Query 000881
Match_columns 1239
No_of_seqs 538 out of 1468
Neff 5.2
Searched_HMMs 46136
Date Tue Apr 2 00:38:03 2013
Command hhsearch -i /work/01045/syshi/lefta3m/000881.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/leftcdd/000881hhsearch_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 1.4E-62 3E-67 537.8 7.2 253 976-1234 21-275 (276)
2 PF14599 zinc_ribbon_6: Zinc-r 99.9 1.5E-25 3.1E-30 195.6 -0.8 61 1164-1224 1-61 (61)
3 PF05495 zf-CHY: CHY zinc fing 99.8 7.3E-21 1.6E-25 172.3 1.0 70 990-1067 1-71 (71)
4 PF01814 Hemerythrin: Hemeryth 99.2 1.6E-10 3.4E-15 112.7 12.2 129 43-176 2-133 (133)
5 PF01814 Hemerythrin: Hemeryth 99.2 3.5E-10 7.7E-15 110.2 14.4 124 293-425 2-133 (133)
6 PF13639 zf-RING_2: Ring finge 99.1 1.1E-11 2.3E-16 102.2 0.7 44 1117-1161 1-44 (44)
7 COG5243 HRD1 HRD ubiquitin lig 98.8 1E-09 2.2E-14 123.6 2.7 57 1113-1169 284-350 (491)
8 KOG4628 Predicted E3 ubiquitin 98.8 1.7E-09 3.7E-14 123.8 2.4 50 1117-1167 230-280 (348)
9 PRK10992 iron-sulfur cluster r 98.8 6.7E-08 1.5E-12 105.9 13.9 132 293-427 75-218 (220)
10 PF12678 zf-rbx1: RING-H2 zinc 98.8 3.7E-09 8E-14 96.7 3.0 47 1115-1161 18-73 (73)
11 KOG0804 Cytoplasmic Zn-finger 98.7 4.2E-09 9.1E-14 121.6 3.1 82 1116-1224 175-258 (493)
12 COG4357 Zinc finger domain con 98.7 1.3E-09 2.8E-14 102.3 -1.0 57 986-1042 11-75 (105)
13 TIGR03652 FeS_repair_RIC iron- 98.7 1.7E-07 3.6E-12 102.5 12.4 129 294-425 72-216 (216)
14 PRK10992 iron-sulfur cluster r 98.6 3.9E-07 8.5E-12 100.0 14.3 129 49-178 82-218 (220)
15 PHA02929 N1R/p28-like protein; 98.5 4.9E-08 1.1E-12 107.6 4.3 54 1113-1166 171-228 (238)
16 COG5540 RING-finger-containing 98.5 4.6E-08 9.9E-13 108.3 2.8 53 1112-1165 319-372 (374)
17 COG3945 Uncharacterized conser 98.5 1.9E-06 4.1E-11 90.2 14.5 140 292-440 8-158 (189)
18 cd00162 RING RING-finger (Real 98.5 7.6E-08 1.6E-12 77.4 3.3 44 1118-1164 1-45 (45)
19 TIGR03652 FeS_repair_RIC iron- 98.5 1.6E-06 3.4E-11 94.9 13.2 127 49-175 78-215 (216)
20 PF13923 zf-C3HC4_2: Zinc fing 98.4 1.1E-07 2.4E-12 76.6 1.9 39 1119-1160 1-39 (39)
21 PRK13276 cell wall biosynthesi 98.3 6.3E-06 1.4E-10 90.5 13.2 128 294-424 79-222 (224)
22 PRK13276 cell wall biosynthesi 98.3 7.2E-06 1.6E-10 90.0 13.4 125 49-174 85-221 (224)
23 PF13920 zf-C3HC4_3: Zinc fing 98.3 4E-07 8.7E-12 77.2 2.1 47 1116-1166 2-49 (50)
24 PF12861 zf-Apc11: Anaphase-pr 98.2 8.3E-07 1.8E-11 83.2 3.4 32 1133-1164 47-81 (85)
25 smart00184 RING Ring finger. E 98.1 1.6E-06 3.5E-11 67.3 2.8 38 1119-1160 1-39 (39)
26 PF14634 zf-RING_5: zinc-RING 98.1 2.2E-06 4.8E-11 71.0 3.1 44 1118-1162 1-44 (44)
27 PLN03208 E3 ubiquitin-protein 98.0 3.7E-06 8.1E-11 89.8 4.3 51 1112-1166 14-80 (193)
28 PF15227 zf-C3HC4_4: zinc fing 98.0 2.4E-06 5.2E-11 70.3 1.9 38 1119-1160 1-42 (42)
29 KOG0802 E3 ubiquitin ligase [P 98.0 1.6E-06 3.4E-11 106.8 1.1 53 1112-1164 287-340 (543)
30 COG2846 Regulator of cell morp 98.0 5.2E-05 1.1E-09 80.7 12.1 128 295-425 79-217 (221)
31 PF00097 zf-C3HC4: Zinc finger 98.0 2.3E-06 5.1E-11 69.2 1.6 39 1119-1160 1-41 (41)
32 COG5194 APC11 Component of SCF 98.0 3.8E-06 8.2E-11 77.1 2.9 48 1117-1164 32-80 (88)
33 KOG0320 Predicted E3 ubiquitin 98.0 3.3E-06 7.2E-11 88.3 2.0 47 1116-1165 131-178 (187)
34 PHA02926 zinc finger-like prot 97.8 8.9E-06 1.9E-10 87.9 3.2 53 1113-1165 167-230 (242)
35 smart00504 Ubox Modified RING 97.8 1.8E-05 4E-10 69.4 3.9 45 1117-1165 2-46 (63)
36 PF13445 zf-RING_UBOX: RING-ty 97.8 1.2E-05 2.7E-10 66.6 2.0 39 1119-1158 1-43 (43)
37 KOG1428 Inhibitor of type V ad 97.7 1.2E-05 2.5E-10 101.5 1.3 122 1020-1165 3408-3544(3738)
38 KOG1493 Anaphase-promoting com 97.7 1.1E-05 2.3E-10 73.7 0.2 28 1137-1164 50-80 (84)
39 COG3945 Uncharacterized conser 97.5 0.00083 1.8E-08 70.9 12.1 139 44-189 10-156 (189)
40 KOG0825 PHD Zn-finger protein 97.5 1.3E-05 2.8E-10 97.7 -1.4 75 1091-1166 96-172 (1134)
41 KOG0317 Predicted E3 ubiquitin 97.5 3.3E-05 7.1E-10 86.3 1.7 46 1116-1165 239-284 (293)
42 TIGR00599 rad18 DNA repair pro 97.5 5.1E-05 1.1E-09 89.6 3.2 47 1116-1166 26-72 (397)
43 COG2846 Regulator of cell morp 97.5 0.00092 2E-08 71.5 12.0 132 45-176 79-217 (221)
44 smart00744 RINGv The RING-vari 97.3 0.00013 2.8E-09 62.2 2.3 42 1118-1161 1-49 (49)
45 KOG2177 Predicted E3 ubiquitin 97.3 0.00025 5.4E-09 77.6 4.9 44 1115-1162 12-55 (386)
46 PF11793 FANCL_C: FANCL C-term 97.3 7.2E-05 1.6E-09 68.3 0.4 50 1116-1165 2-66 (70)
47 KOG0287 Postreplication repair 97.3 0.00014 3E-09 82.3 2.5 60 1117-1180 24-84 (442)
48 TIGR00570 cdk7 CDK-activating 97.2 0.00023 4.9E-09 81.3 4.0 51 1116-1166 3-55 (309)
49 KOG0823 Predicted E3 ubiquitin 97.2 0.00015 3.2E-09 79.2 2.4 52 1113-1168 44-98 (230)
50 KOG2930 SCF ubiquitin ligase, 97.2 7.1E-05 1.5E-09 72.0 -0.2 28 1136-1163 79-106 (114)
51 KOG0827 Predicted E3 ubiquitin 97.2 0.00013 2.7E-09 84.0 1.3 48 1116-1164 4-55 (465)
52 KOG2164 Predicted E3 ubiquitin 97.2 0.00018 3.9E-09 85.8 2.5 49 1114-1166 184-237 (513)
53 KOG0828 Predicted E3 ubiquitin 97.1 0.00018 3.8E-09 84.7 1.0 32 1134-1165 602-634 (636)
54 KOG1734 Predicted RING-contain 97.0 0.00017 3.7E-09 79.7 0.0 50 1116-1165 224-281 (328)
55 PF04564 U-box: U-box domain; 96.7 0.0012 2.7E-08 60.5 2.9 47 1116-1166 4-51 (73)
56 COG5574 PEX10 RING-finger-cont 96.7 0.00075 1.6E-08 75.0 1.7 46 1116-1165 215-262 (271)
57 KOG1039 Predicted E3 ubiquitin 96.5 0.0012 2.6E-08 76.9 2.1 82 1113-1196 158-252 (344)
58 PF14835 zf-RING_6: zf-RING of 96.2 0.0028 6.1E-08 56.8 2.3 56 1117-1178 8-65 (65)
59 COG5432 RAD18 RING-finger-cont 96.1 0.0024 5.2E-08 71.3 1.9 46 1116-1165 25-70 (391)
60 KOG4172 Predicted E3 ubiquitin 96.0 0.0015 3.3E-08 56.4 -0.5 52 1115-1170 6-59 (62)
61 KOG1941 Acetylcholine receptor 95.9 0.0016 3.5E-08 75.1 -0.7 61 1107-1168 357-419 (518)
62 COG5219 Uncharacterized conser 95.9 0.0026 5.7E-08 79.6 0.6 53 1112-1164 1465-1522(1525)
63 KOG1645 RING-finger-containing 95.7 0.0054 1.2E-07 71.6 2.5 49 1116-1164 4-55 (463)
64 COG2461 Uncharacterized conser 95.6 0.074 1.6E-06 62.6 11.0 132 291-441 85-223 (409)
65 KOG4265 Predicted E3 ubiquitin 95.4 0.0092 2E-07 69.1 2.6 51 1112-1166 286-337 (349)
66 KOG0311 Predicted E3 ubiquitin 95.3 0.0028 6.2E-08 72.8 -1.6 47 1116-1165 43-90 (381)
67 KOG0978 E3 ubiquitin ligase in 95.2 0.0063 1.4E-07 76.1 0.6 46 1117-1166 644-690 (698)
68 KOG1785 Tyrosine kinase negati 94.9 0.0069 1.5E-07 70.2 0.0 54 1108-1165 361-416 (563)
69 KOG1940 Zn-finger protein [Gen 94.9 0.0025 5.4E-08 72.1 -3.6 133 690-854 17-149 (276)
70 KOG2879 Predicted E3 ubiquitin 94.2 0.036 7.8E-07 62.2 3.3 52 1114-1168 237-290 (298)
71 KOG3970 Predicted E3 ubiquitin 93.9 0.039 8.4E-07 60.1 2.8 51 1114-1166 48-106 (299)
72 KOG3268 Predicted E3 ubiquitin 93.5 0.041 8.8E-07 58.1 2.0 31 1135-1165 187-228 (234)
73 KOG4445 Uncharacterized conser 93.4 0.021 4.6E-07 64.5 -0.1 54 1112-1166 111-187 (368)
74 PF14570 zf-RING_4: RING/Ubox 93.4 0.058 1.3E-06 46.1 2.5 45 1119-1163 1-46 (48)
75 PF11789 zf-Nse: Zinc-finger o 93.0 0.054 1.2E-06 47.9 1.8 42 1115-1159 10-53 (57)
76 KOG3002 Zn finger protein [Gen 92.7 0.086 1.9E-06 60.9 3.4 64 1116-1189 48-113 (299)
77 KOG1701 Focal adhesion adaptor 92.7 0.014 3.1E-07 68.6 -2.9 62 1070-1147 295-361 (468)
78 PF10367 Vps39_2: Vacuolar sor 92.7 0.048 1E-06 52.7 1.1 38 1109-1148 71-108 (109)
79 KOG0824 Predicted E3 ubiquitin 92.5 0.067 1.4E-06 60.9 2.1 48 1114-1165 5-53 (324)
80 KOG2272 Focal adhesion protein 92.4 0.049 1.1E-06 60.3 0.8 141 989-1170 63-237 (332)
81 KOG0309 Conserved WD40 repeat- 92.3 0.074 1.6E-06 66.1 2.3 49 1109-1159 1021-1069(1081)
82 PF12906 RINGv: RING-variant d 91.8 0.1 2.2E-06 44.3 1.9 40 1119-1160 1-47 (47)
83 KOG3039 Uncharacterized conser 91.7 0.12 2.7E-06 57.2 3.0 55 1112-1167 217-272 (303)
84 KOG0297 TNF receptor-associate 91.6 0.11 2.3E-06 62.3 2.6 54 1114-1170 19-72 (391)
85 PF05883 Baculo_RING: Baculovi 91.3 0.076 1.7E-06 54.4 0.8 43 1116-1159 26-74 (134)
86 KOG2660 Locus-specific chromos 90.5 0.067 1.5E-06 61.6 -0.5 49 1115-1166 14-62 (331)
87 COG5152 Uncharacterized conser 90.4 0.13 2.8E-06 55.3 1.5 58 1117-1178 197-254 (259)
88 KOG1002 Nucleotide excision re 89.6 0.12 2.5E-06 62.3 0.5 51 1111-1165 531-586 (791)
89 COG2461 Uncharacterized conser 89.4 1.7 3.8E-05 51.6 9.6 138 40-191 84-222 (409)
90 PF14447 Prok-RING_4: Prokaryo 89.4 0.17 3.6E-06 44.4 1.1 31 1133-1165 20-50 (55)
91 KOG3800 Predicted E3 ubiquitin 88.8 0.28 6E-06 55.9 2.6 48 1118-1165 2-51 (300)
92 COG5175 MOT2 Transcriptional r 88.2 0.17 3.7E-06 58.1 0.5 58 1116-1173 14-72 (480)
93 PF04641 Rtf2: Rtf2 RING-finge 88.0 0.35 7.7E-06 54.9 2.9 51 1113-1165 110-161 (260)
94 KOG1571 Predicted E3 ubiquitin 87.8 0.26 5.6E-06 57.6 1.6 47 1112-1165 301-347 (355)
95 KOG1813 Predicted E3 ubiquitin 87.5 0.32 6.9E-06 55.5 2.1 63 1116-1182 241-303 (313)
96 COG5592 Uncharacterized conser 87.3 1.5 3.3E-05 46.3 6.7 100 681-817 30-136 (171)
97 COG5592 Uncharacterized conser 87.2 0.93 2E-05 47.8 5.1 71 654-734 74-144 (171)
98 KOG4159 Predicted E3 ubiquitin 85.8 0.65 1.4E-05 55.7 3.6 49 1114-1166 82-130 (398)
99 PHA02862 5L protein; Provision 85.8 0.41 8.9E-06 49.6 1.7 46 1115-1165 1-53 (156)
100 KOG4692 Predicted E3 ubiquitin 84.8 0.52 1.1E-05 54.7 2.0 52 1111-1166 417-468 (489)
101 KOG4275 Predicted E3 ubiquitin 84.3 0.17 3.8E-06 57.3 -1.9 49 1116-1171 300-348 (350)
102 KOG4739 Uncharacterized protei 84.1 0.52 1.1E-05 52.6 1.7 37 1127-1165 12-48 (233)
103 KOG1814 Predicted E3 ubiquitin 83.8 0.52 1.1E-05 55.9 1.5 47 1116-1163 184-238 (445)
104 TIGR00100 hypA hydrogenase nic 83.1 0.68 1.5E-05 46.5 1.9 34 1190-1225 67-100 (115)
105 PRK00564 hypA hydrogenase nick 82.7 0.75 1.6E-05 46.4 2.0 34 1190-1225 68-102 (117)
106 COG5236 Uncharacterized conser 81.8 1.1 2.4E-05 51.9 3.1 65 1096-1164 40-107 (493)
107 PF07800 DUF1644: Protein of u 81.1 1.2 2.7E-05 46.9 2.9 32 1116-1151 2-46 (162)
108 PRK03824 hypA hydrogenase nick 80.3 0.93 2E-05 46.8 1.7 34 1192-1225 69-121 (135)
109 KOG2114 Vacuolar assembly/sort 80.2 0.99 2.1E-05 57.7 2.2 41 1117-1163 841-881 (933)
110 TIGR02481 hemeryth_dom hemeryt 79.9 6.4 0.00014 39.3 7.5 51 361-421 12-62 (126)
111 PRK12380 hydrogenase nickel in 79.7 0.99 2.1E-05 45.2 1.7 33 1191-1225 68-100 (113)
112 PRK03681 hypA hydrogenase nick 79.4 1.1 2.3E-05 45.1 1.8 35 1191-1226 68-102 (114)
113 KOG0269 WD40 repeat-containing 78.1 1.6 3.4E-05 55.3 3.1 70 1070-1159 751-820 (839)
114 PF07191 zinc-ribbons_6: zinc- 77.8 0.43 9.4E-06 43.9 -1.4 65 1117-1209 2-69 (70)
115 KOG0827 Predicted E3 ubiquitin 76.8 0.21 4.5E-06 58.5 -4.6 53 1114-1166 194-246 (465)
116 PF03854 zf-P11: P-11 zinc fin 76.8 0.76 1.6E-05 39.3 -0.1 43 1117-1165 3-46 (50)
117 KOG3161 Predicted E3 ubiquitin 76.5 0.8 1.7E-05 56.7 -0.1 54 1117-1173 12-69 (861)
118 PRK04023 DNA polymerase II lar 76.2 2.3 4.9E-05 55.7 3.7 43 1031-1079 628-670 (1121)
119 KOG4185 Predicted E3 ubiquitin 75.4 2.5 5.4E-05 48.6 3.5 47 1117-1164 4-54 (296)
120 PHA02825 LAP/PHD finger-like p 75.1 2.1 4.5E-05 45.3 2.5 45 1115-1164 7-58 (162)
121 KOG1952 Transcription factor N 72.7 1.5 3.3E-05 56.0 1.1 49 1115-1164 190-246 (950)
122 PF01155 HypA: Hydrogenase exp 72.7 1.1 2.5E-05 44.7 -0.0 33 1191-1225 68-100 (113)
123 PF02084 Bindin: Bindin; Inte 71.6 11 0.00024 41.9 7.1 46 72-128 124-170 (238)
124 KOG4443 Putative transcription 70.2 3.4 7.3E-05 51.8 3.1 71 1116-1191 145-226 (694)
125 KOG2034 Vacuolar sorting prote 70.0 1.8 3.9E-05 55.8 0.8 44 1107-1152 808-851 (911)
126 KOG2817 Predicted E3 ubiquitin 69.1 3.4 7.4E-05 49.2 2.7 46 1117-1163 335-383 (394)
127 KOG1044 Actin-binding LIM Zn-f 68.5 5.3 0.00012 49.5 4.3 78 1135-1220 80-169 (670)
128 PF14446 Prok-RING_1: Prokaryo 67.8 4.3 9.4E-05 35.8 2.4 37 1114-1150 3-39 (54)
129 PF08746 zf-RING-like: RING-li 67.4 3.2 6.9E-05 34.8 1.5 41 1119-1160 1-43 (43)
130 PRK00762 hypA hydrogenase nick 67.3 3.1 6.7E-05 42.4 1.7 34 1191-1225 68-106 (124)
131 KOG0801 Predicted E3 ubiquitin 66.7 2.6 5.7E-05 44.5 1.0 31 1113-1144 174-204 (205)
132 TIGR02481 hemeryth_dom hemeryt 66.2 87 0.0019 31.2 11.8 109 297-424 13-125 (126)
133 PF01529 zf-DHHC: DHHC palmito 65.5 4.5 9.8E-05 42.4 2.6 47 1052-1104 43-89 (174)
134 smart00132 LIM Zinc-binding do 64.8 4.3 9.3E-05 31.6 1.7 38 1118-1165 1-38 (39)
135 COG5220 TFB3 Cdk activating ki 64.3 1.8 3.9E-05 48.1 -0.6 51 1115-1165 9-64 (314)
136 KOG2068 MOT2 transcription fac 63.6 5.2 0.00011 46.8 2.8 52 1114-1165 247-298 (327)
137 COG5222 Uncharacterized conser 63.3 4.4 9.6E-05 46.4 2.1 43 1117-1162 275-318 (427)
138 PRK14890 putative Zn-ribbon RN 63.2 5.6 0.00012 35.7 2.3 45 1029-1080 7-56 (59)
139 PF06524 NOA36: NOA36 protein; 61.6 4 8.6E-05 46.1 1.3 50 1005-1065 140-190 (314)
140 COG0375 HybF Zn finger protein 59.3 5.9 0.00013 40.1 2.0 35 1190-1226 67-101 (115)
141 TIGR00595 priA primosomal prot 57.9 7.1 0.00015 48.6 2.8 48 999-1052 214-261 (505)
142 KOG0298 DEAD box-containing he 57.3 2.9 6.2E-05 55.9 -0.7 70 145-214 237-306 (1394)
143 PF05502 Dynactin_p62: Dynacti 56.5 7.8 0.00017 48.0 2.8 13 1053-1065 22-34 (483)
144 KOG2066 Vacuolar assembly/sort 56.0 4.3 9.3E-05 51.9 0.5 88 405-496 393-485 (846)
145 PF14357 DUF4404: Domain of un 56.0 72 0.0016 30.7 8.5 82 54-139 2-83 (85)
146 PRK01917 cation-binding hemery 54.8 31 0.00066 35.7 6.4 95 363-465 11-118 (139)
147 PHA03096 p28-like protein; Pro 54.6 6.3 0.00014 45.6 1.5 46 1117-1162 179-231 (284)
148 cd00350 rubredoxin_like Rubred 54.4 8.9 0.00019 30.3 1.8 24 1057-1080 1-25 (33)
149 KOG1001 Helicase-like transcri 53.3 5.9 0.00013 51.0 1.1 43 1117-1164 455-499 (674)
150 PF02891 zf-MIZ: MIZ/SP-RING z 52.8 10 0.00022 32.8 2.1 41 1117-1163 3-50 (50)
151 cd00522 Hemerythrin Hemerythri 52.8 57 0.0012 32.4 7.7 28 401-428 37-68 (113)
152 PRK14714 DNA polymerase II lar 52.0 13 0.00028 50.3 3.7 17 1212-1228 914-930 (1337)
153 KOG2462 C2H2-type Zn-finger pr 50.7 14 0.0003 42.4 3.4 70 1073-1168 131-229 (279)
154 PF09538 FYDLN_acid: Protein o 50.6 9.6 0.00021 38.2 1.9 17 1064-1080 18-34 (108)
155 PF09538 FYDLN_acid: Protein o 50.6 9 0.00019 38.4 1.6 32 997-1042 8-39 (108)
156 COG1198 PriA Primosomal protei 49.3 13 0.00028 48.2 3.2 55 998-1059 435-489 (730)
157 COG5109 Uncharacterized conser 48.8 11 0.00024 43.7 2.3 44 1117-1161 337-383 (396)
158 PRK05580 primosome assembly pr 48.2 12 0.00026 48.4 2.7 49 998-1052 381-429 (679)
159 TIGR02605 CxxC_CxxC_SSSS putat 47.9 9.8 0.00021 32.6 1.3 33 1193-1225 5-41 (52)
160 PLN03086 PRLI-interacting fact 46.7 13 0.00027 47.0 2.5 52 1070-1125 451-513 (567)
161 PRK04023 DNA polymerase II lar 46.6 17 0.00036 48.2 3.5 35 1042-1081 626-660 (1121)
162 TIGR01562 FdhE formate dehydro 46.6 14 0.00031 43.2 2.7 37 902-948 91-127 (305)
163 PRK14873 primosome assembly pr 46.2 13 0.00028 47.9 2.6 47 999-1052 384-430 (665)
164 PRK12286 rpmF 50S ribosomal pr 46.1 16 0.00034 32.7 2.3 29 1192-1225 26-54 (57)
165 PF14353 CpXC: CpXC protein 45.9 20 0.00044 36.3 3.4 56 1155-1212 2-57 (128)
166 COG2888 Predicted Zn-ribbon RN 45.7 16 0.00034 33.0 2.2 45 1029-1080 9-58 (61)
167 PRK00808 hypothetical protein; 45.6 3.8E+02 0.0082 28.0 13.0 110 297-428 17-130 (150)
168 COG5183 SSM4 Protein involved 45.5 10 0.00022 48.6 1.4 50 1114-1165 10-66 (1175)
169 KOG3850 Predicted membrane pro 45.0 5.8E+02 0.013 31.1 15.1 129 301-445 262-396 (455)
170 KOG1609 Protein involved in mR 44.9 8.5 0.00018 44.1 0.6 50 1116-1165 78-134 (323)
171 PRK03564 formate dehydrogenase 44.8 17 0.00037 42.7 2.9 15 902-916 94-108 (309)
172 KOG0826 Predicted E3 ubiquitin 44.7 15 0.00032 43.1 2.4 46 1116-1164 300-345 (357)
173 TIGR01562 FdhE formate dehydro 44.3 14 0.0003 43.4 2.1 27 1132-1163 207-233 (305)
174 COG4888 Uncharacterized Zn rib 44.2 10 0.00022 37.5 0.8 32 1070-1101 20-56 (104)
175 PLN03086 PRLI-interacting fact 42.5 32 0.0007 43.5 5.0 77 1075-1165 436-515 (567)
176 PRK00808 hypothetical protein; 42.3 1.1E+02 0.0025 31.9 8.4 109 656-809 17-130 (150)
177 PRK00398 rpoP DNA-directed RNA 42.0 14 0.00031 31.0 1.4 30 1193-1222 3-32 (46)
178 PF12773 DZR: Double zinc ribb 41.4 22 0.00048 30.1 2.4 22 1032-1056 1-23 (50)
179 smart00734 ZnF_Rad18 Rad18-lik 41.3 19 0.00041 27.2 1.7 21 1155-1176 2-22 (26)
180 KOG1829 Uncharacterized conser 40.2 9.3 0.0002 48.1 -0.0 29 989-1018 345-377 (580)
181 TIGR01031 rpmF_bact ribosomal 39.5 17 0.00038 32.1 1.5 29 1192-1225 25-53 (55)
182 COG1656 Uncharacterized conser 38.9 21 0.00046 38.2 2.4 50 1154-1210 97-147 (165)
183 cd00522 Hemerythrin Hemerythri 38.5 1.9E+02 0.0041 28.7 8.9 37 783-821 38-78 (113)
184 PRK14559 putative protein seri 37.4 24 0.00052 45.4 2.9 32 1030-1064 2-34 (645)
185 KOG0006 E3 ubiquitin-protein l 37.3 29 0.00062 40.5 3.2 74 1066-1150 169-253 (446)
186 KOG1280 Uncharacterized conser 37.0 25 0.00054 41.6 2.7 26 1052-1080 60-87 (381)
187 KOG4399 C2HC-type Zn-finger pr 36.3 9.2 0.0002 43.3 -0.8 63 1031-1102 240-302 (325)
188 PF13597 NRDD: Anaerobic ribon 35.2 21 0.00044 45.1 1.8 57 1166-1228 465-521 (546)
189 TIGR02300 FYDLN_acid conserved 35.1 24 0.00051 36.4 1.9 18 1064-1081 18-35 (129)
190 smart00659 RPOLCX RNA polymera 35.0 23 0.00049 30.1 1.5 26 1193-1219 2-27 (44)
191 PF14631 FancD2: Fanconi anaem 34.7 8.1E+02 0.018 35.0 16.7 100 126-228 191-306 (1426)
192 COG1996 RPC10 DNA-directed RNA 34.6 19 0.00041 31.4 0.9 28 1192-1219 5-32 (49)
193 KOG1044 Actin-binding LIM Zn-f 34.2 31 0.00068 43.2 3.0 162 1029-1222 42-229 (670)
194 PRK03564 formate dehydrogenase 34.2 18 0.00039 42.5 1.0 26 1132-1162 209-234 (309)
195 PF01783 Ribosomal_L32p: Ribos 34.2 26 0.00057 31.0 1.8 29 1192-1225 25-53 (56)
196 cd01675 RNR_III Class III ribo 33.5 36 0.00077 43.2 3.5 56 1166-1227 493-548 (555)
197 PF04216 FdhE: Protein involve 33.1 13 0.00029 42.8 -0.2 24 1142-1165 199-222 (290)
198 PF13901 DUF4206: Domain of un 32.9 24 0.00051 39.0 1.6 27 1131-1162 171-197 (202)
199 KOG2807 RNA polymerase II tran 32.9 12 0.00026 43.7 -0.6 84 1083-1219 273-375 (378)
200 KOG3362 Predicted BBOX Zn-fing 31.9 15 0.00033 38.4 -0.1 26 1055-1084 116-143 (156)
201 PRK00398 rpoP DNA-directed RNA 31.6 37 0.0008 28.6 2.2 8 1072-1079 21-28 (46)
202 TIGR00373 conserved hypothetic 31.5 16 0.00035 38.8 0.0 22 1058-1079 110-135 (158)
203 PRK07219 DNA topoisomerase I; 31.4 67 0.0015 42.7 5.6 63 1060-1127 672-744 (822)
204 PF00539 Tat: Transactivating 31.2 45 0.00097 31.0 2.8 18 1072-1092 36-53 (68)
205 KOG3053 Uncharacterized conser 31.0 19 0.00042 40.9 0.6 54 1111-1164 15-81 (293)
206 KOG2593 Transcription initiati 31.0 21 0.00046 43.3 0.9 19 912-930 50-68 (436)
207 PF00628 PHD: PHD-finger; Int 30.9 7.7 0.00017 32.8 -2.0 42 1119-1161 2-49 (51)
208 cd00729 rubredoxin_SM Rubredox 30.3 36 0.00077 27.3 1.8 23 1057-1079 2-25 (34)
209 PRK06266 transcription initiat 30.2 18 0.00039 39.2 0.2 23 1057-1079 117-143 (178)
210 PRK14892 putative transcriptio 29.6 33 0.00072 34.0 1.9 31 1090-1125 20-51 (99)
211 KOG1812 Predicted E3 ubiquitin 29.5 24 0.00053 42.6 1.1 37 1116-1152 146-182 (384)
212 smart00249 PHD PHD zinc finger 29.3 23 0.00051 28.3 0.7 42 1118-1160 1-47 (47)
213 PRK00366 ispG 4-hydroxy-3-meth 29.1 49 0.0011 39.6 3.4 53 1155-1211 269-323 (360)
214 KOG4443 Putative transcription 29.1 29 0.00062 44.1 1.6 47 1117-1165 19-73 (694)
215 PF05290 Baculo_IE-1: Baculovi 28.8 32 0.0007 35.7 1.7 47 1116-1166 80-133 (140)
216 KOG2231 Predicted E3 ubiquitin 28.7 37 0.0008 43.6 2.5 45 1117-1165 1-52 (669)
217 PLN02189 cellulose synthase 28.5 44 0.00096 44.9 3.2 53 1112-1165 30-87 (1040)
218 PF07227 DUF1423: Protein of u 27.8 44 0.00095 41.0 2.8 31 920-952 21-51 (446)
219 TIGR02300 FYDLN_acid conserved 27.6 36 0.00077 35.2 1.7 32 997-1042 8-39 (129)
220 PF01907 Ribosomal_L37e: Ribos 27.5 25 0.00054 31.3 0.5 27 1189-1218 11-37 (55)
221 PF07191 zinc-ribbons_6: zinc- 27.0 23 0.0005 33.0 0.2 10 1055-1064 48-57 (70)
222 COG0143 MetG Methionyl-tRNA sy 27.0 41 0.00088 42.7 2.5 44 1054-1103 123-167 (558)
223 KOG1100 Predicted E3 ubiquitin 26.8 32 0.00069 38.3 1.3 39 1119-1165 161-200 (207)
224 KOG2932 E3 ubiquitin ligase in 26.6 24 0.00053 41.0 0.4 31 1134-1166 105-135 (389)
225 PLN02436 cellulose synthase A 26.6 50 0.0011 44.5 3.2 53 1112-1165 32-89 (1094)
226 PF03833 PolC_DP2: DNA polymer 26.5 22 0.00047 46.5 0.0 34 1029-1065 655-688 (900)
227 KOG3576 Ovo and related transc 26.2 17 0.00036 40.1 -0.9 96 1090-1204 116-223 (267)
228 KOG1311 DHHC-type Zn-finger pr 25.7 56 0.0012 37.8 3.2 48 1051-1104 107-154 (299)
229 KOG4399 C2HC-type Zn-finger pr 25.7 20 0.00044 40.7 -0.4 71 1052-1125 199-270 (325)
230 PRK00420 hypothetical protein; 25.7 41 0.00088 34.1 1.7 30 1115-1165 22-51 (112)
231 PF13894 zf-C2H2_4: C2H2-type 25.6 36 0.00077 23.5 1.0 19 1155-1173 1-19 (24)
232 PF06937 EURL: EURL protein; 25.5 43 0.00092 38.5 2.0 45 1113-1158 27-74 (285)
233 PRK08271 anaerobic ribonucleos 25.5 56 0.0012 42.0 3.3 54 1166-1225 541-594 (623)
234 TIGR00058 Hemerythrin hemeryth 25.3 3E+02 0.0065 27.6 7.8 96 361-467 10-110 (115)
235 KOG0802 E3 ubiquitin ligase [P 24.8 32 0.0007 43.3 1.0 44 1114-1165 477-520 (543)
236 PRK10722 hypothetical protein; 24.7 4.5E+02 0.0098 30.2 9.7 115 180-319 88-203 (247)
237 PF01780 Ribosomal_L37ae: Ribo 24.5 28 0.00061 34.0 0.3 26 1070-1099 33-61 (90)
238 COG1198 PriA Primosomal protei 24.2 54 0.0012 42.9 2.8 43 1154-1222 444-486 (730)
239 PF00412 LIM: LIM domain; Int 24.0 31 0.00068 29.5 0.5 40 1119-1168 1-40 (58)
240 KOG2272 Focal adhesion protein 23.4 42 0.00092 38.1 1.5 77 993-1083 115-203 (332)
241 PHA00626 hypothetical protein 22.9 52 0.0011 29.5 1.6 11 1056-1066 22-32 (59)
242 PF14952 zf-tcix: Putative tre 22.8 39 0.00083 28.8 0.8 22 1213-1235 13-34 (44)
243 KOG2129 Uncharacterized conser 22.5 3.7E+02 0.0081 33.0 8.9 15 183-197 197-211 (552)
244 KOG4718 Non-SMC (structural ma 22.4 38 0.00083 37.7 0.9 26 1136-1161 198-223 (235)
245 PF05502 Dynactin_p62: Dynacti 22.3 66 0.0014 40.2 3.0 10 1007-1016 5-14 (483)
246 PF08271 TF_Zn_Ribbon: TFIIB z 22.3 40 0.00087 28.0 0.8 6 1093-1098 21-26 (43)
247 smart00451 ZnF_U1 U1-like zinc 22.2 43 0.00093 25.9 0.9 11 1056-1066 2-12 (35)
248 PF06220 zf-U1: U1 zinc finger 22.2 34 0.00074 28.1 0.4 13 1055-1067 1-13 (38)
249 PRK01110 rpmF 50S ribosomal pr 22.1 56 0.0012 29.6 1.7 28 1193-1226 27-54 (60)
250 PRK00432 30S ribosomal protein 22.1 47 0.001 29.0 1.2 24 1074-1099 22-45 (50)
251 PF13824 zf-Mss51: Zinc-finger 22.0 54 0.0012 29.3 1.6 11 1070-1080 12-22 (55)
252 PF09723 Zn-ribbon_8: Zinc rib 21.8 46 0.001 27.7 1.1 31 1193-1223 5-38 (42)
253 KOG4367 Predicted Zn-finger pr 21.6 35 0.00077 41.1 0.5 33 1115-1151 3-35 (699)
254 COG3809 Uncharacterized protei 21.2 63 0.0014 30.8 1.9 52 1117-1190 2-55 (88)
255 PF09332 Mcm10: Mcm10 replicat 21.0 19 0.00042 42.8 -1.8 34 1191-1224 283-316 (344)
256 PRK12775 putative trifunctiona 20.8 34 0.00075 46.3 0.2 52 1154-1220 796-847 (1006)
257 PF15353 HECA: Headcase protei 20.8 43 0.00093 33.6 0.8 16 1137-1152 39-54 (107)
258 PF02701 zf-Dof: Dof domain, z 20.7 48 0.001 30.2 1.0 15 1212-1226 6-20 (63)
259 PF05129 Elf1: Transcription e 20.4 40 0.00086 32.2 0.5 31 1071-1101 21-56 (81)
260 KOG3842 Adaptor protein Pellin 20.4 82 0.0018 37.0 3.0 32 1135-1166 375-415 (429)
261 TIGR00622 ssl1 transcription f 20.2 2.1E+02 0.0046 29.1 5.5 46 1116-1161 55-110 (112)
262 PF12126 DUF3583: Protein of u 20.1 8.1E+02 0.018 29.0 10.6 131 46-197 14-152 (324)
No 1
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=100.00 E-value=1.4e-62 Score=537.78 Aligned_cols=253 Identities=50% Similarity=1.090 Sum_probs=240.8
Q ss_pred CCCCcccccccccCcccccccccccccccCCcccCcccccccCCCCCccccccccccccccccccCCCCCCCccCCCCcc
Q 000881 976 CSPSFRDAEKQVFGCEHYKRNCKLRAACCGKLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVGPVCTTLSCSGLSM 1055 (1239)
Q Consensus 976 ~~~~~~~~~~~~~gC~HY~r~c~l~~~cC~~~y~Cr~CHde~~~H~~~r~~~~~v~C~~C~~~q~~~~~C~~~~C~~~~~ 1055 (1239)
..+++.|+...++||+||+|+|++++|||+++|+||+||++..+|.++|+.+.+++|+.|.++||++++|.+ | +..|
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 356788999999999999999999999999999999999999999999999999999999999999999999 4 7789
Q ss_pred ceEecccccCcCCC-CccccCCCCCccccCCCCCccccccCCccccccccc-cccccccCCCCCCCcccccccccCCCcc
Q 000881 1056 AKYYCGICKFFDDE-RVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLAKKL-VDHKCREKGLETNCPICCDFLFTSSATV 1133 (1239)
Q Consensus 1056 ~~y~C~~C~l~dd~-k~~yHC~~CgiCRvG~gl~~~~fHC~~C~~C~~~~l-~~H~C~e~~~~~~CpICle~lf~s~~~v 1133 (1239)
|+|||.+||||||+ ..||||++|||||+|.++ |||||++|+.|++..+ +.|+|+|++++.|||||.|++|++...+
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 9999999999999999 6699999999999999999999999999
Q ss_pred eecCCCCccChhhHHHhhhcCCCCCCCCcCccChhhHhhhhHHHHhhcCCChhhhccCCceeccCCCCCCCCCceeeecc
Q 000881 1134 RALPCGHFMHSDCFQAYTCSHYICPICSKSLGDMAVYFGMLDALLASEQLPEEYRDRCQEILCNDCDKKGSAPFHWLYHK 1213 (1239)
Q Consensus 1134 ~~LpCGH~fH~~Ci~~wl~~~~~CPiCrksv~dm~~~~~~lD~~i~~~pmP~ey~~~~~~I~CnDC~~~s~~~~h~lg~k 1213 (1239)
..++|||++|..|+.++...+|+||+|.+ ++||..+|+++|.+|+.+|||++|++++++|+||||+.+++++|||||+|
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 000881 1214 CGFCGSYNTRVIKVESTNTYC 1234 (1239)
Q Consensus 1214 C~~C~syNT~~~~~~~~~~~~ 1234 (1239)
|+.|+|||||+++.+.....|
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=99.90 E-value=1.5e-25 Score=195.64 Aligned_cols=61 Identities=56% Similarity=1.049 Sum_probs=22.5
Q ss_pred ccChhhHhhhhHHHHhhcCCChhhhccCCceeccCCCCCCCCCceeeeccCCCCCCccccc
Q 000881 1164 LGDMAVYFGMLDALLASEQLPEEYRDRCQEILCNDCDKKGSAPFHWLYHKCGFCGSYNTRV 1224 (1239)
Q Consensus 1164 v~dm~~~~~~lD~~i~~~pmP~ey~~~~~~I~CnDC~~~s~~~~h~lg~kC~~C~syNT~~ 1224 (1239)
|+||+.+|++||++|+++|||++|++++++|+||||+++|.++||||||||++|+||||||
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=7.3e-21 Score=172.26 Aligned_cols=70 Identities=44% Similarity=1.197 Sum_probs=53.9
Q ss_pred ccccccc-ccccccccCCcccCcccccccCCCCCccccccccccccccccccCCCCCCCccCCCCccceEecccccCcC
Q 000881 990 CEHYKRN-CKLRAACCGKLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVGPVCTTLSCSGLSMAKYYCGICKFFD 1067 (1239)
Q Consensus 990 C~HY~r~-c~l~~~cC~~~y~Cr~CHde~~~H~~~r~~~~~v~C~~C~~~q~~~~~C~~~~C~~~~~~~y~C~~C~l~d 1067 (1239)
|+||+|+ |+|+||||++|||||+|||+.++|+++|+.+++|+||.|+++|++++. + | + |+|+|++|++||
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=99.19 E-value=1.6e-10 Score=112.70 Aligned_cols=129 Identities=33% Similarity=0.412 Sum_probs=115.6
Q ss_pred ChhHHHHHHHHHHHHHHHHHHHHHhhccCCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHhhh---hhhHHHHHH
Q 000881 43 PILIFLFFHKAIKSELDVLHRAAMAFATNLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIR---VKNIARTYS 119 (1239)
Q Consensus 43 Pi~~~~~~HkAlRreL~~l~~~a~~~~~~~gd~~~~~~l~~r~~~l~~~~~~H~~aEDevI~PaL~~R---v~~v~~~~~ 119 (1239)
||+.+...|+.||+.+..+...+... ++......+...+.+|...+..|+..|++++||.|+.+ .++.+..+.
