Query 028139
Match_columns 213
No_of_seqs 220 out of 1961
Neff 7.6
Searched_HMMs 46136
Date Fri Mar 29 06:50:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028139.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028139hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF13639 zf-RING_2: Ring finge 99.7 2E-17 4.3E-22 103.8 2.7 44 159-202 1-44 (44)
2 KOG4628 Predicted E3 ubiquitin 99.5 6.9E-15 1.5E-19 128.5 4.9 52 159-210 230-282 (348)
3 PF12678 zf-rbx1: RING-H2 zinc 99.5 2E-14 4.4E-19 99.8 4.5 47 156-202 17-73 (73)
4 COG5243 HRD1 HRD ubiquitin lig 99.4 2E-13 4.4E-18 118.7 3.7 54 156-209 285-348 (491)
5 PHA02929 N1R/p28-like protein; 99.3 7.4E-13 1.6E-17 111.0 4.2 50 157-206 173-227 (238)
6 PF12861 zf-Apc11: Anaphase-pr 99.3 8.3E-13 1.8E-17 93.2 3.4 53 157-209 20-85 (85)
7 PF13920 zf-C3HC4_3: Zinc fing 99.3 3.2E-12 6.9E-17 82.2 4.0 46 158-206 2-48 (50)
8 PF13923 zf-C3HC4_2: Zinc fing 99.3 3.4E-12 7.3E-17 77.9 3.4 39 161-201 1-39 (39)
9 cd00162 RING RING-finger (Real 99.2 1.1E-11 2.3E-16 76.6 3.6 44 160-205 1-45 (45)
10 COG5540 RING-finger-containing 99.2 6.3E-12 1.4E-16 106.9 2.9 49 158-206 323-372 (374)
11 KOG0320 Predicted E3 ubiquitin 99.2 2.6E-11 5.6E-16 96.1 5.9 54 156-210 129-182 (187)
12 PLN03208 E3 ubiquitin-protein 99.2 1.3E-11 2.9E-16 99.8 3.8 50 157-209 17-82 (193)
13 KOG0317 Predicted E3 ubiquitin 99.2 1.6E-11 3.4E-16 104.0 2.8 54 155-211 236-289 (293)
14 KOG0823 Predicted E3 ubiquitin 99.1 2.1E-11 4.5E-16 100.5 2.9 52 156-210 45-99 (230)
15 PF14634 zf-RING_5: zinc-RING 99.1 3.5E-11 7.7E-16 75.3 3.1 44 160-203 1-44 (44)
16 PF15227 zf-C3HC4_4: zinc fing 99.1 1.1E-10 2.3E-15 72.4 3.5 38 161-201 1-42 (42)
17 PHA02926 zinc finger-like prot 99.1 8.2E-11 1.8E-15 96.5 3.5 53 157-209 169-233 (242)
18 smart00504 Ubox Modified RING 99.0 2.3E-10 5E-15 76.5 4.4 48 159-209 2-49 (63)
19 PF00097 zf-C3HC4: Zinc finger 99.0 2.3E-10 5.1E-15 70.2 3.8 39 161-201 1-41 (41)
20 COG5194 APC11 Component of SCF 99.0 1.2E-10 2.6E-15 80.4 2.5 54 158-211 20-86 (88)
21 KOG0802 E3 ubiquitin ligase [P 99.0 1.8E-10 3.9E-15 107.8 2.1 49 157-205 290-340 (543)
22 smart00184 RING Ring finger. E 99.0 5.1E-10 1.1E-14 66.6 3.1 38 161-201 1-39 (39)
23 TIGR00599 rad18 DNA repair pro 98.9 1.2E-09 2.7E-14 97.7 3.9 51 155-208 23-73 (397)
24 PF13445 zf-RING_UBOX: RING-ty 98.9 2.1E-09 4.7E-14 66.8 3.2 34 161-195 1-35 (43)
25 KOG1493 Anaphase-promoting com 98.8 7.3E-10 1.6E-14 75.9 -0.3 52 158-209 20-84 (84)
26 smart00744 RINGv The RING-vari 98.6 3.5E-08 7.5E-13 63.1 3.1 42 160-202 1-49 (49)
27 COG5574 PEX10 RING-finger-cont 98.6 2.2E-08 4.8E-13 84.1 2.2 51 156-209 213-265 (271)
28 KOG2164 Predicted E3 ubiquitin 98.5 3.7E-08 7.9E-13 89.5 2.9 49 158-209 186-239 (513)
29 PF11793 FANCL_C: FANCL C-term 98.5 1.6E-08 3.4E-13 69.6 -0.1 51 158-208 2-68 (70)
30 PF04564 U-box: U-box domain; 98.5 8.7E-08 1.9E-12 66.3 3.0 51 157-210 3-54 (73)
31 KOG2930 SCF ubiquitin ligase, 98.5 6.5E-08 1.4E-12 70.2 1.5 67 143-209 30-111 (114)
32 KOG0828 Predicted E3 ubiquitin 98.4 7.1E-08 1.5E-12 87.1 1.7 50 157-206 570-634 (636)
33 KOG1734 Predicted RING-contain 98.3 9E-08 2E-12 80.6 0.0 53 156-208 222-283 (328)
34 KOG0287 Postreplication repair 98.3 1.6E-07 3.5E-12 81.4 0.6 48 156-206 21-68 (442)
35 KOG1039 Predicted E3 ubiquitin 98.3 4.6E-07 1E-11 79.9 2.4 55 156-210 159-225 (344)
36 KOG2177 Predicted E3 ubiquitin 98.2 4E-07 8.6E-12 76.8 1.4 45 156-203 11-55 (386)
37 COG5432 RAD18 RING-finger-cont 98.2 6.2E-07 1.3E-11 76.4 1.9 48 156-206 23-70 (391)
38 COG5219 Uncharacterized conser 98.1 7.4E-07 1.6E-11 85.9 1.4 56 152-207 1463-1524(1525)
39 KOG0804 Cytoplasmic Zn-finger 98.1 7.7E-07 1.7E-11 79.7 1.3 49 156-206 173-222 (493)
40 PF14835 zf-RING_6: zf-RING of 98.1 4.8E-07 1E-11 60.4 -0.1 50 156-209 5-54 (65)
41 KOG0311 Predicted E3 ubiquitin 98.0 7.8E-07 1.7E-11 77.6 -1.4 54 156-211 41-95 (381)
42 KOG4265 Predicted E3 ubiquitin 97.9 8.9E-06 1.9E-10 71.3 3.2 47 156-205 288-335 (349)
43 KOG0825 PHD Zn-finger protein 97.8 2.9E-06 6.3E-11 80.5 -0.6 51 157-207 122-172 (1134)
44 KOG0978 E3 ubiquitin ligase in 97.8 4.7E-06 1E-10 79.1 0.8 49 159-210 644-693 (698)
45 KOG1428 Inhibitor of type V ad 97.7 2.2E-05 4.8E-10 78.6 2.8 51 155-205 3483-3543(3738)
46 PF11789 zf-Nse: Zinc-finger o 97.6 3.8E-05 8.3E-10 50.6 2.5 43 156-200 9-53 (57)
47 KOG0297 TNF receptor-associate 97.5 3.7E-05 8.1E-10 69.4 2.0 53 156-210 19-71 (391)
48 KOG4172 Predicted E3 ubiquitin 97.5 1.9E-05 4.1E-10 50.9 -0.3 44 159-205 8-53 (62)
49 KOG4445 Uncharacterized conser 97.5 3.2E-05 6.9E-10 66.4 0.4 51 159-209 116-189 (368)
50 COG5152 Uncharacterized conser 97.4 5.1E-05 1.1E-09 61.6 1.4 45 158-205 196-240 (259)
51 KOG1785 Tyrosine kinase negati 97.4 5.7E-05 1.2E-09 67.1 1.2 49 159-210 370-420 (563)
52 PF12906 RINGv: RING-variant d 97.3 0.00021 4.5E-09 45.2 2.4 40 161-201 1-47 (47)
53 KOG1952 Transcription factor N 97.2 0.0013 2.7E-08 63.6 8.3 49 155-203 188-244 (950)
54 KOG4159 Predicted E3 ubiquitin 97.2 0.0002 4.3E-09 64.6 2.9 48 156-206 82-129 (398)
55 TIGR00570 cdk7 CDK-activating 97.2 0.00023 5E-09 61.9 2.3 36 174-209 21-57 (309)
56 KOG1813 Predicted E3 ubiquitin 97.1 0.00017 3.6E-09 61.9 1.0 44 159-205 242-285 (313)
57 KOG1941 Acetylcholine receptor 97.1 0.00015 3.2E-09 64.4 0.2 48 156-203 363-413 (518)
58 KOG0827 Predicted E3 ubiquitin 97.0 0.00028 6.1E-09 62.6 1.2 27 176-202 23-52 (465)
59 PF05883 Baculo_RING: Baculovi 97.0 0.00028 6E-09 54.1 1.0 35 158-192 26-66 (134)
60 KOG3039 Uncharacterized conser 96.8 0.0011 2.4E-08 55.6 3.4 55 157-211 220-275 (303)
61 KOG2660 Locus-specific chromos 96.8 0.00033 7E-09 61.0 0.2 51 157-209 14-64 (331)
62 KOG2879 Predicted E3 ubiquitin 96.8 0.0014 3.1E-08 55.7 3.8 49 156-206 237-287 (298)
63 PF14447 Prok-RING_4: Prokaryo 96.7 0.00091 2E-08 43.4 1.9 47 159-210 8-54 (55)
64 PHA02825 LAP/PHD finger-like p 96.7 0.0013 2.7E-08 51.9 2.8 51 154-208 4-61 (162)
65 PF10367 Vps39_2: Vacuolar sor 96.7 0.0015 3.3E-08 47.6 3.2 33 156-189 76-108 (109)
66 KOG4692 Predicted E3 ubiquitin 96.7 0.0013 2.7E-08 58.0 2.8 49 155-206 419-467 (489)
67 PHA02862 5L protein; Provision 96.7 0.001 2.2E-08 51.5 2.0 48 158-209 2-56 (156)
68 PF14570 zf-RING_4: RING/Ubox 96.6 0.0017 3.8E-08 41.1 2.6 45 161-205 1-47 (48)
69 PF03854 zf-P11: P-11 zinc fin 96.6 0.0011 2.4E-08 41.5 1.3 43 161-208 5-48 (50)
70 PF04641 Rtf2: Rtf2 RING-finge 96.3 0.0038 8.1E-08 53.4 3.7 53 156-209 111-164 (260)
71 KOG4275 Predicted E3 ubiquitin 96.3 0.00085 1.8E-08 57.6 -0.5 42 157-205 299-341 (350)
72 KOG1645 RING-finger-containing 96.2 0.0027 5.8E-08 56.8 2.4 37 169-205 17-55 (463)
73 PHA03096 p28-like protein; Pro 96.2 0.0023 5.1E-08 55.3 1.8 45 159-203 179-231 (284)
74 KOG1814 Predicted E3 ubiquitin 96.0 0.0033 7.1E-08 56.4 1.8 46 158-203 184-237 (445)
75 KOG1571 Predicted E3 ubiquitin 96.0 0.0048 1E-07 54.4 2.7 45 156-206 303-347 (355)
76 KOG3268 Predicted E3 ubiquitin 96.0 0.0045 9.9E-08 49.6 2.3 54 155-208 162-230 (234)
77 COG5175 MOT2 Transcriptional r 96.0 0.0042 9.1E-08 54.5 2.2 54 152-205 8-63 (480)
78 KOG1002 Nucleotide excision re 95.8 0.0035 7.7E-08 57.9 1.3 51 156-209 534-589 (791)
79 COG5236 Uncharacterized conser 95.6 0.01 2.3E-07 52.2 3.0 50 153-205 56-107 (493)
80 KOG2114 Vacuolar assembly/sort 94.8 0.02 4.2E-07 55.7 2.7 42 158-204 840-881 (933)
81 PF08746 zf-RING-like: RING-li 94.8 0.015 3.3E-07 35.9 1.3 41 161-201 1-43 (43)
82 KOG2817 Predicted E3 ubiquitin 94.8 0.026 5.6E-07 50.5 3.1 47 158-204 334-383 (394)
83 KOG0801 Predicted E3 ubiquitin 94.7 0.012 2.6E-07 46.5 0.9 30 156-185 175-204 (205)
84 KOG1940 Zn-finger protein [Gen 94.7 0.017 3.7E-07 49.7 1.7 45 159-203 159-204 (276)
85 KOG0827 Predicted E3 ubiquitin 94.4 0.0023 4.9E-08 57.0 -4.3 49 159-207 197-246 (465)
86 KOG1001 Helicase-like transcri 94.3 0.01 2.2E-07 57.1 -0.5 47 159-209 455-503 (674)
87 KOG3970 Predicted E3 ubiquitin 94.1 0.045 9.8E-07 45.6 2.9 51 156-207 48-106 (299)
88 KOG0826 Predicted E3 ubiquitin 94.1 0.037 7.9E-07 48.4 2.5 51 157-209 299-349 (357)
89 KOG3002 Zn finger protein [Gen 93.8 0.037 7.9E-07 48.3 2.0 43 157-206 47-91 (299)
90 COG5222 Uncharacterized conser 93.1 0.056 1.2E-06 46.8 1.9 49 159-209 275-325 (427)
91 KOG0298 DEAD box-containing he 92.6 0.028 6E-07 56.9 -0.7 44 158-203 1153-1196(1394)
92 PF07800 DUF1644: Protein of u 92.6 0.13 2.8E-06 40.6 3.2 33 158-193 2-47 (162)
93 KOG0309 Conserved WD40 repeat- 91.9 0.087 1.9E-06 50.8 1.8 29 172-200 1041-1069(1081)
94 KOG3053 Uncharacterized conser 91.7 0.074 1.6E-06 45.1 1.0 51 155-205 17-81 (293)
95 KOG2034 Vacuolar sorting prote 91.2 0.096 2.1E-06 51.3 1.3 40 153-193 812-851 (911)
96 COG5183 SSM4 Protein involved 91.2 0.12 2.7E-06 50.2 2.0 53 156-209 10-69 (1175)
97 KOG1609 Protein involved in mR 90.5 0.15 3.3E-06 44.1 1.7 49 158-206 78-134 (323)
98 KOG2932 E3 ubiquitin ligase in 89.6 0.13 2.8E-06 44.8 0.6 42 160-205 92-133 (389)
99 PF02891 zf-MIZ: MIZ/SP-RING z 88.8 0.55 1.2E-05 29.8 3.0 42 160-204 4-50 (50)
100 KOG3161 Predicted E3 ubiquitin 88.8 0.14 3.1E-06 48.6 0.3 42 159-203 12-54 (861)
101 TIGR03602 streptolysinS bacter 88.8 0.13 2.8E-06 32.4 0.1 8 2-9 24-31 (56)
102 PF10272 Tmpp129: Putative tra 88.5 0.85 1.8E-05 40.8 5.0 52 156-209 269-354 (358)
103 KOG1812 Predicted E3 ubiquitin 88.4 0.15 3.3E-06 46.0 0.3 38 158-195 146-184 (384)
104 KOG1829 Uncharacterized conser 87.4 0.19 4.1E-06 47.5 0.3 43 157-202 510-557 (580)
105 PF14446 Prok-RING_1: Prokaryo 86.4 1 2.2E-05 29.2 3.2 47 157-207 4-53 (54)
106 KOG0802 E3 ubiquitin ligase [P 86.3 0.35 7.6E-06 45.6 1.4 49 156-211 477-525 (543)
107 COG5109 Uncharacterized conser 86.0 0.55 1.2E-05 41.1 2.3 45 159-203 337-384 (396)
108 KOG1100 Predicted E3 ubiquitin 85.6 0.47 1E-05 39.3 1.6 40 161-207 161-201 (207)
109 KOG4185 Predicted E3 ubiquitin 85.6 0.61 1.3E-05 40.3 2.4 35 171-205 19-54 (296)
110 KOG2066 Vacuolar assembly/sort 85.4 0.45 9.7E-06 46.3 1.6 44 159-203 785-832 (846)
111 KOG4362 Transcriptional regula 84.9 0.2 4.4E-06 48.1 -0.9 44 159-205 22-68 (684)
112 KOG0825 PHD Zn-finger protein 84.5 0.5 1.1E-05 46.0 1.5 49 157-205 95-153 (1134)
113 PF13901 DUF4206: Domain of un 84.2 0.75 1.6E-05 37.9 2.2 42 157-203 151-197 (202)
114 PF05290 Baculo_IE-1: Baculovi 83.1 0.91 2E-05 34.9 2.1 51 157-209 79-135 (140)
115 smart00249 PHD PHD zinc finger 81.2 0.89 1.9E-05 27.1 1.2 31 160-190 1-31 (47)
116 KOG3899 Uncharacterized conser 81.1 0.72 1.6E-05 40.0 1.0 31 179-209 325-368 (381)
117 KOG0269 WD40 repeat-containing 79.6 1.7 3.7E-05 42.3 3.0 46 160-206 781-828 (839)
118 PF00628 PHD: PHD-finger; Int 78.8 1.2 2.5E-05 27.8 1.2 43 160-202 1-49 (51)
119 KOG1815 Predicted E3 ubiquitin 78.2 1.2 2.7E-05 40.9 1.7 38 156-195 68-105 (444)
120 COG5220 TFB3 Cdk activating ki 76.3 0.92 2E-05 38.3 0.3 47 158-204 10-62 (314)
121 PF01363 FYVE: FYVE zinc finge 74.1 2.1 4.5E-05 28.6 1.5 38 155-192 6-44 (69)
122 KOG3579 Predicted E3 ubiquitin 74.0 1.6 3.5E-05 37.7 1.2 48 156-206 266-328 (352)
123 KOG1812 Predicted E3 ubiquitin 73.8 1.7 3.8E-05 39.3 1.4 42 159-201 307-351 (384)
124 KOG2068 MOT2 transcription fac 72.5 3 6.5E-05 36.8 2.5 50 159-208 250-300 (327)
125 PF07975 C1_4: TFIIH C1-like d 71.3 2.1 4.6E-05 27.4 1.0 42 161-202 2-50 (51)
126 KOG3005 GIY-YIG type nuclease 67.8 1.1 2.4E-05 38.4 -1.2 51 159-209 183-246 (276)
127 PF07191 zinc-ribbons_6: zinc- 66.7 0.7 1.5E-05 31.6 -2.1 40 159-206 2-41 (70)
128 PF13717 zinc_ribbon_4: zinc-r 66.0 4.2 9E-05 23.9 1.4 25 160-184 4-36 (36)
129 PF04710 Pellino: Pellino; In 65.4 2 4.4E-05 38.8 0.0 43 159-204 278-337 (416)
130 smart00064 FYVE Protein presen 64.8 3.3 7.1E-05 27.5 0.9 38 156-193 8-46 (68)
131 KOG0824 Predicted E3 ubiquitin 64.5 2.3 5.1E-05 37.0 0.2 48 156-205 103-150 (324)
132 KOG4718 Non-SMC (structural ma 64.1 3.5 7.6E-05 34.2 1.1 44 158-203 181-224 (235)
133 TIGR00622 ssl1 transcription f 61.9 10 0.00022 28.3 3.2 44 159-202 56-110 (112)
134 PRK05978 hypothetical protein; 60.7 5.3 0.00011 31.4 1.5 36 160-213 35-70 (148)
135 PF13719 zinc_ribbon_5: zinc-r 60.5 6.1 0.00013 23.3 1.4 25 160-184 4-36 (37)
136 PF02318 FYVE_2: FYVE-type zin 60.2 7.6 0.00017 29.0 2.3 46 157-203 53-102 (118)
137 PF10571 UPF0547: Uncharacteri 59.3 5.3 0.00012 21.8 1.0 23 160-183 2-24 (26)
138 KOG3113 Uncharacterized conser 58.1 9.2 0.0002 32.7 2.6 51 157-209 110-161 (293)
139 PF14169 YdjO: Cold-inducible 57.8 5.3 0.00011 26.4 0.9 14 195-208 39-52 (59)
140 PF07649 C1_3: C1-like domain; 56.2 7.9 0.00017 21.5 1.4 29 160-188 2-30 (30)
141 KOG3039 Uncharacterized conser 55.4 11 0.00024 32.1 2.6 35 156-193 41-75 (303)
142 cd00350 rubredoxin_like Rubred 54.4 9.3 0.0002 21.8 1.5 10 194-203 16-25 (33)
143 KOG1814 Predicted E3 ubiquitin 52.8 8.7 0.00019 35.0 1.7 37 155-191 365-404 (445)
144 KOG2807 RNA polymerase II tran 51.7 14 0.00029 32.8 2.7 45 159-203 331-375 (378)
145 KOG2071 mRNA cleavage and poly 51.3 11 0.00024 35.8 2.3 37 156-192 511-557 (579)
146 PF04423 Rad50_zn_hook: Rad50 51.1 5.2 0.00011 25.5 0.1 11 196-206 21-31 (54)
147 PRK00418 DNA gyrase inhibitor; 49.4 11 0.00025 25.1 1.5 14 195-208 6-19 (62)
148 smart00647 IBR In Between Ring 47.3 5.2 0.00011 25.8 -0.4 18 175-192 42-59 (64)
149 cd00065 FYVE FYVE domain; Zinc 46.5 15 0.00032 23.2 1.7 35 159-193 3-38 (57)
150 PF10235 Cript: Microtubule-as 45.7 9.7 0.00021 27.3 0.8 37 158-206 44-80 (90)
151 PF06844 DUF1244: Protein of u 45.2 14 0.00029 25.0 1.3 11 183-193 12-22 (68)
152 PF14311 DUF4379: Domain of un 43.4 18 0.00039 23.0 1.7 24 177-201 32-55 (55)
153 KOG3842 Adaptor protein Pellin 42.8 25 0.00053 31.2 2.9 51 158-208 341-416 (429)
154 KOG4185 Predicted E3 ubiquitin 41.9 4.1 8.9E-05 35.1 -2.0 46 159-204 208-265 (296)
155 PRK13130 H/ACA RNA-protein com 41.7 20 0.00043 23.4 1.7 19 195-213 17-35 (56)
156 PF13832 zf-HC5HC2H_2: PHD-zin 41.3 15 0.00033 26.6 1.3 33 157-191 54-88 (110)
157 PLN02189 cellulose synthase 40.9 25 0.00054 35.9 3.0 50 157-206 33-87 (1040)
158 PF09723 Zn-ribbon_8: Zinc rib 40.8 8.6 0.00019 23.3 -0.1 28 175-203 7-34 (42)
159 KOG1729 FYVE finger containing 40.7 4.8 0.0001 35.0 -1.7 36 160-195 216-251 (288)
160 KOG3799 Rab3 effector RIM1 and 40.1 6.6 0.00014 30.3 -0.8 49 156-204 63-116 (169)
161 PF06906 DUF1272: Protein of u 39.1 31 0.00068 22.5 2.3 44 161-208 8-54 (57)
162 smart00132 LIM Zinc-binding do 38.6 32 0.00069 19.2 2.2 37 161-206 2-38 (39)
163 PF14569 zf-UDP: Zinc-binding 38.5 44 0.00095 23.3 3.1 50 157-206 8-62 (80)
164 PF00412 LIM: LIM domain; Int 37.7 35 0.00076 21.2 2.5 38 161-207 1-38 (58)
165 smart00734 ZnF_Rad18 Rad18-lik 37.4 16 0.00034 19.8 0.6 9 197-205 3-11 (26)
166 PF11023 DUF2614: Protein of u 36.7 25 0.00053 26.3 1.7 22 190-211 80-101 (114)
167 PF13771 zf-HC5HC2H: PHD-like 36.4 23 0.0005 24.5 1.6 33 158-190 36-68 (90)
168 COG3364 Zn-ribbon containing p 36.3 21 0.00046 26.2 1.3 25 174-202 3-27 (112)
169 COG2824 PhnA Uncharacterized Z 36.3 13 0.00028 27.5 0.2 30 159-194 4-33 (112)
170 PF03884 DUF329: Domain of unk 35.6 14 0.0003 24.2 0.3 11 197-207 4-14 (57)
171 KOG2113 Predicted RNA binding 34.8 1.1E+02 0.0023 27.2 5.6 41 159-204 344-385 (394)
172 PRK11827 hypothetical protein; 34.5 14 0.00031 24.4 0.2 19 190-208 3-21 (60)
173 PF14353 CpXC: CpXC protein 32.7 32 0.0007 25.7 1.9 17 196-212 39-55 (128)
174 cd00729 rubredoxin_SM Rubredox 32.2 32 0.0007 19.8 1.4 9 196-204 19-27 (34)
175 PF12660 zf-TFIIIC: Putative z 32.1 4.2 9.1E-05 29.6 -3.0 48 159-208 15-68 (99)
176 PF03119 DNA_ligase_ZBD: NAD-d 31.5 19 0.00042 19.8 0.4 11 197-207 1-11 (28)
177 PTZ00303 phosphatidylinositol 30.6 1.2E+02 0.0026 30.4 5.7 35 158-192 460-500 (1374)
178 PF09889 DUF2116: Uncharacteri 29.9 28 0.0006 22.9 1.0 16 194-209 2-17 (59)
179 PRK01343 zinc-binding protein; 29.2 32 0.00069 22.5 1.1 12 195-206 9-20 (57)
180 PF01485 IBR: IBR domain; Int 28.8 9.3 0.0002 24.5 -1.5 33 159-191 19-58 (64)
181 COG2260 Predicted Zn-ribbon RN 28.7 42 0.00091 22.1 1.6 19 195-213 17-35 (59)
182 KOG2169 Zn-finger transcriptio 28.5 36 0.00077 33.0 1.8 44 160-210 308-360 (636)
183 TIGR02605 CxxC_CxxC_SSSS putat 28.2 25 0.00053 21.9 0.5 24 175-203 7-34 (52)
184 PLN02638 cellulose synthase A 28.2 55 0.0012 33.6 3.1 50 157-206 16-70 (1079)
185 PF11671 Apis_Csd: Complementa 26.1 1.3E+02 0.0028 23.1 4.1 50 17-66 86-136 (146)
186 KOG1512 PHD Zn-finger protein 25.8 77 0.0017 27.7 3.2 50 159-208 259-327 (381)
187 TIGR00686 phnA alkylphosphonat 25.7 42 0.00091 24.9 1.4 23 160-182 4-28 (109)
188 PF05191 ADK_lid: Adenylate ki 25.6 35 0.00075 20.0 0.8 31 175-207 3-33 (36)
189 PF06749 DUF1218: Protein of u 25.4 25 0.00055 25.2 0.2 10 1-10 16-25 (97)
190 COG2835 Uncharacterized conser 25.4 30 0.00064 22.9 0.5 13 197-209 10-22 (60)
191 PRK03564 formate dehydrogenase 25.3 33 0.00071 30.2 0.9 45 157-203 186-234 (309)
192 PF04216 FdhE: Protein involve 25.2 8.2 0.00018 33.4 -2.9 45 157-203 171-219 (290)
193 PF02148 zf-UBP: Zn-finger in 24.9 50 0.0011 21.5 1.5 31 161-193 1-35 (63)
194 KOG1356 Putative transcription 24.6 27 0.00059 34.7 0.3 45 159-204 230-280 (889)
195 PF09237 GAGA: GAGA factor; I 24.2 23 0.0005 22.7 -0.2 9 197-205 26-34 (54)
196 TIGR01562 FdhE formate dehydro 23.4 25 0.00054 30.9 -0.2 47 157-203 183-232 (305)
197 PLN02248 cellulose synthase-li 23.2 63 0.0014 33.4 2.5 32 178-209 149-180 (1135)
198 PF00130 C1_1: Phorbol esters/ 23.1 65 0.0014 19.8 1.8 34 157-190 10-45 (53)
199 PLN02436 cellulose synthase A 23.0 78 0.0017 32.6 3.1 50 157-206 35-89 (1094)
200 PF13240 zinc_ribbon_2: zinc-r 22.9 13 0.00029 19.5 -1.3 7 161-167 2-8 (23)
201 PLN02195 cellulose synthase A 22.3 1.2E+02 0.0025 31.1 4.1 50 158-209 6-62 (977)
202 TIGR01206 lysW lysine biosynth 22.2 48 0.0011 21.4 1.0 15 196-210 3-17 (54)
203 COG4647 AcxC Acetone carboxyla 22.1 48 0.001 25.5 1.1 21 162-185 61-81 (165)
204 KOG4224 Armadillo repeat prote 21.9 47 0.001 30.3 1.2 16 1-16 1-17 (550)
205 PF10497 zf-4CXXC_R1: Zinc-fin 21.8 1.3E+02 0.0027 22.0 3.3 24 180-203 37-69 (105)
206 PF08274 PhnA_Zn_Ribbon: PhnA 21.7 73 0.0016 18.0 1.6 24 160-183 4-29 (30)
207 COG3492 Uncharacterized protei 21.2 47 0.001 23.9 0.9 12 183-194 43-54 (104)
208 PF05502 Dynactin_p62: Dynacti 21.1 49 0.0011 31.0 1.2 38 157-207 25-64 (483)
209 COG1592 Rubrerythrin [Energy p 20.7 43 0.00093 26.8 0.7 9 195-203 149-157 (166)
210 PF06750 DiS_P_DiS: Bacterial 20.6 78 0.0017 22.5 1.9 38 158-207 33-70 (92)
211 smart00531 TFIIE Transcription 20.6 71 0.0015 24.6 1.9 14 196-209 124-137 (147)
212 TIGR00373 conserved hypothetic 20.5 1.1E+02 0.0023 24.1 2.9 35 157-209 108-142 (158)
213 PLN02400 cellulose synthase 20.5 68 0.0015 33.0 2.1 48 157-206 35-89 (1085)
214 KOG4218 Nuclear hormone recept 20.4 36 0.00078 30.5 0.2 23 156-179 13-35 (475)
215 KOG1512 PHD Zn-finger protein 20.1 42 0.00091 29.3 0.5 30 160-189 316-345 (381)
No 1
>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=99.67 E-value=2e-17 Score=103.79 Aligned_cols=44 Identities=45% Similarity=1.152 Sum_probs=40.1
Q ss_pred CccccccccccCCCCeEEcCcCCeechhHHHHHHhcCCCccccc
Q 028139 159 DVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCN 202 (213)
Q Consensus 159 ~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr 202 (213)
+.|+||+++|..++.++.++|||.||.+||.+|++++.+||+||
T Consensus 1 d~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~~~CP~CR 44 (44)
T PF13639_consen 1 DECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRNNSCPVCR 44 (44)
T ss_dssp -CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHSSB-TTTH
T ss_pred CCCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhCCcCCccC
Confidence 46999999998888899999999999999999999999999997
No 2
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.53 E-value=6.9e-15 Score=128.47 Aligned_cols=52 Identities=38% Similarity=0.957 Sum_probs=46.9
Q ss_pred CccccccccccCCCCeEEcCcCCeechhHHHHHHhcCCC-cccccccccCCCC
Q 028139 159 DVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDT-CPVCNQEMIFDLP 210 (213)
Q Consensus 159 ~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~~~~-CPvCr~~l~~~~~ 210 (213)
+.|+||||+|..++.+++|||+|.||..||++||....+ ||+||+.+.....
