Query 001016
Match_columns 1190
No_of_seqs 552 out of 1652
Neff 5.3
Searched_HMMs 46136
Date Thu Mar 28 13:27:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001016.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001016hhsearch_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 6.8E-45 1.5E-49 397.3 2.9 199 976-1180 21-221 (276)
2 PF05495 zf-CHY: CHY zinc fing 99.8 3.1E-21 6.7E-26 173.9 1.9 70 990-1067 1-71 (71)
3 PF01814 Hemerythrin: Hemeryth 99.2 2.3E-10 5.1E-15 111.0 14.0 124 293-425 2-133 (133)
4 PF01814 Hemerythrin: Hemeryth 99.2 2.4E-10 5.3E-15 110.9 12.4 129 43-176 2-133 (133)
5 PF13639 zf-RING_2: Ring finge 99.2 1E-11 2.2E-16 101.8 1.7 44 1117-1161 1-44 (44)
6 KOG4628 Predicted E3 ubiquitin 98.9 5.1E-10 1.1E-14 127.5 3.3 49 1117-1166 230-279 (348)
7 COG4357 Zinc finger domain con 98.9 1.7E-10 3.6E-15 107.7 -0.6 66 987-1055 12-90 (105)
8 PF12678 zf-rbx1: RING-H2 zinc 98.8 2.9E-09 6.2E-14 97.0 3.8 47 1115-1161 18-73 (73)
9 COG5243 HRD1 HRD ubiquitin lig 98.8 2.1E-09 4.6E-14 120.6 2.8 57 1113-1169 284-350 (491)
10 PF12861 zf-Apc11: Anaphase-pr 98.8 4.3E-09 9.3E-14 97.8 3.8 47 1116-1164 32-81 (85)
11 PRK10992 iron-sulfur cluster r 98.8 8.5E-08 1.8E-12 104.7 13.8 131 294-427 76-218 (220)
12 TIGR03652 FeS_repair_RIC iron- 98.6 2E-07 4.4E-12 101.5 12.2 126 297-425 76-216 (216)
13 PRK10992 iron-sulfur cluster r 98.6 4.5E-07 9.7E-12 99.1 14.3 129 49-178 82-218 (220)
14 COG5540 RING-finger-containing 98.6 1.8E-08 3.8E-13 111.1 3.4 57 1109-1166 316-373 (374)
15 PHA02929 N1R/p28-like protein; 98.6 4.8E-08 1E-12 107.3 4.6 54 1113-1166 171-228 (238)
16 COG3945 Uncharacterized conser 98.5 1.9E-06 4E-11 89.9 14.7 140 292-440 8-158 (189)
17 cd00162 RING RING-finger (Real 98.5 8.5E-08 1.8E-12 76.8 3.7 44 1118-1164 1-45 (45)
18 TIGR03652 FeS_repair_RIC iron- 98.5 1.4E-06 2.9E-11 95.0 13.1 127 49-175 78-215 (216)
19 COG5194 APC11 Component of SCF 98.4 1.1E-07 2.5E-12 86.4 3.3 50 1116-1165 31-81 (88)
20 PF13923 zf-C3HC4_2: Zinc fing 98.3 2.7E-07 5.9E-12 74.0 2.8 39 1119-1160 1-39 (39)
21 PRK13276 cell wall biosynthesi 98.3 5.8E-06 1.3E-10 90.4 13.8 125 49-174 85-221 (224)
22 PRK13276 cell wall biosynthesi 98.3 6.4E-06 1.4E-10 90.1 13.1 125 297-424 83-222 (224)
23 PF13920 zf-C3HC4_3: Zinc fing 98.3 4E-07 8.7E-12 76.8 2.5 47 1116-1166 2-49 (50)
24 KOG1493 Anaphase-promoting com 98.2 3.2E-07 6.9E-12 82.9 -0.4 46 1117-1164 32-80 (84)
25 smart00184 RING Ring finger. E 98.1 2.3E-06 4.9E-11 66.1 3.1 38 1119-1160 1-39 (39)
26 PF14634 zf-RING_5: zinc-RING 98.1 2.6E-06 5.7E-11 70.2 3.3 44 1118-1162 1-44 (44)
27 PLN03208 E3 ubiquitin-protein 98.0 3.8E-06 8.3E-11 89.4 4.5 54 1109-1166 11-80 (193)
28 COG2846 Regulator of cell morp 98.0 4.1E-05 8.9E-10 81.2 12.0 128 295-425 79-217 (221)
29 PF00097 zf-C3HC4: Zinc finger 98.0 3.7E-06 7.9E-11 67.8 3.0 39 1119-1160 1-41 (41)
30 KOG0802 E3 ubiquitin ligase [P 98.0 1.6E-06 3.5E-11 106.2 1.4 53 1112-1164 287-340 (543)
31 KOG0320 Predicted E3 ubiquitin 98.0 3E-06 6.6E-11 88.2 2.7 48 1115-1165 130-178 (187)
32 PHA02926 zinc finger-like prot 98.0 3.6E-06 7.9E-11 90.4 3.3 54 1112-1165 166-230 (242)
33 PF15227 zf-C3HC4_4: zinc fing 97.9 7.4E-06 1.6E-10 67.2 2.5 38 1119-1160 1-42 (42)
34 smart00504 Ubox Modified RING 97.8 2.5E-05 5.4E-10 68.3 4.1 45 1117-1165 2-46 (63)
35 PF13445 zf-RING_UBOX: RING-ty 97.7 2E-05 4.4E-10 65.0 2.6 39 1119-1158 1-43 (43)
36 KOG2930 SCF ubiquitin ligase, 97.7 1E-05 2.2E-10 77.2 0.1 32 1133-1164 76-107 (114)
37 KOG0317 Predicted E3 ubiquitin 97.6 2.4E-05 5.2E-10 87.1 2.4 47 1116-1166 239-285 (293)
38 KOG0823 Predicted E3 ubiquitin 97.6 3.3E-05 7.1E-10 83.8 3.3 50 1113-1166 44-96 (230)
39 COG2846 Regulator of cell morp 97.6 0.00064 1.4E-08 72.4 12.2 132 45-176 79-217 (221)
40 KOG0828 Predicted E3 ubiquitin 97.6 2.3E-05 4.9E-10 91.6 1.4 51 1116-1166 571-635 (636)
41 COG3945 Uncharacterized conser 97.5 0.0012 2.6E-08 69.4 12.2 139 44-189 10-156 (189)
42 KOG0804 Cytoplasmic Zn-finger 97.4 5.4E-05 1.2E-09 88.1 1.8 48 1116-1165 175-222 (493)
43 TIGR00599 rad18 DNA repair pro 97.4 8.6E-05 1.9E-09 87.4 3.5 48 1115-1166 25-72 (397)
44 TIGR00570 cdk7 CDK-activating 97.4 0.00011 2.4E-09 83.4 4.1 51 1116-1166 3-55 (309)
45 smart00744 RINGv The RING-vari 97.3 0.00016 3.4E-09 61.4 2.8 42 1118-1161 1-49 (49)
46 KOG2164 Predicted E3 ubiquitin 97.2 0.00016 3.4E-09 85.9 2.7 49 1114-1166 184-237 (513)
47 KOG1734 Predicted RING-contain 97.1 0.00013 2.9E-09 80.1 0.3 50 1116-1165 224-281 (328)
48 PF11793 FANCL_C: FANCL C-term 97.1 0.00017 3.6E-09 65.6 0.6 50 1116-1165 2-66 (70)
49 KOG0827 Predicted E3 ubiquitin 97.0 0.00024 5.3E-09 81.4 1.6 48 1116-1164 4-55 (465)
50 KOG0825 PHD Zn-finger protein 97.0 0.00016 3.5E-09 88.2 -0.1 53 1113-1166 120-172 (1134)
51 KOG1428 Inhibitor of type V ad 97.0 0.0003 6.5E-09 89.2 2.1 111 1031-1165 3419-3544(3738)
52 COG5574 PEX10 RING-finger-cont 96.9 0.00045 9.7E-09 76.4 2.2 48 1115-1166 214-263 (271)
53 KOG0287 Postreplication repair 96.9 0.00041 8.9E-09 78.4 1.5 58 1117-1178 24-82 (442)
54 KOG2177 Predicted E3 ubiquitin 96.8 0.00049 1.1E-08 75.0 1.9 44 1115-1162 12-55 (386)
55 KOG4172 Predicted E3 ubiquitin 96.7 0.00039 8.4E-09 59.7 0.2 53 1116-1172 7-61 (62)
56 KOG4265 Predicted E3 ubiquitin 96.6 0.0013 2.9E-08 75.5 3.0 51 1112-1166 286-337 (349)
57 PF04564 U-box: U-box domain; 96.4 0.0019 4.2E-08 59.0 2.3 47 1116-1166 4-51 (73)
58 KOG1941 Acetylcholine receptor 96.2 0.0013 2.7E-08 75.7 -0.1 60 1108-1168 358-419 (518)
59 KOG1940 Zn-finger protein [Gen 96.1 0.00045 9.8E-09 77.6 -3.9 133 690-854 17-149 (276)
60 COG5432 RAD18 RING-finger-cont 96.1 0.0028 6.1E-08 70.5 2.1 46 1116-1165 25-70 (391)
61 KOG1645 RING-finger-containing 96.0 0.0038 8.3E-08 72.5 2.9 49 1116-1164 4-55 (463)
62 KOG1039 Predicted E3 ubiquitin 95.9 0.0049 1.1E-07 71.6 3.2 54 1112-1165 157-221 (344)
63 PF14835 zf-RING_6: zf-RING of 95.8 0.0031 6.6E-08 56.3 0.5 56 1117-1177 8-64 (65)
64 COG2461 Uncharacterized conser 95.6 0.076 1.7E-06 62.2 10.9 132 291-441 85-223 (409)
65 COG5219 Uncharacterized conser 95.5 0.0045 9.7E-08 77.4 0.7 53 1113-1165 1466-1523(1525)
66 KOG2879 Predicted E3 ubiquitin 94.8 0.021 4.6E-07 63.7 3.5 52 1114-1168 237-290 (298)
67 KOG1785 Tyrosine kinase negati 94.5 0.011 2.4E-07 68.3 0.3 54 1109-1166 362-417 (563)
68 KOG4445 Uncharacterized conser 94.4 0.012 2.6E-07 66.2 0.2 54 1112-1166 111-187 (368)
69 KOG0824 Predicted E3 ubiquitin 94.3 0.022 4.8E-07 64.4 2.0 49 1114-1166 5-54 (324)
70 KOG0978 E3 ubiquitin ligase in 94.1 0.015 3.2E-07 72.6 0.3 46 1117-1166 644-690 (698)
71 KOG0311 Predicted E3 ubiquitin 93.3 0.013 2.8E-07 67.3 -2.0 48 1116-1166 43-91 (381)
72 PF11789 zf-Nse: Zinc-finger o 93.3 0.054 1.2E-06 47.6 2.2 42 1115-1159 10-53 (57)
73 KOG2272 Focal adhesion protein 93.3 0.023 5.1E-07 62.4 -0.1 108 989-1124 63-200 (332)
74 KOG3039 Uncharacterized conser 92.7 0.086 1.9E-06 58.1 3.1 55 1111-1166 216-271 (303)
75 PF10367 Vps39_2: Vacuolar sor 92.4 0.061 1.3E-06 51.7 1.5 38 1109-1148 71-108 (109)
76 PF14570 zf-RING_4: RING/Ubox 92.4 0.096 2.1E-06 44.6 2.4 46 1119-1164 1-47 (48)
77 KOG0309 Conserved WD40 repeat- 91.9 0.095 2.1E-06 64.9 2.5 45 1113-1159 1025-1069(1081)
78 KOG3268 Predicted E3 ubiquitin 91.5 0.12 2.5E-06 54.6 2.4 30 1136-1165 188-228 (234)
79 PF12906 RINGv: RING-variant d 91.3 0.12 2.5E-06 43.7 1.8 40 1119-1160 1-47 (47)
80 KOG3970 Predicted E3 ubiquitin 91.3 0.15 3.2E-06 55.5 3.0 51 1114-1166 48-106 (299)
81 KOG4739 Uncharacterized protei 91.1 0.086 1.9E-06 58.3 1.0 37 1127-1165 12-48 (233)
82 KOG4275 Predicted E3 ubiquitin 90.6 0.053 1.2E-06 61.0 -1.2 49 1116-1172 300-349 (350)
83 KOG0297 TNF receptor-associate 90.1 0.15 3.2E-06 61.0 1.8 53 1114-1169 19-71 (391)
84 PF05883 Baculo_RING: Baculovi 90.1 0.14 2.9E-06 52.4 1.3 43 1116-1159 26-74 (134)
85 KOG1002 Nucleotide excision re 89.3 0.13 2.9E-06 61.5 0.7 51 1111-1165 531-586 (791)
86 KOG1571 Predicted E3 ubiquitin 88.7 0.25 5.4E-06 57.5 2.3 48 1112-1166 301-348 (355)
87 KOG4159 Predicted E3 ubiquitin 88.6 0.31 6.8E-06 58.1 3.1 49 1114-1166 82-130 (398)
88 PF14447 Prok-RING_4: Prokaryo 88.5 0.2 4.3E-06 43.7 1.0 45 1116-1166 7-51 (55)
89 COG2461 Uncharacterized conser 87.7 2.4 5.1E-05 50.3 9.3 137 41-191 85-222 (409)
90 KOG3800 Predicted E3 ubiquitin 87.4 0.41 8.8E-06 54.3 2.8 48 1118-1165 2-51 (300)
91 COG5152 Uncharacterized conser 87.3 0.23 4.9E-06 53.3 0.8 45 1117-1165 197-241 (259)
92 PF04641 Rtf2: Rtf2 RING-finge 87.2 0.48 1.1E-05 53.5 3.4 52 1113-1166 110-162 (260)
93 KOG2660 Locus-specific chromos 86.3 0.19 4.1E-06 57.8 -0.5 49 1115-1166 14-62 (331)
94 KOG4692 Predicted E3 ubiquitin 86.1 0.53 1.2E-05 54.3 2.9 53 1110-1166 416-468 (489)
95 KOG1814 Predicted E3 ubiquitin 86.0 0.42 9.1E-06 56.4 2.1 45 1116-1161 184-236 (445)
96 KOG2114 Vacuolar assembly/sort 85.7 0.45 9.8E-06 60.3 2.3 44 643-686 332-375 (933)
97 KOG0269 WD40 repeat-containing 85.5 0.64 1.4E-05 58.4 3.4 70 1070-1159 751-820 (839)
98 PF07800 DUF1644: Protein of u 85.4 0.7 1.5E-05 48.4 3.1 32 1116-1151 2-46 (162)
99 COG5175 MOT2 Transcriptional r 84.9 0.35 7.6E-06 55.5 0.8 57 1116-1172 14-71 (480)
100 PRK14890 putative Zn-ribbon RN 83.4 0.83 1.8E-05 40.5 2.2 47 1027-1080 5-56 (59)
101 COG5236 Uncharacterized conser 83.2 1.1 2.4E-05 51.7 3.8 67 1095-1165 39-108 (493)
102 PHA02862 5L protein; Provision 82.4 0.85 1.8E-05 47.1 2.2 45 1116-1165 2-53 (156)
103 PRK04023 DNA polymerase II lar 81.9 1.2 2.5E-05 58.0 3.7 44 1031-1080 628-671 (1121)
104 KOG4185 Predicted E3 ubiquitin 81.4 1 2.2E-05 51.4 2.8 47 1117-1164 4-54 (296)
105 KOG1813 Predicted E3 ubiquitin 81.1 0.6 1.3E-05 53.2 0.7 45 1117-1165 242-286 (313)
106 KOG0827 Predicted E3 ubiquitin 80.5 0.14 3.1E-06 59.6 -4.4 51 1116-1166 196-246 (465)
107 PF03854 zf-P11: P-11 zinc fin 79.1 0.82 1.8E-05 38.9 0.7 44 1117-1166 3-47 (50)
108 COG5592 Uncharacterized conser 78.5 6 0.00013 41.8 6.8 110 681-827 30-148 (171)
109 COG2888 Predicted Zn-ribbon RN 78.3 1.5 3.2E-05 39.0 2.1 45 1029-1080 9-58 (61)
110 PHA02825 LAP/PHD finger-like p 77.3 1.9 4E-05 45.5 2.8 46 1115-1165 7-59 (162)
111 KOG0801 Predicted E3 ubiquitin 76.4 1.2 2.6E-05 46.7 1.1 30 1114-1144 175-204 (205)
112 TIGR02481 hemeryth_dom hemeryt 76.0 13 0.00027 37.0 8.3 58 361-428 12-73 (126)
113 KOG2034 Vacuolar sorting prote 75.8 1.2 2.6E-05 57.1 1.2 43 1107-1151 808-850 (911)
114 PF08746 zf-RING-like: RING-li 74.0 1.9 4.1E-05 36.0 1.5 41 1119-1160 1-43 (43)
115 PF09538 FYDLN_acid: Protein o 73.2 1.8 3.8E-05 43.1 1.4 18 1064-1081 18-35 (108)
116 COG5592 Uncharacterized conser 73.0 19 0.00041 38.2 8.8 92 330-435 30-135 (171)
117 COG5220 TFB3 Cdk activating ki 72.8 1.2 2.6E-05 49.3 0.1 51 1116-1166 10-65 (314)
118 KOG3161 Predicted E3 ubiquitin 72.6 1.2 2.6E-05 55.0 0.1 55 1117-1174 12-70 (861)
119 TIGR02481 hemeryth_dom hemeryt 70.4 68 0.0015 31.8 12.0 110 296-424 12-125 (126)
120 KOG2817 Predicted E3 ubiquitin 69.6 3.4 7.3E-05 49.1 2.8 47 1117-1164 335-384 (394)
121 PF02084 Bindin: Bindin; Inte 68.9 14 0.0003 41.1 7.0 45 72-127 124-169 (238)
122 PF06524 NOA36: NOA36 protein; 68.7 2.5 5.3E-05 47.5 1.4 66 1005-1081 140-218 (314)
123 KOG1952 Transcription factor N 67.8 2.6 5.7E-05 53.8 1.6 54 1114-1168 189-250 (950)
124 PRK14714 DNA polymerase II lar 67.7 4.8 0.0001 53.9 3.9 52 1029-1084 667-721 (1337)
125 TIGR02300 FYDLN_acid conserved 67.2 3 6.4E-05 42.5 1.5 19 1064-1082 18-36 (129)
126 smart00132 LIM Zinc-binding do 67.1 3.8 8.3E-05 31.7 1.9 38 1118-1165 1-38 (39)
127 KOG1701 Focal adhesion adaptor 66.7 2.6 5.7E-05 50.2 1.2 133 1018-1164 266-437 (468)
128 PF01529 zf-DHHC: DHHC palmito 66.3 4.3 9.3E-05 42.3 2.6 47 1052-1104 43-89 (174)
129 TIGR00595 priA primosomal prot 65.9 4.8 0.0001 49.9 3.3 45 999-1047 214-258 (505)
130 PF05502 Dynactin_p62: Dynacti 65.6 4.2 9.2E-05 50.1 2.7 15 1050-1064 19-33 (483)
131 PF07191 zinc-ribbons_6: zinc- 65.2 3 6.5E-05 38.4 1.0 34 1028-1064 16-57 (70)
132 PHA03096 p28-like protein; Pro 64.6 3.5 7.5E-05 47.5 1.6 48 1117-1164 179-236 (284)
133 KOG2462 C2H2-type Zn-finger pr 64.2 5.7 0.00012 45.3 3.1 15 1070-1084 159-173 (279)
134 PRK00808 hypothetical protein; 63.7 24 0.00052 36.7 7.5 96 361-467 16-122 (150)
135 KOG4443 Putative transcription 63.3 2.7 5.9E-05 52.4 0.5 45 1116-1161 145-200 (694)
136 COG1198 PriA Primosomal protei 62.2 6.5 0.00014 50.7 3.5 54 999-1059 436-489 (730)
137 KOG1829 Uncharacterized conser 61.0 3 6.4E-05 52.1 0.3 29 989-1018 345-377 (580)
138 KOG1001 Helicase-like transcri 59.9 4 8.7E-05 52.2 1.1 45 1117-1166 455-501 (674)
139 PF12773 DZR: Double zinc ribb 59.8 7.7 0.00017 32.7 2.5 22 1032-1056 1-23 (50)
140 KOG0298 DEAD box-containing he 58.2 2.6 5.6E-05 56.0 -0.9 48 1116-1166 1153-1200(1394)
141 PRK04023 DNA polymerase II lar 57.9 8.8 0.00019 50.4 3.6 48 1042-1101 626-673 (1121)
142 PRK05580 primosome assembly pr 56.5 8.4 0.00018 49.5 3.2 49 999-1054 382-430 (679)
143 KOG2068 MOT2 transcription fac 56.2 7.3 0.00016 45.4 2.3 52 1114-1165 247-298 (327)
144 COG1198 PriA Primosomal protei 55.9 10 0.00022 49.0 3.7 46 1027-1081 433-484 (730)
145 KOG2066 Vacuolar assembly/sort 55.7 4.6 9.9E-05 51.5 0.6 88 405-496 393-485 (846)
146 COG5222 Uncharacterized conser 55.3 6.3 0.00014 45.0 1.6 43 1117-1162 275-318 (427)
147 cd00350 rubredoxin_like Rubred 55.0 8.6 0.00019 30.2 1.8 24 1057-1080 1-25 (33)
148 KOG3002 Zn finger protein [Gen 54.2 9.8 0.00021 44.2 2.9 46 1116-1167 48-93 (299)
149 PRK14873 primosome assembly pr 54.0 9.4 0.0002 49.0 3.0 44 999-1047 384-427 (665)
150 PF14357 DUF4404: Domain of un 53.6 91 0.002 29.8 8.8 82 54-139 2-83 (85)
151 PRK14559 putative protein seri 52.6 9.7 0.00021 48.6 2.8 46 1030-1079 2-48 (645)
152 PF07227 DUF1423: Protein of u 52.0 13 0.00028 45.1 3.5 31 920-952 21-51 (446)
153 PF14446 Prok-RING_1: Prokaryo 51.7 15 0.00033 32.4 3.0 35 1115-1149 4-38 (54)
154 PRK01917 cation-binding hemery 51.7 37 0.00081 34.9 6.4 70 398-467 38-120 (139)
155 COG4888 Uncharacterized Zn rib 51.3 6.8 0.00015 38.4 0.9 33 1070-1102 20-57 (104)
156 KOG0826 Predicted E3 ubiquitin 51.1 13 0.00028 43.4 3.2 47 1116-1165 300-346 (357)
157 PLN03086 PRLI-interacting fact 49.9 8.1 0.00018 48.4 1.5 90 1070-1170 451-559 (567)
158 PF09538 FYDLN_acid: Protein o 49.3 9.4 0.0002 38.1 1.5 32 997-1042 8-39 (108)
159 PRK00808 hypothetical protein; 48.8 3.2E+02 0.0069 28.4 12.8 110 297-428 17-130 (150)
160 KOG1280 Uncharacterized conser 48.1 11 0.00025 44.0 2.2 27 1052-1081 60-88 (381)
161 KOG3850 Predicted membrane pro 48.0 5.4E+02 0.012 31.3 15.4 137 293-445 254-396 (455)
162 KOG2932 E3 ubiquitin ligase in 47.2 11 0.00023 43.6 1.7 33 1134-1168 105-137 (389)
163 cd00522 Hemerythrin Hemerythri 46.8 76 0.0016 31.4 7.5 51 361-428 14-68 (113)
164 KOG1100 Predicted E3 ubiquitin 46.1 10 0.00023 41.8 1.5 39 1119-1165 161-200 (207)
165 PF05502 Dynactin_p62: Dynacti 42.7 12 0.00025 46.4 1.3 35 1006-1041 4-38 (483)
166 PF03833 PolC_DP2: DNA polymer 42.5 8.3 0.00018 49.9 0.0 45 1029-1079 655-699 (900)
167 COG5109 Uncharacterized conser 42.3 17 0.00036 42.2 2.4 43 1118-1161 338-383 (396)
168 PF13901 DUF4206: Domain of un 41.3 15 0.00032 40.3 1.7 31 1127-1162 167-197 (202)
169 PF02891 zf-MIZ: MIZ/SP-RING z 41.2 27 0.00059 30.0 2.9 41 1117-1163 3-50 (50)
170 PHA00626 hypothetical protein 40.7 23 0.00051 31.4 2.4 19 1059-1080 13-31 (59)
171 PRK14714 DNA polymerase II lar 40.6 24 0.00052 47.7 3.6 33 1043-1080 668-700 (1337)
172 KOG1609 Protein involved in mR 40.3 12 0.00027 42.6 1.0 51 1116-1166 78-135 (323)
173 PRK00398 rpoP DNA-directed RNA 39.1 24 0.00053 29.5 2.3 8 1072-1079 21-28 (46)
174 KOG1812 Predicted E3 ubiquitin 38.1 15 0.00032 44.3 1.1 37 1116-1152 146-182 (384)
175 TIGR00373 conserved hypothetic 36.4 12 0.00026 39.5 0.1 10 1070-1079 126-135 (158)
176 KOG2593 Transcription initiati 36.4 15 0.00032 44.3 0.8 19 912-930 50-68 (436)
177 KOG3362 Predicted BBOX Zn-fing 36.1 12 0.00026 38.9 0.0 26 1055-1084 116-143 (156)
178 COG5183 SSM4 Protein involved 35.9 20 0.00044 45.9 1.9 50 1114-1165 10-66 (1175)
179 PF14631 FancD2: Fanconi anaem 35.2 8.8E+02 0.019 34.6 17.0 99 127-228 192-306 (1426)
180 PRK06266 transcription initiat 35.2 14 0.00029 39.9 0.2 22 1058-1079 118-143 (178)
181 KOG1311 DHHC-type Zn-finger pr 35.1 29 0.00063 39.9 2.9 47 1052-1104 108-154 (299)
182 COG0143 MetG Methionyl-tRNA sy 34.5 25 0.00055 44.2 2.4 45 1054-1104 123-168 (558)
183 PF10272 Tmpp129: Putative tra 34.2 36 0.00079 40.6 3.5 17 1148-1164 334-350 (358)
184 cd00729 rubredoxin_SM Rubredox 33.6 30 0.00065 27.5 1.9 24 1057-1080 2-26 (34)
185 PF00412 LIM: LIM domain; Int 33.3 18 0.0004 30.8 0.7 40 1119-1168 1-40 (58)
186 smart00734 ZnF_Rad18 Rad18-lik 33.0 28 0.00061 26.1 1.5 20 1155-1175 2-21 (26)
187 PF08271 TF_Zn_Ribbon: TFIIB z 32.8 22 0.00048 29.4 1.0 13 1067-1079 14-26 (43)
188 PRK07219 DNA topoisomerase I; 32.7 50 0.0011 43.6 4.8 12 1072-1083 733-744 (822)
189 KOG3842 Adaptor protein Pellin 32.2 25 0.00054 40.8 1.7 63 1110-1172 333-421 (429)
190 PF06220 zf-U1: U1 zinc finger 31.9 18 0.00039 29.5 0.4 13 1055-1067 1-13 (38)
191 PF00628 PHD: PHD-finger; Int 31.1 10 0.00022 31.8 -1.2 43 1119-1162 2-50 (51)
192 PF05290 Baculo_IE-1: Baculovi 30.5 29 0.00062 35.9 1.6 48 1115-1166 79-133 (140)
193 PRK14559 putative protein seri 30.4 33 0.00072 44.0 2.6 34 1029-1066 15-50 (645)
194 KOG1044 Actin-binding LIM Zn-f 30.0 47 0.001 41.5 3.5 107 1029-1147 42-161 (670)
195 KOG4399 C2HC-type Zn-finger pr 29.9 13 0.00027 42.1 -1.1 47 1052-1102 256-302 (325)
196 COG1996 RPC10 DNA-directed RNA 29.8 28 0.00062 30.1 1.2 30 1054-1083 3-35 (49)
197 PRK03564 formate dehydrogenase 29.7 56 0.0012 38.3 4.0 22 1026-1047 209-231 (309)
198 smart00249 PHD PHD zinc finger 28.9 24 0.00053 28.1 0.7 42 1118-1160 1-47 (47)
199 KOG4718 Non-SMC (structural ma 28.6 28 0.00061 38.5 1.3 42 1117-1161 182-223 (235)
200 PF00301 Rubredoxin: Rubredoxi 28.4 38 0.00083 29.0 1.8 9 1057-1065 1-9 (47)
201 KOG2807 RNA polymerase II tran 27.9 50 0.0011 38.7 3.1 103 1053-1163 272-376 (378)
202 PRK14873 primosome assembly pr 27.8 45 0.00098 43.0 3.1 49 1023-1081 376-431 (665)
203 TIGR00622 ssl1 transcription f 26.8 1.2E+02 0.0027 30.6 5.2 45 1116-1161 55-110 (112)
204 PF06937 EURL: EURL protein; 26.4 39 0.00085 38.6 2.0 42 1114-1158 28-74 (285)
205 KOG2272 Focal adhesion protein 26.0 45 0.00098 37.7 2.3 79 992-1084 114-204 (332)
206 KOG4654 Uncharacterized conser 26.0 9.3E+02 0.02 26.7 12.4 55 43-103 41-99 (252)
207 PF01780 Ribosomal_L37ae: Ribo 25.9 25 0.00054 34.1 0.3 22 1073-1098 36-60 (90)
208 PRK14892 putative transcriptio 25.8 44 0.00095 33.0 1.9 33 1071-1105 20-56 (99)
209 PF14445 Prok-RING_2: Prokaryo 25.8 6.6 0.00014 33.9 -3.1 45 1053-1102 3-52 (57)
210 TIGR02300 FYDLN_acid conserved 25.5 38 0.00083 34.8 1.5 32 997-1042 8-39 (129)
211 KOG3842 Adaptor protein Pellin 25.4 33 0.00072 39.8 1.2 45 1113-1162 287-349 (429)
212 PF13824 zf-Mss51: Zinc-finger 25.1 45 0.00096 29.7 1.6 12 1070-1081 12-23 (55)
213 KOG4399 C2HC-type Zn-finger pr 25.0 21 0.00046 40.3 -0.4 71 1052-1125 199-270 (325)
214 PRK00420 hypothetical protein; 24.9 41 0.0009 33.9 1.6 29 1116-1165 23-51 (112)
215 KOG0825 PHD Zn-finger protein 24.6 45 0.00098 42.9 2.2 53 1116-1168 96-157 (1134)
216 PLN02189 cellulose synthase 24.6 53 0.0012 43.9 2.9 52 1113-1165 31-87 (1040)
217 PHA00626 hypothetical protein 24.5 43 0.00094 29.8 1.4 34 1030-1068 1-34 (59)
218 PF06377 Adipokin_hormo: Adipo 24.2 1.7E+02 0.0036 25.5 4.8 37 629-665 7-45 (48)
219 KOG0802 E3 ubiquitin ligase [P 24.0 35 0.00075 42.9 1.1 44 1115-1166 478-521 (543)
220 cd00522 Hemerythrin Hemerythri 22.9 4.1E+02 0.0088 26.2 8.2 61 117-195 14-78 (113)
221 PRK10722 hypothetical protein; 22.8 5.1E+02 0.011 29.7 9.6 115 180-319 88-203 (247)
222 PF01599 Ribosomal_S27: Riboso 22.8 41 0.0009 28.9 1.0 28 1038-1065 14-46 (47)
223 KOG0006 E3 ubiquitin-protein l 22.4 74 0.0016 37.1 3.1 75 1066-1151 169-254 (446)
224 smart00451 ZnF_U1 U1-like zinc 22.4 42 0.00092 25.8 0.9 12 1055-1066 1-12 (35)
225 PRK00432 30S ribosomal protein 22.1 49 0.0011 28.6 1.3 9 1090-1098 36-44 (50)
226 smart00531 TFIIE Transcription 22.0 32 0.00068 35.8 0.2 7 1073-1079 124-130 (147)
227 PF09788 Tmemb_55A: Transmembr 21.9 72 0.0016 36.3 2.9 64 1088-1164 103-187 (256)
228 PLN02436 cellulose synthase A 21.2 68 0.0015 43.1 2.9 52 1113-1165 33-89 (1094)
229 KOG3053 Uncharacterized conser 21.0 38 0.00082 38.5 0.5 53 1112-1164 16-81 (293)
230 PRK03824 hypA hydrogenase nick 20.8 53 0.0012 33.9 1.5 9 1072-1080 107-115 (135)
231 COG5273 Uncharacterized protei 20.5 60 0.0013 38.1 2.0 47 1052-1104 104-150 (309)
232 PRK07219 DNA topoisomerase I; 20.5 1.4E+02 0.0031 39.6 5.6 63 1060-1127 672-744 (822)
233 TIGR00595 priA primosomal prot 20.4 74 0.0016 39.7 2.9 47 1026-1082 210-263 (505)
234 cd02341 ZZ_ZZZ3 Zinc finger, Z 20.4 57 0.0012 28.1 1.3 21 1073-1098 1-22 (48)
235 KOG1428 Inhibitor of type V ad 20.3 32 0.0007 46.7 -0.2 74 978-1063 3587-3662(3738)
236 PRK14890 putative Zn-ribbon RN 20.3 82 0.0018 28.4 2.3 35 1027-1066 23-57 (59)
No 1
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=100.00 E-value=6.8e-45 Score=397.27 Aligned_cols=199 Identities=47% Similarity=1.039 Sum_probs=189.8
Q ss_pred CCCCcccccccCCCCccccccccccccccCCcccCcccccccCCCCCCccccceeeccccCccccCCCCCCCCCCCCCcc
Q 001016 976 CSPSFRDAEKQVFGCEHYKRNCKLRAACCGKLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVGPVCTTLSCSGLSM 1055 (1190)
Q Consensus 976 ~~~~~~~~~~~~~gC~HY~r~ckl~~pcC~k~y~Cr~CHde~~dH~~~r~~~~~~~C~~C~~~q~~~~~C~~~~Cc~~~f 1055 (1190)
..+++.|+...++||+||+|+|++++|||+++|+|++||++..+|.++|+.+.+|+||.|.++|++++.|.+ |+..+
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---CHVEL 97 (276)
T ss_pred cccccccccccccCCchhhhccccccccccceeeeEEecChhhhcccchhhhhhhhhhhHHhhhhhhhcccc---chhhh
Confidence 346788999999999999999999999999999999999999999999999999999999999999999999 58889
Q ss_pred ceEeccccccccCC-CCcccCCCCCccccCCCCCccccccCCccccccccc-cccccccCCCCCCCcccccccccCCCee
Q 001016 1056 AKYYCGICKFFDDE-RVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLAKKL-VDHKCREKGLETNCPICCDFLFTSSATV 1133 (1190)
Q Consensus 1056 a~Y~C~~C~l~dd~-k~~yHC~~CgiCrvg~gl~~~~fHC~~C~~C~s~~l-~~H~C~e~~~~~~CpICle~lf~s~~~v 1133 (1190)
|+|||.+|++|||+ ..||||++|||||+|.++ +||||++|+.|++..+ ++|+|+|+..+.+||||.+++|.+...+
T Consensus 98 g~~~c~~C~l~dd~~~~~~hC~~C~icr~g~~~--~~fhc~~c~~c~~~~~~~~H~c~e~~~~~ncPic~e~l~~s~~~~ 175 (276)
T KOG1940|consen 98 GEYYCLICKLFDDDPSKQYHCDLCGICREGLGL--DFFHCKKCKACLSAYLSNWHKCVERSSEFNCPICKEYLFLSFEDA 175 (276)
T ss_pred hhhcCcccccccccccceecccccccccccccc--chhHHhhhHhHHhhhcccccchhhhcccCCCchhHHHhccccccC
Confidence 99999999999988 599999999999999875 9999999999999998 6699999999999999999999999999
Q ss_pred EecCCCCccCHhhHHHHHhcCCCCCCCcccccchhHHHHhhhccccc
Q 001016 1134 RALPCGHFMHSDCFQAYTCSHYICPICSKSLGDMALYEGFCSLFSGL 1180 (1190)
Q Consensus 1134 ~~LpCgH~fH~~Ci~~wl~~~~~CPiCrk~l~~m~~~~~~lD~~~~~ 1180 (1190)
..++|||+.|..|+.+....+|+||+|.+ +.||..+|+++|..++.
