Query 001028
Match_columns 1184
No_of_seqs 531 out of 1512
Neff 5.2
Searched_HMMs 46136
Date Thu Mar 28 13:48:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001028.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001028hhsearch_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 3.6E-44 7.7E-49 391.4 0.6 199 976-1180 21-221 (276)
2 PF05495 zf-CHY: CHY zinc fing 99.8 6.3E-21 1.4E-25 171.9 1.7 70 990-1067 1-71 (71)
3 PF01814 Hemerythrin: Hemeryth 99.2 2.3E-10 5.1E-15 110.7 14.0 124 293-425 2-133 (133)
4 PF13639 zf-RING_2: Ring finge 99.2 5.9E-12 1.3E-16 103.2 0.8 44 1117-1161 1-44 (44)
5 PF01814 Hemerythrin: Hemeryth 99.2 2.5E-10 5.4E-15 110.5 12.4 129 43-176 2-133 (133)
6 COG4357 Zinc finger domain con 98.9 1.3E-10 2.7E-15 108.6 -0.6 57 986-1042 11-75 (105)
7 KOG4628 Predicted E3 ubiquitin 98.9 4.6E-10 1E-14 127.8 3.2 49 1117-1166 230-279 (348)
8 COG5243 HRD1 HRD ubiquitin lig 98.9 5.2E-10 1.1E-14 125.3 3.3 66 1113-1178 284-363 (491)
9 PF12678 zf-rbx1: RING-H2 zinc 98.9 1.2E-09 2.7E-14 99.3 2.9 47 1115-1161 18-73 (73)
10 PF12861 zf-Apc11: Anaphase-pr 98.8 2.8E-09 6.1E-14 99.0 3.4 47 1116-1164 32-81 (85)
11 PRK10992 iron-sulfur cluster r 98.8 7.1E-08 1.5E-12 105.2 13.9 131 294-427 76-218 (220)
12 TIGR03652 FeS_repair_RIC iron- 98.7 1.6E-07 3.4E-12 102.1 12.2 129 294-425 72-216 (216)
13 COG5540 RING-finger-containing 98.6 1.5E-08 3.2E-13 111.7 3.3 57 1109-1166 316-373 (374)
14 PRK10992 iron-sulfur cluster r 98.6 3.9E-07 8.5E-12 99.4 14.3 130 49-178 82-218 (220)
15 PHA02929 N1R/p28-like protein; 98.6 2.5E-08 5.5E-13 109.4 4.4 53 1114-1166 172-228 (238)
16 cd00162 RING RING-finger (Real 98.6 5.1E-08 1.1E-12 78.0 3.5 44 1118-1164 1-45 (45)
17 COG3945 Uncharacterized conser 98.5 2.2E-06 4.8E-11 89.4 14.8 140 292-440 8-158 (189)
18 TIGR03652 FeS_repair_RIC iron- 98.5 1.3E-06 2.8E-11 95.0 13.3 127 49-175 78-215 (216)
19 PF13923 zf-C3HC4_2: Zinc fing 98.4 1E-07 2.3E-12 76.4 1.8 39 1119-1160 1-39 (39)
20 COG5194 APC11 Component of SCF 98.4 2.1E-07 4.6E-12 84.8 2.7 50 1116-1165 31-81 (88)
21 PF13920 zf-C3HC4_3: Zinc fing 98.3 2.4E-07 5.3E-12 78.1 2.1 47 1116-1166 2-49 (50)
22 PRK13276 cell wall biosynthesi 98.3 5.9E-06 1.3E-10 90.2 13.2 125 297-424 83-222 (224)
23 PRK13276 cell wall biosynthesi 98.3 8.4E-06 1.8E-10 89.1 13.6 127 48-174 84-221 (224)
24 smart00184 RING Ring finger. E 98.2 1.2E-06 2.5E-11 67.7 2.7 38 1119-1160 1-39 (39)
25 KOG1493 Anaphase-promoting com 98.1 3.7E-07 8E-12 82.6 -1.0 47 1116-1164 31-80 (84)
26 KOG0802 E3 ubiquitin ligase [P 98.1 9.8E-07 2.1E-11 107.9 1.2 53 1112-1164 287-340 (543)
27 PLN03208 E3 ubiquitin-protein 98.1 3.1E-06 6.8E-11 90.0 4.1 52 1111-1166 13-80 (193)
28 PF14634 zf-RING_5: zinc-RING 98.0 2.9E-06 6.3E-11 69.9 3.0 44 1118-1162 1-44 (44)
29 COG2846 Regulator of cell morp 98.0 4E-05 8.6E-10 81.3 12.0 128 295-425 79-217 (221)
30 PF00097 zf-C3HC4: Zinc finger 98.0 2.3E-06 5.1E-11 68.9 2.1 39 1119-1160 1-41 (41)
31 PHA02926 zinc finger-like prot 98.0 3E-06 6.5E-11 91.1 3.4 61 1113-1173 167-240 (242)
32 KOG0320 Predicted E3 ubiquitin 98.0 2.9E-06 6.3E-11 88.4 1.9 47 1117-1165 132-178 (187)
33 PF15227 zf-C3HC4_4: zinc fing 97.9 4.4E-06 9.5E-11 68.5 1.8 38 1119-1160 1-42 (42)
34 smart00504 Ubox Modified RING 97.8 1.4E-05 3E-10 69.8 3.6 45 1117-1165 2-46 (63)
35 PF13445 zf-RING_UBOX: RING-ty 97.7 1.8E-05 3.8E-10 65.4 1.8 39 1119-1158 1-43 (43)
36 KOG2930 SCF ubiquitin ligase, 97.6 9.3E-06 2E-10 77.6 -0.5 32 1134-1165 77-108 (114)
37 KOG0317 Predicted E3 ubiquitin 97.6 2.3E-05 5E-10 87.1 2.1 48 1116-1167 239-286 (293)
38 KOG0828 Predicted E3 ubiquitin 97.6 2E-05 4.3E-10 92.0 1.3 51 1116-1166 571-635 (636)
39 KOG0804 Cytoplasmic Zn-finger 97.6 2.6E-05 5.7E-10 90.6 1.8 48 1116-1165 175-222 (493)
40 COG2846 Regulator of cell morp 97.5 0.00083 1.8E-08 71.6 12.0 133 45-177 79-218 (221)
41 TIGR00599 rad18 DNA repair pro 97.5 5E-05 1.1E-09 89.3 3.2 47 1116-1166 26-72 (397)
42 KOG0823 Predicted E3 ubiquitin 97.5 5.3E-05 1.2E-09 82.2 3.0 51 1114-1168 45-98 (230)
43 COG3945 Uncharacterized conser 97.5 0.0012 2.7E-08 69.4 12.3 140 44-190 10-157 (189)
44 smart00744 RINGv The RING-vari 97.4 0.0001 2.3E-09 62.5 2.3 42 1118-1161 1-49 (49)
45 KOG1734 Predicted RING-contain 97.2 7.5E-05 1.6E-09 82.1 0.2 50 1116-1165 224-281 (328)
46 KOG2164 Predicted E3 ubiquitin 97.2 0.00014 3.1E-09 86.2 2.4 48 1115-1166 185-237 (513)
47 PF11793 FANCL_C: FANCL C-term 97.2 8.7E-05 1.9E-09 67.4 0.5 50 1116-1165 2-66 (70)
48 TIGR00570 cdk7 CDK-activating 97.2 0.00024 5.2E-09 80.8 3.9 51 1116-1166 3-55 (309)
49 KOG0827 Predicted E3 ubiquitin 97.2 0.00012 2.6E-09 83.8 1.4 49 1116-1165 4-56 (465)
50 KOG1428 Inhibitor of type V ad 97.0 0.00022 4.8E-09 90.3 1.4 114 1028-1165 3416-3544(3738)
51 COG5574 PEX10 RING-finger-cont 96.9 0.00037 7.9E-09 77.0 1.9 47 1116-1166 215-263 (271)
52 KOG0825 PHD Zn-finger protein 96.9 0.00021 4.6E-09 87.2 -0.0 52 1115-1167 122-173 (1134)
53 KOG2177 Predicted E3 ubiquitin 96.9 0.00043 9.3E-09 75.2 1.7 44 1115-1162 12-55 (386)
54 KOG0287 Postreplication repair 96.7 0.00057 1.2E-08 77.2 1.3 46 1117-1166 24-69 (442)
55 KOG4265 Predicted E3 ubiquitin 96.6 0.0011 2.3E-08 76.2 2.8 51 1113-1167 287-338 (349)
56 KOG1940 Zn-finger protein [Gen 96.6 0.00016 3.5E-09 81.1 -4.0 133 690-854 17-149 (276)
57 PF04564 U-box: U-box domain; 96.5 0.0012 2.5E-08 60.4 1.5 47 1116-1166 4-51 (73)
58 KOG1941 Acetylcholine receptor 96.4 0.00065 1.4E-08 78.0 -1.0 61 1107-1168 357-419 (518)
59 KOG4172 Predicted E3 ubiquitin 96.2 0.00071 1.5E-08 58.2 -1.2 50 1115-1168 6-57 (62)
60 COG5432 RAD18 RING-finger-cont 96.1 0.0027 5.9E-08 70.7 2.2 45 1116-1164 25-69 (391)
61 KOG1645 RING-finger-containing 96.0 0.004 8.8E-08 72.3 2.7 49 1116-1164 4-55 (463)
62 KOG1039 Predicted E3 ubiquitin 95.9 0.0051 1.1E-07 71.5 3.2 52 1113-1164 158-220 (344)
63 COG5219 Uncharacterized conser 95.8 0.003 6.4E-08 78.8 0.5 51 1114-1164 1467-1522(1525)
64 COG2461 Uncharacterized conser 95.4 0.094 2E-06 61.5 11.0 132 291-441 85-223 (409)
65 KOG2879 Predicted E3 ubiquitin 95.3 0.012 2.6E-07 65.6 3.2 52 1114-1168 237-290 (298)
66 PF14835 zf-RING_6: zf-RING of 94.7 0.013 2.8E-07 52.5 1.1 44 1117-1165 8-51 (65)
67 KOG4445 Uncharacterized conser 94.4 0.011 2.4E-07 66.4 -0.1 55 1111-1166 110-187 (368)
68 KOG0978 E3 ubiquitin ligase in 94.3 0.013 2.8E-07 73.1 0.3 46 1117-1166 644-690 (698)
69 KOG0311 Predicted E3 ubiquitin 94.1 0.0068 1.5E-07 69.5 -2.6 48 1116-1166 43-91 (381)
70 PF11789 zf-Nse: Zinc-finger o 94.0 0.027 5.9E-07 49.5 1.6 43 1114-1159 9-53 (57)
71 KOG1785 Tyrosine kinase negati 93.9 0.017 3.6E-07 66.9 0.2 55 1109-1167 362-418 (563)
72 PF14570 zf-RING_4: RING/Ubox 93.7 0.047 1E-06 46.5 2.5 45 1119-1163 1-46 (48)
73 PF10367 Vps39_2: Vacuolar sor 93.2 0.034 7.3E-07 53.4 0.9 37 1110-1148 72-108 (109)
74 KOG0824 Predicted E3 ubiquitin 93.0 0.051 1.1E-06 61.5 2.0 48 1114-1165 5-53 (324)
75 KOG0309 Conserved WD40 repeat- 92.7 0.067 1.4E-06 66.2 2.5 49 1109-1159 1021-1069(1081)
76 KOG3268 Predicted E3 ubiquitin 92.6 0.066 1.4E-06 56.4 2.1 30 1136-1165 188-228 (234)
77 KOG0297 TNF receptor-associate 92.5 0.067 1.4E-06 63.7 2.2 62 1114-1178 19-80 (391)
78 PF05883 Baculo_RING: Baculovi 92.2 0.051 1.1E-06 55.3 0.7 42 1116-1158 26-73 (134)
79 KOG3039 Uncharacterized conser 92.0 0.11 2.4E-06 57.4 2.9 52 1114-1166 219-271 (303)
80 KOG4275 Predicted E3 ubiquitin 91.9 0.028 6E-07 63.2 -1.7 50 1116-1172 300-349 (350)
81 PF12906 RINGv: RING-variant d 91.5 0.11 2.3E-06 44.0 1.8 40 1119-1160 1-47 (47)
82 KOG2272 Focal adhesion protein 91.1 0.052 1.1E-06 59.8 -0.6 91 1008-1124 100-200 (332)
83 KOG1571 Predicted E3 ubiquitin 90.6 0.12 2.7E-06 59.9 1.7 46 1113-1165 302-347 (355)
84 KOG3970 Predicted E3 ubiquitin 90.6 0.18 3.9E-06 55.0 2.8 51 1114-1166 48-106 (299)
85 KOG4739 Uncharacterized protei 90.2 0.12 2.6E-06 57.2 1.1 37 1127-1165 12-48 (233)
86 KOG1002 Nucleotide excision re 89.6 0.11 2.4E-06 62.3 0.2 51 1111-1165 531-586 (791)
87 COG2461 Uncharacterized conser 88.9 1.8 3.8E-05 51.3 9.2 137 41-191 85-222 (409)
88 PF14447 Prok-RING_4: Prokaryo 88.9 0.18 4E-06 44.0 1.0 45 1116-1166 7-51 (55)
89 PF07800 DUF1644: Protein of u 88.1 0.37 8E-06 50.4 2.8 49 1116-1168 2-94 (162)
90 KOG2660 Locus-specific chromos 87.3 0.14 3E-06 58.8 -0.8 50 1115-1167 14-63 (331)
91 PF04641 Rtf2: Rtf2 RING-finge 87.1 0.44 9.6E-06 53.8 3.0 52 1113-1166 110-162 (260)
92 KOG0269 WD40 repeat-containing 87.0 0.52 1.1E-05 59.1 3.7 70 1070-1159 751-820 (839)
93 KOG3800 Predicted E3 ubiquitin 86.6 0.43 9.3E-06 54.1 2.5 49 1118-1166 2-52 (300)
94 KOG1814 Predicted E3 ubiquitin 86.5 0.32 7E-06 57.3 1.5 47 1115-1162 183-237 (445)
95 COG5175 MOT2 Transcriptional r 86.1 0.34 7.4E-06 55.5 1.4 56 1116-1171 14-70 (480)
96 KOG4159 Predicted E3 ubiquitin 85.5 0.48 1E-05 56.5 2.3 49 1114-1166 82-130 (398)
97 KOG2114 Vacuolar assembly/sort 84.5 0.42 9.1E-06 60.6 1.2 41 1117-1163 841-881 (933)
98 PHA02862 5L protein; Provision 83.8 0.64 1.4E-05 48.0 2.0 45 1116-1165 2-53 (156)
99 COG5152 Uncharacterized conser 83.5 0.4 8.7E-06 51.5 0.4 45 1117-1165 197-241 (259)
100 COG5236 Uncharacterized conser 83.0 1 2.2E-05 52.0 3.3 66 1096-1165 40-108 (493)
101 KOG0827 Predicted E3 ubiquitin 83.0 0.11 2.3E-06 60.6 -4.4 52 1115-1166 195-246 (465)
102 PRK04023 DNA polymerase II lar 82.2 1.1 2.4E-05 58.1 3.7 44 1031-1080 628-671 (1121)
103 KOG4692 Predicted E3 ubiquitin 82.2 0.78 1.7E-05 53.1 2.1 51 1112-1166 418-468 (489)
104 KOG2034 Vacuolar sorting prote 82.0 0.55 1.2E-05 59.9 0.9 43 1107-1151 808-850 (911)
105 KOG1813 Predicted E3 ubiquitin 80.6 0.62 1.4E-05 53.0 0.6 47 1116-1166 241-287 (313)
106 COG5592 Uncharacterized conser 79.9 5 0.00011 42.4 6.8 100 681-817 30-136 (171)
107 TIGR02481 hemeryth_dom hemeryt 79.5 6.6 0.00014 39.0 7.4 51 361-421 12-62 (126)
108 PRK14890 putative Zn-ribbon RN 78.7 1.6 3.4E-05 38.9 2.4 46 1028-1080 6-56 (59)
109 PHA02825 LAP/PHD finger-like p 78.5 1.5 3.2E-05 46.2 2.5 45 1115-1164 7-58 (162)
110 PF06524 NOA36: NOA36 protein; 75.5 1.4 2.9E-05 49.5 1.3 65 1005-1080 140-217 (314)
111 KOG1701 Focal adhesion adaptor 74.0 1.6 3.4E-05 52.0 1.5 123 1031-1164 276-437 (468)
112 PF08746 zf-RING-like: RING-li 73.1 1.7 3.8E-05 36.2 1.1 41 1119-1160 1-43 (43)
113 PF09538 FYDLN_acid: Protein o 72.9 1.8 3.9E-05 43.0 1.4 17 1064-1080 18-34 (108)
114 KOG1952 Transcription factor N 72.7 2.1 4.5E-05 54.7 2.1 51 1115-1165 190-247 (950)
115 TIGR00595 priA primosomal prot 72.7 2.7 5.9E-05 51.9 3.2 48 999-1052 214-261 (505)
116 KOG3161 Predicted E3 ubiquitin 72.7 1.3 2.8E-05 54.8 0.3 53 1117-1172 12-68 (861)
117 KOG4185 Predicted E3 ubiquitin 71.8 2.4 5.2E-05 48.4 2.3 47 1117-1164 4-54 (296)
118 PF03854 zf-P11: P-11 zinc fin 70.4 1.2 2.6E-05 37.9 -0.4 44 1117-1166 3-47 (50)
119 KOG2817 Predicted E3 ubiquitin 69.6 3.2 6.9E-05 49.2 2.6 47 1117-1164 335-384 (394)
120 PF01529 zf-DHHC: DHHC palmito 69.1 3.4 7.5E-05 43.0 2.6 47 1052-1104 43-89 (174)
121 smart00132 LIM Zinc-binding do 68.0 3.7 8E-05 31.8 1.9 38 1118-1165 1-38 (39)
122 PRK14714 DNA polymerase II lar 68.0 5.2 0.00011 53.5 4.2 52 1029-1083 667-720 (1337)
123 TIGR02300 FYDLN_acid conserved 67.4 2.9 6.2E-05 42.6 1.5 18 1064-1081 18-35 (129)
124 TIGR02481 hemeryth_dom hemeryt 67.0 88 0.0019 31.0 11.9 109 297-424 13-125 (126)
125 PF05502 Dynactin_p62: Dynacti 65.6 4.2 9.2E-05 50.1 2.7 16 1050-1065 19-34 (483)
126 PF02084 Bindin: Bindin; Inte 64.6 22 0.00048 39.5 7.5 40 72-127 124-169 (238)
127 PRK05580 primosome assembly pr 64.3 4.9 0.00011 51.5 3.0 48 999-1052 382-429 (679)
128 COG1198 PriA Primosomal protei 64.2 5.7 0.00012 51.1 3.6 54 999-1059 436-489 (730)
129 PHA03096 p28-like protein; Pro 63.2 3.5 7.6E-05 47.4 1.3 46 1117-1162 179-231 (284)
130 KOG0801 Predicted E3 ubiquitin 63.0 3.5 7.6E-05 43.4 1.2 29 1115-1144 176-204 (205)
131 KOG2066 Vacuolar assembly/sort 62.5 2.9 6.3E-05 53.1 0.6 88 405-496 393-485 (846)
132 PF14446 Prok-RING_1: Prokaryo 61.8 7.3 0.00016 34.3 2.7 35 1115-1149 4-38 (54)
133 KOG1001 Helicase-like transcri 61.4 3.2 6.9E-05 53.0 0.7 44 1117-1165 455-500 (674)
134 PRK00808 hypothetical protein; 61.3 28 0.00061 36.2 7.4 96 361-467 16-122 (150)
135 PRK14873 primosome assembly pr 60.9 6 0.00013 50.6 2.9 47 999-1052 384-430 (665)
136 cd00350 rubredoxin_like Rubred 60.8 6.1 0.00013 31.0 1.9 24 1057-1080 1-25 (33)
137 KOG3002 Zn finger protein [Gen 60.8 5.4 0.00012 46.3 2.3 44 1116-1167 48-93 (299)
138 COG5592 Uncharacterized conser 60.6 29 0.00064 36.9 7.3 94 329-436 29-136 (171)
139 COG5220 TFB3 Cdk activating ki 60.5 2.4 5.1E-05 47.1 -0.6 52 1115-1166 9-65 (314)
140 KOG1100 Predicted E3 ubiquitin 60.1 4.7 0.0001 44.4 1.6 39 1119-1165 161-200 (207)
141 KOG1829 Uncharacterized conser 59.5 2.9 6.2E-05 52.2 -0.2 29 989-1018 345-377 (580)
142 COG2888 Predicted Zn-ribbon RN 59.4 7.6 0.00016 34.8 2.4 45 1029-1080 9-58 (61)
143 KOG2462 C2H2-type Zn-finger pr 59.3 7 0.00015 44.5 2.8 15 1070-1084 159-173 (279)
144 KOG2068 MOT2 transcription fac 56.6 7.2 0.00016 45.5 2.4 52 1114-1165 247-298 (327)
145 PF12773 DZR: Double zinc ribb 56.0 9.8 0.00021 32.1 2.5 22 1032-1056 1-23 (50)
146 PF14357 DUF4404: Domain of un 55.5 83 0.0018 30.1 8.9 82 54-139 2-83 (85)
147 KOG0298 DEAD box-containing he 55.4 3.2 6.9E-05 55.2 -0.8 70 145-214 237-306 (1394)
148 COG4888 Uncharacterized Zn rib 54.0 5.6 0.00012 39.0 0.8 33 1070-1102 20-57 (104)
149 PRK04023 DNA polymerase II lar 53.6 11 0.00025 49.4 3.6 48 1042-1101 626-673 (1121)
150 COG5222 Uncharacterized conser 53.0 6.6 0.00014 44.9 1.3 43 1117-1162 275-318 (427)
151 PF07227 DUF1423: Protein of u 52.2 13 0.00028 45.1 3.5 31 920-952 21-51 (446)
152 KOG1280 Uncharacterized conser 51.7 12 0.00025 44.0 3.0 26 1052-1080 60-87 (381)
153 PF07191 zinc-ribbons_6: zinc- 49.9 7.2 0.00016 36.0 0.8 10 1055-1064 48-57 (70)
154 PRK00808 hypothetical protein; 49.6 3.2E+02 0.007 28.4 13.0 110 297-428 17-130 (150)
155 PF09538 FYDLN_acid: Protein o 49.5 9.4 0.0002 38.1 1.6 32 997-1042 8-39 (108)
156 KOG1609 Protein involved in mR 47.6 6.8 0.00015 44.6 0.4 51 1116-1166 78-135 (323)
157 PRK14559 putative protein seri 47.2 13 0.00029 47.4 2.8 30 1031-1063 3-33 (645)
158 KOG2932 E3 ubiquitin ligase in 47.2 9.3 0.0002 44.1 1.3 32 1134-1167 105-136 (389)
159 PRK01917 cation-binding hemery 46.8 49 0.0011 34.0 6.4 70 398-467 38-120 (139)
160 KOG3850 Predicted membrane pro 46.7 5.7E+02 0.012 31.1 15.3 129 301-445 262-396 (455)
161 PF09788 Tmemb_55A: Transmembr 43.8 16 0.00036 41.3 2.5 82 1088-1182 103-205 (256)
162 PRK00398 rpoP DNA-directed RNA 42.8 20 0.00043 30.1 2.3 23 1057-1079 3-28 (46)
163 PF03833 PolC_DP2: DNA polymer 42.3 8.3 0.00018 49.8 0.0 44 1030-1079 656-699 (900)
164 cd00522 Hemerythrin Hemerythri 42.2 98 0.0021 30.6 7.5 51 361-428 14-68 (113)
165 PHA00626 hypothetical protein 41.2 20 0.00043 31.9 2.1 8 1072-1079 23-30 (59)
166 KOG2593 Transcription initiati 40.3 12 0.00027 45.0 1.0 19 912-930 50-68 (436)
167 cd00729 rubredoxin_SM Rubredox 40.2 21 0.00045 28.5 1.9 24 1057-1080 2-26 (34)
168 COG5109 Uncharacterized conser 39.2 18 0.00038 42.0 1.9 45 1117-1162 337-384 (396)
169 KOG1812 Predicted E3 ubiquitin 39.1 13 0.00029 44.5 1.1 37 1116-1152 146-182 (384)
170 KOG3362 Predicted BBOX Zn-fing 38.8 10 0.00022 39.5 -0.0 26 1055-1084 116-143 (156)
171 KOG0826 Predicted E3 ubiquitin 38.4 20 0.00043 41.9 2.2 46 1116-1164 300-345 (357)
172 PF06220 zf-U1: U1 zinc finger 38.1 12 0.00027 30.5 0.4 13 1055-1067 1-13 (38)
173 KOG1311 DHHC-type Zn-finger pr 37.8 26 0.00056 40.3 3.1 48 1051-1104 107-154 (299)
174 TIGR00373 conserved hypothetic 37.8 11 0.00025 39.7 0.1 23 1057-1079 109-135 (158)
175 PF13901 DUF4206: Domain of un 37.7 15 0.00033 40.2 1.1 31 1127-1162 167-197 (202)
176 PF14631 FancD2: Fanconi anaem 37.0 6E+02 0.013 36.1 15.9 99 127-228 192-306 (1426)
177 PRK06266 transcription initiat 36.6 13 0.00027 40.2 0.3 23 1057-1079 117-143 (178)
178 PF02891 zf-MIZ: MIZ/SP-RING z 35.8 28 0.0006 30.0 2.2 41 1117-1163 3-50 (50)
179 PF00412 LIM: LIM domain; Int 35.7 15 0.00033 31.3 0.6 40 1119-1168 1-40 (58)
180 COG1198 PriA Primosomal protei 35.1 35 0.00075 44.3 3.8 44 1027-1079 433-482 (730)
181 PLN03086 PRLI-interacting fact 34.9 16 0.00034 45.9 0.8 31 1092-1125 479-513 (567)
182 PF04216 FdhE: Protein involve 34.6 87 0.0019 36.1 6.6 42 911-952 111-153 (290)
183 PF05502 Dynactin_p62: Dynacti 34.3 31 0.00068 42.7 3.1 10 1007-1016 5-14 (483)
184 PRK14714 DNA polymerase II lar 34.2 35 0.00075 46.3 3.6 33 1043-1080 668-700 (1337)
185 PF08271 TF_Zn_Ribbon: TFIIB z 34.1 19 0.00042 29.7 0.9 13 1067-1079 14-26 (43)
186 COG0143 MetG Methionyl-tRNA sy 34.1 26 0.00057 44.1 2.5 45 1054-1104 123-168 (558)
187 PF00301 Rubredoxin: Rubredoxi 32.8 29 0.00062 29.8 1.8 9 1057-1065 1-9 (47)
188 PLN02189 cellulose synthase 32.7 33 0.00071 45.8 3.1 51 1114-1165 32-87 (1040)
189 PF00628 PHD: PHD-finger; Int 32.6 8.2 0.00018 32.4 -1.5 43 1119-1162 2-50 (51)
190 KOG2807 RNA polymerase II tran 32.5 48 0.001 38.9 3.9 103 1053-1163 272-376 (378)
191 TIGR00622 ssl1 transcription f 32.2 92 0.002 31.5 5.4 47 1116-1162 55-111 (112)
192 PRK07219 DNA topoisomerase I; 30.7 73 0.0016 42.1 5.8 63 1060-1127 672-744 (822)
193 COG5183 SSM4 Protein involved 30.2 25 0.00055 45.1 1.4 49 1115-1165 11-66 (1175)
194 PLN02436 cellulose synthase A 29.8 39 0.00085 45.2 3.1 51 1114-1165 34-89 (1094)
195 COG1996 RPC10 DNA-directed RNA 29.7 29 0.00062 30.2 1.2 30 1054-1083 3-35 (49)
196 KOG4399 C2HC-type Zn-finger pr 29.7 13 0.00028 42.1 -1.1 47 1052-1102 256-302 (325)
197 PRK14559 putative protein seri 29.7 38 0.00082 43.4 2.9 33 1029-1065 15-49 (645)
198 KOG0006 E3 ubiquitin-protein l 28.7 46 0.001 38.7 3.0 78 1066-1151 169-254 (446)
199 KOG3842 Adaptor protein Pellin 28.2 51 0.0011 38.4 3.3 57 1116-1172 341-421 (429)
200 PRK14892 putative transcriptio 28.0 38 0.00082 33.4 1.9 33 1071-1105 20-56 (99)
201 KOG1044 Actin-binding LIM Zn-f 27.7 54 0.0012 41.0 3.5 116 998-1129 16-146 (670)
202 PF06937 EURL: EURL protein; 27.7 37 0.00081 38.8 2.0 44 1114-1158 28-74 (285)
203 smart00249 PHD PHD zinc finger 27.4 26 0.00057 27.8 0.6 41 1119-1160 2-47 (47)
204 KOG2272 Focal adhesion protein 26.9 42 0.0009 38.0 2.2 143 993-1165 115-291 (332)
205 KOG4654 Uncharacterized conser 26.7 9.1E+02 0.02 26.8 12.3 150 43-200 41-213 (252)
206 KOG4718 Non-SMC (structural ma 26.7 31 0.00066 38.2 1.1 42 1117-1161 182-223 (235)
207 KOG4362 Transcriptional regula 26.7 19 0.00042 45.9 -0.4 48 1115-1166 20-70 (684)
208 TIGR02300 FYDLN_acid conserved 26.0 38 0.00082 34.8 1.6 32 997-1042 8-39 (129)
209 KOG0802 E3 ubiquitin ligase [P 26.0 30 0.00065 43.3 1.1 43 1115-1165 478-520 (543)
210 PF04710 Pellino: Pellino; In 25.6 23 0.0005 42.4 0.0 35 1128-1162 299-336 (416)
211 PF06377 Adipokin_hormo: Adipo 25.0 1.6E+02 0.0034 25.7 4.8 37 629-665 7-45 (48)
212 KOG1312 DHHC-type Zn-finger pr 25.0 23 0.0005 40.7 -0.1 32 1076-1111 149-180 (341)
213 PF13824 zf-Mss51: Zinc-finger 24.9 45 0.00099 29.6 1.7 12 1070-1081 12-23 (55)
214 smart00451 ZnF_U1 U1-like zinc 24.8 36 0.00077 26.2 0.9 11 1056-1066 2-12 (35)
215 cd00522 Hemerythrin Hemerythri 24.8 3.4E+02 0.0075 26.7 8.1 61 117-195 14-78 (113)
216 PRK13428 F0F1 ATP synthase sub 24.7 9.6E+02 0.021 29.7 13.5 30 923-952 216-245 (445)
217 PHA00626 hypothetical protein 24.6 42 0.00092 29.9 1.4 34 1030-1068 1-34 (59)
218 PRK00432 30S ribosomal protein 24.3 42 0.0009 29.1 1.3 24 1074-1099 22-45 (50)
219 PF14445 Prok-RING_2: Prokaryo 23.9 7.6 0.00016 33.7 -3.1 45 1054-1103 4-53 (57)
220 KOG3053 Uncharacterized conser 23.7 27 0.00059 39.6 0.1 54 1111-1164 15-81 (293)
221 PF15353 HECA: Headcase protei 23.7 36 0.00078 33.9 0.9 16 1137-1152 39-54 (107)
222 PRK00420 hypothetical protein; 23.7 45 0.00097 33.7 1.6 30 1115-1165 22-51 (112)
223 PF01780 Ribosomal_L37ae: Ribo 23.5 29 0.00063 33.7 0.2 28 1071-1099 34-61 (90)
224 PRK03824 hypA hydrogenase nick 23.5 47 0.001 34.3 1.8 10 1071-1080 106-115 (135)
225 smart00531 TFIIE Transcription 22.9 30 0.00064 36.0 0.2 7 1073-1079 124-130 (147)
226 PLN02638 cellulose synthase A 22.7 61 0.0013 43.6 2.9 51 1113-1164 14-69 (1079)
227 PRK03564 formate dehydrogenase 22.3 93 0.002 36.6 4.0 62 998-1079 187-259 (309)
228 PF10272 Tmpp129: Putative tra 22.0 74 0.0016 38.1 3.2 18 1148-1165 334-351 (358)
229 KOG1428 Inhibitor of type V ad 21.7 29 0.00063 47.0 -0.1 75 978-1064 3587-3663(3738)
230 PF01780 Ribosomal_L37ae: Ribo 21.4 38 0.00082 32.9 0.6 30 1055-1084 33-65 (90)
231 PF05129 Elf1: Transcription e 21.1 37 0.0008 32.2 0.4 9 1071-1079 21-29 (81)
232 PF05290 Baculo_IE-1: Baculovi 20.8 49 0.0011 34.3 1.2 48 1115-1166 79-133 (140)
233 KOG4577 Transcription factor L 20.3 21 0.00046 40.8 -1.5 59 1107-1175 80-141 (383)
234 KOG1311 DHHC-type Zn-finger pr 20.3 53 0.0012 37.7 1.6 33 1071-1110 112-144 (299)
235 PTZ00255 60S ribosomal protein 20.1 48 0.001 32.2 1.0 29 1070-1099 34-62 (90)
No 1
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=100.00 E-value=3.6e-44 Score=391.40 Aligned_cols=199 Identities=47% Similarity=1.054 Sum_probs=189.2
Q ss_pred CCCCccccccccCCCccccccccccccccCCcccCcccccccCCCCCCccccceeeccccCccccCCCCCCCCCCCCccc
Q 001028 976 CSPSFRDAEKQVFGCEHYKRNCKLRAACCGKLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVGPVCTTLSCSGLSM 1055 (1184)
Q Consensus 976 ~~~~~~~~~~~~~gC~HY~r~c~l~~~cC~~~y~Cr~CHde~~~H~~~r~~~~~~~C~~C~~~q~~~~~C~~~~C~~~~~ 1055 (1184)
..+++.|+...++||+||+|+|++++|||+++|+|++||++..+|.++|+.+.+++|+.|.++||++++|.+ | +..+
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 346788999999999999999999999999999999999999999999999999999999999999999998 4 7789
Q ss_pred ceEecccccCccCC-CCcccCCCCCccccCCCCCccccccCCCcccccccc-ccccccccCccCcccccccccccCCCce
Q 001028 1056 AKYYCGICKFFDDE-RVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLAKKL-VDHKCREKGLETNCPICCDFLFTSSATV 1133 (1184)
Q Consensus 1056 a~Y~C~iC~l~dd~-k~~yHC~~CgiCRvG~gl~~~~fHC~~C~~C~s~~l-~~H~C~e~~~~~~CpICle~lf~s~~~v 1133 (1184)
++|||.+|++|||+ ..||||++|||||+|.++ |||||++|+.|+++.+ +.|+|+|++.+.+||||.+++|.+...+
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 EecCCCCCCChhhHHHHhhcCCCCCCCCccccccCccccccccchhh
Q 001028 1134 RALPCGHFMHSDCFQAYTCSHYICPICSKSLGDMAVSPLFRTTSVVL 1180 (1184)
Q Consensus 1134 ~~LpCGH~fH~~Ci~~wl~~~~tCPiCrk~v~~m~~y~~~~~~~v~~ 1180 (1184)
..++|||.+|..|++.+...+|+||+|.+ ++||..||++.+.+|+-
T Consensus 176 ~~~~CgH~~h~~cf~e~~~~~y~CP~C~~-~~d~~~~~~~~d~~l~~ 221 (276)
T KOG1940|consen 176 GVLKCGHYMHSRCFEEMICEGYTCPICSK-PGDMSHYFRKLDKELAG 221 (276)
T ss_pred CccCcccchHHHHHHHHhccCCCCCcccc-hHHHHHHHHHHHHHHhc
Confidence 99999999999999999988899999999 99999999999888864
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=99.80 E-value=6.3e-21 Score=171.88 Aligned_cols=70 Identities=44% Similarity=1.197 Sum_probs=53.7
Q ss_pred Ccccccc-ccccccccCCcccCcccccccCCCCCCccccceeeccccCccccCCCCCCCCCCCCcccceEecccccCcc
Q 001028 990 CEHYKRN-CKLRAACCGKLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVGPVCTTLSCSGLSMAKYYCGICKFFD 1067 (1184)
Q Consensus 990 C~HY~r~-c~l~~~cC~~~y~Cr~CHde~~~H~~~r~~~~~~~C~~C~~~q~~~~~C~~~~C~~~~~a~Y~C~iC~l~d 1067 (1184)
|+||+|+ |+|+||||++|||||+|||+.++|+++|+.+++|+||.|+++|++++. + | + |+|+|++|++||
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=2.3e-10 Score=110.74 Aligned_cols=124 Identities=26% Similarity=0.366 Sum_probs=110.1
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcccHHHHHHHHHHHHHHHHhhhhccccchhhhhhhhh--------hhHH
Q 001028 293 PIDEIMLWHNAIKRELNDIAEAARKIQLSGDFSDLSAFNKRLQFIAEVCIFHSIAEDKVIFPAVDVEL--------SFAQ 364 (1184)
Q Consensus 293 pid~l~~~HkALRrEL~~L~~~a~~i~~~gd~~~L~~L~~r~~fl~~vl~~Hs~aEDevlFPaL~~r~--------~me~ 364 (1184)
+++.|...|+.||+.++.+...+... ++..++..+...+.+|...+..|+..||.++||.|..+. .+..