T Consensus 230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~di~~~~~ 282 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRDIRTDSG 282 (348)
T ss_pred ceEEEeecccccCCeeeEecCCCchhhccchhhHhhcCccCCCCCCcCCCCCC
Confidence 489999999999999999999999999999999988755 9999998866553
No 3
>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=99.50 E-value=2e-14 Score=99.76 Aligned_cols=47 Identities=36% Similarity=0.965 Sum_probs=37.8
Q ss_pred CCCCccccccccccC----------CCCeEEcCcCCeechhHHHHHHhcCCCccccc
Q 028139 156 EEEDVCPTCLEEYDA----------ENPRIITKCEHHFHLACIFEWMERSDTCPVCN 202 (213)
Q Consensus 156 ee~~~C~ICle~~~~----------~~~~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr 202 (213)
..++.|+||++.|.. +..+...+|||.||..||.+||+.+.+||+||
T Consensus 17 ~~~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR 73 (73)
T PF12678_consen 17 IADDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQNNTCPLCR 73 (73)
T ss_dssp SCCSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred CcCCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcCCcCCCCC
Confidence 345569999999932 23456678999999999999999999999997
No 4
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=99.39 E-value=2e-13 Score=118.69 Aligned_cols=54 Identities=33% Similarity=0.934 Sum_probs=46.2
Q ss_pred CCCCcccccccc-ccCC---------CCeEEcCcCCeechhHHHHHHhcCCCcccccccccCCC
Q 028139 156 EEEDVCPTCLEE-YDAE---------NPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDL 209 (213)
Q Consensus 156 ee~~~C~ICle~-~~~~---------~~~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr~~l~~~~ 209 (213)
..+..|.||||+ |..+ ..+..++|||.||.+|++.||+|+.+||+||.++.+|.
T Consensus 285 n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERqQTCPICr~p~ifd~ 348 (491)
T COG5243 285 NSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQTCPICRRPVIFDQ 348 (491)
T ss_pred CCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhccCCCcccCcccccc
Confidence 455689999999 5444 23468999999999999999999999999999988876
No 5
>PHA02929 N1R/p28-like protein; Provisional
Probab=99.34 E-value=7.4e-13 Score=110.97 Aligned_cols=50 Identities=32% Similarity=0.845 Sum_probs=41.7
Q ss_pred CCCccccccccccCCC-----CeEEcCcCCeechhHHHHHHhcCCCccccccccc
Q 028139 157 EEDVCPTCLEEYDAEN-----PRIITKCEHHFHLACIFEWMERSDTCPVCNQEMI 206 (213)
Q Consensus 157 e~~~C~ICle~~~~~~-----~~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr~~l~ 206 (213)
.+..|+|||+.+.... -.++++|+|.||..||.+|++++.+||+||+.+.
T Consensus 173 ~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~ 227 (238)
T PHA02929 173 KDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFI 227 (238)
T ss_pred CCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEee
Confidence 3467999999975432 1356789999999999999999999999999774
No 6
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=99.33 E-value=8.3e-13 Score=93.17 Aligned_cols=53 Identities=36% Similarity=0.931 Sum_probs=43.8
Q ss_pred CCCccccccccccCC----------CCeEEcCcCCeechhHHHHHHhc---CCCcccccccccCCC
Q 028139 157 EEDVCPTCLEEYDAE----------NPRIITKCEHHFHLACIFEWMER---SDTCPVCNQEMIFDL 209 (213)
Q Consensus 157 e~~~C~ICle~~~~~----------~~~~~l~CgH~Fh~~CI~~Wl~~---~~~CPvCr~~l~~~~ 209 (213)
+++.|.||...|+.. -+++.-.|+|.||..||.+||+. +..||+||++..+++
T Consensus 20 ~dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~~k~ 85 (85)
T PF12861_consen 20 NDDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWKFKE 85 (85)
T ss_pred CCCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeeeeCC
Confidence 467799999999752 25566779999999999999975 478999999988764
No 7
>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=99.29 E-value=3.2e-12 Score=82.18 Aligned_cols=46 Identities=28% Similarity=0.782 Sum_probs=39.5
Q ss_pred CCccccccccccCCCCeEEcCcCCe-echhHHHHHHhcCCCccccccccc
Q 028139 158 EDVCPTCLEEYDAENPRIITKCEHH-FHLACIFEWMERSDTCPVCNQEMI 206 (213)
Q Consensus 158 ~~~C~ICle~~~~~~~~~~l~CgH~-Fh~~CI~~Wl~~~~~CPvCr~~l~ 206 (213)
+..|.||++.... .++++|||. ||..|+.+|++.+..||+||+++.
T Consensus 2 ~~~C~iC~~~~~~---~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFENPRD---VVLLPCGHLCFCEECAERLLKRKKKCPICRQPIE 48 (50)
T ss_dssp HSB-TTTSSSBSS---EEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred cCCCccCCccCCc---eEEeCCCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence 4569999998654 789999999 999999999999999999999874
No 8
>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=99.27 E-value=3.4e-12 Score=77.88 Aligned_cols=39 Identities=44% Similarity=1.142 Sum_probs=34.0
Q ss_pred cccccccccCCCCeEEcCcCCeechhHHHHHHhcCCCcccc
Q 028139 161 CPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVC 201 (213)
Q Consensus 161 C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~~~~CPvC 201 (213)
|+||++.+.. +++.++|||.||..||.+|++.+.+||+|
T Consensus 1 C~iC~~~~~~--~~~~~~CGH~fC~~C~~~~~~~~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDELRD--PVVVTPCGHSFCKECIEKYLEKNPKCPVC 39 (39)
T ss_dssp ETTTTSB-SS--EEEECTTSEEEEHHHHHHHHHCTSB-TTT
T ss_pred CCCCCCcccC--cCEECCCCCchhHHHHHHHHHCcCCCcCC
Confidence 8999998865 55899999999999999999999999998
No 9
>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=99.22 E-value=1.1e-11 Score=76.56 Aligned_cols=44 Identities=39% Similarity=1.092 Sum_probs=37.7
Q ss_pred ccccccccccCCCCeEEcCcCCeechhHHHHHHhc-CCCcccccccc
Q 028139 160 VCPTCLEEYDAENPRIITKCEHHFHLACIFEWMER-SDTCPVCNQEM 205 (213)
Q Consensus 160 ~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~-~~~CPvCr~~l 205 (213)
.|+||++.+ .+...+++|||.||..|+..|++. +..||+||+.+
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 499999998 345667779999999999999998 78899999864
No 10
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.21 E-value=6.3e-12 Score=106.94 Aligned_cols=49 Identities=27% Similarity=0.811 Sum_probs=44.8
Q ss_pred CCccccccccccCCCCeEEcCcCCeechhHHHHHHh-cCCCccccccccc
Q 028139 158 EDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWME-RSDTCPVCNQEMI 206 (213)
Q Consensus 158 ~~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~-~~~~CPvCr~~l~ 206 (213)
.-.|+|||+.|...+...+|||.|.||..||.+||. -+..||+||.+++
T Consensus 323 GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iP 372 (374)
T COG5540 323 GVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIP 372 (374)
T ss_pred CceEEEEhhhhcccceEEEeccCceechhHHHHHHhhhcccCCccCCCCC
Confidence 357999999998888899999999999999999998 6889999999875
No 11
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.20 E-value=2.6e-11 Score=96.13 Aligned_cols=54 Identities=28% Similarity=0.664 Sum_probs=45.1
Q ss_pred CCCCccccccccccCCCCeEEcCcCCeechhHHHHHHhcCCCcccccccccCCCC
Q 028139 156 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDLP 210 (213)
Q Consensus 156 ee~~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr~~l~~~~~ 210 (213)
+....|+|||+.|.... .+.++|||+||..||+..++...+||+|++.|..++-
T Consensus 129 ~~~~~CPiCl~~~sek~-~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~k~~ 182 (187)
T KOG0320|consen 129 EGTYKCPICLDSVSEKV-PVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITHKQF 182 (187)
T ss_pred ccccCCCceecchhhcc-ccccccchhHHHHHHHHHHHhCCCCCCcccccchhhh
Confidence 44468999999986533 3569999999999999999999999999998866543
No 12
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=99.19 E-value=1.3e-11 Score=99.81 Aligned_cols=50 Identities=28% Similarity=0.715 Sum_probs=40.9
Q ss_pred CCCccccccccccCCCCeEEcCcCCeechhHHHHHHhc----------------CCCcccccccccCCC
Q 028139 157 EEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMER----------------SDTCPVCNQEMIFDL 209 (213)
Q Consensus 157 e~~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~----------------~~~CPvCr~~l~~~~ 209 (213)
++..|+||++.+.. .++++|||.||..||.+|+.. ...||+||..+...+
T Consensus 17 ~~~~CpICld~~~d---PVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~ 82 (193)
T PLN03208 17 GDFDCNICLDQVRD---PVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEAT 82 (193)
T ss_pred CccCCccCCCcCCC---cEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhc
Confidence 45679999998754 567899999999999999853 247999999886544
No 13
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=99.15 E-value=1.6e-11 Score=104.02 Aligned_cols=54 Identities=30% Similarity=0.696 Sum_probs=45.9
Q ss_pred cCCCCccccccccccCCCCeEEcCcCCeechhHHHHHHhcCCCcccccccccCCCCC
Q 028139 155 IEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDLPV 211 (213)
Q Consensus 155 ~ee~~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr~~l~~~~~~ 211 (213)
.+....|.||||.-.. +..++|||+||..||.+|...+..||+||..+..++.+
T Consensus 236 ~~a~~kC~LCLe~~~~---pSaTpCGHiFCWsCI~~w~~ek~eCPlCR~~~~pskvi 289 (293)
T KOG0317|consen 236 PEATRKCSLCLENRSN---PSATPCGHIFCWSCILEWCSEKAECPLCREKFQPSKVI 289 (293)
T ss_pred CCCCCceEEEecCCCC---CCcCcCcchHHHHHHHHHHccccCCCcccccCCCccee
Confidence 3556789999997543 67999999999999999999999999999988766543
No 14
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.14 E-value=2.1e-11 Score=100.45 Aligned_cols=52 Identities=31% Similarity=0.763 Sum_probs=42.1
Q ss_pred CCCCccccccccccCCCCeEEcCcCCeechhHHHHHHhc---CCCcccccccccCCCC
Q 028139 156 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMER---SDTCPVCNQEMIFDLP 210 (213)
Q Consensus 156 ee~~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~---~~~CPvCr~~l~~~~~ 210 (213)
.....|.||||.-.. .+++.|||+||..||++||.. ++.|||||..|..+..
T Consensus 45 ~~~FdCNICLd~akd---PVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~v 99 (230)
T KOG0823|consen 45 GGFFDCNICLDLAKD---PVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDTV 99 (230)
T ss_pred CCceeeeeeccccCC---CEEeecccceehHHHHHHHhhcCCCeeCCccccccccceE
Confidence 445679999996433 668889999999999999976 4679999998876653
No 15
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=99.13 E-value=3.5e-11 Score=75.31 Aligned_cols=44 Identities=32% Similarity=0.785 Sum_probs=39.7
Q ss_pred ccccccccccCCCCeEEcCcCCeechhHHHHHHhcCCCcccccc
Q 028139 160 VCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQ 203 (213)
Q Consensus 160 ~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr~ 203 (213)
.|+||++.|..+....++.|||.||..||..++.....||+||+
T Consensus 1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~~~~~~CP~C~k 44 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLKGKSVKCPICRK 44 (44)
T ss_pred CCcCcCccccCCCCeEEcccCCHHHHHHHHhhcCCCCCCcCCCC
Confidence 39999999966677899999999999999999977788999986
No 16
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=99.08 E-value=1.1e-10 Score=72.42 Aligned_cols=38 Identities=29% Similarity=0.838 Sum_probs=29.9
Q ss_pred cccccccccCCCCeEEcCcCCeechhHHHHHHhcC----CCcccc
Q 028139 161 CPTCLEEYDAENPRIITKCEHHFHLACIFEWMERS----DTCPVC 201 (213)
Q Consensus 161 C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~~----~~CPvC 201 (213)
|+||++.|.. .+.++|||.|+..||..|.+.. -.||+|
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 8999999976 7889999999999999999764 369987
No 17
>PHA02926 zinc finger-like protein; Provisional
Probab=99.07 E-value=8.2e-11 Score=96.52 Aligned_cols=53 Identities=26% Similarity=0.644 Sum_probs=40.3
Q ss_pred CCCccccccccccCC------CCeEEcCcCCeechhHHHHHHhcC------CCcccccccccCCC
Q 028139 157 EEDVCPTCLEEYDAE------NPRIITKCEHHFHLACIFEWMERS------DTCPVCNQEMIFDL 209 (213)
Q Consensus 157 e~~~C~ICle~~~~~------~~~~~l~CgH~Fh~~CI~~Wl~~~------~~CPvCr~~l~~~~ 209 (213)
++.+|+||||..... .-.++.+|+|.||..||..|.+.+ .+||+||..+.+=-
T Consensus 169 kE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~I~ 233 (242)
T PHA02926 169 KEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFRNIT 233 (242)
T ss_pred CCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceeeeec
Confidence 456799999986321 124567899999999999999753 46999999875533
No 18
>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=99.05 E-value=2.3e-10 Score=76.51 Aligned_cols=48 Identities=23% Similarity=0.402 Sum_probs=41.9
Q ss_pred CccccccccccCCCCeEEcCcCCeechhHHHHHHhcCCCcccccccccCCC
Q 028139 159 DVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDL 209 (213)
Q Consensus 159 ~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr~~l~~~~ 209 (213)
..|+||++.+.. .++++|||.|+..||.+|++.+.+||+|++.+..++
T Consensus 2 ~~Cpi~~~~~~~---Pv~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~~~ 49 (63)
T smart00504 2 FLCPISLEVMKD---PVILPSGQTYERRAIEKWLLSHGTDPVTGQPLTHED 49 (63)
T ss_pred cCCcCCCCcCCC---CEECCCCCEEeHHHHHHHHHHCCCCCCCcCCCChhh
Confidence 469999998865 467899999999999999999999999999886554
No 19
>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=99.04 E-value=2.3e-10 Score=70.20 Aligned_cols=39 Identities=44% Similarity=1.182 Sum_probs=33.9
Q ss_pred cccccccccCCCCeEEcCcCCeechhHHHHHHh--cCCCcccc
Q 028139 161 CPTCLEEYDAENPRIITKCEHHFHLACIFEWME--RSDTCPVC 201 (213)
Q Consensus 161 C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~--~~~~CPvC 201 (213)
|+||++.+.. +..+++|||.||..||.+|++ ....||+|
T Consensus 1 C~iC~~~~~~--~~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEPFED--PVILLPCGHSFCRDCLRKWLENSGSVKCPLC 41 (41)
T ss_dssp ETTTSSBCSS--EEEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred CCcCCccccC--CCEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence 8999998865 345999999999999999998 55779998
No 20
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=99.03 E-value=1.2e-10 Score=80.39 Aligned_cols=54 Identities=30% Similarity=0.691 Sum_probs=42.6
Q ss_pred CCccccccccccC-------------CCCeEEcCcCCeechhHHHHHHhcCCCcccccccccCCCCC
Q 028139 158 EDVCPTCLEEYDA-------------ENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDLPV 211 (213)
Q Consensus 158 ~~~C~ICle~~~~-------------~~~~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr~~l~~~~~~ 211 (213)
-++|+||...|.. +-++..-.|.|.||..||.+||..++.||++|++..+.+..
T Consensus 20 id~CaICRnhim~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~Tk~~CPld~q~w~~~~~~ 86 (88)
T COG5194 20 IDVCAICRNHIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQTWVLADGG 86 (88)
T ss_pred cchhhhhhccccCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhhCCCCCCCCceeEEeccc
Confidence 3678888776633 12345566999999999999999999999999998776643
No 21
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.97 E-value=1.8e-10 Score=107.77 Aligned_cols=49 Identities=35% Similarity=0.867 Sum_probs=42.8
Q ss_pred CCCccccccccccCCCC--eEEcCcCCeechhHHHHHHhcCCCcccccccc
Q 028139 157 EEDVCPTCLEEYDAENP--RIITKCEHHFHLACIFEWMERSDTCPVCNQEM 205 (213)
Q Consensus 157 e~~~C~ICle~~~~~~~--~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr~~l 205 (213)
..+.|+||+|+...+.. ...++|||.||..|++.||+++++||+||..+
T Consensus 290 ~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~qtCP~CR~~~ 340 (543)
T KOG0802|consen 290 SDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQQTCPTCRTVL 340 (543)
T ss_pred cCCeeeeechhhccccccccceeecccchHHHHHHHHHHHhCcCCcchhhh
Confidence 36789999999876543 67899999999999999999999999999944
No 22
>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=98.96 E-value=5.1e-10 Score=66.58 Aligned_cols=38 Identities=42% Similarity=1.189 Sum_probs=33.0
Q ss_pred cccccccccCCCCeEEcCcCCeechhHHHHHHh-cCCCcccc
Q 028139 161 CPTCLEEYDAENPRIITKCEHHFHLACIFEWME-RSDTCPVC 201 (213)
Q Consensus 161 C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~-~~~~CPvC 201 (213)
|+||++.. ...+.++|||.||..||..|++ .+..||+|
T Consensus 1 C~iC~~~~---~~~~~~~C~H~~c~~C~~~~~~~~~~~CP~C 39 (39)
T smart00184 1 CPICLEEL---KDPVVLPCGHTFCRSCIRKWLKSGNNTCPIC 39 (39)
T ss_pred CCcCccCC---CCcEEecCCChHHHHHHHHHHHhCcCCCCCC
Confidence 78999973 3477889999999999999998 66789987
No 23
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.88 E-value=1.2e-09 Score=97.72 Aligned_cols=51 Identities=25% Similarity=0.636 Sum_probs=43.8
Q ss_pred cCCCCccccccccccCCCCeEEcCcCCeechhHHHHHHhcCCCcccccccccCC
Q 028139 155 IEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFD 208 (213)
Q Consensus 155 ~ee~~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr~~l~~~ 208 (213)
.+....|+||++.|.. .++++|||.||..||..|+.....||+|+..+...
T Consensus 23 Le~~l~C~IC~d~~~~---PvitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~~~ 73 (397)
T TIGR00599 23 LDTSLRCHICKDFFDV---PVLTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQES 73 (397)
T ss_pred cccccCCCcCchhhhC---ccCCCCCCchhHHHHHHHHhCCCCCCCCCCccccc
Confidence 3566789999998854 45789999999999999999988999999987543
No 24
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.86 E-value=2.1e-09 Score=66.79 Aligned_cols=34 Identities=35% Similarity=0.875 Sum_probs=23.4
Q ss_pred cccccccc-cCCCCeEEcCcCCeechhHHHHHHhcC
Q 028139 161 CPTCLEEY-DAENPRIITKCEHHFHLACIFEWMERS 195 (213)
Q Consensus 161 C~ICle~~-~~~~~~~~l~CgH~Fh~~CI~~Wl~~~ 195 (213)
|+||+| | ..+++.++|+|||.|+.+||.+|++.+
T Consensus 1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~ 35 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKS 35 (43)
T ss_dssp -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH-
T ss_pred CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcC
Confidence 899999 7 557788899999999999999999864
No 25
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=98.80 E-value=7.3e-10 Score=75.93 Aligned_cols=52 Identities=31% Similarity=0.827 Sum_probs=41.0
Q ss_pred CCccccccccccCC----------CCeEEcCcCCeechhHHHHHHhc---CCCcccccccccCCC
Q 028139 158 EDVCPTCLEEYDAE----------NPRIITKCEHHFHLACIFEWMER---SDTCPVCNQEMIFDL 209 (213)
Q Consensus 158 ~~~C~ICle~~~~~----------~~~~~l~CgH~Fh~~CI~~Wl~~---~~~CPvCr~~l~~~~ 209 (213)
.++|.||.-.|+.. -+++.-.|.|.||..||.+|+.. +..||+||+.+.+++
T Consensus 20 ~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~~~e 84 (84)
T KOG1493|consen 20 DETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQFKE 84 (84)
T ss_pred CCccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeEecC
Confidence 34799999999662 24444569999999999999965 467999999987653
No 26
>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=98.60 E-value=3.5e-08 Score=63.15 Aligned_cols=42 Identities=29% Similarity=0.867 Sum_probs=33.0
Q ss_pred ccccccccccCCCCeEEcCcC-----CeechhHHHHHHhcC--CCccccc
Q 028139 160 VCPTCLEEYDAENPRIITKCE-----HHFHLACIFEWMERS--DTCPVCN 202 (213)
Q Consensus 160 ~C~ICle~~~~~~~~~~l~Cg-----H~Fh~~CI~~Wl~~~--~~CPvCr 202 (213)
.|.||++..+.+ ...+.||. |.||..|+.+|+..+ .+||+|+
T Consensus 1 ~CrIC~~~~~~~-~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~ 49 (49)
T smart00744 1 ICRICHDEGDEG-DPLVSPCRCKGSLKYVHQECLERWINESGNKTCEICK 49 (49)
T ss_pred CccCCCCCCCCC-CeeEeccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence 489999944444 45578884 999999999999654 5899995
No 27
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.58 E-value=2.2e-08 Score=84.11 Aligned_cols=51 Identities=29% Similarity=0.675 Sum_probs=42.0
Q ss_pred CCCCccccccccccCCCCeEEcCcCCeechhHHHH-HHhcCC-CcccccccccCCC
Q 028139 156 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFE-WMERSD-TCPVCNQEMIFDL 209 (213)
Q Consensus 156 ee~~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~-Wl~~~~-~CPvCr~~l~~~~ 209 (213)
+.+..|+||++.... ...++|||+||..||.. |-+++- .||+||+....++
T Consensus 213 ~~d~kC~lC~e~~~~---ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk~ 265 (271)
T COG5574 213 LADYKCFLCLEEPEV---PSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVYPKK 265 (271)
T ss_pred ccccceeeeecccCC---cccccccchhhHHHHHHHHHhhccccCchhhhhccchh
Confidence 456689999997543 77999999999999999 987764 5999999876554
No 28
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.55 E-value=3.7e-08 Score=89.45 Aligned_cols=49 Identities=31% Similarity=0.737 Sum_probs=40.4
Q ss_pred CCccccccccccCCCCeEEcCcCCeechhHHHHHHhcC-----CCcccccccccCCC
Q 028139 158 EDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERS-----DTCPVCNQEMIFDL 209 (213)
Q Consensus 158 ~~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~~-----~~CPvCr~~l~~~~ 209 (213)
+..|||||+.... ..++.|||.||..||...+..+ ..||+|+..+..++
T Consensus 186 ~~~CPICL~~~~~---p~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kd 239 (513)
T KOG2164|consen 186 DMQCPICLEPPSV---PVRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKD 239 (513)
T ss_pred CCcCCcccCCCCc---ccccccCceeeHHHHHHHHhhhcccCCccCCchhhhccccc
Confidence 5679999998755 5577799999999999988654 67999999876654
No 29
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=98.53 E-value=1.6e-08 Score=69.61 Aligned_cols=51 Identities=27% Similarity=0.690 Sum_probs=25.3
Q ss_pred CCcccccccccc-CCC-C-eEE--cCcCCeechhHHHHHHhc-----------CCCcccccccccCC
Q 028139 158 EDVCPTCLEEYD-AEN-P-RII--TKCEHHFHLACIFEWMER-----------SDTCPVCNQEMIFD 208 (213)
Q Consensus 158 ~~~C~ICle~~~-~~~-~-~~~--l~CgH~Fh~~CI~~Wl~~-----------~~~CPvCr~~l~~~ 208 (213)
+..|.||++.+. .+. + ++. ..|++.||..||.+||.. .++||.|+++|.++
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~~ 68 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISWS 68 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEGG
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeEe
Confidence 346999999875 322 2 223 369999999999999964 14699999998654
No 30
>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=98.50 E-value=8.7e-08 Score=66.35 Aligned_cols=51 Identities=24% Similarity=0.359 Sum_probs=39.6
Q ss_pred CCCccccccccccCCCCeEEcCcCCeechhHHHHHHhc-CCCcccccccccCCCC
Q 028139 157 EEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMER-SDTCPVCNQEMIFDLP 210 (213)
Q Consensus 157 e~~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~-~~~CPvCr~~l~~~~~ 210 (213)
++..|+|+.+-+.. .+++++||.|...+|.+|++. ..+||+|++.+..++.
