Query psy3884
Match_columns 95
No_of_seqs 217 out of 1284
Neff 9.4
Searched_HMMs 46136
Date Fri Aug 16 19:50:36 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3884.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3884hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00504 Ubox Modified RING 99.6 9.6E-16 2.1E-20 80.4 3.9 62 33-94 1-62 (63)
2 PF15227 zf-C3HC4_4: zinc fing 99.6 1.1E-15 2.4E-20 74.3 3.0 38 36-73 1-42 (42)
3 PLN03208 E3 ubiquitin-protein 99.6 2.2E-15 4.8E-20 93.8 5.0 52 31-82 16-83 (193)
4 TIGR00599 rad18 DNA repair pro 99.6 2.6E-15 5.6E-20 102.6 4.0 68 28-95 21-88 (397)
5 KOG0317|consensus 99.5 3.9E-15 8.4E-20 96.9 3.9 55 29-83 235-289 (293)
6 PF13639 zf-RING_2: Ring finge 99.5 1.5E-15 3.2E-20 74.6 1.0 40 35-74 2-44 (44)
7 PF13923 zf-C3HC4_2: Zinc fing 99.5 7E-15 1.5E-19 70.4 2.5 38 36-73 1-39 (39)
8 PF13920 zf-C3HC4_3: Zinc fing 99.5 1.2E-14 2.7E-19 73.1 3.0 46 33-78 2-48 (50)
9 KOG0287|consensus 99.5 2.1E-15 4.5E-20 100.3 0.2 65 31-95 21-85 (442)
10 KOG0823|consensus 99.5 1.8E-14 3.9E-19 91.4 3.8 53 30-82 44-99 (230)
11 PHA02929 N1R/p28-like protein; 99.5 4.7E-14 1E-18 90.9 4.6 47 32-78 173-227 (238)
12 PF04564 U-box: U-box domain; 99.5 2.6E-14 5.7E-19 77.2 1.7 65 31-95 2-67 (73)
13 KOG0320|consensus 99.4 1.4E-13 3E-18 84.4 2.9 52 32-83 130-183 (187)
14 COG5243 HRD1 HRD ubiquitin lig 99.4 4.9E-13 1.1E-17 90.1 5.0 53 26-78 280-345 (491)
15 KOG4628|consensus 99.4 6.7E-13 1.4E-17 89.2 5.1 47 34-80 230-280 (348)
16 PF00097 zf-C3HC4: Zinc finger 99.4 3.9E-13 8.5E-18 64.9 2.7 38 36-73 1-41 (41)
17 COG5432 RAD18 RING-finger-cont 99.3 3.4E-13 7.4E-18 88.4 2.1 64 32-95 24-87 (391)
18 cd00162 RING RING-finger (Real 99.3 1.2E-12 2.6E-17 63.6 3.4 43 35-77 1-45 (45)
19 PF12678 zf-rbx1: RING-H2 zinc 99.3 1.1E-12 2.4E-17 70.8 3.4 42 33-74 19-73 (73)
20 PF14835 zf-RING_6: zf-RING of 99.3 5.1E-13 1.1E-17 69.4 0.3 59 32-92 6-65 (65)
21 PF14634 zf-RING_5: zinc-RING 99.3 4.7E-12 1E-16 62.0 3.2 41 35-75 1-44 (44)
22 smart00184 RING Ring finger. E 99.2 1.2E-11 2.5E-16 58.2 3.6 38 36-73 1-39 (39)
23 KOG0802|consensus 99.2 5.6E-12 1.2E-16 89.8 3.1 52 29-80 287-343 (543)
24 PF13445 zf-RING_UBOX: RING-ty 99.2 5.9E-12 1.3E-16 61.2 2.2 35 36-71 1-43 (43)
25 PHA02926 zinc finger-like prot 99.2 9.2E-12 2E-16 79.0 3.3 48 31-78 168-230 (242)
26 COG5574 PEX10 RING-finger-cont 99.2 9.5E-12 2.1E-16 80.4 2.6 51 32-82 214-266 (271)
27 KOG2164|consensus 99.2 1.1E-11 2.4E-16 86.1 3.1 50 33-82 186-240 (513)
28 COG5540 RING-finger-containing 99.2 2.2E-11 4.7E-16 80.3 3.0 48 32-79 322-373 (374)
29 KOG2177|consensus 99.0 7.4E-11 1.6E-15 77.0 1.9 47 29-75 9-55 (386)
30 PF12861 zf-Apc11: Anaphase-pr 99.0 2.3E-10 5E-15 62.8 3.5 46 33-78 21-82 (85)
31 TIGR00570 cdk7 CDK-activating 98.9 9.4E-10 2E-14 73.2 3.9 49 33-81 3-57 (309)
32 KOG0978|consensus 98.9 3.2E-10 7E-15 81.9 1.4 55 30-84 640-695 (698)
33 KOG4159|consensus 98.8 2.4E-09 5.2E-14 73.7 3.2 55 26-80 77-131 (398)
34 KOG0311|consensus 98.8 5.2E-10 1.1E-14 75.0 -1.2 64 29-92 39-105 (381)
35 KOG4265|consensus 98.8 4.5E-09 9.8E-14 70.7 3.1 50 31-80 288-338 (349)
36 KOG4172|consensus 98.8 2E-09 4.3E-14 54.1 0.6 45 34-78 8-54 (62)
37 KOG2879|consensus 98.7 4.4E-08 9.6E-13 64.0 5.8 51 28-78 234-287 (298)
38 KOG0824|consensus 98.7 8.2E-09 1.8E-13 68.1 2.0 48 33-80 7-55 (324)
39 COG5152 Uncharacterized conser 98.7 8.8E-09 1.9E-13 64.6 2.0 48 31-78 194-241 (259)
40 KOG2660|consensus 98.6 1.1E-08 2.5E-13 68.1 1.2 55 31-85 13-68 (331)
41 KOG1734|consensus 98.6 3.7E-08 8E-13 64.4 2.3 61 23-83 214-286 (328)
42 KOG0828|consensus 98.5 4.4E-08 9.6E-13 68.5 2.3 50 30-79 568-635 (636)
43 COG5194 APC11 Component of SCF 98.5 8.2E-08 1.8E-12 51.9 2.5 30 50-79 53-82 (88)
44 KOG0804|consensus 98.4 1.3E-07 2.8E-12 65.4 2.6 46 31-78 173-222 (493)
45 COG5219 Uncharacterized conser 98.4 8.8E-08 1.9E-12 71.4 1.8 76 3-78 1432-1523(1525)
46 KOG0297|consensus 98.4 1.2E-07 2.6E-12 65.5 2.2 54 30-83 18-72 (391)
47 KOG1813|consensus 98.4 7.4E-08 1.6E-12 63.5 1.0 49 31-79 239-287 (313)
48 PF11793 FANCL_C: FANCL C-term 98.4 3.8E-08 8.1E-13 52.7 -0.3 46 33-78 2-66 (70)
49 PF11789 zf-Nse: Zinc-finger o 98.3 3.5E-07 7.5E-12 47.0 1.9 41 32-72 10-53 (57)
50 smart00744 RINGv The RING-vari 98.3 9.6E-07 2.1E-11 44.0 2.9 40 35-74 1-49 (49)
51 COG5222 Uncharacterized conser 98.2 2.1E-06 4.7E-11 57.1 4.8 43 33-75 274-318 (427)
52 KOG1493|consensus 98.2 2.5E-07 5.4E-12 49.6 0.1 45 34-78 21-81 (84)
53 KOG1039|consensus 98.2 1E-06 2.2E-11 59.9 2.4 48 31-78 159-221 (344)
54 KOG0827|consensus 98.1 1.3E-06 2.8E-11 59.8 2.2 50 34-83 5-61 (465)
55 KOG4692|consensus 98.1 4.3E-06 9.4E-11 56.8 3.6 48 31-78 420-467 (489)
56 KOG2930|consensus 98.0 5E-06 1.1E-10 47.1 1.9 28 50-77 80-107 (114)
57 KOG1785|consensus 97.9 5.3E-06 1.1E-10 57.2 1.6 47 34-80 370-418 (563)
58 KOG4275|consensus 97.9 5.3E-06 1.2E-10 55.0 1.2 42 33-78 300-342 (350)
59 KOG3039|consensus 97.8 2.1E-05 4.6E-10 51.1 3.3 54 32-85 220-277 (303)
60 KOG0825|consensus 97.8 3.4E-06 7.3E-11 62.2 -0.8 49 33-81 123-174 (1134)
61 KOG1002|consensus 97.8 1.4E-05 3.1E-10 56.9 2.1 50 31-80 534-588 (791)
62 KOG1645|consensus 97.7 1.3E-05 2.9E-10 55.2 1.5 50 32-81 3-59 (463)
63 PF04641 Rtf2: Rtf2 RING-finge 97.7 7.4E-05 1.6E-09 49.2 4.3 56 30-86 110-169 (260)
64 KOG0826|consensus 97.7 3.6E-05 7.8E-10 51.8 2.7 50 29-78 296-346 (357)
65 PF14447 Prok-RING_4: Prokaryo 97.7 3E-05 6.6E-10 39.2 1.7 47 33-81 7-53 (55)
66 PF14570 zf-RING_4: RING/Ubox 97.6 6.2E-05 1.3E-09 37.2 2.3 42 36-77 1-47 (48)
67 KOG4185|consensus 97.5 7E-05 1.5E-09 49.9 2.8 45 33-77 3-54 (296)
68 KOG1571|consensus 97.5 6.5E-05 1.4E-09 51.1 2.2 47 29-78 301-347 (355)
69 COG5236 Uncharacterized conser 97.5 0.00011 2.5E-09 50.0 3.3 52 26-77 54-107 (493)
70 KOG4367|consensus 97.5 7.1E-05 1.5E-09 52.4 2.1 35 31-65 2-36 (699)
71 KOG1814|consensus 97.4 4.8E-05 1E-09 52.6 0.6 39 27-65 178-219 (445)
72 KOG1941|consensus 97.4 6.4E-05 1.4E-09 51.9 0.8 44 32-75 364-413 (518)
73 KOG2114|consensus 97.3 0.00033 7.3E-09 52.3 3.9 41 34-77 841-882 (933)
74 KOG1001|consensus 97.3 6.8E-05 1.5E-09 55.2 0.3 52 34-86 455-508 (674)
75 PF10367 Vps39_2: Vacuolar sor 97.1 0.00035 7.6E-09 39.7 1.9 32 30-61 75-108 (109)
76 KOG4739|consensus 97.1 0.00029 6.3E-09 45.6 1.5 44 35-80 5-50 (233)
77 KOG2817|consensus 97.0 0.00056 1.2E-08 47.2 2.4 49 29-77 330-384 (394)
78 PF08746 zf-RING-like: RING-li 96.9 0.0017 3.6E-08 31.4 2.9 38 36-73 1-43 (43)
79 PF07800 DUF1644: Protein of u 96.8 0.0021 4.6E-08 39.3 3.7 33 33-65 2-47 (162)
80 PF05290 Baculo_IE-1: Baculovi 96.7 0.0021 4.6E-08 38.2 3.2 50 32-81 79-135 (140)
81 KOG4445|consensus 96.7 0.00043 9.3E-09 46.4 0.1 49 32-80 114-188 (368)
82 KOG3800|consensus 96.7 0.0018 3.9E-08 43.1 2.9 46 35-80 2-53 (300)
83 PF03854 zf-P11: P-11 zinc fin 96.7 0.00069 1.5E-08 33.2 0.7 35 45-79 12-47 (50)
84 KOG1428|consensus 96.7 0.0015 3.2E-08 52.1 2.6 49 31-79 3484-3545(3738)
85 KOG3002|consensus 96.5 0.0021 4.6E-08 43.3 2.5 48 29-79 44-92 (299)
86 KOG1952|consensus 96.5 0.0042 9.2E-08 46.7 4.2 47 30-76 188-245 (950)
87 PHA02825 LAP/PHD finger-like p 96.5 0.0046 1E-07 37.9 3.7 48 31-79 6-60 (162)
88 KOG3970|consensus 96.5 0.0031 6.8E-08 40.8 3.1 47 34-80 51-107 (299)
89 KOG1940|consensus 96.4 0.0023 4.9E-08 42.6 2.0 42 34-75 159-204 (276)
90 KOG4362|consensus 96.3 0.00093 2E-08 49.1 -0.4 49 32-80 20-71 (684)
91 KOG2932|consensus 96.2 0.0021 4.5E-08 43.4 1.2 42 35-78 92-134 (389)
92 KOG3268|consensus 96.2 0.0043 9.3E-08 38.8 2.4 47 34-80 166-230 (234)
93 PHA03096 p28-like protein; Pro 96.2 0.0034 7.3E-08 42.0 1.9 42 34-75 179-231 (284)
94 PHA02862 5L protein; Provision 96.1 0.0083 1.8E-07 36.3 3.1 46 34-80 3-55 (156)
95 COG5175 MOT2 Transcriptional r 95.9 0.0069 1.5E-07 41.5 2.4 49 33-81 14-67 (480)
96 PF02891 zf-MIZ: MIZ/SP-RING z 95.7 0.0077 1.7E-07 30.0 1.7 43 33-76 2-50 (50)
97 KOG3113|consensus 95.6 0.012 2.6E-07 38.7 2.7 62 30-93 108-173 (293)
98 KOG0298|consensus 95.6 0.0068 1.5E-07 47.4 1.7 46 31-76 1151-1197(1394)
99 PF05883 Baculo_RING: Baculovi 95.4 0.0098 2.1E-07 35.5 1.7 33 33-65 26-67 (134)
100 PF12906 RINGv: RING-variant d 95.0 0.018 3.8E-07 28.3 1.5 38 36-73 1-47 (47)
101 PF10272 Tmpp129: Putative tra 94.7 0.026 5.7E-07 39.0 2.2 31 51-81 311-354 (358)
102 KOG1100|consensus 94.6 0.019 4.2E-07 36.8 1.5 40 36-79 161-201 (207)
103 KOG3039|consensus 94.4 0.041 8.8E-07 36.2 2.5 36 30-65 40-75 (303)
104 KOG3161|consensus 94.4 0.014 3E-07 43.1 0.4 38 32-71 10-51 (861)
105 PF06906 DUF1272: Protein of u 93.9 0.08 1.7E-06 26.9 2.5 46 35-82 7-56 (57)
106 COG5109 Uncharacterized conser 93.8 0.055 1.2E-06 36.8 2.4 47 30-76 333-385 (396)
107 KOG3899|consensus 92.8 0.062 1.3E-06 36.3 1.4 31 51-81 325-368 (381)
108 KOG0309|consensus 92.8 0.071 1.5E-06 40.3 1.8 38 35-72 1030-1069(1081)
109 KOG3579|consensus 92.7 0.11 2.3E-06 35.0 2.4 37 31-67 266-306 (352)
110 KOG2034|consensus 92.7 0.12 2.6E-06 39.5 2.9 35 30-64 814-850 (911)
111 COG5220 TFB3 Cdk activating ki 92.6 0.071 1.5E-06 35.0 1.4 45 33-77 10-63 (314)
112 KOG1815|consensus 92.3 0.1 2.2E-06 37.1 2.1 35 31-65 68-103 (444)
113 KOG1812|consensus 92.3 0.059 1.3E-06 37.6 0.9 48 33-80 146-205 (384)
114 COG3813 Uncharacterized protei 91.3 0.12 2.6E-06 27.7 1.2 33 51-85 27-59 (84)
115 PF04216 FdhE: Protein involve 90.6 0.054 1.2E-06 36.3 -0.7 46 32-77 171-221 (290)
116 PF14446 Prok-RING_1: Prokaryo 90.4 0.48 1E-05 24.0 2.8 30 33-62 5-38 (54)
117 KOG1812|consensus 90.1 0.16 3.4E-06 35.5 1.2 41 33-73 306-351 (384)
118 PF07191 zinc-ribbons_6: zinc- 89.7 0.0097 2.1E-07 31.7 -3.8 40 34-78 2-41 (70)
119 PF10571 UPF0547: Uncharacteri 89.3 0.22 4.7E-06 21.3 0.9 10 35-44 2-11 (26)
120 COG5183 SSM4 Protein involved 89.1 0.54 1.2E-05 36.1 3.3 53 31-83 10-71 (1175)
121 PF10235 Cript: Microtubule-as 89.0 0.44 9.4E-06 26.7 2.2 42 34-84 45-86 (90)
122 KOG4718|consensus 88.4 0.28 6.1E-06 31.6 1.4 43 33-75 181-224 (235)
123 PF07975 C1_4: TFIIH C1-like d 87.9 0.74 1.6E-05 23.0 2.4 25 50-74 26-50 (51)
124 PF02318 FYVE_2: FYVE-type zin 87.9 0.92 2E-05 26.4 3.2 43 33-75 54-102 (118)
125 KOG2068|consensus 87.7 0.61 1.3E-05 32.0 2.7 48 33-80 249-300 (327)
126 TIGR01562 FdhE formate dehydro 86.9 0.36 7.9E-06 32.8 1.3 45 32-76 183-233 (305)
127 PRK03564 formate dehydrogenase 86.7 0.52 1.1E-05 32.1 2.0 44 32-75 186-234 (309)
128 PF06844 DUF1244: Protein of u 85.1 0.59 1.3E-05 24.6 1.3 12 54-65 11-22 (68)
129 KOG0827|consensus 84.6 0.047 1E-06 38.1 -3.8 47 34-80 197-247 (465)
130 KOG0802|consensus 83.3 0.91 2E-05 33.2 2.0 52 29-84 475-526 (543)
131 KOG2169|consensus 83.1 1.2 2.7E-05 33.2 2.7 67 27-93 300-371 (636)
132 KOG1609|consensus 82.0 1.5 3.2E-05 29.3 2.5 46 33-78 78-134 (323)
133 KOG3053|consensus 81.6 1.1 2.4E-05 29.9 1.7 47 32-78 19-82 (293)
134 smart00132 LIM Zinc-binding do 80.5 1.9 4E-05 19.2 1.9 35 36-78 2-38 (39)
135 KOG0825|consensus 80.1 1.5 3.3E-05 33.7 2.2 46 32-77 95-153 (1134)
136 PF01363 FYVE: FYVE zinc finge 79.3 0.41 8.8E-06 24.9 -0.7 30 33-62 9-42 (69)
137 KOG1829|consensus 78.6 0.97 2.1E-05 33.4 0.8 39 32-73 510-556 (580)
138 KOG0824|consensus 78.5 0.92 2E-05 30.8 0.7 49 29-77 101-150 (324)
139 cd00065 FYVE FYVE domain; Zinc 78.4 1.7 3.6E-05 21.6 1.5 30 35-64 4-37 (57)
140 KOG2979|consensus 77.9 1.3 2.8E-05 29.4 1.2 43 32-74 175-220 (262)
141 COG0068 HypF Hydrogenase matur 77.8 2.3 4.9E-05 32.3 2.5 50 29-78 97-184 (750)
142 smart00064 FYVE Protein presen 77.7 2 4.4E-05 22.1 1.8 31 34-64 11-45 (68)
143 PF09889 DUF2116: Uncharacteri 77.1 1.7 3.6E-05 22.4 1.2 18 66-83 2-19 (59)
144 KOG0801|consensus 76.5 0.76 1.6E-05 28.6 -0.1 26 32-57 176-204 (205)
145 KOG0269|consensus 76.2 3.8 8.2E-05 31.4 3.3 39 34-72 780-820 (839)
146 PF14353 CpXC: CpXC protein 76.1 2.3 5E-05 24.9 1.9 47 34-80 2-51 (128)
147 KOG2066|consensus 76.1 2.3 5E-05 32.6 2.2 39 34-73 785-830 (846)
148 KOG0289|consensus 75.8 2.8 6.1E-05 30.1 2.4 49 35-83 2-51 (506)
149 cd00350 rubredoxin_like Rubred 75.3 2.5 5.4E-05 18.8 1.5 10 66-75 16-25 (33)
150 PF10497 zf-4CXXC_R1: Zinc-fin 75.0 2.9 6.4E-05 23.9 2.0 24 52-75 37-69 (105)
151 KOG2807|consensus 74.6 5.1 0.00011 27.7 3.4 42 34-75 331-375 (378)
152 PF14569 zf-UDP: Zinc-binding 74.5 4.9 0.00011 21.9 2.7 47 33-79 9-63 (80)
153 PF04423 Rad50_zn_hook: Rad50 74.4 1.1 2.3E-05 22.3 0.1 13 68-80 21-33 (54)
154 PF12773 DZR: Double zinc ribb 74.2 3.1 6.8E-05 20.1 1.8 27 54-80 13-42 (50)
155 PF00412 LIM: LIM domain; Int 72.5 1.6 3.4E-05 21.6 0.5 37 36-80 1-39 (58)
156 PF13901 DUF4206: Domain of un 70.9 4.1 9E-05 26.0 2.2 38 32-74 151-196 (202)
157 KOG2042|consensus 70.7 5.5 0.00012 31.3 3.1 64 30-93 867-931 (943)
158 TIGR00622 ssl1 transcription f 70.6 7.3 0.00016 22.7 3.0 41 34-74 56-110 (112)
159 TIGR00373 conserved hypothetic 69.9 15 0.00033 22.5 4.5 36 31-81 107-142 (158)
160 PLN02195 cellulose synthase A 69.4 8.5 0.00018 30.4 3.9 48 33-80 6-61 (977)
161 KOG2231|consensus 69.3 4.7 0.0001 30.5 2.4 46 35-80 2-54 (669)
162 PF00628 PHD: PHD-finger; Int 67.8 2.1 4.5E-05 20.7 0.3 40 35-74 1-49 (51)
163 COG4647 AcxC Acetone carboxyla 66.8 2.9 6.4E-05 25.0 0.8 22 37-58 61-82 (165)
164 PLN02638 cellulose synthase A 66.4 10 0.00022 30.4 3.8 47 32-78 16-70 (1079)
165 smart00647 IBR In Between Ring 65.9 0.8 1.7E-05 23.1 -1.5 14 50-63 45-58 (64)
166 PF14311 DUF4379: Domain of un 65.7 4.3 9.4E-05 20.1 1.3 9 65-73 47-55 (55)
167 COG3492 Uncharacterized protei 65.6 4 8.6E-05 22.9 1.1 12 54-65 42-53 (104)
168 smart00249 PHD PHD zinc finger 65.4 4.7 0.0001 18.4 1.3 27 36-62 2-31 (47)
169 COG5151 SSL1 RNA polymerase II 65.1 11 0.00025 26.0 3.4 44 32-75 361-418 (421)
170 COG3058 FdhE Uncharacterized p 64.8 16 0.00034 24.9 4.0 45 32-76 184-234 (308)
171 KOG2113|consensus 64.0 8.5 0.00018 26.6 2.7 44 31-76 341-385 (394)
172 PRK11595 DNA utilization prote 62.6 9.5 0.00021 24.6 2.7 38 35-77 7-44 (227)
173 KOG3476|consensus 62.4 1 2.3E-05 24.9 -1.5 43 34-85 55-97 (100)
174 PLN02189 cellulose synthase 61.3 8.4 0.00018 30.6 2.5 47 32-78 33-87 (1040)
175 KOG3799|consensus 60.2 3.4 7.3E-05 25.0 0.3 27 30-60 62-88 (169)
176 PRK06266 transcription initiat 60.2 11 0.00023 23.7 2.5 35 32-81 116-150 (178)
177 KOG3842|consensus 59.5 14 0.00031 25.7 3.1 48 33-80 341-416 (429)
178 KOG2462|consensus 59.3 3.2 6.9E-05 27.9 0.1 51 32-82 160-230 (279)
179 PLN02248 cellulose synthase-li 58.8 10 0.00023 30.4 2.7 30 50-79 149-178 (1135)
180 KOG1729|consensus 58.7 13 0.00029 25.2 2.9 47 32-78 167-225 (288)
181 COG4640 Predicted membrane pro 57.9 2.4 5.3E-05 30.0 -0.7 38 55-92 3-40 (465)
182 KOG4021|consensus 56.3 4.7 0.0001 25.9 0.5 26 57-82 97-123 (239)
183 smart00154 ZnF_AN1 AN1-like Zi 55.5 9.7 0.00021 17.7 1.4 7 51-57 18-24 (39)
184 KOG3362|consensus 54.8 9.2 0.0002 23.3 1.5 29 31-60 116-145 (156)
185 PLN02436 cellulose synthase A 53.2 13 0.00029 29.7 2.5 46 33-78 36-89 (1094)
186 PLN02915 cellulose synthase A 51.9 14 0.00031 29.5 2.4 46 33-78 15-68 (1044)
187 smart00734 ZnF_Rad18 Rad18-lik 51.8 8.1 0.00018 16.3 0.7 10 69-78 3-12 (26)
188 PLN02400 cellulose synthase 51.6 12 0.00026 30.0 2.0 47 32-78 35-89 (1085)
189 smart00290 ZnF_UBP Ubiquitin C 50.9 12 0.00025 17.9 1.3 22 36-57 2-23 (50)
190 PRK14559 putative protein seri 50.8 9.7 0.00021 28.8 1.4 8 35-42 3-10 (645)
191 PF10146 zf-C4H2: Zinc finger- 49.6 18 0.00039 23.7 2.4 26 55-80 196-221 (230)
192 PF09723 Zn-ribbon_8: Zinc rib 48.9 2.9 6.3E-05 19.7 -1.0 9 67-75 26-34 (42)
193 PF10083 DUF2321: Uncharacteri 48.4 13 0.00027 23.0 1.4 25 53-80 28-52 (158)
194 PF13832 zf-HC5HC2H_2: PHD-zin 48.4 20 0.00044 20.2 2.2 29 32-62 54-87 (110)
195 COG2093 DNA-directed RNA polym 48.0 7.5 0.00016 20.3 0.3 21 56-76 7-27 (64)
196 PF07503 zf-HYPF: HypF finger; 48.0 24 0.00051 16.0 2.0 23 56-78 2-32 (35)
197 KOG4451|consensus 47.4 19 0.00041 23.8 2.2 26 55-80 251-276 (286)
198 PRK08351 DNA-directed RNA poly 47.2 14 0.0003 19.2 1.3 13 66-78 14-26 (61)
199 PF14169 YdjO: Cold-inducible 46.9 14 0.0003 19.0 1.2 14 67-80 39-52 (59)
200 PRK01343 zinc-binding protein; 46.8 15 0.00032 18.8 1.3 12 67-78 9-20 (57)
201 TIGR00143 hypF [NiFe] hydrogen 46.6 13 0.00028 28.4 1.5 49 30-78 65-151 (711)
202 PRK06393 rpoE DNA-directed RNA 45.4 16 0.00034 19.2 1.3 21 56-78 8-28 (64)
203 PF13719 zinc_ribbon_5: zinc-r 45.3 12 0.00025 17.1 0.8 12 35-46 4-15 (37)
204 PF01485 IBR: IBR domain; Int 45.3 1.4 3E-05 22.2 -2.7 29 35-63 20-58 (64)
205 PRK11088 rrmA 23S rRNA methylt 44.5 16 0.00034 24.1 1.6 22 34-55 3-27 (272)
206 KOG2789|consensus 44.0 53 0.0011 23.7 4.0 32 32-63 73-106 (482)
207 PF09297 zf-NADH-PPase: NADH p 43.5 2.5 5.3E-05 18.6 -1.7 10 53-62 3-12 (32)
208 COG5627 MMS21 DNA repair prote 43.2 14 0.00029 24.6 1.0 48 33-80 189-241 (275)
209 PF03119 DNA_ligase_ZBD: NAD-d 41.7 9.4 0.0002 16.4 0.1 11 69-79 1-11 (28)
210 PF11023 DUF2614: Protein of u 41.6 8.4 0.00018 22.5 -0.1 21 64-84 82-102 (114)
211 PRK00418 DNA gyrase inhibitor; 41.0 15 0.00033 19.1 0.8 11 68-78 7-17 (62)
212 KOG1701|consensus 40.9 2.3 5.1E-05 30.3 -2.8 11 69-79 396-406 (468)
213 PF13717 zinc_ribbon_4: zinc-r 40.4 16 0.00034 16.6 0.8 10 35-44 4-13 (36)
214 PRK04023 DNA polymerase II lar 39.9 23 0.0005 28.4 2.0 47 32-80 625-676 (1121)
215 KOG1842|consensus 39.8 4.9 0.00011 28.9 -1.4 31 32-62 179-213 (505)
216 PF05605 zf-Di19: Drought indu 39.3 22 0.00048 17.4 1.3 7 69-75 4-10 (54)
217 PF15616 TerY-C: TerY-C metal 38.8 13 0.00028 22.3 0.5 41 32-78 76-116 (131)
218 PF06827 zf-FPG_IleRS: Zinc fi 37.7 5.4 0.00012 17.2 -1.0 10 35-44 3-12 (30)
219 KOG4218|consensus 36.5 27 0.00059 24.6 1.7 13 33-45 15-27 (475)
220 PF06750 DiS_P_DiS: Bacterial 36.3 35 0.00077 18.9 1.9 39 33-80 33-71 (92)
221 COG4357 Zinc finger domain con 36.3 35 0.00077 19.4 1.9 14 67-80 80-93 (105)
222 COG4306 Uncharacterized protei 36.1 29 0.00062 20.8 1.6 22 55-79 30-51 (160)
223 KOG4443|consensus 36.0 20 0.00044 27.2 1.2 47 30-76 15-71 (694)
224 PF00096 zf-C2H2: Zinc finger, 35.9 9.1 0.0002 14.9 -0.4 9 36-44 3-11 (23)
225 COG3809 Uncharacterized protei 35.4 5.9 0.00013 21.6 -1.2 12 34-45 2-13 (88)
226 PF13894 zf-C2H2_4: C2H2-type 35.4 17 0.00037 13.8 0.4 10 70-79 3-12 (24)
227 PF10013 DUF2256: Uncharacteri 35.2 26 0.00057 16.7 1.1 12 67-78 8-19 (42)
228 PF09237 GAGA: GAGA factor; I 34.9 12 0.00026 18.8 -0.1 13 68-80 25-37 (54)
229 COG4068 Uncharacterized protei 34.9 28 0.00061 17.9 1.2 16 66-81 7-22 (64)
230 PF06416 DUF1076: Protein of u 34.8 60 0.0013 19.0 2.7 73 11-83 18-96 (113)
231 PF01428 zf-AN1: AN1-like Zinc 34.7 24 0.00052 16.5 1.0 20 39-58 6-26 (43)
232 KOG3005|consensus 34.5 22 0.00048 24.0 1.0 44 34-77 183-242 (276)
233 KOG4642|consensus 33.7 26 0.00056 23.6 1.2 65 30-94 208-273 (284)
234 PF09538 FYDLN_acid: Protein o 33.3 23 0.0005 20.4 0.9 13 68-80 27-39 (108)
235 PF10186 Atg14: UV radiation r 32.8 34 0.00073 22.5 1.7 21 35-63 1-21 (302)
236 PRK05452 anaerobic nitric oxid 32.7 1.2E+02 0.0025 22.1 4.5 40 31-76 423-467 (479)
237 PF12132 DUF3587: Protein of u 32.7 40 0.00086 21.7 1.9 23 43-65 151-177 (199)
238 TIGR02652 conserved hypothetic 32.7 16 0.00035 22.3 0.2 14 66-79 8-21 (163)
239 PF02132 RecR: RecR protein; 32.5 57 0.0012 15.1 2.1 17 3-19 2-18 (41)
240 PF09654 DUF2396: Protein of u 32.2 17 0.00037 22.1 0.2 13 67-79 6-18 (161)
241 PF13913 zf-C2HC_2: zinc-finge 32.2 15 0.00032 15.2 -0.0 10 69-78 4-13 (25)
242 cd00729 rubredoxin_SM Rubredox 32.0 25 0.00055 15.7 0.7 9 68-76 19-27 (34)
243 COG5200 LUC7 U1 snRNP componen 31.7 27 0.00059 22.8 1.1 41 1-44 156-196 (258)
244 PF14369 zf-RING_3: zinc-finge 31.6 22 0.00048 16.1 0.5 10 69-78 23-32 (35)
245 PF03884 DUF329: Domain of unk 31.1 16 0.00035 18.6 0.0 11 69-79 4-14 (57)
246 COG1592 Rubrerythrin [Energy p 30.8 30 0.00065 21.6 1.1 11 66-76 148-158 (166)
247 COG2816 NPY1 NTP pyrophosphohy 30.8 13 0.00028 25.2 -0.5 28 51-78 109-140 (279)
248 PF13771 zf-HC5HC2H: PHD-like 30.6 53 0.0012 17.6 2.1 29 32-62 35-68 (90)
249 KOG2071|consensus 30.5 24 0.00052 26.4 0.8 33 32-64 512-557 (579)
250 PF13453 zf-TFIIB: Transcripti 30.1 28 0.00061 16.0 0.7 12 69-80 1-12 (41)
251 PF08882 Acetone_carb_G: Aceto 29.9 28 0.00061 20.3 0.9 11 48-58 26-36 (112)
252 PF14319 Zn_Tnp_IS91: Transpos 29.8 31 0.00067 19.9 1.0 25 34-60 43-67 (111)
253 KOG1356|consensus 29.5 38 0.00083 26.6 1.7 34 31-64 227-262 (889)
254 PF06677 Auto_anti-p27: Sjogre 29.4 42 0.00091 15.8 1.3 17 63-79 13-29 (41)
255 KOG0006|consensus 29.2 50 0.0011 23.1 2.0 32 32-63 220-253 (446)
256 PF02148 zf-UBP: Zn-finger in 29.0 27 0.00058 17.8 0.6 23 36-58 1-24 (63)
257 COG3357 Predicted transcriptio 28.9 17 0.00038 20.4 -0.1 28 50-81 63-90 (97)
258 COG5242 TFB4 RNA polymerase II 28.6 23 0.0005 23.5 0.4 14 33-46 260-273 (296)
259 cd00730 rubredoxin Rubredoxin; 27.8 40 0.00087 16.6 1.1 11 66-76 33-43 (50)
260 TIGR00100 hypA hydrogenase nic 27.3 1E+02 0.0022 17.8 2.9 10 67-76 86-95 (115)
261 PF07649 C1_3: C1-like domain; 27.2 56 0.0012 13.8 1.4 25 35-59 2-29 (30)
262 PF14577 SEO_C: Sieve element 27.2 41 0.00089 22.3 1.3 28 26-53 207-234 (235)
263 COG4098 comFA Superfamily II D 26.5 27 0.00059 24.8 0.5 31 31-61 37-68 (441)
264 COG3677 Transposase and inacti 26.0 34 0.00073 20.3 0.7 37 33-81 30-67 (129)
265 PRK00564 hypA hydrogenase nick 25.5 22 0.00048 20.7 -0.1 8 69-76 90-97 (117)
266 COG4338 Uncharacterized protei 25.2 25 0.00055 17.3 0.1 11 68-78 13-23 (54)
267 PF09986 DUF2225: Uncharacteri 24.9 41 0.00088 21.7 1.0 50 32-81 4-62 (214)
268 PF05502 Dynactin_p62: Dynacti 24.8 28 0.0006 25.4 0.3 10 69-78 54-63 (483)
269 PF04710 Pellino: Pellino; In 24.8 24 0.00053 25.2 0.0 48 33-80 328-403 (416)
270 COG2835 Uncharacterized conser 24.7 37 0.0008 17.5 0.6 11 68-78 9-19 (60)
271 KOG2593|consensus 24.6 88 0.0019 22.7 2.6 41 31-80 126-166 (436)
272 PF12874 zf-met: Zinc-finger o 24.4 19 0.00041 14.3 -0.4 10 35-44 2-11 (25)
273 TIGR01206 lysW lysine biosynth 24.2 38 0.00082 17.0 0.6 13 68-80 3-15 (54)
274 PTZ00303 phosphatidylinositol 24.1 40 0.00088 26.6 1.0 31 34-64 461-500 (1374)
275 KOG2186|consensus 24.1 38 0.00083 22.7 0.8 13 34-46 4-16 (276)
276 KOG1244|consensus 24.0 13 0.00027 25.3 -1.4 42 35-76 283-331 (336)
277 COG3024 Uncharacterized protei 23.4 44 0.00095 17.5 0.8 12 68-79 8-19 (65)
278 PRK02935 hypothetical protein; 23.2 67 0.0015 18.6 1.6 22 64-85 83-104 (110)
279 PF00643 zf-B_box: B-box zinc 22.9 67 0.0014 14.5 1.3 29 34-62 4-32 (42)
280 PF13912 zf-C2H2_6: C2H2-type 22.8 27 0.00059 14.1 -0.0 11 35-45 3-13 (27)
281 cd04718 BAH_plant_2 BAH, or Br 22.7 26 0.00057 21.5 -0.1 24 55-78 2-29 (148)
282 PF14471 DUF4428: Domain of un 22.5 1.2E+02 0.0025 14.9 2.2 28 35-63 1-30 (51)
283 PF06676 DUF1178: Protein of u 22.4 1.3E+02 0.0027 18.5 2.7 11 68-78 33-43 (148)
284 PRK00420 hypothetical protein; 22.3 78 0.0017 18.4 1.8 11 68-78 41-51 (112)
285 PF13465 zf-H2C2_2: Zinc-finge 22.1 40 0.00086 13.8 0.4 11 33-43 14-24 (26)
286 PRK11827 hypothetical protein; 21.8 30 0.00066 17.8 0.0 13 67-79 8-20 (60)
287 smart00531 TFIIE Transcription 21.7 33 0.00071 20.7 0.1 15 67-81 123-137 (147)
288 PF00301 Rubredoxin: Rubredoxi 21.5 54 0.0012 15.9 0.8 15 28-42 29-43 (47)
289 PF14255 Cys_rich_CPXG: Cystei 21.4 46 0.001 16.6 0.6 10 69-78 2-11 (52)
290 COG1675 TFA1 Transcription ini 21.1 76 0.0016 20.1 1.6 18 64-81 129-146 (176)
291 TIGR00627 tfb4 transcription f 20.9 24 0.00052 23.9 -0.6 9 68-76 270-278 (279)
292 KOG0314|consensus 20.7 2.2E+02 0.0048 20.8 4.0 35 27-61 300-335 (448)
293 PF06221 zf-C2HC5: Putative zi 20.5 76 0.0016 16.1 1.3 27 47-79 20-47 (57)
294 PF12907 zf-met2: Zinc-binding 20.5 20 0.00042 16.9 -0.8 7 35-41 3-9 (40)
295 PF05715 zf-piccolo: Piccolo Z 20.2 86 0.0019 16.2 1.5 27 34-60 3-29 (61)
296 PRK00398 rpoP DNA-directed RNA 20.2 47 0.001 15.6 0.5 14 67-80 21-34 (46)
No 1
>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=99.60 E-value=9.6e-16 Score=80.41 Aligned_cols=62 Identities=23% Similarity=0.366 Sum_probs=55.4
Q ss_pred cccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCccCCCCccccCCcchhhhhc
Q psy3884 33 GCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRDGATSYFVQI 94 (95)
Q Consensus 33 ~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~~~~~~~q~ 94 (95)
++.|+||.+.+.+|+.++|||+||..|+..|+..+..||.|+.++..++...+..+.+.++-
T Consensus 1 ~~~Cpi~~~~~~~Pv~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~~~l~~~~~l~~~i~~ 62 (63)
T smart00504 1 EFLCPISLEVMKDPVILPSGQTYERRAIEKWLLSHGTDPVTGQPLTHEDLIPNLALKSAIQE 62 (63)
T ss_pred CcCCcCCCCcCCCCEECCCCCEEeHHHHHHHHHHCCCCCCCcCCCChhhceeCHHHHHHHHh
Confidence 35899999999999999999999999999999988899999999988888888777776653
No 2
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=99.59 E-value=1.1e-15 Score=74.27 Aligned_cols=38 Identities=50% Similarity=1.233 Sum_probs=30.6
Q ss_pred ccccccCCCCCeecCCCCcchHHhHHHHhhCC----CCCCCC
Q psy3884 36 CPICHDEFKTPVQLTCCHIFCESCVTKWFDRE----QTCPLC 73 (95)
Q Consensus 36 C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~----~~CP~C 73 (95)
|+||++.+.+|+.++|||+||..||.+|.+.. ..||.|
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 89999999999999999999999999998744 469987
No 3
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=99.59 E-value=2.2e-15 Score=93.83 Aligned_cols=52 Identities=33% Similarity=0.870 Sum_probs=44.7
Q ss_pred CCcccccccccCCCCCeecCCCCcchHHhHHHHhhC----------------CCCCCCCCccCCCCcc
Q psy3884 31 GVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDR----------------EQTCPLCRATLVDDPA 82 (95)
Q Consensus 31 ~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~----------------~~~CP~Cr~~~~~~~~ 82 (95)
...+.|+||++.+.+|++++|||.||..||..|+.. ...||+||..+.....