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 24556899999999999999999999999999999944 457889999
Q ss_pred hhhhhHhHHHHHHHHHHHhhhcCchHHHHHHHHHHHHHHHHHHHhhHHHHHHHhhHH
Q 000881 120 LEHEGESVLFDQLFELLNSSMRNEESYRRELASCTGALQTSISQHMSKEEEQVFPLL 176 (1239)
Q Consensus 120 ~EH~~~~~l~~~L~~~l~~~~~~~~~~~~eLa~~l~~l~~~l~qHm~~EE~qv~PLl 176 (1239)
.||..+...++.+...+..+. ........+...+..+...+.+||.+||+.++|++
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 33466788888888888899999999999999986
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=99.18 E-value=3.5e-10 Score=110.23 Aligned_cols=124 Identities=26% Similarity=0.366 Sum_probs=110.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhhcccCCcccHHHHHHHHHHHHHHHHhhhhcccccchhhhhhhh--------hhHH
Q 000881 293 PIDEIMLWHNAIKRELNDIAEAARKIQLSGDFSDLSAFNKRLQFIAEVCIFHSIAEDKVIFPAVDVEL--------SFAQ 364 (1239)
Q Consensus 293 pid~L~~~HkALRrEL~~L~~~a~~~~~~gd~~~L~~L~~r~~fl~~vl~~Hs~aEDevlFPaL~~r~--------~me~ 364 (1239)
+++.|...|+.||+.++.+...+... ++..++..+...+.+|...+..|+..||+++||.|..+. .+..
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 000881 365 EHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPLA 425 (1239)
Q Consensus 365 EH~~ie~l~e~l~~ll~~~~~a~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qvfPLl 425 (1239)
||..+...++.+...+...... ......+...+..+...+..|+.+||+.+||++
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 9999999999999999776411 355778889999999999999999999999986
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=102.18 Aligned_cols=44 Identities=34% Similarity=0.951 Sum_probs=37.8
Q ss_pred CCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCC
Q 000881 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICS 1161 (1239)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCr 1161 (1239)
++||||++.+ ...+.+..++|||.||..|+.+|++.+++||+||
T Consensus 1 d~C~IC~~~~-~~~~~~~~l~C~H~fh~~Ci~~~~~~~~~CP~CR 44 (44)
T PF13639_consen 1 DECPICLEEF-EDGEKVVKLPCGHVFHRSCIKEWLKRNNSCPVCR 44 (44)
T ss_dssp -CETTTTCBH-HTTSCEEEETTSEEEEHHHHHHHHHHSSB-TTTH
T ss_pred CCCcCCChhh-cCCCeEEEccCCCeeCHHHHHHHHHhCCcCCccC
Confidence 4799999994 4466788899999999999999999999999997
No 7
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=98.85 E-value=1e-09 Score=123.58 Aligned_cols=57 Identities=32% Similarity=0.800 Sum_probs=49.4
Q ss_pred CCCCCCCcccccccccCC---------CcceecCCCCccChhhHHHhhhcCCCCCCCCcC-ccChhh
Q 000881 1113 KGLETNCPICCDFLFTSS---------ATVRALPCGHFMHSDCFQAYTCSHYICPICSKS-LGDMAV 1169 (1239)
Q Consensus 1113 ~~~~~~CpICle~lf~s~---------~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrks-v~dm~~ 1169 (1239)
...+..|.||+|+|+.++ .+.+.|||||.+|.+|++.|+.++.+|||||.+ ++|++.
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 678765
No 8
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.80 E-value=1.7e-09 Score=123.77 Aligned_cols=50 Identities=26% Similarity=0.808 Sum_probs=45.0
Q ss_pred CCCcccccccccCCCcceecCCCCccChhhHHHhhhcC-CCCCCCCcCccCh
Q 000881 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSH-YICPICSKSLGDM 1167 (1239)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~-~~CPiCrksv~dm 1167 (1239)
..|.||+|+ |..+++++.|||+|.||..||+.|+..+ ..||+|+..+..-
T Consensus 230 ~~CaIClEd-Y~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~di~~~ 280 (348)
T KOG4628|consen 230 DTCAICLED-YEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRDIRTD 280 (348)
T ss_pred ceEEEeecc-cccCCeeeEecCCCchhhccchhhHhhcCccCCCCCCcCCCC
Confidence 699999999 8889999999999999999999998766 5599999988653
No 9
>PRK10992 iron-sulfur cluster repair di-iron protein; Provisional
Probab=98.78 E-value=6.7e-08 Score=105.92 Aligned_cols=132 Identities=17% Similarity=0.310 Sum_probs=107.2
Q ss_pred hHHHH-HHHHHHHHHHHHHHHHHHHhhcc--cCCcccHHHHHHHHHHHHHHHHhhhhcccccchhhhhhhh---------
Q 000881 293 PIDEI-MLWHNAIKRELNDIAEAARKIQL--SGDFSDLSAFNKRLQFIAEVCIFHSIAEDKVIFPAVDVEL--------- 360 (1239)
Q Consensus 293 pid~L-~~~HkALRrEL~~L~~~a~~~~~--~gd~~~L~~L~~r~~fl~~vl~~Hs~aEDevlFPaL~~r~--------- 360 (1239)
-||.+ ..-|..+|++|..|.+.+.++.. .++...+..+..-+..|...+..|+..|++++||+|....
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 35555 78899999999999999977642 2334567888899999999999999999999999999621
Q ss_pred hhHHhHHHHHHHHHHHHHHHHHHhhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHh
Q 000881 361 SFAQEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPLARR 427 (1239)
Q Consensus 361 ~me~EH~~ie~l~e~l~~ll~~~~~a~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qvfPLl~~ 427 (1239)
.|..||+.+...+.+|..++...... ..+...++.+-..+..+...|.+|+.+||+.+||++..
T Consensus 155 vm~~EHd~~~~~l~~L~~lt~~~~~p---~~ac~~~~~l~~~l~~~~~dL~~HI~~EnniLFP~a~~ 218 (220)
T PRK10992 155 VMESEHDEAGELLEVIKHLTNNVTPP---PEACTTWRALYNGINELIDDLMEHIHLENNVLFPRALA 218 (220)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCC---hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Confidence 88999999999999999888664221 11134577777888889999999999999999998764
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=98.76 E-value=3.7e-09 Score=96.73 Aligned_cols=47 Identities=30% Similarity=0.756 Sum_probs=37.2
Q ss_pred CCCCCcccccccccCC---------CcceecCCCCccChhhHHHhhhcCCCCCCCC
Q 000881 1115 LETNCPICCDFLFTSS---------ATVRALPCGHFMHSDCFQAYTCSHYICPICS 1161 (1239)
Q Consensus 1115 ~~~~CpICle~lf~s~---------~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCr 1161 (1239)
.+++|+||++.+.+.. -++...+|||.||..||.+|+..+.+||+||
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 2445569999999999999999999999997
No 11
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=98.74 E-value=4.2e-09 Score=121.61 Aligned_cols=82 Identities=24% Similarity=0.659 Sum_probs=68.3
Q ss_pred CCCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcCccChhhHhhhhHHHHhhcCCChhhhccCCcee
Q 000881 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGDMAVYFGMLDALLASEQLPEEYRDRCQEIL 1195 (1239)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrksv~dm~~~~~~lD~~i~~~pmP~ey~~~~~~I~ 1195 (1239)
-.+||||||.|..+.+.+....|.|.||..|+.+|. ..+||+||.... |-+. ..-.
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 479999999999999999999999999999999995 679999996532 1111 1347
Q ss_pred ccCCCCCCCCCceeeeccCCC--CCCccccc
Q 000881 1196 CNDCDKKGSAPFHWLYHKCGF--CGSYNTRV 1224 (1239)
Q Consensus 1196 CnDC~~~s~~~~h~lg~kC~~--C~syNT~~ 1224 (1239)
|+.|+...+. |+.+.|++ ||.|+-.-
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 9999988777 99999987 99999754
No 12
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=98.73 E-value=1.3e-09 Score=102.29 Aligned_cols=57 Identities=30% Similarity=0.725 Sum_probs=49.5
Q ss_pred cccCccccccc---ccccccccCCcccCcccccccCCCCCccc-----cccccccccccccccCC
Q 000881 986 QVFGCEHYKRN---CKLRAACCGKLFTCRFCHDKVSDHSMDRK-----ATTEMMCMRCLKVQPVG 1042 (1239)
Q Consensus 986 ~~~gC~HY~r~---c~l~~~cC~~~y~Cr~CHde~~~H~~~r~-----~~~~v~C~~C~~~q~~~ 1042 (1239)
+..+|.||+.. ++|+|.||+|||+|..|||+.++|++.+. ..+.|+||.|.++-.++
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 56799999999 78999999999999999999999999864 34679999998766554
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=98.66 E-value=1.7e-07 Score=102.53 Aligned_cols=129 Identities=20% Similarity=0.296 Sum_probs=103.6
Q ss_pred HHHH-HHHHHHHHHHHHHHHHHHHhhcc--cCCcccHHHHHHHHHHHHHHHHhhhhcccccchhhhhhh-----------
Q 000881 294 IDEI-MLWHNAIKRELNDIAEAARKIQL--SGDFSDLSAFNKRLQFIAEVCIFHSIAEDKVIFPAVDVE----------- 359 (1239)
Q Consensus 294 id~L-~~~HkALRrEL~~L~~~a~~~~~--~gd~~~L~~L~~r~~fl~~vl~~Hs~aEDevlFPaL~~r----------- 359 (1239)
||.+ ...|..||++|..|...+.++.. ..+...+..+..-+..|..-+..|+..|++++||+|...
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 000881 360 L--SFAQEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPLA 425 (1239)
Q Consensus 360 ~--~me~EH~~ie~l~e~l~~ll~~~~~a~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qvfPLl 425 (1239)
. .|..||+++...+.+|..++..... +..+...++.+...+..+...|.+|..+||+.+||.+
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=3.9e-07 Score=99.98 Aligned_cols=129 Identities=17% Similarity=0.222 Sum_probs=109.1
Q ss_pred HHHHHHHHHHHHHHHHHHhhcc--CCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHhhh----hhhHHHHHHhhh
Q 000881 49 FFHKAIKSELDVLHRAAMAFAT--NLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIR----VKNIARTYSLEH 122 (1239)
Q Consensus 49 ~~HkAlRreL~~l~~~a~~~~~--~~gd~~~~~~l~~r~~~l~~~~~~H~~aEDevI~PaL~~R----v~~v~~~~~~EH 122 (1239)
.-|.-+|++|..|.+++..+.. + ++......+.+-++.|..-+..|+..|.+++||+|... +.+....|..||
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 5699999999999999988774 2 45567788899999999999999999999999999962 446789999999
Q ss_pred hhHhHHHHHHHHHHHhhhcCch--HHHHHHHHHHHHHHHHHHHhhHHHHHHHhhHHhh
Q 000881 123 EGESVLFDQLFELLNSSMRNEE--SYRRELASCTGALQTSISQHMSKEEEQVFPLLIE 178 (1239)
Q Consensus 123 ~~~~~l~~~L~~~l~~~~~~~~--~~~~eLa~~l~~l~~~l~qHm~~EE~qv~PLl~~ 178 (1239)
.++..++..|..+.+......+ ..++.|...+..+..-|.+|.++||..+||.+.+
T Consensus 161 d~~~~~l~~L~~lt~~~~~p~~ac~~~~~l~~~l~~~~~dL~~HI~~EnniLFP~a~~ 218 (220)
T PRK10992 161 DEAGELLEVIKHLTNNVTPPPEACTTWRALYNGINELIDDLMEHIHLENNVLFPRALA 218 (220)
T ss_pred HHHHHHHHHHHHHHhcCCCChhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Confidence 9999999999999988754332 5577777777777777999999999999998764
No 15
>PHA02929 N1R/p28-like protein; Provisional
Probab=98.54 E-value=4.9e-08 Score=107.63 Aligned_cols=54 Identities=17% Similarity=0.549 Sum_probs=42.9
Q ss_pred CCCCCCCcccccccccCCC----cceecCCCCccChhhHHHhhhcCCCCCCCCcCccC
Q 000881 1113 KGLETNCPICCDFLFTSSA----TVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1166 (1239)
Q Consensus 1113 ~~~~~~CpICle~lf~s~~----~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrksv~d 1166 (1239)
.+.+..||||+|.+..... -....+|||.||..||.+|+..+.+||+||..+..
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 12345899999999999999999999999998753
No 16
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.51 E-value=4.6e-08 Score=108.35 Aligned_cols=53 Identities=28% Similarity=0.723 Sum_probs=46.4
Q ss_pred cCCCCCCCcccccccccCCCcceecCCCCccChhhHHHhhh-cCCCCCCCCcCcc
Q 000881 1112 EKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC-SHYICPICSKSLG 1165 (1239)
Q Consensus 1112 e~~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~-~~~~CPiCrksv~ 1165 (1239)
|....-+|.||+++ |...+.+++|||.|.||..|+++|+. .+..||+||..+.
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 77888899999999999999999985 7899999998764
No 17
>COG3945 Uncharacterized conserved protein [Function unknown]
Probab=98.51 E-value=1.9e-06 Score=90.19 Aligned_cols=140 Identities=21% Similarity=0.284 Sum_probs=109.4
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHHhhcccC--CcccHHHHHHHHHHHHHHHHhhhhcccccchhhhhhhh---------
Q 000881 292 CPIDEIMLWHNAIKRELNDIAEAARKIQLSG--DFSDLSAFNKRLQFIAEVCIFHSIAEDKVIFPAVDVEL--------- 360 (1239)
Q Consensus 292 ~pid~L~~~HkALRrEL~~L~~~a~~~~~~g--d~~~L~~L~~r~~fl~~vl~~Hs~aEDevlFPaL~~r~--------- 360 (1239)
.-++.|+-.|+.|.+-|.-|+..+..+. +| +.+++..+.+-++-|++- .||..|+.++||-|..+.
T Consensus 8 ~~i~~lvEeH~yIlraL~iLr~~~~~~~-~g~i~y~~v~~iidFi~nfaDk--cHH~KEE~~LF~~m~~~g~~~~~~~i~ 84 (189)
T COG3945 8 DSIKLLVEEHTYILRALSILRKALDLIK-NGPIDYSDVKEIIDFIRNFADK--CHHGKEEKLLFNYMEHEGGPFEEGPIY 84 (189)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhccc-CCCCCHHHHHHHHHHHHHHHHh--ccchHHHHHHHHHHHHhCCCcccCcee
Confidence 3578889999999999999988887775 43 233444444444444443 578889999999999765
Q ss_pred hhHHhHHHHHHHHHHHHHHHHHHhhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhhCCHHHHHHHHHh
Q 000881 361 SFAQEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPLARRHFSPKRQRELLYQ 440 (1239)
Q Consensus 361 ~me~EH~~ie~l~e~l~~ll~~~~~a~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qvfPLl~~~fS~eEq~eL~~~ 440 (1239)
.|..||...-.++..|.+.+..+...+. +....++..+......+.+|+.+|+.++||++++.||.+ |.++..+
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 223556666667788999999999999999999999999 6666544
No 18
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=98.50 E-value=7.6e-08 Score=77.42 Aligned_cols=44 Identities=34% Similarity=0.921 Sum_probs=36.9
Q ss_pred CCcccccccccCCCcceecCCCCccChhhHHHhhhc-CCCCCCCCcCc
Q 000881 1118 NCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS-HYICPICSKSL 1164 (1239)
Q Consensus 1118 ~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~-~~~CPiCrksv 1164 (1239)
.|+||++.+ ...+...+|||.||..|+..|+.. +.+||+|++.+
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 345566779999999999999987 78899999764
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=1.6e-06 Score=94.94 Aligned_cols=127 Identities=24% Similarity=0.303 Sum_probs=105.0
Q ss_pred HHHHHHHHHHHHHHHHHHhhcc-CCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHhh--h-h-----hhHHHHHH
Q 000881 49 FFHKAIKSELDVLHRAAMAFAT-NLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDI--R-V-----KNIARTYS 119 (1239)
Q Consensus 49 ~~HkAlRreL~~l~~~a~~~~~-~~gd~~~~~~l~~r~~~l~~~~~~H~~aEDevI~PaL~~--R-v-----~~v~~~~~ 119 (1239)
.-|..||++|..|..++..+.. .-.+...+..+.+-++.|..-+..|+..|.+++||+|.. + . .+.+..|.
T Consensus 78 ~hH~~i~~~l~~L~~l~~kv~~~hg~~~~~l~~l~~~~~~~~~eL~~H~~kEE~~LFP~l~~~~~g~~~~~~~~pi~~m~ 157 (216)
T TIGR03652 78 RHHEYLREELPELIPLATKVARVHGDHHPELIGLAELFRELKAELEQHLMKEEQILFPAIIEYKRGNPAQAIGTPISVME 157 (216)
T ss_pred HHhHHHHHHHHHHHHHHHHHHHHhCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHccCccccccchHHHHH
Confidence 7799999999999998888774 114456778999999999999999999999999999984 2 1 23889999
Q ss_pred hhhhhHhHHHHHHHHHHHhhhcCch--HHHHHHHHHHHHHHHHHHHhhHHHHHHHhhH
Q 000881 120 LEHEGESVLFDQLFELLNSSMRNEE--SYRRELASCTGALQTSISQHMSKEEEQVFPL 175 (1239)
Q Consensus 120 ~EH~~~~~l~~~L~~~l~~~~~~~~--~~~~eLa~~l~~l~~~l~qHm~~EE~qv~PL 175 (1239)
.||.++...+.+|..+.+.....++ ..++.+...+.++..-|.+|.++||..+||.
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 4566666666777777999999999999994
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=98.40 E-value=1.1e-07 Score=76.63 Aligned_cols=39 Identities=41% Similarity=0.974 Sum_probs=33.4
Q ss_pred CcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCC
Q 000881 1119 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPIC 1160 (1239)
Q Consensus 1119 CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiC 1160 (1239)
||||++.+.+ ++..++|||.|+..|+.+|+..+.+||+|
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 8999988543 56789999999999999999889999998
No 21
>PRK13276 cell wall biosynthesis protein ScdA; Provisional
Probab=98.31 E-value=6.3e-06 Score=90.51 Aligned_cols=128 Identities=13% Similarity=0.173 Sum_probs=107.4
Q ss_pred HHH-HHHHHHHHHHHHHHHHHHHHhhcc--cCCcccHHHHHHHHHHHHHHHHhhhhcccccchhhhhhhh----------
Q 000881 294 IDE-IMLWHNAIKRELNDIAEAARKIQL--SGDFSDLSAFNKRLQFIAEVCIFHSIAEDKVIFPAVDVEL---------- 360 (1239)
Q Consensus 294 id~-L~~~HkALRrEL~~L~~~a~~~~~--~gd~~~L~~L~~r~~fl~~vl~~Hs~aEDevlFPaL~~r~---------- 360 (1239)
||. +...|..+|++|..|...+.++.. .++...+..+...+..+..-|..|-..|+.++||++....
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 443 367899999999999999988742 3445578999999999999999999999999999996411
Q ss_pred ---hhHHhHHHHHHHHHHHHHHHHHHhhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 000881 361 ---SFAQEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPL 424 (1239)
Q Consensus 361 ---~me~EH~~ie~l~e~l~~ll~~~~~a~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qvfPL 424 (1239)
.|+.||+.+.+.+.+|++++...... ..+...|+.|=..+.++...|.+|.+.|-+.+||-
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 22
>PRK13276 cell wall biosynthesis protein ScdA; Provisional
Probab=98.29 E-value=7.2e-06 Score=90.02 Aligned_cols=125 Identities=21% Similarity=0.253 Sum_probs=108.6
Q ss_pred HHHHHHHHHHHHHHHHHHhhcc--CCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHhhh--------hhhHHHHH
Q 000881 49 FFHKAIKSELDVLHRAAMAFAT--NLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIR--------VKNIARTY 118 (1239)
Q Consensus 49 ~~HkAlRreL~~l~~~a~~~~~--~~gd~~~~~~l~~r~~~l~~~~~~H~~aEDevI~PaL~~R--------v~~v~~~~ 118 (1239)
..|.-+|++|..|..++..|.. + ++......|.+.|..|+.=+..|..-|.+++||++... +.+.+..|
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 34678999
Q ss_pred HhhhhhHhHHHHHHHHHHHhhhcCch--HHHHHHHHHHHHHHHHHHHhhHHHHHHHhh
Q 000881 119 SLEHEGESVLFDQLFELLNSSMRNEE--SYRRELASCTGALQTSISQHMSKEEEQVFP 174 (1239)
Q Consensus 119 ~~EH~~~~~l~~~L~~~l~~~~~~~~--~~~~eLa~~l~~l~~~l~qHm~~EE~qv~P 174 (1239)
..||+++.+.+.+|.++.+-++..++ ..|+.|=.-+.++..-|.+|.+.|-.-+||
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 566666666666777799999999999988
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=98.26 E-value=4e-07 Score=77.17 Aligned_cols=47 Identities=32% Similarity=0.824 Sum_probs=38.8
Q ss_pred CCCCcccccccccCCCcceecCCCCc-cChhhHHHhhhcCCCCCCCCcCccC
Q 000881 1116 ETNCPICCDFLFTSSATVRALPCGHF-MHSDCFQAYTCSHYICPICSKSLGD 1166 (1239)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCGH~-fH~~Ci~~wl~~~~~CPiCrksv~d 1166 (1239)
+..|+||++.. ..+..+||||. |...|+..|.....+||+||++|.+
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 46899998872 34678899999 9999999999999999999998753
No 24
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=98.22 E-value=8.3e-07 Score=83.18 Aligned_cols=32 Identities=22% Similarity=0.587 Sum_probs=26.6
Q ss_pred ceecCCCCccChhhHHHhhhc---CCCCCCCCcCc
Q 000881 1133 VRALPCGHFMHSDCFQAYTCS---HYICPICSKSL 1164 (1239)
Q Consensus 1133 v~~LpCGH~fH~~Ci~~wl~~---~~~CPiCrksv 1164 (1239)
+..-.|||.||.+||.+|+.. +.+||+||...
T Consensus 47 lv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w 81 (85)
T PF12861_consen 47 LVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPW 81 (85)
T ss_pred eeeccCccHHHHHHHHHHHccccCCCCCCCcCCee
Confidence 344579999999999999964 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=32.7
Q ss_pred CcccccccccCCCcceecCCCCccChhhHHHhhh-cCCCCCCC
Q 000881 1119 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC-SHYICPIC 1160 (1239)
Q Consensus 1119 CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~-~~~~CPiC 1160 (1239)
|+||++. ......++|||.||..|++.|+. .+.+||+|
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 34567889999999999999987 66789998
No 26
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.09 E-value=2.2e-06 Score=70.97 Aligned_cols=44 Identities=30% Similarity=0.764 Sum_probs=37.9
Q ss_pred CCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCc
Q 000881 1118 NCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSK 1162 (1239)
Q Consensus 1118 ~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrk 1162 (1239)
.|+||.+.+ +......+++|||+|...|+..+......||+|++
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
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.03 E-value=3.7e-06 Score=89.81 Aligned_cols=51 Identities=25% Similarity=0.682 Sum_probs=39.8
Q ss_pred cCCCCCCCcccccccccCCCcceecCCCCccChhhHHHhhhc----------------CCCCCCCCcCccC
Q 000881 1112 EKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS----------------HYICPICSKSLGD 1166 (1239)
Q Consensus 1112 e~~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~----------------~~~CPiCrksv~d 1166 (1239)
+...+..||||++.+ . + .++++|||.|+..||.+|+.. ..+||+||..+..
T Consensus 14 ~~~~~~~CpICld~~-~--d-PVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~ 80 (193)
T PLN03208 14 DSGGDFDCNICLDQV-R--D-PVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE 80 (193)
T ss_pred cCCCccCCccCCCcC-C--C-cEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence 344568999999973 2 2 355799999999999999742 3589999999854
No 28
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.01 E-value=2.4e-06 Score=70.34 Aligned_cols=38 Identities=37% Similarity=0.946 Sum_probs=27.4
Q ss_pred CcccccccccCCCcceecCCCCccChhhHHHhhhcC----CCCCCC
Q 000881 1119 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSH----YICPIC 1160 (1239)
Q Consensus 1119 CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~----~~CPiC 1160 (1239)
||||++.+.+ .+.|+|||.|...||..|.+.. +.||+|
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 3669999999999999987542 689998
No 29
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.01 E-value=1.6e-06 Score=106.79 Aligned_cols=53 Identities=30% Similarity=0.702 Sum_probs=45.0
Q ss_pred cCCCCCCCcccccccccCCC-cceecCCCCccChhhHHHhhhcCCCCCCCCcCc
Q 000881 1112 EKGLETNCPICCDFLFTSSA-TVRALPCGHFMHSDCFQAYTCSHYICPICSKSL 1164 (1239)
Q Consensus 1112 e~~~~~~CpICle~lf~s~~-~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrksv 1164 (1239)
....+..|+||.|.|+.+.. ....|||||.||..|+..|++..++||+||..+
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 34557899999999887533 356799999999999999999999999999943
No 30
>COG2846 Regulator of cell morphogenesis and NO signaling [Cell division and chromosome partitioning]
Probab=98.01 E-value=5.2e-05 Score=80.75 Aligned_cols=128 Identities=18% Similarity=0.316 Sum_probs=105.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcc-cCC-cccHHHHHHHHHHHHHHHHhhhhcccccchhhhhhhh---------hhH
Q 000881 295 DEIMLWHNAIKRELNDIAEAARKIQL-SGD-FSDLSAFNKRLQFIAEVCIFHSIAEDKVIFPAVDVEL---------SFA 363 (1239)
Q Consensus 295 d~L~~~HkALRrEL~~L~~~a~~~~~-~gd-~~~L~~L~~r~~fl~~vl~~Hs~aEDevlFPaL~~r~---------~me 363 (1239)
.++..+|+-.|.+|.+|-..+.++.. -|| ++-...|.+-+..|...|.-|-..|++++||++..-. .|+
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 45688999999999999999988732 344 3456888888999999999999999999999998432 899
Q ss_pred HhHHHHHHHHHHHHHHHHHHhhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 000881 364 QEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPLA 425 (1239)
Q Consensus 364 ~EH~~ie~l~e~l~~ll~~~~~a~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qvfPLl 425 (1239)
.||++...+++.+..++...... ..+...++.|=.-+..+.+.+.+|++-|=..+||=+
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 222445677777788889999999999999999954
No 31
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=98.00 E-value=2.3e-06 Score=69.22 Aligned_cols=39 Identities=38% Similarity=0.961 Sum_probs=32.9
Q ss_pred CcccccccccCCCcceecCCCCccChhhHHHhhh--cCCCCCCC
Q 000881 1119 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC--SHYICPIC 1160 (1239)
Q Consensus 1119 CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~--~~~~CPiC 1160 (1239)
||||++.+.. ++..++|||.|+..|+.+|+. ...+||+|
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 8999988432 346899999999999999987 56889998
No 32
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=97.99 E-value=3.8e-06 Score=77.06 Aligned_cols=48 Identities=21% Similarity=0.444 Sum_probs=36.9
Q ss_pred CCCcccccccccCCCc-ceecCCCCccChhhHHHhhhcCCCCCCCCcCc
Q 000881 1117 TNCPICCDFLFTSSAT-VRALPCGHFMHSDCFQAYTCSHYICPICSKSL 1164 (1239)
Q Consensus 1117 ~~CpICle~lf~s~~~-v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrksv 1164 (1239)
..||-|.-.+....+- +.---|.|.||.+||.+|+.+...||+++++.
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 4577776655344432 23348999999999999999999999999875
No 33
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.95 E-value=3.3e-06 Score=88.31 Aligned_cols=47 Identities=32% Similarity=0.732 Sum_probs=39.4
Q ss_pred CCCCcccccccccCCCcc-eecCCCCccChhhHHHhhhcCCCCCCCCcCcc
Q 000881 1116 ETNCPICCDFLFTSSATV-RALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1165 (1239)
Q Consensus 1116 ~~~CpICle~lf~s~~~v-~~LpCGH~fH~~Ci~~wl~~~~~CPiCrksv~ 1165 (1239)
-..|||||+. +.. .+ ....|||.|.+.||+..++...+||+|+|.|.
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 23 34799999999999999999999999999654
No 34
>PHA02926 zinc finger-like protein; Provisional
Probab=97.85 E-value=8.9e-06 Score=87.92 Aligned_cols=53 Identities=21% Similarity=0.541 Sum_probs=40.6
Q ss_pred CCCCCCCcccccccccCCC-----cceecCCCCccChhhHHHhhhc------CCCCCCCCcCcc
Q 000881 1113 KGLETNCPICCDFLFTSSA-----TVRALPCGHFMHSDCFQAYTCS------HYICPICSKSLG 1165 (1239)
Q Consensus 1113 ~~~~~~CpICle~lf~s~~-----~v~~LpCGH~fH~~Ci~~wl~~------~~~CPiCrksv~ 1165 (1239)
.+.+..|+||+|.++.... --...+|+|.|+..||..|... ..+||+||..+.
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=97.80 E-value=1.8e-05 Score=69.44 Aligned_cols=45 Identities=22% Similarity=0.394 Sum_probs=38.4
Q ss_pred CCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcCcc
Q 000881 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1165 (1239)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrksv~ 1165 (1239)
-.||||++.|.+ + ..++|||.|...||.+|+..+.+||+|++.+.