T Consensus 176 ~~~~CgH~~h~~cf~e~~~~~y~CP~C~~-~~d~~~~~~~~d~~l~~ 221 (276)
T KOG1940|consen 176 GVLKCGHYMHSRCFEEMICEGYTCPICSK-PGDMSHYFRKLDKELAG 221 (276)
T ss_pred CccCcccchHHHHHHHHhccCCCCCcccc-hHHHHHHHHHHHHHHhc
Confidence 99999999999999999988899999999 99999999999998853
No 2
>PF05495 zf-CHY: CHY zinc finger; InterPro: IPR008913 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Pirh2 is an eukaryotic ubiquitin protein ligase, which has been shown to promote p53 degradation in mammals. Pirh2 physically interacts with p53 and promotes ubiquitination of p53 independently of MDM2. Like MDM2, Pirh2 is thought to participate in an autoregulatory feedback loop that controls p53 function. Pirh2 proteins contain three distinct zinc fingers, the CHY-type, the CTCHY-type which is C-terminal to the CHY-type zinc finger and a RING finger. The CHY-type zinc finger has no currently known function []. As well as Pirh2, the CHY-type zinc finger is also found in the following proteins: Yeast helper of Tim protein 13. Hot13 may have a role in the assembly and recycling of the small Tims, a complex of the mitochondrial intermembrane space that participates in the TIM22 import pathway for assembly of the inner membrane [] Several plant hypothetical proteins that also contain haemerythrin cation binding domains Several protozoan hypothetical proteins that also contain a Myb domain The solution structure of this zinc finger has been solved and binds 3 zinc atoms as shown in the following schematic representation: ++---------+-----+ || | | CXHYxxxxxxxxxCCxxxxxCxxCHxxxxxHxxxxxxxxxxxCxxCxxxxxxxxxCxxC | | | | | | | | +-+-----------------+--+ +--+---------+--+ 'C': conserved cysteine involved in the binding of one zinc atom. 'H': conserved histidine involved in the binding of one zinc atom. More information about these proteins can be found at Protein of the Month: Zinc Fingers []; GO: 0008270 zinc ion binding; PDB: 2DKT_A 2K2C_A.
Probab=99.81 E-value=3.1e-21 Score=173.94 Aligned_cols=70 Identities=44% Similarity=1.197 Sum_probs=53.6
Q ss_pred Ccccccc-ccccccccCCcccCcccccccCCCCCCccccceeeccccCccccCCCCCCCCCCCCCccceEecccccccc
Q 001016 990 CEHYKRN-CKLRAACCGKLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVGPVCTTLSCSGLSMAKYYCGICKFFD 1067 (1190)
Q Consensus 990 C~HY~r~-ckl~~pcC~k~y~Cr~CHde~~dH~~~r~~~~~~~C~~C~~~q~~~~~C~~~~Cc~~~fa~Y~C~~C~l~d 1067 (1190)
|+||+|+ |+|+||||++|||||+|||+.++|+++|+.+++|+||.|+++|+++++ + | + |+|+|++|++||
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 999999999999999999999999999999999999999999999987 4 4 5 999999999986
No 3
>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=99.20 E-value=2.3e-10 Score=111.03 Aligned_cols=124 Identities=26% Similarity=0.366 Sum_probs=110.3
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhhcccCCcccHHHHHHHHHHHHHHHHhhhhccccchhhhhhhhh--------hhHH
Q 001016 293 PIDEIMLWHNAIKRELNDIAEAARKIQLSGDFSDLSAFNKRLQFIAEVCIFHSIAEDKVIFPAVDVEL--------SFAQ 364 (1190)
Q Consensus 293 PId~l~~~HkALRrEL~~L~~~a~~~~~~gd~~~L~~L~~r~~fl~~vl~~Hs~aEDevlFPaL~~r~--------~me~ 364 (1190)
+|+.|...|+.||+.++.+...+... ++..++..+...+.+|...+..|+..||+++||.|..+. .+..
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 455678999999999999999999999999999999332 8899
Q ss_pred hHHHHHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 001016 365 EHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPLA 425 (1190)
Q Consensus 365 EH~~ie~l~e~l~~ll~~l~~~~~~~~~~~~~~eLa~~l~~L~~~L~~Hf~~EE~qvfPLl 425 (1190)
||..+...++.+...+...... ......+...+..+...+..|+.+||+.+||++
T Consensus 79 eH~~~~~~l~~l~~~~~~~~~~------~~~~~~~~~~~~~l~~~l~~H~~~Ee~~l~P~~ 133 (133)
T PF01814_consen 79 EHEEIRALLDELEEALARYSGD------EEDAEELREALRALAEWLRRHIAKEEEVLFPLL 133 (133)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHTHGGGHHHH
T ss_pred HHHHHHHHHHHHHHHHhhCccc------cchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 9999999999999999776511 255778889999999999999999999999986
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=99.17 E-value=2.4e-10 Score=110.94 Aligned_cols=129 Identities=33% Similarity=0.416 Sum_probs=115.5
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHhhccCCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHHHh---hhhHHHHHH
Q 001016 43 PILIFLFFHKAIKSELDVLHRAAMAFATNLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIR---VKNIARTYS 119 (1190)
Q Consensus 43 Pi~~~~~~HkAlR~eL~~l~~~a~~~~~~~gd~~~~~~l~~r~~~L~~~~~~H~~aEDevI~PaLd~R---v~~v~~~~~ 119 (1190)
||+.+...|+.||+.+..+...+... + +......+...+.+|...+..|+..|++++||.|+.+ .++.+..+.
T Consensus 2 ~i~~l~~~H~~~~~~~~~l~~~~~~~-~---~~~~~~~l~~~~~~l~~~l~~H~~~EE~~l~p~l~~~~~~~~~~~~~~~ 77 (133)
T PF01814_consen 2 PIDELRRDHRALRRLLAELEEALDEL-P---DDEDLRALRELLDELRRELRHHHAREEEYLFPALERRDPRGDALIAELR 77 (133)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHH-C---CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHHHH-CCCHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhC-c---CchhHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhccccchhhHH
Confidence 78899999999999999999998888 2 4556899999999999999999999999999999944 367889999
Q ss_pred hhhhhHHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHHHHHhHHHHHHHhhhhH
Q 001016 120 LEHEGESVLFDQLFELLNSSMRNEESYRRELASCTGALQTSISQHMSKEEEQVFPLL 176 (1190)
Q Consensus 120 ~EH~~~~~lf~~l~~~l~~~~~~~~~~~~eLa~~l~~l~~~l~qHm~~EE~~v~PLl 176 (1190)
.||..+...++.+...+..+. ........+...+.++...+.+||.+||+.++|++
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 33466778888888888899999999999999985
No 5
>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=99.15 E-value=1e-11 Score=101.82 Aligned_cols=44 Identities=36% Similarity=0.989 Sum_probs=38.7
Q ss_pred CCCcccccccccCCCeeEecCCCCccCHhhHHHHHhcCCCCCCCc
Q 001016 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICS 1161 (1190)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCr 1161 (1190)
++|+||+++ +..++.+..++|||.||.+|+.+|++.+++||+||
T Consensus 1 d~C~IC~~~-~~~~~~~~~l~C~H~fh~~Ci~~~~~~~~~CP~CR 44 (44)
T PF13639_consen 1 DECPICLEE-FEDGEKVVKLPCGHVFHRSCIKEWLKRNNSCPVCR 44 (44)
T ss_dssp -CETTTTCB-HHTTSCEEEETTSEEEEHHHHHHHHHHSSB-TTTH
T ss_pred CCCcCCChh-hcCCCeEEEccCCCeeCHHHHHHHHHhCCcCCccC
Confidence 479999999 55677788999999999999999999999999997
No 6
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.91 E-value=5.1e-10 Score=127.48 Aligned_cols=49 Identities=27% Similarity=0.845 Sum_probs=45.0
Q ss_pred CCCcccccccccCCCeeEecCCCCccCHhhHHHHHhcC-CCCCCCcccccc
Q 001016 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSH-YICPICSKSLGD 1166 (1190)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~-~~CPiCrk~l~~ 1166 (1190)
..|+||+|+ |..++++++|||+|.||..||+.|+..+ ..||+|++.+..
T Consensus 230 ~~CaIClEd-Y~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~di~~ 279 (348)
T KOG4628|consen 230 DTCAICLED-YEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRDIRT 279 (348)
T ss_pred ceEEEeecc-cccCCeeeEecCCCchhhccchhhHhhcCccCCCCCCcCCC
Confidence 599999999 9999999999999999999999998776 459999998864
No 7
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=98.91 E-value=1.7e-10 Score=107.70 Aligned_cols=66 Identities=26% Similarity=0.631 Sum_probs=53.4
Q ss_pred CCCCcccccc---ccccccccCCcccCcccccccCCCCCCcc-----ccceeeccccCccccC-----CCCCCCCCCCCC
Q 001016 987 VFGCEHYKRN---CKLRAACCGKLFTCRFCHDKVSDHSMDRK-----ATTEMMCMRCLKVQPV-----GPVCTTLSCSGL 1053 (1190)
Q Consensus 987 ~~gC~HY~r~---ckl~~pcC~k~y~Cr~CHde~~dH~~~r~-----~~~~~~C~~C~~~q~~-----~~~C~~~~Cc~~ 1053 (1190)
..-|.||+.. ++|+|.||+|||+|..||||.++||+.++ ..+.|+||.|.++... ...|++ |..
T Consensus 12 etRC~Hyht~~Diialkc~~C~kyYaCy~CHdel~~Hpf~p~~~~~~~~~~iiCGvC~~~LT~~EY~~~~~Cp~---C~s 88 (105)
T COG4357 12 ETRCLHYHTPLDIIALKCKCCQKYYACYHCHDELEDHPFEPWGLQEFNPKAIICGVCRKLLTRAEYGMCGSCPY---CQS 88 (105)
T ss_pred cceeeEecCccceEeeeechhhhhhhHHHHHhHHhcCCCccCChhhcCCccEEhhhhhhhhhHHHHhhcCCCCC---cCC
Confidence 4469999999 88999999999999999999999988774 4567999999876432 235777 455
Q ss_pred cc
Q 001016 1054 SM 1055 (1190)
Q Consensus 1054 ~f 1055 (1190)
.|
T Consensus 89 pF 90 (105)
T COG4357 89 PF 90 (105)
T ss_pred CC
Confidence 54
No 8
>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=98.81 E-value=2.9e-09 Score=97.04 Aligned_cols=47 Identities=30% Similarity=0.757 Sum_probs=37.6
Q ss_pred CCCCCcccccccccC---------CCeeEecCCCCccCHhhHHHHHhcCCCCCCCc
Q 001016 1115 LETNCPICCDFLFTS---------SATVRALPCGHFMHSDCFQAYTCSHYICPICS 1161 (1190)
Q Consensus 1115 ~~~~CpICle~lf~s---------~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCr 1161 (1190)
.+++|+||++.+.+. ...+...+|||.||.+||.+|++.+.+||+||
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 466799999996322 23566679999999999999999999999998
No 9
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=98.79 E-value=2.1e-09 Score=120.57 Aligned_cols=57 Identities=32% Similarity=0.793 Sum_probs=48.6
Q ss_pred CCCCCCCcccccccccCC---------CeeEecCCCCccCHhhHHHHHhcCCCCCCCccc-ccchhH
Q 001016 1113 KGLETNCPICCDFLFTSS---------ATVRALPCGHFMHSDCFQAYTCSHYICPICSKS-LGDMAL 1169 (1190)
Q Consensus 1113 ~~~~~~CpICle~lf~s~---------~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrk~-l~~m~~ 1169 (1190)
..++..|.||+|+|+.++ .+.+.|||||.+|-+|++.|+..+.+|||||.+ +.|++.
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 556889999999987665 234779999999999999999999999999999 567654
No 10
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=98.77 E-value=4.3e-09 Score=97.79 Aligned_cols=47 Identities=21% Similarity=0.514 Sum_probs=36.4
Q ss_pred CCCCcccccccccCCCeeEecCCCCccCHhhHHHHHhc---CCCCCCCcccc
Q 001016 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS---HYICPICSKSL 1164 (1190)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~---~~~CPiCrk~l 1164 (1190)
+..||.|..+ ....++....|+|.||.+||.+|+.+ +.+||+||+..
T Consensus 32 dg~Cp~Ck~P--gd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w 81 (85)
T PF12861_consen 32 DGCCPDCKFP--GDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPW 81 (85)
T ss_pred ccCCCCccCC--CCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCee
Confidence 4567777755 23335666789999999999999975 57899999875
No 11
>PRK10992 iron-sulfur cluster repair di-iron protein; Provisional
Probab=98.76 E-value=8.5e-08 Score=104.71 Aligned_cols=131 Identities=18% Similarity=0.328 Sum_probs=106.1
Q ss_pred HHHH-HHHHHHHHHHHHHHHHHHHhhcc-cC-CcccHHHHHHHHHHHHHHHHhhhhccccchhhhhhhhh---------h
Q 001016 294 IDEI-MLWHNAIKRELNDIAEAARKIQL-SG-DFSDLSAFNKRLQFIAEVCIFHSIAEDKVIFPAVDVEL---------S 361 (1190)
Q Consensus 294 Id~l-~~~HkALRrEL~~L~~~a~~~~~-~g-d~~~L~~L~~r~~fl~~vl~~Hs~aEDevlFPaL~~r~---------~ 361 (1190)
||.+ ..-|..+|++|..|.+.+.++.. .| +...+..+..-+..|...+..|+..|++++||+|.+.. .
T Consensus 76 idyI~~~~H~~~r~~lp~L~~l~~kv~~vhg~~~~~~~~~~~l~~~~~~el~~H~~kEE~~LFP~l~~~~~~~~~~pi~v 155 (220)
T PRK10992 76 IDHIIVRYHDRHREQLPELILLATKVERVHGDKPDCPRGLAKYLTALHEELSSHMMKEEQILFPMIKQGMGSQAMGPISV 155 (220)
T ss_pred HHHHHHHHhHHHHHHHHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHhcccccccchHHH
Confidence 4554 78899999999999999977642 23 34567888888999999999999999999999999631 8
Q ss_pred hHHhHHHHHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHh
Q 001016 362 FAQEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPLARR 427 (1190)
Q Consensus 362 me~EH~~ie~l~e~l~~ll~~l~~~~~~~~~~~~~~eLa~~l~~L~~~L~~Hf~~EE~qvfPLl~~ 427 (1190)
|..||+++...+.+|..++....... .+...++.+-..+..+...|.+|..+||+.+||++..
T Consensus 156 m~~EHd~~~~~l~~L~~lt~~~~~p~---~ac~~~~~l~~~l~~~~~dL~~HI~~EnniLFP~a~~ 218 (220)
T PRK10992 156 MESEHDEAGELLEVIKHLTNNVTPPP---EACTTWRALYNGINELIDDLMEHIHLENNVLFPRALA 218 (220)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCCCh---hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Confidence 99999999999999998886642221 1124577777888889999999999999999998764
No 12
>TIGR03652 FeS_repair_RIC iron-sulfur cluster repair di-iron protein. Members of this protein family, designated variously as YftE, NorA, DrnN, and NipC, are di-iron proteins involved in the repair of iron-sulfur clusters. Previously assigned names reflect pleiotropic effects of damage from NO or other oxidative stress when this protein is mutated. The suggested name now is RIC, for Repair of Iron Centers.
Probab=98.64 E-value=2e-07 Score=101.45 Aligned_cols=126 Identities=18% Similarity=0.290 Sum_probs=101.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcc--cCCcccHHHHHHHHHHHHHHHHhhhhccccchhhhhhhh------------h-h
Q 001016 297 IMLWHNAIKRELNDIAEAARKIQL--SGDFSDLSAFNKRLQFIAEVCIFHSIAEDKVIFPAVDVE------------L-S 361 (1190)
Q Consensus 297 l~~~HkALRrEL~~L~~~a~~~~~--~gd~~~L~~L~~r~~fl~~vl~~Hs~aEDevlFPaL~~r------------~-~ 361 (1190)
....|..||++|..|...+.++.. ..+...+..+..-+..|..-+..|+..|++++||+|... + .
T Consensus 76 ~~~hH~~i~~~l~~L~~l~~kv~~~hg~~~~~l~~l~~~~~~~~~eL~~H~~kEE~~LFP~l~~~~~g~~~~~~~~pi~~ 155 (216)
T TIGR03652 76 VDRHHEYLREELPELIPLATKVARVHGDHHPELIGLAELFRELKAELEQHLMKEEQILFPAIIEYKRGNPAQAIGTPISV 155 (216)
T ss_pred HHHHhHHHHHHHHHHHHHHHHHHHHhCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHccCccccccchHHH
Confidence 367899999999999998877642 233446788889999999999999999999999999741 1 7
Q ss_pred hHHhHHHHHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 001016 362 FAQEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPLA 425 (1190)
Q Consensus 362 me~EH~~ie~l~e~l~~ll~~l~~~~~~~~~~~~~~eLa~~l~~L~~~L~~Hf~~EE~qvfPLl 425 (1190)
|..||+++...+.+|..++....... .....++.+...+..+...|.+|..+||+.+||.+
T Consensus 156 m~~EH~~~~~~l~~L~~l~~~~~~p~---~ac~~~~~~~~~l~~~~~~L~~HI~~En~iLFP~~ 216 (216)
T TIGR03652 156 MESEHDEAGDLLKELRELTNDYTPPE---DACNTWRALYSGLEELEDDLHEHIHLENNILFPRA 216 (216)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCCCCc---chhHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCC
Confidence 99999999999999998886543221 11345677778888899999999999999999963
No 13
>PRK10992 iron-sulfur cluster repair di-iron protein; Provisional
Probab=98.62 E-value=4.5e-07 Score=99.12 Aligned_cols=129 Identities=17% Similarity=0.222 Sum_probs=110.3
Q ss_pred HHHHHHHHHHHHHHHHHHhhcc--CCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHHHh----hhhHHHHHHhhh
Q 001016 49 FFHKAIKSELDVLHRAAMAFAT--NLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIR----VKNIARTYSLEH 122 (1190)
Q Consensus 49 ~~HkAlR~eL~~l~~~a~~~~~--~~gd~~~~~~l~~r~~~L~~~~~~H~~aEDevI~PaLd~R----v~~v~~~~~~EH 122 (1190)
.-|.-+|++|..|.+++..+.. + ++......+.+-++-|..-+..|+..|.+++||.|... +.+.+..|..||
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 6699999999999999988874 2 45567788888999999999999999999999999962 356789999999
Q ss_pred hhHHHHHHHHHHHHHhhhcCch--hHHHHHHHHHHHHHHHHHHhHHHHHHHhhhhHhh
Q 001016 123 EGESVLFDQLFELLNSSMRNEE--SYRRELASCTGALQTSISQHMSKEEEQVFPLLIE 178 (1190)
Q Consensus 123 ~~~~~lf~~l~~~l~~~~~~~~--~~~~eLa~~l~~l~~~l~qHm~~EE~~v~PLl~~ 178 (1190)
.++..++..|..+.+......+ ..++.+...+..+...|.+|.++|+..+||.+.+
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 9999999999999988744333 5678888888888889999999999999998763
No 14
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.62 E-value=1.8e-08 Score=111.12 Aligned_cols=57 Identities=26% Similarity=0.676 Sum_probs=49.0
Q ss_pred ccccCCCCCCCcccccccccCCCeeEecCCCCccCHhhHHHHHh-cCCCCCCCcccccc
Q 001016 1109 KCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC-SHYICPICSKSLGD 1166 (1190)
Q Consensus 1109 ~C~e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~-~~~~CPiCrk~l~~ 1166 (1190)
.-.|.....+|+|||++ |...+.++++||.|.||..|+++|+. .+..||+||..++.
T Consensus 316 ~~~ea~~GveCaICms~-fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iPP 373 (374)
T COG5540 316 RAVEADKGVECAICMSN-FIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIPP 373 (374)
T ss_pred hHHhcCCCceEEEEhhh-hcccceEEEeccCceechhHHHHHHhhhcccCCccCCCCCC
Confidence 33455556899999999 67788899999999999999999986 78999999998864
No 15
>PHA02929 N1R/p28-like protein; Provisional
Probab=98.56 E-value=4.8e-08 Score=107.27 Aligned_cols=54 Identities=17% Similarity=0.551 Sum_probs=42.8
Q ss_pred CCCCCCCcccccccccCCC---e-eEecCCCCccCHhhHHHHHhcCCCCCCCcccccc
Q 001016 1113 KGLETNCPICCDFLFTSSA---T-VRALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1166 (1190)
Q Consensus 1113 ~~~~~~CpICle~lf~s~~---~-v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrk~l~~ 1166 (1190)
.+.+..||||++.+..... . ....+|||.||..||.+|++.+.+||+||..+..
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 3456899999998554321 1 2345899999999999999999999999998763
No 16
>COG3945 Uncharacterized conserved protein [Function unknown]
Probab=98.52 E-value=1.9e-06 Score=89.90 Aligned_cols=140 Identities=21% Similarity=0.284 Sum_probs=112.4
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHHhhcccC--CcccHHHHHHHHHHHHHHHHhhhhccccchhhhhhhhh---------
Q 001016 292 CPIDEIMLWHNAIKRELNDIAEAARKIQLSG--DFSDLSAFNKRLQFIAEVCIFHSIAEDKVIFPAVDVEL--------- 360 (1190)
Q Consensus 292 ~PId~l~~~HkALRrEL~~L~~~a~~~~~~g--d~~~L~~L~~r~~fl~~vl~~Hs~aEDevlFPaL~~r~--------- 360 (1190)
.-|+.|+-.|+.|.+-|.-|...+..+. .| +.+++..+.+-++-|++- .||..|+.++||-|..+.
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 3578899999999999999988888775 44 344556665555555554 578889999999999774
Q ss_pred hhHHhHHHHHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhhCCHHHHHHHHHh
Q 001016 361 SFAQEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPLARRHFSPKRQRELLYQ 440 (1190)
Q Consensus 361 ~me~EH~~ie~l~e~l~~ll~~l~~~~~~~~~~~~~~eLa~~l~~L~~~L~~Hf~~EE~qvfPLl~~~fS~eEq~~L~~~ 440 (1190)
.|..||...-.++..|.+.+..+.+.+. +....++..+......+.+|..+|+.++||++.+.||.+ |.++..+
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 8999999999999999999999876543 224566667777789999999999999999999999999 6666544
No 17
>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=98.51 E-value=8.5e-08 Score=76.79 Aligned_cols=44 Identities=34% Similarity=0.921 Sum_probs=37.4
Q ss_pred CCcccccccccCCCeeEecCCCCccCHhhHHHHHhc-CCCCCCCcccc
Q 001016 1118 NCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS-HYICPICSKSL 1164 (1190)
Q Consensus 1118 ~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~-~~~CPiCrk~l 1164 (1190)
.|+||++.+ ...+...+|||.||..|++.|+.. +..||+|++.+
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 599999984 445666789999999999999987 78899999864
No 18
>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=98.47 E-value=1.4e-06 Score=95.03 Aligned_cols=127 Identities=24% Similarity=0.300 Sum_probs=106.8
Q ss_pred HHHHHHHHHHHHHHHHHHhhcc-CCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHHH--hh------hhHHHHHH
Q 001016 49 FFHKAIKSELDVLHRAAMAFAT-NLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDI--RV------KNIARTYS 119 (1190)
Q Consensus 49 ~~HkAlR~eL~~l~~~a~~~~~-~~gd~~~~~~l~~r~~~L~~~~~~H~~aEDevI~PaLd~--Rv------~~v~~~~~ 119 (1190)
.-|..+|++|..|..++..+.. .-.+...+..+.+-++.|..-+..|+..|.+++||+|.. +. .+.+..|.
T Consensus 78 ~hH~~i~~~l~~L~~l~~kv~~~hg~~~~~l~~l~~~~~~~~~eL~~H~~kEE~~LFP~l~~~~~g~~~~~~~~pi~~m~ 157 (216)
T TIGR03652 78 RHHEYLREELPELIPLATKVARVHGDHHPELIGLAELFRELKAELEQHLMKEEQILFPAIIEYKRGNPAQAIGTPISVME 157 (216)
T ss_pred HHhHHHHHHHHHHHHHHHHHHHHhCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHccCccccccchHHHHH
Confidence 7799999999999998888774 114456778999999999999999999999999999984 21 22889999
Q ss_pred hhhhhHHHHHHHHHHHHHhhhcCch--hHHHHHHHHHHHHHHHHHHhHHHHHHHhhhh
Q 001016 120 LEHEGESVLFDQLFELLNSSMRNEE--SYRRELASCTGALQTSISQHMSKEEEQVFPL 175 (1190)
Q Consensus 120 ~EH~~~~~lf~~l~~~l~~~~~~~~--~~~~eLa~~l~~l~~~l~qHm~~EE~~v~PL 175 (1190)
.||.++...+++|...++......+ ..++.+...+.++...|.+|.++||..+||.
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 5577777778888889999999999999995
No 19
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=98.45 E-value=1.1e-07 Score=86.39 Aligned_cols=50 Identities=20% Similarity=0.395 Sum_probs=39.5
Q ss_pred CCCCcccccccccCCC-eeEecCCCCccCHhhHHHHHhcCCCCCCCccccc
Q 001016 1116 ETNCPICCDFLFTSSA-TVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1165 (1190)
Q Consensus 1116 ~~~CpICle~lf~s~~-~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrk~l~ 1165 (1190)
.+.||-|.-.+-..++ ++.-.-|.|.||.+||..||.+...||++|++..
T Consensus 31 m~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~Tk~~CPld~q~w~ 81 (88)
T COG5194 31 MGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQTWV 81 (88)
T ss_pred cCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhhCCCCCCCCceeE
Confidence 4568888765433333 4556789999999999999999999999998764
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=98.34 E-value=2.7e-07 Score=73.99 Aligned_cols=39 Identities=41% Similarity=0.997 Sum_probs=33.4
Q ss_pred CcccccccccCCCeeEecCCCCccCHhhHHHHHhcCCCCCCC
Q 001016 1119 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPIC 1160 (1190)
Q Consensus 1119 CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiC 1160 (1190)
||||++.+ .+++..++|||.|+..|+.+|++.+.+||+|
T Consensus 1 C~iC~~~~---~~~~~~~~CGH~fC~~C~~~~~~~~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDEL---RDPVVVTPCGHSFCKECIEKYLEKNPKCPVC 39 (39)
T ss_dssp ETTTTSB----SSEEEECTTSEEEEHHHHHHHHHCTSB-TTT
T ss_pred CCCCCCcc---cCcCEECCCCCchhHHHHHHHHHCcCCCcCC
Confidence 89999883 2367889999999999999999989999998
No 21
>PRK13276 cell wall biosynthesis protein ScdA; Provisional
Probab=98.34 E-value=5.8e-06 Score=90.39 Aligned_cols=125 Identities=21% Similarity=0.253 Sum_probs=111.3
Q ss_pred HHHHHHHHHHHHHHHHHHhhcc--CCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHHHh--------hhhHHHHH
Q 001016 49 FFHKAIKSELDVLHRAAMAFAT--NLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIR--------VKNIARTY 118 (1190)
Q Consensus 49 ~~HkAlR~eL~~l~~~a~~~~~--~~gd~~~~~~l~~r~~~L~~~~~~H~~aEDevI~PaLd~R--------v~~v~~~~ 118 (1190)
..|.-+|++|..|..++..|.. + ++......|.+.|..|+.=+..|..-|.+++||.+... +.+.+..|
T Consensus 85 ~hH~~~r~~lp~l~~l~~kV~~VHg-~~~p~l~~l~~lf~~l~~eL~~H~~KEE~ilFP~i~~~~~~~~~~~~~~pI~~m 163 (224)
T PRK13276 85 AYHEPLREEFKNLTPYVTKLSKVHG-PNHPYLVELKETYDTFKNGMLEHMQKEDDVDFPKLIKYEQGEVVDDINTVIDDL 163 (224)
T ss_pred HHhHHHHHHHHHHHHHHHHHHHHhC-CCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHhhccccchhhhhHHHHH
Confidence 7899999999999999999986 3 45668999999999999999999999999999999752 35578999
Q ss_pred HhhhhhHHHHHHHHHHHHHhhhcCch--hHHHHHHHHHHHHHHHHHHhHHHHHHHhhh
Q 001016 119 SLEHEGESVLFDQLFELLNSSMRNEE--SYRRELASCTGALQTSISQHMSKEEEQVFP 174 (1190)
Q Consensus 119 ~~EH~~~~~lf~~l~~~l~~~~~~~~--~~~~eLa~~l~~l~~~l~qHm~~EE~~v~P 174 (1190)
..||+++.+.+.+|.++.+-++...+ ..|+.|=.-+.++...|.+|.+.|-.-+||
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 778888888888888999999999999988
No 22
>PRK13276 cell wall biosynthesis protein ScdA; Provisional
Probab=98.30 E-value=6.4e-06 Score=90.06 Aligned_cols=125 Identities=13% Similarity=0.168 Sum_probs=105.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcc--cCCcccHHHHHHHHHHHHHHHHhhhhccccchhhhhhhh-------------hh
Q 001016 297 IMLWHNAIKRELNDIAEAARKIQL--SGDFSDLSAFNKRLQFIAEVCIFHSIAEDKVIFPAVDVE-------------LS 361 (1190)
Q Consensus 297 l~~~HkALRrEL~~L~~~a~~~~~--~gd~~~L~~L~~r~~fl~~vl~~Hs~aEDevlFPaL~~r-------------~~ 361 (1190)
+...|..+|++|-.|...+.++.. .++...+..+...+..+..-|..|-..|+.++||++... ..
T Consensus 83 ~~~hH~~~r~~lp~l~~l~~kV~~VHg~~~p~l~~l~~lf~~l~~eL~~H~~KEE~ilFP~i~~~~~~~~~~~~~~pI~~ 162 (224)
T PRK13276 83 QSAYHEPLREEFKNLTPYVTKLSKVHGPNHPYLVELKETYDTFKNGMLEHMQKEDDVDFPKLIKYEQGEVVDDINTVIDD 162 (224)
T ss_pred HHHHhHHHHHHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHhhccccchhhhhHHHH
Confidence 467899999999999999988743 244557899999999999999999999999999999651 18
Q ss_pred hHHhHHHHHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 001016 362 FAQEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPL 424 (1190)
Q Consensus 362 me~EH~~ie~l~e~l~~ll~~l~~~~~~~~~~~~~~eLa~~l~~L~~~L~~Hf~~EE~qvfPL 424 (1190)
|+.||+.+.+.+.+|++++...... .+++..++.|=..+.++...|.+|.+.|-+.+||-
T Consensus 163 m~~EH~~~g~~l~~i~~lTn~yt~P---~~AC~t~r~ly~~L~~fe~dL~~HIhLENnILFPr 222 (224)
T PRK13276 163 LVSDHIATGQLLVKMSELTSSYEPP---IEACGTWRLVYQRLKALEVLTHEHVHLENHVLFKK 222 (224)
T ss_pred HHHHHHHHHHHHHHHHHHhCCCCCC---cchhHHHHHHHHHHHHHHHHHHHHHHHHHHHcccC
Confidence 9999999999999999998766433 22356688888888999999999999999999993
No 23
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=98.28 E-value=4e-07 Score=76.81 Aligned_cols=47 Identities=32% Similarity=0.844 Sum_probs=39.0
Q ss_pred CCCCcccccccccCCCeeEecCCCCc-cCHhhHHHHHhcCCCCCCCcccccc
Q 001016 1116 ETNCPICCDFLFTSSATVRALPCGHF-MHSDCFQAYTCSHYICPICSKSLGD 1166 (1190)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCgH~-fH~~Ci~~wl~~~~~CPiCrk~l~~ 1166 (1190)
+..|+||++. ...+..+||||. |...|+..|++...+||+||+++.+
T Consensus 2 ~~~C~iC~~~----~~~~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~~ 49 (50)
T PF13920_consen 2 DEECPICFEN----PRDVVLLPCGHLCFCEECAERLLKRKKKCPICRQPIES 49 (50)
T ss_dssp HSB-TTTSSS----BSSEEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-SE
T ss_pred cCCCccCCcc----CCceEEeCCCChHHHHHHhHHhcccCCCCCcCChhhcC
Confidence 4679999986 234778899999 9999999999999999999998864
No 24
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=98.17 E-value=3.2e-07 Score=82.93 Aligned_cols=46 Identities=22% Similarity=0.478 Sum_probs=33.0
Q ss_pred CCCcccccccccCCCeeEecCCCCccCHhhHHHHHhc---CCCCCCCcccc
Q 001016 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS---HYICPICSKSL 1164 (1190)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~---~~~CPiCrk~l 1164 (1190)
..||-|.-+ ++.-++...-|.|.||.+||.+|+.. ...||+||++.
T Consensus 32 g~Cp~Ck~P--gDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~ 80 (84)
T KOG1493|consen 32 GCCPDCKLP--GDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTW 80 (84)
T ss_pred CcCCCCcCC--CCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchhee
Confidence 456666543 23334444579999999999999854 46799999865
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=98.09 E-value=2.3e-06 Score=66.13 Aligned_cols=38 Identities=37% Similarity=0.943 Sum_probs=32.9
Q ss_pred CcccccccccCCCeeEecCCCCccCHhhHHHHHh-cCCCCCCC
Q 001016 1119 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC-SHYICPIC 1160 (1190)
Q Consensus 1119 CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~-~~~~CPiC 1160 (1190)
|+||++. ......++|||.||..|++.|+. ...+||+|
T Consensus 1 C~iC~~~----~~~~~~~~C~H~~c~~C~~~~~~~~~~~CP~C 39 (39)
T smart00184 1 CPICLEE----LKDPVVLPCGHTFCRSCIRKWLKSGNNTCPIC 39 (39)
T ss_pred CCcCccC----CCCcEEecCCChHHHHHHHHHHHhCcCCCCCC
Confidence 8999987 34577889999999999999987 67789998
No 26
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.08 E-value=2.6e-06 Score=70.19 Aligned_cols=44 Identities=30% Similarity=0.803 Sum_probs=38.4
Q ss_pred CCcccccccccCCCeeEecCCCCccCHhhHHHHHhcCCCCCCCcc
Q 001016 1118 NCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSK 1162 (1190)
Q Consensus 1118 ~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrk 1162 (1190)
.|+||.+. |.......+++|||.|...|+..+......||+||+
T Consensus 1 ~C~~C~~~-~~~~~~~~l~~CgH~~C~~C~~~~~~~~~~CP~C~k 44 (44)
T PF14634_consen 1 HCNICFEK-YSEERRPRLTSCGHIFCEKCLKKLKGKSVKCPICRK 44 (44)
T ss_pred CCcCcCcc-ccCCCCeEEcccCCHHHHHHHHhhcCCCCCCcCCCC
Confidence 49999999 555667888999999999999999877788999986
No 27
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.04 E-value=3.8e-06 Score=89.36 Aligned_cols=54 Identities=24% Similarity=0.613 Sum_probs=41.5
Q ss_pred ccccCCCCCCCcccccccccCCCeeEecCCCCccCHhhHHHHHhc----------------CCCCCCCcccccc
Q 001016 1109 KCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS----------------HYICPICSKSLGD 1166 (1190)
Q Consensus 1109 ~C~e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~----------------~~~CPiCrk~l~~ 1166 (1190)
+-++...+..||||++. +. + ..+++|||.|+..||..|+.. ..+||+||..+..