T Consensus 16 ~~~~~CpICld~~~dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~L 83 (193)
T PLN03208 16 GGDFDCNICLDQVRDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEATL 83 (193)
T ss_pred CCccCCccCCCcCCCcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhcE
Confidence 456899999999999999999999999999999742 2479999999976543
No 4
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.56 E-value=2.6e-15 Score=102.59 Aligned_cols=68 Identities=32% Similarity=0.679 Sum_probs=60.0
Q ss_pred ccCCCcccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCccCCCCccccCCcchhhhhcC
Q psy3884 28 TLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRDGATSYFVQIF 95 (95)
Q Consensus 28 ~~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~~~~~~~q~~ 95 (95)
......+.|+||.+.+..|++++|||.||..|+..|+.....||.|+..+.......+..+.++++.|
T Consensus 21 ~~Le~~l~C~IC~d~~~~PvitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~~~~Lr~N~~L~~iVe~~ 88 (397)
T TIGR00599 21 YPLDTSLRCHICKDFFDVPVLTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQESKLRSNWLVSEIVESF 88 (397)
T ss_pred cccccccCCCcCchhhhCccCCCCCCchhHHHHHHHHhCCCCCCCCCCccccccCccchHHHHHHHHH
Confidence 34567789999999999999999999999999999999888999999999877777788888888765
No 5
>KOG0317|consensus
Probab=99.55 E-value=3.9e-15 Score=96.94 Aligned_cols=55 Identities=29% Similarity=0.775 Sum_probs=49.2
Q ss_pred cCCCcccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCccCCCCccc
Q psy3884 29 LLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAW 83 (95)
Q Consensus 29 ~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~ 83 (95)
..+....|.+|++...+|..+||||.||..||..|......||+||..+...++.
T Consensus 235 i~~a~~kC~LCLe~~~~pSaTpCGHiFCWsCI~~w~~ek~eCPlCR~~~~pskvi 289 (293)
T KOG0317|consen 235 IPEATRKCSLCLENRSNPSATPCGHIFCWSCILEWCSEKAECPLCREKFQPSKVI 289 (293)
T ss_pred CCCCCCceEEEecCCCCCCcCcCcchHHHHHHHHHHccccCCCcccccCCCccee
Confidence 3445679999999999999999999999999999999999999999999877543
No 6
>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=99.54 E-value=1.5e-15 Score=74.57 Aligned_cols=40 Identities=48% Similarity=1.299 Sum_probs=35.3
Q ss_pred cccccccCCCC---CeecCCCCcchHHhHHHHhhCCCCCCCCC
Q psy3884 35 ICPICHDEFKT---PVQLTCCHIFCESCVTKWFDREQTCPLCR 74 (95)
Q Consensus 35 ~C~IC~~~~~~---p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr 74 (95)
.|+||++.+.. .+.++|||.||..|+.+|++.+.+||+||
T Consensus 2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~~~CP~CR 44 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRNNSCPVCR 44 (44)
T ss_dssp CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHSSB-TTTH
T ss_pred CCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhCCcCCccC
Confidence 79999999853 46789999999999999999999999997
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=7e-15 Score=70.41 Aligned_cols=38 Identities=45% Similarity=1.314 Sum_probs=33.8
Q ss_pred ccccccCCCCC-eecCCCCcchHHhHHHHhhCCCCCCCC
Q psy3884 36 CPICHDEFKTP-VQLTCCHIFCESCVTKWFDREQTCPLC 73 (95)
Q Consensus 36 C~IC~~~~~~p-~~~~CgH~fc~~Ci~~~~~~~~~CP~C 73 (95)
|+||++.+.+| +.++|||+||..|+.+|++.+..||.|
T Consensus 1 C~iC~~~~~~~~~~~~CGH~fC~~C~~~~~~~~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDELRDPVVVTPCGHSFCKECIEKYLEKNPKCPVC 39 (39)
T ss_dssp ETTTTSB-SSEEEECTTSEEEEHHHHHHHHHCTSB-TTT
T ss_pred CCCCCCcccCcCEECCCCCchhHHHHHHHHHCcCCCcCC
Confidence 89999999999 578999999999999999998899987
No 8
>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=99.51 E-value=1.2e-14 Score=73.09 Aligned_cols=46 Identities=37% Similarity=1.003 Sum_probs=41.2
Q ss_pred cccccccccCCCCCeecCCCCc-chHHhHHHHhhCCCCCCCCCccCC
Q psy3884 33 GCICPICHDEFKTPVQLTCCHI-FCESCVTKWFDREQTCPLCRATLV 78 (95)
Q Consensus 33 ~~~C~IC~~~~~~p~~~~CgH~-fc~~Ci~~~~~~~~~CP~Cr~~~~ 78 (95)
+..|.||++...+.+.+||||. ||..|+.+|+.....||+||+++.
T Consensus 2 ~~~C~iC~~~~~~~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFENPRDVVLLPCGHLCFCEECAERLLKRKKKCPICRQPIE 48 (50)
T ss_dssp HSB-TTTSSSBSSEEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred cCCCccCCccCCceEEeCCCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence 4589999999999999999999 999999999999999999999875
No 9
>KOG0287|consensus
Probab=99.51 E-value=2.1e-15 Score=100.30 Aligned_cols=65 Identities=25% Similarity=0.608 Sum_probs=60.3
Q ss_pred CCcccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCccCCCCccccCCcchhhhhcC
Q psy3884 31 GVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRDGATSYFVQIF 95 (95)
Q Consensus 31 ~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~~~~~~~q~~ 95 (95)
.+.+.|.||.++|..|+++||+|+||.-||+.++..+..||.|+.++.+.+...+..++.++|.|
T Consensus 21 D~lLRC~IC~eyf~ip~itpCsHtfCSlCIR~~L~~~p~CP~C~~~~~Es~Lr~n~il~Eiv~S~ 85 (442)
T KOG0287|consen 21 DDLLRCGICFEYFNIPMITPCSHTFCSLCIRKFLSYKPQCPTCCVTVTESDLRNNRILDEIVKSL 85 (442)
T ss_pred HHHHHHhHHHHHhcCceeccccchHHHHHHHHHhccCCCCCceecccchhhhhhhhHHHHHHHHH
Confidence 45679999999999999999999999999999999999999999999999888888888888865
No 10
>KOG0823|consensus
Probab=99.50 E-value=1.8e-14 Score=91.39 Aligned_cols=53 Identities=36% Similarity=0.799 Sum_probs=46.4
Q ss_pred CCCcccccccccCCCCCeecCCCCcchHHhHHHHhhC---CCCCCCCCccCCCCcc
Q psy3884 30 LGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDR---EQTCPLCRATLVDDPA 82 (95)
Q Consensus 30 ~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~---~~~CP~Cr~~~~~~~~ 82 (95)
....+.|.||++..++|+++.|||.||..||.+|+.. ...||+|+..+..+..
T Consensus 44 ~~~~FdCNICLd~akdPVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~v 99 (230)
T KOG0823|consen 44 DGGFFDCNICLDLAKDPVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDTV 99 (230)
T ss_pred CCCceeeeeeccccCCCEEeecccceehHHHHHHHhhcCCCeeCCccccccccceE
Confidence 3467899999999999999999999999999999984 3578999999887743
No 11
>PHA02929 N1R/p28-like protein; Provisional
Probab=99.48 E-value=4.7e-14 Score=90.90 Aligned_cols=47 Identities=30% Similarity=0.897 Sum_probs=40.8
Q ss_pred CcccccccccCCCCC--------eecCCCCcchHHhHHHHhhCCCCCCCCCccCC
Q psy3884 32 VGCICPICHDEFKTP--------VQLTCCHIFCESCVTKWFDREQTCPLCRATLV 78 (95)
Q Consensus 32 ~~~~C~IC~~~~~~p--------~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~ 78 (95)
.+..|+||++.+.++ +.++|||.||..|+.+|+....+||+||.++.
T Consensus 173 ~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~ 227 (238)
T PHA02929 173 KDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFI 227 (238)
T ss_pred CCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEee
Confidence 467999999987653 45589999999999999999999999999876
No 12
>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=99.45 E-value=2.6e-14 Score=77.18 Aligned_cols=65 Identities=22% Similarity=0.446 Sum_probs=53.2
Q ss_pred CCcccccccccCCCCCeecCCCCcchHHhHHHHhhC-CCCCCCCCccCCCCccccCCcchhhhhcC
Q psy3884 31 GVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDR-EQTCPLCRATLVDDPAWRDGATSYFVQIF 95 (95)
Q Consensus 31 ~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~~~~~~~~~~~~~~~~q~~ 95 (95)
.+.+.|||+.+.+.+|+++++||+|...+|..|+.. +..||.++.++...+..++..+.+.|+.|
T Consensus 2 P~~f~CpIt~~lM~dPVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~~l~pn~~Lk~~I~~~ 67 (73)
T PF04564_consen 2 PDEFLCPITGELMRDPVILPSGHTYERSAIERWLEQNGGTDPFTRQPLSESDLIPNRALKSAIEEW 67 (73)
T ss_dssp SGGGB-TTTSSB-SSEEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SGGGSEE-HHHHHHHHHH
T ss_pred CcccCCcCcCcHhhCceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCcccceECHHHHHHHHHH
Confidence 467899999999999999999999999999999998 78999999999988888888887777654
No 13
>KOG0320|consensus
Probab=99.41 E-value=1.4e-13 Score=84.36 Aligned_cols=52 Identities=31% Similarity=0.816 Sum_probs=45.2
Q ss_pred CcccccccccCCCC--CeecCCCCcchHHhHHHHhhCCCCCCCCCccCCCCccc
Q psy3884 32 VGCICPICHDEFKT--PVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAW 83 (95)
Q Consensus 32 ~~~~C~IC~~~~~~--p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~ 83 (95)
..+.||||++.+.+ |+.+.|||+||..||...++....||+|++.+..+.++
T Consensus 130 ~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~k~~~ 183 (187)
T KOG0320|consen 130 GTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITHKQFH 183 (187)
T ss_pred cccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCcccccchhhhe
Confidence 45799999999886 45689999999999999999999999999988776543
No 14
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=99.39 E-value=4.9e-13 Score=90.08 Aligned_cols=53 Identities=40% Similarity=0.983 Sum_probs=44.5
Q ss_pred ccccCCCcccccccccCC-CC------------CeecCCCCcchHHhHHHHhhCCCCCCCCCccCC
Q psy3884 26 KETLLGVGCICPICHDEF-KT------------PVQLTCCHIFCESCVTKWFDREQTCPLCRATLV 78 (95)
Q Consensus 26 ~~~~~~~~~~C~IC~~~~-~~------------p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~ 78 (95)
.++...++..|.||++.+ .. |..+||||.+|..|+..|++++.+||+||.++.
T Consensus 280 ~eql~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERqQTCPICr~p~i 345 (491)
T COG5243 280 EEQLTNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQTCPICRRPVI 345 (491)
T ss_pred hhhhcCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhccCCCcccCccc
Confidence 444456677999999983 33 478899999999999999999999999999953
No 15
>KOG4628|consensus
Probab=99.38 E-value=6.7e-13 Score=89.21 Aligned_cols=47 Identities=28% Similarity=0.873 Sum_probs=41.0
Q ss_pred ccccccccCCCCC---eecCCCCcchHHhHHHHhhCCC-CCCCCCccCCCC
Q psy3884 34 CICPICHDEFKTP---VQLTCCHIFCESCVTKWFDREQ-TCPLCRATLVDD 80 (95)
Q Consensus 34 ~~C~IC~~~~~~p---~~~~CgH~fc~~Ci~~~~~~~~-~CP~Cr~~~~~~ 80 (95)
..|+||++.|... +++||+|.||..||.+|+.+.. .||+|+..+...
T Consensus 230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~di~~~ 280 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRDIRTD 280 (348)
T ss_pred ceEEEeecccccCCeeeEecCCCchhhccchhhHhhcCccCCCCCCcCCCC
Confidence 5999999999975 5789999999999999999875 599999977543
No 16
>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=99.37 E-value=3.9e-13 Score=64.85 Aligned_cols=38 Identities=50% Similarity=1.378 Sum_probs=34.9
Q ss_pred ccccccCCCCCe-ecCCCCcchHHhHHHHhh--CCCCCCCC
Q psy3884 36 CPICHDEFKTPV-QLTCCHIFCESCVTKWFD--REQTCPLC 73 (95)
Q Consensus 36 C~IC~~~~~~p~-~~~CgH~fc~~Ci~~~~~--~~~~CP~C 73 (95)
|+||++.+.++. .++|||.||..|+.+|++ ....||.|
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 899999999998 889999999999999998 55689987
No 17
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=99.35 E-value=3.4e-13 Score=88.36 Aligned_cols=64 Identities=22% Similarity=0.559 Sum_probs=53.6
Q ss_pred CcccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCccCCCCccccCCcchhhhhcC
Q psy3884 32 VGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRDGATSYFVQIF 95 (95)
Q Consensus 32 ~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~~~~~~~q~~ 95 (95)
..+.|.||.+.+..|..++|||+||.-||..++..+..||+||.+...........+..++|.|
T Consensus 24 s~lrC~IC~~~i~ip~~TtCgHtFCslCIR~hL~~qp~CP~Cr~~~~esrlr~~s~~~ei~es~ 87 (391)
T COG5432 24 SMLRCRICDCRISIPCETTCGHTFCSLCIRRHLGTQPFCPVCREDPCESRLRGSSGSREINESH 87 (391)
T ss_pred hHHHhhhhhheeecceecccccchhHHHHHHHhcCCCCCccccccHHhhhcccchhHHHHHHhh
Confidence 4569999999999999999999999999999999999999999988766555555555555543
No 18
>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=99.34 E-value=1.2e-12 Score=63.64 Aligned_cols=43 Identities=53% Similarity=1.388 Sum_probs=37.1
Q ss_pred cccccccCCCCCeecC-CCCcchHHhHHHHhhC-CCCCCCCCccC
Q psy3884 35 ICPICHDEFKTPVQLT-CCHIFCESCVTKWFDR-EQTCPLCRATL 77 (95)
Q Consensus 35 ~C~IC~~~~~~p~~~~-CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~ 77 (95)
.|+||++.+..++.++ |||.||..|+..|+.. ...||.|+..+
T Consensus 1 ~C~iC~~~~~~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~~ 45 (45)
T cd00162 1 ECPICLEEFREPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45 (45)
T ss_pred CCCcCchhhhCceEecCCCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence 4899999997776665 9999999999999987 67899998754
No 19
>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=99.34 E-value=1.1e-12 Score=70.80 Aligned_cols=42 Identities=40% Similarity=1.044 Sum_probs=34.5
Q ss_pred cccccccccCCCCC-------------eecCCCCcchHHhHHHHhhCCCCCCCCC
Q psy3884 33 GCICPICHDEFKTP-------------VQLTCCHIFCESCVTKWFDREQTCPLCR 74 (95)
Q Consensus 33 ~~~C~IC~~~~~~p-------------~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr 74 (95)
...|+||++.+.++ +..+|||.||..||.+|++.+.+||+||
T Consensus 19 ~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR 73 (73)
T PF12678_consen 19 DDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQNNTCPLCR 73 (73)
T ss_dssp CSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred CCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcCCcCCCCC
Confidence 34699999998432 3448999999999999999999999997
No 20
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=99.29 E-value=5.1e-13 Score=69.36 Aligned_cols=59 Identities=29% Similarity=0.595 Sum_probs=32.8
Q ss_pred CcccccccccCCCCCee-cCCCCcchHHhHHHHhhCCCCCCCCCccCCCCccccCCcchhhh
Q psy3884 32 VGCICPICHDEFKTPVQ-LTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRDGATSYFV 92 (95)
Q Consensus 32 ~~~~C~IC~~~~~~p~~-~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~~~~~~~ 92 (95)
..+.|++|.+.+++|+. ..|.|.||..|+...+. ..||+|+.+....+...+..++++|
T Consensus 6 ~lLrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~--~~CPvC~~Paw~qD~~~NrqLd~~i 65 (65)
T PF14835_consen 6 ELLRCSICFDILKEPVCLGGCEHIFCSSCIRDCIG--SECPVCHTPAWIQDIQINRQLDSMI 65 (65)
T ss_dssp HTTS-SSS-S--SS-B---SSS--B-TTTGGGGTT--TB-SSS--B-S-SS----HHHHHHH
T ss_pred HhcCCcHHHHHhcCCceeccCccHHHHHHhHHhcC--CCCCCcCChHHHHHHHhhhhhhccC
Confidence 45699999999999985 58999999999977544 4599999999999988888777664
No 21
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=99.27 E-value=4.7e-12 Score=62.03 Aligned_cols=41 Identities=39% Similarity=1.060 Sum_probs=35.2
Q ss_pred cccccccCCC---CCeecCCCCcchHHhHHHHhhCCCCCCCCCc
Q psy3884 35 ICPICHDEFK---TPVQLTCCHIFCESCVTKWFDREQTCPLCRA 75 (95)
Q Consensus 35 ~C~IC~~~~~---~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~ 75 (95)
.|+||++.+. .+.+++|||+||..|+..+......||+|++
T Consensus 1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~~~~~~CP~C~k 44 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLKGKSVKCPICRK 44 (44)
T ss_pred CCcCcCccccCCCCeEEcccCCHHHHHHHHhhcCCCCCCcCCCC
Confidence 4899999982 4678899999999999998866789999974
No 22
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=99.24 E-value=1.2e-11 Score=58.19 Aligned_cols=38 Identities=55% Similarity=1.441 Sum_probs=34.4
Q ss_pred ccccccCCCCCeecCCCCcchHHhHHHHhh-CCCCCCCC
Q psy3884 36 CPICHDEFKTPVQLTCCHIFCESCVTKWFD-REQTCPLC 73 (95)
Q Consensus 36 C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~-~~~~CP~C 73 (95)
|+||++....++.++|||.||..|+..|+. ....||.|
T Consensus 1 C~iC~~~~~~~~~~~C~H~~c~~C~~~~~~~~~~~CP~C 39 (39)
T smart00184 1 CPICLEELKDPVVLPCGHTFCRSCIRKWLKSGNNTCPIC 39 (39)
T ss_pred CCcCccCCCCcEEecCCChHHHHHHHHHHHhCcCCCCCC
Confidence 789999988889999999999999999998 55679987
No 23
>KOG0802|consensus
Probab=99.23 E-value=5.6e-12 Score=89.77 Aligned_cols=52 Identities=46% Similarity=1.024 Sum_probs=45.7
Q ss_pred cCCCcccccccccCCCC-----CeecCCCCcchHHhHHHHhhCCCCCCCCCccCCCC
Q psy3884 29 LLGVGCICPICHDEFKT-----PVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD 80 (95)
Q Consensus 29 ~~~~~~~C~IC~~~~~~-----p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~ 80 (95)
.......|+||.+.+.. +.+++|||.||..|+..|+++..+||.||..+...
T Consensus 287 ~~~~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~qtCP~CR~~~~~~ 343 (543)
T KOG0802|consen 287 LALSDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQQTCPTCRTVLYDY 343 (543)
T ss_pred hhhcCCeeeeechhhccccccccceeecccchHHHHHHHHHHHhCcCCcchhhhhcc
Confidence 33457799999999998 78999999999999999999999999999965544
No 24
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=99.23 E-value=5.9e-12 Score=61.22 Aligned_cols=35 Identities=46% Similarity=1.247 Sum_probs=22.2
Q ss_pred ccccccCCCC----CeecCCCCcchHHhHHHHhhCC----CCCC
Q psy3884 36 CPICHDEFKT----PVQLTCCHIFCESCVTKWFDRE----QTCP 71 (95)
Q Consensus 36 C~IC~~~~~~----p~~~~CgH~fc~~Ci~~~~~~~----~~CP 71 (95)
||||.+ +.+ |++++|||+||..|+.++...+ ..||
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 8999999999999999998733 3565
No 25
>PHA02926 zinc finger-like protein; Provisional
Probab=99.22 E-value=9.2e-12 Score=78.97 Aligned_cols=48 Identities=29% Similarity=0.805 Sum_probs=38.3
Q ss_pred CCcccccccccCCCC---------CeecCCCCcchHHhHHHHhhCC------CCCCCCCccCC
Q psy3884 31 GVGCICPICHDEFKT---------PVQLTCCHIFCESCVTKWFDRE------QTCPLCRATLV 78 (95)
Q Consensus 31 ~~~~~C~IC~~~~~~---------p~~~~CgH~fc~~Ci~~~~~~~------~~CP~Cr~~~~ 78 (95)
..+.+|+||++...+ ++..+|+|.||..|+..|.... ..||+||..+.
T Consensus 168 SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~ 230 (242)
T PHA02926 168 SKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFR 230 (242)
T ss_pred cCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceee
Confidence 356799999998633 2455899999999999999742 46999999865
No 26
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.19 E-value=9.5e-12 Score=80.43 Aligned_cols=51 Identities=33% Similarity=0.829 Sum_probs=45.0
Q ss_pred CcccccccccCCCCCeecCCCCcchHHhHHH-HhhCCCC-CCCCCccCCCCcc
Q psy3884 32 VGCICPICHDEFKTPVQLTCCHIFCESCVTK-WFDREQT-CPLCRATLVDDPA 82 (95)
Q Consensus 32 ~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~-~~~~~~~-CP~Cr~~~~~~~~ 82 (95)
.++.|+||++....|..++|||.||..||.. |-.+... ||+||+....+++
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 4678999999999999999999999999999 8877665 9999998876654
No 27
>KOG2164|consensus
Probab=99.19 E-value=1.1e-11 Score=86.12 Aligned_cols=50 Identities=34% Similarity=0.927 Sum_probs=44.1
Q ss_pred cccccccccCCCCCeecCCCCcchHHhHHHHhhCC-----CCCCCCCccCCCCcc
Q psy3884 33 GCICPICHDEFKTPVQLTCCHIFCESCVTKWFDRE-----QTCPLCRATLVDDPA 82 (95)
Q Consensus 33 ~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~-----~~CP~Cr~~~~~~~~ 82 (95)
+..||||++...-|+.+.|||.||..||..++... ..||+|+..+..++.
T Consensus 186 ~~~CPICL~~~~~p~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kdl 240 (513)
T KOG2164|consen 186 DMQCPICLEPPSVPVRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKDL 240 (513)
T ss_pred CCcCCcccCCCCcccccccCceeeHHHHHHHHhhhcccCCccCCchhhhccccce
Confidence 77999999999999999999999999999988743 589999999887544
No 28
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.16 E-value=2.2e-11 Score=80.32 Aligned_cols=48 Identities=35% Similarity=0.823 Sum_probs=41.8
Q ss_pred CcccccccccCCCCC---eecCCCCcchHHhHHHHhh-CCCCCCCCCccCCC
Q psy3884 32 VGCICPICHDEFKTP---VQLTCCHIFCESCVTKWFD-REQTCPLCRATLVD 79 (95)
Q Consensus 32 ~~~~C~IC~~~~~~p---~~~~CgH~fc~~Ci~~~~~-~~~~CP~Cr~~~~~ 79 (95)
...+|+||++.+... +++||.|.||..|+.+|+. ....||+||.+++.
T Consensus 322 ~GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iPP 373 (374)
T COG5540 322 KGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIPP 373 (374)
T ss_pred CCceEEEEhhhhcccceEEEeccCceechhHHHHHHhhhcccCCccCCCCCC
Confidence 446999999998753 6789999999999999998 56799999999874
No 29
>KOG2177|consensus
Probab=99.05 E-value=7.4e-11 Score=77.05 Aligned_cols=47 Identities=40% Similarity=1.033 Sum_probs=41.6
Q ss_pred cCCCcccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCc
Q psy3884 29 LLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRA 75 (95)
Q Consensus 29 ~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~ 75 (95)
...+.+.|+||++.+..|.+++|||+||..|+..++.....||.||.
T Consensus 9 ~~~~~~~C~iC~~~~~~p~~l~C~H~~c~~C~~~~~~~~~~Cp~cr~ 55 (386)
T KOG2177|consen 9 VLQEELTCPICLEYFREPVLLPCGHNFCRACLTRSWEGPLSCPVCRP 55 (386)
T ss_pred hccccccChhhHHHhhcCccccccchHhHHHHHHhcCCCcCCcccCC
Confidence 34567899999999999989999999999999998875578999994
No 30
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=99.05 E-value=2.3e-10 Score=62.83 Aligned_cols=46 Identities=33% Similarity=0.893 Sum_probs=36.6
Q ss_pred cccccccccCCCC------------Ceec-CCCCcchHHhHHHHhhC---CCCCCCCCccCC
Q psy3884 33 GCICPICHDEFKT------------PVQL-TCCHIFCESCVTKWFDR---EQTCPLCRATLV 78 (95)
Q Consensus 33 ~~~C~IC~~~~~~------------p~~~-~CgH~fc~~Ci~~~~~~---~~~CP~Cr~~~~ 78 (95)
+..|.||...|.. |.++ .|+|.||..||.+|+.. +..||+||++..
T Consensus 21 dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~ 82 (85)
T PF12861_consen 21 DDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWK 82 (85)
T ss_pred CCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeee
Confidence 5688888887763 2322 79999999999999985 368999999865
No 31
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.94 E-value=9.4e-10 Score=73.20 Aligned_cols=49 Identities=33% Similarity=0.814 Sum_probs=38.0
Q ss_pred cccccccccC-CCCCe---ec-CCCCcchHHhHHHHhh-CCCCCCCCCccCCCCc
Q psy3884 33 GCICPICHDE-FKTPV---QL-TCCHIFCESCVTKWFD-REQTCPLCRATLVDDP 81 (95)
Q Consensus 33 ~~~C~IC~~~-~~~p~---~~-~CgH~fc~~Ci~~~~~-~~~~CP~Cr~~~~~~~ 81 (95)
+..||+|... +.+|. .+ +|||.||..|+...+. ....||.|+.++....
T Consensus 3 ~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk~~ 57 (309)
T TIGR00570 3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLRKNN 57 (309)
T ss_pred CCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCccchhh
Confidence 4589999985 33442 22 7999999999999664 4568999999988765
No 32
>KOG0978|consensus
Probab=98.93 E-value=3.2e-10 Score=81.90 Aligned_cols=55 Identities=31% Similarity=0.790 Sum_probs=48.2
Q ss_pred CCCcccccccccCCCCCeecCCCCcchHHhHHHHhh-CCCCCCCCCccCCCCcccc
Q psy3884 30 LGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFD-REQTCPLCRATLVDDPAWR 84 (95)
Q Consensus 30 ~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~-~~~~CP~Cr~~~~~~~~~~ 84 (95)
....+.|++|....++.+++.|||.||..|+.+... +...||.|...|..+|+..
T Consensus 640 yK~~LkCs~Cn~R~Kd~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganDv~~ 695 (698)
T KOG0978|consen 640 YKELLKCSVCNTRWKDAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGANDVHR 695 (698)
T ss_pred HHhceeCCCccCchhhHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCcccccc
Confidence 356789999999999999999999999999998776 6789999999999887643
No 33
>KOG4159|consensus
Probab=98.84 E-value=2.4e-09 Score=73.67 Aligned_cols=55 Identities=33% Similarity=0.738 Sum_probs=48.6
Q ss_pred ccccCCCcccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCccCCCC
Q psy3884 26 KETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD 80 (95)
Q Consensus 26 ~~~~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~ 80 (95)
.+.....++.|.||+..+.+|+++||||.||..|+.+.+.....||.||.++...
T Consensus 77 ~~~~~~sef~c~vc~~~l~~pv~tpcghs~c~~Cl~r~ld~~~~cp~Cr~~l~e~ 131 (398)
T KOG4159|consen 77 GPEEIRSEFECCVCSRALYPPVVTPCGHSFCLECLDRSLDQETECPLCRDELVEL 131 (398)
T ss_pred cCccccchhhhhhhHhhcCCCccccccccccHHHHHHHhccCCCCcccccccccc
Confidence 3344478899999999999999999999999999999888889999999998863
No 34
>KOG0311|consensus
Probab=98.79 E-value=5.2e-10 Score=75.04 Aligned_cols=64 Identities=30% Similarity=0.677 Sum_probs=50.2
Q ss_pred cCCCcccccccccCCCCCeec-CCCCcchHHhHHHHhh-CCCCCCCCCccCCCC-ccccCCcchhhh
Q psy3884 29 LLGVGCICPICHDEFKTPVQL-TCCHIFCESCVTKWFD-REQTCPLCRATLVDD-PAWRDGATSYFV 92 (95)
Q Consensus 29 ~~~~~~~C~IC~~~~~~p~~~-~CgH~fc~~Ci~~~~~-~~~~CP~Cr~~~~~~-~~~~~~~~~~~~ 92 (95)
.+...+.|+||++.++..+++ .|+|.||..||..-+. .++.||.||+.+... .+..|..++.+|
T Consensus 39 ~~~~~v~c~icl~llk~tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~SkrsLr~Dp~fdaLi 105 (381)
T KOG0311|consen 39 MFDIQVICPICLSLLKKTMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVSKRSLRIDPNFDALI 105 (381)
T ss_pred HhhhhhccHHHHHHHHhhcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhccccccCCCCccHHHHH
Confidence 345678999999999988766 6999999999988776 457999999998876 444555555443
No 35
>KOG4265|consensus
Probab=98.78 E-value=4.5e-09 Score=70.66 Aligned_cols=50 Identities=30% Similarity=0.735 Sum_probs=44.7
Q ss_pred CCcccccccccCCCCCeecCCCCc-chHHhHHHHhhCCCCCCCCCccCCCC
Q psy3884 31 GVGCICPICHDEFKTPVQLTCCHI-FCESCVTKWFDREQTCPLCRATLVDD 80 (95)
Q Consensus 31 ~~~~~C~IC~~~~~~p~~~~CgH~-fc~~Ci~~~~~~~~~CP~Cr~~~~~~ 80 (95)
....+|.||+...++-+++||.|. .|..|.....-++..||+||+++...
T Consensus 288 ~~gkeCVIClse~rdt~vLPCRHLCLCs~Ca~~Lr~q~n~CPICRqpi~~l 338 (349)
T KOG4265|consen 288 ESGKECVICLSESRDTVVLPCRHLCLCSGCAKSLRYQTNNCPICRQPIEEL 338 (349)
T ss_pred cCCCeeEEEecCCcceEEecchhhehhHhHHHHHHHhhcCCCccccchHhh
Confidence 456799999999999999999998 89999998877889999999998653
No 36
>KOG4172|consensus
Probab=98.76 E-value=2e-09 Score=54.11 Aligned_cols=45 Identities=31% Similarity=0.706 Sum_probs=39.5
Q ss_pred ccccccccCCCCCeecCCCCc-chHHhHHHHhh-CCCCCCCCCccCC
Q psy3884 34 CICPICHDEFKTPVQLTCCHI-FCESCVTKWFD-REQTCPLCRATLV 78 (95)
Q Consensus 34 ~~C~IC~~~~~~p~~~~CgH~-fc~~Ci~~~~~-~~~~CP~Cr~~~~ 78 (95)
.+|.||++...+.+...|||. +|..|..+.++ .+..||+||+++.
T Consensus 8 dECTICye~pvdsVlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~ 54 (62)
T KOG4172|consen 8 DECTICYEHPVDSVLYTCGHMCMCYACGLRLKKALHGCCPICRAPIK 54 (62)
T ss_pred cceeeeccCcchHHHHHcchHHhHHHHHHHHHHccCCcCcchhhHHH
Confidence 599999999888888899996 89999988776 5679999999875
No 37
>KOG2879|consensus
Probab=98.71 E-value=4.4e-08 Score=64.02 Aligned_cols=51 Identities=27% Similarity=0.638 Sum_probs=42.0
Q ss_pred ccCCCcccccccccCCCCCeec-CCCCcchHHhHHHHhh--CCCCCCCCCccCC
Q psy3884 28 TLLGVGCICPICHDEFKTPVQL-TCCHIFCESCVTKWFD--REQTCPLCRATLV 78 (95)
Q Consensus 28 ~~~~~~~~C~IC~~~~~~p~~~-~CgH~fc~~Ci~~~~~--~~~~CP~Cr~~~~ 78 (95)
.....+.+|++|.+....|.++ +|||+||..|+..-.. ..+.||.|..+..
