Query psy10800
Match_columns 81
No_of_seqs 163 out of 1256
Neff 9.4
Searched_HMMs 46136
Date Fri Aug 16 18:50:04 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10800.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/10800hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03208 E3 ubiquitin-protein 99.7 4E-17 8.8E-22 97.4 4.5 61 19-79 13-88 (193)
2 KOG0978|consensus 99.7 4.1E-17 9E-22 111.5 3.7 77 3-79 622-698 (698)
3 PF15227 zf-C3HC4_4: zinc fing 99.6 1.3E-16 2.8E-21 74.7 2.5 39 27-65 1-42 (42)
4 KOG0320|consensus 99.6 4.4E-16 9.5E-21 91.5 3.9 56 23-79 130-187 (187)
5 KOG0823|consensus 99.6 8E-16 1.7E-20 93.5 3.5 58 22-79 45-104 (230)
6 smart00504 Ubox Modified RING 99.5 1.2E-14 2.7E-19 73.1 4.4 53 24-77 1-53 (63)
7 PF13923 zf-C3HC4_2: Zinc fing 99.5 5.8E-15 1.2E-19 68.1 2.1 38 27-65 1-39 (39)
8 KOG0317|consensus 99.5 1.2E-14 2.7E-19 90.7 3.2 56 22-78 237-292 (293)
9 PF13920 zf-C3HC4_3: Zinc fing 99.5 2.9E-14 6.3E-19 69.0 2.6 46 24-70 2-48 (50)
10 TIGR00599 rad18 DNA repair pro 99.4 7.6E-14 1.6E-18 91.3 3.7 58 18-76 20-77 (397)
11 PF13639 zf-RING_2: Ring finge 99.4 2.7E-14 5.9E-19 67.4 0.6 40 26-66 2-44 (44)
12 PHA02929 N1R/p28-like protein; 99.4 2.7E-13 5.8E-18 83.7 4.8 49 22-71 172-228 (238)
13 PF00097 zf-C3HC4: Zinc finger 99.4 1.3E-13 2.9E-18 64.0 2.4 39 27-65 1-41 (41)
14 KOG0287|consensus 99.4 6.2E-14 1.3E-18 89.6 0.6 61 17-78 16-76 (442)
15 KOG2164|consensus 99.4 3.7E-13 8.1E-18 89.4 3.8 57 24-80 186-246 (513)
16 cd00162 RING RING-finger (Real 99.4 1.1E-12 2.4E-17 61.2 3.8 44 26-69 1-45 (45)
17 PF14634 zf-RING_5: zinc-RING 99.4 1.4E-12 3E-17 61.5 3.8 41 26-67 1-44 (44)
18 PHA02926 zinc finger-like prot 99.4 2.2E-12 4.7E-17 78.5 5.6 54 18-71 164-231 (242)
19 PF04564 U-box: U-box domain; 99.3 8.2E-13 1.8E-17 68.5 2.8 55 23-77 3-57 (73)
20 PF13445 zf-RING_UBOX: RING-ty 99.3 9.3E-13 2E-17 61.7 1.8 36 27-63 1-43 (43)
21 smart00184 RING Ring finger. E 99.3 5.7E-12 1.2E-16 57.0 4.3 39 27-65 1-39 (39)
22 PF14835 zf-RING_6: zf-RING of 99.2 7.2E-13 1.5E-17 66.3 -1.0 54 20-76 3-57 (65)
23 COG5432 RAD18 RING-finger-cont 99.2 1.2E-11 2.6E-16 78.0 1.9 55 19-74 20-74 (391)
24 TIGR00570 cdk7 CDK-activating 99.2 5.2E-11 1.1E-15 75.8 4.5 57 24-80 3-64 (309)
25 COG5574 PEX10 RING-finger-cont 99.1 2.9E-11 6.3E-16 75.0 3.0 52 23-74 214-266 (271)
26 KOG2177|consensus 99.1 6.3E-11 1.4E-15 73.6 2.8 49 18-67 7-55 (386)
27 KOG4628|consensus 99.0 1.2E-10 2.5E-15 75.2 2.6 47 25-71 230-279 (348)
28 PF12678 zf-rbx1: RING-H2 zinc 99.0 1.2E-10 2.7E-15 60.3 2.1 40 26-66 21-73 (73)
29 KOG0311|consensus 98.9 6.8E-11 1.5E-15 76.0 -1.2 58 14-71 33-91 (381)
30 COG5540 RING-finger-containing 98.9 1.4E-09 3E-14 69.1 3.6 54 18-71 317-373 (374)
31 PF12861 zf-Apc11: Anaphase-pr 98.9 2.2E-09 4.7E-14 56.8 3.6 48 24-71 21-83 (85)
32 KOG0802|consensus 98.8 2E-09 4.4E-14 73.3 2.3 50 22-72 289-343 (543)
33 KOG0824|consensus 98.8 4.1E-09 9E-14 66.7 2.3 49 24-72 7-55 (324)
34 COG5243 HRD1 HRD ubiquitin lig 98.8 6.2E-09 1.3E-13 67.8 3.0 48 21-69 284-344 (491)
35 KOG4172|consensus 98.7 7E-09 1.5E-13 50.3 0.9 47 24-70 7-54 (62)
36 KOG4159|consensus 98.6 1.7E-08 3.6E-13 66.6 1.7 52 19-71 79-130 (398)
37 KOG2660|consensus 98.6 1.7E-08 3.8E-13 64.5 1.5 56 17-73 8-64 (331)
38 KOG4265|consensus 98.6 3.6E-08 7.7E-13 63.6 2.6 56 21-79 287-343 (349)
39 COG5152 Uncharacterized conser 98.6 1.9E-08 4.2E-13 60.7 0.9 46 24-70 196-241 (259)
40 COG5222 Uncharacterized conser 98.4 9.8E-08 2.1E-12 60.9 1.5 43 25-67 275-318 (427)
41 PF11789 zf-Nse: Zinc-finger o 98.4 1.1E-07 2.5E-12 47.0 1.3 44 21-64 8-53 (57)
42 KOG0297|consensus 98.3 3.1E-07 6.7E-12 60.7 1.9 52 21-73 18-70 (391)
43 KOG2879|consensus 98.3 7E-07 1.5E-11 56.2 3.0 49 22-70 237-287 (298)
44 KOG1813|consensus 98.2 2.9E-07 6.2E-12 58.4 0.5 46 24-70 241-286 (313)
45 KOG1039|consensus 98.2 1.8E-06 3.9E-11 56.2 3.2 50 22-71 159-222 (344)
46 KOG0804|consensus 98.2 7.1E-07 1.5E-11 59.4 1.1 50 18-70 169-222 (493)
47 KOG0828|consensus 98.1 2E-06 4.3E-11 58.0 2.8 51 21-71 568-635 (636)
48 KOG3039|consensus 98.1 4.8E-06 1E-10 51.9 4.2 57 21-78 218-278 (303)
49 PF04641 Rtf2: Rtf2 RING-finge 98.1 5E-06 1.1E-10 52.3 4.4 58 21-80 110-171 (260)
50 KOG1785|consensus 98.1 1.9E-06 4.1E-11 57.0 2.6 49 25-73 370-419 (563)
51 KOG2817|consensus 98.1 2.1E-06 4.7E-11 56.3 2.6 59 21-79 331-394 (394)
52 KOG1645|consensus 98.1 1E-06 2.3E-11 58.0 0.5 55 23-77 3-63 (463)
53 PF11793 FANCL_C: FANCL C-term 98.1 5.7E-07 1.2E-11 46.2 -0.6 48 24-71 2-67 (70)
54 smart00744 RINGv The RING-vari 98.0 1.9E-05 4.1E-10 37.8 4.1 41 26-66 1-49 (49)
55 PF14447 Prok-RING_4: Prokaryo 98.0 3.2E-06 6.8E-11 41.2 1.0 48 23-73 6-53 (55)
56 PF14570 zf-RING_4: RING/Ubox 97.9 8.5E-06 1.8E-10 38.8 2.4 43 27-69 1-47 (48)
57 KOG1493|consensus 97.9 4.4E-06 9.6E-11 43.3 1.2 31 41-71 50-82 (84)
58 KOG4367|consensus 97.9 8.9E-06 1.9E-10 54.5 2.7 36 22-57 2-37 (699)
59 KOG1734|consensus 97.9 2.6E-06 5.7E-11 53.7 -0.1 48 23-70 223-281 (328)
60 KOG0827|consensus 97.9 8.5E-06 1.8E-10 53.6 2.2 49 25-73 5-59 (465)
61 COG5194 APC11 Component of SCF 97.9 2.8E-05 6.2E-10 40.6 3.7 30 41-71 53-82 (88)
62 KOG4275|consensus 97.8 7.3E-07 1.6E-11 56.6 -3.0 43 24-71 300-343 (350)
63 COG5219 Uncharacterized conser 97.8 8.2E-06 1.8E-10 58.9 1.7 50 21-70 1466-1523(1525)
64 KOG4185|consensus 97.8 9.3E-06 2E-10 51.7 1.6 46 24-69 3-54 (296)
65 KOG1002|consensus 97.8 1.2E-05 2.6E-10 55.0 2.1 50 23-72 535-588 (791)
66 KOG3800|consensus 97.8 2.8E-05 6.1E-10 49.4 3.4 50 26-75 2-56 (300)
67 KOG4692|consensus 97.7 1.9E-05 4.2E-10 51.6 1.8 48 22-70 420-467 (489)
68 KOG0826|consensus 97.7 7.7E-06 1.7E-10 52.7 -0.1 57 22-79 298-355 (357)
69 KOG4739|consensus 97.5 2.5E-05 5.5E-10 48.4 0.5 46 24-72 3-50 (233)
70 KOG3002|consensus 97.5 7.1E-05 1.5E-09 48.1 2.1 45 21-70 45-91 (299)
71 KOG1814|consensus 97.5 0.00017 3.8E-09 47.9 3.9 38 20-57 180-220 (445)
72 KOG1001|consensus 97.5 6.2E-05 1.4E-09 52.9 1.7 49 25-74 455-504 (674)
73 KOG0825|consensus 97.4 2.6E-05 5.7E-10 55.3 -0.6 51 24-75 123-176 (1134)
74 COG5175 MOT2 Transcriptional r 97.4 0.00032 7E-09 45.9 4.0 56 24-79 14-73 (480)
75 KOG2930|consensus 97.4 0.00023 5E-09 38.9 2.9 29 41-70 80-108 (114)
76 KOG1941|consensus 97.4 9.8E-05 2.1E-09 48.9 1.7 46 23-68 364-414 (518)
77 PF05290 Baculo_IE-1: Baculovi 97.3 0.0005 1.1E-08 39.3 3.8 51 23-73 79-135 (140)
78 COG5220 TFB3 Cdk activating ki 97.2 8.6E-05 1.9E-09 46.4 0.3 52 24-75 10-69 (314)
79 PF10367 Vps39_2: Vacuolar sor 97.0 0.00018 4E-09 39.1 0.3 31 22-52 76-108 (109)
80 KOG1571|consensus 97.0 0.00024 5.3E-09 46.4 0.8 47 20-70 301-347 (355)
81 COG5109 Uncharacterized conser 97.0 0.00046 1E-08 44.7 2.0 60 20-79 332-396 (396)
82 PF07800 DUF1644: Protein of u 97.0 0.0013 2.8E-08 38.6 3.6 34 23-56 1-47 (162)
83 COG5236 Uncharacterized conser 97.0 0.00047 1E-08 45.3 1.9 48 22-69 59-107 (493)
84 KOG2114|consensus 96.8 0.0012 2.7E-08 47.4 2.7 42 24-69 840-882 (933)
85 PF08746 zf-RING-like: RING-li 96.7 0.0024 5.3E-08 29.7 2.6 39 27-65 1-43 (43)
86 PF02891 zf-MIZ: MIZ/SP-RING z 96.7 0.0028 6E-08 30.4 2.9 45 24-68 2-50 (50)
87 KOG4362|consensus 96.6 0.0006 1.3E-08 48.0 0.5 59 16-74 13-73 (684)
88 KOG3970|consensus 96.3 0.0052 1.1E-07 38.3 3.2 48 22-69 48-104 (299)
89 PHA03096 p28-like protein; Pro 96.1 0.0048 1E-07 39.6 2.4 44 25-68 179-232 (284)
90 KOG1940|consensus 96.0 0.0058 1.3E-07 39.0 2.2 43 24-67 158-204 (276)
91 KOG3268|consensus 95.7 0.012 2.6E-07 35.5 2.8 31 41-71 189-229 (234)
92 KOG1952|consensus 95.7 0.015 3.3E-07 42.1 3.5 48 22-69 189-246 (950)
93 KOG2932|consensus 95.7 0.0075 1.6E-07 39.2 1.8 43 24-69 90-133 (389)
94 KOG1812|consensus 95.6 0.0065 1.4E-07 40.5 1.5 50 23-72 145-205 (384)
95 KOG3113|consensus 95.5 0.021 4.5E-07 36.2 3.4 54 22-78 109-166 (293)
96 KOG4445|consensus 95.5 0.0045 9.7E-08 40.0 0.4 48 23-70 114-186 (368)
97 KOG1815|consensus 95.4 0.027 5.9E-07 38.1 3.9 54 24-77 70-133 (444)
98 KOG3161|consensus 95.4 0.0049 1.1E-07 43.5 0.2 40 21-63 8-51 (861)
99 PF10272 Tmpp129: Putative tra 95.3 0.019 4.1E-07 38.0 2.8 34 42-75 311-356 (358)
100 KOG0298|consensus 95.1 0.009 2E-07 44.9 1.0 51 17-68 1146-1197(1394)
101 KOG1100|consensus 95.1 0.011 2.4E-07 36.3 1.2 40 26-70 160-200 (207)
102 KOG1428|consensus 94.9 0.023 5.1E-07 44.0 2.5 51 21-71 3483-3545(3738)
103 PHA02825 LAP/PHD finger-like p 94.7 0.054 1.2E-06 32.0 3.3 48 22-70 6-59 (162)
104 KOG3899|consensus 94.7 0.032 7E-07 36.1 2.6 38 42-79 325-374 (381)
105 KOG3039|consensus 94.6 0.034 7.4E-07 35.2 2.4 39 18-56 37-75 (303)
106 KOG2034|consensus 94.3 0.025 5.5E-07 41.1 1.6 38 19-56 812-851 (911)
107 PF03854 zf-P11: P-11 zinc fin 94.0 0.012 2.7E-07 27.9 -0.3 37 34-71 10-47 (50)
108 PHA02862 5L protein; Provision 93.9 0.079 1.7E-06 30.9 2.8 45 25-70 3-53 (156)
109 PF05883 Baculo_RING: Baculovi 93.8 0.06 1.3E-06 31.0 2.2 44 13-56 13-67 (134)
110 PF06906 DUF1272: Protein of u 93.8 0.068 1.5E-06 26.2 2.1 45 26-73 7-55 (57)
111 KOG3579|consensus 93.6 0.023 5.1E-07 36.6 0.4 36 23-58 267-306 (352)
112 COG3813 Uncharacterized protei 92.9 0.09 1.9E-06 27.1 1.7 32 41-75 26-57 (84)
113 PF14446 Prok-RING_1: Prokaryo 91.8 0.22 4.7E-06 24.3 2.3 30 24-53 5-38 (54)
114 PF10571 UPF0547: Uncharacteri 91.7 0.1 2.2E-06 21.6 0.9 9 26-34 2-10 (26)
115 PF07975 C1_4: TFIIH C1-like d 91.7 0.18 3.9E-06 24.3 1.9 25 41-66 26-50 (51)
116 PF12906 RINGv: RING-variant d 90.4 0.088 1.9E-06 24.8 0.1 39 27-65 1-47 (47)
117 PF07191 zinc-ribbons_6: zinc- 90.3 0.0041 9E-08 31.8 -4.7 40 25-70 2-41 (70)
118 PF10235 Cript: Microtubule-as 89.8 0.21 4.6E-06 26.8 1.3 37 24-70 44-80 (90)
119 KOG1812|consensus 89.7 0.31 6.7E-06 32.7 2.3 36 22-57 304-344 (384)
120 PF14353 CpXC: CpXC protein 89.5 0.36 7.9E-06 27.2 2.2 47 25-71 2-50 (128)
121 PF14569 zf-UDP: Zinc-binding 88.2 1.2 2.6E-05 23.3 3.4 47 24-70 9-62 (80)
122 KOG2979|consensus 87.2 0.77 1.7E-05 29.3 2.7 44 24-67 176-221 (262)
123 KOG0309|consensus 86.9 0.4 8.7E-06 35.0 1.5 40 24-64 1028-1069(1081)
124 PF05605 zf-Di19: Drought indu 85.9 0.8 1.7E-05 21.9 1.9 41 23-70 1-42 (54)
125 KOG4718|consensus 84.7 0.77 1.7E-05 28.6 1.8 46 24-70 181-227 (235)
126 KOG4185|consensus 84.0 0.3 6.4E-06 31.2 -0.2 44 25-68 208-265 (296)
127 KOG2462|consensus 83.7 1.4 3E-05 28.4 2.7 13 60-72 216-228 (279)
128 PF06844 DUF1244: Protein of u 83.5 0.89 1.9E-05 23.0 1.5 13 45-57 11-23 (68)
129 KOG0289|consensus 83.2 2.3 5E-05 29.3 3.7 53 26-79 2-55 (506)
130 KOG2068|consensus 82.2 1.7 3.7E-05 28.7 2.7 46 25-71 250-299 (327)
131 PF12773 DZR: Double zinc ribb 82.0 1.2 2.6E-05 20.8 1.6 25 46-70 14-40 (50)
132 PF04216 FdhE: Protein involve 81.9 0.08 1.7E-06 33.9 -3.3 44 24-68 172-220 (290)
133 cd00350 rubredoxin_like Rubred 81.5 1.5 3.3E-05 18.9 1.7 11 58-68 16-26 (33)
134 cd00065 FYVE FYVE domain; Zinc 80.8 1.2 2.5E-05 21.3 1.3 32 25-56 3-38 (57)
135 PF10497 zf-4CXXC_R1: Zinc-fin 80.2 3.5 7.7E-05 22.7 3.2 26 43-68 37-70 (105)
136 PF15616 TerY-C: TerY-C metal 79.9 0.37 8E-06 27.7 -0.7 48 17-71 70-117 (131)
137 PF04710 Pellino: Pellino; In 79.6 0.58 1.3E-05 31.6 0.0 30 38-70 305-339 (416)
138 smart00064 FYVE Protein presen 79.6 1.6 3.4E-05 21.7 1.6 33 24-56 10-46 (68)
139 PF09986 DUF2225: Uncharacteri 79.3 0.51 1.1E-05 29.1 -0.3 55 22-77 3-66 (214)
140 COG5183 SSM4 Protein involved 77.4 2.8 6.1E-05 31.2 2.8 48 24-71 12-67 (1175)
141 TIGR01562 FdhE formate dehydro 76.8 0.46 1E-05 31.0 -1.0 44 24-68 184-233 (305)
142 TIGR00622 ssl1 transcription f 75.1 2.9 6.2E-05 23.4 1.9 41 25-66 56-110 (112)
143 PRK03564 formate dehydrogenase 75.0 1.5 3.3E-05 28.7 0.9 44 23-67 186-234 (309)
144 PF01363 FYVE: FYVE zinc finge 73.5 0.31 6.7E-06 24.4 -2.0 31 23-53 8-42 (69)
145 KOG2807|consensus 72.9 1.6 3.4E-05 29.0 0.6 41 25-66 331-374 (378)
146 KOG2231|consensus 71.3 3.8 8.2E-05 29.7 2.2 46 26-71 2-53 (669)
147 KOG3053|consensus 71.2 2.3 5E-05 27.3 1.1 52 18-69 14-81 (293)
148 KOG0825|consensus 70.4 3 6.4E-05 31.0 1.6 46 24-69 96-153 (1134)
149 smart00249 PHD PHD zinc finger 69.8 2.1 4.6E-05 18.9 0.5 28 26-53 1-31 (47)
150 PLN02189 cellulose synthase 69.6 4.5 9.8E-05 30.7 2.4 47 24-70 34-87 (1040)
151 COG3492 Uncharacterized protei 67.7 4.5 9.9E-05 21.9 1.6 13 45-57 42-54 (104)
152 smart00132 LIM Zinc-binding do 66.8 4.9 0.00011 17.0 1.4 11 26-36 1-11 (39)
153 PF04423 Rad50_zn_hook: Rad50 65.8 5.4 0.00012 19.0 1.6 10 26-35 22-31 (54)
154 PLN02436 cellulose synthase A 65.1 6.2 0.00013 30.2 2.3 47 24-70 36-89 (1094)
155 COG3058 FdhE Uncharacterized p 64.4 7 0.00015 25.5 2.2 45 22-67 183-233 (308)
156 PRK10144 formate-dependent nit 64.0 5.7 0.00012 22.7 1.6 22 11-32 27-48 (126)
157 smart00290 ZnF_UBP Ubiquitin C 63.8 5.3 0.00012 18.4 1.3 22 27-48 2-23 (50)
158 KOG2169|consensus 63.1 5.8 0.00013 28.5 1.9 53 21-74 303-360 (636)
159 COG4647 AcxC Acetone carboxyla 62.9 2.9 6.2E-05 24.2 0.3 21 29-49 62-82 (165)
160 PF07503 zf-HYPF: HypF finger; 62.4 10 0.00022 16.7 2.0 24 46-69 1-31 (35)
161 KOG0269|consensus 62.2 10 0.00022 28.1 2.9 49 24-73 779-831 (839)
162 PF13719 zinc_ribbon_5: zinc-r 62.0 4.6 0.0001 17.8 0.8 13 25-37 3-15 (37)
163 smart00734 ZnF_Rad18 Rad18-lik 62.0 4.4 9.5E-05 16.5 0.7 9 26-34 3-11 (26)
164 PF14311 DUF4379: Domain of un 61.9 4.3 9.4E-05 19.4 0.8 23 41-65 33-55 (55)
165 PF13717 zinc_ribbon_4: zinc-r 61.8 4.2 9.1E-05 17.9 0.7 12 25-36 3-14 (36)
166 PRK11595 DNA utilization prote 61.2 8.7 0.00019 23.8 2.2 38 26-69 7-44 (227)
167 KOG2042|consensus 59.5 11 0.00023 28.6 2.7 57 18-75 864-921 (943)
168 PF06676 DUF1178: Protein of u 58.9 14 0.00031 21.7 2.7 12 58-69 31-42 (148)
169 PRK00420 hypothetical protein; 58.5 7.1 0.00015 21.9 1.3 12 24-35 23-34 (112)
170 PRK11088 rrmA 23S rRNA methylt 58.4 7.1 0.00015 24.6 1.5 22 25-46 3-27 (272)
171 PF13901 DUF4206: Domain of un 57.9 10 0.00022 23.2 2.1 39 23-67 151-197 (202)
172 smart00154 ZnF_AN1 AN1-like Zi 57.8 7.6 0.00016 17.4 1.2 22 27-48 1-24 (39)
173 PF10083 DUF2321: Uncharacteri 57.4 13 0.00027 22.2 2.3 26 43-72 27-52 (158)
174 TIGR03147 cyt_nit_nrfF cytochr 57.2 8.7 0.00019 22.0 1.6 22 11-32 27-48 (126)
175 smart00647 IBR In Between Ring 57.1 0.74 1.6E-05 22.3 -2.5 32 23-54 17-58 (64)
176 KOG1829|consensus 57.0 5.5 0.00012 28.4 0.9 22 41-66 536-557 (580)
177 PF00412 LIM: LIM domain; Int 56.9 6.8 0.00015 18.4 1.0 30 24-53 26-56 (58)
178 PF14471 DUF4428: Domain of un 56.7 18 0.00039 17.2 2.4 28 26-54 1-30 (51)
179 PF13453 zf-TFIIB: Transcripti 56.1 4.5 9.7E-05 18.1 0.3 6 62-67 22-27 (41)
180 KOG2113|consensus 56.1 10 0.00022 25.3 1.9 46 20-68 339-385 (394)
181 COG3088 CcmH Uncharacterized p 56.1 7.2 0.00016 23.0 1.2 23 11-33 31-53 (153)
182 KOG3799|consensus 56.1 8.9 0.00019 22.4 1.5 25 21-50 62-87 (169)
183 PF09538 FYDLN_acid: Protein o 55.9 8 0.00017 21.5 1.3 14 59-72 26-39 (108)
184 KOG2789|consensus 55.6 6.7 0.00015 26.8 1.1 33 23-55 73-107 (482)
185 COG4357 Zinc finger domain con 54.6 16 0.00034 20.0 2.2 13 60-72 81-93 (105)
186 PRK04023 DNA polymerase II lar 54.4 11 0.00024 28.8 2.1 52 23-77 625-681 (1121)
187 PLN02248 cellulose synthase-li 52.5 19 0.00042 27.8 3.1 33 41-74 149-181 (1135)
188 COG1592 Rubrerythrin [Energy p 52.0 14 0.00031 22.1 2.0 11 58-68 148-158 (166)
189 PF13240 zinc_ribbon_2: zinc-r 51.7 10 0.00022 14.9 0.9 6 62-67 16-21 (23)
190 PF13248 zf-ribbon_3: zinc-rib 51.4 1.6 3.4E-05 17.8 -1.6 6 62-67 19-24 (26)
191 PF13913 zf-C2HC_2: zinc-finge 51.3 8.7 0.00019 15.4 0.7 8 62-69 5-12 (25)
192 PF10146 zf-C4H2: Zinc finger- 51.1 18 0.00039 22.8 2.4 28 46-74 196-223 (230)
193 PLN02638 cellulose synthase A 50.7 17 0.00037 28.0 2.5 47 24-70 17-70 (1079)
194 COG4306 Uncharacterized protei 50.5 18 0.00039 20.9 2.1 24 45-72 29-52 (160)
195 PF09889 DUF2116: Uncharacteri 49.5 13 0.00029 18.3 1.4 13 59-71 3-15 (59)
196 PF00096 zf-C2H2: Zinc finger, 48.9 4.3 9.3E-05 15.4 -0.4 11 26-36 2-12 (23)
197 PF06827 zf-FPG_IleRS: Zinc fi 48.8 1.8 4E-05 18.0 -1.6 11 26-36 3-13 (30)
198 KOG2272|consensus 48.7 12 0.00026 24.2 1.4 32 13-44 172-203 (332)
199 PF13894 zf-C2H2_4: C2H2-type 47.9 7.2 0.00016 14.4 0.2 8 27-34 3-10 (24)
200 PF02318 FYVE_2: FYVE-type zin 47.9 5.2 0.00011 22.3 -0.3 30 23-52 53-87 (118)
201 PLN02915 cellulose synthase A 47.3 19 0.00042 27.6 2.4 48 23-70 14-68 (1044)
202 PRK14559 putative protein seri 47.2 10 0.00022 27.5 1.0 8 26-33 3-10 (645)
203 COG5627 MMS21 DNA repair prote 46.3 14 0.00031 23.6 1.4 41 24-64 189-231 (275)
204 PF10186 Atg14: UV radiation r 45.8 18 0.00039 22.8 1.9 22 26-55 1-22 (302)
205 KOG3476|consensus 45.7 1.7 3.6E-05 23.3 -2.3 36 25-70 55-90 (100)
206 PLN02195 cellulose synthase A 45.5 29 0.00063 26.5 3.1 46 24-70 6-59 (977)
207 PF00643 zf-B_box: B-box zinc 45.1 16 0.00035 16.0 1.2 30 24-53 3-32 (42)
208 PRK01343 zinc-binding protein; 44.8 17 0.00038 17.9 1.3 11 60-70 10-20 (57)
209 KOG4451|consensus 44.3 24 0.00053 22.5 2.2 27 46-73 251-277 (286)
210 KOG3362|consensus 43.9 6 0.00013 23.2 -0.4 28 24-52 118-146 (156)
211 COG0068 HypF Hydrogenase matur 43.8 9.3 0.0002 28.0 0.4 21 47-67 154-181 (750)
212 TIGR00627 tfb4 transcription f 42.8 24 0.00052 22.9 2.1 9 60-68 270-278 (279)
213 KOG4218|consensus 42.6 31 0.00066 23.5 2.6 14 23-36 14-27 (475)
214 COG4098 comFA Superfamily II D 41.8 9.3 0.0002 26.0 0.1 30 23-52 38-68 (441)
215 PF06221 zf-C2HC5: Putative zi 40.1 21 0.00046 17.5 1.2 28 37-71 19-47 (57)
216 PF00628 PHD: PHD-finger; Int 40.1 4.9 0.00011 18.5 -1.0 26 27-52 2-30 (51)
217 PLN02400 cellulose synthase 39.5 20 0.00044 27.6 1.6 47 24-70 36-89 (1085)
218 cd00730 rubredoxin Rubredoxin; 38.9 22 0.00048 16.9 1.2 15 18-32 28-42 (50)
219 PRK00418 DNA gyrase inhibitor; 38.8 18 0.00038 18.1 0.9 11 60-70 7-17 (62)
220 PF01428 zf-AN1: AN1-like Zinc 38.0 17 0.00038 16.4 0.7 20 30-49 6-26 (43)
221 KOG0801|consensus 37.8 24 0.00053 21.3 1.5 15 60-74 139-153 (205)
222 PF00301 Rubredoxin: Rubredoxi 37.6 20 0.00044 16.8 0.9 16 17-32 27-42 (47)
223 TIGR02300 FYDLN_acid conserved 36.8 23 0.0005 20.4 1.2 11 24-34 9-19 (129)
224 KOG1729|consensus 36.6 15 0.00032 24.0 0.5 31 23-53 167-202 (288)
225 PF03119 DNA_ligase_ZBD: NAD-d 35.3 13 0.00027 15.4 0.0 9 62-70 2-10 (28)
226 PF02148 zf-UBP: Zn-finger in 34.6 14 0.00031 18.0 0.2 23 27-49 1-24 (63)
227 COG1997 RPL43A Ribosomal prote 34.3 58 0.0013 17.5 2.4 17 18-34 29-45 (89)
228 KOG2066|consensus 34.1 15 0.00032 27.4 0.2 33 24-56 784-823 (846)
229 COG3364 Zn-ribbon containing p 34.0 19 0.00041 20.0 0.6 24 39-67 5-28 (112)
230 PF13465 zf-H2C2_2: Zinc-finge 33.9 16 0.00036 14.5 0.2 12 23-34 13-24 (26)
231 KOG3842|consensus 33.9 54 0.0012 22.1 2.7 47 23-70 340-414 (429)
232 KOG3475|consensus 33.6 33 0.00072 18.3 1.4 28 43-70 15-42 (92)
233 KOG1609|consensus 33.2 47 0.001 21.1 2.4 48 24-71 78-135 (323)
234 COG2093 DNA-directed RNA polym 32.9 22 0.00047 17.9 0.6 21 47-68 7-27 (64)
235 PF09654 DUF2396: Protein of u 32.8 21 0.00045 21.0 0.6 11 60-70 7-17 (161)
236 TIGR02652 conserved hypothetic 32.6 20 0.00044 21.0 0.6 12 60-71 10-21 (163)
237 PF06750 DiS_P_DiS: Bacterial 32.6 28 0.00061 18.6 1.1 16 61-76 35-50 (92)
238 PF03884 DUF329: Domain of unk 32.5 15 0.00033 18.0 0.0 11 61-71 4-14 (57)
239 PF14205 Cys_rich_KTR: Cystein 32.5 12 0.00027 18.2 -0.3 12 23-34 3-14 (55)
240 PF12874 zf-met: Zinc-finger o 32.4 11 0.00024 14.4 -0.4 11 26-36 2-12 (25)
241 cd00729 rubredoxin_SM Rubredox 31.9 26 0.00057 15.1 0.8 9 60-68 19-27 (34)
242 PF13912 zf-C2H2_6: C2H2-type 31.8 14 0.0003 14.5 -0.2 12 25-36 2-13 (27)
243 PF10013 DUF2256: Uncharacteri 31.2 35 0.00076 15.7 1.1 11 60-70 9-19 (42)
244 KOG4642|consensus 31.1 46 0.001 21.6 2.0 54 23-76 210-263 (284)
245 PRK13130 H/ACA RNA-protein com 31.1 37 0.00081 16.6 1.3 15 60-74 18-32 (56)
246 COG3024 Uncharacterized protei 31.0 31 0.00067 17.4 1.0 10 61-70 9-18 (65)
247 PRK14714 DNA polymerase II lar 31.0 22 0.00048 28.0 0.7 54 24-77 667-727 (1337)
248 KOG0006|consensus 30.7 69 0.0015 21.6 2.8 37 19-55 216-254 (446)
249 PRK06266 transcription initiat 30.1 31 0.00067 20.8 1.1 31 23-71 116-148 (178)
250 PF12292 DUF3624: Protein of u 29.9 14 0.00031 19.3 -0.3 19 47-65 3-21 (77)
251 KOG0396|consensus 29.8 26 0.00056 23.8 0.8 43 37-79 346-388 (389)
252 PF12171 zf-C2H2_jaz: Zinc-fin 29.8 39 0.00084 13.3 1.1 12 25-36 2-13 (27)
253 PF05502 Dynactin_p62: Dynacti 29.8 14 0.00031 25.7 -0.4 50 22-71 3-64 (483)
254 PF07649 C1_3: C1-like domain; 29.8 52 0.0011 13.4 1.7 11 26-36 2-12 (30)
255 COG5151 SSL1 RNA polymerase II 29.1 47 0.001 22.3 1.8 43 24-67 362-418 (421)
256 TIGR01206 lysW lysine biosynth 28.9 32 0.0007 16.6 0.8 8 62-69 25-32 (54)
257 KOG2071|consensus 28.8 22 0.00048 25.5 0.4 34 22-55 511-557 (579)
258 COG4338 Uncharacterized protei 28.6 19 0.0004 17.2 -0.0 13 23-35 11-23 (54)
259 COG1645 Uncharacterized Zn-fin 28.6 11 0.00024 21.7 -0.9 13 24-36 28-40 (131)
260 PF09237 GAGA: GAGA factor; I 28.1 24 0.00052 17.1 0.3 12 60-71 25-36 (54)
261 PF10217 DUF2039: Uncharacteri 27.9 45 0.00097 18.1 1.4 20 44-68 71-90 (92)
262 KOG1356|consensus 27.9 19 0.00041 27.0 -0.1 32 24-55 229-262 (889)
263 TIGR00373 conserved hypothetic 27.8 27 0.00058 20.6 0.5 31 23-71 108-140 (158)
264 PF06937 EURL: EURL protein; 27.5 62 0.0013 21.1 2.1 37 24-63 30-74 (285)
265 smart00714 LITAF Possible memb 27.3 22 0.00048 17.5 0.1 13 59-71 52-64 (67)
266 PF12132 DUF3587: Protein of u 26.7 53 0.0011 20.3 1.7 24 34-57 151-178 (199)
267 PF01485 IBR: IBR domain; Int 26.7 7.1 0.00015 18.6 -1.8 30 25-54 19-58 (64)
268 PRK00398 rpoP DNA-directed RNA 26.6 27 0.00059 15.9 0.4 11 60-70 22-32 (46)
269 KOG0883|consensus 26.6 76 0.0017 22.1 2.5 55 24-79 40-94 (518)
270 PF03833 PolC_DP2: DNA polymer 26.6 22 0.00047 26.8 0.0 50 23-75 654-708 (900)
271 smart00355 ZnF_C2H2 zinc finge 26.5 40 0.00087 12.2 0.8 8 27-34 3-10 (26)
272 COG1655 Uncharacterized protei 26.1 51 0.0011 21.1 1.5 11 60-70 20-30 (267)
273 PF03918 CcmH: Cytochrome C bi 26.1 33 0.00072 20.0 0.7 22 11-32 27-48 (148)
274 KOG4080|consensus 26.1 70 0.0015 19.3 2.1 28 22-56 91-118 (176)
275 PF08882 Acetone_carb_G: Aceto 25.7 29 0.00063 19.5 0.4 12 38-49 25-36 (112)
276 PF05810 NinF: NinF protein; 25.1 72 0.0016 15.7 1.7 33 18-56 12-44 (58)
277 KOG0314|consensus 24.9 15 0.00033 25.5 -1.0 43 15-57 210-255 (448)
278 PF14255 Cys_rich_CPXG: Cystei 24.7 37 0.00081 16.3 0.6 9 61-69 2-10 (52)
279 TIGR03826 YvyF flagellar opero 24.5 37 0.00079 19.7 0.7 23 25-52 4-26 (137)
280 KOG1842|consensus 24.4 37 0.0008 23.8 0.8 31 23-53 179-213 (505)
281 PF14169 YdjO: Cold-inducible 24.3 67 0.0015 15.9 1.5 10 60-69 40-49 (59)
282 smart00531 TFIIE Transcription 23.8 43 0.00094 19.3 0.9 13 60-72 124-136 (147)
283 KOG4021|consensus 23.6 36 0.00077 21.2 0.5 12 60-71 109-120 (239)
284 PF10764 Gin: Inhibitor of sig 23.5 51 0.0011 15.3 1.0 31 26-57 1-31 (46)
285 PF11781 RRN7: RNA polymerase 23.3 37 0.0008 14.9 0.4 10 25-34 9-18 (36)
286 PTZ00303 phosphatidylinositol 23.2 41 0.00089 25.6 0.9 30 25-54 461-499 (1374)
287 PF10601 zf-LITAF-like: LITAF- 23.1 17 0.00037 18.3 -0.8 15 23-37 6-20 (73)
288 KOG3608|consensus 22.9 65 0.0014 22.1 1.7 48 23-70 206-274 (467)
289 PF13771 zf-HC5HC2H: PHD-like 22.5 1.3E+02 0.0027 15.4 2.6 33 21-53 33-68 (90)
290 KOG3993|consensus 22.5 6.8 0.00015 27.1 -2.9 42 19-70 262-306 (500)
291 PF13832 zf-HC5HC2H_2: PHD-zin 22.3 87 0.0019 16.8 1.9 29 23-53 54-87 (110)
292 PF14577 SEO_C: Sieve element 22.3 52 0.0011 20.9 1.1 23 22-44 212-234 (235)
293 PRK06393 rpoE DNA-directed RNA 22.2 69 0.0015 16.1 1.3 16 59-74 17-32 (64)
294 KOG1313|consensus 21.8 12 0.00027 24.4 -1.7 9 44-52 102-110 (309)
295 PRK09678 DNA-binding transcrip 21.6 33 0.00072 17.6 0.1 7 40-46 33-39 (72)
296 PF08209 Sgf11: Sgf11 (transcr 21.1 27 0.00058 15.1 -0.2 11 61-71 6-16 (33)
297 smart00834 CxxC_CXXC_SSSS Puta 21.1 48 0.001 14.2 0.6 10 59-68 26-35 (41)
298 PF04981 NMD3: NMD3 family ; 20.8 73 0.0016 19.9 1.6 43 27-74 1-50 (236)
299 PF01412 ArfGap: Putative GTPa 20.8 1.7E+02 0.0036 16.1 3.0 38 17-54 6-43 (116)
300 PF12088 DUF3565: Protein of u 20.8 48 0.001 16.5 0.6 11 38-48 13-23 (61)
301 PF13834 DUF4193: Domain of un 20.8 17 0.00038 19.9 -1.1 12 23-34 69-80 (99)
302 PF12907 zf-met2: Zinc-binding 20.6 19 0.0004 16.4 -0.8 10 25-34 2-11 (40)
303 COG1545 Predicted nucleic-acid 20.5 42 0.00092 19.3 0.4 10 60-69 44-53 (140)
304 PF09862 DUF2089: Protein of u 20.4 43 0.00093 18.8 0.4 9 27-35 1-9 (113)
305 PHA02768 hypothetical protein; 20.4 47 0.001 16.2 0.5 37 24-71 5-43 (55)
No 1
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=99.68 E-value=4e-17 Score=97.41 Aligned_cols=61 Identities=26% Similarity=0.651 Sum_probs=52.4
Q ss_pred HhcCCcccCccCccCccCceecCCCChhHHHHHHHHHhh---------------CCCCCCCCCcCcCcCCceeeec
Q psy10800 19 REYKETLTCPSCKVKRKDAVLTKCFHVFCWDCLRTRYET---------------RQRKCPKCNAAFGANDYHRLYL 79 (81)
Q Consensus 19 ~~~~~~~~C~iC~~~~~~~~~~~CgH~fc~~Ci~~~~~~---------------~~~~CP~Cr~~~~~~~~~~~~~ 79 (81)
......+.|+||++.+.+|++++|||.||+.||.+|+.. ....||.||..+...++.++|-
T Consensus 13 ~~~~~~~~CpICld~~~dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~LvPiyg 88 (193)
T PLN03208 13 VDSGGDFDCNICLDQVRDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEATLVPIYG 88 (193)
T ss_pred ccCCCccCCccCCCcCCCcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhcEEEeec
Confidence 344567999999999999999999999999999999853 1246999999999999998874
No 2
>KOG0978|consensus
Probab=99.67 E-value=4.1e-17 Score=111.53 Aligned_cols=77 Identities=65% Similarity=1.142 Sum_probs=71.5
Q ss_pred cccccCCchHHHHHHHHhcCCcccCccCccCccCceecCCCChhHHHHHHHHHhhCCCCCCCCCcCcCcCCceeeec
Q psy10800 3 KIEQAGTLDEVMLEEIREYKETLTCPSCKVKRKDAVLTKCFHVFCWDCLRTRYETRQRKCPKCNAAFGANDYHRLYL 79 (81)
Q Consensus 3 k~~~~~~~~~~~~~~~~~~~~~~~C~iC~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~~~~~ 79 (81)
+.+.++..++.+.+++..++..+.||+|...+.+.+++.|||.||..|+...+..+.++||.|...|+.+|+++||+
T Consensus 622 ~~~~~~s~d~~L~EElk~yK~~LkCs~Cn~R~Kd~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganDv~~I~l 698 (698)
T KOG0978|consen 622 KEESGASADEVLAEELKEYKELLKCSVCNTRWKDAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGANDVHRIHL 698 (698)
T ss_pred cccccccccHHHHHHHHHHHhceeCCCccCchhhHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCcccccccCC
Confidence 44555667899999999999999999999999999999999999999999999999999999999999999999985
No 3
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=99.64 E-value=1.3e-16 Score=74.69 Aligned_cols=39 Identities=38% Similarity=0.886 Sum_probs=31.8
Q ss_pred CccCccCccCceecCCCChhHHHHHHHHHhhCCC---CCCCC
Q psy10800 27 CPSCKVKRKDAVLTKCFHVFCWDCLRTRYETRQR---KCPKC 65 (81)
Q Consensus 27 C~iC~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~---~CP~C 65 (81)
||||+++|.+|+.++|||+||..||.++++.... .||.|
T Consensus 1 CpiC~~~~~~Pv~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDLFKDPVSLPCGHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB-SSEEE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCccchhhCCccccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 8999999999999999999999999999986543 48876
No 4
>KOG0320|consensus
Probab=99.62 E-value=4.4e-16 Score=91.47 Aligned_cols=56 Identities=38% Similarity=0.883 Sum_probs=49.8
Q ss_pred CcccCccCccCccC--ceecCCCChhHHHHHHHHHhhCCCCCCCCCcCcCcCCceeeec
Q psy10800 23 ETLTCPSCKVKRKD--AVLTKCFHVFCWDCLRTRYETRQRKCPKCNAAFGANDYHRLYL 79 (81)
Q Consensus 23 ~~~~C~iC~~~~~~--~~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~~~~~ 79 (81)
..+.||||++.+.+ |+.++|||+||..||++.++ ....||.|++.+..+.+.+||+
T Consensus 130 ~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk-~~~~CP~C~kkIt~k~~~rI~L 187 (187)
T KOG0320|consen 130 GTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALK-NTNKCPTCRKKITHKQFHRIYL 187 (187)
T ss_pred cccCCCceecchhhccccccccchhHHHHHHHHHHH-hCCCCCCcccccchhhheeccC
Confidence 35899999998865 46789999999999999999 4588999999999999999986
No 5
>KOG0823|consensus
Probab=99.59 E-value=8e-16 Score=93.51 Aligned_cols=58 Identities=36% Similarity=0.748 Sum_probs=52.1
Q ss_pred CCcccCccCccCccCceecCCCChhHHHHHHHHHhhCCC--CCCCCCcCcCcCCceeeec
Q psy10800 22 KETLTCPSCKVKRKDAVLTKCFHVFCWDCLRTRYETRQR--KCPKCNAAFGANDYHRLYL 79 (81)
Q Consensus 22 ~~~~~C~iC~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~--~CP~Cr~~~~~~~~~~~~~ 79 (81)
...+.|.||++.-++||++.|||.||+.||.+|+..... .||+|+..+....+.+||=
T Consensus 45 ~~~FdCNICLd~akdPVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~vvPlYG 104 (230)
T KOG0823|consen 45 GGFFDCNICLDLAKDPVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDTVVPLYG 104 (230)
T ss_pred CCceeeeeeccccCCCEEeecccceehHHHHHHHhhcCCCeeCCccccccccceEEeeec
Confidence 447999999999999999999999999999999987643 3899999999999999873
No 6
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=99.54 E-value=1.2e-14 Score=73.10 Aligned_cols=53 Identities=13% Similarity=0.146 Sum_probs=47.5
Q ss_pred cccCccCccCccCceecCCCChhHHHHHHHHHhhCCCCCCCCCcCcCcCCceee
Q psy10800 24 TLTCPSCKVKRKDAVLTKCFHVFCWDCLRTRYETRQRKCPKCNAAFGANDYHRL 77 (81)
Q Consensus 24 ~~~C~iC~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~~~ 77 (81)
.+.||||.+.+.+|+.++|||+||..|+.+|+.. ...||.|+..+...++.++
T Consensus 1 ~~~Cpi~~~~~~~Pv~~~~G~v~~~~~i~~~~~~-~~~cP~~~~~~~~~~l~~~ 53 (63)
T smart00504 1 EFLCPISLEVMKDPVILPSGQTYERRAIEKWLLS-HGTDPVTGQPLTHEDLIPN 53 (63)
T ss_pred CcCCcCCCCcCCCCEECCCCCEEeHHHHHHHHHH-CCCCCCCcCCCChhhceeC
Confidence 3689999999999999999999999999999986 5789999999987777654
No 7
>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=99.52 E-value=5.8e-15 Score=68.09 Aligned_cols=38 Identities=42% Similarity=1.010 Sum_probs=33.2
Q ss_pred CccCccCccCc-eecCCCChhHHHHHHHHHhhCCCCCCCC
Q psy10800 27 CPSCKVKRKDA-VLTKCFHVFCWDCLRTRYETRQRKCPKC 65 (81)
Q Consensus 27 C~iC~~~~~~~-~~~~CgH~fc~~Ci~~~~~~~~~~CP~C 65 (81)
|+||++.+.+| +.++|||+||..|+.+|+.. ...||.|
T Consensus 1 C~iC~~~~~~~~~~~~CGH~fC~~C~~~~~~~-~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDELRDPVVVTPCGHSFCKECIEKYLEK-NPKCPVC 39 (39)
T ss_dssp ETTTTSB-SSEEEECTTSEEEEHHHHHHHHHC-TSB-TTT
T ss_pred CCCCCCcccCcCEECCCCCchhHHHHHHHHHC-cCCCcCC
Confidence 79999999999 68899999999999999996 6789987
No 8
>KOG0317|consensus
Probab=99.50 E-value=1.2e-14 Score=90.73 Aligned_cols=56 Identities=29% Similarity=0.723 Sum_probs=49.2
Q ss_pred CCcccCccCccCccCceecCCCChhHHHHHHHHHhhCCCCCCCCCcCcCcCCceeee
Q psy10800 22 KETLTCPSCKVKRKDAVLTKCFHVFCWDCLRTRYETRQRKCPKCNAAFGANDYHRLY 78 (81)
Q Consensus 22 ~~~~~C~iC~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~~~~ 78 (81)
+....|.+|++...+|..++|||.||+.||.+|.... ..||.||..+.++++.-++
T Consensus 237 ~a~~kC~LCLe~~~~pSaTpCGHiFCWsCI~~w~~ek-~eCPlCR~~~~pskvi~Lr 292 (293)
T KOG0317|consen 237 EATRKCSLCLENRSNPSATPCGHIFCWSCILEWCSEK-AECPLCREKFQPSKVICLR 292 (293)
T ss_pred CCCCceEEEecCCCCCCcCcCcchHHHHHHHHHHccc-cCCCcccccCCCcceeeec
Confidence 3468999999999999999999999999999999954 6699999999988876543
No 9
>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=99.47 E-value=2.9e-14 Score=68.99 Aligned_cols=46 Identities=35% Similarity=0.835 Sum_probs=40.2
Q ss_pred cccCccCccCccCceecCCCCh-hHHHHHHHHHhhCCCCCCCCCcCcC
Q psy10800 24 TLTCPSCKVKRKDAVLTKCFHV-FCWDCLRTRYETRQRKCPKCNAAFG 70 (81)
Q Consensus 24 ~~~C~iC~~~~~~~~~~~CgH~-fc~~Ci~~~~~~~~~~CP~Cr~~~~ 70 (81)
+..|+||++...+.+.++|||. ||..|+.+|+. ....||+||+++.