T Consensus 3 ~~f~CpIt~~lM~d---PVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~~l 54 (73)
T PF04564_consen 3 DEFLCPITGELMRD---PVILPSGHTYERSAIERWLEQNGGTDPFTRQPLSESDL 54 (73)
T ss_dssp GGGB-TTTSSB-SS---EEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SGGGS
T ss_pred cccCCcCcCcHhhC---ceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCcccc
Confidence 35679999998866 678899999999999999998 8999999998876543
No 31
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=98.45 E-value=6.5e-08 Score=70.15 Aligned_cols=67 Identities=28% Similarity=0.535 Sum_probs=48.3
Q ss_pred HHhhhccccccc-cCCCCccccccccccC-------------CC-CeEEcCcCCeechhHHHHHHhcCCCcccccccccC
Q 028139 143 ELSKSVHHVVAV-IEEEDVCPTCLEEYDA-------------EN-PRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIF 207 (213)
Q Consensus 143 ~~~~~~~~~~~~-~ee~~~C~ICle~~~~-------------~~-~~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr~~l~~ 207 (213)
+++|+....... +...+.|+||..-+.. ++ .+.---|.|.||..||.+||+.++.||+|.++..+
T Consensus 30 ~lKKWnAvAlWaWDi~vDnCAICRnHIMd~CieCQa~~~~~~~EC~VaWG~CNHaFH~hCisrWlktr~vCPLdn~eW~~ 109 (114)
T KOG2930|consen 30 ELKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQSATSEECTVAWGVCNHAFHFHCISRWLKTRNVCPLDNKEWVF 109 (114)
T ss_pred EEeeeeeeeeeeeeeeechhHHHHHHHHHHHHhhccCCCCCCCceEEEeeecchHHHHHHHHHHHhhcCcCCCcCcceeE
Confidence 466665444433 3567889999755411 12 23335599999999999999999999999998876
Q ss_pred CC
Q 028139 208 DL 209 (213)
Q Consensus 208 ~~ 209 (213)
..
T Consensus 110 qr 111 (114)
T KOG2930|consen 110 QR 111 (114)
T ss_pred ee
Confidence 54
No 32
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.44 E-value=7.1e-08 Score=87.11 Aligned_cols=50 Identities=30% Similarity=0.804 Sum_probs=39.7
Q ss_pred CCCccccccccccC---CC-----------CeEEcCcCCeechhHHHHHHh-cCCCccccccccc
Q 028139 157 EEDVCPTCLEEYDA---EN-----------PRIITKCEHHFHLACIFEWME-RSDTCPVCNQEMI 206 (213)
Q Consensus 157 e~~~C~ICle~~~~---~~-----------~~~~l~CgH~Fh~~CI~~Wl~-~~~~CPvCr~~l~ 206 (213)
....|+|||..++. +. .-.++||.|+||..|+..||. .+--||+||.+++
T Consensus 570 ~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLP 634 (636)
T KOG0828|consen 570 RTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLP 634 (636)
T ss_pred ccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCCC
Confidence 34469999998744 11 134579999999999999999 5668999999875
No 33
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.34 E-value=9e-08 Score=80.63 Aligned_cols=53 Identities=28% Similarity=0.700 Sum_probs=42.3
Q ss_pred CCCCccccccccccCCC-------CeEEcCcCCeechhHHHHHH--hcCCCcccccccccCC
Q 028139 156 EEEDVCPTCLEEYDAEN-------PRIITKCEHHFHLACIFEWM--ERSDTCPVCNQEMIFD 208 (213)
Q Consensus 156 ee~~~C~ICle~~~~~~-------~~~~l~CgH~Fh~~CI~~Wl--~~~~~CPvCr~~l~~~ 208 (213)
.++.+|+||-..+.... +...|.|+|.||..||+-|- -.+.+||.||..+..+
T Consensus 222 l~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVdl~ 283 (328)
T KOG1734|consen 222 LSDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVDLK 283 (328)
T ss_pred CCcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhhHh
Confidence 45567999988875543 56678999999999999998 4578999999877443
No 34
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=98.30 E-value=1.6e-07 Score=81.40 Aligned_cols=48 Identities=27% Similarity=0.695 Sum_probs=42.5
Q ss_pred CCCCccccccccccCCCCeEEcCcCCeechhHHHHHHhcCCCccccccccc
Q 028139 156 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMI 206 (213)
Q Consensus 156 ee~~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr~~l~ 206 (213)
+.-..|.||.|-|.+ ..+++|+|.||.-||+..|..+..||.|+.++.
T Consensus 21 D~lLRC~IC~eyf~i---p~itpCsHtfCSlCIR~~L~~~p~CP~C~~~~~ 68 (442)
T KOG0287|consen 21 DDLLRCGICFEYFNI---PMITPCSHTFCSLCIRKFLSYKPQCPTCCVTVT 68 (442)
T ss_pred HHHHHHhHHHHHhcC---ceeccccchHHHHHHHHHhccCCCCCceecccc
Confidence 445679999999977 678899999999999999999999999998764
No 35
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.25 E-value=4.6e-07 Score=79.89 Aligned_cols=55 Identities=33% Similarity=0.780 Sum_probs=41.4
Q ss_pred CCCCccccccccccCCC-----CeEEcCcCCeechhHHHHHH--hc-----CCCcccccccccCCCC
Q 028139 156 EEEDVCPTCLEEYDAEN-----PRIITKCEHHFHLACIFEWM--ER-----SDTCPVCNQEMIFDLP 210 (213)
Q Consensus 156 ee~~~C~ICle~~~~~~-----~~~~l~CgH~Fh~~CI~~Wl--~~-----~~~CPvCr~~l~~~~~ 210 (213)
..+.+|.||||....-. -.++.+|.|.||..||..|. .+ ++.||.||....+--+
T Consensus 159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~~v~p 225 (344)
T KOG1039|consen 159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSSFVNP 225 (344)
T ss_pred cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccccccc
Confidence 34567999999874432 23447799999999999999 44 5789999987655443
No 36
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.23 E-value=4e-07 Score=76.76 Aligned_cols=45 Identities=38% Similarity=0.849 Sum_probs=39.6
Q ss_pred CCCCccccccccccCCCCeEEcCcCCeechhHHHHHHhcCCCcccccc
Q 028139 156 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQ 203 (213)
Q Consensus 156 ee~~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr~ 203 (213)
+++..|+||++.|... .+++|||.||..||..|+...-.||.||.
T Consensus 11 ~~~~~C~iC~~~~~~p---~~l~C~H~~c~~C~~~~~~~~~~Cp~cr~ 55 (386)
T KOG2177|consen 11 QEELTCPICLEYFREP---VLLPCGHNFCRACLTRSWEGPLSCPVCRP 55 (386)
T ss_pred cccccChhhHHHhhcC---ccccccchHhHHHHHHhcCCCcCCcccCC
Confidence 5677899999999764 78999999999999999986678999993
No 37
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=98.20 E-value=6.2e-07 Score=76.44 Aligned_cols=48 Identities=25% Similarity=0.499 Sum_probs=42.1
Q ss_pred CCCCccccccccccCCCCeEEcCcCCeechhHHHHHHhcCCCccccccccc
Q 028139 156 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMI 206 (213)
Q Consensus 156 ee~~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr~~l~ 206 (213)
+.-..|-||-+.|.+ ...++|||.||.-||+..|..+..||+||.+..
T Consensus 23 Ds~lrC~IC~~~i~i---p~~TtCgHtFCslCIR~hL~~qp~CP~Cr~~~~ 70 (391)
T COG5432 23 DSMLRCRICDCRISI---PCETTCGHTFCSLCIRRHLGTQPFCPVCREDPC 70 (391)
T ss_pred hhHHHhhhhhheeec---ceecccccchhHHHHHHHhcCCCCCccccccHH
Confidence 344679999998877 678999999999999999999999999998653
No 38
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=98.14 E-value=7.4e-07 Score=85.89 Aligned_cols=56 Identities=25% Similarity=0.807 Sum_probs=42.1
Q ss_pred ccccCCCCccccccccccC-CC---CeEEcCcCCeechhHHHHHHhcC--CCcccccccccC
Q 028139 152 VAVIEEEDVCPTCLEEYDA-EN---PRIITKCEHHFHLACIFEWMERS--DTCPVCNQEMIF 207 (213)
Q Consensus 152 ~~~~ee~~~C~ICle~~~~-~~---~~~~l~CgH~Fh~~CI~~Wl~~~--~~CPvCr~~l~~ 207 (213)
...-+....|+||+..... +. ...+..|.|-||..|+++|++.+ ++||+||.++.+
T Consensus 1463 ~~~fsG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseitf 1524 (1525)
T COG5219 1463 DEKFSGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEITF 1524 (1525)
T ss_pred hhhcCCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCcccccccc
Confidence 3333455679999987752 21 23456699999999999999875 689999988865
No 39
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=98.14 E-value=7.7e-07 Score=79.74 Aligned_cols=49 Identities=35% Similarity=0.889 Sum_probs=38.8
Q ss_pred CCCCccccccccccCCC-CeEEcCcCCeechhHHHHHHhcCCCccccccccc
Q 028139 156 EEEDVCPTCLEEYDAEN-PRIITKCEHHFHLACIFEWMERSDTCPVCNQEMI 206 (213)
Q Consensus 156 ee~~~C~ICle~~~~~~-~~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr~~l~ 206 (213)
.|..+||||||.++... .++.+.|.|.||..|+.+|- ..+|||||....
T Consensus 173 tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~--~~scpvcR~~q~ 222 (493)
T KOG0804|consen 173 TELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWW--DSSCPVCRYCQS 222 (493)
T ss_pred ccCCCcchhHhhcCccccceeeeecccccchHHHhhcc--cCcChhhhhhcC
Confidence 45568999999997654 34556799999999999995 455999997544
No 40
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=98.13 E-value=4.8e-07 Score=60.43 Aligned_cols=50 Identities=30% Similarity=0.659 Sum_probs=26.3
Q ss_pred CCCCccccccccccCCCCeEEcCcCCeechhHHHHHHhcCCCcccccccccCCC
Q 028139 156 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDL 209 (213)
Q Consensus 156 ee~~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr~~l~~~~ 209 (213)
++...|+||.+.+. +++.+..|+|.||..||..-+.. .||+|+.+.+.+|
T Consensus 5 e~lLrCs~C~~~l~--~pv~l~~CeH~fCs~Ci~~~~~~--~CPvC~~Paw~qD 54 (65)
T PF14835_consen 5 EELLRCSICFDILK--EPVCLGGCEHIFCSSCIRDCIGS--ECPVCHTPAWIQD 54 (65)
T ss_dssp HHTTS-SSS-S--S--S-B---SSS--B-TTTGGGGTTT--B-SSS--B-S-SS
T ss_pred HHhcCCcHHHHHhc--CCceeccCccHHHHHHhHHhcCC--CCCCcCChHHHHH
Confidence 34567999999864 45677889999999999885553 4999999987766
No 41
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.99 E-value=7.8e-07 Score=77.60 Aligned_cols=54 Identities=22% Similarity=0.707 Sum_probs=41.7
Q ss_pred CCCCccccccccccCCCCeEEcCcCCeechhHHHHHHhc-CCCcccccccccCCCCC
Q 028139 156 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMER-SDTCPVCNQEMIFDLPV 211 (213)
Q Consensus 156 ee~~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~-~~~CPvCr~~l~~~~~~ 211 (213)
.-+..|+|||+-+.. ......|+|.||..||..-|+. .+.||.||+.+..+-.|
T Consensus 41 ~~~v~c~icl~llk~--tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~SkrsL 95 (381)
T KOG0311|consen 41 DIQVICPICLSLLKK--TMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVSKRSL 95 (381)
T ss_pred hhhhccHHHHHHHHh--hcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhccccccC
Confidence 345679999998754 2334559999999999999976 57899999988655433
No 42
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.88 E-value=8.9e-06 Score=71.25 Aligned_cols=47 Identities=26% Similarity=0.668 Sum_probs=40.2
Q ss_pred CCCCccccccccccCCCCeEEcCcCC-eechhHHHHHHhcCCCcccccccc
Q 028139 156 EEEDVCPTCLEEYDAENPRIITKCEH-HFHLACIFEWMERSDTCPVCNQEM 205 (213)
Q Consensus 156 ee~~~C~ICle~~~~~~~~~~l~CgH-~Fh~~CI~~Wl~~~~~CPvCr~~l 205 (213)
+....|.|||.+-.. ..+|||-| ..|..|-+...-..+.||+||+.+
T Consensus 288 ~~gkeCVIClse~rd---t~vLPCRHLCLCs~Ca~~Lr~q~n~CPICRqpi 335 (349)
T KOG4265|consen 288 ESGKECVICLSESRD---TVVLPCRHLCLCSGCAKSLRYQTNNCPICRQPI 335 (349)
T ss_pred cCCCeeEEEecCCcc---eEEecchhhehhHhHHHHHHHhhcCCCccccch
Confidence 445689999998654 77999999 799999999877788999999976
No 43
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.84 E-value=2.9e-06 Score=80.51 Aligned_cols=51 Identities=27% Similarity=0.535 Sum_probs=42.5
Q ss_pred CCCccccccccccCCCCeEEcCcCCeechhHHHHHHhcCCCcccccccccC
Q 028139 157 EEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIF 207 (213)
Q Consensus 157 e~~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr~~l~~ 207 (213)
....|+|||..|..+......+|+|.||..||..|-+.-.+||+||.++..
T Consensus 122 ~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~aqTCPiDR~EF~~ 172 (1134)
T KOG0825|consen 122 VENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCAQTCPVDRGEFGE 172 (1134)
T ss_pred hhhhhhHHHHHHHHHhhccccccccccHHHHhhhhhhhcccCchhhhhhhe
Confidence 345699999999665544556799999999999999999999999997743
No 44
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=97.84 E-value=4.7e-06 Score=79.06 Aligned_cols=49 Identities=31% Similarity=0.621 Sum_probs=42.5
Q ss_pred CccccccccccCCCCeEEcCcCCeechhHHHHHHh-cCCCcccccccccCCCC
Q 028139 159 DVCPTCLEEYDAENPRIITKCEHHFHLACIFEWME-RSDTCPVCNQEMIFDLP 210 (213)
Q Consensus 159 ~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~-~~~~CPvCr~~l~~~~~ 210 (213)
..|+.|-..|.. .++++|||.||..||..-++ |..+||.|...+-.+|-
T Consensus 644 LkCs~Cn~R~Kd---~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganDv 693 (698)
T KOG0978|consen 644 LKCSVCNTRWKD---AVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGANDV 693 (698)
T ss_pred eeCCCccCchhh---HHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCcccc
Confidence 489999998876 77899999999999999995 46889999998877663
No 45
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=97.69 E-value=2.2e-05 Score=78.64 Aligned_cols=51 Identities=31% Similarity=0.775 Sum_probs=44.6
Q ss_pred cCCCCccccccccccCCCCeEEcCcCCeechhHHHHHHhcC----------CCcccccccc
Q 028139 155 IEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERS----------DTCPVCNQEM 205 (213)
Q Consensus 155 ~ee~~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~~----------~~CPvCr~~l 205 (213)
.+.+|+|.||+.+--...+.+.|.|+|+||..|.+.-|++. -.||+|+.++
T Consensus 3483 QD~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~I 3543 (3738)
T KOG1428|consen 3483 QDADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKI 3543 (3738)
T ss_pred cccCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchh
Confidence 36678999999988777889999999999999999988775 4799999876
No 46
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=97.64 E-value=3.8e-05 Score=50.58 Aligned_cols=43 Identities=33% Similarity=0.758 Sum_probs=29.6
Q ss_pred CCCCccccccccccCCCCeEEcCcCCeechhHHHHHHhc--CCCccc
Q 028139 156 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMER--SDTCPV 200 (213)
Q Consensus 156 ee~~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~--~~~CPv 200 (213)
.....|||.+..|. ++++...|||.|-.+.|.+||++ ...||+
T Consensus 9 ~~~~~CPiT~~~~~--~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv 53 (57)
T PF11789_consen 9 TISLKCPITLQPFE--DPVKSKKCGHTFEKEAILQYIQRNGSKRCPV 53 (57)
T ss_dssp B--SB-TTTSSB-S--SEEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred EeccCCCCcCChhh--CCcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence 34468999999885 57777899999999999999944 457998
No 47
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=97.54 E-value=3.7e-05 Score=69.40 Aligned_cols=53 Identities=32% Similarity=0.760 Sum_probs=43.7
Q ss_pred CCCCccccccccccCCCCeEEcCcCCeechhHHHHHHhcCCCcccccccccCCCC
Q 028139 156 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDLP 210 (213)
Q Consensus 156 ee~~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr~~l~~~~~ 210 (213)
++...|+||...+.. ++..+.|||.||..||.+|+..+..||.|+..+.....
T Consensus 19 ~~~l~C~~C~~vl~~--p~~~~~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~~ 71 (391)
T KOG0297|consen 19 DENLLCPICMSVLRD--PVQTTTCGHRFCAGCLLESLSNHQKCPVCRQELTQAEE 71 (391)
T ss_pred cccccCccccccccC--CCCCCCCCCcccccccchhhccCcCCcccccccchhhc
Confidence 455679999998754 33336899999999999999999999999998876553
No 48
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.50 E-value=1.9e-05 Score=50.94 Aligned_cols=44 Identities=25% Similarity=0.656 Sum_probs=33.6
Q ss_pred CccccccccccCCCCeEEcCcCC-eechhHHHHHHh-cCCCcccccccc
Q 028139 159 DVCPTCLEEYDAENPRIITKCEH-HFHLACIFEWME-RSDTCPVCNQEM 205 (213)
Q Consensus 159 ~~C~ICle~~~~~~~~~~l~CgH-~Fh~~CI~~Wl~-~~~~CPvCr~~l 205 (213)
++|.||+|.-.. .++-.||| ..|..|-.+.++ .+..||+||.++
T Consensus 8 dECTICye~pvd---sVlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi 53 (62)
T KOG4172|consen 8 DECTICYEHPVD---SVLYTCGHMCMCYACGLRLKKALHGCCPICRAPI 53 (62)
T ss_pred cceeeeccCcch---HHHHHcchHHhHHHHHHHHHHccCCcCcchhhHH
Confidence 679999996432 34556999 578899766555 688999999876
No 49
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=97.46 E-value=3.2e-05 Score=66.40 Aligned_cols=51 Identities=25% Similarity=0.744 Sum_probs=42.8
Q ss_pred CccccccccccCCCCeEEcCcCCeechhHHHHHHhc-----------------------CCCcccccccccCCC
Q 028139 159 DVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMER-----------------------SDTCPVCNQEMIFDL 209 (213)
Q Consensus 159 ~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~-----------------------~~~CPvCr~~l~~~~ 209 (213)
..|.|||-.|..+...+.+.|-|.||..|+.+.|.. ...|||||..|..+.
T Consensus 116 gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~e~ 189 (368)
T KOG4445|consen 116 GQCVICLYGFASSPAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKIEE 189 (368)
T ss_pred CceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccccc
Confidence 459999999988888899999999999999887731 257999999887654
No 50
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=97.45 E-value=5.1e-05 Score=61.60 Aligned_cols=45 Identities=27% Similarity=0.761 Sum_probs=40.3
Q ss_pred CCccccccccccCCCCeEEcCcCCeechhHHHHHHhcCCCcccccccc
Q 028139 158 EDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEM 205 (213)
Q Consensus 158 ~~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr~~l 205 (213)
...|.||-++|.. ++++.|||.||..|...-++....|-+|.+.+
T Consensus 196 PF~C~iCKkdy~s---pvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t 240 (259)
T COG5152 196 PFLCGICKKDYES---PVVTECGHSFCSLCAIRKYQKGDECGVCGKAT 240 (259)
T ss_pred ceeehhchhhccc---hhhhhcchhHHHHHHHHHhccCCcceecchhh
Confidence 3589999999976 67899999999999999999999999998764
No 51
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=97.40 E-value=5.7e-05 Score=67.14 Aligned_cols=49 Identities=29% Similarity=0.752 Sum_probs=40.1
Q ss_pred CccccccccccCCCCeEEcCcCCeechhHHHHHHhc--CCCcccccccccCCCC
Q 028139 159 DVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMER--SDTCPVCNQEMIFDLP 210 (213)
Q Consensus 159 ~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~--~~~CPvCr~~l~~~~~ 210 (213)
..|-||-|. +..+.+-+|||..|..|+..|-.. .++||.||.+|.--++
T Consensus 370 eLCKICaen---dKdvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKGte~ 420 (563)
T KOG1785|consen 370 ELCKICAEN---DKDVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIKGTEP 420 (563)
T ss_pred HHHHHhhcc---CCCcccccccchHHHHHHHhhcccCCCCCCCceeeEeccccc
Confidence 359999884 444788999999999999999844 5799999999865543
No 52
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=97.27 E-value=0.00021 Score=45.18 Aligned_cols=40 Identities=28% Similarity=0.904 Sum_probs=28.1
Q ss_pred cccccccccCCCCeEEcCcC-----CeechhHHHHHHhc--CCCcccc
Q 028139 161 CPTCLEEYDAENPRIITKCE-----HHFHLACIFEWMER--SDTCPVC 201 (213)
Q Consensus 161 C~ICle~~~~~~~~~~l~Cg-----H~Fh~~CI~~Wl~~--~~~CPvC 201 (213)
|-||++....+. ..+.||. -..|..|+.+|+.. +.+|++|
T Consensus 1 CrIC~~~~~~~~-~li~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C 47 (47)
T PF12906_consen 1 CRICLEGEEEDE-PLISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC 47 (47)
T ss_dssp ETTTTEE-SSSS--EE-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred CeEeCCcCCCCC-ceecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence 779999876655 5577874 47899999999974 5679987
No 53
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=97.24 E-value=0.0013 Score=63.55 Aligned_cols=49 Identities=33% Similarity=0.717 Sum_probs=37.5
Q ss_pred cCCCCccccccccccCCCCeE-EcCcCCeechhHHHHHHhcC-------CCcccccc
Q 028139 155 IEEEDVCPTCLEEYDAENPRI-ITKCEHHFHLACIFEWMERS-------DTCPVCNQ 203 (213)
Q Consensus 155 ~ee~~~C~ICle~~~~~~~~~-~l~CgH~Fh~~CI~~Wl~~~-------~~CPvCr~ 203 (213)
.....+|.||++.+....++. ...|=|+||+.||.+|-+.. -.||.|..
T Consensus 188 ~~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqs 244 (950)
T KOG1952|consen 188 SNRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQS 244 (950)
T ss_pred hcCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccc
Confidence 345568999999996655443 35589999999999999653 25999973
No 54
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.24 E-value=0.0002 Score=64.56 Aligned_cols=48 Identities=27% Similarity=0.722 Sum_probs=41.1
Q ss_pred CCCCccccccccccCCCCeEEcCcCCeechhHHHHHHhcCCCccccccccc
Q 028139 156 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMI 206 (213)
Q Consensus 156 ee~~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr~~l~ 206 (213)
..+..|.||+..+.. ++.++|||.||..||.+-|..+.-||.||.++.
T Consensus 82 ~sef~c~vc~~~l~~---pv~tpcghs~c~~Cl~r~ld~~~~cp~Cr~~l~ 129 (398)
T KOG4159|consen 82 RSEFECCVCSRALYP---PVVTPCGHSFCLECLDRSLDQETECPLCRDELV 129 (398)
T ss_pred cchhhhhhhHhhcCC---CccccccccccHHHHHHHhccCCCCcccccccc
Confidence 345679999887654 667899999999999999998999999999875
No 55
>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=97.15 E-value=0.00023 Score=61.88 Aligned_cols=36 Identities=19% Similarity=0.516 Sum_probs=27.9
Q ss_pred eEEcCcCCeechhHHHHHH-hcCCCcccccccccCCC
Q 028139 174 RIITKCEHHFHLACIFEWM-ERSDTCPVCNQEMIFDL 209 (213)
Q Consensus 174 ~~~l~CgH~Fh~~CI~~Wl-~~~~~CPvCr~~l~~~~ 209 (213)
+.+..|||.||..||...+ .....||+|++.+..+.
T Consensus 21 l~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk~~ 57 (309)
T TIGR00570 21 LMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLRKNN 57 (309)
T ss_pred cccCCCCCcccHHHHHHHhcCCCCCCCCCCCccchhh
Confidence 3344899999999999955 55678999998775443
No 56
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.10 E-value=0.00017 Score=61.87 Aligned_cols=44 Identities=27% Similarity=0.631 Sum_probs=39.9
Q ss_pred CccccccccccCCCCeEEcCcCCeechhHHHHHHhcCCCcccccccc
Q 028139 159 DVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEM 205 (213)
Q Consensus 159 ~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr~~l 205 (213)
+.|-||...|.. .+++.|+|.||..|-..-+++...|.+|.+.+
T Consensus 242 f~c~icr~~f~~---pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t 285 (313)
T KOG1813|consen 242 FKCFICRKYFYR---PVVTKCGHYFCEVCALKPYQKGEKCYVCSQQT 285 (313)
T ss_pred cccccccccccc---chhhcCCceeehhhhccccccCCcceeccccc
Confidence 469999999976 67899999999999999999999999998865
No 57
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=97.06 E-value=0.00015 Score=64.39 Aligned_cols=48 Identities=33% Similarity=0.684 Sum_probs=39.7
Q ss_pred CCCCccccccccccCC-CCeEEcCcCCeechhHHHHHHhcC--CCcccccc
Q 028139 156 EEEDVCPTCLEEYDAE-NPRIITKCEHHFHLACIFEWMERS--DTCPVCNQ 203 (213)
Q Consensus 156 ee~~~C~ICle~~~~~-~~~~~l~CgH~Fh~~CI~~Wl~~~--~~CPvCr~ 203 (213)
+-+..|..|=|.|... +.+..+||.|+||..|+.+.|+++ .+||-||+
T Consensus 363 e~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~Crk 413 (518)
T KOG1941|consen 363 ETELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRK 413 (518)
T ss_pred HHhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHH
Confidence 4456899999998553 346679999999999999999776 68999995
No 58
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.98 E-value=0.00028 Score=62.57 Aligned_cols=27 Identities=41% Similarity=1.178 Sum_probs=23.8
Q ss_pred EcCcCCeechhHHHHHHhcC---CCccccc
Q 028139 176 ITKCEHHFHLACIFEWMERS---DTCPVCN 202 (213)
Q Consensus 176 ~l~CgH~Fh~~CI~~Wl~~~---~~CPvCr 202 (213)
+-.|||.||..|+.+|++.- ..||+|+
T Consensus 23 i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ 52 (465)
T KOG0827|consen 23 IGTCGHIFHTTCLTQWFEGDPSNRGCPICQ 52 (465)
T ss_pred ccchhhHHHHHHHHHHHccCCccCCCCcee
Confidence 55699999999999999873 5899998
No 59
>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=96.97 E-value=0.00028 Score=54.13 Aligned_cols=35 Identities=17% Similarity=0.429 Sum_probs=29.8
Q ss_pred CCccccccccccCCCCeEEcCcC------CeechhHHHHHH
Q 028139 158 EDVCPTCLEEYDAENPRIITKCE------HHFHLACIFEWM 192 (213)
Q Consensus 158 ~~~C~ICle~~~~~~~~~~l~Cg------H~Fh~~CI~~Wl 192 (213)
...|.||++.+.....++.+.|| |.||..|+.+|-
T Consensus 26 ~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~ 66 (134)
T PF05883_consen 26 TVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWR 66 (134)
T ss_pred CeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHH
Confidence 45699999999775667778886 999999999994
No 60
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=96.81 E-value=0.0011 Score=55.62 Aligned_cols=55 Identities=13% Similarity=0.279 Sum_probs=46.6
Q ss_pred CCCccccccccccCCCCeE-EcCcCCeechhHHHHHHhcCCCcccccccccCCCCC
Q 028139 157 EEDVCPTCLEEYDAENPRI-ITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDLPV 211 (213)
Q Consensus 157 e~~~C~ICle~~~~~~~~~-~l~CgH~Fh~~CI~~Wl~~~~~CPvCr~~l~~~~~~ 211 (213)
...+||||.+.+.+..+.. +-+|||+|+.+|+.+.+..-..||||.+++.-++.|
T Consensus 220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdrdiI 275 (303)
T KOG3039|consen 220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDRDII 275 (303)
T ss_pred cceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCcccceE
Confidence 4568999999998766554 456999999999999999999999999998877643
No 61
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=96.81 E-value=0.00033 Score=60.99 Aligned_cols=51 Identities=27% Similarity=0.546 Sum_probs=41.0
Q ss_pred CCCccccccccccCCCCeEEcCcCCeechhHHHHHHhcCCCcccccccccCCC
Q 028139 157 EEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDL 209 (213)
Q Consensus 157 e~~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr~~l~~~~ 209 (213)
...+|.+|---|... ..++-|-|.||.+||.+.|+.++.||.|+..+-...