T Consensus 2 ~~Cpi~~~~~~~---P-v~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~ 46 (63)
T smart00504 2 FLCPISLEVMKD---P-VILPSGQTYERRAIEKWLLSHGTDPVTGQPLT 46 (63)
T ss_pred cCCcCCCCcCCC---C-EECCCCCEEeHHHHHHHHHHCCCCCCCcCCCC
Confidence 469999998543 3 45799999999999999988899999999873
No 36
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=97.76 E-value=1.2e-05 Score=66.63 Aligned_cols=39 Identities=38% Similarity=0.950 Sum_probs=23.4
Q ss_pred CcccccccccCCCcceecCCCCccChhhHHHhhhc----CCCCC
Q 000881 1119 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS----HYICP 1158 (1239)
Q Consensus 1119 CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~----~~~CP 1158 (1239)
||||.| +.+...+.++|+|||+|-..|++++... ..+||
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 4454556678999999999999999863 35787
No 37
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=97.70 E-value=1.2e-05 Score=101.50 Aligned_cols=122 Identities=25% Similarity=0.555 Sum_probs=80.8
Q ss_pred CCCccccccccccccccc-----cccCCCCCCCccCCCCccceEecccccCcCCCCccccCCCCCccccCCCCCcccccc
Q 000881 1020 HSMDRKATTEMMCMRCLK-----VQPVGPVCTTLSCSGLSMAKYYCGICKFFDDERVVYHCPFCNLCRVGRGLGVDFFHC 1094 (1239)
Q Consensus 1020 H~~~r~~~~~v~C~~C~~-----~q~~~~~C~~~~C~~~~~~~y~C~~C~l~dd~k~~yHC~~CgiCRvG~gl~~~~fHC 1094 (1239)
|...-..+..--|..|+. .|.++.+|....| ++.|+--|++=+--. ..|| |- +|--||
T Consensus 3408 ~T~~PTtsS~~aCRFCGs~~~tE~sav~~vCs~aDC--~eYAK~ACs~~H~C~--------H~CG----Gv---kNEE~C 3470 (3738)
T KOG1428|consen 3408 HTGKPTTSSSEACRFCGSRSGTELSAVGSVCSDADC--QEYAKIACSKTHPCG--------HPCG----GV---KNEEHC 3470 (3738)
T ss_pred hcCCCCccchhHhhhccCCCCcchhcccCccccHHH--HHHHHHHHhccCcCC--------Cccc----Cc---cchhhc
Confidence 333333334457999974 3667889998888 467777776522110 2354 21 377888
Q ss_pred CCccccccccccccccccCCCCCCCcccccccccCCCcceecCCCCccChhhHHH-----hhhc-----CCCCCCCCcCc
Q 000881 1095 MTCNCCLAKKLVDHKCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQA-----YTCS-----HYICPICSKSL 1164 (1239)
Q Consensus 1095 ~~C~~C~~~~l~~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~-----wl~~-----~~~CPiCrksv 1164 (1239)
.-|-.|-.-. ..+..++.|.||.-+ --+-.+.+.|.|||.||.+|... |+.- -..||||...|
T Consensus 3471 LPCl~Cdks~------tkQD~DDmCmICFTE-~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~I 3543 (3738)
T KOG1428|consen 3471 LPCLHCDKSA------TKQDADDMCMICFTE-ALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKI 3543 (3738)
T ss_pred ccccccChhh------hhcccCceEEEEehh-hhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchh
Confidence 8888773211 134567899999765 34556788999999999999865 5432 24799999988
Q ss_pred c
Q 000881 1165 G 1165 (1239)
Q Consensus 1165 ~ 1165 (1239)
.
T Consensus 3544 n 3544 (3738)
T KOG1428|consen 3544 N 3544 (3738)
T ss_pred h
Confidence 4
No 38
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=97.66 E-value=1.1e-05 Score=73.67 Aligned_cols=28 Identities=25% Similarity=0.718 Sum_probs=23.9
Q ss_pred CCCCccChhhHHHhhhc---CCCCCCCCcCc
Q 000881 1137 PCGHFMHSDCFQAYTCS---HYICPICSKSL 1164 (1239)
Q Consensus 1137 pCGH~fH~~Ci~~wl~~---~~~CPiCrksv 1164 (1239)
-|.|.||.+||.+|+.. ...||+||...
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 47799999753
No 39
>COG3945 Uncharacterized conserved protein [Function unknown]
Probab=97.55 E-value=0.00083 Score=70.93 Aligned_cols=139 Identities=18% Similarity=0.237 Sum_probs=109.8
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHhhccCCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHhhhh----hhHHHHHH
Q 000881 44 ILIFLFFHKAIKSELDVLHRAAMAFATNLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIRV----KNIARTYS 119 (1239)
Q Consensus 44 i~~~~~~HkAlRreL~~l~~~a~~~~~~~gd~~~~~~l~~r~~~l~~~~~~H~~aEDevI~PaL~~Rv----~~v~~~~~ 119 (1239)
|..|+==|+-|-|-|.-|....--+..+-=|.+++..+++-++-+.+ ++||.-|+.++||-+..+- ++....|.
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 56777789999998888877776666511245566666655555544 5688999999999999885 47899999
Q ss_pred hhhhhHhHHHHHHHHHHHhhhcCch----HHHHHHHHHHHHHHHHHHHhhHHHHHHHhhHHhhcCCHHHHHHHH
Q 000881 120 LEHEGESVLFDQLFELLNSSMRNEE----SYRRELASCTGALQTSISQHMSKEEEQVFPLLIEKFSFEEQASLV 189 (1239)
Q Consensus 120 ~EH~~~~~l~~~L~~~l~~~~~~~~----~~~~eLa~~l~~l~~~l~qHm~~EE~qv~PLl~~~fS~~E~a~L~ 189 (1239)
-||..--.++..+.+++.+|.-.++ .+...+++.+.- +.+|.++|+..+||.+.+.||.+ |..+.
T Consensus 88 ~EH~~~R~i~r~lee~~~~~kngd~~~~~~~i~~A~~y~~l----ikrHIdkEdnvlfp~a~~~~s~e-~~~v~ 156 (189)
T COG3945 88 VEHGEGRYIIRDLEEAYERLKNGDEDSKDDVIDYAVAYLNL----IKRHIDKEDNVLFPFAESTLSEE-LNEVN 156 (189)
T ss_pred hhhhhHHHHHHHHHHHHHHHHccccchHHHHHHHHHHHHHH----HHHHHhhhhhHHHHHHHHHHHHH-HHHHH
Confidence 9999999999999999999975544 555566666666 99999999999999999999999 55443
No 40
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.54 E-value=1.3e-05 Score=97.67 Aligned_cols=75 Identities=15% Similarity=0.389 Sum_probs=51.9
Q ss_pred ccccCCccccccccc-cccccc-cCCCCCCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcCccC
Q 000881 1091 FFHCMTCNCCLAKKL-VDHKCR-EKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1166 (1239)
Q Consensus 1091 ~fHC~~C~~C~~~~l-~~H~C~-e~~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrksv~d 1166 (1239)
--.|..|-.|.|-.. ..-.|+ .+.....||+|+-. |.........+|+|+||.+||..|.+.-.+||+||+.+..
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 344555555555422 222333 23446789999976 4333334457999999999999999999999999998764
No 41
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=97.53 E-value=3.3e-05 Score=86.35 Aligned_cols=46 Identities=24% Similarity=0.693 Sum_probs=38.9
Q ss_pred CCCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcCcc
Q 000881 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1165 (1239)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrksv~ 1165 (1239)
...|.+|||.... ....||||.|+..||..|.....-||+||..+.
T Consensus 239 ~~kC~LCLe~~~~----pSaTpCGHiFCWsCI~~w~~ek~eCPlCR~~~~ 284 (293)
T KOG0317|consen 239 TRKCSLCLENRSN----PSATPCGHIFCWSCILEWCSEKAECPLCREKFQ 284 (293)
T ss_pred CCceEEEecCCCC----CCcCcCcchHHHHHHHHHHccccCCCcccccCC
Confidence 3579999998433 356899999999999999998888999998754
No 42
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.52 E-value=5.1e-05 Score=89.60 Aligned_cols=47 Identities=26% Similarity=0.575 Sum_probs=39.6
Q ss_pred CCCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcCccC
Q 000881 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1166 (1239)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrksv~d 1166 (1239)
...|+||++.+.. + ++++|||.|+..||..|+.....||+|+..+..
T Consensus 26 ~l~C~IC~d~~~~---P-vitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~~ 72 (397)
T TIGR00599 26 SLRCHICKDFFDV---P-VLTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQE 72 (397)
T ss_pred ccCCCcCchhhhC---c-cCCCCCCchhHHHHHHHHhCCCCCCCCCCcccc
Confidence 4689999998432 3 358999999999999999888899999998863
No 43
>COG2846 Regulator of cell morphogenesis and NO signaling [Cell division and chromosome partitioning]
Probab=97.51 E-value=0.00092 Score=71.53 Aligned_cols=132 Identities=18% Similarity=0.239 Sum_probs=106.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHhhcc-CCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHhhh----hhhHHHHHH
Q 000881 45 LIFLFFHKAIKSELDVLHRAAMAFAT-NLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIR----VKNIARTYS 119 (1239)
Q Consensus 45 ~~~~~~HkAlRreL~~l~~~a~~~~~-~~gd~~~~~~l~~r~~~l~~~~~~H~~aEDevI~PaL~~R----v~~v~~~~~ 119 (1239)
.|..-+|.-.|.+|..|..+|..|.. -.+.+...+.|.+-+.-|..-+--|-.-|++++||.+..= +.+....|+
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 1155678889999999999999999999999999999642 236889999
Q ss_pred hhhhhHhHHHHHHHHHHHhhhcCch--HHHHHHHHHHHHHHHHHHHhhHHHHHHHhhHH
Q 000881 120 LEHEGESVLFDQLFELLNSSMRNEE--SYRRELASCTGALQTSISQHMSKEEEQVFPLL 176 (1239)
Q Consensus 120 ~EH~~~~~l~~~L~~~l~~~~~~~~--~~~~eLa~~l~~l~~~l~qHm~~EE~qv~PLl 176 (1239)
.||+++..+++.+.++.+..+-..+ ..++.|=.-+.++.+-+.+|++.|---+||=+
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 34444444444555559999999988888744
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=97.31 E-value=0.00013 Score=62.23 Aligned_cols=42 Identities=26% Similarity=0.736 Sum_probs=32.2
Q ss_pred CCcccccccccCCCcceecCCC-----CccChhhHHHhhhc--CCCCCCCC
Q 000881 1118 NCPICCDFLFTSSATVRALPCG-----HFMHSDCFQAYTCS--HYICPICS 1161 (1239)
Q Consensus 1118 ~CpICle~lf~s~~~v~~LpCG-----H~fH~~Ci~~wl~~--~~~CPiCr 1161 (1239)
.|-||+++ ...+...+.||. |++|..|+.+|+.. +.+||+|+
T Consensus 1 ~CrIC~~~--~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~ 49 (49)
T smart00744 1 ICRICHDE--GDEGDPLVSPCRCKGSLKYVHQECLERWINESGNKTCEICK 49 (49)
T ss_pred CccCCCCC--CCCCCeeEeccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence 48999983 333445578985 99999999999854 45899995
No 45
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.28 E-value=0.00025 Score=77.59 Aligned_cols=44 Identities=32% Similarity=0.813 Sum_probs=37.1
Q ss_pred CCCCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCc
Q 000881 1115 LETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSK 1162 (1239)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrk 1162 (1239)
....||||++++ ... ..+||||.|...|+..+......||.||.
T Consensus 12 ~~~~C~iC~~~~-~~p---~~l~C~H~~c~~C~~~~~~~~~~Cp~cr~ 55 (386)
T KOG2177|consen 12 EELTCPICLEYF-REP---VLLPCGHNFCRACLTRSWEGPLSCPVCRP 55 (386)
T ss_pred ccccChhhHHHh-hcC---ccccccchHhHHHHHHhcCCCcCCcccCC
Confidence 457899999994 432 78999999999999998766689999994
No 46
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=97.28 E-value=7.2e-05 Score=68.29 Aligned_cols=50 Identities=26% Similarity=0.594 Sum_probs=23.7
Q ss_pred CCCCcccccccccC-CCccee---cCCCCccChhhHHHhhhc-----------CCCCCCCCcCcc
Q 000881 1116 ETNCPICCDFLFTS-SATVRA---LPCGHFMHSDCFQAYTCS-----------HYICPICSKSLG 1165 (1239)
Q Consensus 1116 ~~~CpICle~lf~s-~~~v~~---LpCGH~fH~~Ci~~wl~~-----------~~~CPiCrksv~ 1165 (1239)
+..|+||+.++.+. ..+..+ -.|+..||..|+.+|+.. ..+||.|++.|.
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 333333 379999999999999742 135999999873
No 47
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=97.25 E-value=0.00014 Score=82.31 Aligned_cols=60 Identities=25% Similarity=0.611 Sum_probs=45.6
Q ss_pred CCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcCccChhh-HhhhhHHHHhh
Q 000881 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGDMAV-YFGMLDALLAS 1180 (1239)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrksv~dm~~-~~~~lD~~i~~ 1180 (1239)
-.|-||.|| |.- .+..||||+|+.-||..++.++..||.|+.++..-.. .-+.+|++|+.
T Consensus 24 LRC~IC~ey-f~i---p~itpCsHtfCSlCIR~~L~~~p~CP~C~~~~~Es~Lr~n~il~Eiv~S 84 (442)
T KOG0287|consen 24 LRCGICFEY-FNI---PMITPCSHTFCSLCIRKFLSYKPQCPTCCVTVTESDLRNNRILDEIVKS 84 (442)
T ss_pred HHHhHHHHH-hcC---ceeccccchHHHHHHHHHhccCCCCCceecccchhhhhhhhHHHHHHHH
Confidence 469999999 432 3556999999999999999999999999999864221 23456665543
No 48
>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=0.00023 Score=81.34 Aligned_cols=51 Identities=22% Similarity=0.560 Sum_probs=38.1
Q ss_pred CCCCcccccccccCCCc-ceecCCCCccChhhHHHh-hhcCCCCCCCCcCccC
Q 000881 1116 ETNCPICCDFLFTSSAT-VRALPCGHFMHSDCFQAY-TCSHYICPICSKSLGD 1166 (1239)
Q Consensus 1116 ~~~CpICle~lf~s~~~-v~~LpCGH~fH~~Ci~~w-l~~~~~CPiCrksv~d 1166 (1239)
+..||||+...+.+.+. ..+-+|||.|+..|++.. ......||+|++++-.
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 46899999965555442 222389999999999994 4556789999998753
No 49
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.23 E-value=0.00015 Score=79.16 Aligned_cols=52 Identities=23% Similarity=0.540 Sum_probs=39.8
Q ss_pred CCCCCCCcccccccccCCCcceecCCCCccChhhHHHhhhc---CCCCCCCCcCccChh
Q 000881 1113 KGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS---HYICPICSKSLGDMA 1168 (1239)
Q Consensus 1113 ~~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~---~~~CPiCrksv~dm~ 1168 (1239)
.+..-+|-||||- ..+ .++..|||.|+..||.+|+.. +..||+|+-.|.+-+
T Consensus 44 ~~~~FdCNICLd~---akd-PVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~ 98 (230)
T KOG0823|consen 44 DGGFFDCNICLDL---AKD-PVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDT 98 (230)
T ss_pred CCCceeeeeeccc---cCC-CEEeecccceehHHHHHHHhhcCCCeeCCccccccccce
Confidence 3456789999876 333 456679999999999999864 356899998886543
No 50
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=97.22 E-value=7.1e-05 Score=71.96 Aligned_cols=28 Identities=25% Similarity=0.637 Sum_probs=26.4
Q ss_pred cCCCCccChhhHHHhhhcCCCCCCCCcC
Q 000881 1136 LPCGHFMHSDCFQAYTCSHYICPICSKS 1163 (1239)
Q Consensus 1136 LpCGH~fH~~Ci~~wl~~~~~CPiCrks 1163 (1239)
--|.|.||.+||..|++++..||+|.+.
T Consensus 79 G~CNHaFH~hCisrWlktr~vCPLdn~e 106 (114)
T KOG2930|consen 79 GVCNHAFHFHCISRWLKTRNVCPLDNKE 106 (114)
T ss_pred eecchHHHHHHHHHHHhhcCcCCCcCcc
Confidence 4799999999999999999999999985
No 51
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.19 E-value=0.00013 Score=84.01 Aligned_cols=48 Identities=27% Similarity=0.632 Sum_probs=38.2
Q ss_pred CCCCcccccccccCCCcceecC-CCCccChhhHHHhhhc---CCCCCCCCcCc
Q 000881 1116 ETNCPICCDFLFTSSATVRALP-CGHFMHSDCFQAYTCS---HYICPICSKSL 1164 (1239)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~Lp-CGH~fH~~Ci~~wl~~---~~~CPiCrksv 1164 (1239)
...|.|| ++++.....+..+. |||+||..|+.+|... +.+||||+-.+
T Consensus 4 ~A~C~Ic-~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~ 55 (465)
T KOG0827|consen 4 MAECHIC-IDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKL 55 (465)
T ss_pred cceeeEe-ccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeecc
Confidence 3579999 66688777777664 9999999999999865 35899999333
No 52
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.18 E-value=0.00018 Score=85.81 Aligned_cols=49 Identities=29% Similarity=0.643 Sum_probs=36.8
Q ss_pred CCCCCCcccccccccCCCcceecCCCCccChhhHHHhhhc-----CCCCCCCCcCccC
Q 000881 1114 GLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS-----HYICPICSKSLGD 1166 (1239)
Q Consensus 1114 ~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~-----~~~CPiCrksv~d 1166 (1239)
+.+..||||+++ . .-+ ..+.|||.|+..||-+|+.. ...||||+..|.-
T Consensus 184 ~t~~~CPICL~~-~--~~p-~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~ 237 (513)
T KOG2164|consen 184 STDMQCPICLEP-P--SVP-VRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITL 237 (513)
T ss_pred CcCCcCCcccCC-C--Ccc-cccccCceeeHHHHHHHHhhhcccCCccCCchhhhccc
Confidence 348899999987 2 122 33469999999999886533 3679999998864
No 53
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.07 E-value=0.00018 Score=84.74 Aligned_cols=32 Identities=31% Similarity=0.802 Sum_probs=27.7
Q ss_pred eecCCCCccChhhHHHhhh-cCCCCCCCCcCcc
Q 000881 1134 RALPCGHFMHSDCFQAYTC-SHYICPICSKSLG 1165 (1239)
Q Consensus 1134 ~~LpCGH~fH~~Ci~~wl~-~~~~CPiCrksv~ 1165 (1239)
+..||.|.||..|+.+|+. .+..||+||.++.
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 5679999998864
No 54
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.99 E-value=0.00017 Score=79.65 Aligned_cols=50 Identities=22% Similarity=0.640 Sum_probs=39.6
Q ss_pred CCCCcccccccccCC------CcceecCCCCccChhhHHHhh--hcCCCCCCCCcCcc
Q 000881 1116 ETNCPICCDFLFTSS------ATVRALPCGHFMHSDCFQAYT--CSHYICPICSKSLG 1165 (1239)
Q Consensus 1116 ~~~CpICle~lf~s~------~~v~~LpCGH~fH~~Ci~~wl--~~~~~CPiCrksv~ 1165 (1239)
++.|.||...++.+. +..-.|.|+|.||..||+-|- ....+||-|++.|.
T Consensus 224 d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVd 281 (328)
T KOG1734|consen 224 DSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVD 281 (328)
T ss_pred cchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhh
Confidence 467888887766554 234579999999999999994 66799999998763
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=96.66 E-value=0.0012 Score=60.52 Aligned_cols=47 Identities=21% Similarity=0.367 Sum_probs=35.3
Q ss_pred CCCCcccccccccCCCcceecCCCCccChhhHHHhhhc-CCCCCCCCcCccC
Q 000881 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS-HYICPICSKSLGD 1166 (1239)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~-~~~CPiCrksv~d 1166 (1239)
+-.|||+.+-|.+ .+.+||||+|-+.||.+|+.. +.+||+|+..+..
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 3469999987643 256899999999999999988 8999999988764
No 56
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.66 E-value=0.00075 Score=74.95 Aligned_cols=46 Identities=26% Similarity=0.694 Sum_probs=38.0
Q ss_pred CCCCcccccccccCCCcceecCCCCccChhhHHH-hhhcCCC-CCCCCcCcc
Q 000881 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQA-YTCSHYI-CPICSKSLG 1165 (1239)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~-wl~~~~~-CPiCrksv~ 1165 (1239)
+..|+||+|.... ....+|||.|...||-. |+...+- ||+||.-+.
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 5679999988543 45689999999999998 9987766 999997654
No 57
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.50 E-value=0.0012 Score=76.91 Aligned_cols=82 Identities=21% Similarity=0.468 Sum_probs=58.1
Q ss_pred CCCCCCCcccccccccCCCc---ce-ecCCCCccChhhHHHhh--hc-----CCCCCCCCcCcc--ChhhHhhhhHHHHh
Q 000881 1113 KGLETNCPICCDFLFTSSAT---VR-ALPCGHFMHSDCFQAYT--CS-----HYICPICSKSLG--DMAVYFGMLDALLA 1179 (1239)
Q Consensus 1113 ~~~~~~CpICle~lf~s~~~---v~-~LpCGH~fH~~Ci~~wl--~~-----~~~CPiCrksv~--dm~~~~~~lD~~i~ 1179 (1239)
++.+..|-||+|.+...... -. .++|.|.|...||..|- .. +..||+||...- .-+.+|-.-.+ +
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 46678999999987655310 11 25699999999999996 33 578999998874 33445644433 6
Q ss_pred hcCCChhhhccCCceec
Q 000881 1180 SEQLPEEYRDRCQEILC 1196 (1239)
Q Consensus 1180 ~~pmP~ey~~~~~~I~C 1196 (1239)
.++++++|...+....|
T Consensus 236 k~~li~e~~~~~s~~~c 252 (344)
T KOG1039|consen 236 KQKLIEEYEAEMSAKDC 252 (344)
T ss_pred ccccHHHHHHHhhccch
Confidence 77888998777655444
No 58
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=96.22 E-value=0.0028 Score=56.83 Aligned_cols=56 Identities=29% Similarity=0.585 Sum_probs=27.6
Q ss_pred CCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcCcc--ChhhHhhhhHHHH
Q 000881 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG--DMAVYFGMLDALL 1178 (1239)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrksv~--dm~~~~~~lD~~i 1178 (1239)
..|++|.+.|. ++|..-.|.|.|.+.|+..-+. +.||+|+.+.- |+. .-+.||.+|
T Consensus 8 LrCs~C~~~l~---~pv~l~~CeH~fCs~Ci~~~~~--~~CPvC~~Paw~qD~~-~NrqLd~~i 65 (65)
T PF14835_consen 8 LRCSICFDILK---EPVCLGGCEHIFCSSCIRDCIG--SECPVCHTPAWIQDIQ-INRQLDSMI 65 (65)
T ss_dssp TS-SSS-S--S---S-B---SSS--B-TTTGGGGTT--TB-SSS--B-S-SS-----HHHHHHH
T ss_pred cCCcHHHHHhc---CCceeccCccHHHHHHhHHhcC--CCCCCcCChHHHHHHH-hhhhhhccC
Confidence 46999998854 3567779999999999988553 56999999983 433 246666654
No 59
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=96.15 E-value=0.0024 Score=71.33 Aligned_cols=46 Identities=24% Similarity=0.490 Sum_probs=38.3
Q ss_pred CCCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcCcc
Q 000881 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1165 (1239)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrksv~ 1165 (1239)
...|-||-+++.. ....+|||+|+.-||..++..+..||+||....
T Consensus 25 ~lrC~IC~~~i~i----p~~TtCgHtFCslCIR~hL~~qp~CP~Cr~~~~ 70 (391)
T COG5432 25 MLRCRICDCRISI----PCETTCGHTFCSLCIRRHLGTQPFCPVCREDPC 70 (391)
T ss_pred HHHhhhhhheeec----ceecccccchhHHHHHHHhcCCCCCccccccHH
Confidence 3579999988432 245699999999999999999999999998763
No 60
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.97 E-value=0.0015 Score=56.36 Aligned_cols=52 Identities=29% Similarity=0.655 Sum_probs=37.7
Q ss_pred CCCCCcccccccccCCCcceecCCCCc-cChhh-HHHhhhcCCCCCCCCcCccChhhH
Q 000881 1115 LETNCPICCDFLFTSSATVRALPCGHF-MHSDC-FQAYTCSHYICPICSKSLGDMAVY 1170 (1239)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~LpCGH~-fH~~C-i~~wl~~~~~CPiCrksv~dm~~~ 1170 (1239)
....|.||+|.-.+| +.--|||. |.-.| +..|...+..|||||.+|-|.-..
T Consensus 6 ~~dECTICye~pvds----VlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~dvIkT 59 (62)
T KOG4172|consen 6 WSDECTICYEHPVDS----VLYTCGHMCMCYACGLRLKKALHGCCPICRAPIKDVIKT 59 (62)
T ss_pred cccceeeeccCcchH----HHHHcchHHhHHHHHHHHHHccCCcCcchhhHHHHHHHh
Confidence 347899999872222 34589996 66777 455766889999999998776543
No 61
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=95.93 E-value=0.0016 Score=75.12 Aligned_cols=61 Identities=31% Similarity=0.658 Sum_probs=48.5
Q ss_pred ccccccCCCCCCCcccccccccCCCcceecCCCCccChhhHHHhhhcC--CCCCCCCcCccChh
Q 000881 1107 DHKCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSH--YICPICSKSLGDMA 1168 (1239)
Q Consensus 1107 ~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~--~~CPiCrksv~dm~ 1168 (1239)
-|.|++ .++-+|-.|.|.+--..+....|||.|+||..|+.+++..+ .+||-|||-...|.
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 455653 46789999999877777778899999999999999998655 68999996554443
No 62
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=95.85 E-value=0.0026 Score=79.58 Aligned_cols=53 Identities=23% Similarity=0.562 Sum_probs=38.2
Q ss_pred cCCCCCCCcccccccc--cCCCcce-ecCCCCccChhhHHHhhhc--CCCCCCCCcCc
Q 000881 1112 EKGLETNCPICCDFLF--TSSATVR-ALPCGHFMHSDCFQAYTCS--HYICPICSKSL 1164 (1239)
Q Consensus 1112 e~~~~~~CpICle~lf--~s~~~v~-~LpCGH~fH~~Ci~~wl~~--~~~CPiCrksv 1164 (1239)
.-+....|+||+--+. +..-|.. --.|.|.||..|+.+|.+. +.+||+||.++
T Consensus 1465 ~fsG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRsei 1522 (1525)
T COG5219 1465 KFSGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEI 1522 (1525)
T ss_pred hcCCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCcccccc
Confidence 3456789999987654 2211222 2457899999999999865 58999999765
No 63
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.75 E-value=0.0054 Score=71.57 Aligned_cols=49 Identities=35% Similarity=0.819 Sum_probs=38.9
Q ss_pred CCCCcccccccccCCC-cceecCCCCccChhhHHHhhhc--CCCCCCCCcCc
Q 000881 1116 ETNCPICCDFLFTSSA-TVRALPCGHFMHSDCFQAYTCS--HYICPICSKSL 1164 (1239)
Q Consensus 1116 ~~~CpICle~lf~s~~-~v~~LpCGH~fH~~Ci~~wl~~--~~~CPiCrksv 1164 (1239)
...||||++..-.+++ .+..|.|||.|-.+||+.|+.. ...||.|.-..
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 4689999998765555 4456899999999999999953 35799998654
No 64
>COG2461 Uncharacterized conserved protein [Function unknown]
Probab=95.61 E-value=0.074 Score=62.56 Aligned_cols=132 Identities=14% Similarity=0.208 Sum_probs=103.6
Q ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHhhcccCCcccH-HHHHHHHHHHHHHHHhhhhcccccchhhhhhhh------hhH
Q 000881 291 SCPIDEIMLWHNAIKRELNDIAEAARKIQLSGDFSDL-SAFNKRLQFIAEVCIFHSIAEDKVIFPAVDVEL------SFA 363 (1239)
Q Consensus 291 ~~pid~L~~~HkALRrEL~~L~~~a~~~~~~gd~~~L-~~L~~r~~fl~~vl~~Hs~aEDevlFPaL~~r~------~me 363 (1239)
-+|+..|+..-++||..|+.+.+. .. + ..+ -.+...+.++-.+=+ |=+++...|||.++.|- .|-
T Consensus 85 gHPv~tl~~EN~~i~~ll~~~l~~---~~---~-~~ik~~l~~lv~~L~~vg~-Hy~RKe~lIfp~~Er~GitapptVmW 156 (409)
T COG2461 85 GHPVRTLKRENKAIRSLLANLLQF---PP---K-KEIKEKLVELVSELDKIGK-HYTRKEMLIFPYIERRGITAPPTVMW 156 (409)
T ss_pred CCcHHHHhcccHHHHHHHHHHhhc---cc---c-HHHHHHHHHHHHHHHHhcc-ccccccccchhHHHHcCCCCCCeeee
Confidence 689999999999999554444333 21 2 233 556666667766666 99999999999999886 889
Q ss_pred HhHHHHHHHHHHHHHHHHHHhhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhhCCHHHHHHHHHhH
Q 000881 364 QEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPLARRHFSPKRQRELLYQS 441 (1239)
Q Consensus 364 ~EH~~ie~l~e~l~~ll~~~~~a~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qvfPLl~~~fS~eEq~eL~~~~ 441 (1239)
-.|+++-..|..+..++... + ..++...+..+.+.+..=+.+||+.+.|.+-..||..||.++-.+.
T Consensus 157 ~~dDeiRe~lk~~~~~l~~~--s---------~~~~ve~~~~~~t~i~dmIFkEe~Ilypt~~d~~te~ew~~i~~~~ 223 (409)
T COG2461 157 VKDDEIREALKELLKLLKEV--S---------IEEFVEKAESVLTEIEDMIFKEENILYPTLLDLLTEGEWEAIKEQS 223 (409)
T ss_pred ccCcHHHHHHHHHHHHhhcc--C---------hHHHHHHHHHHHHHHHHHHHhhhhhHHhHHHHhcCHHHHHHHHhcC
Confidence 99999988898888887621 1 2456667777888899999999999999999999999999987553
No 65
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.35 E-value=0.0092 Score=69.12 Aligned_cols=51 Identities=29% Similarity=0.671 Sum_probs=40.4
Q ss_pred cCCCCCCCcccccccccCCCcceecCCCCc-cChhhHHHhhhcCCCCCCCCcCccC
Q 000881 1112 EKGLETNCPICCDFLFTSSATVRALPCGHF-MHSDCFQAYTCSHYICPICSKSLGD 1166 (1239)
Q Consensus 1112 e~~~~~~CpICle~lf~s~~~v~~LpCGH~-fH~~Ci~~wl~~~~~CPiCrksv~d 1166 (1239)
++.....|.||+.+ + ..+.+|||-|. +++.|-+...-..+.|||||..|..
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 33446789999876 3 34678999996 8999998877678899999998753
No 66
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.33 E-value=0.0028 Score=72.82 Aligned_cols=47 Identities=30% Similarity=0.591 Sum_probs=38.4
Q ss_pred CCCCcccccccccCCCcceecCCCCccChhhHHHhhh-cCCCCCCCCcCcc
Q 000881 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC-SHYICPICSKSLG 1165 (1239)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~-~~~~CPiCrksv~ 1165 (1239)
+-.|||||+-|... +...-|+|-|...||..-++ .+..||.|||.+.
T Consensus 43 ~v~c~icl~llk~t---mttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~ 90 (381)
T KOG0311|consen 43 QVICPICLSLLKKT---MTTKECLHRFCFDCIWKALRSGNNECPTCRKKLV 90 (381)
T ss_pred hhccHHHHHHHHhh---cccHHHHHHHHHHHHHHHHHhcCCCCchHHhhcc
Confidence 46899999876433 45678999999999988764 5789999999985
No 67
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=95.17 E-value=0.0063 Score=76.11 Aligned_cols=46 Identities=24% Similarity=0.642 Sum_probs=36.6
Q ss_pred CCCcccccccccCCCcceecCCCCccChhhHHHhhhc-CCCCCCCCcCccC
Q 000881 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS-HYICPICSKSLGD 1166 (1239)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~-~~~CPiCrksv~d 1166 (1239)
-.||+|-. ....++...|||.|+..|+..-+.. ..+||.|..+++.
T Consensus 644 LkCs~Cn~----R~Kd~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFga 690 (698)
T KOG0978|consen 644 LKCSVCNT----RWKDAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGA 690 (698)
T ss_pred eeCCCccC----chhhHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCc
Confidence 46888853 3445677899999999999997754 6899999999874
No 68
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=94.94 E-value=0.0069 Score=70.19 Aligned_cols=54 Identities=28% Similarity=0.672 Sum_probs=44.5
Q ss_pred cccccCCCCCCCcccccccccCCCcceecCCCCccChhhHHHhhhc--CCCCCCCCcCcc
Q 000881 1108 HKCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS--HYICPICSKSLG 1165 (1239)
Q Consensus 1108 H~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~--~~~CPiCrksv~ 1165 (1239)
-.|.-+++-.-|-||-|. ...|++=||||.++..|+..|-.. +.+||-||..|-
T Consensus 361 LYceMgsTFeLCKICaen----dKdvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIK 416 (563)
T KOG1785|consen 361 LYCEMGSTFELCKICAEN----DKDVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIK 416 (563)
T ss_pred HHHHccchHHHHHHhhcc----CCCcccccccchHHHHHHHhhcccCCCCCCCceeeEec
Confidence 346667778899999765 456788899999999999999743 689999999873
No 69
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=94.90 E-value=0.0025 Score=72.14 Aligned_cols=133 Identities=17% Similarity=0.114 Sum_probs=92.7
Q ss_pred HHHHHHhhhccccccccccccccccccccccchhhHHHHHHHHHHHHHHHhhhhhhhhcccCcCCcccccccccccchhh
Q 000881 690 GLYRAHSNAEDDIVFPALESKETLSNVSHSYTLDHKQEEKLFEDISSALSELTELHECLSTDLTGDLTRNSLESCDQNET 769 (1239)
Q Consensus 690 ~v~~~HS~AEDeivfPALe~k~~~~nvs~s~~~EH~~ee~lfedi~~~L~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 769 (1239)
.++..|+.++|++-||+...+....+.+++...||--.=.+..+.+.... . .+
T Consensus 17 ~~~~~~~~~~d~~~~~~~c~hy~r~~~~~a~ccd~~~~C~hCH~~s~~h~--------------------------~-~r 69 (276)
T KOG1940|consen 17 ALSSIHSDAEDEIAFPYGCPHYRRNCKSRAPCCDREITCRHCHNESEDHD--------------------------L-DR 69 (276)
T ss_pred hhhhcccccccccccccCCchhhhccccccccccceeeeEEecChhhhcc--------------------------c-ch
Confidence 78999999999999999999877767777666665444444444311000 0 12
Q ss_pred HhhHHHHHHHHHHHHHHHHHHHHHhhHhhhhhhhhHHhhhCCHHHHHHHHHHHhhccCHHHHHHhhhHHhhcCCHHHHHH
Q 000881 770 VRKYNEKATELQGMCKSIRVTLDQHVFREELELWPLFDRHFSVEEQDKIVGRIIGTTGAEVLQSMLPWVTSALTQEEQNT 849 (1239)
Q Consensus 770 ~~~~~e~~~kL~~~~ksl~~~L~~Hi~~EE~ElfPL~~k~fS~eeQ~~Lv~~~l~~~p~~~Lq~~LPWl~~~Lte~E~~~ 849 (1239)
..++.-...+.....++....+..|+. +.++|=++.+.|+++.+ +++..+.+.+--+.++. |||.-.....++.+
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 223334455555555566688888888 99999999999999999 88888866554333332 99998888887776
Q ss_pred HHHHh
Q 000881 850 MMDTW 854 (1239)
Q Consensus 850 ml~~~ 854 (1239)
-|.+|
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=94.16 E-value=0.036 Score=62.23 Aligned_cols=52 Identities=21% Similarity=0.624 Sum_probs=41.8
Q ss_pred CCCCCCcccccccccCCCcceecCCCCccChhhHHHhhh--cCCCCCCCCcCccChh
Q 000881 1114 GLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC--SHYICPICSKSLGDMA 1168 (1239)
Q Consensus 1114 ~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~--~~~~CPiCrksv~dm~ 1168 (1239)
.....||+|.++ +..|-...+|||.|+--|+..-.. .+.+||.|+.++..|.
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 446789999887 455667789999999999987643 3589999999887664
No 71
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.89 E-value=0.039 Score=60.13 Aligned_cols=51 Identities=27% Similarity=0.645 Sum_probs=41.6
Q ss_pred CCCCCCcccccccccCCCcceecCCCCccChhhHHHhhh--------cCCCCCCCCcCccC
Q 000881 1114 GLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC--------SHYICPICSKSLGD 1166 (1239)
Q Consensus 1114 ~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~--------~~~~CPiCrksv~d 1166 (1239)
....||..|.-.|-.. + ...|-|=|.||..|+++|.. ..|.||-|+..|..