T Consensus 2 ~~~C~iC~~~~~~~~~~pCgH~~~C~~C~~~~~~-~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFENPRDVVLLPCGHLCFCEECAERLLK-RKKKCPICRQPIE 48 (50)
T ss_dssp HSB-TTTSSSBSSEEEETTCEEEEEHHHHHHHHH-TTSBBTTTTBB-S
T ss_pred cCCCccCCccCCceEEeCCCChHHHHHHhHHhcc-cCCCCCcCChhhc
Confidence 5789999999999999999999 99999999998 5578999999875
No 10
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.44 E-value=7.6e-14 Score=91.30 Aligned_cols=58 Identities=33% Similarity=0.596 Sum_probs=50.0
Q ss_pred HHhcCCcccCccCccCccCceecCCCChhHHHHHHHHHhhCCCCCCCCCcCcCcCCcee
Q psy10800 18 IREYKETLTCPSCKVKRKDAVLTKCFHVFCWDCLRTRYETRQRKCPKCNAAFGANDYHR 76 (81)
Q Consensus 18 ~~~~~~~~~C~iC~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~~ 76 (81)
...++..+.|+||.+.+.+|++++|||.||..|+..|+.. ...||.|+..+....+..
T Consensus 20 l~~Le~~l~C~IC~d~~~~PvitpCgH~FCs~CI~~~l~~-~~~CP~Cr~~~~~~~Lr~ 77 (397)
T TIGR00599 20 LYPLDTSLRCHICKDFFDVPVLTSCSHTFCSLCIRRCLSN-QPKCPLCRAEDQESKLRS 77 (397)
T ss_pred ccccccccCCCcCchhhhCccCCCCCCchhHHHHHHHHhC-CCCCCCCCCccccccCcc
Confidence 4567778999999999999999999999999999999985 467999999887655543
No 11
>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=99.43 E-value=2.7e-14 Score=67.36 Aligned_cols=40 Identities=30% Similarity=0.753 Sum_probs=33.9
Q ss_pred cCccCccCcc---CceecCCCChhHHHHHHHHHhhCCCCCCCCC
Q psy10800 26 TCPSCKVKRK---DAVLTKCFHVFCWDCLRTRYETRQRKCPKCN 66 (81)
Q Consensus 26 ~C~iC~~~~~---~~~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr 66 (81)
.|+||++.+. ..+.++|||.||.+|+.+|+... .+||+||
T Consensus 2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~-~~CP~CR 44 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRN-NSCPVCR 44 (44)
T ss_dssp CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHS-SB-TTTH
T ss_pred CCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhC-CcCCccC
Confidence 6999999884 34788999999999999999964 6899996
No 12
>PHA02929 N1R/p28-like protein; Provisional
Probab=99.42 E-value=2.7e-13 Score=83.72 Aligned_cols=49 Identities=31% Similarity=0.777 Sum_probs=40.8
Q ss_pred CCcccCccCccCccCc--------eecCCCChhHHHHHHHHHhhCCCCCCCCCcCcCc
Q psy10800 22 KETLTCPSCKVKRKDA--------VLTKCFHVFCWDCLRTRYETRQRKCPKCNAAFGA 71 (81)
Q Consensus 22 ~~~~~C~iC~~~~~~~--------~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~~ 71 (81)
..+.+|+||++.+.++ ++++|||.||..|+.+|+. ....||+||..+..
T Consensus 172 ~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~-~~~tCPlCR~~~~~ 228 (238)
T PHA02929 172 SKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKK-EKNTCPVCRTPFIS 228 (238)
T ss_pred CCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHh-cCCCCCCCCCEeeE
Confidence 4578999999976542 5668999999999999998 45789999998764
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=99.41 E-value=1.3e-13 Score=63.99 Aligned_cols=39 Identities=49% Similarity=1.010 Sum_probs=35.0
Q ss_pred CccCccCccCce-ecCCCChhHHHHHHHHHh-hCCCCCCCC
Q psy10800 27 CPSCKVKRKDAV-LTKCFHVFCWDCLRTRYE-TRQRKCPKC 65 (81)
Q Consensus 27 C~iC~~~~~~~~-~~~CgH~fc~~Ci~~~~~-~~~~~CP~C 65 (81)
|+||.+.+.+++ +++|||.||..|+.+|+. .....||.|
T Consensus 1 C~iC~~~~~~~~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEPFEDPVILLPCGHSFCRDCLRKWLENSGSVKCPLC 41 (41)
T ss_dssp ETTTSSBCSSEEEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred CCcCCccccCCCEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence 799999999998 899999999999999999 445669987
No 14
>KOG0287|consensus
Probab=99.39 E-value=6.2e-14 Score=89.58 Aligned_cols=61 Identities=23% Similarity=0.528 Sum_probs=53.1
Q ss_pred HHHhcCCcccCccCccCccCceecCCCChhHHHHHHHHHhhCCCCCCCCCcCcCcCCceeee
Q psy10800 17 EIREYKETLTCPSCKVKRKDAVLTKCFHVFCWDCLRTRYETRQRKCPKCNAAFGANDYHRLY 78 (81)
Q Consensus 17 ~~~~~~~~~~C~iC~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~~~~ 78 (81)
....+...++|-||+++|..|++++|+|+||.-||..++.. ...||.|+..+...+++..+
T Consensus 16 slk~lD~lLRC~IC~eyf~ip~itpCsHtfCSlCIR~~L~~-~p~CP~C~~~~~Es~Lr~n~ 76 (442)
T KOG0287|consen 16 SLKTLDDLLRCGICFEYFNIPMITPCSHTFCSLCIRKFLSY-KPQCPTCCVTVTESDLRNNR 76 (442)
T ss_pred hhhhhHHHHHHhHHHHHhcCceeccccchHHHHHHHHHhcc-CCCCCceecccchhhhhhhh
Confidence 34556778999999999999999999999999999999984 47799999999988877654
No 15
>KOG2164|consensus
Probab=99.38 E-value=3.7e-13 Score=89.38 Aligned_cols=57 Identities=25% Similarity=0.638 Sum_probs=51.4
Q ss_pred cccCccCccCccCceecCCCChhHHHHHHHHHhhCC----CCCCCCCcCcCcCCceeeecC
Q psy10800 24 TLTCPSCKVKRKDAVLTKCFHVFCWDCLRTRYETRQ----RKCPKCNAAFGANDYHRLYLG 80 (81)
Q Consensus 24 ~~~C~iC~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~----~~CP~Cr~~~~~~~~~~~~~~ 80 (81)
+..||||++....|+.+.|||.||..||..+|.... ..||+|+..+..+++..++..
T Consensus 186 ~~~CPICL~~~~~p~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kdl~pv~~e 246 (513)
T KOG2164|consen 186 DMQCPICLEPPSVPVRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKDLLPVFIE 246 (513)
T ss_pred CCcCCcccCCCCcccccccCceeeHHHHHHHHhhhcccCCccCCchhhhccccceeeeeec
Confidence 789999999999999999999999999999998652 459999999999999988764
No 16
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=99.36 E-value=1.1e-12 Score=61.25 Aligned_cols=44 Identities=30% Similarity=0.845 Sum_probs=37.0
Q ss_pred cCccCccCccCceec-CCCChhHHHHHHHHHhhCCCCCCCCCcCc
Q psy10800 26 TCPSCKVKRKDAVLT-KCFHVFCWDCLRTRYETRQRKCPKCNAAF 69 (81)
Q Consensus 26 ~C~iC~~~~~~~~~~-~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~ 69 (81)
.|+||.+.+..++.+ +|||.||..|+..|+......||.|+..+
T Consensus 1 ~C~iC~~~~~~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~~ 45 (45)
T cd00162 1 ECPICLEEFREPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45 (45)
T ss_pred CCCcCchhhhCceEecCCCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence 489999998777555 59999999999999997567799998753
No 17
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=99.35 E-value=1.4e-12 Score=61.52 Aligned_cols=41 Identities=37% Similarity=0.805 Sum_probs=34.4
Q ss_pred cCccCccCc---cCceecCCCChhHHHHHHHHHhhCCCCCCCCCc
Q psy10800 26 TCPSCKVKR---KDAVLTKCFHVFCWDCLRTRYETRQRKCPKCNA 67 (81)
Q Consensus 26 ~C~iC~~~~---~~~~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~ 67 (81)
.|++|.+.+ ..+++++|||+||..|+..+. .....||+|++
T Consensus 1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~-~~~~~CP~C~k 44 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLK-GKSVKCPICRK 44 (44)
T ss_pred CCcCcCccccCCCCeEEcccCCHHHHHHHHhhc-CCCCCCcCCCC
Confidence 489999988 346889999999999999877 34567999975
No 18
>PHA02926 zinc finger-like protein; Provisional
Probab=99.35 E-value=2.2e-12 Score=78.49 Aligned_cols=54 Identities=26% Similarity=0.639 Sum_probs=41.8
Q ss_pred HHhcCCcccCccCccCccC---------ceecCCCChhHHHHHHHHHhhC-----CCCCCCCCcCcCc
Q psy10800 18 IREYKETLTCPSCKVKRKD---------AVLTKCFHVFCWDCLRTRYETR-----QRKCPKCNAAFGA 71 (81)
Q Consensus 18 ~~~~~~~~~C~iC~~~~~~---------~~~~~CgH~fc~~Ci~~~~~~~-----~~~CP~Cr~~~~~ 71 (81)
.-....+.+|+||++...+ +++.+|+|.||..|+..|.... ...||+||..+..
T Consensus 164 ~~~~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~ 231 (242)
T PHA02926 164 VYRVSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFRN 231 (242)
T ss_pred HHhccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceeee
Confidence 3345567999999987532 3566999999999999999853 2459999998764
No 19
>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=99.34 E-value=8.2e-13 Score=68.49 Aligned_cols=55 Identities=15% Similarity=0.208 Sum_probs=44.7
Q ss_pred CcccCccCccCccCceecCCCChhHHHHHHHHHhhCCCCCCCCCcCcCcCCceee
Q psy10800 23 ETLTCPSCKVKRKDAVLTKCFHVFCWDCLRTRYETRQRKCPKCNAAFGANDYHRL 77 (81)
Q Consensus 23 ~~~~C~iC~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~~~ 77 (81)
+.+.|||+.+++.+|+++++||+|...+|.+|+......||.++..+...++...
T Consensus 3 ~~f~CpIt~~lM~dPVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~~l~pn 57 (73)
T PF04564_consen 3 DEFLCPITGELMRDPVILPSGHTYERSAIERWLEQNGGTDPFTRQPLSESDLIPN 57 (73)
T ss_dssp GGGB-TTTSSB-SSEEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SGGGSEE-
T ss_pred cccCCcCcCcHhhCceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCcccceEC
Confidence 5789999999999999999999999999999999767889999999988777654
No 20
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=99.31 E-value=9.3e-13 Score=61.73 Aligned_cols=36 Identities=42% Similarity=0.915 Sum_probs=22.6
Q ss_pred CccCccCccC----ceecCCCChhHHHHHHHHHhhC---CCCCC
Q psy10800 27 CPSCKVKRKD----AVLTKCFHVFCWDCLRTRYETR---QRKCP 63 (81)
Q Consensus 27 C~iC~~~~~~----~~~~~CgH~fc~~Ci~~~~~~~---~~~CP 63 (81)
||||.+ +.+ |++|+|||+||.+|+.+++..+ ..+||
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 777 8999999999999999999854 23465
No 21
>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=99.30 E-value=5.7e-12 Score=56.96 Aligned_cols=39 Identities=38% Similarity=0.972 Sum_probs=34.9
Q ss_pred CccCccCccCceecCCCChhHHHHHHHHHhhCCCCCCCC
Q psy10800 27 CPSCKVKRKDAVLTKCFHVFCWDCLRTRYETRQRKCPKC 65 (81)
Q Consensus 27 C~iC~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~~CP~C 65 (81)
|+||++....++.++|||.||..|+..|+......||.|
T Consensus 1 C~iC~~~~~~~~~~~C~H~~c~~C~~~~~~~~~~~CP~C 39 (39)
T smart00184 1 CPICLEELKDPVVLPCGHTFCRSCIRKWLKSGNNTCPIC 39 (39)
T ss_pred CCcCccCCCCcEEecCCChHHHHHHHHHHHhCcCCCCCC
Confidence 789999988899999999999999999998555679986
No 22
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=99.23 E-value=7.2e-13 Score=66.33 Aligned_cols=54 Identities=30% Similarity=0.622 Sum_probs=29.9
Q ss_pred hcCCcccCccCccCccCcee-cCCCChhHHHHHHHHHhhCCCCCCCCCcCcCcCCcee
Q psy10800 20 EYKETLTCPSCKVKRKDAVL-TKCFHVFCWDCLRTRYETRQRKCPKCNAAFGANDYHR 76 (81)
Q Consensus 20 ~~~~~~~C~iC~~~~~~~~~-~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~~ 76 (81)
.+++.+.|++|.+.+++|+. ..|.|.||..|+...+. ..||.|+.+....|++-
T Consensus 3 ~le~lLrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~---~~CPvC~~Paw~qD~~~ 57 (65)
T PF14835_consen 3 RLEELLRCSICFDILKEPVCLGGCEHIFCSSCIRDCIG---SECPVCHTPAWIQDIQI 57 (65)
T ss_dssp HHHHTTS-SSS-S--SS-B---SSS--B-TTTGGGGTT---TB-SSS--B-S-SS---
T ss_pred HHHHhcCCcHHHHHhcCCceeccCccHHHHHHhHHhcC---CCCCCcCChHHHHHHHh
Confidence 45667899999999999975 59999999999987554 45999999998888764
No 23
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=99.16 E-value=1.2e-11 Score=77.99 Aligned_cols=55 Identities=25% Similarity=0.539 Sum_probs=46.9
Q ss_pred HhcCCcccCccCccCccCceecCCCChhHHHHHHHHHhhCCCCCCCCCcCcCcCCc
Q psy10800 19 REYKETLTCPSCKVKRKDAVLTKCFHVFCWDCLRTRYETRQRKCPKCNAAFGANDY 74 (81)
Q Consensus 19 ~~~~~~~~C~iC~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~~~~~ 74 (81)
..+...+.|-||.+.+..|+.++|||+||.-||.+++... ..||.||.......+
T Consensus 20 ~~LDs~lrC~IC~~~i~ip~~TtCgHtFCslCIR~hL~~q-p~CP~Cr~~~~esrl 74 (391)
T COG5432 20 KGLDSMLRCRICDCRISIPCETTCGHTFCSLCIRRHLGTQ-PFCPVCREDPCESRL 74 (391)
T ss_pred hcchhHHHhhhhhheeecceecccccchhHHHHHHHhcCC-CCCccccccHHhhhc
Confidence 4455678999999999999999999999999999999954 669999988755433
No 24
>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=99.15 E-value=5.2e-11 Score=75.75 Aligned_cols=57 Identities=21% Similarity=0.668 Sum_probs=44.1
Q ss_pred cccCccCccC-ccCc----eecCCCChhHHHHHHHHHhhCCCCCCCCCcCcCcCCceeeecC
Q psy10800 24 TLTCPSCKVK-RKDA----VLTKCFHVFCWDCLRTRYETRQRKCPKCNAAFGANDYHRLYLG 80 (81)
Q Consensus 24 ~~~C~iC~~~-~~~~----~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~~~~~~ 80 (81)
+..||+|... +.+| .+.+|||.||..|+..+|..+...||.|+..+...++....+.
T Consensus 3 ~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk~~fr~q~F~ 64 (309)
T TIGR00570 3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLRKNNFRVQLFE 64 (309)
T ss_pred CCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCccchhhccccccc
Confidence 4689999973 3344 2227999999999999987666789999999988887655443
No 25
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.15 E-value=2.9e-11 Score=75.03 Aligned_cols=52 Identities=25% Similarity=0.513 Sum_probs=44.4
Q ss_pred CcccCccCccCccCceecCCCChhHHHHHHH-HHhhCCCCCCCCCcCcCcCCc
Q psy10800 23 ETLTCPSCKVKRKDAVLTKCFHVFCWDCLRT-RYETRQRKCPKCNAAFGANDY 74 (81)
Q Consensus 23 ~~~~C~iC~~~~~~~~~~~CgH~fc~~Ci~~-~~~~~~~~CP~Cr~~~~~~~~ 74 (81)
.++.|+||++....|..++|||.||..||.. |-....-.||.||+....+.+
T Consensus 214 ~d~kC~lC~e~~~~ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk~v 266 (271)
T COG5574 214 ADYKCFLCLEEPEVPSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVYPKKV 266 (271)
T ss_pred cccceeeeecccCCcccccccchhhHHHHHHHHHhhccccCchhhhhccchhh
Confidence 4789999999999999999999999999998 666444459999998876655
No 26
>KOG2177|consensus
Probab=99.09 E-value=6.3e-11 Score=73.63 Aligned_cols=49 Identities=37% Similarity=0.809 Sum_probs=43.5
Q ss_pred HHhcCCcccCccCccCccCceecCCCChhHHHHHHHHHhhCCCCCCCCCc
Q psy10800 18 IREYKETLTCPSCKVKRKDAVLTKCFHVFCWDCLRTRYETRQRKCPKCNA 67 (81)
Q Consensus 18 ~~~~~~~~~C~iC~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~ 67 (81)
...+.+.+.|+||++.|..|.+++|||+||..|+..++. ....||.||.
T Consensus 7 ~~~~~~~~~C~iC~~~~~~p~~l~C~H~~c~~C~~~~~~-~~~~Cp~cr~ 55 (386)
T KOG2177|consen 7 LEVLQEELTCPICLEYFREPVLLPCGHNFCRACLTRSWE-GPLSCPVCRP 55 (386)
T ss_pred hhhccccccChhhHHHhhcCccccccchHhHHHHHHhcC-CCcCCcccCC
Confidence 455678899999999999999999999999999999988 5567999993
No 27
>KOG4628|consensus
Probab=99.04 E-value=1.2e-10 Score=75.20 Aligned_cols=47 Identities=21% Similarity=0.523 Sum_probs=40.5
Q ss_pred ccCccCccCccCc---eecCCCChhHHHHHHHHHhhCCCCCCCCCcCcCc
Q psy10800 25 LTCPSCKVKRKDA---VLTKCFHVFCWDCLRTRYETRQRKCPKCNAAFGA 71 (81)
Q Consensus 25 ~~C~iC~~~~~~~---~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~~ 71 (81)
..|.||+|.|... .+|+|+|.|+..||..|+.+....||+|+..+..
T Consensus 230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~di~~ 279 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRDIRT 279 (348)
T ss_pred ceEEEeecccccCCeeeEecCCCchhhccchhhHhhcCccCCCCCCcCCC
Confidence 4999999999875 6789999999999999999764559999987654
No 28
>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=99.04 E-value=1.2e-10 Score=60.33 Aligned_cols=40 Identities=28% Similarity=0.796 Sum_probs=31.7
Q ss_pred cCccCccCccC------------c-eecCCCChhHHHHHHHHHhhCCCCCCCCC
Q psy10800 26 TCPSCKVKRKD------------A-VLTKCFHVFCWDCLRTRYETRQRKCPKCN 66 (81)
Q Consensus 26 ~C~iC~~~~~~------------~-~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr 66 (81)
.|+||++.+.+ + +..+|||.|+..||.+|+... ..||+||
T Consensus 21 ~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~-~~CP~CR 73 (73)
T PF12678_consen 21 NCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQN-NTCPLCR 73 (73)
T ss_dssp BETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTS-SB-TTSS
T ss_pred cccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcC-CcCCCCC
Confidence 49999998832 1 444899999999999999854 6899997
No 29
>KOG0311|consensus
Probab=98.95 E-value=6.8e-11 Score=75.96 Aligned_cols=58 Identities=24% Similarity=0.745 Sum_probs=49.5
Q ss_pred HHHHHHhcCCcccCccCccCccCceec-CCCChhHHHHHHHHHhhCCCCCCCCCcCcCc
Q psy10800 14 MLEEIREYKETLTCPSCKVKRKDAVLT-KCFHVFCWDCLRTRYETRQRKCPKCNAAFGA 71 (81)
Q Consensus 14 ~~~~~~~~~~~~~C~iC~~~~~~~~~~-~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~~ 71 (81)
.......+..++.|+||+.+++..+.+ .|+|.||..||...+...+..||.||+.+..
T Consensus 33 i~~~l~~~~~~v~c~icl~llk~tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~S 91 (381)
T KOG0311|consen 33 IMVDLAMFDIQVICPICLSLLKKTMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVS 91 (381)
T ss_pred heecHHHhhhhhccHHHHHHHHhhcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhccc
Confidence 334456677789999999999988766 8999999999999999888899999988754
No 30
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.91 E-value=1.4e-09 Score=69.06 Aligned_cols=54 Identities=22% Similarity=0.428 Sum_probs=44.4
Q ss_pred HHhcCCcccCccCccCccCc---eecCCCChhHHHHHHHHHhhCCCCCCCCCcCcCc
Q psy10800 18 IREYKETLTCPSCKVKRKDA---VLTKCFHVFCWDCLRTRYETRQRKCPKCNAAFGA 71 (81)
Q Consensus 18 ~~~~~~~~~C~iC~~~~~~~---~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~~ 71 (81)
+..-..+.+|.||++.+... +.+||.|.|+..|+.+|+..-...||.||..+++
T Consensus 317 ~~ea~~GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iPP 373 (374)
T COG5540 317 AVEADKGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIPP 373 (374)
T ss_pred HHhcCCCceEEEEhhhhcccceEEEeccCceechhHHHHHHhhhcccCCccCCCCCC
Confidence 33444578999999877543 7889999999999999999666889999998764
No 31
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=98.90 E-value=2.2e-09 Score=56.76 Aligned_cols=48 Identities=27% Similarity=0.630 Sum_probs=35.6
Q ss_pred cccCccCccCcc-----------C-c-eecCCCChhHHHHHHHHHhhC--CCCCCCCCcCcCc
Q psy10800 24 TLTCPSCKVKRK-----------D-A-VLTKCFHVFCWDCLRTRYETR--QRKCPKCNAAFGA 71 (81)
Q Consensus 24 ~~~C~iC~~~~~-----------~-~-~~~~CgH~fc~~Ci~~~~~~~--~~~CP~Cr~~~~~ 71 (81)
+..|+||...|. + | +.-.|+|.|+..||.+|+... ...||+||+.+..
T Consensus 21 dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~~ 83 (85)
T PF12861_consen 21 DDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWKF 83 (85)
T ss_pred CCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeeee
Confidence 456666665553 2 2 344899999999999999964 3569999998753
No 32
>KOG0802|consensus
Probab=98.82 E-value=2e-09 Score=73.29 Aligned_cols=50 Identities=26% Similarity=0.537 Sum_probs=42.8
Q ss_pred CCcccCccCccCccC-----ceecCCCChhHHHHHHHHHhhCCCCCCCCCcCcCcC
Q psy10800 22 KETLTCPSCKVKRKD-----AVLTKCFHVFCWDCLRTRYETRQRKCPKCNAAFGAN 72 (81)
Q Consensus 22 ~~~~~C~iC~~~~~~-----~~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~~~ 72 (81)
.....|+||.+.+.. +..++|||.|+..|+..|++. ...||+||..+...
T Consensus 289 ~~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er-~qtCP~CR~~~~~~ 343 (543)
T KOG0802|consen 289 LSDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFER-QQTCPTCRTVLYDY 343 (543)
T ss_pred hcCCeeeeechhhccccccccceeecccchHHHHHHHHHHH-hCcCCcchhhhhcc
Confidence 346799999999887 789999999999999999995 58899999955433
No 33
>KOG0824|consensus
Probab=98.77 E-value=4.1e-09 Score=66.69 Aligned_cols=49 Identities=24% Similarity=0.680 Sum_probs=44.1
Q ss_pred cccCccCccCccCceecCCCChhHHHHHHHHHhhCCCCCCCCCcCcCcC
Q psy10800 24 TLTCPSCKVKRKDAVLTKCFHVFCWDCLRTRYETRQRKCPKCNAAFGAN 72 (81)
Q Consensus 24 ~~~C~iC~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~~~ 72 (81)
.-+|+||+.....|+.++|+|.||.-||+.....+...|++||.++...
T Consensus 7 ~~eC~IC~nt~n~Pv~l~C~HkFCyiCiKGsy~ndk~~CavCR~pids~ 55 (324)
T KOG0824|consen 7 KKECLICYNTGNCPVNLYCFHKFCYICIKGSYKNDKKTCAVCRFPIDST 55 (324)
T ss_pred CCcceeeeccCCcCccccccchhhhhhhcchhhcCCCCCceecCCCCcc
Confidence 4589999999999999999999999999988887778899999998754
No 34
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=98.76 E-value=6.2e-09 Score=67.76 Aligned_cols=48 Identities=27% Similarity=0.587 Sum_probs=39.7
Q ss_pred cCCcccCccCccCc-cC------------ceecCCCChhHHHHHHHHHhhCCCCCCCCCcCc
Q psy10800 21 YKETLTCPSCKVKR-KD------------AVLTKCFHVFCWDCLRTRYETRQRKCPKCNAAF 69 (81)
Q Consensus 21 ~~~~~~C~iC~~~~-~~------------~~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~ 69 (81)
-..+..|.||++.+ .. |..++|||.++..|++.|+. +...||+||.++
T Consensus 284 ~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~E-RqQTCPICr~p~ 344 (491)
T COG5243 284 TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLE-RQQTCPICRRPV 344 (491)
T ss_pred cCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHH-hccCCCcccCcc
Confidence 34578999999863 32 37889999999999999999 557899999984
No 35
>KOG4172|consensus
Probab=98.66 E-value=7e-09 Score=50.34 Aligned_cols=47 Identities=28% Similarity=0.594 Sum_probs=41.4
Q ss_pred cccCccCccCccCceecCCCCh-hHHHHHHHHHhhCCCCCCCCCcCcC
Q psy10800 24 TLTCPSCKVKRKDAVLTKCFHV-FCWDCLRTRYETRQRKCPKCNAAFG 70 (81)
Q Consensus 24 ~~~C~iC~~~~~~~~~~~CgH~-fc~~Ci~~~~~~~~~~CP~Cr~~~~ 70 (81)
.-+|.||.+...+.++..|||. .|..|-.+.++.....||+||+++.
T Consensus 7 ~dECTICye~pvdsVlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~ 54 (62)
T KOG4172|consen 7 SDECTICYEHPVDSVLYTCGHMCMCYACGLRLKKALHGCCPICRAPIK 54 (62)
T ss_pred ccceeeeccCcchHHHHHcchHHhHHHHHHHHHHccCCcCcchhhHHH
Confidence 4689999999999999999997 5999999998876678999999864
No 36
>KOG4159|consensus
Probab=98.61 E-value=1.7e-08 Score=66.56 Aligned_cols=52 Identities=27% Similarity=0.691 Sum_probs=45.1
Q ss_pred HhcCCcccCccCccCccCceecCCCChhHHHHHHHHHhhCCCCCCCCCcCcCc
Q psy10800 19 REYKETLTCPSCKVKRKDAVLTKCFHVFCWDCLRTRYETRQRKCPKCNAAFGA 71 (81)
Q Consensus 19 ~~~~~~~~C~iC~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~~ 71 (81)
..+..++.|.||...+..|+.++|||+||..||.+.+. ....||.||..+..
T Consensus 79 ~~~~sef~c~vc~~~l~~pv~tpcghs~c~~Cl~r~ld-~~~~cp~Cr~~l~e 130 (398)
T KOG4159|consen 79 EEIRSEFECCVCSRALYPPVVTPCGHSFCLECLDRSLD-QETECPLCRDELVE 130 (398)
T ss_pred ccccchhhhhhhHhhcCCCccccccccccHHHHHHHhc-cCCCCccccccccc
Confidence 34467899999999999999999999999999999777 44679999988764
No 37
>KOG2660|consensus
Probab=98.60 E-value=1.7e-08 Score=64.49 Aligned_cols=56 Identities=29% Similarity=0.701 Sum_probs=47.3
Q ss_pred HHHhcCCcccCccCccCccCc-eecCCCChhHHHHHHHHHhhCCCCCCCCCcCcCcCC
Q psy10800 17 EIREYKETLTCPSCKVKRKDA-VLTKCFHVFCWDCLRTRYETRQRKCPKCNAAFGAND 73 (81)
Q Consensus 17 ~~~~~~~~~~C~iC~~~~~~~-~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~~~~ 73 (81)
....+.....|.+|..++.++ .++.|-|+||.+||.+++.. ...||.|...+....
T Consensus 8 k~~~~n~~itC~LC~GYliDATTI~eCLHTFCkSCivk~l~~-~~~CP~C~i~ih~t~ 64 (331)
T KOG2660|consen 8 KLTELNPHITCRLCGGYLIDATTITECLHTFCKSCIVKYLEE-SKYCPTCDIVIHKTH 64 (331)
T ss_pred hhhhcccceehhhccceeecchhHHHHHHHHHHHHHHHHHHH-hccCCccceeccCcc
Confidence 355667789999999999998 45599999999999999996 577999998887653
No 38
>KOG4265|consensus
Probab=98.58 E-value=3.6e-08 Score=63.64 Aligned_cols=56 Identities=21% Similarity=0.593 Sum_probs=45.7
Q ss_pred cCCcccCccCccCccCceecCCCChh-HHHHHHHHHhhCCCCCCCCCcCcCcCCceeeec
Q psy10800 21 YKETLTCPSCKVKRKDAVLTKCFHVF-CWDCLRTRYETRQRKCPKCNAAFGANDYHRLYL 79 (81)
Q Consensus 21 ~~~~~~C~iC~~~~~~~~~~~CgH~f-c~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~~~~~ 79 (81)
-+...+|.||+...++.+++||.|.- |..|.+.+. -..+.||+||+.+.. +..++.
