence 567888889999954 333 67899998888888642 3455666654
No 264
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=20.17 E-value=90 Score=40.99 Aligned_cols=53 Identities=21% Similarity=0.361 Sum_probs=30.7
Q ss_pred chhhhhhhHHHHHhhcCCChhhhccCCcEeccCCCCCCCCCceeeeccCCCCCCCccccc
Q 000895 1162 DMAVYFGMLDALLASEQLPEEYRDRCQEILCNDCDKKGSAPFHWLYHKCGFCGSYNTRVI 1221 (1235)
Q Consensus 1162 dm~~~~~~lD~~i~~~pmP~ey~~~~~~i~CnDC~~~s~~~~h~lg~kC~~C~SYNT~~~ 1221 (1235)
|.+.....++. +..+.+|----+. ..-.|++||-.+. .| .+||.|||-|+.++
T Consensus 655 n~eal~~lvk~-~~~~~i~Y~sin~-~~~~C~~CG~~~~--~~---~~CP~CG~~~~~~~ 707 (735)
T PRK07111 655 NVEAFEIIVKA-MKNTNIGYGSINH-PVDRCPVCGYLGV--IE---DKCPKCGSTNIQRI 707 (735)
T ss_pred CHHHHHHHHHH-HHhCCCceEEeCC-CCeecCCCCCCCC--cC---ccCcCCCCccceee
Confidence 33444444443 4455565322222 3456999996443 44 59999999776555
No 265
>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=20.13 E-value=78 Score=39.56 Aligned_cols=10 Identities=40% Similarity=1.152 Sum_probs=5.4
Q ss_pred cccCcccccc
Q 000895 1003 LFTCRFCHDK 1012 (1235)
Q Consensus 1003 ~y~Cr~CHde 1012 (1235)
.|-|+.||.-
T Consensus 5 L~fC~~C~~i 14 (483)
T PF05502_consen 5 LYFCEHCHKI 14 (483)
T ss_pred ceeccccccc
Confidence 4556666544
No 266
>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=20.11 E-value=5.1e+02 Score=25.91 Aligned_cols=69 Identities=14% Similarity=0.218 Sum_probs=37.5
Q ss_pred HHHhhhhhHHHHHHHHHHHHHhhhcCchHHHHHHHHHHHHHHHHHHHhHHHHHHHHhhHHhhcC-CHHHHHHHHHHHhc
Q 000895 117 TYSLEHEGESVLFDQLFELLNSSMRNEESYRRELASCTGALQTSISQHMSKEEEQVFPLLIEKF-SFEEQASLVWQFLC 194 (1235)
Q Consensus 117 ~~~~EH~~~~~lf~~l~~~l~~~~~~~~~~~~eLa~~l~~l~~~l~qHm~~EE~qv~PLl~~~f-S~~Eq~~L~~~~i~ 194 (1235)
.|+.-+..+|..=..|+++++.+..... +..+..|..-...|+..||.-.-. ..| ..++-.+-+.+|+.
T Consensus 10 ~~~~G~~~ID~qH~~L~~lin~l~~~~~------~~~l~~L~~y~~~HF~~EE~lM~~---~~yp~~~~H~~~H~~f~~ 79 (115)
T TIGR00058 10 SFKVFYDNLDEEHKTLFNGIFALAADNS------ATALKELIDVTVLHFLDEEAMMIA---ANYSDYDEHKKAHDDFLA 79 (115)
T ss_pred hhhcCCHHHHHHHHHHHHHHHHHHhcch------HHHHHHHHHHHHHHHHHHHHHHHH---cCCCChHHHHHHHHHHHH
Confidence 3444444444444455555555533221 345677777788999999975431 122 23344555666654
Done!