Query psy10659
Match_columns 140
No_of_seqs 189 out of 1584
Neff 9.2
Searched_HMMs 46136
Date Fri Aug 16 15:19:18 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10659.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/10659hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00504 Ubox Modified RING 99.7 1.3E-16 2.8E-21 92.5 4.7 62 21-83 1-62 (63)
2 TIGR00599 rad18 DNA repair pro 99.6 5.6E-16 1.2E-20 117.9 5.6 75 16-91 21-95 (397)
3 PF15227 zf-C3HC4_4: zinc fing 99.6 3.1E-16 6.7E-21 83.5 2.6 38 24-61 1-42 (42)
4 PF04564 U-box: U-box domain; 99.6 1.1E-15 2.3E-20 91.2 4.2 70 19-89 2-72 (73)
5 KOG0287|consensus 99.6 8.5E-16 1.8E-20 112.8 2.0 72 17-89 19-90 (442)
6 PLN03208 E3 ubiquitin-protein 99.5 3.1E-15 6.8E-20 103.1 3.6 53 17-69 14-82 (193)
7 PF13923 zf-C3HC4_2: Zinc fing 99.5 9.5E-15 2.1E-19 76.7 2.3 38 24-61 1-39 (39)
8 COG5432 RAD18 RING-finger-cont 99.5 2.3E-14 4.9E-19 103.5 3.1 73 17-90 21-93 (391)
9 PF14835 zf-RING_6: zf-RING of 99.4 1.2E-14 2.7E-19 82.5 0.3 60 19-81 5-65 (65)
10 PF13920 zf-C3HC4_3: Zinc fing 99.4 4.7E-14 1E-18 78.1 2.4 47 20-66 1-48 (50)
11 PF13639 zf-RING_2: Ring finge 99.4 3.1E-14 6.7E-19 76.7 1.3 40 23-62 2-44 (44)
12 KOG0320|consensus 99.4 8.3E-14 1.8E-18 94.1 3.4 51 19-69 129-181 (187)
13 KOG0823|consensus 99.4 6.3E-14 1.4E-18 98.4 2.6 52 18-69 44-98 (230)
14 KOG0317|consensus 99.4 9.8E-14 2.1E-18 100.1 3.1 52 18-69 236-287 (293)
15 PHA02929 N1R/p28-like protein; 99.4 2.6E-13 5.7E-18 97.1 3.8 50 18-67 171-228 (238)
16 PF00097 zf-C3HC4: Zinc finger 99.4 4.3E-13 9.3E-18 71.1 2.4 38 24-61 1-41 (41)
17 PF13445 zf-RING_UBOX: RING-ty 99.3 3E-12 6.5E-17 68.1 2.3 35 24-59 1-43 (43)
18 cd00162 RING RING-finger (Real 99.3 6.1E-12 1.3E-16 67.3 3.4 42 23-64 1-44 (45)
19 PF14634 zf-RING_5: zinc-RING 99.2 5.6E-12 1.2E-16 67.8 2.7 41 23-63 1-44 (44)
20 PF12678 zf-rbx1: RING-H2 zinc 99.2 1.3E-11 2.9E-16 73.4 3.1 40 23-62 21-73 (73)
21 smart00184 RING Ring finger. E 99.2 2.3E-11 4.9E-16 63.0 2.8 38 24-61 1-39 (39)
22 TIGR00570 cdk7 CDK-activating 99.2 1.1E-10 2.4E-15 86.0 7.3 50 20-69 2-57 (309)
23 PHA02926 zinc finger-like prot 99.2 2.1E-11 4.5E-16 85.4 2.9 51 17-67 166-231 (242)
24 KOG2177|consensus 99.1 4.7E-11 1E-15 87.8 4.5 71 17-90 9-79 (386)
25 KOG0978|consensus 99.1 1.2E-11 2.5E-16 99.4 1.2 59 11-69 633-692 (698)
26 COG5574 PEX10 RING-finger-cont 99.1 2.8E-11 6.1E-16 86.6 2.0 51 19-69 213-265 (271)
27 KOG2164|consensus 99.1 3E-11 6.5E-16 93.3 2.3 49 21-69 186-239 (513)
28 KOG4628|consensus 99.0 2.5E-10 5.5E-15 85.4 2.6 47 22-68 230-280 (348)
29 COG5243 HRD1 HRD ubiquitin lig 99.0 2.9E-10 6.4E-15 84.9 2.6 47 19-65 285-344 (491)
30 KOG0311|consensus 98.9 3.4E-10 7.3E-15 84.0 0.8 70 18-87 40-111 (381)
31 KOG1002|consensus 98.9 3.2E-09 7E-14 82.7 5.2 107 17-124 532-660 (791)
32 PF12861 zf-Apc11: Anaphase-pr 98.9 1.7E-09 3.6E-14 65.3 2.7 48 19-66 19-82 (85)
33 KOG2660|consensus 98.8 2.6E-09 5.7E-14 78.7 2.5 86 15-100 9-99 (331)
34 KOG0802|consensus 98.8 2.1E-09 4.6E-14 86.0 1.6 49 19-67 289-342 (543)
35 COG5540 RING-finger-containing 98.7 8.4E-09 1.8E-13 75.4 2.7 48 20-67 322-373 (374)
36 KOG0297|consensus 98.7 1.6E-08 3.4E-13 77.9 4.3 81 6-86 6-87 (391)
37 COG5152 Uncharacterized conser 98.7 1.1E-08 2.3E-13 70.7 1.8 47 21-67 196-242 (259)
38 KOG4159|consensus 98.6 2.2E-08 4.9E-13 76.7 3.7 72 16-87 79-154 (398)
39 PF11789 zf-Nse: Zinc-finger o 98.6 2.6E-08 5.7E-13 56.2 1.5 41 20-60 10-53 (57)
40 KOG0824|consensus 98.6 2.9E-08 6.2E-13 72.5 2.1 49 21-69 7-56 (324)
41 KOG1813|consensus 98.5 4.8E-08 1E-12 71.2 2.4 47 21-67 241-287 (313)
42 KOG2879|consensus 98.5 1.2E-07 2.6E-12 68.5 3.0 51 16-66 234-287 (298)
43 COG5222 Uncharacterized conser 98.4 2.7E-07 5.8E-12 67.6 4.4 65 22-86 275-341 (427)
44 KOG1734|consensus 98.3 1.9E-07 4.1E-12 67.4 -0.0 55 19-74 222-288 (328)
45 COG5194 APC11 Component of SCF 98.2 7E-07 1.5E-11 52.8 1.9 46 22-67 21-82 (88)
46 KOG4172|consensus 98.1 5.9E-07 1.3E-11 49.3 0.2 46 21-66 7-54 (62)
47 KOG0804|consensus 98.1 1.8E-06 3.8E-11 66.4 1.7 48 17-66 171-222 (493)
48 PF11793 FANCL_C: FANCL C-term 98.1 5.8E-07 1.2E-11 52.9 -0.7 46 21-66 2-66 (70)
49 KOG1645|consensus 98.0 5.2E-06 1.1E-10 63.2 4.0 56 20-76 3-65 (463)
50 KOG0828|consensus 98.0 3.2E-06 6.8E-11 65.8 1.8 50 18-67 568-635 (636)
51 KOG1039|consensus 97.9 5.5E-06 1.2E-10 62.6 2.4 50 19-68 159-223 (344)
52 KOG3039|consensus 97.9 8E-06 1.7E-10 58.4 3.0 51 19-69 219-273 (303)
53 KOG4265|consensus 97.9 5.2E-06 1.1E-10 62.2 2.1 49 19-67 288-337 (349)
54 smart00744 RINGv The RING-vari 97.9 9.3E-06 2E-10 44.4 2.3 40 23-62 1-49 (49)
55 KOG4692|consensus 97.9 7.6E-06 1.6E-10 61.4 2.5 50 17-66 418-467 (489)
56 KOG1785|consensus 97.9 4.2E-06 9.2E-11 63.6 0.8 49 23-71 371-421 (563)
57 KOG0827|consensus 97.8 7E-06 1.5E-10 62.2 1.3 46 22-67 5-57 (465)
58 KOG4367|consensus 97.8 1.1E-05 2.4E-10 62.2 1.7 36 18-53 1-36 (699)
59 COG5219 Uncharacterized conser 97.7 1.4E-05 3E-10 66.7 1.8 49 18-66 1466-1523(1525)
60 PF14447 Prok-RING_4: Prokaryo 97.7 1.7E-05 3.6E-10 43.9 1.5 48 20-69 6-53 (55)
61 KOG0825|consensus 97.7 9.1E-06 2E-10 66.4 0.5 51 19-69 121-174 (1134)
62 PF04641 Rtf2: Rtf2 RING-finge 97.7 3.9E-05 8.5E-10 56.2 3.7 53 18-71 110-166 (260)
63 KOG2930|consensus 97.6 2.7E-05 5.9E-10 48.4 1.8 44 21-64 46-106 (114)
64 KOG0826|consensus 97.6 6.9E-05 1.5E-09 55.7 3.3 47 19-65 298-345 (357)
65 KOG4739|consensus 97.6 0.00011 2.4E-09 52.5 4.1 45 22-68 4-50 (233)
66 KOG4185|consensus 97.5 0.00012 2.5E-09 54.6 3.7 64 21-84 3-77 (296)
67 KOG1493|consensus 97.4 3.8E-05 8.2E-10 45.2 0.2 44 23-66 22-81 (84)
68 PF14570 zf-RING_4: RING/Ubox 97.4 0.00015 3.3E-09 39.2 2.1 42 24-65 1-47 (48)
69 KOG1814|consensus 97.3 0.0003 6.6E-09 53.9 3.6 45 19-63 182-237 (445)
70 KOG1001|consensus 97.2 0.00018 3.8E-09 59.2 1.9 47 22-69 455-503 (674)
71 KOG0298|consensus 97.2 0.00027 5.8E-09 60.8 3.0 92 17-122 1149-1241(1394)
72 KOG3800|consensus 97.2 0.00035 7.6E-09 51.2 3.0 47 23-69 2-54 (300)
73 KOG4275|consensus 97.1 5.4E-05 1.2E-09 55.5 -1.6 41 21-65 300-341 (350)
74 PF05290 Baculo_IE-1: Baculovi 97.0 0.00063 1.4E-08 44.4 2.8 50 20-69 79-135 (140)
75 KOG1571|consensus 97.0 0.00031 6.7E-09 52.9 1.3 47 18-67 302-348 (355)
76 KOG3002|consensus 96.9 0.00094 2E-08 49.9 3.3 65 18-89 45-110 (299)
77 KOG1941|consensus 96.9 0.0003 6.5E-09 53.7 0.6 45 20-64 364-414 (518)
78 PF10367 Vps39_2: Vacuolar sor 96.8 0.00037 8.1E-09 43.9 0.2 33 17-49 74-108 (109)
79 KOG2114|consensus 96.7 0.002 4.4E-08 53.5 4.1 41 20-63 839-880 (933)
80 PF07800 DUF1644: Protein of u 96.5 0.014 3.1E-07 39.4 6.5 103 20-128 1-154 (162)
81 KOG2817|consensus 96.5 0.0018 3.8E-08 49.6 2.5 48 20-67 333-386 (394)
82 KOG3970|consensus 96.5 0.0046 1E-07 44.0 4.3 51 19-69 48-108 (299)
83 COG5236 Uncharacterized conser 96.5 0.0026 5.7E-08 48.0 3.0 48 18-65 58-107 (493)
84 COG5175 MOT2 Transcriptional r 96.4 0.0052 1.1E-07 46.3 4.0 53 17-69 10-67 (480)
85 KOG4362|consensus 96.3 0.00052 1.1E-08 56.0 -1.5 64 18-82 18-84 (684)
86 PF08746 zf-RING-like: RING-li 96.3 0.0038 8.1E-08 33.0 2.2 38 24-61 1-43 (43)
87 KOG1940|consensus 96.2 0.0032 6.9E-08 46.4 2.2 43 21-63 158-204 (276)
88 COG5220 TFB3 Cdk activating ki 96.2 0.0035 7.6E-08 45.0 2.3 48 20-67 9-65 (314)
89 PHA03096 p28-like protein; Pro 95.8 0.0061 1.3E-07 45.3 2.1 42 22-63 179-231 (284)
90 KOG3579|consensus 95.6 0.012 2.5E-07 43.4 2.8 38 17-54 264-305 (352)
91 KOG1428|consensus 95.6 0.023 5E-07 50.5 4.8 51 17-67 3482-3545(3738)
92 KOG3268|consensus 95.5 0.01 2.3E-07 40.8 2.2 32 37-68 188-230 (234)
93 KOG3161|consensus 95.4 0.0067 1.4E-07 49.3 1.2 38 20-59 10-51 (861)
94 PF02891 zf-MIZ: MIZ/SP-RING z 95.4 0.011 2.3E-07 32.3 1.7 42 22-64 3-50 (50)
95 KOG3039|consensus 95.4 0.011 2.3E-07 42.7 2.1 37 17-53 39-75 (303)
96 KOG2932|consensus 95.3 0.0071 1.5E-07 45.0 1.0 44 22-67 91-135 (389)
97 PHA02825 LAP/PHD finger-like p 95.2 0.026 5.6E-07 38.2 3.3 48 19-67 6-60 (162)
98 PF12906 RINGv: RING-variant d 94.6 0.026 5.7E-07 30.4 1.7 38 24-61 1-47 (47)
99 PF03854 zf-P11: P-11 zinc fin 94.4 0.012 2.7E-07 31.5 0.2 32 36-67 15-47 (50)
100 PF05883 Baculo_RING: Baculovi 94.3 0.026 5.6E-07 37.1 1.5 42 21-62 26-76 (134)
101 KOG3113|consensus 94.2 0.044 9.5E-07 39.8 2.6 53 20-74 110-166 (293)
102 KOG1952|consensus 94.1 0.024 5.1E-07 47.5 1.3 46 19-64 189-245 (950)
103 PHA02862 5L protein; Provision 94.1 0.038 8.2E-07 36.8 2.0 46 22-68 3-55 (156)
104 KOG1812|consensus 94.1 0.046 1E-06 42.4 2.8 48 20-67 145-204 (384)
105 KOG4445|consensus 94.1 0.01 2.2E-07 44.1 -0.8 48 20-67 114-187 (368)
106 COG5109 Uncharacterized conser 93.5 0.056 1.2E-06 40.5 2.2 46 20-65 335-386 (396)
107 KOG1100|consensus 93.0 0.039 8.4E-07 39.2 0.8 40 24-67 161-201 (207)
108 KOG1815|consensus 92.7 0.072 1.6E-06 42.1 1.9 36 19-54 68-104 (444)
109 KOG2034|consensus 92.2 0.073 1.6E-06 44.9 1.4 36 18-53 814-851 (911)
110 COG3813 Uncharacterized protei 92.1 0.18 3.9E-06 29.5 2.6 35 38-75 26-60 (84)
111 KOG4718|consensus 91.6 0.11 2.3E-06 36.8 1.5 46 20-65 180-226 (235)
112 PF04216 FdhE: Protein involve 91.6 0.033 7.2E-07 41.5 -1.1 46 19-64 170-220 (290)
113 PF10272 Tmpp129: Putative tra 91.4 0.13 2.8E-06 39.5 1.9 31 39-69 311-354 (358)
114 TIGR01562 FdhE formate dehydro 90.8 0.079 1.7E-06 39.8 0.3 45 20-64 183-233 (305)
115 PF07191 zinc-ribbons_6: zinc- 90.5 0.024 5.3E-07 33.0 -2.1 41 21-66 1-41 (70)
116 PF10235 Cript: Microtubule-as 90.5 0.13 2.9E-06 31.5 1.0 38 21-67 44-81 (90)
117 PF13240 zinc_ribbon_2: zinc-r 90.5 0.041 8.8E-07 25.0 -1.0 11 54-64 12-22 (23)
118 KOG0825|consensus 90.1 0.18 4E-06 42.3 1.8 50 18-67 93-155 (1134)
119 KOG2979|consensus 89.4 0.2 4.2E-06 36.6 1.3 44 21-64 176-222 (262)
120 KOG1812|consensus 89.0 0.18 4E-06 39.1 1.0 42 21-62 306-352 (384)
121 KOG3899|consensus 88.7 0.26 5.6E-06 36.7 1.5 31 39-69 325-368 (381)
122 PRK03564 formate dehydrogenase 88.6 0.19 4.1E-06 37.9 0.8 44 20-63 186-234 (309)
123 KOG2042|consensus 88.4 0.95 2.1E-05 39.0 4.8 72 17-89 866-938 (943)
124 KOG4642|consensus 87.1 1.1 2.5E-05 32.7 4.0 75 14-89 204-279 (284)
125 PF14569 zf-UDP: Zinc-binding 87.0 0.76 1.6E-05 27.3 2.5 48 21-68 9-64 (80)
126 PF07975 C1_4: TFIIH C1-like d 86.6 0.53 1.1E-05 25.8 1.6 25 38-62 26-50 (51)
127 PF14353 CpXC: CpXC protein 86.5 0.54 1.2E-05 30.6 2.0 47 22-68 2-51 (128)
128 PF14446 Prok-RING_1: Prokaryo 86.5 0.52 1.1E-05 26.1 1.6 31 20-50 4-38 (54)
129 KOG0309|consensus 86.3 0.41 9E-06 40.1 1.6 43 21-63 1028-1073(1081)
130 PF10571 UPF0547: Uncharacteri 86.3 0.23 5E-06 23.2 0.1 8 24-31 3-10 (26)
131 PF05605 zf-Di19: Drought indu 86.2 0.42 9E-06 26.3 1.1 37 20-63 1-39 (54)
132 PF06906 DUF1272: Protein of u 86.1 1.1 2.3E-05 25.0 2.6 44 23-68 7-54 (57)
133 KOG0827|consensus 85.8 0.09 2E-06 40.5 -2.2 48 22-69 197-248 (465)
134 PF13248 zf-ribbon_3: zinc-rib 82.9 0.22 4.7E-06 23.2 -0.8 9 56-64 17-25 (26)
135 KOG3053|consensus 82.7 0.71 1.5E-05 33.8 1.3 52 15-66 14-82 (293)
136 PF01363 FYVE: FYVE zinc finge 82.3 0.32 7E-06 28.0 -0.5 31 20-50 8-42 (69)
137 PF10186 Atg14: UV radiation r 82.3 6.8 0.00015 28.8 6.5 21 23-51 1-21 (302)
138 COG5183 SSM4 Protein involved 81.6 0.98 2.1E-05 38.3 1.9 51 19-69 10-69 (1175)
139 COG5627 MMS21 DNA repair prote 81.5 2.6 5.6E-05 30.6 3.7 40 21-60 189-231 (275)
140 smart00064 FYVE Protein presen 81.1 1.3 2.8E-05 25.3 1.8 32 21-52 10-45 (68)
141 PF06844 DUF1244: Protein of u 80.2 1.1 2.3E-05 25.8 1.2 12 42-53 11-22 (68)
142 cd00065 FYVE FYVE domain; Zinc 79.2 1.3 2.9E-05 24.2 1.4 31 22-52 3-37 (57)
143 KOG4185|consensus 78.6 0.4 8.6E-06 35.7 -1.2 43 22-64 208-265 (296)
144 KOG0269|consensus 78.5 2.3 5E-05 35.8 3.0 48 22-69 780-831 (839)
145 KOG2169|consensus 78.1 3 6.4E-05 34.8 3.6 67 20-87 305-376 (636)
146 PRK04023 DNA polymerase II lar 78.0 2.7 5.9E-05 36.6 3.4 49 19-69 624-677 (1121)
147 PF04710 Pellino: Pellino; In 77.8 0.72 1.6E-05 35.8 0.0 45 22-66 278-339 (416)
148 KOG2068|consensus 77.6 2.1 4.6E-05 32.5 2.4 47 22-68 250-300 (327)
149 PF04710 Pellino: Pellino; In 76.9 0.78 1.7E-05 35.6 0.0 48 21-68 328-403 (416)
150 KOG0289|consensus 76.0 3.7 8.1E-05 32.5 3.4 48 22-69 1-49 (506)
151 smart00132 LIM Zinc-binding do 75.9 2.5 5.4E-05 20.7 1.8 35 23-65 1-37 (39)
152 KOG2789|consensus 75.8 1.2 2.5E-05 34.7 0.7 33 20-52 73-107 (482)
153 PRK11595 DNA utilization prote 75.3 2.3 5E-05 30.5 2.1 39 22-65 6-44 (227)
154 PRK06266 transcription initiat 75.0 1.4 2.9E-05 30.7 0.8 17 53-69 134-150 (178)
155 cd00350 rubredoxin_like Rubred 74.9 2.2 4.9E-05 20.8 1.4 11 54-64 16-26 (33)
156 KOG1829|consensus 74.8 1.1 2.4E-05 36.6 0.3 23 38-63 536-558 (580)
157 smart00647 IBR In Between Ring 73.7 0.57 1.2E-05 26.2 -1.1 33 20-52 17-59 (64)
158 PF10146 zf-C4H2: Zinc finger- 73.4 2.9 6.3E-05 30.3 2.2 27 43-69 196-222 (230)
159 PF04423 Rad50_zn_hook: Rad50 72.9 1.1 2.3E-05 24.6 -0.1 12 56-67 21-32 (54)
160 KOG3993|consensus 72.8 0.7 1.5E-05 36.2 -1.2 43 17-68 263-308 (500)
161 PF15616 TerY-C: TerY-C metal 71.9 1.7 3.8E-05 28.6 0.7 46 17-68 73-118 (131)
162 TIGR00622 ssl1 transcription f 70.7 4.4 9.6E-05 26.0 2.3 41 22-62 56-110 (112)
163 PF12773 DZR: Double zinc ribb 70.3 3.3 7.1E-05 22.1 1.5 26 42-67 13-41 (50)
164 PLN02195 cellulose synthase A 69.3 4.1 8.8E-05 35.4 2.5 46 21-67 6-60 (977)
165 KOG0824|consensus 69.3 1.9 4E-05 32.4 0.4 48 17-64 101-149 (324)
166 PF10497 zf-4CXXC_R1: Zinc-fin 69.1 5.5 0.00012 25.1 2.5 25 40-64 37-70 (105)
167 KOG2807|consensus 69.0 3.1 6.7E-05 31.6 1.5 42 21-62 330-374 (378)
168 PLN02436 cellulose synthase A 68.9 3.8 8.2E-05 36.0 2.2 46 21-66 36-89 (1094)
169 COG4647 AcxC Acetone carboxyla 68.8 2 4.3E-05 28.2 0.5 21 26-46 62-82 (165)
170 PLN02189 cellulose synthase 68.4 4 8.6E-05 35.7 2.2 47 21-67 34-88 (1040)
171 KOG1074|consensus 67.6 4.8 0.0001 34.4 2.5 42 17-69 601-647 (958)
172 KOG4451|consensus 66.7 4.5 9.8E-05 29.2 1.9 28 42-69 250-277 (286)
173 KOG2113|consensus 65.9 4.5 9.7E-05 30.7 1.8 44 19-64 341-385 (394)
174 COG4640 Predicted membrane pro 65.8 3.1 6.8E-05 32.5 1.0 41 43-84 3-43 (465)
175 KOG3476|consensus 65.7 0.63 1.4E-05 28.2 -2.1 38 21-67 54-91 (100)
176 PF09723 Zn-ribbon_8: Zinc rib 65.7 1.2 2.7E-05 23.1 -0.8 25 38-63 10-34 (42)
177 TIGR00373 conserved hypothetic 65.6 1.7 3.7E-05 29.5 -0.3 16 54-69 127-142 (158)
178 KOG3842|consensus 65.2 5.4 0.00012 30.3 2.2 49 20-68 340-416 (429)
179 PF13719 zinc_ribbon_5: zinc-r 64.4 3.5 7.7E-05 20.7 0.8 13 22-34 3-15 (37)
180 PLN02638 cellulose synthase A 63.7 5.3 0.00011 35.2 2.1 45 21-66 17-70 (1079)
181 PRK14559 putative protein seri 63.2 2.3 4.9E-05 35.5 -0.1 22 44-65 30-51 (645)
182 smart00154 ZnF_AN1 AN1-like Zi 63.1 4.6 0.0001 20.6 1.1 23 24-46 1-25 (39)
183 KOG0314|consensus 62.2 9.6 0.00021 30.4 3.1 67 14-81 212-281 (448)
184 PF09986 DUF2225: Uncharacteri 62.1 5 0.00011 28.6 1.5 51 19-69 3-62 (214)
185 PF10083 DUF2321: Uncharacteri 61.9 32 0.0007 23.4 5.2 24 41-67 28-51 (158)
186 PLN02248 cellulose synthase-li 61.2 7.3 0.00016 34.5 2.5 31 38-68 149-179 (1135)
187 COG0068 HypF Hydrogenase matur 60.7 5.7 0.00012 33.4 1.7 52 17-68 97-186 (750)
188 PRK14714 DNA polymerase II lar 60.6 6.8 0.00015 35.1 2.2 67 21-87 667-743 (1337)
189 KOG2231|consensus 60.6 6.2 0.00014 33.0 1.9 45 23-67 2-53 (669)
190 COG3492 Uncharacterized protei 60.4 4.6 0.0001 24.8 0.9 12 42-53 42-53 (104)
191 COG5242 TFB4 RNA polymerase II 59.5 5.4 0.00012 28.9 1.2 12 55-66 274-285 (296)
192 PF09889 DUF2116: Uncharacteri 59.3 16 0.00036 20.5 3.0 14 55-68 3-16 (59)
193 PF00412 LIM: LIM domain; Int 58.9 5.4 0.00012 21.6 1.0 37 24-68 1-39 (58)
194 KOG1609|consensus 58.6 5.5 0.00012 29.6 1.2 47 21-67 78-135 (323)
195 PF13717 zinc_ribbon_4: zinc-r 58.3 5.2 0.00011 20.0 0.8 12 22-33 3-14 (36)
196 PF07503 zf-HYPF: HypF finger; 57.6 10 0.00023 18.9 1.8 24 43-66 1-32 (35)
197 PLN02400 cellulose synthase 56.4 6.4 0.00014 34.7 1.4 46 21-67 36-90 (1085)
198 PF01485 IBR: IBR domain; Int 56.3 1.1 2.4E-05 24.9 -2.2 31 21-51 18-58 (64)
199 PLN02915 cellulose synthase A 56.2 8.7 0.00019 33.8 2.1 47 20-67 14-69 (1044)
200 PF02318 FYVE_2: FYVE-type zin 55.7 5.8 0.00013 25.4 0.9 31 20-50 53-88 (118)
201 PF14311 DUF4379: Domain of un 54.8 8.6 0.00019 21.0 1.3 8 54-61 48-55 (55)
202 PF13901 DUF4206: Domain of un 54.3 8.2 0.00018 27.3 1.5 39 20-63 151-197 (202)
203 PF00628 PHD: PHD-finger; Int 54.3 5.2 0.00011 21.2 0.4 29 23-51 1-32 (51)
204 PRK11088 rrmA 23S rRNA methylt 53.6 8 0.00017 28.3 1.4 22 22-43 3-27 (272)
205 COG5113 UFD2 Ubiquitin fusion 53.6 39 0.00084 28.5 5.2 74 16-90 849-923 (929)
206 KOG1356|consensus 52.9 6.6 0.00014 33.6 0.9 34 19-52 227-262 (889)
207 PF13824 zf-Mss51: Zinc-finger 52.9 13 0.00029 20.6 1.8 14 55-68 14-27 (55)
208 PRK00420 hypothetical protein; 52.8 22 0.00047 22.8 3.1 13 55-67 40-52 (112)
209 smart00290 ZnF_UBP Ubiquitin C 52.6 9 0.00019 20.2 1.2 23 24-46 2-24 (50)
210 PF05502 Dynactin_p62: Dynacti 51.9 5.5 0.00012 32.1 0.3 9 57-65 54-62 (483)
211 KOG1815|consensus 51.1 5.8 0.00013 31.5 0.3 19 34-52 179-197 (444)
212 PTZ00303 phosphatidylinositol 50.6 9.6 0.00021 32.7 1.5 31 22-52 461-500 (1374)
213 KOG2272|consensus 50.5 7.1 0.00015 28.7 0.7 55 13-67 175-233 (332)
214 COG1675 TFA1 Transcription ini 49.4 27 0.00058 24.3 3.3 18 52-69 129-146 (176)
215 KOG2593|consensus 48.8 16 0.00035 28.9 2.4 56 19-83 126-181 (436)
216 KOG2462|consensus 48.6 5.6 0.00012 29.5 -0.1 50 20-69 160-229 (279)
217 PF10013 DUF2256: Uncharacteri 48.3 11 0.00024 19.6 1.0 13 55-67 8-20 (42)
218 PF01428 zf-AN1: AN1-like Zinc 48.1 8.7 0.00019 19.9 0.6 21 27-47 6-27 (43)
219 COG4068 Uncharacterized protei 47.8 33 0.00072 19.3 2.9 16 54-69 7-22 (64)
220 PF06221 zf-C2HC5: Putative zi 47.3 13 0.00027 20.8 1.2 26 36-67 21-47 (57)
221 KOG1729|consensus 47.2 8.4 0.00018 28.9 0.6 32 19-50 166-202 (288)
222 KOG2487|consensus 46.8 9.7 0.00021 28.3 0.9 24 44-67 276-299 (314)
223 KOG2066|consensus 46.6 6.4 0.00014 33.4 -0.0 40 21-61 784-830 (846)
224 PF06827 zf-FPG_IleRS: Zinc fi 46.4 5.7 0.00012 18.8 -0.2 25 23-47 3-27 (30)
225 PF05265 DUF723: Protein of un 45.8 18 0.0004 20.4 1.7 29 33-62 29-60 (60)
226 COG5151 SSL1 RNA polymerase II 45.5 11 0.00024 28.7 1.0 42 21-62 362-417 (421)
227 PRK01343 zinc-binding protein; 45.2 15 0.00032 20.6 1.3 12 55-66 9-20 (57)
228 smart00734 ZnF_Rad18 Rad18-lik 44.9 11 0.00024 17.3 0.7 11 56-66 2-12 (26)
229 PF09538 FYDLN_acid: Protein o 44.9 10 0.00022 24.2 0.7 13 56-68 27-39 (108)
230 PRK12496 hypothetical protein; 44.9 6.4 0.00014 26.9 -0.2 26 44-69 130-157 (164)
231 smart00834 CxxC_CXXC_SSSS Puta 44.8 6.1 0.00013 19.8 -0.3 11 55-65 26-36 (41)
232 KOG3799|consensus 44.6 13 0.00028 24.7 1.2 31 16-50 60-90 (169)
233 KOG3362|consensus 44.6 6.9 0.00015 26.2 -0.1 30 20-50 117-147 (156)
234 smart00249 PHD PHD zinc finger 44.5 11 0.00025 18.9 0.8 28 23-50 1-31 (47)
235 KOG1701|consensus 44.1 5.1 0.00011 31.6 -0.9 12 56-67 361-372 (468)
236 PF13834 DUF4193: Domain of un 43.5 9.9 0.00022 23.8 0.5 31 17-47 66-98 (99)
237 cd00730 rubredoxin Rubredoxin; 43.2 11 0.00025 20.4 0.6 13 17-29 30-42 (50)
238 PF15135 UPF0515: Uncharacteri 42.9 12 0.00026 27.5 0.8 17 15-31 106-122 (278)
239 COG2093 DNA-directed RNA polym 42.8 8.7 0.00019 21.9 0.1 21 44-64 7-27 (64)
240 PRK00418 DNA gyrase inhibitor; 41.5 16 0.00035 20.8 1.1 12 55-66 6-17 (62)
241 PF00301 Rubredoxin: Rubredoxi 41.1 11 0.00023 20.2 0.3 13 17-29 30-42 (47)
242 COG3024 Uncharacterized protei 40.7 16 0.00034 20.9 1.0 14 55-68 7-20 (65)
243 KOG4317|consensus 40.6 30 0.00065 26.4 2.6 11 56-66 20-30 (383)
244 PRK05978 hypothetical protein; 40.3 22 0.00049 23.9 1.8 20 50-69 47-66 (148)
245 KOG3183|consensus 40.1 27 0.00059 25.5 2.3 53 22-74 9-74 (250)
246 KOG4218|consensus 40.0 24 0.00051 27.4 2.0 17 18-34 12-28 (475)
247 PF03119 DNA_ligase_ZBD: NAD-d 39.2 10 0.00022 17.8 0.0 11 57-67 1-11 (28)
248 COG4098 comFA Superfamily II D 38.7 15 0.00033 28.6 0.9 33 19-51 37-70 (441)
249 PF13913 zf-C2HC_2: zinc-finge 38.2 16 0.00034 16.6 0.6 9 57-65 4-12 (25)
250 PF14205 Cys_rich_KTR: Cystein 37.0 15 0.00032 20.4 0.4 10 22-31 5-14 (55)
251 KOG1818|consensus 37.0 15 0.00031 30.7 0.6 34 19-52 163-200 (634)
252 PRK06393 rpoE DNA-directed RNA 36.8 23 0.0005 20.3 1.2 12 54-65 16-27 (64)
253 COG1592 Rubrerythrin [Energy p 36.5 24 0.00052 24.3 1.5 10 55-64 149-158 (166)
254 PF00096 zf-C2H2: Zinc finger, 36.2 10 0.00022 16.3 -0.3 9 58-66 3-11 (23)
255 PF08882 Acetone_carb_G: Aceto 35.9 16 0.00035 23.4 0.5 11 35-45 25-35 (112)
256 PRK00564 hypA hydrogenase nick 35.7 11 0.00024 24.2 -0.2 8 57-64 90-97 (117)
257 KOG3896|consensus 35.7 9.1 0.0002 29.4 -0.7 53 17-69 20-84 (449)
258 PF11290 DUF3090: Protein of u 35.6 33 0.00072 23.7 2.1 16 54-69 153-168 (171)
259 COG3058 FdhE Uncharacterized p 35.3 24 0.00052 26.4 1.4 46 19-64 183-234 (308)
260 COG1645 Uncharacterized Zn-fin 35.2 13 0.00029 24.5 0.1 9 55-63 44-52 (131)
261 KOG0396|consensus 35.0 65 0.0014 25.2 3.7 33 34-66 346-379 (389)
262 COG1439 Predicted nucleic acid 34.7 11 0.00025 26.1 -0.3 24 44-67 142-165 (177)
263 PF09237 GAGA: GAGA factor; I 33.6 11 0.00025 20.6 -0.3 12 56-67 25-36 (54)
264 COG3364 Zn-ribbon containing p 33.5 21 0.00045 22.5 0.7 25 36-64 5-29 (112)
265 KOG1819|consensus 33.4 20 0.00043 29.2 0.8 30 20-49 900-933 (990)
266 PRK12380 hydrogenase nickel in 33.0 9 0.00019 24.5 -1.0 10 55-64 86-95 (113)
267 PRK03681 hypA hydrogenase nick 32.8 10 0.00022 24.3 -0.8 9 56-64 88-96 (114)
268 KOG3726|consensus 32.5 22 0.00047 29.9 0.9 41 23-66 656-700 (717)
269 TIGR00143 hypF [NiFe] hydrogen 32.3 27 0.00059 29.7 1.5 50 18-67 65-152 (711)
270 PRK08351 DNA-directed RNA poly 32.0 24 0.00051 20.0 0.8 12 54-65 14-25 (61)
271 PF06676 DUF1178: Protein of u 32.0 21 0.00046 24.0 0.7 23 38-65 9-42 (148)
272 PF07754 DUF1610: Domain of un 31.9 22 0.00047 16.2 0.5 8 55-62 16-23 (24)
273 PF14319 Zn_Tnp_IS91: Transpos 31.9 21 0.00045 22.7 0.6 25 22-48 43-67 (111)
274 PRK14127 cell division protein 31.8 1.3E+02 0.0027 19.2 4.1 29 105-133 22-50 (109)
275 PF07649 C1_3: C1-like domain; 31.1 35 0.00075 16.0 1.2 25 23-47 2-29 (30)
276 PF06869 DUF1258: Protein of u 31.0 29 0.00062 25.6 1.3 45 40-86 17-63 (258)
277 PF13894 zf-C2H2_4: C2H2-type 30.9 15 0.00033 15.4 -0.1 9 58-66 3-11 (24)
278 COG4338 Uncharacterized protei 30.9 15 0.00033 19.8 -0.1 13 55-67 12-24 (54)
279 TIGR03847 conserved hypothetic 30.8 66 0.0014 22.3 2.9 18 54-71 155-172 (177)
280 TIGR00100 hypA hydrogenase nic 30.7 10 0.00022 24.3 -1.0 10 55-64 86-95 (115)
281 PF02148 zf-UBP: Zn-finger in 30.3 24 0.00052 19.8 0.6 23 24-46 1-24 (63)
282 TIGR02605 CxxC_CxxC_SSSS putat 30.2 15 0.00032 19.6 -0.2 9 55-63 26-34 (52)
283 cd00729 rubredoxin_SM Rubredox 29.9 29 0.00062 17.0 0.8 9 56-64 19-27 (34)
284 KOG0802|consensus 29.7 35 0.00076 27.9 1.7 47 19-69 477-523 (543)
285 PF00643 zf-B_box: B-box zinc 29.5 45 0.00097 16.7 1.6 30 21-50 3-32 (42)
286 PF15372 DUF4600: Domain of un 29.5 1.7E+02 0.0037 19.3 6.6 34 105-138 50-83 (129)
287 PRK02224 chromosome segregatio 29.0 1.3E+02 0.0029 26.0 5.1 16 54-69 450-465 (880)
288 COG4357 Zinc finger domain con 28.7 34 0.00074 21.3 1.1 27 42-68 63-93 (105)
289 KOG2857|consensus 28.6 1.9E+02 0.0041 19.5 6.6 29 21-49 5-34 (157)
290 PF09845 DUF2072: Zn-ribbon co 28.6 33 0.00073 22.6 1.1 24 37-64 5-28 (131)
291 PF05715 zf-piccolo: Piccolo Z 28.6 44 0.00095 18.9 1.4 10 56-65 3-12 (61)
292 TIGR01206 lysW lysine biosynth 28.4 30 0.00065 19.1 0.8 10 57-66 4-13 (54)
293 PF03833 PolC_DP2: DNA polymer 28.4 19 0.00042 31.1 0.0 47 20-68 654-705 (900)
294 COG1198 PriA Primosomal protei 28.0 25 0.00054 30.0 0.6 24 40-64 461-484 (730)
295 PF14169 YdjO: Cold-inducible 27.5 46 0.001 18.7 1.4 12 55-66 39-50 (59)
296 smart00531 TFIIE Transcription 27.5 34 0.00074 22.8 1.1 15 55-69 123-137 (147)
297 KOG2071|consensus 27.1 30 0.00065 28.6 0.9 34 19-52 511-557 (579)
298 PF03884 DUF329: Domain of unk 27.0 19 0.00041 20.1 -0.2 12 56-67 3-14 (57)
299 COG2824 PhnA Uncharacterized Z 26.9 16 0.00035 23.1 -0.5 28 22-52 4-31 (112)
300 PF01155 HypA: Hydrogenase exp 26.9 6.7 0.00015 25.0 -2.3 9 56-64 87-95 (113)
301 COG3809 Uncharacterized protei 26.2 13 0.00028 22.2 -1.0 11 22-32 2-12 (88)
302 PF05103 DivIVA: DivIVA protei 26.0 1.3E+02 0.0028 19.1 3.6 32 105-136 17-48 (131)
303 PF11002 RDM: RFPL defining mo 25.9 23 0.00049 18.5 0.0 26 66-91 3-28 (42)
304 COG4306 Uncharacterized protei 25.7 41 0.00088 22.1 1.1 23 42-67 29-51 (160)
305 PF12874 zf-met: Zinc-finger o 25.5 20 0.00043 15.7 -0.3 10 23-32 2-11 (25)
306 PF14471 DUF4428: Domain of un 25.5 68 0.0015 17.3 1.9 28 23-51 1-30 (51)
307 TIGR03826 YvyF flagellar opero 25.3 50 0.0011 22.0 1.5 24 21-49 3-26 (137)
308 COG1040 ComFC Predicted amidop 25.1 21 0.00047 25.6 -0.2 17 74-90 75-91 (225)
309 TIGR02300 FYDLN_acid conserved 24.8 27 0.00058 22.9 0.2 12 56-67 27-38 (129)
310 COG1885 Uncharacterized protei 24.3 48 0.001 21.0 1.2 14 55-68 49-62 (115)
311 smart00659 RPOLCX RNA polymera 24.3 30 0.00064 18.2 0.3 14 54-67 18-31 (44)
312 PF13453 zf-TFIIB: Transcripti 24.2 41 0.00088 17.0 0.8 11 57-67 1-11 (41)
313 TIGR00375 conserved hypothetic 24.2 18 0.00039 28.2 -0.8 27 39-66 238-269 (374)
314 cd04766 HTH_HspR Helix-Turn-He 24.1 1.7E+02 0.0036 17.5 3.7 33 105-138 58-90 (91)
315 PF14818 DUF4482: Domain of un 23.8 2.3E+02 0.0051 19.0 4.6 24 113-136 20-43 (141)
316 KOG3475|consensus 23.8 43 0.00093 20.3 0.9 30 40-69 15-45 (92)
317 PF12660 zf-TFIIIC: Putative z 23.6 27 0.00059 21.7 0.0 45 22-67 15-67 (99)
318 PF12675 DUF3795: Protein of u 23.5 65 0.0014 18.9 1.7 27 37-64 3-43 (78)
319 KOG4443|consensus 23.4 43 0.00092 28.1 1.1 45 19-63 16-70 (694)
320 KOG2906|consensus 22.9 23 0.00051 22.1 -0.3 26 22-47 2-27 (105)
321 KOG1842|consensus 22.3 40 0.00087 27.0 0.7 32 20-51 179-214 (505)
322 KOG0801|consensus 22.2 48 0.001 22.8 1.0 15 55-69 138-152 (205)
323 COG3677 Transposase and inacti 22.1 69 0.0015 21.0 1.7 15 55-69 53-67 (129)
324 PF09340 NuA4: Histone acetylt 21.8 1.9E+02 0.0041 17.2 3.5 21 117-137 6-26 (80)
325 KOG0006|consensus 21.7 60 0.0013 24.9 1.5 38 15-52 215-254 (446)
326 KOG3005|consensus 21.6 49 0.0011 24.6 1.0 44 22-65 183-242 (276)
327 PF04606 Ogr_Delta: Ogr/Delta- 21.6 36 0.00079 17.9 0.3 7 38-44 32-38 (47)
328 PRK00241 nudC NADH pyrophospha 21.5 76 0.0016 23.3 2.0 27 39-65 97-127 (256)
329 PLN03086 PRLI-interacting fact 21.4 1.2E+02 0.0025 25.3 3.2 50 17-66 449-515 (567)
330 PF11023 DUF2614: Protein of u 21.3 38 0.00083 21.7 0.4 16 54-69 84-99 (114)
331 KOG3576|consensus 21.1 41 0.00089 24.2 0.5 51 19-69 115-187 (267)
332 cd04772 HTH_TioE_rpt1 First He 21.1 2E+02 0.0044 17.5 3.7 27 110-136 73-99 (99)
333 PF14255 Cys_rich_CPXG: Cystei 20.8 46 0.001 18.2 0.6 10 57-66 2-11 (52)
334 PF05190 MutS_IV: MutS family 20.8 1.7E+02 0.0036 17.0 3.2 27 112-138 3-29 (92)
335 TIGR03830 CxxCG_CxxCG_HTH puta 20.6 1.4E+02 0.003 18.8 3.0 40 24-69 1-45 (127)
336 PRK00398 rpoP DNA-directed RNA 20.5 44 0.00096 17.3 0.5 14 55-68 21-34 (46)
337 PF06937 EURL: EURL protein; 20.4 85 0.0018 23.4 2.0 38 19-59 28-74 (285)
338 PRK14890 putative Zn-ribbon RN 20.3 65 0.0014 18.1 1.1 18 44-63 39-56 (59)
339 PF03107 C1_2: C1 domain; Int 20.2 53 0.0011 15.4 0.7 12 23-34 2-13 (30)
340 PTZ00218 40S ribosomal protein 20.2 66 0.0014 17.8 1.1 31 21-53 16-46 (54)
341 KOG0883|consensus 20.1 97 0.0021 24.6 2.4 34 21-54 40-73 (518)
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=99.66 E-value=1.3e-16 Score=92.48 Aligned_cols=62 Identities=26% Similarity=0.486 Sum_probs=56.7
Q ss_pred CcccccccchhhhceecCCCCcccHhhHHHHhhcCCCCCCCCCCCCCCCCCccchHHHHHHHH
Q psy10659 21 DLLCPICFELIREAHITRCGHTFCFSCISKCVELQIKCPKCSASLPDMNSVFPNFLLNELVQK 83 (140)
Q Consensus 21 ~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~CP~C~~~~~~~~~~~~~~~~~~~~~~ 83 (140)
++.||||.+.+.+|+.++|||+||..||..|+.....||.|+.+++..+ +.+|..+.+.++.