T Consensus 14 ~~itC~LC~GYliDA--TTI~eCLHTFCkSCivk~l~~~~~CP~C~i~ih~t~ 64 (331)
T KOG2660|consen 14 PHITCRLCGGYLIDA--TTITECLHTFCKSCIVKYLEESKYCPTCDIVIHKTH 64 (331)
T ss_pred cceehhhccceeecc--hhHHHHHHHHHHHHHHHHHHHhccCCccceeccCcc
Confidence 456799998877442 346679999999999999999999999988764443
No 62
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.77 E-value=0.0014 Score=55.72 Aligned_cols=49 Identities=33% Similarity=0.653 Sum_probs=39.3
Q ss_pred CCCCccccccccccCCCCeEEcCcCCeechhHHHHHHhc--CCCccccccccc
Q 028139 156 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMER--SDTCPVCNQEMI 206 (213)
Q Consensus 156 ee~~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~--~~~CPvCr~~l~ 206 (213)
....+|++|-+.- ..|-++.+|||+||.-||..-+.- +-+||.|.....
T Consensus 237 t~~~~C~~Cg~~P--tiP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~ 287 (298)
T KOG2879|consen 237 TSDTECPVCGEPP--TIPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVE 287 (298)
T ss_pred cCCceeeccCCCC--CCCeeeccccceeehhhhhhhhcchhhcccCccCCCCc
Confidence 4556899999864 456778889999999999997754 478999987664
No 63
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=96.75 E-value=0.00091 Score=43.38 Aligned_cols=47 Identities=28% Similarity=0.547 Sum_probs=36.9
Q ss_pred CccccccccccCCCCeEEcCcCCeechhHHHHHHhcCCCcccccccccCCCC
Q 028139 159 DVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDLP 210 (213)
Q Consensus 159 ~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr~~l~~~~~ 210 (213)
..|..|... +....+++|||..+..|..- ++.+-||+|.+++.++++
T Consensus 8 ~~~~~~~~~---~~~~~~~pCgH~I~~~~f~~--~rYngCPfC~~~~~~~~~ 54 (55)
T PF14447_consen 8 QPCVFCGFV---GTKGTVLPCGHLICDNCFPG--ERYNGCPFCGTPFEFDDP 54 (55)
T ss_pred eeEEEcccc---ccccccccccceeeccccCh--hhccCCCCCCCcccCCCC
Confidence 446666553 44567899999999999876 488889999999988765
No 64
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=96.71 E-value=0.0013 Score=51.85 Aligned_cols=51 Identities=29% Similarity=0.702 Sum_probs=37.3
Q ss_pred ccCCCCccccccccccCCCCeEEcCcC--C---eechhHHHHHHhcC--CCcccccccccCC
Q 028139 154 VIEEEDVCPTCLEEYDAENPRIITKCE--H---HFHLACIFEWMERS--DTCPVCNQEMIFD 208 (213)
Q Consensus 154 ~~ee~~~C~ICle~~~~~~~~~~l~Cg--H---~Fh~~CI~~Wl~~~--~~CPvCr~~l~~~ 208 (213)
.+..+..|-||.++.... .-||. . ..|.+|+.+|+..+ .+|++|+++..+.
T Consensus 4 ~s~~~~~CRIC~~~~~~~----~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i~ 61 (162)
T PHA02825 4 VSLMDKCCWICKDEYDVV----TNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNIK 61 (162)
T ss_pred cCCCCCeeEecCCCCCCc----cCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEEE
Confidence 345667899999985432 24654 3 66999999999664 6799999987543
No 65
>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=96.71 E-value=0.0015 Score=47.62 Aligned_cols=33 Identities=24% Similarity=0.555 Sum_probs=27.1
Q ss_pred CCCCccccccccccCCCCeEEcCcCCeechhHHH
Q 028139 156 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIF 189 (213)
Q Consensus 156 ee~~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~ 189 (213)
.+...|+||-..+.. ....+.||||.||..|+.
T Consensus 76 ~~~~~C~vC~k~l~~-~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 76 TESTKCSVCGKPLGN-SVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCCCccCcCCcCCC-ceEEEeCCCeEEeccccc
Confidence 345569999999866 557789999999999975
No 66
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.67 E-value=0.0013 Score=57.97 Aligned_cols=49 Identities=22% Similarity=0.621 Sum_probs=41.8
Q ss_pred cCCCCccccccccccCCCCeEEcCcCCeechhHHHHHHhcCCCccccccccc
Q 028139 155 IEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMI 206 (213)
Q Consensus 155 ~ee~~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr~~l~ 206 (213)
+.|++.|+||.-. ....+..||+|.-|..||.+-|-+.+.|=.|+..+.
T Consensus 419 ~sEd~lCpICyA~---pi~Avf~PC~H~SC~~CI~qHlmN~k~CFfCktTv~ 467 (489)
T KOG4692|consen 419 DSEDNLCPICYAG---PINAVFAPCSHRSCYGCITQHLMNCKRCFFCKTTVI 467 (489)
T ss_pred CcccccCcceecc---cchhhccCCCCchHHHHHHHHHhcCCeeeEecceee
Confidence 3567789999874 344678999999999999999999999999998765
No 67
>PHA02862 5L protein; Provisional
Probab=96.67 E-value=0.001 Score=51.48 Aligned_cols=48 Identities=21% Similarity=0.593 Sum_probs=35.9
Q ss_pred CCccccccccccCCCCeEEcCc-----CCeechhHHHHHHhc--CCCcccccccccCCC
Q 028139 158 EDVCPTCLEEYDAENPRIITKC-----EHHFHLACIFEWMER--SDTCPVCNQEMIFDL 209 (213)
Q Consensus 158 ~~~C~ICle~~~~~~~~~~l~C-----gH~Fh~~CI~~Wl~~--~~~CPvCr~~l~~~~ 209 (213)
.+.|-||+++.+.+ .-|| --..|..|+.+|++. +..|++|+.+..++.
T Consensus 2 ~diCWIC~~~~~e~----~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~Ik~ 56 (156)
T PHA02862 2 SDICWICNDVCDER----NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNIKK 56 (156)
T ss_pred CCEEEEecCcCCCC----cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEEEEE
Confidence 35799999986432 2455 357899999999965 467999999875543
No 68
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=96.64 E-value=0.0017 Score=41.06 Aligned_cols=45 Identities=27% Similarity=0.645 Sum_probs=23.0
Q ss_pred cccccccccCCC-CeEEcCcCCeechhHHHHHHh-cCCCcccccccc
Q 028139 161 CPTCLEEYDAEN-PRIITKCEHHFHLACIFEWME-RSDTCPVCNQEM 205 (213)
Q Consensus 161 C~ICle~~~~~~-~~~~l~CgH~Fh~~CI~~Wl~-~~~~CPvCr~~l 205 (213)
|++|.++++... ...-=+||+.+|..|...-++ ..+.||-||++.
T Consensus 1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y 47 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILENEGGRCPGCREPY 47 (48)
T ss_dssp -TTTS-B--CCCTT--SSTTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred CCCcccccccCCCccccCcCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence 799999984432 333344799999999999886 478999999864
No 69
>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=96.56 E-value=0.0011 Score=41.54 Aligned_cols=43 Identities=30% Similarity=0.798 Sum_probs=26.6
Q ss_pred cccccccccCCCCeEEcCc-CCeechhHHHHHHhcCCCcccccccccCC
Q 028139 161 CPTCLEEYDAENPRIITKC-EHHFHLACIFEWMERSDTCPVCNQEMIFD 208 (213)
Q Consensus 161 C~ICle~~~~~~~~~~l~C-gH~Fh~~CI~~Wl~~~~~CPvCr~~l~~~ 208 (213)
|--|+-.... +..| .|..|..|+...|.++..||+|+.+++++
T Consensus 5 CKsCWf~~k~-----Li~C~dHYLCl~CLt~ml~~s~~C~iC~~~LPtk 48 (50)
T PF03854_consen 5 CKSCWFANKG-----LIKCSDHYLCLNCLTLMLSRSDRCPICGKPLPTK 48 (50)
T ss_dssp --SS-S--SS-----EEE-SS-EEEHHHHHHT-SSSSEETTTTEE----
T ss_pred ChhhhhcCCC-----eeeecchhHHHHHHHHHhccccCCCcccCcCccc
Confidence 6666654433 5678 59999999999999999999999998764
No 70
>PF04641 Rtf2: Rtf2 RING-finger
Probab=96.33 E-value=0.0038 Score=53.40 Aligned_cols=53 Identities=23% Similarity=0.506 Sum_probs=41.7
Q ss_pred CCCCccccccccccCCCCe-EEcCcCCeechhHHHHHHhcCCCcccccccccCCC
Q 028139 156 EEEDVCPTCLEEYDAENPR-IITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDL 209 (213)
Q Consensus 156 ee~~~C~ICle~~~~~~~~-~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr~~l~~~~ 209 (213)
.....|||...+|...... .+-+|||+|...+|.+- .....||+|.+++...+
T Consensus 111 ~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~-k~~~~Cp~c~~~f~~~D 164 (260)
T PF04641_consen 111 EGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKEL-KKSKKCPVCGKPFTEED 164 (260)
T ss_pred CceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhh-cccccccccCCccccCC
Confidence 5567999999999554444 44589999999999996 34668999999887554
No 71
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.29 E-value=0.00085 Score=57.57 Aligned_cols=42 Identities=21% Similarity=0.623 Sum_probs=32.1
Q ss_pred CCCccccccccccCCCCeEEcCcCC-eechhHHHHHHhcCCCcccccccc
Q 028139 157 EEDVCPTCLEEYDAENPRIITKCEH-HFHLACIFEWMERSDTCPVCNQEM 205 (213)
Q Consensus 157 e~~~C~ICle~~~~~~~~~~l~CgH-~Fh~~CI~~Wl~~~~~CPvCr~~l 205 (213)
....|.|||+.-. ..+.|.||| .-|.+|-.. -+.|||||+.|
T Consensus 299 ~~~LC~ICmDaP~---DCvfLeCGHmVtCt~CGkr----m~eCPICRqyi 341 (350)
T KOG4275|consen 299 TRRLCAICMDAPR---DCVFLECGHMVTCTKCGKR----MNECPICRQYI 341 (350)
T ss_pred HHHHHHHHhcCCc---ceEEeecCcEEeehhhccc----cccCchHHHHH
Confidence 3568999999643 367899999 568888654 34899999876
No 72
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.25 E-value=0.0027 Score=56.83 Aligned_cols=37 Identities=24% Similarity=0.723 Sum_probs=29.4
Q ss_pred cCCCCeEEcCcCCeechhHHHHHHhc--CCCcccccccc
Q 028139 169 DAENPRIITKCEHHFHLACIFEWMER--SDTCPVCNQEM 205 (213)
Q Consensus 169 ~~~~~~~~l~CgH~Fh~~CI~~Wl~~--~~~CPvCr~~l 205 (213)
..++..+.+.|||.|...||.+||-. ...||.|..+.
T Consensus 17 ~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~ka 55 (463)
T KOG1645|consen 17 AGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKA 55 (463)
T ss_pred cCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChh
Confidence 34556678999999999999999953 35699998654
No 73
>PHA03096 p28-like protein; Provisional
Probab=96.22 E-value=0.0023 Score=55.35 Aligned_cols=45 Identities=33% Similarity=0.696 Sum_probs=31.8
Q ss_pred CccccccccccCCC-----CeEEcCcCCeechhHHHHHHhcC---CCcccccc
Q 028139 159 DVCPTCLEEYDAEN-----PRIITKCEHHFHLACIFEWMERS---DTCPVCNQ 203 (213)
Q Consensus 159 ~~C~ICle~~~~~~-----~~~~l~CgH~Fh~~CI~~Wl~~~---~~CPvCr~ 203 (213)
..|.||||...... --++..|.|.||..||..|...+ .+||.||.
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 66999999864321 12345699999999999999553 44555544
No 74
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.02 E-value=0.0033 Score=56.37 Aligned_cols=46 Identities=22% Similarity=0.383 Sum_probs=37.9
Q ss_pred CCccccccccccCCCCeEEcCcCCeechhHHHHHHhc--------CCCcccccc
Q 028139 158 EDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMER--------SDTCPVCNQ 203 (213)
Q Consensus 158 ~~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~--------~~~CPvCr~ 203 (213)
...|.||+++.......+.++|+|+||..|+...+.. .-.||-++-
T Consensus 184 lf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C 237 (445)
T KOG1814|consen 184 LFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKC 237 (445)
T ss_pred cccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCC
Confidence 3469999999987788899999999999999999854 246877653
No 75
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.00 E-value=0.0048 Score=54.44 Aligned_cols=45 Identities=29% Similarity=0.689 Sum_probs=33.2
Q ss_pred CCCCccccccccccCCCCeEEcCcCCeechhHHHHHHhcCCCccccccccc
Q 028139 156 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMI 206 (213)
Q Consensus 156 ee~~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr~~l~ 206 (213)
...+.|.||+++... .+.++|||.-| |+.--.. -.+||+||+.+.
T Consensus 303 ~~p~lcVVcl~e~~~---~~fvpcGh~cc--ct~cs~~-l~~CPvCR~rI~ 347 (355)
T KOG1571|consen 303 PQPDLCVVCLDEPKS---AVFVPCGHVCC--CTLCSKH-LPQCPVCRQRIR 347 (355)
T ss_pred CCCCceEEecCCccc---eeeecCCcEEE--chHHHhh-CCCCchhHHHHH
Confidence 344679999998755 77899999966 7665433 345999998763
No 76
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.00 E-value=0.0045 Score=49.63 Aligned_cols=54 Identities=22% Similarity=0.575 Sum_probs=38.2
Q ss_pred cCCCCccccccccccCCC----CeEEcCcCCeechhHHHHHHhc------C-----CCcccccccccCC
Q 028139 155 IEEEDVCPTCLEEYDAEN----PRIITKCEHHFHLACIFEWMER------S-----DTCPVCNQEMIFD 208 (213)
Q Consensus 155 ~ee~~~C~ICle~~~~~~----~~~~l~CgH~Fh~~CI~~Wl~~------~-----~~CPvCr~~l~~~ 208 (213)
+++...|.||+-.--.+. ..--..||.-||.-|+..||+. + +.||+|-+++..+
T Consensus 162 dd~~~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialK 230 (234)
T KOG3268|consen 162 DDELGACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALK 230 (234)
T ss_pred chhhhcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceee
Confidence 455567999986432222 1223569999999999999964 1 6799999887654
No 77
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=95.97 E-value=0.0042 Score=54.48 Aligned_cols=54 Identities=24% Similarity=0.534 Sum_probs=38.2
Q ss_pred ccccCCCCccccccccccCCCC-eEEcCcCCeechhHHHHHHh-cCCCcccccccc
Q 028139 152 VAVIEEEDVCPTCLEEYDAENP-RIITKCEHHFHLACIFEWME-RSDTCPVCNQEM 205 (213)
Q Consensus 152 ~~~~ee~~~C~ICle~~~~~~~-~~~l~CgH~Fh~~CI~~Wl~-~~~~CPvCr~~l 205 (213)
..+.+++|.||.|+|+++..+. ..--+||-..|..|+..--+ -++.||.||...
T Consensus 8 ~~sedeed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y 63 (480)
T COG5175 8 HNSEDEEDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKY 63 (480)
T ss_pred cccccccccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhc
Confidence 3455677889999999976543 34466898888888655332 257899999854
No 78
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=95.85 E-value=0.0035 Score=57.87 Aligned_cols=51 Identities=35% Similarity=0.721 Sum_probs=40.6
Q ss_pred CCCCccccccccccCCCCeEEcCcCCeechhHHHHHHhc-----CCCcccccccccCCC
Q 028139 156 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMER-----SDTCPVCNQEMIFDL 209 (213)
Q Consensus 156 ee~~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~-----~~~CPvCr~~l~~~~ 209 (213)
.++.+|.+|-+.-+. .+...|.|.||.-||.++++. +-+||+|-..+..+.
T Consensus 534 k~~~~C~lc~d~aed---~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiDl 589 (791)
T KOG1002|consen 534 KGEVECGLCHDPAED---YIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSIDL 589 (791)
T ss_pred cCceeecccCChhhh---hHhhhhhHHHHHHHHHHHHHhhhcccCCCCccccccccccc
Confidence 455689999986433 678899999999999888843 468999988886653
No 79
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=95.58 E-value=0.01 Score=52.22 Aligned_cols=50 Identities=24% Similarity=0.458 Sum_probs=39.8
Q ss_pred cccCCCCccccccccccCCCCeEEcCcCCeechhHHHH--HHhcCCCcccccccc
Q 028139 153 AVIEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFE--WMERSDTCPVCNQEM 205 (213)
Q Consensus 153 ~~~ee~~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~--Wl~~~~~CPvCr~~l 205 (213)
..+|++..|-||-+.... ..++||+|..|.-|-.. .|-..+.||+||.+.
T Consensus 56 dtDEen~~C~ICA~~~TY---s~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~ 107 (493)
T COG5236 56 DTDEENMNCQICAGSTTY---SARYPCGHQICHACAVRLRALYMQKGCPLCRTET 107 (493)
T ss_pred ccccccceeEEecCCceE---EEeccCCchHHHHHHHHHHHHHhccCCCcccccc
Confidence 345777889999998765 66899999999999765 345578899999863
No 80
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=94.82 E-value=0.02 Score=55.67 Aligned_cols=42 Identities=31% Similarity=0.755 Sum_probs=34.2
Q ss_pred CCccccccccccCCCCeEEcCcCCeechhHHHHHHhcCCCccccccc
Q 028139 158 EDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQE 204 (213)
Q Consensus 158 ~~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr~~ 204 (213)
..+|.+|--..+ -|.+...|||.||..|+. .....||-|+-+
T Consensus 840 ~skCs~C~~~Ld--lP~VhF~CgHsyHqhC~e---~~~~~CP~C~~e 881 (933)
T KOG2114|consen 840 VSKCSACEGTLD--LPFVHFLCGHSYHQHCLE---DKEDKCPKCLPE 881 (933)
T ss_pred eeeecccCCccc--cceeeeecccHHHHHhhc---cCcccCCccchh
Confidence 357999977654 478889999999999988 456789999864
No 81
>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=94.79 E-value=0.015 Score=35.89 Aligned_cols=41 Identities=22% Similarity=0.600 Sum_probs=22.2
Q ss_pred cccccccccCCCCeEEcCcCCeechhHHHHHHhcCC--Ccccc
Q 028139 161 CPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSD--TCPVC 201 (213)
Q Consensus 161 C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~~~--~CPvC 201 (213)
|.+|-+....+..-....|+=.+|..|+..+++... .||.|
T Consensus 1 C~~C~~iv~~G~~C~~~~C~~r~H~~C~~~y~r~~~~~~CP~C 43 (43)
T PF08746_consen 1 CEACKEIVTQGQRCSNRDCNVRLHDDCFKKYFRHRSNPKCPNC 43 (43)
T ss_dssp -TTT-SB-SSSEE-SS--S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred CcccchhHeeeccCCCCccCchHHHHHHHHHHhcCCCCCCcCC
Confidence 567777665543222235888999999999997765 79987
No 82
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.77 E-value=0.026 Score=50.51 Aligned_cols=47 Identities=26% Similarity=0.506 Sum_probs=40.5
Q ss_pred CCccccccccccCCCCeEEcCcCCeechhHHHHHHhcC---CCccccccc
Q 028139 158 EDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERS---DTCPVCNQE 204 (213)
Q Consensus 158 ~~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~~---~~CPvCr~~ 204 (213)
..+|||=-+.-..+|++..|.|||+...+=|.+..+.. -+||+|-.+
T Consensus 334 vF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~e 383 (394)
T KOG2817|consen 334 VFICPVLKEQTSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPVE 383 (394)
T ss_pred eeecccchhhccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCcc
Confidence 35899999999999999999999999999999977554 479999554
No 83
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.74 E-value=0.012 Score=46.52 Aligned_cols=30 Identities=23% Similarity=0.545 Sum_probs=26.8
Q ss_pred CCCCccccccccccCCCCeEEcCcCCeech
Q 028139 156 EEEDVCPTCLEEYDAENPRIITKCEHHFHL 185 (213)
Q Consensus 156 ee~~~C~ICle~~~~~~~~~~l~CgH~Fh~ 185 (213)
++.-+|.||||++..++....|||-.+||+
T Consensus 175 ddkGECvICLEdL~~GdtIARLPCLCIYHK 204 (205)
T KOG0801|consen 175 DDKGECVICLEDLEAGDTIARLPCLCIYHK 204 (205)
T ss_pred ccCCcEEEEhhhccCCCceeccceEEEeec
Confidence 455579999999999999999999999996
No 84
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=94.66 E-value=0.017 Score=49.70 Aligned_cols=45 Identities=31% Similarity=0.588 Sum_probs=37.3
Q ss_pred CccccccccccC-CCCeEEcCcCCeechhHHHHHHhcCCCcccccc
Q 028139 159 DVCPTCLEEYDA-ENPRIITKCEHHFHLACIFEWMERSDTCPVCNQ 203 (213)
Q Consensus 159 ~~C~ICle~~~~-~~~~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr~ 203 (213)
..||||.+.+.. ...+..++|||.-|..|..+.....=+||+|.+
T Consensus 159 ~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~~y~CP~C~~ 204 (276)
T KOG1940|consen 159 FNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICEGYTCPICSK 204 (276)
T ss_pred CCCchhHHHhccccccCCccCcccchHHHHHHHHhccCCCCCcccc
Confidence 349999998744 345677999999999999998877789999987
No 85
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.40 E-value=0.0023 Score=56.98 Aligned_cols=49 Identities=18% Similarity=0.466 Sum_probs=41.1
Q ss_pred CccccccccccCC-CCeEEcCcCCeechhHHHHHHhcCCCcccccccccC
Q 028139 159 DVCPTCLEEYDAE-NPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIF 207 (213)
Q Consensus 159 ~~C~ICle~~~~~-~~~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr~~l~~ 207 (213)
..|+||.+.|... .....+.|||.+|..||.+||.....||-|+.++..
T Consensus 197 ~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~~~~kl~~~~rel~~ 246 (465)
T KOG0827|consen 197 GSLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLATKRKLPSCRRELPK 246 (465)
T ss_pred hhhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHHHhHHHHhhhhh
Confidence 3699999988554 345567799999999999999999999999988754
No 86
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=94.27 E-value=0.01 Score=57.14 Aligned_cols=47 Identities=26% Similarity=0.674 Sum_probs=38.5
Q ss_pred CccccccccccCCCCeEEcCcCCeechhHHHHHHhcC--CCcccccccccCCC
Q 028139 159 DVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERS--DTCPVCNQEMIFDL 209 (213)
Q Consensus 159 ~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~~--~~CPvCr~~l~~~~ 209 (213)
..|.||++ .+..+++.|||.||..|+.+-++.. ..||+||..+..+.
T Consensus 455 ~~c~ic~~----~~~~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~~~ 503 (674)
T KOG1001|consen 455 HWCHICCD----LDSFFITRCGHDFCVECLKKSIQQSENAPCPLCRNVLKEKK 503 (674)
T ss_pred cccccccc----cccceeecccchHHHHHHHhccccccCCCCcHHHHHHHHHH
Confidence 67999999 3457889999999999999988664 35999998775544
No 87
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.11 E-value=0.045 Score=45.59 Aligned_cols=51 Identities=25% Similarity=0.551 Sum_probs=40.0
Q ss_pred CCCCccccccccccCCCCeEEcCcCCeechhHHHHHHhc--------CCCcccccccccC
Q 028139 156 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMER--------SDTCPVCNQEMIF 207 (213)
Q Consensus 156 ee~~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~--------~~~CPvCr~~l~~ 207 (213)
+-...|..|-.....++. +.|.|-|.||.+|+.+|-.. .-.||.|.++|..
T Consensus 48 DY~pNC~LC~t~La~gdt-~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFP 106 (299)
T KOG3970|consen 48 DYNPNCRLCNTPLASGDT-TRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFP 106 (299)
T ss_pred CCCCCCceeCCccccCcc-eeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCC
Confidence 334568889888877664 47789999999999999854 2469999998854
No 88
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=94.08 E-value=0.037 Score=48.44 Aligned_cols=51 Identities=29% Similarity=0.699 Sum_probs=40.8
Q ss_pred CCCccccccccccCCCCeEEcCcCCeechhHHHHHHhcCCCcccccccccCCC
Q 028139 157 EEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDL 209 (213)
Q Consensus 157 e~~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr~~l~~~~ 209 (213)
+...|+||+..-. |+.++.-=|-+||..||-..+...+.|||=..++..++
T Consensus 299 ~~~~CpvClk~r~--Nptvl~vSGyVfCY~Ci~~Yv~~~~~CPVT~~p~~v~~ 349 (357)
T KOG0826|consen 299 DREVCPVCLKKRQ--NPTVLEVSGYVFCYPCIFSYVVNYGHCPVTGYPASVDH 349 (357)
T ss_pred ccccChhHHhccC--CCceEEecceEEeHHHHHHHHHhcCCCCccCCcchHHH
Confidence 3457999999754 44555556999999999999999999999877776554
No 89
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=93.82 E-value=0.037 Score=48.35 Aligned_cols=43 Identities=26% Similarity=0.583 Sum_probs=34.3
Q ss_pred CCCccccccccccCCCCeEEcCc--CCeechhHHHHHHhcCCCccccccccc
Q 028139 157 EEDVCPTCLEEYDAENPRIITKC--EHHFHLACIFEWMERSDTCPVCNQEMI 206 (213)
Q Consensus 157 e~~~C~ICle~~~~~~~~~~l~C--gH~Fh~~CI~~Wl~~~~~CPvCr~~l~ 206 (213)
+-..||||.+.+.. -+.+| ||+.|..|-. +.++.||.||.+|.
T Consensus 47 ~lleCPvC~~~l~~----Pi~QC~nGHlaCssC~~---~~~~~CP~Cr~~~g 91 (299)
T KOG3002|consen 47 DLLDCPVCFNPLSP----PIFQCDNGHLACSSCRT---KVSNKCPTCRLPIG 91 (299)
T ss_pred hhccCchhhccCcc----cceecCCCcEehhhhhh---hhcccCCccccccc
Confidence 44569999998865 25678 8999999976 46888999999875
No 90
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=93.05 E-value=0.056 Score=46.85 Aligned_cols=49 Identities=29% Similarity=0.550 Sum_probs=35.5
Q ss_pred CccccccccccCCCCeEEcCcCCeechhHHHHHHhc-CCCcccc-cccccCCC
Q 028139 159 DVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMER-SDTCPVC-NQEMIFDL 209 (213)
Q Consensus 159 ~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~-~~~CPvC-r~~l~~~~ 209 (213)
..|+.|---. .++....-|+|.||.+||...|.. -..||.| |+.++.+.
T Consensus 275 LkCplc~~Ll--rnp~kT~cC~~~fc~eci~~al~dsDf~CpnC~rkdvlld~ 325 (427)
T COG5222 275 LKCPLCHCLL--RNPMKTPCCGHTFCDECIGTALLDSDFKCPNCSRKDVLLDG 325 (427)
T ss_pred ccCcchhhhh--hCcccCccccchHHHHHHhhhhhhccccCCCcccccchhhc
Confidence 5799987654 344555568999999999988754 5689999 55555443
No 91
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=92.59 E-value=0.028 Score=56.88 Aligned_cols=44 Identities=30% Similarity=0.638 Sum_probs=37.3
Q ss_pred CCccccccccccCCCCeEEcCcCCeechhHHHHHHhcCCCcccccc
Q 028139 158 EDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQ 203 (213)
Q Consensus 158 ~~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr~ 203 (213)
...|.||++.... -..+..|||.||..|+..|+..+..||+|+.