T Consensus 11 ~~~~~~~~~~CpICld~-~~--d-PVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~ 80 (193)
T PLN03208 11 TLVDSGGDFDCNICLDQ-VR--D-PVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE 80 (193)
T ss_pred eeccCCCccCCccCCCc-CC--C-cEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence 33445567899999997 32 3 345799999999999999742 3579999998864
No 28
>COG2846 Regulator of cell morphogenesis and NO signaling [Cell division and chromosome partitioning]
Probab=98.04 E-value=4.1e-05 Score=81.19 Aligned_cols=128 Identities=18% Similarity=0.316 Sum_probs=105.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcc-cCC-cccHHHHHHHHHHHHHHHHhhhhccccchhhhhhhhh---------hhH
Q 001016 295 DEIMLWHNAIKRELNDIAEAARKIQL-SGD-FSDLSAFNKRLQFIAEVCIFHSIAEDKVIFPAVDVEL---------SFA 363 (1190)
Q Consensus 295 d~l~~~HkALRrEL~~L~~~a~~~~~-~gd-~~~L~~L~~r~~fl~~vl~~Hs~aEDevlFPaL~~r~---------~me 363 (1190)
.++...|+-.|.+|.+|-..+.++.. -|| ++-...|.+-+..|...|.-|-..|++++||++..-. .|+
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 45688999999999999999888732 344 3456888888999999999999999999999998532 999
Q ss_pred HhHHHHHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 001016 364 QEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPLA 425 (1190)
Q Consensus 364 ~EH~~ie~l~e~l~~ll~~l~~~~~~~~~~~~~~eLa~~l~~L~~~L~~Hf~~EE~qvfPLl 425 (1190)
.||++...+++.+..++...... ..++..++.|=.-+..+.+.+.+|++-|=..+||=+
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 99999999999999998766422 122445677777788889999999999999999954
No 29
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=98.02 E-value=3.7e-06 Score=67.76 Aligned_cols=39 Identities=41% Similarity=1.036 Sum_probs=33.2
Q ss_pred CcccccccccCCCeeEecCCCCccCHhhHHHHHh--cCCCCCCC
Q 001016 1119 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC--SHYICPIC 1160 (1190)
Q Consensus 1119 CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~--~~~~CPiC 1160 (1190)
|+||++. + .+++..++|||.|+..|+.+|++ ....||+|
T Consensus 1 C~iC~~~-~--~~~~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEP-F--EDPVILLPCGHSFCRDCLRKWLENSGSVKCPLC 41 (41)
T ss_dssp ETTTSSB-C--SSEEEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred CCcCCcc-c--cCCCEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence 8999998 3 23456899999999999999987 67889998
No 30
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.02 E-value=1.6e-06 Score=106.24 Aligned_cols=53 Identities=30% Similarity=0.702 Sum_probs=44.6
Q ss_pred cCCCCCCCcccccccccCCC-eeEecCCCCccCHhhHHHHHhcCCCCCCCcccc
Q 001016 1112 EKGLETNCPICCDFLFTSSA-TVRALPCGHFMHSDCFQAYTCSHYICPICSKSL 1164 (1190)
Q Consensus 1112 e~~~~~~CpICle~lf~s~~-~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrk~l 1164 (1190)
.......|+||+|.|..... ....|||||.||..|+..|++...+||+||..+
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 44557899999999876433 356799999999999999999999999999844
No 31
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.99 E-value=3e-06 Score=88.21 Aligned_cols=48 Identities=31% Similarity=0.686 Sum_probs=39.9
Q ss_pred CCCCCcccccccccCCCee-EecCCCCccCHhhHHHHHhcCCCCCCCccccc
Q 001016 1115 LETNCPICCDFLFTSSATV-RALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1165 (1190)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v-~~LpCgH~fH~~Ci~~wl~~~~~CPiCrk~l~ 1165 (1190)
....|||||+. +.. ++ ....|||.|++.||+.-++...+||+|+|.|-
T Consensus 130 ~~~~CPiCl~~-~se--k~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt 178 (187)
T KOG0320|consen 130 GTYKCPICLDS-VSE--KVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKIT 178 (187)
T ss_pred cccCCCceecc-hhh--ccccccccchhHHHHHHHHHHHhCCCCCCcccccc
Confidence 34789999998 433 33 34799999999999999999999999999654
No 32
>PHA02926 zinc finger-like protein; Provisional
Probab=97.99 E-value=3.6e-06 Score=90.45 Aligned_cols=54 Identities=20% Similarity=0.544 Sum_probs=41.1
Q ss_pred cCCCCCCCcccccccccCC----Ce-eEecCCCCccCHhhHHHHHhcC------CCCCCCccccc
Q 001016 1112 EKGLETNCPICCDFLFTSS----AT-VRALPCGHFMHSDCFQAYTCSH------YICPICSKSLG 1165 (1190)
Q Consensus 1112 e~~~~~~CpICle~lf~s~----~~-v~~LpCgH~fH~~Ci~~wl~~~------~~CPiCrk~l~ 1165 (1190)
..+.+..|+||+|.+++.. .. -...+|+|.|+..||..|.+.. .+||+||..+.
T Consensus 166 ~~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~ 230 (242)
T PHA02926 166 RVSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFR 230 (242)
T ss_pred hccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceee
Confidence 3456789999999876532 11 2345999999999999998642 45999998875
No 33
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=97.88 E-value=7.4e-06 Score=67.16 Aligned_cols=38 Identities=37% Similarity=0.980 Sum_probs=27.3
Q ss_pred CcccccccccCCCeeEecCCCCccCHhhHHHHHhcC----CCCCCC
Q 001016 1119 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSH----YICPIC 1160 (1190)
Q Consensus 1119 CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~----~~CPiC 1160 (1190)
||||++.+ .. -+.|+|||.|...||..|.+.. +.||.|
T Consensus 1 CpiC~~~~-~~---Pv~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDLF-KD---PVSLPCGHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB--SS---EEE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCccchhh-CC---ccccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 89999984 32 3569999999999999987543 679998
No 34
>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=97.77 E-value=2.5e-05 Score=68.28 Aligned_cols=45 Identities=22% Similarity=0.422 Sum_probs=38.3
Q ss_pred CCCcccccccccCCCeeEecCCCCccCHhhHHHHHhcCCCCCCCccccc
Q 001016 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1165 (1190)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrk~l~ 1165 (1190)
-.||||++.| .. + ..++|||.|...||.+|++.+.+||+|++.+.
T Consensus 2 ~~Cpi~~~~~-~~--P-v~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~ 46 (63)
T smart00504 2 FLCPISLEVM-KD--P-VILPSGQTYERRAIEKWLLSHGTDPVTGQPLT 46 (63)
T ss_pred cCCcCCCCcC-CC--C-EECCCCCEEeHHHHHHHHHHCCCCCCCcCCCC
Confidence 4699999984 32 3 45799999999999999988999999999874
No 35
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=97.72 E-value=2e-05 Score=65.00 Aligned_cols=39 Identities=38% Similarity=0.950 Sum_probs=23.3
Q ss_pred CcccccccccCCCeeEecCCCCccCHhhHHHHHhc----CCCCC
Q 001016 1119 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS----HYICP 1158 (1190)
Q Consensus 1119 CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~----~~~CP 1158 (1190)
||||.| +-+...+-++|+|||.|..+|++++++. ..+||
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 4444556677999999999999999864 45687
No 36
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=97.66 E-value=1e-05 Score=77.21 Aligned_cols=32 Identities=25% Similarity=0.542 Sum_probs=28.6
Q ss_pred eEecCCCCccCHhhHHHHHhcCCCCCCCcccc
Q 001016 1133 VRALPCGHFMHSDCFQAYTCSHYICPICSKSL 1164 (1190)
Q Consensus 1133 v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrk~l 1164 (1190)
+.-.-|.|.||.+||..|++++..||+|.+.-
T Consensus 76 VaWG~CNHaFH~hCisrWlktr~vCPLdn~eW 107 (114)
T KOG2930|consen 76 VAWGVCNHAFHFHCISRWLKTRNVCPLDNKEW 107 (114)
T ss_pred EEeeecchHHHHHHHHHHHhhcCcCCCcCcce
Confidence 44468999999999999999999999999864
No 37
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=97.63 E-value=2.4e-05 Score=87.06 Aligned_cols=47 Identities=23% Similarity=0.701 Sum_probs=39.5
Q ss_pred CCCCcccccccccCCCeeEecCCCCccCHhhHHHHHhcCCCCCCCcccccc
Q 001016 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1166 (1190)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrk~l~~ 1166 (1190)
...|.+|||.. ......||||.|+..||..|.....-||+||..+..
T Consensus 239 ~~kC~LCLe~~----~~pSaTpCGHiFCWsCI~~w~~ek~eCPlCR~~~~p 285 (293)
T KOG0317|consen 239 TRKCSLCLENR----SNPSATPCGHIFCWSCILEWCSEKAECPLCREKFQP 285 (293)
T ss_pred CCceEEEecCC----CCCCcCcCcchHHHHHHHHHHccccCCCcccccCCC
Confidence 45799999873 223458999999999999999999999999988764
No 38
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.63 E-value=3.3e-05 Score=83.80 Aligned_cols=50 Identities=26% Similarity=0.626 Sum_probs=39.2
Q ss_pred CCCCCCCcccccccccCCCeeEecCCCCccCHhhHHHHHhc---CCCCCCCcccccc
Q 001016 1113 KGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS---HYICPICSKSLGD 1166 (1190)
Q Consensus 1113 ~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~---~~~CPiCrk~l~~ 1166 (1190)
.+..-+|.||||. ..++| +..|||+|+..||-+|+.. +..||+|+..|..
T Consensus 44 ~~~~FdCNICLd~---akdPV-vTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~ 96 (230)
T KOG0823|consen 44 DGGFFDCNICLDL---AKDPV-VTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSI 96 (230)
T ss_pred CCCceeeeeeccc---cCCCE-EeecccceehHHHHHHHhhcCCCeeCCcccccccc
Confidence 4567899999986 44555 4569999999999999864 3558999987764
No 39
>COG2846 Regulator of cell morphogenesis and NO signaling [Cell division and chromosome partitioning]
Probab=97.59 E-value=0.00064 Score=72.39 Aligned_cols=132 Identities=18% Similarity=0.239 Sum_probs=109.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcc-CCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHHHh----hhhHHHHHH
Q 001016 45 LIFLFFHKAIKSELDVLHRAAMAFAT-NLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIR----VKNIARTYS 119 (1190)
Q Consensus 45 ~~~~~~HkAlR~eL~~l~~~a~~~~~-~~gd~~~~~~l~~r~~~L~~~~~~H~~aEDevI~PaLd~R----v~~v~~~~~ 119 (1190)
.|..-+|.-.|.+|..|..+|..|.. -.+.+.-.+.|.+-+.-|..-+..|-.-|++++||.+..= +.+....|+
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 1145567888999999999999999999999999999743 256889999
Q ss_pred hhhhhHHHHHHHHHHHHHhhhcCch--hHHHHHHHHHHHHHHHHHHhHHHHHHHhhhhH
Q 001016 120 LEHEGESVLFDQLFELLNSSMRNEE--SYRRELASCTGALQTSISQHMSKEEEQVFPLL 176 (1190)
Q Consensus 120 ~EH~~~~~lf~~l~~~l~~~~~~~~--~~~~eLa~~l~~l~~~l~qHm~~EE~~v~PLl 176 (1190)
.||+++..+++.+.+..+..+-..+ ..++.|=.-+.++.+.+.+|++-|---+||=+
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 55566666666666699999999988888754
No 40
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.58 E-value=2.3e-05 Score=91.59 Aligned_cols=51 Identities=25% Similarity=0.616 Sum_probs=38.8
Q ss_pred CCCCcccccccc----c---------CCCeeEecCCCCccCHhhHHHHHh-cCCCCCCCcccccc
Q 001016 1116 ETNCPICCDFLF----T---------SSATVRALPCGHFMHSDCFQAYTC-SHYICPICSKSLGD 1166 (1190)
Q Consensus 1116 ~~~CpICle~lf----~---------s~~~v~~LpCgH~fH~~Ci~~wl~-~~~~CPiCrk~l~~ 1166 (1190)
..+|+|||.++- + -...++..||.|.||..|+.+|+. .+..||+||.++..
T Consensus 571 t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLPp 635 (636)
T KOG0828|consen 571 TNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLPP 635 (636)
T ss_pred cccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCCCC
Confidence 467888887651 1 111355669999999999999998 56799999998864
No 41
>COG3945 Uncharacterized conserved protein [Function unknown]
Probab=97.48 E-value=0.0012 Score=69.40 Aligned_cols=139 Identities=18% Similarity=0.235 Sum_probs=109.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHhhccCCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHHHhh----hhHHHHHH
Q 001016 44 ILIFLFFHKAIKSELDVLHRAAMAFATNLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIRV----KNIARTYS 119 (1190)
Q Consensus 44 i~~~~~~HkAlR~eL~~l~~~a~~~~~~~gd~~~~~~l~~r~~~L~~~~~~H~~aEDevI~PaLd~Rv----~~v~~~~~ 119 (1190)
|..|+==|+-|-|-|.-|....--+..+-=|.+++..+++-++-+.+ ++||.-|+.++||-+..+. ++....|.
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 5688999999999999886 57899999
Q ss_pred hhhhhHHHHHHHHHHHHHhhhcCch----hHHHHHHHHHHHHHHHHHHhHHHHHHHhhhhHhhcCCHHHHHHHH
Q 001016 120 LEHEGESVLFDQLFELLNSSMRNEE----SYRRELASCTGALQTSISQHMSKEEEQVFPLLIEKFSFEEQASLV 189 (1190)
Q Consensus 120 ~EH~~~~~lf~~l~~~l~~~~~~~~----~~~~eLa~~l~~l~~~l~qHm~~EE~~v~PLl~~~fS~~E~a~L~ 189 (1190)
-||..--.++..+.+.+.+|.-.++ .+...+++.+. .+.+|.++|+..+||.+.+.||.+ |..+.
T Consensus 88 ~EH~~~R~i~r~lee~~~~~kngd~~~~~~~i~~A~~y~~----likrHIdkEdnvlfp~a~~~~s~e-~~~v~ 156 (189)
T COG3945 88 VEHGEGRYIIRDLEEAYERLKNGDEDSKDDVIDYAVAYLN----LIKRHIDKEDNVLFPFAESTLSEE-LNEVN 156 (189)
T ss_pred hhhhhHHHHHHHHHHHHHHHHccccchHHHHHHHHHHHHH----HHHHHHhhhhhHHHHHHHHHHHHH-HHHHH
Confidence 9999999999999999999975544 45555555665 999999999999999999999999 55543
No 42
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=97.42 E-value=5.4e-05 Score=88.13 Aligned_cols=48 Identities=23% Similarity=0.679 Sum_probs=42.5
Q ss_pred CCCCcccccccccCCCeeEecCCCCccCHhhHHHHHhcCCCCCCCccccc
Q 001016 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1165 (1190)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrk~l~ 1165 (1190)
--+||||||.|-.+...+....|.|.||-.|+..| ...+||+||....
T Consensus 175 LPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w--~~~scpvcR~~q~ 222 (493)
T KOG0804|consen 175 LPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKW--WDSSCPVCRYCQS 222 (493)
T ss_pred CCCcchhHhhcCccccceeeeecccccchHHHhhc--ccCcChhhhhhcC
Confidence 46899999999888888888899999999999999 5678999997765
No 43
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.42 E-value=8.6e-05 Score=87.36 Aligned_cols=48 Identities=27% Similarity=0.613 Sum_probs=40.3
Q ss_pred CCCCCcccccccccCCCeeEecCCCCccCHhhHHHHHhcCCCCCCCcccccc
Q 001016 1115 LETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1166 (1190)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrk~l~~ 1166 (1190)
....|+||++. |.. + ++++|||.|+..||..|+.....||+|+..+..
T Consensus 25 ~~l~C~IC~d~-~~~--P-vitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~~ 72 (397)
T TIGR00599 25 TSLRCHICKDF-FDV--P-VLTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQE 72 (397)
T ss_pred cccCCCcCchh-hhC--c-cCCCCCCchhHHHHHHHHhCCCCCCCCCCcccc
Confidence 35789999998 432 3 358999999999999999888899999998864
No 44
>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=97.41 E-value=0.00011 Score=83.44 Aligned_cols=51 Identities=22% Similarity=0.602 Sum_probs=39.4
Q ss_pred CCCCcccccccccCCC-eeEecCCCCccCHhhHHH-HHhcCCCCCCCcccccc
Q 001016 1116 ETNCPICCDFLFTSSA-TVRALPCGHFMHSDCFQA-YTCSHYICPICSKSLGD 1166 (1190)
Q Consensus 1116 ~~~CpICle~lf~s~~-~v~~LpCgH~fH~~Ci~~-wl~~~~~CPiCrk~l~~ 1166 (1190)
+..||||+.+.+.+.. .+.+.+|||.|+.+|++. |......||.|++++..
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 4689999997655544 233348999999999999 45666789999988754
No 45
>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class
Probab=97.30 E-value=0.00016 Score=61.36 Aligned_cols=42 Identities=26% Similarity=0.736 Sum_probs=32.6
Q ss_pred CCcccccccccCCCeeEecCCC-----CccCHhhHHHHHhc--CCCCCCCc
Q 001016 1118 NCPICCDFLFTSSATVRALPCG-----HFMHSDCFQAYTCS--HYICPICS 1161 (1190)
Q Consensus 1118 ~CpICle~lf~s~~~v~~LpCg-----H~fH~~Ci~~wl~~--~~~CPiCr 1161 (1190)
.|-||++. ...+...+.||. |++|..|+.+|+.. +.+||+|+
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 38999983 334445678995 99999999999854 45899995
No 46
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.23 E-value=0.00016 Score=85.90 Aligned_cols=49 Identities=33% Similarity=0.744 Sum_probs=37.2
Q ss_pred CCCCCCcccccccccCCCeeEecCCCCccCHhhHHHHHhc-----CCCCCCCcccccc
Q 001016 1114 GLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS-----HYICPICSKSLGD 1166 (1190)
Q Consensus 1114 ~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~-----~~~CPiCrk~l~~ 1166 (1190)
+++..||||+++ ...+++ +.|||.|+-.||-+|+.. ...||+|+..|.-
T Consensus 184 ~t~~~CPICL~~---~~~p~~-t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~ 237 (513)
T KOG2164|consen 184 STDMQCPICLEP---PSVPVR-TNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITL 237 (513)
T ss_pred CcCCcCCcccCC---CCcccc-cccCceeeHHHHHHHHhhhcccCCccCCchhhhccc
Confidence 348899999987 223333 459999999999987643 3669999988864
No 47
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.09 E-value=0.00013 Score=80.11 Aligned_cols=50 Identities=22% Similarity=0.643 Sum_probs=40.0
Q ss_pred CCCCcccccccccCC------CeeEecCCCCccCHhhHHHH--HhcCCCCCCCccccc
Q 001016 1116 ETNCPICCDFLFTSS------ATVRALPCGHFMHSDCFQAY--TCSHYICPICSKSLG 1165 (1190)
Q Consensus 1116 ~~~CpICle~lf~s~------~~v~~LpCgH~fH~~Ci~~w--l~~~~~CPiCrk~l~ 1165 (1190)
++.|+||...+..+. ++.-.|.|+|.||..||+.| +..+.+||.|++.+.
T Consensus 224 d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVd 281 (328)
T KOG1734|consen 224 DSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVD 281 (328)
T ss_pred cchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhh
Confidence 567889988765443 24567999999999999999 467899999998764
No 48
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=97.06 E-value=0.00017 Score=65.62 Aligned_cols=50 Identities=26% Similarity=0.600 Sum_probs=23.8
Q ss_pred CCCCcccccccccCCC-eeEe---cCCCCccCHhhHHHHHhc-----------CCCCCCCccccc
Q 001016 1116 ETNCPICCDFLFTSSA-TVRA---LPCGHFMHSDCFQAYTCS-----------HYICPICSKSLG 1165 (1190)
Q Consensus 1116 ~~~CpICle~lf~s~~-~v~~---LpCgH~fH~~Ci~~wl~~-----------~~~CPiCrk~l~ 1165 (1190)
+..|+||.+++.+.++ +..+ -.|+..||..|+.+|+.. ..+||.|+++|.
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 4679999998653332 3333 279999999999999752 135999999874
No 49
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.03 E-value=0.00024 Score=81.42 Aligned_cols=48 Identities=27% Similarity=0.643 Sum_probs=38.3
Q ss_pred CCCCcccccccccCCCeeEec-CCCCccCHhhHHHHHhc---CCCCCCCcccc
Q 001016 1116 ETNCPICCDFLFTSSATVRAL-PCGHFMHSDCFQAYTCS---HYICPICSKSL 1164 (1190)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~L-pCgH~fH~~Ci~~wl~~---~~~CPiCrk~l 1164 (1190)
...|.|| ++++.....+... .|||.||..|+.+|... +..||+|+-.+
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 3569999 6668887777766 49999999999999864 35799999333
No 50
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.00 E-value=0.00016 Score=88.17 Aligned_cols=53 Identities=17% Similarity=0.496 Sum_probs=43.4
Q ss_pred CCCCCCCcccccccccCCCeeEecCCCCccCHhhHHHHHhcCCCCCCCcccccc
Q 001016 1113 KGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1166 (1190)
Q Consensus 1113 ~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrk~l~~ 1166 (1190)
......||+|+.. +.........+|+|+||.+||..|.+.-.+||+||+.+..
T Consensus 120 ~~~~~~CP~Ci~s-~~DqL~~~~k~c~H~FC~~Ci~sWsR~aqTCPiDR~EF~~ 172 (1134)
T KOG0825|consen 120 THVENQCPNCLKS-CNDQLEESEKHTAHYFCEECVGSWSRCAQTCPVDRGEFGE 172 (1134)
T ss_pred hhhhhhhhHHHHH-HHHHhhccccccccccHHHHhhhhhhhcccCchhhhhhhe
Confidence 3456789999987 4444444557999999999999999999999999987764
No 51
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=97.00 E-value=0.0003 Score=89.23 Aligned_cols=111 Identities=27% Similarity=0.569 Sum_probs=73.7
Q ss_pred eccccCcc-----ccCCCCCCCCCCCCCccceEeccccccccCCCCcccCCCCCccccCCCCCccccccCCccccccccc
Q 001016 1031 MCMRCLKV-----QPVGPVCTTLSCSGLSMAKYYCGICKFFDDERVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLAKKL 1105 (1190)
Q Consensus 1031 ~C~~C~~~-----q~~~~~C~~~~Cc~~~fa~Y~C~~C~l~dd~k~~yHC~~CgiCrvg~gl~~~~fHC~~C~~C~s~~l 1105 (1190)
-|.+|+.. |.++..|....| ...|+--|.+-+-... .|| |- +|--||.-|=.|-.-.
T Consensus 3419 aCRFCGs~~~tE~sav~~vCs~aDC--~eYAK~ACs~~H~C~H--------~CG----Gv---kNEE~CLPCl~Cdks~- 3480 (3738)
T KOG1428|consen 3419 ACRFCGSRSGTELSAVGSVCSDADC--QEYAKIACSKTHPCGH--------PCG----GV---KNEEHCLPCLHCDKSA- 3480 (3738)
T ss_pred HhhhccCCCCcchhcccCccccHHH--HHHHHHHHhccCcCCC--------ccc----Cc---cchhhcccccccChhh-
Confidence 68888754 667888988777 5677777765332211 233 11 2556666665553211
Q ss_pred cccccccCCCCCCCcccccccccCCCeeEecCCCCccCHhhHHHHHhc----------CCCCCCCccccc
Q 001016 1106 VDHKCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS----------HYICPICSKSLG 1165 (1190)
Q Consensus 1106 ~~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~----------~~~CPiCrk~l~ 1165 (1190)
.....++.|.||.-+ --+-.+.+.|.|||.||.+|...-+.. -..||+|+..|.
T Consensus 3481 -----tkQD~DDmCmICFTE-~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~In 3544 (3738)
T KOG1428|consen 3481 -----TKQDADDMCMICFTE-ALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKIN 3544 (3738)
T ss_pred -----hhcccCceEEEEehh-hhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchhh
Confidence 123457889999876 445668889999999999998765432 246999998875
No 52
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.89 E-value=0.00045 Score=76.36 Aligned_cols=48 Identities=25% Similarity=0.652 Sum_probs=39.4
Q ss_pred CCCCCcccccccccCCCeeEecCCCCccCHhhHHH-HHhcCCC-CCCCcccccc
Q 001016 1115 LETNCPICCDFLFTSSATVRALPCGHFMHSDCFQA-YTCSHYI-CPICSKSLGD 1166 (1190)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~-wl~~~~~-CPiCrk~l~~ 1166 (1190)
.+..|+||+|... .....||||.|+..||-. |++..+- ||+||.-+..
T Consensus 214 ~d~kC~lC~e~~~----~ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~p 263 (271)
T COG5574 214 ADYKCFLCLEEPE----VPSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVYP 263 (271)
T ss_pred cccceeeeecccC----CcccccccchhhHHHHHHHHHhhccccCchhhhhccc
Confidence 3677999998743 345589999999999998 9988877 9999987654
No 53
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=96.86 E-value=0.00041 Score=78.35 Aligned_cols=58 Identities=21% Similarity=0.523 Sum_probs=44.9
Q ss_pred CCCcccccccccCCCeeEecCCCCccCHhhHHHHHhcCCCCCCCcccccchh-HHHHhhhccc
Q 001016 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGDMA-LYEGFCSLFS 1178 (1190)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrk~l~~m~-~~~~~lD~~~ 1178 (1190)
..|-||.|+ |. ..++.||||.|+.-||..++..+..||.|+.++.+-. +--++||+++
T Consensus 24 LRC~IC~ey-f~---ip~itpCsHtfCSlCIR~~L~~~p~CP~C~~~~~Es~Lr~n~il~Eiv 82 (442)
T KOG0287|consen 24 LRCGICFEY-FN---IPMITPCSHTFCSLCIRKFLSYKPQCPTCCVTVTESDLRNNRILDEIV 82 (442)
T ss_pred HHHhHHHHH-hc---CceeccccchHHHHHHHHHhccCCCCCceecccchhhhhhhhHHHHHH
Confidence 459999999 43 2356799999999999999999999999999886422 2234555554
No 54
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.83 E-value=0.00049 Score=74.99 Aligned_cols=44 Identities=34% Similarity=0.851 Sum_probs=37.4
Q ss_pred CCCCCcccccccccCCCeeEecCCCCccCHhhHHHHHhcCCCCCCCcc
Q 001016 1115 LETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSK 1162 (1190)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrk 1162 (1190)
....||||+++ |... +.+||||.|...|+..+......||.||.
T Consensus 12 ~~~~C~iC~~~-~~~p---~~l~C~H~~c~~C~~~~~~~~~~Cp~cr~ 55 (386)
T KOG2177|consen 12 EELTCPICLEY-FREP---VLLPCGHNFCRACLTRSWEGPLSCPVCRP 55 (386)
T ss_pred ccccChhhHHH-hhcC---ccccccchHhHHHHHHhcCCCcCCcccCC
Confidence 46789999999 4433 78999999999999998777788999993
No 55
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.74 E-value=0.00039 Score=59.67 Aligned_cols=53 Identities=26% Similarity=0.580 Sum_probs=38.9
Q ss_pred CCCCcccccccccCCCeeEecCCCCc-cCHhhH-HHHHhcCCCCCCCcccccchhHHHH
Q 001016 1116 ETNCPICCDFLFTSSATVRALPCGHF-MHSDCF-QAYTCSHYICPICSKSLGDMALYEG 1172 (1190)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCgH~-fH~~Ci-~~wl~~~~~CPiCrk~l~~m~~~~~ 1172 (1190)
.+.|.||+|. ..+. +.--|||+ +.-.|- ..|...+.+||+||.++.+.-+.|+
T Consensus 7 ~dECTICye~---pvds-VlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~dvIkTY~ 61 (62)
T KOG4172|consen 7 SDECTICYEH---PVDS-VLYTCGHMCMCYACGLRLKKALHGCCPICRAPIKDVIKTYR 61 (62)
T ss_pred ccceeeeccC---cchH-HHHHcchHHhHHHHHHHHHHccCCcCcchhhHHHHHHHhhc
Confidence 4789999986 2222 23479998 788884 4566689999999999988665543
No 56
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.57 E-value=0.0013 Score=75.49 Aligned_cols=51 Identities=29% Similarity=0.671 Sum_probs=42.2
Q ss_pred cCCCCCCCcccccccccCCCeeEecCCCCc-cCHhhHHHHHhcCCCCCCCcccccc
Q 001016 1112 EKGLETNCPICCDFLFTSSATVRALPCGHF-MHSDCFQAYTCSHYICPICSKSLGD 1166 (1190)
Q Consensus 1112 e~~~~~~CpICle~lf~s~~~v~~LpCgH~-fH~~Ci~~wl~~~~~CPiCrk~l~~ 1166 (1190)
++.....|.||+.+ .....+|||-|+ +++.|.+...-+...|||||+.+..
T Consensus 286 ~~~~gkeCVIClse----~rdt~vLPCRHLCLCs~Ca~~Lr~q~n~CPICRqpi~~ 337 (349)
T KOG4265|consen 286 ESESGKECVICLSE----SRDTVVLPCRHLCLCSGCAKSLRYQTNNCPICRQPIEE 337 (349)
T ss_pred cccCCCeeEEEecC----CcceEEecchhhehhHhHHHHHHHhhcCCCccccchHh
Confidence 33446789999976 345788999998 9999999988788899999998864
No 57
>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=96.39 E-value=0.0019 Score=59.00 Aligned_cols=47 Identities=21% Similarity=0.378 Sum_probs=35.2
Q ss_pred CCCCcccccccccCCCeeEecCCCCccCHhhHHHHHhc-CCCCCCCcccccc
Q 001016 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS-HYICPICSKSLGD 1166 (1190)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~-~~~CPiCrk~l~~ 1166 (1190)
+-.|||+.+-|. ++ +++|+||+|-..||..|+.. +.+||+|+..+..
T Consensus 4 ~f~CpIt~~lM~---dP-Vi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~ 51 (73)
T PF04564_consen 4 EFLCPITGELMR---DP-VILPSGHTYERSAIERWLEQNGGTDPFTRQPLSE 51 (73)
T ss_dssp GGB-TTTSSB-S---SE-EEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SG
T ss_pred ccCCcCcCcHhh---Cc-eeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCc
Confidence 456999998743 33 46899999999999999988 8999999988864
No 58
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=96.17 E-value=0.0013 Score=75.67 Aligned_cols=60 Identities=32% Similarity=0.671 Sum_probs=47.4
Q ss_pred cccccCCCCCCCcccccccccCCCeeEecCCCCccCHhhHHHHHhcC--CCCCCCcccccchh
Q 001016 1108 HKCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSH--YICPICSKSLGDMA 1168 (1190)
Q Consensus 1108 H~C~e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~--~~CPiCrk~l~~m~ 1168 (1190)
|.|.+ .++-.|-.|.|.+-...+....|||.|.||..|+.+++.++ .+||-||+-...|+
T Consensus 358 ~~~~~-e~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~CrklrSs~~ 419 (518)
T KOG1941|consen 358 HECVE-ETELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRKLRSSMK 419 (518)
T ss_pred HHHHH-HHhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHHHHhhcc
Confidence 44543 35788999999876667778889999999999999998665 67999996655444
No 59
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=96.13 E-value=0.00045 Score=77.63 Aligned_cols=133 Identities=17% Similarity=0.114 Sum_probs=97.8
Q ss_pred HHHHHhhhcccccccccccccccccccCcccchhhHHHHHHHHHHHHHHHhhhhhhhhccccccccccccccccccchhh
Q 001016 690 GLYRAHSNAEDDIVFPALESKETLSNVSHSYTLDHKQEEKLFEDISSALSELTELHECLSTDLTGDLTRNSLESCDQNET 769 (1190)
Q Consensus 690 ~v~~~HS~AEDeivfPaLe~k~~~~nvs~s~~~DH~~ee~lfe~i~~~L~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 769 (1190)
.++..|+.++|++-||+..+.....+..+++..||.-.=.+.++.+.... . .+
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 78999999999999999999887777777777777666555555422110 0 12
Q ss_pred HhhHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhcCCHHHHHHHHHHHHhccCHHHHHHhHhHHhhcCCHHHHHH
Q 001016 770 VRKYNEKATELQGMCKSIRVTLDQHVFREELELWPLFDRHFSVEEQDKIVGRIIGTTGAEVLQSMLPWVTSALTQEEQNT 849 (1190)
Q Consensus 770 ~~~~~e~~~kL~~~~~sl~~~L~~Hl~~EE~Ev~PL~~k~fS~eeQ~~lv~~~l~~~p~~~Lq~~LPWl~~~Lte~E~~~ 849 (1190)
..++.-++.+.....++..+.+..|.. +.+.|=++.+.|.+++| +++.-+.+.+--+.++. |||.-.....+..+
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 223334555555666666688888988 99999999999999999 88888877665544443 99998887777776
Q ss_pred HHHHh
Q 001016 850 MMDTW 854 (1190)
Q Consensus 850 ml~~~ 854 (1190)
-|.+|
T Consensus 145 ~~~~~ 149 (276)
T KOG1940|consen 145 YLSNW 149 (276)
T ss_pred hcccc
Confidence 66665
No 60
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=96.10 E-value=0.0028 Score=70.53 Aligned_cols=46 Identities=24% Similarity=0.521 Sum_probs=37.9
Q ss_pred CCCCcccccccccCCCeeEecCCCCccCHhhHHHHHhcCCCCCCCccccc
Q 001016 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1165 (1190)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrk~l~ 1165 (1190)
...|-||.+++ . .....+|||.|+.-||..++..+..||+||...-
T Consensus 25 ~lrC~IC~~~i-~---ip~~TtCgHtFCslCIR~hL~~qp~CP~Cr~~~~ 70 (391)
T COG5432 25 MLRCRICDCRI-S---IPCETTCGHTFCSLCIRRHLGTQPFCPVCREDPC 70 (391)
T ss_pred HHHhhhhhhee-e---cceecccccchhHHHHHHHhcCCCCCccccccHH
Confidence 45699999984 2 1234699999999999999999999999997653
No 61
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.04 E-value=0.0038 Score=72.50 Aligned_cols=49 Identities=35% Similarity=0.819 Sum_probs=38.8
Q ss_pred CCCCcccccccccCCC-eeEecCCCCccCHhhHHHHHhc--CCCCCCCcccc
Q 001016 1116 ETNCPICCDFLFTSSA-TVRALPCGHFMHSDCFQAYTCS--HYICPICSKSL 1164 (1190)
Q Consensus 1116 ~~~CpICle~lf~s~~-~v~~LpCgH~fH~~Ci~~wl~~--~~~CPiCrk~l 1164 (1190)
..+||||++.+-..++ .+..+.|||.|-.+||+.|+-+ ...||.|.-..
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 4689999998655555 4556899999999999999953 35699998543
No 62
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.93 E-value=0.0049 Score=71.63 Aligned_cols=54 Identities=20% Similarity=0.525 Sum_probs=40.3
Q ss_pred cCCCCCCCcccccccccCC---CeeEe-cCCCCccCHhhHHHHH--hc-----CCCCCCCccccc
Q 001016 1112 EKGLETNCPICCDFLFTSS---ATVRA-LPCGHFMHSDCFQAYT--CS-----HYICPICSKSLG 1165 (1190)
Q Consensus 1112 e~~~~~~CpICle~lf~s~---~~v~~-LpCgH~fH~~Ci~~wl--~~-----~~~CPiCrk~l~ 1165 (1190)
.++.+..|-||+|.+.... ....+ .+|.|.|...||..|- .+ ...||.||....
T Consensus 157 ~~s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~ 221 (344)
T KOG1039|consen 157 QKSSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSS 221 (344)
T ss_pred CccccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccc
Confidence 3466889999999865443 11233 4699999999999997 34 577999997764
No 63
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=95.77 E-value=0.0031 Score=56.33 Aligned_cols=56 Identities=23% Similarity=0.438 Sum_probs=27.1
Q ss_pred CCCcccccccccCCCeeEecCCCCccCHhhHHHHHhcCCCCCCCcccccchh-HHHHhhhcc
Q 001016 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGDMA-LYEGFCSLF 1177 (1190)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrk~l~~m~-~~~~~lD~~ 1177 (1190)
..|++|.+.| ++++....|.|.|.+.|+..-+. +.||+|+.+.-.-+ +..+.||.+
T Consensus 8 LrCs~C~~~l---~~pv~l~~CeH~fCs~Ci~~~~~--~~CPvC~~Paw~qD~~~NrqLd~~ 64 (65)
T PF14835_consen 8 LRCSICFDIL---KEPVCLGGCEHIFCSSCIRDCIG--SECPVCHTPAWIQDIQINRQLDSM 64 (65)
T ss_dssp TS-SSS-S-----SS-B---SSS--B-TTTGGGGTT--TB-SSS--B-S-SS----HHHHHH
T ss_pred cCCcHHHHHh---cCCceeccCccHHHHHHhHHhcC--CCCCCcCChHHHHHHHhhhhhhcc
Confidence 4599999874 35677789999999999987544 55999999884322 233666654
No 64
>COG2461 Uncharacterized conserved protein [Function unknown]
Probab=95.58 E-value=0.076 Score=62.20 Aligned_cols=132 Identities=14% Similarity=0.208 Sum_probs=103.3
Q ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHhhcccCCcccH-HHHHHHHHHHHHHHHhhhhccccchhhhhhhhh------hhH
Q 001016 291 SCPIDEIMLWHNAIKRELNDIAEAARKIQLSGDFSDL-SAFNKRLQFIAEVCIFHSIAEDKVIFPAVDVEL------SFA 363 (1190)
Q Consensus 291 ~~PId~l~~~HkALRrEL~~L~~~a~~~~~~gd~~~L-~~L~~r~~fl~~vl~~Hs~aEDevlFPaL~~r~------~me 363 (1190)
-+|+..|...-++||..|+.+.+. .. + ..+ ..+...+.++..+=+ |=.++...|||.++.|- .|-
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 555666666666666 88999999999999885 889
Q ss_pred HhHHHHHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhhCCHHHHHHHHHhH
Q 001016 364 QEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPLARRHFSPKRQRELLYQS 441 (1190)
Q Consensus 364 ~EH~~ie~l~e~l~~ll~~l~~~~~~~~~~~~~~eLa~~l~~L~~~L~~Hf~~EE~qvfPLl~~~fS~eEq~~L~~~~ 441 (1190)
-.|+++-..|..+...+... + ..++......+.+.+..=+.+||+.+.|.+-..||..||.++-.+.
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 99999988888888887621 1 3456667777888899999999999999999999999999987654
No 65
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=95.49 E-value=0.0045 Score=77.36 Aligned_cols=53 Identities=23% Similarity=0.545 Sum_probs=37.9
Q ss_pred CCCCCCCcccccccccCCC--ee-EecCCCCccCHhhHHHHHhc--CCCCCCCccccc
Q 001016 1113 KGLETNCPICCDFLFTSSA--TV-RALPCGHFMHSDCFQAYTCS--HYICPICSKSLG 1165 (1190)
Q Consensus 1113 ~~~~~~CpICle~lf~s~~--~v-~~LpCgH~fH~~Ci~~wl~~--~~~CPiCrk~l~ 1165 (1190)
-++...||||..-+.--.. +. +--.|.|.||..|+.+|.+. +.+||+||.++.