T Consensus 1 ~~~Cpi~~~~~~~Pv~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~~~-l~~~~~l~~~i~~ 62 (63)
T smart00504 1 EFLCPISLEVMKDPVILPSGQTYERRAIEKWLLSHGTDPVTGQPLTHED-LIPNLALKSAIQE 62 (63)
T ss_pred CcCCcCCCCcCCCCEECCCCCEEeHHHHHHHHHHCCCCCCCcCCCChhh-ceeCHHHHHHHHh
Confidence 4789999999999999999999999999999998889999999997777 8899888887764
No 2
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.62 E-value=5.6e-16 Score=117.87 Aligned_cols=75 Identities=35% Similarity=0.685 Sum_probs=67.2
Q ss_pred CCCCCCcccccccchhhhceecCCCCcccHhhHHHHhhcCCCCCCCCCCCCCCCCCccchHHHHHHHHHHhcCCCC
Q psy10659 16 SPPDNDLLCPICFELIREAHITRCGHTFCFSCISKCVELQIKCPKCSASLPDMNSVFPNFLLNELVQKHKIKSAQD 91 (140)
Q Consensus 16 ~~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~CP~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 91 (140)
..++..+.|+||++.|.+|++++|||+||..||..|+.....||.|+..+.... +..|..+.++++.|....+..
T Consensus 21 ~~Le~~l~C~IC~d~~~~PvitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~~~~-Lr~N~~L~~iVe~~~~~R~~L 95 (397)
T TIGR00599 21 YPLDTSLRCHICKDFFDVPVLTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQESK-LRSNWLVSEIVESFKNLRPSL 95 (397)
T ss_pred cccccccCCCcCchhhhCccCCCCCCchhHHHHHHHHhCCCCCCCCCCcccccc-CccchHHHHHHHHHHHhhHHH
Confidence 467788999999999999999999999999999999988888999999988765 899999999999998765543
No 3
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=99.61 E-value=3.1e-16 Score=83.52 Aligned_cols=38 Identities=39% Similarity=1.150 Sum_probs=30.6
Q ss_pred cccccchhhhceecCCCCcccHhhHHHHhhcC----CCCCCC
Q psy10659 24 CPICFELIREAHITRCGHTFCFSCISKCVELQ----IKCPKC 61 (140)
Q Consensus 24 C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~----~~CP~C 61 (140)
||||+++|.+|+.++|||+||..||..|++.. ..||.|
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 89999999999999999999999999999743 569987
No 4
>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=99.60 E-value=1.1e-15 Score=91.17 Aligned_cols=70 Identities=27% Similarity=0.438 Sum_probs=58.7
Q ss_pred CCCcccccccchhhhceecCCCCcccHhhHHHHhhc-CCCCCCCCCCCCCCCCCccchHHHHHHHHHHhcCC
Q psy10659 19 DNDLLCPICFELIREAHITRCGHTFCFSCISKCVEL-QIKCPKCSASLPDMNSVFPNFLLNELVQKHKIKSA 89 (140)
Q Consensus 19 ~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~-~~~CP~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 89 (140)
.+.+.|||+.++|.+||.+++||+|++.+|..|+.. ...||.|+.++...+ +.+|..+...++.|.....
T Consensus 2 P~~f~CpIt~~lM~dPVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~~-l~pn~~Lk~~I~~~~~~~~ 72 (73)
T PF04564_consen 2 PDEFLCPITGELMRDPVILPSGHTYERSAIERWLEQNGGTDPFTRQPLSESD-LIPNRALKSAIEEWCAENK 72 (73)
T ss_dssp SGGGB-TTTSSB-SSEEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SGGG-SEE-HHHHHHHHHHHHHCT
T ss_pred CcccCCcCcCcHhhCceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCccc-ceECHHHHHHHHHHHHHcc
Confidence 468999999999999999999999999999999987 889999999999877 9999999999999987653
No 5
>KOG0287|consensus
Probab=99.56 E-value=8.5e-16 Score=112.82 Aligned_cols=72 Identities=33% Similarity=0.701 Sum_probs=65.8
Q ss_pred CCCCCcccccccchhhhceecCCCCcccHhhHHHHhhcCCCCCCCCCCCCCCCCCccchHHHHHHHHHHhcCC
Q psy10659 17 PPDNDLLCPICFELIREAHITRCGHTFCFSCISKCVELQIKCPKCSASLPDMNSVFPNFLLNELVQKHKIKSA 89 (140)
Q Consensus 17 ~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~CP~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 89 (140)
.+++.++|.||+++|..|+++||||+||.-||..++..+..||.|..++...+ ++.|..+.++++.+.....
T Consensus 19 ~lD~lLRC~IC~eyf~ip~itpCsHtfCSlCIR~~L~~~p~CP~C~~~~~Es~-Lr~n~il~Eiv~S~~~~R~ 90 (442)
T KOG0287|consen 19 TLDDLLRCGICFEYFNIPMITPCSHTFCSLCIRKFLSYKPQCPTCCVTVTESD-LRNNRILDEIVKSLNFARN 90 (442)
T ss_pred hhHHHHHHhHHHHHhcCceeccccchHHHHHHHHHhccCCCCCceecccchhh-hhhhhHHHHHHHHHHHHHH
Confidence 45678999999999999999999999999999999999999999999999988 9999999999988766543
No 6
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=99.55 E-value=3.1e-15 Score=103.09 Aligned_cols=53 Identities=34% Similarity=0.873 Sum_probs=46.0
Q ss_pred CCCCCcccccccchhhhceecCCCCcccHhhHHHHhhc----------------CCCCCCCCCCCCCCC
Q psy10659 17 PPDNDLLCPICFELIREAHITRCGHTFCFSCISKCVEL----------------QIKCPKCSASLPDMN 69 (140)
Q Consensus 17 ~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~----------------~~~CP~C~~~~~~~~ 69 (140)
+..+++.|+||++.+.+|++++|||+||..||..|+.. ...||.|+..++...
T Consensus 14 ~~~~~~~CpICld~~~dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~ 82 (193)
T PLN03208 14 DSGGDFDCNICLDQVRDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEAT 82 (193)
T ss_pred cCCCccCCccCCCcCCCcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhc
Confidence 44567999999999999999999999999999999742 357999999987754
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=99.50 E-value=9.5e-15 Score=76.74 Aligned_cols=38 Identities=50% Similarity=1.249 Sum_probs=33.8
Q ss_pred cccccchhhhc-eecCCCCcccHhhHHHHhhcCCCCCCC
Q psy10659 24 CPICFELIREA-HITRCGHTFCFSCISKCVELQIKCPKC 61 (140)
Q Consensus 24 C~IC~~~~~~p-~~~~CgH~fC~~Ci~~~~~~~~~CP~C 61 (140)
|+||.+.+.+| +.++|||+||..|+.+|++....||.|
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 578999999999999999988899987
No 8
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=99.47 E-value=2.3e-14 Score=103.52 Aligned_cols=73 Identities=29% Similarity=0.422 Sum_probs=64.4
Q ss_pred CCCCCcccccccchhhhceecCCCCcccHhhHHHHhhcCCCCCCCCCCCCCCCCCccchHHHHHHHHHHhcCCC
Q psy10659 17 PPDNDLLCPICFELIREAHITRCGHTFCFSCISKCVELQIKCPKCSASLPDMNSVFPNFLLNELVQKHKIKSAQ 90 (140)
Q Consensus 17 ~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~CP~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 90 (140)
.++..+.|.||.+.++.|+.++|||+||.-||..++..+..||+|+....... ++.+..+.++++.+......
T Consensus 21 ~LDs~lrC~IC~~~i~ip~~TtCgHtFCslCIR~hL~~qp~CP~Cr~~~~esr-lr~~s~~~ei~es~~~~r~~ 93 (391)
T COG5432 21 GLDSMLRCRICDCRISIPCETTCGHTFCSLCIRRHLGTQPFCPVCREDPCESR-LRGSSGSREINESHARNRDL 93 (391)
T ss_pred cchhHHHhhhhhheeecceecccccchhHHHHHHHhcCCCCCccccccHHhhh-cccchhHHHHHHhhhhccHH
Confidence 45677999999999999999999999999999999999999999999888777 77788888888877766554
No 9
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=99.45 E-value=1.2e-14 Score=82.50 Aligned_cols=60 Identities=32% Similarity=0.769 Sum_probs=34.5
Q ss_pred CCCcccccccchhhhceec-CCCCcccHhhHHHHhhcCCCCCCCCCCCCCCCCCccchHHHHHH
Q psy10659 19 DNDLLCPICFELIREAHIT-RCGHTFCFSCISKCVELQIKCPKCSASLPDMNSVFPNFLLNELV 81 (140)
Q Consensus 19 ~~~~~C~IC~~~~~~p~~~-~CgH~fC~~Ci~~~~~~~~~CP~C~~~~~~~~~~~~~~~~~~~~ 81 (140)
++.+.|++|.+++++||.+ .|.|+||..||...+. ..||+|..+....+ +..|..+.+++
T Consensus 5 e~lLrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~--~~CPvC~~Paw~qD-~~~NrqLd~~i 65 (65)
T PF14835_consen 5 EELLRCSICFDILKEPVCLGGCEHIFCSSCIRDCIG--SECPVCHTPAWIQD-IQINRQLDSMI 65 (65)
T ss_dssp HHTTS-SSS-S--SS-B---SSS--B-TTTGGGGTT--TB-SSS--B-S-SS-----HHHHHHH
T ss_pred HHhcCCcHHHHHhcCCceeccCccHHHHHHhHHhcC--CCCCCcCChHHHHH-HHhhhhhhccC
Confidence 4578999999999999865 9999999999987553 45999999998888 99999988775
No 10
>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=99.44 E-value=4.7e-14 Score=78.05 Aligned_cols=47 Identities=38% Similarity=0.918 Sum_probs=41.5
Q ss_pred CCcccccccchhhhceecCCCCc-ccHhhHHHHhhcCCCCCCCCCCCC
Q psy10659 20 NDLLCPICFELIREAHITRCGHT-FCFSCISKCVELQIKCPKCSASLP 66 (140)
Q Consensus 20 ~~~~C~IC~~~~~~p~~~~CgH~-fC~~Ci~~~~~~~~~CP~C~~~~~ 66 (140)
++..|+||++...+++.+||||. ||..|+.+|+.....||+||+++.
T Consensus 1 ~~~~C~iC~~~~~~~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 1 EDEECPICFENPRDVVLLPCGHLCFCEECAERLLKRKKKCPICRQPIE 48 (50)
T ss_dssp -HSB-TTTSSSBSSEEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred CcCCCccCCccCCceEEeCCCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence 35789999999999999999999 999999999999999999998765
No 11
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=99.44 E-value=3.1e-14 Score=76.72 Aligned_cols=40 Identities=38% Similarity=0.871 Sum_probs=34.8
Q ss_pred ccccccchhhh---ceecCCCCcccHhhHHHHhhcCCCCCCCC
Q psy10659 23 LCPICFELIRE---AHITRCGHTFCFSCISKCVELQIKCPKCS 62 (140)
Q Consensus 23 ~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~CP~C~ 62 (140)
.|+||++.+.. .+.++|||.||.+|+..|++.+..||+||
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 69999999953 45679999999999999999999999996
No 12
>KOG0320|consensus
Probab=99.43 E-value=8.3e-14 Score=94.07 Aligned_cols=51 Identities=33% Similarity=0.885 Sum_probs=45.0
Q ss_pred CCCcccccccchhhhc--eecCCCCcccHhhHHHHhhcCCCCCCCCCCCCCCC
Q psy10659 19 DNDLLCPICFELIREA--HITRCGHTFCFSCISKCVELQIKCPKCSASLPDMN 69 (140)
Q Consensus 19 ~~~~~C~IC~~~~~~p--~~~~CgH~fC~~Ci~~~~~~~~~CP~C~~~~~~~~ 69 (140)
+....||||++.+.+. +.+.|||+||..||+..++....||+|++.++.+.
T Consensus 129 ~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~k~ 181 (187)
T KOG0320|consen 129 EGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITHKQ 181 (187)
T ss_pred ccccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCcccccchhh
Confidence 4568999999999764 56899999999999999999999999999877665
No 13
>KOG0823|consensus
Probab=99.43 E-value=6.3e-14 Score=98.37 Aligned_cols=52 Identities=29% Similarity=0.779 Sum_probs=46.0
Q ss_pred CCCCcccccccchhhhceecCCCCcccHhhHHHHhhc---CCCCCCCCCCCCCCC
Q psy10659 18 PDNDLLCPICFELIREAHITRCGHTFCFSCISKCVEL---QIKCPKCSASLPDMN 69 (140)
Q Consensus 18 ~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~---~~~CP~C~~~~~~~~ 69 (140)
....+.|.||++.-++||++.|||.||+.||.+|+.. ...||+|+..++...
T Consensus 44 ~~~~FdCNICLd~akdPVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~ 98 (230)
T KOG0823|consen 44 DGGFFDCNICLDLAKDPVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDT 98 (230)
T ss_pred CCCceeeeeeccccCCCEEeecccceehHHHHHHHhhcCCCeeCCccccccccce
Confidence 3567999999999999999999999999999999974 456899999887765
No 14
>KOG0317|consensus
Probab=99.42 E-value=9.8e-14 Score=100.14 Aligned_cols=52 Identities=31% Similarity=0.790 Sum_probs=47.7
Q ss_pred CCCCcccccccchhhhceecCCCCcccHhhHHHHhhcCCCCCCCCCCCCCCC
Q psy10659 18 PDNDLLCPICFELIREAHITRCGHTFCFSCISKCVELQIKCPKCSASLPDMN 69 (140)
Q Consensus 18 ~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~CP~C~~~~~~~~ 69 (140)
.+....|.+|++...+|..+||||.||..||..|......||+||..+...+
T Consensus 236 ~~a~~kC~LCLe~~~~pSaTpCGHiFCWsCI~~w~~ek~eCPlCR~~~~psk 287 (293)
T KOG0317|consen 236 PEATRKCSLCLENRSNPSATPCGHIFCWSCILEWCSEKAECPLCREKFQPSK 287 (293)
T ss_pred CCCCCceEEEecCCCCCCcCcCcchHHHHHHHHHHccccCCCcccccCCCcc
Confidence 3456899999999999999999999999999999999899999999888765
No 15
>PHA02929 N1R/p28-like protein; Provisional
Probab=99.39 E-value=2.6e-13 Score=97.09 Aligned_cols=50 Identities=28% Similarity=0.748 Sum_probs=42.7
Q ss_pred CCCCcccccccchhhhc--------eecCCCCcccHhhHHHHhhcCCCCCCCCCCCCC
Q psy10659 18 PDNDLLCPICFELIREA--------HITRCGHTFCFSCISKCVELQIKCPKCSASLPD 67 (140)
Q Consensus 18 ~~~~~~C~IC~~~~~~p--------~~~~CgH~fC~~Ci~~~~~~~~~CP~C~~~~~~ 67 (140)
..++..|+||++.+.++ +.++|||.||..||.+|+.....||+||..+..
T Consensus 171 ~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~~ 228 (238)
T PHA02929 171 RSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFIS 228 (238)
T ss_pred CCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEeeE
Confidence 35578999999987653 456899999999999999999999999988764
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=99.35 E-value=4.3e-13 Score=71.10 Aligned_cols=38 Identities=45% Similarity=1.179 Sum_probs=35.2
Q ss_pred cccccchhhhce-ecCCCCcccHhhHHHHhh--cCCCCCCC
Q psy10659 24 CPICFELIREAH-ITRCGHTFCFSCISKCVE--LQIKCPKC 61 (140)
Q Consensus 24 C~IC~~~~~~p~-~~~CgH~fC~~Ci~~~~~--~~~~CP~C 61 (140)
|+||++.+.+|+ .++|||.||..|+..|++ ....||.|
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 899999999999 789999999999999998 56789987
No 17
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=99.26 E-value=3e-12 Score=68.14 Aligned_cols=35 Identities=43% Similarity=1.088 Sum_probs=22.6
Q ss_pred cccccchhhh----ceecCCCCcccHhhHHHHhhc----CCCCC
Q psy10659 24 CPICFELIRE----AHITRCGHTFCFSCISKCVEL----QIKCP 59 (140)
Q Consensus 24 C~IC~~~~~~----p~~~~CgH~fC~~Ci~~~~~~----~~~CP 59 (140)
||||.+ +.+ |+.++|||+||.+|+.++... ..+||
T Consensus 1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~~~~~~kCP 43 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKSDRNRFKCP 43 (43)
T ss_dssp -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcCCCCeeeCc
Confidence 899999 887 899999999999999999973 34676
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=99.25 E-value=6.1e-12 Score=67.34 Aligned_cols=42 Identities=45% Similarity=1.046 Sum_probs=37.0
Q ss_pred ccccccchhhhceec-CCCCcccHhhHHHHhhc-CCCCCCCCCC
Q psy10659 23 LCPICFELIREAHIT-RCGHTFCFSCISKCVEL-QIKCPKCSAS 64 (140)
Q Consensus 23 ~C~IC~~~~~~p~~~-~CgH~fC~~Ci~~~~~~-~~~CP~C~~~ 64 (140)
.|+||.+.+.+++.+ +|||.||..|+..|+.. ...||.|+..
T Consensus 1 ~C~iC~~~~~~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~ 44 (45)
T cd00162 1 ECPICLEEFREPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTP 44 (45)
T ss_pred CCCcCchhhhCceEecCCCChhcHHHHHHHHHhCcCCCCCCCCc
Confidence 599999999777766 59999999999999986 7789999875
No 19
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=99.24 E-value=5.6e-12 Score=67.79 Aligned_cols=41 Identities=44% Similarity=1.033 Sum_probs=35.5
Q ss_pred ccccccchh---hhceecCCCCcccHhhHHHHhhcCCCCCCCCC
Q psy10659 23 LCPICFELI---REAHITRCGHTFCFSCISKCVELQIKCPKCSA 63 (140)
Q Consensus 23 ~C~IC~~~~---~~p~~~~CgH~fC~~Ci~~~~~~~~~CP~C~~ 63 (140)
.|+||++.+ ..|+.++|||+||..|+..+......||+|++
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 499999999 34677899999999999999866788999984
No 20
>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=99.19 E-value=1.3e-11 Score=73.39 Aligned_cols=40 Identities=38% Similarity=0.870 Sum_probs=33.4
Q ss_pred ccccccchhhhc------------e-ecCCCCcccHhhHHHHhhcCCCCCCCC
Q psy10659 23 LCPICFELIREA------------H-ITRCGHTFCFSCISKCVELQIKCPKCS 62 (140)
Q Consensus 23 ~C~IC~~~~~~p------------~-~~~CgH~fC~~Ci~~~~~~~~~CP~C~ 62 (140)
.|+||++.+.++ + ..+|||.|+..||.+|++....||+||
T Consensus 21 ~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR 73 (73)
T PF12678_consen 21 NCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQNNTCPLCR 73 (73)
T ss_dssp BETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred cccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcCCcCCCCC
Confidence 499999999433 2 348999999999999999999999997
No 21
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=99.17 E-value=2.3e-11 Score=62.97 Aligned_cols=38 Identities=47% Similarity=1.152 Sum_probs=34.8
Q ss_pred cccccchhhhceecCCCCcccHhhHHHHhh-cCCCCCCC
Q psy10659 24 CPICFELIREAHITRCGHTFCFSCISKCVE-LQIKCPKC 61 (140)
Q Consensus 24 C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~-~~~~CP~C 61 (140)
|+||++....++.++|||.||..|+..|+. ....||.|
T Consensus 1 C~iC~~~~~~~~~~~C~H~~c~~C~~~~~~~~~~~CP~C 39 (39)
T smart00184 1 CPICLEELKDPVVLPCGHTFCRSCIRKWLKSGNNTCPIC 39 (39)
T ss_pred CCcCccCCCCcEEecCCChHHHHHHHHHHHhCcCCCCCC
Confidence 899999988899999999999999999998 66779987
No 22
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.16 E-value=1.1e-10 Score=86.05 Aligned_cols=50 Identities=34% Similarity=0.719 Sum_probs=39.0
Q ss_pred CCcccccccch-hhhce---ec-CCCCcccHhhHHHHhh-cCCCCCCCCCCCCCCC
Q psy10659 20 NDLLCPICFEL-IREAH---IT-RCGHTFCFSCISKCVE-LQIKCPKCSASLPDMN 69 (140)
Q Consensus 20 ~~~~C~IC~~~-~~~p~---~~-~CgH~fC~~Ci~~~~~-~~~~CP~C~~~~~~~~ 69 (140)
++..||+|... +.+|- .+ +|||.||..|+..++. +...||.|+..+....
T Consensus 2 d~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk~~ 57 (309)
T TIGR00570 2 DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLRKNN 57 (309)
T ss_pred CCCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCccchhh
Confidence 45789999993 44452 22 7999999999999775 4568999999887765
No 23
>PHA02926 zinc finger-like protein; Provisional
Probab=99.15 E-value=2.1e-11 Score=85.42 Aligned_cols=51 Identities=25% Similarity=0.746 Sum_probs=40.5
Q ss_pred CCCCCcccccccchhhh---------ceecCCCCcccHhhHHHHhhcC------CCCCCCCCCCCC
Q psy10659 17 PPDNDLLCPICFELIRE---------AHITRCGHTFCFSCISKCVELQ------IKCPKCSASLPD 67 (140)
Q Consensus 17 ~~~~~~~C~IC~~~~~~---------p~~~~CgH~fC~~Ci~~~~~~~------~~CP~C~~~~~~ 67 (140)
....+..|+||++...+ ++..+|+|+||..||..|.... ..||+||..+..
T Consensus 166 ~~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~ 231 (242)
T PHA02926 166 RVSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFRN 231 (242)
T ss_pred hccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceeee
Confidence 45678999999997633 2445999999999999999742 459999998764
No 24
>KOG2177|consensus
Probab=99.14 E-value=4.7e-11 Score=87.82 Aligned_cols=71 Identities=35% Similarity=0.784 Sum_probs=60.3
Q ss_pred CCCCCcccccccchhhhceecCCCCcccHhhHHHHhhcCCCCCCCCCCCCCCCCCccchHHHHHHHHHHhcCCC
Q psy10659 17 PPDNDLLCPICFELIREAHITRCGHTFCFSCISKCVELQIKCPKCSASLPDMNSVFPNFLLNELVQKHKIKSAQ 90 (140)
Q Consensus 17 ~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~CP~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 90 (140)
...+.+.|+||++.|.+|.+++|||+||..|+..++.....||.|+. ... . +.+|..+.++++.+......
T Consensus 9 ~~~~~~~C~iC~~~~~~p~~l~C~H~~c~~C~~~~~~~~~~Cp~cr~-~~~-~-~~~n~~l~~~~~~~~~~~~~ 79 (386)
T KOG2177|consen 9 VLQEELTCPICLEYFREPVLLPCGHNFCRACLTRSWEGPLSCPVCRP-PSR-N-LRPNVLLANLVERLRQLRLS 79 (386)
T ss_pred hccccccChhhHHHhhcCccccccchHhHHHHHHhcCCCcCCcccCC-chh-c-cCccHHHHHHHHHHHhcCCc
Confidence 45678999999999999988899999999999999986678999996 333 3 77999999999998876544
No 25
>KOG0978|consensus
Probab=99.14 E-value=1.2e-11 Score=99.35 Aligned_cols=59 Identities=36% Similarity=0.721 Sum_probs=51.5
Q ss_pred hhhcCCCCCCCcccccccchhhhceecCCCCcccHhhHHHHhh-cCCCCCCCCCCCCCCC
Q psy10659 11 LKRQHSPPDNDLLCPICFELIREAHITRCGHTFCFSCISKCVE-LQIKCPKCSASLPDMN 69 (140)
Q Consensus 11 ~~~~~~~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~-~~~~CP~C~~~~~~~~ 69 (140)
+..........+.||+|..-+++.+++.|||.||..|+...+. +..+||.|+..|..++
T Consensus 633 L~EElk~yK~~LkCs~Cn~R~Kd~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganD 692 (698)
T KOG0978|consen 633 LAEELKEYKELLKCSVCNTRWKDAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGAND 692 (698)
T ss_pred HHHHHHHHHhceeCCCccCchhhHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCccc
Confidence 3444445567899999999999999999999999999999987 5789999999999887
No 26
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.11 E-value=2.8e-11 Score=86.58 Aligned_cols=51 Identities=31% Similarity=0.677 Sum_probs=45.1
Q ss_pred CCCcccccccchhhhceecCCCCcccHhhHHH-HhhcCCC-CCCCCCCCCCCC
Q psy10659 19 DNDLLCPICFELIREAHITRCGHTFCFSCISK-CVELQIK-CPKCSASLPDMN 69 (140)
Q Consensus 19 ~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~-~~~~~~~-CP~C~~~~~~~~ 69 (140)
..+..|+||++....|..++|||.||..||.. |-..... ||+||..+..++
T Consensus 213 ~~d~kC~lC~e~~~~ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk~ 265 (271)
T COG5574 213 LADYKCFLCLEEPEVPSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVYPKK 265 (271)
T ss_pred ccccceeeeecccCCcccccccchhhHHHHHHHHHhhccccCchhhhhccchh
Confidence 55899999999999999999999999999999 8776665 999998776655
No 27
>KOG2164|consensus
Probab=99.11 E-value=3e-11 Score=93.29 Aligned_cols=49 Identities=35% Similarity=0.799 Sum_probs=44.4
Q ss_pred CcccccccchhhhceecCCCCcccHhhHHHHhhcC-----CCCCCCCCCCCCCC
Q psy10659 21 DLLCPICFELIREAHITRCGHTFCFSCISKCVELQ-----IKCPKCSASLPDMN 69 (140)
Q Consensus 21 ~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~-----~~CP~C~~~~~~~~ 69 (140)
+..||||+....-|+.+.|||.||..||.+|+... ..||+|+..+..++
T Consensus 186 ~~~CPICL~~~~~p~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kd 239 (513)
T KOG2164|consen 186 DMQCPICLEPPSVPVRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKD 239 (513)
T ss_pred CCcCCcccCCCCcccccccCceeeHHHHHHHHhhhcccCCccCCchhhhccccc
Confidence 78999999999999999999999999999999643 57999999988876
No 28
>KOG4628|consensus
Probab=98.98 E-value=2.5e-10 Score=85.42 Aligned_cols=47 Identities=28% Similarity=0.629 Sum_probs=39.9
Q ss_pred cccccccchhhhc---eecCCCCcccHhhHHHHhhcCC-CCCCCCCCCCCC
Q psy10659 22 LLCPICFELIREA---HITRCGHTFCFSCISKCVELQI-KCPKCSASLPDM 68 (140)
Q Consensus 22 ~~C~IC~~~~~~p---~~~~CgH~fC~~Ci~~~~~~~~-~CP~C~~~~~~~ 68 (140)
..|.||++.|... ..|||+|.||..||..|+.... .||+|+..+...
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 5999999999854 4579999999999999998764 499999876543
No 29
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=98.97 E-value=2.9e-10 Score=84.95 Aligned_cols=47 Identities=28% Similarity=0.725 Sum_probs=41.3
Q ss_pred CCCcccccccchhh-h------------ceecCCCCcccHhhHHHHhhcCCCCCCCCCCC
Q psy10659 19 DNDLLCPICFELIR-E------------AHITRCGHTFCFSCISKCVELQIKCPKCSASL 65 (140)
Q Consensus 19 ~~~~~C~IC~~~~~-~------------p~~~~CgH~fC~~Ci~~~~~~~~~CP~C~~~~ 65 (140)
.++-.|.||.+.+. . |..+||||.|+.+|++.|.+++.+||.||.++
T Consensus 285 n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERqQTCPICr~p~ 344 (491)
T COG5243 285 NSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQTCPICRRPV 344 (491)
T ss_pred CCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhccCCCcccCcc
Confidence 56789999999853 2 36789999999999999999999999999984
No 30
>KOG0311|consensus
Probab=98.90 E-value=3.4e-10 Score=84.02 Aligned_cols=70 Identities=31% Similarity=0.656 Sum_probs=58.8
Q ss_pred CCCCcccccccchhhhceec-CCCCcccHhhHHHHhh-cCCCCCCCCCCCCCCCCCccchHHHHHHHHHHhc
Q psy10659 18 PDNDLLCPICFELIREAHIT-RCGHTFCFSCISKCVE-LQIKCPKCSASLPDMNSVFPNFLLNELVQKHKIK 87 (140)
Q Consensus 18 ~~~~~~C~IC~~~~~~p~~~-~CgH~fC~~Ci~~~~~-~~~~CP~C~~~~~~~~~~~~~~~~~~~~~~~~~~ 87 (140)
+.-++.|+||+++++..+++ .|+|.||..||..-++ +...||.||+.+..+..+.++.....++.++...
T Consensus 40 ~~~~v~c~icl~llk~tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~SkrsLr~Dp~fdaLis~i~~s 111 (381)
T KOG0311|consen 40 FDIQVICPICLSLLKKTMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVSKRSLRIDPNFDALISKIYPS 111 (381)
T ss_pred hhhhhccHHHHHHHHhhcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhccccccCCCCccHHHHHHHHhcc
Confidence 35678999999999999887 7999999999998887 5678999999998887788877777777665544
No 31
>KOG1002|consensus
Probab=98.87 E-value=3.2e-09 Score=82.68 Aligned_cols=107 Identities=20% Similarity=0.432 Sum_probs=71.5
Q ss_pred CCCCCcccccccchhhhceecCCCCcccHhhHHHHhhc-----CCCCCCCCCCCCCCCCCccc--------hHHHHHHHH
Q psy10659 17 PPDNDLLCPICFELIREAHITRCGHTFCFSCISKCVEL-----QIKCPKCSASLPDMNSVFPN--------FLLNELVQK 83 (140)
Q Consensus 17 ~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~-----~~~CP~C~~~~~~~~~~~~~--------~~~~~~~~~ 83 (140)
+......|.+|.+.-.+++.++|.|.||..|+.+|..+ ..+||.|...++... ..+. +....++..
T Consensus 532 enk~~~~C~lc~d~aed~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiDl-se~alek~~l~~Fk~sSIlnR 610 (791)
T KOG1002|consen 532 ENKGEVECGLCHDPAEDYIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSIDL-SEPALEKTDLKGFKASSILNR 610 (791)
T ss_pred cccCceeecccCChhhhhHhhhhhHHHHHHHHHHHHHhhhcccCCCCccccccccccc-cchhhhhcchhhhhhHHHhhh
Confidence 34567899999999999999999999999999999863 478999988765432 1111 111122221
Q ss_pred HH---hcCCCChHHHHHHhh------hcCCCcccccHHHHHHHHHHHHHH
Q psy10659 84 HK---IKSAQDSDGLRDFVA------SESQNLSLPDVNLMLEVLNQRKHL 124 (140)
Q Consensus 84 ~~---~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~l~~~~~~~~~ 124 (140)
+. -....+.+.+++.+- ...+++.|++++++|+.+.++..+
T Consensus 611 inm~~~qsSTKIEAL~EEl~~l~~rd~t~KsIVFSQFTSmLDLi~~rL~k 660 (791)
T KOG1002|consen 611 INMDDWQSSTKIEALVEELYFLRERDRTAKSIVFSQFTSMLDLIEWRLGK 660 (791)
T ss_pred cchhhhcchhHHHHHHHHHHHHHHcccchhhhhHHHHHHHHHHHHHHhhc
Confidence 11 112224444433222 234678899999999999988754
No 32
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=98.86 E-value=1.7e-09 Score=65.30 Aligned_cols=48 Identities=29% Similarity=0.661 Sum_probs=37.8
Q ss_pred CCCcccccccchhhh------------cee-cCCCCcccHhhHHHHhhc---CCCCCCCCCCCC
Q psy10659 19 DNDLLCPICFELIRE------------AHI-TRCGHTFCFSCISKCVEL---QIKCPKCSASLP 66 (140)
Q Consensus 19 ~~~~~C~IC~~~~~~------------p~~-~~CgH~fC~~Ci~~~~~~---~~~CP~C~~~~~ 66 (140)
.++..|+||+..|.. |+. -.|+|.|+..||.+|+.+ +..||+||.+..
T Consensus 19 ~~dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~ 82 (85)
T PF12861_consen 19 ANDDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWK 82 (85)
T ss_pred CCCCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeee
Confidence 347788888888762 233 379999999999999974 478999998754
No 33
>KOG2660|consensus
Probab=98.80 E-value=2.6e-09 Score=78.75 Aligned_cols=86 Identities=26% Similarity=0.480 Sum_probs=66.9
Q ss_pred CCCCCCCcccccccchhhhceec-CCCCcccHhhHHHHhhcCCCCCCCCCCCCCCC---CCccchHHHHHHHHHHhcCC-
Q psy10659 15 HSPPDNDLLCPICFELIREAHIT-RCGHTFCFSCISKCVELQIKCPKCSASLPDMN---SVFPNFLLNELVQKHKIKSA- 89 (140)
Q Consensus 15 ~~~~~~~~~C~IC~~~~~~p~~~-~CgH~fC~~Ci~~~~~~~~~CP~C~~~~~~~~---~~~~~~~~~~~~~~~~~~~~- 89 (140)
..++.....|.+|..+|.++-++ -|-|+||++||..++.....||.|+..+.... .+..+..++.++.++-....
T Consensus 9 ~~~~n~~itC~LC~GYliDATTI~eCLHTFCkSCivk~l~~~~~CP~C~i~ih~t~pl~ni~~DrtlqdiVyKLVPgl~e 88 (331)
T KOG2660|consen 9 LTELNPHITCRLCGGYLIDATTITECLHTFCKSCIVKYLEESKYCPTCDIVIHKTHPLLNIRSDRTLQDIVYKLVPGLQE 88 (331)
T ss_pred hhhcccceehhhccceeecchhHHHHHHHHHHHHHHHHHHHhccCCccceeccCccccccCCcchHHHHHHHHHcchHHH
Confidence 44667789999999999999765 79999999999999999999999998876542 46777888888877655432
Q ss_pred CChHHHHHHhh
Q psy10659 90 QDSDGLRDFVA 100 (140)
Q Consensus 90 ~~~~~~~~~~~ 100 (140)
....+++.|..
T Consensus 89 rE~k~~rdFy~ 99 (331)
T KOG2660|consen 89 REMKRRRDFYK 99 (331)
T ss_pred HHHHHHHHHHH
Confidence 24444555554
No 34
>KOG0802|consensus
Probab=98.78 E-value=2.1e-09 Score=85.97 Aligned_cols=49 Identities=39% Similarity=0.735 Sum_probs=43.8
Q ss_pred CCCcccccccchhhh-----ceecCCCCcccHhhHHHHhhcCCCCCCCCCCCCC
Q psy10659 19 DNDLLCPICFELIRE-----AHITRCGHTFCFSCISKCVELQIKCPKCSASLPD 67 (140)
Q Consensus 19 ~~~~~C~IC~~~~~~-----p~~~~CgH~fC~~Ci~~~~~~~~~CP~C~~~~~~ 67 (140)
..+..|+||.+.+.. |..++|||.||..|+..|++....||.||..+..
T Consensus 289 ~~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~qtCP~CR~~~~~ 342 (543)
T KOG0802|consen 289 LSDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQQTCPTCRTVLYD 342 (543)
T ss_pred hcCCeeeeechhhccccccccceeecccchHHHHHHHHHHHhCcCCcchhhhhc
Confidence 347899999999998 7889999999999999999999999999984433
No 35
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.71 E-value=8.4e-09 Score=75.39 Aligned_cols=48 Identities=27% Similarity=0.747 Sum_probs=40.5
Q ss_pred CCcccccccchhhhc---eecCCCCcccHhhHHHHhh-cCCCCCCCCCCCCC
Q psy10659 20 NDLLCPICFELIREA---HITRCGHTFCFSCISKCVE-LQIKCPKCSASLPD 67 (140)
Q Consensus 20 ~~~~C~IC~~~~~~p---~~~~CgH~fC~~Ci~~~~~-~~~~CP~C~~~~~~ 67 (140)
....|.||++.+.+- +.+||.|.||..|+..|+. .+..||+||.++..
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 347999999988642 5689999999999999998 56789999987754
No 36
>KOG0297|consensus
Probab=98.70 E-value=1.6e-08 Score=77.93 Aligned_cols=81 Identities=33% Similarity=0.650 Sum_probs=62.6
Q ss_pred CCChhhhhcCCCCCCCcccccccchhhhceec-CCCCcccHhhHHHHhhcCCCCCCCCCCCCCCCCCccchHHHHHHHHH
Q psy10659 6 TPSRSLKRQHSPPDNDLLCPICFELIREAHIT-RCGHTFCFSCISKCVELQIKCPKCSASLPDMNSVFPNFLLNELVQKH 84 (140)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~C~IC~~~~~~p~~~-~CgH~fC~~Ci~~~~~~~~~CP~C~~~~~~~~~~~~~~~~~~~~~~~ 84 (140)
.+...+.....++++++.|++|...+.+|+.+ .|||.||..|+..|...+..||.|+..+.....+.........+...
T Consensus 6 ~~~~~~~~~~~~~~~~l~C~~C~~vl~~p~~~~~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~~~~~~~~~~~~~~~l 85 (391)
T KOG0297|consen 6 TMGFDLKHLGRPLDENLLCPICMSVLRDPVQTTTCGHRFCAGCLLESLSNHQKCPVCRQELTQAEELPVPRALRRELLKL 85 (391)
T ss_pred cccccccccCCCCcccccCccccccccCCCCCCCCCCcccccccchhhccCcCCcccccccchhhccCchHHHHHHHHhc
Confidence 34445555666688999999999999999985 99999999999999999999999988877766444344444444444
Q ss_pred Hh
Q psy10659 85 KI 86 (140)
Q Consensus 85 ~~ 86 (140)
..
T Consensus 86 ~i 87 (391)
T KOG0297|consen 86 PI 87 (391)
T ss_pred cc
Confidence 33
No 37
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=98.65 E-value=1.1e-08 Score=70.73 Aligned_cols=47 Identities=28% Similarity=0.626 Sum_probs=42.8
Q ss_pred CcccccccchhhhceecCCCCcccHhhHHHHhhcCCCCCCCCCCCCC
Q psy10659 21 DLLCPICFELIREAHITRCGHTFCFSCISKCVELQIKCPKCSASLPD 67 (140)
Q Consensus 21 ~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~CP~C~~~~~~ 67 (140)
.+.|.||...|..||++.|||.||..|...-.+....|-+|++...-
T Consensus 196 PF~C~iCKkdy~spvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~G 242 (259)
T COG5152 196 PFLCGICKKDYESPVVTECGHSFCSLCAIRKYQKGDECGVCGKATYG 242 (259)
T ss_pred ceeehhchhhccchhhhhcchhHHHHHHHHHhccCCcceecchhhcc
Confidence 47999999999999999999999999999888888999999986544
No 38
>KOG4159|consensus
Probab=98.65 E-value=2.2e-08 Score=76.71 Aligned_cols=72 Identities=25% Similarity=0.643 Sum_probs=55.6
Q ss_pred CCCCCCcccccccchhhhceecCCCCcccHhhHHHHhhcCCCCCCCCCCCCCCC---CCc-cchHHHHHHHHHHhc
Q psy10659 16 SPPDNDLLCPICFELIREAHITRCGHTFCFSCISKCVELQIKCPKCSASLPDMN---SVF-PNFLLNELVQKHKIK 87 (140)
Q Consensus 16 ~~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~CP~C~~~~~~~~---~~~-~~~~~~~~~~~~~~~ 87 (140)
..+..++.|-||...+..|++++|||+||..||.+.+.....||.|+..+.... ... .|.....++..+...
T Consensus 79 ~~~~sef~c~vc~~~l~~pv~tpcghs~c~~Cl~r~ld~~~~cp~Cr~~l~e~~~~~~~~~~~r~~~~li~~F~~~ 154 (398)
T KOG4159|consen 79 EEIRSEFECCVCSRALYPPVVTPCGHSFCLECLDRSLDQETECPLCRDELVELPALEQALSLNRLLCKLITKFLEG 154 (398)
T ss_pred ccccchhhhhhhHhhcCCCccccccccccHHHHHHHhccCCCCcccccccccchHHHHHHHHHHHHHHHHHHhhhh
Confidence 345778999999999999999999999999999998888889999999887532 111 244444666655544
No 39
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=98.57 E-value=2.6e-08 Score=56.22 Aligned_cols=41 Identities=29% Similarity=0.631 Sum_probs=29.9
Q ss_pred CCcccccccchhhhceec-CCCCcccHhhHHHHhh--cCCCCCC
Q psy10659 20 NDLLCPICFELIREAHIT-RCGHTFCFSCISKCVE--LQIKCPK 60 (140)
Q Consensus 20 ~~~~C~IC~~~~~~p~~~-~CgH~fC~~Ci~~~~~--~~~~CP~ 60 (140)
-.+.|||.+..|.+||.. .|||+|.+..|.+|+. ....||+
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 458999999999999985 9999999999999994 4567998
No 40
>KOG0824|consensus
Probab=98.56 E-value=2.9e-08 Score=72.53 Aligned_cols=49 Identities=22% Similarity=0.502 Sum_probs=43.0
Q ss_pred CcccccccchhhhceecCCCCcccHhhHHHHhhcC-CCCCCCCCCCCCCC
Q psy10659 21 DLLCPICFELIREAHITRCGHTFCFSCISKCVELQ-IKCPKCSASLPDMN 69 (140)
Q Consensus 21 ~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~-~~CP~C~~~~~~~~ 69 (140)
.-.|+||+....-|+.++|+|.||.-||+...... ..|++||.++...-
T Consensus 7 ~~eC~IC~nt~n~Pv~l~C~HkFCyiCiKGsy~ndk~~CavCR~pids~i 56 (324)
T KOG0824|consen 7 KKECLICYNTGNCPVNLYCFHKFCYICIKGSYKNDKKTCAVCRFPIDSTI 56 (324)
T ss_pred CCcceeeeccCCcCccccccchhhhhhhcchhhcCCCCCceecCCCCcch
Confidence 56899999999999999999999999999877654 56999999988754
No 41
>KOG1813|consensus
Probab=98.53 E-value=4.8e-08 Score=71.19 Aligned_cols=47 Identities=32% Similarity=0.619 Sum_probs=43.0
Q ss_pred CcccccccchhhhceecCCCCcccHhhHHHHhhcCCCCCCCCCCCCC
Q psy10659 21 DLLCPICFELIREAHITRCGHTFCFSCISKCVELQIKCPKCSASLPD 67 (140)
Q Consensus 21 ~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~CP~C~~~~~~ 67 (140)
.+.|-||...|..||++.|||.||..|...-++....|++|.+....
