Query 000886
Match_columns 1237
No_of_seqs 560 out of 1553
Neff 5.3
Searched_HMMs 46136
Date Tue Apr 2 00:31:13 2013
Command hhsearch -i /work/01045/syshi/lefta3m/000886.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/leftcdd/000886hhsearch_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 7.9E-62 1.7E-66 531.8 7.5 253 974-1232 21-275 (276)
2 PF14599 zinc_ribbon_6: Zinc-r 99.9 5.3E-25 1.1E-29 192.0 -0.7 61 1162-1222 1-61 (61)
3 PF05495 zf-CHY: CHY zinc fing 99.8 4.3E-21 9.3E-26 173.7 0.8 70 988-1065 1-71 (71)
4 PF01814 Hemerythrin: Hemeryth 99.2 3.8E-10 8.3E-15 110.1 14.5 124 293-425 2-133 (133)
5 PF01814 Hemerythrin: Hemeryth 99.2 2.2E-10 4.9E-15 111.7 11.9 129 43-176 2-133 (133)
6 PF13639 zf-RING_2: Ring finge 99.1 1.1E-11 2.3E-16 102.2 0.9 44 1115-1159 1-44 (44)
7 COG4357 Zinc finger domain con 98.9 9.6E-11 2.1E-15 109.6 -1.2 57 984-1040 11-75 (105)
8 COG5243 HRD1 HRD ubiquitin lig 98.8 1.2E-09 2.5E-14 123.1 2.8 57 1111-1167 284-350 (491)
9 KOG4628 Predicted E3 ubiquitin 98.8 1.3E-09 2.8E-14 124.8 2.4 54 1110-1165 226-280 (348)
10 PF12678 zf-rbx1: RING-H2 zinc 98.8 3E-09 6.5E-14 97.3 3.2 47 1113-1159 18-73 (73)
11 KOG0804 Cytoplasmic Zn-finger 98.8 2.5E-09 5.4E-14 123.4 3.0 82 1114-1222 175-258 (493)
12 PRK10992 iron-sulfur cluster r 98.8 7.5E-08 1.6E-12 105.6 13.9 132 293-427 75-218 (220)
13 TIGR03652 FeS_repair_RIC iron- 98.6 1.9E-07 4.1E-12 102.1 12.4 129 294-425 72-216 (216)
14 PRK10992 iron-sulfur cluster r 98.6 4.4E-07 9.6E-12 99.6 14.5 129 49-178 82-218 (220)
15 PHA02929 N1R/p28-like protein; 98.5 4.6E-08 1E-12 107.8 4.2 54 1111-1164 171-228 (238)
16 cd00162 RING RING-finger (Real 98.5 7.8E-08 1.7E-12 77.4 3.3 44 1116-1162 1-45 (45)
17 COG3945 Uncharacterized conser 98.5 2.4E-06 5.3E-11 89.3 14.5 140 292-440 8-158 (189)
18 COG5540 RING-finger-containing 98.5 6.1E-08 1.3E-12 107.3 2.9 53 1110-1163 319-372 (374)
19 TIGR03652 FeS_repair_RIC iron- 98.5 1.7E-06 3.6E-11 94.8 13.4 127 49-175 78-215 (216)
20 PF13923 zf-C3HC4_2: Zinc fing 98.4 1E-07 2.2E-12 76.8 2.0 39 1117-1158 1-39 (39)
21 PRK13276 cell wall biosynthesi 98.3 6E-06 1.3E-10 90.6 13.8 125 49-174 85-221 (224)
22 PRK13276 cell wall biosynthesi 98.3 6.4E-06 1.4E-10 90.4 13.2 128 294-424 79-222 (224)
23 PF13920 zf-C3HC4_3: Zinc fing 98.3 3.5E-07 7.5E-12 77.5 2.2 47 1114-1164 2-49 (50)
24 PF12861 zf-Apc11: Anaphase-pr 98.2 6.6E-07 1.4E-11 83.8 3.4 46 1115-1162 33-81 (85)
25 smart00184 RING Ring finger. E 98.1 1.6E-06 3.5E-11 67.3 2.8 38 1117-1158 1-39 (39)
26 PF14634 zf-RING_5: zinc-RING 98.1 2.1E-06 4.7E-11 71.0 3.0 44 1116-1160 1-44 (44)
27 PF15227 zf-C3HC4_4: zinc fing 98.0 2.1E-06 4.6E-11 70.6 2.1 38 1117-1158 1-42 (42)
28 PLN03208 E3 ubiquitin-protein 98.0 3.8E-06 8.2E-11 89.7 4.3 52 1109-1164 13-80 (193)
29 PF00097 zf-C3HC4: Zinc finger 98.0 2.3E-06 4.9E-11 69.3 1.9 39 1117-1158 1-41 (41)
30 COG2846 Regulator of cell morp 98.0 5.1E-05 1.1E-09 80.7 11.9 128 295-425 79-217 (221)
31 KOG0802 E3 ubiquitin ligase [P 98.0 1.7E-06 3.8E-11 106.4 1.1 53 1110-1162 287-340 (543)
32 COG5194 APC11 Component of SCF 98.0 3.9E-06 8.4E-11 76.9 2.9 48 1115-1162 32-80 (88)
33 KOG0320 Predicted E3 ubiquitin 97.9 4.6E-06 9.9E-11 87.2 2.4 47 1114-1163 131-178 (187)
34 PHA02926 zinc finger-like prot 97.9 6.3E-06 1.4E-10 89.0 3.2 53 1111-1163 167-230 (242)
35 smart00504 Ubox Modified RING 97.8 1.7E-05 3.7E-10 69.7 3.8 45 1115-1163 2-46 (63)
36 PF13445 zf-RING_UBOX: RING-ty 97.8 1.1E-05 2.4E-10 66.8 2.1 39 1117-1156 1-43 (43)
37 KOG1493 Anaphase-promoting com 97.7 9.3E-06 2E-10 73.9 0.3 28 1135-1162 50-80 (84)
38 KOG1428 Inhibitor of type V ad 97.7 1.9E-05 4.1E-10 99.6 2.5 114 1026-1163 3416-3544(3738)
39 COG2846 Regulator of cell morp 97.6 0.00053 1.2E-08 73.2 12.1 132 45-176 79-217 (221)
40 KOG0317 Predicted E3 ubiquitin 97.6 2.6E-05 5.7E-10 87.0 1.8 46 1115-1164 240-285 (293)
41 KOG0825 PHD Zn-finger protein 97.6 1.2E-05 2.5E-10 98.0 -1.3 75 1089-1164 96-172 (1134)
42 COG3945 Uncharacterized conser 97.5 0.00096 2.1E-08 70.4 12.2 139 44-189 10-156 (189)
43 TIGR00599 rad18 DNA repair pro 97.5 5.1E-05 1.1E-09 89.6 3.2 47 1114-1164 26-72 (397)
44 smart00744 RINGv The RING-vari 97.3 0.00012 2.5E-09 62.4 2.3 42 1116-1159 1-49 (49)
45 KOG2930 SCF ubiquitin ligase, 97.3 5.3E-05 1.2E-09 72.7 -0.1 28 1134-1161 79-106 (114)
46 PF11793 FANCL_C: FANCL C-term 97.3 7.6E-05 1.6E-09 68.1 0.7 50 1114-1163 2-66 (70)
47 KOG2177 Predicted E3 ubiquitin 97.3 0.00028 6E-09 77.4 5.0 44 1113-1160 12-55 (386)
48 KOG0287 Postreplication repair 97.2 0.00014 3.1E-09 82.2 2.5 59 1115-1177 24-83 (442)
49 TIGR00570 cdk7 CDK-activating 97.2 0.00022 4.8E-09 81.5 4.0 51 1114-1164 3-55 (309)
50 KOG0823 Predicted E3 ubiquitin 97.2 0.00016 3.4E-09 79.0 2.4 51 1111-1165 44-97 (230)
51 KOG0827 Predicted E3 ubiquitin 97.2 0.00011 2.5E-09 84.3 1.4 47 1115-1162 5-55 (465)
52 KOG2164 Predicted E3 ubiquitin 97.2 0.00015 3.3E-09 86.3 2.5 49 1112-1164 184-237 (513)
53 KOG0828 Predicted E3 ubiquitin 97.0 0.00021 4.6E-09 84.1 1.3 32 1132-1163 602-634 (636)
54 KOG1734 Predicted RING-contain 96.9 0.00021 4.6E-09 78.9 0.1 50 1114-1163 224-281 (328)
55 PF04564 U-box: U-box domain; 96.8 0.001 2.2E-08 61.0 3.2 47 1114-1164 4-51 (73)
56 COG5574 PEX10 RING-finger-cont 96.7 0.00068 1.5E-08 75.3 1.8 46 1114-1163 215-262 (271)
57 KOG1039 Predicted E3 ubiquitin 96.6 0.00088 1.9E-08 78.0 2.0 82 1111-1194 158-252 (344)
58 PF14835 zf-RING_6: zf-RING of 96.4 0.002 4.3E-08 57.7 2.5 56 1115-1176 8-65 (65)
59 COG5432 RAD18 RING-finger-cont 96.1 0.003 6.4E-08 70.6 2.0 44 1115-1162 26-69 (391)
60 KOG4172 Predicted E3 ubiquitin 96.0 0.0016 3.4E-08 56.2 -0.4 52 1113-1168 6-59 (62)
61 KOG1941 Acetylcholine receptor 95.9 0.0017 3.6E-08 75.0 -0.5 61 1105-1166 357-419 (518)
62 KOG1645 RING-finger-containing 95.7 0.006 1.3E-07 71.2 2.5 49 1114-1162 4-55 (463)
63 KOG4265 Predicted E3 ubiquitin 95.7 0.0061 1.3E-07 70.5 2.5 51 1110-1164 286-337 (349)
64 KOG0311 Predicted E3 ubiquitin 95.7 0.0021 4.5E-08 73.9 -1.3 47 1114-1163 43-90 (381)
65 COG5219 Uncharacterized conser 95.6 0.0037 8.1E-08 78.3 0.7 52 1111-1162 1466-1522(1525)
66 COG2461 Uncharacterized conser 95.6 0.075 1.6E-06 62.5 11.0 133 291-441 85-223 (409)
67 KOG0978 E3 ubiquitin ligase in 95.4 0.005 1.1E-07 76.9 0.6 47 1115-1165 644-691 (698)
68 KOG1785 Tyrosine kinase negati 95.0 0.0067 1.4E-07 70.3 0.1 53 1107-1163 362-416 (563)
69 KOG1940 Zn-finger protein [Gen 94.9 0.0025 5.3E-08 72.2 -3.7 133 688-852 17-149 (276)
70 KOG2879 Predicted E3 ubiquitin 94.2 0.033 7.2E-07 62.5 3.2 52 1112-1166 237-290 (298)
71 PF14570 zf-RING_4: RING/Ubox 94.0 0.041 8.9E-07 47.0 2.5 45 1117-1161 1-46 (48)
72 KOG1701 Focal adhesion adaptor 93.7 0.0098 2.1E-07 69.9 -2.1 71 1068-1163 295-371 (468)
73 KOG4445 Uncharacterized conser 93.7 0.019 4.1E-07 64.8 0.0 55 1110-1165 111-188 (368)
74 KOG3970 Predicted E3 ubiquitin 93.4 0.055 1.2E-06 58.9 2.9 52 1111-1164 47-106 (299)
75 PF11789 zf-Nse: Zinc-finger o 93.3 0.047 1E-06 48.2 1.8 43 1112-1157 9-53 (57)
76 KOG3268 Predicted E3 ubiquitin 93.2 0.048 1E-06 57.6 2.1 31 1133-1163 187-228 (234)
77 PF10367 Vps39_2: Vacuolar sor 92.8 0.044 9.6E-07 52.9 1.0 37 1108-1146 72-108 (109)
78 KOG0309 Conserved WD40 repeat- 92.7 0.061 1.3E-06 66.8 2.3 49 1107-1157 1021-1069(1081)
79 KOG3039 Uncharacterized conser 92.6 0.082 1.8E-06 58.5 2.9 56 1109-1165 216-272 (303)
80 KOG0824 Predicted E3 ubiquitin 92.3 0.073 1.6E-06 60.6 2.1 48 1112-1163 5-53 (324)
81 PF12906 RINGv: RING-variant d 92.1 0.094 2E-06 44.5 2.1 40 1117-1158 1-47 (47)
82 KOG0297 TNF receptor-associate 92.0 0.088 1.9E-06 63.1 2.4 54 1112-1168 19-72 (391)
83 KOG4739 Uncharacterized protei 92.0 0.062 1.3E-06 59.7 1.0 37 1125-1163 12-48 (233)
84 PF05883 Baculo_RING: Baculovi 91.9 0.061 1.3E-06 55.0 0.8 45 1114-1159 26-76 (134)
85 KOG2272 Focal adhesion protein 91.8 0.06 1.3E-06 59.6 0.7 141 987-1168 63-237 (332)
86 KOG3002 Zn finger protein [Gen 91.7 0.12 2.7E-06 59.6 3.2 62 1114-1185 48-111 (299)
87 COG5152 Uncharacterized conser 91.3 0.097 2.1E-06 56.2 1.6 58 1115-1176 197-254 (259)
88 KOG2660 Locus-specific chromos 91.2 0.054 1.2E-06 62.3 -0.5 50 1112-1164 13-62 (331)
89 COG5175 MOT2 Transcriptional r 89.1 0.13 2.9E-06 58.9 0.4 57 1114-1170 14-71 (480)
90 KOG1002 Nucleotide excision re 89.0 0.14 3E-06 61.6 0.6 51 1109-1163 531-586 (791)
91 PF14447 Prok-RING_4: Prokaryo 89.0 0.19 4.2E-06 44.0 1.2 33 1130-1164 19-51 (55)
92 PF04641 Rtf2: Rtf2 RING-finge 88.7 0.29 6.3E-06 55.5 2.9 51 1111-1163 110-161 (260)
93 KOG2034 Vacuolar sorting prote 88.7 0.19 4.1E-06 64.2 1.4 44 1105-1150 808-851 (911)
94 KOG3800 Predicted E3 ubiquitin 88.5 0.29 6.4E-06 55.6 2.6 48 1116-1163 2-51 (300)
95 COG5592 Uncharacterized conser 88.3 0.74 1.6E-05 48.5 5.1 71 652-732 74-144 (171)
96 KOG1813 Predicted E3 ubiquitin 88.0 0.28 6.1E-06 55.9 2.1 63 1114-1180 241-303 (313)
97 KOG1571 Predicted E3 ubiquitin 87.9 0.26 5.5E-06 57.6 1.7 47 1110-1163 301-347 (355)
98 PHA02862 5L protein; Provision 86.4 0.37 8.1E-06 49.8 1.7 46 1113-1163 1-53 (156)
99 COG5592 Uncharacterized conser 86.4 1.8 4E-05 45.7 6.7 101 678-815 29-136 (171)
100 COG2461 Uncharacterized conser 86.4 3 6.5E-05 49.6 9.2 138 40-191 84-222 (409)
101 KOG4159 Predicted E3 ubiquitin 85.3 0.47 1E-05 57.0 2.1 49 1112-1164 82-130 (398)
102 KOG4275 Predicted E3 ubiquitin 85.1 0.15 3.2E-06 57.8 -2.0 48 1114-1169 300-348 (350)
103 KOG1814 Predicted E3 ubiquitin 84.7 0.46 9.9E-06 56.3 1.6 55 1105-1161 176-238 (445)
104 KOG4692 Predicted E3 ubiquitin 83.4 0.63 1.4E-05 53.9 2.0 51 1110-1164 418-468 (489)
105 KOG2114 Vacuolar assembly/sort 82.2 0.76 1.6E-05 58.6 2.2 42 1115-1162 841-882 (933)
106 TIGR00100 hypA hydrogenase nic 81.4 0.92 2E-05 45.5 2.1 35 1187-1223 66-100 (115)
107 PRK00564 hypA hydrogenase nick 81.0 1 2.2E-05 45.4 2.2 35 1187-1223 67-102 (117)
108 COG5236 Uncharacterized conser 80.8 1.2 2.6E-05 51.6 3.0 65 1094-1162 40-107 (493)
109 PF03854 zf-P11: P-11 zinc fin 80.2 0.55 1.2E-05 40.0 0.1 43 1115-1163 3-46 (50)
110 TIGR02481 hemeryth_dom hemeryt 79.8 6.7 0.00015 39.2 7.6 51 361-421 12-62 (126)
111 KOG0827 Predicted E3 ubiquitin 79.4 0.16 3.5E-06 59.3 -4.4 53 1112-1164 194-246 (465)
112 KOG4185 Predicted E3 ubiquitin 78.1 1.9 4.1E-05 49.5 3.6 47 1115-1162 4-54 (296)
113 PRK12380 hydrogenase nickel in 77.9 1.3 2.8E-05 44.4 1.9 35 1188-1224 67-101 (113)
114 PRK03681 hypA hydrogenase nick 77.9 1.4 3E-05 44.3 2.0 36 1188-1224 67-102 (114)
115 PRK03824 hypA hydrogenase nick 77.5 1.4 2.9E-05 45.6 1.9 34 1190-1223 69-121 (135)
116 PHA02825 LAP/PHD finger-like p 76.9 1.8 3.9E-05 45.7 2.6 46 1112-1162 6-58 (162)
117 PF07800 DUF1644: Protein of u 76.3 2.1 4.5E-05 45.3 2.9 33 1114-1150 2-47 (162)
118 KOG0269 WD40 repeat-containing 76.3 1.9 4.1E-05 54.6 3.0 73 1068-1160 751-825 (839)
119 PRK04023 DNA polymerase II lar 75.6 2.4 5.1E-05 55.5 3.7 43 1029-1077 628-670 (1121)
120 KOG3161 Predicted E3 ubiquitin 75.4 0.93 2E-05 56.1 0.1 44 1115-1161 12-55 (861)
121 KOG1952 Transcription factor N 74.0 1.4 3E-05 56.4 1.1 51 1112-1163 189-247 (950)
122 PF07191 zinc-ribbons_6: zinc- 73.5 0.67 1.4E-05 42.7 -1.3 64 1115-1206 2-68 (70)
123 PF08746 zf-RING-like: RING-li 70.2 2.6 5.6E-05 35.3 1.5 41 1117-1158 1-43 (43)
124 KOG1044 Actin-binding LIM Zn-f 69.8 4.7 0.0001 49.9 4.1 80 1133-1220 80-171 (670)
125 KOG2817 Predicted E3 ubiquitin 69.4 3.3 7.1E-05 49.3 2.7 47 1115-1162 335-384 (394)
126 PF01155 HypA: Hydrogenase exp 69.4 1.5 3.3E-05 43.8 -0.0 34 1188-1223 67-100 (113)
127 PF02084 Bindin: Bindin; Inte 68.9 14 0.0003 41.2 7.1 45 72-127 124-169 (238)
128 KOG0801 Predicted E3 ubiquitin 68.6 2.3 5E-05 44.8 1.1 31 1111-1142 174-204 (205)
129 PF14446 Prok-RING_1: Prokaryo 67.7 4.3 9.2E-05 35.8 2.4 37 1112-1148 3-39 (54)
130 COG5222 Uncharacterized conser 66.8 3.4 7.5E-05 47.2 2.1 44 1115-1161 275-319 (427)
131 TIGR02481 hemeryth_dom hemeryt 65.8 90 0.0019 31.1 11.8 109 297-424 13-125 (126)
132 COG5220 TFB3 Cdk activating ki 65.5 1.8 3.9E-05 48.1 -0.4 51 1113-1163 9-64 (314)
133 PRK00762 hypA hydrogenase nick 65.2 3.9 8.4E-05 41.7 1.9 35 1188-1223 67-106 (124)
134 smart00132 LIM Zinc-binding do 64.1 4.4 9.6E-05 31.5 1.7 38 1116-1163 1-38 (39)
135 PF01529 zf-DHHC: DHHC palmito 63.9 5 0.00011 42.1 2.5 47 1050-1102 43-89 (174)
136 PF06524 NOA36: NOA36 protein; 63.7 3.5 7.6E-05 46.5 1.4 50 1003-1063 140-190 (314)
137 PRK14890 putative Zn-ribbon RN 63.7 5.5 0.00012 35.7 2.3 45 1027-1078 7-56 (59)
138 KOG4443 Putative transcription 63.5 5.5 0.00012 50.1 3.1 70 1114-1188 145-225 (694)
139 KOG2068 MOT2 transcription fac 62.5 5.5 0.00012 46.6 2.7 52 1112-1163 247-298 (327)
140 PHA03096 p28-like protein; Pro 62.5 3.9 8.3E-05 47.3 1.5 47 1115-1161 179-232 (284)
141 TIGR00595 priA primosomal prot 61.7 5.7 0.00012 49.5 2.9 48 997-1050 214-261 (505)
142 PF05502 Dynactin_p62: Dynacti 60.0 6.3 0.00014 48.9 2.8 13 1154-1166 88-100 (483)
143 KOG0298 DEAD box-containing he 59.4 2.5 5.5E-05 56.3 -0.7 70 145-214 237-306 (1394)
144 KOG2066 Vacuolar assembly/sort 58.9 3.6 7.7E-05 52.6 0.5 90 405-496 393-487 (846)
145 COG0375 HybF Zn finger protein 57.4 6.3 0.00014 39.8 1.8 36 1187-1224 66-101 (115)
146 PF02891 zf-MIZ: MIZ/SP-RING z 56.2 4.4 9.6E-05 35.0 0.4 41 1115-1161 3-50 (50)
147 cd00350 rubredoxin_like Rubred 55.7 8.1 0.00018 30.5 1.8 24 1055-1078 1-25 (33)
148 PRK01917 cation-binding hemery 55.6 31 0.00066 35.7 6.5 50 363-420 11-60 (139)
149 KOG1001 Helicase-like transcri 55.4 5.2 0.00011 51.4 1.1 43 1115-1162 455-499 (674)
150 PF14357 DUF4404: Domain of un 54.8 85 0.0018 30.2 8.8 82 54-139 2-83 (85)
151 COG1198 PriA Primosomal protei 52.9 11 0.00023 49.0 3.3 55 996-1057 435-489 (730)
152 PRK05580 primosome assembly pr 52.5 9.4 0.0002 49.3 2.7 49 996-1050 381-429 (679)
153 PRK14714 DNA polymerase II lar 50.7 14 0.00029 50.1 3.7 23 297-319 7-29 (1337)
154 PRK12286 rpmF 50S ribosomal pr 49.4 13 0.00027 33.2 2.2 29 1190-1223 26-54 (57)
155 cd00522 Hemerythrin Hemerythri 49.2 82 0.0018 31.3 8.2 28 401-428 37-68 (113)
156 KOG2932 E3 ubiquitin ligase in 48.8 8.7 0.00019 44.4 1.4 31 1132-1164 105-135 (389)
157 PF09538 FYDLN_acid: Protein o 48.4 10 0.00022 38.0 1.6 32 995-1040 8-39 (108)
158 PF14353 CpXC: CpXC protein 48.1 17 0.00037 36.8 3.2 56 1153-1210 2-57 (128)
159 PF09538 FYDLN_acid: Protein o 47.6 12 0.00025 37.6 1.9 17 1062-1078 18-34 (108)
160 PRK14873 primosome assembly pr 47.5 12 0.00026 48.2 2.6 46 997-1049 384-429 (665)
161 KOG3850 Predicted membrane pro 47.4 5.4E+02 0.012 31.4 15.3 129 301-445 262-396 (455)
162 COG2888 Predicted Zn-ribbon RN 47.2 13 0.00028 33.4 1.9 45 1027-1078 9-58 (61)
163 PRK00808 hypothetical protein; 46.1 3.7E+02 0.0081 28.1 13.0 110 297-428 17-130 (150)
164 KOG1609 Protein involved in mR 46.0 8.4 0.00018 44.2 0.8 50 1114-1163 78-134 (323)
165 KOG1829 Uncharacterized conser 45.5 7 0.00015 49.1 0.0 29 987-1016 345-377 (580)
166 TIGR01562 FdhE formate dehydro 45.3 16 0.00034 42.9 2.8 23 1191-1217 210-232 (305)
167 COG5183 SSM4 Protein involved 44.6 11 0.00024 48.3 1.5 50 1112-1163 10-66 (1175)
168 PRK03564 formate dehydrogenase 44.2 21 0.00045 41.9 3.6 47 1151-1224 186-239 (309)
169 COG5109 Uncharacterized conser 44.0 15 0.00032 42.8 2.2 45 1115-1160 337-384 (396)
170 COG4888 Uncharacterized Zn rib 42.2 11 0.00025 37.1 0.9 32 1068-1099 20-56 (104)
171 PRK04023 DNA polymerase II lar 42.0 22 0.00047 47.2 3.5 47 1041-1099 627-673 (1121)
172 KOG0826 Predicted E3 ubiquitin 41.6 18 0.00039 42.4 2.4 47 1114-1163 300-346 (357)
173 KOG1044 Actin-binding LIM Zn-f 41.2 21 0.00046 44.6 3.1 188 996-1220 16-229 (670)
174 PF12773 DZR: Double zinc ribb 40.8 23 0.00049 30.0 2.4 22 1030-1054 1-23 (50)
175 TIGR02605 CxxC_CxxC_SSSS putat 40.7 16 0.00034 31.3 1.4 31 1191-1221 5-38 (52)
176 PRK00808 hypothetical protein; 40.5 1.4E+02 0.003 31.2 8.7 109 654-807 17-130 (150)
177 PF01783 Ribosomal_L32p: Ribos 40.2 23 0.0005 31.3 2.4 29 1190-1223 25-53 (56)
178 TIGR01031 rpmF_bact ribosomal 39.2 18 0.00038 32.1 1.5 29 1190-1223 25-53 (55)
179 PLN03086 PRLI-interacting fact 39.2 39 0.00085 42.8 5.1 12 1152-1163 504-515 (567)
180 KOG1280 Uncharacterized conser 38.5 23 0.00049 41.8 2.7 25 1051-1078 61-87 (381)
181 PF14631 FancD2: Fanconi anaem 37.5 4.4E+02 0.0096 37.5 14.9 99 127-228 192-306 (1426)
182 KOG3362 Predicted BBOX Zn-fing 37.3 11 0.00024 39.3 -0.0 26 1053-1082 116-143 (156)
183 PRK00398 rpoP DNA-directed RNA 36.9 20 0.00044 30.1 1.5 30 1191-1220 3-32 (46)
184 smart00734 ZnF_Rad18 Rad18-lik 36.5 25 0.00055 26.5 1.8 20 1153-1173 2-21 (26)
185 KOG3053 Uncharacterized conser 36.2 14 0.00031 41.9 0.6 54 1109-1162 15-81 (293)
186 PRK14559 putative protein seri 36.0 26 0.00057 45.0 3.0 31 1029-1062 3-34 (645)
187 PF13901 DUF4206: Domain of un 35.8 20 0.00043 39.6 1.6 27 1129-1160 171-197 (202)
188 COG1656 Uncharacterized conser 35.1 29 0.00062 37.3 2.6 50 1152-1208 97-147 (165)
189 PF07191 zinc-ribbons_6: zinc- 33.0 17 0.00037 33.8 0.5 10 1053-1062 48-57 (70)
190 TIGR02300 FYDLN_acid conserved 32.7 27 0.00059 35.9 1.9 18 1062-1079 18-35 (129)
191 KOG2807 RNA polymerase II tran 32.6 20 0.00044 41.9 1.1 21 855-875 84-104 (378)
192 KOG0006 E3 ubiquitin-protein l 32.0 38 0.00081 39.5 3.0 100 1064-1174 169-295 (446)
193 COG1996 RPC10 DNA-directed RNA 32.0 22 0.00048 30.9 1.0 28 1190-1217 5-32 (49)
194 PLN03086 PRLI-interacting fact 31.7 27 0.00058 44.2 2.0 52 1068-1123 451-513 (567)
195 KOG1812 Predicted E3 ubiquitin 31.6 21 0.00046 43.1 1.1 37 1114-1150 146-182 (384)
196 PF00628 PHD: PHD-finger; Int 31.3 8.1 0.00018 32.6 -1.8 42 1117-1159 2-49 (51)
197 cd00729 rubredoxin_SM Rubredox 31.2 34 0.00073 27.4 1.8 23 1055-1077 2-25 (34)
198 TIGR00373 conserved hypothetic 31.1 16 0.00035 38.8 -0.0 22 1056-1077 110-135 (158)
199 PRK07219 DNA topoisomerase I; 30.7 70 0.0015 42.5 5.6 63 1058-1125 672-744 (822)
200 smart00659 RPOLCX RNA polymera 30.5 31 0.00068 29.2 1.6 26 1191-1217 2-27 (44)
201 PF01907 Ribosomal_L37e: Ribos 30.2 23 0.0005 31.5 0.8 27 1187-1216 11-37 (55)
202 KOG4399 C2HC-type Zn-finger pr 30.2 13 0.00029 42.0 -0.8 63 1029-1100 240-302 (325)
203 PRK06266 transcription initiat 30.1 18 0.00039 39.2 0.1 23 1055-1077 117-143 (178)
204 PRK00398 rpoP DNA-directed RNA 29.6 41 0.00088 28.3 2.2 8 1070-1077 21-28 (46)
205 PF04216 FdhE: Protein involve 29.5 17 0.00037 42.0 -0.1 25 1139-1163 198-222 (290)
206 KOG2593 Transcription initiati 29.4 22 0.00047 43.2 0.7 19 910-928 50-68 (436)
207 KOG4654 Uncharacterized conser 29.4 8.2E+02 0.018 27.2 12.3 55 43-103 41-99 (252)
208 KOG4443 Putative transcription 28.9 29 0.00063 44.0 1.6 47 1115-1163 19-73 (694)
209 PF03833 PolC_DP2: DNA polymer 28.8 19 0.00041 47.0 0.0 44 1028-1077 656-699 (900)
210 PF07227 DUF1423: Protein of u 28.7 41 0.00089 41.2 2.8 31 918-950 21-51 (446)
211 KOG1100 Predicted E3 ubiquitin 28.7 28 0.0006 38.7 1.3 39 1117-1163 161-200 (207)
212 smart00249 PHD PHD zinc finger 28.5 23 0.00051 28.3 0.5 42 1116-1158 1-47 (47)
213 PF09788 Tmemb_55A: Transmembr 28.3 56 0.0012 37.3 3.6 93 1058-1160 68-185 (256)
214 PF13597 NRDD: Anaerobic ribon 28.1 30 0.00064 43.8 1.6 57 1164-1226 465-521 (546)
215 PF05290 Baculo_IE-1: Baculovi 28.1 35 0.00075 35.5 1.7 48 1113-1164 79-133 (140)
216 PF00539 Tat: Transactivating 27.2 58 0.0013 30.2 2.8 18 1070-1090 36-53 (68)
217 cd01675 RNR_III Class III ribo 27.1 54 0.0012 41.5 3.6 56 1164-1225 493-548 (555)
218 PLN02189 cellulose synthase 27.1 48 0.001 44.6 3.2 52 1111-1163 31-87 (1040)
219 cd00522 Hemerythrin Hemerythri 27.1 3E+02 0.0065 27.3 8.1 61 117-195 14-78 (113)
220 PF00301 Rubredoxin: Rubredoxi 26.8 42 0.0009 28.9 1.7 10 1055-1064 1-10 (47)
221 PF06937 EURL: EURL protein; 25.9 42 0.0009 38.5 2.0 45 1111-1156 27-74 (285)
222 KOG2272 Focal adhesion protein 25.8 39 0.00084 38.4 1.7 77 991-1081 115-203 (332)
223 TIGR02300 FYDLN_acid conserved 25.8 40 0.00086 34.8 1.7 32 995-1040 8-39 (129)
224 PF06220 zf-U1: U1 zinc finger 25.8 26 0.00057 28.7 0.3 13 1053-1065 1-13 (38)
225 COG0143 MetG Methionyl-tRNA sy 25.7 42 0.00092 42.5 2.3 44 1052-1101 123-167 (558)
226 PRK00366 ispG 4-hydroxy-3-meth 25.6 60 0.0013 38.8 3.3 53 1153-1209 269-323 (360)
227 TIGR00622 ssl1 transcription f 25.4 1.4E+02 0.0031 30.3 5.5 45 1114-1159 55-110 (112)
228 PRK00420 hypothetical protein; 25.2 42 0.0009 34.0 1.7 30 1113-1163 22-51 (112)
229 PLN02436 cellulose synthase A 25.0 55 0.0012 44.1 3.2 53 1110-1163 32-89 (1094)
230 PRK14892 putative transcriptio 24.6 46 0.001 33.0 1.8 33 1069-1103 20-56 (99)
231 PF14952 zf-tcix: Putative tre 24.6 47 0.001 28.3 1.6 22 1211-1233 13-34 (44)
232 KOG1311 DHHC-type Zn-finger pr 24.5 58 0.0013 37.7 3.0 48 1049-1102 107-154 (299)
233 KOG2231 Predicted E3 ubiquitin 24.4 50 0.0011 42.5 2.6 45 1115-1163 1-52 (669)
234 TIGR00058 Hemerythrin hemeryth 24.1 3.6E+02 0.0077 27.0 8.1 96 361-467 10-110 (115)
235 PF00412 LIM: LIM domain; Int 24.1 34 0.00073 29.3 0.7 40 1117-1166 1-40 (58)
236 KOG0802 E3 ubiquitin ligase [P 24.1 34 0.00074 43.1 1.1 44 1112-1163 477-520 (543)
237 KOG4718 Non-SMC (structural ma 23.9 35 0.00075 37.9 0.9 28 1132-1159 196-223 (235)
238 KOG3896 Dynactin, subunit p62 23.9 31 0.00067 40.6 0.6 49 1094-1164 34-82 (449)
239 KOG2807 RNA polymerase II tran 23.6 83 0.0018 37.1 3.9 102 1051-1160 272-375 (378)
240 PF09328 Phytochelatin_C: Doma 23.6 3.1E+02 0.0067 31.7 8.1 74 171-252 26-116 (264)
241 PF01780 Ribosomal_L37ae: Ribo 23.4 30 0.00066 33.7 0.3 26 1068-1097 33-61 (90)
242 smart00451 ZnF_U1 U1-like zinc 23.3 39 0.00085 26.1 0.9 11 1054-1064 2-12 (35)
243 PRK01917 cation-binding hemery 23.2 2.6E+02 0.0056 28.9 7.1 54 117-173 9-62 (139)
244 KOG2129 Uncharacterized conser 22.6 4.5E+02 0.0098 32.3 9.5 14 183-196 197-210 (552)
245 KOG4399 C2HC-type Zn-finger pr 22.4 25 0.00055 39.9 -0.4 70 1050-1123 199-270 (325)
246 PF12126 DUF3583: Protein of u 22.3 8.1E+02 0.018 29.0 11.2 132 46-197 14-152 (324)
247 PHA00626 hypothetical protein 22.2 54 0.0012 29.3 1.6 11 1054-1064 22-32 (59)
248 PRK10722 hypothetical protein; 22.0 4.4E+02 0.0096 30.3 9.0 115 180-319 88-203 (247)
249 COG3809 Uncharacterized protei 22.0 60 0.0013 30.9 1.9 52 1115-1188 2-55 (88)
250 KOG1312 DHHC-type Zn-finger pr 21.8 30 0.00064 40.1 -0.1 32 1074-1109 149-180 (341)
251 PF08271 TF_Zn_Ribbon: TFIIB z 21.8 40 0.00088 27.9 0.7 6 1091-1096 21-26 (43)
252 PRK00432 30S ribosomal protein 21.5 48 0.001 28.8 1.2 24 1072-1097 22-45 (50)
253 PF05605 zf-Di19: Drought indu 21.3 80 0.0017 27.4 2.5 10 1152-1161 31-40 (54)
254 KOG3842 Adaptor protein Pellin 21.2 52 0.0011 38.5 1.7 34 1133-1166 375-417 (429)
255 PRK08271 anaerobic ribonucleos 21.0 77 0.0017 40.8 3.2 54 1164-1223 541-594 (623)
256 PF02701 zf-Dof: Dof domain, z 20.8 48 0.001 30.2 1.0 16 1209-1224 5-20 (63)
257 PF13824 zf-Mss51: Zinc-finger 20.8 60 0.0013 29.0 1.6 11 1068-1078 12-22 (55)
258 KOG4367 Predicted Zn-finger pr 20.8 39 0.00084 40.8 0.6 32 1114-1149 4-35 (699)
259 PF15353 HECA: Headcase protei 20.6 44 0.00095 33.4 0.8 16 1135-1150 39-54 (107)
260 PRK01110 rpmF 50S ribosomal pr 20.2 67 0.0014 29.0 1.8 28 1191-1224 27-54 (60)
261 PRK12775 putative trifunctiona 20.1 37 0.00081 46.0 0.3 52 1152-1218 796-847 (1006)
No 1
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=100.00 E-value=7.9e-62 Score=531.84 Aligned_cols=253 Identities=50% Similarity=1.090 Sum_probs=240.8
Q ss_pred CCCCcccccccccCcccccccccccccccCCcccCcccccccCCCCCccccccccccccccccccCCCCCCCccCCCCcc
Q 000886 974 CSPSFRDAEKQVFGCEHYKRNCKLRAACCGKLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVGPVCTTLSCSGLSM 1053 (1237)
Q Consensus 974 ~~~~~~~~~~~~~gC~HY~r~c~l~~~cC~~~y~Cr~CHde~~~H~~~r~~~~~v~C~~C~~~Q~~~~~C~~~~C~~~~~ 1053 (1237)
..+++.|+...++||+||+|+|++++|||+++|+|++||++..+|.++|+.+.+|+|+.|+++||++++|.+ | +..+
T Consensus 21 ~~~~~~d~~~~~~~c~hy~r~~~~~a~ccd~~~~C~hCH~~s~~h~~~r~~v~~~~C~~C~~~q~~~~~c~~--c-~~~~ 97 (276)
T KOG1940|consen 21 IHSDAEDEIAFPYGCPHYRRNCKSRAPCCDREITCRHCHNESEDHDLDRKTVYELLCMKCRKIQPVGQICSN--C-HVEL 97 (276)
T ss_pred cccccccccccccCCchhhhccccccccccceeeeEEecChhhhcccchhhhhhhhhhhHHhhhhhhhcccc--c-hhhh
Confidence 346788999999999999999999999999999999999999999999999999999999999999999999 4 7789
Q ss_pred ceEecccccCCCCC-CccccCCCCCccccCCCCCccccccCCccccccccc-ccccccccCCCCCCcccccccccCCCcc
Q 000886 1054 AKYYCGICKFFDDE-RVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLAKKL-VDHKCREKGLETNCPICCDFLFTSSATV 1131 (1237)
Q Consensus 1054 ~~y~C~~C~~~d~~-k~~yHC~~CgiCR~g~gl~~~~fHC~~C~~C~s~~l-~~H~C~e~~~~~~CpICle~lf~s~~~v 1131 (1237)
|+|||.+||||||+ ..||||++|||||+|+++ |||||++|+.|+++.+ +.|+|+|++++.|||||.|++|++...+
T Consensus 98 g~~~c~~C~l~dd~~~~~~hC~~C~icr~g~~~--~~fhc~~c~~c~~~~~~~~H~c~e~~~~~ncPic~e~l~~s~~~~ 175 (276)
T KOG1940|consen 98 GEYYCLICKLFDDDPSKQYHCDLCGICREGLGL--DFFHCKKCKACLSAYLSNWHKCVERSSEFNCPICKEYLFLSFEDA 175 (276)
T ss_pred hhhcCcccccccccccceecccccccccccccc--chhHHhhhHhHHhhhcccccchhhhcccCCCchhHHHhccccccC
Confidence 99999999999988 599999999999999875 9999999999999998 6699999999999999999999999999
Q ss_pred eecCCCCccChhhHHHhhhcCCCCCCCCcccCChhhHHHhHHHHHhhcCCChhhhccCCceecCCCCCCCCCCceeeccc
Q 000886 1132 RALPCGHFMHSDCFQAYTCSHYICPICSKSLGDMAVYFGMLDALLASEQLPEEYRDRCQEILCNDCDKKGSAPFHWLYHK 1211 (1237)
Q Consensus 1132 ~~LpCgH~fH~~Ci~~wl~~~~~CPiCr~sv~dm~~~~~~lD~~i~~~pmP~ey~~~~~~i~CnDC~~~s~~~~h~lg~k 1211 (1237)
..++|||++|..|+.++...+|+||+|.+ ++||..+|+++|.+|+.+|||++|.+++++|+||||+.+++++|||||+|
T Consensus 176 ~~~~CgH~~h~~cf~e~~~~~y~CP~C~~-~~d~~~~~~~~d~~l~~~~~p~~y~~~~~~i~cndC~~~~~~k~~~l~~k 254 (276)
T KOG1940|consen 176 GVLKCGHYMHSRCFEEMICEGYTCPICSK-PGDMSHYFRKLDKELAGSPMPEEYKNKTQDILCNDCGSGTNVKYHILYHK 254 (276)
T ss_pred CccCcccchHHHHHHHHhccCCCCCcccc-hHHHHHHHHHHHHHHhcCCCCchhhchhheeeccCCCCCCccceehhhhh
Confidence 99999999999999999988899999999 99999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCcccccccccCCCCcc
Q 000886 1212 CGFCGSYNTRVIKVESTNTYC 1232 (1237)
Q Consensus 1212 C~~C~SYNT~~~~~~~~~~~~ 1232 (1237)
|+.|+|||||+++.+.....|
T Consensus 255 c~~c~~~~~r~~~~~~~~~~~ 275 (276)
T KOG1940|consen 255 CGKCGSYNTRMISDPSKYDPQ 275 (276)
T ss_pred CCCcccceeeeccCCCccCCC
Confidence 999999999999855544443
No 2
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=99.89 E-value=5.3e-25 Score=191.98 Aligned_cols=61 Identities=56% Similarity=1.049 Sum_probs=22.5
Q ss_pred cCChhhHHHhHHHHHhhcCCChhhhccCCceecCCCCCCCCCCceeecccCCCCCCccccc
Q 000886 1162 LGDMAVYFGMLDALLASEQLPEEYRDRCQEILCNDCDKKGSAPFHWLYHKCGFCGSYNTRV 1222 (1237)
Q Consensus 1162 v~dm~~~~~~lD~~i~~~pmP~ey~~~~~~i~CnDC~~~s~~~~h~lg~kC~~C~SYNT~~ 1222 (1237)
|+||+.+|++||++|+.+|||++|++++++|+||||+++|.++||||||||++|+||||||
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=4.3e-21 Score=173.70 Aligned_cols=70 Identities=44% Similarity=1.197 Sum_probs=53.8
Q ss_pred ccccccc-ccccccccCCcccCcccccccCCCCCccccccccccccccccccCCCCCCCccCCCCccceEecccccCCC
Q 000886 988 CEHYKRN-CKLRAACCGKLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVGPVCTTLSCSGLSMAKYYCGICKFFD 1065 (1237)
Q Consensus 988 C~HY~r~-c~l~~~cC~~~y~Cr~CHde~~~H~~~r~~~~~v~C~~C~~~Q~~~~~C~~~~C~~~~~~~y~C~~C~~~d 1065 (1237)
|+||+|+ |+|+||||++|||||+|||+.++|+++|+.+++|+||.|+++|++++. + | + |+|+|++|++||
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 4 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=3.8e-10 Score=110.13 Aligned_cols=124 Identities=26% Similarity=0.366 Sum_probs=110.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhhcccCCcccHHHHHHHHHHHHHHHHhhhhcccccchhhhhhhh--------hhHH
Q 000886 293 PIDEIMLWHNAIKRELNDIAEAARKIQLSGDFSDLSAFNKRLQFIAEVCIFHSIAEDKVIFPAVDVEL--------SFAQ 364 (1237)
Q Consensus 293 pid~l~~~HkALRrEL~~L~~~a~~~~~~gd~~~L~~L~~r~~fl~~vl~~Hs~aEDevlFPaL~~r~--------~me~ 364 (1237)
+|+.|...|+.||+.++.+...+... ++..++..+...+.+|...+..|+..||+++||.|..+. .+..