T Consensus 234 s~~t~~~~C~~Cg~~PtiP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~ 287 (298)
T KOG2879|consen 234 STGTSDTECPVCGEPPTIPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVE 287 (298)
T ss_pred ccccCCceeeccCCCCCCCeeeccccceeehhhhhhhhcchhhcccCccCCCCc
Confidence 3345677999999999999766 5999999999987665 3479999988766
No 38
>KOG0824|consensus
Probab=98.69 E-value=8.2e-09 Score=68.14 Aligned_cols=48 Identities=31% Similarity=0.739 Sum_probs=41.9
Q ss_pred cccccccccCCCCCeecCCCCcchHHhHHHHhhCC-CCCCCCCccCCCC
Q psy3884 33 GCICPICHDEFKTPVQLTCCHIFCESCVTKWFDRE-QTCPLCRATLVDD 80 (95)
Q Consensus 33 ~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~-~~CP~Cr~~~~~~ 80 (95)
...|+||+....-|+.++|+|.||.-||....... ..|++||.++.+.
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 34899999999999999999999999998766554 5699999999866
No 39
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=98.69 E-value=8.8e-09 Score=64.64 Aligned_cols=48 Identities=25% Similarity=0.810 Sum_probs=42.8
Q ss_pred CCcccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCccCC
Q psy3884 31 GVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLV 78 (95)
Q Consensus 31 ~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~ 78 (95)
.-.+.|.||.+++..|+++.|||.||..|...-.+....|-+|.+...
T Consensus 194 ~IPF~C~iCKkdy~spvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~ 241 (259)
T COG5152 194 KIPFLCGICKKDYESPVVTECGHSFCSLCAIRKYQKGDECGVCGKATY 241 (259)
T ss_pred CCceeehhchhhccchhhhhcchhHHHHHHHHHhccCCcceecchhhc
Confidence 346799999999999999999999999999998888899999977543
No 40
>KOG2660|consensus
Probab=98.62 E-value=1.1e-08 Score=68.12 Aligned_cols=55 Identities=22% Similarity=0.675 Sum_probs=46.3
Q ss_pred CCcccccccccCCCCCeec-CCCCcchHHhHHHHhhCCCCCCCCCccCCCCccccC
Q psy3884 31 GVGCICPICHDEFKTPVQL-TCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRD 85 (95)
Q Consensus 31 ~~~~~C~IC~~~~~~p~~~-~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~ 85 (95)
.....|.+|..++.++.++ .|-|+||.+||.+++.....||.|...+.......+
T Consensus 13 n~~itC~LC~GYliDATTI~eCLHTFCkSCivk~l~~~~~CP~C~i~ih~t~pl~n 68 (331)
T KOG2660|consen 13 NPHITCRLCGGYLIDATTITECLHTFCKSCIVKYLEESKYCPTCDIVIHKTHPLLN 68 (331)
T ss_pred ccceehhhccceeecchhHHHHHHHHHHHHHHHHHHHhccCCccceeccCcccccc
Confidence 3466999999999999655 799999999999999999999999888776643333
No 41
>KOG1734|consensus
Probab=98.56 E-value=3.7e-08 Score=64.37 Aligned_cols=61 Identities=25% Similarity=0.638 Sum_probs=45.7
Q ss_pred CCcccccCCCcccccccccCCCC----------CeecCCCCcchHHhHHHHhh--CCCCCCCCCccCCCCccc
Q psy3884 23 SPTKETLLGVGCICPICHDEFKT----------PVQLTCCHIFCESCVTKWFD--REQTCPLCRATLVDDPAW 83 (95)
Q Consensus 23 ~~~~~~~~~~~~~C~IC~~~~~~----------p~~~~CgH~fc~~Ci~~~~~--~~~~CP~Cr~~~~~~~~~ 83 (95)
.........++..|+||...+.. -..++|+|+||..||+.|.. +..+||.|++.+..+..+
T Consensus 214 ~~glPtkhl~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVdl~rmf 286 (328)
T KOG1734|consen 214 PSGLPTKHLSDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVDLKRMF 286 (328)
T ss_pred CCCCCCCCCCcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhhHhhhc
Confidence 33444444567799999987653 35779999999999999986 446999999887655433
No 42
>KOG0828|consensus
Probab=98.54 E-value=4.4e-08 Score=68.53 Aligned_cols=50 Identities=30% Similarity=0.722 Sum_probs=40.4
Q ss_pred CCCcccccccccCCCC-----------------CeecCCCCcchHHhHHHHhh-CCCCCCCCCccCCC
Q psy3884 30 LGVGCICPICHDEFKT-----------------PVQLTCCHIFCESCVTKWFD-REQTCPLCRATLVD 79 (95)
Q Consensus 30 ~~~~~~C~IC~~~~~~-----------------p~~~~CgH~fc~~Ci~~~~~-~~~~CP~Cr~~~~~ 79 (95)
.+....|+||+..+.- -..+||.|.||..|+..|+. ..-.||+||.+++.
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 4556799999987642 14559999999999999999 44599999999874
No 43
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=98.52 E-value=8.2e-08 Score=51.87 Aligned_cols=30 Identities=40% Similarity=0.944 Sum_probs=27.6
Q ss_pred CCCCcchHHhHHHHhhCCCCCCCCCccCCC
Q psy3884 50 TCCHIFCESCVTKWFDREQTCPLCRATLVD 79 (95)
Q Consensus 50 ~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~ 79 (95)
.|.|.||..||.+|+.....||++|+++..
T Consensus 53 ~CnHaFH~HCI~rWL~Tk~~CPld~q~w~~ 82 (88)
T COG5194 53 VCNHAFHDHCIYRWLDTKGVCPLDRQTWVL 82 (88)
T ss_pred ecchHHHHHHHHHHHhhCCCCCCCCceeEE
Confidence 599999999999999999999999998753
No 44
>KOG0804|consensus
Probab=98.44 E-value=1.3e-07 Score=65.43 Aligned_cols=46 Identities=30% Similarity=0.868 Sum_probs=38.0
Q ss_pred CCcccccccccCCCCC----eecCCCCcchHHhHHHHhhCCCCCCCCCccCC
Q psy3884 31 GVGCICPICHDEFKTP----VQLTCCHIFCESCVTKWFDREQTCPLCRATLV 78 (95)
Q Consensus 31 ~~~~~C~IC~~~~~~p----~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~ 78 (95)
....+||||++.+... +.+.|.|+||..|+..|. ..+||+||....
T Consensus 173 tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~--~~scpvcR~~q~ 222 (493)
T KOG0804|consen 173 TELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWW--DSSCPVCRYCQS 222 (493)
T ss_pred ccCCCcchhHhhcCccccceeeeecccccchHHHhhcc--cCcChhhhhhcC
Confidence 3456999999999875 355899999999999995 478999988665
No 45
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=98.43 E-value=8.8e-08 Score=71.44 Aligned_cols=76 Identities=24% Similarity=0.504 Sum_probs=49.4
Q ss_pred hHHHHHHHHHHHHhhccCCCCC-------cccccCCCcccccccccCCC-C----C--eecCCCCcchHHhHHHHhhC--
Q psy3884 3 AAKAWWKSFTKLLNNIQLGVSP-------TKETLLGVGCICPICHDEFK-T----P--VQLTCCHIFCESCVTKWFDR-- 66 (95)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~C~IC~~~~~-~----p--~~~~CgH~fc~~Ci~~~~~~-- 66 (95)
+.+.|..+.+..+......... ..........+|+||...+. - | .-..|.|.||..|+.+|+..
T Consensus 1432 ~wkswI~~~q~~~~~~ngs~~D~l~l~kkNi~~~fsG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~ 1511 (1525)
T COG5219 1432 GWKSWINLRQNEMIKKNGSFMDLLGLWKKNIDEKFSGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSA 1511 (1525)
T ss_pred HHHHHHHHHHHHHHhccchHHHHHHHHHhhhhhhcCCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcC
Confidence 3456666655555443321111 12223445679999998765 1 2 23369999999999999984
Q ss_pred CCCCCCCCccCC
Q psy3884 67 EQTCPLCRATLV 78 (95)
Q Consensus 67 ~~~CP~Cr~~~~ 78 (95)
+.+||+||.+++
T Consensus 1512 ~s~CPlCRseit 1523 (1525)
T COG5219 1512 RSNCPLCRSEIT 1523 (1525)
T ss_pred CCCCCccccccc
Confidence 468999998775
No 46
>KOG0297|consensus
Probab=98.43 E-value=1.2e-07 Score=65.50 Aligned_cols=54 Identities=37% Similarity=0.885 Sum_probs=47.5
Q ss_pred CCCcccccccccCCCCCee-cCCCCcchHHhHHHHhhCCCCCCCCCccCCCCccc
Q psy3884 30 LGVGCICPICHDEFKTPVQ-LTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAW 83 (95)
Q Consensus 30 ~~~~~~C~IC~~~~~~p~~-~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~ 83 (95)
....+.|++|...+.+|+. +.|||.||..|+..|+..+..||.|+.++......
T Consensus 18 ~~~~l~C~~C~~vl~~p~~~~~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~~~ 72 (391)
T KOG0297|consen 18 LDENLLCPICMSVLRDPVQTTTCGHRFCAGCLLESLSNHQKCPVCRQELTQAEEL 72 (391)
T ss_pred CcccccCccccccccCCCCCCCCCCcccccccchhhccCcCCcccccccchhhcc
Confidence 4567899999999999988 49999999999999999999999998887765443
No 47
>KOG1813|consensus
Probab=98.42 E-value=7.4e-08 Score=63.54 Aligned_cols=49 Identities=31% Similarity=0.678 Sum_probs=43.5
Q ss_pred CCcccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCccCCC
Q psy3884 31 GVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVD 79 (95)
Q Consensus 31 ~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~ 79 (95)
.-.+.|-||...|.+|+++.|||.||..|...-++....|++|.+....
T Consensus 239 ~~Pf~c~icr~~f~~pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g 287 (313)
T KOG1813|consen 239 LLPFKCFICRKYFYRPVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHG 287 (313)
T ss_pred cCCccccccccccccchhhcCCceeehhhhccccccCCcceeccccccc
Confidence 3456899999999999999999999999999988888999999876543
No 48
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=98.42 E-value=3.8e-08 Score=52.66 Aligned_cols=46 Identities=26% Similarity=0.663 Sum_probs=23.2
Q ss_pred cccccccccCCC-C---Ceec----CCCCcchHHhHHHHhhC---C--------CCCCCCCccCC
Q psy3884 33 GCICPICHDEFK-T---PVQL----TCCHIFCESCVTKWFDR---E--------QTCPLCRATLV 78 (95)
Q Consensus 33 ~~~C~IC~~~~~-~---p~~~----~CgH~fc~~Ci~~~~~~---~--------~~CP~Cr~~~~ 78 (95)
+..|+||++... . |... .|+..||..|+.+|+.. . ..||.|+.++.
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~ 66 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPIS 66 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEE
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeee
Confidence 458999999865 2 2222 69999999999999862 1 36999998875
No 49
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=98.32 E-value=3.5e-07 Score=47.01 Aligned_cols=41 Identities=29% Similarity=0.788 Sum_probs=29.2
Q ss_pred CcccccccccCCCCCeec-CCCCcchHHhHHHHhhC--CCCCCC
Q psy3884 32 VGCICPICHDEFKTPVQL-TCCHIFCESCVTKWFDR--EQTCPL 72 (95)
Q Consensus 32 ~~~~C~IC~~~~~~p~~~-~CgH~fc~~Ci~~~~~~--~~~CP~ 72 (95)
..+.|||.+..+.+|++. .|||+|-+..|..++.+ ...||.
T Consensus 10 ~~~~CPiT~~~~~~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv 53 (57)
T PF11789_consen 10 ISLKCPITLQPFEDPVKSKKCGHTFEKEAILQYIQRNGSKRCPV 53 (57)
T ss_dssp --SB-TTTSSB-SSEEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred eccCCCCcCChhhCCcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence 457999999999999865 89999999999999943 457997
No 50
>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=98.28 E-value=9.6e-07 Score=44.03 Aligned_cols=40 Identities=33% Similarity=1.001 Sum_probs=31.3
Q ss_pred ccccccc--CCCCCeecCCC-----CcchHHhHHHHhhCC--CCCCCCC
Q psy3884 35 ICPICHD--EFKTPVQLTCC-----HIFCESCVTKWFDRE--QTCPLCR 74 (95)
Q Consensus 35 ~C~IC~~--~~~~p~~~~Cg-----H~fc~~Ci~~~~~~~--~~CP~Cr 74 (95)
.|.||++ ...++.+.||. |.+|..|+.+|+..+ ..||+|+
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 4889997 33456777885 789999999999744 5899984
No 51
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=98.25 E-value=2.1e-06 Score=57.14 Aligned_cols=43 Identities=30% Similarity=0.894 Sum_probs=37.0
Q ss_pred cccccccccCCCCCeec-CCCCcchHHhHHHHhh-CCCCCCCCCc
Q psy3884 33 GCICPICHDEFKTPVQL-TCCHIFCESCVTKWFD-REQTCPLCRA 75 (95)
Q Consensus 33 ~~~C~IC~~~~~~p~~~-~CgH~fc~~Ci~~~~~-~~~~CP~Cr~ 75 (95)
.+.|+.|..++.+|+.+ .|+|.||..||...+. ..+.||.|..
T Consensus 274 ~LkCplc~~Llrnp~kT~cC~~~fc~eci~~al~dsDf~CpnC~r 318 (427)
T COG5222 274 SLKCPLCHCLLRNPMKTPCCGHTFCDECIGTALLDSDFKCPNCSR 318 (427)
T ss_pred cccCcchhhhhhCcccCccccchHHHHHHhhhhhhccccCCCccc
Confidence 47999999999999988 5899999999986655 5689999944
No 52
>KOG1493|consensus
Probab=98.22 E-value=2.5e-07 Score=49.61 Aligned_cols=45 Identities=36% Similarity=0.925 Sum_probs=34.4
Q ss_pred ccccccccCCCC------------Ceec-CCCCcchHHhHHHHhh---CCCCCCCCCccCC
Q psy3884 34 CICPICHDEFKT------------PVQL-TCCHIFCESCVTKWFD---REQTCPLCRATLV 78 (95)
Q Consensus 34 ~~C~IC~~~~~~------------p~~~-~CgH~fc~~Ci~~~~~---~~~~CP~Cr~~~~ 78 (95)
..|.||.-.|.. |.++ .|.|.|+..||.+|+. .+..||+||+.+.
T Consensus 21 e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~ 81 (84)
T KOG1493|consen 21 ETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQ 81 (84)
T ss_pred CccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeE
Confidence 378888776653 2333 5999999999999997 3468999999764
No 53
>KOG1039|consensus
Probab=98.19 E-value=1e-06 Score=59.90 Aligned_cols=48 Identities=29% Similarity=0.803 Sum_probs=38.6
Q ss_pred CCcccccccccCCCCCe-----e---cCCCCcchHHhHHHHhh--C-----CCCCCCCCccCC
Q psy3884 31 GVGCICPICHDEFKTPV-----Q---LTCCHIFCESCVTKWFD--R-----EQTCPLCRATLV 78 (95)
Q Consensus 31 ~~~~~C~IC~~~~~~p~-----~---~~CgH~fc~~Ci~~~~~--~-----~~~CP~Cr~~~~ 78 (95)
..+.+|.||++...... . .+|.|.||..|+..|.. + .+.||.||.+..
T Consensus 159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~ 221 (344)
T KOG1039|consen 159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSS 221 (344)
T ss_pred cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccc
Confidence 34679999999877653 2 46999999999999983 4 478999998754
No 54
>KOG0827|consensus
Probab=98.15 E-value=1.3e-06 Score=59.81 Aligned_cols=50 Identities=34% Similarity=0.801 Sum_probs=36.7
Q ss_pred ccccccccCCCCC----eecCCCCcchHHhHHHHhhCC---CCCCCCCccCCCCccc
Q psy3884 34 CICPICHDEFKTP----VQLTCCHIFCESCVTKWFDRE---QTCPLCRATLVDDPAW 83 (95)
Q Consensus 34 ~~C~IC~~~~~~p----~~~~CgH~fc~~Ci~~~~~~~---~~CP~Cr~~~~~~~~~ 83 (95)
..|.||.+.+.+. .+-.|||+||..|+..|+... ..||+|+-.+..+.++
T Consensus 5 A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~~~r~~~ 61 (465)
T KOG0827|consen 5 AECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKLQERHVA 61 (465)
T ss_pred ceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeecccceeee
Confidence 4899995554432 233599999999999999843 5899999666655544
No 55
>KOG4692|consensus
Probab=98.08 E-value=4.3e-06 Score=56.83 Aligned_cols=48 Identities=27% Similarity=0.656 Sum_probs=43.8
Q ss_pred CCcccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCccCC
Q psy3884 31 GVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLV 78 (95)
Q Consensus 31 ~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~ 78 (95)
.++..||||..-..+.+..||+|.-|+.||.+.+.+.+.|-.|+..+.
T Consensus 420 sEd~lCpICyA~pi~Avf~PC~H~SC~~CI~qHlmN~k~CFfCktTv~ 467 (489)
T KOG4692|consen 420 SEDNLCPICYAGPINAVFAPCSHRSCYGCITQHLMNCKRCFFCKTTVI 467 (489)
T ss_pred cccccCcceecccchhhccCCCCchHHHHHHHHHhcCCeeeEecceee
Confidence 356699999999999999999999999999999999999999988765
No 56
>KOG2930|consensus
Probab=97.96 E-value=5e-06 Score=47.09 Aligned_cols=28 Identities=29% Similarity=0.856 Sum_probs=25.8
Q ss_pred CCCCcchHHhHHHHhhCCCCCCCCCccC
Q psy3884 50 TCCHIFCESCVTKWFDREQTCPLCRATL 77 (95)
Q Consensus 50 ~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~ 77 (95)
.|.|.||..||.+|++....||++.++-
T Consensus 80 ~CNHaFH~hCisrWlktr~vCPLdn~eW 107 (114)
T KOG2930|consen 80 VCNHAFHFHCISRWLKTRNVCPLDNKEW 107 (114)
T ss_pred ecchHHHHHHHHHHHhhcCcCCCcCcce
Confidence 5999999999999999999999997754
No 57
>KOG1785|consensus
Probab=97.90 E-value=5.3e-06 Score=57.22 Aligned_cols=47 Identities=36% Similarity=0.896 Sum_probs=39.8
Q ss_pred ccccccccCCCCCeecCCCCcchHHhHHHHhhC--CCCCCCCCccCCCC
Q psy3884 34 CICPICHDEFKTPVQLTCCHIFCESCVTKWFDR--EQTCPLCRATLVDD 80 (95)
Q Consensus 34 ~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~--~~~CP~Cr~~~~~~ 80 (95)
..|-||.+.-++-.+-||||..|..|+..|... ...||.||.++...
T Consensus 370 eLCKICaendKdvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKGt 418 (563)
T KOG1785|consen 370 ELCKICAENDKDVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIKGT 418 (563)
T ss_pred HHHHHhhccCCCcccccccchHHHHHHHhhcccCCCCCCCceeeEeccc
Confidence 479999998777777799999999999999853 57999999988644
No 58
>KOG4275|consensus
Probab=97.87 E-value=5.3e-06 Score=55.00 Aligned_cols=42 Identities=36% Similarity=0.876 Sum_probs=35.5
Q ss_pred cccccccccCCCCCeecCCCC-cchHHhHHHHhhCCCCCCCCCccCC
Q psy3884 33 GCICPICHDEFKTPVQLTCCH-IFCESCVTKWFDREQTCPLCRATLV 78 (95)
Q Consensus 33 ~~~C~IC~~~~~~p~~~~CgH-~fc~~Ci~~~~~~~~~CP~Cr~~~~ 78 (95)
...|.||++...+-+.++||| +-|..|-.+ ...||+||+.+.
T Consensus 300 ~~LC~ICmDaP~DCvfLeCGHmVtCt~CGkr----m~eCPICRqyi~ 342 (350)
T KOG4275|consen 300 RRLCAICMDAPRDCVFLECGHMVTCTKCGKR----MNECPICRQYIV 342 (350)
T ss_pred HHHHHHHhcCCcceEEeecCcEEeehhhccc----cccCchHHHHHH
Confidence 569999999999999999999 479999754 348999998654
No 59
>KOG3039|consensus
Probab=97.82 E-value=2.1e-05 Score=51.11 Aligned_cols=54 Identities=22% Similarity=0.397 Sum_probs=47.1
Q ss_pred CcccccccccCCCCC----eecCCCCcchHHhHHHHhhCCCCCCCCCccCCCCccccC
Q psy3884 32 VGCICPICHDEFKTP----VQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRD 85 (95)
Q Consensus 32 ~~~~C~IC~~~~~~p----~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~ 85 (95)
..+.||+|.+.+.+. +.-+|||+|+..|+.+++.....||+|..++.++++...
T Consensus 220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdrdiI~L 277 (303)
T KOG3039|consen 220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDRDIIGL 277 (303)
T ss_pred cceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCcccceEee
Confidence 567999999999985 333999999999999999999999999999999877543
No 60
>KOG0825|consensus
Probab=97.79 E-value=3.4e-06 Score=62.20 Aligned_cols=49 Identities=31% Similarity=0.657 Sum_probs=38.3
Q ss_pred cccccccccCCCCC---eecCCCCcchHHhHHHHhhCCCCCCCCCccCCCCc
Q psy3884 33 GCICPICHDEFKTP---VQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDP 81 (95)
Q Consensus 33 ~~~C~IC~~~~~~p---~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~ 81 (95)
...|++|+..+.+. ...+|+|.||..|+..|.....+||+||..|..-.
T Consensus 123 ~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~aqTCPiDR~EF~~v~ 174 (1134)
T KOG0825|consen 123 ENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCAQTCPVDRGEFGEVK 174 (1134)
T ss_pred hhhhhHHHHHHHHHhhccccccccccHHHHhhhhhhhcccCchhhhhhheee
Confidence 34677777655543 24479999999999999999999999999886543
No 61
>KOG1002|consensus
Probab=97.77 E-value=1.4e-05 Score=56.88 Aligned_cols=50 Identities=30% Similarity=0.782 Sum_probs=42.8
Q ss_pred CCcccccccccCCCCCeecCCCCcchHHhHHHHhh-----CCCCCCCCCccCCCC
Q psy3884 31 GVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFD-----REQTCPLCRATLVDD 80 (95)
Q Consensus 31 ~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~-----~~~~CP~Cr~~~~~~ 80 (95)
.....|.+|.+.-.+++...|.|.||..|+..+.. .+-+||.|...+..+
T Consensus 534 k~~~~C~lc~d~aed~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiD 588 (791)
T KOG1002|consen 534 KGEVECGLCHDPAEDYIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSID 588 (791)
T ss_pred cCceeecccCChhhhhHhhhhhHHHHHHHHHHHHHhhhcccCCCCcccccccccc
Confidence 45669999999999999999999999999988876 336899998887654
No 62
>KOG1645|consensus
Probab=97.74 E-value=1.3e-05 Score=55.22 Aligned_cols=50 Identities=38% Similarity=1.020 Sum_probs=39.5
Q ss_pred CcccccccccCCCCC-----eecCCCCcchHHhHHHHhhCC--CCCCCCCccCCCCc
Q psy3884 32 VGCICPICHDEFKTP-----VQLTCCHIFCESCVTKWFDRE--QTCPLCRATLVDDP 81 (95)
Q Consensus 32 ~~~~C~IC~~~~~~p-----~~~~CgH~fc~~Ci~~~~~~~--~~CP~Cr~~~~~~~ 81 (95)
....||||++.+.-+ +.+.|||.|-..|+.+|+.+. ..||.|......+.
T Consensus 3 ~g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~katkr~ 59 (463)
T KOG1645|consen 3 CGTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKATKRQ 59 (463)
T ss_pred ccccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChhHHHH
Confidence 356899999998765 456899999999999999632 58999976655443
No 63
>PF04641 Rtf2: Rtf2 RING-finger
Probab=97.68 E-value=7.4e-05 Score=49.24 Aligned_cols=56 Identities=20% Similarity=0.469 Sum_probs=44.4
Q ss_pred CCCcccccccccCCCCC----eecCCCCcchHHhHHHHhhCCCCCCCCCccCCCCccccCC
Q psy3884 30 LGVGCICPICHDEFKTP----VQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRDG 86 (95)
Q Consensus 30 ~~~~~~C~IC~~~~~~p----~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~ 86 (95)
....+.|||....+... ...+|||+|...++...- ....||+|..++...++....
T Consensus 110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k-~~~~Cp~c~~~f~~~DiI~Ln 169 (260)
T PF04641_consen 110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK-KSKKCPVCGKPFTEEDIIPLN 169 (260)
T ss_pred CCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc-ccccccccCCccccCCEEEec
Confidence 35678999999998653 234999999999998873 466899999999988776543
No 64
>KOG0826|consensus
Probab=97.67 E-value=3.6e-05 Score=51.79 Aligned_cols=50 Identities=22% Similarity=0.527 Sum_probs=42.1
Q ss_pred cCCCcccccccccCCCCCeecC-CCCcchHHhHHHHhhCCCCCCCCCccCC
Q psy3884 29 LLGVGCICPICHDEFKTPVQLT-CCHIFCESCVTKWFDREQTCPLCRATLV 78 (95)
Q Consensus 29 ~~~~~~~C~IC~~~~~~p~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~ 78 (95)
...+...||+|.....+|.++. -|-+||..|+..++...+.||+-..+..
T Consensus 296 l~~~~~~CpvClk~r~Nptvl~vSGyVfCY~Ci~~Yv~~~~~CPVT~~p~~ 346 (357)
T KOG0826|consen 296 LPPDREVCPVCLKKRQNPTVLEVSGYVFCYPCIFSYVVNYGHCPVTGYPAS 346 (357)
T ss_pred CCCccccChhHHhccCCCceEEecceEEeHHHHHHHHHhcCCCCccCCcch
Confidence 3456779999999999997775 5999999999999999999998765543
No 65
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=97.66 E-value=3e-05 Score=39.19 Aligned_cols=47 Identities=26% Similarity=0.609 Sum_probs=36.7
Q ss_pred cccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCccCCCCc
Q psy3884 33 GCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDP 81 (95)
Q Consensus 33 ~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~ 81 (95)
...|-.|...-...++++|||..|..|..- .+-+.||.|..++...+
T Consensus 7 ~~~~~~~~~~~~~~~~~pCgH~I~~~~f~~--~rYngCPfC~~~~~~~~ 53 (55)
T PF14447_consen 7 EQPCVFCGFVGTKGTVLPCGHLICDNCFPG--ERYNGCPFCGTPFEFDD 53 (55)
T ss_pred ceeEEEccccccccccccccceeeccccCh--hhccCCCCCCCcccCCC
Confidence 346677777767788999999999999754 35578999999887554
No 66
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=97.60 E-value=6.2e-05 Score=37.19 Aligned_cols=42 Identities=26% Similarity=0.774 Sum_probs=21.5
Q ss_pred ccccccCCCCC--eec--CCCCcchHHhHHHHhh-CCCCCCCCCccC
Q psy3884 36 CPICHDEFKTP--VQL--TCCHIFCESCVTKWFD-REQTCPLCRATL 77 (95)
Q Consensus 36 C~IC~~~~~~p--~~~--~CgH~fc~~Ci~~~~~-~~~~CP~Cr~~~ 77 (95)
||+|.+.+... ... +||...|..|...... ....||.||.+.
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 68888887432 233 6899999999998886 578999999874
No 67
>KOG4185|consensus
Probab=97.55 E-value=7e-05 Score=49.94 Aligned_cols=45 Identities=33% Similarity=0.892 Sum_probs=37.4
Q ss_pred cccccccccCCCC------CeecCCCCcchHHhHHHHhhCC-CCCCCCCccC
Q psy3884 33 GCICPICHDEFKT------PVQLTCCHIFCESCVTKWFDRE-QTCPLCRATL 77 (95)
Q Consensus 33 ~~~C~IC~~~~~~------p~~~~CgH~fc~~Ci~~~~~~~-~~CP~Cr~~~ 77 (95)
...|-||-+.|.. |..+.|||++|..|+...+... ..||.||.+.
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 4589999988764 6788899999999999887755 4789999984
No 68
>KOG1571|consensus
Probab=97.50 E-value=6.5e-05 Score=51.07 Aligned_cols=47 Identities=32% Similarity=0.707 Sum_probs=35.6
Q ss_pred cCCCcccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCccCC
Q psy3884 29 LLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLV 78 (95)
Q Consensus 29 ~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~ 78 (95)
.......|.||.+...+.+.+||||.-| |..-. +....||+||+.+.
T Consensus 301 ~~~~p~lcVVcl~e~~~~~fvpcGh~cc--ct~cs-~~l~~CPvCR~rI~ 347 (355)
T KOG1571|consen 301 ELPQPDLCVVCLDEPKSAVFVPCGHVCC--CTLCS-KHLPQCPVCRQRIR 347 (355)
T ss_pred ccCCCCceEEecCCccceeeecCCcEEE--chHHH-hhCCCCchhHHHHH
Confidence 3456679999999999999999999855 54322 33355999998765
No 69
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=97.49 E-value=0.00011 Score=50.01 Aligned_cols=52 Identities=23% Similarity=0.607 Sum_probs=41.9
Q ss_pred ccccCCCcccccccccCCCCCeecCCCCcchHHhHHHH--hhCCCCCCCCCccC
Q psy3884 26 KETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKW--FDREQTCPLCRATL 77 (95)
Q Consensus 26 ~~~~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~--~~~~~~CP~Cr~~~ 77 (95)
..+...+...|.||.+-+.-..++||+|..|.-|..+. +-..+.||.||..-
T Consensus 54 addtDEen~~C~ICA~~~TYs~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~ 107 (493)
T COG5236 54 ADDTDEENMNCQICAGSTTYSARYPCGHQICHACAVRLRALYMQKGCPLCRTET 107 (493)
T ss_pred ccccccccceeEEecCCceEEEeccCCchHHHHHHHHHHHHHhccCCCcccccc
Confidence 33344566799999999988889999999999998764 34678999999864
No 70
>KOG4367|consensus
Probab=97.47 E-value=7.1e-05 Score=52.43 Aligned_cols=35 Identities=26% Similarity=0.790 Sum_probs=31.5
Q ss_pred CCcccccccccCCCCCeecCCCCcchHHhHHHHhh
Q psy3884 31 GVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFD 65 (95)
Q Consensus 31 ~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~ 65 (95)
++++.|+||...|.+|++++|+|..|..|....+.
T Consensus 2 eeelkc~vc~~f~~epiil~c~h~lc~~ca~~~~~ 36 (699)
T KOG4367|consen 2 EEELKCPVCGSFYREPIILPCSHNLCQACARNILV 36 (699)
T ss_pred cccccCceehhhccCceEeecccHHHHHHHHhhcc
Confidence 35789999999999999999999999999987654
No 71
>KOG1814|consensus
Probab=97.40 E-value=4.8e-05 Score=52.58 Aligned_cols=39 Identities=33% Similarity=0.770 Sum_probs=31.8
Q ss_pred cccCCCcccccccccCCCCC---eecCCCCcchHHhHHHHhh
Q psy3884 27 ETLLGVGCICPICHDEFKTP---VQLTCCHIFCESCVTKWFD 65 (95)
Q Consensus 27 ~~~~~~~~~C~IC~~~~~~p---~~~~CgH~fc~~Ci~~~~~ 65 (95)
..+....+.|.||++..... +.+||+|+||..|+..++.
T Consensus 178 ~~F~~slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~ 219 (445)
T KOG1814|consen 178 EKFVNSLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFT 219 (445)
T ss_pred HHHHhhcccceeeehhhcCcceeeecccchHHHHHHHHHHHH
Confidence 33455678999999987763 5779999999999999886
No 72
>KOG1941|consensus
Probab=97.35 E-value=6.4e-05 Score=51.87 Aligned_cols=44 Identities=27% Similarity=0.762 Sum_probs=36.2
Q ss_pred CcccccccccCCCC-C---eecCCCCcchHHhHHHHhhCC--CCCCCCCc
Q psy3884 32 VGCICPICHDEFKT-P---VQLTCCHIFCESCVTKWFDRE--QTCPLCRA 75 (95)
Q Consensus 32 ~~~~C~IC~~~~~~-p---~~~~CgH~fc~~Ci~~~~~~~--~~CP~Cr~ 75 (95)
-++.|..|.+.+-. + -.+||.|+||..|+..++.++ .+||.||+
T Consensus 364 ~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~Crk 413 (518)
T KOG1941|consen 364 TELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRK 413 (518)
T ss_pred HhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHH
Confidence 46799999998753 2 467999999999999998755 68999984
No 73
>KOG2114|consensus
Probab=97.30 E-value=0.00033 Score=52.30 Aligned_cols=41 Identities=29% Similarity=0.865 Sum_probs=35.1
Q ss_pred ccccccccCCCCCe-ecCCCCcchHHhHHHHhhCCCCCCCCCccC
Q psy3884 34 CICPICHDEFKTPV-QLTCCHIFCESCVTKWFDREQTCPLCRATL 77 (95)
Q Consensus 34 ~~C~IC~~~~~~p~-~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~ 77 (95)
-.|..|...+.-|. ...|||.||..|+. .....||.|+...
T Consensus 841 skCs~C~~~LdlP~VhF~CgHsyHqhC~e---~~~~~CP~C~~e~ 882 (933)
T KOG2114|consen 841 SKCSACEGTLDLPFVHFLCGHSYHQHCLE---DKEDKCPKCLPEL 882 (933)
T ss_pred eeecccCCccccceeeeecccHHHHHhhc---cCcccCCccchhh
Confidence 49999999999884 66999999999997 4668999998743
No 74
>KOG1001|consensus
Probab=97.28 E-value=6.8e-05 Score=55.18 Aligned_cols=52 Identities=31% Similarity=0.707 Sum_probs=42.8
Q ss_pred ccccccccCCCCCeecCCCCcchHHhHHHHhhCC--CCCCCCCccCCCCccccCC
Q psy3884 34 CICPICHDEFKTPVQLTCCHIFCESCVTKWFDRE--QTCPLCRATLVDDPAWRDG 86 (95)
Q Consensus 34 ~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~--~~CP~Cr~~~~~~~~~~~~ 86 (95)
..|.+|.+ ...+++++|||.||..|+...+... ..||.||..+.....+...
T Consensus 455 ~~c~ic~~-~~~~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~~~l~s~~ 508 (674)
T KOG1001|consen 455 HWCHICCD-LDSFFITRCGHDFCVECLKKSIQQSENAPCPLCRNVLKEKKLLSAN 508 (674)
T ss_pred cccccccc-cccceeecccchHHHHHHHhccccccCCCCcHHHHHHHHHHHhhcc
Confidence 79999999 7788899999999999999887743 4799999988766555443
No 75
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=97.09 E-value=0.00035 Score=39.69 Aligned_cols=32 Identities=22% Similarity=0.626 Sum_probs=26.2
Q ss_pred CCCcccccccccCCCCCe--ecCCCCcchHHhHH
Q psy3884 30 LGVGCICPICHDEFKTPV--QLTCCHIFCESCVT 61 (95)
Q Consensus 30 ~~~~~~C~IC~~~~~~p~--~~~CgH~fc~~Ci~ 61 (95)
......|++|...+.+.. +.||||.||..|+.
T Consensus 75 i~~~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 75 ITESTKCSVCGKPLGNSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred ECCCCCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence 345668999999998764 55999999999974
No 76
>KOG4739|consensus
Probab=97.07 E-value=0.00029 Score=45.61 Aligned_cols=44 Identities=30% Similarity=0.739 Sum_probs=30.8
Q ss_pred cccccccCCC-CC-eecCCCCcchHHhHHHHhhCCCCCCCCCccCCCC
Q psy3884 35 ICPICHDEFK-TP-VQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD 80 (95)
Q Consensus 35 ~C~IC~~~~~-~p-~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~ 80 (95)
.|..|..... .+ ..+.|+|+||..|...- ....||+|++++...
T Consensus 5 hCn~C~~~~~~~~f~LTaC~HvfC~~C~k~~--~~~~C~lCkk~ir~i 50 (233)
T KOG4739|consen 5 HCNKCFRFPSQDPFFLTACRHVFCEPCLKAS--SPDVCPLCKKSIRII 50 (233)
T ss_pred EeccccccCCCCceeeeechhhhhhhhcccC--Cccccccccceeeee
Confidence 5777766544 23 46699999999998532 223899999986543
No 77
>KOG2817|consensus
Probab=96.98 E-value=0.00056 Score=47.18 Aligned_cols=49 Identities=20% Similarity=0.558 Sum_probs=38.1
Q ss_pred cCCCcccccccccCCC---CCeecCCCCcchHHhHHHHhhCC---CCCCCCCccC
Q psy3884 29 LLGVGCICPICHDEFK---TPVQLTCCHIFCESCVTKWFDRE---QTCPLCRATL 77 (95)
Q Consensus 29 ~~~~~~~C~IC~~~~~---~p~~~~CgH~fc~~Ci~~~~~~~---~~CP~Cr~~~ 77 (95)
.....+.|||=.+.-. .|+.+.|||+.+..-+.+..++. +.||.|-...
