Query 032467
Match_columns 140
No_of_seqs 219 out of 1749
Neff 7.5
Searched_HMMs 46136
Date Fri Mar 29 14:27:50 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032467.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032467hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1940 Zn-finger protein [Gen 99.9 2.5E-23 5.5E-28 162.6 7.2 124 2-127 147-270 (276)
2 PF14599 zinc_ribbon_6: Zinc-r 99.8 1E-19 2.2E-24 112.7 -0.2 60 63-122 2-61 (61)
3 PF13639 zf-RING_2: Ring finge 99.5 1.7E-14 3.6E-19 83.9 2.0 43 15-59 2-44 (44)
4 PF15227 zf-C3HC4_4: zinc fing 99.3 1E-12 2.3E-17 75.8 3.5 39 16-58 1-42 (42)
5 PLN03208 E3 ubiquitin-protein 99.2 9.7E-12 2.1E-16 93.0 4.6 58 3-64 8-80 (193)
6 PF12678 zf-rbx1: RING-H2 zinc 99.2 1.2E-11 2.6E-16 79.5 4.0 46 13-59 19-73 (73)
7 PF13920 zf-C3HC4_3: Zinc fing 99.2 8.6E-12 1.9E-16 74.3 3.1 46 13-63 2-48 (50)
8 PF13923 zf-C3HC4_2: Zinc fing 99.2 8.5E-12 1.8E-16 70.7 2.7 38 16-58 1-39 (39)
9 PHA02929 N1R/p28-like protein; 99.2 1.2E-11 2.6E-16 95.6 4.0 54 10-64 171-228 (238)
10 PF13445 zf-RING_UBOX: RING-ty 99.2 1.4E-11 2.9E-16 71.4 2.4 40 16-56 1-43 (43)
11 cd00162 RING RING-finger (Real 99.2 3.3E-11 7.2E-16 68.7 3.5 45 15-62 1-45 (45)
12 PF14634 zf-RING_5: zinc-RING 99.2 3.5E-11 7.6E-16 69.9 3.4 44 15-60 1-44 (44)
13 PF00097 zf-C3HC4: Zinc finger 99.1 6.2E-11 1.3E-15 67.5 3.0 39 16-58 1-41 (41)
14 KOG4628 Predicted E3 ubiquitin 99.1 4.5E-11 9.7E-16 96.5 3.0 50 14-64 230-279 (348)
15 COG5243 HRD1 HRD ubiquitin lig 99.1 3.7E-11 8.1E-16 97.1 2.2 52 10-62 284-344 (491)
16 KOG0320 Predicted E3 ubiquitin 99.1 9.8E-11 2.1E-15 86.2 3.2 57 3-63 122-178 (187)
17 PHA02926 zinc finger-like prot 99.0 1.5E-10 3.2E-15 88.1 3.2 55 9-63 166-230 (242)
18 KOG0823 Predicted E3 ubiquitin 99.0 1.7E-10 3.7E-15 88.0 3.2 50 10-63 44-95 (230)
19 smart00184 RING Ring finger. E 99.0 4.9E-10 1.1E-14 61.7 3.2 39 16-58 1-39 (39)
20 KOG0804 Cytoplasmic Zn-finger 99.0 1.7E-10 3.7E-15 95.0 1.8 83 13-123 175-259 (493)
21 smart00504 Ubox Modified RING 98.9 1.5E-09 3.1E-14 67.0 4.0 46 13-63 1-46 (63)
22 KOG0317 Predicted E3 ubiquitin 98.9 5.5E-10 1.2E-14 87.6 2.5 47 13-64 239-285 (293)
23 PF12861 zf-Apc11: Anaphase-pr 98.8 4.2E-09 9.2E-14 69.2 3.7 50 13-62 21-81 (85)
24 COG5540 RING-finger-containing 98.8 3E-09 6.5E-14 84.2 3.2 52 11-63 321-372 (374)
25 TIGR00599 rad18 DNA repair pro 98.7 1E-08 2.2E-13 84.6 3.2 48 11-63 24-71 (397)
26 KOG2164 Predicted E3 ubiquitin 98.6 1.4E-08 3.1E-13 84.9 2.6 48 12-63 185-236 (513)
27 KOG0287 Postreplication repair 98.6 2.1E-08 4.5E-13 80.6 2.6 47 13-64 23-69 (442)
28 KOG2177 Predicted E3 ubiquitin 98.5 2.5E-08 5.5E-13 76.3 1.6 45 11-60 11-55 (386)
29 KOG0802 E3 ubiquitin ligase [P 98.5 2.7E-08 5.8E-13 85.2 1.8 51 11-62 289-340 (543)
30 TIGR00570 cdk7 CDK-activating 98.5 6.5E-08 1.4E-12 77.2 3.7 51 13-63 3-54 (309)
31 COG5574 PEX10 RING-finger-cont 98.5 4.3E-08 9.3E-13 76.2 2.2 47 12-62 214-261 (271)
32 PF04564 U-box: U-box domain; 98.5 1.4E-07 3E-12 60.4 3.7 49 12-64 3-51 (73)
33 COG5194 APC11 Component of SCF 98.3 6.2E-07 1.4E-11 58.0 3.4 52 10-62 28-80 (88)
34 PF11793 FANCL_C: FANCL C-term 98.3 1.3E-07 2.8E-12 60.2 0.2 50 13-62 2-65 (70)
35 KOG1039 Predicted E3 ubiquitin 98.3 1.8E-07 3.8E-12 76.0 0.3 83 10-92 158-250 (344)
36 COG5432 RAD18 RING-finger-cont 98.2 6.3E-07 1.4E-11 70.9 2.2 45 13-62 25-69 (391)
37 smart00744 RINGv The RING-vari 98.2 1.6E-06 3.5E-11 51.5 3.1 43 15-59 1-49 (49)
38 KOG4172 Predicted E3 ubiquitin 98.2 3.4E-07 7.5E-12 55.1 -0.2 51 12-66 6-57 (62)
39 PF14835 zf-RING_6: zf-RING of 98.1 1.2E-06 2.6E-11 54.6 1.7 43 13-62 7-50 (65)
40 KOG0824 Predicted E3 ubiquitin 98.1 1.6E-06 3.6E-11 68.7 2.2 51 9-63 3-53 (324)
41 KOG0828 Predicted E3 ubiquitin 98.0 2.6E-06 5.6E-11 71.5 1.9 51 13-63 571-634 (636)
42 KOG0827 Predicted E3 ubiquitin 98.0 3.8E-06 8.2E-11 68.7 2.1 48 13-61 4-54 (465)
43 KOG4265 Predicted E3 ubiquitin 97.9 7.2E-06 1.6E-10 66.3 3.0 50 10-64 287-337 (349)
44 KOG0978 E3 ubiquitin ligase in 97.9 2.8E-06 6.1E-11 74.2 0.3 47 13-63 643-689 (698)
45 KOG0311 Predicted E3 ubiquitin 97.9 1.4E-06 3.1E-11 70.3 -1.4 48 13-63 43-90 (381)
46 PF14570 zf-RING_4: RING/Ubox 97.9 1E-05 2.3E-10 47.7 2.3 47 16-62 1-47 (48)
47 KOG1493 Anaphase-promoting com 97.9 3.2E-06 6.9E-11 54.3 0.0 33 30-62 45-80 (84)
48 KOG1734 Predicted RING-contain 97.8 5.6E-06 1.2E-10 64.9 0.5 51 12-62 223-280 (328)
49 KOG4159 Predicted E3 ubiquitin 97.7 2.1E-05 4.5E-10 65.2 3.1 49 11-64 82-130 (398)
50 KOG2930 SCF ubiquitin ligase, 97.5 7E-05 1.5E-09 50.8 2.8 29 32-61 78-106 (114)
51 KOG2879 Predicted E3 ubiquitin 97.5 8.3E-05 1.8E-09 58.5 3.5 50 11-63 237-287 (298)
52 KOG4185 Predicted E3 ubiquitin 97.5 0.00011 2.4E-09 58.2 3.8 50 13-62 3-54 (296)
53 PF11789 zf-Nse: Zinc-finger o 97.5 9.8E-05 2.1E-09 45.1 2.6 43 11-57 9-53 (57)
54 KOG1785 Tyrosine kinase negati 97.4 4.8E-05 1E-09 62.7 1.1 47 12-62 368-415 (563)
55 COG5219 Uncharacterized conser 97.4 4.6E-05 9.9E-10 68.5 0.9 52 11-62 1467-1522(1525)
56 KOG1645 RING-finger-containing 97.4 0.0002 4.4E-09 59.1 4.0 50 13-62 4-55 (463)
57 KOG0825 PHD Zn-finger protein 97.4 2.6E-05 5.6E-10 68.7 -1.3 52 11-64 121-172 (1134)
58 KOG1941 Acetylcholine receptor 97.2 9.1E-05 2E-09 61.0 0.2 56 5-61 358-414 (518)
59 COG5175 MOT2 Transcriptional r 97.1 0.00015 3.2E-09 58.8 0.5 55 9-64 11-65 (480)
60 KOG1814 Predicted E3 ubiquitin 97.1 0.00039 8.5E-09 57.5 2.8 48 13-61 184-238 (445)
61 KOG4275 Predicted E3 ubiquitin 97.1 8E-05 1.7E-09 59.1 -1.1 46 13-67 300-346 (350)
62 COG5152 Uncharacterized conser 97.1 0.00033 7.1E-09 53.0 2.0 45 13-62 196-240 (259)
63 KOG3970 Predicted E3 ubiquitin 97.0 0.0011 2.4E-08 51.1 4.4 51 12-64 49-106 (299)
64 KOG0297 TNF receptor-associate 96.9 0.00043 9.4E-09 57.4 1.7 49 11-64 19-68 (391)
65 KOG1813 Predicted E3 ubiquitin 96.9 0.0006 1.3E-08 54.2 2.0 59 13-76 241-299 (313)
66 KOG2660 Locus-specific chromos 96.8 0.00028 6E-09 56.8 -0.3 50 10-63 12-61 (331)
67 PF12906 RINGv: RING-variant d 96.7 0.001 2.2E-08 39.0 1.6 41 16-58 1-47 (47)
68 PF14447 Prok-RING_4: Prokaryo 96.6 0.0011 2.4E-08 40.0 1.3 43 14-63 8-50 (55)
69 KOG1002 Nucleotide excision re 96.6 0.00084 1.8E-08 57.3 1.0 51 8-62 531-585 (791)
70 KOG3039 Uncharacterized conser 96.4 0.0031 6.7E-08 49.2 3.4 53 11-64 219-271 (303)
71 KOG4692 Predicted E3 ubiquitin 96.4 0.0018 3.9E-08 52.9 2.1 51 9-64 418-468 (489)
72 KOG1952 Transcription factor N 96.4 0.0015 3.3E-08 58.3 1.7 49 12-62 190-246 (950)
73 KOG3800 Predicted E3 ubiquitin 96.4 0.0024 5.3E-08 50.7 2.7 49 15-63 2-51 (300)
74 PF04641 Rtf2: Rtf2 RING-finge 96.4 0.0035 7.7E-08 49.2 3.6 52 10-63 110-161 (260)
75 PF10367 Vps39_2: Vacuolar sor 96.4 0.0015 3.3E-08 43.8 1.1 39 6-46 71-109 (109)
76 KOG4445 Uncharacterized conser 96.3 0.0012 2.5E-08 52.8 0.5 53 10-63 112-186 (368)
77 KOG1571 Predicted E3 ubiquitin 96.2 0.0029 6.2E-08 51.6 2.0 47 9-63 301-347 (355)
78 KOG1428 Inhibitor of type V ad 96.0 0.0078 1.7E-07 57.0 4.1 53 10-63 3483-3544(3738)
79 PF05883 Baculo_RING: Baculovi 95.9 0.0034 7.4E-08 44.6 1.1 35 13-48 26-66 (134)
80 KOG4739 Uncharacterized protei 95.8 0.004 8.6E-08 48.2 1.3 43 15-62 5-47 (233)
81 PHA02862 5L protein; Provision 95.7 0.0096 2.1E-07 42.9 2.6 47 12-63 1-53 (156)
82 COG5222 Uncharacterized conser 95.6 0.0074 1.6E-07 48.4 2.1 46 13-61 274-319 (427)
83 KOG2817 Predicted E3 ubiquitin 95.6 0.01 2.3E-07 48.9 3.0 48 14-62 335-384 (394)
84 KOG3161 Predicted E3 ubiquitin 95.6 0.0039 8.5E-08 54.4 0.5 44 14-61 12-55 (861)
85 PHA02825 LAP/PHD finger-like p 95.5 0.013 2.7E-07 42.9 2.7 47 11-62 6-58 (162)
86 PHA03096 p28-like protein; Pro 95.5 0.0079 1.7E-07 48.0 1.7 48 14-61 179-232 (284)
87 PF03854 zf-P11: P-11 zinc fin 95.3 0.007 1.5E-07 35.5 0.8 42 14-62 3-45 (50)
88 PF07800 DUF1644: Protein of u 95.1 0.025 5.4E-07 41.3 3.3 33 13-49 2-47 (162)
89 COG5236 Uncharacterized conser 95.1 0.018 4E-07 47.1 2.8 48 10-61 58-106 (493)
90 KOG3002 Zn finger protein [Gen 94.7 0.046 1E-06 43.9 4.1 46 12-66 47-94 (299)
91 COG5220 TFB3 Cdk activating ki 94.3 0.011 2.4E-07 46.0 -0.2 50 12-62 9-63 (314)
92 KOG2114 Vacuolar assembly/sort 94.2 0.043 9.2E-07 49.4 3.2 44 14-64 841-884 (933)
93 KOG1001 Helicase-like transcri 94.2 0.026 5.6E-07 50.0 1.7 44 14-62 455-499 (674)
94 KOG3268 Predicted E3 ubiquitin 94.0 0.046 9.9E-07 40.9 2.5 50 13-62 165-227 (234)
95 KOG4367 Predicted Zn-finger pr 93.9 0.033 7.1E-07 47.0 1.8 35 11-49 2-36 (699)
96 PF02891 zf-MIZ: MIZ/SP-RING z 93.3 0.049 1.1E-06 32.2 1.4 44 14-61 3-50 (50)
97 KOG2932 E3 ubiquitin ligase in 92.8 0.043 9.3E-07 44.3 0.8 30 31-63 105-134 (389)
98 PF10272 Tmpp129: Putative tra 92.6 0.11 2.4E-06 42.7 2.9 27 36-62 312-350 (358)
99 KOG1812 Predicted E3 ubiquitin 92.3 0.063 1.4E-06 44.5 1.2 50 13-62 146-202 (384)
100 PF05290 Baculo_IE-1: Baculovi 92.3 0.1 2.3E-06 37.1 2.1 49 12-64 79-133 (140)
101 KOG0827 Predicted E3 ubiquitin 90.1 0.022 4.8E-07 47.1 -3.4 53 11-64 194-246 (465)
102 KOG2068 MOT2 transcription fac 89.3 0.31 6.7E-06 39.6 2.6 49 13-62 249-297 (327)
103 KOG2034 Vacuolar sorting prote 89.3 0.17 3.7E-06 45.8 1.2 42 6-49 810-851 (911)
104 PF08746 zf-RING-like: RING-li 88.9 0.55 1.2E-05 26.8 2.7 40 16-58 1-43 (43)
105 KOG0826 Predicted E3 ubiquitin 88.4 0.39 8.4E-06 39.1 2.5 46 12-62 299-345 (357)
106 PF07191 zinc-ribbons_6: zinc- 88.3 0.083 1.8E-06 33.5 -1.1 40 13-62 1-40 (70)
107 KOG0298 DEAD box-containing he 87.6 0.1 2.2E-06 48.9 -1.3 51 10-64 1150-1200(1394)
108 TIGR00100 hypA hydrogenase nic 87.0 0.4 8.6E-06 33.1 1.6 38 87-126 66-103 (115)
109 PF14569 zf-UDP: Zinc-binding 86.8 0.83 1.8E-05 29.6 2.9 54 10-63 6-62 (80)
110 COG5109 Uncharacterized conser 86.5 0.57 1.2E-05 38.1 2.5 47 14-61 337-385 (396)
111 PF14446 Prok-RING_1: Prokaryo 86.5 0.69 1.5E-05 27.8 2.3 35 12-46 4-38 (54)
112 KOG0309 Conserved WD40 repeat- 86.1 0.5 1.1E-05 42.5 2.1 45 10-57 1025-1069(1081)
113 KOG1100 Predicted E3 ubiquitin 85.9 0.36 7.8E-06 36.8 1.0 38 16-62 161-199 (207)
114 PRK12380 hydrogenase nickel in 85.1 0.6 1.3E-05 32.2 1.7 36 88-125 67-102 (113)
115 KOG1815 Predicted E3 ubiquitin 84.6 0.58 1.3E-05 39.4 1.8 38 10-50 67-104 (444)
116 KOG4185 Predicted E3 ubiquitin 83.5 0.17 3.8E-06 40.0 -1.7 49 13-61 207-265 (296)
117 PRK00564 hypA hydrogenase nick 82.8 0.81 1.8E-05 31.7 1.6 38 87-125 67-104 (117)
118 PRK03681 hypA hydrogenase nick 81.6 0.88 1.9E-05 31.4 1.4 39 87-126 66-104 (114)
119 PF01155 HypA: Hydrogenase exp 80.7 0.6 1.3E-05 32.1 0.3 37 88-126 67-103 (113)
120 COG5183 SSM4 Protein involved 80.3 1.1 2.5E-05 40.6 2.0 51 10-62 9-65 (1175)
121 KOG3899 Uncharacterized conser 79.9 1 2.2E-05 36.3 1.4 29 34-62 324-364 (381)
122 KOG4362 Transcriptional regula 79.7 0.51 1.1E-05 41.9 -0.4 48 12-63 20-69 (684)
123 KOG3113 Uncharacterized conser 79.6 1.8 3.8E-05 34.2 2.7 50 11-63 109-158 (293)
124 smart00064 FYVE Protein presen 79.0 1.1 2.4E-05 27.5 1.1 40 10-49 7-46 (68)
125 KOG3053 Uncharacterized conser 78.7 1 2.2E-05 35.6 1.1 52 9-63 16-82 (293)
126 TIGR02605 CxxC_CxxC_SSSS putat 78.7 2 4.3E-05 25.0 2.2 34 90-124 4-41 (52)
127 PRK03824 hypA hydrogenase nick 77.3 1.7 3.6E-05 30.9 1.8 37 89-125 68-123 (135)
128 PLN02189 cellulose synthase 77.1 2.8 6.1E-05 39.0 3.5 55 9-63 30-87 (1040)
129 PLN02436 cellulose synthase A 76.3 2.7 5.9E-05 39.3 3.2 56 8-63 31-89 (1094)
130 PF14353 CpXC: CpXC protein 75.8 0.43 9.2E-06 33.2 -1.6 19 87-105 34-52 (128)
131 KOG2807 RNA polymerase II tran 75.5 0.77 1.7E-05 37.4 -0.4 22 91-116 353-374 (378)
132 PF00628 PHD: PHD-finger; Int 75.0 0.54 1.2E-05 27.1 -1.1 41 16-59 2-49 (51)
133 PF01363 FYVE: FYVE zinc finge 74.8 1.2 2.6E-05 27.4 0.4 39 9-48 5-44 (69)
134 smart00249 PHD PHD zinc finger 73.8 1.6 3.4E-05 23.9 0.7 41 16-58 2-47 (47)
135 PRK00398 rpoP DNA-directed RNA 72.9 3.1 6.8E-05 23.7 1.9 30 90-119 2-31 (46)
136 PF06906 DUF1272: Protein of u 71.8 8.9 0.00019 23.2 3.7 49 12-63 4-52 (57)
137 PF04710 Pellino: Pellino; In 71.6 1.3 2.9E-05 36.9 0.1 48 11-61 275-337 (416)
138 COG0375 HybF Zn finger protein 71.5 2.6 5.5E-05 29.3 1.5 40 85-126 64-103 (115)
139 COG1996 RPC10 DNA-directed RNA 70.5 2.2 4.9E-05 25.1 0.9 30 89-118 4-33 (49)
140 PRK00762 hypA hydrogenase nick 70.2 2.6 5.5E-05 29.5 1.3 37 88-125 67-108 (124)
141 KOG1609 Protein involved in mR 69.4 2.6 5.7E-05 33.1 1.4 50 13-62 78-133 (323)
142 TIGR01562 FdhE formate dehydro 69.0 4.9 0.00011 32.5 2.8 25 89-117 208-232 (305)
143 cd00065 FYVE FYVE domain; Zinc 68.8 3.6 7.8E-05 24.1 1.6 36 14-49 3-38 (57)
144 PLN02638 cellulose synthase A 68.5 5.3 0.00012 37.4 3.2 56 8-63 12-70 (1079)
145 smart00659 RPOLCX RNA polymera 68.0 4 8.8E-05 23.3 1.6 26 91-117 2-27 (44)
146 PF06844 DUF1244: Protein of u 67.4 3.1 6.7E-05 26.1 1.1 12 38-49 11-22 (68)
147 PF10122 Mu-like_Com: Mu-like 67.2 3.7 8E-05 24.4 1.3 42 91-132 4-48 (51)
148 KOG4443 Putative transcription 66.7 7 0.00015 34.7 3.4 48 13-62 18-72 (694)
149 KOG2462 C2H2-type Zn-finger pr 63.5 3.8 8.2E-05 32.6 1.2 80 12-103 160-255 (279)
150 COG1198 PriA Primosomal protei 63.3 6.4 0.00014 35.5 2.7 26 90-120 461-486 (730)
151 PF04216 FdhE: Protein involve 63.2 3.5 7.7E-05 32.7 1.0 30 90-123 196-225 (290)
152 PLN02400 cellulose synthase 63.0 6 0.00013 37.1 2.5 55 9-63 32-89 (1085)
153 cd02339 ZZ_Mind_bomb Zinc fing 61.5 6.2 0.00013 22.7 1.6 26 92-120 1-26 (45)
154 COG4647 AcxC Acetone carboxyla 61.4 4.8 0.0001 28.7 1.2 21 28-49 68-88 (165)
155 COG1066 Sms Predicted ATP-depe 61.4 5.6 0.00012 33.7 1.9 29 90-122 6-34 (456)
156 PRK03564 formate dehydrogenase 61.1 9.1 0.0002 31.0 3.0 25 89-117 210-234 (309)
157 smart00647 IBR In Between Ring 59.5 3.1 6.7E-05 24.7 0.0 34 15-48 20-59 (64)
158 KOG3039 Uncharacterized conser 58.8 6.7 0.00015 31.0 1.8 32 14-49 44-75 (303)
159 TIGR00416 sms DNA repair prote 55.5 9.2 0.0002 32.5 2.2 31 89-123 5-35 (454)
160 PF10571 UPF0547: Uncharacteri 54.2 7 0.00015 19.8 0.8 8 15-22 2-9 (26)
161 PLN02195 cellulose synthase A 54.2 17 0.00036 33.9 3.8 53 11-63 4-59 (977)
162 cd02334 ZZ_dystrophin Zinc fin 54.0 11 0.00025 22.0 1.8 28 92-122 1-28 (49)
163 KOG2066 Vacuolar assembly/sort 53.8 5.4 0.00012 36.1 0.6 45 13-59 784-831 (846)
164 PLN02915 cellulose synthase A 53.8 16 0.00035 34.3 3.6 52 12-63 14-68 (1044)
165 PF10497 zf-4CXXC_R1: Zinc-fin 52.9 14 0.00029 25.1 2.3 26 36-61 37-70 (105)
166 TIGR00595 priA primosomal prot 52.8 13 0.00028 32.0 2.7 25 90-119 239-263 (505)
167 cd02344 ZZ_HERC2 Zinc finger, 52.3 11 0.00023 21.7 1.5 28 92-122 1-28 (45)
168 PF09986 DUF2225: Uncharacteri 52.1 2.9 6.4E-05 31.8 -1.1 12 52-63 5-16 (214)
169 PF12773 DZR: Double zinc ribb 51.7 15 0.00032 20.9 2.1 11 90-100 28-38 (50)
170 KOG1812 Predicted E3 ubiquitin 51.1 9.9 0.00021 31.6 1.7 44 14-58 307-351 (384)
171 COG3813 Uncharacterized protei 51.0 24 0.00051 22.6 3.0 47 14-63 6-52 (84)
172 KOG2807 RNA polymerase II tran 50.8 7.5 0.00016 31.8 0.9 25 91-118 330-354 (378)
173 cd02345 ZZ_dah Zinc finger, ZZ 50.5 14 0.00031 21.4 1.9 28 92-122 1-28 (49)
174 PRK11823 DNA repair protein Ra 50.1 13 0.00027 31.5 2.2 31 89-123 5-35 (446)
175 PRK12286 rpmF 50S ribosomal pr 50.1 15 0.00032 22.2 2.0 29 90-123 26-54 (57)
176 smart00834 CxxC_CXXC_SSSS Puta 48.3 15 0.00032 19.8 1.7 8 110-117 27-34 (41)
177 KOG3842 Adaptor protein Pellin 47.6 11 0.00024 30.8 1.5 48 11-61 288-350 (429)
178 PF13901 DUF4206: Domain of un 47.6 13 0.00029 28.0 1.8 41 13-60 152-197 (202)
179 KOG0825 PHD Zn-finger protein 47.5 11 0.00023 34.6 1.4 50 14-63 97-154 (1134)
180 PF08792 A2L_zn_ribbon: A2L zi 47.1 16 0.00034 19.6 1.6 27 91-117 3-29 (33)
181 smart00734 ZnF_Rad18 Rad18-lik 47.0 20 0.00043 18.0 1.9 9 54-62 3-11 (26)
182 PF09723 Zn-ribbon_8: Zinc rib 46.1 18 0.00038 20.2 1.8 27 91-117 5-34 (42)
183 KOG3579 Predicted E3 ubiquitin 44.9 20 0.00044 28.9 2.5 58 11-77 266-337 (352)
184 PF04423 Rad50_zn_hook: Rad50 44.3 18 0.0004 21.1 1.7 12 53-64 21-32 (54)
185 cd02338 ZZ_PCMF_like Zinc fing 44.1 20 0.00043 20.8 1.8 28 92-122 1-28 (49)
186 PF13248 zf-ribbon_3: zinc-rib 43.4 14 0.00031 18.4 1.0 8 92-99 3-10 (26)
187 KOG3842 Adaptor protein Pellin 43.3 25 0.00054 28.9 2.8 56 7-62 333-413 (429)
188 PF01907 Ribosomal_L37e: Ribos 43.0 16 0.00035 22.0 1.3 27 87-116 11-37 (55)
189 cd00350 rubredoxin_like Rubred 43.0 14 0.00031 19.5 1.0 10 52-61 17-26 (33)
190 smart00132 LIM Zinc-binding do 42.9 27 0.00058 18.0 2.2 36 16-62 2-37 (39)
191 PF07754 DUF1610: Domain of un 42.6 19 0.00042 17.9 1.4 7 110-116 17-23 (24)
192 PF05605 zf-Di19: Drought indu 42.4 38 0.00083 19.7 2.9 8 53-60 3-10 (54)
193 PF13894 zf-C2H2_4: C2H2-type 41.8 11 0.00024 17.2 0.4 13 54-66 2-14 (24)
194 TIGR02098 MJ0042_CXXC MJ0042 f 41.8 14 0.0003 19.8 0.9 11 90-100 24-34 (38)
195 TIGR01031 rpmF_bact ribosomal 41.2 20 0.00043 21.4 1.5 29 90-123 25-53 (55)
196 cd02340 ZZ_NBR1_like Zinc fing 41.2 20 0.00043 20.2 1.5 26 92-121 1-26 (43)
197 PF10058 DUF2296: Predicted in 41.1 19 0.00042 21.4 1.5 33 87-119 18-54 (54)
198 COG2126 RPL37A Ribosomal prote 40.7 16 0.00035 22.3 1.1 27 87-116 12-38 (61)
199 PF09297 zf-NADH-PPase: NADH p 40.6 13 0.00028 19.4 0.6 26 92-117 4-29 (32)
200 TIGR02159 PA_CoA_Oxy4 phenylac 40.3 14 0.00031 26.6 0.9 20 109-128 105-126 (146)
201 cd02342 ZZ_UBA_plant Zinc fing 40.2 21 0.00046 20.4 1.5 27 92-121 1-27 (43)
202 PF00569 ZZ: Zinc finger, ZZ t 40.0 18 0.00038 20.6 1.2 28 91-121 4-31 (46)
203 PF13240 zinc_ribbon_2: zinc-r 39.9 17 0.00038 17.7 1.0 7 94-100 2-8 (23)
204 PF03604 DNA_RNApol_7kD: DNA d 39.9 18 0.00039 19.2 1.1 23 93-116 2-24 (32)
205 PRK05580 primosome assembly pr 39.9 26 0.00057 31.3 2.7 25 90-119 407-431 (679)
206 COG1656 Uncharacterized conser 39.7 19 0.00041 26.6 1.5 42 52-100 97-139 (165)
207 PF01485 IBR: IBR domain; Int 39.7 4.2 9.2E-05 24.0 -1.6 34 14-47 19-58 (64)
208 COG5132 BUD31 Cell cycle contr 39.3 13 0.00027 26.2 0.5 23 38-61 100-122 (146)
209 PF14205 Cys_rich_KTR: Cystein 39.1 28 0.00061 20.9 1.9 8 54-61 6-13 (55)
210 KOG1829 Uncharacterized conser 39.0 11 0.00023 33.3 0.1 43 13-59 511-557 (580)
211 PF14803 Nudix_N_2: Nudix N-te 37.7 21 0.00045 19.3 1.1 9 108-116 21-29 (34)
212 KOG4718 Non-SMC (structural ma 37.6 17 0.00037 28.0 1.1 42 14-59 182-223 (235)
213 cd04718 BAH_plant_2 BAH, or Br 36.8 10 0.00023 27.4 -0.2 23 39-61 2-27 (148)
214 PRK00420 hypothetical protein; 36.3 31 0.00066 23.8 2.0 10 53-62 24-33 (112)
215 PF00412 LIM: LIM domain; Int 36.2 28 0.00062 20.0 1.7 38 16-64 1-38 (58)
216 COG3492 Uncharacterized protei 35.9 18 0.00038 24.2 0.8 12 38-49 42-53 (104)
217 PF13719 zinc_ribbon_5: zinc-r 35.8 15 0.00034 19.9 0.4 11 13-23 2-12 (37)
218 PRK14873 primosome assembly pr 35.0 30 0.00065 31.0 2.3 27 90-122 409-435 (665)
219 KOG3005 GIY-YIG type nuclease 34.7 39 0.00084 26.9 2.6 49 14-62 183-242 (276)
220 PRK04179 rpl37e 50S ribosomal 33.6 23 0.0005 21.9 1.0 25 90-117 16-40 (62)
221 PF02318 FYVE_2: FYVE-type zin 33.0 26 0.00057 24.0 1.3 50 12-61 53-103 (118)
222 KOG0269 WD40 repeat-containing 31.9 42 0.00091 30.6 2.7 41 14-57 780-820 (839)
223 PF06677 Auto_anti-p27: Sjogre 31.7 44 0.00096 18.8 1.9 11 52-62 17-27 (41)
224 KOG2907 RNA polymerase I trans 31.3 19 0.00042 24.9 0.4 18 108-125 73-94 (116)
225 PF10235 Cript: Microtubule-as 31.2 28 0.00061 23.1 1.2 39 14-66 45-83 (90)
226 PF00096 zf-C2H2: Zinc finger, 31.1 15 0.00033 17.1 -0.1 11 54-64 2-12 (23)
227 TIGR00622 ssl1 transcription f 30.8 31 0.00066 23.9 1.3 13 104-116 98-110 (112)
228 PF09538 FYDLN_acid: Protein o 29.3 39 0.00085 23.1 1.7 20 11-30 7-26 (108)
229 PTZ00073 60S ribosomal protein 29.2 30 0.00065 23.0 1.0 28 87-117 12-39 (91)
230 PF13717 zinc_ribbon_4: zinc-r 29.1 40 0.00087 18.2 1.4 10 53-62 3-12 (36)
231 KOG4323 Polycomb-like PHD Zn-f 28.6 28 0.00061 29.8 1.0 48 13-62 168-225 (464)
232 PRK01110 rpmF 50S ribosomal pr 28.5 45 0.00099 20.3 1.7 29 90-124 26-54 (60)
233 PRK14559 putative protein seri 28.0 61 0.0013 29.0 3.0 22 93-118 29-50 (645)
234 PF04981 NMD3: NMD3 family ; 27.8 35 0.00077 26.2 1.4 7 55-61 1-7 (236)
235 PF12172 DUF35_N: Rubredoxin-l 27.6 40 0.00086 18.0 1.2 26 90-119 10-35 (37)
236 PRK00432 30S ribosomal protein 27.1 39 0.00084 19.7 1.2 24 92-116 21-44 (50)
237 PRK11088 rrmA 23S rRNA methylt 26.6 47 0.001 25.7 1.9 27 13-40 2-28 (272)
238 KOG4684 Uncharacterized conser 26.5 17 0.00036 28.2 -0.6 36 87-122 166-202 (275)
239 PRK14714 DNA polymerase II lar 26.2 51 0.0011 31.8 2.3 9 53-61 668-676 (1337)
240 PF07975 C1_4: TFIIH C1-like d 26.0 67 0.0015 19.0 2.0 26 33-59 25-50 (51)
241 PF05502 Dynactin_p62: Dynacti 25.4 25 0.00054 30.2 0.2 44 53-101 53-96 (483)
242 KOG3726 Uncharacterized conser 25.4 44 0.00096 30.1 1.7 44 14-61 655-698 (717)
243 PF15616 TerY-C: TerY-C metal 24.8 53 0.0012 23.3 1.7 38 14-62 78-115 (131)
244 PRK01343 zinc-binding protein; 24.8 44 0.00096 20.3 1.1 11 52-62 9-19 (57)
245 KOG2857 Predicted MYND Zn-fing 24.6 35 0.00076 24.7 0.8 10 53-62 18-27 (157)
246 PF09845 DUF2072: Zn-ribbon co 24.4 59 0.0013 23.1 1.9 24 93-116 3-26 (131)
247 PF15353 HECA: Headcase protei 24.4 46 0.00099 22.8 1.3 16 34-49 39-54 (107)
248 PRK00418 DNA gyrase inhibitor; 24.3 42 0.00092 20.7 1.0 10 53-62 7-16 (62)
249 cd02343 ZZ_EF Zinc finger, ZZ 23.9 61 0.0013 18.9 1.6 27 92-122 1-27 (48)
250 PF06676 DUF1178: Protein of u 23.8 42 0.0009 24.3 1.0 23 34-61 9-41 (148)
251 PF01783 Ribosomal_L32p: Ribos 23.4 80 0.0017 18.7 2.1 29 90-123 25-53 (56)
252 PF10164 DUF2367: Uncharacteri 22.7 73 0.0016 21.5 2.0 12 53-64 50-61 (98)
253 cd02335 ZZ_ADA2 Zinc finger, Z 22.4 73 0.0016 18.2 1.7 23 94-119 3-25 (49)
254 PRK00366 ispG 4-hydroxy-3-meth 22.1 1.5E+02 0.0032 24.7 4.0 47 53-103 269-317 (360)
255 COG1998 RPS31 Ribosomal protei 21.8 52 0.0011 19.5 1.0 27 91-117 19-45 (51)
256 cd02341 ZZ_ZZZ3 Zinc finger, Z 21.6 73 0.0016 18.4 1.6 27 93-122 2-30 (48)
257 PRK11827 hypothetical protein; 21.2 70 0.0015 19.5 1.5 10 53-62 9-18 (60)
258 COG2835 Uncharacterized conser 21.1 56 0.0012 20.0 1.1 10 53-62 9-18 (60)
259 PF13832 zf-HC5HC2H_2: PHD-zin 20.8 97 0.0021 20.4 2.4 31 11-47 53-88 (110)
260 smart00154 ZnF_AN1 AN1-like Zi 20.7 96 0.0021 17.0 1.9 16 109-124 12-28 (39)
261 KOG4582 Uncharacterized conser 20.6 62 0.0013 25.7 1.5 27 91-120 152-178 (278)
262 cd00730 rubredoxin Rubredoxin; 20.5 60 0.0013 19.0 1.1 11 51-61 33-43 (50)
263 PF12088 DUF3565: Protein of u 20.0 61 0.0013 19.9 1.1 16 27-42 9-24 (61)
No 1
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=99.89 E-value=2.5e-23 Score=162.59 Aligned_cols=124 Identities=48% Similarity=0.979 Sum_probs=117.7
Q ss_pred CCCccccccCcccccccccccccccCCccEEecCCCcccHHHHHhhhccccCCCCCCCCCCchhhhHHHHHHHHHhcCCC
Q 032467 2 KDKHRCVERAMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLWDMSKLWSKIDQEIASTPM 81 (140)
Q Consensus 2 ~~~h~c~e~~~~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~~~~~~~~~~l~~~~~~~~~ 81 (140)
.++|.|+|++.+..||||.|.++.+...+..++|||..|.+|++.....+ ++||+|.+ +.+++.+|+.++.++...++
T Consensus 147 ~~~H~c~e~~~~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~~-y~CP~C~~-~~d~~~~~~~~d~~l~~~~~ 224 (276)
T KOG1940|consen 147 SNWHKCVERSSEFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICEG-YTCPICSK-PGDMSHYFRKLDKELAGSPM 224 (276)
T ss_pred ccccchhhhcccCCCchhHHHhccccccCCccCcccchHHHHHHHHhccC-CCCCcccc-hHHHHHHHHHHHHHHhcCCC
Confidence 46799999999999999999999999999999999999999999998756 99999999 99999999999999999999
Q ss_pred ChhhhcccceecCCCCCCCcccceeeeccccccCCCcccccccCCC
Q 032467 82 PAMYQNKMVWILCNDCGANSHVQFHVIAHKCLSCKSYNTRQTRGDT 127 (140)
Q Consensus 82 ~~~~~~~~~~i~C~~C~~~~~~~~~~~~~~C~~C~~~~~~~~~~~~ 127 (140)
|++|+++..++.|++|+...+++||+++++|+.|++||+++++.|.
