Query 001043
Match_columns 1177
No_of_seqs 531 out of 1560
Neff 5.2
Searched_HMMs 46136
Date Thu Mar 28 14:13:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001043.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001043hhsearch_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 5.3E-44 1.1E-48 389.8 0.4 193 976-1174 21-215 (276)
2 PF05495 zf-CHY: CHY zinc fing 99.8 4.9E-21 1.1E-25 172.5 1.8 70 990-1067 1-71 (71)
3 PF01814 Hemerythrin: Hemeryth 99.2 2.4E-10 5.1E-15 110.6 14.1 124 293-425 2-133 (133)
4 PF13639 zf-RING_2: Ring finge 99.2 4.9E-12 1.1E-16 103.6 1.5 44 1117-1161 1-44 (44)
5 PF01814 Hemerythrin: Hemeryth 99.2 2.4E-10 5.1E-15 110.6 12.4 129 43-176 2-133 (133)
6 COG4357 Zinc finger domain con 99.0 5.2E-11 1.1E-15 111.0 -0.7 57 986-1042 11-75 (105)
7 KOG4628 Predicted E3 ubiquitin 98.9 2.9E-10 6.2E-15 129.3 2.5 49 1117-1166 230-279 (348)
8 COG5243 HRD1 HRD ubiquitin lig 98.9 7.8E-10 1.7E-14 123.9 3.2 57 1113-1169 284-350 (491)
9 PF12678 zf-rbx1: RING-H2 zinc 98.9 1.3E-09 2.7E-14 99.2 3.5 47 1115-1161 18-73 (73)
10 PF12861 zf-Apc11: Anaphase-pr 98.8 2.1E-09 4.5E-14 99.9 3.7 47 1116-1164 32-81 (85)
11 PRK10992 iron-sulfur cluster r 98.8 7.3E-08 1.6E-12 105.0 13.9 131 294-427 76-218 (220)
12 COG5540 RING-finger-containing 98.7 1E-08 2.3E-13 112.8 3.3 56 1110-1166 317-373 (374)
13 TIGR03652 FeS_repair_RIC iron- 98.7 1.6E-07 3.6E-12 101.9 12.2 129 294-425 72-216 (216)
14 PRK10992 iron-sulfur cluster r 98.6 3.7E-07 8.1E-12 99.6 14.3 130 49-178 82-218 (220)
15 PHA02929 N1R/p28-like protein; 98.6 2.5E-08 5.4E-13 109.3 4.7 53 1114-1166 172-228 (238)
16 cd00162 RING RING-finger (Real 98.6 5.3E-08 1.1E-12 77.8 3.7 44 1118-1164 1-45 (45)
17 COG3945 Uncharacterized conser 98.5 1.9E-06 4.2E-11 89.7 14.8 140 292-440 8-158 (189)
18 TIGR03652 FeS_repair_RIC iron- 98.5 1.2E-06 2.7E-11 95.1 13.3 127 49-175 78-215 (216)
19 PF13923 zf-C3HC4_2: Zinc fing 98.5 8.8E-08 1.9E-12 76.7 2.4 39 1119-1160 1-39 (39)
20 COG5194 APC11 Component of SCF 98.4 1.5E-07 3.2E-12 85.7 3.1 50 1116-1165 31-81 (88)
21 PF13920 zf-C3HC4_3: Zinc fing 98.3 2.3E-07 4.9E-12 78.2 2.6 47 1116-1166 2-49 (50)
22 PRK13276 cell wall biosynthesi 98.3 6.1E-06 1.3E-10 90.1 13.2 125 297-424 83-222 (224)
23 PRK13276 cell wall biosynthesi 98.3 8E-06 1.7E-10 89.2 13.6 127 48-174 84-221 (224)
24 KOG1493 Anaphase-promoting com 98.3 1.6E-07 3.6E-12 84.8 -0.4 47 1116-1164 31-80 (84)
25 smart00184 RING Ring finger. E 98.2 1.2E-06 2.5E-11 67.6 3.0 38 1119-1160 1-39 (39)
26 PF14634 zf-RING_5: zinc-RING 98.1 1.9E-06 4.2E-11 70.9 3.3 44 1118-1162 1-44 (44)
27 PHA02926 zinc finger-like prot 98.1 1.9E-06 4.2E-11 92.5 3.7 62 1113-1174 167-241 (242)
28 PF00097 zf-C3HC4: Zinc finger 98.1 2E-06 4.2E-11 69.3 2.8 39 1119-1160 1-41 (41)
29 KOG0802 E3 ubiquitin ligase [P 98.1 1.2E-06 2.5E-11 107.2 2.1 54 1112-1165 287-341 (543)
30 PLN03208 E3 ubiquitin-protein 98.1 2.8E-06 6E-11 90.3 4.5 52 1111-1166 13-80 (193)
31 COG2846 Regulator of cell morp 98.0 4.2E-05 9.2E-10 81.0 12.1 128 295-425 79-217 (221)
32 KOG0320 Predicted E3 ubiquitin 98.0 2.3E-06 4.9E-11 89.1 2.4 46 1117-1165 132-178 (187)
33 PF15227 zf-C3HC4_4: zinc fing 98.0 4.1E-06 8.9E-11 68.6 2.4 38 1119-1160 1-42 (42)
34 smart00504 Ubox Modified RING 97.8 1.5E-05 3.2E-10 69.6 4.0 45 1117-1165 2-46 (63)
35 PF13445 zf-RING_UBOX: RING-ty 97.8 1.2E-05 2.7E-10 66.2 2.6 39 1119-1158 1-43 (43)
36 KOG0317 Predicted E3 ubiquitin 97.8 1.2E-05 2.6E-10 89.4 2.5 50 1116-1169 239-288 (293)
37 KOG2930 SCF ubiquitin ligase, 97.7 7.4E-06 1.6E-10 78.2 -0.2 32 1133-1164 76-107 (114)
38 KOG0823 Predicted E3 ubiquitin 97.6 3.4E-05 7.4E-10 83.6 3.1 50 1114-1167 45-97 (230)
39 KOG0828 Predicted E3 ubiquitin 97.6 2.1E-05 4.7E-10 91.7 1.6 51 1116-1166 571-635 (636)
40 COG2846 Regulator of cell morp 97.5 0.0008 1.7E-08 71.7 12.0 133 45-177 79-218 (221)
41 TIGR00599 rad18 DNA repair pro 97.5 4.9E-05 1.1E-09 89.2 3.3 47 1116-1166 26-72 (397)
42 KOG0804 Cytoplasmic Zn-finger 97.5 3.5E-05 7.6E-10 89.6 1.9 48 1116-1165 175-222 (493)
43 COG3945 Uncharacterized conser 97.5 0.0012 2.5E-08 69.5 12.3 140 44-190 10-157 (189)
44 smart00744 RINGv The RING-vari 97.4 0.00011 2.4E-09 62.3 2.7 42 1118-1161 1-49 (49)
45 KOG2164 Predicted E3 ubiquitin 97.3 0.0001 2.3E-09 87.3 2.7 48 1115-1166 185-237 (513)
46 TIGR00570 cdk7 CDK-activating 97.3 0.00019 4E-09 81.6 4.1 51 1116-1166 3-55 (309)
47 PF11793 FANCL_C: FANCL C-term 97.2 0.0001 2.3E-09 66.9 0.4 50 1116-1165 2-66 (70)
48 KOG0827 Predicted E3 ubiquitin 97.1 0.00018 3.9E-09 82.4 1.6 48 1116-1164 4-55 (465)
49 KOG1428 Inhibitor of type V ad 97.1 0.00024 5.2E-09 90.0 2.3 112 1030-1165 3418-3544(3738)
50 KOG1734 Predicted RING-contain 97.0 0.00018 3.9E-09 79.2 0.4 49 1116-1164 224-280 (328)
51 KOG0825 PHD Zn-finger protein 97.0 0.00019 4E-09 87.6 0.4 52 1115-1167 122-173 (1134)
52 COG5574 PEX10 RING-finger-cont 97.0 0.00037 8.1E-09 76.9 2.2 49 1116-1168 215-265 (271)
53 KOG2177 Predicted E3 ubiquitin 96.9 0.0004 8.7E-09 75.4 1.9 44 1115-1162 12-55 (386)
54 KOG4172 Predicted E3 ubiquitin 96.7 0.00032 6.9E-09 60.2 -0.3 54 1115-1172 6-61 (62)
55 KOG0287 Postreplication repair 96.7 0.00059 1.3E-08 77.1 1.4 45 1117-1165 24-68 (442)
56 KOG4265 Predicted E3 ubiquitin 96.6 0.0011 2.5E-08 75.9 2.9 49 1114-1166 288-337 (349)
57 KOG1941 Acetylcholine receptor 96.5 0.00062 1.3E-08 78.1 0.1 61 1107-1168 357-419 (518)
58 PF04564 U-box: U-box domain; 96.5 0.0013 2.9E-08 60.0 2.1 47 1116-1166 4-51 (73)
59 COG5432 RAD18 RING-finger-cont 96.5 0.0013 2.9E-08 73.0 2.0 45 1116-1164 25-69 (391)
60 KOG1940 Zn-finger protein [Gen 96.3 0.0003 6.4E-09 79.0 -3.9 133 690-854 17-149 (276)
61 KOG1645 RING-finger-containing 96.1 0.0034 7.3E-08 72.9 3.0 48 1116-1163 4-54 (463)
62 KOG1039 Predicted E3 ubiquitin 96.0 0.0045 9.8E-08 71.9 3.3 52 1113-1164 158-220 (344)
63 COG5219 Uncharacterized conser 95.7 0.0036 7.8E-08 78.1 0.8 51 1114-1164 1467-1522(1525)
64 COG2461 Uncharacterized conser 95.4 0.1 2.2E-06 61.2 11.0 132 291-441 85-223 (409)
65 KOG2879 Predicted E3 ubiquitin 95.3 0.013 2.9E-07 65.3 3.3 51 1115-1168 238-290 (298)
66 PF14835 zf-RING_6: zf-RING of 95.0 0.0079 1.7E-07 53.8 0.6 43 1117-1164 8-50 (65)
67 KOG4445 Uncharacterized conser 94.9 0.0093 2E-07 66.9 0.9 56 1111-1167 110-188 (368)
68 PF11789 zf-Nse: Zinc-finger o 94.5 0.024 5.2E-07 49.8 2.3 42 1115-1159 10-53 (57)
69 KOG0311 Predicted E3 ubiquitin 94.4 0.0059 1.3E-07 70.0 -2.1 48 1116-1166 43-91 (381)
70 KOG0978 E3 ubiquitin ligase in 94.3 0.014 3E-07 72.8 0.5 46 1117-1166 644-690 (698)
71 KOG4739 Uncharacterized protei 94.1 0.015 3.4E-07 64.0 0.3 48 1127-1176 12-69 (233)
72 KOG1785 Tyrosine kinase negati 94.0 0.017 3.6E-07 66.9 0.4 54 1109-1166 362-417 (563)
73 KOG0824 Predicted E3 ubiquitin 93.8 0.032 6.9E-07 63.1 2.1 48 1114-1165 5-53 (324)
74 PF14570 zf-RING_4: RING/Ubox 93.5 0.059 1.3E-06 45.8 2.7 45 1119-1163 1-46 (48)
75 PF10367 Vps39_2: Vacuolar sor 93.4 0.034 7.4E-07 53.3 1.3 38 1109-1148 71-108 (109)
76 KOG0309 Conserved WD40 repeat- 92.8 0.068 1.5E-06 66.1 2.8 49 1109-1159 1021-1069(1081)
77 KOG3970 Predicted E3 ubiquitin 92.3 0.096 2.1E-06 56.9 2.9 53 1113-1167 47-107 (299)
78 PF12906 RINGv: RING-variant d 92.1 0.083 1.8E-06 44.6 1.7 40 1119-1160 1-47 (47)
79 COG5175 MOT2 Transcriptional r 91.9 0.069 1.5E-06 60.9 1.3 63 1115-1177 13-76 (480)
80 PF05883 Baculo_RING: Baculovi 91.7 0.074 1.6E-06 54.2 1.2 40 1116-1156 26-71 (134)
81 KOG4275 Predicted E3 ubiquitin 91.7 0.031 6.7E-07 62.7 -1.6 49 1116-1172 300-349 (350)
82 KOG3268 Predicted E3 ubiquitin 91.2 0.13 2.9E-06 54.2 2.4 30 1136-1165 188-228 (234)
83 KOG0297 TNF receptor-associate 91.1 0.11 2.5E-06 61.7 2.1 54 1115-1171 20-73 (391)
84 KOG1571 Predicted E3 ubiquitin 90.9 0.12 2.6E-06 60.0 2.0 47 1113-1166 302-348 (355)
85 KOG1002 Nucleotide excision re 90.4 0.1 2.2E-06 62.5 0.8 51 1111-1165 531-586 (791)
86 KOG3039 Uncharacterized conser 90.2 0.23 5E-06 54.9 3.2 52 1115-1167 220-272 (303)
87 PF14447 Prok-RING_4: Prokaryo 89.6 0.15 3.2E-06 44.6 1.0 45 1116-1166 7-51 (55)
88 KOG3800 Predicted E3 ubiquitin 89.6 0.24 5.3E-06 56.0 2.9 48 1118-1165 2-51 (300)
89 PF07800 DUF1644: Protein of u 89.4 0.29 6.4E-06 51.1 3.2 49 1116-1168 2-94 (162)
90 KOG0269 WD40 repeat-containing 89.3 0.31 6.8E-06 60.9 3.8 80 1070-1169 751-837 (839)
91 KOG2272 Focal adhesion protein 89.1 0.1 2.2E-06 57.6 -0.5 69 1008-1102 100-174 (332)
92 COG2461 Uncharacterized conser 89.0 1.7 3.7E-05 51.4 9.2 137 41-191 85-222 (409)
93 KOG2660 Locus-specific chromos 88.8 0.11 2.3E-06 59.7 -0.5 49 1115-1166 14-62 (331)
94 PF04641 Rtf2: Rtf2 RING-finge 88.2 0.43 9.4E-06 53.8 3.8 52 1114-1167 111-163 (260)
95 KOG1814 Predicted E3 ubiquitin 87.3 0.32 6.9E-06 57.3 2.0 46 1116-1162 184-237 (445)
96 COG5152 Uncharacterized conser 87.0 0.24 5.3E-06 53.1 0.8 45 1117-1165 197-241 (259)
97 KOG4159 Predicted E3 ubiquitin 86.8 0.4 8.7E-06 57.2 2.5 49 1114-1166 82-130 (398)
98 KOG2114 Vacuolar assembly/sort 86.1 0.28 6.1E-06 62.0 0.8 40 1117-1162 841-880 (933)
99 PHA02862 5L protein; Provision 85.8 0.51 1.1E-05 48.7 2.3 50 1116-1171 2-58 (156)
100 COG5236 Uncharacterized conser 84.4 0.84 1.8E-05 52.6 3.5 66 1095-1164 39-107 (493)
101 KOG0827 Predicted E3 ubiquitin 82.9 0.11 2.4E-06 60.4 -4.2 51 1115-1165 195-245 (465)
102 KOG2034 Vacuolar sorting prote 82.9 0.53 1.1E-05 60.1 1.2 43 1107-1151 808-850 (911)
103 KOG1813 Predicted E3 ubiquitin 82.9 0.47 1E-05 53.9 0.7 46 1116-1165 241-286 (313)
104 KOG4692 Predicted E3 ubiquitin 82.7 0.8 1.7E-05 52.9 2.4 51 1112-1166 418-468 (489)
105 PHA02825 LAP/PHD finger-like p 81.1 1.3 2.8E-05 46.6 3.0 52 1115-1172 7-65 (162)
106 TIGR02481 hemeryth_dom hemeryt 79.9 6.3 0.00014 39.1 7.4 51 361-421 12-62 (126)
107 PRK04023 DNA polymerase II lar 79.9 1.5 3.3E-05 57.0 3.6 18 925-942 555-572 (1121)
108 KOG1701 Focal adhesion adaptor 79.8 0.16 3.6E-06 59.8 -4.3 86 1056-1167 271-373 (468)
109 COG5592 Uncharacterized conser 79.6 5.3 0.00011 42.2 6.8 99 682-817 31-136 (171)
110 KOG4185 Predicted E3 ubiquitin 76.3 1.7 3.6E-05 49.6 2.5 47 1117-1164 4-54 (296)
111 PRK14890 putative Zn-ribbon RN 75.6 2.2 4.7E-05 38.0 2.4 46 1028-1080 6-56 (59)
112 PF08746 zf-RING-like: RING-li 73.1 2 4.2E-05 35.8 1.4 41 1119-1160 1-43 (43)
113 KOG1952 Transcription factor N 72.5 2.1 4.6E-05 54.5 2.2 50 1115-1165 190-247 (950)
114 KOG2817 Predicted E3 ubiquitin 72.5 2.7 5.8E-05 49.8 2.8 47 1117-1164 335-384 (394)
115 KOG3161 Predicted E3 ubiquitin 72.0 1.3 2.9E-05 54.6 0.3 43 1117-1162 12-54 (861)
116 PF06524 NOA36: NOA36 protein; 71.4 1.8 3.9E-05 48.5 1.1 65 1005-1080 140-217 (314)
117 PF09538 FYDLN_acid: Protein o 71.0 2.1 4.6E-05 42.5 1.4 17 1064-1080 18-34 (108)
118 PF03854 zf-P11: P-11 zinc fin 70.9 1.5 3.2E-05 37.4 0.3 42 1118-1165 4-46 (50)
119 KOG3002 Zn finger protein [Gen 68.5 3 6.5E-05 48.3 2.1 44 1116-1167 48-93 (299)
120 smart00132 LIM Zinc-binding do 68.0 3.4 7.4E-05 32.0 1.7 38 1118-1165 1-38 (39)
121 TIGR02481 hemeryth_dom hemeryt 67.3 87 0.0019 31.0 12.0 109 297-424 13-125 (126)
122 PF01529 zf-DHHC: DHHC palmito 66.9 4 8.7E-05 42.5 2.5 47 1052-1104 43-89 (174)
123 COG5220 TFB3 Cdk activating ki 66.8 1.9 4E-05 47.8 0.0 50 1116-1165 10-64 (314)
124 KOG2462 C2H2-type Zn-finger pr 66.6 4.4 9.6E-05 46.1 2.9 15 1070-1084 159-173 (279)
125 PHA03096 p28-like protein; Pro 65.9 3.2 7E-05 47.7 1.7 46 1117-1162 179-231 (284)
126 TIGR00595 priA primosomal prot 65.7 4.7 0.0001 49.9 3.2 48 999-1052 214-261 (505)
127 TIGR02300 FYDLN_acid conserved 65.1 3.4 7.3E-05 42.1 1.5 19 1064-1082 18-36 (129)
128 PF02084 Bindin: Bindin; Inte 65.0 21 0.00047 39.6 7.5 40 72-127 124-169 (238)
129 PF05502 Dynactin_p62: Dynacti 64.8 4.5 9.7E-05 49.8 2.7 14 1052-1065 21-34 (483)
130 KOG1001 Helicase-like transcri 64.1 2.9 6.4E-05 53.3 1.0 44 1117-1165 455-500 (674)
131 KOG2066 Vacuolar assembly/sort 62.5 2.8 6.1E-05 53.2 0.5 88 405-496 393-485 (846)
132 PRK14714 DNA polymerase II lar 62.2 7.3 0.00016 52.2 4.0 52 1029-1083 667-720 (1337)
133 PRK00808 hypothetical protein; 61.9 26 0.00056 36.4 7.3 96 361-467 16-122 (150)
134 KOG0298 DEAD box-containing he 61.6 1.9 4E-05 57.3 -1.3 70 145-214 237-306 (1394)
135 KOG1829 Uncharacterized conser 60.9 2.9 6.2E-05 52.1 0.2 29 989-1018 345-377 (580)
136 COG5592 Uncharacterized conser 60.1 31 0.00067 36.7 7.3 94 329-436 29-136 (171)
137 KOG2068 MOT2 transcription fac 60.0 6.9 0.00015 45.6 2.9 50 1115-1164 248-297 (327)
138 PF14446 Prok-RING_1: Prokaryo 59.5 9.2 0.0002 33.7 2.9 35 1115-1149 4-38 (54)
139 COG2888 Predicted Zn-ribbon RN 59.0 7.8 0.00017 34.7 2.4 45 1029-1080 9-58 (61)
140 COG5222 Uncharacterized conser 58.3 5.5 0.00012 45.4 1.7 43 1117-1162 275-318 (427)
141 KOG1100 Predicted E3 ubiquitin 58.3 5.1 0.00011 44.1 1.5 39 1119-1165 161-200 (207)
142 KOG0801 Predicted E3 ubiquitin 57.6 4.8 0.0001 42.4 1.0 30 1114-1144 175-204 (205)
143 COG1198 PriA Primosomal protei 57.4 8.9 0.00019 49.4 3.5 55 998-1059 435-489 (730)
144 PRK05580 primosome assembly pr 57.1 7.8 0.00017 49.7 3.1 49 998-1052 381-429 (679)
145 cd00350 rubredoxin_like Rubred 57.0 7.7 0.00017 30.4 1.9 24 1057-1080 1-25 (33)
146 PF14357 DUF4404: Domain of un 56.2 80 0.0017 30.2 8.9 82 54-139 2-83 (85)
147 KOG0826 Predicted E3 ubiquitin 55.5 7.4 0.00016 45.2 2.2 46 1116-1164 300-345 (357)
148 PF07227 DUF1423: Protein of u 54.1 11 0.00024 45.6 3.4 31 920-952 21-51 (446)
149 COG4888 Uncharacterized Zn rib 53.7 5.6 0.00012 38.9 0.8 33 1070-1102 20-57 (104)
150 KOG1609 Protein involved in mR 53.5 5.9 0.00013 45.1 1.0 51 1116-1166 78-135 (323)
151 KOG1280 Uncharacterized conser 53.5 10 0.00023 44.3 2.9 26 1052-1080 60-87 (381)
152 PRK14873 primosome assembly pr 52.9 9.8 0.00021 48.7 2.9 47 999-1052 384-430 (665)
153 PF09538 FYDLN_acid: Protein o 52.4 7.8 0.00017 38.6 1.5 32 997-1042 8-39 (108)
154 PRK00808 hypothetical protein; 50.2 3.1E+02 0.0068 28.4 13.1 110 297-428 17-130 (150)
155 PRK04023 DNA polymerase II lar 49.9 14 0.00031 48.6 3.6 48 1028-1081 625-672 (1121)
156 KOG4443 Putative transcription 48.9 6.3 0.00014 49.3 0.4 46 1116-1162 145-201 (694)
157 PRK01917 cation-binding hemery 48.1 47 0.001 34.1 6.4 70 398-467 38-120 (139)
158 KOG2932 E3 ubiquitin ligase in 46.5 11 0.00023 43.6 1.6 32 1134-1167 105-136 (389)
159 COG5183 SSM4 Protein involved 46.3 13 0.00029 47.5 2.5 59 1115-1175 11-76 (1175)
160 PF02891 zf-MIZ: MIZ/SP-RING z 45.5 20 0.00044 30.8 2.8 41 1117-1163 3-50 (50)
161 KOG3850 Predicted membrane pro 45.5 6.1E+02 0.013 30.8 15.3 129 301-445 262-396 (455)
162 COG5109 Uncharacterized conser 44.5 15 0.00032 42.6 2.3 45 1117-1162 337-384 (396)
163 PF12773 DZR: Double zinc ribb 44.3 19 0.00042 30.2 2.5 22 1032-1056 1-23 (50)
164 cd00522 Hemerythrin Hemerythri 43.6 92 0.002 30.8 7.5 51 361-428 14-68 (113)
165 PRK00398 rpoP DNA-directed RNA 42.4 20 0.00043 30.0 2.3 23 1057-1079 3-28 (46)
166 KOG1812 Predicted E3 ubiquitin 42.4 12 0.00026 44.9 1.3 36 1116-1152 146-182 (384)
167 PF07191 zinc-ribbons_6: zinc- 42.2 11 0.00025 34.7 0.8 9 1056-1064 49-57 (70)
168 PRK14559 putative protein seri 40.8 19 0.00042 46.0 2.8 32 1030-1064 2-34 (645)
169 COG0143 MetG Methionyl-tRNA sy 39.7 19 0.00041 45.2 2.5 45 1054-1104 123-168 (558)
170 KOG3362 Predicted BBOX Zn-fing 39.4 9.7 0.00021 39.5 -0.0 26 1055-1084 116-143 (156)
171 PF13901 DUF4206: Domain of un 39.4 14 0.00031 40.4 1.2 31 1127-1162 167-197 (202)
172 KOG2593 Transcription initiati 39.3 13 0.00029 44.7 1.0 20 912-931 50-69 (436)
173 PF14631 FancD2: Fanconi anaem 38.9 5.5E+02 0.012 36.4 16.0 99 127-228 192-306 (1426)
174 TIGR00373 conserved hypothetic 37.7 11 0.00025 39.7 0.1 23 1057-1079 109-135 (158)
175 PRK06266 transcription initiat 36.4 13 0.00027 40.1 0.3 24 1056-1079 116-143 (178)
176 PF06220 zf-U1: U1 zinc finger 36.1 14 0.0003 30.2 0.4 13 1055-1067 1-13 (38)
177 KOG1311 DHHC-type Zn-finger pr 35.6 29 0.00063 39.8 3.0 48 1051-1104 107-154 (299)
178 PF00412 LIM: LIM domain; Int 35.5 15 0.00032 31.3 0.5 40 1119-1168 1-40 (58)
179 cd00729 rubredoxin_SM Rubredox 35.5 27 0.00058 27.8 1.9 24 1057-1080 2-26 (34)
180 PF03833 PolC_DP2: DNA polymer 34.8 13 0.00028 48.2 0.0 21 923-943 581-601 (900)
181 PF00628 PHD: PHD-finger; Int 32.9 9.1 0.0002 32.1 -1.2 43 1119-1162 2-50 (51)
182 COG1996 RPC10 DNA-directed RNA 32.5 24 0.00052 30.6 1.3 30 1054-1083 3-35 (49)
183 PF06937 EURL: EURL protein; 32.2 28 0.0006 39.7 2.0 43 1113-1158 27-74 (285)
184 KOG3842 Adaptor protein Pellin 31.7 39 0.00085 39.3 3.1 56 1116-1171 341-420 (429)
185 PF08271 TF_Zn_Ribbon: TFIIB z 31.4 23 0.00051 29.2 1.0 13 1067-1079 14-26 (43)
186 COG1198 PriA Primosomal protei 31.0 44 0.00095 43.4 3.8 44 1027-1079 433-482 (730)
187 PF05502 Dynactin_p62: Dynacti 30.0 39 0.00085 41.8 3.0 10 1007-1016 5-14 (483)
188 KOG1044 Actin-binding LIM Zn-f 29.7 59 0.0013 40.7 4.3 124 998-1136 16-152 (670)
189 PLN02189 cellulose synthase 28.9 39 0.00085 45.0 2.9 52 1113-1165 31-87 (1040)
190 TIGR02300 FYDLN_acid conserved 28.4 32 0.00069 35.3 1.5 32 997-1042 8-39 (129)
191 PRK14714 DNA polymerase II lar 28.4 49 0.0011 44.9 3.6 21 298-318 8-28 (1337)
192 PHA00626 hypothetical protein 28.2 43 0.00094 29.8 2.1 7 1073-1079 24-30 (59)
193 PF04216 FdhE: Protein involve 28.1 1.3E+02 0.0029 34.6 6.7 42 911-952 111-153 (290)
194 KOG4654 Uncharacterized conser 27.5 8.8E+02 0.019 26.9 12.3 150 43-200 41-213 (252)
195 PRK14892 putative transcriptio 27.3 39 0.00085 33.3 1.9 12 1114-1125 40-51 (99)
196 KOG4718 Non-SMC (structural ma 27.3 30 0.00066 38.2 1.2 41 1118-1161 183-223 (235)
197 PRK07219 DNA topoisomerase I; 27.2 88 0.0019 41.3 5.6 63 1060-1127 672-744 (822)
198 KOG0006 E3 ubiquitin-protein l 27.1 52 0.0011 38.3 3.0 76 1066-1151 169-254 (446)
199 TIGR00622 ssl1 transcription f 26.9 1.2E+02 0.0026 30.7 5.2 46 1116-1162 55-111 (112)
200 PF09788 Tmemb_55A: Transmembr 26.8 52 0.0011 37.4 3.0 63 1088-1163 103-186 (256)
201 KOG4399 C2HC-type Zn-finger pr 26.5 16 0.00034 41.3 -1.0 47 1052-1102 256-302 (325)
202 smart00249 PHD PHD zinc finger 26.3 28 0.00061 27.7 0.6 42 1118-1160 1-47 (47)
203 KOG3842 Adaptor protein Pellin 26.3 31 0.00067 40.1 1.1 45 1113-1162 287-349 (429)
204 KOG2807 RNA polymerase II tran 26.3 70 0.0015 37.6 3.9 46 1116-1162 330-375 (378)
205 PLN02436 cellulose synthase A 26.1 47 0.001 44.5 2.8 51 1114-1165 34-89 (1094)
206 PLN03086 PRLI-interacting fact 25.8 27 0.00059 43.9 0.7 53 1070-1125 451-513 (567)
207 PRK00420 hypothetical protein; 25.7 39 0.00085 34.0 1.6 14 1115-1128 22-35 (112)
208 KOG0802 E3 ubiquitin ligase [P 25.7 32 0.0007 43.1 1.3 43 1115-1165 478-520 (543)
209 cd00522 Hemerythrin Hemerythri 25.2 3.4E+02 0.0073 26.8 8.1 61 117-195 14-78 (113)
210 PF06377 Adipokin_hormo: Adipo 25.2 1.6E+02 0.0034 25.7 4.8 37 629-665 7-45 (48)
211 smart00451 ZnF_U1 U1-like zinc 25.0 35 0.00076 26.2 0.9 12 1055-1066 1-12 (35)
212 KOG2272 Focal adhesion protein 24.9 43 0.00093 37.9 1.9 78 993-1084 115-204 (332)
213 KOG4399 C2HC-type Zn-finger pr 24.6 22 0.00048 40.2 -0.3 71 1052-1125 199-270 (325)
214 KOG3053 Uncharacterized conser 24.1 30 0.00066 39.2 0.6 51 1112-1164 16-81 (293)
215 PF13824 zf-Mss51: Zinc-finger 23.3 51 0.0011 29.3 1.6 12 1070-1081 12-23 (55)
216 PF15353 HECA: Headcase protei 23.2 42 0.00091 33.4 1.3 15 1137-1151 39-53 (107)
217 PF04710 Pellino: Pellino; In 23.1 28 0.0006 41.8 0.0 35 1128-1162 299-336 (416)
218 KOG1312 DHHC-type Zn-finger pr 22.9 28 0.0006 40.1 -0.0 32 1076-1111 149-180 (341)
219 KOG1044 Actin-binding LIM Zn-f 22.7 46 0.001 41.6 1.7 11 1137-1147 82-92 (670)
220 smart00531 TFIIE Transcription 22.7 30 0.00065 36.0 0.2 7 1073-1079 124-130 (147)
221 PRK00432 30S ribosomal protein 22.6 47 0.001 28.8 1.3 24 1074-1099 22-45 (50)
222 PF01780 Ribosomal_L37ae: Ribo 22.6 31 0.00068 33.4 0.3 22 1073-1098 36-60 (90)
223 PRK14559 putative protein seri 22.3 60 0.0013 41.7 2.7 34 1029-1066 15-50 (645)
224 PHA00626 hypothetical protein 22.3 51 0.0011 29.4 1.4 34 1030-1068 1-34 (59)
225 KOG4362 Transcriptional regula 22.0 27 0.00059 44.5 -0.3 47 1115-1165 20-69 (684)
226 PF05129 Elf1: Transcription e 21.9 35 0.00076 32.4 0.4 31 1071-1101 21-56 (81)
227 PF05290 Baculo_IE-1: Baculovi 21.7 55 0.0012 33.9 1.8 48 1116-1167 80-134 (140)
228 PF10272 Tmpp129: Putative tra 21.6 88 0.0019 37.5 3.7 18 1148-1165 334-351 (358)
229 PRK03824 hypA hydrogenase nick 21.3 52 0.0011 34.0 1.6 10 1071-1080 106-115 (135)
230 PF10235 Cript: Microtubule-as 21.3 66 0.0014 31.3 2.1 45 1116-1173 44-88 (90)
231 TIGR00058 Hemerythrin hemeryth 20.6 4.4E+02 0.0096 26.2 7.9 20 401-420 39-58 (115)
232 PF03604 DNA_RNApol_7kD: DNA d 20.4 64 0.0014 25.6 1.5 22 1058-1079 1-24 (32)
233 KOG1812 Predicted E3 ubiquitin 20.4 52 0.0011 39.6 1.5 48 1115-1162 305-353 (384)
234 PRK14892 putative transcriptio 20.1 58 0.0013 32.2 1.5 31 1006-1037 20-50 (99)
No 1
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=100.00 E-value=5.3e-44 Score=389.84 Aligned_cols=193 Identities=49% Similarity=1.114 Sum_probs=183.4
Q ss_pred CCCCcccccccccCCccccccccccccccCCcccCcccccccCCCCCCccccceeeccccCccccCCCCCCCCCCCCccc
Q 001043 976 CSPSFRDAEKQVFGCEHYKRNCKLRAACCGKLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVGPVCTTLSCSGLSM 1055 (1177)
Q Consensus 976 ~~~~~~~~~~~~~gC~HY~r~c~l~~~cC~k~y~Cr~CHde~~~H~~~r~~~~~~~C~~C~~~q~~~~~C~~~~C~~~~~ 1055 (1177)
..+++.|+...++||+||+|+|++++|||+++|+|++||++..+|.++|+.+.+++|+.|.++||++++|.+ | +..+
T Consensus 21 ~~~~~~d~~~~~~~c~hy~r~~~~~a~ccd~~~~C~hCH~~s~~h~~~r~~v~~~~C~~C~~~q~~~~~c~~--c-~~~~ 97 (276)
T KOG1940|consen 21 IHSDAEDEIAFPYGCPHYRRNCKSRAPCCDREITCRHCHNESEDHDLDRKTVYELLCMKCRKIQPVGQICSN--C-HVEL 97 (276)
T ss_pred cccccccccccccCCchhhhccccccccccceeeeEEecChhhhcccchhhhhhhhhhhHHhhhhhhhcccc--c-hhhh
Confidence 356788989999999999999999999999999999999999999999999999999999999999999999 4 7789
Q ss_pred ceEeccccccccCC-CCcccCCCCCccccCCCCCccccccCCccccccccc-ccccccccCCCCCCcccccccccCCCce
Q 001043 1056 AKYYCGICKFFDDE-RVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLAKKL-VDHKCREKGLETNCPICCDFLFTSSATV 1133 (1177)
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 (1177)
++|||.+|++|||+ ..||||++|||||+|.++ +||||++|+.|++..+ ++|+|+|+..+.+||||.|++|.+...+
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 599999999999999876 9999999999999998 6699999999999999999999999999
Q ss_pred EecCCCCcccHhhHHHHHhcCCCCCCCcccccccccccCCC
Q 001043 1134 RALPCGHFMHSDCFQAYTCSHYICPICSKSLGDMAVLHLPI 1174 (1177)
Q Consensus 1134 ~~LpCGH~fH~~Ci~~wl~~~~~CPiCrk~v~dm~~~~~~~ 1174 (1177)
..++|||.+|..|++++...+|+||+|.+ ++||..||+..