T Consensus 48 DY~pNC~LC~t~La~g-d-t~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFP 106 (299)
T KOG3970|consen 48 DYNPNCRLCNTPLASG-D-TTRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFP 106 (299)
T ss_pred CCCCCCceeCCccccC-c-ceeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCC
Confidence 4578999999886544 3 46789999999999999953 26999999999863
No 72
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.48 E-value=0.041 Score=58.13 Aligned_cols=31 Identities=26% Similarity=0.698 Sum_probs=26.0
Q ss_pred ecCCCCccChhhHHHhhhc-----------CCCCCCCCcCcc
Q 000881 1135 ALPCGHFMHSDCFQAYTCS-----------HYICPICSKSLG 1165 (1239)
Q Consensus 1135 ~LpCGH~fH~~Ci~~wl~~-----------~~~CPiCrksv~ 1165 (1239)
...||-.||+-|+..|++. -..||.|+++|.
T Consensus 187 N~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~Pia 228 (234)
T KOG3268|consen 187 NIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIA 228 (234)
T ss_pred ccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcce
Confidence 3689999999999999852 156999999984
No 73
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=93.43 E-value=0.021 Score=64.47 Aligned_cols=54 Identities=28% Similarity=0.663 Sum_probs=42.8
Q ss_pred cCCCCCCCcccccccccCCCcceecCCCCccChhhHHHhhh-----------------------cCCCCCCCCcCccC
Q 000881 1112 EKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC-----------------------SHYICPICSKSLGD 1166 (1239)
Q Consensus 1112 e~~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~-----------------------~~~~CPiCrksv~d 1166 (1239)
.+--.+.|.|||=- |.+.....+.+|-|+||..|+..|+. ....|||||..|.+
T Consensus 111 nn~p~gqCvICLyg-fa~~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~ 187 (368)
T KOG4445|consen 111 NNHPNGQCVICLYG-FASSPAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKI 187 (368)
T ss_pred CCCCCCceEEEEEe-ecCCCceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccc
Confidence 45567899999965 77777788899999999999987752 02359999998875
No 74
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=93.41 E-value=0.058 Score=46.10 Aligned_cols=45 Identities=22% Similarity=0.526 Sum_probs=23.9
Q ss_pred CcccccccccCCCcceecCCCCccChhhHHHhhh-cCCCCCCCCcC
Q 000881 1119 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC-SHYICPICSKS 1163 (1239)
Q Consensus 1119 CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~-~~~~CPiCrks 1163 (1239)
||+|.++|..++....-=+||+.+...|+..-+. .+..||-||++
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 8999999854443333336799999999998876 48999999986
No 75
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=93.02 E-value=0.054 Score=47.85 Aligned_cols=42 Identities=26% Similarity=0.643 Sum_probs=29.3
Q ss_pred CCCCCcccccccccCCCcceecCCCCccChhhHHHhhh--cCCCCCC
Q 000881 1115 LETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC--SHYICPI 1159 (1239)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~--~~~~CPi 1159 (1239)
....|||.+.. |. ++|+...|||+|=+..|.+|+. ....||+
T Consensus 10 ~~~~CPiT~~~-~~--~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv 53 (57)
T PF11789_consen 10 ISLKCPITLQP-FE--DPVKSKKCGHTFEKEAILQYIQRNGSKRCPV 53 (57)
T ss_dssp --SB-TTTSSB--S--SEEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred eccCCCCcCCh-hh--CCcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence 45789999987 43 5788899999999999999994 3578999
No 76
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=92.71 E-value=0.086 Score=60.92 Aligned_cols=64 Identities=22% Similarity=0.562 Sum_probs=48.6
Q ss_pred CCCCcccccccccCCCcceecCC--CCccChhhHHHhhhcCCCCCCCCcCccChhhHhhhhHHHHhhcCCChhhhc
Q 000881 1116 ETNCPICCDFLFTSSATVRALPC--GHFMHSDCFQAYTCSHYICPICSKSLGDMAVYFGMLDALLASEQLPEEYRD 1189 (1239)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpC--GH~fH~~Ci~~wl~~~~~CPiCrksv~dm~~~~~~lD~~i~~~pmP~ey~~ 1189 (1239)
-.+||||.++|.. -.+.| ||.-...|-. +..++||.||.++++... +.++.+++....|=.|.+
T Consensus 48 lleCPvC~~~l~~-----Pi~QC~nGHlaCssC~~---~~~~~CP~Cr~~~g~~R~--~amEkV~e~~~vpC~~~~ 113 (299)
T KOG3002|consen 48 LLDCPVCFNPLSP-----PIFQCDNGHLACSSCRT---KVSNKCPTCRLPIGNIRC--RAMEKVAEAVLVPCKNAK 113 (299)
T ss_pred hccCchhhccCcc-----cceecCCCcEehhhhhh---hhcccCCccccccccHHH--HHHHHHHHhceecccccc
Confidence 4689999998643 34667 7888888874 457899999999997643 467788888888765543
No 77
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=92.68 E-value=0.014 Score=68.56 Aligned_cols=62 Identities=26% Similarity=0.668 Sum_probs=33.6
Q ss_pred Ccccc--CCCCCccccCCCCCccccccCC---ccccccccccccccccCCCCCCCcccccccccCCCcceecCCCCccCh
Q 000881 1070 RVVYH--CPFCNLCRVGRGLGVDFFHCMT---CNCCLAKKLVDHKCREKGLETNCPICCDFLFTSSATVRALPCGHFMHS 1144 (1239)
Q Consensus 1070 k~~yH--C~~CgiCRvG~gl~~~~fHC~~---C~~C~~~~l~~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~fH~ 1144 (1239)
+.+|| |=.|+.||.-.. |..||.-+. |--||-..+ ..|..|-+.+.+. +.-.||-.||.
T Consensus 295 ~~~fHv~CFtC~~C~r~L~-Gq~FY~v~~k~~CE~cyq~tl-----------ekC~~Cg~~I~d~----iLrA~GkayHp 358 (468)
T KOG1701|consen 295 DQLFHVQCFTCRTCRRQLA-GQSFYQVDGKPYCEGCYQDTL-----------EKCNKCGEPIMDR----ILRALGKAYHP 358 (468)
T ss_pred hhhhcccceehHhhhhhhc-cccccccCCcccchHHHHHHH-----------HHHhhhhhHHHHH----HHHhcccccCC
Confidence 46777 777888887654 566776543 222332222 3466665553221 12256666776
Q ss_pred hhH
Q 000881 1145 DCF 1147 (1239)
Q Consensus 1145 ~Ci 1147 (1239)
.||
T Consensus 359 ~CF 361 (468)
T KOG1701|consen 359 GCF 361 (468)
T ss_pred Cce
Confidence 665
No 78
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=92.67 E-value=0.048 Score=52.66 Aligned_cols=38 Identities=29% Similarity=0.626 Sum_probs=29.9
Q ss_pred ccccCCCCCCCcccccccccCCCcceecCCCCccChhhHH
Q 000881 1109 KCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQ 1148 (1239)
Q Consensus 1109 ~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~ 1148 (1239)
.++.-.....|+||...++.+ ...+.||||.||..|++
T Consensus 71 ~~v~i~~~~~C~vC~k~l~~~--~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 71 RSVVITESTKCSVCGKPLGNS--VFVVFPCGHVVHYSCIK 108 (109)
T ss_pred ceEEECCCCCccCcCCcCCCc--eEEEeCCCeEEeccccc
Confidence 344445577899999997763 56778999999999985
No 79
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.50 E-value=0.067 Score=60.88 Aligned_cols=48 Identities=19% Similarity=0.383 Sum_probs=37.4
Q ss_pred CCCCCCcccccccccCCCcceecCCCCccChhhHHHhhh-cCCCCCCCCcCcc
Q 000881 1114 GLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC-SHYICPICSKSLG 1165 (1239)
Q Consensus 1114 ~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~-~~~~CPiCrksv~ 1165 (1239)
.+...|+||+... .-+ ..|+|+|.|...||+--.. ...+||+||.+|.
T Consensus 5 ~~~~eC~IC~nt~---n~P-v~l~C~HkFCyiCiKGsy~ndk~~CavCR~pid 53 (324)
T KOG0824|consen 5 TKKKECLICYNTG---NCP-VNLYCFHKFCYICIKGSYKNDKKTCAVCRFPID 53 (324)
T ss_pred ccCCcceeeeccC---CcC-ccccccchhhhhhhcchhhcCCCCCceecCCCC
Confidence 4567899998663 233 5699999999999987543 3567999999985
No 80
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=92.40 E-value=0.049 Score=60.29 Aligned_cols=141 Identities=26% Similarity=0.578 Sum_probs=86.8
Q ss_pred CcccccccccccccccCC--------------------cccCcccccccCCCCCccccccccccccccccccCCCCCCCc
Q 000881 989 GCEHYKRNCKLRAACCGK--------------------LFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVGPVCTTL 1048 (1239)
Q Consensus 989 gC~HY~r~c~l~~~cC~~--------------------~y~Cr~CHde~~~H~~~r~~~~~v~C~~C~~~q~~~~~C~~~ 1048 (1239)
-|.|=-. -|.+|||+| -|.|..|.....|--+-|.+ ...+|..|+..-.+
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 4766321 377888876 36777787776666666654 47889988754332
Q ss_pred cCCCCccceEecccccC-cCCC-----CccccCCCCCccccCCCCCccccccCCccccccccc----cccccccCCCCCC
Q 000881 1049 SCSGLSMAKYYCGICKF-FDDE-----RVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLAKKL----VDHKCREKGLETN 1118 (1239)
Q Consensus 1049 ~C~~~~~~~y~C~~C~l-~dd~-----k~~yHC~~CgiCRvG~gl~~~~fHC~~C~~C~~~~l----~~H~C~e~~~~~~ 1118 (1239)
.--|+|.|.+|+- +|++ .++|| -..|.|.+||-=+.... +.--|..-....-
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 1367999999995 5666 67888 26799999987664322 3334444444455
Q ss_pred CcccccccccCCCcceecCCCCccChhhH----HHhhhcCCCCCCCCcCccChhhH
Q 000881 1119 CPICCDFLFTSSATVRALPCGHFMHSDCF----QAYTCSHYICPICSKSLGDMAVY 1170 (1239)
Q Consensus 1119 CpICle~lf~s~~~v~~LpCGH~fH~~Ci----~~wl~~~~~CPiCrksv~dm~~~ 1170 (1239)
||||..- .-.+-..-| ..|--.++.|-.|-|++.--.-|
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 23545578899999988765444
No 81
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=92.33 E-value=0.074 Score=66.10 Aligned_cols=49 Identities=24% Similarity=0.486 Sum_probs=35.3
Q ss_pred ccccCCCCCCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCC
Q 000881 1109 KCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPI 1159 (1239)
Q Consensus 1109 ~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPi 1159 (1239)
+|+-......|.||.-.+.. ....-..|||.+|..|..+|.+..-.||.
T Consensus 1021 ~~~~~~~~~~C~~C~l~V~g--ss~~Cg~C~Hv~H~sc~~eWf~~gd~Cps 1069 (1081)
T KOG0309|consen 1021 CAICKGFTFQCAICHLAVRG--SSNFCGTCGHVGHTSCMMEWFRTGDVCPS 1069 (1081)
T ss_pred ccccccceeeeeeEeeEeec--cchhhccccccccHHHHHHHHhcCCcCCC
Confidence 33334444558888644332 33456789999999999999999989985
No 82
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=91.76 E-value=0.1 Score=44.29 Aligned_cols=40 Identities=25% Similarity=0.674 Sum_probs=26.7
Q ss_pred CcccccccccCCCcceecCCC-----CccChhhHHHhhh--cCCCCCCC
Q 000881 1119 CPICCDFLFTSSATVRALPCG-----HFMHSDCFQAYTC--SHYICPIC 1160 (1239)
Q Consensus 1119 CpICle~lf~s~~~v~~LpCG-----H~fH~~Ci~~wl~--~~~~CPiC 1160 (1239)
|-||++.-.++. ..+.||+ -+.|..|+.+|+. .+.+|++|
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 679988733332 3456774 6899999999985 46789998
No 83
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=91.74 E-value=0.12 Score=57.18 Aligned_cols=55 Identities=24% Similarity=0.480 Sum_probs=45.6
Q ss_pred cCCCCCCCcccccccccCCCcceec-CCCCccChhhHHHhhhcCCCCCCCCcCccCh
Q 000881 1112 EKGLETNCPICCDFLFTSSATVRAL-PCGHFMHSDCFQAYTCSHYICPICSKSLGDM 1167 (1239)
Q Consensus 1112 e~~~~~~CpICle~lf~s~~~v~~L-pCGH~fH~~Ci~~wl~~~~~CPiCrksv~dm 1167 (1239)
..+..-.||||.+.|- +..+..+| ||||+|...|..+.++....||||.+++-|.
T Consensus 217 a~s~ryiCpvtrd~Lt-Nt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdr 272 (303)
T KOG3039|consen 217 AASKRYICPVTRDTLT-NTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDR 272 (303)
T ss_pred hhccceecccchhhhc-CccceEEeccCCcEeeHHHHHHhccccccccCCCCcCccc
Confidence 3445678999999954 45566666 9999999999999999999999999998764
No 84
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=91.62 E-value=0.11 Score=62.34 Aligned_cols=54 Identities=28% Similarity=0.641 Sum_probs=43.0
Q ss_pred CCCCCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcCccChhhH
Q 000881 1114 GLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGDMAVY 1170 (1239)
Q Consensus 1114 ~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrksv~dm~~~ 1170 (1239)
..+..||||..-+- +++....|||.|...|+..|+..+..||.|+..+.....+
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 44578999986643 3444579999999999999998899999999887654444
No 85
>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=91.28 E-value=0.076 Score=54.37 Aligned_cols=43 Identities=21% Similarity=0.400 Sum_probs=35.3
Q ss_pred CCCCcccccccccCCCcceecCCC------CccChhhHHHhhhcCCCCCC
Q 000881 1116 ETNCPICCDFLFTSSATVRALPCG------HFMHSDCFQAYTCSHYICPI 1159 (1239)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCG------H~fH~~Ci~~wl~~~~~CPi 1159 (1239)
...|.||++.+.. ..+|+.++|| |.||..|+.+|.+.+.+=|-
T Consensus 26 ~~EC~IC~~~I~~-~~GvV~vt~~g~lnLEkmfc~~C~~rw~~~~~rDPf 74 (134)
T PF05883_consen 26 TVECQICFDRIDN-NDGVVYVTDGGTLNLEKMFCADCDKRWRRERNRDPF 74 (134)
T ss_pred Ceeehhhhhhhhc-CCCEEEEecCCeehHHHHHHHHHHHHHHhhccCCCc
Confidence 4689999999877 6789999998 99999999999655544443
No 86
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=90.51 E-value=0.067 Score=61.60 Aligned_cols=49 Identities=20% Similarity=0.567 Sum_probs=41.6
Q ss_pred CCCCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcCccC
Q 000881 1115 LETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1166 (1239)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrksv~d 1166 (1239)
....|++|..||-+.+ .+.-|=|+|+..||-+++..+.+||.|...|..
T Consensus 14 ~~itC~LC~GYliDAT---TI~eCLHTFCkSCivk~l~~~~~CP~C~i~ih~ 62 (331)
T KOG2660|consen 14 PHITCRLCGGYLIDAT---TITECLHTFCKSCIVKYLEESKYCPTCDIVIHK 62 (331)
T ss_pred cceehhhccceeecch---hHHHHHHHHHHHHHHHHHHHhccCCccceeccC
Confidence 3568999999976653 346799999999999999999999999998864
No 87
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=90.37 E-value=0.13 Score=55.32 Aligned_cols=58 Identities=24% Similarity=0.309 Sum_probs=42.4
Q ss_pred CCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcCccChhhHhhhhHHHH
Q 000881 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGDMAVYFGMLDALL 1178 (1239)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrksv~dm~~~~~~lD~~i 1178 (1239)
-.|-||.++ |.+ .++..|||.|+..|.-.-.+...+|-+|.+...-.-..-..+|+.+
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 555 3567999999999987766778999999998754333334455544
No 88
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=89.61 E-value=0.12 Score=62.25 Aligned_cols=51 Identities=25% Similarity=0.570 Sum_probs=41.2
Q ss_pred ccCCCCCCCcccccccccCCCcceecCCCCccChhhHHHhhh-----cCCCCCCCCcCcc
Q 000881 1111 REKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC-----SHYICPICSKSLG 1165 (1239)
Q Consensus 1111 ~e~~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~-----~~~~CPiCrksv~ 1165 (1239)
+++..+..|-+|.|. .+....-.|.|.|++-|+.+|.. .+.+||+|.+.+.
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 466778899999876 23456789999999999999963 3689999998874
No 89
>COG2461 Uncharacterized conserved protein [Function unknown]
Probab=89.37 E-value=1.7 Score=51.58 Aligned_cols=138 Identities=22% Similarity=0.214 Sum_probs=104.0
Q ss_pred CCCChhHHHHHHHHHHHHHHHHHHHHHhhccCCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHhhhh-hhHHHHH
Q 000881 40 LKSPILIFLFFHKAIKSELDVLHRAAMAFATNLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIRV-KNIARTY 118 (1239)
Q Consensus 40 ~~~Pi~~~~~~HkAlRreL~~l~~~a~~~~~~~gd~~~~~~l~~r~~~l~~~~~~H~~aEDevI~PaL~~Rv-~~v~~~~ 118 (1239)
-.+|+..|.-=-+++|..|+.+.+. . .+..-...+...+.+|..+=+ |-+-+-..|||-++.|- ..+.-.|
T Consensus 84 ~gHPv~tl~~EN~~i~~ll~~~l~~---~----~~~~ik~~l~~lv~~L~~vg~-Hy~RKe~lIfp~~Er~GitapptVm 155 (409)
T COG2461 84 PGHPVRTLKRENKAIRSLLANLLQF---P----PKKEIKEKLVELVSELDKIGK-HYTRKEMLIFPYIERRGITAPPTVM 155 (409)
T ss_pred CCCcHHHHhcccHHHHHHHHHHhhc---c----ccHHHHHHHHHHHHHHHHhcc-ccccccccchhHHHHcCCCCCCeee
Confidence 3569988888888899665555332 1 123344556667777777777 99999999999999884 3577778
Q ss_pred HhhhhhHhHHHHHHHHHHHhhhcCchHHHHHHHHHHHHHHHHHHHhhHHHHHHHhhHHhhcCCHHHHHHHHHH
Q 000881 119 SLEHEGESVLFDQLFELLNSSMRNEESYRRELASCTGALQTSISQHMSKEEEQVFPLLIEKFSFEEQASLVWQ 191 (1239)
Q Consensus 119 ~~EH~~~~~l~~~L~~~l~~~~~~~~~~~~eLa~~l~~l~~~l~qHm~~EE~qv~PLl~~~fS~~E~a~L~~~ 191 (1239)
-.-|.++-..|..+...+. ..+. .+++.....+.+.+..=+.+||.-+.|-+..-||..||.++..+
T Consensus 156 W~~dDeiRe~lk~~~~~l~--~~s~----~~~ve~~~~~~t~i~dmIFkEe~Ilypt~~d~~te~ew~~i~~~ 222 (409)
T COG2461 156 WVKDDEIREALKELLKLLK--EVSI----EEFVEKAESVLTEIEDMIFKEENILYPTLLDLLTEGEWEAIKEQ 222 (409)
T ss_pred eccCcHHHHHHHHHHHHhh--ccCh----HHHHHHHHHHHHHHHHHHHhhhhhHHhHHHHhcCHHHHHHHHhc
Confidence 8899999999999888887 2222 33333344455568888999999999999999999999999876
No 90
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=89.36 E-value=0.17 Score=44.44 Aligned_cols=31 Identities=32% Similarity=0.857 Sum_probs=25.0
Q ss_pred ceecCCCCccChhhHHHhhhcCCCCCCCCcCcc
Q 000881 1133 VRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1165 (1239)
Q Consensus 1133 v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrksv~ 1165 (1239)
-.++||||.+-..|++-+ +-+-||+|.+.+.
T Consensus 20 ~~~~pCgH~I~~~~f~~~--rYngCPfC~~~~~ 50 (55)
T PF14447_consen 20 GTVLPCGHLICDNCFPGE--RYNGCPFCGTPFE 50 (55)
T ss_pred cccccccceeeccccChh--hccCCCCCCCccc
Confidence 457899999999998755 3456999999875
No 91
>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=88.76 E-value=0.28 Score=55.86 Aligned_cols=48 Identities=23% Similarity=0.470 Sum_probs=37.5
Q ss_pred CCcccccccccCCCccee-cCCCCccChhhHHHhhh-cCCCCCCCCcCcc
Q 000881 1118 NCPICCDFLFTSSATVRA-LPCGHFMHSDCFQAYTC-SHYICPICSKSLG 1165 (1239)
Q Consensus 1118 ~CpICle~lf~s~~~v~~-LpCGH~fH~~Ci~~wl~-~~~~CPiCrksv~ 1165 (1239)
.||+|.-+.+.+.+-+.. -+|||.++..|++.... ..+.||.|.+.+.
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 29999999999999764 5699999998874
No 92
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=88.23 E-value=0.17 Score=58.13 Aligned_cols=58 Identities=22% Similarity=0.522 Sum_probs=43.2
Q ss_pred CCCCcccccccccCCCcceecCCCCccChhhHHHhhh-cCCCCCCCCcCccChhhHhhh
Q 000881 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC-SHYICPICSKSLGDMAVYFGM 1173 (1239)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~-~~~~CPiCrksv~dm~~~~~~ 1173 (1239)
++.||.|+|+|.-+...-.--|||--++.-|+..--. -+.+||-||+-..|-...|.-
T Consensus 14 ed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~denv~~~~ 72 (480)
T COG5175 14 EDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDENVRYVT 72 (480)
T ss_pred cccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhccccceeEEe
Confidence 4559999999877765445568998888888776543 378999999988765554443
No 93
>PF04641 Rtf2: Rtf2 RING-finger
Probab=88.02 E-value=0.35 Score=54.87 Aligned_cols=51 Identities=20% Similarity=0.483 Sum_probs=40.5
Q ss_pred CCCCCCCcccccccccCCCcceec-CCCCccChhhHHHhhhcCCCCCCCCcCcc
Q 000881 1113 KGLETNCPICCDFLFTSSATVRAL-PCGHFMHSDCFQAYTCSHYICPICSKSLG 1165 (1239)
Q Consensus 1113 ~~~~~~CpICle~lf~s~~~v~~L-pCGH~fH~~Ci~~wl~~~~~CPiCrksv~ 1165 (1239)
....--|||....| ++....+.| ||||+|=..++.+.- ....||+|.+++.
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 45567899999985 554555555 999999999999984 4678999999974
No 94
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.79 E-value=0.26 Score=57.63 Aligned_cols=47 Identities=28% Similarity=0.547 Sum_probs=33.7
Q ss_pred cCCCCCCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcCcc
Q 000881 1112 EKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1165 (1239)
Q Consensus 1112 e~~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrksv~ 1165 (1239)
+.....+|.||++. +.+ ...+||||+-. |..-. +...+||+||.+|.
T Consensus 301 ~~~~p~lcVVcl~e-~~~---~~fvpcGh~cc--ct~cs-~~l~~CPvCR~rI~ 347 (355)
T KOG1571|consen 301 ELPQPDLCVVCLDE-PKS---AVFVPCGHVCC--CTLCS-KHLPQCPVCRQRIR 347 (355)
T ss_pred ccCCCCceEEecCC-ccc---eeeecCCcEEE--chHHH-hhCCCCchhHHHHH
Confidence 44567899999987 333 68899999944 55433 23456999998774
No 95
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.49 E-value=0.32 Score=55.48 Aligned_cols=63 Identities=21% Similarity=0.311 Sum_probs=44.4
Q ss_pred CCCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcCccChhhHhhhhHHHHhhcC
Q 000881 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGDMAVYFGMLDALLASEQ 1182 (1239)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrksv~dm~~~~~~lD~~i~~~p 1182 (1239)
-..|-||..+ |.+ .++..|||+|...|.-.-++.+..|+||.+.+-.....=..|...+...+
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 443 25679999999999887777789999999988543222233444444333
No 96
>COG5592 Uncharacterized conserved protein [Function unknown]
Probab=87.26 E-value=1.5 Score=46.31 Aligned_cols=100 Identities=21% Similarity=0.209 Sum_probs=69.6
Q ss_pred HHHHHHHHHHHHHHHhhhccccccccccc-----ccccccc--ccccchhhHHHHHHHHHHHHHHHhhhhhhhhcccCcC
Q 000881 681 FTGRFRLLWGLYRAHSNAEDDIVFPALES-----KETLSNV--SHSYTLDHKQEEKLFEDISSALSELTELHECLSTDLT 753 (1239)
Q Consensus 681 f~~rf~~L~~v~~~HS~AEDeivfPALe~-----k~~~~nv--s~s~~~EH~~ee~lfedi~~~L~~~~~l~~~~~~~~~ 753 (1239)
..+...|+|.++..|-.-|.++.||+.=- .-..++. ..-+..||+.++.|+..+..-
T Consensus 30 ~le~~gf~~k~~k~h~e~Ee~ilF~v~Vd~~~ed~~~fkdt~~~~~i~~DHkliE~l~tnlik~---------------- 93 (171)
T COG5592 30 ILEFEGFNEKLGKDHVELEEKILFPVIVDADMEDLYVFKDTPEVDRIKNDHKLIETLATNLIKW---------------- 93 (171)
T ss_pred HHhhcchHHHHhhhHHHHHHHhhhhhccchHHHHHHhhhccchhhHhHhhHHHHHHHHHHHHhh----------------
Confidence 34444589999999999999999998632 1112222 336889999999999888110
Q ss_pred CcccccccccccchhhHhhHHHHHHHHHHHHHHHHHHHHHhhHhhhhhhhhHHhhhCCHHHHHH
Q 000881 754 GDLTRNSLESCDQNETVRKYNEKATELQGMCKSIRVTLDQHVFREELELWPLFDRHFSVEEQDK 817 (1239)
Q Consensus 754 ~~~~~~~~~~~~~~~~~~~~~e~~~kL~~~~ksl~~~L~~Hi~~EE~ElfPL~~k~fS~eeQ~~ 817 (1239)
.+..|+.++. -.+.++|..|=..||.-+||..++.=...||.+
T Consensus 94 --------------kR~~k~~e~~-------p~fyK~LtdHn~aEE~~IfPrvks~~~E~~~~~ 136 (171)
T COG5592 94 --------------KRPDKIKERV-------PLFYKTLTDHNLAEEEYIFPRVKSLKGEDEQSA 136 (171)
T ss_pred --------------ccchHHHHHH-------HHHHHHHHHccccccchhhHHHHhhcchhhHHH
Confidence 0112333333 566778889999999999999988776655554
No 97
>COG5592 Uncharacterized conserved protein [Function unknown]
Probab=87.25 E-value=0.93 Score=47.85 Aligned_cols=71 Identities=18% Similarity=0.288 Sum_probs=55.9
Q ss_pred HHHHHHHHHHHHHhccccCCChhhHHHHHHHHHHHHHHHHHHhhhccccccccccccccccccccccchhhHHHHHHHHH
Q 000881 654 KAIRKDLEYLDGESGKLNDCNETFLRQFTGRFRLLWGLYRAHSNAEDDIVFPALESKETLSNVSHSYTLDHKQEEKLFED 733 (1239)
Q Consensus 654 kAIRkDLe~l~~~~~kL~~~d~~~l~~f~~rf~~L~~v~~~HS~AEDeivfPALe~k~~~~nvs~s~~~EH~~ee~lfed 733 (1239)
+-||.||+.+.-++.-+...... +.+..|+..+...+..|--||++.+||-+++.. .+.+..+...+++.
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 55788888888888887754222 478999999999999999999999999998763 23455666666777
Q ss_pred H
Q 000881 734 I 734 (1239)
Q Consensus 734 i 734 (1239)
|
T Consensus 144 I 144 (171)
T COG5592 144 I 144 (171)
T ss_pred H
Confidence 7
No 98
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.81 E-value=0.65 Score=55.74 Aligned_cols=49 Identities=27% Similarity=0.657 Sum_probs=40.0
Q ss_pred CCCCCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcCccC
Q 000881 1114 GLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1166 (1239)
Q Consensus 1114 ~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrksv~d 1166 (1239)
..+-.|-||+.-++.. +.+||||.|...|++.-+....-||+||..+..
T Consensus 82 ~sef~c~vc~~~l~~p----v~tpcghs~c~~Cl~r~ld~~~~cp~Cr~~l~e 130 (398)
T KOG4159|consen 82 RSEFECCVCSRALYPP----VVTPCGHSFCLECLDRSLDQETECPLCRDELVE 130 (398)
T ss_pred cchhhhhhhHhhcCCC----ccccccccccHHHHHHHhccCCCCccccccccc
Confidence 4567899998775542 445999999999999977778889999999874
No 99
>PHA02862 5L protein; Provisional
Probab=85.78 E-value=0.41 Score=49.57 Aligned_cols=46 Identities=24% Similarity=0.569 Sum_probs=34.0
Q ss_pred CCCCCcccccccccCCCcceecCCC-----CccChhhHHHhhhc--CCCCCCCCcCcc
Q 000881 1115 LETNCPICCDFLFTSSATVRALPCG-----HFMHSDCFQAYTCS--HYICPICSKSLG 1165 (1239)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~LpCG-----H~fH~~Ci~~wl~~--~~~CPiCrksv~ 1165 (1239)
+...|=||.+. . .+. .-||. -..|..|+.+|+.. +.+||+|+....
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 2 222 34663 78999999999864 478999998763
No 100
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=84.80 E-value=0.52 Score=54.66 Aligned_cols=52 Identities=21% Similarity=0.409 Sum_probs=43.2
Q ss_pred ccCCCCCCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcCccC
Q 000881 1111 REKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1166 (1239)
Q Consensus 1111 ~e~~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrksv~d 1166 (1239)
...+.++.||||+-. ....+.-||||--+..||.+.+.++..|=-|+.++.+
T Consensus 417 lp~sEd~lCpICyA~----pi~Avf~PC~H~SC~~CI~qHlmN~k~CFfCktTv~~ 468 (489)
T KOG4692|consen 417 LPDSEDNLCPICYAG----PINAVFAPCSHRSCYGCITQHLMNCKRCFFCKTTVID 468 (489)
T ss_pred CCCcccccCcceecc----cchhhccCCCCchHHHHHHHHHhcCCeeeEecceeee
Confidence 356778999999643 2334567999999999999999999999999999876
No 101
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=84.35 E-value=0.17 Score=57.28 Aligned_cols=49 Identities=29% Similarity=0.615 Sum_probs=32.7
Q ss_pred CCCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcCccChhhHh
Q 000881 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGDMAVYF 1171 (1239)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrksv~dm~~~~ 1171 (1239)
+.-|.||+|- ......|+|||.. .|+.== +.-..|||||+-|...-..|
T Consensus 300 ~~LC~ICmDa----P~DCvfLeCGHmV--tCt~CG-krm~eCPICRqyi~rvvrif 348 (350)
T KOG4275|consen 300 RRLCAICMDA----PRDCVFLECGHMV--TCTKCG-KRMNECPICRQYIVRVVRIF 348 (350)
T ss_pred HHHHHHHhcC----CcceEEeecCcEE--eehhhc-cccccCchHHHHHHHHHhhh
Confidence 7889999764 4457889999974 344211 11238999998776554444
No 102
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=84.13 E-value=0.52 Score=52.59 Aligned_cols=37 Identities=30% Similarity=0.696 Sum_probs=27.8
Q ss_pred ccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcCcc
Q 000881 1127 FTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1165 (1239)
Q Consensus 1127 f~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrksv~ 1165 (1239)
|.+.++-....|+|+|+..|...-. ...||+|+++|-
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 4444555677999999999986532 239999999973
No 103
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=83.85 E-value=0.52 Score=55.92 Aligned_cols=47 Identities=26% Similarity=0.530 Sum_probs=36.9
Q ss_pred CCCCcccccccccCCCcceecCCCCccChhhHHHhhh--------cCCCCCCCCcC
Q 000881 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC--------SHYICPICSKS 1163 (1239)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~--------~~~~CPiCrks 1163 (1239)
--.|-||.+. +.+......+||+|+|...|...|.. ...+||-|...
T Consensus 184 lf~C~ICf~e-~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C~ 238 (445)
T KOG1814|consen 184 LFDCCICFEE-QMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCG 238 (445)
T ss_pred cccceeeehh-hcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCCc
Confidence 4689999987 66656778899999999999999853 24679877643
No 104
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=83.08 E-value=0.68 Score=46.49 Aligned_cols=34 Identities=24% Similarity=0.423 Sum_probs=25.7
Q ss_pred cCCceeccCCCCCCCCCceeeeccCCCCCCcccccc
Q 000881 1190 RCQEILCNDCDKKGSAPFHWLYHKCGFCGSYNTRVI 1225 (1239)
Q Consensus 1190 ~~~~I~CnDC~~~s~~~~h~lg~kC~~C~syNT~~~ 1225 (1239)
..+...|++|+.......+ +..||.|||++++++
T Consensus 67 ~p~~~~C~~Cg~~~~~~~~--~~~CP~Cgs~~~~i~ 100 (115)
T TIGR00100 67 EPVECECEDCSEEVSPEID--LYRCPKCHGIMLQVR 100 (115)
T ss_pred eCcEEEcccCCCEEecCCc--CccCcCCcCCCcEEe
Confidence 3456899999987665422 347999999998875
No 105
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=82.72 E-value=0.75 Score=46.37 Aligned_cols=34 Identities=24% Similarity=0.460 Sum_probs=26.0
Q ss_pred cCCceeccCCCCCCCCC-ceeeeccCCCCCCcccccc
Q 000881 1190 RCQEILCNDCDKKGSAP-FHWLYHKCGFCGSYNTRVI 1225 (1239)
Q Consensus 1190 ~~~~I~CnDC~~~s~~~-~h~lg~kC~~C~syNT~~~ 1225 (1239)
..+...|++||...... +++ .+||.|||++..++
T Consensus 68 vp~~~~C~~Cg~~~~~~~~~~--~~CP~Cgs~~~~i~ 102 (117)
T PRK00564 68 EKVELECKDCSHVFKPNALDY--GVCEKCHSKNVIIT 102 (117)
T ss_pred cCCEEEhhhCCCccccCCccC--CcCcCCCCCceEEe
Confidence 34678999999877654 333 47999999998775
No 106
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=81.83 E-value=1.1 Score=51.94 Aligned_cols=65 Identities=22% Similarity=0.418 Sum_probs=45.3
Q ss_pred Cccccccccc-cccccccCCCCCCCcccccccccCCCcceecCCCCccChhhHHHh--hhcCCCCCCCCcCc
Q 000881 1096 TCNCCLAKKL-VDHKCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAY--TCSHYICPICSKSL 1164 (1239)
Q Consensus 1096 ~C~~C~~~~l-~~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~w--l~~~~~CPiCrksv 1164 (1239)
+=+.|..-++ +.-+=.....+++|-||-+.+ +-+.++||||-+.-.|--.. +.....||+||..-
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 3455665555 333333445678999998763 34578999999999996543 55678899999764
No 107
>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.
Probab=81.06 E-value=1.2 Score=46.93 Aligned_cols=32 Identities=28% Similarity=0.841 Sum_probs=22.1
Q ss_pred CCCCcccccccccCCCcceecCC------------C-CccChhhHHHhh
Q 000881 1116 ETNCPICCDFLFTSSATVRALPC------------G-HFMHSDCFQAYT 1151 (1239)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpC------------G-H~fH~~Ci~~wl 1151 (1239)
+..||||||.=. ..+.|-| + -+-|+.|++++-
T Consensus 2 d~~CpICme~PH----NAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfk 46 (162)
T PF07800_consen 2 DVTCPICMEHPH----NAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFK 46 (162)
T ss_pred CccCceeccCCC----ceEEEEeccccCCccccccCCccchhHHHHHHH
Confidence 468999999722 2344555 3 356999999984
No 108
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=80.32 E-value=0.93 Score=46.81 Aligned_cols=34 Identities=26% Similarity=0.687 Sum_probs=24.4
Q ss_pred CceeccCCCCCCCCC-------------cee------eeccCCCCCCcccccc
Q 000881 1192 QEILCNDCDKKGSAP-------------FHW------LYHKCGFCGSYNTRVI 1225 (1239)
Q Consensus 1192 ~~I~CnDC~~~s~~~-------------~h~------lg~kC~~C~syNT~~~ 1225 (1239)
....|++||...... +|+ .+.+|+.|||++.+++
T Consensus 69 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~ 121 (135)
T PRK03824 69 AVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRDFEIV 121 (135)
T ss_pred eEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCCcEEe
Confidence 567899999765443 222 2357999999998765
No 109
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=80.18 E-value=0.99 Score=57.68 Aligned_cols=41 Identities=27% Similarity=0.663 Sum_probs=31.6
Q ss_pred CCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcC
Q 000881 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKS 1163 (1239)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrks 1163 (1239)
..|..|--.| .-|.+...|||.||.+|+. .....||-|+-.