T Consensus 287 ~~~gkeCVIClse~rdt~vLPCRHLCLCs~Ca~~Lr-~q~n~CPICRqpi~~--ll~i~~ 343 (349)
T KOG4265|consen 287 SESGKECVICLSESRDTVVLPCRHLCLCSGCAKSLR-YQTNNCPICRQPIEE--LLEIYV 343 (349)
T ss_pred ccCCCeeEEEecCCcceEEecchhhehhHhHHHHHH-HhhcCCCccccchHh--hheecc
Confidence 35578999999999999999999974 999998755 355789999998765 555554
No 39
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=98.56 E-value=1.9e-08 Score=60.68 Aligned_cols=46 Identities=30% Similarity=0.670 Sum_probs=39.4
Q ss_pred cccCccCccCccCceecCCCChhHHHHHHHHHhhCCCCCCCCCcCcC
Q psy10800 24 TLTCPSCKVKRKDAVLTKCFHVFCWDCLRTRYETRQRKCPKCNAAFG 70 (81)
Q Consensus 24 ~~~C~iC~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~ 70 (81)
.+.|.||.+.+..|+.+.|||.||..|..+-.. ....|-+|.+...
T Consensus 196 PF~C~iCKkdy~spvvt~CGH~FC~~Cai~~y~-kg~~C~~Cgk~t~ 241 (259)
T COG5152 196 PFLCGICKKDYESPVVTECGHSFCSLCAIRKYQ-KGDECGVCGKATY 241 (259)
T ss_pred ceeehhchhhccchhhhhcchhHHHHHHHHHhc-cCCcceecchhhc
Confidence 578999999999999999999999999987666 4467999987643
No 40
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=98.42 E-value=9.8e-08 Score=60.88 Aligned_cols=43 Identities=35% Similarity=0.824 Sum_probs=39.1
Q ss_pred ccCccCccCccCceec-CCCChhHHHHHHHHHhhCCCCCCCCCc
Q psy10800 25 LTCPSCKVKRKDAVLT-KCFHVFCWDCLRTRYETRQRKCPKCNA 67 (81)
Q Consensus 25 ~~C~iC~~~~~~~~~~-~CgH~fc~~Ci~~~~~~~~~~CP~Cr~ 67 (81)
+.||+|..++++|+.+ -|||.||..||...+-...+.||.|..
T Consensus 275 LkCplc~~Llrnp~kT~cC~~~fc~eci~~al~dsDf~CpnC~r 318 (427)
T COG5222 275 LKCPLCHCLLRNPMKTPCCGHTFCDECIGTALLDSDFKCPNCSR 318 (427)
T ss_pred ccCcchhhhhhCcccCccccchHHHHHHhhhhhhccccCCCccc
Confidence 8999999999999988 579999999999988877889999954
No 41
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=98.41 E-value=1.1e-07 Score=46.97 Aligned_cols=44 Identities=25% Similarity=0.431 Sum_probs=30.0
Q ss_pred cCCcccCccCccCccCcee-cCCCChhHHHHHHHHHhh-CCCCCCC
Q psy10800 21 YKETLTCPSCKVKRKDAVL-TKCFHVFCWDCLRTRYET-RQRKCPK 64 (81)
Q Consensus 21 ~~~~~~C~iC~~~~~~~~~-~~CgH~fc~~Ci~~~~~~-~~~~CP~ 64 (81)
....+.|||.+..+.+|+. ..|||+|-...|..++.. ....||.
T Consensus 8 ~~~~~~CPiT~~~~~~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv 53 (57)
T PF11789_consen 8 GTISLKCPITLQPFEDPVKSKKCGHTFEKEAILQYIQRNGSKRCPV 53 (57)
T ss_dssp SB--SB-TTTSSB-SSEEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred cEeccCCCCcCChhhCCcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence 4457899999999999976 499999999999999943 2345998
No 42
>KOG0297|consensus
Probab=98.31 E-value=3.1e-07 Score=60.68 Aligned_cols=52 Identities=35% Similarity=0.762 Sum_probs=45.4
Q ss_pred cCCcccCccCccCccCcee-cCCCChhHHHHHHHHHhhCCCCCCCCCcCcCcCC
Q psy10800 21 YKETLTCPSCKVKRKDAVL-TKCFHVFCWDCLRTRYETRQRKCPKCNAAFGAND 73 (81)
Q Consensus 21 ~~~~~~C~iC~~~~~~~~~-~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~~~~ 73 (81)
+++++.|++|...+.+|+. +.|||.||..|+..|+.. ...||.|+..+....
T Consensus 18 ~~~~l~C~~C~~vl~~p~~~~~cgh~fC~~C~~~~~~~-~~~cp~~~~~~~~~~ 70 (391)
T KOG0297|consen 18 LDENLLCPICMSVLRDPVQTTTCGHRFCAGCLLESLSN-HQKCPVCRQELTQAE 70 (391)
T ss_pred CcccccCccccccccCCCCCCCCCCcccccccchhhcc-CcCCcccccccchhh
Confidence 6778999999999999988 499999999999999996 678999987765543
No 43
>KOG2879|consensus
Probab=98.28 E-value=7e-07 Score=56.16 Aligned_cols=49 Identities=24% Similarity=0.605 Sum_probs=39.9
Q ss_pred CCcccCccCccCccCceec-CCCChhHHHHHHHHHhhC-CCCCCCCCcCcC
Q psy10800 22 KETLTCPSCKVKRKDAVLT-KCFHVFCWDCLRTRYETR-QRKCPKCNAAFG 70 (81)
Q Consensus 22 ~~~~~C~iC~~~~~~~~~~-~CgH~fc~~Ci~~~~~~~-~~~CP~Cr~~~~ 70 (81)
..+.+||+|.+....|.+. +|||.||..|+....... ...||.|+....
T Consensus 237 t~~~~C~~Cg~~PtiP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~ 287 (298)
T KOG2879|consen 237 TSDTECPVCGEPPTIPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVE 287 (298)
T ss_pred cCCceeeccCCCCCCCeeeccccceeehhhhhhhhcchhhcccCccCCCCc
Confidence 3478999999999999665 699999999998766533 357999988765
No 44
>KOG1813|consensus
Probab=98.23 E-value=2.9e-07 Score=58.36 Aligned_cols=46 Identities=30% Similarity=0.608 Sum_probs=39.4
Q ss_pred cccCccCccCccCceecCCCChhHHHHHHHHHhhCCCCCCCCCcCcC
Q psy10800 24 TLTCPSCKVKRKDAVLTKCFHVFCWDCLRTRYETRQRKCPKCNAAFG 70 (81)
Q Consensus 24 ~~~C~iC~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~ 70 (81)
.+.|-||.+.|.+||.+.|||.||..|...-+. ....|.+|.+.+.
T Consensus 241 Pf~c~icr~~f~~pVvt~c~h~fc~~ca~~~~q-k~~~c~vC~~~t~ 286 (313)
T KOG1813|consen 241 PFKCFICRKYFYRPVVTKCGHYFCEVCALKPYQ-KGEKCYVCSQQTH 286 (313)
T ss_pred CccccccccccccchhhcCCceeehhhhccccc-cCCcceecccccc
Confidence 467999999999999999999999999887665 3466999987764
No 45
>KOG1039|consensus
Probab=98.17 E-value=1.8e-06 Score=56.19 Aligned_cols=50 Identities=26% Similarity=0.668 Sum_probs=39.0
Q ss_pred CCcccCccCccCccCce--------ecCCCChhHHHHHHHHHhhCC------CCCCCCCcCcCc
Q psy10800 22 KETLTCPSCKVKRKDAV--------LTKCFHVFCWDCLRTRYETRQ------RKCPKCNAAFGA 71 (81)
Q Consensus 22 ~~~~~C~iC~~~~~~~~--------~~~CgH~fc~~Ci~~~~~~~~------~~CP~Cr~~~~~ 71 (81)
..+..|.||++...+.. +.+|.|.||..|+..|-.... ..||.||.....
T Consensus 159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~~ 222 (344)
T KOG1039|consen 159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSSF 222 (344)
T ss_pred cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCcccc
Confidence 34789999998776543 357999999999999984333 569999987654
No 46
>KOG0804|consensus
Probab=98.16 E-value=7.1e-07 Score=59.36 Aligned_cols=50 Identities=26% Similarity=0.590 Sum_probs=40.0
Q ss_pred HHhcCCcccCccCccCccCc----eecCCCChhHHHHHHHHHhhCCCCCCCCCcCcC
Q psy10800 18 IREYKETLTCPSCKVKRKDA----VLTKCFHVFCWDCLRTRYETRQRKCPKCNAAFG 70 (81)
Q Consensus 18 ~~~~~~~~~C~iC~~~~~~~----~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~ 70 (81)
...+.+.-+||||++.+... +.+.|.|+|...|+..|+. .+||+||-...
T Consensus 169 ~~~~tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~~---~scpvcR~~q~ 222 (493)
T KOG0804|consen 169 PTGLTELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWWD---SSCPVCRYCQS 222 (493)
T ss_pred CCCcccCCCcchhHhhcCccccceeeeecccccchHHHhhccc---CcChhhhhhcC
Confidence 34456778999999988765 3458999999999999877 56999987654
No 47
>KOG0828|consensus
Probab=98.13 E-value=2e-06 Score=58.04 Aligned_cols=51 Identities=27% Similarity=0.607 Sum_probs=40.1
Q ss_pred cCCcccCccCccCcc-----------------CceecCCCChhHHHHHHHHHhhCCCCCCCCCcCcCc
Q psy10800 21 YKETLTCPSCKVKRK-----------------DAVLTKCFHVFCWDCLRTRYETRQRKCPKCNAAFGA 71 (81)
Q Consensus 21 ~~~~~~C~iC~~~~~-----------------~~~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~~ 71 (81)
.+....|+||+..+. +-+.+||.|.|+..|+++|+....-.||.||.+++.
T Consensus 568 ~~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLPp 635 (636)
T KOG0828|consen 568 VRRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLPP 635 (636)
T ss_pred hhccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCCCC
Confidence 345678999986441 135669999999999999999766679999998753
No 48
>KOG3039|consensus
Probab=98.12 E-value=4.8e-06 Score=51.95 Aligned_cols=57 Identities=18% Similarity=0.255 Sum_probs=48.2
Q ss_pred cCCcccCccCccCccCc----eecCCCChhHHHHHHHHHhhCCCCCCCCCcCcCcCCceeee
Q psy10800 21 YKETLTCPSCKVKRKDA----VLTKCFHVFCWDCLRTRYETRQRKCPKCNAAFGANDYHRLY 78 (81)
Q Consensus 21 ~~~~~~C~iC~~~~~~~----~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~~~~ 78 (81)
-...+.||+|.+.+.+. ++-+|||+++..|+++++.. ...||+|..++..+++..+.
T Consensus 218 ~s~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~-D~v~pv~d~plkdrdiI~Lq 278 (303)
T KOG3039|consen 218 ASKRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRK-DMVDPVTDKPLKDRDIIGLQ 278 (303)
T ss_pred hccceecccchhhhcCccceEEeccCCcEeeHHHHHHhccc-cccccCCCCcCcccceEeee
Confidence 34679999999999875 45599999999999998884 46799999999999988763
No 49
>PF04641 Rtf2: Rtf2 RING-finger
Probab=98.12 E-value=5e-06 Score=52.32 Aligned_cols=58 Identities=24% Similarity=0.426 Sum_probs=46.8
Q ss_pred cCCcccCccCccCccCc----eecCCCChhHHHHHHHHHhhCCCCCCCCCcCcCcCCceeeecC
Q psy10800 21 YKETLTCPSCKVKRKDA----VLTKCFHVFCWDCLRTRYETRQRKCPKCNAAFGANDYHRLYLG 80 (81)
Q Consensus 21 ~~~~~~C~iC~~~~~~~----~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~~~~~~ 80 (81)
....+.|||....+..- ++.+|||+|+..++.+.- ....||.|..++...|+..|..+
T Consensus 110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k--~~~~Cp~c~~~f~~~DiI~Lnp~ 171 (260)
T PF04641_consen 110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK--KSKKCPVCGKPFTEEDIIPLNPP 171 (260)
T ss_pred CCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc--ccccccccCCccccCCEEEecCC
Confidence 45579999999888542 445999999999999863 34569999999999999988654
No 50
>KOG1785|consensus
Probab=98.12 E-value=1.9e-06 Score=56.95 Aligned_cols=49 Identities=24% Similarity=0.654 Sum_probs=41.2
Q ss_pred ccCccCccCccCceecCCCChhHHHHHHHHHhhC-CCCCCCCCcCcCcCC
Q psy10800 25 LTCPSCKVKRKDAVLTKCFHVFCWDCLRTRYETR-QRKCPKCNAAFGAND 73 (81)
Q Consensus 25 ~~C~iC~~~~~~~~~~~CgH~fc~~Ci~~~~~~~-~~~CP~Cr~~~~~~~ 73 (81)
..|.||-+.=++-.+-+|||..|..|+..|.... ...||+||..+....
T Consensus 370 eLCKICaendKdvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKGte 419 (563)
T KOG1785|consen 370 ELCKICAENDKDVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIKGTE 419 (563)
T ss_pred HHHHHhhccCCCcccccccchHHHHHHHhhcccCCCCCCCceeeEecccc
Confidence 4799999988887788999999999999998655 467999999886543
No 51
>KOG2817|consensus
Probab=98.11 E-value=2.1e-06 Score=56.28 Aligned_cols=59 Identities=27% Similarity=0.505 Sum_probs=48.2
Q ss_pred cCCcccCccCccCcc---CceecCCCChhHHHHHHHHHhhCC--CCCCCCCcCcCcCCceeeec
Q psy10800 21 YKETLTCPSCKVKRK---DAVLTKCFHVFCWDCLRTRYETRQ--RKCPKCNAAFGANDYHRLYL 79 (81)
Q Consensus 21 ~~~~~~C~iC~~~~~---~~~~~~CgH~fc~~Ci~~~~~~~~--~~CP~Cr~~~~~~~~~~~~~ 79 (81)
....+.|||=.+.-. .|+.+.|||+.+.+-+.+...++. .+||+|.......+.+++|+
T Consensus 331 fHSvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~e~~~~~~kql~F 394 (394)
T KOG2817|consen 331 FHSVFICPVLKEQTSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPVEQLASDTKQLYF 394 (394)
T ss_pred ccceeecccchhhccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCcccCHHhcccccC
Confidence 455789999776443 369999999999999999888766 67999998888888887765
No 52
>KOG1645|consensus
Probab=98.06 E-value=1e-06 Score=58.03 Aligned_cols=55 Identities=24% Similarity=0.474 Sum_probs=43.3
Q ss_pred CcccCccCccCccCc-----eecCCCChhHHHHHHHHHhhCC-CCCCCCCcCcCcCCceee
Q psy10800 23 ETLTCPSCKVKRKDA-----VLTKCFHVFCWDCLRTRYETRQ-RKCPKCNAAFGANDYHRL 77 (81)
Q Consensus 23 ~~~~C~iC~~~~~~~-----~~~~CgH~fc~~Ci~~~~~~~~-~~CP~Cr~~~~~~~~~~~ 77 (81)
....||||++.+.-+ +.+.|||.|-..||++|+.... ..||.|......++++..
T Consensus 3 ~g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~katkr~i~~e 63 (463)
T KOG1645|consen 3 CGTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKATKRQIRPE 63 (463)
T ss_pred ccccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChhHHHHHHHH
Confidence 357899999988665 6779999999999999996332 349999887777666544
No 53
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=98.06 E-value=5.7e-07 Score=46.21 Aligned_cols=48 Identities=25% Similarity=0.523 Sum_probs=23.6
Q ss_pred cccCccCccCcc-C---ceec----CCCChhHHHHHHHHHhhC--C--------CCCCCCCcCcCc
Q psy10800 24 TLTCPSCKVKRK-D---AVLT----KCFHVFCWDCLRTRYETR--Q--------RKCPKCNAAFGA 71 (81)
Q Consensus 24 ~~~C~iC~~~~~-~---~~~~----~CgH~fc~~Ci~~~~~~~--~--------~~CP~Cr~~~~~ 71 (81)
+..|+||...+. . |... .|+..|+..|+.+|+... . ..||.|+.++.-
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~ 67 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISW 67 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEG
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeE
Confidence 468999998654 2 2222 799999999999999742 1 239999987753
No 54
>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=98.00 E-value=1.9e-05 Score=37.84 Aligned_cols=41 Identities=20% Similarity=0.572 Sum_probs=31.2
Q ss_pred cCccCcc--CccCceecCCC-----ChhHHHHHHHHHhhCC-CCCCCCC
Q psy10800 26 TCPSCKV--KRKDAVLTKCF-----HVFCWDCLRTRYETRQ-RKCPKCN 66 (81)
Q Consensus 26 ~C~iC~~--~~~~~~~~~Cg-----H~fc~~Ci~~~~~~~~-~~CP~Cr 66 (81)
.|-||++ .-.++.+.||. +.++..|+.+|+.... ..||+|+
T Consensus 1 ~CrIC~~~~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~ 49 (49)
T smart00744 1 ICRICHDEGDEGDPLVSPCRCKGSLKYVHQECLERWINESGNKTCEICK 49 (49)
T ss_pred CccCCCCCCCCCCeeEeccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence 3788986 33456777884 7899999999998653 4699984
No 55
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=97.96 E-value=3.2e-06 Score=41.23 Aligned_cols=48 Identities=25% Similarity=0.627 Sum_probs=36.9
Q ss_pred CcccCccCccCccCceecCCCChhHHHHHHHHHhhCCCCCCCCCcCcCcCC
Q psy10800 23 ETLTCPSCKVKRKDAVLTKCFHVFCWDCLRTRYETRQRKCPKCNAAFGAND 73 (81)
Q Consensus 23 ~~~~C~iC~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~~~~ 73 (81)
....|-.|...-...++++|||..|..|..- .+-+.||+|..++...+
T Consensus 6 ~~~~~~~~~~~~~~~~~~pCgH~I~~~~f~~---~rYngCPfC~~~~~~~~ 53 (55)
T PF14447_consen 6 PEQPCVFCGFVGTKGTVLPCGHLICDNCFPG---ERYNGCPFCGTPFEFDD 53 (55)
T ss_pred cceeEEEccccccccccccccceeeccccCh---hhccCCCCCCCcccCCC
Confidence 3456777777777788999999999999753 24467999999887654
No 56
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=97.95 E-value=8.5e-06 Score=38.81 Aligned_cols=43 Identities=23% Similarity=0.694 Sum_probs=22.1
Q ss_pred CccCccCccCc--eec--CCCChhHHHHHHHHHhhCCCCCCCCCcCc
Q psy10800 27 CPSCKVKRKDA--VLT--KCFHVFCWDCLRTRYETRQRKCPKCNAAF 69 (81)
Q Consensus 27 C~iC~~~~~~~--~~~--~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~ 69 (81)
||+|.+.+... -.. +||..+|..|+.+.+......||.||.+.
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 68888877332 222 68999999999998876667899999864
No 57
>KOG1493|consensus
Probab=97.92 E-value=4.4e-06 Score=43.25 Aligned_cols=31 Identities=26% Similarity=0.695 Sum_probs=26.2
Q ss_pred CCCChhHHHHHHHHHhhCCC--CCCCCCcCcCc
Q psy10800 41 KCFHVFCWDCLRTRYETRQR--KCPKCNAAFGA 71 (81)
Q Consensus 41 ~CgH~fc~~Ci~~~~~~~~~--~CP~Cr~~~~~ 71 (81)
.|.|.|...||.+|+....+ .||+||+.+..
T Consensus 50 ~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~~ 82 (84)
T KOG1493|consen 50 YCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQF 82 (84)
T ss_pred HHHHHHHHHHHHHHhcCccccccCCcchheeEe
Confidence 79999999999999986544 49999987653
No 58
>KOG4367|consensus
Probab=97.91 E-value=8.9e-06 Score=54.52 Aligned_cols=36 Identities=28% Similarity=0.695 Sum_probs=32.7
Q ss_pred CCcccCccCccCccCceecCCCChhHHHHHHHHHhh
Q psy10800 22 KETLTCPSCKVKRKDAVLTKCFHVFCWDCLRTRYET 57 (81)
Q Consensus 22 ~~~~~C~iC~~~~~~~~~~~CgH~fc~~Ci~~~~~~ 57 (81)
++++.||||...|++|++++|+|..|..|....+.+
T Consensus 2 eeelkc~vc~~f~~epiil~c~h~lc~~ca~~~~~~ 37 (699)
T KOG4367|consen 2 EEELKCPVCGSFYREPIILPCSHNLCQACARNILVQ 37 (699)
T ss_pred cccccCceehhhccCceEeecccHHHHHHHHhhccc
Confidence 568999999999999999999999999999877654
No 59
>KOG1734|consensus
Probab=97.88 E-value=2.6e-06 Score=53.68 Aligned_cols=48 Identities=23% Similarity=0.520 Sum_probs=37.5
Q ss_pred CcccCccCccCcc----------CceecCCCChhHHHHHHHHHhhCC-CCCCCCCcCcC
Q psy10800 23 ETLTCPSCKVKRK----------DAVLTKCFHVFCWDCLRTRYETRQ-RKCPKCNAAFG 70 (81)
Q Consensus 23 ~~~~C~iC~~~~~----------~~~~~~CgH~fc~~Ci~~~~~~~~-~~CP~Cr~~~~ 70 (81)
++..|.||...+. +...++|+|+|+..||..|-.-+. ..||.|+..+.
T Consensus 223 ~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVd 281 (328)
T KOG1734|consen 223 SDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVD 281 (328)
T ss_pred CcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhh
Confidence 3678999987553 346789999999999999987553 45999987664
No 60
>KOG0827|consensus
Probab=97.88 E-value=8.5e-06 Score=53.64 Aligned_cols=49 Identities=27% Similarity=0.615 Sum_probs=35.8
Q ss_pred ccCccCccCccCc----eecCCCChhHHHHHHHHHhhCC--CCCCCCCcCcCcCC
Q psy10800 25 LTCPSCKVKRKDA----VLTKCFHVFCWDCLRTRYETRQ--RKCPKCNAAFGAND 73 (81)
Q Consensus 25 ~~C~iC~~~~~~~----~~~~CgH~fc~~Ci~~~~~~~~--~~CP~Cr~~~~~~~ 73 (81)
-.|.||.+.+-+. .+-.|||+|+..|+..|+.... +.||+|+-.+....
T Consensus 5 A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~~~r~ 59 (465)
T KOG0827|consen 5 AECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKLQERH 59 (465)
T ss_pred ceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeeccccee
Confidence 4799996655432 2336999999999999998754 47999995444433
No 61
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=97.88 E-value=2.8e-05 Score=40.61 Aligned_cols=30 Identities=23% Similarity=0.481 Sum_probs=26.4
Q ss_pred CCCChhHHHHHHHHHhhCCCCCCCCCcCcCc
Q psy10800 41 KCFHVFCWDCLRTRYETRQRKCPKCNAAFGA 71 (81)
Q Consensus 41 ~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~~ 71 (81)
-|.|.|+..||.+|+..+ ..||++|+.+..
T Consensus 53 ~CnHaFH~HCI~rWL~Tk-~~CPld~q~w~~ 82 (88)
T COG5194 53 VCNHAFHDHCIYRWLDTK-GVCPLDRQTWVL 82 (88)
T ss_pred ecchHHHHHHHHHHHhhC-CCCCCCCceeEE
Confidence 699999999999999964 779999988754
No 62
>KOG4275|consensus
Probab=97.84 E-value=7.3e-07 Score=56.63 Aligned_cols=43 Identities=28% Similarity=0.670 Sum_probs=35.4
Q ss_pred cccCccCccCccCceecCCCChh-HHHHHHHHHhhCCCCCCCCCcCcCc
Q psy10800 24 TLTCPSCKVKRKDAVLTKCFHVF-CWDCLRTRYETRQRKCPKCNAAFGA 71 (81)
Q Consensus 24 ~~~C~iC~~~~~~~~~~~CgH~f-c~~Ci~~~~~~~~~~CP~Cr~~~~~ 71 (81)
...|.||++..++.+.|+|||.. |..|=+ ....||+||+.+..
T Consensus 300 ~~LC~ICmDaP~DCvfLeCGHmVtCt~CGk-----rm~eCPICRqyi~r 343 (350)
T KOG4275|consen 300 RRLCAICMDAPRDCVFLECGHMVTCTKCGK-----RMNECPICRQYIVR 343 (350)
T ss_pred HHHHHHHhcCCcceEEeecCcEEeehhhcc-----ccccCchHHHHHHH
Confidence 56899999999999999999964 888854 34579999987643
No 63
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=97.83 E-value=8.2e-06 Score=58.87 Aligned_cols=50 Identities=18% Similarity=0.462 Sum_probs=38.3
Q ss_pred cCCcccCccCccCccC-----c--eecCCCChhHHHHHHHHHhhCC-CCCCCCCcCcC
Q psy10800 21 YKETLTCPSCKVKRKD-----A--VLTKCFHVFCWDCLRTRYETRQ-RKCPKCNAAFG 70 (81)
Q Consensus 21 ~~~~~~C~iC~~~~~~-----~--~~~~CgH~fc~~Ci~~~~~~~~-~~CP~Cr~~~~ 70 (81)
.....+|+||...+.. | .-..|.|.|+..|+.+|++... +.||.||..++
T Consensus 1466 fsG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219 1466 FSGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred cCCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence 3446799999876541 1 3336999999999999999765 45999998775
No 64
>KOG4185|consensus
Probab=97.82 E-value=9.3e-06 Score=51.68 Aligned_cols=46 Identities=22% Similarity=0.485 Sum_probs=38.4
Q ss_pred cccCccCccCcc------CceecCCCChhHHHHHHHHHhhCCCCCCCCCcCc
Q psy10800 24 TLTCPSCKVKRK------DAVLTKCFHVFCWDCLRTRYETRQRKCPKCNAAF 69 (81)
Q Consensus 24 ~~~C~iC~~~~~------~~~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~ 69 (81)
.+.|-||.+.|. .|..+.|||++|..|+...+......||.||...
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 357889988774 3678899999999999998887777799999983
No 65
>KOG1002|consensus
Probab=97.81 E-value=1.2e-05 Score=54.97 Aligned_cols=50 Identities=24% Similarity=0.661 Sum_probs=42.3
Q ss_pred CcccCccCccCccCceecCCCChhHHHHHHHHHhhC----CCCCCCCCcCcCcC
Q psy10800 23 ETLTCPSCKVKRKDAVLTKCFHVFCWDCLRTRYETR----QRKCPKCNAAFGAN 72 (81)
Q Consensus 23 ~~~~C~iC~~~~~~~~~~~CgH~fc~~Ci~~~~~~~----~~~CP~Cr~~~~~~ 72 (81)
....|.+|.+.-.+++...|.|.||.-|+.+++... +-.||.|...++..
T Consensus 535 ~~~~C~lc~d~aed~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiD 588 (791)
T KOG1002|consen 535 GEVECGLCHDPAEDYIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSID 588 (791)
T ss_pred CceeecccCChhhhhHhhhhhHHHHHHHHHHHHHhhhcccCCCCcccccccccc
Confidence 468999999999999999999999999998888642 34699998877644
No 66
>KOG3800|consensus
Probab=97.79 E-value=2.8e-05 Score=49.38 Aligned_cols=50 Identities=24% Similarity=0.781 Sum_probs=39.9
Q ss_pred cCccCcc-CccCc----eecCCCChhHHHHHHHHHhhCCCCCCCCCcCcCcCCce
Q psy10800 26 TCPSCKV-KRKDA----VLTKCFHVFCWDCLRTRYETRQRKCPKCNAAFGANDYH 75 (81)
Q Consensus 26 ~C~iC~~-~~~~~----~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~ 75 (81)
.||+|.. .+.+| ++-+|||..|.+|+.+++..+...||-|...+....++
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iLRk~nfr 56 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGPAQCPECMVILRKNNFR 56 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHhcCCCCCCcccchhhhcccc
Confidence 5999974 45555 22399999999999999998888899999887766654
No 67
>KOG4692|consensus
Probab=97.71 E-value=1.9e-05 Score=51.61 Aligned_cols=48 Identities=25% Similarity=0.607 Sum_probs=41.2
Q ss_pred CCcccCccCccCccCceecCCCChhHHHHHHHHHhhCCCCCCCCCcCcC
Q psy10800 22 KETLTCPSCKVKRKDAVLTKCFHVFCWDCLRTRYETRQRKCPKCNAAFG 70 (81)
Q Consensus 22 ~~~~~C~iC~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~ 70 (81)
.++..||||..-..+.+..||+|.-|..||.+.+-+ ...|-+|+..+.
T Consensus 420 sEd~lCpICyA~pi~Avf~PC~H~SC~~CI~qHlmN-~k~CFfCktTv~ 467 (489)
T KOG4692|consen 420 SEDNLCPICYAGPINAVFAPCSHRSCYGCITQHLMN-CKRCFFCKTTVI 467 (489)
T ss_pred cccccCcceecccchhhccCCCCchHHHHHHHHHhc-CCeeeEecceee
Confidence 357899999999999999999999999999998874 466999987654
No 68
>KOG0826|consensus
Probab=97.69 E-value=7.7e-06 Score=52.69 Aligned_cols=57 Identities=23% Similarity=0.494 Sum_probs=46.7
Q ss_pred CCcccCccCccCccCceec-CCCChhHHHHHHHHHhhCCCCCCCCCcCcCcCCceeeec
Q psy10800 22 KETLTCPSCKVKRKDAVLT-KCFHVFCWDCLRTRYETRQRKCPKCNAAFGANDYHRLYL 79 (81)
Q Consensus 22 ~~~~~C~iC~~~~~~~~~~-~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~~~~~ 79 (81)
.+...||+|.....+|..+ --|-+||..|+..++. ....||+-..+....++.++|-
T Consensus 298 ~~~~~CpvClk~r~Nptvl~vSGyVfCY~Ci~~Yv~-~~~~CPVT~~p~~v~~l~rl~~ 355 (357)
T KOG0826|consen 298 PDREVCPVCLKKRQNPTVLEVSGYVFCYPCIFSYVV-NYGHCPVTGYPASVDHLIRLFN 355 (357)
T ss_pred CccccChhHHhccCCCceEEecceEEeHHHHHHHHH-hcCCCCccCCcchHHHHHHHhc
Confidence 3467999999999998555 5599999999999999 5577999988887777766653
No 69
>KOG4739|consensus
Probab=97.53 E-value=2.5e-05 Score=48.37 Aligned_cols=46 Identities=33% Similarity=0.691 Sum_probs=32.5
Q ss_pred cccCccCccCcc-Cc-eecCCCChhHHHHHHHHHhhCCCCCCCCCcCcCcC
Q psy10800 24 TLTCPSCKVKRK-DA-VLTKCFHVFCWDCLRTRYETRQRKCPKCNAAFGAN 72 (81)
Q Consensus 24 ~~~C~iC~~~~~-~~-~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~~~ 72 (81)
...|..|..... .+ .+++|+|+||..|...-. ...||.|++.+...
T Consensus 3 ~VhCn~C~~~~~~~~f~LTaC~HvfC~~C~k~~~---~~~C~lCkk~ir~i 50 (233)
T KOG4739|consen 3 FVHCNKCFRFPSQDPFFLTACRHVFCEPCLKASS---PDVCPLCKKSIRII 50 (233)
T ss_pred eEEeccccccCCCCceeeeechhhhhhhhcccCC---ccccccccceeeee
Confidence 356888876444 33 677999999999986422 23799999986543
No 70
>KOG3002|consensus
Probab=97.48 E-value=7.1e-05 Score=48.11 Aligned_cols=45 Identities=29% Similarity=0.687 Sum_probs=36.3
Q ss_pred cCCcccCccCccCccCceecCC--CChhHHHHHHHHHhhCCCCCCCCCcCcC
Q psy10800 21 YKETLTCPSCKVKRKDAVLTKC--FHVFCWDCLRTRYETRQRKCPKCNAAFG 70 (81)
Q Consensus 21 ~~~~~~C~iC~~~~~~~~~~~C--gH~fc~~Ci~~~~~~~~~~CP~Cr~~~~ 70 (81)
..+.+.||||.+.+..| +..| ||..|..|-.+ ....||.||.+++
T Consensus 45 ~~~lleCPvC~~~l~~P-i~QC~nGHlaCssC~~~----~~~~CP~Cr~~~g 91 (299)
T KOG3002|consen 45 DLDLLDCPVCFNPLSPP-IFQCDNGHLACSSCRTK----VSNKCPTCRLPIG 91 (299)
T ss_pred chhhccCchhhccCccc-ceecCCCcEehhhhhhh----hcccCCccccccc
Confidence 45679999999999988 3455 89999999753 3356999999887
No 71
>KOG1814|consensus
Probab=97.48 E-value=0.00017 Score=47.87 Aligned_cols=38 Identities=24% Similarity=0.558 Sum_probs=30.9
Q ss_pred hcCCcccCccCccCccCc---eecCCCChhHHHHHHHHHhh
Q psy10800 20 EYKETLTCPSCKVKRKDA---VLTKCFHVFCWDCLRTRYET 57 (81)
Q Consensus 20 ~~~~~~~C~iC~~~~~~~---~~~~CgH~fc~~Ci~~~~~~ 57 (81)
-....+.|.||++..... +.++|+|+||..|+..++..
T Consensus 180 F~~slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~ 220 (445)
T KOG1814|consen 180 FVNSLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTI 220 (445)
T ss_pred HHhhcccceeeehhhcCcceeeecccchHHHHHHHHHHHHH
Confidence 344579999999876553 67799999999999999864
No 72
>KOG1001|consensus
Probab=97.46 E-value=6.2e-05 Score=52.93 Aligned_cols=49 Identities=24% Similarity=0.631 Sum_probs=41.5
Q ss_pred ccCccCccCccCceecCCCChhHHHHHHHHHhhCCC-CCCCCCcCcCcCCc
Q psy10800 25 LTCPSCKVKRKDAVLTKCFHVFCWDCLRTRYETRQR-KCPKCNAAFGANDY 74 (81)
Q Consensus 25 ~~C~iC~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~-~CP~Cr~~~~~~~~ 74 (81)
..|.+|.+ ...++++.|||.||..|+...+..... .||.||..+....+
T Consensus 455 ~~c~ic~~-~~~~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~~~l 504 (674)
T KOG1001|consen 455 HWCHICCD-LDSFFITRCGHDFCVECLKKSIQQSENAPCPLCRNVLKEKKL 504 (674)
T ss_pred cccccccc-cccceeecccchHHHHHHHhccccccCCCCcHHHHHHHHHHH
Confidence 89999999 778899999999999999998886554 49999987765443
No 73
>KOG0825|consensus
Probab=97.41 E-value=2.6e-05 Score=55.35 Aligned_cols=51 Identities=24% Similarity=0.507 Sum_probs=37.8
Q ss_pred cccCccCccCccCc---eecCCCChhHHHHHHHHHhhCCCCCCCCCcCcCcCCce
Q psy10800 24 TLTCPSCKVKRKDA---VLTKCFHVFCWDCLRTRYETRQRKCPKCNAAFGANDYH 75 (81)
Q Consensus 24 ~~~C~iC~~~~~~~---~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~ 75 (81)
...||+|+..+.+. ....|+|.||..|+..|-+ ....||+||..|..-.+.
T Consensus 123 ~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR-~aqTCPiDR~EF~~v~V~ 176 (1134)
T KOG0825|consen 123 ENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSR-CAQTCPVDRGEFGEVKVL 176 (1134)
T ss_pred hhhhhHHHHHHHHHhhccccccccccHHHHhhhhhh-hcccCchhhhhhheeeee
Confidence 45678887665543 2347999999999999887 447799999988764443
No 74
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=97.37 E-value=0.00032 Score=45.88 Aligned_cols=56 Identities=18% Similarity=0.404 Sum_probs=41.7
Q ss_pred cccCccCccCccCc----eecCCCChhHHHHHHHHHhhCCCCCCCCCcCcCcCCceeeec
Q psy10800 24 TLTCPSCKVKRKDA----VLTKCFHVFCWDCLRTRYETRQRKCPKCNAAFGANDYHRLYL 79 (81)
Q Consensus 24 ~~~C~iC~~~~~~~----~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~~~~~ 79 (81)
+-.||+|.+.+... .--+||...|..|+..+-..-+..||.||......+++...+
T Consensus 14 ed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~denv~~~~~ 73 (480)
T COG5175 14 EDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDENVRYVTL 73 (480)
T ss_pred cccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhccccceeEEec
Confidence 44599999877432 223789999999998766655567999999988888776543
No 75
>KOG2930|consensus
Probab=97.37 E-value=0.00023 Score=38.94 Aligned_cols=29 Identities=31% Similarity=0.682 Sum_probs=25.2
Q ss_pred CCCChhHHHHHHHHHhhCCCCCCCCCcCcC
Q psy10800 41 KCFHVFCWDCLRTRYETRQRKCPKCNAAFG 70 (81)
Q Consensus 41 ~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~ 70 (81)
.|.|.|+..||.+|++++ ..||++.+...
T Consensus 80 ~CNHaFH~hCisrWlktr-~vCPLdn~eW~ 108 (114)
T KOG2930|consen 80 VCNHAFHFHCISRWLKTR-NVCPLDNKEWV 108 (114)
T ss_pred ecchHHHHHHHHHHHhhc-CcCCCcCccee
Confidence 699999999999999976 66999987653
No 76
>KOG1941|consensus
Probab=97.36 E-value=9.8e-05 Score=48.94 Aligned_cols=46 Identities=28% Similarity=0.596 Sum_probs=36.6
Q ss_pred CcccCccCccCccC-c---eecCCCChhHHHHHHHHHhhC-CCCCCCCCcC
Q psy10800 23 ETLTCPSCKVKRKD-A---VLTKCFHVFCWDCLRTRYETR-QRKCPKCNAA 68 (81)
Q Consensus 23 ~~~~C~iC~~~~~~-~---~~~~CgH~fc~~Ci~~~~~~~-~~~CP~Cr~~ 68 (81)
-++-|..|.+.+-. + --++|.|+|+.+|+.+++.++ ..+||.||+.
T Consensus 364 ~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~Crkl 414 (518)
T KOG1941|consen 364 TELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRKL 414 (518)
T ss_pred HhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHHH
Confidence 37899999987632 1 456999999999999999754 3679999954
No 77
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=97.29 E-value=0.0005 Score=39.28 Aligned_cols=51 Identities=20% Similarity=0.518 Sum_probs=41.8
Q ss_pred CcccCccCccCccCceec----CCCChhHHHHHHHHHhhCC--CCCCCCCcCcCcCC
Q psy10800 23 ETLTCPSCKVKRKDAVLT----KCFHVFCWDCLRTRYETRQ--RKCPKCNAAFGAND 73 (81)
Q Consensus 23 ~~~~C~iC~~~~~~~~~~----~CgH~fc~~Ci~~~~~~~~--~~CP~Cr~~~~~~~ 73 (81)
...+|.||.+...+...+ =||-..|..|....|+... ..||.|+.++..+.