T Consensus 2 ~i~~l~~~H~~~~~~~~~l~~~~~~~---~~~~~~~~l~~~~~~l~~~l~~H~~~EE~~l~p~l~~~~~~~~~~~~~~~~ 78 (133)
T PF01814_consen 2 PIDELRRDHRALRRLLAELEEALDEL---PDDEDLRALRELLDELRRELRHHHAREEEYLFPALERRDPRGDALIAELRR 78 (133)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHH---CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHHHH-CCCHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhC---cCchhHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhccccchhhHHH
Confidence 78999999999999999999999987 455678999999999999999999999999999999332 8899
Q ss_pred hHHHHHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 001028 365 EHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPLA 425 (1184)
Q Consensus 365 EH~~ie~l~e~l~~ll~~~~~~~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qvfPLl 425 (1184)
||..+...++.+...+...... ......+...+..+...+..|+.+||+.+||++
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=99.17 E-value=5.9e-12 Score=103.19 Aligned_cols=44 Identities=34% Similarity=0.951 Sum_probs=38.1
Q ss_pred CcccccccccccCCCceEecCCCCCCChhhHHHHhhcCCCCCCCC
Q 001028 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICS 1161 (1184)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~tCPiCr 1161 (1184)
++|+||++++ ...+.+..++|||.||.+|+.+|++.+++||+||
T Consensus 1 d~C~IC~~~~-~~~~~~~~l~C~H~fh~~Ci~~~~~~~~~CP~CR 44 (44)
T PF13639_consen 1 DECPICLEEF-EDGEKVVKLPCGHVFHRSCIKEWLKRNNSCPVCR 44 (44)
T ss_dssp -CETTTTCBH-HTTSCEEEETTSEEEEHHHHHHHHHHSSB-TTTH
T ss_pred CCCcCCChhh-cCCCeEEEccCCCeeCHHHHHHHHHhCCcCCccC
Confidence 4799999995 4467788999999999999999999999999997
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=2.5e-10 Score=110.54 Aligned_cols=129 Identities=33% Similarity=0.416 Sum_probs=115.6
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHHHh---hhHHHHHHH
Q 001028 43 PILIFLFFHKAIKSELDVLHRAAMAFATNLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIR---VKNIARTYS 119 (1184)
Q Consensus 43 Pi~~~~~~HkAlR~el~~l~~~~~~~~~~~~d~~~~~~l~~r~~~L~~~~~~H~~aEDevI~PaL~~R---v~~v~~~~~ 119 (1184)
||+.+...|+.||+.+..+...+... + +......+...+.+|...+..|+..|++++||.|+.+ .++.+..+.
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 001028 120 LEHEGESVLFDQLFELLNSSMRNEESYRRELASCTGALQTSISQHMSKEEEQVFPLL 176 (1184)
Q Consensus 120 ~EH~~~~~lf~~l~~~l~~~~~~~~~~~~eLa~~l~~l~~~l~qHm~~EE~~v~PLl 176 (1184)
.||..+...++.+...+..+. ........+...+.++...+.+||.+||+.++|++
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=98.93 E-value=1.3e-10 Score=108.55 Aligned_cols=57 Identities=30% Similarity=0.725 Sum_probs=50.0
Q ss_pred ccCCCcccccc---ccccccccCCcccCcccccccCCCCCCcc-----ccceeeccccCccccCC
Q 001028 986 QVFGCEHYKRN---CKLRAACCGKLFTCRFCHDKVSDHSMDRK-----ATTEMMCMRCLKVQPVG 1042 (1184)
Q Consensus 986 ~~~gC~HY~r~---c~l~~~cC~~~y~Cr~CHde~~~H~~~r~-----~~~~~~C~~C~~~q~~~ 1042 (1184)
+.++|.||+.. ++|+|.||+|||+|..|||+.++||+.++ ..+.|+||.|.++..+.
T Consensus 11 ~etRC~Hyht~~Diialkc~~C~kyYaCy~CHdel~~Hpf~p~~~~~~~~~~iiCGvC~~~LT~~ 75 (105)
T COG4357 11 QETRCLHYHTPLDIIALKCKCCQKYYACYHCHDELEDHPFEPWGLQEFNPKAIICGVCRKLLTRA 75 (105)
T ss_pred ccceeeEecCccceEeeeechhhhhhhHHHHHhHHhcCCCccCChhhcCCccEEhhhhhhhhhHH
Confidence 56799999999 78999999999999999999999999864 34679999999877543
No 7
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.92 E-value=4.6e-10 Score=127.78 Aligned_cols=49 Identities=27% Similarity=0.846 Sum_probs=44.8
Q ss_pred CcccccccccccCCCceEecCCCCCCChhhHHHHhhcCC-CCCCCCccccc
Q 001028 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHY-ICPICSKSLGD 1166 (1184)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~-tCPiCrk~v~~ 1166 (1184)
..|+||+|+ |..++.++.|||+|.||..||++||..+. .||+|++++..
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 689999999 88999999999999999999999997765 49999999875
No 8
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=98.91 E-value=5.2e-10 Score=125.34 Aligned_cols=66 Identities=33% Similarity=0.781 Sum_probs=52.6
Q ss_pred cCccCcccccccccccCC---------CceEecCCCCCCChhhHHHHhhcCCCCCCCCcc-ccccCc----cccccccch
Q 001028 1113 KGLETNCPICCDFLFTSS---------ATVRALPCGHFMHSDCFQAYTCSHYICPICSKS-LGDMAV----SPLFRTTSV 1178 (1184)
Q Consensus 1113 ~~~~~~CpICle~lf~s~---------~~v~~LpCGH~fH~~Ci~~wl~~~~tCPiCrk~-v~~m~~----y~~~~~~~v 1178 (1184)
...+..|.||||+|+.++ ..-+.|||||.+|.+|++.|+.++.+|||||.+ +.||+. -+.-+++++
T Consensus 284 ~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERqQTCPICr~p~ifd~~~~~~~s~~v~nt~I 363 (491)
T COG5243 284 TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQTCPICRRPVIFDQSSPTPASPNVRNTQI 363 (491)
T ss_pred cCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhccCCCcccCccccccCCCCcCCccccccee
Confidence 446788999999987664 234789999999999999999999999999999 667764 344444444
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=98.85 E-value=1.2e-09 Score=99.33 Aligned_cols=47 Identities=30% Similarity=0.757 Sum_probs=37.7
Q ss_pred ccCcccccccccccC---------CCceEecCCCCCCChhhHHHHhhcCCCCCCCC
Q 001028 1115 LETNCPICCDFLFTS---------SATVRALPCGHFMHSDCFQAYTCSHYICPICS 1161 (1184)
Q Consensus 1115 ~~~~CpICle~lf~s---------~~~v~~LpCGH~fH~~Ci~~wl~~~~tCPiCr 1161 (1184)
.+++|+||++.+.+. ...+...+|||.||..||.+|+..+.+||+||
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=98.80 E-value=2.8e-09 Score=99.02 Aligned_cols=47 Identities=21% Similarity=0.514 Sum_probs=37.2
Q ss_pred cCcccccccccccCCCceEecCCCCCCChhhHHHHhhc---CCCCCCCCccc
Q 001028 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS---HYICPICSKSL 1164 (1184)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~---~~tCPiCrk~v 1164 (1184)
+..||.|..+ ...-++....|+|.||.+||.+|+.. +.+||+||+..
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 5678888765 33446666789999999999999975 57899999874
No 11
>PRK10992 iron-sulfur cluster repair di-iron protein; Provisional
Probab=98.77 E-value=7.1e-08 Score=105.19 Aligned_cols=131 Identities=18% Similarity=0.318 Sum_probs=106.4
Q ss_pred HHHH-HHHHHHHHHHHHHHHHHHHHhcc--cCCcccHHHHHHHHHHHHHHHHhhhhccccchhhhhhhhh---------h
Q 001028 294 IDEI-MLWHNAIKRELNDIAEAARKIQL--SGDFSDLSAFNKRLQFIAEVCIFHSIAEDKVIFPAVDVEL---------S 361 (1184)
Q Consensus 294 id~l-~~~HkALRrEL~~L~~~a~~i~~--~gd~~~L~~L~~r~~fl~~vl~~Hs~aEDevlFPaL~~r~---------~ 361 (1184)
||.+ ..-|..+|++|..|.+.+.++.. .++...+..+..-+..|...+..|+..|++++||+|.+.. .
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 2334567888888999999999999999999999999631 8
Q ss_pred hHHhHHHHHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHh
Q 001028 362 FAQEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPLARR 427 (1184)
Q Consensus 362 me~EH~~ie~l~e~l~~ll~~~~~~~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qvfPLl~~ 427 (1184)
|..||+++...+.+|..++...... ..+...++.+-..+..+...|.+|..+||+.+||++..
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 9999999999999999888664211 11124577777888889999999999999999998764
No 12
>TIGR03652 FeS_repair_RIC iron-sulfur cluster repair di-iron protein. Members of this protein family, designated variously as YftE, NorA, DrnN, and NipC, are di-iron proteins involved in the repair of iron-sulfur clusters. Previously assigned names reflect pleiotropic effects of damage from NO or other oxidative stress when this protein is mutated. The suggested name now is RIC, for Repair of Iron Centers.
Probab=98.66 E-value=1.6e-07 Score=102.11 Aligned_cols=129 Identities=20% Similarity=0.309 Sum_probs=103.2
Q ss_pred HHHH-HHHHHHHHHHHHHHHHHHHHhcc--cCCcccHHHHHHHHHHHHHHHHhhhhccccchhhhhhhh-----------
Q 001028 294 IDEI-MLWHNAIKRELNDIAEAARKIQL--SGDFSDLSAFNKRLQFIAEVCIFHSIAEDKVIFPAVDVE----------- 359 (1184)
Q Consensus 294 id~l-~~~HkALRrEL~~L~~~a~~i~~--~gd~~~L~~L~~r~~fl~~vl~~Hs~aEDevlFPaL~~r----------- 359 (1184)
||.+ ...|..||++|..|...+.++.. ..+...+..+..-+..|..-+..|+..|++++||+|.+.
T Consensus 72 id~i~~~hH~~i~~~l~~L~~l~~kv~~~hg~~~~~l~~l~~~~~~~~~eL~~H~~kEE~~LFP~l~~~~~g~~~~~~~~ 151 (216)
T TIGR03652 72 IDHIVDRHHEYLREELPELIPLATKVARVHGDHHPELIGLAELFRELKAELEQHLMKEEQILFPAIIEYKRGNPAQAIGT 151 (216)
T ss_pred HHHHHHHHhHHHHHHHHHHHHHHHHHHHHhCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHccCccccccc
Confidence 4443 77899999999999998877642 233446788889999999999999999999999999741
Q ss_pred -h-hhHHhHHHHHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 001028 360 -L-SFAQEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPLA 425 (1184)
Q Consensus 360 -~-~me~EH~~ie~l~e~l~~ll~~~~~~~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qvfPLl 425 (1184)
+ .|..||+++...+.+|..++..... |......++.+...+..+...|.+|..+||+.+||.+
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 13
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.63 E-value=1.5e-08 Score=111.69 Aligned_cols=57 Identities=26% Similarity=0.676 Sum_probs=49.0
Q ss_pred cccccCccCcccccccccccCCCceEecCCCCCCChhhHHHHhh-cCCCCCCCCccccc
Q 001028 1109 KCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC-SHYICPICSKSLGD 1166 (1184)
Q Consensus 1109 ~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~-~~~tCPiCrk~v~~ 1166 (1184)
.-.|.....+|+|||++ |...+.++++||.|.||..|+++|+. .+..||+||..+.+
T Consensus 316 ~~~ea~~GveCaICms~-fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iPP 373 (374)
T COG5540 316 RAVEADKGVECAICMSN-FIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIPP 373 (374)
T ss_pred hHHhcCCCceEEEEhhh-hcccceEEEeccCceechhHHHHHHhhhcccCCccCCCCCC
Confidence 33455566899999999 67788899999999999999999986 68899999998764
No 14
>PRK10992 iron-sulfur cluster repair di-iron protein; Provisional
Probab=98.63 E-value=3.9e-07 Score=99.45 Aligned_cols=130 Identities=17% Similarity=0.211 Sum_probs=110.2
Q ss_pred HHHHHHHHHHHHHHHHHHHhcc-CCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHHHh----hhHHHHHHHhhhh
Q 001028 49 FFHKAIKSELDVLHRAAMAFAT-NLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIR----VKNIARTYSLEHE 123 (1184)
Q Consensus 49 ~~HkAlR~el~~l~~~~~~~~~-~~~d~~~~~~l~~r~~~L~~~~~~H~~aEDevI~PaL~~R----v~~v~~~~~~EH~ 123 (1184)
.-|.-+|++|..|.+++..+.. --++......+..-++.|..-+..|+..|.+++||.|... ..+.+..|..||+
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 1144566778888899999999999999999999999962 3567899999999
Q ss_pred hHHHHHHHHHHHHHhhhcCch--hHHHHHHHHHHHHHHHHHHhHHHHHHHhhhHHHh
Q 001028 124 GESVLFDQLFELLNSSMRNEE--SYRRELASCTGALQTSISQHMSKEEEQVFPLLIE 178 (1184)
Q Consensus 124 ~~~~lf~~l~~~l~~~~~~~~--~~~~eLa~~l~~l~~~l~qHm~~EE~~v~PLl~~ 178 (1184)
++..++..|.+..+......+ ..++.+...+..+...|.+|.++|+..+||.+.+
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=98.61 E-value=2.5e-08 Score=109.35 Aligned_cols=53 Identities=17% Similarity=0.542 Sum_probs=42.5
Q ss_pred CccCcccccccccccCCC----ceEecCCCCCCChhhHHHHhhcCCCCCCCCccccc
Q 001028 1114 GLETNCPICCDFLFTSSA----TVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1166 (1184)
Q Consensus 1114 ~~~~~CpICle~lf~s~~----~v~~LpCGH~fH~~Ci~~wl~~~~tCPiCrk~v~~ 1166 (1184)
+.+..||||++.+..... -....+|||.||..||.+|+..+.+||+||..+..
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 12345899999999999999999999999998764
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=98.55 E-value=5.1e-08 Score=77.95 Aligned_cols=44 Identities=34% Similarity=0.921 Sum_probs=37.3
Q ss_pred cccccccccccCCCceEecCCCCCCChhhHHHHhhc-CCCCCCCCccc
Q 001028 1118 NCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS-HYICPICSKSL 1164 (1184)
Q Consensus 1118 ~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~-~~tCPiCrk~v 1164 (1184)
.|+||++.+ ...+...+|||.||..|+..|+.. +..||+|++.+
T Consensus 1 ~C~iC~~~~---~~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~~ 45 (45)
T cd00162 1 ECPICLEEF---REPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45 (45)
T ss_pred CCCcCchhh---hCceEecCCCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence 599999985 345666789999999999999987 78899999864
No 17
>COG3945 Uncharacterized conserved protein [Function unknown]
Probab=98.50 E-value=2.2e-06 Score=89.37 Aligned_cols=140 Identities=21% Similarity=0.284 Sum_probs=112.2
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHhcccC--CcccHHHHHHHHHHHHHHHHhhhhccccchhhhhhhhh---------
Q 001028 292 CPIDEIMLWHNAIKRELNDIAEAARKIQLSG--DFSDLSAFNKRLQFIAEVCIFHSIAEDKVIFPAVDVEL--------- 360 (1184)
Q Consensus 292 ~pid~l~~~HkALRrEL~~L~~~a~~i~~~g--d~~~L~~L~~r~~fl~~vl~~Hs~aEDevlFPaL~~r~--------- 360 (1184)
.-++.|+-.|+.|.+-|.-|...+-.+. .| +.+++..+.+-++-|++- .||..|+.++||-|..+.
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 4578889999999999999988888775 44 344556665555555554 578889999999999774
Q ss_pred hhHHhHHHHHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhhCCHHHHHHHHHh
Q 001028 361 SFAQEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPLARRHFSPKRQRELLYQ 440 (1184)
Q Consensus 361 ~me~EH~~ie~l~e~l~~ll~~~~~~~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qvfPLl~~~fS~eEq~eL~~~ 440 (1184)
.|..||.....++..|.+.+..+.+.+. +....++..+......+.+|..+|+.++||++.+.||.+ |.++..+
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 224556667777788999999999999999999999999 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=98.48 E-value=1.3e-06 Score=95.01 Aligned_cols=127 Identities=24% Similarity=0.300 Sum_probs=106.8
Q ss_pred HHHHHHHHHHHHHHHHHHHhcc-CCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHHH--hh------hHHHHHHH
Q 001028 49 FFHKAIKSELDVLHRAAMAFAT-NLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDI--RV------KNIARTYS 119 (1184)
Q Consensus 49 ~~HkAlR~el~~l~~~~~~~~~-~~~d~~~~~~l~~r~~~L~~~~~~H~~aEDevI~PaL~~--Rv------~~v~~~~~ 119 (1184)
.-|+.+|++|..|..++..+.. .-.+...+..+.+-++.|..-+..|+..|.+++||.|.. +. .+.+..|.
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 001028 120 LEHEGESVLFDQLFELLNSSMRNEE--SYRRELASCTGALQTSISQHMSKEEEQVFPL 175 (1184)
Q Consensus 120 ~EH~~~~~lf~~l~~~l~~~~~~~~--~~~~eLa~~l~~l~~~l~qHm~~EE~~v~PL 175 (1184)
.||+++...+++|....+......+ ..++.+...+.++...|.+|.++||..+||.
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=98.41 E-value=1e-07 Score=76.38 Aligned_cols=39 Identities=41% Similarity=0.972 Sum_probs=33.5
Q ss_pred ccccccccccCCCceEecCCCCCCChhhHHHHhhcCCCCCCC
Q 001028 1119 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPIC 1160 (1184)
Q Consensus 1119 CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~tCPiC 1160 (1184)
||||++.+. +++..++|||.|+..|+.+|++.+.+||+|
T Consensus 1 C~iC~~~~~---~~~~~~~CGH~fC~~C~~~~~~~~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDELR---DPVVVTPCGHSFCKECIEKYLEKNPKCPVC 39 (39)
T ss_dssp ETTTTSB-S---SEEEECTTSEEEEHHHHHHHHHCTSB-TTT
T ss_pred CCCCCCccc---CcCEECCCCCchhHHHHHHHHHCcCCCcCC
Confidence 899998743 367889999999999999999999999998
No 20
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=98.35 E-value=2.1e-07 Score=84.76 Aligned_cols=50 Identities=20% Similarity=0.395 Sum_probs=38.6
Q ss_pred cCcccccccccccCCC-ceEecCCCCCCChhhHHHHhhcCCCCCCCCcccc
Q 001028 1116 ETNCPICCDFLFTSSA-TVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1165 (1184)
Q Consensus 1116 ~~~CpICle~lf~s~~-~v~~LpCGH~fH~~Ci~~wl~~~~tCPiCrk~v~ 1165 (1184)
.+.||-|...+...++ ++.-.-|.|.||.+||..||.+...||+||+...
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 4567778765433332 3444689999999999999999999999999754
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=98.32 E-value=2.4e-07 Score=78.07 Aligned_cols=47 Identities=32% Similarity=0.844 Sum_probs=39.2
Q ss_pred cCcccccccccccCCCceEecCCCCC-CChhhHHHHhhcCCCCCCCCccccc
Q 001028 1116 ETNCPICCDFLFTSSATVRALPCGHF-MHSDCFQAYTCSHYICPICSKSLGD 1166 (1184)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCGH~-fH~~Ci~~wl~~~~tCPiCrk~v~~ 1166 (1184)
+..|+||++. ...+..+||||. |...|+..|+....+||+||+.|.+
T Consensus 2 ~~~C~iC~~~----~~~~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~~ 49 (50)
T PF13920_consen 2 DEECPICFEN----PRDVVLLPCGHLCFCEECAERLLKRKKKCPICRQPIES 49 (50)
T ss_dssp HSB-TTTSSS----BSSEEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-SE
T ss_pred cCCCccCCcc----CCceEEeCCCChHHHHHHhHHhcccCCCCCcCChhhcC
Confidence 4689999986 234788899999 9999999999999999999998753
No 22
>PRK13276 cell wall biosynthesis protein ScdA; Provisional
Probab=98.31 E-value=5.9e-06 Score=90.25 Aligned_cols=125 Identities=13% Similarity=0.165 Sum_probs=105.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcc--cCCcccHHHHHHHHHHHHHHHHhhhhccccchhhhhhhh-------------hh
Q 001028 297 IMLWHNAIKRELNDIAEAARKIQL--SGDFSDLSAFNKRLQFIAEVCIFHSIAEDKVIFPAVDVE-------------LS 361 (1184)
Q Consensus 297 l~~~HkALRrEL~~L~~~a~~i~~--~gd~~~L~~L~~r~~fl~~vl~~Hs~aEDevlFPaL~~r-------------~~ 361 (1184)
+...|..+|++|..|...+.++.. .++...+..+...+..+..-|..|-..|+.++||++.+. ..
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 18
Q ss_pred hHHhHHHHHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 001028 362 FAQEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPL 424 (1184)
Q Consensus 362 me~EH~~ie~l~e~l~~ll~~~~~~~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qvfPL 424 (1184)
|+.||+.+.+.+.+|++++..... |.++...|+.|=..+.++...|.+|.+.|-+.+||-
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 999999999999999999976642 223356788888888999999999999999999993
No 23
>PRK13276 cell wall biosynthesis protein ScdA; Provisional
Probab=98.29 E-value=8.4e-06 Score=89.07 Aligned_cols=127 Identities=20% Similarity=0.235 Sum_probs=111.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcc-CCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHHHh--------hhHHHHHH
Q 001028 48 LFFHKAIKSELDVLHRAAMAFAT-NLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIR--------VKNIARTY 118 (1184)
Q Consensus 48 ~~~HkAlR~el~~l~~~~~~~~~-~~~d~~~~~~l~~r~~~L~~~~~~H~~aEDevI~PaL~~R--------v~~v~~~~ 118 (1184)
-..|.-+|++|..|..++..|.. --++......|.+.|..|+.=+..|..-|.+++||.+... +.+.+..|
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 001028 119 SLEHEGESVLFDQLFELLNSSMRNEE--SYRRELASCTGALQTSISQHMSKEEEQVFP 174 (1184)
Q Consensus 119 ~~EH~~~~~lf~~l~~~l~~~~~~~~--~~~~eLa~~l~~l~~~l~qHm~~EE~~v~P 174 (1184)
..||+++.+++.+|.++.+.+...++ ..|+.|=.-+.++...|.+|.+.|-.-+||
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
>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=98.16 E-value=1.2e-06 Score=67.68 Aligned_cols=38 Identities=37% Similarity=0.943 Sum_probs=33.0
Q ss_pred ccccccccccCCCceEecCCCCCCChhhHHHHhh-cCCCCCCC
Q 001028 1119 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC-SHYICPIC 1160 (1184)
Q Consensus 1119 CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~-~~~tCPiC 1160 (1184)
|+||++. ......++|||.||..|++.|+. ...+||+|
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 25
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=98.12 E-value=3.7e-07 Score=82.62 Aligned_cols=47 Identities=21% Similarity=0.487 Sum_probs=33.9
Q ss_pred cCcccccccccccCCCceEecCCCCCCChhhHHHHhhc---CCCCCCCCccc
Q 001028 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS---HYICPICSKSL 1164 (1184)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~---~~tCPiCrk~v 1164 (1184)
+..||-|.-+ ++.-+.+..-|.|.||.+||.+|+.. ...||+||+..
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 4567777643 33334444479999999999999854 46799999874
No 26
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.08 E-value=9.8e-07 Score=107.92 Aligned_cols=53 Identities=30% Similarity=0.702 Sum_probs=44.4
Q ss_pred ccCccCcccccccccccCCC-ceEecCCCCCCChhhHHHHhhcCCCCCCCCccc
Q 001028 1112 EKGLETNCPICCDFLFTSSA-TVRALPCGHFMHSDCFQAYTCSHYICPICSKSL 1164 (1184)
Q Consensus 1112 e~~~~~~CpICle~lf~s~~-~v~~LpCGH~fH~~Ci~~wl~~~~tCPiCrk~v 1164 (1184)
....+..|+||+|.|..... ....|||||.||..|+..|++...+||+||..+
T Consensus 287 ~~~~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~qtCP~CR~~~ 340 (543)
T KOG0802|consen 287 LALSDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQQTCPTCRTVL 340 (543)
T ss_pred hhhcCCeeeeechhhccccccccceeecccchHHHHHHHHHHHhCcCCcchhhh
Confidence 34457889999999876422 257799999999999999999999999999944
No 27
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.05 E-value=3.1e-06 Score=89.98 Aligned_cols=52 Identities=25% Similarity=0.668 Sum_probs=40.1
Q ss_pred cccCccCcccccccccccCCCceEecCCCCCCChhhHHHHhhc----------------CCCCCCCCccccc
Q 001028 1111 REKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS----------------HYICPICSKSLGD 1166 (1184)
Q Consensus 1111 ~e~~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~----------------~~tCPiCrk~v~~ 1166 (1184)
++...+..||||++.+ .++ +..+|||.|+..||.+|+.. ..+||+||..+..
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 3444578899999973 233 45789999999999999742 3579999999864
No 28
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.05 E-value=2.9e-06 Score=69.91 Aligned_cols=44 Identities=30% Similarity=0.764 Sum_probs=38.2
Q ss_pred cccccccccccCCCceEecCCCCCCChhhHHHHhhcCCCCCCCCc
Q 001028 1118 NCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSK 1162 (1184)
Q Consensus 1118 ~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~tCPiCrk 1162 (1184)
.|+||.+.+ ........++|||+|...|+..+......||+||+
T Consensus 1 ~C~~C~~~~-~~~~~~~l~~CgH~~C~~C~~~~~~~~~~CP~C~k 44 (44)
T PF14634_consen 1 HCNICFEKY-SEERRPRLTSCGHIFCEKCLKKLKGKSVKCPICRK 44 (44)
T ss_pred CCcCcCccc-cCCCCeEEcccCCHHHHHHHHhhcCCCCCCcCCCC
Confidence 499999984 55566788999999999999999877789999986
No 29
>COG2846 Regulator of cell morphogenesis and NO signaling [Cell division and chromosome partitioning]
Probab=98.04 E-value=4e-05 Score=81.30 Aligned_cols=128 Identities=18% Similarity=0.313 Sum_probs=105.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcc-cCC-cccHHHHHHHHHHHHHHHHhhhhccccchhhhhhhhh---------hhH
Q 001028 295 DEIMLWHNAIKRELNDIAEAARKIQL-SGD-FSDLSAFNKRLQFIAEVCIFHSIAEDKVIFPAVDVEL---------SFA 363 (1184)
Q Consensus 295 d~l~~~HkALRrEL~~L~~~a~~i~~-~gd-~~~L~~L~~r~~fl~~vl~~Hs~aEDevlFPaL~~r~---------~me 363 (1184)
.++...|+-.|.+|.+|-..+.++.. -|| ++-...|.+-+..|...|.-|-..|++++||++..-. .|+
T Consensus 79 hIi~ryH~~hReqlpeLi~latKverVHgd~p~~p~gl~~~L~~l~~eL~~HMmKEEqIlFPmi~~G~g~~a~~pI~vm~ 158 (221)
T COG2846 79 HIIVRYHERHREQLPELIPLATKVERVHGDKPSCPAGLAELLEALKEELESHMMKEEQILFPMIKQGMGSQAAGPISVME 158 (221)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHhhHHHHhccCcccCcchHHHH
Confidence 45688999999999999999988742 344 3456888888999999999999999999999998532 999
Q ss_pred HhHHHHHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 001028 364 QEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPLA 425 (1184)
Q Consensus 364 ~EH~~ie~l~e~l~~ll~~~~~~~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qvfPLl 425 (1184)
.||++...+++.+..++..... |..+...++.|=.-+..+.+.+.+|++-|-..+||=+
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 2222345677777788889999999999999999954
No 30
>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=98.03 E-value=2.3e-06 Score=68.86 Aligned_cols=39 Identities=38% Similarity=0.958 Sum_probs=33.2
Q ss_pred ccccccccccCCCceEecCCCCCCChhhHHHHhh--cCCCCCCC
Q 001028 1119 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC--SHYICPIC 1160 (1184)
Q Consensus 1119 CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~--~~~tCPiC 1160 (1184)
|+||++.+. .++..++|||.|+..|+.+|+. ...+||+|
T Consensus 1 C~iC~~~~~---~~~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEPFE---DPVILLPCGHSFCRDCLRKWLENSGSVKCPLC 41 (41)
T ss_dssp ETTTSSBCS---SEEEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred CCcCCcccc---CCCEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence 899999732 3456899999999999999998 56789998
No 31
>PHA02926 zinc finger-like protein; Provisional
Probab=98.02 E-value=3e-06 Score=91.07 Aligned_cols=61 Identities=20% Similarity=0.457 Sum_probs=44.5
Q ss_pred cCccCcccccccccccCC-----CceEecCCCCCCChhhHHHHhhcC------CCCCCCCcccc--ccCccccc
Q 001028 1113 KGLETNCPICCDFLFTSS-----ATVRALPCGHFMHSDCFQAYTCSH------YICPICSKSLG--DMAVSPLF 1173 (1184)
Q Consensus 1113 ~~~~~~CpICle~lf~s~-----~~v~~LpCGH~fH~~Ci~~wl~~~------~tCPiCrk~v~--~m~~y~~~ 1173 (1184)
.+.+..|+||||.++... .-....+|+|.|+..||..|.+.. .+||+||.... .++.+|..