T Consensus 841 skCs~C~~~L---dlP~VhF~CgHsyHqhC~e---~~~~~CP~C~~e 881 (933)
T KOG2114|consen 841 SKCSACEGTL---DLPFVHFLCGHSYHQHCLE---DKEDKCPKCLPE 881 (933)
T ss_pred eeecccCCcc---ccceeeeecccHHHHHhhc---cCcccCCccchh
Confidence 4677775443 3467778999999999997 456889999983
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=79.92 E-value=6.4 Score=39.32 Aligned_cols=51 Identities=18% Similarity=0.181 Sum_probs=36.4
Q ss_pred hhHHhHHHHHHHHHHHHHHHHHHhhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 000881 361 SFAQEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQV 421 (1239)
Q Consensus 361 ~me~EH~~ie~l~e~l~~ll~~~~~a~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qv 421 (1239)
.+..+|++.-.+++.|..++..- . + ..++...+..|..-+..||..||.-.
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 45678887777777776655321 1 1 24667788888999999999999765
No 111
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=79.74 E-value=0.99 Score=45.25 Aligned_cols=33 Identities=24% Similarity=0.390 Sum_probs=24.6
Q ss_pred CCceeccCCCCCCCCCceeeeccCCCCCCcccccc
Q 000881 1191 CQEILCNDCDKKGSAPFHWLYHKCGFCGSYNTRVI 1225 (1239)
Q Consensus 1191 ~~~I~CnDC~~~s~~~~h~lg~kC~~C~syNT~~~ 1225 (1239)
.....|++|+........ ...||.|||++..++
T Consensus 68 p~~~~C~~Cg~~~~~~~~--~~~CP~Cgs~~~~i~ 100 (113)
T PRK12380 68 PAQAWCWDCSQVVEIHQH--DAQCPHCHGERLRVD 100 (113)
T ss_pred CcEEEcccCCCEEecCCc--CccCcCCCCCCcEEc
Confidence 456899999987665422 235999999998775
No 112
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=79.44 E-value=1.1 Score=45.10 Aligned_cols=35 Identities=17% Similarity=0.374 Sum_probs=25.3
Q ss_pred CCceeccCCCCCCCCCceeeeccCCCCCCccccccc
Q 000881 1191 CQEILCNDCDKKGSAPFHWLYHKCGFCGSYNTRVIK 1226 (1239)
Q Consensus 1191 ~~~I~CnDC~~~s~~~~h~lg~kC~~C~syNT~~~~ 1226 (1239)
.....|++|+.......+. ...||.|||+++.++.
T Consensus 68 p~~~~C~~Cg~~~~~~~~~-~~~CP~Cgs~~~~i~~ 102 (114)
T PRK03681 68 EAECWCETCQQYVTLLTQR-VRRCPQCHGDMLRIVA 102 (114)
T ss_pred CcEEEcccCCCeeecCCcc-CCcCcCcCCCCcEEcc
Confidence 3567899999876553221 2469999999988753
No 113
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=78.15 E-value=1.6 Score=55.30 Aligned_cols=70 Identities=23% Similarity=0.512 Sum_probs=47.1
Q ss_pred CccccCCCCCccccCCCCCccccccCCccccccccccccccccCCCCCCCcccccccccCCCcceecCCCCccChhhHHH
Q 000881 1070 RVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLAKKLVDHKCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQA 1149 (1239)
Q Consensus 1070 k~~yHC~~CgiCRvG~gl~~~~fHC~~C~~C~~~~l~~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~ 1149 (1239)
--+|-|+.|+-=-+++++ .-|++|-.|-+ ..|.+|-..+. +..+.---|||-.|..|+.+
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 55666666633 46999965432 12233347999999999999
Q ss_pred hhhcCCCCCC
Q 000881 1150 YTCSHYICPI 1159 (1239)
Q Consensus 1150 wl~~~~~CPi 1159 (1239)
|...+.-||.
T Consensus 811 w~~~~s~ca~ 820 (839)
T KOG0269|consen 811 WFFKASPCAK 820 (839)
T ss_pred HHhcCCCCcc
Confidence 9987777765
No 114
>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=77.83 E-value=0.43 Score=43.93 Aligned_cols=65 Identities=26% Similarity=0.637 Sum_probs=36.3
Q ss_pred CCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcCccChhhHhhhhHHHHhhcCCChhhhccCCceec
Q 000881 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGDMAVYFGMLDALLASEQLPEEYRDRCQEILC 1196 (1239)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrksv~dm~~~~~~lD~~i~~~pmP~ey~~~~~~I~C 1196 (1239)
..||.|..+|-..+ ||++...|-..+. ....||-|..++..+.. =-.++++|
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 57999998864432 7888888887654 35679999988754321 01258999
Q ss_pred cCCC---CCCCCCcee
Q 000881 1197 NDCD---KKGSAPFHW 1209 (1239)
Q Consensus 1197 nDC~---~~s~~~~h~ 1209 (1239)
|.|+ +|+.|.|.+
T Consensus 54 ~~c~gLiSKkrV~f~~ 69 (70)
T PF07191_consen 54 NHCHGLISKKRVRFEF 69 (70)
T ss_dssp TTTT-EE-TTTSEEEE
T ss_pred ccCCceeecceEEEEe
Confidence 9998 445565543
No 115
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=76.82 E-value=0.21 Score=58.54 Aligned_cols=53 Identities=23% Similarity=0.468 Sum_probs=45.6
Q ss_pred CCCCCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcCccC
Q 000881 1114 GLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1166 (1239)
Q Consensus 1114 ~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrksv~d 1166 (1239)
+.-..|.||.+.+...-+.+..+.|||.+|..|+.+|+.....||.|++.+..
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 34568999999877665678889999999999999999889999999999853
No 116
>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=76.77 E-value=0.76 Score=39.28 Aligned_cols=43 Identities=30% Similarity=0.783 Sum_probs=26.4
Q ss_pred CCCcccccccccCCCcceecCCC-CccChhhHHHhhhcCCCCCCCCcCcc
Q 000881 1117 TNCPICCDFLFTSSATVRALPCG-HFMHSDCFQAYTCSHYICPICSKSLG 1165 (1239)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCG-H~fH~~Ci~~wl~~~~~CPiCrksv~ 1165 (1239)
.||--|. |... ..+.|. |+....|+..++..+..||||.+++.
T Consensus 3 ~nCKsCW---f~~k---~Li~C~dHYLCl~CLt~ml~~s~~C~iC~~~LP 46 (50)
T PF03854_consen 3 YNCKSCW---FANK---GLIKCSDHYLCLNCLTLMLSRSDRCPICGKPLP 46 (50)
T ss_dssp ----SS----S--S---SEEE-SS-EEEHHHHHHT-SSSSEETTTTEE--
T ss_pred ccChhhh---hcCC---CeeeecchhHHHHHHHHHhccccCCCcccCcCc
Confidence 3566675 4332 346786 99999999999999999999999875
No 117
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=76.46 E-value=0.8 Score=56.68 Aligned_cols=54 Identities=22% Similarity=0.452 Sum_probs=39.8
Q ss_pred CCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcC----ccChhhHhhh
Q 000881 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKS----LGDMAVYFGM 1173 (1239)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrks----v~dm~~~~~~ 1173 (1239)
.+|+||+..++...-..+.|-|||++...|+... .+.+|| |... +.+.+.|++.
T Consensus 12 l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~l--yn~scp-~~~De~~~~~~~~e~p~n 69 (861)
T KOG3161|consen 12 LLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLL--YNASCP-TKRDEDSSLMQLKEEPRN 69 (861)
T ss_pred hhchHHHHHHHHHhcCcccccccchHHHHHHHhH--hhccCC-CCccccchhcChhhcchh
Confidence 4799998887777666678999999999999764 478899 7643 3344555433
No 118
>PRK04023 DNA polymerase II large subunit; Validated
Probab=76.22 E-value=2.3 Score=55.72 Aligned_cols=43 Identities=26% Similarity=0.508 Sum_probs=19.8
Q ss_pred ccccccccccCCCCCCCccCCCCccceEecccccCcCCCCccccCCCCC
Q 000881 1031 MCMRCLKVQPVGPVCTTLSCSGLSMAKYYCGICKFFDDERVVYHCPFCN 1079 (1239)
Q Consensus 1031 ~C~~C~~~q~~~~~C~~~~C~~~~~~~y~C~~C~l~dd~k~~yHC~~Cg 1079 (1239)
.|..|+++. +...|.+ |+...-.-|||+.|.- .-..|.|+.||
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 119
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=75.40 E-value=2.5 Score=48.57 Aligned_cols=47 Identities=28% Similarity=0.742 Sum_probs=37.7
Q ss_pred CCCcccccccccCCCc---ceecCCCCccChhhHHHhhhcC-CCCCCCCcCc
Q 000881 1117 TNCPICCDFLFTSSAT---VRALPCGHFMHSDCFQAYTCSH-YICPICSKSL 1164 (1239)
Q Consensus 1117 ~~CpICle~lf~s~~~---v~~LpCGH~fH~~Ci~~wl~~~-~~CPiCrksv 1164 (1239)
..|-||-++ |.+.++ .+.|.|||+|...|+...+.++ ..||-||.+.
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 468999998 666543 3568999999999999887654 5699999995
No 120
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=75.11 E-value=2.1 Score=45.35 Aligned_cols=45 Identities=22% Similarity=0.617 Sum_probs=32.8
Q ss_pred CCCCCcccccccccCCCcceecCCC--C---ccChhhHHHhhhc--CCCCCCCCcCc
Q 000881 1115 LETNCPICCDFLFTSSATVRALPCG--H---FMHSDCFQAYTCS--HYICPICSKSL 1164 (1239)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~LpCG--H---~fH~~Ci~~wl~~--~~~CPiCrksv 1164 (1239)
++..|-||.+.- + . ..-||. . ..|..|++.|+.. ..+||+|+...
T Consensus 7 ~~~~CRIC~~~~-~--~--~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y 58 (162)
T PHA02825 7 MDKCCWICKDEY-D--V--VTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPY 58 (162)
T ss_pred CCCeeEecCCCC-C--C--ccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeE
Confidence 467899998772 1 1 224664 4 6799999999854 57899999875
No 121
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=72.75 E-value=1.5 Score=56.00 Aligned_cols=49 Identities=27% Similarity=0.633 Sum_probs=35.7
Q ss_pred CCCCCcccccccccCCCccee-cCCCCccChhhHHHhhhc-------CCCCCCCCcCc
Q 000881 1115 LETNCPICCDFLFTSSATVRA-LPCGHFMHSDCFQAYTCS-------HYICPICSKSL 1164 (1239)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~-LpCGH~fH~~Ci~~wl~~-------~~~CPiCrksv 1164 (1239)
..-.|.||+|.+..+ .++-. -.|=|+||..||.+|.+. .-+||-|+...
T Consensus 190 ~~yeCmIC~e~I~~t-~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv~ 246 (950)
T KOG1952|consen 190 RKYECMICTERIKRT-APVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSVS 246 (950)
T ss_pred CceEEEEeeeecccc-CCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccchh
Confidence 346899999996544 33322 346699999999999642 46899999543
No 122
>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=72.69 E-value=1.1 Score=44.71 Aligned_cols=33 Identities=24% Similarity=0.435 Sum_probs=21.9
Q ss_pred CCceeccCCCCCCCCCceeeeccCCCCCCcccccc
Q 000881 1191 CQEILCNDCDKKGSAPFHWLYHKCGFCGSYNTRVI 1225 (1239)
Q Consensus 1191 ~~~I~CnDC~~~s~~~~h~lg~kC~~C~syNT~~~ 1225 (1239)
.....|++||..+....+. ..||.|||++..++
T Consensus 68 p~~~~C~~Cg~~~~~~~~~--~~CP~Cgs~~~~i~ 100 (113)
T PF01155_consen 68 PARARCRDCGHEFEPDEFD--FSCPRCGSPDVEII 100 (113)
T ss_dssp --EEEETTTS-EEECHHCC--HH-SSSSSS-EEEE
T ss_pred CCcEECCCCCCEEecCCCC--CCCcCCcCCCcEEc
Confidence 4568899999988655443 46999999998765
No 123
>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=71.62 E-value=11 Score=41.90 Aligned_cols=46 Identities=24% Similarity=0.300 Sum_probs=27.2
Q ss_pred CCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHhhhhh-hHHHHHHhhhhhHhHH
Q 000881 72 LGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIRVK-NIARTYSLEHEGESVL 128 (1239)
Q Consensus 72 ~gd~~~~~~l~~r~~~l~~~~~~H~~aEDevI~PaL~~Rv~-~v~~~~~~EH~~~~~l 128 (1239)
+.|+=++.-|++| ||||++ +|==.=|--|+ -|+.+|..|-++++.-
T Consensus 124 INDPYDlGLLLRh-------LRHHSN----LLAnIgdP~VreqVLsAMqEeeeEEe~D 170 (238)
T PF02084_consen 124 INDPYDLGLLLRH-------LRHHSN----LLANIGDPEVREQVLSAMQEEEEEEEQD 170 (238)
T ss_pred cCChhhHHHHHHH-------HHHHHH----HHhhcCCHHHHHHHHHHHhhhHHHHHHH
Confidence 4677777666555 578998 22111112244 3888998876665543
No 124
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=70.24 E-value=3.4 Score=51.83 Aligned_cols=71 Identities=17% Similarity=0.384 Sum_probs=45.3
Q ss_pred CCCCcccccccccCCCcceecC---CCCccChhhHHHh----h----hcCCCCCCCCcCccChhhHhhhhHHHHhhcCCC
Q 000881 1116 ETNCPICCDFLFTSSATVRALP---CGHFMHSDCFQAY----T----CSHYICPICSKSLGDMAVYFGMLDALLASEQLP 1184 (1239)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~Lp---CGH~fH~~Ci~~w----l----~~~~~CPiCrksv~dm~~~~~~lD~~i~~~pmP 1184 (1239)
-..||+|+-. +-..+....+. |.--.|..|..-. . ...|.|-+|| ..+..-+.|-..+...-+|
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 43334343333 5566888885332 2 1379999999 3344456777778888888
Q ss_pred hhhhccC
Q 000881 1185 EEYRDRC 1191 (1239)
Q Consensus 1185 ~ey~~~~ 1191 (1239)
..|.+..
T Consensus 220 k~~~~~~ 226 (694)
T KOG4443|consen 220 KDKPDKI 226 (694)
T ss_pred hhccccc
Confidence 7775543
No 125
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=70.00 E-value=1.8 Score=55.80 Aligned_cols=44 Identities=25% Similarity=0.558 Sum_probs=32.7
Q ss_pred ccccccCCCCCCCcccccccccCCCcceecCCCCccChhhHHHhhh
Q 000881 1107 DHKCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC 1152 (1239)
Q Consensus 1107 ~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~ 1152 (1239)
.|.|.--.....|-+|.-.++.. +-.+.||||.||..|+.+-..
T Consensus 808 ~~ry~v~ep~d~C~~C~~~ll~~--pF~vf~CgH~FH~~Cl~~~v~ 851 (911)
T KOG2034|consen 808 RQRYRVLEPQDSCDHCGRPLLIK--PFYVFPCGHCFHRDCLIRHVL 851 (911)
T ss_pred hcceEEecCccchHHhcchhhcC--cceeeeccchHHHHHHHHHHH
Confidence 45554445567899998776543 567789999999999987653
No 126
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=69.09 E-value=3.4 Score=49.21 Aligned_cols=46 Identities=22% Similarity=0.536 Sum_probs=37.0
Q ss_pred CCCcccccccccCCCcceecCCCCccChhhHHHhhhcC---CCCCCCCcC
Q 000881 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSH---YICPICSKS 1163 (1239)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~---~~CPiCrks 1163 (1239)
-.|||=.|. -+...|.+.|.|||++-.+=+++..+++ .+||.|-..
T Consensus 335 F~CPVlKeq-tsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~e 383 (394)
T KOG2817|consen 335 FICPVLKEQ-TSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPVE 383 (394)
T ss_pred eecccchhh-ccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCcc
Confidence 468887766 5556688899999999999999987543 789999754
No 127
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=68.54 E-value=5.3 Score=49.48 Aligned_cols=78 Identities=21% Similarity=0.442 Sum_probs=44.2
Q ss_pred ecCCCCccChhhHHHhhhcCCCCCCCCcCccChhh-Hhhhh--HHHHhhcCCChhhhccCCceeccCCCCC---C-----
Q 000881 1135 ALPCGHFMHSDCFQAYTCSHYICPICSKSLGDMAV-YFGML--DALLASEQLPEEYRDRCQEILCNDCDKK---G----- 1203 (1239)
Q Consensus 1135 ~LpCGH~fH~~Ci~~wl~~~~~CPiCrksv~dm~~-~~~~l--D~~i~~~pmP~ey~~~~~~I~CnDC~~~---s----- 1203 (1239)
+..=|-+||..|+ +|-+|+++...-+. .|.-- --+.-.++||--=.....--.|-.|+.. +
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 3344899999987 66777776632111 11111 1122345565431222334568888754 1
Q ss_pred -CCCceeeeccCCCCCCc
Q 000881 1204 -SAPFHWLYHKCGFCGSY 1220 (1239)
Q Consensus 1204 -~~~~h~lg~kC~~C~sy 1220 (1239)
..++|+.+-||..|+.-
T Consensus 152 ld~qwhv~cfkc~~c~~v 169 (670)
T KOG1044|consen 152 LDKQWHVSCFKCKSCSAV 169 (670)
T ss_pred eccceeeeeeehhhhccc
Confidence 36799999999987654
No 128
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=67.76 E-value=4.3 Score=35.83 Aligned_cols=37 Identities=24% Similarity=0.518 Sum_probs=28.7
Q ss_pred CCCCCCcccccccccCCCcceecCCCCccChhhHHHh
Q 000881 1114 GLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAY 1150 (1239)
Q Consensus 1114 ~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~w 1150 (1239)
.....|++|.+.+.+..+.|+-.-||-.+|+.|..+-
T Consensus 3 ~~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~ 39 (54)
T PF14446_consen 3 YEGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKA 39 (54)
T ss_pred ccCccChhhCCcccCCCCEEECCCCCCcccHHHHhhC
Confidence 3467899999996556555555789999999998653
No 129
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=67.44 E-value=3.2 Score=34.81 Aligned_cols=41 Identities=27% Similarity=0.705 Sum_probs=20.0
Q ss_pred CcccccccccCCCcceecCCCCccChhhHHHhhhcCC--CCCCC
Q 000881 1119 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHY--ICPIC 1160 (1239)
Q Consensus 1119 CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~--~CPiC 1160 (1239)
|-+|.+-... +..-..-.|+=.+|..|+..|++... +||.|
T Consensus 1 C~~C~~iv~~-G~~C~~~~C~~r~H~~C~~~y~r~~~~~~CP~C 43 (43)
T PF08746_consen 1 CEACKEIVTQ-GQRCSNRDCNVRLHDDCFKKYFRHRSNPKCPNC 43 (43)
T ss_dssp -TTT-SB-SS-SEE-SS--S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred CcccchhHee-eccCCCCccCchHHHHHHHHHHhcCCCCCCcCC
Confidence 5566654322 21111235777899999999986643 79988
No 130
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=67.34 E-value=3.1 Score=42.44 Aligned_cols=34 Identities=26% Similarity=0.654 Sum_probs=23.4
Q ss_pred CCceeccCCCCCCCCC-c---ee-eeccCCCCCCcccccc
Q 000881 1191 CQEILCNDCDKKGSAP-F---HW-LYHKCGFCGSYNTRVI 1225 (1239)
Q Consensus 1191 ~~~I~CnDC~~~s~~~-~---h~-lg~kC~~C~syNT~~~ 1225 (1239)
.....| +||..+... + |+ .+..||.|||++..++
T Consensus 68 p~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~ 106 (124)
T PRK00762 68 PVEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKRAHIL 106 (124)
T ss_pred CeeEEe-eCcCcccccccchhccccCCcCcCCCCCCCEEe
Confidence 356789 999875432 1 12 1346999999998875
No 131
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=66.67 E-value=2.6 Score=44.47 Aligned_cols=31 Identities=32% Similarity=0.556 Sum_probs=24.6
Q ss_pred CCCCCCCcccccccccCCCcceecCCCCccCh
Q 000881 1113 KGLETNCPICCDFLFTSSATVRALPCGHFMHS 1144 (1239)
Q Consensus 1113 ~~~~~~CpICle~lf~s~~~v~~LpCGH~fH~ 1144 (1239)
+.....|.||||+|-. ++.+..|||==+||+
T Consensus 174 ~ddkGECvICLEdL~~-GdtIARLPCLCIYHK 204 (205)
T KOG0801|consen 174 KDDKGECVICLEDLEA-GDTIARLPCLCIYHK 204 (205)
T ss_pred cccCCcEEEEhhhccC-CCceeccceEEEeec
Confidence 3446789999999654 567889999888886
No 132
>TIGR02481 hemeryth_dom hemerythrin-like metal-binding domain. This model describes both members of the hemerythrin (TIGR00058) family of marine invertebrates and a broader collection of bacterial and archaeal homologs. Many of the latter group are multidomain proteins with signal-transducing domains such as the GGDEF diguanylate cyclase domain (TIGR00254, pfam00990) and methyl-accepting chemotaxis protein signaling domain (pfam00015). Most hemerythrins are oxygen-carriers with a bound non-heme iron, but at least one example is a cadmium-binding protein, apparently with a role in sequestering toxic metals rather than in binding oxygen. Patterns of conserved residues suggest that all prokaryotic instances of this domain bind iron or another heavy metal, but the exact function is unknown. Not surprisingly, the prokaryote with the most instances of this domain is Magnetococcus sp. MC-1, a magnetotactic bacterium.
Probab=66.23 E-value=87 Score=31.25 Aligned_cols=109 Identities=17% Similarity=0.273 Sum_probs=68.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcccCCcccHHHHHHHHHHHHHHHHhhhhcccccc----hhhhhhhhhhHHhHHHHHHH
Q 000881 297 IMLWHNAIKRELNDIAEAARKIQLSGDFSDLSAFNKRLQFIAEVCIFHSIAEDKVI----FPAVDVELSFAQEHAEEEIQ 372 (1239)
Q Consensus 297 L~~~HkALRrEL~~L~~~a~~~~~~gd~~~L~~L~~r~~fl~~vl~~Hs~aEDevl----FPaL~~r~~me~EH~~ie~l 372 (1239)
+=.-|+.|=..++.|...+..- .....+...+.+|.+....|-..|+.++ ||.+..+. .+|+ ..
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 000881 373 FDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPL 424 (1239)
Q Consensus 373 ~e~l~~ll~~~~~a~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qvfPL 424 (1239)
++.+..+...+.. +.. ..... ..+..+.+-|..|+..+-..+.+.
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 4555555444432 101 11222 344557788999999888776553
No 133
>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=65.50 E-value=4.5 Score=42.39 Aligned_cols=47 Identities=26% Similarity=0.579 Sum_probs=39.1
Q ss_pred CCccceEecccccCcCCCCccccCCCCCccccCCCCCccccccCCcccccccc
Q 000881 1052 GLSMAKYYCGICKFFDDERVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLAKK 1104 (1239)
Q Consensus 1052 ~~~~~~y~C~~C~l~dd~k~~yHC~~CgiCRvG~gl~~~~fHC~~C~~C~~~~ 1104 (1239)
+......||..|+.+... ..+||..||.|-.+- -.||.=-|.|+...
T Consensus 43 ~~~~~~~~C~~C~~~kp~-Rs~HC~~C~~CV~~~-----DHHC~w~~~cIG~~ 89 (174)
T PF01529_consen 43 DENGELKYCSTCKIIKPP-RSHHCRVCNRCVLRF-----DHHCPWLGNCIGRR 89 (174)
T ss_pred ccCCCCEECcccCCcCCC-cceeccccccccccc-----cccchhhccccccc
Confidence 456778899999999766 489999999999874 47999999998754
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=64.83 E-value=4.3 Score=31.61 Aligned_cols=38 Identities=32% Similarity=0.747 Sum_probs=25.7
Q ss_pred CCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcCcc
Q 000881 1118 NCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1165 (1239)
Q Consensus 1118 ~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrksv~ 1165 (1239)
.|+.|.+.+......+. .=|..||..|+ +|..|++++.
T Consensus 1 ~C~~C~~~i~~~~~~~~--~~~~~~H~~Cf--------~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLR--ALGKVWHPECF--------KCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEE--eCCccccccCC--------CCcccCCcCc
Confidence 37888887655422222 22789999887 7888988764
No 135
>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=64.32 E-value=1.8 Score=48.11 Aligned_cols=51 Identities=25% Similarity=0.539 Sum_probs=39.1
Q ss_pred CCCCCcccccccccCCCcceec-C-CCCccChhhHHHhhhcC-CCCC--CCCcCcc
Q 000881 1115 LETNCPICCDFLFTSSATVRAL-P-CGHFMHSDCFQAYTCSH-YICP--ICSKSLG 1165 (1239)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~L-p-CGH~fH~~Ci~~wl~~~-~~CP--iCrksv~ 1165 (1239)
.+..||||.-+.+-+.+-...+ | |=|-|+.+|++.-...+ ..|| -|.|.+.
T Consensus 9 ~d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kILR 64 (314)
T COG5220 9 EDRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKILR 64 (314)
T ss_pred hcccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHHH
Confidence 3458999998877776633333 6 99999999999987654 6899 8987663
No 136
>KOG2068 consensus MOT2 transcription factor [Transcription]
Probab=63.59 E-value=5.2 Score=46.81 Aligned_cols=52 Identities=25% Similarity=0.545 Sum_probs=39.8
Q ss_pred CCCCCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcCcc
Q 000881 1114 GLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1165 (1239)
Q Consensus 1114 ~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrksv~ 1165 (1239)
+-...||||.+++........--|||+.++..|...-...+.+||.||+...
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 4457899999986444333334478999999999888888999999997753
No 137
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=63.27 E-value=4.4 Score=46.38 Aligned_cols=43 Identities=30% Similarity=0.772 Sum_probs=33.9
Q ss_pred CCCcccccccccCCCcceecCCCCccChhhHHHhh-hcCCCCCCCCc
Q 000881 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYT-CSHYICPICSK 1162 (1239)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl-~~~~~CPiCrk 1162 (1239)
..||.|.--+. .+++.--|||.|...||..-+ ...+.||.|.+
T Consensus 275 LkCplc~~Llr---np~kT~cC~~~fc~eci~~al~dsDf~CpnC~r 318 (427)
T COG5222 275 LKCPLCHCLLR---NPMKTPCCGHTFCDECIGTALLDSDFKCPNCSR 318 (427)
T ss_pred ccCcchhhhhh---CcccCccccchHHHHHHhhhhhhccccCCCccc
Confidence 57999976543 355666789999999999765 66799999987
No 138
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=63.22 E-value=5.6 Score=35.68 Aligned_cols=45 Identities=27% Similarity=0.641 Sum_probs=21.8
Q ss_pred ccccccccccccCCC-----CCCCccCCCCccceEecccccCcCCCCccccCCCCCc
Q 000881 1029 EMMCMRCLKVQPVGP-----VCTTLSCSGLSMAKYYCGICKFFDDERVVYHCPFCNL 1080 (1239)
Q Consensus 1029 ~v~C~~C~~~q~~~~-----~C~~~~C~~~~~~~y~C~~C~l~dd~k~~yHC~~Cgi 1080 (1239)
...|..|+..-.... .|-| | |.. -=|-|.+|+-.. ..|.|++||+
T Consensus 7 ~~~CtSCg~~i~~~~~~~~F~CPn--C-G~~-~I~RC~~CRk~~---~~Y~CP~CGF 56 (59)
T PRK14890 7 PPKCTSCGIEIAPREKAVKFLCPN--C-GEV-IIYRCEKCRKQS---NPYTCPKCGF 56 (59)
T ss_pred CccccCCCCcccCCCccCEeeCCC--C-CCe-eEeechhHHhcC---CceECCCCCC
Confidence 345666664433322 3444 3 321 123455555543 3566776664
No 139
>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=61.59 E-value=4 Score=46.13 Aligned_cols=50 Identities=28% Similarity=0.824 Sum_probs=35.0
Q ss_pred CCcccCccccccc-CCCCCccccccccccccccccccCCCCCCCccCCCCccceEecccccC
Q 000881 1005 GKLFTCRFCHDKV-SDHSMDRKATTEMMCMRCLKVQPVGPVCTTLSCSGLSMAKYYCGICKF 1065 (1239)
Q Consensus 1005 ~~~y~Cr~CHde~-~~H~~~r~~~~~v~C~~C~~~q~~~~~C~~~~C~~~~~~~y~C~~C~l 1065 (1239)
|+.|.|-||++-. +|-.|+-.+ .|+....-+-.|.+ | + .+|.|.|-.||.
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 6789999999873 454454332 36666666677876 6 3 689999999985
No 140
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=59.26 E-value=5.9 Score=40.06 Aligned_cols=35 Identities=31% Similarity=0.460 Sum_probs=27.6
Q ss_pred cCCceeccCCCCCCCCCceeeeccCCCCCCccccccc
Q 000881 1190 RCQEILCNDCDKKGSAPFHWLYHKCGFCGSYNTRVIK 1226 (1239)
Q Consensus 1190 ~~~~I~CnDC~~~s~~~~h~lg~kC~~C~syNT~~~~ 1226 (1239)
..+.+.|-||+......-|.++ ||.|||-|.+++.
T Consensus 67 ~p~~~~C~~C~~~~~~e~~~~~--CP~C~s~~~~i~~ 101 (115)
T COG0375 67 EPAECWCLDCGQEVELEELDYR--CPKCGSINLRIIG 101 (115)
T ss_pred eccEEEeccCCCeecchhheeE--CCCCCCCceEEec
Confidence 3467899999887766666544 9999999999863
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=57.94 E-value=7.1 Score=48.63 Aligned_cols=48 Identities=23% Similarity=0.632 Sum_probs=41.1
Q ss_pred ccccccCCcccCcccccccCCCCCccccccccccccccccccCCCCCCCccCCC
Q 000881 999 LRAACCGKLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVGPVCTTLSCSG 1052 (1239)
Q Consensus 999 l~~~cC~~~y~Cr~CHde~~~H~~~r~~~~~v~C~~C~~~q~~~~~C~~~~C~~ 1052 (1239)
+.|.-||....|..|.-...-|.- ...+.|-.|+..+++...|-+ |.+
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 789999999999999887777743 458999999999999999987 743
No 142
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=57.30 E-value=2.9 Score=55.88 Aligned_cols=70 Identities=10% Similarity=0.031 Sum_probs=47.5
Q ss_pred HHHHHHHHHHHHHHHHHHHhhHHHHHHHhhHHhhcCCHHHHHHHHHHHhcCCCHHHHHHHHhhhcCCCCH
Q 000881 145 SYRRELASCTGALQTSISQHMSKEEEQVFPLLIEKFSFEEQASLVWQFLCSIPVNMMAEFLPWLSSSISS 214 (1239)
Q Consensus 145 ~~~~eLa~~l~~l~~~l~qHm~~EE~qv~PLl~~~fS~~E~a~L~~~~~~siP~~~m~~~Lpwm~~~lsp 214 (1239)
++..-+-..+.-.+--...||--+|.+..-.=...+|..+-.++...|.-++|..-...-.+....++++
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 4444444445555555677888888887766677788888888888888888866555444455555555
No 143
>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=56.55 E-value=7.8 Score=48.05 Aligned_cols=13 Identities=38% Similarity=0.994 Sum_probs=6.6
Q ss_pred CccceEecccccC
Q 000881 1053 LSMAKYYCGICKF 1065 (1239)
Q Consensus 1053 ~~~~~y~C~~C~l 1065 (1239)
.+.-.|||+.|-+
T Consensus 22 ~Ei~~~yCp~CL~ 34 (483)
T PF05502_consen 22 EEIDSYYCPNCLF 34 (483)
T ss_pred cccceeECccccc
Confidence 3455555555543
No 144
>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]
Probab=56.02 E-value=4.3 Score=51.91 Aligned_cols=88 Identities=13% Similarity=0.053 Sum_probs=60.1
Q ss_pred HHHHHHHHhHHHHHH-----HHHHHHHhhCCHHHHHHHHHhHhhcCCHHHHHHHHhhhcCCCCHHHHHHHHHHhhhhCCC
Q 000881 405 LIMASIQKHFRNEEV-----QVLPLARRHFSPKRQRELLYQSLCVMPLKLIECVLPWLVGSLSEEEARSFLQNIYMAAPA 479 (1239)
Q Consensus 405 ~L~~~L~~Hf~~EE~-----qvfPLl~~~fS~eEq~eL~~~~l~smPl~~L~~vLPWl~~~Ls~~E~~~~L~~l~~~aP~ 479 (1239)
.+-...-.|+..|++ -+.|.+=.. +-+||+..+.+|.-.--+..+.-+||=.-+.|.|.-...+|...=. |-
T Consensus 393 kv~~~yI~HLl~~~~y~~Aas~~p~m~gn-~~~eWe~~V~~f~e~~~l~~Ia~~lPt~~~rL~p~vYemvLve~L~--~~ 469 (846)
T KOG2066|consen 393 KVGKTYIDHLLFEGKYDEAASLCPKMLGN-NAAEWELWVFKFAELDQLTDIAPYLPTGPPRLKPLVYEMVLVEFLA--SD 469 (846)
T ss_pred HHHHHHHHHHHhcchHHHHHhhhHHHhcc-hHHHHHHHHHHhccccccchhhccCCCCCcccCchHHHHHHHHHHH--HH
Confidence 334445666654443 344444333 4578999998888777777888888888889999999998887443 54
Q ss_pred CchHHHHHHHHHhhcCC
Q 000881 480 SDSALITLFAGWACKGH 496 (1239)
Q Consensus 480 ~~~~~~~l~~~w~~~~~ 496 (1239)
.+. |-.+++.|-+.-|
T Consensus 470 ~~~-F~e~i~~Wp~~Ly 485 (846)
T KOG2066|consen 470 VKG-FLELIKEWPGHLY 485 (846)
T ss_pred HHH-HHHHHHhCChhhh
Confidence 444 7888899954434
No 145
>PF14357 DUF4404: Domain of unknown function (DUF4404)
Probab=55.98 E-value=72 Score=30.70 Aligned_cols=82 Identities=13% Similarity=0.095 Sum_probs=64.7
Q ss_pred HHHHHHHHHHHHHhhccCCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHhhhhhhHHHHHHhhhhhHhHHHHHHH
Q 000881 54 IKSELDVLHRAAMAFATNLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIRVKNIARTYSLEHEGESVLFDQLF 133 (1239)
Q Consensus 54 lRreL~~l~~~a~~~~~~~gd~~~~~~l~~r~~~l~~~~~~H~~aEDevI~PaL~~Rv~~v~~~~~~EH~~~~~l~~~L~ 133 (1239)
||..|..|+.-+...++ -|......|..=-+.+...+.. ..|.+.--+.|..|+...+.+++.+|=.....+..|-
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 5666666665555556666654 5677788999999999999999999999999998888
Q ss_pred HHHHhh
Q 000881 134 ELLNSS 139 (1239)
Q Consensus 134 ~~l~~~ 139 (1239)
..|..+
T Consensus 78 ~sLa~M 83 (85)
T PF14357_consen 78 DSLANM 83 (85)
T ss_pred HHHHHC
Confidence 777654
No 146
>PRK01917 cation-binding hemerythrin HHE family protein; Provisional
Probab=54.83 E-value=31 Score=35.70 Aligned_cols=95 Identities=11% Similarity=0.135 Sum_probs=49.6
Q ss_pred HHhHHHHHHHHHHHHHHHHHHhhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHH----HHHHHhhCCH-----HH
Q 000881 363 AQEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQV----LPLARRHFSP-----KR 433 (1239)
Q Consensus 363 e~EH~~ie~l~e~l~~ll~~~~~a~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qv----fPLl~~~fS~-----eE 433 (1239)
+..+..||..-..|..++..+..+. ...+...++.|..-...||..||.-. +|-+..|--. ++
T Consensus 11 ~vGi~~ID~qH~~Lf~lin~l~~~~--------~~~i~~~l~~L~~y~~~HF~~EE~lM~~~~YP~~~~H~~eH~~fl~~ 82 (139)
T PRK01917 11 HLGDPFTDATHAEFVQLLNAVARAD--------DADFLQALDAWIDHTRHHFAQEERWMEATKFGPRHCHRAEHDEVLAV 82 (139)
T ss_pred hcCChhhhHHHHHHHHHHHHHHcCC--------HHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHH
Confidence 3344444444445555555443221 13356778888999999999999653 3433333211 12
Q ss_pred HHHHHHhHhh----cCCHHHHHHHHhhhcCCCCHHH
Q 000881 434 QRELLYQSLC----VMPLKLIECVLPWLVGSLSEEE 465 (1239)
Q Consensus 434 q~eL~~~~l~----smPl~~L~~vLPWl~~~Ls~~E 465 (1239)
..++..+... .+...++..+..||+.++.-..