T Consensus 1153 ~~~c~ic~dil~~--~~~I~~cgh~~c~~c~~~~l~~~s~~~~~ks 1196 (1394)
T KOG0298|consen 1153 HFVCEICLDILRN--QGGIAGCGHEPCCRCDELWLYASSRCPICKS 1196 (1394)
T ss_pred ccchHHHHHHHHh--cCCeeeechhHhhhHHHHHHHHhccCcchhh
Confidence 3489999998753 2346779999999999999999999999974
No 92
>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=92.58 E-value=0.13 Score=40.64 Aligned_cols=33 Identities=21% Similarity=0.609 Sum_probs=22.3
Q ss_pred CCccccccccccCCCCeEEcCcC-------------CeechhHHHHHHh
Q 028139 158 EDVCPTCLEEYDAENPRIITKCE-------------HHFHLACIFEWME 193 (213)
Q Consensus 158 ~~~C~ICle~~~~~~~~~~l~Cg-------------H~Fh~~CI~~Wl~ 193 (213)
+..|+||||-- ...++|-|. -.-|.-|+++.-+
T Consensus 2 d~~CpICme~P---HNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkk 47 (162)
T PF07800_consen 2 DVTCPICMEHP---HNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKK 47 (162)
T ss_pred CccCceeccCC---CceEEEEeccccCCccccccCCccchhHHHHHHHH
Confidence 45799999953 335666663 2457889988654
No 93
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=91.91 E-value=0.087 Score=50.82 Aligned_cols=29 Identities=31% Similarity=0.853 Sum_probs=25.3
Q ss_pred CCeEEcCcCCeechhHHHHHHhcCCCccc
Q 028139 172 NPRIITKCEHHFHLACIFEWMERSDTCPV 200 (213)
Q Consensus 172 ~~~~~l~CgH~Fh~~CI~~Wl~~~~~CPv 200 (213)
-..++..|+|..|.+|.++|++....||-
T Consensus 1041 ss~~Cg~C~Hv~H~sc~~eWf~~gd~Cps 1069 (1081)
T KOG0309|consen 1041 SSNFCGTCGHVGHTSCMMEWFRTGDVCPS 1069 (1081)
T ss_pred cchhhccccccccHHHHHHHHhcCCcCCC
Confidence 34566789999999999999999999984
No 94
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=91.70 E-value=0.074 Score=45.10 Aligned_cols=51 Identities=24% Similarity=0.672 Sum_probs=35.6
Q ss_pred cCCCCccccccccccCCC-CeEEcCc-----CCeechhHHHHHHhcC--------CCcccccccc
Q 028139 155 IEEEDVCPTCLEEYDAEN-PRIITKC-----EHHFHLACIFEWMERS--------DTCPVCNQEM 205 (213)
Q Consensus 155 ~ee~~~C~ICle~~~~~~-~~~~l~C-----gH~Fh~~CI~~Wl~~~--------~~CPvCr~~l 205 (213)
.+.+..|=||+..=++.. ...+-|| .|-.|..|+..|+..+ -+||.|+.+.
T Consensus 17 ~e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEY 81 (293)
T KOG3053|consen 17 QELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEY 81 (293)
T ss_pred cccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchh
Confidence 356678999998632211 1134566 4889999999999543 3699999875
No 95
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=91.19 E-value=0.096 Score=51.30 Aligned_cols=40 Identities=28% Similarity=0.594 Sum_probs=32.3
Q ss_pred cccCCCCccccccccccCCCCeEEcCcCCeechhHHHHHHh
Q 028139 153 AVIEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWME 193 (213)
Q Consensus 153 ~~~ee~~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~ 193 (213)
...+-.+.|.||.-.+.. .+-.+.+|||.||..||.+-+.
T Consensus 812 ~v~ep~d~C~~C~~~ll~-~pF~vf~CgH~FH~~Cl~~~v~ 851 (911)
T KOG2034|consen 812 RVLEPQDSCDHCGRPLLI-KPFYVFPCGHCFHRDCLIRHVL 851 (911)
T ss_pred EEecCccchHHhcchhhc-CcceeeeccchHHHHHHHHHHH
Confidence 344667789999988754 4678899999999999998773
No 96
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=91.17 E-value=0.12 Score=50.18 Aligned_cols=53 Identities=32% Similarity=0.755 Sum_probs=40.9
Q ss_pred CCCCccccccccccCCCCeEEcCcC-----CeechhHHHHHHhcC--CCcccccccccCCC
Q 028139 156 EEEDVCPTCLEEYDAENPRIITKCE-----HHFHLACIFEWMERS--DTCPVCNQEMIFDL 209 (213)
Q Consensus 156 ee~~~C~ICle~~~~~~~~~~l~Cg-----H~Fh~~CI~~Wl~~~--~~CPvCr~~l~~~~ 209 (213)
++...|-||..+-..++++ .-||. -..|.+|+.+||+-+ .+|-+|+.++.+++
T Consensus 10 ~d~~~CRICr~e~~~d~pL-fhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~Fk~ 69 (1175)
T COG5183 10 EDKRSCRICRTEDIRDDPL-FHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKFKD 69 (1175)
T ss_pred ccchhceeecCCCCCCCcC-cccccccchhHHHHHHHHHHHHhcCCCcceeeecceeeeee
Confidence 4456799999987666665 34553 468999999999765 57999999988775
No 97
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=90.45 E-value=0.15 Score=44.07 Aligned_cols=49 Identities=29% Similarity=0.710 Sum_probs=36.9
Q ss_pred CCccccccccccCCCC-eEEcCcC-----CeechhHHHHHHh--cCCCccccccccc
Q 028139 158 EDVCPTCLEEYDAENP-RIITKCE-----HHFHLACIFEWME--RSDTCPVCNQEMI 206 (213)
Q Consensus 158 ~~~C~ICle~~~~~~~-~~~l~Cg-----H~Fh~~CI~~Wl~--~~~~CPvCr~~l~ 206 (213)
+..|-||.++....+. ....+|. +..|..|+..|+. .+..|.+|.....
T Consensus 78 ~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~ 134 (323)
T KOG1609|consen 78 GPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFI 134 (323)
T ss_pred CCcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhccccCeeeecccccce
Confidence 4679999997754332 4567773 6789999999997 5678999987553
No 98
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=89.59 E-value=0.13 Score=44.82 Aligned_cols=42 Identities=24% Similarity=0.645 Sum_probs=28.6
Q ss_pred ccccccccccCCCCeEEcCcCCeechhHHHHHHhcCCCcccccccc
Q 028139 160 VCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEM 205 (213)
Q Consensus 160 ~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr~~l 205 (213)
.|--|=-.+.. =-++.+|.|+||++|-.. ..-+.||.|...+
T Consensus 92 fCd~Cd~PI~I--YGRmIPCkHvFCl~CAr~--~~dK~Cp~C~d~V 133 (389)
T KOG2932|consen 92 FCDRCDFPIAI--YGRMIPCKHVFCLECARS--DSDKICPLCDDRV 133 (389)
T ss_pred eecccCCccee--eecccccchhhhhhhhhc--CccccCcCcccHH
Confidence 56666444322 135789999999999654 3356899996644
No 99
>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=88.82 E-value=0.55 Score=29.81 Aligned_cols=42 Identities=24% Similarity=0.589 Sum_probs=20.3
Q ss_pred ccccccccccCCCCeEEcCcCCeechhHHHHHHhc---C--CCccccccc
Q 028139 160 VCPTCLEEYDAENPRIITKCEHHFHLACIFEWMER---S--DTCPVCNQE 204 (213)
Q Consensus 160 ~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~---~--~~CPvCr~~ 204 (213)
.|+|....+. .+++...|.|.-|.+ +..||+. . =.||+|+++
T Consensus 4 ~CPls~~~i~--~P~Rg~~C~H~~CFD-l~~fl~~~~~~~~W~CPiC~~~ 50 (50)
T PF02891_consen 4 RCPLSFQRIR--IPVRGKNCKHLQCFD-LESFLESNQRTPKWKCPICNKP 50 (50)
T ss_dssp B-TTTSSB-S--SEEEETT--SS--EE-HHHHHHHHHHS---B-TTT---
T ss_pred eCCCCCCEEE--eCccCCcCcccceEC-HHHHHHHhhccCCeECcCCcCc
Confidence 5888888764 477888899984432 3445533 2 259999874
No 100
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.78 E-value=0.14 Score=48.56 Aligned_cols=42 Identities=21% Similarity=0.519 Sum_probs=32.1
Q ss_pred CccccccccccCC-CCeEEcCcCCeechhHHHHHHhcCCCcccccc
Q 028139 159 DVCPTCLEEYDAE-NPRIITKCEHHFHLACIFEWMERSDTCPVCNQ 203 (213)
Q Consensus 159 ~~C~ICle~~~~~-~~~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr~ 203 (213)
..|.||+..|.++ -..+.+.|||..|..|+..-..++ || |+.
T Consensus 12 l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~lyn~s--cp-~~~ 54 (861)
T KOG3161|consen 12 LLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLYNAS--CP-TKR 54 (861)
T ss_pred hhchHHHHHHHHHhcCcccccccchHHHHHHHhHhhcc--CC-CCc
Confidence 4699999988553 345678899999999999865554 88 543
No 101
>TIGR03602 streptolysinS bacteriocin protoxin, streptolysin S family. Members of this family are bacteriocin precursors. These small, ribosomally produced polypeptide precursors are extensively processed post-translationally. This family belongs to a class of heterocycle-containing bacteriocins, including streptolysin S from Streptococcus pyogenes, and related bacteriocins from Streptococcus iniae and Clostridium botulinum. Streptolysin S is hemolytic. Bacteriocin genes in general are small and highly diverse, with odd sequence composition, and are easily missed by many gene-finding programs.
Probab=88.78 E-value=0.13 Score=32.44 Aligned_cols=8 Identities=75% Similarity=2.469 Sum_probs=5.7
Q ss_pred CCccccCC
Q 028139 2 GGCCCCSS 9 (213)
Q Consensus 2 ~~~~~~~~ 9 (213)
||||||+-
T Consensus 24 ggcccccc 31 (56)
T TIGR03602 24 GGCCCCCC 31 (56)
T ss_pred CCeEEEec
Confidence 78887753
No 102
>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=88.53 E-value=0.85 Score=40.84 Aligned_cols=52 Identities=21% Similarity=0.634 Sum_probs=34.7
Q ss_pred CCCCccccccccccCCCCeEEc----------------C-----cCCeechhHHHHHHhc-------------CCCcccc
Q 028139 156 EEEDVCPTCLEEYDAENPRIIT----------------K-----CEHHFHLACIFEWMER-------------SDTCPVC 201 (213)
Q Consensus 156 ee~~~C~ICle~~~~~~~~~~l----------------~-----CgH~Fh~~CI~~Wl~~-------------~~~CPvC 201 (213)
++.+.|--|+..- .+.++.- + |.=.+|.+|+-+|+-. +-.||.|
T Consensus 269 ~e~e~CigC~~~~--~~vkl~k~C~~~~~~g~~~~~~~~C~~C~CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtC 346 (358)
T PF10272_consen 269 QELEPCIGCMQAQ--PNVKLVKRCADEEQEGSPLPNEPPCQQCYCRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTC 346 (358)
T ss_pred cccCCccccccCC--CCcEEEeccCCcccCCcccccCCCCccccccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCC
Confidence 6777899999753 1222221 2 2345689999999943 3579999
Q ss_pred cccccCCC
Q 028139 202 NQEMIFDL 209 (213)
Q Consensus 202 r~~l~~~~ 209 (213)
|+.+..-|
T Consensus 347 Ra~FCilD 354 (358)
T PF10272_consen 347 RAKFCILD 354 (358)
T ss_pred cccceeee
Confidence 99876543
No 103
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.39 E-value=0.15 Score=46.04 Aligned_cols=38 Identities=29% Similarity=0.645 Sum_probs=29.0
Q ss_pred CCcccccc-ccccCCCCeEEcCcCCeechhHHHHHHhcC
Q 028139 158 EDVCPTCL-EEYDAENPRIITKCEHHFHLACIFEWMERS 195 (213)
Q Consensus 158 ~~~C~ICl-e~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~~ 195 (213)
...|.||+ +....+.-..+..|+|.||..|+.+-++.+
T Consensus 146 ~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~ 184 (384)
T KOG1812|consen 146 KEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVK 184 (384)
T ss_pred cccCccCccccccHhhhHHHhcccchhhhHHhHHHhhhh
Confidence 45799999 444443444478899999999999988754
No 104
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=87.43 E-value=0.19 Score=47.54 Aligned_cols=43 Identities=28% Similarity=0.748 Sum_probs=29.9
Q ss_pred CCCcccccccc-----ccCCCCeEEcCcCCeechhHHHHHHhcCCCccccc
Q 028139 157 EEDVCPTCLEE-----YDAENPRIITKCEHHFHLACIFEWMERSDTCPVCN 202 (213)
Q Consensus 157 e~~~C~ICle~-----~~~~~~~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr 202 (213)
....|.||... |..++......|++.||.+|+.. .+.-||.|-
T Consensus 510 ~gfiCe~Cq~~~iiyPF~~~~~~rC~~C~avfH~~C~~r---~s~~CPrC~ 557 (580)
T KOG1829|consen 510 KGFICELCQHNDIIYPFETRNTRRCSTCLAVFHKKCLRR---KSPCCPRCE 557 (580)
T ss_pred CeeeeeeccCCCcccccccccceeHHHHHHHHHHHHHhc---cCCCCCchH
Confidence 45578888432 33455667788999999999554 344499993
No 105
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=86.37 E-value=1 Score=29.17 Aligned_cols=47 Identities=19% Similarity=0.575 Sum_probs=34.0
Q ss_pred CCCcccccccccc-CCCCeEEcCcCCeechhHHHHHHhcCCCccc--ccccccC
Q 028139 157 EEDVCPTCLEEYD-AENPRIITKCEHHFHLACIFEWMERSDTCPV--CNQEMIF 207 (213)
Q Consensus 157 e~~~C~ICle~~~-~~~~~~~l~CgH~Fh~~CI~~Wl~~~~~CPv--Cr~~l~~ 207 (213)
+...|++|-+.|. .++-++...||--||..|..+ ...|-+ |...+.+
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~----~g~C~~~~c~~~~~~ 53 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK----AGGCINYSCGTGFEW 53 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCCCcccHHHHhh----CCceEeccCCCCccc
Confidence 3456999999996 445566677999999999654 566765 6655443
No 106
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=86.30 E-value=0.35 Score=45.65 Aligned_cols=49 Identities=35% Similarity=0.775 Sum_probs=40.7
Q ss_pred CCCCccccccccccCCCCeEEcCcCCeechhHHHHHHhcCCCcccccccccCCCCC
Q 028139 156 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDLPV 211 (213)
Q Consensus 156 ee~~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr~~l~~~~~~ 211 (213)
+..+.|.||+++. ....++|. |.-|+.+|+-.+..||+|.+.+..++..
T Consensus 477 ~~~~~~~~~~~~~----~~~~~~~~---~~~~l~~~~~~~~~~pl~~~~~~~~~~~ 525 (543)
T KOG0802|consen 477 EPNDVCAICYQEM----SARITPCS---HALCLRKWLYVQEVCPLCHTYMKEDDFL 525 (543)
T ss_pred cccCcchHHHHHH----Hhcccccc---chhHHHhhhhhccccCCCchhhhccccc
Confidence 4557799999987 24566777 9999999999999999999998887754
No 107
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=85.96 E-value=0.55 Score=41.13 Aligned_cols=45 Identities=27% Similarity=0.547 Sum_probs=37.9
Q ss_pred CccccccccccCCCCeEEcCcCCeechhHHHHHHhc---CCCcccccc
Q 028139 159 DVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMER---SDTCPVCNQ 203 (213)
Q Consensus 159 ~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~---~~~CPvCr~ 203 (213)
..||+=-|.-..+|++.++.|||+.-++=++..-++ +-+||+|--
T Consensus 337 FiCPVlKe~~t~ENpP~ml~CgHVIskeal~~LS~nG~~~FKCPYCP~ 384 (396)
T COG5109 337 FICPVLKELCTDENPPVMLECGHVISKEALSVLSQNGVLSFKCPYCPE 384 (396)
T ss_pred eeccccHhhhcccCCCeeeeccceeeHHHHHHHhhcCcEEeeCCCCCc
Confidence 489999998899999999999999999888885544 247999954
No 108
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.57 E-value=0.47 Score=39.28 Aligned_cols=40 Identities=25% Similarity=0.575 Sum_probs=29.4
Q ss_pred cccccccccCCCCeEEcCcCC-eechhHHHHHHhcCCCcccccccccC
Q 028139 161 CPTCLEEYDAENPRIITKCEH-HFHLACIFEWMERSDTCPVCNQEMIF 207 (213)
Q Consensus 161 C~ICle~~~~~~~~~~l~CgH-~Fh~~CI~~Wl~~~~~CPvCr~~l~~ 207 (213)
|-+|-+. +..+.++||.| .+|..|=.. -..||+|+.....
T Consensus 161 Cr~C~~~---~~~VlllPCrHl~lC~~C~~~----~~~CPiC~~~~~s 201 (207)
T KOG1100|consen 161 CRKCGER---EATVLLLPCRHLCLCGICDES----LRICPICRSPKTS 201 (207)
T ss_pred ceecCcC---CceEEeecccceEeccccccc----CccCCCCcChhhc
Confidence 8888874 44588999988 678888433 4569999876543
No 109
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.55 E-value=0.61 Score=40.27 Aligned_cols=35 Identities=23% Similarity=0.544 Sum_probs=28.5
Q ss_pred CCCeEEcCcCCeechhHHHHHHhcC-CCcccccccc
Q 028139 171 ENPRIITKCEHHFHLACIFEWMERS-DTCPVCNQEM 205 (213)
Q Consensus 171 ~~~~~~l~CgH~Fh~~CI~~Wl~~~-~~CPvCr~~l 205 (213)
...+..+.|||.|+..|+.+-+... ..||.||...
T Consensus 19 ~~~p~~l~c~h~~c~~c~~~l~~~~~i~cpfcR~~~ 54 (296)
T KOG4185|consen 19 DHIPRVLKCGHTICQNCASKLLGNSRILCPFCRETT 54 (296)
T ss_pred ccCCcccccCceehHhHHHHHhcCceeeccCCCCcc
Confidence 3345678899999999999988664 5799999984
No 110
>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]
Probab=85.41 E-value=0.45 Score=46.25 Aligned_cols=44 Identities=20% Similarity=0.574 Sum_probs=34.2
Q ss_pred CccccccccccC-C---CCeEEcCcCCeechhHHHHHHhcCCCcccccc
Q 028139 159 DVCPTCLEEYDA-E---NPRIITKCEHHFHLACIFEWMERSDTCPVCNQ 203 (213)
Q Consensus 159 ~~C~ICle~~~~-~---~~~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr~ 203 (213)
..|.-|++.... + +..+++.|||.||+.|+.--+.+++ |-.|..
T Consensus 785 ~rc~~c~~~~l~~~~~~~~~~v~~c~h~yhk~c~~~~~~~~~-~~~~~~ 832 (846)
T KOG2066|consen 785 ERCSSCFEPNLPSGAAFDSVVVFHCGHMYHKECLMMESLRNA-CNIESG 832 (846)
T ss_pred hhhhhhcccccccCcccceeeEEEccchhhhcccccHHHhcc-cChhhc
Confidence 369999998743 2 4678899999999999998887766 666643
No 111
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=84.91 E-value=0.2 Score=48.06 Aligned_cols=44 Identities=30% Similarity=0.764 Sum_probs=35.7
Q ss_pred CccccccccccCCCCeEEcCcCCeechhHHHHHHhcC---CCcccccccc
Q 028139 159 DVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERS---DTCPVCNQEM 205 (213)
Q Consensus 159 ~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~~---~~CPvCr~~l 205 (213)
..|+||++.|.. .+.++|.|.|+..|+..-|... ..||+|+..+
T Consensus 22 lEc~ic~~~~~~---p~~~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~ 68 (684)
T KOG4362|consen 22 LECPICLEHVKE---PSLLKCDHIFLKFCLNKLFESKKGPKQCALCKSDI 68 (684)
T ss_pred ccCCceeEEeec---cchhhhhHHHHhhhhhceeeccCccccchhhhhhh
Confidence 459999999866 3789999999999998877554 4699998543
No 112
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=84.48 E-value=0.5 Score=46.03 Aligned_cols=49 Identities=16% Similarity=0.281 Sum_probs=34.2
Q ss_pred CCCccccccccccC----CCCeEEcCcCCeechhHHHHHHhc------CCCcccccccc
Q 028139 157 EEDVCPTCLEEYDA----ENPRIITKCEHHFHLACIFEWMER------SDTCPVCNQEM 205 (213)
Q Consensus 157 e~~~C~ICle~~~~----~~~~~~l~CgH~Fh~~CI~~Wl~~------~~~CPvCr~~l 205 (213)
+.+.|.||.-++.. -....+-.|+|.||..||..|+.+ .-.|+.|..-|
T Consensus 95 ~s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci 153 (1134)
T KOG0825|consen 95 ESDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESEKHTAHYFCEECV 153 (1134)
T ss_pred cccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhccccccccccHHHHh
Confidence 44578888888755 122234459999999999999954 34578886543
No 113
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=84.19 E-value=0.75 Score=37.85 Aligned_cols=42 Identities=24% Similarity=0.723 Sum_probs=31.6
Q ss_pred CCCcccccccc-----ccCCCCeEEcCcCCeechhHHHHHHhcCCCcccccc
Q 028139 157 EEDVCPTCLEE-----YDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQ 203 (213)
Q Consensus 157 e~~~C~ICle~-----~~~~~~~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr~ 203 (213)
.+..|-||-+. |+.++......|+-.||..|.. +..||-|..
T Consensus 151 kGfiCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~~C~~-----~~~CpkC~R 197 (202)
T PF13901_consen 151 KGFICEICNSDDIIFPFQIDTTVRCPKCKSVFHKSCFR-----KKSCPKCAR 197 (202)
T ss_pred CCCCCccCCCCCCCCCCCCCCeeeCCcCccccchhhcC-----CCCCCCcHh
Confidence 45678888753 4555667778899999999976 267999943
No 114
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=83.14 E-value=0.91 Score=34.90 Aligned_cols=51 Identities=22% Similarity=0.408 Sum_probs=36.7
Q ss_pred CCCccccccccccCCCCeEEcC---cCCeechhHHHHHHhc---CCCcccccccccCCC
Q 028139 157 EEDVCPTCLEEYDAENPRIITK---CEHHFHLACIFEWMER---SDTCPVCNQEMIFDL 209 (213)
Q Consensus 157 e~~~C~ICle~~~~~~~~~~l~---CgH~Fh~~CI~~Wl~~---~~~CPvCr~~l~~~~ 209 (213)
.--.|-||.|.-..+. .+-| ||-..|..|.....+. ..+||+|+..+....
T Consensus 79 ~lYeCnIC~etS~ee~--FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKss~ 135 (140)
T PF05290_consen 79 KLYECNICKETSAEER--FLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKSSS 135 (140)
T ss_pred CceeccCcccccchhh--cCCcccccchHHHHHHHHHHHHHcccCCCCCcccccccccc
Confidence 3457999999765432 2222 8999999988775554 478999999886654
No 115
>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 KOG3899 consensus Uncharacterized conserved protein [Function unknown]
Probab=81.12 E-value=0.72 Score=40.02 Aligned_cols=31 Identities=19% Similarity=0.563 Sum_probs=23.7
Q ss_pred cCCeechhHHHHHHh-------------cCCCcccccccccCCC
Q 028139 179 CEHHFHLACIFEWME-------------RSDTCPVCNQEMIFDL 209 (213)
Q Consensus 179 CgH~Fh~~CI~~Wl~-------------~~~~CPvCr~~l~~~~ 209 (213)
|.-.+|.+|+.+|+. .+-+||.||+.+...+
T Consensus 325 crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fci~d 368 (381)
T KOG3899|consen 325 CRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFCIRD 368 (381)
T ss_pred cccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceEEee
Confidence 456778999998883 3568999999886554
No 117
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=79.59 E-value=1.7 Score=42.28 Aligned_cols=46 Identities=17% Similarity=0.330 Sum_probs=33.8
Q ss_pred ccccccccccCCCCeEEcCcCCeechhHHHHHHhcCCCccc--cccccc
Q 028139 160 VCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPV--CNQEMI 206 (213)
Q Consensus 160 ~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~~~~CPv--Cr~~l~ 206 (213)
.|.+|-..+. |.-+....|||.-|.+|+++|+.....||. |-..--
T Consensus 781 ~CtVC~~vi~-G~~~~c~~C~H~gH~sh~~sw~~~~s~ca~~~C~~~c~ 828 (839)
T KOG0269|consen 781 KCTVCDLVIR-GVDVWCQVCGHGGHDSHLKSWFFKASPCAKSICPHLCH 828 (839)
T ss_pred Cceeecceee-eeEeecccccccccHHHHHHHHhcCCCCccccCCcccc
Confidence 5788866543 222445669999999999999999988877 655433
No 118
>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=78.80 E-value=1.2 Score=27.84 Aligned_cols=43 Identities=23% Similarity=0.533 Sum_probs=29.7
Q ss_pred ccccccccccCCCCeEEcCcCCeechhHHHHHHhc------CCCccccc
Q 028139 160 VCPTCLEEYDAENPRIITKCEHHFHLACIFEWMER------SDTCPVCN 202 (213)
Q Consensus 160 ~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~------~~~CPvCr 202 (213)
.|.||......+.-+..-.|+..||..|+..=.+. .=.||.|+
T Consensus 1 ~C~vC~~~~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~ 49 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCR 49 (51)
T ss_dssp EBTTTTSSCTTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHH
T ss_pred eCcCCCCcCCCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCc
Confidence 48899985555555555779999999998765431 23577775
No 119
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=78.15 E-value=1.2 Score=40.88 Aligned_cols=38 Identities=26% Similarity=0.565 Sum_probs=31.4
Q ss_pred CCCCccccccccccCCCCeEEcCcCCeechhHHHHHHhcC
Q 028139 156 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERS 195 (213)
Q Consensus 156 ee~~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~~ 195 (213)
.....|.||.+.+.. ..+.+.|||.||..|+..-+.++
T Consensus 68 ~~~~~c~ic~~~~~~--~~~~~~c~H~~c~~cw~~yl~~k 105 (444)
T KOG1815|consen 68 KGDVQCGICVESYDG--EIIGLGCGHPFCPPCWTGYLGTK 105 (444)
T ss_pred CccccCCcccCCCcc--hhhhcCCCcHHHHHHHHHHhhhe
Confidence 344679999999865 56778999999999999988664
No 120
>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=76.34 E-value=0.92 Score=38.33 Aligned_cols=47 Identities=23% Similarity=0.639 Sum_probs=34.3
Q ss_pred CCccccccccc-cCCCCeEE-cC-cCCeechhHHHHHHhcC-CCcc--ccccc
Q 028139 158 EDVCPTCLEEY-DAENPRII-TK-CEHHFHLACIFEWMERS-DTCP--VCNQE 204 (213)
Q Consensus 158 ~~~C~ICle~~-~~~~~~~~-l~-CgH~Fh~~CI~~Wl~~~-~~CP--vCr~~ 204 (213)
+..||||..+- -..+-+++ -| |=|..|.+|++.-+.+. .-|| -|.+-
T Consensus 10 d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kI 62 (314)
T COG5220 10 DRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKI 62 (314)
T ss_pred cccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHH
Confidence 34799999764 33343333 34 99999999999999775 5699 78663
No 121
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 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 FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=74.11 E-value=2.1 Score=28.56 Aligned_cols=38 Identities=16% Similarity=0.307 Sum_probs=20.2
Q ss_pred cCCCCccccccccccCCCCe-EEcCcCCeechhHHHHHH
Q 028139 155 IEEEDVCPTCLEEYDAENPR-IITKCEHHFHLACIFEWM 192 (213)
Q Consensus 155 ~ee~~~C~ICle~~~~~~~~-~~l~CgH~Fh~~CI~~Wl 192 (213)
+.+...|.+|...|..-... ..-.||++||..|....+
T Consensus 6 d~~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~~~ 44 (69)
T PF01363_consen 6 DSEASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQRI 44 (69)
T ss_dssp GGG-SB-TTT--B-BSSS-EEE-TTT--EEECCCS-EEE
T ss_pred CCCCCcCcCcCCcCCCceeeEccCCCCCEECCchhCCEE
Confidence 35567899999999664333 346699999999987654
No 122
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=73.96 E-value=1.6 Score=37.72 Aligned_cols=48 Identities=23% Similarity=0.627 Sum_probs=35.6
Q ss_pred CCCCccccccccccCCCCeEEcCc----CCeechhHHHHHHhcC-----------CCccccccccc
Q 028139 156 EEEDVCPTCLEEYDAENPRIITKC----EHHFHLACIFEWMERS-----------DTCPVCNQEMI 206 (213)
Q Consensus 156 ee~~~C~ICle~~~~~~~~~~l~C----gH~Fh~~CI~~Wl~~~-----------~~CPvCr~~l~ 206 (213)
.....|.+|.|.+++.+ ..+| .|.||.-|-++-+++. .+||+=...|.