T Consensus 330 ~fHSvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~e~ 384 (394)
T KOG2817|consen 330 HFHSVFICPVLKEQTSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPVEQ 384 (394)
T ss_pred cccceeecccchhhccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCccc
Confidence 3567789999665433 47899999999999999988754 5899995543
No 78
>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=96.88 E-value=0.0017 Score=31.39 Aligned_cols=38 Identities=24% Similarity=0.743 Sum_probs=23.3
Q ss_pred ccccccCCCCCeecC---CCCcchHHhHHHHhhCCC--CCCCC
Q psy3884 36 CPICHDEFKTPVQLT---CCHIFCESCVTKWFDREQ--TCPLC 73 (95)
Q Consensus 36 C~IC~~~~~~p~~~~---CgH~fc~~Ci~~~~~~~~--~CP~C 73 (95)
|.+|.+.....+.=+ |+-.+|..|+..++.... .||.|
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 667888877765544 888999999999998654 79987
No 79
>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=96.82 E-value=0.0021 Score=39.32 Aligned_cols=33 Identities=24% Similarity=0.570 Sum_probs=24.6
Q ss_pred cccccccccCCCCCeecC------------CCCc-chHHhHHHHhh
Q psy3884 33 GCICPICHDEFKTPVQLT------------CCHI-FCESCVTKWFD 65 (95)
Q Consensus 33 ~~~C~IC~~~~~~p~~~~------------CgH~-fc~~Ci~~~~~ 65 (95)
+..||||++...++|.|- |+.. -|..|+.++-+
T Consensus 2 d~~CpICme~PHNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkk 47 (162)
T PF07800_consen 2 DVTCPICMEHPHNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKK 47 (162)
T ss_pred CccCceeccCCCceEEEEeccccCCccccccCCccchhHHHHHHHH
Confidence 458999999999998874 4432 36788887653
No 80
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=96.74 E-value=0.0021 Score=38.21 Aligned_cols=50 Identities=20% Similarity=0.561 Sum_probs=40.8
Q ss_pred CcccccccccCCCCCeec----CCCCcchHHhHHHHhh---CCCCCCCCCccCCCCc
Q psy3884 32 VGCICPICHDEFKTPVQL----TCCHIFCESCVTKWFD---REQTCPLCRATLVDDP 81 (95)
Q Consensus 32 ~~~~C~IC~~~~~~p~~~----~CgH~fc~~Ci~~~~~---~~~~CP~Cr~~~~~~~ 81 (95)
...+|.||.+...+...+ -||-..|.-|....++ -...||.|+.++....
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 356999999998888777 3999999999987766 3468999999887553
No 81
>KOG4445|consensus
Probab=96.69 E-value=0.00043 Score=46.37 Aligned_cols=49 Identities=27% Similarity=0.680 Sum_probs=37.7
Q ss_pred CcccccccccCCCC-C--eecCCCCcchHHhHHHHhh-----------------------CCCCCCCCCccCCCC
Q psy3884 32 VGCICPICHDEFKT-P--VQLTCCHIFCESCVTKWFD-----------------------REQTCPLCRATLVDD 80 (95)
Q Consensus 32 ~~~~C~IC~~~~~~-p--~~~~CgH~fc~~Ci~~~~~-----------------------~~~~CP~Cr~~~~~~ 80 (95)
....|.||+--|.. + .+++|-|.||..|+.+++. ....||+||..+...
T Consensus 114 p~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~e 188 (368)
T KOG4445|consen 114 PNGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKIE 188 (368)
T ss_pred CCCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhcccc
Confidence 34589999877764 3 5779999999999988774 113799999998755
No 82
>KOG3800|consensus
Probab=96.68 E-value=0.0018 Score=43.10 Aligned_cols=46 Identities=35% Similarity=0.882 Sum_probs=34.8
Q ss_pred cccccccC-CCCC----eecCCCCcchHHhHHHHhhC-CCCCCCCCccCCCC
Q psy3884 35 ICPICHDE-FKTP----VQLTCCHIFCESCVTKWFDR-EQTCPLCRATLVDD 80 (95)
Q Consensus 35 ~C~IC~~~-~~~p----~~~~CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~~~~ 80 (95)
.||+|... +.+| .+-+|||..|.+|+...+.. ...||.|...+...
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iLRk~ 53 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGPAQCPECMVILRKN 53 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHhcCCCCCCcccchhhhc
Confidence 58999865 3455 12289999999999998874 57999998776544
No 83
>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.
Probab=96.66 E-value=0.00069 Score=33.21 Aligned_cols=35 Identities=29% Similarity=0.776 Sum_probs=24.4
Q ss_pred CCeecCCC-CcchHHhHHHHhhCCCCCCCCCccCCC
Q psy3884 45 TPVQLTCC-HIFCESCVTKWFDREQTCPLCRATLVD 79 (95)
Q Consensus 45 ~p~~~~Cg-H~fc~~Ci~~~~~~~~~CP~Cr~~~~~ 79 (95)
+.-.+.|. |..|..|+...+..+..||+|..+++.
T Consensus 12 ~k~Li~C~dHYLCl~CLt~ml~~s~~C~iC~~~LPt 47 (50)
T PF03854_consen 12 NKGLIKCSDHYLCLNCLTLMLSRSDRCPICGKPLPT 47 (50)
T ss_dssp -SSEEE-SS-EEEHHHHHHT-SSSSEETTTTEE---
T ss_pred CCCeeeecchhHHHHHHHHHhccccCCCcccCcCcc
Confidence 33456676 888999999999999999999998874
No 84
>KOG1428|consensus
Probab=96.65 E-value=0.0015 Score=52.06 Aligned_cols=49 Identities=29% Similarity=0.768 Sum_probs=37.9
Q ss_pred CCcccccccccCCCC---CeecCCCCcchHHhHHHHhhCC----------CCCCCCCccCCC
Q psy3884 31 GVGCICPICHDEFKT---PVQLTCCHIFCESCVTKWFDRE----------QTCPLCRATLVD 79 (95)
Q Consensus 31 ~~~~~C~IC~~~~~~---p~~~~CgH~fc~~Ci~~~~~~~----------~~CP~Cr~~~~~ 79 (95)
..+..|.||+..--. .+.+.|+|.||..|.+..+++. ..||+|..++..
T Consensus 3484 D~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~InH 3545 (3738)
T KOG1428|consen 3484 DADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKINH 3545 (3738)
T ss_pred ccCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchhhh
Confidence 456699999975432 3788999999999998777643 389999988764
No 85
>KOG3002|consensus
Probab=96.53 E-value=0.0021 Score=43.29 Aligned_cols=48 Identities=29% Similarity=0.624 Sum_probs=37.9
Q ss_pred cCCCcccccccccCCCCCee-cCCCCcchHHhHHHHhhCCCCCCCCCccCCC
Q psy3884 29 LLGVGCICPICHDEFKTPVQ-LTCCHIFCESCVTKWFDREQTCPLCRATLVD 79 (95)
Q Consensus 29 ~~~~~~~C~IC~~~~~~p~~-~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~ 79 (95)
...+.+.||||.+.+..|+. -.=||..|..|-. +....||.||.++..
T Consensus 44 ~~~~lleCPvC~~~l~~Pi~QC~nGHlaCssC~~---~~~~~CP~Cr~~~g~ 92 (299)
T KOG3002|consen 44 LDLDLLDCPVCFNPLSPPIFQCDNGHLACSSCRT---KVSNKCPTCRLPIGN 92 (299)
T ss_pred cchhhccCchhhccCcccceecCCCcEehhhhhh---hhcccCCcccccccc
Confidence 34567899999999998842 2457999999975 356789999999883
No 86
>KOG1952|consensus
Probab=96.52 E-value=0.0042 Score=46.72 Aligned_cols=47 Identities=28% Similarity=0.740 Sum_probs=36.0
Q ss_pred CCCcccccccccCCCCCe-ec---CCCCcchHHhHHHHhhC-------CCCCCCCCcc
Q psy3884 30 LGVGCICPICHDEFKTPV-QL---TCCHIFCESCVTKWFDR-------EQTCPLCRAT 76 (95)
Q Consensus 30 ~~~~~~C~IC~~~~~~p~-~~---~CgH~fc~~Ci~~~~~~-------~~~CP~Cr~~ 76 (95)
....++|.||.+.+.... +. .|-|+||..||.+|... ...||.|+..
T Consensus 188 ~~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv 245 (950)
T KOG1952|consen 188 SNRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSV 245 (950)
T ss_pred hcCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccch
Confidence 346679999999987532 22 57799999999999863 2589999843
No 87
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=96.52 E-value=0.0046 Score=37.89 Aligned_cols=48 Identities=25% Similarity=0.654 Sum_probs=35.2
Q ss_pred CCcccccccccCCCCCeecCCCC-----cchHHhHHHHhhCC--CCCCCCCccCCC
Q psy3884 31 GVGCICPICHDEFKTPVQLTCCH-----IFCESCVTKWFDRE--QTCPLCRATLVD 79 (95)
Q Consensus 31 ~~~~~C~IC~~~~~~p~~~~CgH-----~fc~~Ci~~~~~~~--~~CP~Cr~~~~~ 79 (95)
..+..|-||.+... +..-||.- ..|.+|+.+|+..+ ..|+.|+.++.-
T Consensus 6 ~~~~~CRIC~~~~~-~~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i 60 (162)
T PHA02825 6 LMDKCCWICKDEYD-VVTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNI 60 (162)
T ss_pred CCCCeeEecCCCCC-CccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEE
Confidence 34559999998854 33446653 24999999999854 689999998753
No 88
>KOG3970|consensus
Probab=96.51 E-value=0.0031 Score=40.82 Aligned_cols=47 Identities=21% Similarity=0.609 Sum_probs=37.9
Q ss_pred ccccccccCCCCC--eecCCCCcchHHhHHHHhh--------CCCCCCCCCccCCCC
Q psy3884 34 CICPICHDEFKTP--VQLTCCHIFCESCVTKWFD--------REQTCPLCRATLVDD 80 (95)
Q Consensus 34 ~~C~IC~~~~~~p--~~~~CgH~fc~~Ci~~~~~--------~~~~CP~Cr~~~~~~ 80 (95)
-.|..|...+... +.+-|-|.||..|+..|.. ....||.|..++...
T Consensus 51 pNC~LC~t~La~gdt~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp 107 (299)
T KOG3970|consen 51 PNCRLCNTPLASGDTTRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPP 107 (299)
T ss_pred CCCceeCCccccCcceeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCC
Confidence 3789998888754 6789999999999999875 235899998887654
No 89
>KOG1940|consensus
Probab=96.39 E-value=0.0023 Score=42.59 Aligned_cols=42 Identities=29% Similarity=0.686 Sum_probs=35.5
Q ss_pred ccccccccCCCC----CeecCCCCcchHHhHHHHhhCCCCCCCCCc
Q psy3884 34 CICPICHDEFKT----PVQLTCCHIFCESCVTKWFDREQTCPLCRA 75 (95)
Q Consensus 34 ~~C~IC~~~~~~----p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~ 75 (95)
..||||.+.+.. +..++|||..+..|+......+..||+|.+
T Consensus 159 ~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~~y~CP~C~~ 204 (276)
T KOG1940|consen 159 FNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICEGYTCPICSK 204 (276)
T ss_pred CCCchhHHHhccccccCCccCcccchHHHHHHHHhccCCCCCcccc
Confidence 359999987653 567799999999999988877799999987
No 90
>KOG4362|consensus
Probab=96.26 E-value=0.00093 Score=49.13 Aligned_cols=49 Identities=35% Similarity=0.809 Sum_probs=40.5
Q ss_pred CcccccccccCCCCCeecCCCCcchHHhHHHHhhC---CCCCCCCCccCCCC
Q psy3884 32 VGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDR---EQTCPLCRATLVDD 80 (95)
Q Consensus 32 ~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~---~~~CP~Cr~~~~~~ 80 (95)
..++|+||...+..|+.+.|-|.||..|+...+.. ...||+|+..+...
T Consensus 20 k~lEc~ic~~~~~~p~~~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~eK~ 71 (684)
T KOG4362|consen 20 KILECPICLEHVKEPSLLKCDHIFLKFCLNKLFESKKGPKQCALCKSDIEKR 71 (684)
T ss_pred hhccCCceeEEeeccchhhhhHHHHhhhhhceeeccCccccchhhhhhhhhh
Confidence 35699999999999999999999999999866553 45899998766544
No 91
>KOG2932|consensus
Probab=96.25 E-value=0.0021 Score=43.38 Aligned_cols=42 Identities=29% Similarity=0.809 Sum_probs=30.4
Q ss_pred cccccccCCCC-CeecCCCCcchHHhHHHHhhCCCCCCCCCccCC
Q psy3884 35 ICPICHDEFKT-PVQLTCCHIFCESCVTKWFDREQTCPLCRATLV 78 (95)
Q Consensus 35 ~C~IC~~~~~~-p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~ 78 (95)
.|--|--.+.. ...++|.|+||.+|... ...+.||.|-..+.
T Consensus 92 fCd~Cd~PI~IYGRmIPCkHvFCl~CAr~--~~dK~Cp~C~d~Vq 134 (389)
T KOG2932|consen 92 FCDRCDFPIAIYGRMIPCKHVFCLECARS--DSDKICPLCDDRVQ 134 (389)
T ss_pred eecccCCcceeeecccccchhhhhhhhhc--CccccCcCcccHHH
Confidence 56666555443 46779999999999864 34678999966554
No 92
>KOG3268|consensus
Probab=96.21 E-value=0.0043 Score=38.83 Aligned_cols=47 Identities=23% Similarity=0.622 Sum_probs=33.1
Q ss_pred ccccccccCCCCCe-------ecCCCCcchHHhHHHHhhC------C-----CCCCCCCccCCCC
Q psy3884 34 CICPICHDEFKTPV-------QLTCCHIFCESCVTKWFDR------E-----QTCPLCRATLVDD 80 (95)
Q Consensus 34 ~~C~IC~~~~~~p~-------~~~CgH~fc~~Ci~~~~~~------~-----~~CP~Cr~~~~~~ 80 (95)
..|.||..+--+.. -+.||..||.-|+..|++. + ..||.|..++..+
T Consensus 166 ~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialK 230 (234)
T KOG3268|consen 166 GACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALK 230 (234)
T ss_pred hcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceee
Confidence 35666665543322 2369999999999999972 1 4799998887644
No 93
>PHA03096 p28-like protein; Provisional
Probab=96.16 E-value=0.0034 Score=42.05 Aligned_cols=42 Identities=29% Similarity=0.542 Sum_probs=29.9
Q ss_pred ccccccccCCCCC--------eecCCCCcchHHhHHHHhhCC---CCCCCCCc
Q psy3884 34 CICPICHDEFKTP--------VQLTCCHIFCESCVTKWFDRE---QTCPLCRA 75 (95)
Q Consensus 34 ~~C~IC~~~~~~p--------~~~~CgH~fc~~Ci~~~~~~~---~~CP~Cr~ 75 (95)
..|.||++..... ....|.|.||..|+..|.... ..||.||.
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~ 231 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRR 231 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCccccc
Confidence 4899999876532 233699999999999998733 34555443
No 94
>PHA02862 5L protein; Provisional
Probab=96.09 E-value=0.0083 Score=36.28 Aligned_cols=46 Identities=24% Similarity=0.585 Sum_probs=34.6
Q ss_pred ccccccccCCCCCeecCCCC-----cchHHhHHHHhhCC--CCCCCCCccCCCC
Q psy3884 34 CICPICHDEFKTPVQLTCCH-----IFCESCVTKWFDRE--QTCPLCRATLVDD 80 (95)
Q Consensus 34 ~~C~IC~~~~~~p~~~~CgH-----~fc~~Ci~~~~~~~--~~CP~Cr~~~~~~ 80 (95)
..|-||.+.-.+. .-||.- ..|..|+.+|+..+ ..|+.|+.++.-+
T Consensus 3 diCWIC~~~~~e~-~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~Ik 55 (156)
T PHA02862 3 DICWICNDVCDER-NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNIK 55 (156)
T ss_pred CEEEEecCcCCCC-cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEEEE
Confidence 4799999886544 456653 36999999999844 5899999987544
No 95
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=95.89 E-value=0.0069 Score=41.50 Aligned_cols=49 Identities=22% Similarity=0.598 Sum_probs=35.4
Q ss_pred cccccccccCCCCC----eecCCCCcchHHhHHHHhh-CCCCCCCCCccCCCCc
Q psy3884 33 GCICPICHDEFKTP----VQLTCCHIFCESCVTKWFD-REQTCPLCRATLVDDP 81 (95)
Q Consensus 33 ~~~C~IC~~~~~~p----~~~~CgH~fc~~Ci~~~~~-~~~~CP~Cr~~~~~~~ 81 (95)
+..||.|++.+... .--+||-..|..|.....+ -+..||.||....++.
T Consensus 14 ed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~den 67 (480)
T COG5175 14 EDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDEN 67 (480)
T ss_pred cccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhccccc
Confidence 33699999987642 2237898889888865544 3479999999877653
No 96
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=95.74 E-value=0.0077 Score=29.96 Aligned_cols=43 Identities=23% Similarity=0.716 Sum_probs=21.3
Q ss_pred cccccccccCCCCCeec-CCCCcchHHhHHHHhh-----CCCCCCCCCcc
Q psy3884 33 GCICPICHDEFKTPVQL-TCCHIFCESCVTKWFD-----REQTCPLCRAT 76 (95)
Q Consensus 33 ~~~C~IC~~~~~~p~~~-~CgH~fc~~Ci~~~~~-----~~~~CP~Cr~~ 76 (95)
.+.|||....+..|+.. .|.|.-|.+- ..|+. ....||+|.++
T Consensus 2 sL~CPls~~~i~~P~Rg~~C~H~~CFDl-~~fl~~~~~~~~W~CPiC~~~ 50 (50)
T PF02891_consen 2 SLRCPLSFQRIRIPVRGKNCKHLQCFDL-ESFLESNQRTPKWKCPICNKP 50 (50)
T ss_dssp ESB-TTTSSB-SSEEEETT--SS--EEH-HHHHHHHHHS---B-TTT---
T ss_pred eeeCCCCCCEEEeCccCCcCcccceECH-HHHHHHhhccCCeECcCCcCc
Confidence 35899999999999755 8999866432 23332 33579999764
No 97
>KOG3113|consensus
Probab=95.64 E-value=0.012 Score=38.72 Aligned_cols=62 Identities=21% Similarity=0.359 Sum_probs=46.0
Q ss_pred CCCcccccccccCCCCC----eecCCCCcchHHhHHHHhhCCCCCCCCCccCCCCccccCCcchhhhh
Q psy3884 30 LGVGCICPICHDEFKTP----VQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRDGATSYFVQ 93 (95)
Q Consensus 30 ~~~~~~C~IC~~~~~~p----~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~~~~~~~q 93 (95)
....+.|||-.-.+..- ...+|||+|-..-+.+. ....|++|.+.+...+.........-++
T Consensus 108 ~~a~fiCPvtgleMng~~~F~~l~~CGcV~SerAlKei--kas~C~~C~a~y~~~dvIvlNg~~E~~d 173 (293)
T KOG3113|consen 108 QRARFICPVTGLEMNGKYRFCALRCCGCVFSERALKEI--KASVCHVCGAAYQEDDVIVLNGTEEDVD 173 (293)
T ss_pred ccceeecccccceecceEEEEEEeccceeccHHHHHHh--hhccccccCCcccccCeEeeCCCHHHHH
Confidence 35678999987777654 34489999998877654 4689999999999888776655554443
No 98
>KOG0298|consensus
Probab=95.61 E-value=0.0068 Score=47.45 Aligned_cols=46 Identities=26% Similarity=0.678 Sum_probs=40.3
Q ss_pred CCcccccccccCCC-CCeecCCCCcchHHhHHHHhhCCCCCCCCCcc
Q psy3884 31 GVGCICPICHDEFK-TPVQLTCCHIFCESCVTKWFDREQTCPLCRAT 76 (95)
Q Consensus 31 ~~~~~C~IC~~~~~-~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~ 76 (95)
.....|.||.+.+. ...+..|||.+|..|...|+..+..||.|...
T Consensus 1151 ~~~~~c~ic~dil~~~~~I~~cgh~~c~~c~~~~l~~~s~~~~~ksi 1197 (1394)
T KOG0298|consen 1151 SGHFVCEICLDILRNQGGIAGCGHEPCCRCDELWLYASSRCPICKSI 1197 (1394)
T ss_pred hcccchHHHHHHHHhcCCeeeechhHhhhHHHHHHHHhccCcchhhh
Confidence 35569999999998 45688999999999999999999999999743
No 99
>PF05883 Baculo_RING: Baculovirus U-box/Ring-like domain; InterPro: IPR008573 This family consists of several Baculovirus proteins of around 130 residues in length. The function of this family is unknown, but it appears to be related to the U-box and ring finger domain by profile-profile comparison.
Probab=95.44 E-value=0.0098 Score=35.52 Aligned_cols=33 Identities=30% Similarity=0.741 Sum_probs=26.2
Q ss_pred cccccccccCCCC--C-eecCCC------CcchHHhHHHHhh
Q psy3884 33 GCICPICHDEFKT--P-VQLTCC------HIFCESCVTKWFD 65 (95)
Q Consensus 33 ~~~C~IC~~~~~~--p-~~~~Cg------H~fc~~Ci~~~~~ 65 (95)
..+|.||++.+.+ . +.++|| |.||..|+.+|-.
T Consensus 26 ~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~~ 67 (134)
T PF05883_consen 26 TVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWRR 67 (134)
T ss_pred CeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHHh
Confidence 5599999999887 4 344666 5699999999954
No 100
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=94.95 E-value=0.018 Score=28.26 Aligned_cols=38 Identities=26% Similarity=0.834 Sum_probs=23.9
Q ss_pred ccccccCCCC--CeecCCCC-----cchHHhHHHHhh--CCCCCCCC
Q psy3884 36 CPICHDEFKT--PVQLTCCH-----IFCESCVTKWFD--REQTCPLC 73 (95)
Q Consensus 36 C~IC~~~~~~--p~~~~CgH-----~fc~~Ci~~~~~--~~~~CP~C 73 (95)
|-||++.-.+ +.+.||+- ..|..|+.+|+. ....|++|
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 5688876543 45667652 469999999998 44678876
No 101
>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=94.67 E-value=0.026 Score=38.99 Aligned_cols=31 Identities=35% Similarity=0.937 Sum_probs=23.7
Q ss_pred CCCcchHHhHHHHhh-------------CCCCCCCCCccCCCCc
Q psy3884 51 CCHIFCESCVTKWFD-------------REQTCPLCRATLVDDP 81 (95)
Q Consensus 51 CgH~fc~~Ci~~~~~-------------~~~~CP~Cr~~~~~~~ 81 (95)
|....|.+|+-+|+. +...||.||+.+...|
T Consensus 311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FCilD 354 (358)
T PF10272_consen 311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFCILD 354 (358)
T ss_pred ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccceeee
Confidence 556679999999885 2247999999987544
No 102
>KOG1100|consensus
Probab=94.64 E-value=0.019 Score=36.78 Aligned_cols=40 Identities=30% Similarity=0.798 Sum_probs=30.8
Q ss_pred ccccccCCCCCeecCCCCc-chHHhHHHHhhCCCCCCCCCccCCC
Q psy3884 36 CPICHDEFKTPVQLTCCHI-FCESCVTKWFDREQTCPLCRATLVD 79 (95)
Q Consensus 36 C~IC~~~~~~p~~~~CgH~-fc~~Ci~~~~~~~~~CP~Cr~~~~~ 79 (95)
|-.|.+.-..-..+||.|. +|..|-.. -..||+|+.+...
T Consensus 161 Cr~C~~~~~~VlllPCrHl~lC~~C~~~----~~~CPiC~~~~~s 201 (207)
T KOG1100|consen 161 CRKCGEREATVLLLPCRHLCLCGICDES----LRICPICRSPKTS 201 (207)
T ss_pred ceecCcCCceEEeecccceEeccccccc----CccCCCCcChhhc
Confidence 8899888766667799985 89999642 4569999876543
No 103
>KOG3039|consensus
Probab=94.38 E-value=0.041 Score=36.25 Aligned_cols=36 Identities=11% Similarity=0.162 Sum_probs=31.2
Q ss_pred CCCcccccccccCCCCCeecCCCCcchHHhHHHHhh
Q psy3884 30 LGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFD 65 (95)
Q Consensus 30 ~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~ 65 (95)
+..-..|..|+....+|++++=||.|+..||.+++.
T Consensus 40 iK~FdcCsLtLqPc~dPvit~~GylfdrEaILe~il 75 (303)
T KOG3039|consen 40 IKPFDCCSLTLQPCRDPVITPDGYLFDREAILEYIL 75 (303)
T ss_pred cCCcceeeeecccccCCccCCCCeeeeHHHHHHHHH
Confidence 344558899999999999999999999999988763
No 104
>KOG3161|consensus
Probab=94.37 E-value=0.014 Score=43.06 Aligned_cols=38 Identities=37% Similarity=0.956 Sum_probs=30.0
Q ss_pred CcccccccccCCC----CCeecCCCCcchHHhHHHHhhCCCCCC
Q psy3884 32 VGCICPICHDEFK----TPVQLTCCHIFCESCVTKWFDREQTCP 71 (95)
Q Consensus 32 ~~~~C~IC~~~~~----~p~~~~CgH~fc~~Ci~~~~~~~~~CP 71 (95)
..+.|+||...|. .|+.+.|||+.|..|+..... .+||
T Consensus 10 ~~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~lyn--~scp 51 (861)
T KOG3161|consen 10 LLLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLYN--ASCP 51 (861)
T ss_pred HHhhchHHHHHHHHHhcCcccccccchHHHHHHHhHhh--ccCC
Confidence 4568999987765 478889999999999987544 4566
No 105
>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=93.92 E-value=0.08 Score=26.90 Aligned_cols=46 Identities=26% Similarity=0.748 Sum_probs=31.6
Q ss_pred cccccccCCCCCe--ecCCC--CcchHHhHHHHhhCCCCCCCCCccCCCCcc
Q psy3884 35 ICPICHDEFKTPV--QLTCC--HIFCESCVTKWFDREQTCPLCRATLVDDPA 82 (95)
Q Consensus 35 ~C~IC~~~~~~p~--~~~Cg--H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~ 82 (95)
.|-.|-..+.... ..-|. .+||..|....+ ...||.|...+..++.
T Consensus 7 nCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l--~~~CPNCgGelv~RP~ 56 (57)
T PF06906_consen 7 NCECCDKDLPPDSPEAYICSFECTFCADCAETML--NGVCPNCGGELVRRPR 56 (57)
T ss_pred CccccCCCCCCCCCcceEEeEeCcccHHHHHHHh--cCcCcCCCCccccCCC
Confidence 5666666655322 22344 479999998765 5789999998876653
No 106
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=93.85 E-value=0.055 Score=36.84 Aligned_cols=47 Identities=23% Similarity=0.565 Sum_probs=35.3
Q ss_pred CCCcccccccccCCC---CCeecCCCCcchHHhHHHHhhCC---CCCCCCCcc
Q psy3884 30 LGVGCICPICHDEFK---TPVQLTCCHIFCESCVTKWFDRE---QTCPLCRAT 76 (95)
Q Consensus 30 ~~~~~~C~IC~~~~~---~p~~~~CgH~fc~~Ci~~~~~~~---~~CP~Cr~~ 76 (95)
...-+.||+=.+.-. .|+.+.|||+.-..-+....+++ +.||.|...
T Consensus 333 fHs~FiCPVlKe~~t~ENpP~ml~CgHVIskeal~~LS~nG~~~FKCPYCP~~ 385 (396)
T COG5109 333 FHSLFICPVLKELCTDENPPVMLECGHVISKEALSVLSQNGVLSFKCPYCPEM 385 (396)
T ss_pred ccceeeccccHhhhcccCCCeeeeccceeeHHHHHHHhhcCcEEeeCCCCCcc
Confidence 456679998665433 47899999999998888776644 689999543
No 107
>KOG3899|consensus
Probab=92.80 E-value=0.062 Score=36.26 Aligned_cols=31 Identities=29% Similarity=0.815 Sum_probs=24.2
Q ss_pred CCCcchHHhHHHHhh-------------CCCCCCCCCccCCCCc
Q psy3884 51 CCHIFCESCVTKWFD-------------REQTCPLCRATLVDDP 81 (95)
Q Consensus 51 CgH~fc~~Ci~~~~~-------------~~~~CP~Cr~~~~~~~ 81 (95)
|....|.+|+-+|+. ++..||+||+.+...+
T Consensus 325 crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fci~d 368 (381)
T KOG3899|consen 325 CRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFCIRD 368 (381)
T ss_pred cccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceEEee
Confidence 566789999988874 3458999999987554
No 108
>KOG0309|consensus
Probab=92.79 E-value=0.071 Score=40.27 Aligned_cols=38 Identities=34% Similarity=0.798 Sum_probs=27.0
Q ss_pred cccccccCCCCC--eecCCCCcchHHhHHHHhhCCCCCCC
Q psy3884 35 ICPICHDEFKTP--VQLTCCHIFCESCVTKWFDREQTCPL 72 (95)
Q Consensus 35 ~C~IC~~~~~~p--~~~~CgH~fc~~Ci~~~~~~~~~CP~ 72 (95)
.|.||--..... +-..|||+.|.+|...|+.....||.
T Consensus 1030 ~C~~C~l~V~gss~~Cg~C~Hv~H~sc~~eWf~~gd~Cps 1069 (1081)
T KOG0309|consen 1030 QCAICHLAVRGSSNFCGTCGHVGHTSCMMEWFRTGDVCPS 1069 (1081)
T ss_pred eeeeEeeEeeccchhhccccccccHHHHHHHHhcCCcCCC
Confidence 344444333332 23369999999999999999889984
No 109
>KOG3579|consensus
Probab=92.74 E-value=0.11 Score=35.02 Aligned_cols=37 Identities=22% Similarity=0.678 Sum_probs=30.5
Q ss_pred CCcccccccccCCCCCeecCC----CCcchHHhHHHHhhCC
Q psy3884 31 GVGCICPICHDEFKTPVQLTC----CHIFCESCVTKWFDRE 67 (95)
Q Consensus 31 ~~~~~C~IC~~~~~~p~~~~C----gH~fc~~Ci~~~~~~~ 67 (95)
...+.|.+|.+.+++-..+.| .|.||..|-++.++++
T Consensus 266 ~apLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSResIK~Q 306 (352)
T KOG3579|consen 266 SAPLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSRESIKQQ 306 (352)
T ss_pred CCceeehhhhhhhccCceeecCCCcccceecccCHHHHHhh
Confidence 345899999999999877766 5899999999888743
No 110
>KOG2034|consensus
Probab=92.69 E-value=0.12 Score=39.47 Aligned_cols=35 Identities=23% Similarity=0.528 Sum_probs=27.5
Q ss_pred CCCcccccccccCCCC-C-eecCCCCcchHHhHHHHh
Q psy3884 30 LGVGCICPICHDEFKT-P-VQLTCCHIFCESCVTKWF 64 (95)
Q Consensus 30 ~~~~~~C~IC~~~~~~-p-~~~~CgH~fc~~Ci~~~~ 64 (95)
......|.+|...+.. | .+.+|||.||..|+.+..
T Consensus 814 ~ep~d~C~~C~~~ll~~pF~vf~CgH~FH~~Cl~~~v 850 (911)
T KOG2034|consen 814 LEPQDSCDHCGRPLLIKPFYVFPCGHCFHRDCLIRHV 850 (911)
T ss_pred ecCccchHHhcchhhcCcceeeeccchHHHHHHHHHH
Confidence 3456699999987654 4 566999999999997654
No 111
>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=92.58 E-value=0.071 Score=35.03 Aligned_cols=45 Identities=38% Similarity=0.977 Sum_probs=33.1
Q ss_pred cccccccccCC-CCC-eec---C-CCCcchHHhHHHHhhCC-CCCC--CCCccC
Q psy3884 33 GCICPICHDEF-KTP-VQL---T-CCHIFCESCVTKWFDRE-QTCP--LCRATL 77 (95)
Q Consensus 33 ~~~C~IC~~~~-~~p-~~~---~-CgH~fc~~Ci~~~~~~~-~~CP--~Cr~~~ 77 (95)
+..||||..+. -+| +.+ | |-|.+|.+|+.+.+... ..|| -|.+-+
T Consensus 10 d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kIL 63 (314)
T COG5220 10 DRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKIL 63 (314)
T ss_pred cccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHH
Confidence 44899999753 355 222 4 99999999999988754 6899 675543
No 112
>KOG1815|consensus
Probab=92.34 E-value=0.1 Score=37.06 Aligned_cols=35 Identities=29% Similarity=0.712 Sum_probs=29.8
Q ss_pred CCcccccccccCCCC-CeecCCCCcchHHhHHHHhh
Q psy3884 31 GVGCICPICHDEFKT-PVQLTCCHIFCESCVTKWFD 65 (95)
Q Consensus 31 ~~~~~C~IC~~~~~~-p~~~~CgH~fc~~Ci~~~~~ 65 (95)
.....|.||.+.+.. ...+.|||.||..|...++.
T Consensus 68 ~~~~~c~ic~~~~~~~~~~~~c~H~~c~~cw~~yl~ 103 (444)
T KOG1815|consen 68 KGDVQCGICVESYDGEIIGLGCGHPFCPPCWTGYLG 103 (444)
T ss_pred CccccCCcccCCCcchhhhcCCCcHHHHHHHHHHhh
Confidence 345799999999885 56779999999999999886
No 113
>KOG1812|consensus
Probab=92.32 E-value=0.059 Score=37.65 Aligned_cols=48 Identities=29% Similarity=0.733 Sum_probs=32.3
Q ss_pred cccccccc-cCCCCC---eecCCCCcchHHhHHHHhhCC------CCCCC--CCccCCCC
Q psy3884 33 GCICPICH-DEFKTP---VQLTCCHIFCESCVTKWFDRE------QTCPL--CRATLVDD 80 (95)
Q Consensus 33 ~~~C~IC~-~~~~~p---~~~~CgH~fc~~Ci~~~~~~~------~~CP~--Cr~~~~~~ 80 (95)
...|.||. +..... .+..|+|.||..|+.+++... ..||. |...++..
T Consensus 146 ~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~~~~~~~~~C~~~~C~~~l~~~ 205 (384)
T KOG1812|consen 146 KEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVKLLSGTVIRCPHDGCESRLTLE 205 (384)
T ss_pred cccCccCccccccHhhhHHHhcccchhhhHHhHHHhhhhhccCCCccCCCCCCCccCCHH
Confidence 56899999 443331 245799999999999888732 36763 54444433
No 114
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=91.35 E-value=0.12 Score=27.66 Aligned_cols=33 Identities=27% Similarity=0.626 Sum_probs=25.4
Q ss_pred CCCcchHHhHHHHhhCCCCCCCCCccCCCCccccC
Q psy3884 51 CCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRD 85 (95)
Q Consensus 51 CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~ 85 (95)
=.++||..|....+ +..||.|...+..+++.+.
T Consensus 27 fEcTFCadCae~~l--~g~CPnCGGelv~RP~RPa 59 (84)
T COG3813 27 FECTFCADCAENRL--HGLCPNCGGELVARPIRPA 59 (84)
T ss_pred EeeehhHhHHHHhh--cCcCCCCCchhhcCcCChH
Confidence 34789999997643 5789999998887766543
No 115
>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=90.61 E-value=0.054 Score=36.27 Aligned_cols=46 Identities=26% Similarity=0.494 Sum_probs=23.2
Q ss_pred CcccccccccCCCCCeecCC---C--CcchHHhHHHHhhCCCCCCCCCccC
Q psy3884 32 VGCICPICHDEFKTPVQLTC---C--HIFCESCVTKWFDREQTCPLCRATL 77 (95)
Q Consensus 32 ~~~~C~IC~~~~~~p~~~~C---g--H~fc~~Ci~~~~~~~~~CP~Cr~~~ 77 (95)
....||||.....-.++..= | +.+|.-|-..|--....||.|...-
T Consensus 171 ~~g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R~~Cp~Cg~~~ 221 (290)
T PF04216_consen 171 QRGYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVRIKCPYCGNTD 221 (290)
T ss_dssp T-SS-TTT---EEEEEEE------EEEEEETTT--EEE--TTS-TTT---S
T ss_pred cCCcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecCCCCcCCCCCC
Confidence 34699999997665444432 3 5689999999988889999996653
No 116
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=90.44 E-value=0.48 Score=23.96 Aligned_cols=30 Identities=33% Similarity=0.950 Sum_probs=23.6
Q ss_pred cccccccccCCC--CCeec--CCCCcchHHhHHH
Q psy3884 33 GCICPICHDEFK--TPVQL--TCCHIFCESCVTK 62 (95)
Q Consensus 33 ~~~C~IC~~~~~--~p~~~--~CgH~fc~~Ci~~ 62 (95)
...|++|.+.|. +.++. .||-.+|+.|...