T Consensus 1466 fsG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219 1466 FSGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred cCCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence 4567889999876531111 11 22458899999999999754 688999997653
No 66
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.85 E-value=0.021 Score=63.71 Aligned_cols=52 Identities=21% Similarity=0.624 Sum_probs=42.9
Q ss_pred CCCCCCcccccccccCCCeeEecCCCCccCHhhHHHHHh--cCCCCCCCcccccchh
Q 001016 1114 GLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC--SHYICPICSKSLGDMA 1168 (1190)
Q Consensus 1114 ~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~--~~~~CPiCrk~l~~m~ 1168 (1190)
....+||+|.++ +.-+....+|||.|+--|+..=.. -..+||.|..++..|.
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 346789999987 666788899999999999987543 3589999999988665
No 67
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=94.50 E-value=0.011 Score=68.30 Aligned_cols=54 Identities=26% Similarity=0.674 Sum_probs=43.7
Q ss_pred ccccCCCCCCCcccccccccCCCeeEecCCCCccCHhhHHHHHh-c-CCCCCCCcccccc
Q 001016 1109 KCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC-S-HYICPICSKSLGD 1166 (1190)
Q Consensus 1109 ~C~e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~-~-~~~CPiCrk~l~~ 1166 (1190)
-|.-.++-.-|-||-|. .+.+++=||||.++..|+..|-. . ..+||.||-.|--
T Consensus 362 YceMgsTFeLCKICaen----dKdvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKG 417 (563)
T KOG1785|consen 362 YCEMGSTFELCKICAEN----DKDVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIKG 417 (563)
T ss_pred HHHccchHHHHHHhhcc----CCCcccccccchHHHHHHHhhcccCCCCCCCceeeEecc
Confidence 35556677889999874 55688889999999999999963 2 6889999988754
No 68
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=94.40 E-value=0.012 Score=66.17 Aligned_cols=54 Identities=28% Similarity=0.663 Sum_probs=44.0
Q ss_pred cCCCCCCCcccccccccCCCeeEecCCCCccCHhhHHHHHh-----------------------cCCCCCCCcccccc
Q 001016 1112 EKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC-----------------------SHYICPICSKSLGD 1166 (1190)
Q Consensus 1112 e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~-----------------------~~~~CPiCrk~l~~ 1166 (1190)
.+--...|.|||-- |.++....+.+|-|+||..|+..|+. ....||+||-.|.+
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 34557899999987 77778788999999999999988863 12459999998875
No 69
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.32 E-value=0.022 Score=64.37 Aligned_cols=49 Identities=18% Similarity=0.432 Sum_probs=38.3
Q ss_pred CCCCCCcccccccccCCCeeEecCCCCccCHhhHHHH-HhcCCCCCCCcccccc
Q 001016 1114 GLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAY-TCSHYICPICSKSLGD 1166 (1190)
Q Consensus 1114 ~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~w-l~~~~~CPiCrk~l~~ 1166 (1190)
.....|+||+.. ...+ ..|+|+|.|...||+.- .....+||+||.++..
T Consensus 5 ~~~~eC~IC~nt---~n~P-v~l~C~HkFCyiCiKGsy~ndk~~CavCR~pids 54 (324)
T KOG0824|consen 5 TKKKECLICYNT---GNCP-VNLYCFHKFCYICIKGSYKNDKKTCAVCRFPIDS 54 (324)
T ss_pred ccCCcceeeecc---CCcC-ccccccchhhhhhhcchhhcCCCCCceecCCCCc
Confidence 456789999976 2333 56999999999999874 4456779999999863
No 70
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=94.15 E-value=0.015 Score=72.64 Aligned_cols=46 Identities=24% Similarity=0.608 Sum_probs=36.9
Q ss_pred CCCcccccccccCCCeeEecCCCCccCHhhHHHHHh-cCCCCCCCcccccc
Q 001016 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC-SHYICPICSKSLGD 1166 (1190)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~-~~~~CPiCrk~l~~ 1166 (1190)
..||+|-.. ...+++..|||.|+..|+..-+. ...+||.|...++.
T Consensus 644 LkCs~Cn~R----~Kd~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFga 690 (698)
T KOG0978|consen 644 LKCSVCNTR----WKDAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGA 690 (698)
T ss_pred eeCCCccCc----hhhHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCc
Confidence 468999643 34566789999999999998764 46889999999884
No 71
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.32 E-value=0.013 Score=67.32 Aligned_cols=48 Identities=31% Similarity=0.605 Sum_probs=38.2
Q ss_pred CCCCcccccccccCCCeeEecCCCCccCHhhHHHHH-hcCCCCCCCcccccc
Q 001016 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYT-CSHYICPICSKSLGD 1166 (1190)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl-~~~~~CPiCrk~l~~ 1166 (1190)
+..|||||+-|-. .....-|+|-|+.+||..-+ ..+..||.||+.+..
T Consensus 43 ~v~c~icl~llk~---tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~S 91 (381)
T KOG0311|consen 43 QVICPICLSLLKK---TMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVS 91 (381)
T ss_pred hhccHHHHHHHHh---hcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhccc
Confidence 6789999987532 34557899999999997655 467899999999873
No 72
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=93.29 E-value=0.054 Score=47.64 Aligned_cols=42 Identities=26% Similarity=0.646 Sum_probs=29.5
Q ss_pred CCCCCcccccccccCCCeeEecCCCCccCHhhHHHHHh--cCCCCCC
Q 001016 1115 LETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC--SHYICPI 1159 (1190)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~--~~~~CPi 1159 (1190)
....|||.+.. | .++|+...|||.|-++.|.+|++ ....||+
T Consensus 10 ~~~~CPiT~~~-~--~~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv 53 (57)
T PF11789_consen 10 ISLKCPITLQP-F--EDPVKSKKCGHTFEKEAILQYIQRNGSKRCPV 53 (57)
T ss_dssp --SB-TTTSSB----SSEEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred eccCCCCcCCh-h--hCCcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence 45789999988 3 35888899999999999999993 4567998
No 73
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=93.27 E-value=0.023 Score=62.42 Aligned_cols=108 Identities=29% Similarity=0.619 Sum_probs=66.9
Q ss_pred CCccccccccccccccCC--------------------cccCcccccccCCCCCCccccceeeccccCccccCCCCCCCC
Q 001016 989 GCEHYKRNCKLRAACCGK--------------------LFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVGPVCTTL 1048 (1190)
Q Consensus 989 gC~HY~r~ckl~~pcC~k--------------------~y~Cr~CHde~~dH~~~r~~~~~~~C~~C~~~q~~~~~C~~~ 1048 (1190)
-|.|=- --|.+|||+| -|.|..|.....|--.-|. ..+.+|-.|...-.+
T Consensus 63 YCEhDF--~~LfaPcC~kC~EFiiGrVikamnnSwHp~CF~Cd~Cn~~Lad~gf~rn-qgr~LC~~Cn~k~Ka------- 132 (332)
T KOG2272|consen 63 YCEHDF--HVLFAPCCGKCGEFIIGRVIKAMNNSWHPACFRCDLCNKHLADQGFYRN-QGRALCRECNQKEKA------- 132 (332)
T ss_pred cccccc--hhhhchhhcccccchhhHHHHhhccccCcccchhHHHHHHHhhhhhHhh-cchHHhhhhhhhhcc-------
Confidence 476632 1377888876 3667777766666555554 347788888654322
Q ss_pred CCCCCccceEeccccc-cccCC-----CCcccCCCCCccccCCCCCccccccCCccccccccc----cccccccCCCCCC
Q 001016 1049 SCSGLSMAKYYCGICK-FFDDE-----RVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLAKKL----VDHKCREKGLETN 1118 (1190)
Q Consensus 1049 ~Cc~~~fa~Y~C~~C~-l~dd~-----k~~yHC~~CgiCrvg~gl~~~~fHC~~C~~C~s~~l----~~H~C~e~~~~~~ 1118 (1190)
.--|+|.|.+|+ +.|++ .++|| -.-|.|.+||.=+.... +.--|..--+..-
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 135799999998 46666 57777 25688888887664432 3333444444455
Q ss_pred Cccccc
Q 001016 1119 CPICCD 1124 (1190)
Q Consensus 1119 CpICle 1124 (1190)
||||..
T Consensus 195 ipiCga 200 (332)
T KOG2272|consen 195 IPICGA 200 (332)
T ss_pred Cccccc
Confidence 666543
No 74
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=92.66 E-value=0.086 Score=58.12 Aligned_cols=55 Identities=24% Similarity=0.492 Sum_probs=46.9
Q ss_pred ccCCCCCCCcccccccccCCCeeEec-CCCCccCHhhHHHHHhcCCCCCCCcccccc
Q 001016 1111 REKGLETNCPICCDFLFTSSATVRAL-PCGHFMHSDCFQAYTCSHYICPICSKSLGD 1166 (1190)
Q Consensus 1111 ~e~~~~~~CpICle~lf~s~~~v~~L-pCgH~fH~~Ci~~wl~~~~~CPiCrk~l~~ 1166 (1190)
+..+....||||.+. .++..+..+| ||||.+..+|++..++....||+|.+++-+
T Consensus 216 ~a~s~ryiCpvtrd~-LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkd 271 (303)
T KOG3039|consen 216 IAASKRYICPVTRDT-LTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKD 271 (303)
T ss_pred hhhccceecccchhh-hcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCcc
Confidence 344467889999999 4666667666 999999999999999999999999999875
No 75
>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=92.44 E-value=0.061 Score=51.65 Aligned_cols=38 Identities=26% Similarity=0.616 Sum_probs=29.9
Q ss_pred ccccCCCCCCCcccccccccCCCeeEecCCCCccCHhhHH
Q 001016 1109 KCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQ 1148 (1190)
Q Consensus 1109 ~C~e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~ 1148 (1190)
.++.-..+..|++|...|.. ....+.||||.||..|++
T Consensus 71 ~~v~i~~~~~C~vC~k~l~~--~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 71 RSVVITESTKCSVCGKPLGN--SVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred ceEEECCCCCccCcCCcCCC--ceEEEeCCCeEEeccccc
Confidence 34444567889999999654 467778999999999975
No 76
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=92.38 E-value=0.096 Score=44.58 Aligned_cols=46 Identities=22% Similarity=0.514 Sum_probs=24.0
Q ss_pred CcccccccccCCCeeEecCCCCccCHhhHHHHHh-cCCCCCCCcccc
Q 001016 1119 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC-SHYICPICSKSL 1164 (1190)
Q Consensus 1119 CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~-~~~~CPiCrk~l 1164 (1190)
||+|.+++...+....-=+||+-+...|+..-+. .+..||-||++.
T Consensus 1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y 47 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILENEGGRCPGCREPY 47 (48)
T ss_dssp -TTTS-B--CCCTT--SSTTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred CCCcccccccCCCccccCcCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence 8999999744444444447899999999888876 589999999863
No 77
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=91.86 E-value=0.095 Score=64.93 Aligned_cols=45 Identities=27% Similarity=0.597 Sum_probs=32.9
Q ss_pred CCCCCCCcccccccccCCCeeEecCCCCccCHhhHHHHHhcCCCCCC
Q 001016 1113 KGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPI 1159 (1190)
Q Consensus 1113 ~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPi 1159 (1190)
..-...|.||.-.+. +....-+.|||..|.+|..+|.+....||.
T Consensus 1025 ~~~~~~C~~C~l~V~--gss~~Cg~C~Hv~H~sc~~eWf~~gd~Cps 1069 (1081)
T KOG0309|consen 1025 KGFTFQCAICHLAVR--GSSNFCGTCGHVGHTSCMMEWFRTGDVCPS 1069 (1081)
T ss_pred ccceeeeeeEeeEee--ccchhhccccccccHHHHHHHHhcCCcCCC
Confidence 333455888865432 223445789999999999999999989984
No 78
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.51 E-value=0.12 Score=54.58 Aligned_cols=30 Identities=27% Similarity=0.723 Sum_probs=25.3
Q ss_pred cCCCCccCHhhHHHHHhc------C-----CCCCCCccccc
Q 001016 1136 LPCGHFMHSDCFQAYTCS------H-----YICPICSKSLG 1165 (1190)
Q Consensus 1136 LpCgH~fH~~Ci~~wl~~------~-----~~CPiCrk~l~ 1165 (1190)
..||--||.-|+..|++. + ..||.|.+++.
T Consensus 188 ~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~Pia 228 (234)
T KOG3268|consen 188 IQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIA 228 (234)
T ss_pred cccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcce
Confidence 579999999999999863 1 45999999884
No 79
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=91.33 E-value=0.12 Score=43.74 Aligned_cols=40 Identities=25% Similarity=0.706 Sum_probs=26.3
Q ss_pred CcccccccccCCCeeEecCCC-----CccCHhhHHHHHh--cCCCCCCC
Q 001016 1119 CPICCDFLFTSSATVRALPCG-----HFMHSDCFQAYTC--SHYICPIC 1160 (1190)
Q Consensus 1119 CpICle~lf~s~~~v~~LpCg-----H~fH~~Ci~~wl~--~~~~CPiC 1160 (1190)
|=||++.- +.. ...+.||+ -+.|..|+.+|+. .+.+|++|
T Consensus 1 CrIC~~~~-~~~-~~li~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C 47 (47)
T PF12906_consen 1 CRICLEGE-EED-EPLISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC 47 (47)
T ss_dssp ETTTTEE--SSS-S-EE-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred CeEeCCcC-CCC-CceecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence 67999872 222 24556886 4789999999985 56789998
No 80
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.31 E-value=0.15 Score=55.55 Aligned_cols=51 Identities=29% Similarity=0.668 Sum_probs=40.7
Q ss_pred CCCCCCcccccccccCCCeeEecCCCCccCHhhHHHHHh--------cCCCCCCCcccccc
Q 001016 1114 GLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC--------SHYICPICSKSLGD 1166 (1190)
Q Consensus 1114 ~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~--------~~~~CPiCrk~l~~ 1166 (1190)
....+|..|.-.| .+++ ...|-|=|.||..|+++|-. ..|.||-|...|..
T Consensus 48 DY~pNC~LC~t~L-a~gd-t~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFP 106 (299)
T KOG3970|consen 48 DYNPNCRLCNTPL-ASGD-TTRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFP 106 (299)
T ss_pred CCCCCCceeCCcc-ccCc-ceeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCC
Confidence 3467899999884 4444 35578999999999999963 26899999999874
No 81
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=91.10 E-value=0.086 Score=58.33 Aligned_cols=37 Identities=32% Similarity=0.703 Sum_probs=28.4
Q ss_pred ccCCCeeEecCCCCccCHhhHHHHHhcCCCCCCCccccc
Q 001016 1127 FTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1165 (1190)
Q Consensus 1127 f~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrk~l~ 1165 (1190)
+.+..+.....|+|+|+..|...- ....||+|++++-
T Consensus 12 ~~~~~~f~LTaC~HvfC~~C~k~~--~~~~C~lCkk~ir 48 (233)
T KOG4739|consen 12 FPSQDPFFLTACRHVFCEPCLKAS--SPDVCPLCKKSIR 48 (233)
T ss_pred cCCCCceeeeechhhhhhhhcccC--Cccccccccceee
Confidence 455566777899999999998553 2338999999974
No 82
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.60 E-value=0.053 Score=60.99 Aligned_cols=49 Identities=27% Similarity=0.558 Sum_probs=35.6
Q ss_pred CCCCcccccccccCCCeeEecCCCCcc-CHhhHHHHHhcCCCCCCCcccccchhHHHH
Q 001016 1116 ETNCPICCDFLFTSSATVRALPCGHFM-HSDCFQAYTCSHYICPICSKSLGDMALYEG 1172 (1190)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCgH~f-H~~Ci~~wl~~~~~CPiCrk~l~~m~~~~~ 1172 (1190)
..-|.||++- ......|+|||.- +..|-.. -..|||||+-|.....+|+
T Consensus 300 ~~LC~ICmDa----P~DCvfLeCGHmVtCt~CGkr----m~eCPICRqyi~rvvrif~ 349 (350)
T KOG4275|consen 300 RRLCAICMDA----PRDCVFLECGHMVTCTKCGKR----MNECPICRQYIVRVVRIFR 349 (350)
T ss_pred HHHHHHHhcC----CcceEEeecCcEEeehhhccc----cccCchHHHHHHHHHhhhc
Confidence 7889999975 3457889999973 3344322 2379999999887777765
No 83
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=90.09 E-value=0.15 Score=60.96 Aligned_cols=53 Identities=28% Similarity=0.666 Sum_probs=42.6
Q ss_pred CCCCCCcccccccccCCCeeEecCCCCccCHhhHHHHHhcCCCCCCCcccccchhH
Q 001016 1114 GLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGDMAL 1169 (1190)
Q Consensus 1114 ~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrk~l~~m~~ 1169 (1190)
..+..||||...+ .+++....|||.|...|+..|+..+..||.|+..+..-..
T Consensus 19 ~~~l~C~~C~~vl---~~p~~~~~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~~ 71 (391)
T KOG0297|consen 19 DENLLCPICMSVL---RDPVQTTTCGHRFCAGCLLESLSNHQKCPVCRQELTQAEE 71 (391)
T ss_pred cccccCccccccc---cCCCCCCCCCCcccccccchhhccCcCCcccccccchhhc
Confidence 4468899999763 3445447999999999999999999999999988765433
No 84
>PF05883 Baculo_RING: Baculovirus U-box/Ring-like domain; InterPro: IPR008573 This family consists of several Baculovirus proteins of around 130 residues in length. The function of this family is unknown, but it appears to be related to the U-box and ring finger domain by profile-profile comparison.
Probab=90.08 E-value=0.14 Score=52.35 Aligned_cols=43 Identities=21% Similarity=0.400 Sum_probs=34.2
Q ss_pred CCCCcccccccccCCCeeEecCCC------CccCHhhHHHHHhcCCCCCC
Q 001016 1116 ETNCPICCDFLFTSSATVRALPCG------HFMHSDCFQAYTCSHYICPI 1159 (1190)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCg------H~fH~~Ci~~wl~~~~~CPi 1159 (1190)
...|.||++.+-. .+.++.++|| |+||.+|++.|.+.+.+=|-
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 5679999999765 5678889998 89999999999655444443
No 85
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=89.32 E-value=0.13 Score=61.51 Aligned_cols=51 Identities=25% Similarity=0.570 Sum_probs=41.9
Q ss_pred ccCCCCCCCcccccccccCCCeeEecCCCCccCHhhHHHHHh-----cCCCCCCCccccc
Q 001016 1111 REKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC-----SHYICPICSKSLG 1165 (1190)
Q Consensus 1111 ~e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~-----~~~~CPiCrk~l~ 1165 (1190)
.++..+..|-+|.|+ .+.+....|.|.|+.-|+.+|+. .+.+||.|...+.
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 467788899999987 23466789999999999999974 3688999998874
No 86
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.72 E-value=0.25 Score=57.47 Aligned_cols=48 Identities=25% Similarity=0.503 Sum_probs=34.4
Q ss_pred cCCCCCCCcccccccccCCCeeEecCCCCccCHhhHHHHHhcCCCCCCCcccccc
Q 001016 1112 EKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1166 (1190)
Q Consensus 1112 e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrk~l~~ 1166 (1190)
+.....+|.||++. +. ....+||||+-. |..-. +...+||+||+.+.-
T Consensus 301 ~~~~p~lcVVcl~e-~~---~~~fvpcGh~cc--ct~cs-~~l~~CPvCR~rI~~ 348 (355)
T KOG1571|consen 301 ELPQPDLCVVCLDE-PK---SAVFVPCGHVCC--CTLCS-KHLPQCPVCRQRIRL 348 (355)
T ss_pred ccCCCCceEEecCC-cc---ceeeecCCcEEE--chHHH-hhCCCCchhHHHHHH
Confidence 34567899999987 32 367899999954 54333 344569999998853
No 87
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.62 E-value=0.31 Score=58.12 Aligned_cols=49 Identities=27% Similarity=0.657 Sum_probs=41.0
Q ss_pred CCCCCCcccccccccCCCeeEecCCCCccCHhhHHHHHhcCCCCCCCcccccc
Q 001016 1114 GLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1166 (1190)
Q Consensus 1114 ~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrk~l~~ 1166 (1190)
..+..|.||+.-++.. ..+||||.|...|++.-+....-||+||..+..
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 4578899998875532 346999999999999988888899999999875
No 88
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=88.51 E-value=0.2 Score=43.75 Aligned_cols=45 Identities=29% Similarity=0.702 Sum_probs=31.3
Q ss_pred CCCCcccccccccCCCeeEecCCCCccCHhhHHHHHhcCCCCCCCcccccc
Q 001016 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1166 (1190)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrk~l~~ 1166 (1190)
+..|-.|... +..-.++||||+....|++-+ .-+-||+|.+.+..
T Consensus 7 ~~~~~~~~~~----~~~~~~~pCgH~I~~~~f~~~--rYngCPfC~~~~~~ 51 (55)
T PF14447_consen 7 EQPCVFCGFV----GTKGTVLPCGHLICDNCFPGE--RYNGCPFCGTPFEF 51 (55)
T ss_pred ceeEEEcccc----ccccccccccceeeccccChh--hccCCCCCCCcccC
Confidence 3445555532 233467899999999997665 44569999998753
No 89
>COG2461 Uncharacterized conserved protein [Function unknown]
Probab=87.75 E-value=2.4 Score=50.27 Aligned_cols=137 Identities=22% Similarity=0.221 Sum_probs=104.5
Q ss_pred CCchHHHHHHHHHHHHHHHHHHHHHHhhccCCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHHHhh-hhHHHHHH
Q 001016 41 KSPILIFLFFHKAIKSELDVLHRAAMAFATNLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIRV-KNIARTYS 119 (1190)
Q Consensus 41 ~~Pi~~~~~~HkAlR~eL~~l~~~a~~~~~~~gd~~~~~~l~~r~~~L~~~~~~H~~aEDevI~PaLd~Rv-~~v~~~~~ 119 (1190)
.+|+..|.-=-+++|..|+.+.+. . .+..-...+...+.+|..+=+ |-+-+-..|||-++.|- ..+.-.|-
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---P----PKKEIKEKLVELVSELDKIGK-HYTRKEMLIFPYIERRGITAPPTVMW 156 (409)
T ss_pred CCcHHHHhcccHHHHHHHHHHhhc---c----ccHHHHHHHHHHHHHHHHhcc-ccccccccchhHHHHcCCCCCCeeee
Confidence 569988888888888665555332 1 123344556667777777777 99999999999999886 45777788
Q ss_pred hhhhhHHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHHHHHhHHHHHHHhhhhHhhcCCHHHHHHHHHH
Q 001016 120 LEHEGESVLFDQLFELLNSSMRNEESYRRELASCTGALQTSISQHMSKEEEQVFPLLIEKFSFEEQASLVWQ 191 (1190)
Q Consensus 120 ~EH~~~~~lf~~l~~~l~~~~~~~~~~~~eLa~~l~~l~~~l~qHm~~EE~~v~PLl~~~fS~~E~a~L~~~ 191 (1190)
.-|.++-..|..+...+. ..+. .+++.....+.+.+..=+.+||.-+.|-+..-||..||.++..+
T Consensus 157 ~~dDeiRe~lk~~~~~l~--~~s~----~~~ve~~~~~~t~i~dmIFkEe~Ilypt~~d~~te~ew~~i~~~ 222 (409)
T COG2461 157 VKDDEIREALKELLKLLK--EVSI----EEFVEKAESVLTEIEDMIFKEENILYPTLLDLLTEGEWEAIKEQ 222 (409)
T ss_pred ccCcHHHHHHHHHHHHhh--ccCh----HHHHHHHHHHHHHHHHHHHhhhhhHHhHHHHhcCHHHHHHHHhc
Confidence 899999999999888887 1122 33334444555688888899999999999999999999999988
No 90
>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=87.37 E-value=0.41 Score=54.34 Aligned_cols=48 Identities=23% Similarity=0.495 Sum_probs=38.7
Q ss_pred CCcccccccccCCC-eeEecCCCCccCHhhHHHHH-hcCCCCCCCccccc
Q 001016 1118 NCPICCDFLFTSSA-TVRALPCGHFMHSDCFQAYT-CSHYICPICSKSLG 1165 (1190)
Q Consensus 1118 ~CpICle~lf~s~~-~v~~LpCgH~fH~~Ci~~wl-~~~~~CPiCrk~l~ 1165 (1190)
.||+|.-+.|.+.+ ..++-+|||.++.+|++... ...+.||-|.+.+.
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 59999988777665 33344999999999999975 56799999998875
No 91
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=87.33 E-value=0.23 Score=53.30 Aligned_cols=45 Identities=27% Similarity=0.389 Sum_probs=37.0
Q ss_pred CCCcccccccccCCCeeEecCCCCccCHhhHHHHHhcCCCCCCCccccc
Q 001016 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1165 (1190)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrk~l~ 1165 (1190)
-.|-||.++ |.+ .++..|||.|+..|+-.-.+....|-+|.+...
T Consensus 197 F~C~iCKkd-y~s---pvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~ 241 (259)
T COG5152 197 FLCGICKKD-YES---PVVTECGHSFCSLCAIRKYQKGDECGVCGKATY 241 (259)
T ss_pred eeehhchhh-ccc---hhhhhcchhHHHHHHHHHhccCCcceecchhhc
Confidence 359999998 654 245689999999998887788899999998764
No 92
>PF04641 Rtf2: Rtf2 RING-finger
Probab=87.24 E-value=0.48 Score=53.54 Aligned_cols=52 Identities=19% Similarity=0.491 Sum_probs=41.2
Q ss_pred CCCCCCCcccccccccCCCeeEec-CCCCccCHhhHHHHHhcCCCCCCCcccccc
Q 001016 1113 KGLETNCPICCDFLFTSSATVRAL-PCGHFMHSDCFQAYTCSHYICPICSKSLGD 1166 (1190)
Q Consensus 1113 ~~~~~~CpICle~lf~s~~~v~~L-pCgH~fH~~Ci~~wl~~~~~CPiCrk~l~~ 1166 (1190)
.....-|||....| .+.....+| ||||+|-..++.+.- ....||+|.+++..
T Consensus 110 ~~~~~~CPvt~~~~-~~~~~fv~l~~cG~V~s~~alke~k-~~~~Cp~c~~~f~~ 162 (260)
T PF04641_consen 110 SEGRFICPVTGKEF-NGKHKFVYLRPCGCVFSEKALKELK-KSKKCPVCGKPFTE 162 (260)
T ss_pred CCceeECCCCCccc-CCceeEEEEcCCCCEeeHHHHHhhc-ccccccccCCcccc
Confidence 45678899999985 555555555 999999999999984 46679999998753
No 93
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=86.32 E-value=0.19 Score=57.82 Aligned_cols=49 Identities=20% Similarity=0.557 Sum_probs=40.6
Q ss_pred CCCCCcccccccccCCCeeEecCCCCccCHhhHHHHHhcCCCCCCCcccccc
Q 001016 1115 LETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1166 (1190)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrk~l~~ 1166 (1190)
....|.+|..+|.+. ..+.-|=|.|+..||..++..+.+||.|.-.+..
T Consensus 14 ~~itC~LC~GYliDA---TTI~eCLHTFCkSCivk~l~~~~~CP~C~i~ih~ 62 (331)
T KOG2660|consen 14 PHITCRLCGGYLIDA---TTITECLHTFCKSCIVKYLEESKYCPTCDIVIHK 62 (331)
T ss_pred cceehhhccceeecc---hhHHHHHHHHHHHHHHHHHHHhccCCccceeccC
Confidence 356899999986543 3456799999999999999999999999987764
No 94
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=86.14 E-value=0.53 Score=54.33 Aligned_cols=53 Identities=21% Similarity=0.381 Sum_probs=44.0
Q ss_pred cccCCCCCCCcccccccccCCCeeEecCCCCccCHhhHHHHHhcCCCCCCCcccccc
Q 001016 1110 CREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1166 (1190)
Q Consensus 1110 C~e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrk~l~~ 1166 (1190)
-...+.++.||||.-. .-..+.-||||-=+..||.+-+.++..|=.|+.++.+
T Consensus 416 ~lp~sEd~lCpICyA~----pi~Avf~PC~H~SC~~CI~qHlmN~k~CFfCktTv~~ 468 (489)
T KOG4692|consen 416 DLPDSEDNLCPICYAG----PINAVFAPCSHRSCYGCITQHLMNCKRCFFCKTTVID 468 (489)
T ss_pred CCCCcccccCcceecc----cchhhccCCCCchHHHHHHHHHhcCCeeeEecceeee
Confidence 3456778999999754 2234567999999999999999999999999999986
No 95
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=86.03 E-value=0.42 Score=56.40 Aligned_cols=45 Identities=27% Similarity=0.572 Sum_probs=35.6
Q ss_pred CCCCcccccccccCCCeeEecCCCCccCHhhHHHHHh--------cCCCCCCCc
Q 001016 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC--------SHYICPICS 1161 (1190)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~--------~~~~CPiCr 1161 (1190)
-..|.||.+. +....-...+||+|+|.+.|...|.. +...||-++
T Consensus 184 lf~C~ICf~e-~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~ 236 (445)
T KOG1814|consen 184 LFDCCICFEE-QMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPK 236 (445)
T ss_pred cccceeeehh-hcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCC
Confidence 5679999998 55556678899999999999999853 236688765
No 96
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=85.66 E-value=0.45 Score=60.32 Aligned_cols=44 Identities=16% Similarity=0.097 Sum_probs=32.4
Q ss_pred CCchhHHHHHHHHHHHHHHHHHHHhcccCCCChhHHHHHHHHHH
Q 001016 643 SRPIDNIFKFHKAIRKDLEYLDGESGKLNDCNETFLRQFTGRFR 686 (1190)
Q Consensus 643 ~~PId~i~~~HkAIRkdL~~L~~ea~~l~~~d~~~l~~f~~r~~ 686 (1190)
-.|+|.=...-.-++|.|-.+|--.++=...|+..++.+...+.
T Consensus 332 L~ek~le~kL~iL~kK~ly~~Ai~LAk~~~~d~d~~~~i~~kYg 375 (933)
T KOG2114|consen 332 LIEKDLETKLDILFKKNLYKVAINLAKSQHLDEDTLAEIHRKYG 375 (933)
T ss_pred eeeccHHHHHHHHHHhhhHHHHHHHHHhcCCCHHHHHHHHHHHH
Confidence 34666667777778899988888888777668888877765543
No 97
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=85.51 E-value=0.64 Score=58.39 Aligned_cols=70 Identities=23% Similarity=0.507 Sum_probs=49.4
Q ss_pred CCcccCCCCCccccCCCCCccccccCCccccccccccccccccCCCCCCCcccccccccCCCeeEecCCCCccCHhhHHH
Q 001016 1070 RVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLAKKLVDHKCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQA 1149 (1190)
Q Consensus 1070 k~~yHC~~CgiCrvg~gl~~~~fHC~~C~~C~s~~l~~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~ 1149 (1190)
--+|-|+.|+---+++++ .-|++|-.|-+. .|.+|-..+- +..+.---|||..|.+|+..
T Consensus 751 ~i~~~~~nc~a~~~~~~~----~~c~rc~s~a~~--------------~CtVC~~vi~--G~~~~c~~C~H~gH~sh~~s 810 (839)
T KOG0269|consen 751 TIHYACPNCDAPMVLTKL----WQCDRCESRASA--------------KCTVCDLVIR--GVDVWCQVCGHGGHDSHLKS 810 (839)
T ss_pred eeeccccccCCccccccc----eeechHHHHhhc--------------Cceeecceee--eeEeecccccccccHHHHHH
Confidence 456778888877777653 456666655553 4999986632 22233347999999999999
Q ss_pred HHhcCCCCCC
Q 001016 1150 YTCSHYICPI 1159 (1190)
Q Consensus 1150 wl~~~~~CPi 1159 (1190)
|...+.-||.
T Consensus 811 w~~~~s~ca~ 820 (839)
T KOG0269|consen 811 WFFKASPCAK 820 (839)
T ss_pred HHhcCCCCcc
Confidence 9988877776
No 98
>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=85.36 E-value=0.7 Score=48.43 Aligned_cols=32 Identities=28% Similarity=0.865 Sum_probs=21.5
Q ss_pred CCCCcccccccccCCCeeEecCCC-------------CccCHhhHHHHH
Q 001016 1116 ETNCPICCDFLFTSSATVRALPCG-------------HFMHSDCFQAYT 1151 (1190)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCg-------------H~fH~~Ci~~wl 1151 (1190)
+..||||||. . -..+.|-|. =+=|+.|++++-
T Consensus 2 d~~CpICme~---P-HNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfk 46 (162)
T PF07800_consen 2 DVTCPICMEH---P-HNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFK 46 (162)
T ss_pred CccCceeccC---C-CceEEEEeccccCCccccccCCccchhHHHHHHH
Confidence 4689999996 1 123344453 246999999985
No 99
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=84.91 E-value=0.35 Score=55.46 Aligned_cols=57 Identities=21% Similarity=0.484 Sum_probs=40.7
Q ss_pred CCCCcccccccccCCCeeEecCCCCccCHhhHHHHH-hcCCCCCCCcccccchhHHHH
Q 001016 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYT-CSHYICPICSKSLGDMALYEG 1172 (1190)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl-~~~~~CPiCrk~l~~m~~~~~ 1172 (1190)
++.||.|+|+|--++....--|||--.+.-|...-- .-+.+||-||+...+..+.|+
T Consensus 14 ed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~denv~~~ 71 (480)
T COG5175 14 EDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDENVRYV 71 (480)
T ss_pred cccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhccccceeEE
Confidence 455999999975555544556889887788855432 237899999998877665554
No 100
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=83.37 E-value=0.83 Score=40.54 Aligned_cols=47 Identities=23% Similarity=0.535 Sum_probs=30.7
Q ss_pred cceeeccccCccccC-----CCCCCCCCCCCCccceEeccccccccCCCCcccCCCCCc
Q 001016 1027 TTEMMCMRCLKVQPV-----GPVCTTLSCSGLSMAKYYCGICKFFDDERVVYHCPFCNL 1080 (1190)
Q Consensus 1027 ~~~~~C~~C~~~q~~-----~~~C~~~~Cc~~~fa~Y~C~~C~l~dd~k~~yHC~~Cgi 1080 (1190)
.....|..|+.+-.. .-.|+| ||.. -=|-|..|+-..+ .|.||+||+
T Consensus 5 ~~~~~CtSCg~~i~~~~~~~~F~CPn---CG~~-~I~RC~~CRk~~~---~Y~CP~CGF 56 (59)
T PRK14890 5 MEPPKCTSCGIEIAPREKAVKFLCPN---CGEV-IIYRCEKCRKQSN---PYTCPKCGF 56 (59)
T ss_pred ccCccccCCCCcccCCCccCEeeCCC---CCCe-eEeechhHHhcCC---ceECCCCCC
Confidence 345578888865432 235888 4653 2345888877654 699999985
No 101
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=83.20 E-value=1.1 Score=51.69 Aligned_cols=67 Identities=21% Similarity=0.395 Sum_probs=47.3
Q ss_pred CCccccccccc-cccccccCCCCCCCcccccccccCCCeeEecCCCCccCHhhHHHH--HhcCCCCCCCccccc
Q 001016 1095 MTCNCCLAKKL-VDHKCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAY--TCSHYICPICSKSLG 1165 (1190)
Q Consensus 1095 ~~C~~C~s~~l-~~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~w--l~~~~~CPiCrk~l~ 1165 (1190)
.+=+.|...++ +..+=.....+..|-||-+.+ .-+.++||||-++--|--.. |.....||+||..-.
T Consensus 39 kKNnlsaEPnlttsSaddtDEen~~C~ICA~~~----TYs~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~e 108 (493)
T COG5236 39 KKNNLSAEPNLTTSSADDTDEENMNCQICAGST----TYSARYPCGHQICHACAVRLRALYMQKGCPLCRTETE 108 (493)
T ss_pred cccccccCCccccccccccccccceeEEecCCc----eEEEeccCCchHHHHHHHHHHHHHhccCCCccccccc
Confidence 34466666665 333333455678999998763 34567899999999996554 566788999997653
No 102
>PHA02862 5L protein; Provisional
Probab=82.39 E-value=0.85 Score=47.13 Aligned_cols=45 Identities=24% Similarity=0.561 Sum_probs=33.8
Q ss_pred CCCCcccccccccCCCeeEecCCC-----CccCHhhHHHHHhc--CCCCCCCccccc
Q 001016 1116 ETNCPICCDFLFTSSATVRALPCG-----HFMHSDCFQAYTCS--HYICPICSKSLG 1165 (1190)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCg-----H~fH~~Ci~~wl~~--~~~CPiCrk~l~ 1165 (1190)
.+.|=||.+. . ++. .-||. -.-|.+|+.+|+.. +..||+|+....