T Consensus 241 Pf~c~icr~~f~~pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g 287 (313)
T KOG1813|consen 241 PFKCFICRKYFYRPVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHG 287 (313)
T ss_pred CccccccccccccchhhcCCceeehhhhccccccCCcceeccccccc
Confidence 36899999999999999999999999999988888999999987654
No 42
>KOG2879|consensus
Probab=98.46 E-value=1.2e-07 Score=68.50 Aligned_cols=51 Identities=31% Similarity=0.813 Sum_probs=43.5
Q ss_pred CCCCCCcccccccchhhhceec-CCCCcccHhhHHHHhh--cCCCCCCCCCCCC
Q psy10659 16 SPPDNDLLCPICFELIREAHIT-RCGHTFCFSCISKCVE--LQIKCPKCSASLP 66 (140)
Q Consensus 16 ~~~~~~~~C~IC~~~~~~p~~~-~CgH~fC~~Ci~~~~~--~~~~CP~C~~~~~ 66 (140)
+....+.+||+|.+....|... +|||.||.-|+..-.. ..+.||.|+.++.
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 3446789999999999999876 6999999999988765 4589999998765
No 43
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=98.44 E-value=2.7e-07 Score=67.63 Aligned_cols=65 Identities=35% Similarity=0.680 Sum_probs=52.5
Q ss_pred cccccccchhhhceec-CCCCcccHhhHHHHhh-cCCCCCCCCCCCCCCCCCccchHHHHHHHHHHh
Q psy10659 22 LLCPICFELIREAHIT-RCGHTFCFSCISKCVE-LQIKCPKCSASLPDMNSVFPNFLLNELVQKHKI 86 (140)
Q Consensus 22 ~~C~IC~~~~~~p~~~-~CgH~fC~~Ci~~~~~-~~~~CP~C~~~~~~~~~~~~~~~~~~~~~~~~~ 86 (140)
+.||.|..++.+|+.+ .|||.||..||...+. ..+.||.|.+.--..+.+.++......|+.+..
T Consensus 275 LkCplc~~Llrnp~kT~cC~~~fc~eci~~al~dsDf~CpnC~rkdvlld~l~pD~dk~~EvE~~lk 341 (427)
T COG5222 275 LKCPLCHCLLRNPMKTPCCGHTFCDECIGTALLDSDFKCPNCSRKDVLLDGLTPDIDKKLEVEKALK 341 (427)
T ss_pred ccCcchhhhhhCcccCccccchHHHHHHhhhhhhccccCCCcccccchhhccCccHHHHHHHHHHHH
Confidence 9999999999999999 6999999999998775 678999998743334447777777766666655
No 44
>KOG1734|consensus
Probab=98.25 E-value=1.9e-07 Score=67.38 Aligned_cols=55 Identities=25% Similarity=0.499 Sum_probs=43.2
Q ss_pred CCCcccccccchhhhc----------eecCCCCcccHhhHHHHhh--cCCCCCCCCCCCCCCCCCccc
Q psy10659 19 DNDLLCPICFELIREA----------HITRCGHTFCFSCISKCVE--LQIKCPKCSASLPDMNSVFPN 74 (140)
Q Consensus 19 ~~~~~C~IC~~~~~~p----------~~~~CgH~fC~~Ci~~~~~--~~~~CP~C~~~~~~~~~~~~~ 74 (140)
.++-.|.||...+... ..++|+|+|+..||..|-. .+.+||.|++.+..+. +..|
T Consensus 222 l~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVdl~r-mfsn 288 (328)
T KOG1734|consen 222 LSDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVDLKR-MFSN 288 (328)
T ss_pred CCcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhhHhh-hccC
Confidence 3578899999877533 3579999999999999975 4678999999887665 4444
No 45
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=98.22 E-value=7e-07 Score=52.83 Aligned_cols=46 Identities=24% Similarity=0.455 Sum_probs=35.8
Q ss_pred cccccccchhhhc---------------ee-cCCCCcccHhhHHHHhhcCCCCCCCCCCCCC
Q psy10659 22 LLCPICFELIREA---------------HI-TRCGHTFCFSCISKCVELQIKCPKCSASLPD 67 (140)
Q Consensus 22 ~~C~IC~~~~~~p---------------~~-~~CgH~fC~~Ci~~~~~~~~~CP~C~~~~~~ 67 (140)
..|.||+.-+.++ +. -.|.|.|+..||.+|+.+...||++++....
T Consensus 21 d~CaICRnhim~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~Tk~~CPld~q~w~~ 82 (88)
T COG5194 21 DVCAICRNHIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQTWVL 82 (88)
T ss_pred chhhhhhccccCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhhCCCCCCCCceeEE
Confidence 5677777765432 22 2599999999999999999999999987543
No 46
>KOG4172|consensus
Probab=98.12 E-value=5.9e-07 Score=49.33 Aligned_cols=46 Identities=30% Similarity=0.762 Sum_probs=39.5
Q ss_pred CcccccccchhhhceecCCCC-cccHhhHHHHhh-cCCCCCCCCCCCC
Q psy10659 21 DLLCPICFELIREAHITRCGH-TFCFSCISKCVE-LQIKCPKCSASLP 66 (140)
Q Consensus 21 ~~~C~IC~~~~~~p~~~~CgH-~fC~~Ci~~~~~-~~~~CP~C~~~~~ 66 (140)
..+|.||.+-..+.|...||| -.|..|-.+.++ .+..||.||.++.
T Consensus 7 ~dECTICye~pvdsVlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~ 54 (62)
T KOG4172|consen 7 SDECTICYEHPVDSVLYTCGHMCMCYACGLRLKKALHGCCPICRAPIK 54 (62)
T ss_pred ccceeeeccCcchHHHHHcchHHhHHHHHHHHHHccCCcCcchhhHHH
Confidence 478999999988888889999 579999988887 5788999998754
No 47
>KOG0804|consensus
Probab=98.05 E-value=1.8e-06 Score=66.36 Aligned_cols=48 Identities=27% Similarity=0.625 Sum_probs=38.8
Q ss_pred CCCCCcccccccchhhhce----ecCCCCcccHhhHHHHhhcCCCCCCCCCCCC
Q psy10659 17 PPDNDLLCPICFELIREAH----ITRCGHTFCFSCISKCVELQIKCPKCSASLP 66 (140)
Q Consensus 17 ~~~~~~~C~IC~~~~~~p~----~~~CgH~fC~~Ci~~~~~~~~~CP~C~~~~~ 66 (140)
...+.-+||||++-+..-+ .+.|.|+|+..|+..|. ...||+||....
T Consensus 171 ~~tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~--~~scpvcR~~q~ 222 (493)
T KOG0804|consen 171 GLTELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWW--DSSCPVCRYCQS 222 (493)
T ss_pred CcccCCCcchhHhhcCccccceeeeecccccchHHHhhcc--cCcChhhhhhcC
Confidence 3457789999999987654 45899999999999997 567888886554
No 48
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=98.05 E-value=5.8e-07 Score=52.93 Aligned_cols=46 Identities=28% Similarity=0.761 Sum_probs=23.1
Q ss_pred Ccccccccchhh-h---cee----cCCCCcccHhhHHHHhhc---C--------CCCCCCCCCCC
Q psy10659 21 DLLCPICFELIR-E---AHI----TRCGHTFCFSCISKCVEL---Q--------IKCPKCSASLP 66 (140)
Q Consensus 21 ~~~C~IC~~~~~-~---p~~----~~CgH~fC~~Ci~~~~~~---~--------~~CP~C~~~~~ 66 (140)
+..|+||..... + |.. ..|+..||..|+.+|+.. . ..||.|+.+++
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 578999999765 2 332 269999999999999962 1 35999998764
No 49
>KOG1645|consensus
Probab=98.04 E-value=5.2e-06 Score=63.18 Aligned_cols=56 Identities=30% Similarity=0.720 Sum_probs=42.4
Q ss_pred CCcccccccchhhhc-----eecCCCCcccHhhHHHHhh--cCCCCCCCCCCCCCCCCCccchH
Q psy10659 20 NDLLCPICFELIREA-----HITRCGHTFCFSCISKCVE--LQIKCPKCSASLPDMNSVFPNFL 76 (140)
Q Consensus 20 ~~~~C~IC~~~~~~p-----~~~~CgH~fC~~Ci~~~~~--~~~~CP~C~~~~~~~~~~~~~~~ 76 (140)
...+||||++.+.-| +.+.|||.|-..||+.|+- ....||.|......+. +++-+.
T Consensus 3 ~g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~katkr~-i~~e~a 65 (463)
T KOG1645|consen 3 CGTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKATKRQ-IRPEYA 65 (463)
T ss_pred ccccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChhHHHH-HHHHHH
Confidence 457899999999876 3468999999999999995 2367999976554444 444433
No 50
>KOG0828|consensus
Probab=97.98 E-value=3.2e-06 Score=65.78 Aligned_cols=50 Identities=28% Similarity=0.636 Sum_probs=39.9
Q ss_pred CCCCcccccccchhhh-----------------ceecCCCCcccHhhHHHHhh-cCCCCCCCCCCCCC
Q psy10659 18 PDNDLLCPICFELIRE-----------------AHITRCGHTFCFSCISKCVE-LQIKCPKCSASLPD 67 (140)
Q Consensus 18 ~~~~~~C~IC~~~~~~-----------------p~~~~CgH~fC~~Ci~~~~~-~~~~CP~C~~~~~~ 67 (140)
.+....|+||.....- -+.+||.|.|+..|+.+|.. .+..||+||.++..
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 4567789999986631 13469999999999999998 45689999988753
No 51
>KOG1039|consensus
Probab=97.93 E-value=5.5e-06 Score=62.58 Aligned_cols=50 Identities=32% Similarity=0.761 Sum_probs=40.4
Q ss_pred CCCcccccccchhhhce-----e---cCCCCcccHhhHHHHhh--c-----CCCCCCCCCCCCCC
Q psy10659 19 DNDLLCPICFELIREAH-----I---TRCGHTFCFSCISKCVE--L-----QIKCPKCSASLPDM 68 (140)
Q Consensus 19 ~~~~~C~IC~~~~~~p~-----~---~~CgH~fC~~Ci~~~~~--~-----~~~CP~C~~~~~~~ 68 (140)
..+..|.||.+...+.. . .+|.|.||..||..|.. . ...||.||......
T Consensus 159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~~v 223 (344)
T KOG1039|consen 159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSSFV 223 (344)
T ss_pred cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccccc
Confidence 56889999999887655 2 47999999999999984 3 47899999876553
No 52
>KOG3039|consensus
Probab=97.93 E-value=8e-06 Score=58.44 Aligned_cols=51 Identities=18% Similarity=0.454 Sum_probs=45.3
Q ss_pred CCCcccccccchhhhce----ecCCCCcccHhhHHHHhhcCCCCCCCCCCCCCCC
Q psy10659 19 DNDLLCPICFELIREAH----ITRCGHTFCFSCISKCVELQIKCPKCSASLPDMN 69 (140)
Q Consensus 19 ~~~~~C~IC~~~~~~p~----~~~CgH~fC~~Ci~~~~~~~~~CP~C~~~~~~~~ 69 (140)
+..+.||+|.+.+.+.+ .-+|||+||..|++.+++....||+|..++...+
T Consensus 219 s~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdrd 273 (303)
T KOG3039|consen 219 SKRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDRD 273 (303)
T ss_pred ccceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCcccc
Confidence 35689999999998763 3399999999999999999999999999998877
No 53
>KOG4265|consensus
Probab=97.93 E-value=5.2e-06 Score=62.21 Aligned_cols=49 Identities=22% Similarity=0.614 Sum_probs=43.5
Q ss_pred CCCcccccccchhhhceecCCCC-cccHhhHHHHhhcCCCCCCCCCCCCC
Q psy10659 19 DNDLLCPICFELIREAHITRCGH-TFCFSCISKCVELQIKCPKCSASLPD 67 (140)
Q Consensus 19 ~~~~~C~IC~~~~~~p~~~~CgH-~fC~~Ci~~~~~~~~~CP~C~~~~~~ 67 (140)
+...+|-||+...++-+++||.| -.|..|.+...-.+..||+||.++..
T Consensus 288 ~~gkeCVIClse~rdt~vLPCRHLCLCs~Ca~~Lr~q~n~CPICRqpi~~ 337 (349)
T KOG4265|consen 288 ESGKECVICLSESRDTVVLPCRHLCLCSGCAKSLRYQTNNCPICRQPIEE 337 (349)
T ss_pred cCCCeeEEEecCCcceEEecchhhehhHhHHHHHHHhhcCCCccccchHh
Confidence 44689999999999999999999 57999999887778899999998765
No 54
>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class
Probab=97.90 E-value=9.3e-06 Score=44.40 Aligned_cols=40 Identities=18% Similarity=0.590 Sum_probs=31.3
Q ss_pred ccccccc--hhhhceecCCC-----CcccHhhHHHHhhc--CCCCCCCC
Q psy10659 23 LCPICFE--LIREAHITRCG-----HTFCFSCISKCVEL--QIKCPKCS 62 (140)
Q Consensus 23 ~C~IC~~--~~~~p~~~~Cg-----H~fC~~Ci~~~~~~--~~~CP~C~ 62 (140)
.|.||++ .-.++...||. |.++..|+.+|+.. ...||+|+
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 33456677885 78999999999964 45899995
No 55
>KOG4692|consensus
Probab=97.89 E-value=7.6e-06 Score=61.41 Aligned_cols=50 Identities=30% Similarity=0.718 Sum_probs=44.7
Q ss_pred CCCCCcccccccchhhhceecCCCCcccHhhHHHHhhcCCCCCCCCCCCC
Q psy10659 17 PPDNDLLCPICFELIREAHITRCGHTFCFSCISKCVELQIKCPKCSASLP 66 (140)
Q Consensus 17 ~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~CP~C~~~~~ 66 (140)
+..++..||||..-..+.+..||+|.-|+.||.+.+-+.+.|-.|+..+.
T Consensus 418 p~sEd~lCpICyA~pi~Avf~PC~H~SC~~CI~qHlmN~k~CFfCktTv~ 467 (489)
T KOG4692|consen 418 PDSEDNLCPICYAGPINAVFAPCSHRSCYGCITQHLMNCKRCFFCKTTVI 467 (489)
T ss_pred CCcccccCcceecccchhhccCCCCchHHHHHHHHHhcCCeeeEecceee
Confidence 33678899999998888999999999999999999999999999987654
No 56
>KOG1785|consensus
Probab=97.87 E-value=4.2e-06 Score=63.64 Aligned_cols=49 Identities=33% Similarity=0.781 Sum_probs=41.3
Q ss_pred ccccccchhhhceecCCCCcccHhhHHHHhhc--CCCCCCCCCCCCCCCCC
Q psy10659 23 LCPICFELIREAHITRCGHTFCFSCISKCVEL--QIKCPKCSASLPDMNSV 71 (140)
Q Consensus 23 ~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~--~~~CP~C~~~~~~~~~~ 71 (140)
.|.||-+--++-.+-||||..|..|+..|... ..+||.||..+.....+
T Consensus 371 LCKICaendKdvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKGte~v 421 (563)
T KOG1785|consen 371 LCKICAENDKDVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIKGTEPV 421 (563)
T ss_pred HHHHhhccCCCcccccccchHHHHHHHhhcccCCCCCCCceeeEeccccce
Confidence 68999998887767799999999999999953 57899999988776533
No 57
>KOG0827|consensus
Probab=97.82 E-value=7e-06 Score=62.15 Aligned_cols=46 Identities=33% Similarity=0.746 Sum_probs=34.2
Q ss_pred cccccccchhhhce----ecCCCCcccHhhHHHHhhc---CCCCCCCCCCCCC
Q psy10659 22 LLCPICFELIREAH----ITRCGHTFCFSCISKCVEL---QIKCPKCSASLPD 67 (140)
Q Consensus 22 ~~C~IC~~~~~~p~----~~~CgH~fC~~Ci~~~~~~---~~~CP~C~~~~~~ 67 (140)
..|.||.+.+-.-. +-.|||+|+..|+..|+.+ ...||.|+-.+..
T Consensus 5 A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~~~ 57 (465)
T KOG0827|consen 5 AECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKLQE 57 (465)
T ss_pred ceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeecccc
Confidence 57999966554332 2259999999999999984 3689999944443
No 58
>KOG4367|consensus
Probab=97.77 E-value=1.1e-05 Score=62.18 Aligned_cols=36 Identities=31% Similarity=0.782 Sum_probs=32.9
Q ss_pred CCCCcccccccchhhhceecCCCCcccHhhHHHHhh
Q psy10659 18 PDNDLLCPICFELIREAHITRCGHTFCFSCISKCVE 53 (140)
Q Consensus 18 ~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~ 53 (140)
+++++.||||...|.+|++++|||+.|..|....+.
T Consensus 1 meeelkc~vc~~f~~epiil~c~h~lc~~ca~~~~~ 36 (699)
T KOG4367|consen 1 MEEELKCPVCGSFYREPIILPCSHNLCQACARNILV 36 (699)
T ss_pred CcccccCceehhhccCceEeecccHHHHHHHHhhcc
Confidence 367899999999999999999999999999987764
No 59
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=97.74 E-value=1.4e-05 Score=66.66 Aligned_cols=49 Identities=20% Similarity=0.584 Sum_probs=38.8
Q ss_pred CCCCcccccccchhhh-----cee--cCCCCcccHhhHHHHhhc--CCCCCCCCCCCC
Q psy10659 18 PDNDLLCPICFELIRE-----AHI--TRCGHTFCFSCISKCVEL--QIKCPKCSASLP 66 (140)
Q Consensus 18 ~~~~~~C~IC~~~~~~-----p~~--~~CgH~fC~~Ci~~~~~~--~~~CP~C~~~~~ 66 (140)
.+..-+|+||..++.- |-. ..|.|.||..|+..|++. ..+||+||..++
T Consensus 1466 fsG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219 1466 FSGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred cCCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence 4566799999998872 222 269999999999999984 578999997654
No 60
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=97.72 E-value=1.7e-05 Score=43.89 Aligned_cols=48 Identities=23% Similarity=0.519 Sum_probs=37.4
Q ss_pred CCcccccccchhhhceecCCCCcccHhhHHHHhhcCCCCCCCCCCCCCCC
Q psy10659 20 NDLLCPICFELIREAHITRCGHTFCFSCISKCVELQIKCPKCSASLPDMN 69 (140)
Q Consensus 20 ~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~CP~C~~~~~~~~ 69 (140)
....|-.|...-...++++|||..|..|+.- ++-..||.|.+++...+
T Consensus 6 ~~~~~~~~~~~~~~~~~~pCgH~I~~~~f~~--~rYngCPfC~~~~~~~~ 53 (55)
T PF14447_consen 6 PEQPCVFCGFVGTKGTVLPCGHLICDNCFPG--ERYNGCPFCGTPFEFDD 53 (55)
T ss_pred cceeEEEccccccccccccccceeeccccCh--hhccCCCCCCCcccCCC
Confidence 4456777777777788999999999999763 34578999999887543
No 61
>KOG0825|consensus
Probab=97.71 E-value=9.1e-06 Score=66.40 Aligned_cols=51 Identities=18% Similarity=0.472 Sum_probs=42.4
Q ss_pred CCCcccccccchhhhcee---cCCCCcccHhhHHHHhhcCCCCCCCCCCCCCCC
Q psy10659 19 DNDLLCPICFELIREAHI---TRCGHTFCFSCISKCVELQIKCPKCSASLPDMN 69 (140)
Q Consensus 19 ~~~~~C~IC~~~~~~p~~---~~CgH~fC~~Ci~~~~~~~~~CP~C~~~~~~~~ 69 (140)
...-.||+|+..+.+... .+|+|.||..|+..|-+-..+||+|+..+....
T Consensus 121 ~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~aqTCPiDR~EF~~v~ 174 (1134)
T KOG0825|consen 121 HVENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCAQTCPVDRGEFGEVK 174 (1134)
T ss_pred hhhhhhhHHHHHHHHHhhccccccccccHHHHhhhhhhhcccCchhhhhhheee
Confidence 345688999988877643 379999999999999999999999999877643
No 62
>PF04641 Rtf2: Rtf2 RING-finger
Probab=97.71 E-value=3.9e-05 Score=56.24 Aligned_cols=53 Identities=17% Similarity=0.469 Sum_probs=42.6
Q ss_pred CCCCcccccccchhhhc---eec-CCCCcccHhhHHHHhhcCCCCCCCCCCCCCCCCC
Q psy10659 18 PDNDLLCPICFELIREA---HIT-RCGHTFCFSCISKCVELQIKCPKCSASLPDMNSV 71 (140)
Q Consensus 18 ~~~~~~C~IC~~~~~~p---~~~-~CgH~fC~~Ci~~~~~~~~~CP~C~~~~~~~~~~ 71 (140)
....+.|||....|..- +.+ +|||+|+..++.+.- ....||+|+.++...+.+
T Consensus 110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k-~~~~Cp~c~~~f~~~DiI 166 (260)
T PF04641_consen 110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK-KSKKCPVCGKPFTEEDII 166 (260)
T ss_pred CCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc-ccccccccCCccccCCEE
Confidence 45679999999999542 333 999999999999984 456799999999987733
No 63
>KOG2930|consensus
Probab=97.65 E-value=2.7e-05 Score=48.41 Aligned_cols=44 Identities=30% Similarity=0.609 Sum_probs=34.9
Q ss_pred Ccccccccchhhhc---------------ee--cCCCCcccHhhHHHHhhcCCCCCCCCCC
Q psy10659 21 DLLCPICFELIREA---------------HI--TRCGHTFCFSCISKCVELQIKCPKCSAS 64 (140)
Q Consensus 21 ~~~C~IC~~~~~~p---------------~~--~~CgH~fC~~Ci~~~~~~~~~CP~C~~~ 64 (140)
-..|.||+.-+-++ .+ -.|.|.|+..||.+|+++...||+|.+.
T Consensus 46 vDnCAICRnHIMd~CieCQa~~~~~~~EC~VaWG~CNHaFH~hCisrWlktr~vCPLdn~e 106 (114)
T KOG2930|consen 46 VDNCAICRNHIMDLCIECQANQSATSEECTVAWGVCNHAFHFHCISRWLKTRNVCPLDNKE 106 (114)
T ss_pred echhHHHHHHHHHHHHhhccCCCCCCCceEEEeeecchHHHHHHHHHHHhhcCcCCCcCcc
Confidence 35799998855432 11 1599999999999999999999999875
No 64
>KOG0826|consensus
Probab=97.57 E-value=6.9e-05 Score=55.72 Aligned_cols=47 Identities=23% Similarity=0.588 Sum_probs=40.9
Q ss_pred CCCcccccccchhhhceec-CCCCcccHhhHHHHhhcCCCCCCCCCCC
Q psy10659 19 DNDLLCPICFELIREAHIT-RCGHTFCFSCISKCVELQIKCPKCSASL 65 (140)
Q Consensus 19 ~~~~~C~IC~~~~~~p~~~-~CgH~fC~~Ci~~~~~~~~~CP~C~~~~ 65 (140)
.+.-.||+|+..-.+|..+ .-|-+||..|+..+......||+-+.+.
T Consensus 298 ~~~~~CpvClk~r~Nptvl~vSGyVfCY~Ci~~Yv~~~~~CPVT~~p~ 345 (357)
T KOG0826|consen 298 PDREVCPVCLKKRQNPTVLEVSGYVFCYPCIFSYVVNYGHCPVTGYPA 345 (357)
T ss_pred CccccChhHHhccCCCceEEecceEEeHHHHHHHHHhcCCCCccCCcc
Confidence 4567999999999999766 6799999999999999999999876653
No 65
>KOG4739|consensus
Probab=97.55 E-value=0.00011 Score=52.53 Aligned_cols=45 Identities=29% Similarity=0.770 Sum_probs=32.1
Q ss_pred cccccccchhh-hce-ecCCCCcccHhhHHHHhhcCCCCCCCCCCCCCC
Q psy10659 22 LLCPICFELIR-EAH-ITRCGHTFCFSCISKCVELQIKCPKCSASLPDM 68 (140)
Q Consensus 22 ~~C~IC~~~~~-~p~-~~~CgH~fC~~Ci~~~~~~~~~CP~C~~~~~~~ 68 (140)
..|..|..--. +|. .+.|+|+||..|...-. ...||.|++++...
T Consensus 4 VhCn~C~~~~~~~~f~LTaC~HvfC~~C~k~~~--~~~C~lCkk~ir~i 50 (233)
T KOG4739|consen 4 VHCNKCFRFPSQDPFFLTACRHVFCEPCLKASS--PDVCPLCKKSIRII 50 (233)
T ss_pred EEeccccccCCCCceeeeechhhhhhhhcccCC--ccccccccceeeee
Confidence 56777777544 344 45999999999976322 23899999986653
No 66
>KOG4185|consensus
Probab=97.49 E-value=0.00012 Score=54.55 Aligned_cols=64 Identities=31% Similarity=0.560 Sum_probs=48.5
Q ss_pred Ccccccccchhh------hceecCCCCcccHhhHHHHhhc-CCCCCCCCCCCCCCC----CCccchHHHHHHHHH
Q psy10659 21 DLLCPICFELIR------EAHITRCGHTFCFSCISKCVEL-QIKCPKCSASLPDMN----SVFPNFLLNELVQKH 84 (140)
Q Consensus 21 ~~~C~IC~~~~~------~p~~~~CgH~fC~~Ci~~~~~~-~~~CP~C~~~~~~~~----~~~~~~~~~~~~~~~ 84 (140)
.+.|-||-+.|. .|..+.|||+||..|+...+.. ...||.||.+..... .+..|+.+...+...
T Consensus 3 ~~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~~~i~cpfcR~~~~~~~~~~~~l~kNf~ll~~~~~~ 77 (296)
T KOG4185|consen 3 FPECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGNSRILCPFCRETTEIPDGDVKSLQKNFALLQAIEHM 77 (296)
T ss_pred CCceeecCccccccCcccCCcccccCceehHhHHHHHhcCceeeccCCCCcccCCchhHhhhhhhHHHHHHHHHH
Confidence 467999999886 3667789999999999988864 456899999843221 456677777777665
No 67
>KOG1493|consensus
Probab=97.41 E-value=3.8e-05 Score=45.17 Aligned_cols=44 Identities=30% Similarity=0.574 Sum_probs=33.8
Q ss_pred ccccccchhhh------------ceec-CCCCcccHhhHHHHhhc---CCCCCCCCCCCC
Q psy10659 23 LCPICFELIRE------------AHIT-RCGHTFCFSCISKCVEL---QIKCPKCSASLP 66 (140)
Q Consensus 23 ~C~IC~~~~~~------------p~~~-~CgH~fC~~Ci~~~~~~---~~~CP~C~~~~~ 66 (140)
.|.||+-.|.. |.++ .|.|.|+..||.+|+.. +..||+||....
T Consensus 22 ~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~ 81 (84)
T KOG1493|consen 22 TCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQ 81 (84)
T ss_pred ccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeE
Confidence 78888877752 2222 69999999999999963 467999998654
No 68
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=97.36 E-value=0.00015 Score=39.18 Aligned_cols=42 Identities=31% Similarity=0.796 Sum_probs=21.7
Q ss_pred cccccchhhhc--eec--CCCCcccHhhHHHHhh-cCCCCCCCCCCC
Q psy10659 24 CPICFELIREA--HIT--RCGHTFCFSCISKCVE-LQIKCPKCSASL 65 (140)
Q Consensus 24 C~IC~~~~~~p--~~~--~CgH~fC~~Ci~~~~~-~~~~CP~C~~~~ 65 (140)
||+|-+.+... ... +||+.+|..|+..... ....||.||++.
T Consensus 1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y 47 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILENEGGRCPGCREPY 47 (48)
T ss_dssp -TTTS-B--CCCTT--SSTTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred CCCcccccccCCCccccCcCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence 78888877322 223 6999999999999886 578999999864
No 69
>KOG1814|consensus
Probab=97.26 E-value=0.0003 Score=53.87 Aligned_cols=45 Identities=31% Similarity=0.717 Sum_probs=35.1
Q ss_pred CCCcccccccchhhhc---eecCCCCcccHhhHHHHhhc--------CCCCCCCCC
Q psy10659 19 DNDLLCPICFELIREA---HITRCGHTFCFSCISKCVEL--------QIKCPKCSA 63 (140)
Q Consensus 19 ~~~~~C~IC~~~~~~p---~~~~CgH~fC~~Ci~~~~~~--------~~~CP~C~~ 63 (140)
...+.|.||.+..... +.+||+|+||..|+..|... ...||.++-
T Consensus 182 ~slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C 237 (445)
T KOG1814|consen 182 NSLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKC 237 (445)
T ss_pred hhcccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCC
Confidence 3467999999988653 35799999999999999852 256887654
No 70
>KOG1001|consensus
Probab=97.20 E-value=0.00018 Score=59.18 Aligned_cols=47 Identities=36% Similarity=0.938 Sum_probs=39.9
Q ss_pred cccccccchhhhceecCCCCcccHhhHHHHhhc--CCCCCCCCCCCCCCC
Q psy10659 22 LLCPICFELIREAHITRCGHTFCFSCISKCVEL--QIKCPKCSASLPDMN 69 (140)
Q Consensus 22 ~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~--~~~CP~C~~~~~~~~ 69 (140)
..|+||.+ ...++.++|||.||..|+...+.. ...||.|+..+....
T Consensus 455 ~~c~ic~~-~~~~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~~~ 503 (674)
T KOG1001|consen 455 HWCHICCD-LDSFFITRCGHDFCVECLKKSIQQSENAPCPLCRNVLKEKK 503 (674)
T ss_pred cccccccc-cccceeecccchHHHHHHHhccccccCCCCcHHHHHHHHHH
Confidence 89999999 777888999999999999999864 346999998766544
No 71
>KOG0298|consensus
Probab=97.20 E-value=0.00027 Score=60.78 Aligned_cols=92 Identities=21% Similarity=0.457 Sum_probs=61.0
Q ss_pred CCCCCcccccccchhh-hceecCCCCcccHhhHHHHhhcCCCCCCCCCCCCCCCCCccchHHHHHHHHHHhcCCCChHHH
Q psy10659 17 PPDNDLLCPICFELIR-EAHITRCGHTFCFSCISKCVELQIKCPKCSASLPDMNSVFPNFLLNELVQKHKIKSAQDSDGL 95 (140)
Q Consensus 17 ~~~~~~~C~IC~~~~~-~p~~~~CgH~fC~~Ci~~~~~~~~~CP~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 95 (140)
.+.....|+||++.+. ...+..|||.+|..|...|+..+..||.|......-. ...... ...+...+....
T Consensus 1149 ~~~~~~~c~ic~dil~~~~~I~~cgh~~c~~c~~~~l~~~s~~~~~ksi~~dfg-~kI~~v-~~~il~iK~k~~------ 1220 (1394)
T KOG0298|consen 1149 NLSGHFVCEICLDILRNQGGIAGCGHEPCCRCDELWLYASSRCPICKSIKGDFG-TKIDSV-VIAILYIKFKNE------ 1220 (1394)
T ss_pred HhhcccchHHHHHHHHhcCCeeeechhHhhhHHHHHHHHhccCcchhhhhhhhc-cCchhH-HHHHHHHhccCc------
Confidence 3456779999999999 4567799999999999999999999999985333211 111111 111111111111
Q ss_pred HHHhhhcCCCcccccHHHHHHHHHHHH
Q psy10659 96 RDFVASESQNLSLPDVNLMLEVLNQRK 122 (140)
Q Consensus 96 ~~~~~~~~~~~~~~~~~~~l~~~~~~~ 122 (140)
..+.+.+++++..+++++...
T Consensus 1221 ------qekvIvfsqws~~ldV~e~~~ 1241 (1394)
T KOG0298|consen 1221 ------QEKVIVFSQWSVVLDVKELRY 1241 (1394)
T ss_pred ------CceEEEEEehHHHHHHHHHHH
Confidence 135678888998888886544
No 72
>KOG3800|consensus
Probab=97.18 E-value=0.00035 Score=51.24 Aligned_cols=47 Identities=32% Similarity=0.766 Sum_probs=36.7
Q ss_pred ccccccc-hhhhce----ecCCCCcccHhhHHHHhh-cCCCCCCCCCCCCCCC
Q psy10659 23 LCPICFE-LIREAH----ITRCGHTFCFSCISKCVE-LQIKCPKCSASLPDMN 69 (140)
Q Consensus 23 ~C~IC~~-~~~~p~----~~~CgH~fC~~Ci~~~~~-~~~~CP~C~~~~~~~~ 69 (140)
.||+|.. .+.+|- +-+|||..|.+|+...+. +...||.|.+.+...+
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iLRk~n 54 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGPAQCPECMVILRKNN 54 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHhcCCCCCCcccchhhhcc
Confidence 5999987 445552 128999999999999886 5678999998776654
No 73
>KOG4275|consensus
Probab=97.12 E-value=5.4e-05 Score=55.52 Aligned_cols=41 Identities=32% Similarity=0.836 Sum_probs=34.6
Q ss_pred CcccccccchhhhceecCCCC-cccHhhHHHHhhcCCCCCCCCCCC
Q psy10659 21 DLLCPICFELIREAHITRCGH-TFCFSCISKCVELQIKCPKCSASL 65 (140)
Q Consensus 21 ~~~C~IC~~~~~~p~~~~CgH-~fC~~Ci~~~~~~~~~CP~C~~~~ 65 (140)
+..|.||.+...+-+.++||| +-|..|-... ..||+||+.+
T Consensus 300 ~~LC~ICmDaP~DCvfLeCGHmVtCt~CGkrm----~eCPICRqyi 341 (350)
T KOG4275|consen 300 RRLCAICMDAPRDCVFLECGHMVTCTKCGKRM----NECPICRQYI 341 (350)
T ss_pred HHHHHHHhcCCcceEEeecCcEEeehhhcccc----ccCchHHHHH
Confidence 678999999999999999999 6788886543 3799999754
No 74
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=97.02 E-value=0.00063 Score=44.42 Aligned_cols=50 Identities=26% Similarity=0.602 Sum_probs=42.6
Q ss_pred CCcccccccchhhhceecC----CCCcccHhhHHHHhhc---CCCCCCCCCCCCCCC
Q psy10659 20 NDLLCPICFELIREAHITR----CGHTFCFSCISKCVEL---QIKCPKCSASLPDMN 69 (140)
Q Consensus 20 ~~~~C~IC~~~~~~p~~~~----CgH~fC~~Ci~~~~~~---~~~CP~C~~~~~~~~ 69 (140)
...+|.||.+.-.++..+. ||-..|..|....|+. .+.||.|+.++....
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 4579999999999988773 9999999999888873 578999999887654
No 75
>KOG1571|consensus
Probab=96.98 E-value=0.00031 Score=52.95 Aligned_cols=47 Identities=26% Similarity=0.602 Sum_probs=36.3
Q ss_pred CCCCcccccccchhhhceecCCCCcccHhhHHHHhhcCCCCCCCCCCCCC
Q psy10659 18 PDNDLLCPICFELIREAHITRCGHTFCFSCISKCVELQIKCPKCSASLPD 67 (140)
Q Consensus 18 ~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~CP~C~~~~~~ 67 (140)
..-..-|.||.+...+.+.+||||.-| |..-.. ....||+||..+..
T Consensus 302 ~~~p~lcVVcl~e~~~~~fvpcGh~cc--ct~cs~-~l~~CPvCR~rI~~ 348 (355)
T KOG1571|consen 302 LPQPDLCVVCLDEPKSAVFVPCGHVCC--CTLCSK-HLPQCPVCRQRIRL 348 (355)
T ss_pred cCCCCceEEecCCccceeeecCCcEEE--chHHHh-hCCCCchhHHHHHH
Confidence 345578999999999999999999977 766543 34559999986543
No 76
>KOG3002|consensus
Probab=96.91 E-value=0.00094 Score=49.88 Aligned_cols=65 Identities=22% Similarity=0.509 Sum_probs=49.8
Q ss_pred CCCCcccccccchhhhceec-CCCCcccHhhHHHHhhcCCCCCCCCCCCCCCCCCccchHHHHHHHHHHhcCC
Q psy10659 18 PDNDLLCPICFELIREAHIT-RCGHTFCFSCISKCVELQIKCPKCSASLPDMNSVFPNFLLNELVQKHKIKSA 89 (140)
Q Consensus 18 ~~~~~~C~IC~~~~~~p~~~-~CgH~fC~~Ci~~~~~~~~~CP~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 89 (140)
..+.+.||||.+.+..|+.- .=||.-|..|-. +....||.|+.++.. .....+..+++.......
T Consensus 45 ~~~lleCPvC~~~l~~Pi~QC~nGHlaCssC~~---~~~~~CP~Cr~~~g~----~R~~amEkV~e~~~vpC~ 110 (299)
T KOG3002|consen 45 DLDLLDCPVCFNPLSPPIFQCDNGHLACSSCRT---KVSNKCPTCRLPIGN----IRCRAMEKVAEAVLVPCK 110 (299)
T ss_pred chhhccCchhhccCcccceecCCCcEehhhhhh---hhcccCCcccccccc----HHHHHHHHHHHhceeccc
Confidence 45679999999999988653 679999999975 346789999988873 356777777766655433
No 77
>KOG1941|consensus
Probab=96.90 E-value=0.0003 Score=53.67 Aligned_cols=45 Identities=29% Similarity=0.696 Sum_probs=36.4
Q ss_pred CCcccccccchhhh-c---eecCCCCcccHhhHHHHhhc--CCCCCCCCCC
Q psy10659 20 NDLLCPICFELIRE-A---HITRCGHTFCFSCISKCVEL--QIKCPKCSAS 64 (140)
Q Consensus 20 ~~~~C~IC~~~~~~-p---~~~~CgH~fC~~Ci~~~~~~--~~~CP~C~~~ 64 (140)
-.+.|..|.+.+.- | -.+||.|+|+..|+.+++.. ...||.||+-
T Consensus 364 ~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~Crkl 414 (518)
T KOG1941|consen 364 TELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRKL 414 (518)
T ss_pred HhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHHH
Confidence 45899999998853 2 24699999999999999974 4679999943
No 78
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=96.76 E-value=0.00037 Score=43.93 Aligned_cols=33 Identities=24% Similarity=0.599 Sum_probs=27.3
Q ss_pred CCCCCcccccccchhhhcee--cCCCCcccHhhHH
Q psy10659 17 PPDNDLLCPICFELIREAHI--TRCGHTFCFSCIS 49 (140)
Q Consensus 17 ~~~~~~~C~IC~~~~~~p~~--~~CgH~fC~~Ci~ 49 (140)
.+++...|++|...+.+... .||||.||..|+.
T Consensus 74 ~i~~~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 74 VITESTKCSVCGKPLGNSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred EECCCCCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence 35678889999999987643 4999999999975
No 79
>KOG2114|consensus
Probab=96.72 E-value=0.002 Score=53.50 Aligned_cols=41 Identities=27% Similarity=0.680 Sum_probs=35.5
Q ss_pred CCcccccccchhhhcee-cCCCCcccHhhHHHHhhcCCCCCCCCC
Q psy10659 20 NDLLCPICFELIREAHI-TRCGHTFCFSCISKCVELQIKCPKCSA 63 (140)
Q Consensus 20 ~~~~C~IC~~~~~~p~~-~~CgH~fC~~Ci~~~~~~~~~CP~C~~ 63 (140)
....|..|...+.-|++ ..|||+||.+|+. .+...||.|+.
T Consensus 839 q~skCs~C~~~LdlP~VhF~CgHsyHqhC~e---~~~~~CP~C~~ 880 (933)
T KOG2114|consen 839 QVSKCSACEGTLDLPFVHFLCGHSYHQHCLE---DKEDKCPKCLP 880 (933)
T ss_pred eeeeecccCCccccceeeeecccHHHHHhhc---cCcccCCccch
Confidence 34699999999999965 5999999999998 56788999975
No 80
>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=96.55 E-value=0.014 Score=39.38 Aligned_cols=103 Identities=21% Similarity=0.403 Sum_probs=60.4
Q ss_pred CCcccccccchhhhceecC------------CCCcc-cHhhHHHHhhc-------------------------------C
Q psy10659 20 NDLLCPICFELIREAHITR------------CGHTF-CFSCISKCVEL-------------------------------Q 55 (140)
Q Consensus 20 ~~~~C~IC~~~~~~p~~~~------------CgH~f-C~~Ci~~~~~~-------------------------------~ 55 (140)
++.+||||++...+.|.|- |+.+| +..|+.++.+. .
T Consensus 1 ed~~CpICme~PHNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkka~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (162)
T PF07800_consen 1 EDVTCPICMEHPHNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKKAYGKSSSSSSQSSSSAPSDSSSSESSESQEQPE 80 (162)
T ss_pred CCccCceeccCCCceEEEEeccccCCccccccCCccchhHHHHHHHHHhcCCCCccccccccCcCCCccccccccccccc
Confidence 4689999999999998773 44433 35788888641 1
Q ss_pred CCCCCCCCCCCCCCCCccchHHHHHHHHHHhcCCC-------ChHHHHHHhhhcCCCcccccHHHHHHHHHHHHHHHHHH
Q psy10659 56 IKCPKCSASLPDMNSVFPNFLLNELVQKHKIKSAQ-------DSDGLRDFVASESQNLSLPDVNLMLEVLNQRKHLLEAE 128 (140)
Q Consensus 56 ~~CP~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~e~~ 128 (140)
..||+||-.+.... +-...+..+...+..... ...++++....+.-......++...+ ..++++|++
T Consensus 81 L~CPLCRG~V~GWt---vve~AR~~LN~K~RsC~~e~C~F~GtY~eLrKHar~~HP~~rP~~vDP~rq---~~W~~le~~ 154 (162)
T PF07800_consen 81 LACPLCRGEVKGWT---VVEPARRFLNAKKRSCSQESCSFSGTYSELRKHARSEHPSARPSEVDPQRQ---RDWERLERE 154 (162)
T ss_pred ccCccccCceeceE---EchHHHHHhccCCccCcccccccccCHHHHHHHHHhhCCCCCCccCCHHHH---HHHHHHHHh
Confidence 36999998887754 112233332222222111 56667777765555555555554433 334555544
No 81
>KOG2817|consensus
Probab=96.54 E-value=0.0018 Score=49.57 Aligned_cols=48 Identities=21% Similarity=0.500 Sum_probs=37.3
Q ss_pred CCcccccccchhh---hceecCCCCcccHhhHHHHhhcC---CCCCCCCCCCCC
Q psy10659 20 NDLLCPICFELIR---EAHITRCGHTFCFSCISKCVELQ---IKCPKCSASLPD 67 (140)
Q Consensus 20 ~~~~C~IC~~~~~---~p~~~~CgH~fC~~Ci~~~~~~~---~~CP~C~~~~~~ 67 (140)
..|.|||=.+.-. .|+.+.|||+.+..-+.+..++. ++||.|......
T Consensus 333 SvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~e~~~ 386 (394)
T KOG2817|consen 333 SVFICPVLKEQTSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPVEQLA 386 (394)
T ss_pred ceeecccchhhccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCcccCH
Confidence 3578998766543 47889999999999999988753 689999765443
No 82
>KOG3970|consensus
Probab=96.52 E-value=0.0046 Score=44.04 Aligned_cols=51 Identities=22% Similarity=0.474 Sum_probs=40.0
Q ss_pred CCCcccccccchhhh--ceecCCCCcccHhhHHHHhhc--------CCCCCCCCCCCCCCC
Q psy10659 19 DNDLLCPICFELIRE--AHITRCGHTFCFSCISKCVEL--------QIKCPKCSASLPDMN 69 (140)
Q Consensus 19 ~~~~~C~IC~~~~~~--p~~~~CgH~fC~~Ci~~~~~~--------~~~CP~C~~~~~~~~ 69 (140)
+-.-.|.+|...+.. .+.+.|-|.|+..|+.+|... ...||.|...+....