T Consensus 176 ~~~~CgH~~h~~cf~e~~~~~y~CP~C~~-~~d~~~~~~~~ 215 (276)
T KOG1940|consen 176 GVLKCGHYMHSRCFEEMICEGYTCPICSK-PGDMSHYFRKL 215 (276)
T ss_pred CccCcccchHHHHHHHHhccCCCCCcccc-hHHHHHHHHHH
Confidence 99999999999999999988899999999 99999999754
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=4.9e-21 Score=172.49 Aligned_cols=70 Identities=44% Similarity=1.197 Sum_probs=53.8
Q ss_pred Ccccccc-ccccccccCCcccCcccccccCCCCCCccccceeeccccCccccCCCCCCCCCCCCcccceEecccccccc
Q 001043 990 CEHYKRN-CKLRAACCGKLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVGPVCTTLSCSGLSMAKYYCGICKFFD 1067 (1177)
Q Consensus 990 C~HY~r~-c~l~~~cC~k~y~Cr~CHde~~~H~~~r~~~~~~~C~~C~~~q~~~~~C~~~~C~~~~~a~Y~C~~C~l~d 1067 (1177)
|+||+|+ |+|+||||++|||||+|||+.++|+++|+.+++|+||.|+++|++++. + | + |+|+|++|++||
T Consensus 1 C~HY~~~~~~~~~~cC~~~y~C~~CHde~~~H~~~~~~~~~v~Cg~C~~~~~~~~~--~--c-~---~~~~C~~C~~~~ 71 (71)
T PF05495_consen 1 CKHYHRSLCAIRFPCCGKYYPCRFCHDELEDHPFDRWPVKRVICGKCRTEQPIDEY--S--C-G---ADYFCPICGLYF 71 (71)
T ss_dssp -SS---S-EEEEETTTTEEESSHHHHHHCSSS---TTT--EEEETTT--EEES-SB--T--T------SEEETTTTEEE
T ss_pred CCCCCCCcEEEECCcccCeecHHHHHHHhccCccccccccCeECCCCCCccChhhh--h--c-C---CCccCcCcCCCC
Confidence 8999999 999999999999999999999999999999999999999999999988 4 5 4 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=2.4e-10 Score=110.65 Aligned_cols=124 Identities=26% Similarity=0.366 Sum_probs=110.1
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcccHHHHHHHHHHHHHHHHhhhhccccchhhhhhhhh--------hhHH
Q 001043 293 PIDEIMLWHNAIKRELNDIAEAARKIQLSGDFSDLSAFNKRLQFIAEVCIFHSIAEDKVIFPAVDVEL--------SFAQ 364 (1177)
Q Consensus 293 pid~l~~~HkALRrEL~~L~~~a~~i~~~gd~~~L~~L~~r~~fl~~vl~~Hs~aEDevlFPaL~~r~--------~me~ 364 (1177)
+++.|...|+.||+.++.+...+... ++..++..+...+.+|...+..|+..||+++||.|..+. .+..
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 455578999999999999999999999999999999332 8999
Q ss_pred hHHHHHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 001043 365 EHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPLA 425 (1177)
Q Consensus 365 EH~~ie~l~e~l~~ll~~~~~~~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qvfPLl 425 (1177)
||..+...++.+...+...... ......+...+..+...+..|+.+||+.+||++
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
>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=99.19 E-value=4.9e-12 Score=103.59 Aligned_cols=44 Identities=36% Similarity=0.989 Sum_probs=38.5
Q ss_pred CCCcccccccccCCCceEecCCCCcccHhhHHHHHhcCCCCCCCc
Q 001043 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICS 1161 (1177)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCr 1161 (1177)
++|+||+++ +..++.+..++|||.||.+||.+|++.+++||+||
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 45577788999999999999999999999999997
No 5
>PF01814 Hemerythrin: Hemerythrin HHE cation binding domain; InterPro: IPR012312 The haemerythrin family is composed of haemerythrin proteins found in invertebrates, and a broader collection of bacterial and archaeal homologues. Haemerythrin is an oxygen-binding protein found in the vascular system and coelemic fluid, or in muscles (myohaemerythrin) in invertebrates []. Many of the homologous proteins found in prokaryotes are multi-domain proteins with signal-transducing domains such as the GGDEF diguanylate cyclase domain (IPR000160 from INTERPRO) and methyl-accepting chemotaxis protein (MCP) signalling domain (IPR004089 from INTERPRO). Most haemerythrins are oxygen-carriers with a bound non-haem iron, but at least one example is a cadmium-binding protein, apparently with a role in sequestering toxic metals rather than in binding oxygen. The prokaryote with the most instances of this domain is Magnetococcus sp. MC-1, a magnetotactic bacterium. Haemerythrins and myohaemerythrins [, ] are small proteins of about 110 to 129 amino acid residues that bind two iron atoms. They are left-twisted 4-alpha-helical bundles, which provide a hydrophobic pocket where dioxygen binds as a peroxo species, interacting with adjacent aliphatic side chains via van der Waals forces []. In both haemerythrins and myohaemerythrins, the active centre is a binuclear iron complex, bound directly to the protein via 7 amino acid side chains [], 5 His, 1 Glu and 1 Asp []. Ovohaemerythrin [], a yolk protein from the leech Theromyzon tessulatum seems to belong to this family of proteins, it may play a role in the detoxification of free iron after a blood meal []. This entry represents a haemerythrin/HHE cation-binding motif that occurs as a duplicated domain in haemerythrin and related proteins. This domain binds iron in haemerythrin, but can bind other metals in related proteins, such as cadmium in a Nereis diversicolor protein (P80255 from SWISSPROT). A bacterial protein, Q7WX96 from SWISSPROT, is a regulator of response to NO, which suggests a different set-up for its metal ligands. A protein from Cryptococcus neoformans (Filobasidiella neoformans) that contains haemerythrin/HHE cation-binding motifs is also involved in NO response []. A Staphylococcus aureus protein (P72360 from SWISSPROT) has been noted to be important when the organism switches to living in environments with low oxygen concentrations; perhaps this protein acts as an oxygen store or scavenger.; PDB: 3CAX_A 3V5Z_B 3U9M_G 3V5Y_A 3U9J_B 3V5X_A 2MHR_A 1A7E_A 1A7D_A 2IGF_P ....
Probab=99.17 E-value=2.4e-10 Score=110.64 Aligned_cols=129 Identities=33% Similarity=0.416 Sum_probs=115.6
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHHHh---hhHHHHHHH
Q 001043 43 PILIFLFFHKAIKSELDVLHRAAMAFATNLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIR---VKNIARTYS 119 (1177)
Q Consensus 43 Pi~~~~~~HkAlR~el~~l~~~~~~~~~~~~d~~~~~~l~~r~~~L~~~~~~H~~aEDevI~PaL~~R---v~~v~~~~~ 119 (1177)
||+.+...|+.||+.+..+...+... + +......+...+.+|...+..|+..|++++||.|+.+ .++.+..+.
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 78899999999999999999999888 3 4556899999999999999999999999999999944 377889999
Q ss_pred hhhhhHHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHHHHHhHHHHHHHhhhHH
Q 001043 120 LEHEGESVLFDQLFELLNSSMRNEESYRRELASCTGALQTSISQHMSKEEEQVFPLL 176 (1177)
Q Consensus 120 ~EH~~~~~lf~~l~~~l~~~~~~~~~~~~eLa~~l~~l~~~l~qHm~~EE~~v~PLl 176 (1177)
.||..+...++.+...+..+. ........+...+.++...+.+||.+||+.++|++
T Consensus 78 ~eH~~~~~~l~~l~~~~~~~~-~~~~~~~~~~~~~~~l~~~l~~H~~~Ee~~l~P~~ 133 (133)
T PF01814_consen 78 REHEEIRALLDELEEALARYS-GDEEDAEELREALRALAEWLRRHIAKEEEVLFPLL 133 (133)
T ss_dssp HHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHTHGGGHHHH
T ss_pred HHHHHHHHHHHHHHHHHhhCc-cccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 999999999999999999997 33466778888888888899999999999999986
No 6
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=98.99 E-value=5.2e-11 Score=111.04 Aligned_cols=57 Identities=30% Similarity=0.725 Sum_probs=50.2
Q ss_pred cccCCcccccc---ccccccccCCcccCcccccccCCCCCCcc-----ccceeeccccCccccCC
Q 001043 986 QVFGCEHYKRN---CKLRAACCGKLFTCRFCHDKVSDHSMDRK-----ATTEMMCMRCLKVQPVG 1042 (1177)
Q Consensus 986 ~~~gC~HY~r~---c~l~~~cC~k~y~Cr~CHde~~~H~~~r~-----~~~~~~C~~C~~~q~~~ 1042 (1177)
+++||.||+.. ++|+|.||+|||+|..|||+.++||+.++ ..+.|+||.|.++..++
T Consensus 11 ~etRC~Hyht~~Diialkc~~C~kyYaCy~CHdel~~Hpf~p~~~~~~~~~~iiCGvC~~~LT~~ 75 (105)
T COG4357 11 QETRCLHYHTPLDIIALKCKCCQKYYACYHCHDELEDHPFEPWGLQEFNPKAIICGVCRKLLTRA 75 (105)
T ss_pred ccceeeEecCccceEeeeechhhhhhhHHHHHhHHhcCCCccCChhhcCCccEEhhhhhhhhhHH
Confidence 67899999999 79999999999999999999999999864 34679999998876554
No 7
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.94 E-value=2.9e-10 Score=129.35 Aligned_cols=49 Identities=27% Similarity=0.845 Sum_probs=44.8
Q ss_pred CCCcccccccccCCCceEecCCCCcccHhhHHHHHhcC-CCCCCCcccccc
Q 001043 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSH-YICPICSKSLGD 1166 (1177)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~-~~CPiCrk~v~d 1166 (1177)
..|+||+|+ |..+++++.|||+|.||..||+.||..+ ..||+|++.+..
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 589999999 8999999999999999999999999776 449999998764
No 8
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=98.88 E-value=7.8e-10 Score=123.94 Aligned_cols=57 Identities=32% Similarity=0.800 Sum_probs=48.7
Q ss_pred cCCCCCCcccccccccCC---------CceEecCCCCcccHhhHHHHHhcCCCCCCCccc-cccccc
Q 001043 1113 KGLETNCPICCDFLFTSS---------ATVRALPCGHFMHSDCFQAYTCSHYICPICSKS-LGDMAV 1169 (1177)
Q Consensus 1113 ~~~~~~CpICle~lf~s~---------~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrk~-v~dm~~ 1169 (1177)
...+..|.||||+|+.++ ...+.|||||.+|.+|++.|+.++.+|||||.+ +.||+.
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 446788999999987765 234789999999999999999999999999999 677754
No 9
>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=98.87 E-value=1.3e-09 Score=99.25 Aligned_cols=47 Identities=30% Similarity=0.757 Sum_probs=37.7
Q ss_pred CCCCCcccccccccC---------CCceEecCCCCcccHhhHHHHHhcCCCCCCCc
Q 001043 1115 LETNCPICCDFLFTS---------SATVRALPCGHFMHSDCFQAYTCSHYICPICS 1161 (1177)
Q Consensus 1115 ~~~~CpICle~lf~s---------~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCr 1161 (1177)
.+++|+||+++|.+. ..++...+|||.||.+||.+|++.+.+||+||
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 456799999997332 24556679999999999999999999999998
No 10
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=98.83 E-value=2.1e-09 Score=99.85 Aligned_cols=47 Identities=21% Similarity=0.514 Sum_probs=37.8
Q ss_pred CCCCcccccccccCCCceEecCCCCcccHhhHHHHHhc---CCCCCCCcccc
Q 001043 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS---HYICPICSKSL 1164 (1177)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~---~~~CPiCrk~v 1164 (1177)
+..||.|..+ +..-++....|+|.||.+||.+|+.+ +.+||+||+..
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 5678888866 34446667789999999999999975 47899999864
No 11
>PRK10992 iron-sulfur cluster repair di-iron protein; Provisional
Probab=98.77 E-value=7.3e-08 Score=105.01 Aligned_cols=131 Identities=18% Similarity=0.318 Sum_probs=106.3
Q ss_pred HHHH-HHHHHHHHHHHHHHHHHHHHhcc--cCCcccHHHHHHHHHHHHHHHHhhhhccccchhhhhhhhh---------h
Q 001043 294 IDEI-MLWHNAIKRELNDIAEAARKIQL--SGDFSDLSAFNKRLQFIAEVCIFHSIAEDKVIFPAVDVEL---------S 361 (1177)
Q Consensus 294 id~l-~~~HkALRrEL~~L~~~a~~i~~--~gd~~~L~~L~~r~~fl~~vl~~Hs~aEDevlFPaL~~r~---------~ 361 (1177)
||.+ ..-|..+|++|..|.+.+.++.. .++...+..+..-+..|...+..|+..|++++||+|.+.. .
T Consensus 76 idyI~~~~H~~~r~~lp~L~~l~~kv~~vhg~~~~~~~~~~~l~~~~~~el~~H~~kEE~~LFP~l~~~~~~~~~~pi~v 155 (220)
T PRK10992 76 IDHIIVRYHDRHREQLPELILLATKVERVHGDKPDCPRGLAKYLTALHEELSSHMMKEEQILFPMIKQGMGSQAMGPISV 155 (220)
T ss_pred HHHHHHHHhHHHHHHHHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHhcccccccchHHH
Confidence 5555 78899999999999999977642 2334567888888998999999999999999999999631 8
Q ss_pred hHHhHHHHHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHh
Q 001043 362 FAQEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPLARR 427 (1177)
Q Consensus 362 me~EH~~ie~l~e~l~~ll~~~~~~~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qvfPLl~~ 427 (1177)
|..||+++...+.+|..++...... ......++.+-..+..+...|.+|..+||+.+||++..
T Consensus 156 m~~EHd~~~~~l~~L~~lt~~~~~p---~~ac~~~~~l~~~l~~~~~dL~~HI~~EnniLFP~a~~ 218 (220)
T PRK10992 156 MESEHDEAGELLEVIKHLTNNVTPP---PEACTTWRALYNGINELIDDLMEHIHLENNVLFPRALA 218 (220)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCCC---hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Confidence 9999999999999999888654211 11124577777888889999999999999999998864
No 12
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.67 E-value=1e-08 Score=112.80 Aligned_cols=56 Identities=27% Similarity=0.672 Sum_probs=48.5
Q ss_pred ccccCCCCCCcccccccccCCCceEecCCCCcccHhhHHHHHh-cCCCCCCCcccccc
Q 001043 1110 CREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC-SHYICPICSKSLGD 1166 (1177)
Q Consensus 1110 C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~-~~~~CPiCrk~v~d 1166 (1177)
-+|.....+|+|||++ |...+.+++|||.|.||..|+++|+- .+.+||+||..+.+
T Consensus 317 ~~ea~~GveCaICms~-fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iPP 373 (374)
T COG5540 317 AVEADKGVECAICMSN-FIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIPP 373 (374)
T ss_pred HHhcCCCceEEEEhhh-hcccceEEEeccCceechhHHHHHHhhhcccCCccCCCCCC
Confidence 3455667899999999 67888899999999999999999986 67899999987753
No 13
>TIGR03652 FeS_repair_RIC iron-sulfur cluster repair di-iron protein. Members of this protein family, designated variously as YftE, NorA, DrnN, and NipC, are di-iron proteins involved in the repair of iron-sulfur clusters. Previously assigned names reflect pleiotropic effects of damage from NO or other oxidative stress when this protein is mutated. The suggested name now is RIC, for Repair of Iron Centers.
Probab=98.66 E-value=1.6e-07 Score=101.93 Aligned_cols=129 Identities=19% Similarity=0.307 Sum_probs=103.1
Q ss_pred HHH-HHHHHHHHHHHHHHHHHHHHHhcc--cCCcccHHHHHHHHHHHHHHHHhhhhccccchhhhhhhh-----------
Q 001043 294 IDE-IMLWHNAIKRELNDIAEAARKIQL--SGDFSDLSAFNKRLQFIAEVCIFHSIAEDKVIFPAVDVE----------- 359 (1177)
Q Consensus 294 id~-l~~~HkALRrEL~~L~~~a~~i~~--~gd~~~L~~L~~r~~fl~~vl~~Hs~aEDevlFPaL~~r----------- 359 (1177)
||. ....|..||++|..|...+.++.. ..+...+..+..-+..|..-+..|+..|+++|||+|...
T Consensus 72 id~i~~~hH~~i~~~l~~L~~l~~kv~~~hg~~~~~l~~l~~~~~~~~~eL~~H~~kEE~~LFP~l~~~~~g~~~~~~~~ 151 (216)
T TIGR03652 72 IDHIVDRHHEYLREELPELIPLATKVARVHGDHHPELIGLAELFRELKAELEQHLMKEEQILFPAIIEYKRGNPAQAIGT 151 (216)
T ss_pred HHHHHHHHhHHHHHHHHHHHHHHHHHHHHhCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHccCccccccc
Confidence 444 377899999999999998877642 233446788889999999999999999999999999741
Q ss_pred -h-hhHHhHHHHHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 001043 360 -L-SFAQEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPLA 425 (1177)
Q Consensus 360 -~-~me~EH~~ie~l~e~l~~ll~~~~~~~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qvfPLl 425 (1177)
+ .|..||+++...+.+|..++..... |......++.+...+..+...|.+|..+||+.+||.+
T Consensus 152 pi~~m~~EH~~~~~~l~~L~~l~~~~~~---p~~ac~~~~~~~~~l~~~~~~L~~HI~~En~iLFP~~ 216 (216)
T TIGR03652 152 PISVMESEHDEAGDLLKELRELTNDYTP---PEDACNTWRALYSGLEELEDDLHEHIHLENNILFPRA 216 (216)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHcCCCC---CcchhHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCC
Confidence 1 7999999999999999988865431 1111245677778888899999999999999999963
No 14
>PRK10992 iron-sulfur cluster repair di-iron protein; Provisional
Probab=98.64 E-value=3.7e-07 Score=99.55 Aligned_cols=130 Identities=17% Similarity=0.211 Sum_probs=110.2
Q ss_pred HHHHHHHHHHHHHHHHHHHhcc-CCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHHHh----hhHHHHHHHhhhh
Q 001043 49 FFHKAIKSELDVLHRAAMAFAT-NLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIR----VKNIARTYSLEHE 123 (1177)
Q Consensus 49 ~~HkAlR~el~~l~~~~~~~~~-~~~d~~~~~~l~~r~~~L~~~~~~H~~aEDevI~PaL~~R----v~~v~~~~~~EH~ 123 (1177)
.-|.-+|++|..|.+++..+.. --++......+..-++.|..-+..|+..|.+++||.|... ..+.+..|..||+
T Consensus 82 ~~H~~~r~~lp~L~~l~~kv~~vhg~~~~~~~~~~~l~~~~~~el~~H~~kEE~~LFP~l~~~~~~~~~~pi~vm~~EHd 161 (220)
T PRK10992 82 RYHDRHREQLPELILLATKVERVHGDKPDCPRGLAKYLTALHEELSSHMMKEEQILFPMIKQGMGSQAMGPISVMESEHD 161 (220)
T ss_pred HHhHHHHHHHHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHhcccccccchHHHHHHHHH
Confidence 5699999999999999988773 1144466778888899999999999999999999999962 3567899999999
Q ss_pred hHHHHHHHHHHHHHhhhcCch--hHHHHHHHHHHHHHHHHHHhHHHHHHHhhhHHHh
Q 001043 124 GESVLFDQLFELLNSSMRNEE--SYRRELASCTGALQTSISQHMSKEEEQVFPLLIE 178 (1177)
Q Consensus 124 ~~~~lf~~l~~~l~~~~~~~~--~~~~eLa~~l~~l~~~l~qHm~~EE~~v~PLl~~ 178 (1177)
++..++..|.+..+......+ ..++.+...+..+...|.+|.++|+..+||.+.+
T Consensus 162 ~~~~~l~~L~~lt~~~~~p~~ac~~~~~l~~~l~~~~~dL~~HI~~EnniLFP~a~~ 218 (220)
T PRK10992 162 EAGELLEVIKHLTNNVTPPPEACTTWRALYNGINELIDDLMEHIHLENNVLFPRALA 218 (220)
T ss_pred HHHHHHHHHHHHHhcCCCChhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Confidence 999999999999988754333 5678888888888889999999999999998764
No 15
>PHA02929 N1R/p28-like protein; Provisional
Probab=98.62 E-value=2.5e-08 Score=109.30 Aligned_cols=53 Identities=17% Similarity=0.542 Sum_probs=42.5
Q ss_pred CCCCCCcccccccccCCC----ceEecCCCCcccHhhHHHHHhcCCCCCCCcccccc
Q 001043 1114 GLETNCPICCDFLFTSSA----TVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1166 (1177)
Q Consensus 1114 ~~~~~CpICle~lf~s~~----~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrk~v~d 1166 (1177)
..+..||||+|.+..... -....+|||.||..||.+|++.+.+||+||+.+..
T Consensus 172 ~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~~ 228 (238)
T PHA02929 172 SKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFIS 228 (238)
T ss_pred CCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEeeE
Confidence 446789999998654321 12445899999999999999999999999998764
No 16
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=98.56 E-value=5.3e-08 Score=77.83 Aligned_cols=44 Identities=34% Similarity=0.921 Sum_probs=37.5
Q ss_pred CCcccccccccCCCceEecCCCCcccHhhHHHHHhc-CCCCCCCcccc
Q 001043 1118 NCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS-HYICPICSKSL 1164 (1177)
Q Consensus 1118 ~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~-~~~CPiCrk~v 1164 (1177)
.|+||++.+ ...+...+|||.||..|+..|+.. +..||+|++.+
T Consensus 1 ~C~iC~~~~---~~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~~ 45 (45)
T cd00162 1 ECPICLEEF---REPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45 (45)
T ss_pred CCCcCchhh---hCceEecCCCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence 599999985 445667789999999999999987 78899999864
No 17
>COG3945 Uncharacterized conserved protein [Function unknown]
Probab=98.52 E-value=1.9e-06 Score=89.72 Aligned_cols=140 Identities=21% Similarity=0.284 Sum_probs=112.0
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHhcccC--CcccHHHHHHHHHHHHHHHHhhhhccccchhhhhhhhh---------
Q 001043 292 CPIDEIMLWHNAIKRELNDIAEAARKIQLSG--DFSDLSAFNKRLQFIAEVCIFHSIAEDKVIFPAVDVEL--------- 360 (1177)
Q Consensus 292 ~pid~l~~~HkALRrEL~~L~~~a~~i~~~g--d~~~L~~L~~r~~fl~~vl~~Hs~aEDevlFPaL~~r~--------- 360 (1177)
.-++.|+-.|+.|.+-|.-|...+-.+. .| +.+++..+.+-++-|++- +||..|+.++||-|..+.
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 4578889999999999999988887775 44 344555555555555554 578889999999999774
Q ss_pred hhHHhHHHHHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhhCCHHHHHHHHHh
Q 001043 361 SFAQEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPLARRHFSPKRQRELLYQ 440 (1177)
Q Consensus 361 ~me~EH~~ie~l~e~l~~ll~~~~~~~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qvfPLl~~~fS~eEq~eL~~~ 440 (1177)
.|..||...-.++..|.+.+..+.+.+. +....++..+......+.+|..+|+.++||++++.||.+ |..+..+
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 8999999999999999999998875532 224556667777789999999999999999999999999 6666544
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=98.49 E-value=1.2e-06 Score=95.11 Aligned_cols=127 Identities=24% Similarity=0.300 Sum_probs=106.8
Q ss_pred HHHHHHHHHHHHHHHHHHHhcc-CCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHHH--hh------hHHHHHHH
Q 001043 49 FFHKAIKSELDVLHRAAMAFAT-NLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDI--RV------KNIARTYS 119 (1177)
Q Consensus 49 ~~HkAlR~el~~l~~~~~~~~~-~~~d~~~~~~l~~r~~~L~~~~~~H~~aEDevI~PaL~~--Rv------~~v~~~~~ 119 (1177)
.-|+.+|++|..|..++..+.. .-.+...+..+.+-++.|..-+..|+..|.+++||+|.. +. .+.+..|.
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 7899999999999998888774 114456778999999999999999999999999999985 22 22889999
Q ss_pred hhhhhHHHHHHHHHHHHHhhhcCch--hHHHHHHHHHHHHHHHHHHhHHHHHHHhhhH
Q 001043 120 LEHEGESVLFDQLFELLNSSMRNEE--SYRRELASCTGALQTSISQHMSKEEEQVFPL 175 (1177)
Q Consensus 120 ~EH~~~~~lf~~l~~~l~~~~~~~~--~~~~eLa~~l~~l~~~l~qHm~~EE~~v~PL 175 (1177)
.||+++...+++|....+......+ ..++.+...+.++...|.+|.++||..+||.
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 5677777778888889999999999999994
No 19
>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=98.45 E-value=8.8e-08 Score=76.75 Aligned_cols=39 Identities=41% Similarity=0.997 Sum_probs=33.6
Q ss_pred CcccccccccCCCceEecCCCCcccHhhHHHHHhcCCCCCCC
Q 001043 1119 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPIC 1160 (1177)
Q Consensus 1119 CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiC 1160 (1177)
||||++.+ .++++.++|||.|+.+|+.+|++.+.+||+|
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 89999974 3377899999999999999999999999998
No 20
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=98.41 E-value=1.5e-07 Score=85.72 Aligned_cols=50 Identities=20% Similarity=0.395 Sum_probs=38.6
Q ss_pred CCCCcccccccccCCC-ceEecCCCCcccHhhHHHHHhcCCCCCCCccccc
Q 001043 1116 ETNCPICCDFLFTSSA-TVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1165 (1177)
Q Consensus 1116 ~~~CpICle~lf~s~~-~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrk~v~ 1165 (1177)
.+.||-|.-.+-..++ ++.-.-|.|.||.+||..||.+...||+||+...
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 4567778765433333 4455689999999999999999999999999754
No 21
>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=98.35 E-value=2.3e-07 Score=78.22 Aligned_cols=47 Identities=32% Similarity=0.824 Sum_probs=39.1
Q ss_pred CCCCcccccccccCCCceEecCCCCc-ccHhhHHHHHhcCCCCCCCcccccc
Q 001043 1116 ETNCPICCDFLFTSSATVRALPCGHF-MHSDCFQAYTCSHYICPICSKSLGD 1166 (1177)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCGH~-fH~~Ci~~wl~~~~~CPiCrk~v~d 1166 (1177)
+..|+||++.. ..+..+||||. |...|+..|++...+||+||+.|.+
T Consensus 2 ~~~C~iC~~~~----~~~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~~ 49 (50)
T PF13920_consen 2 DEECPICFENP----RDVVLLPCGHLCFCEECAERLLKRKKKCPICRQPIES 49 (50)
T ss_dssp HSB-TTTSSSB----SSEEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-SE
T ss_pred cCCCccCCccC----CceEEeCCCChHHHHHHhHHhcccCCCCCcCChhhcC
Confidence 46799999872 34778899999 9999999999999999999998854
No 22
>PRK13276 cell wall biosynthesis protein ScdA; Provisional
Probab=98.31 E-value=6.1e-06 Score=90.10 Aligned_cols=125 Identities=13% Similarity=0.183 Sum_probs=105.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcc--cCCcccHHHHHHHHHHHHHHHHhhhhccccchhhhhhhh------------h-h
Q 001043 297 IMLWHNAIKRELNDIAEAARKIQL--SGDFSDLSAFNKRLQFIAEVCIFHSIAEDKVIFPAVDVE------------L-S 361 (1177)
Q Consensus 297 l~~~HkALRrEL~~L~~~a~~i~~--~gd~~~L~~L~~r~~fl~~vl~~Hs~aEDevlFPaL~~r------------~-~ 361 (1177)
+...|..+|++|..|...+.++.. .++...+..+...+..+..-|..|-..|+.++||++.+. + .
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 344557899999999999999999999999999999751 1 8
Q ss_pred hHHhHHHHHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 001043 362 FAQEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPL 424 (1177)
Q Consensus 362 me~EH~~ie~l~e~l~~ll~~~~~~~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qvfPL 424 (1177)
|+.||+.+.+.+.+|++++..... |.++...|+.|=..+.++...|.+|.+.|-+.+||-
T Consensus 163 m~~EH~~~g~~l~~i~~lTn~yt~---P~~AC~t~r~ly~~L~~fe~dL~~HIhLENnILFPr 222 (224)
T PRK13276 163 LVSDHIATGQLLVKMSELTSSYEP---PIEACGTWRLVYQRLKALEVLTHEHVHLENHVLFKK 222 (224)
T ss_pred HHHHHHHHHHHHHHHHHHhCCCCC---CcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHcccC
Confidence 999999999999999999876542 223346788888888999999999999999999993
No 23
>PRK13276 cell wall biosynthesis protein ScdA; Provisional
Probab=98.29 E-value=8e-06 Score=89.19 Aligned_cols=127 Identities=20% Similarity=0.235 Sum_probs=111.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcc-CCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHHHh--------hhHHHHHH
Q 001043 48 LFFHKAIKSELDVLHRAAMAFAT-NLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIR--------VKNIARTY 118 (1177)
Q Consensus 48 ~~~HkAlR~el~~l~~~~~~~~~-~~~d~~~~~~l~~r~~~L~~~~~~H~~aEDevI~PaL~~R--------v~~v~~~~ 118 (1177)
-..|.-+|++|..|..++..|.. --++......|.+.|..|+.=+..|..-|.+++||.+... +.+.+..|
T Consensus 84 ~~hH~~~r~~lp~l~~l~~kV~~VHg~~~p~l~~l~~lf~~l~~eL~~H~~KEE~ilFP~i~~~~~~~~~~~~~~pI~~m 163 (224)
T PRK13276 84 SAYHEPLREEFKNLTPYVTKLSKVHGPNHPYLVELKETYDTFKNGMLEHMQKEDDVDFPKLIKYEQGEVVDDINTVIDDL 163 (224)
T ss_pred HHHhHHHHHHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHhhccccchhhhhHHHHH
Confidence 37899999999999999999886 1135558899999999999999999999999999999752 35578999
Q ss_pred HhhhhhHHHHHHHHHHHHHhhhcCch--hHHHHHHHHHHHHHHHHHHhHHHHHHHhhh
Q 001043 119 SLEHEGESVLFDQLFELLNSSMRNEE--SYRRELASCTGALQTSISQHMSKEEEQVFP 174 (1177)
Q Consensus 119 ~~EH~~~~~lf~~l~~~l~~~~~~~~--~~~~eLa~~l~~l~~~l~qHm~~EE~~v~P 174 (1177)
..||+++.+++.+|.++.+.+...++ ..|+.|=.-+.++...|.+|.+.|-.-+||
T Consensus 164 ~~EH~~~g~~l~~i~~lTn~yt~P~~AC~t~r~ly~~L~~fe~dL~~HIhLENnILFP 221 (224)
T PRK13276 164 VSDHIATGQLLVKMSELTSSYEPPIEACGTWRLVYQRLKALEVLTHEHVHLENHVLFK 221 (224)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHccc
Confidence 99999999999999999998876544 778888888888888999999999999998
No 24
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=98.25 E-value=1.6e-07 Score=84.79 Aligned_cols=47 Identities=21% Similarity=0.487 Sum_probs=35.0
Q ss_pred CCCCcccccccccCCCceEecCCCCcccHhhHHHHHhc---CCCCCCCcccc
Q 001043 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS---HYICPICSKSL 1164 (1177)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~---~~~CPiCrk~v 1164 (1177)
+..||-|.-+ +++-+++..-|.|.||.+||.+|+.. ...||+||+..
T Consensus 31 dg~Cp~Ck~P--gDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~ 80 (84)
T KOG1493|consen 31 DGCCPDCKLP--GDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTW 80 (84)
T ss_pred CCcCCCCcCC--CCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchhee
Confidence 4567777754 33445555589999999999999854 46799999864
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=98.18 E-value=1.2e-06 Score=67.63 Aligned_cols=38 Identities=37% Similarity=0.943 Sum_probs=33.0
Q ss_pred CcccccccccCCCceEecCCCCcccHhhHHHHHh-cCCCCCCC
Q 001043 1119 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC-SHYICPIC 1160 (1177)
Q Consensus 1119 CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~-~~~~CPiC 1160 (1177)
|+||++. ......++|||.||..|++.|+. ...+||+|
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 34577889999999999999998 67789998
No 26
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.12 E-value=1.9e-06 Score=70.92 Aligned_cols=44 Identities=30% Similarity=0.803 Sum_probs=38.4
Q ss_pred CCcccccccccCCCceEecCCCCcccHhhHHHHHhcCCCCCCCcc
Q 001043 1118 NCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSK 1162 (1177)
Q Consensus 1118 ~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrk 1162 (1177)
.|+||.+. |.......+++|||.|...|+..+......||+||+
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 49999998 455667888999999999999999977788999996
No 27
>PHA02926 zinc finger-like protein; Provisional
Probab=98.10 E-value=1.9e-06 Score=92.46 Aligned_cols=62 Identities=19% Similarity=0.469 Sum_probs=45.4
Q ss_pred cCCCCCCcccccccccCC-----CceEecCCCCcccHhhHHHHHhc------CCCCCCCccccc--ccccccCCC
Q 001043 1113 KGLETNCPICCDFLFTSS-----ATVRALPCGHFMHSDCFQAYTCS------HYICPICSKSLG--DMAVLHLPI 1174 (1177)
Q Consensus 1113 ~~~~~~CpICle~lf~s~-----~~v~~LpCGH~fH~~Ci~~wl~~------~~~CPiCrk~v~--dm~~~~~~~ 1174 (1177)
.+.+..|+||||.++... .-....+|+|.|+..||..|.+. ..+||+||..+. .++.+|..+
T Consensus 167 ~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~I~pSrf~~~~ 241 (242)
T PHA02926 167 VSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFRNITMSKFYKLV 241 (242)
T ss_pred ccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceeeeeccccceecc
Confidence 455789999999876531 11244599999999999999864 245999999765 456666543
No 28
>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=98.09 E-value=2e-06 Score=69.27 Aligned_cols=39 Identities=38% Similarity=0.993 Sum_probs=33.4
Q ss_pred CcccccccccCCCceEecCCCCcccHhhHHHHHh--cCCCCCCC
Q 001043 1119 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC--SHYICPIC 1160 (1177)
Q Consensus 1119 CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~--~~~~CPiC 1160 (1177)
|+||++.+ .+++..++|||.|+..|+.+|++ ....||+|
T Consensus 1 C~iC~~~~---~~~~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEPF---EDPVILLPCGHSFCRDCLRKWLENSGSVKCPLC 41 (41)
T ss_dssp ETTTSSBC---SSEEEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred CCcCCccc---cCCCEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence 89999983 33457899999999999999998 56889998
No 29
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.09 E-value=1.2e-06 Score=107.22 Aligned_cols=54 Identities=30% Similarity=0.664 Sum_probs=44.6
Q ss_pred ccCCCCCCcccccccccCCC-ceEecCCCCcccHhhHHHHHhcCCCCCCCccccc
Q 001043 1112 EKGLETNCPICCDFLFTSSA-TVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1165 (1177)
Q Consensus 1112 e~~~~~~CpICle~lf~s~~-~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrk~v~ 1165 (1177)
....+..|+||+|.|+.... ..+.|||||.||..|+..|++...+||+||..+.