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 hHHHHHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 000886 365 EHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPLA 425 (1237)
Q Consensus 365 EH~~ie~l~e~l~~ll~~~~~a~~~~~~~~~~~eLa~~le~L~~~L~~H~~~EE~qvfPLl 425 (1237)
||..+...++.+...+...... ......+...+..+...+..|+.+||+.+||++
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 355778889999999999999999999999986
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=99.16 E-value=2.2e-10 Score=111.75 Aligned_cols=129 Identities=33% Similarity=0.413 Sum_probs=115.3
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHHhhccCCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHHHhh---hhHHHHHH
Q 000886 43 PILIFLFFHKAIKSELDVLHRAAMAFATNLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIRV---KNIARTYS 119 (1237)
Q Consensus 43 Pi~~~~~~HkAlR~eL~~l~~~a~~~~~~~gd~~~~~~l~~r~~~L~~~~~~H~~aEDevI~PaLd~Rv---~~v~~~~~ 119 (1237)
||+.+...|+.||+.+..+...+... ++......+...+.+|...+..|+..|++++||.|+.+. ++.+..+.
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 245568999999999999999999999999999999443 67889999
Q ss_pred hhhhhHHHHHHHHHHHHHhhccCchHHHHHHHHHHHHHHHHHHHhHHHHHHHHhhHH
Q 000886 120 LEHEGESVLFDQLFELLNSSMRNEESYRRELASCTGALQTSISQHMSKEEEQVFPLL 176 (1237)
Q Consensus 120 ~EH~~~~~lf~~l~~~l~~~~~~~~~~~~eLa~~l~~l~~~l~qHm~~EE~qv~PLl 176 (1237)
.||..+...++.+...+..+. ........+...+.++...+.+||.+||+.++|++
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 33466778888888888899999999999999986
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=99.13 E-value=1.1e-11 Score=102.17 Aligned_cols=44 Identities=34% Similarity=0.951 Sum_probs=37.9
Q ss_pred CCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCC
Q 000886 1115 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICS 1159 (1237)
Q Consensus 1115 ~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCr 1159 (1237)
++||||++.+ ...+.+..++|||.||.+|+.+|++.+++||+||
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 4799999995 4466788899999999999999999999999997
No 7
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=98.94 E-value=9.6e-11 Score=109.61 Aligned_cols=57 Identities=30% Similarity=0.725 Sum_probs=50.1
Q ss_pred cccCccccccc---ccccccccCCcccCcccccccCCCCCccc-----cccccccccccccccCC
Q 000886 984 QVFGCEHYKRN---CKLRAACCGKLFTCRFCHDKVSDHSMDRK-----ATTEMMCMRCLKVQPVG 1040 (1237)
Q Consensus 984 ~~~gC~HY~r~---c~l~~~cC~~~y~Cr~CHde~~~H~~~r~-----~~~~v~C~~C~~~Q~~~ 1040 (1237)
++++|.||+.. ++|+|.||+|||+|..|||+.++||+.++ ..+.|+||.|.++-.++
T Consensus 11 ~etRC~Hyht~~Diialkc~~C~kyYaCy~CHdel~~Hpf~p~~~~~~~~~~iiCGvC~~~LT~~ 75 (105)
T COG4357 11 QETRCLHYHTPLDIIALKCKCCQKYYACYHCHDELEDHPFEPWGLQEFNPKAIICGVCRKLLTRA 75 (105)
T ss_pred ccceeeEecCccceEeeeechhhhhhhHHHHHhHHhcCCCccCChhhcCCccEEhhhhhhhhhHH
Confidence 57899999999 79999999999999999999999999865 34679999998776654
No 8
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=98.84 E-value=1.2e-09 Score=123.05 Aligned_cols=57 Identities=32% Similarity=0.800 Sum_probs=49.2
Q ss_pred cCCCCCCcccccccccCC---------CcceecCCCCccChhhHHHhhhcCCCCCCCCcc-cCChhh
Q 000886 1111 KGLETNCPICCDFLFTSS---------ATVRALPCGHFMHSDCFQAYTCSHYICPICSKS-LGDMAV 1167 (1237)
Q Consensus 1111 ~~~~~~CpICle~lf~s~---------~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCr~s-v~dm~~ 1167 (1237)
...+..|.||+|+|+.+. ...+.|||||.+|.+|++.|++++.||||||.+ ++|++.
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 456789999999988765 234789999999999999999999999999999 577765
No 9
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.82 E-value=1.3e-09 Score=124.78 Aligned_cols=54 Identities=26% Similarity=0.769 Sum_probs=46.6
Q ss_pred ccCCCCCCcccccccccCCCcceecCCCCccChhhHHHhhhcC-CCCCCCCcccCCh
Q 000886 1110 EKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSH-YICPICSKSLGDM 1165 (1237)
Q Consensus 1110 e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~-~~CPiCr~sv~dm 1165 (1237)
+++. ..|.||+|+ |..++.+++|||+|.||..||+.|+..+ ..||+|+..+..-
T Consensus 226 ~~~~-~~CaIClEd-Y~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~di~~~ 280 (348)
T KOG4628|consen 226 EDAT-DTCAICLED-YEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRDIRTD 280 (348)
T ss_pred cCCC-ceEEEeecc-cccCCeeeEecCCCchhhccchhhHhhcCccCCCCCCcCCCC
Confidence 3444 699999999 8899999999999999999999998665 5599999988643
No 10
>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=98.79 E-value=3e-09 Score=97.31 Aligned_cols=47 Identities=30% Similarity=0.756 Sum_probs=37.2
Q ss_pred CCCCCcccccccccCC---------CcceecCCCCccChhhHHHhhhcCCCCCCCC
Q 000886 1113 LETNCPICCDFLFTSS---------ATVRALPCGHFMHSDCFQAYTCSHYICPICS 1159 (1237)
Q Consensus 1113 ~~~~CpICle~lf~s~---------~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCr 1159 (1237)
.+.+|+||++.+.+.. -.+...+|||.||..||.+|+..+.+||+||
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 4567999999974332 2345569999999999999999999999998
No 11
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=98.78 E-value=2.5e-09 Score=123.41 Aligned_cols=82 Identities=24% Similarity=0.659 Sum_probs=68.1
Q ss_pred CCCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcccCChhhHHHhHHHHHhhcCCChhhhccCCcee
Q 000886 1114 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGDMAVYFGMLDALLASEQLPEEYRDRCQEIL 1193 (1237)
Q Consensus 1114 ~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCr~sv~dm~~~~~~lD~~i~~~pmP~ey~~~~~~i~ 1193 (1237)
-..||||||.|..+.+.+....|.|.||..|+.+|. ..+||+||.... |-+. ..-.
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 779999996532 1111 1346
Q ss_pred cCCCCCCCCCCceeecccCCC--CCCccccc
Q 000886 1194 CNDCDKKGSAPFHWLYHKCGF--CGSYNTRV 1222 (1237)
Q Consensus 1194 CnDC~~~s~~~~h~lg~kC~~--C~SYNT~~ 1222 (1237)
|.+|+...+. |+++.|++ ||.|+-.-
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 9999997777 99999986 99999754
No 12
>PRK10992 iron-sulfur cluster repair di-iron protein; Provisional
Probab=98.77 E-value=7.5e-08 Score=105.56 Aligned_cols=132 Identities=17% Similarity=0.317 Sum_probs=107.2
Q ss_pred hHHHH-HHHHHHHHHHHHHHHHHHHhhc-c-cCCcccHHHHHHHHHHHHHHHHhhhhcccccchhhhhhhh---------
Q 000886 293 PIDEI-MLWHNAIKRELNDIAEAARKIQ-L-SGDFSDLSAFNKRLQFIAEVCIFHSIAEDKVIFPAVDVEL--------- 360 (1237)
Q Consensus 293 pid~l-~~~HkALRrEL~~L~~~a~~~~-~-~gd~~~L~~L~~r~~fl~~vl~~Hs~aEDevlFPaL~~r~--------- 360 (1237)
-||.+ ..-|..+|++|..|.+.+.++. . .++...+..+...+..|...+..|+..|++++||+|....
T Consensus 75 LidyI~~~~H~~~r~~lp~L~~l~~kv~~vhg~~~~~~~~~~~l~~~~~~el~~H~~kEE~~LFP~l~~~~~~~~~~pi~ 154 (220)
T PRK10992 75 LIDHIIVRYHDRHREQLPELILLATKVERVHGDKPDCPRGLAKYLTALHEELSSHMMKEEQILFPMIKQGMGSQAMGPIS 154 (220)
T ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHhcccccccchHH
Confidence 35655 7889999999999999997764 1 2334567888889999999999999999999999999621
Q ss_pred hhHHhHHHHHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHh
Q 000886 361 SFAQEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPLARR 427 (1237)
Q Consensus 361 ~me~EH~~ie~l~e~l~~ll~~~~~a~~~~~~~~~~~eLa~~le~L~~~L~~H~~~EE~qvfPLl~~ 427 (1237)
.|..||+.+...+.+|..++..... +..+...++.+-..+..+...|.+|+.+||+.+||++..
T Consensus 155 vm~~EHd~~~~~l~~L~~lt~~~~~---p~~ac~~~~~l~~~l~~~~~dL~~HI~~EnniLFP~a~~ 218 (220)
T PRK10992 155 VMESEHDEAGELLEVIKHLTNNVTP---PPEACTTWRALYNGINELIDDLMEHIHLENNVLFPRALA 218 (220)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCC---ChhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Confidence 8899999999999999988866422 111124577777888889999999999999999998764
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=98.64 E-value=1.9e-07 Score=102.09 Aligned_cols=129 Identities=20% Similarity=0.296 Sum_probs=103.6
Q ss_pred HHHH-HHHHHHHHHHHHHHHHHHHhhcc--cCCcccHHHHHHHHHHHHHHHHhhhhcccccchhhhhhh-----------
Q 000886 294 IDEI-MLWHNAIKRELNDIAEAARKIQL--SGDFSDLSAFNKRLQFIAEVCIFHSIAEDKVIFPAVDVE----------- 359 (1237)
Q Consensus 294 id~l-~~~HkALRrEL~~L~~~a~~~~~--~gd~~~L~~L~~r~~fl~~vl~~Hs~aEDevlFPaL~~r----------- 359 (1237)
||.+ ...|..||++|..|...+.++.. ..+...+..+..-+..|...+..|+..|++++||+|...
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 4444 67899999999999998877642 233446788889999999999999999999999999741
Q ss_pred h--hhHHhHHHHHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 000886 360 L--SFAQEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPLA 425 (1237)
Q Consensus 360 ~--~me~EH~~ie~l~e~l~~ll~~~~~a~~~~~~~~~~~eLa~~le~L~~~L~~H~~~EE~qvfPLl 425 (1237)
. .|..||+++...+.+|..++..... +..+...++.+...+..+...|.+|+.+||+.+||.+
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 6899999999999999988865432 1111345777778888899999999999999999963
No 14
>PRK10992 iron-sulfur cluster repair di-iron protein; Provisional
Probab=98.63 E-value=4.4e-07 Score=99.60 Aligned_cols=129 Identities=17% Similarity=0.222 Sum_probs=110.6
Q ss_pred HHHHHHHHHHHHHHHHHHhhcc--CCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHHHh----hhhHHHHHHhhh
Q 000886 49 FFHKAIKSELDVLHRAAMAFAT--NLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIR----VKNIARTYSLEH 122 (1237)
Q Consensus 49 ~~HkAlR~eL~~l~~~a~~~~~--~~gd~~~~~~l~~r~~~L~~~~~~H~~aEDevI~PaLd~R----v~~v~~~~~~EH 122 (1237)
.-|.-+|++|..|.+++..+.. + ++......+.+-++.|..-+..|+..|.+++||.|... +.+.+..|..||
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 6699999999999999988774 2 45567788899999999999999999999999999962 356789999999
Q ss_pred hhHHHHHHHHHHHHHhhccCch--HHHHHHHHHHHHHHHHHHHhHHHHHHHHhhHHHh
Q 000886 123 EGESVLFDQLFELLNSSMRNEE--SYRRELASCTGALQTSISQHMSKEEEQVFPLLIE 178 (1237)
Q Consensus 123 ~~~~~lf~~l~~~l~~~~~~~~--~~~~eLa~~l~~l~~~l~qHm~~EE~qv~PLl~~ 178 (1237)
.++..++..|..+.+......+ ..++.+...+..+...|.+|.++|+..+||.+.+
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 9999999999999988754333 5678888888888889999999999999998764
No 15
>PHA02929 N1R/p28-like protein; Provisional
Probab=98.55 E-value=4.6e-08 Score=107.84 Aligned_cols=54 Identities=17% Similarity=0.551 Sum_probs=42.7
Q ss_pred cCCCCCCcccccccccCCC---c-ceecCCCCccChhhHHHhhhcCCCCCCCCcccCC
Q 000886 1111 KGLETNCPICCDFLFTSSA---T-VRALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1164 (1237)
Q Consensus 1111 ~~~~~~CpICle~lf~s~~---~-v~~LpCgH~fH~~Ci~~wl~~~~~CPiCr~sv~d 1164 (1237)
.+.+..||||+|.+..... . ....+|||.||..||.+|+..+.+||+||..+..
T Consensus 171 ~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~~ 228 (238)
T PHA02929 171 RSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFIS 228 (238)
T ss_pred CCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEeeE
Confidence 3456899999998654321 1 2345899999999999999999999999998753
No 16
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=98.50 E-value=7.8e-08 Score=77.38 Aligned_cols=44 Identities=34% Similarity=0.921 Sum_probs=36.9
Q ss_pred CCcccccccccCCCcceecCCCCccChhhHHHhhhc-CCCCCCCCccc
Q 000886 1116 NCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS-HYICPICSKSL 1162 (1237)
Q Consensus 1116 ~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~-~~~CPiCr~sv 1162 (1237)
.|+||++.+ ...+...+|||.||..|+..|+.. +.+||+|++.+
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 345666779999999999999987 78899999764
No 17
>COG3945 Uncharacterized conserved protein [Function unknown]
Probab=98.48 E-value=2.4e-06 Score=89.34 Aligned_cols=140 Identities=21% Similarity=0.284 Sum_probs=110.0
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHHhhcccC--CcccHHHHHHHHHHHHHHHHhhhhcccccchhhhhhhh---------
Q 000886 292 CPIDEIMLWHNAIKRELNDIAEAARKIQLSG--DFSDLSAFNKRLQFIAEVCIFHSIAEDKVIFPAVDVEL--------- 360 (1237)
Q Consensus 292 ~pid~l~~~HkALRrEL~~L~~~a~~~~~~g--d~~~L~~L~~r~~fl~~vl~~Hs~aEDevlFPaL~~r~--------- 360 (1237)
.-++.|+-.|+.|.+-|.-|+..+..+. .| +.+++..+.+-++-|++- .||..|+.++||-|..+.
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 3578899999999999999998887775 43 233444444444444443 578889999999999765
Q ss_pred hhHHhHHHHHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhhCCHHHHHHHHHh
Q 000886 361 SFAQEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPLARRHFSPKRQRELLYQ 440 (1237)
Q Consensus 361 ~me~EH~~ie~l~e~l~~ll~~~~~a~~~~~~~~~~~eLa~~le~L~~~L~~H~~~EE~qvfPLl~~~fS~eEq~~L~~~ 440 (1237)
.|.-||...-.++..|.+.+..+...+. +....+...+......+.+|+.+|+.++||++++.||.+ |..+..+
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 8999999999999999999998865432 224556667777788999999999999999999999999 7766644
No 18
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.48 E-value=6.1e-08 Score=107.32 Aligned_cols=53 Identities=28% Similarity=0.723 Sum_probs=46.2
Q ss_pred ccCCCCCCcccccccccCCCcceecCCCCccChhhHHHhhh-cCCCCCCCCcccC
Q 000886 1110 EKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC-SHYICPICSKSLG 1163 (1237)
Q Consensus 1110 e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~-~~~~CPiCr~sv~ 1163 (1237)
|.....+|+||+++ |...+.+++|||.|.||..|+++|+. .+..||+||..+.
T Consensus 319 ea~~GveCaICms~-fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iP 372 (374)
T COG5540 319 EADKGVECAICMSN-FIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIP 372 (374)
T ss_pred hcCCCceEEEEhhh-hcccceEEEeccCceechhHHHHHHhhhcccCCccCCCCC
Confidence 44455899999999 77888899999999999999999986 6789999998764
No 19
>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=98.46 E-value=1.7e-06 Score=94.79 Aligned_cols=127 Identities=24% Similarity=0.300 Sum_probs=106.8
Q ss_pred HHHHHHHHHHHHHHHHHHhhcc-CCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHHH--hh------hhHHHHHH
Q 000886 49 FFHKAIKSELDVLHRAAMAFAT-NLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDI--RV------KNIARTYS 119 (1237)
Q Consensus 49 ~~HkAlR~eL~~l~~~a~~~~~-~~gd~~~~~~l~~r~~~L~~~~~~H~~aEDevI~PaLd~--Rv------~~v~~~~~ 119 (1237)
.-|..||++|..|..++..+.. .-.+...+..+.+-++.|..-+..|+..|.+++||+|.. +. .+.+..|.
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 114456778999999999999999999999999999985 21 22889999
Q ss_pred hhhhhHHHHHHHHHHHHHhhccCch--HHHHHHHHHHHHHHHHHHHhHHHHHHHHhhH
Q 000886 120 LEHEGESVLFDQLFELLNSSMRNEE--SYRRELASCTGALQTSISQHMSKEEEQVFPL 175 (1237)
Q Consensus 120 ~EH~~~~~lf~~l~~~l~~~~~~~~--~~~~eLa~~l~~l~~~l~qHm~~EE~qv~PL 175 (1237)
.||.++...+++|...++......+ ..++.+...+.++...|.+|.++||..+||.
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 9999999999999999987754332 5577777778888889999999999999994
No 20
>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=98.42 E-value=1e-07 Score=76.79 Aligned_cols=39 Identities=41% Similarity=0.974 Sum_probs=33.4
Q ss_pred CcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCC
Q 000886 1117 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPIC 1158 (1237)
Q Consensus 1117 CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiC 1158 (1237)
||||++.+.+ ++..++|||.|+..|+.+|+..+.+||+|
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 8999987543 66889999999999999999889999998
No 21
>PRK13276 cell wall biosynthesis protein ScdA; Provisional
Probab=98.33 E-value=6e-06 Score=90.63 Aligned_cols=125 Identities=21% Similarity=0.253 Sum_probs=111.4
Q ss_pred HHHHHHHHHHHHHHHHHHhhcc--CCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHHHh--------hhhHHHHH
Q 000886 49 FFHKAIKSELDVLHRAAMAFAT--NLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIR--------VKNIARTY 118 (1237)
Q Consensus 49 ~~HkAlR~eL~~l~~~a~~~~~--~~gd~~~~~~l~~r~~~L~~~~~~H~~aEDevI~PaLd~R--------v~~v~~~~ 118 (1237)
..|.-+|++|..|..++..|.. + ++......|.+.|..|+.=+..|..-|.+++||.+... +.+.+..|
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 7899999999999999999886 3 55668999999999999999999999999999999752 35578999
Q ss_pred HhhhhhHHHHHHHHHHHHHhhccCch--HHHHHHHHHHHHHHHHHHHhHHHHHHHHhh
Q 000886 119 SLEHEGESVLFDQLFELLNSSMRNEE--SYRRELASCTGALQTSISQHMSKEEEQVFP 174 (1237)
Q Consensus 119 ~~EH~~~~~lf~~l~~~l~~~~~~~~--~~~~eLa~~l~~l~~~l~qHm~~EE~qv~P 174 (1237)
..||+++.+++.+|.++.+-++...+ ..|+.|=.-+.++...|.+|.+.|-.-+||
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 99999999999999999998876554 778888888888888999999999999998
No 22
>PRK13276 cell wall biosynthesis protein ScdA; Provisional
Probab=98.30 E-value=6.4e-06 Score=90.39 Aligned_cols=128 Identities=14% Similarity=0.188 Sum_probs=107.4
Q ss_pred HHHH-HHHHHHHHHHHHHHHHHHHhhcc--cCCcccHHHHHHHHHHHHHHHHhhhhcccccchhhhhhhh----------
Q 000886 294 IDEI-MLWHNAIKRELNDIAEAARKIQL--SGDFSDLSAFNKRLQFIAEVCIFHSIAEDKVIFPAVDVEL---------- 360 (1237)
Q Consensus 294 id~l-~~~HkALRrEL~~L~~~a~~~~~--~gd~~~L~~L~~r~~fl~~vl~~Hs~aEDevlFPaL~~r~---------- 360 (1237)
||.+ ...|..+|++|..|...+.++.. .++...+..+...+..+..-|..|-..|+.++||++....
T Consensus 79 id~I~~~hH~~~r~~lp~l~~l~~kV~~VHg~~~p~l~~l~~lf~~l~~eL~~H~~KEE~ilFP~i~~~~~~~~~~~~~~ 158 (224)
T PRK13276 79 IQYIQSAYHEPLREEFKNLTPYVTKLSKVHGPNHPYLVELKETYDTFKNGMLEHMQKEDDVDFPKLIKYEQGEVVDDINT 158 (224)
T ss_pred HHHHHHHHhHHHHHHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHhhccccchhhhh
Confidence 4443 67899999999999999988742 3445578999999999999999999999999999996411
Q ss_pred ---hhHHhHHHHHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 000886 361 ---SFAQEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPL 424 (1237)
Q Consensus 361 ---~me~EH~~ie~l~e~l~~ll~~~~~a~~~~~~~~~~~eLa~~le~L~~~L~~H~~~EE~qvfPL 424 (1237)
.|+.||+.+.+.+.+|++++...... ..+...|+.|=..+.++...|.+|.+.|-+.+||-
T Consensus 159 pI~~m~~EH~~~g~~l~~i~~lTn~yt~P---~~AC~t~r~ly~~L~~fe~dL~~HIhLENnILFPr 222 (224)
T PRK13276 159 VIDDLVSDHIATGQLLVKMSELTSSYEPP---IEACGTWRLVYQRLKALEVLTHEHVHLENHVLFKK 222 (224)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCCCCC---cchhHHHHHHHHHHHHHHHHHHHHHHHHHHHcccC
Confidence 89999999999999999999776432 22356788888889999999999999999999993
No 23
>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=98.28 E-value=3.5e-07 Score=77.54 Aligned_cols=47 Identities=32% Similarity=0.824 Sum_probs=38.9
Q ss_pred CCCCcccccccccCCCcceecCCCCc-cChhhHHHhhhcCCCCCCCCcccCC
Q 000886 1114 ETNCPICCDFLFTSSATVRALPCGHF-MHSDCFQAYTCSHYICPICSKSLGD 1164 (1237)
Q Consensus 1114 ~~~CpICle~lf~s~~~v~~LpCgH~-fH~~Ci~~wl~~~~~CPiCr~sv~d 1164 (1237)
+..|+||++.. ..+..+||||. |...|+.+|.....+||+||++|.+
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 46899999862 24678899999 9999999999999999999998753
No 24
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=98.25 E-value=6.6e-07 Score=83.78 Aligned_cols=46 Identities=22% Similarity=0.445 Sum_probs=31.9
Q ss_pred CCCcccccccccCCCcceecCCCCccChhhHHHhhhc---CCCCCCCCccc
Q 000886 1115 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS---HYICPICSKSL 1162 (1237)
Q Consensus 1115 ~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~---~~~CPiCr~sv 1162 (1237)
..||.|..+-. .-++..-.|+|.||.+||.+|+.+ +.+||+||.+.
T Consensus 33 g~Cp~Ck~Pgd--~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w 81 (85)
T PF12861_consen 33 GCCPDCKFPGD--DCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPW 81 (85)
T ss_pred cCCCCccCCCC--CCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCee
Confidence 34555553311 113344579999999999999964 57899999864
No 25
>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=1.6e-06 Score=67.26 Aligned_cols=38 Identities=37% Similarity=0.943 Sum_probs=32.8
Q ss_pred CcccccccccCCCcceecCCCCccChhhHHHhhh-cCCCCCCC
Q 000886 1117 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC-SHYICPIC 1158 (1237)
Q Consensus 1117 CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~-~~~~CPiC 1158 (1237)
|+||++. ......++|||.||..|++.|+. .+.+||+|
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 8999887 24567889999999999999987 66789998
No 26
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.09 E-value=2.1e-06 Score=71.01 Aligned_cols=44 Identities=30% Similarity=0.764 Sum_probs=37.9
Q ss_pred CCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCc
Q 000886 1116 NCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSK 1160 (1237)
Q Consensus 1116 ~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCr~ 1160 (1237)
.|+||.+.+ .......+++|||+|...|+..+......||+||+
T Consensus 1 ~C~~C~~~~-~~~~~~~l~~CgH~~C~~C~~~~~~~~~~CP~C~k 44 (44)
T PF14634_consen 1 HCNICFEKY-SEERRPRLTSCGHIFCEKCLKKLKGKSVKCPICRK 44 (44)
T ss_pred CCcCcCccc-cCCCCeEEcccCCHHHHHHHHhhcCCCCCCcCCCC
Confidence 499999984 55556788999999999999999866789999986
No 27
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.04 E-value=2.1e-06 Score=70.60 Aligned_cols=38 Identities=37% Similarity=0.946 Sum_probs=27.5
Q ss_pred CcccccccccCCCcceecCCCCccChhhHHHhhhcC----CCCCCC
Q 000886 1117 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSH----YICPIC 1158 (1237)
Q Consensus 1117 CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~----~~CPiC 1158 (1237)
||||++.+.+ .+.|+|||.|...||..|.+.. ..||+|
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 679998
No 28
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.03 E-value=3.8e-06 Score=89.74 Aligned_cols=52 Identities=25% Similarity=0.656 Sum_probs=40.3
Q ss_pred cccCCCCCCcccccccccCCCcceecCCCCccChhhHHHhhhc----------------CCCCCCCCcccCC
Q 000886 1109 REKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS----------------HYICPICSKSLGD 1164 (1237)
Q Consensus 1109 ~e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~----------------~~~CPiCr~sv~d 1164 (1237)
++...+..||||++.+ . + .++++|||.|+..||.+|+.. ..+||+||..+..
T Consensus 13 ~~~~~~~~CpICld~~-~--d-PVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~ 80 (193)
T PLN03208 13 VDSGGDFDCNICLDQV-R--D-PVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE 80 (193)
T ss_pred ccCCCccCCccCCCcC-C--C-cEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence 3444568999999973 2 2 355799999999999999742 3589999999854
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=98.02 E-value=2.3e-06 Score=69.27 Aligned_cols=39 Identities=38% Similarity=0.961 Sum_probs=33.0
Q ss_pred CcccccccccCCCcceecCCCCccChhhHHHhhh--cCCCCCCC
Q 000886 1117 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC--SHYICPIC 1158 (1237)
Q Consensus 1117 CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~--~~~~CPiC 1158 (1237)
||||++.+.. ++..++|||.|+..|+.+|+. ...+||+|
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 8999998432 346899999999999999987 56889998
No 30
>COG2846 Regulator of cell morphogenesis and NO signaling [Cell division and chromosome partitioning]
Probab=98.00 E-value=5.1e-05 Score=80.74 Aligned_cols=128 Identities=18% Similarity=0.316 Sum_probs=105.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcc-cCC-cccHHHHHHHHHHHHHHHHhhhhcccccchhhhhhhh---------hhH
Q 000886 295 DEIMLWHNAIKRELNDIAEAARKIQL-SGD-FSDLSAFNKRLQFIAEVCIFHSIAEDKVIFPAVDVEL---------SFA 363 (1237)
Q Consensus 295 d~l~~~HkALRrEL~~L~~~a~~~~~-~gd-~~~L~~L~~r~~fl~~vl~~Hs~aEDevlFPaL~~r~---------~me 363 (1237)
.++..+|+-.|.+|.+|-..+.++.. .|| ++-...|.+-+..|...|.-|-..|++++||++..-. .|+
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 45588999999999999999988732 344 3456888888999999999999999999999998532 899
Q ss_pred HhHHHHHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 000886 364 QEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPLA 425 (1237)
Q Consensus 364 ~EH~~ie~l~e~l~~ll~~~~~a~~~~~~~~~~~eLa~~le~L~~~L~~H~~~EE~qvfPLl 425 (1237)
.||++...+++.+..+....... ..+...++.|=.-+..+.+.+.+|++-|=..+||=+
T Consensus 159 ~EHde~g~~l~~lk~lT~n~tpP---~~AC~tWkalY~gl~~~~dDl~~HIHLENnvLFpr~ 217 (221)
T COG2846 159 SEHDEAGELLEVLKHLTNNYTPP---EEACGTWKALYNGLNEFIDDLMEHIHLENNVLFPRV 217 (221)
T ss_pred HHHHHHHHHHHHHHHHhcCCCCC---hHHHhHHHHHHHHHHHHHHHHHHHHHhhhccccchh
Confidence 99999999999999999776432 222345667777778889999999999999999954
No 31
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.99 E-value=1.7e-06 Score=106.43 Aligned_cols=53 Identities=30% Similarity=0.702 Sum_probs=44.7
Q ss_pred ccCCCCCCcccccccccCCC-cceecCCCCccChhhHHHhhhcCCCCCCCCccc
Q 000886 1110 EKGLETNCPICCDFLFTSSA-TVRALPCGHFMHSDCFQAYTCSHYICPICSKSL 1162 (1237)
Q Consensus 1110 e~~~~~~CpICle~lf~s~~-~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCr~sv 1162 (1237)
....+..|+||.|.|+.+.. ..+.|||||.||..|+..|++...+||+||..+
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 34557899999999886532 357799999999999999999999999999944
No 32
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=97.98 E-value=3.9e-06 Score=76.91 Aligned_cols=48 Identities=19% Similarity=0.408 Sum_probs=36.6
Q ss_pred CCCcccccccccCCCcc-eecCCCCccChhhHHHhhhcCCCCCCCCccc
Q 000886 1115 TNCPICCDFLFTSSATV-RALPCGHFMHSDCFQAYTCSHYICPICSKSL 1162 (1237)
Q Consensus 1115 ~~CpICle~lf~s~~~v-~~LpCgH~fH~~Ci~~wl~~~~~CPiCr~sv 1162 (1237)
..||-|.-.+....+-. .---|.|.||.+||.+|+.+...||++|++.