T Consensus 167 ~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~I~pSrf~~~ 240 (242)
T PHA02926 167 VSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFRNITMSKFYKL 240 (242)
T ss_pred ccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceeeeeccccceec
Confidence 456789999999876431 112345999999999999998642 45999999875 34555543
No 32
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.96 E-value=2.9e-06 Score=88.39 Aligned_cols=47 Identities=30% Similarity=0.697 Sum_probs=39.0
Q ss_pred CcccccccccccCCCceEecCCCCCCChhhHHHHhhcCCCCCCCCcccc
Q 001028 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1165 (1184)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~tCPiCrk~v~ 1165 (1184)
..|||||+. +.... ...-.|||+|.+.||+.-++...+||+|+|.|.
T Consensus 132 ~~CPiCl~~-~sek~-~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt 178 (187)
T KOG0320|consen 132 YKCPICLDS-VSEKV-PVSTKCGHVFCSQCIKDALKNTNKCPTCRKKIT 178 (187)
T ss_pred cCCCceecc-hhhcc-ccccccchhHHHHHHHHHHHhCCCCCCcccccc
Confidence 789999998 43322 234799999999999999999999999999664
No 33
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=97.92 E-value=4.4e-06 Score=68.51 Aligned_cols=38 Identities=37% Similarity=0.946 Sum_probs=27.5
Q ss_pred ccccccccccCCCceEecCCCCCCChhhHHHHhhcC----CCCCCC
Q 001028 1119 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSH----YICPIC 1160 (1184)
Q Consensus 1119 CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~----~tCPiC 1160 (1184)
||||++.+.. -+.|+|||.|...||..|.+.. ..||+|
T Consensus 1 CpiC~~~~~~----Pv~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDLFKD----PVSLPCGHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB-SS----EEE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCccchhhCC----ccccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 8999998432 3569999999999999998643 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=97.84 E-value=1.4e-05 Score=69.84 Aligned_cols=45 Identities=22% Similarity=0.391 Sum_probs=38.2
Q ss_pred CcccccccccccCCCceEecCCCCCCChhhHHHHhhcCCCCCCCCcccc
Q 001028 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1165 (1184)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~tCPiCrk~v~ 1165 (1184)
-.||||++.|. ++ +.++|||.|.+.||.+|+..+.+||+|++.+.
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 46999999743 24 45799999999999999988999999999874
No 35
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=97.69 E-value=1.8e-05 Score=65.41 Aligned_cols=39 Identities=38% Similarity=0.950 Sum_probs=23.3
Q ss_pred ccccccccccCCCceEecCCCCCCChhhHHHHhhc----CCCCC
Q 001028 1119 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS----HYICP 1158 (1184)
Q Consensus 1119 CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~----~~tCP 1158 (1184)
||||.| +.+...+-+.|+|||+|-.+|++++++. ..+||
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 4444555677999999999999999874 34687
No 36
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=97.64 E-value=9.3e-06 Score=77.57 Aligned_cols=32 Identities=22% Similarity=0.473 Sum_probs=28.5
Q ss_pred EecCCCCCCChhhHHHHhhcCCCCCCCCcccc
Q 001028 1134 RALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1165 (1184)
Q Consensus 1134 ~~LpCGH~fH~~Ci~~wl~~~~tCPiCrk~v~ 1165 (1184)
.-.-|.|.||.+||.+||+++..||+|.+...
T Consensus 77 aWG~CNHaFH~hCisrWlktr~vCPLdn~eW~ 108 (114)
T KOG2930|consen 77 AWGVCNHAFHFHCISRWLKTRNVCPLDNKEWV 108 (114)
T ss_pred EeeecchHHHHHHHHHHHhhcCcCCCcCccee
Confidence 33579999999999999999999999998753
No 37
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=97.62 E-value=2.3e-05 Score=87.13 Aligned_cols=48 Identities=23% Similarity=0.650 Sum_probs=40.4
Q ss_pred cCcccccccccccCCCceEecCCCCCCChhhHHHHhhcCCCCCCCCcccccc
Q 001028 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGDM 1167 (1184)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~tCPiCrk~v~~m 1167 (1184)
...|.+|||... .-...||||.|+..||..|.....-||+||...-+-
T Consensus 239 ~~kC~LCLe~~~----~pSaTpCGHiFCWsCI~~w~~ek~eCPlCR~~~~ps 286 (293)
T KOG0317|consen 239 TRKCSLCLENRS----NPSATPCGHIFCWSCILEWCSEKAECPLCREKFQPS 286 (293)
T ss_pred CCceEEEecCCC----CCCcCcCcchHHHHHHHHHHccccCCCcccccCCCc
Confidence 467999999742 335689999999999999999999999999987653
No 38
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.60 E-value=2e-05 Score=92.03 Aligned_cols=51 Identities=27% Similarity=0.636 Sum_probs=38.7
Q ss_pred cCccccccccccc----C---------CCceEecCCCCCCChhhHHHHhh-cCCCCCCCCccccc
Q 001028 1116 ETNCPICCDFLFT----S---------SATVRALPCGHFMHSDCFQAYTC-SHYICPICSKSLGD 1166 (1184)
Q Consensus 1116 ~~~CpICle~lf~----s---------~~~v~~LpCGH~fH~~Ci~~wl~-~~~tCPiCrk~v~~ 1166 (1184)
..+|+|||.++.- + ....+.-||.|.||..|+.+|+. .+..||+||..+..
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 4679999877521 1 11244559999999999999998 56799999998764
No 39
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=97.57 E-value=2.6e-05 Score=90.62 Aligned_cols=48 Identities=23% Similarity=0.679 Sum_probs=43.2
Q ss_pred cCcccccccccccCCCceEecCCCCCCChhhHHHHhhcCCCCCCCCcccc
Q 001028 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1165 (1184)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~tCPiCrk~v~ 1165 (1184)
-.+||||+|.|..+...+....|.|.||-.|+.+| ...+||+||....
T Consensus 175 LPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w--~~~scpvcR~~q~ 222 (493)
T KOG0804|consen 175 LPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKW--WDSSCPVCRYCQS 222 (493)
T ss_pred CCCcchhHhhcCccccceeeeecccccchHHHhhc--ccCcChhhhhhcC
Confidence 46899999999999888888999999999999999 4789999998655
No 40
>COG2846 Regulator of cell morphogenesis and NO signaling [Cell division and chromosome partitioning]
Probab=97.53 E-value=0.00083 Score=71.57 Aligned_cols=133 Identities=18% Similarity=0.244 Sum_probs=109.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcc-CCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHHHh----hhHHHHHHH
Q 001028 45 LIFLFFHKAIKSELDVLHRAAMAFAT-NLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIR----VKNIARTYS 119 (1184)
Q Consensus 45 ~~~~~~HkAlR~el~~l~~~~~~~~~-~~~d~~~~~~l~~r~~~L~~~~~~H~~aEDevI~PaL~~R----v~~v~~~~~ 119 (1184)
.|..-+|.-.|.+|..|..++..|.. -.+.+.-.+.|..-+.-|..-+..|-.-|++++||.+..= +.+....|+
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 001028 120 LEHEGESVLFDQLFELLNSSMRNEE--SYRRELASCTGALQTSISQHMSKEEEQVFPLLI 177 (1184)
Q Consensus 120 ~EH~~~~~lf~~l~~~l~~~~~~~~--~~~~eLa~~l~~l~~~l~qHm~~EE~~v~PLl~ 177 (1184)
.||+++..+++.+.+..+...-..+ ..++.|=.-+.++.+.+.+|++.|---+||=+.
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=97.52 E-value=5e-05 Score=89.26 Aligned_cols=47 Identities=26% Similarity=0.576 Sum_probs=39.8
Q ss_pred cCcccccccccccCCCceEecCCCCCCChhhHHHHhhcCCCCCCCCccccc
Q 001028 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1166 (1184)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~tCPiCrk~v~~ 1166 (1184)
...|+||++.+. .+ +.++|||.|+..||..|+.....||+|+..+..
T Consensus 26 ~l~C~IC~d~~~---~P-vitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~~ 72 (397)
T TIGR00599 26 SLRCHICKDFFD---VP-VLTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQE 72 (397)
T ss_pred ccCCCcCchhhh---Cc-cCCCCCCchhHHHHHHHHhCCCCCCCCCCcccc
Confidence 568999999743 23 358999999999999999888899999998764
No 42
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.51 E-value=5.3e-05 Score=82.20 Aligned_cols=51 Identities=27% Similarity=0.635 Sum_probs=39.6
Q ss_pred CccCcccccccccccCCCceEecCCCCCCChhhHHHHhhc---CCCCCCCCccccccC
Q 001028 1114 GLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS---HYICPICSKSLGDMA 1168 (1184)
Q Consensus 1114 ~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~---~~tCPiCrk~v~~m~ 1168 (1184)
+..-+|-||+|- ..++|+.+ |||.|.-.||.+|+.. +..||+|+..|..-+
T Consensus 45 ~~~FdCNICLd~---akdPVvTl-CGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~ 98 (230)
T KOG0823|consen 45 GGFFDCNICLDL---AKDPVVTL-CGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDT 98 (230)
T ss_pred CCceeeeeeccc---cCCCEEee-cccceehHHHHHHHhhcCCCeeCCccccccccce
Confidence 456789999975 45566554 9999999999999964 345899999887543
No 43
>COG3945 Uncharacterized conserved protein [Function unknown]
Probab=97.48 E-value=0.0012 Score=69.39 Aligned_cols=140 Identities=18% Similarity=0.226 Sum_probs=110.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHHHhh----hHHHHHHH
Q 001028 44 ILIFLFFHKAIKSELDVLHRAAMAFATNLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIRV----KNIARTYS 119 (1184)
Q Consensus 44 i~~~~~~HkAlR~el~~l~~~~~~~~~~~~d~~~~~~l~~r~~~L~~~~~~H~~aEDevI~PaL~~Rv----~~v~~~~~ 119 (1184)
|..|+==|+-|-+-|.-|....--+..+-=|.+++..+++-++-+.+ ++||.-|+-++||-+..+. ++....|.
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 56777789888888888777776666521245566666665555554 5688999999999999886 57899999
Q ss_pred hhhhhHHHHHHHHHHHHHhhhcCch----hHHHHHHHHHHHHHHHHHHhHHHHHHHhhhHHHhhCCHHHHHHHHH
Q 001028 120 LEHEGESVLFDQLFELLNSSMRNEE----SYRRELASCTGALQTSISQHMSKEEEQVFPLLIEKFSFEEQASLVW 190 (1184)
Q Consensus 120 ~EH~~~~~lf~~l~~~l~~~~~~~~----~~~~eLa~~l~~l~~~l~qHm~~EE~~v~PLl~~~fS~~E~a~L~~ 190 (1184)
-||..--.++..+.+.+.+|.-.++ .+...+++.+. .+.+|.++|+..+||.+.+.||.+ |..+..
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=97.36 E-value=0.0001 Score=62.47 Aligned_cols=42 Identities=26% Similarity=0.736 Sum_probs=32.7
Q ss_pred cccccccccccCCCceEecCCC-----CCCChhhHHHHhhc--CCCCCCCC
Q 001028 1118 NCPICCDFLFTSSATVRALPCG-----HFMHSDCFQAYTCS--HYICPICS 1161 (1184)
Q Consensus 1118 ~CpICle~lf~s~~~v~~LpCG-----H~fH~~Ci~~wl~~--~~tCPiCr 1161 (1184)
.|-||+++ .+.+.....||. |++|..|+.+|+.. +.+||+|+
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 334455678995 99999999999954 45899995
No 45
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.24 E-value=7.5e-05 Score=82.07 Aligned_cols=50 Identities=22% Similarity=0.640 Sum_probs=40.0
Q ss_pred cCcccccccccccCC------CceEecCCCCCCChhhHHHHh--hcCCCCCCCCcccc
Q 001028 1116 ETNCPICCDFLFTSS------ATVRALPCGHFMHSDCFQAYT--CSHYICPICSKSLG 1165 (1184)
Q Consensus 1116 ~~~CpICle~lf~s~------~~v~~LpCGH~fH~~Ci~~wl--~~~~tCPiCrk~v~ 1165 (1184)
++.|+||...++.+. ++.-.|.|+|.||..||+-|- ....+||.|++.+.
T Consensus 224 d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVd 281 (328)
T KOG1734|consen 224 DSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVD 281 (328)
T ss_pred cchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhh
Confidence 567888887765543 245679999999999999993 66889999998864
No 46
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.23 E-value=0.00014 Score=86.19 Aligned_cols=48 Identities=33% Similarity=0.756 Sum_probs=37.3
Q ss_pred ccCcccccccccccCCCceEecCCCCCCChhhHHHHhhc-----CCCCCCCCccccc
Q 001028 1115 LETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS-----HYICPICSKSLGD 1166 (1184)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~-----~~tCPiCrk~v~~ 1166 (1184)
++..||||+++ ...+++ +.|||.|+-.||-+|+.. ...||||+..|..
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 222333 459999999999998754 3679999999875
No 47
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=97.23 E-value=8.7e-05 Score=67.40 Aligned_cols=50 Identities=26% Similarity=0.594 Sum_probs=23.7
Q ss_pred cCcccccccccccC-CCceEe---cCCCCCCChhhHHHHhhc-----------CCCCCCCCcccc
Q 001028 1116 ETNCPICCDFLFTS-SATVRA---LPCGHFMHSDCFQAYTCS-----------HYICPICSKSLG 1165 (1184)
Q Consensus 1116 ~~~CpICle~lf~s-~~~v~~---LpCGH~fH~~Ci~~wl~~-----------~~tCPiCrk~v~ 1165 (1184)
+.+|+||..++... ..+... -.|+..||..|+.+|+.. ..+||.|++.|.
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 46899999986522 223333 379999999999999852 135999999874
No 48
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.22 E-value=0.00024 Score=80.81 Aligned_cols=51 Identities=22% Similarity=0.546 Sum_probs=38.4
Q ss_pred cCcccccccccccCCCc-eEecCCCCCCChhhHHHHh-hcCCCCCCCCccccc
Q 001028 1116 ETNCPICCDFLFTSSAT-VRALPCGHFMHSDCFQAYT-CSHYICPICSKSLGD 1166 (1184)
Q Consensus 1116 ~~~CpICle~lf~s~~~-v~~LpCGH~fH~~Ci~~wl-~~~~tCPiCrk~v~~ 1166 (1184)
+..||||+.+.+.+... ..+-+|||.|+..|++..+ .....||.|++.+-.
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 2223899999999999954 556789999998754
No 49
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.20 E-value=0.00012 Score=83.83 Aligned_cols=49 Identities=27% Similarity=0.612 Sum_probs=38.6
Q ss_pred cCcccccccccccCCCceEecC-CCCCCChhhHHHHhhc---CCCCCCCCcccc
Q 001028 1116 ETNCPICCDFLFTSSATVRALP-CGHFMHSDCFQAYTCS---HYICPICSKSLG 1165 (1184)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~Lp-CGH~fH~~Ci~~wl~~---~~tCPiCrk~v~ 1165 (1184)
...|.|| ++++.....+.... |||+||..|+.+|+.. +.+||+|+-.++
T Consensus 4 ~A~C~Ic-~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~~ 56 (465)
T KOG0827|consen 4 MAECHIC-IDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKLQ 56 (465)
T ss_pred cceeeEe-ccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeeccc
Confidence 3569999 66687777776664 9999999999999965 358999994444
No 50
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=97.03 E-value=0.00022 Score=90.31 Aligned_cols=114 Identities=26% Similarity=0.564 Sum_probs=75.8
Q ss_pred ceeeccccCcc-----ccCCCCCCCCCCCCcccceEecccccCccCCCCcccCCCCCccccCCCCCccccccCCCccccc
Q 001028 1028 TEMMCMRCLKV-----QPVGPVCTTLSCSGLSMAKYYCGICKFFDDERVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLA 1102 (1184)
Q Consensus 1028 ~~~~C~~C~~~-----q~~~~~C~~~~C~~~~~a~Y~C~iC~l~dd~k~~yHC~~CgiCRvG~gl~~~~fHC~~C~~C~s 1102 (1184)
..--|.+|+.. |.++.+|...+| .+.|+--|++-+-... .|| | . ++--||.-|=.|-.
T Consensus 3416 S~~aCRFCGs~~~tE~sav~~vCs~aDC--~eYAK~ACs~~H~C~H--------~CG----G--v-kNEE~CLPCl~Cdk 3478 (3738)
T KOG1428|consen 3416 SSEACRFCGSRSGTELSAVGSVCSDADC--QEYAKIACSKTHPCGH--------PCG----G--V-KNEEHCLPCLHCDK 3478 (3738)
T ss_pred chhHhhhccCCCCcchhcccCccccHHH--HHHHHHHHhccCcCCC--------ccc----C--c-cchhhcccccccCh
Confidence 34478888743 567889998888 5677878865332211 233 1 1 25566666655532
Q ss_pred cccccccccccCccCcccccccccccCCCceEecCCCCCCChhhHHHHhhc----------CCCCCCCCcccc
Q 001028 1103 KKLVDHKCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS----------HYICPICSKSLG 1165 (1184)
Q Consensus 1103 ~~l~~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~----------~~tCPiCrk~v~ 1165 (1184)
-. .....++.|.||.-+ .-+-.+...|.|||.||.+|.+.-|.+ -..||||...|.
T Consensus 3479 s~------tkQD~DDmCmICFTE-~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~In 3544 (3738)
T KOG1428|consen 3479 SA------TKQDADDMCMICFTE-ALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKIN 3544 (3738)
T ss_pred hh------hhcccCceEEEEehh-hhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchhh
Confidence 11 123356789999876 446678899999999999999765532 246999998874
No 51
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.93 E-value=0.00037 Score=77.03 Aligned_cols=47 Identities=26% Similarity=0.674 Sum_probs=39.2
Q ss_pred cCcccccccccccCCCceEecCCCCCCChhhHHH-HhhcCCC-CCCCCccccc
Q 001028 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQA-YTCSHYI-CPICSKSLGD 1166 (1184)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~-wl~~~~t-CPiCrk~v~~ 1166 (1184)
+..|+||++... .....||||.|...||.. |....+- ||+||..+..
T Consensus 215 d~kC~lC~e~~~----~ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~p 263 (271)
T COG5574 215 DYKCFLCLEEPE----VPSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVYP 263 (271)
T ss_pred ccceeeeecccC----CcccccccchhhHHHHHHHHHhhccccCchhhhhccc
Confidence 567999998743 345689999999999999 9988776 9999998764
No 52
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=96.92 E-value=0.00021 Score=87.18 Aligned_cols=52 Identities=17% Similarity=0.524 Sum_probs=42.8
Q ss_pred ccCcccccccccccCCCceEecCCCCCCChhhHHHHhhcCCCCCCCCcccccc
Q 001028 1115 LETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGDM 1167 (1184)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~tCPiCrk~v~~m 1167 (1184)
....||||+.. +.........+|+|+||..||..|.+.-.+||+||+.+...
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 35679999976 44444455679999999999999999999999999988653
No 53
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.85 E-value=0.00043 Score=75.18 Aligned_cols=44 Identities=32% Similarity=0.811 Sum_probs=37.3
Q ss_pred ccCcccccccccccCCCceEecCCCCCCChhhHHHHhhcCCCCCCCCc
Q 001028 1115 LETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSK 1162 (1184)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~tCPiCrk 1162 (1184)
.+..||||++++ .. + +.+||||.|...|+..+......||.||.
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 78999999999999998776788999994
No 54
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=96.71 E-value=0.00057 Score=77.23 Aligned_cols=46 Identities=24% Similarity=0.655 Sum_probs=39.1
Q ss_pred CcccccccccccCCCceEecCCCCCCChhhHHHHhhcCCCCCCCCccccc
Q 001028 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1166 (1184)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~tCPiCrk~v~~ 1166 (1184)
-.|-||.|++. ..+..||||.|+.-||+.+|..+..||.|+..+..
T Consensus 24 LRC~IC~eyf~----ip~itpCsHtfCSlCIR~~L~~~p~CP~C~~~~~E 69 (442)
T KOG0287|consen 24 LRCGICFEYFN----IPMITPCSHTFCSLCIRKFLSYKPQCPTCCVTVTE 69 (442)
T ss_pred HHHhHHHHHhc----CceeccccchHHHHHHHHHhccCCCCCceecccch
Confidence 46999999843 23556899999999999999999999999988753
No 55
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.64 E-value=0.0011 Score=76.25 Aligned_cols=51 Identities=27% Similarity=0.666 Sum_probs=42.1
Q ss_pred cCccCcccccccccccCCCceEecCCCCC-CChhhHHHHhhcCCCCCCCCcccccc
Q 001028 1113 KGLETNCPICCDFLFTSSATVRALPCGHF-MHSDCFQAYTCSHYICPICSKSLGDM 1167 (1184)
Q Consensus 1113 ~~~~~~CpICle~lf~s~~~v~~LpCGH~-fH~~Ci~~wl~~~~tCPiCrk~v~~m 1167 (1184)
+....+|.|||.+ ...+.+|||.|. +++.|.+.....++.|||||..+...
T Consensus 287 ~~~gkeCVIClse----~rdt~vLPCRHLCLCs~Ca~~Lr~q~n~CPICRqpi~~l 338 (349)
T KOG4265|consen 287 SESGKECVICLSE----SRDTVVLPCRHLCLCSGCAKSLRYQTNNCPICRQPIEEL 338 (349)
T ss_pred ccCCCeeEEEecC----CcceEEecchhhehhHhHHHHHHHhhcCCCccccchHhh
Confidence 3446789999976 335788999997 89999998877889999999998753
No 56
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=96.60 E-value=0.00016 Score=81.06 Aligned_cols=133 Identities=17% Similarity=0.114 Sum_probs=98.7
Q ss_pred HHHHHhhccccccccccccccccccccCcccchhhhHHHHHHHHHHHHHHhhhhhhhhccccccccccccccccccchhh
Q 001028 690 GLYRAHSNAEDDIVFPALESKETLSNVSHSYTLDHKQEEKLFEDISSALSELTELHECLSTDLTGDLTRNSLESCDQNET 769 (1184)
Q Consensus 690 ~v~~~HS~AEDeivFPaLe~k~~~~nvs~s~~~dH~~ee~lf~~i~~~L~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 769 (1184)
.++..|+.++|++-||+..+.....+..+++..||--.=.++.+.+.... . .+
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 78999999999999999999988878888877777666666655422110 0 13
Q ss_pred HHhHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhcCCHHHHHHHHHHHHhccCHHHHHHhhhHHhhcCCHHHHHH
Q 001028 770 VRKYNEKATELQGMCKSIRVTLDQHVFREELELWPLFDRHFSVEEQDKIVGRIIGTTGAEVLQSMLPWVTSALTQEEQNT 849 (1184)
Q Consensus 770 ~~~~~el~~kL~~~~~sl~~~L~~H~~~EE~Ev~PL~~k~fS~eeQ~~lv~~~l~~~p~~~Lq~~LPWl~~~LteeE~~~ 849 (1184)
..++.-++.+.....++..+.+..|.. +.++|=++.+.|.+++| +++..+.+.+--+.++. |||.-.....++.+
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 334444566666666666688899988 99999999999999999 88888866554333332 99998888888777
Q ss_pred HHHHh
Q 001028 850 MMDTW 854 (1184)
Q Consensus 850 ml~~~ 854 (1184)
-|.+|
T Consensus 145 ~~~~~ 149 (276)
T KOG1940|consen 145 YLSNW 149 (276)
T ss_pred hcccc
Confidence 66665
No 57
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=96.48 E-value=0.0012 Score=60.37 Aligned_cols=47 Identities=21% Similarity=0.378 Sum_probs=35.0
Q ss_pred cCcccccccccccCCCceEecCCCCCCChhhHHHHhhc-CCCCCCCCccccc
Q 001028 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS-HYICPICSKSLGD 1166 (1184)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~-~~tCPiCrk~v~~ 1166 (1184)
+-.|||+.+-|. ++ +.+||||+|-+.||.+|+.. +.+||+|+..+..
T Consensus 4 ~f~CpIt~~lM~---dP-Vi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~ 51 (73)
T PF04564_consen 4 EFLCPITGELMR---DP-VILPSGHTYERSAIERWLEQNGGTDPFTRQPLSE 51 (73)
T ss_dssp GGB-TTTSSB-S---SE-EEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SG
T ss_pred ccCCcCcCcHhh---Cc-eeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCc
Confidence 457999998643 33 46799999999999999988 8999999988764
No 58
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=96.37 E-value=0.00065 Score=77.95 Aligned_cols=61 Identities=31% Similarity=0.669 Sum_probs=49.1
Q ss_pred cccccccCccCcccccccccccCCCceEecCCCCCCChhhHHHHhhcC--CCCCCCCccccccC
Q 001028 1107 DHKCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSH--YICPICSKSLGDMA 1168 (1184)
Q Consensus 1107 ~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~--~tCPiCrk~v~~m~ 1168 (1184)
-|.|++. ++-.|-.|.|.+-...+....|||.|+||..|+..++.++ .+||-|||....|.
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 4556543 5788999999887777788899999999999999999665 57999996655443
No 59
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.25 E-value=0.00071 Score=58.20 Aligned_cols=50 Identities=28% Similarity=0.640 Sum_probs=36.3
Q ss_pred ccCcccccccccccCCCceEecCCCCC-CChhhHH-HHhhcCCCCCCCCccccccC
Q 001028 1115 LETNCPICCDFLFTSSATVRALPCGHF-MHSDCFQ-AYTCSHYICPICSKSLGDMA 1168 (1184)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~LpCGH~-fH~~Ci~-~wl~~~~tCPiCrk~v~~m~ 1168 (1184)
.+.+|.||+|. ..+. +.--|||+ +.-.|-. .|...+.+|||||.+|-+.-
T Consensus 6 ~~dECTICye~---pvds-VlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~dvI 57 (62)
T KOG4172|consen 6 WSDECTICYEH---PVDS-VLYTCGHMCMCYACGLRLKKALHGCCPICRAPIKDVI 57 (62)
T ss_pred cccceeeeccC---cchH-HHHHcchHHhHHHHHHHHHHccCCcCcchhhHHHHHH
Confidence 35789999986 2222 33469997 6778855 46568999999999987643
No 60
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=96.12 E-value=0.0027 Score=70.65 Aligned_cols=45 Identities=24% Similarity=0.515 Sum_probs=37.7
Q ss_pred cCcccccccccccCCCceEecCCCCCCChhhHHHHhhcCCCCCCCCccc
Q 001028 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSL 1164 (1184)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~tCPiCrk~v 1164 (1184)
...|-||.+++.. -..-+|||.|+.-||..+|..+..||+||...
T Consensus 25 ~lrC~IC~~~i~i----p~~TtCgHtFCslCIR~hL~~qp~CP~Cr~~~ 69 (391)
T COG5432 25 MLRCRICDCRISI----PCETTCGHTFCSLCIRRHLGTQPFCPVCREDP 69 (391)
T ss_pred HHHhhhhhheeec----ceecccccchhHHHHHHHhcCCCCCccccccH
Confidence 3569999988431 23469999999999999999999999999865
No 61
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.98 E-value=0.004 Score=72.30 Aligned_cols=49 Identities=35% Similarity=0.819 Sum_probs=38.5
Q ss_pred cCcccccccccccCCC-ceEecCCCCCCChhhHHHHhhcC--CCCCCCCccc
Q 001028 1116 ETNCPICCDFLFTSSA-TVRALPCGHFMHSDCFQAYTCSH--YICPICSKSL 1164 (1184)
Q Consensus 1116 ~~~CpICle~lf~s~~-~v~~LpCGH~fH~~Ci~~wl~~~--~tCPiCrk~v 1164 (1184)
...||||++.+-.+++ .+..|.|||.|-.+||+.||... ..||.|.-..
T Consensus 4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~ka 55 (463)
T KOG1645|consen 4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKA 55 (463)
T ss_pred cccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChh
Confidence 4679999998655544 44568999999999999999543 4699998653
No 62
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.91 E-value=0.0051 Score=71.50 Aligned_cols=52 Identities=23% Similarity=0.561 Sum_probs=39.1
Q ss_pred cCccCcccccccccccCCCc---eEe-cCCCCCCChhhHHHHh--hc-----CCCCCCCCccc
Q 001028 1113 KGLETNCPICCDFLFTSSAT---VRA-LPCGHFMHSDCFQAYT--CS-----HYICPICSKSL 1164 (1184)
Q Consensus 1113 ~~~~~~CpICle~lf~s~~~---v~~-LpCGH~fH~~Ci~~wl--~~-----~~tCPiCrk~v 1164 (1184)
++.+..|-||||.+...... -.. .+|.|.|...||..|- .. ...||.||...
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 46688999999986544310 122 4699999999999997 33 46799999875
No 63
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=95.76 E-value=0.003 Score=78.83 Aligned_cols=51 Identities=24% Similarity=0.595 Sum_probs=36.6
Q ss_pred CccCcccccccccccCCC--ce-EecCCCCCCChhhHHHHhhc--CCCCCCCCccc
Q 001028 1114 GLETNCPICCDFLFTSSA--TV-RALPCGHFMHSDCFQAYTCS--HYICPICSKSL 1164 (1184)
Q Consensus 1114 ~~~~~CpICle~lf~s~~--~v-~~LpCGH~fH~~Ci~~wl~~--~~tCPiCrk~v 1164 (1184)
+...+||||..-|..-.. +. +--.|.|.||..|+.+|.+. +.+||+||.++
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 457789999865541111 11 22457899999999999864 67899999765
No 64
>COG2461 Uncharacterized conserved protein [Function unknown]
Probab=95.45 E-value=0.094 Score=61.46 Aligned_cols=132 Identities=14% Similarity=0.208 Sum_probs=103.1
Q ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcccH-HHHHHHHHHHHHHHHhhhhccccchhhhhhhhh------hhH
Q 001028 291 SCPIDEIMLWHNAIKRELNDIAEAARKIQLSGDFSDL-SAFNKRLQFIAEVCIFHSIAEDKVIFPAVDVEL------SFA 363 (1184)
Q Consensus 291 ~~pid~l~~~HkALRrEL~~L~~~a~~i~~~gd~~~L-~~L~~r~~fl~~vl~~Hs~aEDevlFPaL~~r~------~me 363 (1184)
-+|+..|...-+++|..|+.+.+. .. + ..+ -.+...+.++..+=+ |=.++...|||.++.|- .|-
T Consensus 85 gHPv~tl~~EN~~i~~ll~~~l~~---~~---~-~~ik~~l~~lv~~L~~vg~-Hy~RKe~lIfp~~Er~GitapptVmW 156 (409)
T COG2461 85 GHPVRTLKRENKAIRSLLANLLQF---PP---K-KEIKEKLVELVSELDKIGK-HYTRKEMLIFPYIERRGITAPPTVMW 156 (409)
T ss_pred CCcHHHHhcccHHHHHHHHHHhhc---cc---c-HHHHHHHHHHHHHHHHhcc-ccccccccchhHHHHcCCCCCCeeee
Confidence 689999999999999554444333 21 2 233 555666667766666 88999999999999885 889
Q ss_pred HhHHHHHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhhCCHHHHHHHHHhH
Q 001028 364 QEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPLARRHFSPKRQRELLYQS 441 (1184)
Q Consensus 364 ~EH~~ie~l~e~l~~ll~~~~~~~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qvfPLl~~~fS~eEq~eL~~~~ 441 (1184)
-.|+++-..|..+...+... + ..++......+.+.+..=+.+||+.+.|.+-..||..||.++-.+.