T Consensus 83 v~~l~~~~~~~g~~~~~~~l~~~L~~Wl~~HI~~~D 118 (139)
T PRK01917 83 AADVREKVARDGDFELGRRLVAELPEWFDQHVRTMD 118 (139)
T ss_pred HHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 2222222221 2334455556678887774333
No 147
>PHA03096 p28-like protein; Provisional
Probab=54.55 E-value=6.3 Score=45.64 Aligned_cols=46 Identities=15% Similarity=0.220 Sum_probs=29.6
Q ss_pred CCCcccccccccCC---Ccceec-CCCCccChhhHHHhhhc---CCCCCCCCc
Q 000881 1117 TNCPICCDFLFTSS---ATVRAL-PCGHFMHSDCFQAYTCS---HYICPICSK 1162 (1239)
Q Consensus 1117 ~~CpICle~lf~s~---~~v~~L-pCGH~fH~~Ci~~wl~~---~~~CPiCrk 1162 (1239)
-.|.||+|...... ..-..| .|.|.|...|+..|... ..+||.|+.
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~ 231 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRR 231 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCccccc
Confidence 46888887655431 111234 79999999999999642 344555554
No 148
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=54.37 E-value=8.9 Score=30.28 Aligned_cols=24 Identities=38% Similarity=1.089 Sum_probs=19.0
Q ss_pred eEecccccCc-CCCCccccCCCCCc
Q 000881 1057 KYYCGICKFF-DDERVVYHCPFCNL 1080 (1239)
Q Consensus 1057 ~y~C~~C~l~-dd~k~~yHC~~Cgi 1080 (1239)
.|-|.+|.+. |.++.++.||.||.
T Consensus 1 ~~~C~~CGy~y~~~~~~~~CP~Cg~ 25 (33)
T cd00350 1 KYVCPVCGYIYDGEEAPWVCPVCGA 25 (33)
T ss_pred CEECCCCCCEECCCcCCCcCcCCCC
Confidence 4788999886 55578999999984
No 149
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=53.31 E-value=5.9 Score=50.96 Aligned_cols=43 Identities=30% Similarity=0.745 Sum_probs=34.2
Q ss_pred CCCcccccccccCCCcceecCCCCccChhhHHHhhhc--CCCCCCCCcCc
Q 000881 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS--HYICPICSKSL 1164 (1239)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~--~~~CPiCrksv 1164 (1239)
..|+||++ .+.....+|||.|...|+.+.+.. ...||+||..+
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
>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=52.84 E-value=10 Score=32.78 Aligned_cols=41 Identities=34% Similarity=0.869 Sum_probs=20.0
Q ss_pred CCCcccccccccCCCcceecCCCCccChhhHH--Hhhhc-----CCCCCCCCcC
Q 000881 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQ--AYTCS-----HYICPICSKS 1163 (1239)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~--~wl~~-----~~~CPiCrks 1163 (1239)
-.|||....|. .+++...|.|. .||| .|+.. ...||+|+++
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 36999987753 46788889866 6765 45532 4679999874
No 151
>cd00522 Hemerythrin Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the muscle tissue of sipunculids as well as in polycheate and oligocheate annelids. In addition to oxygen transport, Mhr proteins are involved in cadmium fixation and host anti-bacterial defense. Hr and Mhr proteins have the same "four alpha helix bundle" motif and active site structure. Hr forms oligomers, the octameric form being most prevalent, while Mhr is monomeric.
Probab=52.84 E-value=57 Score=32.42 Aligned_cols=28 Identities=25% Similarity=0.411 Sum_probs=20.2
Q ss_pred HHHHHHHHHHHHhHHHHHHHH----HHHHHhh
Q 000881 401 SQADLIMASIQKHFRNEEVQV----LPLARRH 428 (1239)
Q Consensus 401 ~~le~L~~~L~~Hf~~EE~qv----fPLl~~~ 428 (1239)
..+..|..-...||..||+-. +|-+..|
T Consensus 37 ~~l~~L~~y~~~HF~~EE~~M~~~~yp~~~~H 68 (113)
T cd00522 37 DNLKELVDYTVKHFKDEEALMEAAGYPDYEEH 68 (113)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCCCHHHH
Confidence 456777888999999999764 4555444
No 152
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=51.96 E-value=13 Score=50.33 Aligned_cols=17 Identities=24% Similarity=0.257 Sum_probs=11.2
Q ss_pred ccCCCCCCccccccccc
Q 000881 1212 HKCGFCGSYNTRVIKVE 1228 (1239)
Q Consensus 1212 ~kC~~C~syNT~~~~~~ 1228 (1239)
.|=++|-.-.|+++-.+
T Consensus 914 AKRRNCF~GDT~IlV~d 930 (1337)
T PRK14714 914 AKRRNCFHGDTRILVQD 930 (1337)
T ss_pred HhhcCCCCCCcEEEEEc
Confidence 35567888888876433
No 153
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=50.70 E-value=14 Score=42.41 Aligned_cols=70 Identities=26% Similarity=0.637 Sum_probs=0.0
Q ss_pred ccCCCCCccccCCCCC-------------ccccccCCccccc------cccccccccccCCCCCCCcccccccccCCCcc
Q 000881 1073 YHCPFCNLCRVGRGLG-------------VDFFHCMTCNCCL------AKKLVDHKCREKGLETNCPICCDFLFTSSATV 1133 (1239)
Q Consensus 1073 yHC~~CgiCRvG~gl~-------------~~~fHC~~C~~C~------~~~l~~H~C~e~~~~~~CpICle~lf~s~~~v 1133 (1239)
|+|++||-=.---. | ..-|+|..|+-=| .+-+-+|. ....|+||.-. |..
T Consensus 131 ~~c~eCgk~ysT~s-nLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~-----l~c~C~iCGKa-FSR---- 199 (279)
T KOG2462|consen 131 YKCPECGKSYSTSS-NLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT-----LPCECGICGKA-FSR---- 199 (279)
T ss_pred eecccccccccccc-ccchhhcccccccccccccCCCCCceeeehHHHhhHhhccC-----CCccccccccc-ccc----
Q ss_pred eecCCCCccChhhHHHhhhcC----------CCCCCCCcCccChh
Q 000881 1134 RALPCGHFMHSDCFQAYTCSH----------YICPICSKSLGDMA 1168 (1239)
Q Consensus 1134 ~~LpCGH~fH~~Ci~~wl~~~----------~~CPiCrksv~dm~ 1168 (1239)
.|+-.. +.||.|+|.+.|.+
T Consensus 200 ---------------PWLLQGHiRTHTGEKPF~C~hC~kAFADRS 229 (279)
T KOG2462|consen 200 ---------------PWLLQGHIRTHTGEKPFSCPHCGKAFADRS 229 (279)
T ss_pred ---------------hHHhhcccccccCCCCccCCcccchhcchH
No 154
>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=50.62 E-value=9.6 Score=38.18 Aligned_cols=17 Identities=35% Similarity=0.757 Sum_probs=15.1
Q ss_pred cCcCCCCccccCCCCCc
Q 000881 1064 KFFDDERVVYHCPFCNL 1080 (1239)
Q Consensus 1064 ~l~dd~k~~yHC~~Cgi 1080 (1239)
||||-+|.+-.||+||-
T Consensus 18 kFYDLnk~PivCP~CG~ 34 (108)
T PF09538_consen 18 KFYDLNKDPIVCPKCGT 34 (108)
T ss_pred hhccCCCCCccCCCCCC
Confidence 78899999999999993
No 155
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=50.60 E-value=9 Score=38.39 Aligned_cols=32 Identities=25% Similarity=0.517 Sum_probs=24.0
Q ss_pred ccccccccCCcccCcccccccCCCCCccccccccccccccccccCC
Q 000881 997 CKLRAACCGKLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVG 1042 (1239)
Q Consensus 997 c~l~~~cC~~~y~Cr~CHde~~~H~~~r~~~~~v~C~~C~~~q~~~ 1042 (1239)
-|-.||-||+-| .+... ..++|.+|+++|++.
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 23333 578999999999987
No 156
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=49.32 E-value=13 Score=48.24 Aligned_cols=55 Identities=24% Similarity=0.529 Sum_probs=43.3
Q ss_pred cccccccCCcccCcccccccCCCCCccccccccccccccccccCCCCCCCccCCCCccceEe
Q 000881 998 KLRAACCGKLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVGPVCTTLSCSGLSMAKYY 1059 (1239)
Q Consensus 998 ~l~~~cC~~~y~Cr~CHde~~~H~~~r~~~~~v~C~~C~~~q~~~~~C~~~~C~~~~~~~y~ 1059 (1239)
-+.|.-||-.+.|++|=.-..=|.- +..+.|-.|+..+++-..|-+ | |...=+|+
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 3899999999999999665555532 369999999999999999987 6 54444444
No 157
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=48.80 E-value=11 Score=43.70 Aligned_cols=44 Identities=23% Similarity=0.637 Sum_probs=34.4
Q ss_pred CCCcccccccccCCCcceecCCCCccChhhHHHhhhc---CCCCCCCC
Q 000881 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS---HYICPICS 1161 (1239)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~---~~~CPiCr 1161 (1239)
-.|||=.|. -+...+...|.|||++-..=++..-++ .++||.|-
T Consensus 337 FiCPVlKe~-~t~ENpP~ml~CgHVIskeal~~LS~nG~~~FKCPYCP 383 (396)
T COG5109 337 FICPVLKEL-CTDENPPVMLECGHVISKEALSVLSQNGVLSFKCPYCP 383 (396)
T ss_pred eeccccHhh-hcccCCCeeeeccceeeHHHHHHHhhcCcEEeeCCCCC
Confidence 357776655 555667888999999999999887654 47899996
No 158
>PRK05580 primosome assembly protein PriA; Validated
Probab=48.18 E-value=12 Score=48.36 Aligned_cols=49 Identities=22% Similarity=0.598 Sum_probs=41.6
Q ss_pred cccccccCCcccCcccccccCCCCCccccccccccccccccccCCCCCCCccCCC
Q 000881 998 KLRAACCGKLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVGPVCTTLSCSG 1052 (1239)
Q Consensus 998 ~l~~~cC~~~y~Cr~CHde~~~H~~~r~~~~~v~C~~C~~~q~~~~~C~~~~C~~ 1052 (1239)
-+.|.-||....|..|.-...-|.. ...+.|-.|+..+++...|-+ |.+
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 3889999999999999888777743 457999999999999999987 743
No 159
>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=47.88 E-value=9.8 Score=32.56 Aligned_cols=33 Identities=21% Similarity=0.452 Sum_probs=21.6
Q ss_pred ceeccCCCCCCCCCcee---eeccCCCCCCccc-ccc
Q 000881 1193 EILCNDCDKKGSAPFHW---LYHKCGFCGSYNT-RVI 1225 (1239)
Q Consensus 1193 ~I~CnDC~~~s~~~~h~---lg~kC~~C~syNT-~~~ 1225 (1239)
.+.|++||....+-..+ -...|+.||+-+. +++
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~r~~ 41 (52)
T TIGR02605 5 EYRCTACGHRFEVLQKMSDDPLATCPECGGEKLRRLL 41 (52)
T ss_pred EEEeCCCCCEeEEEEecCCCCCCCCCCCCCCceeEEe
Confidence 46799999876543211 1236999999876 444
No 160
>PLN03086 PRLI-interacting factor K; Provisional
Probab=46.73 E-value=13 Score=46.96 Aligned_cols=52 Identities=25% Similarity=0.626 Sum_probs=26.9
Q ss_pred CccccCCCCCccccCC-CCCc------cccccCCccccccccc-cccc---cccCCCCCCCcccccc
Q 000881 1070 RVVYHCPFCNLCRVGR-GLGV------DFFHCMTCNCCLAKKL-VDHK---CREKGLETNCPICCDF 1125 (1239)
Q Consensus 1070 k~~yHC~~CgiCRvG~-gl~~------~~fHC~~C~~C~~~~l-~~H~---C~e~~~~~~CpICle~ 1125 (1239)
+..+||+.||- .++. .|.+ .-+.|. ||..+.... ..|. |.++ ...|+.|...
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 124566 765443332 5563 5443 4678888755
No 161
>PRK04023 DNA polymerase II large subunit; Validated
Probab=46.62 E-value=17 Score=48.23 Aligned_cols=35 Identities=29% Similarity=0.705 Sum_probs=18.7
Q ss_pred CCCCCCccCCCCccceEecccccCcCCCCccccCCCCCcc
Q 000881 1042 GPVCTTLSCSGLSMAKYYCGICKFFDDERVVYHCPFCNLC 1081 (1239)
Q Consensus 1042 ~~~C~~~~C~~~~~~~y~C~~C~l~dd~k~~yHC~~CgiC 1081 (1239)
...|.+ | |......+|+.|.=- .+.+|.|+.||..
T Consensus 626 ~RfCps--C-G~~t~~frCP~CG~~--Te~i~fCP~CG~~ 660 (1121)
T PRK04023 626 RRKCPS--C-GKETFYRRCPFCGTH--TEPVYRCPRCGIE 660 (1121)
T ss_pred CccCCC--C-CCcCCcccCCCCCCC--CCcceeCccccCc
Confidence 345654 4 555555566666533 2456666666433
No 162
>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=46.58 E-value=14 Score=43.21 Aligned_cols=37 Identities=8% Similarity=0.027 Sum_probs=17.5
Q ss_pred CCCCCCCCChhHHHhcCHHHHHHHHhhhccCCCCChHHHHHHHHHHH
Q 000881 902 HSDHTFKPGWNDIFRMNQNELEAEIRKVSRDSTLDPRRKAYLIQNLM 948 (1239)
Q Consensus 902 ~~~~~~~~~~~~~~~~~q~~L~~~Ir~i~~~~~l~~~~ka~liq~Lm 948 (1239)
...-.+-|.|..+|. +-|.++. +. .+..-+-.|++|+
T Consensus 91 ~~~~~~d~~w~~~l~-------~LL~~l~--~~-~~~~~~~~l~~l~ 127 (305)
T TIGR01562 91 YDLLVREGAWLPWLD-------ALLAGYP--AP-ANAAAGAALEQLR 127 (305)
T ss_pred hhhcccCHHHHHHHH-------HHHHHhc--cc-ccHHHHHHHHHHH
Confidence 333445566766654 3333331 11 3344455666665
No 163
>PRK14873 primosome assembly protein PriA; Provisional
Probab=46.22 E-value=13 Score=47.91 Aligned_cols=47 Identities=26% Similarity=0.461 Sum_probs=38.4
Q ss_pred ccccccCCcccCcccccccCCCCCccccccccccccccccccCCCCCCCccCCC
Q 000881 999 LRAACCGKLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVGPVCTTLSCSG 1052 (1239)
Q Consensus 999 l~~~cC~~~y~Cr~CHde~~~H~~~r~~~~~v~C~~C~~~q~~~~~C~~~~C~~ 1052 (1239)
+.|..|+....|..|.--..=|. ....+.|-.|+..+ +...|-+ |.+
T Consensus 384 l~C~~Cg~~~~C~~C~~~L~~h~----~~~~l~Ch~CG~~~-~p~~Cp~--Cgs 430 (665)
T PRK14873 384 LACARCRTPARCRHCTGPLGLPS----AGGTPRCRWCGRAA-PDWRCPR--CGS 430 (665)
T ss_pred eEhhhCcCeeECCCCCCceeEec----CCCeeECCCCcCCC-cCccCCC--CcC
Confidence 79999999999999988877663 24579999999977 5789977 643
No 164
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=46.13 E-value=16 Score=32.70 Aligned_cols=29 Identities=28% Similarity=0.651 Sum_probs=22.4
Q ss_pred CceeccCCCCCCCCCceeeeccCCCCCCcccccc
Q 000881 1192 QEILCNDCDKKGSAPFHWLYHKCGFCGSYNTRVI 1225 (1239)
Q Consensus 1192 ~~I~CnDC~~~s~~~~h~lg~kC~~C~syNT~~~ 1225 (1239)
..+.|..||.. ...| +-|+.||.||.+++
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 46999999999985
No 165
>PF14353 CpXC: CpXC protein
Probab=45.85 E-value=20 Score=36.29 Aligned_cols=56 Identities=20% Similarity=0.344 Sum_probs=29.6
Q ss_pred CCCCCCCcCccChhhHhhhhHHHHhhcCCChhhhccCCceeccCCCCCCCCCceeeec
Q 000881 1155 YICPICSKSLGDMAVYFGMLDALLASEQLPEEYRDRCQEILCNDCDKKGSAPFHWLYH 1212 (1239)
Q Consensus 1155 ~~CPiCrksv~dm~~~~~~lD~~i~~~pmP~ey~~~~~~I~CnDC~~~s~~~~h~lg~ 1212 (1239)
.+||.|++...- ..|..+|......-...-..+..-.+.|..||.+..+.|=++|+
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 489999987631 12333321000000000113344568899999988777666664
No 166
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=45.68 E-value=16 Score=32.96 Aligned_cols=45 Identities=29% Similarity=0.833 Sum_probs=25.2
Q ss_pred ccccccccccccCCC-----CCCCccCCCCccceEecccccCcCCCCccccCCCCCc
Q 000881 1029 EMMCMRCLKVQPVGP-----VCTTLSCSGLSMAKYYCGICKFFDDERVVYHCPFCNL 1080 (1239)
Q Consensus 1029 ~v~C~~C~~~q~~~~-----~C~~~~C~~~~~~~y~C~~C~l~dd~k~~yHC~~Cgi 1080 (1239)
...|..|+.+-.+.. .|-| | |. .-=|-|..|+-..+ .|.|++||+
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 456777776664432 3544 4 41 22355666665543 677777774
No 167
>PRK00808 hypothetical protein; Provisional
Probab=45.59 E-value=3.8e+02 Score=28.03 Aligned_cols=110 Identities=17% Similarity=0.252 Sum_probs=71.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcccCCcccHHHHHHHHHHHHHHHHhhhhcccccc----hhhhhhhhhhHHhHHHHHHH
Q 000881 297 IMLWHNAIKRELNDIAEAARKIQLSGDFSDLSAFNKRLQFIAEVCIFHSIAEDKVI----FPAVDVELSFAQEHAEEEIQ 372 (1239)
Q Consensus 297 L~~~HkALRrEL~~L~~~a~~~~~~gd~~~L~~L~~r~~fl~~vl~~Hs~aEDevl----FPaL~~r~~me~EH~~ie~l 372 (1239)
+=.-|+.|=.-++.|...+. .++ ...+..-+.+|.+....|=..|+.++ ||.++.+. .+| +..
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 000881 373 FDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPLARRH 428 (1239)
Q Consensus 373 ~e~l~~ll~~~~~a~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qvfPLl~~~ 428 (1239)
++.+..+...... +. ... ...+.-|..-|..|+..+-....+.+.+.
T Consensus 84 l~~l~~l~~~~~~-g~-----~~~---~~l~~~L~~WL~~HI~~~D~~~~~~l~~~ 130 (150)
T PRK00808 84 IKRVEEYRERFQA-GE-----DVA---DELHGMLSRWLFNHIRNDDAAYVDAVKAN 130 (150)
T ss_pred HHHHHHHHHHHHc-cc-----hHH---HHHHHHHHHHHHHHHHHHhHHHHHHHHHh
Confidence 5555555544432 21 122 23445678889999999999999998885
No 168
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=45.50 E-value=10 Score=48.60 Aligned_cols=50 Identities=20% Similarity=0.469 Sum_probs=35.1
Q ss_pred CCCCCCcccccccccCCCcceecCCC-----CccChhhHHHhhhcC--CCCCCCCcCcc
Q 000881 1114 GLETNCPICCDFLFTSSATVRALPCG-----HFMHSDCFQAYTCSH--YICPICSKSLG 1165 (1239)
Q Consensus 1114 ~~~~~CpICle~lf~s~~~v~~LpCG-----H~fH~~Ci~~wl~~~--~~CPiCrksv~ 1165 (1239)
.....|-||.-+ ...++ .-.-||. -++|.+|+-+|+..+ .+|-||...+.
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 445789999755 22222 2334663 789999999999654 67999998764
No 169
>KOG3850 consensus Predicted membrane protein [Function unknown]
Probab=45.02 E-value=5.8e+02 Score=31.14 Aligned_cols=129 Identities=19% Similarity=0.244 Sum_probs=75.4
Q ss_pred HHHHHHHHHHHHHHHHhhcccCCcccH-HHHHHHHHHHHHHHHhhhhcccccchhhhhhhh--hhHHhHHHHHHHHHHHH
Q 000881 301 HNAIKRELNDIAEAARKIQLSGDFSDL-SAFNKRLQFIAEVCIFHSIAEDKVIFPAVDVEL--SFAQEHAEEEIQFDKLR 377 (1239)
Q Consensus 301 HkALRrEL~~L~~~a~~~~~~gd~~~L-~~L~~r~~fl~~vl~~Hs~aEDevlFPaL~~r~--~me~EH~~ie~l~e~l~ 377 (1239)
=+||-.||++|.+.-..++ .+..+| .++..-+.|+.+.|. |+.+-.-.|++.+ ..+....+|..+=-++.
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 4677788888888877774 334456 667777788888776 7766666666555 33444444333222222
Q ss_pred HHHHHHhhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH---HHHHhhCCHHHHHHHHHhHhhcC
Q 000881 378 CLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVL---PLARRHFSPKRQRELLYQSLCVM 445 (1239)
Q Consensus 378 ~ll~~~~~a~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qvf---PLl~~~fS~eEq~eL~~~~l~sm 445 (1239)
..-..++= .-|+ =+..+.+.+++...|+.+=|.+.- -+--++++++-|..|+.+++-.+
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 0111 245566667777777777776544 22335677778888888877543
No 170
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=44.85 E-value=8.5 Score=44.13 Aligned_cols=50 Identities=22% Similarity=0.543 Sum_probs=37.5
Q ss_pred CCCCcccccccccCCCcceecCCC-----CccChhhHHHhhh--cCCCCCCCCcCcc
Q 000881 1116 ETNCPICCDFLFTSSATVRALPCG-----HFMHSDCFQAYTC--SHYICPICSKSLG 1165 (1239)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCG-----H~fH~~Ci~~wl~--~~~~CPiCrksv~ 1165 (1239)
...|-||.+..+.........||. ++.|..|+..|.. .+.+|.+|.....
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 468999998765543323456773 8889999999986 5688999998653
No 171
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=44.78 E-value=17 Score=42.71 Aligned_cols=15 Identities=7% Similarity=0.191 Sum_probs=8.3
Q ss_pred CCCCCCCCChhHHHh
Q 000881 902 HSDHTFKPGWNDIFR 916 (1239)
Q Consensus 902 ~~~~~~~~~~~~~~~ 916 (1239)
.+.-...|.|.++|+
T Consensus 94 ~~~~~r~~~w~~~L~ 108 (309)
T PRK03564 94 IHVFPRDKHWQKLLM 108 (309)
T ss_pred ccccccChHHHHHHH
Confidence 333445566766655
No 172
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=44.72 E-value=15 Score=43.07 Aligned_cols=46 Identities=17% Similarity=0.366 Sum_probs=34.7
Q ss_pred CCCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcCc
Q 000881 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSL 1164 (1239)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrksv 1164 (1239)
...||||+... .++...--=|=+|+-.|+..++.+..+|||=.+++
T Consensus 300 ~~~CpvClk~r---~Nptvl~vSGyVfCY~Ci~~Yv~~~~~CPVT~~p~ 345 (357)
T KOG0826|consen 300 REVCPVCLKKR---QNPTVLEVSGYVFCYPCIFSYVVNYGHCPVTGYPA 345 (357)
T ss_pred cccChhHHhcc---CCCceEEecceEEeHHHHHHHHHhcCCCCccCCcc
Confidence 46799998652 22222223499999999999999999999988775
No 173
>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=44.28 E-value=14 Score=43.36 Aligned_cols=27 Identities=26% Similarity=0.608 Sum_probs=20.3
Q ss_pred cceecCCCCccChhhHHHhhhcCCCCCCCCcC
Q 000881 1132 TVRALPCGHFMHSDCFQAYTCSHYICPICSKS 1163 (1239)
Q Consensus 1132 ~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrks 1163 (1239)
..+.|-|+ -|-.+|-.....||.|..+
T Consensus 207 G~RyL~Cs-----lC~teW~~~R~~C~~Cg~~ 233 (305)
T TIGR01562 207 GLRYLSCS-----LCATEWHYVRVKCSHCEES 233 (305)
T ss_pred CceEEEcC-----CCCCcccccCccCCCCCCC
Confidence 44556655 5777898788999999964
No 174
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=44.16 E-value=10 Score=37.46 Aligned_cols=32 Identities=22% Similarity=0.656 Sum_probs=24.8
Q ss_pred CccccCCCCC-----ccccCCCCCccccccCCccccc
Q 000881 1070 RVVYHCPFCN-----LCRVGRGLGVDFFHCMTCNCCL 1101 (1239)
Q Consensus 1070 k~~yHC~~Cg-----iCRvG~gl~~~~fHC~~C~~C~ 1101 (1239)
+..|-|+.|| +|-|-+++++-+-||..||.-.
T Consensus 20 ~k~FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~ 56 (104)
T COG4888 20 PKTFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSF 56 (104)
T ss_pred CceEecCccCCeeeeEEEEEecCceeEEEcccCcceE
Confidence 4678888888 7888877777788888888653
No 175
>PLN03086 PRLI-interacting factor K; Provisional
Probab=42.45 E-value=32 Score=43.51 Aligned_cols=77 Identities=19% Similarity=0.411 Sum_probs=41.1
Q ss_pred CC--CCCccccCCCCCccccccCCccccccccc-cccccccCCCCCCCcccccccccCCCcceecCCCCccChhhHHHhh
Q 000881 1075 CP--FCNLCRVGRGLGVDFFHCMTCNCCLAKKL-VDHKCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYT 1151 (1239)
Q Consensus 1075 C~--~CgiCRvG~gl~~~~fHC~~C~~C~~~~l-~~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl 1151 (1239)
|+ +||.-=.-.- .++-+||..|+.=++.+. ..|.=+- .....|| |... +... .|. -|. ..+|-
T Consensus 436 Cp~~~Cg~v~~r~e-l~~H~~C~~Cgk~f~~s~LekH~~~~-Hkpv~Cp-Cg~~-~~R~----~L~-~H~-~thCp---- 501 (567)
T PLN03086 436 CPHDGCGIVLRVEE-AKNHVHCEKCGQAFQQGEMEKHMKVF-HEPLQCP-CGVV-LEKE----QMV-QHQ-ASTCP---- 501 (567)
T ss_pred CCcccccceeeccc-cccCccCCCCCCccchHHHHHHHHhc-CCCccCC-CCCC-cchh----HHH-hhh-hccCC----
Confidence 55 4775333322 257889999987665432 5564221 2456788 8633 2221 111 121 12232
Q ss_pred hcCCCCCCCCcCcc
Q 000881 1152 CSHYICPICSKSLG 1165 (1239)
Q Consensus 1152 ~~~~~CPiCrksv~ 1165 (1239)
..-+.||.|.+.+.
T Consensus 502 ~Kpi~C~fC~~~v~ 515 (567)
T PLN03086 502 LRLITCRFCGDMVQ 515 (567)
T ss_pred CCceeCCCCCCccc
Confidence 23578999999884
No 176
>PRK00808 hypothetical protein; Provisional
Probab=42.26 E-value=1.1e+02 Score=31.86 Aligned_cols=109 Identities=11% Similarity=0.106 Sum_probs=64.8
Q ss_pred HHHHHHHHHHHhccccCC-ChhhHHHHHHHHHHHHHHHHHHhhhccccc----cccccccccccccccccchhhHHHHHH
Q 000881 656 IRKDLEYLDGESGKLNDC-NETFLRQFTGRFRLLWGLYRAHSNAEDDIV----FPALESKETLSNVSHSYTLDHKQEEKL 730 (1239)
Q Consensus 656 IRkDLe~l~~~~~kL~~~-d~~~l~~f~~rf~~L~~v~~~HS~AEDeiv----fPALe~k~~~~nvs~s~~~EH~~ee~l 730 (1239)
|-.+|+.|-..+.+|..+ .......+...|..|....+.|=..|+.+. ||.++... .+|+..
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 334444444444444321 001134677789999999999999998765 88775321 244333
Q ss_pred HHHHHHHHHhhhhhhhhcccCcCCcccccccccccchhhHhhHHHHHHHHHHHHHHHHHHHHHhhHhhhhhhhhHHhhh
Q 000881 731 FEDISSALSELTELHECLSTDLTGDLTRNSLESCDQNETVRKYNEKATELQGMCKSIRVTLDQHVFREELELWPLFDRH 809 (1239)
Q Consensus 731 fedi~~~L~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~kL~~~~ksl~~~L~~Hi~~EE~ElfPL~~k~ 809 (1239)
+.+|..+...+. . + + ..+. .+.+.|..-|..||..+-..+.+.++..
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 444433332210 0 0 0 1122 3346788889999999999999998885
No 177
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=41.96 E-value=14 Score=31.03 Aligned_cols=30 Identities=20% Similarity=0.366 Sum_probs=19.3
Q ss_pred ceeccCCCCCCCCCceeeeccCCCCCCccc
Q 000881 1193 EILCNDCDKKGSAPFHWLYHKCGFCGSYNT 1222 (1239)
Q Consensus 1193 ~I~CnDC~~~s~~~~h~lg~kC~~C~syNT 1222 (1239)
.+.|.+||......-..-..+|+.||+.-.
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCGYRIL 32 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCCCeEE
Confidence 467999997643222222568999997543
No 178
>PF12773 DZR: Double zinc ribbon
Probab=41.42 E-value=22 Score=30.08 Aligned_cols=22 Identities=27% Similarity=0.789 Sum_probs=11.6
Q ss_pred cccccccccC-CCCCCCccCCCCccc
Q 000881 1032 CMRCLKVQPV-GPVCTTLSCSGLSMA 1056 (1239)
Q Consensus 1032 C~~C~~~q~~-~~~C~~~~C~~~~~~ 1056 (1239)
|..|+++.+. +..|.+ | |..+.
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 5566665444 455665 4 55444
No 179
>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=41.32 E-value=19 Score=27.18 Aligned_cols=21 Identities=24% Similarity=0.580 Sum_probs=14.9
Q ss_pred CCCCCCCcCccChhhHhhhhHH
Q 000881 1155 YICPICSKSLGDMAVYFGMLDA 1176 (1239)
Q Consensus 1155 ~~CPiCrksv~dm~~~~~~lD~ 1176 (1239)
..||||.+.+ .+....+.||.
T Consensus 2 v~CPiC~~~v-~~~~in~HLD~ 22 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLDS 22 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHHH
Confidence 3699999998 55555666663
No 180
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=40.24 E-value=9.3 Score=48.09 Aligned_cols=29 Identities=31% Similarity=0.595 Sum_probs=23.1
Q ss_pred Cccccccc----ccccccccCCcccCcccccccC
Q 000881 989 GCEHYKRN----CKLRAACCGKLFTCRFCHDKVS 1018 (1239)
Q Consensus 989 gC~HY~r~----c~l~~~cC~~~y~Cr~CHde~~ 1018 (1239)
||.|+--. ..-.|.-+|+|| |..||....
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 999998754
No 181
>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=39.46 E-value=17 Score=32.14 Aligned_cols=29 Identities=28% Similarity=0.689 Sum_probs=22.2
Q ss_pred CceeccCCCCCCCCCceeeeccCCCCCCcccccc
Q 000881 1192 QEILCNDCDKKGSAPFHWLYHKCGFCGSYNTRVI 1225 (1239)
Q Consensus 1192 ~~I~CnDC~~~s~~~~h~lg~kC~~C~syNT~~~ 1225 (1239)
..+.|..||+- ...| +-|+.||.|+-+++
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 45789999973 3334 46999999999886
No 182
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=38.91 E-value=21 Score=38.23 Aligned_cols=50 Identities=28% Similarity=0.489 Sum_probs=36.7
Q ss_pred CCCCCCCCcCccChhhHhhhhHHHHhhcCCCh-hhhccCCceeccCCCCCCCCCceee
Q 000881 1154 HYICPICSKSLGDMAVYFGMLDALLASEQLPE-EYRDRCQEILCNDCDKKGSAPFHWL 1210 (1239)
Q Consensus 1154 ~~~CPiCrksv~dm~~~~~~lD~~i~~~pmP~-ey~~~~~~I~CnDC~~~s~~~~h~l 1210 (1239)
-.+||.|+.++...+. +.....+|+ .|.+......|..||+.....-||=
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 4689999999876543 334444554 4777777788999999888888873
No 183
>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=38.52 E-value=1.9e+02 Score=28.72 Aligned_cols=37 Identities=19% Similarity=0.280 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHhhHhhhhhh----hhHHhhhCCHHHHHHHHHH
Q 000881 783 MCKSIRVTLDQHVFREELEL----WPLFDRHFSVEEQDKIVGR 821 (1239)
Q Consensus 783 ~~ksl~~~L~~Hi~~EE~El----fPL~~k~fS~eeQ~~Lv~~ 821 (1239)
..+.|..-+..||..||.=+ +|-+..| .++-+.++.+
T Consensus 38 ~l~~L~~y~~~HF~~EE~~M~~~~yp~~~~H--~~~H~~f~~~ 78 (113)
T cd00522 38 NLKELVDYTVKHFKDEEALMEAAGYPDYEEH--KKIHEDFVEK 78 (113)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCCCHHHH--HHHHHHHHHH
Confidence 45888889999999999653 7877777 4444455443
No 184
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=37.37 E-value=24 Score=45.39 Aligned_cols=32 Identities=28% Similarity=0.772 Sum_probs=16.1
Q ss_pred cccccccccccCC-CCCCCccCCCCccceEeccccc
Q 000881 1030 MMCMRCLKVQPVG-PVCTTLSCSGLSMAKYYCGICK 1064 (1239)
Q Consensus 1030 v~C~~C~~~q~~~-~~C~~~~C~~~~~~~y~C~~C~ 1064 (1239)
++|..|+++-|.+ ..|.+ | |..+..-.|..|.