T Consensus 2 ~diCWIC~~~-~--~e~--~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~ 53 (156)
T PHA02862 2 SDICWICNDV-C--DER--NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYN 53 (156)
T ss_pred CCEEEEecCc-C--CCC--cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEE
Confidence 4679999986 2 222 35775 57999999999854 577999998774
No 103
>PRK04023 DNA polymerase II large subunit; Validated
Probab=81.95 E-value=1.2 Score=57.98 Aligned_cols=44 Identities=25% Similarity=0.480 Sum_probs=21.2
Q ss_pred eccccCccccCCCCCCCCCCCCCccceEeccccccccCCCCcccCCCCCc
Q 001016 1031 MCMRCLKVQPVGPVCTTLSCSGLSMAKYYCGICKFFDDERVVYHCPFCNL 1080 (1190)
Q Consensus 1031 ~C~~C~~~q~~~~~C~~~~Cc~~~fa~Y~C~~C~l~dd~k~~yHC~~Cgi 1080 (1190)
.|..|+++. +...|++ |......-|+|+.|.- .-..|.||.||.
T Consensus 628 fCpsCG~~t-~~frCP~--CG~~Te~i~fCP~CG~---~~~~y~CPKCG~ 671 (1121)
T PRK04023 628 KCPSCGKET-FYRRCPF--CGTHTEPVYRCPRCGI---EVEEDECEKCGR 671 (1121)
T ss_pred cCCCCCCcC-CcccCCC--CCCCCCcceeCccccC---cCCCCcCCCCCC
Confidence 455555554 2336665 3222344556666622 122355666664
No 104
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=81.41 E-value=1 Score=51.41 Aligned_cols=47 Identities=28% Similarity=0.752 Sum_probs=37.7
Q ss_pred CCCcccccccccCCC---eeEecCCCCccCHhhHHHHHhc-CCCCCCCcccc
Q 001016 1117 TNCPICCDFLFTSSA---TVRALPCGHFMHSDCFQAYTCS-HYICPICSKSL 1164 (1190)
Q Consensus 1117 ~~CpICle~lf~s~~---~v~~LpCgH~fH~~Ci~~wl~~-~~~CPiCrk~l 1164 (1190)
..|-||-++ |.+.+ ..+.|.|||.+...|+...+.. ...||.||.+.
T Consensus 4 ~~c~~c~~~-~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~~~i~cpfcR~~~ 54 (296)
T KOG4185|consen 4 PECEICNED-YSSEDGDHIPRVLKCGHTICQNCASKLLGNSRILCPFCRETT 54 (296)
T ss_pred CceeecCcc-ccccCcccCCcccccCceehHhHHHHHhcCceeeccCCCCcc
Confidence 469999999 66654 3367899999999999888754 45699999994
No 105
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=81.12 E-value=0.6 Score=53.15 Aligned_cols=45 Identities=24% Similarity=0.513 Sum_probs=37.1
Q ss_pred CCCcccccccccCCCeeEecCCCCccCHhhHHHHHhcCCCCCCCccccc
Q 001016 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1165 (1190)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrk~l~ 1165 (1190)
..|-||..+ |.+ -++..|||+|+..|...=++....|++|.+.+-
T Consensus 242 f~c~icr~~-f~~---pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~ 286 (313)
T KOG1813|consen 242 FKCFICRKY-FYR---PVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTH 286 (313)
T ss_pred ccccccccc-ccc---chhhcCCceeehhhhccccccCCcceecccccc
Confidence 459999998 433 245789999999998887788899999998875
No 106
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=80.52 E-value=0.14 Score=59.56 Aligned_cols=51 Identities=22% Similarity=0.458 Sum_probs=43.9
Q ss_pred CCCCcccccccccCCCeeEecCCCCccCHhhHHHHHhcCCCCCCCcccccc
Q 001016 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1166 (1190)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrk~l~~ 1166 (1190)
-..|.||.+.+...-+++..+.|||.+|..|+.+|+.....||.|++.+..
T Consensus 196 v~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~~~~kl~~~~rel~~ 246 (465)
T KOG0827|consen 196 VGSLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLATKRKLPSCRRELPK 246 (465)
T ss_pred HhhhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHHHhHHHHhhhhh
Confidence 457999999865554677889999999999999999989999999999863
No 107
>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=79.06 E-value=0.82 Score=38.88 Aligned_cols=44 Identities=30% Similarity=0.776 Sum_probs=26.3
Q ss_pred CCCcccccccccCCCeeEecCCC-CccCHhhHHHHHhcCCCCCCCcccccc
Q 001016 1117 TNCPICCDFLFTSSATVRALPCG-HFMHSDCFQAYTCSHYICPICSKSLGD 1166 (1190)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCg-H~fH~~Ci~~wl~~~~~CPiCrk~l~~ 1166 (1190)
.+|--|. |.... .+.|. |+....|+.-.+..+..||||.++++.
T Consensus 3 ~nCKsCW---f~~k~---Li~C~dHYLCl~CLt~ml~~s~~C~iC~~~LPt 47 (50)
T PF03854_consen 3 YNCKSCW---FANKG---LIKCSDHYLCLNCLTLMLSRSDRCPICGKPLPT 47 (50)
T ss_dssp ----SS----S--SS---EEE-SS-EEEHHHHHHT-SSSSEETTTTEE---
T ss_pred ccChhhh---hcCCC---eeeecchhHHHHHHHHHhccccCCCcccCcCcc
Confidence 4566676 33322 45787 999999999999999999999999874
No 108
>COG5592 Uncharacterized conserved protein [Function unknown]
Probab=78.46 E-value=6 Score=41.84 Aligned_cols=110 Identities=21% Similarity=0.215 Sum_probs=74.1
Q ss_pred HHHHHHHHHHHHHHhhhcccccccccccc-----ccccccc--CcccchhhHHHHHHHHHHHHHHHhhhhhhhhcccccc
Q 001016 681 FTGRFRLLWGLYRAHSNAEDDIVFPALES-----KETLSNV--SHSYTLDHKQEEKLFEDISSALSELTELHECLSTDLT 753 (1190)
Q Consensus 681 f~~r~~fl~~v~~~HS~AEDeivfPaLe~-----k~~~~nv--s~s~~~DH~~ee~lfe~i~~~L~~~~~l~~~~~~~~~ 753 (1190)
.....+|+|.++..|---|-++.||+.=- .-..... .--+..||+.+|.|+..+-..
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 33445589999999999999999997532 1111222 236889999999999887111
Q ss_pred ccccccccccccchhhHhhHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhcCCHHHHH--HHHHHHHhccC
Q 001016 754 GDLTRNSLESCDQNETVRKYNEKATELQGMCKSIRVTLDQHVFREELELWPLFDRHFSVEEQD--KIVGRIIGTTG 827 (1190)
Q Consensus 754 ~~~~~~~~~~~~~~~~~~~~~e~~~kL~~~~~sl~~~L~~Hl~~EE~Ev~PL~~k~fS~eeQ~--~lv~~~l~~~p 827 (1190)
.++ .|.+.-.-.+.++|..|=..||..++|-.++.=...+|. +++=.+|-..+
T Consensus 94 --------------kR~-------~k~~e~~p~fyK~LtdHn~aEE~~IfPrvks~~~E~~~~~~kl~LeiI~~~~ 148 (171)
T COG5592 94 --------------KRP-------DKIKERVPLFYKTLTDHNLAEEEYIFPRVKSLKGEDEQSALKLALEIIEQYG 148 (171)
T ss_pred --------------ccc-------hHHHHHHHHHHHHHHHccccccchhhHHHHhhcchhhHHHHHHHHHHHHHhC
Confidence 011 244455577888999999999999999987765444444 44444444444
No 109
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=78.28 E-value=1.5 Score=39.00 Aligned_cols=45 Identities=27% Similarity=0.724 Sum_probs=32.0
Q ss_pred eeeccccCccccCC-----CCCCCCCCCCCccceEeccccccccCCCCcccCCCCCc
Q 001016 1029 EMMCMRCLKVQPVG-----PVCTTLSCSGLSMAKYYCGICKFFDDERVVYHCPFCNL 1080 (1190)
Q Consensus 1029 ~~~C~~C~~~q~~~-----~~C~~~~Cc~~~fa~Y~C~~C~l~dd~k~~yHC~~Cgi 1080 (1190)
...|..|+.+-.++ -.|+| ||. .-=|-|..|+-..+ +|.||+||+
T Consensus 9 ~~~CtSCg~~i~p~e~~v~F~CPn---CGe-~~I~Rc~~CRk~g~---~Y~Cp~CGF 58 (61)
T COG2888 9 PPVCTSCGREIAPGETAVKFPCPN---CGE-VEIYRCAKCRKLGN---PYRCPKCGF 58 (61)
T ss_pred CceeccCCCEeccCCceeEeeCCC---CCc-eeeehhhhHHHcCC---ceECCCcCc
Confidence 56899999876443 34888 462 33477888887755 699999986
No 110
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=77.35 E-value=1.9 Score=45.46 Aligned_cols=46 Identities=22% Similarity=0.625 Sum_probs=33.8
Q ss_pred CCCCCcccccccccCCCeeEecCCCC-----ccCHhhHHHHHhc--CCCCCCCccccc
Q 001016 1115 LETNCPICCDFLFTSSATVRALPCGH-----FMHSDCFQAYTCS--HYICPICSKSLG 1165 (1190)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~LpCgH-----~fH~~Ci~~wl~~--~~~CPiCrk~l~ 1165 (1190)
.+..|=||.+. .+ . ..-||.- ..|.+|++.|+.. ..+||+|+....
T Consensus 7 ~~~~CRIC~~~-~~--~--~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~ 59 (162)
T PHA02825 7 MDKCCWICKDE-YD--V--VTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYN 59 (162)
T ss_pred CCCeeEecCCC-CC--C--ccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEE
Confidence 46789999877 21 2 2347764 5699999999854 577999998764
No 111
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=76.38 E-value=1.2 Score=46.67 Aligned_cols=30 Identities=30% Similarity=0.587 Sum_probs=25.2
Q ss_pred CCCCCCcccccccccCCCeeEecCCCCccCH
Q 001016 1114 GLETNCPICCDFLFTSSATVRALPCGHFMHS 1144 (1190)
Q Consensus 1114 ~~~~~CpICle~lf~s~~~v~~LpCgH~fH~ 1144 (1190)
.....|.||||+| ..++.+..|||=..||+
T Consensus 175 ddkGECvICLEdL-~~GdtIARLPCLCIYHK 204 (205)
T KOG0801|consen 175 DDKGECVICLEDL-EAGDTIARLPCLCIYHK 204 (205)
T ss_pred ccCCcEEEEhhhc-cCCCceeccceEEEeec
Confidence 3467899999994 66778999999999996
No 112
>TIGR02481 hemeryth_dom hemerythrin-like metal-binding domain. This model describes both members of the hemerythrin (TIGR00058) family of marine invertebrates and a broader collection of bacterial and archaeal homologs. Many of the latter group are multidomain proteins with signal-transducing domains such as the GGDEF diguanylate cyclase domain (TIGR00254, pfam00990) and methyl-accepting chemotaxis protein signaling domain (pfam00015). Most hemerythrins are oxygen-carriers with a bound non-heme iron, but at least one example is a cadmium-binding protein, apparently with a role in sequestering toxic metals rather than in binding oxygen. Patterns of conserved residues suggest that all prokaryotic instances of this domain bind iron or another heavy metal, but the exact function is unknown. Not surprisingly, the prokaryote with the most instances of this domain is Magnetococcus sp. MC-1, a magnetotactic bacterium.
Probab=76.04 E-value=13 Score=37.04 Aligned_cols=58 Identities=19% Similarity=0.241 Sum_probs=40.1
Q ss_pred hhHHhHHHHHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHH----HHHHHhh
Q 001016 361 SFAQEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQV----LPLARRH 428 (1190)
Q Consensus 361 ~me~EH~~ie~l~e~l~~ll~~l~~~~~~~~~~~~~~eLa~~l~~L~~~L~~Hf~~EE~qv----fPLl~~~ 428 (1190)
.+..+|++.-++++.|..++.. ..+ ..++...+..|..-+..||..||.-. +|-+..|
T Consensus 12 ~ID~qH~~l~~~in~l~~a~~~---~~~-------~~~~~~~l~~L~~y~~~HF~~EE~~M~~~~yp~~~~H 73 (126)
T TIGR02481 12 EIDAQHKELFELINELYDALSA---GNG-------KDELKEILDELIDYTENHFADEEELMEEYGYPDLEEH 73 (126)
T ss_pred HHHHHHHHHHHHHHHHHHHHHc---CCC-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCHHHH
Confidence 5667888877777777765532 111 34667788888999999999999765 4444444
No 113
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=75.83 E-value=1.2 Score=57.09 Aligned_cols=43 Identities=26% Similarity=0.579 Sum_probs=31.3
Q ss_pred ccccccCCCCCCCcccccccccCCCeeEecCCCCccCHhhHHHHH
Q 001016 1107 DHKCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYT 1151 (1190)
Q Consensus 1107 ~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl 1151 (1190)
++.|.--.....|-+|.-+|+. ++-.+.||||.||.+|+..-.
T Consensus 808 ~~ry~v~ep~d~C~~C~~~ll~--~pF~vf~CgH~FH~~Cl~~~v 850 (911)
T KOG2034|consen 808 RQRYRVLEPQDSCDHCGRPLLI--KPFYVFPCGHCFHRDCLIRHV 850 (911)
T ss_pred hcceEEecCccchHHhcchhhc--CcceeeeccchHHHHHHHHHH
Confidence 3444433446789999988653 466778999999999997653
No 114
>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=73.97 E-value=1.9 Score=35.96 Aligned_cols=41 Identities=29% Similarity=0.745 Sum_probs=20.3
Q ss_pred CcccccccccCCCeeEecCCCCccCHhhHHHHHhcCC--CCCCC
Q 001016 1119 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHY--ICPIC 1160 (1190)
Q Consensus 1119 CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~--~CPiC 1160 (1190)
|.+|.+-+ ..+..-..-.|+=.+|..|++.|++... +||.|
T Consensus 1 C~~C~~iv-~~G~~C~~~~C~~r~H~~C~~~y~r~~~~~~CP~C 43 (43)
T PF08746_consen 1 CEACKEIV-TQGQRCSNRDCNVRLHDDCFKKYFRHRSNPKCPNC 43 (43)
T ss_dssp -TTT-SB--SSSEE-SS--S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred CcccchhH-eeeccCCCCccCchHHHHHHHHHHhcCCCCCCcCC
Confidence 56676642 2222111224777899999999987654 79988
No 115
>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=73.22 E-value=1.8 Score=43.10 Aligned_cols=18 Identities=33% Similarity=0.659 Sum_probs=15.3
Q ss_pred ccccCCCCcccCCCCCcc
Q 001016 1064 KFFDDERVVYHCPFCNLC 1081 (1190)
Q Consensus 1064 ~l~dd~k~~yHC~~CgiC 1081 (1190)
||||=.|.+..||+||-=
T Consensus 18 kFYDLnk~PivCP~CG~~ 35 (108)
T PF09538_consen 18 KFYDLNKDPIVCPKCGTE 35 (108)
T ss_pred hhccCCCCCccCCCCCCc
Confidence 678888999999999943
No 116
>COG5592 Uncharacterized conserved protein [Function unknown]
Probab=72.99 E-value=19 Score=38.25 Aligned_cols=92 Identities=17% Similarity=0.151 Sum_probs=66.4
Q ss_pred HHHHHHHHHHHHHhhhhccccchhhhhhhhh--------------hhHHhHHHHHHHHHHHHHHHHHHHhcCCCCChHHH
Q 001016 330 FNKRLQFIAEVCIFHSIAEDKVIFPAVDVEL--------------SFAQEHAEEEIQFDKLRCLIESIQSAGANSSTAEF 395 (1190)
Q Consensus 330 L~~r~~fl~~vl~~Hs~aEDevlFPaL~~r~--------------~me~EH~~ie~l~e~l~~ll~~l~~~~~~~~~~~~ 395 (1190)
+.+-..|...+.+.|-.-|.+.+||+.-... ++..+|..|+-+.+.+...- +
T Consensus 30 ~le~~gf~~k~~k~h~e~Ee~ilF~v~Vd~~~ed~~~fkdt~~~~~i~~DHkliE~l~tnlik~k--------R------ 95 (171)
T COG5592 30 ILEFEGFNEKLGKDHVELEEKILFPVIVDADMEDLYVFKDTPEVDRIKNDHKLIETLATNLIKWK--------R------ 95 (171)
T ss_pred HHhhcchHHHHhhhHHHHHHHhhhhhccchHHHHHHhhhccchhhHhHhhHHHHHHHHHHHHhhc--------c------
Confidence 3344448899999999999999999864211 77889998888777654321 1
Q ss_pred HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhhCCHHHHH
Q 001016 396 YTKLCSQADLIMASIQKHFRNEEVQVLPLARRHFSPKRQR 435 (1190)
Q Consensus 396 ~~eLa~~l~~L~~~L~~Hf~~EE~qvfPLl~~~fS~eEq~ 435 (1190)
.++.-.-+..++.+|++|=..||..+||-+...--..||.
T Consensus 96 ~~k~~e~~p~fyK~LtdHn~aEE~~IfPrvks~~~E~~~~ 135 (171)
T COG5592 96 PDKIKERVPLFYKTLTDHNLAEEEYIFPRVKSLKGEDEQS 135 (171)
T ss_pred chHHHHHHHHHHHHHHHccccccchhhHHHHhhcchhhHH
Confidence 1234456777799999999999999999876655443333
No 117
>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=72.79 E-value=1.2 Score=49.31 Aligned_cols=51 Identities=25% Similarity=0.531 Sum_probs=39.4
Q ss_pred CCCCcccccccccCCCeeE-ecC-CCCccCHhhHHHHHh-cCCCCC--CCcccccc
Q 001016 1116 ETNCPICCDFLFTSSATVR-ALP-CGHFMHSDCFQAYTC-SHYICP--ICSKSLGD 1166 (1190)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~-~Lp-CgH~fH~~Ci~~wl~-~~~~CP--iCrk~l~~ 1166 (1190)
+..||||..+.|-+.+-.. +-| |=|-++.+|++.-.. ....|| -|.+.+-.
T Consensus 10 d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kILRK 65 (314)
T COG5220 10 DRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKILRK 65 (314)
T ss_pred cccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHHHH
Confidence 4589999999887766333 336 999999999999764 557899 89877643
No 118
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=72.59 E-value=1.2 Score=54.98 Aligned_cols=55 Identities=22% Similarity=0.449 Sum_probs=39.1
Q ss_pred CCCcccccccccCCCeeEecCCCCccCHhhHHHHHhcCCCCCCCccc----ccchhHHHHhh
Q 001016 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKS----LGDMALYEGFC 1174 (1190)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrk~----l~~m~~~~~~l 1174 (1190)
..|+||+..++...-.-+.|-|||+++.+|+... .+.+|| |++. +.+.+.++++.
T Consensus 12 l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~l--yn~scp-~~~De~~~~~~~~e~p~n~ 70 (861)
T KOG3161|consen 12 LLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLL--YNASCP-TKRDEDSSLMQLKEEPRNY 70 (861)
T ss_pred hhchHHHHHHHHHhcCcccccccchHHHHHHHhH--hhccCC-CCccccchhcChhhcchhH
Confidence 4699998776666666677899999999999764 467798 7643 33444555443
No 119
>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=70.38 E-value=68 Score=31.83 Aligned_cols=110 Identities=18% Similarity=0.294 Sum_probs=68.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhcccCCcccHHHHHHHHHHHHHHHHhhhhccccch----hhhhhhhhhhHHhHHHHHH
Q 001016 296 EIMLWHNAIKRELNDIAEAARKIQLSGDFSDLSAFNKRLQFIAEVCIFHSIAEDKVI----FPAVDVELSFAQEHAEEEI 371 (1190)
Q Consensus 296 ~l~~~HkALRrEL~~L~~~a~~~~~~gd~~~L~~L~~r~~fl~~vl~~Hs~aEDevl----FPaL~~r~~me~EH~~ie~ 371 (1190)
.+=.-|+.|=..++.+.+.+.. + .....+...+.+|.+....|-..|+.++ ||.+..+. .+| +.
T Consensus 12 ~ID~qH~~l~~~in~l~~a~~~----~--~~~~~~~~~l~~L~~y~~~HF~~EE~~M~~~~yp~~~~H~---~~H---~~ 79 (126)
T TIGR02481 12 EIDAQHKELFELINELYDALSA----G--NGKDELKEILDELIDYTENHFADEEELMEEYGYPDLEEHK---KEH---EK 79 (126)
T ss_pred HHHHHHHHHHHHHHHHHHHHHc----C--CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHH---HHH---HH
Confidence 3335688887888887776543 1 1245677778888999999999998765 77776543 344 44
Q ss_pred HHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 001016 372 QFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPL 424 (1190)
Q Consensus 372 l~e~l~~ll~~l~~~~~~~~~~~~~~eLa~~l~~L~~~L~~Hf~~EE~qvfPL 424 (1190)
.++.+..+...+..... ..... ..+..+.+-|..|+..+-..+.+.
T Consensus 80 ~l~~l~~l~~~~~~~~~----~~~~~---~~~~~l~~Wl~~HI~~~D~~~~~~ 125 (126)
T TIGR02481 80 FVKKIEELQEAVAEGAD----ESLAE---ELLDFLKDWLVNHILKEDKKYAPY 125 (126)
T ss_pred HHHHHHHHHHHHHcCCc----hhHHH---HHHHHHHHHHHHHhHHHhHHHHhh
Confidence 45555555544432211 11222 344456778999999888776553
No 120
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=69.64 E-value=3.4 Score=49.06 Aligned_cols=47 Identities=21% Similarity=0.513 Sum_probs=37.0
Q ss_pred CCCcccccccccCCCeeEecCCCCccCHhhHHHHHhcC---CCCCCCcccc
Q 001016 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSH---YICPICSKSL 1164 (1190)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~---~~CPiCrk~l 1164 (1190)
-.|||=.+. -+...+.+.|.|||.+-.+-++...+++ ++||.|-...
T Consensus 335 F~CPVlKeq-tsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~e~ 384 (394)
T KOG2817|consen 335 FICPVLKEQ-TSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPVEQ 384 (394)
T ss_pred eecccchhh-ccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCccc
Confidence 468887776 4555678889999999999999997653 6899997543
No 121
>PF02084 Bindin: Bindin; InterPro: IPR000775 Bindin, the major protein component of the acrosome granule of sea urchin sperm, mediates species-specific adhesion of sperm to the egg surface during fertilisation [, ]. The protein coats the acrosomal process after externalisation by the acrosome reaction; it binds to sulphated, fucose-containing polysaccharides on the vitelline-layer receptor proteoglycans that cover the egg plasma membrane. Bindins from different genera show high levels of sequence similarity in both the mature bindin domain and in the probindin precursor region. The most highly conserved region is a 42-residue segment in the central portion of the mature bindin protein. This domain may be responsible for conserved functions of bindin, while the more highly divergent flanking regions may be responsible for its species-specific properties [].; GO: 0007342 fusion of sperm to egg plasma membrane
Probab=68.86 E-value=14 Score=41.08 Aligned_cols=45 Identities=24% Similarity=0.336 Sum_probs=26.6
Q ss_pred CCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHHHhhh-hHHHHHHhhhhhHHH
Q 001016 72 LGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIRVK-NIARTYSLEHEGESV 127 (1190)
Q Consensus 72 ~gd~~~~~~l~~r~~~L~~~~~~H~~aEDevI~PaLd~Rv~-~v~~~~~~EH~~~~~ 127 (1190)
+.|+=++.-|++| ||||++ +|==.=|--|+ -|+.+|..|-++++.
T Consensus 124 INDPYDlGLLLRh-------LRHHSN----LLAnIgdP~VreqVLsAMqEeeeEEe~ 169 (238)
T PF02084_consen 124 INDPYDLGLLLRH-------LRHHSN----LLANIGDPEVREQVLSAMQEEEEEEEQ 169 (238)
T ss_pred cCChhhHHHHHHH-------HHHHHH----HHhhcCCHHHHHHHHHHHhhhHHHHHH
Confidence 4677777766655 578988 22111112234 488899887665554
No 122
>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=68.66 E-value=2.5 Score=47.51 Aligned_cols=66 Identities=30% Similarity=0.776 Sum_probs=41.6
Q ss_pred CCcccCcccccc-cCCCCCCccccceeeccccCccccCCCCCCCCCCCCCccceEecccccc-c-cCC----------CC
Q 001016 1005 GKLFTCRFCHDK-VSDHSMDRKATTEMMCMRCLKVQPVGPVCTTLSCSGLSMAKYYCGICKF-F-DDE----------RV 1071 (1190)
Q Consensus 1005 ~k~y~Cr~CHde-~~dH~~~r~~~~~~~C~~C~~~q~~~~~C~~~~Cc~~~fa~Y~C~~C~l-~-dd~----------k~ 1071 (1190)
|+.|.|-||++- -+|-.++-.+ .|+....-+-.|.. | ..+|.|.|-.||. | ||. ..
T Consensus 140 Grif~CsfC~~flCEDDQFEHQA-------sCQvLe~E~~KC~S--C--NrlGq~sCLRCK~cfCddHvrrKg~ky~k~k 208 (314)
T PF06524_consen 140 GRIFKCSFCDNFLCEDDQFEHQA-------SCQVLESETFKCQS--C--NRLGQYSCLRCKICFCDDHVRRKGFKYEKGK 208 (314)
T ss_pred CeEEEeecCCCeeeccchhhhhh-------hhhhhhcccccccc--c--ccccchhhhheeeeehhhhhhhcccccccCC
Confidence 678889888877 3444444322 24444444556776 5 3789999999985 3 433 34
Q ss_pred cccCCCCCcc
Q 001016 1072 VYHCPFCNLC 1081 (1190)
Q Consensus 1072 ~yHC~~CgiC 1081 (1190)
++-||+||.=
T Consensus 209 ~~PCPKCg~e 218 (314)
T PF06524_consen 209 PIPCPKCGYE 218 (314)
T ss_pred CCCCCCCCCc
Confidence 6677777743
No 123
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=67.83 E-value=2.6 Score=53.80 Aligned_cols=54 Identities=24% Similarity=0.582 Sum_probs=37.7
Q ss_pred CCCCCCcccccccccCCCeeEe-cCCCCccCHhhHHHHHhc-------CCCCCCCcccccchh
Q 001016 1114 GLETNCPICCDFLFTSSATVRA-LPCGHFMHSDCFQAYTCS-------HYICPICSKSLGDMA 1168 (1190)
Q Consensus 1114 ~~~~~CpICle~lf~s~~~v~~-LpCgH~fH~~Ci~~wl~~-------~~~CPiCrk~l~~m~ 1168 (1190)
.....|.||.|.|. ...++-. -.|=|+||..||..|-+. .-.||-|+.....+.
T Consensus 189 ~~~yeCmIC~e~I~-~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv~~~~~ 250 (950)
T KOG1952|consen 189 NRKYECMICTERIK-RTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSVSKTVP 250 (950)
T ss_pred cCceEEEEeeeecc-ccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccchhccCC
Confidence 35678999999853 3333322 356799999999999653 356999995544443
No 124
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=67.71 E-value=4.8 Score=53.86 Aligned_cols=52 Identities=25% Similarity=0.457 Sum_probs=28.5
Q ss_pred eeeccccCccccCCCCCCCCCCCCCc-cceEeccccccc--cCCCCcccCCCCCccccC
Q 001016 1029 EMMCMRCLKVQPVGPVCTTLSCSGLS-MAKYYCGICKFF--DDERVVYHCPFCNLCRVG 1084 (1190)
Q Consensus 1029 ~~~C~~C~~~q~~~~~C~~~~Cc~~~-fa~Y~C~~C~l~--dd~k~~yHC~~CgiCrvg 1084 (1190)
.-.|..|+++-+. ..|+. | |.. -..|+|..|+.- .++....+||+||.=.+.
T Consensus 667 ~rkCPkCG~~t~~-~fCP~--C-Gs~te~vy~CPsCGaev~~des~a~~CP~CGtplv~ 721 (1337)
T PRK14714 667 RRRCPSCGTETYE-NRCPD--C-GTHTEPVYVCPDCGAEVPPDESGRVECPRCDVELTP 721 (1337)
T ss_pred EEECCCCCCcccc-ccCcc--c-CCcCCCceeCccCCCccCCCccccccCCCCCCcccc
Confidence 4556666665433 26665 3 443 345667777652 122236678888854443
No 125
>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=67.24 E-value=3 Score=42.48 Aligned_cols=19 Identities=26% Similarity=0.315 Sum_probs=16.1
Q ss_pred ccccCCCCcccCCCCCccc
Q 001016 1064 KFFDDERVVYHCPFCNLCR 1082 (1190)
Q Consensus 1064 ~l~dd~k~~yHC~~CgiCr 1082 (1190)
||||-.|.+..||+||.=.
T Consensus 18 kFYDLnk~p~vcP~cg~~~ 36 (129)
T TIGR02300 18 KFYDLNRRPAVSPYTGEQF 36 (129)
T ss_pred cccccCCCCccCCCcCCcc
Confidence 6788889999999999653
No 126
>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=67.12 E-value=3.8 Score=31.71 Aligned_cols=38 Identities=34% Similarity=0.766 Sum_probs=25.8
Q ss_pred CCcccccccccCCCeeEecCCCCccCHhhHHHHHhcCCCCCCCccccc
Q 001016 1118 NCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1165 (1190)
Q Consensus 1118 ~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrk~l~ 1165 (1190)
.|+.|.+.+......+.. =|..||.+|+ +|..|+++|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~--~~~~~H~~Cf--------~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRA--LGKVWHPECF--------KCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEe--CCccccccCC--------CCcccCCcCc
Confidence 378888886544222222 3789999886 6888888774
No 127
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=66.72 E-value=2.6 Score=50.22 Aligned_cols=133 Identities=23% Similarity=0.538 Sum_probs=0.0
Q ss_pred CCCCCCccccceeeccccCcc---ccCCCCCCCCCCCCCccceEeccccc-------cccCCCCccc----------CCC
Q 001016 1018 SDHSMDRKATTEMMCMRCLKV---QPVGPVCTTLSCSGLSMAKYYCGICK-------FFDDERVVYH----------CPF 1077 (1190)
Q Consensus 1018 ~dH~~~r~~~~~~~C~~C~~~---q~~~~~C~~~~Cc~~~fa~Y~C~~C~-------l~dd~k~~yH----------C~~ 1077 (1190)
+.++.+.+.. +|..|++. +..+-.-.+ --....-+.|..|. ||.-|..+|= |..
T Consensus 266 ~~~p~~~~~~---iC~~C~K~V~g~~~ac~Am~---~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~tlekC~~ 339 (468)
T KOG1701|consen 266 EAEPVEDYFG---ICAFCHKTVSGQGLAVEAMD---QLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDTLEKCNK 339 (468)
T ss_pred CCChhhhhhh---hhhhcCCcccCcchHHHHhh---hhhcccceehHhhhhhhccccccccCCcccchHHHHHHHHHHhh
Q ss_pred CC-------ccccCCCCCccccccCCccccc---cccc---ccccccc---CCCCCCCccccccc---ccCCCeeEecCC
Q 001016 1078 CN-------LCRVGRGLGVDFFHCMTCNCCL---AKKL---VDHKCRE---KGLETNCPICCDFL---FTSSATVRALPC 1138 (1190)
Q Consensus 1078 Cg-------iCrvg~gl~~~~fHC~~C~~C~---s~~l---~~H~C~e---~~~~~~CpICle~l---f~s~~~v~~LpC 1138 (1190)
|| +=-.|+--.-.-|.|-.|+-|+ +..+ ++--|++ +.-.-.|+||-+.| -...+.+++..=
T Consensus 340 Cg~~I~d~iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAPrCs~C~~PI~P~~G~~etvRvvam 419 (468)
T KOG1701|consen 340 CGEPIMDRILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAPRCSVCGNPILPRDGKDETVRVVAM 419 (468)
T ss_pred hhhHHHHHHHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcCcchhhccCCccCCCCCcceEEEEEc
Q ss_pred CCccCHhhHHHHHhcCCCCCCCcccc
Q 001016 1139 GHFMHSDCFQAYTCSHYICPICSKSL 1164 (1190)
Q Consensus 1139 gH~fH~~Ci~~wl~~~~~CPiCrk~l 1164 (1190)
+--||.+| |.|--|+..|
T Consensus 420 dr~fHv~C--------Y~CEDCg~~L 437 (468)
T KOG1701|consen 420 DRDFHVNC--------YKCEDCGLLL 437 (468)
T ss_pred cccccccc--------eehhhcCccc
No 128
>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=66.26 E-value=4.3 Score=42.33 Aligned_cols=47 Identities=26% Similarity=0.579 Sum_probs=39.6
Q ss_pred CCccceEeccccccccCCCCcccCCCCCccccCCCCCccccccCCcccccccc
Q 001016 1052 GLSMAKYYCGICKFFDDERVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLAKK 1104 (1190)
Q Consensus 1052 ~~~fa~Y~C~~C~l~dd~k~~yHC~~CgiCrvg~gl~~~~fHC~~C~~C~s~~ 1104 (1190)
+......||..|+.+-.. ..+||..||.|-.+. -.||.=-|.|+...
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 567788899999999766 489999999999985 36999999998764
No 129
>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=65.91 E-value=4.8 Score=49.87 Aligned_cols=45 Identities=22% Similarity=0.583 Sum_probs=39.5
Q ss_pred ccccccCCcccCcccccccCCCCCCccccceeeccccCccccCCCCCCC
Q 001016 999 LRAACCGKLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVGPVCTT 1047 (1190)
Q Consensus 999 l~~pcC~k~y~Cr~CHde~~dH~~~r~~~~~~~C~~C~~~q~~~~~C~~ 1047 (1190)
+.|.-||....|..|.-...-|.. ...+.|-+|+..+++...|++
T Consensus 214 ~~C~~Cg~~~~C~~C~~~l~~h~~----~~~l~Ch~Cg~~~~~~~~Cp~ 258 (505)
T TIGR00595 214 LLCRSCGYILCCPNCDVSLTYHKK----EGKLRCHYCGYQEPIPKTCPQ 258 (505)
T ss_pred eEhhhCcCccCCCCCCCceEEecC----CCeEEcCCCcCcCCCCCCCCC
Confidence 789999999999999877777753 448999999999999999998
No 130
>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=65.63 E-value=4.2 Score=50.10 Aligned_cols=15 Identities=33% Similarity=0.948 Sum_probs=7.7
Q ss_pred CCCCccceEeccccc
Q 001016 1050 CSGLSMAKYYCGICK 1064 (1190)
Q Consensus 1050 Cc~~~fa~Y~C~~C~ 1064 (1190)
|.....-.|||+.|-
T Consensus 19 c~~~Ei~~~yCp~CL 33 (483)
T PF05502_consen 19 CVSEEIDSYYCPNCL 33 (483)
T ss_pred hcccccceeECcccc
Confidence 334455555555554
No 131
>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=65.21 E-value=3 Score=38.39 Aligned_cols=34 Identities=26% Similarity=0.741 Sum_probs=16.7
Q ss_pred ceeeccccCccccCCCCCCCCCCCCCc--------cceEeccccc
Q 001016 1028 TEMMCMRCLKVQPVGPVCTTLSCSGLS--------MAKYYCGICK 1064 (1190)
Q Consensus 1028 ~~~~C~~C~~~q~~~~~C~~~~Cc~~~--------fa~Y~C~~C~ 1064 (1190)
....|..|.........|+. | +.. -+.|||..|+
T Consensus 16 ~~~~C~~C~~~~~~~a~CPd--C-~~~Le~LkACGAvdYFC~~c~ 57 (70)
T PF07191_consen 16 GHYHCEACQKDYKKEAFCPD--C-GQPLEVLKACGAVDYFCNHCH 57 (70)
T ss_dssp TEEEETTT--EEEEEEE-TT--T--SB-EEEEETTEEEEE-TTTT
T ss_pred CEEECccccccceecccCCC--c-ccHHHHHHHhcccceeeccCC
Confidence 35566666655444445555 2 322 3688888886
No 132
>PHA03096 p28-like protein; Provisional
Probab=64.58 E-value=3.5 Score=47.50 Aligned_cols=48 Identities=13% Similarity=0.180 Sum_probs=31.9
Q ss_pred CCCcccccccccC---CCeeEec-CCCCccCHhhHHHHHhc---CCC---CCCCcccc
Q 001016 1117 TNCPICCDFLFTS---SATVRAL-PCGHFMHSDCFQAYTCS---HYI---CPICSKSL 1164 (1190)
Q Consensus 1117 ~~CpICle~lf~s---~~~v~~L-pCgH~fH~~Ci~~wl~~---~~~---CPiCrk~l 1164 (1190)
..|.||+|..... ......| .|.|.|...|+..|... .-+ ||.|+..+
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~~~~~~ 236 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRRLNTVI 236 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCccccchhhHH
Confidence 5799999886543 1222334 89999999999999643 233 55555444
No 133
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=64.21 E-value=5.7 Score=45.26 Aligned_cols=15 Identities=20% Similarity=0.751 Sum_probs=10.5
Q ss_pred CCcccCCCCCccccC
Q 001016 1070 RVVYHCPFCNLCRVG 1084 (1190)
Q Consensus 1070 k~~yHC~~CgiCrvg 1084 (1190)
+..++|++||.=.|.