T Consensus 266 ~apLcCTLC~ERLEDTH---FVQCPSVp~HKFCFPCSResIK~Qg~sgevYCPSGdkCPLvgS~vP 328 (352)
T KOG3579|consen 266 SAPLCCTLCHERLEDTH---FVQCPSVPSHKFCFPCSRESIKQQGASGEVYCPSGDKCPLVGSNVP 328 (352)
T ss_pred CCceeehhhhhhhccCc---eeecCCCcccceecccCHHHHHhhcCCCceeCCCCCcCcccCCccc
Confidence 34468999999987633 4457 7999999999999874 46776655443
No 123
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=73.78 E-value=1.7 Score=39.29 Aligned_cols=42 Identities=26% Similarity=0.628 Sum_probs=30.7
Q ss_pred Cccccccccc---cCCCCeEEcCcCCeechhHHHHHHhcCCCcccc
Q 028139 159 DVCPTCLEEY---DAENPRIITKCEHHFHLACIFEWMERSDTCPVC 201 (213)
Q Consensus 159 ~~C~ICle~~---~~~~~~~~l~CgH~Fh~~CI~~Wl~~~~~CPvC 201 (213)
..|++|.-.+ ..-+..... |||.||..|...|......|.-|
T Consensus 307 r~CpkC~~~ie~~~GCnhm~Cr-C~~~fcy~C~~~~~~~~~~~~~~ 351 (384)
T KOG1812|consen 307 RQCPKCKFMIELSEGCNHMTCR-CGHQFCYMCGGDWKTHNGECYEC 351 (384)
T ss_pred CcCcccceeeeecCCcceEEee-ccccchhhcCcchhhCCccccCc
Confidence 3477776554 333455555 99999999999998888777555
No 124
>KOG2068 consensus MOT2 transcription factor [Transcription]
Probab=72.51 E-value=3 Score=36.78 Aligned_cols=50 Identities=22% Similarity=0.533 Sum_probs=39.1
Q ss_pred CccccccccccC-CCCeEEcCcCCeechhHHHHHHhcCCCcccccccccCC
Q 028139 159 DVCPTCLEEYDA-ENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFD 208 (213)
Q Consensus 159 ~~C~ICle~~~~-~~~~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr~~l~~~ 208 (213)
..|+||-+.... ....+-.+|+|..|+.|...-......||.||+.....
T Consensus 250 ~s~p~~~~~~~~~d~~~lP~~~~~~~~l~~~~t~~~~~~~~~~~rk~~~~~ 300 (327)
T KOG2068|consen 250 PSCPICYEDLDLTDSNFLPCPCGFRLCLFCHKTISDGDGRCPGCRKPYERN 300 (327)
T ss_pred CCCCCCCCcccccccccccccccccchhhhhhcccccCCCCCccCCccccC
Confidence 479999998733 33444566899999999988888899999999876543
No 125
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=71.33 E-value=2.1 Score=27.38 Aligned_cols=42 Identities=26% Similarity=0.618 Sum_probs=21.0
Q ss_pred cccccccccCC-------CCeEEcCcCCeechhHHHHHHhcCCCccccc
Q 028139 161 CPTCLEEYDAE-------NPRIITKCEHHFHLACIFEWMERSDTCPVCN 202 (213)
Q Consensus 161 C~ICle~~~~~-------~~~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr 202 (213)
|--|+..|... .......|+++||.+|=.---+.=.+||-|-
T Consensus 2 CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHE~LH~CPGC~ 50 (51)
T PF07975_consen 2 CFGCQKPFPDGPEKKADSSRYRCPKCKNHFCIDCDVFIHETLHNCPGCE 50 (51)
T ss_dssp ETTTTEE-TTS-------EEE--TTTT--B-HHHHHTTTTTS-SSSTT-
T ss_pred CccCCCCCCCcccccccCCeEECCCCCCccccCcChhhhccccCCcCCC
Confidence 44566666443 2234577999999999443334456799883
No 126
>KOG3005 consensus GIY-YIG type nuclease [General function prediction only]
Probab=67.79 E-value=1.1 Score=38.36 Aligned_cols=51 Identities=24% Similarity=0.483 Sum_probs=35.1
Q ss_pred CccccccccccCCCCeEE----cCcCCeechhHHHHHH-hc--------CCCcccccccccCCC
Q 028139 159 DVCPTCLEEYDAENPRII----TKCEHHFHLACIFEWM-ER--------SDTCPVCNQEMIFDL 209 (213)
Q Consensus 159 ~~C~ICle~~~~~~~~~~----l~CgH~Fh~~CI~~Wl-~~--------~~~CPvCr~~l~~~~ 209 (213)
..|-||..++......+. ..|+-++|..|+..-+ .. ...||.|++.+.+.+
T Consensus 183 ~~celc~~ei~e~~~~~a~c~~~~c~~~~h~~CLa~~~~~~e~g~~~p~eg~cp~C~~~~~w~~ 246 (276)
T KOG3005|consen 183 VECELCEKEILETDWSRATCPNPDCDSLNHLTCLAEELLEVEPGQLIPLEGMCPKCEKFLSWTT 246 (276)
T ss_pred hhhHHHHHHhccccceeccCCCCCCCchhhhhhhhHHHhccCCCceeccCCCCCchhceeeHHH
Confidence 479999999943222211 3388899999999833 22 378999999765433
No 127
>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=66.68 E-value=0.7 Score=31.57 Aligned_cols=40 Identities=28% Similarity=0.665 Sum_probs=21.3
Q ss_pred CccccccccccCCCCeEEcCcCCeechhHHHHHHhcCCCccccccccc
Q 028139 159 DVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMI 206 (213)
Q Consensus 159 ~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr~~l~ 206 (213)
..||+|..++.... +|.+|..|-.. ++....||-|.++|.
T Consensus 2 ~~CP~C~~~L~~~~-------~~~~C~~C~~~-~~~~a~CPdC~~~Le 41 (70)
T PF07191_consen 2 NTCPKCQQELEWQG-------GHYHCEACQKD-YKKEAFCPDCGQPLE 41 (70)
T ss_dssp -B-SSS-SBEEEET-------TEEEETTT--E-EEEEEE-TTT-SB-E
T ss_pred CcCCCCCCccEEeC-------CEEECcccccc-ceecccCCCcccHHH
Confidence 35999988754321 66777777554 455677999988763
No 128
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=65.96 E-value=4.2 Score=23.91 Aligned_cols=25 Identities=32% Similarity=0.873 Sum_probs=16.8
Q ss_pred ccccccccccCCC--------CeEEcCcCCeec
Q 028139 160 VCPTCLEEYDAEN--------PRIITKCEHHFH 184 (213)
Q Consensus 160 ~C~ICle~~~~~~--------~~~~l~CgH~Fh 184 (213)
.|+-|.-.|...+ .+....|+|.|+
T Consensus 4 ~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f~ 36 (36)
T PF13717_consen 4 TCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVFF 36 (36)
T ss_pred ECCCCCCEEeCCHHHCCCCCcEEECCCCCCEeC
Confidence 4888888886543 345567888874
No 129
>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=65.40 E-value=2 Score=38.75 Aligned_cols=43 Identities=30% Similarity=0.678 Sum_probs=0.0
Q ss_pred CccccccccccC-----------CCCeEEcCcCCeechhHHHHHHhc------CCCccccccc
Q 028139 159 DVCPTCLEEYDA-----------ENPRIITKCEHHFHLACIFEWMER------SDTCPVCNQE 204 (213)
Q Consensus 159 ~~C~ICle~~~~-----------~~~~~~l~CgH~Fh~~CI~~Wl~~------~~~CPvCr~~ 204 (213)
.-||+=|....- ..+-+-+.|||++.. ..|-.. ..+||+||+.
T Consensus 278 pQCPVglnTL~fp~~~~~~~~~~~qP~VYl~CGHVhG~---h~Wg~~~~~~~~~r~CPlCr~~ 337 (416)
T PF04710_consen 278 PQCPVGLNTLVFPSKSRKDVPDERQPWVYLNCGHVHGY---HNWGQDSDRDPRSRTCPLCRQV 337 (416)
T ss_dssp ---------------------------------------------------------------
T ss_pred CCCCcCCCccccccccccccccccCceeeccccceeee---cccccccccccccccCCCcccc
Confidence 347776655421 235566899998875 467632 4689999985
No 130
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=64.51 E-value=2.3 Score=37.04 Aligned_cols=48 Identities=23% Similarity=0.615 Sum_probs=38.1
Q ss_pred CCCCccccccccccCCCCeEEcCcCCeechhHHHHHHhcCCCcccccccc
Q 028139 156 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEM 205 (213)
Q Consensus 156 ee~~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr~~l 205 (213)
...+.|-||.--|.... ....|+|.|+..|...|.++.+.||.|+...
T Consensus 103 ~~~~~~~~~~g~l~vpt--~~qg~w~qf~~~~p~~~~~~~~~~~d~~~~~ 150 (324)
T KOG0824|consen 103 QDHDICYICYGKLTVPT--RIQGCWHQFCYVCPKSNFAMGNDCPDCRGKI 150 (324)
T ss_pred CCccceeeeeeeEEecc--cccCceeeeeecCCchhhhhhhccchhhcCc
Confidence 45567899988775522 2344999999999999999999999998754
No 132
>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]
Probab=64.09 E-value=3.5 Score=34.20 Aligned_cols=44 Identities=25% Similarity=0.580 Sum_probs=35.0
Q ss_pred CCccccccccccCCCCeEEcCcCCeechhHHHHHHhcCCCcccccc
Q 028139 158 EDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQ 203 (213)
Q Consensus 158 ~~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr~ 203 (213)
-..|.+|-+-.-.+ ...-.||-.||..||...+++...||.|..
T Consensus 181 lk~Cn~Ch~LvIqg--~rCg~c~i~~h~~c~qty~q~~~~cphc~d 224 (235)
T KOG4718|consen 181 LKNCNLCHCLVIQG--IRCGSCNIQYHRGCIQTYLQRRDICPHCGD 224 (235)
T ss_pred HHHHhHhHHHhhee--eccCcccchhhhHHHHHHhcccCcCCchhc
Confidence 34799998865332 445668889999999999999999999954
No 133
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=61.90 E-value=10 Score=28.34 Aligned_cols=44 Identities=20% Similarity=0.476 Sum_probs=34.7
Q ss_pred CccccccccccCC-----------CCeEEcCcCCeechhHHHHHHhcCCCccccc
Q 028139 159 DVCPTCLEEYDAE-----------NPRIITKCEHHFHLACIFEWMERSDTCPVCN 202 (213)
Q Consensus 159 ~~C~ICle~~~~~-----------~~~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr 202 (213)
..|--|+..|... ..-....|++.||.+|=.-|-+.=..||-|.
T Consensus 56 ~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~CPGC~ 110 (112)
T TIGR00622 56 RFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHESLHCCPGCI 110 (112)
T ss_pred CcccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhhccCCcCCC
Confidence 4599999988542 1123578999999999888888888899995
No 134
>PRK05978 hypothetical protein; Provisional
Probab=60.72 E-value=5.3 Score=31.36 Aligned_cols=36 Identities=25% Similarity=0.680 Sum_probs=27.3
Q ss_pred ccccccccccCCCCeEEcCcCCeechhHHHHHHhcCCCcccccccccCCCCCCC
Q 028139 160 VCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDLPVDY 213 (213)
Q Consensus 160 ~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr~~l~~~~~~~~ 213 (213)
.||-|-+ |+.|+ .+|+.+..||.|...+...+.-||
T Consensus 35 rCP~CG~-------------G~LF~-----g~Lkv~~~C~~CG~~~~~~~a~Dg 70 (148)
T PRK05978 35 RCPACGE-------------GKLFR-----AFLKPVDHCAACGEDFTHHRADDL 70 (148)
T ss_pred cCCCCCC-------------Ccccc-----cccccCCCccccCCccccCCcccc
Confidence 4887765 45565 788999999999999877765543
No 135
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=60.48 E-value=6.1 Score=23.28 Aligned_cols=25 Identities=28% Similarity=0.745 Sum_probs=16.6
Q ss_pred ccccccccccCCC--------CeEEcCcCCeec
Q 028139 160 VCPTCLEEYDAEN--------PRIITKCEHHFH 184 (213)
Q Consensus 160 ~C~ICle~~~~~~--------~~~~l~CgH~Fh 184 (213)
.||-|...|...+ .+....|+|.|.
T Consensus 4 ~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 4 TCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred ECCCCCceEEcCHHHcccCCcEEECCCCCcEee
Confidence 4888888875532 345566788775
No 136
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=60.24 E-value=7.6 Score=28.97 Aligned_cols=46 Identities=22% Similarity=0.568 Sum_probs=30.6
Q ss_pred CCCcccccccccc--CCCCeEEcCcCCeechhHHHHHHhcCC--Ccccccc
Q 028139 157 EEDVCPTCLEEYD--AENPRIITKCEHHFHLACIFEWMERSD--TCPVCNQ 203 (213)
Q Consensus 157 e~~~C~ICle~~~--~~~~~~~l~CgH~Fh~~CI~~Wl~~~~--~CPvCr~ 203 (213)
.+..|.+|...|. .........|.|.+|..|-.. ..... .|-+|.+
T Consensus 53 ~~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~-~~~~~~WlC~vC~k 102 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVY-SKKEPIWLCKVCQK 102 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEE-TSSSCCEEEHHHHH
T ss_pred CCcchhhhCCcccccCCCCCcCCcCCccccCccCCc-CCCCCCEEChhhHH
Confidence 4568999999873 344677889999999999655 11111 4888865
No 137
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=59.26 E-value=5.3 Score=21.79 Aligned_cols=23 Identities=26% Similarity=0.681 Sum_probs=12.5
Q ss_pred ccccccccccCCCCeEEcCcCCee
Q 028139 160 VCPTCLEEYDAENPRIITKCEHHF 183 (213)
Q Consensus 160 ~C~ICle~~~~~~~~~~l~CgH~F 183 (213)
.||-|-.++.... .....|||.|
T Consensus 2 ~CP~C~~~V~~~~-~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCPECGAEVPESA-KFCPHCGYDF 24 (26)
T ss_pred cCCCCcCCchhhc-CcCCCCCCCC
Confidence 3777776663322 2344467766
No 138
>KOG3113 consensus Uncharacterized conserved protein [Function unknown]
Probab=58.08 E-value=9.2 Score=32.66 Aligned_cols=51 Identities=20% Similarity=0.324 Sum_probs=36.3
Q ss_pred CCCccccccccccCCCC-eEEcCcCCeechhHHHHHHhcCCCcccccccccCCC
Q 028139 157 EEDVCPTCLEEYDAENP-RIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDL 209 (213)
Q Consensus 157 e~~~C~ICle~~~~~~~-~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr~~l~~~~ 209 (213)
....|||=--++..... ..+-.|||+|-..=+.+- ...+|++|.+.+..++
T Consensus 110 a~fiCPvtgleMng~~~F~~l~~CGcV~SerAlKei--kas~C~~C~a~y~~~d 161 (293)
T KOG3113|consen 110 ARFICPVTGLEMNGKYRFCALRCCGCVFSERALKEI--KASVCHVCGAAYQEDD 161 (293)
T ss_pred ceeecccccceecceEEEEEEeccceeccHHHHHHh--hhccccccCCcccccC
Confidence 44589987666644332 345679999999887774 3678999998876655
No 139
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=57.85 E-value=5.3 Score=26.37 Aligned_cols=14 Identities=29% Similarity=0.883 Sum_probs=11.2
Q ss_pred CCCcccccccccCC
Q 028139 195 SDTCPVCNQEMIFD 208 (213)
Q Consensus 195 ~~~CPvCr~~l~~~ 208 (213)
..+||+|+.+|...
T Consensus 39 ~p~CPlC~s~M~~~ 52 (59)
T PF14169_consen 39 EPVCPLCKSPMVSG 52 (59)
T ss_pred CccCCCcCCccccc
Confidence 47899999988654
No 140
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=56.22 E-value=7.9 Score=21.48 Aligned_cols=29 Identities=21% Similarity=0.476 Sum_probs=11.5
Q ss_pred ccccccccccCCCCeEEcCcCCeechhHH
Q 028139 160 VCPTCLEEYDAENPRIITKCEHHFHLACI 188 (213)
Q Consensus 160 ~C~ICle~~~~~~~~~~l~CgH~Fh~~CI 188 (213)
.|.+|.+....+..-....|.-.+|..|+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~Cdf~lH~~Ca 30 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSECDFDLHEECA 30 (30)
T ss_dssp --TTTS----S--EEE-TTT-----HHHH
T ss_pred cCCcCCCcCCCCceEECccCCCccChhcC
Confidence 48888887755444566889999999986
No 141
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=55.42 E-value=11 Score=32.15 Aligned_cols=35 Identities=23% Similarity=0.333 Sum_probs=29.3
Q ss_pred CCCCccccccccccCCCCeEEcCcCCeechhHHHHHHh
Q 028139 156 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWME 193 (213)
Q Consensus 156 ee~~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~ 193 (213)
..-+.|..||..+.. +++++=||+|+.+||.+.+-
T Consensus 41 K~FdcCsLtLqPc~d---Pvit~~GylfdrEaILe~il 75 (303)
T KOG3039|consen 41 KPFDCCSLTLQPCRD---PVITPDGYLFDREAILEYIL 75 (303)
T ss_pred CCcceeeeecccccC---CccCCCCeeeeHHHHHHHHH
Confidence 455789999998855 56888899999999999873
No 142
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=54.45 E-value=9.3 Score=21.83 Aligned_cols=10 Identities=40% Similarity=0.959 Sum_probs=7.2
Q ss_pred cCCCcccccc
Q 028139 194 RSDTCPVCNQ 203 (213)
Q Consensus 194 ~~~~CPvCr~ 203 (213)
....||+|..
T Consensus 16 ~~~~CP~Cg~ 25 (33)
T cd00350 16 APWVCPVCGA 25 (33)
T ss_pred CCCcCcCCCC
Confidence 3457999975
No 143
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=52.75 E-value=8.7 Score=35.00 Aligned_cols=37 Identities=24% Similarity=0.371 Sum_probs=27.6
Q ss_pred cCCCCccccccccc---cCCCCeEEcCcCCeechhHHHHH
Q 028139 155 IEEEDVCPTCLEEY---DAENPRIITKCEHHFHLACIFEW 191 (213)
Q Consensus 155 ~ee~~~C~ICle~~---~~~~~~~~l~CgH~Fh~~CI~~W 191 (213)
......||-|.-.+ +.-++...+.|||.||.-|-.--
T Consensus 365 ~~N~krCP~C~v~IEr~eGCnKM~C~~c~~~fc~~c~~~l 404 (445)
T KOG1814|consen 365 ESNSKRCPKCKVVIERSEGCNKMHCTKCGTYFCWICAELL 404 (445)
T ss_pred HhcCCCCCcccceeecCCCccceeeccccccceeehhhhc
Confidence 34556799888766 33577888999999999886553
No 144
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=51.67 E-value=14 Score=32.82 Aligned_cols=45 Identities=24% Similarity=0.490 Sum_probs=35.3
Q ss_pred CccccccccccCCCCeEEcCcCCeechhHHHHHHhcCCCcccccc
Q 028139 159 DVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQ 203 (213)
Q Consensus 159 ~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr~ 203 (213)
..|-.|.++.........-.|.|.||..|=.---+.=..||.|..
T Consensus 331 ~~Cf~C~~~~~~~~~y~C~~Ck~~FCldCDv~iHesLh~CpgCeh 375 (378)
T KOG2807|consen 331 RFCFACQGELLSSGRYRCESCKNVFCLDCDVFIHESLHNCPGCEH 375 (378)
T ss_pred cceeeeccccCCCCcEEchhccceeeccchHHHHhhhhcCCCcCC
Confidence 349999888777777778889999999996554455578999963
No 145
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=51.30 E-value=11 Score=35.79 Aligned_cols=37 Identities=27% Similarity=0.615 Sum_probs=25.7
Q ss_pred CCCCccccccccccC----CC------CeEEcCcCCeechhHHHHHH
Q 028139 156 EEEDVCPTCLEEYDA----EN------PRIITKCEHHFHLACIFEWM 192 (213)
Q Consensus 156 ee~~~C~ICle~~~~----~~------~~~~l~CgH~Fh~~CI~~Wl 192 (213)
+....|+||.|.|+. +. ..+-+.=|-+||..|+.+--
T Consensus 511 e~~~~C~IC~EkFe~v~d~e~~~Wm~kdaV~le~G~ifH~~Cl~e~~ 557 (579)
T KOG2071|consen 511 ERQASCPICQEKFEVVFDQEEDLWMYKDAVYLEFGRIFHSKCLSEKR 557 (579)
T ss_pred ccccCCcccccccceeecchhhheeecceeeeccCceeeccccchHH
Confidence 667789999999865 11 11222258899999987754
No 146
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=51.14 E-value=5.2 Score=25.49 Aligned_cols=11 Identities=27% Similarity=0.981 Sum_probs=5.3
Q ss_pred CCccccccccc
Q 028139 196 DTCPVCNQEMI 206 (213)
Q Consensus 196 ~~CPvCr~~l~ 206 (213)
..||+|..+|.
T Consensus 21 ~~CPlC~r~l~ 31 (54)
T PF04423_consen 21 GCCPLCGRPLD 31 (54)
T ss_dssp EE-TTT--EE-
T ss_pred CcCCCCCCCCC
Confidence 38999988764
No 147
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=49.39 E-value=11 Score=25.05 Aligned_cols=14 Identities=21% Similarity=0.802 Sum_probs=10.2
Q ss_pred CCCcccccccccCC
Q 028139 195 SDTCPVCNQEMIFD 208 (213)
Q Consensus 195 ~~~CPvCr~~l~~~ 208 (213)
.-.||+|++.+.+.
T Consensus 6 ~v~CP~C~k~~~w~ 19 (62)
T PRK00418 6 TVNCPTCGKPVEWG 19 (62)
T ss_pred cccCCCCCCccccc
Confidence 35699999987653
No 148
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=47.27 E-value=5.2 Score=25.76 Aligned_cols=18 Identities=28% Similarity=0.759 Sum_probs=14.5
Q ss_pred EEcCcCCeechhHHHHHH
Q 028139 175 IITKCEHHFHLACIFEWM 192 (213)
Q Consensus 175 ~~l~CgH~Fh~~CI~~Wl 192 (213)
....|+|.||..|-.+|-
T Consensus 42 ~C~~C~~~fC~~C~~~~H 59 (64)
T smart00647 42 TCPKCGFSFCFRCKVPWH 59 (64)
T ss_pred ECCCCCCeECCCCCCcCC
Confidence 334799999999998884
No 149
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=46.55 E-value=15 Score=23.20 Aligned_cols=35 Identities=14% Similarity=0.353 Sum_probs=26.3
Q ss_pred CccccccccccCCC-CeEEcCcCCeechhHHHHHHh
Q 028139 159 DVCPTCLEEYDAEN-PRIITKCEHHFHLACIFEWME 193 (213)
Q Consensus 159 ~~C~ICle~~~~~~-~~~~l~CgH~Fh~~CI~~Wl~ 193 (213)
..|.+|-..|..-. ......||++|+..|....+.
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~~ 38 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRIP 38 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCcChHHcCCeee
Confidence 45999998886633 234466999999999887664
No 150
>PF10235 Cript: Microtubule-associated protein CRIPT; InterPro: IPR019367 The CRIPT protein is a cytoskeletal protein involved in microtubule production. This C-terminal domain is essential for binding to the PDZ3 domain of the SAP90 protein, one of a super-family of PDZ-containing proteins that play an important role in coupling the membrane ion channels with their signalling partners [].
Probab=45.68 E-value=9.7 Score=27.32 Aligned_cols=37 Identities=14% Similarity=0.617 Sum_probs=27.9
Q ss_pred CCccccccccccCCCCeEEcCcCCeechhHHHHHHhcCCCccccccccc
Q 028139 158 EDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMI 206 (213)
Q Consensus 158 ~~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr~~l~ 206 (213)
...|-||-... -+=||.||..|-++ +..|.+|.+.|.
T Consensus 44 ~~~C~~CK~~v--------~q~g~~YCq~CAYk----kGiCamCGKki~ 80 (90)
T PF10235_consen 44 SSKCKICKTKV--------HQPGAKYCQTCAYK----KGICAMCGKKIL 80 (90)
T ss_pred Ccccccccccc--------ccCCCccChhhhcc----cCcccccCCeec
Confidence 34699997643 23488999999766 789999988774
No 151
>PF06844 DUF1244: Protein of unknown function (DUF1244); InterPro: IPR009654 This family consists of several short bacterial proteins of around 100 residues in length. The function of this family is unknown.; PDB: 2O35_A 3FYB_B.
Probab=45.21 E-value=14 Score=24.98 Aligned_cols=11 Identities=27% Similarity=0.918 Sum_probs=8.3
Q ss_pred echhHHHHHHh
Q 028139 183 FHLACIFEWME 193 (213)
Q Consensus 183 Fh~~CI~~Wl~ 193 (213)
||..|+.+|+.
T Consensus 12 FCRNCLskWy~ 22 (68)
T PF06844_consen 12 FCRNCLSKWYR 22 (68)
T ss_dssp --HHHHHHHHH
T ss_pred HHHHHHHHHHH
Confidence 99999999985
No 152
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=43.36 E-value=18 Score=22.98 Aligned_cols=24 Identities=29% Similarity=0.782 Sum_probs=14.4
Q ss_pred cCcCCeechhHHHHHHhcCCCcccc
Q 028139 177 TKCEHHFHLACIFEWMERSDTCPVC 201 (213)
Q Consensus 177 l~CgH~Fh~~CI~~Wl~~~~~CPvC 201 (213)
..|||.|-..= ..-..+...||.|
T Consensus 32 ~~Cgh~w~~~v-~~R~~~~~~CP~C 55 (55)
T PF14311_consen 32 PKCGHEWKASV-NDRTRRGKGCPYC 55 (55)
T ss_pred CCCCCeeEccH-hhhccCCCCCCCC
Confidence 34677666542 2223567789988
No 153
>KOG3842 consensus Adaptor protein Pellino [Signal transduction mechanisms]
Probab=42.76 E-value=25 Score=31.16 Aligned_cols=51 Identities=22% Similarity=0.498 Sum_probs=35.5
Q ss_pred CCccccccccccC---------------CCC-eEEcCcCCeechhHHHHHHhc---------CCCcccccccccCC
Q 028139 158 EDVCPTCLEEYDA---------------ENP-RIITKCEHHFHLACIFEWMER---------SDTCPVCNQEMIFD 208 (213)
Q Consensus 158 ~~~C~ICle~~~~---------------~~~-~~~l~CgH~Fh~~CI~~Wl~~---------~~~CPvCr~~l~~~ 208 (213)
+..||+|+..-.. +-+ -...||||+--.+=..-|-+. ...||.|-+.|...