T Consensus 48 DY~pNC~LC~t~La~gdt~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp~ 108 (299)
T KOG3970|consen 48 DYNPNCRLCNTPLASGDTTRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPPI 108 (299)
T ss_pred CCCCCCceeCCccccCcceeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCCc
Confidence 344679999998864 467799999999999999852 467999998776543
No 83
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=96.47 E-value=0.0026 Score=48.02 Aligned_cols=48 Identities=25% Similarity=0.639 Sum_probs=39.3
Q ss_pred CCCCcccccccchhhhceecCCCCcccHhhHHHHh--hcCCCCCCCCCCC
Q psy10659 18 PDNDLLCPICFELIREAHITRCGHTFCFSCISKCV--ELQIKCPKCSASL 65 (140)
Q Consensus 18 ~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~--~~~~~CP~C~~~~ 65 (140)
-++...|-||-.-+.--..+||+|..|+-|..+.. -....||+|+..-
T Consensus 58 DEen~~C~ICA~~~TYs~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~ 107 (493)
T COG5236 58 DEENMNCQICAGSTTYSARYPCGHQICHACAVRLRALYMQKGCPLCRTET 107 (493)
T ss_pred ccccceeEEecCCceEEEeccCCchHHHHHHHHHHHHHhccCCCcccccc
Confidence 35567899999988777788999999999987654 3678899999753
No 84
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=96.37 E-value=0.0052 Score=46.35 Aligned_cols=53 Identities=26% Similarity=0.668 Sum_probs=39.2
Q ss_pred CCCCCcccccccchhhhc--ee--cCCCCcccHhhHHHHhhc-CCCCCCCCCCCCCCC
Q psy10659 17 PPDNDLLCPICFELIREA--HI--TRCGHTFCFSCISKCVEL-QIKCPKCSASLPDMN 69 (140)
Q Consensus 17 ~~~~~~~C~IC~~~~~~p--~~--~~CgH~fC~~Ci~~~~~~-~~~CP~C~~~~~~~~ 69 (140)
..+++..||+|.+.+... -. -+||...|..|+....+. ...||.||+.....+
T Consensus 10 sedeed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~den 67 (480)
T COG5175 10 SEDEEDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDEN 67 (480)
T ss_pred cccccccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhccccc
Confidence 344556699999977532 22 379999999998876653 578999999877655
No 85
>KOG4362|consensus
Probab=96.34 E-value=0.00052 Score=55.96 Aligned_cols=64 Identities=25% Similarity=0.572 Sum_probs=47.1
Q ss_pred CCCCcccccccchhhhceecCCCCcccHhhHHHHhhc---CCCCCCCCCCCCCCCCCccchHHHHHHH
Q psy10659 18 PDNDLLCPICFELIREAHITRCGHTFCFSCISKCVEL---QIKCPKCSASLPDMNSVFPNFLLNELVQ 82 (140)
Q Consensus 18 ~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~---~~~CP~C~~~~~~~~~~~~~~~~~~~~~ 82 (140)
+--.++|+||...+..|+.+.|.|.||..|+...+.. ...||+|+..+.... .+.......+++
T Consensus 18 ~~k~lEc~ic~~~~~~p~~~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~eK~s-~~Es~r~sq~vq 84 (684)
T KOG4362|consen 18 MQKILECPICLEHVKEPSLLKCDHIFLKFCLNKLFESKKGPKQCALCKSDIEKRS-LRESPRFSQLSK 84 (684)
T ss_pred HhhhccCCceeEEeeccchhhhhHHHHhhhhhceeeccCccccchhhhhhhhhhh-ccccchHHHHHH
Confidence 3457899999999999999999999999999776653 457999997655443 333333444444
No 86
>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=96.31 E-value=0.0038 Score=33.05 Aligned_cols=38 Identities=26% Similarity=0.724 Sum_probs=23.1
Q ss_pred cccccchhhhceec---CCCCcccHhhHHHHhhcCC--CCCCC
Q psy10659 24 CPICFELIREAHIT---RCGHTFCFSCISKCVELQI--KCPKC 61 (140)
Q Consensus 24 C~IC~~~~~~p~~~---~CgH~fC~~Ci~~~~~~~~--~CP~C 61 (140)
|.+|.++....+.= .|+-.++..|+..|++... .||.|
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 67788877766553 4999999999999998654 79987
No 87
>KOG1940|consensus
Probab=96.20 E-value=0.0032 Score=46.38 Aligned_cols=43 Identities=33% Similarity=0.797 Sum_probs=36.5
Q ss_pred Ccccccccchhh----hceecCCCCcccHhhHHHHhhcCCCCCCCCC
Q psy10659 21 DLLCPICFELIR----EAHITRCGHTFCFSCISKCVELQIKCPKCSA 63 (140)
Q Consensus 21 ~~~C~IC~~~~~----~p~~~~CgH~fC~~Ci~~~~~~~~~CP~C~~ 63 (140)
...||||.+.+. .|..++|||..+..|+.........||.|.+
T Consensus 158 ~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~~y~CP~C~~ 204 (276)
T KOG1940|consen 158 EFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICEGYTCPICSK 204 (276)
T ss_pred cCCCchhHHHhccccccCCccCcccchHHHHHHHHhccCCCCCcccc
Confidence 455999999775 3556799999999999999887799999987
No 88
>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=96.20 E-value=0.0035 Score=45.03 Aligned_cols=48 Identities=27% Similarity=0.632 Sum_probs=35.6
Q ss_pred CCcccccccch-hhhc-ee-c--C-CCCcccHhhHHHHhhc-CCCCC--CCCCCCCC
Q psy10659 20 NDLLCPICFEL-IREA-HI-T--R-CGHTFCFSCISKCVEL-QIKCP--KCSASLPD 67 (140)
Q Consensus 20 ~~~~C~IC~~~-~~~p-~~-~--~-CgH~fC~~Ci~~~~~~-~~~CP--~C~~~~~~ 67 (140)
.+-.||||... +-+| +. + | |-|..|.+|+.+.+.. ...|| .|++-+..
T Consensus 9 ~d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kILRK 65 (314)
T COG5220 9 EDRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKILRK 65 (314)
T ss_pred hcccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHHHH
Confidence 46799999873 3445 22 2 4 9999999999999875 46799 78875544
No 89
>PHA03096 p28-like protein; Provisional
Probab=95.78 E-value=0.0061 Score=45.26 Aligned_cols=42 Identities=24% Similarity=0.460 Sum_probs=30.4
Q ss_pred cccccccchhhhc--------eecCCCCcccHhhHHHHhhc---CCCCCCCCC
Q psy10659 22 LLCPICFELIREA--------HITRCGHTFCFSCISKCVEL---QIKCPKCSA 63 (140)
Q Consensus 22 ~~C~IC~~~~~~p--------~~~~CgH~fC~~Ci~~~~~~---~~~CP~C~~ 63 (140)
-.|.||++..... ....|.|.||..|+..|... ...||.|+.
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 6799999965432 12379999999999999863 345666654
No 90
>KOG3579|consensus
Probab=95.57 E-value=0.012 Score=43.39 Aligned_cols=38 Identities=32% Similarity=0.960 Sum_probs=32.8
Q ss_pred CCCCCcccccccchhhhceecCC----CCcccHhhHHHHhhc
Q psy10659 17 PPDNDLLCPICFELIREAHITRC----GHTFCFSCISKCVEL 54 (140)
Q Consensus 17 ~~~~~~~C~IC~~~~~~p~~~~C----gH~fC~~Ci~~~~~~ 54 (140)
.....+.|.+|.+-+.+.....| .|.||..|-.+.++.
T Consensus 264 A~~apLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSResIK~ 305 (352)
T KOG3579|consen 264 APSAPLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSRESIKQ 305 (352)
T ss_pred CCCCceeehhhhhhhccCceeecCCCcccceecccCHHHHHh
Confidence 34566999999999999988776 899999999999874
No 91
>KOG1428|consensus
Probab=95.55 E-value=0.023 Score=50.51 Aligned_cols=51 Identities=29% Similarity=0.681 Sum_probs=38.3
Q ss_pred CCCCCcccccccchhh--hc-eecCCCCcccHhhHHHHhhcC----------CCCCCCCCCCCC
Q psy10659 17 PPDNDLLCPICFELIR--EA-HITRCGHTFCFSCISKCVELQ----------IKCPKCSASLPD 67 (140)
Q Consensus 17 ~~~~~~~C~IC~~~~~--~p-~~~~CgH~fC~~Ci~~~~~~~----------~~CP~C~~~~~~ 67 (140)
..+.+..|-||+..-- .| +.+.|+|.|+..|....+++. ..||.|..++..
T Consensus 3482 kQD~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~InH 3545 (3738)
T KOG1428|consen 3482 KQDADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKINH 3545 (3738)
T ss_pred hcccCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchhhh
Confidence 4466789999998543 23 568999999999998877632 369999876544
No 92
>KOG3268|consensus
Probab=95.51 E-value=0.01 Score=40.79 Aligned_cols=32 Identities=25% Similarity=0.598 Sum_probs=26.3
Q ss_pred cCCCCcccHhhHHHHhhcC-----------CCCCCCCCCCCCC
Q psy10659 37 TRCGHTFCFSCISKCVELQ-----------IKCPKCSASLPDM 68 (140)
Q Consensus 37 ~~CgH~fC~~Ci~~~~~~~-----------~~CP~C~~~~~~~ 68 (140)
..||..|+.-|+..|+++- ..||.|..++..+
T Consensus 188 ~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialK 230 (234)
T KOG3268|consen 188 IQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALK 230 (234)
T ss_pred cccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceee
Confidence 4799999999999999741 4699999887654
No 93
>KOG3161|consensus
Probab=95.43 E-value=0.0067 Score=49.27 Aligned_cols=38 Identities=39% Similarity=0.847 Sum_probs=30.7
Q ss_pred CCcccccccchhh----hceecCCCCcccHhhHHHHhhcCCCCC
Q psy10659 20 NDLLCPICFELIR----EAHITRCGHTFCFSCISKCVELQIKCP 59 (140)
Q Consensus 20 ~~~~C~IC~~~~~----~p~~~~CgH~fC~~Ci~~~~~~~~~CP 59 (140)
+.+.|+||+..|. .|+.+.|||+.|..|++.... ..||
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 3588999988885 478899999999999987654 4565
No 94
>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=95.43 E-value=0.011 Score=32.34 Aligned_cols=42 Identities=36% Similarity=0.764 Sum_probs=22.4
Q ss_pred cccccccchhhhceec-CCCCcccHhhHHHHhh-----cCCCCCCCCCC
Q psy10659 22 LLCPICFELIREAHIT-RCGHTFCFSCISKCVE-----LQIKCPKCSAS 64 (140)
Q Consensus 22 ~~C~IC~~~~~~p~~~-~CgH~fC~~Ci~~~~~-----~~~~CP~C~~~ 64 (140)
+.|||....+..|+.. .|.|.-|.+= ..|+. ..-.||.|+++
T Consensus 3 L~CPls~~~i~~P~Rg~~C~H~~CFDl-~~fl~~~~~~~~W~CPiC~~~ 50 (50)
T PF02891_consen 3 LRCPLSFQRIRIPVRGKNCKHLQCFDL-ESFLESNQRTPKWKCPICNKP 50 (50)
T ss_dssp SB-TTTSSB-SSEEEETT--SS--EEH-HHHHHHHHHS---B-TTT---
T ss_pred eeCCCCCCEEEeCccCCcCcccceECH-HHHHHHhhccCCeECcCCcCc
Confidence 7899999999999976 8999977653 33443 23579999863
No 95
>KOG3039|consensus
Probab=95.40 E-value=0.011 Score=42.75 Aligned_cols=37 Identities=19% Similarity=0.158 Sum_probs=32.7
Q ss_pred CCCCCcccccccchhhhceecCCCCcccHhhHHHHhh
Q psy10659 17 PPDNDLLCPICFELIREAHITRCGHTFCFSCISKCVE 53 (140)
Q Consensus 17 ~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~ 53 (140)
.+.+-.-|.+|+..+.+||+++=||.||..||.+++-
T Consensus 39 siK~FdcCsLtLqPc~dPvit~~GylfdrEaILe~il 75 (303)
T KOG3039|consen 39 SIKPFDCCSLTLQPCRDPVITPDGYLFDREAILEYIL 75 (303)
T ss_pred ccCCcceeeeecccccCCccCCCCeeeeHHHHHHHHH
Confidence 4455667899999999999999999999999999873
No 96
>KOG2932|consensus
Probab=95.32 E-value=0.0071 Score=45.04 Aligned_cols=44 Identities=25% Similarity=0.638 Sum_probs=29.6
Q ss_pred cccccccchhhhc-eecCCCCcccHhhHHHHhhcCCCCCCCCCCCCC
Q psy10659 22 LLCPICFELIREA-HITRCGHTFCFSCISKCVELQIKCPKCSASLPD 67 (140)
Q Consensus 22 ~~C~IC~~~~~~p-~~~~CgH~fC~~Ci~~~~~~~~~CP~C~~~~~~ 67 (140)
-.|.-|--.+..- ..++|.|+||.+|... ...+.||.|...+..
T Consensus 91 HfCd~Cd~PI~IYGRmIPCkHvFCl~CAr~--~~dK~Cp~C~d~Vqr 135 (389)
T KOG2932|consen 91 HFCDRCDFPIAIYGRMIPCKHVFCLECARS--DSDKICPLCDDRVQR 135 (389)
T ss_pred EeecccCCcceeeecccccchhhhhhhhhc--CccccCcCcccHHHH
Confidence 3566665544332 3569999999999763 335789999766543
No 97
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=95.21 E-value=0.026 Score=38.18 Aligned_cols=48 Identities=17% Similarity=0.334 Sum_probs=35.1
Q ss_pred CCCcccccccchhhhceecCCCC-----cccHhhHHHHhhc--CCCCCCCCCCCCC
Q psy10659 19 DNDLLCPICFELIREAHITRCGH-----TFCFSCISKCVEL--QIKCPKCSASLPD 67 (140)
Q Consensus 19 ~~~~~C~IC~~~~~~p~~~~CgH-----~fC~~Ci~~~~~~--~~~CP~C~~~~~~ 67 (140)
..+..|-||++... +...||.. ..|.+|+.+|+.. ...|+.|+.++..
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 35679999998754 33446544 3489999999974 4679999987643
No 98
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=94.58 E-value=0.026 Score=30.36 Aligned_cols=38 Identities=32% Similarity=0.648 Sum_probs=23.8
Q ss_pred cccccchhhh--ceecCCCC-----cccHhhHHHHhh--cCCCCCCC
Q psy10659 24 CPICFELIRE--AHITRCGH-----TFCFSCISKCVE--LQIKCPKC 61 (140)
Q Consensus 24 C~IC~~~~~~--p~~~~CgH-----~fC~~Ci~~~~~--~~~~CP~C 61 (140)
|-||++.-.+ |.+.||+- ..|..|+.+|+. +...|++|
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 6788886543 45666643 568999999997 45678877
No 99
>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.
Probab=94.38 E-value=0.012 Score=31.46 Aligned_cols=32 Identities=28% Similarity=0.928 Sum_probs=22.9
Q ss_pred ecCC-CCcccHhhHHHHhhcCCCCCCCCCCCCC
Q psy10659 36 ITRC-GHTFCFSCISKCVELQIKCPKCSASLPD 67 (140)
Q Consensus 36 ~~~C-gH~fC~~Ci~~~~~~~~~CP~C~~~~~~ 67 (140)
.+.| .|-.|..|+...+..+..||+|+.++..
T Consensus 15 Li~C~dHYLCl~CLt~ml~~s~~C~iC~~~LPt 47 (50)
T PF03854_consen 15 LIKCSDHYLCLNCLTLMLSRSDRCPICGKPLPT 47 (50)
T ss_dssp EEE-SS-EEEHHHHHHT-SSSSEETTTTEE---
T ss_pred eeeecchhHHHHHHHHHhccccCCCcccCcCcc
Confidence 4455 6889999999999999999999988754
No 100
>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=94.26 E-value=0.026 Score=37.14 Aligned_cols=42 Identities=24% Similarity=0.486 Sum_probs=31.0
Q ss_pred Ccccccccchhhh--ce-ecCCC------CcccHhhHHHHhhcCCCCCCCC
Q psy10659 21 DLLCPICFELIRE--AH-ITRCG------HTFCFSCISKCVELQIKCPKCS 62 (140)
Q Consensus 21 ~~~C~IC~~~~~~--p~-~~~Cg------H~fC~~Ci~~~~~~~~~CP~C~ 62 (140)
..+|.||++.+.+ .+ .++|| |.||..|+.+|.+....=|.=|
T Consensus 26 ~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~~~~~rDPfnR 76 (134)
T PF05883_consen 26 TVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWRRERNRDPFNR 76 (134)
T ss_pred CeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHHhhccCCCccc
Confidence 6899999998877 43 34665 6899999999965555445444
No 101
>KOG3113|consensus
Probab=94.18 E-value=0.044 Score=39.81 Aligned_cols=53 Identities=17% Similarity=0.393 Sum_probs=42.1
Q ss_pred CCcccccccchhhhce----ecCCCCcccHhhHHHHhhcCCCCCCCCCCCCCCCCCccc
Q psy10659 20 NDLLCPICFELIREAH----ITRCGHTFCFSCISKCVELQIKCPKCSASLPDMNSVFPN 74 (140)
Q Consensus 20 ~~~~C~IC~~~~~~p~----~~~CgH~fC~~Ci~~~~~~~~~CP~C~~~~~~~~~~~~~ 74 (140)
..+.|||-.-.|.... ..+|||+|-..-+.+.- ...|++|+..+...+.+..|
T Consensus 110 a~fiCPvtgleMng~~~F~~l~~CGcV~SerAlKeik--as~C~~C~a~y~~~dvIvlN 166 (293)
T KOG3113|consen 110 ARFICPVTGLEMNGKYRFCALRCCGCVFSERALKEIK--ASVCHVCGAAYQEDDVIVLN 166 (293)
T ss_pred ceeecccccceecceEEEEEEeccceeccHHHHHHhh--hccccccCCcccccCeEeeC
Confidence 4589999888887653 34899999999988754 67899999999988855555
No 102
>KOG1952|consensus
Probab=94.14 E-value=0.024 Score=47.47 Aligned_cols=46 Identities=30% Similarity=0.704 Sum_probs=36.3
Q ss_pred CCCcccccccchhh--hceec--CCCCcccHhhHHHHhhc-------CCCCCCCCCC
Q psy10659 19 DNDLLCPICFELIR--EAHIT--RCGHTFCFSCISKCVEL-------QIKCPKCSAS 64 (140)
Q Consensus 19 ~~~~~C~IC~~~~~--~p~~~--~CgH~fC~~Ci~~~~~~-------~~~CP~C~~~ 64 (140)
.+..+|.||.+.+. .|+.. .|-|+|+..||..|.+. .-.||.|...
T Consensus 189 ~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv 245 (950)
T KOG1952|consen 189 NRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSV 245 (950)
T ss_pred cCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccch
Confidence 45689999999875 45543 79999999999999863 2469999843
No 103
>PHA02862 5L protein; Provisional
Probab=94.10 E-value=0.038 Score=36.79 Aligned_cols=46 Identities=20% Similarity=0.475 Sum_probs=34.0
Q ss_pred cccccccchhhhceecCCCC-----cccHhhHHHHhhc--CCCCCCCCCCCCCC
Q psy10659 22 LLCPICFELIREAHITRCGH-----TFCFSCISKCVEL--QIKCPKCSASLPDM 68 (140)
Q Consensus 22 ~~C~IC~~~~~~p~~~~CgH-----~fC~~Ci~~~~~~--~~~CP~C~~~~~~~ 68 (140)
..|-||++.-.+. ..||.. -.|..|+.+|+.. ...||.|+.++..+
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 4689999976544 356543 5689999999974 46799999876543
No 104
>KOG1812|consensus
Probab=94.08 E-value=0.046 Score=42.43 Aligned_cols=48 Identities=38% Similarity=0.888 Sum_probs=32.6
Q ss_pred CCcccccccchhhhc----eecCCCCcccHhhHHHHhhc------CCCCCC--CCCCCCC
Q psy10659 20 NDLLCPICFELIREA----HITRCGHTFCFSCISKCVEL------QIKCPK--CSASLPD 67 (140)
Q Consensus 20 ~~~~C~IC~~~~~~p----~~~~CgH~fC~~Ci~~~~~~------~~~CP~--C~~~~~~ 67 (140)
....|.||......+ ....|+|.||..|+.+++.. ...||. |...++.
T Consensus 145 ~~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~~~~~~~~~C~~~~C~~~l~~ 204 (384)
T KOG1812|consen 145 PKEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVKLLSGTVIRCPHDGCESRLTL 204 (384)
T ss_pred ccccCccCccccccHhhhHHHhcccchhhhHHhHHHhhhhhccCCCccCCCCCCCccCCH
Confidence 367999999433322 24579999999999999862 356764 4444433
No 105
>KOG4445|consensus
Probab=94.06 E-value=0.01 Score=44.08 Aligned_cols=48 Identities=23% Similarity=0.609 Sum_probs=36.7
Q ss_pred CCcccccccchhhh-c--eecCCCCcccHhhHHHHhhc-----------------------CCCCCCCCCCCCC
Q psy10659 20 NDLLCPICFELIRE-A--HITRCGHTFCFSCISKCVEL-----------------------QIKCPKCSASLPD 67 (140)
Q Consensus 20 ~~~~C~IC~~~~~~-p--~~~~CgH~fC~~Ci~~~~~~-----------------------~~~CP~C~~~~~~ 67 (140)
..-.|.||+-=|.+ | ..++|.|-|+..|+.+|+.. ...||+||..+..
T Consensus 114 p~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~ 187 (368)
T KOG4445|consen 114 PNGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKI 187 (368)
T ss_pred CCCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccc
Confidence 35689999987754 4 35699999999999988731 1359999988765
No 106
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=93.50 E-value=0.056 Score=40.52 Aligned_cols=46 Identities=26% Similarity=0.556 Sum_probs=35.6
Q ss_pred CCcccccccchhh---hceecCCCCcccHhhHHHHhhc---CCCCCCCCCCC
Q psy10659 20 NDLLCPICFELIR---EAHITRCGHTFCFSCISKCVEL---QIKCPKCSASL 65 (140)
Q Consensus 20 ~~~~C~IC~~~~~---~p~~~~CgH~fC~~Ci~~~~~~---~~~CP~C~~~~ 65 (140)
..+.||+=.+.-. .|+.+.|||+.-...+....+. .++||.|...-
T Consensus 335 s~FiCPVlKe~~t~ENpP~ml~CgHVIskeal~~LS~nG~~~FKCPYCP~~~ 386 (396)
T COG5109 335 SLFICPVLKELCTDENPPVMLECGHVISKEALSVLSQNGVLSFKCPYCPEMS 386 (396)
T ss_pred ceeeccccHhhhcccCCCeeeeccceeeHHHHHHHhhcCcEEeeCCCCCcch
Confidence 3578998666553 4688999999999999988764 37899996543
No 107
>KOG1100|consensus
Probab=93.05 E-value=0.039 Score=39.22 Aligned_cols=40 Identities=25% Similarity=0.536 Sum_probs=31.1
Q ss_pred cccccchhhhceecCCCC-cccHhhHHHHhhcCCCCCCCCCCCCC
Q psy10659 24 CPICFELIREAHITRCGH-TFCFSCISKCVELQIKCPKCSASLPD 67 (140)
Q Consensus 24 C~IC~~~~~~p~~~~CgH-~fC~~Ci~~~~~~~~~CP~C~~~~~~ 67 (140)
|-.|...-..-..+||.| .+|..|-.. ...||+|+.+...
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 888988777766779999 889999543 4669999876544
No 108
>KOG1815|consensus
Probab=92.68 E-value=0.072 Score=42.11 Aligned_cols=36 Identities=31% Similarity=0.647 Sum_probs=30.6
Q ss_pred CCCcccccccchhhh-ceecCCCCcccHhhHHHHhhc
Q psy10659 19 DNDLLCPICFELIRE-AHITRCGHTFCFSCISKCVEL 54 (140)
Q Consensus 19 ~~~~~C~IC~~~~~~-p~~~~CgH~fC~~Ci~~~~~~ 54 (140)
.....|.||.+.+.. ...+.|||.||..|+..++..
T Consensus 68 ~~~~~c~ic~~~~~~~~~~~~c~H~~c~~cw~~yl~~ 104 (444)
T KOG1815|consen 68 KGDVQCGICVESYDGEIIGLGCGHPFCPPCWTGYLGT 104 (444)
T ss_pred CccccCCcccCCCcchhhhcCCCcHHHHHHHHHHhhh
Confidence 456899999998886 556699999999999999863
No 109
>KOG2034|consensus
Probab=92.17 E-value=0.073 Score=44.89 Aligned_cols=36 Identities=22% Similarity=0.431 Sum_probs=28.8
Q ss_pred CCCCcccccccchh-hhcee-cCCCCcccHhhHHHHhh
Q psy10659 18 PDNDLLCPICFELI-REAHI-TRCGHTFCFSCISKCVE 53 (140)
Q Consensus 18 ~~~~~~C~IC~~~~-~~p~~-~~CgH~fC~~Ci~~~~~ 53 (140)
++....|.+|...+ ..|.. .+|||.|+.+|+.+...
T Consensus 814 ~ep~d~C~~C~~~ll~~pF~vf~CgH~FH~~Cl~~~v~ 851 (911)
T KOG2034|consen 814 LEPQDSCDHCGRPLLIKPFYVFPCGHCFHRDCLIRHVL 851 (911)
T ss_pred ecCccchHHhcchhhcCcceeeeccchHHHHHHHHHHH
Confidence 46678999999865 45654 59999999999987763
No 110
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=92.13 E-value=0.18 Score=29.52 Aligned_cols=35 Identities=26% Similarity=0.560 Sum_probs=26.6
Q ss_pred CCCCcccHhhHHHHhhcCCCCCCCCCCCCCCCCCccch
Q psy10659 38 RCGHTFCFSCISKCVELQIKCPKCSASLPDMNSVFPNF 75 (140)
Q Consensus 38 ~CgH~fC~~Ci~~~~~~~~~CP~C~~~~~~~~~~~~~~ 75 (140)
.-.|+||..|.+..+ ...||.|+-.+.... +++..
T Consensus 26 tfEcTFCadCae~~l--~g~CPnCGGelv~RP-~RPaa 60 (84)
T COG3813 26 TFECTFCADCAENRL--HGLCPNCGGELVARP-IRPAA 60 (84)
T ss_pred EEeeehhHhHHHHhh--cCcCCCCCchhhcCc-CChHH
Confidence 456789999998765 678999998877655 55543
No 111
>KOG4718|consensus
Probab=91.61 E-value=0.11 Score=36.85 Aligned_cols=46 Identities=22% Similarity=0.504 Sum_probs=38.6
Q ss_pred CCcccccccchhhhceec-CCCCcccHhhHHHHhhcCCCCCCCCCCC
Q psy10659 20 NDLLCPICFELIREAHIT-RCGHTFCFSCISKCVELQIKCPKCSASL 65 (140)
Q Consensus 20 ~~~~C~IC~~~~~~p~~~-~CgH~fC~~Ci~~~~~~~~~CP~C~~~~ 65 (140)
..-.|.+|..+....+.- +||-.++..|+..++.....||.|+--.
T Consensus 180 nlk~Cn~Ch~LvIqg~rCg~c~i~~h~~c~qty~q~~~~cphc~d~w 226 (235)
T KOG4718|consen 180 NLKNCNLCHCLVIQGIRCGSCNIQYHRGCIQTYLQRRDICPHCGDLW 226 (235)
T ss_pred HHHHHhHhHHHhheeeccCcccchhhhHHHHHHhcccCcCCchhccc
Confidence 446899999988876654 8999999999999999999999997533
No 112
>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=91.55 E-value=0.033 Score=41.50 Aligned_cols=46 Identities=22% Similarity=0.386 Sum_probs=24.8
Q ss_pred CCCcccccccchhhhceecC-----CCCcccHhhHHHHhhcCCCCCCCCCC
Q psy10659 19 DNDLLCPICFELIREAHITR-----CGHTFCFSCISKCVELQIKCPKCSAS 64 (140)
Q Consensus 19 ~~~~~C~IC~~~~~~p~~~~-----CgH~fC~~Ci~~~~~~~~~CP~C~~~ 64 (140)
...-.||||.....-.++.. =.|.+|..|-.+|.-....||.|+..
T Consensus 170 w~~g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R~~Cp~Cg~~ 220 (290)
T PF04216_consen 170 WQRGYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVRIKCPYCGNT 220 (290)
T ss_dssp TT-SS-TTT---EEEEEEE------EEEEEETTT--EEE--TTS-TTT---
T ss_pred ccCCcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecCCCCcCCCCC
Confidence 34579999999776544432 35789999999998888899999874
No 113
>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=91.40 E-value=0.13 Score=39.47 Aligned_cols=31 Identities=26% Similarity=0.791 Sum_probs=24.1
Q ss_pred CCCcccHhhHHHHhhc-------------CCCCCCCCCCCCCCC
Q psy10659 39 CGHTFCFSCISKCVEL-------------QIKCPKCSASLPDMN 69 (140)
Q Consensus 39 CgH~fC~~Ci~~~~~~-------------~~~CP~C~~~~~~~~ 69 (140)
|.-.+|.+|+-+|+.. +..||.||+.+.-.+
T Consensus 311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FCilD 354 (358)
T PF10272_consen 311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFCILD 354 (358)
T ss_pred ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccceeee
Confidence 5667799999999842 357999999887654
No 114
>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=90.80 E-value=0.079 Score=39.83 Aligned_cols=45 Identities=22% Similarity=0.478 Sum_probs=34.4
Q ss_pred CCcccccccchhhhceec------CCCCcccHhhHHHHhhcCCCCCCCCCC
Q psy10659 20 NDLLCPICFELIREAHIT------RCGHTFCFSCISKCVELQIKCPKCSAS 64 (140)
Q Consensus 20 ~~~~C~IC~~~~~~p~~~------~CgH~fC~~Ci~~~~~~~~~CP~C~~~ 64 (140)
..-.||+|.....-.++. .=.+.+|..|-.+|--....||.|+..
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 356999999977544322 123678999999999888999999974
No 115
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=90.55 E-value=0.024 Score=33.05 Aligned_cols=41 Identities=27% Similarity=0.662 Sum_probs=22.4
Q ss_pred CcccccccchhhhceecCCCCcccHhhHHHHhhcCCCCCCCCCCCC
Q psy10659 21 DLLCPICFELIREAHITRCGHTFCFSCISKCVELQIKCPKCSASLP 66 (140)
Q Consensus 21 ~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~CP~C~~~~~ 66 (140)
++.||.|...+.-.- ||.+|..|-..+ .....||.|..++.
T Consensus 1 e~~CP~C~~~L~~~~----~~~~C~~C~~~~-~~~a~CPdC~~~Le 41 (70)
T PF07191_consen 1 ENTCPKCQQELEWQG----GHYHCEACQKDY-KKEAFCPDCGQPLE 41 (70)
T ss_dssp --B-SSS-SBEEEET----TEEEETTT--EE-EEEEE-TTT-SB-E
T ss_pred CCcCCCCCCccEEeC----CEEECccccccc-eecccCCCcccHHH
Confidence 367999998754221 888888887653 34567999988764
No 116
>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=90.49 E-value=0.13 Score=31.52 Aligned_cols=38 Identities=26% Similarity=0.688 Sum_probs=30.1
Q ss_pred CcccccccchhhhceecCCCCcccHhhHHHHhhcCCCCCCCCCCCCC
Q psy10659 21 DLLCPICFELIREAHITRCGHTFCFSCISKCVELQIKCPKCSASLPD 67 (140)
Q Consensus 21 ~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~CP~C~~~~~~ 67 (140)
.-.|.||......+ ||.||..|... ...|.+|++.+..
T Consensus 44 ~~~C~~CK~~v~q~-----g~~YCq~CAYk----kGiCamCGKki~d 81 (90)
T PF10235_consen 44 SSKCKICKTKVHQP-----GAKYCQTCAYK----KGICAMCGKKILD 81 (90)
T ss_pred CccccccccccccC-----CCccChhhhcc----cCcccccCCeecc
Confidence 45899998877765 88999999553 6789999998744
No 117
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=90.48 E-value=0.041 Score=24.99 Aligned_cols=11 Identities=27% Similarity=0.703 Sum_probs=5.5
Q ss_pred cCCCCCCCCCC
Q psy10659 54 LQIKCPKCSAS 64 (140)
Q Consensus 54 ~~~~CP~C~~~ 64 (140)
....||.|+.+
T Consensus 12 ~~~fC~~CG~~ 22 (23)
T PF13240_consen 12 DAKFCPNCGTP 22 (23)
T ss_pred cCcchhhhCCc
Confidence 34445555543
No 118
>KOG0825|consensus
Probab=90.08 E-value=0.18 Score=42.29 Aligned_cols=50 Identities=14% Similarity=0.284 Sum_probs=36.3
Q ss_pred CCCCcccccccchhhhce----ecC---CCCcccHhhHHHHhhc------CCCCCCCCCCCCC
Q psy10659 18 PDNDLLCPICFELIREAH----ITR---CGHTFCFSCISKCVEL------QIKCPKCSASLPD 67 (140)
Q Consensus 18 ~~~~~~C~IC~~~~~~p~----~~~---CgH~fC~~Ci~~~~~~------~~~CP~C~~~~~~ 67 (140)
..+...|++|...+.+|+ ..+ |+|.||..||..|..+ .-.|++|..-+..
T Consensus 93 ~a~s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~s 155 (1134)
T KOG0825|consen 93 TAESDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESEKHTAHYFCEECVGS 155 (1134)
T ss_pred cccccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhccccccccccHHHHhhh
Confidence 345678888888888753 224 9999999999999863 2457777765544
No 119
>KOG2979|consensus
Probab=89.40 E-value=0.2 Score=36.58 Aligned_cols=44 Identities=25% Similarity=0.408 Sum_probs=37.0
Q ss_pred Ccccccccchhhhceec-CCCCcccHhhHHHHhhc--CCCCCCCCCC
Q psy10659 21 DLLCPICFELIREAHIT-RCGHTFCFSCISKCVEL--QIKCPKCSAS 64 (140)
Q Consensus 21 ~~~C~IC~~~~~~p~~~-~CgH~fC~~Ci~~~~~~--~~~CP~C~~~ 64 (140)
.++|||-...+.+|+.. .|||+|=.+-|..++.. ...||+=+..
T Consensus 176 s~rdPis~~~I~nPviSkkC~HvydrDsI~~~l~~~~~i~CPv~gC~ 222 (262)
T KOG2979|consen 176 SNRDPISKKPIVNPVISKKCGHVYDRDSIMQILCDEITIRCPVLGCE 222 (262)
T ss_pred cccCchhhhhhhchhhhcCcCcchhhhhHHHHhccCceeecccccCC
Confidence 57999999999999865 89999999999999975 5679976554
No 120
>KOG1812|consensus
Probab=89.02 E-value=0.18 Score=39.14 Aligned_cols=42 Identities=31% Similarity=0.685 Sum_probs=31.3
Q ss_pred Ccccccccchhhh-----ceecCCCCcccHhhHHHHhhcCCCCCCCC
Q psy10659 21 DLLCPICFELIRE-----AHITRCGHTFCFSCISKCVELQIKCPKCS 62 (140)
Q Consensus 21 ~~~C~IC~~~~~~-----p~~~~CgH~fC~~Ci~~~~~~~~~CP~C~ 62 (140)
-..||.|...+.. .++-.|||-||+.|...|......|..|-
T Consensus 306 wr~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~~~~~~~~~~~~~~~ 352 (384)
T KOG1812|consen 306 WRQCPKCKFMIELSEGCNHMTCRCGHQFCYMCGGDWKTHNGECYECC 352 (384)
T ss_pred cCcCcccceeeeecCCcceEEeeccccchhhcCcchhhCCccccCcc
Confidence 4689999887642 23336999999999999987777665553
No 121
>KOG3899|consensus
Probab=88.67 E-value=0.26 Score=36.73 Aligned_cols=31 Identities=23% Similarity=0.629 Sum_probs=24.8
Q ss_pred CCCcccHhhHHHHhh-------------cCCCCCCCCCCCCCCC
Q psy10659 39 CGHTFCFSCISKCVE-------------LQIKCPKCSASLPDMN 69 (140)
Q Consensus 39 CgH~fC~~Ci~~~~~-------------~~~~CP~C~~~~~~~~ 69 (140)
|...+|.+|+-+|+. ++-.||.||+.+.-.+
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 677889999999884 2457999999887655
No 122
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=88.56 E-value=0.19 Score=37.87 Aligned_cols=44 Identities=20% Similarity=0.529 Sum_probs=34.4
Q ss_pred CCcccccccchhhhcee-c----CCCCcccHhhHHHHhhcCCCCCCCCC
Q psy10659 20 NDLLCPICFELIREAHI-T----RCGHTFCFSCISKCVELQIKCPKCSA 63 (140)
Q Consensus 20 ~~~~C~IC~~~~~~p~~-~----~CgH~fC~~Ci~~~~~~~~~CP~C~~ 63 (140)
..-.||+|.....-.++ . .=.+.+|..|-.+|--....||.|+.
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 56899999997654432 1 23467899999999988899999996
No 123
>KOG2042|consensus
Probab=88.37 E-value=0.95 Score=38.96 Aligned_cols=72 Identities=17% Similarity=0.110 Sum_probs=64.0
Q ss_pred CCCCCcccccccchhhhceecC-CCCcccHhhHHHHhhcCCCCCCCCCCCCCCCCCccchHHHHHHHHHHhcCC
Q psy10659 17 PPDNDLLCPICFELIREAHITR-CGHTFCFSCISKCVELQIKCPKCSASLPDMNSVFPNFLLNELVQKHKIKSA 89 (140)
Q Consensus 17 ~~~~~~~C~IC~~~~~~p~~~~-CgH~fC~~Ci~~~~~~~~~CP~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 89 (140)
+..+++.=|+-...+.+||.+| -|++.++.=|.+++-...+=|.||.+++... +.+|..+...+..|.....
T Consensus 866 dvpdef~DPlm~Tlm~dPV~LP~Srv~vDRsti~rhlLs~~tdPFNR~pLt~d~-v~pn~eLK~kI~~~~~ek~ 938 (943)
T KOG2042|consen 866 DVPDEFLDPLMSTLMSDPVVLPSSRVTVDRSTIERHLLSDCTDPFNREPLTEDM-VSPNEELKAKIRCWIKEKR 938 (943)
T ss_pred cCchhhhCccccccCCCCccCCcccccccHHHHHHHHhcCCCCccccccCchhh-cCCCHHHHHHHHHHHHHhh
Confidence 5677888899999999999997 9999999999999998889999999999988 8999999998888876543
No 124
>KOG4642|consensus
Probab=87.08 E-value=1.1 Score=32.73 Aligned_cols=75 Identities=23% Similarity=0.266 Sum_probs=62.8
Q ss_pred cCCCCCCCcccccccchhhhceecCCCCcccHhhHHHHhhcC-CCCCCCCCCCCCCCCCccchHHHHHHHHHHhcCC
Q psy10659 14 QHSPPDNDLLCPICFELIREAHITRCGHTFCFSCISKCVELQ-IKCPKCSASLPDMNSVFPNFLLNELVQKHKIKSA 89 (140)
Q Consensus 14 ~~~~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~-~~CP~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 89 (140)
...++.+.+.|.|-++++.+|+++|-|-++=..=|.+.+... ..=|+-|.+++... +.+|..+...|+.|.....
T Consensus 204 k~rEvpd~lcgkIt~el~~~pvi~psgIty~ra~I~Ehl~rvghfdpvtr~~Lte~q-~ipN~alkevIa~fl~~n~ 279 (284)
T KOG4642|consen 204 KKREVPDYLCGKITLELMREPVITPSGITYDRADIEEHLQRVGHFDPVTRWPLTEYQ-LIPNLALKEVIAAFLKENE 279 (284)
T ss_pred ccccccchhhhhhhHHhhcCCccCccccchhHHHHHHHHHHhccCCchhcccCCHHh-hccchHHHHHHHHHHHhcc
Confidence 334566788889999999999999999999999999998753 44578888888877 8999999999999887654
No 125
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=87.01 E-value=0.76 Score=27.34 Aligned_cols=48 Identities=21% Similarity=0.559 Sum_probs=20.0
Q ss_pred Ccccccccchhh-----hceec--CCCCcccHhhHHHHhh-cCCCCCCCCCCCCCC
Q psy10659 21 DLLCPICFELIR-----EAHIT--RCGHTFCFSCISKCVE-LQIKCPKCSASLPDM 68 (140)
Q Consensus 21 ~~~C~IC~~~~~-----~p~~~--~CgH~fC~~Ci~~~~~-~~~~CP~C~~~~~~~ 68 (140)
...|.||.+... ++.+. .|+--.|+.|.+--.+ +...||.|+......
T Consensus 9 ~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg~q~CpqCkt~ykr~ 64 (80)
T PF14569_consen 9 GQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEGNQVCPQCKTRYKRH 64 (80)
T ss_dssp S-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS-SB-TTT--B----
T ss_pred CcccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcCcccccccCCCcccc
Confidence 568999999774 23333 6898999999975444 668899999876653
No 126
>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=86.57 E-value=0.53 Score=25.77 Aligned_cols=25 Identities=32% Similarity=0.844 Sum_probs=14.5
Q ss_pred CCCCcccHhhHHHHhhcCCCCCCCC
Q psy10659 38 RCGHTFCFSCISKCVELQIKCPKCS 62 (140)
Q Consensus 38 ~CgH~fC~~Ci~~~~~~~~~CP~C~ 62 (140)
.|++.||.+|=.-.-+.-..||.|.
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 6999999999553334556799884
No 127
>PF14353 CpXC: CpXC protein
Probab=86.52 E-value=0.54 Score=30.60 Aligned_cols=47 Identities=17% Similarity=0.227 Sum_probs=30.5
Q ss_pred cccccccchhhhceecCCCCcccHhhHHHHhhcC---CCCCCCCCCCCCC
Q psy10659 22 LLCPICFELIREAHITRCGHTFCFSCISKCVELQ---IKCPKCSASLPDM 68 (140)
Q Consensus 22 ~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~---~~CP~C~~~~~~~ 68 (140)
++||-|...+...+.+.-.-..=..=....+.+. ..||.|+..+...
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 6799998888766554433333344455555443 5799999987553
No 128
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=86.47 E-value=0.52 Score=26.08 Aligned_cols=31 Identities=23% Similarity=0.649 Sum_probs=24.5
Q ss_pred CCcccccccchh--hhceec--CCCCcccHhhHHH
Q psy10659 20 NDLLCPICFELI--REAHIT--RCGHTFCFSCISK 50 (140)
Q Consensus 20 ~~~~C~IC~~~~--~~p~~~--~CgH~fC~~Ci~~ 50 (140)
..-.|++|...| .+.++. .||-.+++.|+..
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~ 38 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK 38 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence 346899999999 455554 7999999999764
No 129
>KOG0309|consensus
Probab=86.33 E-value=0.41 Score=40.11 Aligned_cols=43 Identities=28% Similarity=0.651 Sum_probs=31.0
Q ss_pred Ccccccccchhhhc--eecCCCCcccHhhHHHHhhcCCCCCC-CCC
Q psy10659 21 DLLCPICFELIREA--HITRCGHTFCFSCISKCVELQIKCPK-CSA 63 (140)
Q Consensus 21 ~~~C~IC~~~~~~p--~~~~CgH~fC~~Ci~~~~~~~~~CP~-C~~ 63 (140)
.+.|.||.-....- +...|||+.+.+|...|++..-.||. |+.