T Consensus 287 ~~~~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~qtCP~CR~~~~ 341 (543)
T KOG0802|consen 287 LALSDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQQTCPTCRTVLY 341 (543)
T ss_pred hhhcCCeeeeechhhccccccccceeecccchHHHHHHHHHHHhCcCCcchhhhh
Confidence 34457889999999875422 2577999999999999999999999999999443
No 30
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.08 E-value=2.8e-06 Score=90.34 Aligned_cols=52 Identities=25% Similarity=0.668 Sum_probs=40.0
Q ss_pred cccCCCCCCcccccccccCCCceEecCCCCcccHhhHHHHHhc----------------CCCCCCCcccccc
Q 001043 1111 REKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS----------------HYICPICSKSLGD 1166 (1177)
Q Consensus 1111 ~e~~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~----------------~~~CPiCrk~v~d 1166 (1177)
++...+..||||++.+ .++ ++++|||.|+..||.+|+.. ..+||+||..+..
T Consensus 13 ~~~~~~~~CpICld~~---~dP-VvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~ 80 (193)
T PLN03208 13 VDSGGDFDCNICLDQV---RDP-VVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE 80 (193)
T ss_pred ccCCCccCCccCCCcC---CCc-EEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence 3444567899999973 233 45799999999999999742 3579999998854
No 31
>COG2846 Regulator of cell morphogenesis and NO signaling [Cell division and chromosome partitioning]
Probab=98.04 E-value=4.2e-05 Score=81.04 Aligned_cols=128 Identities=18% Similarity=0.313 Sum_probs=105.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcc-cCC-cccHHHHHHHHHHHHHHHHhhhhccccchhhhhhhhh---------hhH
Q 001043 295 DEIMLWHNAIKRELNDIAEAARKIQL-SGD-FSDLSAFNKRLQFIAEVCIFHSIAEDKVIFPAVDVEL---------SFA 363 (1177)
Q Consensus 295 d~l~~~HkALRrEL~~L~~~a~~i~~-~gd-~~~L~~L~~r~~fl~~vl~~Hs~aEDevlFPaL~~r~---------~me 363 (1177)
.++...|+-.|.+|.+|-..+.++.. -|| ++-...|.+-+..|...|.-|-..|++++||++..-. .|+
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 45688999999999999999888742 344 3456888888899999999999999999999998532 999
Q ss_pred HhHHHHHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 001043 364 QEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPLA 425 (1177)
Q Consensus 364 ~EH~~ie~l~e~l~~ll~~~~~~~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qvfPLl 425 (1177)
.||++...+++.+..++..... |..+...++.|=.-+..+.+.+.+|++-|=..+||=+
T Consensus 159 ~EHde~g~~l~~lk~lT~n~tp---P~~AC~tWkalY~gl~~~~dDl~~HIHLENnvLFpr~ 217 (221)
T COG2846 159 SEHDEAGELLEVLKHLTNNYTP---PEEACGTWKALYNGLNEFIDDLMEHIHLENNVLFPRV 217 (221)
T ss_pred HHHHHHHHHHHHHHHHhcCCCC---ChHHHhHHHHHHHHHHHHHHHHHHHHHhhhccccchh
Confidence 9999999999999999876632 2222345677777888889999999999999999954
No 32
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.02 E-value=2.3e-06 Score=89.09 Aligned_cols=46 Identities=33% Similarity=0.748 Sum_probs=38.9
Q ss_pred CCCcccccccccCCCce-EecCCCCcccHhhHHHHHhcCCCCCCCccccc
Q 001043 1117 TNCPICCDFLFTSSATV-RALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1165 (1177)
Q Consensus 1117 ~~CpICle~lf~s~~~v-~~LpCGH~fH~~Ci~~wl~~~~~CPiCrk~v~ 1165 (1177)
-.|||||+. +.. .+ ....|||.|+++||+.-++...+||+|+|.|-
T Consensus 132 ~~CPiCl~~-~se--k~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt 178 (187)
T KOG0320|consen 132 YKCPICLDS-VSE--KVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKIT 178 (187)
T ss_pred cCCCceecc-hhh--ccccccccchhHHHHHHHHHHHhCCCCCCcccccc
Confidence 679999998 332 34 34799999999999999999999999999663
No 33
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=97.96 E-value=4.1e-06 Score=68.62 Aligned_cols=38 Identities=37% Similarity=0.946 Sum_probs=27.4
Q ss_pred CcccccccccCCCceEecCCCCcccHhhHHHHHhcC----CCCCCC
Q 001043 1119 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSH----YICPIC 1160 (1177)
Q Consensus 1119 CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~----~~CPiC 1160 (1177)
||||++.+. .-+.|+|||.|...||..|.+.. ..||+|
T Consensus 1 CpiC~~~~~----~Pv~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDLFK----DPVSLPCGHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB-S----SEEE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCccchhhC----CccccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 899999843 23569999999999999997543 579998
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=97.85 E-value=1.5e-05 Score=69.62 Aligned_cols=45 Identities=22% Similarity=0.391 Sum_probs=38.1
Q ss_pred CCCcccccccccCCCceEecCCCCcccHhhHHHHHhcCCCCCCCccccc
Q 001043 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1165 (1177)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrk~v~ 1165 (1177)
-.||||++.|- ++ +.++|||.|...||.+|++.+.+||+|++.+.
T Consensus 2 ~~Cpi~~~~~~---~P-v~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~ 46 (63)
T smart00504 2 FLCPISLEVMK---DP-VILPSGQTYERRAIEKWLLSHGTDPVTGQPLT 46 (63)
T ss_pred cCCcCCCCcCC---CC-EECCCCCEEeHHHHHHHHHHCCCCCCCcCCCC
Confidence 36999999752 24 45799999999999999988999999999873
No 35
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=97.80 E-value=1.2e-05 Score=66.25 Aligned_cols=39 Identities=38% Similarity=0.950 Sum_probs=23.5
Q ss_pred CcccccccccCCCceEecCCCCcccHhhHHHHHhc----CCCCC
Q 001043 1119 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS----HYICP 1158 (1177)
Q Consensus 1119 CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~----~~~CP 1158 (1177)
||||.| +-+...+-++|+|||.|..+|++++++. ..+||
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 4455556678999999999999999874 35687
No 36
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=97.76 E-value=1.2e-05 Score=89.35 Aligned_cols=50 Identities=24% Similarity=0.644 Sum_probs=41.1
Q ss_pred CCCCcccccccccCCCceEecCCCCcccHhhHHHHHhcCCCCCCCccccccccc
Q 001043 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGDMAV 1169 (1177)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrk~v~dm~~ 1169 (1177)
...|.+|||... .....||||.|+..||..|.....-||+||...-.-+.
T Consensus 239 ~~kC~LCLe~~~----~pSaTpCGHiFCWsCI~~w~~ek~eCPlCR~~~~pskv 288 (293)
T KOG0317|consen 239 TRKCSLCLENRS----NPSATPCGHIFCWSCILEWCSEKAECPLCREKFQPSKV 288 (293)
T ss_pred CCceEEEecCCC----CCCcCcCcchHHHHHHHHHHccccCCCcccccCCCcce
Confidence 356999999742 34568999999999999999999999999998765443
No 37
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=97.70 E-value=7.4e-06 Score=78.19 Aligned_cols=32 Identities=25% Similarity=0.542 Sum_probs=28.2
Q ss_pred eEecCCCCcccHhhHHHHHhcCCCCCCCcccc
Q 001043 1133 VRALPCGHFMHSDCFQAYTCSHYICPICSKSL 1164 (1177)
Q Consensus 1133 v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrk~v 1164 (1177)
|.-.-|.|.||.+||.+||+++..||+|.+.-
T Consensus 76 VaWG~CNHaFH~hCisrWlktr~vCPLdn~eW 107 (114)
T KOG2930|consen 76 VAWGVCNHAFHFHCISRWLKTRNVCPLDNKEW 107 (114)
T ss_pred EEeeecchHHHHHHHHHHHhhcCcCCCcCcce
Confidence 34468999999999999999999999999853
No 38
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.60 E-value=3.4e-05 Score=83.61 Aligned_cols=50 Identities=26% Similarity=0.589 Sum_probs=38.5
Q ss_pred CCCCCCcccccccccCCCceEecCCCCcccHhhHHHHHhc---CCCCCCCccccccc
Q 001043 1114 GLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS---HYICPICSKSLGDM 1167 (1177)
Q Consensus 1114 ~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~---~~~CPiCrk~v~dm 1167 (1177)
+..-+|-||+|- ..++|+ ..|||.|+..||-+||.. +..||+|+..|.+-
T Consensus 45 ~~~FdCNICLd~---akdPVv-TlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~ 97 (230)
T KOG0823|consen 45 GGFFDCNICLDL---AKDPVV-TLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSID 97 (230)
T ss_pred CCceeeeeeccc---cCCCEE-eecccceehHHHHHHHhhcCCCeeCCccccccccc
Confidence 345689999975 455555 459999999999999864 34589999887653
No 39
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.60 E-value=2.1e-05 Score=91.72 Aligned_cols=51 Identities=27% Similarity=0.637 Sum_probs=38.3
Q ss_pred CCCCcccccccc----cC---------CCceEecCCCCcccHhhHHHHHh-cCCCCCCCcccccc
Q 001043 1116 ETNCPICCDFLF----TS---------SATVRALPCGHFMHSDCFQAYTC-SHYICPICSKSLGD 1166 (1177)
Q Consensus 1116 ~~~CpICle~lf----~s---------~~~v~~LpCGH~fH~~Ci~~wl~-~~~~CPiCrk~v~d 1166 (1177)
..+|+|||.++- ++ ...++..||.|.||..|+.+|+. .+..||+||..+..
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 357888887651 11 12345569999999999999998 56689999998753
No 40
>COG2846 Regulator of cell morphogenesis and NO signaling [Cell division and chromosome partitioning]
Probab=97.54 E-value=0.0008 Score=71.66 Aligned_cols=133 Identities=18% Similarity=0.244 Sum_probs=109.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcc-CCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHHHh----hhHHHHHHH
Q 001043 45 LIFLFFHKAIKSELDVLHRAAMAFAT-NLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIR----VKNIARTYS 119 (1177)
Q Consensus 45 ~~~~~~HkAlR~el~~l~~~~~~~~~-~~~d~~~~~~l~~r~~~L~~~~~~H~~aEDevI~PaL~~R----v~~v~~~~~ 119 (1177)
.|..-+|.-.|.+|..|..++..|.. -.+.+.-.+.|..-+.-|..-+..|-.-|++++||.+..= +.+....|+
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 45668999999999999999998885 1244567788889999999999999999999999999642 256889999
Q ss_pred hhhhhHHHHHHHHHHHHHhhhcCch--hHHHHHHHHHHHHHHHHHHhHHHHHHHhhhHHH
Q 001043 120 LEHEGESVLFDQLFELLNSSMRNEE--SYRRELASCTGALQTSISQHMSKEEEQVFPLLI 177 (1177)
Q Consensus 120 ~EH~~~~~lf~~l~~~l~~~~~~~~--~~~~eLa~~l~~l~~~l~qHm~~EE~~v~PLl~ 177 (1177)
.||+++..+++.+.+..+...-..+ ..++.|=.-+.++.+.+.+|++.|---+||=+.
T Consensus 159 ~EHde~g~~l~~lk~lT~n~tpP~~AC~tWkalY~gl~~~~dDl~~HIHLENnvLFpr~~ 218 (221)
T COG2846 159 SEHDEAGELLEVLKHLTNNYTPPEEACGTWKALYNGLNEFIDDLMEHIHLENNVLFPRVL 218 (221)
T ss_pred HHHHHHHHHHHHHHHHhcCCCCChHHHhHHHHHHHHHHHHHHHHHHHHHhhhccccchhc
Confidence 9999999999999999888875444 556666666667777999999999888888543
No 41
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.53 E-value=4.9e-05 Score=89.24 Aligned_cols=47 Identities=28% Similarity=0.646 Sum_probs=39.6
Q ss_pred CCCCcccccccccCCCceEecCCCCcccHhhHHHHHhcCCCCCCCcccccc
Q 001043 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1166 (1177)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrk~v~d 1166 (1177)
...|+||++.+ . .++ .++|||.|+..||..|+.....||+|+..+..
T Consensus 26 ~l~C~IC~d~~-~--~Pv-itpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~~ 72 (397)
T TIGR00599 26 SLRCHICKDFF-D--VPV-LTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQE 72 (397)
T ss_pred ccCCCcCchhh-h--Ccc-CCCCCCchhHHHHHHHHhCCCCCCCCCCcccc
Confidence 56899999974 2 233 68999999999999999888899999998763
No 42
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=97.52 E-value=3.5e-05 Score=89.59 Aligned_cols=48 Identities=23% Similarity=0.677 Sum_probs=42.4
Q ss_pred CCCCcccccccccCCCceEecCCCCcccHhhHHHHHhcCCCCCCCccccc
Q 001043 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1165 (1177)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrk~v~ 1165 (1177)
-.+||||+|.|..+.+.+....|.|.||-.|+..|- ..+||+||....
T Consensus 175 LPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~--~~scpvcR~~q~ 222 (493)
T KOG0804|consen 175 LPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWW--DSSCPVCRYCQS 222 (493)
T ss_pred CCCcchhHhhcCccccceeeeecccccchHHHhhcc--cCcChhhhhhcC
Confidence 458999999998888888889999999999999995 677999997554
No 43
>COG3945 Uncharacterized conserved protein [Function unknown]
Probab=97.49 E-value=0.0012 Score=69.51 Aligned_cols=140 Identities=18% Similarity=0.226 Sum_probs=110.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHHHhh----hHHHHHHH
Q 001043 44 ILIFLFFHKAIKSELDVLHRAAMAFATNLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIRV----KNIARTYS 119 (1177)
Q Consensus 44 i~~~~~~HkAlR~el~~l~~~~~~~~~~~~d~~~~~~l~~r~~~L~~~~~~H~~aEDevI~PaL~~Rv----~~v~~~~~ 119 (1177)
|..|+==|+-|-+-|.-|....--+..+-=|.+++..+++-++-+.+ ++||.-|+-++||-+..+. ++....|.
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 56777789988888888777776666521245566666665555554 5688999999999999886 57899999
Q ss_pred hhhhhHHHHHHHHHHHHHhhhcCch----hHHHHHHHHHHHHHHHHHHhHHHHHHHhhhHHHhhCCHHHHHHHHH
Q 001043 120 LEHEGESVLFDQLFELLNSSMRNEE----SYRRELASCTGALQTSISQHMSKEEEQVFPLLIEKFSFEEQASLVW 190 (1177)
Q Consensus 120 ~EH~~~~~lf~~l~~~l~~~~~~~~----~~~~eLa~~l~~l~~~l~qHm~~EE~~v~PLl~~~fS~~E~a~L~~ 190 (1177)
-||..--.++..+.+.+.+|.-.++ .+...+++.+. .+.+|.++|+..+||.+.+.||.+ |..+..
T Consensus 88 ~EH~~~R~i~r~lee~~~~~kngd~~~~~~~i~~A~~y~~----likrHIdkEdnvlfp~a~~~~s~e-~~~v~~ 157 (189)
T COG3945 88 VEHGEGRYIIRDLEEAYERLKNGDEDSKDDVIDYAVAYLN----LIKRHIDKEDNVLFPFAESTLSEE-LNEVNS 157 (189)
T ss_pred hhhhhHHHHHHHHHHHHHHHHccccchHHHHHHHHHHHHH----HHHHHHhhhhhHHHHHHHHHHHHH-HHHHHH
Confidence 9999999999999999999975544 44555555555 999999999999999999999999 555443
No 44
>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class
Probab=97.38 E-value=0.00011 Score=62.28 Aligned_cols=42 Identities=26% Similarity=0.736 Sum_probs=32.6
Q ss_pred CCcccccccccCCCceEecCCC-----CcccHhhHHHHHhc--CCCCCCCc
Q 001043 1118 NCPICCDFLFTSSATVRALPCG-----HFMHSDCFQAYTCS--HYICPICS 1161 (1177)
Q Consensus 1118 ~CpICle~lf~s~~~v~~LpCG-----H~fH~~Ci~~wl~~--~~~CPiCr 1161 (1177)
.|-||+++ .+.+...+.||. |++|..|+.+|+.. +.+||+|+
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 99999999999954 45899995
No 45
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.33 E-value=0.0001 Score=87.28 Aligned_cols=48 Identities=33% Similarity=0.756 Sum_probs=37.2
Q ss_pred CCCCCcccccccccCCCceEecCCCCcccHhhHHHHHhc-----CCCCCCCcccccc
Q 001043 1115 LETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS-----HYICPICSKSLGD 1166 (1177)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~-----~~~CPiCrk~v~d 1166 (1177)
++..||||+++ ...+++ +.|||.|+-.||-+|+.. ...||||+..|..
T Consensus 185 t~~~CPICL~~---~~~p~~-t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~ 237 (513)
T KOG2164|consen 185 TDMQCPICLEP---PSVPVR-TNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITL 237 (513)
T ss_pred cCCcCCcccCC---CCcccc-cccCceeeHHHHHHHHhhhcccCCccCCchhhhccc
Confidence 37899999987 223344 459999999999998643 3669999998864
No 46
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.29 E-value=0.00019 Score=81.60 Aligned_cols=51 Identities=22% Similarity=0.560 Sum_probs=38.3
Q ss_pred CCCCcccccccccCCCc-eEecCCCCcccHhhHHHH-HhcCCCCCCCcccccc
Q 001043 1116 ETNCPICCDFLFTSSAT-VRALPCGHFMHSDCFQAY-TCSHYICPICSKSLGD 1166 (1177)
Q Consensus 1116 ~~~CpICle~lf~s~~~-v~~LpCGH~fH~~Ci~~w-l~~~~~CPiCrk~v~d 1166 (1177)
+..||||+.+.+.+.+. ..+.+|||.|+..|++.. ......||.|++.+-.
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 45799999965554432 223389999999999995 4556789999997753
No 47
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=97.17 E-value=0.0001 Score=66.86 Aligned_cols=50 Identities=26% Similarity=0.594 Sum_probs=23.6
Q ss_pred CCCCcccccccccC-CCceEe---cCCCCcccHhhHHHHHhc-----------CCCCCCCccccc
Q 001043 1116 ETNCPICCDFLFTS-SATVRA---LPCGHFMHSDCFQAYTCS-----------HYICPICSKSLG 1165 (1177)
Q Consensus 1116 ~~~CpICle~lf~s-~~~v~~---LpCGH~fH~~Ci~~wl~~-----------~~~CPiCrk~v~ 1165 (1177)
+..|+||+.++.+. ..+..+ -.|+..||..|+.+|+.. ..+||.|++.|.
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 46799999986523 233333 279999999999999752 135999999774
No 48
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.12 E-value=0.00018 Score=82.42 Aligned_cols=48 Identities=27% Similarity=0.643 Sum_probs=37.7
Q ss_pred CCCCcccccccccCCCceEec-CCCCcccHhhHHHHHhc---CCCCCCCcccc
Q 001043 1116 ETNCPICCDFLFTSSATVRAL-PCGHFMHSDCFQAYTCS---HYICPICSKSL 1164 (1177)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~L-pCGH~fH~~Ci~~wl~~---~~~CPiCrk~v 1164 (1177)
...|.|| ++++.....+... .|||+||..|+.+|... +..||+|+-.+
T Consensus 4 ~A~C~Ic-~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~ 55 (465)
T KOG0827|consen 4 MAECHIC-IDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKL 55 (465)
T ss_pred cceeeEe-ccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeecc
Confidence 3579999 5667777667665 59999999999999875 35799999433
No 49
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=97.08 E-value=0.00024 Score=89.98 Aligned_cols=112 Identities=27% Similarity=0.569 Sum_probs=73.1
Q ss_pred eeccccCcc-----ccCCCCCCCCCCCCcccceEeccccccccCCCCcccCCCCCccccCCCCCccccccCCcccccccc
Q 001043 1030 MMCMRCLKV-----QPVGPVCTTLSCSGLSMAKYYCGICKFFDDERVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLAKK 1104 (1177)
Q Consensus 1030 ~~C~~C~~~-----q~~~~~C~~~~C~~~~~a~Y~C~~C~l~dd~k~~yHC~~CgiCrvg~gl~~~~fhC~~C~~C~s~~ 1104 (1177)
--|.+|+.. |.++.+|....| ...|+--|++-+-... .|| | . +|--||.-|=.|-.-.
T Consensus 3418 ~aCRFCGs~~~tE~sav~~vCs~aDC--~eYAK~ACs~~H~C~H--------~CG----G--v-kNEE~CLPCl~Cdks~ 3480 (3738)
T KOG1428|consen 3418 EACRFCGSRSGTELSAVGSVCSDADC--QEYAKIACSKTHPCGH--------PCG----G--V-KNEEHCLPCLHCDKSA 3480 (3738)
T ss_pred hHhhhccCCCCcchhcccCccccHHH--HHHHHHHHhccCcCCC--------ccc----C--c-cchhhcccccccChhh
Confidence 368888743 567889988877 5677777865332211 233 1 1 2445555554443211
Q ss_pred cccccccccCCCCCCcccccccccCCCceEecCCCCcccHhhHHHHHhc----------CCCCCCCccccc
Q 001043 1105 LVDHKCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS----------HYICPICSKSLG 1165 (1177)
Q Consensus 1105 l~~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~----------~~~CPiCrk~v~ 1165 (1177)
.....++.|.||..+ --+..+.+.|.|||.||.+|.+.-|.+ -..||||...|.
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 023357789999876 446678899999999999999875542 245999998764
No 50
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.02 E-value=0.00018 Score=79.16 Aligned_cols=49 Identities=22% Similarity=0.655 Sum_probs=39.3
Q ss_pred CCCCcccccccccCC------CceEecCCCCcccHhhHHHH--HhcCCCCCCCcccc
Q 001043 1116 ETNCPICCDFLFTSS------ATVRALPCGHFMHSDCFQAY--TCSHYICPICSKSL 1164 (1177)
Q Consensus 1116 ~~~CpICle~lf~s~------~~v~~LpCGH~fH~~Ci~~w--l~~~~~CPiCrk~v 1164 (1177)
+..|+||...++.+. ++.-.|.|+|.||.-||+-| +.+..+||-|++.+
T Consensus 224 d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekV 280 (328)
T KOG1734|consen 224 DSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKV 280 (328)
T ss_pred cchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHh
Confidence 566888887765443 24567999999999999999 46789999999876
No 51
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.00 E-value=0.00019 Score=87.62 Aligned_cols=52 Identities=17% Similarity=0.524 Sum_probs=42.8
Q ss_pred CCCCCcccccccccCCCceEecCCCCcccHhhHHHHHhcCCCCCCCccccccc
Q 001043 1115 LETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGDM 1167 (1177)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrk~v~dm 1167 (1177)
....||+|+.. +........-+|+|+||.+||..|.+.-.+||+||+.+...
T Consensus 122 ~~~~CP~Ci~s-~~DqL~~~~k~c~H~FC~~Ci~sWsR~aqTCPiDR~EF~~v 173 (1134)
T KOG0825|consen 122 VENQCPNCLKS-CNDQLEESEKHTAHYFCEECVGSWSRCAQTCPVDRGEFGEV 173 (1134)
T ss_pred hhhhhhHHHHH-HHHHhhccccccccccHHHHhhhhhhhcccCchhhhhhhee
Confidence 45679999976 44444445679999999999999999999999999987643
No 52
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.96 E-value=0.00037 Score=76.91 Aligned_cols=49 Identities=24% Similarity=0.634 Sum_probs=39.7
Q ss_pred CCCCcccccccccCCCceEecCCCCcccHhhHHH-HHhcCCC-CCCCcccccccc
Q 001043 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQA-YTCSHYI-CPICSKSLGDMA 1168 (1177)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~-wl~~~~~-CPiCrk~v~dm~ 1168 (1177)
+-.|+||+|... .....||||.|...||.. |....+- ||+||.-+..-.
T Consensus 215 d~kC~lC~e~~~----~ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk~ 265 (271)
T COG5574 215 DYKCFLCLEEPE----VPSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVYPKK 265 (271)
T ss_pred ccceeeeecccC----CcccccccchhhHHHHHHHHHhhccccCchhhhhccchh
Confidence 456999999743 345689999999999999 9988766 999998776433
No 53
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.90 E-value=0.0004 Score=75.36 Aligned_cols=44 Identities=32% Similarity=0.811 Sum_probs=37.2
Q ss_pred CCCCCcccccccccCCCceEecCCCCcccHhhHHHHHhcCCCCCCCcc
Q 001043 1115 LETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSK 1162 (1177)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrk 1162 (1177)
....||||++++ .. + +.+||||.|...|+..+......||.||.
T Consensus 12 ~~~~C~iC~~~~-~~--p-~~l~C~H~~c~~C~~~~~~~~~~Cp~cr~ 55 (386)
T KOG2177|consen 12 EELTCPICLEYF-RE--P-VLLPCGHNFCRACLTRSWEGPLSCPVCRP 55 (386)
T ss_pred ccccChhhHHHh-hc--C-ccccccchHhHHHHHHhcCCCcCCcccCC
Confidence 467899999984 33 2 78999999999999998777788999993
No 54
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.75 E-value=0.00032 Score=60.21 Aligned_cols=54 Identities=26% Similarity=0.551 Sum_probs=39.4
Q ss_pred CCCCCcccccccccCCCceEecCCCCc-ccHhhHHH-HHhcCCCCCCCcccccccccccC
Q 001043 1115 LETNCPICCDFLFTSSATVRALPCGHF-MHSDCFQA-YTCSHYICPICSKSLGDMAVLHL 1172 (1177)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~LpCGH~-fH~~Ci~~-wl~~~~~CPiCrk~v~dm~~~~~ 1172 (1177)
..++|.||+|. ..+. +.--|||. +...|-.+ |...+.+|||||..|-|.-..|+
T Consensus 6 ~~dECTICye~---pvds-VlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~dvIkTY~ 61 (62)
T KOG4172|consen 6 WSDECTICYEH---PVDS-VLYTCGHMCMCYACGLRLKKALHGCCPICRAPIKDVIKTYR 61 (62)
T ss_pred cccceeeeccC---cchH-HHHHcchHHhHHHHHHHHHHccCCcCcchhhHHHHHHHhhc
Confidence 35789999986 2222 33479998 78888665 55589999999999987655443
No 55
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=96.72 E-value=0.00059 Score=77.13 Aligned_cols=45 Identities=27% Similarity=0.713 Sum_probs=38.4
Q ss_pred CCCcccccccccCCCceEecCCCCcccHhhHHHHHhcCCCCCCCccccc
Q 001043 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1165 (1177)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrk~v~ 1165 (1177)
-.|-||.|+ |. ..+..||||.|+.-||+.+|..+..||.|+..+.
T Consensus 24 LRC~IC~ey-f~---ip~itpCsHtfCSlCIR~~L~~~p~CP~C~~~~~ 68 (442)
T KOG0287|consen 24 LRCGICFEY-FN---IPMITPCSHTFCSLCIRKFLSYKPQCPTCCVTVT 68 (442)
T ss_pred HHHhHHHHH-hc---CceeccccchHHHHHHHHHhccCCCCCceecccc
Confidence 369999998 43 2355799999999999999999999999998764
No 56
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.62 E-value=0.0011 Score=75.94 Aligned_cols=49 Identities=29% Similarity=0.674 Sum_probs=41.1
Q ss_pred CCCCCCcccccccccCCCceEecCCCCc-ccHhhHHHHHhcCCCCCCCcccccc
Q 001043 1114 GLETNCPICCDFLFTSSATVRALPCGHF-MHSDCFQAYTCSHYICPICSKSLGD 1166 (1177)
Q Consensus 1114 ~~~~~CpICle~lf~s~~~v~~LpCGH~-fH~~Ci~~wl~~~~~CPiCrk~v~d 1166 (1177)
.....|.|||.+ ...+.+|||-|. ++..|.+...-..+.|||||..+..
T Consensus 288 ~~gkeCVIClse----~rdt~vLPCRHLCLCs~Ca~~Lr~q~n~CPICRqpi~~ 337 (349)
T KOG4265|consen 288 ESGKECVICLSE----SRDTVVLPCRHLCLCSGCAKSLRYQTNNCPICRQPIEE 337 (349)
T ss_pred cCCCeeEEEecC----CcceEEecchhhehhHhHHHHHHHhhcCCCccccchHh
Confidence 446789999976 234788999998 9999999887778899999998864
No 57
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=96.54 E-value=0.00062 Score=78.11 Aligned_cols=61 Identities=31% Similarity=0.669 Sum_probs=50.1
Q ss_pred cccccccCCCCCCcccccccccCCCceEecCCCCcccHhhHHHHHhcC--CCCCCCcccccccc
Q 001043 1107 DHKCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSH--YICPICSKSLGDMA 1168 (1177)
Q Consensus 1107 ~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~--~~CPiCrk~v~dm~ 1168 (1177)
-|.|++. ++-.|-.|.|.+-...+....|||.|+||..|+.++|.++ .+||-|||-...|.
T Consensus 357 a~~~~~e-~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~CrklrSs~~ 419 (518)
T KOG1941|consen 357 AHECVEE-TELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRKLRSSMK 419 (518)
T ss_pred HHHHHHH-HhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHHHHhhcc
Confidence 4556544 6788999999877777778899999999999999999765 66999998776665
No 58
>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=96.52 E-value=0.0013 Score=59.98 Aligned_cols=47 Identities=23% Similarity=0.417 Sum_probs=34.8
Q ss_pred CCCCcccccccccCCCceEecCCCCcccHhhHHHHHhc-CCCCCCCcccccc
Q 001043 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS-HYICPICSKSLGD 1166 (1177)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~-~~~CPiCrk~v~d 1166 (1177)
+-.|||+.+-|. ++| .+||||+|-+.||.+|+.. +.+||+|+..+..
T Consensus 4 ~f~CpIt~~lM~---dPV-i~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~ 51 (73)
T PF04564_consen 4 EFLCPITGELMR---DPV-ILPSGHTYERSAIERWLEQNGGTDPFTRQPLSE 51 (73)
T ss_dssp GGB-TTTSSB-S---SEE-EETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SG
T ss_pred ccCCcCcCcHhh---Cce-eCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCc
Confidence 346999998752 344 5799999999999999988 8999999987753
No 59
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=96.46 E-value=0.0013 Score=73.03 Aligned_cols=45 Identities=24% Similarity=0.515 Sum_probs=37.3
Q ss_pred CCCCcccccccccCCCceEecCCCCcccHhhHHHHHhcCCCCCCCcccc
Q 001043 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSL 1164 (1177)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrk~v 1164 (1177)
...|-||.+++- .-...+|||.|+.-||..+|..+..||+||...
T Consensus 25 ~lrC~IC~~~i~----ip~~TtCgHtFCslCIR~hL~~qp~CP~Cr~~~ 69 (391)
T COG5432 25 MLRCRICDCRIS----IPCETTCGHTFCSLCIRRHLGTQPFCPVCREDP 69 (391)
T ss_pred HHHhhhhhheee----cceecccccchhHHHHHHHhcCCCCCccccccH
Confidence 356999999842 123469999999999999999999999999754
No 60
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=96.35 E-value=0.0003 Score=78.99 Aligned_cols=133 Identities=17% Similarity=0.114 Sum_probs=97.4
Q ss_pred HHHHHhhccccccccccccccccccccCcccchhhhHHHHHHHHHHHHHHhhhhhhhhccccccCccccccccccchhhh
Q 001043 690 GLYRAHSNAEDDIVFPALESKETLSNVSHSYTLDHKQEEKLFEDISSALSELTELHECLSTDLTGDLTRNSLESCDQNET 769 (1177)
Q Consensus 690 ~v~~~HS~AEDeivFPaLe~k~~~~nvs~s~~~dH~~ee~lf~~i~~~L~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 769 (1177)
.++..|+.++|++-||+..+.....+..+++..||--.=.++.+.+.... . .+
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 78999999999999999999988778888877777666666655422110 0 12
Q ss_pred HhhHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhcCCHHHHHHHHHHHHhccCHHHHHHhhhHHhhcCCHHHHHH
Q 001043 770 VRKYNEKATELQGMCKSIRVTLDQHVFREELELWPLFDRHFSVEEQDKIVGRIIGTTGAEVLQSMLPWVTSALTQEEQNT 849 (1177)
Q Consensus 770 ~~~~~el~~kL~~~~~sl~~~L~~H~~~EE~Ev~PL~~k~fS~eeQ~~lv~~~l~~~p~~~Lq~~LPWl~~~LteeE~~~ 849 (1177)
..++.-++.+.....++..+.+..|.. +.++|=++.+.|.++.| +++..+.+.+--+.++. |||.-.....++.+
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 233344555555566666688889988 99999999999999999 88888866554333332 99998887777776
Q ss_pred HHHHh
Q 001043 850 MMDTW 854 (1177)
Q Consensus 850 ml~~~ 854 (1177)
-|.+|
T Consensus 145 ~~~~~ 149 (276)
T KOG1940|consen 145 YLSNW 149 (276)
T ss_pred hcccc
Confidence 66665
No 61
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.12 E-value=0.0034 Score=72.89 Aligned_cols=48 Identities=35% Similarity=0.845 Sum_probs=38.2
Q ss_pred CCCCcccccccccCCC-ceEecCCCCcccHhhHHHHHhcC--CCCCCCccc
Q 001043 1116 ETNCPICCDFLFTSSA-TVRALPCGHFMHSDCFQAYTCSH--YICPICSKS 1163 (1177)
Q Consensus 1116 ~~~CpICle~lf~s~~-~v~~LpCGH~fH~~Ci~~wl~~~--~~CPiCrk~ 1163 (1177)
...||||++.+-.+++ .+..|.|||.|-.+||+.||.+. ..||.|...