T Consensus 79 ~lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKss~ 135 (140)
T PF05290_consen 79 KLYECNICKETSAEERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKSSS 135 (140)
T ss_pred CceeccCcccccchhhcCCcccccchHHHHHHHHHHHHHcccCCCCCcccccccccc
Confidence 468999999988877655 3899999999999998653 46999999886544
No 78
>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=97.23 E-value=8.6e-05 Score=46.37 Aligned_cols=52 Identities=21% Similarity=0.688 Sum_probs=38.9
Q ss_pred cccCccCcc-CccCc-eec----CCCChhHHHHHHHHHhhCCCCCC--CCCcCcCcCCce
Q psy10800 24 TLTCPSCKV-KRKDA-VLT----KCFHVFCWDCLRTRYETRQRKCP--KCNAAFGANDYH 75 (81)
Q Consensus 24 ~~~C~iC~~-~~~~~-~~~----~CgH~fc~~Ci~~~~~~~~~~CP--~Cr~~~~~~~~~ 75 (81)
+..||+|.. .+-+| +.+ .|-|..|.+|+.+.+..+...|| -|.+.+....+.
T Consensus 10 d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kILRK~kf~ 69 (314)
T COG5220 10 DRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKILRKIKFI 69 (314)
T ss_pred cccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHHHHhccc
Confidence 568999984 44555 222 59999999999999998888999 587765544443
No 79
>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=97.02 E-value=0.00018 Score=39.14 Aligned_cols=31 Identities=26% Similarity=0.661 Sum_probs=25.9
Q ss_pred CCcccCccCccCccCc--eecCCCChhHHHHHH
Q psy10800 22 KETLTCPSCKVKRKDA--VLTKCFHVFCWDCLR 52 (81)
Q Consensus 22 ~~~~~C~iC~~~~~~~--~~~~CgH~fc~~Ci~ 52 (81)
.+...|++|...+.+. +..||||.|+..|+.
T Consensus 76 ~~~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 76 TESTKCSVCGKPLGNSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCCCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence 4578899999988776 566999999999975
No 80
>KOG1571|consensus
Probab=97.01 E-value=0.00024 Score=46.37 Aligned_cols=47 Identities=30% Similarity=0.605 Sum_probs=36.0
Q ss_pred hcCCcccCccCccCccCceecCCCChhHHHHHHHHHhhCCCCCCCCCcCcC
Q psy10800 20 EYKETLTCPSCKVKRKDAVLTKCFHVFCWDCLRTRYETRQRKCPKCNAAFG 70 (81)
Q Consensus 20 ~~~~~~~C~iC~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~ 70 (81)
.......|.||.+...+.+.++|||.-| |..-... ...||.||..+.
T Consensus 301 ~~~~p~lcVVcl~e~~~~~fvpcGh~cc--ct~cs~~--l~~CPvCR~rI~ 347 (355)
T KOG1571|consen 301 ELPQPDLCVVCLDEPKSAVFVPCGHVCC--CTLCSKH--LPQCPVCRQRIR 347 (355)
T ss_pred ccCCCCceEEecCCccceeeecCCcEEE--chHHHhh--CCCCchhHHHHH
Confidence 3445678999999999999999999876 6554333 356999998764
No 81
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=97.01 E-value=0.00046 Score=44.67 Aligned_cols=60 Identities=22% Similarity=0.388 Sum_probs=45.0
Q ss_pred hcCCcccCccCccCcc---CceecCCCChhHHHHHHHHHhhCC--CCCCCCCcCcCcCCceeeec
Q psy10800 20 EYKETLTCPSCKVKRK---DAVLTKCFHVFCWDCLRTRYETRQ--RKCPKCNAAFGANDYHRLYL 79 (81)
Q Consensus 20 ~~~~~~~C~iC~~~~~---~~~~~~CgH~fc~~Ci~~~~~~~~--~~CP~Cr~~~~~~~~~~~~~ 79 (81)
.....+.||+=.+.-. .|+.++|||+.-..-+...-+++. ++||+|.......+..++++
T Consensus 332 hfHs~FiCPVlKe~~t~ENpP~ml~CgHVIskeal~~LS~nG~~~FKCPYCP~~~~~~~~~rvrf 396 (396)
T COG5109 332 HFHSLFICPVLKELCTDENPPVMLECGHVISKEALSVLSQNGVLSFKCPYCPEMSKYENILRVRF 396 (396)
T ss_pred cccceeeccccHhhhcccCCCeeeeccceeeHHHHHHHhhcCcEEeeCCCCCcchhhhhhhcccC
Confidence 4556789998776443 369999999999988887665443 56999988777777776654
No 82
>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=96.99 E-value=0.0013 Score=38.64 Aligned_cols=34 Identities=32% Similarity=0.606 Sum_probs=25.6
Q ss_pred CcccCccCccCccCceecC------------CCChh-HHHHHHHHHh
Q psy10800 23 ETLTCPSCKVKRKDAVLTK------------CFHVF-CWDCLRTRYE 56 (81)
Q Consensus 23 ~~~~C~iC~~~~~~~~~~~------------CgH~f-c~~Ci~~~~~ 56 (81)
++..||||++...++|+|- |+..| +..|+.++-+
T Consensus 1 ed~~CpICme~PHNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkk 47 (162)
T PF07800_consen 1 EDVTCPICMEHPHNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKK 47 (162)
T ss_pred CCccCceeccCCCceEEEEeccccCCccccccCCccchhHHHHHHHH
Confidence 3578999999999998884 34333 6788887664
No 83
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=96.99 E-value=0.00047 Score=45.27 Aligned_cols=48 Identities=23% Similarity=0.517 Sum_probs=37.9
Q ss_pred CCcccCccCccCccCceecCCCChhHHHHHHHHHhh-CCCCCCCCCcCc
Q psy10800 22 KETLTCPSCKVKRKDAVLTKCFHVFCWDCLRTRYET-RQRKCPKCNAAF 69 (81)
Q Consensus 22 ~~~~~C~iC~~~~~~~~~~~CgH~fc~~Ci~~~~~~-~~~~CP~Cr~~~ 69 (81)
++...|.||-+-+.-...+||+|..|.-|..+.-.- ....||+||...
T Consensus 59 Een~~C~ICA~~~TYs~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~ 107 (493)
T COG5236 59 EENMNCQICAGSTTYSARYPCGHQICHACAVRLRALYMQKGCPLCRTET 107 (493)
T ss_pred cccceeEEecCCceEEEeccCCchHHHHHHHHHHHHHhccCCCcccccc
Confidence 446789999998888889999999999998764332 235699999764
No 84
>KOG2114|consensus
Probab=96.77 E-value=0.0012 Score=47.35 Aligned_cols=42 Identities=29% Similarity=0.646 Sum_probs=34.9
Q ss_pred cccCccCccCccCc-eecCCCChhHHHHHHHHHhhCCCCCCCCCcCc
Q psy10800 24 TLTCPSCKVKRKDA-VLTKCFHVFCWDCLRTRYETRQRKCPKCNAAF 69 (81)
Q Consensus 24 ~~~C~iC~~~~~~~-~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~ 69 (81)
...|..|.-.+.-| |...|||.|+..|+. .....||.|+...
T Consensus 840 ~skCs~C~~~LdlP~VhF~CgHsyHqhC~e----~~~~~CP~C~~e~ 882 (933)
T KOG2114|consen 840 VSKCSACEGTLDLPFVHFLCGHSYHQHCLE----DKEDKCPKCLPEL 882 (933)
T ss_pred eeeecccCCccccceeeeecccHHHHHhhc----cCcccCCccchhh
Confidence 35899999999888 677999999999988 2557799998743
No 85
>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=96.68 E-value=0.0024 Score=29.66 Aligned_cols=39 Identities=28% Similarity=0.707 Sum_probs=22.6
Q ss_pred CccCccCccCceec---CCCChhHHHHHHHHHhhCCC-CCCCC
Q psy10800 27 CPSCKVKRKDAVLT---KCFHVFCWDCLRTRYETRQR-KCPKC 65 (81)
Q Consensus 27 C~iC~~~~~~~~~~---~CgH~fc~~Ci~~~~~~~~~-~CP~C 65 (81)
|.+|.++....+.= .|+-.++..|+..++..... .||.|
T Consensus 1 C~~C~~iv~~G~~C~~~~C~~r~H~~C~~~y~r~~~~~~CP~C 43 (43)
T PF08746_consen 1 CEACKEIVTQGQRCSNRDCNVRLHDDCFKKYFRHRSNPKCPNC 43 (43)
T ss_dssp -TTT-SB-SSSEE-SS--S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred CcccchhHeeeccCCCCccCchHHHHHHHHHHhcCCCCCCcCC
Confidence 56788877666444 48888999999999997654 49977
No 86
>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=96.68 E-value=0.0028 Score=30.40 Aligned_cols=45 Identities=33% Similarity=0.683 Sum_probs=21.5
Q ss_pred cccCccCccCccCceec-CCCChhHHH---HHHHHHhhCCCCCCCCCcC
Q psy10800 24 TLTCPSCKVKRKDAVLT-KCFHVFCWD---CLRTRYETRQRKCPKCNAA 68 (81)
Q Consensus 24 ~~~C~iC~~~~~~~~~~-~CgH~fc~~---Ci~~~~~~~~~~CP~Cr~~ 68 (81)
.+.||+....+..|+.. .|.|..|.+ -+..........||+|.++
T Consensus 2 sL~CPls~~~i~~P~Rg~~C~H~~CFDl~~fl~~~~~~~~W~CPiC~~~ 50 (50)
T PF02891_consen 2 SLRCPLSFQRIRIPVRGKNCKHLQCFDLESFLESNQRTPKWKCPICNKP 50 (50)
T ss_dssp ESB-TTTSSB-SSEEEETT--SS--EEHHHHHHHHHHS---B-TTT---
T ss_pred eeeCCCCCCEEEeCccCCcCcccceECHHHHHHHhhccCCeECcCCcCc
Confidence 36899999999999655 899987643 2222222334679999763
No 87
>KOG4362|consensus
Probab=96.63 E-value=0.0006 Score=47.97 Aligned_cols=59 Identities=27% Similarity=0.643 Sum_probs=46.1
Q ss_pred HHHHhcCCcccCccCccCccCceecCCCChhHHHHHHHHHhhCC--CCCCCCCcCcCcCCc
Q psy10800 16 EEIREYKETLTCPSCKVKRKDAVLTKCFHVFCWDCLRTRYETRQ--RKCPKCNAAFGANDY 74 (81)
Q Consensus 16 ~~~~~~~~~~~C~iC~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~--~~CP~Cr~~~~~~~~ 74 (81)
..+......++|+||...+.+|+.+.|.|.||..|+...+.... ..||+|+..+.....
T Consensus 13 ~vi~~~~k~lEc~ic~~~~~~p~~~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~eK~s~ 73 (684)
T KOG4362|consen 13 QVINAMQKILECPICLEHVKEPSLLKCDHIFLKFCLNKLFESKKGPKQCALCKSDIEKRSL 73 (684)
T ss_pred hHHHHHhhhccCCceeEEeeccchhhhhHHHHhhhhhceeeccCccccchhhhhhhhhhhc
Confidence 34555667899999999999999999999999999876665432 359999876655443
No 88
>KOG3970|consensus
Probab=96.33 E-value=0.0052 Score=38.28 Aligned_cols=48 Identities=25% Similarity=0.691 Sum_probs=38.1
Q ss_pred CCcccCccCccCccC--ceecCCCChhHHHHHHHHHhhC-------CCCCCCCCcCc
Q psy10800 22 KETLTCPSCKVKRKD--AVLTKCFHVFCWDCLRTRYETR-------QRKCPKCNAAF 69 (81)
Q Consensus 22 ~~~~~C~iC~~~~~~--~~~~~CgH~fc~~Ci~~~~~~~-------~~~CP~Cr~~~ 69 (81)
+-.--|.+|...+.. .+.+-|-|.|+++|+.+|..+- ...||.|..++
T Consensus 48 DY~pNC~LC~t~La~gdt~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~ei 104 (299)
T KOG3970|consen 48 DYNPNCRLCNTPLASGDTTRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEI 104 (299)
T ss_pred CCCCCCceeCCccccCcceeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCcc
Confidence 345679999988754 4888999999999999988652 24699998765
No 89
>PHA03096 p28-like protein; Provisional
Probab=96.13 E-value=0.0048 Score=39.59 Aligned_cols=44 Identities=18% Similarity=0.295 Sum_probs=31.7
Q ss_pred ccCccCccCccC--------ceecCCCChhHHHHHHHHHhhCC--CCCCCCCcC
Q psy10800 25 LTCPSCKVKRKD--------AVLTKCFHVFCWDCLRTRYETRQ--RKCPKCNAA 68 (81)
Q Consensus 25 ~~C~iC~~~~~~--------~~~~~CgH~fc~~Ci~~~~~~~~--~~CP~Cr~~ 68 (81)
..|.||++.... .++..|.|.||..|+..|..... ..||.||..
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 789999985532 24558999999999999987643 235555543
No 90
>KOG1940|consensus
Probab=95.96 E-value=0.0058 Score=39.02 Aligned_cols=43 Identities=30% Similarity=0.581 Sum_probs=35.0
Q ss_pred cccCccCccCcc----CceecCCCChhHHHHHHHHHhhCCCCCCCCCc
Q psy10800 24 TLTCPSCKVKRK----DAVLTKCFHVFCWDCLRTRYETRQRKCPKCNA 67 (81)
Q Consensus 24 ~~~C~iC~~~~~----~~~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~ 67 (81)
..-||||.+.+. .+..++|||.....|+....... ..||+|.+
T Consensus 158 ~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~~-y~CP~C~~ 204 (276)
T KOG1940|consen 158 EFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICEG-YTCPICSK 204 (276)
T ss_pred cCCCchhHHHhccccccCCccCcccchHHHHHHHHhccC-CCCCcccc
Confidence 345999987553 45677999999999999888866 88999987
No 91
>KOG3268|consensus
Probab=95.74 E-value=0.012 Score=35.48 Aligned_cols=31 Identities=23% Similarity=0.482 Sum_probs=25.1
Q ss_pred CCCChhHHHHHHHHHhhCC----------CCCCCCCcCcCc
Q psy10800 41 KCFHVFCWDCLRTRYETRQ----------RKCPKCNAAFGA 71 (81)
Q Consensus 41 ~CgH~fc~~Ci~~~~~~~~----------~~CP~Cr~~~~~ 71 (81)
.||..|+.-|+..|++.-. ..||+|..++..
T Consensus 189 qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~Pial 229 (234)
T KOG3268|consen 189 QCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIAL 229 (234)
T ss_pred ccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCccee
Confidence 7999999999999998521 249999887754
No 92
>KOG1952|consensus
Probab=95.67 E-value=0.015 Score=42.11 Aligned_cols=48 Identities=25% Similarity=0.722 Sum_probs=36.6
Q ss_pred CCcccCccCccCccCc--eec--CCCChhHHHHHHHHHhhC------CCCCCCCCcCc
Q psy10800 22 KETLTCPSCKVKRKDA--VLT--KCFHVFCWDCLRTRYETR------QRKCPKCNAAF 69 (81)
Q Consensus 22 ~~~~~C~iC~~~~~~~--~~~--~CgH~fc~~Ci~~~~~~~------~~~CP~Cr~~~ 69 (81)
...++|.||.+.+... +.- .|=|+|+..||.+|-... ...||.|....
T Consensus 189 ~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv~ 246 (950)
T KOG1952|consen 189 NRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSVS 246 (950)
T ss_pred cCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccchh
Confidence 4579999999987643 322 688999999999998753 35699998543
No 93
>KOG2932|consensus
Probab=95.67 E-value=0.0075 Score=39.20 Aligned_cols=43 Identities=28% Similarity=0.775 Sum_probs=29.6
Q ss_pred cccCccCccCccC-ceecCCCChhHHHHHHHHHhhCCCCCCCCCcCc
Q psy10800 24 TLTCPSCKVKRKD-AVLTKCFHVFCWDCLRTRYETRQRKCPKCNAAF 69 (81)
Q Consensus 24 ~~~C~iC~~~~~~-~~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~ 69 (81)
.-.|.-|...+.. ...++|.|+||.+|... . ....||.|-..+
T Consensus 90 VHfCd~Cd~PI~IYGRmIPCkHvFCl~CAr~--~-~dK~Cp~C~d~V 133 (389)
T KOG2932|consen 90 VHFCDRCDFPIAIYGRMIPCKHVFCLECARS--D-SDKICPLCDDRV 133 (389)
T ss_pred eEeecccCCcceeeecccccchhhhhhhhhc--C-ccccCcCcccHH
Confidence 3456677655443 36779999999999752 2 345799996554
No 94
>KOG1812|consensus
Probab=95.62 E-value=0.0065 Score=40.46 Aligned_cols=50 Identities=26% Similarity=0.657 Sum_probs=33.8
Q ss_pred CcccCccCc-cCccCc---eecCCCChhHHHHHHHHHhhC-----CCCCCC--CCcCcCcC
Q psy10800 23 ETLTCPSCK-VKRKDA---VLTKCFHVFCWDCLRTRYETR-----QRKCPK--CNAAFGAN 72 (81)
Q Consensus 23 ~~~~C~iC~-~~~~~~---~~~~CgH~fc~~Ci~~~~~~~-----~~~CP~--Cr~~~~~~ 72 (81)
....|.||. +..... ....|+|.||..|+.+++... ...||. |...++..
T Consensus 145 ~~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~~~~~~~~~C~~~~C~~~l~~~ 205 (384)
T KOG1812|consen 145 PKEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVKLLSGTVIRCPHDGCESRLTLE 205 (384)
T ss_pred ccccCccCccccccHhhhHHHhcccchhhhHHhHHHhhhhhccCCCccCCCCCCCccCCHH
Confidence 367899999 444331 345899999999999988743 234655 55544443
No 95
>KOG3113|consensus
Probab=95.54 E-value=0.021 Score=36.18 Aligned_cols=54 Identities=24% Similarity=0.423 Sum_probs=41.5
Q ss_pred CCcccCccCccCccCc----eecCCCChhHHHHHHHHHhhCCCCCCCCCcCcCcCCceeee
Q psy10800 22 KETLTCPSCKVKRKDA----VLTKCFHVFCWDCLRTRYETRQRKCPKCNAAFGANDYHRLY 78 (81)
Q Consensus 22 ~~~~~C~iC~~~~~~~----~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~~~~ 78 (81)
+..+.|||-.-.+..- ++-.|||+|-.+-++++- ...|+.|.+.+...++.-|.
T Consensus 109 ~a~fiCPvtgleMng~~~F~~l~~CGcV~SerAlKeik---as~C~~C~a~y~~~dvIvlN 166 (293)
T KOG3113|consen 109 RARFICPVTGLEMNGKYRFCALRCCGCVFSERALKEIK---ASVCHVCGAAYQEDDVIVLN 166 (293)
T ss_pred cceeecccccceecceEEEEEEeccceeccHHHHHHhh---hccccccCCcccccCeEeeC
Confidence 3478999987666543 455999999998887643 36799999999988887664
No 96
>KOG4445|consensus
Probab=95.51 E-value=0.0045 Score=40.01 Aligned_cols=48 Identities=21% Similarity=0.464 Sum_probs=37.0
Q ss_pred CcccCccCccCccCc---eecCCCChhHHHHHHHHHhh----------------------CCCCCCCCCcCcC
Q psy10800 23 ETLTCPSCKVKRKDA---VLTKCFHVFCWDCLRTRYET----------------------RQRKCPKCNAAFG 70 (81)
Q Consensus 23 ~~~~C~iC~~~~~~~---~~~~CgH~fc~~Ci~~~~~~----------------------~~~~CP~Cr~~~~ 70 (81)
..-.|.||+.-|.+. +.++|-|.|+..|+.+++.. ....||+||..+.
T Consensus 114 p~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~ 186 (368)
T KOG4445|consen 114 PNGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIK 186 (368)
T ss_pred CCCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhcc
Confidence 356899999877543 67799999999999998852 0134999998775
No 97
>KOG1815|consensus
Probab=95.43 E-value=0.027 Score=38.11 Aligned_cols=54 Identities=28% Similarity=0.568 Sum_probs=39.2
Q ss_pred cccCccCccCccC-ceecCCCChhHHHHHHHHHhhCC-------CCCCC--CCcCcCcCCceee
Q psy10800 24 TLTCPSCKVKRKD-AVLTKCFHVFCWDCLRTRYETRQ-------RKCPK--CNAAFGANDYHRL 77 (81)
Q Consensus 24 ~~~C~iC~~~~~~-~~~~~CgH~fc~~Ci~~~~~~~~-------~~CP~--Cr~~~~~~~~~~~ 77 (81)
...|.||.+.+.. .+.+.|||.||..|+..++.... .+||. |.+.+....+..+
T Consensus 70 ~~~c~ic~~~~~~~~~~~~c~H~~c~~cw~~yl~~kI~~~~~~~i~cp~~~C~a~v~~~~i~~~ 133 (444)
T KOG1815|consen 70 DVQCGICVESYDGEIIGLGCGHPFCPPCWTGYLGTKIHEGEEAKIKCPAHGCPALVGEDTVEKL 133 (444)
T ss_pred cccCCcccCCCcchhhhcCCCcHHHHHHHHHHhhheeeccccccccCCCCCccccCCCceeeee
Confidence 4789999988875 66779999999999999887531 24655 6666555444433
No 98
>KOG3161|consensus
Probab=95.36 E-value=0.0049 Score=43.48 Aligned_cols=40 Identities=28% Similarity=0.621 Sum_probs=30.9
Q ss_pred cCCcccCccCccCcc----CceecCCCChhHHHHHHHHHhhCCCCCC
Q psy10800 21 YKETLTCPSCKVKRK----DAVLTKCFHVFCWDCLRTRYETRQRKCP 63 (81)
Q Consensus 21 ~~~~~~C~iC~~~~~----~~~~~~CgH~fc~~Ci~~~~~~~~~~CP 63 (81)
+.+.+.|+||...|. .|+.+.|||+.|..|+..... .+||
T Consensus 8 w~~~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~lyn---~scp 51 (861)
T KOG3161|consen 8 WVLLLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLYN---ASCP 51 (861)
T ss_pred hHHHhhchHHHHHHHHHhcCcccccccchHHHHHHHhHhh---ccCC
Confidence 344578999977663 578999999999999986544 4577
No 99
>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=95.30 E-value=0.019 Score=38.00 Aligned_cols=34 Identities=32% Similarity=0.837 Sum_probs=25.9
Q ss_pred CCChhHHHHHHHHHhhCC------------CCCCCCCcCcCcCCce
Q psy10800 42 CFHVFCWDCLRTRYETRQ------------RKCPKCNAAFGANDYH 75 (81)
Q Consensus 42 CgH~fc~~Ci~~~~~~~~------------~~CP~Cr~~~~~~~~~ 75 (81)
|....|.+|+-+|+..+. ..||+||+.|-..|+.
T Consensus 311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FCilDV~ 356 (358)
T PF10272_consen 311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFCILDVC 356 (358)
T ss_pred ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccceeeeee
Confidence 445569999999997543 3499999998776653
No 100
>KOG0298|consensus
Probab=95.13 E-value=0.009 Score=44.86 Aligned_cols=51 Identities=18% Similarity=0.435 Sum_probs=42.1
Q ss_pred HHHhcCCcccCccCccCcc-CceecCCCChhHHHHHHHHHhhCCCCCCCCCcC
Q psy10800 17 EIREYKETLTCPSCKVKRK-DAVLTKCFHVFCWDCLRTRYETRQRKCPKCNAA 68 (81)
Q Consensus 17 ~~~~~~~~~~C~iC~~~~~-~~~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~ 68 (81)
...++.....|++|.+.+. ...++.|||.+|..|...|+... ..||+|...
T Consensus 1146 y~~~~~~~~~c~ic~dil~~~~~I~~cgh~~c~~c~~~~l~~~-s~~~~~ksi 1197 (1394)
T KOG0298|consen 1146 YLMNLSGHFVCEICLDILRNQGGIAGCGHEPCCRCDELWLYAS-SRCPICKSI 1197 (1394)
T ss_pred HHHHhhcccchHHHHHHHHhcCCeeeechhHhhhHHHHHHHHh-ccCcchhhh
Confidence 4455666779999999998 56888999999999999999854 779999743
No 101
>KOG1100|consensus
Probab=95.10 E-value=0.011 Score=36.33 Aligned_cols=40 Identities=28% Similarity=0.712 Sum_probs=31.2
Q ss_pred cCccCccCccCceecCCCCh-hHHHHHHHHHhhCCCCCCCCCcCcC
Q psy10800 26 TCPSCKVKRKDAVLTKCFHV-FCWDCLRTRYETRQRKCPKCNAAFG 70 (81)
Q Consensus 26 ~C~iC~~~~~~~~~~~CgH~-fc~~Ci~~~~~~~~~~CP~Cr~~~~ 70 (81)
.|-.|.+.-...+++||.|. +|..|-.. ...||+|+....
T Consensus 160 ~Cr~C~~~~~~VlllPCrHl~lC~~C~~~-----~~~CPiC~~~~~ 200 (207)
T KOG1100|consen 160 SCRKCGEREATVLLLPCRHLCLCGICDES-----LRICPICRSPKT 200 (207)
T ss_pred cceecCcCCceEEeecccceEeccccccc-----CccCCCCcChhh
Confidence 39999988888888899985 69999542 456999987643
No 102
>KOG1428|consensus
Probab=94.88 E-value=0.023 Score=43.99 Aligned_cols=51 Identities=25% Similarity=0.529 Sum_probs=37.3
Q ss_pred cCCcccCccCccC-cc-C-ceecCCCChhHHHHHHHHHhhCC---------CCCCCCCcCcCc
Q psy10800 21 YKETLTCPSCKVK-RK-D-AVLTKCFHVFCWDCLRTRYETRQ---------RKCPKCNAAFGA 71 (81)
Q Consensus 21 ~~~~~~C~iC~~~-~~-~-~~~~~CgH~fc~~Ci~~~~~~~~---------~~CP~Cr~~~~~ 71 (81)
...+-.|.||+.. +. . .+.+.|+|.|+..|..+.+..+= ..||+|...+..
T Consensus 3483 QD~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~InH 3545 (3738)
T KOG1428|consen 3483 QDADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKINH 3545 (3738)
T ss_pred cccCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchhhh
Confidence 3446689999853 32 2 38899999999999988776531 359999887754
No 103
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=94.74 E-value=0.054 Score=32.02 Aligned_cols=48 Identities=23% Similarity=0.486 Sum_probs=34.3
Q ss_pred CCcccCccCccCccCceecCCCC-----hhHHHHHHHHHhhCC-CCCCCCCcCcC
Q psy10800 22 KETLTCPSCKVKRKDAVLTKCFH-----VFCWDCLRTRYETRQ-RKCPKCNAAFG 70 (81)
Q Consensus 22 ~~~~~C~iC~~~~~~~~~~~CgH-----~fc~~Ci~~~~~~~~-~~CP~Cr~~~~ 70 (81)
..+..|=||++... +..-||.- ..+.+|+.+|+.... ..|+.|+..+.
T Consensus 6 ~~~~~CRIC~~~~~-~~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~ 59 (162)
T PHA02825 6 LMDKCCWICKDEYD-VVTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYN 59 (162)
T ss_pred CCCCeeEecCCCCC-CccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEE
Confidence 34678999987654 33446643 338999999998654 45999998764
No 104
>KOG3899|consensus
Probab=94.72 E-value=0.032 Score=36.10 Aligned_cols=38 Identities=32% Similarity=0.774 Sum_probs=29.1
Q ss_pred CCChhHHHHHHHHHhhCC------------CCCCCCCcCcCcCCceeeec
Q psy10800 42 CFHVFCWDCLRTRYETRQ------------RKCPKCNAAFGANDYHRLYL 79 (81)
Q Consensus 42 CgH~fc~~Ci~~~~~~~~------------~~CP~Cr~~~~~~~~~~~~~ 79 (81)
|....|.+|+.+|+..+. ..||+||+.+-..|+.-+-+
T Consensus 325 crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fci~dv~~v~~ 374 (381)
T KOG3899|consen 325 CRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFCIRDVHCVDF 374 (381)
T ss_pred cccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceEEeeeeEEEe
Confidence 556679999999997532 46999999998877765543
No 105
>KOG3039|consensus
Probab=94.60 E-value=0.034 Score=35.17 Aligned_cols=39 Identities=15% Similarity=0.031 Sum_probs=33.5
Q ss_pred HHhcCCcccCccCccCccCceecCCCChhHHHHHHHHHh
Q psy10800 18 IREYKETLTCPSCKVKRKDAVLTKCFHVFCWDCLRTRYE 56 (81)
Q Consensus 18 ~~~~~~~~~C~iC~~~~~~~~~~~CgH~fc~~Ci~~~~~ 56 (81)
.+.+.+---|.+|+..+.+|++++=||.|+..||.+++-
T Consensus 37 rDsiK~FdcCsLtLqPc~dPvit~~GylfdrEaILe~il 75 (303)
T KOG3039|consen 37 RDSIKPFDCCSLTLQPCRDPVITPDGYLFDREAILEYIL 75 (303)
T ss_pred ccccCCcceeeeecccccCCccCCCCeeeeHHHHHHHHH
Confidence 345566667899999999999999999999999988874
No 106
>KOG2034|consensus
Probab=94.33 E-value=0.025 Score=41.11 Aligned_cols=38 Identities=24% Similarity=0.391 Sum_probs=29.6
Q ss_pred HhcCCcccCccCccCcc-Cc-eecCCCChhHHHHHHHHHh
Q psy10800 19 REYKETLTCPSCKVKRK-DA-VLTKCFHVFCWDCLRTRYE 56 (81)
Q Consensus 19 ~~~~~~~~C~iC~~~~~-~~-~~~~CgH~fc~~Ci~~~~~ 56 (81)
..++.+-.|.+|...+. .| ++.+|||.|++.|+.+...
T Consensus 812 ~v~ep~d~C~~C~~~ll~~pF~vf~CgH~FH~~Cl~~~v~ 851 (911)
T KOG2034|consen 812 RVLEPQDSCDHCGRPLLIKPFYVFPCGHCFHRDCLIRHVL 851 (911)
T ss_pred EEecCccchHHhcchhhcCcceeeeccchHHHHHHHHHHH
Confidence 34456889999987653 45 7779999999999987664
No 107
>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.
Probab=94.04 E-value=0.012 Score=27.86 Aligned_cols=37 Identities=30% Similarity=0.718 Sum_probs=21.9
Q ss_pred ccCceecCCC-ChhHHHHHHHHHhhCCCCCCCCCcCcCc
Q psy10800 34 RKDAVLTKCF-HVFCWDCLRTRYETRQRKCPKCNAAFGA 71 (81)
Q Consensus 34 ~~~~~~~~Cg-H~fc~~Ci~~~~~~~~~~CP~Cr~~~~~ 71 (81)
|.+.-.+.|. |..|..|+...+. ....||+|..+++.
T Consensus 10 f~~k~Li~C~dHYLCl~CLt~ml~-~s~~C~iC~~~LPt 47 (50)
T PF03854_consen 10 FANKGLIKCSDHYLCLNCLTLMLS-RSDRCPICGKPLPT 47 (50)
T ss_dssp S--SSEEE-SS-EEEHHHHHHT-S-SSSEETTTTEE---
T ss_pred hcCCCeeeecchhHHHHHHHHHhc-cccCCCcccCcCcc
Confidence 3344456775 6679999997776 44669999988764
No 108
>PHA02862 5L protein; Provisional
Probab=93.94 E-value=0.079 Score=30.92 Aligned_cols=45 Identities=16% Similarity=0.380 Sum_probs=31.6
Q ss_pred ccCccCccCccCceecCCCC-----hhHHHHHHHHHhhCC-CCCCCCCcCcC
Q psy10800 25 LTCPSCKVKRKDAVLTKCFH-----VFCWDCLRTRYETRQ-RKCPKCNAAFG 70 (81)
Q Consensus 25 ~~C~iC~~~~~~~~~~~CgH-----~fc~~Ci~~~~~~~~-~~CP~Cr~~~~ 70 (81)
-.|=||++.-.+. .-||.- .-+..|+.+|+.... ..|+.|+.++.
T Consensus 3 diCWIC~~~~~e~-~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~ 53 (156)
T PHA02862 3 DICWICNDVCDER-NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYN 53 (156)
T ss_pred CEEEEecCcCCCC-cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEE
Confidence 3678888765443 356543 348999999998654 35999998764
No 109
>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=93.80 E-value=0.06 Score=30.98 Aligned_cols=44 Identities=18% Similarity=0.314 Sum_probs=30.7
Q ss_pred HHHHHHHhcCC--cccCccCccCccC--c-eecCCC------ChhHHHHHHHHHh
Q psy10800 13 VMLEEIREYKE--TLTCPSCKVKRKD--A-VLTKCF------HVFCWDCLRTRYE 56 (81)
Q Consensus 13 ~~~~~~~~~~~--~~~C~iC~~~~~~--~-~~~~Cg------H~fc~~Ci~~~~~ 56 (81)
.+......... ..+|.||.+.+.+ . +.++|| |.||..|+++|-+
T Consensus 13 ~l~~lf~~~w~~~~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~~ 67 (134)
T PF05883_consen 13 YLERLFNDQWPRCTVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWRR 67 (134)
T ss_pred HHHHHHHHHccccCeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHHh
Confidence 33444455555 7899999998876 3 344554 6789999999954
No 110
>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=93.79 E-value=0.068 Score=26.18 Aligned_cols=45 Identities=24% Similarity=0.563 Sum_probs=28.8
Q ss_pred cCccCccCccC----ceecCCCChhHHHHHHHHHhhCCCCCCCCCcCcCcCC
Q psy10800 26 TCPSCKVKRKD----AVLTKCFHVFCWDCLRTRYETRQRKCPKCNAAFGAND 73 (81)
Q Consensus 26 ~C~iC~~~~~~----~~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~~~~ 73 (81)
.|-.|...+.. ..+-+=-.+||..|....+. ..||.|+..+..+.
T Consensus 7 nCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~---~~CPNCgGelv~RP 55 (57)
T PF06906_consen 7 NCECCDKDLPPDSPEAYICSFECTFCADCAETMLN---GVCPNCGGELVRRP 55 (57)
T ss_pred CccccCCCCCCCCCcceEEeEeCcccHHHHHHHhc---CcCcCCCCccccCC
Confidence 45556554432 22223334799999998765 56999998876654
No 111
>KOG3579|consensus
Probab=93.65 E-value=0.023 Score=36.55 Aligned_cols=36 Identities=28% Similarity=0.759 Sum_probs=30.4
Q ss_pred CcccCccCccCccCceecCC----CChhHHHHHHHHHhhC
Q psy10800 23 ETLTCPSCKVKRKDAVLTKC----FHVFCWDCLRTRYETR 58 (81)
Q Consensus 23 ~~~~C~iC~~~~~~~~~~~C----gH~fc~~Ci~~~~~~~ 58 (81)
..+.|.+|++.+.+.-...| .|.||..|-.+.++..
T Consensus 267 apLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSResIK~Q 306 (352)
T KOG3579|consen 267 APLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSRESIKQQ 306 (352)
T ss_pred CceeehhhhhhhccCceeecCCCcccceecccCHHHHHhh
Confidence 35899999999999866666 7999999999888864
No 112
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=92.87 E-value=0.09 Score=27.14 Aligned_cols=32 Identities=28% Similarity=0.623 Sum_probs=23.8
Q ss_pred CCCChhHHHHHHHHHhhCCCCCCCCCcCcCcCCce
Q psy10800 41 KCFHVFCWDCLRTRYETRQRKCPKCNAAFGANDYH 75 (81)
Q Consensus 41 ~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~ 75 (81)
.=.++||..|.+..+. ..||.|...+..+.++
T Consensus 26 tfEcTFCadCae~~l~---g~CPnCGGelv~RP~R 57 (84)
T COG3813 26 TFECTFCADCAENRLH---GLCPNCGGELVARPIR 57 (84)
T ss_pred EEeeehhHhHHHHhhc---CcCCCCCchhhcCcCC
Confidence 3457899999987665 4699998877665543
No 113
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=91.84 E-value=0.22 Score=24.27 Aligned_cols=30 Identities=27% Similarity=0.618 Sum_probs=23.7
Q ss_pred cccCccCccCc--cCceec--CCCChhHHHHHHH
Q psy10800 24 TLTCPSCKVKR--KDAVLT--KCFHVFCWDCLRT 53 (81)
Q Consensus 24 ~~~C~iC~~~~--~~~~~~--~CgH~fc~~Ci~~ 53 (81)
...|++|.+.| .+.++. .||-.+++.|+.+
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~ 38 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK 38 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence 56899999999 445444 8999999999763
No 114
>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=91.74 E-value=0.1 Score=21.60 Aligned_cols=9 Identities=44% Similarity=1.165 Sum_probs=5.0
Q ss_pred cCccCccCc
Q psy10800 26 TCPSCKVKR 34 (81)
Q Consensus 26 ~C~iC~~~~ 34 (81)
.||-|...+
T Consensus 2 ~CP~C~~~V 10 (26)
T PF10571_consen 2 TCPECGAEV 10 (26)
T ss_pred cCCCCcCCc
Confidence 466665544
No 115
>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=91.70 E-value=0.18 Score=24.29 Aligned_cols=25 Identities=36% Similarity=0.852 Sum_probs=14.3
Q ss_pred CCCChhHHHHHHHHHhhCCCCCCCCC
Q psy10800 41 KCFHVFCWDCLRTRYETRQRKCPKCN 66 (81)
Q Consensus 41 ~CgH~fc~~Ci~~~~~~~~~~CP~Cr 66 (81)
.|++.||.+|=. ++.+....||-|.
T Consensus 26 ~C~~~FC~dCD~-fiHE~LH~CPGC~ 50 (51)
T PF07975_consen 26 KCKNHFCIDCDV-FIHETLHNCPGCE 50 (51)
T ss_dssp TTT--B-HHHHH-TTTTTS-SSSTT-
T ss_pred CCCCccccCcCh-hhhccccCCcCCC
Confidence 689999999943 4454556799883
No 116
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=90.42 E-value=0.088 Score=24.79 Aligned_cols=39 Identities=23% Similarity=0.611 Sum_probs=22.3
Q ss_pred CccCccCcc--CceecCCCC-----hhHHHHHHHHHhhC-CCCCCCC
Q psy10800 27 CPSCKVKRK--DAVLTKCFH-----VFCWDCLRTRYETR-QRKCPKC 65 (81)
Q Consensus 27 C~iC~~~~~--~~~~~~CgH-----~fc~~Ci~~~~~~~-~~~CP~C 65 (81)
|-||++.-. .+.+.||+- ..+..|+.+|+... ...|++|
T Consensus 1 CrIC~~~~~~~~~li~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C 47 (47)
T PF12906_consen 1 CRICLEGEEEDEPLISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC 47 (47)
T ss_dssp ETTTTEE-SSSS-EE-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred CeEeCCcCCCCCceecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence 457775433 246677742 24889999999864 3458776
No 117
>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=90.33 E-value=0.0041 Score=31.84 Aligned_cols=40 Identities=25% Similarity=0.573 Sum_probs=19.6
Q ss_pred ccCccCccCccCceecCCCChhHHHHHHHHHhhCCCCCCCCCcCcC
Q psy10800 25 LTCPSCKVKRKDAVLTKCFHVFCWDCLRTRYETRQRKCPKCNAAFG 70 (81)
Q Consensus 25 ~~C~iC~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~ 70 (81)
+.||.|...+...- |+.+|..|-..+.. ...||.|..++.