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~ 38 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK 38 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence 458999999994 45544 6999999999753
No 117
>KOG1812|consensus
Probab=90.12 E-value=0.16 Score=35.54 Aligned_cols=41 Identities=27% Similarity=0.636 Sum_probs=30.8
Q ss_pred cccccccccCCCC-----CeecCCCCcchHHhHHHHhhCCCCCCCC
Q psy3884 33 GCICPICHDEFKT-----PVQLTCCHIFCESCVTKWFDREQTCPLC 73 (95)
Q Consensus 33 ~~~C~IC~~~~~~-----p~~~~CgH~fc~~Ci~~~~~~~~~CP~C 73 (95)
-..||.|...+.. .++-.|||.||+.|...|...+..|..|
T Consensus 306 wr~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~~~~~~~~~~~~~~ 351 (384)
T KOG1812|consen 306 WRQCPKCKFMIELSEGCNHMTCRCGHQFCYMCGGDWKTHNGECYEC 351 (384)
T ss_pred cCcCcccceeeeecCCcceEEeeccccchhhcCcchhhCCccccCc
Confidence 3489999887653 2333699999999999998877766544
No 118
>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=89.68 E-value=0.0097 Score=31.66 Aligned_cols=40 Identities=33% Similarity=0.803 Sum_probs=21.6
Q ss_pred ccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCccCC
Q psy3884 34 CICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLV 78 (95)
Q Consensus 34 ~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~ 78 (95)
+.||.|...+... =|+.+|..|-.. +.....||.|.+++.
T Consensus 2 ~~CP~C~~~L~~~----~~~~~C~~C~~~-~~~~a~CPdC~~~Le 41 (70)
T PF07191_consen 2 NTCPKCQQELEWQ----GGHYHCEACQKD-YKKEAFCPDCGQPLE 41 (70)
T ss_dssp -B-SSS-SBEEEE----TTEEEETTT--E-EEEEEE-TTT-SB-E
T ss_pred CcCCCCCCccEEe----CCEEECcccccc-ceecccCCCcccHHH
Confidence 5799998875421 167778888754 234567999988875
No 119
>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=89.31 E-value=0.22 Score=21.33 Aligned_cols=10 Identities=40% Similarity=0.956 Sum_probs=5.1
Q ss_pred cccccccCCC
Q psy3884 35 ICPICHDEFK 44 (95)
Q Consensus 35 ~C~IC~~~~~ 44 (95)
.||-|...+.
T Consensus 2 ~CP~C~~~V~ 11 (26)
T PF10571_consen 2 TCPECGAEVP 11 (26)
T ss_pred cCCCCcCCch
Confidence 3555555543
No 120
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=89.08 E-value=0.54 Score=36.10 Aligned_cols=53 Identities=19% Similarity=0.492 Sum_probs=38.5
Q ss_pred CCcccccccccCCC--CCeecCCCCc-----chHHhHHHHhhCC--CCCCCCCccCCCCccc
Q psy3884 31 GVGCICPICHDEFK--TPVQLTCCHI-----FCESCVTKWFDRE--QTCPLCRATLVDDPAW 83 (95)
Q Consensus 31 ~~~~~C~IC~~~~~--~p~~~~CgH~-----fc~~Ci~~~~~~~--~~CP~Cr~~~~~~~~~ 83 (95)
.+...|.||...-. +|..-||.-+ .|..|+.+|+..+ ..|-+|..++.-++++
T Consensus 10 ~d~~~CRICr~e~~~d~pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~Fk~IY 71 (1175)
T COG5183 10 EDKRSCRICRTEDIRDDPLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKFKDIY 71 (1175)
T ss_pred ccchhceeecCCCCCCCcCcccccccchhHHHHHHHHHHHHhcCCCcceeeecceeeeeeec
Confidence 34569999986543 4555577643 6999999999854 5899999887655443
No 121
>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=88.99 E-value=0.44 Score=26.66 Aligned_cols=42 Identities=21% Similarity=0.804 Sum_probs=31.3
Q ss_pred ccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCccCCCCcccc
Q psy3884 34 CICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWR 84 (95)
Q Consensus 34 ~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~ 84 (95)
..|.||......+ ||.||..|.. ....|.+|...+.+...+.
T Consensus 45 ~~C~~CK~~v~q~-----g~~YCq~CAY----kkGiCamCGKki~dtk~yk 86 (90)
T PF10235_consen 45 SKCKICKTKVHQP-----GAKYCQTCAY----KKGICAMCGKKILDTKNYK 86 (90)
T ss_pred ccccccccccccC-----CCccChhhhc----ccCcccccCCeeccccccc
Confidence 4788888865543 7889999974 4578999999886654443
No 122
>KOG4718|consensus
Probab=88.44 E-value=0.28 Score=31.63 Aligned_cols=43 Identities=21% Similarity=0.625 Sum_probs=35.0
Q ss_pred cccccccccCCCCCeec-CCCCcchHHhHHHHhhCCCCCCCCCc
Q psy3884 33 GCICPICHDEFKTPVQL-TCCHIFCESCVTKWFDREQTCPLCRA 75 (95)
Q Consensus 33 ~~~C~IC~~~~~~p~~~-~CgH~fc~~Ci~~~~~~~~~CP~Cr~ 75 (95)
...|.+|.......+.- .||-.++..|+..++.+...||.|.-
T Consensus 181 lk~Cn~Ch~LvIqg~rCg~c~i~~h~~c~qty~q~~~~cphc~d 224 (235)
T KOG4718|consen 181 LKNCNLCHCLVIQGIRCGSCNIQYHRGCIQTYLQRRDICPHCGD 224 (235)
T ss_pred HHHHhHhHHHhheeeccCcccchhhhHHHHHHhcccCcCCchhc
Confidence 35899999987765433 67778999999999999999999943
No 123
>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=87.91 E-value=0.74 Score=22.99 Aligned_cols=25 Identities=28% Similarity=0.740 Sum_probs=13.3
Q ss_pred CCCCcchHHhHHHHhhCCCCCCCCC
Q psy3884 50 TCCHIFCESCVTKWFDREQTCPLCR 74 (95)
Q Consensus 50 ~CgH~fc~~Ci~~~~~~~~~CP~Cr 74 (95)
.|++.||.+|=.-.-+.-..||-|.
T Consensus 26 ~C~~~FC~dCD~fiHE~LH~CPGC~ 50 (51)
T PF07975_consen 26 KCKNHFCIDCDVFIHETLHNCPGCE 50 (51)
T ss_dssp TTT--B-HHHHHTTTTTS-SSSTT-
T ss_pred CCCCccccCcChhhhccccCCcCCC
Confidence 5889999999432223346899884
No 124
>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=87.87 E-value=0.92 Score=26.40 Aligned_cols=43 Identities=23% Similarity=0.508 Sum_probs=24.2
Q ss_pred cccccccccCCC---CC--eecCCCCcchHHhHHHHhh-CCCCCCCCCc
Q psy3884 33 GCICPICHDEFK---TP--VQLTCCHIFCESCVTKWFD-REQTCPLCRA 75 (95)
Q Consensus 33 ~~~C~IC~~~~~---~p--~~~~CgH~fc~~Ci~~~~~-~~~~CP~Cr~ 75 (95)
...|.+|...|. +. .-..|+|.+|..|-..-.. ....|.+|.+
T Consensus 54 ~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~~~~~~~WlC~vC~k 102 (118)
T PF02318_consen 54 ERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVYSKKEPIWLCKVCQK 102 (118)
T ss_dssp CSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEETSSSCCEEEHHHHH
T ss_pred CcchhhhCCcccccCCCCCcCCcCCccccCccCCcCCCCCCEEChhhHH
Confidence 449999988653 22 3347999999988643111 1125666643
No 125
>KOG2068|consensus
Probab=87.68 E-value=0.61 Score=31.96 Aligned_cols=48 Identities=25% Similarity=0.618 Sum_probs=37.3
Q ss_pred cccccccccCCCC--C--eecCCCCcchHHhHHHHhhCCCCCCCCCccCCCC
Q psy3884 33 GCICPICHDEFKT--P--VQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD 80 (95)
Q Consensus 33 ~~~C~IC~~~~~~--p--~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~ 80 (95)
...|+||.+.... . .-.+||+..|..|+......+..||.||.+....
T Consensus 249 ~~s~p~~~~~~~~~d~~~lP~~~~~~~~l~~~~t~~~~~~~~~~~rk~~~~~ 300 (327)
T KOG2068|consen 249 PPSCPICYEDLDLTDSNFLPCPCGFRLCLFCHKTISDGDGRCPGCRKPYERN 300 (327)
T ss_pred CCCCCCCCCcccccccccccccccccchhhhhhcccccCCCCCccCCccccC
Confidence 3689999997642 2 2337899999999988888889999999776543
No 126
>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=86.94 E-value=0.36 Score=32.80 Aligned_cols=45 Identities=20% Similarity=0.548 Sum_probs=33.3
Q ss_pred CcccccccccCCCCCeec----CCC--CcchHHhHHHHhhCCCCCCCCCcc
Q psy3884 32 VGCICPICHDEFKTPVQL----TCC--HIFCESCVTKWFDREQTCPLCRAT 76 (95)
Q Consensus 32 ~~~~C~IC~~~~~~p~~~----~Cg--H~fc~~Ci~~~~~~~~~CP~Cr~~ 76 (95)
....||||.....-.++. .=| +.+|.-|-..|-.....||.|...
T Consensus 183 ~~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~~ 233 (305)
T TIGR01562 183 SRTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHYVRVKCSHCEES 233 (305)
T ss_pred CCCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCcccccCccCCCCCCC
Confidence 345999999986544322 233 457899999998888999999764
No 127
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=86.73 E-value=0.52 Score=32.14 Aligned_cols=44 Identities=23% Similarity=0.591 Sum_probs=33.1
Q ss_pred CcccccccccCCCCCee-c--CCC--CcchHHhHHHHhhCCCCCCCCCc
Q psy3884 32 VGCICPICHDEFKTPVQ-L--TCC--HIFCESCVTKWFDREQTCPLCRA 75 (95)
Q Consensus 32 ~~~~C~IC~~~~~~p~~-~--~Cg--H~fc~~Ci~~~~~~~~~CP~Cr~ 75 (95)
....||||.....-.++ + .=| +.+|.-|-..|--....||.|..
T Consensus 186 ~~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~ 234 (309)
T PRK03564 186 QRQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVVRVKCSNCEQ 234 (309)
T ss_pred CCCCCCCCCCcchhheeeccCCCCceEEEcCCCCCcccccCccCCCCCC
Confidence 45699999998654432 1 233 45789999999888899999975
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=85.05 E-value=0.59 Score=24.55 Aligned_cols=12 Identities=42% Similarity=1.450 Sum_probs=8.7
Q ss_pred cchHHhHHHHhh
Q psy3884 54 IFCESCVTKWFD 65 (95)
Q Consensus 54 ~fc~~Ci~~~~~ 65 (95)
.||+.|+.+|..
T Consensus 11 gFCRNCLskWy~ 22 (68)
T PF06844_consen 11 GFCRNCLSKWYR 22 (68)
T ss_dssp S--HHHHHHHHH
T ss_pred HHHHHHHHHHHH
Confidence 499999999985
No 129
>KOG0827|consensus
Probab=84.64 E-value=0.047 Score=38.11 Aligned_cols=47 Identities=26% Similarity=0.639 Sum_probs=39.6
Q ss_pred ccccccccCCCCC----eecCCCCcchHHhHHHHhhCCCCCCCCCccCCCC
Q psy3884 34 CICPICHDEFKTP----VQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD 80 (95)
Q Consensus 34 ~~C~IC~~~~~~p----~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~ 80 (95)
..|+||...++.- ..+.|||.++..|+..|+.....||.|+..++..
T Consensus 197 ~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~~~~kl~~~~rel~~~ 247 (465)
T KOG0827|consen 197 GSLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLATKRKLPSCRRELPKN 247 (465)
T ss_pred hhhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHHHhHHHHhhhhhh
Confidence 3789999887653 4568999999999999999888999999988754
No 130
>KOG0802|consensus
Probab=83.26 E-value=0.91 Score=33.15 Aligned_cols=52 Identities=27% Similarity=0.675 Sum_probs=39.6
Q ss_pred cCCCcccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCccCCCCcccc
Q psy3884 29 LLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWR 84 (95)
Q Consensus 29 ~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~ 84 (95)
.......|.+|.... ....++|. +..|+..|......||.|+..+..++...
T Consensus 475 l~~~~~~~~~~~~~~-~~~~~~~~---~~~~l~~~~~~~~~~pl~~~~~~~~~~~~ 526 (543)
T KOG0802|consen 475 LREPNDVCAICYQEM-SARITPCS---HALCLRKWLYVQEVCPLCHTYMKEDDFLS 526 (543)
T ss_pred hhcccCcchHHHHHH-Hhcccccc---chhHHHhhhhhccccCCCchhhhcccccC
Confidence 334556899999988 55666777 57888899999999999988877664433
No 131
>KOG2169|consensus
Probab=83.14 E-value=1.2 Score=33.20 Aligned_cols=67 Identities=24% Similarity=0.380 Sum_probs=43.4
Q ss_pred cccCCCcccccccccCCCCCe-ecCCCCcchHHhHHHHhh----CCCCCCCCCccCCCCccccCCcchhhhh
Q psy3884 27 ETLLGVGCICPICHDEFKTPV-QLTCCHIFCESCVTKWFD----REQTCPLCRATLVDDPAWRDGATSYFVQ 93 (95)
Q Consensus 27 ~~~~~~~~~C~IC~~~~~~p~-~~~CgH~fc~~Ci~~~~~----~~~~CP~Cr~~~~~~~~~~~~~~~~~~q 93 (95)
.......+.|+|....+.-|. -..|.|.-|.+-..-.-. ....||+|.+....+....|..+..+++
T Consensus 300 tt~~~vSL~CPl~~~Rm~~P~r~~~CkHlQcFD~~~~lq~n~~~pTW~CPVC~~~~~~e~l~iD~~~~~iL~ 371 (636)
T KOG2169|consen 300 TTSLRVSLNCPLSKMRMSLPARGHTCKHLQCFDALSYLQMNEQKPTWRCPVCQKAAPFEGLIIDGYFLNILQ 371 (636)
T ss_pred eccceeEecCCcccceeecCCcccccccceecchhhhHHhccCCCeeeCccCCccccccchhhhHHHHHHHh
Confidence 334456789999988877764 457888766554422111 2248999998888776666655555443
No 132
>KOG1609|consensus
Probab=81.95 E-value=1.5 Score=29.32 Aligned_cols=46 Identities=35% Similarity=0.870 Sum_probs=34.3
Q ss_pred cccccccccCCCC----CeecCCC-----CcchHHhHHHHhh--CCCCCCCCCccCC
Q psy3884 33 GCICPICHDEFKT----PVQLTCC-----HIFCESCVTKWFD--REQTCPLCRATLV 78 (95)
Q Consensus 33 ~~~C~IC~~~~~~----p~~~~Cg-----H~fc~~Ci~~~~~--~~~~CP~Cr~~~~ 78 (95)
...|-||...... +...||. ...|..|+..|.. +...|..|...+.
T Consensus 78 ~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~ 134 (323)
T KOG1609|consen 78 GPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFI 134 (323)
T ss_pred CCcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhccccCeeeecccccce
Confidence 4689999986543 3556664 2369999999998 5678999987654
No 133
>KOG3053|consensus
Probab=81.56 E-value=1.1 Score=29.87 Aligned_cols=47 Identities=23% Similarity=0.663 Sum_probs=33.5
Q ss_pred CcccccccccCCCCCee----cCCC-----CcchHHhHHHHhhCC--------CCCCCCCccCC
Q psy3884 32 VGCICPICHDEFKTPVQ----LTCC-----HIFCESCVTKWFDRE--------QTCPLCRATLV 78 (95)
Q Consensus 32 ~~~~C~IC~~~~~~p~~----~~Cg-----H~fc~~Ci~~~~~~~--------~~CP~Cr~~~~ 78 (95)
.+-.|=||+..-++... -||. |=.|..|+..|+... -.||.|+.+..
T Consensus 19 ~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYi 82 (293)
T KOG3053|consen 19 LERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYI 82 (293)
T ss_pred cceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchhe
Confidence 44589999988765432 2654 337999999999622 37999998753
No 134
>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=80.51 E-value=1.9 Score=19.15 Aligned_cols=35 Identities=20% Similarity=0.482 Sum_probs=20.6
Q ss_pred ccccccCCCCC--eecCCCCcchHHhHHHHhhCCCCCCCCCccCC
Q psy3884 36 CPICHDEFKTP--VQLTCCHIFCESCVTKWFDREQTCPLCRATLV 78 (95)
Q Consensus 36 C~IC~~~~~~p--~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~ 78 (95)
|+.|.+.+... ....=+..||..| +.|..|+.++.
T Consensus 2 C~~C~~~i~~~~~~~~~~~~~~H~~C--------f~C~~C~~~L~ 38 (39)
T smart00132 2 CAGCGKPIRGGELVLRALGKVWHPEC--------FKCSKCGKPLG 38 (39)
T ss_pred ccccCCcccCCcEEEEeCCccccccC--------CCCcccCCcCc
Confidence 66777766653 2333456666666 34777766553
No 135
>KOG0825|consensus
Probab=80.12 E-value=1.5 Score=33.71 Aligned_cols=46 Identities=15% Similarity=0.352 Sum_probs=31.7
Q ss_pred CcccccccccCCCCC----eecC---CCCcchHHhHHHHhhC------CCCCCCCCccC
Q psy3884 32 VGCICPICHDEFKTP----VQLT---CCHIFCESCVTKWFDR------EQTCPLCRATL 77 (95)
Q Consensus 32 ~~~~C~IC~~~~~~p----~~~~---CgH~fc~~Ci~~~~~~------~~~CP~Cr~~~ 77 (95)
....|.+|...+.++ -..+ |+|.||..||..|..+ .-.|+.|..-|
T Consensus 95 ~s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci 153 (1134)
T KOG0825|consen 95 ESDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESEKHTAHYFCEECV 153 (1134)
T ss_pred cccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhccccccccccHHHHh
Confidence 445777777776663 2334 9999999999999863 23567775544
No 136
>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=79.31 E-value=0.41 Score=24.94 Aligned_cols=30 Identities=27% Similarity=0.659 Sum_probs=15.0
Q ss_pred cccccccccCCCCCe----ecCCCCcchHHhHHH
Q psy3884 33 GCICPICHDEFKTPV----QLTCCHIFCESCVTK 62 (95)
Q Consensus 33 ~~~C~IC~~~~~~p~----~~~CgH~fc~~Ci~~ 62 (95)
...|.+|...|.--. --.||++||..|...
T Consensus 9 ~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~ 42 (69)
T PF01363_consen 9 ASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQ 42 (69)
T ss_dssp -SB-TTT--B-BSSS-EEE-TTT--EEECCCS-E
T ss_pred CCcCcCcCCcCCCceeeEccCCCCCEECCchhCC
Confidence 348999999985321 116999999998754
No 137
>KOG1829|consensus
Probab=78.55 E-value=0.97 Score=33.38 Aligned_cols=39 Identities=31% Similarity=0.826 Sum_probs=24.8
Q ss_pred CcccccccccCC-CCC-------eecCCCCcchHHhHHHHhhCCCCCCCC
Q psy3884 32 VGCICPICHDEF-KTP-------VQLTCCHIFCESCVTKWFDREQTCPLC 73 (95)
Q Consensus 32 ~~~~C~IC~~~~-~~p-------~~~~CgH~fc~~Ci~~~~~~~~~CP~C 73 (95)
..+.|.+|...- .-| .-..||+.||..|+.+ .+..||.|
T Consensus 510 ~gfiCe~Cq~~~iiyPF~~~~~~rC~~C~avfH~~C~~r---~s~~CPrC 556 (580)
T KOG1829|consen 510 KGFICELCQHNDIIYPFETRNTRRCSTCLAVFHKKCLRR---KSPCCPRC 556 (580)
T ss_pred CeeeeeeccCCCcccccccccceeHHHHHHHHHHHHHhc---cCCCCCch
Confidence 456778884321 112 1226999999999864 44459999
No 138
>KOG0824|consensus
Probab=78.51 E-value=0.92 Score=30.83 Aligned_cols=49 Identities=31% Similarity=0.728 Sum_probs=38.9
Q ss_pred cCCCcccccccccCCCCCeec-CCCCcchHHhHHHHhhCCCCCCCCCccC
Q psy3884 29 LLGVGCICPICHDEFKTPVQL-TCCHIFCESCVTKWFDREQTCPLCRATL 77 (95)
Q Consensus 29 ~~~~~~~C~IC~~~~~~p~~~-~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~ 77 (95)
...+...|-||...+.-|... .|+|.||..|...|......||.|+...
T Consensus 101 ~~~~~~~~~~~~g~l~vpt~~qg~w~qf~~~~p~~~~~~~~~~~d~~~~~ 150 (324)
T KOG0824|consen 101 FQQDHDICYICYGKLTVPTRIQGCWHQFCYVCPKSNFAMGNDCPDCRGKI 150 (324)
T ss_pred ccCCccceeeeeeeEEecccccCceeeeeecCCchhhhhhhccchhhcCc
Confidence 344566899999988877655 5999999999999988888888776643
No 139
>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=78.41 E-value=1.7 Score=21.57 Aligned_cols=30 Identities=27% Similarity=0.643 Sum_probs=21.2
Q ss_pred cccccccCCCCC----eecCCCCcchHHhHHHHh
Q psy3884 35 ICPICHDEFKTP----VQLTCCHIFCESCVTKWF 64 (95)
Q Consensus 35 ~C~IC~~~~~~p----~~~~CgH~fc~~Ci~~~~ 64 (95)
.|.+|...|..- .-..||++||..|.....
T Consensus 4 ~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~ 37 (57)
T cd00065 4 SCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRI 37 (57)
T ss_pred cCcccCccccCCccccccCcCcCCcChHHcCCee
Confidence 688888766542 223799999999986543
No 140
>KOG2979|consensus
Probab=77.92 E-value=1.3 Score=29.44 Aligned_cols=43 Identities=19% Similarity=0.394 Sum_probs=34.5
Q ss_pred CcccccccccCCCCCee-cCCCCcchHHhHHHHhhC--CCCCCCCC
Q psy3884 32 VGCICPICHDEFKTPVQ-LTCCHIFCESCVTKWFDR--EQTCPLCR 74 (95)
Q Consensus 32 ~~~~C~IC~~~~~~p~~-~~CgH~fc~~Ci~~~~~~--~~~CP~Cr 74 (95)
..+.|||-...+.+|++ ..|||+|=++-+...+.. .-.||+-.
T Consensus 175 fs~rdPis~~~I~nPviSkkC~HvydrDsI~~~l~~~~~i~CPv~g 220 (262)
T KOG2979|consen 175 FSNRDPISKKPIVNPVISKKCGHVYDRDSIMQILCDEITIRCPVLG 220 (262)
T ss_pred hcccCchhhhhhhchhhhcCcCcchhhhhHHHHhccCceeeccccc
Confidence 35699999888999964 489999999999988876 45788643
No 141
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=77.81 E-value=2.3 Score=32.28 Aligned_cols=50 Identities=26% Similarity=0.582 Sum_probs=36.0
Q ss_pred cCCCcccccccccCCCCC----------eecCCCCcc--------------------hHHhHHHHhh--------CCCCC
Q psy3884 29 LLGVGCICPICHDEFKTP----------VQLTCCHIF--------------------CESCVTKWFD--------REQTC 70 (95)
Q Consensus 29 ~~~~~~~C~IC~~~~~~p----------~~~~CgH~f--------------------c~~Ci~~~~~--------~~~~C 70 (95)
...+...|.-|++.+.+| .-+.||..| |..|..++-. +...|
T Consensus 97 I~pD~a~C~~Cl~Ei~dp~~rrY~YPF~~CT~CGPRfTIi~alPYDR~nTsM~~F~lC~~C~~EY~dP~nRRfHAQp~aC 176 (750)
T COG0068 97 IPPDAATCEDCLEEIFDPNSRRYLYPFINCTNCGPRFTIIEALPYDRENTSMADFPLCPFCDKEYKDPLNRRFHAQPIAC 176 (750)
T ss_pred cCCchhhhHHHHHHhcCCCCcceeccccccCCCCcceeeeccCCCCcccCccccCcCCHHHHHHhcCccccccccccccC
Confidence 356677999999988765 233577776 9999988765 22479
Q ss_pred CCCCccCC
Q psy3884 71 PLCRATLV 78 (95)
Q Consensus 71 P~Cr~~~~ 78 (95)
|.|.-.+.
T Consensus 177 p~CGP~~~ 184 (750)
T COG0068 177 PKCGPHLF 184 (750)
T ss_pred cccCCCeE
Confidence 99976554
No 142
>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 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=77.14 E-value=1.7 Score=22.41 Aligned_cols=18 Identities=22% Similarity=0.759 Sum_probs=13.6
Q ss_pred CCCCCCCCCccCCCCccc
Q psy3884 66 REQTCPLCRATLVDDPAW 83 (95)
Q Consensus 66 ~~~~CP~Cr~~~~~~~~~ 83 (95)
.++.||.|..+++.+..+
T Consensus 2 ~HkHC~~CG~~Ip~~~~f 19 (59)
T PF09889_consen 2 PHKHCPVCGKPIPPDESF 19 (59)
T ss_pred CCCcCCcCCCcCCcchhh
Confidence 467899999998876544
No 144
>KOG0801|consensus
Probab=76.54 E-value=0.76 Score=28.58 Aligned_cols=26 Identities=23% Similarity=0.585 Sum_probs=16.8
Q ss_pred CcccccccccCCCCC---eecCCCCcchH
Q psy3884 32 VGCICPICHDEFKTP---VQLTCCHIFCE 57 (95)
Q Consensus 32 ~~~~C~IC~~~~~~p---~~~~CgH~fc~ 57 (95)
+.-+|.||++++... ..+||--+||+
T Consensus 176 dkGECvICLEdL~~GdtIARLPCLCIYHK 204 (205)
T KOG0801|consen 176 DKGECVICLEDLEAGDTIARLPCLCIYHK 204 (205)
T ss_pred cCCcEEEEhhhccCCCceeccceEEEeec
Confidence 445788888877653 45577655553
No 145
>KOG0269|consensus
Probab=76.18 E-value=3.8 Score=31.37 Aligned_cols=39 Identities=21% Similarity=0.465 Sum_probs=29.4
Q ss_pred ccccccccCCCCCeec--CCCCcchHHhHHHHhhCCCCCCC
Q psy3884 34 CICPICHDEFKTPVQL--TCCHIFCESCVTKWFDREQTCPL 72 (95)
Q Consensus 34 ~~C~IC~~~~~~p~~~--~CgH~fc~~Ci~~~~~~~~~CP~ 72 (95)
..|.+|--.+..-..- .|||.-|..++..|+.....||.
T Consensus 780 ~~CtVC~~vi~G~~~~c~~C~H~gH~sh~~sw~~~~s~ca~ 820 (839)
T KOG0269|consen 780 AKCTVCDLVIRGVDVWCQVCGHGGHDSHLKSWFFKASPCAK 820 (839)
T ss_pred cCceeecceeeeeEeecccccccccHHHHHHHHhcCCCCcc
Confidence 4677776665543222 59999999999999998887765
No 146
>PF14353 CpXC: CpXC protein
Probab=76.09 E-value=2.3 Score=24.87 Aligned_cols=47 Identities=26% Similarity=0.357 Sum_probs=25.1
Q ss_pred ccccccccCCCCCeecCCCCcchHHhHHHHhhCC---CCCCCCCccCCCC
Q psy3884 34 CICPICHDEFKTPVQLTCCHIFCESCVTKWFDRE---QTCPLCRATLVDD 80 (95)
Q Consensus 34 ~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~---~~CP~Cr~~~~~~ 80 (95)
.+||-|...+.-.+-+.-.-..-..=....+.+. .+||.|...+...
T Consensus 2 itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~ 51 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLE 51 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecC
Confidence 4788888877654332222111222233333332 5899998876533
No 147
>KOG2066|consensus
Probab=76.06 E-value=2.3 Score=32.57 Aligned_cols=39 Identities=21% Similarity=0.464 Sum_probs=27.6
Q ss_pred ccccccccCCCC-------CeecCCCCcchHHhHHHHhhCCCCCCCC
Q psy3884 34 CICPICHDEFKT-------PVQLTCCHIFCESCVTKWFDREQTCPLC 73 (95)
Q Consensus 34 ~~C~IC~~~~~~-------p~~~~CgH~fc~~Ci~~~~~~~~~CP~C 73 (95)
..|.-|.+.... -++..|||.||..|+.....++. |-.|
T Consensus 785 ~rc~~c~~~~l~~~~~~~~~~v~~c~h~yhk~c~~~~~~~~~-~~~~ 830 (846)
T KOG2066|consen 785 ERCSSCFEPNLPSGAAFDSVVVFHCGHMYHKECLMMESLRNA-CNIE 830 (846)
T ss_pred hhhhhhcccccccCcccceeeEEEccchhhhcccccHHHhcc-cChh
Confidence 388888876542 25678999999999976555444 5444
No 148
>KOG0289|consensus
Probab=75.84 E-value=2.8 Score=30.07 Aligned_cols=49 Identities=16% Similarity=0.323 Sum_probs=42.7
Q ss_pred cccccccCCCCCeecC-CCCcchHHhHHHHhhCCCCCCCCCccCCCCccc
Q psy3884 35 ICPICHDEFKTPVQLT-CCHIFCESCVTKWFDREQTCPLCRATLVDDPAW 83 (95)
Q Consensus 35 ~C~IC~~~~~~p~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~ 83 (95)
.|+|-.+..++|++-+ -||+|=+.-|.+++.....+|+-.+++..+++.
T Consensus 2 ~CaISgEvP~~PVvS~~Sg~vfEkrLIEqyI~e~G~DPIt~~pLs~eelV 51 (506)
T KOG0289|consen 2 VCAISGEVPEEPVVSPVSGHVFEKRLIEQYIAETGKDPITNEPLSIEELV 51 (506)
T ss_pred eecccCCCCCCccccccccchHHHHHHHHHHHHcCCCCCCCCcCCHHHee
Confidence 6999999999998764 889999999999999999999999998766443
No 149
>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=75.26 E-value=2.5 Score=18.84 Aligned_cols=10 Identities=40% Similarity=0.999 Sum_probs=6.8
Q ss_pred CCCCCCCCCc
Q psy3884 66 REQTCPLCRA 75 (95)
Q Consensus 66 ~~~~CP~Cr~ 75 (95)
....||+|..
T Consensus 16 ~~~~CP~Cg~ 25 (33)
T cd00350 16 APWVCPVCGA 25 (33)
T ss_pred CCCcCcCCCC
Confidence 4457888865
No 150
>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=75.04 E-value=2.9 Score=23.95 Aligned_cols=24 Identities=29% Similarity=0.847 Sum_probs=17.9
Q ss_pred CCcchHHhHHHHhh---------CCCCCCCCCc
Q psy3884 52 CHIFCESCVTKWFD---------REQTCPLCRA 75 (95)
Q Consensus 52 gH~fc~~Ci~~~~~---------~~~~CP~Cr~ 75 (95)
.-.||..||..... ....||.||.
T Consensus 37 ~~~fC~~CL~~ryge~~~ev~~~~~W~CP~Crg 69 (105)
T PF10497_consen 37 RGKFCGGCLRNRYGENVEEVLEDPNWKCPKCRG 69 (105)
T ss_pred cceehHhHHHHHHhhhHHHHhcCCceECCCCCC
Confidence 56799999987654 2357998876
No 151
>KOG2807|consensus
Probab=74.60 E-value=5.1 Score=27.74 Aligned_cols=42 Identities=24% Similarity=0.609 Sum_probs=28.4
Q ss_pred ccccccccCCCCCe---ecCCCCcchHHhHHHHhhCCCCCCCCCc
Q psy3884 34 CICPICHDEFKTPV---QLTCCHIFCESCVTKWFDREQTCPLCRA 75 (95)
Q Consensus 34 ~~C~IC~~~~~~p~---~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~ 75 (95)
..|-.|.+...... --.|.++||.+|=.-.-+.-..||.|..
T Consensus 331 ~~Cf~C~~~~~~~~~y~C~~Ck~~FCldCDv~iHesLh~CpgCeh 375 (378)
T KOG2807|consen 331 RFCFACQGELLSSGRYRCESCKNVFCLDCDVFIHESLHNCPGCEH 375 (378)
T ss_pred cceeeeccccCCCCcEEchhccceeeccchHHHHhhhhcCCCcCC
Confidence 35999966555432 2269999999996543344468999963
No 152
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=74.54 E-value=4.9 Score=21.89 Aligned_cols=47 Identities=30% Similarity=0.699 Sum_probs=18.6
Q ss_pred cccccccccCCCC----Ceec---CCCCcchHHhHHHHh-hCCCCCCCCCccCCC
Q psy3884 33 GCICPICHDEFKT----PVQL---TCCHIFCESCVTKWF-DREQTCPLCRATLVD 79 (95)
Q Consensus 33 ~~~C~IC~~~~~~----p~~~---~CgH~fc~~Ci~~~~-~~~~~CP~Cr~~~~~ 79 (95)
.-.|.||.+..-. .+.+ .|+-..|+.|..--. ..+..||.|+.+...
T Consensus 9 ~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg~q~CpqCkt~ykr 63 (80)
T PF14569_consen 9 GQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEGNQVCPQCKTRYKR 63 (80)
T ss_dssp S-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS-SB-TTT--B---
T ss_pred CcccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcCcccccccCCCccc
Confidence 4489999987642 1233 567778999986433 356899999987753
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=74.41 E-value=1.1 Score=22.34 Aligned_cols=13 Identities=38% Similarity=0.976 Sum_probs=6.8
Q ss_pred CCCCCCCccCCCC
Q psy3884 68 QTCPLCRATLVDD 80 (95)
Q Consensus 68 ~~CP~Cr~~~~~~ 80 (95)
..||+|..++...
T Consensus 21 ~~CPlC~r~l~~e 33 (54)
T PF04423_consen 21 GCCPLCGRPLDEE 33 (54)
T ss_dssp EE-TTT--EE-HH
T ss_pred CcCCCCCCCCCHH
Confidence 3899999888754
No 154
>PF12773 DZR: Double zinc ribbon
Probab=74.20 E-value=3.1 Score=20.06 Aligned_cols=27 Identities=33% Similarity=0.661 Sum_probs=14.4
Q ss_pred cchHHhHHHHh--h-CCCCCCCCCccCCCC
Q psy3884 54 IFCESCVTKWF--D-REQTCPLCRATLVDD 80 (95)
Q Consensus 54 ~fc~~Ci~~~~--~-~~~~CP~Cr~~~~~~ 80 (95)
.||..|-.... . ....||.|...+...
T Consensus 13 ~fC~~CG~~l~~~~~~~~~C~~Cg~~~~~~ 42 (50)
T PF12773_consen 13 KFCPHCGTPLPPPDQSKKICPNCGAENPPN 42 (50)
T ss_pred cCChhhcCChhhccCCCCCCcCCcCCCcCC
Confidence 35555554443 1 235688887765543
No 155
>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=72.54 E-value=1.6 Score=21.58 Aligned_cols=37 Identities=19% Similarity=0.486 Sum_probs=17.5
Q ss_pred ccccccCCCCC-ee-cCCCCcchHHhHHHHhhCCCCCCCCCccCCCC
Q psy3884 36 CPICHDEFKTP-VQ-LTCCHIFCESCVTKWFDREQTCPLCRATLVDD 80 (95)
Q Consensus 36 C~IC~~~~~~p-~~-~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~ 80 (95)
|+.|.+.+... .. ..-|..||..| ..|-.|+.++...