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=95.31 E-value=0.012 Score=65.62 Aligned_cols=52 Identities=21% Similarity=0.624 Sum_probs=43.6
Q ss_pred CccCcccccccccccCCCceEecCCCCCCChhhHHHHhh--cCCCCCCCCccccccC
Q 001028 1114 GLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC--SHYICPICSKSLGDMA 1168 (1184)
Q Consensus 1114 ~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~--~~~tCPiCrk~v~~m~ 1168 (1184)
....+||+|.++ +..+....+|||.|+--|+..=.. .+.+||.|...+..|+
T Consensus 237 t~~~~C~~Cg~~---PtiP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~~lq 290 (298)
T KOG2879|consen 237 TSDTECPVCGEP---PTIPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVEPLQ 290 (298)
T ss_pred cCCceeeccCCC---CCCCeeeccccceeehhhhhhhhcchhhcccCccCCCCcchh
Confidence 346789999987 667788889999999999988654 3589999999998776
No 66
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=94.71 E-value=0.013 Score=52.49 Aligned_cols=44 Identities=30% Similarity=0.619 Sum_probs=23.1
Q ss_pred CcccccccccccCCCceEecCCCCCCChhhHHHHhhcCCCCCCCCcccc
Q 001028 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1165 (1184)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~tCPiCrk~v~ 1165 (1184)
..|++|.+.|. ++|....|.|.|.+.|+..-+. +.||+|+.+..
T Consensus 8 LrCs~C~~~l~---~pv~l~~CeH~fCs~Ci~~~~~--~~CPvC~~Paw 51 (65)
T PF14835_consen 8 LRCSICFDILK---EPVCLGGCEHIFCSSCIRDCIG--SECPVCHTPAW 51 (65)
T ss_dssp TS-SSS-S--S---S-B---SSS--B-TTTGGGGTT--TB-SSS--B-S
T ss_pred cCCcHHHHHhc---CCceeccCccHHHHHHhHHhcC--CCCCCcCChHH
Confidence 46999998753 4677789999999999988654 45999999874
No 67
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=94.37 E-value=0.011 Score=66.39 Aligned_cols=55 Identities=27% Similarity=0.654 Sum_probs=44.3
Q ss_pred cccCccCcccccccccccCCCceEecCCCCCCChhhHHHHhh-----------------------cCCCCCCCCccccc
Q 001028 1111 REKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC-----------------------SHYICPICSKSLGD 1166 (1184)
Q Consensus 1111 ~e~~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~-----------------------~~~tCPiCrk~v~~ 1166 (1184)
..+-..+.|.||+-. |.+.....+.+|-|+||..|+..||. ....||+||-.|++
T Consensus 110 ~nn~p~gqCvICLyg-fa~~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~ 187 (368)
T KOG4445|consen 110 ENNHPNGQCVICLYG-FASSPAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKI 187 (368)
T ss_pred cCCCCCCceEEEEEe-ecCCCceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccc
Confidence 445668899999977 66777788899999999999988863 12349999998875
No 68
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=94.33 E-value=0.013 Score=73.09 Aligned_cols=46 Identities=24% Similarity=0.608 Sum_probs=37.2
Q ss_pred CcccccccccccCCCceEecCCCCCCChhhHHHHhh-cCCCCCCCCccccc
Q 001028 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC-SHYICPICSKSLGD 1166 (1184)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~-~~~tCPiCrk~v~~ 1166 (1184)
-.||+|-.. ...++...|||.|+..|++.-+. +..+||.|...+|.
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 459999744 33466779999999999999875 46889999999885
No 69
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.06 E-value=0.0068 Score=69.51 Aligned_cols=48 Identities=31% Similarity=0.589 Sum_probs=39.0
Q ss_pred cCcccccccccccCCCceEecCCCCCCChhhHHHHhh-cCCCCCCCCccccc
Q 001028 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC-SHYICPICSKSLGD 1166 (1184)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~-~~~tCPiCrk~v~~ 1166 (1184)
+..||||++-|.. .+...-|+|-|..+||..-++ .+..||.||+.++.
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 5689999986543 356678999999999987664 57899999999864
No 70
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=94.03 E-value=0.027 Score=49.46 Aligned_cols=43 Identities=26% Similarity=0.622 Sum_probs=29.7
Q ss_pred CccCcccccccccccCCCceEecCCCCCCChhhHHHHhh--cCCCCCC
Q 001028 1114 GLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC--SHYICPI 1159 (1184)
Q Consensus 1114 ~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~--~~~tCPi 1159 (1184)
.....|||.+.. + .++|+...|||+|=+..|.+|++ ....||+
T Consensus 9 ~~~~~CPiT~~~-~--~~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv 53 (57)
T PF11789_consen 9 TISLKCPITLQP-F--EDPVKSKKCGHTFEKEAILQYIQRNGSKRCPV 53 (57)
T ss_dssp B--SB-TTTSSB----SSEEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred EeccCCCCcCCh-h--hCCcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence 345789999987 3 35888899999999999999994 3567998
No 71
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=93.94 E-value=0.017 Score=66.95 Aligned_cols=55 Identities=27% Similarity=0.668 Sum_probs=44.4
Q ss_pred cccccCccCcccccccccccCCCceEecCCCCCCChhhHHHHhhc--CCCCCCCCcccccc
Q 001028 1109 KCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS--HYICPICSKSLGDM 1167 (1184)
Q Consensus 1109 ~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~--~~tCPiCrk~v~~m 1167 (1184)
-|.-.++-.-|-||-|. +..|+.=||||.++..|+..|-.. ..+||-||..|-..
T Consensus 362 YceMgsTFeLCKICaen----dKdvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKGt 418 (563)
T KOG1785|consen 362 YCEMGSTFELCKICAEN----DKDVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIKGT 418 (563)
T ss_pred HHHccchHHHHHHhhcc----CCCcccccccchHHHHHHHhhcccCCCCCCCceeeEeccc
Confidence 45556677789999875 456888899999999999999733 68999999988543
No 72
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=93.75 E-value=0.047 Score=46.46 Aligned_cols=45 Identities=22% Similarity=0.526 Sum_probs=24.6
Q ss_pred ccccccccccCCCceEecCCCCCCChhhHHHHhh-cCCCCCCCCcc
Q 001028 1119 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC-SHYICPICSKS 1163 (1184)
Q Consensus 1119 CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~-~~~tCPiCrk~ 1163 (1184)
||+|.+++..++....-=+||+-+...|+..-+. .+..||-||+.
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 58899999986
No 73
>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=93.23 E-value=0.034 Score=53.38 Aligned_cols=37 Identities=27% Similarity=0.608 Sum_probs=29.5
Q ss_pred ccccCccCcccccccccccCCCceEecCCCCCCChhhHH
Q 001028 1110 CREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQ 1148 (1184)
Q Consensus 1110 C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~ 1148 (1184)
++.-.....|+||...|.. ....+.||||.||..|++
T Consensus 72 ~v~i~~~~~C~vC~k~l~~--~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 72 SVVITESTKCSVCGKPLGN--SVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred eEEECCCCCccCcCCcCCC--ceEEEeCCCeEEeccccc
Confidence 3444557789999999765 467788999999999975
No 74
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.96 E-value=0.051 Score=61.52 Aligned_cols=48 Identities=19% Similarity=0.423 Sum_probs=37.7
Q ss_pred CccCcccccccccccCCCceEecCCCCCCChhhHHHHh-hcCCCCCCCCcccc
Q 001028 1114 GLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYT-CSHYICPICSKSLG 1165 (1184)
Q Consensus 1114 ~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl-~~~~tCPiCrk~v~ 1165 (1184)
....+|+||+.. ...+ +.|+|+|.|..-||+--. ....+||+||..|.
T Consensus 5 ~~~~eC~IC~nt---~n~P-v~l~C~HkFCyiCiKGsy~ndk~~CavCR~pid 53 (324)
T KOG0824|consen 5 TKKKECLICYNT---GNCP-VNLYCFHKFCYICIKGSYKNDKKTCAVCRFPID 53 (324)
T ss_pred ccCCcceeeecc---CCcC-ccccccchhhhhhhcchhhcCCCCCceecCCCC
Confidence 356789999865 3334 679999999999998644 44677999999985
No 75
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=92.68 E-value=0.067 Score=66.21 Aligned_cols=49 Identities=27% Similarity=0.493 Sum_probs=36.1
Q ss_pred cccccCccCcccccccccccCCCceEecCCCCCCChhhHHHHhhcCCCCCC
Q 001028 1109 KCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPI 1159 (1184)
Q Consensus 1109 ~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~tCPi 1159 (1184)
+|+.......|.||.-.+..+ ...-+.|||.+|..|...|.+....||.
T Consensus 1021 ~~~~~~~~~~C~~C~l~V~gs--s~~Cg~C~Hv~H~sc~~eWf~~gd~Cps 1069 (1081)
T KOG0309|consen 1021 CAICKGFTFQCAICHLAVRGS--SNFCGTCGHVGHTSCMMEWFRTGDVCPS 1069 (1081)
T ss_pred ccccccceeeeeeEeeEeecc--chhhccccccccHHHHHHHHhcCCcCCC
Confidence 333344455699997554433 3456789999999999999999999984
No 76
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.60 E-value=0.066 Score=56.38 Aligned_cols=30 Identities=27% Similarity=0.724 Sum_probs=25.5
Q ss_pred cCCCCCCChhhHHHHhhc-----------CCCCCCCCcccc
Q 001028 1136 LPCGHFMHSDCFQAYTCS-----------HYICPICSKSLG 1165 (1184)
Q Consensus 1136 LpCGH~fH~~Ci~~wl~~-----------~~tCPiCrk~v~ 1165 (1184)
..||-.||+-|+..||+. -..||.|.+++.
T Consensus 188 ~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~Pia 228 (234)
T KOG3268|consen 188 IQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIA 228 (234)
T ss_pred cccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcce
Confidence 579999999999999863 145999999984
No 77
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=92.47 E-value=0.067 Score=63.71 Aligned_cols=62 Identities=27% Similarity=0.603 Sum_probs=48.1
Q ss_pred CccCcccccccccccCCCceEecCCCCCCChhhHHHHhhcCCCCCCCCccccccCccccccccch
Q 001028 1114 GLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGDMAVSPLFRTTSV 1178 (1184)
Q Consensus 1114 ~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~tCPiCrk~v~~m~~y~~~~~~~v 1178 (1184)
..+..||||+..+ .+++....|||.|...|+..|+..+..||.|+..+..-..++..+....
T Consensus 19 ~~~l~C~~C~~vl---~~p~~~~~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~~~~~~~~~~~ 80 (391)
T KOG0297|consen 19 DENLLCPICMSVL---RDPVQTTTCGHRFCAGCLLESLSNHQKCPVCRQELTQAEELPVPRALRR 80 (391)
T ss_pred cccccCccccccc---cCCCCCCCCCCcccccccchhhccCcCCcccccccchhhccCchHHHHH
Confidence 3457899999764 3345557899999999999999999999999999877666764443333
No 78
>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=92.25 E-value=0.051 Score=55.34 Aligned_cols=42 Identities=21% Similarity=0.401 Sum_probs=34.4
Q ss_pred cCcccccccccccCCCceEecCCC------CCCChhhHHHHhhcCCCCC
Q 001028 1116 ETNCPICCDFLFTSSATVRALPCG------HFMHSDCFQAYTCSHYICP 1158 (1184)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCG------H~fH~~Ci~~wl~~~~tCP 1158 (1184)
..+|.||++.+.. ...++.++|| |+||.+|++.|.+.+.+=|
T Consensus 26 ~~EC~IC~~~I~~-~~GvV~vt~~g~lnLEkmfc~~C~~rw~~~~~rDP 73 (134)
T PF05883_consen 26 TVECQICFDRIDN-NDGVVYVTDGGTLNLEKMFCADCDKRWRRERNRDP 73 (134)
T ss_pred Ceeehhhhhhhhc-CCCEEEEecCCeehHHHHHHHHHHHHHHhhccCCC
Confidence 5689999999876 6789999998 9999999999965444433
No 79
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=92.01 E-value=0.11 Score=57.36 Aligned_cols=52 Identities=25% Similarity=0.521 Sum_probs=44.5
Q ss_pred CccCcccccccccccCCCceEec-CCCCCCChhhHHHHhhcCCCCCCCCccccc
Q 001028 1114 GLETNCPICCDFLFTSSATVRAL-PCGHFMHSDCFQAYTCSHYICPICSKSLGD 1166 (1184)
Q Consensus 1114 ~~~~~CpICle~lf~s~~~v~~L-pCGH~fH~~Ci~~wl~~~~tCPiCrk~v~~ 1166 (1184)
+....||||.+.|. +..+..+| ||||++..+|.++.++....||+|.+.+-+
T Consensus 219 s~ryiCpvtrd~Lt-Nt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkd 271 (303)
T KOG3039|consen 219 SKRYICPVTRDTLT-NTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKD 271 (303)
T ss_pred ccceecccchhhhc-CccceEEeccCCcEeeHHHHHHhccccccccCCCCcCcc
Confidence 35678999999854 55566666 999999999999999999999999999865
No 80
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.90 E-value=0.028 Score=63.16 Aligned_cols=50 Identities=26% Similarity=0.515 Sum_probs=35.0
Q ss_pred cCcccccccccccCCCceEecCCCCCCChhhHHHHhhcCCCCCCCCccccccCcccc
Q 001028 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGDMAVSPL 1172 (1184)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~tCPiCrk~v~~m~~y~~ 1172 (1184)
+.-|.|||+- ......|+|||.- .|++-=.+ -..|||||+.|......|+
T Consensus 300 ~~LC~ICmDa----P~DCvfLeCGHmV--tCt~CGkr-m~eCPICRqyi~rvvrif~ 349 (350)
T KOG4275|consen 300 RRLCAICMDA----PRDCVFLECGHMV--TCTKCGKR-MNECPICRQYIVRVVRIFR 349 (350)
T ss_pred HHHHHHHhcC----CcceEEeecCcEE--eehhhccc-cccCchHHHHHHHHHhhhc
Confidence 6789999975 3457899999974 34322111 2379999999887666664
No 81
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=91.50 E-value=0.11 Score=43.96 Aligned_cols=40 Identities=25% Similarity=0.672 Sum_probs=26.5
Q ss_pred ccccccccccCCCceEecCCC-----CCCChhhHHHHhh--cCCCCCCC
Q 001028 1119 CPICCDFLFTSSATVRALPCG-----HFMHSDCFQAYTC--SHYICPIC 1160 (1184)
Q Consensus 1119 CpICle~lf~s~~~v~~LpCG-----H~fH~~Ci~~wl~--~~~tCPiC 1160 (1184)
|-||++.-..+ ...+.||+ -+.|..|+.+|+. .+.+|++|
T Consensus 1 CrIC~~~~~~~--~~li~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C 47 (47)
T PF12906_consen 1 CRICLEGEEED--EPLISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC 47 (47)
T ss_dssp ETTTTEE-SSS--S-EE-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred CeEeCCcCCCC--CceecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence 67999873322 23456775 5899999999986 56789998
No 82
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=91.11 E-value=0.052 Score=59.83 Aligned_cols=91 Identities=24% Similarity=0.577 Sum_probs=56.6
Q ss_pred ccCcccccccCCCCCCccccceeeccccCccccCCCCCCCCCCCCcccceEeccccc-CccCC-----CCcccCCCCCcc
Q 001028 1008 FTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVGPVCTTLSCSGLSMAKYYCGICK-FFDDE-----RVVYHCPFCNLC 1081 (1184)
Q Consensus 1008 y~Cr~CHde~~~H~~~r~~~~~~~C~~C~~~q~~~~~C~~~~C~~~~~a~Y~C~iC~-l~dd~-----k~~yHC~~CgiC 1081 (1184)
|.|.+|.....|--+-|. ..+.+|-.|+..-.+ .--++|.|.+|+ +.|++ .++||
T Consensus 100 F~Cd~Cn~~Lad~gf~rn-qgr~LC~~Cn~k~Ka-----------~~~g~YvC~KCh~~iD~~~l~fr~d~yH------- 160 (332)
T KOG2272|consen 100 FRCDLCNKHLADQGFYRN-QGRALCRECNQKEKA-----------KGRGRYVCQKCHAHIDEQPLTFRGDPYH------- 160 (332)
T ss_pred chhHHHHHHHhhhhhHhh-cchHHhhhhhhhhcc-----------cccceeehhhhhhhcccccccccCCCCC-------
Confidence 667777777666666564 347788877654322 235799999998 46666 57777
Q ss_pred ccCCCCCccccccCCCcccccccc----ccccccccCccCccccccc
Q 001028 1082 RVGRGLGVDFFHCMTCNCCLAKKL----VDHKCREKGLETNCPICCD 1124 (1184)
Q Consensus 1082 RvG~gl~~~~fHC~~C~~C~s~~l----~~H~C~e~~~~~~CpICle 1124 (1184)
-..|.|.+||.=+...- +.--|..-....-||||..
T Consensus 161 -------~yHFkCt~C~keL~sdaRevk~eLyClrChD~mgipiCga 200 (332)
T KOG2272|consen 161 -------PYHFKCTTCGKELTSDAREVKGELYCLRCHDKMGIPICGA 200 (332)
T ss_pred -------ccceecccccccccchhhhhccceeccccccccCCccccc
Confidence 25688888887664431 3334444444455666653
No 83
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.61 E-value=0.12 Score=59.92 Aligned_cols=46 Identities=24% Similarity=0.525 Sum_probs=33.3
Q ss_pred cCccCcccccccccccCCCceEecCCCCCCChhhHHHHhhcCCCCCCCCcccc
Q 001028 1113 KGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1165 (1184)
Q Consensus 1113 ~~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~tCPiCrk~v~ 1165 (1184)
.....+|.||++. + .....+||||+-. |..-. +...+||+||..+.
T Consensus 302 ~~~p~lcVVcl~e-~---~~~~fvpcGh~cc--ct~cs-~~l~~CPvCR~rI~ 347 (355)
T KOG1571|consen 302 LPQPDLCVVCLDE-P---KSAVFVPCGHVCC--CTLCS-KHLPQCPVCRQRIR 347 (355)
T ss_pred cCCCCceEEecCC-c---cceeeecCCcEEE--chHHH-hhCCCCchhHHHHH
Confidence 3457899999987 2 2378899999954 54433 23456999999874
No 84
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.59 E-value=0.18 Score=55.00 Aligned_cols=51 Identities=29% Similarity=0.649 Sum_probs=41.1
Q ss_pred CccCcccccccccccCCCceEecCCCCCCChhhHHHHhh--------cCCCCCCCCccccc
Q 001028 1114 GLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC--------SHYICPICSKSLGD 1166 (1184)
Q Consensus 1114 ~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~--------~~~tCPiCrk~v~~ 1166 (1184)
....+|..|.-.|- +++ ...|-|=|.||-.|+++|-. ..|.||-|...|..
T Consensus 48 DY~pNC~LC~t~La-~gd-t~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFP 106 (299)
T KOG3970|consen 48 DYNPNCRLCNTPLA-SGD-TTRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFP 106 (299)
T ss_pred CCCCCCceeCCccc-cCc-ceeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCC
Confidence 45789999998865 344 45688999999999999963 26889999998864
No 85
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=90.18 E-value=0.12 Score=57.23 Aligned_cols=37 Identities=32% Similarity=0.703 Sum_probs=27.7
Q ss_pred ccCCCceEecCCCCCCChhhHHHHhhcCCCCCCCCcccc
Q 001028 1127 FTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1165 (1184)
Q Consensus 1127 f~s~~~v~~LpCGH~fH~~Ci~~wl~~~~tCPiCrk~v~ 1165 (1184)
+.+..+-....|+|+|+..|...- ....||+|++++-
T Consensus 12 ~~~~~~f~LTaC~HvfC~~C~k~~--~~~~C~lCkk~ir 48 (233)
T KOG4739|consen 12 FPSQDPFFLTACRHVFCEPCLKAS--SPDVCPLCKKSIR 48 (233)
T ss_pred cCCCCceeeeechhhhhhhhcccC--Cccccccccceee
Confidence 444455667799999999998653 2238999999974
No 86
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=89.63 E-value=0.11 Score=62.26 Aligned_cols=51 Identities=25% Similarity=0.570 Sum_probs=41.6
Q ss_pred cccCccCcccccccccccCCCceEecCCCCCCChhhHHHHhh-----cCCCCCCCCcccc
Q 001028 1111 REKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC-----SHYICPICSKSLG 1165 (1184)
Q Consensus 1111 ~e~~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~-----~~~tCPiCrk~v~ 1165 (1184)
+++..+..|-+|.|+ .+....-.|.|.|++-|+.+|+. .+.+||+|...+.
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 467778899999986 23456778999999999999974 3689999998774
No 87
>COG2461 Uncharacterized conserved protein [Function unknown]
Probab=88.91 E-value=1.8 Score=51.29 Aligned_cols=137 Identities=22% Similarity=0.229 Sum_probs=105.1
Q ss_pred CCChHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHHHhh-hHHHHHHH
Q 001028 41 KSPILIFLFFHKAIKSELDVLHRAAMAFATNLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIRV-KNIARTYS 119 (1184)
Q Consensus 41 ~~Pi~~~~~~HkAlR~el~~l~~~~~~~~~~~~d~~~~~~l~~r~~~L~~~~~~H~~aEDevI~PaL~~Rv-~~v~~~~~ 119 (1184)
.+|+..|.-=-+++|..++.+.+.. .+..-...+...+.+|..+=+ |-+-+-..|||-++.|- ..+.-.|-
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 001028 120 LEHEGESVLFDQLFELLNSSMRNEESYRRELASCTGALQTSISQHMSKEEEQVFPLLIEKFSFEEQASLVWQ 191 (1184)
Q Consensus 120 ~EH~~~~~lf~~l~~~l~~~~~~~~~~~~eLa~~l~~l~~~l~qHm~~EE~~v~PLl~~~fS~~E~a~L~~~ 191 (1184)
.-|.++-..|..+...+. .. .. .+++.....+.+.+..=+.+||.-+.|-+..-||..||.++..+
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 33344444555788888899999999999999999999999988
No 88
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=88.87 E-value=0.18 Score=44.02 Aligned_cols=45 Identities=29% Similarity=0.702 Sum_probs=31.5
Q ss_pred cCcccccccccccCCCceEecCCCCCCChhhHHHHhhcCCCCCCCCccccc
Q 001028 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1166 (1184)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~tCPiCrk~v~~ 1166 (1184)
+..|-.|... ...-.++||||+.-..|++-+ +-+-||+|.+.+..
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 3455566532 233467899999999997654 45679999998753
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=88.09 E-value=0.37 Score=50.44 Aligned_cols=49 Identities=24% Similarity=0.753 Sum_probs=33.3
Q ss_pred cCcccccccccccCCCceEecC------------CC-CCCChhhHHHHhhc-----------------------------
Q 001028 1116 ETNCPICCDFLFTSSATVRALP------------CG-HFMHSDCFQAYTCS----------------------------- 1153 (1184)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~Lp------------CG-H~fH~~Ci~~wl~~----------------------------- 1153 (1184)
+..||||||.= -..+.|- |+ =+=|..|++++-+.
T Consensus 2 d~~CpICme~P----HNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkka~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 77 (162)
T PF07800_consen 2 DVTCPICMEHP----HNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKKAYGKSSSSSSQSSSSAPSDSSSSESSESQE 77 (162)
T ss_pred CccCceeccCC----CceEEEEeccccCCccccccCCccchhHHHHHHHHHhcCCCCccccccccCcCCCcccccccccc
Confidence 46799999962 1233344 44 35589999998531
Q ss_pred --CCCCCCCCccccccC
Q 001028 1154 --HYICPICSKSLGDMA 1168 (1184)
Q Consensus 1154 --~~tCPiCrk~v~~m~ 1168 (1184)
...||+||-.|..+.
T Consensus 78 ~~~L~CPLCRG~V~GWt 94 (162)
T PF07800_consen 78 QPELACPLCRGEVKGWT 94 (162)
T ss_pred cccccCccccCceeceE
Confidence 346999999987654
No 90
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=87.33 E-value=0.14 Score=58.81 Aligned_cols=50 Identities=20% Similarity=0.542 Sum_probs=41.7
Q ss_pred ccCcccccccccccCCCceEecCCCCCCChhhHHHHhhcCCCCCCCCcccccc
Q 001028 1115 LETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGDM 1167 (1184)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~tCPiCrk~v~~m 1167 (1184)
....|.+|..+|... ..+.-|=|.|++.||..++..+.+||.|...|..-
T Consensus 14 ~~itC~LC~GYliDA---TTI~eCLHTFCkSCivk~l~~~~~CP~C~i~ih~t 63 (331)
T KOG2660|consen 14 PHITCRLCGGYLIDA---TTITECLHTFCKSCIVKYLEESKYCPTCDIVIHKT 63 (331)
T ss_pred cceehhhccceeecc---hhHHHHHHHHHHHHHHHHHHHhccCCccceeccCc
Confidence 456899999986543 34567999999999999999999999999998763
No 91
>PF04641 Rtf2: Rtf2 RING-finger
Probab=87.07 E-value=0.44 Score=53.77 Aligned_cols=52 Identities=19% Similarity=0.491 Sum_probs=40.7
Q ss_pred cCccCcccccccccccCCCceEec-CCCCCCChhhHHHHhhcCCCCCCCCccccc
Q 001028 1113 KGLETNCPICCDFLFTSSATVRAL-PCGHFMHSDCFQAYTCSHYICPICSKSLGD 1166 (1184)
Q Consensus 1113 ~~~~~~CpICle~lf~s~~~v~~L-pCGH~fH~~Ci~~wl~~~~tCPiCrk~v~~ 1166 (1184)
....--|||....| .+....++| ||||+|-..++.+.- ....||+|.+.+..
T Consensus 110 ~~~~~~CPvt~~~~-~~~~~fv~l~~cG~V~s~~alke~k-~~~~Cp~c~~~f~~ 162 (260)
T PF04641_consen 110 SEGRFICPVTGKEF-NGKHKFVYLRPCGCVFSEKALKELK-KSKKCPVCGKPFTE 162 (260)
T ss_pred CCceeECCCCCccc-CCceeEEEEcCCCCEeeHHHHHhhc-ccccccccCCcccc
Confidence 34566899999985 444555555 999999999999983 46789999998753
No 92
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=87.01 E-value=0.52 Score=59.11 Aligned_cols=70 Identities=23% Similarity=0.505 Sum_probs=50.6
Q ss_pred CCcccCCCCCccccCCCCCccccccCCCccccccccccccccccCccCcccccccccccCCCceEecCCCCCCChhhHHH
Q 001028 1070 RVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLAKKLVDHKCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQA 1149 (1184)
Q Consensus 1070 k~~yHC~~CgiCRvG~gl~~~~fHC~~C~~C~s~~l~~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~ 1149 (1184)
.-+|-|+.|+---+++++ .-|++|-.|-+ ..|.+|-..+.+ ..+.---|||..|.+|+.+
T Consensus 751 ~i~~~~~nc~a~~~~~~~----~~c~rc~s~a~--------------~~CtVC~~vi~G--~~~~c~~C~H~gH~sh~~s 810 (839)
T KOG0269|consen 751 TIHYACPNCDAPMVLTKL----WQCDRCESRAS--------------AKCTVCDLVIRG--VDVWCQVCGHGGHDSHLKS 810 (839)
T ss_pred eeeccccccCCccccccc----eeechHHHHhh--------------cCceeecceeee--eEeecccccccccHHHHHH
Confidence 457888888877777653 45666665544 459999866432 2233347999999999999
Q ss_pred HhhcCCCCCC
Q 001028 1150 YTCSHYICPI 1159 (1184)
Q Consensus 1150 wl~~~~tCPi 1159 (1184)
|+..+.-||.
T Consensus 811 w~~~~s~ca~ 820 (839)
T KOG0269|consen 811 WFFKASPCAK 820 (839)
T ss_pred HHhcCCCCcc
Confidence 9988888776
No 93
>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=86.60 E-value=0.43 Score=54.13 Aligned_cols=49 Identities=22% Similarity=0.452 Sum_probs=38.0
Q ss_pred cccccccccccCCCceE-ecCCCCCCChhhHHHHh-hcCCCCCCCCccccc
Q 001028 1118 NCPICCDFLFTSSATVR-ALPCGHFMHSDCFQAYT-CSHYICPICSKSLGD 1166 (1184)
Q Consensus 1118 ~CpICle~lf~s~~~v~-~LpCGH~fH~~Ci~~wl-~~~~tCPiCrk~v~~ 1166 (1184)
.||+|.-+.+.+.+-.. +=+|||.+...|++.-. ...+.||-|.+.+..
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iLRk 52 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGPAQCPECMVILRK 52 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHhcCCCCCCcccchhhh
Confidence 59999987666544222 23999999999999976 567899999988753
No 94
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=86.53 E-value=0.32 Score=57.31 Aligned_cols=47 Identities=26% Similarity=0.513 Sum_probs=36.4
Q ss_pred ccCcccccccccccCCCceEecCCCCCCChhhHHHHhh--------cCCCCCCCCc
Q 001028 1115 LETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC--------SHYICPICSK 1162 (1184)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~--------~~~tCPiCrk 1162 (1184)
.--.|.||++. +....-...+||+|+|.+.|...|.. +..+||-|.-
T Consensus 183 slf~C~ICf~e-~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C 237 (445)
T KOG1814|consen 183 SLFDCCICFEE-QMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKC 237 (445)
T ss_pred hcccceeeehh-hcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCC
Confidence 35689999987 44445678899999999999999963 2356987664
No 95
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=86.07 E-value=0.34 Score=55.54 Aligned_cols=56 Identities=23% Similarity=0.525 Sum_probs=42.1
Q ss_pred cCcccccccccccCCCceEecCCCCCCChhhHHHHhh-cCCCCCCCCccccccCccc
Q 001028 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC-SHYICPICSKSLGDMAVSP 1171 (1184)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~-~~~tCPiCrk~v~~m~~y~ 1171 (1184)
++-||.|+|+|.-++....--|||--+++-|+..--+ -+.+||-||+...+-.+.|
T Consensus 14 ed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~denv~~ 70 (480)
T COG5175 14 EDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDENVRY 70 (480)
T ss_pred cccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhccccceeE
Confidence 4559999999887766666668998888888655433 3789999999877654444
No 96
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.52 E-value=0.48 Score=56.55 Aligned_cols=49 Identities=27% Similarity=0.655 Sum_probs=39.8
Q ss_pred CccCcccccccccccCCCceEecCCCCCCChhhHHHHhhcCCCCCCCCccccc
Q 001028 1114 GLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1166 (1184)
Q Consensus 1114 ~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~tCPiCrk~v~~ 1166 (1184)
..+-.|.||+.-++. + +..||||.|...|+++-+....-||+||-.+..
T Consensus 82 ~sef~c~vc~~~l~~---p-v~tpcghs~c~~Cl~r~ld~~~~cp~Cr~~l~e 130 (398)
T KOG4159|consen 82 RSEFECCVCSRALYP---P-VVTPCGHSFCLECLDRSLDQETECPLCRDELVE 130 (398)
T ss_pred cchhhhhhhHhhcCC---C-ccccccccccHHHHHHHhccCCCCccccccccc
Confidence 456789999876553 2 335999999999999988888889999998764
No 97
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=84.46 E-value=0.42 Score=60.56 Aligned_cols=41 Identities=27% Similarity=0.663 Sum_probs=33.3
Q ss_pred CcccccccccccCCCceEecCCCCCCChhhHHHHhhcCCCCCCCCcc
Q 001028 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKS 1163 (1184)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~tCPiCrk~ 1163 (1184)
..|..|--.| .-|++...|||.||++|+. .....||-|+-.
T Consensus 841 skCs~C~~~L---dlP~VhF~CgHsyHqhC~e---~~~~~CP~C~~e 881 (933)
T KOG2114|consen 841 SKCSACEGTL---DLPFVHFLCGHSYHQHCLE---DKEDKCPKCLPE 881 (933)
T ss_pred eeecccCCcc---ccceeeeecccHHHHHhhc---cCcccCCccchh
Confidence 4788997654 3467778899999999998 567889999983
No 98
>PHA02862 5L protein; Provisional
Probab=83.78 E-value=0.64 Score=48.02 Aligned_cols=45 Identities=24% Similarity=0.561 Sum_probs=33.4
Q ss_pred cCcccccccccccCCCceEecCCC-----CCCChhhHHHHhhc--CCCCCCCCcccc
Q 001028 1116 ETNCPICCDFLFTSSATVRALPCG-----HFMHSDCFQAYTCS--HYICPICSKSLG 1165 (1184)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCG-----H~fH~~Ci~~wl~~--~~tCPiCrk~v~ 1165 (1184)
...|=||.+. . ++. .-||. -.-|+.|+.+|+.. +.+||+|+....