T Consensus 225 p~~y~~~~~~i~cndC~~~~~~k~~~l~~kc~~c~~~~~r~~~~~~ 270 (276)
T KOG1940|consen 225 PEEYKNKTQDILCNDCGSGTNVKYHILYHKCGKCGSYNTRMISDPS 270 (276)
T ss_pred CchhhchhheeeccCCCCCCccceehhhhhCCCcccceeeeccCCC
Confidence 9999999999999999999999999999999999999999998443
No 2
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=99.75 E-value=1e-19 Score=112.68 Aligned_cols=60 Identities=63% Similarity=1.162 Sum_probs=22.2
Q ss_pred chhhhHHHHHHHHHhcCCCChhhhcccceecCCCCCCCcccceeeeccccccCCCccccc
Q 032467 63 WDMSKLWSKIDQEIASTPMPAMYQNKMVWILCNDCGANSHVQFHVIAHKCLSCKSYNTRQ 122 (140)
Q Consensus 63 ~~~~~~~~~l~~~~~~~~~~~~~~~~~~~i~C~~C~~~~~~~~~~~~~~C~~C~~~~~~~ 122 (140)
.+|+..|+.|+.+++.++||++|++.+++|+|+||++++.+.||++|+||..|+||||++
T Consensus 2 ~dM~~~w~~LD~~i~~~pmP~~Y~~~~v~IlCNDC~~~s~v~fH~lg~KC~~C~SYNT~q 61 (61)
T PF14599_consen 2 VDMSAYWRMLDAEIAATPMPEEYRNKKVWILCNDCNAKSEVPFHFLGHKCSHCGSYNTRQ 61 (61)
T ss_dssp --------------------------EEEEEESSS--EEEEE--TT----TTTS---EEE
T ss_pred CCHHHHHHHHHHHHHhCCCCHHHhCCEEEEECCCCCCccceeeeHhhhcCCCCCCcccCC
Confidence 467889999999999999999999999999999999999999999999999999999985
No 3
>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=99.47 E-value=1.7e-14 Score=83.90 Aligned_cols=43 Identities=44% Similarity=0.977 Sum_probs=36.8
Q ss_pred ccccccccccccCCccEEecCCCcccHHHHHhhhccccCCCCCCC
Q 032467 15 NCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCS 59 (140)
Q Consensus 15 ~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR 59 (140)
+|+||++.+.. ...++.++|||.||.+||.+|+.. +.+||+||
T Consensus 2 ~C~IC~~~~~~-~~~~~~l~C~H~fh~~Ci~~~~~~-~~~CP~CR 44 (44)
T PF13639_consen 2 ECPICLEEFED-GEKVVKLPCGHVFHRSCIKEWLKR-NNSCPVCR 44 (44)
T ss_dssp CETTTTCBHHT-TSCEEEETTSEEEEHHHHHHHHHH-SSB-TTTH
T ss_pred CCcCCChhhcC-CCeEEEccCCCeeCHHHHHHHHHh-CCcCCccC
Confidence 69999999754 567788999999999999999985 57999997
No 4
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=99.34 E-value=1e-12 Score=75.82 Aligned_cols=39 Identities=41% Similarity=1.059 Sum_probs=29.8
Q ss_pred cccccccccccCCccEEecCCCcccHHHHHhhhccc---cCCCCCC
Q 032467 16 CPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHY---RYTCPVC 58 (140)
Q Consensus 16 C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~---~~~CP~C 58 (140)
||||++. +.+|++|+|||+||..||.+|+... .+.||+|
T Consensus 1 CpiC~~~----~~~Pv~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDL----FKDPVSLPCGHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB-----SSEEE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCccchh----hCCccccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 8999975 5789999999999999999998753 2579987
No 5
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=99.23 E-value=9.7e-12 Score=93.02 Aligned_cols=58 Identities=26% Similarity=0.608 Sum_probs=46.2
Q ss_pred CCccccccCcccccccccccccccCCccEEecCCCcccHHHHHhhhcc---------------ccCCCCCCCCCCch
Q 032467 3 DKHRCVERAMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKH---------------YRYTCPVCSKSLWD 64 (140)
Q Consensus 3 ~~h~c~e~~~~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~---------------~~~~CP~CR~~~~~ 64 (140)
|+-.-++...+.+|+||++. ..++++++|||.||..||.+|+.. ....||+||..+..
T Consensus 8 ~~~~~~~~~~~~~CpICld~----~~dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~ 80 (193)
T PLN03208 8 DDTTLVDSGGDFDCNICLDQ----VRDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE 80 (193)
T ss_pred ccceeccCCCccCCccCCCc----CCCcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence 44455666778999999985 467888999999999999999742 23579999999754
No 6
>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=99.22 E-value=1.2e-11 Score=79.49 Aligned_cols=46 Identities=37% Similarity=0.768 Sum_probs=35.0
Q ss_pred cccccccccccccc---------CCccEEecCCCcccHHHHHhhhccccCCCCCCC
Q 032467 13 HHNCPICFEFIFDT---------MKDITVLRCGHTIHLECLKEMEKHYRYTCPVCS 59 (140)
Q Consensus 13 ~~~C~IC~e~l~~~---------~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR 59 (140)
+..|+||++.|.+. ...++..+|||.||..||.+|+.. +.+||+||
T Consensus 19 ~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~-~~~CP~CR 73 (73)
T PF12678_consen 19 DDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQ-NNTCPLCR 73 (73)
T ss_dssp CSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTT-SSB-TTSS
T ss_pred CCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhc-CCcCCCCC
Confidence 55699999988332 133455699999999999999984 46999998
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=99.22 E-value=8.6e-12 Score=74.32 Aligned_cols=46 Identities=37% Similarity=0.927 Sum_probs=38.4
Q ss_pred ccccccccccccccCCccEEecCCCc-ccHHHHHhhhccccCCCCCCCCCCc
Q 032467 13 HHNCPICFEFIFDTMKDITVLRCGHT-IHLECLKEMEKHYRYTCPVCSKSLW 63 (140)
Q Consensus 13 ~~~C~IC~e~l~~~~~~~~~l~CgH~-Fc~~Cl~~~~~~~~~~CP~CR~~~~ 63 (140)
+..|.||++. ...++.+||||. ||..|+.+|+. ....||+||+.+.
T Consensus 2 ~~~C~iC~~~----~~~~~~~pCgH~~~C~~C~~~~~~-~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFEN----PRDVVLLPCGHLCFCEECAERLLK-RKKKCPICRQPIE 48 (50)
T ss_dssp HSB-TTTSSS----BSSEEEETTCEEEEEHHHHHHHHH-TTSBBTTTTBB-S
T ss_pred cCCCccCCcc----CCceEEeCCCChHHHHHHhHHhcc-cCCCCCcCChhhc
Confidence 5789999975 466788899999 99999999988 6688999999874
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=99.21 E-value=8.5e-12 Score=70.69 Aligned_cols=38 Identities=39% Similarity=1.032 Sum_probs=31.4
Q ss_pred cccccccccccCCcc-EEecCCCcccHHHHHhhhccccCCCCCC
Q 032467 16 CPICFEFIFDTMKDI-TVLRCGHTIHLECLKEMEKHYRYTCPVC 58 (140)
Q Consensus 16 C~IC~e~l~~~~~~~-~~l~CgH~Fc~~Cl~~~~~~~~~~CP~C 58 (140)
|+||++.+ .++ +.++|||+||.+|+.+|++. +.+||+|
T Consensus 1 C~iC~~~~----~~~~~~~~CGH~fC~~C~~~~~~~-~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDEL----RDPVVVTPCGHSFCKECIEKYLEK-NPKCPVC 39 (39)
T ss_dssp ETTTTSB-----SSEEEECTTSEEEEHHHHHHHHHC-TSB-TTT
T ss_pred CCCCCCcc----cCcCEECCCCCchhHHHHHHHHHC-cCCCcCC
Confidence 89999863 335 67899999999999999996 7899998
No 9
>PHA02929 N1R/p28-like protein; Provisional
Probab=99.20 E-value=1.2e-11 Score=95.58 Aligned_cols=54 Identities=30% Similarity=0.682 Sum_probs=42.1
Q ss_pred cCcccccccccccccccCC----ccEEecCCCcccHHHHHhhhccccCCCCCCCCCCch
Q 032467 10 RAMHHNCPICFEFIFDTMK----DITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLWD 64 (140)
Q Consensus 10 ~~~~~~C~IC~e~l~~~~~----~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~~~ 64 (140)
.+.+.+|+||++.+.+... -++.++|||.||..||.+|+. .+.+||+||..+..
T Consensus 171 ~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~-~~~tCPlCR~~~~~ 228 (238)
T PHA02929 171 RSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKK-EKNTCPVCRTPFIS 228 (238)
T ss_pred CCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHh-cCCCCCCCCCEeeE
Confidence 4557899999998654221 135568999999999999998 56789999998743
No 10
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=99.18 E-value=1.4e-11 Score=71.43 Aligned_cols=40 Identities=40% Similarity=0.924 Sum_probs=25.1
Q ss_pred cccccccccccCCccEEecCCCcccHHHHHhhhccc---cCCCC
Q 032467 16 CPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHY---RYTCP 56 (140)
Q Consensus 16 C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~---~~~CP 56 (140)
||||.| +.+....|+.|+|||+||.+||++++..+ .++||
T Consensus 1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~~~~~~kCP 43 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKSDRNRFKCP 43 (43)
T ss_dssp -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcCCCCeeeCc
Confidence 899999 76667889999999999999999998753 46677
No 11
>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=99.16 E-value=3.3e-11 Score=68.67 Aligned_cols=45 Identities=33% Similarity=0.868 Sum_probs=35.7
Q ss_pred ccccccccccccCCccEEecCCCcccHHHHHhhhccccCCCCCCCCCC
Q 032467 15 NCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSL 62 (140)
Q Consensus 15 ~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~ 62 (140)
.|+||++.+ ......++|||.||..|+..|+......||+||..+
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 599999864 233444569999999999999986567899999763
No 12
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=99.15 E-value=3.5e-11 Score=69.92 Aligned_cols=44 Identities=34% Similarity=0.831 Sum_probs=37.2
Q ss_pred ccccccccccccCCccEEecCCCcccHHHHHhhhccccCCCCCCCC
Q 032467 15 NCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSK 60 (140)
Q Consensus 15 ~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~ 60 (140)
.|+||++.+ +....+.+++|||+||..|+.++. .....||+||+
T Consensus 1 ~C~~C~~~~-~~~~~~~l~~CgH~~C~~C~~~~~-~~~~~CP~C~k 44 (44)
T PF14634_consen 1 HCNICFEKY-SEERRPRLTSCGHIFCEKCLKKLK-GKSVKCPICRK 44 (44)
T ss_pred CCcCcCccc-cCCCCeEEcccCCHHHHHHHHhhc-CCCCCCcCCCC
Confidence 489999987 445678899999999999999998 34578999985
No 13
>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=99.10 E-value=6.2e-11 Score=67.53 Aligned_cols=39 Identities=38% Similarity=0.984 Sum_probs=32.7
Q ss_pred cccccccccccCCccE-EecCCCcccHHHHHhhhc-cccCCCCCC
Q 032467 16 CPICFEFIFDTMKDIT-VLRCGHTIHLECLKEMEK-HYRYTCPVC 58 (140)
Q Consensus 16 C~IC~e~l~~~~~~~~-~l~CgH~Fc~~Cl~~~~~-~~~~~CP~C 58 (140)
|+||++.+ ..+. +++|||.||..|+.+|++ .....||+|
T Consensus 1 C~iC~~~~----~~~~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEPF----EDPVILLPCGHSFCRDCLRKWLENSGSVKCPLC 41 (41)
T ss_dssp ETTTSSBC----SSEEEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred CCcCCccc----cCCCEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence 89999863 3444 889999999999999998 566789998
No 14
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.10 E-value=4.5e-11 Score=96.53 Aligned_cols=50 Identities=28% Similarity=0.721 Sum_probs=42.9
Q ss_pred cccccccccccccCCccEEecCCCcccHHHHHhhhccccCCCCCCCCCCch
Q 032467 14 HNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLWD 64 (140)
Q Consensus 14 ~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~~~ 64 (140)
..|+||+|++.. .+..+.|||+|.||..||+.|+...+..||+|+..+.+
T Consensus 230 ~~CaIClEdY~~-GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~di~~ 279 (348)
T KOG4628|consen 230 DTCAICLEDYEK-GDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRDIRT 279 (348)
T ss_pred ceEEEeeccccc-CCeeeEecCCCchhhccchhhHhhcCccCCCCCCcCCC
Confidence 499999999654 56778899999999999999998666679999998744
No 15
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=99.09 E-value=3.7e-11 Score=97.14 Aligned_cols=52 Identities=33% Similarity=0.809 Sum_probs=44.4
Q ss_pred cCcccccccccccccccC---------CccEEecCCCcccHHHHHhhhccccCCCCCCCCCC
Q 032467 10 RAMHHNCPICFEFIFDTM---------KDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSL 62 (140)
Q Consensus 10 ~~~~~~C~IC~e~l~~~~---------~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~ 62 (140)
-+.|..|.||+|+|+... ..|+.|||||.||.+|++.|+++ +.+||+||.++
T Consensus 284 ~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ER-qQTCPICr~p~ 344 (491)
T COG5243 284 TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLER-QQTCPICRRPV 344 (491)
T ss_pred cCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHh-ccCCCcccCcc
Confidence 567899999999976544 34688999999999999999994 57899999994
No 16
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.06 E-value=9.8e-11 Score=86.17 Aligned_cols=57 Identities=28% Similarity=0.659 Sum_probs=44.2
Q ss_pred CCccccccCcccccccccccccccCCccEEecCCCcccHHHHHhhhccccCCCCCCCCCCc
Q 032467 3 DKHRCVERAMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLW 63 (140)
Q Consensus 3 ~~h~c~e~~~~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~~ 63 (140)
+.|.-.+.+ -+.|||||+.+ ....++.+.|||+||..||+..+.. ...||+||+.+.
T Consensus 122 ~v~~~~~~~-~~~CPiCl~~~--sek~~vsTkCGHvFC~~Cik~alk~-~~~CP~C~kkIt 178 (187)
T KOG0320|consen 122 DVDPLRKEG-TYKCPICLDSV--SEKVPVSTKCGHVFCSQCIKDALKN-TNKCPTCRKKIT 178 (187)
T ss_pred ccccccccc-ccCCCceecch--hhccccccccchhHHHHHHHHHHHh-CCCCCCcccccc
Confidence 444444443 48999999974 3456677999999999999999984 478999998763
No 17
>PHA02926 zinc finger-like protein; Provisional
Probab=99.03 E-value=1.5e-10 Score=88.10 Aligned_cols=55 Identities=18% Similarity=0.538 Sum_probs=41.3
Q ss_pred ccCccccccccccccccc----C-CccEEecCCCcccHHHHHhhhccc-----cCCCCCCCCCCc
Q 032467 9 ERAMHHNCPICFEFIFDT----M-KDITVLRCGHTIHLECLKEMEKHY-----RYTCPVCSKSLW 63 (140)
Q Consensus 9 e~~~~~~C~IC~e~l~~~----~-~~~~~l~CgH~Fc~~Cl~~~~~~~-----~~~CP~CR~~~~ 63 (140)
+.+.+.+|+||+|.++.. . .-.+..+|+|.||..||.+|.... ...||+||..+.
T Consensus 166 ~~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~ 230 (242)
T PHA02926 166 RVSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFR 230 (242)
T ss_pred hccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceee
Confidence 346689999999976432 1 123455999999999999998742 345999999864
No 18
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.02 E-value=1.7e-10 Score=87.99 Aligned_cols=50 Identities=30% Similarity=0.656 Sum_probs=42.3
Q ss_pred cCcccccccccccccccCCccEEecCCCcccHHHHHhhhcc--ccCCCCCCCCCCc
Q 032467 10 RAMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKH--YRYTCPVCSKSLW 63 (140)
Q Consensus 10 ~~~~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~--~~~~CP~CR~~~~ 63 (140)
.....+|.||||. .++|+++.|||.||+-||-+|+.. ....||+|+..+.
T Consensus 44 ~~~~FdCNICLd~----akdPVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs 95 (230)
T KOG0823|consen 44 DGGFFDCNICLDL----AKDPVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVS 95 (230)
T ss_pred CCCceeeeeeccc----cCCCEEeecccceehHHHHHHHhhcCCCeeCCccccccc
Confidence 4567899999973 678999999999999999999975 3456999998874
No 19
>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=98.98 E-value=4.9e-10 Score=61.66 Aligned_cols=39 Identities=49% Similarity=1.056 Sum_probs=33.5
Q ss_pred cccccccccccCCccEEecCCCcccHHHHHhhhccccCCCCCC
Q 032467 16 CPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVC 58 (140)
Q Consensus 16 C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~C 58 (140)
|+||++. ...++.++|||.||..|+..|+......||+|
T Consensus 1 C~iC~~~----~~~~~~~~C~H~~c~~C~~~~~~~~~~~CP~C 39 (39)
T smart00184 1 CPICLEE----LKDPVVLPCGHTFCRSCIRKWLKSGNNTCPIC 39 (39)
T ss_pred CCcCccC----CCCcEEecCCChHHHHHHHHHHHhCcCCCCCC
Confidence 7899975 56788899999999999999988556779987
No 20
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=98.98 E-value=1.7e-10 Score=95.04 Aligned_cols=83 Identities=27% Similarity=0.606 Sum_probs=67.2
Q ss_pred ccccccccccccccCCccEEecCCCcccHHHHHhhhccccCCCCCCCCCCchhhhHHHHHHHHHhcCCCChhhhccccee
Q 032467 13 HHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLWDMSKLWSKIDQEIASTPMPAMYQNKMVWI 92 (140)
Q Consensus 13 ~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~i 92 (140)
-..||||+|.|+++..-.+.+.|.|+||..|+.+|+. .+||+||....+ ......
T Consensus 175 LPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~~---~scpvcR~~q~p----------------------~~ve~~ 229 (493)
T KOG0804|consen 175 LPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWWD---SSCPVCRYCQSP----------------------SVVESS 229 (493)
T ss_pred CCCcchhHhhcCccccceeeeecccccchHHHhhccc---CcChhhhhhcCc----------------------chhhhh
Confidence 3689999999988877788889999999999999987 579999976321 011245
Q ss_pred cCCCCCCCcccceeeecccccc--CCCcccccc
Q 032467 93 LCNDCGANSHVQFHVIAHKCLS--CKSYNTRQT 123 (140)
Q Consensus 93 ~C~~C~~~~~~~~~~~~~~C~~--C~~~~~~~~ 123 (140)
.|..|+...+. |+.+.|.. ||.|...+.
T Consensus 230 ~c~~c~~~~~L---wicliCg~vgcgrY~eghA 259 (493)
T KOG0804|consen 230 LCLACGCTEDL---WICLICGNVGCGRYKEGHA 259 (493)
T ss_pred hhhhhcccccE---EEEEEccceecccccchhH
Confidence 68889877666 89999996 999999886
No 21
>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=98.92 E-value=1.5e-09 Score=67.04 Aligned_cols=46 Identities=30% Similarity=0.429 Sum_probs=39.5
Q ss_pred ccccccccccccccCCccEEecCCCcccHHHHHhhhccccCCCCCCCCCCc
Q 032467 13 HHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLW 63 (140)
Q Consensus 13 ~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~~ 63 (140)
+..||||++. +.+|+.++|||+|+..||.+|+.. +..||+|+..+.
T Consensus 1 ~~~Cpi~~~~----~~~Pv~~~~G~v~~~~~i~~~~~~-~~~cP~~~~~~~ 46 (63)
T smart00504 1 EFLCPISLEV----MKDPVILPSGQTYERRAIEKWLLS-HGTDPVTGQPLT 46 (63)
T ss_pred CcCCcCCCCc----CCCCEECCCCCEEeHHHHHHHHHH-CCCCCCCcCCCC
Confidence 3679999986 455789999999999999999985 678999998873
No 22
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=98.91 E-value=5.5e-10 Score=87.63 Aligned_cols=47 Identities=23% Similarity=0.650 Sum_probs=40.2
Q ss_pred ccccccccccccccCCccEEecCCCcccHHHHHhhhccccCCCCCCCCCCch
Q 032467 13 HHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLWD 64 (140)
Q Consensus 13 ~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~~~ 64 (140)
...|.+|+|. ...|..+||||.||+.||..|.. ....||+||..+..
T Consensus 239 ~~kC~LCLe~----~~~pSaTpCGHiFCWsCI~~w~~-ek~eCPlCR~~~~p 285 (293)
T KOG0317|consen 239 TRKCSLCLEN----RSNPSATPCGHIFCWSCILEWCS-EKAECPLCREKFQP 285 (293)
T ss_pred CCceEEEecC----CCCCCcCcCcchHHHHHHHHHHc-cccCCCcccccCCC
Confidence 4689999974 56788899999999999999997 45679999998743
No 23
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=98.82 E-value=4.2e-09 Score=69.16 Aligned_cols=50 Identities=20% Similarity=0.466 Sum_probs=36.3
Q ss_pred cccccccccccc--------ccC-CccEEecCCCcccHHHHHhhhcc--ccCCCCCCCCCC
Q 032467 13 HHNCPICFEFIF--------DTM-KDITVLRCGHTIHLECLKEMEKH--YRYTCPVCSKSL 62 (140)
Q Consensus 13 ~~~C~IC~e~l~--------~~~-~~~~~l~CgH~Fc~~Cl~~~~~~--~~~~CP~CR~~~ 62 (140)
+..|+||...|. .+. -+++.-.|+|.||..||.+|++. ++..||+||...
T Consensus 21 dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w 81 (85)
T PF12861_consen 21 DDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPW 81 (85)
T ss_pred CCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCee
Confidence 566777766542 111 23455599999999999999985 357899999875
No 24
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.80 E-value=3e-09 Score=84.19 Aligned_cols=52 Identities=27% Similarity=0.662 Sum_probs=43.1
Q ss_pred CcccccccccccccccCCccEEecCCCcccHHHHHhhhccccCCCCCCCCCCc
Q 032467 11 AMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLW 63 (140)
Q Consensus 11 ~~~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~~ 63 (140)
....+|+|||+.+. ..+..+.|||.|.||..|+++|+...+..||+||..+.
T Consensus 321 ~~GveCaICms~fi-K~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iP 372 (374)
T COG5540 321 DKGVECAICMSNFI-KNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIP 372 (374)
T ss_pred CCCceEEEEhhhhc-ccceEEEeccCceechhHHHHHHhhhcccCCccCCCCC
Confidence 33478999999875 34557889999999999999999855678999998864
No 25
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.69 E-value=1e-08 Score=84.58 Aligned_cols=48 Identities=23% Similarity=0.555 Sum_probs=40.2
Q ss_pred CcccccccccccccccCCccEEecCCCcccHHHHHhhhccccCCCCCCCCCCc
Q 032467 11 AMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLW 63 (140)
Q Consensus 11 ~~~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~~ 63 (140)
...+.|+||++.| ..|++++|||+||..||..|+.. ...||+||..+.
T Consensus 24 e~~l~C~IC~d~~----~~PvitpCgH~FCs~CI~~~l~~-~~~CP~Cr~~~~ 71 (397)
T TIGR00599 24 DTSLRCHICKDFF----DVPVLTSCSHTFCSLCIRRCLSN-QPKCPLCRAEDQ 71 (397)
T ss_pred ccccCCCcCchhh----hCccCCCCCCchhHHHHHHHHhC-CCCCCCCCCccc
Confidence 3468999999863 56778999999999999999974 457999999864
No 26
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.64 E-value=1.4e-08 Score=84.95 Aligned_cols=48 Identities=25% Similarity=0.582 Sum_probs=38.6
Q ss_pred cccccccccccccccCCccEEecCCCcccHHHHHhhhccc----cCCCCCCCCCCc
Q 032467 12 MHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHY----RYTCPVCSKSLW 63 (140)
Q Consensus 12 ~~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~----~~~CP~CR~~~~ 63 (140)
.+..||||++. ...++.+.|||.||..||.++|..+ ...||+||..+.
T Consensus 185 t~~~CPICL~~----~~~p~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~ 236 (513)
T KOG2164|consen 185 TDMQCPICLEP----PSVPVRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTIT 236 (513)
T ss_pred cCCcCCcccCC----CCcccccccCceeeHHHHHHHHhhhcccCCccCCchhhhcc
Confidence 38899999985 3445666799999999999987653 357999998864
No 27
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=98.61 E-value=2.1e-08 Score=80.57 Aligned_cols=47 Identities=28% Similarity=0.745 Sum_probs=40.9
Q ss_pred ccccccccccccccCCccEEecCCCcccHHHHHhhhccccCCCCCCCCCCch
Q 032467 13 HHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLWD 64 (140)
Q Consensus 13 ~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~~~ 64 (140)
-+.|.||.|+ +..|+++||||+||.-||+.++. .+..||.|+.++..
T Consensus 23 lLRC~IC~ey----f~ip~itpCsHtfCSlCIR~~L~-~~p~CP~C~~~~~E 69 (442)
T KOG0287|consen 23 LLRCGICFEY----FNIPMITPCSHTFCSLCIRKFLS-YKPQCPTCCVTVTE 69 (442)
T ss_pred HHHHhHHHHH----hcCceeccccchHHHHHHHHHhc-cCCCCCceecccch
Confidence 4689999997 46789999999999999999998 56889999998753
No 28
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.55 E-value=2.5e-08 Score=76.31 Aligned_cols=45 Identities=33% Similarity=0.846 Sum_probs=38.4
Q ss_pred CcccccccccccccccCCccEEecCCCcccHHHHHhhhccccCCCCCCCC
Q 032467 11 AMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSK 60 (140)
Q Consensus 11 ~~~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~ 60 (140)
.....|+||++.| ..|++++|||+||..|+..++. ....||.||.
T Consensus 11 ~~~~~C~iC~~~~----~~p~~l~C~H~~c~~C~~~~~~-~~~~Cp~cr~ 55 (386)
T KOG2177|consen 11 QEELTCPICLEYF----REPVLLPCGHNFCRACLTRSWE-GPLSCPVCRP 55 (386)
T ss_pred cccccChhhHHHh----hcCccccccchHhHHHHHHhcC-CCcCCcccCC
Confidence 3578999999874 4448899999999999999988 6688999994
No 29
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.55 E-value=2.7e-08 Score=85.25 Aligned_cols=51 Identities=31% Similarity=0.630 Sum_probs=41.9
Q ss_pred CcccccccccccccccC-CccEEecCCCcccHHHHHhhhccccCCCCCCCCCC
Q 032467 11 AMHHNCPICFEFIFDTM-KDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSL 62 (140)
Q Consensus 11 ~~~~~C~IC~e~l~~~~-~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~ 62 (140)
..+..|+||+|.|.... ..+..|+|||.||..|+.+|++. ..+||+||..+
T Consensus 289 ~~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er-~qtCP~CR~~~ 340 (543)
T KOG0802|consen 289 LSDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFER-QQTCPTCRTVL 340 (543)
T ss_pred hcCCeeeeechhhccccccccceeecccchHHHHHHHHHHH-hCcCCcchhhh
Confidence 44889999999875422 23678999999999999999995 68899999954
No 30
>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=98.54 E-value=6.5e-08 Score=77.24 Aligned_cols=51 Identities=25% Similarity=0.535 Sum_probs=37.1
Q ss_pred ccccccccccccccCCc-cEEecCCCcccHHHHHhhhccccCCCCCCCCCCc
Q 032467 13 HHNCPICFEFIFDTMKD-ITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLW 63 (140)
Q Consensus 13 ~~~C~IC~e~l~~~~~~-~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~~ 63 (140)
+..||||....+..... ..+.+|||.||..|+..++..+...||.|+..+.
T Consensus 3 ~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lr 54 (309)
T TIGR00570 3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLR 54 (309)
T ss_pred CCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCccc
Confidence 46899999853221121 1222799999999999987766778999998764
No 31
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.52 E-value=4.3e-08 Score=76.25 Aligned_cols=47 Identities=28% Similarity=0.565 Sum_probs=38.5
Q ss_pred cccccccccccccccCCccEEecCCCcccHHHHHh-hhccccCCCCCCCCCC
Q 032467 12 MHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKE-MEKHYRYTCPVCSKSL 62 (140)
Q Consensus 12 ~~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~-~~~~~~~~CP~CR~~~ 62 (140)
.+..|+||++. ...+..++|||.||..||.. |-......||+||..+
T Consensus 214 ~d~kC~lC~e~----~~~ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~ 261 (271)
T COG5574 214 ADYKCFLCLEE----PEVPSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKV 261 (271)
T ss_pred cccceeeeecc----cCCcccccccchhhHHHHHHHHHhhccccCchhhhhc
Confidence 47889999985 56788899999999999999 7654333499999885
No 32
>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=1.4e-07 Score=60.42 Aligned_cols=49 Identities=27% Similarity=0.370 Sum_probs=38.9
Q ss_pred cccccccccccccccCCccEEecCCCcccHHHHHhhhccccCCCCCCCCCCch
Q 032467 12 MHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLWD 64 (140)
Q Consensus 12 ~~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~~~ 64 (140)
.++.|||+.+. +.+|+++++||+|.+.+|.+|+......||+++..+..