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~C--------f~C~~C~~~l~~~ 39 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPEC--------FKCSKCGKPLNDG 39 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETTT--------SBETTTTCBTTTS
T ss_pred CCCCCCCccCcEEEEEeCCcEEEccc--------cccCCCCCccCCC
Confidence 34455544432 22 14445555554 2366666555544
No 156
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=70.95 E-value=4.1 Score=25.99 Aligned_cols=38 Identities=34% Similarity=0.959 Sum_probs=25.5
Q ss_pred CcccccccccC-CCCC----eec---CCCCcchHHhHHHHhhCCCCCCCCC
Q psy3884 32 VGCICPICHDE-FKTP----VQL---TCCHIFCESCVTKWFDREQTCPLCR 74 (95)
Q Consensus 32 ~~~~C~IC~~~-~~~p----~~~---~CgH~fc~~Ci~~~~~~~~~CP~Cr 74 (95)
.++.|.+|.+. +.=| .+. .|+..||..|.. ...||.|.
T Consensus 151 kGfiCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~~C~~-----~~~CpkC~ 196 (202)
T PF13901_consen 151 KGFICEICNSDDIIFPFQIDTTVRCPKCKSVFHKSCFR-----KKSCPKCA 196 (202)
T ss_pred CCCCCccCCCCCCCCCCCCCCeeeCCcCccccchhhcC-----CCCCCCcH
Confidence 45688888753 1112 122 689999999985 26799994
No 157
>KOG2042|consensus
Probab=70.74 E-value=5.5 Score=31.26 Aligned_cols=64 Identities=16% Similarity=0.161 Sum_probs=52.8
Q ss_pred CCCcccccccccCCCCCeecC-CCCcchHHhHHHHhhCCCCCCCCCccCCCCccccCCcchhhhh
Q psy3884 30 LGVGCICPICHDEFKTPVQLT-CCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRDGATSYFVQ 93 (95)
Q Consensus 30 ~~~~~~C~IC~~~~~~p~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~~~~~~~q 93 (95)
..+++.=|+-...+.+|+++| -|++.++.=+.+.+....+=|.||.++..+...++..+...|+
T Consensus 867 vpdef~DPlm~Tlm~dPV~LP~Srv~vDRsti~rhlLs~~tdPFNR~pLt~d~v~pn~eLK~kI~ 931 (943)
T KOG2042|consen 867 VPDEFLDPLMSTLMSDPVVLPSSRVTVDRSTIERHLLSDCTDPFNREPLTEDMVSPNEELKAKIR 931 (943)
T ss_pred CchhhhCccccccCCCCccCCcccccccHHHHHHHHhcCCCCccccccCchhhcCCCHHHHHHHH
Confidence 345566678888899999998 8899999999999988888899999999988777766655554
No 158
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=70.62 E-value=7.3 Score=22.72 Aligned_cols=41 Identities=27% Similarity=0.650 Sum_probs=29.8
Q ss_pred ccccccccCCCCCe--------------ecCCCCcchHHhHHHHhhCCCCCCCCC
Q psy3884 34 CICPICHDEFKTPV--------------QLTCCHIFCESCVTKWFDREQTCPLCR 74 (95)
Q Consensus 34 ~~C~IC~~~~~~p~--------------~~~CgH~fc~~Ci~~~~~~~~~CP~Cr 74 (95)
..|--|+..|..+. -..|++.||.+|=.-+-+.-..||-|.
T Consensus 56 ~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~CPGC~ 110 (112)
T TIGR00622 56 RFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHESLHCCPGCI 110 (112)
T ss_pred CcccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhhccCCcCCC
Confidence 46999999876531 226889999999655555557899885
No 159
>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=69.85 E-value=15 Score=22.48 Aligned_cols=36 Identities=28% Similarity=0.374 Sum_probs=23.4
Q ss_pred CCcccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCccCCCCc
Q psy3884 31 GVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDP 81 (95)
Q Consensus 31 ~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~ 81 (95)
...+.||.|...+.- ...+...+.||.|..++...+
T Consensus 107 ~~~Y~Cp~c~~r~tf---------------~eA~~~~F~Cp~Cg~~L~~~d 142 (158)
T TIGR00373 107 NMFFICPNMCVRFTF---------------NEAMELNFTCPRCGAMLDYLD 142 (158)
T ss_pred CCeEECCCCCcEeeH---------------HHHHHcCCcCCCCCCEeeecc
Confidence 356688887765442 122235789999999876543
No 160
>PLN02195 cellulose synthase A
Probab=69.45 E-value=8.5 Score=30.41 Aligned_cols=48 Identities=19% Similarity=0.513 Sum_probs=33.4
Q ss_pred cccccccccCCCC-----Ce--ecCCCCcchHHhHHH-HhhCCCCCCCCCccCCCC
Q psy3884 33 GCICPICHDEFKT-----PV--QLTCCHIFCESCVTK-WFDREQTCPLCRATLVDD 80 (95)
Q Consensus 33 ~~~C~IC~~~~~~-----p~--~~~CgH~fc~~Ci~~-~~~~~~~CP~Cr~~~~~~ 80 (95)
...|.||.+.... +- .-.|+--.|+.|..- ..+.+..||.|+....++
T Consensus 6 ~~~c~~cgd~~~~~~~g~~fvaC~eC~~pvCrpCyeyer~eg~q~CpqCkt~Yk~~ 61 (977)
T PLN02195 6 APICATCGEEVGVDSNGEAFVACHECSYPLCKACLEYEIKEGRKVCLRCGGPYDAE 61 (977)
T ss_pred CccceecccccCcCCCCCeEEEeccCCCccccchhhhhhhcCCccCCccCCccccc
Confidence 3489999986542 22 226888889999842 223567999999988844
No 161
>KOG2231|consensus
Probab=69.25 E-value=4.7 Score=30.47 Aligned_cols=46 Identities=26% Similarity=0.590 Sum_probs=35.1
Q ss_pred cccccccCCCCCeecCCCC-cchHHhHHHHhh--C----CCCCCCCCccCCCC
Q psy3884 35 ICPICHDEFKTPVQLTCCH-IFCESCVTKWFD--R----EQTCPLCRATLVDD 80 (95)
Q Consensus 35 ~C~IC~~~~~~p~~~~CgH-~fc~~Ci~~~~~--~----~~~CP~Cr~~~~~~ 80 (95)
.|+||-....-...-.||| ..|..|..+... . ...||+|+..+...
T Consensus 2 ~c~ic~~s~~~~~~~s~~h~~v~~~~~~R~~~~~~~~~~~~~~~vcr~~~~~~ 54 (669)
T KOG2231|consen 2 SCAICAFSPDFVGRGSCGHNEVCATCVVRLRFELNNRKCSNECPVCRREVETK 54 (669)
T ss_pred CcceeecCccccccccccccccchhhhhhhhhhcccccccccCcccccceeee
Confidence 5889988877766779999 799999987653 2 35689999866543
No 162
>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=67.83 E-value=2.1 Score=20.68 Aligned_cols=40 Identities=25% Similarity=0.633 Sum_probs=24.7
Q ss_pred cccccccCCCCCeec---CCCCcchHHhHHHHhh------CCCCCCCCC
Q psy3884 35 ICPICHDEFKTPVQL---TCCHIFCESCVTKWFD------REQTCPLCR 74 (95)
Q Consensus 35 ~C~IC~~~~~~p~~~---~CgH~fc~~Ci~~~~~------~~~~CP~Cr 74 (95)
.|.||.....+...+ .|+..||..|+..-.. ....||.|+
T Consensus 1 ~C~vC~~~~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~ 49 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCR 49 (51)
T ss_dssp EBTTTTSSCTTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHH
T ss_pred eCcCCCCcCCCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCc
Confidence 378888844443344 6788899999854322 235677664
No 163
>COG4647 AcxC Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=66.84 E-value=2.9 Score=25.05 Aligned_cols=22 Identities=27% Similarity=0.523 Sum_probs=15.3
Q ss_pred cccccCCCCCeecCCCCcchHH
Q psy3884 37 PICHDEFKTPVQLTCCHIFCES 58 (95)
Q Consensus 37 ~IC~~~~~~p~~~~CgH~fc~~ 58 (95)
-||++.-..-+.-.|||.||..
T Consensus 61 fi~qs~~~rv~rcecghsf~d~ 82 (165)
T COG4647 61 FICQSAQKRVIRCECGHSFGDY 82 (165)
T ss_pred EEEecccccEEEEeccccccCh
Confidence 4677665554455899999864
No 164
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=66.42 E-value=10 Score=30.36 Aligned_cols=47 Identities=28% Similarity=0.705 Sum_probs=32.9
Q ss_pred CcccccccccCCCCC----eec---CCCCcchHHhHH-HHhhCCCCCCCCCccCC
Q psy3884 32 VGCICPICHDEFKTP----VQL---TCCHIFCESCVT-KWFDREQTCPLCRATLV 78 (95)
Q Consensus 32 ~~~~C~IC~~~~~~p----~~~---~CgH~fc~~Ci~-~~~~~~~~CP~Cr~~~~ 78 (95)
..-.|.||.+..... ... .|+--.|+.|.. +.-+.+..||.|+....
T Consensus 16 ~~qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCYEYEr~eG~q~CPqCktrYk 70 (1079)
T PLN02638 16 GGQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCYEYERKDGNQSCPQCKTKYK 70 (1079)
T ss_pred CCceeeecccccCcCCCCCEEEEeccCCCccccchhhhhhhcCCccCCccCCchh
Confidence 344999999986521 222 577778999994 22235679999998876
No 165
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=65.85 E-value=0.8 Score=23.11 Aligned_cols=14 Identities=36% Similarity=1.082 Sum_probs=11.9
Q ss_pred CCCCcchHHhHHHH
Q psy3884 50 TCCHIFCESCVTKW 63 (95)
Q Consensus 50 ~CgH~fc~~Ci~~~ 63 (95)
.||+.||..|...|
T Consensus 45 ~C~~~fC~~C~~~~ 58 (64)
T smart00647 45 KCGFSFCFRCKVPW 58 (64)
T ss_pred CCCCeECCCCCCcC
Confidence 58999999998766
No 166
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=65.72 E-value=4.3 Score=20.15 Aligned_cols=9 Identities=44% Similarity=1.280 Sum_probs=6.1
Q ss_pred hCCCCCCCC
Q psy3884 65 DREQTCPLC 73 (95)
Q Consensus 65 ~~~~~CP~C 73 (95)
.....||.|
T Consensus 47 ~~~~~CP~C 55 (55)
T PF14311_consen 47 RRGKGCPYC 55 (55)
T ss_pred cCCCCCCCC
Confidence 355678877
No 167
>COG3492 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=65.57 E-value=4 Score=22.92 Aligned_cols=12 Identities=33% Similarity=1.384 Sum_probs=10.6
Q ss_pred cchHHhHHHHhh
Q psy3884 54 IFCESCVTKWFD 65 (95)
Q Consensus 54 ~fc~~Ci~~~~~ 65 (95)
.||..|+..|..
T Consensus 42 gFCRNCLs~Wy~ 53 (104)
T COG3492 42 GFCRNCLSNWYR 53 (104)
T ss_pred HHHHHHHHHHHH
Confidence 399999999986
No 168
>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 COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=65.08 E-value=11 Score=26.02 Aligned_cols=44 Identities=23% Similarity=0.538 Sum_probs=29.4
Q ss_pred CcccccccccCCCCCeec--------------CCCCcchHHhHHHHhhCCCCCCCCCc
Q psy3884 32 VGCICPICHDEFKTPVQL--------------TCCHIFCESCVTKWFDREQTCPLCRA 75 (95)
Q Consensus 32 ~~~~C~IC~~~~~~p~~~--------------~CgH~fc~~Ci~~~~~~~~~CP~Cr~ 75 (95)
....|-+|+..|..|..- .|...||.+|=.-.-+.-..|+.|..
T Consensus 361 ks~~Cf~CQ~~fp~~~~~~~~~~~ss~rY~Ce~CK~~FC~dCdvfiHe~Lh~C~gCe~ 418 (421)
T COG5151 361 KSTHCFVCQGPFPKPPVSPFDESTSSGRYQCELCKSTFCSDCDVFIHETLHFCIGCEL 418 (421)
T ss_pred CCccceeccCCCCCCCCCcccccccccceechhhhhhhhhhhHHHHHHHHhhCCCCcC
Confidence 345899999988754221 38888999996433334467888854
No 170
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=64.83 E-value=16 Score=24.90 Aligned_cols=45 Identities=20% Similarity=0.510 Sum_probs=31.5
Q ss_pred CcccccccccCCCCCeecC----CCC--cchHHhHHHHhhCCCCCCCCCcc
Q psy3884 32 VGCICPICHDEFKTPVQLT----CCH--IFCESCVTKWFDREQTCPLCRAT 76 (95)
Q Consensus 32 ~~~~C~IC~~~~~~p~~~~----CgH--~fc~~Ci~~~~~~~~~CP~Cr~~ 76 (95)
..-.||+|.......++.- -|- .-|.-|...|......|-.|.+.
T Consensus 184 ~~~~CPvCGS~PvaSmV~~g~~~~GlRYL~CslC~teW~~VR~KC~nC~~t 234 (308)
T COG3058 184 SRQYCPVCGSMPVASMVQIGETEQGLRYLHCSLCETEWHYVRVKCSNCEQS 234 (308)
T ss_pred ccccCCCcCCCCcceeeeecCccccchhhhhhhHHHHHHHHHHHhcccccc
Confidence 4459999999876654332 232 24899999998877777777553
No 171
>KOG2113|consensus
Probab=64.04 E-value=8.5 Score=26.62 Aligned_cols=44 Identities=7% Similarity=-0.156 Sum_probs=33.2
Q ss_pred CCcccccccccCCCCCeecCCCCc-chHHhHHHHhhCCCCCCCCCcc
Q psy3884 31 GVGCICPICHDEFKTPVQLTCCHI-FCESCVTKWFDREQTCPLCRAT 76 (95)
Q Consensus 31 ~~~~~C~IC~~~~~~p~~~~CgH~-fc~~Ci~~~~~~~~~CP~Cr~~ 76 (95)
-..++|..|..-.-.-+..+|+|. ||..|.. +.-...||.|...
T Consensus 341 ~s~~~~~~~~~~~~st~~~~~~~n~~~~~~a~--~s~~~~~~~c~~~ 385 (394)
T KOG2113|consen 341 MSSLKGTSAGFGLLSTIWSGGNMNLSPGSLAS--ASASPTSSTCDHN 385 (394)
T ss_pred hhhcccccccCceeeeEeecCCcccChhhhhh--cccCCcccccccc
Confidence 345688888877666667799985 8999986 4556789999654
No 172
>PRK11595 DNA utilization protein GntX; Provisional
Probab=62.63 E-value=9.5 Score=24.63 Aligned_cols=38 Identities=18% Similarity=0.498 Sum_probs=22.1
Q ss_pred cccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCccC
Q psy3884 35 ICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATL 77 (95)
Q Consensus 35 ~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~ 77 (95)
.|.+|...+... ....|..|...+..-...||.|..++
T Consensus 7 ~C~~C~~~~~~~-----~~~lC~~C~~~l~~~~~~C~~Cg~~~ 44 (227)
T PRK11595 7 LCWLCRMPLALS-----HWGICSVCSRALRTLKTCCPQCGLPA 44 (227)
T ss_pred cCccCCCccCCC-----CCcccHHHHhhCCcccCcCccCCCcC
Confidence 688887765321 12367777765432234677776654
No 173
>KOG3476|consensus
Probab=62.40 E-value=1 Score=24.95 Aligned_cols=43 Identities=21% Similarity=0.758 Sum_probs=31.2
Q ss_pred ccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCccCCCCccccC
Q psy3884 34 CICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRD 85 (95)
Q Consensus 34 ~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~ 85 (95)
..|.||......| |..||..|... ...|.+|.+.+.....+..
T Consensus 55 ~kC~iCk~~vHQ~-----GshYC~tCAY~----KgiCAMCGKki~nTK~ykQ 97 (100)
T KOG3476|consen 55 AKCRICKQLVHQP-----GSHYCQTCAYK----KGICAMCGKKILNTKNYKQ 97 (100)
T ss_pred chhHHHHHHhcCC-----cchhHhHhhhh----hhHHHHhhhHhhccccccc
Confidence 4788998887776 54589999753 4679999888776654443
No 174
>PLN02189 cellulose synthase
Probab=61.26 E-value=8.4 Score=30.64 Aligned_cols=47 Identities=28% Similarity=0.651 Sum_probs=32.7
Q ss_pred CcccccccccCCCC----Ceec---CCCCcchHHhHHHH-hhCCCCCCCCCccCC
Q psy3884 32 VGCICPICHDEFKT----PVQL---TCCHIFCESCVTKW-FDREQTCPLCRATLV 78 (95)
Q Consensus 32 ~~~~C~IC~~~~~~----p~~~---~CgH~fc~~Ci~~~-~~~~~~CP~Cr~~~~ 78 (95)
....|.||.+.+.. .... .|+--.|..|..-= -+.+..||.|+....
T Consensus 33 ~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cyeyer~eg~q~CpqCkt~Y~ 87 (1040)
T PLN02189 33 DGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCYEYERREGTQNCPQCKTRYK 87 (1040)
T ss_pred cCccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchh
Confidence 34499999998652 1223 47777899999422 235579999998876
No 175
>KOG3799|consensus
Probab=60.23 E-value=3.4 Score=24.98 Aligned_cols=27 Identities=33% Similarity=0.715 Sum_probs=16.0
Q ss_pred CCCcccccccccCCCCCeecCCCCcchHHhH
Q psy3884 30 LGVGCICPICHDEFKTPVQLTCCHIFCESCV 60 (95)
Q Consensus 30 ~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci 60 (95)
..++..|.||...-. .-.|||. |.+|-
T Consensus 62 v~ddatC~IC~KTKF---ADG~GH~-C~YCq 88 (169)
T KOG3799|consen 62 VGDDATCGICHKTKF---ADGCGHN-CSYCQ 88 (169)
T ss_pred cCcCcchhhhhhccc---ccccCcc-cchhh
Confidence 345679999997532 2246764 44443
No 176
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=60.16 E-value=11 Score=23.70 Aligned_cols=35 Identities=26% Similarity=0.538 Sum_probs=23.0
Q ss_pred CcccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCccCCCCc
Q psy3884 32 VGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDP 81 (95)
Q Consensus 32 ~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~ 81 (95)
..+.||.|...+.-- ..+...+.||.|...+...+
T Consensus 116 ~~Y~Cp~C~~rytf~---------------eA~~~~F~Cp~Cg~~L~~~d 150 (178)
T PRK06266 116 MFFFCPNCHIRFTFD---------------EAMEYGFRCPQCGEMLEEYD 150 (178)
T ss_pred CEEECCCCCcEEeHH---------------HHhhcCCcCCCCCCCCeecc
Confidence 456788776554411 22346799999999887643
No 177
>KOG3842|consensus
Probab=59.54 E-value=14 Score=25.65 Aligned_cols=48 Identities=27% Similarity=0.636 Sum_probs=30.8
Q ss_pred cccccccccCCC-----------------CC--eecCCCCcchHHhHHHHhh---------CCCCCCCCCccCCCC
Q psy3884 33 GCICPICHDEFK-----------------TP--VQLTCCHIFCESCVTKWFD---------REQTCPLCRATLVDD 80 (95)
Q Consensus 33 ~~~C~IC~~~~~-----------------~p--~~~~CgH~fc~~Ci~~~~~---------~~~~CP~Cr~~~~~~ 80 (95)
+-+||+|+..-. .| ...||||.--..=..-|.+ -+..||.|-..+...
T Consensus 341 ~r~CPmC~~~gp~V~L~lG~E~~f~vD~G~pthaF~PCGHv~sekt~~YWs~iplPhGT~~f~a~CPFC~~~L~ge 416 (429)
T KOG3842|consen 341 ERECPMCRVVGPYVPLWLGCEAGFYVDAGPPTHAFNPCGHVCSEKTVKYWSQIPLPHGTHAFHAACPFCATQLAGE 416 (429)
T ss_pred cCcCCeeeeecceeeeeccccceeEecCCCcccccCCcccccchhhhhHhhcCcCCCccccccccCcchhhhhccC
Confidence 569999987421 01 3448999755555555654 124799998887654
No 178
>KOG2462|consensus
Probab=59.26 E-value=3.2 Score=27.90 Aligned_cols=51 Identities=22% Similarity=0.593 Sum_probs=31.5
Q ss_pred CcccccccccCCCC-C--------eecCCCCcchHHhH-HHHhhC----------CCCCCCCCccCCCCcc
Q psy3884 32 VGCICPICHDEFKT-P--------VQLTCCHIFCESCV-TKWFDR----------EQTCPLCRATLVDDPA 82 (95)
Q Consensus 32 ~~~~C~IC~~~~~~-p--------~~~~CgH~fc~~Ci-~~~~~~----------~~~CP~Cr~~~~~~~~ 82 (95)
....|.+|-..+.. | -.++|.-.+|.+=+ ++|+.+ .+.||.|++.|.++..
T Consensus 160 ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSN 230 (279)
T KOG2462|consen 160 KAFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSN 230 (279)
T ss_pred ccccCCCCCceeeehHHHhhHhhccCCCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHH
Confidence 45688888887653 1 12355444554443 367652 3689999988887643
No 179
>PLN02248 cellulose synthase-like protein
Probab=58.82 E-value=10 Score=30.39 Aligned_cols=30 Identities=20% Similarity=0.553 Sum_probs=25.9
Q ss_pred CCCCcchHHhHHHHhhCCCCCCCCCccCCC
Q psy3884 50 TCCHIFCESCVTKWFDREQTCPLCRATLVD 79 (95)
Q Consensus 50 ~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~ 79 (95)
.|+...|.+|....+.....||-|+.+...
T Consensus 149 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 178 (1135)
T PLN02248 149 ECGFKICRDCYIDAVKSGGICPGCKEPYKV 178 (1135)
T ss_pred cccchhHHhHhhhhhhcCCCCCCCcccccc
Confidence 477888999999998888999999998754
No 180
>KOG1729|consensus
Probab=58.72 E-value=13 Score=25.21 Aligned_cols=47 Identities=26% Similarity=0.582 Sum_probs=29.4
Q ss_pred Cccccccccc-CCCCC----eecCCCCcchHHhHHHHhh------C-CCCCCCCCccCC
Q psy3884 32 VGCICPICHD-EFKTP----VQLTCCHIFCESCVTKWFD------R-EQTCPLCRATLV 78 (95)
Q Consensus 32 ~~~~C~IC~~-~~~~p----~~~~CgH~fc~~Ci~~~~~------~-~~~CP~Cr~~~~ 78 (95)
+...|.+|.. .|..- .--.||++||..|-..-+. + ...|+.|-..+.
T Consensus 167 ea~~C~~C~~~~Ftl~~RRHHCR~CG~ivC~~Cs~n~~~l~~~~~k~~rvC~~CF~el~ 225 (288)
T KOG1729|consen 167 EATECMVCGCTEFTLSERRHHCRNCGDIVCAPCSRNRFLLPNLSTKPIRVCDICFEELE 225 (288)
T ss_pred cceecccCCCccccHHHHHHHHHhcchHhhhhhhcCcccccccCCCCceecHHHHHHHh
Confidence 4569999998 44321 1226999999998765221 1 126777755553
No 181
>COG4640 Predicted membrane protein [Function unknown]
Probab=57.85 E-value=2.4 Score=30.00 Aligned_cols=38 Identities=16% Similarity=0.472 Sum_probs=21.8
Q ss_pred chHHhHHHHhhCCCCCCCCCccCCCCccccCCcchhhh
Q psy3884 55 FCESCVTKWFDREQTCPLCRATLVDDPAWRDGATSYFV 92 (95)
Q Consensus 55 fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~~~~~~~ 92 (95)
||..|-..-.+....||.|..++.....+-+..+..++
T Consensus 3 fC~kcG~qk~Ed~~qC~qCG~~~t~~~sqan~~tn~i~ 40 (465)
T COG4640 3 FCPKCGSQKAEDDVQCTQCGHKFTSRQSQANKSTNEII 40 (465)
T ss_pred cccccccccccccccccccCCcCCchhhhhhHHHHHHH
Confidence 56666544344444578887777766555554444443
No 182
>KOG4021|consensus
Probab=56.27 E-value=4.7 Score=25.87 Aligned_cols=26 Identities=23% Similarity=0.492 Sum_probs=15.7
Q ss_pred HHhHHHHhh-CCCCCCCCCccCCCCcc
Q psy3884 57 ESCVTKWFD-REQTCPLCRATLVDDPA 82 (95)
Q Consensus 57 ~~Ci~~~~~-~~~~CP~Cr~~~~~~~~ 82 (95)
..||.+.-. -...||+||-....-+.
T Consensus 97 ktCIrkn~~~~gnpCPICRDeyL~~Dy 123 (239)
T KOG4021|consen 97 KTCIRKNGRFLGNPCPICRDEYLYFDY 123 (239)
T ss_pred hHHHhhcCeecCCCCCccccceEEEec
Confidence 456655333 34679999987554333
No 183
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=55.53 E-value=9.7 Score=17.67 Aligned_cols=7 Identities=43% Similarity=1.483 Sum_probs=4.1
Q ss_pred CCCcchH
Q psy3884 51 CCHIFCE 57 (95)
Q Consensus 51 CgH~fc~ 57 (95)
|+..||.
T Consensus 18 C~~~FC~ 24 (39)
T smart00154 18 CGNLFCG 24 (39)
T ss_pred cCCcccc
Confidence 6666654
No 184
>KOG3362|consensus
Probab=54.82 E-value=9.2 Score=23.35 Aligned_cols=29 Identities=17% Similarity=0.555 Sum_probs=19.7
Q ss_pred CCcccccccccCCCCCeecCCCCcchH-HhH
Q psy3884 31 GVGCICPICHDEFKTPVQLTCCHIFCE-SCV 60 (95)
Q Consensus 31 ~~~~~C~IC~~~~~~p~~~~CgH~fc~-~Ci 60 (95)
+..-.|+||. .+..-.-+.||..+|. .|+
T Consensus 116 P~r~fCaVCG-~~S~ysC~~CG~kyCsv~C~ 145 (156)
T KOG3362|consen 116 PLRKFCAVCG-YDSKYSCVNCGTKYCSVRCL 145 (156)
T ss_pred CcchhhhhcC-CCchhHHHhcCCceeechhh
Confidence 4456999999 4444456789988764 444
No 185
>PLN02436 cellulose synthase A
Probab=53.16 E-value=13 Score=29.73 Aligned_cols=46 Identities=28% Similarity=0.684 Sum_probs=32.2
Q ss_pred cccccccccCCCCC----eec---CCCCcchHHhHHHH-hhCCCCCCCCCccCC
Q psy3884 33 GCICPICHDEFKTP----VQL---TCCHIFCESCVTKW-FDREQTCPLCRATLV 78 (95)
Q Consensus 33 ~~~C~IC~~~~~~p----~~~---~CgH~fc~~Ci~~~-~~~~~~CP~Cr~~~~ 78 (95)
.-.|.||.+..... ..+ .|+--.|..|..-= -+.+..||.|+....
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 44999999986421 223 57777899999422 225579999998876
No 186
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=51.94 E-value=14 Score=29.49 Aligned_cols=46 Identities=24% Similarity=0.592 Sum_probs=32.3
Q ss_pred cccccccccCCCCC----eec---CCCCcchHHhHHH-HhhCCCCCCCCCccCC
Q psy3884 33 GCICPICHDEFKTP----VQL---TCCHIFCESCVTK-WFDREQTCPLCRATLV 78 (95)
Q Consensus 33 ~~~C~IC~~~~~~p----~~~---~CgH~fc~~Ci~~-~~~~~~~CP~Cr~~~~ 78 (95)
...|.||.+..... ..+ .|+--.|..|..- .-+.+..||.|+....
T Consensus 15 ~~~c~iCGd~vg~~~~Ge~FVAC~eC~fpvCr~cyeye~~~g~~~cp~c~t~y~ 68 (1044)
T PLN02915 15 AKTCRVCGDEVGVKEDGQPFVACHVCGFPVCKPCYEYERSEGNQCCPQCNTRYK 68 (1044)
T ss_pred cchhhccccccCcCCCCCEEEEeccCCCccccchhhhhhhcCCccCCccCCchh
Confidence 44899999986531 222 5777789999942 2235579999998876
No 187
>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=51.76 E-value=8.1 Score=16.26 Aligned_cols=10 Identities=30% Similarity=0.949 Sum_probs=7.5
Q ss_pred CCCCCCccCC
Q psy3884 69 TCPLCRATLV 78 (95)
Q Consensus 69 ~CP~Cr~~~~ 78 (95)
.||+|.+.+.
T Consensus 3 ~CPiC~~~v~ 12 (26)
T smart00734 3 QCPVCFREVP 12 (26)
T ss_pred cCCCCcCccc
Confidence 5899977763
No 188
>PLN02400 cellulose synthase
Probab=51.62 E-value=12 Score=29.97 Aligned_cols=47 Identities=32% Similarity=0.719 Sum_probs=32.4
Q ss_pred CcccccccccCCCCC----eec---CCCCcchHHhHHH-HhhCCCCCCCCCccCC
Q psy3884 32 VGCICPICHDEFKTP----VQL---TCCHIFCESCVTK-WFDREQTCPLCRATLV 78 (95)
Q Consensus 32 ~~~~C~IC~~~~~~p----~~~---~CgH~fc~~Ci~~-~~~~~~~CP~Cr~~~~ 78 (95)
..-.|-||.+..... ..+ .|+--.|+.|..- .-+.+..||.|+....
T Consensus 35 ~gqiCqICGD~VG~t~dGe~FVAC~eCaFPVCRpCYEYERkeGnq~CPQCkTrYk 89 (1085)
T PLN02400 35 NGQICQICGDDVGVTETGDVFVACNECAFPVCRPCYEYERKDGTQCCPQCKTRYR 89 (1085)
T ss_pred CCceeeecccccCcCCCCCEEEEEccCCCccccchhheecccCCccCcccCCccc
Confidence 344999999986531 222 5777789999831 2235579999998876
No 189
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=50.93 E-value=12 Score=17.89 Aligned_cols=22 Identities=27% Similarity=0.579 Sum_probs=13.2
Q ss_pred ccccccCCCCCeecCCCCcchH
Q psy3884 36 CPICHDEFKTPVQLTCCHIFCE 57 (95)
Q Consensus 36 C~IC~~~~~~p~~~~CgH~fc~ 57 (95)
|..|......-+-+.|++++|.
T Consensus 2 C~~C~~~~~l~~CL~C~~~~c~ 23 (50)
T smart00290 2 CSVCGTIENLWLCLTCGQVGCG 23 (50)
T ss_pred cccCCCcCCeEEecCCCCcccC
Confidence 5566654433355678887774
No 190
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=50.77 E-value=9.7 Score=28.76 Aligned_cols=8 Identities=63% Similarity=1.373 Sum_probs=4.4
Q ss_pred cccccccC
Q psy3884 35 ICPICHDE 42 (95)
Q Consensus 35 ~C~IC~~~ 42 (95)
.||-|...
T Consensus 3 ~Cp~Cg~~ 10 (645)
T PRK14559 3 ICPQCQFE 10 (645)
T ss_pred cCCCCCCc
Confidence 45555554
No 191
>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=49.60 E-value=18 Score=23.74 Aligned_cols=26 Identities=31% Similarity=0.736 Sum_probs=20.1
Q ss_pred chHHhHHHHhhCCCCCCCCCccCCCC
Q psy3884 55 FCESCVTKWFDREQTCPLCRATLVDD 80 (95)
Q Consensus 55 fc~~Ci~~~~~~~~~CP~Cr~~~~~~ 80 (95)
-|.+|....-.+...||+|+..-..+
T Consensus 196 ~C~sC~qqIHRNAPiCPlCK~KsRSr 221 (230)
T PF10146_consen 196 TCQSCHQQIHRNAPICPLCKAKSRSR 221 (230)
T ss_pred hhHhHHHHHhcCCCCCcccccccccC
Confidence 48889887777778999998766543
No 192
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=48.93 E-value=2.9 Score=19.71 Aligned_cols=9 Identities=33% Similarity=0.962 Sum_probs=7.0
Q ss_pred CCCCCCCCc
Q psy3884 67 EQTCPLCRA 75 (95)
Q Consensus 67 ~~~CP~Cr~ 75 (95)
...||.|+.
T Consensus 26 ~~~CP~Cg~ 34 (42)
T PF09723_consen 26 PVPCPECGS 34 (42)
T ss_pred CCcCCCCCC
Confidence 457999977
No 193
>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=48.45 E-value=13 Score=23.02 Aligned_cols=25 Identities=32% Similarity=0.824 Sum_probs=18.9
Q ss_pred CcchHHhHHHHhhCCCCCCCCCccCCCC
Q psy3884 53 HIFCESCVTKWFDREQTCPLCRATLVDD 80 (95)
Q Consensus 53 H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~ 80 (95)
+.||..|-.+-+. .||.|..++...
T Consensus 28 ~~fC~kCG~~tI~---~Cp~C~~~IrG~ 52 (158)
T PF10083_consen 28 EKFCSKCGAKTIT---SCPNCSTPIRGD 52 (158)
T ss_pred HHHHHHhhHHHHH---HCcCCCCCCCCc
Confidence 4599999876543 599998888754
No 194
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=48.36 E-value=20 Score=20.16 Aligned_cols=29 Identities=24% Similarity=0.582 Sum_probs=21.6
Q ss_pred CcccccccccCCCCCeec-----CCCCcchHHhHHH
Q psy3884 32 VGCICPICHDEFKTPVQL-----TCCHIFCESCVTK 62 (95)
Q Consensus 32 ~~~~C~IC~~~~~~p~~~-----~CgH~fc~~Ci~~ 62 (95)
....|.||... ....+ .|...||..|...
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 46799999997 34444 3677899999865
No 195
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=47.96 E-value=7.5 Score=20.25 Aligned_cols=21 Identities=29% Similarity=0.828 Sum_probs=12.6
Q ss_pred hHHhHHHHhhCCCCCCCCCcc
Q psy3884 56 CESCVTKWFDREQTCPLCRAT 76 (95)
Q Consensus 56 c~~Ci~~~~~~~~~CP~Cr~~ 76 (95)
|..|..-.-.....||.|..+
T Consensus 7 C~~Ck~l~~~d~e~CP~Cgs~ 27 (64)
T COG2093 7 CKNCKRLTPEDTEICPVCGST 27 (64)
T ss_pred HhhccccCCCCCccCCCCCCc
Confidence 556643222344569999877
No 196
>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=47.96 E-value=24 Score=16.04 Aligned_cols=23 Identities=26% Similarity=0.842 Sum_probs=11.7
Q ss_pred hHHhHHHHhhC--------CCCCCCCCccCC
Q psy3884 56 CESCVTKWFDR--------EQTCPLCRATLV 78 (95)
Q Consensus 56 c~~Ci~~~~~~--------~~~CP~Cr~~~~ 78 (95)
|..|+.++... ..+|+.|.-.+.
T Consensus 2 C~~C~~Ey~~p~~RR~~~~~isC~~CGPr~~ 32 (35)
T PF07503_consen 2 CDDCLKEYFDPSNRRFHYQFISCTNCGPRYS 32 (35)
T ss_dssp -HHHHHHHCSTTSTTTT-TT--BTTCC-SCC
T ss_pred CHHHHHHHcCCCCCcccCcCccCCCCCCCEE
Confidence 66777766542 237888865543
No 197
>KOG4451|consensus
Probab=47.42 E-value=19 Score=23.83 Aligned_cols=26 Identities=31% Similarity=0.708 Sum_probs=19.7
Q ss_pred chHHhHHHHhhCCCCCCCCCccCCCC
Q psy3884 55 FCESCVTKWFDREQTCPLCRATLVDD 80 (95)
Q Consensus 55 fc~~Ci~~~~~~~~~CP~Cr~~~~~~ 80 (95)
.|.+|....-.+...||+|+.....+
T Consensus 251 ~ClsChqqIHRNAPiCPlCKaKsRSr 276 (286)
T KOG4451|consen 251 VCLSCHQQIHRNAPICPLCKAKSRSR 276 (286)
T ss_pred HHHHHHHHHhcCCCCCcchhhccccC
Confidence 47888877767778999998766543
No 198
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=47.24 E-value=14 Score=19.15 Aligned_cols=13 Identities=31% Similarity=0.876 Sum_probs=9.1
Q ss_pred CCCCCCCCCccCC
Q psy3884 66 REQTCPLCRATLV 78 (95)
Q Consensus 66 ~~~~CP~Cr~~~~ 78 (95)
....||.|...-.