T Consensus 4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~k 54 (463)
T KOG1645|consen 4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGK 54 (463)
T ss_pred cccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCCh
Confidence 4679999998755555 44568999999999999999543 559999753
No 62
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.99 E-value=0.0045 Score=71.85 Aligned_cols=52 Identities=21% Similarity=0.531 Sum_probs=38.8
Q ss_pred cCCCCCCcccccccccCC---CceEe-cCCCCcccHhhHHHHH--hc-----CCCCCCCcccc
Q 001043 1113 KGLETNCPICCDFLFTSS---ATVRA-LPCGHFMHSDCFQAYT--CS-----HYICPICSKSL 1164 (1177)
Q Consensus 1113 ~~~~~~CpICle~lf~s~---~~v~~-LpCGH~fH~~Ci~~wl--~~-----~~~CPiCrk~v 1164 (1177)
+..+..|.||||.+.... ..-.. .+|.|.|...||..|- .. +..||.||...
T Consensus 158 ~s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s 220 (344)
T KOG1039|consen 158 KSSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPS 220 (344)
T ss_pred ccccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCcc
Confidence 356789999999865443 11122 4699999999999997 33 56799999865
No 63
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=95.68 E-value=0.0036 Score=78.10 Aligned_cols=51 Identities=24% Similarity=0.595 Sum_probs=36.6
Q ss_pred CCCCCCcccccccccCCC--ce-EecCCCCcccHhhHHHHHhc--CCCCCCCcccc
Q 001043 1114 GLETNCPICCDFLFTSSA--TV-RALPCGHFMHSDCFQAYTCS--HYICPICSKSL 1164 (1177)
Q Consensus 1114 ~~~~~CpICle~lf~s~~--~v-~~LpCGH~fH~~Ci~~wl~~--~~~CPiCrk~v 1164 (1177)
+....|+||..-|..-.. |. +--.|.|.||..|+.+|.++ +.+||+||.++
T Consensus 1467 sG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRsei 1522 (1525)
T COG5219 1467 SGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEI 1522 (1525)
T ss_pred CCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCcccccc
Confidence 456789999875531111 11 23457899999999999865 58899999765
No 64
>COG2461 Uncharacterized conserved protein [Function unknown]
Probab=95.39 E-value=0.1 Score=61.17 Aligned_cols=132 Identities=14% Similarity=0.208 Sum_probs=102.9
Q ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcccH-HHHHHHHHHHHHHHHhhhhccccchhhhhhhhh------hhH
Q 001043 291 SCPIDEIMLWHNAIKRELNDIAEAARKIQLSGDFSDL-SAFNKRLQFIAEVCIFHSIAEDKVIFPAVDVEL------SFA 363 (1177)
Q Consensus 291 ~~pid~l~~~HkALRrEL~~L~~~a~~i~~~gd~~~L-~~L~~r~~fl~~vl~~Hs~aEDevlFPaL~~r~------~me 363 (1177)
-+|+..|...-+++|..|+.+.+. .. + ..+ -.+...+.++-.+=+ |=+++...|||.++.|- .|-
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 1 233 555666666666666 88999999999999885 889
Q ss_pred HhHHHHHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhhCCHHHHHHHHHhH
Q 001043 364 QEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPLARRHFSPKRQRELLYQS 441 (1177)
Q Consensus 364 ~EH~~ie~l~e~l~~ll~~~~~~~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qvfPLl~~~fS~eEq~eL~~~~ 441 (1177)
-.|+++-..|..+...+... + ..++...+..+.+.+..=+.+||+.+.|.+-..||..||.++-.+.
T Consensus 157 ~~dDeiRe~lk~~~~~l~~~--s---------~~~~ve~~~~~~t~i~dmIFkEe~Ilypt~~d~~te~ew~~i~~~~ 223 (409)
T COG2461 157 VKDDEIREALKELLKLLKEV--S---------IEEFVEKAESVLTEIEDMIFKEENILYPTLLDLLTEGEWEAIKEQS 223 (409)
T ss_pred ccCcHHHHHHHHHHHHhhcc--C---------hHHHHHHHHHHHHHHHHHHHhhhhhHHhHHHHhcCHHHHHHHHhcC
Confidence 99999988898888887621 1 2456667777888899999999999999999999999999987654
No 65
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.25 E-value=0.013 Score=65.25 Aligned_cols=51 Identities=22% Similarity=0.643 Sum_probs=43.3
Q ss_pred CCCCCcccccccccCCCceEecCCCCcccHhhHHHHHh--cCCCCCCCcccccccc
Q 001043 1115 LETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC--SHYICPICSKSLGDMA 1168 (1177)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~--~~~~CPiCrk~v~dm~ 1168 (1177)
...+||+|.++ +..|....+|||.|+--|+..=.. -+.+||.|...+..|+
T Consensus 238 ~~~~C~~Cg~~---PtiP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~~lq 290 (298)
T KOG2879|consen 238 SDTECPVCGEP---PTIPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVEPLQ 290 (298)
T ss_pred CCceeeccCCC---CCCCeeeccccceeehhhhhhhhcchhhcccCccCCCCcchh
Confidence 46789999987 677888899999999999998654 3589999999988776
No 66
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=95.04 E-value=0.0079 Score=53.79 Aligned_cols=43 Identities=30% Similarity=0.690 Sum_probs=22.6
Q ss_pred CCCcccccccccCCCceEecCCCCcccHhhHHHHHhcCCCCCCCcccc
Q 001043 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSL 1164 (1177)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrk~v 1164 (1177)
..|++|.+.| .++|....|.|.|.+.||..-+. +.||+|+.+.
T Consensus 8 LrCs~C~~~l---~~pv~l~~CeH~fCs~Ci~~~~~--~~CPvC~~Pa 50 (65)
T PF14835_consen 8 LRCSICFDIL---KEPVCLGGCEHIFCSSCIRDCIG--SECPVCHTPA 50 (65)
T ss_dssp TS-SSS-S-----SS-B---SSS--B-TTTGGGGTT--TB-SSS--B-
T ss_pred cCCcHHHHHh---cCCceeccCccHHHHHHhHHhcC--CCCCCcCChH
Confidence 4699999875 45677789999999999988654 4599999876
No 67
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=94.91 E-value=0.0093 Score=66.94 Aligned_cols=56 Identities=27% Similarity=0.630 Sum_probs=44.9
Q ss_pred cccCCCCCCcccccccccCCCceEecCCCCcccHhhHHHHHh-----------------------cCCCCCCCccccccc
Q 001043 1111 REKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC-----------------------SHYICPICSKSLGDM 1167 (1177)
Q Consensus 1111 ~e~~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~-----------------------~~~~CPiCrk~v~dm 1167 (1177)
..+...+.|.||+-- |.++....+.+|-|+||..|+..||. ....|||||-.|++-
T Consensus 110 ~nn~p~gqCvICLyg-fa~~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~e 188 (368)
T KOG4445|consen 110 ENNHPNGQCVICLYG-FASSPAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKIE 188 (368)
T ss_pred cCCCCCCceEEEEEe-ecCCCceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhcccc
Confidence 345567899999977 77777789999999999999998863 123499999988753
No 68
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=94.53 E-value=0.024 Score=49.80 Aligned_cols=42 Identities=24% Similarity=0.606 Sum_probs=29.7
Q ss_pred CCCCCcccccccccCCCceEecCCCCcccHhhHHHHHh--cCCCCCC
Q 001043 1115 LETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC--SHYICPI 1159 (1177)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~--~~~~CPi 1159 (1177)
....|||.+..+ .++|+...|||.|=++.|.+|++ ....||+
T Consensus 10 ~~~~CPiT~~~~---~~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv 53 (57)
T PF11789_consen 10 ISLKCPITLQPF---EDPVKSKKCGHTFEKEAILQYIQRNGSKRCPV 53 (57)
T ss_dssp --SB-TTTSSB----SSEEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred eccCCCCcCChh---hCCcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence 457899999884 46899999999999999999994 3567998
No 69
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.41 E-value=0.0059 Score=69.98 Aligned_cols=48 Identities=31% Similarity=0.589 Sum_probs=38.5
Q ss_pred CCCCcccccccccCCCceEecCCCCcccHhhHHHHHh-cCCCCCCCcccccc
Q 001043 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC-SHYICPICSKSLGD 1166 (1177)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~-~~~~CPiCrk~v~d 1166 (1177)
+..||||++-|-. .....-|+|-|+.+||..-++ .+..||.||+.++.
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 5679999986532 345678999999999987664 57889999998863
No 70
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=94.33 E-value=0.014 Score=72.84 Aligned_cols=46 Identities=24% Similarity=0.608 Sum_probs=37.1
Q ss_pred CCCcccccccccCCCceEecCCCCcccHhhHHHHHh-cCCCCCCCcccccc
Q 001043 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC-SHYICPICSKSLGD 1166 (1177)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~-~~~~CPiCrk~v~d 1166 (1177)
-.||+|-.. ...++...|||.|+..|++.-+. +..+||.|...++.
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 459999754 23456679999999999999875 46889999999884
No 71
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=94.09 E-value=0.015 Score=63.96 Aligned_cols=48 Identities=29% Similarity=0.581 Sum_probs=34.3
Q ss_pred ccCCCceEecCCCCcccHhhHHHHHhcCCCCCCCccccc----------ccccccCCCCC
Q 001043 1127 FTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG----------DMAVLHLPIPF 1176 (1177)
Q Consensus 1127 f~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrk~v~----------dm~~~~~~~~~ 1176 (1177)
+.+..+.....|+|+|+..|...= ....||+|++++- +...||.++|+
T Consensus 12 ~~~~~~f~LTaC~HvfC~~C~k~~--~~~~C~lCkk~ir~i~l~~slp~~ik~~F~d~~~ 69 (233)
T KOG4739|consen 12 FPSQDPFFLTACRHVFCEPCLKAS--SPDVCPLCKKSIRIIQLNRSLPTDIKSYFADPPR 69 (233)
T ss_pred cCCCCceeeeechhhhhhhhcccC--CccccccccceeeeeecccccchhHHHHccCcHH
Confidence 445556677899999999997542 2238999999864 23557777663
No 72
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=94.02 E-value=0.017 Score=66.87 Aligned_cols=54 Identities=28% Similarity=0.684 Sum_probs=43.5
Q ss_pred cccccCCCCCCcccccccccCCCceEecCCCCcccHhhHHHHHhc--CCCCCCCcccccc
Q 001043 1109 KCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS--HYICPICSKSLGD 1166 (1177)
Q Consensus 1109 ~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~--~~~CPiCrk~v~d 1166 (1177)
-|.-+++-.-|-||-|. ...|++=||||.++..|+..|-.. ..+||.||..|-.
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 35555667789999875 456888899999999999999733 6889999998754
No 73
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.84 E-value=0.032 Score=63.09 Aligned_cols=48 Identities=19% Similarity=0.390 Sum_probs=37.4
Q ss_pred CCCCCCcccccccccCCCceEecCCCCcccHhhHHHHH-hcCCCCCCCccccc
Q 001043 1114 GLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYT-CSHYICPICSKSLG 1165 (1177)
Q Consensus 1114 ~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl-~~~~~CPiCrk~v~ 1165 (1177)
.+...|+||+... ..+ +.|+|+|.|..-||+--. ....+||+||..|-
T Consensus 5 ~~~~eC~IC~nt~---n~P-v~l~C~HkFCyiCiKGsy~ndk~~CavCR~pid 53 (324)
T KOG0824|consen 5 TKKKECLICYNTG---NCP-VNLYCFHKFCYICIKGSYKNDKKTCAVCRFPID 53 (324)
T ss_pred ccCCcceeeeccC---CcC-ccccccchhhhhhhcchhhcCCCCCceecCCCC
Confidence 3567899999752 333 679999999999998743 44567999999884
No 74
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=93.53 E-value=0.059 Score=45.85 Aligned_cols=45 Identities=22% Similarity=0.526 Sum_probs=24.5
Q ss_pred CcccccccccCCCceEecCCCCcccHhhHHHHHh-cCCCCCCCccc
Q 001043 1119 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC-SHYICPICSKS 1163 (1177)
Q Consensus 1119 CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~-~~~~CPiCrk~ 1163 (1177)
||+|.+++..++....-=+||+.+...|+..-+. .+..||-||+.
T Consensus 1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~ 46 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILENEGGRCPGCREP 46 (48)
T ss_dssp -TTTS-B--CCCTT--SSTTS----HHHHHHHTTSS-SB-TTT--B
T ss_pred CCCcccccccCCCccccCcCCCcHHHHHHHHHHhccCCCCCCCCCC
Confidence 8999999855544444447899999999988886 58999999985
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=93.43 E-value=0.034 Score=53.28 Aligned_cols=38 Identities=26% Similarity=0.616 Sum_probs=29.9
Q ss_pred cccccCCCCCCcccccccccCCCceEecCCCCcccHhhHH
Q 001043 1109 KCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQ 1148 (1177)
Q Consensus 1109 ~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~ 1148 (1177)
.++.-.....|+||...|.. ....+.||||.||..|++
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 34444557789999999765 467788999999999975
No 76
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=92.77 E-value=0.068 Score=66.12 Aligned_cols=49 Identities=24% Similarity=0.486 Sum_probs=36.1
Q ss_pred cccccCCCCCCcccccccccCCCceEecCCCCcccHhhHHHHHhcCCCCCC
Q 001043 1109 KCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPI 1159 (1177)
Q Consensus 1109 ~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPi 1159 (1177)
+|+.......|.||.-.+.. ....-+-|||.+|..|..+|.+....||.
T Consensus 1021 ~~~~~~~~~~C~~C~l~V~g--ss~~Cg~C~Hv~H~sc~~eWf~~gd~Cps 1069 (1081)
T KOG0309|consen 1021 CAICKGFTFQCAICHLAVRG--SSNFCGTCGHVGHTSCMMEWFRTGDVCPS 1069 (1081)
T ss_pred ccccccceeeeeeEeeEeec--cchhhccccccccHHHHHHHHhcCCcCCC
Confidence 33334445568888765433 33456789999999999999999989984
No 77
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.32 E-value=0.096 Score=56.95 Aligned_cols=53 Identities=28% Similarity=0.629 Sum_probs=41.8
Q ss_pred cCCCCCCcccccccccCCCceEecCCCCcccHhhHHHHHh--------cCCCCCCCccccccc
Q 001043 1113 KGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC--------SHYICPICSKSLGDM 1167 (1177)
Q Consensus 1113 ~~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~--------~~~~CPiCrk~v~dm 1167 (1177)
.....+|..|.-.| .+++ ...|-|=|.||..|+++|-. ..|.||-|...|..-
T Consensus 47 sDY~pNC~LC~t~L-a~gd-t~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp 107 (299)
T KOG3970|consen 47 SDYNPNCRLCNTPL-ASGD-TTRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPP 107 (299)
T ss_pred cCCCCCCceeCCcc-ccCc-ceeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCC
Confidence 34578999999986 4455 35578999999999999953 258899999988653
No 78
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=92.13 E-value=0.083 Score=44.60 Aligned_cols=40 Identities=25% Similarity=0.665 Sum_probs=26.4
Q ss_pred CcccccccccCCCceEecCCC-----CcccHhhHHHHHh--cCCCCCCC
Q 001043 1119 CPICCDFLFTSSATVRALPCG-----HFMHSDCFQAYTC--SHYICPIC 1160 (1177)
Q Consensus 1119 CpICle~lf~s~~~v~~LpCG-----H~fH~~Ci~~wl~--~~~~CPiC 1160 (1177)
|-||++.-.+ +...+.||+ -+.|..|+.+|+. .+.+|++|
T Consensus 1 CrIC~~~~~~--~~~li~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C 47 (47)
T PF12906_consen 1 CRICLEGEEE--DEPLISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC 47 (47)
T ss_dssp ETTTTEE-SS--SS-EE-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred CeEeCCcCCC--CCceecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence 6799987322 223456775 5899999999986 56789998
No 79
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=91.91 E-value=0.069 Score=60.91 Aligned_cols=63 Identities=22% Similarity=0.472 Sum_probs=48.2
Q ss_pred CCCCCcccccccccCCCceEecCCCCcccHhhHHHHHh-cCCCCCCCcccccccccccCCCCCC
Q 001043 1115 LETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC-SHYICPICSKSLGDMAVLHLPIPFE 1177 (1177)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~-~~~~CPiCrk~v~dm~~~~~~~~~~ 1177 (1177)
.++.||.|+|+|.-++....--|||--+++-|...--. -+.+||-||+..-+-.+.|.++.+|
T Consensus 13 eed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~denv~~~~~s~e 76 (480)
T COG5175 13 EEDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDENVRYVTLSPE 76 (480)
T ss_pred ccccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhccccceeEEecCHH
Confidence 35569999999866555555568998888888665432 3789999999998888888877654
No 80
>PF05883 Baculo_RING: Baculovirus U-box/Ring-like domain; InterPro: IPR008573 This family consists of several Baculovirus proteins of around 130 residues in length. The function of this family is unknown, but it appears to be related to the U-box and ring finger domain by profile-profile comparison.
Probab=91.70 E-value=0.074 Score=54.17 Aligned_cols=40 Identities=20% Similarity=0.384 Sum_probs=32.9
Q ss_pred CCCCcccccccccCCCceEecCCC------CcccHhhHHHHHhcCCC
Q 001043 1116 ETNCPICCDFLFTSSATVRALPCG------HFMHSDCFQAYTCSHYI 1156 (1177)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCG------H~fH~~Ci~~wl~~~~~ 1156 (1177)
...|.||++.+.. ...|+.++|| |+||.+|+..|.+...+
T Consensus 26 ~~EC~IC~~~I~~-~~GvV~vt~~g~lnLEkmfc~~C~~rw~~~~~r 71 (134)
T PF05883_consen 26 TVECQICFDRIDN-NDGVVYVTDGGTLNLEKMFCADCDKRWRRERNR 71 (134)
T ss_pred Ceeehhhhhhhhc-CCCEEEEecCCeehHHHHHHHHHHHHHHhhccC
Confidence 5679999999866 6678999998 89999999999654433
No 81
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.69 E-value=0.031 Score=62.74 Aligned_cols=49 Identities=27% Similarity=0.600 Sum_probs=36.0
Q ss_pred CCCCcccccccccCCCceEecCCCCcc-cHhhHHHHHhcCCCCCCCcccccccccccC
Q 001043 1116 ETNCPICCDFLFTSSATVRALPCGHFM-HSDCFQAYTCSHYICPICSKSLGDMAVLHL 1172 (1177)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCGH~f-H~~Ci~~wl~~~~~CPiCrk~v~dm~~~~~ 1172 (1177)
..-|.|||+- ......|+|||.- ..+|-.. -..|||||+-|.....+|+
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 6789999975 3457889999973 4445322 2379999999988777765
No 82
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.19 E-value=0.13 Score=54.18 Aligned_cols=30 Identities=27% Similarity=0.724 Sum_probs=25.2
Q ss_pred cCCCCcccHhhHHHHHhc-----------CCCCCCCccccc
Q 001043 1136 LPCGHFMHSDCFQAYTCS-----------HYICPICSKSLG 1165 (1177)
Q Consensus 1136 LpCGH~fH~~Ci~~wl~~-----------~~~CPiCrk~v~ 1165 (1177)
..||-.||+-|+..||+. -..||.|.+++.
T Consensus 188 ~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~Pia 228 (234)
T KOG3268|consen 188 IQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIA 228 (234)
T ss_pred cccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcce
Confidence 579999999999999863 145999999874
No 83
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=91.10 E-value=0.11 Score=61.74 Aligned_cols=54 Identities=30% Similarity=0.677 Sum_probs=43.5
Q ss_pred CCCCCcccccccccCCCceEecCCCCcccHhhHHHHHhcCCCCCCCccccccccccc
Q 001043 1115 LETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGDMAVLH 1171 (1177)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrk~v~dm~~~~ 1171 (1177)
.+..||||+..+ .+++....|||.|...|+..|+..+..||.|+..+..-..+.
T Consensus 20 ~~l~C~~C~~vl---~~p~~~~~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~~~~ 73 (391)
T KOG0297|consen 20 ENLLCPICMSVL---RDPVQTTTCGHRFCAGCLLESLSNHQKCPVCRQELTQAEELP 73 (391)
T ss_pred ccccCccccccc---cCCCCCCCCCCcccccccchhhccCcCCcccccccchhhccC
Confidence 457899999764 445555799999999999999999999999998876554443
No 84
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.94 E-value=0.12 Score=59.98 Aligned_cols=47 Identities=23% Similarity=0.509 Sum_probs=33.9
Q ss_pred cCCCCCCcccccccccCCCceEecCCCCcccHhhHHHHHhcCCCCCCCcccccc
Q 001043 1113 KGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1166 (1177)
Q Consensus 1113 ~~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrk~v~d 1166 (1177)
.....+|.||++. +. ....+||||+-. |..-.. ...+||+||.+|.-
T Consensus 302 ~~~p~lcVVcl~e-~~---~~~fvpcGh~cc--ct~cs~-~l~~CPvCR~rI~~ 348 (355)
T KOG1571|consen 302 LPQPDLCVVCLDE-PK---SAVFVPCGHVCC--CTLCSK-HLPQCPVCRQRIRL 348 (355)
T ss_pred cCCCCceEEecCC-cc---ceeeecCCcEEE--chHHHh-hCCCCchhHHHHHH
Confidence 3457899999987 22 378899999955 554432 34559999998853
No 85
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=90.38 E-value=0.1 Score=62.48 Aligned_cols=51 Identities=25% Similarity=0.570 Sum_probs=41.3
Q ss_pred cccCCCCCCcccccccccCCCceEecCCCCcccHhhHHHHHh-----cCCCCCCCccccc
Q 001043 1111 REKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC-----SHYICPICSKSLG 1165 (1177)
Q Consensus 1111 ~e~~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~-----~~~~CPiCrk~v~ 1165 (1177)
.++..+..|-+|.|+ .+......|.|.|++-|+.+|+. .+-+||+|...+.
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 466778899999987 23466789999999999999974 3688999998663
No 86
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=90.19 E-value=0.23 Score=54.89 Aligned_cols=52 Identities=27% Similarity=0.537 Sum_probs=44.1
Q ss_pred CCCCCcccccccccCCCceEec-CCCCcccHhhHHHHHhcCCCCCCCccccccc
Q 001043 1115 LETNCPICCDFLFTSSATVRAL-PCGHFMHSDCFQAYTCSHYICPICSKSLGDM 1167 (1177)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~L-pCGH~fH~~Ci~~wl~~~~~CPiCrk~v~dm 1167 (1177)
..-.||||.+.| +...+..+| ||||++..+|..+.++....||+|.+.+-+-
T Consensus 220 ~ryiCpvtrd~L-tNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdr 272 (303)
T KOG3039|consen 220 KRYICPVTRDTL-TNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDR 272 (303)
T ss_pred cceecccchhhh-cCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCccc
Confidence 456799999996 455566666 9999999999999999999999999988654
No 87
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=89.61 E-value=0.15 Score=44.55 Aligned_cols=45 Identities=29% Similarity=0.702 Sum_probs=31.4
Q ss_pred CCCCcccccccccCCCceEecCCCCcccHhhHHHHHhcCCCCCCCcccccc
Q 001043 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1166 (1177)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrk~v~d 1166 (1177)
+..|-.|... +..-.++||||+....|++-+ +-+-||+|.+.+..
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 334567999999999997654 45569999998753
No 88
>KOG3800 consensus Predicted E3 ubiquitin ligase containing RING finger, subunit of transcription/repair factor TFIIH and CDK-activating kinase assembly factor [Posttranslational modification, protein turnover, chaperones]
Probab=89.61 E-value=0.24 Score=56.01 Aligned_cols=48 Identities=23% Similarity=0.461 Sum_probs=37.5
Q ss_pred CCcccccccccCCCce-EecCCCCcccHhhHHHHH-hcCCCCCCCccccc
Q 001043 1118 NCPICCDFLFTSSATV-RALPCGHFMHSDCFQAYT-CSHYICPICSKSLG 1165 (1177)
Q Consensus 1118 ~CpICle~lf~s~~~v-~~LpCGH~fH~~Ci~~wl-~~~~~CPiCrk~v~ 1165 (1177)
.||+|.-+.+.+.+-+ .+=+|||.++.+|++.-. ...+.||-|.+.+.
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 5999998776654422 223999999999999975 56799999998764
No 89
>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=89.44 E-value=0.29 Score=51.13 Aligned_cols=49 Identities=24% Similarity=0.758 Sum_probs=33.0
Q ss_pred CCCCcccccccccCCCceEecCC------------C-CcccHhhHHHHHhc-----------------------------
Q 001043 1116 ETNCPICCDFLFTSSATVRALPC------------G-HFMHSDCFQAYTCS----------------------------- 1153 (1177)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpC------------G-H~fH~~Ci~~wl~~----------------------------- 1153 (1177)
+..||||||.=. ..+.|-| + =+-|..|++++-+.
T Consensus 2 d~~CpICme~PH----NAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkka~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 77 (162)
T PF07800_consen 2 DVTCPICMEHPH----NAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKKAYGKSSSSSSQSSSSAPSDSSSSESSESQE 77 (162)
T ss_pred CccCceeccCCC----ceEEEEeccccCCccccccCCccchhHHHHHHHHHhcCCCCccccccccCcCCCcccccccccc
Confidence 467999999621 2344444 3 24699999998531
Q ss_pred --CCCCCCCcccccccc
Q 001043 1154 --HYICPICSKSLGDMA 1168 (1177)
Q Consensus 1154 --~~~CPiCrk~v~dm~ 1168 (1177)
...||+||-.|....
T Consensus 78 ~~~L~CPLCRG~V~GWt 94 (162)
T PF07800_consen 78 QPELACPLCRGEVKGWT 94 (162)
T ss_pred cccccCccccCceeceE
Confidence 245999999887543
No 90
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=89.28 E-value=0.31 Score=60.93 Aligned_cols=80 Identities=24% Similarity=0.502 Sum_probs=55.9
Q ss_pred CCcccCCCCCccccCCCCCccccccCCcccccccccccccccccCCCCCCcccccccccCCCceEecCCCCcccHhhHHH
Q 001043 1070 RVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLAKKLVDHKCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQA 1149 (1177)
Q Consensus 1070 k~~yHC~~CgiCrvg~gl~~~~fhC~~C~~C~s~~l~~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~ 1149 (1177)
.-+|-|+.|+---+++++ .-|++|-.|-+ ..|.+|-..+- +..+----|||..|.+|+.+
T Consensus 751 ~i~~~~~nc~a~~~~~~~----~~c~rc~s~a~--------------~~CtVC~~vi~--G~~~~c~~C~H~gH~sh~~s 810 (839)
T KOG0269|consen 751 TIHYACPNCDAPMVLTKL----WQCDRCESRAS--------------AKCTVCDLVIR--GVDVWCQVCGHGGHDSHLKS 810 (839)
T ss_pred eeeccccccCCccccccc----eeechHHHHhh--------------cCceeecceee--eeEeecccccccccHHHHHH
Confidence 467888888877777654 45666666554 35999987642 22233347999999999999
Q ss_pred HHhcCCCCCC--C-----ccccccccc
Q 001043 1150 YTCSHYICPI--C-----SKSLGDMAV 1169 (1177)
Q Consensus 1150 wl~~~~~CPi--C-----rk~v~dm~~ 1169 (1177)
|+..+.-||. | +.++.||..
T Consensus 811 w~~~~s~ca~~~C~~~c~~~~~~D~~~ 837 (839)
T KOG0269|consen 811 WFFKASPCAKSICPHLCHYSSFIDTFM 837 (839)
T ss_pred HHhcCCCCccccCCccccccccchhhh
Confidence 9988877776 4 445556543
No 91
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=89.11 E-value=0.1 Score=57.64 Aligned_cols=69 Identities=26% Similarity=0.667 Sum_probs=45.4
Q ss_pred ccCcccccccCCCCCCccccceeeccccCccccCCCCCCCCCCCCcccceEecccccc-ccCC-----CCcccCCCCCcc
Q 001043 1008 FTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVGPVCTTLSCSGLSMAKYYCGICKF-FDDE-----RVVYHCPFCNLC 1081 (1177)
Q Consensus 1008 y~Cr~CHde~~~H~~~r~~~~~~~C~~C~~~q~~~~~C~~~~C~~~~~a~Y~C~~C~l-~dd~-----k~~yHC~~CgiC 1081 (1177)
|.|..|.....|--+-|.+ ..++|-.|+..-.+ .--|+|.|.+|+- .|++ .++||
T Consensus 100 F~Cd~Cn~~Lad~gf~rnq-gr~LC~~Cn~k~Ka-----------~~~g~YvC~KCh~~iD~~~l~fr~d~yH------- 160 (332)
T KOG2272|consen 100 FRCDLCNKHLADQGFYRNQ-GRALCRECNQKEKA-----------KGRGRYVCQKCHAHIDEQPLTFRGDPYH------- 160 (332)
T ss_pred chhHHHHHHHhhhhhHhhc-chHHhhhhhhhhcc-----------cccceeehhhhhhhcccccccccCCCCC-------
Confidence 6677777777776666653 47788887654332 2357999999974 5665 56777
Q ss_pred ccCCCCCccccccCCcccccc
Q 001043 1082 RVGRGLGVDFFHCMTCNCCLA 1102 (1177)
Q Consensus 1082 rvg~gl~~~~fhC~~C~~C~s 1102 (1177)
-.-|.|.+||-=+.
T Consensus 161 -------~yHFkCt~C~keL~ 174 (332)
T KOG2272|consen 161 -------PYHFKCTTCGKELT 174 (332)
T ss_pred -------ccceeccccccccc
Confidence 24566666665543
No 92
>COG2461 Uncharacterized conserved protein [Function unknown]
Probab=89.04 E-value=1.7 Score=51.37 Aligned_cols=137 Identities=22% Similarity=0.229 Sum_probs=105.1
Q ss_pred CCchHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHHHhh-hHHHHHHH
Q 001043 41 KSPILIFLFFHKAIKSELDVLHRAAMAFATNLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIRV-KNIARTYS 119 (1177)
Q Consensus 41 ~~Pi~~~~~~HkAlR~el~~l~~~~~~~~~~~~d~~~~~~l~~r~~~L~~~~~~H~~aEDevI~PaL~~Rv-~~v~~~~~ 119 (1177)
.+|+..|.-=-+++|..++.+.+.. .+..-...+...+.+|..+=+ |-+-+-..|||-++.|- ..+.-.|-
T Consensus 85 gHPv~tl~~EN~~i~~ll~~~l~~~-------~~~~ik~~l~~lv~~L~~vg~-Hy~RKe~lIfp~~Er~GitapptVmW 156 (409)
T COG2461 85 GHPVRTLKRENKAIRSLLANLLQFP-------PKKEIKEKLVELVSELDKIGK-HYTRKEMLIFPYIERRGITAPPTVMW 156 (409)
T ss_pred CCcHHHHhcccHHHHHHHHHHhhcc-------ccHHHHHHHHHHHHHHHHhcc-ccccccccchhHHHHcCCCCCCeeee
Confidence 5699888888889996665544332 123344566677777777777 99999999999999886 45777788
Q ss_pred hhhhhHHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHHHHHhHHHHHHHhhhHHHhhCCHHHHHHHHHH
Q 001043 120 LEHEGESVLFDQLFELLNSSMRNEESYRRELASCTGALQTSISQHMSKEEEQVFPLLIEKFSFEEQASLVWQ 191 (1177)
Q Consensus 120 ~EH~~~~~lf~~l~~~l~~~~~~~~~~~~eLa~~l~~l~~~l~qHm~~EE~~v~PLl~~~fS~~E~a~L~~~ 191 (1177)
.-|.++-..|..+...+. .. .. .+++.....+.+.+..=+.+||.-+.|-+..-||..||.++..+
T Consensus 157 ~~dDeiRe~lk~~~~~l~--~~-s~---~~~ve~~~~~~t~i~dmIFkEe~Ilypt~~d~~te~ew~~i~~~ 222 (409)
T COG2461 157 VKDDEIREALKELLKLLK--EV-SI---EEFVEKAESVLTEIEDMIFKEENILYPTLLDLLTEGEWEAIKEQ 222 (409)
T ss_pred ccCcHHHHHHHHHHHHhh--cc-Ch---HHHHHHHHHHHHHHHHHHHhhhhhHHhHHHHhcCHHHHHHHHhc
Confidence 899999999999888887 11 22 33344444555788888899999999999999999999999888
No 93
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=88.85 E-value=0.11 Score=59.68 Aligned_cols=49 Identities=20% Similarity=0.557 Sum_probs=41.1
Q ss_pred CCCCCcccccccccCCCceEecCCCCcccHhhHHHHHhcCCCCCCCcccccc
Q 001043 1115 LETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1166 (1177)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrk~v~d 1166 (1177)
....|.+|.-+|.+. ..+.-|=|.|++.||..++..+.+||.|...|..
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 456899999986543 3456799999999999999999999999988874
No 94
>PF04641 Rtf2: Rtf2 RING-finger
Probab=88.24 E-value=0.43 Score=53.81 Aligned_cols=52 Identities=19% Similarity=0.478 Sum_probs=40.9
Q ss_pred CCCCCCcccccccccCCCceEec-CCCCcccHhhHHHHHhcCCCCCCCccccccc
Q 001043 1114 GLETNCPICCDFLFTSSATVRAL-PCGHFMHSDCFQAYTCSHYICPICSKSLGDM 1167 (1177)
Q Consensus 1114 ~~~~~CpICle~lf~s~~~v~~L-pCGH~fH~~Ci~~wl~~~~~CPiCrk~v~dm 1167 (1177)
...-.|||....| +.....++| ||||+|-..++.+.- ....||+|.+.+..-
T Consensus 111 ~~~~~CPvt~~~~-~~~~~fv~l~~cG~V~s~~alke~k-~~~~Cp~c~~~f~~~ 163 (260)
T PF04641_consen 111 EGRFICPVTGKEF-NGKHKFVYLRPCGCVFSEKALKELK-KSKKCPVCGKPFTEE 163 (260)
T ss_pred CceeECCCCCccc-CCceeEEEEcCCCCEeeHHHHHhhc-ccccccccCCccccC
Confidence 4556799999985 555555555 999999999999984 466799999987643
No 95
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.31 E-value=0.32 Score=57.34 Aligned_cols=46 Identities=26% Similarity=0.539 Sum_probs=35.7
Q ss_pred CCCCcccccccccCCCceEecCCCCcccHhhHHHHHh--------cCCCCCCCcc
Q 001043 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC--------SHYICPICSK 1162 (1177)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~--------~~~~CPiCrk 1162 (1177)
--.|.||++. +........+||+|+|.+.|...|.. +.-+||-|.-
T Consensus 184 lf~C~ICf~e-~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C 237 (445)
T KOG1814|consen 184 LFDCCICFEE-QMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKC 237 (445)
T ss_pred cccceeeehh-hcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCC
Confidence 4579999998 55556678899999999999999963 2356887653
No 96
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=86.95 E-value=0.24 Score=53.08 Aligned_cols=45 Identities=27% Similarity=0.389 Sum_probs=37.0
Q ss_pred CCCcccccccccCCCceEecCCCCcccHhhHHHHHhcCCCCCCCccccc
Q 001043 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1165 (1177)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrk~v~ 1165 (1177)
-.|-||.++ |.+ .++..|||.|+..|+-.-.+....|-+|.+...