T Consensus 2 ~diCWIC~~~-~--~e~--~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~ 53 (156)
T PHA02862 2 SDICWICNDV-C--DER--NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYN 53 (156)
T ss_pred CCEEEEecCc-C--CCC--cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEE
Confidence 4679999986 2 222 24664 78999999999954 567999998764
No 99
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=83.47 E-value=0.4 Score=51.54 Aligned_cols=45 Identities=27% Similarity=0.389 Sum_probs=36.9
Q ss_pred CcccccccccccCCCceEecCCCCCCChhhHHHHhhcCCCCCCCCcccc
Q 001028 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1165 (1184)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~tCPiCrk~v~ 1165 (1184)
-.|.||.++ |.+ .++-.|||.|+..|+..=.+...+|-+|.+...
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 469999988 544 245689999999999888888899999998754
No 100
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=82.97 E-value=1 Score=52.05 Aligned_cols=66 Identities=21% Similarity=0.408 Sum_probs=45.7
Q ss_pred CCcccccccc-ccccccccCccCcccccccccccCCCceEecCCCCCCChhhHHHH--hhcCCCCCCCCcccc
Q 001028 1096 TCNCCLAKKL-VDHKCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAY--TCSHYICPICSKSLG 1165 (1184)
Q Consensus 1096 ~C~~C~s~~l-~~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~w--l~~~~tCPiCrk~v~ 1165 (1184)
+=+.|..-++ ...+-.....+..|.||-+.+ +-+.++||||-+..-|--.. |.....||+||....
T Consensus 40 KNnlsaEPnlttsSaddtDEen~~C~ICA~~~----TYs~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~e 108 (493)
T COG5236 40 KNNLSAEPNLTTSSADDTDEENMNCQICAGST----TYSARYPCGHQICHACAVRLRALYMQKGCPLCRTETE 108 (493)
T ss_pred ccccccCCccccccccccccccceeEEecCCc----eEEEeccCCchHHHHHHHHHHHHHhccCCCccccccc
Confidence 3355554444 333333345578899998763 34567899999999997654 677889999998754
No 101
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=82.95 E-value=0.11 Score=60.63 Aligned_cols=52 Identities=23% Similarity=0.475 Sum_probs=44.9
Q ss_pred ccCcccccccccccCCCceEecCCCCCCChhhHHHHhhcCCCCCCCCccccc
Q 001028 1115 LETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1166 (1184)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~tCPiCrk~v~~ 1166 (1184)
....|.||.+.+...-+.+..+.|||.+|..|+.+||.....||.|++.+..
T Consensus 195 lv~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~~~~kl~~~~rel~~ 246 (465)
T KOG0827|consen 195 LVGSLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLATKRKLPSCRRELPK 246 (465)
T ss_pred HHhhhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHHHhHHHHhhhhh
Confidence 4567999999876555677889999999999999999999999999998864
No 102
>PRK04023 DNA polymerase II large subunit; Validated
Probab=82.25 E-value=1.1 Score=58.11 Aligned_cols=44 Identities=23% Similarity=0.423 Sum_probs=21.0
Q ss_pred eccccCccccCCCCCCCCCCCCcccceEecccccCccCCCCcccCCCCCc
Q 001028 1031 MCMRCLKVQPVGPVCTTLSCSGLSMAKYYCGICKFFDDERVVYHCPFCNL 1080 (1184)
Q Consensus 1031 ~C~~C~~~q~~~~~C~~~~C~~~~~a~Y~C~iC~l~dd~k~~yHC~~Cgi 1080 (1184)
.|..|+++. +...|.+ |+.....-|+|+.|.-- -..|.||.||.
T Consensus 628 fCpsCG~~t-~~frCP~--CG~~Te~i~fCP~CG~~---~~~y~CPKCG~ 671 (1121)
T PRK04023 628 KCPSCGKET-FYRRCPF--CGTHTEPVYRCPRCGIE---VEEDECEKCGR 671 (1121)
T ss_pred cCCCCCCcC-CcccCCC--CCCCCCcceeCccccCc---CCCCcCCCCCC
Confidence 455555443 3345554 53333445566666221 22355666663
No 103
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=82.20 E-value=0.78 Score=53.07 Aligned_cols=51 Identities=22% Similarity=0.431 Sum_probs=42.5
Q ss_pred ccCccCcccccccccccCCCceEecCCCCCCChhhHHHHhhcCCCCCCCCccccc
Q 001028 1112 EKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1166 (1184)
Q Consensus 1112 e~~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~tCPiCrk~v~~ 1166 (1184)
..+.+..||||.-. ....+.-||||--+..||.+-+.++..|=.|+..+.+
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 44668899999753 3345667999999999999999999999999998874
No 104
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=81.97 E-value=0.55 Score=59.91 Aligned_cols=43 Identities=26% Similarity=0.579 Sum_probs=32.1
Q ss_pred cccccccCccCcccccccccccCCCceEecCCCCCCChhhHHHHh
Q 001028 1107 DHKCREKGLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYT 1151 (1184)
Q Consensus 1107 ~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl 1151 (1184)
++.|.--.....|-+|.-.|+. .+-.+.||||.||++|+.+-.
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 3444433456789999988664 367788999999999997754
No 105
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=80.62 E-value=0.62 Score=53.00 Aligned_cols=47 Identities=23% Similarity=0.489 Sum_probs=38.4
Q ss_pred cCcccccccccccCCCceEecCCCCCCChhhHHHHhhcCCCCCCCCccccc
Q 001028 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGD 1166 (1184)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~tCPiCrk~v~~ 1166 (1184)
...|-||..+ |.+ -++-.|||+|...|...=++....|+||.+.+..
T Consensus 241 Pf~c~icr~~-f~~---pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g 287 (313)
T KOG1813|consen 241 PFKCFICRKY-FYR---PVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHG 287 (313)
T ss_pred Cccccccccc-ccc---chhhcCCceeehhhhccccccCCcceeccccccc
Confidence 4569999998 433 2456899999999998888888999999998753
No 106
>COG5592 Uncharacterized conserved protein [Function unknown]
Probab=79.90 E-value=5 Score=42.40 Aligned_cols=100 Identities=19% Similarity=0.194 Sum_probs=69.6
Q ss_pred HHHHHHHHHHHHHHhhcccccccccccccc-----cccccc--CcccchhhhHHHHHHHHHHHHHHhhhhhhhhcccccc
Q 001028 681 FTGRFRLLWGLYRAHSNAEDDIVFPALESK-----ETLSNV--SHSYTLDHKQEEKLFEDISSALSELTELHECLSTDLT 753 (1184)
Q Consensus 681 f~~Rf~fl~~v~~~HS~AEDeivFPaLe~k-----~~~~nv--s~s~~~dH~~ee~lf~~i~~~L~~~~~l~~~~~~~~~ 753 (1184)
...-..|+|.++..|---|-++.||+.=-. -..... .--+..||+.+|-++.++..-
T Consensus 30 ~le~~gf~~k~~k~h~e~Ee~ilF~v~Vd~~~ed~~~fkdt~~~~~i~~DHkliE~l~tnlik~---------------- 93 (171)
T COG5592 30 ILEFEGFNEKLGKDHVELEEKILFPVIVDADMEDLYVFKDTPEVDRIKNDHKLIETLATNLIKW---------------- 93 (171)
T ss_pred HHhhcchHHHHhhhHHHHHHHhhhhhccchHHHHHHhhhccchhhHhHhhHHHHHHHHHHHHhh----------------
Confidence 333444899999999999999999975331 111111 236889999999999887111
Q ss_pred ccccccccccccchhhHHhHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhcCCHHHHHH
Q 001028 754 GDLTRNSLESCDQNETVRKYNEKATELQGMCKSIRVTLDQHVFREELELWPLFDRHFSVEEQDK 817 (1184)
Q Consensus 754 ~~~~~~~~~~~~~~~~~~~~~el~~kL~~~~~sl~~~L~~H~~~EE~Ev~PL~~k~fS~eeQ~~ 817 (1184)
.|+ .|.+.-.-.+.++|..|=..||.-++|-.++.=...+|.+
T Consensus 94 --------------kR~-------~k~~e~~p~fyK~LtdHn~aEE~~IfPrvks~~~E~~~~~ 136 (171)
T COG5592 94 --------------KRP-------DKIKERVPLFYKTLTDHNLAEEEYIFPRVKSLKGEDEQSA 136 (171)
T ss_pred --------------ccc-------hHHHHHHHHHHHHHHHccccccchhhHHHHhhcchhhHHH
Confidence 022 2344455778889999999999999999877655544444
No 107
>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=79.50 E-value=6.6 Score=38.99 Aligned_cols=51 Identities=18% Similarity=0.214 Sum_probs=36.9
Q ss_pred hhHHhHHHHHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 001028 361 SFAQEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQV 421 (1184)
Q Consensus 361 ~me~EH~~ie~l~e~l~~ll~~~~~~~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qv 421 (1184)
.+..+|++.-++++.|..++.. ..+ ..++...+..|..-...||..||.-.
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 5667888877777777765532 111 24667788888999999999999765
No 108
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=78.75 E-value=1.6 Score=38.90 Aligned_cols=46 Identities=26% Similarity=0.626 Sum_probs=28.2
Q ss_pred ceeeccccCccccCCC-----CCCCCCCCCcccceEecccccCccCCCCcccCCCCCc
Q 001028 1028 TEMMCMRCLKVQPVGP-----VCTTLSCSGLSMAKYYCGICKFFDDERVVYHCPFCNL 1080 (1184)
Q Consensus 1028 ~~~~C~~C~~~q~~~~-----~C~~~~C~~~~~a~Y~C~iC~l~dd~k~~yHC~~Cgi 1080 (1184)
....|..|+..-.+.. .|.+ | |.. -=|-|..|+-.. ..|.||+||+
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 3456778876654333 4665 5 432 134477777664 4688888885
No 109
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=78.49 E-value=1.5 Score=46.23 Aligned_cols=45 Identities=22% Similarity=0.673 Sum_probs=32.8
Q ss_pred ccCcccccccccccCCCceEecCCC--C---CCChhhHHHHhhc--CCCCCCCCccc
Q 001028 1115 LETNCPICCDFLFTSSATVRALPCG--H---FMHSDCFQAYTCS--HYICPICSKSL 1164 (1184)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~LpCG--H---~fH~~Ci~~wl~~--~~tCPiCrk~v 1164 (1184)
.+..|=||.++ . +.. .-||. . ..|.+|++.|+.. ..+||+|+...
T Consensus 7 ~~~~CRIC~~~-~--~~~--~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y 58 (162)
T PHA02825 7 MDKCCWICKDE-Y--DVV--TNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPY 58 (162)
T ss_pred CCCeeEecCCC-C--CCc--cCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeE
Confidence 46789999877 2 122 24664 4 6699999999854 56799999875
No 110
>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=75.51 E-value=1.4 Score=49.48 Aligned_cols=65 Identities=31% Similarity=0.812 Sum_probs=44.4
Q ss_pred CCcccCccccccc-CCCCCCccccceeeccccCccccCCCCCCCCCCCCcccceEecccccC-c-cCC----------CC
Q 001028 1005 GKLFTCRFCHDKV-SDHSMDRKATTEMMCMRCLKVQPVGPVCTTLSCSGLSMAKYYCGICKF-F-DDE----------RV 1071 (1184)
Q Consensus 1005 ~~~y~Cr~CHde~-~~H~~~r~~~~~~~C~~C~~~q~~~~~C~~~~C~~~~~a~Y~C~iC~l-~-dd~----------k~ 1071 (1184)
|+.|.|-+|++-. +|-.|+-.+ .|+....-+-.|.+ | ..++.|.|-.||. | ||. ..
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 6789999999873 555555432 25556666667865 6 3789999999985 3 332 35
Q ss_pred cccCCCCCc
Q 001028 1072 VYHCPFCNL 1080 (1184)
Q Consensus 1072 ~yHC~~Cgi 1080 (1184)
++-||+||.
T Consensus 209 ~~PCPKCg~ 217 (314)
T PF06524_consen 209 PIPCPKCGY 217 (314)
T ss_pred CCCCCCCCC
Confidence 667888874
No 111
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=74.05 E-value=1.6 Score=51.98 Aligned_cols=123 Identities=24% Similarity=0.571 Sum_probs=0.0
Q ss_pred eccccCccc-cCCCCCCCCCCCCcc--cceEeccccc-------CccCCCCccc----------CCCCC-------cccc
Q 001028 1031 MCMRCLKVQ-PVGPVCTTLSCSGLS--MAKYYCGICK-------FFDDERVVYH----------CPFCN-------LCRV 1083 (1184)
Q Consensus 1031 ~C~~C~~~q-~~~~~C~~~~C~~~~--~a~Y~C~iC~-------l~dd~k~~yH----------C~~Cg-------iCRv 1083 (1184)
+|..|++.- ..+.-|.. =+.. ..-+.|..|. ||.-|..+|= |..|| +=-.
T Consensus 276 iC~~C~K~V~g~~~ac~A---m~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~tlekC~~Cg~~I~d~iLrA~ 352 (468)
T KOG1701|consen 276 ICAFCHKTVSGQGLAVEA---MDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDTLEKCNKCGEPIMDRILRAL 352 (468)
T ss_pred hhhhcCCcccCcchHHHH---hhhhhcccceehHhhhhhhccccccccCCcccchHHHHHHHHHHhhhhhHHHHHHHHhc
Q ss_pred CCCCCccccccCCCcccc---cccc---cccccccc---CccCccccccccc---ccCCCceEecCCCCCCChhhHHHHh
Q 001028 1084 GRGLGVDFFHCMTCNCCL---AKKL---VDHKCREK---GLETNCPICCDFL---FTSSATVRALPCGHFMHSDCFQAYT 1151 (1184)
Q Consensus 1084 G~gl~~~~fHC~~C~~C~---s~~l---~~H~C~e~---~~~~~CpICle~l---f~s~~~v~~LpCGH~fH~~Ci~~wl 1151 (1184)
|+--.-.-|.|-.|+-|+ +..+ ++--|++. ...-.|+||-+.| -..++.|++..=+--||.+|
T Consensus 353 GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAPrCs~C~~PI~P~~G~~etvRvvamdr~fHv~C----- 427 (468)
T KOG1701|consen 353 GKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAPRCSVCGNPILPRDGKDETVRVVAMDRDFHVNC----- 427 (468)
T ss_pred ccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcCcchhhccCCccCCCCCcceEEEEEccccccccc-----
Q ss_pred hcCCCCCCCCccc
Q 001028 1152 CSHYICPICSKSL 1164 (1184)
Q Consensus 1152 ~~~~tCPiCrk~v 1164 (1184)
|.|--|+..+
T Consensus 428 ---Y~CEDCg~~L 437 (468)
T KOG1701|consen 428 ---YKCEDCGLLL 437 (468)
T ss_pred ---eehhhcCccc
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=73.09 E-value=1.7 Score=36.18 Aligned_cols=41 Identities=29% Similarity=0.731 Sum_probs=20.4
Q ss_pred ccccccccccCCCceEecCCCCCCChhhHHHHhhcCC--CCCCC
Q 001028 1119 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHY--ICPIC 1160 (1184)
Q Consensus 1119 CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~--tCPiC 1160 (1184)
|.+|.+- ...+..-..-.|+=-+|..|++.|++... +||.|
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 5566654 22222222234777899999999987654 79988
No 113
>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=72.90 E-value=1.8 Score=43.01 Aligned_cols=17 Identities=35% Similarity=0.757 Sum_probs=15.0
Q ss_pred cCccCCCCcccCCCCCc
Q 001028 1064 KFFDDERVVYHCPFCNL 1080 (1184)
Q Consensus 1064 ~l~dd~k~~yHC~~Cgi 1080 (1184)
||||=.|.+..||+||-
T Consensus 18 kFYDLnk~PivCP~CG~ 34 (108)
T PF09538_consen 18 KFYDLNKDPIVCPKCGT 34 (108)
T ss_pred hhccCCCCCccCCCCCC
Confidence 67898899999999994
No 114
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=72.75 E-value=2.1 Score=54.68 Aligned_cols=51 Identities=22% Similarity=0.560 Sum_probs=35.4
Q ss_pred ccCcccccccccccCCCceEecCCCCCCChhhHHHHhhc-------CCCCCCCCcccc
Q 001028 1115 LETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS-------HYICPICSKSLG 1165 (1184)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~-------~~tCPiCrk~v~ 1165 (1184)
....|.||.|.|..+...-.--.|=|+||..||..|-+. .-.||-|+....
T Consensus 190 ~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv~~ 247 (950)
T KOG1952|consen 190 RKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSVSK 247 (950)
T ss_pred CceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccchhc
Confidence 456899999986543221122346699999999999753 356999995443
No 115
>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=72.69 E-value=2.7 Score=51.91 Aligned_cols=48 Identities=23% Similarity=0.632 Sum_probs=41.5
Q ss_pred ccccccCCcccCcccccccCCCCCCccccceeeccccCccccCCCCCCCCCCCC
Q 001028 999 LRAACCGKLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVGPVCTTLSCSG 1052 (1184)
Q Consensus 999 l~~~cC~~~y~Cr~CHde~~~H~~~r~~~~~~~C~~C~~~q~~~~~C~~~~C~~ 1052 (1184)
+.|.-||....|..|.-...-|.- ...+.|-.|+..+++...|.+ |++
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 789999999999999888777743 458999999999999999987 744
No 116
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=72.67 E-value=1.3 Score=54.79 Aligned_cols=53 Identities=25% Similarity=0.556 Sum_probs=38.7
Q ss_pred CcccccccccccCCCceEecCCCCCCChhhHHHHhhcCCCCCCCCcc----ccccCcccc
Q 001028 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKS----LGDMAVSPL 1172 (1184)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~tCPiCrk~----v~~m~~y~~ 1172 (1184)
-.|+||+...+.+.-.-+.|-|||++...|...- .+.+|| |..+ +.+.+.|++
T Consensus 12 l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~l--yn~scp-~~~De~~~~~~~~e~p~ 68 (861)
T KOG3161|consen 12 LLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLL--YNASCP-TKRDEDSSLMQLKEEPR 68 (861)
T ss_pred hhchHHHHHHHHHhcCcccccccchHHHHHHHhH--hhccCC-CCccccchhcChhhcch
Confidence 4799998776666666677899999999999764 477899 7654 233445553
No 117
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=71.83 E-value=2.4 Score=48.39 Aligned_cols=47 Identities=28% Similarity=0.742 Sum_probs=37.1
Q ss_pred CcccccccccccCCCc---eEecCCCCCCChhhHHHHhhcC-CCCCCCCccc
Q 001028 1117 TNCPICCDFLFTSSAT---VRALPCGHFMHSDCFQAYTCSH-YICPICSKSL 1164 (1184)
Q Consensus 1117 ~~CpICle~lf~s~~~---v~~LpCGH~fH~~Ci~~wl~~~-~tCPiCrk~v 1164 (1184)
..|-||-++ |.+.+. -+.|.|||.|...|+.+-+... ..||-||...
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 555432 3668999999999999887654 4699999995
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=70.44 E-value=1.2 Score=37.95 Aligned_cols=44 Identities=27% Similarity=0.656 Sum_probs=26.3
Q ss_pred CcccccccccccCCCceEecCCC-CCCChhhHHHHhhcCCCCCCCCccccc
Q 001028 1117 TNCPICCDFLFTSSATVRALPCG-HFMHSDCFQAYTCSHYICPICSKSLGD 1166 (1184)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCG-H~fH~~Ci~~wl~~~~tCPiCrk~v~~ 1166 (1184)
.+|--|... .. ..+.|. |+....|+...+..+..||||.+++..
T Consensus 3 ~nCKsCWf~---~k---~Li~C~dHYLCl~CLt~ml~~s~~C~iC~~~LPt 47 (50)
T PF03854_consen 3 YNCKSCWFA---NK---GLIKCSDHYLCLNCLTLMLSRSDRCPICGKPLPT 47 (50)
T ss_dssp ----SS-S-----S---SEEE-SS-EEEHHHHHHT-SSSSEETTTTEE---
T ss_pred ccChhhhhc---CC---CeeeecchhHHHHHHHHHhccccCCCcccCcCcc
Confidence 356667633 22 245787 999999999999999999999998763
No 119
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=69.58 E-value=3.2 Score=49.24 Aligned_cols=47 Identities=21% Similarity=0.513 Sum_probs=36.8
Q ss_pred CcccccccccccCCCceEecCCCCCCChhhHHHHhhcC---CCCCCCCccc
Q 001028 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSH---YICPICSKSL 1164 (1184)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~---~tCPiCrk~v 1164 (1184)
-.|||=.|. -+...+-+.|.|||++-++-+++..++. .+||.|-...
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 568887665 4555677889999999999999987653 6899997653
No 120
>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=69.07 E-value=3.4 Score=42.99 Aligned_cols=47 Identities=26% Similarity=0.579 Sum_probs=39.8
Q ss_pred CcccceEecccccCccCCCCcccCCCCCccccCCCCCccccccCCCccccccc
Q 001028 1052 GLSMAKYYCGICKFFDDERVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLAKK 1104 (1184)
Q Consensus 1052 ~~~~a~Y~C~iC~l~dd~k~~yHC~~CgiCRvG~gl~~~~fHC~~C~~C~s~~ 1104 (1184)
+......||..|+.+-.. ..+||..||.|-.+- -.||.=-|.|+...
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 456788899999999766 589999999999984 47999999998865
No 121
>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=68.02 E-value=3.7 Score=31.80 Aligned_cols=38 Identities=34% Similarity=0.766 Sum_probs=26.0
Q ss_pred cccccccccccCCCceEecCCCCCCChhhHHHHhhcCCCCCCCCcccc
Q 001028 1118 NCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1165 (1184)
Q Consensus 1118 ~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~tCPiCrk~v~ 1165 (1184)
.|+.|.+.+......+.. =|..||.+|+ +|..|++++.
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 378888886554222222 3789999886 7888888764
No 122
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=67.97 E-value=5.2 Score=53.55 Aligned_cols=52 Identities=23% Similarity=0.427 Sum_probs=25.5
Q ss_pred eeeccccCccccCCCCCCCCCCCCcccceEecccccCc--cCCCCcccCCCCCcccc
Q 001028 1029 EMMCMRCLKVQPVGPVCTTLSCSGLSMAKYYCGICKFF--DDERVVYHCPFCNLCRV 1083 (1184)
Q Consensus 1029 ~~~C~~C~~~q~~~~~C~~~~C~~~~~a~Y~C~iC~l~--dd~k~~yHC~~CgiCRv 1083 (1184)
...|..|+++-+. ..|.. |+...-..|+|..|+.- .++....+||+||.=-+
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 3445555544322 25544 43222345666666552 12223667888884433
No 123
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=67.44 E-value=2.9 Score=42.60 Aligned_cols=18 Identities=28% Similarity=0.392 Sum_probs=15.8
Q ss_pred cCccCCCCcccCCCCCcc
Q 001028 1064 KFFDDERVVYHCPFCNLC 1081 (1184)
Q Consensus 1064 ~l~dd~k~~yHC~~CgiC 1081 (1184)
||||-.|.+..||+||.=
T Consensus 18 kFYDLnk~p~vcP~cg~~ 35 (129)
T TIGR02300 18 KFYDLNRRPAVSPYTGEQ 35 (129)
T ss_pred cccccCCCCccCCCcCCc
Confidence 688988999999999954
No 124
>TIGR02481 hemeryth_dom hemerythrin-like metal-binding domain. This model describes both members of the hemerythrin (TIGR00058) family of marine invertebrates and a broader collection of bacterial and archaeal homologs. Many of the latter group are multidomain proteins with signal-transducing domains such as the GGDEF diguanylate cyclase domain (TIGR00254, pfam00990) and methyl-accepting chemotaxis protein signaling domain (pfam00015). Most hemerythrins are oxygen-carriers with a bound non-heme iron, but at least one example is a cadmium-binding protein, apparently with a role in sequestering toxic metals rather than in binding oxygen. Patterns of conserved residues suggest that all prokaryotic instances of this domain bind iron or another heavy metal, but the exact function is unknown. Not surprisingly, the prokaryote with the most instances of this domain is Magnetococcus sp. MC-1, a magnetotactic bacterium.
Probab=66.98 E-value=88 Score=31.01 Aligned_cols=109 Identities=18% Similarity=0.299 Sum_probs=68.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcccCCcccHHHHHHHHHHHHHHHHhhhhccccch----hhhhhhhhhhHHhHHHHHHH
Q 001028 297 IMLWHNAIKRELNDIAEAARKIQLSGDFSDLSAFNKRLQFIAEVCIFHSIAEDKVI----FPAVDVELSFAQEHAEEEIQ 372 (1184)
Q Consensus 297 l~~~HkALRrEL~~L~~~a~~i~~~gd~~~L~~L~~r~~fl~~vl~~Hs~aEDevl----FPaL~~r~~me~EH~~ie~l 372 (1184)
+=.-|+.|=..++.+.+.+.. + .....+...+.+|.+....|-..|+.++ ||.+..+. .+| +..
T Consensus 13 ID~qH~~l~~~in~l~~a~~~----~--~~~~~~~~~l~~L~~y~~~HF~~EE~~M~~~~yp~~~~H~---~~H---~~~ 80 (126)
T TIGR02481 13 IDAQHKELFELINELYDALSA----G--NGKDELKEILDELIDYTENHFADEEELMEEYGYPDLEEHK---KEH---EKF 80 (126)
T ss_pred HHHHHHHHHHHHHHHHHHHHc----C--CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHH---HHH---HHH
Confidence 335688887787777776543 1 1245677778888999999999998765 77776543 344 444
Q ss_pred HHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 001028 373 FDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPL 424 (1184)
Q Consensus 373 ~e~l~~ll~~~~~~~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qvfPL 424 (1184)
++.+..+...+... .+ ..... ..+..+.+-|..|+..+-..+.+.
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 125
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=65.58 E-value=4.2 Score=50.06 Aligned_cols=16 Identities=38% Similarity=1.034 Sum_probs=8.8
Q ss_pred CCCcccceEecccccC
Q 001028 1050 CSGLSMAKYYCGICKF 1065 (1184)
Q Consensus 1050 C~~~~~a~Y~C~iC~l 1065 (1184)
|...++-.|||+.|-+
T Consensus 19 c~~~Ei~~~yCp~CL~ 34 (483)
T PF05502_consen 19 CVSEEIDSYYCPNCLF 34 (483)
T ss_pred hcccccceeECccccc
Confidence 3344566666666643
No 126
>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=64.64 E-value=22 Score=39.54 Aligned_cols=40 Identities=28% Similarity=0.385 Sum_probs=26.6
Q ss_pred CCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHHHh-----hh-HHHHHHHhhhhhHHH
Q 001028 72 LGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIR-----VK-NIARTYSLEHEGESV 127 (1184)
Q Consensus 72 ~~d~~~~~~l~~r~~~L~~~~~~H~~aEDevI~PaL~~R-----v~-~v~~~~~~EH~~~~~ 127 (1184)
+.|+=++.-|++| ||||++ |.+. |+ -|+.+|..|-++++.
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 488999887666554
No 127
>PRK05580 primosome assembly protein PriA; Validated
Probab=64.27 E-value=4.9 Score=51.50 Aligned_cols=48 Identities=23% Similarity=0.633 Sum_probs=41.6
Q ss_pred ccccccCCcccCcccccccCCCCCCccccceeeccccCccccCCCCCCCCCCCC
Q 001028 999 LRAACCGKLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVGPVCTTLSCSG 1052 (1184)
Q Consensus 999 l~~~cC~~~y~Cr~CHde~~~H~~~r~~~~~~~C~~C~~~q~~~~~C~~~~C~~ 1052 (1184)
+.|.-||....|..|.-...-|.. ...+.|-.|+..+++...|.+ |++
T Consensus 382 ~~C~~Cg~~~~C~~C~~~l~~h~~----~~~l~Ch~Cg~~~~~~~~Cp~--Cg~ 429 (679)
T PRK05580 382 LLCRDCGWVAECPHCDASLTLHRF----QRRLRCHHCGYQEPIPKACPE--CGS 429 (679)
T ss_pred eEhhhCcCccCCCCCCCceeEECC----CCeEECCCCcCCCCCCCCCCC--CcC
Confidence 899999999999999988777753 458999999999999999987 744
No 128
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=64.24 E-value=5.7 Score=51.12 Aligned_cols=54 Identities=24% Similarity=0.551 Sum_probs=43.5
Q ss_pred ccccccCCcccCcccccccCCCCCCccccceeeccccCccccCCCCCCCCCCCCcccceEe
Q 001028 999 LRAACCGKLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVGPVCTTLSCSGLSMAKYY 1059 (1184)
Q Consensus 999 l~~~cC~~~y~Cr~CHde~~~H~~~r~~~~~~~C~~C~~~q~~~~~C~~~~C~~~~~a~Y~ 1059 (1184)
+.|.-||-.+.|+.|=.-..=|.. +..+.|-+|+..+++-..|.+ | |...=+|+
T Consensus 436 l~C~~Cg~v~~Cp~Cd~~lt~H~~----~~~L~CH~Cg~~~~~p~~Cp~--C-gs~~L~~~ 489 (730)
T COG1198 436 LLCRDCGYIAECPNCDSPLTLHKA----TGQLRCHYCGYQEPIPQSCPE--C-GSEHLRAV 489 (730)
T ss_pred eecccCCCcccCCCCCcceEEecC----CCeeEeCCCCCCCCCCCCCCC--C-CCCeeEEe
Confidence 899999999999999666655543 469999999999999999977 6 54444444
No 129
>PHA03096 p28-like protein; Provisional
Probab=63.19 E-value=3.5 Score=47.44 Aligned_cols=46 Identities=15% Similarity=0.220 Sum_probs=30.3
Q ss_pred CcccccccccccCC---CceEec-CCCCCCChhhHHHHhhc---CCCCCCCCc
Q 001028 1117 TNCPICCDFLFTSS---ATVRAL-PCGHFMHSDCFQAYTCS---HYICPICSK 1162 (1184)
Q Consensus 1117 ~~CpICle~lf~s~---~~v~~L-pCGH~fH~~Ci~~wl~~---~~tCPiCrk 1162 (1184)
..|.||+|...... ..-..| .|.|.|...|+..|... ..+||.||.
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 56999998765431 111234 79999999999999643 234555544
No 130
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=62.99 E-value=3.5 Score=43.38 Aligned_cols=29 Identities=31% Similarity=0.563 Sum_probs=23.9
Q ss_pred ccCcccccccccccCCCceEecCCCCCCCh
Q 001028 1115 LETNCPICCDFLFTSSATVRALPCGHFMHS 1144 (1184)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~LpCGH~fH~ 1144 (1184)
...+|.||+|+|. ..+.+..|||==+||+
T Consensus 176 dkGECvICLEdL~-~GdtIARLPCLCIYHK 204 (205)
T KOG0801|consen 176 DKGECVICLEDLE-AGDTIARLPCLCIYHK 204 (205)
T ss_pred cCCcEEEEhhhcc-CCCceeccceEEEeec
Confidence 4678999999965 5677999999888886
No 131
>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]
Probab=62.53 E-value=2.9 Score=53.10 Aligned_cols=88 Identities=13% Similarity=0.053 Sum_probs=60.7
Q ss_pred HHHHHHHHhHHHHHH-----HHHHHHHhhCCHHHHHHHHHhHhhcCCHHHHHHHHhhhcCCCCHHHHHHHHHHhhhhCCC
Q 001028 405 LIMASIQKHFRNEEV-----QVLPLARRHFSPKRQRELLYQSLCVMPLKLIECVLPWLVGSLSEEEARSFLQNIYMAAPA 479 (1184)
Q Consensus 405 ~L~~~L~~Hf~~EE~-----qvfPLl~~~fS~eEq~eL~~~~l~smPl~~L~~vLpWl~~~Ls~~E~~~~L~~l~~~aP~ 479 (1184)
.+-...-.|+..|++ -+.|.+=.. +-+||+..+.+|.-.--+..+.-+||=.-+.|.|.-...+|.-.=. |.