T Consensus 14 ~~~~CP~Cgs~~~ 26 (61)
T PRK08351 14 TEDRCPVCGSRDL 26 (61)
T ss_pred CCCcCCCCcCCcc
Confidence 4457999977653
No 199
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=46.89 E-value=14 Score=19.03 Aligned_cols=14 Identities=43% Similarity=1.158 Sum_probs=10.5
Q ss_pred CCCCCCCCccCCCC
Q psy3884 67 EQTCPLCRATLVDD 80 (95)
Q Consensus 67 ~~~CP~Cr~~~~~~ 80 (95)
...||+|..+....
T Consensus 39 ~p~CPlC~s~M~~~ 52 (59)
T PF14169_consen 39 EPVCPLCKSPMVSG 52 (59)
T ss_pred CccCCCcCCccccc
Confidence 36899998886644
No 200
>PRK01343 zinc-binding protein; Provisional
Probab=46.84 E-value=15 Score=18.80 Aligned_cols=12 Identities=25% Similarity=0.719 Sum_probs=8.9
Q ss_pred CCCCCCCCccCC
Q psy3884 67 EQTCPLCRATLV 78 (95)
Q Consensus 67 ~~~CP~Cr~~~~ 78 (95)
...||+|++++.
T Consensus 9 ~~~CP~C~k~~~ 20 (57)
T PRK01343 9 TRPCPECGKPST 20 (57)
T ss_pred CCcCCCCCCcCc
Confidence 457899988765
No 201
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF. A previously described regulatory effect of HypF mutatation is attributable to loss of activity of a regulatory hydrogenase. A zinc finger-like region CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported the regulatory hypothesis. However, more recent work (PUBMED:11375153) shows the direct effect is on the activity of expressed hydrogenases with nickel/iron centers, rather than on expression.
Probab=46.59 E-value=13 Score=28.44 Aligned_cols=49 Identities=24% Similarity=0.541 Sum_probs=34.6
Q ss_pred CCCcccccccccCCCCC----------eecCCCCcc--------------------hHHhHHHHhhC--------CCCCC
Q psy3884 30 LGVGCICPICHDEFKTP----------VQLTCCHIF--------------------CESCVTKWFDR--------EQTCP 71 (95)
Q Consensus 30 ~~~~~~C~IC~~~~~~p----------~~~~CgH~f--------------------c~~Ci~~~~~~--------~~~CP 71 (95)
..+.-.|.-|+..+.+| --+.||..| |..|..++... ...||
T Consensus 65 ppD~a~C~~Cl~E~~dp~~Rry~YpF~nCt~CGPr~~i~~~lpydr~~t~m~~f~~C~~C~~ey~~p~~rr~h~~~~~C~ 144 (711)
T TIGR00143 65 PADVATCSDCLEEMLDKNDRRYLYPFISCTHCGPRFTIIEALPYDRENTSMADFPLCPDCAKEYKDPLDRRFHAQPIACP 144 (711)
T ss_pred CCchhhHHHHHHHhcCCCcccccCCcccccCCCCCeEEeecCCCCCCCcCCCCCcCCHHHHHHhcCCccccCCCCCccCC
Confidence 45667999999888765 122576665 99999988552 14799
Q ss_pred CCCccCC
Q psy3884 72 LCRATLV 78 (95)
Q Consensus 72 ~Cr~~~~ 78 (95)
.|.-.+.
T Consensus 145 ~Cgp~l~ 151 (711)
T TIGR00143 145 RCGPQLN 151 (711)
T ss_pred CCCcEEE
Confidence 9977664
No 202
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=45.36 E-value=16 Score=19.15 Aligned_cols=21 Identities=29% Similarity=0.727 Sum_probs=12.6
Q ss_pred hHHhHHHHhhCCCCCCCCCccCC
Q psy3884 56 CESCVTKWFDREQTCPLCRATLV 78 (95)
Q Consensus 56 c~~Ci~~~~~~~~~CP~Cr~~~~ 78 (95)
|..|- .+.....||.|...-.
T Consensus 8 C~~C~--~i~~~~~Cp~Cgs~~~ 28 (64)
T PRK06393 8 CKKCK--RLTPEKTCPVHGDEKT 28 (64)
T ss_pred HhhCC--cccCCCcCCCCCCCcC
Confidence 45553 2234568999987643
No 203
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=45.31 E-value=12 Score=17.10 Aligned_cols=12 Identities=42% Similarity=1.279 Sum_probs=7.7
Q ss_pred cccccccCCCCC
Q psy3884 35 ICPICHDEFKTP 46 (95)
Q Consensus 35 ~C~IC~~~~~~p 46 (95)
.||-|...|.-+
T Consensus 4 ~CP~C~~~f~v~ 15 (37)
T PF13719_consen 4 TCPNCQTRFRVP 15 (37)
T ss_pred ECCCCCceEEcC
Confidence 677777766543
No 204
>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=45.30 E-value=1.4 Score=22.16 Aligned_cols=29 Identities=31% Similarity=0.787 Sum_probs=15.3
Q ss_pred cccc--cccCCCC-----C--eecC-CCCcchHHhHHHH
Q psy3884 35 ICPI--CHDEFKT-----P--VQLT-CCHIFCESCVTKW 63 (95)
Q Consensus 35 ~C~I--C~~~~~~-----p--~~~~-CgH~fc~~Ci~~~ 63 (95)
.||- |...+.. . +.=+ |++.||..|-..|
T Consensus 20 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~ 58 (64)
T PF01485_consen 20 WCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPW 58 (64)
T ss_dssp --TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSES
T ss_pred CCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCccc
Confidence 7766 7765542 1 2224 9999999887655
No 205
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=44.52 E-value=16 Score=24.09 Aligned_cols=22 Identities=27% Similarity=0.637 Sum_probs=14.8
Q ss_pred ccccccccCCCC-Ceec--CCCCcc
Q psy3884 34 CICPICHDEFKT-PVQL--TCCHIF 55 (95)
Q Consensus 34 ~~C~IC~~~~~~-p~~~--~CgH~f 55 (95)
+.||+|.+.+.. ...+ +.||.|
T Consensus 3 ~~CP~C~~~l~~~~~~~~C~~~h~f 27 (272)
T PRK11088 3 YQCPLCHQPLTLEENSWICPQNHQF 27 (272)
T ss_pred ccCCCCCcchhcCCCEEEcCCCCCC
Confidence 689999998862 2223 456776
No 206
>KOG2789|consensus
Probab=43.99 E-value=53 Score=23.67 Aligned_cols=32 Identities=22% Similarity=0.666 Sum_probs=24.2
Q ss_pred CcccccccccCCCCC--eecCCCCcchHHhHHHH
Q psy3884 32 VGCICPICHDEFKTP--VQLTCCHIFCESCVTKW 63 (95)
Q Consensus 32 ~~~~C~IC~~~~~~p--~~~~CgH~fc~~Ci~~~ 63 (95)
....|+||+-.+... .+.-|.-..|..|+.+.
T Consensus 73 r~~ecpicflyyps~~n~~rcC~~~Ic~ecf~~~ 106 (482)
T KOG2789|consen 73 RKTECPICFLYYPSAKNLVRCCSETICGECFAPF 106 (482)
T ss_pred ccccCceeeeecccccchhhhhccchhhhheecc
Confidence 346999999887654 34468889999998754
No 207
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=43.47 E-value=2.5 Score=18.65 Aligned_cols=10 Identities=40% Similarity=0.976 Sum_probs=3.6
Q ss_pred CcchHHhHHH
Q psy3884 53 HIFCESCVTK 62 (95)
Q Consensus 53 H~fc~~Ci~~ 62 (95)
|.||..|-.+
T Consensus 3 ~rfC~~CG~~ 12 (32)
T PF09297_consen 3 HRFCGRCGAP 12 (32)
T ss_dssp TSB-TTT--B
T ss_pred CcccCcCCcc
Confidence 4555555543
No 208
>COG5627 MMS21 DNA repair protein MMS21 [DNA replication, recombination, and repair]
Probab=43.25 E-value=14 Score=24.59 Aligned_cols=48 Identities=25% Similarity=0.402 Sum_probs=34.8
Q ss_pred cccccccccCCCCCe-ecCCCCcchHHhHHHHhhC--CCCCCC--CCccCCCC
Q psy3884 33 GCICPICHDEFKTPV-QLTCCHIFCESCVTKWFDR--EQTCPL--CRATLVDD 80 (95)
Q Consensus 33 ~~~C~IC~~~~~~p~-~~~CgH~fc~~Ci~~~~~~--~~~CP~--Cr~~~~~~ 80 (95)
+..|||-+..+.-|+ ...|.|.|=.+-|...++. ...||. |.+.+.-+
T Consensus 189 ~nrCpitl~p~~~pils~kcnh~~e~D~I~~~lq~~~trvcp~~~Csq~~~~~ 241 (275)
T COG5627 189 SNRCPITLNPDFYPILSSKCNHKPEMDLINKKLQVECTRVCPRLICSQKEVVD 241 (275)
T ss_pred cccCCcccCcchhHHHHhhhcccccHHHHHHHhcCCceeecchhhcchheecc
Confidence 468999877777774 4489999999999998874 356774 64444433
No 209
>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=41.69 E-value=9.4 Score=16.39 Aligned_cols=11 Identities=55% Similarity=1.277 Sum_probs=5.9
Q ss_pred CCCCCCccCCC
Q psy3884 69 TCPLCRATLVD 79 (95)
Q Consensus 69 ~CP~Cr~~~~~ 79 (95)
.||.|...+..
T Consensus 1 ~CP~C~s~l~~ 11 (28)
T PF03119_consen 1 TCPVCGSKLVR 11 (28)
T ss_dssp B-TTT--BEEE
T ss_pred CcCCCCCEeEc
Confidence 48999888763
No 210
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=41.58 E-value=8.4 Score=22.47 Aligned_cols=21 Identities=29% Similarity=0.651 Sum_probs=15.4
Q ss_pred hhCCCCCCCCCccCCCCcccc
Q psy3884 64 FDREQTCPLCRATLVDDPAWR 84 (95)
Q Consensus 64 ~~~~~~CP~Cr~~~~~~~~~~ 84 (95)
+.+...|+.|++++..++.+.
T Consensus 82 LGr~D~CM~C~~pLTLd~~le 102 (114)
T PF11023_consen 82 LGRVDACMHCKEPLTLDPSLE 102 (114)
T ss_pred hchhhccCcCCCcCccCchhh
Confidence 445578999999998765443
No 211
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=40.98 E-value=15 Score=19.07 Aligned_cols=11 Identities=27% Similarity=0.815 Sum_probs=8.9
Q ss_pred CCCCCCCccCC
Q psy3884 68 QTCPLCRATLV 78 (95)
Q Consensus 68 ~~CP~Cr~~~~ 78 (95)
..||+|++++.
T Consensus 7 v~CP~C~k~~~ 17 (62)
T PRK00418 7 VNCPTCGKPVE 17 (62)
T ss_pred ccCCCCCCccc
Confidence 57999999864
No 212
>KOG1701|consensus
Probab=40.91 E-value=2.3 Score=30.31 Aligned_cols=11 Identities=18% Similarity=0.839 Sum_probs=5.7
Q ss_pred CCCCCCccCCC
Q psy3884 69 TCPLCRATLVD 79 (95)
Q Consensus 69 ~CP~Cr~~~~~ 79 (95)
.|-+|..+|..
T Consensus 396 rCs~C~~PI~P 406 (468)
T KOG1701|consen 396 RCSVCGNPILP 406 (468)
T ss_pred chhhccCCccC
Confidence 45555555543
No 213
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=40.37 E-value=16 Score=16.62 Aligned_cols=10 Identities=30% Similarity=1.185 Sum_probs=6.0
Q ss_pred cccccccCCC
Q psy3884 35 ICPICHDEFK 44 (95)
Q Consensus 35 ~C~IC~~~~~ 44 (95)
.|+-|...|.
T Consensus 4 ~Cp~C~~~y~ 13 (36)
T PF13717_consen 4 TCPNCQAKYE 13 (36)
T ss_pred ECCCCCCEEe
Confidence 5666666554
No 214
>PRK04023 DNA polymerase II large subunit; Validated
Probab=39.91 E-value=23 Score=28.38 Aligned_cols=47 Identities=21% Similarity=0.287 Sum_probs=30.3
Q ss_pred CcccccccccCCCCCeecCCCC-----cchHHhHHHHhhCCCCCCCCCccCCCC
Q psy3884 32 VGCICPICHDEFKTPVQLTCCH-----IFCESCVTKWFDREQTCPLCRATLVDD 80 (95)
Q Consensus 32 ~~~~C~IC~~~~~~p~~~~CgH-----~fc~~Ci~~~~~~~~~CP~Cr~~~~~~ 80 (95)
....|+-|........--.||. .||..|-. ......||.|.......
T Consensus 625 g~RfCpsCG~~t~~frCP~CG~~Te~i~fCP~CG~--~~~~y~CPKCG~El~~~ 676 (1121)
T PRK04023 625 GRRKCPSCGKETFYRRCPFCGTHTEPVYRCPRCGI--EVEEDECEKCGREPTPY 676 (1121)
T ss_pred cCccCCCCCCcCCcccCCCCCCCCCcceeCccccC--cCCCCcCCCCCCCCCcc
Confidence 3458888887753333334874 48999943 23446799998877644
No 215
>KOG1842|consensus
Probab=39.84 E-value=4.9 Score=28.94 Aligned_cols=31 Identities=23% Similarity=0.635 Sum_probs=23.4
Q ss_pred CcccccccccCCCCCee----cCCCCcchHHhHHH
Q psy3884 32 VGCICPICHDEFKTPVQ----LTCCHIFCESCVTK 62 (95)
Q Consensus 32 ~~~~C~IC~~~~~~p~~----~~CgH~fc~~Ci~~ 62 (95)
+...||+|.+.|.-... --||.+.|.+|..-
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 44589999999875322 25999999999864
No 216
>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=39.32 E-value=22 Score=17.43 Aligned_cols=7 Identities=57% Similarity=1.507 Sum_probs=3.1
Q ss_pred CCCCCCc
Q psy3884 69 TCPLCRA 75 (95)
Q Consensus 69 ~CP~Cr~ 75 (95)
.||.|.+
T Consensus 4 ~CP~C~~ 10 (54)
T PF05605_consen 4 TCPYCGK 10 (54)
T ss_pred CCCCCCC
Confidence 4444443
No 217
>PF15616 TerY-C: TerY-C metal binding domain
Probab=38.77 E-value=13 Score=22.27 Aligned_cols=41 Identities=27% Similarity=0.617 Sum_probs=28.9
Q ss_pred CcccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCccCC
Q psy3884 32 VGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLV 78 (95)
Q Consensus 32 ~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~ 78 (95)
....||-|-..+.-. +-.||+.||..= ....+||-|.....
T Consensus 76 g~PgCP~CGn~~~fa-~C~CGkl~Ci~g-----~~~~~CPwCg~~g~ 116 (131)
T PF15616_consen 76 GAPGCPHCGNQYAFA-VCGCGKLFCIDG-----EGEVTCPWCGNEGS 116 (131)
T ss_pred CCCCCCCCcChhcEE-EecCCCEEEeCC-----CCCEECCCCCCeee
Confidence 346999999875433 338999998642 23568999987654
No 218
>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=37.75 E-value=5.4 Score=17.16 Aligned_cols=10 Identities=30% Similarity=0.899 Sum_probs=3.4
Q ss_pred cccccccCCC
Q psy3884 35 ICPICHDEFK 44 (95)
Q Consensus 35 ~C~IC~~~~~ 44 (95)
.|+.|...+.
T Consensus 3 ~C~rC~~~~~ 12 (30)
T PF06827_consen 3 KCPRCWNYIE 12 (30)
T ss_dssp B-TTT--BBE
T ss_pred cCccCCCcce
Confidence 4555555543
No 219
>KOG4218|consensus
Probab=36.46 E-value=27 Score=24.64 Aligned_cols=13 Identities=38% Similarity=1.119 Sum_probs=10.1
Q ss_pred cccccccccCCCC
Q psy3884 33 GCICPICHDEFKT 45 (95)
Q Consensus 33 ~~~C~IC~~~~~~ 45 (95)
+..||+|.+....
T Consensus 15 ~ElCPVCGDkVSG 27 (475)
T KOG4218|consen 15 GELCPVCGDKVSG 27 (475)
T ss_pred ccccccccCcccc
Confidence 4589999987664
No 220
>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=36.34 E-value=35 Score=18.94 Aligned_cols=39 Identities=15% Similarity=0.347 Sum_probs=26.5
Q ss_pred cccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCccCCCC
Q psy3884 33 GCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD 80 (95)
Q Consensus 33 ~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~ 80 (95)
.-.|+-|...+.---.+| +..|+.....|..|+++++..
T Consensus 33 rS~C~~C~~~L~~~~lIP---------i~S~l~lrGrCr~C~~~I~~~ 71 (92)
T PF06750_consen 33 RSHCPHCGHPLSWWDLIP---------ILSYLLLRGRCRYCGAPIPPR 71 (92)
T ss_pred CCcCcCCCCcCcccccch---------HHHHHHhCCCCcccCCCCChH
Confidence 347777777665432333 346777889999999988754
No 221
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=36.33 E-value=35 Score=19.41 Aligned_cols=14 Identities=21% Similarity=0.714 Sum_probs=11.1
Q ss_pred CCCCCCCCccCCCC
Q psy3884 67 EQTCPLCRATLVDD 80 (95)
Q Consensus 67 ~~~CP~Cr~~~~~~ 80 (95)
...||.|+.++...
T Consensus 80 ~~~Cp~C~spFNp~ 93 (105)
T COG4357 80 CGSCPYCQSPFNPG 93 (105)
T ss_pred cCCCCCcCCCCCcc
Confidence 35799999998754
No 222
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.09 E-value=29 Score=20.83 Aligned_cols=22 Identities=32% Similarity=0.939 Sum_probs=12.7
Q ss_pred chHHhHHHHhhCCCCCCCCCccCCC
Q psy3884 55 FCESCVTKWFDREQTCPLCRATLVD 79 (95)
Q Consensus 55 fc~~Ci~~~~~~~~~CP~Cr~~~~~ 79 (95)
||..|-..-+ ..||.|..++..
T Consensus 30 fcskcgeati---~qcp~csasirg 51 (160)
T COG4306 30 FCSKCGEATI---TQCPICSASIRG 51 (160)
T ss_pred HHhhhchHHH---hcCCccCCcccc
Confidence 6666654322 347777666653
No 223
>KOG4443|consensus
Probab=36.04 E-value=20 Score=27.16 Aligned_cols=47 Identities=32% Similarity=0.697 Sum_probs=31.4
Q ss_pred CCCcccccccccCCCCC--eec---CCCCcchHHhHHHHhh-----CCCCCCCCCcc
Q psy3884 30 LGVGCICPICHDEFKTP--VQL---TCCHIFCESCVTKWFD-----REQTCPLCRAT 76 (95)
Q Consensus 30 ~~~~~~C~IC~~~~~~p--~~~---~CgH~fc~~Ci~~~~~-----~~~~CP~Cr~~ 76 (95)
....+.|++|...=..+ ..+ .||-.+|..|+..|+. +...||-||.-
T Consensus 15 ~~~~~mc~l~~s~G~~~ag~m~ac~~c~~~yH~~cvt~~~~~~~l~~gWrC~~crvC 71 (694)
T KOG4443|consen 15 IIVCLMCPLCGSSGKGRAGRLLACSDCGQKYHPYCVTSWAQHAVLSGGWRCPSCRVC 71 (694)
T ss_pred hhhhhhhhhhccccccccCcchhhhhhcccCCcchhhHHHhHHHhcCCcccCCceee
Confidence 34456888887654433 122 6888999999998876 23468877653
No 224
>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=35.94 E-value=9.1 Score=14.92 Aligned_cols=9 Identities=56% Similarity=1.516 Sum_probs=3.9
Q ss_pred ccccccCCC
Q psy3884 36 CPICHDEFK 44 (95)
Q Consensus 36 C~IC~~~~~ 44 (95)
|++|...|.
T Consensus 3 C~~C~~~f~ 11 (23)
T PF00096_consen 3 CPICGKSFS 11 (23)
T ss_dssp ETTTTEEES
T ss_pred CCCCCCccC
Confidence 444444433
No 225
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.44 E-value=5.9 Score=21.63 Aligned_cols=12 Identities=42% Similarity=0.968 Sum_probs=8.0
Q ss_pred ccccccccCCCC
Q psy3884 34 CICPICHDEFKT 45 (95)
Q Consensus 34 ~~C~IC~~~~~~ 45 (95)
+.||||.-.+..
T Consensus 2 llCP~C~v~l~~ 13 (88)
T COG3809 2 LLCPICGVELVM 13 (88)
T ss_pred cccCcCCceeee
Confidence 468888766553
No 226
>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=35.44 E-value=17 Score=13.77 Aligned_cols=10 Identities=30% Similarity=1.132 Sum_probs=4.6
Q ss_pred CCCCCccCCC
Q psy3884 70 CPLCRATLVD 79 (95)
Q Consensus 70 CP~Cr~~~~~ 79 (95)
|+.|...+..
T Consensus 3 C~~C~~~~~~ 12 (24)
T PF13894_consen 3 CPICGKSFRS 12 (24)
T ss_dssp -SSTS-EESS
T ss_pred CcCCCCcCCc
Confidence 6667655543
No 227
>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=35.19 E-value=26 Score=16.71 Aligned_cols=12 Identities=25% Similarity=0.944 Sum_probs=8.6
Q ss_pred CCCCCCCCccCC
Q psy3884 67 EQTCPLCRATLV 78 (95)
Q Consensus 67 ~~~CP~Cr~~~~ 78 (95)
...||+|..+|.
T Consensus 8 ~K~C~~C~rpf~ 19 (42)
T PF10013_consen 8 SKICPVCGRPFT 19 (42)
T ss_pred CCcCcccCCcch
Confidence 467888877765
No 228
>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=34.92 E-value=12 Score=18.78 Aligned_cols=13 Identities=38% Similarity=1.007 Sum_probs=5.8
Q ss_pred CCCCCCCccCCCC
Q psy3884 68 QTCPLCRATLVDD 80 (95)
Q Consensus 68 ~~CP~Cr~~~~~~ 80 (95)
.+||+|...+...
T Consensus 25 atCP~C~a~~~~s 37 (54)
T PF09237_consen 25 ATCPICGAVIRQS 37 (54)
T ss_dssp EE-TTT--EESSH
T ss_pred CCCCcchhhccch
Confidence 3677776665543
No 229
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=34.87 E-value=28 Score=17.92 Aligned_cols=16 Identities=19% Similarity=0.571 Sum_probs=12.5
Q ss_pred CCCCCCCCCccCCCCc
Q psy3884 66 REQTCPLCRATLVDDP 81 (95)
Q Consensus 66 ~~~~CP~Cr~~~~~~~ 81 (95)
.+..|++|.+.++.+.
T Consensus 7 PH~HC~VCg~aIp~de 22 (64)
T COG4068 7 PHRHCVVCGKAIPPDE 22 (64)
T ss_pred CCccccccCCcCCCcc
Confidence 4577999999888664
No 230
>PF06416 DUF1076: Protein of unknown function (DUF1076); InterPro: IPR010489 This entry is represented by Bacteriophage 2851, Orf74 (EP2851_74). The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; PDB: 2KKX_A 2KKY_A.
Probab=34.84 E-value=60 Score=18.97 Aligned_cols=73 Identities=11% Similarity=0.154 Sum_probs=37.0
Q ss_pred HHHHHhhccCCCCCcccccCCCcccccccccCCCCCeecC--CC----CcchHHhHHHHhhCCCCCCCCCccCCCCccc
Q psy3884 11 FTKLLNNIQLGVSPTKETLLGVGCICPICHDEFKTPVQLT--CC----HIFCESCVTKWFDREQTCPLCRATLVDDPAW 83 (95)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~~~~~~~~C~IC~~~~~~p~~~~--Cg----H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~ 83 (95)
++..+..-+....+..-.-..+.+.|||-++..++.+.+. =+ ..|=..-+.+....+..=|+-|.++....+.
T Consensus 18 l~~kI~~csF~V~~~~f~C~ee~L~CPITL~iPe~GVFvkNs~~S~VC~LyD~~Al~~Lv~~~~~HPLSREpit~sMIv 96 (113)
T PF06416_consen 18 LQDKISSCSFSVNSEEFQCPEEHLTCPITLCIPENGVFVKNSSGSDVCSLYDKEALSRLVREGAPHPLSREPITPSMIV 96 (113)
T ss_dssp HHHHHHHC-EE--CCCCTS-CHHH-BTTTTC--SCEEEEECTTTSSEEEEEEHHHHHHHHHCT---TTT-----TTTEE
T ss_pred HHHHHHhcccccChhhccCCHHHcCCCeEEeecCCceEEecCCCCccceecCHHHHHHHHHcCCCCCCccCCCChhhEe
Confidence 3344444444444444444556789999999999987662 11 3466777777777777778889988766443
No 231
>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=34.67 E-value=24 Score=16.52 Aligned_cols=20 Identities=25% Similarity=0.610 Sum_probs=8.0
Q ss_pred cccCCCCCeecC-CCCcchHH
Q psy3884 39 CHDEFKTPVQLT-CCHIFCES 58 (95)
Q Consensus 39 C~~~~~~p~~~~-CgH~fc~~ 58 (95)
|......|..=+ |+..||..
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 554444444444 77777754
No 232
>KOG3005|consensus
Probab=34.46 E-value=22 Score=23.98 Aligned_cols=44 Identities=23% Similarity=0.488 Sum_probs=30.6
Q ss_pred ccccccccCCCC--Ceec-----CCCCcchHHhHHHHhh---------CCCCCCCCCccC
Q psy3884 34 CICPICHDEFKT--PVQL-----TCCHIFCESCVTKWFD---------REQTCPLCRATL 77 (95)
Q Consensus 34 ~~C~IC~~~~~~--p~~~-----~CgH~fc~~Ci~~~~~---------~~~~CP~Cr~~~ 77 (95)
..|.+|.+.+.+ ..++ .|+-++|..|+...+. ....||.|++.+
T Consensus 183 ~~celc~~ei~e~~~~~a~c~~~~c~~~~h~~CLa~~~~~~e~g~~~p~eg~cp~C~~~~ 242 (276)
T KOG3005|consen 183 VECELCEKEILETDWSRATCPNPDCDSLNHLTCLAEELLEVEPGQLIPLEGMCPKCEKFL 242 (276)
T ss_pred hhhHHHHHHhccccceeccCCCCCCCchhhhhhhhHHHhccCCCceeccCCCCCchhcee
Confidence 489999988843 2333 4777889999987433 125799998744
No 233
>KOG4642|consensus
Probab=33.71 E-value=26 Score=23.61 Aligned_cols=65 Identities=12% Similarity=0.056 Sum_probs=50.4
Q ss_pred CCCcccccccccCCCCCeecCCCCcchHHhHHHHhhCC-CCCCCCCccCCCCccccCCcchhhhhc
Q psy3884 30 LGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDRE-QTCPLCRATLVDDPAWRDGATSYFVQI 94 (95)
Q Consensus 30 ~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~-~~CP~Cr~~~~~~~~~~~~~~~~~~q~ 94 (95)
..+.+.|.|=++.+..|+++|-|=++=..=|...+.+- .-=|+-|.++.+....++-++...|..
T Consensus 208 vpd~lcgkIt~el~~~pvi~psgIty~ra~I~Ehl~rvghfdpvtr~~Lte~q~ipN~alkevIa~ 273 (284)
T KOG4642|consen 208 VPDYLCGKITLELMREPVITPSGITYDRADIEEHLQRVGHFDPVTRWPLTEYQLIPNLALKEVIAA 273 (284)
T ss_pred ccchhhhhhhHHhhcCCccCccccchhHHHHHHHHHHhccCCchhcccCCHHhhccchHHHHHHHH
Confidence 34566778999999999999999999998888887743 334888888888877777766555443
No 234
>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=33.28 E-value=23 Score=20.42 Aligned_cols=13 Identities=23% Similarity=0.726 Sum_probs=8.6
Q ss_pred CCCCCCCccCCCC
Q psy3884 68 QTCPLCRATLVDD 80 (95)
Q Consensus 68 ~~CP~Cr~~~~~~ 80 (95)
..||.|...+...
T Consensus 27 ivCP~CG~~~~~~ 39 (108)
T PF09538_consen 27 IVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCCCccCcc
Confidence 3577777766654
No 235
>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=32.76 E-value=34 Score=22.53 Aligned_cols=21 Identities=38% Similarity=1.054 Sum_probs=13.9
Q ss_pred cccccccCCCCCeecCCCCcchHHhHHHH
Q psy3884 35 ICPICHDEFKTPVQLTCCHIFCESCVTKW 63 (95)
Q Consensus 35 ~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~ 63 (95)
.|+||. .+-.+.+|..|+..-
T Consensus 1 ~C~iC~--------~~~~~~~C~~C~~~~ 21 (302)
T PF10186_consen 1 QCPICH--------NSRRRFYCANCVNNR 21 (302)
T ss_pred CCCCCC--------CCCCCeECHHHHHHH
Confidence 488888 234455788888653
No 236
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=32.70 E-value=1.2e+02 Score=22.13 Aligned_cols=40 Identities=18% Similarity=0.410 Sum_probs=22.7
Q ss_pred CCcccccccccCCCCCe-----ecCCCCcchHHhHHHHhhCCCCCCCCCcc
Q psy3884 31 GVGCICPICHDEFKTPV-----QLTCCHIFCESCVTKWFDREQTCPLCRAT 76 (95)
Q Consensus 31 ~~~~~C~IC~~~~~~p~-----~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~ 76 (95)
.....|.+|.-.+.... -++=|..|=. +-....||.|..+
T Consensus 423 ~~~~~c~~c~~~yd~~~g~~~~~~~~gt~~~~------lp~~~~cp~c~~~ 467 (479)
T PRK05452 423 GPRMQCSVCQWIYDPAKGEPMQDVAPGTPWSE------VPDNFLCPECSLG 467 (479)
T ss_pred CCeEEECCCCeEECCCCCCcccCCCCCCChhh------CCCCCcCcCCCCc
Confidence 45568999987665421 2233332211 2245689999764
No 237
>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=32.67 E-value=40 Score=21.73 Aligned_cols=23 Identities=30% Similarity=0.823 Sum_probs=15.9
Q ss_pred CCCCeecCCC----CcchHHhHHHHhh
Q psy3884 43 FKTPVQLTCC----HIFCESCVTKWFD 65 (95)
Q Consensus 43 ~~~p~~~~Cg----H~fc~~Ci~~~~~ 65 (95)
+..|....|. |.||...+..|+.
T Consensus 151 f~~p~~~~C~~gHfHHyCs~HV~~WL~ 177 (199)
T PF12132_consen 151 FVKPSVDECEYGHFHHYCSQHVNSWLN 177 (199)
T ss_pred ccCCCCCCCCCCCcChhhHHHHHHHHH
Confidence 4445555565 5688888889986
No 238
>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=32.66 E-value=16 Score=22.25 Aligned_cols=14 Identities=36% Similarity=0.833 Sum_probs=10.5
Q ss_pred CCCCCCCCCccCCC
Q psy3884 66 REQTCPLCRATLVD 79 (95)
Q Consensus 66 ~~~~CP~Cr~~~~~ 79 (95)
..-.||.||+.++.
T Consensus 8 pei~CPhCRQ~ipA 21 (163)
T TIGR02652 8 PEIRCPHCRQNIPA 21 (163)
T ss_pred CcCcCchhhcccch
Confidence 34579999998753
No 239
>PF02132 RecR: RecR protein; InterPro: IPR023628 The bacterial protein RecR seems to play a role in a recombinational process of DNA repair []. It may act with RecF and RecO. RecR's structure consists of a N-terminal helix-hairpin-helix (HhH) motif, followed by a Cys4 zinc-finger motif, a Toprim domain and a Walker B motif []. This entry represents the C4-type zinc finger.; PDB: 1VDD_D 2V1C_B.
Probab=32.51 E-value=57 Score=15.09 Aligned_cols=17 Identities=18% Similarity=0.216 Sum_probs=9.3
Q ss_pred hHHHHHHHHHHHHhhcc
Q psy3884 3 AAKAWWKSFTKLLNNIQ 19 (95)
Q Consensus 3 ~~~~~~~~~~~~~~~~~ 19 (95)
.+..+.+++..+.....
T Consensus 2 ~~~~La~al~~~~~~i~ 18 (41)
T PF02132_consen 2 EAEQLADALKEAKENIK 18 (41)
T ss_dssp HHHHHHHHHHHHHHH-E
T ss_pred cHHHHHHHHHHHHHcCC
Confidence 45566666666655543
No 240
>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=32.24 E-value=17 Score=22.13 Aligned_cols=13 Identities=46% Similarity=0.976 Sum_probs=10.0
Q ss_pred CCCCCCCCccCCC
Q psy3884 67 EQTCPLCRATLVD 79 (95)
Q Consensus 67 ~~~CP~Cr~~~~~ 79 (95)
.-.||.||+.++.
T Consensus 6 ei~CPhCRq~ipA 18 (161)
T PF09654_consen 6 EIQCPHCRQTIPA 18 (161)
T ss_pred cCcCchhhcccch
Confidence 4579999998753
No 241
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=32.15 E-value=15 Score=15.19 Aligned_cols=10 Identities=30% Similarity=1.059 Sum_probs=6.1
Q ss_pred CCCCCCccCC
Q psy3884 69 TCPLCRATLV 78 (95)
Q Consensus 69 ~CP~Cr~~~~ 78 (95)
.||.|...|.
T Consensus 4 ~C~~CgR~F~ 13 (25)
T PF13913_consen 4 PCPICGRKFN 13 (25)
T ss_pred cCCCCCCEEC
Confidence 4777766554
No 242
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=32.01 E-value=25 Score=15.69 Aligned_cols=9 Identities=44% Similarity=1.357 Sum_probs=6.7
Q ss_pred CCCCCCCcc
Q psy3884 68 QTCPLCRAT 76 (95)
Q Consensus 68 ~~CP~Cr~~ 76 (95)
..||+|.++
T Consensus 19 ~~CP~Cg~~ 27 (34)
T cd00729 19 EKCPICGAP 27 (34)
T ss_pred CcCcCCCCc
Confidence 579999764
No 243
>COG5200 LUC7 U1 snRNP component, mediates U1 snRNP association with cap-binding complex [RNA processing and modification]
Probab=31.71 E-value=27 Score=22.84 Aligned_cols=41 Identities=10% Similarity=0.153 Sum_probs=23.7
Q ss_pred ChhHHHHHHHHHHHHhhccCCCCCcccccCCCcccccccccCCC
Q psy3884 1 MQAAKAWWKSFTKLLNNIQLGVSPTKETLLGVGCICPICHDEFK 44 (95)
Q Consensus 1 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~IC~~~~~ 44 (95)
+++++..++.+.....+....+..+..+. .-.|.||...+.
T Consensus 156 l~rl~~~rkei~~~v~sm~en~gq~thqk---lqvC~iCgayLs 196 (258)
T COG5200 156 LERLREERKEIKEAVYSMVENNGQGTHQK---LQVCGICGAYLS 196 (258)
T ss_pred HHHHHHHHHHHHHHHHHHhhCcchhhhhh---hhhhhhhhhHHH
Confidence 35667777776665554443333333333 238999987654
No 244
>PF14369 zf-RING_3: zinc-finger
Probab=31.64 E-value=22 Score=16.07 Aligned_cols=10 Identities=40% Similarity=1.145 Sum_probs=6.1
Q ss_pred CCCCCCccCC
Q psy3884 69 TCPLCRATLV 78 (95)
Q Consensus 69 ~CP~Cr~~~~ 78 (95)
.||.|...|.
T Consensus 23 ~CP~C~~gFv 32 (35)
T PF14369_consen 23 ACPRCHGGFV 32 (35)
T ss_pred CCcCCCCcEe
Confidence 3777766554
No 245
>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=31.11 E-value=16 Score=18.59 Aligned_cols=11 Identities=27% Similarity=0.815 Sum_probs=5.5
Q ss_pred CCCCCCccCCC
Q psy3884 69 TCPLCRATLVD 79 (95)
Q Consensus 69 ~CP~Cr~~~~~ 79 (95)
.||+|++++..