T Consensus 1028 ~~~C~~C~l~V~gss~~Cg~C~Hv~H~sc~~eWf~~gd~CpsGCGC 1073 (1081)
T KOG0309|consen 1028 TFQCAICHLAVRGSSNFCGTCGHVGHTSCMMEWFRTGDVCPSGCGC 1073 (1081)
T ss_pred eeeeeeEeeEeeccchhhccccccccHHHHHHHHhcCCcCCCCCCc
Confidence 45566666544433 23479999999999999998888883 443
No 130
>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=86.33 E-value=0.23 Score=23.22 Aligned_cols=8 Identities=38% Similarity=0.957 Sum_probs=3.8
Q ss_pred cccccchh
Q psy10659 24 CPICFELI 31 (140)
Q Consensus 24 C~IC~~~~ 31 (140)
||-|....
T Consensus 3 CP~C~~~V 10 (26)
T PF10571_consen 3 CPECGAEV 10 (26)
T ss_pred CCCCcCCc
Confidence 45454444
No 131
>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=86.21 E-value=0.42 Score=26.27 Aligned_cols=37 Identities=24% Similarity=0.622 Sum_probs=22.7
Q ss_pred CCcccccccchhhhceecCCCCcccHhhHHHHhh--cCCCCCCCCC
Q psy10659 20 NDLLCPICFELIREAHITRCGHTFCFSCISKCVE--LQIKCPKCSA 63 (140)
Q Consensus 20 ~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~--~~~~CP~C~~ 63 (140)
+.+.||.|...+... .+...|...... ....||+|..
T Consensus 1 ~~f~CP~C~~~~~~~-------~L~~H~~~~H~~~~~~v~CPiC~~ 39 (54)
T PF05605_consen 1 DSFTCPYCGKGFSES-------SLVEHCEDEHRSESKNVVCPICSS 39 (54)
T ss_pred CCcCCCCCCCccCHH-------HHHHHHHhHCcCCCCCccCCCchh
Confidence 468899999955432 234444444433 2467999975
No 132
>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=86.06 E-value=1.1 Score=24.99 Aligned_cols=44 Identities=25% Similarity=0.521 Sum_probs=28.9
Q ss_pred ccccccchhhhc----eecCCCCcccHhhHHHHhhcCCCCCCCCCCCCCC
Q psy10659 23 LCPICFELIREA----HITRCGHTFCFSCISKCVELQIKCPKCSASLPDM 68 (140)
Q Consensus 23 ~C~IC~~~~~~p----~~~~CgH~fC~~Ci~~~~~~~~~CP~C~~~~~~~ 68 (140)
.|-.|-..+... .+-+=..+||..|....+ ...||.|+-.+..+
T Consensus 7 nCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l--~~~CPNCgGelv~R 54 (57)
T PF06906_consen 7 NCECCDKDLPPDSPEAYICSFECTFCADCAETML--NGVCPNCGGELVRR 54 (57)
T ss_pred CccccCCCCCCCCCcceEEeEeCcccHHHHHHHh--cCcCcCCCCccccC
Confidence 455565555322 222344589999999877 67899998766543
No 133
>KOG0827|consensus
Probab=85.81 E-value=0.09 Score=40.50 Aligned_cols=48 Identities=29% Similarity=0.569 Sum_probs=40.1
Q ss_pred cccccccchhhhc----eecCCCCcccHhhHHHHhhcCCCCCCCCCCCCCCC
Q psy10659 22 LLCPICFELIREA----HITRCGHTFCFSCISKCVELQIKCPKCSASLPDMN 69 (140)
Q Consensus 22 ~~C~IC~~~~~~p----~~~~CgH~fC~~Ci~~~~~~~~~CP~C~~~~~~~~ 69 (140)
-.|.||...++.- -.+.|||.+...|+..|+.....||.|+..+....
T Consensus 197 ~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~~~~kl~~~~rel~~~~ 248 (465)
T KOG0827|consen 197 GSLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLATKRKLPSCRRELPKNG 248 (465)
T ss_pred hhhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHHHhHHHHhhhhhhh
Confidence 4688999888754 24589999999999999999999999998876644
No 134
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=82.90 E-value=0.22 Score=23.16 Aligned_cols=9 Identities=44% Similarity=1.069 Sum_probs=4.4
Q ss_pred CCCCCCCCC
Q psy10659 56 IKCPKCSAS 64 (140)
Q Consensus 56 ~~CP~C~~~ 64 (140)
..||.|+.+
T Consensus 17 ~fC~~CG~~ 25 (26)
T PF13248_consen 17 KFCPNCGAK 25 (26)
T ss_pred ccChhhCCC
Confidence 445555543
No 135
>KOG3053|consensus
Probab=82.73 E-value=0.71 Score=33.80 Aligned_cols=52 Identities=21% Similarity=0.564 Sum_probs=36.9
Q ss_pred CCCCCCCcccccccchhhhce----ecCC-----CCcccHhhHHHHhhc--------CCCCCCCCCCCC
Q psy10659 15 HSPPDNDLLCPICFELIREAH----ITRC-----GHTFCFSCISKCVEL--------QIKCPKCSASLP 66 (140)
Q Consensus 15 ~~~~~~~~~C~IC~~~~~~p~----~~~C-----gH~fC~~Ci~~~~~~--------~~~CP~C~~~~~ 66 (140)
.+..+.+-.|=||+..-++.. +-|| .|=.|..|+..|+.. ...||.|+....
T Consensus 14 ~~~~e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYi 82 (293)
T KOG3053|consen 14 SDNQELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYI 82 (293)
T ss_pred CCccccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchhe
Confidence 345667789999999776542 2255 345789999999952 246999987643
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=82.34 E-value=0.32 Score=27.99 Aligned_cols=31 Identities=32% Similarity=0.622 Sum_probs=15.8
Q ss_pred CCcccccccchhhhc---e-ecCCCCcccHhhHHH
Q psy10659 20 NDLLCPICFELIREA---H-ITRCGHTFCFSCISK 50 (140)
Q Consensus 20 ~~~~C~IC~~~~~~p---~-~~~CgH~fC~~Ci~~ 50 (140)
+...|.+|...|.-- . --.||++||..|...
T Consensus 8 ~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~ 42 (69)
T PF01363_consen 8 EASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQ 42 (69)
T ss_dssp G-SB-TTT--B-BSSS-EEE-TTT--EEECCCS-E
T ss_pred CCCcCcCcCCcCCCceeeEccCCCCCEECCchhCC
Confidence 457899999988421 1 137999999999754
No 137
>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=82.30 E-value=6.8 Score=28.81 Aligned_cols=21 Identities=29% Similarity=0.915 Sum_probs=16.4
Q ss_pred ccccccchhhhceecCCCCcccHhhHHHH
Q psy10659 23 LCPICFELIREAHITRCGHTFCFSCISKC 51 (140)
Q Consensus 23 ~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~ 51 (140)
.|+||. .+-.+.+|..|+..-
T Consensus 1 ~C~iC~--------~~~~~~~C~~C~~~~ 21 (302)
T PF10186_consen 1 QCPICH--------NSRRRFYCANCVNNR 21 (302)
T ss_pred CCCCCC--------CCCCCeECHHHHHHH
Confidence 499998 456677999998874
No 138
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=81.59 E-value=0.98 Score=38.31 Aligned_cols=51 Identities=18% Similarity=0.354 Sum_probs=38.3
Q ss_pred CCCcccccccchh--hhceecCCCCc-----ccHhhHHHHhh--cCCCCCCCCCCCCCCC
Q psy10659 19 DNDLLCPICFELI--REAHITRCGHT-----FCFSCISKCVE--LQIKCPKCSASLPDMN 69 (140)
Q Consensus 19 ~~~~~C~IC~~~~--~~p~~~~CgH~-----fC~~Ci~~~~~--~~~~CP~C~~~~~~~~ 69 (140)
+++..|.||+..- .+|..-||..+ .|.+|+.+|+. +..+|-.|..++.-++
T Consensus 10 ~d~~~CRICr~e~~~d~pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~Fk~ 69 (1175)
T COG5183 10 EDKRSCRICRTEDIRDDPLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKFKD 69 (1175)
T ss_pred ccchhceeecCCCCCCCcCcccccccchhHHHHHHHHHHHHhcCCCcceeeecceeeeee
Confidence 4668999998744 45666677653 68899999997 4578999998775543
No 139
>COG5627 MMS21 DNA repair protein MMS21 [DNA replication, recombination, and repair]
Probab=81.53 E-value=2.6 Score=30.59 Aligned_cols=40 Identities=23% Similarity=0.424 Sum_probs=33.5
Q ss_pred Ccccccccchhhhcee-cCCCCcccHhhHHHHhh--cCCCCCC
Q psy10659 21 DLLCPICFELIREAHI-TRCGHTFCFSCISKCVE--LQIKCPK 60 (140)
Q Consensus 21 ~~~C~IC~~~~~~p~~-~~CgH~fC~~Ci~~~~~--~~~~CP~ 60 (140)
+.+|||-+..+.-|+. ..|.|.|=.+-|..++. ....||.
T Consensus 189 ~nrCpitl~p~~~pils~kcnh~~e~D~I~~~lq~~~trvcp~ 231 (275)
T COG5627 189 SNRCPITLNPDFYPILSSKCNHKPEMDLINKKLQVECTRVCPR 231 (275)
T ss_pred cccCCcccCcchhHHHHhhhcccccHHHHHHHhcCCceeecch
Confidence 5799999998888875 58999999999999997 4466774
No 140
>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 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=80.25 E-value=1.1 Score=25.82 Aligned_cols=12 Identities=42% Similarity=0.918 Sum_probs=8.8
Q ss_pred cccHhhHHHHhh
Q psy10659 42 TFCFSCISKCVE 53 (140)
Q Consensus 42 ~fC~~Ci~~~~~ 53 (140)
.||+.|+..|..
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 142
>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=79.17 E-value=1.3 Score=24.19 Aligned_cols=31 Identities=29% Similarity=0.610 Sum_probs=22.1
Q ss_pred cccccccchhhhc----eecCCCCcccHhhHHHHh
Q psy10659 22 LLCPICFELIREA----HITRCGHTFCFSCISKCV 52 (140)
Q Consensus 22 ~~C~IC~~~~~~p----~~~~CgH~fC~~Ci~~~~ 52 (140)
..|.+|...|.-- .-..||++||..|.....
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~ 37 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRI 37 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCcChHHcCCee
Confidence 4688888766532 223799999999977544
No 143
>KOG4185|consensus
Probab=78.59 E-value=0.4 Score=35.70 Aligned_cols=43 Identities=40% Similarity=0.766 Sum_probs=33.9
Q ss_pred cccccccchhhh------ceecC--------CCCcccHhhHHHHhhc-CCCCCCCCCC
Q psy10659 22 LLCPICFELIRE------AHITR--------CGHTFCFSCISKCVEL-QIKCPKCSAS 64 (140)
Q Consensus 22 ~~C~IC~~~~~~------p~~~~--------CgH~fC~~Ci~~~~~~-~~~CP~C~~~ 64 (140)
..|.||...+.. |.++. |||+.|..|+...+.. ...||.|+..
T Consensus 208 ~~c~ic~~~~~~n~~~~~p~vl~~~~~~~~~c~htlc~~c~~~~l~~~~~~cp~~~~~ 265 (296)
T KOG4185|consen 208 KLCEICERIYSENDEKLAPLVLSLSRLKEKIEGHTLCKECIDTILLQAGIKCPFCTWS 265 (296)
T ss_pred HHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcchHHHHHHhhhcCCcccce
Confidence 568999988872 44455 9999999999988753 3789999863
No 144
>KOG0269|consensus
Probab=78.48 E-value=2.3 Score=35.78 Aligned_cols=48 Identities=23% Similarity=0.334 Sum_probs=35.6
Q ss_pred cccccccchhhhceec--CCCCcccHhhHHHHhhcCCCCCC--CCCCCCCCC
Q psy10659 22 LLCPICFELIREAHIT--RCGHTFCFSCISKCVELQIKCPK--CSASLPDMN 69 (140)
Q Consensus 22 ~~C~IC~~~~~~p~~~--~CgH~fC~~Ci~~~~~~~~~CP~--C~~~~~~~~ 69 (140)
..|.+|...+..-..- .|||.-+.+|+..|+.....||. |........
T Consensus 780 ~~CtVC~~vi~G~~~~c~~C~H~gH~sh~~sw~~~~s~ca~~~C~~~c~~~~ 831 (839)
T KOG0269|consen 780 AKCTVCDLVIRGVDVWCQVCGHGGHDSHLKSWFFKASPCAKSICPHLCHYSS 831 (839)
T ss_pred cCceeecceeeeeEeecccccccccHHHHHHHHhcCCCCccccCCccccccc
Confidence 4677777766543322 69999999999999999888887 776554443
No 145
>KOG2169|consensus
Probab=78.12 E-value=3 Score=34.76 Aligned_cols=67 Identities=19% Similarity=0.365 Sum_probs=47.0
Q ss_pred CCcccccccchhhhcee-cCCCCcccHhhHHHHhh----cCCCCCCCCCCCCCCCCCccchHHHHHHHHHHhc
Q psy10659 20 NDLLCPICFELIREAHI-TRCGHTFCFSCISKCVE----LQIKCPKCSASLPDMNSVFPNFLLNELVQKHKIK 87 (140)
Q Consensus 20 ~~~~C~IC~~~~~~p~~-~~CgH~fC~~Ci~~~~~----~~~~CP~C~~~~~~~~~~~~~~~~~~~~~~~~~~ 87 (140)
-.+.|||+..-+.-|.. ..|+|.=|.+-..-... ..-.||+|.+.....+ +..+..+.+++......
T Consensus 305 vSL~CPl~~~Rm~~P~r~~~CkHlQcFD~~~~lq~n~~~pTW~CPVC~~~~~~e~-l~iD~~~~~iL~~~~~~ 376 (636)
T KOG2169|consen 305 VSLNCPLSKMRMSLPARGHTCKHLQCFDALSYLQMNEQKPTWRCPVCQKAAPFEG-LIIDGYFLNILQSCQAN 376 (636)
T ss_pred eEecCCcccceeecCCcccccccceecchhhhHHhccCCCeeeCccCCccccccc-hhhhHHHHHHHhhccCC
Confidence 35789999888877765 47888777765442221 2346999999877766 77777777777666553
No 146
>PRK04023 DNA polymerase II large subunit; Validated
Probab=78.04 E-value=2.7 Score=36.62 Aligned_cols=49 Identities=20% Similarity=0.306 Sum_probs=33.5
Q ss_pred CCCcccccccchhhhceecCCCC-----cccHhhHHHHhhcCCCCCCCCCCCCCCC
Q psy10659 19 DNDLLCPICFELIREAHITRCGH-----TFCFSCISKCVELQIKCPKCSASLPDMN 69 (140)
Q Consensus 19 ~~~~~C~IC~~~~~~p~~~~CgH-----~fC~~Ci~~~~~~~~~CP~C~~~~~~~~ 69 (140)
.....|+-|........--.||. .||..|-. ......||.|+.......
T Consensus 624 Vg~RfCpsCG~~t~~frCP~CG~~Te~i~fCP~CG~--~~~~y~CPKCG~El~~~s 677 (1121)
T PRK04023 624 IGRRKCPSCGKETFYRRCPFCGTHTEPVYRCPRCGI--EVEEDECEKCGREPTPYS 677 (1121)
T ss_pred ccCccCCCCCCcCCcccCCCCCCCCCcceeCccccC--cCCCCcCCCCCCCCCccc
Confidence 45679999998753322335885 59999933 233467999998877644
No 147
>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=77.76 E-value=0.72 Score=35.82 Aligned_cols=45 Identities=20% Similarity=0.454 Sum_probs=0.0
Q ss_pred cccccccchhhh-------------c-eecCCCCcccHhhHHHHhh---cCCCCCCCCCCCC
Q psy10659 22 LLCPICFELIRE-------------A-HITRCGHTFCFSCISKCVE---LQIKCPKCSASLP 66 (140)
Q Consensus 22 ~~C~IC~~~~~~-------------p-~~~~CgH~fC~~Ci~~~~~---~~~~CP~C~~~~~ 66 (140)
..||+=+..+.- | |.+.|||++-+.=+..-.. ....||+|+..-.
T Consensus 278 pQCPVglnTL~fp~~~~~~~~~~~qP~VYl~CGHVhG~h~Wg~~~~~~~~~r~CPlCr~~g~ 339 (416)
T PF04710_consen 278 PQCPVGLNTLVFPSKSRKDVPDERQPWVYLNCGHVHGYHNWGQDSDRDPRSRTCPLCRQVGP 339 (416)
T ss_dssp --------------------------------------------------------------
T ss_pred CCCCcCCCccccccccccccccccCceeeccccceeeecccccccccccccccCCCccccCC
Confidence 577776665532 2 4578999987754322111 2578999997543
No 148
>KOG2068|consensus
Probab=77.55 E-value=2.1 Score=32.45 Aligned_cols=47 Identities=26% Similarity=0.696 Sum_probs=36.3
Q ss_pred cccccccchhhh--cee--cCCCCcccHhhHHHHhhcCCCCCCCCCCCCCC
Q psy10659 22 LLCPICFELIRE--AHI--TRCGHTFCFSCISKCVELQIKCPKCSASLPDM 68 (140)
Q Consensus 22 ~~C~IC~~~~~~--p~~--~~CgH~fC~~Ci~~~~~~~~~CP~C~~~~~~~ 68 (140)
-.||||-+.... --. .+||+..|..|..........||.|+++....
T Consensus 250 ~s~p~~~~~~~~~d~~~lP~~~~~~~~l~~~~t~~~~~~~~~~~rk~~~~~ 300 (327)
T KOG2068|consen 250 PSCPICYEDLDLTDSNFLPCPCGFRLCLFCHKTISDGDGRCPGCRKPYERN 300 (327)
T ss_pred CCCCCCCCcccccccccccccccccchhhhhhcccccCCCCCccCCccccC
Confidence 679999997632 222 37999999999988888889999999765543
No 149
>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=76.94 E-value=0.78 Score=35.62 Aligned_cols=48 Identities=21% Similarity=0.540 Sum_probs=0.0
Q ss_pred Ccccccccchhh--------------h---c--eecCCCCcccHhhHHHHhhc---------CCCCCCCCCCCCCC
Q psy10659 21 DLLCPICFELIR--------------E---A--HITRCGHTFCFSCISKCVEL---------QIKCPKCSASLPDM 68 (140)
Q Consensus 21 ~~~C~IC~~~~~--------------~---p--~~~~CgH~fC~~Ci~~~~~~---------~~~CP~C~~~~~~~ 68 (140)
.-+||+|+..-. + | ...||||.--.....-|..- +..||+|..++...
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 689999997421 1 1 23489998777777777641 25799999887643
No 150
>KOG0289|consensus
Probab=76.01 E-value=3.7 Score=32.46 Aligned_cols=48 Identities=23% Similarity=0.290 Sum_probs=42.3
Q ss_pred cccccccchhhhceec-CCCCcccHhhHHHHhhcCCCCCCCCCCCCCCC
Q psy10659 22 LLCPICFELIREAHIT-RCGHTFCFSCISKCVELQIKCPKCSASLPDMN 69 (140)
Q Consensus 22 ~~C~IC~~~~~~p~~~-~CgH~fC~~Ci~~~~~~~~~CP~C~~~~~~~~ 69 (140)
+.|.|-.+....||+. .-||+|=++=|++++....+||+-+.+++..+
T Consensus 1 m~CaISgEvP~~PVvS~~Sg~vfEkrLIEqyI~e~G~DPIt~~pLs~ee 49 (506)
T KOG0289|consen 1 MVCAISGEVPEEPVVSPVSGHVFEKRLIEQYIAETGKDPITNEPLSIEE 49 (506)
T ss_pred CeecccCCCCCCccccccccchHHHHHHHHHHHHcCCCCCCCCcCCHHH
Confidence 3699999999999987 69999999999999999999999988876543
No 151
>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=75.88 E-value=2.5 Score=20.68 Aligned_cols=35 Identities=31% Similarity=0.650 Sum_probs=21.0
Q ss_pred ccccccchhhh--ceecCCCCcccHhhHHHHhhcCCCCCCCCCCC
Q psy10659 23 LCPICFELIRE--AHITRCGHTFCFSCISKCVELQIKCPKCSASL 65 (140)
Q Consensus 23 ~C~IC~~~~~~--p~~~~CgH~fC~~Ci~~~~~~~~~CP~C~~~~ 65 (140)
.|..|...+.. .....=+..|+..| +.|..|+.++
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~C--------f~C~~C~~~L 37 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPEC--------FKCSKCGKPL 37 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccC--------CCCcccCCcC
Confidence 36777776665 23334456666666 4477777654
No 152
>KOG2789|consensus
Probab=75.80 E-value=1.2 Score=34.70 Aligned_cols=33 Identities=30% Similarity=0.627 Sum_probs=26.2
Q ss_pred CCcccccccchhhhceec--CCCCcccHhhHHHHh
Q psy10659 20 NDLLCPICFELIREAHIT--RCGHTFCFSCISKCV 52 (140)
Q Consensus 20 ~~~~C~IC~~~~~~p~~~--~CgH~fC~~Ci~~~~ 52 (140)
....||||+-++-....+ -|..+.|..|+.++-
T Consensus 73 r~~ecpicflyyps~~n~~rcC~~~Ic~ecf~~~~ 107 (482)
T KOG2789|consen 73 RKTECPICFLYYPSAKNLVRCCSETICGECFAPFG 107 (482)
T ss_pred ccccCceeeeecccccchhhhhccchhhhheeccc
Confidence 357999999988765433 699999999998765
No 153
>PRK11595 DNA utilization protein GntX; Provisional
Probab=75.29 E-value=2.3 Score=30.48 Aligned_cols=39 Identities=23% Similarity=0.487 Sum_probs=23.3
Q ss_pred cccccccchhhhceecCCCCcccHhhHHHHhhcCCCCCCCCCCC
Q psy10659 22 LLCPICFELIREAHITRCGHTFCFSCISKCVELQIKCPKCSASL 65 (140)
Q Consensus 22 ~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~CP~C~~~~ 65 (140)
-.|.+|...+... ....|..|...+-.....||.|+.+.
T Consensus 6 ~~C~~C~~~~~~~-----~~~lC~~C~~~l~~~~~~C~~Cg~~~ 44 (227)
T PRK11595 6 GLCWLCRMPLALS-----HWGICSVCSRALRTLKTCCPQCGLPA 44 (227)
T ss_pred CcCccCCCccCCC-----CCcccHHHHhhCCcccCcCccCCCcC
Confidence 3588888765321 12467888766533234677777654
No 154
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=74.95 E-value=1.4 Score=30.65 Aligned_cols=17 Identities=29% Similarity=0.894 Sum_probs=13.9
Q ss_pred hcCCCCCCCCCCCCCCC
Q psy10659 53 ELQIKCPKCSASLPDMN 69 (140)
Q Consensus 53 ~~~~~CP~C~~~~~~~~ 69 (140)
...+.||.|+..+..-+
T Consensus 134 ~~~F~Cp~Cg~~L~~~d 150 (178)
T PRK06266 134 EYGFRCPQCGEMLEEYD 150 (178)
T ss_pred hcCCcCCCCCCCCeecc
Confidence 45899999999887754
No 155
>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=74.94 E-value=2.2 Score=20.85 Aligned_cols=11 Identities=36% Similarity=0.824 Sum_probs=7.5
Q ss_pred cCCCCCCCCCC
Q psy10659 54 LQIKCPKCSAS 64 (140)
Q Consensus 54 ~~~~CP~C~~~ 64 (140)
....||.|+..
T Consensus 16 ~~~~CP~Cg~~ 26 (33)
T cd00350 16 APWVCPVCGAP 26 (33)
T ss_pred CCCcCcCCCCc
Confidence 35578988763
No 156
>KOG1829|consensus
Probab=74.83 E-value=1.1 Score=36.64 Aligned_cols=23 Identities=26% Similarity=0.739 Sum_probs=17.8
Q ss_pred CCCCcccHhhHHHHhhcCCCCCCCCC
Q psy10659 38 RCGHTFCFSCISKCVELQIKCPKCSA 63 (140)
Q Consensus 38 ~CgH~fC~~Ci~~~~~~~~~CP~C~~ 63 (140)
.||+.||..|+.. .+..||.|-+
T Consensus 536 ~C~avfH~~C~~r---~s~~CPrC~R 558 (580)
T KOG1829|consen 536 TCLAVFHKKCLRR---KSPCCPRCER 558 (580)
T ss_pred HHHHHHHHHHHhc---cCCCCCchHH
Confidence 6999999999653 4555999954
No 157
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=73.68 E-value=0.57 Score=26.18 Aligned_cols=33 Identities=30% Similarity=0.684 Sum_probs=21.9
Q ss_pred CCcccc--cccchhhhc-------eec-CCCCcccHhhHHHHh
Q psy10659 20 NDLLCP--ICFELIREA-------HIT-RCGHTFCFSCISKCV 52 (140)
Q Consensus 20 ~~~~C~--IC~~~~~~p-------~~~-~CgH~fC~~Ci~~~~ 52 (140)
....|| -|...+... +.- .||+.||..|...|-
T Consensus 17 ~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H 59 (64)
T smart00647 17 DLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWH 59 (64)
T ss_pred CccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcCC
Confidence 345688 676644322 233 689999999988774
No 158
>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=73.41 E-value=2.9 Score=30.27 Aligned_cols=27 Identities=30% Similarity=0.495 Sum_probs=22.2
Q ss_pred ccHhhHHHHhhcCCCCCCCCCCCCCCC
Q psy10659 43 FCFSCISKCVELQIKCPKCSASLPDMN 69 (140)
Q Consensus 43 fC~~Ci~~~~~~~~~CP~C~~~~~~~~ 69 (140)
-|.+|-...-+..+.||+|+.....++
T Consensus 196 ~C~sC~qqIHRNAPiCPlCK~KsRSrn 222 (230)
T PF10146_consen 196 TCQSCHQQIHRNAPICPLCKAKSRSRN 222 (230)
T ss_pred hhHhHHHHHhcCCCCCcccccccccCC
Confidence 588999998889999999997655543
No 159
>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=72.89 E-value=1.1 Score=24.59 Aligned_cols=12 Identities=33% Similarity=0.761 Sum_probs=6.3
Q ss_pred CCCCCCCCCCCC
Q psy10659 56 IKCPKCSASLPD 67 (140)
Q Consensus 56 ~~CP~C~~~~~~ 67 (140)
..||+|+++++.
T Consensus 21 ~~CPlC~r~l~~ 32 (54)
T PF04423_consen 21 GCCPLCGRPLDE 32 (54)
T ss_dssp EE-TTT--EE-H
T ss_pred CcCCCCCCCCCH
Confidence 389999998765
No 160
>KOG3993|consensus
Probab=72.76 E-value=0.7 Score=36.21 Aligned_cols=43 Identities=23% Similarity=0.564 Sum_probs=30.9
Q ss_pred CCCCCcccccccchhhhceec---CCCCcccHhhHHHHhhcCCCCCCCCCCCCCC
Q psy10659 17 PPDNDLLCPICFELIREAHIT---RCGHTFCFSCISKCVELQIKCPKCSASLPDM 68 (140)
Q Consensus 17 ~~~~~~~C~IC~~~~~~p~~~---~CgH~fC~~Ci~~~~~~~~~CP~C~~~~~~~ 68 (140)
....++.|.+|...|.|+..| .|-.+.+. ..+||.|.++|.-.
T Consensus 263 n~iGdyiCqLCK~kYeD~F~LAQHrC~RIV~v---------EYrCPEC~KVFsCP 308 (500)
T KOG3993|consen 263 NVIGDYICQLCKEKYEDAFALAQHRCPRIVHV---------EYRCPECDKVFSCP 308 (500)
T ss_pred ccHHHHHHHHHHHhhhhHHHHhhccCCeeEEe---------eecCCcccccccCc
Confidence 344578899999999888766 46544332 57899999988654
No 161
>PF15616 TerY-C: TerY-C metal binding domain
Probab=71.91 E-value=1.7 Score=28.60 Aligned_cols=46 Identities=26% Similarity=0.416 Sum_probs=33.5
Q ss_pred CCCCCcccccccchhhhceecCCCCcccHhhHHHHhhcCCCCCCCCCCCCCC
Q psy10659 17 PPDNDLLCPICFELIREAHITRCGHTFCFSCISKCVELQIKCPKCSASLPDM 68 (140)
Q Consensus 17 ~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~CP~C~~~~~~~ 68 (140)
++...-.||-|...+.-.+- .||+.||..= .....||-|+......
T Consensus 73 eL~g~PgCP~CGn~~~fa~C-~CGkl~Ci~g-----~~~~~CPwCg~~g~~~ 118 (131)
T PF15616_consen 73 ELIGAPGCPHCGNQYAFAVC-GCGKLFCIDG-----EGEVTCPWCGNEGSFG 118 (131)
T ss_pred HhcCCCCCCCCcChhcEEEe-cCCCEEEeCC-----CCCEECCCCCCeeeec
Confidence 44556899999998764444 8999999642 2357899999876543
No 162
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=70.67 E-value=4.4 Score=25.95 Aligned_cols=41 Identities=24% Similarity=0.501 Sum_probs=31.0
Q ss_pred cccccccchhhhce--------------ecCCCCcccHhhHHHHhhcCCCCCCCC
Q psy10659 22 LLCPICFELIREAH--------------ITRCGHTFCFSCISKCVELQIKCPKCS 62 (140)
Q Consensus 22 ~~C~IC~~~~~~p~--------------~~~CgH~fC~~Ci~~~~~~~~~CP~C~ 62 (140)
..|--|...|..+. -..|++.||.+|=.-+-+.-..||.|.
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 45999999886541 236999999999776666667899985
No 163
>PF12773 DZR: Double zinc ribbon
Probab=70.35 E-value=3.3 Score=22.06 Aligned_cols=26 Identities=31% Similarity=0.710 Sum_probs=14.2
Q ss_pred cccHhhHHHHh--h-cCCCCCCCCCCCCC
Q psy10659 42 TFCFSCISKCV--E-LQIKCPKCSASLPD 67 (140)
Q Consensus 42 ~fC~~Ci~~~~--~-~~~~CP~C~~~~~~ 67 (140)
.||..|-.... . ....||.|+..+..
T Consensus 13 ~fC~~CG~~l~~~~~~~~~C~~Cg~~~~~ 41 (50)
T PF12773_consen 13 KFCPHCGTPLPPPDQSKKICPNCGAENPP 41 (50)
T ss_pred cCChhhcCChhhccCCCCCCcCCcCCCcC
Confidence 35555544443 1 23568888776544
No 164
>PLN02195 cellulose synthase A
Probab=69.32 E-value=4.1 Score=35.45 Aligned_cols=46 Identities=22% Similarity=0.566 Sum_probs=34.3
Q ss_pred Ccccccccchhh-----hceec--CCCCcccHhhHHHHhh--cCCCCCCCCCCCCC
Q psy10659 21 DLLCPICFELIR-----EAHIT--RCGHTFCFSCISKCVE--LQIKCPKCSASLPD 67 (140)
Q Consensus 21 ~~~C~IC~~~~~-----~p~~~--~CgH~fC~~Ci~~~~~--~~~~CP~C~~~~~~ 67 (140)
...|.||.+... +|.+. .||--.|+.|.+ |-+ ++..||.|+.....
T Consensus 6 ~~~c~~cgd~~~~~~~g~~fvaC~eC~~pvCrpCye-yer~eg~q~CpqCkt~Yk~ 60 (977)
T PLN02195 6 APICATCGEEVGVDSNGEAFVACHECSYPLCKACLE-YEIKEGRKVCLRCGGPYDA 60 (977)
T ss_pred CccceecccccCcCCCCCeEEEeccCCCccccchhh-hhhhcCCccCCccCCcccc
Confidence 357999999664 34332 799999999994 433 56889999998774
No 165
>KOG0824|consensus
Probab=69.26 E-value=1.9 Score=32.40 Aligned_cols=48 Identities=23% Similarity=0.664 Sum_probs=38.1
Q ss_pred CCCCCcccccccchhhhceec-CCCCcccHhhHHHHhhcCCCCCCCCCC
Q psy10659 17 PPDNDLLCPICFELIREAHIT-RCGHTFCFSCISKCVELQIKCPKCSAS 64 (140)
Q Consensus 17 ~~~~~~~C~IC~~~~~~p~~~-~CgH~fC~~Ci~~~~~~~~~CP~C~~~ 64 (140)
-..+...|-||...+.-|-.. .|+|-||..|...|......||.|+..
T Consensus 101 ~~~~~~~~~~~~g~l~vpt~~qg~w~qf~~~~p~~~~~~~~~~~d~~~~ 149 (324)
T KOG0824|consen 101 FQQDHDICYICYGKLTVPTRIQGCWHQFCYVCPKSNFAMGNDCPDCRGK 149 (324)
T ss_pred ccCCccceeeeeeeEEecccccCceeeeeecCCchhhhhhhccchhhcC
Confidence 345667888999988887665 699999999999999877777776643
No 166
>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=69.09 E-value=5.5 Score=25.15 Aligned_cols=25 Identities=32% Similarity=0.724 Sum_probs=18.6
Q ss_pred CCcccHhhHHHHhh---------cCCCCCCCCCC
Q psy10659 40 GHTFCFSCISKCVE---------LQIKCPKCSAS 64 (140)
Q Consensus 40 gH~fC~~Ci~~~~~---------~~~~CP~C~~~ 64 (140)
.-.||..|+..+.. ..-.||.|+-.
T Consensus 37 ~~~fC~~CL~~ryge~~~ev~~~~~W~CP~Crgi 70 (105)
T PF10497_consen 37 RGKFCGGCLRNRYGENVEEVLEDPNWKCPKCRGI 70 (105)
T ss_pred cceehHhHHHHHHhhhHHHHhcCCceECCCCCCe
Confidence 77899999987763 23469988763
No 167
>KOG2807|consensus
Probab=69.04 E-value=3.1 Score=31.64 Aligned_cols=42 Identities=24% Similarity=0.591 Sum_probs=29.2
Q ss_pred Ccccccccchhhh-ceec--CCCCcccHhhHHHHhhcCCCCCCCC
Q psy10659 21 DLLCPICFELIRE-AHIT--RCGHTFCFSCISKCVELQIKCPKCS 62 (140)
Q Consensus 21 ~~~C~IC~~~~~~-p~~~--~CgH~fC~~Ci~~~~~~~~~CP~C~ 62 (140)
...|-.|...... +... .|.++||.+|=.-.-+.-..||.|.
T Consensus 330 ~~~Cf~C~~~~~~~~~y~C~~Ck~~FCldCDv~iHesLh~CpgCe 374 (378)
T KOG2807|consen 330 SRFCFACQGELLSSGRYRCESCKNVFCLDCDVFIHESLHNCPGCE 374 (378)
T ss_pred CcceeeeccccCCCCcEEchhccceeeccchHHHHhhhhcCCCcC
Confidence 3458889554443 3332 7999999999665555667899996
No 168
>PLN02436 cellulose synthase A
Probab=68.90 E-value=3.8 Score=35.99 Aligned_cols=46 Identities=24% Similarity=0.595 Sum_probs=33.5
Q ss_pred Ccccccccchhh-----hceec--CCCCcccHhhHHHHhh-cCCCCCCCCCCCC
Q psy10659 21 DLLCPICFELIR-----EAHIT--RCGHTFCFSCISKCVE-LQIKCPKCSASLP 66 (140)
Q Consensus 21 ~~~C~IC~~~~~-----~p~~~--~CgH~fC~~Ci~~~~~-~~~~CP~C~~~~~ 66 (140)
...|.||.+... ++.+. .||--.|..|.+-=.+ ++..||.|+....
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 348999999874 23332 5888899999943222 5678999998876
No 169
>COG4647 AcxC Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=68.83 E-value=2 Score=28.20 Aligned_cols=21 Identities=29% Similarity=0.520 Sum_probs=13.2
Q ss_pred cccchhhhceecCCCCcccHh
Q psy10659 26 ICFELIREAHITRCGHTFCFS 46 (140)
Q Consensus 26 IC~~~~~~p~~~~CgH~fC~~ 46 (140)
||.+.-..-..-.|||+||..
T Consensus 62 i~qs~~~rv~rcecghsf~d~ 82 (165)
T COG4647 62 ICQSAQKRVIRCECGHSFGDY 82 (165)
T ss_pred EEecccccEEEEeccccccCh
Confidence 455544443345899999973
No 170
>PLN02189 cellulose synthase
Probab=68.40 E-value=4 Score=35.75 Aligned_cols=47 Identities=26% Similarity=0.604 Sum_probs=33.8
Q ss_pred Ccccccccchhhh-----ceec--CCCCcccHhhHHHHh-hcCCCCCCCCCCCCC
Q psy10659 21 DLLCPICFELIRE-----AHIT--RCGHTFCFSCISKCV-ELQIKCPKCSASLPD 67 (140)
Q Consensus 21 ~~~C~IC~~~~~~-----p~~~--~CgH~fC~~Ci~~~~-~~~~~CP~C~~~~~~ 67 (140)
...|.||.+.... +.+. .||--.|..|.+-=. +++..||.|+.....
T Consensus 34 ~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cyeyer~eg~q~CpqCkt~Y~r 88 (1040)
T PLN02189 34 GQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCYEYERREGTQNCPQCKTRYKR 88 (1040)
T ss_pred CccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchhh
Confidence 3489999998752 3222 588889999994322 256789999988763
No 171
>KOG1074|consensus
Probab=67.58 E-value=4.8 Score=34.42 Aligned_cols=42 Identities=19% Similarity=0.490 Sum_probs=25.9
Q ss_pred CCCCCcccccccchhhhceecCCCCcccHhhHHHHhhc-----CCCCCCCCCCCCCCC
Q psy10659 17 PPDNDLLCPICFELIREAHITRCGHTFCFSCISKCVEL-----QIKCPKCSASLPDMN 69 (140)
Q Consensus 17 ~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~-----~~~CP~C~~~~~~~~ 69 (140)
...+-..|.||+.++. |.+-++-.++. -++|-+|++.|+.+.
T Consensus 601 ~~TdPNqCiiC~rVlS-----------C~saLqmHyrtHtGERPFkCKiCgRAFtTkG 647 (958)
T KOG1074|consen 601 KRTDPNQCIICLRVLS-----------CPSALQMHYRTHTGERPFKCKICGRAFTTKG 647 (958)
T ss_pred ccCCccceeeeeeccc-----------chhhhhhhhhcccCcCccccccccchhcccc
Confidence 4456789999999886 33444444432 255666666665554
No 172
>KOG4451|consensus
Probab=66.68 E-value=4.5 Score=29.22 Aligned_cols=28 Identities=29% Similarity=0.560 Sum_probs=22.0
Q ss_pred cccHhhHHHHhhcCCCCCCCCCCCCCCC
Q psy10659 42 TFCFSCISKCVELQIKCPKCSASLPDMN 69 (140)
Q Consensus 42 ~fC~~Ci~~~~~~~~~CP~C~~~~~~~~ 69 (140)
..|.+|-.+.-+..+.||+|+.....++
T Consensus 250 K~ClsChqqIHRNAPiCPlCKaKsRSrN 277 (286)
T KOG4451|consen 250 KVCLSCHQQIHRNAPICPLCKAKSRSRN 277 (286)
T ss_pred hHHHHHHHHHhcCCCCCcchhhccccCC
Confidence 3678888888888899999987655543
No 173
>KOG2113|consensus
Probab=65.86 E-value=4.5 Score=30.68 Aligned_cols=44 Identities=9% Similarity=-0.165 Sum_probs=34.0
Q ss_pred CCCcccccccchhhhceecCCCC-cccHhhHHHHhhcCCCCCCCCCC
Q psy10659 19 DNDLLCPICFELIREAHITRCGH-TFCFSCISKCVELQIKCPKCSAS 64 (140)
Q Consensus 19 ~~~~~C~IC~~~~~~p~~~~CgH-~fC~~Ci~~~~~~~~~CP~C~~~ 64 (140)
-..++|-.|..-+...+..+||| .||.+|.. +.....||.|...
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 34568888887777667779999 68999987 4557889999753
No 174
>COG4640 Predicted membrane protein [Function unknown]
Probab=65.81 E-value=3.1 Score=32.46 Aligned_cols=41 Identities=27% Similarity=0.524 Sum_probs=24.4
Q ss_pred ccHhhHHHHhhcCCCCCCCCCCCCCCCCCccchHHHHHHHHH
Q psy10659 43 FCFSCISKCVELQIKCPKCSASLPDMNSVFPNFLLNELVQKH 84 (140)
Q Consensus 43 fC~~Ci~~~~~~~~~CP~C~~~~~~~~~~~~~~~~~~~~~~~ 84 (140)
||..|-.+-.+....||.|+.++.... -..|..+.++++..
T Consensus 3 fC~kcG~qk~Ed~~qC~qCG~~~t~~~-sqan~~tn~i~~tr 43 (465)
T COG4640 3 FCPKCGSQKAEDDVQCTQCGHKFTSRQ-SQANKSTNEIIQTR 43 (465)
T ss_pred cccccccccccccccccccCCcCCchh-hhhhHHHHHHHHhh
Confidence 677776555555555888888777655 34454444444443
No 175
>KOG3476|consensus
Probab=65.72 E-value=0.63 Score=28.23 Aligned_cols=38 Identities=26% Similarity=0.703 Sum_probs=29.6
Q ss_pred CcccccccchhhhceecCCCCcccHhhHHHHhhcCCCCCCCCCCCCC
Q psy10659 21 DLLCPICFELIREAHITRCGHTFCFSCISKCVELQIKCPKCSASLPD 67 (140)
Q Consensus 21 ~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~CP~C~~~~~~ 67 (140)
...|.||....++| |..||..|... ...|.+|++.+..
T Consensus 54 ~~kC~iCk~~vHQ~-----GshYC~tCAY~----KgiCAMCGKki~n 91 (100)
T KOG3476|consen 54 LAKCRICKQLVHQP-----GSHYCQTCAYK----KGICAMCGKKILN 91 (100)
T ss_pred cchhHHHHHHhcCC-----cchhHhHhhhh----hhHHHHhhhHhhc
Confidence 46899999988887 66699999764 5679999886544
No 176
>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=65.67 E-value=1.2 Score=23.11 Aligned_cols=25 Identities=28% Similarity=0.691 Sum_probs=14.1
Q ss_pred CCCCcccHhhHHHHhhcCCCCCCCCC
Q psy10659 38 RCGHTFCFSCISKCVELQIKCPKCSA 63 (140)
Q Consensus 38 ~CgH~fC~~Ci~~~~~~~~~CP~C~~ 63 (140)
.|||.|-..--..- .....||.|+.