T Consensus 393 kv~~~yI~HLl~~~~y~~Aas~~p~m~gn-~~~eWe~~V~~f~e~~~l~~Ia~~lPt~~~rL~p~vYemvLve~L~--~~ 469 (846)
T KOG2066|consen 393 KVGKTYIDHLLFEGKYDEAASLCPKMLGN-NAAEWELWVFKFAELDQLTDIAPYLPTGPPRLKPLVYEMVLVEFLA--SD 469 (846)
T ss_pred HHHHHHHHHHHhcchHHHHHhhhHHHhcc-hHHHHHHHHHHhccccccchhhccCCCCCcccCchHHHHHHHHHHH--HH
Confidence 334445666654443 344444333 4578999998888777777888888888888999999988876554 55
Q ss_pred ChhHHHHHHHHhhhcCC
Q 001028 480 SDSALITLFAGWACKGH 496 (1184)
Q Consensus 480 ~~~~l~~l~~~w~~~~~ 496 (1184)
.+. |-.+++.|-+.-|
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
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=61.78 E-value=7.3 Score=34.29 Aligned_cols=35 Identities=26% Similarity=0.606 Sum_probs=27.7
Q ss_pred ccCcccccccccccCCCceEecCCCCCCChhhHHH
Q 001028 1115 LETNCPICCDFLFTSSATVRALPCGHFMHSDCFQA 1149 (1184)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~ 1149 (1184)
....|++|.+.+...++.|+---||=.+|+.|...
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~ 38 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK 38 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence 45789999999665666566678999999999643
No 133
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=61.42 E-value=3.2 Score=52.99 Aligned_cols=44 Identities=30% Similarity=0.720 Sum_probs=35.4
Q ss_pred CcccccccccccCCCceEecCCCCCCChhhHHHHhhc--CCCCCCCCcccc
Q 001028 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS--HYICPICSKSLG 1165 (1184)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~--~~tCPiCrk~v~ 1165 (1184)
..|+||++ .+.....+|||.|...|+.+.+.. ...||+||..+.
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 234667899999999999998753 346999998764
No 134
>PRK00808 hypothetical protein; Provisional
Probab=61.28 E-value=28 Score=36.16 Aligned_cols=96 Identities=19% Similarity=0.197 Sum_probs=56.8
Q ss_pred hhHHhHHHHHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHH----HHHHHhhCCH-----
Q 001028 361 SFAQEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQV----LPLARRHFSP----- 431 (1184)
Q Consensus 361 ~me~EH~~ie~l~e~l~~ll~~~~~~~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qv----fPLl~~~fS~----- 431 (1184)
.+..+|.+.-.+++.|..++.. .+ ...+...+..|.+-...||..||.-. +|-+..|--.
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 5677888777777776655521 11 24567778899999999999999753 4444443221
Q ss_pred HHHHHHHHhHhh--cCCHHHHHHHHhhhcCCCCHHHHH
Q 001028 432 KRQRELLYQSLC--VMPLKLIECVLPWLVGSLSEEEAR 467 (1184)
Q Consensus 432 eEq~eL~~~~l~--smPl~~L~~vLpWl~~~Ls~~E~~ 467 (1184)
++..++..++.. .+...++..+..||+.++.-..++
T Consensus 85 ~~l~~l~~~~~~g~~~~~~l~~~L~~WL~~HI~~~D~~ 122 (150)
T PRK00808 85 KRVEEYRERFQAGEDVADELHGMLSRWLFNHIRNDDAA 122 (150)
T ss_pred HHHHHHHHHHHccchHHHHHHHHHHHHHHHHHHHHhHH
Confidence 222222222211 123345556777887777666544
No 135
>PRK14873 primosome assembly protein PriA; Provisional
Probab=60.89 E-value=6 Score=50.60 Aligned_cols=47 Identities=26% Similarity=0.461 Sum_probs=38.6
Q ss_pred ccccccCCcccCcccccccCCCCCCccccceeeccccCccccCCCCCCCCCCCC
Q 001028 999 LRAACCGKLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVGPVCTTLSCSG 1052 (1184)
Q Consensus 999 l~~~cC~~~y~Cr~CHde~~~H~~~r~~~~~~~C~~C~~~q~~~~~C~~~~C~~ 1052 (1184)
+.|..||....|..|.-...=|. ....+.|-.|+..+ +...|.+ |++
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 5789977 743
No 136
>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=60.84 E-value=6.1 Score=31.03 Aligned_cols=24 Identities=38% Similarity=1.089 Sum_probs=19.2
Q ss_pred eEecccccCc-cCCCCcccCCCCCc
Q 001028 1057 KYYCGICKFF-DDERVVYHCPFCNL 1080 (1184)
Q Consensus 1057 ~Y~C~iC~l~-dd~k~~yHC~~Cgi 1080 (1184)
.|-|.+|.+. +.++.++.||.||.
T Consensus 1 ~~~C~~CGy~y~~~~~~~~CP~Cg~ 25 (33)
T cd00350 1 KYVCPVCGYIYDGEEAPWVCPVCGA 25 (33)
T ss_pred CEECCCCCCEECCCcCCCcCcCCCC
Confidence 4789999875 55578999999985
No 137
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=60.83 E-value=5.4 Score=46.30 Aligned_cols=44 Identities=30% Similarity=0.772 Sum_probs=34.3
Q ss_pred cCcccccccccccCCCceEecCC--CCCCChhhHHHHhhcCCCCCCCCcccccc
Q 001028 1116 ETNCPICCDFLFTSSATVRALPC--GHFMHSDCFQAYTCSHYICPICSKSLGDM 1167 (1184)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpC--GH~fH~~Ci~~wl~~~~tCPiCrk~v~~m 1167 (1184)
-.+||||.++|... .+.| ||.-...|-. +....||.||..+++.
T Consensus 48 lleCPvC~~~l~~P-----i~QC~nGHlaCssC~~---~~~~~CP~Cr~~~g~~ 93 (299)
T KOG3002|consen 48 LLDCPVCFNPLSPP-----IFQCDNGHLACSSCRT---KVSNKCPTCRLPIGNI 93 (299)
T ss_pred hccCchhhccCccc-----ceecCCCcEehhhhhh---hhcccCCccccccccH
Confidence 46899999986532 3556 7999888865 4688999999999964
No 138
>COG5592 Uncharacterized conserved protein [Function unknown]
Probab=60.61 E-value=29 Score=36.91 Aligned_cols=94 Identities=17% Similarity=0.160 Sum_probs=67.3
Q ss_pred HHHHHHHHHHHHHHhhhhccccchhhhhhhhh--------------hhHHhHHHHHHHHHHHHHHHHHHHhcCCCCChHH
Q 001028 329 AFNKRLQFIAEVCIFHSIAEDKVIFPAVDVEL--------------SFAQEHAEEEIQFDKLRCLIESIQSAGANSSTAE 394 (1184)
Q Consensus 329 ~L~~r~~fl~~vl~~Hs~aEDevlFPaL~~r~--------------~me~EH~~ie~l~e~l~~ll~~~~~~~~~~~~~~ 394 (1184)
.+.+-..|...+.+.|-.-|.+.+||+.-... ++..+|..|+-+.+.+...- +.
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 001028 395 FYTKLCSQADLIMASIQKHFRNEEVQVLPLARRHFSPKRQRE 436 (1184)
Q Consensus 395 ~~~eLa~~le~L~~~L~~Hf~~EE~qvfPLl~~~fS~eEq~e 436 (1184)
++.-.-+...+.+|++|=..||..+||-+...--..||.+
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 139
>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=60.45 E-value=2.4 Score=47.07 Aligned_cols=52 Identities=25% Similarity=0.533 Sum_probs=39.9
Q ss_pred ccCcccccccccccCCCceEec-C-CCCCCChhhHHHHhhc-CCCCC--CCCccccc
Q 001028 1115 LETNCPICCDFLFTSSATVRAL-P-CGHFMHSDCFQAYTCS-HYICP--ICSKSLGD 1166 (1184)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~L-p-CGH~fH~~Ci~~wl~~-~~tCP--iCrk~v~~ 1166 (1184)
.+..||||..+.+-+.+-...+ | |=|-++..|.+.-+.. .-.|| -|.+.+..
T Consensus 9 ~d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kILRK 65 (314)
T COG5220 9 EDRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKILRK 65 (314)
T ss_pred hcccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHHHH
Confidence 3458999999888776533332 6 9999999999997754 56799 89887754
No 140
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=60.08 E-value=4.7 Score=44.38 Aligned_cols=39 Identities=38% Similarity=0.791 Sum_probs=28.8
Q ss_pred ccccccccccCCCceEecCCCCC-CChhhHHHHhhcCCCCCCCCcccc
Q 001028 1119 CPICCDFLFTSSATVRALPCGHF-MHSDCFQAYTCSHYICPICSKSLG 1165 (1184)
Q Consensus 1119 CpICle~lf~s~~~v~~LpCGH~-fH~~Ci~~wl~~~~tCPiCrk~v~ 1165 (1184)
|-+|-+. ...|..+||.|. +...|-.. -.+||+|+....
T Consensus 161 Cr~C~~~----~~~VlllPCrHl~lC~~C~~~----~~~CPiC~~~~~ 200 (207)
T KOG1100|consen 161 CRKCGER----EATVLLLPCRHLCLCGICDES----LRICPICRSPKT 200 (207)
T ss_pred ceecCcC----CceEEeecccceEeccccccc----CccCCCCcChhh
Confidence 8888765 345888999976 55788543 456999998764
No 141
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=59.48 E-value=2.9 Score=52.19 Aligned_cols=29 Identities=31% Similarity=0.595 Sum_probs=23.0
Q ss_pred CCcccccc----ccccccccCCcccCcccccccC
Q 001028 989 GCEHYKRN----CKLRAACCGKLFTCRFCHDKVS 1018 (1184)
Q Consensus 989 gC~HY~r~----c~l~~~cC~~~y~Cr~CHde~~ 1018 (1184)
||.||--. +.-.|.-+|+|| |..||....
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 457788899977 999998854
No 142
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=59.36 E-value=7.6 Score=34.76 Aligned_cols=45 Identities=29% Similarity=0.822 Sum_probs=30.0
Q ss_pred eeeccccCccccCCC-----CCCCCCCCCcccceEecccccCccCCCCcccCCCCCc
Q 001028 1029 EMMCMRCLKVQPVGP-----VCTTLSCSGLSMAKYYCGICKFFDDERVVYHCPFCNL 1080 (1184)
Q Consensus 1029 ~~~C~~C~~~q~~~~-----~C~~~~C~~~~~a~Y~C~iC~l~dd~k~~yHC~~Cgi 1080 (1184)
...|..|+.+-.+++ .|.| | | ..-=|-|..|+-.. ..|.||+||+
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 467888888774432 4766 5 4 23346677777664 4688999985
No 143
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=59.33 E-value=7 Score=44.53 Aligned_cols=15 Identities=20% Similarity=0.751 Sum_probs=8.6
Q ss_pred CCcccCCCCCccccC
Q 001028 1070 RVVYHCPFCNLCRVG 1084 (1184)
Q Consensus 1070 k~~yHC~~CgiCRvG 1084 (1184)
+..++|++||.=.|-
T Consensus 159 ~ka~~C~~C~K~YvS 173 (279)
T KOG2462|consen 159 KKAFSCKYCGKVYVS 173 (279)
T ss_pred cccccCCCCCceeee
Confidence 555666666655554
No 144
>KOG2068 consensus MOT2 transcription factor [Transcription]
Probab=56.58 E-value=7.2 Score=45.45 Aligned_cols=52 Identities=25% Similarity=0.545 Sum_probs=40.5
Q ss_pred CccCcccccccccccCCCceEecCCCCCCChhhHHHHhhcCCCCCCCCcccc
Q 001028 1114 GLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1165 (1184)
Q Consensus 1114 ~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~tCPiCrk~v~ 1165 (1184)
+....||||-+++...+....--|||+-++..|...-...+.+||.||+...
T Consensus 247 ~v~~s~p~~~~~~~~~d~~~lP~~~~~~~~l~~~~t~~~~~~~~~~~rk~~~ 298 (327)
T KOG2068|consen 247 SVPPSCPICYEDLDLTDSNFLPCPCGFRLCLFCHKTISDGDGRCPGCRKPYE 298 (327)
T ss_pred ccCCCCCCCCCcccccccccccccccccchhhhhhcccccCCCCCccCCccc
Confidence 3457899999987544444444578999999999888888999999997754
No 145
>PF12773 DZR: Double zinc ribbon
Probab=55.98 E-value=9.8 Score=32.05 Aligned_cols=22 Identities=27% Similarity=0.783 Sum_probs=11.6
Q ss_pred ccccCccccCC-CCCCCCCCCCcccc
Q 001028 1032 CMRCLKVQPVG-PVCTTLSCSGLSMA 1056 (1184)
Q Consensus 1032 C~~C~~~q~~~-~~C~~~~C~~~~~a 1056 (1184)
|..|+++.+.+ ..|.+ | |..+.
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 55666655443 55655 4 54443
No 146
>PF14357 DUF4404: Domain of unknown function (DUF4404)
Probab=55.52 E-value=83 Score=30.12 Aligned_cols=82 Identities=13% Similarity=0.095 Sum_probs=65.0
Q ss_pred HHHHHHHHHHHHHHhccCCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHHHhhhHHHHHHHhhhhhHHHHHHHHH
Q 001028 54 IKSELDVLHRAAMAFATNLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIRVKNIARTYSLEHEGESVLFDQLF 133 (1184)
Q Consensus 54 lR~el~~l~~~~~~~~~~~~d~~~~~~l~~r~~~L~~~~~~H~~aEDevI~PaL~~Rv~~v~~~~~~EH~~~~~lf~~l~ 133 (1184)
||..|..|+.-+...++ -|......|..=-+.+...+.. ..|.+.--+.|..|+...+.+++.+|=.....+..|-
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 5677788999999999999999999999999888887
Q ss_pred HHHHhh
Q 001028 134 ELLNSS 139 (1184)
Q Consensus 134 ~~l~~~ 139 (1184)
..|..+
T Consensus 78 ~sLa~M 83 (85)
T PF14357_consen 78 DSLANM 83 (85)
T ss_pred HHHHHC
Confidence 777543
No 147
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=55.44 E-value=3.2 Score=55.25 Aligned_cols=70 Identities=10% Similarity=0.031 Sum_probs=48.1
Q ss_pred hHHHHHHHHHHHHHHHHHHhHHHHHHHhhhHHHhhCCHHHHHHHHHHHhhcCCHHHHHHHHhhhcCCCCH
Q 001028 145 SYRRELASCTGALQTSISQHMSKEEEQVFPLLIEKFSFEEQASLVWQFLCSIPVNMMAEFLPWLSSSISS 214 (1184)
Q Consensus 145 ~~~~eLa~~l~~l~~~l~qHm~~EE~~v~PLl~~~fS~~E~a~L~~~~i~siP~~~m~~~LpWm~~~lsp 214 (1184)
++..-+-.-+.-.+-....||--+|.+..-.=...+|..+-.++...|.-++|..-...-......++++
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 4444444445555556677888777776655566678888889999998888887666655566666666
No 148
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=54.04 E-value=5.6 Score=38.98 Aligned_cols=33 Identities=21% Similarity=0.637 Sum_probs=27.1
Q ss_pred CCcccCCCCC-----ccccCCCCCccccccCCCccccc
Q 001028 1070 RVVYHCPFCN-----LCRVGRGLGVDFFHCMTCNCCLA 1102 (1184)
Q Consensus 1070 k~~yHC~~Cg-----iCRvG~gl~~~~fHC~~C~~C~s 1102 (1184)
+..|-||.|| +|.|.+++++-+-+|..||.-..
T Consensus 20 ~k~FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e 57 (104)
T COG4888 20 PKTFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSFE 57 (104)
T ss_pred CceEecCccCCeeeeEEEEEecCceeEEEcccCcceEE
Confidence 4678899998 89999888888999999987543
No 149
>PRK04023 DNA polymerase II large subunit; Validated
Probab=53.60 E-value=11 Score=49.40 Aligned_cols=48 Identities=25% Similarity=0.551 Sum_probs=31.8
Q ss_pred CCCCCCCCCCCcccceEecccccCccCCCCcccCCCCCccccCCCCCccccccCCCcccc
Q 001028 1042 GPVCTTLSCSGLSMAKYYCGICKFFDDERVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCL 1101 (1184)
Q Consensus 1042 ~~~C~~~~C~~~~~a~Y~C~iC~l~dd~k~~yHC~~CgiCRvG~gl~~~~fHC~~C~~C~ 1101 (1184)
...|.. | |......+|+.|.-- ...+|.|+.||..-.+ ..|.+||.=.
T Consensus 626 ~RfCps--C-G~~t~~frCP~CG~~--Te~i~fCP~CG~~~~~-------y~CPKCG~El 673 (1121)
T PRK04023 626 RRKCPS--C-GKETFYRRCPFCGTH--TEPVYRCPRCGIEVEE-------DECEKCGREP 673 (1121)
T ss_pred CccCCC--C-CCcCCcccCCCCCCC--CCcceeCccccCcCCC-------CcCCCCCCCC
Confidence 357865 5 666667778888644 3577888888655332 4577777654
No 150
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=53.02 E-value=6.6 Score=44.87 Aligned_cols=43 Identities=30% Similarity=0.795 Sum_probs=34.0
Q ss_pred CcccccccccccCCCceEecCCCCCCChhhHHHHh-hcCCCCCCCCc
Q 001028 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYT-CSHYICPICSK 1162 (1184)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl-~~~~tCPiCrk 1162 (1184)
..||.|.--+ +.+++.--|||.|..+||..-| ...+.||.|.+
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 3456666789999999999764 67799999987
No 151
>PF07227 DUF1423: Protein of unknown function (DUF1423); InterPro: IPR004082 A total of 715 potential protein-coding genes have been identified in the nucleotide sequence of Arabidopsis thaliana chromosome 5, with an average gene density of 1 gene per 4001 bp []. Amongst the gene products is a well-conserved family of 130.7kDa proteins that share no sequence similarity with any other known proteins, other than in plants. The sequences are characterised by an N-terminal domain of variable length, a central cysteine-rich region and a relatively acidic C-terminal domain. The sequences may possess a PHD finger.
Probab=52.17 E-value=13 Score=45.14 Aligned_cols=31 Identities=23% Similarity=0.356 Sum_probs=18.6
Q ss_pred HHHHHHHhhhccCCCCChHHHHHHHHHHHHHHH
Q 001028 920 NELEAEIRKVSRDSTLDPRRKAYLIQNLMTSRW 952 (1184)
Q Consensus 920 ~~l~~~Ir~i~~~~~l~~~~ka~liq~Lm~~~~ 952 (1184)
..|+..||.|--. .+.+..-...|+++-.|-
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 3567777777633 444455566677765554
No 152
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=51.73 E-value=12 Score=43.96 Aligned_cols=26 Identities=19% Similarity=0.734 Sum_probs=19.9
Q ss_pred CcccceEe--cccccCccCCCCcccCCCCCc
Q 001028 1052 GLSMAKYY--CGICKFFDDERVVYHCPFCNL 1080 (1184)
Q Consensus 1052 ~~~~a~Y~--C~iC~l~dd~k~~yHC~~Cgi 1080 (1184)
...|--|| |.||++++. .|.||+||+
T Consensus 60 ~~dfeL~f~Ge~i~~y~~q---SftCPyC~~ 87 (381)
T KOG1280|consen 60 RVDFELYFGGEPISHYDPQ---SFTCPYCGI 87 (381)
T ss_pred ccceeeEecCccccccccc---cccCCcccc
Confidence 34566666 788888765 899999995
No 153
>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=49.87 E-value=7.2 Score=36.05 Aligned_cols=10 Identities=30% Similarity=1.152 Sum_probs=6.5
Q ss_pred cceEeccccc
Q 001028 1055 MAKYYCGICK 1064 (1184)
Q Consensus 1055 ~a~Y~C~iC~ 1064 (1184)
-+.|||..||
T Consensus 48 AvdYFC~~c~ 57 (70)
T PF07191_consen 48 AVDYFCNHCH 57 (70)
T ss_dssp EEEEE-TTTT
T ss_pred ccceeeccCC
Confidence 3678888876
No 154
>PRK00808 hypothetical protein; Provisional
Probab=49.60 E-value=3.2e+02 Score=28.37 Aligned_cols=110 Identities=16% Similarity=0.228 Sum_probs=71.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcccCCcccHHHHHHHHHHHHHHHHhhhhccccch----hhhhhhhhhhHHhHHHHHHH
Q 001028 297 IMLWHNAIKRELNDIAEAARKIQLSGDFSDLSAFNKRLQFIAEVCIFHSIAEDKVI----FPAVDVELSFAQEHAEEEIQ 372 (1184)
Q Consensus 297 l~~~HkALRrEL~~L~~~a~~i~~~gd~~~L~~L~~r~~fl~~vl~~Hs~aEDevl----FPaL~~r~~me~EH~~ie~l 372 (1184)
+=.-|+.|=.-++.|...+. .++ ...+..-+.+|.+....|=..|+.++ ||.++.+. .+++..
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 001028 373 FDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVLPLARRH 428 (1184)
Q Consensus 373 ~e~l~~ll~~~~~~~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qvfPLl~~~ 428 (1184)
++.+..+...... +. ... ...+.-|..-|.+|+..+-....+.+.+.
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
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=49.49 E-value=9.4 Score=38.06 Aligned_cols=32 Identities=25% Similarity=0.517 Sum_probs=23.5
Q ss_pred ccccccccCCcccCcccccccCCCCCCccccceeeccccCccccCC
Q 001028 997 CKLRAACCGKLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVG 1042 (1184)
Q Consensus 997 c~l~~~cC~~~y~Cr~CHde~~~H~~~r~~~~~~~C~~C~~~q~~~ 1042 (1184)
-|-.||.||+-| .+... ..|+|.+|+++|++.
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 456789998733 33332 578999999999886
No 156
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=47.62 E-value=6.8 Score=44.61 Aligned_cols=51 Identities=22% Similarity=0.546 Sum_probs=37.6
Q ss_pred cCcccccccccccCCCceEecCCC-----CCCChhhHHHHhh--cCCCCCCCCccccc
Q 001028 1116 ETNCPICCDFLFTSSATVRALPCG-----HFMHSDCFQAYTC--SHYICPICSKSLGD 1166 (1184)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCG-----H~fH~~Ci~~wl~--~~~tCPiCrk~v~~ 1166 (1184)
+..|=||.++...........||. ++.|+.|++.|+. .+.+|.+|......
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 467999998755432223456774 8889999999986 66789999986543
No 157
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=47.21 E-value=13 Score=47.38 Aligned_cols=30 Identities=30% Similarity=0.804 Sum_probs=13.4
Q ss_pred eccccCccccCC-CCCCCCCCCCcccceEecccc
Q 001028 1031 MCMRCLKVQPVG-PVCTTLSCSGLSMAKYYCGIC 1063 (1184)
Q Consensus 1031 ~C~~C~~~q~~~-~~C~~~~C~~~~~a~Y~C~iC 1063 (1184)
+|..|+.+-|.+ ..|.+ | |..+..-.|..|
T Consensus 3 ~Cp~Cg~~n~~~akFC~~--C-G~~l~~~~Cp~C 33 (645)
T PRK14559 3 ICPQCQFENPNNNRFCQK--C-GTSLTHKPCPQC 33 (645)
T ss_pred cCCCCCCcCCCCCccccc--c-CCCCCCCcCCCC
Confidence 455555554433 34544 3 444433334444
No 158
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=47.19 E-value=9.3 Score=44.07 Aligned_cols=32 Identities=31% Similarity=0.855 Sum_probs=24.4
Q ss_pred EecCCCCCCChhhHHHHhhcCCCCCCCCcccccc
Q 001028 1134 RALPCGHFMHSDCFQAYTCSHYICPICSKSLGDM 1167 (1184)
Q Consensus 1134 ~~LpCGH~fH~~Ci~~wl~~~~tCPiCrk~v~~m 1167 (1184)
+.+||.|+|+.+|... .....||.|.-.|..+
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 4579999999999743 2356899998887653
No 159
>PRK01917 cation-binding hemerythrin HHE family protein; Provisional
Probab=46.78 E-value=49 Score=33.99 Aligned_cols=70 Identities=13% Similarity=0.159 Sum_probs=38.8
Q ss_pred HHHHHHHHHHHHHHHhHHHHHHHH----HHHHHhhCCH-----HHHHHHHHhHhh----cCCHHHHHHHHhhhcCCCCHH
Q 001028 398 KLCSQADLIMASIQKHFRNEEVQV----LPLARRHFSP-----KRQRELLYQSLC----VMPLKLIECVLPWLVGSLSEE 464 (1184)
Q Consensus 398 eLa~~le~L~~~L~~Hf~~EE~qv----fPLl~~~fS~-----eEq~eL~~~~l~----smPl~~L~~vLpWl~~~Ls~~ 464 (1184)
.+...++.|..-...||..||.-. +|-+..|--. ++..++..+... .+...++..+..||+.++.-.
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 233444555667777776555
Q ss_pred HHH
Q 001028 465 EAR 467 (1184)
Q Consensus 465 E~~ 467 (1184)
.++
T Consensus 118 D~~ 120 (139)
T PRK01917 118 DAM 120 (139)
T ss_pred HHH
Confidence 443
No 160
>KOG3850 consensus Predicted membrane protein [Function unknown]
Probab=46.73 E-value=5.7e+02 Score=31.10 Aligned_cols=129 Identities=19% Similarity=0.247 Sum_probs=75.5
Q ss_pred HHHHHHHHHHHHHHHHHhcccCCcccH-HHHHHHHHHHHHHHHhhhhccccchhhhhhhhh--hhHHhHHHHHHHHHHHH
Q 001028 301 HNAIKRELNDIAEAARKIQLSGDFSDL-SAFNKRLQFIAEVCIFHSIAEDKVIFPAVDVEL--SFAQEHAEEEIQFDKLR 377 (1184)
Q Consensus 301 HkALRrEL~~L~~~a~~i~~~gd~~~L-~~L~~r~~fl~~vl~~Hs~aEDevlFPaL~~r~--~me~EH~~ie~l~e~l~ 377 (1184)
=+||..||++|.+.-..++ .+..+| .++..-+.|+.+.|. |+.+-+-.|++.+ ..+....+|..+=-++.
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 7767666666555 44444444443322222
Q ss_pred HHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH---HHHHhhCCHHHHHHHHHhHhhcC
Q 001028 378 CLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQVL---PLARRHFSPKRQRELLYQSLCVM 445 (1184)
Q Consensus 378 ~ll~~~~~~~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qvf---PLl~~~fS~eEq~eL~~~~l~sm 445 (1184)
..-..+.= .-| +=+..+.+.+++...|+.+=|.+.- -+--++++++-|..|+.+++-.+
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 011 2245566677777778777776544 22345677778888888777543
No 161
>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=43.75 E-value=16 Score=41.27 Aligned_cols=82 Identities=27% Similarity=0.587 Sum_probs=43.8
Q ss_pred CccccccCCCccccccccccccccccCccCcccc--cccccccCCC-------------ceEecCCCCCCChhhHHHHhh
Q 001028 1088 GVDFFHCMTCNCCLAKKLVDHKCREKGLETNCPI--CCDFLFTSSA-------------TVRALPCGHFMHSDCFQAYTC 1152 (1184)
Q Consensus 1088 ~~~~fHC~~C~~C~s~~l~~H~C~e~~~~~~CpI--Cle~lf~s~~-------------~v~~LpCGH~fH~~Ci~~wl~ 1152 (1184)
|+.|.-|. ||+-+ .|.+.+..-.||- |.--+..... ....+.||| |-+.++-
T Consensus 103 GKKYVRCP-CNCLL-------ICk~sS~rIaCPRp~CkRiI~L~~~~~~p~~~~~~~~p~~~rv~Cgh-----C~~~Fl~ 169 (256)
T PF09788_consen 103 GKKYVRCP-CNCLL-------ICKSSSQRIACPRPNCKRIINLGPSHQGPVTPPVPTQPGSCRVICGH-----CSNTFLF 169 (256)
T ss_pred CCeeEecC-CceEE-------EeecccccccCCCCCCcceEEeCCccCCCCCCCCCCCCCceeEECCC-----CCCcEec
Confidence 46788886 55432 3556666667776 7643321111 123467888 4444331
Q ss_pred -----cC-CCCCCCCccccccCccccccccchhhhc
Q 001028 1153 -----SH-YICPICSKSLGDMAVSPLFRTTSVVLLG 1182 (1184)
Q Consensus 1153 -----~~-~tCPiCrk~v~~m~~y~~~~~~~v~~~~ 1182 (1184)
+. -+||-|||.-..=.+|=+.|..--.++|
T Consensus 170 ~~~~~~tlARCPHCrKvSSVG~~faRkR~i~f~llg 205 (256)
T PF09788_consen 170 NTLTSNTLARCPHCRKVSSVGPRFARKRAIIFFLLG 205 (256)
T ss_pred cCCCCCccccCCCCceeccccchHhhhHHHHHHHHH
Confidence 12 3799999853322345555554444444
No 162
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=42.76 E-value=20 Score=30.05 Aligned_cols=23 Identities=30% Similarity=0.894 Sum_probs=11.2
Q ss_pred eEecccccC---ccCCCCcccCCCCC
Q 001028 1057 KYYCGICKF---FDDERVVYHCPFCN 1079 (1184)
Q Consensus 1057 ~Y~C~iC~l---~dd~k~~yHC~~Cg 1079 (1184)
.|-|..|.- +++.....+||+||
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG 28 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCG 28 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCC
Confidence 455555542 22223356666666
No 163
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=42.33 E-value=8.3 Score=49.81 Aligned_cols=44 Identities=27% Similarity=0.618 Sum_probs=0.0
Q ss_pred eeccccCccccCCCCCCCCCCCCcccceEecccccCccCCCCcccCCCCC
Q 001028 1030 MMCMRCLKVQPVGPVCTTLSCSGLSMAKYYCGICKFFDDERVVYHCPFCN 1079 (1184)
Q Consensus 1030 ~~C~~C~~~q~~~~~C~~~~C~~~~~a~Y~C~iC~l~dd~k~~yHC~~Cg 1079 (1184)
-.|..|+++. ....|.. |+....-.|+|+.|+.--++. +||.||
T Consensus 656 r~Cp~Cg~~t-~~~~Cp~--CG~~T~~~~~Cp~C~~~~~~~---~C~~C~ 699 (900)
T PF03833_consen 656 RRCPKCGKET-FYNRCPE--CGSHTEPVYVCPDCGIEVEED---ECPKCG 699 (900)
T ss_dssp --------------------------------------------------
T ss_pred ccCcccCCcc-hhhcCcc--cCCccccceeccccccccCcc---cccccc
Confidence 3455555442 2234543 544445566666665421111 566665
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=42.17 E-value=98 Score=30.56 Aligned_cols=51 Identities=20% Similarity=0.232 Sum_probs=31.8
Q ss_pred hhHHhHHHHHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHhHHHHHHHH----HHHHHhh
Q 001028 361 SFAQEHAEEEIQFDKLRCLIESIQSAGANSSTAEFYTKLCSQADLIMASIQKHFRNEEVQV----LPLARRH 428 (1184)
Q Consensus 361 ~me~EH~~ie~l~e~l~~ll~~~~~~~~~~~~~~~~~eLa~~le~L~~~L~~Hf~~EE~qv----fPLl~~~ 428 (1184)
.+..+|++.-.+++.|..++.. ...+..|..-...||..||.-. +|-+..|
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 4556666665555555544422 2346677777899999999764 4555444
No 165
>PHA00626 hypothetical protein
Probab=41.24 E-value=20 Score=31.87 Aligned_cols=8 Identities=38% Similarity=0.779 Sum_probs=4.0
Q ss_pred cccCCCCC
Q 001028 1072 VYHCPFCN 1079 (1184)
Q Consensus 1072 ~yHC~~Cg 1079 (1184)
.|.|++||
T Consensus 23 rYkCkdCG 30 (59)
T PHA00626 23 DYVCCDCG 30 (59)
T ss_pred ceEcCCCC
Confidence 35555555
No 166
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=40.27 E-value=12 Score=44.97 Aligned_cols=19 Identities=16% Similarity=0.469 Sum_probs=14.4
Q ss_pred hHHHhcCHHHHHHHHhhhc
Q 001028 912 NDIFRMNQNELEAEIRKVS 930 (1184)
Q Consensus 912 ~~~~~~~q~~l~~~Ir~i~ 930 (1184)
...+++|+.+||..|++.-
T Consensus 50 ~~llk~~~KqLR~li~~Lr 68 (436)
T KOG2593|consen 50 KELLKFNKKQLRKLIASLR 68 (436)
T ss_pred HHHhcccHHHHHHHHHHhh
Confidence 3456788899888888774
No 167
>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=40.19 E-value=21 Score=28.46 Aligned_cols=24 Identities=25% Similarity=0.897 Sum_probs=17.6
Q ss_pred eEecccccCc-cCCCCcccCCCCCc
Q 001028 1057 KYYCGICKFF-DDERVVYHCPFCNL 1080 (1184)
Q Consensus 1057 ~Y~C~iC~l~-dd~k~~yHC~~Cgi 1080 (1184)
.|-|.+|.+. +.++.+..||-||.