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 369999998 544 245689999999999888888899999998653
No 97
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=86.75 E-value=0.4 Score=57.16 Aligned_cols=49 Identities=27% Similarity=0.642 Sum_probs=39.7
Q ss_pred CCCCCCcccccccccCCCceEecCCCCcccHhhHHHHHhcCCCCCCCcccccc
Q 001043 1114 GLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1166 (1177)
Q Consensus 1114 ~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrk~v~d 1166 (1177)
..+-.|.||+.-++. .+.+||||.|...|+++-+....-||+||-.+..
T Consensus 82 ~sef~c~vc~~~l~~----pv~tpcghs~c~~Cl~r~ld~~~~cp~Cr~~l~e 130 (398)
T KOG4159|consen 82 RSEFECCVCSRALYP----PVVTPCGHSFCLECLDRSLDQETECPLCRDELVE 130 (398)
T ss_pred cchhhhhhhHhhcCC----CccccccccccHHHHHHHhccCCCCccccccccc
Confidence 346789999887553 2345999999999999988888889999988764
No 98
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=86.12 E-value=0.28 Score=61.98 Aligned_cols=40 Identities=28% Similarity=0.678 Sum_probs=32.7
Q ss_pred CCCcccccccccCCCceEecCCCCcccHhhHHHHHhcCCCCCCCcc
Q 001043 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSK 1162 (1177)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrk 1162 (1177)
..|..|--.| .-|.+-..|||.||++|+. .....||-|+-
T Consensus 841 skCs~C~~~L---dlP~VhF~CgHsyHqhC~e---~~~~~CP~C~~ 880 (933)
T KOG2114|consen 841 SKCSACEGTL---DLPFVHFLCGHSYHQHCLE---DKEDKCPKCLP 880 (933)
T ss_pred eeecccCCcc---ccceeeeecccHHHHHhhc---cCcccCCccch
Confidence 4788887554 4467778899999999998 56788999998
No 99
>PHA02862 5L protein; Provisional
Probab=85.78 E-value=0.51 Score=48.70 Aligned_cols=50 Identities=22% Similarity=0.491 Sum_probs=35.6
Q ss_pred CCCCcccccccccCCCceEecCCC-----CcccHhhHHHHHhc--CCCCCCCccccccccccc
Q 001043 1116 ETNCPICCDFLFTSSATVRALPCG-----HFMHSDCFQAYTCS--HYICPICSKSLGDMAVLH 1171 (1177)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCG-----H~fH~~Ci~~wl~~--~~~CPiCrk~v~dm~~~~ 1171 (1177)
.+.|=||.+. .++. .-||. -.-|++|+.+|+.. +..||+|+.... +..-|
T Consensus 2 ~diCWIC~~~---~~e~--~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~-Ik~~y 58 (156)
T PHA02862 2 SDICWICNDV---CDER--NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYN-IKKTY 58 (156)
T ss_pred CCEEEEecCc---CCCC--cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEE-EEEcc
Confidence 4679999986 2222 34664 67999999999964 467999998764 44433
No 100
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=84.44 E-value=0.84 Score=52.63 Aligned_cols=66 Identities=21% Similarity=0.405 Sum_probs=46.1
Q ss_pred CCccccccccc-ccccccccCCCCCCcccccccccCCCceEecCCCCcccHhhHHHH--HhcCCCCCCCcccc
Q 001043 1095 MTCNCCLAKKL-VDHKCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAY--TCSHYICPICSKSL 1164 (1177)
Q Consensus 1095 ~~C~~C~s~~l-~~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~w--l~~~~~CPiCrk~v 1164 (1177)
.+=+.|....+ ...+=.....++.|-||-+.+ +-+.++||||-++--|--.. |.....||+||..-
T Consensus 39 kKNnlsaEPnlttsSaddtDEen~~C~ICA~~~----TYs~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~ 107 (493)
T COG5236 39 KKNNLSAEPNLTTSSADDTDEENMNCQICAGST----TYSARYPCGHQICHACAVRLRALYMQKGCPLCRTET 107 (493)
T ss_pred cccccccCCccccccccccccccceeEEecCCc----eEEEeccCCchHHHHHHHHHHHHHhccCCCcccccc
Confidence 34456665555 333333344578899998763 34567899999999997764 66778899999853
No 101
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=82.88 E-value=0.11 Score=60.37 Aligned_cols=51 Identities=24% Similarity=0.481 Sum_probs=43.4
Q ss_pred CCCCCcccccccccCCCceEecCCCCcccHhhHHHHHhcCCCCCCCccccc
Q 001043 1115 LETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1165 (1177)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrk~v~ 1165 (1177)
....|+||.+.+...-+.+..+.|||.+|..|+.+||.....||.|++.+.
T Consensus 195 lv~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~~~~kl~~~~rel~ 245 (465)
T KOG0827|consen 195 LVGSLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLATKRKLPSCRRELP 245 (465)
T ss_pred HHhhhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHHHhHHHHhhhh
Confidence 356799999987555467788999999999999999998899999999775
No 102
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=82.88 E-value=0.53 Score=60.06 Aligned_cols=43 Identities=26% Similarity=0.579 Sum_probs=33.0
Q ss_pred cccccccCCCCCCcccccccccCCCceEecCCCCcccHhhHHHHH
Q 001043 1107 DHKCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYT 1151 (1177)
Q Consensus 1107 ~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl 1151 (1177)
++.|+--.....|-+|.-+|+. .+-.+.||||.||.+|+.+-.
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 4455444557889999988653 467788999999999998764
No 103
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=82.86 E-value=0.47 Score=53.90 Aligned_cols=46 Identities=22% Similarity=0.513 Sum_probs=37.8
Q ss_pred CCCCcccccccccCCCceEecCCCCcccHhhHHHHHhcCCCCCCCccccc
Q 001043 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1165 (1177)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrk~v~ 1165 (1177)
...|-||..++. + -++..|||+|...|...-++....|+||.+.+.
T Consensus 241 Pf~c~icr~~f~-~---pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~ 286 (313)
T KOG1813|consen 241 PFKCFICRKYFY-R---PVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTH 286 (313)
T ss_pred Cccccccccccc-c---chhhcCCceeehhhhccccccCCcceecccccc
Confidence 456999999843 2 245789999999999888888899999999765
No 104
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=82.73 E-value=0.8 Score=52.94 Aligned_cols=51 Identities=22% Similarity=0.431 Sum_probs=42.1
Q ss_pred ccCCCCCCcccccccccCCCceEecCCCCcccHhhHHHHHhcCCCCCCCcccccc
Q 001043 1112 EKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1166 (1177)
Q Consensus 1112 e~~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrk~v~d 1166 (1177)
..+.+..||||.-. ....+.-||||--+..||.+.+.++..|=.|+.++.+
T Consensus 418 p~sEd~lCpICyA~----pi~Avf~PC~H~SC~~CI~qHlmN~k~CFfCktTv~~ 468 (489)
T KOG4692|consen 418 PDSEDNLCPICYAG----PINAVFAPCSHRSCYGCITQHLMNCKRCFFCKTTVID 468 (489)
T ss_pred CCcccccCcceecc----cchhhccCCCCchHHHHHHHHHhcCCeeeEecceeee
Confidence 34567899999753 2234567999999999999999999999999998875
No 105
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=81.05 E-value=1.3 Score=46.57 Aligned_cols=52 Identities=19% Similarity=0.541 Sum_probs=35.6
Q ss_pred CCCCCcccccccccCCCceEecCCC--C---cccHhhHHHHHhc--CCCCCCCcccccccccccC
Q 001043 1115 LETNCPICCDFLFTSSATVRALPCG--H---FMHSDCFQAYTCS--HYICPICSKSLGDMAVLHL 1172 (1177)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~LpCG--H---~fH~~Ci~~wl~~--~~~CPiCrk~v~dm~~~~~ 1172 (1177)
.+..|=||.+. . +.. .-||. . ..|.+|++.|+.. ..+||+|+.... +...++
T Consensus 7 ~~~~CRIC~~~-~--~~~--~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~-i~~~~k 65 (162)
T PHA02825 7 MDKCCWICKDE-Y--DVV--TNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYN-IKKNYK 65 (162)
T ss_pred CCCeeEecCCC-C--CCc--cCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEE-EEEecC
Confidence 46789999877 1 222 24665 4 5799999999854 567999998763 433333
No 106
>TIGR02481 hemeryth_dom hemerythrin-like metal-binding domain. This model describes both members of the hemerythrin (TIGR00058) family of marine invertebrates and a broader collection of bacterial and archaeal homologs. Many of the latter group are multidomain proteins with signal-transducing domains such as the GGDEF diguanylate cyclase domain (TIGR00254, pfam00990) and methyl-accepting chemotaxis protein signaling domain (pfam00015). Most hemerythrins are oxygen-carriers with a bound non-heme iron, but at least one example is a cadmium-binding protein, apparently with a role in sequestering toxic metals rather than in binding oxygen. Patterns of conserved residues suggest that all prokaryotic instances of this domain bind iron or another heavy metal, but the exact function is unknown. Not surprisingly, the prokaryote with the most instances of this domain is Magnetococcus sp. MC-1, a magnetotactic bacterium.
Probab=79.87 E-value=6.3 Score=39.11 Aligned_cols=51 Identities=18% Similarity=0.214 Sum_probs=37.0
Q ss_pred hhHHhHHHHHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 001043 361 SFAQEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQV 421 (1177)
Q Consensus 361 ~me~EH~~ie~l~e~l~~ll~~~~~~~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qv 421 (1177)
.+..+|++.-++++.|..++.. ..+ ..++...+..|..-+..||..||.-.
T Consensus 12 ~ID~qH~~l~~~in~l~~a~~~---~~~-------~~~~~~~l~~L~~y~~~HF~~EE~~M 62 (126)
T TIGR02481 12 EIDAQHKELFELINELYDALSA---GNG-------KDELKEILDELIDYTENHFADEEELM 62 (126)
T ss_pred HHHHHHHHHHHHHHHHHHHHHc---CCC-------HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5667888877777777766532 111 24667788888999999999999765
No 107
>PRK04023 DNA polymerase II large subunit; Validated
Probab=79.86 E-value=1.5 Score=56.95 Aligned_cols=18 Identities=28% Similarity=0.207 Sum_probs=10.5
Q ss_pred HHhhhccCCCCChHHHHH
Q 001043 925 EIRKVSRDSTLDPRRKAY 942 (1177)
Q Consensus 925 ~Ir~i~~~~~l~~~~k~~ 942 (1177)
.|.-|+..+.+.=+.||.
T Consensus 555 ~~~~vn~~s~~~ir~ra~ 572 (1121)
T PRK04023 555 VLEAVNELSGFEIRPKAP 572 (1121)
T ss_pred HHHHHHHhCCcEEeccCC
Confidence 455566666666566553
No 108
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=79.79 E-value=0.16 Score=59.80 Aligned_cols=86 Identities=28% Similarity=0.772 Sum_probs=0.0
Q ss_pred ceEeccccccccCC-----------CCccc--CCCCCccccCCCCCccccccCC---cccccccccccccccccCCCCCC
Q 001043 1056 AKYYCGICKFFDDE-----------RVVYH--CPFCNLCRVGRGLGVDFFHCMT---CNCCLAKKLVDHKCREKGLETNC 1119 (1177)
Q Consensus 1056 a~Y~C~~C~l~dd~-----------k~~yH--C~~CgiCrvg~gl~~~~fhC~~---C~~C~s~~l~~H~C~e~~~~~~C 1119 (1177)
.+||- ||-+...+ +.+|| |=.|+.|+.-.. |..||.-+. |--|+..+ -..|
T Consensus 271 ~~~~~-iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~-Gq~FY~v~~k~~CE~cyq~t-----------lekC 337 (468)
T KOG1701|consen 271 EDYFG-ICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLA-GQSFYQVDGKPYCEGCYQDT-----------LEKC 337 (468)
T ss_pred hhhhh-hhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhc-cccccccCCcccchHHHHHH-----------HHHH
Q ss_pred cccccccccCCCceEec-CCCCcccHhhHHHHHhcCCCCCCCccccccc
Q 001043 1120 PICCDFLFTSSATVRAL-PCGHFMHSDCFQAYTCSHYICPICSKSLGDM 1167 (1177)
Q Consensus 1120 pICle~lf~s~~~v~~L-pCGH~fH~~Ci~~wl~~~~~CPiCrk~v~dm 1167 (1177)
..|-+.|-+ ++| .||-.||..|| +|=+|.+.+...
T Consensus 338 ~~Cg~~I~d-----~iLrA~GkayHp~CF--------~Cv~C~r~ldgi 373 (468)
T KOG1701|consen 338 NKCGEPIMD-----RILRALGKAYHPGCF--------TCVVCARCLDGI 373 (468)
T ss_pred hhhhhHHHH-----HHHHhcccccCCCce--------EEEEeccccCCc
No 109
>COG5592 Uncharacterized conserved protein [Function unknown]
Probab=79.61 E-value=5.3 Score=42.23 Aligned_cols=99 Identities=19% Similarity=0.195 Sum_probs=69.4
Q ss_pred HHHHHHHHHHHHHhhcccccccccccccc-----cccccc--CcccchhhhHHHHHHHHHHHHHHhhhhhhhhccccccC
Q 001043 682 TGRFRLLWGLYRAHSNAEDDIVFPALESK-----ETLSNV--SHSYTLDHKQEEKLFEDISSALSELTELHECLSTDLTG 754 (1177)
Q Consensus 682 ~~Rf~fl~~v~~~HS~AEDeivFPaLe~k-----~~~~nv--s~s~~~dH~~ee~lf~~i~~~L~~~~~l~~~~~~~~~~ 754 (1177)
..-..|+|.++..|---|-++.||+.=-. -..... .--+..||+.+|-++.++..-
T Consensus 31 le~~gf~~k~~k~h~e~Ee~ilF~v~Vd~~~ed~~~fkdt~~~~~i~~DHkliE~l~tnlik~----------------- 93 (171)
T COG5592 31 LEFEGFNEKLGKDHVELEEKILFPVIVDADMEDLYVFKDTPEVDRIKNDHKLIETLATNLIKW----------------- 93 (171)
T ss_pred HhhcchHHHHhhhHHHHHHHhhhhhccchHHHHHHhhhccchhhHhHhhHHHHHHHHHHHHhh-----------------
Confidence 33444899999999999999999975331 111122 225889999999999887111
Q ss_pred ccccccccccchhhhHhhHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhcCCHHHHHH
Q 001043 755 DLTRNSLESCDQNETVRKYNEKATELQGMCKSIRVTLDQHVFREELELWPLFDRHFSVEEQDK 817 (1177)
Q Consensus 755 ~~~~~~~~~~~~~~~~~~~~el~~kL~~~~~sl~~~L~~H~~~EE~Ev~PL~~k~fS~eeQ~~ 817 (1177)
.+ . .|.+.-.-.+.++|..|=..||.-++|-.++.=...+|.+
T Consensus 94 -------------kR----~---~k~~e~~p~fyK~LtdHn~aEE~~IfPrvks~~~E~~~~~ 136 (171)
T COG5592 94 -------------KR----P---DKIKERVPLFYKTLTDHNLAEEEYIFPRVKSLKGEDEQSA 136 (171)
T ss_pred -------------cc----c---hHHHHHHHHHHHHHHHccccccchhhHHHHhhcchhhHHH
Confidence 01 1 2444555778889999999999999999877655544444
No 110
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=76.35 E-value=1.7 Score=49.62 Aligned_cols=47 Identities=28% Similarity=0.742 Sum_probs=37.3
Q ss_pred CCCcccccccccCCCc---eEecCCCCcccHhhHHHHHhcC-CCCCCCcccc
Q 001043 1117 TNCPICCDFLFTSSAT---VRALPCGHFMHSDCFQAYTCSH-YICPICSKSL 1164 (1177)
Q Consensus 1117 ~~CpICle~lf~s~~~---v~~LpCGH~fH~~Ci~~wl~~~-~~CPiCrk~v 1164 (1177)
..|-||-++ |.+.+. .+.|.|||.+...|+...+... ..||.||...
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 469999998 555532 3678999999999999887654 5599999985
No 111
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=75.62 E-value=2.2 Score=38.02 Aligned_cols=46 Identities=26% Similarity=0.626 Sum_probs=27.5
Q ss_pred ceeeccccCccccCCC-----CCCCCCCCCcccceEeccccccccCCCCcccCCCCCc
Q 001043 1028 TEMMCMRCLKVQPVGP-----VCTTLSCSGLSMAKYYCGICKFFDDERVVYHCPFCNL 1080 (1177)
Q Consensus 1028 ~~~~C~~C~~~q~~~~-----~C~~~~C~~~~~a~Y~C~~C~l~dd~k~~yHC~~Cgi 1080 (1177)
....|..|+..-.+.. .|-| | |.. -=|-|..|+-.. ..|.||+||+
T Consensus 6 ~~~~CtSCg~~i~~~~~~~~F~CPn--C-G~~-~I~RC~~CRk~~---~~Y~CP~CGF 56 (59)
T PRK14890 6 EPPKCTSCGIEIAPREKAVKFLCPN--C-GEV-IIYRCEKCRKQS---NPYTCPKCGF 56 (59)
T ss_pred cCccccCCCCcccCCCccCEeeCCC--C-CCe-eEeechhHHhcC---CceECCCCCC
Confidence 3456778876554333 4655 5 432 134477776664 4688888885
No 112
>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=73.08 E-value=2 Score=35.84 Aligned_cols=41 Identities=29% Similarity=0.731 Sum_probs=20.4
Q ss_pred CcccccccccCCCceEecCCCCcccHhhHHHHHhcCC--CCCCC
Q 001043 1119 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHY--ICPIC 1160 (1177)
Q Consensus 1119 CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~--~CPiC 1160 (1177)
|.+|.+- .+-+..-..-.|+=.+|..|++.|++... +||.|
T Consensus 1 C~~C~~i-v~~G~~C~~~~C~~r~H~~C~~~y~r~~~~~~CP~C 43 (43)
T PF08746_consen 1 CEACKEI-VTQGQRCSNRDCNVRLHDDCFKKYFRHRSNPKCPNC 43 (43)
T ss_dssp -TTT-SB--SSSEE-SS--S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred Ccccchh-HeeeccCCCCccCchHHHHHHHHHHhcCCCCCCcCC
Confidence 5667654 22222112224777899999999987654 79988
No 113
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=72.48 E-value=2.1 Score=54.53 Aligned_cols=50 Identities=26% Similarity=0.618 Sum_probs=35.0
Q ss_pred CCCCCcccccccccCCCce-EecCCCCcccHhhHHHHHhc-------CCCCCCCccccc
Q 001043 1115 LETNCPICCDFLFTSSATV-RALPCGHFMHSDCFQAYTCS-------HYICPICSKSLG 1165 (1177)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v-~~LpCGH~fH~~Ci~~wl~~-------~~~CPiCrk~v~ 1165 (1177)
..-.|.||.|.|..+ .++ .--.|=|+||..||..|-+. .-.||-|+....
T Consensus 190 ~~yeCmIC~e~I~~t-~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv~~ 247 (950)
T KOG1952|consen 190 RKYECMICTERIKRT-APVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSVSK 247 (950)
T ss_pred CceEEEEeeeecccc-CCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccchhc
Confidence 345799999986433 322 22346699999999999643 356999995443
No 114
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=72.48 E-value=2.7 Score=49.82 Aligned_cols=47 Identities=21% Similarity=0.513 Sum_probs=37.1
Q ss_pred CCCcccccccccCCCceEecCCCCcccHhhHHHHHhcC---CCCCCCcccc
Q 001043 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSH---YICPICSKSL 1164 (1177)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~---~~CPiCrk~v 1164 (1177)
-.|||=.|. -+...|-+.|.|||++-++-+++..++. .+||.|-...
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 468887765 4556677889999999999999987653 6899997643
No 115
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=72.03 E-value=1.3 Score=54.59 Aligned_cols=43 Identities=26% Similarity=0.623 Sum_probs=34.1
Q ss_pred CCCcccccccccCCCceEecCCCCcccHhhHHHHHhcCCCCCCCcc
Q 001043 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSK 1162 (1177)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrk 1162 (1177)
-.|+||+..++.+.-.-+.|-|||+++..|...- .+.+|| |.+
T Consensus 12 l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~l--yn~scp-~~~ 54 (861)
T KOG3161|consen 12 LLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLL--YNASCP-TKR 54 (861)
T ss_pred hhchHHHHHHHHHhcCcccccccchHHHHHHHhH--hhccCC-CCc
Confidence 4799998776666666678999999999999764 366799 765
No 116
>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=71.35 E-value=1.8 Score=48.51 Aligned_cols=65 Identities=31% Similarity=0.812 Sum_probs=43.7
Q ss_pred CCcccCccccccc-CCCCCCccccceeeccccCccccCCCCCCCCCCCCcccceEecccccc-c-cCC----------CC
Q 001043 1005 GKLFTCRFCHDKV-SDHSMDRKATTEMMCMRCLKVQPVGPVCTTLSCSGLSMAKYYCGICKF-F-DDE----------RV 1071 (1177)
Q Consensus 1005 ~k~y~Cr~CHde~-~~H~~~r~~~~~~~C~~C~~~q~~~~~C~~~~C~~~~~a~Y~C~~C~l-~-dd~----------k~ 1071 (1177)
|+.|.|-+|++-+ +|-.|+-.+ .|+....-+-.|.+ | ..+|.|.|-.||. | ||. ..
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 6789999999874 555555432 35566666667875 6 3789999999986 3 332 24
Q ss_pred cccCCCCCc
Q 001043 1072 VYHCPFCNL 1080 (1177)
Q Consensus 1072 ~yHC~~Cgi 1080 (1177)
++-||+||.
T Consensus 209 ~~PCPKCg~ 217 (314)
T PF06524_consen 209 PIPCPKCGY 217 (314)
T ss_pred CCCCCCCCC
Confidence 566777774
No 117
>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=70.95 E-value=2.1 Score=42.49 Aligned_cols=17 Identities=35% Similarity=0.757 Sum_probs=15.0
Q ss_pred ccccCCCCcccCCCCCc
Q 001043 1064 KFFDDERVVYHCPFCNL 1080 (1177)
Q Consensus 1064 ~l~dd~k~~yHC~~Cgi 1080 (1177)
||||=.|.+..||+||.
T Consensus 18 kFYDLnk~PivCP~CG~ 34 (108)
T PF09538_consen 18 KFYDLNKDPIVCPKCGT 34 (108)
T ss_pred hhccCCCCCccCCCCCC
Confidence 67888899999999994
No 118
>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=70.88 E-value=1.5 Score=37.39 Aligned_cols=42 Identities=29% Similarity=0.725 Sum_probs=26.0
Q ss_pred CCcccccccccCCCceEecCCC-CcccHhhHHHHHhcCCCCCCCccccc
Q 001043 1118 NCPICCDFLFTSSATVRALPCG-HFMHSDCFQAYTCSHYICPICSKSLG 1165 (1177)
Q Consensus 1118 ~CpICle~lf~s~~~v~~LpCG-H~fH~~Ci~~wl~~~~~CPiCrk~v~ 1165 (1177)
+|--|.. ... ..+.|. |+....|+.-.+..+..||||.+++.
T Consensus 4 nCKsCWf---~~k---~Li~C~dHYLCl~CLt~ml~~s~~C~iC~~~LP 46 (50)
T PF03854_consen 4 NCKSCWF---ANK---GLIKCSDHYLCLNCLTLMLSRSDRCPICGKPLP 46 (50)
T ss_dssp ---SS-S-----S---SEEE-SS-EEEHHHHHHT-SSSSEETTTTEE--
T ss_pred cChhhhh---cCC---CeeeecchhHHHHHHHHHhccccCCCcccCcCc
Confidence 5666663 222 235787 99999999999999999999999875
No 119
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=68.49 E-value=3 Score=48.27 Aligned_cols=44 Identities=30% Similarity=0.799 Sum_probs=34.2
Q ss_pred CCCCcccccccccCCCceEecCC--CCcccHhhHHHHHhcCCCCCCCccccccc
Q 001043 1116 ETNCPICCDFLFTSSATVRALPC--GHFMHSDCFQAYTCSHYICPICSKSLGDM 1167 (1177)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpC--GH~fH~~Ci~~wl~~~~~CPiCrk~v~dm 1167 (1177)
-.+||||.++|.. ++ +.| ||.-...|-. +..+.||.||..+++.
T Consensus 48 lleCPvC~~~l~~---Pi--~QC~nGHlaCssC~~---~~~~~CP~Cr~~~g~~ 93 (299)
T KOG3002|consen 48 LLDCPVCFNPLSP---PI--FQCDNGHLACSSCRT---KVSNKCPTCRLPIGNI 93 (299)
T ss_pred hccCchhhccCcc---cc--eecCCCcEehhhhhh---hhcccCCccccccccH
Confidence 4689999998632 23 455 7999999864 4678999999999964
No 120
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=68.03 E-value=3.4 Score=31.97 Aligned_cols=38 Identities=34% Similarity=0.766 Sum_probs=26.1
Q ss_pred CCcccccccccCCCceEecCCCCcccHhhHHHHHhcCCCCCCCccccc
Q 001043 1118 NCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1165 (1177)
Q Consensus 1118 ~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrk~v~ 1165 (1177)
.|+.|.+.+......+.. =|..||.+|+ +|..|++++.
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 388898886544222222 3789999886 6888888764
No 121
>TIGR02481 hemeryth_dom hemerythrin-like metal-binding domain. This model describes both members of the hemerythrin (TIGR00058) family of marine invertebrates and a broader collection of bacterial and archaeal homologs. Many of the latter group are multidomain proteins with signal-transducing domains such as the GGDEF diguanylate cyclase domain (TIGR00254, pfam00990) and methyl-accepting chemotaxis protein signaling domain (pfam00015). Most hemerythrins are oxygen-carriers with a bound non-heme iron, but at least one example is a cadmium-binding protein, apparently with a role in sequestering toxic metals rather than in binding oxygen. Patterns of conserved residues suggest that all prokaryotic instances of this domain bind iron or another heavy metal, but the exact function is unknown. Not surprisingly, the prokaryote with the most instances of this domain is Magnetococcus sp. MC-1, a magnetotactic bacterium.
Probab=67.34 E-value=87 Score=31.01 Aligned_cols=109 Identities=17% Similarity=0.288 Sum_probs=68.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcccCCcccHHHHHHHHHHHHHHHHhhhhccccch----hhhhhhhhhhHHhHHHHHHH
Q 001043 297 IMLWHNAIKRELNDIAEAARKIQLSGDFSDLSAFNKRLQFIAEVCIFHSIAEDKVI----FPAVDVELSFAQEHAEEEIQ 372 (1177)
Q Consensus 297 l~~~HkALRrEL~~L~~~a~~i~~~gd~~~L~~L~~r~~fl~~vl~~Hs~aEDevl----FPaL~~r~~me~EH~~ie~l 372 (1177)
+=.-|+.|=..++.+.+.+.. + .....+...+.+|.+....|-..|+.++ ||.+..+. .+|+ ..
T Consensus 13 ID~qH~~l~~~in~l~~a~~~----~--~~~~~~~~~l~~L~~y~~~HF~~EE~~M~~~~yp~~~~H~---~~H~---~~ 80 (126)
T TIGR02481 13 IDAQHKELFELINELYDALSA----G--NGKDELKEILDELIDYTENHFADEEELMEEYGYPDLEEHK---KEHE---KF 80 (126)
T ss_pred HHHHHHHHHHHHHHHHHHHHc----C--CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHH---HHHH---HH
Confidence 335688777777777776543 1 1245677778888999999999998765 77776543 3444 44
Q ss_pred HHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 001043 373 FDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPL 424 (1177)
Q Consensus 373 ~e~l~~ll~~~~~~~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qvfPL 424 (1177)
++.+..+...+... .. ..... ..+..+.+-|..|+..+-..+.+.
T Consensus 81 l~~l~~l~~~~~~~-~~---~~~~~---~~~~~l~~Wl~~HI~~~D~~~~~~ 125 (126)
T TIGR02481 81 VKKIEELQEAVAEG-AD---ESLAE---ELLDFLKDWLVNHILKEDKKYAPY 125 (126)
T ss_pred HHHHHHHHHHHHcC-Cc---hhHHH---HHHHHHHHHHHHHhHHHhHHHHhh
Confidence 55555555444322 11 01222 344556778999999888776553
No 122
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=66.91 E-value=4 Score=42.46 Aligned_cols=47 Identities=26% Similarity=0.579 Sum_probs=39.5
Q ss_pred CcccceEeccccccccCCCCcccCCCCCccccCCCCCccccccCCcccccccc
Q 001043 1052 GLSMAKYYCGICKFFDDERVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLAKK 1104 (1177)
Q Consensus 1052 ~~~~a~Y~C~~C~l~dd~k~~yHC~~CgiCrvg~gl~~~~fhC~~C~~C~s~~ 1104 (1177)
+......||..|+.+-.. ..+||..||.|..+- -.||.=-|.|+...
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 456788899999999665 589999999999984 47999999998765
No 123
>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=66.82 E-value=1.9 Score=47.84 Aligned_cols=50 Identities=26% Similarity=0.570 Sum_probs=38.4
Q ss_pred CCCCcccccccccCCCceEec-C-CCCcccHhhHHHHHhc-CCCCC--CCccccc
Q 001043 1116 ETNCPICCDFLFTSSATVRAL-P-CGHFMHSDCFQAYTCS-HYICP--ICSKSLG 1165 (1177)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~L-p-CGH~fH~~Ci~~wl~~-~~~CP--iCrk~v~ 1165 (1177)
+..||||..+.|-+.+-.... | |=|-|+.+|++.-+.. ...|| -|.|.+.
T Consensus 10 d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kILR 64 (314)
T COG5220 10 DRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKILR 64 (314)
T ss_pred cccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHHH
Confidence 457999999877766533332 6 9999999999997654 57799 8988664
No 124
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=66.55 E-value=4.4 Score=46.05 Aligned_cols=15 Identities=20% Similarity=0.751 Sum_probs=9.1
Q ss_pred CCcccCCCCCccccC
Q 001043 1070 RVVYHCPFCNLCRVG 1084 (1177)
Q Consensus 1070 k~~yHC~~CgiCrvg 1084 (1177)
+..++|++||.=.|.
T Consensus 159 ~ka~~C~~C~K~YvS 173 (279)
T KOG2462|consen 159 KKAFSCKYCGKVYVS 173 (279)
T ss_pred cccccCCCCCceeee
Confidence 556666666655554
No 125
>PHA03096 p28-like protein; Provisional
Probab=65.92 E-value=3.2 Score=47.70 Aligned_cols=46 Identities=15% Similarity=0.220 Sum_probs=30.3
Q ss_pred CCCcccccccccCC---CceEec-CCCCcccHhhHHHHHhc---CCCCCCCcc
Q 001043 1117 TNCPICCDFLFTSS---ATVRAL-PCGHFMHSDCFQAYTCS---HYICPICSK 1162 (1177)
Q Consensus 1117 ~~CpICle~lf~s~---~~v~~L-pCGH~fH~~Ci~~wl~~---~~~CPiCrk 1162 (1177)
..|.||+|...... ..-..| .|.|.|...|+..|... .-+||.||.
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~ 231 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRR 231 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCccccc
Confidence 57999998765431 111234 89999999999999643 233555544
No 126
>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=65.69 E-value=4.7 Score=49.85 Aligned_cols=48 Identities=23% Similarity=0.632 Sum_probs=41.1
Q ss_pred ccccccCCcccCcccccccCCCCCCccccceeeccccCccccCCCCCCCCCCCC
Q 001043 999 LRAACCGKLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVGPVCTTLSCSG 1052 (1177)
Q Consensus 999 l~~~cC~k~y~Cr~CHde~~~H~~~r~~~~~~~C~~C~~~q~~~~~C~~~~C~~ 1052 (1177)
+.|.-||....|..|.-...-|.- ...+.|-.|+..+++...|.+ |++
T Consensus 214 ~~C~~Cg~~~~C~~C~~~l~~h~~----~~~l~Ch~Cg~~~~~~~~Cp~--C~s 261 (505)
T TIGR00595 214 LLCRSCGYILCCPNCDVSLTYHKK----EGKLRCHYCGYQEPIPKTCPQ--CGS 261 (505)
T ss_pred eEhhhCcCccCCCCCCCceEEecC----CCeEEcCCCcCcCCCCCCCCC--CCC
Confidence 789999999999999887777743 458999999999999999976 743
No 127
>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=65.12 E-value=3.4 Score=42.07 Aligned_cols=19 Identities=26% Similarity=0.315 Sum_probs=16.2
Q ss_pred ccccCCCCcccCCCCCccc
Q 001043 1064 KFFDDERVVYHCPFCNLCR 1082 (1177)
Q Consensus 1064 ~l~dd~k~~yHC~~CgiCr 1082 (1177)
||||-.|.+..||+||.=.