T Consensus 159 ~ka~~C~~C~K~YvS 173 (279)
T KOG2462|consen 159 KKAFSCKYCGKVYVS 173 (279)
T ss_pred cccccCCCCCceeee
Confidence 667777777766665
No 134
>PRK00808 hypothetical protein; Provisional
Probab=63.66 E-value=24 Score=36.68 Aligned_cols=96 Identities=19% Similarity=0.197 Sum_probs=57.0
Q ss_pred hhHHhHHHHHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHH----HHHHHhhCCH-----
Q 001016 361 SFAQEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQV----LPLARRHFSP----- 431 (1190)
Q Consensus 361 ~me~EH~~ie~l~e~l~~ll~~l~~~~~~~~~~~~~~eLa~~l~~L~~~L~~Hf~~EE~qv----fPLl~~~fS~----- 431 (1190)
.+..+|++.-.+++.|..++.. .+ ...+...+..|.+-...||..||.-. +|-+..|--.
T Consensus 16 ~ID~qH~~L~~lin~l~~a~~~---~~--------~~~i~~~l~~L~~y~~~HF~~EE~lM~~~~Yp~~~~H~~~H~~fl 84 (150)
T PRK00808 16 VIDQQHKRIVDYINHLHDAQDS---PD--------RLAVAEVIDELIDYTLSHFAFEESLMEEAGYPFLVPHKRVHELFI 84 (150)
T ss_pred HHHHHHHHHHHHHHHHHHHHHc---Cc--------HHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHH
Confidence 5667888777777776655421 11 24567778899999999999999753 4444443221
Q ss_pred HHHHHHHHhHhh--cCCHHHHHHHHhhhcCCCCHHHHH
Q 001016 432 KRQRELLYQSLC--VMPLKLIECVLPWLVGSLSEEEAR 467 (1190)
Q Consensus 432 eEq~~L~~~~l~--smPl~~l~~vLpWl~~~Ls~eE~~ 467 (1190)
++..++..++.. .+...++..+..||+.++.-..++
T Consensus 85 ~~l~~l~~~~~~g~~~~~~l~~~L~~WL~~HI~~~D~~ 122 (150)
T PRK00808 85 KRVEEYRERFQAGEDVADELHGMLSRWLFNHIRNDDAA 122 (150)
T ss_pred HHHHHHHHHHHccchHHHHHHHHHHHHHHHHHHHHhHH
Confidence 222222222211 123345556777887777666544
No 135
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=63.33 E-value=2.7 Score=52.41 Aligned_cols=45 Identities=24% Similarity=0.680 Sum_probs=28.8
Q ss_pred CCCCcccccccccCCCeeEecCCC---CccCHhhHHH----HH----hcCCCCCCCc
Q 001016 1116 ETNCPICCDFLFTSSATVRALPCG---HFMHSDCFQA----YT----CSHYICPICS 1161 (1190)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCg---H~fH~~Ci~~----wl----~~~~~CPiCr 1161 (1190)
-..||+|+-. |...+....+.|. --.|-.|..- +. ...|.|-+||
T Consensus 145 ~~~cPvc~~~-Y~~~e~~~~~~c~~c~rwsh~~c~~~sdd~~~q~~vD~~~~CS~CR 200 (694)
T KOG4443|consen 145 LSYCPVCLIV-YQDSESLPMVCCSICQRWSHGGCDGISDDKYMQAQVDLQYKCSTCR 200 (694)
T ss_pred cccCchHHHh-hhhccchhhHHHHHhcccccCCCCccchHHHHHHhhhhhcccceee
Confidence 4679999864 5555555444444 4478888532 22 2368999999
No 136
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=62.23 E-value=6.5 Score=50.69 Aligned_cols=54 Identities=22% Similarity=0.481 Sum_probs=43.1
Q ss_pred ccccccCCcccCcccccccCCCCCCccccceeeccccCccccCCCCCCCCCCCCCccceEe
Q 001016 999 LRAACCGKLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVGPVCTTLSCSGLSMAKYY 1059 (1190)
Q Consensus 999 l~~pcC~k~y~Cr~CHde~~dH~~~r~~~~~~~C~~C~~~q~~~~~C~~~~Cc~~~fa~Y~ 1059 (1190)
+.|.-||-.+.|++|=.-..=|.- +..+.|-+|+..+++-..|++ ||...=+|+
T Consensus 436 l~C~~Cg~v~~Cp~Cd~~lt~H~~----~~~L~CH~Cg~~~~~p~~Cp~---Cgs~~L~~~ 489 (730)
T COG1198 436 LLCRDCGYIAECPNCDSPLTLHKA----TGQLRCHYCGYQEPIPQSCPE---CGSEHLRAV 489 (730)
T ss_pred eecccCCCcccCCCCCcceEEecC----CCeeEeCCCCCCCCCCCCCCC---CCCCeeEEe
Confidence 899999999999999665555543 369999999999999999998 476544444
No 137
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=60.96 E-value=3 Score=52.09 Aligned_cols=29 Identities=31% Similarity=0.595 Sum_probs=23.5
Q ss_pred CCcccccc----ccccccccCCcccCcccccccC
Q 001016 989 GCEHYKRN----CKLRAACCGKLFTCRFCHDKVS 1018 (1190)
Q Consensus 989 gC~HY~r~----ckl~~pcC~k~y~Cr~CHde~~ 1018 (1190)
||.||--. +.-.|.-+|+|| |..||....
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 89998773 557788899977 999998754
No 138
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=59.89 E-value=4 Score=52.19 Aligned_cols=45 Identities=29% Similarity=0.724 Sum_probs=35.4
Q ss_pred CCCcccccccccCCCeeEecCCCCccCHhhHHHHHhc--CCCCCCCcccccc
Q 001016 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS--HYICPICSKSLGD 1166 (1190)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~--~~~CPiCrk~l~~ 1166 (1190)
..|+||++ .+.....+|||.|..+|+...+.. ...||+||..+..
T Consensus 455 ~~c~ic~~-----~~~~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~ 501 (674)
T KOG1001|consen 455 HWCHICCD-----LDSFFITRCGHDFCVECLKKSIQQSENAPCPLCRNVLKE 501 (674)
T ss_pred cccccccc-----cccceeecccchHHHHHHHhccccccCCCCcHHHHHHHH
Confidence 78999998 245667899999999999987643 3469999976653
No 139
>PF12773 DZR: Double zinc ribbon
Probab=59.80 E-value=7.7 Score=32.67 Aligned_cols=22 Identities=23% Similarity=0.617 Sum_probs=13.4
Q ss_pred ccccCccccC-CCCCCCCCCCCCccc
Q 001016 1032 CMRCLKVQPV-GPVCTTLSCSGLSMA 1056 (1190)
Q Consensus 1032 C~~C~~~q~~-~~~C~~~~Cc~~~fa 1056 (1190)
|..|+++.+. ...|++ ||..+.
T Consensus 1 Cp~Cg~~~~~~~~fC~~---CG~~l~ 23 (50)
T PF12773_consen 1 CPHCGTPNPDDAKFCPH---CGTPLP 23 (50)
T ss_pred CCCcCCcCCccccCChh---hcCChh
Confidence 5667766443 456777 466655
No 140
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=58.15 E-value=2.6 Score=56.04 Aligned_cols=48 Identities=31% Similarity=0.591 Sum_probs=39.3
Q ss_pred CCCCcccccccccCCCeeEecCCCCccCHhhHHHHHhcCCCCCCCcccccc
Q 001016 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1166 (1190)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrk~l~~ 1166 (1190)
...|+||++.+-. .-.+.-|||.+...|+..|+..+..||+|+...++
T Consensus 1153 ~~~c~ic~dil~~---~~~I~~cgh~~c~~c~~~~l~~~s~~~~~ksi~~d 1200 (1394)
T KOG0298|consen 1153 HFVCEICLDILRN---QGGIAGCGHEPCCRCDELWLYASSRCPICKSIKGD 1200 (1394)
T ss_pred ccchHHHHHHHHh---cCCeeeechhHhhhHHHHHHHHhccCcchhhhhhh
Confidence 4489999987531 22456799999999999999999999999976665
No 141
>PRK04023 DNA polymerase II large subunit; Validated
Probab=57.95 E-value=8.8 Score=50.39 Aligned_cols=48 Identities=23% Similarity=0.472 Sum_probs=31.2
Q ss_pred CCCCCCCCCCCCccceEeccccccccCCCCcccCCCCCccccCCCCCccccccCCccccc
Q 001016 1042 GPVCTTLSCSGLSMAKYYCGICKFFDDERVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCL 1101 (1190)
Q Consensus 1042 ~~~C~~~~Cc~~~fa~Y~C~~C~l~dd~k~~yHC~~CgiCrvg~gl~~~~fHC~~C~~C~ 1101 (1190)
...|+. ||......+|+.|.-- ...+|.|+.||..-.+ +.|.+||.=.
T Consensus 626 ~RfCps---CG~~t~~frCP~CG~~--Te~i~fCP~CG~~~~~-------y~CPKCG~El 673 (1121)
T PRK04023 626 RRKCPS---CGKETFYRRCPFCGTH--TEPVYRCPRCGIEVEE-------DECEKCGREP 673 (1121)
T ss_pred CccCCC---CCCcCCcccCCCCCCC--CCcceeCccccCcCCC-------CcCCCCCCCC
Confidence 356876 4777667778888644 3567888888655332 4477777644
No 142
>PRK05580 primosome assembly protein PriA; Validated
Probab=56.53 E-value=8.4 Score=49.51 Aligned_cols=49 Identities=24% Similarity=0.655 Sum_probs=41.5
Q ss_pred ccccccCCcccCcccccccCCCCCCccccceeeccccCccccCCCCCCCCCCCCCc
Q 001016 999 LRAACCGKLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVGPVCTTLSCSGLS 1054 (1190)
Q Consensus 999 l~~pcC~k~y~Cr~CHde~~dH~~~r~~~~~~~C~~C~~~q~~~~~C~~~~Cc~~~ 1054 (1190)
+.|.-||....|..|.-...-|.. ...+.|-+|+..++....|++ | |..
T Consensus 382 ~~C~~Cg~~~~C~~C~~~l~~h~~----~~~l~Ch~Cg~~~~~~~~Cp~--C-g~~ 430 (679)
T PRK05580 382 LLCRDCGWVAECPHCDASLTLHRF----QRRLRCHHCGYQEPIPKACPE--C-GST 430 (679)
T ss_pred eEhhhCcCccCCCCCCCceeEECC----CCeEECCCCcCCCCCCCCCCC--C-cCC
Confidence 889999999999999887766653 458999999999998899998 5 544
No 143
>KOG2068 consensus MOT2 transcription factor [Transcription]
Probab=56.18 E-value=7.3 Score=45.41 Aligned_cols=52 Identities=25% Similarity=0.545 Sum_probs=39.8
Q ss_pred CCCCCCcccccccccCCCeeEecCCCCccCHhhHHHHHhcCCCCCCCccccc
Q 001016 1114 GLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1165 (1190)
Q Consensus 1114 ~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrk~l~ 1165 (1190)
.....||||.+++-..+....--|||+..+..|...-...+.+||.||++..
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 3457899999986444434444578888888898888888999999997765
No 144
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=55.95 E-value=10 Score=49.01 Aligned_cols=46 Identities=20% Similarity=0.574 Sum_probs=30.0
Q ss_pred cceeeccccCccccCCCCCCCCCCCCCccc------eEeccccccccCCCCcccCCCCCcc
Q 001016 1027 TTEMMCMRCLKVQPVGPVCTTLSCSGLSMA------KYYCGICKFFDDERVVYHCPFCNLC 1081 (1190)
Q Consensus 1027 ~~~~~C~~C~~~q~~~~~C~~~~Cc~~~fa------~Y~C~~C~l~dd~k~~yHC~~CgiC 1081 (1190)
.+.++|..|+.+- .|+| |...+. ...|..|..= .+.+.+||.||-=
T Consensus 433 s~~l~C~~Cg~v~----~Cp~---Cd~~lt~H~~~~~L~CH~Cg~~--~~~p~~Cp~Cgs~ 484 (730)
T COG1198 433 APLLLCRDCGYIA----ECPN---CDSPLTLHKATGQLRCHYCGYQ--EPIPQSCPECGSE 484 (730)
T ss_pred cceeecccCCCcc----cCCC---CCcceEEecCCCeeEeCCCCCC--CCCCCCCCCCCCC
Confidence 4589999999886 7988 455443 3345444432 2667777777743
No 145
>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]
Probab=55.71 E-value=4.6 Score=51.48 Aligned_cols=88 Identities=13% Similarity=0.053 Sum_probs=62.0
Q ss_pred HHHHHHHHhHHHHHH-----HHHHHHHhhCCHHHHHHHHHhHhhcCCHHHHHHHHhhhcCCCCHHHHHHHHHHhHhhCCC
Q 001016 405 LIMASIQKHFRNEEV-----QVLPLARRHFSPKRQRELLYQSLCVMPLKLIECVLPWLVGSLSEEEARSFLQNIYMAAPA 479 (1190)
Q Consensus 405 ~L~~~L~~Hf~~EE~-----qvfPLl~~~fS~eEq~~L~~~~l~smPl~~l~~vLpWl~~~Ls~eE~~~~L~~l~~~aP~ 479 (1190)
.+-...-.|+..|++ -+.|.+=.. +-+||+..+.++.-.--+..+.-+||=.-+.|.|.-...+|.-.=. |.
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 334446666654443 344444433 4578999999888777777888889988899999999988876554 55
Q ss_pred ChhHHHHHHHHhhhcCC
Q 001016 480 SDSALITLFAGWACKGH 496 (1190)
Q Consensus 480 ~~~~~~~l~~~w~~~~~ 496 (1190)
.+. |-.+++.|-+.-|
T Consensus 470 ~~~-F~e~i~~Wp~~Ly 485 (846)
T KOG2066|consen 470 VKG-FLELIKEWPGHLY 485 (846)
T ss_pred HHH-HHHHHHhCChhhh
Confidence 555 8889999955444
No 146
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=55.33 E-value=6.3 Score=45.00 Aligned_cols=43 Identities=30% Similarity=0.795 Sum_probs=33.5
Q ss_pred CCCcccccccccCCCeeEecCCCCccCHhhHHHH-HhcCCCCCCCcc
Q 001016 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAY-TCSHYICPICSK 1162 (1190)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~w-l~~~~~CPiCrk 1162 (1190)
..||.|.--+ +.+++.--|||.|+.+||..- +...+.||.|.+
T Consensus 275 LkCplc~~Ll---rnp~kT~cC~~~fc~eci~~al~dsDf~CpnC~r 318 (427)
T COG5222 275 LKCPLCHCLL---RNPMKTPCCGHTFCDECIGTALLDSDFKCPNCSR 318 (427)
T ss_pred ccCcchhhhh---hCcccCccccchHHHHHHhhhhhhccccCCCccc
Confidence 6799998643 345555568999999999875 567899999986
No 147
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=55.00 E-value=8.6 Score=30.17 Aligned_cols=24 Identities=38% Similarity=1.089 Sum_probs=18.9
Q ss_pred eEeccccccc-cCCCCcccCCCCCc
Q 001016 1057 KYYCGICKFF-DDERVVYHCPFCNL 1080 (1190)
Q Consensus 1057 ~Y~C~~C~l~-dd~k~~yHC~~Cgi 1080 (1190)
.|-|.+|.+. +.++.++.||.||.
T Consensus 1 ~~~C~~CGy~y~~~~~~~~CP~Cg~ 25 (33)
T cd00350 1 KYVCPVCGYIYDGEEAPWVCPVCGA 25 (33)
T ss_pred CEECCCCCCEECCCcCCCcCcCCCC
Confidence 4788999765 55578999999985
No 148
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=54.16 E-value=9.8 Score=44.22 Aligned_cols=46 Identities=26% Similarity=0.615 Sum_probs=34.2
Q ss_pred CCCCcccccccccCCCeeEecCCCCccCHhhHHHHHhcCCCCCCCcccccch
Q 001016 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGDM 1167 (1190)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrk~l~~m 1167 (1190)
-.+||||.++|.. ++.+=+=||+-...|-. +....||.||.++++.
T Consensus 48 lleCPvC~~~l~~---Pi~QC~nGHlaCssC~~---~~~~~CP~Cr~~~g~~ 93 (299)
T KOG3002|consen 48 LLDCPVCFNPLSP---PIFQCDNGHLACSSCRT---KVSNKCPTCRLPIGNI 93 (299)
T ss_pred hccCchhhccCcc---cceecCCCcEehhhhhh---hhcccCCccccccccH
Confidence 4689999998532 23332338999999964 4578999999999964
No 149
>PRK14873 primosome assembly protein PriA; Provisional
Probab=54.00 E-value=9.4 Score=48.96 Aligned_cols=44 Identities=25% Similarity=0.400 Sum_probs=36.7
Q ss_pred ccccccCCcccCcccccccCCCCCCccccceeeccccCccccCCCCCCC
Q 001016 999 LRAACCGKLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVGPVCTT 1047 (1190)
Q Consensus 999 l~~pcC~k~y~Cr~CHde~~dH~~~r~~~~~~~C~~C~~~q~~~~~C~~ 1047 (1190)
+.|.-||....|..|.--..=|. ....+.|-+|+..+ ....|++
T Consensus 384 l~C~~Cg~~~~C~~C~~~L~~h~----~~~~l~Ch~CG~~~-~p~~Cp~ 427 (665)
T PRK14873 384 LACARCRTPARCRHCTGPLGLPS----AGGTPRCRWCGRAA-PDWRCPR 427 (665)
T ss_pred eEhhhCcCeeECCCCCCceeEec----CCCeeECCCCcCCC-cCccCCC
Confidence 79999999999999988876664 24589999999976 4679988
No 150
>PF14357 DUF4404: Domain of unknown function (DUF4404)
Probab=53.56 E-value=91 Score=29.84 Aligned_cols=82 Identities=13% Similarity=0.095 Sum_probs=64.0
Q ss_pred HHHHHHHHHHHHHhhccCCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHHHhhhhHHHHHHhhhhhHHHHHHHHH
Q 001016 54 IKSELDVLHRAAMAFATNLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIRVKNIARTYSLEHEGESVLFDQLF 133 (1190)
Q Consensus 54 lR~eL~~l~~~a~~~~~~~gd~~~~~~l~~r~~~L~~~~~~H~~aEDevI~PaLd~Rv~~v~~~~~~EH~~~~~lf~~l~ 133 (1190)
||..|..|+.-+...++ -|......|..=-+.+...+.. ..|...--+.|..|+...+.+++.+|=.....+..|-
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 57888888888888887 5666666665555556666654 5677788899999999999999999999998888887
Q ss_pred HHHHhh
Q 001016 134 ELLNSS 139 (1190)
Q Consensus 134 ~~l~~~ 139 (1190)
..|..+
T Consensus 78 ~sLa~M 83 (85)
T PF14357_consen 78 DSLANM 83 (85)
T ss_pred HHHHHC
Confidence 777543
No 151
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=52.59 E-value=9.7 Score=48.59 Aligned_cols=46 Identities=26% Similarity=0.566 Sum_probs=23.0
Q ss_pred eeccccCccccC-CCCCCCCCCCCCccceEeccccccccCCCCcccCCCCC
Q 001016 1030 MMCMRCLKVQPV-GPVCTTLSCSGLSMAKYYCGICKFFDDERVVYHCPFCN 1079 (1190)
Q Consensus 1030 ~~C~~C~~~q~~-~~~C~~~~Cc~~~fa~Y~C~~C~l~dd~k~~yHC~~Cg 1079 (1190)
++|..|+.+-+. +..|++ ||..+..-.|..|.--- ..+.-.|+.||
T Consensus 2 ~~Cp~Cg~~n~~~akFC~~---CG~~l~~~~Cp~CG~~~-~~~~~fC~~CG 48 (645)
T PRK14559 2 LICPQCQFENPNNNRFCQK---CGTSLTHKPCPQCGTEV-PVDEAHCPNCG 48 (645)
T ss_pred CcCCCCCCcCCCCCccccc---cCCCCCCCcCCCCCCCC-CcccccccccC
Confidence 356666666443 345666 36665544455554321 12333455555
No 152
>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=52.01 E-value=13 Score=45.14 Aligned_cols=31 Identities=23% Similarity=0.356 Sum_probs=18.1
Q ss_pred HHHHHHHhhhccCCCCChHHHHHHHHHHHHHHH
Q 001016 920 NELEAEIRKVSRDSTLDPRRKAYLIQNLMTSRW 952 (1190)
Q Consensus 920 ~~l~~~Ir~i~~~~~l~~~~ka~liq~Lm~~~~ 952 (1190)
..|+..||.|--. .+.+..-...|+++-.|-
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 3566777777533 444445556677765554
No 153
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=51.72 E-value=15 Score=32.37 Aligned_cols=35 Identities=26% Similarity=0.606 Sum_probs=26.9
Q ss_pred CCCCCcccccccccCCCeeEecCCCCccCHhhHHH
Q 001016 1115 LETNCPICCDFLFTSSATVRALPCGHFMHSDCFQA 1149 (1190)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~ 1149 (1190)
....|++|.+.+...++.|+---||=.+|..|.+.
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~ 38 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK 38 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence 45689999999554555555578999999999543
No 154
>PRK01917 cation-binding hemerythrin HHE family protein; Provisional
Probab=51.68 E-value=37 Score=34.89 Aligned_cols=70 Identities=13% Similarity=0.159 Sum_probs=38.9
Q ss_pred HHHHHHHHHHHHHHHhHHHHHHHH----HHHHHhhCCH-----HHHHHHHHhHhh----cCCHHHHHHHHhhhcCCCCHH
Q 001016 398 KLCSQADLIMASIQKHFRNEEVQV----LPLARRHFSP-----KRQRELLYQSLC----VMPLKLIECVLPWLVGSLSEE 464 (1190)
Q Consensus 398 eLa~~l~~L~~~L~~Hf~~EE~qv----fPLl~~~fS~-----eEq~~L~~~~l~----smPl~~l~~vLpWl~~~Ls~e 464 (1190)
.+...++.|..-...||..||.-. +|-+..|--. ++..++..+... .+...++..+..||+.++.-.
T Consensus 38 ~i~~~l~~L~~y~~~HF~~EE~lM~~~~YP~~~~H~~eH~~fl~~v~~l~~~~~~~g~~~~~~~l~~~L~~Wl~~HI~~~ 117 (139)
T PRK01917 38 DFLQALDAWIDHTRHHFAQEERWMEATKFGPRHCHRAEHDEVLAVAADVREKVARDGDFELGRRLVAELPEWFDQHVRTM 117 (139)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 356778888999999999999643 3434333211 122222222211 233444555667777776555
Q ss_pred HHH
Q 001016 465 EAR 467 (1190)
Q Consensus 465 E~~ 467 (1190)
.++
T Consensus 118 D~~ 120 (139)
T PRK01917 118 DAM 120 (139)
T ss_pred HHH
Confidence 543
No 155
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=51.33 E-value=6.8 Score=38.41 Aligned_cols=33 Identities=21% Similarity=0.637 Sum_probs=26.0
Q ss_pred CCcccCCCCC-----ccccCCCCCccccccCCcccccc
Q 001016 1070 RVVYHCPFCN-----LCRVGRGLGVDFFHCMTCNCCLA 1102 (1190)
Q Consensus 1070 k~~yHC~~Cg-----iCrvg~gl~~~~fHC~~C~~C~s 1102 (1190)
+..|-||.|| +|.|.+++++-+-+|..||.-..
T Consensus 20 ~k~FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e 57 (104)
T COG4888 20 PKTFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSFE 57 (104)
T ss_pred CceEecCccCCeeeeEEEEEecCceeEEEcccCcceEE
Confidence 4567888888 88888888888889988886543
No 156
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=51.10 E-value=13 Score=43.39 Aligned_cols=47 Identities=17% Similarity=0.374 Sum_probs=35.1
Q ss_pred CCCCcccccccccCCCeeEecCCCCccCHhhHHHHHhcCCCCCCCccccc
Q 001016 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1165 (1190)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrk~l~ 1165 (1190)
...||||+... .+.. ..--=|=.|+-.|+-.|+....+||+=.+++.
T Consensus 300 ~~~CpvClk~r-~Npt--vl~vSGyVfCY~Ci~~Yv~~~~~CPVT~~p~~ 346 (357)
T KOG0826|consen 300 REVCPVCLKKR-QNPT--VLEVSGYVFCYPCIFSYVVNYGHCPVTGYPAS 346 (357)
T ss_pred cccChhHHhcc-CCCc--eEEecceEEeHHHHHHHHHhcCCCCccCCcch
Confidence 56799999762 2222 22223899999999999999999999777654
No 157
>PLN03086 PRLI-interacting factor K; Provisional
Probab=49.90 E-value=8.1 Score=48.40 Aligned_cols=90 Identities=22% Similarity=0.534 Sum_probs=43.1
Q ss_pred CCcccCCCCCccccCCCCCc------cccccCCcccccccc-ccccc---cccCCCCCCCcccccccccCCCe-------
Q 001016 1070 RVVYHCPFCNLCRVGRGLGV------DFFHCMTCNCCLAKK-LVDHK---CREKGLETNCPICCDFLFTSSAT------- 1132 (1190)
Q Consensus 1070 k~~yHC~~CgiCrvg~gl~~------~~fHC~~C~~C~s~~-l~~H~---C~e~~~~~~CpICle~lf~s~~~------- 1132 (1190)
+..+||+.||-=-....|.+ .-+.|. ||..+... +..|. |.++ ...|+.|... +..++.
T Consensus 451 ~~H~~C~~Cgk~f~~s~LekH~~~~Hkpv~Cp-Cg~~~~R~~L~~H~~thCp~K--pi~C~fC~~~-v~~g~~~~d~~d~ 526 (567)
T PLN03086 451 KNHVHCEKCGQAFQQGEMEKHMKVFHEPLQCP-CGVVLEKEQMVQHQASTCPLR--LITCRFCGDM-VQAGGSAMDVRDR 526 (567)
T ss_pred ccCccCCCCCCccchHHHHHHHHhcCCCccCC-CCCCcchhHHHhhhhccCCCC--ceeCCCCCCc-cccCccccchhhh
Confidence 55677777764111111100 123466 66544333 25663 5544 5679999866 321110
Q ss_pred eEecCCCCccCHhhHHHHHhcCCCCCCCccccc--chhHH
Q 001016 1133 VRALPCGHFMHSDCFQAYTCSHYICPICSKSLG--DMALY 1170 (1190)
Q Consensus 1133 v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrk~l~--~m~~~ 1170 (1190)
...|. .|... | -...+.|..|++.+. +|..+
T Consensus 527 ~s~Lt-~HE~~--C----G~rt~~C~~Cgk~Vrlrdm~~H 559 (567)
T PLN03086 527 LRGMS-EHESI--C----GSRTAPCDSCGRSVMLKEMDIH 559 (567)
T ss_pred hhhHH-HHHHh--c----CCcceEccccCCeeeehhHHHH
Confidence 11111 12111 2 134577999998886 44443
No 158
>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=49.26 E-value=9.4 Score=38.07 Aligned_cols=32 Identities=25% Similarity=0.517 Sum_probs=23.5
Q ss_pred ccccccccCCcccCcccccccCCCCCCccccceeeccccCccccCC
Q 001016 997 CKLRAACCGKLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVG 1042 (1190)
Q Consensus 997 ckl~~pcC~k~y~Cr~CHde~~dH~~~r~~~~~~~C~~C~~~q~~~ 1042 (1190)
-|-.||-||+-| .+... ..|+|.+|+++|++.
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 33333 578999999998876
No 159
>PRK00808 hypothetical protein; Provisional
Probab=48.77 E-value=3.2e+02 Score=28.44 Aligned_cols=110 Identities=16% Similarity=0.228 Sum_probs=71.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcccCCcccHHHHHHHHHHHHHHHHhhhhccccch----hhhhhhhhhhHHhHHHHHHH
Q 001016 297 IMLWHNAIKRELNDIAEAARKIQLSGDFSDLSAFNKRLQFIAEVCIFHSIAEDKVI----FPAVDVELSFAQEHAEEEIQ 372 (1190)
Q Consensus 297 l~~~HkALRrEL~~L~~~a~~~~~~gd~~~L~~L~~r~~fl~~vl~~Hs~aEDevl----FPaL~~r~~me~EH~~ie~l 372 (1190)
+=.-|+.|=.-++.|...+. .++ ...+..-+.+|.+....|=..|+.++ ||.++.+. .+++..
T Consensus 17 ID~qH~~L~~lin~l~~a~~----~~~---~~~i~~~l~~L~~y~~~HF~~EE~lM~~~~Yp~~~~H~------~~H~~f 83 (150)
T PRK00808 17 IDQQHKRIVDYINHLHDAQD----SPD---RLAVAEVIDELIDYTLSHFAFEESLMEEAGYPFLVPHK------RVHELF 83 (150)
T ss_pred HHHHHHHHHHHHHHHHHHHH----cCc---HHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHH------HHHHHH
Confidence 33568777677777665542 222 24566668888899999999898765 77776444 334444
Q ss_pred HHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhh
Q 001016 373 FDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPLARRH 428 (1190)
Q Consensus 373 ~e~l~~ll~~l~~~~~~~~~~~~~~eLa~~l~~L~~~L~~Hf~~EE~qvfPLl~~~ 428 (1190)
++.+..+...... +. ... ...+.-|..-|.+|+..+-....+.+.+.
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 160
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=48.08 E-value=11 Score=44.04 Aligned_cols=27 Identities=19% Similarity=0.696 Sum_probs=20.3
Q ss_pred CCccceEe--ccccccccCCCCcccCCCCCcc
Q 001016 1052 GLSMAKYY--CGICKFFDDERVVYHCPFCNLC 1081 (1190)
Q Consensus 1052 ~~~fa~Y~--C~~C~l~dd~k~~yHC~~CgiC 1081 (1190)
...|--|| |.||++++. .|.||+||+=
T Consensus 60 ~~dfeL~f~Ge~i~~y~~q---SftCPyC~~~ 88 (381)
T KOG1280|consen 60 RVDFELYFGGEPISHYDPQ---SFTCPYCGIM 88 (381)
T ss_pred ccceeeEecCccccccccc---cccCCccccc
Confidence 34576676 788887765 8999999963
No 161
>KOG3850 consensus Predicted membrane protein [Function unknown]
Probab=48.04 E-value=5.4e+02 Score=31.29 Aligned_cols=137 Identities=18% Similarity=0.226 Sum_probs=77.8
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhhcccCCcccH-HHHHHHHHHHHHHHHhhhhccccchhhhhhhhh--hhHHhHHHH
Q 001016 293 PIDEIMLWHNAIKRELNDIAEAARKIQLSGDFSDL-SAFNKRLQFIAEVCIFHSIAEDKVIFPAVDVEL--SFAQEHAEE 369 (1190)
Q Consensus 293 PId~l~~~HkALRrEL~~L~~~a~~~~~~gd~~~L-~~L~~r~~fl~~vl~~Hs~aEDevlFPaL~~r~--~me~EH~~i 369 (1190)
|.+.=-..=+||..||++|.+.-..++ .+..+| .++..-+.|+.+.|. |+.+-.-.|++.+ ..+....+|
T Consensus 254 ~~~s~~~~l~aileeL~eIk~~q~~Le--esye~Lke~~krdy~fi~etLQ-----EERyR~erLEEqLNdlteLqQnEi 326 (455)
T KOG3850|consen 254 PYHSQGAALDAILEELREIKETQALLE--ESYERLKEQIKRDYKFIAETLQ-----EERYRYERLEEQLNDLTELQQNEI 326 (455)
T ss_pred cccccchHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHhHHHHHHHHHH
Confidence 443333335677788888888777764 334456 666666778877776 6666666666555 444444444
Q ss_pred HHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH---HHHHhhCCHHHHHHHHHhHhhcC
Q 001016 370 EIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVL---PLARRHFSPKRQRELLYQSLCVM 445 (1190)
Q Consensus 370 e~l~e~l~~ll~~l~~~~~~~~~~~~~~eLa~~l~~L~~~L~~Hf~~EE~qvf---PLl~~~fS~eEq~~L~~~~l~sm 445 (1190)
..+=-++...-..++= --| +=+..+.+.+++...|+.+=|.+.- -+--++++++-|..|+.+++-.+
T Consensus 327 ~nLKqElasmeervaY--------Qsy-ERaRdIqEalEscqtrisKlEl~qq~qqv~Q~e~~~na~a~~llgk~iNii 396 (455)
T KOG3850|consen 327 ANLKQELASMEERVAY--------QSY-ERARDIQEALESCQTRISKLELQQQQQQVVQLEGLENAVARRLLGKFINII 396 (455)
T ss_pred HHHHHHHHHHHHHHHH--------HHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccHHHHHHHHHHHH
Confidence 3332222211111100 001 1244566667777777777776544 22335677778888888777543
No 162
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=47.24 E-value=11 Score=43.63 Aligned_cols=33 Identities=30% Similarity=0.829 Sum_probs=24.2
Q ss_pred EecCCCCccCHhhHHHHHhcCCCCCCCcccccchh
Q 001016 1134 RALPCGHFMHSDCFQAYTCSHYICPICSKSLGDMA 1168 (1190)
Q Consensus 1134 ~~LpCgH~fH~~Ci~~wl~~~~~CPiCrk~l~~m~ 1168 (1190)
+.+||.|+|+.+|... .....||.|.-.|..++
T Consensus 105 RmIPCkHvFCl~CAr~--~~dK~Cp~C~d~VqrIe 137 (389)
T KOG2932|consen 105 RMIPCKHVFCLECARS--DSDKICPLCDDRVQRIE 137 (389)
T ss_pred cccccchhhhhhhhhc--CccccCcCcccHHHHHH
Confidence 5579999999999643 22457999987776543
No 163
>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=46.80 E-value=76 Score=31.37 Aligned_cols=51 Identities=20% Similarity=0.232 Sum_probs=32.2
Q ss_pred hhHHhHHHHHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHH----HHHHHhh
Q 001016 361 SFAQEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQV----LPLARRH 428 (1190)
Q Consensus 361 ~me~EH~~ie~l~e~l~~ll~~l~~~~~~~~~~~~~~eLa~~l~~L~~~L~~Hf~~EE~qv----fPLl~~~ 428 (1190)
.+..+|++.-.+++.|..++.. ...+..|..-...||..||.-. +|-+..|
T Consensus 14 ~ID~qH~~L~~l~n~l~~a~~~-----------------~~~l~~L~~y~~~HF~~EE~~M~~~~yp~~~~H 68 (113)
T cd00522 14 VIDDEHKTLFNGINDLSEANNR-----------------ADNLKELVDYTVKHFKDEEALMEAAGYPDYEEH 68 (113)
T ss_pred HHHHHHHHHHHHHHHHHHHHhH-----------------HHHHHHHHHHHHHHHHHHHHHHHHcCCCCHHHH
Confidence 4556666666665555544422 2356677777899999999764 4555544
No 164
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=46.10 E-value=10 Score=41.79 Aligned_cols=39 Identities=38% Similarity=0.791 Sum_probs=28.2
Q ss_pred CcccccccccCCCeeEecCCCCc-cCHhhHHHHHhcCCCCCCCccccc
Q 001016 1119 CPICCDFLFTSSATVRALPCGHF-MHSDCFQAYTCSHYICPICSKSLG 1165 (1190)
Q Consensus 1119 CpICle~lf~s~~~v~~LpCgH~-fH~~Ci~~wl~~~~~CPiCrk~l~ 1165 (1190)
|-+|-+. ...|..+||-|. ++..|-.. -.+||+|+....
T Consensus 161 Cr~C~~~----~~~VlllPCrHl~lC~~C~~~----~~~CPiC~~~~~ 200 (207)
T KOG1100|consen 161 CRKCGER----EATVLLLPCRHLCLCGICDES----LRICPICRSPKT 200 (207)
T ss_pred ceecCcC----CceEEeecccceEeccccccc----CccCCCCcChhh
Confidence 8888765 335788999976 66788533 455999997654
No 165
>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=42.74 E-value=12 Score=46.36 Aligned_cols=35 Identities=23% Similarity=0.524 Sum_probs=19.4
Q ss_pred CcccCcccccccCCCCCCccccceeeccccCccccC
Q 001016 1006 KLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPV 1041 (1190)
Q Consensus 1006 k~y~Cr~CHde~~dH~~~r~~~~~~~C~~C~~~q~~ 1041 (1190)
+.|-|+.||.-.... .--..+.-..|..|..+.|.