T Consensus 2 ~~CP~C~~~L~~~~----~~~~C~~C~~~~~~--~a~CPdC~~~Le 41 (70)
T PF07191_consen 2 NTCPKCQQELEWQG----GHYHCEACQKDYKK--EAFCPDCGQPLE 41 (70)
T ss_dssp -B-SSS-SBEEEET----TEEEETTT--EEEE--EEE-TTT-SB-E
T ss_pred CcCCCCCCccEEeC----CEEECcccccccee--cccCCCcccHHH
Confidence 57999988754321 67777777664332 245888877653
No 118
>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=89.77 E-value=0.21 Score=26.85 Aligned_cols=37 Identities=22% Similarity=0.543 Sum_probs=27.8
Q ss_pred cccCccCccCccCceecCCCChhHHHHHHHHHhhCCCCCCCCCcCcC
Q psy10800 24 TLTCPSCKVKRKDAVLTKCFHVFCWDCLRTRYETRQRKCPKCNAAFG 70 (81)
Q Consensus 24 ~~~C~iC~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~ 70 (81)
.-.|-+|...+..+ ||.||..|.. ....|.+|.+.+.
T Consensus 44 ~~~C~~CK~~v~q~-----g~~YCq~CAY-----kkGiCamCGKki~ 80 (90)
T PF10235_consen 44 SSKCKICKTKVHQP-----GAKYCQTCAY-----KKGICAMCGKKIL 80 (90)
T ss_pred CccccccccccccC-----CCccChhhhc-----ccCcccccCCeec
Confidence 34788888766554 8889999976 3356999998874
No 119
>KOG1812|consensus
Probab=89.72 E-value=0.31 Score=32.66 Aligned_cols=36 Identities=28% Similarity=0.568 Sum_probs=26.4
Q ss_pred CCcccCccCccCccCc-----eecCCCChhHHHHHHHHHhh
Q psy10800 22 KETLTCPSCKVKRKDA-----VLTKCFHVFCWDCLRTRYET 57 (81)
Q Consensus 22 ~~~~~C~iC~~~~~~~-----~~~~CgH~fc~~Ci~~~~~~ 57 (81)
.....||.|.-.+.-. ++=.|||-||+.|.-.|...
T Consensus 304 ~~wr~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~~~~~~~ 344 (384)
T KOG1812|consen 304 KRWRQCPKCKFMIELSEGCNHMTCRCGHQFCYMCGGDWKTH 344 (384)
T ss_pred HhcCcCcccceeeeecCCcceEEeeccccchhhcCcchhhC
Confidence 5567899998665321 33369999999999887663
No 120
>PF14353 CpXC: CpXC protein
Probab=89.45 E-value=0.36 Score=27.16 Aligned_cols=47 Identities=21% Similarity=0.294 Sum_probs=26.3
Q ss_pred ccCccCccCccCceecCCCChhHHHHHHHHHhhCC--CCCCCCCcCcCc
Q psy10800 25 LTCPSCKVKRKDAVLTKCFHVFCWDCLRTRYETRQ--RKCPKCNAAFGA 71 (81)
Q Consensus 25 ~~C~iC~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~--~~CP~Cr~~~~~ 71 (81)
++||.|...+...+.+.-.-..=..=..+.+...- ..||.|+..+..
T Consensus 2 itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~ 50 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRL 50 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceec
Confidence 68999998876654332221122233344443221 359999987753
No 121
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=88.16 E-value=1.2 Score=23.32 Aligned_cols=47 Identities=19% Similarity=0.546 Sum_probs=19.7
Q ss_pred cccCccCccCccC---c-eec---CCCChhHHHHHHHHHhhCCCCCCCCCcCcC
Q psy10800 24 TLTCPSCKVKRKD---A-VLT---KCFHVFCWDCLRTRYETRQRKCPKCNAAFG 70 (81)
Q Consensus 24 ~~~C~iC~~~~~~---~-~~~---~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~ 70 (81)
...|.||.+..-- . +.. .|+-..|..|++-=.+.....||.|+....
T Consensus 9 ~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg~q~CpqCkt~yk 62 (80)
T PF14569_consen 9 GQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEGNQVCPQCKTRYK 62 (80)
T ss_dssp S-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS-SB-TTT--B--
T ss_pred CcccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcCcccccccCCCcc
Confidence 4689999875521 1 222 677777999997555656667999987654
No 122
>KOG2979|consensus
Probab=87.23 E-value=0.77 Score=29.26 Aligned_cols=44 Identities=20% Similarity=0.294 Sum_probs=35.1
Q ss_pred cccCccCccCccCc-eecCCCChhHHHHHHHHHhhC-CCCCCCCCc
Q psy10800 24 TLTCPSCKVKRKDA-VLTKCFHVFCWDCLRTRYETR-QRKCPKCNA 67 (81)
Q Consensus 24 ~~~C~iC~~~~~~~-~~~~CgH~fc~~Ci~~~~~~~-~~~CP~Cr~ 67 (81)
.+.||+-...+.+| +...|||+|=.+-+..++... ...||+-+.
T Consensus 176 s~rdPis~~~I~nPviSkkC~HvydrDsI~~~l~~~~~i~CPv~gC 221 (262)
T KOG2979|consen 176 SNRDPISKKPIVNPVISKKCGHVYDRDSIMQILCDEITIRCPVLGC 221 (262)
T ss_pred cccCchhhhhhhchhhhcCcCcchhhhhHHHHhccCceeecccccC
Confidence 68999999999999 456999999999999888742 345888443
No 123
>KOG0309|consensus
Probab=86.92 E-value=0.4 Score=35.04 Aligned_cols=40 Identities=25% Similarity=0.574 Sum_probs=29.2
Q ss_pred cccCccCccCccCc--eecCCCChhHHHHHHHHHhhCCCCCCC
Q psy10800 24 TLTCPSCKVKRKDA--VLTKCFHVFCWDCLRTRYETRQRKCPK 64 (81)
Q Consensus 24 ~~~C~iC~~~~~~~--~~~~CgH~fc~~Ci~~~~~~~~~~CP~ 64 (81)
.+.|.+|.-..... +-..|||+.+.+|+.+||..+ -.||.
T Consensus 1028 ~~~C~~C~l~V~gss~~Cg~C~Hv~H~sc~~eWf~~g-d~Cps 1069 (1081)
T KOG0309|consen 1028 TFQCAICHLAVRGSSNFCGTCGHVGHTSCMMEWFRTG-DVCPS 1069 (1081)
T ss_pred eeeeeeEeeEeeccchhhccccccccHHHHHHHHhcC-CcCCC
Confidence 45577776544433 445899999999999999965 46775
No 124
>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=85.88 E-value=0.8 Score=21.91 Aligned_cols=41 Identities=20% Similarity=0.546 Sum_probs=22.1
Q ss_pred CcccCccCccCccCceecCCCChhHHHHHHHHHhh-CCCCCCCCCcCcC
Q psy10800 23 ETLTCPSCKVKRKDAVLTKCFHVFCWDCLRTRYET-RQRKCPKCNAAFG 70 (81)
Q Consensus 23 ~~~~C~iC~~~~~~~~~~~CgH~fc~~Ci~~~~~~-~~~~CP~Cr~~~~ 70 (81)
+.+.||.|.+.+... .+..-+...-... ....||+|...+.
T Consensus 1 ~~f~CP~C~~~~~~~-------~L~~H~~~~H~~~~~~v~CPiC~~~~~ 42 (54)
T PF05605_consen 1 DSFTCPYCGKGFSES-------SLVEHCEDEHRSESKNVVCPICSSRVT 42 (54)
T ss_pred CCcCCCCCCCccCHH-------HHHHHHHhHCcCCCCCccCCCchhhhh
Confidence 357899999854432 1333333322222 1245999987544
No 125
>KOG4718|consensus
Probab=84.68 E-value=0.77 Score=28.56 Aligned_cols=46 Identities=17% Similarity=0.504 Sum_probs=35.8
Q ss_pred cccCccCccCccCcee-cCCCChhHHHHHHHHHhhCCCCCCCCCcCcC
Q psy10800 24 TLTCPSCKVKRKDAVL-TKCFHVFCWDCLRTRYETRQRKCPKCNAAFG 70 (81)
Q Consensus 24 ~~~C~iC~~~~~~~~~-~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~ 70 (81)
...|.+|+.+....+. -+||-.+...|+..++.. ...||.|+.-++
T Consensus 181 lk~Cn~Ch~LvIqg~rCg~c~i~~h~~c~qty~q~-~~~cphc~d~w~ 227 (235)
T KOG4718|consen 181 LKNCNLCHCLVIQGIRCGSCNIQYHRGCIQTYLQR-RDICPHCGDLWT 227 (235)
T ss_pred HHHHhHhHHHhheeeccCcccchhhhHHHHHHhcc-cCcCCchhcccC
Confidence 4689999987766543 377878899999999985 567999976554
No 126
>KOG4185|consensus
Probab=83.95 E-value=0.3 Score=31.21 Aligned_cols=44 Identities=23% Similarity=0.466 Sum_probs=34.5
Q ss_pred ccCccCccCcc------CceecC--------CCChhHHHHHHHHHhhCCCCCCCCCcC
Q psy10800 25 LTCPSCKVKRK------DAVLTK--------CFHVFCWDCLRTRYETRQRKCPKCNAA 68 (81)
Q Consensus 25 ~~C~iC~~~~~------~~~~~~--------CgH~fc~~Ci~~~~~~~~~~CP~Cr~~ 68 (81)
..|.+|...+. .|.++. |||..|..|+...+.+....||.|+..
T Consensus 208 ~~c~ic~~~~~~n~~~~~p~vl~~~~~~~~~c~htlc~~c~~~~l~~~~~~cp~~~~~ 265 (296)
T KOG4185|consen 208 KLCEICERIYSENDEKLAPLVLSLSRLKEKIEGHTLCKECIDTILLQAGIKCPFCTWS 265 (296)
T ss_pred HHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcchHHHHHHhhhcCCcccce
Confidence 56888876665 244555 999999999999988776789999863
No 127
>KOG2462|consensus
Probab=83.72 E-value=1.4 Score=28.44 Aligned_cols=13 Identities=38% Similarity=0.973 Sum_probs=8.7
Q ss_pred CCCCCCCcCcCcC
Q psy10800 60 RKCPKCNAAFGAN 72 (81)
Q Consensus 60 ~~CP~Cr~~~~~~ 72 (81)
+.||.|++.|..+
T Consensus 216 F~C~hC~kAFADR 228 (279)
T KOG2462|consen 216 FSCPHCGKAFADR 228 (279)
T ss_pred ccCCcccchhcch
Confidence 4588887777543
No 128
>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=83.48 E-value=0.89 Score=23.04 Aligned_cols=13 Identities=38% Similarity=0.966 Sum_probs=9.3
Q ss_pred hhHHHHHHHHHhh
Q psy10800 45 VFCWDCLRTRYET 57 (81)
Q Consensus 45 ~fc~~Ci~~~~~~ 57 (81)
.||..|+.+|...
T Consensus 11 gFCRNCLskWy~~ 23 (68)
T PF06844_consen 11 GFCRNCLSKWYRE 23 (68)
T ss_dssp S--HHHHHHHHHH
T ss_pred HHHHHHHHHHHHH
Confidence 3999999999864
No 129
>KOG0289|consensus
Probab=83.25 E-value=2.3 Score=29.29 Aligned_cols=53 Identities=15% Similarity=0.203 Sum_probs=44.9
Q ss_pred cCccCccCccCceec-CCCChhHHHHHHHHHhhCCCCCCCCCcCcCcCCceeeec
Q psy10800 26 TCPSCKVKRKDAVLT-KCFHVFCWDCLRTRYETRQRKCPKCNAAFGANDYHRLYL 79 (81)
Q Consensus 26 ~C~iC~~~~~~~~~~-~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~~~~~ 79 (81)
.|.|-.+..++|++- .-||+|=++=|++++. ....+|+-..++...++.+|..
T Consensus 2 ~CaISgEvP~~PVvS~~Sg~vfEkrLIEqyI~-e~G~DPIt~~pLs~eelV~Ik~ 55 (506)
T KOG0289|consen 2 VCAISGEVPEEPVVSPVSGHVFEKRLIEQYIA-ETGKDPITNEPLSIEELVEIKV 55 (506)
T ss_pred eecccCCCCCCccccccccchHHHHHHHHHHH-HcCCCCCCCCcCCHHHeeeccc
Confidence 589999999999655 6799999999999988 4577999999999888877754
No 130
>KOG2068|consensus
Probab=82.17 E-value=1.7 Score=28.68 Aligned_cols=46 Identities=22% Similarity=0.573 Sum_probs=33.4
Q ss_pred ccCccCccCccC--c--eecCCCChhHHHHHHHHHhhCCCCCCCCCcCcCc
Q psy10800 25 LTCPSCKVKRKD--A--VLTKCFHVFCWDCLRTRYETRQRKCPKCNAAFGA 71 (81)
Q Consensus 25 ~~C~iC~~~~~~--~--~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~~ 71 (81)
-.||+|.+.... . +-.+||+..|..|+..... ....||.||+....
T Consensus 250 ~s~p~~~~~~~~~d~~~lP~~~~~~~~l~~~~t~~~-~~~~~~~~rk~~~~ 299 (327)
T KOG2068|consen 250 PSCPICYEDLDLTDSNFLPCPCGFRLCLFCHKTISD-GDGRCPGCRKPYER 299 (327)
T ss_pred CCCCCCCCcccccccccccccccccchhhhhhcccc-cCCCCCccCCcccc
Confidence 689999986622 1 2337888889999887665 45779999976643
No 131
>PF12773 DZR: Double zinc ribbon
Probab=81.97 E-value=1.2 Score=20.75 Aligned_cols=25 Identities=28% Similarity=0.663 Sum_probs=13.1
Q ss_pred hHHHHHHHHH--hhCCCCCCCCCcCcC
Q psy10800 46 FCWDCLRTRY--ETRQRKCPKCNAAFG 70 (81)
Q Consensus 46 fc~~Ci~~~~--~~~~~~CP~Cr~~~~ 70 (81)
||..|=..+. ......||.|...+.
T Consensus 14 fC~~CG~~l~~~~~~~~~C~~Cg~~~~ 40 (50)
T PF12773_consen 14 FCPHCGTPLPPPDQSKKICPNCGAENP 40 (50)
T ss_pred CChhhcCChhhccCCCCCCcCCcCCCc
Confidence 4445544333 222345888877654
No 132
>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=81.93 E-value=0.08 Score=33.92 Aligned_cols=44 Identities=27% Similarity=0.393 Sum_probs=20.2
Q ss_pred cccCccCccCccCceecCC---C--ChhHHHHHHHHHhhCCCCCCCCCcC
Q psy10800 24 TLTCPSCKVKRKDAVLTKC---F--HVFCWDCLRTRYETRQRKCPKCNAA 68 (81)
Q Consensus 24 ~~~C~iC~~~~~~~~~~~C---g--H~fc~~Ci~~~~~~~~~~CP~Cr~~ 68 (81)
.-.||||.....-.++..= | +.+|.-|-.+|-..+ ..||.|...
T Consensus 172 ~g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R-~~Cp~Cg~~ 220 (290)
T PF04216_consen 172 RGYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVR-IKCPYCGNT 220 (290)
T ss_dssp -SS-TTT---EEEEEEE------EEEEEETTT--EEE--T-TS-TTT---
T ss_pred CCcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecC-CCCcCCCCC
Confidence 4699999987665544433 4 345888888876643 679999764
No 133
>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=81.48 E-value=1.5 Score=18.85 Aligned_cols=11 Identities=36% Similarity=0.845 Sum_probs=7.6
Q ss_pred CCCCCCCCCcC
Q psy10800 58 RQRKCPKCNAA 68 (81)
Q Consensus 58 ~~~~CP~Cr~~ 68 (81)
....||.|+..
T Consensus 16 ~~~~CP~Cg~~ 26 (33)
T cd00350 16 APWVCPVCGAP 26 (33)
T ss_pred CCCcCcCCCCc
Confidence 34579999764
No 134
>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=80.83 E-value=1.2 Score=21.25 Aligned_cols=32 Identities=22% Similarity=0.485 Sum_probs=21.7
Q ss_pred ccCccCccCccCc----eecCCCChhHHHHHHHHHh
Q psy10800 25 LTCPSCKVKRKDA----VLTKCFHVFCWDCLRTRYE 56 (81)
Q Consensus 25 ~~C~iC~~~~~~~----~~~~CgH~fc~~Ci~~~~~ 56 (81)
..|.+|...|.-- --..||++||..|......
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~~ 38 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRIP 38 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCcChHHcCCeee
Confidence 4688887655432 2237999999999875433
No 135
>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=80.21 E-value=3.5 Score=22.68 Aligned_cols=26 Identities=46% Similarity=0.971 Sum_probs=19.1
Q ss_pred CChhHHHHHHHHHhh--------CCCCCCCCCcC
Q psy10800 43 FHVFCWDCLRTRYET--------RQRKCPKCNAA 68 (81)
Q Consensus 43 gH~fc~~Ci~~~~~~--------~~~~CP~Cr~~ 68 (81)
.-.||..||...... ....||.||..
T Consensus 37 ~~~fC~~CL~~ryge~~~ev~~~~~W~CP~Crgi 70 (105)
T PF10497_consen 37 RGKFCGGCLRNRYGENVEEVLEDPNWKCPKCRGI 70 (105)
T ss_pred cceehHhHHHHHHhhhHHHHhcCCceECCCCCCe
Confidence 667999998877753 23569999863
No 136
>PF15616 TerY-C: TerY-C metal binding domain
Probab=79.91 E-value=0.37 Score=27.68 Aligned_cols=48 Identities=27% Similarity=0.495 Sum_probs=33.6
Q ss_pred HHHhcCCcccCccCccCccCceecCCCChhHHHHHHHHHhhCCCCCCCCCcCcCc
Q psy10800 17 EIREYKETLTCPSCKVKRKDAVLTKCFHVFCWDCLRTRYETRQRKCPKCNAAFGA 71 (81)
Q Consensus 17 ~~~~~~~~~~C~iC~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~~ 71 (81)
....+...-.||-|...+.-.+- .||+.||.. ......||-|......
T Consensus 70 ntseL~g~PgCP~CGn~~~fa~C-~CGkl~Ci~------g~~~~~CPwCg~~g~~ 117 (131)
T PF15616_consen 70 NTSELIGAPGCPHCGNQYAFAVC-GCGKLFCID------GEGEVTCPWCGNEGSF 117 (131)
T ss_pred ehHHhcCCCCCCCCcChhcEEEe-cCCCEEEeC------CCCCEECCCCCCeeee
Confidence 34556667899999986654433 899999864 2344679999877653
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=79.61 E-value=0.58 Score=31.58 Aligned_cols=30 Identities=30% Similarity=0.522 Sum_probs=0.0
Q ss_pred eecCCCChhHHHHHHHHHhh-----CCCCCCCCCcCcC
Q psy10800 38 VLTKCFHVFCWDCLRTRYET-----RQRKCPKCNAAFG 70 (81)
Q Consensus 38 ~~~~CgH~fc~~Ci~~~~~~-----~~~~CP~Cr~~~~ 70 (81)
+.+.|||++-..= |... ..+.||+|+..-.
T Consensus 305 VYl~CGHVhG~h~---Wg~~~~~~~~~r~CPlCr~~g~ 339 (416)
T PF04710_consen 305 VYLNCGHVHGYHN---WGQDSDRDPRSRTCPLCRQVGP 339 (416)
T ss_dssp --------------------------------------
T ss_pred eeccccceeeecc---cccccccccccccCCCccccCC
Confidence 5678999885542 3321 2467999987644
No 138
>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 PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=79.29 E-value=0.51 Score=29.13 Aligned_cols=55 Identities=24% Similarity=0.480 Sum_probs=30.3
Q ss_pred CCcccCccCccCccCceecCCC-------ChhHHHH--HHHHHhhCCCCCCCCCcCcCcCCceee
Q psy10800 22 KETLTCPSCKVKRKDAVLTKCF-------HVFCWDC--LRTRYETRQRKCPKCNAAFGANDYHRL 77 (81)
Q Consensus 22 ~~~~~C~iC~~~~~~~~~~~Cg-------H~fc~~C--i~~~~~~~~~~CP~Cr~~~~~~~~~~~ 77 (81)
.....||+|...|....+.+-+ --||..- +.+++- ....||.|+-.+...++..+
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y-~V~vCP~CgyA~~~~~F~~l 66 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFY-EVWVCPHCGYAAFEEDFEKL 66 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeee-eEEECCCCCCcccccccccC
Confidence 4568999999988765333211 1111110 111111 12459999988887776654
No 140
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=77.43 E-value=2.8 Score=31.22 Aligned_cols=48 Identities=23% Similarity=0.561 Sum_probs=34.3
Q ss_pred cccCccCcc--CccCceecCCCCh-----hHHHHHHHHHhhCC-CCCCCCCcCcCc
Q psy10800 24 TLTCPSCKV--KRKDAVLTKCFHV-----FCWDCLRTRYETRQ-RKCPKCNAAFGA 71 (81)
Q Consensus 24 ~~~C~iC~~--~~~~~~~~~CgH~-----fc~~Ci~~~~~~~~-~~CP~Cr~~~~~ 71 (81)
...|-||.. ...+|..-||..+ .+.+|+.+|+..+. .+|-+|..++.-
T Consensus 12 ~~~CRICr~e~~~d~pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~F 67 (1175)
T COG5183 12 KRSCRICRTEDIRDDPLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKF 67 (1175)
T ss_pred chhceeecCCCCCCCcCcccccccchhHHHHHHHHHHHHhcCCCcceeeecceeee
Confidence 468999974 3445655576432 48999999998654 459999887654
No 141
>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=76.84 E-value=0.46 Score=30.98 Aligned_cols=44 Identities=18% Similarity=0.430 Sum_probs=29.7
Q ss_pred cccCccCccCccCceec----CCCC--hhHHHHHHHHHhhCCCCCCCCCcC
Q psy10800 24 TLTCPSCKVKRKDAVLT----KCFH--VFCWDCLRTRYETRQRKCPKCNAA 68 (81)
Q Consensus 24 ~~~C~iC~~~~~~~~~~----~CgH--~fc~~Ci~~~~~~~~~~CP~Cr~~ 68 (81)
.-.||||.....-.++. .=|+ .+|.-|-.+|--. ...||.|...
T Consensus 184 ~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~~-R~~C~~Cg~~ 233 (305)
T TIGR01562 184 RTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHYV-RVKCSHCEES 233 (305)
T ss_pred CCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCccccc-CccCCCCCCC
Confidence 45999999876544322 2343 3488888887664 3679999763
No 142
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=75.09 E-value=2.9 Score=23.45 Aligned_cols=41 Identities=27% Similarity=0.513 Sum_probs=28.5
Q ss_pred ccCccCccCccCce--------------ecCCCChhHHHHHHHHHhhCCCCCCCCC
Q psy10800 25 LTCPSCKVKRKDAV--------------LTKCFHVFCWDCLRTRYETRQRKCPKCN 66 (81)
Q Consensus 25 ~~C~iC~~~~~~~~--------------~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr 66 (81)
..|--|+..|..+. -..|++.||.+|=. ++.+.-..||.|.
T Consensus 56 ~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~-fiHe~Lh~CPGC~ 110 (112)
T TIGR00622 56 RFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDV-FVHESLHCCPGCI 110 (112)
T ss_pred CcccCcCCCCCCcccccccccccccceeCCCCCCccccccch-hhhhhccCCcCCC
Confidence 45999988775431 23789999999944 4444556799885
No 143
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=75.00 E-value=1.5 Score=28.73 Aligned_cols=44 Identities=20% Similarity=0.381 Sum_probs=30.0
Q ss_pred CcccCccCccCccCcee-c--CCCCh--hHHHHHHHHHhhCCCCCCCCCc
Q psy10800 23 ETLTCPSCKVKRKDAVL-T--KCFHV--FCWDCLRTRYETRQRKCPKCNA 67 (81)
Q Consensus 23 ~~~~C~iC~~~~~~~~~-~--~CgH~--fc~~Ci~~~~~~~~~~CP~Cr~ 67 (81)
..-.||+|.....-.++ + .=|+. +|.-|-.+|--. ...||.|..
T Consensus 186 ~~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~~-R~~C~~Cg~ 234 (309)
T PRK03564 186 QRQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVV-RVKCSNCEQ 234 (309)
T ss_pred CCCCCCCCCCcchhheeeccCCCCceEEEcCCCCCccccc-CccCCCCCC
Confidence 45799999987654432 1 23433 488888887664 367999986
No 144
>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=73.50 E-value=0.31 Score=24.39 Aligned_cols=31 Identities=26% Similarity=0.407 Sum_probs=14.8
Q ss_pred CcccCccCccCccCc----eecCCCChhHHHHHHH
Q psy10800 23 ETLTCPSCKVKRKDA----VLTKCFHVFCWDCLRT 53 (81)
Q Consensus 23 ~~~~C~iC~~~~~~~----~~~~CgH~fc~~Ci~~ 53 (81)
+...|.+|...|.-- ---.||++||..|...
T Consensus 8 ~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~ 42 (69)
T PF01363_consen 8 EASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQ 42 (69)
T ss_dssp G-SB-TTT--B-BSSS-EEE-TTT--EEECCCS-E
T ss_pred CCCcCcCcCCcCCCceeeEccCCCCCEECCchhCC
Confidence 356899999888421 1127999999888753
No 145
>KOG2807|consensus
Probab=72.85 E-value=1.6 Score=28.95 Aligned_cols=41 Identities=27% Similarity=0.621 Sum_probs=26.7
Q ss_pred ccCccCccCccCc---eecCCCChhHHHHHHHHHhhCCCCCCCCC
Q psy10800 25 LTCPSCKVKRKDA---VLTKCFHVFCWDCLRTRYETRQRKCPKCN 66 (81)
Q Consensus 25 ~~C~iC~~~~~~~---~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr 66 (81)
..|-.|+...... .--.|.++||.+|=. ++.+.-..||.|.
T Consensus 331 ~~Cf~C~~~~~~~~~y~C~~Ck~~FCldCDv-~iHesLh~CpgCe 374 (378)
T KOG2807|consen 331 RFCFACQGELLSSGRYRCESCKNVFCLDCDV-FIHESLHNCPGCE 374 (378)
T ss_pred cceeeeccccCCCCcEEchhccceeeccchH-HHHhhhhcCCCcC
Confidence 3488885444332 223789999999943 5554556699985
No 146
>KOG2231|consensus
Probab=71.34 E-value=3.8 Score=29.67 Aligned_cols=46 Identities=20% Similarity=0.447 Sum_probs=34.8
Q ss_pred cCccCccCccCceecCCCC-hhHHHHHHHHHhhCC-----CCCCCCCcCcCc
Q psy10800 26 TCPSCKVKRKDAVLTKCFH-VFCWDCLRTRYETRQ-----RKCPKCNAAFGA 71 (81)
Q Consensus 26 ~C~iC~~~~~~~~~~~CgH-~fc~~Ci~~~~~~~~-----~~CP~Cr~~~~~ 71 (81)
.|+||-..+.-...-+||| ..|..|..+.....+ ..||.|+..+..
T Consensus 2 ~c~ic~~s~~~~~~~s~~h~~v~~~~~~R~~~~~~~~~~~~~~~vcr~~~~~ 53 (669)
T KOG2231|consen 2 SCAICAFSPDFVGRGSCGHNEVCATCVVRLRFELNNRKCSNECPVCRREVET 53 (669)
T ss_pred CcceeecCccccccccccccccchhhhhhhhhhcccccccccCcccccceee
Confidence 4889988777777889999 789999987665433 337999876543
No 147
>KOG3053|consensus
Probab=71.22 E-value=2.3 Score=27.30 Aligned_cols=52 Identities=21% Similarity=0.497 Sum_probs=35.4
Q ss_pred HHhcCCcccCccCccCccCc----eecCC-----CChhHHHHHHHHHhhCCC-------CCCCCCcCc
Q psy10800 18 IREYKETLTCPSCKVKRKDA----VLTKC-----FHVFCWDCLRTRYETRQR-------KCPKCNAAF 69 (81)
Q Consensus 18 ~~~~~~~~~C~iC~~~~~~~----~~~~C-----gH~fc~~Ci~~~~~~~~~-------~CP~Cr~~~ 69 (81)
.++.+.+..|=||+..=++. .+-|| .|..+..|+.+|+.+.+. .||.|+...
T Consensus 14 ~~~~e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEY 81 (293)
T KOG3053|consen 14 SDNQELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEY 81 (293)
T ss_pred CCccccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchh
Confidence 34455677899998754442 23355 245699999999986542 499998764
No 148
>KOG0825|consensus
Probab=70.41 E-value=3 Score=31.00 Aligned_cols=46 Identities=15% Similarity=0.327 Sum_probs=30.8
Q ss_pred cccCccCccCccCc----eec---CCCChhHHHHHHHHHhhCC-----CCCCCCCcCc
Q psy10800 24 TLTCPSCKVKRKDA----VLT---KCFHVFCWDCLRTRYETRQ-----RKCPKCNAAF 69 (81)
Q Consensus 24 ~~~C~iC~~~~~~~----~~~---~CgH~fc~~Ci~~~~~~~~-----~~CP~Cr~~~ 69 (81)
...|++|...+.++ -+. .|+|.||..||..|..+-. -.|++|...+
T Consensus 96 s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci 153 (1134)
T KOG0825|consen 96 SDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESEKHTAHYFCEECV 153 (1134)
T ss_pred ccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhccccccccccHHHHh
Confidence 45777777666552 222 5999999999999987522 2367775443
No 149
>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 PLN02189 cellulose synthase
Probab=69.64 E-value=4.5 Score=30.73 Aligned_cols=47 Identities=17% Similarity=0.526 Sum_probs=32.3
Q ss_pred cccCccCccCccCc----eec---CCCChhHHHHHHHHHhhCCCCCCCCCcCcC
Q psy10800 24 TLTCPSCKVKRKDA----VLT---KCFHVFCWDCLRTRYETRQRKCPKCNAAFG 70 (81)
Q Consensus 24 ~~~C~iC~~~~~~~----~~~---~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~ 70 (81)
...|.||.+.+... ... .|+--.|..|.+--.++++..||.|+....
T Consensus 34 ~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cyeyer~eg~q~CpqCkt~Y~ 87 (1040)
T PLN02189 34 GQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCYEYERREGTQNCPQCKTRYK 87 (1040)
T ss_pred CccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchh
Confidence 45899999875421 222 577778999996444445567999988765
No 151
>COG3492 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=67.70 E-value=4.5 Score=21.87 Aligned_cols=13 Identities=38% Similarity=0.976 Sum_probs=11.4
Q ss_pred hhHHHHHHHHHhh
Q psy10800 45 VFCWDCLRTRYET 57 (81)
Q Consensus 45 ~fc~~Ci~~~~~~ 57 (81)
.||..|+..|...
T Consensus 42 gFCRNCLs~Wy~e 54 (104)
T COG3492 42 GFCRNCLSNWYRE 54 (104)
T ss_pred HHHHHHHHHHHHH
Confidence 4999999999975
No 152
>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=66.76 E-value=4.9 Score=16.97 Aligned_cols=11 Identities=18% Similarity=0.631 Sum_probs=7.0
Q ss_pred cCccCccCccC
Q psy10800 26 TCPSCKVKRKD 36 (81)
Q Consensus 26 ~C~iC~~~~~~ 36 (81)
.|..|.+.+..
T Consensus 1 ~C~~C~~~i~~ 11 (39)
T smart00132 1 KCAGCGKPIRG 11 (39)
T ss_pred CccccCCcccC
Confidence 36677776655
No 153
>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=65.79 E-value=5.4 Score=18.96 Aligned_cols=10 Identities=30% Similarity=0.753 Sum_probs=3.5
Q ss_pred cCccCccCcc
Q psy10800 26 TCPSCKVKRK 35 (81)
Q Consensus 26 ~C~iC~~~~~ 35 (81)
.||+|...|.
T Consensus 22 ~CPlC~r~l~ 31 (54)
T PF04423_consen 22 CCPLCGRPLD 31 (54)
T ss_dssp E-TTT--EE-
T ss_pred cCCCCCCCCC
Confidence 6666665443
No 154
>PLN02436 cellulose synthase A
Probab=65.09 E-value=6.2 Score=30.19 Aligned_cols=47 Identities=19% Similarity=0.554 Sum_probs=32.2
Q ss_pred cccCccCccCccCc----eec---CCCChhHHHHHHHHHhhCCCCCCCCCcCcC
Q psy10800 24 TLTCPSCKVKRKDA----VLT---KCFHVFCWDCLRTRYETRQRKCPKCNAAFG 70 (81)
Q Consensus 24 ~~~C~iC~~~~~~~----~~~---~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~ 70 (81)
...|.||.+..... ... .|+-..|..|.+--.++.+..||.|+....
T Consensus 36 ~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cyeyer~eg~~~Cpqckt~Y~ 89 (1094)
T PLN02436 36 GQTCQICGDEIELTVDGEPFVACNECAFPVCRPCYEYERREGNQACPQCKTRYK 89 (1094)
T ss_pred CccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchh
Confidence 44899999865321 222 577778999996444445567999988765
No 155
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=64.44 E-value=7 Score=25.48 Aligned_cols=45 Identities=20% Similarity=0.424 Sum_probs=31.2
Q ss_pred CCcccCccCccCccCceec----CCCChh--HHHHHHHHHhhCCCCCCCCCc
Q psy10800 22 KETLTCPSCKVKRKDAVLT----KCFHVF--CWDCLRTRYETRQRKCPKCNA 67 (81)
Q Consensus 22 ~~~~~C~iC~~~~~~~~~~----~CgH~f--c~~Ci~~~~~~~~~~CP~Cr~ 67 (81)
+....||+|.......++. .=|-.| |.-|..+|...+ .+|-.|..
T Consensus 183 e~~~~CPvCGS~PvaSmV~~g~~~~GlRYL~CslC~teW~~VR-~KC~nC~~ 233 (308)
T COG3058 183 ESRQYCPVCGSMPVASMVQIGETEQGLRYLHCSLCETEWHYVR-VKCSNCEQ 233 (308)
T ss_pred cccccCCCcCCCCcceeeeecCccccchhhhhhhHHHHHHHHH-HHhccccc
Confidence 3455899999887766433 234444 999999998755 55777755
No 156
>PRK10144 formate-dependent nitrite reductase complex subunit NrfF; Provisional
Probab=63.96 E-value=5.7 Score=22.73 Aligned_cols=22 Identities=18% Similarity=0.484 Sum_probs=17.2
Q ss_pred hHHHHHHHHhcCCcccCccCcc
Q psy10800 11 DEVMLEEIREYKETLTCPSCKV 32 (81)
Q Consensus 11 ~~~~~~~~~~~~~~~~C~iC~~ 32 (81)
+...+.....+...+.||+|+.
T Consensus 27 ~~~~e~r~~~L~~~LRC~vCqn 48 (126)
T PRK10144 27 NPQQQQQALNIASQLRCPQCQN 48 (126)
T ss_pred CHHHHHHHHHHHHcCCCCCCCC
Confidence 3555666778888999999986
No 157
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=63.85 E-value=5.3 Score=18.40 Aligned_cols=22 Identities=23% Similarity=0.381 Sum_probs=14.5
Q ss_pred CccCccCccCceecCCCChhHH
Q psy10800 27 CPSCKVKRKDAVLTKCFHVFCW 48 (81)
Q Consensus 27 C~iC~~~~~~~~~~~CgH~fc~ 48 (81)
|..|...-..-+-+.|++++|.
T Consensus 2 C~~C~~~~~l~~CL~C~~~~c~ 23 (50)
T smart00290 2 CSVCGTIENLWLCLTCGQVGCG 23 (50)
T ss_pred cccCCCcCCeEEecCCCCcccC
Confidence 6666654444466788888884
No 158
>KOG2169|consensus
Probab=63.06 E-value=5.8 Score=28.53 Aligned_cols=53 Identities=25% Similarity=0.522 Sum_probs=35.1
Q ss_pred cCCcccCccCccCccCc-eecCCCChhHHHHHHHHHhh----CCCCCCCCCcCcCcCCc
Q psy10800 21 YKETLTCPSCKVKRKDA-VLTKCFHVFCWDCLRTRYET----RQRKCPKCNAAFGANDY 74 (81)
Q Consensus 21 ~~~~~~C~iC~~~~~~~-~~~~CgH~fc~~Ci~~~~~~----~~~~CP~Cr~~~~~~~~ 74 (81)
+.-.+.||+....+.-| .-..|.|.-|.+-+. ++.. ..+.||+|.+.+...++
T Consensus 303 ~~vSL~CPl~~~Rm~~P~r~~~CkHlQcFD~~~-~lq~n~~~pTW~CPVC~~~~~~e~l 360 (636)
T KOG2169|consen 303 LRVSLNCPLSKMRMSLPARGHTCKHLQCFDALS-YLQMNEQKPTWRCPVCQKAAPFEGL 360 (636)
T ss_pred ceeEecCCcccceeecCCcccccccceecchhh-hHHhccCCCeeeCccCCccccccch
Confidence 44578999988777766 344899887776543 2222 22569999887765543
No 159
>COG4647 AcxC Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=62.86 E-value=2.9 Score=24.18 Aligned_cols=21 Identities=24% Similarity=0.385 Sum_probs=12.6
Q ss_pred cCccCccCceecCCCChhHHH
Q psy10800 29 SCKVKRKDAVLTKCFHVFCWD 49 (81)
Q Consensus 29 iC~~~~~~~~~~~CgH~fc~~ 49 (81)
||+..-...+.-.|||+||..