T Consensus 18 kFYDLnk~p~vcP~cg~~~ 36 (129)
T TIGR02300 18 KFYDLNRRPAVSPYTGEQF 36 (129)
T ss_pred cccccCCCCccCCCcCCcc
Confidence 6888889999999999653
No 128
>PF02084 Bindin: Bindin; InterPro: IPR000775 Bindin, the major protein component of the acrosome granule of sea urchin sperm, mediates species-specific adhesion of sperm to the egg surface during fertilisation [, ]. The protein coats the acrosomal process after externalisation by the acrosome reaction; it binds to sulphated, fucose-containing polysaccharides on the vitelline-layer receptor proteoglycans that cover the egg plasma membrane. Bindins from different genera show high levels of sequence similarity in both the mature bindin domain and in the probindin precursor region. The most highly conserved region is a 42-residue segment in the central portion of the mature bindin protein. This domain may be responsible for conserved functions of bindin, while the more highly divergent flanking regions may be responsible for its species-specific properties [].; GO: 0007342 fusion of sperm to egg plasma membrane
Probab=64.96 E-value=21 Score=39.60 Aligned_cols=40 Identities=28% Similarity=0.385 Sum_probs=26.6
Q ss_pred CCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHHHh-----hh-HHHHHHHhhhhhHHH
Q 001043 72 LGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIR-----VK-NIARTYSLEHEGESV 127 (1177)
Q Consensus 72 ~~d~~~~~~l~~r~~~L~~~~~~H~~aEDevI~PaL~~R-----v~-~v~~~~~~EH~~~~~ 127 (1177)
+.|+=++.-|++| ||||++ |.+. |+ -|+.+|..|-++++.
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 4777777766655 578988 4444 34 488999887665554
No 129
>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=64.77 E-value=4.5 Score=49.81 Aligned_cols=14 Identities=36% Similarity=0.933 Sum_probs=7.8
Q ss_pred CcccceEecccccc
Q 001043 1052 GLSMAKYYCGICKF 1065 (1177)
Q Consensus 1052 ~~~~a~Y~C~~C~l 1065 (1177)
..++-.|||+.|-+
T Consensus 21 ~~Ei~~~yCp~CL~ 34 (483)
T PF05502_consen 21 SEEIDSYYCPNCLF 34 (483)
T ss_pred ccccceeECccccc
Confidence 44555666666643
No 130
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=64.07 E-value=2.9 Score=53.26 Aligned_cols=44 Identities=30% Similarity=0.720 Sum_probs=35.3
Q ss_pred CCCcccccccccCCCceEecCCCCcccHhhHHHHHhc--CCCCCCCccccc
Q 001043 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS--HYICPICSKSLG 1165 (1177)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~--~~~CPiCrk~v~ 1165 (1177)
..|+||++ .+.....+|||.|..+|+.+.+.. ...||+||..+.
T Consensus 455 ~~c~ic~~-----~~~~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~ 500 (674)
T KOG1001|consen 455 HWCHICCD-----LDSFFITRCGHDFCVECLKKSIQQSENAPCPLCRNVLK 500 (674)
T ss_pred cccccccc-----cccceeecccchHHHHHHHhccccccCCCCcHHHHHHH
Confidence 78999998 234667899999999999998643 346999998764
No 131
>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]
Probab=62.55 E-value=2.8 Score=53.20 Aligned_cols=88 Identities=13% Similarity=0.053 Sum_probs=60.3
Q ss_pred HHHHHHHHhHHHHHH-----HHHHHHHhhCCHHHHHHHHHhHhhcCCHHHHHHHHhhhcCCCCHHHHHHHHHHhhhhCCC
Q 001043 405 LIMASIQKHFRNEEV-----QVLPLARRHFSPKRQRELLYQSLCVMPLKLIECVLPWLVGSLSEEEARSFLQNIYMAAPA 479 (1177)
Q Consensus 405 ~L~~~L~~Hf~~EE~-----qvfPLl~~~fS~eEq~eL~~~~l~smPl~~L~~vLPWl~~~Ls~~E~~~~L~~l~~~aP~ 479 (1177)
.+-...-.|+..|++ -+.|.+=.. +.+||+..+.+|.-.--+..+.-+||=.-+.|.|.-...+|.-.=. |-
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 344444333 4578999888888777777888888888888999999888876554 54
Q ss_pred ChhHHHHHHHHhhhcCC
Q 001043 480 SDSALITLFAGWACKGH 496 (1177)
Q Consensus 480 ~~~~~~~l~~~w~~~~~ 496 (1177)
.+. |-.+++.|-+.-|
T Consensus 470 ~~~-F~e~i~~Wp~~Ly 485 (846)
T KOG2066|consen 470 VKG-FLELIKEWPGHLY 485 (846)
T ss_pred HHH-HHHHHHhCChhhh
Confidence 554 8888999954444
No 132
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=62.18 E-value=7.3 Score=52.21 Aligned_cols=52 Identities=23% Similarity=0.427 Sum_probs=26.5
Q ss_pred eeeccccCccccCCCCCCCCCCCCcccceEeccccccc--cCCCCcccCCCCCcccc
Q 001043 1029 EMMCMRCLKVQPVGPVCTTLSCSGLSMAKYYCGICKFF--DDERVVYHCPFCNLCRV 1083 (1177)
Q Consensus 1029 ~~~C~~C~~~q~~~~~C~~~~C~~~~~a~Y~C~~C~l~--dd~k~~yHC~~CgiCrv 1083 (1177)
...|..|+++-+. ..|.. |+...-..|+|..|+.- .|+....+||+||.=.+
T Consensus 667 ~rkCPkCG~~t~~-~fCP~--CGs~te~vy~CPsCGaev~~des~a~~CP~CGtplv 720 (1337)
T PRK14714 667 RRRCPSCGTETYE-NRCPD--CGTHTEPVYVCPDCGAEVPPDESGRVECPRCDVELT 720 (1337)
T ss_pred EEECCCCCCcccc-ccCcc--cCCcCCCceeCccCCCccCCCccccccCCCCCCccc
Confidence 3455555554332 25544 43222345666666652 12223667888885443
No 133
>PRK00808 hypothetical protein; Provisional
Probab=61.91 E-value=26 Score=36.40 Aligned_cols=96 Identities=19% Similarity=0.197 Sum_probs=57.0
Q ss_pred hhHHhHHHHHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHH----HHHHHhhCCH-----
Q 001043 361 SFAQEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQV----LPLARRHFSP----- 431 (1177)
Q Consensus 361 ~me~EH~~ie~l~e~l~~ll~~~~~~~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qv----fPLl~~~fS~----- 431 (1177)
.+..+|++.-.+++.|..++.. .+ ...+...+..|.+-...||..||.-. +|-+..|--.
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 5667888777777776655521 11 24577778899999999999999753 4444443221
Q ss_pred HHHHHHHHhHhh--cCCHHHHHHHHhhhcCCCCHHHHH
Q 001043 432 KRQRELLYQSLC--VMPLKLIECVLPWLVGSLSEEEAR 467 (1177)
Q Consensus 432 eEq~eL~~~~l~--smPl~~L~~vLPWl~~~Ls~~E~~ 467 (1177)
++..++..++.. .+...++..+..||+.++.-..++
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 134
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=61.63 E-value=1.9 Score=57.27 Aligned_cols=70 Identities=10% Similarity=0.031 Sum_probs=48.1
Q ss_pred hHHHHHHHHHHHHHHHHHHhHHHHHHHhhhHHHhhCCHHHHHHHHHHHhhcCCHHHHHHHHhhhcCCCCH
Q 001043 145 SYRRELASCTGALQTSISQHMSKEEEQVFPLLIEKFSFEEQASLVWQFLCSIPVNMMAEFLPWLSSSISS 214 (1177)
Q Consensus 145 ~~~~eLa~~l~~l~~~l~qHm~~EE~~v~PLl~~~fS~~E~a~L~~~~i~siP~~~m~~~LpWm~~~lsp 214 (1177)
++..-+-.-+.-.+-....||--+|.+..-.=...+|..+-.++...|.-++|..-...-.+....++++
T Consensus 237 D~~~~~~~~~r~~~~r~~~~~~~~~~e~~~~s~~~It~~~~~di~~~~~~~l~~~~~~~~~~l~~e~l~~ 306 (1394)
T KOG0298|consen 237 DLIKRFQSQLRKYQQRTVSWMPSREQEYTQVSANFITLHLIDDITRVFKLKLCFQFYSFEEELPKESLSP 306 (1394)
T ss_pred hHHHHhhhhccHHHHHHHHhccccchhhhhccccccccccccchHHHhhhccceecccccccchhccCCC
Confidence 4444444445555556677888777776655566678888889999998888887666655666666666
No 135
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=60.94 E-value=2.9 Score=52.12 Aligned_cols=29 Identities=31% Similarity=0.595 Sum_probs=23.1
Q ss_pred CCcccccc----ccccccccCCcccCcccccccC
Q 001043 989 GCEHYKRN----CKLRAACCGKLFTCRFCHDKVS 1018 (1177)
Q Consensus 989 gC~HY~r~----c~l~~~cC~k~y~Cr~CHde~~ 1018 (1177)
||.||--. +.-.|.-+|+|| |..||....
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 78888773 557788999977 999998854
No 136
>COG5592 Uncharacterized conserved protein [Function unknown]
Probab=60.13 E-value=31 Score=36.75 Aligned_cols=94 Identities=17% Similarity=0.160 Sum_probs=67.3
Q ss_pred HHHHHHHHHHHHHHhhhhccccchhhhhhhhh--------------hhHHhHHHHHHHHHHHHHHHHHHHhcCCCCChHH
Q 001043 329 AFNKRLQFIAEVCIFHSIAEDKVIFPAVDVEL--------------SFAQEHAEEEIQFDKLRCLIESIQSAGANSSTAE 394 (1177)
Q Consensus 329 ~L~~r~~fl~~vl~~Hs~aEDevlFPaL~~r~--------------~me~EH~~ie~l~e~l~~ll~~~~~~~~~~~~~~ 394 (1177)
.+.+-..|...+.+.|-.-|.+.+||+.-... ++..+|..|+-+.+.+...- +.
T Consensus 29 e~le~~gf~~k~~k~h~e~Ee~ilF~v~Vd~~~ed~~~fkdt~~~~~i~~DHkliE~l~tnlik~k--------R~---- 96 (171)
T COG5592 29 EILEFEGFNEKLGKDHVELEEKILFPVIVDADMEDLYVFKDTPEVDRIKNDHKLIETLATNLIKWK--------RP---- 96 (171)
T ss_pred HHHhhcchHHHHhhhHHHHHHHhhhhhccchHHHHHHhhhccchhhHhHhhHHHHHHHHHHHHhhc--------cc----
Confidence 33344448899999999999999999864211 77889998888777654321 11
Q ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhhCCHHHHHH
Q 001043 395 FYTKLCSQADLIMASIQKHFRNEEVQVLPLARRHFSPKRQRE 436 (1177)
Q Consensus 395 ~~~eLa~~le~L~~~L~~Hf~~EE~qvfPLl~~~fS~eEq~e 436 (1177)
++.-.-+...+.+|++|=..||..+||-+...--..||.+
T Consensus 97 --~k~~e~~p~fyK~LtdHn~aEE~~IfPrvks~~~E~~~~~ 136 (171)
T COG5592 97 --DKIKERVPLFYKTLTDHNLAEEEYIFPRVKSLKGEDEQSA 136 (171)
T ss_pred --hHHHHHHHHHHHHHHHccccccchhhHHHHhhcchhhHHH
Confidence 2344566777999999999999999998776654434433
No 137
>KOG2068 consensus MOT2 transcription factor [Transcription]
Probab=60.03 E-value=6.9 Score=45.61 Aligned_cols=50 Identities=26% Similarity=0.570 Sum_probs=39.0
Q ss_pred CCCCCcccccccccCCCceEecCCCCcccHhhHHHHHhcCCCCCCCcccc
Q 001043 1115 LETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSL 1164 (1177)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrk~v 1164 (1177)
....||||-+++...+....--|||+.++..|...-...+.+||.||+..
T Consensus 248 v~~s~p~~~~~~~~~d~~~lP~~~~~~~~l~~~~t~~~~~~~~~~~rk~~ 297 (327)
T KOG2068|consen 248 VPPSCPICYEDLDLTDSNFLPCPCGFRLCLFCHKTISDGDGRCPGCRKPY 297 (327)
T ss_pred cCCCCCCCCCcccccccccccccccccchhhhhhcccccCCCCCccCCcc
Confidence 35689999998644444444458899999999988888899999999654
No 138
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=59.47 E-value=9.2 Score=33.66 Aligned_cols=35 Identities=26% Similarity=0.606 Sum_probs=27.6
Q ss_pred CCCCCcccccccccCCCceEecCCCCcccHhhHHH
Q 001043 1115 LETNCPICCDFLFTSSATVRALPCGHFMHSDCFQA 1149 (1177)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~ 1149 (1177)
....|++|.+.+...++.|+---||=.+|+.|...
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~ 38 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK 38 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence 45689999999655666666679999999999543
No 139
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=59.01 E-value=7.8 Score=34.67 Aligned_cols=45 Identities=29% Similarity=0.822 Sum_probs=29.5
Q ss_pred eeeccccCccccCCC-----CCCCCCCCCcccceEeccccccccCCCCcccCCCCCc
Q 001043 1029 EMMCMRCLKVQPVGP-----VCTTLSCSGLSMAKYYCGICKFFDDERVVYHCPFCNL 1080 (1177)
Q Consensus 1029 ~~~C~~C~~~q~~~~-----~C~~~~C~~~~~a~Y~C~~C~l~dd~k~~yHC~~Cgi 1080 (1177)
...|..|+.+-.+.+ .|-| | | ..-=|-|..|+-.. .+|.||+||+
T Consensus 9 ~~~CtSCg~~i~p~e~~v~F~CPn--C-G-e~~I~Rc~~CRk~g---~~Y~Cp~CGF 58 (61)
T COG2888 9 PPVCTSCGREIAPGETAVKFPCPN--C-G-EVEIYRCAKCRKLG---NPYRCPKCGF 58 (61)
T ss_pred CceeccCCCEeccCCceeEeeCCC--C-C-ceeeehhhhHHHcC---CceECCCcCc
Confidence 467888888775443 4655 5 4 22346677777664 4688888885
No 140
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=58.33 E-value=5.5 Score=45.44 Aligned_cols=43 Identities=30% Similarity=0.795 Sum_probs=34.4
Q ss_pred CCCcccccccccCCCceEecCCCCcccHhhHHHH-HhcCCCCCCCcc
Q 001043 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAY-TCSHYICPICSK 1162 (1177)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~w-l~~~~~CPiCrk 1162 (1177)
..||.|.--+ +.+++.--|||.|..+||..- +...+.||.|.+
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 5799998643 456666678999999999976 467799999987
No 141
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=58.33 E-value=5.1 Score=44.12 Aligned_cols=39 Identities=38% Similarity=0.791 Sum_probs=28.5
Q ss_pred CcccccccccCCCceEecCCCCc-ccHhhHHHHHhcCCCCCCCccccc
Q 001043 1119 CPICCDFLFTSSATVRALPCGHF-MHSDCFQAYTCSHYICPICSKSLG 1165 (1177)
Q Consensus 1119 CpICle~lf~s~~~v~~LpCGH~-fH~~Ci~~wl~~~~~CPiCrk~v~ 1165 (1177)
|-.|.+. ...|..+||.|. +...|-.. -.+||+|+....
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 8888775 345888999976 66788533 456999998664
No 142
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=57.61 E-value=4.8 Score=42.41 Aligned_cols=30 Identities=30% Similarity=0.587 Sum_probs=24.8
Q ss_pred CCCCCCcccccccccCCCceEecCCCCcccH
Q 001043 1114 GLETNCPICCDFLFTSSATVRALPCGHFMHS 1144 (1177)
Q Consensus 1114 ~~~~~CpICle~lf~s~~~v~~LpCGH~fH~ 1144 (1177)
....+|.||+|+| ..++.+..|||==+||+
T Consensus 175 ddkGECvICLEdL-~~GdtIARLPCLCIYHK 204 (205)
T KOG0801|consen 175 DDKGECVICLEDL-EAGDTIARLPCLCIYHK 204 (205)
T ss_pred ccCCcEEEEhhhc-cCCCceeccceEEEeec
Confidence 3467899999996 56778999999988886
No 143
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=57.36 E-value=8.9 Score=49.43 Aligned_cols=55 Identities=24% Similarity=0.529 Sum_probs=43.3
Q ss_pred cccccccCCcccCcccccccCCCCCCccccceeeccccCccccCCCCCCCCCCCCcccceEe
Q 001043 998 KLRAACCGKLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVGPVCTTLSCSGLSMAKYY 1059 (1177)
Q Consensus 998 ~l~~~cC~k~y~Cr~CHde~~~H~~~r~~~~~~~C~~C~~~q~~~~~C~~~~C~~~~~a~Y~ 1059 (1177)
-+.|..||-.+.|+.|=.-..=|.. +..+.|-.|+..+++-..|.+ | |...=+|+
T Consensus 435 ~l~C~~Cg~v~~Cp~Cd~~lt~H~~----~~~L~CH~Cg~~~~~p~~Cp~--C-gs~~L~~~ 489 (730)
T COG1198 435 LLLCRDCGYIAECPNCDSPLTLHKA----TGQLRCHYCGYQEPIPQSCPE--C-GSEHLRAV 489 (730)
T ss_pred eeecccCCCcccCCCCCcceEEecC----CCeeEeCCCCCCCCCCCCCCC--C-CCCeeEEe
Confidence 3899999999999999655555533 369999999999999999976 6 54544554
No 144
>PRK05580 primosome assembly protein PriA; Validated
Probab=57.13 E-value=7.8 Score=49.67 Aligned_cols=49 Identities=22% Similarity=0.598 Sum_probs=41.6
Q ss_pred cccccccCCcccCcccccccCCCCCCccccceeeccccCccccCCCCCCCCCCCC
Q 001043 998 KLRAACCGKLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVGPVCTTLSCSG 1052 (1177)
Q Consensus 998 ~l~~~cC~k~y~Cr~CHde~~~H~~~r~~~~~~~C~~C~~~q~~~~~C~~~~C~~ 1052 (1177)
-+.|.-||....|..|.-...-|.. ...+.|-.|+..+++...|.+ |++
T Consensus 381 ~~~C~~Cg~~~~C~~C~~~l~~h~~----~~~l~Ch~Cg~~~~~~~~Cp~--Cg~ 429 (679)
T PRK05580 381 FLLCRDCGWVAECPHCDASLTLHRF----QRRLRCHHCGYQEPIPKACPE--CGS 429 (679)
T ss_pred ceEhhhCcCccCCCCCCCceeEECC----CCeEECCCCcCCCCCCCCCCC--CcC
Confidence 3889999999999999888777743 458999999999999999977 744
No 145
>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=57.03 E-value=7.7 Score=30.45 Aligned_cols=24 Identities=38% Similarity=1.089 Sum_probs=19.0
Q ss_pred eEeccccccc-cCCCCcccCCCCCc
Q 001043 1057 KYYCGICKFF-DDERVVYHCPFCNL 1080 (1177)
Q Consensus 1057 ~Y~C~~C~l~-dd~k~~yHC~~Cgi 1080 (1177)
.|-|.+|.+. +.++.++.||.||.
T Consensus 1 ~~~C~~CGy~y~~~~~~~~CP~Cg~ 25 (33)
T cd00350 1 KYVCPVCGYIYDGEEAPWVCPVCGA 25 (33)
T ss_pred CEECCCCCCEECCCcCCCcCcCCCC
Confidence 4789999775 55578999999985
No 146
>PF14357 DUF4404: Domain of unknown function (DUF4404)
Probab=56.20 E-value=80 Score=30.21 Aligned_cols=82 Identities=13% Similarity=0.095 Sum_probs=65.0
Q ss_pred HHHHHHHHHHHHHHhccCCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHHHhhhHHHHHHHhhhhhHHHHHHHHH
Q 001043 54 IKSELDVLHRAAMAFATNLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIRVKNIARTYSLEHEGESVLFDQLF 133 (1177)
Q Consensus 54 lR~el~~l~~~~~~~~~~~~d~~~~~~l~~r~~~L~~~~~~H~~aEDevI~PaL~~Rv~~v~~~~~~EH~~~~~lf~~l~ 133 (1177)
||..|..|+.-+...++ -|......|..=-+.+...+.. ..|.+.--+.|..|+...+.+++.+|=.....+..|-
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 6666666666666666666655 5677788999999999999999999999999988887
Q ss_pred HHHHhh
Q 001043 134 ELLNSS 139 (1177)
Q Consensus 134 ~~l~~~ 139 (1177)
..|..+
T Consensus 78 ~sLa~M 83 (85)
T PF14357_consen 78 DSLANM 83 (85)
T ss_pred HHHHHC
Confidence 777553
No 147
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=55.47 E-value=7.4 Score=45.23 Aligned_cols=46 Identities=17% Similarity=0.345 Sum_probs=34.3
Q ss_pred CCCCcccccccccCCCceEecCCCCcccHhhHHHHHhcCCCCCCCcccc
Q 001043 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSL 1164 (1177)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrk~v 1164 (1177)
...||||+...- ++.+.--=|=+|+..|+..|+.+..+||+=.+++
T Consensus 300 ~~~CpvClk~r~---Nptvl~vSGyVfCY~Ci~~Yv~~~~~CPVT~~p~ 345 (357)
T KOG0826|consen 300 REVCPVCLKKRQ---NPTVLEVSGYVFCYPCIFSYVVNYGHCPVTGYPA 345 (357)
T ss_pred cccChhHHhccC---CCceEEecceEEeHHHHHHHHHhcCCCCccCCcc
Confidence 567999996532 2222223499999999999999999999876654
No 148
>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=54.07 E-value=11 Score=45.57 Aligned_cols=31 Identities=23% Similarity=0.356 Sum_probs=19.4
Q ss_pred HHHHHHHhhhccCCCCChHHHHHHHHHHHHHHH
Q 001043 920 NELEAEIRKVSRDSTLDPRRKAYLIQNLMTSRW 952 (1177)
Q Consensus 920 ~~L~~~Ir~i~~~~~l~~~~k~~~~q~l~~~~~ 952 (1177)
..|+..||.|--. .+.+..-...|+++-.|-
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 3577778887754 444455566777765554
No 149
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=53.70 E-value=5.6 Score=38.94 Aligned_cols=33 Identities=21% Similarity=0.637 Sum_probs=27.2
Q ss_pred CCcccCCCCC-----ccccCCCCCccccccCCcccccc
Q 001043 1070 RVVYHCPFCN-----LCRVGRGLGVDFFHCMTCNCCLA 1102 (1177)
Q Consensus 1070 k~~yHC~~Cg-----iCrvg~gl~~~~fhC~~C~~C~s 1102 (1177)
+..|-||.|| +|.|.+++++-+-+|..||.-..
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 4578899998 89999888888999999987553
No 150
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=53.48 E-value=5.9 Score=45.08 Aligned_cols=51 Identities=22% Similarity=0.546 Sum_probs=37.5
Q ss_pred CCCCcccccccccCCCceEecCCC-----CcccHhhHHHHHh--cCCCCCCCcccccc
Q 001043 1116 ETNCPICCDFLFTSSATVRALPCG-----HFMHSDCFQAYTC--SHYICPICSKSLGD 1166 (1177)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCG-----H~fH~~Ci~~wl~--~~~~CPiCrk~v~d 1166 (1177)
+..|=||.+............||. .+.|..|++.|+. .+.+|.+|......
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 467999998754432223456774 7889999999986 56789999986554
No 151
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=53.47 E-value=10 Score=44.32 Aligned_cols=26 Identities=19% Similarity=0.734 Sum_probs=19.9
Q ss_pred CcccceEe--ccccccccCCCCcccCCCCCc
Q 001043 1052 GLSMAKYY--CGICKFFDDERVVYHCPFCNL 1080 (1177)
Q Consensus 1052 ~~~~a~Y~--C~~C~l~dd~k~~yHC~~Cgi 1080 (1177)
...|--|| |.||++++. .|.||+||+
T Consensus 60 ~~dfeL~f~Ge~i~~y~~q---SftCPyC~~ 87 (381)
T KOG1280|consen 60 RVDFELYFGGEPISHYDPQ---SFTCPYCGI 87 (381)
T ss_pred ccceeeEecCccccccccc---cccCCcccc
Confidence 44566666 788887755 899999996
No 152
>PRK14873 primosome assembly protein PriA; Provisional
Probab=52.90 E-value=9.8 Score=48.69 Aligned_cols=47 Identities=26% Similarity=0.461 Sum_probs=38.2
Q ss_pred ccccccCCcccCcccccccCCCCCCccccceeeccccCccccCCCCCCCCCCCC
Q 001043 999 LRAACCGKLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVGPVCTTLSCSG 1052 (1177)
Q Consensus 999 l~~~cC~k~y~Cr~CHde~~~H~~~r~~~~~~~C~~C~~~q~~~~~C~~~~C~~ 1052 (1177)
+.|..||....|..|.-...=|. ....+.|-.|+..+ +...|.+ |++
T Consensus 384 l~C~~Cg~~~~C~~C~~~L~~h~----~~~~l~Ch~CG~~~-~p~~Cp~--Cgs 430 (665)
T PRK14873 384 LACARCRTPARCRHCTGPLGLPS----AGGTPRCRWCGRAA-PDWRCPR--CGS 430 (665)
T ss_pred eEhhhCcCeeECCCCCCceeEec----CCCeeECCCCcCCC-cCccCCC--CcC
Confidence 89999999999999988877664 24589999999976 5789976 743
No 153
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=52.37 E-value=7.8 Score=38.60 Aligned_cols=32 Identities=25% Similarity=0.517 Sum_probs=23.9
Q ss_pred ccccccccCCcccCcccccccCCCCCCccccceeeccccCccccCC
Q 001043 997 CKLRAACCGKLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVG 1042 (1177)
Q Consensus 997 c~l~~~cC~k~y~Cr~CHde~~~H~~~r~~~~~~~C~~C~~~q~~~ 1042 (1177)
-|-.||-||+-| .+... ..|+|.+|+++|++.
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 456789998743 34333 579999999999887
No 154
>PRK00808 hypothetical protein; Provisional
Probab=50.17 E-value=3.1e+02 Score=28.42 Aligned_cols=110 Identities=16% Similarity=0.228 Sum_probs=71.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcccCCcccHHHHHHHHHHHHHHHHhhhhccccch----hhhhhhhhhhHHhHHHHHHH
Q 001043 297 IMLWHNAIKRELNDIAEAARKIQLSGDFSDLSAFNKRLQFIAEVCIFHSIAEDKVI----FPAVDVELSFAQEHAEEEIQ 372 (1177)
Q Consensus 297 l~~~HkALRrEL~~L~~~a~~i~~~gd~~~L~~L~~r~~fl~~vl~~Hs~aEDevl----FPaL~~r~~me~EH~~ie~l 372 (1177)
+=.-|+.|=.-++.|...+. .++ ...+..-+.+|.+....|=..|+.++ ||.++.+. .+++..
T Consensus 17 ID~qH~~L~~lin~l~~a~~----~~~---~~~i~~~l~~L~~y~~~HF~~EE~lM~~~~Yp~~~~H~------~~H~~f 83 (150)
T PRK00808 17 IDQQHKRIVDYINHLHDAQD----SPD---RLAVAEVIDELIDYTLSHFAFEESLMEEAGYPFLVPHK------RVHELF 83 (150)
T ss_pred HHHHHHHHHHHHHHHHHHHH----cCc---HHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHH------HHHHHH
Confidence 33467777666666665542 222 24566668888999999999898764 77776444 333444
Q ss_pred HHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhh
Q 001043 373 FDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPLARRH 428 (1177)
Q Consensus 373 ~e~l~~ll~~~~~~~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qvfPLl~~~ 428 (1177)
++.+..+...... +. ... ...+.-|..-|.+|+..+-....+.+.+.
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 155
>PRK04023 DNA polymerase II large subunit; Validated
Probab=49.93 E-value=14 Score=48.58 Aligned_cols=48 Identities=21% Similarity=0.351 Sum_probs=30.2
Q ss_pred ceeeccccCccccCCCCCCCCCCCCcccceEeccccccccCCCCcccCCCCCcc
Q 001043 1028 TEMMCMRCLKVQPVGPVCTTLSCSGLSMAKYYCGICKFFDDERVVYHCPFCNLC 1081 (1177)
Q Consensus 1028 ~~~~C~~C~~~q~~~~~C~~~~C~~~~~a~Y~C~~C~l~dd~k~~yHC~~CgiC 1081 (1177)
..-.|..|+++. +...|.+ |+.....-|+|+.|.-- -..|.||.||.=
T Consensus 625 g~RfCpsCG~~t-~~frCP~--CG~~Te~i~fCP~CG~~---~~~y~CPKCG~E 672 (1121)
T PRK04023 625 GRRKCPSCGKET-FYRRCPF--CGTHTEPVYRCPRCGIE---VEEDECEKCGRE 672 (1121)
T ss_pred cCccCCCCCCcC-CcccCCC--CCCCCCcceeCccccCc---CCCCcCCCCCCC
Confidence 455788888875 4567866 64444566777777322 334667777743
No 156
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=48.89 E-value=6.3 Score=49.31 Aligned_cols=46 Identities=22% Similarity=0.571 Sum_probs=29.0
Q ss_pred CCCCcccccccccCCCceEecCCCC---cccHhhHHHHH--------hcCCCCCCCcc
Q 001043 1116 ETNCPICCDFLFTSSATVRALPCGH---FMHSDCFQAYT--------CSHYICPICSK 1162 (1177)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCGH---~fH~~Ci~~wl--------~~~~~CPiCrk 1162 (1177)
-..||+|+-. |...+....+.|.| ..|-.|..-.. ...|.|-+||-
T Consensus 145 ~~~cPvc~~~-Y~~~e~~~~~~c~~c~rwsh~~c~~~sdd~~~q~~vD~~~~CS~CR~ 201 (694)
T KOG4443|consen 145 LSYCPVCLIV-YQDSESLPMVCCSICQRWSHGGCDGISDDKYMQAQVDLQYKCSTCRG 201 (694)
T ss_pred cccCchHHHh-hhhccchhhHHHHHhcccccCCCCccchHHHHHHhhhhhcccceeeh
Confidence 4679999865 44444444444544 47888865332 23689999993
No 157
>PRK01917 cation-binding hemerythrin HHE family protein; Provisional
Probab=48.08 E-value=47 Score=34.15 Aligned_cols=70 Identities=13% Similarity=0.159 Sum_probs=38.9
Q ss_pred HHHHHHHHHHHHHHHhHHHHHHHH----HHHHHhhCCH-----HHHHHHHHhHhh----cCCHHHHHHHHhhhcCCCCHH
Q 001043 398 KLCSQADLIMASIQKHFRNEEVQV----LPLARRHFSP-----KRQRELLYQSLC----VMPLKLIECVLPWLVGSLSEE 464 (1177)
Q Consensus 398 eLa~~le~L~~~L~~Hf~~EE~qv----fPLl~~~fS~-----eEq~eL~~~~l~----smPl~~L~~vLPWl~~~Ls~~ 464 (1177)
.+...++.|..-...||..||.-. +|-+..|--. ++..++..+... .+...++..+..||+.++.-.
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 3433333211 112222222211 233444555667777776655
Q ss_pred HHH
Q 001043 465 EAR 467 (1177)
Q Consensus 465 E~~ 467 (1177)
.++
T Consensus 118 D~~ 120 (139)
T PRK01917 118 DAM 120 (139)
T ss_pred HHH
Confidence 543
No 158
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=46.50 E-value=11 Score=43.58 Aligned_cols=32 Identities=31% Similarity=0.855 Sum_probs=23.6
Q ss_pred EecCCCCcccHhhHHHHHhcCCCCCCCccccccc
Q 001043 1134 RALPCGHFMHSDCFQAYTCSHYICPICSKSLGDM 1167 (1177)
Q Consensus 1134 ~~LpCGH~fH~~Ci~~wl~~~~~CPiCrk~v~dm 1167 (1177)
+.+||.|+|+.+|... .....||.|.-.|..+
T Consensus 105 RmIPCkHvFCl~CAr~--~~dK~Cp~C~d~VqrI 136 (389)
T KOG2932|consen 105 RMIPCKHVFCLECARS--DSDKICPLCDDRVQRI 136 (389)
T ss_pred cccccchhhhhhhhhc--CccccCcCcccHHHHH
Confidence 5679999999999743 2345799998766543
No 159
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=46.30 E-value=13 Score=47.46 Aligned_cols=59 Identities=19% Similarity=0.436 Sum_probs=39.8
Q ss_pred CCCCCcccccccccCCCceEecCCC-----CcccHhhHHHHHhcC--CCCCCCcccccccccccCCCC
Q 001043 1115 LETNCPICCDFLFTSSATVRALPCG-----HFMHSDCFQAYTCSH--YICPICSKSLGDMAVLHLPIP 1175 (1177)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~LpCG-----H~fH~~Ci~~wl~~~--~~CPiCrk~v~dm~~~~~~~~ 1175 (1177)
....|-||.-+ -..+++ -.-||. -++|.+|+.+|+..+ ..|-+|...+.=-+.|=..||
T Consensus 11 d~~~CRICr~e-~~~d~p-LfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~Fk~IY~e~mP 76 (1175)
T COG5183 11 DKRSCRICRTE-DIRDDP-LFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKFKDIYKEDMP 76 (1175)
T ss_pred cchhceeecCC-CCCCCc-CcccccccchhHHHHHHHHHHHHhcCCCcceeeecceeeeeeecccCCC
Confidence 44679999855 222222 223664 679999999999654 569999998765555555555
No 160
>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=45.53 E-value=20 Score=30.80 Aligned_cols=41 Identities=34% Similarity=0.874 Sum_probs=20.6
Q ss_pred CCCcccccccccCCCceEecCCCCcccHhhHHH--HHhc-----CCCCCCCccc
Q 001043 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQA--YTCS-----HYICPICSKS 1163 (1177)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~--wl~~-----~~~CPiCrk~ 1163 (1177)
-.|||....| ..+++...|.|. +||+- |+.. ...||+|.++
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 3699988775 457888889877 56653 5532 3569999874
No 161
>KOG3850 consensus Predicted membrane protein [Function unknown]
Probab=45.52 E-value=6.1e+02 Score=30.82 Aligned_cols=129 Identities=19% Similarity=0.247 Sum_probs=75.1
Q ss_pred HHHHHHHHHHHHHHHHHhcccCCcccH-HHHHHHHHHHHHHHHhhhhccccchhhhhhhhh--hhHHhHHHHHHHHHHHH
Q 001043 301 HNAIKRELNDIAEAARKIQLSGDFSDL-SAFNKRLQFIAEVCIFHSIAEDKVIFPAVDVEL--SFAQEHAEEEIQFDKLR 377 (1177)
Q Consensus 301 HkALRrEL~~L~~~a~~i~~~gd~~~L-~~L~~r~~fl~~vl~~Hs~aEDevlFPaL~~r~--~me~EH~~ie~l~e~l~ 377 (1177)
=+||..||++|.+.-..++ .+..+| .++..-+.|+.+.|. |+.+-.-.|++.+ ..+....+|..+=-++.