T Consensus 10 ~Cg~~fe~~~~~~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 10 ECGHEFEVLQSISE-DDPVPCPECGS 34 (42)
T ss_pred CCCCEEEEEEEcCC-CCCCcCCCCCC
Confidence 56666655321111 23567999987
No 177
>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=65.58 E-value=1.7 Score=29.50 Aligned_cols=16 Identities=38% Similarity=0.958 Sum_probs=13.1
Q ss_pred cCCCCCCCCCCCCCCC
Q psy10659 54 LQIKCPKCSASLPDMN 69 (140)
Q Consensus 54 ~~~~CP~C~~~~~~~~ 69 (140)
..+.||.|+.++..-+
T Consensus 127 ~~F~Cp~Cg~~L~~~d 142 (158)
T TIGR00373 127 LNFTCPRCGAMLDYLD 142 (158)
T ss_pred cCCcCCCCCCEeeecc
Confidence 4799999999887644
No 178
>KOG3842|consensus
Probab=65.21 E-value=5.4 Score=30.31 Aligned_cols=49 Identities=20% Similarity=0.541 Sum_probs=30.5
Q ss_pred CCcccccccchhh--------------h---c--eecCCCCcccHhhHHHHhhc---------CCCCCCCCCCCCCC
Q psy10659 20 NDLLCPICFELIR--------------E---A--HITRCGHTFCFSCISKCVEL---------QIKCPKCSASLPDM 68 (140)
Q Consensus 20 ~~~~C~IC~~~~~--------------~---p--~~~~CgH~fC~~Ci~~~~~~---------~~~CP~C~~~~~~~ 68 (140)
.+-+||+|+..-. + | ...||||.--..=..-|..- +..||+|...+.-.
T Consensus 340 ~~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 340 RERECPMCRVVGPYVPLWLGCEAGFYVDAGPPTHAFNPCGHVCSEKTVKYWSQIPLPHGTHAFHAACPFCATQLAGE 416 (429)
T ss_pred ccCcCCeeeeecceeeeeccccceeEecCCCcccccCCcccccchhhhhHhhcCcCCCccccccccCcchhhhhccC
Confidence 3678999987431 1 1 23489996555555555431 35799998876543
No 179
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=64.37 E-value=3.5 Score=20.73 Aligned_cols=13 Identities=31% Similarity=0.731 Sum_probs=9.1
Q ss_pred cccccccchhhhc
Q psy10659 22 LLCPICFELIREA 34 (140)
Q Consensus 22 ~~C~IC~~~~~~p 34 (140)
..||-|...|.-|
T Consensus 3 i~CP~C~~~f~v~ 15 (37)
T PF13719_consen 3 ITCPNCQTRFRVP 15 (37)
T ss_pred EECCCCCceEEcC
Confidence 5688888877644
No 180
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=63.69 E-value=5.3 Score=35.15 Aligned_cols=45 Identities=22% Similarity=0.653 Sum_probs=33.8
Q ss_pred Ccccccccchhh-----hceec--CCCCcccHhhHHHHh--hcCCCCCCCCCCCC
Q psy10659 21 DLLCPICFELIR-----EAHIT--RCGHTFCFSCISKCV--ELQIKCPKCSASLP 66 (140)
Q Consensus 21 ~~~C~IC~~~~~-----~p~~~--~CgH~fC~~Ci~~~~--~~~~~CP~C~~~~~ 66 (140)
...|.||.+... ++.+. .||--.|+.|.+ |- +++..||.|+....
T Consensus 17 ~qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCYE-YEr~eG~q~CPqCktrYk 70 (1079)
T PLN02638 17 GQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCYE-YERKDGNQSCPQCKTKYK 70 (1079)
T ss_pred CceeeecccccCcCCCCCEEEEeccCCCccccchhh-hhhhcCCccCCccCCchh
Confidence 458999999864 23332 688889999994 43 35688999998876
No 181
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=63.20 E-value=2.3 Score=35.46 Aligned_cols=22 Identities=27% Similarity=0.674 Sum_probs=9.5
Q ss_pred cHhhHHHHhhcCCCCCCCCCCC
Q psy10659 44 CFSCISKCVELQIKCPKCSASL 65 (140)
Q Consensus 44 C~~Ci~~~~~~~~~CP~C~~~~ 65 (140)
|..|-...-.+...||.|+..+
T Consensus 30 Cp~CG~~~~~~~~fC~~CG~~~ 51 (645)
T PRK14559 30 CPQCGTEVPVDEAHCPNCGAET 51 (645)
T ss_pred CCCCCCCCCcccccccccCCcc
Confidence 3444333223334555555543
No 182
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=63.13 E-value=4.6 Score=20.63 Aligned_cols=23 Identities=30% Similarity=0.755 Sum_probs=13.0
Q ss_pred cccccchhhh-ceecC-CCCcccHh
Q psy10659 24 CPICFELIRE-AHITR-CGHTFCFS 46 (140)
Q Consensus 24 C~IC~~~~~~-p~~~~-CgH~fC~~ 46 (140)
|.+|.....- |..-. |+..||..
T Consensus 1 C~~C~~~~~l~~f~C~~C~~~FC~~ 25 (39)
T smart00154 1 CHFCRKKVGLTGFKCRHCGNLFCGE 25 (39)
T ss_pred CcccCCcccccCeECCccCCccccc
Confidence 4455554443 55544 77777763
No 183
>KOG0314|consensus
Probab=62.18 E-value=9.6 Score=30.37 Aligned_cols=67 Identities=24% Similarity=0.454 Sum_probs=42.8
Q ss_pred cCCCCCCCcccccc-cchhhhceec--CCCCcccHhhHHHHhhcCCCCCCCCCCCCCCCCCccchHHHHHH
Q psy10659 14 QHSPPDNDLLCPIC-FELIREAHIT--RCGHTFCFSCISKCVELQIKCPKCSASLPDMNSVFPNFLLNELV 81 (140)
Q Consensus 14 ~~~~~~~~~~C~IC-~~~~~~p~~~--~CgH~fC~~Ci~~~~~~~~~CP~C~~~~~~~~~~~~~~~~~~~~ 81 (140)
.+-...+.+.|++| ...|.+...+ -|.-+||..||...+.. ..++.|.+.-.....+.++..+....
T Consensus 212 ~v~~~~e~~~c~~~~~~~~~~~~l~~~~~~~~~~~~~i~~~l~~-~~~~~c~~~~~~~~~~~~p~~~r~~~ 281 (448)
T KOG0314|consen 212 TVGELPEGLQCPLCGKEVMLDAALLSKCCLKSFCDKCIRDALIS-KSMCVCGASNVLADDLLPPKTLRDTI 281 (448)
T ss_pred HhccCCccccCceecchhhHHHHHhhhhhcccCCcccccccccc-ccCCcchhhcccccccCCchhhHHHH
Confidence 44456788999999 7777777666 58999999999887653 33444444322222344554444433
No 184
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=62.07 E-value=5 Score=28.64 Aligned_cols=51 Identities=18% Similarity=0.441 Sum_probs=28.3
Q ss_pred CCCcccccccchhhhceec-CCCC------cccHhh--HHHHhhcCCCCCCCCCCCCCCC
Q psy10659 19 DNDLLCPICFELIREAHIT-RCGH------TFCFSC--ISKCVELQIKCPKCSASLPDMN 69 (140)
Q Consensus 19 ~~~~~C~IC~~~~~~p~~~-~CgH------~fC~~C--i~~~~~~~~~CP~C~~~~~~~~ 69 (140)
+....||+|...|....+. .=+. -||..- +.+.+-....||.|+-.....+
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~~ 62 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEED 62 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCcccccc
Confidence 3568999999999865332 1111 111110 1122222357999998777654
No 185
>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=61.92 E-value=32 Score=23.39 Aligned_cols=24 Identities=33% Similarity=0.920 Sum_probs=14.7
Q ss_pred CcccHhhHHHHhhcCCCCCCCCCCCCC
Q psy10659 41 HTFCFSCISKCVELQIKCPKCSASLPD 67 (140)
Q Consensus 41 H~fC~~Ci~~~~~~~~~CP~C~~~~~~ 67 (140)
+.||..|-..-+ ..||.|..++.-
T Consensus 28 ~~fC~kCG~~tI---~~Cp~C~~~IrG 51 (158)
T PF10083_consen 28 EKFCSKCGAKTI---TSCPNCSTPIRG 51 (158)
T ss_pred HHHHHHhhHHHH---HHCcCCCCCCCC
Confidence 457777766543 346777666544
No 186
>PLN02248 cellulose synthase-like protein
Probab=61.24 E-value=7.3 Score=34.47 Aligned_cols=31 Identities=26% Similarity=0.636 Sum_probs=27.1
Q ss_pred CCCCcccHhhHHHHhhcCCCCCCCCCCCCCC
Q psy10659 38 RCGHTFCFSCISKCVELQIKCPKCSASLPDM 68 (140)
Q Consensus 38 ~CgH~fC~~Ci~~~~~~~~~CP~C~~~~~~~ 68 (140)
.|+...|.+|....+.....||.|+.+....
T Consensus 149 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 179 (1135)
T PLN02248 149 ECGFKICRDCYIDAVKSGGICPGCKEPYKVT 179 (1135)
T ss_pred cccchhHHhHhhhhhhcCCCCCCCccccccc
Confidence 5899999999999998889999999887543
No 187
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=60.73 E-value=5.7 Score=33.42 Aligned_cols=52 Identities=33% Similarity=0.662 Sum_probs=38.3
Q ss_pred CCCCCcccccccchhhhce----------ecCCCCcc--------------------cHhhHHHHhhc--------CCCC
Q psy10659 17 PPDNDLLCPICFELIREAH----------ITRCGHTF--------------------CFSCISKCVEL--------QIKC 58 (140)
Q Consensus 17 ~~~~~~~C~IC~~~~~~p~----------~~~CgH~f--------------------C~~Ci~~~~~~--------~~~C 58 (140)
.+.|.-.|+-|+..+.+|- .+.||..| |..|-.+|... ...|
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 3567789999999998872 24577665 88999988742 2469
Q ss_pred CCCCCCCCCC
Q psy10659 59 PKCSASLPDM 68 (140)
Q Consensus 59 P~C~~~~~~~ 68 (140)
|.|+-.+...
T Consensus 177 p~CGP~~~l~ 186 (750)
T COG0068 177 PKCGPHLFLV 186 (750)
T ss_pred cccCCCeEEE
Confidence 9999766543
No 188
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=60.63 E-value=6.8 Score=35.10 Aligned_cols=67 Identities=18% Similarity=0.415 Sum_probs=38.6
Q ss_pred CcccccccchhhhceecCCCCc-----ccHhhHHHHhhc---CCCCCCCCCCCCCCC--CCccchHHHHHHHHHHhc
Q psy10659 21 DLLCPICFELIREAHITRCGHT-----FCFSCISKCVEL---QIKCPKCSASLPDMN--SVFPNFLLNELVQKHKIK 87 (140)
Q Consensus 21 ~~~C~IC~~~~~~p~~~~CgH~-----fC~~Ci~~~~~~---~~~CP~C~~~~~~~~--~~~~~~~~~~~~~~~~~~ 87 (140)
.+.||-|.........-.||.. +|..|-...-.. ...||.|+.++.... .+.....+...++.....
T Consensus 667 ~rkCPkCG~~t~~~fCP~CGs~te~vy~CPsCGaev~~des~a~~CP~CGtplv~~~~~~i~~~~~~~~A~~~~g~~ 743 (1337)
T PRK14714 667 RRRCPSCGTETYENRCPDCGTHTEPVYVCPDCGAEVPPDESGRVECPRCDVELTPYQRRTINVKEEYRSALENVGER 743 (1337)
T ss_pred EEECCCCCCccccccCcccCCcCCCceeCccCCCccCCCccccccCCCCCCcccccceEEecHHHHHHHHHHHhCcc
Confidence 4799999986544333358865 388886543221 247999998776644 123333444444444333
No 189
>KOG2231|consensus
Probab=60.63 E-value=6.2 Score=32.97 Aligned_cols=45 Identities=24% Similarity=0.549 Sum_probs=35.2
Q ss_pred ccccccchhhhceecCCCC-cccHhhHHHHhh--c----CCCCCCCCCCCCC
Q psy10659 23 LCPICFELIREAHITRCGH-TFCFSCISKCVE--L----QIKCPKCSASLPD 67 (140)
Q Consensus 23 ~C~IC~~~~~~p~~~~CgH-~fC~~Ci~~~~~--~----~~~CP~C~~~~~~ 67 (140)
.|+||-.-+.-+..-+||| ..|..|..+... . ...||+|+..+..
T Consensus 2 ~c~ic~~s~~~~~~~s~~h~~v~~~~~~R~~~~~~~~~~~~~~~vcr~~~~~ 53 (669)
T KOG2231|consen 2 SCAICAFSPDFVGRGSCGHNEVCATCVVRLRFELNNRKCSNECPVCRREVET 53 (669)
T ss_pred CcceeecCccccccccccccccchhhhhhhhhhcccccccccCcccccceee
Confidence 5889988777777779999 999999987763 2 3568999986544
No 190
>COG3492 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=60.40 E-value=4.6 Score=24.79 Aligned_cols=12 Identities=33% Similarity=0.852 Sum_probs=10.9
Q ss_pred cccHhhHHHHhh
Q psy10659 42 TFCFSCISKCVE 53 (140)
Q Consensus 42 ~fC~~Ci~~~~~ 53 (140)
.||..|+..|..
T Consensus 42 gFCRNCLs~Wy~ 53 (104)
T COG3492 42 GFCRNCLSNWYR 53 (104)
T ss_pred HHHHHHHHHHHH
Confidence 499999999986
No 191
>COG5242 TFB4 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB4 [Transcription / DNA replication, recombination, and repair]
Probab=59.45 E-value=5.4 Score=28.90 Aligned_cols=12 Identities=25% Similarity=0.653 Sum_probs=7.7
Q ss_pred CCCCCCCCCCCC
Q psy10659 55 QIKCPKCSASLP 66 (140)
Q Consensus 55 ~~~CP~C~~~~~ 66 (140)
...||.|...+.
T Consensus 274 ~~~C~~C~skF~ 285 (296)
T COG5242 274 VPVCKKCKSKFS 285 (296)
T ss_pred cCcCcccccccc
Confidence 556777766654
No 192
>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=59.31 E-value=16 Score=20.54 Aligned_cols=14 Identities=29% Similarity=0.850 Sum_probs=8.9
Q ss_pred CCCCCCCCCCCCCC
Q psy10659 55 QIKCPKCSASLPDM 68 (140)
Q Consensus 55 ~~~CP~C~~~~~~~ 68 (140)
+..||.|++++...
T Consensus 3 HkHC~~CG~~Ip~~ 16 (59)
T PF09889_consen 3 HKHCPVCGKPIPPD 16 (59)
T ss_pred CCcCCcCCCcCCcc
Confidence 45677777766543
No 193
>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=58.87 E-value=5.4 Score=21.61 Aligned_cols=37 Identities=30% Similarity=0.626 Sum_probs=18.6
Q ss_pred cccccchhhhce-e-cCCCCcccHhhHHHHhhcCCCCCCCCCCCCCC
Q psy10659 24 CPICFELIREAH-I-TRCGHTFCFSCISKCVELQIKCPKCSASLPDM 68 (140)
Q Consensus 24 C~IC~~~~~~p~-~-~~CgH~fC~~Ci~~~~~~~~~CP~C~~~~~~~ 68 (140)
|.-|...+.... . ..-|..|+..| ..|-.|+.++...
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 444555444222 2 25555666655 3466666665543
No 194
>KOG1609|consensus
Probab=58.60 E-value=5.5 Score=29.63 Aligned_cols=47 Identities=28% Similarity=0.525 Sum_probs=34.2
Q ss_pred Ccccccccchhhh----ceecCCC-----CcccHhhHHHHhh--cCCCCCCCCCCCCC
Q psy10659 21 DLLCPICFELIRE----AHITRCG-----HTFCFSCISKCVE--LQIKCPKCSASLPD 67 (140)
Q Consensus 21 ~~~C~IC~~~~~~----p~~~~Cg-----H~fC~~Ci~~~~~--~~~~CP~C~~~~~~ 67 (140)
...|.||...... +...||. +..+..|+..|.. +...|..|......
T Consensus 78 ~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~~ 135 (323)
T KOG1609|consen 78 GPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFIN 135 (323)
T ss_pred CCcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhccccCeeeeccccccee
Confidence 4789999996643 4455653 3457999999997 56789999875544
No 195
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=58.33 E-value=5.2 Score=20.01 Aligned_cols=12 Identities=25% Similarity=0.600 Sum_probs=7.8
Q ss_pred cccccccchhhh
Q psy10659 22 LLCPICFELIRE 33 (140)
Q Consensus 22 ~~C~IC~~~~~~ 33 (140)
..||-|...|.-
T Consensus 3 i~Cp~C~~~y~i 14 (36)
T PF13717_consen 3 ITCPNCQAKYEI 14 (36)
T ss_pred EECCCCCCEEeC
Confidence 467777776653
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=57.59 E-value=10 Score=18.89 Aligned_cols=24 Identities=21% Similarity=0.714 Sum_probs=13.1
Q ss_pred ccHhhHHHHhhc--------CCCCCCCCCCCC
Q psy10659 43 FCFSCISKCVEL--------QIKCPKCSASLP 66 (140)
Q Consensus 43 fC~~Ci~~~~~~--------~~~CP~C~~~~~ 66 (140)
.|..|+.++... ...|+.|+-.++
T Consensus 1 lC~~C~~Ey~~p~~RR~~~~~isC~~CGPr~~ 32 (35)
T PF07503_consen 1 LCDDCLKEYFDPSNRRFHYQFISCTNCGPRYS 32 (35)
T ss_dssp --HHHHHHHCSTTSTTTT-TT--BTTCC-SCC
T ss_pred CCHHHHHHHcCCCCCcccCcCccCCCCCCCEE
Confidence 477788877642 246999986654
No 197
>PLN02400 cellulose synthase
Probab=56.37 E-value=6.4 Score=34.70 Aligned_cols=46 Identities=20% Similarity=0.582 Sum_probs=33.9
Q ss_pred Ccccccccchhhh-----ceec--CCCCcccHhhHHHHh--hcCCCCCCCCCCCCC
Q psy10659 21 DLLCPICFELIRE-----AHIT--RCGHTFCFSCISKCV--ELQIKCPKCSASLPD 67 (140)
Q Consensus 21 ~~~C~IC~~~~~~-----p~~~--~CgH~fC~~Ci~~~~--~~~~~CP~C~~~~~~ 67 (140)
...|.||.+.... +.+. .|+--.|+.|.+ |- +++..||.|+.....
T Consensus 36 gqiCqICGD~VG~t~dGe~FVAC~eCaFPVCRpCYE-YERkeGnq~CPQCkTrYkR 90 (1085)
T PLN02400 36 GQICQICGDDVGVTETGDVFVACNECAFPVCRPCYE-YERKDGTQCCPQCKTRYRR 90 (1085)
T ss_pred CceeeecccccCcCCCCCEEEEEccCCCccccchhh-eecccCCccCcccCCcccc
Confidence 3489999998742 3332 688889999984 33 256789999988763
No 198
>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=56.34 E-value=1.1 Score=24.93 Aligned_cols=31 Identities=32% Similarity=0.726 Sum_probs=17.5
Q ss_pred Cccccc--ccchhhhc-------eecC-CCCcccHhhHHHH
Q psy10659 21 DLLCPI--CFELIREA-------HITR-CGHTFCFSCISKC 51 (140)
Q Consensus 21 ~~~C~I--C~~~~~~p-------~~~~-CgH~fC~~Ci~~~ 51 (140)
...||- |...+... +.=+ ||+.||..|-..|
T Consensus 18 ~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~ 58 (64)
T PF01485_consen 18 IRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPW 58 (64)
T ss_dssp CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSES
T ss_pred ccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCccc
Confidence 358877 88877532 2224 9999999997766
No 199
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=56.17 E-value=8.7 Score=33.80 Aligned_cols=47 Identities=19% Similarity=0.596 Sum_probs=34.7
Q ss_pred CCcccccccchhh-----hceec--CCCCcccHhhHHHHhh--cCCCCCCCCCCCCC
Q psy10659 20 NDLLCPICFELIR-----EAHIT--RCGHTFCFSCISKCVE--LQIKCPKCSASLPD 67 (140)
Q Consensus 20 ~~~~C~IC~~~~~-----~p~~~--~CgH~fC~~Ci~~~~~--~~~~CP~C~~~~~~ 67 (140)
....|.||.+... +|.+. .|+--.|+.|.+ +-+ ++..||.|+.....
T Consensus 14 ~~~~c~iCGd~vg~~~~Ge~FVAC~eC~fpvCr~cye-ye~~~g~~~cp~c~t~y~~ 69 (1044)
T PLN02915 14 DAKTCRVCGDEVGVKEDGQPFVACHVCGFPVCKPCYE-YERSEGNQCCPQCNTRYKR 69 (1044)
T ss_pred CcchhhccccccCcCCCCCEEEEeccCCCccccchhh-hhhhcCCccCCccCCchhh
Confidence 3568999999764 23332 688889999994 432 56789999988763
No 200
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=55.74 E-value=5.8 Score=25.45 Aligned_cols=31 Identities=19% Similarity=0.420 Sum_probs=19.9
Q ss_pred CCcccccccchhh---hc--eecCCCCcccHhhHHH
Q psy10659 20 NDLLCPICFELIR---EA--HITRCGHTFCFSCISK 50 (140)
Q Consensus 20 ~~~~C~IC~~~~~---~p--~~~~CgH~fC~~Ci~~ 50 (140)
..-.|.+|...|. ++ +-..|+|.+|..|-..
T Consensus 53 ~~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~ 88 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVY 88 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEE
T ss_pred CCcchhhhCCcccccCCCCCcCCcCCccccCccCCc
Confidence 4679999988653 22 2247999999988543
No 201
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=54.77 E-value=8.6 Score=20.97 Aligned_cols=8 Identities=38% Similarity=0.920 Sum_probs=5.4
Q ss_pred cCCCCCCC
Q psy10659 54 LQIKCPKC 61 (140)
Q Consensus 54 ~~~~CP~C 61 (140)
....||.|
T Consensus 48 ~~~~CP~C 55 (55)
T PF14311_consen 48 RGKGCPYC 55 (55)
T ss_pred CCCCCCCC
Confidence 45668877
No 202
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=54.33 E-value=8.2 Score=27.27 Aligned_cols=39 Identities=31% Similarity=0.769 Sum_probs=26.5
Q ss_pred CCcccccccch-hhhce-----e--cCCCCcccHhhHHHHhhcCCCCCCCCC
Q psy10659 20 NDLLCPICFEL-IREAH-----I--TRCGHTFCFSCISKCVELQIKCPKCSA 63 (140)
Q Consensus 20 ~~~~C~IC~~~-~~~p~-----~--~~CgH~fC~~Ci~~~~~~~~~CP~C~~ 63 (140)
..+.|-+|.+. ..=|. . -.|+..|+..|+. ...||-|.+
T Consensus 151 kGfiCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~~C~~-----~~~CpkC~R 197 (202)
T PF13901_consen 151 KGFICEICNSDDIIFPFQIDTTVRCPKCKSVFHKSCFR-----KKSCPKCAR 197 (202)
T ss_pred CCCCCccCCCCCCCCCCCCCCeeeCCcCccccchhhcC-----CCCCCCcHh
Confidence 35788899852 21121 1 2699999999976 266999964
No 203
>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=54.27 E-value=5.2 Score=21.21 Aligned_cols=29 Identities=17% Similarity=0.587 Sum_probs=18.6
Q ss_pred ccccccchhhhceec---CCCCcccHhhHHHH
Q psy10659 23 LCPICFELIREAHIT---RCGHTFCFSCISKC 51 (140)
Q Consensus 23 ~C~IC~~~~~~p~~~---~CgH~fC~~Ci~~~ 51 (140)
.|.||......--.+ .|+..||..|+..-
T Consensus 1 ~C~vC~~~~~~~~~i~C~~C~~~~H~~C~~~~ 32 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDSCNRWYHQECVGPP 32 (51)
T ss_dssp EBTTTTSSCTTSSEEEBSTTSCEEETTTSTSS
T ss_pred eCcCCCCcCCCCCeEEcCCCChhhCcccCCCC
Confidence 478888833322222 68888999887543
No 204
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=53.59 E-value=8 Score=28.33 Aligned_cols=22 Identities=23% Similarity=0.560 Sum_probs=15.4
Q ss_pred cccccccchhhh-ceec--CCCCcc
Q psy10659 22 LLCPICFELIRE-AHIT--RCGHTF 43 (140)
Q Consensus 22 ~~C~IC~~~~~~-p~~~--~CgH~f 43 (140)
+.||+|...+.. +..+ +.||+|
T Consensus 3 ~~CP~C~~~l~~~~~~~~C~~~h~f 27 (272)
T PRK11088 3 YQCPLCHQPLTLEENSWICPQNHQF 27 (272)
T ss_pred ccCCCCCcchhcCCCEEEcCCCCCC
Confidence 789999998852 2223 567877
No 205
>COG5113 UFD2 Ubiquitin fusion degradation protein 2 [Posttranslational modification, protein turnover, chaperones]
Probab=53.59 E-value=39 Score=28.55 Aligned_cols=74 Identities=19% Similarity=0.144 Sum_probs=62.8
Q ss_pred CCCCCCcccccccchhhhceecC-CCCcccHhhHHHHhhcCCCCCCCCCCCCCCCCCccchHHHHHHHHHHhcCCC
Q psy10659 16 SPPDNDLLCPICFELIREAHITR-CGHTFCFSCISKCVELQIKCPKCSASLPDMNSVFPNFLLNELVQKHKIKSAQ 90 (140)
Q Consensus 16 ~~~~~~~~C~IC~~~~~~p~~~~-CgH~fC~~Ci~~~~~~~~~CP~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 90 (140)
.++++++.=|.-..++++||.+| -|-+.=++=|...+-...+=|.=|.+++..+ +.+|..+++.+..+.....+
T Consensus 849 GDvPDeFlDPLmftimkdPV~Lp~S~i~IDRSTikahllsd~tDPFNRmPLtldd-Vtpn~eLrekIn~f~k~k~~ 923 (929)
T COG5113 849 GDVPDEFLDPLMFTIMKDPVKLPTSRITIDRSTIKAHLLSDGTDPFNRMPLTLDD-VTPNAELREKINRFYKCKGQ 923 (929)
T ss_pred cCCchhhhCchhhhcccCCeecccccccccHHHHHHHHhcCCCCccccCCCchhh-cCCCHHHHHHHHHHHhcccc
Confidence 35778888899999999999985 6777888888888888888999999999888 89999999999888776554
No 206
>KOG1356|consensus
Probab=52.91 E-value=6.6 Score=33.58 Aligned_cols=34 Identities=26% Similarity=0.618 Sum_probs=26.6
Q ss_pred CCCcccccccchhhhcee--cCCCCcccHhhHHHHh
Q psy10659 19 DNDLLCPICFELIREAHI--TRCGHTFCFSCISKCV 52 (140)
Q Consensus 19 ~~~~~C~IC~~~~~~p~~--~~CgH~fC~~Ci~~~~ 52 (140)
.-.-.|..|.....+-+. ..||+.+|..|+..|.
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 334678888887776443 3899999999999995
No 207
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=52.88 E-value=13 Score=20.62 Aligned_cols=14 Identities=21% Similarity=0.643 Sum_probs=10.3
Q ss_pred CCCCCCCCCCCCCC
Q psy10659 55 QIKCPKCSASLPDM 68 (140)
Q Consensus 55 ~~~CP~C~~~~~~~ 68 (140)
.+.||.|+-++--+
T Consensus 14 ~~~Cp~cGipthcS 27 (55)
T PF13824_consen 14 NFECPDCGIPTHCS 27 (55)
T ss_pred CCcCCCCCCcCccC
Confidence 57899998776543
No 208
>PRK00420 hypothetical protein; Validated
Probab=52.81 E-value=22 Score=22.80 Aligned_cols=13 Identities=15% Similarity=0.327 Sum_probs=8.5
Q ss_pred CCCCCCCCCCCCC
Q psy10659 55 QIKCPKCSASLPD 67 (140)
Q Consensus 55 ~~~CP~C~~~~~~ 67 (140)
...||.|+..+.-
T Consensus 40 ~~~Cp~Cg~~~~v 52 (112)
T PRK00420 40 EVVCPVHGKVYIV 52 (112)
T ss_pred ceECCCCCCeeee
Confidence 4568888876543
No 209
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=52.65 E-value=9 Score=20.21 Aligned_cols=23 Identities=22% Similarity=0.449 Sum_probs=13.8
Q ss_pred cccccchhhhceecCCCCcccHh
Q psy10659 24 CPICFELIREAHITRCGHTFCFS 46 (140)
Q Consensus 24 C~IC~~~~~~p~~~~CgH~fC~~ 46 (140)
|..|...-..-+-+.|+|++|..
T Consensus 2 C~~C~~~~~l~~CL~C~~~~c~~ 24 (50)
T smart00290 2 CSVCGTIENLWLCLTCGQVGCGR 24 (50)
T ss_pred cccCCCcCCeEEecCCCCcccCC
Confidence 66666544322446788888854
No 210
>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=51.91 E-value=5.5 Score=32.08 Aligned_cols=9 Identities=44% Similarity=1.172 Sum_probs=4.5
Q ss_pred CCCCCCCCC
Q psy10659 57 KCPKCSASL 65 (140)
Q Consensus 57 ~CP~C~~~~ 65 (140)
.||.|...+
T Consensus 54 ~CP~C~~~L 62 (483)
T PF05502_consen 54 DCPICFSPL 62 (483)
T ss_pred cCCCCCCcc
Confidence 355555443
No 211
>KOG1815|consensus
Probab=51.12 E-value=5.8 Score=31.49 Aligned_cols=19 Identities=37% Similarity=0.873 Sum_probs=15.1
Q ss_pred ceecCCCCcccHhhHHHHh
Q psy10659 34 AHITRCGHTFCFSCISKCV 52 (140)
Q Consensus 34 p~~~~CgH~fC~~Ci~~~~ 52 (140)
+|.-.|||.||..|...|.
T Consensus 179 ~v~C~~g~~FC~~C~~~~H 197 (444)
T KOG1815|consen 179 EVDCGCGHEFCFACGEESH 197 (444)
T ss_pred ceeCCCCchhHhhcccccc
Confidence 3455899999999987664
No 212
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=50.59 E-value=9.6 Score=32.72 Aligned_cols=31 Identities=35% Similarity=0.720 Sum_probs=23.2
Q ss_pred cccccccchhhh--------c-eecCCCCcccHhhHHHHh
Q psy10659 22 LLCPICFELIRE--------A-HITRCGHTFCFSCISKCV 52 (140)
Q Consensus 22 ~~C~IC~~~~~~--------p-~~~~CgH~fC~~Ci~~~~ 52 (140)
..|..|...|.. . .--.||.+||..|-....
T Consensus 461 dtC~~C~kkFfSlsK~L~~RKHHCRkCGrVFC~~CSSnRs 500 (1374)
T PTZ00303 461 DSCPSCGRAFISLSRPLGTRAHHCRSCGIRLCVFCITKRA 500 (1374)
T ss_pred CcccCcCCcccccccccccccccccCCccccCccccCCcc
Confidence 569999999852 1 123799999999986544
No 213
>KOG2272|consensus
Probab=50.54 E-value=7.1 Score=28.74 Aligned_cols=55 Identities=15% Similarity=0.286 Sum_probs=31.9
Q ss_pred hcCCCCCCCcccccccchhhhceecCCCCcccHhhH----HHHhhcCCCCCCCCCCCCC
Q psy10659 13 RQHSPPDNDLLCPICFELIREAHITRCGHTFCFSCI----SKCVELQIKCPKCSASLPD 67 (140)
Q Consensus 13 ~~~~~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci----~~~~~~~~~CP~C~~~~~~ 67 (140)
.+...+.+++.|+-|.+.+..|+--.|....=..=| ..|-..++.|..|-+++-.
T Consensus 175 sdaRevk~eLyClrChD~mgipiCgaC~rpIeervi~amgKhWHveHFvCa~CekPFlG 233 (332)
T KOG2272|consen 175 SDAREVKGELYCLRCHDKMGIPICGACRRPIEERVIFAMGKHWHVEHFVCAKCEKPFLG 233 (332)
T ss_pred chhhhhccceeccccccccCCcccccccCchHHHHHHHhccccchhheeehhcCCcccc
Confidence 334455678888888888887765555433322222 2233345667777766543
No 214
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=49.40 E-value=27 Score=24.29 Aligned_cols=18 Identities=39% Similarity=0.966 Sum_probs=14.4
Q ss_pred hhcCCCCCCCCCCCCCCC
Q psy10659 52 VELQIKCPKCSASLPDMN 69 (140)
Q Consensus 52 ~~~~~~CP~C~~~~~~~~ 69 (140)
....+.||.|+..+...+
T Consensus 129 ~~~~F~Cp~Cg~~L~~~d 146 (176)
T COG1675 129 MELGFTCPKCGEDLEEYD 146 (176)
T ss_pred HHhCCCCCCCCchhhhcc
Confidence 344699999999988766
No 215
>KOG2593|consensus
Probab=48.80 E-value=16 Score=28.93 Aligned_cols=56 Identities=13% Similarity=0.243 Sum_probs=29.9
Q ss_pred CCCcccccccchhhhceecCCCCcccHhhHHHHhhcCCCCCCCCCCCCCCCCCccchHHHHHHHH
Q psy10659 19 DNDLLCPICFELIREAHITRCGHTFCFSCISKCVELQIKCPKCSASLPDMNSVFPNFLLNELVQK 83 (140)
Q Consensus 19 ~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~CP~C~~~~~~~~~~~~~~~~~~~~~~ 83 (140)
...+.||+|...|..- =..++...-.+.+.|-.|+..+.....-.++...+..+..
T Consensus 126 ~~~Y~Cp~C~kkyt~L---------ea~~L~~~~~~~F~C~~C~gelveDe~~~~~~e~~~~l~~ 181 (436)
T KOG2593|consen 126 VAGYVCPNCQKKYTSL---------EALQLLDNETGEFHCENCGGELVEDENKLPSKESRTALNR 181 (436)
T ss_pred cccccCCccccchhhh---------HHHHhhcccCceEEEecCCCchhcccccCchHHHHHHHHH
Confidence 3568899999887642 0122222223456788888776554333344333333333
No 216
>KOG2462|consensus
Probab=48.61 E-value=5.6 Score=29.51 Aligned_cols=50 Identities=20% Similarity=0.504 Sum_probs=34.4
Q ss_pred CCcccccccchhhh-c--------eecCCCCcccHhhHH-HHhhc----------CCCCCCCCCCCCCCC
Q psy10659 20 NDLLCPICFELIRE-A--------HITRCGHTFCFSCIS-KCVEL----------QIKCPKCSASLPDMN 69 (140)
Q Consensus 20 ~~~~C~IC~~~~~~-p--------~~~~CgH~fC~~Ci~-~~~~~----------~~~CP~C~~~~~~~~ 69 (140)
..+.|++|-..|.. | ..++|...+|..-+. .|+-. -+.||.|++.|..+.
T Consensus 160 ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRS 229 (279)
T KOG2462|consen 160 KAFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRS 229 (279)
T ss_pred ccccCCCCCceeeehHHHhhHhhccCCCcccccccccccchHHhhcccccccCCCCccCCcccchhcchH
Confidence 45788888887753 2 235788788887774 56631 267999999887644
No 217
>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=48.26 E-value=11 Score=19.64 Aligned_cols=13 Identities=23% Similarity=0.565 Sum_probs=9.8
Q ss_pred CCCCCCCCCCCCC
Q psy10659 55 QIKCPKCSASLPD 67 (140)
Q Consensus 55 ~~~CP~C~~~~~~ 67 (140)
...||+|+.+++-
T Consensus 8 ~K~C~~C~rpf~W 20 (42)
T PF10013_consen 8 SKICPVCGRPFTW 20 (42)
T ss_pred CCcCcccCCcchH
Confidence 4679999888753
No 218
>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=48.11 E-value=8.7 Score=19.91 Aligned_cols=21 Identities=24% Similarity=0.592 Sum_probs=10.7
Q ss_pred ccchhhhceecC-CCCcccHhh
Q psy10659 27 CFELIREAHITR-CGHTFCFSC 47 (140)
Q Consensus 27 C~~~~~~p~~~~-CgH~fC~~C 47 (140)
|......|+.=+ |+..||..-
T Consensus 6 C~~~~~~~~~C~~C~~~FC~~H 27 (43)
T PF01428_consen 6 CKKKDFLPFKCKHCGKSFCLKH 27 (43)
T ss_dssp T--BCTSHEE-TTTS-EE-TTT
T ss_pred CcCccCCCeECCCCCcccCccc
Confidence 666555566554 999998754
No 219
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=47.80 E-value=33 Score=19.30 Aligned_cols=16 Identities=19% Similarity=0.528 Sum_probs=12.0
Q ss_pred cCCCCCCCCCCCCCCC
Q psy10659 54 LQIKCPKCSASLPDMN 69 (140)
Q Consensus 54 ~~~~CP~C~~~~~~~~ 69 (140)
.+..||+|++.+....
T Consensus 7 PH~HC~VCg~aIp~de 22 (64)
T COG4068 7 PHRHCVVCGKAIPPDE 22 (64)
T ss_pred CCccccccCCcCCCcc
Confidence 4567999998877654
No 220
>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=47.27 E-value=13 Score=20.85 Aligned_cols=26 Identities=31% Similarity=0.597 Sum_probs=19.1
Q ss_pred ecCCCCcccHhhHHHHhhc-CCCCCCCCCCCCC
Q psy10659 36 ITRCGHTFCFSCISKCVEL-QIKCPKCSASLPD 67 (140)
Q Consensus 36 ~~~CgH~fC~~Ci~~~~~~-~~~CP~C~~~~~~ 67 (140)
-+.||-+.|. .++ ...||.|+.++..
T Consensus 21 Cl~CGkIiC~------~Eg~~~pC~fCg~~l~~ 47 (57)
T PF06221_consen 21 CLNCGKIICE------QEGPLGPCPFCGTPLLS 47 (57)
T ss_pred ccccChhhcc------cccCcCcCCCCCCcccC
Confidence 4579988887 345 5789999976544
No 221
>KOG1729|consensus
Probab=47.23 E-value=8.4 Score=28.91 Aligned_cols=32 Identities=22% Similarity=0.539 Sum_probs=22.9
Q ss_pred CCCcccccccc-hhhhc----eecCCCCcccHhhHHH
Q psy10659 19 DNDLLCPICFE-LIREA----HITRCGHTFCFSCISK 50 (140)
Q Consensus 19 ~~~~~C~IC~~-~~~~p----~~~~CgH~fC~~Ci~~ 50 (140)
.+...|.+|.. .|.-- ..-.||++||..|-..
T Consensus 166 ~ea~~C~~C~~~~Ftl~~RRHHCR~CG~ivC~~Cs~n 202 (288)
T KOG1729|consen 166 SEATECMVCGCTEFTLSERRHHCRNCGDIVCAPCSRN 202 (288)
T ss_pred ccceecccCCCccccHHHHHHHHHhcchHhhhhhhcC
Confidence 46789999998 43211 2237999999999765
No 222
>KOG2487|consensus
Probab=46.80 E-value=9.7 Score=28.35 Aligned_cols=24 Identities=21% Similarity=0.551 Sum_probs=13.9
Q ss_pred cHhhHHHHhhcCCCCCCCCCCCCC
Q psy10659 44 CFSCISKCVELQIKCPKCSASLPD 67 (140)
Q Consensus 44 C~~Ci~~~~~~~~~CP~C~~~~~~ 67 (140)
|.-|+.-+-+..+.|+.|...++.
T Consensus 276 CSVCLSVfC~~~PiC~~C~s~F~~ 299 (314)
T KOG2487|consen 276 CSVCLSVFCRFVPICKTCKSKFSF 299 (314)
T ss_pred hHHHHHHhhCCCCccchhhhhccc
Confidence 333443333446678888877753
No 223
>KOG2066|consensus
Probab=46.64 E-value=6.4 Score=33.43 Aligned_cols=40 Identities=23% Similarity=0.476 Sum_probs=28.0
Q ss_pred Ccccccccchhh------h-ceecCCCCcccHhhHHHHhhcCCCCCCC
Q psy10659 21 DLLCPICFELIR------E-AHITRCGHTFCFSCISKCVELQIKCPKC 61 (140)
Q Consensus 21 ~~~C~IC~~~~~------~-p~~~~CgH~fC~~Ci~~~~~~~~~CP~C 61 (140)
+-+|..|.+... + -+.+.|||.|+..|+.....+.. |-.|
T Consensus 784 e~rc~~c~~~~l~~~~~~~~~~v~~c~h~yhk~c~~~~~~~~~-~~~~ 830 (846)
T KOG2066|consen 784 EERCSSCFEPNLPSGAAFDSVVVFHCGHMYHKECLMMESLRNA-CNIE 830 (846)
T ss_pred hhhhhhhcccccccCcccceeeEEEccchhhhcccccHHHhcc-cChh
Confidence 448999988654 2 24568999999999987665433 4444
No 224
>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=46.36 E-value=5.7 Score=18.77 Aligned_cols=25 Identities=28% Similarity=0.747 Sum_probs=10.6
Q ss_pred ccccccchhhhceecCCCCcccHhh
Q psy10659 23 LCPICFELIREAHITRCGHTFCFSC 47 (140)
Q Consensus 23 ~C~IC~~~~~~p~~~~CgH~fC~~C 47 (140)
.|+.|...+.+.....=+..||..|
T Consensus 3 ~C~rC~~~~~~~~~~~r~~~~C~rC 27 (30)
T PF06827_consen 3 KCPRCWNYIEDIGINGRSTYLCPRC 27 (30)
T ss_dssp B-TTT--BBEEEEETTEEEEE-TTT
T ss_pred cCccCCCcceEeEecCCCCeECcCC
Confidence 5777777665444333334455444
No 225
>PF05265 DUF723: Protein of unknown function (DUF723); InterPro: IPR007929 This family contains several uncharacterised proteins from Neisseria meningitidis. These proteins may have a role in DNA binding.
Probab=45.79 E-value=18 Score=20.43 Aligned_cols=29 Identities=24% Similarity=0.697 Sum_probs=15.9
Q ss_pred hceecCC---CCcccHhhHHHHhhcCCCCCCCC
Q psy10659 33 EAHITRC---GHTFCFSCISKCVELQIKCPKCS 62 (140)
Q Consensus 33 ~p~~~~C---gH~fC~~Ci~~~~~~~~~CP~C~ 62 (140)
.|+++.| |-..+.. ...++..+..||.|.
T Consensus 29 ~PvtI~CP~HG~~~~s~-~~~~~~sk~GCP~Cg 60 (60)
T PF05265_consen 29 TPVTIRCPKHGNFTCST-FNSFIKSKHGCPECG 60 (60)
T ss_pred CceEEECCCCCcEEecc-HHhhhhhccCCCCCC
Confidence 4555555 2233322 255555667899984
No 226
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=45.52 E-value=11 Score=28.65 Aligned_cols=42 Identities=24% Similarity=0.483 Sum_probs=26.4
Q ss_pred Ccccccccchhhhceec--------------CCCCcccHhhHHHHhhcCCCCCCCC
Q psy10659 21 DLLCPICFELIREAHIT--------------RCGHTFCFSCISKCVELQIKCPKCS 62 (140)
Q Consensus 21 ~~~C~IC~~~~~~p~~~--------------~CgH~fC~~Ci~~~~~~~~~CP~C~ 62 (140)
...|-.|...|-.|... .|...||.+|=.-.-+.-..||.|.
T Consensus 362 s~~Cf~CQ~~fp~~~~~~~~~~~ss~rY~Ce~CK~~FC~dCdvfiHe~Lh~C~gCe 417 (421)
T COG5151 362 STHCFVCQGPFPKPPVSPFDESTSSGRYQCELCKSTFCSDCDVFIHETLHFCIGCE 417 (421)
T ss_pred CccceeccCCCCCCCCCcccccccccceechhhhhhhhhhhHHHHHHHHhhCCCCc
Confidence 34677888776554211 2777888888554444456688774
No 227
>PRK01343 zinc-binding protein; Provisional
Probab=45.21 E-value=15 Score=20.61 Aligned_cols=12 Identities=25% Similarity=0.755 Sum_probs=9.2
Q ss_pred CCCCCCCCCCCC
Q psy10659 55 QIKCPKCSASLP 66 (140)
Q Consensus 55 ~~~CP~C~~~~~ 66 (140)
...||.|++++.