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 45777766553333322 2347999999999999999999999999875
No 33
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.92 E-value=4.6e-06 Score=87.24 Aligned_cols=47 Identities=32% Similarity=0.732 Sum_probs=39.3
Q ss_pred CCCCcccccccccCCCcc-eecCCCCccChhhHHHhhhcCCCCCCCCcccC
Q 000886 1114 ETNCPICCDFLFTSSATV-RALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1163 (1237)
Q Consensus 1114 ~~~CpICle~lf~s~~~v-~~LpCgH~fH~~Ci~~wl~~~~~CPiCr~sv~ 1163 (1237)
-..|||||+. +.. .+ ..-.|||.|+++||+..++...+||+|+|.|.
T Consensus 131 ~~~CPiCl~~-~se--k~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt 178 (187)
T KOG0320|consen 131 TYKCPICLDS-VSE--KVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKIT 178 (187)
T ss_pred ccCCCceecc-hhh--ccccccccchhHHHHHHHHHHHhCCCCCCcccccc
Confidence 3789999998 433 33 34799999999999999999999999999654
No 34
>PHA02926 zinc finger-like protein; Provisional
Probab=97.90 E-value=6.3e-06 Score=88.96 Aligned_cols=53 Identities=21% Similarity=0.541 Sum_probs=40.5
Q ss_pred cCCCCCCcccccccccCCC-----cceecCCCCccChhhHHHhhhc------CCCCCCCCcccC
Q 000886 1111 KGLETNCPICCDFLFTSSA-----TVRALPCGHFMHSDCFQAYTCS------HYICPICSKSLG 1163 (1237)
Q Consensus 1111 ~~~~~~CpICle~lf~s~~-----~v~~LpCgH~fH~~Ci~~wl~~------~~~CPiCr~sv~ 1163 (1237)
.+.+..|+||+|.++.... -....+|+|.|+..||..|... ..+||+||..+.
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 4567899999998765321 1234599999999999999864 245999998874
No 35
>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=97.81 E-value=1.7e-05 Score=69.66 Aligned_cols=45 Identities=22% Similarity=0.394 Sum_probs=38.4
Q ss_pred CCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcccC
Q 000886 1115 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1163 (1237)
Q Consensus 1115 ~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCr~sv~ 1163 (1237)
-.||||++.|.+ + ..++|||.|...||.+|+..+.+||+|++.+.
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 469999997543 3 55799999999999999988899999999873
No 36
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=97.78 E-value=1.1e-05 Score=66.78 Aligned_cols=39 Identities=38% Similarity=0.950 Sum_probs=23.2
Q ss_pred CcccccccccCCCcceecCCCCccChhhHHHhhhc----CCCCC
Q 000886 1117 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS----HYICP 1156 (1237)
Q Consensus 1117 CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~----~~~CP 1156 (1237)
||||.| +.+...+.++|+|||+|..+|++++... ..+||
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 4444555677999999999999999863 35687
No 37
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=97.69 E-value=9.3e-06 Score=73.90 Aligned_cols=28 Identities=25% Similarity=0.718 Sum_probs=23.9
Q ss_pred CCCCccChhhHHHhhhc---CCCCCCCCccc
Q 000886 1135 PCGHFMHSDCFQAYTCS---HYICPICSKSL 1162 (1237)
Q Consensus 1135 pCgH~fH~~Ci~~wl~~---~~~CPiCr~sv 1162 (1237)
-|.|.||.+||.+|+.. ...||+||...
T Consensus 50 ~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~ 80 (84)
T KOG1493|consen 50 YCLHAFHAHCILKWLNTPTSQGQCPMCRQTW 80 (84)
T ss_pred HHHHHHHHHHHHHHhcCccccccCCcchhee
Confidence 69999999999999853 46799999764
No 38
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=97.67 E-value=1.9e-05 Score=99.61 Aligned_cols=114 Identities=26% Similarity=0.560 Sum_probs=77.4
Q ss_pred cccccccccc-----cccCCCCCCCccCCCCccceEecccccCCCCCCccccCCCCCccccCCCCCccccccCCcccccc
Q 000886 1026 TEMMCMRCLK-----VQPVGPVCTTLSCSGLSMAKYYCGICKFFDDERVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLA 1100 (1237)
Q Consensus 1026 ~~v~C~~C~~-----~Q~~~~~C~~~~C~~~~~~~y~C~~C~~~d~~k~~yHC~~CgiCR~g~gl~~~~fHC~~C~~C~s 1100 (1237)
..--|..|+. .|.++.+|....| +..|+--|++=+--. ..|| |- +|--||.-|--|-.
T Consensus 3416 S~~aCRFCGs~~~tE~sav~~vCs~aDC--~eYAK~ACs~~H~C~--------H~CG----Gv---kNEE~CLPCl~Cdk 3478 (3738)
T KOG1428|consen 3416 SSEACRFCGSRSGTELSAVGSVCSDADC--QEYAKIACSKTHPCG--------HPCG----GV---KNEEHCLPCLHCDK 3478 (3738)
T ss_pred chhHhhhccCCCCcchhcccCccccHHH--HHHHHHHHhccCcCC--------Cccc----Cc---cchhhcccccccCh
Confidence 3447888874 3667889998888 567777776522110 2344 21 37788888877732
Q ss_pred cccccccccccCCCCCCcccccccccCCCcceecCCCCccChhhHHHhhhc----------CCCCCCCCcccC
Q 000886 1101 KKLVDHKCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS----------HYICPICSKSLG 1163 (1237)
Q Consensus 1101 ~~l~~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~----------~~~CPiCr~sv~ 1163 (1237)
-. .....++.|.||.-+ --+..+...|.|||.||.+|.+.-+.+ -..||||...|.
T Consensus 3479 s~------tkQD~DDmCmICFTE-~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~In 3544 (3738)
T KOG1428|consen 3479 SA------TKQDADDMCMICFTE-ALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKIN 3544 (3738)
T ss_pred hh------hhcccCceEEEEehh-hhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchhh
Confidence 11 124457899999865 334567888999999999998764432 246999999885
No 39
>COG2846 Regulator of cell morphogenesis and NO signaling [Cell division and chromosome partitioning]
Probab=97.62 E-value=0.00053 Score=73.23 Aligned_cols=132 Identities=18% Similarity=0.239 Sum_probs=109.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcc-CCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHHHh----hhhHHHHHH
Q 000886 45 LIFLFFHKAIKSELDVLHRAAMAFAT-NLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIR----VKNIARTYS 119 (1237)
Q Consensus 45 ~~~~~~HkAlR~eL~~l~~~a~~~~~-~~gd~~~~~~l~~r~~~L~~~~~~H~~aEDevI~PaLd~R----v~~v~~~~~ 119 (1237)
.|..-+|.-.|.+|..|..+|..|.. -.+.+...+.|.+-+.-|..-+..|-.-|++++||.+..= +.+....|+
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 45668999999999999999998886 1155678889999999999999999999999999999643 256889999
Q ss_pred hhhhhHHHHHHHHHHHHHhhccCch--HHHHHHHHHHHHHHHHHHHhHHHHHHHHhhHH
Q 000886 120 LEHEGESVLFDQLFELLNSSMRNEE--SYRRELASCTGALQTSISQHMSKEEEQVFPLL 176 (1237)
Q Consensus 120 ~EH~~~~~lf~~l~~~l~~~~~~~~--~~~~eLa~~l~~l~~~l~qHm~~EE~qv~PLl 176 (1237)
.||+++..+++.+.++.+..+-..+ ..++.|=.-+.++.+.+.+|++-|---+||=+
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 9999999999999999988865544 55566666666666699999999988888744
No 40
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=97.58 E-value=2.6e-05 Score=87.03 Aligned_cols=46 Identities=24% Similarity=0.689 Sum_probs=38.9
Q ss_pred CCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcccCC
Q 000886 1115 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1164 (1237)
Q Consensus 1115 ~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCr~sv~d 1164 (1237)
..|.+|||.... ....||||.|+..||..|.....-||+||..+..
T Consensus 240 ~kC~LCLe~~~~----pSaTpCGHiFCWsCI~~w~~ek~eCPlCR~~~~p 285 (293)
T KOG0317|consen 240 RKCSLCLENRSN----PSATPCGHIFCWSCILEWCSEKAECPLCREKFQP 285 (293)
T ss_pred CceEEEecCCCC----CCcCcCcchHHHHHHHHHHccccCCCcccccCCC
Confidence 579999997432 3568999999999999999988889999987643
No 41
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.57 E-value=1.2e-05 Score=98.03 Aligned_cols=75 Identities=15% Similarity=0.389 Sum_probs=50.7
Q ss_pred ccccCCccccccccc-cccccc-ccCCCCCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcccCC
Q 000886 1089 FFHCMTCNCCLAKKL-VDHKCR-EKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1164 (1237)
Q Consensus 1089 ~fHC~~C~~C~s~~l-~~H~C~-e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCr~sv~d 1164 (1237)
--.|..|-.|.|-.. ..-.|+ .+.....||+|+-. +.........+|+|+||..||..|.+.-.+||+||+.+..
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 344445555554422 122232 23345689999976 4333334457999999999999999999999999998854
No 42
>COG3945 Uncharacterized conserved protein [Function unknown]
Probab=97.52 E-value=0.00096 Score=70.40 Aligned_cols=139 Identities=18% Similarity=0.235 Sum_probs=109.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHhhccCCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHHHhh----hhHHHHHH
Q 000886 44 ILIFLFFHKAIKSELDVLHRAAMAFATNLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIRV----KNIARTYS 119 (1237)
Q Consensus 44 i~~~~~~HkAlR~eL~~l~~~a~~~~~~~gd~~~~~~l~~r~~~L~~~~~~H~~aEDevI~PaLd~Rv----~~v~~~~~ 119 (1237)
|..|+==|+-|-|-|.-|....--+..+-=|.+++..+++-++-+.+ ++||.-|+.++||-+..+. ++....|.
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 56777789999998888877776666511245566666655555444 5688999999999999886 57899999
Q ss_pred hhhhhHHHHHHHHHHHHHhhccCch----HHHHHHHHHHHHHHHHHHHhHHHHHHHHhhHHHhcCCHHHHHHHH
Q 000886 120 LEHEGESVLFDQLFELLNSSMRNEE----SYRRELASCTGALQTSISQHMSKEEEQVFPLLIEKFSFEEQASLV 189 (1237)
Q Consensus 120 ~EH~~~~~lf~~l~~~l~~~~~~~~----~~~~eLa~~l~~l~~~l~qHm~~EE~qv~PLl~~~~S~~Eqa~L~ 189 (1237)
-||..--.++..+.+++.+|.-.++ .+...+++.+. .+.+|.++|+-.+||.+.+.||.+ |..+.
T Consensus 88 ~EH~~~R~i~r~lee~~~~~kngd~~~~~~~i~~A~~y~~----likrHIdkEdnvlfp~a~~~~s~e-~~~v~ 156 (189)
T COG3945 88 VEHGEGRYIIRDLEEAYERLKNGDEDSKDDVIDYAVAYLN----LIKRHIDKEDNVLFPFAESTLSEE-LNEVN 156 (189)
T ss_pred hhhhhHHHHHHHHHHHHHHHHccccchHHHHHHHHHHHHH----HHHHHHhhhhhHHHHHHHHHHHHH-HHHHH
Confidence 9999999999999999999975554 55555666666 999999999999999999999999 55544
No 43
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.51 E-value=5.1e-05 Score=89.57 Aligned_cols=47 Identities=26% Similarity=0.568 Sum_probs=39.6
Q ss_pred CCCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcccCC
Q 000886 1114 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1164 (1237)
Q Consensus 1114 ~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCr~sv~d 1164 (1237)
...|+||++.+. . + ++++|||.|+..||..|+.....||+|+..+..
T Consensus 26 ~l~C~IC~d~~~-~--P-vitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~~ 72 (397)
T TIGR00599 26 SLRCHICKDFFD-V--P-VLTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQE 72 (397)
T ss_pred ccCCCcCchhhh-C--c-cCCCCCCchhHHHHHHHHhCCCCCCCCCCcccc
Confidence 468999999743 2 3 368999999999999999888899999998863
No 44
>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=97.33 E-value=0.00012 Score=62.42 Aligned_cols=42 Identities=26% Similarity=0.736 Sum_probs=32.3
Q ss_pred CCcccccccccCCCcceecCCC-----CccChhhHHHhhhc--CCCCCCCC
Q 000886 1116 NCPICCDFLFTSSATVRALPCG-----HFMHSDCFQAYTCS--HYICPICS 1159 (1237)
Q Consensus 1116 ~CpICle~lf~s~~~v~~LpCg-----H~fH~~Ci~~wl~~--~~~CPiCr 1159 (1237)
.|-||+++ ...+...+.||. |++|..|+.+|+.. +.+||+|+
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 48999982 333445678985 99999999999854 46899995
No 45
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=97.30 E-value=5.3e-05 Score=72.72 Aligned_cols=28 Identities=25% Similarity=0.637 Sum_probs=26.4
Q ss_pred cCCCCccChhhHHHhhhcCCCCCCCCcc
Q 000886 1134 LPCGHFMHSDCFQAYTCSHYICPICSKS 1161 (1237)
Q Consensus 1134 LpCgH~fH~~Ci~~wl~~~~~CPiCr~s 1161 (1237)
--|.|.||.+||.+|++++..||+|.+.
T Consensus 79 G~CNHaFH~hCisrWlktr~vCPLdn~e 106 (114)
T KOG2930|consen 79 GVCNHAFHFHCISRWLKTRNVCPLDNKE 106 (114)
T ss_pred eecchHHHHHHHHHHHhhcCcCCCcCcc
Confidence 4799999999999999999999999986
No 46
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=97.29 E-value=7.6e-05 Score=68.10 Aligned_cols=50 Identities=26% Similarity=0.594 Sum_probs=23.7
Q ss_pred CCCCcccccccccC-CCccee---cCCCCccChhhHHHhhhc-----------CCCCCCCCcccC
Q 000886 1114 ETNCPICCDFLFTS-SATVRA---LPCGHFMHSDCFQAYTCS-----------HYICPICSKSLG 1163 (1237)
Q Consensus 1114 ~~~CpICle~lf~s-~~~v~~---LpCgH~fH~~Ci~~wl~~-----------~~~CPiCr~sv~ 1163 (1237)
+..|+||+.++.+. ..+..+ -.|+..||..|+.+|+.. ..+||.|+++|.
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 46899999986623 233333 279999999999999752 135999999873
No 47
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.26 E-value=0.00028 Score=77.43 Aligned_cols=44 Identities=34% Similarity=0.851 Sum_probs=37.1
Q ss_pred CCCCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCc
Q 000886 1113 LETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSK 1160 (1237)
Q Consensus 1113 ~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCr~ 1160 (1237)
....||||+++ |... +++||||.|...|+..+......||.||.
T Consensus 12 ~~~~C~iC~~~-~~~p---~~l~C~H~~c~~C~~~~~~~~~~Cp~cr~ 55 (386)
T KOG2177|consen 12 EELTCPICLEY-FREP---VLLPCGHNFCRACLTRSWEGPLSCPVCRP 55 (386)
T ss_pred ccccChhhHHH-hhcC---ccccccchHhHHHHHHhcCCCcCCcccCC
Confidence 45789999998 4432 78999999999999998766689999994
No 48
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=97.24 E-value=0.00014 Score=82.15 Aligned_cols=59 Identities=24% Similarity=0.616 Sum_probs=44.9
Q ss_pred CCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcccCChhh-HHHhHHHHHh
Q 000886 1115 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGDMAV-YFGMLDALLA 1177 (1237)
Q Consensus 1115 ~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCr~sv~dm~~-~~~~lD~~i~ 1177 (1237)
-.|-||.|| |. ..++.||||+|+.-||+.++..+..||.|+.++..-.. .-+.+|++|+
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 469999999 43 23556999999999999999999999999999863221 2345666543
No 49
>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=97.24 E-value=0.00022 Score=81.45 Aligned_cols=51 Identities=22% Similarity=0.560 Sum_probs=38.0
Q ss_pred CCCCcccccccccCCCc-ceecCCCCccChhhHHHh-hhcCCCCCCCCcccCC
Q 000886 1114 ETNCPICCDFLFTSSAT-VRALPCGHFMHSDCFQAY-TCSHYICPICSKSLGD 1164 (1237)
Q Consensus 1114 ~~~CpICle~lf~s~~~-v~~LpCgH~fH~~Ci~~w-l~~~~~CPiCr~sv~d 1164 (1237)
+..||||+...+.+.+. ..+-+|||.|+..|++.. ......||+|++++-.
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 45799999965555432 222289999999999995 4556789999998753
No 50
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.22 E-value=0.00016 Score=78.99 Aligned_cols=51 Identities=24% Similarity=0.547 Sum_probs=39.1
Q ss_pred cCCCCCCcccccccccCCCcceecCCCCccChhhHHHhhhc---CCCCCCCCcccCCh
Q 000886 1111 KGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS---HYICPICSKSLGDM 1165 (1237)
Q Consensus 1111 ~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~---~~~CPiCr~sv~dm 1165 (1237)
.+..-+|-||||- ..+ .++-.|||.|+..||.+|+.. +..||+|+-.|.+-
T Consensus 44 ~~~~FdCNICLd~---akd-PVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~ 97 (230)
T KOG0823|consen 44 DGGFFDCNICLDL---AKD-PVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSID 97 (230)
T ss_pred CCCceeeeeeccc---cCC-CEEeecccceehHHHHHHHhhcCCCeeCCccccccccc
Confidence 3455789999875 333 455679999999999999864 35689999888654
No 51
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.22 E-value=0.00011 Score=84.35 Aligned_cols=47 Identities=28% Similarity=0.659 Sum_probs=37.7
Q ss_pred CCCcccccccccCCCcceecC-CCCccChhhHHHhhhc---CCCCCCCCccc
Q 000886 1115 TNCPICCDFLFTSSATVRALP-CGHFMHSDCFQAYTCS---HYICPICSKSL 1162 (1237)
Q Consensus 1115 ~~CpICle~lf~s~~~v~~Lp-CgH~fH~~Ci~~wl~~---~~~CPiCr~sv 1162 (1237)
..|.|| ++++.....+..+. |||+||..|+.+|... +.+||||+-.+
T Consensus 5 A~C~Ic-~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~ 55 (465)
T KOG0827|consen 5 AECHIC-IDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKL 55 (465)
T ss_pred ceeeEe-ccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeecc
Confidence 579999 66687777676664 9999999999999865 36899999433
No 52
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.22 E-value=0.00015 Score=86.33 Aligned_cols=49 Identities=31% Similarity=0.679 Sum_probs=36.8
Q ss_pred CCCCCCcccccccccCCCcceecCCCCccChhhHHHhhhc-----CCCCCCCCcccCC
Q 000886 1112 GLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS-----HYICPICSKSLGD 1164 (1237)
Q Consensus 1112 ~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~-----~~~CPiCr~sv~d 1164 (1237)
+++..||||+++ . ..++ .+.|||.|+..||-+|+.. -..||||+..|.-
T Consensus 184 ~t~~~CPICL~~-~--~~p~-~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~ 237 (513)
T KOG2164|consen 184 STDMQCPICLEP-P--SVPV-RTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITL 237 (513)
T ss_pred CcCCcCCcccCC-C--Cccc-ccccCceeeHHHHHHHHhhhcccCCccCCchhhhccc
Confidence 338899999987 2 1223 3459999999999887543 3679999998864
No 53
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.04 E-value=0.00021 Score=84.08 Aligned_cols=32 Identities=31% Similarity=0.802 Sum_probs=27.5
Q ss_pred eecCCCCccChhhHHHhhh-cCCCCCCCCcccC
Q 000886 1132 RALPCGHFMHSDCFQAYTC-SHYICPICSKSLG 1163 (1237)
Q Consensus 1132 ~~LpCgH~fH~~Ci~~wl~-~~~~CPiCr~sv~ 1163 (1237)
+..||.|.||..|+.+|+. .+..||+||.++.
T Consensus 602 m~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLP 634 (636)
T KOG0828|consen 602 MLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLP 634 (636)
T ss_pred cccchHHHHHHHHHHHHHhhhcccCCccCCCCC
Confidence 3459999999999999997 5669999998864
No 54
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.93 E-value=0.00021 Score=78.90 Aligned_cols=50 Identities=22% Similarity=0.640 Sum_probs=39.2
Q ss_pred CCCCcccccccccCC------CcceecCCCCccChhhHHHhh--hcCCCCCCCCcccC
Q 000886 1114 ETNCPICCDFLFTSS------ATVRALPCGHFMHSDCFQAYT--CSHYICPICSKSLG 1163 (1237)
Q Consensus 1114 ~~~CpICle~lf~s~------~~v~~LpCgH~fH~~Ci~~wl--~~~~~CPiCr~sv~ 1163 (1237)
++.|.||...++.+. +..-.|.|+|.||..||+-|- ....+||.|++.|.
T Consensus 224 d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVd 281 (328)
T KOG1734|consen 224 DSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVD 281 (328)
T ss_pred cchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhh
Confidence 467888887766554 134679999999999999994 56789999998763
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=96.77 E-value=0.001 Score=61.02 Aligned_cols=47 Identities=21% Similarity=0.367 Sum_probs=35.3
Q ss_pred CCCCcccccccccCCCcceecCCCCccChhhHHHhhhc-CCCCCCCCcccCC
Q 000886 1114 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS-HYICPICSKSLGD 1164 (1237)
Q Consensus 1114 ~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~-~~~CPiCr~sv~d 1164 (1237)
+-.|||+.+-|.+ .+++||||+|-+.||.+|+.. +.+||+|+..+..
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 3469999987543 356899999999999999988 8999999998864
No 56
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.72 E-value=0.00068 Score=75.28 Aligned_cols=46 Identities=26% Similarity=0.694 Sum_probs=38.0
Q ss_pred CCCCcccccccccCCCcceecCCCCccChhhHHH-hhhcCCC-CCCCCcccC
Q 000886 1114 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQA-YTCSHYI-CPICSKSLG 1163 (1237)
Q Consensus 1114 ~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~-wl~~~~~-CPiCr~sv~ 1163 (1237)
+..|+||+|.... ....+|||.|+..||-. |+...+- ||+||..+.
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 4579999987543 45689999999999998 9988766 999998764
No 57
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.62 E-value=0.00088 Score=77.99 Aligned_cols=82 Identities=21% Similarity=0.463 Sum_probs=57.0
Q ss_pred cCCCCCCcccccccccCCC---ccee-cCCCCccChhhHHHhh--hc-----CCCCCCCCcccC--ChhhHHHhHHHHHh
Q 000886 1111 KGLETNCPICCDFLFTSSA---TVRA-LPCGHFMHSDCFQAYT--CS-----HYICPICSKSLG--DMAVYFGMLDALLA 1177 (1237)
Q Consensus 1111 ~~~~~~CpICle~lf~s~~---~v~~-LpCgH~fH~~Ci~~wl--~~-----~~~CPiCr~sv~--dm~~~~~~lD~~i~ 1177 (1237)
++.+..|-||+|.+..... .-.+ ++|.|.|...||+.|- .. +..||+||.... .-+.+|-.-.. +
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 4667899999998765431 0122 4699999999999997 33 578999998874 33444543333 6
Q ss_pred hcCCChhhhccCCceec
Q 000886 1178 SEQLPEEYRDRCQEILC 1194 (1237)
Q Consensus 1178 ~~pmP~ey~~~~~~i~C 1194 (1237)
.++++++|...+....|
T Consensus 236 k~~li~e~~~~~s~~~c 252 (344)
T KOG1039|consen 236 KQKLIEEYEAEMSAKDC 252 (344)
T ss_pred ccccHHHHHHHhhccch
Confidence 77888888776654444
No 58
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=96.42 E-value=0.002 Score=57.69 Aligned_cols=56 Identities=29% Similarity=0.611 Sum_probs=27.8
Q ss_pred CCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcccC--ChhhHHHhHHHHH
Q 000886 1115 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG--DMAVYFGMLDALL 1176 (1237)
Q Consensus 1115 ~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCr~sv~--dm~~~~~~lD~~i 1176 (1237)
..|++|.+.|. ++|..-.|.|.|.+.|+.+-+ ++.||+|+.+.- |+.. -+.||..|
T Consensus 8 LrCs~C~~~l~---~pv~l~~CeH~fCs~Ci~~~~--~~~CPvC~~Paw~qD~~~-NrqLd~~i 65 (65)
T PF14835_consen 8 LRCSICFDILK---EPVCLGGCEHIFCSSCIRDCI--GSECPVCHTPAWIQDIQI-NRQLDSMI 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--CCCCCCcCChHHHHHHHh-hhhhhccC
Confidence 46999998854 356777999999999998855 356999999984 4432 46677654
No 59
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=96.05 E-value=0.003 Score=70.61 Aligned_cols=44 Identities=25% Similarity=0.542 Sum_probs=37.3
Q ss_pred CCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCccc
Q 000886 1115 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSL 1162 (1237)
Q Consensus 1115 ~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCr~sv 1162 (1237)
..|-||.+++.. ....+|||.|+.-||..++..+..||+||...
T Consensus 26 lrC~IC~~~i~i----p~~TtCgHtFCslCIR~hL~~qp~CP~Cr~~~ 69 (391)
T COG5432 26 LRCRICDCRISI----PCETTCGHTFCSLCIRRHLGTQPFCPVCREDP 69 (391)
T ss_pred HHhhhhhheeec----ceecccccchhHHHHHHHhcCCCCCccccccH
Confidence 579999988431 24469999999999999999999999999875
No 60
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.97 E-value=0.0016 Score=56.23 Aligned_cols=52 Identities=27% Similarity=0.634 Sum_probs=37.4
Q ss_pred CCCCCcccccccccCCCcceecCCCCc-cChhh-HHHhhhcCCCCCCCCcccCChhhH
Q 000886 1113 LETNCPICCDFLFTSSATVRALPCGHF-MHSDC-FQAYTCSHYICPICSKSLGDMAVY 1168 (1237)
Q Consensus 1113 ~~~~CpICle~lf~s~~~v~~LpCgH~-fH~~C-i~~wl~~~~~CPiCr~sv~dm~~~ 1168 (1237)
...+|.||+|.-.+ .+.--|||. +.-.| ++.|...+.+|||||.+|.|.-..
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 34789999986222 234489996 56677 455766889999999998775443
No 61
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=95.93 E-value=0.0017 Score=74.96 Aligned_cols=61 Identities=31% Similarity=0.658 Sum_probs=48.5
Q ss_pred cccccccCCCCCCcccccccccCCCcceecCCCCccChhhHHHhhhcC--CCCCCCCcccCChh
Q 000886 1105 DHKCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSH--YICPICSKSLGDMA 1166 (1237)
Q Consensus 1105 ~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~--~~CPiCr~sv~dm~ 1166 (1237)
-|.|++ .++-+|-.|.|.+--..+....|||.|+||..|+.+++..+ .+||-||+-...|.
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 46789999999877667778889999999999999998665 67999996554443
No 62
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.66 E-value=0.006 Score=71.18 Aligned_cols=49 Identities=35% Similarity=0.819 Sum_probs=38.7
Q ss_pred CCCCcccccccccCCC-cceecCCCCccChhhHHHhhhc--CCCCCCCCccc
Q 000886 1114 ETNCPICCDFLFTSSA-TVRALPCGHFMHSDCFQAYTCS--HYICPICSKSL 1162 (1237)
Q Consensus 1114 ~~~CpICle~lf~s~~-~v~~LpCgH~fH~~Ci~~wl~~--~~~CPiCr~sv 1162 (1237)
...||||++..-.+++ .+..|.|||.|-.+||+.|+.. ...||.|.-..
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 4689999998655554 4456899999999999999953 36799998654
No 63
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.66 E-value=0.0061 Score=70.49 Aligned_cols=51 Identities=29% Similarity=0.671 Sum_probs=40.7
Q ss_pred ccCCCCCCcccccccccCCCcceecCCCCc-cChhhHHHhhhcCCCCCCCCcccCC
Q 000886 1110 EKGLETNCPICCDFLFTSSATVRALPCGHF-MHSDCFQAYTCSHYICPICSKSLGD 1164 (1237)
Q Consensus 1110 e~~~~~~CpICle~lf~s~~~v~~LpCgH~-fH~~Ci~~wl~~~~~CPiCr~sv~d 1164 (1237)
++.....|.||+.+ + ..+.+|||-|. ++..|-+...-..+.|||||..|..
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 34456799999876 2 34788999996 8999998877678899999998753
No 64
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.65 E-value=0.0021 Score=73.87 Aligned_cols=47 Identities=32% Similarity=0.598 Sum_probs=38.3
Q ss_pred CCCCcccccccccCCCcceecCCCCccChhhHHHhhh-cCCCCCCCCcccC
Q 000886 1114 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC-SHYICPICSKSLG 1163 (1237)
Q Consensus 1114 ~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~-~~~~CPiCr~sv~ 1163 (1237)
+..|||||+-|.. .+...-|+|-|+.+||..-++ .+..||.||+.++
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 4689999986543 355678999999999988764 5789999999985
No 65
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=95.63 E-value=0.0037 Score=78.27 Aligned_cols=52 Identities=25% Similarity=0.578 Sum_probs=37.6
Q ss_pred cCCCCCCcccccccc--cCCCcc-eecCCCCccChhhHHHhhhc--CCCCCCCCccc
Q 000886 1111 KGLETNCPICCDFLF--TSSATV-RALPCGHFMHSDCFQAYTCS--HYICPICSKSL 1162 (1237)
Q Consensus 1111 ~~~~~~CpICle~lf--~s~~~v-~~LpCgH~fH~~Ci~~wl~~--~~~CPiCr~sv 1162 (1237)
-+....|+||+--+. +..-|. +.-.|.|.||..|+.+|.++ +.+||+||-++
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 455789999987554 221122 22458899999999999865 58999999765
No 66
>COG2461 Uncharacterized conserved protein [Function unknown]
Probab=95.61 E-value=0.075 Score=62.50 Aligned_cols=133 Identities=14% Similarity=0.170 Sum_probs=104.0
Q ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHhhcccCCcccHHHHHHHHHHHHHHHHhhhhcccccchhhhhhhh------hhHH
Q 000886 291 SCPIDEIMLWHNAIKRELNDIAEAARKIQLSGDFSDLSAFNKRLQFIAEVCIFHSIAEDKVIFPAVDVEL------SFAQ 364 (1237)
Q Consensus 291 ~~pid~l~~~HkALRrEL~~L~~~a~~~~~~gd~~~L~~L~~r~~fl~~vl~~Hs~aEDevlFPaL~~r~------~me~ 364 (1237)
-+|+..|+..-++||..|+.+.+. .. +..-...+...+.++..+=+ |=+.+...|||.++.+- .|--
T Consensus 85 gHPv~tl~~EN~~i~~ll~~~l~~---~~---~~~ik~~l~~lv~~L~~vg~-Hy~RKe~lIfp~~Er~GitapptVmW~ 157 (409)
T COG2461 85 GHPVRTLKRENKAIRSLLANLLQF---PP---KKEIKEKLVELVSELDKIGK-HYTRKEMLIFPYIERRGITAPPTVMWV 157 (409)
T ss_pred CCcHHHHhcccHHHHHHHHHHhhc---cc---cHHHHHHHHHHHHHHHHhcc-ccccccccchhHHHHcCCCCCCeeeec
Confidence 689999999999999554444333 21 21222566666777777767 88999999999999886 8889
Q ss_pred hHHHHHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhhCCHHHHHHHHHhH
Q 000886 365 EHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPLARRHFSPKRQRELLYQS 441 (1237)
Q Consensus 365 EH~~ie~l~e~l~~ll~~~~~a~~~~~~~~~~~eLa~~le~L~~~L~~H~~~EE~qvfPLl~~~fS~eEq~~L~~~~ 441 (1237)
.|+++-..+..+..++... + ..++......+.+.+..=+.+||+.+.|.+-..||..||.++-.+.
T Consensus 158 ~dDeiRe~lk~~~~~l~~~--s---------~~~~ve~~~~~~t~i~dmIFkEe~Ilypt~~d~~te~ew~~i~~~~ 223 (409)
T COG2461 158 KDDEIREALKELLKLLKEV--S---------IEEFVEKAESVLTEIEDMIFKEENILYPTLLDLLTEGEWEAIKEQS 223 (409)
T ss_pred cCcHHHHHHHHHHHHhhcc--C---------hHHHHHHHHHHHHHHHHHHHhhhhhHHhHHHHhcCHHHHHHHHhcC
Confidence 9999988899988888621 1 2456667777888899999999999999999999999999987553
No 67
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=95.38 E-value=0.005 Score=76.93 Aligned_cols=47 Identities=23% Similarity=0.612 Sum_probs=37.3
Q ss_pred CCCcccccccccCCCcceecCCCCccChhhHHHhhhc-CCCCCCCCcccCCh
Q 000886 1115 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS-HYICPICSKSLGDM 1165 (1237)
Q Consensus 1115 ~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~-~~~CPiCr~sv~dm 1165 (1237)
-.||+|-+ ....+++..|||.|+..|+..-+.. ..+||.|..+++.-
T Consensus 644 LkCs~Cn~----R~Kd~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFgan 691 (698)
T KOG0978|consen 644 LKCSVCNT----RWKDAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGAN 691 (698)
T ss_pred eeCCCccC----chhhHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCcc
Confidence 45888853 3445677899999999999998754 68999999998753
No 68
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=95.00 E-value=0.0067 Score=70.28 Aligned_cols=53 Identities=28% Similarity=0.696 Sum_probs=43.9
Q ss_pred cccccCCCCCCcccccccccCCCcceecCCCCccChhhHHHhhhc--CCCCCCCCcccC
Q 000886 1107 KCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS--HYICPICSKSLG 1163 (1237)
Q Consensus 1107 ~C~e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~--~~~CPiCr~sv~ 1163 (1237)
.|.-.++-.-|-||-|. .+.|++=||||.++..|+..|-.. +.+||-||..|-
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 46666777899999875 456888899999999999999743 689999999884
No 69
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=94.88 E-value=0.0025 Score=72.16 Aligned_cols=133 Identities=17% Similarity=0.124 Sum_probs=92.2
Q ss_pred HHHHHHhhhhcccccccccccccccccccccchhhHHHHHHHHHHHHHHHhhhhhhhccccCcCCcccccccccccchhh
Q 000886 688 GLYRAHSNAEDDIVFPALESKETLSNVSHSYTLDHKQEEKLFEDISSALSELTELHECLSTDLTGDLTRNSLESCDQNET 767 (1237)
Q Consensus 688 ~v~~~HS~AEDeivfPALe~k~~~~n~s~s~~~DH~~ee~lfedi~~~L~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 767 (1237)
.++..|+.++|++-||+..++....+.+++...||.-.=.+..+.+... +. .+
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 7899999999999999999887666666666555544444444431100 00 11
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHhhHhHHHhhhhHHhhcCCHHHHHHHHHHHHhccCHHHHHHhhhHHhhcCCHHHHHH
Q 000886 768 VRKYNEKATELQGMCKSIRVTLDQHVFREELELWPLFDRHFSVEEQDKIVGRIIGTTGAEVLQSMLPWVTSALTQEEQNT 847 (1237)
Q Consensus 768 ~~~~~e~~~kL~~~~ksl~~~L~~Hl~~EE~ElfPL~rk~fS~eeQ~~Lv~~~l~~~p~~~L~~~LPWl~~~Lte~E~~~ 847 (1237)
..++.-...+.....++.......|.. +.++|=++.+.|+++++ +++.-+.+.+--+.++. |||.-.....+..+
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 123233455555555556678888888 99999999999999999 88888877665544443 99998777777776
Q ss_pred HHHHh
Q 000886 848 MMDTW 852 (1237)
Q Consensus 848 ml~~~ 852 (1237)
-|.+|
T Consensus 145 ~~~~~ 149 (276)
T KOG1940|consen 145 YLSNW 149 (276)
T ss_pred hcccc
Confidence 66665
No 70
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.25 E-value=0.033 Score=62.48 Aligned_cols=52 Identities=21% Similarity=0.624 Sum_probs=41.8
Q ss_pred CCCCCCcccccccccCCCcceecCCCCccChhhHHHhhh--cCCCCCCCCcccCChh
Q 000886 1112 GLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC--SHYICPICSKSLGDMA 1166 (1237)
Q Consensus 1112 ~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~--~~~~CPiCr~sv~dm~ 1166 (1237)
.....||+|.++ +.-|....+|||.|+--|+..-.. -+.+||.|+-++..|.
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 446789999986 455677789999999999988654 3589999999887664
No 71
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=94.00 E-value=0.041 Score=46.96 Aligned_cols=45 Identities=22% Similarity=0.526 Sum_probs=24.0
Q ss_pred CcccccccccCCCcceecCCCCccChhhHHHhhh-cCCCCCCCCcc
Q 000886 1117 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC-SHYICPICSKS 1161 (1237)
Q Consensus 1117 CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~-~~~~CPiCr~s 1161 (1237)
||+|.++|..+.....-=+||+.+...|+..-+. .+..||-||++
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 8999999854443333336899999999999886 48999999986
No 72
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=93.74 E-value=0.0098 Score=69.90 Aligned_cols=71 Identities=30% Similarity=0.797 Sum_probs=40.9
Q ss_pred Ccccc--CCCCCccccCCCCCccccccCC---cccccccccccccccccCCCCCCcccccccccCCCcceec-CCCCccC
Q 000886 1068 RVVYH--CPFCNLCRVGRGLGVDFFHCMT---CNCCLAKKLVDHKCREKGLETNCPICCDFLFTSSATVRAL-PCGHFMH 1141 (1237)
Q Consensus 1068 k~~yH--C~~CgiCR~g~gl~~~~fHC~~---C~~C~s~~l~~H~C~e~~~~~~CpICle~lf~s~~~v~~L-pCgH~fH 1141 (1237)
+.+|| |=.|+.||.-.. |..||.-+. |--|+-.++ ..|-.|-+.+.+ ++| .||-.||
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 778888887654 567776544 333332222 346666655322 223 5777777
Q ss_pred hhhHHHhhhcCCCCCCCCcccC
Q 000886 1142 SDCFQAYTCSHYICPICSKSLG 1163 (1237)
Q Consensus 1142 ~~Ci~~wl~~~~~CPiCr~sv~ 1163 (1237)
..|| +|=+|.+.+.