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 59999887754
No 246
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=30.76 E-value=30 Score=21.63 Aligned_cols=11 Identities=36% Similarity=1.075 Sum_probs=7.5
Q ss_pred CCCCCCCCCcc
Q psy3884 66 REQTCPLCRAT 76 (95)
Q Consensus 66 ~~~~CP~Cr~~ 76 (95)
....||+|..+
T Consensus 148 ~P~~CPiCga~ 158 (166)
T COG1592 148 APEVCPICGAP 158 (166)
T ss_pred CCCcCCCCCCh
Confidence 44678888654
No 247
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=30.75 E-value=13 Score=25.20 Aligned_cols=28 Identities=39% Similarity=0.814 Sum_probs=17.6
Q ss_pred CCCcchHHhHHHHhhCC----CCCCCCCccCC
Q psy3884 51 CCHIFCESCVTKWFDRE----QTCPLCRATLV 78 (95)
Q Consensus 51 CgH~fc~~Ci~~~~~~~----~~CP~Cr~~~~ 78 (95)
=.|.||..|-.+..... ..||.|+...-
T Consensus 109 ~~~RFCg~CG~~~~~~~~g~~~~C~~cg~~~f 140 (279)
T COG2816 109 RSHRFCGRCGTKTYPREGGWARVCPKCGHEHF 140 (279)
T ss_pred hhCcCCCCCCCcCccccCceeeeCCCCCCccC
Confidence 45777887776544322 46888876543
No 248
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=30.56 E-value=53 Score=17.57 Aligned_cols=29 Identities=24% Similarity=0.516 Sum_probs=20.9
Q ss_pred CcccccccccCCCCCeec-----CCCCcchHHhHHH
Q psy3884 32 VGCICPICHDEFKTPVQL-----TCCHIFCESCVTK 62 (95)
Q Consensus 32 ~~~~C~IC~~~~~~p~~~-----~CgH~fc~~Ci~~ 62 (95)
....|.+|.... ...+ .|...||..|...
T Consensus 35 ~~~~C~~C~~~~--Ga~i~C~~~~C~~~fH~~CA~~ 68 (90)
T PF13771_consen 35 RKLKCSICKKKG--GACIGCSHPGCSRSFHVPCARK 68 (90)
T ss_pred hCCCCcCCCCCC--CeEEEEeCCCCCcEEChHHHcc
Confidence 456999999762 2333 5778899999864
No 249
>KOG2071|consensus
Probab=30.50 E-value=24 Score=26.36 Aligned_cols=33 Identities=30% Similarity=0.673 Sum_probs=23.9
Q ss_pred CcccccccccCCCC-------------CeecCCCCcchHHhHHHHh
Q psy3884 32 VGCICPICHDEFKT-------------PVQLTCCHIFCESCVTKWF 64 (95)
Q Consensus 32 ~~~~C~IC~~~~~~-------------p~~~~CgH~fc~~Ci~~~~ 64 (95)
....|+||.+.|.. .+-+.=|-.||..|+..-.
T Consensus 512 ~~~~C~IC~EkFe~v~d~e~~~Wm~kdaV~le~G~ifH~~Cl~e~~ 557 (579)
T KOG2071|consen 512 RQASCPICQEKFEVVFDQEEDLWMYKDAVYLEFGRIFHSKCLSEKR 557 (579)
T ss_pred cccCCcccccccceeecchhhheeecceeeeccCceeeccccchHH
Confidence 45699999998764 2333458899999987543
No 250
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=30.06 E-value=28 Score=16.04 Aligned_cols=12 Identities=33% Similarity=0.736 Sum_probs=8.2
Q ss_pred CCCCCCccCCCC
Q psy3884 69 TCPLCRATLVDD 80 (95)
Q Consensus 69 ~CP~Cr~~~~~~ 80 (95)
.||.|+..+...
T Consensus 1 ~CP~C~~~l~~~ 12 (41)
T PF13453_consen 1 KCPRCGTELEPV 12 (41)
T ss_pred CcCCCCcccceE
Confidence 489998765533
No 251
>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=29.88 E-value=28 Score=20.27 Aligned_cols=11 Identities=36% Similarity=1.062 Sum_probs=8.3
Q ss_pred ecCCCCcchHH
Q psy3884 48 QLTCCHIFCES 58 (95)
Q Consensus 48 ~~~CgH~fc~~ 58 (95)
.-.|||.||..
T Consensus 26 kc~CGh~f~d~ 36 (112)
T PF08882_consen 26 KCDCGHEFCDA 36 (112)
T ss_pred eccCCCeecCh
Confidence 44799999864
No 252
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=29.82 E-value=31 Score=19.85 Aligned_cols=25 Identities=32% Similarity=0.578 Sum_probs=13.3
Q ss_pred ccccccccCCCCCeecCCCCcchHHhH
Q psy3884 34 CICPICHDEFKTPVQLTCCHIFCESCV 60 (95)
Q Consensus 34 ~~C~IC~~~~~~p~~~~CgH~fc~~Ci 60 (95)
..|+-|.... -+-.+|+|.+|..|-
T Consensus 43 ~~C~~Cg~~~--~~~~SCk~R~CP~C~ 67 (111)
T PF14319_consen 43 YRCEDCGHEK--IVYNSCKNRHCPSCQ 67 (111)
T ss_pred eecCCCCceE--EecCcccCcCCCCCC
Confidence 3555555432 123367776666665
No 253
>KOG1356|consensus
Probab=29.54 E-value=38 Score=26.59 Aligned_cols=34 Identities=24% Similarity=0.638 Sum_probs=26.8
Q ss_pred CCcccccccccCCCCC--eecCCCCcchHHhHHHHh
Q psy3884 31 GVGCICPICHDEFKTP--VQLTCCHIFCESCVTKWF 64 (95)
Q Consensus 31 ~~~~~C~IC~~~~~~p--~~~~CgH~fc~~Ci~~~~ 64 (95)
.....|..|.....+- +-..||+.+|..|+..|.
T Consensus 227 g~~~mC~~C~~tlfn~hw~C~~C~~~~Cl~C~r~~~ 262 (889)
T KOG1356|consen 227 GIREMCDRCETTLFNIHWRCPRCGFGVCLDCYRKWY 262 (889)
T ss_pred CcchhhhhhcccccceeEEccccCCeeeecchhhcc
Confidence 3455899999887763 344799999999999994
No 254
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=29.38 E-value=42 Score=15.81 Aligned_cols=17 Identities=29% Similarity=0.833 Sum_probs=11.4
Q ss_pred HhhCCCCCCCCCccCCC
Q psy3884 63 WFDREQTCPLCRATLVD 79 (95)
Q Consensus 63 ~~~~~~~CP~Cr~~~~~ 79 (95)
|..-...||.|..++..
T Consensus 13 ~~ML~~~Cp~C~~PL~~ 29 (41)
T PF06677_consen 13 WTMLDEHCPDCGTPLMR 29 (41)
T ss_pred HhHhcCccCCCCCeeEE
Confidence 44455789999777654
No 255
>KOG0006|consensus
Probab=29.23 E-value=50 Score=23.13 Aligned_cols=32 Identities=22% Similarity=0.581 Sum_probs=23.3
Q ss_pred CcccccccccCCCCCeecCCC--CcchHHhHHHH
Q psy3884 32 VGCICPICHDEFKTPVQLTCC--HIFCESCVTKW 63 (95)
Q Consensus 32 ~~~~C~IC~~~~~~p~~~~Cg--H~fc~~Ci~~~ 63 (95)
....|-.|-+.-..-.+++|. |+-|..|..-+
T Consensus 220 ~ni~C~~Ctdv~~~vlvf~Cns~HvtC~dCFr~y 253 (446)
T KOG0006|consen 220 RNITCITCTDVRSPVLVFQCNSRHVTCLDCFRLY 253 (446)
T ss_pred ccceeEEecCCccceEEEecCCceeehHHhhhhH
Confidence 345788888765544567898 99999998744
No 256
>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=29.02 E-value=27 Score=17.75 Aligned_cols=23 Identities=26% Similarity=0.563 Sum_probs=12.3
Q ss_pred ccccccC-CCCCeecCCCCcchHH
Q psy3884 36 CPICHDE-FKTPVQLTCCHIFCES 58 (95)
Q Consensus 36 C~IC~~~-~~~p~~~~CgH~fc~~ 58 (95)
|..|... -..-+-+.||+.+|..
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 4556654 1112456899998875
No 257
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=28.86 E-value=17 Score=20.40 Aligned_cols=28 Identities=21% Similarity=0.745 Sum_probs=16.3
Q ss_pred CCCCcchHHhHHHHhhCCCCCCCCCccCCCCc
Q psy3884 50 TCCHIFCESCVTKWFDREQTCPLCRATLVDDP 81 (95)
Q Consensus 50 ~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~ 81 (95)
.||-.|-.. -++..+.||.|+..--+.+
T Consensus 63 kCGfef~~~----~ik~pSRCP~CKSE~Ie~p 90 (97)
T COG3357 63 KCGFEFRDD----KIKKPSRCPKCKSEWIEEP 90 (97)
T ss_pred ccCcccccc----ccCCcccCCcchhhcccCC
Confidence 466554431 1234578999987755444
No 258
>COG5242 TFB4 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB4 [Transcription / DNA replication, recombination, and repair]
Probab=28.64 E-value=23 Score=23.48 Aligned_cols=14 Identities=36% Similarity=1.039 Sum_probs=7.9
Q ss_pred cccccccccCCCCC
Q psy3884 33 GCICPICHDEFKTP 46 (95)
Q Consensus 33 ~~~C~IC~~~~~~p 46 (95)
.+.|+||+..|-.|
T Consensus 260 GfvCsVCLsvfc~p 273 (296)
T COG5242 260 GFVCSVCLSVFCRP 273 (296)
T ss_pred eeehhhhheeecCC
Confidence 45666666665433
No 259
>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=27.82 E-value=40 Score=16.59 Aligned_cols=11 Identities=36% Similarity=0.981 Sum_probs=7.5
Q ss_pred CCCCCCCCCcc
Q psy3884 66 REQTCPLCRAT 76 (95)
Q Consensus 66 ~~~~CP~Cr~~ 76 (95)
....||+|..+
T Consensus 33 ~~w~CP~C~a~ 43 (50)
T cd00730 33 DDWVCPVCGAG 43 (50)
T ss_pred CCCCCCCCCCc
Confidence 45688888653
No 260
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=27.27 E-value=1e+02 Score=17.77 Aligned_cols=10 Identities=30% Similarity=0.810 Sum_probs=7.5
Q ss_pred CCCCCCCCcc
Q psy3884 67 EQTCPLCRAT 76 (95)
Q Consensus 67 ~~~CP~Cr~~ 76 (95)
...||.|...
T Consensus 86 ~~~CP~Cgs~ 95 (115)
T TIGR00100 86 LYRCPKCHGI 95 (115)
T ss_pred CccCcCCcCC
Confidence 4579999764
No 261
>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=27.21 E-value=56 Score=13.80 Aligned_cols=25 Identities=20% Similarity=0.397 Sum_probs=5.8
Q ss_pred cccccccCCCCCe---ecCCCCcchHHh
Q psy3884 35 ICPICHDEFKTPV---QLTCCHIFCESC 59 (95)
Q Consensus 35 ~C~IC~~~~~~p~---~~~CgH~fc~~C 59 (95)
.|.+|........ -..|.-.+|..|
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~Cdf~lH~~C 29 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSECDFDLHEEC 29 (30)
T ss_dssp --TTTS----S--EEE-TTT-----HHH
T ss_pred cCCcCCCcCCCCceEECccCCCccChhc
Confidence 4666666555411 124555555555
No 262
>PF14577 SEO_C: Sieve element occlusion C-terminus
Probab=27.19 E-value=41 Score=22.26 Aligned_cols=28 Identities=25% Similarity=0.635 Sum_probs=21.0
Q ss_pred ccccCCCcccccccccCCCCCeecCCCC
Q psy3884 26 KETLLGVGCICPICHDEFKTPVQLTCCH 53 (95)
Q Consensus 26 ~~~~~~~~~~C~IC~~~~~~p~~~~CgH 53 (95)
......+...||-|...++.-+...|-|
T Consensus 207 ~~g~ipe~i~CpeC~R~MEk~v~YkCCh 234 (235)
T PF14577_consen 207 SAGRIPETIVCPECGRPMEKFVMYKCCH 234 (235)
T ss_pred cccCCCceeECCCCCCchhhceeeeccC
Confidence 4455567788999988888777777876
No 263
>COG4098 comFA Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [DNA replication, recombination, and repair]
Probab=26.54 E-value=27 Score=24.81 Aligned_cols=31 Identities=19% Similarity=0.605 Sum_probs=24.5
Q ss_pred CCcccccccc-cCCCCCeecCCCCcchHHhHH
Q psy3884 31 GVGCICPICH-DEFKTPVQLTCCHIFCESCVT 61 (95)
Q Consensus 31 ~~~~~C~IC~-~~~~~p~~~~CgH~fc~~Ci~ 61 (95)
.....|.=|. .....-..+|||-.||..|+.
T Consensus 37 ~gk~~C~RC~~~~~~~~~~lp~~~~YCr~Cl~ 68 (441)
T COG4098 37 NGKYRCNRCGNTHIELFAKLPCGCLYCRNCLM 68 (441)
T ss_pred cCcEEehhcCCcchhhhcccccceEeehhhhh
Confidence 3456898888 555566789999999999985
No 264
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=26.02 E-value=34 Score=20.34 Aligned_cols=37 Identities=16% Similarity=0.343 Sum_probs=22.1
Q ss_pred cccccccccCCC-CCeecCCCCcchHHhHHHHhhCCCCCCCCCccCCCCc
Q psy3884 33 GCICPICHDEFK-TPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDP 81 (95)
Q Consensus 33 ~~~C~IC~~~~~-~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~ 81 (95)
...||.|..... .--....| .+...|+.|+..+....
T Consensus 30 ~~~cP~C~s~~~~k~g~~~~~------------~qRyrC~~C~~tf~~~~ 67 (129)
T COG3677 30 KVNCPRCKSSNVVKIGGIRRG------------HQRYKCKSCGSTFTVET 67 (129)
T ss_pred cCcCCCCCccceeeECCcccc------------ccccccCCcCcceeeec
Confidence 458888887651 10111233 24578999988877553
No 265
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=25.50 E-value=22 Score=20.67 Aligned_cols=8 Identities=25% Similarity=0.924 Sum_probs=6.4
Q ss_pred CCCCCCcc
Q psy3884 69 TCPLCRAT 76 (95)
Q Consensus 69 ~CP~Cr~~ 76 (95)
.||.|...
T Consensus 90 ~CP~Cgs~ 97 (117)
T PRK00564 90 VCEKCHSK 97 (117)
T ss_pred cCcCCCCC
Confidence 49999765
No 266
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.22 E-value=25 Score=17.33 Aligned_cols=11 Identities=27% Similarity=1.068 Sum_probs=7.5
Q ss_pred CCCCCCCccCC
Q psy3884 68 QTCPLCRATLV 78 (95)
Q Consensus 68 ~~CP~Cr~~~~ 78 (95)
+.||+|..+|.
T Consensus 13 KICpvCqRPFs 23 (54)
T COG4338 13 KICPVCQRPFS 23 (54)
T ss_pred hhhhhhcCchH
Confidence 46788877664
No 267
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=24.94 E-value=41 Score=21.68 Aligned_cols=50 Identities=28% Similarity=0.535 Sum_probs=27.4
Q ss_pred CcccccccccCCCCCeecCCC-C------cchHH--hHHHHhhCCCCCCCCCccCCCCc
Q psy3884 32 VGCICPICHDEFKTPVQLTCC-H------IFCES--CVTKWFDREQTCPLCRATLVDDP 81 (95)
Q Consensus 32 ~~~~C~IC~~~~~~p~~~~Cg-H------~fc~~--Ci~~~~~~~~~CP~Cr~~~~~~~ 81 (95)
....||+|...|....+.+=+ . -||.. =+.+.+-.-..||.|.-...+.+
T Consensus 4 k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~~ 62 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEED 62 (214)
T ss_pred CceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCcccccc
Confidence 456999999999865333211 0 01111 02222222358999988776554
No 268
>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=24.82 E-value=28 Score=25.42 Aligned_cols=10 Identities=40% Similarity=1.145 Sum_probs=6.2
Q ss_pred CCCCCCccCC
Q psy3884 69 TCPLCRATLV 78 (95)
Q Consensus 69 ~CP~Cr~~~~ 78 (95)
.||.|..++.
T Consensus 54 ~CP~C~~~L~ 63 (483)
T PF05502_consen 54 DCPICFSPLS 63 (483)
T ss_pred cCCCCCCcce
Confidence 4677766554
No 269
>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=24.79 E-value=24 Score=25.15 Aligned_cols=48 Identities=25% Similarity=0.650 Sum_probs=0.0
Q ss_pred cccccccccCCC-----------------CC--eecCCCCcchHHhHHHHhhC---------CCCCCCCCccCCCC
Q psy3884 33 GCICPICHDEFK-----------------TP--VQLTCCHIFCESCVTKWFDR---------EQTCPLCRATLVDD 80 (95)
Q Consensus 33 ~~~C~IC~~~~~-----------------~p--~~~~CgH~fc~~Ci~~~~~~---------~~~CP~Cr~~~~~~ 80 (95)
.-.||+|...-. .| +..||||.--.....-|.+- +..||.|-.++..+
T Consensus 328 ~r~CPlCr~~g~~V~L~mG~E~afyvD~~~pthaF~PCGHv~SekTa~yWs~i~lPhGt~~f~a~CPFCa~~L~g~ 403 (416)
T PF04710_consen 328 SRTCPLCRQVGPYVPLWMGCEPAFYVDSGPPTHAFNPCGHVCSEKTAKYWSQIPLPHGTHAFHAACPFCATPLDGE 403 (416)
T ss_dssp ----------------------------------------------------------------------------
T ss_pred cccCCCccccCCceeEeeccccceeecCCCCceeecccccccchhhhhhhhcCCCCCCcccccccCCcccCcccCC
Confidence 559999996421 12 34489998766677667651 24799998888754
No 270
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=24.68 E-value=37 Score=17.53 Aligned_cols=11 Identities=45% Similarity=1.274 Sum_probs=8.5
Q ss_pred CCCCCCCccCC
Q psy3884 68 QTCPLCRATLV 78 (95)
Q Consensus 68 ~~CP~Cr~~~~ 78 (95)
-.||.|+.++.
T Consensus 9 LaCP~~kg~L~ 19 (60)
T COG2835 9 LACPVCKGPLV 19 (60)
T ss_pred eeccCcCCcce
Confidence 36999998864
No 271
>KOG2593|consensus
Probab=24.61 E-value=88 Score=22.70 Aligned_cols=41 Identities=24% Similarity=0.493 Sum_probs=24.3
Q ss_pred CCcccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCccCCCC
Q psy3884 31 GVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD 80 (95)
Q Consensus 31 ~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~ 80 (95)
...+.||+|...|..= =..++.......+.|-.|..++...
T Consensus 126 ~~~Y~Cp~C~kkyt~L---------ea~~L~~~~~~~F~C~~C~gelveD 166 (436)
T KOG2593|consen 126 VAGYVCPNCQKKYTSL---------EALQLLDNETGEFHCENCGGELVED 166 (436)
T ss_pred cccccCCccccchhhh---------HHHHhhcccCceEEEecCCCchhcc
Confidence 4678999999987631 0112222222346777787776644
No 272
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=24.39 E-value=19 Score=14.26 Aligned_cols=10 Identities=40% Similarity=1.152 Sum_probs=4.9
Q ss_pred cccccccCCC
Q psy3884 35 ICPICHDEFK 44 (95)
Q Consensus 35 ~C~IC~~~~~ 44 (95)
.|.||...+.
T Consensus 2 ~C~~C~~~f~ 11 (25)
T PF12874_consen 2 YCDICNKSFS 11 (25)
T ss_dssp EETTTTEEES
T ss_pred CCCCCCCCcC
Confidence 3555554444
No 273
>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=24.24 E-value=38 Score=17.01 Aligned_cols=13 Identities=31% Similarity=0.636 Sum_probs=8.7
Q ss_pred CCCCCCCccCCCC
Q psy3884 68 QTCPLCRATLVDD 80 (95)
Q Consensus 68 ~~CP~Cr~~~~~~ 80 (95)
+.||.|.+.+.-.
T Consensus 3 ~~CP~CG~~iev~ 15 (54)
T TIGR01206 3 FECPDCGAEIELE 15 (54)
T ss_pred cCCCCCCCEEecC
Confidence 4688887776543
No 274
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=24.14 E-value=40 Score=26.64 Aligned_cols=31 Identities=29% Similarity=0.592 Sum_probs=22.7
Q ss_pred ccccccccCCCCC---e------ecCCCCcchHHhHHHHh
Q psy3884 34 CICPICHDEFKTP---V------QLTCCHIFCESCVTKWF 64 (95)
Q Consensus 34 ~~C~IC~~~~~~p---~------~~~CgH~fc~~Ci~~~~ 64 (95)
..|..|...|..- . --.||.+||..|-....
T Consensus 461 dtC~~C~kkFfSlsK~L~~RKHHCRkCGrVFC~~CSSnRs 500 (1374)
T PTZ00303 461 DSCPSCGRAFISLSRPLGTRAHHCRSCGIRLCVFCITKRA 500 (1374)
T ss_pred CcccCcCCcccccccccccccccccCCccccCccccCCcc
Confidence 4699999998531 1 22699999999986543
No 275
>KOG2186|consensus
Probab=24.09 E-value=38 Score=22.75 Aligned_cols=13 Identities=31% Similarity=0.930 Sum_probs=9.1
Q ss_pred ccccccccCCCCC
Q psy3884 34 CICPICHDEFKTP 46 (95)
Q Consensus 34 ~~C~IC~~~~~~p 46 (95)
+.|-+|.+....|
T Consensus 4 FtCnvCgEsvKKp 16 (276)
T KOG2186|consen 4 FTCNVCGESVKKP 16 (276)
T ss_pred Eehhhhhhhcccc
Confidence 5677777776655
No 276
>KOG1244|consensus
Probab=24.05 E-value=13 Score=25.31 Aligned_cols=42 Identities=21% Similarity=0.449 Sum_probs=25.2
Q ss_pred cccccccCCCCCeec---CCCCcchHHhHHHHhh----CCCCCCCCCcc
Q psy3884 35 ICPICHDEFKTPVQL---TCCHIFCESCVTKWFD----REQTCPLCRAT 76 (95)
Q Consensus 35 ~C~IC~~~~~~p~~~---~CgH~fc~~Ci~~~~~----~~~~CP~Cr~~ 76 (95)
.|.||...-.+...+ .|...||.+|+.+-+. .+.+|-+|-..
T Consensus 283 ~csicgtsenddqllfcddcdrgyhmyclsppm~eppegswsc~KOG~~ 331 (336)
T KOG1244|consen 283 YCSICGTSENDDQLLFCDDCDRGYHMYCLSPPMVEPPEGSWSCHLCLEE 331 (336)
T ss_pred eeccccCcCCCceeEeecccCCceeeEecCCCcCCCCCCchhHHHHHHH
Confidence 566776654444444 5777788888766443 33467776443
No 277
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.40 E-value=44 Score=17.51 Aligned_cols=12 Identities=33% Similarity=0.739 Sum_probs=9.5
Q ss_pred CCCCCCCccCCC
Q psy3884 68 QTCPLCRATLVD 79 (95)
Q Consensus 68 ~~CP~Cr~~~~~ 79 (95)
..||.|.+++.-
T Consensus 8 v~CP~Cgkpv~w 19 (65)
T COG3024 8 VPCPTCGKPVVW 19 (65)
T ss_pred ccCCCCCCcccc
Confidence 479999888764
No 278
>PRK02935 hypothetical protein; Provisional
Probab=23.17 E-value=67 Score=18.61 Aligned_cols=22 Identities=23% Similarity=0.456 Sum_probs=15.7
Q ss_pred hhCCCCCCCCCccCCCCccccC
Q psy3884 64 FDREQTCPLCRATLVDDPAWRD 85 (95)
Q Consensus 64 ~~~~~~CP~Cr~~~~~~~~~~~ 85 (95)
+.+...|..|++++..++.+.-
T Consensus 83 LGrvD~CM~C~~PLTLd~~leg 104 (110)
T PRK02935 83 LGRVDACMHCNQPLTLDRSLEG 104 (110)
T ss_pred ccceeecCcCCCcCCcCccccc
Confidence 3455689999999987665443
No 279
>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=22.91 E-value=67 Score=14.47 Aligned_cols=29 Identities=21% Similarity=0.418 Sum_probs=16.4
Q ss_pred ccccccccCCCCCeecCCCCcchHHhHHH
Q psy3884 34 CICPICHDEFKTPVQLTCCHIFCESCVTK 62 (95)
Q Consensus 34 ~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~ 62 (95)
..|..+.+....-.-..|+-.+|..|...
T Consensus 4 ~~C~~H~~~~~~~~C~~C~~~~C~~C~~~ 32 (42)
T PF00643_consen 4 PKCPEHPEEPLSLFCEDCNEPLCSECTVS 32 (42)
T ss_dssp SB-SSTTTSBEEEEETTTTEEEEHHHHHT
T ss_pred ccCccCCccceEEEecCCCCccCccCCCC
Confidence 35666655322223337888888888753
No 280
>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=22.79 E-value=27 Score=14.07 Aligned_cols=11 Identities=27% Similarity=0.742 Sum_probs=6.2
Q ss_pred cccccccCCCC
Q psy3884 35 ICPICHDEFKT 45 (95)
Q Consensus 35 ~C~IC~~~~~~ 45 (95)
.|.+|...|..
T Consensus 3 ~C~~C~~~F~~ 13 (27)
T PF13912_consen 3 ECDECGKTFSS 13 (27)
T ss_dssp EETTTTEEESS
T ss_pred CCCccCCccCC
Confidence 56666655543
No 281
>cd04718 BAH_plant_2 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=22.75 E-value=26 Score=21.45 Aligned_cols=24 Identities=21% Similarity=0.574 Sum_probs=14.4
Q ss_pred chHHhHHHHhh----CCCCCCCCCccCC
Q psy3884 55 FCESCVTKWFD----REQTCPLCRATLV 78 (95)
Q Consensus 55 fc~~Ci~~~~~----~~~~CP~Cr~~~~ 78 (95)
||..|+.+-+. ..-.||.|...-.
T Consensus 2 ~H~~CL~Ppl~~~P~g~W~Cp~C~~~~~ 29 (148)
T cd04718 2 FHLCCLRPPLKEVPEGDWICPFCEVEKS 29 (148)
T ss_pred cccccCCCCCCCCCCCCcCCCCCcCCCC
Confidence 56667665554 2347888876543
No 282
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=22.46 E-value=1.2e+02 Score=14.92 Aligned_cols=28 Identities=21% Similarity=0.618 Sum_probs=17.5
Q ss_pred cccccccCCCC--CeecCCCCcchHHhHHHH
Q psy3884 35 ICPICHDEFKT--PVQLTCCHIFCESCVTKW 63 (95)
Q Consensus 35 ~C~IC~~~~~~--p~~~~CgH~fc~~Ci~~~ 63 (95)
.|+||...+.- ...+.=| ..|.+|+...
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 37888876432 2445555 5788888664
No 283
>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=22.38 E-value=1.3e+02 Score=18.51 Aligned_cols=11 Identities=45% Similarity=1.078 Sum_probs=8.1
Q ss_pred CCCCCCCccCC
Q psy3884 68 QTCPLCRATLV 78 (95)
Q Consensus 68 ~~CP~Cr~~~~ 78 (95)
-.||+|...-.
T Consensus 33 v~CP~Cgs~~V 43 (148)
T PF06676_consen 33 VSCPVCGSTEV 43 (148)
T ss_pred ccCCCCCCCeE
Confidence 48999977543
No 284
>PRK00420 hypothetical protein; Validated
Probab=22.32 E-value=78 Score=18.44 Aligned_cols=11 Identities=18% Similarity=0.600 Sum_probs=7.1
Q ss_pred CCCCCCCccCC
Q psy3884 68 QTCPLCRATLV 78 (95)
Q Consensus 68 ~~CP~Cr~~~~ 78 (95)
..||.|...+.
T Consensus 41 ~~Cp~Cg~~~~ 51 (112)
T PRK00420 41 VVCPVHGKVYI 51 (112)
T ss_pred eECCCCCCeee
Confidence 46787766544
No 285
>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=22.07 E-value=40 Score=13.81 Aligned_cols=11 Identities=36% Similarity=0.969 Sum_probs=7.1
Q ss_pred cccccccccCC
Q psy3884 33 GCICPICHDEF 43 (95)
Q Consensus 33 ~~~C~IC~~~~ 43 (95)
.+.|++|...|
T Consensus 14 ~~~C~~C~k~F 24 (26)
T PF13465_consen 14 PYKCPYCGKSF 24 (26)
T ss_dssp SEEESSSSEEE
T ss_pred CCCCCCCcCee
Confidence 35777776654
No 286
>PRK11827 hypothetical protein; Provisional
Probab=21.82 E-value=30 Score=17.80 Aligned_cols=13 Identities=31% Similarity=0.715 Sum_probs=8.2
Q ss_pred CCCCCCCCccCCC
Q psy3884 67 EQTCPLCRATLVD 79 (95)
Q Consensus 67 ~~~CP~Cr~~~~~ 79 (95)
--.||.|+.++..
T Consensus 8 ILaCP~ckg~L~~ 20 (60)
T PRK11827 8 IIACPVCNGKLWY 20 (60)
T ss_pred heECCCCCCcCeE
Confidence 3457777776653
No 287
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=21.65 E-value=33 Score=20.65 Aligned_cols=15 Identities=40% Similarity=0.798 Sum_probs=11.7
Q ss_pred CCCCCCCCccCCCCc
Q psy3884 67 EQTCPLCRATLVDDP 81 (95)
Q Consensus 67 ~~~CP~Cr~~~~~~~ 81 (95)
.+.||.|...+...+
T Consensus 123 ~f~Cp~Cg~~l~~~d 137 (147)
T smart00531 123 TFTCPRCGEELEEDD 137 (147)
T ss_pred cEECCCCCCEEEEcC
Confidence 378999999887543
No 288
>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=21.47 E-value=54 Score=15.92 Aligned_cols=15 Identities=27% Similarity=0.647 Sum_probs=7.9
Q ss_pred ccCCCcccccccccC
Q psy3884 28 TLLGVGCICPICHDE 42 (95)
Q Consensus 28 ~~~~~~~~C~IC~~~ 42 (95)
+.+.+...||+|...
T Consensus 29 ~~Lp~~w~CP~C~a~ 43 (47)
T PF00301_consen 29 EDLPDDWVCPVCGAP 43 (47)
T ss_dssp GGS-TT-B-TTTSSB
T ss_pred HHCCCCCcCcCCCCc
Confidence 345667789988653
No 289
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=21.42 E-value=46 Score=16.56 Aligned_cols=10 Identities=30% Similarity=1.019 Sum_probs=7.1
Q ss_pred CCCCCCccCC
Q psy3884 69 TCPLCRATLV 78 (95)
Q Consensus 69 ~CP~Cr~~~~ 78 (95)
.||.|...+.
T Consensus 2 ~CPyCge~~~ 11 (52)
T PF14255_consen 2 QCPYCGEPIE 11 (52)
T ss_pred CCCCCCCeeE
Confidence 4888877654
No 290
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=21.06 E-value=76 Score=20.05 Aligned_cols=18 Identities=28% Similarity=0.556 Sum_probs=13.6
Q ss_pred hhCCCCCCCCCccCCCCc
Q psy3884 64 FDREQTCPLCRATLVDDP 81 (95)
Q Consensus 64 ~~~~~~CP~Cr~~~~~~~ 81 (95)
....+.||.|...+...+
T Consensus 129 ~~~~F~Cp~Cg~~L~~~d 146 (176)
T COG1675 129 MELGFTCPKCGEDLEEYD 146 (176)
T ss_pred HHhCCCCCCCCchhhhcc
Confidence 345689999999887554
No 291
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=20.92 E-value=24 Score=23.85 Aligned_cols=9 Identities=22% Similarity=0.896 Sum_probs=5.2
Q ss_pred CCCCCCCcc
Q psy3884 68 QTCPLCRAT 76 (95)
Q Consensus 68 ~~CP~Cr~~ 76 (95)
..||.|+..
T Consensus 270 ~~C~~Cgt~ 278 (279)
T TIGR00627 270 PICKTCKTA 278 (279)
T ss_pred CCCCCCCCC
Confidence 456666543
No 292
>KOG0314|consensus
Probab=20.65 E-value=2.2e+02 Score=20.84 Aligned_cols=35 Identities=14% Similarity=-0.147 Sum_probs=26.0
Q ss_pred cccCCCcccccccccCCCCCeecCCCC-cchHHhHH
Q psy3884 27 ETLLGVGCICPICHDEFKTPVQLTCCH-IFCESCVT 61 (95)
Q Consensus 27 ~~~~~~~~~C~IC~~~~~~p~~~~CgH-~fc~~Ci~ 61 (95)
.....+...|+++......++..+++| ..+..++.
T Consensus 300 ~~~~~~~~~~p~~k~v~~~~~~~s~~~~~~~~~~~~ 335 (448)
T KOG0314|consen 300 RTQDPESLRCPPPKALSPTTSVASPGEKKPLPSNNN 335 (448)
T ss_pred ccCCCccccCCcccccCCcccccCCCCcccCCcCCC
Confidence 334557789999999999998887776 45665554
No 293
>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=20.51 E-value=76 Score=16.15 Aligned_cols=27 Identities=33% Similarity=0.826 Sum_probs=18.7
Q ss_pred eecCCCCcchHHhHHHHhhC-CCCCCCCCccCCC
Q psy3884 47 VQLTCCHIFCESCVTKWFDR-EQTCPLCRATLVD 79 (95)
Q Consensus 47 ~~~~CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~~~ 79 (95)
--+.||-+.|.. +. ...||.|..++..
T Consensus 20 NCl~CGkIiC~~------Eg~~~pC~fCg~~l~~ 47 (57)
T PF06221_consen 20 NCLNCGKIICEQ------EGPLGPCPFCGTPLLS 47 (57)
T ss_pred cccccChhhccc------ccCcCcCCCCCCcccC
Confidence 345788877763 34 5789999877654
No 294
>PF12907 zf-met2: Zinc-binding
Probab=20.49 E-value=20 Score=16.93 Aligned_cols=7 Identities=57% Similarity=1.516 Sum_probs=3.5
Q ss_pred ccccccc
Q psy3884 35 ICPICHD 41 (95)
Q Consensus 35 ~C~IC~~ 41 (95)
.|.||+.
T Consensus 3 ~C~iC~q 9 (40)
T PF12907_consen 3 ICKICRQ 9 (40)
T ss_pred CcHHhhH
Confidence 4555553
No 295
>PF05715 zf-piccolo: Piccolo Zn-finger; InterPro: IPR008899 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 (predicted) zinc finger is found in the bassoon and piccolo proteins, both of which are components of the presynaptic cytoskeletal matrix (PCM) assembled at the active zone of neurotransmitter release, where Piccolo plays a role in the trafficking of synaptic vesicles (SVs) [, , ]. The Piccolo zinc fingers were found to interact with the dual prenylated rab3A and VAMP2/Synaptobrevin II receptor PRA1. There are eight conserved cysteines in Piccolo-type zinc fingers, suggesting that they coordinates two zinc ligands. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding, 0045202 synapse
Probab=20.22 E-value=86 Score=16.19 Aligned_cols=27 Identities=19% Similarity=0.543 Sum_probs=14.2
Q ss_pred ccccccccCCCCCeecCCCCcchHHhH
Q psy3884 34 CICPICHDEFKTPVQLTCCHIFCESCV 60 (95)
Q Consensus 34 ~~C~IC~~~~~~p~~~~CgH~fc~~Ci 60 (95)
..||+|.........-+=.+.-|..|-
T Consensus 3 ~~CPlCkt~~n~gsk~~pNyntCT~Ck 29 (61)
T PF05715_consen 3 SLCPLCKTTLNVGSKDPPNYNTCTECK 29 (61)
T ss_pred ccCCcccchhhcCCCCCCCccHHHHHh
Confidence 368888876533222233344455553
No 296
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=20.21 E-value=47 Score=15.65 Aligned_cols=14 Identities=21% Similarity=0.603 Sum_probs=9.9
Q ss_pred CCCCCCCCccCCCC
Q psy3884 67 EQTCPLCRATLVDD 80 (95)
Q Consensus 67 ~~~CP~Cr~~~~~~ 80 (95)
...||.|..++...
T Consensus 21 ~~~Cp~CG~~~~~~ 34 (46)
T PRK00398 21 GVRCPYCGYRILFK 34 (46)
T ss_pred ceECCCCCCeEEEc
Confidence 35799998876533
Done!