T Consensus 3 ~~f~CpIt~~l----M~dPVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~ 51 (73)
T PF04564_consen 3 DEFLCPITGEL----MRDPVILPSGHTYERSAIERWLEQNGGTDPFTRQPLSE 51 (73)
T ss_dssp GGGB-TTTSSB-----SSEEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SG
T ss_pred cccCCcCcCcH----hhCceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCc
Confidence 46889999975 57899999999999999999999767899999988754
No 33
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=98.32 E-value=6.2e-07 Score=57.99 Aligned_cols=52 Identities=17% Similarity=0.305 Sum_probs=37.4
Q ss_pred cCcccccccccccccccCCcc-EEecCCCcccHHHHHhhhccccCCCCCCCCCC
Q 032467 10 RAMHHNCPICFEFIFDTMKDI-TVLRCGHTIHLECLKEMEKHYRYTCPVCSKSL 62 (140)
Q Consensus 10 ~~~~~~C~IC~e~l~~~~~~~-~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~ 62 (140)
+.....|+-|+..+....+-+ +.-.|.|.||..||.+|+.. +..||++|++.
T Consensus 28 nhim~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~T-k~~CPld~q~w 80 (88)
T COG5194 28 NHIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDT-KGVCPLDRQTW 80 (88)
T ss_pred ccccCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhh-CCCCCCCCcee
Confidence 344556777775443333333 33499999999999999984 67899999885
No 34
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=98.31 E-value=1.3e-07 Score=60.24 Aligned_cols=50 Identities=32% Similarity=0.683 Sum_probs=23.2
Q ss_pred ccccccccccccccCCccEEe----cCCCcccHHHHHhhhccc----------cCCCCCCCCCC
Q 032467 13 HHNCPICFEFIFDTMKDITVL----RCGHTIHLECLKEMEKHY----------RYTCPVCSKSL 62 (140)
Q Consensus 13 ~~~C~IC~e~l~~~~~~~~~l----~CgH~Fc~~Cl~~~~~~~----------~~~CP~CR~~~ 62 (140)
+.+|+||++.+.+....|... .|+..||..||.+|+... ...||.|+.++
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i 65 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPI 65 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEE
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCee
Confidence 578999998765333333222 899999999999998641 13599999886
No 35
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.27 E-value=1.8e-07 Score=75.96 Aligned_cols=83 Identities=17% Similarity=0.396 Sum_probs=51.7
Q ss_pred cCcccccccccccccccC---CccEE-ecCCCcccHHHHHhhhccc------cCCCCCCCCCCchhhhHHHHHHHHHhcC
Q 032467 10 RAMHHNCPICFEFIFDTM---KDITV-LRCGHTIHLECLKEMEKHY------RYTCPVCSKSLWDMSKLWSKIDQEIAST 79 (140)
Q Consensus 10 ~~~~~~C~IC~e~l~~~~---~~~~~-l~CgH~Fc~~Cl~~~~~~~------~~~CP~CR~~~~~~~~~~~~l~~~~~~~ 79 (140)
++.+..|.||+|.+.... ..-.+ ++|.|.||..||.+|.... ...||.||.....+...........+..
T Consensus 158 ~s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~~v~pS~~Wv~t~~~k~ 237 (344)
T KOG1039|consen 158 KSSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSSFVNPSSFWVETKEEKQ 237 (344)
T ss_pred ccccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccccccccceeeeeccccc
Confidence 466889999999765432 11233 4799999999999998432 3679999998643222110112222444
Q ss_pred CCChhhhccccee
Q 032467 80 PMPAMYQNKMVWI 92 (140)
Q Consensus 80 ~~~~~~~~~~~~i 92 (140)
.++++|...+...
T Consensus 238 ~li~e~~~~~s~~ 250 (344)
T KOG1039|consen 238 KLIEEYEAEMSAK 250 (344)
T ss_pred ccHHHHHHHhhcc
Confidence 5566666655443
No 36
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=98.22 E-value=6.3e-07 Score=70.93 Aligned_cols=45 Identities=27% Similarity=0.489 Sum_probs=39.0
Q ss_pred ccccccccccccccCCccEEecCCCcccHHHHHhhhccccCCCCCCCCCC
Q 032467 13 HHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSL 62 (140)
Q Consensus 13 ~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~ 62 (140)
-+.|-||-+. +..|..++|||+||.-||+..+. .+..||+||...
T Consensus 25 ~lrC~IC~~~----i~ip~~TtCgHtFCslCIR~hL~-~qp~CP~Cr~~~ 69 (391)
T COG5432 25 MLRCRICDCR----ISIPCETTCGHTFCSLCIRRHLG-TQPFCPVCREDP 69 (391)
T ss_pred HHHhhhhhhe----eecceecccccchhHHHHHHHhc-CCCCCccccccH
Confidence 4679999975 46788999999999999999997 568899999884
No 37
>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=98.19 E-value=1.6e-06 Score=51.45 Aligned_cols=43 Identities=30% Similarity=0.617 Sum_probs=33.7
Q ss_pred ccccccccccccCCccEEecCC-----CcccHHHHHhhhccc-cCCCCCCC
Q 032467 15 NCPICFEFIFDTMKDITVLRCG-----HTIHLECLKEMEKHY-RYTCPVCS 59 (140)
Q Consensus 15 ~C~IC~e~l~~~~~~~~~l~Cg-----H~Fc~~Cl~~~~~~~-~~~CP~CR 59 (140)
.|-||++. .....+...||. |.+|..||.+|+... ..+||+|+
T Consensus 1 ~CrIC~~~--~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~ 49 (49)
T smart00744 1 ICRICHDE--GDEGDPLVSPCRCKGSLKYVHQECLERWINESGNKTCEICK 49 (49)
T ss_pred CccCCCCC--CCCCCeeEeccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence 48899972 345666778995 899999999999753 56899995
No 38
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.16 E-value=3.4e-07 Score=55.13 Aligned_cols=51 Identities=27% Similarity=0.694 Sum_probs=39.9
Q ss_pred cccccccccccccccCCccEEecCCCc-ccHHHHHhhhccccCCCCCCCCCCchhh
Q 032467 12 MHHNCPICFEFIFDTMKDITVLRCGHT-IHLECLKEMEKHYRYTCPVCSKSLWDMS 66 (140)
Q Consensus 12 ~~~~C~IC~e~l~~~~~~~~~l~CgH~-Fc~~Cl~~~~~~~~~~CP~CR~~~~~~~ 66 (140)
-+.+|.||+|- ..+.++..|||. +|..|-.+.+...+..||+||+++.++-
T Consensus 6 ~~dECTICye~----pvdsVlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~dvI 57 (62)
T KOG4172|consen 6 WSDECTICYEH----PVDSVLYTCGHMCMCYACGLRLKKALHGCCPICRAPIKDVI 57 (62)
T ss_pred cccceeeeccC----cchHHHHHcchHHhHHHHHHHHHHccCCcCcchhhHHHHHH
Confidence 34799999974 344566699996 9999988877656789999999986643
No 39
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=98.13 E-value=1.2e-06 Score=54.57 Aligned_cols=43 Identities=28% Similarity=0.739 Sum_probs=23.5
Q ss_pred ccccccccccccccCCccEE-ecCCCcccHHHHHhhhccccCCCCCCCCCC
Q 032467 13 HHNCPICFEFIFDTMKDITV-LRCGHTIHLECLKEMEKHYRYTCPVCSKSL 62 (140)
Q Consensus 13 ~~~C~IC~e~l~~~~~~~~~-l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~ 62 (140)
-+.|++|.+. .+.|+. ..|.|+||..|+...+. ..||+|+.+.
T Consensus 7 lLrCs~C~~~----l~~pv~l~~CeH~fCs~Ci~~~~~---~~CPvC~~Pa 50 (65)
T PF14835_consen 7 LLRCSICFDI----LKEPVCLGGCEHIFCSSCIRDCIG---SECPVCHTPA 50 (65)
T ss_dssp TTS-SSS-S------SS-B---SSS--B-TTTGGGGTT---TB-SSS--B-
T ss_pred hcCCcHHHHH----hcCCceeccCccHHHHHHhHHhcC---CCCCCcCChH
Confidence 4679999975 345554 59999999999988765 3599999885
No 40
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.09 E-value=1.6e-06 Score=68.68 Aligned_cols=51 Identities=27% Similarity=0.481 Sum_probs=42.4
Q ss_pred ccCcccccccccccccccCCccEEecCCCcccHHHHHhhhccccCCCCCCCCCCc
Q 032467 9 ERAMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLW 63 (140)
Q Consensus 9 e~~~~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~~ 63 (140)
+..+..+|+||+.. ...|+.|+|+|.||.-||+.........|++||.++.
T Consensus 3 p~~~~~eC~IC~nt----~n~Pv~l~C~HkFCyiCiKGsy~ndk~~CavCR~pid 53 (324)
T KOG0824|consen 3 PRTKKKECLICYNT----GNCPVNLYCFHKFCYICIKGSYKNDKKTCAVCRFPID 53 (324)
T ss_pred CcccCCcceeeecc----CCcCccccccchhhhhhhcchhhcCCCCCceecCCCC
Confidence 34567899999964 5667999999999999999976656677999999974
No 41
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.00 E-value=2.6e-06 Score=71.53 Aligned_cols=51 Identities=31% Similarity=0.643 Sum_probs=38.7
Q ss_pred ccccccccccccc--cC-----------CccEEecCCCcccHHHHHhhhccccCCCCCCCCCCc
Q 032467 13 HHNCPICFEFIFD--TM-----------KDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLW 63 (140)
Q Consensus 13 ~~~C~IC~e~l~~--~~-----------~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~~ 63 (140)
..+|+||+.++.- .. +..+.+||.|.||..|+.+|.+..+..||+||..+.
T Consensus 571 t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLP 634 (636)
T KOG0828|consen 571 TNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLP 634 (636)
T ss_pred cccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCCC
Confidence 5689999986421 00 123456999999999999999855568999998863
No 42
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.96 E-value=3.8e-06 Score=68.72 Aligned_cols=48 Identities=25% Similarity=0.557 Sum_probs=37.2
Q ss_pred ccccccccccccccCCccEEe-cCCCcccHHHHHhhhccc--cCCCCCCCCC
Q 032467 13 HHNCPICFEFIFDTMKDITVL-RCGHTIHLECLKEMEKHY--RYTCPVCSKS 61 (140)
Q Consensus 13 ~~~C~IC~e~l~~~~~~~~~l-~CgH~Fc~~Cl~~~~~~~--~~~CP~CR~~ 61 (140)
...|.|| ++++....+...+ .|||+||..|+.+|++.. +..||+|+-.
T Consensus 4 ~A~C~Ic-~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik 54 (465)
T KOG0827|consen 4 MAECHIC-IDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIK 54 (465)
T ss_pred cceeeEe-ccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeec
Confidence 4689999 5566655666666 599999999999999863 2479999944
No 43
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.92 E-value=7.2e-06 Score=66.34 Aligned_cols=50 Identities=26% Similarity=0.642 Sum_probs=40.4
Q ss_pred cCcccccccccccccccCCccEEecCCCc-ccHHHHHhhhccccCCCCCCCCCCch
Q 032467 10 RAMHHNCPICFEFIFDTMKDITVLRCGHT-IHLECLKEMEKHYRYTCPVCSKSLWD 64 (140)
Q Consensus 10 ~~~~~~C~IC~e~l~~~~~~~~~l~CgH~-Fc~~Cl~~~~~~~~~~CP~CR~~~~~ 64 (140)
+....+|.|||.+ .++.++|||.|. +|..|.+.+.- ....||+||..+..
T Consensus 287 ~~~gkeCVIClse----~rdt~vLPCRHLCLCs~Ca~~Lr~-q~n~CPICRqpi~~ 337 (349)
T KOG4265|consen 287 SESGKECVICLSE----SRDTVVLPCRHLCLCSGCAKSLRY-QTNNCPICRQPIEE 337 (349)
T ss_pred ccCCCeeEEEecC----CcceEEecchhhehhHhHHHHHHH-hhcCCCccccchHh
Confidence 3446799999964 577889999997 99999998763 45679999999743
No 44
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=97.90 E-value=2.8e-06 Score=74.17 Aligned_cols=47 Identities=26% Similarity=0.660 Sum_probs=40.5
Q ss_pred ccccccccccccccCCccEEecCCCcccHHHHHhhhccccCCCCCCCCCCc
Q 032467 13 HHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLW 63 (140)
Q Consensus 13 ~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~~ 63 (140)
-+.||+|-. ...+.+++.|||.||..|+...+.....+||.|...|+
T Consensus 643 ~LkCs~Cn~----R~Kd~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFg 689 (698)
T KOG0978|consen 643 LLKCSVCNT----RWKDAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFG 689 (698)
T ss_pred ceeCCCccC----chhhHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCC
Confidence 468999994 35677888999999999999998877789999999975
No 45
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.89 E-value=1.4e-06 Score=70.35 Aligned_cols=48 Identities=27% Similarity=0.672 Sum_probs=39.9
Q ss_pred ccccccccccccccCCccEEecCCCcccHHHHHhhhccccCCCCCCCCCCc
Q 032467 13 HHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLW 63 (140)
Q Consensus 13 ~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~~ 63 (140)
+..|+|||+.|.. ...+..|+|.||..||..-+..++..||.||+.+.
T Consensus 43 ~v~c~icl~llk~---tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~ 90 (381)
T KOG0311|consen 43 QVICPICLSLLKK---TMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLV 90 (381)
T ss_pred hhccHHHHHHHHh---hcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhcc
Confidence 6789999987543 23445999999999999998888899999999863
No 46
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=97.87 E-value=1e-05 Score=47.67 Aligned_cols=47 Identities=30% Similarity=0.607 Sum_probs=25.4
Q ss_pred cccccccccccCCccEEecCCCcccHHHHHhhhccccCCCCCCCCCC
Q 032467 16 CPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSL 62 (140)
Q Consensus 16 C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~ 62 (140)
||+|.++|........--+||+.+|+.|+...++.....||-||+.+
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 78999998544443333489999999999998876678999999875
No 47
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=97.86 E-value=3.2e-06 Score=54.29 Aligned_cols=33 Identities=24% Similarity=0.575 Sum_probs=26.9
Q ss_pred cEEe-cCCCcccHHHHHhhhcc--ccCCCCCCCCCC
Q 032467 30 ITVL-RCGHTIHLECLKEMEKH--YRYTCPVCSKSL 62 (140)
Q Consensus 30 ~~~l-~CgH~Fc~~Cl~~~~~~--~~~~CP~CR~~~ 62 (140)
|.++ .|.|.||..||.+|+.. ++..||+||.+.
T Consensus 45 PLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~ 80 (84)
T KOG1493|consen 45 PLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTW 80 (84)
T ss_pred ccHHHHHHHHHHHHHHHHHhcCccccccCCcchhee
Confidence 4434 89999999999999875 346799999875
No 48
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.80 E-value=5.6e-06 Score=64.95 Aligned_cols=51 Identities=24% Similarity=0.511 Sum_probs=39.8
Q ss_pred cccccccccccccccC------CccEEecCCCcccHHHHHhhhccc-cCCCCCCCCCC
Q 032467 12 MHHNCPICFEFIFDTM------KDITVLRCGHTIHLECLKEMEKHY-RYTCPVCSKSL 62 (140)
Q Consensus 12 ~~~~C~IC~e~l~~~~------~~~~~l~CgH~Fc~~Cl~~~~~~~-~~~CP~CR~~~ 62 (140)
.+..|+||-..++.+. +..-.|.|+|+||..||+.|---+ ..+||-|++.+
T Consensus 223 ~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekV 280 (328)
T KOG1734|consen 223 SDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKV 280 (328)
T ss_pred CcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHh
Confidence 4688999988765433 134578999999999999996543 46899999886
No 49
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.74 E-value=2.1e-05 Score=65.17 Aligned_cols=49 Identities=29% Similarity=0.649 Sum_probs=41.3
Q ss_pred CcccccccccccccccCCccEEecCCCcccHHHHHhhhccccCCCCCCCCCCch
Q 032467 11 AMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLWD 64 (140)
Q Consensus 11 ~~~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~~~ 64 (140)
..+++|.||+.. ..+|+.+||||+||..||.+.+. ....||.||..+..
T Consensus 82 ~sef~c~vc~~~----l~~pv~tpcghs~c~~Cl~r~ld-~~~~cp~Cr~~l~e 130 (398)
T KOG4159|consen 82 RSEFECCVCSRA----LYPPVVTPCGHSFCLECLDRSLD-QETECPLCRDELVE 130 (398)
T ss_pred cchhhhhhhHhh----cCCCccccccccccHHHHHHHhc-cCCCCccccccccc
Confidence 568899999864 56788889999999999999776 56789999999864
No 50
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=97.54 E-value=7e-05 Score=50.81 Aligned_cols=29 Identities=31% Similarity=0.650 Sum_probs=25.6
Q ss_pred EecCCCcccHHHHHhhhccccCCCCCCCCC
Q 032467 32 VLRCGHTIHLECLKEMEKHYRYTCPVCSKS 61 (140)
Q Consensus 32 ~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~ 61 (140)
--.|.|.||..||.+|+. .+..||++.+.
T Consensus 78 WG~CNHaFH~hCisrWlk-tr~vCPLdn~e 106 (114)
T KOG2930|consen 78 WGVCNHAFHFHCISRWLK-TRNVCPLDNKE 106 (114)
T ss_pred eeecchHHHHHHHHHHHh-hcCcCCCcCcc
Confidence 348999999999999998 56889999876
No 51
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.53 E-value=8.3e-05 Score=58.47 Aligned_cols=50 Identities=24% Similarity=0.605 Sum_probs=38.3
Q ss_pred CcccccccccccccccCCccEEecCCCcccHHHHHhhhcc-ccCCCCCCCCCCc
Q 032467 11 AMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKH-YRYTCPVCSKSLW 63 (140)
Q Consensus 11 ~~~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~-~~~~CP~CR~~~~ 63 (140)
+.+.+||+|.+. ...+-+..+|||.||-.|+..-... ..++||.|...+.
T Consensus 237 t~~~~C~~Cg~~---PtiP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~ 287 (298)
T KOG2879|consen 237 TSDTECPVCGEP---PTIPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVE 287 (298)
T ss_pred cCCceeeccCCC---CCCCeeeccccceeehhhhhhhhcchhhcccCccCCCCc
Confidence 457899999985 3344445579999999999986553 3589999998864
No 52
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.49 E-value=0.00011 Score=58.24 Aligned_cols=50 Identities=32% Similarity=0.622 Sum_probs=42.3
Q ss_pred cccccccccccccc--CCccEEecCCCcccHHHHHhhhccccCCCCCCCCCC
Q 032467 13 HHNCPICFEFIFDT--MKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSL 62 (140)
Q Consensus 13 ~~~C~IC~e~l~~~--~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~ 62 (140)
-..|-||-++|... ...|+.|.|||+||..|+.+.+..+...||.||...
T Consensus 3 ~~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~~~i~cpfcR~~~ 54 (296)
T KOG4185|consen 3 FPECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGNSRILCPFCRETT 54 (296)
T ss_pred CCceeecCccccccCcccCCcccccCceehHhHHHHHhcCceeeccCCCCcc
Confidence 35799999887543 456899999999999999999987778899999984
No 53
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=97.48 E-value=9.8e-05 Score=45.11 Aligned_cols=43 Identities=28% Similarity=0.594 Sum_probs=27.8
Q ss_pred CcccccccccccccccCCcc-EEecCCCcccHHHHHhhhcc-ccCCCCC
Q 032467 11 AMHHNCPICFEFIFDTMKDI-TVLRCGHTIHLECLKEMEKH-YRYTCPV 57 (140)
Q Consensus 11 ~~~~~C~IC~e~l~~~~~~~-~~l~CgH~Fc~~Cl~~~~~~-~~~~CP~ 57 (140)
...+.|||.+.. +.+| +...|||+|-.+.|.+|+.. +...||+
T Consensus 9 ~~~~~CPiT~~~----~~~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv 53 (57)
T PF11789_consen 9 TISLKCPITLQP----FEDPVKSKKCGHTFEKEAILQYIQRNGSKRCPV 53 (57)
T ss_dssp B--SB-TTTSSB-----SSEEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred EeccCCCCcCCh----hhCCcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence 456899999975 3445 45699999999999999942 4577998
No 54
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=97.44 E-value=4.8e-05 Score=62.73 Aligned_cols=47 Identities=32% Similarity=0.680 Sum_probs=38.9
Q ss_pred cccccccccccccccCCccEEecCCCcccHHHHHhhhccc-cCCCCCCCCCC
Q 032467 12 MHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHY-RYTCPVCSKSL 62 (140)
Q Consensus 12 ~~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~-~~~CP~CR~~~ 62 (140)
.=..|-||-|. ..++.+=||||.+|..|+..|-.+. ...||.||-.+
T Consensus 368 TFeLCKICaen----dKdvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEI 415 (563)
T KOG1785|consen 368 TFELCKICAEN----DKDVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEI 415 (563)
T ss_pred hHHHHHHhhcc----CCCcccccccchHHHHHHHhhcccCCCCCCCceeeEe
Confidence 34579999973 5777888999999999999998653 67899999876
No 55
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=97.42 E-value=4.6e-05 Score=68.48 Aligned_cols=52 Identities=23% Similarity=0.563 Sum_probs=38.2
Q ss_pred CcccccccccccccccCC-cc--EEecCCCcccHHHHHhhhcc-ccCCCCCCCCCC
Q 032467 11 AMHHNCPICFEFIFDTMK-DI--TVLRCGHTIHLECLKEMEKH-YRYTCPVCSKSL 62 (140)
Q Consensus 11 ~~~~~C~IC~e~l~~~~~-~~--~~l~CgH~Fc~~Cl~~~~~~-~~~~CP~CR~~~ 62 (140)
+...+|+||+..+....+ -| +-..|.|.||.+|+-+|+.+ ++.+||+||..+
T Consensus 1467 sG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRsei 1522 (1525)
T COG5219 1467 SGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEI 1522 (1525)
T ss_pred CCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCcccccc
Confidence 446789999987541111 11 23478899999999999976 467899999776
No 56
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.37 E-value=0.0002 Score=59.11 Aligned_cols=50 Identities=28% Similarity=0.702 Sum_probs=38.9
Q ss_pred ccccccccccccc-cCCccEEecCCCcccHHHHHhhhcc-ccCCCCCCCCCC
Q 032467 13 HHNCPICFEFIFD-TMKDITVLRCGHTIHLECLKEMEKH-YRYTCPVCSKSL 62 (140)
Q Consensus 13 ~~~C~IC~e~l~~-~~~~~~~l~CgH~Fc~~Cl~~~~~~-~~~~CP~CR~~~ 62 (140)
-..||||++.+.. .....+.|.|||.|-..||++|+-+ ....||.|....
T Consensus 4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~ka 55 (463)
T KOG1645|consen 4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKA 55 (463)
T ss_pred cccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChh
Confidence 3689999987632 3345677899999999999999953 346799998774
No 57
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.36 E-value=2.6e-05 Score=68.73 Aligned_cols=52 Identities=21% Similarity=0.420 Sum_probs=37.7
Q ss_pred CcccccccccccccccCCccEEecCCCcccHHHHHhhhccccCCCCCCCCCCch
Q 032467 11 AMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLWD 64 (140)
Q Consensus 11 ~~~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~~~ 64 (140)
.....||+|+..+.+. ......+|+|.||..||..|-. ...+||+||..|..
T Consensus 121 ~~~~~CP~Ci~s~~Dq-L~~~~k~c~H~FC~~Ci~sWsR-~aqTCPiDR~EF~~ 172 (1134)
T KOG0825|consen 121 HVENQCPNCLKSCNDQ-LEESEKHTAHYFCEECVGSWSR-CAQTCPVDRGEFGE 172 (1134)
T ss_pred hhhhhhhHHHHHHHHH-hhccccccccccHHHHhhhhhh-hcccCchhhhhhhe
Confidence 4456799998653321 1123358999999999999976 45789999998753
No 58
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=97.19 E-value=9.1e-05 Score=60.95 Aligned_cols=56 Identities=36% Similarity=0.697 Sum_probs=43.1
Q ss_pred ccccccCcccccccccccccccCCccEEecCCCcccHHHHHhhhcc-ccCCCCCCCCC
Q 032467 5 HRCVERAMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKH-YRYTCPVCSKS 61 (140)
Q Consensus 5 h~c~e~~~~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~-~~~~CP~CR~~ 61 (140)
|-|++ .+++.|..|-|.+-........|||.|.||.+|+..++++ +..+||-||+-
T Consensus 358 ~~~~~-e~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~Crkl 414 (518)
T KOG1941|consen 358 HECVE-ETELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRKL 414 (518)
T ss_pred HHHHH-HHhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHHH
Confidence 45554 4678999999876444455567899999999999998865 45689999943
No 59
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=97.09 E-value=0.00015 Score=58.79 Aligned_cols=55 Identities=27% Similarity=0.535 Sum_probs=42.8
Q ss_pred ccCcccccccccccccccCCccEEecCCCcccHHHHHhhhccccCCCCCCCCCCch
Q 032467 9 ERAMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLWD 64 (140)
Q Consensus 9 e~~~~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~~~ 64 (140)
|+..|+ ||.|+|+|+-....-.--+||-..|..|.....+.-+.+||.||+.+.+
T Consensus 11 edeed~-cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~d 65 (480)
T COG5175 11 EDEEDY-CPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDD 65 (480)
T ss_pred cccccc-CcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhccc
Confidence 344445 9999999876555555569999999999887766556789999999865
No 60
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.08 E-value=0.00039 Score=57.47 Aligned_cols=48 Identities=27% Similarity=0.472 Sum_probs=35.7
Q ss_pred ccccccccccccccCCccEEecCCCcccHHHHHhhhcc-------ccCCCCCCCCC
Q 032467 13 HHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKH-------YRYTCPVCSKS 61 (140)
Q Consensus 13 ~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~-------~~~~CP~CR~~ 61 (140)
...|.||++... +......+||+|+||..|+..+... +..+||-+.-.
T Consensus 184 lf~C~ICf~e~~-G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C~ 238 (445)
T KOG1814|consen 184 LFDCCICFEEQM-GQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCG 238 (445)
T ss_pred cccceeeehhhc-CcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCCc
Confidence 568999999732 3355677899999999999998653 23568876543
No 61
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.08 E-value=8e-05 Score=59.11 Aligned_cols=46 Identities=30% Similarity=0.819 Sum_probs=35.6
Q ss_pred ccccccccccccccCCccEEecCCC-cccHHHHHhhhccccCCCCCCCCCCchhhh
Q 032467 13 HHNCPICFEFIFDTMKDITVLRCGH-TIHLECLKEMEKHYRYTCPVCSKSLWDMSK 67 (140)
Q Consensus 13 ~~~C~IC~e~l~~~~~~~~~l~CgH-~Fc~~Cl~~~~~~~~~~CP~CR~~~~~~~~ 67 (140)
+..|.||++ ...+-+.|+||| +-|.+|=.+.- .||+||+.+..+..
T Consensus 300 ~~LC~ICmD----aP~DCvfLeCGHmVtCt~CGkrm~-----eCPICRqyi~rvvr 346 (350)
T KOG4275|consen 300 RRLCAICMD----APRDCVFLECGHMVTCTKCGKRMN-----ECPICRQYIVRVVR 346 (350)
T ss_pred HHHHHHHhc----CCcceEEeecCcEEeehhhccccc-----cCchHHHHHHHHHh
Confidence 789999996 467889999999 47888865543 59999988654433
No 62
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=97.05 E-value=0.00033 Score=53.00 Aligned_cols=45 Identities=27% Similarity=0.479 Sum_probs=37.2
Q ss_pred ccccccccccccccCCccEEecCCCcccHHHHHhhhccccCCCCCCCCCC
Q 032467 13 HHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSL 62 (140)
Q Consensus 13 ~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~ 62 (140)
...|.||-++ +..|+.+.|||.||..|..+-.. ....|-+|.+..
T Consensus 196 PF~C~iCKkd----y~spvvt~CGH~FC~~Cai~~y~-kg~~C~~Cgk~t 240 (259)
T COG5152 196 PFLCGICKKD----YESPVVTECGHSFCSLCAIRKYQ-KGDECGVCGKAT 240 (259)
T ss_pred ceeehhchhh----ccchhhhhcchhHHHHHHHHHhc-cCCcceecchhh
Confidence 4689999985 56788899999999999887665 347899998875
No 63
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.00 E-value=0.0011 Score=51.09 Aligned_cols=51 Identities=33% Similarity=0.729 Sum_probs=40.7
Q ss_pred cccccccccccccccCCccEEecCCCcccHHHHHhhhcc-------ccCCCCCCCCCCch
Q 032467 12 MHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKH-------YRYTCPVCSKSLWD 64 (140)
Q Consensus 12 ~~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~-------~~~~CP~CR~~~~~ 64 (140)
++..|..|--.|-+ .+-+.|.|-|.||..|+..|... ..+.||-|...+..
T Consensus 49 Y~pNC~LC~t~La~--gdt~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFP 106 (299)
T KOG3970|consen 49 YNPNCRLCNTPLAS--GDTTRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFP 106 (299)
T ss_pred CCCCCceeCCcccc--CcceeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCC
Confidence 46789999876543 45578999999999999999753 35889999999754
No 64
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=96.91 E-value=0.00043 Score=57.37 Aligned_cols=49 Identities=33% Similarity=0.726 Sum_probs=39.9
Q ss_pred CcccccccccccccccCCccEE-ecCCCcccHHHHHhhhccccCCCCCCCCCCch
Q 032467 11 AMHHNCPICFEFIFDTMKDITV-LRCGHTIHLECLKEMEKHYRYTCPVCSKSLWD 64 (140)
Q Consensus 11 ~~~~~C~IC~e~l~~~~~~~~~-l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~~~ 64 (140)
..++.|++|... ..+|.. +.|||.||..|+..|+.. +..||.|+..+..
T Consensus 19 ~~~l~C~~C~~v----l~~p~~~~~cgh~fC~~C~~~~~~~-~~~cp~~~~~~~~ 68 (391)
T KOG0297|consen 19 DENLLCPICMSV----LRDPVQTTTCGHRFCAGCLLESLSN-HQKCPVCRQELTQ 68 (391)
T ss_pred cccccCcccccc----ccCCCCCCCCCCcccccccchhhcc-CcCCcccccccch
Confidence 456899999975 344555 699999999999999985 7889999988643
No 65
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.85 E-value=0.0006 Score=54.21 Aligned_cols=59 Identities=20% Similarity=0.390 Sum_probs=42.7
Q ss_pred ccccccccccccccCCccEEecCCCcccHHHHHhhhccccCCCCCCCCCCchhhhHHHHHHHHH
Q 032467 13 HHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLWDMSKLWSKIDQEI 76 (140)
Q Consensus 13 ~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~~~~~~~~~~l~~~~ 76 (140)
...|-||.++ +..|+...|||+||..|..+-+.. ...|++|.+.+.........|...+
T Consensus 241 Pf~c~icr~~----f~~pVvt~c~h~fc~~ca~~~~qk-~~~c~vC~~~t~g~~~~akeL~~~L 299 (313)
T KOG1813|consen 241 PFKCFICRKY----FYRPVVTKCGHYFCEVCALKPYQK-GEKCYVCSQQTHGSFNVAKELLVSL 299 (313)
T ss_pred Cccccccccc----cccchhhcCCceeehhhhcccccc-CCcceecccccccccchHHHHHHHH
Confidence 4569999975 567889999999999998887663 4689999988644333333333333
No 66
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=96.80 E-value=0.00028 Score=56.79 Aligned_cols=50 Identities=24% Similarity=0.582 Sum_probs=39.7
Q ss_pred cCcccccccccccccccCCccEEecCCCcccHHHHHhhhccccCCCCCCCCCCc
Q 032467 10 RAMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLW 63 (140)
Q Consensus 10 ~~~~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~~ 63 (140)
-.....|.+|..+|.+ +-.+.-|-|+||..||.+++.. ...||.|...+.
T Consensus 12 ~n~~itC~LC~GYliD---ATTI~eCLHTFCkSCivk~l~~-~~~CP~C~i~ih 61 (331)
T KOG2660|consen 12 LNPHITCRLCGGYLID---ATTITECLHTFCKSCIVKYLEE-SKYCPTCDIVIH 61 (331)
T ss_pred cccceehhhccceeec---chhHHHHHHHHHHHHHHHHHHH-hccCCccceecc
Confidence 3456789999987643 2244599999999999999985 678999998763
No 67
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=96.68 E-value=0.001 Score=39.00 Aligned_cols=41 Identities=24% Similarity=0.587 Sum_probs=26.4
Q ss_pred cccccccccccCCccEEecCCC-----cccHHHHHhhhcc-ccCCCCCC
Q 032467 16 CPICFEFIFDTMKDITVLRCGH-----TIHLECLKEMEKH-YRYTCPVC 58 (140)
Q Consensus 16 C~IC~e~l~~~~~~~~~l~CgH-----~Fc~~Cl~~~~~~-~~~~CP~C 58 (140)
|-||++.- ....+.+.||+- ..|..||.+|+.. +..+|++|
T Consensus 1 CrIC~~~~--~~~~~li~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C 47 (47)
T PF12906_consen 1 CRICLEGE--EEDEPLISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC 47 (47)
T ss_dssp ETTTTEE---SSSS-EE-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred CeEeCCcC--CCCCceecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence 67999862 233356678863 6799999999875 45679887
No 68
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=96.57 E-value=0.0011 Score=40.03 Aligned_cols=43 Identities=30% Similarity=0.584 Sum_probs=30.5
Q ss_pred cccccccccccccCCccEEecCCCcccHHHHHhhhccccCCCCCCCCCCc
Q 032467 14 HNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLW 63 (140)
Q Consensus 14 ~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~~ 63 (140)
..|-.|... ....+.++|||..|..|+.-+..+ .||+|.+++.