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 5556666554
No 73
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=93.66 E-value=0.019 Score=64.80 Aligned_cols=55 Identities=27% Similarity=0.639 Sum_probs=43.5
Q ss_pred ccCCCCCCcccccccccCCCcceecCCCCccChhhHHHhhh-----------------------cCCCCCCCCcccCCh
Q 000886 1110 EKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC-----------------------SHYICPICSKSLGDM 1165 (1237)
Q Consensus 1110 e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~-----------------------~~~~CPiCr~sv~dm 1165 (1237)
.+-..+.|.|||=- |.+.....+.+|-|+||..|+..|+. ....|||||-.|++-
T Consensus 111 nn~p~gqCvICLyg-fa~~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~e 188 (368)
T KOG4445|consen 111 NNHPNGQCVICLYG-FASSPAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKIE 188 (368)
T ss_pred CCCCCCceEEEEEe-ecCCCceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhcccc
Confidence 45567899999955 77777788899999999999988753 124599999988653
No 74
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.39 E-value=0.055 Score=58.93 Aligned_cols=52 Identities=27% Similarity=0.633 Sum_probs=41.9
Q ss_pred cCCCCCCcccccccccCCCcceecCCCCccChhhHHHhhh--------cCCCCCCCCcccCC
Q 000886 1111 KGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC--------SHYICPICSKSLGD 1164 (1237)
Q Consensus 1111 ~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~--------~~~~CPiCr~sv~d 1164 (1237)
.....||..|.-.|-.. + ...|-|=|.||..|+++|.. .+|.||-|+..|..
T Consensus 47 sDY~pNC~LC~t~La~g-d-t~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFP 106 (299)
T KOG3970|consen 47 SDYNPNCRLCNTPLASG-D-TTRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFP 106 (299)
T ss_pred cCCCCCCceeCCccccC-c-ceeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCC
Confidence 34578999999886543 3 46689999999999999953 36999999999964
No 75
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=93.27 E-value=0.047 Score=48.18 Aligned_cols=43 Identities=26% Similarity=0.620 Sum_probs=29.7
Q ss_pred CCCCCCcccccccccCCCcceecCCCCccChhhHHHhhh--cCCCCCC
Q 000886 1112 GLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC--SHYICPI 1157 (1237)
Q Consensus 1112 ~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~--~~~~CPi 1157 (1237)
.....|||.+.. |. ++|+...|||+|=+..|.+|+. ....||+
T Consensus 9 ~~~~~CPiT~~~-~~--~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv 53 (57)
T PF11789_consen 9 TISLKCPITLQP-FE--DPVKSKKCGHTFEKEAILQYIQRNGSKRCPV 53 (57)
T ss_dssp B--SB-TTTSSB--S--SEEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred EeccCCCCcCCh-hh--CCcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence 345789999987 43 4788899999999999999994 3578999
No 76
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.22 E-value=0.048 Score=57.56 Aligned_cols=31 Identities=26% Similarity=0.698 Sum_probs=26.0
Q ss_pred ecCCCCccChhhHHHhhhc-----------CCCCCCCCcccC
Q 000886 1133 ALPCGHFMHSDCFQAYTCS-----------HYICPICSKSLG 1163 (1237)
Q Consensus 1133 ~LpCgH~fH~~Ci~~wl~~-----------~~~CPiCr~sv~ 1163 (1237)
...||-.||.-|+..|++. -..||.|+++|.
T Consensus 187 N~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~Pia 228 (234)
T KOG3268|consen 187 NIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIA 228 (234)
T ss_pred ccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcce
Confidence 3689999999999999863 156999999984
No 77
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=92.77 E-value=0.044 Score=52.88 Aligned_cols=37 Identities=27% Similarity=0.608 Sum_probs=29.5
Q ss_pred ccccCCCCCCcccccccccCCCcceecCCCCccChhhHH
Q 000886 1108 CREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQ 1146 (1237)
Q Consensus 1108 C~e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~ 1146 (1237)
++.-.....|+||...+.. ....+.||||.||..|++
T Consensus 72 ~v~i~~~~~C~vC~k~l~~--~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 72 SVVITESTKCSVCGKPLGN--SVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred eEEECCCCCccCcCCcCCC--ceEEEeCCCeEEeccccc
Confidence 3444556789999999776 357778999999999985
No 78
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=92.74 E-value=0.061 Score=66.76 Aligned_cols=49 Identities=24% Similarity=0.516 Sum_probs=35.3
Q ss_pred cccccCCCCCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCC
Q 000886 1107 KCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPI 1157 (1237)
Q Consensus 1107 ~C~e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPi 1157 (1237)
+|+-......|.||.-.+ .+.....+.|||.+|..|..+|.+....||.
T Consensus 1021 ~~~~~~~~~~C~~C~l~V--~gss~~Cg~C~Hv~H~sc~~eWf~~gd~Cps 1069 (1081)
T KOG0309|consen 1021 CAICKGFTFQCAICHLAV--RGSSNFCGTCGHVGHTSCMMEWFRTGDVCPS 1069 (1081)
T ss_pred ccccccceeeeeeEeeEe--eccchhhccccccccHHHHHHHHhcCCcCCC
Confidence 333344445588886443 2334556789999999999999999999995
No 79
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=92.64 E-value=0.082 Score=58.50 Aligned_cols=56 Identities=25% Similarity=0.485 Sum_probs=46.5
Q ss_pred cccCCCCCCcccccccccCCCcceec-CCCCccChhhHHHhhhcCCCCCCCCcccCCh
Q 000886 1109 REKGLETNCPICCDFLFTSSATVRAL-PCGHFMHSDCFQAYTCSHYICPICSKSLGDM 1165 (1237)
Q Consensus 1109 ~e~~~~~~CpICle~lf~s~~~v~~L-pCgH~fH~~Ci~~wl~~~~~CPiCr~sv~dm 1165 (1237)
+..+..-.||||.+.| ++..+..+| ||||+|...|..+.++....||||.+++-+.
T Consensus 216 ~a~s~ryiCpvtrd~L-tNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdr 272 (303)
T KOG3039|consen 216 IAASKRYICPVTRDTL-TNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDR 272 (303)
T ss_pred hhhccceecccchhhh-cCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCccc
Confidence 3344567899999985 455666666 9999999999999999999999999998754
No 80
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.31 E-value=0.073 Score=60.56 Aligned_cols=48 Identities=19% Similarity=0.358 Sum_probs=37.4
Q ss_pred CCCCCCcccccccccCCCcceecCCCCccChhhHHHhhhc-CCCCCCCCcccC
Q 000886 1112 GLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS-HYICPICSKSLG 1163 (1237)
Q Consensus 1112 ~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~-~~~CPiCr~sv~ 1163 (1237)
.+...|+||+.... -+ ..|+|+|.|.-.||+--... ..+||+||.+|.
T Consensus 5 ~~~~eC~IC~nt~n---~P-v~l~C~HkFCyiCiKGsy~ndk~~CavCR~pid 53 (324)
T KOG0824|consen 5 TKKKECLICYNTGN---CP-VNLYCFHKFCYICIKGSYKNDKKTCAVCRFPID 53 (324)
T ss_pred ccCCcceeeeccCC---cC-ccccccchhhhhhhcchhhcCCCCCceecCCCC
Confidence 45678999986532 23 66999999999999875443 567999999985
No 81
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=92.14 E-value=0.094 Score=44.48 Aligned_cols=40 Identities=25% Similarity=0.674 Sum_probs=26.6
Q ss_pred CcccccccccCCCcceecCCC-----CccChhhHHHhhh--cCCCCCCC
Q 000886 1117 CPICCDFLFTSSATVRALPCG-----HFMHSDCFQAYTC--SHYICPIC 1158 (1237)
Q Consensus 1117 CpICle~lf~s~~~v~~LpCg-----H~fH~~Ci~~wl~--~~~~CPiC 1158 (1237)
|-||++.-.++. ..+.||+ -+.|..|+.+|+. .+.+|++|
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 3456774 6899999999985 46789998
No 82
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=91.99 E-value=0.088 Score=63.08 Aligned_cols=54 Identities=28% Similarity=0.641 Sum_probs=43.0
Q ss_pred CCCCCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcccCChhhH
Q 000886 1112 GLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGDMAVY 1168 (1237)
Q Consensus 1112 ~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCr~sv~dm~~~ 1168 (1237)
..+..||||..-+- +++....|||.|...|+..|+..+..||.|+..+.....+
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 34578999986643 3455579999999999999998899999999887655444
No 83
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=91.97 E-value=0.062 Score=59.66 Aligned_cols=37 Identities=30% Similarity=0.696 Sum_probs=28.1
Q ss_pred ccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcccC
Q 000886 1125 FTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1163 (1237)
Q Consensus 1125 f~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCr~sv~ 1163 (1237)
+.+.++-....|+|+|+..|...-. ...||+|++++-
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 4455556677999999999986532 239999999973
No 84
>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=91.91 E-value=0.061 Score=55.02 Aligned_cols=45 Identities=20% Similarity=0.367 Sum_probs=36.4
Q ss_pred CCCCcccccccccCCCcceecCCC------CccChhhHHHhhhcCCCCCCCC
Q 000886 1114 ETNCPICCDFLFTSSATVRALPCG------HFMHSDCFQAYTCSHYICPICS 1159 (1237)
Q Consensus 1114 ~~~CpICle~lf~s~~~v~~LpCg------H~fH~~Ci~~wl~~~~~CPiCr 1159 (1237)
...|.||++.+.. .+.|+.++|| |+||.+|+.+|.+.+.+=|-=|
T Consensus 26 ~~EC~IC~~~I~~-~~GvV~vt~~g~lnLEkmfc~~C~~rw~~~~~rDPfnR 76 (134)
T PF05883_consen 26 TVECQICFDRIDN-NDGVVYVTDGGTLNLEKMFCADCDKRWRRERNRDPFNR 76 (134)
T ss_pred Ceeehhhhhhhhc-CCCEEEEecCCeehHHHHHHHHHHHHHHhhccCCCccc
Confidence 4689999999877 6789999998 9999999999965555555433
No 85
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=91.82 E-value=0.06 Score=59.57 Aligned_cols=141 Identities=26% Similarity=0.578 Sum_probs=86.2
Q ss_pred CcccccccccccccccCC--------------------cccCcccccccCCCCCccccccccccccccccccCCCCCCCc
Q 000886 987 GCEHYKRNCKLRAACCGK--------------------LFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVGPVCTTL 1046 (1237)
Q Consensus 987 gC~HY~r~c~l~~~cC~~--------------------~y~Cr~CHde~~~H~~~r~~~~~v~C~~C~~~Q~~~~~C~~~ 1046 (1237)
-|.|=-. -|.+|||+| -|.|..|.....|--+-|.+ ...+|-.|+..-.+
T Consensus 63 YCEhDF~--~LfaPcC~kC~EFiiGrVikamnnSwHp~CF~Cd~Cn~~Lad~gf~rnq-gr~LC~~Cn~k~Ka------- 132 (332)
T KOG2272|consen 63 YCEHDFH--VLFAPCCGKCGEFIIGRVIKAMNNSWHPACFRCDLCNKHLADQGFYRNQ-GRALCRECNQKEKA------- 132 (332)
T ss_pred cccccch--hhhchhhcccccchhhHHHHhhccccCcccchhHHHHHHHhhhhhHhhc-chHHhhhhhhhhcc-------
Confidence 3766321 377888876 36677777776666666653 47788888654332
Q ss_pred cCCCCccceEecccccC-CCCC-----CccccCCCCCccccCCCCCccccccCCccccccccc----ccccccccCCCCC
Q 000886 1047 SCSGLSMAKYYCGICKF-FDDE-----RVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLAKKL----VDHKCREKGLETN 1116 (1237)
Q Consensus 1047 ~C~~~~~~~y~C~~C~~-~d~~-----k~~yHC~~CgiCR~g~gl~~~~fHC~~C~~C~s~~l----~~H~C~e~~~~~~ 1116 (1237)
.--|+|.|.+|+- +|++ .++|| -..|.|.+||-=+.... +.--|..=....-
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 1257999999995 5666 67888 26799999987764332 3333443333455
Q ss_pred CcccccccccCCCcceecCCCCccChhhH----HHhhhcCCCCCCCCcccCChhhH
Q 000886 1117 CPICCDFLFTSSATVRALPCGHFMHSDCF----QAYTCSHYICPICSKSLGDMAVY 1168 (1237)
Q Consensus 1117 CpICle~lf~s~~~v~~LpCgH~fH~~Ci----~~wl~~~~~CPiCr~sv~dm~~~ 1168 (1237)
||||..- .-.+-..-| ..|-..+..|-.|-|++..-..|
T Consensus 195 ipiCgaC-------------~rpIeervi~amgKhWHveHFvCa~CekPFlGHrHY 237 (332)
T KOG2272|consen 195 IPICGAC-------------RRPIEERVIFAMGKHWHVEHFVCAKCEKPFLGHRHY 237 (332)
T ss_pred Ccccccc-------------cCchHHHHHHHhccccchhheeehhcCCcccchhhh
Confidence 6666432 111111112 23555678899999988765544
No 86
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=91.72 E-value=0.12 Score=59.61 Aligned_cols=62 Identities=23% Similarity=0.580 Sum_probs=46.5
Q ss_pred CCCCcccccccccCCCcceecCC--CCccChhhHHHhhhcCCCCCCCCcccCChhhHHHhHHHHHhhcCCChhh
Q 000886 1114 ETNCPICCDFLFTSSATVRALPC--GHFMHSDCFQAYTCSHYICPICSKSLGDMAVYFGMLDALLASEQLPEEY 1185 (1237)
Q Consensus 1114 ~~~CpICle~lf~s~~~v~~LpC--gH~fH~~Ci~~wl~~~~~CPiCr~sv~dm~~~~~~lD~~i~~~pmP~ey 1185 (1237)
-.+||||.++|.. -++.| ||.....|-. +..++||.||.++++... +.++.+++....|=.|
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 3689999998643 34667 7999998874 458899999999996532 4666777777776544
No 87
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=91.32 E-value=0.097 Score=56.18 Aligned_cols=58 Identities=24% Similarity=0.309 Sum_probs=43.3
Q ss_pred CCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcccCChhhHHHhHHHHH
Q 000886 1115 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGDMAVYFGMLDALL 1176 (1237)
Q Consensus 1115 ~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCr~sv~dm~~~~~~lD~~i 1176 (1237)
-.|-||.++ |.+ .++..|||.|+..|...-.+...+|-+|.+.....-..-..+|+.+
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 368999988 554 3567899999999987777778999999998754433345555544
No 88
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=91.18 E-value=0.054 Score=62.33 Aligned_cols=50 Identities=20% Similarity=0.559 Sum_probs=42.1
Q ss_pred CCCCCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcccCC
Q 000886 1112 GLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1164 (1237)
Q Consensus 1112 ~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCr~sv~d 1164 (1237)
.....|++|..||.+.+ .+.-|=|+|++.||-+++..+.+||.|...|..
T Consensus 13 n~~itC~LC~GYliDAT---TI~eCLHTFCkSCivk~l~~~~~CP~C~i~ih~ 62 (331)
T KOG2660|consen 13 NPHITCRLCGGYLIDAT---TITECLHTFCKSCIVKYLEESKYCPTCDIVIHK 62 (331)
T ss_pred ccceehhhccceeecch---hHHHHHHHHHHHHHHHHHHHhccCCccceeccC
Confidence 34568999999976653 456799999999999999999999999998864
No 89
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=89.14 E-value=0.13 Score=58.94 Aligned_cols=57 Identities=23% Similarity=0.535 Sum_probs=43.3
Q ss_pred CCCCcccccccccCCCcceecCCCCccChhhHHHhhh-cCCCCCCCCcccCChhhHHH
Q 000886 1114 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC-SHYICPICSKSLGDMAVYFG 1170 (1237)
Q Consensus 1114 ~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~-~~~~CPiCr~sv~dm~~~~~ 1170 (1237)
++.||.|+|+|.-+.....--|||--++.-|+..-.. -+.+||-||+...+-...|+
T Consensus 14 ed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~denv~~~ 71 (480)
T COG5175 14 EDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDENVRYV 71 (480)
T ss_pred cccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhccccceeEE
Confidence 4559999999877765555568999999999876543 37899999998876555553
No 90
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=89.03 E-value=0.14 Score=61.59 Aligned_cols=51 Identities=25% Similarity=0.570 Sum_probs=41.3
Q ss_pred cccCCCCCCcccccccccCCCcceecCCCCccChhhHHHhhh-----cCCCCCCCCcccC
Q 000886 1109 REKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC-----SHYICPICSKSLG 1163 (1237)
Q Consensus 1109 ~e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~-----~~~~CPiCr~sv~ 1163 (1237)
.++..+..|-+|.|+ .+....-.|.|.|++-|+.+|.. .+.+||+|.+.+.
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 467778899999876 23456679999999999999964 3689999999874
No 91
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=88.99 E-value=0.19 Score=44.02 Aligned_cols=33 Identities=30% Similarity=0.760 Sum_probs=25.9
Q ss_pred cceecCCCCccChhhHHHhhhcCCCCCCCCcccCC
Q 000886 1130 TVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1164 (1237)
Q Consensus 1130 ~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCr~sv~d 1164 (1237)
.-.++||||.+...|++-+ +-+-||+|.+.+..
T Consensus 19 ~~~~~pCgH~I~~~~f~~~--rYngCPfC~~~~~~ 51 (55)
T PF14447_consen 19 KGTVLPCGHLICDNCFPGE--RYNGCPFCGTPFEF 51 (55)
T ss_pred ccccccccceeeccccChh--hccCCCCCCCcccC
Confidence 3467899999999998655 34579999998753
No 92
>PF04641 Rtf2: Rtf2 RING-finger
Probab=88.74 E-value=0.29 Score=55.54 Aligned_cols=51 Identities=20% Similarity=0.483 Sum_probs=40.2
Q ss_pred cCCCCCCcccccccccCCCcceec-CCCCccChhhHHHhhhcCCCCCCCCcccC
Q 000886 1111 KGLETNCPICCDFLFTSSATVRAL-PCGHFMHSDCFQAYTCSHYICPICSKSLG 1163 (1237)
Q Consensus 1111 ~~~~~~CpICle~lf~s~~~v~~L-pCgH~fH~~Ci~~wl~~~~~CPiCr~sv~ 1163 (1237)
....--|||....| ++....+.| ||||+|-..++.+.- ....||+|.+++.
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 45567899999986 444445554 999999999999984 4678999999974
No 93
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=88.72 E-value=0.19 Score=64.18 Aligned_cols=44 Identities=25% Similarity=0.554 Sum_probs=33.3
Q ss_pred cccccccCCCCCCcccccccccCCCcceecCCCCccChhhHHHhhh
Q 000886 1105 DHKCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC 1150 (1237)
Q Consensus 1105 ~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~ 1150 (1237)
.|.|.--.....|-+|.-.++. .+-.+.||||.||++|+.+-..
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 4555544557889999887654 3667789999999999988653
No 94
>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=88.51 E-value=0.29 Score=55.63 Aligned_cols=48 Identities=23% Similarity=0.459 Sum_probs=37.4
Q ss_pred CCcccccccccCCCccee-cCCCCccChhhHHHhh-hcCCCCCCCCcccC
Q 000886 1116 NCPICCDFLFTSSATVRA-LPCGHFMHSDCFQAYT-CSHYICPICSKSLG 1163 (1237)
Q Consensus 1116 ~CpICle~lf~s~~~v~~-LpCgH~fH~~Ci~~wl-~~~~~CPiCr~sv~ 1163 (1237)
.||+|.-+.+.+.+-+.. -+|||.++..|++.-. ...+.||.|.+.+.
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 599999776666543322 2999999999999976 45699999998874
No 95
>COG5592 Uncharacterized conserved protein [Function unknown]
Probab=88.31 E-value=0.74 Score=48.51 Aligned_cols=71 Identities=18% Similarity=0.288 Sum_probs=56.1
Q ss_pred HHHHHHHHHHHHHhccccCCChhhHHHHHHHHHHHHHHHHHHhhhhcccccccccccccccccccccchhhHHHHHHHHH
Q 000886 652 KAIRKDLEYLDGESGKLNDCNETFLRQFTGRFRLLWGLYRAHSNAEDDIVFPALESKETLSNVSHSYTLDHKQEEKLFED 731 (1237)
Q Consensus 652 kAIRkDLe~l~~~~~kL~~~d~~~L~~f~~rf~~L~~v~~~HS~AEDeivfPALe~k~~~~n~s~s~~~DH~~ee~lfed 731 (1237)
+-||.||+.+.-+..-+.++... +.+..|+..+...+..|--||++.+||-+++.. .+.+..+...+++.
T Consensus 74 ~~i~~DHkliE~l~tnlik~kR~--~k~~e~~p~fyK~LtdHn~aEE~~IfPrvks~~--------~E~~~~~~kl~Lei 143 (171)
T COG5592 74 DRIKNDHKLIETLATNLIKWKRP--DKIKERVPLFYKTLTDHNLAEEEYIFPRVKSLK--------GEDEQSALKLALEI 143 (171)
T ss_pred hHhHhhHHHHHHHHHHHHhhccc--hHHHHHHHHHHHHHHHccccccchhhHHHHhhc--------chhhHHHHHHHHHH
Confidence 45788888888888888766333 478999999999999999999999999998763 33455666666777
Q ss_pred H
Q 000886 732 I 732 (1237)
Q Consensus 732 i 732 (1237)
|
T Consensus 144 I 144 (171)
T COG5592 144 I 144 (171)
T ss_pred H
Confidence 7
No 96
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.05 E-value=0.28 Score=55.86 Aligned_cols=63 Identities=21% Similarity=0.311 Sum_probs=45.2
Q ss_pred CCCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcccCChhhHHHhHHHHHhhcC
Q 000886 1114 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGDMAVYFGMLDALLASEQ 1180 (1237)
Q Consensus 1114 ~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCr~sv~dm~~~~~~lD~~i~~~p 1180 (1237)
-..|-||..+ |.+ .++-.|||+|...|...-++.+..|+||.+.+-.....-..|...+...+
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 3569999998 433 35679999999999988777889999999988544333344444444433
No 97
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.85 E-value=0.26 Score=57.63 Aligned_cols=47 Identities=26% Similarity=0.542 Sum_probs=33.5
Q ss_pred ccCCCCCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcccC
Q 000886 1110 EKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1163 (1237)
Q Consensus 1110 e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCr~sv~ 1163 (1237)
+.....+|.||++. +. ....+||||+-. |..-. +...+||+||..|.
T Consensus 301 ~~~~p~lcVVcl~e-~~---~~~fvpcGh~cc--ct~cs-~~l~~CPvCR~rI~ 347 (355)
T KOG1571|consen 301 ELPQPDLCVVCLDE-PK---SAVFVPCGHVCC--CTLCS-KHLPQCPVCRQRIR 347 (355)
T ss_pred ccCCCCceEEecCC-cc---ceeeecCCcEEE--chHHH-hhCCCCchhHHHHH
Confidence 44567899999987 33 367899999954 54333 23456999998764
No 98
>PHA02862 5L protein; Provisional
Probab=86.44 E-value=0.37 Score=49.82 Aligned_cols=46 Identities=24% Similarity=0.569 Sum_probs=34.0
Q ss_pred CCCCCcccccccccCCCcceecCCC-----CccChhhHHHhhhc--CCCCCCCCcccC
Q 000886 1113 LETNCPICCDFLFTSSATVRALPCG-----HFMHSDCFQAYTCS--HYICPICSKSLG 1163 (1237)
Q Consensus 1113 ~~~~CpICle~lf~s~~~v~~LpCg-----H~fH~~Ci~~wl~~--~~~CPiCr~sv~ 1163 (1237)
+...|=||.+. . .+. .-||. -..|..|+.+|+.. +.+||+|+.+..
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 35679999876 2 122 34663 78999999999864 478999998864
No 99
>COG5592 Uncharacterized conserved protein [Function unknown]
Probab=86.41 E-value=1.8 Score=45.66 Aligned_cols=101 Identities=21% Similarity=0.207 Sum_probs=69.1
Q ss_pred HHHHHHHHHHHHHHHHhhhhcccccccccc-----cccccc--cccccchhhHHHHHHHHHHHHHHHhhhhhhhccccCc
Q 000886 678 QFTGRFRLLWGLYRAHSNAEDDIVFPALES-----KETLSN--VSHSYTLDHKQEEKLFEDISSALSELTELHECLSTDL 750 (1237)
Q Consensus 678 ~f~~rf~~L~~v~~~HS~AEDeivfPALe~-----k~~~~n--~s~s~~~DH~~ee~lfedi~~~L~~l~~l~~~~~~~~ 750 (1237)
...+...|+|.++..|-.-|+++.||+.=- .-..++ ...-+..||+.++.|+..+- ..
T Consensus 29 e~le~~gf~~k~~k~h~e~Ee~ilF~v~Vd~~~ed~~~fkdt~~~~~i~~DHkliE~l~tnli-------------k~-- 93 (171)
T COG5592 29 EILEFEGFNEKLGKDHVELEEKILFPVIVDADMEDLYVFKDTPEVDRIKNDHKLIETLATNLI-------------KW-- 93 (171)
T ss_pred HHHhhcchHHHHhhhHHHHHHHhhhhhccchHHHHHHhhhccchhhHhHhhHHHHHHHHHHHH-------------hh--
Confidence 344455589999999999999999998632 111122 12368889999999998871 10
Q ss_pred CCcccccccccccchhhhhhHHHHHHHHHHHHHHHHHHHHHhhHhHHHhhhhHHhhcCCHHHHHH
Q 000886 751 TGDLTRNSLESCDQNETVRKYNEKATELQGMCKSIRVTLDQHVFREELELWPLFDRHFSVEEQDK 815 (1237)
Q Consensus 751 ~~~~~~~~~~~~~~~~~~~~~~e~~~kL~~~~ksl~~~L~~Hl~~EE~ElfPL~rk~fS~eeQ~~ 815 (1237)
.+..|+.++. -.+.++|..|=..||.-+||..++.=...+|.+
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 0112323333 556778899999999999999988776655554
No 100
>COG2461 Uncharacterized conserved protein [Function unknown]
Probab=86.38 E-value=3 Score=49.62 Aligned_cols=138 Identities=22% Similarity=0.224 Sum_probs=104.5
Q ss_pred CCCChHHHHHHHHHHHHHHHHHHHHHHhhccCCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHHHhh-hhHHHHH
Q 000886 40 LKSPILIFLFFHKAIKSELDVLHRAAMAFATNLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIRV-KNIARTY 118 (1237)
Q Consensus 40 ~~~Pi~~~~~~HkAlR~eL~~l~~~a~~~~~~~gd~~~~~~l~~r~~~L~~~~~~H~~aEDevI~PaLd~Rv-~~v~~~~ 118 (1237)
-.+|+..|.-=-+++|..|+.+.+.. .+..-...+...+.+|..+=+ |-+-+-..|||-++.|- ..+.-.|
T Consensus 84 ~gHPv~tl~~EN~~i~~ll~~~l~~~-------~~~~ik~~l~~lv~~L~~vg~-Hy~RKe~lIfp~~Er~GitapptVm 155 (409)
T COG2461 84 PGHPVRTLKRENKAIRSLLANLLQFP-------PKKEIKEKLVELVSELDKIGK-HYTRKEMLIFPYIERRGITAPPTVM 155 (409)
T ss_pred CCCcHHHHhcccHHHHHHHHHHhhcc-------ccHHHHHHHHHHHHHHHHhcc-ccccccccchhHHHHcCCCCCCeee
Confidence 35699888888888996655553321 123344556667777777777 99999999999999886 4577778
Q ss_pred HhhhhhHHHHHHHHHHHHHhhccCchHHHHHHHHHHHHHHHHHHHhHHHHHHHHhhHHHhcCCHHHHHHHHHH
Q 000886 119 SLEHEGESVLFDQLFELLNSSMRNEESYRRELASCTGALQTSISQHMSKEEEQVFPLLIEKFSFEEQASLVWQ 191 (1237)
Q Consensus 119 ~~EH~~~~~lf~~l~~~l~~~~~~~~~~~~eLa~~l~~l~~~l~qHm~~EE~qv~PLl~~~~S~~Eqa~L~~~ 191 (1237)
-.-|.++-..|..+...+. ..+. .+++.....+.+.+..=+.+||.-+.|-+..-||..||.++..+
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 8899999899999888887 2222 33333444555688888999999999999999999999999876
No 101
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.31 E-value=0.47 Score=56.95 Aligned_cols=49 Identities=27% Similarity=0.642 Sum_probs=39.9
Q ss_pred CCCCCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcccCC
Q 000886 1112 GLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1164 (1237)
Q Consensus 1112 ~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCr~sv~d 1164 (1237)
..+-.|-||+.-++. .+.+||||.|...|+++-+....-||+||..+..
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 456789999876553 2445999999999999977778889999999864
No 102
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.13 E-value=0.15 Score=57.82 Aligned_cols=48 Identities=29% Similarity=0.653 Sum_probs=32.9
Q ss_pred CCCCcccccccccCCCcceecCCCCcc-ChhhHHHhhhcCCCCCCCCcccCChhhHH
Q 000886 1114 ETNCPICCDFLFTSSATVRALPCGHFM-HSDCFQAYTCSHYICPICSKSLGDMAVYF 1169 (1237)
Q Consensus 1114 ~~~CpICle~lf~s~~~v~~LpCgH~f-H~~Ci~~wl~~~~~CPiCr~sv~dm~~~~ 1169 (1237)
+.-|.||+|- ......|+|||.. ..+|-.. -..|||||+-|......|
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 7889999764 3457889999975 2344322 238999998776554444
No 103
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=84.67 E-value=0.46 Score=56.32 Aligned_cols=55 Identities=22% Similarity=0.394 Sum_probs=40.1
Q ss_pred cccccccCCCCCCcccccccccCCCcceecCCCCccChhhHHHhhh--------cCCCCCCCCcc
Q 000886 1105 DHKCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC--------SHYICPICSKS 1161 (1237)
Q Consensus 1105 ~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~--------~~~~CPiCr~s 1161 (1237)
+|.+..+ .--.|-||.+. +.+......+||+|+|.+.|...|.. +..+||-|.-.
T Consensus 176 ~~~~F~~-slf~C~ICf~e-~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C~ 238 (445)
T KOG1814|consen 176 TLEKFVN-SLFDCCICFEE-QMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCG 238 (445)
T ss_pred HHHHHHh-hcccceeeehh-hcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCCc
Confidence 3444333 34689999987 55556778899999999999999853 24679987654
No 104
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=83.42 E-value=0.63 Score=53.95 Aligned_cols=51 Identities=22% Similarity=0.431 Sum_probs=42.2
Q ss_pred ccCCCCCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcccCC
Q 000886 1110 EKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1164 (1237)
Q Consensus 1110 e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCr~sv~d 1164 (1237)
..+.++.||||.-. .-..+.-||||--+..||.+.+.++..|=.|+..+.+
T Consensus 418 p~sEd~lCpICyA~----pi~Avf~PC~H~SC~~CI~qHlmN~k~CFfCktTv~~ 468 (489)
T KOG4692|consen 418 PDSEDNLCPICYAG----PINAVFAPCSHRSCYGCITQHLMNCKRCFFCKTTVID 468 (489)
T ss_pred CCcccccCcceecc----cchhhccCCCCchHHHHHHHHHhcCCeeeEecceeee
Confidence 45678999999743 2234556999999999999999999999999999876
No 105
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=82.19 E-value=0.76 Score=58.63 Aligned_cols=42 Identities=29% Similarity=0.639 Sum_probs=32.0
Q ss_pred CCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCccc
Q 000886 1115 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSL 1162 (1237)
Q Consensus 1115 ~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCr~sv 1162 (1237)
..|..|--.|. -|++...|||.||.+|+. .....||-|+-..
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 46777754432 366778999999999997 4568899999844
No 106
>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=81.39 E-value=0.92 Score=45.55 Aligned_cols=35 Identities=26% Similarity=0.455 Sum_probs=26.1
Q ss_pred ccCCceecCCCCCCCCCCceeecccCCCCCCcccccc
Q 000886 1187 DRCQEILCNDCDKKGSAPFHWLYHKCGFCGSYNTRVI 1223 (1237)
Q Consensus 1187 ~~~~~i~CnDC~~~s~~~~h~lg~kC~~C~SYNT~~~ 1223 (1237)
.......|++|+.......+ +..|+.|||++++++
T Consensus 66 ~~p~~~~C~~Cg~~~~~~~~--~~~CP~Cgs~~~~i~ 100 (115)
T TIGR00100 66 DEPVECECEDCSEEVSPEID--LYRCPKCHGIMLQVR 100 (115)
T ss_pred eeCcEEEcccCCCEEecCCc--CccCcCCcCCCcEEe
Confidence 34466899999987665422 347999999998875
No 107
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=81.04 E-value=1 Score=45.41 Aligned_cols=35 Identities=26% Similarity=0.491 Sum_probs=26.4
Q ss_pred ccCCceecCCCCCCCCCC-ceeecccCCCCCCcccccc
Q 000886 1187 DRCQEILCNDCDKKGSAP-FHWLYHKCGFCGSYNTRVI 1223 (1237)
Q Consensus 1187 ~~~~~i~CnDC~~~s~~~-~h~lg~kC~~C~SYNT~~~ 1223 (1237)
.......|++||...... +++ .+|+.|||++..++
T Consensus 67 ~vp~~~~C~~Cg~~~~~~~~~~--~~CP~Cgs~~~~i~ 102 (117)
T PRK00564 67 DEKVELECKDCSHVFKPNALDY--GVCEKCHSKNVIIT 102 (117)
T ss_pred ecCCEEEhhhCCCccccCCccC--CcCcCCCCCceEEe
Confidence 345678999999877654 333 47999999998765
No 108
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=80.85 E-value=1.2 Score=51.58 Aligned_cols=65 Identities=22% Similarity=0.418 Sum_probs=44.8
Q ss_pred Cccccccccc-ccccccccCCCCCCcccccccccCCCcceecCCCCccChhhHHHh--hhcCCCCCCCCccc
Q 000886 1094 TCNCCLAKKL-VDHKCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAY--TCSHYICPICSKSL 1162 (1237)
Q Consensus 1094 ~C~~C~s~~l-~~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~w--l~~~~~CPiCr~sv 1162 (1237)
+=+.|..-++ ..-+=..+...++|-||-+.+ +-+.++||||-++..|--.. +.....||+||..-
T Consensus 40 KNnlsaEPnlttsSaddtDEen~~C~ICA~~~----TYs~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~ 107 (493)
T COG5236 40 KNNLSAEPNLTTSSADDTDEENMNCQICAGST----TYSARYPCGHQICHACAVRLRALYMQKGCPLCRTET 107 (493)
T ss_pred ccccccCCccccccccccccccceeEEecCCc----eEEEeccCCchHHHHHHHHHHHHHhccCCCcccccc
Confidence 3455555444 333333345578999998753 45678999999999996443 56678899999764
No 109
>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.
Probab=80.25 E-value=0.55 Score=39.99 Aligned_cols=43 Identities=30% Similarity=0.769 Sum_probs=26.2
Q ss_pred CCCcccccccccCCCcceecCCC-CccChhhHHHhhhcCCCCCCCCcccC
Q 000886 1115 TNCPICCDFLFTSSATVRALPCG-HFMHSDCFQAYTCSHYICPICSKSLG 1163 (1237)
Q Consensus 1115 ~~CpICle~lf~s~~~v~~LpCg-H~fH~~Ci~~wl~~~~~CPiCr~sv~ 1163 (1237)
.+|--|. |.. -..+.|. |+....|+..++..+..||||.+++.
T Consensus 3 ~nCKsCW---f~~---k~Li~C~dHYLCl~CLt~ml~~s~~C~iC~~~LP 46 (50)
T PF03854_consen 3 YNCKSCW---FAN---KGLIKCSDHYLCLNCLTLMLSRSDRCPICGKPLP 46 (50)
T ss_dssp ----SS----S-----SSEEE-SS-EEEHHHHHHT-SSSSEETTTTEE--
T ss_pred ccChhhh---hcC---CCeeeecchhHHHHHHHHHhccccCCCcccCcCc
Confidence 3566675 332 1345787 99999999999999999999999874
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=79.77 E-value=6.7 Score=39.18 Aligned_cols=51 Identities=18% Similarity=0.181 Sum_probs=36.3
Q ss_pred hhHHhHHHHHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 000886 361 SFAQEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQV 421 (1237)
Q Consensus 361 ~me~EH~~ie~l~e~l~~ll~~~~~a~~~~~~~~~~~eLa~~le~L~~~L~~H~~~EE~qv 421 (1237)
.+..+|+..-.+++.|..++... . + ..++...+..|..-+..||..||.-.