T Consensus 341 ~r~CPmC~~~gp~V~L~lG~E~~f~vD~G~pthaF~PCGHv~sekt~~YWs~iplPhGT~~f~a~CPFC~~~L~ge 416 (429)
T KOG3842|consen 341 ERECPMCRVVGPYVPLWLGCEAGFYVDAGPPTHAFNPCGHVCSEKTVKYWSQIPLPHGTHAFHAACPFCATQLAGE 416 (429)
T ss_pred cCcCCeeeeecceeeeeccccceeEecCCCcccccCCcccccchhhhhHhhcCcCCCccccccccCcchhhhhccC
Confidence 4589999986211 111 123689999988889999865 36799998876443
No 154
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=41.89 E-value=4.1 Score=35.07 Aligned_cols=46 Identities=20% Similarity=0.483 Sum_probs=35.4
Q ss_pred CccccccccccCC---CCeEEcC--------cCCeechhHHHHHHhcC-CCccccccc
Q 028139 159 DVCPTCLEEYDAE---NPRIITK--------CEHHFHLACIFEWMERS-DTCPVCNQE 204 (213)
Q Consensus 159 ~~C~ICle~~~~~---~~~~~l~--------CgH~Fh~~CI~~Wl~~~-~~CPvCr~~ 204 (213)
..|.||...|... ....++. |||..+..|+..-+... -.||.|+..
T Consensus 208 ~~c~ic~~~~~~n~~~~~p~vl~~~~~~~~~c~htlc~~c~~~~l~~~~~~cp~~~~~ 265 (296)
T KOG4185|consen 208 KLCEICERIYSENDEKLAPLVLSLSRLKEKIEGHTLCKECIDTILLQAGIKCPFCTWS 265 (296)
T ss_pred HHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcchHHHHHHhhhcCCcccce
Confidence 4699999999732 2233455 99999999999988665 589999874
No 155
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=41.73 E-value=20 Score=23.39 Aligned_cols=19 Identities=26% Similarity=0.684 Sum_probs=15.6
Q ss_pred CCCcccccccccCCCCCCC
Q 028139 195 SDTCPVCNQEMIFDLPVDY 213 (213)
Q Consensus 195 ~~~CPvCr~~l~~~~~~~~ 213 (213)
+..||.|...+..-+|..|
T Consensus 17 k~~CP~CG~~t~~~~P~rf 35 (56)
T PRK13130 17 KEICPVCGGKTKNPHPPRF 35 (56)
T ss_pred cccCcCCCCCCCCCCCCCC
Confidence 6779999998888877765
No 156
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=41.26 E-value=15 Score=26.61 Aligned_cols=33 Identities=21% Similarity=0.307 Sum_probs=22.7
Q ss_pred CCCccccccccccCCCCeEEcC--cCCeechhHHHHH
Q 028139 157 EEDVCPTCLEEYDAENPRIITK--CEHHFHLACIFEW 191 (213)
Q Consensus 157 e~~~C~ICle~~~~~~~~~~l~--CgH~Fh~~CI~~W 191 (213)
....|.||...... .+.... |...||..|...+
T Consensus 54 ~~~~C~iC~~~~G~--~i~C~~~~C~~~fH~~CA~~~ 88 (110)
T PF13832_consen 54 FKLKCSICGKSGGA--CIKCSHPGCSTAFHPTCARKA 88 (110)
T ss_pred cCCcCcCCCCCCce--eEEcCCCCCCcCCCHHHHHHC
Confidence 34679999997432 233333 7889999998663
No 157
>PLN02189 cellulose synthase
Probab=40.90 E-value=25 Score=35.89 Aligned_cols=50 Identities=20% Similarity=0.460 Sum_probs=33.2
Q ss_pred CCCccccccccccC---CCCeEE-cCcCCeechhHHHH-HHhcCCCccccccccc
Q 028139 157 EEDVCPTCLEEYDA---ENPRII-TKCEHHFHLACIFE-WMERSDTCPVCNQEMI 206 (213)
Q Consensus 157 e~~~C~ICle~~~~---~~~~~~-l~CgH~Fh~~CI~~-Wl~~~~~CPvCr~~l~ 206 (213)
...+|.||-++... ++.-+. --|+--.|..|..- .-+.++.||.||+...
T Consensus 33 ~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cyeyer~eg~q~CpqCkt~Y~ 87 (1040)
T PLN02189 33 DGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCYEYERREGTQNCPQCKTRYK 87 (1040)
T ss_pred cCccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchh
Confidence 34579999999743 333332 23777789999832 1133578999998765
No 158
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=40.83 E-value=8.6 Score=23.25 Aligned_cols=28 Identities=21% Similarity=0.533 Sum_probs=16.6
Q ss_pred EEcCcCCeechhHHHHHHhcCCCcccccc
Q 028139 175 IITKCEHHFHLACIFEWMERSDTCPVCNQ 203 (213)
Q Consensus 175 ~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr~ 203 (213)
....|||.|-..--..= .....||.|..
T Consensus 7 ~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 7 RCEECGHEFEVLQSISE-DDPVPCPECGS 34 (42)
T ss_pred EeCCCCCEEEEEEEcCC-CCCCcCCCCCC
Confidence 35678888875321111 22457999987
No 159
>KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=40.68 E-value=4.8 Score=35.05 Aligned_cols=36 Identities=25% Similarity=0.512 Sum_probs=27.6
Q ss_pred ccccccccccCCCCeEEcCcCCeechhHHHHHHhcC
Q 028139 160 VCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERS 195 (213)
Q Consensus 160 ~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~~ 195 (213)
+|.||+++|..+.....+.|--.||..|+..|+...
T Consensus 216 vC~~CF~el~~~~~~~~~~~~~~~~~~~~~~~~~~~ 251 (288)
T KOG1729|consen 216 VCDICFEELEKGARGDREDSLPVFHGKCYPNWLTTG 251 (288)
T ss_pred ecHHHHHHHhcccccchhhccccccccccccccccc
Confidence 899999999654444455555599999999999654
No 160
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=40.08 E-value=6.6 Score=30.32 Aligned_cols=49 Identities=18% Similarity=0.477 Sum_probs=27.1
Q ss_pred CCCCcccccccc-ccCCCCeEEcCcCCeechhHHHHHHhcCC----Cccccccc
Q 028139 156 EEEDVCPTCLEE-YDAENPRIITKCEHHFHLACIFEWMERSD----TCPVCNQE 204 (213)
Q Consensus 156 ee~~~C~ICle~-~~~~~~~~~l~CgH~Fh~~CI~~Wl~~~~----~CPvCr~~ 204 (213)
.++.+|.||+.. |..+-.-...-|.-.||..|--+--.+++ .|-+|++.
T Consensus 63 ~ddatC~IC~KTKFADG~GH~C~YCq~r~CARCGGrv~lrsNKv~wvcnlc~k~ 116 (169)
T KOG3799|consen 63 GDDATCGICHKTKFADGCGHNCSYCQTRFCARCGGRVSLRSNKVMWVCNLCRKQ 116 (169)
T ss_pred CcCcchhhhhhcccccccCcccchhhhhHHHhcCCeeeeccCceEEeccCCcHH
Confidence 566789999975 44433333334444555555444333332 47777653
No 161
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=39.11 E-value=31 Score=22.48 Aligned_cols=44 Identities=23% Similarity=0.643 Sum_probs=28.7
Q ss_pred cccccccccCCC-CeEEcCcC--CeechhHHHHHHhcCCCcccccccccCC
Q 028139 161 CPTCLEEYDAEN-PRIITKCE--HHFHLACIFEWMERSDTCPVCNQEMIFD 208 (213)
Q Consensus 161 C~ICle~~~~~~-~~~~l~Cg--H~Fh~~CI~~Wl~~~~~CPvCr~~l~~~ 208 (213)
|-.|-.++..+. ...+ |. ..||..|...-| .+.||-|.-.|+-.
T Consensus 8 CE~C~~dLp~~s~~A~I--CSfECTFC~~C~e~~l--~~~CPNCgGelv~R 54 (57)
T PF06906_consen 8 CECCDKDLPPDSPEAYI--CSFECTFCADCAETML--NGVCPNCGGELVRR 54 (57)
T ss_pred ccccCCCCCCCCCcceE--EeEeCcccHHHHHHHh--cCcCcCCCCccccC
Confidence 555655553332 1222 43 479999999976 67799998877643
No 162
>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=38.56 E-value=32 Score=19.19 Aligned_cols=37 Identities=16% Similarity=0.530 Sum_probs=22.7
Q ss_pred cccccccccCCCCeEEcCcCCeechhHHHHHHhcCCCccccccccc
Q 028139 161 CPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMI 206 (213)
Q Consensus 161 C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr~~l~ 206 (213)
|..|-+.+.... ..+..=+..||..|. .|..|+..|.
T Consensus 2 C~~C~~~i~~~~-~~~~~~~~~~H~~Cf--------~C~~C~~~L~ 38 (39)
T smart00132 2 CAGCGKPIRGGE-LVLRALGKVWHPECF--------KCSKCGKPLG 38 (39)
T ss_pred ccccCCcccCCc-EEEEeCCccccccCC--------CCcccCCcCc
Confidence 777877765542 222234778888773 4777777653
No 163
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=38.45 E-value=44 Score=23.33 Aligned_cols=50 Identities=16% Similarity=0.407 Sum_probs=19.7
Q ss_pred CCCccccccccccC---CCCeE-EcCcCCeechhHHHHHH-hcCCCccccccccc
Q 028139 157 EEDVCPTCLEEYDA---ENPRI-ITKCEHHFHLACIFEWM-ERSDTCPVCNQEMI 206 (213)
Q Consensus 157 e~~~C~ICle~~~~---~~~~~-~l~CgH~Fh~~CI~~Wl-~~~~~CPvCr~~l~ 206 (213)
...+|-||=+++.. ++..+ .--|+--.|..|..-=. +.++.||.|+....
T Consensus 8 ~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg~q~CpqCkt~yk 62 (80)
T PF14569_consen 8 NGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEGNQVCPQCKTRYK 62 (80)
T ss_dssp SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS-SB-TTT--B--
T ss_pred CCcccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcCcccccccCCCcc
Confidence 45679999998733 33222 24477788888875433 34688999997653
No 164
>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=37.73 E-value=35 Score=21.25 Aligned_cols=38 Identities=18% Similarity=0.469 Sum_probs=20.0
Q ss_pred cccccccccCCCCeEEcCcCCeechhHHHHHHhcCCCcccccccccC
Q 028139 161 CPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIF 207 (213)
Q Consensus 161 C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr~~l~~ 207 (213)
|..|-..+.... .++..-|..||..| -+|-.|++.|..
T Consensus 1 C~~C~~~I~~~~-~~~~~~~~~~H~~C--------f~C~~C~~~l~~ 38 (58)
T PF00412_consen 1 CARCGKPIYGTE-IVIKAMGKFWHPEC--------FKCSKCGKPLND 38 (58)
T ss_dssp BTTTSSBESSSS-EEEEETTEEEETTT--------SBETTTTCBTTT
T ss_pred CCCCCCCccCcE-EEEEeCCcEEEccc--------cccCCCCCccCC
Confidence 455555554322 33334566677665 246666665543
No 165
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=37.39 E-value=16 Score=19.81 Aligned_cols=9 Identities=56% Similarity=1.390 Sum_probs=7.0
Q ss_pred Ccccccccc
Q 028139 197 TCPVCNQEM 205 (213)
Q Consensus 197 ~CPvCr~~l 205 (213)
.||+|.+.+
T Consensus 3 ~CPiC~~~v 11 (26)
T smart00734 3 QCPVCFREV 11 (26)
T ss_pred cCCCCcCcc
Confidence 589997766
No 166
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=36.65 E-value=25 Score=26.29 Aligned_cols=22 Identities=23% Similarity=0.616 Sum_probs=17.3
Q ss_pred HHHhcCCCcccccccccCCCCC
Q 028139 190 EWMERSDTCPVCNQEMIFDLPV 211 (213)
Q Consensus 190 ~Wl~~~~~CPvCr~~l~~~~~~ 211 (213)
+-+.+...|+.|++++..|+.+
T Consensus 80 KmLGr~D~CM~C~~pLTLd~~l 101 (114)
T PF11023_consen 80 KMLGRVDACMHCKEPLTLDPSL 101 (114)
T ss_pred hhhchhhccCcCCCcCccCchh
Confidence 3466778899999999888754
No 167
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=36.45 E-value=23 Score=24.51 Aligned_cols=33 Identities=21% Similarity=0.389 Sum_probs=23.2
Q ss_pred CCccccccccccCCCCeEEcCcCCeechhHHHH
Q 028139 158 EDVCPTCLEEYDAENPRIITKCEHHFHLACIFE 190 (213)
Q Consensus 158 ~~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~ 190 (213)
...|.+|-.....-..-....|.-.||..|...
T Consensus 36 ~~~C~~C~~~~Ga~i~C~~~~C~~~fH~~CA~~ 68 (90)
T PF13771_consen 36 KLKCSICKKKGGACIGCSHPGCSRSFHVPCARK 68 (90)
T ss_pred CCCCcCCCCCCCeEEEEeCCCCCcEEChHHHcc
Confidence 356999998744432333456899999999765
No 168
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=36.34 E-value=21 Score=26.20 Aligned_cols=25 Identities=28% Similarity=0.554 Sum_probs=16.5
Q ss_pred eEEcCcCCeechhHHHHHHhcCCCccccc
Q 028139 174 RIITKCEHHFHLACIFEWMERSDTCPVCN 202 (213)
Q Consensus 174 ~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr 202 (213)
-..++|||+|-.. ++-|.+. ||-|.
T Consensus 3 H~CtrCG~vf~~g--~~~il~G--Cp~CG 27 (112)
T COG3364 3 HQCTRCGEVFDDG--SEEILSG--CPKCG 27 (112)
T ss_pred ceecccccccccc--cHHHHcc--Ccccc
Confidence 3578899999875 4433333 88774
No 169
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=36.31 E-value=13 Score=27.51 Aligned_cols=30 Identities=33% Similarity=0.718 Sum_probs=22.1
Q ss_pred CccccccccccCCCCeEEcCcCCeechhHHHHHHhc
Q 028139 159 DVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMER 194 (213)
Q Consensus 159 ~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~ 194 (213)
..|++|-.+|..++.. +.+|..|..+|-+.
T Consensus 4 p~cp~c~sEytYed~~------~~~cpec~~ew~~~ 33 (112)
T COG2824 4 PPCPKCNSEYTYEDGG------QLICPECAHEWNEN 33 (112)
T ss_pred CCCCccCCceEEecCc------eEeCchhccccccc
Confidence 3599999999775533 45788888888743
No 170
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=35.59 E-value=14 Score=24.19 Aligned_cols=11 Identities=27% Similarity=1.141 Sum_probs=5.4
Q ss_pred CcccccccccC
Q 028139 197 TCPVCNQEMIF 207 (213)
Q Consensus 197 ~CPvCr~~l~~ 207 (213)
.||+|++.+.+
T Consensus 4 ~CP~C~k~~~~ 14 (57)
T PF03884_consen 4 KCPICGKPVEW 14 (57)
T ss_dssp E-TTT--EEE-
T ss_pred cCCCCCCeecc
Confidence 58899887766
No 171
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=34.84 E-value=1.1e+02 Score=27.25 Aligned_cols=41 Identities=10% Similarity=-0.100 Sum_probs=30.4
Q ss_pred CccccccccccCCCCeEEcCcCC-eechhHHHHHHhcCCCccccccc
Q 028139 159 DVCPTCLEEYDAENPRIITKCEH-HFHLACIFEWMERSDTCPVCNQE 204 (213)
Q Consensus 159 ~~C~ICle~~~~~~~~~~l~CgH-~Fh~~CI~~Wl~~~~~CPvCr~~ 204 (213)
..|-.|-+.... .+..+|+| .|+.+|-. +....+||+|...
T Consensus 344 ~~~~~~~~~~~s---t~~~~~~~n~~~~~~a~--~s~~~~~~~c~~~ 385 (394)
T KOG2113|consen 344 LKGTSAGFGLLS---TIWSGGNMNLSPGSLAS--ASASPTSSTCDHN 385 (394)
T ss_pred cccccccCceee---eEeecCCcccChhhhhh--cccCCcccccccc
Confidence 357777664432 46778998 78999987 6778899999764
No 172
>PRK11827 hypothetical protein; Provisional
Probab=34.51 E-value=14 Score=24.42 Aligned_cols=19 Identities=26% Similarity=0.711 Sum_probs=12.3
Q ss_pred HHHhcCCCcccccccccCC
Q 028139 190 EWMERSDTCPVCNQEMIFD 208 (213)
Q Consensus 190 ~Wl~~~~~CPvCr~~l~~~ 208 (213)
+||..--.||+|+.++..+
T Consensus 3 ~~LLeILaCP~ckg~L~~~ 21 (60)
T PRK11827 3 HRLLEIIACPVCNGKLWYN 21 (60)
T ss_pred hHHHhheECCCCCCcCeEc
Confidence 4555555678887777654
No 173
>PF14353 CpXC: CpXC protein
Probab=32.67 E-value=32 Score=25.69 Aligned_cols=17 Identities=29% Similarity=0.778 Sum_probs=12.3
Q ss_pred CCcccccccccCCCCCC
Q 028139 196 DTCPVCNQEMIFDLPVD 212 (213)
Q Consensus 196 ~~CPvCr~~l~~~~~~~ 212 (213)
-+||.|.+.+..+-++-
T Consensus 39 ~~CP~Cg~~~~~~~p~l 55 (128)
T PF14353_consen 39 FTCPSCGHKFRLEYPLL 55 (128)
T ss_pred EECCCCCCceecCCCEE
Confidence 57999988877665543
No 174
>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=32.21 E-value=32 Score=19.78 Aligned_cols=9 Identities=33% Similarity=1.339 Sum_probs=6.7
Q ss_pred CCccccccc
Q 028139 196 DTCPVCNQE 204 (213)
Q Consensus 196 ~~CPvCr~~ 204 (213)
..||+|...
T Consensus 19 ~~CP~Cg~~ 27 (34)
T cd00729 19 EKCPICGAP 27 (34)
T ss_pred CcCcCCCCc
Confidence 579999763
No 175
>PF12660 zf-TFIIIC: Putative zinc-finger of transcription factor IIIC complex; InterPro: IPR024764 This zinc-finger domain is at the very C terminus of a number of different TFIIIC subunit proteins. This domain might be involved in protein-DNA and/or protein-protein interactions [].; PDB: 2J04_C.
Probab=32.08 E-value=4.2 Score=29.57 Aligned_cols=48 Identities=19% Similarity=0.544 Sum_probs=12.9
Q ss_pred CccccccccccCCCCeEEcCc--CCeechhHHHHHHhc----CCCcccccccccCC
Q 028139 159 DVCPTCLEEYDAENPRIITKC--EHHFHLACIFEWMER----SDTCPVCNQEMIFD 208 (213)
Q Consensus 159 ~~C~ICle~~~~~~~~~~l~C--gH~Fh~~CI~~Wl~~----~~~CPvCr~~l~~~ 208 (213)
..|+||.+.+...+.. ...| ||.|-.-.+ --|-- -..|++|+..+...
T Consensus 15 E~C~~C~~~i~~~~~~-~~~C~~GH~w~RC~l-T~l~i~~~~~r~C~~C~~~~l~~ 68 (99)
T PF12660_consen 15 EKCPICGAPIPFDDLD-EAQCENGHVWPRCAL-TFLPIQTPGVRVCPVCGRRALDP 68 (99)
T ss_dssp --------------SS-EEE-TTS-EEEB-SS-S-SBS-SS-EEE-TTT--EEE-G
T ss_pred ccccccccccccCCcC-EeECCCCCEEeeeee-eeeeeccCCeeEcCCCCCEEecC
Confidence 4599999887544422 2336 788754332 22211 16799998766443
No 176
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 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 zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=31.53 E-value=19 Score=19.84 Aligned_cols=11 Identities=45% Similarity=1.241 Sum_probs=5.9
Q ss_pred CcccccccccC
Q 028139 197 TCPVCNQEMIF 207 (213)
Q Consensus 197 ~CPvCr~~l~~ 207 (213)
.||+|...+..
T Consensus 1 ~CP~C~s~l~~ 11 (28)
T PF03119_consen 1 TCPVCGSKLVR 11 (28)
T ss_dssp B-TTT--BEEE
T ss_pred CcCCCCCEeEc
Confidence 49999888763
No 177
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=30.61 E-value=1.2e+02 Score=30.43 Aligned_cols=35 Identities=20% Similarity=0.486 Sum_probs=26.0
Q ss_pred CCccccccccccCC------CCeEEcCcCCeechhHHHHHH
Q 028139 158 EDVCPTCLEEYDAE------NPRIITKCEHHFHLACIFEWM 192 (213)
Q Consensus 158 ~~~C~ICle~~~~~------~~~~~l~CgH~Fh~~CI~~Wl 192 (213)
.+.|.+|-..|..- ..-.+-.||.+||..|-..+.
T Consensus 460 SdtC~~C~kkFfSlsK~L~~RKHHCRkCGrVFC~~CSSnRs 500 (1374)
T PTZ00303 460 SDSCPSCGRAFISLSRPLGTRAHHCRSCGIRLCVFCITKRA 500 (1374)
T ss_pred CCcccCcCCcccccccccccccccccCCccccCccccCCcc
Confidence 36899999999531 122345799999999987765
No 178
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=29.92 E-value=28 Score=22.93 Aligned_cols=16 Identities=31% Similarity=0.677 Sum_probs=12.2
Q ss_pred cCCCcccccccccCCC
Q 028139 194 RSDTCPVCNQEMIFDL 209 (213)
Q Consensus 194 ~~~~CPvCr~~l~~~~ 209 (213)
.++.||+|.+++..+.
T Consensus 2 ~HkHC~~CG~~Ip~~~ 17 (59)
T PF09889_consen 2 PHKHCPVCGKPIPPDE 17 (59)
T ss_pred CCCcCCcCCCcCCcch
Confidence 3567999999887654
No 179
>PRK01343 zinc-binding protein; Provisional
Probab=29.17 E-value=32 Score=22.52 Aligned_cols=12 Identities=25% Similarity=0.816 Sum_probs=8.5
Q ss_pred CCCccccccccc
Q 028139 195 SDTCPVCNQEMI 206 (213)
Q Consensus 195 ~~~CPvCr~~l~ 206 (213)
...||+|++.+.
T Consensus 9 ~~~CP~C~k~~~ 20 (57)
T PRK01343 9 TRPCPECGKPST 20 (57)
T ss_pred CCcCCCCCCcCc
Confidence 456888888754
No 180
>PF01485 IBR: IBR domain; InterPro: IPR002867 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 cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=28.76 E-value=9.3 Score=24.45 Aligned_cols=33 Identities=21% Similarity=0.589 Sum_probs=18.5
Q ss_pred Ccccc--ccccccCCC---C--eEEcCcCCeechhHHHHH
Q 028139 159 DVCPT--CLEEYDAEN---P--RIITKCEHHFHLACIFEW 191 (213)
Q Consensus 159 ~~C~I--Cle~~~~~~---~--~~~l~CgH~Fh~~CI~~W 191 (213)
..|+- |-..+.... . +....|++.||..|-.+|
T Consensus 19 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~ 58 (64)
T PF01485_consen 19 RWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPW 58 (64)
T ss_dssp C--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSES
T ss_pred cCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCccc
Confidence 46877 777664322 2 444559999999998777
No 181
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=28.66 E-value=42 Score=22.06 Aligned_cols=19 Identities=26% Similarity=0.779 Sum_probs=13.6
Q ss_pred CCCcccccccccCCCCCCC
Q 028139 195 SDTCPVCNQEMIFDLPVDY 213 (213)
Q Consensus 195 ~~~CPvCr~~l~~~~~~~~ 213 (213)
+.+||+|........|..|
T Consensus 17 ke~Cp~CG~~t~~~~PprF 35 (59)
T COG2260 17 KEKCPVCGGDTKVPHPPRF 35 (59)
T ss_pred cccCCCCCCccccCCCCCC
Confidence 3679999877776666554
No 182
>KOG2169 consensus Zn-finger transcription factor [Transcription]
Probab=28.48 E-value=36 Score=33.01 Aligned_cols=44 Identities=23% Similarity=0.369 Sum_probs=26.4
Q ss_pred ccccccccccCCCCeEEcCcCCeech--hHHHH-HHhc----C--CCcccccccccCCCC
Q 028139 160 VCPTCLEEYDAENPRIITKCEHHFHL--ACIFE-WMER----S--DTCPVCNQEMIFDLP 210 (213)
Q Consensus 160 ~C~ICle~~~~~~~~~~l~CgH~Fh~--~CI~~-Wl~~----~--~~CPvCr~~l~~~~~ 210 (213)
.|+|+.- ...++|.++.|+ .|.+. |+-. . -.||||.+...++.+
T Consensus 308 ~CPl~~~-------Rm~~P~r~~~CkHlQcFD~~~~lq~n~~~pTW~CPVC~~~~~~e~l 360 (636)
T KOG2169|consen 308 NCPLSKM-------RMSLPARGHTCKHLQCFDALSYLQMNEQKPTWRCPVCQKAAPFEGL 360 (636)
T ss_pred cCCcccc-------eeecCCcccccccceecchhhhHHhccCCCeeeCccCCccccccch
Confidence 5665544 345566555554 66554 3311 1 259999999888774
No 183
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=28.17 E-value=25 Score=21.89 Aligned_cols=24 Identities=33% Similarity=0.721 Sum_probs=15.5
Q ss_pred EEcCcCCeechhHHHHHHh----cCCCcccccc
Q 028139 175 IITKCEHHFHLACIFEWME----RSDTCPVCNQ 203 (213)
Q Consensus 175 ~~l~CgH~Fh~~CI~~Wl~----~~~~CPvCr~ 203 (213)
....|||.|-. |.. ....||.|..
T Consensus 7 ~C~~Cg~~fe~-----~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 7 RCTACGHRFEV-----LQKMSDDPLATCPECGG 34 (52)
T ss_pred EeCCCCCEeEE-----EEecCCCCCCCCCCCCC
Confidence 45678888774 322 2246999986
No 184
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=28.16 E-value=55 Score=33.62 Aligned_cols=50 Identities=20% Similarity=0.507 Sum_probs=32.7
Q ss_pred CCCccccccccccC---CCCeE-EcCcCCeechhHHH-HHHhcCCCccccccccc
Q 028139 157 EEDVCPTCLEEYDA---ENPRI-ITKCEHHFHLACIF-EWMERSDTCPVCNQEMI 206 (213)
Q Consensus 157 e~~~C~ICle~~~~---~~~~~-~l~CgH~Fh~~CI~-~Wl~~~~~CPvCr~~l~ 206 (213)
...+|-||=+++.. ++.-+ +--|+-=.|..|.. +.-+.++.||.|+....
T Consensus 16 ~~qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCYEYEr~eG~q~CPqCktrYk 70 (1079)
T PLN02638 16 GGQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCYEYERKDGNQSCPQCKTKYK 70 (1079)
T ss_pred CCceeeecccccCcCCCCCEEEEeccCCCccccchhhhhhhcCCccCCccCCchh
Confidence 34579999999743 33322 23366668999983 22233678999998765
No 185
>PF11671 Apis_Csd: Complementary sex determiner protein; InterPro: IPR021007 Sex determination proteins are found in eukaryotes. Proteins in this family are typically between 168 and 410 amino acids in length. It plays a role in the gender determination of around 20% of all animals. In the honeybee, the mechanism of sex determination depends on the complementary sex determiner (csd) gene which produces an SR-type protein. Males are homozygous while females are homozygous for the csd gene. Heterozygosity generates an active protein which initiates female development []. This entry represents the C-terminal end of the sex determination protein.