T Consensus 8 ~~~~~~~~~----~~~~~~~pCgH~I~~~~f~~~rYn---gCPfC~~~~~ 50 (55)
T PF14447_consen 8 QPCVFCGFV----GTKGTVLPCGHLICDNCFPGERYN---GCPFCGTPFE 50 (55)
T ss_pred eeEEEcccc----ccccccccccceeeccccChhhcc---CCCCCCCccc
Confidence 345555532 244577899999999998776553 4999998873
No 69
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=96.56 E-value=0.00084 Score=57.34 Aligned_cols=51 Identities=29% Similarity=0.565 Sum_probs=42.0
Q ss_pred cccCcccccccccccccccCCccEEecCCCcccHHHHHhhhcc----ccCCCCCCCCCC
Q 032467 8 VERAMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKH----YRYTCPVCSKSL 62 (140)
Q Consensus 8 ~e~~~~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~----~~~~CP~CR~~~ 62 (140)
.++..+.+|.+|-++ ..++....|.|.||+-|+..++.. .+.+||+|...+
T Consensus 531 ~enk~~~~C~lc~d~----aed~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~L 585 (791)
T KOG1002|consen 531 DENKGEVECGLCHDP----AEDYIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGL 585 (791)
T ss_pred ccccCceeecccCCh----hhhhHhhhhhHHHHHHHHHHHHHhhhcccCCCCccccccc
Confidence 467778899999975 566778899999999999888653 357899998775
No 70
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=96.45 E-value=0.0031 Score=49.22 Aligned_cols=53 Identities=23% Similarity=0.395 Sum_probs=43.1
Q ss_pred CcccccccccccccccCCccEEecCCCcccHHHHHhhhccccCCCCCCCCCCch
Q 032467 11 AMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLWD 64 (140)
Q Consensus 11 ~~~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~~~ 64 (140)
+..+.||||.+.|.+...-.++-+|||+|+.+|.++++. ....||+|.+++.+
T Consensus 219 s~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir-~D~v~pv~d~plkd 271 (303)
T KOG3039|consen 219 SKRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIR-KDMVDPVTDKPLKD 271 (303)
T ss_pred ccceecccchhhhcCccceEEeccCCcEeeHHHHHHhcc-ccccccCCCCcCcc
Confidence 457899999999876444444449999999999999987 56789999998754
No 71
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.43 E-value=0.0018 Score=52.93 Aligned_cols=51 Identities=20% Similarity=0.488 Sum_probs=42.1
Q ss_pred ccCcccccccccccccccCCccEEecCCCcccHHHHHhhhccccCCCCCCCCCCch
Q 032467 9 ERAMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLWD 64 (140)
Q Consensus 9 e~~~~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~~~ 64 (140)
..+.+..||||+. .....+..||||.-|..||.+-+. ....|-.|+.++.+
T Consensus 418 p~sEd~lCpICyA----~pi~Avf~PC~H~SC~~CI~qHlm-N~k~CFfCktTv~~ 468 (489)
T KOG4692|consen 418 PDSEDNLCPICYA----GPINAVFAPCSHRSCYGCITQHLM-NCKRCFFCKTTVID 468 (489)
T ss_pred CCcccccCcceec----ccchhhccCCCCchHHHHHHHHHh-cCCeeeEecceeee
Confidence 4577899999995 345567889999999999999887 45789999998754
No 72
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=96.42 E-value=0.0015 Score=58.25 Aligned_cols=49 Identities=29% Similarity=0.590 Sum_probs=37.1
Q ss_pred cccccccccccccccCCccEE--ecCCCcccHHHHHhhhcc------ccCCCCCCCCCC
Q 032467 12 MHHNCPICFEFIFDTMKDITV--LRCGHTIHLECLKEMEKH------YRYTCPVCSKSL 62 (140)
Q Consensus 12 ~~~~C~IC~e~l~~~~~~~~~--l~CgH~Fc~~Cl~~~~~~------~~~~CP~CR~~~ 62 (140)
..++|.||++.+.. ..++. -.|-|+||..||.+|..+ ..++||.|....
T Consensus 190 ~~yeCmIC~e~I~~--t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv~ 246 (950)
T KOG1952|consen 190 RKYECMICTERIKR--TAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSVS 246 (950)
T ss_pred CceEEEEeeeeccc--cCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccchh
Confidence 46799999998643 33333 368899999999999764 258899998553
No 73
>KOG3800 consensus Predicted E3 ubiquitin ligase containing RING finger, subunit of transcription/repair factor TFIIH and CDK-activating kinase assembly factor [Posttranslational modification, protein turnover, chaperones]
Probab=96.42 E-value=0.0024 Score=50.66 Aligned_cols=49 Identities=22% Similarity=0.502 Sum_probs=36.1
Q ss_pred ccccccccccccCC-ccEEecCCCcccHHHHHhhhccccCCCCCCCCCCc
Q 032467 15 NCPICFEFIFDTMK-DITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLW 63 (140)
Q Consensus 15 ~C~IC~e~l~~~~~-~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~~ 63 (140)
.||+|....+-... ...+-+|||..|.+|+...+..+...||.|.+.+.
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iLR 51 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGPAQCPECMVILR 51 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHhcCCCCCCcccchhh
Confidence 58999865322111 11222999999999999999888899999988753
No 74
>PF04641 Rtf2: Rtf2 RING-finger
Probab=96.40 E-value=0.0035 Score=49.17 Aligned_cols=52 Identities=25% Similarity=0.429 Sum_probs=40.0
Q ss_pred cCcccccccccccccccCCccEEecCCCcccHHHHHhhhccccCCCCCCCCCCc
Q 032467 10 RAMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLW 63 (140)
Q Consensus 10 ~~~~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~~ 63 (140)
....+.|||...+|.....-+.+-+|||+|...+|.+.- ....||+|..+|.
T Consensus 110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k--~~~~Cp~c~~~f~ 161 (260)
T PF04641_consen 110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK--KSKKCPVCGKPFT 161 (260)
T ss_pred CCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc--ccccccccCCccc
Confidence 456789999999875433333444999999999999984 3467999999974
No 75
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=96.35 E-value=0.0015 Score=43.77 Aligned_cols=39 Identities=28% Similarity=0.644 Sum_probs=30.4
Q ss_pred cccccCcccccccccccccccCCccEEecCCCcccHHHHHh
Q 032467 6 RCVERAMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKE 46 (140)
Q Consensus 6 ~c~e~~~~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~ 46 (140)
..+..+.+..|++|...|.+ ...+..||||.||..|+.+
T Consensus 71 ~~v~i~~~~~C~vC~k~l~~--~~f~~~p~~~v~H~~C~~r 109 (109)
T PF10367_consen 71 RSVVITESTKCSVCGKPLGN--SVFVVFPCGHVVHYSCIKR 109 (109)
T ss_pred ceEEECCCCCccCcCCcCCC--ceEEEeCCCeEEecccccC
Confidence 34556678889999998754 4556779999999999753
No 76
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=96.34 E-value=0.0012 Score=52.84 Aligned_cols=53 Identities=26% Similarity=0.562 Sum_probs=39.1
Q ss_pred cCcccccccccccccccCCccEEecCCCcccHHHHHhhhcc----------------------ccCCCCCCCCCCc
Q 032467 10 RAMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKH----------------------YRYTCPVCSKSLW 63 (140)
Q Consensus 10 ~~~~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~----------------------~~~~CP~CR~~~~ 63 (140)
+-....|.|||-.|-+ ......++|-|.||..||.+++.. ....||+||..+.
T Consensus 112 n~p~gqCvICLygfa~-~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~ 186 (368)
T KOG4445|consen 112 NHPNGQCVICLYGFAS-SPAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIK 186 (368)
T ss_pred CCCCCceEEEEEeecC-CCceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhcc
Confidence 3446899999976432 334567899999999999988752 1245999999874
No 77
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.19 E-value=0.0029 Score=51.56 Aligned_cols=47 Identities=26% Similarity=0.581 Sum_probs=34.6
Q ss_pred ccCcccccccccccccccCCccEEecCCCcccHHHHHhhhccccCCCCCCCCCCc
Q 032467 9 ERAMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLW 63 (140)
Q Consensus 9 e~~~~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~~ 63 (140)
+.+.+..|.||++. ....+.+||||+-| |..-... ...||+||..+.
T Consensus 301 ~~~~p~lcVVcl~e----~~~~~fvpcGh~cc--ct~cs~~--l~~CPvCR~rI~ 347 (355)
T KOG1571|consen 301 ELPQPDLCVVCLDE----PKSAVFVPCGHVCC--CTLCSKH--LPQCPVCRQRIR 347 (355)
T ss_pred ccCCCCceEEecCC----ccceeeecCCcEEE--chHHHhh--CCCCchhHHHHH
Confidence 44567899999975 45578899999977 6554433 245999998864
No 78
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=96.02 E-value=0.0078 Score=56.97 Aligned_cols=53 Identities=25% Similarity=0.631 Sum_probs=39.4
Q ss_pred cCcccccccccccccccCCccEEecCCCcccHHHHHhhhcc---------ccCCCCCCCCCCc
Q 032467 10 RAMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKH---------YRYTCPVCSKSLW 63 (140)
Q Consensus 10 ~~~~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~---------~~~~CP~CR~~~~ 63 (140)
+..|..|.||+.+-. +..+...|.|||.||..|.+..+++ +-..||+|...+.
T Consensus 3483 QD~DDmCmICFTE~L-~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~In 3544 (3738)
T KOG1428|consen 3483 QDADDMCMICFTEAL-SAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKIN 3544 (3738)
T ss_pred cccCceEEEEehhhh-CCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchhh
Confidence 345778999987632 2355677999999999999887653 2356999998863
No 79
>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=95.90 E-value=0.0034 Score=44.65 Aligned_cols=35 Identities=23% Similarity=0.484 Sum_probs=29.2
Q ss_pred ccccccccccccccCCccEEecCC------CcccHHHHHhhh
Q 032467 13 HHNCPICFEFIFDTMKDITVLRCG------HTIHLECLKEME 48 (140)
Q Consensus 13 ~~~C~IC~e~l~~~~~~~~~l~Cg------H~Fc~~Cl~~~~ 48 (140)
..+|.||++.+.+ ...++.++|| |.||..|+.+|.
T Consensus 26 ~~EC~IC~~~I~~-~~GvV~vt~~g~lnLEkmfc~~C~~rw~ 66 (134)
T PF05883_consen 26 TVECQICFDRIDN-NDGVVYVTDGGTLNLEKMFCADCDKRWR 66 (134)
T ss_pred Ceeehhhhhhhhc-CCCEEEEecCCeehHHHHHHHHHHHHHH
Confidence 5799999998765 4566777888 899999999994
No 80
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=95.82 E-value=0.004 Score=48.19 Aligned_cols=43 Identities=33% Similarity=0.787 Sum_probs=30.7
Q ss_pred ccccccccccccCCccEEecCCCcccHHHHHhhhccccCCCCCCCCCC
Q 032467 15 NCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSL 62 (140)
Q Consensus 15 ~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~ 62 (140)
.|..|.- +.+...--++.|+|+||..|...-.. ..||+|++.+
T Consensus 5 hCn~C~~--~~~~~~f~LTaC~HvfC~~C~k~~~~---~~C~lCkk~i 47 (233)
T KOG4739|consen 5 HCNKCFR--FPSQDPFFLTACRHVFCEPCLKASSP---DVCPLCKKSI 47 (233)
T ss_pred Eeccccc--cCCCCceeeeechhhhhhhhcccCCc---ccccccccee
Confidence 4666664 23444446679999999999876433 3799999985
No 81
>PHA02862 5L protein; Provisional
Probab=95.65 E-value=0.0096 Score=42.91 Aligned_cols=47 Identities=21% Similarity=0.487 Sum_probs=34.4
Q ss_pred cccccccccccccccCCccEEecCC-----CcccHHHHHhhhccc-cCCCCCCCCCCc
Q 032467 12 MHHNCPICFEFIFDTMKDITVLRCG-----HTIHLECLKEMEKHY-RYTCPVCSKSLW 63 (140)
Q Consensus 12 ~~~~C~IC~e~l~~~~~~~~~l~Cg-----H~Fc~~Cl~~~~~~~-~~~CP~CR~~~~ 63 (140)
+...|-||++. + ... .-||. -.-|.+|+.+|+..+ ...|++|+.++.
T Consensus 1 ~~diCWIC~~~--~-~e~--~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~ 53 (156)
T PHA02862 1 MSDICWICNDV--C-DER--NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYN 53 (156)
T ss_pred CCCEEEEecCc--C-CCC--cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEE
Confidence 35679999985 2 121 35665 478999999999753 567999999973
No 82
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=95.63 E-value=0.0074 Score=48.42 Aligned_cols=46 Identities=28% Similarity=0.717 Sum_probs=35.5
Q ss_pred ccccccccccccccCCccEEecCCCcccHHHHHhhhccccCCCCCCCCC
Q 032467 13 HHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKS 61 (140)
Q Consensus 13 ~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~ 61 (140)
.+-|+.|...|. .+..+.-|||.||.+||...|....+.||.|.+.
T Consensus 274 ~LkCplc~~Llr---np~kT~cC~~~fc~eci~~al~dsDf~CpnC~rk 319 (427)
T COG5222 274 SLKCPLCHCLLR---NPMKTPCCGHTFCDECIGTALLDSDFKCPNCSRK 319 (427)
T ss_pred cccCcchhhhhh---CcccCccccchHHHHHHhhhhhhccccCCCcccc
Confidence 488999987532 2333447899999999998776677999999764
No 83
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.61 E-value=0.01 Score=48.92 Aligned_cols=48 Identities=27% Similarity=0.565 Sum_probs=39.3
Q ss_pred cccccccccccccCCccEEecCCCcccHHHHHhhhcccc--CCCCCCCCCC
Q 032467 14 HNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYR--YTCPVCSKSL 62 (140)
Q Consensus 14 ~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~--~~CP~CR~~~ 62 (140)
..|||=.|. .+...+|+.|.|||+...+-+.+....+. +.||.|-...
T Consensus 335 F~CPVlKeq-tsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~e~ 384 (394)
T KOG2817|consen 335 FICPVLKEQ-TSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPVEQ 384 (394)
T ss_pred eecccchhh-ccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCccc
Confidence 478887664 44568999999999999999999987765 8899997663
No 84
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.61 E-value=0.0039 Score=54.38 Aligned_cols=44 Identities=27% Similarity=0.642 Sum_probs=36.6
Q ss_pred cccccccccccccCCccEEecCCCcccHHHHHhhhccccCCCCCCCCC
Q 032467 14 HNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKS 61 (140)
Q Consensus 14 ~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~ 61 (140)
+.|+||+..++.....|+.|.|||+.|..|++.... .+|| |++.
T Consensus 12 l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~lyn---~scp-~~~D 55 (861)
T KOG3161|consen 12 LLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLYN---ASCP-TKRD 55 (861)
T ss_pred hhchHHHHHHHHHhcCcccccccchHHHHHHHhHhh---ccCC-CCcc
Confidence 579999988887778899999999999999998755 4688 5443
No 85
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=95.46 E-value=0.013 Score=42.89 Aligned_cols=47 Identities=26% Similarity=0.579 Sum_probs=34.5
Q ss_pred CcccccccccccccccCCccEEecCC--C---cccHHHHHhhhccc-cCCCCCCCCCC
Q 032467 11 AMHHNCPICFEFIFDTMKDITVLRCG--H---TIHLECLKEMEKHY-RYTCPVCSKSL 62 (140)
Q Consensus 11 ~~~~~C~IC~e~l~~~~~~~~~l~Cg--H---~Fc~~Cl~~~~~~~-~~~CP~CR~~~ 62 (140)
.++..|-||.++- . ...-||. . ..|.+|+++|+..+ ..+|++|+.++
T Consensus 6 ~~~~~CRIC~~~~----~-~~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y 58 (162)
T PHA02825 6 LMDKCCWICKDEY----D-VVTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPY 58 (162)
T ss_pred CCCCeeEecCCCC----C-CccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeE
Confidence 4577899999862 1 1224665 4 55999999999763 57899999886
No 86
>PHA03096 p28-like protein; Provisional
Probab=95.46 E-value=0.0079 Score=47.98 Aligned_cols=48 Identities=25% Similarity=0.348 Sum_probs=32.0
Q ss_pred ccccccccccccc---CCccEEe-cCCCcccHHHHHhhhccc--cCCCCCCCCC
Q 032467 14 HNCPICFEFIFDT---MKDITVL-RCGHTIHLECLKEMEKHY--RYTCPVCSKS 61 (140)
Q Consensus 14 ~~C~IC~e~l~~~---~~~~~~l-~CgH~Fc~~Cl~~~~~~~--~~~CP~CR~~ 61 (140)
-.|.||+|..... .+.-.+| .|.|.||..|+..|.... ...||.||.-
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~~ 232 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRRL 232 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCccccch
Confidence 5799999975432 1122334 999999999999997642 2345555543
No 87
>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=95.31 E-value=0.007 Score=35.49 Aligned_cols=42 Identities=33% Similarity=0.804 Sum_probs=25.0
Q ss_pred cccccccccccccCCccEEecCC-CcccHHHHHhhhccccCCCCCCCCCC
Q 032467 14 HNCPICFEFIFDTMKDITVLRCG-HTIHLECLKEMEKHYRYTCPVCSKSL 62 (140)
Q Consensus 14 ~~C~IC~e~l~~~~~~~~~l~Cg-H~Fc~~Cl~~~~~~~~~~CP~CR~~~ 62 (140)
..|--|+- ..-..+.|. |..|..|+...+. ....||+|.+++
T Consensus 3 ~nCKsCWf------~~k~Li~C~dHYLCl~CLt~ml~-~s~~C~iC~~~L 45 (50)
T PF03854_consen 3 YNCKSCWF------ANKGLIKCSDHYLCLNCLTLMLS-RSDRCPICGKPL 45 (50)
T ss_dssp ----SS-S--------SSEEE-SS-EEEHHHHHHT-S-SSSEETTTTEE-
T ss_pred ccChhhhh------cCCCeeeecchhHHHHHHHHHhc-cccCCCcccCcC
Confidence 45666772 233456887 9999999999987 457899999886
No 88
>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=95.13 E-value=0.025 Score=41.34 Aligned_cols=33 Identities=33% Similarity=0.784 Sum_probs=22.8
Q ss_pred ccccccccccccccCCccEEecCC------------C-cccHHHHHhhhc
Q 032467 13 HHNCPICFEFIFDTMKDITVLRCG------------H-TIHLECLKEMEK 49 (140)
Q Consensus 13 ~~~C~IC~e~l~~~~~~~~~l~Cg------------H-~Fc~~Cl~~~~~ 49 (140)
+..||||||. ....++|-|. - .-|..||+++..
T Consensus 2 d~~CpICme~----PHNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkk 47 (162)
T PF07800_consen 2 DVTCPICMEH----PHNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKK 47 (162)
T ss_pred CccCceeccC----CCceEEEEeccccCCccccccCCccchhHHHHHHHH
Confidence 5789999984 4455666553 2 347889999854
No 89
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=95.09 E-value=0.018 Score=47.09 Aligned_cols=48 Identities=25% Similarity=0.558 Sum_probs=36.7
Q ss_pred cCcccccccccccccccCCccEEecCCCcccHHHHHhhhcc-ccCCCCCCCCC
Q 032467 10 RAMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKH-YRYTCPVCSKS 61 (140)
Q Consensus 10 ~~~~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~-~~~~CP~CR~~ 61 (140)
+..+..|.||-+. ..-...+||||.+|.-|..+...- ....||+||..
T Consensus 58 DEen~~C~ICA~~----~TYs~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE 106 (493)
T COG5236 58 DEENMNCQICAGS----TTYSARYPCGHQICHACAVRLRALYMQKGCPLCRTE 106 (493)
T ss_pred ccccceeEEecCC----ceEEEeccCCchHHHHHHHHHHHHHhccCCCccccc
Confidence 4456789999975 344567899999999998775332 34679999987
No 90
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=94.69 E-value=0.046 Score=43.93 Aligned_cols=46 Identities=24% Similarity=0.713 Sum_probs=34.5
Q ss_pred cccccccccccccccCCccEEecC--CCcccHHHHHhhhccccCCCCCCCCCCchhh
Q 032467 12 MHHNCPICFEFIFDTMKDITVLRC--GHTIHLECLKEMEKHYRYTCPVCSKSLWDMS 66 (140)
Q Consensus 12 ~~~~C~IC~e~l~~~~~~~~~l~C--gH~Fc~~Cl~~~~~~~~~~CP~CR~~~~~~~ 66 (140)
.-++||||.+.|. +| +.+| ||..|..|-.+.. ..||.||..+.++.
T Consensus 47 ~lleCPvC~~~l~----~P-i~QC~nGHlaCssC~~~~~----~~CP~Cr~~~g~~R 94 (299)
T KOG3002|consen 47 DLLDCPVCFNPLS----PP-IFQCDNGHLACSSCRTKVS----NKCPTCRLPIGNIR 94 (299)
T ss_pred hhccCchhhccCc----cc-ceecCCCcEehhhhhhhhc----ccCCccccccccHH
Confidence 3469999998643 33 3556 7999999987543 46999999998653
No 91
>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=94.27 E-value=0.011 Score=46.03 Aligned_cols=50 Identities=26% Similarity=0.563 Sum_probs=36.9
Q ss_pred cccccccccccccccCCccEEe--c-CCCcccHHHHHhhhccccCCCC--CCCCCC
Q 032467 12 MHHNCPICFEFIFDTMKDITVL--R-CGHTIHLECLKEMEKHYRYTCP--VCSKSL 62 (140)
Q Consensus 12 ~~~~C~IC~e~l~~~~~~~~~l--~-CgH~Fc~~Cl~~~~~~~~~~CP--~CR~~~ 62 (140)
.+..||||..+-+-... .++| | |-|.+|.+|..+.+..+...|| -|.+.+
T Consensus 9 ~d~~CPvCksDrYLnPd-ik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kIL 63 (314)
T COG5220 9 EDRRCPVCKSDRYLNPD-IKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKIL 63 (314)
T ss_pred hcccCCccccccccCCC-eEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHH
Confidence 35689999976432222 2333 4 9999999999999988888999 786554
No 92
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=94.23 E-value=0.043 Score=49.36 Aligned_cols=44 Identities=27% Similarity=0.632 Sum_probs=33.7
Q ss_pred cccccccccccccCCccEEecCCCcccHHHHHhhhccccCCCCCCCCCCch
Q 032467 14 HNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLWD 64 (140)
Q Consensus 14 ~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~~~ 64 (140)
..|..|--.| .-+.+.-.|||.||.+|+. .+...||.|+..+..
T Consensus 841 skCs~C~~~L---dlP~VhF~CgHsyHqhC~e----~~~~~CP~C~~e~~~ 884 (933)
T KOG2114|consen 841 SKCSACEGTL---DLPFVHFLCGHSYHQHCLE----DKEDKCPKCLPELRG 884 (933)
T ss_pred eeecccCCcc---ccceeeeecccHHHHHhhc----cCcccCCccchhhhh
Confidence 4788998643 3456777999999999998 245689999986543
No 93
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=94.17 E-value=0.026 Score=50.02 Aligned_cols=44 Identities=36% Similarity=0.904 Sum_probs=36.6
Q ss_pred cccccccccccccCCccEEecCCCcccHHHHHhhhcccc-CCCCCCCCCC
Q 032467 14 HNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYR-YTCPVCSKSL 62 (140)
Q Consensus 14 ~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~-~~CP~CR~~~ 62 (140)
..|.||++ ...+...+|||.||..|+...+.... ..||+||..+
T Consensus 455 ~~c~ic~~-----~~~~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l 499 (674)
T KOG1001|consen 455 HWCHICCD-----LDSFFITRCGHDFCVECLKKSIQQSENAPCPLCRNVL 499 (674)
T ss_pred cccccccc-----cccceeecccchHHHHHHHhccccccCCCCcHHHHHH
Confidence 78999997 35678889999999999999887543 3699999875
No 94
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.01 E-value=0.046 Score=40.91 Aligned_cols=50 Identities=26% Similarity=0.647 Sum_probs=35.1
Q ss_pred ccccccccccccccCCc---cEEecCCCcccHHHHHhhhcc-----c-----cCCCCCCCCCC
Q 032467 13 HHNCPICFEFIFDTMKD---ITVLRCGHTIHLECLKEMEKH-----Y-----RYTCPVCSKSL 62 (140)
Q Consensus 13 ~~~C~IC~e~l~~~~~~---~~~l~CgH~Fc~~Cl~~~~~~-----~-----~~~CP~CR~~~ 62 (140)
-..|.||+.+-.++..+ --...||-.||.-|+..|+.. + -..||.|..++
T Consensus 165 ~~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~Pi 227 (234)
T KOG3268|consen 165 LGACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPI 227 (234)
T ss_pred hhcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcc
Confidence 45788888754333222 234599999999999999863 1 13599998886
No 95
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=93.90 E-value=0.033 Score=46.95 Aligned_cols=35 Identities=23% Similarity=0.680 Sum_probs=29.6
Q ss_pred CcccccccccccccccCCccEEecCCCcccHHHHHhhhc
Q 032467 11 AMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEK 49 (140)
Q Consensus 11 ~~~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~ 49 (140)
..++.|+||... +++|.+|+|||..|..|....+.
T Consensus 2 eeelkc~vc~~f----~~epiil~c~h~lc~~ca~~~~~ 36 (699)
T KOG4367|consen 2 EEELKCPVCGSF----YREPIILPCSHNLCQACARNILV 36 (699)
T ss_pred cccccCceehhh----ccCceEeecccHHHHHHHHhhcc
Confidence 457899999964 57899999999999999987654
No 96
>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=93.33 E-value=0.049 Score=32.18 Aligned_cols=44 Identities=25% Similarity=0.659 Sum_probs=20.9
Q ss_pred cccccccccccccCCccEEecCCCcccHHHHHhhhcc----ccCCCCCCCCC
Q 032467 14 HNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKH----YRYTCPVCSKS 61 (140)
Q Consensus 14 ~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~----~~~~CP~CR~~ 61 (140)
+.|||-...+ ..+.+...|.|.-|.+ ++.|++. ..+.||+|+++
T Consensus 3 L~CPls~~~i---~~P~Rg~~C~H~~CFD-l~~fl~~~~~~~~W~CPiC~~~ 50 (50)
T PF02891_consen 3 LRCPLSFQRI---RIPVRGKNCKHLQCFD-LESFLESNQRTPKWKCPICNKP 50 (50)
T ss_dssp SB-TTTSSB----SSEEEETT--SS--EE-HHHHHHHHHHS---B-TTT---
T ss_pred eeCCCCCCEE---EeCccCCcCcccceEC-HHHHHHHhhccCCeECcCCcCc
Confidence 5789888753 2455666999987654 4555543 45789999863
No 97
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=92.77 E-value=0.043 Score=44.28 Aligned_cols=30 Identities=27% Similarity=0.718 Sum_probs=23.4
Q ss_pred EEecCCCcccHHHHHhhhccccCCCCCCCCCCc
Q 032467 31 TVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLW 63 (140)
Q Consensus 31 ~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~~ 63 (140)
++++|.|+||.+|...- ..+.||.|...+.
T Consensus 105 RmIPCkHvFCl~CAr~~---~dK~Cp~C~d~Vq 134 (389)
T KOG2932|consen 105 RMIPCKHVFCLECARSD---SDKICPLCDDRVQ 134 (389)
T ss_pred cccccchhhhhhhhhcC---ccccCcCcccHHH
Confidence 56799999999997642 2467999987753
No 98
>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=92.57 E-value=0.11 Score=42.74 Aligned_cols=27 Identities=22% Similarity=0.508 Sum_probs=20.8
Q ss_pred CCcccHHHHHhhhcc------------ccCCCCCCCCCC
Q 032467 36 GHTIHLECLKEMEKH------------YRYTCPVCSKSL 62 (140)
Q Consensus 36 gH~Fc~~Cl~~~~~~------------~~~~CP~CR~~~ 62 (140)
.=.+|.+|+.+|+.+ ++-.||+||+.+
T Consensus 312 RPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~F 350 (358)
T PF10272_consen 312 RPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKF 350 (358)
T ss_pred cchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccc
Confidence 345799999999864 235699999985
No 99
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.28 E-value=0.063 Score=44.55 Aligned_cols=50 Identities=30% Similarity=0.652 Sum_probs=32.8
Q ss_pred ccccccccccccccCCccEEecCCCcccHHHHHhhhcc-----ccCCCCC--CCCCC
Q 032467 13 HHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKH-----YRYTCPV--CSKSL 62 (140)
Q Consensus 13 ~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~-----~~~~CP~--CR~~~ 62 (140)
..+|.||+.+..........+.|+|.||..|+.+.++. ...+||. |...+
T Consensus 146 ~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~~~~~~~~~C~~~~C~~~l 202 (384)
T KOG1812|consen 146 KEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVKLLSGTVIRCPHDGCESRL 202 (384)
T ss_pred cccCccCccccccHhhhHHHhcccchhhhHHhHHHhhhhhccCCCccCCCCCCCccC
Confidence 56899999433222222336799999999999998763 2356763 44443
No 100
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=92.26 E-value=0.1 Score=37.10 Aligned_cols=49 Identities=31% Similarity=0.546 Sum_probs=37.1
Q ss_pred cccccccccccccccCCccEEe----cCCCcccHHHHHhhhccc--cCCCCCCCCCCch
Q 032467 12 MHHNCPICFEFIFDTMKDITVL----RCGHTIHLECLKEMEKHY--RYTCPVCSKSLWD 64 (140)
Q Consensus 12 ~~~~C~IC~e~l~~~~~~~~~l----~CgH~Fc~~Cl~~~~~~~--~~~CP~CR~~~~~ 64 (140)
.-++|.||.|. ..+...| =||=..|.-|..++|... ...||+|+.++..
T Consensus 79 ~lYeCnIC~et----S~ee~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKs 133 (140)
T PF05290_consen 79 KLYECNICKET----SAEERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKS 133 (140)
T ss_pred CceeccCcccc----cchhhcCCcccccchHHHHHHHHHHHHHcccCCCCCcccccccc
Confidence 45799999985 2333444 489999999999987653 4689999999743
No 101
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.08 E-value=0.022 Score=47.10 Aligned_cols=53 Identities=25% Similarity=0.476 Sum_probs=43.2
Q ss_pred CcccccccccccccccCCccEEecCCCcccHHHHHhhhccccCCCCCCCCCCch
Q 032467 11 AMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLWD 64 (140)
Q Consensus 11 ~~~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~~~ 64 (140)
+....|.||.+.|.........+.|||.++..+|.+|+.. ...||.|+..+..
T Consensus 194 slv~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~~-~~kl~~~~rel~~ 246 (465)
T KOG0827|consen 194 SLVGSLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLAT-KRKLPSCRRELPK 246 (465)
T ss_pred HHHhhhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHHH-HHHhHHHHhhhhh
Confidence 3456799999887765566677899999999999999985 6789999998743
No 102
>KOG2068 consensus MOT2 transcription factor [Transcription]
Probab=89.34 E-value=0.31 Score=39.56 Aligned_cols=49 Identities=31% Similarity=0.590 Sum_probs=38.3
Q ss_pred ccccccccccccccCCccEEecCCCcccHHHHHhhhccccCCCCCCCCCC
Q 032467 13 HHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSL 62 (140)
Q Consensus 13 ~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~ 62 (140)
...||||.+++........-.+||+..|..|+..... +..+||.||+.+
T Consensus 249 ~~s~p~~~~~~~~~d~~~lP~~~~~~~~l~~~~t~~~-~~~~~~~~rk~~ 297 (327)
T KOG2068|consen 249 PPSCPICYEDLDLTDSNFLPCPCGFRLCLFCHKTISD-GDGRCPGCRKPY 297 (327)
T ss_pred CCCCCCCCCcccccccccccccccccchhhhhhcccc-cCCCCCccCCcc
Confidence 4789999998754444444458999999999988776 568999999875
No 103
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=89.33 E-value=0.17 Score=45.81 Aligned_cols=42 Identities=26% Similarity=0.449 Sum_probs=31.0
Q ss_pred cccccCcccccccccccccccCCccEEecCCCcccHHHHHhhhc
Q 032467 6 RCVERAMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEK 49 (140)
Q Consensus 6 ~c~e~~~~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~ 49 (140)
.+.--..+..|.+|...|.. ++-..-+|||.||..||.+-..