T Consensus 12 ~ID~qH~~l~~~in~l~~a~~~~---~-~------~~~~~~~l~~L~~y~~~HF~~EE~~M 62 (126)
T TIGR02481 12 EIDAQHKELFELINELYDALSAG---N-G------KDELKEILDELIDYTENHFADEEELM 62 (126)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcC---C-C------HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45677887777777776655321 1 1 24677788888999999999999765
No 111
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=79.44 E-value=0.16 Score=59.34 Aligned_cols=53 Identities=23% Similarity=0.468 Sum_probs=45.5
Q ss_pred CCCCCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcccCC
Q 000886 1112 GLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1164 (1237)
Q Consensus 1112 ~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCr~sv~d 1164 (1237)
+.-..|.||.+.+...-+.+..+.|||.+|..|+.+|+.....||.|++.+..
T Consensus 194 slv~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~~~~kl~~~~rel~~ 246 (465)
T KOG0827|consen 194 SLVGSLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLATKRKLPSCRRELPK 246 (465)
T ss_pred HHHhhhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHHHhHHHHhhhhh
Confidence 33568999999876665677889999999999999999999999999998853
No 112
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=78.13 E-value=1.9 Score=49.51 Aligned_cols=47 Identities=28% Similarity=0.742 Sum_probs=37.6
Q ss_pred CCCcccccccccCCCc---ceecCCCCccChhhHHHhhhcC-CCCCCCCccc
Q 000886 1115 TNCPICCDFLFTSSAT---VRALPCGHFMHSDCFQAYTCSH-YICPICSKSL 1162 (1237)
Q Consensus 1115 ~~CpICle~lf~s~~~---v~~LpCgH~fH~~Ci~~wl~~~-~~CPiCr~sv 1162 (1237)
..|-||-++ |.+.+. .+.|.|||+|...|+...+..+ ..||-||.+.
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 468999988 666533 3568999999999999887654 5699999995
No 113
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=77.93 E-value=1.3 Score=44.36 Aligned_cols=35 Identities=23% Similarity=0.395 Sum_probs=25.3
Q ss_pred cCCceecCCCCCCCCCCceeecccCCCCCCccccccc
Q 000886 1188 RCQEILCNDCDKKGSAPFHWLYHKCGFCGSYNTRVIK 1224 (1237)
Q Consensus 1188 ~~~~i~CnDC~~~s~~~~h~lg~kC~~C~SYNT~~~~ 1224 (1237)
......|++|+........ ...|+.|||++..+++
T Consensus 67 vp~~~~C~~Cg~~~~~~~~--~~~CP~Cgs~~~~i~~ 101 (113)
T PRK12380 67 KPAQAWCWDCSQVVEIHQH--DAQCPHCHGERLRVDT 101 (113)
T ss_pred eCcEEEcccCCCEEecCCc--CccCcCCCCCCcEEcc
Confidence 3456899999977665422 2359999999987753
No 114
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=77.88 E-value=1.4 Score=44.30 Aligned_cols=36 Identities=17% Similarity=0.377 Sum_probs=25.7
Q ss_pred cCCceecCCCCCCCCCCceeecccCCCCCCccccccc
Q 000886 1188 RCQEILCNDCDKKGSAPFHWLYHKCGFCGSYNTRVIK 1224 (1237)
Q Consensus 1188 ~~~~i~CnDC~~~s~~~~h~lg~kC~~C~SYNT~~~~ 1224 (1237)
......|++|+.......+. ...|+.|||+++.+++
T Consensus 67 ~p~~~~C~~Cg~~~~~~~~~-~~~CP~Cgs~~~~i~~ 102 (114)
T PRK03681 67 QEAECWCETCQQYVTLLTQR-VRRCPQCHGDMLRIVA 102 (114)
T ss_pred eCcEEEcccCCCeeecCCcc-CCcCcCcCCCCcEEcc
Confidence 34568999999876553221 2469999999988753
No 115
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=77.52 E-value=1.4 Score=45.59 Aligned_cols=34 Identities=26% Similarity=0.687 Sum_probs=24.3
Q ss_pred CceecCCCCCCCCCC-------------cee------ecccCCCCCCcccccc
Q 000886 1190 QEILCNDCDKKGSAP-------------FHW------LYHKCGFCGSYNTRVI 1223 (1237)
Q Consensus 1190 ~~i~CnDC~~~s~~~-------------~h~------lg~kC~~C~SYNT~~~ 1223 (1237)
....|++||...... +|+ .+.+|+.|||++..++
T Consensus 69 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~ 121 (135)
T PRK03824 69 AVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRDFEIV 121 (135)
T ss_pred eEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCCcEEe
Confidence 567899999765442 222 2357999999998765
No 116
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=76.86 E-value=1.8 Score=45.74 Aligned_cols=46 Identities=22% Similarity=0.586 Sum_probs=33.2
Q ss_pred CCCCCCcccccccccCCCcceecCCC--C---ccChhhHHHhhhc--CCCCCCCCccc
Q 000886 1112 GLETNCPICCDFLFTSSATVRALPCG--H---FMHSDCFQAYTCS--HYICPICSKSL 1162 (1237)
Q Consensus 1112 ~~~~~CpICle~lf~s~~~v~~LpCg--H---~fH~~Ci~~wl~~--~~~CPiCr~sv 1162 (1237)
..+..|=||.+.- + .. .-||. . ..|.+|+..|+.. ..+||+|+...
T Consensus 6 ~~~~~CRIC~~~~-~--~~--~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y 58 (162)
T PHA02825 6 LMDKCCWICKDEY-D--VV--TNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPY 58 (162)
T ss_pred CCCCeeEecCCCC-C--Cc--cCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeE
Confidence 3467899998762 1 22 24664 4 6799999999854 57899999875
No 117
>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=76.34 E-value=2.1 Score=45.26 Aligned_cols=33 Identities=27% Similarity=0.788 Sum_probs=21.9
Q ss_pred CCCCcccccccccCCCcceecCC------------C-CccChhhHHHhhh
Q 000886 1114 ETNCPICCDFLFTSSATVRALPC------------G-HFMHSDCFQAYTC 1150 (1237)
Q Consensus 1114 ~~~CpICle~lf~s~~~v~~LpC------------g-H~fH~~Ci~~wl~ 1150 (1237)
+..||||||.=. ..+.|-| + =+=|..|++++-+
T Consensus 2 d~~CpICme~PH----NAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkk 47 (162)
T PF07800_consen 2 DVTCPICMEHPH----NAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKK 47 (162)
T ss_pred CccCceeccCCC----ceEEEEeccccCCccccccCCccchhHHHHHHHH
Confidence 468999999722 2234444 3 3558999999853
No 118
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=76.29 E-value=1.9 Score=54.63 Aligned_cols=73 Identities=23% Similarity=0.548 Sum_probs=48.7
Q ss_pred CccccCCCCCccccCCCCCccccccCCcccccccccccccccccCCCCCCcccccccccCCCcceecCCCCccChhhHHH
Q 000886 1068 RVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLAKKLVDHKCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQA 1147 (1237)
Q Consensus 1068 k~~yHC~~CgiCR~g~gl~~~~fHC~~C~~C~s~~l~~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~ 1147 (1237)
--+|-|+.|+-=-+++++ .-|.+|-.|-+ ..|.+|-..+. +..+..--|||..|.+|+.+
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--------------AKCTVCDLVIR--GVDVWCQVCGHGGHDSHLKS 810 (839)
T ss_pred eeeccccccCCccccccc----eeechHHHHhh--------------cCceeecceee--eeEeecccccccccHHHHHH
Confidence 457778888755555542 45666655533 46999965432 12233346999999999999
Q ss_pred hhhcCCCCCC--CCc
Q 000886 1148 YTCSHYICPI--CSK 1160 (1237)
Q Consensus 1148 wl~~~~~CPi--Cr~ 1160 (1237)
|...+.-||. |.+
T Consensus 811 w~~~~s~ca~~~C~~ 825 (839)
T KOG0269|consen 811 WFFKASPCAKSICPH 825 (839)
T ss_pred HHhcCCCCccccCCc
Confidence 9988777776 544
No 119
>PRK04023 DNA polymerase II large subunit; Validated
Probab=75.61 E-value=2.4 Score=55.52 Aligned_cols=43 Identities=26% Similarity=0.508 Sum_probs=19.8
Q ss_pred ccccccccccCCCCCCCccCCCCccceEecccccCCCCCCccccCCCCC
Q 000886 1029 MCMRCLKVQPVGPVCTTLSCSGLSMAKYYCGICKFFDDERVVYHCPFCN 1077 (1237)
Q Consensus 1029 ~C~~C~~~Q~~~~~C~~~~C~~~~~~~y~C~~C~~~d~~k~~yHC~~Cg 1077 (1237)
.|..|+++. +...|.+ |+...-.-|||..|.- .-..|.|+.||
T Consensus 628 fCpsCG~~t-~~frCP~--CG~~Te~i~fCP~CG~---~~~~y~CPKCG 670 (1121)
T PRK04023 628 KCPSCGKET-FYRRCPF--CGTHTEPVYRCPRCGI---EVEEDECEKCG 670 (1121)
T ss_pred cCCCCCCcC-CcccCCC--CCCCCCcceeCccccC---cCCCCcCCCCC
Confidence 455555443 3345554 4322344455555521 12235566665
No 120
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=75.41 E-value=0.93 Score=56.12 Aligned_cols=44 Identities=25% Similarity=0.612 Sum_probs=35.3
Q ss_pred CCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcc
Q 000886 1115 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKS 1161 (1237)
Q Consensus 1115 ~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCr~s 1161 (1237)
-+|+||+...+.++-..+.|-|||+++..|+... .+.+|| |.+.
T Consensus 12 l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~l--yn~scp-~~~D 55 (861)
T KOG3161|consen 12 LLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLL--YNASCP-TKRD 55 (861)
T ss_pred hhchHHHHHHHHHhcCcccccccchHHHHHHHhH--hhccCC-CCcc
Confidence 4799998876777666678999999999999764 478899 7653
No 121
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=74.05 E-value=1.4 Score=56.36 Aligned_cols=51 Identities=25% Similarity=0.604 Sum_probs=36.4
Q ss_pred CCCCCCcccccccccCCCccee-cCCCCccChhhHHHhhhc-------CCCCCCCCcccC
Q 000886 1112 GLETNCPICCDFLFTSSATVRA-LPCGHFMHSDCFQAYTCS-------HYICPICSKSLG 1163 (1237)
Q Consensus 1112 ~~~~~CpICle~lf~s~~~v~~-LpCgH~fH~~Ci~~wl~~-------~~~CPiCr~sv~ 1163 (1237)
.....|.||+|.+..+ .++-. -.|=|+||..||.+|.+. .-+||-|+....
T Consensus 189 ~~~yeCmIC~e~I~~t-~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv~~ 247 (950)
T KOG1952|consen 189 NRKYECMICTERIKRT-APVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSVSK 247 (950)
T ss_pred cCceEEEEeeeecccc-CCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccchhc
Confidence 3456899999986544 33322 246699999999999642 468999995443
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=73.52 E-value=0.67 Score=42.70 Aligned_cols=64 Identities=27% Similarity=0.628 Sum_probs=35.8
Q ss_pred CCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcccCChhhHHHhHHHHHhhcCCChhhhccCCceec
Q 000886 1115 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGDMAVYFGMLDALLASEQLPEEYRDRCQEILC 1194 (1237)
Q Consensus 1115 ~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCr~sv~dm~~~~~~lD~~i~~~pmP~ey~~~~~~i~C 1194 (1237)
..||.|..+|-..+ ||++...|-..+. ....||-|..++..+.. =-.++++|
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 57999998865432 7888888887653 35679999998754321 11257899
Q ss_pred CCCC---CCCCCCce
Q 000886 1195 NDCD---KKGSAPFH 1206 (1237)
Q Consensus 1195 nDC~---~~s~~~~h 1206 (1237)
|.|+ +|+.+.|.
T Consensus 54 ~~c~gLiSKkrV~f~ 68 (70)
T PF07191_consen 54 NHCHGLISKKRVRFE 68 (70)
T ss_dssp TTTT-EE-TTTSEEE
T ss_pred ccCCceeecceEEEE
Confidence 9998 44555554
No 123
>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=70.21 E-value=2.6 Score=35.30 Aligned_cols=41 Identities=29% Similarity=0.731 Sum_probs=20.3
Q ss_pred CcccccccccCCCcceecCCCCccChhhHHHhhhcCC--CCCCC
Q 000886 1117 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHY--ICPIC 1158 (1237)
Q Consensus 1117 CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~--~CPiC 1158 (1237)
|-+|.+- .+-+..-..-.|+=.+|..|++.|++... +||.|
T Consensus 1 C~~C~~i-v~~G~~C~~~~C~~r~H~~C~~~y~r~~~~~~CP~C 43 (43)
T PF08746_consen 1 CEACKEI-VTQGQRCSNRDCNVRLHDDCFKKYFRHRSNPKCPNC 43 (43)
T ss_dssp -TTT-SB--SSSEE-SS--S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred Ccccchh-HeeeccCCCCccCchHHHHHHHHHHhcCCCCCCcCC
Confidence 5667654 22222122235887899999999987644 79988
No 124
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=69.76 E-value=4.7 Score=49.93 Aligned_cols=80 Identities=19% Similarity=0.403 Sum_probs=45.5
Q ss_pred ecCCCCccChhhHHHhhhcCCCCCCCCcccCChhh-HHHhHH--HHHhhcCCChhhhccCCceecCCCCCCC--------
Q 000886 1133 ALPCGHFMHSDCFQAYTCSHYICPICSKSLGDMAV-YFGMLD--ALLASEQLPEEYRDRCQEILCNDCDKKG-------- 1201 (1237)
Q Consensus 1133 ~LpCgH~fH~~Ci~~wl~~~~~CPiCr~sv~dm~~-~~~~lD--~~i~~~pmP~ey~~~~~~i~CnDC~~~s-------- 1201 (1237)
+..=|-+||..|+ +|-+|+++.-.-+. .|.--+ -+.-.++||--=.....--.|--|+..-
T Consensus 80 vsa~gktyh~~cf--------~cs~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk~gq~lla 151 (670)
T KOG1044|consen 80 VSTLGKTYHPKCF--------SCSTCKSPFKSGDKVTFSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELKNGQALLA 151 (670)
T ss_pred Eecccceeccccc--------eecccCCCCCCCCeeeecchhhhhhhhcCcccCCcccccCCccccchhhhhhccceeee
Confidence 3344889999987 67778777632111 111111 1222455553312223334688887541
Q ss_pred -CCCceeecccCCCCCCccc
Q 000886 1202 -SAPFHWLYHKCGFCGSYNT 1220 (1237)
Q Consensus 1202 -~~~~h~lg~kC~~C~SYNT 1220 (1237)
..++|+.+-||..|+.-=+
T Consensus 152 ld~qwhv~cfkc~~c~~vL~ 171 (670)
T KOG1044|consen 152 LDKQWHVSCFKCKSCSAVLN 171 (670)
T ss_pred eccceeeeeeehhhhccccc
Confidence 4679999999998765433
No 125
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=69.44 E-value=3.3 Score=49.32 Aligned_cols=47 Identities=21% Similarity=0.513 Sum_probs=37.3
Q ss_pred CCCcccccccccCCCcceecCCCCccChhhHHHhhhcC---CCCCCCCccc
Q 000886 1115 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSH---YICPICSKSL 1162 (1237)
Q Consensus 1115 ~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~---~~CPiCr~sv 1162 (1237)
-.|||=.|. -+...+.+.|.|||++-.+=+++..+++ .+||.|-...
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 468887776 4555678889999999999999987653 6899997643
No 126
>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=69.36 E-value=1.5 Score=43.83 Aligned_cols=34 Identities=24% Similarity=0.403 Sum_probs=22.2
Q ss_pred cCCceecCCCCCCCCCCceeecccCCCCCCcccccc
Q 000886 1188 RCQEILCNDCDKKGSAPFHWLYHKCGFCGSYNTRVI 1223 (1237)
Q Consensus 1188 ~~~~i~CnDC~~~s~~~~h~lg~kC~~C~SYNT~~~ 1223 (1237)
......|++||.......+. ..|+.|||++..++
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 44568999999987655433 46999999998765
No 127
>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=68.87 E-value=14 Score=41.17 Aligned_cols=45 Identities=24% Similarity=0.336 Sum_probs=26.5
Q ss_pred CCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHHHhhh-hHHHHHHhhhhhHHH
Q 000886 72 LGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIRVK-NIARTYSLEHEGESV 127 (1237)
Q Consensus 72 ~gd~~~~~~l~~r~~~L~~~~~~H~~aEDevI~PaLd~Rv~-~v~~~~~~EH~~~~~ 127 (1237)
+.|+=++.-|++| ||||++ +|==.=|--|+ -|+.+|..|-++++.
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 22111112234 488899887665554
No 128
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=68.60 E-value=2.3 Score=44.78 Aligned_cols=31 Identities=32% Similarity=0.556 Sum_probs=24.7
Q ss_pred cCCCCCCcccccccccCCCcceecCCCCccCh
Q 000886 1111 KGLETNCPICCDFLFTSSATVRALPCGHFMHS 1142 (1237)
Q Consensus 1111 ~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~ 1142 (1237)
+....+|.||||+|-. ++.+..|||-=+||+
T Consensus 174 ~ddkGECvICLEdL~~-GdtIARLPCLCIYHK 204 (205)
T KOG0801|consen 174 KDDKGECVICLEDLEA-GDTIARLPCLCIYHK 204 (205)
T ss_pred cccCCcEEEEhhhccC-CCceeccceEEEeec
Confidence 3446789999999654 567889999988886
No 129
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=67.73 E-value=4.3 Score=35.82 Aligned_cols=37 Identities=24% Similarity=0.518 Sum_probs=28.6
Q ss_pred CCCCCCcccccccccCCCcceecCCCCccChhhHHHh
Q 000886 1112 GLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAY 1148 (1237)
Q Consensus 1112 ~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~w 1148 (1237)
.....|++|.+.+....+.|+---||-.+|+.|...-
T Consensus 3 ~~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~ 39 (54)
T PF14446_consen 3 YEGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKA 39 (54)
T ss_pred ccCccChhhCCcccCCCCEEECCCCCCcccHHHHhhC
Confidence 3467899999996555555555689999999998653
No 130
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=66.77 E-value=3.4 Score=47.17 Aligned_cols=44 Identities=30% Similarity=0.755 Sum_probs=34.4
Q ss_pred CCCcccccccccCCCcceecCCCCccChhhHHHhh-hcCCCCCCCCcc
Q 000886 1115 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYT-CSHYICPICSKS 1161 (1237)
Q Consensus 1115 ~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl-~~~~~CPiCr~s 1161 (1237)
..||.|.--+- .+++.--|||.|..+||..-+ .....||.|.+.
T Consensus 275 LkCplc~~Llr---np~kT~cC~~~fc~eci~~al~dsDf~CpnC~rk 319 (427)
T COG5222 275 LKCPLCHCLLR---NPMKTPCCGHTFCDECIGTALLDSDFKCPNCSRK 319 (427)
T ss_pred ccCcchhhhhh---CcccCccccchHHHHHHhhhhhhccccCCCcccc
Confidence 57999976532 356666789999999999765 567999999873
No 131
>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=65.79 E-value=90 Score=31.13 Aligned_cols=109 Identities=17% Similarity=0.273 Sum_probs=68.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcccCCcccHHHHHHHHHHHHHHHHhhhhcccccc----hhhhhhhhhhHHhHHHHHHH
Q 000886 297 IMLWHNAIKRELNDIAEAARKIQLSGDFSDLSAFNKRLQFIAEVCIFHSIAEDKVI----FPAVDVELSFAQEHAEEEIQ 372 (1237)
Q Consensus 297 l~~~HkALRrEL~~L~~~a~~~~~~gd~~~L~~L~~r~~fl~~vl~~Hs~aEDevl----FPaL~~r~~me~EH~~ie~l 372 (1237)
+=.-|+.|=..++.|...+..- .....+...+.+|.+....|-..|+.++ ||.+..+. .+|+ ..
T Consensus 13 ID~qH~~l~~~in~l~~a~~~~------~~~~~~~~~l~~L~~y~~~HF~~EE~~M~~~~yp~~~~H~---~~H~---~~ 80 (126)
T TIGR02481 13 IDAQHKELFELINELYDALSAG------NGKDELKEILDELIDYTENHFADEEELMEEYGYPDLEEHK---KEHE---KF 80 (126)
T ss_pred HHHHHHHHHHHHHHHHHHHHcC------CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHH---HHHH---HH
Confidence 3356887777777777765431 1245677788888999999999998765 77776543 3444 44
Q ss_pred HHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 000886 373 FDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPL 424 (1237)
Q Consensus 373 ~e~l~~ll~~~~~a~~~~~~~~~~~eLa~~le~L~~~L~~H~~~EE~qvfPL 424 (1237)
++.+..+...+.. +.. ..... ..+..+..-|..|+..+-..+.+.
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 5555555444432 111 12222 344556778999999888776553
No 132
>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=65.46 E-value=1.8 Score=48.14 Aligned_cols=51 Identities=25% Similarity=0.539 Sum_probs=38.8
Q ss_pred CCCCCcccccccccCCCcceec-C-CCCccChhhHHHhhhcC-CCCC--CCCcccC
Q 000886 1113 LETNCPICCDFLFTSSATVRAL-P-CGHFMHSDCFQAYTCSH-YICP--ICSKSLG 1163 (1237)
Q Consensus 1113 ~~~~CpICle~lf~s~~~v~~L-p-CgH~fH~~Ci~~wl~~~-~~CP--iCr~sv~ 1163 (1237)
.+..||||.-+.+-+.+-...+ | |=|-|+.+|++.-...+ ..|| -|.+.+.
T Consensus 9 ~d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kILR 64 (314)
T COG5220 9 EDRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKILR 64 (314)
T ss_pred hcccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHHH
Confidence 3468999998877776533332 6 99999999999987654 6899 8887653
No 133
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=65.16 E-value=3.9 Score=41.71 Aligned_cols=35 Identities=26% Similarity=0.613 Sum_probs=23.8
Q ss_pred cCCceecCCCCCCCCCC-c---ee-ecccCCCCCCcccccc
Q 000886 1188 RCQEILCNDCDKKGSAP-F---HW-LYHKCGFCGSYNTRVI 1223 (1237)
Q Consensus 1188 ~~~~i~CnDC~~~s~~~-~---h~-lg~kC~~C~SYNT~~~ 1223 (1237)
......| +|+...... + |+ .+..|+.|||++..++
T Consensus 67 vp~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~ 106 (124)
T PRK00762 67 IPVEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKRAHIL 106 (124)
T ss_pred cCeeEEe-eCcCcccccccchhccccCCcCcCCCCCCCEEe
Confidence 3456889 999874422 1 22 1346999999998875
No 134
>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=64.12 E-value=4.4 Score=31.52 Aligned_cols=38 Identities=29% Similarity=0.643 Sum_probs=25.7
Q ss_pred CCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcccC
Q 000886 1116 NCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1163 (1237)
Q Consensus 1116 ~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCr~sv~ 1163 (1237)
.|+.|.+.+..... .+..=|..||.+|+ +|..|++++.
T Consensus 1 ~C~~C~~~i~~~~~--~~~~~~~~~H~~Cf--------~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGEL--VLRALGKVWHPECF--------KCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcE--EEEeCCccccccCC--------CCcccCCcCc
Confidence 37888887655412 22223789999887 7888988764
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=63.94 E-value=5 Score=42.10 Aligned_cols=47 Identities=26% Similarity=0.579 Sum_probs=39.1
Q ss_pred CCccceEecccccCCCCCCccccCCCCCccccCCCCCccccccCCcccccccc
Q 000886 1050 GLSMAKYYCGICKFFDDERVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLAKK 1102 (1237)
Q Consensus 1050 ~~~~~~y~C~~C~~~d~~k~~yHC~~CgiCR~g~gl~~~~fHC~~C~~C~s~~ 1102 (1237)
+......||..|+.+-.. ..+||..||.|-.+- -.||.=-|.|+...
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 456778999999999766 489999999999874 47999999998754
No 136
>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=63.67 E-value=3.5 Score=46.53 Aligned_cols=50 Identities=28% Similarity=0.824 Sum_probs=36.3
Q ss_pred CCcccCccccccc-CCCCCccccccccccccccccccCCCCCCCccCCCCccceEecccccC
Q 000886 1003 GKLFTCRFCHDKV-SDHSMDRKATTEMMCMRCLKVQPVGPVCTTLSCSGLSMAKYYCGICKF 1063 (1237)
Q Consensus 1003 ~~~y~Cr~CHde~-~~H~~~r~~~~~v~C~~C~~~Q~~~~~C~~~~C~~~~~~~y~C~~C~~ 1063 (1237)
|+.|.|-+|++-. +|-.|+-.+ .|+....-+-.|.+ | + .+|.|.|-.||.
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 6789999999874 555555432 36666666777876 6 3 589999999985
No 137
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=63.66 E-value=5.5 Score=35.69 Aligned_cols=45 Identities=27% Similarity=0.673 Sum_probs=23.6
Q ss_pred ccccccccccccCCC-----CCCCccCCCCccceEecccccCCCCCCccccCCCCCc
Q 000886 1027 EMMCMRCLKVQPVGP-----VCTTLSCSGLSMAKYYCGICKFFDDERVVYHCPFCNL 1078 (1237)
Q Consensus 1027 ~v~C~~C~~~Q~~~~-----~C~~~~C~~~~~~~y~C~~C~~~d~~k~~yHC~~Cgi 1078 (1237)
...|..|+..-.... .|-| | |.. -=|-|.+|+-..+ .|.|++||+
T Consensus 7 ~~~CtSCg~~i~~~~~~~~F~CPn--C-G~~-~I~RC~~CRk~~~---~Y~CP~CGF 56 (59)
T PRK14890 7 PPKCTSCGIEIAPREKAVKFLCPN--C-GEV-IIYRCEKCRKQSN---PYTCPKCGF 56 (59)
T ss_pred CccccCCCCcccCCCccCEeeCCC--C-CCe-eEeechhHHhcCC---ceECCCCCC
Confidence 445666665444332 3544 4 431 1244666665543 577777774
No 138
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=63.49 E-value=5.5 Score=50.07 Aligned_cols=70 Identities=17% Similarity=0.397 Sum_probs=43.9
Q ss_pred CCCCcccccccccCCCcceec---CCCCccChhhHHHh----h----hcCCCCCCCCcccCChhhHHHhHHHHHhhcCCC
Q 000886 1114 ETNCPICCDFLFTSSATVRAL---PCGHFMHSDCFQAY----T----CSHYICPICSKSLGDMAVYFGMLDALLASEQLP 1182 (1237)
Q Consensus 1114 ~~~CpICle~lf~s~~~v~~L---pCgH~fH~~Ci~~w----l----~~~~~CPiCr~sv~dm~~~~~~lD~~i~~~pmP 1182 (1237)
-..||+|+-. +-..+....+ -|.--.|..|..-. . ...|.|-+|| ..+.+...|-..+...-+|
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 4689999854 4333434333 35567888885322 1 1379999999 3344456666667777778
Q ss_pred hhhhcc
Q 000886 1183 EEYRDR 1188 (1237)
Q Consensus 1183 ~ey~~~ 1188 (1237)
..|.+.
T Consensus 220 k~~~~~ 225 (694)
T KOG4443|consen 220 KDKPDK 225 (694)
T ss_pred hhcccc
Confidence 776544
No 139
>KOG2068 consensus MOT2 transcription factor [Transcription]
Probab=62.49 E-value=5.5 Score=46.56 Aligned_cols=52 Identities=25% Similarity=0.545 Sum_probs=39.6
Q ss_pred CCCCCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcccC
Q 000886 1112 GLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1163 (1237)
Q Consensus 1112 ~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCr~sv~ 1163 (1237)
+-...||||.+++........--|||+-++..|...-...+.+||+||++..
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 4457899999986444333333478999999999888888999999997753
No 140
>PHA03096 p28-like protein; Provisional
Probab=62.47 E-value=3.9 Score=47.35 Aligned_cols=47 Identities=15% Similarity=0.200 Sum_probs=31.2
Q ss_pred CCCcccccccccCC---Ccceec-CCCCccChhhHHHhhhc---CCCCCCCCcc
Q 000886 1115 TNCPICCDFLFTSS---ATVRAL-PCGHFMHSDCFQAYTCS---HYICPICSKS 1161 (1237)
Q Consensus 1115 ~~CpICle~lf~s~---~~v~~L-pCgH~fH~~Ci~~wl~~---~~~CPiCr~s 1161 (1237)
-.|.||+|...... ..-..| .|.|.|...|+..|... ..+||.|+.-
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~~ 232 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRRL 232 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCccccch
Confidence 56888888755432 111234 79999999999999643 3456666643
No 141
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=61.69 E-value=5.7 Score=49.47 Aligned_cols=48 Identities=23% Similarity=0.632 Sum_probs=41.3
Q ss_pred ccccccCCcccCcccccccCCCCCccccccccccccccccccCCCCCCCccCCC
Q 000886 997 LRAACCGKLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVGPVCTTLSCSG 1050 (1237)
Q Consensus 997 l~~~cC~~~y~Cr~CHde~~~H~~~r~~~~~v~C~~C~~~Q~~~~~C~~~~C~~ 1050 (1237)
+.|.-||....|..|.-...-|.- ...+.|-.|+..+++...|.+ |.+
T Consensus 214 ~~C~~Cg~~~~C~~C~~~l~~h~~----~~~l~Ch~Cg~~~~~~~~Cp~--C~s 261 (505)
T TIGR00595 214 LLCRSCGYILCCPNCDVSLTYHKK----EGKLRCHYCGYQEPIPKTCPQ--CGS 261 (505)
T ss_pred eEhhhCcCccCCCCCCCceEEecC----CCeEEcCCCcCcCCCCCCCCC--CCC
Confidence 789999999999999888777753 448999999999999999987 643
No 142
>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=59.98 E-value=6.3 Score=48.85 Aligned_cols=13 Identities=31% Similarity=0.616 Sum_probs=7.1
Q ss_pred CCCCCCcccCChh
Q 000886 1154 ICPICSKSLGDMA 1166 (1237)
Q Consensus 1154 ~CPiCr~sv~dm~ 1166 (1237)
.|+.|+-+-.+..
T Consensus 88 ~C~~C~Wss~~ig 100 (483)
T PF05502_consen 88 SCSYCRWSSRDIG 100 (483)
T ss_pred ECCCceeeccccC
Confidence 5666666554433
No 143
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=59.41 E-value=2.5 Score=56.35 Aligned_cols=70 Identities=10% Similarity=0.031 Sum_probs=48.2
Q ss_pred HHHHHHHHHHHHHHHHHHHhHHHHHHHHhhHHHhcCCHHHHHHHHHHHhcccCHHHHHHHHhhhcCCCCH
Q 000886 145 SYRRELASCTGALQTSISQHMSKEEEQVFPLLIEKFSFEEQASLVWQFLCSIPVNMMAEFLPWLSSSISS 214 (1237)
Q Consensus 145 ~~~~eLa~~l~~l~~~l~qHm~~EE~qv~PLl~~~~S~~Eqa~L~~~~i~siP~~~m~~~LpWm~~~lsp 214 (1237)
++..-+-+.+.-.+-....||-.+|.+..-.=-..+|..+-.++...|.-++|..-...-......++++
T Consensus 237 D~~~~~~~~~r~~~~r~~~~~~~~~~e~~~~s~~~It~~~~~di~~~~~~~l~~~~~~~~~~l~~e~l~~ 306 (1394)
T KOG0298|consen 237 DLIKRFQSQLRKYQQRTVSWMPSREQEYTQVSANFITLHLIDDITRVFKLKLCFQFYSFEEELPKESLSP 306 (1394)
T ss_pred hHHHHhhhhccHHHHHHHHhccccchhhhhccccccccccccchHHHhhhccceecccccccchhccCCC
Confidence 4445555555556666777888888877666667778888888888888888866555545555555555
No 144
>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]
Probab=58.95 E-value=3.6 Score=52.57 Aligned_cols=90 Identities=13% Similarity=0.050 Sum_probs=64.5
Q ss_pred HHHHHHHHhHHHHHH-----HHHHHHHhhCCHHHHHHHHHhHhhcCCHHHHHHHHhhhhCCCCHHHHHHHHHHhhhhcCh
Q 000886 405 LIMASIQKHFRNEEV-----QVLPLARRHFSPKRQRELLYQSLCVMPLKLIECVLPWLVGSLSEEEARSFLQNIYMAASD 479 (1237)
Q Consensus 405 ~L~~~L~~H~~~EE~-----qvfPLl~~~fS~eEq~~L~~~~l~smPl~~L~~vLPWl~~~Ls~~E~~~~L~~l~~~a~~ 479 (1237)
.+-...-.|+..|++ -+.|.+=.. +-+||+..+.+|.-.--+..+.-+||=.-+.|.|.-...+|.-.-. +--
T Consensus 393 kv~~~yI~HLl~~~~y~~Aas~~p~m~gn-~~~eWe~~V~~f~e~~~l~~Ia~~lPt~~~rL~p~vYemvLve~L~-~~~ 470 (846)
T KOG2066|consen 393 KVGKTYIDHLLFEGKYDEAASLCPKMLGN-NAAEWELWVFKFAELDQLTDIAPYLPTGPPRLKPLVYEMVLVEFLA-SDV 470 (846)
T ss_pred HHHHHHHHHHHhcchHHHHHhhhHHHhcc-hHHHHHHHHHHhccccccchhhccCCCCCcccCchHHHHHHHHHHH-HHH
Confidence 344456667755443 344444333 4578999999988777777888899988899999999998877644 566
Q ss_pred hHHHHHHHHHhccCCCC
Q 000886 480 SALITLFAGWACKGHSR 496 (1237)
Q Consensus 480 ~~l~~ll~~W~~~~~~~ 496 (1237)
.-|.+++..|=..-|+.
T Consensus 471 ~~F~e~i~~Wp~~Lys~ 487 (846)
T KOG2066|consen 471 KGFLELIKEWPGHLYSV 487 (846)
T ss_pred HHHHHHHHhCChhhhhh
Confidence 88999999997555543
No 145
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=57.43 E-value=6.3 Score=39.82 Aligned_cols=36 Identities=31% Similarity=0.472 Sum_probs=28.0
Q ss_pred ccCCceecCCCCCCCCCCceeecccCCCCCCccccccc
Q 000886 1187 DRCQEILCNDCDKKGSAPFHWLYHKCGFCGSYNTRVIK 1224 (1237)
Q Consensus 1187 ~~~~~i~CnDC~~~s~~~~h~lg~kC~~C~SYNT~~~~ 1224 (1237)
...+.+.|-||+......-|.++ ||.|||-|.++++
T Consensus 66 ~~p~~~~C~~C~~~~~~e~~~~~--CP~C~s~~~~i~~ 101 (115)
T COG0375 66 EEPAECWCLDCGQEVELEELDYR--CPKCGSINLRIIG 101 (115)
T ss_pred EeccEEEeccCCCeecchhheeE--CCCCCCCceEEec
Confidence 34567899999887766655544 9999999998864
No 146
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=56.20 E-value=4.4 Score=34.96 Aligned_cols=41 Identities=34% Similarity=0.869 Sum_probs=20.0
Q ss_pred CCCcccccccccCCCcceecCCCCccChhhHH--Hhhhc-----CCCCCCCCcc
Q 000886 1115 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQ--AYTCS-----HYICPICSKS 1161 (1237)
Q Consensus 1115 ~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~--~wl~~-----~~~CPiCr~s 1161 (1237)
-.|||....|. .+++...|.|. +|++ .|+.. ...||+|+++
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 46999987753 36788889866 5754 45532 4679999874
No 147
>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=55.68 E-value=8.1 Score=30.46 Aligned_cols=24 Identities=38% Similarity=1.089 Sum_probs=19.1
Q ss_pred eEecccccCC-CCCCccccCCCCCc
Q 000886 1055 KYYCGICKFF-DDERVVYHCPFCNL 1078 (1237)
Q Consensus 1055 ~y~C~~C~~~-d~~k~~yHC~~Cgi 1078 (1237)
.|-|.+|.+. |.++.++.||.||.