T Consensus 262 l~aileeL~eIk~~q~~Le--esye~Lke~~krdy~fi~etLQ-----EERyR~erLEEqLNdlteLqQnEi~nLKqEla 334 (455)
T KOG3850|consen 262 LDAILEELREIKETQALLE--ESYERLKEQIKRDYKFIAETLQ-----EERYRYERLEEQLNDLTELQQNEIANLKQELA 334 (455)
T ss_pred HHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHH
Confidence 4677788888888777764 334455 666666778877776 7777777776655 44444444433322222
Q ss_pred HHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH---HHHHhhCCHHHHHHHHHhHhhcC
Q 001043 378 CLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVL---PLARRHFSPKRQRELLYQSLCVM 445 (1177)
Q Consensus 378 ~ll~~~~~~~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qvf---PLl~~~fS~eEq~eL~~~~l~sm 445 (1177)
..-..+.= .-| +=+..+.+.+++...|+.+=|.+.- -+--++++++-|..|+.+++-.+
T Consensus 335 smeervaY--------Qsy-ERaRdIqEalEscqtrisKlEl~qq~qqv~Q~e~~~na~a~~llgk~iNii 396 (455)
T KOG3850|consen 335 SMEERVAY--------QSY-ERARDIQEALESCQTRISKLELQQQQQQVVQLEGLENAVARRLLGKFINII 396 (455)
T ss_pred HHHHHHHH--------HHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccHHHHHHHHHHHH
Confidence 11111100 001 1245566667777777777776544 22345677778888888777543
No 162
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=44.50 E-value=15 Score=42.57 Aligned_cols=45 Identities=22% Similarity=0.631 Sum_probs=34.1
Q ss_pred CCCcccccccccCCCceEecCCCCcccHhhHHHHHhc---CCCCCCCcc
Q 001043 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS---HYICPICSK 1162 (1177)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~---~~~CPiCrk 1162 (1177)
-.|||=.|. -+...+...|.|||.+-..-++..-+. .+.||.|-.
T Consensus 337 FiCPVlKe~-~t~ENpP~ml~CgHVIskeal~~LS~nG~~~FKCPYCP~ 384 (396)
T COG5109 337 FICPVLKEL-CTDENPPVMLECGHVISKEALSVLSQNGVLSFKCPYCPE 384 (396)
T ss_pred eeccccHhh-hcccCCCeeeeccceeeHHHHHHHhhcCcEEeeCCCCCc
Confidence 357776664 556667788999999999999887654 477999963
No 163
>PF12773 DZR: Double zinc ribbon
Probab=44.26 E-value=19 Score=30.24 Aligned_cols=22 Identities=27% Similarity=0.789 Sum_probs=11.9
Q ss_pred ccccCccccC-CCCCCCCCCCCcccc
Q 001043 1032 CMRCLKVQPV-GPVCTTLSCSGLSMA 1056 (1177)
Q Consensus 1032 C~~C~~~q~~-~~~C~~~~C~~~~~a 1056 (1177)
|..|+++.+. ...|.+ | |..+.
T Consensus 1 Cp~Cg~~~~~~~~fC~~--C-G~~l~ 23 (50)
T PF12773_consen 1 CPHCGTPNPDDAKFCPH--C-GTPLP 23 (50)
T ss_pred CCCcCCcCCccccCChh--h-cCChh
Confidence 5566665544 355665 4 55544
No 164
>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=43.60 E-value=92 Score=30.75 Aligned_cols=51 Identities=20% Similarity=0.232 Sum_probs=31.7
Q ss_pred hhHHhHHHHHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHH----HHHHHhh
Q 001043 361 SFAQEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQV----LPLARRH 428 (1177)
Q Consensus 361 ~me~EH~~ie~l~e~l~~ll~~~~~~~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qv----fPLl~~~ 428 (1177)
.+..+|++.-.+++.|..++.. ...+..|..-...||..||.-. +|-+..|
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 4455666655555555544422 2346677777899999999764 4555444
No 165
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=42.41 E-value=20 Score=30.00 Aligned_cols=23 Identities=30% Similarity=0.894 Sum_probs=11.2
Q ss_pred eEecccccc---ccCCCCcccCCCCC
Q 001043 1057 KYYCGICKF---FDDERVVYHCPFCN 1079 (1177)
Q Consensus 1057 ~Y~C~~C~l---~dd~k~~yHC~~Cg 1079 (1177)
.|-|..|.- +++.....+||+||
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG 28 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCG 28 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCC
Confidence 455555542 22223356666666
No 166
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=42.36 E-value=12 Score=44.93 Aligned_cols=36 Identities=25% Similarity=0.550 Sum_probs=26.5
Q ss_pred CCCCcccc-cccccCCCceEecCCCCcccHhhHHHHHh
Q 001043 1116 ETNCPICC-DFLFTSSATVRALPCGHFMHSDCFQAYTC 1152 (1177)
Q Consensus 1116 ~~~CpICl-e~lf~s~~~v~~LpCGH~fH~~Ci~~wl~ 1152 (1177)
...|.||. ++. ..........|||.|..+|..+++.
T Consensus 146 ~~~C~iC~~e~~-~~~~~f~~~~C~H~fC~~C~k~~ie 182 (384)
T KOG1812|consen 146 KEECGICFVEDP-EAEDMFSVLKCGHRFCKDCVKQHIE 182 (384)
T ss_pred cccCccCccccc-cHhhhHHHhcccchhhhHHhHHHhh
Confidence 46799999 543 2222233678999999999999975
No 167
>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=42.19 E-value=11 Score=34.75 Aligned_cols=9 Identities=33% Similarity=1.305 Sum_probs=5.7
Q ss_pred ceEeccccc
Q 001043 1056 AKYYCGICK 1064 (1177)
Q Consensus 1056 a~Y~C~~C~ 1064 (1177)
+.|||..|+
T Consensus 49 vdYFC~~c~ 57 (70)
T PF07191_consen 49 VDYFCNHCH 57 (70)
T ss_dssp EEEE-TTTT
T ss_pred cceeeccCC
Confidence 577777775
No 168
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=40.81 E-value=19 Score=45.96 Aligned_cols=32 Identities=28% Similarity=0.772 Sum_probs=16.0
Q ss_pred eeccccCccccCC-CCCCCCCCCCcccceEeccccc
Q 001043 1030 MMCMRCLKVQPVG-PVCTTLSCSGLSMAKYYCGICK 1064 (1177)
Q Consensus 1030 ~~C~~C~~~q~~~-~~C~~~~C~~~~~a~Y~C~~C~ 1064 (1177)
++|..|+.+-|.+ ..|.+ | |..+..-.|..|.
T Consensus 2 ~~Cp~Cg~~n~~~akFC~~--C-G~~l~~~~Cp~CG 34 (645)
T PRK14559 2 LICPQCQFENPNNNRFCQK--C-GTSLTHKPCPQCG 34 (645)
T ss_pred CcCCCCCCcCCCCCccccc--c-CCCCCCCcCCCCC
Confidence 3566666665443 34655 4 5555433444443
No 169
>COG0143 MetG Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=39.67 E-value=19 Score=45.21 Aligned_cols=45 Identities=24% Similarity=0.447 Sum_probs=35.6
Q ss_pred ccceEeccccccccCC-CCcccCCCCCccccCCCCCccccccCCcccccccc
Q 001043 1054 SMAKYYCGICKFFDDE-RVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLAKK 1104 (1177)
Q Consensus 1054 ~~a~Y~C~~C~l~dd~-k~~yHC~~CgiCrvg~gl~~~~fhC~~C~~C~s~~ 1104 (1177)
....+||..|.-|=.| .-.=.||+||.+..++ -+|+.||.++...
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 4667899999877665 4455799999999984 4899999998764
No 170
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=39.38 E-value=9.7 Score=39.54 Aligned_cols=26 Identities=27% Similarity=0.837 Sum_probs=19.7
Q ss_pred cceEeccccccccCCCCcccCCCCC--ccccC
Q 001043 1055 MAKYYCGICKFFDDERVVYHCPFCN--LCRVG 1084 (1177)
Q Consensus 1055 ~a~Y~C~~C~l~dd~k~~yHC~~Cg--iCrvg 1084 (1177)
-.+-||.+|.+| ++|-|-.|| +|-|+
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 455678888865 678888888 67776
No 171
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=39.36 E-value=14 Score=40.37 Aligned_cols=31 Identities=35% Similarity=0.881 Sum_probs=22.7
Q ss_pred ccCCCceEecCCCCcccHhhHHHHHhcCCCCCCCcc
Q 001043 1127 FTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSK 1162 (1177)
Q Consensus 1127 f~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrk 1162 (1177)
|.....++--.|+-.||..|+. ...||-|.+
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 266999965
No 172
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=39.33 E-value=13 Score=44.70 Aligned_cols=20 Identities=15% Similarity=0.453 Sum_probs=15.1
Q ss_pred hHHHhcCHHHHHHHHhhhcc
Q 001043 912 NDIFRMNQNELEAEIRKVSR 931 (1177)
Q Consensus 912 ~~~~~~~q~~L~~~Ir~i~~ 931 (1177)
...+++|+.+||..|++.-.
T Consensus 50 ~~llk~~~KqLR~li~~Lre 69 (436)
T KOG2593|consen 50 KELLKFNKKQLRKLIASLRE 69 (436)
T ss_pred HHHhcccHHHHHHHHHHhhh
Confidence 34567888888888887765
No 173
>PF14631 FancD2: Fanconi anaemia protein FancD2 nuclease; PDB: 3S4W_B.
Probab=38.86 E-value=5.5e+02 Score=36.44 Aligned_cols=99 Identities=20% Similarity=0.277 Sum_probs=59.5
Q ss_pred HHHHHHHHHHHhhhcCchhHHHHHHHHHH---------HHHHHHHHhHHHHHHHhhhHHHh----hCCHHHHHH---HHH
Q 001043 127 VLFDQLFELLNSSMRNEESYRRELASCTG---------ALQTSISQHMSKEEEQVFPLLIE----KFSFEEQAS---LVW 190 (1177)
Q Consensus 127 ~lf~~l~~~l~~~~~~~~~~~~eLa~~l~---------~l~~~l~qHm~~EE~~v~PLl~~----~fS~~E~a~---L~~ 190 (1177)
.++++|++.+... +..+-+++...+- ++-..|.+=|..++.-+.|.|.. .+|++.+.. .+-
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 5556666665543 2233344444442 22223334444444556666654 345555544 455
Q ss_pred HHhhcCCHHHHHHHHhhhcCCCCHHHHHHHHHHHhhcC
Q 001043 191 QFLCSIPVNMMAEFLPWLSSSISSDEHQDMRKCLCKII 228 (1177)
Q Consensus 191 ~~i~siP~~~m~~~LpWm~~~lsp~Er~~~l~~l~~~~ 228 (1177)
..+.+++++.|..++..++.++++.+-..+...||+..
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 57789999999999999999999999999999999864
No 174
>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=37.70 E-value=11 Score=39.66 Aligned_cols=23 Identities=22% Similarity=0.711 Sum_probs=13.1
Q ss_pred eEecccccc---ccCC-CCcccCCCCC
Q 001043 1057 KYYCGICKF---FDDE-RVVYHCPFCN 1079 (1177)
Q Consensus 1057 ~Y~C~~C~l---~dd~-k~~yHC~~Cg 1079 (1177)
-|+|+.|+. |++. ..-|+||.||
T Consensus 109 ~Y~Cp~c~~r~tf~eA~~~~F~Cp~Cg 135 (158)
T TIGR00373 109 FFICPNMCVRFTFNEAMELNFTCPRCG 135 (158)
T ss_pred eEECCCCCcEeeHHHHHHcCCcCCCCC
Confidence 456666652 3443 4457777776
No 175
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=36.43 E-value=13 Score=40.11 Aligned_cols=24 Identities=29% Similarity=0.984 Sum_probs=13.6
Q ss_pred ceEecccccc---ccCC-CCcccCCCCC
Q 001043 1056 AKYYCGICKF---FDDE-RVVYHCPFCN 1079 (1177)
Q Consensus 1056 a~Y~C~~C~l---~dd~-k~~yHC~~Cg 1079 (1177)
.-|+|+.|+. |++. ...|+||.||
T Consensus 116 ~~Y~Cp~C~~rytf~eA~~~~F~Cp~Cg 143 (178)
T PRK06266 116 MFFFCPNCHIRFTFDEAMEYGFRCPQCG 143 (178)
T ss_pred CEEECCCCCcEEeHHHHhhcCCcCCCCC
Confidence 3466766653 3333 4456777766
No 176
>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=36.07 E-value=14 Score=30.17 Aligned_cols=13 Identities=46% Similarity=1.185 Sum_probs=5.5
Q ss_pred cceEecccccccc
Q 001043 1055 MAKYYCGICKFFD 1067 (1177)
Q Consensus 1055 ~a~Y~C~~C~l~d 1067 (1177)
|.+|||+.|+.|=
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 5689999998774
No 177
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=35.61 E-value=29 Score=39.82 Aligned_cols=48 Identities=27% Similarity=0.710 Sum_probs=38.6
Q ss_pred CCcccceEeccccccccCCCCcccCCCCCccccCCCCCccccccCCcccccccc
Q 001043 1051 SGLSMAKYYCGICKFFDDERVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLAKK 1104 (1177)
Q Consensus 1051 ~~~~~a~Y~C~~C~l~dd~k~~yHC~~CgiCrvg~gl~~~~fhC~~C~~C~s~~ 1104 (1177)
.|....-+||+.|+++-. +...||.-||.|-.+- --||.=-|.|+...
T Consensus 107 ~~~~~~~~~C~~C~~~rP-pRs~HCsvC~~CV~rf-----DHHC~WvnnCVG~r 154 (299)
T KOG1311|consen 107 NGIQVEWKYCDTCQLYRP-PRSSHCSVCNNCVLRF-----DHHCPWLNNCIGER 154 (299)
T ss_pred CCcccceEEcCcCcccCC-CCcccchhhccccccc-----CCCCCCccceECCC
Confidence 367788899999999955 4678999999998874 37999888888654
No 178
>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=35.51 E-value=15 Score=31.33 Aligned_cols=40 Identities=30% Similarity=0.757 Sum_probs=28.7
Q ss_pred CcccccccccCCCceEecCCCCcccHhhHHHHHhcCCCCCCCcccccccc
Q 001043 1119 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGDMA 1168 (1177)
Q Consensus 1119 CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrk~v~dm~ 1168 (1177)
|+.|...+... . +.+..-|..||..|+ +|-.|++.+.+-.
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 77888886532 2 332345899999885 7999999987655
No 179
>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=35.50 E-value=27 Score=27.79 Aligned_cols=24 Identities=25% Similarity=0.897 Sum_probs=17.4
Q ss_pred eEeccccccc-cCCCCcccCCCCCc
Q 001043 1057 KYYCGICKFF-DDERVVYHCPFCNL 1080 (1177)
Q Consensus 1057 ~Y~C~~C~l~-dd~k~~yHC~~Cgi 1080 (1177)
.|-|.+|.+. +.++.+..||-||.
T Consensus 2 ~~~C~~CG~i~~g~~~p~~CP~Cg~ 26 (34)
T cd00729 2 VWVCPVCGYIHEGEEAPEKCPICGA 26 (34)
T ss_pred eEECCCCCCEeECCcCCCcCcCCCC
Confidence 4778888775 44467778888874
No 180
>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=34.79 E-value=13 Score=48.16 Aligned_cols=21 Identities=19% Similarity=0.169 Sum_probs=0.0
Q ss_pred HHHHhhhccCCCCChHHHHHH
Q 001043 923 EAEIRKVSRDSTLDPRRKAYL 943 (1177)
Q Consensus 923 ~~~Ir~i~~~~~l~~~~k~~~ 943 (1177)
...+.-|+..|.+.=+.||.-
T Consensus 581 ~~~l~~vn~~sg~~ir~rapt 601 (900)
T PF03833_consen 581 KNALEAVNELSGFKIRDRAPT 601 (900)
T ss_dssp ---------------------
T ss_pred ccHHHHHHHhCCCEecccCcc
Confidence 344555555556665666543
No 181
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=32.92 E-value=9.1 Score=32.12 Aligned_cols=43 Identities=21% Similarity=0.680 Sum_probs=29.8
Q ss_pred CcccccccccCCCceEecCCCCcccHhhHHHHHh------cCCCCCCCcc
Q 001043 1119 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC------SHYICPICSK 1162 (1177)
Q Consensus 1119 CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~------~~~~CPiCrk 1162 (1177)
|+||... ...+.-+.=-.|+-.||..|+..=.. ..+.||.|+.
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 33333333458999999999976432 3688998864
No 182
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=32.51 E-value=24 Score=30.57 Aligned_cols=30 Identities=23% Similarity=0.609 Sum_probs=21.9
Q ss_pred ccceEeccccc-cccCC--CCcccCCCCCcccc
Q 001043 1054 SMAKYYCGICK-FFDDE--RVVYHCPFCNLCRV 1083 (1177)
Q Consensus 1054 ~~a~Y~C~~C~-l~dd~--k~~yHC~~CgiCrv 1083 (1177)
.+..|-|..|. .++.+ ..-+.|++||.=.+
T Consensus 3 ~~~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~rIl 35 (49)
T COG1996 3 AMMEYKCARCGREVELDQETRGIRCPYCGSRIL 35 (49)
T ss_pred ceEEEEhhhcCCeeehhhccCceeCCCCCcEEE
Confidence 46789999994 45533 78889999995443
No 183
>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=32.19 E-value=28 Score=39.74 Aligned_cols=43 Identities=28% Similarity=0.544 Sum_probs=26.8
Q ss_pred cCCCCCCcccccccccCCCceEecCCCCc----ccHhhHHHH-HhcCCCCC
Q 001043 1113 KGLETNCPICCDFLFTSSATVRALPCGHF----MHSDCFQAY-TCSHYICP 1158 (1177)
Q Consensus 1113 ~~~~~~CpICle~lf~s~~~v~~LpCGH~----fH~~Ci~~w-l~~~~~CP 1158 (1177)
..+-.-|+||.|- ...+.+-.-| =|. =|++||.+| +--+..||
T Consensus 27 ~~tLsfChiCfEl-~iegvpks~l--lHtkSlRGHrdCFEK~HlIanQ~~p 74 (285)
T PF06937_consen 27 TETLSFCHICFEL-SIEGVPKSNL--LHTKSLRGHRDCFEKYHLIANQDCP 74 (285)
T ss_pred ccceeecceeecc-ccccCccccc--cccccccchHHHHHHHHHHHcCCCC
Confidence 3345679999874 3333222212 132 489999999 56677898
No 184
>KOG3842 consensus Adaptor protein Pellino [Signal transduction mechanisms]
Probab=31.69 E-value=39 Score=39.26 Aligned_cols=56 Identities=25% Similarity=0.578 Sum_probs=36.8
Q ss_pred CCCCcccccc-----c---------ccCCCce-EecCCCCcccHhhHHHHHhc---------CCCCCCCccccccccccc
Q 001043 1116 ETNCPICCDF-----L---------FTSSATV-RALPCGHFMHSDCFQAYTCS---------HYICPICSKSLGDMAVLH 1171 (1177)
Q Consensus 1116 ~~~CpICle~-----l---------f~s~~~v-~~LpCGH~fH~~Ci~~wl~~---------~~~CPiCrk~v~dm~~~~ 1171 (1177)
+..||+|+.. | .+.+-+. ..-||||+--.+=..-|-+. +..||.|-..+..-.-|+
T Consensus 341 ~r~CPmC~~~gp~V~L~lG~E~~f~vD~G~pthaF~PCGHv~sekt~~YWs~iplPhGT~~f~a~CPFC~~~L~ge~~~i 420 (429)
T KOG3842|consen 341 ERECPMCRVVGPYVPLWLGCEAGFYVDAGPPTHAFNPCGHVCSEKTVKYWSQIPLPHGTHAFHAACPFCATQLAGEQGYI 420 (429)
T ss_pred cCcCCeeeeecceeeeeccccceeEecCCCcccccCCcccccchhhhhHhhcCcCCCccccccccCcchhhhhccCCceE
Confidence 6789999853 0 1122222 34599999888888888542 456999998876544443
No 185
>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=31.38 E-value=23 Score=29.21 Aligned_cols=13 Identities=46% Similarity=0.846 Sum_probs=5.7
Q ss_pred cCCCCcccCCCCC
Q 001043 1067 DDERVVYHCPFCN 1079 (1177)
Q Consensus 1067 dd~k~~yHC~~Cg 1079 (1177)
|...+.|-|..||
T Consensus 14 D~~~g~~vC~~CG 26 (43)
T PF08271_consen 14 DPERGELVCPNCG 26 (43)
T ss_dssp ETTTTEEEETTT-
T ss_pred cCCCCeEECCCCC
Confidence 3334455555554
No 186
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=30.99 E-value=44 Score=43.39 Aligned_cols=44 Identities=23% Similarity=0.723 Sum_probs=25.4
Q ss_pred cceeeccccCccccCCCCCCCCCCCCccc------ceEeccccccccCCCCcccCCCCC
Q 001043 1027 TTEMMCMRCLKVQPVGPVCTTLSCSGLSM------AKYYCGICKFFDDERVVYHCPFCN 1079 (1177)
Q Consensus 1027 ~~~~~C~~C~~~q~~~~~C~~~~C~~~~~------a~Y~C~~C~l~dd~k~~yHC~~Cg 1079 (1177)
.+.++|..|+.+- .|.+ | ...+ ....|-.|+.= .+.+.+||.||
T Consensus 433 s~~l~C~~Cg~v~----~Cp~--C-d~~lt~H~~~~~L~CH~Cg~~--~~~p~~Cp~Cg 482 (730)
T COG1198 433 APLLLCRDCGYIA----ECPN--C-DSPLTLHKATGQLRCHYCGYQ--EPIPQSCPECG 482 (730)
T ss_pred cceeecccCCCcc----cCCC--C-CcceEEecCCCeeEeCCCCCC--CCCCCCCCCCC
Confidence 3589999999874 4766 5 4333 23334333322 25566666666
No 187
>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=29.98 E-value=39 Score=41.82 Aligned_cols=10 Identities=40% Similarity=1.152 Sum_probs=5.2
Q ss_pred cccCcccccc
Q 001043 1007 LFTCRFCHDK 1016 (1177)
Q Consensus 1007 ~y~Cr~CHde 1016 (1177)
.|-|+.||.-
T Consensus 5 L~fC~~C~~i 14 (483)
T PF05502_consen 5 LYFCEHCHKI 14 (483)
T ss_pred ceeccccccc
Confidence 4556555543
No 188
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=29.67 E-value=59 Score=40.74 Aligned_cols=124 Identities=20% Similarity=0.338 Sum_probs=58.7
Q ss_pred cccccccCCcccCcccccccCCCCCCccccceeeccccCccccCCCCCCCCCCCCcccceEec-cccccccCC------C
Q 001043 998 KLRAACCGKLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVGPVCTTLSCSGLSMAKYYC-GICKFFDDE------R 1070 (1177)
Q Consensus 998 ~l~~~cC~k~y~Cr~CHde~~~H~~~r~~~~~~~C~~C~~~q~~~~~C~~~~C~~~~~a~Y~C-~~C~l~dd~------k 1070 (1177)
.++|..|++ .|-.++-.-.-.-+-+.-..|-.|+.-...+..|.. | +. +||| ..|.-|--. -
T Consensus 16 ~i~c~~c~~-----kc~gevlrv~d~~fhi~cf~c~~cg~~la~~gff~k--~-~~---~~ygt~~c~~~~~gevvsa~g 84 (670)
T KOG1044|consen 16 GIKCDKCRK-----KCSGEVLRVNDNHFHINCFQCKKCGRNLAEGGFFTK--P-EN---RLYGTDDCRAFVEGEVVSTLG 84 (670)
T ss_pred ceehhhhCC-----ccccceeEeeccccceeeeeccccCCCcccccceec--c-cc---eeecccchhhhccceeEeccc
Confidence 466776766 454442211111122334556666655555556665 3 32 7777 444444221 4
Q ss_pred Cccc--CCCCCccccCCCCCccccccCC---cccccccc-cccccccccCCCCCCcccccccccCCCceEec
Q 001043 1071 VVYH--CPFCNLCRVGRGLGVDFFHCMT---CNCCLAKK-LVDHKCREKGLETNCPICCDFLFTSSATVRAL 1136 (1177)
Q Consensus 1071 ~~yH--C~~CgiCrvg~gl~~~~fhC~~---C~~C~s~~-l~~H~C~e~~~~~~CpICle~lf~s~~~v~~L 1136 (1177)
..|| |-.|.+|+..-.-|....-|.+ |..|.... +. =.+...-.+|+-|.+.|.. +.....|
T Consensus 85 ktyh~~cf~cs~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~---p~~~~~ps~cagc~~~lk~-gq~llal 152 (670)
T KOG1044|consen 85 KTYHPKCFSCSTCKSPFKSGDKVTFSGKECLCQTCSQPMPVS---PAESYGPSTCAGCGEELKN-GQALLAL 152 (670)
T ss_pred ceeccccceecccCCCCCCCCeeeecchhhhhhhhcCcccCC---cccccCCccccchhhhhhc-cceeeee
Confidence 5676 6777777765333321111111 22222111 01 1122356789999998654 4434333
No 189
>PLN02189 cellulose synthase
Probab=28.86 E-value=39 Score=45.04 Aligned_cols=52 Identities=23% Similarity=0.435 Sum_probs=35.0
Q ss_pred cCCCCCCccccccccc--CCCceEec-CCCCcccHhhHHHHHh--cCCCCCCCccccc
Q 001043 1113 KGLETNCPICCDFLFT--SSATVRAL-PCGHFMHSDCFQAYTC--SHYICPICSKSLG 1165 (1177)
Q Consensus 1113 ~~~~~~CpICle~lf~--s~~~v~~L-pCGH~fH~~Ci~~wl~--~~~~CPiCrk~v~ 1165 (1177)
+.....|.||.|++-. .++.-+.- -||--.++.|+ +|-+ .+..||-|+...-
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 3345689999998653 23332222 36666999999 6643 4678999998654
No 190
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=28.43 E-value=32 Score=35.34 Aligned_cols=32 Identities=16% Similarity=0.044 Sum_probs=22.8
Q ss_pred ccccccccCCcccCcccccccCCCCCCccccceeeccccCccccCC
Q 001043 997 CKLRAACCGKLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVG 1042 (1177)
Q Consensus 997 c~l~~~cC~k~y~Cr~CHde~~~H~~~r~~~~~~~C~~C~~~q~~~ 1042 (1177)
-|-.||.||+-| .+... ..++|.+|++.+++.
T Consensus 8 tKr~Cp~cg~kF-------------YDLnk-~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 8 TKRICPNTGSKF-------------YDLNR-RPAVSPYTGEQFPPE 39 (129)
T ss_pred ccccCCCcCccc-------------cccCC-CCccCCCcCCccCcc
Confidence 355788898743 23222 689999999999876
No 191
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=28.37 E-value=49 Score=44.92 Aligned_cols=21 Identities=24% Similarity=0.341 Sum_probs=11.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHh
Q 001043 298 MLWHNAIKRELNDIAEAARKI 318 (1177)
Q Consensus 298 ~~~HkALRrEL~~L~~~a~~i 318 (1177)
..-++-|.+++.++.+.|.+.
T Consensus 8 ~~Yf~~l~~~~~~~~~iA~~a 28 (1337)
T PRK14714 8 ERYFERLERELDKAYEVAEAA 28 (1337)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 344555666666655555554
No 192
>PHA00626 hypothetical protein
Probab=28.18 E-value=43 Score=29.84 Aligned_cols=7 Identities=43% Similarity=1.027 Sum_probs=3.4
Q ss_pred ccCCCCC
Q 001043 1073 YHCPFCN 1079 (1177)
Q Consensus 1073 yHC~~Cg 1079 (1177)
|.|++||
T Consensus 24 YkCkdCG 30 (59)
T PHA00626 24 YVCCDCG 30 (59)
T ss_pred eEcCCCC
Confidence 4444444
No 193
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=28.09 E-value=1.3e+02 Score=34.58 Aligned_cols=42 Identities=14% Similarity=0.254 Sum_probs=30.3
Q ss_pred hhHHHhcCHHHHHHHHhhhcc-CCCCChHHHHHHHHHHHHHHH
Q 001043 911 WNDIFRMNQNELEAEIRKVSR-DSTLDPRRKAYLIQNLMTSRW 952 (1177)
Q Consensus 911 ~~~~~~~~q~~L~~~Ir~i~~-~~~l~~~~k~~~~q~l~~~~~ 952 (1177)
.+.+...+..++++-++.+.. +...++..-+.+++..+.--|
T Consensus 111 l~~l~~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~aaL~~~~ 153 (290)
T PF04216_consen 111 LEALRAADEEDLEALAEALLAGEMPVDPEALAFFLWAALQPFL 153 (290)
T ss_dssp HHHHHH--HHHHHHHHHHHHTT-GGGS-GGGHHHHHHHHHHHH
T ss_pred HHHHHhCCHHHHHHHHHHHHhcccCCCcHHHHHHHHHHHHHHH
Confidence 677777899999999998877 455677778888888887655
No 194
>KOG4654 consensus Uncharacterized conserved protein [Function unknown]
Probab=27.50 E-value=8.8e+02 Score=26.86 Aligned_cols=150 Identities=20% Similarity=0.184 Sum_probs=71.6
Q ss_pred chHHHH----HHHHHHHHHHHHHHHHHHHhccCCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHHHhh-------
Q 001043 43 PILIFL----FFHKAIKSELDVLHRAAMAFATNLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIRV------- 111 (1177)
Q Consensus 43 Pi~~~~----~~HkAlR~el~~l~~~~~~~~~~~~d~~~~~~l~~r~~~L~~~~~~H~~aEDevI~PaL~~Rv------- 111 (1177)
|+|+|. ++|||+-..-.. --|+-- -=...|++|..-++|+.+..-.-...||.+-...|---+
T Consensus 41 p~dlY~~c~q~Vhk~lc~~kkc----~iRl~Y--~W~ELW~aL~n~L~Flmsne~~llak~dif~La~lIldlf~mfIs~ 114 (252)
T KOG4654|consen 41 PADLYFLCFQFVHKALCSLKKC----GIRLEY--HWLELWRALFNFLDFLMSNEINLLAKEDIFRLAELILDLFAMFISN 114 (252)
T ss_pred ChhHHHHHHHHHHHHHHHHHhh----cceeee--HHHHHHHHHHHHHHHHHHhHhhhcchhhHHHHHHHHHHHHHHHHhC
Confidence 777776 788887654332 111111 112367777778888887777777777765333221111
Q ss_pred -------hHHH--HHHHhhhhhHHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHH--HHHHHhHH-HHHHHhhhHHHhh
Q 001043 112 -------KNIA--RTYSLEHEGESVLFDQLFELLNSSMRNEESYRRELASCTGALQ--TSISQHMS-KEEEQVFPLLIEK 179 (1177)
Q Consensus 112 -------~~v~--~~~~~EH~~~~~lf~~l~~~l~~~~~~~~~~~~eLa~~l~~l~--~~l~qHm~-~EE~~v~PLl~~~ 179 (1177)
+.-. .=|+.=|. ..-|+.+..-+-++..+++...++-...++++- ..+.+|+. |-|...----.-.
T Consensus 115 GDafl~~pde~ddLfYeii~m--hknFdn~~S~vlrlstnagq~kdaaskv~~AL~ni~aiiehfnpKiedyaavnhi~q 192 (252)
T KOG4654|consen 115 GDAFLIRPDELDDLFYEIIHM--HKNFDNFSSKVLRLSTNAGQIKDAASKVLGALNNILAIIEHFNPKIEDYAAVNHIPQ 192 (252)
T ss_pred CCeeeeCchHHHHHHHHHHHH--hcchhhHHHHHHHhccccccCchHHHHHHHHHHHHHHHHHhcCchhhhHHHhccccc
Confidence 1111 11222221 234555555555665554422222211222111 12445554 3333111111223
Q ss_pred CCHHHHHHHHHHHhhcCCHHH
Q 001043 180 FSFEEQASLVWQFLCSIPVNM 200 (1177)
Q Consensus 180 fS~~E~a~L~~~~i~siP~~~ 200 (1177)
.|.+|-.+++..=..|||+..
T Consensus 193 lsadeV~eVikae~dsi~la~ 213 (252)
T KOG4654|consen 193 LSADEVEEVIKAELDSIPLAK 213 (252)
T ss_pred ccHHHHHHHHHHhccccchhh
Confidence 456777777777777777654
No 195
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=27.26 E-value=39 Score=33.31 Aligned_cols=12 Identities=17% Similarity=0.257 Sum_probs=7.5
Q ss_pred CCCCCCcccccc
Q 001043 1114 GLETNCPICCDF 1125 (1177)
Q Consensus 1114 ~~~~~CpICle~ 1125 (1177)
..+..|++|..+
T Consensus 40 ~~h~~C~~CG~y 51 (99)
T PRK14892 40 IAIITCGNCGLY 51 (99)
T ss_pred cceEECCCCCCc
Confidence 345667777755
No 196
>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]
Probab=27.25 E-value=30 Score=38.22 Aligned_cols=41 Identities=32% Similarity=0.750 Sum_probs=28.5
Q ss_pred CCcccccccccCCCceEecCCCCcccHhhHHHHHhcCCCCCCCc
Q 001043 1118 NCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICS 1161 (1177)
Q Consensus 1118 ~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCr 1161 (1177)
+|-+|..=+ -..++--.||=-||..|++.|+.....||-|.
T Consensus 183 ~Cn~Ch~Lv---Iqg~rCg~c~i~~h~~c~qty~q~~~~cphc~ 223 (235)
T KOG4718|consen 183 NCNLCHCLV---IQGIRCGSCNIQYHRGCIQTYLQRRDICPHCG 223 (235)
T ss_pred HHhHhHHHh---heeeccCcccchhhhHHHHHHhcccCcCCchh
Confidence 455555431 12234456677799999999999999999884
No 197
>PRK07219 DNA topoisomerase I; Validated
Probab=27.23 E-value=88 Score=41.32 Aligned_cols=63 Identities=25% Similarity=0.495 Sum_probs=34.2
Q ss_pred ccccccccCC----CCcccCCCCCcc---ccCCCCCccccccCC---cccccccccccccccccCCCCCCcccccccc
Q 001043 1060 CGICKFFDDE----RVVYHCPFCNLC---RVGRGLGVDFFHCMT---CNCCLAKKLVDHKCREKGLETNCPICCDFLF 1127 (1177)
Q Consensus 1060 C~~C~l~dd~----k~~yHC~~CgiC---rvg~gl~~~~fhC~~---C~~C~s~~l~~H~C~e~~~~~~CpICle~lf 1127 (1177)
|+.|+..... .....||.||-- |.|+. | .|+-|.+ |+.-..+.-..+. ......||-|-.++.