T Consensus 9 ~~~CP~C~k~~~ 20 (57)
T PRK01343 9 TRPCPECGKPST 20 (57)
T ss_pred CCcCCCCCCcCc
Confidence 467999998765
No 228
>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=44.93 E-value=11 Score=17.32 Aligned_cols=11 Identities=36% Similarity=1.201 Sum_probs=8.1
Q ss_pred CCCCCCCCCCC
Q psy10659 56 IKCPKCSASLP 66 (140)
Q Consensus 56 ~~CP~C~~~~~ 66 (140)
..||+|.+.+.
T Consensus 2 v~CPiC~~~v~ 12 (26)
T smart00734 2 VQCPVCFREVP 12 (26)
T ss_pred CcCCCCcCccc
Confidence 35999988763
No 229
>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=44.90 E-value=10 Score=24.15 Aligned_cols=13 Identities=46% Similarity=1.132 Sum_probs=9.0
Q ss_pred CCCCCCCCCCCCC
Q psy10659 56 IKCPKCSASLPDM 68 (140)
Q Consensus 56 ~~CP~C~~~~~~~ 68 (140)
..||.|+..+...
T Consensus 27 ivCP~CG~~~~~~ 39 (108)
T PF09538_consen 27 IVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCCCccCcc
Confidence 4588888776554
No 230
>PRK12496 hypothetical protein; Provisional
Probab=44.87 E-value=6.4 Score=26.91 Aligned_cols=26 Identities=23% Similarity=0.454 Sum_probs=16.7
Q ss_pred cHhhHHHHhh--cCCCCCCCCCCCCCCC
Q psy10659 44 CFSCISKCVE--LQIKCPKCSASLPDMN 69 (140)
Q Consensus 44 C~~Ci~~~~~--~~~~CP~C~~~~~~~~ 69 (140)
|..|-..|-. ....||.|+.++..+.
T Consensus 130 C~gC~~~~~~~~~~~~C~~CG~~~~r~~ 157 (164)
T PRK12496 130 CKGCKKKYPEDYPDDVCEICGSPVKRKM 157 (164)
T ss_pred CCCCCccccCCCCCCcCCCCCChhhhcc
Confidence 6666655533 2346999998876654
No 231
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=44.76 E-value=6.1 Score=19.84 Aligned_cols=11 Identities=27% Similarity=0.990 Sum_probs=8.0
Q ss_pred CCCCCCCCCCC
Q psy10659 55 QIKCPKCSASL 65 (140)
Q Consensus 55 ~~~CP~C~~~~ 65 (140)
...||.|+..+
T Consensus 26 ~~~CP~Cg~~~ 36 (41)
T smart00834 26 LATCPECGGDV 36 (41)
T ss_pred CCCCCCCCCcc
Confidence 45799998743
No 232
>KOG3799|consensus
Probab=44.60 E-value=13 Score=24.66 Aligned_cols=31 Identities=29% Similarity=0.666 Sum_probs=19.5
Q ss_pred CCCCCCcccccccchhhhceecCCCCcccHhhHHH
Q psy10659 16 SPPDNDLLCPICFELIREAHITRCGHTFCFSCISK 50 (140)
Q Consensus 16 ~~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~ 50 (140)
..+.++..|.||+..-. .-.||| -|..|-.+
T Consensus 60 aGv~ddatC~IC~KTKF---ADG~GH-~C~YCq~r 90 (169)
T KOG3799|consen 60 AGVGDDATCGICHKTKF---ADGCGH-NCSYCQTR 90 (169)
T ss_pred cccCcCcchhhhhhccc---ccccCc-ccchhhhh
Confidence 34578899999987322 125888 35555443
No 233
>KOG3362|consensus
Probab=44.58 E-value=6.9 Score=26.18 Aligned_cols=30 Identities=20% Similarity=0.642 Sum_probs=21.2
Q ss_pred CCcccccccchhhhceecCCCCcccH-hhHHH
Q psy10659 20 NDLLCPICFELIREAHITRCGHTFCF-SCISK 50 (140)
Q Consensus 20 ~~~~C~IC~~~~~~p~~~~CgH~fC~-~Ci~~ 50 (140)
.--.|.||. ++..-.-+.||..+|. .|+..
T Consensus 117 ~r~fCaVCG-~~S~ysC~~CG~kyCsv~C~~~ 147 (156)
T KOG3362|consen 117 LRKFCAVCG-YDSKYSCVNCGTKYCSVRCLKT 147 (156)
T ss_pred cchhhhhcC-CCchhHHHhcCCceeechhhhh
Confidence 346899999 5555556789998885 55543
No 234
>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 KOG1701|consensus
Probab=44.05 E-value=5.1 Score=31.59 Aligned_cols=12 Identities=25% Similarity=0.683 Sum_probs=6.4
Q ss_pred CCCCCCCCCCCC
Q psy10659 56 IKCPKCSASLPD 67 (140)
Q Consensus 56 ~~CP~C~~~~~~ 67 (140)
++|-+|.+.+.-
T Consensus 361 F~Cv~C~r~ldg 372 (468)
T KOG1701|consen 361 FTCVVCARCLDG 372 (468)
T ss_pred eEEEEeccccCC
Confidence 346666655544
No 236
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=43.45 E-value=9.9 Score=23.76 Aligned_cols=31 Identities=19% Similarity=0.695 Sum_probs=21.3
Q ss_pred CCCCCcccccccchhhhcee--cCCCCcccHhh
Q psy10659 17 PPDNDLLCPICFELIREAHI--TRCGHTFCFSC 47 (140)
Q Consensus 17 ~~~~~~~C~IC~~~~~~p~~--~~CgH~fC~~C 47 (140)
.-.++|+|.-|+-+-+.-.. ..=|+.+|..|
T Consensus 66 ~q~DEFTCssCFLV~HRSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 66 KQADEFTCSSCFLVHHRSQLAREKDGQPICRDC 98 (99)
T ss_pred CCCCceeeeeeeeEechhhhccccCCCEecccc
Confidence 34678999999877654322 24478888877
No 237
>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=43.24 E-value=11 Score=20.37 Aligned_cols=13 Identities=31% Similarity=0.841 Sum_probs=10.5
Q ss_pred CCCCCcccccccc
Q psy10659 17 PPDNDLLCPICFE 29 (140)
Q Consensus 17 ~~~~~~~C~IC~~ 29 (140)
++.++..||+|..
T Consensus 30 ~Lp~~w~CP~C~a 42 (50)
T cd00730 30 DLPDDWVCPVCGA 42 (50)
T ss_pred HCCCCCCCCCCCC
Confidence 4678899999975
No 238
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=42.89 E-value=12 Score=27.49 Aligned_cols=17 Identities=18% Similarity=0.432 Sum_probs=10.3
Q ss_pred CCCCCCCcccccccchh
Q psy10659 15 HSPPDNDLLCPICFELI 31 (140)
Q Consensus 15 ~~~~~~~~~C~IC~~~~ 31 (140)
+...+..|.|..|-..+
T Consensus 106 ip~~drqFaC~~Cd~~W 122 (278)
T PF15135_consen 106 IPSVDRQFACSSCDHMW 122 (278)
T ss_pred ccccceeeeccccchHH
Confidence 33445567777776554
No 239
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=42.79 E-value=8.7 Score=21.88 Aligned_cols=21 Identities=29% Similarity=0.645 Sum_probs=12.1
Q ss_pred cHhhHHHHhhcCCCCCCCCCC
Q psy10659 44 CFSCISKCVELQIKCPKCSAS 64 (140)
Q Consensus 44 C~~Ci~~~~~~~~~CP~C~~~ 64 (140)
|..|..-.-.....||.|+..
T Consensus 7 C~~Ck~l~~~d~e~CP~Cgs~ 27 (64)
T COG2093 7 CKNCKRLTPEDTEICPVCGST 27 (64)
T ss_pred HhhccccCCCCCccCCCCCCc
Confidence 555533222234569999875
No 240
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=41.48 E-value=16 Score=20.79 Aligned_cols=12 Identities=25% Similarity=1.007 Sum_probs=9.6
Q ss_pred CCCCCCCCCCCC
Q psy10659 55 QIKCPKCSASLP 66 (140)
Q Consensus 55 ~~~CP~C~~~~~ 66 (140)
...||.|++++.
T Consensus 6 ~v~CP~C~k~~~ 17 (62)
T PRK00418 6 TVNCPTCGKPVE 17 (62)
T ss_pred cccCCCCCCccc
Confidence 467999999864
No 241
>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=41.09 E-value=11 Score=20.19 Aligned_cols=13 Identities=31% Similarity=0.841 Sum_probs=7.9
Q ss_pred CCCCCcccccccc
Q psy10659 17 PPDNDLLCPICFE 29 (140)
Q Consensus 17 ~~~~~~~C~IC~~ 29 (140)
++.++..||+|..
T Consensus 30 ~Lp~~w~CP~C~a 42 (47)
T PF00301_consen 30 DLPDDWVCPVCGA 42 (47)
T ss_dssp GS-TT-B-TTTSS
T ss_pred HCCCCCcCcCCCC
Confidence 5678899999975
No 242
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=40.69 E-value=16 Score=20.94 Aligned_cols=14 Identities=21% Similarity=0.593 Sum_probs=11.1
Q ss_pred CCCCCCCCCCCCCC
Q psy10659 55 QIKCPKCSASLPDM 68 (140)
Q Consensus 55 ~~~CP~C~~~~~~~ 68 (140)
...||.|++++.-.
T Consensus 7 ~v~CP~Cgkpv~w~ 20 (65)
T COG3024 7 TVPCPTCGKPVVWG 20 (65)
T ss_pred cccCCCCCCccccc
Confidence 46799999988653
No 243
>KOG4317|consensus
Probab=40.62 E-value=30 Score=26.41 Aligned_cols=11 Identities=27% Similarity=0.824 Sum_probs=6.7
Q ss_pred CCCCCCCCCCC
Q psy10659 56 IKCPKCSASLP 66 (140)
Q Consensus 56 ~~CP~C~~~~~ 66 (140)
.+||-|+....
T Consensus 20 YtCPRCn~~YC 30 (383)
T KOG4317|consen 20 YTCPRCNLLYC 30 (383)
T ss_pred ccCCCCCccce
Confidence 66777765543
No 244
>PRK05978 hypothetical protein; Provisional
Probab=40.32 E-value=22 Score=23.93 Aligned_cols=20 Identities=10% Similarity=0.336 Sum_probs=16.0
Q ss_pred HHhhcCCCCCCCCCCCCCCC
Q psy10659 50 KCVELQIKCPKCSASLPDMN 69 (140)
Q Consensus 50 ~~~~~~~~CP~C~~~~~~~~ 69 (140)
.+++-...||.|+..+...+
T Consensus 47 g~Lkv~~~C~~CG~~~~~~~ 66 (148)
T PRK05978 47 AFLKPVDHCAACGEDFTHHR 66 (148)
T ss_pred cccccCCCccccCCccccCC
Confidence 56777889999999887653
No 245
>KOG3183|consensus
Probab=40.05 E-value=27 Score=25.47 Aligned_cols=53 Identities=25% Similarity=0.421 Sum_probs=34.5
Q ss_pred cccc--cccchhhhceec-CCCCcccHhhHHHHh----------hcCCCCCCCCCCCCCCCCCccc
Q psy10659 22 LLCP--ICFELIREAHIT-RCGHTFCFSCISKCV----------ELQIKCPKCSASLPDMNSVFPN 74 (140)
Q Consensus 22 ~~C~--IC~~~~~~p~~~-~CgH~fC~~Ci~~~~----------~~~~~CP~C~~~~~~~~~~~~~ 74 (140)
-.|. .|..+-.-|+.- .|++.||.+=...-. .....||.|.+++..+.+-.++
T Consensus 9 kHCs~~~CkqlDFLPf~Cd~C~~~FC~eHrsye~H~Cp~~~~~~~~v~icp~cs~pv~~~~de~~~ 74 (250)
T KOG3183|consen 9 KHCSVPYCKQLDFLPFKCDGCSGIFCLEHRSYESHHCPKGLRIDVQVPICPLCSKPVPTKKDEAPD 74 (250)
T ss_pred cccCcchhhhccccceeeCCccchhhhccchHhhcCCCcccccceeecccCCCCCCCCCCCCcchh
Confidence 4565 687777777765 799999986432111 1236899999988765433333
No 246
>KOG4218|consensus
Probab=39.99 E-value=24 Score=27.36 Aligned_cols=17 Identities=29% Similarity=0.618 Sum_probs=12.6
Q ss_pred CCCCcccccccchhhhc
Q psy10659 18 PDNDLLCPICFELIREA 34 (140)
Q Consensus 18 ~~~~~~C~IC~~~~~~p 34 (140)
.+.+-.||+|.+..+.-
T Consensus 12 edl~ElCPVCGDkVSGY 28 (475)
T KOG4218|consen 12 EDLGELCPVCGDKVSGY 28 (475)
T ss_pred cccccccccccCccccc
Confidence 34567899999977654
No 247
>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=39.21 E-value=10 Score=17.85 Aligned_cols=11 Identities=36% Similarity=0.984 Sum_probs=5.5
Q ss_pred CCCCCCCCCCC
Q psy10659 57 KCPKCSASLPD 67 (140)
Q Consensus 57 ~CP~C~~~~~~ 67 (140)
.||.|+..+..
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 48999887653
No 248
>COG4098 comFA Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [DNA replication, recombination, and repair]
Probab=38.75 E-value=15 Score=28.55 Aligned_cols=33 Identities=21% Similarity=0.485 Sum_probs=25.4
Q ss_pred CCCcccccccc-hhhhceecCCCCcccHhhHHHH
Q psy10659 19 DNDLLCPICFE-LIREAHITRCGHTFCFSCISKC 51 (140)
Q Consensus 19 ~~~~~C~IC~~-~~~~p~~~~CgH~fC~~Ci~~~ 51 (140)
.....|.-|.. ....-..+|||..||..|+.--
T Consensus 37 ~gk~~C~RC~~~~~~~~~~lp~~~~YCr~Cl~mg 70 (441)
T COG4098 37 NGKYRCNRCGNTHIELFAKLPCGCLYCRNCLMMG 70 (441)
T ss_pred cCcEEehhcCCcchhhhcccccceEeehhhhhcc
Confidence 45678999984 4445567899999999999743
No 249
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=38.17 E-value=16 Score=16.59 Aligned_cols=9 Identities=33% Similarity=1.102 Sum_probs=4.8
Q ss_pred CCCCCCCCC
Q psy10659 57 KCPKCSASL 65 (140)
Q Consensus 57 ~CP~C~~~~ 65 (140)
.||.|++.+
T Consensus 4 ~C~~CgR~F 12 (25)
T PF13913_consen 4 PCPICGRKF 12 (25)
T ss_pred cCCCCCCEE
Confidence 355555544
No 250
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=37.01 E-value=15 Score=20.37 Aligned_cols=10 Identities=50% Similarity=1.145 Sum_probs=6.9
Q ss_pred cccccccchh
Q psy10659 22 LLCPICFELI 31 (140)
Q Consensus 22 ~~C~IC~~~~ 31 (140)
+.||+|...-
T Consensus 5 i~CP~CgnKT 14 (55)
T PF14205_consen 5 ILCPICGNKT 14 (55)
T ss_pred EECCCCCCcc
Confidence 5688888644
No 251
>KOG1818|consensus
Probab=36.98 E-value=15 Score=30.68 Aligned_cols=34 Identities=29% Similarity=0.546 Sum_probs=26.1
Q ss_pred CCCcccccccchhhh----ceecCCCCcccHhhHHHHh
Q psy10659 19 DNDLLCPICFELIRE----AHITRCGHTFCFSCISKCV 52 (140)
Q Consensus 19 ~~~~~C~IC~~~~~~----p~~~~CgH~fC~~Ci~~~~ 52 (140)
.+...|-.|...|.. -....||-+||..|-...+
T Consensus 163 ~D~~~C~rCr~~F~~~~rkHHCr~CG~vFC~qcss~s~ 200 (634)
T KOG1818|consen 163 IDSEECLRCRVKFGLTNRKHHCRNCGQVFCGQCSSKSL 200 (634)
T ss_pred ccccccceeeeeeeeccccccccccchhhccCcccccc
Confidence 455789999988853 2345899999999987665
No 252
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=36.79 E-value=23 Score=20.31 Aligned_cols=12 Identities=17% Similarity=0.326 Sum_probs=9.0
Q ss_pred cCCCCCCCCCCC
Q psy10659 54 LQIKCPKCSASL 65 (140)
Q Consensus 54 ~~~~CP~C~~~~ 65 (140)
....||.|+..-
T Consensus 16 ~~~~Cp~Cgs~~ 27 (64)
T PRK06393 16 PEKTCPVHGDEK 27 (64)
T ss_pred CCCcCCCCCCCc
Confidence 456899999753
No 253
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=36.51 E-value=24 Score=24.27 Aligned_cols=10 Identities=40% Similarity=0.903 Sum_probs=7.3
Q ss_pred CCCCCCCCCC
Q psy10659 55 QIKCPKCSAS 64 (140)
Q Consensus 55 ~~~CP~C~~~ 64 (140)
...||+|+.+
T Consensus 149 P~~CPiCga~ 158 (166)
T COG1592 149 PEVCPICGAP 158 (166)
T ss_pred CCcCCCCCCh
Confidence 4579999864
No 254
>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=36.23 E-value=10 Score=16.28 Aligned_cols=9 Identities=44% Similarity=1.224 Sum_probs=4.5
Q ss_pred CCCCCCCCC
Q psy10659 58 CPKCSASLP 66 (140)
Q Consensus 58 CP~C~~~~~ 66 (140)
||.|++.+.
T Consensus 3 C~~C~~~f~ 11 (23)
T PF00096_consen 3 CPICGKSFS 11 (23)
T ss_dssp ETTTTEEES
T ss_pred CCCCCCccC
Confidence 555555443
No 255
>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=35.90 E-value=16 Score=23.36 Aligned_cols=11 Identities=45% Similarity=1.002 Sum_probs=8.6
Q ss_pred eecCCCCcccH
Q psy10659 35 HITRCGHTFCF 45 (140)
Q Consensus 35 ~~~~CgH~fC~ 45 (140)
+.-.|||.||.
T Consensus 25 vkc~CGh~f~d 35 (112)
T PF08882_consen 25 VKCDCGHEFCD 35 (112)
T ss_pred eeccCCCeecC
Confidence 34479999997
No 256
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=35.68 E-value=11 Score=24.17 Aligned_cols=8 Identities=38% Similarity=1.041 Sum_probs=6.3
Q ss_pred CCCCCCCC
Q psy10659 57 KCPKCSAS 64 (140)
Q Consensus 57 ~CP~C~~~ 64 (140)
.||.|+..
T Consensus 90 ~CP~Cgs~ 97 (117)
T PRK00564 90 VCEKCHSK 97 (117)
T ss_pred cCcCCCCC
Confidence 49999864
No 257
>KOG3896|consensus
Probab=35.67 E-value=9.1 Score=29.41 Aligned_cols=53 Identities=25% Similarity=0.639 Sum_probs=35.1
Q ss_pred CCCCCcccccccchhhhceec-CCCCcccHhhHHHHhh------c-----CCCCCCCCCCCCCCC
Q psy10659 17 PPDNDLLCPICFELIREAHIT-RCGHTFCFSCISKCVE------L-----QIKCPKCSASLPDMN 69 (140)
Q Consensus 17 ~~~~~~~C~IC~~~~~~p~~~-~CgH~fC~~Ci~~~~~------~-----~~~CP~C~~~~~~~~ 69 (140)
.+.+.+.|.-|..+-.+-..+ .=...||..|++..-. . =+.||.|...++.+.
T Consensus 20 pl~~L~FCRyC~klrc~~Cv~hEvdshfCp~CLEn~ps~EArlKKn~CAnCfDCP~C~htLSaRa 84 (449)
T KOG3896|consen 20 PLPDLVFCRYCFKLRCDDCVLHEVDSHFCPRCLENSPSPEARLKKNKCANCFDCPKCAHTLSARA 84 (449)
T ss_pred cccceeeeecccccccccccccccccccchhhccCCCchHHHhhhccccccccCcchhhhhhhhc
Confidence 556778888888766544333 4455799999875432 1 156999987776543
No 258
>PF11290 DUF3090: Protein of unknown function (DUF3090); InterPro: IPR021441 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=35.62 E-value=33 Score=23.70 Aligned_cols=16 Identities=25% Similarity=0.505 Sum_probs=13.0
Q ss_pred cCCCCCCCCCCCCCCC
Q psy10659 54 LQIKCPKCSASLPDMN 69 (140)
Q Consensus 54 ~~~~CP~C~~~~~~~~ 69 (140)
+.+.||+|+.++....
T Consensus 153 GRP~CPlCg~PlDP~G 168 (171)
T PF11290_consen 153 GRPPCPLCGEPLDPEG 168 (171)
T ss_pred CCCCCCCCCCCCCCCC
Confidence 4678999999987654
No 259
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=35.32 E-value=24 Score=26.43 Aligned_cols=46 Identities=22% Similarity=0.587 Sum_probs=33.6
Q ss_pred CCCcccccccchhhhceec----CCC--CcccHhhHHHHhhcCCCCCCCCCC
Q psy10659 19 DNDLLCPICFELIREAHIT----RCG--HTFCFSCISKCVELQIKCPKCSAS 64 (140)
Q Consensus 19 ~~~~~C~IC~~~~~~p~~~----~Cg--H~fC~~Ci~~~~~~~~~CP~C~~~ 64 (140)
+....||+|......-++. .=| -.-|.-|...|..-..+|-.|...
T Consensus 183 e~~~~CPvCGS~PvaSmV~~g~~~~GlRYL~CslC~teW~~VR~KC~nC~~t 234 (308)
T COG3058 183 ESRQYCPVCGSMPVASMVQIGETEQGLRYLHCSLCETEWHYVRVKCSNCEQS 234 (308)
T ss_pred cccccCCCcCCCCcceeeeecCccccchhhhhhhHHHHHHHHHHHhcccccc
Confidence 4567999999976654331 122 245889999999888899999864
No 260
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=35.21 E-value=13 Score=24.48 Aligned_cols=9 Identities=33% Similarity=1.058 Sum_probs=6.1
Q ss_pred CCCCCCCCC
Q psy10659 55 QIKCPKCSA 63 (140)
Q Consensus 55 ~~~CP~C~~ 63 (140)
...||+|..
T Consensus 44 ~v~CPvC~~ 52 (131)
T COG1645 44 EVFCPVCGY 52 (131)
T ss_pred eEECCCCCc
Confidence 355888874
No 261
>KOG0396|consensus
Probab=34.96 E-value=65 Score=25.18 Aligned_cols=33 Identities=15% Similarity=0.197 Sum_probs=21.0
Q ss_pred ceecCCCCcccHhhHHHHhhcC-CCCCCCCCCCC
Q psy10659 34 AHITRCGHTFCFSCISKCVELQ-IKCPKCSASLP 66 (140)
Q Consensus 34 p~~~~CgH~fC~~Ci~~~~~~~-~~CP~C~~~~~ 66 (140)
|+..|=||++-..-+.+|-... ..||.-++.+.
T Consensus 346 P~lfpnG~Vyg~~~L~s~~~~~~i~dP~~~k~f~ 379 (389)
T KOG0396|consen 346 PHLFPNGYVYGTKALESLNEDDGIGDPRTKKVFR 379 (389)
T ss_pred cccccCceeehhHHHHhhcccCCCcCCCCCcccc
Confidence 3455677777777777776654 56666655444
No 262
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=34.73 E-value=11 Score=26.08 Aligned_cols=24 Identities=29% Similarity=0.632 Sum_probs=13.6
Q ss_pred cHhhHHHHhhcCCCCCCCCCCCCC
Q psy10659 44 CFSCISKCVELQIKCPKCSASLPD 67 (140)
Q Consensus 44 C~~Ci~~~~~~~~~CP~C~~~~~~ 67 (140)
|..|...+-.....||.|+.++..
T Consensus 142 C~GC~~~f~~~~~~Cp~CG~~~~~ 165 (177)
T COG1439 142 CHGCKRIFPEPKDFCPICGSPLKR 165 (177)
T ss_pred EecCceecCCCCCcCCCCCCceEE
Confidence 334433333345678888877544
No 263
>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=33.62 E-value=11 Score=20.61 Aligned_cols=12 Identities=33% Similarity=0.899 Sum_probs=6.5
Q ss_pred CCCCCCCCCCCC
Q psy10659 56 IKCPKCSASLPD 67 (140)
Q Consensus 56 ~~CP~C~~~~~~ 67 (140)
.+||.|+..+..
T Consensus 25 atCP~C~a~~~~ 36 (54)
T PF09237_consen 25 ATCPICGAVIRQ 36 (54)
T ss_dssp EE-TTT--EESS
T ss_pred CCCCcchhhccc
Confidence 469999887665
No 264
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=33.45 E-value=21 Score=22.54 Aligned_cols=25 Identities=36% Similarity=0.719 Sum_probs=15.6
Q ss_pred ecCCCCcccHhhHHHHhhcCCCCCCCCCC
Q psy10659 36 ITRCGHTFCFSCISKCVELQIKCPKCSAS 64 (140)
Q Consensus 36 ~~~CgH~fC~~Ci~~~~~~~~~CP~C~~~ 64 (140)
.+.|||.|-.. -... -..||.|+-.
T Consensus 5 CtrCG~vf~~g-~~~i---l~GCp~CG~n 29 (112)
T COG3364 5 CTRCGEVFDDG-SEEI---LSGCPKCGCN 29 (112)
T ss_pred ecccccccccc-cHHH---HccCccccch
Confidence 36799988764 1111 2579988764
No 265
>KOG1819|consensus
Probab=33.41 E-value=20 Score=29.22 Aligned_cols=30 Identities=27% Similarity=0.616 Sum_probs=20.2
Q ss_pred CCcccccccchhhh---c-eecCCCCcccHhhHH
Q psy10659 20 NDLLCPICFELIRE---A-HITRCGHTFCFSCIS 49 (140)
Q Consensus 20 ~~~~C~IC~~~~~~---p-~~~~CgH~fC~~Ci~ 49 (140)
+.-.|-.|.-.|.. . ..-.||.+||..|-.
T Consensus 900 ~a~~cmacq~pf~afrrrhhcrncggifcg~cs~ 933 (990)
T KOG1819|consen 900 DAEQCMACQMPFNAFRRRHHCRNCGGIFCGKCSC 933 (990)
T ss_pred cchhhhhccCcHHHHHHhhhhcccCceeeccccc
Confidence 34567777776642 2 234899999999954
No 266
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=32.95 E-value=9 Score=24.47 Aligned_cols=10 Identities=30% Similarity=1.109 Sum_probs=7.1
Q ss_pred CCCCCCCCCC
Q psy10659 55 QIKCPKCSAS 64 (140)
Q Consensus 55 ~~~CP~C~~~ 64 (140)
...||.|+..
T Consensus 86 ~~~CP~Cgs~ 95 (113)
T PRK12380 86 DAQCPHCHGE 95 (113)
T ss_pred CccCcCCCCC
Confidence 3459999853
No 267
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=32.82 E-value=10 Score=24.29 Aligned_cols=9 Identities=33% Similarity=1.228 Sum_probs=6.8
Q ss_pred CCCCCCCCC
Q psy10659 56 IKCPKCSAS 64 (140)
Q Consensus 56 ~~CP~C~~~ 64 (140)
..||.|+..
T Consensus 88 ~~CP~Cgs~ 96 (114)
T PRK03681 88 RRCPQCHGD 96 (114)
T ss_pred CcCcCcCCC
Confidence 459999854
No 268
>KOG3726|consensus
Probab=32.47 E-value=22 Score=29.91 Aligned_cols=41 Identities=17% Similarity=0.405 Sum_probs=27.1
Q ss_pred ccccccchhh----hceecCCCCcccHhhHHHHhhcCCCCCCCCCCCC
Q psy10659 23 LCPICFELIR----EAHITRCGHTFCFSCISKCVELQIKCPKCSASLP 66 (140)
Q Consensus 23 ~C~IC~~~~~----~p~~~~CgH~fC~~Ci~~~~~~~~~CP~C~~~~~ 66 (140)
+|-+|...-. -+.++.|+-.||..|...+ ...||+|+-...
T Consensus 656 ~C~vcq~pedse~~v~rt~~C~~~~C~~c~~~~---~~~~~vC~~~~~ 700 (717)
T KOG3726|consen 656 TCKVCQLPEDSETDVCRTTFCYTPYCVACSLDY---ASISEVCGPDAA 700 (717)
T ss_pred HHHHhcCCcCccccccCccccCCcchHhhhhhh---hccCcccCchhh
Confidence 5667765322 1234579999999985554 677999976443
No 269
>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=32.30 E-value=27 Score=29.67 Aligned_cols=50 Identities=28% Similarity=0.705 Sum_probs=36.1
Q ss_pred CCCCcccccccchhhhce----------ecCCCCc--------------------ccHhhHHHHhhc--------CCCCC
Q psy10659 18 PDNDLLCPICFELIREAH----------ITRCGHT--------------------FCFSCISKCVEL--------QIKCP 59 (140)
Q Consensus 18 ~~~~~~C~IC~~~~~~p~----------~~~CgH~--------------------fC~~Ci~~~~~~--------~~~CP 59 (140)
..|.-.|+-|+..+.+|- -+.||-. .|..|..++... -..||
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 356789999999998872 1346644 489999998642 14699
Q ss_pred CCCCCCCC
Q psy10659 60 KCSASLPD 67 (140)
Q Consensus 60 ~C~~~~~~ 67 (140)
.|+-.+..
T Consensus 145 ~Cgp~l~l 152 (711)
T TIGR00143 145 RCGPQLNF 152 (711)
T ss_pred CCCcEEEE
Confidence 99987754
No 270
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=32.04 E-value=24 Score=20.05 Aligned_cols=12 Identities=25% Similarity=0.708 Sum_probs=8.6
Q ss_pred cCCCCCCCCCCC
Q psy10659 54 LQIKCPKCSASL 65 (140)
Q Consensus 54 ~~~~CP~C~~~~ 65 (140)
....||.|+...
T Consensus 14 ~~~~CP~Cgs~~ 25 (61)
T PRK08351 14 TEDRCPVCGSRD 25 (61)
T ss_pred CCCcCCCCcCCc
Confidence 345799998754
No 271
>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=31.95 E-value=21 Score=24.05 Aligned_cols=23 Identities=26% Similarity=0.657 Sum_probs=15.3
Q ss_pred CCCCcccHhhHHHHhhc-----------CCCCCCCCCCC
Q psy10659 38 RCGHTFCFSCISKCVEL-----------QIKCPKCSASL 65 (140)
Q Consensus 38 ~CgH~fC~~Ci~~~~~~-----------~~~CP~C~~~~ 65 (140)
.+||.| ..|+.+ -..||+|+..-
T Consensus 9 ~~gH~F-----EgWF~ss~~fd~Q~~~glv~CP~Cgs~~ 42 (148)
T PF06676_consen 9 ENGHEF-----EGWFRSSAAFDRQQARGLVSCPVCGSTE 42 (148)
T ss_pred CCCCcc-----ceecCCHHHHHHHHHcCCccCCCCCCCe
Confidence 467776 447743 25799999754
No 272
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=31.89 E-value=22 Score=16.19 Aligned_cols=8 Identities=38% Similarity=1.331 Sum_probs=5.3
Q ss_pred CCCCCCCC
Q psy10659 55 QIKCPKCS 62 (140)
Q Consensus 55 ~~~CP~C~ 62 (140)
.+.||.|+
T Consensus 16 ~f~CPnCG 23 (24)
T PF07754_consen 16 PFPCPNCG 23 (24)
T ss_pred eEeCCCCC
Confidence 35677775
No 273
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=31.89 E-value=21 Score=22.73 Aligned_cols=25 Identities=24% Similarity=0.459 Sum_probs=13.9
Q ss_pred cccccccchhhhceecCCCCcccHhhH
Q psy10659 22 LLCPICFELIREAHITRCGHTFCFSCI 48 (140)
Q Consensus 22 ~~C~IC~~~~~~p~~~~CgH~fC~~Ci 48 (140)
..|+-|.... -+..+|+|.||..|-
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 4555555433 233467777776664
No 274
>PRK14127 cell division protein GpsB; Provisional
Probab=31.81 E-value=1.3e+02 Score=19.23 Aligned_cols=29 Identities=14% Similarity=0.145 Sum_probs=13.6
Q ss_pred CcccccHHHHHHHHHHHHHHHHHHHHHHH
Q psy10659 105 NLSLPDVNLMLEVLNQRKHLLEAESSVAQ 133 (140)
Q Consensus 105 ~~~~~~~~~~l~~~~~~~~~~e~~~~~~~ 133 (140)
..+..+++.+|+.+...+..+..+...++
T Consensus 22 GYd~~EVD~FLd~V~~dye~l~~e~~~Lk 50 (109)
T PRK14127 22 GYDQDEVDKFLDDVIKDYEAFQKEIEELQ 50 (109)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444555555555544444444443333
No 275
>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=31.14 E-value=35 Score=15.96 Aligned_cols=25 Identities=20% Similarity=0.446 Sum_probs=6.6
Q ss_pred ccccccchhhh-cee--cCCCCcccHhh
Q psy10659 23 LCPICFELIRE-AHI--TRCGHTFCFSC 47 (140)
Q Consensus 23 ~C~IC~~~~~~-p~~--~~CgH~fC~~C 47 (140)
.|.+|...... ... ..|.-.++..|
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 46666666554 222 25555555555
No 276
>PF06869 DUF1258: Protein of unknown function (DUF1258); InterPro: IPR009667 This family represents a conserved region approximately 260 residues long within a number of hypothetical proteins of unknown function that seem to be specific to Caenorhabditis elegans. Note that this family contains a number of conserved cysteine and histidine residues.
Probab=31.03 E-value=29 Score=25.63 Aligned_cols=45 Identities=27% Similarity=0.321 Sum_probs=25.7
Q ss_pred CCcccHhhHHHHhhcCCCCCCC--CCCCCCCCCCccchHHHHHHHHHHh
Q psy10659 40 GHTFCFSCISKCVELQIKCPKC--SASLPDMNSVFPNFLLNELVQKHKI 86 (140)
Q Consensus 40 gH~fC~~Ci~~~~~~~~~CP~C--~~~~~~~~~~~~~~~~~~~~~~~~~ 86 (140)
.|.||..|.. .......|-.| ........ +-....+..+++.+..
T Consensus 17 ~h~~CN~CG~-~~~~~~kC~~c~~~~vakfvR-ig~~~QL~dLV~~y~~ 63 (258)
T PF06869_consen 17 THFICNSCGK-VVESNEKCSCCGCGPVAKFVR-IGGFSQLQDLVEQYLE 63 (258)
T ss_pred eehhhhhhhh-hhccCceeeccCCCccEEEEE-EcHHHHHHHHHHHHHH
Confidence 5889999988 45555667555 43333222 2233556666666543
No 277
>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=30.94 E-value=15 Score=15.39 Aligned_cols=9 Identities=44% Similarity=1.176 Sum_probs=3.6
Q ss_pred CCCCCCCCC
Q psy10659 58 CPKCSASLP 66 (140)
Q Consensus 58 CP~C~~~~~ 66 (140)
||.|+..+.
T Consensus 3 C~~C~~~~~ 11 (24)
T PF13894_consen 3 CPICGKSFR 11 (24)
T ss_dssp -SSTS-EES
T ss_pred CcCCCCcCC
Confidence 555555443
No 278
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.87 E-value=15 Score=19.75 Aligned_cols=13 Identities=23% Similarity=0.585 Sum_probs=9.2
Q ss_pred CCCCCCCCCCCCC
Q psy10659 55 QIKCPKCSASLPD 67 (140)
Q Consensus 55 ~~~CP~C~~~~~~ 67 (140)
...||+|..++.-
T Consensus 12 ~KICpvCqRPFsW 24 (54)
T COG4338 12 DKICPVCQRPFSW 24 (54)
T ss_pred hhhhhhhcCchHH
Confidence 3568889887653
No 279
>TIGR03847 conserved hypothetical protein. The conserved hypothetical protein described here occurs as part of the trio of uncharacterized proteins common in the Actinobacteria.
Probab=30.81 E-value=66 Score=22.34 Aligned_cols=18 Identities=17% Similarity=0.451 Sum_probs=14.2
Q ss_pred cCCCCCCCCCCCCCCCCC
Q psy10659 54 LQIKCPKCSASLPDMNSV 71 (140)
Q Consensus 54 ~~~~CP~C~~~~~~~~~~ 71 (140)
+.+.||.|+.++....++
T Consensus 155 GRP~CPlCg~PldP~GH~ 172 (177)
T TIGR03847 155 GRPPCPLCGRPIDPDGHI 172 (177)
T ss_pred CCCCCCCCCCCCCCCCcc
Confidence 568899999999876543
No 280
>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=30.73 E-value=10 Score=24.27 Aligned_cols=10 Identities=40% Similarity=1.089 Sum_probs=7.5
Q ss_pred CCCCCCCCCC
Q psy10659 55 QIKCPKCSAS 64 (140)
Q Consensus 55 ~~~CP~C~~~ 64 (140)
...||.|+..
T Consensus 86 ~~~CP~Cgs~ 95 (115)
T TIGR00100 86 LYRCPKCHGI 95 (115)
T ss_pred CccCcCCcCC
Confidence 4569999864
No 281
>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=30.30 E-value=24 Score=19.78 Aligned_cols=23 Identities=22% Similarity=0.424 Sum_probs=12.9
Q ss_pred cccccchhhhc-eecCCCCcccHh
Q psy10659 24 CPICFELIREA-HITRCGHTFCFS 46 (140)
Q Consensus 24 C~IC~~~~~~p-~~~~CgH~fC~~ 46 (140)
|..|.....+. +-+.||+.+|..
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 55666541222 236899999995
No 282
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=30.19 E-value=15 Score=19.60 Aligned_cols=9 Identities=33% Similarity=1.125 Sum_probs=7.1
Q ss_pred CCCCCCCCC
Q psy10659 55 QIKCPKCSA 63 (140)
Q Consensus 55 ~~~CP~C~~ 63 (140)
...||.|+.
T Consensus 26 ~~~CP~Cg~ 34 (52)
T TIGR02605 26 LATCPECGG 34 (52)
T ss_pred CCCCCCCCC
Confidence 457999997
No 283
>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=29.87 E-value=29 Score=17.02 Aligned_cols=9 Identities=56% Similarity=1.191 Sum_probs=7.0
Q ss_pred CCCCCCCCC
Q psy10659 56 IKCPKCSAS 64 (140)
Q Consensus 56 ~~CP~C~~~ 64 (140)
..||.|+.+
T Consensus 19 ~~CP~Cg~~ 27 (34)
T cd00729 19 EKCPICGAP 27 (34)
T ss_pred CcCcCCCCc
Confidence 579999864
No 284
>KOG0802|consensus
Probab=29.66 E-value=35 Score=27.90 Aligned_cols=47 Identities=28% Similarity=0.689 Sum_probs=35.7
Q ss_pred CCCcccccccchhhhceecCCCCcccHhhHHHHhhcCCCCCCCCCCCCCCC
Q psy10659 19 DNDLLCPICFELIREAHITRCGHTFCFSCISKCVELQIKCPKCSASLPDMN 69 (140)
Q Consensus 19 ~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~CP~C~~~~~~~~ 69 (140)
.....|.+|.... ....++|. ...|+..|...+..||.|.......+
T Consensus 477 ~~~~~~~~~~~~~-~~~~~~~~---~~~~l~~~~~~~~~~pl~~~~~~~~~ 523 (543)
T KOG0802|consen 477 EPNDVCAICYQEM-SARITPCS---HALCLRKWLYVQEVCPLCHTYMKEDD 523 (543)
T ss_pred cccCcchHHHHHH-Hhcccccc---chhHHHhhhhhccccCCCchhhhccc
Confidence 3456889999888 55566777 56788888888899999987765544
No 285
>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=29.51 E-value=45 Score=16.66 Aligned_cols=30 Identities=20% Similarity=0.404 Sum_probs=18.5
Q ss_pred CcccccccchhhhceecCCCCcccHhhHHH
Q psy10659 21 DLLCPICFELIREAHITRCGHTFCFSCISK 50 (140)
Q Consensus 21 ~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~ 50 (140)
...|+.+.+....-.-..|+-.+|..|...
T Consensus 3 ~~~C~~H~~~~~~~~C~~C~~~~C~~C~~~ 32 (42)
T PF00643_consen 3 EPKCPEHPEEPLSLFCEDCNEPLCSECTVS 32 (42)
T ss_dssp SSB-SSTTTSBEEEEETTTTEEEEHHHHHT
T ss_pred CccCccCCccceEEEecCCCCccCccCCCC
Confidence 456777765332223347888999999764
No 286
>PF15372 DUF4600: Domain of unknown function (DUF4600)
Probab=29.46 E-value=1.7e+02 Score=19.28 Aligned_cols=34 Identities=24% Similarity=0.358 Sum_probs=27.4
Q ss_pred CcccccHHHHHHHHHHHHHHHHHHHHHHHhHhhh
Q psy10659 105 NLSLPDVNLMLEVLNQRKHLLEAESSVAQYKLLY 138 (140)
Q Consensus 105 ~~~~~~~~~~l~~~~~~~~~~e~~~~~~~~~i~~ 138 (140)
.+.....+.++..++..++.++.+.....++|-.
T Consensus 50 ~Ms~~~l~~llkqLEkeK~~Le~qlk~~e~rLeQ 83 (129)
T PF15372_consen 50 QMSVESLNQLLKQLEKEKRSLENQLKDYEWRLEQ 83 (129)
T ss_pred hccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4566788888999999999999888888887643
No 287
>PRK02224 chromosome segregation protein; Provisional
Probab=29.01 E-value=1.3e+02 Score=25.95 Aligned_cols=16 Identities=25% Similarity=0.567 Sum_probs=12.7
Q ss_pred cCCCCCCCCCCCCCCC
Q psy10659 54 LQIKCPKCSASLPDMN 69 (140)
Q Consensus 54 ~~~~CP~C~~~~~~~~ 69 (140)
....||+|+.++....
T Consensus 450 ~~~~Cp~C~r~~~~~~ 465 (880)
T PRK02224 450 EAGKCPECGQPVEGSP 465 (880)
T ss_pred hcccCCCCCCcCCCcc
Confidence 3578999999887755
No 288
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=28.68 E-value=34 Score=21.33 Aligned_cols=27 Identities=19% Similarity=0.431 Sum_probs=15.7
Q ss_pred cccHhhHHHHhh----cCCCCCCCCCCCCCC
Q psy10659 42 TFCFSCISKCVE----LQIKCPKCSASLPDM 68 (140)
Q Consensus 42 ~fC~~Ci~~~~~----~~~~CP~C~~~~~~~ 68 (140)
+.|.-|...... ....||.|+.++...
T Consensus 63 iiCGvC~~~LT~~EY~~~~~Cp~C~spFNp~ 93 (105)
T COG4357 63 IICGVCRKLLTRAEYGMCGSCPYCQSPFNPG 93 (105)
T ss_pred EEhhhhhhhhhHHHHhhcCCCCCcCCCCCcc
Confidence 344455544332 135699999887653
No 289
>KOG2857|consensus
Probab=28.61 E-value=1.9e+02 Score=19.49 Aligned_cols=29 Identities=24% Similarity=0.679 Sum_probs=15.6
Q ss_pred CcccccccchhhhceecCCCCcccH-hhHH
Q psy10659 21 DLLCPICFELIREAHITRCGHTFCF-SCIS 49 (140)
Q Consensus 21 ~~~C~IC~~~~~~p~~~~CgH~fC~-~Ci~ 49 (140)
...|.||++.-..-.--+|.--||. .|+.