T Consensus 1 ~~~C~~CGy~y~~~~~~~~CP~Cg~ 25 (33)
T cd00350 1 KYVCPVCGYIYDGEEAPWVCPVCGA 25 (33)
T ss_pred CEECCCCCCEECCCcCCCcCcCCCC
Confidence 4789999986 55578999999984
No 148
>PRK01917 cation-binding hemerythrin HHE family protein; Provisional
Probab=55.58 E-value=31 Score=35.70 Aligned_cols=50 Identities=14% Similarity=0.177 Sum_probs=31.1
Q ss_pred HHhHHHHHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHH
Q 000886 363 AQEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQ 420 (1237)
Q Consensus 363 e~EH~~ie~l~e~l~~ll~~~~~a~~~~~~~~~~~eLa~~le~L~~~L~~H~~~EE~q 420 (1237)
+..+..||..-.+|..++..+..+. ...+...++.|..-...||..||.-
T Consensus 11 ~vGi~~ID~qH~~Lf~lin~l~~~~--------~~~i~~~l~~L~~y~~~HF~~EE~l 60 (139)
T PRK01917 11 HLGDPFTDATHAEFVQLLNAVARAD--------DADFLQALDAWIDHTRHHFAQEERW 60 (139)
T ss_pred hcCChhhhHHHHHHHHHHHHHHcCC--------HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344444444445555555443221 1336677888899999999999964
No 149
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=55.37 E-value=5.2 Score=51.42 Aligned_cols=43 Identities=30% Similarity=0.745 Sum_probs=34.2
Q ss_pred CCCcccccccccCCCcceecCCCCccChhhHHHhhhc--CCCCCCCCccc
Q 000886 1115 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS--HYICPICSKSL 1162 (1237)
Q Consensus 1115 ~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~--~~~CPiCr~sv 1162 (1237)
..|+||++ .+.....+|||.|...|+.+.+.. ...||+||..+
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 244677899999999999987643 34699999654
No 150
>PF14357 DUF4404: Domain of unknown function (DUF4404)
Probab=54.83 E-value=85 Score=30.18 Aligned_cols=82 Identities=13% Similarity=0.095 Sum_probs=64.2
Q ss_pred HHHHHHHHHHHHHhhccCCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHHHhhhhHHHHHHhhhhhHHHHHHHHH
Q 000886 54 IKSELDVLHRAAMAFATNLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIRVKNIARTYSLEHEGESVLFDQLF 133 (1237)
Q Consensus 54 lR~eL~~l~~~a~~~~~~~gd~~~~~~l~~r~~~L~~~~~~H~~aEDevI~PaLd~Rv~~v~~~~~~EH~~~~~lf~~l~ 133 (1237)
||..|..|+.-+...++ -|......|..=-+.+...+.. ..|...--+.|..|+...+.+|+.+|=.....+..|-
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 67888888888888887 5666666665555555666654 5677788999999999999999999999999888887
Q ss_pred HHHHhh
Q 000886 134 ELLNSS 139 (1237)
Q Consensus 134 ~~l~~~ 139 (1237)
..|..+
T Consensus 78 ~sLa~M 83 (85)
T PF14357_consen 78 DSLANM 83 (85)
T ss_pred HHHHHC
Confidence 777654
No 151
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=52.93 E-value=11 Score=48.99 Aligned_cols=55 Identities=24% Similarity=0.529 Sum_probs=43.7
Q ss_pred cccccccCCcccCcccccccCCCCCccccccccccccccccccCCCCCCCccCCCCccceEe
Q 000886 996 KLRAACCGKLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVGPVCTTLSCSGLSMAKYY 1057 (1237)
Q Consensus 996 ~l~~~cC~~~y~Cr~CHde~~~H~~~r~~~~~v~C~~C~~~Q~~~~~C~~~~C~~~~~~~y~ 1057 (1237)
-+.|.-||-.+.|++|=.-..=|.- +..+.|-+|+..+++-..|-+ | |...=+|+
T Consensus 435 ~l~C~~Cg~v~~Cp~Cd~~lt~H~~----~~~L~CH~Cg~~~~~p~~Cp~--C-gs~~L~~~ 489 (730)
T COG1198 435 LLLCRDCGYIAECPNCDSPLTLHKA----TGQLRCHYCGYQEPIPQSCPE--C-GSEHLRAV 489 (730)
T ss_pred eeecccCCCcccCCCCCcceEEecC----CCeeEeCCCCCCCCCCCCCCC--C-CCCeeEEe
Confidence 3899999999999999666555543 369999999999999999987 6 55544444
No 152
>PRK05580 primosome assembly protein PriA; Validated
Probab=52.53 E-value=9.4 Score=49.29 Aligned_cols=49 Identities=22% Similarity=0.598 Sum_probs=41.7
Q ss_pred cccccccCCcccCcccccccCCCCCccccccccccccccccccCCCCCCCccCCC
Q 000886 996 KLRAACCGKLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVGPVCTTLSCSG 1050 (1237)
Q Consensus 996 ~l~~~cC~~~y~Cr~CHde~~~H~~~r~~~~~v~C~~C~~~Q~~~~~C~~~~C~~ 1050 (1237)
-+.|.-||....|..|.-...-|.. ...+.|-.|+..+++...|.+ |.+
T Consensus 381 ~~~C~~Cg~~~~C~~C~~~l~~h~~----~~~l~Ch~Cg~~~~~~~~Cp~--Cg~ 429 (679)
T PRK05580 381 FLLCRDCGWVAECPHCDASLTLHRF----QRRLRCHHCGYQEPIPKACPE--CGS 429 (679)
T ss_pred ceEhhhCcCccCCCCCCCceeEECC----CCeEECCCCcCCCCCCCCCCC--CcC
Confidence 3889999999999999988777753 458999999999999999988 643
No 153
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=50.74 E-value=14 Score=50.09 Aligned_cols=23 Identities=22% Similarity=0.369 Sum_probs=13.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhc
Q 000886 297 IMLWHNAIKRELNDIAEAARKIQ 319 (1237)
Q Consensus 297 l~~~HkALRrEL~~L~~~a~~~~ 319 (1237)
+..-++-|.+++.++.+.|.+.+
T Consensus 7 ~~~Yf~~l~~~~~~~~~iA~~ar 29 (1337)
T PRK14714 7 MERYFERLERELDKAYEVAEAAR 29 (1337)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455666666666666665553
No 154
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=49.40 E-value=13 Score=33.23 Aligned_cols=29 Identities=28% Similarity=0.651 Sum_probs=22.3
Q ss_pred CceecCCCCCCCCCCceeecccCCCCCCcccccc
Q 000886 1190 QEILCNDCDKKGSAPFHWLYHKCGFCGSYNTRVI 1223 (1237)
Q Consensus 1190 ~~i~CnDC~~~s~~~~h~lg~kC~~C~SYNT~~~ 1223 (1237)
..+.|..||.. ...| +-|++||.||.+++
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 3334 46999999999885
No 155
>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=49.18 E-value=82 Score=31.27 Aligned_cols=28 Identities=25% Similarity=0.411 Sum_probs=20.0
Q ss_pred HHHHHHHHHHHHhHHHHHHHH----HHHHHhh
Q 000886 401 SQADLIMASIQKHFRNEEVQV----LPLARRH 428 (1237)
Q Consensus 401 ~~le~L~~~L~~H~~~EE~qv----fPLl~~~ 428 (1237)
..+..|..-...||..||+-. +|-+..|
T Consensus 37 ~~l~~L~~y~~~HF~~EE~~M~~~~yp~~~~H 68 (113)
T cd00522 37 DNLKELVDYTVKHFKDEEALMEAAGYPDYEEH 68 (113)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCCCHHHH
Confidence 456777888999999999754 4544444
No 156
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=48.81 E-value=8.7 Score=44.45 Aligned_cols=31 Identities=32% Similarity=0.860 Sum_probs=23.4
Q ss_pred eecCCCCccChhhHHHhhhcCCCCCCCCcccCC
Q 000886 1132 RALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1164 (1237)
Q Consensus 1132 ~~LpCgH~fH~~Ci~~wl~~~~~CPiCr~sv~d 1164 (1237)
+.+||.|+|+.+|-..- ....||.|.-.|..
T Consensus 105 RmIPCkHvFCl~CAr~~--~dK~Cp~C~d~Vqr 135 (389)
T KOG2932|consen 105 RMIPCKHVFCLECARSD--SDKICPLCDDRVQR 135 (389)
T ss_pred cccccchhhhhhhhhcC--ccccCcCcccHHHH
Confidence 56899999999997432 25689999877643
No 157
>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=48.39 E-value=10 Score=38.02 Aligned_cols=32 Identities=25% Similarity=0.517 Sum_probs=23.8
Q ss_pred ccccccccCCcccCcccccccCCCCCccccccccccccccccccCC
Q 000886 995 CKLRAACCGKLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVG 1040 (1237)
Q Consensus 995 c~l~~~cC~~~y~Cr~CHde~~~H~~~r~~~~~v~C~~C~~~Q~~~ 1040 (1237)
-|-.||-||+-| .+... ..++|.+|+++|++.
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 578999999999987
No 158
>PF14353 CpXC: CpXC protein
Probab=48.08 E-value=17 Score=36.83 Aligned_cols=56 Identities=20% Similarity=0.344 Sum_probs=29.1
Q ss_pred CCCCCCCcccCChhhHHHhHHHHHhhcCCChhhhccCCceecCCCCCCCCCCceeecc
Q 000886 1153 YICPICSKSLGDMAVYFGMLDALLASEQLPEEYRDRCQEILCNDCDKKGSAPFHWLYH 1210 (1237)
Q Consensus 1153 ~~CPiCr~sv~dm~~~~~~lD~~i~~~pmP~ey~~~~~~i~CnDC~~~s~~~~h~lg~ 1210 (1237)
.+||.|++...- ..|..+|......-...-..+..-.+.|..||.+..+.|=++|+
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 489999988631 11222221000000000113444568899999988766655554
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=47.61 E-value=12 Score=37.62 Aligned_cols=17 Identities=35% Similarity=0.757 Sum_probs=15.1
Q ss_pred cCCCCCCccccCCCCCc
Q 000886 1062 KFFDDERVVYHCPFCNL 1078 (1237)
Q Consensus 1062 ~~~d~~k~~yHC~~Cgi 1078 (1237)
||||-.|.+-.||+||-
T Consensus 18 kFYDLnk~PivCP~CG~ 34 (108)
T PF09538_consen 18 KFYDLNKDPIVCPKCGT 34 (108)
T ss_pred hhccCCCCCccCCCCCC
Confidence 78899999999999993
No 160
>PRK14873 primosome assembly protein PriA; Provisional
Probab=47.52 E-value=12 Score=48.17 Aligned_cols=46 Identities=26% Similarity=0.468 Sum_probs=38.0
Q ss_pred ccccccCCcccCcccccccCCCCCccccccccccccccccccCCCCCCCccCC
Q 000886 997 LRAACCGKLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVGPVCTTLSCS 1049 (1237)
Q Consensus 997 l~~~cC~~~y~Cr~CHde~~~H~~~r~~~~~v~C~~C~~~Q~~~~~C~~~~C~ 1049 (1237)
+.|..||....|..|.-...=|. ....+.|-.|+..+ +...|.+ |.
T Consensus 384 l~C~~Cg~~~~C~~C~~~L~~h~----~~~~l~Ch~CG~~~-~p~~Cp~--Cg 429 (665)
T PRK14873 384 LACARCRTPARCRHCTGPLGLPS----AGGTPRCRWCGRAA-PDWRCPR--CG 429 (665)
T ss_pred eEhhhCcCeeECCCCCCceeEec----CCCeeECCCCcCCC-cCccCCC--Cc
Confidence 89999999999999988877664 24578999999976 5789987 64
No 161
>KOG3850 consensus Predicted membrane protein [Function unknown]
Probab=47.43 E-value=5.4e+02 Score=31.39 Aligned_cols=129 Identities=19% Similarity=0.244 Sum_probs=75.0
Q ss_pred HHHHHHHHHHHHHHHHhhcccCCcccH-HHHHHHHHHHHHHHHhhhhcccccchhhhhhhh--hhHHhHHHHHHHHHHHH
Q 000886 301 HNAIKRELNDIAEAARKIQLSGDFSDL-SAFNKRLQFIAEVCIFHSIAEDKVIFPAVDVEL--SFAQEHAEEEIQFDKLR 377 (1237)
Q Consensus 301 HkALRrEL~~L~~~a~~~~~~gd~~~L-~~L~~r~~fl~~vl~~Hs~aEDevlFPaL~~r~--~me~EH~~ie~l~e~l~ 377 (1237)
=+||..||++|.+.-..++ .+..+| .++..-+.|+.+.|. |+.+-.-.|++.+ ..+....+|..+=-++.
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 344466 677777888888776 7767666666555 34444444433322222
Q ss_pred HHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH---HHHHhhCCHHHHHHHHHhHhhcC
Q 000886 378 CLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVL---PLARRHFSPKRQRELLYQSLCVM 445 (1237)
Q Consensus 378 ~ll~~~~~a~~~~~~~~~~~eLa~~le~L~~~L~~H~~~EE~qvf---PLl~~~fS~eEq~~L~~~~l~sm 445 (1237)
..-..++= ..|+ =+..+.+.+++...|+.+=|.+.- -+--++++++-|..|+.+++-.+
T Consensus 335 smeervaY--------QsyE-RaRdIqEalEscqtrisKlEl~qq~qqv~Q~e~~~na~a~~llgk~iNii 396 (455)
T KOG3850|consen 335 SMEERVAY--------QSYE-RARDIQEALESCQTRISKLELQQQQQQVVQLEGLENAVARRLLGKFINII 396 (455)
T ss_pred HHHHHHHH--------HHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccHHHHHHHHHHHH
Confidence 11111100 0011 234455666677777777665544 22345677788888888877643
No 162
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=47.24 E-value=13 Score=33.43 Aligned_cols=45 Identities=29% Similarity=0.833 Sum_probs=27.4
Q ss_pred ccccccccccccCCC-----CCCCccCCCCccceEecccccCCCCCCccccCCCCCc
Q 000886 1027 EMMCMRCLKVQPVGP-----VCTTLSCSGLSMAKYYCGICKFFDDERVVYHCPFCNL 1078 (1237)
Q Consensus 1027 ~v~C~~C~~~Q~~~~-----~C~~~~C~~~~~~~y~C~~C~~~d~~k~~yHC~~Cgi 1078 (1237)
...|..|+.+-.+.+ .|-| | |. .-=|-|..|+-..+ .|.|++||+
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 457888877764433 3655 4 42 23366777766644 678888874
No 163
>PRK00808 hypothetical protein; Provisional
Probab=46.07 E-value=3.7e+02 Score=28.07 Aligned_cols=110 Identities=17% Similarity=0.254 Sum_probs=71.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcccCCcccHHHHHHHHHHHHHHHHhhhhcccccc----hhhhhhhhhhHHhHHHHHHH
Q 000886 297 IMLWHNAIKRELNDIAEAARKIQLSGDFSDLSAFNKRLQFIAEVCIFHSIAEDKVI----FPAVDVELSFAQEHAEEEIQ 372 (1237)
Q Consensus 297 l~~~HkALRrEL~~L~~~a~~~~~~gd~~~L~~L~~r~~fl~~vl~~Hs~aEDevl----FPaL~~r~~me~EH~~ie~l 372 (1237)
+=.-|+.|=.-++.|...+. .++ ...+..-+.+|.+....|=..|+.++ ||.++.+. .+| +..
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---RVH---ELF 83 (150)
T ss_pred HHHHHHHHHHHHHHHHHHHH----cCc---HHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHH---HHH---HHH
Confidence 33467777666666665542 222 24566678888999999999898764 77776444 244 444
Q ss_pred HHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhh
Q 000886 373 FDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPLARRH 428 (1237)
Q Consensus 373 ~e~l~~ll~~~~~a~~~~~~~~~~~eLa~~le~L~~~L~~H~~~EE~qvfPLl~~~ 428 (1237)
++.+..+...... + . ... ...+.-|..-|..|+..+-....+.+.+.
T Consensus 84 l~~l~~l~~~~~~-g-~----~~~---~~l~~~L~~WL~~HI~~~D~~~~~~l~~~ 130 (150)
T PRK00808 84 IKRVEEYRERFQA-G-E----DVA---DELHGMLSRWLFNHIRNDDAAYVDAVKAN 130 (150)
T ss_pred HHHHHHHHHHHHc-c-c----hHH---HHHHHHHHHHHHHHHHHHhHHHHHHHHHh
Confidence 5555555544432 2 1 122 23445678889999999999999998885
No 164
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=46.00 E-value=8.4 Score=44.19 Aligned_cols=50 Identities=22% Similarity=0.543 Sum_probs=37.4
Q ss_pred CCCCcccccccccCCCcceecCCC-----CccChhhHHHhhh--cCCCCCCCCcccC
Q 000886 1114 ETNCPICCDFLFTSSATVRALPCG-----HFMHSDCFQAYTC--SHYICPICSKSLG 1163 (1237)
Q Consensus 1114 ~~~CpICle~lf~s~~~v~~LpCg-----H~fH~~Ci~~wl~--~~~~CPiCr~sv~ 1163 (1237)
+..|-||.+............||. ++.|..|+..|.. .+.+|.+|.....
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 468999998765443223445773 8889999999986 5688999998653
No 165
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=45.48 E-value=7 Score=49.12 Aligned_cols=29 Identities=31% Similarity=0.595 Sum_probs=23.0
Q ss_pred Cccccccc----ccccccccCCcccCcccccccC
Q 000886 987 GCEHYKRN----CKLRAACCGKLFTCRFCHDKVS 1016 (1237)
Q Consensus 987 gC~HY~r~----c~l~~~cC~~~y~Cr~CHde~~ 1016 (1237)
||.|+--. ..-.|.-+|+|| |..||....
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 78888762 557788899988 999998854
No 166
>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=45.32 E-value=16 Score=42.89 Aligned_cols=23 Identities=26% Similarity=0.801 Sum_probs=12.6
Q ss_pred ceecCCCCCCCCCCceeecccCCCCCC
Q 000886 1191 EILCNDCDKKGSAPFHWLYHKCGFCGS 1217 (1237)
Q Consensus 1191 ~i~CnDC~~~s~~~~h~lg~kC~~C~S 1217 (1237)
.-.|+=|+ ..+|+.-.||++||+
T Consensus 210 yL~CslC~----teW~~~R~~C~~Cg~ 232 (305)
T TIGR01562 210 YLSCSLCA----TEWHYVRVKCSHCEE 232 (305)
T ss_pred EEEcCCCC----CcccccCccCCCCCC
Confidence 34555555 445555556666653
No 167
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=44.58 E-value=11 Score=48.29 Aligned_cols=50 Identities=20% Similarity=0.469 Sum_probs=34.9
Q ss_pred CCCCCCcccccccccCCCcceecCCC-----CccChhhHHHhhhcC--CCCCCCCcccC
Q 000886 1112 GLETNCPICCDFLFTSSATVRALPCG-----HFMHSDCFQAYTCSH--YICPICSKSLG 1163 (1237)
Q Consensus 1112 ~~~~~CpICle~lf~s~~~v~~LpCg-----H~fH~~Ci~~wl~~~--~~CPiCr~sv~ 1163 (1237)
.....|-||.-+ ....+ .-.-||. -++|.+|+-+|+..+ ..|-||..++.
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 345789999755 22222 2233664 789999999999754 67999998874
No 168
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=44.24 E-value=21 Score=41.95 Aligned_cols=47 Identities=21% Similarity=0.583 Sum_probs=0.0
Q ss_pred cCCCCCCCCcccCChhhHHHhHHHHHhhcCCChhhh-------ccCCceecCCCCCCCCCCceeecccCCCCCCcccccc
Q 000886 1151 SHYICPICSKSLGDMAVYFGMLDALLASEQLPEEYR-------DRCQEILCNDCDKKGSAPFHWLYHKCGFCGSYNTRVI 1223 (1237)
Q Consensus 1151 ~~~~CPiCr~sv~dm~~~~~~lD~~i~~~pmP~ey~-------~~~~~i~CnDC~~~s~~~~h~lg~kC~~C~SYNT~~~ 1223 (1237)
....||+|+. ++... +-.-...|.=|+ ..+|+.-.+|++|| |+..+
T Consensus 186 ~~~~CPvCGs---------------------~P~~s~v~~~~~~G~RyL~CslC~----teW~~~R~~C~~Cg--~~~~l 238 (309)
T PRK03564 186 QRQFCPVCGS---------------------MPVSSVVQIGTTQGLRYLHCNLCE----SEWHVVRVKCSNCE--QSGKL 238 (309)
T ss_pred CCCCCCCCCC---------------------cchhheeeccCCCCceEEEcCCCC----CcccccCccCCCCC--CCCce
Q ss_pred c
Q 000886 1224 K 1224 (1237)
Q Consensus 1224 ~ 1224 (1237)
.
T Consensus 239 ~ 239 (309)
T PRK03564 239 H 239 (309)
T ss_pred e
No 169
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=44.04 E-value=15 Score=42.77 Aligned_cols=45 Identities=22% Similarity=0.631 Sum_probs=34.5
Q ss_pred CCCcccccccccCCCcceecCCCCccChhhHHHhhhc---CCCCCCCCc
Q 000886 1115 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS---HYICPICSK 1160 (1237)
Q Consensus 1115 ~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~---~~~CPiCr~ 1160 (1237)
-.|||=.|. -+...+...|.|||++-..=++..-++ ...||.|-.
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 357776664 555567788999999999999887655 478999963
No 170
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=42.19 E-value=11 Score=37.06 Aligned_cols=32 Identities=22% Similarity=0.656 Sum_probs=24.8
Q ss_pred CccccCCCCC-----ccccCCCCCccccccCCccccc
Q 000886 1068 RVVYHCPFCN-----LCRVGRGLGVDFFHCMTCNCCL 1099 (1237)
Q Consensus 1068 k~~yHC~~Cg-----iCR~g~gl~~~~fHC~~C~~C~ 1099 (1237)
+..|-|+.|| +|-|-++++.-+-+|..||.-.
T Consensus 20 ~k~FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~ 56 (104)
T COG4888 20 PKTFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSF 56 (104)
T ss_pred CceEecCccCCeeeeEEEEEecCceeEEEcccCcceE
Confidence 4677888888 7888877777788888888653
No 171
>PRK04023 DNA polymerase II large subunit; Validated
Probab=41.96 E-value=22 Score=47.21 Aligned_cols=47 Identities=26% Similarity=0.569 Sum_probs=24.6
Q ss_pred CCCCCccCCCCccceEecccccCCCCCCccccCCCCCccccCCCCCccccccCCccccc
Q 000886 1041 PVCTTLSCSGLSMAKYYCGICKFFDDERVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCL 1099 (1237)
Q Consensus 1041 ~~C~~~~C~~~~~~~y~C~~C~~~d~~k~~yHC~~CgiCR~g~gl~~~~fHC~~C~~C~ 1099 (1237)
..|.+ | |......+|+.|.=. .+.+|.|+.||..-.+ +.|.+||.=.
T Consensus 627 RfCps--C-G~~t~~frCP~CG~~--Te~i~fCP~CG~~~~~-------y~CPKCG~El 673 (1121)
T PRK04023 627 RKCPS--C-GKETFYRRCPFCGTH--TEPVYRCPRCGIEVEE-------DECEKCGREP 673 (1121)
T ss_pred ccCCC--C-CCcCCcccCCCCCCC--CCcceeCccccCcCCC-------CcCCCCCCCC
Confidence 45655 4 555555566666533 2456666666443221 3466666543
No 172
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=41.62 E-value=18 Score=42.42 Aligned_cols=47 Identities=17% Similarity=0.341 Sum_probs=35.0
Q ss_pred CCCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcccC
Q 000886 1114 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1163 (1237)
Q Consensus 1114 ~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCr~sv~ 1163 (1237)
...||||+-..- .+.+.--=|=+|+-.|+-.++.+..+||+=.+++.
T Consensus 300 ~~~CpvClk~r~---Nptvl~vSGyVfCY~Ci~~Yv~~~~~CPVT~~p~~ 346 (357)
T KOG0826|consen 300 REVCPVCLKKRQ---NPTVLEVSGYVFCYPCIFSYVVNYGHCPVTGYPAS 346 (357)
T ss_pred cccChhHHhccC---CCceEEecceEEeHHHHHHHHHhcCCCCccCCcch
Confidence 467999985421 22222234999999999999999999999888753
No 173
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=41.20 E-value=21 Score=44.57 Aligned_cols=188 Identities=23% Similarity=0.466 Sum_probs=96.7
Q ss_pred cccccccCCcccCcccccccCCCCCccccccccccccccccccCCCCCCCccCCCCccceEec-ccccCCCCC------C
Q 000886 996 KLRAACCGKLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVGPVCTTLSCSGLSMAKYYC-GICKFFDDE------R 1068 (1237)
Q Consensus 996 ~l~~~cC~~~y~Cr~CHde~~~H~~~r~~~~~v~C~~C~~~Q~~~~~C~~~~C~~~~~~~y~C-~~C~~~d~~------k 1068 (1237)
.++|.-|++ .|-.++-.-.-.-+.+.-..|-.|+.--..+.-|.. | +. +||| ..|.-|-.. -
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 466766665 454453211111222345556666665555666666 3 32 6776 445444221 5
Q ss_pred cccc--CCCCCccccCCCCCcc------ccccCCcccccccccccccccccCCCCCCcccccccccCCCcceecCCCCcc
Q 000886 1069 VVYH--CPFCNLCRVGRGLGVD------FFHCMTCNCCLAKKLVDHKCREKGLETNCPICCDFLFTSSATVRALPCGHFM 1140 (1237)
Q Consensus 1069 ~~yH--C~~CgiCR~g~gl~~~------~fHC~~C~~C~s~~l~~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCgH~f 1140 (1237)
+.|| |-.|-+|+..-.-|.. +--|.+|-.=+++. =.+...-.+|.-|.+.+... +....| +
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 6666677654222221 12233332222222 11223457899999886554 333333 2
Q ss_pred ChhhHHHhhhcCCCCCCCCcccCChhhHHHhHHHHHhhcCCC---hhhhccCCceecCCCCCC--------CCCCceeec
Q 000886 1141 HSDCFQAYTCSHYICPICSKSLGDMAVYFGMLDALLASEQLP---EEYRDRCQEILCNDCDKK--------GSAPFHWLY 1209 (1237)
Q Consensus 1141 H~~Ci~~wl~~~~~CPiCr~sv~dm~~~~~~lD~~i~~~pmP---~ey~~~~~~i~CnDC~~~--------s~~~~h~lg 1209 (1237)
++|-.....|--|.+.+..- | |...-.| ..|.... -|.|-.|.+- +.-.||--+
T Consensus 154 -----~qwhv~cfkc~~c~~vL~ge--y-------~skdg~pyce~dy~~~f-gvkc~~c~~fisgkvLqag~kh~HPtC 218 (670)
T KOG1044|consen 154 -----KQWHVSCFKCKSCSAVLNGE--Y-------MSKDGVPYCEKDYQAKF-GVKCEECEKFISGKVLQAGDKHFHPTC 218 (670)
T ss_pred -----cceeeeeeehhhhcccccce--e-------eccCCCcchhhhhhhhc-CeehHHhhhhhhhhhhhccCcccCcch
Confidence 34444445777888766321 1 1222222 2465555 4789999643 234577777
Q ss_pred ccCCCCCCccc
Q 000886 1210 HKCGFCGSYNT 1220 (1237)
Q Consensus 1210 ~kC~~C~SYNT 1220 (1237)
-+|..||.-=|
T Consensus 219 ARCsRCgqmF~ 229 (670)
T KOG1044|consen 219 ARCSRCGQMFG 229 (670)
T ss_pred hhhhhhccccc
Confidence 77888887544
No 174
>PF12773 DZR: Double zinc ribbon
Probab=40.77 E-value=23 Score=29.97 Aligned_cols=22 Identities=27% Similarity=0.789 Sum_probs=11.3
Q ss_pred cccccccccC-CCCCCCccCCCCccc
Q 000886 1030 CMRCLKVQPV-GPVCTTLSCSGLSMA 1054 (1237)
Q Consensus 1030 C~~C~~~Q~~-~~~C~~~~C~~~~~~ 1054 (1237)
|..|+++.+. ...|.+ | |..+.
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 4556655444 345665 3 55443
No 175
>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=40.67 E-value=16 Score=31.30 Aligned_cols=31 Identities=23% Similarity=0.432 Sum_probs=20.3
Q ss_pred ceecCCCCCCCCCCcee---ecccCCCCCCcccc
Q 000886 1191 EILCNDCDKKGSAPFHW---LYHKCGFCGSYNTR 1221 (1237)
Q Consensus 1191 ~i~CnDC~~~s~~~~h~---lg~kC~~C~SYNT~ 1221 (1237)
...|++|+....+-..+ -...|+.||+-+.+
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~ 38 (52)
T TIGR02605 5 EYRCTACGHRFEVLQKMSDDPLATCPECGGEKLR 38 (52)
T ss_pred EEEeCCCCCEeEEEEecCCCCCCCCCCCCCCcee
Confidence 45799999865542211 12479999998763
No 176
>PRK00808 hypothetical protein; Provisional
Probab=40.53 E-value=1.4e+02 Score=31.21 Aligned_cols=109 Identities=11% Similarity=0.097 Sum_probs=64.0
Q ss_pred HHHHHHHHHHHhccccCC-ChhhHHHHHHHHHHHHHHHHHHhhhhcccc----cccccccccccccccccchhhHHHHHH
Q 000886 654 IRKDLEYLDGESGKLNDC-NETFLRQFTGRFRLLWGLYRAHSNAEDDIV----FPALESKETLSNVSHSYTLDHKQEEKL 728 (1237)
Q Consensus 654 IRkDLe~l~~~~~kL~~~-d~~~L~~f~~rf~~L~~v~~~HS~AEDeiv----fPALe~k~~~~n~s~s~~~DH~~ee~l 728 (1237)
|=.+|+.|-..+.+|... ....-..+...+..|......|=..|+.+. ||.++... .+|+..
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 IDQQHKRIVDYINHLHDAQDSPDRLAVAEVIDELIDYTLSHFAFEESLMEEAGYPFLVPHK----------RVHELF--- 83 (150)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHH----------HHHHHH---
Confidence 344455554444444321 001134667778999999999999888765 77764321 244443
Q ss_pred HHHHHHHHHhhhhhhhccccCcCCcccccccccccchhhhhhHHHHHHHHHHHHHHHHHHHHHhhHhHHHhhhhHHhhc
Q 000886 729 FEDISSALSELTELHECLSTDLTGDLTRNSLESCDQNETVRKYNEKATELQGMCKSIRVTLDQHVFREELELWPLFDRH 807 (1237)
Q Consensus 729 fedi~~~L~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~kL~~~~ksl~~~L~~Hl~~EE~ElfPL~rk~ 807 (1237)
+.+|..+...+. . + . .... .+.+.|..-|.+||..+-....+.++..
T Consensus 84 l~~l~~l~~~~~-------~--g---------------~-----~~~~---~l~~~L~~WL~~HI~~~D~~~~~~l~~~ 130 (150)
T PRK00808 84 IKRVEEYRERFQ-------A--G---------------E-----DVAD---ELHGMLSRWLFNHIRNDDAAYVDAVKAN 130 (150)
T ss_pred HHHHHHHHHHHH-------c--c---------------c-----hHHH---HHHHHHHHHHHHHHHHHhHHHHHHHHHh
Confidence 444433332211 0 0 0 1112 2346678889999999999999998885
No 177
>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=40.19 E-value=23 Score=31.32 Aligned_cols=29 Identities=28% Similarity=0.683 Sum_probs=21.9
Q ss_pred CceecCCCCCCCCCCceeecccCCCCCCcccccc
Q 000886 1190 QEILCNDCDKKGSAPFHWLYHKCGFCGSYNTRVI 1223 (1237)
Q Consensus 1190 ~~i~CnDC~~~s~~~~h~lg~kC~~C~SYNT~~~ 1223 (1237)
..+.|..||+- ...| +.|++||-|+.+++
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 45789999963 2223 57999999999985
No 178
>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=39.24 E-value=18 Score=32.08 Aligned_cols=29 Identities=28% Similarity=0.689 Sum_probs=22.1
Q ss_pred CceecCCCCCCCCCCceeecccCCCCCCcccccc
Q 000886 1190 QEILCNDCDKKGSAPFHWLYHKCGFCGSYNTRVI 1223 (1237)
Q Consensus 1190 ~~i~CnDC~~~s~~~~h~lg~kC~~C~SYNT~~~ 1223 (1237)
..+.|..||+- ...| +-|..||.||-+++
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 45789999972 3344 46999999999876
No 179
>PLN03086 PRLI-interacting factor K; Provisional
Probab=39.15 E-value=39 Score=42.75 Aligned_cols=12 Identities=17% Similarity=0.562 Sum_probs=9.6
Q ss_pred CCCCCCCCcccC
Q 000886 1152 HYICPICSKSLG 1163 (1237)
Q Consensus 1152 ~~~CPiCr~sv~ 1163 (1237)
-+.||.|.+.+.
T Consensus 504 pi~C~fC~~~v~ 515 (567)
T PLN03086 504 LITCRFCGDMVQ 515 (567)
T ss_pred ceeCCCCCCccc
Confidence 478999998874
No 180
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=38.51 E-value=23 Score=41.83 Aligned_cols=25 Identities=20% Similarity=0.777 Sum_probs=19.5
Q ss_pred CccceEe--cccccCCCCCCccccCCCCCc
Q 000886 1051 LSMAKYY--CGICKFFDDERVVYHCPFCNL 1078 (1237)
Q Consensus 1051 ~~~~~y~--C~~C~~~d~~k~~yHC~~Cgi 1078 (1237)
+.|--|| |.||++++. .|.|++||+
T Consensus 61 ~dfeL~f~Ge~i~~y~~q---SftCPyC~~ 87 (381)
T KOG1280|consen 61 VDFELYFGGEPISHYDPQ---SFTCPYCGI 87 (381)
T ss_pred cceeeEecCccccccccc---cccCCcccc
Confidence 4566666 788888765 899999995
No 181
>PF14631 FancD2: Fanconi anaemia protein FancD2 nuclease; PDB: 3S4W_B.
Probab=37.54 E-value=4.4e+02 Score=37.51 Aligned_cols=99 Identities=20% Similarity=0.280 Sum_probs=59.1
Q ss_pred HHHHHHHHHHHhhccCchHHHHHHHHHHHHHH---------HHHHHhHHHHHHHHhhHHHh----cCCHHHHH---HHHH
Q 000886 127 VLFDQLFELLNSSMRNEESYRRELASCTGALQ---------TSISQHMSKEEEQVFPLLIE----KFSFEEQA---SLVW 190 (1237)
Q Consensus 127 ~lf~~l~~~l~~~~~~~~~~~~eLa~~l~~l~---------~~l~qHm~~EE~qv~PLl~~----~~S~~Eqa---~L~~ 190 (1237)
.++++|++.++.. +..+-+++...+-+|- ..|.+=|..++.-+.|.|.. .++++.+. ..+-
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 5566666665543 2233344444443222 22333344444445566554 34555554 4455
Q ss_pred HHhcccCHHHHHHHHhhhcCCCCHHHHHHHHHHHhhhC
Q 000886 191 QFLCSIPVNMMAEFLPWLSSSISSDEHQDMRKCLCKII 228 (1237)
Q Consensus 191 ~~i~siP~~~m~~~LpWm~~~lsp~Er~~~l~~l~~~~ 228 (1237)
.++.+++++.|..++..++.++++.+-..+...||+..
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 182
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=37.26 E-value=11 Score=39.32 Aligned_cols=26 Identities=27% Similarity=0.837 Sum_probs=18.6
Q ss_pred cceEecccccCCCCCCccccCCCCC--ccccC
Q 000886 1053 MAKYYCGICKFFDDERVVYHCPFCN--LCRVG 1082 (1237)
Q Consensus 1053 ~~~y~C~~C~~~d~~k~~yHC~~Cg--iCR~g 1082 (1237)
-.+-||.+|.+| ++|-|-.|| +|-|+
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 345678888865 578888888 67665
No 183
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=36.88 E-value=20 Score=30.12 Aligned_cols=30 Identities=20% Similarity=0.366 Sum_probs=18.9
Q ss_pred ceecCCCCCCCCCCceeecccCCCCCCccc
Q 000886 1191 EILCNDCDKKGSAPFHWLYHKCGFCGSYNT 1220 (1237)
Q Consensus 1191 ~i~CnDC~~~s~~~~h~lg~kC~~C~SYNT 1220 (1237)
.+.|.+||..-...-..-..+|+.||+.-.
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCGYRIL 32 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCCCeEE
Confidence 467999987643222222568999997543
No 184
>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=36.45 E-value=25 Score=26.47 Aligned_cols=20 Identities=25% Similarity=0.590 Sum_probs=13.9
Q ss_pred CCCCCCCcccCChhhHHHhHH
Q 000886 1153 YICPICSKSLGDMAVYFGMLD 1173 (1237)
Q Consensus 1153 ~~CPiCr~sv~dm~~~~~~lD 1173 (1237)
..||||.+.+ .+....+-+|
T Consensus 2 v~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLD 21 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHH
Confidence 3699999988 4444456666
No 185
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=36.20 E-value=14 Score=41.87 Aligned_cols=54 Identities=22% Similarity=0.524 Sum_probs=36.4
Q ss_pred cccCCCCCCcccccccccCCCcceecCCC-----CccChhhHHHhhhc--------CCCCCCCCccc
Q 000886 1109 REKGLETNCPICCDFLFTSSATVRALPCG-----HFMHSDCFQAYTCS--------HYICPICSKSL 1162 (1237)
Q Consensus 1109 ~e~~~~~~CpICle~lf~s~~~v~~LpCg-----H~fH~~Ci~~wl~~--------~~~CPiCr~sv 1162 (1237)
.+...+.-|=||...=-+.+...-+-||- |..|..|+..|+.. .-+||-|+...