Probab=26.12 E-value=1.3e+02 Score=23.11 Aligned_cols=50 Identities=24% Similarity=0.309 Sum_probs=27.6
Q ss_pred CCcceecCCCCCCCCCCCCCCCCCCCccc-ccccccCCCCCCCCCCCCCCC
Q 028139 17 TPAYYYQYPRASEERLPLSSHHGAGSALS-RGLLVDTNLETSVPDAYRPPP 66 (213)
Q Consensus 17 ~p~~~~~~~~~~~~~~~~ss~~~~~~~~s-~~~~~~~~~~~s~~d~~r~pp 66 (213)
-||||=.||+++-.-.+--+.++..+-+. -|.+...-..--+||+||..|
T Consensus 86 VPvyy~nfpp~pi~v~pwv~~~~qvpr~r~igp~~pfPPrFippn~yr~rp 136 (146)
T PF11671_consen 86 VPVYYGNFPPRPIMVGPWVSMQEQVPRFRYIGPLTPFPPRFIPPNMYRLRP 136 (146)
T ss_pred cceEecCCCCCcccccCcccccccCCCccccCCCCCCCCccCCccccccCC
Confidence 48888779999886666556666444432 122221112223567776433
No 186
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=25.81 E-value=77 Score=27.74 Aligned_cols=50 Identities=16% Similarity=0.260 Sum_probs=32.5
Q ss_pred CccccccccccC-----CCC-eEEcCcCCeechhHHHHHHhc-------------CCCcccccccccCC
Q 028139 159 DVCPTCLEEYDA-----ENP-RIITKCEHHFHLACIFEWMER-------------SDTCPVCNQEMIFD 208 (213)
Q Consensus 159 ~~C~ICle~~~~-----~~~-~~~l~CgH~Fh~~CI~~Wl~~-------------~~~CPvCr~~l~~~ 208 (213)
..|.|||+.-+. .+. ....+|...+|-.||.--++. -.+|-+|.++...+
T Consensus 259 ~~~~~~~~~~~~~~~~r~~S~I~C~~C~~~~HP~Ci~M~~elv~~~KTY~W~C~~C~lC~IC~~P~~E~ 327 (381)
T KOG1512|consen 259 NERKHFWDIQTNIIQSRRNSWIVCKPCATRPHPYCVAMIPELVGQYKTYFWKCSSCELCRICLGPVIES 327 (381)
T ss_pred hhhhhhhcchhhhhhhhhccceeecccccCCCCcchhcCHHHHhHHhhcchhhcccHhhhccCCcccch
Confidence 469999986432 122 345779999999998643322 25788887765433
No 187
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=25.65 E-value=42 Score=24.89 Aligned_cols=23 Identities=30% Similarity=0.635 Sum_probs=14.2
Q ss_pred ccccccccccCC--CCeEEcCcCCe
Q 028139 160 VCPTCLEEYDAE--NPRIITKCEHH 182 (213)
Q Consensus 160 ~C~ICle~~~~~--~~~~~l~CgH~ 182 (213)
.||-|..+|..+ .-.+..-|+|.
T Consensus 4 ~CP~C~seytY~dg~~~iCpeC~~E 28 (109)
T TIGR00686 4 PCPKCNSEYTYHDGTQLICPSCLYE 28 (109)
T ss_pred cCCcCCCcceEecCCeeECcccccc
Confidence 499999998553 33444445554
No 188
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=25.63 E-value=35 Score=20.01 Aligned_cols=31 Identities=23% Similarity=0.508 Sum_probs=19.8
Q ss_pred EEcCcCCeechhHHHHHHhcCCCcccccccccC
Q 028139 175 IITKCEHHFHLACIFEWMERSDTCPVCNQEMIF 207 (213)
Q Consensus 175 ~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr~~l~~ 207 (213)
+...||+.||..=--+ +....|..|..+|..
T Consensus 3 ~C~~Cg~~Yh~~~~pP--~~~~~Cd~cg~~L~q 33 (36)
T PF05191_consen 3 ICPKCGRIYHIEFNPP--KVEGVCDNCGGELVQ 33 (36)
T ss_dssp EETTTTEEEETTTB----SSTTBCTTTTEBEBE
T ss_pred CcCCCCCccccccCCC--CCCCccCCCCCeeEe
Confidence 4567999999532111 345789999887654
No 189
>PF06749 DUF1218: Protein of unknown function (DUF1218); InterPro: IPR009606 This family contains hypothetical plant proteins of unknown function. Family members contain a number of conserved cysteine residues.
Probab=25.41 E-value=25 Score=25.24 Aligned_cols=10 Identities=50% Similarity=1.620 Sum_probs=6.5
Q ss_pred CCCccccCCC
Q 028139 1 MGGCCCCSSK 10 (213)
Q Consensus 1 ~~~~~~~~~~ 10 (213)
+|||+||+.+
T Consensus 16 ~~gC~cc~~~ 25 (97)
T PF06749_consen 16 AGGCLCCGKR 25 (97)
T ss_pred HhcceEeCCC
Confidence 3788878543
No 190
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=25.39 E-value=30 Score=22.90 Aligned_cols=13 Identities=38% Similarity=1.198 Sum_probs=9.9
Q ss_pred CcccccccccCCC
Q 028139 197 TCPVCNQEMIFDL 209 (213)
Q Consensus 197 ~CPvCr~~l~~~~ 209 (213)
.||+||.++..+.
T Consensus 10 aCP~~kg~L~~~~ 22 (60)
T COG2835 10 ACPVCKGPLVYDE 22 (60)
T ss_pred eccCcCCcceEec
Confidence 4999998876654
No 191
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=25.32 E-value=33 Score=30.23 Aligned_cols=45 Identities=20% Similarity=0.373 Sum_probs=29.8
Q ss_pred CCCccccccccccCCCCeEEc--Cc--CCeechhHHHHHHhcCCCcccccc
Q 028139 157 EEDVCPTCLEEYDAENPRIIT--KC--EHHFHLACIFEWMERSDTCPVCNQ 203 (213)
Q Consensus 157 e~~~C~ICle~~~~~~~~~~l--~C--gH~Fh~~CI~~Wl~~~~~CPvCr~ 203 (213)
....||||=..-... ++.. .= -|.+|.-|=.+|--....||.|..
T Consensus 186 ~~~~CPvCGs~P~~s--~v~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~ 234 (309)
T PRK03564 186 QRQFCPVCGSMPVSS--VVQIGTTQGLRYLHCNLCESEWHVVRVKCSNCEQ 234 (309)
T ss_pred CCCCCCCCCCcchhh--eeeccCCCCceEEEcCCCCCcccccCccCCCCCC
Confidence 456899997653211 1111 11 356778888899888899999975
No 192
>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=25.23 E-value=8.2 Score=33.36 Aligned_cols=45 Identities=20% Similarity=0.347 Sum_probs=20.6
Q ss_pred CCCccccccccccCCCCeEEc----CcCCeechhHHHHHHhcCCCcccccc
Q 028139 157 EEDVCPTCLEEYDAENPRIIT----KCEHHFHLACIFEWMERSDTCPVCNQ 203 (213)
Q Consensus 157 e~~~C~ICle~~~~~~~~~~l----~CgH~Fh~~CI~~Wl~~~~~CPvCr~ 203 (213)
....||||=..-... .+.- .=-|.+|.-|=.+|--....||.|..
T Consensus 171 ~~g~CPvCGs~P~~s--~l~~~~~~G~R~L~Cs~C~t~W~~~R~~Cp~Cg~ 219 (290)
T PF04216_consen 171 QRGYCPVCGSPPVLS--VLRGGEREGKRYLHCSLCGTEWRFVRIKCPYCGN 219 (290)
T ss_dssp T-SS-TTT---EEEE--EEE------EEEEEETTT--EEE--TTS-TTT--
T ss_pred cCCcCCCCCCcCceE--EEecCCCCccEEEEcCCCCCeeeecCCCCcCCCC
Confidence 345899997653221 0111 01467888888899888889999965
No 193
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 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 UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=24.90 E-value=50 Score=21.52 Aligned_cols=31 Identities=13% Similarity=0.171 Sum_probs=19.2
Q ss_pred cccccccccCCCCeEEcCcCCeechh----HHHHHHh
Q 028139 161 CPTCLEEYDAENPRIITKCEHHFHLA----CIFEWME 193 (213)
Q Consensus 161 C~ICle~~~~~~~~~~l~CgH~Fh~~----CI~~Wl~ 193 (213)
|.+|... ..+.-+.|.||+++|.. .+.+=++
T Consensus 1 C~~C~~~--~~~lw~CL~Cg~~~C~~~~~~Ha~~H~~ 35 (63)
T PF02148_consen 1 CSVCGST--NSNLWLCLTCGYVGCGRYSNGHALKHYK 35 (63)
T ss_dssp -SSSHTC--SSSEEEETTTS-EEETTTSTSHHHHHHH
T ss_pred CCCCCCc--CCceEEeCCCCcccccCCcCcHHHHhhc
Confidence 5566643 34556789999999985 5555544
No 194
>KOG1356 consensus Putative transcription factor 5qNCA, contains JmjC domain [Transcription]
Probab=24.60 E-value=27 Score=34.69 Aligned_cols=45 Identities=16% Similarity=0.428 Sum_probs=30.2
Q ss_pred CccccccccccCCCCeEEcCcCCeechhHHHHHH-h-----cCCCccccccc
Q 028139 159 DVCPTCLEEYDAENPRIITKCEHHFHLACIFEWM-E-----RSDTCPVCNQE 204 (213)
Q Consensus 159 ~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl-~-----~~~~CPvCr~~ 204 (213)
..|-.|.-..- ....+...|||.||..|++.|. . .-..|+.|+..
T Consensus 230 ~mC~~C~~tlf-n~hw~C~~C~~~~Cl~C~r~~~p~~~~~e~a~k~~~~~~~ 280 (889)
T KOG1356|consen 230 EMCDRCETTLF-NIHWRCPRCGFGVCLDCYRKWYPRLSKEEVAEKCEFSWLK 280 (889)
T ss_pred hhhhhhccccc-ceeEEccccCCeeeecchhhccccchHhHhhhhhhHHHHh
Confidence 35777765431 1245678899999999999995 1 12467776654
No 195
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 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. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=24.17 E-value=23 Score=22.74 Aligned_cols=9 Identities=44% Similarity=1.368 Sum_probs=3.2
Q ss_pred Ccccccccc
Q 028139 197 TCPVCNQEM 205 (213)
Q Consensus 197 ~CPvCr~~l 205 (213)
+||+|...+
T Consensus 26 tCP~C~a~~ 34 (54)
T PF09237_consen 26 TCPICGAVI 34 (54)
T ss_dssp E-TTT--EE
T ss_pred CCCcchhhc
Confidence 466665543
No 196
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=23.37 E-value=25 Score=30.93 Aligned_cols=47 Identities=21% Similarity=0.362 Sum_probs=29.2
Q ss_pred CCCccccccccccCCCCeEE-cCc--CCeechhHHHHHHhcCCCcccccc
Q 028139 157 EEDVCPTCLEEYDAENPRII-TKC--EHHFHLACIFEWMERSDTCPVCNQ 203 (213)
Q Consensus 157 e~~~C~ICle~~~~~~~~~~-l~C--gH~Fh~~CI~~Wl~~~~~CPvCr~ 203 (213)
....||||=..-....-... ..= -|.+|.-|=.+|--..-.||.|..
T Consensus 183 ~~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~ 232 (305)
T TIGR01562 183 SRTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHYVRVKCSHCEE 232 (305)
T ss_pred CCCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCcccccCccCCCCCC
Confidence 34489999765321100000 011 256777788899888899999976
No 197
>PLN02248 cellulose synthase-like protein
Probab=23.21 E-value=63 Score=33.38 Aligned_cols=32 Identities=16% Similarity=0.481 Sum_probs=27.6
Q ss_pred CcCCeechhHHHHHHhcCCCcccccccccCCC
Q 028139 178 KCEHHFHLACIFEWMERSDTCPVCNQEMIFDL 209 (213)
Q Consensus 178 ~CgH~Fh~~CI~~Wl~~~~~CPvCr~~l~~~~ 209 (213)
.|++..|.+|...-++....||-|+.+....+
T Consensus 149 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 180 (1135)
T PLN02248 149 ECGFKICRDCYIDAVKSGGICPGCKEPYKVTD 180 (1135)
T ss_pred cccchhHHhHhhhhhhcCCCCCCCcccccccc
Confidence 36889999999999999999999998875543
No 198
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=23.14 E-value=65 Score=19.83 Aligned_cols=34 Identities=15% Similarity=0.255 Sum_probs=24.2
Q ss_pred CCCccccccccc--cCCCCeEEcCcCCeechhHHHH
Q 028139 157 EEDVCPTCLEEY--DAENPRIITKCEHHFHLACIFE 190 (213)
Q Consensus 157 e~~~C~ICle~~--~~~~~~~~l~CgH~Fh~~CI~~ 190 (213)
....|.+|-+.+ ..........|+-.+|.+|+..
T Consensus 10 ~~~~C~~C~~~i~g~~~~g~~C~~C~~~~H~~C~~~ 45 (53)
T PF00130_consen 10 KPTYCDVCGKFIWGLGKQGYRCSWCGLVCHKKCLSK 45 (53)
T ss_dssp STEB-TTSSSBECSSSSCEEEETTTT-EEETTGGCT
T ss_pred CCCCCcccCcccCCCCCCeEEECCCCChHhhhhhhh
Confidence 445699999887 3445567788999999999765
No 199
>PLN02436 cellulose synthase A
Probab=23.01 E-value=78 Score=32.59 Aligned_cols=50 Identities=20% Similarity=0.482 Sum_probs=32.7
Q ss_pred CCCccccccccccC---CCCeEE-cCcCCeechhHHHHHH-hcCCCccccccccc
Q 028139 157 EEDVCPTCLEEYDA---ENPRII-TKCEHHFHLACIFEWM-ERSDTCPVCNQEMI 206 (213)
Q Consensus 157 e~~~C~ICle~~~~---~~~~~~-l~CgH~Fh~~CI~~Wl-~~~~~CPvCr~~l~ 206 (213)
...+|.||-+++.. ++.-+. --|+--.|..|..-=- +.++.||.|++...
T Consensus 35 ~~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cyeyer~eg~~~Cpqckt~Y~ 89 (1094)
T PLN02436 35 SGQTCQICGDEIELTVDGEPFVACNECAFPVCRPCYEYERREGNQACPQCKTRYK 89 (1094)
T ss_pred CCccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchh
Confidence 34579999999733 333322 2266678999983211 23578999998765
No 200
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=22.90 E-value=13 Score=19.50 Aligned_cols=7 Identities=57% Similarity=1.440 Sum_probs=2.6
Q ss_pred ccccccc
Q 028139 161 CPTCLEE 167 (213)
Q Consensus 161 C~ICle~ 167 (213)
|+-|=.+
T Consensus 2 Cp~CG~~ 8 (23)
T PF13240_consen 2 CPNCGAE 8 (23)
T ss_pred CcccCCC
Confidence 3333333
No 201
>PLN02195 cellulose synthase A
Probab=22.27 E-value=1.2e+02 Score=31.06 Aligned_cols=50 Identities=22% Similarity=0.390 Sum_probs=34.0
Q ss_pred CCccccccccccC---CCCe-EEcCcCCeechhHHHHHHhc---CCCcccccccccCCC
Q 028139 158 EDVCPTCLEEYDA---ENPR-IITKCEHHFHLACIFEWMER---SDTCPVCNQEMIFDL 209 (213)
Q Consensus 158 ~~~C~ICle~~~~---~~~~-~~l~CgH~Fh~~CI~~Wl~~---~~~CPvCr~~l~~~~ 209 (213)
...|.||=++... +++- .+--|+--.|..|.. .+| ++.||.|+....-++
T Consensus 6 ~~~c~~cgd~~~~~~~g~~fvaC~eC~~pvCrpCye--yer~eg~q~CpqCkt~Yk~~~ 62 (977)
T PLN02195 6 APICATCGEEVGVDSNGEAFVACHECSYPLCKACLE--YEIKEGRKVCLRCGGPYDAEN 62 (977)
T ss_pred CccceecccccCcCCCCCeEEEeccCCCccccchhh--hhhhcCCccCCccCCcccccc
Confidence 4579999998743 3332 233477789999983 244 478999999887433
No 202
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=22.17 E-value=48 Score=21.35 Aligned_cols=15 Identities=33% Similarity=0.800 Sum_probs=10.3
Q ss_pred CCcccccccccCCCC
Q 028139 196 DTCPVCNQEMIFDLP 210 (213)
Q Consensus 196 ~~CPvCr~~l~~~~~ 210 (213)
.+||.|.+.|.+.++
T Consensus 3 ~~CP~CG~~iev~~~ 17 (54)
T TIGR01206 3 FECPDCGAEIELENP 17 (54)
T ss_pred cCCCCCCCEEecCCC
Confidence 368888887766543
No 203
>COG4647 AcxC Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=22.08 E-value=48 Score=25.51 Aligned_cols=21 Identities=24% Similarity=0.409 Sum_probs=14.8
Q ss_pred ccccccccCCCCeEEcCcCCeech
Q 028139 162 PTCLEEYDAENPRIITKCEHHFHL 185 (213)
Q Consensus 162 ~ICle~~~~~~~~~~l~CgH~Fh~ 185 (213)
-||++. +..++.-.|||.|+.
T Consensus 61 fi~qs~---~~rv~rcecghsf~d 81 (165)
T COG4647 61 FICQSA---QKRVIRCECGHSFGD 81 (165)
T ss_pred EEEecc---cccEEEEeccccccC
Confidence 467663 444667779999986
No 204
>KOG4224 consensus Armadillo repeat protein VAC8 required for vacuole fusion, inheritance and cytosol-to-vacuole protein targeting [Intracellular trafficking, secretion, and vesicular transport]
Probab=21.94 E-value=47 Score=30.34 Aligned_cols=16 Identities=50% Similarity=1.032 Sum_probs=11.3
Q ss_pred CCCcc-ccCCCCcccCC
Q 028139 1 MGGCC-CCSSKGVERNS 16 (213)
Q Consensus 1 ~~~~~-~~~~~~~~~~~ 16 (213)
||.|| ||-+-+.+-..
T Consensus 1 MG~c~sc~~~S~dEs~~ 17 (550)
T KOG4224|consen 1 MGNCLSCCESSEDESES 17 (550)
T ss_pred CCccccccccccccccc
Confidence 99999 88666655444
No 205
>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type [].
Probab=21.76 E-value=1.3e+02 Score=22.05 Aligned_cols=24 Identities=21% Similarity=0.490 Sum_probs=19.0
Q ss_pred CCeechhHHHHHHhc---------CCCcccccc
Q 028139 180 EHHFHLACIFEWMER---------SDTCPVCNQ 203 (213)
Q Consensus 180 gH~Fh~~CI~~Wl~~---------~~~CPvCr~ 203 (213)
.=.||..||..++.. .-.||.||.
T Consensus 37 ~~~fC~~CL~~ryge~~~ev~~~~~W~CP~Crg 69 (105)
T PF10497_consen 37 RGKFCGGCLRNRYGENVEEVLEDPNWKCPKCRG 69 (105)
T ss_pred cceehHhHHHHHHhhhHHHHhcCCceECCCCCC
Confidence 668999999998843 246999986
No 206
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=21.71 E-value=73 Score=17.95 Aligned_cols=24 Identities=29% Similarity=0.751 Sum_probs=9.6
Q ss_pred cccccccccc--CCCCeEEcCcCCee
Q 028139 160 VCPTCLEEYD--AENPRIITKCEHHF 183 (213)
Q Consensus 160 ~C~ICle~~~--~~~~~~~l~CgH~F 183 (213)
.|+-|-.+|. .+...+...|+|.+
T Consensus 4 ~Cp~C~se~~y~D~~~~vCp~C~~ew 29 (30)
T PF08274_consen 4 KCPLCGSEYTYEDGELLVCPECGHEW 29 (30)
T ss_dssp --TTT-----EE-SSSEEETTTTEEE
T ss_pred CCCCCCCcceeccCCEEeCCcccccC
Confidence 4778877763 34445556666643
No 207
>COG3492 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.22 E-value=47 Score=23.89 Aligned_cols=12 Identities=25% Similarity=0.844 Sum_probs=10.6
Q ss_pred echhHHHHHHhc
Q 028139 183 FHLACIFEWMER 194 (213)
Q Consensus 183 Fh~~CI~~Wl~~ 194 (213)
||..|+..|+..
T Consensus 43 FCRNCLs~Wy~e 54 (104)
T COG3492 43 FCRNCLSNWYRE 54 (104)
T ss_pred HHHHHHHHHHHH
Confidence 999999999853
No 208
>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=21.09 E-value=49 Score=30.96 Aligned_cols=38 Identities=26% Similarity=0.725 Sum_probs=22.1
Q ss_pred CCCccccccccccCCCC-eEEcCcC-CeechhHHHHHHhcCCCcccccccccC
Q 028139 157 EEDVCPTCLEEYDAENP-RIITKCE-HHFHLACIFEWMERSDTCPVCNQEMIF 207 (213)
Q Consensus 157 e~~~C~ICle~~~~~~~-~~~l~Cg-H~Fh~~CI~~Wl~~~~~CPvCr~~l~~ 207 (213)
+-..|+-||+++...+- ...-.|. +.| .||+|...|.+
T Consensus 25 ~~~yCp~CL~~~p~~e~~~~~nrC~r~Cf-------------~CP~C~~~L~~ 64 (483)
T PF05502_consen 25 DSYYCPNCLFEVPSSEARSEKNRCSRNCF-------------DCPICFSPLSV 64 (483)
T ss_pred ceeECccccccCChhhheeccceeccccc-------------cCCCCCCccee
Confidence 34579999999855332 1122354 333 38888776643
No 209
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=20.66 E-value=43 Score=26.77 Aligned_cols=9 Identities=33% Similarity=1.368 Sum_probs=6.4
Q ss_pred CCCcccccc
Q 028139 195 SDTCPVCNQ 203 (213)
Q Consensus 195 ~~~CPvCr~ 203 (213)
-..||+|..
T Consensus 149 P~~CPiCga 157 (166)
T COG1592 149 PEVCPICGA 157 (166)
T ss_pred CCcCCCCCC
Confidence 456888875
No 210
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=20.59 E-value=78 Score=22.53 Aligned_cols=38 Identities=16% Similarity=0.320 Sum_probs=27.2
Q ss_pred CCccccccccccCCCCeEEcCcCCeechhHHHHHHhcCCCcccccccccC
Q 028139 158 EDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIF 207 (213)
Q Consensus 158 ~~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr~~l~~ 207 (213)
...|+-|.....--+.. =|..|+-.++.|..|++++..
T Consensus 33 rS~C~~C~~~L~~~~lI------------Pi~S~l~lrGrCr~C~~~I~~ 70 (92)
T PF06750_consen 33 RSHCPHCGHPLSWWDLI------------PILSYLLLRGRCRYCGAPIPP 70 (92)
T ss_pred CCcCcCCCCcCcccccc------------hHHHHHHhCCCCcccCCCCCh
Confidence 45688887766442211 177899999999999998864
No 211
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=20.58 E-value=71 Score=24.64 Aligned_cols=14 Identities=43% Similarity=0.695 Sum_probs=11.5
Q ss_pred CCcccccccccCCC
Q 028139 196 DTCPVCNQEMIFDL 209 (213)
Q Consensus 196 ~~CPvCr~~l~~~~ 209 (213)
-.||.|...|..++
T Consensus 124 f~Cp~Cg~~l~~~d 137 (147)
T smart00531 124 FTCPRCGEELEEDD 137 (147)
T ss_pred EECCCCCCEEEEcC
Confidence 57999999987665
No 212
>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=20.47 E-value=1.1e+02 Score=24.06 Aligned_cols=35 Identities=26% Similarity=0.340 Sum_probs=23.4
Q ss_pred CCCccccccccccCCCCeEEcCcCCeechhHHHHHHhcCCCcccccccccCCC
Q 028139 157 EEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDL 209 (213)
Q Consensus 157 e~~~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~~Wl~~~~~CPvCr~~l~~~~ 209 (213)
....|+.|--.|.. .+.|+..-.||.|...|...+
T Consensus 108 ~~Y~Cp~c~~r~tf------------------~eA~~~~F~Cp~Cg~~L~~~d 142 (158)
T TIGR00373 108 MFFICPNMCVRFTF------------------NEAMELNFTCPRCGAMLDYLD 142 (158)
T ss_pred CeEECCCCCcEeeH------------------HHHHHcCCcCCCCCCEeeecc
Confidence 44578777665533 334455778999999887655
No 213
>PLN02400 cellulose synthase
Probab=20.46 E-value=68 Score=33.01 Aligned_cols=48 Identities=19% Similarity=0.544 Sum_probs=32.4
Q ss_pred CCCccccccccccC---CCCeE-EcCcCCeechhHHHHHHhc---CCCccccccccc
Q 028139 157 EEDVCPTCLEEYDA---ENPRI-ITKCEHHFHLACIFEWMER---SDTCPVCNQEMI 206 (213)
Q Consensus 157 e~~~C~ICle~~~~---~~~~~-~l~CgH~Fh~~CI~~Wl~~---~~~CPvCr~~l~ 206 (213)
...+|-||=+++.. ++.-+ +--|+--.|.-|.. ++| ++.||.||....
T Consensus 35 ~gqiCqICGD~VG~t~dGe~FVAC~eCaFPVCRpCYE--YERkeGnq~CPQCkTrYk 89 (1085)
T PLN02400 35 NGQICQICGDDVGVTETGDVFVACNECAFPVCRPCYE--YERKDGTQCCPQCKTRYR 89 (1085)
T ss_pred CCceeeecccccCcCCCCCEEEEEccCCCccccchhh--eecccCCccCcccCCccc
Confidence 44579999999733 33322 23366668999973 344 578999998765
No 214
>KOG4218 consensus Nuclear hormone receptor betaFTZ-F1 [Transcription]
Probab=20.39 E-value=36 Score=30.52 Aligned_cols=23 Identities=17% Similarity=0.531 Sum_probs=14.2
Q ss_pred CCCCccccccccccCCCCeEEcCc
Q 028139 156 EEEDVCPTCLEEYDAENPRIITKC 179 (213)
Q Consensus 156 ee~~~C~ICle~~~~~~~~~~l~C 179 (213)
+.+..||+|=+... |..-.++.|
T Consensus 13 dl~ElCPVCGDkVS-GYHYGLLTC 35 (475)
T KOG4218|consen 13 DLGELCPVCGDKVS-GYHYGLLTC 35 (475)
T ss_pred ccccccccccCccc-cceeeeeeh
Confidence 34456999988764 333445555
No 215
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=20.14 E-value=42 Score=29.31 Aligned_cols=30 Identities=20% Similarity=0.441 Sum_probs=23.8
Q ss_pred ccccccccccCCCCeEEcCcCCeechhHHH
Q 028139 160 VCPTCLEEYDAENPRIITKCEHHFHLACIF 189 (213)
Q Consensus 160 ~C~ICle~~~~~~~~~~l~CgH~Fh~~CI~ 189 (213)
.|.||+.....++.+..--|..-||.-|+-
T Consensus 316 lC~IC~~P~~E~E~~FCD~CDRG~HT~CVG 345 (381)
T KOG1512|consen 316 LCRICLGPVIESEHLFCDVCDRGPHTLCVG 345 (381)
T ss_pred hhhccCCcccchheeccccccCCCCccccc
Confidence 688998887777767777788888888874
Done!