T Consensus 4 ~L~fC~~C~~irc~~-c~~~Ei~~~yCp~CL~~~p~ 38 (483)
T PF05502_consen 4 ELYFCEHCHKIRCPR-CVSEEIDSYYCPNCLFEVPS 38 (483)
T ss_pred cceecccccccCChh-hcccccceeECccccccCCh
Confidence 467788888654322 11122445567777666554
No 166
>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=42.47 E-value=8.3 Score=49.85 Aligned_cols=45 Identities=27% Similarity=0.600 Sum_probs=0.0
Q ss_pred eeeccccCccccCCCCCCCCCCCCCccceEeccccccccCCCCcccCCCCC
Q 001016 1029 EMMCMRCLKVQPVGPVCTTLSCSGLSMAKYYCGICKFFDDERVVYHCPFCN 1079 (1190)
Q Consensus 1029 ~~~C~~C~~~q~~~~~C~~~~Cc~~~fa~Y~C~~C~l~dd~k~~yHC~~Cg 1079 (1190)
.-.|..|+++... ..|+. |.....-.|+|+.|+.--++. +||.||
T Consensus 655 ~r~Cp~Cg~~t~~-~~Cp~--CG~~T~~~~~Cp~C~~~~~~~---~C~~C~ 699 (900)
T PF03833_consen 655 RRRCPKCGKETFY-NRCPE--CGSHTEPVYVCPDCGIEVEED---ECPKCG 699 (900)
T ss_dssp ---------------------------------------------------
T ss_pred cccCcccCCcchh-hcCcc--cCCccccceeccccccccCcc---cccccc
Confidence 4456666655422 35655 433345566666665421111 566666
No 167
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=42.34 E-value=17 Score=42.16 Aligned_cols=43 Identities=23% Similarity=0.668 Sum_probs=33.0
Q ss_pred CCcccccccccCCCeeEecCCCCccCHhhHHHHHhc---CCCCCCCc
Q 001016 1118 NCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS---HYICPICS 1161 (1190)
Q Consensus 1118 ~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~---~~~CPiCr 1161 (1190)
.||+=.|. -+...+...|.|||.+-..-++...+. .+.||.|-
T Consensus 338 iCPVlKe~-~t~ENpP~ml~CgHVIskeal~~LS~nG~~~FKCPYCP 383 (396)
T COG5109 338 ICPVLKEL-CTDENPPVMLECGHVISKEALSVLSQNGVLSFKCPYCP 383 (396)
T ss_pred eccccHhh-hcccCCCeeeeccceeeHHHHHHHhhcCcEEeeCCCCC
Confidence 47776554 445556778999999999999988765 47799995
No 168
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=41.30 E-value=15 Score=40.35 Aligned_cols=31 Identities=35% Similarity=0.881 Sum_probs=22.5
Q ss_pred ccCCCeeEecCCCCccCHhhHHHHHhcCCCCCCCcc
Q 001016 1127 FTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSK 1162 (1190)
Q Consensus 1127 f~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrk 1162 (1190)
|.....++--.|+-.||..|+. ...||-|.+
T Consensus 167 F~~~~~~~C~~C~~v~H~~C~~-----~~~CpkC~R 197 (202)
T PF13901_consen 167 FQIDTTVRCPKCKSVFHKSCFR-----KKSCPKCAR 197 (202)
T ss_pred CCCCCeeeCCcCccccchhhcC-----CCCCCCcHh
Confidence 3443445557899999999975 266999964
No 169
>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=41.18 E-value=27 Score=30.04 Aligned_cols=41 Identities=32% Similarity=0.878 Sum_probs=19.9
Q ss_pred CCCcccccccccCCCeeEecCCCCccCHhhHH--HHHh-----cCCCCCCCccc
Q 001016 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQ--AYTC-----SHYICPICSKS 1163 (1190)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~--~wl~-----~~~~CPiCrk~ 1163 (1190)
..|||....| ..+++...|.|. .||| .|+. ....||+|+++
T Consensus 3 L~CPls~~~i---~~P~Rg~~C~H~---~CFDl~~fl~~~~~~~~W~CPiC~~~ 50 (50)
T PF02891_consen 3 LRCPLSFQRI---RIPVRGKNCKHL---QCFDLESFLESNQRTPKWKCPICNKP 50 (50)
T ss_dssp SB-TTTSSB----SSEEEETT--SS-----EEHHHHHHHHHHS---B-TTT---
T ss_pred eeCCCCCCEE---EeCccCCcCccc---ceECHHHHHHHhhccCCeECcCCcCc
Confidence 3689988764 347888889877 5654 3553 24679999874
No 170
>PHA00626 hypothetical protein
Probab=40.68 E-value=23 Score=31.40 Aligned_cols=19 Identities=16% Similarity=0.160 Sum_probs=9.2
Q ss_pred eccccccccCCCCcccCCCCCc
Q 001016 1059 YCGICKFFDDERVVYHCPFCNL 1080 (1190)
Q Consensus 1059 ~C~~C~l~dd~k~~yHC~~Cgi 1080 (1190)
-|.+|+-+ ++.|.|++||.
T Consensus 13 rcg~cr~~---snrYkCkdCGY 31 (59)
T PHA00626 13 KEKTMRGW---SDDYVCCDCGY 31 (59)
T ss_pred eeceeccc---CcceEcCCCCC
Confidence 44555444 23455555553
No 171
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=40.64 E-value=24 Score=47.73 Aligned_cols=33 Identities=30% Similarity=0.704 Sum_probs=19.3
Q ss_pred CCCCCCCCCCCccceEeccccccccCCCCcccCCCCCc
Q 001016 1043 PVCTTLSCSGLSMAKYYCGICKFFDDERVVYHCPFCNL 1080 (1190)
Q Consensus 1043 ~~C~~~~Cc~~~fa~Y~C~~C~l~dd~k~~yHC~~Cgi 1080 (1190)
..|++ | |..--..||+.|.-.- +.+|+|+.||.
T Consensus 668 rkCPk--C-G~~t~~~fCP~CGs~t--e~vy~CPsCGa 700 (1337)
T PRK14714 668 RRCPS--C-GTETYENRCPDCGTHT--EPVYVCPDCGA 700 (1337)
T ss_pred EECCC--C-CCccccccCcccCCcC--CCceeCccCCC
Confidence 35776 3 5543334777775432 34677777776
No 172
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=40.34 E-value=12 Score=42.63 Aligned_cols=51 Identities=22% Similarity=0.546 Sum_probs=37.5
Q ss_pred CCCCcccccccccCCCeeEecCCC-----CccCHhhHHHHHh--cCCCCCCCcccccc
Q 001016 1116 ETNCPICCDFLFTSSATVRALPCG-----HFMHSDCFQAYTC--SHYICPICSKSLGD 1166 (1190)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCg-----H~fH~~Ci~~wl~--~~~~CPiCrk~l~~ 1166 (1190)
...|=||.+............||. .+.|..|++.|.. .+.+|.+|......
T Consensus 78 ~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~~ 135 (323)
T KOG1609|consen 78 GPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFIN 135 (323)
T ss_pred CCcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhccccCeeeeccccccee
Confidence 467999998754332223456874 6789999999986 67889999976643
No 173
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=39.11 E-value=24 Score=29.50 Aligned_cols=8 Identities=38% Similarity=1.344 Sum_probs=4.9
Q ss_pred cccCCCCC
Q 001016 1072 VYHCPFCN 1079 (1190)
Q Consensus 1072 ~yHC~~Cg 1079 (1190)
..+||+||
T Consensus 21 ~~~Cp~CG 28 (46)
T PRK00398 21 GVRCPYCG 28 (46)
T ss_pred ceECCCCC
Confidence 55666665
No 174
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=38.11 E-value=15 Score=44.26 Aligned_cols=37 Identities=24% Similarity=0.441 Sum_probs=26.2
Q ss_pred CCCCcccccccccCCCeeEecCCCCccCHhhHHHHHh
Q 001016 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC 1152 (1190)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~ 1152 (1190)
..+|.||..+............|||.|..+|+.+++.
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 4679999933222322233679999999999999875
No 175
>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=36.40 E-value=12 Score=39.48 Aligned_cols=10 Identities=30% Similarity=1.085 Sum_probs=6.4
Q ss_pred CCcccCCCCC
Q 001016 1070 RVVYHCPFCN 1079 (1190)
Q Consensus 1070 k~~yHC~~Cg 1079 (1190)
..-|+||.||
T Consensus 126 ~~~F~Cp~Cg 135 (158)
T TIGR00373 126 ELNFTCPRCG 135 (158)
T ss_pred HcCCcCCCCC
Confidence 4457777776
No 176
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=36.38 E-value=15 Score=44.35 Aligned_cols=19 Identities=16% Similarity=0.469 Sum_probs=14.4
Q ss_pred hHHHhcCHHHHHHHHhhhc
Q 001016 912 NDIFRMNQNELEAEIRKVS 930 (1190)
Q Consensus 912 ~~~~~~~q~~l~~~Ir~i~ 930 (1190)
...+++|+.+||..|++.-
T Consensus 50 ~~llk~~~KqLR~li~~Lr 68 (436)
T KOG2593|consen 50 KELLKFNKKQLRKLIASLR 68 (436)
T ss_pred HHHhcccHHHHHHHHHHhh
Confidence 3456788889888888774
No 177
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=36.10 E-value=12 Score=38.91 Aligned_cols=26 Identities=27% Similarity=0.837 Sum_probs=18.9
Q ss_pred cceEeccccccccCCCCcccCCCCC--ccccC
Q 001016 1055 MAKYYCGICKFFDDERVVYHCPFCN--LCRVG 1084 (1190)
Q Consensus 1055 fa~Y~C~~C~l~dd~k~~yHC~~Cg--iCrvg 1084 (1190)
-.+-||.+|.+| ++|-|-.|| +|-|+
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 345578888855 678888888 67776
No 178
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=35.93 E-value=20 Score=45.92 Aligned_cols=50 Identities=20% Similarity=0.469 Sum_probs=34.5
Q ss_pred CCCCCCcccccccccCCCeeEecCCC-----CccCHhhHHHHHhc--CCCCCCCccccc
Q 001016 1114 GLETNCPICCDFLFTSSATVRALPCG-----HFMHSDCFQAYTCS--HYICPICSKSLG 1165 (1190)
Q Consensus 1114 ~~~~~CpICle~lf~s~~~v~~LpCg-----H~fH~~Ci~~wl~~--~~~CPiCrk~l~ 1165 (1190)
.+...|-||.-+ -..++ --.-||. -++|.+|+.+|+.. ...|-+|+..+.
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 445779999865 22222 2234675 46999999999965 466999998764
No 179
>PF14631 FancD2: Fanconi anaemia protein FancD2 nuclease; PDB: 3S4W_B.
Probab=35.21 E-value=8.8e+02 Score=34.58 Aligned_cols=99 Identities=20% Similarity=0.290 Sum_probs=58.4
Q ss_pred HHHHHHHHHHHhhhcCchhHHHHHHHHHH---------HHHHHHHHhHHHHHHHhhhhHhh----cCCHHHHHHH---HH
Q 001016 127 VLFDQLFELLNSSMRNEESYRRELASCTG---------ALQTSISQHMSKEEEQVFPLLIE----KFSFEEQASL---VW 190 (1190)
Q Consensus 127 ~lf~~l~~~l~~~~~~~~~~~~eLa~~l~---------~l~~~l~qHm~~EE~~v~PLl~~----~fS~~E~a~L---~~ 190 (1190)
.++++|++.++.. +..+-+++...+- .+-..|.+=|..++.-+.|.|.. .++++.+..+ +-
T Consensus 192 ~l~~kl~~~l~~a---p~~lq~eiI~~LPeIl~ds~h~~v~~~L~~ll~~~~~L~~~iLd~Ls~L~Ls~~~l~~vr~~vl 268 (1426)
T PF14631_consen 192 ELTDKLFEVLSIA---PVELQKEIISSLPEILDDSQHDEVVEELLELLQENPELTVPILDALSNLNLSPELLEEVREKVL 268 (1426)
T ss_dssp HHHHHHHHHHHHS----TTTHHHHHHTHHHHS-GGGHHHHHHHHHHHHHH-STTHHHHHHHHHHS---HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhC---CHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHhcCCchhhhHHHHHhcCCCCHHHHHHHHHHHH
Confidence 5556666655543 2223344444442 22223333344444445566554 3455555444 45
Q ss_pred HHhcccCHHHHHHHHhhhcCCCCHHHHHHHHHHHhhcC
Q 001016 191 QFLCSIPVNMMAEFLPWLSSSISSDEHQDMRKCLCKII 228 (1190)
Q Consensus 191 ~~i~siP~~~m~~~LpWm~~~lsp~Er~~~l~~l~~~~ 228 (1190)
..+.+++++.|..++..++.++++.+-..+...||+..
T Consensus 269 ~~L~s~~~e~LP~lirFLL~s~t~~da~evI~~LR~~L 306 (1426)
T PF14631_consen 269 EKLSSVDLEDLPVLIRFLLQSITPSDAVEVISELRENL 306 (1426)
T ss_dssp HSTTSS-TTHHHHHHHHHHHS-SSTTHHHHHHHHHHHH
T ss_pred HHHhcCChhhhHHHHHHHHHhCCcccHHHHHHHHHHHc
Confidence 57788999999999999999999999999999999864
No 180
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=35.19 E-value=14 Score=39.94 Aligned_cols=22 Identities=32% Similarity=1.133 Sum_probs=11.5
Q ss_pred Eecccccc---ccCC-CCcccCCCCC
Q 001016 1058 YYCGICKF---FDDE-RVVYHCPFCN 1079 (1190)
Q Consensus 1058 Y~C~~C~l---~dd~-k~~yHC~~Cg 1079 (1190)
|+|+.|+. |++. ...|+||.||
T Consensus 118 Y~Cp~C~~rytf~eA~~~~F~Cp~Cg 143 (178)
T PRK06266 118 FFCPNCHIRFTFDEAMEYGFRCPQCG 143 (178)
T ss_pred EECCCCCcEEeHHHHhhcCCcCCCCC
Confidence 44555532 3333 4457777776
No 181
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=35.11 E-value=29 Score=39.91 Aligned_cols=47 Identities=28% Similarity=0.754 Sum_probs=38.3
Q ss_pred CCccceEeccccccccCCCCcccCCCCCccccCCCCCccccccCCcccccccc
Q 001016 1052 GLSMAKYYCGICKFFDDERVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLAKK 1104 (1190)
Q Consensus 1052 ~~~fa~Y~C~~C~l~dd~k~~yHC~~CgiCrvg~gl~~~~fHC~~C~~C~s~~ 1104 (1190)
|....-+||..|+++-.. ...||.-||.|-.+.. -||.=-|.|+...
T Consensus 108 ~~~~~~~~C~~C~~~rPp-Rs~HCsvC~~CV~rfD-----HHC~WvnnCVG~r 154 (299)
T KOG1311|consen 108 GIQVEWKYCDTCQLYRPP-RSSHCSVCNNCVLRFD-----HHCPWLNNCIGER 154 (299)
T ss_pred CcccceEEcCcCcccCCC-CcccchhhcccccccC-----CCCCCccceECCC
Confidence 677888999999999554 6789999999988752 6998888888654
No 182
>COG0143 MetG Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=34.54 E-value=25 Score=44.24 Aligned_cols=45 Identities=24% Similarity=0.447 Sum_probs=34.6
Q ss_pred ccceEeccccccccCC-CCcccCCCCCccccCCCCCccccccCCcccccccc
Q 001016 1054 SMAKYYCGICKFFDDE-RVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLAKK 1104 (1190)
Q Consensus 1054 ~fa~Y~C~~C~l~dd~-k~~yHC~~CgiCrvg~gl~~~~fHC~~C~~C~s~~ 1104 (1190)
....+||..|.-|=.| .-.=.||+||.+..++ -+|+.||.++...
T Consensus 123 ~~~~~Yc~~~e~fl~dr~v~g~cp~cg~~~arG------D~Ce~Cg~~~~P~ 168 (558)
T COG0143 123 EYEGLYCVSCERFLPDRYVEGTCPKCGGEDARG------DQCENCGRTLDPT 168 (558)
T ss_pred ceeeeEcccccccccchheeccCCCcCccccCc------chhhhccCcCCch
Confidence 4556788888766555 4455799999999985 4899999998764
No 183
>PF10272 Tmpp129: Putative transmembrane protein precursor; InterPro: IPR018801 This entry consists of proteins conserved from worms to humans. They are purported to be transmembrane protein-precursors but their function is unknown.
Probab=34.17 E-value=36 Score=40.59 Aligned_cols=17 Identities=18% Similarity=0.679 Sum_probs=12.8
Q ss_pred HHHHhcCCCCCCCcccc
Q 001016 1148 QAYTCSHYICPICSKSL 1164 (1190)
Q Consensus 1148 ~~wl~~~~~CPiCrk~l 1164 (1190)
+.|+.++-+||.||+.+
T Consensus 334 ~~Wl~~~~~CPtCRa~F 350 (358)
T PF10272_consen 334 ETWLSGKCPCPTCRAKF 350 (358)
T ss_pred hhhhcCCCCCCCCcccc
Confidence 34556678899999865
No 184
>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=33.58 E-value=30 Score=27.53 Aligned_cols=24 Identities=25% Similarity=0.897 Sum_probs=17.0
Q ss_pred eEeccccccc-cCCCCcccCCCCCc
Q 001016 1057 KYYCGICKFF-DDERVVYHCPFCNL 1080 (1190)
Q Consensus 1057 ~Y~C~~C~l~-dd~k~~yHC~~Cgi 1080 (1190)
.|-|.+|.+. +.++.+..||-||.
T Consensus 2 ~~~C~~CG~i~~g~~~p~~CP~Cg~ 26 (34)
T cd00729 2 VWVCPVCGYIHEGEEAPEKCPICGA 26 (34)
T ss_pred eEECCCCCCEeECCcCCCcCcCCCC
Confidence 4778888765 54467778888874
No 185
>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=33.29 E-value=18 Score=30.80 Aligned_cols=40 Identities=30% Similarity=0.757 Sum_probs=28.1
Q ss_pred CcccccccccCCCeeEecCCCCccCHhhHHHHHhcCCCCCCCcccccchh
Q 001016 1119 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGDMA 1168 (1190)
Q Consensus 1119 CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrk~l~~m~ 1168 (1190)
|+.|...+... . +.+..-|..||..|+ +|-.|+++|.+..
T Consensus 1 C~~C~~~I~~~-~-~~~~~~~~~~H~~Cf--------~C~~C~~~l~~~~ 40 (58)
T PF00412_consen 1 CARCGKPIYGT-E-IVIKAMGKFWHPECF--------KCSKCGKPLNDGD 40 (58)
T ss_dssp BTTTSSBESSS-S-EEEEETTEEEETTTS--------BETTTTCBTTTSS
T ss_pred CCCCCCCccCc-E-EEEEeCCcEEEcccc--------ccCCCCCccCCCe
Confidence 77788886532 2 232345899999885 7889999987644
No 186
>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=32.98 E-value=28 Score=26.10 Aligned_cols=20 Identities=20% Similarity=0.552 Sum_probs=14.7
Q ss_pred CCCCCCcccccchhHHHHhhh
Q 001016 1155 YICPICSKSLGDMALYEGFCS 1175 (1190)
Q Consensus 1155 ~~CPiCrk~l~~m~~~~~~lD 1175 (1190)
..||+|.+.+ .+....+-||
T Consensus 2 v~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLD 21 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHH
Confidence 3699999998 5556666676
No 187
>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=32.82 E-value=22 Score=29.38 Aligned_cols=13 Identities=46% Similarity=0.846 Sum_probs=5.9
Q ss_pred cCCCCcccCCCCC
Q 001016 1067 DDERVVYHCPFCN 1079 (1190)
Q Consensus 1067 dd~k~~yHC~~Cg 1079 (1190)
|...+.|-|..||
T Consensus 14 D~~~g~~vC~~CG 26 (43)
T PF08271_consen 14 DPERGELVCPNCG 26 (43)
T ss_dssp ETTTTEEEETTT-
T ss_pred cCCCCeEECCCCC
Confidence 3334555555554
No 188
>PRK07219 DNA topoisomerase I; Validated
Probab=32.68 E-value=50 Score=43.58 Aligned_cols=12 Identities=33% Similarity=0.628 Sum_probs=8.0
Q ss_pred cccCCCCCcccc
Q 001016 1072 VYHCPFCNLCRV 1083 (1190)
Q Consensus 1072 ~yHC~~CgiCrv 1083 (1190)
...||.||-.-+
T Consensus 733 ~~~CpkCg~~l~ 744 (822)
T PRK07219 733 DEKCPECGLPLL 744 (822)
T ss_pred cCCCCCCCCeEE
Confidence 367888886533
No 189
>KOG3842 consensus Adaptor protein Pellino [Signal transduction mechanisms]
Probab=32.19 E-value=25 Score=40.76 Aligned_cols=63 Identities=27% Similarity=0.560 Sum_probs=39.6
Q ss_pred cccCCC--CCCCcccccc-----c---------ccCCCee-EecCCCCccCHhhHHHHHhc---------CCCCCCCccc
Q 001016 1110 CREKGL--ETNCPICCDF-----L---------FTSSATV-RALPCGHFMHSDCFQAYTCS---------HYICPICSKS 1163 (1190)
Q Consensus 1110 C~e~~~--~~~CpICle~-----l---------f~s~~~v-~~LpCgH~fH~~Ci~~wl~~---------~~~CPiCrk~ 1163 (1190)
+.|+.. +..||+|+.. | .+.+-+. ..-||||+--..=..-|.+. +..||.|-..
T Consensus 333 ~~e~~g~~~r~CPmC~~~gp~V~L~lG~E~~f~vD~G~pthaF~PCGHv~sekt~~YWs~iplPhGT~~f~a~CPFC~~~ 412 (429)
T KOG3842|consen 333 VRENTGQRERECPMCRVVGPYVPLWLGCEAGFYVDAGPPTHAFNPCGHVCSEKTVKYWSQIPLPHGTHAFHAACPFCATQ 412 (429)
T ss_pred cccccCcccCcCCeeeeecceeeeeccccceeEecCCCcccccCCcccccchhhhhHhhcCcCCCccccccccCcchhhh
Confidence 344443 6789999752 0 1122222 34599999888888888642 4669999988
Q ss_pred ccchhHHHH
Q 001016 1164 LGDMALYEG 1172 (1190)
Q Consensus 1164 l~~m~~~~~ 1172 (1190)
+....-|++
T Consensus 413 L~ge~~~ik 421 (429)
T KOG3842|consen 413 LAGEQGYIK 421 (429)
T ss_pred hccCCceEE
Confidence 865444433
No 190
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=31.92 E-value=18 Score=29.54 Aligned_cols=13 Identities=46% Similarity=1.185 Sum_probs=5.5
Q ss_pred cceEecccccccc
Q 001016 1055 MAKYYCGICKFFD 1067 (1190)
Q Consensus 1055 fa~Y~C~~C~l~d 1067 (1190)
|.+|||+.|+.|=
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 5689999998764
No 191
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=31.08 E-value=10 Score=31.84 Aligned_cols=43 Identities=21% Similarity=0.702 Sum_probs=29.2
Q ss_pred CcccccccccCCCeeEecCCCCccCHhhHHHHH------hcCCCCCCCcc
Q 001016 1119 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYT------CSHYICPICSK 1162 (1190)
Q Consensus 1119 CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl------~~~~~CPiCrk 1162 (1190)
|+||... ...+.-+.=-.|+-.||..|+..-. ...+.||.|+.
T Consensus 2 C~vC~~~-~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~~ 50 (51)
T PF00628_consen 2 CPVCGQS-DDDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCRP 50 (51)
T ss_dssp BTTTTSS-CTTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHHH
T ss_pred CcCCCCc-CCCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCcC
Confidence 8899884 3333333335899999999986532 23688998863
No 192
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=30.46 E-value=29 Score=35.92 Aligned_cols=48 Identities=27% Similarity=0.620 Sum_probs=34.0
Q ss_pred CCCCCcccccccccCCCeeEec----CCCCccCHhhHHH-HH--hcCCCCCCCcccccc
Q 001016 1115 LETNCPICCDFLFTSSATVRAL----PCGHFMHSDCFQA-YT--CSHYICPICSKSLGD 1166 (1190)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~L----pCgH~fH~~Ci~~-wl--~~~~~CPiCrk~l~~ 1166 (1190)
.-..|.||.|. |.+ -+.| =||=.+..-|... |- ..+..||+|+.++-.
T Consensus 79 ~lYeCnIC~et---S~e-e~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKs 133 (140)
T PF05290_consen 79 KLYECNICKET---SAE-ERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKS 133 (140)
T ss_pred CceeccCcccc---cch-hhcCCcccccchHHHHHHHHHHHHHcccCCCCCcccccccc
Confidence 35679999986 322 2333 2898899999776 63 346889999998764
No 193
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=30.39 E-value=33 Score=43.95 Aligned_cols=34 Identities=18% Similarity=0.404 Sum_probs=19.1
Q ss_pred eeeccccCccccCCCCCCCCCCCCC--ccceEeccccccc
Q 001016 1029 EMMCMRCLKVQPVGPVCTTLSCSGL--SMAKYYCGICKFF 1066 (1190)
Q Consensus 1029 ~~~C~~C~~~q~~~~~C~~~~Cc~~--~fa~Y~C~~C~l~ 1066 (1190)
.-+|..|++.... ..|++ ||. ..+.-||+.|...
T Consensus 15 akFC~~CG~~l~~-~~Cp~---CG~~~~~~~~fC~~CG~~ 50 (645)
T PRK14559 15 NRFCQKCGTSLTH-KPCPQ---CGTEVPVDEAHCPNCGAE 50 (645)
T ss_pred CccccccCCCCCC-CcCCC---CCCCCCcccccccccCCc
Confidence 3466667665532 35666 344 3555677777643
No 194
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=29.97 E-value=47 Score=41.54 Aligned_cols=107 Identities=22% Similarity=0.406 Sum_probs=52.5
Q ss_pred eeeccccCccccCCCCCCCCCCCCCccceEec-cccccccCC------CCccc--CCCCCccccCCCCCccccccCC---
Q 001016 1029 EMMCMRCLKVQPVGPVCTTLSCSGLSMAKYYC-GICKFFDDE------RVVYH--CPFCNLCRVGRGLGVDFFHCMT--- 1096 (1190)
Q Consensus 1029 ~~~C~~C~~~q~~~~~C~~~~Cc~~~fa~Y~C-~~C~l~dd~------k~~yH--C~~CgiCrvg~gl~~~~fHC~~--- 1096 (1190)
-..|-.|+.--..+..|.. ++. +||| ..|.-|--. -..|| |-.|-+|+....-|....-|.+
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---PEN---RLYGTDDCRAFVEGEVVSTLGKTYHPKCFSCSTCKSPFKSGDKVTFSGKECL 115 (670)
T ss_pred eeeccccCCCcccccceec---ccc---eeecccchhhhccceeEecccceeccccceecccCCCCCCCCeeeecchhhh
Confidence 4445555544433445555 232 6776 444443221 45676 6777777776444432222211
Q ss_pred cccccccc-ccccccccCCCCCCCcccccccccCCCeeEecCCCCccCHhhH
Q 001016 1097 CNCCLAKK-LVDHKCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCF 1147 (1190)
Q Consensus 1097 C~~C~s~~-l~~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci 1147 (1190)
|-.|.... +. =.+...-.+|+-|.+.|. +++.+..| +--+|..|+
T Consensus 116 c~~c~~~~~~~---p~~~~~ps~cagc~~~lk-~gq~llal--d~qwhv~cf 161 (670)
T KOG1044|consen 116 CQTCSQPMPVS---PAESYGPSTCAGCGEELK-NGQALLAL--DKQWHVSCF 161 (670)
T ss_pred hhhhcCcccCC---cccccCCccccchhhhhh-ccceeeee--ccceeeeee
Confidence 22222111 11 112345678999999854 44544444 445555554
No 195
>KOG4399 consensus C2HC-type Zn-finger protein [General function prediction only]
Probab=29.90 E-value=13 Score=42.06 Aligned_cols=47 Identities=19% Similarity=0.149 Sum_probs=36.6
Q ss_pred CCccceEeccccccccCCCCcccCCCCCccccCCCCCccccccCCcccccc
Q 001016 1052 GLSMAKYYCGICKFFDDERVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLA 1102 (1190)
Q Consensus 1052 ~~~fa~Y~C~~C~l~dd~k~~yHC~~CgiCrvg~gl~~~~fHC~~C~~C~s 1102 (1190)
+...+.-+|.||.=+|.++ -|||.|.-||--+. ...-||.+|..|..
T Consensus 256 ~~~A~~~~C~iC~~~~~~R--~~C~~~kA~~~~~Q--~K~N~~~~~~~~~q 302 (325)
T KOG4399|consen 256 NHCAVKHGCFICGELDHKR--STCPNIKAVRKQKQ--RKSNKMKMETTKGQ 302 (325)
T ss_pred cchhhhcceeecccccccc--ccCccHHHHHHHHh--cccchhhhhhhhhh
Confidence 4455677899999998877 89999999997542 25678888888764
No 196
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=29.77 E-value=28 Score=30.14 Aligned_cols=30 Identities=23% Similarity=0.609 Sum_probs=21.4
Q ss_pred ccceEeccccc-cccCC--CCcccCCCCCcccc
Q 001016 1054 SMAKYYCGICK-FFDDE--RVVYHCPFCNLCRV 1083 (1190)
Q Consensus 1054 ~fa~Y~C~~C~-l~dd~--k~~yHC~~CgiCrv 1083 (1190)
.+..|-|..|. .++.+ ..-+.||+||.=.+
T Consensus 3 ~~~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~rIl 35 (49)
T COG1996 3 AMMEYKCARCGREVELDQETRGIRCPYCGSRIL 35 (49)
T ss_pred ceEEEEhhhcCCeeehhhccCceeCCCCCcEEE
Confidence 35678888884 45533 78889999995433
No 197
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=29.68 E-value=56 Score=38.34 Aligned_cols=22 Identities=18% Similarity=0.311 Sum_probs=16.2
Q ss_pred ccceeeccccCccccC-CCCCCC
Q 001016 1026 ATTEMMCMRCLKVQPV-GPVCTT 1047 (1190)
Q Consensus 1026 ~~~~~~C~~C~~~q~~-~~~C~~ 1047 (1190)
..+-..|..|.++=.. --.|++
T Consensus 209 G~RyL~CslC~teW~~~R~~C~~ 231 (309)
T PRK03564 209 GLRYLHCNLCESEWHVVRVKCSN 231 (309)
T ss_pred CceEEEcCCCCCcccccCccCCC
Confidence 3468999999998543 347988
No 198
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]
Probab=28.64 E-value=28 Score=38.49 Aligned_cols=42 Identities=31% Similarity=0.755 Sum_probs=29.4
Q ss_pred CCCcccccccccCCCeeEecCCCCccCHhhHHHHHhcCCCCCCCc
Q 001016 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICS 1161 (1190)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCr 1161 (1190)
.+|.+|..-+. ..++--.||=-||..|+..|+.....||-|.
T Consensus 182 k~Cn~Ch~LvI---qg~rCg~c~i~~h~~c~qty~q~~~~cphc~ 223 (235)
T KOG4718|consen 182 KNCNLCHCLVI---QGIRCGSCNIQYHRGCIQTYLQRRDICPHCG 223 (235)
T ss_pred HHHhHhHHHhh---eeeccCcccchhhhHHHHHHhcccCcCCchh
Confidence 35666665421 2233445667799999999999899999995
No 200
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=28.43 E-value=38 Score=29.04 Aligned_cols=9 Identities=44% Similarity=1.397 Sum_probs=5.7
Q ss_pred eEecccccc
Q 001016 1057 KYYCGICKF 1065 (1190)
Q Consensus 1057 ~Y~C~~C~l 1065 (1190)
+|.|.+|.+
T Consensus 1 ky~C~~Cgy 9 (47)
T PF00301_consen 1 KYQCPVCGY 9 (47)
T ss_dssp EEEETTTSB
T ss_pred CcCCCCCCE
Confidence 466677764
No 201
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=27.90 E-value=50 Score=38.71 Aligned_cols=103 Identities=28% Similarity=0.408 Sum_probs=56.7
Q ss_pred CccceEeccccccccCCCCcccCCCCCccccC-CCCCccccccCCccccccccc-cccccccCCCCCCCcccccccccCC
Q 001016 1053 LSMAKYYCGICKFFDDERVVYHCPFCNLCRVG-RGLGVDFFHCMTCNCCLAKKL-VDHKCREKGLETNCPICCDFLFTSS 1130 (1190)
Q Consensus 1053 ~~fa~Y~C~~C~l~dd~k~~yHC~~CgiCrvg-~gl~~~~fHC~~C~~C~s~~l-~~H~C~e~~~~~~CpICle~lf~s~ 1130 (1190)
..-|-|+|+.||--=- .-+-.||-|+.--|- .-|-..|.|=. +..- ..-.=.++-....|-.|.+.+ .+.
T Consensus 272 ~~~~Gy~CP~CkakvC-sLP~eCpiC~ltLVss~hLARSyhhL~------PL~~F~Eip~~~~~~~~~Cf~C~~~~-~~~ 343 (378)
T KOG2807|consen 272 LSGGGYFCPQCKAKVC-SLPIECPICSLTLVSSPHLARSYHHLF------PLKPFVEIPETEYNGSRFCFACQGEL-LSS 343 (378)
T ss_pred cccCceeCCcccCeee-cCCccCCccceeEecchHHHHHHHhhc------CCcchhhccccccCCCcceeeecccc-CCC
Confidence 3567888888874211 134567777766554 22323343311 1110 111111222345599997773 444
Q ss_pred CeeEecCCCCccCHhhHHHHHhcCCCCCCCccc
Q 001016 1131 ATVRALPCGHFMHSDCFQAYTCSHYICPICSKS 1163 (1190)
Q Consensus 1131 ~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrk~ 1163 (1190)
..++--.|.+.|+.+|-.=--.+-..||-|...
T Consensus 344 ~~y~C~~Ck~~FCldCDv~iHesLh~CpgCeh~ 376 (378)
T KOG2807|consen 344 GRYRCESCKNVFCLDCDVFIHESLHNCPGCEHK 376 (378)
T ss_pred CcEEchhccceeeccchHHHHhhhhcCCCcCCC
Confidence 556667899999999953322334679999743
No 202
>PRK14873 primosome assembly protein PriA; Provisional
Probab=27.80 E-value=45 Score=42.96 Aligned_cols=49 Identities=20% Similarity=0.496 Sum_probs=29.9
Q ss_pred Cccc-cceeeccccCccccCCCCCCCCCCCCCccc------eEeccccccccCCCCcccCCCCCcc
Q 001016 1023 DRKA-TTEMMCMRCLKVQPVGPVCTTLSCSGLSMA------KYYCGICKFFDDERVVYHCPFCNLC 1081 (1190)
Q Consensus 1023 ~r~~-~~~~~C~~C~~~q~~~~~C~~~~Cc~~~fa------~Y~C~~C~l~dd~k~~yHC~~CgiC 1081 (1190)
+|+. .+.++|..|+..- .|++ |+..+. .-.|..|.+ ...+..||.||--
T Consensus 376 nRrGyap~l~C~~Cg~~~----~C~~---C~~~L~~h~~~~~l~Ch~CG~---~~~p~~Cp~Cgs~ 431 (665)
T PRK14873 376 PRRGYVPSLACARCRTPA----RCRH---CTGPLGLPSAGGTPRCRWCGR---AAPDWRCPRCGSD 431 (665)
T ss_pred cCCCCCCeeEhhhCcCee----ECCC---CCCceeEecCCCeeECCCCcC---CCcCccCCCCcCC
Confidence 4433 3578999999876 7888 455543 233555554 2236677777754
No 203
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=26.80 E-value=1.2e+02 Score=30.62 Aligned_cols=45 Identities=22% Similarity=0.315 Sum_probs=29.3
Q ss_pred CCCCcccccccccCC-----------CeeEecCCCCccCHhhHHHHHhcCCCCCCCc
Q 001016 1116 ETNCPICCDFLFTSS-----------ATVRALPCGHFMHSDCFQAYTCSHYICPICS 1161 (1190)
Q Consensus 1116 ~~~CpICle~lf~s~-----------~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCr 1161 (1190)
...|--|+.. |... ..+.--.|++.|..+|-.=+-..=..||-|.