T Consensus 62 i~qs~~~rv~rcecghsf~d~ 82 (165)
T COG4647 62 ICQSAQKRVIRCECGHSFGDY 82 (165)
T ss_pred EEecccccEEEEeccccccCh
Confidence 344433333455899999854
No 160
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 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. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=62.40 E-value=10 Score=16.66 Aligned_cols=24 Identities=25% Similarity=0.895 Sum_probs=12.8
Q ss_pred hHHHHHHHHHhhCC-------CCCCCCCcCc
Q psy10800 46 FCWDCLRTRYETRQ-------RKCPKCNAAF 69 (81)
Q Consensus 46 fc~~Ci~~~~~~~~-------~~CP~Cr~~~ 69 (81)
.|..|++++..... ..|+.|+-.+
T Consensus 1 lC~~C~~Ey~~p~~RR~~~~~isC~~CGPr~ 31 (35)
T PF07503_consen 1 LCDDCLKEYFDPSNRRFHYQFISCTNCGPRY 31 (35)
T ss_dssp --HHHHHHHCSTTSTTTT-TT--BTTCC-SC
T ss_pred CCHHHHHHHcCCCCCcccCcCccCCCCCCCE
Confidence 37788887765432 3588886544
No 161
>KOG0269|consensus
Probab=62.24 E-value=10 Score=28.07 Aligned_cols=49 Identities=16% Similarity=0.301 Sum_probs=32.8
Q ss_pred cccCccCccCccCce--ecCCCChhHHHHHHHHHhhCCCCCCC--CCcCcCcCC
Q psy10800 24 TLTCPSCKVKRKDAV--LTKCFHVFCWDCLRTRYETRQRKCPK--CNAAFGAND 73 (81)
Q Consensus 24 ~~~C~iC~~~~~~~~--~~~CgH~fc~~Ci~~~~~~~~~~CP~--Cr~~~~~~~ 73 (81)
.-.|.+|...++.-. ---|||.-+..+++.|+. ....||. |........
T Consensus 779 ~~~CtVC~~vi~G~~~~c~~C~H~gH~sh~~sw~~-~~s~ca~~~C~~~c~~~~ 831 (839)
T KOG0269|consen 779 SAKCTVCDLVIRGVDVWCQVCGHGGHDSHLKSWFF-KASPCAKSICPHLCHYSS 831 (839)
T ss_pred hcCceeecceeeeeEeecccccccccHHHHHHHHh-cCCCCccccCCccccccc
Confidence 447888877665432 226999999999999998 4455665 655444433
No 162
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=61.98 E-value=4.6 Score=17.79 Aligned_cols=13 Identities=31% Similarity=0.971 Sum_probs=8.9
Q ss_pred ccCccCccCccCc
Q psy10800 25 LTCPSCKVKRKDA 37 (81)
Q Consensus 25 ~~C~iC~~~~~~~ 37 (81)
+.||-|...|..+
T Consensus 3 i~CP~C~~~f~v~ 15 (37)
T PF13719_consen 3 ITCPNCQTRFRVP 15 (37)
T ss_pred EECCCCCceEEcC
Confidence 5688887766544
No 163
>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=61.95 E-value=4.4 Score=16.50 Aligned_cols=9 Identities=33% Similarity=0.870 Sum_probs=5.2
Q ss_pred cCccCccCc
Q psy10800 26 TCPSCKVKR 34 (81)
Q Consensus 26 ~C~iC~~~~ 34 (81)
.||||...+
T Consensus 3 ~CPiC~~~v 11 (26)
T smart00734 3 QCPVCFREV 11 (26)
T ss_pred cCCCCcCcc
Confidence 466665544
No 164
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=61.88 E-value=4.3 Score=19.37 Aligned_cols=23 Identities=30% Similarity=0.598 Sum_probs=11.6
Q ss_pred CCCChhHHHHHHHHHhhCCCCCCCC
Q psy10800 41 KCFHVFCWDCLRTRYETRQRKCPKC 65 (81)
Q Consensus 41 ~CgH~fc~~Ci~~~~~~~~~~CP~C 65 (81)
.|||.|=..=-.+. .....||.|
T Consensus 33 ~Cgh~w~~~v~~R~--~~~~~CP~C 55 (55)
T PF14311_consen 33 KCGHEWKASVNDRT--RRGKGCPYC 55 (55)
T ss_pred CCCCeeEccHhhhc--cCCCCCCCC
Confidence 46666633322221 234568887
No 165
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=61.80 E-value=4.2 Score=17.88 Aligned_cols=12 Identities=42% Similarity=1.032 Sum_probs=7.4
Q ss_pred ccCccCccCccC
Q psy10800 25 LTCPSCKVKRKD 36 (81)
Q Consensus 25 ~~C~iC~~~~~~ 36 (81)
+.||-|...|..
T Consensus 3 i~Cp~C~~~y~i 14 (36)
T PF13717_consen 3 ITCPNCQAKYEI 14 (36)
T ss_pred EECCCCCCEEeC
Confidence 467777765543
No 166
>PRK11595 DNA utilization protein GntX; Provisional
Probab=61.20 E-value=8.7 Score=23.78 Aligned_cols=38 Identities=21% Similarity=0.449 Sum_probs=22.4
Q ss_pred cCccCccCccCceecCCCChhHHHHHHHHHhhCCCCCCCCCcCc
Q psy10800 26 TCPSCKVKRKDAVLTKCFHVFCWDCLRTRYETRQRKCPKCNAAF 69 (81)
Q Consensus 26 ~C~iC~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~ 69 (81)
.|.+|...+... ....|..|...+-. -...||.|..+.
T Consensus 7 ~C~~C~~~~~~~-----~~~lC~~C~~~l~~-~~~~C~~Cg~~~ 44 (227)
T PRK11595 7 LCWLCRMPLALS-----HWGICSVCSRALRT-LKTCCPQCGLPA 44 (227)
T ss_pred cCccCCCccCCC-----CCcccHHHHhhCCc-ccCcCccCCCcC
Confidence 688888765322 12367888765432 124588887654
No 167
>KOG2042|consensus
Probab=59.53 E-value=11 Score=28.56 Aligned_cols=57 Identities=7% Similarity=0.008 Sum_probs=44.7
Q ss_pred HHhcCCcccCccCccCccCceecC-CCChhHHHHHHHHHhhCCCCCCCCCcCcCcCCce
Q psy10800 18 IREYKETLTCPSCKVKRKDAVLTK-CFHVFCWDCLRTRYETRQRKCPKCNAAFGANDYH 75 (81)
Q Consensus 18 ~~~~~~~~~C~iC~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~ 75 (81)
.....+.+.=|+-...+.+|+++| -|++.++.=+.+.+-.. ..=|+||.+++..++.
T Consensus 864 l~dvpdef~DPlm~Tlm~dPV~LP~Srv~vDRsti~rhlLs~-~tdPFNR~pLt~d~v~ 921 (943)
T KOG2042|consen 864 LGDVPDEFLDPLMSTLMSDPVVLPSSRVTVDRSTIERHLLSD-CTDPFNREPLTEDMVS 921 (943)
T ss_pred hccCchhhhCccccccCCCCccCCcccccccHHHHHHHHhcC-CCCccccccCchhhcC
Confidence 344556788889999999999998 88999999888887743 4459999998876654
No 168
>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=58.93 E-value=14 Score=21.69 Aligned_cols=12 Identities=25% Similarity=0.628 Sum_probs=8.3
Q ss_pred CCCCCCCCCcCc
Q psy10800 58 RQRKCPKCNAAF 69 (81)
Q Consensus 58 ~~~~CP~Cr~~~ 69 (81)
+...||+|...-
T Consensus 31 glv~CP~Cgs~~ 42 (148)
T PF06676_consen 31 GLVSCPVCGSTE 42 (148)
T ss_pred CCccCCCCCCCe
Confidence 345699997653
No 169
>PRK00420 hypothetical protein; Validated
Probab=58.49 E-value=7.1 Score=21.88 Aligned_cols=12 Identities=25% Similarity=0.647 Sum_probs=8.5
Q ss_pred cccCccCccCcc
Q psy10800 24 TLTCPSCKVKRK 35 (81)
Q Consensus 24 ~~~C~iC~~~~~ 35 (81)
...||+|...+.
T Consensus 23 ~~~CP~Cg~pLf 34 (112)
T PRK00420 23 SKHCPVCGLPLF 34 (112)
T ss_pred cCCCCCCCCcce
Confidence 368998886554
No 170
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=58.39 E-value=7.1 Score=24.63 Aligned_cols=22 Identities=23% Similarity=0.395 Sum_probs=14.9
Q ss_pred ccCccCccCccC-c--eecCCCChh
Q psy10800 25 LTCPSCKVKRKD-A--VLTKCFHVF 46 (81)
Q Consensus 25 ~~C~iC~~~~~~-~--~~~~CgH~f 46 (81)
+.||+|...+.. . ..-+.||+|
T Consensus 3 ~~CP~C~~~l~~~~~~~~C~~~h~f 27 (272)
T PRK11088 3 YQCPLCHQPLTLEENSWICPQNHQF 27 (272)
T ss_pred ccCCCCCcchhcCCCEEEcCCCCCC
Confidence 789999987752 2 222457877
No 171
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=57.91 E-value=10 Score=23.19 Aligned_cols=39 Identities=31% Similarity=0.770 Sum_probs=25.4
Q ss_pred CcccCccCccC-----ccC-ce--ecCCCChhHHHHHHHHHhhCCCCCCCCCc
Q psy10800 23 ETLTCPSCKVK-----RKD-AV--LTKCFHVFCWDCLRTRYETRQRKCPKCNA 67 (81)
Q Consensus 23 ~~~~C~iC~~~-----~~~-~~--~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~ 67 (81)
.++.|-+|... |.. .+ -..|+..|+..|.. . ..||.|..
T Consensus 151 kGfiCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~~C~~-----~-~~CpkC~R 197 (202)
T PF13901_consen 151 KGFICEICNSDDIIFPFQIDTTVRCPKCKSVFHKSCFR-----K-KSCPKCAR 197 (202)
T ss_pred CCCCCccCCCCCCCCCCCCCCeeeCCcCccccchhhcC-----C-CCCCCcHh
Confidence 37888888741 111 11 12789999999975 2 55999954
No 172
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=57.82 E-value=7.6 Score=17.38 Aligned_cols=22 Identities=27% Similarity=0.617 Sum_probs=11.3
Q ss_pred CccCccCccC-ceecC-CCChhHH
Q psy10800 27 CPSCKVKRKD-AVLTK-CFHVFCW 48 (81)
Q Consensus 27 C~iC~~~~~~-~~~~~-CgH~fc~ 48 (81)
|.+|.....- |..=+ |+..||.
T Consensus 1 C~~C~~~~~l~~f~C~~C~~~FC~ 24 (39)
T smart00154 1 CHFCRKKVGLTGFKCRHCGNLFCG 24 (39)
T ss_pred CcccCCcccccCeECCccCCcccc
Confidence 4455543333 44334 7777765
No 173
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=57.42 E-value=13 Score=22.17 Aligned_cols=26 Identities=23% Similarity=0.677 Sum_probs=19.8
Q ss_pred CChhHHHHHHHHHhhCCCCCCCCCcCcCcC
Q psy10800 43 FHVFCWDCLRTRYETRQRKCPKCNAAFGAN 72 (81)
Q Consensus 43 gH~fc~~Ci~~~~~~~~~~CP~Cr~~~~~~ 72 (81)
.+.||..|=.+.+. .||.|..++...
T Consensus 27 ~~~fC~kCG~~tI~----~Cp~C~~~IrG~ 52 (158)
T PF10083_consen 27 REKFCSKCGAKTIT----SCPNCSTPIRGD 52 (158)
T ss_pred HHHHHHHhhHHHHH----HCcCCCCCCCCc
Confidence 46799999887665 399998887543
No 174
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=57.21 E-value=8.7 Score=21.98 Aligned_cols=22 Identities=18% Similarity=0.460 Sum_probs=17.1
Q ss_pred hHHHHHHHHhcCCcccCccCcc
Q psy10800 11 DEVMLEEIREYKETLTCPSCKV 32 (81)
Q Consensus 11 ~~~~~~~~~~~~~~~~C~iC~~ 32 (81)
+...+.....+...+.|++|+.
T Consensus 27 ~~~~e~r~~~L~~~LRC~vCqn 48 (126)
T TIGR03147 27 NPEQRTRAVALAKSLRCPQCQN 48 (126)
T ss_pred CHHHHHHHHHHHHhCCCCCCCC
Confidence 3555666778888999999986
No 175
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=57.09 E-value=0.74 Score=22.30 Aligned_cols=32 Identities=28% Similarity=0.588 Sum_probs=20.7
Q ss_pred CcccCc--cCccCccC-------ceec-CCCChhHHHHHHHH
Q psy10800 23 ETLTCP--SCKVKRKD-------AVLT-KCFHVFCWDCLRTR 54 (81)
Q Consensus 23 ~~~~C~--iC~~~~~~-------~~~~-~CgH~fc~~Ci~~~ 54 (81)
....|| -|...+.. .+.- .||+.||..|...|
T Consensus 17 ~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~ 58 (64)
T smart00647 17 DLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPW 58 (64)
T ss_pred CccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcC
Confidence 445688 78654322 1333 68999999887765
No 176
>KOG1829|consensus
Probab=56.99 E-value=5.5 Score=28.43 Aligned_cols=22 Identities=41% Similarity=1.094 Sum_probs=17.1
Q ss_pred CCCChhHHHHHHHHHhhCCCCCCCCC
Q psy10800 41 KCFHVFCWDCLRTRYETRQRKCPKCN 66 (81)
Q Consensus 41 ~CgH~fc~~Ci~~~~~~~~~~CP~Cr 66 (81)
.||+.|+..|+.+ ....||.|-
T Consensus 536 ~C~avfH~~C~~r----~s~~CPrC~ 557 (580)
T KOG1829|consen 536 TCLAVFHKKCLRR----KSPCCPRCE 557 (580)
T ss_pred HHHHHHHHHHHhc----cCCCCCchH
Confidence 6999999999874 334499994
No 177
>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=56.95 E-value=6.8 Score=18.38 Aligned_cols=30 Identities=23% Similarity=0.556 Sum_probs=16.2
Q ss_pred cccCccCccCccCc-eecCCCChhHHHHHHH
Q psy10800 24 TLTCPSCKVKRKDA-VLTKCFHVFCWDCLRT 53 (81)
Q Consensus 24 ~~~C~iC~~~~~~~-~~~~CgH~fc~~Ci~~ 53 (81)
=+.|..|...+... ....=|..+|..|..+
T Consensus 26 Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~ 56 (58)
T PF00412_consen 26 CFKCSKCGKPLNDGDFYEKDGKPYCKDCYQK 56 (58)
T ss_dssp TSBETTTTCBTTTSSEEEETTEEEEHHHHHH
T ss_pred ccccCCCCCccCCCeeEeECCEEECHHHHhh
Confidence 35666666655544 3333445566666543
No 178
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=56.71 E-value=18 Score=17.19 Aligned_cols=28 Identities=29% Similarity=0.469 Sum_probs=19.4
Q ss_pred cCccCccCcc--CceecCCCChhHHHHHHHH
Q psy10800 26 TCPSCKVKRK--DAVLTKCFHVFCWDCLRTR 54 (81)
Q Consensus 26 ~C~iC~~~~~--~~~~~~CgH~fc~~Ci~~~ 54 (81)
.|+||.+.+. ..+.+.=| ..|.+|+.+.
T Consensus 1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDG-YICKDCLKKL 30 (51)
T ss_pred CCCccccccccccceeccCc-cchHHHHHHh
Confidence 4899987443 23556667 5799999875
No 179
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=56.13 E-value=4.5 Score=18.14 Aligned_cols=6 Identities=50% Similarity=1.752 Sum_probs=3.0
Q ss_pred CCCCCc
Q psy10800 62 CPKCNA 67 (81)
Q Consensus 62 CP~Cr~ 67 (81)
||.|..
T Consensus 22 C~~C~G 27 (41)
T PF13453_consen 22 CPSCGG 27 (41)
T ss_pred CCCCCe
Confidence 555543
No 180
>KOG2113|consensus
Probab=56.11 E-value=10 Score=25.30 Aligned_cols=46 Identities=7% Similarity=-0.062 Sum_probs=34.3
Q ss_pred hcCCcccCccCccCccCceecCCCCh-hHHHHHHHHHhhCCCCCCCCCcC
Q psy10800 20 EYKETLTCPSCKVKRKDAVLTKCFHV-FCWDCLRTRYETRQRKCPKCNAA 68 (81)
Q Consensus 20 ~~~~~~~C~iC~~~~~~~~~~~CgH~-fc~~Ci~~~~~~~~~~CP~Cr~~ 68 (81)
.+-..++|-+|.+-+...+..+|+|. ||..|.. +. ....||.|...
T Consensus 339 ~~~s~~~~~~~~~~~~st~~~~~~~n~~~~~~a~--~s-~~~~~~~c~~~ 385 (394)
T KOG2113|consen 339 GLMSSLKGTSAGFGLLSTIWSGGNMNLSPGSLAS--AS-ASPTSSTCDHN 385 (394)
T ss_pred cchhhcccccccCceeeeEeecCCcccChhhhhh--cc-cCCcccccccc
Confidence 34446789999988888888899985 6999977 22 33679999653
No 181
>COG3088 CcmH Uncharacterized protein involved in biosynthesis of c-type cytochromes [Posttranslational modification, protein turnover, chaperones]
Probab=56.11 E-value=7.2 Score=23.03 Aligned_cols=23 Identities=30% Similarity=0.660 Sum_probs=17.8
Q ss_pred hHHHHHHHHhcCCcccCccCccC
Q psy10800 11 DEVMLEEIREYKETLTCPSCKVK 33 (81)
Q Consensus 11 ~~~~~~~~~~~~~~~~C~iC~~~ 33 (81)
+.........+...+.||.|++.
T Consensus 31 ~~~qe~ra~~Lt~~LRCp~CQNq 53 (153)
T COG3088 31 DPAQEQRARALTEELRCPQCQNQ 53 (153)
T ss_pred CHHHHHHHHHHHHhcCCCcCCCC
Confidence 45556677888899999999863
No 182
>KOG3799|consensus
Probab=56.06 E-value=8.9 Score=22.35 Aligned_cols=25 Identities=32% Similarity=0.632 Sum_probs=15.3
Q ss_pred cCCcccCccCccC-ccCceecCCCChhHHHH
Q psy10800 21 YKETLTCPSCKVK-RKDAVLTKCFHVFCWDC 50 (81)
Q Consensus 21 ~~~~~~C~iC~~~-~~~~~~~~CgH~fc~~C 50 (81)
..++-.|.||+.. |.+ .|||. |..|
T Consensus 62 v~ddatC~IC~KTKFAD----G~GH~-C~YC 87 (169)
T KOG3799|consen 62 VGDDATCGICHKTKFAD----GCGHN-CSYC 87 (169)
T ss_pred cCcCcchhhhhhccccc----ccCcc-cchh
Confidence 3567899999863 433 46663 3444
No 183
>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=55.88 E-value=8 Score=21.46 Aligned_cols=14 Identities=36% Similarity=0.883 Sum_probs=8.7
Q ss_pred CCCCCCCCcCcCcC
Q psy10800 59 QRKCPKCNAAFGAN 72 (81)
Q Consensus 59 ~~~CP~Cr~~~~~~ 72 (81)
...||.|+..+...
T Consensus 26 PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 26 PIVCPKCGTEFPPE 39 (108)
T ss_pred CccCCCCCCccCcc
Confidence 34577777766544
No 184
>KOG2789|consensus
Probab=55.64 E-value=6.7 Score=26.85 Aligned_cols=33 Identities=21% Similarity=0.521 Sum_probs=24.2
Q ss_pred CcccCccCccCccCc--eecCCCChhHHHHHHHHH
Q psy10800 23 ETLTCPSCKVKRKDA--VLTKCFHVFCWDCLRTRY 55 (81)
Q Consensus 23 ~~~~C~iC~~~~~~~--~~~~CgH~fc~~Ci~~~~ 55 (81)
...+||||+-++-.. ...-|....|..|+.++-
T Consensus 73 r~~ecpicflyyps~~n~~rcC~~~Ic~ecf~~~~ 107 (482)
T KOG2789|consen 73 RKTECPICFLYYPSAKNLVRCCSETICGECFAPFG 107 (482)
T ss_pred ccccCceeeeecccccchhhhhccchhhhheeccc
Confidence 356999999877554 334688899999986643
No 185
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=54.61 E-value=16 Score=20.04 Aligned_cols=13 Identities=31% Similarity=0.968 Sum_probs=10.1
Q ss_pred CCCCCCCcCcCcC
Q psy10800 60 RKCPKCNAAFGAN 72 (81)
Q Consensus 60 ~~CP~Cr~~~~~~ 72 (81)
..||.|+.+|...
T Consensus 81 ~~Cp~C~spFNp~ 93 (105)
T COG4357 81 GSCPYCQSPFNPG 93 (105)
T ss_pred CCCCCcCCCCCcc
Confidence 4599999988653
No 186
>PRK04023 DNA polymerase II large subunit; Validated
Probab=54.38 E-value=11 Score=28.81 Aligned_cols=52 Identities=19% Similarity=0.335 Sum_probs=34.8
Q ss_pred CcccCccCccCccCceecCCCC-----hhHHHHHHHHHhhCCCCCCCCCcCcCcCCceee
Q psy10800 23 ETLTCPSCKVKRKDAVLTKCFH-----VFCWDCLRTRYETRQRKCPKCNAAFGANDYHRL 77 (81)
Q Consensus 23 ~~~~C~iC~~~~~~~~~~~CgH-----~fc~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~~~ 77 (81)
....|+-|........-..||. .||..|-.. . ....||.|...........+
T Consensus 625 g~RfCpsCG~~t~~frCP~CG~~Te~i~fCP~CG~~--~-~~y~CPKCG~El~~~s~~~i 681 (1121)
T PRK04023 625 GRRKCPSCGKETFYRRCPFCGTHTEPVYRCPRCGIE--V-EEDECEKCGREPTPYSKRKI 681 (1121)
T ss_pred cCccCCCCCCcCCcccCCCCCCCCCcceeCccccCc--C-CCCcCCCCCCCCCccceEEe
Confidence 3679999998764444446884 489999332 1 22459999988876655544
No 187
>PLN02248 cellulose synthase-like protein
Probab=52.47 E-value=19 Score=27.85 Aligned_cols=33 Identities=24% Similarity=0.679 Sum_probs=26.0
Q ss_pred CCCChhHHHHHHHHHhhCCCCCCCCCcCcCcCCc
Q psy10800 41 KCFHVFCWDCLRTRYETRQRKCPKCNAAFGANDY 74 (81)
Q Consensus 41 ~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~~~~~ 74 (81)
.|+...|.+|....++. ...||-|+.+....+.
T Consensus 149 ~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~ 181 (1135)
T PLN02248 149 ECGFKICRDCYIDAVKS-GGICPGCKEPYKVTDL 181 (1135)
T ss_pred cccchhHHhHhhhhhhc-CCCCCCCccccccccc
Confidence 57788899999998885 4679999887755443
No 188
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=51.98 E-value=14 Score=22.13 Aligned_cols=11 Identities=36% Similarity=0.893 Sum_probs=7.6
Q ss_pred CCCCCCCCCcC
Q psy10800 58 RQRKCPKCNAA 68 (81)
Q Consensus 58 ~~~~CP~Cr~~ 68 (81)
....||+|..+
T Consensus 148 ~P~~CPiCga~ 158 (166)
T COG1592 148 APEVCPICGAP 158 (166)
T ss_pred CCCcCCCCCCh
Confidence 34569999764
No 189
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=51.72 E-value=10 Score=14.94 Aligned_cols=6 Identities=50% Similarity=1.796 Sum_probs=2.6
Q ss_pred CCCCCc
Q psy10800 62 CPKCNA 67 (81)
Q Consensus 62 CP~Cr~ 67 (81)
||.|+.
T Consensus 16 C~~CG~ 21 (23)
T PF13240_consen 16 CPNCGT 21 (23)
T ss_pred hhhhCC
Confidence 444433
No 190
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=51.45 E-value=1.6 Score=17.75 Aligned_cols=6 Identities=67% Similarity=1.896 Sum_probs=2.8
Q ss_pred CCCCCc
Q psy10800 62 CPKCNA 67 (81)
Q Consensus 62 CP~Cr~ 67 (81)
||.|..
T Consensus 19 C~~CG~ 24 (26)
T PF13248_consen 19 CPNCGA 24 (26)
T ss_pred ChhhCC
Confidence 555443
No 191
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=51.30 E-value=8.7 Score=15.35 Aligned_cols=8 Identities=50% Similarity=1.451 Sum_probs=3.6
Q ss_pred CCCCCcCc
Q psy10800 62 CPKCNAAF 69 (81)
Q Consensus 62 CP~Cr~~~ 69 (81)
||.|+..|
T Consensus 5 C~~CgR~F 12 (25)
T PF13913_consen 5 CPICGRKF 12 (25)
T ss_pred CCCCCCEE
Confidence 44444444
No 192
>PF10146 zf-C4H2: Zinc finger-containing protein ; InterPro: IPR018482 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 family of proteins which appears to have a highly conserved zinc finger domain at the C-terminal end, described as -C-X2-CH-X3-H-X5-C-X2-C-. The structure is predicted to contain a coiled coil. Members of this family are annotated as being tumour-associated antigen HCA127 in humans, but this could not be confirmed.
Probab=51.07 E-value=18 Score=22.81 Aligned_cols=28 Identities=21% Similarity=0.466 Sum_probs=19.8
Q ss_pred hHHHHHHHHHhhCCCCCCCCCcCcCcCCc
Q psy10800 46 FCWDCLRTRYETRQRKCPKCNAAFGANDY 74 (81)
Q Consensus 46 fc~~Ci~~~~~~~~~~CP~Cr~~~~~~~~ 74 (81)
-|.+|-..+-+ ....||+|++....++.
T Consensus 196 ~C~sC~qqIHR-NAPiCPlCK~KsRSrnp 223 (230)
T PF10146_consen 196 TCQSCHQQIHR-NAPICPLCKAKSRSRNP 223 (230)
T ss_pred hhHhHHHHHhc-CCCCCcccccccccCCC
Confidence 38999887655 34679999887655443
No 193
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=50.68 E-value=17 Score=28.01 Aligned_cols=47 Identities=17% Similarity=0.529 Sum_probs=31.2
Q ss_pred cccCccCccCccC-----ce--ecCCCChhHHHHHHHHHhhCCCCCCCCCcCcC
Q psy10800 24 TLTCPSCKVKRKD-----AV--LTKCFHVFCWDCLRTRYETRQRKCPKCNAAFG 70 (81)
Q Consensus 24 ~~~C~iC~~~~~~-----~~--~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~ 70 (81)
...|.||.+...- +. --.||-..|..|.+==.++++..||.|+....
T Consensus 17 ~qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCYEYEr~eG~q~CPqCktrYk 70 (1079)
T PLN02638 17 GQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCYEYERKDGNQSCPQCKTKYK 70 (1079)
T ss_pred CceeeecccccCcCCCCCEEEEeccCCCccccchhhhhhhcCCccCCccCCchh
Confidence 4589999986532 21 22678778999985322334456999987764
No 194
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=50.45 E-value=18 Score=20.88 Aligned_cols=24 Identities=29% Similarity=0.833 Sum_probs=14.6
Q ss_pred hhHHHHHHHHHhhCCCCCCCCCcCcCcC
Q psy10800 45 VFCWDCLRTRYETRQRKCPKCNAAFGAN 72 (81)
Q Consensus 45 ~fc~~Ci~~~~~~~~~~CP~Cr~~~~~~ 72 (81)
.||..|-...+. .||.|..++...
T Consensus 29 afcskcgeati~----qcp~csasirgd 52 (160)
T COG4306 29 AFCSKCGEATIT----QCPICSASIRGD 52 (160)
T ss_pred HHHhhhchHHHh----cCCccCCccccc
Confidence 477777554333 378887776543
No 195
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=49.53 E-value=13 Score=18.33 Aligned_cols=13 Identities=23% Similarity=0.856 Sum_probs=8.8
Q ss_pred CCCCCCCCcCcCc
Q psy10800 59 QRKCPKCNAAFGA 71 (81)
Q Consensus 59 ~~~CP~Cr~~~~~ 71 (81)
++.||.|++++..
T Consensus 3 HkHC~~CG~~Ip~ 15 (59)
T PF09889_consen 3 HKHCPVCGKPIPP 15 (59)
T ss_pred CCcCCcCCCcCCc
Confidence 3458888777764
No 196
>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=48.86 E-value=4.3 Score=15.35 Aligned_cols=11 Identities=27% Similarity=0.715 Sum_probs=5.2
Q ss_pred cCccCccCccC
Q psy10800 26 TCPSCKVKRKD 36 (81)
Q Consensus 26 ~C~iC~~~~~~ 36 (81)
.|++|...|..
T Consensus 2 ~C~~C~~~f~~ 12 (23)
T PF00096_consen 2 KCPICGKSFSS 12 (23)
T ss_dssp EETTTTEEESS
T ss_pred CCCCCCCccCC
Confidence 35555544443
No 197
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=48.77 E-value=1.8 Score=18.01 Aligned_cols=11 Identities=36% Similarity=0.794 Sum_probs=4.1
Q ss_pred cCccCccCccC
Q psy10800 26 TCPSCKVKRKD 36 (81)
Q Consensus 26 ~C~iC~~~~~~ 36 (81)
.|+.|...+..
T Consensus 3 ~C~rC~~~~~~ 13 (30)
T PF06827_consen 3 KCPRCWNYIED 13 (30)
T ss_dssp B-TTT--BBEE
T ss_pred cCccCCCcceE
Confidence 45666555443
No 198
>KOG2272|consensus
Probab=48.72 E-value=12 Score=24.23 Aligned_cols=32 Identities=25% Similarity=0.391 Sum_probs=22.0
Q ss_pred HHHHHHHhcCCcccCccCccCccCceecCCCC
Q psy10800 13 VMLEEIREYKETLTCPSCKVKRKDAVLTKCFH 44 (81)
Q Consensus 13 ~~~~~~~~~~~~~~C~iC~~~~~~~~~~~CgH 44 (81)
.+...+..+..++-|+-|.+.+..|+-..|..
T Consensus 172 eL~sdaRevk~eLyClrChD~mgipiCgaC~r 203 (332)
T KOG2272|consen 172 ELTSDAREVKGELYCLRCHDKMGIPICGACRR 203 (332)
T ss_pred cccchhhhhccceeccccccccCCcccccccC
Confidence 34455667777888888888777776555543
No 199
>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=47.89 E-value=7.2 Score=14.38 Aligned_cols=8 Identities=38% Similarity=0.953 Sum_probs=2.7
Q ss_pred CccCccCc
Q psy10800 27 CPSCKVKR 34 (81)
Q Consensus 27 C~iC~~~~ 34 (81)
|++|...+
T Consensus 3 C~~C~~~~ 10 (24)
T PF13894_consen 3 CPICGKSF 10 (24)
T ss_dssp -SSTS-EE
T ss_pred CcCCCCcC
Confidence 44444433
No 200
>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=47.86 E-value=5.2 Score=22.28 Aligned_cols=30 Identities=23% Similarity=0.466 Sum_probs=19.4
Q ss_pred CcccCccCccCcc---Cc--eecCCCChhHHHHHH
Q psy10800 23 ETLTCPSCKVKRK---DA--VLTKCFHVFCWDCLR 52 (81)
Q Consensus 23 ~~~~C~iC~~~~~---~~--~~~~CgH~fc~~Ci~ 52 (81)
....|.+|...|. +. +-..|+|.+|..|-.
T Consensus 53 ~~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~ 87 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGV 87 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEE
T ss_pred CCcchhhhCCcccccCCCCCcCCcCCccccCccCC
Confidence 4679999987542 22 445788888888854
No 201
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=47.25 E-value=19 Score=27.63 Aligned_cols=48 Identities=21% Similarity=0.499 Sum_probs=32.3
Q ss_pred CcccCccCccCccC-----ce--ecCCCChhHHHHHHHHHhhCCCCCCCCCcCcC
Q psy10800 23 ETLTCPSCKVKRKD-----AV--LTKCFHVFCWDCLRTRYETRQRKCPKCNAAFG 70 (81)
Q Consensus 23 ~~~~C~iC~~~~~~-----~~--~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~ 70 (81)
....|.||.+.... +. --.|+-..|..|.+-=.+++...||.|+....
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 35689999986532 22 22678778999995333444456999987765
No 202
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=47.21 E-value=10 Score=27.50 Aligned_cols=8 Identities=38% Similarity=1.373 Sum_probs=4.7
Q ss_pred cCccCccC
Q psy10800 26 TCPSCKVK 33 (81)
Q Consensus 26 ~C~iC~~~ 33 (81)
.||-|...
T Consensus 3 ~Cp~Cg~~ 10 (645)
T PRK14559 3 ICPQCQFE 10 (645)
T ss_pred cCCCCCCc
Confidence 56666654
No 203
>COG5627 MMS21 DNA repair protein MMS21 [DNA replication, recombination, and repair]
Probab=46.28 E-value=14 Score=23.55 Aligned_cols=41 Identities=22% Similarity=0.403 Sum_probs=31.4
Q ss_pred cccCccCccCccCc-eecCCCChhHHHHHHHHHhhC-CCCCCC
Q psy10800 24 TLTCPSCKVKRKDA-VLTKCFHVFCWDCLRTRYETR-QRKCPK 64 (81)
Q Consensus 24 ~~~C~iC~~~~~~~-~~~~CgH~fc~~Ci~~~~~~~-~~~CP~ 64 (81)
..+|||-...+..| ....|.|.|=.+-|..++... .+.||.
T Consensus 189 ~nrCpitl~p~~~pils~kcnh~~e~D~I~~~lq~~~trvcp~ 231 (275)
T COG5627 189 SNRCPITLNPDFYPILSSKCNHKPEMDLINKKLQVECTRVCPR 231 (275)
T ss_pred cccCCcccCcchhHHHHhhhcccccHHHHHHHhcCCceeecch
Confidence 57999988888777 455899999999888877632 245775
No 204
>PF10186 Atg14: UV radiation resistance protein and autophagy-related subunit 14; InterPro: IPR018791 Class III phosphatidylinositol 3-kinase (PI3-kinase) regulates multiple membrane trafficking. In yeast, two distinct PI3-kinase complexes are known: complex I (Vps34, Vps15, Vps30/Atg6, and Atg14) is involved in autophagy, and complex II (Vps34, Vps15, Vps30/Atg6, and Vps38) functions in the vacuolar protein sorting pathway. In mammals, the counterparts of Vps34, Vps15, and Vps30/Atg6 are Vps34, p150, and Beclin 1, respectively. Mammalian UV irradiation resistance-associated gene (UVRAG) has been identified as identical to yeast Vps38 []. The Atg14 (autophagy-related protein 14) proteins are hydrophilic proteins and have a coiled-coil motif at the N terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole []. This entry represents Atg14 and UVRAG, which bind Beclin 1 to forms two distinct PI3-kinase complexes. This entry also includes Bakor (beclin-1-associated autophagy-related key regulator), also known as autophagy-related protein 14-like protein, which share sequence similarity to the yeast Atg14 protein []. Barkor positively regulates autophagy through its interaction with Beclin-1, with decreased levels of autophagosome formation observed when Barkor expression is eliminated []. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. ; GO: 0010508 positive regulation of autophagy
Probab=45.78 E-value=18 Score=22.78 Aligned_cols=22 Identities=27% Similarity=0.898 Sum_probs=15.1
Q ss_pred cCccCccCccCceecCCCChhHHHHHHHHH
Q psy10800 26 TCPSCKVKRKDAVLTKCFHVFCWDCLRTRY 55 (81)
Q Consensus 26 ~C~iC~~~~~~~~~~~CgH~fc~~Ci~~~~ 55 (81)
.|+||. ..-.+.+|..|+..-+
T Consensus 1 ~C~iC~--------~~~~~~~C~~C~~~~L 22 (302)
T PF10186_consen 1 QCPICH--------NSRRRFYCANCVNNRL 22 (302)
T ss_pred CCCCCC--------CCCCCeECHHHHHHHH
Confidence 489998 2334557889987654
No 205
>KOG3476|consensus
Probab=45.67 E-value=1.7 Score=23.30 Aligned_cols=36 Identities=19% Similarity=0.466 Sum_probs=26.0
Q ss_pred ccCccCccCccCceecCCCChhHHHHHHHHHhhCCCCCCCCCcCcC
Q psy10800 25 LTCPSCKVKRKDAVLTKCFHVFCWDCLRTRYETRQRKCPKCNAAFG 70 (81)
Q Consensus 25 ~~C~iC~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~ 70 (81)
..|-||......| |..||..|... ...|-+|.+.+.
T Consensus 55 ~kC~iCk~~vHQ~-----GshYC~tCAY~-----KgiCAMCGKki~ 90 (100)
T KOG3476|consen 55 AKCRICKQLVHQP-----GSHYCQTCAYK-----KGICAMCGKKIL 90 (100)
T ss_pred chhHHHHHHhcCC-----cchhHhHhhhh-----hhHHHHhhhHhh
Confidence 5788888877776 66689999763 244888877654
No 206
>PLN02195 cellulose synthase A
Probab=45.50 E-value=29 Score=26.53 Aligned_cols=46 Identities=20% Similarity=0.555 Sum_probs=31.5
Q ss_pred cccCccCccCcc-----Cce--ecCCCChhHHHHHHHHHh-hCCCCCCCCCcCcC
Q psy10800 24 TLTCPSCKVKRK-----DAV--LTKCFHVFCWDCLRTRYE-TRQRKCPKCNAAFG 70 (81)
Q Consensus 24 ~~~C~iC~~~~~-----~~~--~~~CgH~fc~~Ci~~~~~-~~~~~CP~Cr~~~~ 70 (81)
...|.||.+... ++. --.|+-..|..|.+ +-+ +++..||.|+....
T Consensus 6 ~~~c~~cgd~~~~~~~g~~fvaC~eC~~pvCrpCye-yer~eg~q~CpqCkt~Yk 59 (977)
T PLN02195 6 APICATCGEEVGVDSNGEAFVACHECSYPLCKACLE-YEIKEGRKVCLRCGGPYD 59 (977)
T ss_pred CccceecccccCcCCCCCeEEEeccCCCccccchhh-hhhhcCCccCCccCCccc
Confidence 457999988553 222 22788888999985 443 34456999998776
No 207
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 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 B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=45.14 E-value=16 Score=16.02 Aligned_cols=30 Identities=17% Similarity=0.438 Sum_probs=19.5
Q ss_pred cccCccCccCccCceecCCCChhHHHHHHH
Q psy10800 24 TLTCPSCKVKRKDAVLTKCFHVFCWDCLRT 53 (81)
Q Consensus 24 ~~~C~iC~~~~~~~~~~~CgH~fc~~Ci~~ 53 (81)
...|+.+.+....-.-..|+-.+|..|+..
T Consensus 3 ~~~C~~H~~~~~~~~C~~C~~~~C~~C~~~ 32 (42)
T PF00643_consen 3 EPKCPEHPEEPLSLFCEDCNEPLCSECTVS 32 (42)
T ss_dssp SSB-SSTTTSBEEEEETTTTEEEEHHHHHT
T ss_pred CccCccCCccceEEEecCCCCccCccCCCC
Confidence 446776665444444558888899999763
No 208
>PRK01343 zinc-binding protein; Provisional
Probab=44.77 E-value=17 Score=17.85 Aligned_cols=11 Identities=36% Similarity=0.978 Sum_probs=8.0
Q ss_pred CCCCCCCcCcC
Q psy10800 60 RKCPKCNAAFG 70 (81)
Q Consensus 60 ~~CP~Cr~~~~ 70 (81)
..||+|++.+.