T Consensus 2 ~~Cp~Cg~~n~~~akFC~~--C-G~~l~~~~Cp~CG 34 (645)
T PRK14559 2 LICPQCQFENPNNNRFCQK--C-GTSLTHKPCPQCG 34 (645)
T ss_pred CcCCCCCCcCCCCCccccc--c-CCCCCCCcCCCCC
Confidence 3566666664443 44665 4 5555433344443
No 185
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=37.30 E-value=29 Score=40.50 Aligned_cols=74 Identities=28% Similarity=0.554 Sum_probs=48.8
Q ss_pred cCCC----CccccCCCCCccccCCCCCc-cccccCCcccccccc--c--cccccccCCCCCCCcccccccccCCCcceec
Q 000881 1066 FDDE----RVVYHCPFCNLCRVGRGLGV-DFFHCMTCNCCLAKK--L--VDHKCREKGLETNCPICCDFLFTSSATVRAL 1136 (1239)
Q Consensus 1066 ~dd~----k~~yHC~~CgiCRvG~gl~~-~~fHC~~C~~C~~~~--l--~~H~C~e~~~~~~CpICle~lf~s~~~v~~L 1136 (1239)
|||= +-+=||..|- --| |-- =||. |+.|.+-. . ..|-=..+.....|-.|-+- .++|.++
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 35555556777899999654 4578889
Q ss_pred CCC--CccChhhHHHh
Q 000881 1137 PCG--HFMHSDCFQAY 1150 (1239)
Q Consensus 1137 pCG--H~fH~~Ci~~w 1150 (1239)
+|. |+....||.-|
T Consensus 238 ~Cns~HvtC~dCFr~y 253 (446)
T KOG0006|consen 238 QCNSRHVTCLDCFRLY 253 (446)
T ss_pred ecCCceeehHHhhhhH
Confidence 999 99999999866
No 186
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=37.01 E-value=25 Score=41.57 Aligned_cols=26 Identities=19% Similarity=0.734 Sum_probs=19.8
Q ss_pred CCccceEe--cccccCcCCCCccccCCCCCc
Q 000881 1052 GLSMAKYY--CGICKFFDDERVVYHCPFCNL 1080 (1239)
Q Consensus 1052 ~~~~~~y~--C~~C~l~dd~k~~yHC~~Cgi 1080 (1239)
.+.|--|| |.||++++. .|.|++||+
T Consensus 60 ~~dfeL~f~Ge~i~~y~~q---SftCPyC~~ 87 (381)
T KOG1280|consen 60 RVDFELYFGGEPISHYDPQ---SFTCPYCGI 87 (381)
T ss_pred ccceeeEecCccccccccc---cccCCcccc
Confidence 34566666 788887765 899999995
No 187
>KOG4399 consensus C2HC-type Zn-finger protein [General function prediction only]
Probab=36.33 E-value=9.2 Score=43.29 Aligned_cols=63 Identities=22% Similarity=0.348 Sum_probs=43.2
Q ss_pred ccccccccccCCCCCCCccCCCCccceEecccccCcCCCCccccCCCCCccccCCCCCccccccCCcccccc
Q 000881 1031 MCMRCLKVQPVGPVCTTLSCSGLSMAKYYCGICKFFDDERVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLA 1102 (1239)
Q Consensus 1031 ~C~~C~~~q~~~~~C~~~~C~~~~~~~y~C~~C~l~dd~k~~yHC~~CgiCRvG~gl~~~~fHC~~C~~C~~ 1102 (1239)
+|..|.+..- -.|+- | +...+.-+|.||.=+|.++ -|||.|.-||--+. ...-||.+|..|..
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 188
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=35.19 E-value=21 Score=45.14 Aligned_cols=57 Identities=21% Similarity=0.279 Sum_probs=25.6
Q ss_pred ChhhHhhhhHHHHhhcCCChhhhccCCceeccCCCCCCCCCceeeeccCCCCCCccccccccc
Q 000881 1166 DMAVYFGMLDALLASEQLPEEYRDRCQEILCNDCDKKGSAPFHWLYHKCGFCGSYNTRVIKVE 1228 (1239)
Q Consensus 1166 dm~~~~~~lD~~i~~~pmP~ey~~~~~~I~CnDC~~~s~~~~h~lg~kC~~C~syNT~~~~~~ 1228 (1239)
+.+.....++.......+|-- .-....-.|++||..... +-+|+.|||-|+.+++..
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 556666666666664555522 112234579999987553 448999999998776543
No 189
>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=35.12 E-value=24 Score=36.43 Aligned_cols=18 Identities=28% Similarity=0.392 Sum_probs=15.6
Q ss_pred cCcCCCCccccCCCCCcc
Q 000881 1064 KFFDDERVVYHCPFCNLC 1081 (1239)
Q Consensus 1064 ~l~dd~k~~yHC~~CgiC 1081 (1239)
||||-.|.+-.||+||.=
T Consensus 18 kFYDLnk~p~vcP~cg~~ 35 (129)
T TIGR02300 18 KFYDLNRRPAVSPYTGEQ 35 (129)
T ss_pred cccccCCCCccCCCcCCc
Confidence 788988999999999954
No 190
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=34.99 E-value=23 Score=30.07 Aligned_cols=26 Identities=19% Similarity=0.524 Sum_probs=16.7
Q ss_pred ceeccCCCCCCCCCceeeeccCCCCCC
Q 000881 1193 EILCNDCDKKGSAPFHWLYHKCGFCGS 1219 (1239)
Q Consensus 1193 ~I~CnDC~~~s~~~~h~lg~kC~~C~s 1219 (1239)
.+.|.+||....... --..+|+.||+
T Consensus 2 ~Y~C~~Cg~~~~~~~-~~~irC~~CG~ 27 (44)
T smart00659 2 IYICGECGRENEIKS-KDVVRCRECGY 27 (44)
T ss_pred EEECCCCCCEeecCC-CCceECCCCCc
Confidence 457888887654431 23567888886
No 191
>PF14631 FancD2: Fanconi anaemia protein FancD2 nuclease; PDB: 3S4W_B.
Probab=34.69 E-value=8.1e+02 Score=35.04 Aligned_cols=100 Identities=20% Similarity=0.275 Sum_probs=60.5
Q ss_pred hHHHHHHHHHHHhhhcCchHHHHHHHHHHHH---------HHHHHHHhhHHHHHHHhhHHhh----cCCHHHHHH---HH
Q 000881 126 SVLFDQLFELLNSSMRNEESYRRELASCTGA---------LQTSISQHMSKEEEQVFPLLIE----KFSFEEQAS---LV 189 (1239)
Q Consensus 126 ~~l~~~L~~~l~~~~~~~~~~~~eLa~~l~~---------l~~~l~qHm~~EE~qv~PLl~~----~fS~~E~a~---L~ 189 (1239)
+.++++|++.++.. +..+-+++...+-+ +-..|.+=|..++.-+.|.|.. .++++.+.. .+
T Consensus 191 ~~l~~kl~~~l~~a---p~~lq~eiI~~LPeIl~ds~h~~v~~~L~~ll~~~~~L~~~iLd~Ls~L~Ls~~~l~~vr~~v 267 (1426)
T PF14631_consen 191 EELTDKLFEVLSIA---PVELQKEIISSLPEILDDSQHDEVVEELLELLQENPELTVPILDALSNLNLSPELLEEVREKV 267 (1426)
T ss_dssp HHHHHHHHHHHHHS----TTTHHHHHHTHHHHS-GGGHHHHHHHHHHHHHH-STTHHHHHHHHHHS---HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhC---CHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHhcCCchhhhHHHHHhcCCCCHHHHHHHHHHH
Confidence 35566666665543 22333444444422 2223444444445556677665 456665544 45
Q ss_pred HHHhcCCCHHHHHHHHhhhcCCCCHHHHHHHHHHHhhcC
Q 000881 190 WQFLCSIPVNMMAEFLPWLSSSISSDEHQDMRKCLCKII 228 (1239)
Q Consensus 190 ~~~~~siP~~~m~~~Lpwm~~~lsp~Er~~~l~~l~~~~ 228 (1239)
-.++.+++++.|..++..++.++++.+-..+...||+..
T Consensus 268 l~~L~s~~~e~LP~lirFLL~s~t~~da~evI~~LR~~L 306 (1426)
T PF14631_consen 268 LEKLSSVDLEDLPVLIRFLLQSITPSDAVEVISELRENL 306 (1426)
T ss_dssp HHSTTSS-TTHHHHHHHHHHHS-SSTTHHHHHHHHHHHH
T ss_pred HHHHhcCChhhhHHHHHHHHHhCCcccHHHHHHHHHHHc
Confidence 566778899999999999999999999999999999874
No 192
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=34.58 E-value=19 Score=31.38 Aligned_cols=28 Identities=25% Similarity=0.538 Sum_probs=20.3
Q ss_pred CceeccCCCCCCCCCceeeeccCCCCCC
Q 000881 1192 QEILCNDCDKKGSAPFHWLYHKCGFCGS 1219 (1239)
Q Consensus 1192 ~~I~CnDC~~~s~~~~h~lg~kC~~C~s 1219 (1239)
..+.|-+||+.-....---|.+|++||+
T Consensus 5 ~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~ 32 (49)
T COG1996 5 MEYKCARCGREVELDQETRGIRCPYCGS 32 (49)
T ss_pred EEEEhhhcCCeeehhhccCceeCCCCCc
Confidence 4577888988765444455778999987
No 193
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=34.21 E-value=31 Score=43.18 Aligned_cols=162 Identities=24% Similarity=0.499 Sum_probs=82.6
Q ss_pred ccccccccccccCCCCCCCccCCCCccceEec-ccccCcCCC------Ccccc--CCCCCccccCCCCCcc------ccc
Q 000881 1029 EMMCMRCLKVQPVGPVCTTLSCSGLSMAKYYC-GICKFFDDE------RVVYH--CPFCNLCRVGRGLGVD------FFH 1093 (1239)
Q Consensus 1029 ~v~C~~C~~~q~~~~~C~~~~C~~~~~~~y~C-~~C~l~dd~------k~~yH--C~~CgiCRvG~gl~~~------~fH 1093 (1239)
-..|-.|+.--..+..|+. | +. +||| ..|.-|-.. -+.|| |-.|-+|+..-.-|.. +--
T Consensus 42 cf~c~~cg~~la~~gff~k--~-~~---~~ygt~~c~~~~~gevvsa~gktyh~~cf~cs~ck~pf~~g~~vt~~gk~~~ 115 (670)
T KOG1044|consen 42 CFQCKKCGRNLAEGGFFTK--P-EN---RLYGTDDCRAFVEGEVVSTLGKTYHPKCFSCSTCKSPFKSGDKVTFSGKECL 115 (670)
T ss_pred eeeccccCCCcccccceec--c-cc---eeecccchhhhccceeEecccceeccccceecccCCCCCCCCeeeecchhhh
Confidence 4445555554444555655 2 32 6666 444444221 45676 6666667654322221 122
Q ss_pred cCCccccccccccccccccCCCCCCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcCccChhhHhhh
Q 000881 1094 CMTCNCCLAKKLVDHKCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGDMAVYFGM 1173 (1239)
Q Consensus 1094 C~~C~~C~~~~l~~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrksv~dm~~~~~~ 1173 (1239)
|.+|-.=++.. =.+...-.+|.-|.+.+..+ +....| + ++|--..++|--|.+.+.- .|
T Consensus 116 c~~c~~~~~~~-----p~~~~~ps~cagc~~~lk~g-q~llal--d--------~qwhv~cfkc~~c~~vL~g--ey--- 174 (670)
T KOG1044|consen 116 CQTCSQPMPVS-----PAESYGPSTCAGCGEELKNG-QALLAL--D--------KQWHVSCFKCKSCSAVLNG--EY--- 174 (670)
T ss_pred hhhhcCcccCC-----cccccCCccccchhhhhhcc-ceeeee--c--------cceeeeeeehhhhcccccc--ee---
Confidence 33333222222 01223457899999886654 333333 2 3444445578888877632 01
Q ss_pred hHHHHhhcCCC---hhhhccCCceeccCCCCC--------CCCCceeeeccCCCCCCccc
Q 000881 1174 LDALLASEQLP---EEYRDRCQEILCNDCDKK--------GSAPFHWLYHKCGFCGSYNT 1222 (1239)
Q Consensus 1174 lD~~i~~~pmP---~ey~~~~~~I~CnDC~~~--------s~~~~h~lg~kC~~C~syNT 1222 (1239)
|...-.| ..|.... -|.|..|.+- +.-.||--.-.|..||+-=|
T Consensus 175 ----~skdg~pyce~dy~~~f-gvkc~~c~~fisgkvLqag~kh~HPtCARCsRCgqmF~ 229 (670)
T KOG1044|consen 175 ----MSKDGVPYCEKDYQAKF-GVKCEECEKFISGKVLQAGDKHFHPTCARCSRCGQMFG 229 (670)
T ss_pred ----eccCCCcchhhhhhhhc-CeehHHhhhhhhhhhhhccCcccCcchhhhhhhccccc
Confidence 1122223 2355444 5789999643 23457776777777776543
No 194
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=34.19 E-value=18 Score=42.49 Aligned_cols=26 Identities=23% Similarity=0.568 Sum_probs=19.3
Q ss_pred cceecCCCCccChhhHHHhhhcCCCCCCCCc
Q 000881 1132 TVRALPCGHFMHSDCFQAYTCSHYICPICSK 1162 (1239)
Q Consensus 1132 ~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrk 1162 (1239)
..+.|-|+ -|-.+|-.....||.|..
T Consensus 209 G~RyL~Cs-----lC~teW~~~R~~C~~Cg~ 234 (309)
T PRK03564 209 GLRYLHCN-----LCESEWHVVRVKCSNCEQ 234 (309)
T ss_pred CceEEEcC-----CCCCcccccCccCCCCCC
Confidence 34555554 577789878899999996
No 195
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=34.19 E-value=26 Score=30.99 Aligned_cols=29 Identities=24% Similarity=0.589 Sum_probs=21.9
Q ss_pred CceeccCCCCCCCCCceeeeccCCCCCCcccccc
Q 000881 1192 QEILCNDCDKKGSAPFHWLYHKCGFCGSYNTRVI 1225 (1239)
Q Consensus 1192 ~~I~CnDC~~~s~~~~h~lg~kC~~C~syNT~~~ 1225 (1239)
..+.|..||.- ... .+-|+.||-|+.+++
T Consensus 25 ~l~~c~~cg~~--~~~---H~vc~~cG~y~~r~v 53 (56)
T PF01783_consen 25 NLVKCPNCGEP--KLP---HRVCPSCGYYKGRQV 53 (56)
T ss_dssp SEEESSSSSSE--EST---TSBCTTTBBSSSSSS
T ss_pred ceeeeccCCCE--ecc---cEeeCCCCeECCEEE
Confidence 45789999953 222 357999999999985
No 196
>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=33.47 E-value=36 Score=43.15 Aligned_cols=56 Identities=21% Similarity=0.279 Sum_probs=33.5
Q ss_pred ChhhHhhhhHHHHhhcCCChhhhccCCceeccCCCCCCCCCceeeeccCCCCCCcccccccc
Q 000881 1166 DMAVYFGMLDALLASEQLPEEYRDRCQEILCNDCDKKGSAPFHWLYHKCGFCGSYNTRVIKV 1227 (1239)
Q Consensus 1166 dm~~~~~~lD~~i~~~pmP~ey~~~~~~I~CnDC~~~s~~~~h~lg~kC~~C~syNT~~~~~ 1227 (1239)
+.+.....++......-++ -.-+.... .|++||.... -.+.+|+.|||-|+.+++.
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 4555555665554432222 11233334 8999997543 2356999999998766543
No 197
>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=33.08 E-value=13 Score=42.85 Aligned_cols=24 Identities=21% Similarity=0.404 Sum_probs=11.7
Q ss_pred cChhhHHHhhhcCCCCCCCCcCcc
Q 000881 1142 MHSDCFQAYTCSHYICPICSKSLG 1165 (1239)
Q Consensus 1142 fH~~Ci~~wl~~~~~CPiCrksv~ 1165 (1239)
++.-|-.+|.....+||.|...=.
T Consensus 199 ~Cs~C~t~W~~~R~~Cp~Cg~~~~ 222 (290)
T PF04216_consen 199 HCSLCGTEWRFVRIKCPYCGNTDH 222 (290)
T ss_dssp EETTT--EEE--TTS-TTT---SS
T ss_pred EcCCCCCeeeecCCCCcCCCCCCC
Confidence 334678889877889999997643
No 198
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=32.91 E-value=24 Score=38.95 Aligned_cols=27 Identities=37% Similarity=0.941 Sum_probs=20.6
Q ss_pred CcceecCCCCccChhhHHHhhhcCCCCCCCCc
Q 000881 1131 ATVRALPCGHFMHSDCFQAYTCSHYICPICSK 1162 (1239)
Q Consensus 1131 ~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrk 1162 (1239)
..++--.|+-.||..|+. ...||-|.+
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 199
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=32.88 E-value=12 Score=43.72 Aligned_cols=84 Identities=31% Similarity=0.691 Sum_probs=0.0
Q ss_pred cCCCCCccccccCCccccccccccccccccCCCCCCCcccccccccCCCcceecCCCCcc------------------Ch
Q 000881 1083 VGRGLGVDFFHCMTCNCCLAKKLVDHKCREKGLETNCPICCDFLFTSSATVRALPCGHFM------------------HS 1144 (1239)
Q Consensus 1083 vG~gl~~~~fHC~~C~~C~~~~l~~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~f------------------H~ 1144 (1239)
.|+| |+|..|++= .|.=. ..||||--.|-.+..-.+.. .|.| ..
T Consensus 273 ~~~G-----y~CP~Ckak--------vCsLP---~eCpiC~ltLVss~hLARSy--hhL~PL~~F~Eip~~~~~~~~~Cf 334 (378)
T KOG2807|consen 273 SGGG-----YFCPQCKAK--------VCSLP---IECPICSLTLVSSPHLARSY--HHLFPLKPFVEIPETEYNGSRFCF 334 (378)
T ss_pred ccCc-----eeCCcccCe--------eecCC---ccCCccceeEecchHHHHHH--HhhcCCcchhhccccccCCCccee
Q ss_pred hhHHHhhhcC-CCCCCCCcCccChhhHhhhhHHHHhhcCCChhhhccCCceeccCCCCCCCCCceeeeccCCCCCC
Q 000881 1145 DCFQAYTCSH-YICPICSKSLGDMAVYFGMLDALLASEQLPEEYRDRCQEILCNDCDKKGSAPFHWLYHKCGFCGS 1219 (1239)
Q Consensus 1145 ~Ci~~wl~~~-~~CPiCrksv~dm~~~~~~lD~~i~~~pmP~ey~~~~~~I~CnDC~~~s~~~~h~lg~kC~~C~s 1219 (1239)
.|..+-+... |+|+.|+ ..+|-||+ +..|=.-|-|+.|..
T Consensus 335 ~C~~~~~~~~~y~C~~Ck-------------------------------~~FCldCD----v~iHesLh~CpgCeh 375 (378)
T KOG2807|consen 335 ACQGELLSSGRYRCESCK-------------------------------NVFCLDCD----VFIHESLHNCPGCEH 375 (378)
T ss_pred eeccccCCCCcEEchhcc-------------------------------ceeeccch----HHHHhhhhcCCCcCC
No 200
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=31.89 E-value=15 Score=38.39 Aligned_cols=26 Identities=27% Similarity=0.837 Sum_probs=18.1
Q ss_pred cceEecccccCcCCCCccccCCCCC--ccccC
Q 000881 1055 MAKYYCGICKFFDDERVVYHCPFCN--LCRVG 1084 (1239)
Q Consensus 1055 ~~~y~C~~C~l~dd~k~~yHC~~Cg--iCRvG 1084 (1239)
-.+-||.+|.+| ++|-|-.|| +|-|+
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 445677888755 578888887 66665
No 201
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=31.64 E-value=37 Score=28.60 Aligned_cols=8 Identities=38% Similarity=1.344 Sum_probs=3.9
Q ss_pred cccCCCCC
Q 000881 1072 VYHCPFCN 1079 (1239)
Q Consensus 1072 ~yHC~~Cg 1079 (1239)
..+|+.||
T Consensus 21 ~~~Cp~CG 28 (46)
T PRK00398 21 GVRCPYCG 28 (46)
T ss_pred ceECCCCC
Confidence 44455554
No 202
>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=31.48 E-value=16 Score=38.80 Aligned_cols=22 Identities=23% Similarity=0.794 Sum_probs=11.1
Q ss_pred EecccccC---cCCC-CccccCCCCC
Q 000881 1058 YYCGICKF---FDDE-RVVYHCPFCN 1079 (1239)
Q Consensus 1058 y~C~~C~l---~dd~-k~~yHC~~Cg 1079 (1239)
|+|+.|+. |++. ..-|+||.||
T Consensus 110 Y~Cp~c~~r~tf~eA~~~~F~Cp~Cg 135 (158)
T TIGR00373 110 FICPNMCVRFTFNEAMELNFTCPRCG 135 (158)
T ss_pred EECCCCCcEeeHHHHHHcCCcCCCCC
Confidence 55555552 3333 4456666665
No 203
>PRK07219 DNA topoisomerase I; Validated
Probab=31.44 E-value=67 Score=42.67 Aligned_cols=63 Identities=25% Similarity=0.495 Sum_probs=34.3
Q ss_pred cccccCcCCC----CccccCCCCCcc---ccCCCCCccccccCC---ccccccccccccccccCCCCCCCcccccccc
Q 000881 1060 CGICKFFDDE----RVVYHCPFCNLC---RVGRGLGVDFFHCMT---CNCCLAKKLVDHKCREKGLETNCPICCDFLF 1127 (1239)
Q Consensus 1060 C~~C~l~dd~----k~~yHC~~CgiC---RvG~gl~~~~fHC~~---C~~C~~~~l~~H~C~e~~~~~~CpICle~lf 1127 (1239)
|+.|+..... .....|+.||-- |.|+. | .|+-|.+ |+.-..+.-..+. ......||-|...+.
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 7888876432 346889999821 22332 3 3888865 6643332111111 123467888866543
No 204
>PF00539 Tat: Transactivating regulatory protein (Tat); InterPro: IPR001831 Like other lentiviruses, Human immunodeficiency virus 1 (HIV-1) encodes a trans-activating regulatory protein (Tat), which is essential for efficient transcription of the viral genome [, ]. Tat acts by binding to an RNA stem-loop structure, the trans-activating response element (TAR), found at the 5' ends of nascent HIV-1 transcripts. In binding to TAR, Tat alters the properties of the transcription complex, recruits a positive transcription elongation complex (P-TEFb) and hence increases the production of full-length viral RNA []. Tat protein also associates with RNA polymerase II complexes during early transcription elongation after the promoter clearance and before the synthesis of full-length TAR RNA transcript. This interaction of Tat with RNA polymerase II elongation complexes is P-TEFb-independent. There are two Tat binding sites on each transcription elongation complex; one is located on TAR RNA and the other one on RNA polymerase II near the exit site for nascent mRNA transcripts which suggests that two Tat molecules are involved in performing various functions during a single round of HIV-1 mRNA synthesis []. The minimum Tat sequence that can mediate specific TAR binding in vitro has been mapped to a basic domain of 10 amino acids, comprising mostly Arg and Lys residues. Regulatory activity, however, also requires the 47 N-terminal residues, which interact with components of the transcription complex and function as a transcriptional activation domain [, , ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0042025 host cell nucleus; PDB: 2W2H_D 1ZBN_B 1TVS_A 1TVT_A 3O6L_C 3O6M_C 3MI9_C 3MIA_C 1JFW_A 1TBC_A ....
Probab=31.18 E-value=45 Score=31.00 Aligned_cols=18 Identities=44% Similarity=1.139 Sum_probs=13.5
Q ss_pred cccCCCCCccccCCCCCcccc
Q 000881 1072 VYHCPFCNLCRVGRGLGVDFF 1092 (1239)
Q Consensus 1072 ~yHC~~CgiCRvG~gl~~~~f 1092 (1239)
-|||. +|-+-+|||+.|.
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 205
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=30.99 E-value=19 Score=40.90 Aligned_cols=54 Identities=24% Similarity=0.570 Sum_probs=36.6
Q ss_pred ccCCCCCCCcccccccccCCCcceecCC---C--CccChhhHHHhhhc--------CCCCCCCCcCc
Q 000881 1111 REKGLETNCPICCDFLFTSSATVRALPC---G--HFMHSDCFQAYTCS--------HYICPICSKSL 1164 (1239)
Q Consensus 1111 ~e~~~~~~CpICle~lf~s~~~v~~LpC---G--H~fH~~Ci~~wl~~--------~~~CPiCrksv 1164 (1239)
.+...+.-|=||...=-+.....-+-|| | |-.|..|+..|+.. .-+||-|+...
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 3455678899997652222222234577 2 99999999999732 24699999865
No 206
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=30.97 E-value=21 Score=43.31 Aligned_cols=19 Identities=16% Similarity=0.469 Sum_probs=14.4
Q ss_pred hHHHhcCHHHHHHHHhhhc
Q 000881 912 NDIFRMNQNELEAEIRKVS 930 (1239)
Q Consensus 912 ~~~~~~~q~~L~~~Ir~i~ 930 (1239)
...+++|+.+||..|++.-
T Consensus 50 ~~llk~~~KqLR~li~~Lr 68 (436)
T KOG2593|consen 50 KELLKFNKKQLRKLIASLR 68 (436)
T ss_pred HHHhcccHHHHHHHHHHhh
Confidence 3456788888888888774
No 207
>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=30.93 E-value=7.7 Score=32.79 Aligned_cols=42 Identities=21% Similarity=0.701 Sum_probs=27.9
Q ss_pred CcccccccccCCCcceecCCCCccChhhHHHhhh------cCCCCCCCC
Q 000881 1119 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC------SHYICPICS 1161 (1239)
Q Consensus 1119 CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~------~~~~CPiCr 1161 (1239)
|+||... .....-+.=-.|+-.||..|+..-.. ..+.||.|+
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 33333233348999999999865421 257888875
No 208
>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=30.31 E-value=36 Score=27.26 Aligned_cols=23 Identities=26% Similarity=0.953 Sum_probs=16.5
Q ss_pred eEecccccCc-CCCCccccCCCCC
Q 000881 1057 KYYCGICKFF-DDERVVYHCPFCN 1079 (1239)
Q Consensus 1057 ~y~C~~C~l~-dd~k~~yHC~~Cg 1079 (1239)
.|-|.+|.+. +.++.+..||-||
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 209
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=30.18 E-value=18 Score=39.22 Aligned_cols=23 Identities=30% Similarity=1.037 Sum_probs=11.3
Q ss_pred eEecccccC---cCCC-CccccCCCCC
Q 000881 1057 KYYCGICKF---FDDE-RVVYHCPFCN 1079 (1239)
Q Consensus 1057 ~y~C~~C~l---~dd~-k~~yHC~~Cg 1079 (1239)
.|+|+.|+. |++. ...|+||.||
T Consensus 117 ~Y~Cp~C~~rytf~eA~~~~F~Cp~Cg 143 (178)
T PRK06266 117 FFFCPNCHIRFTFDEAMEYGFRCPQCG 143 (178)
T ss_pred EEECCCCCcEEeHHHHhhcCCcCCCCC
Confidence 355655543 3332 3445555555
No 210
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=29.57 E-value=33 Score=33.97 Aligned_cols=31 Identities=19% Similarity=0.504 Sum_probs=18.5
Q ss_pred cccccCCcc-ccccccccccccccCCCCCCCcccccc
Q 000881 1090 DFFHCMTCN-CCLAKKLVDHKCREKGLETNCPICCDF 1125 (1239)
Q Consensus 1090 ~~fHC~~C~-~C~~~~l~~H~C~e~~~~~~CpICle~ 1125 (1239)
.+|+|..|| ..+++.++. +..+..||+|..+
T Consensus 20 t~f~CP~Cge~~v~v~~~k-----~~~h~~C~~CG~y 51 (99)
T PRK14892 20 KIFECPRCGKVSISVKIKK-----NIAIITCGNCGLY 51 (99)
T ss_pred cEeECCCCCCeEeeeecCC-----CcceEECCCCCCc
Confidence 567777777 333333322 4556788888766
No 211
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=29.46 E-value=24 Score=42.63 Aligned_cols=37 Identities=24% Similarity=0.441 Sum_probs=26.3
Q ss_pred CCCCcccccccccCCCcceecCCCCccChhhHHHhhh
Q 000881 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC 1152 (1239)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~ 1152 (1239)
...|.||..+.......-.+..|||.|...|..+++.
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 4679999843233323333678999999999998865
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 PRK00366 ispG 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed
Probab=29.07 E-value=49 Score=39.59 Aligned_cols=53 Identities=17% Similarity=0.268 Sum_probs=43.1
Q ss_pred CCCCCCCcCccChhhHhhhhHHHHhhcCCChhhhccCCceec--cCCCCCCCCCceeee
Q 000881 1155 YICPICSKSLGDMAVYFGMLDALLASEQLPEEYRDRCQEILC--NDCDKKGSAPFHWLY 1211 (1239)
Q Consensus 1155 ~~CPiCrksv~dm~~~~~~lD~~i~~~pmP~ey~~~~~~I~C--nDC~~~s~~~~h~lg 1211 (1239)
..||-|++...|....-..+++.+...++| -+....=| |.|++.....+=+.|
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 569999999999988889999999988888 34556678 999988777665544
No 214
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=29.06 E-value=29 Score=44.08 Aligned_cols=47 Identities=23% Similarity=0.584 Sum_probs=31.5
Q ss_pred CCCcccccccccCCCccee---cCCCCccChhhHHHhhh-----cCCCCCCCCcCcc
Q 000881 1117 TNCPICCDFLFTSSATVRA---LPCGHFMHSDCFQAYTC-----SHYICPICSKSLG 1165 (1239)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~---LpCGH~fH~~Ci~~wl~-----~~~~CPiCrksv~ 1165 (1239)
..|+||--. .+...-.. -.||-.+|..|+.-|+. ...+||-|++...
T Consensus 19 ~mc~l~~s~--G~~~ag~m~ac~~c~~~yH~~cvt~~~~~~~l~~gWrC~~crvCe~ 73 (694)
T KOG4443|consen 19 LMCPLCGSS--GKGRAGRLLACSDCGQKYHPYCVTSWAQHAVLSGGWRCPSCRVCEA 73 (694)
T ss_pred hhhhhhccc--cccccCcchhhhhhcccCCcchhhHHHhHHHhcCCcccCCceeeee
Confidence 467777532 22222222 36899999999999964 3468999998763
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=28.84 E-value=32 Score=35.72 Aligned_cols=47 Identities=30% Similarity=0.723 Sum_probs=33.3
Q ss_pred CCCCcccccccccCCCcceec-C---CCCccChhhHHH-hh--hcCCCCCCCCcCccC
Q 000881 1116 ETNCPICCDFLFTSSATVRAL-P---CGHFMHSDCFQA-YT--CSHYICPICSKSLGD 1166 (1239)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~L-p---CGH~fH~~Ci~~-wl--~~~~~CPiCrksv~d 1166 (1239)
--.|-||.|- |.+ -+.| | ||=.+...|+.. |- .....||+|+.|.-.
T Consensus 80 lYeCnIC~et---S~e-e~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKs 133 (140)
T PF05290_consen 80 LYECNICKET---SAE-ERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKS 133 (140)
T ss_pred ceeccCcccc---cch-hhcCCcccccchHHHHHHHHHHHHHcccCCCCCcccccccc
Confidence 4579999875 322 2444 3 899999999877 64 235789999998753
No 216
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=28.71 E-value=37 Score=43.61 Aligned_cols=45 Identities=24% Similarity=0.597 Sum_probs=32.8
Q ss_pred CCCcccccccccCCCcceecCCCC-ccChhhHHHhh--hc----CCCCCCCCcCcc
Q 000881 1117 TNCPICCDFLFTSSATVRALPCGH-FMHSDCFQAYT--CS----HYICPICSKSLG 1165 (1239)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCGH-~fH~~Ci~~wl--~~----~~~CPiCrksv~ 1165 (1239)
.+|+||-.. .+-+..-.||| .....|..... .. ...||+|+..+.
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 479999754 33455668999 89999987753 23 466899999764
No 217
>PLN02189 cellulose synthase
Probab=28.49 E-value=44 Score=44.85 Aligned_cols=53 Identities=21% Similarity=0.394 Sum_probs=36.8
Q ss_pred cCCCCCCCcccccccccCCCcceec---CCCCccChhhHHHhh--hcCCCCCCCCcCcc
Q 000881 1112 EKGLETNCPICCDFLFTSSATVRAL---PCGHFMHSDCFQAYT--CSHYICPICSKSLG 1165 (1239)
Q Consensus 1112 e~~~~~~CpICle~lf~s~~~v~~L---pCGH~fH~~Ci~~wl--~~~~~CPiCrksv~ 1165 (1239)
++.....|.||.|++-...+.-... -||--.++.|+ ++- ..+..||-|+...-
T Consensus 30 ~~~~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cy-eyer~eg~q~CpqCkt~Y~ 87 (1040)
T PLN02189 30 RNLDGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCY-EYERREGTQNCPQCKTRYK 87 (1040)
T ss_pred ccccCccccccccccCcCCCCCEEEeeccCCCccccchh-hhhhhcCCccCcccCCchh
Confidence 3445568999999976443332333 47788999999 553 34788999998763
No 218
>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=27.82 E-value=44 Score=40.98 Aligned_cols=31 Identities=23% Similarity=0.356 Sum_probs=19.0
Q ss_pred HHHHHHHhhhccCCCCChHHHHHHHHHHHHHHH
Q 000881 920 NELEAEIRKVSRDSTLDPRRKAYLIQNLMTSRW 952 (1239)
Q Consensus 920 ~~L~~~Ir~i~~~~~l~~~~ka~liq~Lm~~~~ 952 (1239)
..|+..||.|--. .+.+..-...|+++-.|-
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 3577778877633 444455566677766554
No 219
>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=27.57 E-value=36 Score=35.17 Aligned_cols=32 Identities=16% Similarity=0.104 Sum_probs=23.1
Q ss_pred ccccccccCCcccCcccccccCCCCCccccccccccccccccccCC
Q 000881 997 CKLRAACCGKLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVG 1042 (1239)
Q Consensus 997 c~l~~~cC~~~y~Cr~CHde~~~H~~~r~~~~~v~C~~C~~~q~~~ 1042 (1239)
-|-.||.|++-|- -|.| ..++|.+|++.+++.
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 3567899987441 1333 689999999999886
No 220
>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=27.53 E-value=25 Score=31.33 Aligned_cols=27 Identities=26% Similarity=0.792 Sum_probs=20.5
Q ss_pred ccCCceeccCCCCCCCCCceeeeccCCCCC
Q 000881 1189 DRCQEILCNDCDKKGSAPFHWLYHKCGFCG 1218 (1239)
Q Consensus 1189 ~~~~~I~CnDC~~~s~~~~h~lg~kC~~C~ 1218 (1239)
+.+..|+|.-||.+ .||+--..|..||
T Consensus 11 ~~ktH~~CrRCG~~---syH~qK~~CasCG 37 (55)
T PF01907_consen 11 HNKTHTLCRRCGRR---SYHIQKKTCASCG 37 (55)
T ss_dssp -S-SEEE-TTTSSE---EEETTTTEETTTB
T ss_pred CCccEeeecccCCe---eeecCCCcccccC
Confidence 45578999999985 6888777899999
No 221
>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=27.02 E-value=23 Score=33.01 Aligned_cols=10 Identities=30% Similarity=1.152 Sum_probs=5.9
Q ss_pred cceEeccccc
Q 000881 1055 MAKYYCGICK 1064 (1239)
Q Consensus 1055 ~~~y~C~~C~ 1064 (1239)
.+.|||..|+
T Consensus 48 AvdYFC~~c~ 57 (70)
T PF07191_consen 48 AVDYFCNHCH 57 (70)
T ss_dssp EEEEE-TTTT
T ss_pred ccceeeccCC
Confidence 3567777766
No 222
>COG0143 MetG Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=27.00 E-value=41 Score=42.66 Aligned_cols=44 Identities=25% Similarity=0.456 Sum_probs=33.7
Q ss_pred ccceEecccccCcCCC-CccccCCCCCccccCCCCCccccccCCccccccc
Q 000881 1054 SMAKYYCGICKFFDDE-RVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLAK 1103 (1239)
Q Consensus 1054 ~~~~y~C~~C~l~dd~-k~~yHC~~CgiCRvG~gl~~~~fHC~~C~~C~~~ 1103 (1239)
...-+||..|.-|=.| .-.=.|++||.+..++ -||+.||.++.-
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 3556788888877666 3445699999999884 489999999764
No 223
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=26.77 E-value=32 Score=38.25 Aligned_cols=39 Identities=38% Similarity=0.760 Sum_probs=26.6
Q ss_pred CcccccccccCCCcceecCCCCcc-ChhhHHHhhhcCCCCCCCCcCcc
Q 000881 1119 CPICCDFLFTSSATVRALPCGHFM-HSDCFQAYTCSHYICPICSKSLG 1165 (1239)
Q Consensus 1119 CpICle~lf~s~~~v~~LpCGH~f-H~~Ci~~wl~~~~~CPiCrksv~ 1165 (1239)
|-+|.+. ...|..+||-|.. ...|-.. -.+||||+....