T Consensus 55 ~~~C~~C~~~-f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~CPGC~ 110 (112)
T TIGR00622 55 SRFCFGCQGP-FPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHESLHCCPGCI 110 (112)
T ss_pred CCcccCcCCC-CCCcccccccccccccceeCCCCCCccccccchhhhhhccCCcCCC
Confidence 3569999887 4321 1123457889998888554544556699886
No 204
>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=26.42 E-value=39 Score=38.57 Aligned_cols=42 Identities=29% Similarity=0.556 Sum_probs=25.2
Q ss_pred CCCCCCcccccccccCCCeeEecCCCCc----cCHhhHHHH-HhcCCCCC
Q 001016 1114 GLETNCPICCDFLFTSSATVRALPCGHF----MHSDCFQAY-TCSHYICP 1158 (1190)
Q Consensus 1114 ~~~~~CpICle~lf~s~~~v~~LpCgH~----fH~~Ci~~w-l~~~~~CP 1158 (1190)
.+-.-|+||.|- .-.+.+-.-| =|. =|++||+.| +--+..||
T Consensus 28 ~tLsfChiCfEl-~iegvpks~l--lHtkSlRGHrdCFEK~HlIanQ~~p 74 (285)
T PF06937_consen 28 ETLSFCHICFEL-SIEGVPKSNL--LHTKSLRGHRDCFEKYHLIANQDCP 74 (285)
T ss_pred cceeecceeecc-ccccCccccc--cccccccchHHHHHHHHHHHcCCCC
Confidence 345668999874 2222211111 122 489999999 55678898
No 205
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=25.99 E-value=45 Score=37.72 Aligned_cols=79 Identities=20% Similarity=0.513 Sum_probs=49.5
Q ss_pred cccccccccccccCC--------cccCcccccccCCCCC----CccccceeeccccCccccCCCCCCCCCCCCCccceEe
Q 001016 992 HYKRNCKLRAACCGK--------LFTCRFCHDKVSDHSM----DRKATTEMMCMRCLKVQPVGPVCTTLSCSGLSMAKYY 1059 (1190)
Q Consensus 992 HY~r~ckl~~pcC~k--------~y~Cr~CHde~~dH~~----~r~~~~~~~C~~C~~~q~~~~~C~~~~Cc~~~fa~Y~ 1059 (1190)
-|+..=...|.-|+. .|.|..||.-..+-++ |-+..-...|..|+++..... ...-+.-|
T Consensus 114 f~rnqgr~LC~~Cn~k~Ka~~~g~YvC~KCh~~iD~~~l~fr~d~yH~yHFkCt~C~keL~sda--------Revk~eLy 185 (332)
T KOG2272|consen 114 FYRNQGRALCRECNQKEKAKGRGRYVCQKCHAHIDEQPLTFRGDPYHPYHFKCTTCGKELTSDA--------REVKGELY 185 (332)
T ss_pred hHhhcchHHhhhhhhhhcccccceeehhhhhhhcccccccccCCCCCccceecccccccccchh--------hhhcccee
Confidence 344444455555643 6999999987655433 334455788999998865431 22345667
Q ss_pred ccccccccCCCCcccCCCCCccccC
Q 001016 1060 CGICKFFDDERVVYHCPFCNLCRVG 1084 (1190)
Q Consensus 1060 C~~C~l~dd~k~~yHC~~CgiCrvg 1084 (1190)
|.-|. +.+-||-||-||..
T Consensus 186 ClrCh------D~mgipiCgaC~rp 204 (332)
T KOG2272|consen 186 CLRCH------DKMGIPICGACRRP 204 (332)
T ss_pred ccccc------cccCCcccccccCc
Confidence 77664 23457888888753
No 206
>KOG4654 consensus Uncharacterized conserved protein [Function unknown]
Probab=25.97 E-value=9.3e+02 Score=26.66 Aligned_cols=55 Identities=18% Similarity=0.097 Sum_probs=33.7
Q ss_pred chHHHH----HHHHHHHHHHHHHHHHHHhhccCCCCcchHHHHHHHHHHHHHHHHHhhccccccc
Q 001016 43 PILIFL----FFHKAIKSELDVLHRAAMAFATNLGGGGDINKLLERYHFFRAIYKHHCNAEDEVI 103 (1190)
Q Consensus 43 Pi~~~~----~~HkAlR~eL~~l~~~a~~~~~~~gd~~~~~~l~~r~~~L~~~~~~H~~aEDevI 103 (1190)
|+|+|. ++|||+-..-..= -|+-- -=...|++|..-++|+.+....-+..||.+-
T Consensus 41 p~dlY~~c~q~Vhk~lc~~kkc~----iRl~Y--~W~ELW~aL~n~L~Flmsne~~llak~dif~ 99 (252)
T KOG4654|consen 41 PADLYFLCFQFVHKALCSLKKCG----IRLEY--HWLELWRALFNFLDFLMSNEINLLAKEDIFR 99 (252)
T ss_pred ChhHHHHHHHHHHHHHHHHHhhc----ceeee--HHHHHHHHHHHHHHHHHHhHhhhcchhhHHH
Confidence 777776 7888875432211 11111 1113677788888888888888888887653
No 207
>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=25.92 E-value=25 Score=34.08 Aligned_cols=22 Identities=45% Similarity=1.313 Sum_probs=0.0
Q ss_pred ccCCCCC---ccccCCCCCccccccCCcc
Q 001016 1073 YHCPFCN---LCRVGRGLGVDFFHCMTCN 1098 (1190)
Q Consensus 1073 yHC~~Cg---iCrvg~gl~~~~fHC~~C~ 1098 (1190)
|.||+|| +=|++.| +.+|.+|+
T Consensus 36 y~Cp~Cgk~~vkR~a~G----IW~C~~C~ 60 (90)
T PF01780_consen 36 YTCPFCGKTSVKRVATG----IWKCKKCG 60 (90)
T ss_dssp BEESSSSSSEEEEEETT----EEEETTTT
T ss_pred CcCCCCCCceeEEeeeE----EeecCCCC
No 208
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=25.80 E-value=44 Score=33.00 Aligned_cols=33 Identities=15% Similarity=0.624 Sum_probs=0.0
Q ss_pred CcccCCCCC----ccccCCCCCccccccCCccccccccc
Q 001016 1071 VVYHCPFCN----LCRVGRGLGVDFFHCMTCNCCLAKKL 1105 (1190)
Q Consensus 1071 ~~yHC~~Cg----iCrvg~gl~~~~fHC~~C~~C~s~~l 1105 (1190)
.+|+||+|| .|.+++ |.-...|.+||.-.....
T Consensus 20 t~f~CP~Cge~~v~v~~~k--~~~h~~C~~CG~y~~~~V 56 (99)
T PRK14892 20 KIFECPRCGKVSISVKIKK--NIAIITCGNCGLYTEFEV 56 (99)
T ss_pred cEeECCCCCCeEeeeecCC--CcceEECCCCCCccCEEC
No 209
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=25.79 E-value=6.6 Score=33.92 Aligned_cols=45 Identities=22% Similarity=0.702 Sum_probs=28.6
Q ss_pred CccceEeccccccccCCCCcccCCCCC-----ccccCCCCCccccccCCcccccc
Q 001016 1053 LSMAKYYCGICKFFDDERVVYHCPFCN-----LCRVGRGLGVDFFHCMTCNCCLA 1102 (1190)
Q Consensus 1053 ~~fa~Y~C~~C~l~dd~k~~yHC~~Cg-----iCrvg~gl~~~~fHC~~C~~C~s 1102 (1190)
.+|++|.|+.|+---.-++.-.|--|| -|-. +.||.|..|+.=+.
T Consensus 3 ~SFsry~CDLCn~~~p~~~LRQCvlCGRWaC~sCW~-----deYY~CksC~Gii~ 52 (57)
T PF14445_consen 3 HSFSRYSCDLCNSSHPISELRQCVLCGRWACNSCWQ-----DEYYTCKSCNGIIN 52 (57)
T ss_pred hHHhhHhHHhhcccCcHHHHHHHhhhchhhhhhhhh-----hhHhHHHhhhchhh
Confidence 468999999997543334445565554 3332 46888888876544
No 210
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=25.51 E-value=38 Score=34.77 Aligned_cols=32 Identities=16% Similarity=0.104 Sum_probs=22.1
Q ss_pred ccccccccCCcccCcccccccCCCCCCccccceeeccccCccccCC
Q 001016 997 CKLRAACCGKLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVG 1042 (1190)
Q Consensus 997 ckl~~pcC~k~y~Cr~CHde~~dH~~~r~~~~~~~C~~C~~~q~~~ 1042 (1190)
-|-.||-||+-|= -+.| ..++|.+|++.+++.
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 3557888887441 1333 588999999998765
No 211
>KOG3842 consensus Adaptor protein Pellino [Signal transduction mechanisms]
Probab=25.36 E-value=33 Score=39.80 Aligned_cols=45 Identities=24% Similarity=0.603 Sum_probs=31.1
Q ss_pred CCCCCCCccccccc----------ccCCCeeEecCCCCc--cCHhhHHHHHh------cCCCCCCCcc
Q 001016 1113 KGLETNCPICCDFL----------FTSSATVRALPCGHF--MHSDCFQAYTC------SHYICPICSK 1162 (1190)
Q Consensus 1113 ~~~~~~CpICle~l----------f~s~~~v~~LpCgH~--fH~~Ci~~wl~------~~~~CPiCrk 1162 (1190)
+...-.||+=+..| ....++..+|.|||. +|. |-. ....||+|+.
T Consensus 287 NA~RPQCPVglnTL~~P~~~~~~~~~~~QP~vYl~CGHV~G~H~-----WG~~e~~g~~~r~CPmC~~ 349 (429)
T KOG3842|consen 287 NAARPQCPVGLNTLAFPSKRRKRVVDEKQPWVYLNCGHVHGYHN-----WGVRENTGQRERECPMCRV 349 (429)
T ss_pred hccCCCCCcccceeecccccccccccccCCeEEEeccccccccc-----cccccccCcccCcCCeeee
Confidence 45677899988765 133456789999976 553 632 2467999994
No 212
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=25.15 E-value=45 Score=29.65 Aligned_cols=12 Identities=33% Similarity=0.930 Sum_probs=9.1
Q ss_pred CCcccCCCCCcc
Q 001016 1070 RVVYHCPFCNLC 1081 (1190)
Q Consensus 1070 k~~yHC~~CgiC 1081 (1190)
...|-||+|||-
T Consensus 12 ~v~~~Cp~cGip 23 (55)
T PF13824_consen 12 HVNFECPDCGIP 23 (55)
T ss_pred ccCCcCCCCCCc
Confidence 567888888874
No 213
>KOG4399 consensus C2HC-type Zn-finger protein [General function prediction only]
Probab=25.02 E-value=21 Score=40.32 Aligned_cols=71 Identities=23% Similarity=0.591 Sum_probs=48.8
Q ss_pred CCccceEeccccccccCCCCcccCCCCCccccCCCCCccccccCCccccccccc-cccccccCCCCCCCcccccc
Q 001016 1052 GLSMAKYYCGICKFFDDERVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLAKKL-VDHKCREKGLETNCPICCDF 1125 (1190)
Q Consensus 1052 ~~~fa~Y~C~~C~l~dd~k~~yHC~~CgiCrvg~gl~~~~fHC~~C~~C~s~~l-~~H~C~e~~~~~~CpICle~ 1125 (1190)
+..-+-+||..|-.|=. +..-||..|+.|..-.| +-+-||.+|-.|+-.++ .--.|.--....-|-||-+.
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 45566677999876632 45669999999987763 68999999999988775 22222223345567788775
No 214
>PRK00420 hypothetical protein; Validated
Probab=24.90 E-value=41 Score=33.88 Aligned_cols=29 Identities=28% Similarity=0.642 Sum_probs=20.3
Q ss_pred CCCCcccccccccCCCeeEecCCCCccCHhhHHHHHhcCCCCCCCccccc
Q 001016 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1165 (1190)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrk~l~ 1165 (1190)
...||+|.-+||...+ ....||.|...+.
T Consensus 23 ~~~CP~Cg~pLf~lk~---------------------g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 23 SKHCPVCGLPLFELKD---------------------GEVVCPVHGKVYI 51 (112)
T ss_pred cCCCCCCCCcceecCC---------------------CceECCCCCCeee
Confidence 5789999988775322 3566888887664
No 215
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=24.63 E-value=45 Score=42.91 Aligned_cols=53 Identities=13% Similarity=0.286 Sum_probs=36.8
Q ss_pred CCCCcccccccccCCCeeEecC---CCCccCHhhHHHHHh------cCCCCCCCcccccchh
Q 001016 1116 ETNCPICCDFLFTSSATVRALP---CGHFMHSDCFQAYTC------SHYICPICSKSLGDMA 1168 (1190)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~Lp---CgH~fH~~Ci~~wl~------~~~~CPiCrk~l~~m~ 1168 (1190)
...|+||.-.+-...+....+| |+|-++..||..|.. .+..|+.|..-|..+.
T Consensus 96 s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWs 157 (1134)
T KOG0825|consen 96 SDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWS 157 (1134)
T ss_pred ccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhccccccccccHHHHhhhhh
Confidence 4567777766322223334455 999999999999963 3567999998887554
No 216
>PLN02189 cellulose synthase
Probab=24.61 E-value=53 Score=43.94 Aligned_cols=52 Identities=23% Similarity=0.435 Sum_probs=35.1
Q ss_pred CCCCCCCccccccccc--CCCeeEec-CCCCccCHhhHHHHHh--cCCCCCCCccccc
Q 001016 1113 KGLETNCPICCDFLFT--SSATVRAL-PCGHFMHSDCFQAYTC--SHYICPICSKSLG 1165 (1190)
Q Consensus 1113 ~~~~~~CpICle~lf~--s~~~v~~L-pCgH~fH~~Ci~~wl~--~~~~CPiCrk~l~ 1165 (1190)
+.....|.||.|++-. +++.-+.- -||--.+..|+ +|.+ .+..||-|+...-
T Consensus 31 ~~~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cy-eyer~eg~q~CpqCkt~Y~ 87 (1040)
T PLN02189 31 NLDGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCY-EYERREGTQNCPQCKTRYK 87 (1040)
T ss_pred cccCccccccccccCcCCCCCEEEeeccCCCccccchh-hhhhhcCCccCcccCCchh
Confidence 3455689999998642 33332222 36667999999 5643 4678999997664
No 217
>PHA00626 hypothetical protein
Probab=24.48 E-value=43 Score=29.82 Aligned_cols=34 Identities=24% Similarity=0.329 Sum_probs=20.5
Q ss_pred eeccccCccccCCCCCCCCCCCCCccceEeccccccccC
Q 001016 1030 MMCMRCLKVQPVGPVCTTLSCSGLSMAKYYCGICKFFDD 1068 (1190)
Q Consensus 1030 ~~C~~C~~~q~~~~~C~~~~Cc~~~fa~Y~C~~C~l~dd 1068 (1190)
|.|..|+..+-+ .|.. |...-.+|-|..|.+++.
T Consensus 1 m~CP~CGS~~Iv--rcg~---cr~~snrYkCkdCGY~ft 34 (59)
T PHA00626 1 MSCPKCGSGNIA--KEKT---MRGWSDDYVCCDCGYNDS 34 (59)
T ss_pred CCCCCCCCceee--eece---ecccCcceEcCCCCCeec
Confidence 467777765433 3433 234456788888887643
No 218
>PF06377 Adipokin_hormo: Adipokinetic hormone; InterPro: IPR010475 This family consists of several insect adipokinetic hormone as well as the related crustacean red pigment concentrating hormone (RPCH) []. Flight activity of insects comprises one of the most intense biochemical processes known in nature, and therefore provides an attractive model system to study the hormonal regulation of metabolism during physical exercise. In long-distance flying insects, such as the migratory locust, both carbohydrate and lipid reserves are utilised as fuels for sustained flight activity. The mobilisation of these energy stores in Locusta migratoria (Migratory locust) is mediated by three structurally related adipokinetic hormones (AKHs), which are all capable of stimulating the release of both carbohydrates and lipids from the fat body [].; GO: 0005179 hormone activity
Probab=24.24 E-value=1.7e+02 Score=25.51 Aligned_cols=37 Identities=14% Similarity=0.260 Sum_probs=25.3
Q ss_pred ccccCCCCCCC--CCCCCchhHHHHHHHHHHHHHHHHHH
Q 001016 629 NWETDLSSADI--GCASRPIDNIFKFHKAIRKDLEYLDG 665 (1190)
Q Consensus 629 ~~~~~~~~~~~--~~~~~PId~i~~~HkAIRkdL~~L~~ 665 (1190)
+|++....... +.-..|+|.+..+-+.|+.|-++|.+
T Consensus 7 ~WGKRs~~~~~~~~~C~~s~e~l~~iy~~iQ~EAqkl~~ 45 (48)
T PF06377_consen 7 GWGKRSAGARGRADDCKSSVESLLHIYKLIQNEAQKLLD 45 (48)
T ss_pred CcccccccCCCCCCCCCCcHHHHHHHHHHHHHHHHHHHh
Confidence 56555332222 12245899999999999999988864
No 219
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=24.04 E-value=35 Score=42.85 Aligned_cols=44 Identities=25% Similarity=0.781 Sum_probs=36.5
Q ss_pred CCCCCcccccccccCCCeeEecCCCCccCHhhHHHHHhcCCCCCCCcccccc
Q 001016 1115 LETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1166 (1190)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~LpCgH~fH~~Ci~~wl~~~~~CPiCrk~l~~ 1166 (1190)
.++.|.||.+.+ ..+.-+|- |..|+..|+.....||.|++.+..
T Consensus 478 ~~~~~~~~~~~~-----~~~~~~~~---~~~~l~~~~~~~~~~pl~~~~~~~ 521 (543)
T KOG0802|consen 478 PNDVCAICYQEM-----SARITPCS---HALCLRKWLYVQEVCPLCHTYMKE 521 (543)
T ss_pred ccCcchHHHHHH-----Hhcccccc---chhHHHhhhhhccccCCCchhhhc
Confidence 478999999985 34556777 999999999999999999987753
No 220
>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=22.92 E-value=4.1e+02 Score=26.24 Aligned_cols=61 Identities=21% Similarity=0.114 Sum_probs=35.1
Q ss_pred HHHhhhhhHHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHHHHHhHHHHHHHhh----hhHhhcCCHHHHHHHHHHH
Q 001016 117 TYSLEHEGESVLFDQLFELLNSSMRNEESYRRELASCTGALQTSISQHMSKEEEQVF----PLLIEKFSFEEQASLVWQF 192 (1190)
Q Consensus 117 ~~~~EH~~~~~lf~~l~~~l~~~~~~~~~~~~eLa~~l~~l~~~l~qHm~~EE~~v~----PLl~~~fS~~E~a~L~~~~ 192 (1190)
.+..||++.=+++++|..++.. ...+..|..-...|...||.-.- |-+..| ...+.+|
T Consensus 14 ~ID~qH~~L~~l~n~l~~a~~~------------~~~l~~L~~y~~~HF~~EE~~M~~~~yp~~~~H------~~~H~~f 75 (113)
T cd00522 14 VIDDEHKTLFNGINDLSEANNR------------ADNLKELVDYTVKHFKDEEALMEAAGYPDYEEH------KKIHEDF 75 (113)
T ss_pred HHHHHHHHHHHHHHHHHHHHhH------------HHHHHHHHHHHHHHHHHHHHHHHHcCCCCHHHH------HHHHHHH
Confidence 4455555444444444444332 34566777788899999998653 444433 5555555
Q ss_pred hcc
Q 001016 193 LCS 195 (1190)
Q Consensus 193 i~s 195 (1190)
+..
T Consensus 76 ~~~ 78 (113)
T cd00522 76 VEK 78 (113)
T ss_pred HHH
Confidence 543
No 221
>PRK10722 hypothetical protein; Provisional
Probab=22.80 E-value=5.1e+02 Score=29.68 Aligned_cols=115 Identities=10% Similarity=0.139 Sum_probs=73.4
Q ss_pred CCHHHHHHHHHHHhcccCHHHHHHHHhhhcCCCCHHHHHHHHHHHhhcCCc-hhHHHHHHHHHhcCCCCCCCcccchhhh
Q 001016 180 FSFEEQASLVWQFLCSIPVNMMAEFLPWLSSSISSDEHQDMRKCLCKIIPK-EKLLRQVIFAWMEGVKVSDKSCEDNLEH 258 (1190)
Q Consensus 180 fS~~E~a~L~~~~i~siP~~~m~~~LpWm~~~lsp~Er~~~l~~l~~~~P~-~~~l~~~~~~W~~~~~~~~~~~~~~~~~ 258 (1190)
++++|......++....|-+.+..-+-.--...++.||+.|+..|-...+. +..|+-++--|..+-- -++
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 455667777777666666665555555555667799999999999866554 7788888888877421 000
Q ss_pred hhccCcccccccccccchhhhhhccCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 001016 259 RCQRWFSCACESSRSSKRKYVELSYDLTDSSMSCPIDEIMLWHNAIKRELNDIAEAARKIQ 319 (1190)
Q Consensus 259 ~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~PId~l~~~HkALRrEL~~L~~~a~~~~ 319 (1190)
... -.+++|...-.+. -.-+|.+..-++.++++|+.+.+-+..+.
T Consensus 159 ~La-----------eEr~Ry~rLQq~s-----D~qlD~lrqq~~~Lq~~L~~t~rKLEnLT 203 (247)
T PRK10722 159 ALA-----------EERQRYQKLQQSS-----DSELDALRQQQQRLQYQLELTTRKLENLT 203 (247)
T ss_pred hHH-----------HHHHHHHHHhhcc-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 000 0112222211000 13688999999999999999888876653
No 222
>PF01599 Ribosomal_S27: Ribosomal protein S27a; InterPro: IPR002906 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP) (IPR000626 from INTERPRO). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis []. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2K4X_A 3U5C_f 3U5G_f 2XZN_9 2XZM_9.
Probab=22.78 E-value=41 Score=28.93 Aligned_cols=28 Identities=25% Similarity=0.774 Sum_probs=14.6
Q ss_pred cccCCCCCCCCCCCC-C----ccceEecccccc
Q 001016 1038 VQPVGPVCTTLSCSG-L----SMAKYYCGICKF 1065 (1190)
Q Consensus 1038 ~q~~~~~C~~~~Cc~-~----~fa~Y~C~~C~l 1065 (1190)
++.....|+++.|+. . .+.++||.+|.+
T Consensus 14 v~r~rk~CP~~~CG~GvFMA~H~dR~~CGKCg~ 46 (47)
T PF01599_consen 14 VKRLRKECPSPRCGAGVFMAEHKDRHYCGKCGY 46 (47)
T ss_dssp EEESSEE-TSTTTTSSSEEEE-SSEEEETTTSS
T ss_pred EEEhhhcCCCcccCCceEeeecCCCccCCCccc
Confidence 344556788666632 1 245667776653
No 223
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=22.40 E-value=74 Score=37.14 Aligned_cols=75 Identities=28% Similarity=0.528 Sum_probs=50.1
Q ss_pred ccCC----CCcccCCCCCccccCCCCC-ccccccCCcccccccc--c--cccccccCCCCCCCcccccccccCCCeeEec
Q 001016 1066 FDDE----RVVYHCPFCNLCRVGRGLG-VDFFHCMTCNCCLAKK--L--VDHKCREKGLETNCPICCDFLFTSSATVRAL 1136 (1190)
Q Consensus 1066 ~dd~----k~~yHC~~CgiCrvg~gl~-~~~fHC~~C~~C~s~~--l--~~H~C~e~~~~~~CpICle~lf~s~~~v~~L 1136 (1190)
|||- +-+=||..|-. -| |- +=|| ||+.|.+.. . ..|-=..++....|-.|-+. .+++.++
T Consensus 169 WdDVLks~Ripg~Ces~~~--pg--~fAEFfF---KC~ah~~~~k~~aa~lhli~~N~~ni~C~~Ctdv----~~~vlvf 237 (446)
T KOG0006|consen 169 WDDVLKSKRIPGVCESCCT--PG--LFAEFFF---KCGAHPTSDKETAAALHLIATNSRNITCITCTDV----RSPVLVF 237 (446)
T ss_pred hhhhhhcccCccccccccC--Cc--chHhhee---hhccCCCccccchhHHHHhhcccccceeEEecCC----ccceEEE
Confidence 6664 66777776632 22 22 3455 455665542 1 35655667778899999764 5678889
Q ss_pred CCC--CccCHhhHHHHH
Q 001016 1137 PCG--HFMHSDCFQAYT 1151 (1190)
Q Consensus 1137 pCg--H~fH~~Ci~~wl 1151 (1190)
+|. |.....||.-|-
T Consensus 238 ~Cns~HvtC~dCFr~yc 254 (446)
T KOG0006|consen 238 QCNSRHVTCLDCFRLYC 254 (446)
T ss_pred ecCCceeehHHhhhhHh
Confidence 999 999999998773
No 224
>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=22.37 E-value=42 Score=25.80 Aligned_cols=12 Identities=25% Similarity=0.974 Sum_probs=8.9
Q ss_pred cceEeccccccc
Q 001016 1055 MAKYYCGICKFF 1066 (1190)
Q Consensus 1055 fa~Y~C~~C~l~ 1066 (1190)
++.|||++|+.+
T Consensus 1 ~~~~~C~~C~~~ 12 (35)
T smart00451 1 TGGFYCKLCNVT 12 (35)
T ss_pred CcCeEccccCCc
Confidence 357889999754
No 225
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=22.07 E-value=49 Score=28.65 Aligned_cols=9 Identities=44% Similarity=1.150 Sum_probs=5.2
Q ss_pred cccccCCcc
Q 001016 1090 DFFHCMTCN 1098 (1190)
Q Consensus 1090 ~~fHC~~C~ 1098 (1190)
+.++|.+||
T Consensus 36 ~r~~C~~Cg 44 (50)
T PRK00432 36 DRWHCGKCG 44 (50)
T ss_pred CcEECCCcC
Confidence 555666555
No 226
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=22.01 E-value=32 Score=35.83 Aligned_cols=7 Identities=43% Similarity=1.549 Sum_probs=4.9
Q ss_pred ccCCCCC
Q 001016 1073 YHCPFCN 1079 (1190)
Q Consensus 1073 yHC~~Cg 1079 (1190)
|.||.||
T Consensus 124 f~Cp~Cg 130 (147)
T smart00531 124 FTCPRCG 130 (147)
T ss_pred EECCCCC
Confidence 6777776
No 227
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=21.91 E-value=72 Score=36.34 Aligned_cols=64 Identities=28% Similarity=0.738 Sum_probs=34.4
Q ss_pred CccccccCCccccccccccccccccCCCCCCCcc--cccccccCCC-------------eeEecCCCCccCHhhHHHHH-
Q 001016 1088 GVDFFHCMTCNCCLAKKLVDHKCREKGLETNCPI--CCDFLFTSSA-------------TVRALPCGHFMHSDCFQAYT- 1151 (1190)
Q Consensus 1088 ~~~~fHC~~C~~C~s~~l~~H~C~e~~~~~~CpI--Cle~lf~s~~-------------~v~~LpCgH~fH~~Ci~~wl- 1151 (1190)
|+.|.-|. ||+-+ .|.+.+..-.||- |.--+.-... ....+.||| |-+..+
T Consensus 103 GKKYVRCP-CNCLL-------ICk~sS~rIaCPRp~CkRiI~L~~~~~~p~~~~~~~~p~~~rv~Cgh-----C~~~Fl~ 169 (256)
T PF09788_consen 103 GKKYVRCP-CNCLL-------ICKSSSQRIACPRPNCKRIINLGPSHQGPVTPPVPTQPGSCRVICGH-----CSNTFLF 169 (256)
T ss_pred CCeeEecC-CceEE-------EeecccccccCCCCCCcceEEeCCccCCCCCCCCCCCCCceeEECCC-----CCCcEec
Confidence 46788886 55332 2555566666765 6543321111 113357887 433322
Q ss_pred ---h--cCCCCCCCcccc
Q 001016 1152 ---C--SHYICPICSKSL 1164 (1190)
Q Consensus 1152 ---~--~~~~CPiCrk~l 1164 (1190)
. .--+||-|||.-
T Consensus 170 ~~~~~~tlARCPHCrKvS 187 (256)
T PF09788_consen 170 NTLTSNTLARCPHCRKVS 187 (256)
T ss_pred cCCCCCccccCCCCceec
Confidence 1 224799999754
No 228
>PLN02436 cellulose synthase A
Probab=21.20 E-value=68 Score=43.10 Aligned_cols=52 Identities=19% Similarity=0.445 Sum_probs=34.9
Q ss_pred CCCCCCCcccccccccCCCeeEec---CCCCccCHhhHHHHHh--cCCCCCCCccccc
Q 001016 1113 KGLETNCPICCDFLFTSSATVRAL---PCGHFMHSDCFQAYTC--SHYICPICSKSLG 1165 (1190)
Q Consensus 1113 ~~~~~~CpICle~lf~s~~~v~~L---pCgH~fH~~Ci~~wl~--~~~~CPiCrk~l~ 1165 (1190)
......|.||.|++-...+.-... -||--.+..|+ +|.+ .+..||-|+...-
T Consensus 33 ~~~~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cy-eyer~eg~~~Cpqckt~Y~ 89 (1094)
T PLN02436 33 ELSGQTCQICGDEIELTVDGEPFVACNECAFPVCRPCY-EYERREGNQACPQCKTRYK 89 (1094)
T ss_pred ccCCccccccccccCcCCCCCEEEeeccCCCccccchh-hhhhhcCCccCcccCCchh
Confidence 344568999999964333322233 45666999999 5643 4678999997664
No 229
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=21.01 E-value=38 Score=38.48 Aligned_cols=53 Identities=23% Similarity=0.535 Sum_probs=35.2
Q ss_pred cCCCCCCCcccccccccCCCeeEecCCC-----CccCHhhHHHHHhc--------CCCCCCCcccc
Q 001016 1112 EKGLETNCPICCDFLFTSSATVRALPCG-----HFMHSDCFQAYTCS--------HYICPICSKSL 1164 (1190)
Q Consensus 1112 e~~~~~~CpICle~lf~s~~~v~~LpCg-----H~fH~~Ci~~wl~~--------~~~CPiCrk~l 1164 (1190)
+...+..|=||...=-++....-+-||- |--|..|+..|+.. .-+||-|+...
T Consensus 16 ~~e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEY 81 (293)
T KOG3053|consen 16 NQELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEY 81 (293)
T ss_pred ccccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchh
Confidence 4456788999986511111122245773 88999999999742 23599999765
No 230
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=20.82 E-value=53 Score=33.91 Aligned_cols=9 Identities=33% Similarity=0.973 Sum_probs=5.5
Q ss_pred cccCCCCCc
Q 001016 1072 VYHCPFCNL 1080 (1190)
Q Consensus 1072 ~yHC~~Cgi 1080 (1190)
.|.||.||-
T Consensus 107 ~~~CP~Cgs 115 (135)
T PRK03824 107 FLKCPKCGS 115 (135)
T ss_pred CcCCcCCCC
Confidence 455777773
No 231
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=20.52 E-value=60 Score=38.05 Aligned_cols=47 Identities=26% Similarity=0.622 Sum_probs=33.8
Q ss_pred CCccceEeccccccccCCCCcccCCCCCccccCCCCCccccccCCcccccccc
Q 001016 1052 GLSMAKYYCGICKFFDDERVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLAKK 1104 (1190)
Q Consensus 1052 ~~~fa~Y~C~~C~l~dd~k~~yHC~~CgiCrvg~gl~~~~fHC~~C~~C~s~~ 1104 (1190)
+....+=||.+|+.|-.+ ...||.-||.|...- =-||.=-|-|+...
T Consensus 104 ~~~~~~~~C~~C~~~KP~-RS~HC~~Cn~CV~k~-----DHHC~Wi~nCVG~~ 150 (309)
T COG5273 104 GKFGTENFCSTCNIYKPP-RSHHCSICNRCVLKF-----DHHCPWINNCVGFR 150 (309)
T ss_pred CccccceeccccccccCC-CCccchhhcchhhcc-----CccCcccccccCcc
Confidence 455556678888888776 356888888888764 26888777777654
No 232
>PRK07219 DNA topoisomerase I; Validated
Probab=20.50 E-value=1.4e+02 Score=39.57 Aligned_cols=63 Identities=25% Similarity=0.495 Sum_probs=33.8
Q ss_pred ccccccccCC----CCcccCCCCCcc---ccCCCCCccccccCC---ccccccccccccccccCCCCCCCcccccccc
Q 001016 1060 CGICKFFDDE----RVVYHCPFCNLC---RVGRGLGVDFFHCMT---CNCCLAKKLVDHKCREKGLETNCPICCDFLF 1127 (1190)
Q Consensus 1060 C~~C~l~dd~----k~~yHC~~CgiC---rvg~gl~~~~fHC~~---C~~C~s~~l~~H~C~e~~~~~~CpICle~lf 1127 (1190)
|+.|+..... .....||.||-- |.|+. | .|+-|.+ |+.-..+.-..+. ......||-|-..+.
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 7777765432 346789999822 22221 3 3888865 6543332111100 123567999976543
No 233
>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=20.36 E-value=74 Score=39.66 Aligned_cols=47 Identities=21% Similarity=0.588 Sum_probs=30.4
Q ss_pred ccceeeccccCccccCCCCCCCCCCCCCccc------eEeccccccccCC-CCcccCCCCCccc
Q 001016 1026 ATTEMMCMRCLKVQPVGPVCTTLSCSGLSMA------KYYCGICKFFDDE-RVVYHCPFCNLCR 1082 (1190)
Q Consensus 1026 ~~~~~~C~~C~~~q~~~~~C~~~~Cc~~~fa------~Y~C~~C~l~dd~-k~~yHC~~CgiCr 1082 (1190)
-.+.++|..|+..- .|++ |+..+. .-.|..|. .. +-+..||.||--.
T Consensus 210 ya~~~~C~~Cg~~~----~C~~---C~~~l~~h~~~~~l~Ch~Cg---~~~~~~~~Cp~C~s~~ 263 (505)
T TIGR00595 210 YSKNLLCRSCGYIL----CCPN---CDVSLTYHKKEGKLRCHYCG---YQEPIPKTCPQCGSED 263 (505)
T ss_pred CCCeeEhhhCcCcc----CCCC---CCCceEEecCCCeEEcCCCc---CcCCCCCCCCCCCCCe
Confidence 35688999999876 7888 465553 22355554 33 4466788887543
No 234
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=20.35 E-value=57 Score=28.05 Aligned_cols=21 Identities=29% Similarity=0.937 Sum_probs=14.0
Q ss_pred ccCCCCCc-cccCCCCCccccccCCcc
Q 001016 1073 YHCPFCNL-CRVGRGLGVDFFHCMTCN 1098 (1190)
Q Consensus 1073 yHC~~Cgi-Crvg~gl~~~~fHC~~C~ 1098 (1190)
|.|+.|+. -.+|. .|||..|.
T Consensus 1 y~Cd~C~~~pI~G~-----R~~C~~C~ 22 (48)
T cd02341 1 FKCDSCGIEPIPGT-----RYHCSECD 22 (48)
T ss_pred CCCCCCCCCccccc-----eEECCCCC
Confidence 67888887 34443 58887664
No 235
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=20.31 E-value=32 Score=46.68 Aligned_cols=74 Identities=20% Similarity=0.441 Sum_probs=48.0
Q ss_pred CCcccccccCCCCccccccccccccccCCcccCc--ccccccCCCCCCccccceeeccccCccccCCCCCCCCCCCCCcc
Q 001016 978 PSFRDAEKQVFGCEHYKRNCKLRAACCGKLFTCR--FCHDKVSDHSMDRKATTEMMCMRCLKVQPVGPVCTTLSCSGLSM 1055 (1190)
Q Consensus 978 ~~~~~~~~~~~gC~HY~r~ckl~~pcC~k~y~Cr--~CHde~~dH~~~r~~~~~~~C~~C~~~q~~~~~C~~~~Cc~~~f 1055 (1190)
.-|.||+...+. |---..|..|.|.|-=- .|-.+.. -+-++..+.+||.|..+..++ .|+. =|..|
T Consensus 3587 ~FYNdPa~YAmn-----RY~Y~vC~KCrKAYFGGEaRCdAe~~---~ddydP~ELiCG~CSDvS~aQ-mCPk---HGtdf 3654 (3738)
T KOG1428|consen 3587 RFYNDPAGYAMN-----RYAYYVCYKCRKAYFGGEARCDAEAG---GDDYDPRELICGACSDVSRAQ-MCPK---HGTDF 3654 (3738)
T ss_pred eeccChhhhhhh-----hhhhhhhhhhhhhhcCchhhcchhcC---CCCCCHHHhhhccccccccce-eccc---ccchh
Confidence 457787664432 11226788888866421 4444433 355667799999999887553 8887 47778
Q ss_pred ceEecccc
Q 001016 1056 AKYYCGIC 1063 (1190)
Q Consensus 1056 a~Y~C~~C 1063 (1190)
=.|.|..|
T Consensus 3655 LEYKCRyC 3662 (3738)
T KOG1428|consen 3655 LEYKCRYC 3662 (3738)
T ss_pred hhhhhhee
Confidence 88777666
No 236
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=20.26 E-value=82 Score=28.43 Aligned_cols=35 Identities=23% Similarity=0.535 Sum_probs=21.2
Q ss_pred cceeeccccCccccCCCCCCCCCCCCCccceEeccccccc
Q 001016 1027 TTEMMCMRCLKVQPVGPVCTTLSCSGLSMAKYYCGICKFF 1066 (1190)
Q Consensus 1027 ~~~~~C~~C~~~q~~~~~C~~~~Cc~~~fa~Y~C~~C~l~ 1066 (1190)
.....|..|+++- +. .|.. |......|.|+.|.|-
T Consensus 23 ~~~F~CPnCG~~~-I~-RC~~---CRk~~~~Y~CP~CGF~ 57 (59)
T PRK14890 23 AVKFLCPNCGEVI-IY-RCEK---CRKQSNPYTCPKCGFE 57 (59)
T ss_pred cCEeeCCCCCCee-Ee-echh---HHhcCCceECCCCCCc
Confidence 3566777776542 11 4665 4666777777777663
Done!