T Consensus 10 ~~CP~C~k~~~ 20 (57)
T PRK01343 10 RPCPECGKPST 20 (57)
T ss_pred CcCCCCCCcCc
Confidence 45888888764
No 209
>KOG4451|consensus
Probab=44.33 E-value=24 Score=22.46 Aligned_cols=27 Identities=22% Similarity=0.575 Sum_probs=19.2
Q ss_pred hHHHHHHHHHhhCCCCCCCCCcCcCcCC
Q psy10800 46 FCWDCLRTRYETRQRKCPKCNAAFGAND 73 (81)
Q Consensus 46 fc~~Ci~~~~~~~~~~CP~Cr~~~~~~~ 73 (81)
.|.+|-..+-+ ....||+|+.....++
T Consensus 251 ~ClsChqqIHR-NAPiCPlCKaKsRSrN 277 (286)
T KOG4451|consen 251 VCLSCHQQIHR-NAPICPLCKAKSRSRN 277 (286)
T ss_pred HHHHHHHHHhc-CCCCCcchhhccccCC
Confidence 48888887655 3467999987765444
No 210
>KOG3362|consensus
Probab=43.86 E-value=6 Score=23.22 Aligned_cols=28 Identities=21% Similarity=0.562 Sum_probs=18.2
Q ss_pred cccCccCccCccCceecCCCChhH-HHHHH
Q psy10800 24 TLTCPSCKVKRKDAVLTKCFHVFC-WDCLR 52 (81)
Q Consensus 24 ~~~C~iC~~~~~~~~~~~CgH~fc-~~Ci~ 52 (81)
...|.||. ++....-+.||..|| ..|+.
T Consensus 118 r~fCaVCG-~~S~ysC~~CG~kyCsv~C~~ 146 (156)
T KOG3362|consen 118 RKFCAVCG-YDSKYSCVNCGTKYCSVRCLK 146 (156)
T ss_pred chhhhhcC-CCchhHHHhcCCceeechhhh
Confidence 45788888 445445668888875 34543
No 211
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=43.84 E-value=9.3 Score=28.03 Aligned_cols=21 Identities=29% Similarity=0.654 Sum_probs=13.1
Q ss_pred HHHHHHHHHhhCC-------CCCCCCCc
Q psy10800 47 CWDCLRTRYETRQ-------RKCPKCNA 67 (81)
Q Consensus 47 c~~Ci~~~~~~~~-------~~CP~Cr~ 67 (81)
|..|.+++-.... ..||.|+-
T Consensus 154 C~~C~~EY~dP~nRRfHAQp~aCp~CGP 181 (750)
T COG0068 154 CPFCDKEYKDPLNRRFHAQPIACPKCGP 181 (750)
T ss_pred CHHHHHHhcCccccccccccccCcccCC
Confidence 7778777655322 34888854
No 212
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=42.83 E-value=24 Score=22.91 Aligned_cols=9 Identities=33% Similarity=0.862 Sum_probs=5.5
Q ss_pred CCCCCCCcC
Q psy10800 60 RKCPKCNAA 68 (81)
Q Consensus 60 ~~CP~Cr~~ 68 (81)
..||.|+..
T Consensus 270 ~~C~~Cgt~ 278 (279)
T TIGR00627 270 PICKTCKTA 278 (279)
T ss_pred CCCCCCCCC
Confidence 457777654
No 213
>KOG4218|consensus
Probab=42.59 E-value=31 Score=23.47 Aligned_cols=14 Identities=29% Similarity=0.453 Sum_probs=10.6
Q ss_pred CcccCccCccCccC
Q psy10800 23 ETLTCPSCKVKRKD 36 (81)
Q Consensus 23 ~~~~C~iC~~~~~~ 36 (81)
.+..||+|.+....
T Consensus 14 l~ElCPVCGDkVSG 27 (475)
T KOG4218|consen 14 LGELCPVCGDKVSG 27 (475)
T ss_pred cccccccccCcccc
Confidence 35689999987654
No 214
>COG4098 comFA Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [DNA replication, recombination, and repair]
Probab=41.76 E-value=9.3 Score=25.98 Aligned_cols=30 Identities=20% Similarity=0.522 Sum_probs=24.3
Q ss_pred CcccCccCc-cCccCceecCCCChhHHHHHH
Q psy10800 23 ETLTCPSCK-VKRKDAVLTKCFHVFCWDCLR 52 (81)
Q Consensus 23 ~~~~C~iC~-~~~~~~~~~~CgH~fc~~Ci~ 52 (81)
..+.|.-|. .....-..++||-.||..|+.
T Consensus 38 gk~~C~RC~~~~~~~~~~lp~~~~YCr~Cl~ 68 (441)
T COG4098 38 GKYRCNRCGNTHIELFAKLPCGCLYCRNCLM 68 (441)
T ss_pred CcEEehhcCCcchhhhcccccceEeehhhhh
Confidence 357899998 556666788999999999985
No 215
>PF06221 zf-C2HC5: Putative zinc finger motif, C2HC5-type; InterPro: IPR009349 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 zinc finger appears to be common in activating signal cointegrator 1/thyroid receptor interacting protein 4. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=40.14 E-value=21 Score=17.51 Aligned_cols=28 Identities=18% Similarity=0.456 Sum_probs=19.2
Q ss_pred ceecCCCChhHHHHHHHHHhhC-CCCCCCCCcCcCc
Q psy10800 37 AVLTKCFHVFCWDCLRTRYETR-QRKCPKCNAAFGA 71 (81)
Q Consensus 37 ~~~~~CgH~fc~~Ci~~~~~~~-~~~CP~Cr~~~~~ 71 (81)
+--+.||-++|.. +. ...||+|..++..
T Consensus 19 ~NCl~CGkIiC~~-------Eg~~~pC~fCg~~l~~ 47 (57)
T PF06221_consen 19 PNCLNCGKIICEQ-------EGPLGPCPFCGTPLLS 47 (57)
T ss_pred ccccccChhhccc-------ccCcCcCCCCCCcccC
Confidence 3456889888763 23 4669999877654
No 216
>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=40.12 E-value=4.9 Score=18.54 Aligned_cols=26 Identities=23% Similarity=0.698 Sum_probs=15.4
Q ss_pred CccCccCccCceec---CCCChhHHHHHH
Q psy10800 27 CPSCKVKRKDAVLT---KCFHVFCWDCLR 52 (81)
Q Consensus 27 C~iC~~~~~~~~~~---~CgH~fc~~Ci~ 52 (81)
|.||........++ .|+..|+..|+.
T Consensus 2 C~vC~~~~~~~~~i~C~~C~~~~H~~C~~ 30 (51)
T PF00628_consen 2 CPVCGQSDDDGDMIQCDSCNRWYHQECVG 30 (51)
T ss_dssp BTTTTSSCTTSSEEEBSTTSCEEETTTST
T ss_pred CcCCCCcCCCCCeEEcCCCChhhCcccCC
Confidence 67777733332222 677777777764
No 217
>PLN02400 cellulose synthase
Probab=39.48 E-value=20 Score=27.64 Aligned_cols=47 Identities=17% Similarity=0.495 Sum_probs=31.0
Q ss_pred cccCccCccCccC-----ce--ecCCCChhHHHHHHHHHhhCCCCCCCCCcCcC
Q psy10800 24 TLTCPSCKVKRKD-----AV--LTKCFHVFCWDCLRTRYETRQRKCPKCNAAFG 70 (81)
Q Consensus 24 ~~~C~iC~~~~~~-----~~--~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~ 70 (81)
...|.||.+.... +. --.|+-..|..|.+==.+.++..||.|+....
T Consensus 36 gqiCqICGD~VG~t~dGe~FVAC~eCaFPVCRpCYEYERkeGnq~CPQCkTrYk 89 (1085)
T PLN02400 36 GQICQICGDDVGVTETGDVFVACNECAFPVCRPCYEYERKDGTQCCPQCKTRYR 89 (1085)
T ss_pred CceeeecccccCcCCCCCEEEEEccCCCccccchhheecccCCccCcccCCccc
Confidence 4589999986532 21 22677778999985222334456999987764
No 218
>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=38.93 E-value=22 Score=16.88 Aligned_cols=15 Identities=20% Similarity=0.758 Sum_probs=10.5
Q ss_pred HHhcCCcccCccCcc
Q psy10800 18 IREYKETLTCPSCKV 32 (81)
Q Consensus 18 ~~~~~~~~~C~iC~~ 32 (81)
...+.++..||+|..
T Consensus 28 f~~Lp~~w~CP~C~a 42 (50)
T cd00730 28 FEDLPDDWVCPVCGA 42 (50)
T ss_pred HhHCCCCCCCCCCCC
Confidence 345677788888864
No 219
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=38.83 E-value=18 Score=18.13 Aligned_cols=11 Identities=27% Similarity=0.881 Sum_probs=8.6
Q ss_pred CCCCCCCcCcC
Q psy10800 60 RKCPKCNAAFG 70 (81)
Q Consensus 60 ~~CP~Cr~~~~ 70 (81)
..||+|++.+.
T Consensus 7 v~CP~C~k~~~ 17 (62)
T PRK00418 7 VNCPTCGKPVE 17 (62)
T ss_pred ccCCCCCCccc
Confidence 46999999863
No 220
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 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 AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=38.00 E-value=17 Score=16.38 Aligned_cols=20 Identities=35% Similarity=0.564 Sum_probs=9.0
Q ss_pred CccCccCceecC-CCChhHHH
Q psy10800 30 CKVKRKDAVLTK-CFHVFCWD 49 (81)
Q Consensus 30 C~~~~~~~~~~~-CgH~fc~~ 49 (81)
|......|+.=+ |+..||..
T Consensus 6 C~~~~~~~~~C~~C~~~FC~~ 26 (43)
T PF01428_consen 6 CKKKDFLPFKCKHCGKSFCLK 26 (43)
T ss_dssp T--BCTSHEE-TTTS-EE-TT
T ss_pred CcCccCCCeECCCCCcccCcc
Confidence 655544554444 88888764
No 221
>KOG0801|consensus
Probab=37.81 E-value=24 Score=21.28 Aligned_cols=15 Identities=33% Similarity=0.791 Sum_probs=11.3
Q ss_pred CCCCCCCcCcCcCCc
Q psy10800 60 RKCPKCNAAFGANDY 74 (81)
Q Consensus 60 ~~CP~Cr~~~~~~~~ 74 (81)
.+||+|.+.+...++
T Consensus 139 ~KCPvC~K~V~sDd~ 153 (205)
T KOG0801|consen 139 MKCPVCHKVVPSDDA 153 (205)
T ss_pred ccCCccccccCCCcc
Confidence 579999888776654
No 222
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=37.61 E-value=20 Score=16.79 Aligned_cols=16 Identities=19% Similarity=0.700 Sum_probs=8.6
Q ss_pred HHHhcCCcccCccCcc
Q psy10800 17 EIREYKETLTCPSCKV 32 (81)
Q Consensus 17 ~~~~~~~~~~C~iC~~ 32 (81)
....+.++..||+|..
T Consensus 27 ~F~~Lp~~w~CP~C~a 42 (47)
T PF00301_consen 27 PFEDLPDDWVCPVCGA 42 (47)
T ss_dssp -GGGS-TT-B-TTTSS
T ss_pred CHHHCCCCCcCcCCCC
Confidence 3456777888888864
No 223
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=36.82 E-value=23 Score=20.37 Aligned_cols=11 Identities=27% Similarity=0.446 Sum_probs=5.9
Q ss_pred cccCccCccCc
Q psy10800 24 TLTCPSCKVKR 34 (81)
Q Consensus 24 ~~~C~iC~~~~ 34 (81)
...||-|...|
T Consensus 9 Kr~Cp~cg~kF 19 (129)
T TIGR02300 9 KRICPNTGSKF 19 (129)
T ss_pred cccCCCcCccc
Confidence 44566655444
No 224
>KOG1729|consensus
Probab=36.61 E-value=15 Score=24.01 Aligned_cols=31 Identities=23% Similarity=0.476 Sum_probs=20.5
Q ss_pred CcccCccCccC-ccCc----eecCCCChhHHHHHHH
Q psy10800 23 ETLTCPSCKVK-RKDA----VLTKCFHVFCWDCLRT 53 (81)
Q Consensus 23 ~~~~C~iC~~~-~~~~----~~~~CgH~fc~~Ci~~ 53 (81)
+...|.+|... |.-- -.-.||++||..|-..
T Consensus 167 ea~~C~~C~~~~Ftl~~RRHHCR~CG~ivC~~Cs~n 202 (288)
T KOG1729|consen 167 EATECMVCGCTEFTLSERRHHCRNCGDIVCAPCSRN 202 (288)
T ss_pred cceecccCCCccccHHHHHHHHHhcchHhhhhhhcC
Confidence 35788888873 3211 1127999999988654
No 225
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=35.35 E-value=13 Score=15.39 Aligned_cols=9 Identities=33% Similarity=1.062 Sum_probs=4.1
Q ss_pred CCCCCcCcC
Q psy10800 62 CPKCNAAFG 70 (81)
Q Consensus 62 CP~Cr~~~~ 70 (81)
||.|...+.
T Consensus 2 CP~C~s~l~ 10 (28)
T PF03119_consen 2 CPVCGSKLV 10 (28)
T ss_dssp -TTT--BEE
T ss_pred cCCCCCEeE
Confidence 777776654
No 226
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=34.62 E-value=14 Score=18.04 Aligned_cols=23 Identities=22% Similarity=0.320 Sum_probs=13.1
Q ss_pred CccCccC-ccCceecCCCChhHHH
Q psy10800 27 CPSCKVK-RKDAVLTKCFHVFCWD 49 (81)
Q Consensus 27 C~iC~~~-~~~~~~~~CgH~fc~~ 49 (81)
|..|... -..-+-|.||+.+|..
T Consensus 1 C~~C~~~~~~lw~CL~Cg~~~C~~ 24 (63)
T PF02148_consen 1 CSVCGSTNSNLWLCLTCGYVGCGR 24 (63)
T ss_dssp -SSSHTCSSSEEEETTTS-EEETT
T ss_pred CCCCCCcCCceEEeCCCCcccccC
Confidence 4566654 1222567899999885
No 227
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=34.35 E-value=58 Score=17.51 Aligned_cols=17 Identities=18% Similarity=0.436 Sum_probs=11.9
Q ss_pred HHhcCCcccCccCccCc
Q psy10800 18 IREYKETLTCPSCKVKR 34 (81)
Q Consensus 18 ~~~~~~~~~C~iC~~~~ 34 (81)
.....+...||.|....
T Consensus 29 e~~~~~~~~Cp~C~~~~ 45 (89)
T COG1997 29 EAQQRAKHVCPFCGRTT 45 (89)
T ss_pred HHHHhcCCcCCCCCCcc
Confidence 34445678999998753
No 228
>KOG2066|consensus
Probab=34.05 E-value=15 Score=27.40 Aligned_cols=33 Identities=24% Similarity=0.454 Sum_probs=24.2
Q ss_pred cccCccCccCcc-------CceecCCCChhHHHHHHHHHh
Q psy10800 24 TLTCPSCKVKRK-------DAVLTKCFHVFCWDCLRTRYE 56 (81)
Q Consensus 24 ~~~C~iC~~~~~-------~~~~~~CgH~fc~~Ci~~~~~ 56 (81)
.-.|..|.+... .-+.+.|||.|+..|+....-
T Consensus 784 e~rc~~c~~~~l~~~~~~~~~~v~~c~h~yhk~c~~~~~~ 823 (846)
T KOG2066|consen 784 EERCSSCFEPNLPSGAAFDSVVVFHCGHMYHKECLMMESL 823 (846)
T ss_pred hhhhhhhcccccccCcccceeeEEEccchhhhcccccHHH
Confidence 448888887543 236779999999999865444
No 229
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=33.99 E-value=19 Score=19.96 Aligned_cols=24 Identities=33% Similarity=0.591 Sum_probs=12.9
Q ss_pred ecCCCChhHHHHHHHHHhhCCCCCCCCCc
Q psy10800 39 LTKCFHVFCWDCLRTRYETRQRKCPKCNA 67 (81)
Q Consensus 39 ~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~ 67 (81)
-+.|||.|-.. ...+. +.||.|..
T Consensus 5 CtrCG~vf~~g--~~~il---~GCp~CG~ 28 (112)
T COG3364 5 CTRCGEVFDDG--SEEIL---SGCPKCGC 28 (112)
T ss_pred ecccccccccc--cHHHH---ccCccccc
Confidence 35788877443 11112 34888853
No 230
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=33.86 E-value=16 Score=14.48 Aligned_cols=12 Identities=25% Similarity=0.672 Sum_probs=7.4
Q ss_pred CcccCccCccCc
Q psy10800 23 ETLTCPSCKVKR 34 (81)
Q Consensus 23 ~~~~C~iC~~~~ 34 (81)
..+.|++|...|
T Consensus 13 k~~~C~~C~k~F 24 (26)
T PF13465_consen 13 KPYKCPYCGKSF 24 (26)
T ss_dssp SSEEESSSSEEE
T ss_pred CCCCCCCCcCee
Confidence 346777776544
No 231
>KOG3842|consensus
Probab=33.85 E-value=54 Score=22.08 Aligned_cols=47 Identities=23% Similarity=0.526 Sum_probs=28.2
Q ss_pred CcccCccCccCc--------------cC---c--eecCCCChhHHHHHHHHHhhC---------CCCCCCCCcCcC
Q psy10800 23 ETLTCPSCKVKR--------------KD---A--VLTKCFHVFCWDCLRTRYETR---------QRKCPKCNAAFG 70 (81)
Q Consensus 23 ~~~~C~iC~~~~--------------~~---~--~~~~CgH~fc~~Ci~~~~~~~---------~~~CP~Cr~~~~ 70 (81)
...+||+|...- .+ | ...+|||.--.. ...+|.+- ...||+|...+.
T Consensus 340 ~~r~CPmC~~~gp~V~L~lG~E~~f~vD~G~pthaF~PCGHv~sek-t~~YWs~iplPhGT~~f~a~CPFC~~~L~ 414 (429)
T KOG3842|consen 340 RERECPMCRVVGPYVPLWLGCEAGFYVDAGPPTHAFNPCGHVCSEK-TVKYWSQIPLPHGTHAFHAACPFCATQLA 414 (429)
T ss_pred ccCcCCeeeeecceeeeeccccceeEecCCCcccccCCcccccchh-hhhHhhcCcCCCccccccccCcchhhhhc
Confidence 367899998521 11 1 234899965444 44455532 135999987764
No 232
>KOG3475|consensus
Probab=33.58 E-value=33 Score=18.29 Aligned_cols=28 Identities=25% Similarity=0.678 Sum_probs=21.6
Q ss_pred CChhHHHHHHHHHhhCCCCCCCCCcCcC
Q psy10800 43 FHVFCWDCLRTRYETRQRKCPKCNAAFG 70 (81)
Q Consensus 43 gH~fc~~Ci~~~~~~~~~~CP~Cr~~~~ 70 (81)
.|+.|..|=.+.+.-+.+.|..|.-+..
T Consensus 15 shtlC~RCG~~syH~QKstC~~CGYpaa 42 (92)
T KOG3475|consen 15 SHTLCRRCGRRSYHIQKSTCSSCGYPAA 42 (92)
T ss_pred chHHHHHhCchhhhhhcccccccCCcch
Confidence 5888999988777766677888876643
No 233
>KOG1609|consensus
Probab=33.15 E-value=47 Score=21.14 Aligned_cols=48 Identities=17% Similarity=0.482 Sum_probs=32.8
Q ss_pred cccCccCccCccC----ceecCCC-----ChhHHHHHHHHHhhCC-CCCCCCCcCcCc
Q psy10800 24 TLTCPSCKVKRKD----AVLTKCF-----HVFCWDCLRTRYETRQ-RKCPKCNAAFGA 71 (81)
Q Consensus 24 ~~~C~iC~~~~~~----~~~~~Cg-----H~fc~~Ci~~~~~~~~-~~CP~Cr~~~~~ 71 (81)
...|-||...... +...+|. ...+..|+..|+.... ..|.+|...+..
T Consensus 78 ~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~~ 135 (323)
T KOG1609|consen 78 GPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFIN 135 (323)
T ss_pred CCcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhccccCeeeeccccccee
Confidence 4679999875432 4566663 2348999999998543 459999776543
No 234
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=32.88 E-value=22 Score=17.88 Aligned_cols=21 Identities=29% Similarity=0.771 Sum_probs=11.7
Q ss_pred HHHHHHHHHhhCCCCCCCCCcC
Q psy10800 47 CWDCLRTRYETRQRKCPKCNAA 68 (81)
Q Consensus 47 c~~Ci~~~~~~~~~~CP~Cr~~ 68 (81)
|..|.. ....+...||.|...
T Consensus 7 C~~Ck~-l~~~d~e~CP~Cgs~ 27 (64)
T COG2093 7 CKNCKR-LTPEDTEICPVCGST 27 (64)
T ss_pred Hhhccc-cCCCCCccCCCCCCc
Confidence 555532 233333459999776
No 235
>PF09654 DUF2396: Protein of unknown function (DUF2396); InterPro: IPR013472 These conserved hypothetical proteins have so far been found only in the Cyanobacteria. They are about 170 amino acids long and contain a CxxCx(14)CxxH motif near the N terminus.
Probab=32.83 E-value=21 Score=20.97 Aligned_cols=11 Identities=27% Similarity=0.920 Sum_probs=6.6
Q ss_pred CCCCCCCcCcC
Q psy10800 60 RKCPKCNAAFG 70 (81)
Q Consensus 60 ~~CP~Cr~~~~ 70 (81)
..||.||+.+.
T Consensus 7 i~CPhCRq~ip 17 (161)
T PF09654_consen 7 IQCPHCRQTIP 17 (161)
T ss_pred CcCchhhcccc
Confidence 45666666554
No 236
>TIGR02652 conserved hypothetical protein TIGR02652, cyanobacterial. Members of this family of conserved hypothetical proteins are found, so far, only in the Cyanobacteria. Members are about 170 amino acids long and share a motif CxxCx(14)CxxH near the amino end.
Probab=32.65 E-value=20 Score=21.03 Aligned_cols=12 Identities=33% Similarity=0.919 Sum_probs=7.4
Q ss_pred CCCCCCCcCcCc
Q psy10800 60 RKCPKCNAAFGA 71 (81)
Q Consensus 60 ~~CP~Cr~~~~~ 71 (81)
..||.||+.+..
T Consensus 10 i~CPhCRQ~ipA 21 (163)
T TIGR02652 10 IRCPHCRQNIPA 21 (163)
T ss_pred CcCchhhcccch
Confidence 457777766543
No 237
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=32.60 E-value=28 Score=18.60 Aligned_cols=16 Identities=25% Similarity=0.594 Sum_probs=8.0
Q ss_pred CCCCCCcCcCcCCcee
Q psy10800 61 KCPKCNAAFGANDYHR 76 (81)
Q Consensus 61 ~CP~Cr~~~~~~~~~~ 76 (81)
.||.|+..+.-.+..+
T Consensus 35 ~C~~C~~~L~~~~lIP 50 (92)
T PF06750_consen 35 HCPHCGHPLSWWDLIP 50 (92)
T ss_pred cCcCCCCcCcccccch
Confidence 3555555555444433
No 238
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=32.49 E-value=15 Score=18.02 Aligned_cols=11 Identities=36% Similarity=0.839 Sum_probs=5.2
Q ss_pred CCCCCCcCcCc
Q psy10800 61 KCPKCNAAFGA 71 (81)
Q Consensus 61 ~CP~Cr~~~~~ 71 (81)
.||.|++.+..
T Consensus 4 ~CP~C~k~~~~ 14 (57)
T PF03884_consen 4 KCPICGKPVEW 14 (57)
T ss_dssp E-TTT--EEE-
T ss_pred cCCCCCCeecc
Confidence 49999887654
No 239
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=32.49 E-value=12 Score=18.22 Aligned_cols=12 Identities=42% Similarity=0.836 Sum_probs=8.5
Q ss_pred CcccCccCccCc
Q psy10800 23 ETLTCPSCKVKR 34 (81)
Q Consensus 23 ~~~~C~iC~~~~ 34 (81)
..+.||+|...-
T Consensus 3 ~Wi~CP~CgnKT 14 (55)
T PF14205_consen 3 EWILCPICGNKT 14 (55)
T ss_pred eEEECCCCCCcc
Confidence 357899998644
No 240
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=32.43 E-value=11 Score=14.43 Aligned_cols=11 Identities=18% Similarity=0.462 Sum_probs=6.0
Q ss_pred cCccCccCccC
Q psy10800 26 TCPSCKVKRKD 36 (81)
Q Consensus 26 ~C~iC~~~~~~ 36 (81)
.|.+|...+..
T Consensus 2 ~C~~C~~~f~s 12 (25)
T PF12874_consen 2 YCDICNKSFSS 12 (25)
T ss_dssp EETTTTEEESS
T ss_pred CCCCCCCCcCC
Confidence 46666555544
No 241
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=31.94 E-value=26 Score=15.06 Aligned_cols=9 Identities=56% Similarity=1.302 Sum_probs=7.0
Q ss_pred CCCCCCCcC
Q psy10800 60 RKCPKCNAA 68 (81)
Q Consensus 60 ~~CP~Cr~~ 68 (81)
..||+|.+.
T Consensus 19 ~~CP~Cg~~ 27 (34)
T cd00729 19 EKCPICGAP 27 (34)
T ss_pred CcCcCCCCc
Confidence 469999874
No 242
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=31.77 E-value=14 Score=14.46 Aligned_cols=12 Identities=17% Similarity=0.531 Sum_probs=7.0
Q ss_pred ccCccCccCccC
Q psy10800 25 LTCPSCKVKRKD 36 (81)
Q Consensus 25 ~~C~iC~~~~~~ 36 (81)
+.|.+|...|..
T Consensus 2 ~~C~~C~~~F~~ 13 (27)
T PF13912_consen 2 FECDECGKTFSS 13 (27)
T ss_dssp EEETTTTEEESS
T ss_pred CCCCccCCccCC
Confidence 356666665543
No 243
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=31.24 E-value=35 Score=15.71 Aligned_cols=11 Identities=36% Similarity=1.074 Sum_probs=7.2
Q ss_pred CCCCCCCcCcC
Q psy10800 60 RKCPKCNAAFG 70 (81)
Q Consensus 60 ~~CP~Cr~~~~ 70 (81)
..||.|..+|+
T Consensus 9 K~C~~C~rpf~ 19 (42)
T PF10013_consen 9 KICPVCGRPFT 19 (42)
T ss_pred CcCcccCCcch
Confidence 45777777664
No 244
>KOG4642|consensus
Probab=31.13 E-value=46 Score=21.59 Aligned_cols=54 Identities=7% Similarity=-0.053 Sum_probs=41.7
Q ss_pred CcccCccCccCccCceecCCCChhHHHHHHHHHhhCCCCCCCCCcCcCcCCcee
Q psy10800 23 ETLTCPSCKVKRKDAVLTKCFHVFCWDCLRTRYETRQRKCPKCNAAFGANDYHR 76 (81)
Q Consensus 23 ~~~~C~iC~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~~ 76 (81)
+.+-+.|-++++.+|++++-|-++=..=|.+.+..-..-=|+-|.+++...+.+
T Consensus 210 d~lcgkIt~el~~~pvi~psgIty~ra~I~Ehl~rvghfdpvtr~~Lte~q~ip 263 (284)
T KOG4642|consen 210 DYLCGKITLELMREPVITPSGITYDRADIEEHLQRVGHFDPVTRWPLTEYQLIP 263 (284)
T ss_pred chhhhhhhHHhhcCCccCccccchhHHHHHHHHHHhccCCchhcccCCHHhhcc
Confidence 355667889999999999999999888888887754444577888777665544
No 245
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=31.09 E-value=37 Score=16.57 Aligned_cols=15 Identities=20% Similarity=0.456 Sum_probs=9.0
Q ss_pred CCCCCCCcCcCcCCc
Q psy10800 60 RKCPKCNAAFGANDY 74 (81)
Q Consensus 60 ~~CP~Cr~~~~~~~~ 74 (81)
..||.|+........
T Consensus 18 ~~CP~CG~~t~~~~P 32 (56)
T PRK13130 18 EICPVCGGKTKNPHP 32 (56)
T ss_pred ccCcCCCCCCCCCCC
Confidence 347888776654433
No 246
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.03 E-value=31 Score=17.42 Aligned_cols=10 Identities=30% Similarity=0.906 Sum_probs=6.1
Q ss_pred CCCCCCcCcC
Q psy10800 61 KCPKCNAAFG 70 (81)
Q Consensus 61 ~CP~Cr~~~~ 70 (81)
.||.|.+++.
T Consensus 9 ~CP~Cgkpv~ 18 (65)
T COG3024 9 PCPTCGKPVV 18 (65)
T ss_pred cCCCCCCccc
Confidence 4777766553
No 247
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=31.02 E-value=22 Score=27.98 Aligned_cols=54 Identities=20% Similarity=0.495 Sum_probs=30.8
Q ss_pred cccCccCccCccCceecCCCChh-----HHHHHHHHHhhC--CCCCCCCCcCcCcCCceee
Q psy10800 24 TLTCPSCKVKRKDAVLTKCFHVF-----CWDCLRTRYETR--QRKCPKCNAAFGANDYHRL 77 (81)
Q Consensus 24 ~~~C~iC~~~~~~~~~~~CgH~f-----c~~Ci~~~~~~~--~~~CP~Cr~~~~~~~~~~~ 77 (81)
.+.||-|........--.||... |..|=.+.-... ...||.|..++....-+.+
T Consensus 667 ~rkCPkCG~~t~~~fCP~CGs~te~vy~CPsCGaev~~des~a~~CP~CGtplv~~~~~~i 727 (1337)
T PRK14714 667 RRRCPSCGTETYENRCPDCGTHTEPVYVCPDCGAEVPPDESGRVECPRCDVELTPYQRRTI 727 (1337)
T ss_pred EEECCCCCCccccccCcccCCcCCCceeCccCCCccCCCccccccCCCCCCcccccceEEe
Confidence 47899999765444444677553 666644321110 1258888877655444333
No 248
>KOG0006|consensus
Probab=30.68 E-value=69 Score=21.62 Aligned_cols=37 Identities=30% Similarity=0.670 Sum_probs=27.3
Q ss_pred HhcCCcccCccCccCccCceecCCC--ChhHHHHHHHHH
Q psy10800 19 REYKETLTCPSCKVKRKDAVLTKCF--HVFCWDCLRTRY 55 (81)
Q Consensus 19 ~~~~~~~~C~iC~~~~~~~~~~~Cg--H~fc~~Ci~~~~ 55 (81)
..-.....|-.|.+.-..-..++|. |+.|.+|..-+-
T Consensus 216 ~~N~~ni~C~~Ctdv~~~vlvf~Cns~HvtC~dCFr~yc 254 (446)
T KOG0006|consen 216 ATNSRNITCITCTDVRSPVLVFQCNSRHVTCLDCFRLYC 254 (446)
T ss_pred hcccccceeEEecCCccceEEEecCCceeehHHhhhhHh
Confidence 3344578899998876666777887 999999987443
No 249
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=30.13 E-value=31 Score=20.77 Aligned_cols=31 Identities=26% Similarity=0.761 Sum_probs=20.5
Q ss_pred CcccCccCccCc--cCceecCCCChhHHHHHHHHHhhCCCCCCCCCcCcCc
Q psy10800 23 ETLTCPSCKVKR--KDAVLTKCFHVFCWDCLRTRYETRQRKCPKCNAAFGA 71 (81)
Q Consensus 23 ~~~~C~iC~~~~--~~~~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~~ 71 (81)
..+.||.|...+ .+++ . ..+.||.|+..+..
T Consensus 116 ~~Y~Cp~C~~rytf~eA~-----------------~-~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 116 MFFFCPNCHIRFTFDEAM-----------------E-YGFRCPQCGEMLEE 148 (178)
T ss_pred CEEECCCCCcEEeHHHHh-----------------h-cCCcCCCCCCCCee
Confidence 468899997644 3432 1 24779999887754
No 250
>PF12292 DUF3624: Protein of unknown function (DUF3624); InterPro: IPR022072 This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. There is a conserved GRC sequence motif.
Probab=29.95 E-value=14 Score=19.30 Aligned_cols=19 Identities=26% Similarity=0.905 Sum_probs=12.5
Q ss_pred HHHHHHHHHhhCCCCCCCC
Q psy10800 47 CWDCLRTRYETRQRKCPKC 65 (81)
Q Consensus 47 c~~Ci~~~~~~~~~~CP~C 65 (81)
|..|-+.|+.++-..|..|
T Consensus 3 C~~C~~~~F~~KiGRC~rC 21 (77)
T PF12292_consen 3 CNDCQESWFWQKIGRCQRC 21 (77)
T ss_pred hhhHHHHHHHHHhccHHHH
Confidence 5667777777655556655
No 251
>KOG0396|consensus
Probab=29.84 E-value=26 Score=23.83 Aligned_cols=43 Identities=19% Similarity=0.195 Sum_probs=30.5
Q ss_pred ceecCCCChhHHHHHHHHHhhCCCCCCCCCcCcCcCCceeeec
Q psy10800 37 AVLTKCFHVFCWDCLRTRYETRQRKCPKCNAAFGANDYHRLYL 79 (81)
Q Consensus 37 ~~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~~~~~ 79 (81)
|..++=|+++-..-+.+|-...+..||.-.+.+....+.++|+
T Consensus 346 P~lfpnG~Vyg~~~L~s~~~~~~i~dP~~~k~f~~~~l~kvy~ 388 (389)
T KOG0396|consen 346 PHLFPNGYVYGTKALESLNEDDGIGDPRTKKVFRYSELCKVYL 388 (389)
T ss_pred cccccCceeehhHHHHhhcccCCCcCCCCCccccHHHHHHHhc
Confidence 4666788888888888766544467888888777666655554
No 252
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=29.78 E-value=39 Score=13.29 Aligned_cols=12 Identities=17% Similarity=0.490 Sum_probs=6.4
Q ss_pred ccCccCccCccC
Q psy10800 25 LTCPSCKVKRKD 36 (81)
Q Consensus 25 ~~C~iC~~~~~~ 36 (81)
+.|.+|...|.+
T Consensus 2 ~~C~~C~k~f~~ 13 (27)
T PF12171_consen 2 FYCDACDKYFSS 13 (27)
T ss_dssp CBBTTTTBBBSS
T ss_pred CCcccCCCCcCC
Confidence 345666555544
No 253
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=29.77 E-value=14 Score=25.72 Aligned_cols=50 Identities=22% Similarity=0.426 Sum_probs=24.4
Q ss_pred CCcccCccCccCccCc-eecCCCChhHHHHHHHHHhhC-----------CCCCCCCCcCcCc
Q psy10800 22 KETLTCPSCKVKRKDA-VLTKCFHVFCWDCLRTRYETR-----------QRKCPKCNAAFGA 71 (81)
Q Consensus 22 ~~~~~C~iC~~~~~~~-~~~~CgH~fc~~Ci~~~~~~~-----------~~~CP~Cr~~~~~ 71 (81)
.+.+.|..|+.+--.. +.-.=--.||..|+...-... -+.||.|...+..
T Consensus 3 ~~L~fC~~C~~irc~~c~~~Ei~~~yCp~CL~~~p~~e~~~~~nrC~r~Cf~CP~C~~~L~~ 64 (483)
T PF05502_consen 3 EELYFCEHCHKIRCPRCVSEEIDSYYCPNCLFEVPSSEARSEKNRCSRNCFDCPICFSPLSV 64 (483)
T ss_pred ccceecccccccCChhhcccccceeECccccccCChhhheeccceeccccccCCCCCCccee
Confidence 3445666666533211 111222346777775432211 1348888776653
No 254
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=29.76 E-value=52 Score=13.40 Aligned_cols=11 Identities=18% Similarity=0.546 Sum_probs=2.9
Q ss_pred cCccCccCccC
Q psy10800 26 TCPSCKVKRKD 36 (81)
Q Consensus 26 ~C~iC~~~~~~ 36 (81)
.|.+|.+....
T Consensus 2 ~C~~C~~~~~~ 12 (30)
T PF07649_consen 2 RCDACGKPIDG 12 (30)
T ss_dssp --TTTS----S
T ss_pred cCCcCCCcCCC
Confidence 45666655544
No 255
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=29.10 E-value=47 Score=22.27 Aligned_cols=43 Identities=21% Similarity=0.426 Sum_probs=26.0
Q ss_pred cccCccCccCccCcee--------------cCCCChhHHHHHHHHHhhCCCCCCCCCc
Q psy10800 24 TLTCPSCKVKRKDAVL--------------TKCFHVFCWDCLRTRYETRQRKCPKCNA 67 (81)
Q Consensus 24 ~~~C~iC~~~~~~~~~--------------~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~ 67 (81)
...|-+|+..|-.|-. -.|...||.+|=. ++.+.-..|+.|..
T Consensus 362 s~~Cf~CQ~~fp~~~~~~~~~~~ss~rY~Ce~CK~~FC~dCdv-fiHe~Lh~C~gCe~ 418 (421)
T COG5151 362 STHCFVCQGPFPKPPVSPFDESTSSGRYQCELCKSTFCSDCDV-FIHETLHFCIGCEL 418 (421)
T ss_pred CccceeccCCCCCCCCCcccccccccceechhhhhhhhhhhHH-HHHHHHhhCCCCcC
Confidence 3458888876643311 1478889998843 34434455888843
No 256
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=28.86 E-value=32 Score=16.63 Aligned_cols=8 Identities=38% Similarity=1.178 Sum_probs=4.1
Q ss_pred CCCCCcCc
Q psy10800 62 CPKCNAAF 69 (81)
Q Consensus 62 CP~Cr~~~ 69 (81)
||.|++.+
T Consensus 25 Cp~CGael 32 (54)
T TIGR01206 25 CDECGAEL 32 (54)
T ss_pred CCCCCCEE
Confidence 55555443
No 257
>KOG2071|consensus
Probab=28.84 E-value=22 Score=25.48 Aligned_cols=34 Identities=29% Similarity=0.575 Sum_probs=24.5
Q ss_pred CCcccCccCccCcc-------------CceecCCCChhHHHHHHHHH
Q psy10800 22 KETLTCPSCKVKRK-------------DAVLTKCFHVFCWDCLRTRY 55 (81)
Q Consensus 22 ~~~~~C~iC~~~~~-------------~~~~~~CgH~fc~~Ci~~~~ 55 (81)
.....|+||.+.|. +.+.+.-|-.|+..|+.+-.
T Consensus 511 e~~~~C~IC~EkFe~v~d~e~~~Wm~kdaV~le~G~ifH~~Cl~e~~ 557 (579)
T KOG2071|consen 511 ERQASCPICQEKFEVVFDQEEDLWMYKDAVYLEFGRIFHSKCLSEKR 557 (579)
T ss_pred ccccCCcccccccceeecchhhheeecceeeeccCceeeccccchHH
Confidence 45689999998663 34555568888888886543
No 258
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.56 E-value=19 Score=17.19 Aligned_cols=13 Identities=23% Similarity=0.570 Sum_probs=9.4
Q ss_pred CcccCccCccCcc
Q psy10800 23 ETLTCPSCKVKRK 35 (81)
Q Consensus 23 ~~~~C~iC~~~~~ 35 (81)
.+..||+|+..|.