T Consensus 810 ry~v~ep~d~C~~C~~~ll~--~pF~vf~CgH~FH~~Cl~~~v~ 851 (911)
T KOG2034|consen 810 RYRVLEPQDSCDHCGRPLLI--KPFYVFPCGHCFHRDCLIRHVL 851 (911)
T ss_pred ceEEecCccchHHhcchhhc--CcceeeeccchHHHHHHHHHHH
Confidence 33334456789999987643 4556679999999999998654
No 104
>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=88.94 E-value=0.55 Score=26.78 Aligned_cols=40 Identities=28% Similarity=0.696 Sum_probs=20.0
Q ss_pred cccccccccccCCccEEe--cCCCcccHHHHHhhhcccc-CCCCCC
Q 032467 16 CPICFEFIFDTMKDITVL--RCGHTIHLECLKEMEKHYR-YTCPVC 58 (140)
Q Consensus 16 C~IC~e~l~~~~~~~~~l--~CgH~Fc~~Cl~~~~~~~~-~~CP~C 58 (140)
|.+|.+.++. ..+-. .|+=.+|..|+..++.... ..||.|
T Consensus 1 C~~C~~iv~~---G~~C~~~~C~~r~H~~C~~~y~r~~~~~~CP~C 43 (43)
T PF08746_consen 1 CEACKEIVTQ---GQRCSNRDCNVRLHDDCFKKYFRHRSNPKCPNC 43 (43)
T ss_dssp -TTT-SB-SS---SEE-SS--S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred CcccchhHee---eccCCCCccCchHHHHHHHHHHhcCCCCCCcCC
Confidence 5667765332 11222 4888999999999987543 369987
No 105
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=88.44 E-value=0.39 Score=39.06 Aligned_cols=46 Identities=17% Similarity=0.356 Sum_probs=35.8
Q ss_pred cccccccccccccccCCcc-EEecCCCcccHHHHHhhhccccCCCCCCCCCC
Q 032467 12 MHHNCPICFEFIFDTMKDI-TVLRCGHTIHLECLKEMEKHYRYTCPVCSKSL 62 (140)
Q Consensus 12 ~~~~C~IC~e~l~~~~~~~-~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~ 62 (140)
....||||+.. ...| +...-|=+||..|+-.++. ....||+=..++
T Consensus 299 ~~~~CpvClk~----r~Nptvl~vSGyVfCY~Ci~~Yv~-~~~~CPVT~~p~ 345 (357)
T KOG0826|consen 299 DREVCPVCLKK----RQNPTVLEVSGYVFCYPCIFSYVV-NYGHCPVTGYPA 345 (357)
T ss_pred ccccChhHHhc----cCCCceEEecceEEeHHHHHHHHH-hcCCCCccCCcc
Confidence 46789999963 3444 4447799999999999988 567899987764
No 106
>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=88.27 E-value=0.083 Score=33.50 Aligned_cols=40 Identities=30% Similarity=0.595 Sum_probs=23.0
Q ss_pred ccccccccccccccCCccEEecCCCcccHHHHHhhhccccCCCCCCCCCC
Q 032467 13 HHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSL 62 (140)
Q Consensus 13 ~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~ 62 (140)
+..||.|..+|.. .. ||.+|..|-..+.. ...||-|..++
T Consensus 1 e~~CP~C~~~L~~-------~~-~~~~C~~C~~~~~~--~a~CPdC~~~L 40 (70)
T PF07191_consen 1 ENTCPKCQQELEW-------QG-GHYHCEACQKDYKK--EAFCPDCGQPL 40 (70)
T ss_dssp --B-SSS-SBEEE-------ET-TEEEETTT--EEEE--EEE-TTT-SB-
T ss_pred CCcCCCCCCccEE-------eC-CEEECcccccccee--cccCCCcccHH
Confidence 4689999986532 12 89999999888755 35799999886
No 107
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=87.62 E-value=0.1 Score=48.87 Aligned_cols=51 Identities=24% Similarity=0.479 Sum_probs=39.4
Q ss_pred cCcccccccccccccccCCccEEecCCCcccHHHHHhhhccccCCCCCCCCCCch
Q 032467 10 RAMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLWD 64 (140)
Q Consensus 10 ~~~~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~~~ 64 (140)
.+....|.||++.+. ..-.+..|||.+|..|+..|+. .+..||+|+....+
T Consensus 1150 ~~~~~~c~ic~dil~---~~~~I~~cgh~~c~~c~~~~l~-~~s~~~~~ksi~~d 1200 (1394)
T KOG0298|consen 1150 LSGHFVCEICLDILR---NQGGIAGCGHEPCCRCDELWLY-ASSRCPICKSIKGD 1200 (1394)
T ss_pred hhcccchHHHHHHHH---hcCCeeeechhHhhhHHHHHHH-HhccCcchhhhhhh
Confidence 344568999998653 2335679999999999999998 45789999876543
No 108
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=87.03 E-value=0.4 Score=33.14 Aligned_cols=38 Identities=18% Similarity=0.398 Sum_probs=27.5
Q ss_pred cccceecCCCCCCCcccceeeeccccccCCCcccccccCC
Q 032467 87 NKMVWILCNDCGANSHVQFHVIAHKCLSCKSYNTRQTRGD 126 (140)
Q Consensus 87 ~~~~~i~C~~C~~~~~~~~~~~~~~C~~C~~~~~~~~~~~ 126 (140)
.......|++|+....... ....||.|++++...+.|.
T Consensus 66 ~~p~~~~C~~Cg~~~~~~~--~~~~CP~Cgs~~~~i~~G~ 103 (115)
T TIGR00100 66 DEPVECECEDCSEEVSPEI--DLYRCPKCHGIMLQVRAGK 103 (115)
T ss_pred eeCcEEEcccCCCEEecCC--cCccCcCCcCCCcEEecCC
Confidence 3346899999997654432 3567999999988776553
No 109
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=86.84 E-value=0.83 Score=29.55 Aligned_cols=54 Identities=19% Similarity=0.354 Sum_probs=23.3
Q ss_pred cCcccccccccccccccCC-cc--EEecCCCcccHHHHHhhhccccCCCCCCCCCCc
Q 032467 10 RAMHHNCPICFEFIFDTMK-DI--TVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLW 63 (140)
Q Consensus 10 ~~~~~~C~IC~e~l~~~~~-~~--~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~~ 63 (140)
+-....|.||-+.+-.... .+ .--.|+--.|+.|++-=...++..||.|+..+.
T Consensus 6 ~~~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg~q~CpqCkt~yk 62 (80)
T PF14569_consen 6 NLNGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEGNQVCPQCKTRYK 62 (80)
T ss_dssp --SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS-SB-TTT--B--
T ss_pred hcCCcccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcCcccccccCCCcc
Confidence 3446789999987522211 22 123788889999998766667889999998763
No 110
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=86.54 E-value=0.57 Score=38.06 Aligned_cols=47 Identities=28% Similarity=0.634 Sum_probs=36.8
Q ss_pred cccccccccccccCCccEEecCCCcccHHHHHhhhccc--cCCCCCCCCC
Q 032467 14 HNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHY--RYTCPVCSKS 61 (140)
Q Consensus 14 ~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~--~~~CP~CR~~ 61 (140)
..|||=-|. .....+|++|.|||+.=.+-+.+.-..+ .+.||.|-..
T Consensus 337 FiCPVlKe~-~t~ENpP~ml~CgHVIskeal~~LS~nG~~~FKCPYCP~~ 385 (396)
T COG5109 337 FICPVLKEL-CTDENPPVMLECGHVISKEALSVLSQNGVLSFKCPYCPEM 385 (396)
T ss_pred eeccccHhh-hcccCCCeeeeccceeeHHHHHHHhhcCcEEeeCCCCCcc
Confidence 468876654 3456889999999999999999886654 5789999654
No 111
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=86.53 E-value=0.69 Score=27.85 Aligned_cols=35 Identities=23% Similarity=0.525 Sum_probs=27.1
Q ss_pred cccccccccccccccCCccEEecCCCcccHHHHHh
Q 032467 12 MHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKE 46 (140)
Q Consensus 12 ~~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~ 46 (140)
....|++|-+.|.+....++-..||=.+|+.|..+
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~ 38 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK 38 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence 45679999998865555555569999999999654
No 112
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=86.07 E-value=0.5 Score=42.51 Aligned_cols=45 Identities=24% Similarity=0.500 Sum_probs=29.0
Q ss_pred cCcccccccccccccccCCccEEecCCCcccHHHHHhhhccccCCCCC
Q 032467 10 RAMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPV 57 (140)
Q Consensus 10 ~~~~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~ 57 (140)
......|.||--.+ ......-..|||+.|..|...|+..+ ..||.
T Consensus 1025 ~~~~~~C~~C~l~V--~gss~~Cg~C~Hv~H~sc~~eWf~~g-d~Cps 1069 (1081)
T KOG0309|consen 1025 KGFTFQCAICHLAV--RGSSNFCGTCGHVGHTSCMMEWFRTG-DVCPS 1069 (1081)
T ss_pred ccceeeeeeEeeEe--eccchhhccccccccHHHHHHHHhcC-CcCCC
Confidence 33445566665221 11223445899999999999999854 57773
No 113
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.89 E-value=0.36 Score=36.82 Aligned_cols=38 Identities=26% Similarity=0.580 Sum_probs=28.5
Q ss_pred cccccccccccCCccEEecCCC-cccHHHHHhhhccccCCCCCCCCCC
Q 032467 16 CPICFEFIFDTMKDITVLRCGH-TIHLECLKEMEKHYRYTCPVCSKSL 62 (140)
Q Consensus 16 C~IC~e~l~~~~~~~~~l~CgH-~Fc~~Cl~~~~~~~~~~CP~CR~~~ 62 (140)
|-.|.+. ...+.++||.| .+|..|-.. -..||+|+...
T Consensus 161 Cr~C~~~----~~~VlllPCrHl~lC~~C~~~-----~~~CPiC~~~~ 199 (207)
T KOG1100|consen 161 CRKCGER----EATVLLLPCRHLCLCGICDES-----LRICPICRSPK 199 (207)
T ss_pred ceecCcC----CceEEeecccceEeccccccc-----CccCCCCcChh
Confidence 9999874 45567789998 589988554 24599998764
No 114
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=85.15 E-value=0.6 Score=32.16 Aligned_cols=36 Identities=22% Similarity=0.422 Sum_probs=26.2
Q ss_pred ccceecCCCCCCCcccceeeeccccccCCCcccccccC
Q 032467 88 KMVWILCNDCGANSHVQFHVIAHKCLSCKSYNTRQTRG 125 (140)
Q Consensus 88 ~~~~i~C~~C~~~~~~~~~~~~~~C~~C~~~~~~~~~~ 125 (140)
......|++|+..+.... ....|+.|++++...+.|
T Consensus 67 vp~~~~C~~Cg~~~~~~~--~~~~CP~Cgs~~~~i~~G 102 (113)
T PRK12380 67 KPAQAWCWDCSQVVEIHQ--HDAQCPHCHGERLRVDTG 102 (113)
T ss_pred eCcEEEcccCCCEEecCC--cCccCcCCCCCCcEEccC
Confidence 346889999997654532 334599999998877665
No 115
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=84.63 E-value=0.58 Score=39.44 Aligned_cols=38 Identities=26% Similarity=0.454 Sum_probs=29.8
Q ss_pred cCcccccccccccccccCCccEEecCCCcccHHHHHhhhcc
Q 032467 10 RAMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKH 50 (140)
Q Consensus 10 ~~~~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~ 50 (140)
...+..|.||.+.+.. ....+.|||.||..|+..++..
T Consensus 67 ~~~~~~c~ic~~~~~~---~~~~~~c~H~~c~~cw~~yl~~ 104 (444)
T KOG1815|consen 67 KKGDVQCGICVESYDG---EIIGLGCGHPFCPPCWTGYLGT 104 (444)
T ss_pred CCccccCCcccCCCcc---hhhhcCCCcHHHHHHHHHHhhh
Confidence 3556899999986322 4567799999999999998864
No 116
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=83.51 E-value=0.17 Score=39.95 Aligned_cols=49 Identities=31% Similarity=0.533 Sum_probs=38.4
Q ss_pred cccccccccccc--ccCCccEEec--------CCCcccHHHHHhhhccccCCCCCCCCC
Q 032467 13 HHNCPICFEFIF--DTMKDITVLR--------CGHTIHLECLKEMEKHYRYTCPVCSKS 61 (140)
Q Consensus 13 ~~~C~IC~e~l~--~~~~~~~~l~--------CgH~Fc~~Cl~~~~~~~~~~CP~CR~~ 61 (140)
+..|.||...+. +....|.++. |||+.|..|+...+......||.|+..
T Consensus 207 ~~~c~ic~~~~~~n~~~~~p~vl~~~~~~~~~c~htlc~~c~~~~l~~~~~~cp~~~~~ 265 (296)
T KOG4185|consen 207 EKLCEICERIYSENDEKLAPLVLSLSRLKEKIEGHTLCKECIDTILLQAGIKCPFCTWS 265 (296)
T ss_pred HHHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcchHHHHHHhhhcCCcccce
Confidence 467999987654 2445667777 999999999999876555889999975
No 117
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=82.82 E-value=0.81 Score=31.69 Aligned_cols=38 Identities=26% Similarity=0.398 Sum_probs=26.6
Q ss_pred cccceecCCCCCCCcccceeeeccccccCCCcccccccC
Q 032467 87 NKMVWILCNDCGANSHVQFHVIAHKCLSCKSYNTRQTRG 125 (140)
Q Consensus 87 ~~~~~i~C~~C~~~~~~~~~~~~~~C~~C~~~~~~~~~~ 125 (140)
.......|++|+..+.... +...+|+.|++.+...+.|
T Consensus 67 ~vp~~~~C~~Cg~~~~~~~-~~~~~CP~Cgs~~~~i~~G 104 (117)
T PRK00564 67 DEKVELECKDCSHVFKPNA-LDYGVCEKCHSKNVIITQG 104 (117)
T ss_pred ecCCEEEhhhCCCccccCC-ccCCcCcCCCCCceEEecC
Confidence 3457899999997654432 1233699999998776655
No 118
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=81.59 E-value=0.88 Score=31.38 Aligned_cols=39 Identities=15% Similarity=0.320 Sum_probs=26.8
Q ss_pred cccceecCCCCCCCcccceeeeccccccCCCcccccccCC
Q 032467 87 NKMVWILCNDCGANSHVQFHVIAHKCLSCKSYNTRQTRGD 126 (140)
Q Consensus 87 ~~~~~i~C~~C~~~~~~~~~~~~~~C~~C~~~~~~~~~~~ 126 (140)
.......|++|+.......+ ....||.|++++...+.|.
T Consensus 66 ~~p~~~~C~~Cg~~~~~~~~-~~~~CP~Cgs~~~~i~~G~ 104 (114)
T PRK03681 66 EQEAECWCETCQQYVTLLTQ-RVRRCPQCHGDMLRIVADD 104 (114)
T ss_pred eeCcEEEcccCCCeeecCCc-cCCcCcCcCCCCcEEccCC
Confidence 33468899999976544321 1245999999988776653
No 119
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=80.72 E-value=0.6 Score=32.10 Aligned_cols=37 Identities=22% Similarity=0.390 Sum_probs=24.0
Q ss_pred ccceecCCCCCCCcccceeeeccccccCCCcccccccCC
Q 032467 88 KMVWILCNDCGANSHVQFHVIAHKCLSCKSYNTRQTRGD 126 (140)
Q Consensus 88 ~~~~i~C~~C~~~~~~~~~~~~~~C~~C~~~~~~~~~~~ 126 (140)
......|.+|+..+....+ ...|+.|++.+...+.|.
T Consensus 67 ~p~~~~C~~Cg~~~~~~~~--~~~CP~Cgs~~~~i~~G~ 103 (113)
T PF01155_consen 67 VPARARCRDCGHEFEPDEF--DFSCPRCGSPDVEIISGR 103 (113)
T ss_dssp E--EEEETTTS-EEECHHC--CHH-SSSSSS-EEEEESS
T ss_pred cCCcEECCCCCCEEecCCC--CCCCcCCcCCCcEEccCC
Confidence 3468899999988766543 367999999987766553
No 120
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=80.26 E-value=1.1 Score=40.62 Aligned_cols=51 Identities=27% Similarity=0.470 Sum_probs=39.9
Q ss_pred cCcccccccccccccccCCccEEecCCC-----cccHHHHHhhhccc-cCCCCCCCCCC
Q 032467 10 RAMHHNCPICFEFIFDTMKDITVLRCGH-----TIHLECLKEMEKHY-RYTCPVCSKSL 62 (140)
Q Consensus 10 ~~~~~~C~IC~e~l~~~~~~~~~l~CgH-----~Fc~~Cl~~~~~~~-~~~CP~CR~~~ 62 (140)
|.++..|-||..+ +...+|..-||.. ..|.+|+.+|+..+ ...|-+|..++
T Consensus 9 N~d~~~CRICr~e--~~~d~pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~ 65 (1175)
T COG5183 9 NEDKRSCRICRTE--DIRDDPLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEY 65 (1175)
T ss_pred CccchhceeecCC--CCCCCcCcccccccchhHHHHHHHHHHHHhcCCCcceeeeccee
Confidence 4456899999976 5556676668864 68999999999864 46799999875
No 121
>KOG3899 consensus Uncharacterized conserved protein [Function unknown]
Probab=79.90 E-value=1 Score=36.30 Aligned_cols=29 Identities=24% Similarity=0.490 Sum_probs=22.1
Q ss_pred cCCCcccHHHHHhhhcc------------ccCCCCCCCCCC
Q 032467 34 RCGHTIHLECLKEMEKH------------YRYTCPVCSKSL 62 (140)
Q Consensus 34 ~CgH~Fc~~Cl~~~~~~------------~~~~CP~CR~~~ 62 (140)
-|.-..|.+|+.+|+.. ++-.||+||+.+
T Consensus 324 ~crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~f 364 (381)
T KOG3899|consen 324 ICRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNF 364 (381)
T ss_pred ccccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhce
Confidence 35567899999999752 345799999985
No 122
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=79.66 E-value=0.51 Score=41.88 Aligned_cols=48 Identities=25% Similarity=0.627 Sum_probs=37.5
Q ss_pred cccccccccccccccCCccEEecCCCcccHHHHHhhhcc--ccCCCCCCCCCCc
Q 032467 12 MHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKH--YRYTCPVCSKSLW 63 (140)
Q Consensus 12 ~~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~--~~~~CP~CR~~~~ 63 (140)
..++|+||.+.++ .+..+.|-|.||..|+...+.. ....||+|+..+.
T Consensus 20 k~lEc~ic~~~~~----~p~~~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~e 69 (684)
T KOG4362|consen 20 KILECPICLEHVK----EPSLLKCDHIFLKFCLNKLFESKKGPKQCALCKSDIE 69 (684)
T ss_pred hhccCCceeEEee----ccchhhhhHHHHhhhhhceeeccCccccchhhhhhhh
Confidence 4789999998654 3478899999999999886543 3467999997653
No 123
>KOG3113 consensus Uncharacterized conserved protein [Function unknown]
Probab=79.62 E-value=1.8 Score=34.20 Aligned_cols=50 Identities=20% Similarity=0.350 Sum_probs=38.3
Q ss_pred CcccccccccccccccCCccEEecCCCcccHHHHHhhhccccCCCCCCCCCCc
Q 032467 11 AMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLW 63 (140)
Q Consensus 11 ~~~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~~ 63 (140)
.....|||=--+|....+=..+-+|||+|=.+-+.+.-. ..|++|...+.
T Consensus 109 ~a~fiCPvtgleMng~~~F~~l~~CGcV~SerAlKeika---s~C~~C~a~y~ 158 (293)
T KOG3113|consen 109 RARFICPVTGLEMNGKYRFCALRCCGCVFSERALKEIKA---SVCHVCGAAYQ 158 (293)
T ss_pred cceeecccccceecceEEEEEEeccceeccHHHHHHhhh---ccccccCCccc
Confidence 456789998776665444445569999999999888754 57999999874
No 124
>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 KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=78.75 E-value=1 Score=35.61 Aligned_cols=52 Identities=25% Similarity=0.564 Sum_probs=36.0
Q ss_pred ccCcccccccccccccccCCccE---EecCC-----CcccHHHHHhhhccc-------cCCCCCCCCCCc
Q 032467 9 ERAMHHNCPICFEFIFDTMKDIT---VLRCG-----HTIHLECLKEMEKHY-------RYTCPVCSKSLW 63 (140)
Q Consensus 9 e~~~~~~C~IC~e~l~~~~~~~~---~l~Cg-----H~Fc~~Cl~~~~~~~-------~~~CP~CR~~~~ 63 (140)
+...+-.|=||++. + .+... .-||. |-.|..||..|+... ...||.|+..+.
T Consensus 16 ~~e~eR~CWiCF~T--d-eDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYi 82 (293)
T KOG3053|consen 16 NQELERCCWICFAT--D-EDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYI 82 (293)
T ss_pred ccccceeEEEEecc--C-cccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchhe
Confidence 45567889999974 2 22221 12664 789999999998642 246999999863
No 126
>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=78.69 E-value=2 Score=24.96 Aligned_cols=34 Identities=21% Similarity=0.381 Sum_probs=21.3
Q ss_pred ceecCCCCCCCcccceeeec----cccccCCCccccccc
Q 032467 90 VWILCNDCGANSHVQFHVIA----HKCLSCKSYNTRQTR 124 (140)
Q Consensus 90 ~~i~C~~C~~~~~~~~~~~~----~~C~~C~~~~~~~~~ 124 (140)
.+..|.+|+..+.+.. .+. ..|+.|++.+.+-+-
T Consensus 4 Yey~C~~Cg~~fe~~~-~~~~~~~~~CP~Cg~~~~~r~~ 41 (52)
T TIGR02605 4 YEYRCTACGHRFEVLQ-KMSDDPLATCPECGGEKLRRLL 41 (52)
T ss_pred EEEEeCCCCCEeEEEE-ecCCCCCCCCCCCCCCceeEEe
Confidence 3567888887665532 222 369999986654443
No 127
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=77.31 E-value=1.7 Score=30.90 Aligned_cols=37 Identities=24% Similarity=0.495 Sum_probs=25.3
Q ss_pred cceecCCCCCCCcccc---e----------e------eeccccccCCCcccccccC
Q 032467 89 MVWILCNDCGANSHVQ---F----------H------VIAHKCLSCKSYNTRQTRG 125 (140)
Q Consensus 89 ~~~i~C~~C~~~~~~~---~----------~------~~~~~C~~C~~~~~~~~~~ 125 (140)
.....|.+|+...... . | .....|+.||+++...+.|
T Consensus 68 p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~G 123 (135)
T PRK03824 68 EAVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRDFEIVKG 123 (135)
T ss_pred ceEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCCcEEecC
Confidence 3678999999654332 0 1 2345799999998776655
No 128
>PLN02189 cellulose synthase
Probab=77.08 E-value=2.8 Score=39.03 Aligned_cols=55 Identities=20% Similarity=0.364 Sum_probs=38.0
Q ss_pred ccCcccccccccccccccCCccEEe---cCCCcccHHHHHhhhccccCCCCCCCCCCc
Q 032467 9 ERAMHHNCPICFEFIFDTMKDITVL---RCGHTIHLECLKEMEKHYRYTCPVCSKSLW 63 (140)
Q Consensus 9 e~~~~~~C~IC~e~l~~~~~~~~~l---~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~~ 63 (140)
++.....|.||.+++-.....-... .||--.|+.|.+-=.+.++..||.|+..+.
T Consensus 30 ~~~~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cyeyer~eg~q~CpqCkt~Y~ 87 (1040)
T PLN02189 30 RNLDGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCYEYERREGTQNCPQCKTRYK 87 (1040)
T ss_pred ccccCccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchh
Confidence 3444569999999863222211222 578889999996655557889999999874
No 129
>PLN02436 cellulose synthase A
Probab=76.33 E-value=2.7 Score=39.26 Aligned_cols=56 Identities=20% Similarity=0.403 Sum_probs=38.3
Q ss_pred cccCcccccccccccccccCCccEEe---cCCCcccHHHHHhhhccccCCCCCCCCCCc
Q 032467 8 VERAMHHNCPICFEFIFDTMKDITVL---RCGHTIHLECLKEMEKHYRYTCPVCSKSLW 63 (140)
Q Consensus 8 ~e~~~~~~C~IC~e~l~~~~~~~~~l---~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~~ 63 (140)
++......|.||-+++-....--... .||--.|+.|.+-=.+.++..||.|+..+.
T Consensus 31 ~~~~~~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cyeyer~eg~~~Cpqckt~Y~ 89 (1094)
T PLN02436 31 VQELSGQTCQICGDEIELTVDGEPFVACNECAFPVCRPCYEYERREGNQACPQCKTRYK 89 (1094)
T ss_pred ccccCCccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchh
Confidence 33444569999999863222211222 677889999996655557889999999874
No 130
>PF14353 CpXC: CpXC protein
Probab=75.77 E-value=0.43 Score=33.21 Aligned_cols=19 Identities=16% Similarity=0.621 Sum_probs=13.1
Q ss_pred cccceecCCCCCCCcccce
Q 032467 87 NKMVWILCNDCGANSHVQF 105 (140)
Q Consensus 87 ~~~~~i~C~~C~~~~~~~~ 105 (140)
+..-...|..|+.+..+.+
T Consensus 34 g~l~~~~CP~Cg~~~~~~~ 52 (128)
T PF14353_consen 34 GSLFSFTCPSCGHKFRLEY 52 (128)
T ss_pred CCcCEEECCCCCCceecCC
Confidence 3345788999998765544
No 131
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=75.47 E-value=0.77 Score=37.43 Aligned_cols=22 Identities=36% Similarity=0.883 Sum_probs=14.6
Q ss_pred eecCCCCCCCcccceeeeccccccCC
Q 032467 91 WILCNDCGANSHVQFHVIAHKCLSCK 116 (140)
Q Consensus 91 ~i~C~~C~~~~~~~~~~~~~~C~~C~ 116 (140)
..+|.||. +..|..-+.|+.|.
T Consensus 353 ~~FCldCD----v~iHesLh~CpgCe 374 (378)
T KOG2807|consen 353 NVFCLDCD----VFIHESLHNCPGCE 374 (378)
T ss_pred ceeeccch----HHHHhhhhcCCCcC
Confidence 34577776 55666667788776
No 132
>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=75.01 E-value=0.54 Score=27.14 Aligned_cols=41 Identities=32% Similarity=0.685 Sum_probs=27.1
Q ss_pred cccccccccccCCccEEe--cCCCcccHHHHHhhhcc-----ccCCCCCCC
Q 032467 16 CPICFEFIFDTMKDITVL--RCGHTIHLECLKEMEKH-----YRYTCPVCS 59 (140)
Q Consensus 16 C~IC~e~l~~~~~~~~~l--~CgH~Fc~~Cl~~~~~~-----~~~~CP~CR 59 (140)
|.||.+. . .....+. .|+-.||..|+..-... ..+.||.|+
T Consensus 2 C~vC~~~--~-~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~ 49 (51)
T PF00628_consen 2 CPVCGQS--D-DDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCR 49 (51)
T ss_dssp BTTTTSS--C-TTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHH
T ss_pred CcCCCCc--C-CCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCc
Confidence 7889873 2 2223333 88899999999765431 257888875
No 133
>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=74.80 E-value=1.2 Score=27.40 Aligned_cols=39 Identities=18% Similarity=0.355 Sum_probs=20.1
Q ss_pred ccCcccccccccccccccCCccEE-ecCCCcccHHHHHhhh
Q 032467 9 ERAMHHNCPICFEFIFDTMKDITV-LRCGHTIHLECLKEME 48 (140)
Q Consensus 9 e~~~~~~C~IC~e~l~~~~~~~~~-l~CgH~Fc~~Cl~~~~ 48 (140)
+++....|.+|...| ..+..... -.||++||..|.....
T Consensus 5 ~d~~~~~C~~C~~~F-~~~~rrhhCr~CG~~vC~~Cs~~~~ 44 (69)
T PF01363_consen 5 PDSEASNCMICGKKF-SLFRRRHHCRNCGRVVCSSCSSQRI 44 (69)
T ss_dssp SGGG-SB-TTT--B--BSSS-EEE-TTT--EEECCCS-EEE
T ss_pred CCCCCCcCcCcCCcC-CCceeeEccCCCCCEECCchhCCEE
Confidence 455677899999886 33332222 3899999999987654
No 134
>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 PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=72.95 E-value=3.1 Score=23.69 Aligned_cols=30 Identities=17% Similarity=0.299 Sum_probs=17.2
Q ss_pred ceecCCCCCCCcccceeeeccccccCCCcc
Q 032467 90 VWILCNDCGANSHVQFHVIAHKCLSCKSYN 119 (140)
Q Consensus 90 ~~i~C~~C~~~~~~~~~~~~~~C~~C~~~~ 119 (140)
....|.+|+......-.....+|+.||+.-
T Consensus 2 ~~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~ 31 (46)
T PRK00398 2 AEYKCARCGREVELDEYGTGVRCPYCGYRI 31 (46)
T ss_pred CEEECCCCCCEEEECCCCCceECCCCCCeE
Confidence 345677777654333322256788887543
No 136
>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=71.82 E-value=8.9 Score=23.24 Aligned_cols=49 Identities=20% Similarity=0.390 Sum_probs=32.4
Q ss_pred cccccccccccccccCCccEEecCCCcccHHHHHhhhccccCCCCCCCCCCc
Q 032467 12 MHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLW 63 (140)
Q Consensus 12 ~~~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~~ 63 (140)
+...|-.|-.+|-....+..+-.=-.+||..|.+..+. ..||-|...+.
T Consensus 4 lrpnCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~---~~CPNCgGelv 52 (57)
T PF06906_consen 4 LRPNCECCDKDLPPDSPEAYICSFECTFCADCAETMLN---GVCPNCGGELV 52 (57)
T ss_pred cCCCccccCCCCCCCCCcceEEeEeCcccHHHHHHHhc---CcCcCCCCccc
Confidence 45567778776643332333322225899999999875 57999988763
No 137
>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=71.62 E-value=1.3 Score=36.91 Aligned_cols=48 Identities=25% Similarity=0.565 Sum_probs=0.0
Q ss_pred Cccccccccccccc----------ccCCccEEecCCCcccHHHHHhhhcc-----ccCCCCCCCCC
Q 032467 11 AMHHNCPICFEFIF----------DTMKDITVLRCGHTIHLECLKEMEKH-----YRYTCPVCSKS 61 (140)
Q Consensus 11 ~~~~~C~IC~e~l~----------~~~~~~~~l~CgH~Fc~~Cl~~~~~~-----~~~~CP~CR~~ 61 (140)
.....|||=+..|. +..++-+.|.|||++-.. .|... ....||+||..
T Consensus 275 a~rpQCPVglnTL~fp~~~~~~~~~~~qP~VYl~CGHVhG~h---~Wg~~~~~~~~~r~CPlCr~~ 337 (416)
T PF04710_consen 275 AGRPQCPVGLNTLVFPSKSRKDVPDERQPWVYLNCGHVHGYH---NWGQDSDRDPRSRTCPLCRQV 337 (416)
T ss_dssp ------------------------------------------------------------------
T ss_pred hcCCCCCcCCCccccccccccccccccCceeeccccceeeec---ccccccccccccccCCCcccc
Confidence 34566777765541 122455788999988743 46431 24679999976
No 138
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=71.53 E-value=2.6 Score=29.33 Aligned_cols=40 Identities=28% Similarity=0.503 Sum_probs=28.4
Q ss_pred hhcccceecCCCCCCCcccceeeeccccccCCCcccccccCC
Q 032467 85 YQNKMVWILCNDCGANSHVQFHVIAHKCLSCKSYNTRQTRGD 126 (140)
Q Consensus 85 ~~~~~~~i~C~~C~~~~~~~~~~~~~~C~~C~~~~~~~~~~~ 126 (140)
+......+.|.+|+......-| ...||.|+|-+.+...|.
T Consensus 64 Ie~~p~~~~C~~C~~~~~~e~~--~~~CP~C~s~~~~i~~G~ 103 (115)
T COG0375 64 IEEEPAECWCLDCGQEVELEEL--DYRCPKCGSINLRIIGGD 103 (115)
T ss_pred EEEeccEEEeccCCCeecchhh--eeECCCCCCCceEEecCC
Confidence 3445578999999876544433 334999999988877654
No 139
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=70.45 E-value=2.2 Score=25.13 Aligned_cols=30 Identities=23% Similarity=0.498 Sum_probs=21.5
Q ss_pred cceecCCCCCCCcccceeeeccccccCCCc
Q 032467 89 MVWILCNDCGANSHVQFHVIAHKCLSCKSY 118 (140)
Q Consensus 89 ~~~i~C~~C~~~~~~~~~~~~~~C~~C~~~ 118 (140)
+....|..|++......-..+..|+.|++-
T Consensus 4 ~~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~r 33 (49)
T COG1996 4 MMEYKCARCGREVELDQETRGIRCPYCGSR 33 (49)
T ss_pred eEEEEhhhcCCeeehhhccCceeCCCCCcE
Confidence 356778888887654555677888888853
No 140
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=70.17 E-value=2.6 Score=29.48 Aligned_cols=37 Identities=27% Similarity=0.447 Sum_probs=24.7
Q ss_pred ccceecCCCCCCCcccc-e---ee-eccccccCCCcccccccC
Q 032467 88 KMVWILCNDCGANSHVQ-F---HV-IAHKCLSCKSYNTRQTRG 125 (140)
Q Consensus 88 ~~~~i~C~~C~~~~~~~-~---~~-~~~~C~~C~~~~~~~~~~ 125 (140)
......| +|+..+... + |+ ....||.|++++...+.|
T Consensus 67 vp~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~G 108 (124)
T PRK00762 67 IPVEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKRAHILGG 108 (124)
T ss_pred cCeeEEe-eCcCcccccccchhccccCCcCcCCCCCCCEEecC
Confidence 3468899 999764332 1 11 124699999998877655
No 141
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=69.37 E-value=2.6 Score=33.09 Aligned_cols=50 Identities=22% Similarity=0.411 Sum_probs=35.8
Q ss_pred ccccccccccccccCCccEEecCC-----CcccHHHHHhhhcc-ccCCCCCCCCCC
Q 032467 13 HHNCPICFEFIFDTMKDITVLRCG-----HTIHLECLKEMEKH-YRYTCPVCSKSL 62 (140)
Q Consensus 13 ~~~C~IC~e~l~~~~~~~~~l~Cg-----H~Fc~~Cl~~~~~~-~~~~CP~CR~~~ 62 (140)
+..|-||.++.......+...||. ...|..|+..|... +...|.+|...+
T Consensus 78 ~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~ 133 (323)
T KOG1609|consen 78 GPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFF 133 (323)
T ss_pred CCcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhccccCeeeecccccc
Confidence 368999998643222224556775 57899999999874 457799998875
No 142
>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=68.99 E-value=4.9 Score=32.51 Aligned_cols=25 Identities=24% Similarity=0.826 Sum_probs=19.0
Q ss_pred cceecCCCCCCCcccceeeeccccccCCC
Q 032467 89 MVWILCNDCGANSHVQFHVIAHKCLSCKS 117 (140)
Q Consensus 89 ~~~i~C~~C~~~~~~~~~~~~~~C~~C~~ 117 (140)
.....|.-|+ ..||+.+.+|++|+.