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 8888665 3457889999764 4555432 456999997653
No 224
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=26.64 E-value=24 Score=41.01 Aligned_cols=31 Identities=32% Similarity=0.860 Sum_probs=23.5
Q ss_pred eecCCCCccChhhHHHhhhcCCCCCCCCcCccC
Q 000881 1134 RALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1166 (1239)
Q Consensus 1134 ~~LpCGH~fH~~Ci~~wl~~~~~CPiCrksv~d 1166 (1239)
+++||.|+|+.+|-..- ....||.|.-.|..
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 225
>PLN02436 cellulose synthase A
Probab=26.64 E-value=50 Score=44.48 Aligned_cols=53 Identities=19% Similarity=0.442 Sum_probs=37.0
Q ss_pred cCCCCCCCcccccccccCCCcceec---CCCCccChhhHHHhh--hcCCCCCCCCcCcc
Q 000881 1112 EKGLETNCPICCDFLFTSSATVRAL---PCGHFMHSDCFQAYT--CSHYICPICSKSLG 1165 (1239)
Q Consensus 1112 e~~~~~~CpICle~lf~s~~~v~~L---pCGH~fH~~Ci~~wl--~~~~~CPiCrksv~ 1165 (1239)
.......|.||.|++-...+.-... -||--.++.|+ ++. ..+..||-|+...-
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 3445679999999975544433334 46677999999 453 34688999997753
No 226
>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=26.51 E-value=22 Score=46.47 Aligned_cols=34 Identities=24% Similarity=0.536 Sum_probs=0.0
Q ss_pred ccccccccccccCCCCCCCccCCCCccceEecccccC
Q 000881 1029 EMMCMRCLKVQPVGPVCTTLSCSGLSMAKYYCGICKF 1065 (1239)
Q Consensus 1029 ~v~C~~C~~~q~~~~~C~~~~C~~~~~~~y~C~~C~l 1065 (1239)
.-.|..|+++. ....|.. |++...-.|+|+.|+.
T Consensus 655 ~r~Cp~Cg~~t-~~~~Cp~--CG~~T~~~~~Cp~C~~ 688 (900)
T PF03833_consen 655 RRRCPKCGKET-FYNRCPE--CGSHTEPVYVCPDCGI 688 (900)
T ss_dssp -------------------------------------
T ss_pred cccCcccCCcc-hhhcCcc--cCCccccceecccccc
Confidence 33455555542 2234533 4333345555555554
No 227
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=26.17 E-value=17 Score=40.10 Aligned_cols=96 Identities=22% Similarity=0.472 Sum_probs=54.5
Q ss_pred cccccCCccccccccc--ccc-ccccCCCCCCCcccccccccCCCcceecCCCCccChhhHHHhhh-----cCCCCCCCC
Q 000881 1090 DFFHCMTCNCCLAKKL--VDH-KCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC-----SHYICPICS 1161 (1239)
Q Consensus 1090 ~~fHC~~C~~C~~~~l--~~H-~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~-----~~~~CPiCr 1161 (1239)
|.|.|..|+-=.+.+- ..| +|-..--...|..|... |...-. +...++ +-|+|-+|.
T Consensus 116 d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkg-fndtfd--------------lkrh~rthtgvrpykc~~c~ 180 (267)
T KOG3576|consen 116 DSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKG-FNDTFD--------------LKRHTRTHTGVRPYKCSLCE 180 (267)
T ss_pred CeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCc-ccchhh--------------hhhhhccccCccccchhhhh
Confidence 6777777776666552 333 56655556677777665 322111 112222 248999999
Q ss_pred cCccC---hhhHhhhhHHHHhhcCCChhhhccCC-ceeccCCCCCCC
Q 000881 1162 KSLGD---MAVYFGMLDALLASEQLPEEYRDRCQ-EILCNDCDKKGS 1204 (1239)
Q Consensus 1162 ksv~d---m~~~~~~lD~~i~~~pmP~ey~~~~~-~I~CnDC~~~s~ 1204 (1239)
|.+.. +++..+++ -..+---.|+.++. .+.|-|||-++.
T Consensus 181 kaftqrcsleshl~kv----hgv~~~yaykerr~kl~vcedcg~t~~ 223 (267)
T KOG3576|consen 181 KAFTQRCSLESHLKKV----HGVQHQYAYKERRAKLYVCEDCGYTSE 223 (267)
T ss_pred HHHHhhccHHHHHHHH----cCchHHHHHHHhhhheeeecccCCCCC
Confidence 99854 33333332 22222234555554 478999998765
No 228
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=25.74 E-value=56 Score=37.79 Aligned_cols=48 Identities=27% Similarity=0.710 Sum_probs=38.1
Q ss_pred CCCccceEecccccCcCCCCccccCCCCCccccCCCCCccccccCCcccccccc
Q 000881 1051 SGLSMAKYYCGICKFFDDERVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLAKK 1104 (1239)
Q Consensus 1051 ~~~~~~~y~C~~C~l~dd~k~~yHC~~CgiCRvG~gl~~~~fHC~~C~~C~~~~ 1104 (1239)
.|....-+||..|+++-. +...||.-||.|-.+- --||.=-|.|+...
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 366777899999999955 4678999999998763 37999999998653
No 229
>KOG4399 consensus C2HC-type Zn-finger protein [General function prediction only]
Probab=25.73 E-value=20 Score=40.70 Aligned_cols=71 Identities=23% Similarity=0.591 Sum_probs=47.2
Q ss_pred CCccceEecccccCcCCCCccccCCCCCccccCCCCCccccccCCccccccccc-cccccccCCCCCCCcccccc
Q 000881 1052 GLSMAKYYCGICKFFDDERVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLAKKL-VDHKCREKGLETNCPICCDF 1125 (1239)
Q Consensus 1052 ~~~~~~y~C~~C~l~dd~k~~yHC~~CgiCRvG~gl~~~~fHC~~C~~C~~~~l-~~H~C~e~~~~~~CpICle~ 1125 (1239)
|..-+-+||..|-.|=. +..-||..|+-|..-.| +-|-||.+|-.|+-.++ .--.|..-+...-|-||-++
T Consensus 199 ~~EE~~~~~~~~~~Yv~-~~~~H~~~~~S~~~~~~--~~~~H~~~~~~~~~~~~i~C~~~~~~A~~~~C~iC~~~ 270 (325)
T KOG4399|consen 199 PTEEGYRFCSPCQRYVS-LENQHCEHCNSCTSKDG--RKWNHCFLCKKCVKPSWIHCSICNHCAVKHGCFICGEL 270 (325)
T ss_pred ccccceEEEeehHHHHH-HHhhhchhhcccccchh--HHHhHhHHhhhhcccceeeeecccchhhhcceeecccc
Confidence 45566677999987743 45679999999987553 57999999999987665 11112222234456666554
No 230
>PRK00420 hypothetical protein; Validated
Probab=25.66 E-value=41 Score=34.10 Aligned_cols=30 Identities=30% Similarity=0.665 Sum_probs=21.3
Q ss_pred CCCCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcCcc
Q 000881 1115 LETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1165 (1239)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrksv~ 1165 (1239)
....||+|.-+||...+ ....||.|+..+.
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 35789999988775221 3567999998764
No 231
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=25.57 E-value=36 Score=23.49 Aligned_cols=19 Identities=32% Similarity=0.656 Sum_probs=12.3
Q ss_pred CCCCCCCcCccChhhHhhh
Q 000881 1155 YICPICSKSLGDMAVYFGM 1173 (1239)
Q Consensus 1155 ~~CPiCrksv~dm~~~~~~ 1173 (1239)
+.||+|.+.+.+...++.-
T Consensus 1 ~~C~~C~~~~~~~~~l~~H 19 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQH 19 (24)
T ss_dssp EE-SSTS-EESSHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHH
Confidence 4699999998877665543
No 232
>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=25.48 E-value=43 Score=38.49 Aligned_cols=45 Identities=24% Similarity=0.469 Sum_probs=25.5
Q ss_pred CCCCCCCcccccccccCCCcceecC-C-CCccChhhHHHh-hhcCCCCC
Q 000881 1113 KGLETNCPICCDFLFTSSATVRALP-C-GHFMHSDCFQAY-TCSHYICP 1158 (1239)
Q Consensus 1113 ~~~~~~CpICle~lf~s~~~v~~Lp-C-GH~fH~~Ci~~w-l~~~~~CP 1158 (1239)
..+-.-|+||.|- ...+.+-..|. = .=-=|+.||.+| +--+..||
T Consensus 27 ~~tLsfChiCfEl-~iegvpks~llHtkSlRGHrdCFEK~HlIanQ~~p 74 (285)
T PF06937_consen 27 TETLSFCHICFEL-SIEGVPKSNLLHTKSLRGHRDCFEKYHLIANQDCP 74 (285)
T ss_pred ccceeecceeecc-ccccCccccccccccccchHHHHHHHHHHHcCCCC
Confidence 3444678888765 32222222111 0 012389999999 45688999
No 233
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=25.47 E-value=56 Score=42.03 Aligned_cols=54 Identities=20% Similarity=0.295 Sum_probs=31.1
Q ss_pred ChhhHhhhhHHHHhhcCCChhhhccCCceeccCCCCCCCCCceeeeccCCCCCCcccccc
Q 000881 1166 DMAVYFGMLDALLASEQLPEEYRDRCQEILCNDCDKKGSAPFHWLYHKCGFCGSYNTRVI 1225 (1239)
Q Consensus 1166 dm~~~~~~lD~~i~~~pmP~ey~~~~~~I~CnDC~~~s~~~~h~lg~kC~~C~syNT~~~ 1225 (1239)
+.+...+.++... .+.+|----+. ..-.|++||.... . .+..||.|||-|+.++
T Consensus 541 n~eal~~lv~~~~-~~~i~Yf~in~-~~~iC~~CG~~~~-g---~~~~CP~CGs~~~ev~ 594 (623)
T PRK08271 541 SEEGYRKLLNIAA-KTGCNYFAFNV-KITICNDCHHIDK-R---TGKRCPICGSENIDYY 594 (623)
T ss_pred CHHHHHHHHHHHH-HcCCceEEeCC-CCccCCCCCCcCC-C---CCcCCcCCCCcchhHH
Confidence 4455545555443 35554321122 3456999997522 2 3469999999887554
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=25.27 E-value=3e+02 Score=27.59 Aligned_cols=96 Identities=14% Similarity=0.197 Sum_probs=0.0
Q ss_pred hhHHhHHHHHHHHHHHHHHHHHHhhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhhCCHHHHH-----
Q 000881 361 SFAQEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPLARRHFSPKRQR----- 435 (1239)
Q Consensus 361 ~me~EH~~ie~l~e~l~~ll~~~~~a~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qvfPLl~~~fS~eEq~----- 435 (1239)
.|+.-+..||..-.+|..++..+..+.. ...++.|..-...||..||.-.-..-=..+..-...
T Consensus 10 ~~~~G~~~ID~qH~~L~~lin~l~~~~~-----------~~~l~~L~~y~~~HF~~EE~lM~~~~yp~~~~H~~~H~~f~ 78 (115)
T TIGR00058 10 SFKVFYDNLDEEHKTLFNGIFALAADNS-----------ATALKELIDVTVLHFLDEEAMMIAANYSDYDEHKKAHDDFL 78 (115)
T ss_pred hhhcCCHHHHHHHHHHHHHHHHHHhcch-----------HHHHHHHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHH
Q ss_pred HHHHhHhhcCCHHHHHHHHhhhcCCCCHHHHH
Q 000881 436 ELLYQSLCVMPLKLIECVLPWLVGSLSEEEAR 467 (1239)
Q Consensus 436 eL~~~~l~smPl~~L~~vLPWl~~~Ls~~E~~ 467 (1239)
+-+..+......+++..+-.|++.++--..++
T Consensus 79 ~~l~~~~~~~~~~~~~~l~~Wl~~HI~~~D~~ 110 (115)
T TIGR00058 79 AVLRGLKAPVPQDDLLYAKDWLVNHIKTTDFK 110 (115)
T ss_pred HHHHHHHHHhhHHHHHHHHHHHHHHhHHHHHH
No 235
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=24.81 E-value=32 Score=43.34 Aligned_cols=44 Identities=25% Similarity=0.754 Sum_probs=36.1
Q ss_pred CCCCCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcCcc
Q 000881 1114 GLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1165 (1239)
Q Consensus 1114 ~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrksv~ 1165 (1239)
..+.+|.||++.+ ..+.-+|- |..|+.+|+.....||.|++.+.
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 236
>PRK10722 hypothetical protein; Provisional
Probab=24.74 E-value=4.5e+02 Score=30.21 Aligned_cols=115 Identities=10% Similarity=0.139 Sum_probs=70.6
Q ss_pred CCHHHHHHHHHHHhcCCCHHHHHHHHhhhcCCCCHHHHHHHHHHHhhcCCc-hhHHHHHHHHHHcCCCCCCCccccchhh
Q 000881 180 FSFEEQASLVWQFLCSIPVNMMAEFLPWLSSSISSDEHQDMRKCLCKIIPK-EKLLRQVIFAWMEGVKVSDKSCEDNLEH 258 (1239)
Q Consensus 180 fS~~E~a~L~~~~~~siP~~~m~~~Lpwm~~~lsp~Er~~~l~~l~~~~P~-~~~l~~~~~~w~~~~~~~~~~~~~~~~~ 258 (1239)
++++|......++....|-+.+-.-+=.--...++.||+.|+..|-...+. +..|+-++--|..+-- -++
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 444555666666555555444333222233456699999999999988766 7888889999887421 001
Q ss_pred hcccCcccccccccccchhhhhhcccCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 000881 259 RCQRWFSCACESSRSSKRKYVELSYDLTDSSMSCPIDEIMLWHNAIKRELNDIAEAARKIQ 319 (1239)
Q Consensus 259 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pid~L~~~HkALRrEL~~L~~~a~~~~ 319 (1239)
+.. -.++.|...-.+. ..-+|.+..-++.++++|+.+.+-+..+.
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 100 0122333221111 23688999999999999999888877663
No 237
>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=24.49 E-value=28 Score=33.95 Aligned_cols=26 Identities=38% Similarity=1.063 Sum_probs=15.4
Q ss_pred CccccCCCCC---ccccCCCCCccccccCCccc
Q 000881 1070 RVVYHCPFCN---LCRVGRGLGVDFFHCMTCNC 1099 (1239)
Q Consensus 1070 k~~yHC~~Cg---iCRvG~gl~~~~fHC~~C~~ 1099 (1239)
+.-|.|++|| +=|++-| ..+|.+|+.
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 4557777777 3344433 577777764
No 238
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=24.17 E-value=54 Score=42.86 Aligned_cols=43 Identities=26% Similarity=0.605 Sum_probs=31.4
Q ss_pred CCCCCCCCcCccChhhHhhhhHHHHhhcCCChhhhccCCceeccCCCCCCCCCceeeeccCCCCCCccc
Q 000881 1154 HYICPICSKSLGDMAVYFGMLDALLASEQLPEEYRDRCQEILCNDCDKKGSAPFHWLYHKCGFCGSYNT 1222 (1239)
Q Consensus 1154 ~~~CPiCrksv~dm~~~~~~lD~~i~~~pmP~ey~~~~~~I~CnDC~~~s~~~~h~lg~kC~~C~syNT 1222 (1239)
-..||-|..++. |........|+=||..+..+ ..|+.|||-.-
T Consensus 444 v~~Cp~Cd~~lt---------------------~H~~~~~L~CH~Cg~~~~~p-----~~Cp~Cgs~~L 486 (730)
T COG1198 444 IAECPNCDSPLT---------------------LHKATGQLRCHYCGYQEPIP-----QSCPECGSEHL 486 (730)
T ss_pred cccCCCCCcceE---------------------EecCCCeeEeCCCCCCCCCC-----CCCCCCCCCee
Confidence 358999997643 23334567899999887665 47999999843
No 239
>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=24.04 E-value=31 Score=29.51 Aligned_cols=40 Identities=30% Similarity=0.756 Sum_probs=28.4
Q ss_pred CcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcCccChh
Q 000881 1119 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGDMA 1168 (1239)
Q Consensus 1119 CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrksv~dm~ 1168 (1239)
|+.|...+... .+.+..=|..||..|+ +|-.|++++.+..
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 2332355899999887 8999999987644
No 240
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=23.42 E-value=42 Score=38.09 Aligned_cols=77 Identities=19% Similarity=0.509 Sum_probs=50.2
Q ss_pred ccccccccccccCC--------cccCcccccccCCCCCc----cccccccccccccccccCCCCCCCccCCCCccceEec
Q 000881 993 YKRNCKLRAACCGK--------LFTCRFCHDKVSDHSMD----RKATTEMMCMRCLKVQPVGPVCTTLSCSGLSMAKYYC 1060 (1239)
Q Consensus 993 Y~r~c~l~~~cC~~--------~y~Cr~CHde~~~H~~~----r~~~~~v~C~~C~~~q~~~~~C~~~~C~~~~~~~y~C 1060 (1239)
|+..=...|.-|+. .|.|..||.-..+-++. -+-.-...|..|+++-.....= .-++-||
T Consensus 115 ~rnqgr~LC~~Cn~k~Ka~~~g~YvC~KCh~~iD~~~l~fr~d~yH~yHFkCt~C~keL~sdaRe--------vk~eLyC 186 (332)
T KOG2272|consen 115 YRNQGRALCRECNQKEKAKGRGRYVCQKCHAHIDEQPLTFRGDPYHPYHFKCTTCGKELTSDARE--------VKGELYC 186 (332)
T ss_pred HhhcchHHhhhhhhhhcccccceeehhhhhhhcccccccccCCCCCccceecccccccccchhhh--------hccceec
Confidence 33334455666654 79999999886654433 2333578899999887664432 2457788
Q ss_pred ccccCcCCCCccccCCCCCcccc
Q 000881 1061 GICKFFDDERVVYHCPFCNLCRV 1083 (1239)
Q Consensus 1061 ~~C~l~dd~k~~yHC~~CgiCRv 1083 (1239)
.-|. +.+-||-||-||.
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 241
>PHA00626 hypothetical protein
Probab=22.94 E-value=52 Score=29.49 Aligned_cols=11 Identities=27% Similarity=0.758 Sum_probs=5.3
Q ss_pred ceEecccccCc
Q 000881 1056 AKYYCGICKFF 1066 (1239)
Q Consensus 1056 ~~y~C~~C~l~ 1066 (1239)
.+|-|..|.++
T Consensus 22 nrYkCkdCGY~ 32 (59)
T PHA00626 22 DDYVCCDCGYN 32 (59)
T ss_pred cceEcCCCCCe
Confidence 34555555544
No 242
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=22.75 E-value=39 Score=28.83 Aligned_cols=22 Identities=36% Similarity=0.747 Sum_probs=15.1
Q ss_pred cCCCCCCcccccccccCCCCccc
Q 000881 1213 KCGFCGSYNTRVIKVESTNTYCS 1235 (1239)
Q Consensus 1213 kC~~C~syNT~~~~~~~~~~~~~ 1235 (1239)
||+.||-||-..- +.=.+.+|+
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 243
>KOG2129 consensus Uncharacterized conserved protein H4 [Function unknown]
Probab=22.51 E-value=3.7e+02 Score=32.96 Aligned_cols=15 Identities=27% Similarity=0.295 Sum_probs=9.9
Q ss_pred HHHHHHHHHHhcCCC
Q 000881 183 EEQASLVWQFLCSIP 197 (1239)
Q Consensus 183 ~E~a~L~~~~~~siP 197 (1239)
.||.+|+..++.-|.
T Consensus 197 QEqEalvN~LwKrmd 211 (552)
T KOG2129|consen 197 QEQEALVNSLWKRMD 211 (552)
T ss_pred HHHHHHHHHHHHHHH
Confidence 467777777765543
No 244
>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]
Probab=22.43 E-value=38 Score=37.66 Aligned_cols=26 Identities=35% Similarity=0.758 Sum_probs=20.6
Q ss_pred cCCCCccChhhHHHhhhcCCCCCCCC
Q 000881 1136 LPCGHFMHSDCFQAYTCSHYICPICS 1161 (1239)
Q Consensus 1136 LpCGH~fH~~Ci~~wl~~~~~CPiCr 1161 (1239)
-.||=-||..|+..++.....||-|+
T Consensus 198 g~c~i~~h~~c~qty~q~~~~cphc~ 223 (235)
T KOG4718|consen 198 GSCNIQYHRGCIQTYLQRRDICPHCG 223 (235)
T ss_pred CcccchhhhHHHHHHhcccCcCCchh
Confidence 45666788888888888888888885
No 245
>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=22.29 E-value=66 Score=40.16 Aligned_cols=10 Identities=40% Similarity=1.152 Sum_probs=5.2
Q ss_pred cccCcccccc
Q 000881 1007 LFTCRFCHDK 1016 (1239)
Q Consensus 1007 ~y~Cr~CHde 1016 (1239)
.|-|+.||.-
T Consensus 5 L~fC~~C~~i 14 (483)
T PF05502_consen 5 LYFCEHCHKI 14 (483)
T ss_pred ceeccccccc
Confidence 4556666543
No 246
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=22.28 E-value=40 Score=28.01 Aligned_cols=6 Identities=33% Similarity=1.082 Sum_probs=1.9
Q ss_pred ccCCcc
Q 000881 1093 HCMTCN 1098 (1239)
Q Consensus 1093 HC~~C~ 1098 (1239)
-|..||
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 247
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=22.19 E-value=43 Score=25.91 Aligned_cols=11 Identities=27% Similarity=1.081 Sum_probs=8.6
Q ss_pred ceEecccccCc
Q 000881 1056 AKYYCGICKFF 1066 (1239)
Q Consensus 1056 ~~y~C~~C~l~ 1066 (1239)
+.|||++|+.+
T Consensus 2 ~~~~C~~C~~~ 12 (35)
T smart00451 2 GGFYCKLCNVT 12 (35)
T ss_pred cCeEccccCCc
Confidence 57888888865
No 248
>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=22.17 E-value=34 Score=28.10 Aligned_cols=13 Identities=46% Similarity=1.185 Sum_probs=5.5
Q ss_pred cceEecccccCcC
Q 000881 1055 MAKYYCGICKFFD 1067 (1239)
Q Consensus 1055 ~~~y~C~~C~l~d 1067 (1239)
|.+|||+-|+.|=
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 5689999999774
No 249
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=22.11 E-value=56 Score=29.56 Aligned_cols=28 Identities=18% Similarity=0.107 Sum_probs=20.9
Q ss_pred ceeccCCCCCCCCCceeeeccCCCCCCccccccc
Q 000881 1193 EILCNDCDKKGSAPFHWLYHKCGFCGSYNTRVIK 1226 (1239)
Q Consensus 1193 ~I~CnDC~~~s~~~~h~lg~kC~~C~syNT~~~~ 1226 (1239)
.+.|..||.. ...| +.|. ||.||.+++-
T Consensus 27 ~~~c~~cg~~--~~pH---~vc~-cG~Y~gr~v~ 54 (60)
T PRK01110 27 LSVDKTTGEY--HLPH---HVSP-KGYYKGRKVL 54 (60)
T ss_pred eeEcCCCCce--eccc---eecC-CcccCCeEee
Confidence 5789999964 2333 3599 9999999863
No 250
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=22.08 E-value=47 Score=28.96 Aligned_cols=24 Identities=29% Similarity=0.664 Sum_probs=14.7
Q ss_pred cCCCCCccccCCCCCccccccCCccc
Q 000881 1074 HCPFCNLCRVGRGLGVDFFHCMTCNC 1099 (1239)
Q Consensus 1074 HC~~CgiCRvG~gl~~~~fHC~~C~~ 1099 (1239)
.||.||-. +-. ...+.++|.+||.
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 67887754 221 1246788888874
No 251
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=22.00 E-value=54 Score=29.30 Aligned_cols=11 Identities=36% Similarity=1.108 Sum_probs=7.9
Q ss_pred CccccCCCCCc
Q 000881 1070 RVVYHCPFCNL 1080 (1239)
Q Consensus 1070 k~~yHC~~Cgi 1080 (1239)
...|-|++|||
T Consensus 12 ~v~~~Cp~cGi 22 (55)
T PF13824_consen 12 HVNFECPDCGI 22 (55)
T ss_pred ccCCcCCCCCC
Confidence 45677888875
No 252
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=21.79 E-value=46 Score=27.69 Aligned_cols=31 Identities=26% Similarity=0.370 Sum_probs=19.4
Q ss_pred ceeccCCCCCCCCCce---eeeccCCCCCCcccc
Q 000881 1193 EILCNDCDKKGSAPFH---WLYHKCGFCGSYNTR 1223 (1239)
Q Consensus 1193 ~I~CnDC~~~s~~~~h---~lg~kC~~C~syNT~ 1223 (1239)
.+.|.+||....+-.. -....|+.||+-+.+
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~ 38 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSISEDDPVPCPECGSTEVR 38 (42)
T ss_pred EEEeCCCCCEEEEEEEcCCCCCCcCCCCCCCceE
Confidence 4679999966543222 134679999995443
No 253
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=21.63 E-value=35 Score=41.14 Aligned_cols=33 Identities=30% Similarity=0.766 Sum_probs=25.6
Q ss_pred CCCCCcccccccccCCCcceecCCCCccChhhHHHhh
Q 000881 1115 LETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYT 1151 (1239)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl 1151 (1239)
.+..||||..+ |.. .++|||||.....|-..-+
T Consensus 3 eelkc~vc~~f-~~e---piil~c~h~lc~~ca~~~~ 35 (699)
T KOG4367|consen 3 EELKCPVCGSF-YRE---PIILPCSHNLCQACARNIL 35 (699)
T ss_pred ccccCceehhh-ccC---ceEeecccHHHHHHHHhhc
Confidence 35679999876 432 4679999999999987654
No 254
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.22 E-value=63 Score=30.78 Aligned_cols=52 Identities=33% Similarity=0.493 Sum_probs=32.8
Q ss_pred CCCcccccccccCCCcceecCCCCccChhhHHHhhhcCCCCCCCCcCccChhhHhhhhHHHHhhc--CCChhhhcc
Q 000881 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGDMAVYFGMLDALLASE--QLPEEYRDR 1190 (1239)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrksv~dm~~~~~~lD~~i~~~--pmP~ey~~~ 1190 (1239)
..||||--.|-.+...-+ .--.||-||-.-.|- ..||.+|+.. |-|.+|+..
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 369999877654421110 124699999877664 5788888876 455566543
No 255
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=21.05 E-value=19 Score=42.82 Aligned_cols=34 Identities=21% Similarity=0.368 Sum_probs=15.1
Q ss_pred CCceeccCCCCCCCCCceeeeccCCCCCCccccc
Q 000881 1191 CQEILCNDCDKKGSAPFHWLYHKCGFCGSYNTRV 1224 (1239)
Q Consensus 1191 ~~~I~CnDC~~~s~~~~h~lg~kC~~C~syNT~~ 1224 (1239)
+-...|-||+.++..-.-+=...|.+||++|-..
T Consensus 283 KRFFkC~~C~~Rt~sl~r~P~~~C~~Cg~~~wer 316 (344)
T PF09332_consen 283 KRFFKCKDCGNRTISLERLPKKHCSNCGSSKWER 316 (344)
T ss_dssp -EEEE-T-TS-EEEESSSS--S--TTT-S---EE
T ss_pred eeeEECCCCCCeeeecccCCCCCCCcCCcCceee
Confidence 4578899999986543333346799999988544
No 256
>PRK12775 putative trifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta/ferritin domain-containing protein; Provisional
Probab=20.80 E-value=34 Score=46.28 Aligned_cols=52 Identities=27% Similarity=0.586 Sum_probs=35.6
Q ss_pred CCCCCCCCcCccChhhHhhhhHHHHhhcCCChhhhccCCceeccCCCCCCCCCceeeeccCCCCCCc
Q 000881 1154 HYICPICSKSLGDMAVYFGMLDALLASEQLPEEYRDRCQEILCNDCDKKGSAPFHWLYHKCGFCGSY 1220 (1239)
Q Consensus 1154 ~~~CPiCrksv~dm~~~~~~lD~~i~~~pmP~ey~~~~~~I~CnDC~~~s~~~~h~lg~kC~~C~sy 1220 (1239)
..+||-|.+++.-.+.|.-- .+..-...|.||++.|.. |-|-|-.|++||..
T Consensus 796 ~~~~~~~~~~~~~~~~~~~~--------------~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~ 847 (1006)
T PRK12775 796 VATCPKCHRPLEGDEEYVCC--------------ATSELQWRCDDCGKVSEG-FAFPYGMCPACGGK 847 (1006)
T ss_pred CccCcccCCCCCCCceeEEe--------------cCcceeeehhhhcccccc-ccCCcCcCcccccc
Confidence 47899999998655444211 112224569999998753 45566799999986
No 257
>PF15353 HECA: Headcase protein family homologue
Probab=20.75 E-value=43 Score=33.56 Aligned_cols=16 Identities=38% Similarity=1.105 Sum_probs=13.8
Q ss_pred CCCCccChhhHHHhhh
Q 000881 1137 PCGHFMHSDCFQAYTC 1152 (1239)
Q Consensus 1137 pCGH~fH~~Ci~~wl~ 1152 (1239)
|.|++||..||++|-.
T Consensus 39 p~~~~MH~~CF~~wE~ 54 (107)
T PF15353_consen 39 PFGQYMHRECFEKWED 54 (107)
T ss_pred CCCCchHHHHHHHHHH
Confidence 5589999999999953
No 258
>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=20.72 E-value=48 Score=30.25 Aligned_cols=15 Identities=33% Similarity=0.490 Sum_probs=12.9
Q ss_pred ccCCCCCCccccccc
Q 000881 1212 HKCGFCGSYNTRVIK 1226 (1239)
Q Consensus 1212 ~kC~~C~syNT~~~~ 1226 (1239)
++|+.|.|+||+.-.
T Consensus 6 ~~CPRC~S~nTKFcY 20 (63)
T PF02701_consen 6 LPCPRCDSTNTKFCY 20 (63)
T ss_pred CCCCCcCCCCCEEEe
Confidence 689999999998743
No 259
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=20.42 E-value=40 Score=32.18 Aligned_cols=31 Identities=29% Similarity=0.909 Sum_probs=10.5
Q ss_pred ccccCCCCC-----ccccCCCCCccccccCCccccc
Q 000881 1071 VVYHCPFCN-----LCRVGRGLGVDFFHCMTCNCCL 1101 (1239)
Q Consensus 1071 ~~yHC~~Cg-----iCRvG~gl~~~~fHC~~C~~C~ 1101 (1239)
..|.||+|| .|.+-+..|.-.-+|..||.-+
T Consensus 21 ~~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~ 56 (81)
T PF05129_consen 21 KVFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESF 56 (81)
T ss_dssp S----TTT--SS-EEEEEETTTTEEEEEESSS--EE
T ss_pred ceEcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeE
Confidence 455566666 3444333233344555554444
No 260
>KOG3842 consensus Adaptor protein Pellino [Signal transduction mechanisms]
Probab=20.39 E-value=82 Score=36.96 Aligned_cols=32 Identities=28% Similarity=0.688 Sum_probs=23.8
Q ss_pred ecCCCCccChhhHHHhhh---------cCCCCCCCCcCccC
Q 000881 1135 ALPCGHFMHSDCFQAYTC---------SHYICPICSKSLGD 1166 (1239)
Q Consensus 1135 ~LpCGH~fH~~Ci~~wl~---------~~~~CPiCrksv~d 1166 (1239)
.-||||.--..=..-|.. .+..||.|-..+.-
T Consensus 375 F~PCGHv~sekt~~YWs~iplPhGT~~f~a~CPFC~~~L~g 415 (429)
T KOG3842|consen 375 FNPCGHVCSEKTVKYWSQIPLPHGTHAFHAACPFCATQLAG 415 (429)
T ss_pred cCCcccccchhhhhHhhcCcCCCccccccccCcchhhhhcc
Confidence 459999988888888853 24679999876643
No 261
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=20.18 E-value=2.1e+02 Score=29.13 Aligned_cols=46 Identities=20% Similarity=0.253 Sum_probs=24.1
Q ss_pred CCCCcccccccccCCC----------cceecCCCCccChhhHHHhhhcCCCCCCCC
Q 000881 1116 ETNCPICCDFLFTSSA----------TVRALPCGHFMHSDCFQAYTCSHYICPICS 1161 (1239)
Q Consensus 1116 ~~~CpICle~lf~s~~----------~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCr 1161 (1239)
...|--|+..+-+... ...--.|++.|..+|-.-+-..=..||-|.
T Consensus 55 ~~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~CPGC~ 110 (112)
T TIGR00622 55 SRFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHESLHCCPGCI 110 (112)
T ss_pred CCcccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhhccCCcCCC
Confidence 3469999887322110 011235667776666444433334577665
No 262
>PF12126 DUF3583: Protein of unknown function (DUF3583); InterPro: IPR021978 This domain is found in eukaryotes, and is typically between 302 and 338 amino acids in length. It is found in association with PF00097 from PFAM and PF00643 from PFAM. Most members are promyelocytic leukemia proteins, and this family lies towards the C terminus.
Probab=20.12 E-value=8.1e+02 Score=29.00 Aligned_cols=131 Identities=17% Similarity=0.211 Sum_probs=82.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhccCCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHhhhhhhHHHHHHhhhhhH
Q 000881 46 IFLFFHKAIKSELDVLHRAAMAFATNLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIRVKNIARTYSLEHEGE 125 (1239)
Q Consensus 46 ~~~~~HkAlRreL~~l~~~a~~~~~~~gd~~~~~~l~~r~~~l~~~~~~H~~aEDevI~PaL~~Rv~~v~~~~~~EH~~~ 125 (1239)
.|--.|..+|.-...|-+.-..+. ..+..|++.+. .|..+.-..|.- .|-.+|+.+|+++
T Consensus 14 ~F~aahaqm~sav~qL~~~r~~te---------elIr~rVrq~V----~hVqaqEreLLe-------~v~~rYqR~y~em 73 (324)
T PF12126_consen 14 AFGAAHAQMRSAVSQLGRARADTE---------ELIRARVRQVV----AHVQAQERELLE-------AVEARYQRDYEEM 73 (324)
T ss_pred hHHHHHHHHHHHHHHHHHHHhhHH---------HHHHHHHHHHH----HHHHHHHHHHHH-------HHHHHHHHHHHHH
Confidence 455667777776666643322222 23344554433 344444433332 4556899999999
Q ss_pred hHHHHHHHHHHHhhhcCch-----HHH---HHHHHHHHHHHHHHHHhhHHHHHHHhhHHhhcCCHHHHHHHHHHHhcCCC
Q 000881 126 SVLFDQLFELLNSSMRNEE-----SYR---RELASCTGALQTSISQHMSKEEEQVFPLLIEKFSFEEQASLVWQFLCSIP 197 (1239)
Q Consensus 126 ~~l~~~L~~~l~~~~~~~~-----~~~---~eLa~~l~~l~~~l~qHm~~EE~qv~PLl~~~fS~~E~a~L~~~~~~siP 197 (1239)
..-+.+|.+-|.+++.... ..| +|+-.-=+-|+. ...+|..||=+.+-.+.++=.++|-..=...++..|.
T Consensus 74 a~~L~~LeavLqRir~G~~LVekM~~YASDQEVLdMh~Flre-AL~rLrqeePq~lqa~V~td~F~E~k~rLQ~L~scIt 152 (324)
T PF12126_consen 74 AGQLGRLEAVLQRIRTGGALVEKMKLYASDQEVLDMHGFLRE-ALERLRQEEPQNLQAAVRTDGFDEFKARLQDLVSCIT 152 (324)
T ss_pred HHHHhHHHHHHHHHHhHHHHHHHHHHhcchHHHHHHHHHHHH-HHHHhhhhcCcccccceecccHHHHHHHHHHHHHHHh
Confidence 9999999999999975432 222 333333333333 4567889999999888888888887766666666555
Done!