T Consensus 15 ~~~e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEY 81 (293)
T KOG3053|consen 15 DNQELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEY 81 (293)
T ss_pred CccccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchh
Confidence 34455778999986522222222345772 99999999999742 24699999875
No 186
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=35.95 E-value=26 Score=45.03 Aligned_cols=31 Identities=29% Similarity=0.766 Sum_probs=14.8
Q ss_pred ccccccccccCC-CCCCCccCCCCccceEeccccc
Q 000886 1029 MCMRCLKVQPVG-PVCTTLSCSGLSMAKYYCGICK 1062 (1237)
Q Consensus 1029 ~C~~C~~~Q~~~-~~C~~~~C~~~~~~~y~C~~C~ 1062 (1237)
+|..|+.+-|.+ ..|.+ | |..+..-.|..|.
T Consensus 3 ~Cp~Cg~~n~~~akFC~~--C-G~~l~~~~Cp~CG 34 (645)
T PRK14559 3 ICPQCQFENPNNNRFCQK--C-GTSLTHKPCPQCG 34 (645)
T ss_pred cCCCCCCcCCCCCccccc--c-CCCCCCCcCCCCC
Confidence 566666654443 34555 3 5554433344443
No 187
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=35.78 E-value=20 Score=39.56 Aligned_cols=27 Identities=37% Similarity=0.941 Sum_probs=20.7
Q ss_pred CcceecCCCCccChhhHHHhhhcCCCCCCCCc
Q 000886 1129 ATVRALPCGHFMHSDCFQAYTCSHYICPICSK 1160 (1237)
Q Consensus 1129 ~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCr~ 1160 (1237)
+.++--.|+-.||..|+. ...||-|.+
T Consensus 171 ~~~~C~~C~~v~H~~C~~-----~~~CpkC~R 197 (202)
T PF13901_consen 171 TTVRCPKCKSVFHKSCFR-----KKSCPKCAR 197 (202)
T ss_pred CeeeCCcCccccchhhcC-----CCCCCCcHh
Confidence 334456899999999996 267999964
No 188
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=35.07 E-value=29 Score=37.28 Aligned_cols=50 Identities=28% Similarity=0.489 Sum_probs=36.3
Q ss_pred CCCCCCCCcccCChhhHHHhHHHHHhhcCCCh-hhhccCCceecCCCCCCCCCCceee
Q 000886 1152 HYICPICSKSLGDMAVYFGMLDALLASEQLPE-EYRDRCQEILCNDCDKKGSAPFHWL 1208 (1237)
Q Consensus 1152 ~~~CPiCr~sv~dm~~~~~~lD~~i~~~pmP~-ey~~~~~~i~CnDC~~~s~~~~h~l 1208 (1237)
-.+||.|+.++...+. +.....+|+ .|.+......|..||+.-...-||=
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 334445554 4666666788999999888777773
No 189
>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=33.04 E-value=17 Score=33.75 Aligned_cols=10 Identities=30% Similarity=1.152 Sum_probs=6.1
Q ss_pred cceEeccccc
Q 000886 1053 MAKYYCGICK 1062 (1237)
Q Consensus 1053 ~~~y~C~~C~ 1062 (1237)
.+.|||..||
T Consensus 48 AvdYFC~~c~ 57 (70)
T PF07191_consen 48 AVDYFCNHCH 57 (70)
T ss_dssp EEEEE-TTTT
T ss_pred ccceeeccCC
Confidence 3577777776
No 190
>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=32.68 E-value=27 Score=35.93 Aligned_cols=18 Identities=28% Similarity=0.392 Sum_probs=15.6
Q ss_pred cCCCCCCccccCCCCCcc
Q 000886 1062 KFFDDERVVYHCPFCNLC 1079 (1237)
Q Consensus 1062 ~~~d~~k~~yHC~~CgiC 1079 (1237)
||||-.|.+-.|++||.=
T Consensus 18 kFYDLnk~p~vcP~cg~~ 35 (129)
T TIGR02300 18 KFYDLNRRPAVSPYTGEQ 35 (129)
T ss_pred cccccCCCCccCCCcCCc
Confidence 788988999999999954
No 191
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=32.60 E-value=20 Score=41.90 Aligned_cols=21 Identities=14% Similarity=0.366 Sum_probs=15.7
Q ss_pred hhhhchHHHHHHHhhcCCCCC
Q 000886 855 ATKNTMFSEWLNEWWEGPPAP 875 (1237)
Q Consensus 855 a~~~t~f~~WL~eW~~~~~~~ 875 (1237)
|...++....+.|.|+..|.|
T Consensus 84 a~~~K~le~Fv~eFFdQNPiS 104 (378)
T KOG2807|consen 84 ANVIKYLEGFVPEFFDQNPIS 104 (378)
T ss_pred HHHHHHHHHHHHHHhccCchh
Confidence 334467888888999988866
No 192
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=32.02 E-value=38 Score=39.54 Aligned_cols=100 Identities=28% Similarity=0.513 Sum_probs=61.8
Q ss_pred CCCC----CccccCCCCCccccCCCCCc-cccccCCcccccccc--c--ccccccccCCCCCCcccccccccCCCcceec
Q 000886 1064 FDDE----RVVYHCPFCNLCRVGRGLGV-DFFHCMTCNCCLAKK--L--VDHKCREKGLETNCPICCDFLFTSSATVRAL 1134 (1237)
Q Consensus 1064 ~d~~----k~~yHC~~CgiCR~g~gl~~-~~fHC~~C~~C~s~~--l--~~H~C~e~~~~~~CpICle~lf~s~~~v~~L 1134 (1237)
|||= +-+=||..|- --| |-- =||. |+.+.+-. . ..|-=..|.....|-.|-+- .++|.++
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 4555 55555432 2 35655567778899999754 4578889
Q ss_pred CCC--CccChhhHHHhhhc-------------CCC--CC-CCCcccCChhhHHHhHHH
Q 000886 1135 PCG--HFMHSDCFQAYTCS-------------HYI--CP-ICSKSLGDMAVYFGMLDA 1174 (1237)
Q Consensus 1135 pCg--H~fH~~Ci~~wl~~-------------~~~--CP-iCr~sv~dm~~~~~~lD~ 1174 (1237)
+|. |+....|+.-|-.. .|+ || -|-.++..--.+|+.|-+
T Consensus 238 ~Cns~HvtC~dCFr~yc~~Rl~~rqf~~~p~~gyslpc~agc~~s~i~e~HHF~ilg~ 295 (446)
T KOG0006|consen 238 QCNSRHVTCLDCFRLYCVTRLNDRQFVHDPQLGYSLPCVAGCPNSLIKELHHFRILGE 295 (446)
T ss_pred ecCCceeehHHhhhhHhhhcccccccccCccccccccccCCCchHHHHhhhhheecch
Confidence 999 99999999876321 244 44 255665544445666543
No 193
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=31.96 E-value=22 Score=30.90 Aligned_cols=28 Identities=25% Similarity=0.538 Sum_probs=19.9
Q ss_pred CceecCCCCCCCCCCceeecccCCCCCC
Q 000886 1190 QEILCNDCDKKGSAPFHWLYHKCGFCGS 1217 (1237)
Q Consensus 1190 ~~i~CnDC~~~s~~~~h~lg~kC~~C~S 1217 (1237)
..+.|.+||+.-....---+.+|+.||+
T Consensus 5 ~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~ 32 (49)
T COG1996 5 MEYKCARCGREVELDQETRGIRCPYCGS 32 (49)
T ss_pred EEEEhhhcCCeeehhhccCceeCCCCCc
Confidence 3577888888765444455778888887
No 194
>PLN03086 PRLI-interacting factor K; Provisional
Probab=31.74 E-value=27 Score=44.21 Aligned_cols=52 Identities=25% Similarity=0.654 Sum_probs=27.6
Q ss_pred CccccCCCCCccccCC-CCCc------cccccCCcccccccc-ccccc---ccccCCCCCCcccccc
Q 000886 1068 RVVYHCPFCNLCRVGR-GLGV------DFFHCMTCNCCLAKK-LVDHK---CREKGLETNCPICCDF 1123 (1237)
Q Consensus 1068 k~~yHC~~CgiCR~g~-gl~~------~~fHC~~C~~C~s~~-l~~H~---C~e~~~~~~CpICle~ 1123 (1237)
+..+||+.||- .++. .|.+ .-+.|. ||..+... +..|. |.++ ...|+.|...
T Consensus 451 ~~H~~C~~Cgk-~f~~s~LekH~~~~Hkpv~Cp-Cg~~~~R~~L~~H~~thCp~K--pi~C~fC~~~ 513 (567)
T PLN03086 451 KNHVHCEKCGQ-AFQQGEMEKHMKVFHEPLQCP-CGVVLEKEQMVQHQASTCPLR--LITCRFCGDM 513 (567)
T ss_pred ccCccCCCCCC-ccchHHHHHHHHhcCCCccCC-CCCCcchhHHHhhhhccCCCC--ceeCCCCCCc
Confidence 56678888863 1221 0100 124576 76554333 25674 5443 4679999765
No 195
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=31.58 E-value=21 Score=43.07 Aligned_cols=37 Identities=24% Similarity=0.441 Sum_probs=26.2
Q ss_pred CCCCcccccccccCCCcceecCCCCccChhhHHHhhh
Q 000886 1114 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC 1150 (1237)
Q Consensus 1114 ~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~ 1150 (1237)
...|.||............+..|||.|..+|..+++.
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 4679999833233323333679999999999999875
No 196
>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=31.26 E-value=8.1 Score=32.63 Aligned_cols=42 Identities=21% Similarity=0.701 Sum_probs=28.0
Q ss_pred CcccccccccCCCcceecCCCCccChhhHHHhhh------cCCCCCCCC
Q 000886 1117 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC------SHYICPICS 1159 (1237)
Q Consensus 1117 CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~------~~~~CPiCr 1159 (1237)
|+||... .....-+.=-.|+-.||..|+..-.. ..+.||.|+
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 8899873 33333333348999999999865421 367888875
No 197
>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=31.19 E-value=34 Score=27.38 Aligned_cols=23 Identities=26% Similarity=0.953 Sum_probs=16.6
Q ss_pred eEecccccCC-CCCCccccCCCCC
Q 000886 1055 KYYCGICKFF-DDERVVYHCPFCN 1077 (1237)
Q Consensus 1055 ~y~C~~C~~~-d~~k~~yHC~~Cg 1077 (1237)
.|-|.+|.+. +.++.+..|+-||
T Consensus 2 ~~~C~~CG~i~~g~~~p~~CP~Cg 25 (34)
T cd00729 2 VWVCPVCGYIHEGEEAPEKCPICG 25 (34)
T ss_pred eEECCCCCCEeECCcCCCcCcCCC
Confidence 4778888876 4446777777777
No 198
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=31.09 E-value=16 Score=38.75 Aligned_cols=22 Identities=23% Similarity=0.794 Sum_probs=10.9
Q ss_pred EecccccC---CCCC-CccccCCCCC
Q 000886 1056 YYCGICKF---FDDE-RVVYHCPFCN 1077 (1237)
Q Consensus 1056 y~C~~C~~---~d~~-k~~yHC~~Cg 1077 (1237)
|+|+.|+. |++. ..-|+||.||
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 44555552 3333 4456666665
No 199
>PRK07219 DNA topoisomerase I; Validated
Probab=30.72 E-value=70 Score=42.51 Aligned_cols=63 Identities=25% Similarity=0.495 Sum_probs=34.3
Q ss_pred cccccCCCCC----CccccCCCCCcc---ccCCCCCccccccCC---cccccccccccccccccCCCCCCcccccccc
Q 000886 1058 CGICKFFDDE----RVVYHCPFCNLC---RVGRGLGVDFFHCMT---CNCCLAKKLVDHKCREKGLETNCPICCDFLF 1125 (1237)
Q Consensus 1058 C~~C~~~d~~----k~~yHC~~CgiC---R~g~gl~~~~fHC~~---C~~C~s~~l~~H~C~e~~~~~~CpICle~lf 1125 (1237)
|..|+..... .....|+.||-- |.|+. | .|+-|.+ |+.-..+.-..+. ......||-|...+.
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 7888776432 346889999821 22332 3 3888865 6543332211111 123467888866543
No 200
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=30.52 E-value=31 Score=29.22 Aligned_cols=26 Identities=19% Similarity=0.524 Sum_probs=16.4
Q ss_pred ceecCCCCCCCCCCceeecccCCCCCC
Q 000886 1191 EILCNDCDKKGSAPFHWLYHKCGFCGS 1217 (1237)
Q Consensus 1191 ~i~CnDC~~~s~~~~h~lg~kC~~C~S 1217 (1237)
.+.|.+||....... --..+|+.||+
T Consensus 2 ~Y~C~~Cg~~~~~~~-~~~irC~~CG~ 27 (44)
T smart00659 2 IYICGECGRENEIKS-KDVVRCRECGY 27 (44)
T ss_pred EEECCCCCCEeecCC-CCceECCCCCc
Confidence 456888887654431 23567888886
No 201
>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=30.24 E-value=23 Score=31.47 Aligned_cols=27 Identities=26% Similarity=0.752 Sum_probs=20.6
Q ss_pred ccCCceecCCCCCCCCCCceeecccCCCCC
Q 000886 1187 DRCQEILCNDCDKKGSAPFHWLYHKCGFCG 1216 (1237)
Q Consensus 1187 ~~~~~i~CnDC~~~s~~~~h~lg~kC~~C~ 1216 (1237)
+.+..|+|.-||. ..||+--..|..||
T Consensus 11 ~~ktH~~CrRCG~---~syH~qK~~CasCG 37 (55)
T PF01907_consen 11 HNKTHTLCRRCGR---RSYHIQKKTCASCG 37 (55)
T ss_dssp -S-SEEE-TTTSS---EEEETTTTEETTTB
T ss_pred CCccEeeecccCC---eeeecCCCcccccC
Confidence 4557899999998 56888777899999
No 202
>KOG4399 consensus C2HC-type Zn-finger protein [General function prediction only]
Probab=30.22 E-value=13 Score=42.05 Aligned_cols=63 Identities=22% Similarity=0.348 Sum_probs=43.1
Q ss_pred ccccccccccCCCCCCCccCCCCccceEecccccCCCCCCccccCCCCCccccCCCCCccccccCCcccccc
Q 000886 1029 MCMRCLKVQPVGPVCTTLSCSGLSMAKYYCGICKFFDDERVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLA 1100 (1237)
Q Consensus 1029 ~C~~C~~~Q~~~~~C~~~~C~~~~~~~y~C~~C~~~d~~k~~yHC~~CgiCR~g~gl~~~~fHC~~C~~C~s 1100 (1237)
+|..|....- -.|+- | +...++-+|.||.=+|.++ -|||.|.-||--+. ...-||.+|..|..
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 3444444333 24544 3 3345677899999998877 89999999997653 24678888888864
No 203
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=30.06 E-value=18 Score=39.22 Aligned_cols=23 Identities=30% Similarity=1.037 Sum_probs=11.2
Q ss_pred eEecccccC---CCCC-CccccCCCCC
Q 000886 1055 KYYCGICKF---FDDE-RVVYHCPFCN 1077 (1237)
Q Consensus 1055 ~y~C~~C~~---~d~~-k~~yHC~~Cg 1077 (1237)
.|+|+.|+. |++. ...|+||.||
T Consensus 117 ~Y~Cp~C~~rytf~eA~~~~F~Cp~Cg 143 (178)
T PRK06266 117 FFFCPNCHIRFTFDEAMEYGFRCPQCG 143 (178)
T ss_pred EEECCCCCcEEeHHHHhhcCCcCCCCC
Confidence 355555542 3332 3445566555
No 204
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=29.64 E-value=41 Score=28.30 Aligned_cols=8 Identities=38% Similarity=1.344 Sum_probs=3.9
Q ss_pred cccCCCCC
Q 000886 1070 VYHCPFCN 1077 (1237)
Q Consensus 1070 ~yHC~~Cg 1077 (1237)
..+|+.||
T Consensus 21 ~~~Cp~CG 28 (46)
T PRK00398 21 GVRCPYCG 28 (46)
T ss_pred ceECCCCC
Confidence 44555554
No 205
>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=29.50 E-value=17 Score=41.97 Aligned_cols=25 Identities=20% Similarity=0.414 Sum_probs=12.1
Q ss_pred ccChhhHHHhhhcCCCCCCCCcccC
Q 000886 1139 FMHSDCFQAYTCSHYICPICSKSLG 1163 (1237)
Q Consensus 1139 ~fH~~Ci~~wl~~~~~CPiCr~sv~ 1163 (1237)
.++.-|-.+|.....+||.|...=.
T Consensus 198 L~Cs~C~t~W~~~R~~Cp~Cg~~~~ 222 (290)
T PF04216_consen 198 LHCSLCGTEWRFVRIKCPYCGNTDH 222 (290)
T ss_dssp EEETTT--EEE--TTS-TTT---SS
T ss_pred EEcCCCCCeeeecCCCCcCCCCCCC
Confidence 3344678889878889999997643
No 206
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=29.41 E-value=22 Score=43.18 Aligned_cols=19 Identities=16% Similarity=0.469 Sum_probs=14.3
Q ss_pred hHHHhcCHHHHHHHHhhhc
Q 000886 910 NDIFRMNQNELEAEIRKVS 928 (1237)
Q Consensus 910 ~~~~~~~q~~L~~~Ir~i~ 928 (1237)
...+++|+.+||..|++.-
T Consensus 50 ~~llk~~~KqLR~li~~Lr 68 (436)
T KOG2593|consen 50 KELLKFNKKQLRKLIASLR 68 (436)
T ss_pred HHHhcccHHHHHHHHHHhh
Confidence 3456788888888887774
No 207
>KOG4654 consensus Uncharacterized conserved protein [Function unknown]
Probab=29.36 E-value=8.2e+02 Score=27.16 Aligned_cols=55 Identities=18% Similarity=0.097 Sum_probs=33.9
Q ss_pred ChHHHH----HHHHHHHHHHHHHHHHHHhhccCCCCcchHHHHHHHHHHHHHHHHHhhccccccc
Q 000886 43 PILIFL----FFHKAIKSELDVLHRAAMAFATNLGGGGDINKLLERYHFFRAIYKHHCNAEDEVI 103 (1237)
Q Consensus 43 Pi~~~~----~~HkAlR~eL~~l~~~a~~~~~~~gd~~~~~~l~~r~~~L~~~~~~H~~aEDevI 103 (1237)
|+|+|. ++|||+-..-..= -|+-- -=...|++|..-++|+.+....-...||.+-
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 7888875432211 11111 1123677788888888888888888887653
No 208
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=28.88 E-value=29 Score=44.02 Aligned_cols=47 Identities=26% Similarity=0.622 Sum_probs=32.1
Q ss_pred CCCcccccccccCCCcceec---CCCCccChhhHHHhhhc-----CCCCCCCCcccC
Q 000886 1115 TNCPICCDFLFTSSATVRAL---PCGHFMHSDCFQAYTCS-----HYICPICSKSLG 1163 (1237)
Q Consensus 1115 ~~CpICle~lf~s~~~v~~L---pCgH~fH~~Ci~~wl~~-----~~~CPiCr~sv~ 1163 (1237)
..|+||-- +.+...-..+ .||-.+|..|+.-|+.. .-+||-|++..+
T Consensus 19 ~mc~l~~s--~G~~~ag~m~ac~~c~~~yH~~cvt~~~~~~~l~~gWrC~~crvCe~ 73 (694)
T KOG4443|consen 19 LMCPLCGS--SGKGRAGRLLACSDCGQKYHPYCVTSWAQHAVLSGGWRCPSCRVCEA 73 (694)
T ss_pred hhhhhhcc--ccccccCcchhhhhhcccCCcchhhHHHhHHHhcCCcccCCceeeee
Confidence 46778753 2232223333 68999999999999743 468999998763
No 209
>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=28.77 E-value=19 Score=47.00 Aligned_cols=44 Identities=27% Similarity=0.618 Sum_probs=0.0
Q ss_pred cccccccccccCCCCCCCccCCCCccceEecccccCCCCCCccccCCCCC
Q 000886 1028 MMCMRCLKVQPVGPVCTTLSCSGLSMAKYYCGICKFFDDERVVYHCPFCN 1077 (1237)
Q Consensus 1028 v~C~~C~~~Q~~~~~C~~~~C~~~~~~~y~C~~C~~~d~~k~~yHC~~Cg 1077 (1237)
-.|..|+++. ....|.. |++...-.|+|..|+.--++. +|+.||
T Consensus 656 r~Cp~Cg~~t-~~~~Cp~--CG~~T~~~~~Cp~C~~~~~~~---~C~~C~ 699 (900)
T PF03833_consen 656 RRCPKCGKET-FYNRCPE--CGSHTEPVYVCPDCGIEVEED---ECPKCG 699 (900)
T ss_dssp --------------------------------------------------
T ss_pred ccCcccCCcc-hhhcCcc--cCCccccceeccccccccCcc---cccccc
Confidence 3455555542 2334543 433345556666665422111 555555
No 210
>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=28.70 E-value=41 Score=41.19 Aligned_cols=31 Identities=23% Similarity=0.356 Sum_probs=17.9
Q ss_pred HHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHH
Q 000886 918 NELEAEIRKVSRDSTLDPRRKAYLIQNLMTSRW 950 (1237)
Q Consensus 918 ~~L~~~Ir~i~~~~~l~~~~ka~liq~Lm~~~~ 950 (1237)
..|+..||.|--. .+.+..-...|+++-.|-
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 3466777777533 444445556677665553
No 211
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=28.65 E-value=28 Score=38.71 Aligned_cols=39 Identities=38% Similarity=0.755 Sum_probs=27.0
Q ss_pred CcccccccccCCCcceecCCCCccC-hhhHHHhhhcCCCCCCCCcccC
Q 000886 1117 CPICCDFLFTSSATVRALPCGHFMH-SDCFQAYTCSHYICPICSKSLG 1163 (1237)
Q Consensus 1117 CpICle~lf~s~~~v~~LpCgH~fH-~~Ci~~wl~~~~~CPiCr~sv~ 1163 (1237)
|-+|.+. ...|..+||-|..+ ..|-.. -.+||||+....
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 23478889997654 466532 456999997653
No 212
>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 PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=28.33 E-value=56 Score=37.34 Aligned_cols=93 Identities=29% Similarity=0.707 Sum_probs=0.0
Q ss_pred ccccc-CCCCC----CccccCCCCC----ccccCCCCCccccccCCcccccccccccccccccCCCCCCcc--ccccccc
Q 000886 1058 CGICK-FFDDE----RVVYHCPFCN----LCRVGRGLGVDFFHCMTCNCCLAKKLVDHKCREKGLETNCPI--CCDFLFT 1126 (1237)
Q Consensus 1058 C~~C~-~~d~~----k~~yHC~~Cg----iCR~g~gl~~~~fHC~~C~~C~s~~l~~H~C~e~~~~~~CpI--Cle~lf~ 1126 (1237)
|.+|. ++|=+ ..+-.|..|+ |=.-..| +.|.-|. ||+-+ .|.+.+..-.||- |.--+.-
T Consensus 68 CrVCq~~I~i~gk~~QhVVkC~~CnEATPIr~aPpG--KKYVRCP-CNCLL-------ICk~sS~rIaCPRp~CkRiI~L 137 (256)
T PF09788_consen 68 CRVCQSLIDIEGKMHQHVVKCSVCNEATPIRNAPPG--KKYVRCP-CNCLL-------ICKSSSQRIACPRPNCKRIINL 137 (256)
T ss_pred eecCCceecccCccceeeEECCCCCccccccCCCCC--CeeEecC-CceEE-------EeecccccccCCCCCCcceEEe
Q ss_pred CCC-------------cceecCCCCccChhhHHHhh-hcCCCCCCCCc
Q 000886 1127 SSA-------------TVRALPCGHFMHSDCFQAYT-CSHYICPICSK 1160 (1237)
Q Consensus 1127 s~~-------------~v~~LpCgH~fH~~Ci~~wl-~~~~~CPiCr~ 1160 (1237)
... ....+.|||---.-=+.... ..--+||-|||
T Consensus 138 ~~~~~~p~~~~~~~~p~~~rv~CghC~~~Fl~~~~~~~tlARCPHCrK 185 (256)
T PF09788_consen 138 GPSHQGPVTPPVPTQPGSCRVICGHCSNTFLFNTLTSNTLARCPHCRK 185 (256)
T ss_pred CCccCCCCCCCCCCCCCceeEECCCCCCcEeccCCCCCccccCCCCce
No 214
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=28.07 E-value=30 Score=43.76 Aligned_cols=57 Identities=21% Similarity=0.279 Sum_probs=25.0
Q ss_pred ChhhHHHhHHHHHhhcCCChhhhccCCceecCCCCCCCCCCceeecccCCCCCCccccccccc
Q 000886 1164 DMAVYFGMLDALLASEQLPEEYRDRCQEILCNDCDKKGSAPFHWLYHKCGFCGSYNTRVIKVE 1226 (1237)
Q Consensus 1164 dm~~~~~~lD~~i~~~pmP~ey~~~~~~i~CnDC~~~s~~~~h~lg~kC~~C~SYNT~~~~~~ 1226 (1237)
+.+.....++.......+|-- .-....-.|++||..... +.+|+.|||-|+.+++..
T Consensus 465 n~~al~~lv~~~~~~~~i~Y~-~in~~~~~C~~CG~~~~~-----~~~CP~CGs~~~~~~~Rv 521 (546)
T PF13597_consen 465 NPEALEKLVRYAMENTGIPYF-TINPPIDICPDCGYIGGE-----GDKCPKCGSENIEVYSRV 521 (546)
T ss_dssp -HHHHHHHHHHHHH--H-SEE-EEE--EEEETTT---S-------EEE-CCC----EEEEB-S
T ss_pred CHHHHHHHHHHHHHhCCCCeE-EEecCcccccCCCcCCCC-----CCCCCCCCCcccceEEEe
Confidence 555566666666654555422 112234579999986543 348999999998776543
No 215
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=28.05 E-value=35 Score=35.47 Aligned_cols=48 Identities=29% Similarity=0.694 Sum_probs=34.1
Q ss_pred CCCCCcccccccccCCCcceec-C---CCCccChhhHHH-hh--hcCCCCCCCCcccCC
Q 000886 1113 LETNCPICCDFLFTSSATVRAL-P---CGHFMHSDCFQA-YT--CSHYICPICSKSLGD 1164 (1237)
Q Consensus 1113 ~~~~CpICle~lf~s~~~v~~L-p---CgH~fH~~Ci~~-wl--~~~~~CPiCr~sv~d 1164 (1237)
.--.|-||.|- |.+ -+.| | ||=.+...|+-. |- .....||+|+.|+-.
T Consensus 79 ~lYeCnIC~et---S~e-e~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKs 133 (140)
T PF05290_consen 79 KLYECNICKET---SAE-ERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKS 133 (140)
T ss_pred CceeccCcccc---cch-hhcCCcccccchHHHHHHHHHHHHHcccCCCCCcccccccc
Confidence 34679999875 332 3444 3 899999999876 63 235789999998754
No 216
>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=27.19 E-value=58 Score=30.25 Aligned_cols=18 Identities=44% Similarity=1.139 Sum_probs=13.5
Q ss_pred cccCCCCCccccCCCCCcccc
Q 000886 1070 VYHCPFCNLCRVGRGLGVDFF 1090 (1237)
Q Consensus 1070 ~yHC~~CgiCR~g~gl~~~~f 1090 (1237)
-|||. +|-+-+|||+.|.
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 46765 7788899998764
No 217
>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=27.12 E-value=54 Score=41.55 Aligned_cols=56 Identities=21% Similarity=0.279 Sum_probs=33.8
Q ss_pred ChhhHHHhHHHHHhhcCCChhhhccCCceecCCCCCCCCCCceeecccCCCCCCcccccccc
Q 000886 1164 DMAVYFGMLDALLASEQLPEEYRDRCQEILCNDCDKKGSAPFHWLYHKCGFCGSYNTRVIKV 1225 (1237)
Q Consensus 1164 dm~~~~~~lD~~i~~~pmP~ey~~~~~~i~CnDC~~~s~~~~h~lg~kC~~C~SYNT~~~~~ 1225 (1237)
+.+.....++......-++ -..+.... .|++||.... -.+.+|+.|||-|+.+++.
T Consensus 493 n~~al~~lv~~a~~~~~~y-~~~~~p~~-~C~~CG~~~~----~~~~~CP~CGs~~~~~~~R 548 (555)
T cd01675 493 NPEALEALVKKAAKRGVIY-FGINTPID-ICNDCGYIGE----GEGFKCPKCGSEDVEVISR 548 (555)
T ss_pred CHHHHHHHHHHHHHcCCce-EEEecCCc-cCCCCCCCCc----CCCCCCcCCCCcCceEEEe
Confidence 4555556666654432222 12333344 8999997543 2356999999988766543
No 218
>PLN02189 cellulose synthase
Probab=27.12 E-value=48 Score=44.55 Aligned_cols=52 Identities=21% Similarity=0.399 Sum_probs=35.7
Q ss_pred cCCCCCCcccccccccCCCcceec---CCCCccChhhHHHhh--hcCCCCCCCCcccC
Q 000886 1111 KGLETNCPICCDFLFTSSATVRAL---PCGHFMHSDCFQAYT--CSHYICPICSKSLG 1163 (1237)
Q Consensus 1111 ~~~~~~CpICle~lf~s~~~v~~L---pCgH~fH~~Ci~~wl--~~~~~CPiCr~sv~ 1163 (1237)
+.....|.||.|++-...+.-... -||--.++.|+ ++. ..+..||-|+...-
T Consensus 31 ~~~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cy-eyer~eg~q~CpqCkt~Y~ 87 (1040)
T PLN02189 31 NLDGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCY-EYERREGTQNCPQCKTRYK 87 (1040)
T ss_pred cccCccccccccccCcCCCCCEEEeeccCCCccccchh-hhhhhcCCccCcccCCchh
Confidence 344568999999865333322222 47788999999 554 34688999997763
No 219
>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=27.06 E-value=3e+02 Score=27.33 Aligned_cols=61 Identities=21% Similarity=0.114 Sum_probs=35.9
Q ss_pred HHHhhhhhHHHHHHHHHHHHHhhccCchHHHHHHHHHHHHHHHHHHHhHHHHHHHHh----hHHHhcCCHHHHHHHHHHH
Q 000886 117 TYSLEHEGESVLFDQLFELLNSSMRNEESYRRELASCTGALQTSISQHMSKEEEQVF----PLLIEKFSFEEQASLVWQF 192 (1237)
Q Consensus 117 ~~~~EH~~~~~lf~~l~~~l~~~~~~~~~~~~eLa~~l~~l~~~l~qHm~~EE~qv~----PLl~~~~S~~Eqa~L~~~~ 192 (1237)
.+..||++.=+++.+|..++.. ...+..|..-...|+..||.-.- |-+..| +..+.+|
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 4455565544444444444432 34567777788899999998654 444433 5555666
Q ss_pred hcc
Q 000886 193 LCS 195 (1237)
Q Consensus 193 i~s 195 (1237)
+..
T Consensus 76 ~~~ 78 (113)
T cd00522 76 VEK 78 (113)
T ss_pred HHH
Confidence 544
No 220
>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=26.78 E-value=42 Score=28.94 Aligned_cols=10 Identities=40% Similarity=1.261 Sum_probs=7.1
Q ss_pred eEecccccCC
Q 000886 1055 KYYCGICKFF 1064 (1237)
Q Consensus 1055 ~y~C~~C~~~ 1064 (1237)
+|.|.+|.+.
T Consensus 1 ky~C~~Cgyv 10 (47)
T PF00301_consen 1 KYQCPVCGYV 10 (47)
T ss_dssp EEEETTTSBE
T ss_pred CcCCCCCCEE
Confidence 5778888763
No 221
>PF06937 EURL: EURL protein; InterPro: IPR009704 This family consists of several animal EURL proteins. EURL is preferentially expressed in chick retinal precursor cells as well as in the anterior epithelial cells of the lens at early stages of development. EURL transcripts are found primarily in the peripheral dorsal retina, i.e., the most undifferentiated part of the dorsal retina. EURL transcripts are also detected in the lens at stage 18 and remain abundant in the proliferating epithelial cells of the lens until at least day 11. The distribution pattern of EURL in the developing retina and lens suggest a role before the events leading to cell determination and differentiation [].
Probab=25.87 E-value=42 Score=38.54 Aligned_cols=45 Identities=24% Similarity=0.469 Sum_probs=26.2
Q ss_pred cCCCCCCcccccccccCCCcceecC-C-CCccChhhHHHh-hhcCCCCC
Q 000886 1111 KGLETNCPICCDFLFTSSATVRALP-C-GHFMHSDCFQAY-TCSHYICP 1156 (1237)
Q Consensus 1111 ~~~~~~CpICle~lf~s~~~v~~Lp-C-gH~fH~~Ci~~w-l~~~~~CP 1156 (1237)
+.+-.-|+||.|- ...+.+-..|. = .=-=|++||.+| +--+..||
T Consensus 27 ~~tLsfChiCfEl-~iegvpks~llHtkSlRGHrdCFEK~HlIanQ~~p 74 (285)
T PF06937_consen 27 TETLSFCHICFEL-SIEGVPKSNLLHTKSLRGHRDCFEKYHLIANQDCP 74 (285)
T ss_pred ccceeecceeecc-ccccCccccccccccccchHHHHHHHHHHHcCCCC
Confidence 3445678888874 43332222111 0 002389999999 45688999
No 222
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=25.80 E-value=39 Score=38.35 Aligned_cols=77 Identities=19% Similarity=0.513 Sum_probs=50.1
Q ss_pred ccccccccccccCC--------cccCcccccccCCCCCc----cccccccccccccccccCCCCCCCccCCCCccceEec
Q 000886 991 YKRNCKLRAACCGK--------LFTCRFCHDKVSDHSMD----RKATTEMMCMRCLKVQPVGPVCTTLSCSGLSMAKYYC 1058 (1237)
Q Consensus 991 Y~r~c~l~~~cC~~--------~y~Cr~CHde~~~H~~~----r~~~~~v~C~~C~~~Q~~~~~C~~~~C~~~~~~~y~C 1058 (1237)
|+..=...|.-|+. .|.|..||.-..+-++. -+......|..|+++-....+=+ -++-||
T Consensus 115 ~rnqgr~LC~~Cn~k~Ka~~~g~YvC~KCh~~iD~~~l~fr~d~yH~yHFkCt~C~keL~sdaRev--------k~eLyC 186 (332)
T KOG2272|consen 115 YRNQGRALCRECNQKEKAKGRGRYVCQKCHAHIDEQPLTFRGDPYHPYHFKCTTCGKELTSDAREV--------KGELYC 186 (332)
T ss_pred HhhcchHHhhhhhhhhcccccceeehhhhhhhcccccccccCCCCCccceecccccccccchhhhh--------ccceec
Confidence 33333455656643 79999999886654433 23345788999998877644322 456788
Q ss_pred ccccCCCCCCccccCCCCCcccc
Q 000886 1059 GICKFFDDERVVYHCPFCNLCRV 1081 (1237)
Q Consensus 1059 ~~C~~~d~~k~~yHC~~CgiCR~ 1081 (1237)
.-|. +.+-|+-||-||.
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 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=25.79 E-value=40 Score=34.81 Aligned_cols=32 Identities=16% Similarity=0.104 Sum_probs=23.0
Q ss_pred ccccccccCCcccCcccccccCCCCCccccccccccccccccccCC
Q 000886 995 CKLRAACCGKLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVG 1040 (1237)
Q Consensus 995 c~l~~~cC~~~y~Cr~CHde~~~H~~~r~~~~~v~C~~C~~~Q~~~ 1040 (1237)
-|-.||.||+-|= -+.| ..++|.+|++.|++.