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 7888765432 346789999822 22322 3 3888865 6543332111100 124567999976643
No 198
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=27.10 E-value=52 Score=38.32 Aligned_cols=76 Identities=26% Similarity=0.520 Sum_probs=50.0
Q ss_pred ccCC----CCcccCCCCCccccCCCCCccccccCCcccccccc--c--ccccccccCCCCCCcccccccccCCCceEecC
Q 001043 1066 FDDE----RVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLAKK--L--VDHKCREKGLETNCPICCDFLFTSSATVRALP 1137 (1177)
Q Consensus 1066 ~dd~----k~~yHC~~CgiCrvg~gl~~~~fhC~~C~~C~s~~--l--~~H~C~e~~~~~~CpICle~lf~s~~~v~~Lp 1137 (1177)
|||- +-+=||..|-. -| -.-+=||.| +.|.+-. . ..|.=..+.....|..|-+- .++|.+++
T Consensus 169 WdDVLks~Ripg~Ces~~~--pg-~fAEFfFKC---~ah~~~~k~~aa~lhli~~N~~ni~C~~Ctdv----~~~vlvf~ 238 (446)
T KOG0006|consen 169 WDDVLKSKRIPGVCESCCT--PG-LFAEFFFKC---GAHPTSDKETAAALHLIATNSRNITCITCTDV----RSPVLVFQ 238 (446)
T ss_pred hhhhhhcccCccccccccC--Cc-chHhheehh---ccCCCccccchhHHHHhhcccccceeEEecCC----ccceEEEe
Confidence 6664 66778877642 22 112345655 4454432 1 35555566677889999764 56788899
Q ss_pred CC--CcccHhhHHHHH
Q 001043 1138 CG--HFMHSDCFQAYT 1151 (1177)
Q Consensus 1138 CG--H~fH~~Ci~~wl 1151 (1177)
|. |.....||.-|-
T Consensus 239 Cns~HvtC~dCFr~yc 254 (446)
T KOG0006|consen 239 CNSRHVTCLDCFRLYC 254 (446)
T ss_pred cCCceeehHHhhhhHh
Confidence 99 999999998773
No 199
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=26.87 E-value=1.2e+02 Score=30.65 Aligned_cols=46 Identities=20% Similarity=0.276 Sum_probs=30.6
Q ss_pred CCCCcccccccccCC-----------CceEecCCCCcccHhhHHHHHhcCCCCCCCcc
Q 001043 1116 ETNCPICCDFLFTSS-----------ATVRALPCGHFMHSDCFQAYTCSHYICPICSK 1162 (1177)
Q Consensus 1116 ~~~CpICle~lf~s~-----------~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrk 1162 (1177)
...|--|+..+ ... ...+--.|++.|..+|-.=+-..=..||-|..
T Consensus 55 ~~~C~~C~~~f-~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~CPGC~~ 111 (112)
T TIGR00622 55 SRFCFGCQGPF-PKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHESLHCCPGCIH 111 (112)
T ss_pred CCcccCcCCCC-CCcccccccccccccceeCCCCCCccccccchhhhhhccCCcCCCC
Confidence 34699999873 321 12234588999999996555555567998863
No 200
>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=26.78 E-value=52 Score=37.39 Aligned_cols=63 Identities=29% Similarity=0.761 Sum_probs=36.0
Q ss_pred CccccccCCcccccccccccccccccCCCCCCcc--cccccccCCC-------------ceEecCCCCcccHhhHHHHH-
Q 001043 1088 GVDFFHCMTCNCCLAKKLVDHKCREKGLETNCPI--CCDFLFTSSA-------------TVRALPCGHFMHSDCFQAYT- 1151 (1177)
Q Consensus 1088 ~~~~fhC~~C~~C~s~~l~~H~C~e~~~~~~CpI--Cle~lf~s~~-------------~v~~LpCGH~fH~~Ci~~wl- 1151 (1177)
|+.|.-|. ||+-+ .|.+.+..-.||- |.--|.-... ....+.||| |-+..+
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 57788887 55443 3566666777776 7643321111 113467888 444432
Q ss_pred ---h--cCCCCCCCccc
Q 001043 1152 ---C--SHYICPICSKS 1163 (1177)
Q Consensus 1152 ---~--~~~~CPiCrk~ 1163 (1177)
. .--+||-|||.
T Consensus 170 ~~~~~~tlARCPHCrKv 186 (256)
T PF09788_consen 170 NTLTSNTLARCPHCRKV 186 (256)
T ss_pred cCCCCCccccCCCCcee
Confidence 1 12469999983
No 201
>KOG4399 consensus C2HC-type Zn-finger protein [General function prediction only]
Probab=26.47 E-value=16 Score=41.31 Aligned_cols=47 Identities=19% Similarity=0.149 Sum_probs=36.0
Q ss_pred CcccceEeccccccccCCCCcccCCCCCccccCCCCCccccccCCcccccc
Q 001043 1052 GLSMAKYYCGICKFFDDERVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLA 1102 (1177)
Q Consensus 1052 ~~~~a~Y~C~~C~l~dd~k~~yHC~~CgiCrvg~gl~~~~fhC~~C~~C~s 1102 (1177)
+...+.-+|.||.=+|.++ -|||.|.-||--+. ...-||.+|..|..
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 3345566899999998877 89999999997542 25678888888765
No 202
>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 KOG3842 consensus Adaptor protein Pellino [Signal transduction mechanisms]
Probab=26.30 E-value=31 Score=40.06 Aligned_cols=45 Identities=24% Similarity=0.586 Sum_probs=30.4
Q ss_pred cCCCCCCcccccccc----------cCCCceEecCCCCc--ccHhhHHHHHh------cCCCCCCCcc
Q 001043 1113 KGLETNCPICCDFLF----------TSSATVRALPCGHF--MHSDCFQAYTC------SHYICPICSK 1162 (1177)
Q Consensus 1113 ~~~~~~CpICle~lf----------~s~~~v~~LpCGH~--fH~~Ci~~wl~------~~~~CPiCrk 1162 (1177)
++....||+=+..|- ....+.++|.|||. +|. |=. +...||+|+.
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 355678999876541 23457789999976 553 632 2466999996
No 204
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=26.26 E-value=70 Score=37.57 Aligned_cols=46 Identities=28% Similarity=0.394 Sum_probs=31.6
Q ss_pred CCCCcccccccccCCCceEecCCCCcccHhhHHHHHhcCCCCCCCcc
Q 001043 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSK 1162 (1177)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrk 1162 (1177)
...|-.|.+.+ .+...++--.|.+.|..+|-.=--.+-..||-|..
T Consensus 330 ~~~Cf~C~~~~-~~~~~y~C~~Ck~~FCldCDv~iHesLh~CpgCeh 375 (378)
T KOG2807|consen 330 SRFCFACQGEL-LSSGRYRCESCKNVFCLDCDVFIHESLHNCPGCEH 375 (378)
T ss_pred Ccceeeecccc-CCCCcEEchhccceeeccchHHHHhhhhcCCCcCC
Confidence 34599997774 34445666789999999995332233467999974
No 205
>PLN02436 cellulose synthase A
Probab=26.05 E-value=47 Score=44.46 Aligned_cols=51 Identities=20% Similarity=0.451 Sum_probs=34.8
Q ss_pred CCCCCCcccccccccCCCceEecC---CCCcccHhhHHHHHh--cCCCCCCCccccc
Q 001043 1114 GLETNCPICCDFLFTSSATVRALP---CGHFMHSDCFQAYTC--SHYICPICSKSLG 1165 (1177)
Q Consensus 1114 ~~~~~CpICle~lf~s~~~v~~Lp---CGH~fH~~Ci~~wl~--~~~~CPiCrk~v~ 1165 (1177)
.....|.||.|++-...+.-.... ||--.++.|+ +|-+ .+..||-|+...-
T Consensus 34 ~~~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cy-eyer~eg~~~Cpqckt~Y~ 89 (1094)
T PLN02436 34 LSGQTCQICGDEIELTVDGEPFVACNECAFPVCRPCY-EYERREGNQACPQCKTRYK 89 (1094)
T ss_pred cCCccccccccccCcCCCCCEEEeeccCCCccccchh-hhhhhcCCccCcccCCchh
Confidence 345689999999743333323344 5556999999 6643 4678999998654
No 206
>PLN03086 PRLI-interacting factor K; Provisional
Probab=25.82 E-value=27 Score=43.89 Aligned_cols=53 Identities=25% Similarity=0.575 Sum_probs=26.8
Q ss_pred CCcccCCCCCccccCCCCCc------cccccCCccccccccc-cccc---ccccCCCCCCcccccc
Q 001043 1070 RVVYHCPFCNLCRVGRGLGV------DFFHCMTCNCCLAKKL-VDHK---CREKGLETNCPICCDF 1125 (1177)
Q Consensus 1070 k~~yHC~~CgiCrvg~gl~~------~~fhC~~C~~C~s~~l-~~H~---C~e~~~~~~CpICle~ 1125 (1177)
+..+||+.||-=-....|.+ .-+.|. ||..+.... ..|. |.++ ...|+.|...
T Consensus 451 ~~H~~C~~Cgk~f~~s~LekH~~~~Hkpv~Cp-Cg~~~~R~~L~~H~~thCp~K--pi~C~fC~~~ 513 (567)
T PLN03086 451 KNHVHCEKCGQAFQQGEMEKHMKVFHEPLQCP-CGVVLEKEQMVQHQASTCPLR--LITCRFCGDM 513 (567)
T ss_pred ccCccCCCCCCccchHHHHHHHHhcCCCccCC-CCCCcchhHHHhhhhccCCCC--ceeCCCCCCc
Confidence 55677777763111111100 123466 665443332 5663 5544 4679999865
No 207
>PRK00420 hypothetical protein; Validated
Probab=25.73 E-value=39 Score=34.02 Aligned_cols=14 Identities=43% Similarity=0.959 Sum_probs=10.5
Q ss_pred CCCCCccccccccc
Q 001043 1115 LETNCPICCDFLFT 1128 (1177)
Q Consensus 1115 ~~~~CpICle~lf~ 1128 (1177)
....||+|.-+||.
T Consensus 22 l~~~CP~Cg~pLf~ 35 (112)
T PRK00420 22 LSKHCPVCGLPLFE 35 (112)
T ss_pred ccCCCCCCCCccee
Confidence 34679999888775
No 208
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=25.72 E-value=32 Score=43.05 Aligned_cols=43 Identities=26% Similarity=0.778 Sum_probs=36.0
Q ss_pred CCCCCcccccccccCCCceEecCCCCcccHhhHHHHHhcCCCCCCCccccc
Q 001043 1115 LETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1165 (1177)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrk~v~ 1165 (1177)
.++.|.||.+.+ ..+.-+|- |..|+.+|+.....||+|++.+.
T Consensus 478 ~~~~~~~~~~~~-----~~~~~~~~---~~~~l~~~~~~~~~~pl~~~~~~ 520 (543)
T KOG0802|consen 478 PNDVCAICYQEM-----SARITPCS---HALCLRKWLYVQEVCPLCHTYMK 520 (543)
T ss_pred ccCcchHHHHHH-----Hhcccccc---chhHHHhhhhhccccCCCchhhh
Confidence 478899999985 34556777 99999999999999999998764
No 209
>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=25.18 E-value=3.4e+02 Score=26.78 Aligned_cols=61 Identities=21% Similarity=0.163 Sum_probs=35.7
Q ss_pred HHHhhhhhHHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHHHHHhHHHHHHHh----hhHHHhhCCHHHHHHHHHHH
Q 001043 117 TYSLEHEGESVLFDQLFELLNSSMRNEESYRRELASCTGALQTSISQHMSKEEEQV----FPLLIEKFSFEEQASLVWQF 192 (1177)
Q Consensus 117 ~~~~EH~~~~~lf~~l~~~l~~~~~~~~~~~~eLa~~l~~l~~~l~qHm~~EE~~v----~PLl~~~fS~~E~a~L~~~~ 192 (1177)
.+..||+..=++++.|..++.. ...+..|..-...|...||.-. .|-+..| ...+.+|
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 4555666555555554444432 3456667778889999999764 3444333 5555556
Q ss_pred hhc
Q 001043 193 LCS 195 (1177)
Q Consensus 193 i~s 195 (1177)
+..
T Consensus 76 ~~~ 78 (113)
T cd00522 76 VEK 78 (113)
T ss_pred HHH
Confidence 544
No 210
>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=25.16 E-value=1.6e+02 Score=25.68 Aligned_cols=37 Identities=14% Similarity=0.260 Sum_probs=25.3
Q ss_pred ccccCCCCCCC--CCCCCchhHHHHHHHHHHHHHHHHHH
Q 001043 629 NWETDLSSADI--GCASRPIDNIFKFHKAIRKDLEYLDG 665 (1177)
Q Consensus 629 ~~~~~~~~~~~--~~~~~PId~i~~~HkAIRkdL~~l~~ 665 (1177)
+|++....... +.-..|+|.+...-+.|+.|-.+|.+
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 211
>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=25.01 E-value=35 Score=26.24 Aligned_cols=12 Identities=25% Similarity=0.974 Sum_probs=8.9
Q ss_pred cceEeccccccc
Q 001043 1055 MAKYYCGICKFF 1066 (1177)
Q Consensus 1055 ~a~Y~C~~C~l~ 1066 (1177)
++.|||++|+.+
T Consensus 1 ~~~~~C~~C~~~ 12 (35)
T smart00451 1 TGGFYCKLCNVT 12 (35)
T ss_pred CcCeEccccCCc
Confidence 357899999764
No 212
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=24.91 E-value=43 Score=37.88 Aligned_cols=78 Identities=19% Similarity=0.500 Sum_probs=50.9
Q ss_pred ccccccccccccCC--------cccCcccccccCCCCCC----ccccceeeccccCccccCCCCCCCCCCCCcccceEec
Q 001043 993 YKRNCKLRAACCGK--------LFTCRFCHDKVSDHSMD----RKATTEMMCMRCLKVQPVGPVCTTLSCSGLSMAKYYC 1060 (1177)
Q Consensus 993 Y~r~c~l~~~cC~k--------~y~Cr~CHde~~~H~~~----r~~~~~~~C~~C~~~q~~~~~C~~~~C~~~~~a~Y~C 1060 (1177)
|+..=...|.-|+. .|.|..||.-..+.++. -+-.-...|..|+++..... ...-+.-||
T Consensus 115 ~rnqgr~LC~~Cn~k~Ka~~~g~YvC~KCh~~iD~~~l~fr~d~yH~yHFkCt~C~keL~sda--------Revk~eLyC 186 (332)
T KOG2272|consen 115 YRNQGRALCRECNQKEKAKGRGRYVCQKCHAHIDEQPLTFRGDPYHPYHFKCTTCGKELTSDA--------REVKGELYC 186 (332)
T ss_pred HhhcchHHhhhhhhhhcccccceeehhhhhhhcccccccccCCCCCccceecccccccccchh--------hhhccceec
Confidence 33333455555643 79999999886664443 23335788999998876533 234567788
Q ss_pred cccccccCCCCcccCCCCCccccC
Q 001043 1061 GICKFFDDERVVYHCPFCNLCRVG 1084 (1177)
Q Consensus 1061 ~~C~l~dd~k~~yHC~~CgiCrvg 1084 (1177)
.-|. +.+-||-||-||..
T Consensus 187 lrCh------D~mgipiCgaC~rp 204 (332)
T KOG2272|consen 187 LRCH------DKMGIPICGACRRP 204 (332)
T ss_pred cccc------cccCCcccccccCc
Confidence 8874 33568899999864
No 213
>KOG4399 consensus C2HC-type Zn-finger protein [General function prediction only]
Probab=24.63 E-value=22 Score=40.20 Aligned_cols=71 Identities=23% Similarity=0.591 Sum_probs=48.6
Q ss_pred CcccceEeccccccccCCCCcccCCCCCccccCCCCCccccccCCccccccccc-ccccccccCCCCCCcccccc
Q 001043 1052 GLSMAKYYCGICKFFDDERVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLAKKL-VDHKCREKGLETNCPICCDF 1125 (1177)
Q Consensus 1052 ~~~~a~Y~C~~C~l~dd~k~~yHC~~CgiCrvg~gl~~~~fhC~~C~~C~s~~l-~~H~C~e~~~~~~CpICle~ 1125 (1177)
+..-+-+||..|-.|=. +..-||+.|+-|..-.| +-+-||-+|-.|+-..+ .--.|..-+...-|-||-+.
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 55666777999977633 45669999999987653 57889999999987765 22222222334568888776
No 214
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=24.14 E-value=30 Score=39.20 Aligned_cols=51 Identities=24% Similarity=0.626 Sum_probs=34.4
Q ss_pred ccCCCCCCcccccccccCCCceE--ecCCC-----CcccHhhHHHHHhc--------CCCCCCCcccc
Q 001043 1112 EKGLETNCPICCDFLFTSSATVR--ALPCG-----HFMHSDCFQAYTCS--------HYICPICSKSL 1164 (1177)
Q Consensus 1112 e~~~~~~CpICle~lf~s~~~v~--~LpCG-----H~fH~~Ci~~wl~~--------~~~CPiCrk~v 1164 (1177)
+...+..|=||... +++.... +=||- |--|..|+..|+.. .-+||-|+...
T Consensus 16 ~~e~eR~CWiCF~T--deDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEY 81 (293)
T KOG3053|consen 16 NQELERCCWICFAT--DEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEY 81 (293)
T ss_pred ccccceeEEEEecc--CcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchh
Confidence 34467789999865 2222222 34773 89999999999843 13499999753
No 215
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=23.30 E-value=51 Score=29.32 Aligned_cols=12 Identities=33% Similarity=0.930 Sum_probs=9.1
Q ss_pred CCcccCCCCCcc
Q 001043 1070 RVVYHCPFCNLC 1081 (1177)
Q Consensus 1070 k~~yHC~~CgiC 1081 (1177)
...|-||+|||-
T Consensus 12 ~v~~~Cp~cGip 23 (55)
T PF13824_consen 12 HVNFECPDCGIP 23 (55)
T ss_pred ccCCcCCCCCCc
Confidence 567888888874
No 216
>PF15353 HECA: Headcase protein family homologue
Probab=23.21 E-value=42 Score=33.43 Aligned_cols=15 Identities=40% Similarity=1.249 Sum_probs=13.4
Q ss_pred CCCCcccHhhHHHHH
Q 001043 1137 PCGHFMHSDCFQAYT 1151 (1177)
Q Consensus 1137 pCGH~fH~~Ci~~wl 1151 (1177)
|.|++||.+||++|-
T Consensus 39 p~~~~MH~~CF~~wE 53 (107)
T PF15353_consen 39 PFGQYMHRECFEKWE 53 (107)
T ss_pred CCCCchHHHHHHHHH
Confidence 568999999999994
No 217
>PF04710 Pellino: Pellino; InterPro: IPR006800 Pellino is involved in Toll-like signalling pathways, and associates with the kinase domain of the Pelle Ser/Thr kinase [, , ].; PDB: 3EGB_B 3EGA_A.
Probab=23.11 E-value=28 Score=41.76 Aligned_cols=35 Identities=20% Similarity=0.422 Sum_probs=0.0
Q ss_pred cCCCceEecCCCCcccHhhHHHHHhc---CCCCCCCcc
Q 001043 1128 TSSATVRALPCGHFMHSDCFQAYTCS---HYICPICSK 1162 (1177)
Q Consensus 1128 ~s~~~v~~LpCGH~fH~~Ci~~wl~~---~~~CPiCrk 1162 (1177)
....+.++|.|||++-.+=--.--.. ..+||+||.
T Consensus 299 ~~~qP~VYl~CGHVhG~h~Wg~~~~~~~~~r~CPlCr~ 336 (416)
T PF04710_consen 299 DERQPWVYLNCGHVHGYHNWGQDSDRDPRSRTCPLCRQ 336 (416)
T ss_dssp --------------------------------------
T ss_pred cccCceeeccccceeeecccccccccccccccCCCccc
No 218
>KOG1312 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=22.95 E-value=28 Score=40.13 Aligned_cols=32 Identities=31% Similarity=0.812 Sum_probs=23.2
Q ss_pred CCCCccccCCCCCccccccCCccccccccccccccc
Q 001043 1076 PFCNLCRVGRGLGVDFFHCMTCNCCLAKKLVDHKCR 1111 (1177)
Q Consensus 1076 ~~CgiCrvg~gl~~~~fhC~~C~~C~s~~l~~H~C~ 1111 (1177)
.+|..|+..|. --..||..||.|+..- +|-|+
T Consensus 149 ~kCSTCki~KP--ARSKHCsiCNrCV~rf--DHHCi 180 (341)
T KOG1312|consen 149 VKCSTCKIRKP--ARSKHCSICNRCVHRF--DHHCI 180 (341)
T ss_pred CccccccCCCc--cccccchHHHHHHHHh--ccceE
Confidence 56777777763 4678999999998653 66664
No 219
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=22.72 E-value=46 Score=41.60 Aligned_cols=11 Identities=36% Similarity=0.872 Sum_probs=7.8
Q ss_pred CCCCcccHhhH
Q 001043 1137 PCGHFMHSDCF 1147 (1177)
Q Consensus 1137 pCGH~fH~~Ci 1147 (1177)
.=|-+||..|+
T Consensus 82 a~gktyh~~cf 92 (670)
T KOG1044|consen 82 TLGKTYHPKCF 92 (670)
T ss_pred cccceeccccc
Confidence 33778888776
No 220
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=22.66 E-value=30 Score=35.96 Aligned_cols=7 Identities=43% Similarity=1.549 Sum_probs=4.7
Q ss_pred ccCCCCC
Q 001043 1073 YHCPFCN 1079 (1177)
Q Consensus 1073 yHC~~Cg 1079 (1177)
|.||.||
T Consensus 124 f~Cp~Cg 130 (147)
T smart00531 124 FTCPRCG 130 (147)
T ss_pred EECCCCC
Confidence 6666666
No 221
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=22.59 E-value=47 Score=28.77 Aligned_cols=24 Identities=29% Similarity=0.704 Sum_probs=13.1
Q ss_pred cCCCCCccccCCCCCccccccCCccc
Q 001043 1074 HCPFCNLCRVGRGLGVDFFHCMTCNC 1099 (1177)
Q Consensus 1074 HC~~CgiCrvg~gl~~~~fhC~~C~~ 1099 (1177)
.||.||-.... ...+.++|.+||.
T Consensus 22 fCP~Cg~~~m~--~~~~r~~C~~Cgy 45 (50)
T PRK00432 22 FCPRCGSGFMA--EHLDRWHCGKCGY 45 (50)
T ss_pred cCcCCCcchhe--ccCCcEECCCcCC
Confidence 57777654111 1236777777764
No 222
>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=22.58 E-value=31 Score=33.44 Aligned_cols=22 Identities=45% Similarity=1.313 Sum_probs=0.0
Q ss_pred ccCCCCC---ccccCCCCCccccccCCcc
Q 001043 1073 YHCPFCN---LCRVGRGLGVDFFHCMTCN 1098 (1177)
Q Consensus 1073 yHC~~Cg---iCrvg~gl~~~~fhC~~C~ 1098 (1177)
|.||+|| +=|++-| +.+|.+|+
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 223
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=22.30 E-value=60 Score=41.66 Aligned_cols=34 Identities=21% Similarity=0.515 Sum_probs=18.6
Q ss_pred eeeccccCccccCCCCCCCCCCCCc--ccceEeccccccc
Q 001043 1029 EMMCMRCLKVQPVGPVCTTLSCSGL--SMAKYYCGICKFF 1066 (1177)
Q Consensus 1029 ~~~C~~C~~~q~~~~~C~~~~C~~~--~~a~Y~C~~C~l~ 1066 (1177)
.-+|..|++..+. ..|.+ | |. ..+.-||+.|...
T Consensus 15 akFC~~CG~~l~~-~~Cp~--C-G~~~~~~~~fC~~CG~~ 50 (645)
T PRK14559 15 NRFCQKCGTSLTH-KPCPQ--C-GTEVPVDEAHCPNCGAE 50 (645)
T ss_pred CccccccCCCCCC-CcCCC--C-CCCCCcccccccccCCc
Confidence 4467777765542 45655 4 32 2455566666543
No 224
>PHA00626 hypothetical protein
Probab=22.26 E-value=51 Score=29.42 Aligned_cols=34 Identities=24% Similarity=0.334 Sum_probs=20.5
Q ss_pred eeccccCccccCCCCCCCCCCCCcccceEeccccccccC
Q 001043 1030 MMCMRCLKVQPVGPVCTTLSCSGLSMAKYYCGICKFFDD 1068 (1177)
Q Consensus 1030 ~~C~~C~~~q~~~~~C~~~~C~~~~~a~Y~C~~C~l~dd 1068 (1177)
|.|..|+..+-+ .|.. | ...-.+|-|..|.+++.
T Consensus 1 m~CP~CGS~~Iv--rcg~--c-r~~snrYkCkdCGY~ft 34 (59)
T PHA00626 1 MSCPKCGSGNIA--KEKT--M-RGWSDDYVCCDCGYNDS 34 (59)
T ss_pred CCCCCCCCceee--eece--e-cccCcceEcCCCCCeec
Confidence 457777765544 3333 2 33456788888887653
No 225
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=22.00 E-value=27 Score=44.52 Aligned_cols=47 Identities=21% Similarity=0.554 Sum_probs=36.4
Q ss_pred CCCCCcccccccccCCCceEecCCCCcccHhhHHHHH---hcCCCCCCCccccc
Q 001043 1115 LETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYT---CSHYICPICSKSLG 1165 (1177)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl---~~~~~CPiCrk~v~ 1165 (1177)
....||||.+.+++. ..+.|-|.|...|+..-+ .....||+|+..+.
T Consensus 20 k~lEc~ic~~~~~~p----~~~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~e 69 (684)
T KOG4362|consen 20 KILECPICLEHVKEP----SLLKCDHIFLKFCLNKLFESKKGPKQCALCKSDIE 69 (684)
T ss_pred hhccCCceeEEeecc----chhhhhHHHHhhhhhceeeccCccccchhhhhhhh
Confidence 457899999987764 458999999999988743 33467999996553
No 226
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=21.94 E-value=35 Score=32.36 Aligned_cols=31 Identities=29% Similarity=0.909 Sum_probs=10.4
Q ss_pred CcccCCCCC-----ccccCCCCCccccccCCccccc
Q 001043 1071 VVYHCPFCN-----LCRVGRGLGVDFFHCMTCNCCL 1101 (1177)
Q Consensus 1071 ~~yHC~~Cg-----iCrvg~gl~~~~fhC~~C~~C~ 1101 (1177)
..|.||+|| .|.+-+..|.-.-+|..||.-+
T Consensus 21 ~~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~ 56 (81)
T PF05129_consen 21 KVFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESF 56 (81)
T ss_dssp S----TTT--SS-EEEEEETTTTEEEEEESSS--EE
T ss_pred ceEcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeE
Confidence 456666666 3333333333344444444433
No 227
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=21.75 E-value=55 Score=33.93 Aligned_cols=48 Identities=27% Similarity=0.625 Sum_probs=33.5
Q ss_pred CCCCcccccccccCCCceEec----CCCCcccHhhHHH-HH--hcCCCCCCCccccccc
Q 001043 1116 ETNCPICCDFLFTSSATVRAL----PCGHFMHSDCFQA-YT--CSHYICPICSKSLGDM 1167 (1177)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~L----pCGH~fH~~Ci~~-wl--~~~~~CPiCrk~v~dm 1167 (1177)
--.|-||.|- |.+ -+.| =||=.+..-|..+ |- ..+..||+|+.|.-.-
T Consensus 80 lYeCnIC~et---S~e-e~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKss 134 (140)
T PF05290_consen 80 LYECNICKET---SAE-ERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKSS 134 (140)
T ss_pred ceeccCcccc---cch-hhcCCcccccchHHHHHHHHHHHHHcccCCCCCccccccccc
Confidence 4579999875 332 2333 3898899999887 53 2467899999987543
No 228
>PF10272 Tmpp129: Putative transmembrane protein precursor; InterPro: IPR018801 This entry consists of proteins conserved from worms to humans. They are purported to be transmembrane protein-precursors but their function is unknown.
Probab=21.56 E-value=88 Score=37.45 Aligned_cols=18 Identities=17% Similarity=0.604 Sum_probs=13.8
Q ss_pred HHHHhcCCCCCCCccccc
Q 001043 1148 QAYTCSHYICPICSKSLG 1165 (1177)
Q Consensus 1148 ~~wl~~~~~CPiCrk~v~ 1165 (1177)
+.|+.+.-.||.||+..-
T Consensus 334 ~~Wl~~~~~CPtCRa~FC 351 (358)
T PF10272_consen 334 ETWLSGKCPCPTCRAKFC 351 (358)
T ss_pred hhhhcCCCCCCCCcccce
Confidence 346667788999999764
No 229
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=21.34 E-value=52 Score=33.96 Aligned_cols=10 Identities=30% Similarity=0.879 Sum_probs=6.1
Q ss_pred CcccCCCCCc
Q 001043 1071 VVYHCPFCNL 1080 (1177)
Q Consensus 1071 ~~yHC~~Cgi 1080 (1177)
..|.||.||-
T Consensus 106 ~~~~CP~Cgs 115 (135)
T PRK03824 106 AFLKCPKCGS 115 (135)
T ss_pred cCcCCcCCCC
Confidence 3455777773
No 230
>PF10235 Cript: Microtubule-associated protein CRIPT; InterPro: IPR019367 The CRIPT protein is a cytoskeletal protein involved in microtubule production. This C-terminal domain is essential for binding to the PDZ3 domain of the SAP90 protein, one of a super-family of PDZ-containing proteins that play an important role in coupling the membrane ion channels with their signalling partners [].
Probab=21.26 E-value=66 Score=31.30 Aligned_cols=45 Identities=22% Similarity=0.451 Sum_probs=33.7
Q ss_pred CCCCcccccccccCCCceEecCCCCcccHhhHHHHHhcCCCCCCCcccccccccccCC
Q 001043 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGDMAVLHLP 1173 (1177)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrk~v~dm~~~~~~ 1173 (1177)
...|-||...+.. =||.|...|- .....|.+|.+.|.|...|-++
T Consensus 44 ~~~C~~CK~~v~q---------~g~~YCq~CA----YkkGiCamCGKki~dtk~ykqs 88 (90)
T PF10235_consen 44 SSKCKICKTKVHQ---------PGAKYCQTCA----YKKGICAMCGKKILDTKNYKQS 88 (90)
T ss_pred Ccccccccccccc---------CCCccChhhh----cccCcccccCCeeccccccccc
Confidence 4579999865432 2788999995 2467899999999998877543
No 231
>TIGR00058 Hemerythrin hemerythrin family non-heme iron proteins. This family includes oxygen carrier proteins of various oligomeric states from the vascular fluid (hemerythrin) and muscle (myohemerythrin) of some marine invertebrates. Each unit binds 2 non-heme Fe using 5 H, one E and one D. One member of this family,from the sandworm Nereis diversicolor, is an unusual (non-metallothionein) cadmium-binding protein. Homologous proteins, excluded from this narrowly defined family, are found in archaea and bacteria (see pfam01814).
Probab=20.60 E-value=4.4e+02 Score=26.19 Aligned_cols=20 Identities=20% Similarity=0.283 Sum_probs=16.3
Q ss_pred HHHHHHHHHHHHhHHHHHHH
Q 001043 401 SQADLIMASIQKHFRNEEVQ 420 (1177)
Q Consensus 401 ~~le~L~~~L~~Hf~~EE~q 420 (1177)
..++.|..-...||..||.-
T Consensus 39 ~~l~~L~~y~~~HF~~EE~l 58 (115)
T TIGR00058 39 TALKELIDVTVLHFLDEEAM 58 (115)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 45677788899999999964
No 232
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=20.40 E-value=64 Score=25.61 Aligned_cols=22 Identities=32% Similarity=0.726 Sum_probs=13.2
Q ss_pred Eeccccccc-cCC-CCcccCCCCC
Q 001043 1058 YYCGICKFF-DDE-RVVYHCPFCN 1079 (1177)
Q Consensus 1058 Y~C~~C~l~-dd~-k~~yHC~~Cg 1079 (1177)
|.|..|..- +.. .+...|++||
T Consensus 1 Y~C~~Cg~~~~~~~~~~irC~~CG 24 (32)
T PF03604_consen 1 YICGECGAEVELKPGDPIRCPECG 24 (32)
T ss_dssp EBESSSSSSE-BSTSSTSSBSSSS
T ss_pred CCCCcCCCeeEcCCCCcEECCcCC
Confidence 556666542 222 5667888887
No 233
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=20.38 E-value=52 Score=39.64 Aligned_cols=48 Identities=21% Similarity=0.364 Sum_probs=32.8
Q ss_pred CCCCCcccccccccCCC-ceEecCCCCcccHhhHHHHHhcCCCCCCCcc
Q 001043 1115 LETNCPICCDFLFTSSA-TVRALPCGHFMHSDCFQAYTCSHYICPICSK 1162 (1177)
Q Consensus 1115 ~~~~CpICle~lf~s~~-~v~~LpCGH~fH~~Ci~~wl~~~~~CPiCrk 1162 (1177)
.-..||+|.-.+-.++- ..+.=.|||-|...|...|...+..|.-|-+
T Consensus 305 ~wr~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~~~~~~~~~~~~~~~r 353 (384)
T KOG1812|consen 305 RWRQCPKCKFMIELSEGCNHMTCRCGHQFCYMCGGDWKTHNGECYECCR 353 (384)
T ss_pred hcCcCcccceeeeecCCcceEEeeccccchhhcCcchhhCCccccCccc
Confidence 35678888865432222 2233379999999999999887776665554
No 234
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=20.12 E-value=58 Score=32.17 Aligned_cols=31 Identities=19% Similarity=0.462 Sum_probs=17.7
Q ss_pred CcccCcccccccCCCCCCccccceeeccccCc
Q 001043 1006 KLFTCRFCHDKVSDHSMDRKATTEMMCMRCLK 1037 (1177)
Q Consensus 1006 k~y~Cr~CHde~~~H~~~r~~~~~~~C~~C~~ 1037 (1177)
++|.|.+|+...-.-++++ .+..+.|..|+.
T Consensus 20 t~f~CP~Cge~~v~v~~~k-~~~h~~C~~CG~ 50 (99)
T PRK14892 20 KIFECPRCGKVSISVKIKK-NIAIITCGNCGL 50 (99)
T ss_pred cEeECCCCCCeEeeeecCC-CcceEECCCCCC
Confidence 5677777774333334444 455666666654
Done!