T Consensus 208 ~RyL~CslC~----teW~~~R~~C~~Cg~ 232 (305)
T TIGR01562 208 LRYLSCSLCA----TEWHYVRVKCSHCEE 232 (305)
T ss_pred ceEEEcCCCC----CcccccCccCCCCCC
Confidence 3567788887 567788888888885
No 143
>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=68.80 E-value=3.6 Score=24.10 Aligned_cols=36 Identities=17% Similarity=0.232 Sum_probs=24.3
Q ss_pred cccccccccccccCCccEEecCCCcccHHHHHhhhc
Q 032467 14 HNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEK 49 (140)
Q Consensus 14 ~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~ 49 (140)
..|.+|...|........--.||++||..|......
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~~ 38 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRIP 38 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCcChHHcCCeee
Confidence 468888876543333334458999999999776543
No 144
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=68.53 E-value=5.3 Score=37.43 Aligned_cols=56 Identities=18% Similarity=0.370 Sum_probs=38.1
Q ss_pred cccCcccccccccccccccCC-cc--EEecCCCcccHHHHHhhhccccCCCCCCCCCCc
Q 032467 8 VERAMHHNCPICFEFIFDTMK-DI--TVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLW 63 (140)
Q Consensus 8 ~e~~~~~~C~IC~e~l~~~~~-~~--~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~~ 63 (140)
+++.....|.||-+++-.... .+ .--.||--.|+.|.+-=...++..||.|+..+.
T Consensus 12 ~~~~~~qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCYEYEr~eG~q~CPqCktrYk 70 (1079)
T PLN02638 12 MKHGGGQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCYEYERKDGNQSCPQCKTKYK 70 (1079)
T ss_pred ccccCCceeeecccccCcCCCCCEEEEeccCCCccccchhhhhhhcCCccCCccCCchh
Confidence 344455699999997522211 11 223777889999996545557889999999874
No 145
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=67.96 E-value=4 Score=23.35 Aligned_cols=26 Identities=19% Similarity=0.671 Sum_probs=16.1
Q ss_pred eecCCCCCCCcccceeeeccccccCCC
Q 032467 91 WILCNDCGANSHVQFHVIAHKCLSCKS 117 (140)
Q Consensus 91 ~i~C~~C~~~~~~~~~~~~~~C~~C~~ 117 (140)
...|.+|+...... .....+|+.||+
T Consensus 2 ~Y~C~~Cg~~~~~~-~~~~irC~~CG~ 27 (44)
T smart00659 2 IYICGECGRENEIK-SKDVVRCRECGY 27 (44)
T ss_pred EEECCCCCCEeecC-CCCceECCCCCc
Confidence 35677777665444 245667777774
No 146
>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=67.35 E-value=3.1 Score=26.08 Aligned_cols=12 Identities=17% Similarity=0.365 Sum_probs=8.8
Q ss_pred cccHHHHHhhhc
Q 032467 38 TIHLECLKEMEK 49 (140)
Q Consensus 38 ~Fc~~Cl~~~~~ 49 (140)
-||+.||.+|..
T Consensus 11 gFCRNCLskWy~ 22 (68)
T PF06844_consen 11 GFCRNCLSKWYR 22 (68)
T ss_dssp S--HHHHHHHHH
T ss_pred HHHHHHHHHHHH
Confidence 499999999986
No 147
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=67.18 E-value=3.7 Score=24.39 Aligned_cols=42 Identities=19% Similarity=0.346 Sum_probs=24.2
Q ss_pred eecCCCCCCCccc--ceeeeccccccCCCcccccc-cCCCCCCCC
Q 032467 91 WILCNDCGANSHV--QFHVIAHKCLSCKSYNTRQT-RGDTATTCS 132 (140)
Q Consensus 91 ~i~C~~C~~~~~~--~~~~~~~~C~~C~~~~~~~~-~~~~~~~~~ 132 (140)
++.|..|++-.-. .+..+..+|+-|+..|..-. ++.+.|+++
T Consensus 4 eiRC~~CnklLa~~g~~~~leIKCpRC~tiN~~~a~~~~~~p~~~ 48 (51)
T PF10122_consen 4 EIRCGHCNKLLAKAGEVIELEIKCPRCKTINHVRATSPEPEPLSE 48 (51)
T ss_pred ceeccchhHHHhhhcCccEEEEECCCCCccceEeccCCCCCchhh
Confidence 4667777642211 22246678888887776554 466666543
No 148
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=66.65 E-value=7 Score=34.73 Aligned_cols=48 Identities=25% Similarity=0.582 Sum_probs=32.6
Q ss_pred ccccccccccccccCCccEEe---cCCCcccHHHHHhhhcc----ccCCCCCCCCCC
Q 032467 13 HHNCPICFEFIFDTMKDITVL---RCGHTIHLECLKEMEKH----YRYTCPVCSKSL 62 (140)
Q Consensus 13 ~~~C~IC~e~l~~~~~~~~~l---~CgH~Fc~~Cl~~~~~~----~~~~CP~CR~~~ 62 (140)
...|++|-.. .....-..+ .||-.+|..|...|+.+ +.++||-||+-.
T Consensus 18 ~~mc~l~~s~--G~~~ag~m~ac~~c~~~yH~~cvt~~~~~~~l~~gWrC~~crvCe 72 (694)
T KOG4443|consen 18 CLMCPLCGSS--GKGRAGRLLACSDCGQKYHPYCVTSWAQHAVLSGGWRCPSCRVCE 72 (694)
T ss_pred hhhhhhhccc--cccccCcchhhhhhcccCCcchhhHHHhHHHhcCCcccCCceeee
Confidence 4567777642 222222233 78999999999999865 458899998763
No 149
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=63.47 E-value=3.8 Score=32.64 Aligned_cols=80 Identities=19% Similarity=0.387 Sum_probs=46.7
Q ss_pred cccccccccccccccCC------ccEEecCCCcccHHHHHh-hhccc---------cCCCCCCCCCCchhhhHHHHHHHH
Q 032467 12 MHHNCPICFEFIFDTMK------DITVLRCGHTIHLECLKE-MEKHY---------RYTCPVCSKSLWDMSKLWSKIDQE 75 (140)
Q Consensus 12 ~~~~C~IC~e~l~~~~~------~~~~l~CgH~Fc~~Cl~~-~~~~~---------~~~CP~CR~~~~~~~~~~~~l~~~ 75 (140)
.-..|.+|-..+.. .- ..-.|+|--.+|..-+.+ ||..+ .+.||.|++.|.|.+. |+..
T Consensus 160 ka~~C~~C~K~YvS-mpALkMHirTH~l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSN----LRAH 234 (279)
T KOG2462|consen 160 KAFSCKYCGKVYVS-MPALKMHIRTHTLPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSN----LRAH 234 (279)
T ss_pred ccccCCCCCceeee-hHHHhhHhhccCCCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHH----HHHH
Confidence 34568888654321 11 112357777777776654 77643 3679999999977543 4444
Q ss_pred HhcCCCChhhhcccceecCCCCCCCccc
Q 032467 76 IASTPMPAMYQNKMVWILCNDCGANSHV 103 (140)
Q Consensus 76 ~~~~~~~~~~~~~~~~i~C~~C~~~~~~ 103 (140)
+++.. +. -...|..|++.+..
T Consensus 235 mQTHS------~~-K~~qC~~C~KsFsl 255 (279)
T KOG2462|consen 235 MQTHS------DV-KKHQCPRCGKSFAL 255 (279)
T ss_pred HHhhc------CC-ccccCcchhhHHHH
Confidence 44322 12 24668888876543
No 150
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=63.34 E-value=6.4 Score=35.54 Aligned_cols=26 Identities=27% Similarity=0.578 Sum_probs=19.7
Q ss_pred ceecCCCCCCCcccceeeeccccccCCCccc
Q 032467 90 VWILCNDCGANSHVQFHVIAHKCLSCKSYNT 120 (140)
Q Consensus 90 ~~i~C~~C~~~~~~~~~~~~~~C~~C~~~~~ 120 (140)
....|+.|+.... +-.+|+.|++..-
T Consensus 461 ~~L~CH~Cg~~~~-----~p~~Cp~Cgs~~L 486 (730)
T COG1198 461 GQLRCHYCGYQEP-----IPQSCPECGSEHL 486 (730)
T ss_pred CeeEeCCCCCCCC-----CCCCCCCCCCCee
Confidence 5788999997643 4458999998833
No 151
>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=63.17 E-value=3.5 Score=32.65 Aligned_cols=30 Identities=20% Similarity=0.647 Sum_probs=17.1
Q ss_pred ceecCCCCCCCcccceeeeccccccCCCcccccc
Q 032467 90 VWILCNDCGANSHVQFHVIAHKCLSCKSYNTRQT 123 (140)
Q Consensus 90 ~~i~C~~C~~~~~~~~~~~~~~C~~C~~~~~~~~ 123 (140)
....|.-|+ ..||+.+.+|++||.-+...+
T Consensus 196 R~L~Cs~C~----t~W~~~R~~Cp~Cg~~~~~~l 225 (290)
T PF04216_consen 196 RYLHCSLCG----TEWRFVRIKCPYCGNTDHEKL 225 (290)
T ss_dssp EEEEETTT------EEE--TTS-TTT---SS-EE
T ss_pred EEEEcCCCC----CeeeecCCCCcCCCCCCCcce
Confidence 678899997 678889999999997666554
No 152
>PLN02400 cellulose synthase
Probab=63.00 E-value=6 Score=37.14 Aligned_cols=55 Identities=20% Similarity=0.368 Sum_probs=37.0
Q ss_pred ccCcccccccccccccccCC-cc--EEecCCCcccHHHHHhhhccccCCCCCCCCCCc
Q 032467 9 ERAMHHNCPICFEFIFDTMK-DI--TVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLW 63 (140)
Q Consensus 9 e~~~~~~C~IC~e~l~~~~~-~~--~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~~ 63 (140)
++.....|.||-+++-.... .+ .--.||--.|+.|.+-=.+.++..||.|+..+.
T Consensus 32 ~~~~gqiCqICGD~VG~t~dGe~FVAC~eCaFPVCRpCYEYERkeGnq~CPQCkTrYk 89 (1085)
T PLN02400 32 KNLNGQICQICGDDVGVTETGDVFVACNECAFPVCRPCYEYERKDGTQCCPQCKTRYR 89 (1085)
T ss_pred cccCCceeeecccccCcCCCCCEEEEEccCCCccccchhheecccCCccCcccCCccc
Confidence 33345699999997532211 11 223777889999996544446788999999874
No 153
>cd02339 ZZ_Mind_bomb Zinc finger, ZZ type. Zinc finger present in Drosophila Mind bomb (D-mib) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Mind bomb is an E3 ubiqitin ligase that has been shown to regulate signaling by the Notch ligand Delta in Drosophila melanogaster.
Probab=61.46 E-value=6.2 Score=22.65 Aligned_cols=26 Identities=31% Similarity=0.820 Sum_probs=17.1
Q ss_pred ecCCCCCCCcccceeeeccccccCCCccc
Q 032467 92 ILCNDCGANSHVQFHVIAHKCLSCKSYNT 120 (140)
Q Consensus 92 i~C~~C~~~~~~~~~~~~~~C~~C~~~~~ 120 (140)
|.|+.|++.. ..+.+.+|..|..|..
T Consensus 1 i~Cd~C~~~~---i~G~RykC~~C~dyDL 26 (45)
T cd02339 1 IICDTCRKQG---IIGIRWKCAECPNYDL 26 (45)
T ss_pred CCCCCCCCCC---cccCeEECCCCCCccc
Confidence 5689998642 2256677888876543
No 154
>COG4647 AcxC Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=61.41 E-value=4.8 Score=28.73 Aligned_cols=21 Identities=19% Similarity=0.300 Sum_probs=13.3
Q ss_pred CccEEecCCCcccHHHHHhhhc
Q 032467 28 KDITVLRCGHTIHLECLKEMEK 49 (140)
Q Consensus 28 ~~~~~l~CgH~Fc~~Cl~~~~~ 49 (140)
..+..-.|||.|+.. -++|..
T Consensus 68 ~rv~rcecghsf~d~-r~nwkl 88 (165)
T COG4647 68 KRVIRCECGHSFGDY-RENWKL 88 (165)
T ss_pred ccEEEEeccccccCh-hhCcee
Confidence 345556999999864 344543
No 155
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=61.36 E-value=5.6 Score=33.72 Aligned_cols=29 Identities=31% Similarity=0.681 Sum_probs=23.1
Q ss_pred ceecCCCCCCCcccceeeeccccccCCCccccc
Q 032467 90 VWILCNDCGANSHVQFHVIAHKCLSCKSYNTRQ 122 (140)
Q Consensus 90 ~~i~C~~C~~~~~~~~~~~~~~C~~C~~~~~~~ 122 (140)
....|..|+..+ ..|++ +|+.|+.+|+-.
T Consensus 6 t~f~C~~CG~~s---~KW~G-kCp~Cg~Wns~v 34 (456)
T COG1066 6 TAFVCQECGYVS---PKWLG-KCPACGAWNTLV 34 (456)
T ss_pred cEEEcccCCCCC---ccccc-cCCCCCCccceE
Confidence 568899999753 33788 899999998765
No 156
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=61.11 E-value=9.1 Score=31.03 Aligned_cols=25 Identities=32% Similarity=0.911 Sum_probs=18.8
Q ss_pred cceecCCCCCCCcccceeeeccccccCCC
Q 032467 89 MVWILCNDCGANSHVQFHVIAHKCLSCKS 117 (140)
Q Consensus 89 ~~~i~C~~C~~~~~~~~~~~~~~C~~C~~ 117 (140)
.....|.-|+ ..||+.+.+|+.|+.
T Consensus 210 ~RyL~CslC~----teW~~~R~~C~~Cg~ 234 (309)
T PRK03564 210 LRYLHCNLCE----SEWHVVRVKCSNCEQ 234 (309)
T ss_pred ceEEEcCCCC----CcccccCccCCCCCC
Confidence 3567788887 567778888888885
No 157
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=59.53 E-value=3.1 Score=24.70 Aligned_cols=34 Identities=24% Similarity=0.448 Sum_probs=21.2
Q ss_pred ccc--ccccccccc---CCccEEe-cCCCcccHHHHHhhh
Q 032467 15 NCP--ICFEFIFDT---MKDITVL-RCGHTIHLECLKEME 48 (140)
Q Consensus 15 ~C~--IC~e~l~~~---~~~~~~l-~CgH~Fc~~Cl~~~~ 48 (140)
-|| =|...+... ....+.- .|||.||..|...|-
T Consensus 20 ~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H 59 (64)
T smart00647 20 WCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWH 59 (64)
T ss_pred CCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcCC
Confidence 466 664433222 2233444 789999999998884
No 158
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=58.83 E-value=6.7 Score=30.97 Aligned_cols=32 Identities=16% Similarity=0.210 Sum_probs=27.1
Q ss_pred cccccccccccccCCccEEecCCCcccHHHHHhhhc
Q 032467 14 HNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEK 49 (140)
Q Consensus 14 ~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~ 49 (140)
.-|..|+.. ..+|++.+=||.|+++||.+++.
T Consensus 44 dcCsLtLqP----c~dPvit~~GylfdrEaILe~il 75 (303)
T KOG3039|consen 44 DCCSLTLQP----CRDPVITPDGYLFDREAILEYIL 75 (303)
T ss_pred ceeeeeccc----ccCCccCCCCeeeeHHHHHHHHH
Confidence 357888864 78899999999999999999865
No 159
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=55.48 E-value=9.2 Score=32.45 Aligned_cols=31 Identities=32% Similarity=0.669 Sum_probs=23.0
Q ss_pred cceecCCCCCCCcccceeeeccccccCCCcccccc
Q 032467 89 MVWILCNDCGANSHVQFHVIAHKCLSCKSYNTRQT 123 (140)
Q Consensus 89 ~~~i~C~~C~~~~~~~~~~~~~~C~~C~~~~~~~~ 123 (140)
+....|..|+..+.. |++ +|++|+++|+-.-
T Consensus 5 ~~~y~C~~Cg~~~~~---~~g-~Cp~C~~w~t~~~ 35 (454)
T TIGR00416 5 KSKFVCQHCGADSPK---WQG-KCPACHAWNTITE 35 (454)
T ss_pred CCeEECCcCCCCCcc---ccE-ECcCCCCccccch
Confidence 456889999975432 344 8999999998765
No 160
>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=54.19 E-value=7 Score=19.81 Aligned_cols=8 Identities=38% Similarity=0.804 Sum_probs=4.4
Q ss_pred cccccccc
Q 032467 15 NCPICFEF 22 (140)
Q Consensus 15 ~C~IC~e~ 22 (140)
.||-|...
T Consensus 2 ~CP~C~~~ 9 (26)
T PF10571_consen 2 TCPECGAE 9 (26)
T ss_pred cCCCCcCC
Confidence 36666654
No 161
>PLN02195 cellulose synthase A
Probab=54.15 E-value=17 Score=33.94 Aligned_cols=53 Identities=19% Similarity=0.249 Sum_probs=36.8
Q ss_pred CcccccccccccccccCC-cc--EEecCCCcccHHHHHhhhccccCCCCCCCCCCc
Q 032467 11 AMHHNCPICFEFIFDTMK-DI--TVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLW 63 (140)
Q Consensus 11 ~~~~~C~IC~e~l~~~~~-~~--~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~~ 63 (140)
+....|.||-+.+..... .+ .--.||--.|+.|.+-=.+.++..||.|+..+.
T Consensus 4 ~~~~~c~~cgd~~~~~~~g~~fvaC~eC~~pvCrpCyeyer~eg~q~CpqCkt~Yk 59 (977)
T PLN02195 4 SGAPICATCGEEVGVDSNGEAFVACHECSYPLCKACLEYEIKEGRKVCLRCGGPYD 59 (977)
T ss_pred CCCccceecccccCcCCCCCeEEEeccCCCccccchhhhhhhcCCccCCccCCccc
Confidence 345689999986522111 11 223788889999996555557789999999985
No 162
>cd02334 ZZ_dystrophin Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan.
Probab=53.97 E-value=11 Score=21.96 Aligned_cols=28 Identities=29% Similarity=0.571 Sum_probs=19.6
Q ss_pred ecCCCCCCCcccceeeeccccccCCCccccc
Q 032467 92 ILCNDCGANSHVQFHVIAHKCLSCKSYNTRQ 122 (140)
Q Consensus 92 i~C~~C~~~~~~~~~~~~~~C~~C~~~~~~~ 122 (140)
+.|+.|++. +..+++.+|..|..|+.-+
T Consensus 1 ~~Cd~C~~~---pi~g~RykC~~C~d~DLC~ 28 (49)
T cd02334 1 AKCNICKEF---PITGFRYRCLKCFNYDLCQ 28 (49)
T ss_pred CCCCCCCCC---CceeeeEECCCCCCcCchH
Confidence 358888863 3346788899988776554
No 163
>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]
Probab=53.81 E-value=5.4 Score=36.14 Aligned_cols=45 Identities=31% Similarity=0.638 Sum_probs=31.1
Q ss_pred ccccccccccccccC---CccEEecCCCcccHHHHHhhhccccCCCCCCC
Q 032467 13 HHNCPICFEFIFDTM---KDITVLRCGHTIHLECLKEMEKHYRYTCPVCS 59 (140)
Q Consensus 13 ~~~C~IC~e~l~~~~---~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR 59 (140)
+..|.-|.+....+. ...+.+.|||.||..|+.....+.. |-.|.
T Consensus 784 e~rc~~c~~~~l~~~~~~~~~~v~~c~h~yhk~c~~~~~~~~~--~~~~~ 831 (846)
T KOG2066|consen 784 EERCSSCFEPNLPSGAAFDSVVVFHCGHMYHKECLMMESLRNA--CNIES 831 (846)
T ss_pred hhhhhhhcccccccCcccceeeEEEccchhhhcccccHHHhcc--cChhh
Confidence 557888988643222 5567889999999999987655332 54443
No 164
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=53.78 E-value=16 Score=34.31 Aligned_cols=52 Identities=15% Similarity=0.331 Sum_probs=36.4
Q ss_pred cccccccccccccccCC-cc--EEecCCCcccHHHHHhhhccccCCCCCCCCCCc
Q 032467 12 MHHNCPICFEFIFDTMK-DI--TVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLW 63 (140)
Q Consensus 12 ~~~~C~IC~e~l~~~~~-~~--~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~~ 63 (140)
....|.||-+++-.... .+ .--.||--.|+.|.+-=.+.++..||.|+..+.
T Consensus 14 ~~~~c~iCGd~vg~~~~Ge~FVAC~eC~fpvCr~cyeye~~~g~~~cp~c~t~y~ 68 (1044)
T PLN02915 14 DAKTCRVCGDEVGVKEDGQPFVACHVCGFPVCKPCYEYERSEGNQCCPQCNTRYK 68 (1044)
T ss_pred CcchhhccccccCcCCCCCEEEEeccCCCccccchhhhhhhcCCccCCccCCchh
Confidence 46789999987522211 11 223777889999996555557789999999874
No 165
>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=52.90 E-value=14 Score=25.13 Aligned_cols=26 Identities=19% Similarity=0.429 Sum_probs=18.8
Q ss_pred CCcccHHHHHhhhc--------cccCCCCCCCCC
Q 032467 36 GHTIHLECLKEMEK--------HYRYTCPVCSKS 61 (140)
Q Consensus 36 gH~Fc~~Cl~~~~~--------~~~~~CP~CR~~ 61 (140)
.=.||..||..... ...+.||.||..
T Consensus 37 ~~~fC~~CL~~ryge~~~ev~~~~~W~CP~Crgi 70 (105)
T PF10497_consen 37 RGKFCGGCLRNRYGENVEEVLEDPNWKCPKCRGI 70 (105)
T ss_pred cceehHhHHHHHHhhhHHHHhcCCceECCCCCCe
Confidence 56799999877542 245789999864
No 166
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=52.77 E-value=13 Score=31.97 Aligned_cols=25 Identities=24% Similarity=0.601 Sum_probs=18.4
Q ss_pred ceecCCCCCCCcccceeeeccccccCCCcc
Q 032467 90 VWILCNDCGANSHVQFHVIAHKCLSCKSYN 119 (140)
Q Consensus 90 ~~i~C~~C~~~~~~~~~~~~~~C~~C~~~~ 119 (140)
....|+.|+..... ...|+.|++..
T Consensus 239 ~~l~Ch~Cg~~~~~-----~~~Cp~C~s~~ 263 (505)
T TIGR00595 239 GKLRCHYCGYQEPI-----PKTCPQCGSED 263 (505)
T ss_pred CeEEcCCCcCcCCC-----CCCCCCCCCCe
Confidence 46789999976433 44899999753
No 167
>cd02344 ZZ_HERC2 Zinc finger, ZZ type. Zinc finger present in HERC2 and related proteins. HERC2 is a potential E3 ubiquitin protein ligase and/or guanine nucleotide exchange factor. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=52.32 E-value=11 Score=21.73 Aligned_cols=28 Identities=18% Similarity=0.581 Sum_probs=19.0
Q ss_pred ecCCCCCCCcccceeeeccccccCCCccccc
Q 032467 92 ILCNDCGANSHVQFHVIAHKCLSCKSYNTRQ 122 (140)
Q Consensus 92 i~C~~C~~~~~~~~~~~~~~C~~C~~~~~~~ 122 (140)
+.|+.|+... .-+.+.+|..|..|..-+
T Consensus 1 V~Cd~C~~~p---I~G~RykC~~C~dyDLC~ 28 (45)
T cd02344 1 VTCDGCQMFP---INGPRFKCRNCDDFDFCE 28 (45)
T ss_pred CCCCCCCCCC---CccCeEECCCCCCccchH
Confidence 4688898632 235777888888776544
No 168
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=52.10 E-value=2.9 Score=31.84 Aligned_cols=12 Identities=50% Similarity=1.132 Sum_probs=9.7
Q ss_pred cCCCCCCCCCCc
Q 032467 52 RYTCPVCSKSLW 63 (140)
Q Consensus 52 ~~~CP~CR~~~~ 63 (140)
..+||+|.+.+.
T Consensus 5 ~~~CPvC~~~F~ 16 (214)
T PF09986_consen 5 KITCPVCGKEFK 16 (214)
T ss_pred ceECCCCCCeee
Confidence 467999999874
No 169
>PF12773 DZR: Double zinc ribbon
Probab=51.72 E-value=15 Score=20.90 Aligned_cols=11 Identities=36% Similarity=0.921 Sum_probs=7.4
Q ss_pred ceecCCCCCCC
Q 032467 90 VWILCNDCGAN 100 (140)
Q Consensus 90 ~~i~C~~C~~~ 100 (140)
..++|..|+..
T Consensus 28 ~~~~C~~Cg~~ 38 (50)
T PF12773_consen 28 SKKICPNCGAE 38 (50)
T ss_pred CCCCCcCCcCC
Confidence 45667777765
No 170
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=51.10 E-value=9.9 Score=31.63 Aligned_cols=44 Identities=27% Similarity=0.546 Sum_probs=27.4
Q ss_pred ccccccccccc-ccCCccEEecCCCcccHHHHHhhhccccCCCCCC
Q 032467 14 HNCPICFEFIF-DTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVC 58 (140)
Q Consensus 14 ~~C~IC~e~l~-~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~C 58 (140)
..||.|.-.+. ...-..++-.|||-||..|...|... +..|..|
T Consensus 307 r~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~~~~~~~-~~~~~~~ 351 (384)
T KOG1812|consen 307 RQCPKCKFMIELSEGCNHMTCRCGHQFCYMCGGDWKTH-NGECYEC 351 (384)
T ss_pred CcCcccceeeeecCCcceEEeeccccchhhcCcchhhC-CccccCc
Confidence 46888865321 11133344479999999999999763 3334333
No 171
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=51.00 E-value=24 Score=22.63 Aligned_cols=47 Identities=21% Similarity=0.362 Sum_probs=31.6
Q ss_pred cccccccccccccCCccEEecCCCcccHHHHHhhhccccCCCCCCCCCCc
Q 032467 14 HNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLW 63 (140)
Q Consensus 14 ~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~~ 63 (140)
..|--|-.+|-....+.++-.=-|+||..|.+.-+. ..||-|...+.
T Consensus 6 PnCECCDrDLpp~s~dA~ICtfEcTFCadCae~~l~---g~CPnCGGelv 52 (84)
T COG3813 6 PNCECCDRDLPPDSTDARICTFECTFCADCAENRLH---GLCPNCGGELV 52 (84)
T ss_pred CCCcccCCCCCCCCCceeEEEEeeehhHhHHHHhhc---CcCCCCCchhh
Confidence 445556655544344444434458999999998776 57999988763
No 172
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=50.83 E-value=7.5 Score=31.85 Aligned_cols=25 Identities=24% Similarity=0.416 Sum_probs=15.1
Q ss_pred eecCCCCCCCcccceeeeccccccCCCc
Q 032467 91 WILCNDCGANSHVQFHVIAHKCLSCKSY 118 (140)
Q Consensus 91 ~i~C~~C~~~~~~~~~~~~~~C~~C~~~ 118 (140)
.-.|-.|+..... ..+.+|..|+.+
T Consensus 330 ~~~Cf~C~~~~~~---~~~y~C~~Ck~~ 354 (378)
T KOG2807|consen 330 SRFCFACQGELLS---SGRYRCESCKNV 354 (378)
T ss_pred CcceeeeccccCC---CCcEEchhccce
Confidence 3448888655333 356677777743
No 173
>cd02345 ZZ_dah Zinc finger, ZZ type. Zinc finger present in Drosophila dah and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dah (discontinuous actin hexagon) is a membrane associated protein essential for cortical furrow formation in Drosophila.
Probab=50.46 E-value=14 Score=21.37 Aligned_cols=28 Identities=21% Similarity=0.643 Sum_probs=18.9
Q ss_pred ecCCCCCCCcccceeeeccccccCCCccccc
Q 032467 92 ILCNDCGANSHVQFHVIAHKCLSCKSYNTRQ 122 (140)
Q Consensus 92 i~C~~C~~~~~~~~~~~~~~C~~C~~~~~~~ 122 (140)
+.|+.|.+.. +. +++.+|..|..|+.-.
T Consensus 1 ~~C~~C~~~~-i~--g~R~~C~~C~dydLC~ 28 (49)
T cd02345 1 LSCSACRKQD-IS--GIRFPCQVCRDYSLCL 28 (49)
T ss_pred CcCCCCCCCC-ce--EeeEECCCCCCcCchH
Confidence 4688888742 22 5777888888776544
No 174
>PRK11823 DNA repair protein RadA; Provisional
Probab=50.09 E-value=13 Score=31.51 Aligned_cols=31 Identities=29% Similarity=0.674 Sum_probs=22.2
Q ss_pred cceecCCCCCCCcccceeeeccccccCCCcccccc
Q 032467 89 MVWILCNDCGANSHVQFHVIAHKCLSCKSYNTRQT 123 (140)
Q Consensus 89 ~~~i~C~~C~~~~~~~~~~~~~~C~~C~~~~~~~~ 123 (140)
+....|..|+..+.. |++ +|++|+.+|+-.=
T Consensus 5 ~~~y~C~~Cg~~~~~---~~g-~Cp~C~~w~t~~e 35 (446)
T PRK11823 5 KTAYVCQECGAESPK---WLG-RCPECGAWNTLVE 35 (446)
T ss_pred CCeEECCcCCCCCcc---cCe-eCcCCCCccceee
Confidence 456889999975422 344 8999998887643
No 175
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=50.07 E-value=15 Score=22.21 Aligned_cols=29 Identities=28% Similarity=0.602 Sum_probs=21.4
Q ss_pred ceecCCCCCCCcccceeeeccccccCCCcccccc
Q 032467 90 VWILCNDCGANSHVQFHVIAHKCLSCKSYNTRQT 123 (140)
Q Consensus 90 ~~i~C~~C~~~~~~~~~~~~~~C~~C~~~~~~~~ 123 (140)
....|..|++. .. -...|+.||-|+.+++
T Consensus 26 ~l~~C~~CG~~--~~---~H~vC~~CG~Y~gr~v 54 (57)
T PRK12286 26 GLVECPNCGEP--KL---PHRVCPSCGYYKGREV 54 (57)
T ss_pred cceECCCCCCc--cC---CeEECCCCCcCCCEEe
Confidence 45779999975 33 3457899999987764
No 176
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS 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=48.28 E-value=15 Score=19.82 Aligned_cols=8 Identities=25% Similarity=0.812 Sum_probs=4.4
Q ss_pred cccccCCC
Q 032467 110 HKCLSCKS 117 (140)
Q Consensus 110 ~~C~~C~~ 117 (140)
..|+.|++
T Consensus 27 ~~CP~Cg~ 34 (41)
T smart00834 27 ATCPECGG 34 (41)
T ss_pred CCCCCCCC
Confidence 34666654
No 177
>KOG3842 consensus Adaptor protein Pellino [Signal transduction mechanisms]
Probab=47.62 E-value=11 Score=30.83 Aligned_cols=48 Identities=23% Similarity=0.530 Sum_probs=29.8
Q ss_pred Ccccccccccccc----------cccCCccEEecCCCcccHHHHHhhhcc-----ccCCCCCCCCC
Q 032467 11 AMHHNCPICFEFI----------FDTMKDITVLRCGHTIHLECLKEMEKH-----YRYTCPVCSKS 61 (140)
Q Consensus 11 ~~~~~C~IC~e~l----------~~~~~~~~~l~CgH~Fc~~Cl~~~~~~-----~~~~CP~CR~~ 61 (140)
.....||+=+..| .+..++-+.|.|||+--. ..|-.. ....||+||..
T Consensus 288 A~RPQCPVglnTL~~P~~~~~~~~~~~QP~vYl~CGHV~G~---H~WG~~e~~g~~~r~CPmC~~~ 350 (429)
T KOG3842|consen 288 AARPQCPVGLNTLAFPSKRRKRVVDEKQPWVYLNCGHVHGY---HNWGVRENTGQRERECPMCRVV 350 (429)
T ss_pred ccCCCCCcccceeecccccccccccccCCeEEEeccccccc---cccccccccCcccCcCCeeeee
Confidence 3456788877654 122345688999987442 246432 13579999965
No 178
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=47.58 E-value=13 Score=27.99 Aligned_cols=41 Identities=27% Similarity=0.767 Sum_probs=26.6
Q ss_pred ccccccccc--cccccCCc-c--EEecCCCcccHHHHHhhhccccCCCCCCCC
Q 032467 13 HHNCPICFE--FIFDTMKD-I--TVLRCGHTIHLECLKEMEKHYRYTCPVCSK 60 (140)
Q Consensus 13 ~~~C~IC~e--~l~~~~~~-~--~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~ 60 (140)
...|-||.+ .+|. ++. - .-..|+-+||..|+.+ ..||-|..
T Consensus 152 GfiCe~C~~~~~IfP-F~~~~~~~C~~C~~v~H~~C~~~------~~CpkC~R 197 (202)
T PF13901_consen 152 GFICEICNSDDIIFP-FQIDTTVRCPKCKSVFHKSCFRK------KSCPKCAR 197 (202)
T ss_pred CCCCccCCCCCCCCC-CCCCCeeeCCcCccccchhhcCC------CCCCCcHh
Confidence 357888874 2332 332 2 2238999999999763 35999953
No 179
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=47.53 E-value=11 Score=34.61 Aligned_cols=50 Identities=12% Similarity=0.199 Sum_probs=31.8
Q ss_pred cccccccccccccCCccEEe---cCCCcccHHHHHhhhcc-----ccCCCCCCCCCCc
Q 032467 14 HNCPICFEFIFDTMKDITVL---RCGHTIHLECLKEMEKH-----YRYTCPVCSKSLW 63 (140)
Q Consensus 14 ~~C~IC~e~l~~~~~~~~~l---~CgH~Fc~~Cl~~~~~~-----~~~~CP~CR~~~~ 63 (140)
..|.||.-++.+.....-++ .|+|.||..||..|... ..-.|++|..-|.