T Consensus 8 tKr~Cp~cg~kFY-----------DLnk---~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 8 TKRICPNTGSKFY-----------DLNR---RPAVSPYTGEQFPPE 39 (129)
T ss_pred ccccCCCcCcccc-----------ccCC---CCccCCCcCCccCcc
Confidence 3567888987441 1333 589999999999886
No 224
>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=25.77 E-value=26 Score=28.72 Aligned_cols=13 Identities=46% Similarity=1.185 Sum_probs=5.5
Q ss_pred cceEecccccCCC
Q 000886 1053 MAKYYCGICKFFD 1065 (1237)
Q Consensus 1053 ~~~y~C~~C~~~d 1065 (1237)
|.+|||+-|+.|=
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 225
>COG0143 MetG Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=25.66 E-value=42 Score=42.51 Aligned_cols=44 Identities=25% Similarity=0.456 Sum_probs=33.7
Q ss_pred ccceEecccccCCCCC-CccccCCCCCccccCCCCCccccccCCccccccc
Q 000886 1052 SMAKYYCGICKFFDDE-RVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLAK 1101 (1237)
Q Consensus 1052 ~~~~y~C~~C~~~d~~-k~~yHC~~CgiCR~g~gl~~~~fHC~~C~~C~s~ 1101 (1237)
...-+||..|.-|=.| .-.=.|++||.+..++ -+|+.||.++.-
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 3556788888877665 3444699999999885 489999999764
No 226
>PRK00366 ispG 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed
Probab=25.59 E-value=60 Score=38.84 Aligned_cols=53 Identities=17% Similarity=0.268 Sum_probs=42.6
Q ss_pred CCCCCCCcccCChhhHHHhHHHHHhhcCCChhhhccCCceec--CCCCCCCCCCceeec
Q 000886 1153 YICPICSKSLGDMAVYFGMLDALLASEQLPEEYRDRCQEILC--NDCDKKGSAPFHWLY 1209 (1237)
Q Consensus 1153 ~~CPiCr~sv~dm~~~~~~lD~~i~~~pmP~ey~~~~~~i~C--nDC~~~s~~~~h~lg 1209 (1237)
..||.|++...|....-..+++.+...++| -+....=| |.|++....++=+.|
T Consensus 269 isCPgCgR~~~D~~~la~~vee~~~~~~~P----lkIAVmGC~VNgpGEa~~aDIGIaG 323 (360)
T PRK00366 269 ISCPTCGRTEFDVIQELAEVEQRLEHIKMP----LKVAVMGCVVNGPGEAKEADIGIAG 323 (360)
T ss_pred EECCCCCCCcccHHHHHHHHHHHhcCCCCC----cEEEEeCCCCCCCCchhhCcEeEec
Confidence 469999999999988889999999988888 34455668 999988777665543
No 227
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=25.44 E-value=1.4e+02 Score=30.28 Aligned_cols=45 Identities=22% Similarity=0.323 Sum_probs=26.5
Q ss_pred CCCCcccccccccCCC-----------cceecCCCCccChhhHHHhhhcCCCCCCCC
Q 000886 1114 ETNCPICCDFLFTSSA-----------TVRALPCGHFMHSDCFQAYTCSHYICPICS 1159 (1237)
Q Consensus 1114 ~~~CpICle~lf~s~~-----------~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCr 1159 (1237)
...|--|+.. |.... ...--.|++.|..+|---+-..=.+||-|.
T Consensus 55 ~~~C~~C~~~-f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~CPGC~ 110 (112)
T TIGR00622 55 SRFCFGCQGP-FPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHESLHCCPGCI 110 (112)
T ss_pred CCcccCcCCC-CCCcccccccccccccceeCCCCCCccccccchhhhhhccCCcCCC
Confidence 3469999887 33210 112346777787777544444445677775
No 228
>PRK00420 hypothetical protein; Validated
Probab=25.16 E-value=42 Score=34.00 Aligned_cols=30 Identities=30% Similarity=0.665 Sum_probs=21.5
Q ss_pred CCCCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcccC
Q 000886 1113 LETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1163 (1237)
Q Consensus 1113 ~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCr~sv~ 1163 (1237)
....||+|.-+||...+ ....||.|+..+.
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 35789999988875221 3567999998764
No 229
>PLN02436 cellulose synthase A
Probab=24.99 E-value=55 Score=44.10 Aligned_cols=53 Identities=19% Similarity=0.447 Sum_probs=36.3
Q ss_pred ccCCCCCCcccccccccCCCcceec---CCCCccChhhHHHhhh--cCCCCCCCCcccC
Q 000886 1110 EKGLETNCPICCDFLFTSSATVRAL---PCGHFMHSDCFQAYTC--SHYICPICSKSLG 1163 (1237)
Q Consensus 1110 e~~~~~~CpICle~lf~s~~~v~~L---pCgH~fH~~Ci~~wl~--~~~~CPiCr~sv~ 1163 (1237)
.......|.||.|++-...+.-... -||--.++.|+ ++.+ .+..||-|+...-
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 3344569999999974443333333 46777999999 5543 4688999997753
No 230
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=24.63 E-value=46 Score=32.99 Aligned_cols=33 Identities=15% Similarity=0.624 Sum_probs=0.0
Q ss_pred ccccCCCCC----ccccCCCCCccccccCCccccccccc
Q 000886 1069 VVYHCPFCN----LCRVGRGLGVDFFHCMTCNCCLAKKL 1103 (1237)
Q Consensus 1069 ~~yHC~~Cg----iCR~g~gl~~~~fHC~~C~~C~s~~l 1103 (1237)
.+|+|++|| .|.+++ |.-...|.+||.-+....
T Consensus 20 t~f~CP~Cge~~v~v~~~k--~~~h~~C~~CG~y~~~~V 56 (99)
T PRK14892 20 KIFECPRCGKVSISVKIKK--NIAIITCGNCGLYTEFEV 56 (99)
T ss_pred cEeECCCCCCeEeeeecCC--CcceEECCCCCCccCEEC
No 231
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=24.56 E-value=47 Score=28.27 Aligned_cols=22 Identities=36% Similarity=0.747 Sum_probs=15.0
Q ss_pred cCCCCCCcccccccccCCCCccc
Q 000886 1211 KCGFCGSYNTRVIKVESTNTYCS 1233 (1237)
Q Consensus 1211 kC~~C~SYNT~~~~~~~~~~~~~ 1233 (1237)
||+.||-||-..- +.=.+.+|+
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 7999999996553 333455665
No 232
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=24.54 E-value=58 Score=37.66 Aligned_cols=48 Identities=27% Similarity=0.710 Sum_probs=37.9
Q ss_pred CCCccceEecccccCCCCCCccccCCCCCccccCCCCCccccccCCcccccccc
Q 000886 1049 SGLSMAKYYCGICKFFDDERVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLAKK 1102 (1237)
Q Consensus 1049 ~~~~~~~y~C~~C~~~d~~k~~yHC~~CgiCR~g~gl~~~~fHC~~C~~C~s~~ 1102 (1237)
.|....-+||+.|+++-. +-..||.-||.|-.+- --||.=-|.|+...
T Consensus 107 ~~~~~~~~~C~~C~~~rP-pRs~HCsvC~~CV~rf-----DHHC~WvnnCVG~r 154 (299)
T KOG1311|consen 107 NGIQVEWKYCDTCQLYRP-PRSSHCSVCNNCVLRF-----DHHCPWLNNCIGER 154 (299)
T ss_pred CCcccceEEcCcCcccCC-CCcccchhhccccccc-----CCCCCCccceECCC
Confidence 366778899999999955 4578999999997763 37998888887644
No 233
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=24.38 E-value=50 Score=42.47 Aligned_cols=45 Identities=24% Similarity=0.597 Sum_probs=33.0
Q ss_pred CCCcccccccccCCCcceecCCCC-ccChhhHHHhh--hc----CCCCCCCCcccC
Q 000886 1115 TNCPICCDFLFTSSATVRALPCGH-FMHSDCFQAYT--CS----HYICPICSKSLG 1163 (1237)
Q Consensus 1115 ~~CpICle~lf~s~~~v~~LpCgH-~fH~~Ci~~wl--~~----~~~CPiCr~sv~ 1163 (1237)
.+|+||-.. .+.+..-.||| .....|.-... .. ...||+|+..+.
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 379999754 33455668999 89999987763 23 466899999764
No 234
>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=24.12 E-value=3.6e+02 Score=27.03 Aligned_cols=96 Identities=14% Similarity=0.198 Sum_probs=0.0
Q ss_pred hhHHhHHHHHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhhCCHHHHH-----
Q 000886 361 SFAQEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPLARRHFSPKRQR----- 435 (1237)
Q Consensus 361 ~me~EH~~ie~l~e~l~~ll~~~~~a~~~~~~~~~~~eLa~~le~L~~~L~~H~~~EE~qvfPLl~~~fS~eEq~----- 435 (1237)
.|+..+..||..-.+|..++..+..+. . ...++.|..-...||..||.-.-..-=..+..-...
T Consensus 10 ~~~~G~~~ID~qH~~L~~lin~l~~~~---------~--~~~l~~L~~y~~~HF~~EE~lM~~~~yp~~~~H~~~H~~f~ 78 (115)
T TIGR00058 10 SFKVFYDNLDEEHKTLFNGIFALAADN---------S--ATALKELIDVTVLHFLDEEAMMIAANYSDYDEHKKAHDDFL 78 (115)
T ss_pred hhhcCCHHHHHHHHHHHHHHHHHHhcc---------h--HHHHHHHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHH
Q ss_pred HHHHhHhhcCCHHHHHHHHhhhhCCCCHHHHH
Q 000886 436 ELLYQSLCVMPLKLIECVLPWLVGSLSEEEAR 467 (1237)
Q Consensus 436 ~L~~~~l~smPl~~L~~vLPWl~~~Ls~~E~~ 467 (1237)
+-+..+......+++..+-.|++.++--..++
T Consensus 79 ~~l~~~~~~~~~~~~~~l~~Wl~~HI~~~D~~ 110 (115)
T TIGR00058 79 AVLRGLKAPVPQDDLLYAKDWLVNHIKTTDFK 110 (115)
T ss_pred HHHHHHHHHhhHHHHHHHHHHHHHHhHHHHHH
No 235
>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=24.08 E-value=34 Score=29.33 Aligned_cols=40 Identities=30% Similarity=0.756 Sum_probs=28.6
Q ss_pred CcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcccCChh
Q 000886 1117 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGDMA 1166 (1237)
Q Consensus 1117 CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCr~sv~dm~ 1166 (1237)
|+.|...+... .+.+..=|..||..|+ +|-.|++++.+..
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 67788876533 2332356899999887 8999999987654
No 236
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=24.06 E-value=34 Score=43.13 Aligned_cols=44 Identities=25% Similarity=0.754 Sum_probs=36.1
Q ss_pred CCCCCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcccC
Q 000886 1112 GLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1163 (1237)
Q Consensus 1112 ~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCr~sv~ 1163 (1237)
..+.+|.||++.+ ..+.-+|- |..|+.+|+.....||.|++.+.
T Consensus 477 ~~~~~~~~~~~~~-----~~~~~~~~---~~~~l~~~~~~~~~~pl~~~~~~ 520 (543)
T KOG0802|consen 477 EPNDVCAICYQEM-----SARITPCS---HALCLRKWLYVQEVCPLCHTYMK 520 (543)
T ss_pred cccCcchHHHHHH-----Hhcccccc---chhHHHhhhhhccccCCCchhhh
Confidence 3468999999986 23455677 99999999999999999998764
No 237
>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]
Probab=23.93 E-value=35 Score=37.95 Aligned_cols=28 Identities=36% Similarity=0.765 Sum_probs=21.2
Q ss_pred eecCCCCccChhhHHHhhhcCCCCCCCC
Q 000886 1132 RALPCGHFMHSDCFQAYTCSHYICPICS 1159 (1237)
Q Consensus 1132 ~~LpCgH~fH~~Ci~~wl~~~~~CPiCr 1159 (1237)
+--.||=-||..|+..++.....||-|+
T Consensus 196 rCg~c~i~~h~~c~qty~q~~~~cphc~ 223 (235)
T KOG4718|consen 196 RCGSCNIQYHRGCIQTYLQRRDICPHCG 223 (235)
T ss_pred ccCcccchhhhHHHHHHhcccCcCCchh
Confidence 3345666788888888888888888885
No 238
>KOG3896 consensus Dynactin, subunit p62 [Cell motility]
Probab=23.86 E-value=31 Score=40.56 Aligned_cols=49 Identities=24% Similarity=0.683 Sum_probs=28.8
Q ss_pred CcccccccccccccccccCCCCCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcccCC
Q 000886 1094 TCNCCLAKKLVDHKCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1164 (1237)
Q Consensus 1094 ~C~~C~s~~l~~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCr~sv~d 1164 (1237)
+|+-|+.-..++| -||-|||.+-......+.-.|. +.+-||-|...+..
T Consensus 34 rc~~Cv~hEvdsh---------fCp~CLEn~ps~EArlKKn~CA-------------nCfDCP~C~htLSa 82 (449)
T KOG3896|consen 34 RCDDCVLHEVDSH---------FCPRCLENSPSPEARLKKNKCA-------------NCFDCPKCAHTLSA 82 (449)
T ss_pred ccccccccccccc---------cchhhccCCCchHHHhhhcccc-------------ccccCcchhhhhhh
Confidence 4677766555555 4889999854322222222333 34579999887653
No 239
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=23.60 E-value=83 Score=37.15 Aligned_cols=102 Identities=27% Similarity=0.422 Sum_probs=51.6
Q ss_pred CccceEecccccCCCCCCccccCCCCCccccC-CCCCccccccCCccccccccc-ccccccccCCCCCCcccccccccCC
Q 000886 1051 LSMAKYYCGICKFFDDERVVYHCPFCNLCRVG-RGLGVDFFHCMTCNCCLAKKL-VDHKCREKGLETNCPICCDFLFTSS 1128 (1237)
Q Consensus 1051 ~~~~~y~C~~C~~~d~~k~~yHC~~CgiCR~g-~gl~~~~fHC~~C~~C~s~~l-~~H~C~e~~~~~~CpICle~lf~s~ 1128 (1237)
..-|-|+|+.||--== .-+-.|+-|+.=-|- ..|-..|-|= ++..- ..-.=.++-....|-.|.+.+.++
T Consensus 272 ~~~~Gy~CP~CkakvC-sLP~eCpiC~ltLVss~hLARSyhhL------~PL~~F~Eip~~~~~~~~~Cf~C~~~~~~~- 343 (378)
T KOG2807|consen 272 LSGGGYFCPQCKAKVC-SLPIECPICSLTLVSSPHLARSYHHL------FPLKPFVEIPETEYNGSRFCFACQGELLSS- 343 (378)
T ss_pred cccCceeCCcccCeee-cCCccCCccceeEecchHHHHHHHhh------cCCcchhhccccccCCCcceeeeccccCCC-
Confidence 4567788888874210 123344544443332 2222233331 12111 111111222344599997764433
Q ss_pred CcceecCCCCccChhhHHHhhhcCCCCCCCCc
Q 000886 1129 ATVRALPCGHFMHSDCFQAYTCSHYICPICSK 1160 (1237)
Q Consensus 1129 ~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCr~ 1160 (1237)
...+--.|.++|+.+|-.---.+--.||-|..
T Consensus 344 ~~y~C~~Ck~~FCldCDv~iHesLh~CpgCeh 375 (378)
T KOG2807|consen 344 GRYRCESCKNVFCLDCDVFIHESLHNCPGCEH 375 (378)
T ss_pred CcEEchhccceeeccchHHHHhhhhcCCCcCC
Confidence 33555678999999995332233467999874
No 240
>PF09328 Phytochelatin_C: Domain of unknown function (DUF1984); InterPro: IPR015407 This entry represents the C-terminal region of plant phytochelatin synthases (also known as glutathione gamma-glutamylcysteinyltransferase; 2.3.2.15 from EC), which is involved in the synthesis of phytochelatins (PC) and homophytochelatins (hPC), the heavy-metal-binding peptides of plants. This enzyme is required for detoxification of heavy metals such as cadmium and arsenate. The N-terminal region of phytochelatin synthase contains the active site, as well as four highly conserved cysteine residues that appear to play an important role in heavy-metal-induced phytochelatin catalysis. The C-terminal region is rich in cysteines, and may act as a metal sensor, whereby the Cys residues bind cadmium ions to bring them into closer proximity and transferring them to the activation site in the N-terminal catalytic domain []. The C-terminal region displays homology to the functional domains of metallothionein and metallochaperone.; GO: 0016756 glutathione gamma-glutamylcysteinyltransferase activity, 0046872 metal ion binding, 0010038 response to metal ion, 0046938 phytochelatin biosynthetic process
Probab=23.56 E-value=3.1e+02 Score=31.68 Aligned_cols=74 Identities=26% Similarity=0.541 Sum_probs=55.8
Q ss_pred HHhhHHHhcCCHHHHHHHHHHHhcccCHHHHHHHHhhhc---------CCCCHHHHHHHHHHHhhhCCchhHHHHH----
Q 000886 171 QVFPLLIEKFSFEEQASLVWQFLCSIPVNMMAEFLPWLS---------SSISSDEHQDMRKCLCKIIPKEKLLRQV---- 237 (1237)
Q Consensus 171 qv~PLl~~~~S~~Eqa~L~~~~i~siP~~~m~~~LpWm~---------~~lsp~Er~~~l~~l~~~~P~e~~lq~v---- 237 (1237)
+-+|.|-+-=+.....++....+.|.|.+. ..|+-|++ +.||.+|...+-- +++.||||
T Consensus 26 eDvP~LLkse~v~~v~~vls~vf~SlPsn~-~~FIKWVaEVRR~Edg~~~LS~EEk~RL~l-------Ke~VL~Qvr~T~ 97 (264)
T PF09328_consen 26 EDVPRLLKSEDVKDVEEVLSVVFKSLPSNF-GEFIKWVAEVRRQEDGGSSLSKEEKERLAL-------KEEVLQQVRETE 97 (264)
T ss_pred HHHHHHhhhcccCcHHHHHHHHHhcCchhH-HHHhhhheeEEecccCCCCCCHHHHHHHHH-------HHHHHHHHHhch
Confidence 346888777788888888999999998775 67999998 5699999876532 36667765
Q ss_pred ----HHHHhcCCccCCCcc
Q 000886 238 ----IFAWMEGVKVSDKSC 252 (1237)
Q Consensus 238 ----~~~Wl~~~~~~~~~~ 252 (1237)
|..||...++.+++|
T Consensus 98 LFk~V~~~L~s~~s~c~~~ 116 (264)
T PF09328_consen 98 LFKHVTKWLSSSNSCCCNC 116 (264)
T ss_pred HHHHHHHHHhccccccccc
Confidence 889999766555444
No 241
>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=23.42 E-value=30 Score=33.68 Aligned_cols=26 Identities=38% Similarity=1.063 Sum_probs=15.0
Q ss_pred CccccCCCCC---ccccCCCCCccccccCCccc
Q 000886 1068 RVVYHCPFCN---LCRVGRGLGVDFFHCMTCNC 1097 (1237)
Q Consensus 1068 k~~yHC~~Cg---iCR~g~gl~~~~fHC~~C~~ 1097 (1237)
+.-|.|++|| +=|++-| ..+|.+|+.
T Consensus 33 ~~ky~Cp~Cgk~~vkR~a~G----IW~C~~C~~ 61 (90)
T PF01780_consen 33 HAKYTCPFCGKTSVKRVATG----IWKCKKCGK 61 (90)
T ss_dssp HS-BEESSSSSSEEEEEETT----EEEETTTTE
T ss_pred hCCCcCCCCCCceeEEeeeE----EeecCCCCC
Confidence 4556777777 3344433 577777764
No 242
>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=23.35 E-value=39 Score=26.11 Aligned_cols=11 Identities=27% Similarity=1.081 Sum_probs=8.6
Q ss_pred ceEecccccCC
Q 000886 1054 AKYYCGICKFF 1064 (1237)
Q Consensus 1054 ~~y~C~~C~~~ 1064 (1237)
+.|||++|+.+
T Consensus 2 ~~~~C~~C~~~ 12 (35)
T smart00451 2 GGFYCKLCNVT 12 (35)
T ss_pred cCeEccccCCc
Confidence 57888888865
No 243
>PRK01917 cation-binding hemerythrin HHE family protein; Provisional
Probab=23.22 E-value=2.6e+02 Score=28.93 Aligned_cols=54 Identities=17% Similarity=0.218 Sum_probs=35.1
Q ss_pred HHHhhhhhHHHHHHHHHHHHHhhccCchHHHHHHHHHHHHHHHHHHHhHHHHHHHHh
Q 000886 117 TYSLEHEGESVLFDQLFELLNSSMRNEESYRRELASCTGALQTSISQHMSKEEEQVF 173 (1237)
Q Consensus 117 ~~~~EH~~~~~lf~~l~~~l~~~~~~~~~~~~eLa~~l~~l~~~l~qHm~~EE~qv~ 173 (1237)
.|+.-+..+|+.=..|++.++.+.... ..++...+..|..-...|...||.-.-
T Consensus 9 ~l~vGi~~ID~qH~~Lf~lin~l~~~~---~~~i~~~l~~L~~y~~~HF~~EE~lM~ 62 (139)
T PRK01917 9 ELHLGDPFTDATHAEFVQLLNAVARAD---DADFLQALDAWIDHTRHHFAQEERWME 62 (139)
T ss_pred HhhcCChhhhHHHHHHHHHHHHHHcCC---HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344445555555556666666664332 234667778888899999999998654
No 244
>KOG2129 consensus Uncharacterized conserved protein H4 [Function unknown]
Probab=22.63 E-value=4.5e+02 Score=32.27 Aligned_cols=14 Identities=29% Similarity=0.332 Sum_probs=8.4
Q ss_pred HHHHHHHHHHhccc
Q 000886 183 EEQASLVWQFLCSI 196 (1237)
Q Consensus 183 ~Eqa~L~~~~i~si 196 (1237)
.||.+|+..++.-|
T Consensus 197 QEqEalvN~LwKrm 210 (552)
T KOG2129|consen 197 QEQEALVNSLWKRM 210 (552)
T ss_pred HHHHHHHHHHHHHH
Confidence 46666776665543
No 245
>KOG4399 consensus C2HC-type Zn-finger protein [General function prediction only]
Probab=22.38 E-value=25 Score=39.90 Aligned_cols=70 Identities=24% Similarity=0.632 Sum_probs=46.5
Q ss_pred CCccceEecccccCCCCCCccccCCCCCccccCCCCCccccccCCccccccccccccc--ccccCCCCCCcccccc
Q 000886 1050 GLSMAKYYCGICKFFDDERVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLAKKLVDHK--CREKGLETNCPICCDF 1123 (1237)
Q Consensus 1050 ~~~~~~y~C~~C~~~d~~k~~yHC~~CgiCR~g~gl~~~~fHC~~C~~C~s~~l~~H~--C~e~~~~~~CpICle~ 1123 (1237)
|.+-+-+||+.|-.|=. +..-||..|+-|..-.| +-|-||.+|-.|+-.++ .|. |..-+...-|-||-++
T Consensus 199 ~~EE~~~~~~~~~~Yv~-~~~~H~~~~~S~~~~~~--~~~~H~~~~~~~~~~~~-i~C~~~~~~A~~~~C~iC~~~ 270 (325)
T KOG4399|consen 199 PTEEGYRFCSPCQRYVS-LENQHCEHCNSCTSKDG--RKWNHCFLCKKCVKPSW-IHCSICNHCAVKHGCFICGEL 270 (325)
T ss_pred ccccceEEEeehHHHHH-HHhhhchhhcccccchh--HHHhHhHHhhhhcccce-eeeecccchhhhcceeecccc
Confidence 45566677999987743 45679999999977553 57999999999987665 111 1111223456666554
No 246
>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=22.27 E-value=8.1e+02 Score=28.97 Aligned_cols=132 Identities=12% Similarity=0.103 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhccCCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHHHhhhhHHHHHHhhhhhH
Q 000886 46 IFLFFHKAIKSELDVLHRAAMAFATNLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIRVKNIARTYSLEHEGE 125 (1237)
Q Consensus 46 ~~~~~HkAlR~eL~~l~~~a~~~~~~~gd~~~~~~l~~r~~~L~~~~~~H~~aEDevI~PaLd~Rv~~v~~~~~~EH~~~ 125 (1237)
.|--.|..+|.-...|-+.-..+.. -=.++++++.++++.=-.-| ...|-.+|+.+|+++
T Consensus 14 ~F~aahaqm~sav~qL~~~r~~tee--lIr~rVrq~V~hVqaqEreL------------------Le~v~~rYqR~y~em 73 (324)
T PF12126_consen 14 AFGAAHAQMRSAVSQLGRARADTEE--LIRARVRQVVAHVQAQEREL------------------LEAVEARYQRDYEEM 73 (324)
T ss_pred hHHHHHHHHHHHHHHHHHHHhhHHH--HHHHHHHHHHHHHHHHHHHH------------------HHHHHHHHHHHHHHH
Q ss_pred HHHHHHHHHHHHhhccCch-----HHH--HHHHHHHHHHHHHHHHhHHHHHHHHhhHHHhcCCHHHHHHHHHHHhcccC
Q 000886 126 SVLFDQLFELLNSSMRNEE-----SYR--RELASCTGALQTSISQHMSKEEEQVFPLLIEKFSFEEQASLVWQFLCSIP 197 (1237)
Q Consensus 126 ~~lf~~l~~~l~~~~~~~~-----~~~--~eLa~~l~~l~~~l~qHm~~EE~qv~PLl~~~~S~~Eqa~L~~~~i~siP 197 (1237)
..-+.+|.+-|.+++.... ..| ++=+.-...+......+|..||=+.+-.+.++=.++|-+.=...++..|.
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 247
>PHA00626 hypothetical protein
Probab=22.19 E-value=54 Score=29.34 Aligned_cols=11 Identities=27% Similarity=0.758 Sum_probs=5.5
Q ss_pred ceEecccccCC
Q 000886 1054 AKYYCGICKFF 1064 (1237)
Q Consensus 1054 ~~y~C~~C~~~ 1064 (1237)
.+|-|..|.|+
T Consensus 22 nrYkCkdCGY~ 32 (59)
T PHA00626 22 DDYVCCDCGYN 32 (59)
T ss_pred cceEcCCCCCe
Confidence 44555555554
No 248
>PRK10722 hypothetical protein; Provisional
Probab=22.04 E-value=4.4e+02 Score=30.27 Aligned_cols=115 Identities=10% Similarity=0.139 Sum_probs=73.5
Q ss_pred CCHHHHHHHHHHHhcccCHHHHHHHHhhhcCCCCHHHHHHHHHHHhhhCCc-hhHHHHHHHHHhcCCccCCCcccchhhh
Q 000886 180 FSFEEQASLVWQFLCSIPVNMMAEFLPWLSSSISSDEHQDMRKCLCKIIPK-EKLLRQVIFAWMEGVKVSDKSCEDNLEH 258 (1237)
Q Consensus 180 ~S~~Eqa~L~~~~i~siP~~~m~~~LpWm~~~lsp~Er~~~l~~l~~~~P~-e~~lq~v~~~Wl~~~~~~~~~~~~~~~~ 258 (1237)
++++|......++...-|-+.+..-+-.--...++.||+.|+..|-...++ +..|+=++--|..+-- -++
T Consensus 88 L~~~ear~ea~~~~~~~w~~afkq~ILL~~a~~t~~err~~l~rl~~~~~~~p~~lrPL~qlwr~~Q~---------l~l 158 (247)
T PRK10722 88 LMPAQARAQAKRLPDDSWQNAFKQGILLADAKITPAERRQIVERLNAYSLQIPAQVRPLYQLWRDGQA---------LQL 158 (247)
T ss_pred cCHHHHHHHHHhcCCCCHHHHHHHHHHHcCCCCChHHHHHHHHHHhhcccccchhhhHHHHHHHHhhH---------HHH
Confidence 355666666666666666555554444455667799999999999976655 7788888999987421 000
Q ss_pred hhccCcccccccccccchhhhhhcccCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 000886 259 RCQRWFSCACESSRSSKRKYVELSYDLTDSSMSCPIDEIMLWHNAIKRELNDIAEAARKIQ 319 (1237)
Q Consensus 259 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pid~l~~~HkALRrEL~~L~~~a~~~~ 319 (1237)
+.. -.++.|...-.+. ..-+|.+..-++.++++|+.+.+-+..+.
T Consensus 159 ~La-----------eEr~Ry~rLQq~s-----D~qlD~lrqq~~~Lq~~L~~t~rKLEnLT 203 (247)
T PRK10722 159 ALA-----------EERQRYQKLQQSS-----DSELDALRQQQQRLQYQLELTTRKLENLT 203 (247)
T ss_pred hHH-----------HHHHHHHHHhhcc-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 000 0112222211110 23688999999999999999888876663
No 249
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.96 E-value=60 Score=30.87 Aligned_cols=52 Identities=33% Similarity=0.493 Sum_probs=32.5
Q ss_pred CCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcccCChhhHHHhHHHHHhhc--CCChhhhcc
Q 000886 1115 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGDMAVYFGMLDALLASE--QLPEEYRDR 1188 (1237)
Q Consensus 1115 ~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCr~sv~dm~~~~~~lD~~i~~~--pmP~ey~~~ 1188 (1237)
..||||--.|-.+...-+ .-..||-||-.-.|- ..||.+|+.. |-|.+|+..
T Consensus 2 llCP~C~v~l~~~~rs~v------------------EiD~CPrCrGVWLDr----GELdKli~r~r~pqpa~ys~~ 55 (88)
T COG3809 2 LLCPICGVELVMSVRSGV------------------EIDYCPRCRGVWLDR----GELDKLIERSRYPQPAEYSQP 55 (88)
T ss_pred cccCcCCceeeeeeecCc------------------eeeeCCccccEeecc----hhHHHHHHHhcCCCCcccCCc
Confidence 369999877654321100 125699999876664 5788888765 555566543
No 250
>KOG1312 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=21.78 E-value=30 Score=40.07 Aligned_cols=32 Identities=31% Similarity=0.847 Sum_probs=24.4
Q ss_pred CCCCccccCCCCCccccccCCccccccccccccccc
Q 000886 1074 PFCNLCRVGRGLGVDFFHCMTCNCCLAKKLVDHKCR 1109 (1237)
Q Consensus 1074 ~~CgiCR~g~gl~~~~fHC~~C~~C~s~~l~~H~C~ 1109 (1237)
.+|..|++-|. -...||..||.|+.. .+|-|+
T Consensus 149 ~kCSTCki~KP--ARSKHCsiCNrCV~r--fDHHCi 180 (341)
T KOG1312|consen 149 VKCSTCKIRKP--ARSKHCSICNRCVHR--FDHHCI 180 (341)
T ss_pred CccccccCCCc--cccccchHHHHHHHH--hccceE
Confidence 57888888774 467899999999654 577776
No 251
>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=21.77 E-value=40 Score=27.95 Aligned_cols=6 Identities=33% Similarity=1.082 Sum_probs=2.0
Q ss_pred ccCCcc
Q 000886 1091 HCMTCN 1096 (1237)
Q Consensus 1091 HC~~C~ 1096 (1237)
-|..||
T Consensus 21 vC~~CG 26 (43)
T PF08271_consen 21 VCPNCG 26 (43)
T ss_dssp EETTT-
T ss_pred ECCCCC
Confidence 333333
No 252
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=21.50 E-value=48 Score=28.82 Aligned_cols=24 Identities=29% Similarity=0.664 Sum_probs=14.7
Q ss_pred cCCCCCccccCCCCCccccccCCccc
Q 000886 1072 HCPFCNLCRVGRGLGVDFFHCMTCNC 1097 (1237)
Q Consensus 1072 HC~~CgiCR~g~gl~~~~fHC~~C~~ 1097 (1237)
.||.||-. +-. ...+.++|.+||.
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 67877754 221 1246788888874
No 253
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=21.31 E-value=80 Score=27.39 Aligned_cols=10 Identities=50% Similarity=1.328 Sum_probs=5.6
Q ss_pred CCCCCCCCcc
Q 000886 1152 HYICPICSKS 1161 (1237)
Q Consensus 1152 ~~~CPiCr~s 1161 (1237)
++.||||...
T Consensus 31 ~v~CPiC~~~ 40 (54)
T PF05605_consen 31 NVVCPICSSR 40 (54)
T ss_pred CccCCCchhh
Confidence 3556666653
No 254
>KOG3842 consensus Adaptor protein Pellino [Signal transduction mechanisms]
Probab=21.21 E-value=52 Score=38.45 Aligned_cols=34 Identities=26% Similarity=0.636 Sum_probs=24.3
Q ss_pred ecCCCCccChhhHHHhhhc---------CCCCCCCCcccCChh
Q 000886 1133 ALPCGHFMHSDCFQAYTCS---------HYICPICSKSLGDMA 1166 (1237)
Q Consensus 1133 ~LpCgH~fH~~Ci~~wl~~---------~~~CPiCr~sv~dm~ 1166 (1237)
.-||||+--..=..-|... +..||.|-..+..-.
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 3599999888778778542 467999987765433
No 255
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=20.96 E-value=77 Score=40.83 Aligned_cols=54 Identities=20% Similarity=0.294 Sum_probs=30.7
Q ss_pred ChhhHHHhHHHHHhhcCCChhhhccCCceecCCCCCCCCCCceeecccCCCCCCcccccc
Q 000886 1164 DMAVYFGMLDALLASEQLPEEYRDRCQEILCNDCDKKGSAPFHWLYHKCGFCGSYNTRVI 1223 (1237)
Q Consensus 1164 dm~~~~~~lD~~i~~~pmP~ey~~~~~~i~CnDC~~~s~~~~h~lg~kC~~C~SYNT~~~ 1223 (1237)
+.+.....++.... ..+|----+. ..-.|++||-.... .+..|+.|||-|+.++
T Consensus 541 n~eal~~lv~~~~~-~~i~Yf~in~-~~~iC~~CG~~~~g----~~~~CP~CGs~~~ev~ 594 (623)
T PRK08271 541 SEEGYRKLLNIAAK-TGCNYFAFNV-KITICNDCHHIDKR----TGKRCPICGSENIDYY 594 (623)
T ss_pred CHHHHHHHHHHHHH-cCCceEEeCC-CCccCCCCCCcCCC----CCcCCcCCCCcchhHH
Confidence 44444445554433 4454221222 23469999975222 3468999999886554
No 256
>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=20.82 E-value=48 Score=30.19 Aligned_cols=16 Identities=31% Similarity=0.395 Sum_probs=13.2
Q ss_pred cccCCCCCCccccccc
Q 000886 1209 YHKCGFCGSYNTRVIK 1224 (1237)
Q Consensus 1209 g~kC~~C~SYNT~~~~ 1224 (1237)
.++|+.|+|+||+.-.
T Consensus 5 ~~~CPRC~S~nTKFcY 20 (63)
T PF02701_consen 5 PLPCPRCDSTNTKFCY 20 (63)
T ss_pred CCCCCCcCCCCCEEEe
Confidence 3689999999998743
No 257
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=20.77 E-value=60 Score=29.00 Aligned_cols=11 Identities=36% Similarity=1.108 Sum_probs=7.8
Q ss_pred CccccCCCCCc
Q 000886 1068 RVVYHCPFCNL 1078 (1237)
Q Consensus 1068 k~~yHC~~Cgi 1078 (1237)
...|-|++|||
T Consensus 12 ~v~~~Cp~cGi 22 (55)
T PF13824_consen 12 HVNFECPDCGI 22 (55)
T ss_pred ccCCcCCCCCC
Confidence 45677888875
No 258
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=20.75 E-value=39 Score=40.79 Aligned_cols=32 Identities=31% Similarity=0.815 Sum_probs=25.4
Q ss_pred CCCCcccccccccCCCcceecCCCCccChhhHHHhh
Q 000886 1114 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYT 1149 (1237)
Q Consensus 1114 ~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl 1149 (1237)
+-.||||... |. ..++|||||.++..|-..-+
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 5679999876 43 35789999999999987654
No 259
>PF15353 HECA: Headcase protein family homologue
Probab=20.59 E-value=44 Score=33.45 Aligned_cols=16 Identities=38% Similarity=1.105 Sum_probs=13.8
Q ss_pred CCCCccChhhHHHhhh
Q 000886 1135 PCGHFMHSDCFQAYTC 1150 (1237)
Q Consensus 1135 pCgH~fH~~Ci~~wl~ 1150 (1237)
|.|++||.+||++|-.
T Consensus 39 p~~~~MH~~CF~~wE~ 54 (107)
T PF15353_consen 39 PFGQYMHRECFEKWED 54 (107)
T ss_pred CCCCchHHHHHHHHHH
Confidence 5589999999999954
No 260
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=20.18 E-value=67 Score=29.03 Aligned_cols=28 Identities=18% Similarity=0.107 Sum_probs=20.8
Q ss_pred ceecCCCCCCCCCCceeecccCCCCCCccccccc
Q 000886 1191 EILCNDCDKKGSAPFHWLYHKCGFCGSYNTRVIK 1224 (1237)
Q Consensus 1191 ~i~CnDC~~~s~~~~h~lg~kC~~C~SYNT~~~~ 1224 (1237)
.+.|..||.. ...| +.|. ||.||.+++-
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 5789999973 3334 3499 9999999863
No 261
>PRK12775 putative trifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta/ferritin domain-containing protein; Provisional
Probab=20.11 E-value=37 Score=45.96 Aligned_cols=52 Identities=27% Similarity=0.586 Sum_probs=35.8
Q ss_pred CCCCCCCCcccCChhhHHHhHHHHHhhcCCChhhhccCCceecCCCCCCCCCCceeecccCCCCCCc
Q 000886 1152 HYICPICSKSLGDMAVYFGMLDALLASEQLPEEYRDRCQEILCNDCDKKGSAPFHWLYHKCGFCGSY 1218 (1237)
Q Consensus 1152 ~~~CPiCr~sv~dm~~~~~~lD~~i~~~pmP~ey~~~~~~i~CnDC~~~s~~~~h~lg~kC~~C~SY 1218 (1237)
..+||-|.+++...+.|.-- .+..-...|.||++.|.. |-|-|-.|+.||..
T Consensus 796 ~~~~~~~~~~~~~~~~~~~~--------------~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~ 847 (1006)
T PRK12775 796 VATCPKCHRPLEGDEEYVCC--------------ATSELQWRCDDCGKVSEG-FAFPYGMCPACGGK 847 (1006)
T ss_pred CccCcccCCCCCCCceeEEe--------------cCcceeeehhhhcccccc-ccCCcCcCcccccc
Confidence 47899999998765544221 122223569999998753 45567799999986
Done!