T Consensus 11 p~KICpvCqRPFs 23 (54)
T COG4338 11 PDKICPVCQRPFS 23 (54)
T ss_pred chhhhhhhcCchH
Confidence 4567888887764
No 259
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=28.55 E-value=11 Score=21.73 Aligned_cols=13 Identities=23% Similarity=0.549 Sum_probs=8.9
Q ss_pred cccCccCccCccC
Q psy10800 24 TLTCPSCKVKRKD 36 (81)
Q Consensus 24 ~~~C~iC~~~~~~ 36 (81)
...||.|...+..
T Consensus 28 ~~hCp~Cg~PLF~ 40 (131)
T COG1645 28 AKHCPKCGTPLFR 40 (131)
T ss_pred HhhCcccCCccee
Confidence 4688888875543
No 260
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=28.06 E-value=24 Score=17.09 Aligned_cols=12 Identities=33% Similarity=0.852 Sum_probs=5.8
Q ss_pred CCCCCCCcCcCc
Q psy10800 60 RKCPKCNAAFGA 71 (81)
Q Consensus 60 ~~CP~Cr~~~~~ 71 (81)
.+||.|...+..
T Consensus 25 atCP~C~a~~~~ 36 (54)
T PF09237_consen 25 ATCPICGAVIRQ 36 (54)
T ss_dssp EE-TTT--EESS
T ss_pred CCCCcchhhccc
Confidence 358988877643
No 261
>PF10217 DUF2039: Uncharacterized conserved protein (DUF2039); InterPro: IPR019351 This entry is a region of approximately 100 residues containing three pairs of cysteine residues. The region is conserved from plants to humans but its function is unknown.
Probab=27.95 E-value=45 Score=18.06 Aligned_cols=20 Identities=35% Similarity=0.918 Sum_probs=13.6
Q ss_pred ChhHHHHHHHHHhhCCCCCCCCCcC
Q psy10800 44 HVFCWDCLRTRYETRQRKCPKCNAA 68 (81)
Q Consensus 44 H~fc~~Ci~~~~~~~~~~CP~Cr~~ 68 (81)
|+.|..|..+ ...|+.|..+
T Consensus 71 h~iC~~Ca~~-----~~vCaKC~k~ 90 (92)
T PF10217_consen 71 HVICDPCAKE-----LKVCAKCGKP 90 (92)
T ss_pred HHHHHHHHHh-----hccCcccCCC
Confidence 5668888764 2558888653
No 262
>KOG1356|consensus
Probab=27.91 E-value=19 Score=27.03 Aligned_cols=32 Identities=25% Similarity=0.584 Sum_probs=25.3
Q ss_pred cccCccCccCccCc--eecCCCChhHHHHHHHHH
Q psy10800 24 TLTCPSCKVKRKDA--VLTKCFHVFCWDCLRTRY 55 (81)
Q Consensus 24 ~~~C~iC~~~~~~~--~~~~CgH~fc~~Ci~~~~ 55 (81)
.-.|-.|.....+- +-..||+.+|..|+..|.
T Consensus 229 ~~mC~~C~~tlfn~hw~C~~C~~~~Cl~C~r~~~ 262 (889)
T KOG1356|consen 229 REMCDRCETTLFNIHWRCPRCGFGVCLDCYRKWY 262 (889)
T ss_pred chhhhhhcccccceeEEccccCCeeeecchhhcc
Confidence 45788888776653 455899999999999884
No 263
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=27.83 E-value=27 Score=20.55 Aligned_cols=31 Identities=26% Similarity=0.558 Sum_probs=20.9
Q ss_pred CcccCccCccCc--cCceecCCCChhHHHHHHHHHhhCCCCCCCCCcCcCc
Q psy10800 23 ETLTCPSCKVKR--KDAVLTKCFHVFCWDCLRTRYETRQRKCPKCNAAFGA 71 (81)
Q Consensus 23 ~~~~C~iC~~~~--~~~~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~~ 71 (81)
..+.||.|...+ .+++. ..+.||.|+..+..
T Consensus 108 ~~Y~Cp~c~~r~tf~eA~~------------------~~F~Cp~Cg~~L~~ 140 (158)
T TIGR00373 108 MFFICPNMCVRFTFNEAME------------------LNFTCPRCGAMLDY 140 (158)
T ss_pred CeEECCCCCcEeeHHHHHH------------------cCCcCCCCCCEeee
Confidence 468899998643 46531 24779999887654
No 264
>PF06937 EURL: EURL protein; InterPro: IPR009704 This family consists of several animal EURL proteins. EURL is preferentially expressed in chick retinal precursor cells as well as in the anterior epithelial cells of the lens at early stages of development. EURL transcripts are found primarily in the peripheral dorsal retina, i.e., the most undifferentiated part of the dorsal retina. EURL transcripts are also detected in the lens at stage 18 and remain abundant in the proliferating epithelial cells of the lens until at least day 11. The distribution pattern of EURL in the developing retina and lens suggest a role before the events leading to cell determination and differentiation [].
Probab=27.46 E-value=62 Score=21.12 Aligned_cols=37 Identities=22% Similarity=0.319 Sum_probs=22.1
Q ss_pred cccCccCccCccCcee----c----CCCChhHHHHHHHHHhhCCCCCC
Q psy10800 24 TLTCPSCKVKRKDAVL----T----KCFHVFCWDCLRTRYETRQRKCP 63 (81)
Q Consensus 24 ~~~C~iC~~~~~~~~~----~----~CgH~fc~~Ci~~~~~~~~~~CP 63 (81)
...|.||+++-.+.+- + --|| .+|.++|---.+..||
T Consensus 30 LsfChiCfEl~iegvpks~llHtkSlRGH---rdCFEK~HlIanQ~~p 74 (285)
T PF06937_consen 30 LSFCHICFELSIEGVPKSNLLHTKSLRGH---RDCFEKYHLIANQDCP 74 (285)
T ss_pred eeecceeeccccccCccccccccccccch---HHHHHHHHHHHcCCCC
Confidence 4568888876544321 1 1355 6788877654555677
No 265
>smart00714 LITAF Possible membrane-associated motif in LPS-induced tumor necrosis factor alpha factor (LITAF), also known as PIG7, and other animal proteins.
Probab=27.26 E-value=22 Score=17.54 Aligned_cols=13 Identities=38% Similarity=1.032 Sum_probs=9.4
Q ss_pred CCCCCCCCcCcCc
Q psy10800 59 QRKCPKCNAAFGA 71 (81)
Q Consensus 59 ~~~CP~Cr~~~~~ 71 (81)
...||.|++.+..
T Consensus 52 ~H~Cp~C~~~lg~ 64 (67)
T smart00714 52 NHYCPNCGAFLGT 64 (67)
T ss_pred cEECCCCCCEeEE
Confidence 3569999887653
No 266
>PF12132 DUF3587: Protein of unknown function (DUF3587); InterPro: IPR021982 This entry is represented by Hyposoter fugitivus ichnovirus, Gp7; it is a family of uncharacterised viral proteins.
Probab=26.73 E-value=53 Score=20.35 Aligned_cols=24 Identities=13% Similarity=0.360 Sum_probs=16.6
Q ss_pred ccCceecCCC----ChhHHHHHHHHHhh
Q psy10800 34 RKDAVLTKCF----HVFCWDCLRTRYET 57 (81)
Q Consensus 34 ~~~~~~~~Cg----H~fc~~Ci~~~~~~ 57 (81)
+..|....|. |.||...+..|+..
T Consensus 151 f~~p~~~~C~~gHfHHyCs~HV~~WL~~ 178 (199)
T PF12132_consen 151 FVKPSVDECEYGHFHHYCSQHVNSWLNN 178 (199)
T ss_pred ccCCCCCCCCCCCcChhhHHHHHHHHHH
Confidence 3444445563 67899999999874
No 267
>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=26.67 E-value=7.1 Score=18.62 Aligned_cols=30 Identities=27% Similarity=0.628 Sum_probs=15.0
Q ss_pred ccCcc--CccCccCc-------eecC-CCChhHHHHHHHH
Q psy10800 25 LTCPS--CKVKRKDA-------VLTK-CFHVFCWDCLRTR 54 (81)
Q Consensus 25 ~~C~i--C~~~~~~~-------~~~~-CgH~fc~~Ci~~~ 54 (81)
..||- |...+... +.=+ |++.||..|-..|
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 48877 87765432 1223 8898888876544
No 268
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=26.64 E-value=27 Score=15.86 Aligned_cols=11 Identities=27% Similarity=0.709 Sum_probs=8.0
Q ss_pred CCCCCCCcCcC
Q psy10800 60 RKCPKCNAAFG 70 (81)
Q Consensus 60 ~~CP~Cr~~~~ 70 (81)
..||.|+..+.
T Consensus 22 ~~Cp~CG~~~~ 32 (46)
T PRK00398 22 VRCPYCGYRIL 32 (46)
T ss_pred eECCCCCCeEE
Confidence 45999987654
No 269
>KOG0883|consensus
Probab=26.61 E-value=76 Score=22.06 Aligned_cols=55 Identities=16% Similarity=0.147 Sum_probs=41.9
Q ss_pred cccCccCccCccCceecCCCChhHHHHHHHHHhhCCCCCCCCCcCcCcCCceeeec
Q psy10800 24 TLTCPSCKVKRKDAVLTKCFHVFCWDCLRTRYETRQRKCPKCNAAFGANDYHRLYL 79 (81)
Q Consensus 24 ~~~C~iC~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~~~~~ 79 (81)
-..|.+-+..|..|+-+.=|.+|=..-|.+|++. ...=|.-++.+..+++..+.+
T Consensus 40 ~~hC~lt~~Pfe~PvC~~dg~vFd~~~Ivp~lkk-~g~nP~tG~kl~~~dLIkL~F 94 (518)
T KOG0883|consen 40 FNHCSLTMLPFEDPVCTVDGTVFDLTAIVPWLKK-HGTNPITGQKLDGKDLIKLKF 94 (518)
T ss_pred hhhceeccccccCcccccCCcEEeeehhhHHHHH-cCCCCCCCCccccccceeeee
Confidence 3568888889999999999999999999999984 234466666666666666544
No 270
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=26.56 E-value=22 Score=26.83 Aligned_cols=50 Identities=22% Similarity=0.430 Sum_probs=0.0
Q ss_pred CcccCccCccCccCceecCCCCh-----hHHHHHHHHHhhCCCCCCCCCcCcCcCCce
Q psy10800 23 ETLTCPSCKVKRKDAVLTKCFHV-----FCWDCLRTRYETRQRKCPKCNAAFGANDYH 75 (81)
Q Consensus 23 ~~~~C~iC~~~~~~~~~~~CgH~-----fc~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~ 75 (81)
....||-|...-....--.||-. +|..|-...- ...||.|........-+
T Consensus 654 ~~r~Cp~Cg~~t~~~~Cp~CG~~T~~~~~Cp~C~~~~~---~~~C~~C~~~~~~~~~~ 708 (900)
T PF03833_consen 654 GRRRCPKCGKETFYNRCPECGSHTEPVYVCPDCGIEVE---EDECPKCGRETTSYSKQ 708 (900)
T ss_dssp ----------------------------------------------------------
T ss_pred ecccCcccCCcchhhcCcccCCccccceeccccccccC---ccccccccccCccccee
Confidence 35789999876544444457643 5888876532 24699998776544333
No 271
>smart00355 ZnF_C2H2 zinc finger.
Probab=26.49 E-value=40 Score=12.18 Aligned_cols=8 Identities=38% Similarity=0.962 Sum_probs=3.4
Q ss_pred CccCccCc
Q psy10800 27 CPSCKVKR 34 (81)
Q Consensus 27 C~iC~~~~ 34 (81)
|+.|...+
T Consensus 3 C~~C~~~f 10 (26)
T smart00355 3 CPECGKVF 10 (26)
T ss_pred CCCCcchh
Confidence 44444433
No 272
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.10 E-value=51 Score=21.13 Aligned_cols=11 Identities=45% Similarity=1.138 Sum_probs=5.2
Q ss_pred CCCCCCCcCcC
Q psy10800 60 RKCPKCNAAFG 70 (81)
Q Consensus 60 ~~CP~Cr~~~~ 70 (81)
..||+|...+.
T Consensus 20 ieCPvC~tkFk 30 (267)
T COG1655 20 IECPVCNTKFK 30 (267)
T ss_pred eccCcccchhh
Confidence 34555544443
No 273
>PF03918 CcmH: Cytochrome C biogenesis protein; InterPro: IPR005616 Members of this family include NrfF, CcmH, CycL, Ccl2.; PDB: 2KW0_A 2HL7_A.
Probab=26.08 E-value=33 Score=20.05 Aligned_cols=22 Identities=32% Similarity=0.603 Sum_probs=16.3
Q ss_pred hHHHHHHHHhcCCcccCccCcc
Q psy10800 11 DEVMLEEIREYKETLTCPSCKV 32 (81)
Q Consensus 11 ~~~~~~~~~~~~~~~~C~iC~~ 32 (81)
+.........+...+.||+|..
T Consensus 27 ~~~~e~r~~~l~~~LrCp~Cq~ 48 (148)
T PF03918_consen 27 DPEQEARARELAKELRCPVCQN 48 (148)
T ss_dssp SHHHHHHHHHHHHCCE-TTTTS
T ss_pred ChhHHHHHHHHHhcccCCCCCC
Confidence 4555667788888999999985
No 274
>KOG4080|consensus
Probab=26.05 E-value=70 Score=19.33 Aligned_cols=28 Identities=25% Similarity=0.511 Sum_probs=17.7
Q ss_pred CCcccCccCccCccCceecCCCChhHHHHHHHHHh
Q psy10800 22 KETLTCPSCKVKRKDAVLTKCFHVFCWDCLRTRYE 56 (81)
Q Consensus 22 ~~~~~C~iC~~~~~~~~~~~CgH~fc~~Ci~~~~~ 56 (81)
.....||+|..+- =.|+.|..|......
T Consensus 91 ~nl~~CP~CGh~k-------~a~~LC~~Cy~kV~k 118 (176)
T KOG4080|consen 91 DNLNTCPACGHIK-------PAHTLCDYCYAKVHK 118 (176)
T ss_pred hccccCcccCccc-------cccccHHHHHHHHHH
Confidence 3456788777532 246678888876553
No 275
>PF08882 Acetone_carb_G: Acetone carboxylase gamma subunit; InterPro: IPR014979 Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO2 to form acetoacetate [] according to the following reaction: CH3COCH3 + CO2 + ATP = CH3COCH2COO- + AMP + 2P(i) + H+ It has the subunit composition: (alpha(2)beta(2)gamma(2) multimers of 85kDa, 78kDa, and 20kDa subunits). It is expressed to high levels (17 to 25% of soluble protein) in cells grown with acetone as the carbon source but are not present at detectable levels in cells grown with other carbon sources []. Acetone carboxylase may enable Helicobacter pylori to survive off acetone in the stomach of humans and other mammals where it is the etiological agent of peptic ulcer disease []. This entry represents the family of gamma subunit-related acetone carboxylase proteins.
Probab=25.65 E-value=29 Score=19.47 Aligned_cols=12 Identities=42% Similarity=0.686 Sum_probs=8.7
Q ss_pred eecCCCChhHHH
Q psy10800 38 VLTKCFHVFCWD 49 (81)
Q Consensus 38 ~~~~CgH~fc~~ 49 (81)
+.-.|||.||..
T Consensus 25 vkc~CGh~f~d~ 36 (112)
T PF08882_consen 25 VKCDCGHEFCDA 36 (112)
T ss_pred eeccCCCeecCh
Confidence 344799999863
No 276
>PF05810 NinF: NinF protein; InterPro: IPR008712 This family consists of several bacteriophage NinF proteins as well as related sequences from Escherichia coli.
Probab=25.11 E-value=72 Score=15.65 Aligned_cols=33 Identities=18% Similarity=0.376 Sum_probs=20.8
Q ss_pred HHhcCCcccCccCccCccCceecCCCChhHHHHHHHHHh
Q psy10800 18 IREYKETLTCPSCKVKRKDAVLTKCFHVFCWDCLRTRYE 56 (81)
Q Consensus 18 ~~~~~~~~~C~iC~~~~~~~~~~~CgH~fc~~Ci~~~~~ 56 (81)
..++...+ |.-|...+..- --..|..|+.+|+.
T Consensus 12 q~Si~RAl-Ca~C~~~L~~~-----E~h~Ce~C~~E~l~ 44 (58)
T PF05810_consen 12 QQSIERAL-CANCGQKLHPD-----ETHVCEECCAEWLV 44 (58)
T ss_pred HHHHHHHH-HhccCcccccc-----hhhHHHHHHHHHHh
Confidence 34444555 88887655432 11258999999887
No 277
>KOG0314|consensus
Probab=24.91 E-value=15 Score=25.49 Aligned_cols=43 Identities=35% Similarity=0.668 Sum_probs=31.4
Q ss_pred HHHHHhcCCcccCccC-ccCccCceec--CCCChhHHHHHHHHHhh
Q psy10800 15 LEEIREYKETLTCPSC-KVKRKDAVLT--KCFHVFCWDCLRTRYET 57 (81)
Q Consensus 15 ~~~~~~~~~~~~C~iC-~~~~~~~~~~--~CgH~fc~~Ci~~~~~~ 57 (81)
...+..+.+++.|++| .+.+.+..++ .|..+||..|+...+..
T Consensus 210 a~~v~~~~e~~~c~~~~~~~~~~~~l~~~~~~~~~~~~~i~~~l~~ 255 (448)
T KOG0314|consen 210 ARTVGELPEGLQCPLCGKEVMLDAALLSKCCLKSFCDKCIRDALIS 255 (448)
T ss_pred hHHhccCCccccCceecchhhHHHHHhhhhhcccCCcccccccccc
Confidence 3345566788999999 6666666555 67889999999876653
No 278
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=24.73 E-value=37 Score=16.27 Aligned_cols=9 Identities=33% Similarity=1.173 Sum_probs=6.1
Q ss_pred CCCCCCcCc
Q psy10800 61 KCPKCNAAF 69 (81)
Q Consensus 61 ~CP~Cr~~~ 69 (81)
.||.|+..+
T Consensus 2 ~CPyCge~~ 10 (52)
T PF14255_consen 2 QCPYCGEPI 10 (52)
T ss_pred CCCCCCCee
Confidence 478887654
No 279
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=24.52 E-value=37 Score=19.71 Aligned_cols=23 Identities=22% Similarity=0.472 Sum_probs=13.7
Q ss_pred ccCccCccCccCceecCCCChhHHHHHH
Q psy10800 25 LTCPSCKVKRKDAVLTKCFHVFCWDCLR 52 (81)
Q Consensus 25 ~~C~iC~~~~~~~~~~~CgH~fc~~Ci~ 52 (81)
..|+.|..+|... |..+|..|+.
T Consensus 4 ~nC~~CgklF~~~-----~~~iCp~C~~ 26 (137)
T TIGR03826 4 ANCPKCGRLFVKT-----GRDVCPSCYE 26 (137)
T ss_pred ccccccchhhhhc-----CCccCHHHhH
Confidence 3577777766541 4456666663
No 280
>KOG1842|consensus
Probab=24.37 E-value=37 Score=23.79 Aligned_cols=31 Identities=26% Similarity=0.513 Sum_probs=23.0
Q ss_pred CcccCccCccCccCce----ecCCCChhHHHHHHH
Q psy10800 23 ETLTCPSCKVKRKDAV----LTKCFHVFCWDCLRT 53 (81)
Q Consensus 23 ~~~~C~iC~~~~~~~~----~~~CgH~fc~~Ci~~ 53 (81)
....||+|.+.|.-.. ---||-+.|.+|.+-
T Consensus 179 ~V~~CP~Ca~~F~l~rRrHHCRLCG~VmC~~C~k~ 213 (505)
T KOG1842|consen 179 SVQFCPECANSFGLTRRRHHCRLCGRVMCRDCSKF 213 (505)
T ss_pred cccccccccchhhhHHHhhhhhhcchHHHHHHHHh
Confidence 3678999999886431 125999999999863
No 281
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=24.28 E-value=67 Score=15.90 Aligned_cols=10 Identities=30% Similarity=0.989 Sum_probs=5.3
Q ss_pred CCCCCCCcCc
Q psy10800 60 RKCPKCNAAF 69 (81)
Q Consensus 60 ~~CP~Cr~~~ 69 (81)
..||+|..+.
T Consensus 40 p~CPlC~s~M 49 (59)
T PF14169_consen 40 PVCPLCKSPM 49 (59)
T ss_pred ccCCCcCCcc
Confidence 4466665544
No 282
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=23.84 E-value=43 Score=19.31 Aligned_cols=13 Identities=23% Similarity=0.871 Sum_probs=9.9
Q ss_pred CCCCCCCcCcCcC
Q psy10800 60 RKCPKCNAAFGAN 72 (81)
Q Consensus 60 ~~CP~Cr~~~~~~ 72 (81)
..||.|+..+...
T Consensus 124 f~Cp~Cg~~l~~~ 136 (147)
T smart00531 124 FTCPRCGEELEED 136 (147)
T ss_pred EECCCCCCEEEEc
Confidence 6799999887543
No 283
>KOG4021|consensus
Probab=23.65 E-value=36 Score=21.21 Aligned_cols=12 Identities=25% Similarity=0.742 Sum_probs=8.6
Q ss_pred CCCCCCCcCcCc
Q psy10800 60 RKCPKCNAAFGA 71 (81)
Q Consensus 60 ~~CP~Cr~~~~~ 71 (81)
+-||+||.....
T Consensus 109 npCPICRDeyL~ 120 (239)
T KOG4021|consen 109 NPCPICRDEYLY 120 (239)
T ss_pred CCCCccccceEE
Confidence 459999976543
No 284
>PF10764 Gin: Inhibitor of sigma-G Gin; InterPro: IPR019700 Gin allows sigma-F to delay late forespore transcription by preventing sigma-G to take over before the cell has reached a critical stage of development. Gin is also known as CsfB [].
Probab=23.53 E-value=51 Score=15.32 Aligned_cols=31 Identities=19% Similarity=0.468 Sum_probs=21.3
Q ss_pred cCccCccCccCceecCCCChhHHHHHHHHHhh
Q psy10800 26 TCPSCKVKRKDAVLTKCFHVFCWDCLRTRYET 57 (81)
Q Consensus 26 ~C~iC~~~~~~~~~~~CgH~fc~~Ci~~~~~~ 57 (81)
.|-||.+...+.+. =.|..+|..|-.+.+..
T Consensus 1 ~CiiC~~~~~~GI~-I~~~fIC~~CE~~iv~~ 31 (46)
T PF10764_consen 1 KCIICGKEKEEGIH-IYGKFICSDCEKEIVNT 31 (46)
T ss_pred CeEeCCCcCCCCEE-EECeEehHHHHHHhccC
Confidence 37788877766533 35666799998877664
No 285
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=23.31 E-value=37 Score=14.87 Aligned_cols=10 Identities=30% Similarity=0.863 Sum_probs=7.1
Q ss_pred ccCccCccCc
Q psy10800 25 LTCPSCKVKR 34 (81)
Q Consensus 25 ~~C~iC~~~~ 34 (81)
..|++|...+
T Consensus 9 ~~C~~C~~~~ 18 (36)
T PF11781_consen 9 EPCPVCGSRW 18 (36)
T ss_pred CcCCCCCCeE
Confidence 4589988763
No 286
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=23.17 E-value=41 Score=25.61 Aligned_cols=30 Identities=27% Similarity=0.538 Sum_probs=21.9
Q ss_pred ccCccCccCccCc---e------ecCCCChhHHHHHHHH
Q psy10800 25 LTCPSCKVKRKDA---V------LTKCFHVFCWDCLRTR 54 (81)
Q Consensus 25 ~~C~iC~~~~~~~---~------~~~CgH~fc~~Ci~~~ 54 (81)
..|..|...|..- + --.||.+||..|-...
T Consensus 461 dtC~~C~kkFfSlsK~L~~RKHHCRkCGrVFC~~CSSnR 499 (1374)
T PTZ00303 461 DSCPSCGRAFISLSRPLGTRAHHCRSCGIRLCVFCITKR 499 (1374)
T ss_pred CcccCcCCcccccccccccccccccCCccccCccccCCc
Confidence 4699999988531 1 1279999999998644
No 287
>PF10601 zf-LITAF-like: LITAF-like zinc ribbon domain; InterPro: IPR006629 Members of this family display a conserved zinc ribbon structure [] with the motif C-XX-C- separated from the more C-terminal HX-C(P)X-C-X4-G-R motif by a variable region of usually 25-30 (hydrophobic) residues. Although it belongs to one of the zinc finger's fold groups (zinc ribbon), this particular domain was first identified in LPS-induced tumour necrosis alpha factor (LITAF) which is produced in mammalian cells after being challenged with lipopolysaccharide (LPS). The hydrophobic region probably inserts into the membrane rather than traversing it. Such an insertion brings together the N- and C-terminal C-XX-C motifs to form a compact Zn2+-binding structure [].
Probab=23.07 E-value=17 Score=18.27 Aligned_cols=15 Identities=20% Similarity=0.620 Sum_probs=10.4
Q ss_pred CcccCccCccCccCc
Q psy10800 23 ETLTCPSCKVKRKDA 37 (81)
Q Consensus 23 ~~~~C~iC~~~~~~~ 37 (81)
....||-|+......
T Consensus 6 ~~~~CP~C~~~~~T~ 20 (73)
T PF10601_consen 6 VRIYCPYCQQQVQTR 20 (73)
T ss_pred eeeECCCCCCEEEEE
Confidence 357899998765443
No 288
>KOG3608|consensus
Probab=22.93 E-value=65 Score=22.09 Aligned_cols=48 Identities=19% Similarity=0.484 Sum_probs=32.1
Q ss_pred CcccCccCccCccCc----------eecCCCChhHHHHHHHHHhhC-----------CCCCCCCCcCcC
Q psy10800 23 ETLTCPSCKVKRKDA----------VLTKCFHVFCWDCLRTRYETR-----------QRKCPKCNAAFG 70 (81)
Q Consensus 23 ~~~~C~iC~~~~~~~----------~~~~CgH~fc~~Ci~~~~~~~-----------~~~CP~Cr~~~~ 70 (81)
..+-||-|.++|... ..+.=.|..|..|.+++-... ..+||+|-...+
T Consensus 206 KvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn~ykCplCdmtc~ 274 (467)
T KOG3608|consen 206 KVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVNCYKCPLCDMTCS 274 (467)
T ss_pred eEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhhcccccccccCCC
Confidence 368899999988653 233456777999987755431 246999865443
No 289
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=22.49 E-value=1.3e+02 Score=15.39 Aligned_cols=33 Identities=27% Similarity=0.524 Sum_probs=21.9
Q ss_pred cCCcccCccCccCccCc---eecCCCChhHHHHHHH
Q psy10800 21 YKETLTCPSCKVKRKDA---VLTKCFHVFCWDCLRT 53 (81)
Q Consensus 21 ~~~~~~C~iC~~~~~~~---~~~~CgH~fc~~Ci~~ 53 (81)
......|.+|....-.. ..-.|...|+..|...
T Consensus 33 ~~~~~~C~~C~~~~Ga~i~C~~~~C~~~fH~~CA~~ 68 (90)
T PF13771_consen 33 RRRKLKCSICKKKGGACIGCSHPGCSRSFHVPCARK 68 (90)
T ss_pred HHhCCCCcCCCCCCCeEEEEeCCCCCcEEChHHHcc
Confidence 34467999999762221 2336788888888753
No 290
>KOG3993|consensus
Probab=22.47 E-value=6.8 Score=27.06 Aligned_cols=42 Identities=26% Similarity=0.634 Sum_probs=24.1
Q ss_pred HhcCCcccCccCccCccCceec---CCCChhHHHHHHHHHhhCCCCCCCCCcCcC
Q psy10800 19 REYKETLTCPSCKVKRKDAVLT---KCFHVFCWDCLRTRYETRQRKCPKCNAAFG 70 (81)
Q Consensus 19 ~~~~~~~~C~iC~~~~~~~~~~---~CgH~fc~~Ci~~~~~~~~~~CP~Cr~~~~ 70 (81)
.+...++.|.+|.+.|.++..| .|..+ .. -...||-|.+.|.
T Consensus 262 ~n~iGdyiCqLCK~kYeD~F~LAQHrC~RI---------V~-vEYrCPEC~KVFs 306 (500)
T KOG3993|consen 262 PNVIGDYICQLCKEKYEDAFALAQHRCPRI---------VH-VEYRCPECDKVFS 306 (500)
T ss_pred cccHHHHHHHHHHHhhhhHHHHhhccCCee---------EE-eeecCCccccccc
Confidence 3334477888888888777444 33211 11 2345787777664
No 291
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=22.33 E-value=87 Score=16.77 Aligned_cols=29 Identities=24% Similarity=0.472 Sum_probs=20.6
Q ss_pred CcccCccCccCccCceec-----CCCChhHHHHHHH
Q psy10800 23 ETLTCPSCKVKRKDAVLT-----KCFHVFCWDCLRT 53 (81)
Q Consensus 23 ~~~~C~iC~~~~~~~~~~-----~CgH~fc~~Ci~~ 53 (81)
....|.+|... ..+.+ .|...|+..|...
T Consensus 54 ~~~~C~iC~~~--~G~~i~C~~~~C~~~fH~~CA~~ 87 (110)
T PF13832_consen 54 FKLKCSICGKS--GGACIKCSHPGCSTAFHPTCARK 87 (110)
T ss_pred cCCcCcCCCCC--CceeEEcCCCCCCcCCCHHHHHH
Confidence 47899999986 33333 4777888888754
No 292
>PF14577 SEO_C: Sieve element occlusion C-terminus
Probab=22.30 E-value=52 Score=20.94 Aligned_cols=23 Identities=39% Similarity=0.830 Sum_probs=12.2
Q ss_pred CCcccCccCccCccCceecCCCC
Q psy10800 22 KETLTCPSCKVKRKDAVLTKCFH 44 (81)
Q Consensus 22 ~~~~~C~iC~~~~~~~~~~~CgH 44 (81)
.+...||-|...+..-+...|-|
T Consensus 212 pe~i~CpeC~R~MEk~v~YkCCh 234 (235)
T PF14577_consen 212 PETIVCPECGRPMEKFVMYKCCH 234 (235)
T ss_pred CceeECCCCCCchhhceeeeccC
Confidence 34455666655555445555544
No 293
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=22.18 E-value=69 Score=16.14 Aligned_cols=16 Identities=13% Similarity=0.505 Sum_probs=10.6
Q ss_pred CCCCCCCCcCcCcCCc
Q psy10800 59 QRKCPKCNAAFGANDY 74 (81)
Q Consensus 59 ~~~CP~Cr~~~~~~~~ 74 (81)
...||.|.......++
T Consensus 17 ~~~Cp~Cgs~~~S~~w 32 (64)
T PRK06393 17 EKTCPVHGDEKTTTEW 32 (64)
T ss_pred CCcCCCCCCCcCCcCc
Confidence 3479999886544444
No 294
>KOG1313|consensus
Probab=21.83 E-value=12 Score=24.39 Aligned_cols=9 Identities=33% Similarity=0.796 Sum_probs=4.3
Q ss_pred ChhHHHHHH
Q psy10800 44 HVFCWDCLR 52 (81)
Q Consensus 44 H~fc~~Ci~ 52 (81)
-+||.+|..
T Consensus 102 ~SfC~KC~~ 110 (309)
T KOG1313|consen 102 DSFCNKCNY 110 (309)
T ss_pred ccHHhhcCC
Confidence 345555543
No 295
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=21.64 E-value=33 Score=17.63 Aligned_cols=7 Identities=29% Similarity=0.747 Sum_probs=5.5
Q ss_pred cCCCChh
Q psy10800 40 TKCFHVF 46 (81)
Q Consensus 40 ~~CgH~f 46 (81)
+.|||+|
T Consensus 33 ~eCg~tF 39 (72)
T PRK09678 33 VNCSATF 39 (72)
T ss_pred CCCCCEE
Confidence 3799987
No 296
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=21.14 E-value=27 Score=15.12 Aligned_cols=11 Identities=36% Similarity=1.081 Sum_probs=5.9
Q ss_pred CCCCCCcCcCc
Q psy10800 61 KCPKCNAAFGA 71 (81)
Q Consensus 61 ~CP~Cr~~~~~ 71 (81)
.||.|...+..
T Consensus 6 ~C~nC~R~v~a 16 (33)
T PF08209_consen 6 ECPNCGRPVAA 16 (33)
T ss_dssp E-TTTSSEEEG
T ss_pred ECCCCcCCcch
Confidence 47777665543
No 297
>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=21.08 E-value=48 Score=14.24 Aligned_cols=10 Identities=30% Similarity=1.009 Sum_probs=7.4
Q ss_pred CCCCCCCCcC
Q psy10800 59 QRKCPKCNAA 68 (81)
Q Consensus 59 ~~~CP~Cr~~ 68 (81)
...||.|+..
T Consensus 26 ~~~CP~Cg~~ 35 (41)
T smart00834 26 LATCPECGGD 35 (41)
T ss_pred CCCCCCCCCc
Confidence 3569999874
No 298
>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=20.82 E-value=73 Score=19.88 Aligned_cols=43 Identities=26% Similarity=0.653 Sum_probs=23.2
Q ss_pred CccCccCccCceecCCCChhHHHHHHHHHhhC-------CCCCCCCCcCcCcCCc
Q psy10800 27 CPSCKVKRKDAVLTKCFHVFCWDCLRTRYETR-------QRKCPKCNAAFGANDY 74 (81)
Q Consensus 27 C~iC~~~~~~~~~~~CgH~fc~~Ci~~~~~~~-------~~~CP~Cr~~~~~~~~ 74 (81)
|+.|..... +. -...|..|+.+-..-. ...||.|++......+
T Consensus 1 C~~CG~~~~-~~----~~~lC~~C~~~~~~i~ei~~~i~v~~C~~Cg~~~~~~~W 50 (236)
T PF04981_consen 1 CPRCGREIE-PL----IDGLCPDCYLKRFDIIEIPDRIEVTICPKCGRYRIGGRW 50 (236)
T ss_pred CCCCCCCCC-Cc----ccccChHHhcccCCeeecCCccCceECCCCCCEECCCEe
Confidence 677776332 11 1147888875433210 1239999887655433
No 299
>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=20.82 E-value=1.7e+02 Score=16.11 Aligned_cols=38 Identities=13% Similarity=0.292 Sum_probs=23.7
Q ss_pred HHHhcCCcccCccCccCccCceecCCCChhHHHHHHHH
Q psy10800 17 EIREYKETLTCPSCKVKRKDAVLTKCFHVFCWDCLRTR 54 (81)
Q Consensus 17 ~~~~~~~~~~C~iC~~~~~~~~~~~CgH~fc~~Ci~~~ 54 (81)
.+........|.-|...-..-+.++=|-..|..|.--.
T Consensus 6 ~l~~~~~N~~CaDCg~~~p~w~s~~~GiflC~~Cag~H 43 (116)
T PF01412_consen 6 ELLKKPGNKVCADCGAPNPTWASLNYGIFLCLECAGIH 43 (116)
T ss_dssp HHHCSTTCTB-TTT-SBS--EEETTTTEEE-HHHHHHH
T ss_pred HHHcCcCcCcCCCCCCCCCCEEEeecChhhhHHHHHHH
Confidence 34445677899999865555577787877799997543
No 300
>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=20.80 E-value=48 Score=16.52 Aligned_cols=11 Identities=18% Similarity=0.060 Sum_probs=8.1
Q ss_pred eecCCCChhHH
Q psy10800 38 VLTKCFHVFCW 48 (81)
Q Consensus 38 ~~~~CgH~fc~ 48 (81)
..|+|||..+.
T Consensus 13 A~L~CGH~QHv 23 (61)
T PF12088_consen 13 AELSCGHTQHV 23 (61)
T ss_pred EEecccccccc
Confidence 56799997653
No 301
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=20.80 E-value=17 Score=19.91 Aligned_cols=12 Identities=33% Similarity=0.836 Sum_probs=7.0
Q ss_pred CcccCccCccCc
Q psy10800 23 ETLTCPSCKVKR 34 (81)
Q Consensus 23 ~~~~C~iC~~~~ 34 (81)
+.|+|.-|+-.-
T Consensus 69 DEFTCssCFLV~ 80 (99)
T PF13834_consen 69 DEFTCSSCFLVH 80 (99)
T ss_pred CceeeeeeeeEe
Confidence 456676666433
No 302
>PF12907 zf-met2: Zinc-binding
Probab=20.65 E-value=19 Score=16.39 Aligned_cols=10 Identities=20% Similarity=0.697 Sum_probs=5.5
Q ss_pred ccCccCccCc
Q psy10800 25 LTCPSCKVKR 34 (81)
Q Consensus 25 ~~C~iC~~~~ 34 (81)
+.|.||...|
T Consensus 2 i~C~iC~qtF 11 (40)
T PF12907_consen 2 IICKICRQTF 11 (40)
T ss_pred cCcHHhhHHH
Confidence 4566666433
No 303
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=20.51 E-value=42 Score=19.34 Aligned_cols=10 Identities=40% Similarity=1.012 Sum_probs=6.7
Q ss_pred CCCCCCCcCc
Q psy10800 60 RKCPKCNAAF 69 (81)
Q Consensus 60 ~~CP~Cr~~~ 69 (81)
..||.|+...
T Consensus 44 ~~Cp~C~~~~ 53 (140)
T COG1545 44 AYCPKCGSET 53 (140)
T ss_pred ccCCCCCCCC
Confidence 4588887653
No 304
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=20.39 E-value=43 Score=18.81 Aligned_cols=9 Identities=33% Similarity=0.833 Sum_probs=5.3
Q ss_pred CccCccCcc
Q psy10800 27 CPSCKVKRK 35 (81)
Q Consensus 27 C~iC~~~~~ 35 (81)
||+|...+.
T Consensus 1 CPvCg~~l~ 9 (113)
T PF09862_consen 1 CPVCGGELV 9 (113)
T ss_pred CCCCCCceE
Confidence 666665554
No 305
>PHA02768 hypothetical protein; Provisional
Probab=20.39 E-value=47 Score=16.18 Aligned_cols=37 Identities=16% Similarity=0.182 Sum_probs=21.6
Q ss_pred cccCccCccCccCceecCCCChhHHHHHHHHHh--hCCCCCCCCCcCcCc
Q psy10800 24 TLTCPSCKVKRKDAVLTKCFHVFCWDCLRTRYE--TRQRKCPKCNAAFGA 71 (81)
Q Consensus 24 ~~~C~iC~~~~~~~~~~~CgH~fc~~Ci~~~~~--~~~~~CP~Cr~~~~~ 71 (81)
++.|+.|...|.....+ ..... .....|..|.+.+..
T Consensus 5 ~y~C~~CGK~Fs~~~~L-----------~~H~r~H~k~~kc~~C~k~f~~ 43 (55)
T PHA02768 5 GYECPICGEIYIKRKSM-----------ITHLRKHNTNLKLSNCKRISLR 43 (55)
T ss_pred ccCcchhCCeeccHHHH-----------HHHHHhcCCcccCCcccceecc
Confidence 46899999888764222 11111 123568888877653
Done!