T Consensus 2 ~~~C~~CG~i~~g~~~p~~CP~Cg~ 26 (34)
T cd00729 2 VWVCPVCGYIHEGEEAPEKCPICGA 26 (34)
T ss_pred eEECCCCCCEeECCcCCCcCcCCCC
Confidence 4778999876 54467778888874
No 168
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=39.16 E-value=18 Score=42.03 Aligned_cols=45 Identities=22% Similarity=0.631 Sum_probs=33.2
Q ss_pred CcccccccccccCCCceEecCCCCCCChhhHHHHhhc---CCCCCCCCc
Q 001028 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCS---HYICPICSK 1162 (1184)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~---~~tCPiCrk 1162 (1184)
-.||+=.|. -+...+-+.|.|||++-..-++..-++ .+.||.|-.
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 357775554 555566778999999999999887654 467999953
No 169
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=39.10 E-value=13 Score=44.50 Aligned_cols=37 Identities=24% Similarity=0.441 Sum_probs=26.4
Q ss_pred cCcccccccccccCCCceEecCCCCCCChhhHHHHhh
Q 001028 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC 1152 (1184)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~ 1152 (1184)
...|.||..+............|||.|..+|..+++.
T Consensus 146 ~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~ie 182 (384)
T KOG1812|consen 146 KEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIE 182 (384)
T ss_pred cccCccCccccccHhhhHHHhcccchhhhHHhHHHhh
Confidence 4679999933222222233678999999999999975
No 170
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=38.85 E-value=10 Score=39.46 Aligned_cols=26 Identities=27% Similarity=0.837 Sum_probs=19.6
Q ss_pred cceEecccccCccCCCCcccCCCCC--ccccC
Q 001028 1055 MAKYYCGICKFFDDERVVYHCPFCN--LCRVG 1084 (1184)
Q Consensus 1055 ~a~Y~C~iC~l~dd~k~~yHC~~Cg--iCRvG 1084 (1184)
-.+-||.+|.+| ++|-|-.|| +|-|+
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 445688888866 678888888 67776
No 171
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=38.37 E-value=20 Score=41.91 Aligned_cols=46 Identities=17% Similarity=0.345 Sum_probs=34.1
Q ss_pred cCcccccccccccCCCceEecCCCCCCChhhHHHHhhcCCCCCCCCccc
Q 001028 1116 ETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSL 1164 (1184)
Q Consensus 1116 ~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~tCPiCrk~v 1164 (1184)
...||||+...- .+.+.--=|=+|+-.|+..|+.++.+||+=.+++
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 567999986522 1222222399999999999999999999876654
No 172
>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=38.12 E-value=12 Score=30.49 Aligned_cols=13 Identities=46% Similarity=1.185 Sum_probs=5.5
Q ss_pred cceEecccccCcc
Q 001028 1055 MAKYYCGICKFFD 1067 (1184)
Q Consensus 1055 ~a~Y~C~iC~l~d 1067 (1184)
|.+|||+.|+.|=
T Consensus 1 m~ryyCdyC~~~~ 13 (38)
T PF06220_consen 1 MPRYYCDYCKKYL 13 (38)
T ss_dssp --S-B-TTT--B-
T ss_pred CcCeeccccccee
Confidence 5689999998764
No 173
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=37.80 E-value=26 Score=40.26 Aligned_cols=48 Identities=27% Similarity=0.710 Sum_probs=39.0
Q ss_pred CCcccceEecccccCccCCCCcccCCCCCccccCCCCCccccccCCCccccccc
Q 001028 1051 SGLSMAKYYCGICKFFDDERVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLAKK 1104 (1184)
Q Consensus 1051 ~~~~~a~Y~C~iC~l~dd~k~~yHC~~CgiCRvG~gl~~~~fHC~~C~~C~s~~ 1104 (1184)
.|....-+||+.|+++-. +...||.-||.|-.+- --||.=-|.|+...
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 367778899999999955 4678999999998874 37999999998754
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=37.80 E-value=11 Score=39.68 Aligned_cols=23 Identities=22% Similarity=0.711 Sum_probs=12.6
Q ss_pred eEecccccC---ccCC-CCcccCCCCC
Q 001028 1057 KYYCGICKF---FDDE-RVVYHCPFCN 1079 (1184)
Q Consensus 1057 ~Y~C~iC~l---~dd~-k~~yHC~~Cg 1079 (1184)
-|+|+.|+. |++. ..-|+||.||
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 355666652 3333 4457777776
No 175
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=37.73 E-value=15 Score=40.22 Aligned_cols=31 Identities=35% Similarity=0.881 Sum_probs=22.2
Q ss_pred ccCCCceEecCCCCCCChhhHHHHhhcCCCCCCCCc
Q 001028 1127 FTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSK 1162 (1184)
Q Consensus 1127 f~s~~~v~~LpCGH~fH~~Ci~~wl~~~~tCPiCrk 1162 (1184)
|.....++--.|+-+||+.|+. ...||-|.+
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 3333344556899999999975 267999965
No 176
>PF14631 FancD2: Fanconi anaemia protein FancD2 nuclease; PDB: 3S4W_B.
Probab=36.97 E-value=6e+02 Score=36.09 Aligned_cols=99 Identities=20% Similarity=0.277 Sum_probs=59.6
Q ss_pred HHHHHHHHHHHhhhcCchhHHHHHHHHHH---------HHHHHHHHhHHHHHHHhhhHHHh----hCCHHHHHH---HHH
Q 001028 127 VLFDQLFELLNSSMRNEESYRRELASCTG---------ALQTSISQHMSKEEEQVFPLLIE----KFSFEEQAS---LVW 190 (1184)
Q Consensus 127 ~lf~~l~~~l~~~~~~~~~~~~eLa~~l~---------~l~~~l~qHm~~EE~~v~PLl~~----~fS~~E~a~---L~~ 190 (1184)
.++++|++.+... +..+-+++...+- ++-..|.+=|..++.-+.|.|.. .+|++.+.. .+-
T Consensus 192 ~l~~kl~~~l~~a---p~~lq~eiI~~LPeIl~ds~h~~v~~~L~~ll~~~~~L~~~iLd~Ls~L~Ls~~~l~~vr~~vl 268 (1426)
T PF14631_consen 192 ELTDKLFEVLSIA---PVELQKEIISSLPEILDDSQHDEVVEELLELLQENPELTVPILDALSNLNLSPELLEEVREKVL 268 (1426)
T ss_dssp HHHHHHHHHHHHS----TTTHHHHHHTHHHHS-GGGHHHHHHHHHHHHHH-STTHHHHHHHHHHS---HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhC---CHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHhcCCchhhhHHHHHhcCCCCHHHHHHHHHHHH
Confidence 5566666665543 2233344444442 22223344444444556666654 345555544 455
Q ss_pred HHhhcCCHHHHHHHHhhhcCCCCHHHHHHHHHHHhhcC
Q 001028 191 QFLCSIPVNMMAEFLPWLSSSISSDEHQDMRKCLCKII 228 (1184)
Q Consensus 191 ~~i~siP~~~m~~~LpWm~~~lsp~Er~~~l~~l~~~~ 228 (1184)
..+.+++++.|..++..++.++++.+-..+...||+..
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 177
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=36.59 E-value=13 Score=40.15 Aligned_cols=23 Identities=30% Similarity=1.037 Sum_probs=12.8
Q ss_pred eEecccccC---ccCC-CCcccCCCCC
Q 001028 1057 KYYCGICKF---FDDE-RVVYHCPFCN 1079 (1184)
Q Consensus 1057 ~Y~C~iC~l---~dd~-k~~yHC~~Cg 1079 (1184)
-|+|+.|+. |++. ...|+||.||
T Consensus 117 ~Y~Cp~C~~rytf~eA~~~~F~Cp~Cg 143 (178)
T PRK06266 117 FFFCPNCHIRFTFDEAMEYGFRCPQCG 143 (178)
T ss_pred EEECCCCCcEEeHHHHhhcCCcCCCCC
Confidence 456666652 3333 4456677666
No 178
>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=35.85 E-value=28 Score=30.00 Aligned_cols=41 Identities=34% Similarity=0.869 Sum_probs=20.3
Q ss_pred CcccccccccccCCCceEecCCCCCCChhhHH--HHhhc-----CCCCCCCCcc
Q 001028 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQ--AYTCS-----HYICPICSKS 1163 (1184)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~--~wl~~-----~~tCPiCrk~ 1163 (1184)
-.|||....|. .+++...|.|. +||+ .|+.. ...||+|+++
T Consensus 3 L~CPls~~~i~---~P~Rg~~C~H~---~CFDl~~fl~~~~~~~~W~CPiC~~~ 50 (50)
T PF02891_consen 3 LRCPLSFQRIR---IPVRGKNCKHL---QCFDLESFLESNQRTPKWKCPICNKP 50 (50)
T ss_dssp SB-TTTSSB-S---SEEEETT--SS-----EEHHHHHHHHHHS---B-TTT---
T ss_pred eeCCCCCCEEE---eCccCCcCccc---ceECHHHHHHHhhccCCeECcCCcCc
Confidence 36999887753 47888888876 5765 35532 3579999874
No 179
>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=35.75 E-value=15 Score=31.29 Aligned_cols=40 Identities=30% Similarity=0.756 Sum_probs=29.0
Q ss_pred ccccccccccCCCceEecCCCCCCChhhHHHHhhcCCCCCCCCccccccC
Q 001028 1119 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGDMA 1168 (1184)
Q Consensus 1119 CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~tCPiCrk~v~~m~ 1168 (1184)
|+.|...+... .+....-|..||..|+ +|-.|++.+.+-.
T Consensus 1 C~~C~~~I~~~--~~~~~~~~~~~H~~Cf--------~C~~C~~~l~~~~ 40 (58)
T PF00412_consen 1 CARCGKPIYGT--EIVIKAMGKFWHPECF--------KCSKCGKPLNDGD 40 (58)
T ss_dssp BTTTSSBESSS--SEEEEETTEEEETTTS--------BETTTTCBTTTSS
T ss_pred CCCCCCCccCc--EEEEEeCCcEEEcccc--------ccCCCCCccCCCe
Confidence 77888886633 2332345899999885 8999999998755
No 180
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=35.09 E-value=35 Score=44.32 Aligned_cols=44 Identities=23% Similarity=0.724 Sum_probs=25.7
Q ss_pred cceeeccccCccccCCCCCCCCCCCCcccc------eEecccccCccCCCCcccCCCCC
Q 001028 1027 TTEMMCMRCLKVQPVGPVCTTLSCSGLSMA------KYYCGICKFFDDERVVYHCPFCN 1079 (1184)
Q Consensus 1027 ~~~~~C~~C~~~q~~~~~C~~~~C~~~~~a------~Y~C~iC~l~dd~k~~yHC~~Cg 1079 (1184)
.+.++|..|+.+- .|.+ | +..+. ...|..|+.= .+.+.+||.||
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 3589999999864 5777 5 44332 2234444332 25566666666
No 181
>PLN03086 PRLI-interacting factor K; Provisional
Probab=34.90 E-value=16 Score=45.90 Aligned_cols=31 Identities=32% Similarity=0.883 Sum_probs=18.0
Q ss_pred cccCCCccccccc-ccccc---ccccCccCcccccccc
Q 001028 1092 FHCMTCNCCLAKK-LVDHK---CREKGLETNCPICCDF 1125 (1184)
Q Consensus 1092 fHC~~C~~C~s~~-l~~H~---C~e~~~~~~CpICle~ 1125 (1184)
+.|. |+..+... +..|. |.++ ...|+.|...
T Consensus 479 v~Cp-Cg~~~~R~~L~~H~~thCp~K--pi~C~fC~~~ 513 (567)
T PLN03086 479 LQCP-CGVVLEKEQMVQHQASTCPLR--LITCRFCGDM 513 (567)
T ss_pred ccCC-CCCCcchhHHHhhhhccCCCC--ceeCCCCCCc
Confidence 3466 66544333 25664 5443 4679999865
No 182
>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=34.63 E-value=87 Score=36.06 Aligned_cols=42 Identities=14% Similarity=0.254 Sum_probs=29.5
Q ss_pred hhHHHhcCHHHHHHHHhhhcc-CCCCChHHHHHHHHHHHHHHH
Q 001028 911 WNDIFRMNQNELEAEIRKVSR-DSTLDPRRKAYLIQNLMTSRW 952 (1184)
Q Consensus 911 ~~~~~~~~q~~l~~~Ir~i~~-~~~l~~~~ka~liq~Lm~~~~ 952 (1184)
.+.+...+..++++-++.+.. +...++..-+.+++..+.--|
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 677777889999999988876 455667777888888877555
No 183
>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=34.28 E-value=31 Score=42.71 Aligned_cols=10 Identities=40% Similarity=1.152 Sum_probs=5.3
Q ss_pred cccCcccccc
Q 001028 1007 LFTCRFCHDK 1016 (1184)
Q Consensus 1007 ~y~Cr~CHde 1016 (1184)
.|-|+.||.-
T Consensus 5 L~fC~~C~~i 14 (483)
T PF05502_consen 5 LYFCEHCHKI 14 (483)
T ss_pred ceeccccccc
Confidence 4556666543
No 184
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=34.20 E-value=35 Score=46.29 Aligned_cols=33 Identities=30% Similarity=0.704 Sum_probs=17.5
Q ss_pred CCCCCCCCCCcccceEecccccCccCCCCcccCCCCCc
Q 001028 1043 PVCTTLSCSGLSMAKYYCGICKFFDDERVVYHCPFCNL 1080 (1184)
Q Consensus 1043 ~~C~~~~C~~~~~a~Y~C~iC~l~dd~k~~yHC~~Cgi 1080 (1184)
..|.+ | |...-..||+.|.-.- +.+|+|+.||.
T Consensus 668 rkCPk--C-G~~t~~~fCP~CGs~t--e~vy~CPsCGa 700 (1337)
T PRK14714 668 RRCPS--C-GTETYENRCPDCGTHT--EPVYVCPDCGA 700 (1337)
T ss_pred EECCC--C-CCccccccCcccCCcC--CCceeCccCCC
Confidence 45655 5 4332234666665332 34667777765
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=34.14 E-value=19 Score=29.72 Aligned_cols=13 Identities=46% Similarity=0.846 Sum_probs=5.7
Q ss_pred cCCCCcccCCCCC
Q 001028 1067 DDERVVYHCPFCN 1079 (1184)
Q Consensus 1067 dd~k~~yHC~~Cg 1079 (1184)
|...+.|-|..||
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
>COG0143 MetG Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=34.05 E-value=26 Score=44.07 Aligned_cols=45 Identities=24% Similarity=0.447 Sum_probs=35.2
Q ss_pred ccceEecccccCccCC-CCcccCCCCCccccCCCCCccccccCCCccccccc
Q 001028 1054 SMAKYYCGICKFFDDE-RVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLAKK 1104 (1184)
Q Consensus 1054 ~~a~Y~C~iC~l~dd~-k~~yHC~~CgiCRvG~gl~~~~fHC~~C~~C~s~~ 1104 (1184)
....+||..|.-|=.| .-.=.||+||.+..++ -+|+.||.++.-.
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 4566799999877665 4555799999999985 4899999998753
No 187
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=32.82 E-value=29 Score=29.79 Aligned_cols=9 Identities=44% Similarity=1.397 Sum_probs=6.6
Q ss_pred eEecccccC
Q 001028 1057 KYYCGICKF 1065 (1184)
Q Consensus 1057 ~Y~C~iC~l 1065 (1184)
+|.|.+|.+
T Consensus 1 ky~C~~Cgy 9 (47)
T PF00301_consen 1 KYQCPVCGY 9 (47)
T ss_dssp EEEETTTSB
T ss_pred CcCCCCCCE
Confidence 577888875
No 188
>PLN02189 cellulose synthase
Probab=32.70 E-value=33 Score=45.76 Aligned_cols=51 Identities=22% Similarity=0.412 Sum_probs=35.2
Q ss_pred CccCcccccccccccCCCceEecC---CCCCCChhhHHHHhh--cCCCCCCCCcccc
Q 001028 1114 GLETNCPICCDFLFTSSATVRALP---CGHFMHSDCFQAYTC--SHYICPICSKSLG 1165 (1184)
Q Consensus 1114 ~~~~~CpICle~lf~s~~~v~~Lp---CGH~fH~~Ci~~wl~--~~~tCPiCrk~v~ 1165 (1184)
.....|.||.|++-...+.-.... ||--.++.|+ +|-+ .+..||-|+...-
T Consensus 32 ~~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cy-eyer~eg~q~CpqCkt~Y~ 87 (1040)
T PLN02189 32 LDGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCY-EYERREGTQNCPQCKTRYK 87 (1040)
T ss_pred ccCccccccccccCcCCCCCEEEeeccCCCccccchh-hhhhhcCCccCcccCCchh
Confidence 345689999999754333333343 6666999999 5653 4678999997654
No 189
>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=32.63 E-value=8.2 Score=32.42 Aligned_cols=43 Identities=21% Similarity=0.680 Sum_probs=29.5
Q ss_pred ccccccccccCCCceEecCCCCCCChhhHHHHhh------cCCCCCCCCc
Q 001028 1119 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTC------SHYICPICSK 1162 (1184)
Q Consensus 1119 CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~------~~~tCPiCrk 1162 (1184)
|+||... ...+..+.=-.|+-.||..|+..=.. ..+.||.|+.
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 8899874 33333333358999999999976432 3678998864
No 190
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=32.46 E-value=48 Score=38.87 Aligned_cols=103 Identities=27% Similarity=0.417 Sum_probs=53.7
Q ss_pred cccceEecccccCccCCCCcccCCCCCccccC-CCCCccccccCCCcccccccc-ccccccccCccCcccccccccccCC
Q 001028 1053 LSMAKYYCGICKFFDDERVVYHCPFCNLCRVG-RGLGVDFFHCMTCNCCLAKKL-VDHKCREKGLETNCPICCDFLFTSS 1130 (1184)
Q Consensus 1053 ~~~a~Y~C~iC~l~dd~k~~yHC~~CgiCRvG-~gl~~~~fHC~~C~~C~s~~l-~~H~C~e~~~~~~CpICle~lf~s~ 1130 (1184)
..-|-|+|+.||--=- .-+-.||-|+.=-|- .-|...|-|=. +..- ..-.-.++-....|-.|.+.+.+ .
T Consensus 272 ~~~~Gy~CP~CkakvC-sLP~eCpiC~ltLVss~hLARSyhhL~------PL~~F~Eip~~~~~~~~~Cf~C~~~~~~-~ 343 (378)
T KOG2807|consen 272 LSGGGYFCPQCKAKVC-SLPIECPICSLTLVSSPHLARSYHHLF------PLKPFVEIPETEYNGSRFCFACQGELLS-S 343 (378)
T ss_pred cccCceeCCcccCeee-cCCccCCccceeEecchHHHHHHHhhc------CCcchhhccccccCCCcceeeeccccCC-C
Confidence 4567788888864211 123456666554443 12222222211 1110 11011112234459999777443 3
Q ss_pred CceEecCCCCCCChhhHHHHhhcCCCCCCCCcc
Q 001028 1131 ATVRALPCGHFMHSDCFQAYTCSHYICPICSKS 1163 (1184)
Q Consensus 1131 ~~v~~LpCGH~fH~~Ci~~wl~~~~tCPiCrk~ 1163 (1184)
..++--.|.+.|..+|-.---..-..||-|...
T Consensus 344 ~~y~C~~Ck~~FCldCDv~iHesLh~CpgCeh~ 376 (378)
T KOG2807|consen 344 GRYRCESCKNVFCLDCDVFIHESLHNCPGCEHK 376 (378)
T ss_pred CcEEchhccceeeccchHHHHhhhhcCCCcCCC
Confidence 446666899999999954333344679999743
No 191
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=32.17 E-value=92 Score=31.50 Aligned_cols=47 Identities=21% Similarity=0.258 Sum_probs=30.7
Q ss_pred cCcccccccccccC----------CCceEecCCCCCCChhhHHHHhhcCCCCCCCCc
Q 001028 1116 ETNCPICCDFLFTS----------SATVRALPCGHFMHSDCFQAYTCSHYICPICSK 1162 (1184)
Q Consensus 1116 ~~~CpICle~lf~s----------~~~v~~LpCGH~fH~~Ci~~wl~~~~tCPiCrk 1162 (1184)
...|--|+..+-.. .....--.|++.|..+|-.-+-..=..||-|..
T Consensus 55 ~~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~CPGC~~ 111 (112)
T TIGR00622 55 SRFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHESLHCCPGCIH 111 (112)
T ss_pred CCcccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhhccCCcCCCC
Confidence 34699998873221 111234578899999996655555677999863
No 192
>PRK07219 DNA topoisomerase I; Validated
Probab=30.72 E-value=73 Score=42.12 Aligned_cols=63 Identities=25% Similarity=0.495 Sum_probs=34.4
Q ss_pred cccccCccCC----CCcccCCCCCcc---ccCCCCCccccccCC---CccccccccccccccccCccCcccccccccc
Q 001028 1060 CGICKFFDDE----RVVYHCPFCNLC---RVGRGLGVDFFHCMT---CNCCLAKKLVDHKCREKGLETNCPICCDFLF 1127 (1184)
Q Consensus 1060 C~iC~l~dd~----k~~yHC~~CgiC---RvG~gl~~~~fHC~~---C~~C~s~~l~~H~C~e~~~~~~CpICle~lf 1127 (1184)
|+.|+..... .....||.||-- |.|+. | .|+-|.+ |+.-.++.-..+. ......||-|...+.
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 346889999822 22322 3 3888865 6644332211101 124568999976543
No 193
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=30.22 E-value=25 Score=45.12 Aligned_cols=49 Identities=20% Similarity=0.497 Sum_probs=34.1
Q ss_pred ccCcccccccccccCCCceEecCCC-----CCCChhhHHHHhhc--CCCCCCCCcccc
Q 001028 1115 LETNCPICCDFLFTSSATVRALPCG-----HFMHSDCFQAYTCS--HYICPICSKSLG 1165 (1184)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~LpCG-----H~fH~~Ci~~wl~~--~~tCPiCrk~v~ 1165 (1184)
....|-||.-+ ...+++ -.-||. -++|++|+.+|+.. ...|-+|...+.
T Consensus 11 d~~~CRICr~e-~~~d~p-LfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~ 66 (1175)
T COG5183 11 DKRSCRICRTE-DIRDDP-LFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYK 66 (1175)
T ss_pred cchhceeecCC-CCCCCc-CcccccccchhHHHHHHHHHHHHhcCCCcceeeecceee
Confidence 44679999865 222222 223663 78999999999965 456999998765
No 194
>PLN02436 cellulose synthase A
Probab=29.79 E-value=39 Score=45.19 Aligned_cols=51 Identities=20% Similarity=0.451 Sum_probs=35.4
Q ss_pred CccCcccccccccccCCCceEecC---CCCCCChhhHHHHhh--cCCCCCCCCcccc
Q 001028 1114 GLETNCPICCDFLFTSSATVRALP---CGHFMHSDCFQAYTC--SHYICPICSKSLG 1165 (1184)
Q Consensus 1114 ~~~~~CpICle~lf~s~~~v~~Lp---CGH~fH~~Ci~~wl~--~~~tCPiCrk~v~ 1165 (1184)
.....|.||.|++-...+.-.... ||--.++.|+ +|-+ .+..||-|+...-
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 345689999999754444334444 5555999999 5654 4678999997654
No 195
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=29.73 E-value=29 Score=30.16 Aligned_cols=30 Identities=23% Similarity=0.609 Sum_probs=21.7
Q ss_pred ccceEeccccc-CccCC--CCcccCCCCCcccc
Q 001028 1054 SMAKYYCGICK-FFDDE--RVVYHCPFCNLCRV 1083 (1184)
Q Consensus 1054 ~~a~Y~C~iC~-l~dd~--k~~yHC~~CgiCRv 1083 (1184)
.+..|-|..|. .++.+ ..-+.|++||.=.+
T Consensus 3 ~~~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~rIl 35 (49)
T COG1996 3 AMMEYKCARCGREVELDQETRGIRCPYCGSRIL 35 (49)
T ss_pred ceEEEEhhhcCCeeehhhccCceeCCCCCcEEE
Confidence 45678999994 45533 78889999995443
No 196
>KOG4399 consensus C2HC-type Zn-finger protein [General function prediction only]
Probab=29.69 E-value=13 Score=42.05 Aligned_cols=47 Identities=19% Similarity=0.149 Sum_probs=36.2
Q ss_pred CcccceEecccccCccCCCCcccCCCCCccccCCCCCccccccCCCccccc
Q 001028 1052 GLSMAKYYCGICKFFDDERVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLA 1102 (1184)
Q Consensus 1052 ~~~~a~Y~C~iC~l~dd~k~~yHC~~CgiCRvG~gl~~~~fHC~~C~~C~s 1102 (1184)
+...+.-+|.||.=+|.++ -|||.|.-||--+. ...-||..|..|..
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 89999999997643 25678888888765
No 197
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=29.68 E-value=38 Score=43.44 Aligned_cols=33 Identities=21% Similarity=0.570 Sum_probs=18.7
Q ss_pred eeeccccCccccCCCCCCCCCCCCc--ccceEecccccC
Q 001028 1029 EMMCMRCLKVQPVGPVCTTLSCSGL--SMAKYYCGICKF 1065 (1184)
Q Consensus 1029 ~~~C~~C~~~q~~~~~C~~~~C~~~--~~a~Y~C~iC~l 1065 (1184)
.-+|..|++..+. ..|.+ | |. ..+.-||+.|..
T Consensus 15 akFC~~CG~~l~~-~~Cp~--C-G~~~~~~~~fC~~CG~ 49 (645)
T PRK14559 15 NRFCQKCGTSLTH-KPCPQ--C-GTEVPVDEAHCPNCGA 49 (645)
T ss_pred CccccccCCCCCC-CcCCC--C-CCCCCcccccccccCC
Confidence 4467777776543 46765 5 43 245556666654
No 198
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=28.72 E-value=46 Score=38.71 Aligned_cols=78 Identities=27% Similarity=0.508 Sum_probs=50.1
Q ss_pred ccCC----CCcccCCCCCccccCCCCCccccccCCCcccccccc--ccccccccCccCcccccccccccCCCceEecCCC
Q 001028 1066 FDDE----RVVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLAKKL--VDHKCREKGLETNCPICCDFLFTSSATVRALPCG 1139 (1184)
Q Consensus 1066 ~dd~----k~~yHC~~CgiCRvG~gl~~~~fHC~~C~~C~s~~l--~~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCG 1139 (1184)
|||- +-+=||..|-. -| -..+=||.|.-|..= .+.. ..|.=..|.....|..|-+- .++|.+++|.
T Consensus 169 WdDVLks~Ripg~Ces~~~--pg-~fAEFfFKC~ah~~~-~k~~aa~lhli~~N~~ni~C~~Ctdv----~~~vlvf~Cn 240 (446)
T KOG0006|consen 169 WDDVLKSKRIPGVCESCCT--PG-LFAEFFFKCGAHPTS-DKETAAALHLIATNSRNITCITCTDV----RSPVLVFQCN 240 (446)
T ss_pred hhhhhhcccCccccccccC--Cc-chHhheehhccCCCc-cccchhHHHHhhcccccceeEEecCC----ccceEEEecC
Confidence 6664 66778877642 22 122446655444332 1112 35555556677889999764 4578889999
Q ss_pred --CCCChhhHHHHh
Q 001028 1140 --HFMHSDCFQAYT 1151 (1184)
Q Consensus 1140 --H~fH~~Ci~~wl 1151 (1184)
|+...+||.-|-
T Consensus 241 s~HvtC~dCFr~yc 254 (446)
T KOG0006|consen 241 SRHVTCLDCFRLYC 254 (446)
T ss_pred CceeehHHhhhhHh
Confidence 999999999774
No 199
>KOG3842 consensus Adaptor protein Pellino [Signal transduction mechanisms]
Probab=28.18 E-value=51 Score=38.36 Aligned_cols=57 Identities=25% Similarity=0.543 Sum_probs=38.2
Q ss_pred cCcccccccc-----c---------ccCCCce-EecCCCCCCChhhHHHHhhc---------CCCCCCCCccccccCccc
Q 001028 1116 ETNCPICCDF-----L---------FTSSATV-RALPCGHFMHSDCFQAYTCS---------HYICPICSKSLGDMAVSP 1171 (1184)
Q Consensus 1116 ~~~CpICle~-----l---------f~s~~~v-~~LpCGH~fH~~Ci~~wl~~---------~~tCPiCrk~v~~m~~y~ 1171 (1184)
+..||+|+.. | .+.+-+. ..-||||+--..=..-|-+. +..||.|-..+..-.-|+
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 6789999753 0 1112222 34599999888888888642 456999999887666665
Q ss_pred c
Q 001028 1172 L 1172 (1184)
Q Consensus 1172 ~ 1172 (1184)
+
T Consensus 421 k 421 (429)
T KOG3842|consen 421 K 421 (429)
T ss_pred E
Confidence 4
No 200
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=27.99 E-value=38 Score=33.42 Aligned_cols=33 Identities=15% Similarity=0.624 Sum_probs=0.0
Q ss_pred CcccCCCCC----ccccCCCCCccccccCCCcccccccc
Q 001028 1071 VVYHCPFCN----LCRVGRGLGVDFFHCMTCNCCLAKKL 1105 (1184)
Q Consensus 1071 ~~yHC~~Cg----iCRvG~gl~~~~fHC~~C~~C~s~~l 1105 (1184)
.+|+||+|| .|.+++ |.-...|.+||.-.....
T Consensus 20 t~f~CP~Cge~~v~v~~~k--~~~h~~C~~CG~y~~~~V 56 (99)
T PRK14892 20 KIFECPRCGKVSISVKIKK--NIAIITCGNCGLYTEFEV 56 (99)
T ss_pred cEeECCCCCCeEeeeecCC--CcceEECCCCCCccCEEC
No 201
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=27.72 E-value=54 Score=41.03 Aligned_cols=116 Identities=21% Similarity=0.344 Sum_probs=60.1
Q ss_pred cccccccCCcccCcccccccCCCCCCccccceeeccccCccccCCCCCCCCCCCCcccceEec-ccccCccCC------C
Q 001028 998 KLRAACCGKLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVGPVCTTLSCSGLSMAKYYC-GICKFFDDE------R 1070 (1184)
Q Consensus 998 ~l~~~cC~~~y~Cr~CHde~~~H~~~r~~~~~~~C~~C~~~q~~~~~C~~~~C~~~~~a~Y~C-~iC~l~dd~------k 1070 (1184)
.++|..|++ .|-.++-.-.-.-+-+.-..|-.|+.--..+.-|.. | +. +||| ..|.-|-.. -
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 455452111011122445667777766666666666 3 32 7777 445444321 5
Q ss_pred Cccc--CCCCCccccCCCCCcc------ccccCCCccccccccccccccccCccCcccccccccccC
Q 001028 1071 VVYH--CPFCNLCRVGRGLGVD------FFHCMTCNCCLAKKLVDHKCREKGLETNCPICCDFLFTS 1129 (1184)
Q Consensus 1071 ~~yH--C~~CgiCRvG~gl~~~------~fHC~~C~~C~s~~l~~H~C~e~~~~~~CpICle~lf~s 1129 (1184)
+.|| |-.|.+|+..-.-|.. .--|.+|..=++.. =.+...-.+|+-|.+.|...