T Consensus 97 ~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~ 154 (1134)
T KOG0825|consen 97 DTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESEKHTAHYFCEECVG 154 (1134)
T ss_pred cccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhccccccccccHHHHhh
Confidence 45677765543312222233 49999999999999764 1345788876653
No 180
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=47.09 E-value=16 Score=19.56 Aligned_cols=27 Identities=30% Similarity=0.540 Sum_probs=15.2
Q ss_pred eecCCCCCCCcccceeeeccccccCCC
Q 032467 91 WILCNDCGANSHVQFHVIAHKCLSCKS 117 (140)
Q Consensus 91 ~i~C~~C~~~~~~~~~~~~~~C~~C~~ 117 (140)
...|..|+....+..-.-+..|..|++
T Consensus 3 ~~~C~~C~~~~i~~~~~~~~~C~~Cg~ 29 (33)
T PF08792_consen 3 LKKCSKCGGNGIVNKEDDYEVCIFCGS 29 (33)
T ss_pred ceEcCCCCCCeEEEecCCeEEcccCCc
Confidence 355777765543323345567777774
No 181
>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=46.98 E-value=20 Score=18.00 Aligned_cols=9 Identities=44% Similarity=1.328 Sum_probs=7.3
Q ss_pred CCCCCCCCC
Q 032467 54 TCPVCSKSL 62 (140)
Q Consensus 54 ~CP~CR~~~ 62 (140)
.||+|.+.+
T Consensus 3 ~CPiC~~~v 11 (26)
T smart00734 3 QCPVCFREV 11 (26)
T ss_pred cCCCCcCcc
Confidence 589998876
No 182
>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=46.08 E-value=18 Score=20.20 Aligned_cols=27 Identities=26% Similarity=0.516 Sum_probs=12.5
Q ss_pred eecCCCCCCCcccceee---eccccccCCC
Q 032467 91 WILCNDCGANSHVQFHV---IAHKCLSCKS 117 (140)
Q Consensus 91 ~i~C~~C~~~~~~~~~~---~~~~C~~C~~ 117 (140)
+..|.+|+..+.+...+ ....|+.|++
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred EEEeCCCCCEEEEEEEcCCCCCCcCCCCCC
Confidence 34566666444332211 2345666665
No 183
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=44.86 E-value=20 Score=28.93 Aligned_cols=58 Identities=26% Similarity=0.598 Sum_probs=38.6
Q ss_pred CcccccccccccccccCCccEEecC----CCcccHHHHHhhhccc----------cCCCCCCCCCCchhhhHHHHHHHHH
Q 032467 11 AMHHNCPICFEFIFDTMKDITVLRC----GHTIHLECLKEMEKHY----------RYTCPVCSKSLWDMSKLWSKIDQEI 76 (140)
Q Consensus 11 ~~~~~C~IC~e~l~~~~~~~~~l~C----gH~Fc~~Cl~~~~~~~----------~~~CP~CR~~~~~~~~~~~~l~~~~ 76 (140)
+..+.|.+|.|.|.+ -....| .|.||.-|-++.++.. ..+||+=...+ -|.-++.++
T Consensus 266 ~apLcCTLC~ERLED----THFVQCPSVp~HKFCFPCSResIK~Qg~sgevYCPSGdkCPLvgS~v-----PWAFMQGEI 336 (352)
T KOG3579|consen 266 SAPLCCTLCHERLED----THFVQCPSVPSHKFCFPCSRESIKQQGASGEVYCPSGDKCPLVGSNV-----PWAFMQGEI 336 (352)
T ss_pred CCceeehhhhhhhcc----CceeecCCCcccceecccCHHHHHhhcCCCceeCCCCCcCcccCCcc-----cHHHhhhhH
Confidence 346899999997533 345566 5999999999988642 24566665554 455555555
Q ss_pred h
Q 032467 77 A 77 (140)
Q Consensus 77 ~ 77 (140)
.
T Consensus 337 a 337 (352)
T KOG3579|consen 337 A 337 (352)
T ss_pred H
Confidence 4
No 184
>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=44.32 E-value=18 Score=21.11 Aligned_cols=12 Identities=33% Similarity=0.913 Sum_probs=6.5
Q ss_pred CCCCCCCCCCch
Q 032467 53 YTCPVCSKSLWD 64 (140)
Q Consensus 53 ~~CP~CR~~~~~ 64 (140)
..||+|.+.+..
T Consensus 21 ~~CPlC~r~l~~ 32 (54)
T PF04423_consen 21 GCCPLCGRPLDE 32 (54)
T ss_dssp EE-TTT--EE-H
T ss_pred CcCCCCCCCCCH
Confidence 389999999865
No 185
>cd02338 ZZ_PCMF_like Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel modulatory factor 1 or FIGC has been shown to possess intrinsic E3 ubiquitin ligase activity and to promote ubiquitination.
Probab=44.10 E-value=20 Score=20.76 Aligned_cols=28 Identities=29% Similarity=0.700 Sum_probs=17.7
Q ss_pred ecCCCCCCCcccceeeeccccccCCCccccc
Q 032467 92 ILCNDCGANSHVQFHVIAHKCLSCKSYNTRQ 122 (140)
Q Consensus 92 i~C~~C~~~~~~~~~~~~~~C~~C~~~~~~~ 122 (140)
|.|+.|++..-. +.+.+|..|..|+.-.
T Consensus 1 i~C~~C~~~~i~---g~R~~C~~C~d~dlC~ 28 (49)
T cd02338 1 VSCDGCGKSNFT---GRRYKCLICYDYDLCA 28 (49)
T ss_pred CCCCCCcCCCcE---EeeEEeCCCCCCccch
Confidence 468888854222 5667777777666543
No 186
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=43.38 E-value=14 Score=18.37 Aligned_cols=8 Identities=50% Similarity=1.572 Sum_probs=4.3
Q ss_pred ecCCCCCC
Q 032467 92 ILCNDCGA 99 (140)
Q Consensus 92 i~C~~C~~ 99 (140)
+.|..|++
T Consensus 3 ~~Cp~Cg~ 10 (26)
T PF13248_consen 3 MFCPNCGA 10 (26)
T ss_pred CCCcccCC
Confidence 34556655
No 187
>KOG3842 consensus Adaptor protein Pellino [Signal transduction mechanisms]
Probab=43.35 E-value=25 Score=28.87 Aligned_cols=56 Identities=21% Similarity=0.478 Sum_probs=33.9
Q ss_pred ccccCc--ccccccccccc-------------cccCCcc--EEecCCCcccHHHHHhhhcc--------ccCCCCCCCCC
Q 032467 7 CVERAM--HHNCPICFEFI-------------FDTMKDI--TVLRCGHTIHLECLKEMEKH--------YRYTCPVCSKS 61 (140)
Q Consensus 7 c~e~~~--~~~C~IC~e~l-------------~~~~~~~--~~l~CgH~Fc~~Cl~~~~~~--------~~~~CP~CR~~ 61 (140)
+.|+.. +.+||+|+..= +-...+| ..-||||.-=..=..-|..- -+..||.|-..
T Consensus 333 ~~e~~g~~~r~CPmC~~~gp~V~L~lG~E~~f~vD~G~pthaF~PCGHv~sekt~~YWs~iplPhGT~~f~a~CPFC~~~ 412 (429)
T KOG3842|consen 333 VRENTGQRERECPMCRVVGPYVPLWLGCEAGFYVDAGPPTHAFNPCGHVCSEKTVKYWSQIPLPHGTHAFHAACPFCATQ 412 (429)
T ss_pred cccccCcccCcCCeeeeecceeeeeccccceeEecCCCcccccCCcccccchhhhhHhhcCcCCCccccccccCcchhhh
Confidence 445555 78999998740 1011122 33499998766666666442 13569999766
Q ss_pred C
Q 032467 62 L 62 (140)
Q Consensus 62 ~ 62 (140)
+
T Consensus 413 L 413 (429)
T KOG3842|consen 413 L 413 (429)
T ss_pred h
Confidence 5
No 188
>PF01907 Ribosomal_L37e: Ribosomal protein L37e; InterPro: IPR001569 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families consists of proteins of 56 to 96 amino-acid residues that share a highly conserved region located in the N-terminal part.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A19_A 4A1D_A 4A18_A 4A1B_A 1S1I_Y 3O5H_d 3IZS_l 3O58_d 2ZKR_2 3IZR_l ....
Probab=43.00 E-value=16 Score=22.01 Aligned_cols=27 Identities=30% Similarity=0.813 Sum_probs=20.2
Q ss_pred cccceecCCCCCCCcccceeeeccccccCC
Q 032467 87 NKMVWILCNDCGANSHVQFHVIAHKCLSCK 116 (140)
Q Consensus 87 ~~~~~i~C~~C~~~~~~~~~~~~~~C~~C~ 116 (140)
..+..++|..|+. ..||.--..|.+|+
T Consensus 11 ~~ktH~~CrRCG~---~syH~qK~~CasCG 37 (55)
T PF01907_consen 11 HNKTHTLCRRCGR---RSYHIQKKTCASCG 37 (55)
T ss_dssp -S-SEEE-TTTSS---EEEETTTTEETTTB
T ss_pred CCccEeeecccCC---eeeecCCCcccccC
Confidence 3457899999987 56788888899998
No 189
>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=42.97 E-value=14 Score=19.45 Aligned_cols=10 Identities=40% Similarity=1.252 Sum_probs=7.8
Q ss_pred cCCCCCCCCC
Q 032467 52 RYTCPVCSKS 61 (140)
Q Consensus 52 ~~~CP~CR~~ 61 (140)
...||+|...
T Consensus 17 ~~~CP~Cg~~ 26 (33)
T cd00350 17 PWVCPVCGAP 26 (33)
T ss_pred CCcCcCCCCc
Confidence 4679999875
No 190
>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=42.93 E-value=27 Score=17.96 Aligned_cols=36 Identities=31% Similarity=0.675 Sum_probs=21.1
Q ss_pred cccccccccccCCccEEecCCCcccHHHHHhhhccccCCCCCCCCCC
Q 032467 16 CPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSL 62 (140)
Q Consensus 16 C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~ 62 (140)
|..|.+.+... ...+..=|..||..| +.|..|+..+
T Consensus 2 C~~C~~~i~~~--~~~~~~~~~~~H~~C---------f~C~~C~~~L 37 (39)
T smart00132 2 CAGCGKPIRGG--ELVLRALGKVWHPEC---------FKCSKCGKPL 37 (39)
T ss_pred ccccCCcccCC--cEEEEeCCccccccC---------CCCcccCCcC
Confidence 67777654332 122333467787766 4577777665
No 191
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=42.57 E-value=19 Score=17.93 Aligned_cols=7 Identities=29% Similarity=0.942 Sum_probs=4.0
Q ss_pred cccccCC
Q 032467 110 HKCLSCK 116 (140)
Q Consensus 110 ~~C~~C~ 116 (140)
..|+.||
T Consensus 17 f~CPnCG 23 (24)
T PF07754_consen 17 FPCPNCG 23 (24)
T ss_pred EeCCCCC
Confidence 3566665
No 192
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=42.42 E-value=38 Score=19.68 Aligned_cols=8 Identities=63% Similarity=1.692 Sum_probs=4.1
Q ss_pred CCCCCCCC
Q 032467 53 YTCPVCSK 60 (140)
Q Consensus 53 ~~CP~CR~ 60 (140)
+.||.|.+
T Consensus 3 f~CP~C~~ 10 (54)
T PF05605_consen 3 FTCPYCGK 10 (54)
T ss_pred cCCCCCCC
Confidence 44555555
No 193
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=41.84 E-value=11 Score=17.24 Aligned_cols=13 Identities=46% Similarity=1.055 Sum_probs=7.2
Q ss_pred CCCCCCCCCchhh
Q 032467 54 TCPVCSKSLWDMS 66 (140)
Q Consensus 54 ~CP~CR~~~~~~~ 66 (140)
.||+|...+....
T Consensus 2 ~C~~C~~~~~~~~ 14 (24)
T PF13894_consen 2 QCPICGKSFRSKS 14 (24)
T ss_dssp E-SSTS-EESSHH
T ss_pred CCcCCCCcCCcHH
Confidence 5888887765533
No 194
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=41.79 E-value=14 Score=19.84 Aligned_cols=11 Identities=27% Similarity=0.655 Sum_probs=7.9
Q ss_pred ceecCCCCCCC
Q 032467 90 VWILCNDCGAN 100 (140)
Q Consensus 90 ~~i~C~~C~~~ 100 (140)
..+.|..|+..
T Consensus 24 ~~v~C~~C~~~ 34 (38)
T TIGR02098 24 GKVRCGKCGHV 34 (38)
T ss_pred CEEECCCCCCE
Confidence 46778888764
No 195
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=41.22 E-value=20 Score=21.44 Aligned_cols=29 Identities=31% Similarity=0.678 Sum_probs=20.6
Q ss_pred ceecCCCCCCCcccceeeeccccccCCCcccccc
Q 032467 90 VWILCNDCGANSHVQFHVIAHKCLSCKSYNTRQT 123 (140)
Q Consensus 90 ~~i~C~~C~~~~~~~~~~~~~~C~~C~~~~~~~~ 123 (140)
..+.|..|++. .. -...|+.||-|.-++.
T Consensus 25 ~l~~C~~cG~~--~~---~H~vc~~cG~Y~gr~v 53 (55)
T TIGR01031 25 TLVVCPNCGEF--KL---PHRVCPSCGYYKGRQV 53 (55)
T ss_pred cceECCCCCCc--cc---CeeECCccCeECCEEc
Confidence 45679999975 33 3457889998887653
No 196
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=41.21 E-value=20 Score=20.23 Aligned_cols=26 Identities=27% Similarity=0.814 Sum_probs=17.0
Q ss_pred ecCCCCCCCcccceeeeccccccCCCcccc
Q 032467 92 ILCNDCGANSHVQFHVIAHKCLSCKSYNTR 121 (140)
Q Consensus 92 i~C~~C~~~~~~~~~~~~~~C~~C~~~~~~ 121 (140)
+.|+.|++. + -+.+.+|..|..|..-
T Consensus 1 v~Cd~C~~~--i--~G~ry~C~~C~d~dLC 26 (43)
T cd02340 1 VICDGCQGP--I--VGVRYKCLVCPDYDLC 26 (43)
T ss_pred CCCCCCCCc--C--cCCeEECCCCCCccch
Confidence 468888863 2 2566788888766543
No 197
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=41.09 E-value=19 Score=21.43 Aligned_cols=33 Identities=21% Similarity=0.584 Sum_probs=21.6
Q ss_pred cccceecCCCCCCCccc----ceeeeccccccCCCcc
Q 032467 87 NKMVWILCNDCGANSHV----QFHVIAHKCLSCKSYN 119 (140)
Q Consensus 87 ~~~~~i~C~~C~~~~~~----~~~~~~~~C~~C~~~~ 119 (140)
+.+..++|..|...+.. .+..+..+|+.|+..|
T Consensus 18 ~~r~aLIC~~C~~hNGla~~~~~~~i~y~C~~Cg~~N 54 (54)
T PF10058_consen 18 SNRYALICSKCFSHNGLAPKEEFEEIQYRCPYCGALN 54 (54)
T ss_pred cCceeEECcccchhhcccccccCCceEEEcCCCCCcC
Confidence 34467779999864432 2344567899998765
No 198
>COG2126 RPL37A Ribosomal protein L37E [Translation, ribosomal structure and biogenesis]
Probab=40.66 E-value=16 Score=22.30 Aligned_cols=27 Identities=37% Similarity=0.812 Sum_probs=22.1
Q ss_pred cccceecCCCCCCCcccceeeeccccccCC
Q 032467 87 NKMVWILCNDCGANSHVQFHVIAHKCLSCK 116 (140)
Q Consensus 87 ~~~~~i~C~~C~~~~~~~~~~~~~~C~~C~ 116 (140)
++...+.|..|+. ..||.--..|..||
T Consensus 12 nk~tH~~CRRCGr---~syhv~k~~CaaCG 38 (61)
T COG2126 12 NKKTHIRCRRCGR---RSYHVRKKYCAACG 38 (61)
T ss_pred CCcceehhhhccc---hheeeccceecccC
Confidence 3467899999997 56777888899998
No 199
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=40.63 E-value=13 Score=19.39 Aligned_cols=26 Identities=31% Similarity=0.615 Sum_probs=12.1
Q ss_pred ecCCCCCCCcccceeeeccccccCCC
Q 032467 92 ILCNDCGANSHVQFHVIAHKCLSCKS 117 (140)
Q Consensus 92 i~C~~C~~~~~~~~~~~~~~C~~C~~ 117 (140)
-+|..|+.+..........+|+.|+.
T Consensus 4 rfC~~CG~~t~~~~~g~~r~C~~Cg~ 29 (32)
T PF09297_consen 4 RFCGRCGAPTKPAPGGWARRCPSCGH 29 (32)
T ss_dssp SB-TTT--BEEE-SSSS-EEESSSS-
T ss_pred cccCcCCccccCCCCcCEeECCCCcC
Confidence 45777776654444445567777764
No 200
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=40.33 E-value=14 Score=26.56 Aligned_cols=20 Identities=40% Similarity=0.596 Sum_probs=16.1
Q ss_pred ccccccCCCccccccc--CCCC
Q 032467 109 AHKCLSCKSYNTRQTR--GDTA 128 (140)
Q Consensus 109 ~~~C~~C~~~~~~~~~--~~~~ 128 (140)
...|+.|||.+|+.+. |+||
T Consensus 105 ~~~cp~c~s~~t~~~s~fg~t~ 126 (146)
T TIGR02159 105 SVQCPRCGSADTTITSIFGPTA 126 (146)
T ss_pred CCcCCCCCCCCcEeecCCCChh
Confidence 3589999999999986 6553
No 201
>cd02342 ZZ_UBA_plant Zinc finger, ZZ type. Zinc finger present in plant ubiquitin-associated (UBA) proteins. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=40.21 E-value=21 Score=20.40 Aligned_cols=27 Identities=22% Similarity=0.364 Sum_probs=18.6
Q ss_pred ecCCCCCCCcccceeeeccccccCCCcccc
Q 032467 92 ILCNDCGANSHVQFHVIAHKCLSCKSYNTR 121 (140)
Q Consensus 92 i~C~~C~~~~~~~~~~~~~~C~~C~~~~~~ 121 (140)
|.|+.|+... .-+.+.+|..|..|..-
T Consensus 1 I~CDgCg~~P---I~G~RykC~~C~dyDLC 27 (43)
T cd02342 1 IQCDGCGVLP---ITGPRYKSKVKEDYDLC 27 (43)
T ss_pred CCCCCCCCCc---ccccceEeCCCCCCccH
Confidence 4688998643 33677788888877543
No 202
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 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 ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=40.00 E-value=18 Score=20.58 Aligned_cols=28 Identities=25% Similarity=0.682 Sum_probs=16.7
Q ss_pred eecCCCCCCCcccceeeeccccccCCCcccc
Q 032467 91 WILCNDCGANSHVQFHVIAHKCLSCKSYNTR 121 (140)
Q Consensus 91 ~i~C~~C~~~~~~~~~~~~~~C~~C~~~~~~ 121 (140)
.+.|+.|+.. ..-+.+.+|..|..|+.-
T Consensus 4 ~~~C~~C~~~---~i~g~Ry~C~~C~d~dLC 31 (46)
T PF00569_consen 4 GYTCDGCGTD---PIIGVRYHCLVCPDYDLC 31 (46)
T ss_dssp SCE-SSS-SS---SEESSEEEESSSSS-EEE
T ss_pred CeECcCCCCC---cCcCCeEECCCCCCCchh
Confidence 5779999873 222566788888877643
No 203
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=39.91 E-value=17 Score=17.68 Aligned_cols=7 Identities=57% Similarity=1.626 Sum_probs=3.5
Q ss_pred CCCCCCC
Q 032467 94 CNDCGAN 100 (140)
Q Consensus 94 C~~C~~~ 100 (140)
|..|+.+
T Consensus 2 Cp~CG~~ 8 (23)
T PF13240_consen 2 CPNCGAE 8 (23)
T ss_pred CcccCCC
Confidence 4555544
No 204
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=39.91 E-value=18 Score=19.23 Aligned_cols=23 Identities=26% Similarity=0.742 Sum_probs=10.3
Q ss_pred cCCCCCCCcccceeeeccccccCC
Q 032467 93 LCNDCGANSHVQFHVIAHKCLSCK 116 (140)
Q Consensus 93 ~C~~C~~~~~~~~~~~~~~C~~C~ 116 (140)
.|.+|+....... .-..+|+.||
T Consensus 2 ~C~~Cg~~~~~~~-~~~irC~~CG 24 (32)
T PF03604_consen 2 ICGECGAEVELKP-GDPIRCPECG 24 (32)
T ss_dssp BESSSSSSE-BST-SSTSSBSSSS
T ss_pred CCCcCCCeeEcCC-CCcEECCcCC
Confidence 3555555443322 2334566665
No 205
>PRK05580 primosome assembly protein PriA; Validated
Probab=39.88 E-value=26 Score=31.25 Aligned_cols=25 Identities=24% Similarity=0.690 Sum_probs=18.3
Q ss_pred ceecCCCCCCCcccceeeeccccccCCCcc
Q 032467 90 VWILCNDCGANSHVQFHVIAHKCLSCKSYN 119 (140)
Q Consensus 90 ~~i~C~~C~~~~~~~~~~~~~~C~~C~~~~ 119 (140)
....|+.|+..... ...|+.|++..
T Consensus 407 ~~l~Ch~Cg~~~~~-----~~~Cp~Cg~~~ 431 (679)
T PRK05580 407 RRLRCHHCGYQEPI-----PKACPECGSTD 431 (679)
T ss_pred CeEECCCCcCCCCC-----CCCCCCCcCCe
Confidence 46789999976433 34799998763
No 206
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=39.74 E-value=19 Score=26.57 Aligned_cols=42 Identities=29% Similarity=0.597 Sum_probs=24.4
Q ss_pred cCCCCCCCCCCchhhhHHHHHHHHHhcCCCCh-hhhcccceecCCCCCCC
Q 032467 52 RYTCPVCSKSLWDMSKLWSKIDQEIASTPMPA-MYQNKMVWILCNDCGAN 100 (140)
Q Consensus 52 ~~~CP~CR~~~~~~~~~~~~l~~~~~~~~~~~-~~~~~~~~i~C~~C~~~ 100 (140)
..+||.|+..+..++. +.....+|+ .+........|..|++.
T Consensus 97 ~~RCp~CN~~L~~vs~-------eev~~~Vp~~~~~~~~~f~~C~~Cgki 139 (165)
T COG1656 97 FSRCPECNGELEKVSR-------EEVKEKVPEKVYRNYEEFYRCPKCGKI 139 (165)
T ss_pred cccCcccCCEeccCcH-------HHHhhccchhhhhcccceeECCCCccc
Confidence 4679999999754332 222223332 34444456669999863
No 207
>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=39.69 E-value=4.2 Score=24.03 Aligned_cols=34 Identities=21% Similarity=0.351 Sum_probs=17.8
Q ss_pred ccccc--ccccccccCCc-c--EEec-CCCcccHHHHHhh
Q 032467 14 HNCPI--CFEFIFDTMKD-I--TVLR-CGHTIHLECLKEM 47 (140)
Q Consensus 14 ~~C~I--C~e~l~~~~~~-~--~~l~-CgH~Fc~~Cl~~~ 47 (140)
..||- |...+...... . +.=+ ||+.||..|...|
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 36766 76554222222 1 2224 9999999998888
No 208
>COG5132 BUD31 Cell cycle control protein, G10 family [Transcription / Cell division and chromosome partitioning]
Probab=39.31 E-value=13 Score=26.21 Aligned_cols=23 Identities=26% Similarity=0.650 Sum_probs=14.7
Q ss_pred cccHHHHHhhhccccCCCCCCCCC
Q 032467 38 TIHLECLKEMEKHYRYTCPVCSKS 61 (140)
Q Consensus 38 ~Fc~~Cl~~~~~~~~~~CP~CR~~ 61 (140)
.-|.+||+.--.....+| +||.+
T Consensus 100 LCCLRCIQ~~esk~GstC-ICRVP 122 (146)
T COG5132 100 LCCLRCIQPIESKHGSTC-ICRVP 122 (146)
T ss_pred hhhHhhcCcccccCCCEE-EEeCc
Confidence 346777777655445566 77766
No 209
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=39.11 E-value=28 Score=20.94 Aligned_cols=8 Identities=38% Similarity=1.402 Sum_probs=4.5
Q ss_pred CCCCCCCC
Q 032467 54 TCPVCSKS 61 (140)
Q Consensus 54 ~CP~CR~~ 61 (140)
.||+|+..
T Consensus 6 ~CP~CgnK 13 (55)
T PF14205_consen 6 LCPICGNK 13 (55)
T ss_pred ECCCCCCc
Confidence 46666544
No 210
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=38.98 E-value=11 Score=33.26 Aligned_cols=43 Identities=26% Similarity=0.585 Sum_probs=26.0
Q ss_pred cccccccccc--ccc--cCCccEEecCCCcccHHHHHhhhccccCCCCCCC
Q 032467 13 HHNCPICFEF--IFD--TMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCS 59 (140)
Q Consensus 13 ~~~C~IC~e~--l~~--~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR 59 (140)
-..|.+|... +|. ......-..||+.||..|+..- ...||.|-
T Consensus 511 gfiCe~Cq~~~iiyPF~~~~~~rC~~C~avfH~~C~~r~----s~~CPrC~ 557 (580)
T KOG1829|consen 511 GFICELCQHNDIIYPFETRNTRRCSTCLAVFHKKCLRRK----SPCCPRCE 557 (580)
T ss_pred eeeeeeccCCCcccccccccceeHHHHHHHHHHHHHhcc----CCCCCchH
Confidence 4567788432 111 1111234589999999997653 34499993
No 211
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=37.74 E-value=21 Score=19.25 Aligned_cols=9 Identities=22% Similarity=0.512 Sum_probs=4.6
Q ss_pred eccccccCC
Q 032467 108 IAHKCLSCK 116 (140)
Q Consensus 108 ~~~~C~~C~ 116 (140)
.++.|+.|+
T Consensus 21 ~R~vC~~Cg 29 (34)
T PF14803_consen 21 ERLVCPACG 29 (34)
T ss_dssp -EEEETTTT
T ss_pred cceECCCCC
Confidence 345566665
No 212
>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]
Probab=37.64 E-value=17 Score=28.01 Aligned_cols=42 Identities=26% Similarity=0.716 Sum_probs=31.3
Q ss_pred cccccccccccccCCccEEecCCCcccHHHHHhhhccccCCCCCCC
Q 032467 14 HNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCS 59 (140)
Q Consensus 14 ~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR 59 (140)
..|.+|...+. ...+--.||=.+|..|+..++.. ...||.|.
T Consensus 182 k~Cn~Ch~LvI---qg~rCg~c~i~~h~~c~qty~q~-~~~cphc~ 223 (235)
T KOG4718|consen 182 KNCNLCHCLVI---QGIRCGSCNIQYHRGCIQTYLQR-RDICPHCG 223 (235)
T ss_pred HHHhHhHHHhh---eeeccCcccchhhhHHHHHHhcc-cCcCCchh
Confidence 47999987532 33333467778999999999985 68899995
No 213
>cd04718 BAH_plant_2 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=36.82 E-value=10 Score=27.44 Aligned_cols=23 Identities=35% Similarity=0.764 Sum_probs=17.1
Q ss_pred ccHHHHHhhhcc---ccCCCCCCCCC
Q 032467 39 IHLECLKEMEKH---YRYTCPVCSKS 61 (140)
Q Consensus 39 Fc~~Cl~~~~~~---~~~~CP~CR~~ 61 (140)
||..||+.=+.. +.+.||.|...
T Consensus 2 ~H~~CL~Ppl~~~P~g~W~Cp~C~~~ 27 (148)
T cd04718 2 FHLCCLRPPLKEVPEGDWICPFCEVE 27 (148)
T ss_pred cccccCCCCCCCCCCCCcCCCCCcCC
Confidence 677788776653 46889999865
No 214
>PRK00420 hypothetical protein; Validated
Probab=36.30 E-value=31 Score=23.84 Aligned_cols=10 Identities=50% Similarity=1.142 Sum_probs=5.1
Q ss_pred CCCCCCCCCC
Q 032467 53 YTCPVCSKSL 62 (140)
Q Consensus 53 ~~CP~CR~~~ 62 (140)
..||.|..++
T Consensus 24 ~~CP~Cg~pL 33 (112)
T PRK00420 24 KHCPVCGLPL 33 (112)
T ss_pred CCCCCCCCcc
Confidence 3455555543
No 215
>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=36.20 E-value=28 Score=19.95 Aligned_cols=38 Identities=34% Similarity=0.760 Sum_probs=24.9
Q ss_pred cccccccccccCCccEEecCCCcccHHHHHhhhccccCCCCCCCCCCch
Q 032467 16 CPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLWD 64 (140)
Q Consensus 16 C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~~~ 64 (140)
|..|.+.+.. ...++..=|..||..| ++|-.|++.+.+
T Consensus 1 C~~C~~~I~~--~~~~~~~~~~~~H~~C---------f~C~~C~~~l~~ 38 (58)
T PF00412_consen 1 CARCGKPIYG--TEIVIKAMGKFWHPEC---------FKCSKCGKPLND 38 (58)
T ss_dssp BTTTSSBESS--SSEEEEETTEEEETTT---------SBETTTTCBTTT
T ss_pred CCCCCCCccC--cEEEEEeCCcEEEccc---------cccCCCCCccCC
Confidence 5667776542 2333346788888777 568899888643
No 216
>COG3492 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.87 E-value=18 Score=24.24 Aligned_cols=12 Identities=17% Similarity=0.357 Sum_probs=10.7
Q ss_pred cccHHHHHhhhc
Q 032467 38 TIHLECLKEMEK 49 (140)
Q Consensus 38 ~Fc~~Cl~~~~~ 49 (140)
-||+.||.+|..
T Consensus 42 gFCRNCLs~Wy~ 53 (104)
T COG3492 42 GFCRNCLSNWYR 53 (104)
T ss_pred HHHHHHHHHHHH
Confidence 499999999975
No 217
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=35.80 E-value=15 Score=19.89 Aligned_cols=11 Identities=27% Similarity=0.576 Sum_probs=6.8
Q ss_pred ccccccccccc
Q 032467 13 HHNCPICFEFI 23 (140)
Q Consensus 13 ~~~C~IC~e~l 23 (140)
...||-|...|
T Consensus 2 ~i~CP~C~~~f 12 (37)
T PF13719_consen 2 IITCPNCQTRF 12 (37)
T ss_pred EEECCCCCceE
Confidence 35677777553
No 218
>PRK14873 primosome assembly protein PriA; Provisional
Probab=34.96 E-value=30 Score=30.98 Aligned_cols=27 Identities=26% Similarity=0.428 Sum_probs=19.2
Q ss_pred ceecCCCCCCCcccceeeeccccccCCCccccc
Q 032467 90 VWILCNDCGANSHVQFHVIAHKCLSCKSYNTRQ 122 (140)
Q Consensus 90 ~~i~C~~C~~~~~~~~~~~~~~C~~C~~~~~~~ 122 (140)
....|+.|+... ....|+.|++..-+.
T Consensus 409 ~~l~Ch~CG~~~------~p~~Cp~Cgs~~l~~ 435 (665)
T PRK14873 409 GTPRCRWCGRAA------PDWRCPRCGSDRLRA 435 (665)
T ss_pred CeeECCCCcCCC------cCccCCCCcCCccee
Confidence 467899999742 245899999865444
No 219
>KOG3005 consensus GIY-YIG type nuclease [General function prediction only]
Probab=34.70 E-value=39 Score=26.95 Aligned_cols=49 Identities=31% Similarity=0.494 Sum_probs=32.2
Q ss_pred cccccccccccccCCccE---EecCCCcccHHHHHhhhc-c-------ccCCCCCCCCCC
Q 032467 14 HNCPICFEFIFDTMKDIT---VLRCGHTIHLECLKEMEK-H-------YRYTCPVCSKSL 62 (140)
Q Consensus 14 ~~C~IC~e~l~~~~~~~~---~l~CgH~Fc~~Cl~~~~~-~-------~~~~CP~CR~~~ 62 (140)
..|-+|.+++.+....+. ...|+-.+|..||...+. . ....||.|++.+
T Consensus 183 ~~celc~~ei~e~~~~~a~c~~~~c~~~~h~~CLa~~~~~~e~g~~~p~eg~cp~C~~~~ 242 (276)
T KOG3005|consen 183 VECELCEKEILETDWSRATCPNPDCDSLNHLTCLAEELLEVEPGQLIPLEGMCPKCEKFL 242 (276)
T ss_pred hhhHHHHHHhccccceeccCCCCCCCchhhhhhhhHHHhccCCCceeccCCCCCchhcee
Confidence 589999988643222111 125778899999988332 1 135699999875
No 220
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=33.61 E-value=23 Score=21.88 Aligned_cols=25 Identities=28% Similarity=0.701 Sum_probs=20.6
Q ss_pred ceecCCCCCCCcccceeeeccccccCCC
Q 032467 90 VWILCNDCGANSHVQFHVIAHKCLSCKS 117 (140)
Q Consensus 90 ~~i~C~~C~~~~~~~~~~~~~~C~~C~~ 117 (140)
..++|..|+. ..||.--..|.+|+=
T Consensus 16 tHt~CrRCG~---~syh~qK~~CasCGy 40 (62)
T PRK04179 16 THIRCRRCGR---HSYNVRKKYCAACGF 40 (62)
T ss_pred ccchhcccCc---ccccccccchhhcCC
Confidence 7899999997 467777888988873
No 221
>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=33.03 E-value=26 Score=23.96 Aligned_cols=50 Identities=20% Similarity=0.369 Sum_probs=31.0
Q ss_pred cccccccccccccccC-CccEEecCCCcccHHHHHhhhccccCCCCCCCCC
Q 032467 12 MHHNCPICFEFIFDTM-KDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKS 61 (140)
Q Consensus 12 ~~~~C~IC~e~l~~~~-~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~ 61 (140)
.+..|.+|...|.-.. ....-..|+|.+|..|-..-.....+.|-+|.+.