T Consensus 5 t~tC~ic~e~~~KYKCpkC~vPYCSl~CfK 34 (157)
T KOG2857|consen 5 TTTCVICLESEIKYKCPKCSVPYCSLPCFK 34 (157)
T ss_pred eeeehhhhcchhhccCCCCCCccccchhhh
Confidence 3578888874433323355555554 4443
No 290
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=28.59 E-value=33 Score=22.60 Aligned_cols=24 Identities=29% Similarity=0.695 Sum_probs=14.5
Q ss_pred cCCCCcccHhhHHHHhhcCCCCCCCCCC
Q psy10659 37 TRCGHTFCFSCISKCVELQIKCPKCSAS 64 (140)
Q Consensus 37 ~~CgH~fC~~Ci~~~~~~~~~CP~C~~~ 64 (140)
+.||++|=..-.. . -..||.|+-.
T Consensus 5 t~Cg~~f~dgs~e-i---l~GCP~CGg~ 28 (131)
T PF09845_consen 5 TKCGRVFEDGSKE-I---LSGCPECGGN 28 (131)
T ss_pred CcCCCCcCCCcHH-H---HccCcccCCc
Confidence 5677777543322 1 2579999854
No 291
>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=28.59 E-value=44 Score=18.87 Aligned_cols=10 Identities=40% Similarity=1.026 Sum_probs=5.9
Q ss_pred CCCCCCCCCC
Q psy10659 56 IKCPKCSASL 65 (140)
Q Consensus 56 ~~CP~C~~~~ 65 (140)
..||+|+..+
T Consensus 3 ~~CPlCkt~~ 12 (61)
T PF05715_consen 3 SLCPLCKTTL 12 (61)
T ss_pred ccCCcccchh
Confidence 4566666554
No 292
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=28.43 E-value=30 Score=19.09 Aligned_cols=10 Identities=40% Similarity=1.252 Sum_probs=5.4
Q ss_pred CCCCCCCCCC
Q psy10659 57 KCPKCSASLP 66 (140)
Q Consensus 57 ~CP~C~~~~~ 66 (140)
.||.|+..+.
T Consensus 4 ~CP~CG~~ie 13 (54)
T TIGR01206 4 ECPDCGAEIE 13 (54)
T ss_pred CCCCCCCEEe
Confidence 4566655443
No 293
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=28.36 E-value=19 Score=31.08 Aligned_cols=47 Identities=23% Similarity=0.518 Sum_probs=0.0
Q ss_pred CCcccccccchhhhceecCCCCc-----ccHhhHHHHhhcCCCCCCCCCCCCCC
Q psy10659 20 NDLLCPICFELIREAHITRCGHT-----FCFSCISKCVELQIKCPKCSASLPDM 68 (140)
Q Consensus 20 ~~~~C~IC~~~~~~p~~~~CgH~-----fC~~Ci~~~~~~~~~CP~C~~~~~~~ 68 (140)
....||-|...-.....-.||-. +|..|-...- ...||.|+......
T Consensus 654 ~~r~Cp~Cg~~t~~~~Cp~CG~~T~~~~~Cp~C~~~~~--~~~C~~C~~~~~~~ 705 (900)
T PF03833_consen 654 GRRRCPKCGKETFYNRCPECGSHTEPVYVCPDCGIEVE--EDECPKCGRETTSY 705 (900)
T ss_dssp ------------------------------------------------------
T ss_pred ecccCcccCCcchhhcCcccCCccccceeccccccccC--ccccccccccCccc
Confidence 45789888876443333347654 7888877543 34899998876543
No 294
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=27.97 E-value=25 Score=29.97 Aligned_cols=24 Identities=25% Similarity=0.712 Sum_probs=15.8
Q ss_pred CCcccHhhHHHHhhcCCCCCCCCCC
Q psy10659 40 GHTFCFSCISKCVELQIKCPKCSAS 64 (140)
Q Consensus 40 gH~fC~~Ci~~~~~~~~~CP~C~~~ 64 (140)
+..+|+.|-.+ ...-..||.|+..
T Consensus 461 ~~L~CH~Cg~~-~~~p~~Cp~Cgs~ 484 (730)
T COG1198 461 GQLRCHYCGYQ-EPIPQSCPECGSE 484 (730)
T ss_pred CeeEeCCCCCC-CCCCCCCCCCCCC
Confidence 66777777554 2223579999876
No 295
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=27.51 E-value=46 Score=18.74 Aligned_cols=12 Identities=25% Similarity=0.791 Sum_probs=6.9
Q ss_pred CCCCCCCCCCCC
Q psy10659 55 QIKCPKCSASLP 66 (140)
Q Consensus 55 ~~~CP~C~~~~~ 66 (140)
.+.||+|+.+..
T Consensus 39 ~p~CPlC~s~M~ 50 (59)
T PF14169_consen 39 EPVCPLCKSPMV 50 (59)
T ss_pred CccCCCcCCccc
Confidence 456666665543
No 296
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=27.45 E-value=34 Score=22.76 Aligned_cols=15 Identities=27% Similarity=0.897 Sum_probs=11.8
Q ss_pred CCCCCCCCCCCCCCC
Q psy10659 55 QIKCPKCSASLPDMN 69 (140)
Q Consensus 55 ~~~CP~C~~~~~~~~ 69 (140)
.+.||.|+..+...+
T Consensus 123 ~f~Cp~Cg~~l~~~d 137 (147)
T smart00531 123 TFTCPRCGEELEEDD 137 (147)
T ss_pred cEECCCCCCEEEEcC
Confidence 488999999886644
No 297
>KOG2071|consensus
Probab=27.12 E-value=30 Score=28.56 Aligned_cols=34 Identities=29% Similarity=0.576 Sum_probs=25.7
Q ss_pred CCCcccccccchhh-------------hceecCCCCcccHhhHHHHh
Q psy10659 19 DNDLLCPICFELIR-------------EAHITRCGHTFCFSCISKCV 52 (140)
Q Consensus 19 ~~~~~C~IC~~~~~-------------~p~~~~CgH~fC~~Ci~~~~ 52 (140)
+....|+||.+.|. +.|.+.-|-.||..|+.+-.
T Consensus 511 e~~~~C~IC~EkFe~v~d~e~~~Wm~kdaV~le~G~ifH~~Cl~e~~ 557 (579)
T KOG2071|consen 511 ERQASCPICQEKFEVVFDQEEDLWMYKDAVYLEFGRIFHSKCLSEKR 557 (579)
T ss_pred ccccCCcccccccceeecchhhheeecceeeeccCceeeccccchHH
Confidence 45689999999885 33545579999999987654
No 298
>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=27.02 E-value=19 Score=20.13 Aligned_cols=12 Identities=33% Similarity=0.869 Sum_probs=6.0
Q ss_pred CCCCCCCCCCCC
Q psy10659 56 IKCPKCSASLPD 67 (140)
Q Consensus 56 ~~CP~C~~~~~~ 67 (140)
..||.|++++..
T Consensus 3 v~CP~C~k~~~~ 14 (57)
T PF03884_consen 3 VKCPICGKPVEW 14 (57)
T ss_dssp EE-TTT--EEE-
T ss_pred ccCCCCCCeecc
Confidence 369999997765
No 299
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=26.90 E-value=16 Score=23.14 Aligned_cols=28 Identities=21% Similarity=0.432 Sum_probs=16.7
Q ss_pred cccccccchhhhceecCCCCcccHhhHHHHh
Q psy10659 22 LLCPICFELIREAHITRCGHTFCFSCISKCV 52 (140)
Q Consensus 22 ~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~ 52 (140)
-.||.|.+.|.-. -=++..|..|..+|.
T Consensus 4 p~cp~c~sEytYe---d~~~~~cpec~~ew~ 31 (112)
T COG2824 4 PPCPKCNSEYTYE---DGGQLICPECAHEWN 31 (112)
T ss_pred CCCCccCCceEEe---cCceEeCchhccccc
Confidence 4688887765421 112556777777776
No 300
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=26.87 E-value=6.7 Score=25.00 Aligned_cols=9 Identities=33% Similarity=1.342 Sum_probs=5.9
Q ss_pred CCCCCCCCC
Q psy10659 56 IKCPKCSAS 64 (140)
Q Consensus 56 ~~CP~C~~~ 64 (140)
..||.|+..
T Consensus 87 ~~CP~Cgs~ 95 (113)
T PF01155_consen 87 FSCPRCGSP 95 (113)
T ss_dssp HH-SSSSSS
T ss_pred CCCcCCcCC
Confidence 459999864
No 301
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.17 E-value=13 Score=22.23 Aligned_cols=11 Identities=55% Similarity=1.014 Sum_probs=7.0
Q ss_pred cccccccchhh
Q psy10659 22 LLCPICFELIR 32 (140)
Q Consensus 22 ~~C~IC~~~~~ 32 (140)
+.||||.-.+.
T Consensus 2 llCP~C~v~l~ 12 (88)
T COG3809 2 LLCPICGVELV 12 (88)
T ss_pred cccCcCCceee
Confidence 45777766554
No 302
>PF05103 DivIVA: DivIVA protein; InterPro: IPR007793 The Bacillus subtilis divIVA1 mutation causes misplacement of the septum during cell division, resulting in the formation of small, circular, anucleate minicells []. Inactivation of divIVA produces a minicell phenotype, whereas overproduction of DivIVA results in a filamentation phenotype []. These proteins appear to contain coiled-coils.; PDB: 2WUK_C 2WUJ_A.
Probab=25.95 E-value=1.3e+02 Score=19.09 Aligned_cols=32 Identities=16% Similarity=0.220 Sum_probs=26.7
Q ss_pred CcccccHHHHHHHHHHHHHHHHHHHHHHHhHh
Q psy10659 105 NLSLPDVNLMLEVLNQRKHLLEAESSVAQYKL 136 (140)
Q Consensus 105 ~~~~~~~~~~l~~~~~~~~~~e~~~~~~~~~i 136 (140)
..+..+++.+|+.+......+..+...++.++
T Consensus 17 GYd~~eVD~fl~~l~~~~~~l~~e~~~L~~~~ 48 (131)
T PF05103_consen 17 GYDPDEVDDFLDELAEELERLQRENAELKEEI 48 (131)
T ss_dssp EEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45678899999999999999988888887765
No 303
>PF11002 RDM: RFPL defining motif (RDM); InterPro: IPR022723 The RFPL defining motif (RDM) is a domain found on RFPL (Ret finger protein like) proteins. In humans, RFPL transcripts can be detected at the onset of neurogenesis in differentiating human embryonic stem cells, and in the developing human neocortex []. The RDM domain is thought to have emerged from a neofunctionalisation event. It is found N-terminal to the SPRY domain (PF00622 from PFAM). ; PDB: 2FBE_B.
Probab=25.86 E-value=23 Score=18.46 Aligned_cols=26 Identities=38% Similarity=0.420 Sum_probs=0.0
Q ss_pred CCCCCCccchHHHHHHHHHHhcCCCC
Q psy10659 66 PDMNSVFPNFLLNELVQKHKIKSAQD 91 (140)
Q Consensus 66 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 91 (140)
+.++++.+|..+..++...++..+..
T Consensus 3 Sqk~Di~p~~qLg~Lvs~iKelEPqL 28 (42)
T PF11002_consen 3 SQKNDIRPNFQLGKLVSKIKELEPQL 28 (42)
T ss_dssp --------------------------
T ss_pred cccccccHHHHHHHHHHHHHHhCHHH
Confidence 34445889999999998888777653
No 304
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.68 E-value=41 Score=22.10 Aligned_cols=23 Identities=39% Similarity=0.855 Sum_probs=12.8
Q ss_pred cccHhhHHHHhhcCCCCCCCCCCCCC
Q psy10659 42 TFCFSCISKCVELQIKCPKCSASLPD 67 (140)
Q Consensus 42 ~fC~~Ci~~~~~~~~~CP~C~~~~~~ 67 (140)
.||..|-..- ...||.|..++.-
T Consensus 29 afcskcgeat---i~qcp~csasirg 51 (160)
T COG4306 29 AFCSKCGEAT---ITQCPICSASIRG 51 (160)
T ss_pred HHHhhhchHH---HhcCCccCCcccc
Confidence 4777775432 2456776665543
No 305
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=25.49 E-value=20 Score=15.65 Aligned_cols=10 Identities=30% Similarity=0.770 Sum_probs=4.7
Q ss_pred ccccccchhh
Q psy10659 23 LCPICFELIR 32 (140)
Q Consensus 23 ~C~IC~~~~~ 32 (140)
.|.||...+.
T Consensus 2 ~C~~C~~~f~ 11 (25)
T PF12874_consen 2 YCDICNKSFS 11 (25)
T ss_dssp EETTTTEEES
T ss_pred CCCCCCCCcC
Confidence 3555544443
No 306
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=25.46 E-value=68 Score=17.32 Aligned_cols=28 Identities=29% Similarity=0.594 Sum_probs=19.2
Q ss_pred ccccccchhh--hceecCCCCcccHhhHHHH
Q psy10659 23 LCPICFELIR--EAHITRCGHTFCFSCISKC 51 (140)
Q Consensus 23 ~C~IC~~~~~--~p~~~~CgH~fC~~Ci~~~ 51 (140)
.|+||..... ..+.+.=| ..|.+|+...
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 4888888654 23456666 6888998764
No 307
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=25.30 E-value=50 Score=21.96 Aligned_cols=24 Identities=33% Similarity=0.674 Sum_probs=16.7
Q ss_pred CcccccccchhhhceecCCCCcccHhhHH
Q psy10659 21 DLLCPICFELIREAHITRCGHTFCFSCIS 49 (140)
Q Consensus 21 ~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~ 49 (140)
...|+.|..+|... |..+|..|+.
T Consensus 3 l~nC~~CgklF~~~-----~~~iCp~C~~ 26 (137)
T TIGR03826 3 LANCPKCGRLFVKT-----GRDVCPSCYE 26 (137)
T ss_pred Cccccccchhhhhc-----CCccCHHHhH
Confidence 34688888877651 6667777774
No 308
>COG1040 ComFC Predicted amidophosphoribosyltransferases [General function prediction only]
Probab=25.13 E-value=21 Score=25.62 Aligned_cols=17 Identities=29% Similarity=0.301 Sum_probs=11.0
Q ss_pred chHHHHHHHHHHhcCCC
Q psy10659 74 NFLLNELVQKHKIKSAQ 90 (140)
Q Consensus 74 ~~~~~~~~~~~~~~~~~ 90 (140)
+..+..++..++-....
T Consensus 75 ~~~l~~~i~~~Kf~~~~ 91 (225)
T COG1040 75 NGPLRELISQLKFQGDL 91 (225)
T ss_pred cHHHHHHHHHhhhCCch
Confidence 45677777777766543
No 309
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=24.83 E-value=27 Score=22.94 Aligned_cols=12 Identities=17% Similarity=0.337 Sum_probs=7.2
Q ss_pred CCCCCCCCCCCC
Q psy10659 56 IKCPKCSASLPD 67 (140)
Q Consensus 56 ~~CP~C~~~~~~ 67 (140)
..||.|+..+..
T Consensus 27 ~vcP~cg~~~~~ 38 (129)
T TIGR02300 27 AVSPYTGEQFPP 38 (129)
T ss_pred ccCCCcCCccCc
Confidence 457777765443
No 310
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=24.34 E-value=48 Score=20.98 Aligned_cols=14 Identities=29% Similarity=0.847 Sum_probs=10.9
Q ss_pred CCCCCCCCCCCCCC
Q psy10659 55 QIKCPKCSASLPDM 68 (140)
Q Consensus 55 ~~~CP~C~~~~~~~ 68 (140)
...||.|+..+..-
T Consensus 49 ~t~CP~Cg~~~e~~ 62 (115)
T COG1885 49 STSCPKCGEPFESA 62 (115)
T ss_pred cccCCCCCCcccee
Confidence 46799999987663
No 311
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=24.34 E-value=30 Score=18.15 Aligned_cols=14 Identities=14% Similarity=0.460 Sum_probs=9.4
Q ss_pred cCCCCCCCCCCCCC
Q psy10659 54 LQIKCPKCSASLPD 67 (140)
Q Consensus 54 ~~~~CP~C~~~~~~ 67 (140)
....||.|+..+-.
T Consensus 18 ~~irC~~CG~rIly 31 (44)
T smart00659 18 DVVRCRECGYRILY 31 (44)
T ss_pred CceECCCCCceEEE
Confidence 34678888876544
No 312
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=24.18 E-value=41 Score=17.04 Aligned_cols=11 Identities=45% Similarity=1.226 Sum_probs=7.6
Q ss_pred CCCCCCCCCCC
Q psy10659 57 KCPKCSASLPD 67 (140)
Q Consensus 57 ~CP~C~~~~~~ 67 (140)
.||.|+..+..
T Consensus 1 ~CP~C~~~l~~ 11 (41)
T PF13453_consen 1 KCPRCGTELEP 11 (41)
T ss_pred CcCCCCcccce
Confidence 48888876544
No 313
>TIGR00375 conserved hypothetical protein TIGR00375. The member of this family from Methanococcus jannaschii, MJ0043, is considerably longer and appears to contain an intein N-terminal to the region of homology.
Probab=24.16 E-value=18 Score=28.22 Aligned_cols=27 Identities=26% Similarity=0.603 Sum_probs=16.5
Q ss_pred CCCcccHhhHHHHhh-----cCCCCCCCCCCCC
Q psy10659 39 CGHTFCFSCISKCVE-----LQIKCPKCSASLP 66 (140)
Q Consensus 39 CgH~fC~~Ci~~~~~-----~~~~CP~C~~~~~ 66 (140)
=-.++|..|-..+-. ....|| |+..++
T Consensus 238 Yh~~~c~~C~~~~~~~~~~~~~~~Cp-CG~~i~ 269 (374)
T TIGR00375 238 YHQTACEACGEPAVSEDAETACANCP-CGGRIK 269 (374)
T ss_pred cchhhhcccCCcCCchhhhhcCCCCC-CCCcce
Confidence 444566666544432 237799 998754
No 314
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=24.08 E-value=1.7e+02 Score=17.45 Aligned_cols=33 Identities=27% Similarity=0.290 Sum_probs=20.3
Q ss_pred CcccccHHHHHHHHHHHHHHHHHHHHHHHhHhhh
Q psy10659 105 NLSLPDVNLMLEVLNQRKHLLEAESSVAQYKLLY 138 (140)
Q Consensus 105 ~~~~~~~~~~l~~~~~~~~~~e~~~~~~~~~i~~ 138 (140)
.+....+..+++ +.++...++++...++.++.+
T Consensus 58 g~~l~~i~~~l~-l~~~~~~l~~~l~~l~~~~~~ 90 (91)
T cd04766 58 GVNLAGVKRILE-LEEELAELRAELDELRARLRR 90 (91)
T ss_pred CCCHHHHHHHHH-HHHHHHHHHHHHHHHHHHhcc
Confidence 344445555554 556777777777777776654
No 315
>PF14818 DUF4482: Domain of unknown function (DUF4482)
Probab=23.85 E-value=2.3e+02 Score=18.96 Aligned_cols=24 Identities=17% Similarity=0.243 Sum_probs=17.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhHh
Q psy10659 113 LMLEVLNQRKHLLEAESSVAQYKL 136 (140)
Q Consensus 113 ~~l~~~~~~~~~~e~~~~~~~~~i 136 (140)
.+|+.+...++..|++...++++|
T Consensus 20 ELLdrfd~ER~eWE~Q~kemq~ki 43 (141)
T PF14818_consen 20 ELLDRFDRERQEWEQQWKEMQRKI 43 (141)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 377777777777777777777766
No 316
>KOG3475|consensus
Probab=23.83 E-value=43 Score=20.28 Aligned_cols=30 Identities=20% Similarity=0.485 Sum_probs=22.4
Q ss_pred CCcccHhhHHHHh-hcCCCCCCCCCCCCCCC
Q psy10659 40 GHTFCFSCISKCV-ELQIKCPKCSASLPDMN 69 (140)
Q Consensus 40 gH~fC~~Ci~~~~-~~~~~CP~C~~~~~~~~ 69 (140)
.|+.|..|-...+ .....|..|+-+-....
T Consensus 15 shtlC~RCG~~syH~QKstC~~CGYpaak~R 45 (92)
T KOG3475|consen 15 SHTLCRRCGRRSYHIQKSTCSSCGYPAAKKR 45 (92)
T ss_pred chHHHHHhCchhhhhhcccccccCCcchhcc
Confidence 5888999986655 46788999998765543
No 317
>PF12660 zf-TFIIIC: Putative zinc-finger of transcription factor IIIC complex; InterPro: IPR024764 This zinc-finger domain is at the very C terminus of a number of different TFIIIC subunit proteins. This domain might be involved in protein-DNA and/or protein-protein interactions [].; PDB: 2J04_C.
Probab=23.60 E-value=27 Score=21.70 Aligned_cols=45 Identities=27% Similarity=0.490 Sum_probs=14.3
Q ss_pred cccccccchh--hhceec--CCCCcccHhhHHHHhh----cCCCCCCCCCCCCC
Q psy10659 22 LLCPICFELI--REAHIT--RCGHTFCFSCISKCVE----LQIKCPKCSASLPD 67 (140)
Q Consensus 22 ~~C~IC~~~~--~~p~~~--~CgH~fC~~Ci~~~~~----~~~~CP~C~~~~~~ 67 (140)
-.|++|...+ .++... +=||+|= .|...++. ....|+.|+..+..
T Consensus 15 E~C~~C~~~i~~~~~~~~~C~~GH~w~-RC~lT~l~i~~~~~r~C~~C~~~~l~ 67 (99)
T PF12660_consen 15 EKCPICGAPIPFDDLDEAQCENGHVWP-RCALTFLPIQTPGVRVCPVCGRRALD 67 (99)
T ss_dssp --------------SSEEE-TTS-EEE-B-SSS-SBS-SS-EEE-TTT--EEE-
T ss_pred ccccccccccccCCcCEeECCCCCEEe-eeeeeeeeeccCCeeEcCCCCCEEec
Confidence 6899999965 344444 4588874 45444442 12679999876544
No 318
>PF12675 DUF3795: Protein of unknown function (DUF3795); InterPro: IPR024227 This family of proteins is functionally uncharacterised and is found in bacteria and archaea. Proteins in this family are typically between 99 and 171 amino acids in length. These proteins are likely to be zinc binding given the conserved cysteines.
Probab=23.54 E-value=65 Score=18.89 Aligned_cols=27 Identities=30% Similarity=0.737 Sum_probs=15.9
Q ss_pred cCCCCcccHhhHHHHhhc--------------CCCCCCCCCC
Q psy10659 37 TRCGHTFCFSCISKCVEL--------------QIKCPKCSAS 64 (140)
Q Consensus 37 ~~CgH~fC~~Ci~~~~~~--------------~~~CP~C~~~ 64 (140)
.+||. +|..|..-.... ...||.|+..
T Consensus 3 ApCGl-~C~~C~~y~~~~~~~~~~~~~~~~~~~~~C~GCr~~ 43 (78)
T PF12675_consen 3 APCGL-DCGNCPAYEAGKISDASLRLKEASPEKIRCPGCRSG 43 (78)
T ss_pred cccCC-ccccchhhhcCCccHHHHHHhhccCCCCcCcCCcCC
Confidence 46775 777776533221 1248888864
No 319
>KOG4443|consensus
Probab=23.38 E-value=43 Score=28.14 Aligned_cols=45 Identities=22% Similarity=0.645 Sum_probs=31.0
Q ss_pred CCCcccccccchhhhce--e---cCCCCcccHhhHHHHhhc-----CCCCCCCCC
Q psy10659 19 DNDLLCPICFELIREAH--I---TRCGHTFCFSCISKCVEL-----QIKCPKCSA 63 (140)
Q Consensus 19 ~~~~~C~IC~~~~~~p~--~---~~CgH~fC~~Ci~~~~~~-----~~~CP~C~~ 63 (140)
.-.+.|++|...-..+. . -.||-.++..|+..|+.. .-.||-|+.
T Consensus 16 ~~~~mc~l~~s~G~~~ag~m~ac~~c~~~yH~~cvt~~~~~~~l~~gWrC~~crv 70 (694)
T KOG4443|consen 16 IVCLMCPLCGSSGKGRAGRLLACSDCGQKYHPYCVTSWAQHAVLSGGWRCPSCRV 70 (694)
T ss_pred hhhhhhhhhccccccccCcchhhhhhcccCCcchhhHHHhHHHhcCCcccCCcee
Confidence 34578888887666542 2 269999999999998853 234776654
No 320
>KOG2906|consensus
Probab=22.89 E-value=23 Score=22.12 Aligned_cols=26 Identities=27% Similarity=0.728 Sum_probs=15.6
Q ss_pred cccccccchhhhceecCCCCcccHhh
Q psy10659 22 LLCPICFELIREAHITRCGHTFCFSC 47 (140)
Q Consensus 22 ~~C~IC~~~~~~p~~~~CgH~fC~~C 47 (140)
+.||-|...+.-..-..|..-+|..|
T Consensus 2 ~FCP~Cgn~Live~g~~~~rf~C~tC 27 (105)
T KOG2906|consen 2 LFCPTCGNMLIVESGESCNRFSCRTC 27 (105)
T ss_pred cccCCCCCEEEEecCCeEeeEEcCCC
Confidence 46777777776444344555555555
No 321
>KOG1842|consensus
Probab=22.34 E-value=40 Score=26.99 Aligned_cols=32 Identities=22% Similarity=0.544 Sum_probs=24.5
Q ss_pred CCcccccccchhhhce----ecCCCCcccHhhHHHH
Q psy10659 20 NDLLCPICFELIREAH----ITRCGHTFCFSCISKC 51 (140)
Q Consensus 20 ~~~~C~IC~~~~~~p~----~~~CgH~fC~~Ci~~~ 51 (140)
+...||+|...|.-.. .-=||-+.|.+|..-.
T Consensus 179 ~V~~CP~Ca~~F~l~rRrHHCRLCG~VmC~~C~k~i 214 (505)
T KOG1842|consen 179 SVQFCPECANSFGLTRRRHHCRLCGRVMCRDCSKFI 214 (505)
T ss_pred cccccccccchhhhHHHhhhhhhcchHHHHHHHHhc
Confidence 4578999999987442 2259999999997643
No 322
>KOG0801|consensus
Probab=22.23 E-value=48 Score=22.82 Aligned_cols=15 Identities=33% Similarity=0.913 Sum_probs=11.6
Q ss_pred CCCCCCCCCCCCCCC
Q psy10659 55 QIKCPKCSASLPDMN 69 (140)
Q Consensus 55 ~~~CP~C~~~~~~~~ 69 (140)
..+||+|.+.+...+
T Consensus 138 g~KCPvC~K~V~sDd 152 (205)
T KOG0801|consen 138 GMKCPVCHKVVPSDD 152 (205)
T ss_pred CccCCccccccCCCc
Confidence 368999999876644
No 323
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=22.09 E-value=69 Score=20.96 Aligned_cols=15 Identities=20% Similarity=0.605 Sum_probs=12.0
Q ss_pred CCCCCCCCCCCCCCC
Q psy10659 55 QIKCPKCSASLPDMN 69 (140)
Q Consensus 55 ~~~CP~C~~~~~~~~ 69 (140)
...|+.|+..+....
T Consensus 53 RyrC~~C~~tf~~~~ 67 (129)
T COG3677 53 RYKCKSCGSTFTVET 67 (129)
T ss_pred ccccCCcCcceeeec
Confidence 578999999887654
No 324
>PF09340 NuA4: Histone acetyltransferase subunit NuA4; InterPro: IPR015418 The NuA4 histone acetyltransferase (HAT) multisubunit complex is responsible for acetylation of histone H4 and H2A N-terminal tails in yeast []. NuA4 complexes are highly conserved in eukaryotes and play primary roles in transcription, cellular response to DNA damage, and cell cycle control [].
Probab=21.78 E-value=1.9e+02 Score=17.19 Aligned_cols=21 Identities=24% Similarity=0.286 Sum_probs=12.3
Q ss_pred HHHHHHHHHHHHHHHHHhHhh
Q psy10659 117 VLNQRKHLLEAESSVAQYKLL 137 (140)
Q Consensus 117 ~~~~~~~~~e~~~~~~~~~i~ 137 (140)
.+-.++++++.+...++.+|.
T Consensus 6 ~l~~~k~~Le~~L~~lE~qIy 26 (80)
T PF09340_consen 6 ELLQKKKKLEKDLAALEKQIY 26 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 334556666666666666653
No 325
>KOG0006|consensus
Probab=21.72 E-value=60 Score=24.94 Aligned_cols=38 Identities=16% Similarity=0.541 Sum_probs=27.6
Q ss_pred CCCCCCCcccccccchhhhceecCCC--CcccHhhHHHHh
Q psy10659 15 HSPPDNDLLCPICFELIREAHITRCG--HTFCFSCISKCV 52 (140)
Q Consensus 15 ~~~~~~~~~C~IC~~~~~~p~~~~Cg--H~fC~~Ci~~~~ 52 (140)
+........|..|-+.-..-..++|. |+-|..|+..|-
T Consensus 215 i~~N~~ni~C~~Ctdv~~~vlvf~Cns~HvtC~dCFr~yc 254 (446)
T KOG0006|consen 215 IATNSRNITCITCTDVRSPVLVFQCNSRHVTCLDCFRLYC 254 (446)
T ss_pred hhcccccceeEEecCCccceEEEecCCceeehHHhhhhHh
Confidence 33445567888898865544456998 999999998664
No 326
>KOG3005|consensus
Probab=21.65 E-value=49 Score=24.62 Aligned_cols=44 Identities=25% Similarity=0.547 Sum_probs=31.0
Q ss_pred cccccccchhhhc--eec-----CCCCcccHhhHHHHhhc---------CCCCCCCCCCC
Q psy10659 22 LLCPICFELIREA--HIT-----RCGHTFCFSCISKCVEL---------QIKCPKCSASL 65 (140)
Q Consensus 22 ~~C~IC~~~~~~p--~~~-----~CgH~fC~~Ci~~~~~~---------~~~CP~C~~~~ 65 (140)
..|.+|-..+.++ ..+ .|+-+++..|+...+.. ...||.|++.+
T Consensus 183 ~~celc~~ei~e~~~~~a~c~~~~c~~~~h~~CLa~~~~~~e~g~~~p~eg~cp~C~~~~ 242 (276)
T KOG3005|consen 183 VECELCEKEILETDWSRATCPNPDCDSLNHLTCLAEELLEVEPGQLIPLEGMCPKCEKFL 242 (276)
T ss_pred hhhHHHHHHhccccceeccCCCCCCCchhhhhhhhHHHhccCCCceeccCCCCCchhcee
Confidence 4899999888332 222 48889999999885431 35799998843
No 327
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=21.60 E-value=36 Score=17.90 Aligned_cols=7 Identities=71% Similarity=1.616 Sum_probs=5.4
Q ss_pred CCCCccc
Q psy10659 38 RCGHTFC 44 (140)
Q Consensus 38 ~CgH~fC 44 (140)
.|||+|=
T Consensus 32 ~Cg~tfv 38 (47)
T PF04606_consen 32 ECGHTFV 38 (47)
T ss_pred cCCCEEE
Confidence 5999884
No 328
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=21.52 E-value=76 Score=23.30 Aligned_cols=27 Identities=26% Similarity=0.582 Sum_probs=15.3
Q ss_pred CCCcccHhhHHHHhhc----CCCCCCCCCCC
Q psy10659 39 CGHTFCFSCISKCVEL----QIKCPKCSASL 65 (140)
Q Consensus 39 CgH~fC~~Ci~~~~~~----~~~CP~C~~~~ 65 (140)
=.|.||..|-...... ...||.|+...
T Consensus 97 ~~~~fC~~CG~~~~~~~~~~~~~C~~c~~~~ 127 (256)
T PRK00241 97 RSHRFCGYCGHPMHPSKTEWAMLCPHCRERY 127 (256)
T ss_pred hcCccccccCCCCeecCCceeEECCCCCCEE
Confidence 3567777776543221 24577777543
No 329
>PLN03086 PRLI-interacting factor K; Provisional
Probab=21.44 E-value=1.2e+02 Score=25.30 Aligned_cols=50 Identities=16% Similarity=0.325 Sum_probs=25.9
Q ss_pred CCCCCcccccccchhhh------------ceecCCCCcccHhhHHHHhh-----cCCCCCCCCCCCC
Q psy10659 17 PPDNDLLCPICFELIRE------------AHITRCGHTFCFSCISKCVE-----LQIKCPKCSASLP 66 (140)
Q Consensus 17 ~~~~~~~C~IC~~~~~~------------p~~~~CgH~fC~~Ci~~~~~-----~~~~CP~C~~~~~ 66 (140)
++++.+.|+.|...|.. |+.-+||..+-..-+..... ....|+.|...+.
T Consensus 449 el~~H~~C~~Cgk~f~~s~LekH~~~~Hkpv~CpCg~~~~R~~L~~H~~thCp~Kpi~C~fC~~~v~ 515 (567)
T PLN03086 449 EAKNHVHCEKCGQAFQQGEMEKHMKVFHEPLQCPCGVVLEKEQMVQHQASTCPLRLITCRFCGDMVQ 515 (567)
T ss_pred ccccCccCCCCCCccchHHHHHHHHhcCCCccCCCCCCcchhHHHhhhhccCCCCceeCCCCCCccc
Confidence 44566788888765531 11112554443333333322 1246888887774
No 330
>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=21.31 E-value=38 Score=21.71 Aligned_cols=16 Identities=19% Similarity=0.210 Sum_probs=11.7
Q ss_pred cCCCCCCCCCCCCCCC
Q psy10659 54 LQIKCPKCSASLPDMN 69 (140)
Q Consensus 54 ~~~~CP~C~~~~~~~~ 69 (140)
+...|+.|+++++...
T Consensus 84 r~D~CM~C~~pLTLd~ 99 (114)
T PF11023_consen 84 RVDACMHCKEPLTLDP 99 (114)
T ss_pred hhhccCcCCCcCccCc
Confidence 3457999999887543
No 331
>KOG3576|consensus
Probab=21.12 E-value=41 Score=24.15 Aligned_cols=51 Identities=16% Similarity=0.424 Sum_probs=29.4
Q ss_pred CCCcccccccchhhhceec----C------------CCCcccHhhH-HHHhhc-----CCCCCCCCCCCCCCC
Q psy10659 19 DNDLLCPICFELIREAHIT----R------------CGHTFCFSCI-SKCVEL-----QIKCPKCSASLPDMN 69 (140)
Q Consensus 19 ~~~~~C~IC~~~~~~p~~~----~------------CgH~fC~~Ci-~~~~~~-----~~~CP~C~~~~~~~~ 69 (140)
.+.+.|.||...|.-...+ . ||-.|-..-= .+..+. -.+|..|.+.++..-
T Consensus 115 ~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrc 187 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRC 187 (267)
T ss_pred CCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhc
Confidence 6779999999988643222 2 3433332211 111111 257999998887754
No 332
>cd04772 HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.
Probab=21.11 E-value=2e+02 Score=17.52 Aligned_cols=27 Identities=19% Similarity=0.167 Sum_probs=21.8
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHHHhHh
Q psy10659 110 DVNLMLEVLNQRKHLLEAESSVAQYKL 136 (140)
Q Consensus 110 ~~~~~l~~~~~~~~~~e~~~~~~~~~i 136 (140)
+....+..+..+...++++.++++.+|
T Consensus 73 ~~~~~~~ll~~~~~~l~~~i~~L~~~~ 99 (99)
T cd04772 73 IVASALALVDAAHALLQRYRQQLDQEL 99 (99)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 345788899999999999998888764
No 333
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=20.84 E-value=46 Score=18.16 Aligned_cols=10 Identities=30% Similarity=1.102 Sum_probs=7.3
Q ss_pred CCCCCCCCCC
Q psy10659 57 KCPKCSASLP 66 (140)
Q Consensus 57 ~CP~C~~~~~ 66 (140)
.||.|+..+.
T Consensus 2 ~CPyCge~~~ 11 (52)
T PF14255_consen 2 QCPYCGEPIE 11 (52)
T ss_pred CCCCCCCeeE
Confidence 5888887654
No 334
>PF05190 MutS_IV: MutS family domain IV C-terminus.; InterPro: IPR007861 Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication []. MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base []. MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch []. MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level []. Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA. MutS is a modular protein with a complex structure [], and is composed of: N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair. Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [].This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions []. Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts []. This entry represents the clamp domain (domain 4) found in proteins of the MutS family. The clamp domain is inserted within the core domain at the top of the lever helices. It has a beta-sheet structure [].; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 2WTU_A 1OH7_A 1OH5_B 1W7A_B 1NG9_A 1OH8_B 1WBD_A 1WB9_A 3K0S_A 1OH6_A ....
Probab=20.79 E-value=1.7e+02 Score=17.02 Aligned_cols=27 Identities=15% Similarity=0.058 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhHhhh
Q psy10659 112 NLMLEVLNQRKHLLEAESSVAQYKLLY 138 (140)
Q Consensus 112 ~~~l~~~~~~~~~~e~~~~~~~~~i~~ 138 (140)
+..|+.+.+....++++..+...++..
T Consensus 3 d~~Ld~~~~~~~~~~~~l~~~~~~~~~ 29 (92)
T PF05190_consen 3 DEELDELREEYEEIEEELEELLEEIRK 29 (92)
T ss_dssp SHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345555656666666666555555544
No 335
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=20.59 E-value=1.4e+02 Score=18.76 Aligned_cols=40 Identities=28% Similarity=0.487 Sum_probs=22.0
Q ss_pred cccccc-hhhhc----eecCCCCcccHhhHHHHhhcCCCCCCCCCCCCCCC
Q psy10659 24 CPICFE-LIREA----HITRCGHTFCFSCISKCVELQIKCPKCSASLPDMN 69 (140)
Q Consensus 24 C~IC~~-~~~~p----~~~~CgH~fC~~Ci~~~~~~~~~CP~C~~~~~~~~ 69 (140)
|++|.. .+... ...-+|+.+-. - .....||.|+..+...+
T Consensus 1 C~~C~~~~~~~~~~~~~~~~~G~~~~v-~-----~~~~~C~~CGe~~~~~e 45 (127)
T TIGR03830 1 CPICGSGELVRDVKDEPYTYKGESITI-G-----VPGWYCPACGEELLDPE 45 (127)
T ss_pred CCCCCCccceeeeecceEEEcCEEEEE-e-----eeeeECCCCCCEEEcHH
Confidence 889974 33221 12246665443 1 12356999998765543
No 336
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=20.48 E-value=44 Score=17.34 Aligned_cols=14 Identities=21% Similarity=0.617 Sum_probs=10.2
Q ss_pred CCCCCCCCCCCCCC
Q psy10659 55 QIKCPKCSASLPDM 68 (140)
Q Consensus 55 ~~~CP~C~~~~~~~ 68 (140)
...||.|+..+...
T Consensus 21 ~~~Cp~CG~~~~~~ 34 (46)
T PRK00398 21 GVRCPYCGYRILFK 34 (46)
T ss_pred ceECCCCCCeEEEc
Confidence 46799999876543
No 337
>PF06937 EURL: EURL protein; InterPro: IPR009704 This family consists of several animal EURL proteins. EURL is preferentially expressed in chick retinal precursor cells as well as in the anterior epithelial cells of the lens at early stages of development. EURL transcripts are found primarily in the peripheral dorsal retina, i.e., the most undifferentiated part of the dorsal retina. EURL transcripts are also detected in the lens at stage 18 and remain abundant in the proliferating epithelial cells of the lens until at least day 11. The distribution pattern of EURL in the developing retina and lens suggest a role before the events leading to cell determination and differentiation [].
Probab=20.45 E-value=85 Score=23.44 Aligned_cols=38 Identities=37% Similarity=0.638 Sum_probs=24.5
Q ss_pred CCCcccccccchhhhcee------c-C-CCCcccHhhHHHHhh-cCCCCC
Q psy10659 19 DNDLLCPICFELIREAHI------T-R-CGHTFCFSCISKCVE-LQIKCP 59 (140)
Q Consensus 19 ~~~~~C~IC~~~~~~p~~------~-~-CgH~fC~~Ci~~~~~-~~~~CP 59 (140)
+....|+||+++-...+- + + =|| ++|++.|-- ....||
T Consensus 28 ~tLsfChiCfEl~iegvpks~llHtkSlRGH---rdCFEK~HlIanQ~~p 74 (285)
T PF06937_consen 28 ETLSFCHICFELSIEGVPKSNLLHTKSLRGH---RDCFEKYHLIANQDCP 74 (285)
T ss_pred cceeecceeeccccccCccccccccccccch---HHHHHHHHHHHcCCCC
Confidence 445578888886654321 1 1 566 789988863 667787
No 338
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=20.31 E-value=65 Score=18.14 Aligned_cols=18 Identities=33% Similarity=0.864 Sum_probs=10.7
Q ss_pred cHhhHHHHhhcCCCCCCCCC
Q psy10659 44 CFSCISKCVELQIKCPKCSA 63 (140)
Q Consensus 44 C~~Ci~~~~~~~~~CP~C~~ 63 (140)
|..|-+. .....||.|+.
T Consensus 39 C~~CRk~--~~~Y~CP~CGF 56 (59)
T PRK14890 39 CEKCRKQ--SNPYTCPKCGF 56 (59)
T ss_pred chhHHhc--CCceECCCCCC
Confidence 5556442 23567888874
No 339
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=20.22 E-value=53 Score=15.40 Aligned_cols=12 Identities=25% Similarity=0.567 Sum_probs=6.6
Q ss_pred ccccccchhhhc
Q psy10659 23 LCPICFELIREA 34 (140)
Q Consensus 23 ~C~IC~~~~~~p 34 (140)
.|.+|.+.....
T Consensus 2 ~C~~C~~~~~~~ 13 (30)
T PF03107_consen 2 WCDVCRRKIDGF 13 (30)
T ss_pred CCCCCCCCcCCC
Confidence 466666555443
No 340
>PTZ00218 40S ribosomal protein S29; Provisional
Probab=20.17 E-value=66 Score=17.77 Aligned_cols=31 Identities=23% Similarity=0.560 Sum_probs=23.8
Q ss_pred CcccccccchhhhceecCCCCcccHhhHHHHhh
Q psy10659 21 DLLCPICFELIREAHITRCGHTFCFSCISKCVE 53 (140)
Q Consensus 21 ~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~ 53 (140)
.-.|.+|... ..++-..|-..|..|+.++..
T Consensus 16 sr~C~vCg~~--~gliRkygL~~CRqCFRe~A~ 46 (54)
T PTZ00218 16 SRQCRVCSNR--HGLIRKYGLNVCRQCFRENAE 46 (54)
T ss_pred CCeeecCCCc--chhhhhcCcchhhHHHHHhhH
Confidence 4789999884 345568888899999987754
No 341
>KOG0883|consensus
Probab=20.14 E-value=97 Score=24.58 Aligned_cols=34 Identities=15% Similarity=0.162 Sum_probs=30.5
Q ss_pred CcccccccchhhhceecCCCCcccHhhHHHHhhc
Q psy10659 21 DLLCPICFELIREAHITRCGHTFCFSCISKCVEL 54 (140)
Q Consensus 21 ~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~ 54 (140)
-..|.+-+-.|.+|+.+.=|.+|=..-|..|++.
T Consensus 40 ~~hC~lt~~Pfe~PvC~~dg~vFd~~~Ivp~lkk 73 (518)
T KOG0883|consen 40 FNHCSLTMLPFEDPVCTVDGTVFDLTAIVPWLKK 73 (518)
T ss_pred hhhceeccccccCcccccCCcEEeeehhhHHHHH
Confidence 4578888999999999999999999999999974
Done!