T Consensus 85 ktyh~~cf~cs~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~-----p~~~~~ps~cagc~~~lk~g 146 (670)
T KOG1044|consen 85 KTYHPKCFSCSTCKSPFKSGDKVTFSGKECLCQTCSQPMPVS-----PAESYGPSTCAGCGEELKNG 146 (670)
T ss_pred ceeccccceecccCCCCCCCCeeeecchhhhhhhhcCcccCC-----cccccCCccccchhhhhhcc
Confidence 6777 7777777765333321 11223332222221 12224567899999986543
No 202
>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=27.71 E-value=37 Score=38.78 Aligned_cols=44 Identities=25% Similarity=0.468 Sum_probs=26.1
Q ss_pred CccCcccccccccccCCCceEecC-CC-CCCChhhHHHH-hhcCCCCC
Q 001028 1114 GLETNCPICCDFLFTSSATVRALP-CG-HFMHSDCFQAY-TCSHYICP 1158 (1184)
Q Consensus 1114 ~~~~~CpICle~lf~s~~~v~~Lp-CG-H~fH~~Ci~~w-l~~~~tCP 1158 (1184)
.+-.-|+||.|- ...+.+-..|. =. =-=|++||.+| +-.+..||
T Consensus 28 ~tLsfChiCfEl-~iegvpks~llHtkSlRGHrdCFEK~HlIanQ~~p 74 (285)
T PF06937_consen 28 ETLSFCHICFEL-SIEGVPKSNLLHTKSLRGHRDCFEKYHLIANQDCP 74 (285)
T ss_pred cceeecceeecc-ccccCccccccccccccchHHHHHHHHHHHcCCCC
Confidence 345679999874 33332222121 00 02389999999 56688898
No 203
>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 KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=26.92 E-value=42 Score=38.00 Aligned_cols=143 Identities=22% Similarity=0.522 Sum_probs=81.0
Q ss_pred ccccccccccccCC--------cccCcccccccCCCCCC----ccccceeeccccCccccCCCCCCCCCCCCcccceEec
Q 001028 993 YKRNCKLRAACCGK--------LFTCRFCHDKVSDHSMD----RKATTEMMCMRCLKVQPVGPVCTTLSCSGLSMAKYYC 1060 (1184)
Q Consensus 993 Y~r~c~l~~~cC~~--------~y~Cr~CHde~~~H~~~----r~~~~~~~C~~C~~~q~~~~~C~~~~C~~~~~a~Y~C 1060 (1184)
|+..=...|.-|+. .|.|..||.-..+.++. .+-.-...|..|+++...... ..-+.-||
T Consensus 115 ~rnqgr~LC~~Cn~k~Ka~~~g~YvC~KCh~~iD~~~l~fr~d~yH~yHFkCt~C~keL~sdaR--------evk~eLyC 186 (332)
T KOG2272|consen 115 YRNQGRALCRECNQKEKAKGRGRYVCQKCHAHIDEQPLTFRGDPYHPYHFKCTTCGKELTSDAR--------EVKGELYC 186 (332)
T ss_pred HhhcchHHhhhhhhhhcccccceeehhhhhhhcccccccccCCCCCccceecccccccccchhh--------hhccceec
Confidence 33333455555643 69999999887664443 233347889999988765332 23456788
Q ss_pred ccccCccCCCCcccCCCCCccccC----------CCCCccccccCCCccccccccccccccccC------------ccCc
Q 001028 1061 GICKFFDDERVVYHCPFCNLCRVG----------RGLGVDFFHCMTCNCCLAKKLVDHKCREKG------------LETN 1118 (1184)
Q Consensus 1061 ~iC~l~dd~k~~yHC~~CgiCRvG----------~gl~~~~fHC~~C~~C~s~~l~~H~C~e~~------------~~~~ 1118 (1184)
.-|. +.+-||-||-||.. +.-..+.|-|.+|-- - +-.|.--|+. ...-
T Consensus 187 lrCh------D~mgipiCgaC~rpIeervi~amgKhWHveHFvCa~Cek---P-FlGHrHYEkkGlaYCe~h~~qLfG~~ 256 (332)
T KOG2272|consen 187 LRCH------DKMGIPICGACRRPIEERVIFAMGKHWHVEHFVCAKCEK---P-FLGHRHYEKKGLAYCETHYHQLFGNL 256 (332)
T ss_pred cccc------cccCCcccccccCchHHHHHHHhccccchhheeehhcCC---c-ccchhhhhhcCchhHHHHHHHHhhhh
Confidence 8874 23568899999853 332335666666532 1 1122222221 2345
Q ss_pred ccccccccccCCCceEecCCCCCCChhhHHHHhhcCCCCCCCCcccc
Q 001028 1119 CPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1165 (1184)
Q Consensus 1119 CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~tCPiCrk~v~ 1165 (1184)
|-||-..+ +|-++|.- -+.|--..+.|..|.+.+.
T Consensus 257 CF~C~~~i-----------~G~vv~al-~KawCv~cf~Cs~Cdkkl~ 291 (332)
T KOG2272|consen 257 CFICNRVI-----------GGDVVSAL-NKAWCVECFSCSTCDKKLT 291 (332)
T ss_pred heecCCcc-----------CccHHHHh-hhhhccccccccccccccc
Confidence 66775542 12222210 2346666788888888764
No 205
>KOG4654 consensus Uncharacterized conserved protein [Function unknown]
Probab=26.72 E-value=9.1e+02 Score=26.77 Aligned_cols=150 Identities=20% Similarity=0.184 Sum_probs=71.5
Q ss_pred ChHHHH----HHHHHHHHHHHHHHHHHHHhccCCCCcchHHHHHHHHHHHHHHHHHhhccccccchhhHHHhh-------
Q 001028 43 PILIFL----FFHKAIKSELDVLHRAAMAFATNLGGGGDINKLLERYHFFRAIYKHHCNAEDEVIFPALDIRV------- 111 (1184)
Q Consensus 43 Pi~~~~----~~HkAlR~el~~l~~~~~~~~~~~~d~~~~~~l~~r~~~L~~~~~~H~~aEDevI~PaL~~Rv------- 111 (1184)
|+|+|. ++|||+-..-.. --|+-- -=...|++|..-++|+.+..-.-...||.+-...|---+
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 001028 112 -------KNIA--RTYSLEHEGESVLFDQLFELLNSSMRNEESYRRELASCTGALQ--TSISQHMS-KEEEQVFPLLIEK 179 (1184)
Q Consensus 112 -------~~v~--~~~~~EH~~~~~lf~~l~~~l~~~~~~~~~~~~eLa~~l~~l~--~~l~qHm~-~EE~~v~PLl~~~ 179 (1184)
+.-. .=|+.=|. ..-|+.+..-+-++..+++...++-...++++- ..+.+|+. |-|...----.-.
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 001028 180 FSFEEQASLVWQFLCSIPVNM 200 (1184)
Q Consensus 180 fS~~E~a~L~~~~i~siP~~~ 200 (1184)
.|.+|-.+++..=..|||+..
T Consensus 193 lsadeV~eVikae~dsi~la~ 213 (252)
T KOG4654|consen 193 LSADEVEEVIKAELDSIPLAK 213 (252)
T ss_pred ccHHHHHHHHHHhccccchhh
Confidence 456777777777777777654
No 206
>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]
Probab=26.71 E-value=31 Score=38.22 Aligned_cols=42 Identities=31% Similarity=0.755 Sum_probs=29.8
Q ss_pred CcccccccccccCCCceEecCCCCCCChhhHHHHhhcCCCCCCCC
Q 001028 1117 TNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICS 1161 (1184)
Q Consensus 1117 ~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~tCPiCr 1161 (1184)
.+|-+|..=+. ..++--.||=-||..|++.|++....||-|.
T Consensus 182 k~Cn~Ch~LvI---qg~rCg~c~i~~h~~c~qty~q~~~~cphc~ 223 (235)
T KOG4718|consen 182 KNCNLCHCLVI---QGIRCGSCNIQYHRGCIQTYLQRRDICPHCG 223 (235)
T ss_pred HHHhHhHHHhh---eeeccCcccchhhhHHHHHHhcccCcCCchh
Confidence 35666654321 2234456777799999999999999999985
No 207
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=26.65 E-value=19 Score=45.85 Aligned_cols=48 Identities=21% Similarity=0.546 Sum_probs=37.2
Q ss_pred ccCcccccccccccCCCceEecCCCCCCChhhHHHHh---hcCCCCCCCCccccc
Q 001028 1115 LETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYT---CSHYICPICSKSLGD 1166 (1184)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl---~~~~tCPiCrk~v~~ 1166 (1184)
..-.||||.+.++.. ..+.|-|.|-..|+..-+ .....||+|+..+..
T Consensus 20 k~lEc~ic~~~~~~p----~~~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~eK 70 (684)
T KOG4362|consen 20 KILECPICLEHVKEP----SLLKCDHIFLKFCLNKLFESKKGPKQCALCKSDIEK 70 (684)
T ss_pred hhccCCceeEEeecc----chhhhhHHHHhhhhhceeeccCccccchhhhhhhhh
Confidence 356899999987754 568999999999987644 334679999977654
No 208
>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=26.00 E-value=38 Score=34.83 Aligned_cols=32 Identities=16% Similarity=0.104 Sum_probs=22.5
Q ss_pred ccccccccCCcccCcccccccCCCCCCccccceeeccccCccccCC
Q 001028 997 CKLRAACCGKLFTCRFCHDKVSDHSMDRKATTEMMCMRCLKVQPVG 1042 (1184)
Q Consensus 997 c~l~~~cC~~~y~Cr~CHde~~~H~~~r~~~~~~~C~~C~~~q~~~ 1042 (1184)
-|-.||.||+-|- -+.| ..++|.+|++.+++.
T Consensus 8 tKr~Cp~cg~kFY-----------DLnk---~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 8 TKRICPNTGSKFY-----------DLNR---RPAVSPYTGEQFPPE 39 (129)
T ss_pred ccccCCCcCcccc-----------ccCC---CCccCCCcCCccCcc
Confidence 3567888987331 1233 689999999999876
No 209
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=25.97 E-value=30 Score=43.34 Aligned_cols=43 Identities=26% Similarity=0.778 Sum_probs=35.8
Q ss_pred ccCcccccccccccCCCceEecCCCCCCChhhHHHHhhcCCCCCCCCcccc
Q 001028 1115 LETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1165 (1184)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~tCPiCrk~v~ 1165 (1184)
.+++|.||.+.+ ..+.-+|- |..|+.+|+.....||+|++.+.
T Consensus 478 ~~~~~~~~~~~~-----~~~~~~~~---~~~~l~~~~~~~~~~pl~~~~~~ 520 (543)
T KOG0802|consen 478 PNDVCAICYQEM-----SARITPCS---HALCLRKWLYVQEVCPLCHTYMK 520 (543)
T ss_pred ccCcchHHHHHH-----Hhcccccc---chhHHHhhhhhccccCCCchhhh
Confidence 478999999985 23445666 99999999999999999998865
No 210
>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=25.64 E-value=23 Score=42.40 Aligned_cols=35 Identities=20% Similarity=0.422 Sum_probs=0.0
Q ss_pred cCCCceEecCCCCCCChhhHHHHhhc---CCCCCCCCc
Q 001028 1128 TSSATVRALPCGHFMHSDCFQAYTCS---HYICPICSK 1162 (1184)
Q Consensus 1128 ~s~~~v~~LpCGH~fH~~Ci~~wl~~---~~tCPiCrk 1162 (1184)
....+.++|.|||++-.+=--.--.. ..+||+||.
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 211
>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=25.04 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 001028 629 NWETDLSSADI--GCASRPIDNIFKFHKAIRKDLEYLDG 665 (1184)
Q Consensus 629 ~~~~~~~~~~~--~~~~~PId~i~~fHkAIRkdL~~l~~ 665 (1184)
+|++....... +.-..|+|.+...-+.|+.|-.+|..
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 12245899999999999999988863
No 212
>KOG1312 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=25.00 E-value=23 Score=40.74 Aligned_cols=32 Identities=31% Similarity=0.812 Sum_probs=23.3
Q ss_pred CCCCccccCCCCCccccccCCCcccccccccccccc
Q 001028 1076 PFCNLCRVGRGLGVDFFHCMTCNCCLAKKLVDHKCR 1111 (1184)
Q Consensus 1076 ~~CgiCRvG~gl~~~~fHC~~C~~C~s~~l~~H~C~ 1111 (1184)
-+|..|++.|. --..||..||.|+..- +|-|+
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 57777777763 4678999999997653 66664
No 213
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=24.95 E-value=45 Score=29.63 Aligned_cols=12 Identities=33% Similarity=0.930 Sum_probs=9.0
Q ss_pred CCcccCCCCCcc
Q 001028 1070 RVVYHCPFCNLC 1081 (1184)
Q Consensus 1070 k~~yHC~~CgiC 1081 (1184)
...|-||+|||-
T Consensus 12 ~v~~~Cp~cGip 23 (55)
T PF13824_consen 12 HVNFECPDCGIP 23 (55)
T ss_pred ccCCcCCCCCCc
Confidence 567888888863
No 214
>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=24.84 E-value=36 Score=26.22 Aligned_cols=11 Identities=27% Similarity=1.081 Sum_probs=8.5
Q ss_pred ceEecccccCc
Q 001028 1056 AKYYCGICKFF 1066 (1184)
Q Consensus 1056 a~Y~C~iC~l~ 1066 (1184)
+.|||++|+.+
T Consensus 2 ~~~~C~~C~~~ 12 (35)
T smart00451 2 GGFYCKLCNVT 12 (35)
T ss_pred cCeEccccCCc
Confidence 57889988764
No 215
>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=24.83 E-value=3.4e+02 Score=26.74 Aligned_cols=61 Identities=21% Similarity=0.163 Sum_probs=35.6
Q ss_pred HHHhhhhhHHHHHHHHHHHHHhhhcCchhHHHHHHHHHHHHHHHHHHhHHHHHHHh----hhHHHhhCCHHHHHHHHHHH
Q 001028 117 TYSLEHEGESVLFDQLFELLNSSMRNEESYRRELASCTGALQTSISQHMSKEEEQV----FPLLIEKFSFEEQASLVWQF 192 (1184)
Q Consensus 117 ~~~~EH~~~~~lf~~l~~~l~~~~~~~~~~~~eLa~~l~~l~~~l~qHm~~EE~~v----~PLl~~~fS~~E~a~L~~~~ 192 (1184)
.+..||+..=++++.|..++.. ...+..|..-...|...||.-. .|-+..| ...+.+|
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 3456666777889999999764 3444333 5555556
Q ss_pred hhc
Q 001028 193 LCS 195 (1184)
Q Consensus 193 i~s 195 (1184)
+..
T Consensus 76 ~~~ 78 (113)
T cd00522 76 VEK 78 (113)
T ss_pred HHH
Confidence 544
No 216
>PRK13428 F0F1 ATP synthase subunit delta; Provisional
Probab=24.73 E-value=9.6e+02 Score=29.65 Aligned_cols=30 Identities=20% Similarity=0.282 Sum_probs=25.0
Q ss_pred HHHHhhhccCCCCChHHHHHHHHHHHHHHH
Q 001028 923 EAEIRKVSRDSTLDPRRKAYLIQNLMTSRW 952 (1184)
Q Consensus 923 ~~~Ir~i~~~~~l~~~~ka~liq~Lm~~~~ 952 (1184)
+..+|+--.|++-++..|+-|+.+|+.++-
T Consensus 216 ~~~lrr~l~d~~~~~~~k~~l~~~l~~~~~ 245 (445)
T PRK13428 216 EPVLTKHLTEPAEDAAPKIRLVERLFSGKV 245 (445)
T ss_pred cHHHHHHcCCCCCChhhHHHHHHHHhCcCC
Confidence 345667778999999999999999997764
No 217
>PHA00626 hypothetical protein
Probab=24.61 E-value=42 Score=29.91 Aligned_cols=34 Identities=24% Similarity=0.334 Sum_probs=19.9
Q ss_pred eeccccCccccCCCCCCCCCCCCcccceEecccccCccC
Q 001028 1030 MMCMRCLKVQPVGPVCTTLSCSGLSMAKYYCGICKFFDD 1068 (1184)
Q Consensus 1030 ~~C~~C~~~q~~~~~C~~~~C~~~~~a~Y~C~iC~l~dd 1068 (1184)
|.|..|+..+-+ .|.. | ...-.+|-|..|.+++.
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 3332 2 23456788888887643
No 218
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=24.34 E-value=42 Score=29.11 Aligned_cols=24 Identities=29% Similarity=0.664 Sum_probs=12.3
Q ss_pred cCCCCCccccCCCCCccccccCCCcc
Q 001028 1074 HCPFCNLCRVGRGLGVDFFHCMTCNC 1099 (1184)
Q Consensus 1074 HC~~CgiCRvG~gl~~~~fHC~~C~~ 1099 (1184)
.||.||-. .-. ...+.++|.+||.
T Consensus 22 fCP~Cg~~-~m~-~~~~r~~C~~Cgy 45 (50)
T PRK00432 22 FCPRCGSG-FMA-EHLDRWHCGKCGY 45 (50)
T ss_pred cCcCCCcc-hhe-ccCCcEECCCcCC
Confidence 56666643 111 1235666666663
No 219
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=23.90 E-value=7.6 Score=33.66 Aligned_cols=45 Identities=22% Similarity=0.700 Sum_probs=28.4
Q ss_pred ccceEecccccCccCCCCcccCCCCC-----ccccCCCCCccccccCCCcccccc
Q 001028 1054 SMAKYYCGICKFFDDERVVYHCPFCN-----LCRVGRGLGVDFFHCMTCNCCLAK 1103 (1184)
Q Consensus 1054 ~~a~Y~C~iC~l~dd~k~~yHC~~Cg-----iCRvG~gl~~~~fHC~~C~~C~s~ 1103 (1184)
.|++|.|+.||---.-++.-.|--|| -|-. +.||.|..|+.-+.+
T Consensus 4 SFsry~CDLCn~~~p~~~LRQCvlCGRWaC~sCW~-----deYY~CksC~Gii~l 53 (57)
T PF14445_consen 4 SFSRYSCDLCNSSHPISELRQCVLCGRWACNSCWQ-----DEYYTCKSCNGIINL 53 (57)
T ss_pred HHhhHhHHhhcccCcHHHHHHHhhhchhhhhhhhh-----hhHhHHHhhhchhhh
Confidence 68888888887543334444454444 3433 468899888876654
No 220
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=23.69 E-value=27 Score=39.59 Aligned_cols=54 Identities=22% Similarity=0.524 Sum_probs=34.9
Q ss_pred cccCccCcccccccccccCCCceEecCCC-----CCCChhhHHHHhhc--------CCCCCCCCccc
Q 001028 1111 REKGLETNCPICCDFLFTSSATVRALPCG-----HFMHSDCFQAYTCS--------HYICPICSKSL 1164 (1184)
Q Consensus 1111 ~e~~~~~~CpICle~lf~s~~~v~~LpCG-----H~fH~~Ci~~wl~~--------~~tCPiCrk~v 1164 (1184)
.+...+..|=||...=.+.....=+=||- |--|..|+..|+.. .-+||-|+...
T Consensus 15 ~~~e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEY 81 (293)
T KOG3053|consen 15 DNQELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEY 81 (293)
T ss_pred CccccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchh
Confidence 34456778999986511111111234772 99999999999842 23599999864
No 221
>PF15353 HECA: Headcase protein family homologue
Probab=23.67 E-value=36 Score=33.92 Aligned_cols=16 Identities=38% Similarity=1.105 Sum_probs=13.8
Q ss_pred CCCCCCChhhHHHHhh
Q 001028 1137 PCGHFMHSDCFQAYTC 1152 (1184)
Q Consensus 1137 pCGH~fH~~Ci~~wl~ 1152 (1184)
|.|++||.+||++|-.
T Consensus 39 p~~~~MH~~CF~~wE~ 54 (107)
T PF15353_consen 39 PFGQYMHRECFEKWED 54 (107)
T ss_pred CCCCchHHHHHHHHHH
Confidence 5689999999999953
No 222
>PRK00420 hypothetical protein; Validated
Probab=23.67 E-value=45 Score=33.66 Aligned_cols=30 Identities=30% Similarity=0.665 Sum_probs=20.4
Q ss_pred ccCcccccccccccCCCceEecCCCCCCChhhHHHHhhcCCCCCCCCcccc
Q 001028 1115 LETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLG 1165 (1184)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~tCPiCrk~v~ 1165 (1184)
....||+|.-+||.... ....||.|...+.
T Consensus 22 l~~~CP~Cg~pLf~lk~---------------------g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 22 LSKHCPVCGLPLFELKD---------------------GEVVCPVHGKVYI 51 (112)
T ss_pred ccCCCCCCCCcceecCC---------------------CceECCCCCCeee
Confidence 34679999888775222 3567888888654
No 223
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=23.52 E-value=29 Score=33.69 Aligned_cols=28 Identities=32% Similarity=0.892 Sum_probs=12.4
Q ss_pred CcccCCCCCccccCCCCCccccccCCCcc
Q 001028 1071 VVYHCPFCNLCRVGRGLGVDFFHCMTCNC 1099 (1184)
Q Consensus 1071 ~~yHC~~CgiCRvG~gl~~~~fHC~~C~~ 1099 (1184)
.-|.||+||--.|.. .+.-..+|.+|+.
T Consensus 34 ~ky~Cp~Cgk~~vkR-~a~GIW~C~~C~~ 61 (90)
T PF01780_consen 34 AKYTCPFCGKTSVKR-VATGIWKCKKCGK 61 (90)
T ss_dssp S-BEESSSSSSEEEE-EETTEEEETTTTE
T ss_pred CCCcCCCCCCceeEE-eeeEEeecCCCCC
Confidence 445566666333321 1122466666653
No 224
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=23.51 E-value=47 Score=34.29 Aligned_cols=10 Identities=30% Similarity=0.879 Sum_probs=6.1
Q ss_pred CcccCCCCCc
Q 001028 1071 VVYHCPFCNL 1080 (1184)
Q Consensus 1071 ~~yHC~~Cgi 1080 (1184)
..|.||.||-
T Consensus 106 ~~~~CP~Cgs 115 (135)
T PRK03824 106 AFLKCPKCGS 115 (135)
T ss_pred cCcCCcCCCC
Confidence 3456777773
No 225
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=22.86 E-value=30 Score=36.01 Aligned_cols=7 Identities=43% Similarity=1.549 Sum_probs=4.7
Q ss_pred ccCCCCC
Q 001028 1073 YHCPFCN 1079 (1184)
Q Consensus 1073 yHC~~Cg 1079 (1184)
|.||.||
T Consensus 124 f~Cp~Cg 130 (147)
T smart00531 124 FTCPRCG 130 (147)
T ss_pred EECCCCC
Confidence 6666666
No 226
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=22.75 E-value=61 Score=43.56 Aligned_cols=51 Identities=22% Similarity=0.496 Sum_probs=34.9
Q ss_pred cCccCcccccccccccCCCceEecC---CCCCCChhhHHHHhh--cCCCCCCCCccc
Q 001028 1113 KGLETNCPICCDFLFTSSATVRALP---CGHFMHSDCFQAYTC--SHYICPICSKSL 1164 (1184)
Q Consensus 1113 ~~~~~~CpICle~lf~s~~~v~~Lp---CGH~fH~~Ci~~wl~--~~~tCPiCrk~v 1164 (1184)
+.....|-||.|++-...+.-.... ||=-.++.|+ +|-+ .+..||-|+...
T Consensus 14 ~~~~qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCY-EYEr~eG~q~CPqCktrY 69 (1079)
T PLN02638 14 HGGGQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCY-EYERKDGNQSCPQCKTKY 69 (1079)
T ss_pred ccCCceeeecccccCcCCCCCEEEEeccCCCccccchh-hhhhhcCCccCCccCCch
Confidence 3445689999999654444334444 4555999999 5643 467899998754
No 227
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=22.27 E-value=93 Score=36.58 Aligned_cols=62 Identities=19% Similarity=0.405 Sum_probs=0.0
Q ss_pred cccccccCCcccCcccccccCCCCCCc-------cccceeeccccCccccCC-CCCCCCCCCCcccceEecccccCccCC
Q 001028 998 KLRAACCGKLFTCRFCHDKVSDHSMDR-------KATTEMMCMRCLKVQPVG-PVCTTLSCSGLSMAKYYCGICKFFDDE 1069 (1184)
Q Consensus 998 ~l~~~cC~~~y~Cr~CHde~~~H~~~r-------~~~~~~~C~~C~~~q~~~-~~C~~~~C~~~~~a~Y~C~iC~l~dd~ 1069 (1184)
+-.||+||. +|.-- ....-..|+.|+++=... -.|.+ |+...-=.|+ -++++
T Consensus 187 ~~~CPvCGs-------------~P~~s~v~~~~~~G~RyL~CslC~teW~~~R~~C~~--Cg~~~~l~y~-----~~~~~ 246 (309)
T PRK03564 187 RQFCPVCGS-------------MPVSSVVQIGTTQGLRYLHCNLCESEWHVVRVKCSN--CEQSGKLHYW-----SLDSE 246 (309)
T ss_pred CCCCCCCCC-------------cchhheeeccCCCCceEEEcCCCCCcccccCccCCC--CCCCCceeee-----eecCC
Q ss_pred ---CCcccCCCCC
Q 001028 1070 ---RVVYHCPFCN 1079 (1184)
Q Consensus 1070 ---k~~yHC~~Cg 1079 (1184)
-.++.|+.||
T Consensus 247 ~~~~r~e~C~~C~ 259 (309)
T PRK03564 247 QAAVKAESCGDCG 259 (309)
T ss_pred CcceEeeeccccc
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=21.95 E-value=74 Score=38.09 Aligned_cols=18 Identities=17% Similarity=0.604 Sum_probs=14.4
Q ss_pred HHHhhcCCCCCCCCcccc
Q 001028 1148 QAYTCSHYICPICSKSLG 1165 (1184)
Q Consensus 1148 ~~wl~~~~tCPiCrk~v~ 1165 (1184)
+.|+.++-+||.||+..-
T Consensus 334 ~~Wl~~~~~CPtCRa~FC 351 (358)
T PF10272_consen 334 ETWLSGKCPCPTCRAKFC 351 (358)
T ss_pred hhhhcCCCCCCCCcccce
Confidence 457777889999999854
No 229
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=21.74 E-value=29 Score=47.05 Aligned_cols=75 Identities=20% Similarity=0.442 Sum_probs=47.8
Q ss_pred CCccccccccCCCccccccccccccccCCcccCc--ccccccCCCCCCccccceeeccccCccccCCCCCCCCCCCCccc
Q 001028 978 PSFRDAEKQVFGCEHYKRNCKLRAACCGKLFTCR--FCHDKVSDHSMDRKATTEMMCMRCLKVQPVGPVCTTLSCSGLSM 1055 (1184)
Q Consensus 978 ~~~~~~~~~~~gC~HY~r~c~l~~~cC~~~y~Cr--~CHde~~~H~~~r~~~~~~~C~~C~~~q~~~~~C~~~~C~~~~~ 1055 (1184)
.-|.||+...+. |---..|..|+|.|-=- .|-.+... +-+...+.+||.|..+..+ +.|.. -|..|
T Consensus 3587 ~FYNdPa~YAmn-----RY~Y~vC~KCrKAYFGGEaRCdAe~~~---ddydP~ELiCG~CSDvS~a-QmCPk---HGtdf 3654 (3738)
T KOG1428|consen 3587 RFYNDPAGYAMN-----RYAYYVCYKCRKAYFGGEARCDAEAGG---DDYDPRELICGACSDVSRA-QMCPK---HGTDF 3654 (3738)
T ss_pred eeccChhhhhhh-----hhhhhhhhhhhhhhcCchhhcchhcCC---CCCCHHHhhhccccccccc-eeccc---ccchh
Confidence 457777664421 11226788888866432 45555443 3345679999999987654 67876 47788
Q ss_pred ceEeccccc
Q 001028 1056 AKYYCGICK 1064 (1184)
Q Consensus 1056 a~Y~C~iC~ 1064 (1184)
-.|.|..|-
T Consensus 3655 LEYKCRyCC 3663 (3738)
T KOG1428|consen 3655 LEYKCRYCC 3663 (3738)
T ss_pred hhhhhheee
Confidence 888776663
No 230
>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=21.39 E-value=38 Score=32.91 Aligned_cols=30 Identities=27% Similarity=0.525 Sum_probs=20.5
Q ss_pred cceEecccccCccCC---CCcccCCCCCccccC
Q 001028 1055 MAKYYCGICKFFDDE---RVVYHCPFCNLCRVG 1084 (1184)
Q Consensus 1055 ~a~Y~C~iC~l~dd~---k~~yHC~~CgiCRvG 1084 (1184)
-++|.|+.|.--.-. -+|++|..||.=--|
T Consensus 33 ~~ky~Cp~Cgk~~vkR~a~GIW~C~~C~~~~AG 65 (90)
T PF01780_consen 33 HAKYTCPFCGKTSVKRVATGIWKCKKCGKKFAG 65 (90)
T ss_dssp HS-BEESSSSSSEEEEEETTEEEETTTTEEEE-
T ss_pred hCCCcCCCCCCceeEEeeeEEeecCCCCCEEeC
Confidence 468899888654322 789999999965555
No 231
>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=21.08 E-value=37 Score=32.23 Aligned_cols=9 Identities=67% Similarity=1.796 Sum_probs=2.3
Q ss_pred CcccCCCCC
Q 001028 1071 VVYHCPFCN 1079 (1184)
Q Consensus 1071 ~~yHC~~Cg 1079 (1184)
..|.||+||
T Consensus 21 ~~F~CPfC~ 29 (81)
T PF05129_consen 21 KVFDCPFCN 29 (81)
T ss_dssp S----TTT-
T ss_pred ceEcCCcCC
Confidence 455666666
No 232
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=20.83 E-value=49 Score=34.31 Aligned_cols=48 Identities=29% Similarity=0.694 Sum_probs=33.2
Q ss_pred ccCcccccccccccCCCceEec-C---CCCCCChhhHHH-Hh--hcCCCCCCCCccccc
Q 001028 1115 LETNCPICCDFLFTSSATVRAL-P---CGHFMHSDCFQA-YT--CSHYICPICSKSLGD 1166 (1184)
Q Consensus 1115 ~~~~CpICle~lf~s~~~v~~L-p---CGH~fH~~Ci~~-wl--~~~~tCPiCrk~v~~ 1166 (1184)
.--.|-||.|- |.+ -+.| | ||=.+..-|... |- ..+..||+|+.+.-.
T Consensus 79 ~lYeCnIC~et---S~e-e~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKs 133 (140)
T PF05290_consen 79 KLYECNICKET---SAE-ERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKS 133 (140)
T ss_pred CceeccCcccc---cch-hhcCCcccccchHHHHHHHHHHHHHcccCCCCCcccccccc
Confidence 34679999875 322 3344 2 898889888876 53 235789999998653
No 233
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=20.32 E-value=21 Score=40.82 Aligned_cols=59 Identities=24% Similarity=0.450 Sum_probs=39.6
Q ss_pred ccccccc---CccCcccccccccccCCCceEecCCCCCCChhhHHHHhhcCCCCCCCCccccccCccccccc
Q 001028 1107 DHKCREK---GLETNCPICCDFLFTSSATVRALPCGHFMHSDCFQAYTCSHYICPICSKSLGDMAVSPLFRT 1175 (1184)
Q Consensus 1107 ~H~C~e~---~~~~~CpICle~lf~s~~~v~~LpCGH~fH~~Ci~~wl~~~~tCPiCrk~v~~m~~y~~~~~ 1175 (1184)
.--|.|. .....|.-|.+.|- . +.|+.-.=.|+||.+|| .|-||++.+..=+.++.|-+
T Consensus 80 s~yCkedFfKrfGTKCsaC~~GIp-P-tqVVRkAqd~VYHl~CF--------~C~iC~R~L~TGdEFYLmeD 141 (383)
T KOG4577|consen 80 SVYCKEDFFKRFGTKCSACQEGIP-P-TQVVRKAQDFVYHLHCF--------ACFICKRQLATGDEFYLMED 141 (383)
T ss_pred ceeehHHHHHHhCCcchhhcCCCC-h-HHHHHHhhcceeehhhh--------hhHhhhcccccCCeeEEecc
Confidence 3445553 35678999998743 2 22333334799999998 68899999876666665554
No 234
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=20.30 E-value=53 Score=37.75 Aligned_cols=33 Identities=39% Similarity=0.806 Sum_probs=25.6
Q ss_pred CcccCCCCCccccCCCCCccccccCCCccccccccccccc
Q 001028 1071 VVYHCPFCNLCRVGRGLGVDFFHCMTCNCCLAKKLVDHKC 1110 (1184)
Q Consensus 1071 ~~yHC~~CgiCRvG~gl~~~~fHC~~C~~C~s~~l~~H~C 1110 (1184)
....|+.|.+-|-.. -.||..||.|+..- +|-|
T Consensus 112 ~~~~C~~C~~~rPpR-----s~HCsvC~~CV~rf--DHHC 144 (299)
T KOG1311|consen 112 EWKYCDTCQLYRPPR-----SSHCSVCNNCVLRF--DHHC 144 (299)
T ss_pred ceEEcCcCcccCCCC-----cccchhhccccccc--CCCC
Confidence 467888888886653 78999999998763 5655
No 235
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=20.13 E-value=48 Score=32.22 Aligned_cols=29 Identities=34% Similarity=0.848 Sum_probs=12.6
Q ss_pred CCcccCCCCCccccCCCCCccccccCCCcc
Q 001028 1070 RVVYHCPFCNLCRVGRGLGVDFFHCMTCNC 1099 (1184)
Q Consensus 1070 k~~yHC~~CgiCRvG~gl~~~~fHC~~C~~ 1099 (1184)
+..|.||+||--.|.. .+.-.-+|..|+.
T Consensus 34 ~a~y~CpfCgk~~vkR-~a~GIW~C~~C~~ 62 (90)
T PTZ00255 34 HAKYFCPFCGKHAVKR-QAVGIWRCKGCKK 62 (90)
T ss_pred hCCccCCCCCCCceee-eeeEEEEcCCCCC
Confidence 4445555555333321 1223455555543
Done!