T Consensus 53 ~~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~~~~~~~WlC~vC~k~ 103 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVYSKKEPIWLCKVCQKQ 103 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEETSSSCCEEEHHHHHH
T ss_pred CCcchhhhCCcccccCCCCCcCCcCCccccCccCCcCCCCCCEEChhhHHH
Confidence 4678999987642222 2345569999999999665222234678888654
No 222
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=31.86 E-value=42 Score=30.60 Aligned_cols=41 Identities=27% Similarity=0.374 Sum_probs=27.6
Q ss_pred cccccccccccccCCccEEecCCCcccHHHHHhhhccccCCCCC
Q 032467 14 HNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPV 57 (140)
Q Consensus 14 ~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~ 57 (140)
..|.+|--.+.. ...---.|||-.|..++.+|+.. ...||.
T Consensus 780 ~~CtVC~~vi~G--~~~~c~~C~H~gH~sh~~sw~~~-~s~ca~ 820 (839)
T KOG0269|consen 780 AKCTVCDLVIRG--VDVWCQVCGHGGHDSHLKSWFFK-ASPCAK 820 (839)
T ss_pred cCceeecceeee--eEeecccccccccHHHHHHHHhc-CCCCcc
Confidence 468888754322 11122389999999999999974 455665
No 223
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=31.72 E-value=44 Score=18.75 Aligned_cols=11 Identities=36% Similarity=0.887 Sum_probs=7.8
Q ss_pred cCCCCCCCCCC
Q 032467 52 RYTCPVCSKSL 62 (140)
Q Consensus 52 ~~~CP~CR~~~ 62 (140)
...||.|..++
T Consensus 17 ~~~Cp~C~~PL 27 (41)
T PF06677_consen 17 DEHCPDCGTPL 27 (41)
T ss_pred cCccCCCCCee
Confidence 35799997664
No 224
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=31.33 E-value=19 Score=24.93 Aligned_cols=18 Identities=56% Similarity=0.934 Sum_probs=14.5
Q ss_pred eccccccCC----CcccccccC
Q 032467 108 IAHKCLSCK----SYNTRQTRG 125 (140)
Q Consensus 108 ~~~~C~~C~----~~~~~~~~~ 125 (140)
+-++|+.|+ +|+|.|||-
T Consensus 73 I~~kCpkCghe~m~Y~T~QlRS 94 (116)
T KOG2907|consen 73 IKHKCPKCGHEEMSYHTLQLRS 94 (116)
T ss_pred hhccCcccCCchhhhhhhhccc
Confidence 566888887 899999983
No 225
>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=31.24 E-value=28 Score=23.09 Aligned_cols=39 Identities=23% Similarity=0.552 Sum_probs=26.0
Q ss_pred cccccccccccccCCccEEecCCCcccHHHHHhhhccccCCCCCCCCCCchhh
Q 032467 14 HNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLWDMS 66 (140)
Q Consensus 14 ~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~~~~~ 66 (140)
..|-||-..+ -.=||.||..|.-+ ...|.+|.+.+.+..
T Consensus 45 ~~C~~CK~~v---------~q~g~~YCq~CAYk-----kGiCamCGKki~dtk 83 (90)
T PF10235_consen 45 SKCKICKTKV---------HQPGAKYCQTCAYK-----KGICAMCGKKILDTK 83 (90)
T ss_pred cccccccccc---------ccCCCccChhhhcc-----cCcccccCCeecccc
Confidence 3677777421 12388999999432 357999999986543
No 226
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 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 C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=31.12 E-value=15 Score=17.08 Aligned_cols=11 Identities=45% Similarity=1.174 Sum_probs=7.7
Q ss_pred CCCCCCCCCch
Q 032467 54 TCPVCSKSLWD 64 (140)
Q Consensus 54 ~CP~CR~~~~~ 64 (140)
.||.|.+.+..
T Consensus 2 ~C~~C~~~f~~ 12 (23)
T PF00096_consen 2 KCPICGKSFSS 12 (23)
T ss_dssp EETTTTEEESS
T ss_pred CCCCCCCccCC
Confidence 57888777654
No 227
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=30.82 E-value=31 Score=23.86 Aligned_cols=13 Identities=31% Similarity=0.534 Sum_probs=6.3
Q ss_pred ceeeeccccccCC
Q 032467 104 QFHVIAHKCLSCK 116 (140)
Q Consensus 104 ~~~~~~~~C~~C~ 116 (140)
..|-.-+.|+.|.
T Consensus 98 fiHe~Lh~CPGC~ 110 (112)
T TIGR00622 98 FVHESLHCCPGCI 110 (112)
T ss_pred hhhhhccCCcCCC
Confidence 3444444555554
No 228
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=29.28 E-value=39 Score=23.07 Aligned_cols=20 Identities=30% Similarity=0.576 Sum_probs=10.3
Q ss_pred CcccccccccccccccCCcc
Q 032467 11 AMHHNCPICFEFIFDTMKDI 30 (140)
Q Consensus 11 ~~~~~C~IC~e~l~~~~~~~ 30 (140)
.....|+-|...|++..+.|
T Consensus 7 GtKR~Cp~CG~kFYDLnk~P 26 (108)
T PF09538_consen 7 GTKRTCPSCGAKFYDLNKDP 26 (108)
T ss_pred CCcccCCCCcchhccCCCCC
Confidence 34456666665555544333
No 229
>PTZ00073 60S ribosomal protein L37; Provisional
Probab=29.16 E-value=30 Score=22.98 Aligned_cols=28 Identities=36% Similarity=0.799 Sum_probs=22.2
Q ss_pred cccceecCCCCCCCcccceeeeccccccCCC
Q 032467 87 NKMVWILCNDCGANSHVQFHVIAHKCLSCKS 117 (140)
Q Consensus 87 ~~~~~i~C~~C~~~~~~~~~~~~~~C~~C~~ 117 (140)
..+..++|..|+. ..||.--..|.+|+=
T Consensus 12 ~~ktHtlCrRCG~---~syH~qK~~CasCGy 39 (91)
T PTZ00073 12 HGKTHTLCRRCGK---RSFHVQKKRCASCGY 39 (91)
T ss_pred cCcCcchhcccCc---cccccccccchhcCC
Confidence 3467899999997 567777888999984
No 230
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=29.12 E-value=40 Score=18.15 Aligned_cols=10 Identities=40% Similarity=1.002 Sum_probs=7.5
Q ss_pred CCCCCCCCCC
Q 032467 53 YTCPVCSKSL 62 (140)
Q Consensus 53 ~~CP~CR~~~ 62 (140)
..||-|.+.+
T Consensus 3 i~Cp~C~~~y 12 (36)
T PF13717_consen 3 ITCPNCQAKY 12 (36)
T ss_pred EECCCCCCEE
Confidence 4688888776
No 231
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=28.58 E-value=28 Score=29.81 Aligned_cols=48 Identities=23% Similarity=0.590 Sum_probs=32.4
Q ss_pred ccccccccccccccCCccEEe---cCCCcccHHHHHhhhcc-------ccCCCCCCCCCC
Q 032467 13 HHNCPICFEFIFDTMKDITVL---RCGHTIHLECLKEMEKH-------YRYTCPVCSKSL 62 (140)
Q Consensus 13 ~~~C~IC~e~l~~~~~~~~~l---~CgH~Fc~~Cl~~~~~~-------~~~~CP~CR~~~ 62 (140)
+..|.+|+........ ++| .|+--||..|.+..... ..+-|=+|+...
T Consensus 168 n~qc~vC~~g~~~~~N--rmlqC~~C~~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~~~ 225 (464)
T KOG4323|consen 168 NLQCSVCYCGGPGAGN--RMLQCDKCRQWYHQACHQPLIKDELAGDPFYEWFCDVCNRGP 225 (464)
T ss_pred cceeeeeecCCcCccc--eeeeecccccHHHHHhccCCCCHhhccCccceEeehhhccch
Confidence 4569999976544333 555 67778888888776542 246688887764
No 232
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=28.50 E-value=45 Score=20.25 Aligned_cols=29 Identities=17% Similarity=0.094 Sum_probs=20.5
Q ss_pred ceecCCCCCCCcccceeeeccccccCCCccccccc
Q 032467 90 VWILCNDCGANSHVQFHVIAHKCLSCKSYNTRQTR 124 (140)
Q Consensus 90 ~~i~C~~C~~~~~~~~~~~~~~C~~C~~~~~~~~~ 124 (140)
....|..|++. ...| ..|+ ||-|+.++.-
T Consensus 26 ~~~~c~~cg~~--~~pH---~vc~-cG~Y~gr~v~ 54 (60)
T PRK01110 26 TLSVDKTTGEY--HLPH---HVSP-KGYYKGRKVL 54 (60)
T ss_pred ceeEcCCCCce--eccc---eecC-CcccCCeEee
Confidence 35779999875 4333 3488 9999888763
No 233
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=27.99 E-value=61 Score=28.98 Aligned_cols=22 Identities=27% Similarity=0.682 Sum_probs=13.5
Q ss_pred cCCCCCCCcccceeeeccccccCCCc
Q 032467 93 LCNDCGANSHVQFHVIAHKCLSCKSY 118 (140)
Q Consensus 93 ~C~~C~~~~~~~~~~~~~~C~~C~~~ 118 (140)
.|..|+..... -..+|+.||..
T Consensus 29 ~Cp~CG~~~~~----~~~fC~~CG~~ 50 (645)
T PRK14559 29 PCPQCGTEVPV----DEAHCPNCGAE 50 (645)
T ss_pred cCCCCCCCCCc----ccccccccCCc
Confidence 48888865322 23478888843
No 234
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=27.78 E-value=35 Score=26.18 Aligned_cols=7 Identities=43% Similarity=1.516 Sum_probs=4.1
Q ss_pred CCCCCCC
Q 032467 55 CPVCSKS 61 (140)
Q Consensus 55 CP~CR~~ 61 (140)
||.|..+
T Consensus 1 C~~CG~~ 7 (236)
T PF04981_consen 1 CPRCGRE 7 (236)
T ss_pred CCCCCCC
Confidence 5666654
No 235
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=27.59 E-value=40 Score=17.97 Aligned_cols=26 Identities=27% Similarity=0.446 Sum_probs=11.1
Q ss_pred ceecCCCCCCCcccceeeeccccccCCCcc
Q 032467 90 VWILCNDCGANSHVQFHVIAHKCLSCKSYN 119 (140)
Q Consensus 90 ~~i~C~~C~~~~~~~~~~~~~~C~~C~~~~ 119 (140)
..-.|.+|+.. ++.-...|+.|++-+
T Consensus 10 ~~~rC~~Cg~~----~~pPr~~Cp~C~s~~ 35 (37)
T PF12172_consen 10 LGQRCRDCGRV----QFPPRPVCPHCGSDE 35 (37)
T ss_dssp EEEE-TTT--E----EES--SEETTTT---
T ss_pred EEEEcCCCCCE----ecCCCcCCCCcCccc
Confidence 45567777753 223456777777644
No 236
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=27.14 E-value=39 Score=19.74 Aligned_cols=24 Identities=25% Similarity=0.667 Sum_probs=13.2
Q ss_pred ecCCCCCCCcccceeeeccccccCC
Q 032467 92 ILCNDCGANSHVQFHVIAHKCLSCK 116 (140)
Q Consensus 92 i~C~~C~~~~~~~~~~~~~~C~~C~ 116 (140)
..|..|+.. -...|.-..+|..|+
T Consensus 21 ~fCP~Cg~~-~m~~~~~r~~C~~Cg 44 (50)
T PRK00432 21 KFCPRCGSG-FMAEHLDRWHCGKCG 44 (50)
T ss_pred CcCcCCCcc-hheccCCcEECCCcC
Confidence 356666643 344445555666665
No 237
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=26.63 E-value=47 Score=25.69 Aligned_cols=27 Identities=15% Similarity=0.351 Sum_probs=16.8
Q ss_pred ccccccccccccccCCccEEecCCCccc
Q 032467 13 HHNCPICFEFIFDTMKDITVLRCGHTIH 40 (140)
Q Consensus 13 ~~~C~IC~e~l~~~~~~~~~l~CgH~Fc 40 (140)
...||+|.+.|.. ......-+.||.|=
T Consensus 2 ~~~CP~C~~~l~~-~~~~~~C~~~h~fd 28 (272)
T PRK11088 2 SYQCPLCHQPLTL-EENSWICPQNHQFD 28 (272)
T ss_pred cccCCCCCcchhc-CCCEEEcCCCCCCc
Confidence 3679999998743 22222235589884
No 238
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=26.50 E-value=17 Score=28.21 Aligned_cols=36 Identities=11% Similarity=0.332 Sum_probs=26.6
Q ss_pred cccceecCCCCCCCc-ccceeeeccccccCCCccccc
Q 032467 87 NKMVWILCNDCGANS-HVQFHVIAHKCLSCKSYNTRQ 122 (140)
Q Consensus 87 ~~~~~i~C~~C~~~~-~~~~~~~~~~C~~C~~~~~~~ 122 (140)
-...-+.|..|.+.+ -..+|..-..|++|++|.+.-
T Consensus 166 P~gcRV~CgHC~~tFLfnt~tnaLArCPHCrKvSsvG 202 (275)
T KOG4684|consen 166 PTGCRVKCGHCNETFLFNTLTNALARCPHCRKVSSVG 202 (275)
T ss_pred CcceEEEecCccceeehhhHHHHHhcCCcccchhhhh
Confidence 334778999999865 235677788999999876543
No 239
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=26.18 E-value=51 Score=31.84 Aligned_cols=9 Identities=33% Similarity=1.047 Sum_probs=5.3
Q ss_pred CCCCCCCCC
Q 032467 53 YTCPVCSKS 61 (140)
Q Consensus 53 ~~CP~CR~~ 61 (140)
..||-|...
T Consensus 668 rkCPkCG~~ 676 (1337)
T PRK14714 668 RRCPSCGTE 676 (1337)
T ss_pred EECCCCCCc
Confidence 456666654
No 240
>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=25.99 E-value=67 Score=18.96 Aligned_cols=26 Identities=19% Similarity=0.568 Sum_probs=12.9
Q ss_pred ecCCCcccHHHHHhhhccccCCCCCCC
Q 032467 33 LRCGHTIHLECLKEMEKHYRYTCPVCS 59 (140)
Q Consensus 33 l~CgH~Fc~~Cl~~~~~~~~~~CP~CR 59 (140)
..|++.||.+|=. ++...--.||-|-
T Consensus 25 ~~C~~~FC~dCD~-fiHE~LH~CPGC~ 50 (51)
T PF07975_consen 25 PKCKNHFCIDCDV-FIHETLHNCPGCE 50 (51)
T ss_dssp TTTT--B-HHHHH-TTTTTS-SSSTT-
T ss_pred CCCCCccccCcCh-hhhccccCCcCCC
Confidence 3788999999943 2221234688773
No 241
>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=25.39 E-value=25 Score=30.19 Aligned_cols=44 Identities=18% Similarity=0.335 Sum_probs=21.3
Q ss_pred CCCCCCCCCCchhhhHHHHHHHHHhcCCCChhhhcccceecCCCCCCCc
Q 032467 53 YTCPVCSKSLWDMSKLWSKIDQEIASTPMPAMYQNKMVWILCNDCGANS 101 (140)
Q Consensus 53 ~~CP~CR~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~i~C~~C~~~~ 101 (140)
+.||+|...+....... .. .................|..|.+.+
T Consensus 53 f~CP~C~~~L~~~~~~~---~~--~~~~~~~~~~~~~~~l~C~~C~Wss 96 (483)
T PF05502_consen 53 FDCPICFSPLSVRASDT---PP--SPPDPSSDSGGKPYYLSCSYCRWSS 96 (483)
T ss_pred ccCCCCCCcceeEeccc---cc--ccccccccCCCCCEEEECCCceeec
Confidence 56999998863311110 00 0001111122334567888888754
No 242
>KOG3726 consensus Uncharacterized conserved protein [Function unknown]
Probab=25.37 E-value=44 Score=30.06 Aligned_cols=44 Identities=14% Similarity=0.236 Sum_probs=30.5
Q ss_pred cccccccccccccCCccEEecCCCcccHHHHHhhhccccCCCCCCCCC
Q 032467 14 HNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKS 61 (140)
Q Consensus 14 ~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~ 61 (140)
..|-+|+..-+....-+.++.|+-.||..|...+. ..||+|.-.
T Consensus 655 r~C~vcq~pedse~~v~rt~~C~~~~C~~c~~~~~----~~~~vC~~~ 698 (717)
T KOG3726|consen 655 RTCKVCQLPEDSETDVCRTTFCYTPYCVACSLDYA----SISEVCGPD 698 (717)
T ss_pred HHHHHhcCCcCccccccCccccCCcchHhhhhhhh----ccCcccCch
Confidence 45888886533334456777999999999855543 469999644
No 243
>PF15616 TerY-C: TerY-C metal binding domain
Probab=24.80 E-value=53 Score=23.30 Aligned_cols=38 Identities=26% Similarity=0.576 Sum_probs=27.1
Q ss_pred cccccccccccccCCccEEecCCCcccHHHHHhhhccccCCCCCCCCCC
Q 032467 14 HNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSL 62 (140)
Q Consensus 14 ~~C~IC~e~l~~~~~~~~~l~CgH~Fc~~Cl~~~~~~~~~~CP~CR~~~ 62 (140)
..||-|-.. ...+.-.||..||.. .....+||-|.+..
T Consensus 78 PgCP~CGn~-----~~fa~C~CGkl~Ci~------g~~~~~CPwCg~~g 115 (131)
T PF15616_consen 78 PGCPHCGNQ-----YAFAVCGCGKLFCID------GEGEVTCPWCGNEG 115 (131)
T ss_pred CCCCCCcCh-----hcEEEecCCCEEEeC------CCCCEECCCCCCee
Confidence 689999863 233455999999842 23457899999875
No 244
>PRK01343 zinc-binding protein; Provisional
Probab=24.78 E-value=44 Score=20.27 Aligned_cols=11 Identities=36% Similarity=0.869 Sum_probs=8.9
Q ss_pred cCCCCCCCCCC
Q 032467 52 RYTCPVCSKSL 62 (140)
Q Consensus 52 ~~~CP~CR~~~ 62 (140)
...||+|++.+
T Consensus 9 ~~~CP~C~k~~ 19 (57)
T PRK01343 9 TRPCPECGKPS 19 (57)
T ss_pred CCcCCCCCCcC
Confidence 36799999985
No 245
>KOG2857 consensus Predicted MYND Zn-finger protein/hormone receptor interactor [Transcription]
Probab=24.61 E-value=35 Score=24.70 Aligned_cols=10 Identities=50% Similarity=1.255 Sum_probs=6.2
Q ss_pred CCCCCCCCCC
Q 032467 53 YTCPVCSKSL 62 (140)
Q Consensus 53 ~~CP~CR~~~ 62 (140)
++||.|+.++
T Consensus 18 YKCpkC~vPY 27 (157)
T KOG2857|consen 18 YKCPKCSVPY 27 (157)
T ss_pred ccCCCCCCcc
Confidence 5566666664
No 246
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=24.41 E-value=59 Score=23.10 Aligned_cols=24 Identities=25% Similarity=0.516 Sum_probs=15.8
Q ss_pred cCCCCCCCcccceeeeccccccCC
Q 032467 93 LCNDCGANSHVQFHVIAHKCLSCK 116 (140)
Q Consensus 93 ~C~~C~~~~~~~~~~~~~~C~~C~ 116 (140)
.|..|+..+....-.|..-|+.||
T Consensus 3 ~Ct~Cg~~f~dgs~eil~GCP~CG 26 (131)
T PF09845_consen 3 QCTKCGRVFEDGSKEILSGCPECG 26 (131)
T ss_pred ccCcCCCCcCCCcHHHHccCcccC
Confidence 377777666554445666788887
No 247
>PF15353 HECA: Headcase protein family homologue
Probab=24.39 E-value=46 Score=22.80 Aligned_cols=16 Identities=31% Similarity=0.690 Sum_probs=13.9
Q ss_pred cCCCcccHHHHHhhhc
Q 032467 34 RCGHTIHLECLKEMEK 49 (140)
Q Consensus 34 ~CgH~Fc~~Cl~~~~~ 49 (140)
|.|+.+|.+|++.|-+
T Consensus 39 p~~~~MH~~CF~~wE~ 54 (107)
T PF15353_consen 39 PFGQYMHRECFEKWED 54 (107)
T ss_pred CCCCchHHHHHHHHHH
Confidence 5589999999999965
No 248
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=24.30 E-value=42 Score=20.70 Aligned_cols=10 Identities=40% Similarity=1.192 Sum_probs=8.6
Q ss_pred CCCCCCCCCC
Q 032467 53 YTCPVCSKSL 62 (140)
Q Consensus 53 ~~CP~CR~~~ 62 (140)
..||+|++.+
T Consensus 7 v~CP~C~k~~ 16 (62)
T PRK00418 7 VNCPTCGKPV 16 (62)
T ss_pred ccCCCCCCcc
Confidence 5799999986
No 249
>cd02343 ZZ_EF Zinc finger, ZZ type. Zinc finger present in proteins with an EF_hand motif. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=23.89 E-value=61 Score=18.90 Aligned_cols=27 Identities=22% Similarity=0.573 Sum_probs=17.9
Q ss_pred ecCCCCCCCcccceeeeccccccCCCccccc
Q 032467 92 ILCNDCGANSHVQFHVIAHKCLSCKSYNTRQ 122 (140)
Q Consensus 92 i~C~~C~~~~~~~~~~~~~~C~~C~~~~~~~ 122 (140)
|.|+.|++. + ...+.+|..|..|.--+
T Consensus 1 i~CdgC~~~--~--~~~RykCl~C~d~DlC~ 27 (48)
T cd02343 1 ISCDGCDEI--A--PWHRYRCLQCTDMDLCK 27 (48)
T ss_pred CCCCCCCCc--C--CCceEECCCCCCchhHH
Confidence 458899874 2 24677888887665443
No 250
>PF06676 DUF1178: Protein of unknown function (DUF1178); InterPro: IPR009562 This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=23.83 E-value=42 Score=24.32 Aligned_cols=23 Identities=26% Similarity=0.585 Sum_probs=16.0
Q ss_pred cCCCcccHHHHHhhhcc----------ccCCCCCCCCC
Q 032467 34 RCGHTIHLECLKEMEKH----------YRYTCPVCSKS 61 (140)
Q Consensus 34 ~CgH~Fc~~Cl~~~~~~----------~~~~CP~CR~~ 61 (140)
.+||.| +.|+.+ +-..||+|...
T Consensus 9 ~~gH~F-----EgWF~ss~~fd~Q~~~glv~CP~Cgs~ 41 (148)
T PF06676_consen 9 ENGHEF-----EGWFRSSAAFDRQQARGLVSCPVCGST 41 (148)
T ss_pred CCCCcc-----ceecCCHHHHHHHHHcCCccCCCCCCC
Confidence 457887 567764 34679999866
No 251
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=23.37 E-value=80 Score=18.70 Aligned_cols=29 Identities=31% Similarity=0.673 Sum_probs=20.6
Q ss_pred ceecCCCCCCCcccceeeeccccccCCCcccccc
Q 032467 90 VWILCNDCGANSHVQFHVIAHKCLSCKSYNTRQT 123 (140)
Q Consensus 90 ~~i~C~~C~~~~~~~~~~~~~~C~~C~~~~~~~~ 123 (140)
....|..|++. . .-...|++||-|..++.
T Consensus 25 ~l~~c~~cg~~--~---~~H~vc~~cG~y~~r~v 53 (56)
T PF01783_consen 25 NLVKCPNCGEP--K---LPHRVCPSCGYYKGRQV 53 (56)
T ss_dssp SEEESSSSSSE--E---STTSBCTTTBBSSSSSS
T ss_pred ceeeeccCCCE--e---cccEeeCCCCeECCEEE
Confidence 56789999864 2 24467889988876653
No 252
>PF10164 DUF2367: Uncharacterized conserved protein (DUF2367); InterPro: IPR019317 This is a highly conserved set of proteins which contains three pairs of cysteine residues within a length of 42 amino acids and is rich in proline residues towards the N terminus. It includes a membrane protein that has been found to be highly expressed in the mouse brain and consequently, several members have been assigned as brain protein i3 (Bri3). Their function is unknown.
Probab=22.71 E-value=73 Score=21.48 Aligned_cols=12 Identities=25% Similarity=0.775 Sum_probs=9.2
Q ss_pred CCCCCCCCCCch
Q 032467 53 YTCPVCSKSLWD 64 (140)
Q Consensus 53 ~~CP~CR~~~~~ 64 (140)
..||.||..+.+
T Consensus 50 ggCp~CrvG~le 61 (98)
T PF10164_consen 50 GGCPACRVGVLE 61 (98)
T ss_pred cCCCCCceeeec
Confidence 459999988654
No 253
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=22.36 E-value=73 Score=18.22 Aligned_cols=23 Identities=26% Similarity=0.765 Sum_probs=11.0
Q ss_pred CCCCCCCcccceeeeccccccCCCcc
Q 032467 94 CNDCGANSHVQFHVIAHKCLSCKSYN 119 (140)
Q Consensus 94 C~~C~~~~~~~~~~~~~~C~~C~~~~ 119 (140)
|+.|.+.... +.+.+|..|..|.
T Consensus 3 Cd~C~~~~~~---g~r~~C~~C~d~d 25 (49)
T cd02335 3 CDYCSKDITG---TIRIKCAECPDFD 25 (49)
T ss_pred CCCcCCCCCC---CcEEECCCCCCcc
Confidence 6666653222 2344555555444
No 254
>PRK00366 ispG 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed
Probab=22.07 E-value=1.5e+02 Score=24.68 Aligned_cols=47 Identities=23% Similarity=0.571 Sum_probs=32.4
Q ss_pred CCCCCCCCCCchhhhHHHHHHHHHhcCCCChhhhcccceecC--CCCCCCccc
Q 032467 53 YTCPVCSKSLWDMSKLWSKIDQEIASTPMPAMYQNKMVWILC--NDCGANSHV 103 (140)
Q Consensus 53 ~~CP~CR~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~i~C--~~C~~~~~~ 103 (140)
..||.|++...+...+...+++.+...++| -+....-| +.|++....
T Consensus 269 isCPgCgR~~~D~~~la~~vee~~~~~~~P----lkIAVmGC~VNgpGEa~~a 317 (360)
T PRK00366 269 ISCPTCGRTEFDVIQELAEVEQRLEHIKMP----LKVAVMGCVVNGPGEAKEA 317 (360)
T ss_pred EECCCCCCCcccHHHHHHHHHHHhcCCCCC----cEEEEeCCCCCCCCchhhC
Confidence 469999999888777777777777666555 33455567 667765444
No 255
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=21.83 E-value=52 Score=19.46 Aligned_cols=27 Identities=22% Similarity=0.437 Sum_probs=19.4
Q ss_pred eecCCCCCCCcccceeeeccccccCCC
Q 032467 91 WILCNDCGANSHVQFHVIAHKCLSCKS 117 (140)
Q Consensus 91 ~i~C~~C~~~~~~~~~~~~~~C~~C~~ 117 (140)
.-.|..|+...-+-.|.-+..|.-|+.
T Consensus 19 ~~~CPrCG~gvfmA~H~dR~~CGkCgy 45 (51)
T COG1998 19 NRFCPRCGPGVFMADHKDRWACGKCGY 45 (51)
T ss_pred cccCCCCCCcchhhhcCceeEeccccc
Confidence 456888887655666777777777774
No 256
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=21.58 E-value=73 Score=18.41 Aligned_cols=27 Identities=22% Similarity=0.656 Sum_probs=16.9
Q ss_pred cCCCCCCCcccceeeeccccccCC--Cccccc
Q 032467 93 LCNDCGANSHVQFHVIAHKCLSCK--SYNTRQ 122 (140)
Q Consensus 93 ~C~~C~~~~~~~~~~~~~~C~~C~--~~~~~~ 122 (140)
.|+.|+... .-+.+.+|..|. .|..-+
T Consensus 2 ~Cd~C~~~p---I~G~R~~C~~C~~~d~DlC~ 30 (48)
T cd02341 2 KCDSCGIEP---IPGTRYHCSECDDGDFDLCQ 30 (48)
T ss_pred CCCCCCCCc---cccceEECCCCCCCCCccCH
Confidence 478888632 225667788887 665443
No 257
>PRK11827 hypothetical protein; Provisional
Probab=21.23 E-value=70 Score=19.55 Aligned_cols=10 Identities=50% Similarity=1.258 Sum_probs=7.8
Q ss_pred CCCCCCCCCC
Q 032467 53 YTCPVCSKSL 62 (140)
Q Consensus 53 ~~CP~CR~~~ 62 (140)
..||+|+..+
T Consensus 9 LaCP~ckg~L 18 (60)
T PRK11827 9 IACPVCNGKL 18 (60)
T ss_pred eECCCCCCcC
Confidence 4599998876
No 258
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=21.11 E-value=56 Score=20.03 Aligned_cols=10 Identities=50% Similarity=1.265 Sum_probs=7.2
Q ss_pred CCCCCCCCCC
Q 032467 53 YTCPVCSKSL 62 (140)
Q Consensus 53 ~~CP~CR~~~ 62 (140)
..||+||..+
T Consensus 9 LaCP~~kg~L 18 (60)
T COG2835 9 LACPVCKGPL 18 (60)
T ss_pred eeccCcCCcc
Confidence 3588888774
No 259
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=20.83 E-value=97 Score=20.44 Aligned_cols=31 Identities=19% Similarity=0.532 Sum_probs=21.1
Q ss_pred CcccccccccccccccCCccEEe-----cCCCcccHHHHHhh
Q 032467 11 AMHHNCPICFEFIFDTMKDITVL-----RCGHTIHLECLKEM 47 (140)
Q Consensus 11 ~~~~~C~IC~e~l~~~~~~~~~l-----~CgH~Fc~~Cl~~~ 47 (140)
.....|.||... .-..+ .|...||..|....
T Consensus 53 ~~~~~C~iC~~~------~G~~i~C~~~~C~~~fH~~CA~~~ 88 (110)
T PF13832_consen 53 RFKLKCSICGKS------GGACIKCSHPGCSTAFHPTCARKA 88 (110)
T ss_pred hcCCcCcCCCCC------CceeEEcCCCCCCcCCCHHHHHHC
Confidence 357889999963 11233 36679999998764
No 260
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=20.74 E-value=96 Score=16.97 Aligned_cols=16 Identities=19% Similarity=0.468 Sum_probs=10.0
Q ss_pred ccccccCC-Cccccccc
Q 032467 109 AHKCLSCK-SYNTRQTR 124 (140)
Q Consensus 109 ~~~C~~C~-~~~~~~~~ 124 (140)
..+|..|+ .|...++.
T Consensus 12 ~f~C~~C~~~FC~~HR~ 28 (39)
T smart00154 12 GFKCRHCGNLFCGEHRL 28 (39)
T ss_pred CeECCccCCccccccCC
Confidence 55677777 56655553
No 261
>KOG4582 consensus Uncharacterized conserved protein, contains ZZ-type Zn-finger [General function prediction only]
Probab=20.56 E-value=62 Score=25.73 Aligned_cols=27 Identities=30% Similarity=0.709 Sum_probs=19.5
Q ss_pred eecCCCCCCCcccceeeeccccccCCCccc
Q 032467 91 WILCNDCGANSHVQFHVIAHKCLSCKSYNT 120 (140)
Q Consensus 91 ~i~C~~C~~~~~~~~~~~~~~C~~C~~~~~ 120 (140)
.+.|+.|++..-+ +.+.||..|..|.-
T Consensus 152 ~v~CD~C~~~~Iv---G~RyKC~~C~dYDL 178 (278)
T KOG4582|consen 152 SVPCDNCGKPGIV---GARYKCTVCPDYDL 178 (278)
T ss_pred cccCCCccCCccc---cceeeecCCCccch
Confidence 4899999984433 57778888777653
No 262
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=20.50 E-value=60 Score=18.99 Aligned_cols=11 Identities=36% Similarity=1.072 Sum_probs=8.9
Q ss_pred ccCCCCCCCCC
Q 032467 51 YRYTCPVCSKS 61 (140)
Q Consensus 51 ~~~~CP~CR~~ 61 (140)
..++||+|+..
T Consensus 33 ~~w~CP~C~a~ 43 (50)
T cd00730 33 DDWVCPVCGAG 43 (50)
T ss_pred CCCCCCCCCCc
Confidence 35899999876
No 263
>PF12088 DUF3565: Protein of unknown function (DUF3565); InterPro: IPR021948 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 30 to 78 amino acids in length. This protein has two conserved sequence motifs: WVA and CGH.
Probab=20.02 E-value=61 Score=19.90 Aligned_cols=16 Identities=38% Similarity=0.634 Sum_probs=12.3
Q ss_pred CCccEEecCCCcccHH
Q 032467 27 MKDITVLRCGHTIHLE 42 (140)
Q Consensus 27 ~~~~~~l~CgH~Fc~~ 42 (140)
...+..|.|||+-|.+
T Consensus 9 ~hWVA~L~CGH~QHvR 24 (61)
T PF12088_consen 9 GHWVAELSCGHTQHVR 24 (61)
T ss_pred CCEEEEeccccccccc
Confidence 3457889999998864
Done!